Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2267
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: 37894
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2801 original size:33 final size:34
Alignment explanation
Indices: 2750--2815 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
2740 TGAGAAAGAC
2750 AAACTATCAAAGTATCAAGTATAAGATCTCGATA
1 AAACTATCAAAGTATCAAGTATAAGATCTCGATA
2784 AAACTATC-AAGTATCAAGTATAAGATCTCGAT
1 AAACTATCAAAGTATCAAGTATAAGATCTCGAT
2816 TATCATCCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.75
34 8 0.25
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (34 bp):
AAACTATCAAAGTATCAAGTATAAGATCTCGATA
Found at i:5543 original size:33 final size:36
Alignment explanation
Indices: 5506--5580 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
5496 TTGTTGATTA
5506 AAGGA-GC-AAATTAAT-AATGCAGTCATCCAAAAG
1 AAGGATGCTAAATTAATCAATGCAGTCATCCAAAAG
* ** *
5539 AAGGATTCTATTTTGATCAATGCAGTCATCCAAAAG
1 AAGGATGCTAAATTAATCAATGCAGTCATCCAAAAG
5575 AAGGAT
1 AAGGAT
5581 TCTATTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 5 0.14
34 1 0.03
35 5 0.14
36 24 0.69
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.24
Consensus pattern (36 bp):
AAGGATGCTAAATTAATCAATGCAGTCATCCAAAAG
Found at i:5561 original size:36 final size:36
Alignment explanation
Indices: 5521--5594 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5511 GCAAATTAAT
5521 AATGCAGTCATCCAAAAGAAGGATTCTATTTTGATC
1 AATGCAGTCATCCAAAAGAAGGATTCTATTTTGATC
5557 AATGCAGTCATCCAAAAGAAGGATTCTATTTTGATC
1 AATGCAGTCATCCAAAAGAAGGATTCTATTTTGATC
5593 AA
1 AA
5595 GTATTAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (36 bp):
AATGCAGTCATCCAAAAGAAGGATTCTATTTTGATC
Found at i:10267 original size:22 final size:23
Alignment explanation
Indices: 10242--10290 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
10232 TTATTATATC
10242 ATATTATTATATT-T-AATTTAAT
1 ATATTATTA-ATTCTAAATTTAAT
10264 ATATTATTAATTCTAAATTTAAT
1 ATATTATTAATTCTAAATTTAAT
10287 -TATT
1 ATATT
10291 GAGCGAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATTATTAATTCTAAATTTAAT
Found at i:18410 original size:21 final size:21
Alignment explanation
Indices: 18385--18434 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
18375 AAAACTTTAA
*
18385 AAATATTATTGTTTACACAAT
1 AAATATTATTGTTTAAACAAT
*
18406 AAATAATATTGTTTAAACAAT
1 AAATATTATTGTTTAAACAAT
18427 AAATATTA
1 AAATATTA
18435 AATCTATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATATTATTGTTTAAACAAT
Found at i:19915 original size:51 final size:51
Alignment explanation
Indices: 19845--19957 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
19835 ATCGGTGTAA
* * * * *
19845 TAATAAATTCAGCCCTAATAATTTATATA-TTCTATCAATTTGGTATTGATT
1 TAATAAATTTAGCCCTAAT-ATTTACACATTTCTATCAATTTAGTATTAATT
* *
19896 TAATAAATTTA-CCCGTAATATTTACACATTTTTATCAATTTAGTCTTAATT
1 TAATAAATTTAGCCC-TAATATTTACACATTTCTATCAATTTAGTATTAATT
*
19947 TAACAAATTTA
1 TAATAAATTTA
19958 ACCTGTACCA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
50 10 0.19
51 42 0.81
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.45
Consensus pattern (51 bp):
TAATAAATTTAGCCCTAATATTTACACATTTCTATCAATTTAGTATTAATT
Found at i:21729 original size:12 final size:12
Alignment explanation
Indices: 21712--21736 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21702 TCACGTTATT
21712 TCTAAAAATATA
1 TCTAAAAATATA
21724 TCTAAAAATATA
1 TCTAAAAATATA
21736 T
1 T
21737 GAATATCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTAAAAATATA
Found at i:28951 original size:16 final size:16
Alignment explanation
Indices: 28918--28951 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28908 TAAGTGTGTT
* *
28918 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
28934 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
28950 AA
1 AA
28952 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:31772 original size:21 final size:21
Alignment explanation
Indices: 31746--31786 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31736 AGACGAGCAA
* *
31746 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
31767 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
31787 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:33721 original size:16 final size:16
Alignment explanation
Indices: 33688--33721 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33678 GGAGATTGTT
* *
33688 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
33704 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
33720 AA
1 AA
33722 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:35279 original size:1 final size:1
Alignment explanation
Indices: 35275--35343 Score: 75
Period size: 1 Copynumber: 69.0 Consensus size: 1
35265 AAACATAAAC
* * * * ** *
35275 AAAAAAAAAAAAAAAACAGAAAAAAATACAAAAAACCAAACAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35340 AAAA
1 AAAA
35344 CACACTTGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.90, C:0.07, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:35315 original size:47 final size:43
Alignment explanation
Indices: 35256--35343 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 43
35246 CTTGTTTAAG
35256 CAAAAAAACAAACATAAACAAAAAAAAAAAAAAAACAGAAAAAAATA
1 CAAAAAAACAAACA-AAA-AAAAAAAAAAAAAAAA-A-AAAAAAATA
*
35303 CAAAAAACCAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 CAAAAAAACAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35344 CACACTTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 7 0.17
44 1 0.03
45 16 0.40
46 3 0.08
47 13 0.32
ACGTcount: A:0.86, C:0.10, G:0.01, T:0.02
Consensus pattern (43 bp):
CAAAAAAACAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAATA
Found at i:35390 original size:21 final size:22
Alignment explanation
Indices: 35355--35395 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
35345 ACACTTGTTA
35355 AAATAAAACAAAAAAAAAGAAG
1 AAATAAAACAAAAAAAAAGAAG
35377 AAATAAAA-AAAAAAAAAGA
1 AAATAAAACAAAAAAAAAGA
35396 CTGAGGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.05
Consensus pattern (22 bp):
AAATAAAACAAAAAAAAAGAAG
Done.