Tandem Repeats Finder Program written by:
Gary Benson
Department of Biomathematical Sciences
Mount Sinai School of Medicine
Version 4.00
Sequence: pNF2 2003-09-03
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 87093
ACGTcount: A:0.16, C:0.35, G:0.34, T:0.16
Found at i:9745 original size:14 final size:14
Alignment explanation
Indices: 9726--9754 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9716 GTTGACCCTC
9726 CCCGCGCCGACGCA
1 CCCGCGCCGACGCA
9740 CCCGCGCCGACGCA
1 CCCGCGCCGACGCA
9754 C
1 C
9755 GGTCATGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.59, G:0.28, T:0.00
Consensus pattern (14 bp):
CCCGCGCCGACGCA
Found at i:32222 original size:15 final size:15
Alignment explanation
Indices: 32202--32231 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32192 TCGATACGCG
*
32202 GGTGACCGCTTCGAC
1 GGTGACCGCCTCGAC
32217 GGTGACCGCCTCGAC
1 GGTGACCGCCTCGAC
32232 ACCGCCGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.37, G:0.33, T:0.17
Consensus pattern (15 bp):
GGTGACCGCCTCGAC
Found at i:33149 original size:15 final size:15
Alignment explanation
Indices: 33111--33149 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
33101 TGGCGGTCGC
*
33111 GGTCGCCGCGATCGT
1 GGTCGCCGCGATCGA
*
33126 GTTCGCCGCGATCGA
1 GGTCGCCGCGATCGA
*
33141 GGTCCCCGC
1 GGTCGCCGC
33150 ACGCGGCTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.38, G:0.36, T:0.18
Consensus pattern (15 bp):
GGTCGCCGCGATCGA
Found at i:46666 original size:126 final size:126
Alignment explanation
Indices: 46457--47557 Score: 871
Period size: 126 Copynumber: 8.7 Consensus size: 126
46447 GTGCTAGGTG
* * *** * **
46457 CCGAGCACCCCCACACTCTGGCCTCCCGTGGCAACCTCGCCGGCGCCTACCAGTCGGTGGGACGG
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGG
* * * * * * * *
46522 CTGGACGAGGCAATCCCGCTCTACGAACAGGCCCGCACCG-GTCAGGAGCGGATTCTCGG-A
66 CTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTC-CGAACGCATACTGGGCA
* * * **** * * *
46582 CCCGACCACCCCGAGACCATGGCCGCGCGCAACAACCTCGCCTACGCCTACCAGTCGGTGGGACG
1 -CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACG
46647 GCTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTCCGAACGCATACTGGGCA
65 GCTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTCCGAACGCATACTGGGCA
*
46709 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGA
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGG
46774 CTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTCCGAACGCATACTGGGCA
66 CTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTCCGAACGCATACTGGGCA
46835 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACC-GATCGGTGGGACG
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAG-TCGGTGGGACG
46899 GCTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTCCGAACGCATACTGGGCA
65 GCTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTCCGAACGCATACTGGGCA
* * * ** * * * * ** *** *
46961 CCGAGCACCCCAATACCTTGACCTTCCGTAGCAACCTCGCTTTCGCTTATGAGTCAACGGGACGA
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGG
* * * * * ** * * * *
