Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2275
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: 181829
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:142630 original size:38 final size:35
Alignment explanation
Indices: 142588--142708 Score: 76
Period size: 38 Copynumber: 3.4 Consensus size: 35
142578 GATAAATATA
142588 ATATTTATATTATATTTATATAATTTTATGTATATTAT
1 ATATTTATATTATATTTATAT-ATTTTAT-T-TATTAT
* *
142626 ATATTTATA-TA-A-TTAT-TAATATA-TTATTAT
1 ATATTTATATTATATTTATATATTTTATTTATTAT
* *
142656 ATTATATTATA-TAAATTTAATGTATTTTATATT-TATAT
1 A-TAT-TTATATTATATTT-ATATATTTTAT-TTAT-TAT
142694 AATATTTATATTATA
1 -ATATTTATATTATA
142709 ATATATTATA
Statistics
Matches: 67, Mismatches: 5, Indels: 22
0.71 0.05 0.23
Matches are distributed among these distances:
30 7 0.10
31 4 0.06
32 7 0.10
33 5 0.07
34 3 0.04
35 6 0.09
36 6 0.09
37 8 0.12
38 20 0.30
39 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (35 bp):
ATATTTATATTATATTTATATATTTTATTTATTAT
Found at i:142636 original size:27 final size:27
Alignment explanation
Indices: 142598--142715 Score: 123
Period size: 27 Copynumber: 4.2 Consensus size: 27
142588 ATATTTATAT
*
142598 TATATTTATATAATTTTATGTATATTA
1 TATATTTATATAATTTTATATATATTA
142625 TATATTTATATAATTATTAATATATTATTA
1 TATATTTATATAATT-TT-ATATA-TATTA
* * *
142655 TATTATATTATATAAATTTA-ATGTATTT
1 TA-TAT-TTATATAATTTTATATATATTA
*
142683 TATATTTATATAATATTTATAT-TATAA
1 TATATTTATATAAT-TTTATATATATTA
142710 TATATT
1 TATATT
142716 ATAATTGTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
26 8 0.10
27 31 0.40
28 10 0.13
29 6 0.08
30 8 0.10
31 5 0.06
32 9 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TATATTTATATAATTTTATATATATTA
Found at i:142679 original size:60 final size:57
Alignment explanation
Indices: 142582--142718 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 57
142572 AGATTAGATA
* *
142582 AATATAATATTTATATTATATTTATATAATTTTATGTATATTATATATTTATATAATTATT
1 AATATATTA-TTATATTATATTTATATAATTTAATGTAT-TT-TATATTTATATAA-TATT
142643 AATATATTATTATATTATA-TTATATAAATTTAATGTATTTTATATTTATATAATATT
1 AATATATTATTATATTATATTTATAT-AATTTAATGTATTTTATATTTATATAATATT
142700 --TATATTATAATATATTATA
1 AATATATTAT--TATATTATA
142719 ATTGTTTTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
55 8 0.11
57 13 0.18
58 13 0.18
59 8 0.11
60 21 0.30
61 8 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (57 bp):
AATATATTATTATATTATATTTATATAATTTAATGTATTTTATATTTATATAATATT
Found at i:142741 original size:85 final size:84
Alignment explanation
Indices: 142597--142759 Score: 188
Period size: 85 Copynumber: 1.9 Consensus size: 84
142587 AATATTTATA
* *
142597 TTATATTTATATAATTTTATGTATATTATATATTTATATAATTATTAATATATTATTATATTATA
1 TTATATTTATATAATTTTATATATATAATATATTTATATAATTATTAATATATTATTATA-TA-A
142662 TTATA-TAAATTTAATGTATT
64 TTATATTAAATTTAATGTATT
** * * * *
142682 TTATATTTATATAATATTTATAT-TATAATATA-TTATAATTGTTTTTATTTTATTTTTATATAA
1 TTATATTTATATAAT-TTTATATATATAATATATTTAT-ATAATTATTAATATATTATTATATAA
*
142745 TTATATTATATTTAA
64 TTATATTAAATTTAA
142760 AATAATTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
83 6 0.09
84 14 0.21
85 40 0.61
86 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (84 bp):
TTATATTTATATAATTTTATATATATAATATATTTATATAATTATTAATATATTATTATATAATT
ATATTAAATTTAATGTATT
Found at i:142779 original size:49 final size:47
Alignment explanation
Indices: 142639--142779 Score: 126
Period size: 49 Copynumber: 2.9 Consensus size: 47
142629 TTTATATAAT
* * * *
142639 TATTAATATATTA-TTATATTATATTATA-TAAATTTAATGTATTTTA
1 TATTTATATAATATTTATATTAAAATATATTAAATTTAAT-TATTTTA
* **
142685 TATTTATATAATATTTATATTATAATATATTATAATTGTTTTTATTTTA
1 TATTTATATAATATTTATATTAAAATATATTA-AATT-TAATTATTTTA
* *
142734 TTTTTATATAATTATATTATATTTAAAATA-ATTAAATTCAATTATT
1 TATTTATATAA-TAT-TTATA-TTAAAATATATTAAATTTAATTATT
142780 AATTGGTTAC
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
46 11 0.14
47 14 0.18
48 2 0.03
49 26 0.33
50 9 0.12
51 9 0.12
52 7 0.09
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (47 bp):
TATTTATATAATATTTATATTAAAATATATTAAATTTAATTATTTTA
Found at i:143145 original size:35 final size:35
Alignment explanation
Indices: 143069--143146 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
