Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008671.1 Hibiscus syriacus cultivar Beakdansim tig00111684_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: 112365
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:4364 original size:20 final size:20
Alignment explanation
Indices: 4335--4377 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4325 ATTTCACCAC
*
4335 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
4355 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
4375 ATG
1 ATG
4378 GTCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:6256 original size:16 final size:16
Alignment explanation
Indices: 6235--6273 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
6225 TTGTGGGTGA
6235 TATGTCGTGGCAATTT
1 TATGTCGTGGCAATTT
6251 TATGTCGTGGCAATTT
1 TATGTCGTGGCAATTT
6267 TATGTCG
1 TATGTCG
6274 CACTCCGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.44
Consensus pattern (16 bp):
TATGTCGTGGCAATTT
Found at i:12915 original size:20 final size:20
Alignment explanation
Indices: 12886--12927 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
12876 ATTTCACCAC
*
12886 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
12906 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
12926 AT
1 AT
12928 AGGCTTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:20256 original size:122 final size:122
Alignment explanation
Indices: 20037--20280 Score: 452
Period size: 122 Copynumber: 2.0 Consensus size: 122
20027 TGTTCCACTC
20037 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
1 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
* *
20102 GACCATCAATATCGATAACACATCAGCCATGAATGAACTGCCCATAGATTGCCATGA
66 GACCATCAATACCGATAACACATCAGCCATGAATGAACTGCCCATAGATTACCATGA
20159 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
1 ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
* *
20224 GACCATCAATACCGATAACACATCAGCTATGAATGAATTGCCCATAGATTACCATGA
66 GACCATCAATACCGATAACACATCAGCCATGAATGAACTGCCCATAGATTACCATGA
20281 CTGAGAAGCG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (122 bp):
ATTCCATAAATCTCTCCTTAAACTGCTATCAGGACTAGCATAAATGCACGTTAAGAAAAAACCCT
GACCATCAATACCGATAACACATCAGCCATGAATGAACTGCCCATAGATTACCATGA
Found at i:21637 original size:23 final size:19
Alignment explanation
Indices: 21592--21629 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21582 TTGCTTTCGC
21592 TATATATCTAAACAAACTT
1 TATATATCTAAACAAACTT
21611 TATATATCTAAACAAACTT
1 TATATATCTAAACAAACTT
21630 CTTGTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATATCTAAACAAACTT
Found at i:22839 original size:93 final size:92
Alignment explanation
Indices: 22728--22910 Score: 321
Period size: 93 Copynumber: 2.0 Consensus size: 92
22718 AGACGAATGA
* *
22728 TATAATATTTAATTTTAATATTAATATAAAAATATTATTTTCTTTATTTAATAATAATGTAATAT
1 TATAATATTTAATATTAATATTAATATAAAAATATTATTTTATTTATTTAATAATAATGTAATAT
22793 TTTTATCTTATAATATTTTCTTATTGG
66 TTTTATCTTATAATATTTTCTTATTGG
* *
22820 TATAATATTTTGATATTAATATTAATATAAAAATATTATTTTATTTATTTAATAATAATGTGATA
1 TATAATA-TTTAATATTAATATTAATATAAAAATATTATTTTATTTATTTAATAATAATGTAATA
22885 TTTTTATCTTATAATATTTTCTTATT
65 TTTTTATCTTATAATATTTTCTTATT
22911 AATATTTAAG
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 7 0.08
93 79 0.92
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (92 bp):
TATAATATTTAATATTAATATTAATATAAAAATATTATTTTATTTATTTAATAATAATGTAATAT
TTTTATCTTATAATATTTTCTTATTGG
Found at i:23820 original size:14 final size:15
Alignment explanation
Indices: 23801--23833 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23791 AGAGTTTGTG
*
23801 TTTAAAA-TTAGGAA
1 TTTAAAATTTAGAAA
23815 TTTAAAATTTAGAAA
1 TTTAAAATTTAGAAA
23830 TTTA
1 TTTA
23834 GGTTTTAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (15 bp):