47026 CTGGAGGCGGCAATCCCTCTGCTA-GAGCA-GACACTGGCGGA-TCGGGAGCGCATATTGGGCGA
66 CTGGACGAGGCAATCCCGCT-CTACGAACAGGTC-CTCACCGACTC-CGAACGCATACTGGGC-A
* * ** * * * *
47088 -CGAGCACCCCCACACCTTGATCTCCCGTGGCAACCTCG-CTGGCGCCTATCAGTCGGCGGGACG
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCT-ACGCCTACCAGTCGGTGGGACG
* * ** * * * *
47151 GCTGGACGAGGCAATCCCGCTCTACCAGCAGACCCTCACCGA-TCGGGAGA-GAATCCTGGGCG
65 GCTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTC-CGA-ACGCATACTGGGCA
* * * ** * * * ** * *
47213 TCAAGCACCCCGACACCTTGATCTCCCGCAACAACCTTGCCTACATCTACAAGTCGGCGGGACGG
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGG
* * ** * * *
47278 CTGGACGAGGCAATCCCGCTCTACCAGCAGACCCTCACCGA-TCGGGAGCGCATATTGGGCGA
66 CTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTC-CGAACGCATACTGGGC-A
* * ** * * * ** * * *
47340 -CGAGCACCCCCACACCTTGATCTCCCGCAACAACCTTGCCGGCGCCTATCAGTCGGCGGGACGA
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGG
* * ** * * * *
47404 CTGGACGAGGCAATCCCGCTCTACCAGCAGACCCTCACCGA-TCGGGAGA-GAATCCTGGGCG
66 CTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTC-CGA-ACGCATACTGGGCA
* * * ** *** * * ** * * *
47465 TCAAGCACCCCGACACCTTGATCTCCTACAACAACCTTGCCGGCGCCTACCAGTTGCTGGGACGA
1 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGG
47530 CTGGACGAGGCAATCCCGCTCTACGAAC
66 CTGGACGAGGCAATCCCGCTCTACGAAC
47558 GAACCCTCAC
Statistics
Matches: 833, Mismatches: 124, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
125 9 0.01
126 813 0.98
127 11 0.01
ACGTcount: A:0.22, C:0.38, G:0.26, T:0.15
Consensus pattern (126 bp):
CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGG
CTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTCCGAACGCATACTGGGCA
Found at i:46902 original size:252 final size:252
Alignment explanation
Indices: 46457--47557 Score: 1045
Period size: 252 Copynumber: 4.4 Consensus size: 252
46447 GTGCTAGGTG
* * * **
46457 CCGAGCACCCCCACA-CTCTGGCCTCCCGTGGCAACCTCGCCGGCGCCTACCAGTCGGTGGGACG
1 CCGAGCACCCCGACACCT-TGACCTCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACG
* * * * * * * *
46521 GCTGGACGAGGCAATCCCGCTCTACGAACAGGCCCGCACCGGTCAGGAGCGGATTCTCGGAC-CC
65 ACTGGACGAGGCAATCCCGCTCTACGAACAGGCCCTCACCGATCGGGAGCGCATACT-GGGCGAC
* * * * ** * * *
46585 GACCACCCCGAGACCATGGCCGCGCGCAACAACCTCGCCTACGCCTACCAGTCGGTGGGACGGCT
129 GAGCACCCCCACACCTTGATCTCCCGCAACAACCTCGCCTACGCCTACCAGTCGGCGGGACGGCT
* ** *
46650 GGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTC-CGA-ACGCATACTGGGCA
194 GGACGAGGCAATCCCGCTCTACCAACAGACCCTCACCGA-TCGCGAGA-GAATACTGGGCA
* **
46709 CCGAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGA
1 CCGAGCACCCCGACACCTTGACCTCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGA
* * *
46774 CTGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTC-CGAACGCATACTGGGC-ACC
66 CTGGACGAGGCAATCCCGCTCTACGAACAGGCCCTCACCGA-TCGGGAGCGCATACTGGGCGA-C
* * ** * * *
46837 GAGCACCCCGACACCCTGAAATCCCGTAGCAACCTCGCCTACGCCTACC-GATCGGTGGGACGGC
129 GAGCACCCCCACACCTTGATCTCCCGCAACAACCTCGCCTACGCCTACCAG-TCGGCGGGACGGC
* ** *
