Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold484
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: 288598
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.28
Warning! 45481 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:279123 original size:51 final size:51
Alignment explanation
Indices: 278887--279168 Score: 213
Period size: 46 Copynumber: 5.9 Consensus size: 51
278877 CATGATTTGT
* * * * *
278887 AGCTTTAATCTGTTCCACTACAATGCCAGAGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGATTCGCTGCCTTC
* * * * *
278938 AGCTTTAATC---T--ACTGCAGCGCCAGGGAAATAAGACTCGCAGCCTTC
1 AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGATTCGCTGCCTTC
* * *
278984 AGCTTTAATCTG-T----TGCAATGCCAGAGAAATAAGACTT-GCTGCCTTC
1 AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGA-TTCGCTGCCTTC
* * ** * *
279030 AACTTTAGTCTG------TGCAACGCTAGGGAAATAAGATTTGCTGCCTTG
1 AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGATTCGCTGCCTTC
*
279075 AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGATTCGTTGCCTTC
1 AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGATTCGCTGCCTTC
* * * *
279126 AGCTTTAATCTGTTTCACTACAACGCCGAGGAAATAA-ATTCGC
1 AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGATTCGC
279169 CATAATGACT
Statistics
Matches: 192, Mismatches: 29, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
44 2 0.01
45 36 0.19
46 75 0.39
47 1 0.01
48 2 0.01
50 5 0.03
51 71 0.37
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (51 bp):
AGCTTTAATCTGTTCCAATGCAACGCCGGGGAAATAAGATTCGCTGCCTTC
Found at i:280438 original size:11 final size:11
Alignment explanation
Indices: 280424--280465 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
280414 GACCTCTCCT
*
280424 TTTTCTTTTCC
1 TTTTCTTTTTC
280435 TTTT-TTTTTC
1 TTTTCTTTTTC
*
280445 TTCTCTTTTTC
1 TTTTCTTTTTC
*
280456 TTTCCTTTTT
1 TTTTCTTTTT
280466 TCATCATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:280481 original size:27 final size:27
Alignment explanation
Indices: 280424--280482 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
280414 GACCTCTCCT
** *
280424 TTTTCTTTTCCTTTTTTTTTCTTCTCT
1 TTTTCTTTTCCTTTTTTCATCTTCTCA
*
280451 TTTTC-TTTCCTTTTTTCATCATTTTCA
1 TTTTCTTTTCCTTTTTTCATC-TTCTCA
280478 TTTTC
1 TTTTC
280483 ATCATTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTCTTTTCCTTTTTTCATCTTCTCA
Found at i:280483 original size:15 final size:15
Alignment explanation
Indices: 280463--280491 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
280453 TTCTTTCCTT
280463 TTTTCATCATTTTCA
1 TTTTCATCATTTTCA
280478 TTTTCATCATTTTC
1 TTTTCATCATTTTC
280492 TTTCTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTCATCATTTTCA
Found at i:280528 original size:24 final size:22
Alignment explanation
Indices: 280501--280544 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 22
280491 CTTTCTTTCT
280501 TTTTTTTTGAAAAATATTTTTTGA
1 TTTTTTTTG--AAATATTTTTTGA
280525 TTTTTTTTGAAATATTTTTT
1 TTTTTTTTGAAATATTTTTT
280545 AATTGGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTTTTTTGAAATATTTTTTGA
Found at i:283964 original size:41 final size:41
Alignment explanation
Indices: 283906--284076 Score: 252
Period size: 41 Copynumber: 4.1 Consensus size: 41
283896 CTTAATTTAA
* *
283906 CAGATTCACAGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * *
283948 CAGATCACCGGCACTTACCCTGCTAGGTTTATAACTTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * *
283989 CAGATCACCTGCACTGAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
284030 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
284071 CAGATC
1 CAGATC
284077 GCATAAGATA
Statistics
Matches: 116, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 112 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:285125 original size:22 final size:22
Alignment explanation
Indices: 285097--285141 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
285087 GAATGTTCCT
285097 TGTCTTCATATAAGTCCACACA
1 TGTCTTCATATAAGTCCACACA
285119 TGTCTTCATATAAGTCCACACA
1 TGTCTTCATATAAGTCCACACA
285141 T
1 T
285142 CTCATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (22 bp):
TGTCTTCATATAAGTCCACACA
Found at i:287095 original size:16 final size:16
Alignment explanation
Indices: 287070--287103 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
287060 TTTTATGATG
*
287070 AAATGCCATGCAGTCA
1 AAATGCCATGCAATCA
*
287086 AAATGTCATGCAATCA
1 AAATGCCATGCAATCA
287102 AA
1 AA
287104 GCAAAACACA
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:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (16 bp):
AAATGCCATGCAATCA
Found at i:287491 original size:27 final size:27
Alignment explanation
Indices: 287461--287520 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
287451 TCTCACTCCC
287461 ACTTAAAGGGGTAAAATTGACCAACTT
1 ACTTAAAGGGGTAAAATTGACCAACTT
*
287488 ACTTAAAGGGGTAAAATTGACTAACTT
1 ACTTAAAGGGGTAAAATTGACCAACTT
287515 ACTTAA
1 ACTTAA
287521 TGCAAAATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (27 bp):
ACTTAAAGGGGTAAAATTGACCAACTT
Done.