Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002783.1 Hibiscus syriacus cultivar Beakdansim tig00005737_pilon, 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: 105818
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:5037 original size:23 final size:23
Alignment explanation
Indices: 5011--5071 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
5001 CAATCTTATA
5011 TGGCACTAT-AGTGCAATTCTACG
1 TGGCACT-TCAGTGCAATTCTACG
*
5034 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTCTACG
*
5057 TGGCACTTCGGTGCA
1 TGGCACTTCAGTGCA
5072 TTTATATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTCTACG
Found at i:6837 original size:13 final size:13
Alignment explanation
Indices: 6819--6843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6809 CTTAATATAT
6819 AAATAATAAAAAG
1 AAATAATAAAAAG
6832 AAATAATAAAAA
1 AAATAATAAAAA
6844 TAAAAGAAAA
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAATAATAAAAAG
Found at i:6845 original size:19 final size:20
Alignment explanation
Indices: 6812--6852 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
6802 AATATAACTT
6812 AATATATAAATAATAAAAAGA
1 AATATATAAATAAT-AAAAGA
6833 AATA-ATAAA-AATAAAAGA
1 AATATATAAATAATAAAAGA
6851 AA
1 AA
6853 AATTATCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 5 0.25
21 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (20 bp):
AATATATAAATAATAAAAGA
Found at i:6955 original size:30 final size:29
Alignment explanation
Indices: 6917--6973 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
6907 AAAAAAATGA
6917 TTTTAAAATCGA-TTTAAAAACTATATAAG
1 TTTTAAAAT-GATTTTAAAAACTATATAAG
* *
6946 TTTTCAAAATTATTTTTAAAACTATATA
1 TTTT-AAAATGATTTTAAAAACTATATA
6974 TTATATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTTAAAATGATTTTAAAAACTATATAAG
Found at i:6986 original size:35 final size:34
Alignment explanation
Indices: 6940--7047 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 34
6930 TTAAAAACTA
*
6940 TATAAGTTTTCAAAATTATTTTTAAAACTATATAT
1 TATATGTTTTCAAAATT-TTTTTAAAACTATATAT
*
6975 TATATGTTTTCAAAATTTTCTTTAAAACTATATAC
1 TATATGTTTTCAAAATTTT-TTTAAAACTATATAT
* *
7010 TATATG-TTTCAAAATGGTTTTAAAAACTATATAT
1 TATATGTTTTCAAAAT-TTTTTTAAAACTATATAT
7044 TATA
1 TATA
7048 CATTTTTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
34 28 0.42
35 38 0.58
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (34 bp):
TATATGTTTTCAAAATTTTTTTAAAACTATATAT
Found at i:23224 original size:4 final size:4
Alignment explanation
Indices: 23215--23245 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
23205 ACTGTTTAAC
23215 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
23246 ACATGGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:24654 original size:20 final size:20
Alignment explanation
Indices: 24629--24683 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
24619 AAATTTTGAA
24629 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
24649 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
*
24669 GGTGCATCAATGCAT
1 GGTGCATCGATGCAT
24684 GAATATTTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.25
Consensus pattern (20 bp):
GGTGCATCGATGCATTAAGG
Found at i:25086 original size:17 final size:16
Alignment explanation
Indices: 25057--25088 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
25047 ATGTATGTTA
25057 TTACATGTTACATGAT
1 TTACATGTTACATGAT
25073 TTACATGCTTACATGA
1 TTACATG-TTACATGA
