Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3649
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: 62325
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:8830 original size:13 final size:13
Alignment explanation
Indices: 8814--8838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8804 AGCGAGGCAA
8814 AAGAAAAAGAAAT
1 AAGAAAAAGAAAT
8827 AAGAAAAAGAAA
1 AAGAAAAAGAAA
8839 GACAAGAAAT
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAGAAAAAGAAAT
Found at i:8950 original size:18 final size:18
Alignment explanation
Indices: 8929--8963 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8919 CAAGAAATCA
*
8929 AAAAAGGAGAGAAAAAAG
1 AAAAAGAAGAGAAAAAAG
*
8947 AAAATGAAGAGAAAAAA
1 AAAAAGAAGAGAAAAAA
8964 TTCAAAAAAG
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:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAAAAGAAGAGAAAAAAG
Found at i:9123 original size:33 final size:32
Alignment explanation
Indices: 9086--9147 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
9076 AAATTGAAAA
*
9086 TGAGAGAGGAAATGAAAAGAGAAAAAAAGAAGT
1 TGAGAGA-GAAAAGAAAAGAGAAAAAAAGAAGT
* * *
9119 TGAGATAGAAAAGAAACGAGAGAAAAAGA
1 TGAGAGAGAAAAGAAAAGAGAAAAAAAGA
9148 GATAAACGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.61, C:0.02, G:0.29, T:0.08
Consensus pattern (32 bp):
TGAGAGAGAAAAGAAAAGAGAAAAAAAGAAGT
Found at i:21599 original size:20 final size:20
Alignment explanation
Indices: 21553--21599 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
21543 AGCTTGTTTC
*
21553 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
21573 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
21593 CAGCTCA
1 CAGCTCA
21600 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25697 original size:16 final size:16
Alignment explanation
Indices: 25665--25698 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25655 AAACACTCAA
**
25665 CACTCAAAAAGTTAAT
1 CACTCAAAAAGAAAAT
25681 CACTCAAAAAGAAAAT
1 CACTCAAAAAGAAAAT
25697 CA
1 CA
25699 AATTCTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.21, G:0.06, T:0.18
Consensus pattern (16 bp):
CACTCAAAAAGAAAAT
Found at i:30158 original size:46 final size:46
Alignment explanation
Indices: 30079--30191 Score: 165
Period size: 46 Copynumber: 2.4 Consensus size: 46
30069 GCTGTAAACA
* *
30079 AGACAAATTAAATTAGTTTAAGACAACTTAAATT-TCTGTAATAATTT
1 AGACAAATTAAATGA-CTTAAGACAACTTAAATTGT-TGTAATAATTT
* *
30126 AGACAAATTAAATGACTTAGGACAACTTAAATTGTTGTAGTAATTT
1 AGACAAATTAAATGACTTAAGACAACTTAAATTGTTGTAATAATTT
30172 AGACAAATTAAATGACTTAA
1 AGACAAATTAAATGACTTAA
30192 CTTATTAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
46 45 0.75
47 15 0.25
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.35
Consensus pattern (46 bp):
AGACAAATTAAATGACTTAAGACAACTTAAATTGTTGTAATAATTT
Found at i:34833 original size:18 final size:18
Alignment explanation
Indices: 34812--34854 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
34802 GAGAGACGAG
34812 AGAAAAAGAAATCGAAAA
1 AGAAAAAGAAATCGAAAA
* *
34830 AGAAAAAGACATTGAAAA
1 AGAAAAAGAAATCGAAAA
34848 AGAAAAA
1 AGAAAAA
34855 AAGAGTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.05, G:0.16, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCGAAAA
Found at i:43820 original size:11 final size:11
Alignment explanation
Indices: 43804--43848 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
43794 TAGTAGTTTC
43804 TTCAAAAAAAA
1 TTCAAAAAAAA
43815 TTCAAAAAAAA
1 TTCAAAAAAAA
*
43826 ATCAAAAAAAAA
1 TTC-AAAAAAAA
43838 TTCAAAAAAAA
1 TTCAAAAAAAA
43849 AATTTGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:43824 original size:12 final size:12
Alignment explanation
Indices: 43807--43849 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
43797 TAGTTTCTTC
43807 AAAAAAAATTCA
1 AAAAAAAATTCA
43819 AAAAAAAA-TCA
1 AAAAAAAATTCA
43830 AAAAAAAATTCA
1 AAAAAAAATTCA
43842 AAAAAAAA
1 AAAAAAAA
43850 ATTTGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:43912 original size:15 final size:15
Alignment explanation
Indices: 43892--43944 Score: 79
Period size: 16 Copynumber: 3.4 Consensus size: 15
43882 TATCAAGTTG
43892 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
*
43907 AAAAAAAATTTGTGAA
1 AAAAAAAATTCGTG-A
43923 AAAAAAAATTTCGTGA
1 AAAAAAAA-TTCGTGA
43939 AAAAAA
1 AAAAAA
43945 GAAGAAGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 13 0.38
16 16 0.47
17 5 0.15
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.21
Consensus pattern (15 bp):
AAAAAAAATTCGTGA
Found at i:43913 original size:16 final size:16
Alignment explanation
Indices: 43892--43944 Score: 81
Period size: 15 Copynumber: 3.3 Consensus size: 16
43882 TATCAAGTTG
43892 AAAAAAAATTCGTG-A
1 AAAAAAAATTCGTGAA
*
43907 AAAAAAAATTTGTGAA
1 AAAAAAAATTCGTGAA
43923 AAAAAAAATTTCGTGAA
1 AAAAAAAA-TTCGTGAA
43940 AAAAA
1 AAAAA
43945 GAAGAAGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.38
16 9 0.26
17 12 0.35
ACGTcount: A:0.64, C:0.04, G:0.11, T:0.21
Consensus pattern (16 bp):
AAAAAAAATTCGTGAA
Found at i:48360 original size:32 final size:34