143059 TATTATAATA
**
143069 ATAAAATAATTAAACATATTTAATTTTTTTATTTT
1 ATAAAATAATTAAACATATTTAATTTAATTATTTT
*
143104 AAAAAATAATTAAA-AT-TTTAATCTTAAATTATTTT
1 ATAAAATAATTAAACATATTTAAT-TT-AATTATTTT
*
143139 TTAAAATA
1 ATAAAATA
143147 TAAAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 6 0.17
34 4 0.11
35 26 0.72
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (35 bp):
ATAAAATAATTAAACATATTTAATTTAATTATTTT
Found at i:144412 original size:17 final size:17
Alignment explanation
Indices: 144386--144426 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
144376 TTAAAAATTA
* *
144386 TTTTTAAAAATAACATTT
1 TTTTTAAAAGTAA-ATAT
144404 TTTTTAAAAGTAAATAT
1 TTTTTAAAAGTAAATAT
144421 TTTTTA
1 TTTTTA
144427 GCCGAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTTTAAAAGTAAATAT
Found at i:145321 original size:16 final size:16
Alignment explanation
Indices: 145302--145352 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
145292 AGTCGACTTT
145302 AATTAATAAATTTTAA
1 AATTAATAAATTTTAA
145318 AATTTAAATATAATTTT-A
1 AA-TT-AATA-AATTTTAA
*
145336 AATCAATTAAATTTTAA
1 AATTAA-TAAATTTTAA
145353 TTTTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
16 10 0.34
17 6 0.21
18 7 0.24
19 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATAAATTTTAA
Found at i:146051 original size:24 final size:26
Alignment explanation
Indices: 146000--146060 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
145990 TAAATTTTTT
*
146000 AAATTATAATTTAAATCTACAATAAA
1 AAATTATAATTTAAAGCTACAATAAA
*
146026 AAATTA-AATTTAAAGCT-GAATAAA
1 AAATTATAATTTAAAGCTACAATAAA
*
146050 AAATTTTAATT
1 AAATTATAATT
146061 ACGTTTTGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.35
25 14 0.45
26 6 0.19
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (26 bp):
AAATTATAATTTAAAGCTACAATAAA
Found at i:146651 original size:11 final size:11
Alignment explanation
Indices: 146637--146767 Score: 76
Period size: 11 Copynumber: 12.8 Consensus size: 11
146627 TAATATGTAT
146637 TAAATATATTA
1 TAAATATATTA
*
146648 TAAATATATATT
1 TAAATATAT-TA
146660 TAAA-AT-TTA
1 TAAATATATTA
146669 TATAATATAAATTA
1 TA-AATAT--ATTA
*
146683 TTAATATATTA
1 TAAATATATTA
*
146694 -AAATTTA-TA
1 TAAATATATTA
146703 T-AA-ATA-TA
1 TAAATATATTA
146711 -AAATAT-TT-
1 TAAATATATTA
146719 TAAATATAATTA
1 TAAATAT-ATTA
146731 T-AATATATTA
1 TAAATATATTA
146741 -AAATATA--A
1 TAAATATATTA
*
146749 -AAATATAATA
1 TAAATATATTA
146759 TAAATATAT
1 TAAATATAT
146768 AAATTATTTA
Statistics
Matches: 95, Mismatches: 7, Indels: 36
0.69 0.05 0.26
Matches are distributed among these distances:
8 14 0.15
9 16 0.17
10 19 0.20
11 31 0.33
12 6 0.06
13 5 0.05
14 4 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATATATTA
Found at i:146670 original size:15 final size:15
Alignment explanation
Indices: 146652--146704 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
146642 ATATTATAAA
146652 TATATATTTAAAATT
1 TATATATTTAAAATT
* *
146667 TATATAATATAAATTAT
1 TATAT-ATTTAAAAT-T
146684 TA-ATATATTAAAATT
1 TATATAT-TTAAAATT
146699 TATATA
1 TATATA
146705 AATATAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 10 0.33
16 17 0.57
17 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATTTAAAATT
Found at i:146676 original size:33 final size:32
Alignment explanation
Indices: 146639--146747 Score: 85
Period size: 32 Copynumber: 3.6 Consensus size: 32
146629 ATATGTATTA
146639 AATATATTATAAATATATATTTAAAATTTATAT
1 AATATATTATAAA-ATATATTTAAAATTTATAT
*
146672 AATATAAATTAT-TAATATA-TTAAAATTTATAT
1 AATAT--ATTATAAAATATATTTAAAATTTATAT
*
146704 -A-A-A-TATAAAATAT-TTT-AAATATAATTAT
1 AATATATTATAAAATATATTTAAAAT-TTA-TAT
146732 AATATA-T-TAAAATATA
1 AATATATTATAAAATATA
146748 AAAATATAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
26 7 0.11
27 10 0.16
28 3 0.05
29 1 0.02
30 10 0.16
31 3 0.05
32 13 0.21
33 10 0.16
34 1 0.02
35 5 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AATATATTATAAAATATATTTAAAATTTATAT
Found at i:146700 original size:32 final size:34
Alignment explanation
Indices: 146653--146760 Score: 107
Period size: 37 Copynumber: 3.1 Consensus size: 34
146643 TATTATAAAT
*
146653 ATATATTTAAAATTTATAT-AATATAAATTATTA
1 ATATATTTAAAATTTATATAAATATAAAATATTA
146686 ATATA-TTAAAATTTATATAAATATAAAATATTTTAA
