Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2471
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: 54870
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:5775 original size:39 final size:40
Alignment explanation
Indices: 5674--5897 Score: 264
Period size: 40 Copynumber: 5.7 Consensus size: 40
5664 TTGAATGATG
* *
5674 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
5713 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
5754 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
5793 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
5832 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
5871 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
5898 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
39 75 0.45
40 77 0.47
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:5869 original size:79 final size:80
Alignment explanation
Indices: 5674--5897 Score: 285
Period size: 79 Copynumber: 2.8 Consensus size: 80
5664 TTGAATGATG
* * * * *
5674 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAGACCCGAAGGCATT
*
5738 TGTGCGAGATACTAAT
65 TGTGCGAGATACTAAA
*
5754 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGACCCGAAGGCATT
*
5816 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* * * * *
5832 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGACCCGAAGGCATTT
5897 G
66 G
5898 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
78 36 0.29
79 57 0.45
80 33 0.26
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:5911 original size:40 final size:38
Alignment explanation
Indices: 5727--5904 Score: 212
Period size: 39 Copynumber: 4.5 Consensus size: 38
5717 GGACTAAGAT
* * *
5727 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTACGAGTTACTAA-ACCGGGCTAAGC
* * *
5766 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTACGAGTTACTAA-ACCGGGCTAAGC
* *
5805 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTACGAGTTACTAAA-CCGGGCTAAG-C
*
5845 CCGAAGGCATTTGTACGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTACGAGTTACTA-AACCGGGCTAAG-C
*
5885 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGTACGAGT
5905 AGCTATATCC
Statistics
Matches: 129, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 73 0.57
40 54 0.42
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGAAGGCATTTGTACGAGTTACTAAACCGGGCTAAGC
Found at i:5920 original size:79 final size:78
Alignment explanation
Indices: 5727--5897 Score: 238
Period size: 78 Copynumber: 2.2 Consensus size: 78
5717 GGACTAAGAT
* *
5727 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGTGCGAGATACTAA-TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGATACTA
*
5791 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
* *
5805 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACT-
1 CCGAAGGCATTTGTGCGAGATACT-AATCCGGGTTAAGTCCCGAAGGCATTTGTACGAGATACTA
*
5869 ATAACCGGGCTATGTC
65 AT-ACCGGGCTAAG-C
5885 CCGAAGGCATTTG
1 CCGAAGGCATTTG
5898 AACGAGTAGC
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
78 35 0.42
79 34 0.41
80 14 0.17
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATCCGGGTTAAGTCCCGAAGGCATTTGTACGAGATACTAA
TACCGGGCTAAGC
Found at i:5928 original size:79 final size:79
Alignment explanation
Indices: 5727--5930 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 79
5717 GGACTAAGAT
** * * * * *
5727 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCT-AAGCCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTTGTACGAGATACTA
*
5791 ATTCCGGGCTAAGC
66 ATACCGGGCTAAGC
** * *
5805 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTTGTACGAGATACTA
*
5869 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* *
5885 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAATCCCGAAGG
5931 TACGTGATTT
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
78 34 0.31
79 49 0.45
80 25 0.23
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTTGTACGAGATACTA
ATACCGGGCTAAGC
Found at i:7522 original size:17 final size:17
Alignment explanation
Indices: 7502--7535 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7492 TTCGTATATT
*
7502 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
7519 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
7536 GCGAGTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:10247 original size:16 final size:15
Alignment explanation
Indices: 10226--10260 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10216 TAAAATCTTG
10226 TATATCTAGATAAAAA
1 TATATCTAGA-AAAAA
*
10242 TATATCTATAAAAAA
1 TATATCTAGAAAAAA
10257 TATA
1 TATA
10261 GACAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATATCTAGAAAAAA
Found at i:10547 original size:19 final size:19
Alignment explanation
Indices: 10523--10566 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
10513 TATTTATTTT
*
10523 TTTAATTAGAATCGAAAAG
1 TTTAATTAGAATAGAAAAG
10542 TTTAATTAGAATAGAAAAG
1 TTTAATTAGAATAGAAAAG
*
10561 TATAAT
1 TTTAAT
10567 AAAAGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (19 bp):
TTTAATTAGAATAGAAAAG
Found at i:11585 original size:15 final size:15
Alignment explanation
Indices: 11565--11598 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
11555 GATCATTTTG
11565 ACATTCTAATTCCAT
1 ACATTCTAATTCCAT
11580 ACATTCTAATTCCAT
1 ACATTCTAATTCCAT
11595 ACAT
1 ACAT
11599 AGACATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (15 bp):
ACATTCTAATTCCAT
Found at i:15340 original size:29 final size:29
