Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_265 ID=scaffold_265-JGI_221_v2.0
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: 8831
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:240 original size:19 final size:19
Alignment explanation
Indices: 202--242 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
192 TTTAATACTA
**
202 ATTTATTATTATTATTATT
1 ATTTATTATTATTAACATT
*
221 ATTTATTGTTATTAACATT
1 ATTTATTATTATTAACATT
240 ATT
1 ATT
243 ATCATACTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTATTATTATTAACATT
Found at i:5250 original size:6 final size:6
Alignment explanation
Indices: 5241--5296 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
5231 CAAAAAAAAT
* ** *
5241 AATCAA AATCAA AATCAA AAACAAA AAT-AA AAGAAA AATCAA AGTCAA
1 AATCAA AATCAA AATCAA AATC-AA AATCAA AATCAA AATCAA AATCAA
*
5289 AAGCAA AA
1 AATCAA AA
5297 AAGAGAAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 4 0.10
6 32 0.80
7 4 0.10
ACGTcount: A:0.71, C:0.12, G:0.05, T:0.11
Consensus pattern (6 bp):
AATCAA
Found at i:5272 original size:24 final size:25
Alignment explanation
Indices: 5230--5283 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
5220 GGGTTCAGAT
**
5230 TCAAAAAAAATAATCAAAATCAAAA
1 TCAAAAAAAATAATCAAAAGAAAAA
5255 TCAAAAACAAA-AAT-AAAAGAAAAA
1 TCAAAAA-AAATAATCAAAAGAAAAA
5279 TCAAA
1 TCAAA
5284 GTCAAAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 13 0.50
25 10 0.38
26 3 0.12
ACGTcount: A:0.74, C:0.11, G:0.02, T:0.13
Consensus pattern (25 bp):
TCAAAAAAAATAATCAAAAGAAAAA
Found at i:5289 original size:24 final size:24
Alignment explanation
Indices: 5251--5325 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 24
5241 AATCAAAATC
**
5251 AAAATCAAAAACAAAAATAAAAGA
1 AAAATCAAAGTCAAAAATAAAAGA
*
5275 AAAATCAAAGTCAAAAGCAAAAAAGAGA
1 AAAATCAAAGTC-AAA--AATAAA-AGA
5303 AATCAATCAAAGTC-AAAATAAAA
1 AA--AATCAAAGTCAAAAATAAAA
5326 TATGAAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
24 10 0.24
25 4 0.10
26 5 0.12
27 5 0.12
28 7 0.17
30 10 0.24
ACGTcount: A:0.71, C:0.11, G:0.08, T:0.11
Consensus pattern (24 bp):
AAAATCAAAGTCAAAAATAAAAGA
Found at i:5311 original size:30 final size:30
Alignment explanation
Indices: 5245--5320 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
5235 AAAAATAATC
*
5245 AAAATCAAAATCAAAAACAAAAATAAAAGA
1 AAAATCAAAGTCAAAAACAAAAATAAAAGA
* *
5275 AAAATCAAAGTCAAAAGC-AAAA-AAGAGA
1 AAAATCAAAGTCAAAAACAAAAATAAAAGA
5303 AATCAATCAAAGTCAAAA
1 AA--AATCAAAGTCAAAA
5321 TAAAATATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 7 0.17
29 4 0.10
30 30 0.73
ACGTcount: A:0.70, C:0.12, G:0.08, T:0.11
Consensus pattern (30 bp):
AAAATCAAAGTCAAAAACAAAAATAAAAGA
Found at i:5738 original size:13 final size:13
Alignment explanation
Indices: 5705--5730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5695 AAAAAAAATG
5705 ATGAAAAATGAAA
1 ATGAAAAATGAAA
5718 ATGAAAAATGAAA
1 ATGAAAAATGAAA
5731 GAGTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:7390 original size:87 final size:87
Alignment explanation
Indices: 6949--7371 Score: 621
Period size: 87 Copynumber: 4.9 Consensus size: 87
6939 AGAACAGATC
* ** * * * *
6949 AGCAGATCGAAAACAAAGAATTGCCTCCATCGGTTGCAGTGGAGTTGTTTAAATATAGTAGATCT
1 AGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
7014 TGCCTTCCTGCATTAACAGCGA
66 TGCCTTCCTGCATTAACAGCGA
* *
7036 AGCAGATCGAAAATAAAGCCTTGCCTTCATCGGTGGCAGTGGAGCTGGTTAAAGATAGCAGATCT
1 AGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
7101 TGCCTTCCTGCATTAACAGCGA
66 TGCCTTCCTGCATTAACAGCGA
* * *
7123 AGCAGATCGAAAACAAAGCCTCGCCTCCATCAGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
1 AGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
**
7188 TGCCTTCCTGTGTTAACAGCGA
66 TGCCTTCCTGCATTAACAGCGA
* * *
7210 AGCAGATCGAAAATAAAGCATTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATAT
1 AGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
* *
7275 TCCCTTCCTACATTAACAGCGA
66 TGCCTTCCTGCATTAACAGCGA
* ** *
7297 ATCAGATAAAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGAAGATCT
1 AGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
* *
7362 TCCCCTCCTG
66 TGCCTTCCTG
7372 TGTCGACAGT
Statistics
Matches: 302, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 302 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (87 bp):
AGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCT
TGCCTTCCTGCATTAACAGCGA
Done.