Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5677.1
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: 19374
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:1455 original size:7 final size:7
Alignment explanation
Indices: 1443--1472 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1433 ATTTGTAAAG
1443 GACTTTT
1 GACTTTT
1450 GACTTTT
1 GACTTTT
1457 GACTTTT
1 GACTTTT
1464 GACTTTT
1 GACTTTT
1471 GA
1 GA
1473 TCATTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (7 bp):
GACTTTT
Found at i:6447 original size:23 final size:22
Alignment explanation
Indices: 6395--6447 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
6385 TCCTCGTCTT
*
6395 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
6417 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
6440 TTTCTTTT
1 TTTCTTTT
6448 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:10476 original size:13 final size:13
Alignment explanation
Indices: 10458--10503 Score: 67
Period size: 14 Copynumber: 3.5 Consensus size: 13
10448 TTGTAGATTC
*
10458 AAAAAAAATCG-A
1 AAAAAAAATTGAA
10470 AAAAAAAATTGAA
1 AAAAAAAATTGAA
10483 AAAAAAAATTTGAA
1 AAAAAAAA-TTGAA
10497 AAAAAAA
1 AAAAAAA
10504 TTGCATACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 10 0.32
13 9 0.29
14 12 0.39
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTGAA
Found at i:10497 original size:26 final size:25
Alignment explanation
Indices: 10458--10506 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
10448 TTGTAGATTC
10458 AAAAAAAATCGAAAAAAAAATTGAA
1 AAAAAAAATCGAAAAAAAAATTGAA
*
10483 AAAAAAAATTTGAAAAAAAAATTG
1 AAAAAAAA-TCGAAAAAAAAATTG
10507 CATACGGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (25 bp):
AAAAAAAATCGAAAAAAAAATTGAA
Found at i:10504 original size:13 final size:12
Alignment explanation
Indices: 10458--10506 Score: 71
Period size: 13 Copynumber: 3.9 Consensus size: 12
10448 TTGTAGATTC
*
10458 AAAAAAAATCGA
1 AAAAAAAATTGA
10470 AAAAAAAATTGAA
1 AAAAAAAATTG-A
10483 AAAAAAAATTTGA
1 AAAAAAAA-TTGA
10496 AAAAAAAATTG
1 AAAAAAAATTG
10507 CATACGGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 13 0.38
13 18 0.53
14 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:11708 original size:13 final size:13
Alignment explanation
Indices: 11690--11735 Score: 67
Period size: 14 Copynumber: 3.5 Consensus size: 13
11680 TTGTAGATTC
*
11690 AAAAAAAATCG-A
1 AAAAAAAATTGAA
11702 AAAAAAAATTGAA
1 AAAAAAAATTGAA
11715 AAAAAAAATTTGAA
1 AAAAAAAA-TTGAA
11729 AAAAAAA
1 AAAAAAA
11736 TTGCATACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 10 0.32
13 9 0.29
14 12 0.39
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTGAA
Found at i:11729 original size:26 final size:25
Alignment explanation
Indices: 11690--11738 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
11680 TTGTAGATTC
11690 AAAAAAAATCGAAAAAAAAATTGAA
1 AAAAAAAATCGAAAAAAAAATTGAA
*
11715 AAAAAAAATTTGAAAAAAAAATTG
1 AAAAAAAA-TCGAAAAAAAAATTG
11739 CATACGGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (25 bp):
AAAAAAAATCGAAAAAAAAATTGAA
Found at i:11736 original size:13 final size:12
Alignment explanation
Indices: 11690--11738 Score: 71
Period size: 13 Copynumber: 3.9 Consensus size: 12
11680 TTGTAGATTC
*
11690 AAAAAAAATCGA
1 AAAAAAAATTGA
11702 AAAAAAAATTGAA
1 AAAAAAAATTG-A
11715 AAAAAAAATTTGA
1 AAAAAAAA-TTGA
11728 AAAAAAAATTG
1 AAAAAAAATTG
11739 CATACGGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 13 0.38
13 18 0.53
14 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:16336 original size:175 final size:177
Alignment explanation
Indices: 16041--16390 Score: 632
Period size: 175 Copynumber: 2.0 Consensus size: 177
16031 TGTAGATAGG
16041 TTCTCAAAAATGGCCCATTTTATAGCATGTCATAAAACTGATGATGCCGTTAATATTGCTAACTT
1 TTCTCAAAAATGGCCCATTTTATAGCATGTCATAAAAC--ATGATGCCGTTAATATTGCTAACTT
16106 ATTTTTCAAAGAAGTGGTCAGGTTGCATGGCATGCCTAGAACGATCGTGTCCGACCGAGACACAA
64 ATTTTTCAAAGAAGTGGTCAGGTTGCATGGCATGCCTAGAACGATCGTGTCCGACCGAGACACAA
16171 AATTCCTTAGCCATTTTTGGAGGACACTATGGGGGCGACTTGGAATGAT
129 AATTCCTTAGCCATTTTTGGAGGACACTATGGGGGCGACTTGGAATGAT
*
16220 TTCTCAAAAATGGCCCATTTTATAGCATGTTATAAAAC-T-ATGCCGTTAATATTGCTAACTTAT
1 TTCTCAAAAATGGCCCATTTTATAGCATGTCATAAAACATGATGCCGTTAATATTGCTAACTTAT
* *
16283 TTTTCAAAGAGGTGGTCAGGTTGCATGGCATGCCTAGAACGATCGTGTCCGACCGAGACGCAAAA
66 TTTTCAAAGAAGTGGTCAGGTTGCATGGCATGCCTAGAACGATCGTGTCCGACCGAGACACAAAA
*
16348 TTCCTTAGCCATTTTTGGAGGACACTATGGGGGCGTCTTGGAA
131 TTCCTTAGCCATTTTTGGAGGACACTATGGGGGCGACTTGGAA
16391 CGAAGTTGCT
Statistics
Matches: 167, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
175 129 0.77
176 1 0.01
179 37 0.22
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (177 bp):
TTCTCAAAAATGGCCCATTTTATAGCATGTCATAAAACATGATGCCGTTAATATTGCTAACTTAT
TTTTCAAAGAAGTGGTCAGGTTGCATGGCATGCCTAGAACGATCGTGTCCGACCGAGACACAAAA
TTCCTTAGCCATTTTTGGAGGACACTATGGGGGCGACTTGGAATGAT
Done.