Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1990
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: 36414
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Found at i:3571 original size:3 final size:3
Alignment explanation
Indices: 3565--3614 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
3555 GAAAAAAAAT
*
3565 ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3613 AT
1 AT
3615 TTGGCATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3752 original size:20 final size:20
Alignment explanation
Indices: 3727--3766 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3717 TGTATTTTAA
*
3727 AAATCAATAAAAAATCAATT
1 AAATCAATAAAAAATAAATT
*
3747 AAATCATTAAAAAATAAATT
1 AAATCAATAAAAAATAAATT
3767 TTAAGCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATCAATAAAAAATAAATT
Found at i:4174 original size:22 final size:22
Alignment explanation
Indices: 4149--4222 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 22
4139 ATTCACTGAT
4149 AATATTTAATATATTAAATATA
1 AATATTTAATATATTAAATATA
**
4171 AATA-AAAAT-TATTAAATAT-
1 AATATTTAATATATTAAATATA
*
4190 AAT-TTTAA-ATTTTAAAATATA
1 AATATTTAATATATT-AAATATA
*
4211 ATATTTTTAATA
1 A-ATATTTAATA
4223 AAAATAAGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
19 8 0.20
20 16 0.40
21 4 0.10
22 6 0.15
23 5 0.12
24 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATTTAATATATTAAATATA
Found at i:4199 original size:20 final size:20
Alignment explanation
Indices: 4147--4212 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
4137 TAATTCACTG
4147 ATAATATTT-AATATATTAAAT
1 ATAAT-TTTAAAT-TATTAAAT
* **
4168 ATAAATAAAAATTATTAAAT
1 ATAATTTTAAATTATTAAAT
4188 ATAATTTTAAATT-TTAAAAT
1 ATAATTTTAAATTATT-AAAT
4208 ATAAT
1 ATAAT
4213 ATTTTTAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
19 2 0.05
20 28 0.76
21 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATTTTAAATTATTAAAT
Found at i:7386 original size:26 final size:26
Alignment explanation
Indices: 7356--7405 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
7346 TCAAGTTCGT
7356 TGATTATTCATTCGACTTATACGTAA
1 TGATTATTCATTCGACTTATACGTAA
7382 TGATTATTCATTCGACTTATACGT
1 TGATTATTCATTCGACTTATACGT
7406 GAAGAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (26 bp):
TGATTATTCATTCGACTTATACGTAA
Found at i:7679 original size:37 final size:37
Alignment explanation
Indices: 7629--7708 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
7619 TTTTTCAAGC
7629 ATGGTGCAGATTGAAATGCAAAAACAATAGGATGAAA
1 ATGGTGCAGATTGAAATGCAAAAACAATAGGATGAAA
7666 ATGGTGCAGATTGAAATGCAAAAACAATAGGATGAAA
1 ATGGTGCAGATTGAAATGCAAAAACAATAGGATGAAA
7703 A-GGTGC
1 ATGGTGC
7709 CACAAAGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 5 0.12
37 38 0.88
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.19
Consensus pattern (37 bp):
ATGGTGCAGATTGAAATGCAAAAACAATAGGATGAAA
Found at i:8590 original size:2 final size:2
Alignment explanation
Indices: 8583--8610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8573 ATCCATCACC
8583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8611 GCAGCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10295 original size:11 final size:11
Alignment explanation
Indices: 10261--10303 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
10251 ATTAAATTTG
*
10261 ATAATTTAAAT
1 ATAATATAAAT
*
10272 ATGATATAAAAAT
1 AT-A-ATATAAAT
10285 ATAATATAAAT
1 ATAATATAAAT
10296 ATAATATA
1 ATAATATA
10304 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
12 2 0.07
13 8 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:10913 original size:26 final size:27
Alignment explanation
Indices: 10864--10918 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
10854 TTAGTTAATT
*
10864 TTAAATTATTTTTAATTACGA-TTTAA
1 TTAAATTATTTTAAATTACGATTTTAA
*
10890 TTAAATTATTATTAAATTA-TATTTTAA
1 TTAAATTATT-TTAAATTACGATTTTAA
10917 TT
1 TT
10919 GAAGTACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAATTATTTTAAATTACGATTTTAA
Found at i:11757 original size:18 final size:20
Alignment explanation
Indices: 11734--11777 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
11724 AATTTTAAGA
11734 TATATTTTAA-TATTATA-T
1 TATATTTTAATTATTATATT
*
11752 TATATTTTAATTATTTTATT
1 TATATTTTAATTATTATATT
11772 TATATT
1 TATATT
