Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168020.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_274, whole genome shotgun sequence
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: 40382
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
File 2 of 2
Found at i:30879 original size:32 final size:30
Alignment explanation
Indices: 30805--30884 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 30
30795 ATGACAATTT
30805 TTTAATTAATATCAATAAATAGTCATAAAAA
1 TTTAATTAATAT-AATAAATAGTCATAAAAA
* * **
30836 TTATTATTAATATAATAATATATTCATATTAA
1 TT-TAATTAATATAATAA-ATAGTCATAAAAA
30868 TTTAATGTAATAATAAT
1 TTTAAT-TAAT-ATAAT
30885 TAATTAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
31 10 0.25
32 25 0.62
33 5 0.12
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTAATTAATATAATAAATAGTCATAAAAA
Found at i:31356 original size:4 final size:4
Alignment explanation
Indices: 31347--31381 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
31337 TTATCAAATA
31347 TAAT TAAT TAAT TAAT TAAT TAA- TAA- TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
31382 GATTTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TAAT
Found at i:31679 original size:15 final size:16
Alignment explanation
Indices: 31658--31701 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
31648 GAGTAATTCA
31658 AATATTATTATTAATT
1 AATATTATTATTAATT
*
31674 -ATATTA-TAATAATT
1 AATATTATTATTAATT
31688 AATATTAATTATTA
1 AATATT-ATTATTA
31702 TAAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 7 0.30
15 11 0.48
16 1 0.04
17 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTATTATTAATT
Found at i:32595 original size:17 final size:17
Alignment explanation
Indices: 32573--32608 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
32563 TTACTATAAA
*
32573 TAGATTATTATATATAT
1 TAGATTATAATATATAT
*
32590 TAGATTATAATCTATAT
1 TAGATTATAATATATAT
32607 TA
1 TA
32609 TAAATCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
TAGATTATAATATATAT
Found at i:32673 original size:23 final size:21
Alignment explanation
Indices: 32606--32679 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 21
32596 ATAATCTATA
*
32606 TTATAAATCATTTATATATAAT
1 TTATAAAT-ATTTATATATTAT
* *
32628 ATTATATATATTTGA-ATAATAT
1 -TTATAAATATTT-ATATATTAT
32650 TTGATTAAATATTTATATATTAT
1 TT-A-TAAATATTTATATATTAT
*
32673 TTTTAAA
1 TTATAAA
32680 CAAATAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
21 6 0.15
22 11 0.27
23 24 0.59
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (21 bp):
TTATAAATATTTATATATTAT
Found at i:32839 original size:17 final size:18
Alignment explanation
Indices: 32793--32852 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 18
32783 TATAGTAATA
32793 ATTAAT-AAATAAA-TAGT
1 ATTAATAAAATAAATTA-T
32810 A-TAATAAAATAAATTAT
1 ATTAATAAAATAAATTAT
*
32827 ATTAAT-AATTAAATTA-
1 ATTAATAAAATAAATTAT
32843 ATATAATAAA
1 AT-TAATAAA
32853 TTAGAATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 6 0.16
17 23 0.62
18 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTAATAAAATAAATTAT
Found at i:32840 original size:21 final size:22
Alignment explanation
Indices: 32783--32847 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 22
32773 TTATTATTAG
32783 TATAGTAATAATT-AATAAATA
1 TATAGTAATAATTAAATAAATA
* *
32804 AATAGT-ATAATAAAATAAAT-
1 TATAGTAATAATTAAATAAATA
* *
32824 TATATTAATAATTAAATTAATA
1 TATAGTAATAATTAAATAAATA
32846 TA
1 TA
32848 ATAAATTAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 9 0.26
21 24 0.69
22 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
TATAGTAATAATTAAATAAATA