1 ATATATTTAAAATTTATATAAATATAAAATA--TT-A
* * *
146722 ATATAATTATAATATAT-TAAAATATAAAA-ATATA
1 ATATATTTAAAATTTATAT-AAATATAAAATAT-TA
146756 ATATA
1 ATATA
146761 AATATATAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
32 13 0.20
33 15 0.23
34 7 0.11
35 3 0.05
36 8 0.12
37 19 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
ATATATTTAAAATTTATATAAATATAAAATATTA
Found at i:149419 original size:16 final size:16
Alignment explanation
Indices: 149398--149431 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
149388 AATGCACAAA
149398 AGATGACATATAAAAT
1 AGATGACATATAAAAT
149414 AGATGACATATAAAAT
1 AGATGACATATAAAAT
149430 AG
1 AG
149432 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (16 bp):
AGATGACATATAAAAT
Found at i:151801 original size:4 final size:4
Alignment explanation
Indices: 151792--151844 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
151782 TATTTTAATG
* *
151792 AAAT AAAT AAAAT AAAT AAAT AAAT AAAT AAATT AAA- ATAT AATT AAAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
151841 AAAT
1 AAAT
151845 TGACAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 32 0.76
5 8 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:151834 original size:20 final size:21
Alignment explanation
Indices: 151792--151844 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
151782 TATTTTAATG
151792 AAATAAATAAAATAAATAAA-T
1 AAATAAAT-AAATAAATAAATT
151813 AAATAAATAAATTAAAATATAATT
1 AAATAAATAAA-T-AAATA-AATT
151837 AAATAAAT
1 AAATAAAT
151845 TGACAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.11
21 9 0.32
22 5 0.18
23 2 0.07
24 9 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAATAAATAAATAAATT
Found at i:151845 original size:20 final size:21
Alignment explanation
Indices: 151792--151845 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
151782 TATTTTAATG
*
151792 AAATAAATAAAATAAATAAAT
1 AAATAAATAAATTAAATAAAT
*
151813 AAATAAATAAATTAAA-ATAT
1 AAATAAATAAATTAAATAAAT
*
151833 AATTAAATAAATT
1 AAATAAATAAATT
151846 GACAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATAAATAAATTAAATAAAT
Found at i:152517 original size:11 final size:12
Alignment explanation
Indices: 152490--152514 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
152480 TTTATTATAA
152490 AATATAAAAATT
1 AATATAAAAATT
152502 AATATAAAAATT
1 AATATAAAAATT
152514 A
1 A
152515 TATTTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAAAAATT
Found at i:152752 original size:9 final size:10
Alignment explanation
Indices: 152723--152755 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
152713 ACCATGGCAG
152723 TTAGTATTATA
1 TTAGTATTA-A
152734 TTAGTATTAA
1 TTAGTATTAA
152744 TTA-TATTAA
1 TTAGTATTAA
152753 TTA
1 TTA
152756 ACATGTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 4 0.18
11 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (10 bp):
TTAGTATTAA
Found at i:153073 original size:20 final size:22
Alignment explanation
Indices: 153024--153073 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
153014 AAATTATTAA
*
153024 ACTTAATTAATAATAATTTTTT
1 ACTTATTTAATAATAATTTTTT
*
153046 ACAT-TTTAA-AAT-ATTTTTT
1 ACTTATTTAATAATAATTTTTT
153065 ACTTATTTA
1 ACTTATTTA
153074 TTTTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.42
20 7 0.29
21 4 0.17
22 3 0.12
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
ACTTATTTAATAATAATTTTTT
Found at i:153104 original size:17 final size:17
Alignment explanation
Indices: 153074--153111 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
153064 TACTTATTTA
*
153074 TTTT-ATATTTAAAAAT
1 TTTTAATATTAAAAAAT
*
153090 TTTTAATATTAAAAATT
1 TTTTAATATTAAAAAAT
153107 TTTTA
1 TTTTA
153112 CTTATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAATATTAAAAAAT
Found at i:153550 original size:9 final size:8
Alignment explanation
Indices: 153523--153581 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
153513 ACACTGAATT
*
153523 AAAATGTA
1 AAAATATA
*
153531 AAAAAATA
1 AAAATATA
*
153539 AATA-ATA
1 AAAATATA
*
153546 AAAATTTA
1 AAAATATA
*
153554 AAAATTTA
1 AAAATATA
153562 AAAATATA
1 AAAATATA
153570 AAAATAATA
1 AAAAT-ATA
153579 AAA
1 AAA
153582 TATTTTTACT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
7 6 0.14
8 31 0.72
9 6 0.14
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (8 bp):
