Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 36352
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1321 original size:46 final size:46
Alignment explanation
Indices: 1268--1443 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
1258 ATTTTGGGCA
*
1268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
1314 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
1361 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
1407 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1444 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
45 3 0.03
46 65 0.59
47 28 0.25
48 3 0.03
50 5 0.05
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:1423 original size:93 final size:93
Alignment explanation
Indices: 1264--1436 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
1254 TAGGATTTTG
* *
1264 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
1329 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
1357 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
1422 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
1437 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:4395 original size:15 final size:15
Alignment explanation
Indices: 4356--4435 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
4346 GTATCTTGGG
*
4356 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
4371 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
4386 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
4401 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
4416 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
4430 TTTCTT
1 TTTCTT
4436 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:4425 original size:30 final size:30
Alignment explanation
Indices: 4347--4434 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
4337 CATAGTATCG
* * *
4347 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
4377 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
4407 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
4435 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:8627 original size:20 final size:20
Alignment explanation
Indices: 8604--8646 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
8594 AGGCACGATG
* *
8604 GTGCAATTAGAGGCACCAAA
1 GTGCAATCAGAGACACCAAA
8624 GTGCAATCAGAGACACCAAA
1 GTGCAATCAGAGACACCAAA
8644 GTG
1 GTG
8647 TAACAAAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.14
Consensus pattern (20 bp):
GTGCAATCAGAGACACCAAA
Found at i:8664 original size:19 final size:20
Alignment explanation
Indices: 8604--8670 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
8594 AGGCACGATG
* *
8604 GTGCAATTAGAGGCACCAAA
1 GTGCAATCAAAGGCACCAAA
* *
8624 GTGCAATCAGAGACACCAAA
1 GTGCAATCAAAGGCACCAAA
* *
8644 GTGTAA-CAAAGGCACCCAA
1 GTGCAATCAAAGGCACCAAA
*
8663 GTACAATC
1 GTGCAATC
8671 CCGTACAAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 14 0.37
20 24 0.63
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.13
Consensus pattern (20 bp):
GTGCAATCAAAGGCACCAAA
Found at i:11114 original size:34 final size:34
Alignment explanation
Indices: 11071--11138 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
11061 TCTACAATTG
11071 ATCTATGTCCCAACTACAATTCAAGAACTTTTTT
1 ATCTATGTCCCAACTACAATTCAAGAACTTTTTT
11105 ATCTATGTCCCAACTACAATTCAAGAACTTTTTT
1 ATCTATGTCCCAACTACAATTCAAGAACTTTTTT
11139 TTTCTTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (34 bp):
ATCTATGTCCCAACTACAATTCAAGAACTTTTTT
Found at i:23240 original size:27 final size:27
Alignment explanation
Indices: 23202--23257 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
23192 TGGATGAAAT
23202 ATGTTTGTTTTATTTCATTTCATCATA
1 ATGTTTGTTTTATTTCATTTCATCATA
*
23229 ATGTTTGTTTTATTTTATTTCATCATA
1 ATGTTTGTTTTATTTCATTTCATCATA
23256 AT
1 AT
23258 ACACTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (27 bp):
ATGTTTGTTTTATTTCATTTCATCATA
Found at i:27371 original size:27 final size:26
Alignment explanation
Indices: 27323--27382 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
27313 AGCGAGCTGC
*
27323 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCAGA-A
* * *
27350 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACAAAGCCACCAGAA
27376 CAGATAT
1 CAGATAT
27383 ATATATATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAGAA
Found at i:27469 original size:27 final size:26
Alignment explanation
Indices: 27421--27472 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
27411 GCGAGGCTGC
*
27421 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
27447 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
27473 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:34759 original size:27 final size:26
Alignment explanation
Indices: 34711--34770 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
34701 GCGAGGCTGC
*
34711 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
34738 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
34764 CAGATAT
1 CAGATAT
34771 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:34857 original size:27 final size:26
Alignment explanation
Indices: 34809--34860 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
34799 GCGAGGCTGC
*
34809 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
34835 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
34861 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Done.