NFAR.fasta.2.3.5.80.10.40.100000.500000.1.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  1  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
2046--2092	47	2218--2264	47	125	85.11	0.00	59	41.49	58.51	40.00	60.00	0.00	4310	4310
77021--77110	90	77154--77243	90	43	75.00	12.50	48	25.00	75.00	18.06	81.94	0.00	154264	154264
104337--104411	75	104632--104706	75	220	75.95	10.13	47	24.00	76.00	21.67	78.33	0.00	209043	209043
176461--176612	152	193315--193465	151	16702	89.54	1.96	220	23.10	76.90	22.63	77.37	0.00	369927	369926
194616--197314	2699	197855--200559	2705	540	71.27	6.65	1203	28.39	71.61	26.46	73.54	0.00	395169	395175
256013--256057	45	256102--256144	43	44	88.89	4.44	61	31.82	68.18	30.00	70.00	0.00	512159	512159
256980--257086	107	258884--258990	107	1797	96.26	0.00	194	29.44	70.56	29.13	70.87	0.00	515970	515970
275182--275242	61	276129--276186	58	886	78.69	4.92	51	28.57	71.43	25.00	75.00	0.00	551371	551368
77068--77232	165	280024--280186	163	202791	88.62	3.59	227	24.70	75.30	24.32	75.68	0.00	357256	357256
77011--77154	144	280024--280166	143	202869	92.41	2.07	229	24.39	75.61	23.88	76.12	0.00	357178	357178
176455--176595	141	280024--280161	138	103428	92.25	3.52	219	22.22	77.78	21.37	78.63	0.00	456619	456618
77021--77234	214	286200--286414	215	208965	85.12	0.47	268	25.87	74.13	23.50	76.50	0.00	363434	363434
77099--77279	181	286233--286414	182	208953	82.97	0.55	207	27.00	73.00	24.50	75.50	0.00	363512	363512
176460--176627	168	286249--286414	166	109621	82.94	3.53	183	24.85	75.15	22.69	77.31	0.00	462876	462875
218824--219515	692	287649--288339	691	68133	83.81	1.86	805	28.13	71.87	28.38	71.62	0.00	507164	507161
94237--95223	987	429994--430974	981	334770	66.24	5.73	200	32.72	67.28	30.10	69.90	0.00	525217	525217
79045--79457	413	474645--475057	413	395187	75.30	1.92	303	32.08	67.92	33.44	66.56	0.00	554102	554102
347060--347186	127	485522--485651	130	138335	71.97	5.30	65	29.57	70.43	27.37	72.63	0.00	832708	832711
464495--464653	159	495512--495666	155	30858	71.78	7.36	72	28.34	71.66	23.08	76.92	0.00	960165	960162
465176--465534	359	496751--497109	359	31216	68.56	5.42	118	28.83	71.17	26.09	73.91	0.00	962285	962285
119217--119330	114	529058--529172	115	409727	73.95	7.56	65	10.48	89.52	5.68	94.32	0.00	648388	648388
296609--296862	254	532011--532264	254	235148	71.26	5.36	119	33.66	66.34	32.26	67.74	0.00	828873	828873
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
504871--505140	270	532887--533156	270	27746	70.44	2.92	127	26.11	73.89	23.83	76.17	0.00	1038027	1038027
467180--468248	1069	548361--549441	1081	80112	69.81	6.83	394	29.77	70.23	27.67	72.33	0.00	1016609	1016621
280024--280165	142	584974--585114	141	304808	89.44	0.70	207	22.97	77.03	22.05	77.95	0.00	865139	865139
193291--193465	175	584984--585151	168	391518	83.52	5.11	189	25.36	74.64	25.17	74.83	0.00	778449	778445
286229--286414	186	585059--585241	183	298644	82.80	1.61	206	25.20	74.80	24.03	75.97	0.00	871473	871471
280024--280161	138	585054--585191	138	304892	87.05	1.44	184	23.91	76.09	22.31	77.69	0.00	865215	865215
529008--529157	150	625364--625519	156	96206	72.05	9.94	65	10.78	89.22	3.45	96.55	0.00	1154521	1154521
152272--152310	39	649858--649895	38	497547	84.62	2.56	46	22.08	77.92	21.21	78.79	0.00	802168	802167
