Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001967.1 Hibiscus syriacus cultivar Beakdansim tig00003975_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: 94565
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5342 original size:26 final size:28
Alignment explanation
Indices: 5309--5373 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
5299 GTCCCCGTGA
* *
5309 TTTT-CTAAGTTTTTA-TATA-AATTTT
1 TTTTACTAAGTTTTTATTATATAATATG
*
5334 TTTTACTAAG-TTTTATTGTATAATATG
1 TTTTACTAAGTTTTTATTATATAATATG
5361 TTTTACTAAGTTT
1 TTTTACTAAGTTT
5374 AATATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 9 0.27
26 8 0.24
27 14 0.42
28 2 0.06
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.60
Consensus pattern (28 bp):
TTTTACTAAGTTTTTATTATATAATATG
Found at i:8684 original size:31 final size:30
Alignment explanation
Indices: 8604--8685 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
8594 AGTACACTCG
* *
8604 TAATAATAAATACTAAAAAAATTAGACCCT
1 TAATAACAAATATTAAAAAAATTAGACCCT
* ** *
8634 TGATAACAGGTATTGAAAAAATTAGACCCT
1 TAATAACAAATATTAAAAAAATTAGACCCT
*
8664 TAATAACAAATGTTAAAAAAAT
1 TAATAACAAATATTAAAAAAAT
8686 GATGACAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.27
Consensus pattern (30 bp):
TAATAACAAATATTAAAAAAATTAGACCCT
Found at i:8809 original size:33 final size:30
Alignment explanation
Indices: 8749--8829 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 30
8739 ATAAGTCTCC
* *
8749 AATAATAAATATTAGAAAAAATGAACCCAT
1 AATAATAAATATTAAAAAAAAAGAACCCAT
*
8779 AATAATAAATATTAAAAACAAAAGCAAACCCTT
1 AATAATAAATATTAAAAA-AAAAG--AACCCAT
*
8812 AATAACAAATATTAAAAA
1 AATAATAAATATTAAAAA
8830 TCATTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 17 0.39
31 4 0.09
33 23 0.52
ACGTcount: A:0.63, C:0.11, G:0.04, T:0.22
Consensus pattern (30 bp):
AATAATAAATATTAAAAAAAAAGAACCCAT
Found at i:8940 original size:59 final size:59
Alignment explanation
Indices: 8868--8986 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 59
8858 AAAAAATTAC
* * *
8868 GGCCCTAGGCAAGTACCTCTCCTGCCCAAGCCCAAATACGACCTTGGGTATCATTAGAA
1 GGCCCTAGGCAAGTACCCCTCCTACCCAAGCCCAAATACGACCCTGGGTATCATTAGAA
* * *
8927 GGCCCTGGGCAAGTGCCCCTCCTACCCAAGCCCAAATACGACCCTGGGTATCGTTAGAA
1 GGCCCTAGGCAAGTACCCCTCCTACCCAAGCCCAAATACGACCCTGGGTATCATTAGAA
8986 G
1 G
8987 ACGTTAGTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.18
Consensus pattern (59 bp):
GGCCCTAGGCAAGTACCCCTCCTACCCAAGCCCAAATACGACCCTGGGTATCATTAGAA
Found at i:13007 original size:2 final size:2
Alignment explanation
Indices: 13000--13033 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12990 TCTTTCAGTT
13000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13034 CACCATGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14696 original size:11 final size:11
Alignment explanation
Indices: 14680--14718 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
14670 AAATTATCTT
14680 TATTAAGTAAA
1 TATTAAGTAAA
*
14691 TATTAA-AAAGA
1 TATTAAGTAA-A
14702 TATTAAGTAAA
1 TATTAAGTAAA
14713 TATTAA
1 TATTAA
14719 AAGGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
TATTAAGTAAA
Found at i:14706 original size:22 final size:22
Alignment explanation
Indices: 14680--14725 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
14670 AAATTATCTT
