NFAR.fasta.2.3.5.80.10.40.100000.500000.2.html

Inverted Repeats Finder Program written by:

Gary Benson
Department of Biomathematical Sciences
Mount Sinai School of Medicine
Version 3.05

Sequence: NFA 2003-09-04
Parameters: 2 3 5 80 10 40 100000 500000 -t7 600000 -d 
Length:  6021225

Tables:   1   2   3   

This is table  2  of  3  ( 282 repeats found )

Click on indices to view alignment

Table Explanation

Left Indices	Length	Right Indices	Length	Loop	Percent Matches	Percent Indels	Score	Percent A/T	Percent G/C	Percent A-T pairs	Percent G-C pairs	Percent G-T pairs	Center times 2	Average Center times 2
2348159--2349293	1135	2724886--2726023	1138	375592	71.52	3.20	591	32.34	67.66	31.48	68.52	0.00	5074179	5074182
2482819--2483500	682	2739892--2740573	682	256391	71.29	5.14	323	28.23	71.77	27.66	72.34	0.00	5223392	5223392
2672140--2673213	1074	2739889--2740965	1077	66675	66.79	7.43	213	29.94	70.06	28.28	71.72	0.00	5413102	5413102
2597301--2598532	1232	2754935--2756167	1233	156402	79.31	2.33	1146	31.64	68.36	31.95	68.05	0.00	5353467	5353468
2526146--2526919	774	2769525--2770302	778	242605	75.83	1.53	595	32.15	67.85	32.21	67.79	0.00	5296444	5296448
2777630--2777655	26	2777660--2777684	25	4	92.31	3.85	40	43.14	56.86	41.67	58.33	0.00	5555315	5555314
2739892--2740925	1034	2788686--2789713	1028	47760	67.42	5.29	281	28.86	71.14	26.75	73.25	0.00	5529611	5529605
2503893--2503954	62	2799700--2799761	62	295745	81.25	6.25	60	19.35	80.65	17.31	82.69	0.00	5303654	5303654
2359946--2359997	52	2801859--2801910	52	441861	77.36	3.77	42	14.42	85.58	12.20	87.80	0.00	5161856	5161856
2828943--2828987	45	2829270--2829314	45	282	80.43	4.35	43	22.22	77.78	18.92	81.08	0.00	5658257	5658257
2519204--2519623	420	2844938--2845358	421	325314	72.56	4.42	232	32.70	67.30	31.09	68.91	0.00	5364561	5364562
2379059--2379121	63	2866613--2866674	62	487491	76.92	7.69	45	14.40	85.60	8.00	92.00	0.00	5245734	5245733
2492861--2493344	484	2869735--2870217	483	376390	74.13	3.06	317	27.61	72.39	27.75	72.25	0.00	5363079	5363079
2445429--2445491	63	2892819--2892880	62	447327	76.56	4.69	47	16.80	83.20	12.24	87.76	0.00	5338310	5338309
2606698--2606910	213	2921474--2921686	213	314563	70.37	2.78	100	29.81	70.19	28.29	71.71	0.00	5528384	5528384
2571338--2571927	590	2949821--2950413	593	377893	70.40	2.17	285	30.35	69.65	29.45	70.55	0.00	5521748	5521748
2782093--2782793	701	2956739--2957433	695	173945	64.86	6.11	87	27.65	72.35	23.77	76.23	0.00	5739532	5739532
2781423--2781581	159	2957891--2958049	159	176309	76.25	1.25	126	24.84	75.16	22.95	77.05	0.00	5739472	5739472
2949947--2950165	219	3006925--3007143	219	56759	67.42	1.81	74	28.08	71.92	26.85	73.15	0.00	5957090	5957090
2680667--2680768	102	3039593--3039694	102	358824	70.75	7.55	41	13.24	86.76	8.00	92.00	0.00	5720361	5720361
3048695--3048714	20	3048719--3048738	20	4	100.00	0.00	40	45.00	55.00	45.00	55.00	0.00	6097433	6097433