585059--585241	183	709569--709754	186	124327	85.48	1.61	231	23.31	76.69	22.01	77.99	0.00	1294810	1294813
726141--726164	24	726304--726327	24	139	95.83	0.00	43	31.25	68.75	30.43	69.57	0.00	1452468	1452468
476978--477018	41	739788--739828	41	262769	83.33	4.76	45	24.39	75.61	20.00	80.00	0.00	1216806	1216806
394709--394788	80	780420--780499	80	385631	79.01	2.47	73	30.00	70.00	28.12	71.88	0.00	1175208	1175208
458836--458962	127	788483--788609	127	329520	71.64	10.45	50	26.38	73.62	21.88	78.12	0.00	1247445	1247445
585847--586273	427	813369--813793	425	227095	66.74	5.92	96	26.17	73.83	21.84	78.16	0.00	1399642	1399642
821468--821492	25	821493--821516	24	0	96.00	4.00	43	22.45	77.55	20.83	79.17	0.00	1642985	1642985
394714--394818	105	830082--830189	108	435263	77.06	4.59	83	30.52	69.48	29.76	70.24	0.00	1224900	1224903
394514--394818	305	835127--835437	311	440308	71.03	8.10	125	25.00	75.00	21.49	78.51	0.00	1229945	1229948
464857--464958	102	862966--863063	98	398007	72.38	9.52	45	23.50	76.50	18.42	81.58	0.00	1327924	1327920
870096--870490	395	878410--878808	399	7919	69.53	4.91	154	27.58	72.42	26.15	73.85	0.00	1748900	1748900
537667--537705	39	907100--907138	39	369394	82.05	0.00	43	11.54	88.46	9.38	90.62	0.00	1444805	1444805
917456--917922	467	942108--942571	464	24185	72.00	4.00	247	27.39	72.61	26.32	73.68	0.00	1860030	1860030
916643--916738	96	943244--943339	96	26505	72.16	2.06	55	21.88	78.12	20.00	80.00	0.00	1859982	1859982
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
993286--993313	28	993436--993464	29	122	89.66	3.45	41	7.02	92.98	3.85	96.15	0.00	1986749	1986750
997865--997888	24	997908--997931	24	19	100.00	0.00	48	29.17	70.83	29.17	70.83	0.00	1995796	1995796
880418--880480	63	998884--998946	63	118403	75.76	9.09	40	16.67	83.33	10.00	90.00	0.00	1879364	1879364
1004813--1004845	33	1005226--1005258	33	380	84.85	0.00	41	16.67	83.33	14.29	85.71	0.00	2010071	2010071
1008314--1008385	72	1008861--1008934	74	475	75.32	10.39	43	15.75	84.25	12.07	87.93	0.00	2017246	2017247
906878--906908	31	1059313--1059343	31	152404	90.32	0.00	47	11.29	88.71	7.14	92.86	0.00	1966221	1966221
1065391--1065410	20	1065414--1065433	20	3	100.00	0.00	40	20.00	80.00	20.00	80.00	0.00	2130824	2130824
584980--585229	250	1071347--1071604	258	486117	79.92	3.86	238	25.39	74.61	23.19	76.81	0.00	1656576	1656580
585057--585241	185	1071572--1071761	190	486330	81.05	2.63	190	24.53	75.47	22.08	77.92	0.00	1656813	1656817
737363--738355	993	1138282--1139280	999	399926	66.44	6.23	203	28.82	71.18	26.65	73.35	0.00	1876637	1876643
1089115--1089397	283	1144211--1144493	283	54813	68.04	5.50	85	30.39	69.61	28.28	71.72	0.00	2233608	2233608
1223163--1223193	31	1258376--1258406	31	35182	87.10	0.00	42	22.58	77.42	22.22	77.78	0.00	2481569	2481569
1293168--1293346	179	1299911--1300092	182	6564	82.42	1.65	198	23.27	76.73	21.33	78.67	0.00	2593257	2593260
1293168--1293352	185	1300060--1300249	190	6707	83.16	2.63	210	22.67	77.33	21.52	78.48	0.00	2593412	2593417
1300027--1300171	145	1300184--1300328	145	12	71.24	10.46	54	22.76	77.24	12.84	87.16	0.00	2600355	2600351
1299925--1300092	168	1300105--1300272	168	12	69.66	11.24	46	23.51	76.49	12.90	87.10	0.00	2600197	2600194
1299947--1300013	67	1300262--1300328	67	248	75.71	8.57	43	20.15	79.85	11.32	88.68	0.00	2600275	2600272
