Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2007
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: 25940
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3649 original size:15 final size:14
Alignment explanation
Indices: 3625--3673 Score: 73
Period size: 13 Copynumber: 3.5 Consensus size: 14
3615 AGGAAACCGA
3625 ATAAAGAAATCCAAG
1 ATAAAGAAATCC-AG
*
3640 ATAGAGAAATCCAG
1 ATAAAGAAATCCAG
3654 ATAAAG-AATCCAG
1 ATAAAGAAATCCAG
3667 ATAAAGA
1 ATAAAGA
3674 TCAGGATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 13 0.42
14 7 0.23
15 11 0.35
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.14
Consensus pattern (14 bp):
ATAAAGAAATCCAG
Found at i:3665 original size:13 final size:13
Alignment explanation
Indices: 3625--3686 Score: 65
Period size: 13 Copynumber: 4.6 Consensus size: 13
3615 AGGAAACCGA
3625 ATAAAGAAATCCAAG
1 ATAAAG-AATCC-AG
*
3640 ATAGAGAAATCCAG
1 ATAAAG-AATCCAG
3654 ATAAAGAATCCAG
1 ATAAAGAATCCAG
3667 ATAAAG-AT-CAGG
1 ATAAAGAATCCA-G
3679 ATAAAGAA
1 ATAAAGAA
3687 ACCCAAGATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
11 2 0.05
12 9 0.21
13 14 0.33
14 7 0.16
15 11 0.26
ACGTcount: A:0.56, C:0.11, G:0.18, T:0.15
Consensus pattern (13 bp):
ATAAAGAATCCAG
Found at i:11564 original size:17 final size:18
Alignment explanation
Indices: 11538--11571 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11528 ATTTTGTTTA
11538 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
11555 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
11572 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:16850 original size:40 final size:40
Alignment explanation
Indices: 16612--16836 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
16602 TTGAATGATG
* * * *
16612 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
16652 TCCGAACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16692 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16731 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
16771 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
16812 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
16837 AATGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:16854 original size:80 final size:80
Alignment explanation
Indices: 16612--16869 Score: 249
Period size: 80 Copynumber: 3.2 Consensus size: 80
16602 TTGAATGATG
* * * * * **
16612 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGAACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
** * *
16675 TTGTGCGAGATACTAAT
64 TTGAACGAGTTACTAAA
* * *
16692 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
**
16756 GTGCGAGTTACTAAA
66 GAACGAGTTACTAAA
*
16771 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
* *
16835 TGAATGAG-TAGCTATA
65 TGAACGAGTTA-CTAAA
* *
16851 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
16870 TACGTGATTT
Statistics
Matches: 153, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 74 0.48
80 76 0.50
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTTACTAAA
Found at i:17165 original size:29 final size:29
Alignment explanation
Indices: 17123--17185 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
17113 AGCTACATGA
17123 ATGCTATACTTTTGTTGTGCTGGAATCCC
1 ATGCTATACTTTTGTTGTGCTGGAATCCC
17152 ATGCTATACTTTTGTTGTGCTGGAATCCC
1 ATGCTATACTTTTGTTGTGCTGGAATCCC
*
17181 TTGCT
1 ATGCT
17186 CAAAACTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (29 bp):
ATGCTATACTTTTGTTGTGCTGGAATCCC
Found at i:24734 original size:40 final size:40
Alignment explanation
Indices: 24594--24815 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
24584 TTGAATGATG
* * * *
24594 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
24634 TCCGGACTAAGAT-CCGAAGGCATTTGT--GAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
24672 TCCGGGCTAAG--CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24710 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24750 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
24791 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24816 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
36 14 0.09
38 34 0.21
40 106 0.65
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.