25089 AAATGCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (16 bp):
TTACATGTTACATGAT
Found at i:25467 original size:31 final size:31
Alignment explanation
Indices: 25356--25464 Score: 173
Period size: 31 Copynumber: 3.5 Consensus size: 31
25346 AGGGTCGAGG
*
25356 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
*
25387 GTTTACCTATGTTATTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
*
25418 GTTTACCTATGTTCTTTGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
* *
25449 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
25465 TGGAATCTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATT
Found at i:25476 original size:31 final size:31
Alignment explanation
Indices: 25358--25479 Score: 120
Period size: 31 Copynumber: 3.9 Consensus size: 31
25348 GGTCGAGGGT
* * * * *
25358 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTAGGTTCTTTGGAACATATGGATTGA
* * * * *
25389 TTACCTATGTTATTCGGGACATATGGATTGT
1 TTACCTAGGTTCTTTGGAACATATGGATTGA
* *
25420 TTACCTATGTTCTTTGGGACATATGGATTGA
1 TTACCTAGGTTCTTTGGAACATATGGATTGA
25451 TTACCTAGGTTCTTTGGAATC-TATGGATT
1 TTACCTAGGTTCTTTGGAA-CATATGGATT
25480 AGTTCTTCGG
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 82 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (31 bp):
TTACCTAGGTTCTTTGGAACATATGGATTGA
Found at i:25476 original size:62 final size:62
Alignment explanation
Indices: 25356--25479 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
25346 AGGGTCGAGG
* * *
25356 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTATTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTATTCGGAACATATGGATT
* * * *
25418 GTTTACCTATGTTCTTTGGGACATATGGATTGATTACCTAGGTTCTTTGGAATC-TATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTATTCGGAA-CATATGGATT
25480 AGTTCTTCGG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 53 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTATTCGGAACATATGGATT
Found at i:36429 original size:32 final size:33
Alignment explanation
Indices: 36393--36455 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
36383 GTTTATTATT
* *
36393 ATTAAAATATTAT-TAGCAATAAAAATATTAAG
1 ATTAAAACATTATATAGAAATAAAAATATTAAG
* *
36425 ATTAATACATTATATTGAAATAAAAATATTA
1 ATTAAAACATTATATAGAAATAAAAATATTA
36456 TAAATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (33 bp):
ATTAAAACATTATATAGAAATAAAAATATTAAG
Found at i:36749 original size:23 final size:24
Alignment explanation
Indices: 36700--36767 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
36690 TATCTTATAT
** *
36700 TATATTATTATAATA-TAATTGAG
1 TATATTATTATAATATTAATAAAA
36723 TATATTATTATAATATTAA-AAAA
1 TATATTATTATAATATTAATAAAA
* *
36746 TATAATATTATATTATTAATAA
1 TATATTATTATAATATTAATAA
36768 TTAATAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 33 0.87
24 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
TATATTATTATAATATTAATAAAA
Found at i:36777 original size:30 final size:30
Alignment explanation
Indices: 36728--36803 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
36718 TTGAGTATAT
*
36728 TATTA-TAAT-ATTAAAAAATATAATATT-A
1 TATTATTAATAATTAATAAATAT-ATATTAA
*
36756 TATTATTAATAATTAATAAATATATTTTAAA
1 TATTATTAATAATTAATAAATATATATT-AA
36787 TATT-TTAATAATTAATA
1 TATTATTAATAATTAATA
36804 TTTTTATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 5 0.12
29 8 0.19
30 24 0.57
31 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TATTATTAATAATTAATAAATATATATTAA
