Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3830
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: 72852
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:5612 original size:18 final size:19
Alignment explanation
Indices: 5579--5619 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5569 TTGAATTCTT
**
5579 TTTTTTATTTTTC-TTTTC
1 TTTTTTATTTCGCTTTTTC
5597 TTTTTTATTTCGCTTTTTC
1 TTTTTTATTTCGCTTTTTC
5616 TTTT
1 TTTT
5620 CTCTCATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTATTTCGCTTTTTC
Found at i:7957 original size:20 final size:20
Alignment explanation
Indices: 7934--7980 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7924 GGGTTAAGAT
*
7934 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
7954 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
7974 TGAGCTG
1 TGAGCTG
7981 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:9702 original size:48 final size:48
Alignment explanation
Indices: 9650--9753 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
9640 TTGTCTTTTC
*
9650 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
9698 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
9746 TTTCTTTT
1 TTTCTTTT
9754 CCATGACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:12384 original size:20 final size:20
Alignment explanation
Indices: 12361--12407 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12351 TGGTTAGGAT
*
12361 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
12381 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
12401 TGAGCTG
1 TGAGCTG
12408 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:14086 original size:22 final size:22
Alignment explanation
Indices: 14056--14099 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
14046 TTTGGTATTT
14056 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
14078 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
14100 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:16449 original size:10 final size:10
Alignment explanation
Indices: 16434--16470 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
16424 CGATATTGTA
16434 AAAAAAATTC
1 AAAAAAATTC
16444 AAAAAAATTC
1 AAAAAAATTC
16454 AAAAAAATTC
1 AAAAAAATTC
16464 AAAAAAA
1 AAAAAAA
16471 AATTTGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:17742 original size:10 final size:11
Alignment explanation
Indices: 17708--17756 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
17698 AGAGAAGAGG
17708 AAATTCAAAAAA
1 AAATT-AAAAAA
*
17720 AAATTTTGAAAAA
1 AAA--TTAAAAAA
*
17733 AAATTGAAAAA
1 AAATTAAAAAA
17744 AAATTAAAAAA
1 AAATTAAAAAA
17755 AA
1 AA
17757 TCGAAGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 20 0.61
12 3 0.09
13 8 0.24
14 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (11 bp):
AAATTAAAAAA
Found at i:17757 original size:10 final size:11
Alignment explanation
Indices: 17715--17757 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
17705 AGGAAATTCA
17715 AAAAAAAATTTTG
1 AAAAAAAA--TTG
17728 AAAAAAAATTG
1 AAAAAAAATTG
17739 AAAAAAAATT-
1 AAAAAAAATTG
17749 AAAAAAAAT
1 AAAAAAAAT
17758 CGAAGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.30
11 13 0.43
13 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:19259 original size:16 final size:15
Alignment explanation
Indices: 19240--19269 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19230 AGTATCAATT
19240 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
19256 TTTGATTGGGATGA
1 TTTGATTGGGATGA
19270 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:23907 original size:20 final size:19
Alignment explanation
Indices: 23884--23948 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
23874 AAGCTCAAAC
23884 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
23904 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
23924 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
23944 GAGCT
1 GAGCT
23949 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:28706 original size:49 final size:49
Alignment explanation
Indices: 28649--28746 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
28639 AAGGTTTGTT
28649 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
* *
28698 TGATACGAGTCACAAAGGCTCAACCCAAGCTTAAGAAGGTGATGGGCTC
1 TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
28747 AAATCAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (49 bp):
TGATACGAGTCACAAAGGCCCAACCCAAGCTCAAGAAGGTGATGGGCTC
Found at i:33424 original size:17 final size:15
Alignment explanation
Indices: 33387--33425 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
33377 TATCTCCCAC
33387 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
33403 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
33420 TCATTT
1 TCATTT
33426 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:34317 original size:29 final size:30
Alignment explanation
Indices: 34275--34343 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
34265 CAATCACTCT
* *
34275 TTTTTTTTTCAATTTCGATTTTTTTTCTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTCTTC
34305 TTTTTTTTT-AATTCCGAATTTTTTTCTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTCTTC
34334 TTTTTTTTTC
1 TTTTTTTTTC
34344 CTTCAATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (30 bp):
TTTTTTTTTCAATTCCGAATTTTTTTCTTC
Found at i:34405 original size:12 final size:11
