Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2287
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: 24083
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:11273 original size:2 final size:2
Alignment explanation
Indices: 11221--11261 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11211 TGTGTGTGTT
11221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11262 GTAAGTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11844 original size:25 final size:23
Alignment explanation
Indices: 11805--11862 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
11795 ATTTAACATG
* *
11805 AAAAATAATACGAACACATGACACA
1 AAAAATAAAACG-A-ACATAACACA
*
11830 AAAAATAAAATGAACATAACACA
1 AAAAATAAAACGAACATAACACA
11853 AAAAATAAAA
1 AAAAATAAAA
11863 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 19 0.63
24 1 0.03
25 10 0.33
ACGTcount: A:0.69, C:0.14, G:0.05, T:0.12
Consensus pattern (23 bp):
AAAAATAAAACGAACATAACACA
Found at i:12358 original size:26 final size:25
Alignment explanation
Indices: 12329--12387 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
12319 CATAACAAAA
*
12329 AATAAAACATTTTGATAAATTAGTTT
1 AATAAAACATTTTGAT-AATTAATTT
*
12355 AATAAAAATATTTTGATAATTAATTT
1 AAT-AAAACATTTTGATAATTAATTT
*
12381 AAAAAAA
1 AATAAAA
12388 TGCTATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 13 0.45
27 12 0.41
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (25 bp):
AATAAAACATTTTGATAATTAATTT
Found at i:12367 original size:27 final size:25
Alignment explanation
Indices: 12332--12388 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
12322 AACAAAAAAT
* *
12332 AAAACATTTTGATAAATTAGTTTAATA
1 AAAATATTTTGAT-AATTAATTTAA-A
12359 AAAATATTTTGATAATTAATTTAAA
1 AAAATATTTTGATAATTAATTTAAA
12384 AAAAT
1 AAAAT
12389 GCTATTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 10 0.36
27 12 0.43
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (25 bp):
AAAATATTTTGATAATTAATTTAAA
Found at i:16665 original size:18 final size:18
Alignment explanation
Indices: 16642--16677 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16632 TTCTGGAGAC
16642 TCAGGTTCGGACACATGG
1 TCAGGTTCGGACACATGG
*
16660 TCAGGTTTGGACACATGG
1 TCAGGTTCGGACACATGG
16678 GTCGGTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (18 bp):
TCAGGTTCGGACACATGG
Found at i:18509 original size:62 final size:62
Alignment explanation
Indices: 18412--18530 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
18402 AACTATCAAA
* * * *
18412 AAAATCAATCAGTAATGAAGGCTGACTGAATGAAATAATTTAGCGATAAAAGCTGATCTAAT
1 AAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTGATCTAAT
*
18474 AAAATCAATCAGCACTGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTGAT
1 AAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTGAT
18531 TCAGAGAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (62 bp):
AAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTGATCTAAT
Found at i:18529 original size:31 final size:31
Alignment explanation
Indices: 18432--18529 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
18422 AGTAATGAAG
* *
18432 GCTGACTGAATGAAATAATTTAGCGATAAAA
1 GCTGACTGAATGAAATAAATCAGCGATAAAA
* * * *
18463 GCTGATCT-AATAAAATCAATCAGC-ACTGAAG
1 GCTGA-CTGAATGAAATAAATCAGCGA-TAAAA
*
18494 GCTGACTGAATGAAATAAATCAACGATAAAA
1 GCTGACTGAATGAAATAAATCAGCGATAAAA
18525 GCTGA
1 GCTGA
18530 TTCAGAGAGA
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
30 3 0.06
31 46 0.88
32 3 0.06
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22
Consensus pattern (31 bp):
GCTGACTGAATGAAATAAATCAGCGATAAAA
Found at i:18576 original size:24 final size:25
Alignment explanation
Indices: 18539--18599 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
18529 ATTCAGAGAG
*
18539 AAAAGGAATCCCAAAA-TTTTTTTTC
1 AAAA-GAATTCCAAAATTTTTTTTTC
18564 AAAAGAATTCCAAAATTTTTTTTTTC
1 AAAAGAATTCCAAAA-TTTTTTTTTC
18590 AAAAGAATTC
1 AAAAGAATTC
18600 GAACCTATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 10 0.30
25 4 0.12
26 19 0.58
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.38
Consensus pattern (25 bp):
AAAAGAATTCCAAAATTTTTTTTTC
Found at i:20488 original size:240 final size:239
Alignment explanation
Indices: 20058--20491 Score: 629
Period size: 240 Copynumber: 1.8 Consensus size: 239
20048 GAAGAAAATC
20058 AATAACTGCTCAAAATCATGAAAATAGGAACTTCGGATATCTCAAGCCCCTCCTCAAATCATTGA
1 AATAACTGCTCAAAATCATGAAAATAGGAACTTCGGATATCTCAAGCCCCTCCTCAAATCATTGA
* * * *
20123 TCACACATTAGGAGAAAGTTGGTTCTACAGATACGTAAACTTATAGGAAAATTAAGATATATAGC
66 ACACACAATAGGAGAAAGGTGGTTCTACAGATACGTAAACTTACAGGAAAATTAAGATATATAGC
* *
20188 AATCAAAAACAAAAAAAAAGATATCAAAAGATAGGAAAAACAAAATTAATAATCATAAAAAAAGA
131 AATCAAAAAC--AAAAAAAGATATCAAAAGATAGGAAAAACAAAAATAATAATAATAAAAAAAGA
20253 GGCCTCCAGTTTACAAGTGGATACTATATAGGATGGGTCGGAAGAA
194 GGCCTCCAGTTTACAAGTGGATACTATATAGGATGGGTCGGAAGAA
* * * * *
20299 AATAACTGTTC-AAATCATGAAAGTAGGAACTTTGGATATTTCAAGCCCCTTCTCAAATCATTGA
1 AATAACTGCTCAAAATCATGAAAATAGGAACTTCGGATATCTCAAGCCCCTCCTCAAATCATTGA
* ** *
20363 ACACACAATAGTAGAAAGGTGGTTCTACAGATGTGTAAATTTACAGGAAAAATTAAGATATATAG
66 ACACACAATAGGAGAAAGGTGGTTCTACAGATACGTAAACTTACAGG-AAAATTAAGATATATAG
* ** * *
20428 CAATCATAAAC-AAAATTGATATCAACATATAGGAAAAACAAATTAATAATAATAATAAAAAAAG
130 CAATCAAAAACAAAAAAAGATATCAAAAGATAGGAAAAACAAA--AATAATAATAATAAAAAAAG
20492 GCAACAGTTT
Statistics
Matches: 170, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
238 27 0.16
240 106 0.62
241 37 0.22
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (239 bp):
AATAACTGCTCAAAATCATGAAAATAGGAACTTCGGATATCTCAAGCCCCTCCTCAAATCATTGA
ACACACAATAGGAGAAAGGTGGTTCTACAGATACGTAAACTTACAGGAAAATTAAGATATATAGC
AATCAAAAACAAAAAAAGATATCAAAAGATAGGAAAAACAAAAATAATAATAATAAAAAAAGAGG
CCTCCAGTTTACAAGTGGATACTATATAGGATGGGTCGGAAGAA
Done.