Found at i:33715 original size:21 final size:21
Alignment explanation
Indices: 33691--33751 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
33681 ATTTAAAATT
33691 ATTTATTAATAATATTATATA
1 ATTTATTAATAATATTATATA
33712 ATTTATT--T-ATATTATATA
1 ATTTATTAATAATATTATATA
33730 ATGTT-TTAATAATAGTT-TATA
1 AT-TTATTAATAATA-TTATATA
33751 A
1 A
33752 ATATAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 14 0.40
19 3 0.09
20 1 0.03
21 15 0.43
22 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTATTAATAATATTATATA
Found at i:34525 original size:23 final size:21
Alignment explanation
Indices: 34464--34527 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
34454 TAAAGTAATA
* *
34464 TTATTTTAATAGTCATAATTAT
1 TTATTTAAATAAT-ATAATTAT
34486 TTATTTAAATAAT-TAATTAT
1 TTATTTAAATAATATAATTAT
**
34506 TATATATTCGATAATATAATTA
1 T-TAT-TTAAATAATATAATTA
34528 ATAAATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.23
21 3 0.09
22 18 0.51
23 6 0.17
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (21 bp):
TTATTTAAATAATATAATTAT
Found at i:34618 original size:23 final size:23
Alignment explanation
Indices: 34588--34636 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
34578 AATTATAGAG
34588 ATATACTAATAA-AATTAATTATT
1 ATATACTAATAATAATTAA-TATT
* *
34611 ATATACTATTAATTATTAATATT
1 ATATACTAATAATAATTAATATT
34634 ATA
1 ATA
34637 ATTATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATACTAATAATAATTAATATT
Found at i:34623 original size:17 final size:17
Alignment explanation
Indices: 34601--34647 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
34591 TACTAATAAA
34601 ATTAATTATTATATACT
1 ATTAATTATTATATACT
*
34618 ATTAATTATTA-ATATT
1 ATTAATTATTATATACT
*
34634 A-TAATTATAATATA
1 ATTAATTATTATATA
34648 TTTATCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.30
16 8 0.30
17 11 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATTATTATATACT
Found at i:34728 original size:23 final size:25
Alignment explanation
Indices: 34701--34755 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 25
34691 TATCTAATAA
* *
34701 AAATAATTTTATAT-GTATTA-TAT
1 AAATAATTTTATATAGTATAATTAC
34724 AAAT-ATTTTATATAGTATAATTAC
1 AAATAATTTTATATAGTATAATTAC
34748 AAATAATT
1 AAATAATT
34756 ATTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.33
23 9 0.33
24 6 0.22
25 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
AAATAATTTTATATAGTATAATTAC
Found at i:34751 original size:24 final size:22
Alignment explanation
Indices: 34695--34752 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
34685 ATATTTTATC
*
34695 TAATAAAAATAATTTTATATGTA
1 TAATACAAAT-ATTTTATATGTA
* *
34718 TTATATAAATATTTTATATAGTA
1 TAATACAAATATTTTATAT-GTA
34741 TAATTACAAATA
1 TAA-TACAAATA
34753 ATTATTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 9 0.31
23 13 0.45
24 7 0.24
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (22 bp):
TAATACAAATATTTTATATGTA
Found at i:35258 original size:16 final size:16
Alignment explanation
Indices: 35237--35267 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35227 TATTATACTA
*
35237 AATTAATCTTAATATT
1 AATTAATATTAATATT
35253 AATTAATATTAATAT
1 AATTAATATTAATAT
35268 AAAATTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAATATTAATATT
Found at i:35443 original size:14 final size:14
Alignment explanation
Indices: 35406--35443 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
35396 ATATCTTATT
*
35406 ATTTATTATTAATA
1 ATTTATTAATAATA
35420 ATGTTA-TAATAATA
1 AT-TTATTAATAATA
35434 ATTTATTAAT
1 ATTTATTAAT
35444 TTATAACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 15 0.71
