Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold970
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: 19228
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:1321 original size:17 final size:17
Alignment explanation
Indices: 1299--1333 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1289 ATTTTTATTA
1299 TAAAAATTAAAA-TTAAT
1 TAAAAA-TAAAATTTAAT
1316 TAAAAATAAAATTTAAT
1 TAAAAATAAAATTTAAT
1333 T
1 T
1334 TGATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAATAAAATTTAAT
Found at i:1548 original size:18 final size:18
Alignment explanation
Indices: 1527--1561 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1517 TAACTTTAAC
* *
1527 TTAAACTCAATTTAAAAG
1 TTAAACTAAAATTAAAAG
1545 TTAAACTAAAATTAAAA
1 TTAAACTAAAATTAAAA
1562 TATATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAAACTAAAATTAAAAG
Found at i:2493 original size:23 final size:22
Alignment explanation
Indices: 2467--2523 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2457 TATACTTATT
2467 TATTTATTATTTAAAATTTTAAA
1 TATTTA-TATTTAAAATTTTAAA
* * *
2490 TATTAAATATTTATATTTTTAAA
1 TATT-TATATTTAAAATTTTAAA
2513 -ATTTATATTTA
1 TATTTATATTTA
2524 CATATGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 7 0.24
22 3 0.10
23 18 0.62
24 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTTATATTTAAAATTTTAAA
Found at i:2516 original size:15 final size:16
Alignment explanation
Indices: 2492--2522 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2482 ATTTTAAATA
2492 TTAAATATTTATATTT
1 TTAAATATTTATATTT
2508 TTAAA-ATTTATATTT
1 TTAAATATTTATATTT
2523 ACATATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAAATATTTATATTT
Found at i:2643 original size:18 final size:19
Alignment explanation
Indices: 2600--2644 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2590 ATAAATTATA
*
2600 AATATAT-ATCTCAAAAAT
1 AATATATAAACTCAAAAAT
*
2618 ATTA-ATAAACTC-AAAAT
1 AATATATAAACTCAAAAAT
2635 AATATATAAA
1 AATATATAAA
2645 AAAATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATATAAACTCAAAAAT
Found at i:5351 original size:15 final size:15
Alignment explanation
Indices: 5331--5361 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5321 GCCAAGTCCA
5331 AAAAAAAAAAAAATT
1 AAAAAAAAAAAAATT
*
5346 AAAAAAAGAAAAATT
1 AAAAAAAAAAAAATT
5361 A
1 A
5362 TGGTTGGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAAAAAAAAAATT
Found at i:5553 original size:34 final size:33
Alignment explanation
Indices: 5527--5676 Score: 147
Period size: 34 Copynumber: 4.4 Consensus size: 33
5517 TGGTGATTTG
5527 CCATTGTTGATTAAATGGGAGATTTGGTAACTTA
1 CCATTGTTGATTAAATGGGAGATTTGGT-ACTTA
* *
5561 CCATTGTTGATTAAATGAGAAATTTGGTAGCTTA
1 CCATTGTTGATTAAATGGGAGATTTGGTA-CTTA
* * * * *
5595 CTATTATTGATTAAATGGGTGATTTGATGGCTTA
1 CCATTGTTGATTAAATGGGAGATTTGGT-ACTTA
* * * * * *
5629 TCATTGTTGACTAAATGGTAGATTTAGTAGGTTG
1 CCATTGTTGATTAAATGGGAGATTTGGTA-CTTA
5663 CCATTGTTGATTAA
1 CCATTGTTGATTAA
5677 TGGTGGTTTT
Statistics
Matches: 91, Mismatches: 22, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
33 1 0.01
34 90 0.99
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.41
Consensus pattern (33 bp):
CCATTGTTGATTAAATGGGAGATTTGGTACTTA
Found at i:5587 original size:68 final size:68
Alignment explanation
Indices: 5524--5676 Score: 182
Period size: 68 Copynumber: 2.2 Consensus size: 68
5514 TTTTGGTGAT
* *
5524 TTGCCATTGTTGATTAAATGGGAGATTTGGTAACTTACCATTGTTGATTAAATGAG-AAATTTGG
1 TTGCCATTGTTGATTAAATGGGAGATTTGATAACTTACCATTGTTGACTAAATG-GTAAATTTGG
5588 TAGC
65 TAGC
* * * * ** * * *
5592 TTACTATTATTGATTAAATGGGTGATTTGATGGCTTATCATTGTTGACTAAATGGTAGATTTAGT
1 TTGCCATTGTTGATTAAATGGGAGATTTGATAACTTACCATTGTTGACTAAATGGTAAATTTGGT
