Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_22285
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: 3408
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Found at i:2552 original size:162 final size:162
Alignment explanation
Indices: 2285--2616 Score: 513
Period size: 162 Copynumber: 2.0 Consensus size: 162
2275 TTACAAATTC
* * * *
2285 TGAAGATAAAGAGGTGCTTTGGAATGGAAGAAATAATTCAAAACTCACCAGTATCAACCATAAGC
1 TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
* *
2350 TTCCAATGTCTAAGGGAAGTACAAGTTACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
66 TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
2415 TGTTGCTAATAATCTTGGG-AGATTGCAAACCT
131 TGTTGCTAATAATCTTGGGCA-ATTGCAAACCT
* * **
2447 TGAAGATAGAGAGATGCTTTGGAATGGCAGAAATAATCCAAGTCTCACAAGTATCAACCATAAAC
1 TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
* * *
2512 TTTCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTTCCGATGTG
66 TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
* *
2577 TGTTGCTAATAGTCTTGGGCAATTGCAAACTT
131 TGTTGCTAATAATCTTGGGCAATTGCAAACCT
2609 TGAAGATA
1 TGAAGATA
2617 TGGAGTTGTT
Statistics
Matches: 154, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
162 153 0.99
163 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (162 bp):
TGAAGATAAAGAGATGCTTTGGAATGGAAGAAATAATCCAAAACTCACAAGTATCAACCATAAAC
TTCCAATGTCTAAGGAAAGTACAAGTCACAGAATGCAATAATTTGAAATTTCTCTTCCCAATGTG
TGTTGCTAATAATCTTGGGCAATTGCAAACCT
Done.