15 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTATTAATAATA
Found at i:35515 original size:6 final size:6
Alignment explanation
Indices: 35491--35568 Score: 54
Period size: 6 Copynumber: 12.7 Consensus size: 6
35481 TGACTTATGA
* *
35491 TAATAT TAACAT ATAATAT TAATAT TACATA- TAATAT TCATTAT T-ATAT
1 TAATAT TAATAT -TAATAT TAATAT TA-ATAT TAATAT T-AATAT TAATAT
* *
35540 TGA-AT TAATAAAT TATTAT TAATAT TAAT
1 TAATAT TAAT--AT TAATAT TAATAT TAAT
35569 TCAATTAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
5 11 0.19
6 28 0.49
7 13 0.23
8 5 0.09
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:35522 original size:18 final size:19
Alignment explanation
Indices: 35491--35528 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
35481 TGACTTATGA
35491 TAATATTAACATATAATAT
1 TAATATTAACATATAATAT
35510 TAATATT-ACATATAATAT
1 TAATATTAACATATAATAT
35528 T
1 T
35529 CATTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATATTAACATATAATAT
Found at i:35578 original size:25 final size:24
Alignment explanation
Indices: 35521--35580 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
35511 AATATTACAT
35521 ATAATATTCATTATTATATTGAATTA
1 ATAA-ATT-ATTATTATATTGAATTA
35547 ATAAATTATTATTAATATT-AATTCA
1 ATAAATTATTATT-ATATTGAATT-A
*
35572 ATTAATTAT
1 ATAAATTAT
35581 GAATTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 10 0.32
25 17 0.55
26 4 0.13
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (24 bp):
ATAAATTATTATTATATTGAATTA
Found at i:35618 original size:14 final size:14
Alignment explanation
Indices: 35597--35630 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35587 TTTATATCAT
35597 AATT-TTAAATATA
1 AATTATTAAATATA
*
35610 AATTATTAAATATT
1 AATTATTAAATATA
35624 AATTATT
1 AATTATT
35631 TTGTCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATTAAATATA
Found at i:36113 original size:17 final size:17
Alignment explanation
Indices: 36091--36127 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
36081 TTATTAATAA
*
36091 TATTATAAAACAGTTAT
1 TATTATAAAACAATTAT
*
36108 TATTATAAAATAATTAT
1 TATTATAAAACAATTAT
36125 TAT
1 TAT
36128 AATGTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TATTATAAAACAATTAT
Found at i:36119 original size:27 final size:28
Alignment explanation
Indices: 36071--36124 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
36061 AATTATATTG
*
36071 AAACAGTTAATTATTAATAAT-ATTATA
1 AAACAGTTAATTATTAAAAATAATTATA
36098 AAACAGTT-ATTATTATAAAATAATTAT
1 AAACAGTTAATTATTA-AAAATAATTAT
36125 TATAATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (28 bp):
AAACAGTTAATTATTAAAAATAATTATA
Found at i:36331 original size:21 final size:21
Alignment explanation
Indices: 36286--36332 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
36276 TATACTAGAT
36286 TATTATAATTTAAATAACAGA
1 TATTATAATTTAAATAACAGA
**
36307 -ATTATAATTGTTCATAACA-A
1 TATTATAATT-TAAATAACAGA
36327 TATTAT
1 TATTAT
36333 TTGTGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
TATTATAATTTAAATAACAGA
Found at i:36834 original size:24 final size:22
Alignment explanation
Indices: 36746--36837 Score: 64
Period size: 22 Copynumber: 4.1 Consensus size: 22
36736 ACTATTATTA
* *
36746 ATTTATAATAATTTCTATTATAAT
1 ATTTATAATAATTT-AATTA-ATT
* * *
36770 ATTCAT-A-AATATAATTTATT
1 ATTTATAATAATTTAATTAATT
* *
36790 ATTTATAATAGTTT-ATAAATT
1 ATTTATAATAATTTAATTAATT
36811 ATTTAATAATAATTTAAATTAATT
1 ATTT-ATAATAATTT-AATTAATT
36835 ATT
1 ATT
36838 ATGCTATTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
20 7 0.14
21 13 0.25
22 16 0.31
23 1 0.02
24 14 0.27
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (22 bp):