AAAATATA
Found at i:153584 original size:16 final size:17
Alignment explanation
Indices: 153538--153581 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
153528 GTAAAAAAAT
*
153538 AAATAATAAAAATTTAA
1 AAATAATAAAAATATAA
*
153555 AAAT-TTAAAAATATAA
1 AAATAATAAAAATATAA
153571 AAATAATAAAA
1 AAATAATAAAA
153582 TATTTTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAATAAAAATATAA
Found at i:153729 original size:31 final size:30
Alignment explanation
Indices: 153667--153747 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 30
153657 CACTATAAAA
* * * *
153667 TTAAAAGAATAAAAAGTGATTAATAATAATTT
1 TTAAAA-AATAAAAAATTATTTATAA-AAATT
*
153699 TTAAAAAATAAAAAATTATTTCTAAAAATT
1 TTAAAAAATAAAAAATTATTTATAAAAATT
153729 TT--AAAATAAAAAATTATTT
1 TTAAAAAATAAAAAATTATTT
153748 TTAACAGTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
28 17 0.39
30 6 0.14
31 15 0.34
32 6 0.14
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (30 bp):
TTAAAAAATAAAAAATTATTTATAAAAATT
Found at i:154450 original size:20 final size:20
Alignment explanation
Indices: 154403--154459 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
154393 ATTACGCTTC
154403 ATTATATTATTATA-A-TTAT
1 ATTA-ATTATTATATATTTAT
154422 ATTTAAATTATTATATATTTAT
1 A-TT-AATTATTATATATTTAT
154444 ATTAATT-TTA-ATATTT
1 ATTAATTATTATATATTT
154460 TAAAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 15 0.44
21 4 0.12
22 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTAATTATTATATATTTAT
Found at i:154543 original size:30 final size:30
Alignment explanation
Indices: 154509--154631 Score: 146
Period size: 30 Copynumber: 4.1 Consensus size: 30
154499 TATCTCTTAT
*
154509 TTTAATTAAAAATATATTTATCTTTTAAAA
1 TTTAATAAAAAATATATTTATCTTTTAAAA
154539 TTTAATAAAAAATATATTTATCTTTTAAAA
1 TTTAATAAAAAATATATTTATCTTTTAAAA
* * *
154569 -TT--TAAAAGATACTCATTTATCTCTTAAAG
1 TTTAATAAAAAATA-T-ATTTATCTTTTAAAA
*
154598 TTTAATAAAAAATAATATTAAT-TTTTAAAA
1 TTTAATAAAAAAT-ATATTTATCTTTTAAAA
154628 TTTA
1 TTTA
154632 TATACTAAGT
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
27 8 0.10
28 1 0.01
29 15 0.19
30 41 0.52
31 5 0.06
32 8 0.10
33 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTAATAAAAAATATATTTATCTTTTAAAA
Found at i:155284 original size:16 final size:16
Alignment explanation
Indices: 155263--155294 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
155253 CATGTACTTG
155263 AATTAAAATATAATTT
1 AATTAAAATATAATTT
*
155279 AATTAAAATTTAATTT
1 AATTAAAATATAATTT
155295 TATAAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAAATATAATTT
Found at i:155934 original size:2 final size:2
Alignment explanation
Indices: 155927--155953 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155917 TATGTTGATT
155927 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
155954 TTTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:165994 original size:24 final size:23
Alignment explanation
Indices: 165942--165994 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
165932 ATATACATAT
* *
165942 AAATAAAACAAAAAAAATATATG
1 AAATAAAACAAAAAAAACAAATG
165965 ATAATAATAA-AAAAAAAACAAATG
1 A-AATAA-AACAAAAAAAACAAATG
165989 CAAATA
1 -AAATA
165995 TCACCAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.04
24 21 0.84
25 3 0.12
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.17
Consensus pattern (23 bp):
AAATAAAACAAAAAAAACAAATG
Found at i:167575 original size:45 final size:48
Alignment explanation
Indices: 167474--167591 Score: 134
Period size: 45 Copynumber: 2.5 Consensus size: 48
167464 AATGTGCCAT
* * * *
167474 TTCAAGGTCAACGACATTGGACTAAGGGAAAAGTGGACCAATGTGCTGA
1 TTCAAGGCCAGCGACATTGGACTTA-GGAAAAGTGGACCAATATGCTGA
* *
167523 CTCAAGGCCAGCGACATTGGACTTA-GAAAGGT-G-CCAATATGCTGA
1 TTCAAGGCCAGCGACATTGGACTTAGGAAAAGTGGACCAATATGCTGA
* *
167568 TTCAAGGCCAGCGATATCGGACTT
1 TTCAAGGCCAGCGACATTGGACTT
167592 TAAGATGACA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
45 32 0.53
46 1 0.02
47 6 0.10
49 21 0.35
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (48 bp):
TTCAAGGCCAGCGACATTGGACTTAGGAAAAGTGGACCAATATGCTGA
Found at i:167661 original size:32 final size:32
Alignment explanation
Indices: 167612--168119 Score: 851
Period size: 32 Copynumber: 15.8 Consensus size: 32