Alignment explanation
Indices: 34388--34426 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
34378 GAATACAAAC
34388 TTTTTTTTGAA
1 TTTTTTTTGAA
34399 TTTTTTTTGAA
1 TTTTTTTTGAA
34410 TTTTTTTT--A
1 TTTTTTTTGAA
34419 TTTTTTTT
1 TTTTTTTT
34427 ACAATACCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.32
11 19 0.68
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:37472 original size:17 final size:15
Alignment explanation
Indices: 37435--37473 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
37425 TATCTCCCAC
37435 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
37451 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
37468 TCATTT
1 TCATTT
37474 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:38358 original size:27 final size:28
Alignment explanation
Indices: 38318--38382 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
38308 TCAATCACTC
* * *
38318 TTTTTTTTTCAATTTCG-ATTTTTTTTT
1 TTTTTTTTTTAATTCCGAATTTTTTTCT
38345 TTTTTTTTTTAATTCCGAATTTTTTTCT
1 TTTTTTTTTTAATTCCGAATTTTTTTCT
*
38373 TCTTTTTTTT
1 TTTTTTTTTT
38383 CTTCAATACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 15 0.45
28 18 0.55
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.77
Consensus pattern (28 bp):
TTTTTTTTTTAATTCCGAATTTTTTTCT
Found at i:38460 original size:13 final size:12
Alignment explanation
Indices: 38427--38459 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
38417 GAATACAAAC
38427 TTTTTTTTTGAA
1 TTTTTTTTTGAA
38439 TTTTTTTTTGAA
1 TTTTTTTTTGAA
38451 TTTTTTTTT
1 TTTTTTTTT
38460 TTTTTTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:50433 original size:56 final size:55
Alignment explanation
Indices: 50317--50434 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
50307 TGCATGCTTT
* * * *
50317 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
50371 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
50427 CATTAAAT
1 CATTAAAT
50435 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:51085 original size:20 final size:20
Alignment explanation
Indices: 51060--51114 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
51050 ACGAGTTAAA
* *
51060 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
51080 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
51100 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
51115 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:53115 original size:22 final size:22
Alignment explanation
Indices: 53085--53128 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53075 TTTGGTATTT
53085 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
53107 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
53129 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:55538 original size:23 final size:23
Alignment explanation
Indices: 55511--55570 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
55501 TCACATGCAA
55511 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATGAGTTTAT
55534 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATGAGTTTAT
55557 TAAACACATTAAAA
1 TAAACACATTAAAA
55571 CACTTATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATGAGTTTAT
Found at i:57963 original size:23 final size:22
Alignment explanation
Indices: 57912--57963 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
57902 CCTCGTCTTT
*
57912 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
57934 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
57957 TTCTTTT
1 TTCTTTT
57964 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:68643 original size:18 final size:19
Alignment explanation
Indices: 68615--68651 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
68605 TGGCTTAGAA
68615 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
68634 AATG-CTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
68652 TTGGCTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:72075 original size:13 final size:13
Alignment explanation
Indices: 72057--72110 Score: 74
Period size: 13 Copynumber: 4.1 Consensus size: 13
72047 AACTAGCTCT
72057 ATTTTTTTTTACA
1 ATTTTTTTTTACA
72070 ATTTTTTTTTCACA
1 ATTTTTTTTT-ACA
72084 ATTTTTTTTT-CAA
1 ATTTTTTTTTAC-A
*
72097 ATTTTTTTTCACA
1 ATTTTTTTTTACA
72110 A
1 A
72111 CTTGATATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
12 1 0.03
13 22 0.59
14 14 0.38
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTTTTTTACA
Found at i:72077 original size:14 final size:14
Alignment explanation
Indices: 72057--72110 Score: 87
Period size: 14 Copynumber: 4.1 Consensus size: 14
72047 AACTAGCTCT
72057 ATTTTTTTTT-ACA
1 ATTTTTTTTTCACA
72070 ATTTTTTTTTCACA
1 ATTTTTTTTTCACA
72084 ATTTTTTTTTCA-A
1 ATTTTTTTTTCACA
72097 A-TTTTTTTTCACA
1 ATTTTTTTTTCACA
72110 A
1 A
72111 CTTGATATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.26
13 14 0.36
14 15 0.38
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTTTTTTCACA
Found at i:72101 original size:26 final size:27
Alignment explanation
Indices: 72057--72110 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
72047 AACTAGCTCT
*
72057 ATTTTTTTTTACAATTTTTTTTTCACA
1 ATTTTTTTTTACAAATTTTTTTTCACA
72084 ATTTTTTTTT-CAAATTTTTTTTCACA
1 ATTTTTTTTTACAAATTTTTTTTCACA
72110 A
1 A
72111 CTTGATATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (27 bp):
ATTTTTTTTTACAAATTTTTTTTCACA
Done.