TTTAAAATTTAGAAA
Found at i:25420 original size:21 final size:23
Alignment explanation
Indices: 25395--25458 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
25385 CTTCTAAGGT
25395 ATATTTTATA-TT-ATATT-TTTA
1 ATATTTTATATTTAAT-TTATTTA
*
25416 ATATTTTGTATTTAATTTATTTA
1 ATATTTTATATTTAATTTATTTA
25439 ATATTTTACTTATTTAATTT
1 ATATTTTA--TATTTAATTT
25459 TTTTGCAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 9 0.25
22 4 0.11
23 13 0.36
25 10 0.28
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
ATATTTTATATTTAATTTATTTA
Found at i:31669 original size:23 final size:21
Alignment explanation
Indices: 31614--31680 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 21
31604 TCAGATTAAG
31614 TATAAAATTTAATATAATCTA
1 TATAAAATTTAATATAATCTA
*
31635 TAAAAAGTATTTGATATATTAAT-TA
1 TATAAA--ATTT-A-ATA-TAATCTA
*
31660 TATAAAATTTAATTTAATCTA
1 TATAAAATTTAATATAATCTA
31681 ACATTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
20 4 0.11
21 9 0.24
22 1 0.03
23 8 0.22
24 1 0.03
25 10 0.27
26 4 0.11
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TATAAAATTTAATATAATCTA
Found at i:40043 original size:20 final size:20
Alignment explanation
Indices: 40018--40076 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
40008 GGCTGCTGGA
*
40018 AACCGGTT-TAACCGATTTTC
1 AACCGGTTCTAACCG-GTTTC
*
40038 AACCGGTTCTGACCGGTTTC
1 AACCGGTTCTAACCGGTTTC
*
40058 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
40077 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
AACCGGTTCTAACCGGTTTC
Found at i:40096 original size:5 final size:5
Alignment explanation
Indices: 40086--40126 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
40076 TGACCGGTCT
*
40086 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
40127 GTTGACTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:40111 original size:22 final size:22
Alignment explanation
Indices: 40085--40132 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
40075 TTGACCGGTC
40085 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
40107 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
40129 TGAC
1 TGAC
40133 TGTTGACCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.10
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCGT
Found at i:40139 original size:7 final size:7
Alignment explanation
Indices: 40123--40153 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
40113 GACCCGACCC
40123 GACCGTT
1 GACCGTT
*
40130 GACTGTT
1 GACCGTT
40137 GACCGTT
1 GACCGTT
40144 GACCGTT
1 GACCGTT
40151 GAC
1 GAC
40154 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:47329 original size:29 final size:29
Alignment explanation
Indices: 47274--47348 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
47264 GGCTGCTGGA
* *
47274 AACCGGTTTAACCGATTTTCAACCGGTTCTG
1 AACCGGTTTGACCG-GTTTCAACCGGTTC-G
*
47305 -ACCGGTTTGACCGGTTTCAAGCGGTTCG
1 AACCGGTTTGACCGGTTTCAACCGGTTCG
*
47333 AACTGGTTTGACCGGT
1 AACCGGTTTGACCGGT
47349 CTGACCCGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 26 0.67
30 12 0.31
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.31
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:47361 original size:5 final size:5
Alignment explanation
Indices: 47351--47391 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
47341 TGACCGGTCT
*
47351 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
47392 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:47376 original size:22 final size:22
Alignment explanation
Indices: 47350--47398 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
47340 TTGACCGGTC
47350 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
47372 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
47394 TGACC
1 TGACC
