Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2964
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: 31850
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Found at i:4320 original size:27 final size:29
Alignment explanation
Indices: 4258--4320 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 29
4248 ATGTGGCCAT
* * *
4258 TGGTTTTTTGCGACTTGTTATAGTTGTCC
1 TGGTTTTTTGCGACTTGTTATAATAGTCA
* *
4287 TGTTTTTTTG-GGC-TGTTATAATAGTCA
1 TGGTTTTTTGCGACTTGTTATAATAGTCA
4314 TGGTTTT
1 TGGTTTT
4321 CGGGTTTCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 17 0.61
28 2 0.07
29 9 0.32
ACGTcount: A:0.13, C:0.10, G:0.24, T:0.54
Consensus pattern (29 bp):
TGGTTTTTTGCGACTTGTTATAATAGTCA
Found at i:11523 original size:19 final size:20
Alignment explanation
Indices: 11499--11538 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11489 CAATTGTTTT
11499 AAAA-TTAA-ATAAGTTTAAA
1 AAAATTTAATATAA-TTTAAA
11518 AAAATTTAATATAATTTAAA
1 AAAATTTAATATAATTTAAA
11538 A
1 A
11539 TTTTAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAATTTAATATAATTTAAA
Found at i:16278 original size:21 final size:20
Alignment explanation
Indices: 16254--16312 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
16244 CAAATTCCGT
16254 TCCGGTTCAGAATTTTTTGTG
1 TCCGGTTCAG-ATTTTTTGTG
16275 TCCGGTTCAG-TTGTTTTGGTG
1 TCCGGTTCAGATT-TTTT-GTG
16296 TCCGGTTCAGATTTTTT
1 TCCGGTTCAGATTTTTT
16313 TGCGTATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.06
20 4 0.11
21 27 0.77
22 2 0.06
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.49
Consensus pattern (20 bp):
TCCGGTTCAGATTTTTTGTG
Found at i:25168 original size:230 final size:230
Alignment explanation
Indices: 24749--25271 Score: 682
Period size: 230 Copynumber: 2.3 Consensus size: 230
24739 TAGCAGAATA
* *
24749 ATTTTTGTAATATCTGCTGAGCAGAATACTTTTCCTCTCTGTTTTTAGTTGATATATTCTTCTTT
1 ATTTTTGTAATATCTGCTGAGCAGAATAATTTTCCTCTCTGTTTTTAGTTAATATATTCTTCTTT
* **
24814 TCTTGTTTTTGCTTAGCAGAGTAATTTTGGGGTTTGGTGTTTTTGAGCCTGAATCACGATTAGAT
66 TCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGAT
* * *
24879 TTTGGCTTTTCATTTATATTTTTGTCATTATAGTTACTTTTCCAATTAACATGACACTAGTTCTA
131 TTCGGCTTATCATTTATATTTTTGTCATTATAGTTACTTTTCCAAATAACATGACACTAGTTCTA
24944 TTCCTCCCAACACTGAAGAAAATATCTATATTAAG
196 TTCCTCCCAACACTGAAGAAAATATCTATATTAAG
*
24979 ATTTTTTTAATAT-TCGCTGAGCAGAATAATTTTCCTCTCTGTTTTTAGTTAATATATTCTTCTT
1 ATTTTTGTAATATCT-GCTGAGCAGAATAATTTTCCTCTCTGTTTTTAGTTAATATATTCTTCTT
* * * * *
25043 TTCTTGTTTTTGCTTAGTAGAATAATTTTGTGGTTTGGTTTTTTTGGGCCCAAATCACGCTTAGA
65 TTCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGA
* *
25108 TTTCGGCTTATCATTTATATTTTTGTCATTATAGTT-CATTTTCCAAATGACATTACACTAGTTC
130 TTTCGGCTTATCATTTATATTTTTGTCATTATAGTTAC-TTTTCCAAATAACATGACACTAGTT-
* * * * * * * *
25172 CT-TTGCTCTCAGA-ACTCAGGATAGTATCTTTA-TAAT
193 CTATTCCTCCCA-ACACTGAAGAAAATATCTATATTAAG
* * * * * * *
25208 ATTTTTGTAATTTCTGCTTAGCAGAATACTATT-C-CTCTGTTTTTAGTTGACATATGCTTCTTT
1 ATTTTTGTAATATCTGCTGAGCAGAATAATTTTCCTCTCTGTTTTTAGTTAATATATTCTTCTTT
25271 T
66 T
25272 TGCTAATATG
Statistics
Matches: 256, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
227 27 0.11
228 1 0.00
229 31 0.12
230 194 0.76
231 3 0.01
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (230 bp):
ATTTTTGTAATATCTGCTGAGCAGAATAATTTTCCTCTCTGTTTTTAGTTAATATATTCTTCTTT
TCTTGTTTTTGCTTAGCAGAATAATTTTGGGGTTTGGTGTTTTTGAGCCCAAATCACGATTAGAT
TTCGGCTTATCATTTATATTTTTGTCATTATAGTTACTTTTCCAAATAACATGACACTAGTTCTA
TTCCTCCCAACACTGAAGAAAATATCTATATTAAG
Found at i:27739 original size:39 final size:40
Alignment explanation
Indices: 27660--27742 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
27650 TTACTGCATC
*
27660 TGTGTTGGCTTGATTTTGGTTCTAGGAACCTGGTGGGAGT
1 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
27700 TGTGTTGGCTTGATTTTGGTTCTA-GAACCCGGTGGGAGT
1 TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
27739 TGTG
1 TGTG
27743 ATGCACGTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 18 0.43
40 24 0.57
ACGTcount: A:0.12, C:0.11, G:0.37, T:0.40
Consensus pattern (40 bp):
TGTGTTGGCTTGATTTTGGTTCTAGGAACCCGGTGGGAGT
Found at i:28552 original size:21 final size:21
Alignment explanation
Indices: 28526--28584 Score: 102
Period size: 21 Copynumber: 2.8 Consensus size: 21
28516 ATATCCCATC
28526 CCGGTTCAGTTCTTTTAGTGT
1 CCGGTTCAGTTCTTTTAGTGT
28547 CCGGTTCAGTTCTTTTAGTGT
1 CCGGTTCAGTTCTTTTAGTGT
28568 CCGGTTCAGATT-TTTTA
1 CCGGTTCAG-TTCTTTTA
28585 TGCTGCAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (21 bp):
CCGGTTCAGTTCTTTTAGTGT
Found at i:30630 original size:14 final size:14
Alignment explanation
Indices: 30613--30646 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30603 ATAGCAATTA
**
30613 TAATATTATTTAAT
1 TAATATTATACAAT
30627 TAATATTATACAAT
1 TAATATTATACAAT
30641 TAATAT
1 TAATAT
30647 AAATGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATACAAT
Done.