Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4392
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: 14981
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:4022 original size:19 final size:19
Alignment explanation
Indices: 3998--4040 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3988 CGTGAAAGTC
*
3998 TAATGCATATG-ATGCAATG
1 TAATGCA-ATGCATGAAATG
4017 TAATGCAATGCATGAAATG
1 TAATGCAATGCATGAAATG
4036 -AATGC
1 TAATGC
4041 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (19 bp):
TAATGCAATGCATGAAATG
Found at i:6113 original size:38 final size:38
Alignment explanation
Indices: 6062--6167 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
6052 GCATTTTAAG
*
6062 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
6099 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
6137 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
6168 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:6558 original size:19 final size:17
Alignment explanation
Indices: 6534--6582 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
6524 TAATACTAGA
6534 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
6553 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
6573 AAAATATATA
1 AAAATATATA
6583 CAATGATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 8 0.30
20 9 0.33
21 2 0.07
22 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:6631 original size:8 final size:8
Alignment explanation
Indices: 6563--6648 Score: 51
Period size: 8 Copynumber: 11.0 Consensus size: 8
6553 AAAATATAAC
6563 TAATAATA
1 TAATAATA
6571 TTAA-AATA
1 -TAATAATA
*
6579 TATACAATGA
1 TA-ATAAT-A
6589 TAATAATA
1 TAATAATA
*
6597 TAA-AAGA
1 TAATAATA
*
6604 T-ATATGTA
1 TAATA-ATA
6612 TATATAAT-
1 TA-ATAATA
6620 TAATAATA
1 TAATAATA
6628 TAAT-AT-
1 TAATAATA
6634 TAA-AATA
1 TAATAATA
6641 TAATAATA
1 TAATAATA
6649 CGACATAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 23
0.69 0.06 0.26
Matches are distributed among these distances:
6 6 0.10
7 17 0.28
8 21 0.34
9 11 0.18
10 6 0.10
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (8 bp):
TAATAATA
Found at i:7034 original size:6 final size:6
Alignment explanation
Indices: 6992--7025 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
6982 ATAAAAATAT
*
6992 ATACTA ATACATA ATAGTA ATACTA ATACTA ATA
1 ATACTA ATAC-TA ATACTA ATACTA ATACTA ATA
7026 ATACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:7524 original size:11 final size:11
Alignment explanation
Indices: 7508--7543 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
7498 AGAAAAAAAA
7508 GAAGAGAGAGG
1 GAAGAGAGAGG
*
7519 GAAGAGAGAAG
1 GAAGAGAGAGG
7530 GAAGAGAGAAGG
1 GAAGAGAG-AGG
7542 GA
1 GA
7544 GGGGGAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:8393 original size:19 final size:19
Alignment explanation
Indices: 8358--8436 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
8348 ATATTACAAG
8358 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
8379 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
8398 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
8415 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
8434 ATC
1 ATC
8437 CTTAAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
20 1 0.02
21 8 0.14
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:8400 original size:14 final size:15
Alignment explanation
Indices: 8380--8436 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
8370 AGATTGCATA
8380 TCATATCTAAGATTG
1 TCATATCTAAGATTG
8395 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
8414 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
8431 -CATATC
1 TCATATC
8437 CTTAAAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:8422 original size:36 final size:39
Alignment explanation
Indices: 8358--8436 Score: 128
Period size: 36 Copynumber: 2.1 Consensus size: 39
8348 ATATTACAAG
8358 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTG-ATATCATATCTAAGATTGCAT
8398 ATCATATC-T-AAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
8434 ATC
1 ATC
8437 CTTAAAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
39 1 0.03
40 8 0.21
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (39 bp):
ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
Found at i:11368 original size:24 final size:24
Alignment explanation
Indices: 11336--11383 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11326 ATAGAATGAA
*
11336 TGAAATAATTGAGTGGTTATTCTT
1 TGAAATAATTGAGTGGCTATTCTT
11360 TGAAATAATTGAGTGGCTATTCTT
1 TGAAATAATTGAGTGGCTATTCTT
11384 ATAATTTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (24 bp):
TGAAATAATTGAGTGGCTATTCTT
Found at i:13509 original size:21 final size:20
Alignment explanation
Indices: 13467--13521 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
13457 TTAGCATATT
13467 TAATA-TATTATTATTACTC
1 TAATATTATTATTATTACTC
*
13486 TAACTATTATTATTATT-TTGC
1 TAA-TATTATTATTATTACT-C
*
13507 TAATATTACTATTAT
1 TAATATTATTATTAT
13522 GATTATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.10
20 14 0.45
21 14 0.45
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.55
Consensus pattern (20 bp):
TAATATTATTATTATTACTC
Found at i:13629 original size:16 final size:15
Alignment explanation
Indices: 13604--13643 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
13594 CATGTCTTGG
*
13604 TATTTTTATTTCTAT
1 TATTTTTATTACTAT
13619 TATTATTTATTACTAT
1 TATT-TTTATTACTAT
13635 TATTTTTAT
1 TATTTTTAT
13644 CTTGATACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTTATTACTAT
Found at i:14095 original size:25 final size:26
Alignment explanation
Indices: 14058--14153 Score: 109
Period size: 25 Copynumber: 4.0 Consensus size: 26
14048 TGGTACAAAT
14058 TGAT-ATGGGTTAGGT-AATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
14082 TGATAATGGATTAGGTAAAT-TT---
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
14104 T-TTTATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
14129 TGATAATGGGTTAGGT-AATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
14154 GATGGATTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
21 15 0.25
22 3 0.05
24 4 0.07
25 22 0.37
26 15 0.25
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:14647 original size:19 final size:19
Alignment explanation
Indices: 14625--14662 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
14615 ACAAGTGTGG
14625 GAAGATAGAAT-AATTATGT
1 GAAGAT-GAATAAATTATGT
*
14644 GAAGCTGAATAAATTATGT
1 GAAGATGAATAAATTATGT
14663 TAATTAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (19 bp):
GAAGATGAATAAATTATGT
Done.