Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold435
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: 14321
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Found at i:1505 original size:47 final size:47
Alignment explanation
Indices: 1427--1786 Score: 566
Period size: 47 Copynumber: 7.7 Consensus size: 47
1417 GCCCTTCGGA
* * * * * *
1427 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1474 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1521 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1568 CTTAT--CATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1613 CTTATCACATATATACACTTTCGCATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1660 CTTATCAAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1707 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1754 CTTATC-CATATATGCA-TTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
1787 AGAATCCTAA
Statistics
Matches: 291, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
45 60 0.21
46 9 0.03
47 222 0.76
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1688 original size:139 final size:140
Alignment explanation
Indices: 1427--1786 Score: 555
Period size: 139 Copynumber: 2.6 Consensus size: 140
1417 GCCCTTCGGA
* * * * * * * *
1427 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
1492 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
65 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAAATATATACACTTTCACATTCATCACATC
1557 GGCCATTAGGC
130 GGCCATTAGGC
*
1568 CTTAT-CATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACT
1 CTTATACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
* *
1632 TTCGCATTCATCACATCGGCTATTAGGCCTTATCAAATATATACACTTTCACATTCATCACATCG
66 TTCACATTCATCACATCGGCCATTAGGCCTTATCAAATATATACACTTTCACATTCATCACATCG
1697 GCCATTAGGC
131 GCCATTAGGC
*
1707 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC-CATATATGCA-
1 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
1770 TTTCACATCCATCACAT
65 TTTCACATTCATCACAT
1787 AGAATCCTAA
Statistics
Matches: 201, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
139 142 0.71
140 9 0.04
141 50 0.25
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (140 bp):
CTTATACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGCCTTATCAAATATATACACTTTCACATTCATCACATCG
GCCATTAGGC
Found at i:1741 original size:186 final size:186
Alignment explanation
Indices: 1427--1786 Score: 587
Period size: 186 Copynumber: 1.9 Consensus size: 186
1417 GCCCTTCGGA
* * * * * *
1427 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCAAATATATACAC
1492 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
1557 GGCCATTAGGCCTTAT-CATATATACACTTTCACATTCATCACATCAGCCATTAGGC
131 GGCCATTAGGCCTTATCCATATATACA-TTTCACATCCATCACATCAGCCATTAGGC
* * * * *
1613 CTTATCACATATATACACTTTCGCATTCATCACATCGGCTATTAGGCCTTATCAAATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCAAATATATACAC
1678 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
1743 GGCCATTAGGCCTTATCCATATATGCATTTCACATCCATCACAT
131 GGCCATTAGGCCTTATCCATATATACATTTCACATCCATCACAT
1787 AGAATCCTAA
Statistics
Matches: 160, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
186 151 0.94
187 9 0.06
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (186 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCAAATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCCATATATACATTTCACATCCATCACATCAGCCATTAGGC
Found at i:3169 original size:40 final size:40
Alignment explanation
Indices: 3117--3346 Score: 336
Period size: 40 Copynumber: 5.8 Consensus size: 40
3107 ATAACCACAA
* * * *
3117 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
3157 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCATCTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
3197 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
3237 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
3277 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
3317 GCATAAATGCCTTCGGGACTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
3347 GTATTCAAAT
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 172 0.98
41 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:10700 original size:40 final size:40
Alignment explanation
Indices: 10649--10878 Score: 336
Period size: 40 Copynumber: 5.8 Consensus size: 40
10639 ATAACCACAA
* * * *
10649 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
10689 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCATCTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
10729 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
10769 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
10809 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
10849 GCATAAATGCCTTCGGGACTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
10879 GTATTCAAAT
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 172 0.98
41 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Done.