Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3751
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: 17379
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4825 original size:51 final size:51
Alignment explanation
Indices: 4711--4840 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 51
4701 TTTTTGTTGT
*
4711 CAGTGTAAGACCTGTCTGGGACATGGCATCGACATCCGATATGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACATCCGATATGATGAAAGC
** * * * * *
4762 CAGTGTGGGACCTGTTCTGGGACATGGCATTGGCCTTCGATAT-ATGAAAGT
1 CAGTGTAAGACCTG-TCTGGGACATGGCATCGACATCCGATATGATGAAAGC
* * *
4813 TAGTGTAAGACCTGTCTAGGACACGGCA
1 CAGTGTAAGACCTGTCTGGGACATGGCA
4841 GATCGACTTC
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
50 12 0.18
51 29 0.45
52 24 0.37
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (51 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACATCCGATATGATGAAAGC
Found at i:8499 original size:40 final size:39
Alignment explanation
Indices: 8447--8564 Score: 134
Period size: 39 Copynumber: 3.0 Consensus size: 39
8437 TCCAATTTCT
* *
8447 AGCACAAAGCCTGCGGGATTTAACCCGGATATCTATTACC
1 AGCACTAAGCCTGCGGGATTTAACCCGGATAT-TAATACC
* * *
8487 AGCACTAGGCCTGC-GGACTATAAGTCCGGATA-TAATACC
1 AGCACTAAGCCTGCGGGA-TTTAA-CCCGGATATTAATACC
*
8526 AGCATTAAGCCTGCGGGATTTAACCCGGATA-TAATACC
1 AGCACTAAGCCTGCGGGATTTAACCCGGATATTAATACC
8564 A
1 A
8565 CATAAATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
38 15 0.23
39 25 0.38
40 19 0.29
41 7 0.11
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (39 bp):
AGCACTAAGCCTGCGGGATTTAACCCGGATATTAATACC
Found at i:13689 original size:5 final size:5
Alignment explanation
Indices: 13681--13740 Score: 77
Period size: 5 Copynumber: 11.6 Consensus size: 5
13671 CCAATTTAAT
*
13681 TTTTA TTTTTA TTTTTT TTTTA TTTTA TTTTA TTTTA TTTTTA TTTTA
1 TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA
13729 TTTTA -TTTA TTT
1 TTTTA TTTTA TTT
13741 CTTGCATGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
4 4 0.08
5 31 0.62
6 15 0.30
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:13706 original size:16 final size:16
Alignment explanation
Indices: 13674--13732 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
13664 AGACAACCCA
*
13674 ATTTAATTTTTATTTTT
1 ATTTTATTTTT-TTTTT
13691 ATTTT-TTTTTTATTTT
1 ATTTTATTTTTT-TTTT
*
13707 ATTTTATTTTATTTTT
1 ATTTTATTTTTTTTTT
13723 ATTTTATTTT
1 ATTTTATTTT
13733 ATTTATTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.74
17 9 0.24
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTATTTTTTTTTT
Found at i:13713 original size:21 final size:21
Alignment explanation
Indices: 13681--13740 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
13671 CCAATTTAAT
*
13681 TTTTATTTTTATTTTTTTTTTA
1 TTTTA-TTTTATTTTATTTTTA
13703 TTTTATTTTATTTTATTTTTA
1 TTTTATTTTATTTTATTTTTA
13724 TTTTATTTTA-TTTATTT
1 TTTTATTTTATTTTATTT
13741 CTTGCATGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
20 7 0.19
21 25 0.68
22 5 0.14
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTATTTTATTTTATTTTTA
Found at i:13733 original size:16 final size:16
Alignment explanation
Indices: 13681--13736 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
13671 CCAATTTAAT
13681 TTTTATTTTTATTTT-
1 TTTTATTTTTATTTTA
*
13696 TTTTTTATTTTATTTTA
1 TTTTAT-TTTTATTTTA
13713 TTTTATTTTTATTTTA
1 TTTTATTTTTATTTTA
13729 TTTTATTT
1 TTTTATTT
13737 ATTTCTTGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 5 0.14
16 27 0.73
17 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:15513 original size:48 final size:48
Alignment explanation
Indices: 15442--15615 Score: 203
Period size: 48 Copynumber: 3.6 Consensus size: 48
15432 ACAACAAGCT
* *
15442 GATGCCATGTCCCAGACAGGTCTTACACTAGCTTGTATATTGCGAGGCC
1 GATG-CATGTCCCAGACATGTCTTACACTAGCTTATATATTGCGAGGCC
* *
15491 GATGCATGTCCCAGACATGTCTTACACTGGCTTAAATATCT-CGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTATATAT-TGCGAGGCC
* * * * *
15539 AATGCATGTCCCAGACATGTCTTACACTAGC-TCT-CA-TGCTGTGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTTATATATTGC-GAGGCC
*
15585 GATGCTTGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
15616 ACACATATCA
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 34 0.31
47 1 0.01
48 67 0.61
49 5 0.05
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTATATATTGCGAGGCC
Found at i:15624 original size:94 final size:96
Alignment explanation
Indices: 15447--15624 Score: 236
Period size: 94 Copynumber: 1.9 Consensus size: 96
15437 AAGCTGATGC
* *
15447 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATTGCGAGGCCGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACAGGTCTTACACTAGCTTCTACATTGCGAGGCCGATGCATGTCCCAGACATGTC
* **
15512 TTACACTGGCTTAAATATCTCGAGGCCAATG
66 TTACACTAGCACAAATATCTCGAGGCCAATG
* * * *
15543 CATGTCCCAGACATGTCTTACACTAGC-TCT-CA-TGCTGTGGCTGATGCTTGTCCCAGACATGT
1 CATGTCCCAGACAGGTCTTACACTAGCTTCTACATTGC-GAGGCCGATGCATGTCCCAGACATGT
*
15605 CTTACACTAGCACACATATC
65 CTTACACTAGCACAAATATC
15625 ACCCATTATC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
93 3 0.04
94 40 0.56
95 2 0.03
96 26 0.37
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (96 bp):
CATGTCCCAGACAGGTCTTACACTAGCTTCTACATTGCGAGGCCGATGCATGTCCCAGACATGTC
TTACACTAGCACAAATATCTCGAGGCCAATG
Done.