Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2771
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: 49767
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:1390 original size:39 final size:40
Alignment explanation
Indices: 1345--1568 Score: 240
Period size: 40 Copynumber: 5.7 Consensus size: 40
1335 GCTCCTCGTT
* * * *
1345 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
1385 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
1424 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
1464 CAAAGGCCTTCGGGGCTTAACCCGGAATT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
1503 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
1544 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
1569 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.01
39 64 0.41
40 80 0.51
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:1434 original size:79 final size:78
Alignment explanation
Indices: 1345--1568 Score: 252
Period size: 79 Copynumber: 2.8 Consensus size: 78
1335 GCTCCTCGTT
* * *
1345 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
*
1410 TTTAATAACTCGCA
66 ATT-ATAACTCGCA
* * * * *
1424 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGG
* *
1489 AATTGTATCTCGCA
65 AATTATAACTCGCA
* * * * * *
1503 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCG
1567 GA
64 GA
1569 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
78 3 0.03
79 89 0.74
80 28 0.23
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA
ATTATAACTCGCA
Found at i:1577 original size:41 final size:41
Alignment explanation
Indices: 1500--1577 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1490 ATTGTATCTC
* * *
1500 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
1541 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
1578 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:9295 original size:39 final size:40
Alignment explanation
Indices: 9222--9444 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
9212 GCTCCTCGTT
* * * *
9222 CAAATGCCTTC-GGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
9261 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
9300 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
9340 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
9379 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
9420 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9445 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
38 11 0.07
39 58 0.37
40 78 0.49
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9342 original size:79 final size:76
Alignment explanation
Indices: 9222--9444 Score: 241
Period size: 79 Copynumber: 2.8 Consensus size: 76
9212 GCTCCTCGTT
* * * *
9222 CAAATGCCTTCGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGAT
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGAT
9287 TTAATAACTCGCA
65 TT-ATAACTCGCA
* *
9300 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
9364 AATTTGTATCTCGCA
63 -ATTTATAACTCGCA
* * * * *
9379 CAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCGG
9444 A
63 A
9445 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
78 14 0.11
79 77 0.63
80 31 0.25
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (76 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGATT
TATAACTCGCA
Found at i:9453 original size:41 final size:41
Alignment explanation
Indices: 9376--9453 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
9366 TTTGTATCTC
* * *
9376 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
9417 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
9454 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28445 original size:43 final size:44
Alignment explanation
Indices: 28302--28448 Score: 117
Period size: 43 Copynumber: 3.4 Consensus size: 44
28292 TGAGACATCG
** * * ** *
28302 TGTAAGACCGTGTCTGGGACACAGGCCTTGAT-TGAGAATTACG
1 TGTAAGACCACGTCTGGGACACAGGCATCGATATCTGAATTACA
* * * *
28345 TATAAGACCATGTCTGGGACATC-GGTATC-ATATCT-AATTTCA
1 TGTAAGACCACGTCTGGGACA-CAGGCATCGATATCTGAATTACA
* *
28387 TTTAAGACC-CTGTCTGGGACAGAGGCATCGATAT-TGAATTACA
1 TGTAAGACCAC-GTCTGGGACACAGGCATCGATATCTGAATTACA
28430 TGTAAGACCACGTCTGGGA
1 TGTAAGACCACGTCTGGGA
28449 TGTCAGCATT
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
42 31 0.38
43 49 0.60
44 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACACAGGCATCGATATCTGAATTACA
Found at i:35626 original size:42 final size:42
Alignment explanation
Indices: 35541--35636 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
35531 AATTACGTAG
** * * *
35541 AAGACCATGTCTGGGACATCGGCATCATATCTGATTTCGTGT
1 AAGACCATGTCTGGGACAAAGGCATCATATCTAATTACATGT
35583 AAGATCC-TGTCTGGGACAAAGGCATCGATAT-TAATTACATGT
1 AAGA-CCATGTCTGGGACAAAGGCATC-ATATCTAATTACATGT
35625 AAGACCATGTCT
1 AAGACCATGTCT
35637 AGGATGTCAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 2 0.04
42 38 0.83
43 6 0.13
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
AAGACCATGTCTGGGACAAAGGCATCATATCTAATTACATGT
Found at i:37046 original size:21 final size:22
Alignment explanation
Indices: 37001--37053 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
36991 GCAGGGCTCT
**
37001 CACGCCCGTGTGGTCCAAGGGA
1 CACGCCCGTGTGACCCAAGGGA
*
37023 CACGCCCGTGTGACCCTA-GGA
1 CACGCCCGTGTGACCCAAGGGA
37044 CACGCCCGTG
1 CACGCCCGTG
37054 CTACAGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.17, C:0.38, G:0.32, T:0.13
Consensus pattern (22 bp):
CACGCCCGTGTGACCCAAGGGA
Found at i:42464 original size:28 final size:28
Alignment explanation
Indices: 42432--42559 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
42422 ATAGTAAGTC
*
42432 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
42460 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
42489 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* ** * *
42517 TGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
42546 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42560 CAATCTCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 44 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42522 original size:57 final size:57
Alignment explanation
Indices: 42431--42559 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
42421 TATAGTAAGT
*
42431 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * * *
42488 TCGCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
42545 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42560 CAATCTCATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Done.