Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2138
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: 36469
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:6443 original size:40 final size:40
Alignment explanation
Indices: 6387--6610 Score: 261
Period size: 40 Copynumber: 5.5 Consensus size: 40
6377 TATTCGGATG
6387 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
6427 ATATCCGGGCTCAGTCCTGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * * *
6470 ATACCCGGGCTAAGTCCAGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * *
6510 ATATCCGGGCTAAGTCTCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
6550 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
6590 ATAT-CTGGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
6611 ATACTTGGGT
Statistics
Matches: 157, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
39 14 0.09
40 107 0.68
41 1 0.01
43 35 0.22
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:6532 original size:83 final size:80
Alignment explanation
Indices: 6391--6594 Score: 252
Period size: 83 Copynumber: 2.5 Consensus size: 80
6381 CGGATGATAT
* * **
6391 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTCAGTCCTGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCTGAAGGCATTCA
6456 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
* *
6474 CCGGGCTAAGTCCAGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGT-CTCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCT-GAAGGCATTC
*
6538 ATGCTAGTGACTATAT
65 ATGCTAGTGACTATAC
* *
6554 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATC
6595 TGGCTAAATC
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
79 2 0.02
80 43 0.40
81 2 0.02
82 2 0.02
83 59 0.55
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCTGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:10295 original size:27 final size:27
Alignment explanation
Indices: 10254--10529 Score: 283
Period size: 27 Copynumber: 10.4 Consensus size: 27
10244 TGGATAAGTT
10254 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
**
10281 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* **
10308 GTAGAATTACCGAAATGCCGTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
10335 GTAGAAATACCGAAATACCCTTGTA--
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
10360 G--GAA-TACCAAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
**
10384 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
10411 GTAGAATTACCGAAATAAGCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
10438 ATAGAATTACCGAAATACCCTTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
10465 GTAGAAATACTGAAATACTCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
10492 GTAGAATTACCGAGATACCCTTATGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
10519 GTAAAATTACC
1 GTAGAATTACC
10530 ATTTTGCCCT
Statistics
Matches: 202, Mismatches: 42, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
22 15 0.07
23 3 0.01
24 1 0.00
25 1 0.00
26 3 0.01
27 179 0.89
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:10365 original size:22 final size:22
Alignment explanation
Indices: 10335--10376 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10325 CCGTTGTAGG
*
10335 GTAGAAATACCGAAATACCCTT
1 GTAGAAATACCAAAATACCCTT
*
10357 GTAGGAATACCAAAATACCC
1 GTAGAAATACCAAAATACCC
10377 CTATAGGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (22 bp):
GTAGAAATACCAAAATACCCTT
Found at i:10383 original size:22 final size:22
Alignment explanation
Indices: 10340--10383 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10330 GTAGGGTAGA
* * *
10340 AATACCGAAATACCCTTGTAGG
1 AATACCAAAATACCCCTATAGG
10362 AATACCAAAATACCCCTATAGG
1 AATACCAAAATACCCCTATAGG
10384 GTAGAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (22 bp):
AATACCAAAATACCCCTATAGG
Found at i:10435 original size:103 final size:104
Alignment explanation
Indices: 10252--10464 Score: 335
Period size: 103 Copynumber: 2.1 Consensus size: 104
10242 AGTGGATAAG
* *
10252 TTGTA-GAATTACCGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATT
1 TTGTAGGAATTACCAAAATACCCCTATAGGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATT
*
10316 ACCGAAATGCCGTTGTAGGGTAGAAATACCGAAATACCC
66 ACCGAAATGCCGTTGTAGGATAGAAATACCGAAATACCC
10355 TTGTAGGAA-TACCAAAATACCCCTATAGGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATT
1 TTGTAGGAATTACCAAAATACCCCTATAGGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATT
*
10419 ACCGAAATAAG-C-TTGTAGGATAGAATTACCGAAATACCC
66 ACCGAAAT--GCCGTTGTAGGATAGAAATACCGAAATACCC
*
10458 TTATAGG
1 TTGTAGG
10465 GTAGAAATAC
Statistics
Matches: 102, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
103 97 0.95
104 4 0.04
105 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (104 bp):
TTGTAGGAATTACCAAAATACCCCTATAGGGTAGAATTATTGAAATACCCCTGTAGGGTAGAATT
ACCGAAATGCCGTTGTAGGATAGAAATACCGAAATACCC
Found at i:10539 original size:27 final size:27
Alignment explanation
Indices: 10509--10565 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
10499 TACCGAGATA
* *
10509 CCCTTATGGGGTAAAATTACCATTTTG
1 CCCTTAAGGGGTAAAATGACCATTTTG
* * *
10536 CCCTTAAGGTGTTAAATGACTATTTTG
1 CCCTTAAGGGGTAAAATGACCATTTTG
10563 CCC
1 CCC
10566 CTCGTGTGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (27 bp):
CCCTTAAGGGGTAAAATGACCATTTTG
Found at i:12266 original size:27 final size:26
Alignment explanation
Indices: 12210--12266 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
12200 CAACCTTAAC
* * *
12210 CCTAAGGGTATATCAGTAATTTTGCT
1 CCTAAGGGTAAATCAGTAATTTTCCA
* *
12236 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAAGGGTAAATCAGT-AATTTTCCA
12263 CCTA
1 CCTA
12267 TAAAGGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (26 bp):
CCTAAGGGTAAATCAGTAATTTTCCA
Found at i:23740 original size:46 final size:46
Alignment explanation
Indices: 23690--23865 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
23680 TGGTTGAGCA
23690 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
23736 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
23781 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
23829 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
23866 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 62 0.57
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:23846 original size:93 final size:93
Alignment explanation
Indices: 23687--23858 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
23677 GGATGGTTGA
*
23687 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
23752 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
23780 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
23844 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
23859 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:27633 original size:41 final size:40
Alignment explanation
Indices: 27516--27739 Score: 247
Period size: 40 Copynumber: 5.6 Consensus size: 40
27506 TCCTCGTTCA
* * * * *
27516 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
27555 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
27595 AATGCCTTCGGGACTTAACCCGGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCC-GGATTTAATAACTCGCACG
* * *
27636 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
27676 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
27716 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
27740 CAGCATTCAA
Statistics
Matches: 162, Mismatches: 18, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
39 37 0.23
40 77 0.48
41 48 0.30
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:27658 original size:81 final size:79
Alignment explanation
Indices: 27514--27739 Score: 247
Period size: 81 Copynumber: 2.8 Consensus size: 79
27504 GCTCCTCGTT
* * *
27514 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGA
27579 TTTAATAACTCGCA
66 TTTAATAACTCGCA
* * *
27593 CGAATGCCTTCGGGACTTAACCCGGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACATAACCC-GGATTTAATAACTCACAC-AATGCCTTCGGGACTTAACCCG
* *
27658 GATTTAGTATCTCGCA
64 GATTTAATAACTCGCA
* * ** * * * * * *
27674 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAATAACTCA-CACAATGCCTTCGGGACTTAACCCG
27738 GA
64 GA
27740 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
79 20 0.16
80 50 0.40
81 54 0.44
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGA
TTTAATAACTCGCA
Found at i:27748 original size:41 final size:41
Alignment explanation
Indices: 27671--27748 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
27661 TTAGTATCTC
* * *
27671 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
27712 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
27749 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:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.