1300184--1300249	66	1300262--1300328	67	12	75.71	10.00	41	20.30	79.70	11.32	88.68	0.00	2600511	2600508
1314779--1314815	37	1315223--1315259	37	407	84.21	5.26	42	13.51	86.49	12.50	87.50	0.00	2630038	2630038
1299874--1300096	223	1316464--1316685	222	16367	81.33	2.22	230	24.49	75.51	22.95	77.05	0.00	2616560	2616559
1300027--1300253	227	1316464--1316690	227	16210	83.04	2.61	253	23.79	76.21	23.04	76.96	0.00	2616717	2616716
1281406--1281603	198	1330475--1330672	198	48871	73.13	2.99	120	29.55	70.45	28.57	71.43	0.00	2612078	2612078
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
1280636--1280997	362	1331102--1331463	362	50104	66.30	3.26	92	27.35	72.65	25.41	74.59	0.00	2612099	2612099
1297642--1297998	357	1337059--1337415	357	39060	69.81	2.22	161	26.05	73.95	22.62	77.38	0.00	2635057	2635057
1350238--1350316	79	1350723--1350801	79	406	71.25	2.50	41	22.78	77.22	19.30	80.70	0.00	2701039	2701039
1326643--1326888	246	1355566--1355811	246	28677	70.63	4.76	110	25.20	74.80	21.35	78.65	0.00	2682454	2682454
1380498--1380520	23	1380541--1380563	23	20	100.00	0.00	46	17.39	82.61	17.39	82.61	0.00	2761061	2761061
1233366--1233928	563	1414869--1415431	563	180940	71.83	4.17	292	29.22	70.78	28.09	71.91	0.00	2648797	2648797
1418621--1418641	21	1418643--1418663	21	1	100.00	0.00	42	19.05	80.95	19.05	80.95	0.00	2837284	2837284
1358638--1361801	3164	1461993--1465204	3212	100191	74.07	4.36	2009	28.58	71.42	26.93	73.07	0.00	2823794	2823842
1345096--1345673	578	1481397--1481974	578	135723	67.00	6.37	133	22.15	77.85	19.50	80.50	0.00	2827070	2827070
1408683--1408716	34	1493492--1493525	34	84775	85.71	5.71	41	13.24	86.76	10.00	90.00	0.00	2902208	2902208
1073675--1073831	157	1505478--1505634	157	431646	71.95	8.54	70	26.43	73.57	27.12	72.88	0.00	2579309	2579309
1419026--1419152	127	1516357--1516484	128	97204	70.68	8.27	49	18.04	81.96	8.51	91.49	0.00	2935509	2935510
1019492--1019522	31	1518403--1518433	31	498880	90.32	0.00	47	6.45	93.55	3.57	96.43	0.00	2537925	2537925
1547794--1547834	41	1548153--1548193	41	318	80.95	4.76	40	25.61	74.39	20.59	79.41	0.00	3095987	3095987
1313448--1314496	1049	1554325--1555373	1049	239828	98.57	0.00	2023	32.22	67.78	32.11	67.89	0.00	2868821	2868821
1468526--1469493	968	1554388--1555347	960	84894	73.52	2.86	605	32.52	67.48	30.88	69.12	0.00	3023881	3023873
1313447--1314495	1049	1564492--1565540	1049	249996	99.24	0.00	2058	32.32	67.68	32.18	67.82	0.00	2878987	2878987
1468526--1469493	968	1564554--1565513	960	95060	73.29	2.66	597	32.62	67.38	30.87	69.13	0.00	3034047	3034039
1628501--1628569	69	1628889--1628957	69	319	75.00	8.33	42	21.01	78.99	12.96	87.04	0.00	3257458	3257459
1549225--1549339	115	1630670--1630778	109	81330	71.79	8.55	49	25.89	74.11	23.81	76.19	0.00	3180009	3180005
1746650--1746897	248	1747177--1747424	248	279	80.65	0.00	256	32.46	67.54	33.00	67.00	0.00	3494074	3494074
1536825--1536918	94	1870897--1870996	100	333978	72.28	7.92	46	20.62	79.38	13.70	86.30	0.00	3407815	3407818
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
1778906--1778934	29	1899458--1899486	29	120523	89.66	0.00	43	10.34	89.66	7.69	92.31	0.00	3678392	3678392
1904176--1904242	67	1904713--1904780	68	470	74.29	7.14	40	14.81	85.19	9.62	90.38	0.00	3808955	3808956
