Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1265
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: 2223
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Found at i:582 original size:130 final size:130
Alignment explanation
Indices: 364--601 Score: 309
Period size: 130 Copynumber: 1.8 Consensus size: 130
354 CATTTTGGAG
* * * * *
364 TTGAGAATTTTAAAAAATTGACTAAAAATTCGAGTTTTCCGTTGAAAAATACCGTGTGATACCGC
1 TTGAGAATTTTAAAAAATGGACTAAAAATTCGAGTTTTCCGTCGAAAAATACCGTCTGACACCGA
* * * *
429 GTTTCACAAGACTCGAACAAACAGAAACCGAGATAGCATTTTAGCCCACGTCCGCCATCTTGAAT
66 ATTTCACAAAAATCCAACAAACAGAAACCGAGATAGCATTTTAGCCCACGTCCGCCATCTTGAAT
494 TTGAGAATTTTAAAAAATGGACTAAAAATTCGAG-TTTCCTGTCGAAAAATACC-TCCTGACACC
1 TTGAGAATTTTAAAAAATGGACTAAAAATTCGAGTTTTCC-GTCGAAAAATACCGT-CTGACACC
* * * ***
557 GAATTTCAGAAAAATCCATCGAACAGGGGCCGAGATAGCATTTTA
64 GAATTTCACAAAAATCCAACAAACAGAAACCGAGATAGCATTTTA
602 AGCCATTTCG
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
129 6 0.07
130 85 0.93
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (130 bp):
TTGAGAATTTTAAAAAATGGACTAAAAATTCGAGTTTTCCGTCGAAAAATACCGTCTGACACCGA
ATTTCACAAAAATCCAACAAACAGAAACCGAGATAGCATTTTAGCCCACGTCCGCCATCTTGAAT
Found at i:886 original size:176 final size:176
Alignment explanation
Indices: 548--1086 Score: 799
Period size: 176 Copynumber: 3.0 Consensus size: 176
538 AAAAATACCT
* * * *
548 CCTGACACCGAATTTCAGAAAAATCCATCGAACAGGGGCCGAGATAGCATTTTAAGCCATTTCGG
1 CCTGACACCGAATTTCAGGAAAATCCATCGAACAGGAGCCGAGATGGCATTTTAAGCCACTTC--
* * * * * * *
613 ATTTTCGAATTTTGAATTTTTTGAATTTTGACAGATTTTGATTTAAAACGCGTGATCCCCAAAAT
64 A--GTC--ATTTCGGA-TTTTTGAA-TTTGA-AAAATTTGACTTAAAACGCGTGATACCCAAAAT
*
678 CGAAGCTCAGATTCGGATTCCTCGTAAAAAATCGATGCGATTTCATGTATCATAC
122 CGAAGTTCAGATTCGGATTCCTCGTAAAAAATCGATGCGATTTCATGTATCATAC
*
733 CCTGACACCGAATTTCAGGAGAATCCATCGAACAGGAGCCGAGATGGCATTTTAAGCCACTTCAG
1 CCTGACACCGAATTTCAGGAAAATCCATCGAACAGGAGCCGAGATGGCATTTTAAGCCACTTCAG
*
798 TCATTTCGGATTTTTGAAGTTGAAAAATTTGACTTAAAACGCGTGATACCCAAAATCGAAGTTCA
66 TCATTTCGGATTTTTGAATTTGAAAAATTTGACTTAAAACGCGTGATACCCAAAATCGAAGTTCA
863 GATTCGGATTCCTCGTAAAAAATCGATGCGATTTCATGTATCATAC
131 GATTCGGATTCCTCGTAAAAAATCGATGCGATTTCATGTATCATAC
*
909 CCTGACACCGAATTTCAGGAAAATCCATCGAACAGGAGCCGAGATGGCATTTTAAGCCACGTCAG
1 CCTGACACCGAATTTCAGGAAAATCCATCGAACAGGAGCCGAGATGGCATTTTAAGCCACTTCAG
* * *
974 TCATTTCAGATTTTCGAATTTGGAAAATTTGACTTAAAACGCGTGATACCCAAAATCGAAGTTCA
66 TCATTTCGGATTTTTGAATTTGAAAAATTTGACTTAAAACGCGTGATACCCAAAATCGAAGTTCA
* * * *
1039 GATTCGGATTCCTCGTTAAAAATTGATACAATTTCATGTATCATAC
131 GATTCGGATTCCTCGTAAAAAATCGATGCGATTTCATGTATCATAC
1085 CC
1 CC
1087 GAGCATAGCG
Statistics
Matches: 330, Mismatches: 24, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
176 251 0.76
177 4 0.01
178 8 0.02
179 6 0.02
181 2 0.01
183 1 0.00
185 58 0.18
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (176 bp):
CCTGACACCGAATTTCAGGAAAATCCATCGAACAGGAGCCGAGATGGCATTTTAAGCCACTTCAG
TCATTTCGGATTTTTGAATTTGAAAAATTTGACTTAAAACGCGTGATACCCAAAATCGAAGTTCA
GATTCGGATTCCTCGTAAAAAATCGATGCGATTTCATGTATCATAC
Done.