14680 TATTAAGTAAATATTAAAAAGA
1 TATTAAGTAAATATTAAAAAGA
*
14702 TATTAAGTAAATATTAAAAGGA
1 TATTAAGTAAATATTAAAAAGA
14724 TA
1 TA
14726 AATTACACGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.33
Consensus pattern (22 bp):
TATTAAGTAAATATTAAAAAGA
Found at i:15453 original size:21 final size:21
Alignment explanation
Indices: 15415--15468 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
15405 CGAAATAATA
* *
15415 AAAAAAATAGT-ATTTTTATTC
1 AAAAAAATAATGA-TTTAATTC
*
15436 AATAAAAATAATGATTTAATTG
1 AA-AAAAATAATGATTTAATTC
15458 AAAAAAATAAT
1 AAAAAAATAAT
15469 ATATAGAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 11 0.39
22 16 0.57
23 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAAAAATAATGATTTAATTC
Found at i:18860 original size:29 final size:30
Alignment explanation
Indices: 18800--18873 Score: 141
Period size: 29 Copynumber: 2.5 Consensus size: 30
18790 AAATGTTTGT
18800 AATTGACTCCATATTTGTTTTTTTATTAAC
1 AATTGACTCCATATTTGTTTTTTTATTAAC
18830 AATTGACTCCATATTTG-TTTTTTATTAAC
1 AATTGACTCCATATTTGTTTTTTTATTAAC
18859 AATTGACTCCATATT
1 AATTGACTCCATATT
18874 CAATATCCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 27 0.61
30 17 0.39
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (30 bp):
AATTGACTCCATATTTGTTTTTTTATTAAC
Found at i:24624 original size:31 final size:32
Alignment explanation
Indices: 24583--24652 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
24573 GGTCAAGTTG
* * *
24583 AGATCTAGTGGATGATATAT-GTTTTTGGGTC
1 AGATCGAGTGGATGATATATAATTTTTGAGTC
24614 AGATCGAGTGGATGATATATAATTTTTGAGTC
1 AGATCGAGTGGATGATATATAATTTTTGAGTC
24646 AGATCGA
1 AGATCGA
24653 ATTCGAATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 19 0.54
32 16 0.46
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (32 bp):
AGATCGAGTGGATGATATATAATTTTTGAGTC
Found at i:28265 original size:17 final size:17
Alignment explanation
Indices: 28243--28276 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28233 TTTACTCGGA
* *
28243 TGATGTTGTGTTTTTCT
1 TGATGTCGTGTTCTTCT
28260 TGATGTCGTGTTCTTCT
1 TGATGTCGTGTTCTTCT
28277 GGGGAACTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.59
Consensus pattern (17 bp):
TGATGTCGTGTTCTTCT
Found at i:38357 original size:60 final size:60
Alignment explanation
Indices: 38275--38387 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
38265 AATGATCCTT
*
38275 TGACTATAAGATAATGTTTTGTTGAGT-TCGTTGACTATAAAAAGTTACAAAATGGTCCCC
1 TGACTATAAGATAATGCTTTGTTGAGTCTC-TTGACTATAAAAAGTTACAAAATGGTCCCC
* *
38335 TGACTATAGGA-AATTGCTTTGTTGAGTCTCTTGACTATTAAAAGTTACAAAAT
1 TGACTATAAGATAA-TGCTTTGTTGAGTCTCTTGACTATAAAAAGTTACAAAAT
38388 AGTCATTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
59 2 0.04
60 44 0.92
61 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (60 bp):
TGACTATAAGATAATGCTTTGTTGAGTCTCTTGACTATAAAAAGTTACAAAATGGTCCCC
Found at i:39411 original size:2 final size:2
Alignment explanation
Indices: 39404--39466 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
39394 CAATAATTAA
39404 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39446 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
39467 CCAAATTCAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45600 original size:20 final size:20
Alignment explanation
