Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1749
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: 365996
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:318814 original size:13 final size:12
Alignment explanation
Indices: 318796--318833 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
318786 ATAATCCCCT
318796 TGTATCGATACA
1 TGTATCGATACA
318808 GTGTATCGATACTA
1 -TGTATCGATAC-A
318822 TGTATCGATACA
1 TGTATCGATACA
318834 AAGAATACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:325156 original size:13 final size:13
Alignment explanation
Indices: 325138--325162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325128 ACAATGCAAC
325138 ATGTATCGATACA
1 ATGTATCGATACA
325151 ATGTATCGATAC
1 ATGTATCGATAC
325163 TGTGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:325157 original size:33 final size:33
Alignment explanation
Indices: 325120--325185 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
325110 TCTTTTTGAA
325120 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
**
325153 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
325186 TAACTGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAAT
Found at i:337434 original size:20 final size:20
Alignment explanation
Indices: 337409--337513 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
337399 TTTTAACTAG
337409 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
337429 ATGTATCGATACATCTGGGCAAAATGATAGA
1 ATGTATCGATACAT-T--G----A--A-A-A
* * *
337460 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
337480 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
337500 ATGTATCGATACAT
1 ATGTATCGATACAT
337514 CTGGGTACTT
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
20 45 0.66
21 2 0.03
23 1 0.01
24 1 0.01
27 1 0.01
29 1 0.01
30 2 0.03
31 15 0.22
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:339608 original size:58 final size:57
Alignment explanation
Indices: 339541--339728 Score: 200
Period size: 58 Copynumber: 3.3 Consensus size: 57
339531 AAAAAGATGC
* ** *
339541 AAAATGCATGAAATTACATATTAACCCCTATATTATGAAAAAAGACTAAGGTG-GTGCT
1 AAAATGCATGAAATTACATAATAACCCCTA-ATTATGAAAAAAGACTAAAATGACT-CT
* * * * *
339599 ATAATGCATGAAGTTACATAATAACTCCTAAATCATGAAAAATGACTAAAATGACTCT
1 AAAATGCATGAAATTACATAATAACCCCT-AATTATGAAAAAAGACTAAAATGACTCT
* * ** *
339657 AAAATGCATGAAATTGCATAATAATCCCTGAATTATGAAAAATTACTAAAATAACTCT
1 AAAATGCATGAAATTACATAATAACCCCT-AATTATGAAAAAAGACTAAAATGACTCT
339715 -AAATGCATGAAATT
1 AAAATGCATGAAATT
339729 GTATAAATAG
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
57 14 0.13
58 94 0.85
59 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (57 bp):
AAAATGCATGAAATTACATAATAACCCCTAATTATGAAAAAAGACTAAAATGACTCT
Found at i:339720 original size:115 final size:115
Alignment explanation
Indices: 339512--339725 Score: 256
Period size: 116 Copynumber: 1.9 Consensus size: 115
339502 TAATTGGTCG
* *
339512 TAAATCATGGAAAATGACAAAAAAGATGCAAAATGCATGAAATTACATATTAACCCCTATATTAT
1 TAAATCATGAAAAATGACAAAAAAGATGCAAAATGCATGAAATTACATAATAACCCCTATATTAT
** **
339577 GAAAAAAGACTAAGGTGGTGCTATAATGCATGAAGTTACATAATAACTCC
66 GAAAAAAGACTAAAATACTGCTATAATGCATGAAGTTACATAATAACTCC
* * * *
339627 TAAATCATGAAAAATGACTAAAATGACT-CTAAAATGCATGAAATTGCATAATAATCCCTGA-AT
1 TAAATCATGAAAAATGACAAAAAAGA-TGC-AAAATGCATGAAATTACATAATAACCCCT-ATAT
**
339690 TATGAAAAATTACTAAAATAACT-CTA-AATGCATGAA
63 TATGAAAAAAGACTAAAAT-ACTGCTATAATGCATGAA
339726 ATTGTATAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
115 34 0.41
116 47 0.57
117 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.26