*
5657 AGG
66 AGC
5660 TTGCCATTGTTGATTAA
1 TTGCCATTGTTGATTAA
5677 TGGTGGTTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
67 1 0.01
68 68 0.99
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (68 bp):
TTGCCATTGTTGATTAAATGGGAGATTTGATAACTTACCATTGTTGACTAAATGGTAAATTTGGT
AGC
Found at i:9996 original size:34 final size:34
Alignment explanation
Indices: 9939--10157 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 34
9929 AAGTGGGAGA
*
9939 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
9972 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
10006 ATTATTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* ** *
10040 ATTGTTGATTAAATGAGAAATTTGATAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
10074 ATTATTGATTAAATGGGTGATTTGGTAACTTACT
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
10108 ATTGTTGACTAAAT-AGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
10142 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
10158 TGGTTTTTAC
Statistics
Matches: 154, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
33 16 0.10
34 138 0.90
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:10084 original size:102 final size:101
Alignment explanation
Indices: 9939--10157 Score: 294
Period size: 102 Copynumber: 2.2 Consensus size: 101
9929 AAGTGGGAGA
** * * * *** *
9939 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTAACTTA
*
10004 CCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTATTGACTAAATAGGAGATTTGGTAGCTTACC
10040 ATTGTTGATTAAATGAGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTAACTT
1 ATTGTTGATTAAATG-GAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTAACTT
* * * * *
10105 ACTATTGTTGACTAAATAGTAGATTTGGTAGGTTGCC
65 ACCATTATTGACTAAATAGGAGATTTGGTAGCTTACC
10142 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
10158 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
101 16 0.16
102 86 0.84
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTAACTTA
CCATTATTGACTAAATAGGAGATTTGGTAGCTTACC
Found at i:12382 original size:29 final size:29
Alignment explanation
Indices: 12325--12382 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
12315 TTTTAGTCAA
* *
12325 TTGATTTGAATTAATATTTAATAAGTATT
1 TTGATTTAAATTAATATTTAATAAATATT
12354 TTGATTTAAATTTAA-ATTATAA-AAATATT
1 TTGATTTAAA-TTAATATT-TAATAAATATT
12383 ATATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (29 bp):
TTGATTTAAATTAATATTTAATAAATATT
Found at i:12815 original size:16 final size:17
Alignment explanation
Indices: 12784--12817 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12774 TGTATTATTT
12784 AAATATATTAAATATAA
1 AAATATATTAAATATAA
*
12801 AAATAT-TTTAATATAA
1 AAATATATTAAATATAA
12817 A
1 A
12818 GTTTATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATATTAAATATAA
Found at i:13355 original size:64 final size:61
Alignment explanation
Indices: 13206--13363 Score: 183
Period size: 62 Copynumber: 2.5 Consensus size: 61
13196 AGAGACTCTT
* * * * * *
13206 ATGGCAATTGAACTGCTGAAATTAGTTGCCAACTTGGATATTGTAGCATTGATTTGGCTGAA
1 ATGGCAATTGAATTGCTG-ATTTAGTTGCCAACTTAGAGATTATAGCATTGATTTGGCCGAA
* *
13268 ATGGCAATTAAATTACTAGATTTAGTTGCCAACTTAAGAGATTATAGCATT-AGTTTGGCCGAAA
1 ATGGCAATTGAATTGCT-GATTTAGTTGCCAACTT-AGAGATTATAGCATTGA-TTTGGCCG-AA
13332 ATGGCAATTGAATTGCTGCATTTAGTTGCCAA
1 ATGGCAATTGAATTGCTG-ATTTAGTTGCCAA
13364 AGTTGGACAC
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
62 30 0.37
63 21 0.26
64 30 0.37
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.34
Consensus pattern (61 bp):
ATGGCAATTGAATTGCTGATTTAGTTGCCAACTTAGAGATTATAGCATTGATTTGGCCGAA
Found at i:13389 original size:64 final size:61
Alignment explanation
