Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2212
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: 6111
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Found at i:652 original size:15 final size:16
Alignment explanation
Indices: 601--672 Score: 62
Period size: 16 Copynumber: 4.5 Consensus size: 16
591 GAATATTTAA
601 AAATAAATTAATATAAAT
1 AAAT-AATTAATA-AAAT
*
619 AAAT-ATTATATATAAT
1 AAATAATTA-ATAAAAT
635 AAATAATTAA-AAAAT
1 AAATAATTAATAAAAT
*
650 AAAT--TTAATAATAT
1 AAATAATTAATAAAAT
664 AACATAATT
1 AA-ATAATT
673 TTTAAAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 10 0.22
16 12 0.27
17 9 0.20
18 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATTAATAAAAT
Found at i:1649 original size:19 final size:20
Alignment explanation
Indices: 1621--1663 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1611 AAGTTCTTGG
1621 TAATAATTTACATAATTT-A
1 TAATAATTTACATAATTTGA
* **
1640 TAATATTTTATTTAATTTGA
1 TAATAATTTACATAATTTGA
1660 TAAT
1 TAAT
1664 CTTATATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATAATTTACATAATTTGA
Found at i:1675 original size:20 final size:19
Alignment explanation
Indices: 1633--1675 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1623 ATAATTTACA
* *
1633 TAATTTATAATATTTTATT
1 TAATTTATAATATTATATG
*
1652 TAATTTGATAATCTTATATG
1 TAATTT-ATAATATTATATG
1672 TAAT
1 TAAT
1676 CTTTTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
TAATTTATAATATTATATG
Found at i:1746 original size:17 final size:17
Alignment explanation
Indices: 1724--1756 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1714 GAAAATTATT
*
1724 AGGTAATGTTTATATAA
1 AGGTAATATTTATATAA
1741 AGGTAATATTTATATA
1 AGGTAATATTTATATA
1757 TATTAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (17 bp):
AGGTAATATTTATATAA
Found at i:1920 original size:21 final size:20
Alignment explanation
Indices: 1871--1923 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1861 AAATTTCTTA
*
1871 AGTAATATTTTATATAATTG
1 AGTAATTTTTTATATAATTG
**
1891 AGTCGTTTTTATATATAATTG
1 AGTAATTTTT-TATATAATTG
*
1912 GGTAATTTTTTA
1 AGTAATTTTTTA
1924 AGCAATTCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (20 bp):
AGTAATTTTTTATATAATTG
Found at i:2100 original size:21 final size:20
Alignment explanation
Indices: 2071--2114 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2061 TATAATGTCC
* *
2071 TATGTAATTTGATAATGATTT
1 TATGCAATTTCATAATG-TTT
2092 TATGCAATTTCATAATGTTT
1 TATGCAATTTCATAATGTTT
2112 TAT
1 TAT
2115 ATAATTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (20 bp):
TATGCAATTTCATAATGTTT
Found at i:2509 original size:19 final size:18
Alignment explanation
Indices: 2482--2555 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 18
2472 TATTTTTTAG
* *
2482 TAATATTTTATATAACTAA
1 TAATGTTTTATGTAA-TAA
*
2501 TAATGTTTTATGTAATTA
1 TAATGTTTTATGTAATAA
2519 TAATGTTTATATGTAAGTAGA
1 TAATGTTT-TATGTAA-TA-A
2540 TAATGTTTTATGTAAT
1 TAATGTTTTATGTAAT
2556 TCATAAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.21
19 21 0.44
20 8 0.17
21 9 0.19
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.50
Consensus pattern (18 bp):
TAATGTTTTATGTAATAA
Found at i:2542 original size:21 final size:18
Alignment explanation
Indices: 2500--2555 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
2490 TATATAACTA
*
2500 ATAATGTTTTATGTAATT
1 ATAATGTTTTATGTAATG
2518 ATAATGTTTATATGTAAGTAG
1 ATAATGTTT-TATGTAA-T-G
2539 ATAATGTTTTATGTAAT
1 ATAATGTTTTATGTAAT
2556 TCATAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.26
19 8 0.24
20 8 0.24
21 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (18 bp):
ATAATGTTTTATGTAATG
Found at i:3304 original size:14 final size:15
Alignment explanation
Indices: 3286--3334 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3276 TTTAAAATAT
3286 TATATATAAATTTTA
1 TATATATAAATTTTA
*
3301 -ATATATTATATTTTA
1 TATATA-TAAATTTTA
3316 TATTATATAAATTTT-
1 TA-TATATAAATTTTA
3331 TATA
1 TATA
3335 CATTCATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 7 0.24
15 10 0.34
16 8 0.28
17 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATAAATTTTA
Found at i:4041 original size:19 final size:17
