Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold353
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: 358750
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:355477 original size:33 final size:33
Alignment explanation
Indices: 355440--355521 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
355430 CATTTCCCCA
*
355440 TATCTCTTCTATCTCTCCTTCTATCATCCCTTC
1 TATCTCTTCTATCTCTCCTCCTATCATCCCTTC
*
355473 TATCTCTACTATCTCTCCTCCTATCATCCCTTC
1 TATCTCTTCTATCTCTCCTCCTATCATCCCTTC
* *
355506 TGTCTCTTCTTTCTCT
1 TATCTCTTCTATCTCT
355522 TTGAGGGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.39, G:0.01, T:0.49
Consensus pattern (33 bp):
TATCTCTTCTATCTCTCCTCCTATCATCCCTTC
Found at i:356839 original size:220 final size:221
Alignment explanation
Indices: 356445--356883 Score: 740
Period size: 220 Copynumber: 2.0 Consensus size: 221
356435 AATAATTATC
*
356445 TTGAGATGAATTTCTAACAACAAACAGAATTATTAATGCAAGAACAGAAATTGAAAGAAGCAAAA
1 TTGAGATGAATTTCTAACAACAAACAGAATTATTAATGCAAGAACAGAAATAGAAAGAAGCAAAA
*
356510 AAAATAACAAAACTGGAATAGATTAGAGATGAAGGATGGTGCCACAATCACAAGATTGATAAGCC
66 AAAAAAACAAAACTGGAATAGATTAGAGATGAAGGATGGTGCCACAATCACAAGATTGATAAGCC
* *
356575 AAAAGGAATGATCACCACAAGAGTTTTGGCCTCTTCTCAAGATCCAAAAAAATTGGCTCACTCAA
131 AAAAGGAATGATCACCACAAGAGTCTTGGCCACTTCTCAAGATCCAAAAAAATTGGCTCACTCAA
356640 GAACCTAAGAATCACACTCTCACATT
196 GAACCTAAGAATCACACTCTCACATT
* * * * *
356666 TTGAGATGGATTTCTAACAATAAATATAATTATTGATGCAAGAACAGAAATAGAAAGAAGCAAAA
1 TTGAGATGAATTTCTAACAACAAACAGAATTATTAATGCAAGAACAGAAATAGAAAGAAGCAAAA
356731 AAAAAAACAAAA-TGGAATAGATTAGAGATGAAGGATGGTGCCACAATCACAAGATTGATAAGCC
66 AAAAAAACAAAACTGGAATAGATTAGAGATGAAGGATGGTGCCACAATCACAAGATTGATAAGCC
* *
356795 AAAAGGAATGATCGCCACAAGAGTCTTGGCCAC-TCGAT-AAGATCCAGAAAAATTGGCTCACTC
131 AAAAGGAATGATCACCACAAGAGTCTTGGCCACTTC--TCAAGATCCAAAAAAATTGGCTCACTC
356858 AAGAACCTAAGAATCACACTCTCACA
194 AAGAACCTAAGAATCACACTCTCACA
356884 CAAAATGTGT
Statistics
Matches: 205, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
219 2 0.01
220 132 0.64
221 71 0.35
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (221 bp):
TTGAGATGAATTTCTAACAACAAACAGAATTATTAATGCAAGAACAGAAATAGAAAGAAGCAAAA
AAAAAAACAAAACTGGAATAGATTAGAGATGAAGGATGGTGCCACAATCACAAGATTGATAAGCC
AAAAGGAATGATCACCACAAGAGTCTTGGCCACTTCTCAAGATCCAAAAAAATTGGCTCACTCAA
GAACCTAAGAATCACACTCTCACATT
Done.