Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold678
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: 30237
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Found at i:4752 original size:34 final size:35
Alignment explanation
Indices: 4714--4780 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
4704 CCTTACAACA
4714 CTATC-TTTC-AAGGCTAAGATAAAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGAT-AAAACCTCTCTCT
*
4748 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAAAACCTCTC
4781 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 13 0.45
37 11 0.38
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAAAACCTCTCTCT
Found at i:5257 original size:13 final size:13
Alignment explanation
Indices: 5239--5263 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5229 AATTTTTTGG
5239 TGTATCGATACAT
1 TGTATCGATACAT
5252 TGTATCGATACA
1 TGTATCGATACA
5264 AGTTTGGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7042 original size:13 final size:13
Alignment explanation
Indices: 7024--7048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7014 ACTCAAGCAA
7024 TGTATCGATACAT
1 TGTATCGATACAT
7037 TGTATCGATACA
1 TGTATCGATACA
7049 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8142 original size:13 final size:13
Alignment explanation
Indices: 8124--8149 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8114 AATTTTTTGG
8124 TGTATCGATACAT
1 TGTATCGATACAT
8137 TGTATCGATACAT
1 TGTATCGATACAT
8150 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12298 original size:26 final size:26
Alignment explanation
Indices: 12248--12298 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
12238 GATAGTATTA
* * *
12248 ATAAAGTTTAACTTTATTTGGGATTG
1 ATAAAGTTCAACTTTATATGAGATTG
12274 ATAAAGTTCAACTTTATATGAGATT
1 ATAAAGTTCAACTTTATATGAGATT
12299 CTAAATAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (26 bp):
ATAAAGTTCAACTTTATATGAGATTG
Found at i:17008 original size:15 final size:16
Alignment explanation
Indices: 16983--17013 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16973 TTTATGAATA
16983 TTTTAATATATAAAAT
1 TTTTAATATATAAAAT
16999 TTTTAA-ATATAAAAT
1 TTTTAATATATAAAAT
17014 AAATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAATATATAAAAT
Found at i:17579 original size:16 final size:16
Alignment explanation
Indices: 17557--17602 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
17547 TTCGGGCAGG
17557 TTCGGGTTCAGGCTCA
1 TTCGGGTTCAGGCTCA
* * *
17573 TTTGGGTTCATGCTCG
1 TTCGGGTTCAGGCTCA
17589 TTCGGGTTCAGGCT
1 TTCGGGTTCAGGCT
17603 TTTTTCAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.09, C:0.22, G:0.33, T:0.37
Consensus pattern (16 bp):
TTCGGGTTCAGGCTCA
Found at i:17648 original size:16 final size:16
Alignment explanation
Indices: 17627--17660 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17617 TTCGGACTCT
17627 TTCAGGTTCAGGCTTA
1 TTCAGGTTCAGGCTTA
*
17643 TTCAGGTTCGGGCTTA
1 TTCAGGTTCAGGCTTA
17659 TT
1 TT
17661 TAGGCTCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.41
Consensus pattern (16 bp):
TTCAGGTTCAGGCTTA
Found at i:17669 original size:16 final size:16
Alignment explanation
Indices: 17627--17670 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
17617 TTCGGACTCT
* *
17627 TTCAGGTTCAGGCTTA
1 TTCAGGCTCGGGCTTA
*
17643 TTCAGGTTCGGGCTTA
1 TTCAGGCTCGGGCTTA
*
17659 TTTAGGCTCGGG
1 TTCAGGCTCGGG
17671 TTTAGGTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (16 bp):
TTCAGGCTCGGGCTTA
Found at i:17867 original size:18 final size:18
Alignment explanation
Indices: 17844--17886 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
17834 TCTATATTTA
17844 TATATAAAATTAATTTTT
1 TATATAAAATTAATTTTT
17862 TATATAAAATTAATTTTT
1 TATATAAAATTAATTTTT
*
17880 TAAATAA
1 TATATAA
17887 TTTATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATAAAATTAATTTTT
Found at i:19043 original size:16 final size:16
Alignment explanation
Indices: 19024--19054 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19014 GGGTTCGAGC
*