Indices: 45577--45615 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
45567 CATTTAGTAC
45577 CTAAACTATCAATTTTGATT
1 CTAAACTATCAATTTTGATT
*
45597 CTAAACTATCCATTTTGAT
1 CTAAACTATCAATTTTGAT
45616 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (20 bp):
CTAAACTATCAATTTTGATT
Found at i:45632 original size:31 final size:31
Alignment explanation
Indices: 45597--45662 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
45587 AATTTTGATT
*
45597 CTAAACTATCCATTTTGATATATTTTAATAC
1 CTAAACTATCAATTTTGATATATTTTAATAC
* * *
45628 CTAAATTATCAATTTTGATCTGTTTTAATAC
1 CTAAACTATCAATTTTGATATATTTTAATAC
45659 CTAA
1 CTAA
45663 CTTCCACGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (31 bp):
CTAAACTATCAATTTTGATATATTTTAATAC
Found at i:47877 original size:141 final size:141
Alignment explanation
Indices: 47518--47867 Score: 468
Period size: 141 Copynumber: 2.5 Consensus size: 141
47508 CCTAAAGGAC
* * * * * *
47518 TAAACCTAAAAATGGAGGCTCTAATACTAATCCTAATCGA-TTTTAACCAATTATTGAGTCGAAT
1 TAAACCT-AAAGTGAAGGCTCTAATATTAATCATAATC-ACTTTTATCCAATTATTGAATCGAAT
* * *
47582 AATCAATGTGGACCCTCAGACATTTTAATGCAAAGATCAAATTGAATTATTCCCTAAATTAAGGG
64 AATCAACGTGGACCCTCAGACATTTTAATGCAAAGATCAAATCGAATTATTCCCTAAATTAAAGG
47647 ACTAAAGTGAAAT
129 ACTAAAGTGAAAT
* * *
47660 TAAGCCTAAAGTGGAGGCTCTAATATTAATCATAATCATTTTTATCCAATTATTGAATCGAATAA
1 TAAACCTAAAGTGAAGGCTCTAATATTAATCATAATCACTTTTATCCAATTATTGAATCGAATAA
* * ** * *
47725 TCAACGTGGACCCTCGGGCATTTTAATGTGAAGGTCAAATCGAATTATTCCCTAAATTAAAGGAG
66 TCAACGTGGACCCTCAGACATTTTAATGCAAAGATCAAATCGAATTATTCCCTAAATTAAAGGAC
47790 TAAAGTGAAAT
131 TAAAGTGAAAT
* * * * *
47801 TAAATCTAAAGTGAAGGCTCTAATATTAATCATAGTTACTTTTATTCAATTATTGAATCAAATAA
1 TAAACCTAAAGTGAAGGCTCTAATATTAATCATAATCACTTTTATCCAATTATTGAATCGAATAA
47866 TC
66 TC
47868 TAAATGGACC
Statistics
Matches: 184, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
140 1 0.01
141 177 0.96
142 6 0.03
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (141 bp):
TAAACCTAAAGTGAAGGCTCTAATATTAATCATAATCACTTTTATCCAATTATTGAATCGAATAA
TCAACGTGGACCCTCAGACATTTTAATGCAAAGATCAAATCGAATTATTCCCTAAATTAAAGGAC
TAAAGTGAAAT
Found at i:50111 original size:22 final size:23
Alignment explanation
Indices: 50080--50126 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
50070 ATCGATACTT
*
50080 GGGGAAGTATTGATACC-ACAGGA
1 GGGGAAGTATCGATACCTA-AGGA
50103 GGGG-AGTATCGATACCTAAGGA
1 GGGGAAGTATCGATACCTAAGGA
50125 GG
1 GG
50127 AGTATCGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.32, C:0.13, G:0.38, T:0.17
Consensus pattern (23 bp):
GGGGAAGTATCGATACCTAAGGA
Found at i:52783 original size:10 final size:10
Alignment explanation
Indices: 52768--52796 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
52758 TATTTGGGGC
52768 TTCTCTTTCT
1 TTCTCTTTCT
52778 TTCTCTTTCT
1 TTCTCTTTCT
52788 TTCTCTTTC
1 TTCTCTTTC
52797 ATAGCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TTCTCTTTCT
Found at i:54624 original size:4 final size:4
Alignment explanation
Indices: 54615--54643 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
54605 AGTGTATACA
54615 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
54644 TTTAATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:57172 original size:4 final size:4
Alignment explanation
Indices: 57165--57211 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
