Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1732
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: 40434
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:5684 original size:1 final size:1
Alignment explanation
Indices: 5678--5708 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
5668 TTTGCTTCCT
5678 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5709 CTTTGGAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7287 original size:85 final size:85
Alignment explanation
Indices: 7184--7465 Score: 279
Period size: 85 Copynumber: 3.3 Consensus size: 85
7174 GATATAATCC
* *
7184 TATCTCCCTGAAGTTACAGTGGAGCGGGTTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
7249 GAGAAGATCACATCAGGTCT
66 GAGAAGATCACATCAGGTCT
* * * ** ** * *
7269 TATCTCCCTG-AGATTACAGTGGAACAGACCAAAGAATTTCA-GATCTTATCTCCCTGAGGTTAC
1 TATCTCCCTGAAG-TTACAGCGGAGCGGA-TTAA-AA-TAAAGGATCTTATCTCTCTGAAGTTAC
** * * * *
7332 AGCGGAGCAGATCGA-A-GATGATCC
62 AGTAGAGAAGATC-ACATCA-GGTCT
7356 TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
* *
7421 GAGTAGATCGCATCAGGTCT
66 GAGAAGATCACATCAGGTCT
7441 TATCTCTCC-G-AGATTACAGCGGAGC
1 TATCTC-CCTGAAG-TTACAGCGGAGC
7466 AGATCGAAGA
Statistics
Matches: 154, Mismatches: 31, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
84 6 0.04
85 77 0.50
86 8 0.05
87 58 0.38
88 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (85 bp):
TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
GAGAAGATCACATCAGGTCT
Found at i:7367 original size:128 final size:131
Alignment explanation
Indices: 7223--7607 Score: 396
Period size: 128 Copynumber: 3.0 Consensus size: 131
7213 TAAAATAAAG
* * * * * * * *
7223 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACAT-CAGG-TCTTATCTCCCTGAGATTAC
1 GATCCTATCTCCCTGAAGTTACAGTGGAGAGGATAAAATAAAGGATCTTATCTCTCTGAGATTAC
**
7286 AGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-A
66 AGTGGAGTAGACC-AAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAA
7350 -T
130 CT
* *
7351 GATCCTATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTT
1 GATCCTATCTCCCTGAAGTTACAGTGGAGAGGA-TAAAATAAAGGATCTTATCTCTCTGAGA-TT
* * * * *
7415 ACAGTAGAGTAGATC--GCA--TCAGGTCTTATCTCTCC-GAGATTACAGCGGAGCAGATCGAAG
64 ACAGTGGAGTAGACCAAGAATTTCAGATCTTATCTC-CCTGAGGTTACAGCGGAGCAGATCGAAG
7475 ACACT
128 A-ACT
* * *
7480 -ATCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCTTATCTCTCTGAGGTTA
1 GATCCTATCTCCCTGAAGTTACAGTGGAG-AGGATAAAATAAAGGATCTTATCTCTCTGAGATTA
* * * * * *
7544 CAGTGGAGTAGACCGAAGAATTGCAGATCTTATCCCCCTGAAGTTACAGTGGAACAGATTGAAG
65 CAGTGGAGTAGACC-AAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG
7608 CCAGAGATCT
Statistics
Matches: 209, Mismatches: 32, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
126 37 0.18
127 2 0.01
128 98 0.47
129 7 0.03
130 4 0.02
131 28 0.13
132 2 0.01
133 31 0.15
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (131 bp):
GATCCTATCTCCCTGAAGTTACAGTGGAGAGGATAAAATAAAGGATCTTATCTCTCTGAGATTAC
AGTGGAGTAGACCAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAAC
T
Found at i:7437 original size:172 final size:173
Alignment explanation
Indices: 7138--7468 Score: 549
Period size: 172 Copynumber: 1.9 Consensus size: 173
7128 AAGCCAGAGG
*
7138 TCTTGTCTCCCTGAGATTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA-ATAATCCTATCTCCCTGAAGTTACAG
* *
7203 TGGAGCGGGTTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
65 CGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
*
7268 TTATCTC-CCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
130 TTATCTCTCC-GAGATTACAGCGGAACAGACCAAAGAATTTCAGA
* *
7312 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-ATGATCCTATCTCCCTGAAGTTACAGC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAATAATCCTATCTCCCTGAAGTTACAGC
* *
7376 GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCT
66 GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
*
7441 TATCTCTCCGAGATTACAGCGGAGCAGA
131 TATCTCTCCGAGATTACAGCGGAACAGA
7469 TCGAAGACAC
Statistics
Matches: 147, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
172 110 0.75
173 2 0.01
174 35 0.24
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (173 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAATAATCCTATCTCCCTGAAGTTACAGC
GGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
TATCTCTCCGAGATTACAGCGGAACAGACCAAAGAATTTCAGA
Found at i:7546 original size:172 final size:171
Alignment explanation
Indices: 7184--7724 Score: 583
Period size: 172 Copynumber: 3.1 Consensus size: 171
7174 GATATAATCC
* *
7184 TATCTCCCTGAAGTTACAGTGGAGCGGGTTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
* * * * *
7249 GAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGAT
66 GAGAAGATCGCATCAGGTCTTATCTCCC-GAGATTACAGCGGAGCAGATCAAAGACA---C-TAT
* * * ** * * * *
7313 CTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT----GATCC
