Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3493
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: 25261
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:5483 original size:27 final size:27
Alignment explanation
Indices: 5453--5602 Score: 169
Period size: 27 Copynumber: 5.6 Consensus size: 27
5443 ATATTGAGTC
* * *
5453 CGCACACTCAGTGCTATATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5480 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
5508 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
5535 CGCACACTTAGTGC-ATCAT-TTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
5561 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5588 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5603 GTACAATTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
26 22 0.21
27 60 0.57
28 23 0.22
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:5585 original size:53 final size:55
Alignment explanation
Indices: 5453--5602 Score: 171
Period size: 53 Copynumber: 2.8 Consensus size: 55
5443 ATATTGAGTC
* * * *
5453 CGCACACTCAGTGCTATATAATCAAATCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTACATAGTCAAACT
** * * * **
5508 CGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCAT-TTC-ATTT
1 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTA-CATAGTCAAACT
5561 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
5603 GTACAATTTA
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
53 39 0.49
54 3 0.04
55 37 0.47
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTACATAGTCAAACT
Found at i:7499 original size:47 final size:47
Alignment explanation
Indices: 7445--7710 Score: 441
Period size: 47 Copynumber: 5.7 Consensus size: 47
7435 GGGCTGTCAC
7445 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
7492 ATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
7539 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
7586 ATCACATATATATACAC-TTCACA-TCATCACATCGGCCATTAGGCCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
7633 ATCAC-TATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
* * *
7679 ATCTCATATATGCA-TGTTCACATCCATCACAT
1 ATCACATATATACACT-TTCACATTCATCACAT
7711 AGAATCCTAA
Statistics
Matches: 208, Mismatches: 5, Indels: 12
0.92 0.02 0.05
Matches are distributed among these distances:
44 9 0.04
45 6 0.03
46 29 0.14
47 148 0.71
48 6 0.03
49 10 0.05
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Found at i:13558 original size:27 final size:27
Alignment explanation
Indices: 13527--13704 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
13517 TAAATTGTAC
13527 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
13554 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13580 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
13608 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
13636 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13663 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13690 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13705 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13641 original size:82 final size:81
Alignment explanation
Indices: 13528--13683 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
13518 AAATTGTACA
* *
13528 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
13592 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
13609 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
13674 TGCGAGTTGA
65 TGCGAATTGA
13684 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:13695 original size:82 final size:81
Alignment explanation
Indices: 13524--13704 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
13514 GATTAAATTG
* *
13524 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
13589 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
13605 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
13669 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
13687 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
13705 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:21665 original size:26 final size:27
Alignment explanation
Indices: 21615--21786 Score: 113
Period size: 26 Copynumber: 6.5 Consensus size: 27
21605 AAATTGTACA
** * *
21615 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAAATGAATATGAT
21642 GCACTAAGTG-GCGAAATGAATATGAT
1 GCACTAAGTGTGCGAAATGAATATGAT
* ** *
21668 GCACTAAGTGTGCGAATTGACCATG-C
1 GCACTAAGTGTGCGAAATGAATATGAT
** *
21694 GCACTAAGTGTGC-AGTTGACTATG-T
1 GCACTAAGTGTGCGAAATGAATATGAT
** * *
21719 AGCACTAAGTGTGCGATTTGATTACG-T
1 -GCACTAAGTGTGCGAAATGAATATGAT
** *
21746 AGCACTAAGTGTGCGAGTTGATTAT-AT
1 -GCACTAAGTGTGCGAAATGAATATGAT
*
21773 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
21787 GACTCATATA
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
25 9 0.07
26 61 0.49
27 54 0.44
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAAATGAATATGAT
Found at i:21753 original size:79 final size:79
Alignment explanation
Indices: 21615--21766 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 79
21605 AAATTGTACA
* * *
21615 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGGCGAAATGAATATGATGCACTAAGTGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGGCGAAATGAATACGATGCACTAAGTGTG
21680 CGAATTGACCATGC
66 CGAATTGACCATGC
** *
21694 GCACTAAGTGTGC-AGTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTG-GCGAAATGAATACGAT-GCACTAAGTG
*
21757 TGCGAGTTGA
64 TGCGAATTGA
21767 TTATATGCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
78 22 0.34
79 42 0.66
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (79 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGGCGAAATGAATACGATGCACTAAGTGTG
CGAATTGACCATGC
Found at i:21777 original size:79 final size:79
Alignment explanation
Indices: 21615--21786 Score: 204
Period size: 79 Copynumber: 2.2 Consensus size: 79
21605 AAATTGTACA
* * *
21615 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGGCGAAATGAATATGATGCACTAAGTGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGGCGAAATGAATACGATGCACTAAGTGTG
*
21680 CGAATTGACCATGC
66 CGAATTGACCATAC
** *
21694 GCACTAAGTGTGC-AGTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTG-GCGAAATGAATACGAT-GCACTAAGTG
* ** *
21757 TGCGAGTTGATTATAT
64 TGCGAATTGACCATAC
*
21773 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
21787 GACTCATATA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 22 0.28
79 56 0.72
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (79 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGGCGAAATGAATACGATGCACTAAGTGTG
CGAATTGACCATAC
Done.