46901 TGGACGAGGCAATCCCGCTCTACGAACAGGTCCTCACCGACTC-CGA-ACGCATACTGGGCA
193 TGGACGAGGCAATCCCGCTCTACCAACAGACCCTCACCGA-TCGCGAGA-GAATACTGGGCA
* * * * * * ** ***
46961 CCGAGCACCCCAATACCTTGACCTTCCGTAGCAACCTCGCTTTCGCTTATGAGTCAACGGGACGA
1 CCGAGCACCCCGACACCTTGACCTCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGA
* * * * * * ** * *
47026 CTGGAGGCGGCAATCCCTCTGCTA-GAGCAGACACTGGCGGATCGGGAGCGCATATTGGGCGACG
66 CTGGACGAGGCAATCCCGCT-CTACGAACAGGCCCTCACCGATCGGGAGCGCATACTGGGCGACG
*** * *
47090 AGCACCCCCACACCTTGATCTCCCGTGGCAACCTCG-CTGGCGCCTATCAGTCGGCGGGACGGCT
130 AGCACCCCCACACCTTGATCTCCCGCAACAACCTCGCCT-ACGCCTACCAGTCGGCGGGACGGCT
* * * *
47154 GGACGAGGCAATCCCGCTCTACCAGCAGACCCTCACCGATCGGGAGAGAATCCTGGGCG
194 GGACGAGGCAATCCCGCTCTACCAACAGACCCTCACCGATCGCGAGAGAATACTGGGCA
* * * * * * ** * * *
47213 TCAAGCACCCCGACACCTTGATCTCCCGCAACAACCTTGCCTACATCTACAAGTCGGCGGGACGG
1 CCGAGCACCCCGACACCTTGACCTCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGA
* * * *
47278 CTGGACGAGGCAATCCCGCTCTACCAGCAGACCCTCACCGATCGGGAGCGCATATTGGGCGACGA
66 CTGGACGAGGCAATCCCGCTCTACGAACAGGCCCTCACCGATCGGGAGCGCATACTGGGCGACGA
* ** * *
47343 GCACCCCCACACCTTGATCTCCCGCAACAACCTTGCCGGCGCCTATCAGTCGGCGGGACGACTGG
131 GCACCCCCACACCTTGATCTCCCGCAACAACCTCGCCTACGCCTACCAGTCGGCGGGACGGCTGG
* * * *
47408 ACGAGGCAATCCCGCTCTACCAGCAGACCCTCACCGATCGGGAGAGAATCCTGGGCG
196 ACGAGGCAATCCCGCTCTACCAACAGACCCTCACCGATCGCGAGAGAATACTGGGCA
* * * *** * * ** * *
47465 TCAAGCACCCCGACACCTTGATCTCCTACAACAACCTTGCCGGCGCCTACCAGTTGCTGGGACGA
1 CCGAGCACCCCGACACCTTGACCTCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGA
47530 CTGGACGAGGCAATCCCGCTCTACGAAC
66 CTGGACGAGGCAATCCCGCTCTACGAAC
47558 GAACCCTCAC
Statistics
Matches: 719, Mismatches: 117, Indels: 26
0.83 0.14 0.03
Matches are distributed among these distances:
251 13 0.02
252 696 0.97
253 10 0.01
ACGTcount: A:0.22, C:0.38, G:0.26, T:0.15
Consensus pattern (252 bp):
CCGAGCACCCCGACACCTTGACCTCCCGTAGCAACCTCGCCTACGCCTACCAGTCGGTGGGACGA
CTGGACGAGGCAATCCCGCTCTACGAACAGGCCCTCACCGATCGGGAGCGCATACTGGGCGACGA
GCACCCCCACACCTTGATCTCCCGCAACAACCTCGCCTACGCCTACCAGTCGGCGGGACGGCTGG
ACGAGGCAATCCCGCTCTACCAACAGACCCTCACCGATCGCGAGAGAATACTGGGCA
Found at i:47600 original size:378 final size:374
Alignment explanation
Indices: 46488--47601 Score: 1037
Period size: 378 Copynumber: 2.9 Consensus size: 374
46478 CCTCCCGTGG
** *
46488 CAACCTCGCCGGCGCCTACCAGTCGGTGGGACGGCTGGACGAGGCAATCCCGCTCTACGAACAGG
1 CAACCTCGCCTACACCTA-CAGTCGGTGGGACGGCTGGACGAGGCAATCCCGCTCTACGAACAGG
* * * * * * * * * * * *
46553 CCCGCACCGGTCAGGAGCGGAT-TCTCGGACCCGACCACCCCGAGACCATGGCCGCGCGCAACAA
65 CCCTCACCGATC-GGAGCGCATAT-T-GGGCACGAGCACCCCAACACCTTGACCTCCCGCAACAA
* * * * **
46617 CCTCGCCTACGCCTACCAGTCGGTGGGACGGCTGGACGAGGCAATCCCGCTCTACGAACAGGTCC
127 CCTCGCCTACGCCTATCAGTCGGCGGGACGACTGGACGAGGCAATCCCGCTCTACGAGCAGACCC
* * **
46682 TCACCGACTC-CGA-ACGCATACTGGGC-ACCGAGCACCCCGACACCCTGAAATCCCGTAGCAAC
192 TCACCGA-TCGGGAGA-GCATACTGGGCGA-CGAGCACCCCGACACCTTGATCTCCCGTAGCAAC
** * **
46744 CTCGCCTACGCCTACCAGTCGGTGGGACGACTGGACGAGGCAATCCCGCTCTACGAACAGGTCCT