Consensus pattern (115 bp):
TAAATCATGAAAAATGACAAAAAAGATGCAAAATGCATGAAATTACATAATAACCCCTATATTAT
GAAAAAAGACTAAAATACTGCTATAATGCATGAAGTTACATAATAACTCC
Found at i:339725 original size:30 final size:29
Alignment explanation
Indices: 339618--339726 Score: 89
Period size: 29 Copynumber: 3.7 Consensus size: 29
339608 GAAGTTACAT
*
339618 AATAACTCCTAAATCATGAAAAATGACTAA
1 AATAACT-CTAAATCATGAAAAATTACTAA
* * *
339648 AATGACTCTAAAATGCATG--AAATTGC-AT
1 AATAACTCT-AAAT-CATGAAAAATTACTAA
* * *
339676 AATAATCCCTGAATTATGAAAAATTACTAA
1 AATAA-CTCTAAATCATGAAAAATTACTAA
339706 AATAACTCTAAATGCATGAAA
1 AATAACTCTAAAT-CATGAAA
339727 TTGTATAAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
27 3 0.05
28 8 0.14
29 22 0.37
30 22 0.37
31 4 0.07
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.27
Consensus pattern (29 bp):
AATAACTCTAAATCATGAAAAATTACTAA
Found at i:339757 original size:57 final size:57
Alignment explanation
Indices: 339427--339784 Score: 183
Period size: 58 Copynumber: 6.2 Consensus size: 57
339417 AATGGTGCTG
* * * * *
339427 AAATGCATGAAATTCCATAATAGT-CCTCAAAACAT-AGAGAATGATTAAAATGGACT-T
1 AAATGCATGAAATTGCATAATAATCCCT-AAAACATGA-AAAATTACTAAAAT-GACTCT
* ** * * * * * * *
339484 AAAATGCATAAAATTGCATAATTGGT-CGTAAATCATGGAAAATGACAAAAAAGA-TGCA
1 -AAATGCATGAAATTGCATAA-TAATCCCTAAAACATGAAAAATTACTAAAATGACT-CT
* * * * ** ** ** *
339542 AAATGCATGAAATTACATATTAACCCCTATATTATGAAAAAAGACTAAGGTG-GTGCT
1 AAATGCATGAAATTGCATAATAATCCCTAAAACATGAAAAATTACTAAAATGACT-CT
* * * *
339599 ATAATGCATGAAGTTACATAATAA-CTCCTAAATCATGAAAAATGACTAAAATGACTCT
1 A-AATGCATGAAATTGCATAATAATC-CCTAAAACATGAAAAATTACTAAAATGACTCT
* ** *
339657 AAAATGCATGAAATTGCATAATAATCCCTGAATTATGAAAAATTACTAAAATAACTCT
1 -AAATGCATGAAATTGCATAATAATCCCTAAAACATGAAAAATTACTAAAATGACTCT
* * * ** **
339715 AAATGCATGAAATTGTATAAATAGT-TCTAAAACATGGCAAATTACTAAAATGACGAT
1 AAATGCATGAAATTGCAT-AATAATCCCTAAAACATGAAAAATTACTAAAATGACTCT
339772 AAAGTGCATGAAA
1 AAA-TGCATGAAA
339785 AGAGATAATA
Statistics
Matches: 235, Mismatches: 52, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
56 2 0.01
57 85 0.36
58 140 0.60
59 8 0.03
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (57 bp):
AAATGCATGAAATTGCATAATAATCCCTAAAACATGAAAAATTACTAAAATGACTCT
Found at i:339860 original size:28 final size:28
Alignment explanation
Indices: 339829--339891 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
339819 TAAATGCACC
*
339829 TAAATGCTTAAAATTACATAGTGATCTT
1 TAAATGCTTAAAATTACATAGTAATCTT
339857 TAAATGCTTAAAATTACATAGTAATCTT
1 TAAATGCTTAAAATTACATAGTAATCTT
339885 TAAATGC
1 TAAATGC
339892 ATGAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (28 bp):
TAAATGCTTAAAATTACATAGTAATCTT
Found at i:343660 original size:20 final size:21
Alignment explanation
Indices: 343635--343689 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
343625 CATTTTAGGC
343635 ATGTATTGATACATTCACT-T
1 ATGTATTGATACATTCACTGT
*
343655 ATGTATTGATACATTTACTGT
1 ATGTATTGATACATTCACTGT
* *
343676 TTGTATCGATACAT
1 ATGTATTGATACAT
343690 ATTTTAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (21 bp):
ATGTATTGATACATTCACTGT
Found at i:343686 original size:21 final size:21
Alignment explanation
Indices: 343615--343689 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
343605 AGGGTGGTTT
* *
343615 TGTATCGATACATTTTA-GGCA
1 TGTATCGATACA-TTTACTGTA
* *
343636 TGTATTGATACATTCACT-TA
1 TGTATCGATACATTTACTGTA
* *
343656 TGTATTGATACATTTACTGTT
1 TGTATCGATACATTTACTGTA
343677 TGTATCGATACAT
1 TGTATCGATACAT
343690 ATTTTAGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
20 21 0.47
21 24 0.53
