Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2210
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: 24353
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:1234 original size:12 final size:13
Alignment explanation
Indices: 1212--1240 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1202 GCGCTCGTTT
1212 TTTTTTGTTTTTG
1 TTTTTTGTTTTTG
1225 TTTTTT-TTTTTG
1 TTTTTTGTTTTTG
1237 TTTT
1 TTTT
1241 GTGGTGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:1430 original size:22 final size:19
Alignment explanation
Indices: 1365--1492 Score: 90
Period size: 18 Copynumber: 6.7 Consensus size: 19
1355 GGTTTTTCAA
1365 CACCCCCCACCCCCAACCACGC
1 CACCCCCC-CCCCCAACC-C-C
* *
1387 C-CCACCCCCCCCAAACGACC
1 CACC-CCCCCCCCCAAC-CCC
1407 CACCCCCTCCCCGCACAACCCC
1 CACCCCC-CCCC-C-CAACCCC
*
1429 CA---ACCCCCCCAACCCC
1 CACCCCCCCCCCCAACCCC
* *
1445 AACCCCCACCCCC-ACCCC
1 CACCCCCCCCCCCAACCCC
1463 CACCCCCCCCCCC-ACCCC
1 CACCCCCCCCCCCAACCCC
1481 C-CCCCCCCCCCC
1 CACCCCCCCCCCC
1493 TTTTTTTTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
16 8 0.09
17 12 0.14
18 26 0.30
19 7 0.08
20 5 0.06
21 16 0.18
22 10 0.11
23 3 0.03
ACGTcount: A:0.19, C:0.78, G:0.02, T:0.01
Consensus pattern (19 bp):
CACCCCCCCCCCCAACCCC
Found at i:1451 original size:1 final size:1
Alignment explanation
Indices: 1447--1492 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
1437 CCAACCCCAA
* * * *
1447 CCCCCACCCCCACCCCCACCCCCCCCCCCACCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1493 TTTTTTTTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.09, C:0.91, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1455 original size:12 final size:12
Alignment explanation
Indices: 1422--1480 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
1412 CCTCCCCGCA
*
1422 CAACCCCCAACC
1 CAACCCCCACCC
*
1434 C--CCCCAACCC
1 CAACCCCCACCC
1444 CAACCCCCACCC
1 CAACCCCCACCC
*
1456 CCACCCCCACCC
1 CAACCCCCACCC
**
1468 CCCCCCCCACCC
1 CAACCCCCACCC
1480 C
1 C
1481 CCCCCCCCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 8 0.20
12 32 0.80
ACGTcount: A:0.20, C:0.80, G:0.00, T:0.00
Consensus pattern (12 bp):
CAACCCCCACCC
Found at i:1492 original size:6 final size:6
Alignment explanation
Indices: 1434--1491 Score: 75
Period size: 6 Copynumber: 9.8 Consensus size: 6
1424 ACCCCCAACC
* *
1434 CCCCCAA CCCCAA CCCCCA CCCCCA CCCCCA CCCCCC CCCCCA CCCCC-
1 CCCCC-A CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA
1482 CCCCC- CCCCC
1 CCCCCA CCCCC
1492 CTTTTTTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
5 10 0.21
6 33 0.70
7 4 0.09
ACGTcount: A:0.14, C:0.86, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCCA
Found at i:2054 original size:1 final size:1
Alignment explanation
Indices: 2050--2114 Score: 112
Period size: 1 Copynumber: 65.0 Consensus size: 1
2040 CTCTTTTTCA
* *
2050 CCCCCCCCACCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2115 AAAAAAAAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:6231 original size:2 final size:2
Alignment explanation
Indices: 6226--6253 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6216 AAAAAATAAA
6226 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6254 CCCAATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7303 original size:24 final size:24
Alignment explanation
Indices: 7221--7318 Score: 60
Period size: 24 Copynumber: 4.0 Consensus size: 24
7211 TATAAAATTA
7221 AATTAATTAAAAA-TAAATTT--T
1 AATTAATTAAAAATTAAATTTAAT
*
7242 AATCTAATTCATATAATTATAATTTTTAAT
1 AAT-TAATT-A-AAAATTA-AA--TTTAAT
*
7272 -TTTCAATTAAAAATTAAATTTAAT
1 AATT-AATTAAAAATTAAATTTAAT
** *
7296 AATTAATTATTATTTAAATTTAA
1 AATTAATTAAAAATTAAATTTAA
7319 AATCAAATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
21 3 0.05
22 5 0.08
23 1 0.02
24 25 0.42
25 4 0.07
26 4 0.07
27 6 0.10
28 5 0.08
29 5 0.08
30 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTAATTAAAAATTAAATTTAAT
Found at i:9505 original size:34 final size:33
Alignment explanation
Indices: 9457--9677 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 33
9447 TGATAAAAAC
* *
9457 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
* * *
9490 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAACTACCAAAT
* *
9524 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
** *
9558 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAACTACCAAAT
* * *
9592 CTCCCATTTAGTTAACAATGGTAAACTACCAAAT
1 C-ACCATTTAATCAACAATGGTAAACTACCAAAT
*
9626 CACCCATTTAATCAACAATTGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
9660 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
9678 TCTCCCACTT
Statistics
