Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4503.1
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: 56210
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.30
Warning! 4343 characters in sequence are not A, C, G, or T
Found at i:4703 original size:12 final size:12
Alignment explanation
Indices: 4683--4716 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4673 TTTCTCTTAT
4683 AAAAAAAATTTC
1 AAAAAAAATTTC
*
4695 AAAACAAATTTC
1 AAAAAAAATTTC
4707 AACAAAAAAT
1 AA-AAAAAAT
4717 ACTTATGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAAAATTTC
Found at i:11450 original size:31 final size:31
Alignment explanation
Indices: 11414--11472 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
11404 AATAACTCAG
11414 TGACTTAAATAAAAACTTTTAAATAGTTTAA
1 TGACTTAAATAAAAACTTTTAAATAGTTTAA
* *
11445 TGACTTGAATGAAAACTTTTAAATAGTT
1 TGACTTAAATAAAAACTTTTAAATAGTT
11473 CAAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTAAATAGTTTAA
Found at i:12390 original size:29 final size:29
Alignment explanation
Indices: 12322--12395 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
12312 TTTAATAGAT
* *
12322 TATAATTTTATAATTTTTAAAGGATTAAAT
1 TATAATTTTAT-ATTTTTAAAGGATCAAAG
*
12352 TA-AATATTTATATTTTT-AAGTGGTCAAAG
1 TATAAT-TTTATATTTTTAAAG-GATCAAAG
12381 TATAATTTTATATTT
1 TATAATTTTATATTT
12396 ACTAATCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 3 0.08
29 25 0.66
30 10 0.26
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.51
Consensus pattern (29 bp):
TATAATTTTATATTTTTAAAGGATCAAAG
Found at i:17497 original size:26 final size:25
Alignment explanation
Indices: 17459--17592 Score: 86
Period size: 24 Copynumber: 5.5 Consensus size: 25
17449 GACTCACCTT
*
17459 AGCTCGTATGAGCTTACTGATATATC
1 AGCTCGTAAGAGCTTACTGAT-TATC
* *
17485 AGCTTGTAAGAGCTTACT-ATTCTC
1 AGCTCGTAAGAGCTTACTGATTATC
* *
17509 AGCTCGTTAGAGCTTACTG-TT-CC
1 AGCTCGTAAGAGCTTACTGATTATC
*
17532 AGCTC--AATGAGCTTGCT-ATTCATC
1 AGCTCGTAA-GAGCTTACTGATT-ATC
* *
17556 AACTCAG-AAGGAGCTTACTGATCAT-
1 AGCTC-GTAA-GAGCTTACTGATTATC
*
17581 AGCTCGAAAGAG
1 AGCTCGTAAGAG
17593 AAAATACGAT
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
21 1 0.01
22 10 0.12
23 6 0.07
24 30 0.35
25 8 0.09
26 28 0.33
27 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (25 bp):
AGCTCGTAAGAGCTTACTGATTATC
Found at i:20991 original size:29 final size:29
Alignment explanation
Indices: 20928--20995 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
20918 TAATCAACCG
*
20928 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
20957 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
20986 CGCACACTTA
1 CGCACACTTA
20996 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:21107 original size:174 final size:174
Alignment explanation
Indices: 20817--21144 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
20807 AACTCAAGGT
* *
20817 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
20882 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
20947 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
20991 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
21056 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATTAACTGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
21121 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
21145 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:21136 original size:29 final size:30
Alignment explanation
Indices: 21104--21175 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
21094 ATTAACTGCG
*
21104 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTTAAACCCA
*
21133 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATTTAAACCCA
21162 CACACTTAGTGCCA
1 CACACTTAGTGCCA
21176 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTTAAACCCA
Found at i:33397 original size:48 final size:48
Alignment explanation
Indices: 33307--33408 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 48
33297 CATCAACATT
* * * * *
33307 GATATGTGATCCTATGTAAAACCTTGTTCGGGATATGGCATTGGCATC
1 GATATGTGATCCCATGTAAAACCATGTTCGGGACAAGACATTGGCATC
* * * *
33355 GTTATGTGATCCCATGTAAGACCATGTTTGGGACAAGACATTGGTATC
1 GATATGTGATCCCATGTAAAACCATGTTCGGGACAAGACATTGGCATC
33403 GATATG
1 GATATG
33409 AGAACATCGT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (48 bp):
GATATGTGATCCCATGTAAAACCATGTTCGGGACAAGACATTGGCATC
Found at i:35927 original size:40 final size:40
Alignment explanation
Indices: 35822--36077 Score: 353
Period size: 40 Copynumber: 6.5 Consensus size: 40
35812 TGGATGATAA
* * *
35822 CCGGGCTAAGTCCCGAAGGCATCTGTGCAAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
35862 CCGGGCTAAG-CCTGAAGGCAATTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
35901 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
35941 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
*
35981 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
36021 CCGGGCTAAGTCCCGAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
36060 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
36078 TACTTGGTTG
Statistics
Matches: 197, Mismatches: 14, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
38 16 0.08
39 42 0.21
40 137 0.70
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.