ATTTATAATAATTTAATTAATT
Found at i:36873 original size:14 final size:14
Alignment explanation
Indices: 36709--36895 Score: 56
Period size: 15 Copynumber: 13.1 Consensus size: 14
36699 TAATTCCAAA
*
36709 AATATAATAATT-T
1 AATATTATAATTAT
*
36722 -ATATTATTATTTAT
1 AATATTA-TAATTAT
*
36736 ACTATTATTAATTTAT
1 AATATTA-TAA-TTAT
*
36752 AATAATT-TCTATTAT
1 AAT-ATTAT-AATTAT
*
36767 AATATTCATAAATAT
1 AATATT-ATAATTAT
*
36782 AAT-TTATTATTTAT
1 AATATTA-TAATTAT
36796 AATAGTTTATAAATTATTT
1 AATA--TTAT-AATTA--T
36815 AATA--ATAATT-T
1 AATATTATAATTAT
*
36826 AA-ATTAATTATTAT
1 AATATT-ATAATTAT
**
36840 GCTATTTATAATTAT
1 AATA-TTATAATTAT
36855 AATATTATATATTAT
1 AATATTATA-ATTAT
36870 -ATA-TA-AATTAAT
1 AATATTATAATT-AT
*
36882 AA-ATTATAAATAT
1 AATATTATAATTAT
36895 A
1 A
36896 TTAATTTAAT
Statistics
Matches: 130, Mismatches: 18, Indels: 52
0.65 0.09 0.26
Matches are distributed among these distances:
10 1 0.01
11 6 0.05
12 9 0.07
13 18 0.14
14 30 0.23
15 40 0.31
16 11 0.08
17 10 0.08
19 5 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (14 bp):
AATATTATAATTAT
Found at i:36887 original size:19 final size:19
Alignment explanation
Indices: 36852--36900 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
36842 TATTTATAAT
*
36852 TATAATATT-ATATATTATA
1 TATAA-ATTAATAAATTATA
36871 TATAAATTAATAAATTATA
1 TATAAATTAATAAATTATA
* *
36890 AATATATTAAT
1 TATAAATTAAT
36901 TTAATCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAAATTAATAAATTATA
Found at i:36904 original size:24 final size:27
Alignment explanation
Indices: 36849--36910 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
36839 TGCTATTTAT
*
36849 AATT-ATAATATTATATATTATATATA
1 AATTAATAATATTATATAATATATATA
36875 AATTAATAA-ATTATA-AATATAT-TA
1 AATTAATAATATTATATAATATATATA
*
36899 ATTTAATCAATA
1 AATTAAT-AATA
36911 ATTAAAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 8 0.26
25 8 0.26
26 11 0.35
27 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AATTAATAATATTATATAATATATATA
Found at i:37484 original size:28 final size:29
Alignment explanation
Indices: 37420--37506 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
37410 TTTAATTTGA
* *
37420 TAATTAAA-C-TAATAAAATATTAATTAT
1 TAATTAAATCATAATAAATTATAAATTAT
*
37447 T-TTTATAATCATAATAAATTA-AAATTAT
1 TAATTA-AATCATAATAAATTATAAATTAT
* * *
37475 TAATTAAATCATCAATGAATTATTAACTAT
1 TAATTAAATCAT-AATAAATTATAAATTAT
37505 TA
1 TA
37507 TTATCTCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 14 0.30
29 20 0.43
30 7 0.15
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (29 bp):
TAATTAAATCATAATAAATTATAAATTAT
Found at i:37770 original size:22 final size:23
Alignment explanation
Indices: 37742--37790 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
37732 ATTATTAAAT
*
37742 ATATTAACTTA-TATAATA-TATA
1 ATATTAACTAATTATAATACTA-A
37764 ATATTAACTAATTATAATACTAA
1 ATATTAACTAATTATAATACTAA
37787 ATAT
1 ATAT
37791 AACATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
23 12 0.50
24 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTAACTAATTATAATACTAA
Found at i:38166 original size:22 final size:21
Alignment explanation
Indices: 38131--38195 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
38121 TATAATAGTT
38131 AATTATTTTAATAATTAATACA
1 AATTATTTT-ATAATTAATACA
* * *
38153 AATTATTCTTATAAATCATATA
1 AATTATT-TTATAATTAATACA
*
38175 AATTATAATTATACATTAATA
1 AATTAT-TTTATA-ATTAATA
38196 TATTATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTATTTTATAATTAATACA
Found at i:38221 original size:18 final size:19
Alignment explanation
Indices: 38177--38223 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