57155 ACGCACGCAC
* * * *
57165 GTAT GTAT GTAT ATAT ATAT -TAT GTAT GTAT ATAT ATAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
57212 ATATATGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (4 bp):
GTAT
Found at i:57190 original size:19 final size:20
Alignment explanation
Indices: 57165--57217 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
57155 ACGCACGCAC
57165 GTATGTATGTATATATATAT
1 GTATGTATGTATATATATAT
57185 -TATGTATGTATATATATAT
1 GTATGTATGTATATATATAT
*
57204 GTATGTATATATAT
1 GTATGTATGTATAT
57218 GTACATTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
GTATGTATGTATATATATAT
Found at i:58106 original size:2 final size:2
Alignment explanation
Indices: 58099--58129 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58089 ATCAAGCTTT
58099 TA TA 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 TA TA T
58130 TCAACACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67018 original size:2 final size:2
Alignment explanation
Indices: 67011--67035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67001 AAATGAGTAC
67011 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 A
67036 ACATGGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68564 original size:17 final size:18
Alignment explanation
Indices: 68520--68564 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
68510 GCTTTGCCAA
68520 ATCTCAAAGTTTTCCCAC
1 ATCTCAAAGTTTTCCCAC
68538 ATCTCAAAGTTTTCCCAC
1 ATCTCAAAGTTTTCCCAC
68556 ATC-CAAAGT
1 ATCTCAAAGT
68565 GCCAAAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (18 bp):
ATCTCAAAGTTTTCCCAC
Found at i:72799 original size:124 final size:123
Alignment explanation
Indices: 72613--72848 Score: 294
Period size: 124 Copynumber: 1.9 Consensus size: 123
72603 TAACGTTAAG
**
72613 TTTTGAAAAAAAAATTAAAAATTTAAGTACTAAAACAACCAAACTAATAGTTTAGGTACTAAACA
1 TTTTGAAAAAAAAATTAAAAATTTAAGTACTAAAACAACCAAACTAATAGGCTAGGTACTAAACA
* *
72678 CATTAAATTTTCAATGATG-GATACTAAAATGAAACAAAAACTAAACGTTAGACATGA
66 CATTAAATTTTCAACGACGAGATACTAAAATGAAACAAAAACTAAACGTTAGACATGA
* * ** * * *
72735 TTTTTAAAAAAAAATTAAAAGTTTTGGTACTAAATCGGACCAAAACTGATAGGCTAGGTACTAAA
1 TTTTGAAAAAAAAATTAAAAATTTAAGTACTAAAAC-AACC-AAACTAATAGGCTAGGTACTAAA
* * * * * *
72800 CGCGTTAAGTTTTTAACGACGAGATACTAAAATGAAATAAAAATTAAAC
64 CACATTAAATTTTCAACGACGAGATACTAAAATGAAACAAAAACTAAAC
72849 ATTAAGTATA
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
122 31 0.33
123 3 0.03
124 35 0.37
125 25 0.27
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (123 bp):
TTTTGAAAAAAAAATTAAAAATTTAAGTACTAAAACAACCAAACTAATAGGCTAGGTACTAAACA
CATTAAATTTTCAACGACGAGATACTAAAATGAAACAAAAACTAAACGTTAGACATGA
Found at i:77710 original size:32 final size:34
Alignment explanation
Indices: 77672--77754 Score: 134
Period size: 32 Copynumber: 2.5 Consensus size: 34
77662 TCCCCAAATA
* *
77672 TATATATATAATATTTTTTATTTTTTATATTAA-
1 TATATATATAATATTTTATATATTTTATATTAAT
77705 T-TATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
77738 TATATATATAATATTTT
1 TATATATATAATATTTT
77755 CGGGTTCAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 29 0.63
33 2 0.04
34 15 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:77741 original size:16 final size:16
Alignment explanation