167602 AAAATGGTGA
* * *
167612 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
167644 TTTTAAATGGGTTGCCACCGACTT-TCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGT-GTGGGC
*
167676 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
167708 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
167740 TTT-AGAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
167772 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
167804 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
167836 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
167868 TTTGAAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAATGGGTTGCCACCGACTTGTGTGGGC
167901 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
167933 TTTGAAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAATGGGTTGCCACCGACTTGTGTGGGC
167966 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
167998 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
168030 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
168062 TTTGGAATGGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
168094 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
168120 GATTTAAAAG
Statistics
Matches: 453, Mismatches: 17, Indels: 13
0.94 0.04 0.03
Matches are distributed among these distances:
31 13 0.03
32 374 0.83
33 66 0.15
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:168137 original size:27 final size:27
Alignment explanation
Indices: 168102--169144 Score: 1595
Period size: 27 Copynumber: 38.0 Consensus size: 27
168092 GCTTTGAAAT
* *
168102 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
**
168129 GGACGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168156 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
168183 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168210 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
168238 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
168265 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
168293 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
168320 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168347 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
168374 GGGTGCCACAAAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168401 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
168429 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
168456 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
168484 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168511 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
168538 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168565 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
168593 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
168620 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
168648 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
168675 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
168703 GGGTGTCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168730 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168757 GGGTGCCACGGAGTTGTGGACTTAAAGGCAA
1 GGGTGCCACGGAGTTGTGGACTT-AA---AA
*
168788 GTGGTAGGCCACAGAGTTGTGGACTTAAAA
1 G-GGT--GCCACGGAGTTGTGGACTTAAAA
*
168818 GGGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
168846 GGGT-CCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
168872 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
168899 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
168926 GGGTGCCACGGAGTTGTGGACTTGAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
168953 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
168980 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
169007 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
169035 GGGT-CCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
169061 GGATGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
169089 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
169116 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
169144 G
1 G
169145 AAAATGCCAC
Statistics
Matches: 938, Mismatches: 58, Indels: 39
0.91 0.06 0.04
Matches are distributed among these distances:
26 18 0.02
27 663 0.71
28 225 0.24
29 3 0.00
30 3 0.00