38167 ATCATATAAA
38177 TTATAAT-TATACATTAAT
1 TTATAATATATACATTAAT
* * *
38195 ATATTATATATA-ATTATT
1 TTATAATATATACATTAAT
38213 TTATAATATAT
1 TTATAATATAT
38224 TTAGATATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATAATATATACATTAAT
Found at i:38293 original size:24 final size:23
Alignment explanation
Indices: 38266--38311 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
38256 AACTAATATT
*
38266 TAATTACAAATATTTGATTATTTG
1 TAATAACAAATATTT-ATTATTTG
*
38290 TAATAATAAATATTTATTATTT
1 TAATAACAAATATTTATTATTT
38312 AAATTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
TAATAACAAATATTTATTATTTG
Found at i:38319 original size:23 final size:23
Alignment explanation
Indices: 38273--38329 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 23
38263 ATTTAATTAC
*
38273 AAATATTTGATTATTTGTAATAAT
1 AAATATTT-ATTATTTGAAATAAT
38297 AAATATTTATTATTT-AAAT--T
1 AAATATTTATTATTTGAAATAAT
38317 AATATATTTATTA
1 AA-ATATTTATTA
38330 ATATTTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 3 0.10
21 10 0.32
22 3 0.10
23 7 0.23
24 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
AAATATTTATTATTTGAAATAAT
Found at i:38919 original size:15 final size:16
Alignment explanation
Indices: 38901--38931 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
38891 TAAATATTTT
38901 AATTATTGATT-AATA
1 AATTATTGATTCAATA
38916 AATTATTGATTCAATA
1 AATTATTGATTCAATA
38932 GACTATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (16 bp):
AATTATTGATTCAATA
Found at i:38981 original size:27 final size:27
Alignment explanation
Indices: 38951--39013 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
38941 CATATACATT
* *
38951 AATTATTATACT-ATTTGATTATTATAA
1 AATTATTA-ACTAATTTAATTATAATAA
*
38978 AATTATTAACTAATTTAATTGTAATAA
1 AATTATTAACTAATTTAATTATAATAA
*
39005 ATTTATTAA
1 AATTATTAA
39014 AATATACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (27 bp):
AATTATTAACTAATTTAATTATAATAA
Found at i:39089 original size:21 final size:19
Alignment explanation
Indices: 39065--39122 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
39055 TGTATTATTA
39065 TAAATTAATATTATACTTAAT
1 TAAATTAATATT-TA-TTAAT
*
39086 TAAAATAAATAATTTATTAAT
1 T-AAATTAAT-ATTTATTAAT
*
39107 TATATTAAATATTTAT
1 TAAATT-AATATTTAT
39123 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 9 0.29
21 10 0.32
22 9 0.29
23 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAATTAATATTTATTAAT
Found at i:39353 original size:15 final size:15
Alignment explanation
Indices: 39329--39394 Score: 55
Period size: 15 Copynumber: 4.2 Consensus size: 15
39319 TAATTTATTA
*
39329 AATTAAATATTAATT
1 AATTATATATTAATT
39344 AATTATATATT-ATT
1 AATTATATATTAATT
*
39358 AATT-TACTAATTAATA
1 AATTATA-T-ATTAATT
39374 AATTAACTAATATTAATT
1 AATT-A-T-ATATTAATT
39392 AAT
1 AAT
39395 AACAATGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.05
14 8 0.20
15 13 0.32
16 6 0.15
18 9 0.22
19 2 0.05
20 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATATATTAATT
Found at i:39468 original size:17 final size:17
Alignment explanation
Indices: 39425--39491 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
39415 CAATTGTTTC
39425 TAATAATATTAATT-ATA
1 TAATAA-ATTAATTAATA
* *
39442 TTATATAATTAGTTAATA
1 TAATA-AATTAATTAATA
*
39460 TAATAAATTAAATAATA
1 TAATAAATTAATTAATA
*
39477 T-ATAAATTAAATAAT
1 TAATAAATTAATTAAT
39492 CATTTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
16 14 0.33
17 21 0.49
18 8 0.19
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
TAATAAATTAATTAATA
Found at i:39527 original size:17 final size:17
Alignment explanation
Indices: 39434--39527 Score: 59
