Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7319.1
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: 7332
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Found at i:55 original size:35 final size:35
Alignment explanation
Indices: 9--77 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
1 GTGTGTGA
9 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
44 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
78 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:840 original size:16 final size:17
Alignment explanation
Indices: 806--840 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
796 TTGATTTTTG
* *
806 AAAAGCATAGATTGAAA
1 AAAAACATAAATTGAAA
823 AAAAACATAAATTGAAA
1 AAAAACATAAATTGAAA
840 A
1 A
841 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAAACATAAATTGAAA
Found at i:1194 original size:192 final size:193
Alignment explanation
Indices: 859--1210 Score: 661
Period size: 192 Copynumber: 1.8 Consensus size: 193
849 CATGTGAGCC
*
859 GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTGTGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGTGAAAAACAAAAATTAAAAGGCTTAACT
924 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
66 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
989 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
131 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
**
1052 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT-TGAAAAACAAAAATTAAAAGGCTTAACT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGTGAAAAACAAAAATTAAAAGGCTTAACT
1116 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
66 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
*
1181 AACTCATTTCTCGCAATATGAGTTGATTTT
131 AACTCACTTCTCGCAATATGAGTTGATTTT
1211 GAAAAACAAA
Statistics
Matches: 155, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
192 122 0.79
193 33 0.21
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (193 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGTGAAAAACAAAAATTAAAAGGCTTAACT
CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTT
Found at i:1201 original size:122 final size:122
Alignment explanation
Indices: 1052--1318 Score: 516
Period size: 122 Copynumber: 2.2 Consensus size: 122
1042 AACGTGTCTT
1052 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
*
1117 ACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCC
66 ACCTCTCACAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCC
1174 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
1239 ACCTCTCACAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCC
66 ACCTCTCACAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCC
*
1296 GAGGCTCAACTCACTTCTCGCAA
1 GAGGCTCAACTCATTTCTCGCAA
1319 AAATTTAAAA
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 143 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (122 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTC
ACCTCTCACAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCC
Done.