2949793--2950197	405	3052384--3052790	407	102186	67.87	5.28	120	30.54	69.46	28.98	71.02	0.00	6002581	6002581
Left Indices	Length	Right Indices	Length	Loop	Percent Matches	Percent Indels	Score	Percent A/T	Percent G/C	Percent A-T pairs	Percent G-C pairs	Percent G-T pairs	Center times 2	Average Center times 2
3073433--3073454	22	3073455--3073476	22	0	100.00	0.00	44	31.82	68.18	31.82	68.18	0.00	6146909	6146909
2906000--2906173	174	3147308--3147483	176	241134	72.07	4.47	92	29.43	70.57	26.36	73.64	0.00	6053481	6053484
2945999--2946952	954	3178891--3179862	972	231938	66.13	6.43	177	31.72	68.28	29.18	70.82	0.00	6125843	6125861
2786299--2786506	208	3183964--3184163	200	397457	81.90	5.71	206	22.55	77.45	19.19	80.81	0.00	5970470	5970467
2786298--2786538	241	3184007--3184239	233	397468	81.07	4.94	232	22.15	77.85	18.27	81.73	0.00	5970545	5970542
3189708--3189757	50	3190378--3190426	49	620	80.77	9.62	44	16.16	83.84	11.90	88.10	0.00	6380135	6380134
2908227--2908814	588	3215778--3216377	600	306963	67.31	7.77	130	24.83	75.17	20.67	79.33	0.00	6124592	6124604
2943944--2944398	455	3229834--3230287	454	285435	66.16	4.09	105	27.94	72.06	28.01	71.99	0.00	6174232	6174232
2945962--2947228	1267	3238113--3239391	1279	290884	66.51	6.24	264	29.85	70.15	27.23	72.77	0.00	6185341	6185344
3266019--3266064	46	3266546--3266591	46	481	78.26	0.00	42	25.00	75.00	22.22	77.78	0.00	6532610	6532610
2921509--2921732	224	3266942--3267165	224	345209	70.61	3.51	105	32.37	67.63	29.81	70.19	0.00	6188674	6188674
3283635--3283992	358	3287558--3287915	358	3565	68.03	4.37	115	26.26	73.74	24.50	75.50	0.00	6571550	6571550
3154356--3154375	20	3289591--3289610	20	135215	100.00	0.00	40	20.00	80.00	20.00	80.00	0.00	6443966	6443966
3296993--3297038	46	3297044--3297089	46	5	80.85	4.26	45	29.35	70.65	28.95	71.05	0.00	6594082	6594082
2976261--2981143	4883	3299841--3304790	4950	318697	66.85	7.69	965	26.45	73.55	23.87	76.13	0.00	6280984	6280963
2968607--2970153	1547	3299914--3301459	1546	329760	67.70	5.23	445	26.87	73.13	23.81	76.19	0.00	6270067	6270067
2983579--2984703	1125	3299437--3300552	1116	314733	66.44	6.14	230	26.91	73.09	24.09	75.91	0.00	6284140	6284140
2973482--2974571	1090	3300065--3301150	1086	325493	68.65	6.75	335	27.76	72.24	25.61	74.39	0.00	6274636	6274636
2976279--2982938	6660	3301223--3307960	6738	318284	67.47	7.78	1521	26.02	73.98	23.39	76.61	0.00	6284161	6284188
2973559--2974725	1167	3303148--3304305	1158	328422	69.06	6.09	397	27.05	72.95	24.76	75.24	0.00	6277873	6277864
2968569--2970182	1614	3303119--3304738	1620	332936	67.82	6.93	423	25.88	74.12	23.24	76.76	0.00	6273301	6273295
2977242--2984209	6968	3303141--3310165	7025	318931	66.50	7.71	1242	26.11	73.89	23.87	76.13	0.00	6287350	6287380
Left Indices	Length	Right Indices	Length	Loop	Percent Matches	Percent Indels	Score	Percent A/T	Percent G/C	Percent A-T pairs	Percent G-C pairs	Percent G-T pairs	Center times 2	Average Center times 2
