Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1111
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: 24998
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:773 original size:21 final size:21
Alignment explanation
Indices: 721--762 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
711 TTTAAAAACA
*
721 TCATCTAATGCCCATTTAAGT
1 TCATCTAATGCCCATTAAAGT
742 TCATCTAATGCCCATTAAAGT
1 TCATCTAATGCCCATTAAAGT
763 CACTTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (21 bp):
TCATCTAATGCCCATTAAAGT
Found at i:8330 original size:20 final size:20
Alignment explanation
Indices: 8307--8357 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
8297 ACCATGGCAT
*
8307 GCATTAAATGACTTAAATGG
1 GCATTAGATGACTTAAATGG
8327 GCATTAGATGACTTAAATGG
1 GCATTAGATGACTTAAATGG
8347 GCATTAGATGA
1 GCATTAGATGA
8358 TGGTTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (20 bp):
GCATTAGATGACTTAAATGG
Found at i:12411 original size:15 final size:15
Alignment explanation
Indices: 12372--12451 Score: 85
Period size: 15 Copynumber: 5.4 Consensus size: 15
12362 GTATCTTGGG
*
12372 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
12387 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
12402 TTTCTTTATTCTGTG-
1 TTTCTTTATTCTG-GA
*
12417 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
12432 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
12446 TTTCTT
1 TTTCTT
12452 GTTATCTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
14 11 0.20
15 41 0.75
16 3 0.05
ACGTcount: A:0.10, C:0.17, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:12441 original size:30 final size:30
Alignment explanation
Indices: 12363--12450 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
12353 CATAGTATCG
* * * *
12363 TATCTTGGGTTTCTTTATCCTG-GATCTCTT
1 TATCTTGGATTTCTTTATTCTGTG-TTTCTC
12393 TAT-TCTGGATTTCTTTATTCTGTGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGTGTTTCTC
*
12423 TATCTTGGATTTCTTTATTCGGT-TTTCT
1 TATCTTGGATTTCTTTATTCTGTGTTTCT
12451 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 6 0.12
30 42 0.84
31 2 0.04
ACGTcount: A:0.10, C:0.17, G:0.15, T:0.58
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGTGTTTCTC
Found at i:14423 original size:46 final size:46
Alignment explanation
Indices: 14373--14548 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
14363 TGGTTGAGCA
14373 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** * *
14419 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
* *
14466 TCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
14512 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
14549 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:14529 original size:93 final size:93
Alignment explanation
Indices: 14370--14540 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
14360 GGATGGTTGA
* *
14370 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
14435 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
14463 GCATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
14528 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
14541 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:16702 original size:43 final size:41
Alignment explanation
Indices: 16547--16703 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 41
16537 TGTGTTATCG
*
16547 TGTAAGACCACGTCTGAGACGTTGGCATCA-ACTTATGATTTAC
1 TGTAAGACCACGTCTGGGACGTTGGCATCATA-TT-TGA-TTAC
* * * * *
16590 GTGTAAGACCATGTTTGGGACATCGGCATCATATTTGATTTC
1 -TGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTAC
* *
16632 GGTCAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGATTAC
1 TGT-AAGACCAC-GTCTGGGA-CGTTGGCATC-ATATTTGATTAC
16675 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 -TGTAAGACCACGTCTGGGACGTTGGCAT
16704 TGTACGAGTT
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
41 2 0.02
42 23 0.26
43 34 0.38
44 30 0.33
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCATATTTGATTAC
Found at i:18660 original size:19 final size:19
Alignment explanation
Indices: 18636--18675 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18626 TTCTGATTTT
*
18636 GTTCCAATTCAAGGATAGA
1 GTTCCAATTCAAGGACAGA
* *
18655 GTTCCACTTCGAGGACAGA
1 GTTCCAATTCAAGGACAGA
18674 GT
1 GT
18676 ATTCTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (19 bp):
GTTCCAATTCAAGGACAGA
Done.