Alignment explanation
Indices: 15298--15355 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
15288 GCAACCCATT
* *
15298 TTTATTATCATATCGAAACGCTATTCCTA
1 TTTATTATCATATCAAAACACTATTCCTA
15327 TTTATTATCATATCAAAACACTATTCCTA
1 TTTATTATCATATCAAAACACTATTCCTA
15356 ATAGAAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTATTATCATATCAAAACACTATTCCTA
Found at i:17723 original size:14 final size:14
Alignment explanation
Indices: 17704--17732 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17694 ACAGATGGAT
17704 TCGTATAATTCTTA
1 TCGTATAATTCTTA
17718 TCGTATAATTCTTA
1 TCGTATAATTCTTA
17732 T
1 T
17733 ATATATTGTA
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:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Found at i:22421 original size:14 final size:14
Alignment explanation
Indices: 22402--22430 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22392 TACAATATAT
22402 ATAAGAATTATACG
1 ATAAGAATTATACG
22416 ATAAGAATTATACG
1 ATAAGAATTATACG
22430 A
1 A
22431 ATCCATCTGT
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:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:24318 original size:19 final size:19
Alignment explanation
Indices: 24294--24337 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
24284 TATTTATTTT
24294 TTTAATTAGAATAGAAAAG
1 TTTAATTAGAATAGAAAAG
24313 TTTAATTAGAATAGAAAAG
1 TTTAATTAGAATAGAAAAG
*
24332 TATAAT
1 TTTAAT
24338 AAAAGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (19 bp):
TTTAATTAGAATAGAAAAG
Found at i:25358 original size:15 final size:15
Alignment explanation
Indices: 25338--25371 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
25328 GATCTTTTTG
25338 ACATTCTAATTCCAT
1 ACATTCTAATTCCAT
25353 ACATTCTAATTCCAT
1 ACATTCTAATTCCAT
25368 ACAT
1 ACAT
25372 AGACATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (15 bp):
ACATTCTAATTCCAT
Found at i:26016 original size:12 final size:12
Alignment explanation
Indices: 25991--26028 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
25981 ACAAAACAAC
25991 ATAAAAT-A-AG
1 ATAAAATAACAG
26001 ATAAAATAACAG
1 ATAAAATAACAG
*
26013 ATAAAATAACAT
1 ATAAAATAACAG
26025 ATAA
1 ATAA
26029 CATATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 7 0.28
11 1 0.04
12 17 0.68
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (12 bp):
ATAAAATAACAG
Found at i:28459 original size:10 final size:10
Alignment explanation
Indices: 28429--28469 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
28419 ATCACAAGTC
28429 TTGTGATATA
1 TTGTGATATA
*
28439 GTGTGATATA
1 TTGTGATATA
28449 TTGTGATATA
1 TTGTGATATA
*
28459 TATATGATATA
1 T-TGTGATATA
28470 CGTAGAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (10 bp):
TTGTGATATA
Found at i:37721 original size:15 final size:15
Alignment explanation
Indices: 37703--37733 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37693 ATCTCTCATC
37703 TATCTATCTATTTTT
1 TATCTATCTATTTTT
37718 TATCTATCTATTTTT
1 TATCTATCTATTTTT
37733 T
1 T
37734 CTTTAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATCTATCTATTTTT
Found at i:45873 original size:32 final size:32
Alignment explanation
Indices: 45832--45893 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
45822 CATCTATTTT
45832 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
45864 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
45894 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:47724 original size:95 final size:96
Alignment explanation
Indices: 47566--47745 Score: 219
Period size: 95 Copynumber: 1.9 Consensus size: 96
47556 TGAATGAAAT
* * *
47566 TGTGAAAGTGTATATATTGATAGGCGCTAATGGCCCGATGTGATGAATGTGAAATGTAATATATA
1 TGTGAAAGTGTATATATTGAGAGGCGCAAATAGCCCGATGTGATGAATGTGAAATGTAATATATA
*
47631 TG-GATAAGGGTCCTAATGGCCGATGGATGTA
66 TGTGATAAGGCT-CTAATGGCCGATGGATGTA
*
47662 TGTGAAAGT-TATATATGTGAGGAGGC-CAAATAG-CCGATGTGATTGAATGTG-AATAGT-GTA
1 TGTGAAAGTGTATATAT-TGA-GAGGCGCAAATAGCCCGATGTGA-TGAATGTGAAAT-GTAATA
*
47722 TATATGTGATGAGGCTCTAATGGC
62 TATATGTGATAAGGCTCTAATGGC
47746 GACTGTTGTA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
95 35 0.48
96 34 0.47
97 4 0.05
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (96 bp):
TGTGAAAGTGTATATATTGAGAGGCGCAAATAGCCCGATGTGATGAATGTGAAATGTAATATATA
TGTGATAAGGCTCTAATGGCCGATGGATGTA
Found at i:47726 original size:49 final size:48
Alignment explanation
Indices: 47545--47773 Score: 188
Period size: 49 Copynumber: 4.7 Consensus size: 48
47535 CACCGAGAGA
*
47545 TAATGG-CGATGTGAATGAAATTGTGAAAGTGTATATAT-TGA-TAGGCGC
1 TAATGGCCGATGTG-ATG-AA-TGTGAAAGTGTATATATGTGAGGAGGCGC
* **
47593 TAATGGCCCGATGTGATGAATGTGAAA-TGTAATATATATGGATAAGG-GTCC
1 TAATGG-CCGATGTGATGAATGTGAAAGTGT-ATATATGT-GAGGAGGCG--C
*
47644 TAATGGCCGATG-GATGTATGTGAAAGT-TATATATGTGAGGAGGC-C
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAGGAGGCGC
* * * *
47689 AAATAGCCGATGTGATTGAATGTGAATAGTGTATATATGTGATGAGGCTC
1 TAATGGCCGATGTGA-TGAATGTGAA-AGTGTATATATGTGAGGAGGCGC
47739 TAATGG-CGACTGTTGTATTGAATGTGAAAGTGTAT
1 TAATGGCCGA-TG-TG-A-TGAATGTGAAAGTGTAT
47774 TAGGTGACAG
Statistics
Matches: 152, Mismatches: 11, Indels: 33
0.78 0.06 0.17
Matches are distributed among these distances:
45 11 0.07
46 5 0.03
47 27 0.18
48 19 0.12
49 38 0.25
50 24 0.16
51 16 0.11
52 12 0.08
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.31
Consensus pattern (48 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAGGAGGCGC
Done.