Alignment explanation
Indices: 4006--4056 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
3996 TATATATAAA
*
4006 ATTTAAAAATTTTATATAT
1 ATTTAAAAA-TATA-ATAT
*
4025 ATGTAAAAATATAATAT
1 ATTTAAAAATATAATAT
4042 ATTTAATAAATATAA
1 ATTTAA-AAATATAA
4057 AAATAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 11 0.39
19 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTAAAAATATAATAT
Found at i:4043 original size:17 final size:18
Alignment explanation
Indices: 4021--4056 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4011 AAAATTTTAT
4021 ATATATGTAA-AAATATA
1 ATATATGTAATAAATATA
*
4038 ATATATTTAATAAATATA
1 ATATATGTAATAAATATA
4056 A
1 A
4057 AAATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
ATATATGTAATAAATATA
Found at i:4462 original size:10 final size:10
Alignment explanation
Indices: 4444--4520 Score: 50
Period size: 10 Copynumber: 7.1 Consensus size: 10
4434 TTAAATATAA
*
4444 TATTAAAATT
1 TATTTAAATT
4454 TATTTAAATTT
1 TATTTAAA-TT
4465 ATATGTATAAATAAT
1 -TAT-T-TAAAT--T
4480 TAATTTAAATT
1 T-ATTTAAATT
4491 TA-TTAAA-T
1 TATTTAAATT
*
4499 TATTTTAATTT
1 TA-TTTAAATT
4510 TATTTAAATT
1 TATTTAAATT
4520 T
1 T
4521 TTTTTAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
8 3 0.06
9 5 0.09
10 20 0.37
11 7 0.13
12 3 0.06
13 7 0.13
14 6 0.11
15 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (10 bp):
TATTTAAATT
Found at i:4505 original size:19 final size:20
Alignment explanation
Indices: 4477--4523 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
4467 ATGTATAAAT
*
4477 AATTAATTTAAATTTA-TTA
1 AATTATTTTAAATTTATTTA
*
4496 AATTATTTTAATTTTATTTA
1 AATTATTTTAAATTTATTTA
4516 AATT-TTTT
1 AATTATTTT
4524 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTATTTTAAATTTATTTA
Found at i:4658 original size:17 final size:17
Alignment explanation
Indices: 4626--4674 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
4616 TTATAAGATT
*
4626 AAATATTTTTATAAATAA
1 AAATA-TTTAATAAATAA
4644 AAATATTTAATAAAT-A
1 AAATATTTAATAAATAA
*
4660 AAATA-TAAATAAATA
1 AAATATTTAATAAATA
4675 TTATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 9 0.32
18 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATATTTAATAAATAA
Found at i:4663 original size:16 final size:16
Alignment explanation
Indices: 4626--4674 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
4616 TTATAAGATT
*
4626 AAATATTTTTATAAATAA
1 AAATA-TTTAATAAAT-A
4644 AAATATTTAATAAATA
1 AAATATTTAATAAATA
*
4660 AAATA-TAAATAAATA
1 AAATATTTAATAAATA
4675 TTATAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 9 0.31
16 6 0.21
17 9 0.31
18 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATTTAATAAATA
Found at i:4772 original size:13 final size:14
Alignment explanation
Indices: 4754--4783 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4744 CTAATTTTTA
4754 TTTAAATTT-ATAT
1 TTTAAATTTAATAT
4767 TTTAAATTTAATAT
1 TTTAAATTTAATAT
4781 TTT
1 TTT
4784 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAAATTTAATAT
Found at i:4914 original size:18 final size:17
Alignment explanation
Indices: 4888--4927 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
4878 TAACACTTGG
* *
4888 AAATGTAGAAATTTAACA
1 AAATATAGAAATGTAA-A
4906 AAATATAGAAATGTAAA
1 AAATATAGAAATGTAAA
4923 AAATA
1 AAATA
4928 AAAGAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (17 bp):
AAATATAGAAATGTAAA
Found at i:5484 original size:12 final size:13
Alignment explanation
Indices: 5456--5485 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5446 CATAAGACTA
5456 TTAAAGGAAGTTG
1 TTAAAGGAAGTTG
5469 TTAAAGGAAG-TG
1 TTAAAGGAAGTTG
5481 TTAAA
1 TTAAA
5486 AATATATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (13 bp):
TTAAAGGAAGTTG
Found at i:5596 original size:17 final size:18
Alignment explanation
Indices: 5576--5624 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
5566 AAATATTAAT
5576 TTAATAAAAATTAAAT-A
1 TTAATAAAAATTAAATAA
*
5593 TTAA-ATATAATT-AATAA
1 TTAATA-AAAATTAAATAA
*
5610 TTAATAAAAACTAAA
1 TTAATAAAAATTAAA
5625 CATTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
16 4 0.16
17 18 0.72
18 3 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAATAAAAATTAAATAA
Done.