Found at i:36788 original size:22 final size:22
Alignment explanation
Indices: 36754--36807 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
36744 AATATAATAT
36754 TATATTATTAATA-ATTAATAAA
1 TATATT-TTAATATATTAATAAA
* *
36776 TATATTTTAAATATTTTAATAAT
1 TATATTTT-AATATATTAATAAA
36799 TAATATTTT
1 T-ATATTTT
36808 TATAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 10 0.37
23 8 0.30
24 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATATTTTAATATATTAATAAA
Found at i:44723 original size:22 final size:22
Alignment explanation
Indices: 44681--44726 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
44671 TAATTTACCA
*
44681 TTTTATAGTTTGTTATGTATTT
1 TTTTATAGTTTGTTATATATTT
*
44703 TTTTAATAGTTTTTTA-ATATTT
1 TTTT-ATAGTTTGTTATATATTT
44725 TT
1 TT
44727 AATATGAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTATAGTTTGTTATATATTT
Found at i:49132 original size:13 final size:13
Alignment explanation
Indices: 49114--49144 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
49104 ACCTTGATCA
*
49114 GATTGAATAGGAG
1 GATTGAATAAGAG
49127 GATTGAATAAGAG
1 GATTGAATAAGAG
49140 GATTG
1 GATTG
49145 CGATTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (13 bp):
GATTGAATAAGAG
Found at i:49702 original size:2 final size:2
Alignment explanation
Indices: 49695--49729 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
49685 ATTAAATTCC
49695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49730 CCTACTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50993 original size:24 final size:23
Alignment explanation
Indices: 50966--51024 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
50956 GATTACATTT
50966 ATATTTATATATATATAAT-ATTAC
1 ATATTTATAT-TAT-TAATAATTAC
*
50990 ATATTTA-ATTATTAATAATTTC
1 ATATTTATATTATTAATAATTAC
51012 ATATATTATATTA
1 ATAT-TTATATTA
51025 AACTAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 4 0.13
22 11 0.35
23 5 0.16
24 11 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTATATTATTAATAATTAC
Found at i:59510 original size:18 final size:18
Alignment explanation
Indices: 59483--59519 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59473 GCTATACAAG
* *
59483 TGTGACTATTTCGAGACT
1 TGTGAATATTCCGAGACT
59501 TGTGAATATTCCGAGACT
1 TGTGAATATTCCGAGACT
59519 T
1 T
59520 ATGCCAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
TGTGAATATTCCGAGACT
Found at i:60686 original size:33 final size:32
Alignment explanation
Indices: 60615--60701 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
60605 TAGTTTTTAT
* *
60615 TATTATAAGATTTATAAATAT-TTAATATTAG
1 TATTATAAGATTTATAAAAATATTAATATTAA
*
60646 TATTATAAGATTTATAATAAATATTAATTTTAA
1 TATTATAAGATTTATAA-AAATATTAATATTAA
*
60679 -ATATATAAAATTTATGAAAAATA
1 TAT-TATAAGATTTAT-AAAAATA
60702 ATATTTTTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 17 0.35
32 5 0.10
33 24 0.50
34 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (32 bp):
TATTATAAGATTTATAAAAATATTAATATTAA
Found at i:60702 original size:16 final size:16
Alignment explanation
Indices: 60683--60732 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
60673 TTTTAAATAT
60683 ATAAAATTTATGAAAA
1 ATAAAATTTATGAAAA
* *
60699 ATAATATTTTTGATAATA
1 ATAAAATTTATGA-AA-A
60717 A-AAAA-TTATGAAAA
1 ATAAAATTTATGAAAA
60731 AT
1 AT
60733 TTATTTATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 16 0.59
17 5 0.19
18 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