Indices: 13206--13390 Score: 190
Period size: 64 Copynumber: 2.9 Consensus size: 61
13196 AGAGACTCTT
* * * * *
13206 ATGGCAATTGAACTGCTGAAATTAGTTGCCAACTTGGATATTGTAGCATTGATTTGGCTGAA
1 ATGGCAATTGAATTGCTG-ATTTAGTTGCCAACTTGGACATTGTAGCATTAATTTGGCCGAA
* * * * * *
13268 ATGGCAATTAAATTACTAGATTTAGTTGCCAACTTAAGAGATTATAGCATTAGTTTGGCCGAAA
1 ATGGCAATTGAATTGCT-GATTTAGTTGCCAACTT-GGACATTGTAGCATTAATTTGGCCG-AA
* * *
13332 ATGGCAATTGAATTGCTGCATTTAGTTGCCAAAGTTGGACACTGTAGCGTTAATTTGGC
1 ATGGCAATTGAATTGCTG-ATTTAGTTGCC-AACTTGGACATTGTAGCATTAATTTGGC
13391 AAAAACGTGA
Statistics
Matches: 99, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
62 29 0.29
63 21 0.21
64 45 0.45
65 4 0.04
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (61 bp):
ATGGCAATTGAATTGCTGATTTAGTTGCCAACTTGGACATTGTAGCATTAATTTGGCCGAA
Found at i:14171 original size:39 final size:40
Alignment explanation
Indices: 14122--14214 Score: 111
Period size: 39 Copynumber: 2.3 Consensus size: 40
14112 AAAACCGTAG
*
14122 TTAAATTTTAAATAA-TATTTTTATAAATTAAAATAT-TTAAT
1 TTAAA-TTTAAATAATTA-TTTTAT-AATAAAAATATGTTAAT
* *
14163 TT-AATTTAAATTATTATTTTATAATAAAAATATGTTTAT
1 TTAAATTTAAATAATTATTTTATAATAAAAATATGTTAAT
14202 TTAAATTTAAATA
1 TTAAATTTAAATA
14215 TAAAATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
38 10 0.22
39 20 0.44
40 13 0.29
41 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (40 bp):
TTAAATTTAAATAATTATTTTATAATAAAAATATGTTAAT
Found at i:17206 original size:17 final size:17
Alignment explanation
Indices: 17176--17223 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
17166 AATATACTTA
*
17176 AAAATAAATTTAAATTT
1 AAAATAATTTTAAATTT
17193 ATAAA-AATTTTAAA-TT
1 A-AAATAATTTTAAATTT
17209 AAAATAATTTTAAAT
1 AAAATAATTTTAAAT
17224 ATTTTTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.11
16 12 0.44
17 9 0.33
18 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATAATTTTAAATTT
Found at i:17660 original size:29 final size:27
Alignment explanation
Indices: 17621--17688 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
17611 TTTAAGTTGA
**
17621 TAAATAATTATCATTATTTATTTTATTTT
1 TAAATAATTAT--TTAAATATTTTATTTT
*
17650 TAAATTATTATTTAAATATTTTATTTT
1 TAAATAATTATTTAAATATTTTATTTT
17677 T-AATAA-TATTTA
1 TAAATAATTATTTA
17689 TCTAATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 6 0.17
26 4 0.11
27 15 0.43
29 10 0.29
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (27 bp):
TAAATAATTATTTAAATATTTTATTTT
Found at i:17681 original size:14 final size:14
Alignment explanation
Indices: 17639--17681 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
17629 TATCATTATT
17639 TATTTTATTTTTAA
1 TATTTTATTTTTAA
*
17653 -ATTATTA-TTTAAA
1 TATT-TTATTTTTAA
17666 TATTTTATTTTTAA
1 TATTTTATTTTTAA
17680 TA
1 TA
17682 ATATTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTATTTTTAA
Found at i:17697 original size:25 final size:27
Alignment explanation
Indices: 17642--17698 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
17632 CATTATTTAT
* *
17642 TTTATTTTTAAATTATTATTTAAATAT
1 TTTATTTTTAAATTAATATTTAAATAA
**
17669 TTTATTTTT-AA-TAATATTTATCTAA
1 TTTATTTTTAAATTAATATTTAAATAA
17694 TTTAT
1 TTTAT
17699 AAGTAATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 15 0.58
26 2 0.08
27 9 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTATTTTTAAATTAATATTTAAATAA
Found at i:17812 original size:15 final size:15
Alignment explanation
Indices: 17792--17827 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
17782 AATAATAATT
*
17792 TATTATAATATTATA
1 TATTATAAGATTATA
17807 TATTATAAGATTATA
1 TATTATAAGATTATA
17822 -ATTATA
1 TATTATA
17828 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TATTATAAGATTATA
Done.