Period size: 17 Copynumber: 5.4 Consensus size: 17
39424 CTAATAATAT
* *
39434 TAATTATATTATATAAT
1 TAATTATATAATATAAA
*
39451 TAGTTAATATAATAAATTAAA
1 TAATT-ATATAAT--A-TAAA
39472 TAA-TATATAA-ATTAAA
1 TAATTATATAATA-TAAA
* * *
39488 TAATCATTTAAAATAAA
1 TAATTATATAATATAAA
39505 -ATATTATATAATATAAA
1 TA-ATTATATAATATAAA
39522 TAATTA
1 TAATTA
39528 ATCTTATTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
16 10 0.17
17 29 0.48
18 8 0.13
19 6 0.10
20 2 0.03
21 5 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
TAATTATATAATATAAA
Found at i:39702 original size:10 final size:9
Alignment explanation
Indices: 39683--39790 Score: 55
Period size: 10 Copynumber: 11.4 Consensus size: 9
39673 CATAAAACTA
39683 ATAATAATT
1 ATAATAATT
39692 ATAACTAATT
1 ATAA-TAATT
39702 AT--TAATT
1 ATAATAATT
39709 A-AAT-ATT
1 ATAATAATT
* *
39716 TTACTTATATT
1 ATA-ATA-ATT
*
39727 ATTAATAAATC
1 A-TAAT-AATT
39738 ATAATATATT
1 ATAATA-ATT
*
39748 ATATTATATT
1 ATAATA-ATT
39758 -TAATAATT
1 ATAATAATT
39766 ATATATAAATT
1 ATA-AT-AATT
39777 ATAACTAATT
1 ATAA-TAATT
39787 ATAA
1 ATAA
39791 AATATTAATT
Statistics
Matches: 77, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
7 9 0.12
8 5 0.06
9 12 0.16
10 33 0.43
11 15 0.19
12 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (9 bp):
ATAATAATT
Found at i:40001 original size:26 final size:29
Alignment explanation
Indices: 39972--40027 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 29
39962 ACATTATATT
39972 TTATAAAAAATTATTT-AT-AAT-TAATA
1 TTATAAAAAATTATTTCATAAATATAATA
* *
39998 TTATATATAATTATTTCATAAATATAATA
1 TTATAAAAAATTATTTCATAAATATAATA
40027 T
1 T
40028 AATTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.56
27 2 0.08
28 3 0.12
29 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TTATAAAAAATTATTTCATAAATATAATA
Found at i:40027 original size:22 final size:21
Alignment explanation
Indices: 39995--40077 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 21
39985 TTTATAATTA
39995 ATAT-TAT-ATATAATTATTT
1 ATATATATAATATAATTATTT
*
40014 CATAAATATAATATAATTTATTT
1 -ATATATATAATATAA-TTATTT
*
40037 ATATATA-ATATATAATTATAT
1 ATATATATA-ATATAATTATTT
*
40058 ATATAGATAATATATATTAT
1 ATATATATAATATA-ATTAT
40078 AGTAAATAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.06
21 20 0.38
22 24 0.45
23 6 0.11
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
ATATATATAATATAATTATTT
Found at i:40044 original size:15 final size:17
Alignment explanation
Indices: 39987--40074 Score: 63
Period size: 16 Copynumber: 5.8 Consensus size: 17
39977 AAAAATTATT
*
39987 TATAATTA-ATATTATA
1 TATAATTATATATAATA
*
40003 TATAATTATTTCATAA-A
1 TATAATTATAT-ATAATA
40020 TATAA-TATA-AT--T-
1 TATAATTATATATAATA
40032 TAT--TTATATATAATA
1 TATAATTATATATAATA
40047 TATAATTATATAT-ATA
1 TATAATTATATATAATA
*
40063 GATAA-TATATAT
1 TATAATTATATAT
40075 TATAGTAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
11 4 0.07
12 5 0.09
14 3 0.05
15 10 0.17
16 18 0.31
17 15 0.26
18 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (17 bp):
TATAATTATATATAATA
Found at i:40294 original size:14 final size:14
Alignment explanation
Indices: 40277--40335 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
40267 TATAGATAAA
*
40277 AATTAATACATTAT
1 AATTAATAAATTAT
40291 AATTAATAAATTAT
1 AATTAATAAATTAT
*
40305 ATAGT-ATAAA-T-T
1 A-ATTAATAAATTAT
*
40317 AATTATTAAATTAT
1 AATTAATAAATTAT
40331 -ATTAA
1 AATTAA
40336 GTAATTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
11 2 0.06
12 6 0.17
13 6 0.17
14 20 0.56
15 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
AATTAATAAATTAT
Done.