Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3613
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: 17898
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:134 original size:8 final size:8
Alignment explanation
Indices: 117--156 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
107 TACCAAAGTG
*
117 GGCCCGTT
1 GGCCCATT
125 GGCCCATT
1 GGCCCATT
*
133 GGCCCGTT
1 GGCCCATT
141 GGCCCATT
1 GGCCCATT
149 GGCCCATT
1 GGCCCATT
157 TTCGGCCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.07, C:0.38, G:0.30, T:0.25
Consensus pattern (8 bp):
GGCCCATT
Found at i:138 original size:16 final size:16
Alignment explanation
Indices: 117--153 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
107 TACCAAAGTG
117 GGCCCGTTGGCCCATT
1 GGCCCGTTGGCCCATT
133 GGCCCGTTGGCCCATT
1 GGCCCGTTGGCCCATT
149 GGCCC
1 GGCCC
154 ATTTTCGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.05, C:0.41, G:0.32, T:0.22
Consensus pattern (16 bp):
GGCCCGTTGGCCCATT
Found at i:9141 original size:13 final size:13
Alignment explanation
Indices: 9123--9148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9113 GCCTAGTGAG
9123 GTATGTAGGAAAA
1 GTATGTAGGAAAA
9136 GTATGTAGGAAAA
1 GTATGTAGGAAAA
9149 AAATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
GTATGTAGGAAAA
Found at i:10634 original size:40 final size:39
Alignment explanation
Indices: 10466--10672 Score: 310
Period size: 39 Copynumber: 5.3 Consensus size: 39
10456 CAAAGATCCA
10466 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
*
10505 AAGGCATTTGTGTGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
10544 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
* * *
10583 AAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCG
1 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCG
* *
10623 AAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCG
1 AAGGCATTTGTGCGAGA-TACTAAT-TCCGGGCTAAG-CCCG
10663 AAGGCATTTG
1 AAGGCATTTG
10673 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 109 0.70
40 46 0.30
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCG
Found at i:10686 original size:40 final size:40
Alignment explanation
Indices: 10411--10672 Score: 260
Period size: 39 Copynumber: 6.7 Consensus size: 40
10401 TTGAATGATG
* *
10411 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
* * * *
10450 TCCGGACAAAGAT-CCAAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
10490 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGATACTA-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
*
10529 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
10568 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
10607 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAA
*
10648 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10673 AACGAGGAGC
Statistics
Matches: 197, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
39 126 0.64
40 61 0.31
41 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:10695 original size:79 final size:79
Alignment explanation
Indices: 10466--10705 Score: 249
Period size: 78 Copynumber: 3.1 Consensus size: 79
10456 CAAAGATCCA
* *** *
10466 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGTGAGAT-ACTAATT
1 AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TGACTAAAT
* *
10530 CCGGGCTAAG-CCCG
65 CCGAGTTAAGTCCCG
* ** *
10544 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATC
*
10609 CGGGTTAAGTCCCG
66 CGAGTTAAGTCCCG
*
10623 AAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTA
1 AAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTA
* * *
10685 TATCC-AGTTAAATTCCG
62 AATCCGAGTTAAGTCCCG
10702 AAGG
1 AAGG
10706 TACGTGATTT
Statistics
Matches: 144, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
77 1 0.01
78 72 0.50
79 46 0.32
80 25 0.17
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATC
CGAGTTAAGTCCCG
Done.