47399 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.10
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCGT
Found at i:54617 original size:29 final size:30
Alignment explanation
Indices: 54565--54637 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
54555 GGCTGCTGGA
* *
54565 AACCGGTTTAACCGATTTTCAACCGGTTCTG
1 AACCGGTTTGACCGAGTTTCAACCGGTTC-G
54596 -ACCGGTTTGACC-AGTTTCAACCGGTTCG
1 AACCGGTTTGACCGAGTTTCAACCGGTTCG
*
54624 AACTGGTTTGACCG
1 AACCGGTTTGACCG
54638 GTCTGACCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 25 0.68
30 11 0.30
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGAGTTTCAACCGGTTCG
Found at i:54669 original size:17 final size:17
Alignment explanation
Indices: 54647--54684 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
54637 GGTCTGACCC
54647 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
54664 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
54681 GACC
1 GACC
54685 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:54684 original size:24 final size:22
Alignment explanation
Indices: 54631--54690 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
54621 TCGAACTGGT
54631 TTGACCGGTCTGACCCGACCCGAC
1 TTGACC-GT-TGACCCGACCCGAC
**
54655 CCGACCGTTGACCCGACCCGATC
1 TTGACCGTTGACCCGACCCGA-C
54678 GTTGACCGTTGAC
1 -TTGACCGTTGAC
54691 TTTCTTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 13 0.43
23 3 0.10
24 14 0.47
ACGTcount: A:0.17, C:0.40, G:0.25, T:0.18
Consensus pattern (22 bp):
TTGACCGTTGACCCGACCCGAC
Found at i:68176 original size:3 final size:3
Alignment explanation
Indices: 68168--68200 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
68158 TTTTCTCTCT
68168 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
68201 GTACCAGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:69713 original size:9 final size:9
Alignment explanation
Indices: 69649--69748 Score: 57
Period size: 9 Copynumber: 11.1 Consensus size: 9
69639 TTTCCCTTCG
*
69649 TTTTGTTTA
1 TTTTATTTA
69658 TTTGT-TTTA
1 TTT-TATTTA
69667 TTTTTATTT-
1 -TTTTATTTA
69676 TCTTTATTTA
1 T-TTTATTTA
* *
69686 -TTGATTCA
1 TTTTATTTA
*
69694 TTTT-TCCTA
1 TTTTAT-TTA
69703 TTTTATTTA
1 TTTTATTTA
69712 -TTTATTTA
1 TTTTATTTA
*
69720 TTTTATTCAA
1 TTTTATT-TA
*
69730 TTGTATTTA
1 TTTTATTTA
*
69739 TTTTTTTTA
1 TTTTATTTA
69748 T
1 T
69749 ATATTCCTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
8 16 0.23
9 39 0.56
10 15 0.21
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:70850 original size:16 final size:16
Alignment explanation
Indices: 70813--70850 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
70803 TCTTGCCATT
*
70813 TTTTTATTTCTATTTA
1 TTTTTATTTCTATTAA
70829 TTTTTATTT-TATTAA
1 TTTTTATTTCTATTAA
70844 TTGTTTA
1 TT-TTTA
70851 CCTTTGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTATTTCTATTAA
Found at i:74270 original size:10 final size:11
Alignment explanation
Indices: 74257--74295 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
74247 AATAAAAAAG
74257 AAAAGAAACAA
1 AAAAGAAACAA
74268 AAAAGAAA-AA
1 AAAAGAAACAA
*
74278 ACAAG-AACAA
1 AAAAGAAACAA
74288 AAAAGAAA
1 AAAAGAAA
74296 AGAAGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 12 0.50
11 10 0.42
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAGAAACAA
Found at i:74271 original size:16 final size:16
Alignment explanation
Indices: 74250--74306 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
74240 AATCAAGAAT
74250 AAAAAAGAAAAGAAAC
1 AAAAAAGAAAAGAAAC
*
74266 AAAAAAGAAAAAACAAGAAC
1 AAAAAAG--AAAA-GA-AAC
*
74286 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAAGAAAC
74302 AAAAA
1 AAAAA
74307 TCAAAAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 14 0.41
17 1 0.03
18 8 0.24
19 1 0.03