ATAAAATTTATGAAAA
Found at i:60894 original size:25 final size:23
Alignment explanation
Indices: 60830--60894 Score: 57
Period size: 25 Copynumber: 2.9 Consensus size: 23
60820 CAAATTATGG
*
60830 CAAATTTATATAGTCATAA-TGA
1 CAAATTTATTTAGTCATAATTGA
*
60852 C-AA-TTATTT-GTAACTAATTGTAA
1 CAAATTTATTTAGTCA-TAATTG--A
60875 CAAATTTATTTAGTCATAAT
1 CAAATTTATTTAGTCATAAT
60895 AATATATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 3 0.09
20 8 0.24
21 4 0.12
22 1 0.03
23 2 0.06
24 2 0.06
25 10 0.30
26 3 0.09
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (23 bp):
CAAATTTATTTAGTCATAATTGA
Found at i:60910 original size:23 final size:23
Alignment explanation
Indices: 60882--60926 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
60872 TAACAAATTT
* *
60882 ATTTAGTCATAATAATATATTAA
1 ATTTAGTCAAAATAATAAATTAA
60905 ATTTAGTCAAAATAATAAATTA
1 ATTTAGTCAAAATAATAAATTA
60927 TGTCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTTAGTCAAAATAATAAATTAA
Found at i:60980 original size:145 final size:146
Alignment explanation
Indices: 60729--60998 Score: 373
Period size: 145 Copynumber: 1.9 Consensus size: 146
60719 AAATTATGAA
*
60729 AAATTTATTTATTCATAACAACATATTAAATTTAATAAAAATAAAAAATATTATGTCAAATTTAT
1 AAATTTATTTAGTCATAACAACATATTAAATTTAATAAAAATAAAAAATATTATGTCAAATTTAT
* * * * * *
60794 TTAGTCACAATATTTTCTTAAAATAACAAATTATGGCAAATTTATATAGTCATAATGACAATTAT
66 TTAGTCACAATATTTTCTCAAAATAACAAATGAT-GAAAAATTATATAGTCAAAATAACAATTAT
60859 TTGTAACTAATTGTAAC
130 TTGTAACTAATTGTAAC
* * * * * *
60876 AAATTTATTTAGTCATAATAATATATTAAATTTAGTCAAAAT-AATAA-ATTATGTCAAATTTGT
1 AAATTTATTTAGTCATAACAACATATTAAATTTAATAAAAATAAAAAATATTATGTCAAATTTAT
* * *
60939 TTTGTCACAATATTTTCTCAAAATAATAAATGATGAAAAATTATTTAGTCAAAATAACAA
66 TTAGTCACAATATTTTCTCAAAATAACAAATGATGAAAAATTATATAGTCAAAATAACAA
60999 ATGACAATAA
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
144 21 0.20
145 45 0.42
146 4 0.04
147 37 0.35
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (146 bp):
AAATTTATTTAGTCATAACAACATATTAAATTTAATAAAAATAAAAAATATTATGTCAAATTTAT
TTAGTCACAATATTTTCTCAAAATAACAAATGATGAAAAATTATATAGTCAAAATAACAATTATT
TGTAACTAATTGTAAC
Found at i:66403 original size:19 final size:20
Alignment explanation
Indices: 66366--66413 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
66356 TCTAAATCCT
*
66366 TTTTCAAAATTTCATTTTAG
1 TTTTCAAAATCTCATTTTAG
66386 TTTTCAAAATCT-ATTTTAG
1 TTTTCAAAATCTCATTTTAG
*
66405 CTTTCAAAA
1 TTTTCAAAA
66414 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTAG
Found at i:73846 original size:14 final size:16
Alignment explanation
Indices: 73815--73851 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
73805 AACCTGAATC
73815 GAGAGAGCAGAGATTA
1 GAGAGAGCAGAGATTA
*
73831 GAGAGAG-ATAGA-TA
1 GAGAGAGCAGAGATTA
73845 GAGAGAG
1 GAGAGAG
73852 GGAATGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.46, C:0.03, G:0.41, T:0.11
Consensus pattern (16 bp):
GAGAGAGCAGAGATTA
Found at i:74436 original size:14 final size:14
Alignment explanation
Indices: 74417--74444 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
74407 GAGTTCAAAG
74417 AAAGACATAGTAGT
1 AAAGACATAGTAGT
74431 AAAGACATAGTAGT
1 AAAGACATAGTAGT
74445 TAATTCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAGACATAGTAGT
Found at i:79858 original size:194 final size:188
Alignment explanation
Indices: 79530--79914 Score: 619
Period size: 194 Copynumber: 2.0 Consensus size: 188
79520 ATTACAAATC
