Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold288
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 32900
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:1847 original size:44 final size:44
Alignment explanation
Indices: 1797--1921 Score: 205
Period size: 44 Copynumber: 2.8 Consensus size: 44
1787 GGAGTTGAGC
*
1797 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1841 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* *
1885 ACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1922 GGGCGGGTTA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
44 44 0.58
46 32 0.42
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:2432 original size:14 final size:14
Alignment explanation
Indices: 2409--2444 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2399 CAATATACTT
*
2409 ATTTTGTGTAAATA
1 ATTTTATGTAAATA
2423 ATTTTATGTAAATA
1 ATTTTATGTAAATA
2437 ATTTTATG
1 ATTTTATG
2445 ATTGGCCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (14 bp):
ATTTTATGTAAATA
Found at i:9320 original size:46 final size:46
Alignment explanation
Indices: 9270--9442 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
9260 TGGTTGAGCA
9270 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
9316 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
9361 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
9409 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
9443 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:9426 original size:93 final size:93
Alignment explanation
Indices: 9267--9437 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
9257 GGATGGTTGA
* *
9267 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
9332 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
9360 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
9425 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
9438 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:13319 original size:40 final size:40
Alignment explanation
Indices: 13235--13418 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
13225 TTGAATGCTG
* * * *
13235 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
13274 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
13315 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
13355 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
13395 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
13419 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:13372 original size:80 final size:81
Alignment explanation
Indices: 13235--13415 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
13225 TTGAATGCTG
* * *
13235 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
13299 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
13315 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
13376 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
13395 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
13416 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:13439 original size:39 final size:38
Alignment explanation
Indices: 13316--13465 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
13306 GTTATTAATT
* ** * *
13316 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
13356 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
13395 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
13435 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
13466 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:15030 original size:77 final size:77
Alignment explanation
Indices: 14949--15111 Score: 181
Period size: 77 Copynumber: 2.1 Consensus size: 77
14939 GAATTTAAAC
* * *
14949 CCGG-TATAATACCAGCT-CGA-AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAGCACGTAG
1 CCGGATATAATACCAG-TAC-ATAGCCTGC-GGACCTTAAGCCCGGACATA-TTCCAACACATAG
*
15010 CCTGCGGACCATAAGT
62 CCTCCGGACCATAAGT
* * * *
15026 CCGGTTATAATTCCAGTACATAGCCTGCGGACCTTAAGTCCGGATATATTCCAACACATAGCCTC
1 CCGGATATAATACCAGTACATAGCCTGCGGACCTTAAGCCCGGACATATTCCAACACATAGCCTC
*
15091 CGGACCTTAAGT
66 CGGACCATAAGT
15103 CCGGATATA
1 CCGGATATA
15112 CTTCATCATT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
77 42 0.58
78 31 0.42
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (77 bp):
CCGGATATAATACCAGTACATAGCCTGCGGACCTTAAGCCCGGACATATTCCAACACATAGCCTC
CGGACCATAAGT
Found at i:15040 original size:39 final size:39
Alignment explanation
Indices: 14916--15111 Score: 177
Period size: 39 Copynumber: 5.1 Consensus size: 39
14906 AACTTGAAAC
** **
14916 TAATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TA
1 TAATT-CCAGCACATAGCCTGC-GGACCTTAAGTCCGGATA
* * * * *
14955 TAATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACA
1 TAATTCCAGCAC-ATAGCCTGC-GGACCTTAAGTCCGGATA
* * * *
14994 TATTTCCAGCACGTAGCCTGCGGACCATAAGTCCGGTTA
1 TAATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATA
*
15033 TAATTCCAGTACATAGCCTGCGGACCTTAAGTCCGGATA
1 TAATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATA
* *
15072 T-ATTCCAACACATAGCCTCCGGACCTTAAGTCCGGATA
1 TAATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATA
15110 TA
1 TA
15112 CTTCATCATT
Statistics
Matches: 129, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
38 52 0.40
39 77 0.60
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (39 bp):
TAATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATA
Found at i:19370 original size:27 final size:27
Alignment explanation
Indices: 19293--19397 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
19283 TAAAACTCTA
**
19293 ATTTATAAAATTACTGAAATATACCCG
1 ATTTATAAAATTACTGAAATACCCCCG
* * * *
19320 GTTTGTAAAATTACTAAAACACCCCCG
1 ATTTATAAAATTACTGAAATACCCCCG
*
19347 ATTTATAAAATTA-TCGAAATACCCCCA
1 ATTTATAAAATTACT-GAAATACCCCCG
*
19374 ATTTTTAAAATTA-TCGAAATACCC
1 ATTTATAAAATTACT-GAAATACCC
19398 TTGTAGTGTA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.02
27 64 0.98
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
ATTTATAAAATTACTGAAATACCCCCG
Found at i:19409 original size:27 final size:27
Alignment explanation
Indices: 19379--19438 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
19369 CCCCAATTTT
* * *
19379 TAAAATTATCGAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTGTAGGG
19406 TAAAATTACCGAAATACCCCTGTAGGG
1 TAAAATTACCGAAATACCCCTGTAGGG
19433 TAAAAT
1 TAAAAT
19439 GACTGGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCTGTAGGG
Found at i:19839 original size:22 final size:22
Alignment explanation
Indices: 19788--19842 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
19778 TTGCTTACTC
19788 TGATTATGGCTCTGTGCCAAAT
1 TGATTATGGCTCTGTGCCAAAT
* * * **
19810 TAAATATGGCTCTGTGCTATGT
1 TGATTATGGCTCTGTGCCAAAT
19832 TGATTATGGCT
1 TGATTATGGCT
19843 TTTTACAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.40
Consensus pattern (22 bp):
TGATTATGGCTCTGTGCCAAAT
Found at i:19928 original size:27 final size:27
Alignment explanation
Indices: 19873--19939 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
19863 AGTGGCTATA
* * *
19873 TGCCTATCATATTTATTGATGACTCTG
1 TGCCGATCATATTTACTCATGACTCTG
* * *
19900 TGTCGATCATATTTACTCATGGCTGTG
1 TGCCGATCATATTTACTCATGACTCTG
*
19927 TGCCGATTATATT
1 TGCCGATCATATT
19940 ACCGTCGCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (27 bp):
TGCCGATCATATTTACTCATGACTCTG
Found at i:20825 original size:14 final size:13
Alignment explanation
Indices: 20801--20826 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20791 TTCTTAATAA
20801 GAAAAAGTTTTTT
1 GAAAAAGTTTTTT
20814 GAAAAAGTTTTTT
1 GAAAAAGTTTTTT
20827 AATGTGACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
GAAAAAGTTTTTT
Found at i:23938 original size:27 final size:26
Alignment explanation
Indices: 23890--23941 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
23880 GCGAGGCTGC
*
23890 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
23916 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
23942 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:31271 original size:27 final size:26
Alignment explanation
Indices: 31223--31282 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
31213 GCGAGGCTGC
*
31223 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
31250 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
31276 CAGATAT
1 CAGATAT
31283 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:31327 original size:71 final size:67
Alignment explanation
Indices: 31250--31391 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
31240 TCACCAGATA
* * *
31250 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
31315 GGCTGC
62 GGCTGC
* *
31321 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
31386 GC
66 GC
31388 CAGA
1 CAGA
31392 ACGCTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 41 0.62
71 25 0.38
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:31369 original size:27 final size:26
Alignment explanation
Indices: 31321--31372 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
31311 GCGAGGCTGC
*
31321 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
31347 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
31373 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Done.