2973543--2974344	802	3306691--3307489	799	332346	68.03	6.88	219	27.30	72.70	25.00	75.00	0.00	6281035	6281029
2968932--2970139	1208	3306327--3307526	1200	336187	67.49	7.67	277	26.04	73.96	23.55	76.45	0.00	6276466	6276460
2973130--2973447	318	3307651--3307968	318	334203	69.37	9.01	96	24.37	75.63	22.08	77.92	0.00	6281098	6281098
2979849--2982285	2437	3308284--3310764	2481	325998	67.12	7.29	537	26.47	73.53	23.18	76.82	0.00	6290569	6290569
2971922--2971977	56	3309139--3309194	56	337161	80.36	0.00	57	25.89	74.11	26.67	73.33	0.00	6281116	6281116
2982970--2984207	1238	3309500--3310773	1274	325292	71.26	6.47	563	26.95	73.05	25.73	74.27	0.00	6293707	6293743
2967720--2970153	2434	3309505--3311983	2479	339351	65.96	9.50	278	26.34	73.66	23.10	76.90	0.00	6279658	6279694
2974072--2974840	769	3309386--3310164	779	334545	67.38	6.50	191	26.10	73.90	23.38	76.62	0.00	6284226	6284230
3039617--3039657	41	3322082--3322122	41	282424	83.33	4.76	45	19.51	80.49	17.14	82.86	0.00	6361739	6361739
3366079--3366106	28	3366111--3366140	30	4	90.00	6.67	41	20.69	79.31	22.22	77.78	0.00	6732217	6732217
3389070--3389116	47	3389495--3389539	45	378	81.25	8.33	43	21.74	78.26	20.51	79.49	0.00	6778611	6778609
3039420--3039595	176	3399352--3399527	176	359756	67.93	8.70	41	16.48	83.52	11.20	88.80	0.00	6438947	6438947
3006927--3007144	218	3402528--3402745	218	395383	69.96	4.48	91	27.52	72.48	25.00	75.00	0.00	6409672	6409672
3052379--3052748	370	3402418--3402783	366	349669	70.29	4.77	158	30.16	69.84	29.06	70.94	0.00	6455166	6455163
3094714--3094940	227	3420794--3421013	220	325853	74.24	4.80	141	32.44	67.56	30.00	70.00	0.00	6515734	6515730
3052384--3052653	270	3434279--3434548	270	381625	69.68	5.05	106	28.70	71.30	26.42	73.58	0.00	6486932	6486932
3006866--3007150	285	3467108--3467392	285	459957	67.01	4.12	78	26.49	73.51	24.62	75.38	0.00	6474258	6474258
3411264--3411613	350	3498571--3498920	350	86957	67.79	3.92	111	27.57	72.43	27.69	72.31	0.00	6910184	6910184
3070721--3071836	1116	3507404--3508520	1117	435567	99.82	0.09	2222	33.99	66.01	33.99	66.01	0.00	6579240	6579241
3339079--3339796	718	3513471--3514188	718	173674	68.43	5.42	231	27.92	72.08	27.33	72.67	0.00	6853267	6853267
3339161--3341471	2311	3513543--3515869	2327	172071	66.38	7.95	386	27.12	72.88	24.20	75.80	0.00	6855014	6855002
3555284--3555312	29	3555318--3555347	30	5	90.00	3.33	43	32.20	67.80	25.93	74.07	0.00	7110630	7110630
Left Indices	Length	Right Indices	Length	Loop	Percent Matches	Percent Indels	Score	Percent A/T	Percent G/C	Percent A-T pairs	Percent G-C pairs	Percent G-T pairs	Center times 2	Average Center times 2
3261586--3261707	122	3573202--3573323	122	311494	72.66	9.38	57	24.59	75.41	19.35	80.65	0.00	6834909	6834909
3557048--3558114	1067	3575621--3576702	1082	17506	74.25	3.74	698	33.78	66.22	33.58	66.42	0.00	7133735	7133750
3495582--3495823	242	3614271--3614515	245	118447	70.08	8.27	86	21.97	78.03	19.66	80.34	0.00	7110094	7110097
3261586--3261836	251	3614267--3614517	251	352430	70.27	6.18	101	24.50	75.50	21.98	78.02	0.00	6876103	6876103