Matches: 164, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
33 19 0.12
34 144 0.88
35 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:9636 original size:102 final size:101
Alignment explanation
Indices: 9457--9677 Score: 334
Period size: 102 Copynumber: 2.2 Consensus size: 101
9447 TGATAAAAAC
*
9457 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
* *
9522 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * * * *
9558 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTTAACAATGGTAAACTACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCA
*
9623 AATCACCCATTTAATCAACAATTGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
9660 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
9678 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:14128 original size:34 final size:33
Alignment explanation
Indices: 14080--14298 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 33
14070 TGGTAAAAAC
*
14080 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
14113 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
14147 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
14181 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
14215 CTCCCATTTAGTCAACAATGGTAA-ATCACCAAAT
1 C-ACCATTTAATCAACAATGGTAACCT-ACCAAAT
* *
14249 CACCCATTTAATCAACAATGATAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
14283 CACCATTTAATCAACA
1 CACCATTTAATCAACA
14299 CAAACATGTA
Statistics
Matches: 161, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
33 19 0.12
34 138 0.86
35 4 0.02
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:14259 original size:102 final size:101
Alignment explanation
Indices: 14080--14298 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
14070 TGGTAAAAAC
*
14080 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
* * *
14145 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAAT
** * * * *
14181 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGTAAATCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCA
14246 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
14283 CACCATTTAATCAACA
1 CACCATTTAATCAACA
14299 CAAACATGTA
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 14 0.13
102 91 0.87
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:15374 original size:33 final size:34
Alignment explanation
Indices: 15336--15400 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
15326 AATTTGTATT
*
15336 ATTA-TTATAAATTAAA-ATAATATTTTTTAAAAA
1 ATTATTTATAAAATAAATA-AATATTTTTTAAAAA
* *
15369 ATTATTTCTAAAATATATAAATATTTTTTAAA
1 ATTATTTATAAAATAAATAAATATTTTTTAAA
15401 TATTTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.15
34 22 0.81
35 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (34 bp):
ATTATTTATAAAATAAATAAATATTTTTTAAAAA
Found at i:15401 original size:19 final size:19
Alignment explanation
Indices: 15379--15421 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
15369 ATTATTTCTA
*
15379 AAATATATAAATATTTTTT
1 AAATATATAAATATATTTT
* *
15398 AAATATTTTAATATATTTT
1 AAATATATAAATATATTTT
15417 AAATA
1 AAATA
15422 ATTATTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATATAAATATATTTT
Found at i:19108 original size:13 final size:13
Alignment explanation
Indices: 19065--19116 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
19055 AATTAAAAAA
*
19065 ATATTAAATATATT
1 ATATTTAATAT-TT
*
19079 -TATTTAGATATTC
1 ATATTTA-ATATTT
19092 ATATTTAATATTT
1 ATATTTAATATTT
19105 ATATTTAA-ATTT
1 ATATTTAATATTT
19117 GAATAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.12
13 19 0.58
14 10 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
ATATTTAATATTT
Found at i:19143 original size:17 final size:17
Alignment explanation
Indices: 19123--19157 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
19113 ATTTGAATAA
*
19123 TATACATATAACAAATC
1 TATAAATATAACAAATC
19140 TATAAATATAACAAATC
1 TATAAATATAACAAATC
19157 T
1 T
19158 CAAACATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (17 bp):
TATAAATATAACAAATC
Found at i:19399 original size:22 final size:22
Alignment explanation
Indices: 19374--19416 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19364 ATATATTTTT
19374 TAAAAAA-ATTTAATTATAAATA
1 TAAAAAATATTTAATTA-AAATA
*
19396 TAAAAAATATTTATTTAAAAT
1 TAAAAAATATTTAATTAAAAT
19417 TTGTGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAAATATTTAATTAAAATA
Found at i:22391 original size:2 final size:2
Alignment explanation
Indices: 22384--22412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22374 TTCTGGAAAA
22384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22413 CTTGGGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.