* * *
79530 GACAATATCAGTGACCTAATTTTTACTTTTAAAATTTTAGTAGTTAAAAAACTTACTCAAACATC
1 GACAATATCAGTGACATAATTTTTACTTTTAAAACTTTAGTAGTAAAAAAACTTACTCAAACATC
79595 AATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAAGC
66 AATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAAGC
* *
79660 TAAAAACTTATGGTCAAAATGTTTTTTTTTATAAAAAAAATTTGGGGATAAAGAATGTCATTA
131 TAAAAACTTAAGGTCAAAATGATTTTTTTT-T----AAAATTTGGGGATAAAGAATGTCATTA
*
79723 GACAATATTAGTGACAT-ATTTGTTACTTTTAAAACTTTAGTAGGTAAAAAAACTTACTCAAACA
1 GACAATATCAGTGACATAATTT-TTACTTTTAAAACTTTAGTA-GTAAAAAAACTTACTCAAACA
*
79787 TCAATGATTATTTTTGTAATTTACCCTAAAATATCATCATTTAGTTTAATTCGAGGTCAAAAGAA
64 TCAATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAA
* *
79852 GCTAAAAACTTAAGGTTAAAATGATTTTTTTTTAAATTTTGGGGATAAAGAATGTCATTA
129 GCTAAAAACTTAAGGTCAAAATGATTTTTTTTTAAAATTTGGGGATAAAGAATGTCATTA
79912 GAC
1 GAC
79915 CTATTTTTTC
Statistics
Matches: 181, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
189 29 0.16
192 4 0.02
193 35 0.19
194 113 0.62
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (188 bp):
GACAATATCAGTGACATAATTTTTACTTTTAAAACTTTAGTAGTAAAAAAACTTACTCAAACATC
AATGATTATTTTTGTAATTTACCCTAAAATACCATCATTTAGTTTAATTCGAGGTCAAAAGAAGC
TAAAAACTTAAGGTCAAAATGATTTTTTTTTAAAATTTGGGGATAAAGAATGTCATTA
Found at i:80194 original size:40 final size:40
Alignment explanation
Indices: 80150--80272 Score: 194
Period size: 40 Copynumber: 3.1 Consensus size: 40
80140 TTTAAGTTGA
80150 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
1 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
* *
80190 AATCGAAAATATTGTCTATTTCGTAATATTTTAGG-TTGA
1 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
* * *
80229 AATCGAAAATATTGTATATTTCGTAATATTTCTGGTTTAT
1 AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
80269 AATC
1 AATC
80273 TAATTATAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
39 35 0.47
40 40 0.53
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (40 bp):
AATCGAAAATATTGTCTATTTCGTAATATTTTTGGTTTGT
Found at i:80249 original size:39 final size:39
Alignment explanation
Indices: 80133--80259 Score: 200
Period size: 39 Copynumber: 3.2 Consensus size: 39
80123 GTTAGACATA
* *
80133 GTAACATTTTAAGTTGAAATCGAAAATATTGTCTATTTC
1 GTAATATTTTAGGTTGAAATCGAAAATATTGTCTATTTC
* *
80172 GTAATATTTTTGGTTTGTAATCGAAAATATTGTCTATTTC
1 GTAATATTTTAGG-TTGAAATCGAAAATATTGTCTATTTC
*
80212 GTAATATTTTAGGTTGAAATCGAAAATATTGTATATTTC
1 GTAATATTTTAGGTTGAAATCGAAAATATTGTCTATTTC
80251 GTAATATTT
1 GTAATATTT
80260 CTGGTTTATA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 43 0.54
40 37 0.46
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (39 bp):
GTAATATTTTAGGTTGAAATCGAAAATATTGTCTATTTC
Found at i:83349 original size:16 final size:16
Alignment explanation
Indices: 83328--83360 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
83318 TACTATATAT
83328 ATATAATATTTAGAAC
1 ATATAATATTTAGAAC
83344 ATATAATATTTAGAAC
1 ATATAATATTTAGAAC
83360 A
1 A
83361 CAGGAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (16 bp):
ATATAATATTTAGAAC
Found at i:88392 original size:31 final size:31
Alignment explanation
Indices: 88339--88422 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
88329 TCATTATAAT
* *
88339 AAAT-TATGTT-TA-GATTTAAATATGTGAA
1 AAATATATGTTATATGATTTGAATATATGAA
88367 AAATATATGTTATATGATTTGAATATATGAA
1 AAATATATGTTATATGATTTGAATATATGAA
* * *
88398 CAATACATGTTATATGGTTTGAATA