3261586--3261647	62	3615233--3615294	62	353585	79.03	0.00	59	20.16	79.84	18.37	81.63	0.00	6876880	6876880
3387757--3387797	41	3630526--3630566	41	242728	80.95	4.76	40	13.41	86.59	8.82	91.18	0.00	7018323	7018323
3179613--3179738	126	3639290--3639415	126	459551	72.66	3.12	73	33.73	66.27	31.18	68.82	0.00	6819028	6819028
3238377--3238523	147	3639979--3640125	147	401455	69.54	5.30	56	27.21	72.79	21.90	78.10	0.00	6878502	6878502
3261579--3261677	99	3656871--3656970	100	395193	74.76	6.80	62	20.60	79.40	20.78	79.22	0.00	6918548	6918549
3495570--3495823	254	3656726--3656973	248	160902	69.23	6.92	84	22.31	77.69	17.78	82.22	0.00	7152549	7152543
3614569--3615307	739	3700283--3701030	748	84975	70.60	4.86	330	28.38	71.62	28.62	71.38	0.00	7315590	7315599
3722301--3722328	28	3722344--3722371	28	15	89.29	0.00	41	26.79	73.21	28.00	72.00	0.00	7444672	7444672
3281473--3282539	1067	3753100--3754151	1052	470560	70.61	4.16	484	30.39	69.61	29.32	70.68	0.00	7035639	7035630
3553929--3554352	424	3755447--3755867	421	201094	69.72	6.19	158	32.90	67.10	29.93	70.07	0.00	7309799	7309796
3298286--3298575	290	3774285--3774574	290	475709	67.34	4.71	81	26.90	73.10	25.50	74.50	0.00	7072860	7072860
3652655--3652983	329	3774376--3774703	328	121392	69.21	7.33	107	26.79	73.21	25.00	75.00	0.00	7427359	7427359
3882510--3882532	23	3882533--3882555	23	0	100.00	0.00	46	30.43	69.57	30.43	69.57	0.00	7765065	7765065
3634219--3634484	266	3896353--3896615	263	261868	75.46	3.35	190	27.98	72.02	27.09	72.91	0.00	7530837	7530834
3721985--3722239	255	3904278--3904532	255	182038	71.65	4.60	128	27.84	72.16	27.81	72.19	0.00	7626517	7626517
3720894--3721359	466	3905149--3905630	482	183789	69.15	8.87	139	27.43	72.57	25.66	74.34	0.00	7626508	7626508
3932825--3932880	56	3933456--3933511	56	575	84.48	6.90	63	37.50	62.50	38.78	61.22	0.00	7866336	7866336
3773974--3774129	156	3941821--3941976	156	167691	72.22	7.41	75	27.56	72.44	23.93	76.07	0.00	7715950	7715950
Left Indices	Length	Right Indices	Length	Loop	Percent Matches	Percent Indels	Score	Percent A/T	Percent G/C	Percent A-T pairs	Percent G-C pairs	Percent G-T pairs	Center times 2	Average Center times 2
3954715--3954737	23	3954740--3954762	23	2	95.65	0.00	41	15.22	84.78	13.64	86.36	0.00	7909477	7909477
3495576--3495684	109	3985477--3985585	109	489792	72.32	5.36	57	20.18	79.82	17.28	82.72	0.00	7481161	7481161
3729462--3729806	345	4013747--4014097	351	283940	68.89	6.67	112	28.74	71.26	28.23	71.77	0.00	7743553	7743559
3635964--3636328	365	4035203--4035567	365	398874	72.04	3.76	196	25.89	74.11	23.88	76.12	0.00	7671531	7671531
4123312--4123332	21	4123334--4123354	21	1	100.00	0.00	42	33.33	66.67	33.33	66.67	0.00	8246666	8246666
3917423--3917596	174	4225490--4225675	186	307893	83.51	8.51	189	25.56	74.44	24.84	75.16	0.00	8143086	8143094
4225417--4225618	202	4233609--4233799	191	7990	83.33	7.35	208	25.45	74.55	25.29	74.71	0.00	8459227	8459217