19024 TTTCTCTAGTTCGGAT
1 TTTCTCAAGTTCGGAT
19040 TTTCTCAAGTTCGGA
1 TTTCTCAAGTTCGGA
19055 CGATTTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (16 bp):
TTTCTCAAGTTCGGAT
Found at i:19904 original size:53 final size:53
Alignment explanation
Indices: 19837--19943 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
19827 AAACCGATAT
19837 ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
1 ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
*
19890 ACCAAATCACACAGATACATATACATATATCAATATGAAAATAAAAATAATAC
1 ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
19943 A
1 A
19944 TTGACTAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.57, C:0.18, G:0.04, T:0.21
Consensus pattern (53 bp):
ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
Found at i:24644 original size:26 final size:26
Alignment explanation
Indices: 24614--24667 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
24604 AAACCCTAAC
*
24614 CCTAATTGACGCCAACCAAACCAAAT
1 CCTAATTGACCCCAACCAAACCAAAT
* *
24640 CCTAATTGACCCCAATCAAACTAAAT
1 CCTAATTGACCCCAACCAAACCAAAT
24666 CC
1 CC
24668 AATCTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.19
Consensus pattern (26 bp):
CCTAATTGACCCCAACCAAACCAAAT
Found at i:25368 original size:15 final size:15
Alignment explanation
Indices: 25348--25425 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
25338 AAAATTTTAA
25348 TTAATTTATTTAAAT
1 TTAATTTATTTAAAT
*
25363 TTAATTTAATTAAA-
1 TTAATTTATTTAAAT
* * *
25377 --AATTAATTAAAAA
1 TTAATTTATTTAAAT
*
25390 TTAATTAATTTAAAT
1 TTAATTTATTTAAAT
* *
25405 ATAAAAATTATTTAAAT
1 -T-TAATTTATTTAAAT
25422 TTAA
1 TTAA
25426 AATAATTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
12 9 0.19
15 26 0.54
16 2 0.04
17 11 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTTATTTAAAT
Found at i:25382 original size:11 final size:11
Alignment explanation
Indices: 25368--25397 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
25358 TAAATTTAAT
25368 TTAATTAAAAA
1 TTAATTAAAAA
25379 TTAATTAAAAA
1 TTAATTAAAAA
25390 TTAATTAA
1 TTAATTAA
25398 TTTAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAATTAAAAA
Found at i:25384 original size:16 final size:16
Alignment explanation
Indices: 25346--25467 Score: 69
Period size: 16 Copynumber: 7.6 Consensus size: 16
25336 TAAAAATTTT
*
25346 AATTAATTT-ATTTAA
1 AATTAATTTAATTAAA
*
25361 ATTTAATTTAATTAAA
1 AATTAATTTAATTAAA
25377 AATTAA-TTAA--AAA
1 AATTAATTTAATTAAA
25390 TTAATTAATTTAAATATAAA
1 --AATTAATTT-AAT-TAAA
*
25410 AATT-ATTTAAATTTAA
1 AATTAATTT-AATTAAA
*
25426 AA-TAATTTAAATATAA
1 AATTAATTTAATTA-AA
* **
25442 AATAAATCGAATATAAA
1 AATTAATTTAAT-TAAA
25459 AA-TAATTTA
1 AATTAATTTA
25468 TACTTAAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 23
0.69 0.11 0.19
Matches are distributed among these distances:
13 3 0.04
15 22 0.27
16 29 0.35
17 19 0.23
18 6 0.07
20 3 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
AATTAATTTAATTAAA
Found at i:25411 original size:23 final size:22
Alignment explanation
Indices: 25384--25430 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
25374 AAAAATTAAT
25384 TAAAAATTAATT-AATTTAAATA
1 TAAAAATTAATTAAATTTAAA-A
*
25406 TAAAAATTATTTAAATTTAAAA
1 TAAAAATTAATTAAATTTAAAA
25428 TAA
1 TAA
25431 TTTAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATTAATTAAATTTAAAA
Found at i:25419 original size:17 final size:17
Alignment explanation
Indices: 25392--25443 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 17
25382 ATTAAAAATT
25392 AATTAATTTAAATATAAA
1 AATT-ATTTAAATATAAA
*
25410 AATTATTTAAAT-TTAA
1 AATTATTTAAATATAAA
*
25426 AATAATTTAAATATAAA
1 AATTATTTAAATATAAA
25443 A
1 A
25444 TAAATCGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.47
17 12 0.40
18 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTATTTAAATATAAA
Found at i:25420 original size:33 final size:33
Alignment explanation
Indices: 25357--25443 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
25347 ATTAATTTAT
25357 TTAAATTTAATTT-AAT-TAAAAATTAATTAAAAA
