Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1706
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: 15914
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Found at i:2284 original size:13 final size:15
Alignment explanation
Indices: 2251--2286 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
2241 TTAAAAAAAT
2251 TTAAAATATAATTAA
1 TTAAAATATAATTAA
2266 TT-AAATA-AATT-A
1 TTAAAATATAATTAA
2278 TTAAAATAT
1 TTAAAATAT
2287 GTTGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.16
13 9 0.47
14 5 0.26
15 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATATAATTAA
Found at i:4219 original size:28 final size:29
Alignment explanation
Indices: 4147--4207 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
4137 CACATAACAA
* *
4147 AAAATAAAAACATTTTGATAAATTATTTT
1 AAAATAAAAATATTTTGATAAATTAATTT
4176 AAAATAAAAATATTTTGAT-AATTAATTT
1 AAAATAAAAATATTTTGATAAATTAATTT
4204 AAAA
1 AAAA
4208 AAATGCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATAAAAATATTTTGATAAATTAATTT
Found at i:4517 original size:45 final size:45
Alignment explanation
Indices: 4453--4542 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
4443 ATTTATATAT
*
4453 ATATATATCTTTATGTTTGGATTAAATTTACTTTTCCTAGACTTA
1 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
4498 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
1 ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
4543 TGTGCTCCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (45 bp):
ATATATATCTTTATGTTTGGATTAAATTTACTTTCCCTAGACTTA
Found at i:8459 original size:42 final size:42
Alignment explanation
Indices: 8412--8492 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
8402 ATCAAGAATG
* *
8412 GGTTCAGATTCTGGAGATTCAGGTTCGAACACATGGTCAATC
1 GGTTCAAATTCTGGAGACTCAGGTTCGAACACATGGTCAATC
*
8454 GGTTCAAATTCTGGAGACTCAGGTTCGGACACATGGTCA
1 GGTTCAAATTCTGGAGACTCAGGTTCGAACACATGGTCA
8493 GGTTTGGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (42 bp):
GGTTCAAATTCTGGAGACTCAGGTTCGAACACATGGTCAATC
Found at i:8495 original size:18 final size:18
Alignment explanation
Indices: 8472--8507 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
8462 TTCTGGAGAC
8472 TCAGGTTCGGACACATGG
1 TCAGGTTCGGACACATGG
*
8490 TCAGGTTTGGACACATGG
1 TCAGGTTCGGACACATGG
8508 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:10343 original size:62 final size:62
Alignment explanation
Indices: 10246--10364 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
10236 AACTATCAAA
* * * *
10246 AAAATCAATCAGTAATGAAGGCTGACTGAATGAAATAATTTAGCGATAAAAGCTGATCTAAT
1 AAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTGATCTAAT
*
10308 AAAATCAATCAGCACTGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTGAT
1 AAAATCAATCAGCAATGAAGGCTGACTGAATGAAATAAATCAACGATAAAAGCTGAT
10365 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:10363 original size:31 final size:31
Alignment explanation
Indices: 10266--10363 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
10256 AGTAATGAAG
* *
10266 GCTGACTGAATGAAATAATTTAGCGATAAAA
1 GCTGACTGAATGAAATAAATCAGCGATAAAA
* * * *
10297 GCTGATCT-AATAAAATCAATCAGC-ACTGAAG
1 GCTGA-CTGAATGAAATAAATCAGCGA-TAAAA
*
10328 GCTGACTGAATGAAATAAATCAACGATAAAA
1 GCTGACTGAATGAAATAAATCAGCGATAAAA
10359 GCTGA
1 GCTGA
10364 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:10410 original size:24 final size:25
Alignment explanation
Indices: 10373--10433 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
10363 ATTCAGAGAG
*
10373 AAAAGGAATCCCAAAA-TTTTTTTTC
1 AAAA-GAATTCCAAAATTTTTTTTTC
10398 AAAAGAATTCCAAAATTTTTTTTTTC
1 AAAAGAATTCCAAAA-TTTTTTTTTC
10424 AAAAGAATTC
1 AAAAGAATTC
10434 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:12322 original size:240 final size:239
Alignment explanation
Indices: 11892--12325 Score: 629
Period size: 240 Copynumber: 1.8 Consensus size: 239
11882 GAAGAAAATC
11892 AATAACTGCTCAAAATCATGAAAATAGGAACTTCGGATATCTCAAGCCCCTCCTCAAATCATTGA
1 AATAACTGCTCAAAATCATGAAAATAGGAACTTCGGATATCTCAAGCCCCTCCTCAAATCATTGA
* * * *
11957 TCACACATTAGGAGAAAGTTGGTTCTACAGATACGTAAACTTATAGGAAAATTAAGATATATAGC
66 ACACACAATAGGAGAAAGGTGGTTCTACAGATACGTAAACTTACAGGAAAATTAAGATATATAGC
* *
12022 AATCAAAAACAAAAAAAAAGATATCAAAAGATAGGAAAAACAAAATTAATAATCATAAAAAAAGA
131 AATCAAAAAC--AAAAAAAGATATCAAAAGATAGGAAAAACAAAAATAATAATAATAAAAAAAGA
12087 GGCCTCCAGTTTACAAGTGGATACTATATAGGATGGGTCGGAAGAA
194 GGCCTCCAGTTTACAAGTGGATACTATATAGGATGGGTCGGAAGAA
* * * * *
12133 AATAACTGTTC-AAATCATGAAAGTAGGAACTTTGGATATTTCAAGCCCCTTCTCAAATCATTGA
1 AATAACTGCTCAAAATCATGAAAATAGGAACTTCGGATATCTCAAGCCCCTCCTCAAATCATTGA
* ** *
12197 ACACACAATAGTAGAAAGGTGGTTCTACAGATGTGTAAATTTACAGGAAAAATTAAGATATATAG
66 ACACACAATAGGAGAAAGGTGGTTCTACAGATACGTAAACTTACAGG-AAAATTAAGATATATAG
* ** * *
12262 CAATCATAAAC-AAAATTGATATCAACATATAGGAAAAACAAATTAATAATAATAATAAAAAAAG
130 CAATCAAAAACAAAAAAAGATATCAAAAGATAGGAAAAACAAA--AATAATAATAATAAAAAAAG
12326 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
Found at i:12644 original size:20 final size:20
Alignment explanation
Indices: 12619--12659 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12609 TAGGAAGAAC
12619 AAAATTAAAAACAATAAAAA
1 AAAATTAAAAACAATAAAAA
*
12639 AAAATTAATAACAATAAAAA
1 AAAATTAAAAACAATAAAAA
12659 A
1 A
12660 TGACGGCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAATTAAAAACAATAAAAA
Done.