Alignment explanation
Indices: 48291--48384 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 34
48281 TCCTCGTTCA
*
48291 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACATAACCCGG-----GTAACTCACAC
48330 AATGCCTTC-GGACAT-ACCCGGGTAACTCACAC
1 AATGCCTTCGGGACATAACCCGGGTAACTCACAC
48362 AATGCCTTCGGGACATAACCCGG
1 AATGCCTTCGGGACATAACCCGG
48385 ATTTAACAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
32 20 0.38
33 6 0.12
34 6 0.12
37 5 0.10
38 6 0.12
39 9 0.17
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (34 bp):
AATGCCTTCGGGACATAACCCGGGTAACTCACAC
Found at i:48408 original size:40 final size:40
Alignment explanation
Indices: 48352--48585 Score: 294
Period size: 40 Copynumber: 5.9 Consensus size: 40
48342 CATACCCGGG
* *
48352 TAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTAA
1 TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAA
* *
48391 CAACTCGCACGACTGCCTTCGGGACTTAACCCGGATTTAA
1 TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAA
48431 TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAA
1 TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAA
*
48471 TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAG
1 TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAA
* * * * * *
48511 TATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGATATAT
1 TAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAA
* * * *
48551 TCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 TAAC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
48586 CAGCATTCAA
Statistics
Matches: 172, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
39 11 0.06
40 153 0.89
41 8 0.05
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAA
Found at i:56383 original size:40 final size:39
Alignment explanation
Indices: 56251--56503 Score: 272
Period size: 40 Copynumber: 6.6 Consensus size: 39
56241 CTCCTCGTTC
* * * *
56251 AATGCCTTCGGGA-ATAGCCCGG-TTTAGTAACTCACAC-
1 AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
* * *
56288 AATGCCTTC-GACGT-ACCC-G--TTAGTAACTCACAC-
1 AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
* *
56321 AATGCCTTCGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
*
56360 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
56400 AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
* * *
56439 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
* *
56479 AAGGCCTTCGGATCTTAATCCGGAT
1 AATGCCTTCGGA-CTTAACCCGGAT
56504 ATTTCACTTA
Statistics
Matches: 191, Mismatches: 15, Indels: 17
0.86 0.07 0.08
Matches are distributed among these distances:
33 23 0.12
34 5 0.03
35 9 0.05
36 2 0.01
37 9 0.05
38 11 0.06
39 50 0.26
40 82 0.43
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:56452 original size:79 final size:78
Alignment explanation
Indices: 56311--56503 Score: 287
Period size: 79 Copynumber: 2.4 Consensus size: 78
56301 TACCCGTTAG
* * *
56311 TAACTCACACAATGCCTTCGGACATAACCCGGATTTAACAACTCGCACGACTGCCTTCGGGACTT
1 TAACTCGCACAATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
56376 AACCCGGATTTAA
66 AACCCGGATTTAA
*
56389 TAACTCGCACGAATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACT
1 TAACTCGCAC-AATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACT
*
56454 TAACCCGGATTTAG
65 TAACCCGGATTTAA
* * *
56468 TATCTCGCACAAAGGCCTTCGGATCTTAATCCGGAT
1 TAACTCGCAC-AATGCCTTCGGA-CTTAACCCGGAT
56504 ATTTCACTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 9 0.09
79 84 0.81
80 11 0.11
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (78 bp):
TAACTCGCACAATGCCTTCGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTT
AACCCGGATTTAA
Found at i:56525 original size:79 final size:78
Alignment explanation
Indices: 56311--56540 Score: 243
Period size: 79 Copynumber: 2.9 Consensus size: 78
56301 TACCCGTTAG
* * * * * **
56311 TAACTCACAC-AATGCCTTCGGACATAACCCGGATTTAACAACTCGCACGACTGCCTTCGGGACT
1 TAACTCGCACAAAGGCCTTCGGACTTAACCCGGATTT-ATAACTAGCACGAAAGCCTTCGGGACT
56375 TAACCCGGATTTAA
65 TAACCCGGATTTAA
* * * *
56389 TAACTCGCACGAATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACT
1 TAACTCGCACAAAGGCCTTCGGACTTAACCCGGATTT-ATAACTAGCACGAAAGCCTTCGGGACT
*
56454 TAACCCGGATTTAG
65 TAACCCGGATTTAA
* * *
56468 TATCTCGCACAAAGGCCTTCGGATCTTAATCCGGATATT-TCACTTAGCAC-AAAGCCTTC-GGA
1 TAACTCGCACAAAGGCCTTCGGA-CTTAACCCGGAT-TTATAAC-TAGCACGAAAGCCTTCGGGA
*
56530 CTTAGCCCGGA
63 CTTAACCCGGA
56541 CAGCATTCAA
Statistics
Matches: 135, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
78 22 0.16
79 95 0.70
80 16 0.12
81 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (78 bp):
TAACTCGCACAAAGGCCTTCGGACTTAACCCGGATTTATAACTAGCACGAAAGCCTTCGGGACTT
AACCCGGATTTAA
Found at i:60940 original size:13 final size:14
Alignment explanation
Indices: 60922--60954 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
60912 TATTGATGCA
60922 TAAATTA-ATTCTT
1 TAAATTATATTCTT
*
60935 TAAATTATCTTCTT
1 TAAATTATATTCTT
60949 TAAATT
1 TAAATT
60955 TAAACTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATTATATTCTT
Done.