Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3076
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: 32444
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Found at i:9709 original size:46 final size:45
Alignment explanation
Indices: 9656--9831 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
9646 TGGTTGAGCA
9656 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-AATG
* * * * * *
9702 TCCGAACTCATTGAGTTGAGTCCGAGTTC-GTGAGATGTA-ACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATACAATG
* * **
9747 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAAC
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAATG
* *
9794 TCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 T-CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
9832 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
45 4 0.04
46 67 0.64
47 33 0.31
48 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAATG
Found at i:9812 original size:93 final size:93
Alignment explanation
Indices: 9653--9824 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
9643 GGATGGTTGA
* *
9653 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTCCGAACTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATGCCCGAACTCATTGAGT
9718 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
9746 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACT-CCCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAA-TGCCCGAACTCATTGAG
9810 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
9825 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:18264 original size:27 final size:27
Alignment explanation
Indices: 18097--18274 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
18087 TAAATTGTAC
*
18097 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
18124 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
18150 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
18178 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
18206 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
18233 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
18260 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
18275 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:18265 original size:82 final size:81
Alignment explanation
Indices: 18094--18274 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
18084 GATTAAATTG
* * * *
18094 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
18159 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
18175 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
18239 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
18257 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
18275 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:26268 original size:27 final size:27
Alignment explanation
Indices: 26101--26278 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
26091 TAAATTGTAC
*
26101 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
26128 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
26154 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
26182 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
26210 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
26237 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
26264 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
26279 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:26269 original size:82 final size:81
Alignment explanation
Indices: 26098--26278 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
26088 GATTAAATTG
* * * *
26098 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
26163 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
26179 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
26243 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
26261 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
26279 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:29943 original size:29 final size:29
Alignment explanation
Indices: 29864--29973 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
29854 ACCCCTCCAT
* *
29864 ACATGCATATAGCCCACTAGGCCCAA-T-
1 ACATTCATATGGCCCACTAGGCCCAATTC
* * * *
29891 ATTATTCAAATGGCCCATTTGGCCCAATTC
1 A-CATTCATATGGCCCACTAGGCCCAATTC
* *
29921 ACATTCTTATGGCTCACTAGGCCCAATTC
1 ACATTCATATGGCCCACTAGGCCCAATTC
* *
29950 ACTTTCATATGGCCCATTAGGCCC
1 ACATTCATATGGCCCACTAGGCCC
29974 GAATCATATT
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
27 1 0.02
28 19 0.30
29 43 0.67
30 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAATTC
Found at i:31463 original size:16 final size:16
Alignment explanation
Indices: 31442--31474 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31432 AAAAATTCAA
31442 GATTTCAGGATTTTTG
1 GATTTCAGGATTTTTG
*
31458 GATTTCGGGATTTTTG
1 GATTTCAGGATTTTTG
31474 G
1 G
31475 GGCGTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.30, T:0.48
Consensus pattern (16 bp):
GATTTCAGGATTTTTG
Done.