1894739--1894767	29	1915684--1915712	29	20916	89.66	0.00	43	20.69	79.31	19.23	80.77	0.00	3810451	3810451
1875082--1875170	89	1916803--1916891	89	41632	72.83	6.52	47	19.66	80.34	14.93	85.07	0.00	3791973	3791973
1870453--1870756	304	1935811--1936116	306	65054	72.52	5.11	164	27.70	72.30	24.67	75.33	0.00	3806567	3806569
1516593--1516640	48	1949788--1949833	46	433147	83.33	4.17	52	26.60	73.40	25.00	75.00	0.00	3466428	3466428
1592178--1592273	96	1996244--1996340	97	403970	75.49	10.78	57	24.35	75.65	25.97	74.03	0.00	3588517	3588518
1895943--1896542	600	2001391--2001996	606	104848	69.13	6.11	208	29.44	70.56	27.21	72.79	0.00	3897933	3897933
1752209--1752567	359	2029397--2029753	357	276829	72.63	5.96	189	28.91	71.09	27.61	72.39	0.00	3781964	3781964
2000700--2000892	193	2160503--2160693	191	159610	68.34	7.04	55	22.66	77.34	18.38	81.62	0.00	4161395	4161395
2223591--2223610	20	2223611--2223630	20	0	100.00	0.00	40	30.00	70.00	30.00	70.00	0.00	4447221	4447221
1810239--1810581	343	2276437--2276785	349	465855	71.63	5.62	167	31.79	68.21	29.41	70.59	0.00	4087018	4087024
2282051--2282088	38	2282475--2282512	38	386	81.58	0.00	41	21.05	78.95	19.35	80.65	0.00	4564563	4564563
1966193--1966649	457	2286505--2286961	457	319855	67.30	7.17	105	25.82	74.18	22.57	77.43	0.00	4253154	4253154
2129663--2129779	117	2295499--2295616	118	165719	76.23	7.38	81	28.94	71.06	24.73	75.27	0.00	4425278	4425278
2000851--2000889	39	2295496--2295534	39	294606	84.62	0.00	48	26.92	73.08	27.27	72.73	0.00	4296385	4296385
2281934--2282071	138	2341662--2341799	138	59590	69.01	5.63	48	26.81	73.19	22.45	77.55	0.00	4623733	4623733
2314744--2316421	1678	2461599--2463292	1694	145177	69.18	6.10	586	28.14	71.86	25.60	74.40	0.00	4778020	4778036
2304392--2305553	1162	2468081--2469239	1159	162527	72.55	2.13	686	30.20	69.80	29.49	70.51	0.00	4773634	4773631
2485924--2485970	47	2486687--2486735	49	716	82.35	11.76	45	13.54	86.46	7.14	92.86	0.00	4972657	4972660
2445366--2445403	38	2486800--2486836	37	41396	84.21	2.63	44	12.00	88.00	6.25	93.75	0.00	4932203	4932202
2433538--2433624	87	2532670--2532756	87	99045	73.91	10.87	44	17.82	82.18	11.76	88.24	0.00	4966294	4966294
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
2554433--2554473	41	2555125--2555165	41	651	82.93	0.00	47	13.41	86.59	11.76	88.24	0.00	5109598	5109598
2255482--2255843	362	2571567--2571928	362	315723	73.91	3.26	232	30.11	69.89	29.04	70.96	0.00	4827410	4827410
2495813--2496065	253	2600627--2600879	253	104561	70.54	3.88	116	24.51	75.49	23.63	76.37	0.00	5096692	5096692
2600706--2600802	97	2606777--2606873	97	5974	75.25	7.92	61	22.68	77.32	21.05	78.95	0.00	5207579	5207579
2129376--2129904	529	2606653--2607181	529	476748	69.61	5.16	205	28.07	71.93	27.25	72.75	0.00	4736557	4736557
2160521--2160669	149	2654226--2654376	151	493556	69.93	3.92	64	24.67	75.33	22.43	77.57	0.00	4814895	4814897
2628110--2628359	250	2664511--2664763	253	36151	69.88	5.79	98	25.45	74.55	23.76	76.24	0.00	5292870	5292873
2680305--2680361	57	2680497--2680554	58	135	76.67	8.33	40	18.26	81.74	15.22	84.78	0.00	5360858	5360858
2600677--2600786	110	2684164--2684273	110	83377	77.48	1.80	93	24.09	75.91	22.09	77.91	0.00	5284950	5284950
2696385--2696886	502	2719160--2719661	502	22273	73.97	3.52	321	30.38	69.62	30.42	69.58	0.00	5416046	5416046

Tables:   1   2   3