Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold743
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: 7855
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Found at i:1098 original size:211 final size:211
Alignment explanation
Indices: 734--1145 Score: 815
Period size: 211 Copynumber: 2.0 Consensus size: 211
724 AATAAGAGGT
734 GTTTGGATGCCAAGAAAATCTAAAAGGTGCAGAAAATTTGAAATAAAACTTTCAATCTTAGATCT
1 GTTTGGATGCCAAGAAAATCTAAAAGGTGCAGAAAATTTGAAATAAAACTTTCAATCTTAGATCT
799 AACAAATTTTTAAAATGAAAAAAAGTATGGTGAGAACTTGGGCGGCAAGTGGCTTTTGTATCCAA
66 AACAAATTTTTAAAATGAAAAAAAGTATGGTGAGAACTTGGGCGGCAAGTGGCTTTTGTATCCAA
*
864 CTAATTTTTTTAAAATTGGGCTATTTACCCTCTAAGTCCTCTCTTATTTCTCCCTTGTTCTAATA
131 CTAATTTTTTTAAAATTGGGCTATTTACCATCTAAGTCCTCTCTTATTTCTCCCTTGTTCTAATA
929 ACTCCCTATGGAATAA
196 ACTCCCTATGGAATAA
945 GTTTGGATGCCAAGAAAATCTAAAAGGTGCAGAAAATTTGAAATAAAACTTTCAATCTTAGATCT
1 GTTTGGATGCCAAGAAAATCTAAAAGGTGCAGAAAATTTGAAATAAAACTTTCAATCTTAGATCT
1010 AACAAATTTTTAAAATGAAAAAAAGTATGGTGAGAACTTGGGCGGCAAGTGGCTTTTGTATCCAA
66 AACAAATTTTTAAAATGAAAAAAAGTATGGTGAGAACTTGGGCGGCAAGTGGCTTTTGTATCCAA
1075 CTAATTTTTTTAAAATTGGGCTATTTACCATCTAAGTCCTCTCTTATTTCTCCCTTGTTCTAATA
131 CTAATTTTTTTAAAATTGGGCTATTTACCATCTAAGTCCTCTCTTATTTCTCCCTTGTTCTAATA
1140 ACTCCC
196 ACTCCC
1146 CTTTTAACTA
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 200 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (211 bp):
GTTTGGATGCCAAGAAAATCTAAAAGGTGCAGAAAATTTGAAATAAAACTTTCAATCTTAGATCT
AACAAATTTTTAAAATGAAAAAAAGTATGGTGAGAACTTGGGCGGCAAGTGGCTTTTGTATCCAA
CTAATTTTTTTAAAATTGGGCTATTTACCATCTAAGTCCTCTCTTATTTCTCCCTTGTTCTAATA
ACTCCCTATGGAATAA
Found at i:1289 original size:27 final size:28
Alignment explanation
Indices: 1234--1287 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1224 CTATTTCCCC
*
1234 AATTATTAATACCATTATTATTTTATTT
1 AATTATTAATAACATTATTATTTTATTT
*
1262 AATTATTATTAAC-TTATTA-TTTATTT
1 AATTATTAATAACATTATTATTTTATTT
1288 TATCCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 6 0.25
28 11 0.46
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (28 bp):
AATTATTAATAACATTATTATTTTATTT
Found at i:5794 original size:106 final size:106
Alignment explanation
Indices: 5673--5884 Score: 408
Period size: 105 Copynumber: 2.0 Consensus size: 106
5663 TTCTAAAGGA
5673 ATCATTCATCAAACTTCTTGTGTTGAAACCCCACAACAAAATGGTCTTGTTGAACGTAGGCATCA
1 ATCATTCATCAAACTTCTTGTGTTGAAACCCCACAACAAAATGGTCTTGTTGAACGTA-GCATCA
5738 ACATATTCTTAATGTTTCACGGGCTCTTTTATTCCATTCTAG
65 ACATATTCTTAATGTTTCACGGGCTCTTTTATTCCATTCTAG
5780 ATCATTCAT-AAACTTCTTGTGTTGAAACCCCACAACAAAATGGTCTTGTTGAACGTAGCATCAA
1 ATCATTCATCAAACTTCTTGTGTTGAAACCCCACAACAAAATGGTCTTGTTGAACGTAGCATCAA
5844 CATATTCTTAATGTTTCACGGGCTCTTTTATTCCATTCTAG
66 CATATTCTTAATGTTTCACGGGCTCTTTTATTCCATTCTAG
5885 TTTGCCTAAG
Statistics
Matches: 105, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 48 0.46
106 48 0.46
107 9 0.09
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (106 bp):
ATCATTCATCAAACTTCTTGTGTTGAAACCCCACAACAAAATGGTCTTGTTGAACGTAGCATCAA
CATATTCTTAATGTTTCACGGGCTCTTTTATTCCATTCTAG
Done.