Indices: 77689--77742 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
77679 ATAATATTTT
*
77689 TTATTTTTTATATTAA
1 TTATATTTTATATTAA
* * *
77705 TTATATATAATATT-T
1 TTATATTTTATATTAA
77720 TATATATTTTATATTAA
1 T-TATATTTTATATTAA
77737 TTATAT
1 TTATAT
77743 ATATAATATT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTTTATATTAA
Found at i:79649 original size:29 final size:29
Alignment explanation
Indices: 79603--79672 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
79593 GTGTTGATCG
* *
79603 TAGGTCGCCATGCTATCCGGGTGACCTAC
1 TAGGTCGCCATGCCATCCGGGCGACCTAC
79632 TAGGTCGCCATGCCATCCGGGCGACCTAC
1 TAGGTCGCCATGCCATCCGGGCGACCTAC
79661 TAGGTCGCCATG
1 TAGGTCGCCATG
79673 TCTTCCGACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCATCCGGGCGACCTAC
Found at i:79752 original size:14 final size:14
Alignment explanation
Indices: 79733--79779 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
79723 CGCTGGGTAT
79733 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
79747 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
* *
79761 TCGAGGCTATCCGA
1 CCGAGGCCATCCGA
*
79775 GCGAG
1 CCGAG
79780 CTATGCGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.34, G:0.34, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:79870 original size:29 final size:29
Alignment explanation
Indices: 79828--79911 Score: 159
Period size: 29 Copynumber: 2.9 Consensus size: 29
79818 GGAGCAGGAG
79828 GGAGTGCATGGCGACCTACAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
79857 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
79886 GGAGTGCATGGCGACCTACAAGGTCG
1 GGAGTGCATGGCGACCTACAAGGTCG
79912 GAGTAGGTCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCA
Found at i:86490 original size:44 final size:42
Alignment explanation
Indices: 86442--86584 Score: 153
Period size: 44 Copynumber: 3.3 Consensus size: 42
86432 GGGATTAAAC
* *
86442 TATAAAAGTAAAAAAGTGTGATTTAAAAAATTACGGAGCTCAAT
1 TATAAAAGT-AAAAAGTGAGATTAAAAAAATTA-GGAGCTCAAT
* * * *
86486 TATAAAGGTAGAAAGTGAGATTAAAAAAATTAGGGGCCCCCAAT
1 TATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGAG--CTCAAT
* * *
86530 TTTAAAAGTAAAATGTGAGATTAAAAAAATTAGGA-CTAAAT
1 TATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGAGCTCAAT
*
86571 TATATAAGTAAAAA
1 TATAAAAGTAAAAA
86585 TAAATTAGGG
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
41 15 0.19
42 3 0.04
43 20 0.25
44 43 0.53
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (42 bp):
TATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGAGCTCAAT
Found at i:86592 original size:30 final size:29
Alignment explanation
Indices: 86552--86610 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
86542 ATGTGAGATT
86552 AAAAAAATTAGGACTAAATTATATAAGTA
1 AAAAAAATTAGGACTAAATTATATAAGTA
* *
86581 AAAATAAATTAGGGCTGAATTATATAAGTA
1 AAAA-AAATTAGGACTAAATTATATAAGTA
86611 GTCGAGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.29
Consensus pattern (29 bp):
AAAAAAATTAGGACTAAATTATATAAGTA
Found at i:88168 original size:3 final size:3
Alignment explanation
Indices: 88160--88196 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
88150 TCGGGTTTCC
* *
88160 ATT ATT ATT ATA ATA ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
88197 ATTTACATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Done.