31 3 0.00
32 3 0.00
33 2 0.00
34 18 0.02
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:168394 original size:164 final size:163
Alignment explanation
Indices: 168087--169144 Score: 1622
Period size: 164 Copynumber: 6.4 Consensus size: 163
168077 CACCAACTTG
* * * *
168087 TGTGGGCTTTGAAATGGGTGCCACAGAGTTGTGGATTTAAAAGGACGCCACGGAGTTGTGGACTT
1 TGTGGACTTT-AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT
* *
168152 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCC
65 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
168217 ACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGT
130 ACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGT
* * * *
168252 TGTGGAC-TTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TGTGGACTTTAAAAG-GGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT
*
168316 AAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
65 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
** *
168381 ACAAAGTTGTGGACTAAAAAGGGTGCCACGGAGT
130 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
168415 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GATGCCACGGAGTTGTGGACTT
168480 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
65 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
168545 ACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGT
130 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
168579 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GATGCCACGGAGTTGTGGACTT
* *
168644 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTTAAAAGGGTGT
65 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
168709 CACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
129 CACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* * *
168744 TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAGGCAAGTGGTAGGCCACAGAGTTGT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTT-AA---AA--GG-ATGCCACGGAGTTGT
* *
168808 GGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGT-CCACAGAGTTGTGGACTTAAAA
59 GGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
168872 GGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
123 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* * * *
168913 TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTGAAAGGGTGCCACAGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
168977 AAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGT-CC
66 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCC
* *
169041 ACAGAGTTGTGGACTTAAAAGGATGCCACGGAGT
130 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
169075 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TT
169140 AAAAG
65 AAAAG
169145 AAAATGCCAC
Statistics
Matches: 831, Mismatches: 46, Indels: 33
0.91 0.05 0.04
Matches are distributed among these distances:
161 9 0.01
162 100 0.12
163 115 0.14
164 393 0.47
165 62 0.07
168 3 0.00
169 82 0.10
170 57 0.07
171 10 0.01
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (163 bp):
TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
CGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
Found at i:170214 original size:13 final size:13
Alignment explanation
Indices: 170196--170220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
170186 AGGGTGAAAA
170196 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
170209 GGTTTTTTTTTT
1 GGTTTTTTTTTT
170221 AGGATTAGGT
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:177044 original size:24 final size:24
Alignment explanation
Indices: 176986--177044 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
176976 ATTTTTTTCT
* *
176986 TTTTTTTTTTCTTTCTTCTTCATC
1 TTTTTTTTTTCTTTCTTCCTCAAC
* * *
177010 TTCTTTCTTTCTTTTTTACCT-AAC
1 TTTTTTTTTTCTTTCTT-CCTCAAC
177034 TTTTTTTTTTC
1 TTTTTTTTTTC
177045 AACCCATAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTTTTTTCTTTCTTCCTCAAC
Found at i:177228 original size:10 final size:10
Alignment explanation
Indices: 177203--177236 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
177193 AATCCGAAAT
177203 TAGATTTTTC
1 TAGATTTTTC
*
177213 TA-ATTTTTT
1 TAGATTTTTC
177222 TAGATTTTTC
1 TAGATTTTTC
177232 TAGAT
1 TAGAT
177237 CTACAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (10 bp):
TAGATTTTTC
Done.