254 CTCGCCGGCGCCTACCAGTCGCTGGGACGACTGGACGAGGCAATCCCGCTCTACGAACAGACCCT
* * * * * *
46809 CACCGA-CTCCGAA-CGCATACTGGGCACCGAGCACCCCGACACCCTGAAATCCCGTAG
319 CACCGATCTCC-AAGAGC-TTCTGGG-GCGGAGCACCCCGACACCCTGAAATCCCGCAA
* *
46866 CAACCTCGCCTACGCCTACCGATCGGTGGGACGGCTGGACGAGGCAATCCCGCTCTACGAACAGG
1 CAACCTCGCCTACACCTACAG-TCGGTGGGACGGCTGGACGAGGCAATCCCGCTCTACGAACAGG
* * * * * * * *
46931 TCCTCACCGACTCCGAACGCATACTGGGCACCGAGCACCCCAATACCTTGACCTTCCGTAGCAAC
65 CCCTCACCGA-TCGGAGCGCATATTGGGCA-CGAGCACCCCAACACCTTGACCTCCCGCAACAAC
* * * * ** * * * *
46996 CTCGCTTTCGCTTATGAGTCAACGGGACGACTGGAGGCGGCAATCCCTCTGCTA-GAGCAGACAC
128 CTCGCCTACGCCTATCAGTCGGCGGGACGACTGGACGAGGCAATCCCGCT-CTACGAGCAGACCC
** * * * * *
47060 TGGCGGATCGGGAGCGCATATTGGGCGACGAGCACCCCCACACCTTGATCTCCCGTGGCAACCTC
192 TCACCGATCGGGAGAGCATACTGGGCGACGAGCACCCCGACACCTTGATCTCCCGTAGCAACCTC
* * * * *
47125 GCTGGCGCCTATCAGTCGGC-GGGACGGCTGGACGAGGCAATCCCGCTCTACCAGCAGACCCTCA
257 GCCGGCGCCTACCAGTC-GCTGGGACGACTGGACGAGGCAATCCCGCTCTACGAACAGACCCTCA
*** * * * * **
47189 CCGATC-GGGAGAGAATCCT-GGGCGTCAAGCACCCCGACACCTTGATCTCCCGCAA
321 CCGATCTCCAAGAG-CTTCTGGGGCG--GAGCACCCCGACACCCTGAAATCCCGCAA
* * * * * *
47244 CAACCTTGCCTACATCTACAAGTCGGCGGGACGGCTGGACGAGGCAATCCCGCTCTACCAGCAGA
1 CAACCTCGCCTACACCTAC-AGTCGGTGGGACGGCTGGACGAGGCAATCCCGCTCTACGAACAGG
* *
47309 CCCTCACCGATCGGGAGCGCATATTGGGCGACGAGCACCCCCACACCTTGATCTCCCGCAACAAC
65 CCCTCACCGATC-GGAGCGCATATTGGGC-ACGAGCACCCCAACACCTTGACCTCCCGCAACAAC
* ** *
47374 CTTGCCGGCGCCTATCAGTCGGCGGGACGACTGGACGAGGCAATCCCGCTCTACCAGCAGACCCT
128 CTCGCCTACGCCTATCAGTCGGCGGGACGACTGGACGAGGCAATCCCGCTCTACGAGCAGACCCT
* * * * *** * *
47439 CACCGATCGGGAGAGAATCCTGGGCGTCAAGCACCCCGACACCTTGATCTCCTACAACAACCTTG
193 CACCGATCGGGAGAGCATACTGGGCGACGAGCACCCCGACACCTTGATCTCCCGTAGCAACCTCG
*
47504 CCGGCGCCTACCAGTTGCTGGGACGACTGGACGAGGCAATCCCGCTCTACGAAC-GAACCCTCAC
258 CCGGCGCCTACCAGTCGCTGGGACGACTGGACGAGGCAATCCCGCTCTACGAACAG-ACCCTCAC
47568 C-ATCTCCAAGGAGCTTCTTGGGGCGGAGCACCCC
322 CGATCTCCAA-GAGCTTC-TGGGGCGGAGCACCCC
47602 ACCACCCGTT
Statistics
Matches: 580, Mismatches: 132, Indels: 48
0.76 0.17 0.06
Matches are distributed among these distances:
376 1 0.00
377 21 0.04
378 539 0.93
379 14 0.02
380 5 0.01
ACGTcount: A:0.22, C:0.37, G:0.26, T:0.15
Consensus pattern (374 bp):
CAACCTCGCCTACACCTACAGTCGGTGGGACGGCTGGACGAGGCAATCCCGCTCTACGAACAGGC
CCTCACCGATCGGAGCGCATATTGGGCACGAGCACCCCAACACCTTGACCTCCCGCAACAACCTC
GCCTACGCCTATCAGTCGGCGGGACGACTGGACGAGGCAATCCCGCTCTACGAGCAGACCCTCAC
CGATCGGGAGAGCATACTGGGCGACGAGCACCCCGACACCTTGATCTCCCGTAGCAACCTCGCCG
GCGCCTACCAGTCGCTGGGACGACTGGACGAGGCAATCCCGCTCTACGAACAGACCCTCACCGAT
CTCCAAGAGCTTCTGGGGCGGAGCACCCCGACACCCTGAAATCCCGCAA
Found at i:52441 original size:15 final size:15
Alignment explanation
Indices: 52421--52458 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52411 CGTCACCTCG
*
52421 TCGGCATCACCCCAC
1 TCGGCATCACCACAC
52436 TCGGCAATCACCACAC
1 TCGGC-ATCACCACAC
52452 -CGGCATC
1 TCGGCATC
52459 GTCGGACCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.24, C:0.47, G:0.16, T:0.13
Consensus pattern (15 bp):
TCGGCATCACCACAC
Done.