1 AAATATATGTTATATGATTTGAATA
88423 AAGTAAATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 4 0.08
29 6 0.12
30 2 0.04
31 36 0.75
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (31 bp):
AAATATATGTTATATGATTTGAATATATGAA
Found at i:90537 original size:19 final size:19
Alignment explanation
Indices: 90513--90559 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
90503 AAGAGCCAGG
*
90513 AGTGCATCGTTGCATGGTC
1 AGTGCATCGATGCATGGTC
90532 AGTGCATCGATGCATGGTC
1 AGTGCATCGATGCATGGTC
*
90551 TGTGCATCG
1 AGTGCATCG
90560 GTACATAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (19 bp):
AGTGCATCGATGCATGGTC
Found at i:92557 original size:44 final size:44
Alignment explanation
Indices: 92452--92558 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
92442 CGATGCACTG
* * * * *
92452 CATAGTGTATCGATGGACATTTAAGGCATGCATTGGTGCACCTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
* *
92496 CATAGTGTATCGATGCATATTCAAGGGATGCATCGGTACACTTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
*
92540 CATAGTGTATCAATGCATA
1 CATAGTGTATCGATGCATA
92559 GTGTACAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (44 bp):
CATAGTGTATCGATGCATATTCAAGGCATGCATCGGTACACCTT
Found at i:96220 original size:20 final size:21
Alignment explanation
Indices: 96181--96220 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
96171 GAAGCTTTAA
* *
96181 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
96202 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
96221 AAGTAGGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:99621 original size:22 final size:20
Alignment explanation
Indices: 99576--99657 Score: 80
Period size: 22 Copynumber: 4.0 Consensus size: 20
99566 AATGCAATTA
99576 ATGCATCGATGCA--TAAGG
1 ATGCATCGATGCACTTAAGG
99594 AGTGCATCGATGCACATTAAGGG
1 A-TGCATCGATGCAC-TTAA-GG
* *
99617 ATGCATCGATACACTGT-AGA
1 ATGCATCGATGCACT-TAAGG
99637 ATGCATCGATGCACTTCAAGG
1 ATGCATCGATGCACTT-AAGG
99658 GAAATTGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.02
19 13 0.25
20 15 0.29
21 4 0.08
22 16 0.31
23 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (20 bp):
ATGCATCGATGCACTTAAGG
Found at i:101242 original size:23 final size:23
Alignment explanation
Indices: 101185--101252 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
101175 CATTTTATAT
* *
101185 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTTGGTGCATTTCTACGC
**
101208 GGCACTACGGTGCATTTCTACGC
1 GGCACTTTGGTGCATTTCTACGC
*
101231 GGCACTTTGGTGCATTTATACG
1 GGCACTTTGGTGCATTTCTACG
101253 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTTGGTGCATTTCTACGC
Found at i:103007 original size:65 final size:65
Alignment explanation
Indices: 102913--103069 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
102903 TACACTTGGG
* * * * *
102913 GTGCATCGGTACACT-AATTACATTTGATGTTTCAA-AAGAGGCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACA-TAAAATACATTCGATGTTTCAATAA-AAGCACGAGTGCATCGATACATGGT
102976 CT
64 CT
* * * *
102978 GTGCATCGGTACATAAAATGCATTCGATGTTTTAATAAAATCACGAGTGCATCGATACATGGTTT
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAATAAAAGCACGAGTGCATCGATACATGGTCT
* *
103043 GTGCACCGGTACACAAAATACATTCGA
1 GTGCATCGGTACATAAAATACATTCGA
103070 ATTAGGATGT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 1 0.01
65 75 0.96
66 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACATAAAATACATTCGATGTTTCAATAAAAGCACGAGTGCATCGATACATGGTCT
Done.