3976651--3976740	90	4360748--4360837	90	384007	74.44	0.00	65	31.11	68.89	31.34	68.66	0.00	8337488	8337488
3976641--3976731	91	4360862--4360955	94	384130	76.60	3.19	72	29.73	70.27	30.56	69.44	0.00	8337593	8337593
4391265--4391983	719	4405879--4406601	723	13895	70.52	4.08	327	26.91	73.09	25.43	74.57	0.00	8797862	8797863
4041247--4041928	682	4471441--4472113	673	429512	66.57	7.25	129	25.31	74.69	23.72	76.28	0.00	8513369	8513360
4233705--4233890	186	4519989--4520176	188	286098	85.19	2.12	230	23.80	76.20	20.50	79.50	0.00	8753879	8753880
4226813--4226975	163	4555835--4556000	166	328859	72.25	9.83	72	25.23	74.77	24.00	76.00	0.00	8782810	8782810
4298919--4299092	174	4663348--4663519	172	364255	67.43	2.29	57	27.75	72.25	26.27	73.73	0.00	8962440	8962439
4311888--4311939	52	4666275--4666326	52	354335	79.25	3.77	47	27.88	72.12	26.19	73.81	0.00	8978214	8978214
4233609--4233731	123	4699284--4699402	119	465552	83.33	7.94	127	28.10	71.90	25.71	74.29	0.00	8933015	8933014
4233683--4233880	198	4699292--4699481	190	465411	86.14	7.92	232	26.80	73.20	24.14	75.86	0.00	8933172	8933167
4744245--4744584	340	4747557--4747893	337	2972	73.41	4.34	202	31.46	68.54	30.32	69.68	0.00	9492141	9492141
4744039--4744103	65	4748068--4748132	65	3964	87.69	0.00	90	40.77	59.23	40.35	59.65	0.00	9492171	9492171
4497281--4497335	55	4793472--4793526	55	296136	83.64	0.00	65	20.00	80.00	15.22	84.78	0.00	9290807	9290807
4402326--4402387	62	4850462--4850523	62	448074	75.81	0.00	49	28.23	71.77	29.79	70.21	0.00	9252849	9252849
4402359--4402463	105	4851748--4851852	105	449284	73.15	5.56	59	24.29	75.71	21.52	78.48	0.00	9254211	9254211
Left Indices	Length	Right Indices	Length	Loop	Percent Matches	Percent Indels	Score	Percent A/T	Percent G/C	Percent A-T pairs	Percent G-C pairs	Percent G-T pairs	Center times 2	Average Center times 2
4854485--4854540	56	4855098--4855151	54	557	80.36	3.57	53	20.00	80.00	20.00	80.00	0.00	9709638	9709636
4497981--4498040	60	4861482--4861541	60	363441	75.41	3.28	43	16.67	83.33	17.39	82.61	0.00	9359522	9359522
4770219--4770324	106	4862524--4862629	106	92199	73.58	0.00	72	30.66	69.34	26.92	73.08	0.00	9632848	9632848
4699292--4699416	125	4873634--4873763	130	174217	86.26	5.34	158	24.31	75.69	21.24	78.76	0.00	9573050	9573053
4699361--4699489	129	4873635--4873769	135	174145	84.56	5.88	151	25.00	75.00	21.74	78.26	0.00	9573124	9573128
4519989--4520130	142	4873634--4873775	142	353503	90.34	4.14	208	22.89	77.11	21.37	78.63	0.00	9393764	9393763
4875367--4875431	65	4875852--4875912	61	420	78.79	9.09	50	20.63	79.37	17.31	82.69	0.00	9751283	9751282
4886962--4887030	69	4887352--4887421	70	321	75.00	6.94	44	12.95	87.05	3.70	96.30	0.00	9774382	9774383
4738613--4738675	63	4891814--4891876	63	153138	75.38	6.15	42	14.29	85.71	8.16	91.84	0.00	9630489	9630489
4445142--4445200	59	4896011--4896069	59	450810	86.67	3.33	76	27.12	72.88	25.00	75.00	0.00	9341211	9341211

Tables:   1   2   3