Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3475
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: 8401
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Found at i:1719 original size:40 final size:40
Alignment explanation
Indices: 1687--1985 Score: 460
Period size: 40 Copynumber: 7.5 Consensus size: 40
1677 CCAGCAAGAT
* * * *
1687 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
1727 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
1767 TGCTCTTCGGAACTTAGCCC-GATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
1806 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
1846 TGCTCTTCGGGACTTAGCCCGGTTACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1886 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
1926 TGCTCTTC-GGACTTAACCCGGATACATCACTAGCTCGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1965 TGCTCTTC-GGACTTAGCCCGG
1 TGCTCTTCGGGACTTAGCCCGG
1986 CTATACAACT
Statistics
Matches: 239, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 85 0.36
40 154 0.64
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:1901 original size:119 final size:120
Alignment explanation
Indices: 1687--1985 Score: 469
Period size: 119 Copynumber: 2.5 Consensus size: 120
1677 CCAGCAAGAT
* * * * * ** *
1687 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
1752 TATCACTAGCACGAATGCTCTTCGGAACTTAGCCC-GATACATCACTAGCACGAA
66 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
1806 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGTTA
1 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
1871 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
66 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
1926 TGCTCTTC-GGACTTAACCCGGATACATCACTAGCTCGAATGCTCTTC-GGACTTAGCCCGG
1 TGCTCTTCGGGACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGG
1986 CTATACAACT
Statistics
Matches: 167, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
118 13 0.08
119 127 0.76
120 27 0.16
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (120 bp):
TGCTCTTCGGGACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
Found at i:1917 original size:159 final size:158
Alignment explanation
Indices: 1687--1985 Score: 465
Period size: 159 Copynumber: 1.9 Consensus size: 158
1677 CCAGCAAGAT
* **
1687 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGGGACCTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGACTTAGCACGGATA
* *
1752 TATCACTAGCACGAATGCTCTTCGGAACTTAGCCC-GATACATCACTAGCACGAATGCTCTTCGG
66 CATCACTAGCACGAATGCTCTTCGG-ACTTAACCCGGATACATCACTAGCACGAATGCTCTTC-G
1816 GACTTAACCCGGATACATCACTAGCACGAA
129 GACTTAACCCGGATACATCACTAGCACGAA
* * * * *
1846 TGCTCTTCGGGACTTAGCCCGGTTACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGGACCTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGACTTAGCACGGATA
*
1911 CATCACTAGCACGAATGCTCTTCGGACTTAACCCGGATACATCACTAGCTCGAATGCTCTTCGGA
66 CATCACTAGCACGAATGCTCTTCGGACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGA
*
1976 CTTAGCCCGG
131 CTTAACCCGG
1986 CTATACAACT
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
158 20 0.16
159 107 0.84
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (158 bp):
TGCTCTTCGGGACCTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGACTTAGCACGGATA
CATCACTAGCACGAATGCTCTTCGGACTTAACCCGGATACATCACTAGCACGAATGCTCTTCGGA
CTTAACCCGGATACATCACTAGCACGAA
Found at i:4098 original size:48 final size:48
Alignment explanation
Indices: 4037--4525 Score: 828
Period size: 48 Copynumber: 10.3 Consensus size: 48
4027 TGTTACAACA
* * *
4037 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
4085 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
4133 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
4181 TTCACATTAGCCATTCGGCTTTACCACATATACATAT--CACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
4227 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
4275 TTCACATTCG-CATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
4322 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
4370 TTCACATTAGCCATTCGGCTTTACCACATATACATAT--CTCATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
4416 TTCACATTCGTCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
4464 TTCACATTAGCCATTCGGCTTTA-CACATACACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
4511 TTCACATTAGCCATT
1 TTCACATTAGCCATT
4526 TTCACCACAC
Statistics
Matches: 417, Mismatches: 19, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
46 89 0.21
47 81 0.19
48 247 0.59
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:4358 original size:189 final size:190
Alignment explanation
Indices: 4037--4525 Score: 892
Period size: 189 Copynumber: 2.6 Consensus size: 190
4027 TGTTACAACA
4037 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
4102 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
4167 TATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACATATAT
131 TATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACATATAT
4227 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCG-CATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
4291 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
*
4356 TATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATAT
131 TATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACATATAT
* * * * * *
4416 TTCACATTCGTCATTCGGCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
*
4481 GCTTTA-CACATACACATATCACACATATATTTCACATTAGCCATT
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATT
4526 TTCACCACAC
Statistics
Matches: 290, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
189 220 0.76
190 70 0.24
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (190 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
TATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACATATAT
Found at i:4463 original size:237 final size:236
Alignment explanation
Indices: 4037--4525 Score: 820
Period size: 237 Copynumber: 2.1 Consensus size: 236
4027 TGTTACAACA
* * *
4037 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATATTTCACATTAGCCATTCG
4102 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
4167 TATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACATATATTTCAC
131 TAT-ACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACATATATTTCAC
* * *
4232 ATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
195 ATTAGCCATTCGGCTTTA-CACATACACATATCACACACATAT
* *
4275 TTCACATTCG-CATTCGGCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATATTTCACATTAGCCATTCG
4339 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
66 GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
* * *
4404 TAT-CTCATATATTTCACATTCGTCATTCGGCTTTACCACATATACATATCACACATATATTTCA
131 TATACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATAT--CACATATATTTCA
*
4468 CATTAGCCATTCGGCTTTACACATACACATATCACACATATAT
194 CATTAGCCATTCGGCTTTACACATACACATATCACACACATAT
4511 TTCACATTAGCCATT
1 TTCACATTAGCCATT
4526 TTCACCACAC
Statistics
Matches: 235, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
235 43 0.18
236 29 0.12
237 154 0.66
238 9 0.04
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (236 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATATTTCACATTAGCCATTCG
GCTTTACCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACA
TATACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACATATATTTCACA
TTAGCCATTCGGCTTTACACATACACATATCACACACATAT
Done.