126 CCTATCTCCCTGAAGTTACAGTGGAGTGGGT-TAAAATAAAGGATCT
7356 TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
* *
7421 GAGTAGATCGCATCAGGTCTTATCTCTCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTA
66 GAGAAGATCGCATCAGGTCTTATCTC-CCGAGATTACAGCGGAGCAGATCAAAGACACTATCCTA
7486 TCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCT
130 TCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCT
* * * ** ** ** * *
7528 TATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCA-GATCTTATCCCCCTGAAGTTACA
1 TATCTCCCTGAAGTTACAGCGGAGCGGA-TTAA-AA-TAAAGGATCTTATCTCTCTGAAGTTACA
* * * *
7592 GTGGA-ACAGATTGAAGCCAGAGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCAAAGACAC
63 GTAGAGA-AGATCGCA-TCAG-G-TCTTATCT-CCCGAGATTACAGCGGAGCAGATCAAAGACAC
7656 TATCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCT
123 TATCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCT
* *
7705 TATCTCTCTGAGGTTACAGC
1 TATCTCCCTGAAGTTACAGC
7725 AGAGTAGGTC
Statistics
Matches: 319, Mismatches: 36, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
168 4 0.01
169 27 0.08
170 1 0.00
172 136 0.43
173 5 0.02
174 33 0.10
175 5 0.02
176 1 0.00
177 106 0.33
178 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (171 bp):
TATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
GAGAAGATCGCATCAGGTCTTATCTCCCGAGATTACAGCGGAGCAGATCAAAGACACTATCCTAT
CTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCT
Found at i:7704 original size:87 final size:87
Alignment explanation
Indices: 7438--7724 Score: 335
Period size: 87 Copynumber: 3.3 Consensus size: 87
7428 TCGCATCAGG
7438 TCTTATCTCTCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCTCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
7503 TGGAGTGGGTTAAAATAAAGGA
66 TGGAGTGGGTTAAAATAAAGGA
* * * * * * * *
7525 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTGCAGATCTTATCCCCCTGAAGTT
1 TCTTATCTCTCCGAGATTACAGCGGAGCAGATCGAAGACA---C-TATCCTATCTCCCTGAAGTT
*** * * ***
7589 ACAGTGGAACAGATT-GAAGCCAGAGA
62 ACAGTGGAGTGGGTTAAAATAAAG-GA
* *
7615 TCTTATCTCCCCGAGATTACAGCGGAGCAGATCAAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCTCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
7680 TGGAGTGGGTTAAAATAAAGGA
66 TGGAGTGGGTTAAAATAAAGGA
* *
7702 TCTTATCTCTCTGAGGTTACAGC
1 TCTTATCTCTCCGAGATTACAGC
7725 AGAGTAGGTC
Statistics
Matches: 156, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
86 1 0.01
87 83 0.53
88 5 0.03
89 5 0.03
90 61 0.39
91 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TCTTATCTCTCCGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
TGGAGTGGGTTAAAATAAAGGA
Found at i:13359 original size:13 final size:13
Alignment explanation
Indices: 13341--13405 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
13331 TTTAAACCAA
13341 ACTTCTCAAAAGC
1 ACTTCTCAAAAGC
13354 ACTTCTCAAAAGC
1 ACTTCTCAAAAGC
* * *
13367 ACTTTTCCACAGC
1 ACTTCTCAAAAGC
*
13380 ACTTTTCAAAAGC
1 ACTTCTCAAAAGC
13393 ACTT-TCAAAAGC
1 ACTTCTCAAAAGC
13405 A
1 A
13406 ATGAAGAACT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
12 9 0.19
13 38 0.81
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (13 bp):
ACTTCTCAAAAGC
Found at i:17034 original size:20 final size:20
Alignment explanation
Indices: 17009--17058 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
16999 TGGCTTAAAA
17009 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
17029 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
17046 GTGGTAGTGGATT
1 TTGGTAGTGGATT
17059 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:21671 original size:20 final size:20
Alignment explanation
Indices: 21646--21695 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
21636 TGGCTTAAAA
21646 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
21666 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
21683 GTGGTAGTGGATT
1 TTGGTAGTGGATT
21696 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:24851 original size:5 final size:5
Alignment explanation
Indices: 24841--24911 Score: 142
Period size: 5 Copynumber: 14.2 Consensus size: 5
24831 TTAAAAGTTA
24841 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
24891 ATTAT ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT A
24912 AAAACAAACA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 66 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:25898 original size:25 final size:25
Alignment explanation
Indices: 25847--25926 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
25837 ACTTTAGCGC
* **
25847 GCTCTCTGATTATTAGCACATTGGT
1 GCTCTCTGATTACTAGCACATCAGT
25872 GCTCTCTGATTACTAGCACGA-CAGT
1 GCTCTCTGATTACTAGCAC-ATCAGT
* *
25897 GCTCTCCG-TT--TAGCACATCTGT
1 GCTCTCTGATTACTAGCACATCAGT
25919 GCTCTCTG
1 GCTCTCTG
25927 TTTATTAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.02
22 16 0.34
24 2 0.04
25 27 0.57
26 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACATCAGT
Done.