11778 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 6 0.26
20 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATATTTTAATTATTATATT
Found at i:13667 original size:18 final size:18
Alignment explanation
Indices: 13620--13667 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
13610 TATTATTATT
* *
13620 TTATATTTTATTAAACAA
1 TTATATTTTATAAAAAAA
13638 TT-TGATTATTATAAAAAAA
1 TTAT-ATT-TTATAAAAAAA
13657 TTATATTTTAT
1 TTATATTTTAT
13668 TATATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 1 0.04
18 9 0.36
19 14 0.56
20 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATATTTTATAAAAAAA
Found at i:14300 original size:11 final size:11
Alignment explanation
Indices: 14271--14304 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
14261 TTATACTCAT
14271 AACAATAAT-A
1 AACAATAATAA
14281 AACAATAATAA
1 AACAATAATAA
*
14292 AATAATAATAA
1 AACAATAATAA
14303 AA
1 AA
14305 AAAAAGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (11 bp):
AACAATAATAA
Found at i:15528 original size:111 final size:115
Alignment explanation
Indices: 15402--15631 Score: 333
Period size: 114 Copynumber: 2.0 Consensus size: 115
15392 GTAAAGCGAA
* * *
15402 ATGAGAAGCAAGGATTCAATAGTTCGAAAAAATATTACAAAATTGAAGAAGATG-A-A-GAAGAA
1 ATGAGAAGCAAGGATTCAAAAGTTCGAAAAAATATCACAAAACTGAAGAAGATGAACAGGAAGAA
* * *
15464 GAAGAGTAAGGAAATGGGATTTAAGTGGAATCCAATGGTGATTAAATCAT
66 GAAGAATAAGGAAATGGGATTTAAGTGGAATCCAATGGTGACTAAATCAG
*** *
15514 ATGA-AAGCAAGGATTCAAAAGTTTTTAAAAATATCACAGAACTGAAGAAGATGAACAGGAAGAA
1 ATGAGAAGCAAGGATTCAAAAGTTCGAAAAAATATCACAAAACTGAAGAAGATGAACAGGAAGAA
*
15578 GAGGAATAAGGAAATGGGATTTAAGTGGAATCCAATGGTGACTAAATCAG
66 GAAGAATAAGGAAATGGGATTTAAGTGGAATCCAATGGTGACTAAATCAG
15628 ATGA
1 ATGA
15632 TCAGTGGTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
111 42 0.40
112 5 0.05
113 1 0.01
114 56 0.54
ACGTcount: A:0.47, C:0.07, G:0.24, T:0.21
Consensus pattern (115 bp):
ATGAGAAGCAAGGATTCAAAAGTTCGAAAAAATATCACAAAACTGAAGAAGATGAACAGGAAGAA
GAAGAATAAGGAAATGGGATTTAAGTGGAATCCAATGGTGACTAAATCAG
Found at i:22965 original size:28 final size:28
Alignment explanation
Indices: 22897--22966 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
22887 GGTTAAATAG
22897 ATTTTTTT-TA-TTAAAATTTATAATTT
1 ATTTTTTTATATTTAAAATTTATAATTT
* * *
22923 -TATTTTTATTTTTAAAATTTATTATTT
1 ATTTTTTTATATTTAAAATTTATAATTT
22950 ATTTTTTTATATTTAAA
1 ATTTTTTTATATTTAAA
22967 TAAAATTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 6 0.17
26 1 0.03
27 15 0.42
28 14 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
ATTTTTTTATATTTAAAATTTATAATTT
Found at i:31991 original size:21 final size:22
Alignment explanation
Indices: 31965--32045 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
31955 TGATTGATTC
31965 AATTAATTTTA-ATAATTTAAA
1 AATTAATTTTATATAATTTAAA
* * *
31986 AATTAAAATTTATATTATATAAA
1 AATT-AATTTTATATAATTTAAA
*
32009 AATT-ATTATATATAATTTTAAA
1 AATTAATTTTATATAA-TTTAAA
* *
32031 AGATTTATATTATAT
1 A-ATTAATTTTATAT
32046 TGTATAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 12 0.26
22 12 0.26
23 15 0.33
24 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
AATTAATTTTATATAATTTAAA
Found at i:34449 original size:32 final size:32
Alignment explanation
Indices: 34377--34450 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
34367 ATTTTTATTT
* *
34377 AATAATAAAAATAATATTTTTAATTTAAATTT
1 AATAATAAAAATAATATTTTTAATATAAATTA
*
34409 AATTATAAAAATAATATTTTACTAATAT-AA-TA
1 AATAATAAAAATAATATTTT--TAATATAAATTA
34441 AATAATAAAA
1 AATAATAAAA
34451 TAAGTTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 29 0.81
33 2 0.06
34 5 0.14
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
AATAATAAAAATAATATTTTTAATATAAATTA
Found at i:35780 original size:2 final size:2
Alignment explanation
Indices: 35773--35802 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35763 CGTCATAGAA
35773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35803 CTCTCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35967 original size:13 final size:13
Alignment explanation
Indices: 35951--35975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35941 TTTTTTATAA
35951 ATATTTATATTTG
1 ATATTTATATTTG
35964 ATATTTATATTT
1 ATATTTATATTT
35976 ATTTAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTG
Done.