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (21 bp):
TGTATCGATACATTTACTGTA
Found at i:350330 original size:91 final size:90
Alignment explanation
Indices: 350169--350339 Score: 229
Period size: 91 Copynumber: 1.9 Consensus size: 90
350159 TCATATGAAC
* * *
350169 GTATCGATACATATGGTTGGCAGTAGCTAAGAAATGCTAAAACCTTGATTTGTATCAGTACAAGT
1 GTATCGATACATATGGTTGACAGTAGCTAAGAAATCCTAAAACCTTGATTTGTATCAATACAAGT
350234 CAAAATCTATCGATACATTAAGTGA
66 CAAAATCTATCGATACATTAAGTGA
* * *
350259 GTATCGATACATTTGGTTGACAGTAGTTAAAGAAATCCTAAAACCCTT-ATTTTTATCAATACAT
1 GTATCGATACATATGGTTGACAGTAGCT-AAGAAATCCTAAAA-CCTTGATTTGTATCAATACA-
* *
350323 A-TGAAAATGTATCGATA
63 AGTCAAAATCTATCGATA
350340 TAATACACAA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
90 25 0.36
91 40 0.57
92 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (90 bp):
GTATCGATACATATGGTTGACAGTAGCTAAGAAATCCTAAAACCTTGATTTGTATCAATACAAGT
CAAAATCTATCGATACATTAAGTGA
Found at i:352825 original size:19 final size:18
Alignment explanation
Indices: 352801--352837 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
352791 ACTCTCCCTG
*
352801 TTGTGATTTCTCCACCTTT
1 TTGTGATCTCTCC-CCTTT
352820 TTGTGATCTCTCCCCTTT
1 TTGTGATCTCTCCCCTTT
352838 ATGTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.30, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTGATCTCTCCCCTTT
Found at i:356009 original size:21 final size:22
Alignment explanation
Indices: 355988--356061 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 22
355978 AGTTAATTCA
*
355988 TTATTTTCTTCTTGTAACTCAT
1 TTATTTTCTTCTTCTAACTCAT
* *
356010 TTCTTTTCTT-TTCCAACTCAT
1 TTATTTTCTTCTTCTAACTCAT
* *
356031 TTATTTTC-TCTTCTAATTCAC
1 TTATTTTCTTCTTCTAACTCAT
*
356052 TTACTTTCTT
1 TTATTTTCTT
356062 TTCGAGATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 31 0.74
22 10 0.24
ACGTcount: A:0.16, C:0.23, G:0.01, T:0.59
Consensus pattern (22 bp):
TTATTTTCTTCTTCTAACTCAT
Found at i:363725 original size:49 final size:49
Alignment explanation
Indices: 363655--363823 Score: 211
Period size: 48 Copynumber: 3.5 Consensus size: 49
363645 TTTGTATTAG
*
363655 TACAATGAATAATGTATCGATATATCTAGGTTTTTCCAGAATGTATCGA
1 TACAATGAATAATGTATCGATACATCTAGGTTTTTCCAGAATGTATCGA
* * *
363704 TATAATGTAA-AATGTAGCGATACATCTAGGTTTTT-CAGAATGTATCAA
1 TACAATG-AATAATGTATCGATACATCTAGGTTTTTCCAGAATGTATCGA
* * *
363752 TACAATGAATAATATATCGATACATCTAAG--TTTCCAGATTGTATCGA
1 TACAATGAATAATGTATCGATACATCTAGGTTTTTCCAGAATGTATCGA
* * *
363799 TACATTCACTAATGTATCGATACAT
1 TACAATGAATAATGTATCGATACAT
363824 ACACGGTATT
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
46 3 0.03
47 34 0.33
48 35 0.34
49 29 0.28
50 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (49 bp):
TACAATGAATAATGTATCGATACATCTAGGTTTTTCCAGAATGTATCGA
Found at i:363773 original size:48 final size:48
Alignment explanation
Indices: 363655--363823 Score: 207
Period size: 47 Copynumber: 3.5 Consensus size: 48
363645 TTTGTATTAG
*
363655 TACAATGAATAATGTATCGATATATCTAGGTTTTTCCAGAATGTATCGA
1 TACAATGAATAATGTATCGATACATCTAGGTTTTT-CAGAATGTATCGA
* * *
363704 TATAATGTAA-AATGTAGCGATACATCTAGGTTTTTCAGAATGTATCAA
1 TACAATG-AATAATGTATCGATACATCTAGGTTTTTCAGAATGTATCGA
* * * *
363752 TACAATGAATAATATATCGATACATCTAAG-TTTCCAGATTGTATCGA
1 TACAATGAATAATGTATCGATACATCTAGGTTTTTCAGAATGTATCGA
* * *
363799 TACATTCACTAATGTATCGATACAT
1 TACAATGAATAATGTATCGATACAT
363824 ACACGGTATT
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
47 37 0.36
48 35 0.34
49 29 0.28
50 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (48 bp):
TACAATGAATAATGTATCGATACATCTAGGTTTTTCAGAATGTATCGA
Done.