1 TTAAA-TTAATTTAAATATAAAAATTAATT-AAAA
* *
25390 TT-AATTAATTTAAATATAAAAATTATTTAAAT
1 TTAAATTAATTTAAATATAAAAATTAATTAAAA
*
25422 TTAAAATAATTTAAATATAAAA
1 TTAAATTAATTTAAATATAAAA
25444 TAAATCGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 7 0.15
32 10 0.21
33 31 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TTAAATTAATTTAAATATAAAAATTAATTAAAA
Found at i:25493 original size:49 final size:49
Alignment explanation
Indices: 25402--25495 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
25392 AATTAATTTA
* * **
25402 AATATAAAAATTATTTAAATTTAAAATAATTTAAATATAAAATAAATCG
1 AATATAAAAATAATTTAAACTTAAAATAATACAAATATAAAATAAATCG
*
25451 AATATAAAAATAATTTATACTTAAAATAATACAAAT-TCAAAATAA
1 AATATAAAAATAATTTAAACTTAAAATAATACAAATAT-AAAATAA
25496 CTCAAATCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.03
49 38 0.97
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (49 bp):
AATATAAAAATAATTTAAACTTAAAATAATACAAATATAAAATAAATCG
Found at i:25642 original size:27 final size:28
Alignment explanation
Indices: 25612--25676 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
25602 TTAATTAATT
*
25612 TAAATTTAAAAT-AATAC-AAATTTAAAA
1 TAAATTTAAAATCAA-ACTAAATATAAAA
*
25639 TAAA-TAAAAATCAAACTAAATATAAAA
1 TAAATTTAAAATCAAACTAAATATAAAA
25666 -ATAATTTAAAA
1 TA-AATTTAAAA
25677 ATTTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 9 0.29
27 17 0.55
28 5 0.16
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (28 bp):
TAAATTTAAAATCAAACTAAATATAAAA
Found at i:25649 original size:17 final size:16
Alignment explanation
Indices: 25613--25649 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
25603 TAATTAATTT
*
25613 AAATTTAAAATAATAC
1 AAATTTAAAATAATAA
25629 AAATTTAAAATAAATAA
1 AAATTTAAAAT-AATAA
25646 AAAT
1 AAAT
25650 CAAACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTTAAAATAATAA
Found at i:25707 original size:18 final size:20
Alignment explanation
Indices: 25686--25733 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
25676 AATTTAAATT
25686 AACTTAA-TCA-TAACTCAA
1 AACTTAATTCATTAACTCAA
25704 AAC-TAATTCATTAACTCAA
1 AACTTAATTCATTAACTCAA
25723 AAC-TAATTCAT
1 AACTTAATTCAT
25734 CATTCATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.11
18 6 0.21
19 19 0.68
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (20 bp):
AACTTAATTCATTAACTCAA
Found at i:25720 original size:19 final size:19
Alignment explanation
Indices: 25696--25733 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25686 AACTTAATCA
25696 TAACTCAAAACTAATTCAT
1 TAACTCAAAACTAATTCAT
25715 TAACTCAAAACTAATTCAT
1 TAACTCAAAACTAATTCAT
25734 CATTCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (19 bp):
TAACTCAAAACTAATTCAT
Found at i:29524 original size:20 final size:20
Alignment explanation
Indices: 29499--29536 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29489 GAGAACCTAG
*
29499 AATGTATGGATACAATTTTA
1 AATGTATCGATACAATTTTA
29519 AATGTATCGATACAATTT
1 AATGTATCGATACAATTT
29537 CCTTTCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACAATTTTA
Found at i:29603 original size:20 final size:20
Alignment explanation
Indices: 29560--29633 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
29550 CACATGGTTC
***
29560 TGTATCGATACATTTCAAGCA
1 TGTATCGATACA-TTCACTTA
29581 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
29601 TGTAT-GAATACATTGC-CTTA
1 TGTATCG-ATACATT-CACTTA
*
29621 TTGTATTGATACA
1 -TGTATCGATACA
29634 AATTGTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.02
20 21 0.46
21 23 0.50
22 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:29632 original size:21 final size:20
Alignment explanation
Indices: 29580--29633 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
29570 CATTTCAAGC
*
29580 ATGTATCGATACATTCACTT
1 ATGTATTGATACATTCACTT
29600 ATGTA-TGAATACATTGC-CTT
1 ATGTATTG-ATACATT-CACTT
29620 ATTGTATTGATACA
1 A-TGTATTGATACA
29634 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 10 0.34
22 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATTGATACATTCACTT
Done.