20 10 0.29
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAC
Found at i:74312 original size:16 final size:15
Alignment explanation
Indices: 74252--74313 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 15
74242 TCAAGAATAA
*
74252 AAAAGAA-AAGAAAC
1 AAAAGAACAAAAAAC
*
74266 AAAA-AAGAAAAAAC
1 AAAAGAACAAAAAAC
*
74280 --AAGAACAAAAAAG
1 AAAAGAACAAAAAAC
*
74293 AAAAGAAGCAAAAATC
1 AAAAGAA-CAAAAAAC
74309 AAAAG
1 AAAAG
74314 GAAAATGGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 2 0.05
13 10 0.26
14 10 0.26
15 5 0.13
16 11 0.29
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAGAACAAAAAAC
Found at i:74312 original size:22 final size:20
Alignment explanation
Indices: 74262--74312 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 20
74252 AAAAGAAAAG
74262 AAACAAAAAAGAAAAAACAA
1 AAACAAAAAAGAAAAAACAA
*
74282 GAACAAAAAAGAAAAGAAGCAA
1 AAACAAAAAAGAAAA-AA-CAA
74304 AAATCAAAA
1 AAA-CAAAA
74313 GGAAAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 14 0.54
21 2 0.08
22 5 0.19
23 5 0.19
ACGTcount: A:0.78, C:0.10, G:0.10, T:0.02
Consensus pattern (20 bp):
AAACAAAAAAGAAAAAACAA
Found at i:75374 original size:32 final size:33
Alignment explanation
Indices: 75332--75395 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
75322 AGAAATGAGG
75332 AATATTTGGGGCATCTTTGAAGATTCAACATCA
1 AATATTTGGGGCATCTTTGAAGATTCAACATCA
*
75365 AATA-TTGGGGCATCTTTGGAGATTCAACATC
1 AATATTTGGGGCATCTTTGAAGATTCAACATC
75396 CTAATGCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (33 bp):
AATATTTGGGGCATCTTTGAAGATTCAACATCA
Found at i:75963 original size:30 final size:32
Alignment explanation
Indices: 75923--75982 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
75913 TCTTGAGACA
75923 GTTTCCCTTGAAA-A-AAAAACCTTTGAAATT
1 GTTTCCCTTGAAACACAAAAACCTTTGAAATT
*
75953 GTTTCTCTTGAAACACAAAAACCTTTGAAA
1 GTTTCCCTTGAAACACAAAAACCTTTGAAA
75983 CATAAACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 12 0.44
31 1 0.04
32 14 0.52
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (32 bp):
GTTTCCCTTGAAACACAAAAACCTTTGAAATT
Found at i:76189 original size:37 final size:37
Alignment explanation
Indices: 76119--76190 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
76109 TGGAACTAAG
* * *
76119 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
76156 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
76191 CAGATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:77234 original size:106 final size:106
Alignment explanation
Indices: 76806--77245 Score: 650
Period size: 106 Copynumber: 4.2 Consensus size: 106
76796 ATATCACGCC
*
76806 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTT-C
1 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCC
* *
76870 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
76912 ACTC-AAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 ACTCGAA-ACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
* * **
76976 CAATTTCAGAGCCAATTTCAACTTCACAACAAAGGGCATTGG
65 CAATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
* * * * *
77018 ACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGACAGCTGATTGTCAATAAACAATTTCCC
1 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
77083 AATTTCAAAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
*
77124 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTTAACAAACAATTTCCC
1 ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * * *
77189 AATTCCATAACCAATTTCAACTTCACGGTAAACGATATTGG
66 AATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
* *
77230 ACTCGGAACAATACAA
1 ACTCGAAACAACACAA
77246 CCTACTTGGA
Statistics
Matches: 301, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
105 4 0.01
106 296 0.98
107 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (106 bp):
ACTCGAAACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAACCAATTTCAACTTCACAGCAAAGGATATTGG
Found at i:78817 original size:9 final size:9
Alignment explanation
Indices: 78803--78875 Score: 60
Period size: 9 Copynumber: 7.7 Consensus size: 9
78793 CTTCGTTTTG
78803 TTTATTTAT
1 TTTATTTAT
78812 TTTATTTTTAT
1 TTTA--TTTAT
*
78823 TTTCTTTAT
1 TTTATTTAT
*
78832 TCATTGATTCAT
1 T--TT-ATTTAT
78844 TTT-TCTTAT
1 TTTAT-TTAT
78853 TTTATTTA-
1 TTTATTTAT
78861 TTTATTTAT
1 TTTATTTAT
78870 TTTATT
1 TTTATT
78876 CCGTTGTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
8 9 0.17
9 25 0.48
10 3 0.06
11 10 0.19
12 5 0.10
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:81607 original size:36 final size:36
Alignment explanation
Indices: 81566--81638 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
81556 TGGAAAATAT
*
81566 TTATAT-ATTTTCTTTAAAAAATT-AAATTCATAAAAA
1 TTATATAATTTT-TTTAAAAAATTGAAAAT-ATAAAAA
*
81602 TTATATAATTTTTTTACAAAATTGAAAATATAAAAA
1 TTATATAATTTTTTTAAAAAATTGAAAATATAAAAA
81638 T
1 T
81639 GTTTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
TTATATAATTTTTTTAAAAAATTGAAAATATAAAAA
Found at i:82097 original size:16 final size:18
Alignment explanation
Indices: 82065--82097 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
82055 TTATTTGACT
82065 GAGAATTTAAGGAGAGAG
1 GAGAATTTAAGGAGAGAG
82083 GAGAA-TTAA-GAGAGA
1 GAGAATTTAAGGAGAGA
82098 AAGTGACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.15
Consensus pattern (18 bp):
GAGAATTTAAGGAGAGAG
Found at i:84415 original size:3 final size:3
Alignment explanation
Indices: 84409--84504 Score: 64
Period size: 3 Copynumber: 34.0 Consensus size: 3
84399 AATTTCGTCC
* * * *
84409 ATT ATT ATT A-T ATAT ATA ATT A-T ATT CTT CTT ATT -TT ATT TTT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
84452 A-T ATT -TT ATT -TT ATT -TT CTT TTT ACTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
84494 ATT -TT ATT ATT
1 ATT ATT ATT ATT
84505 TTGTTCTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
2 16 0.21
3 53 0.71
4 6 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:84468 original size:23 final size:25
Alignment explanation
Indices: 84439--84506 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 25
84429 TATATTCTTC
84439 TTATTTTATTTTTA-TATTTTATT-
1 TTATTTTATTTTTACTATTTTATTA
* *
84462 TTATTTTCTTTTTACT-TATTATTA
1 TTATTTTATTTTTACTATTTTATTA
*
84486 TTATTATTA-TTTTATTATTTT
1 TTATT-TTATTTTTACTATTTT
84507 GTTCTATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
23 19 0.53
24 12 0.33
25 5 0.14
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (25 bp):
TTATTTTATTTTTACTATTTTATTA
Found at i:84876 original size:18 final size:18
Alignment explanation
Indices: 84855--84911 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
84845 TGTTTTTAAT
84855 TTTTTATTTCATTTTATA
1 TTTTTATTTCATTTTATA
*
84873 TTTTTAGTTT-ATTTAATA
1 TTTTTA-TTTCATTTTATA
*
84891 TTTTT-TATCATTTT-TA
1 TTTTTATTTCATTTTATA
84907 TTTTT
1 TTTTT
84912 TTCTAACATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 18 0.53
19 3 0.09
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTATTTCATTTTATA
Found at i:84925 original size:28 final size:27
Alignment explanation
Indices: 84866--84924 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
84856 TTTTATTTCA
*
84866 TTTTATATTTTTAGTTTATTTAATATT
1 TTTTATATTTTTAGTTTATTTAACATT
* *
84893 TTTTATCATTTTTATTTTTTTCTAACATT
1 TTTTAT-ATTTTTAGTTTATT-TAACATT
84922 TTT
1 TTT
84925 AACTTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 6 0.22
28 12 0.44
29 9 0.33
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTATATTTTTAGTTTATTTAACATT
Found at i:85390 original size:16 final size:15
Alignment explanation
Indices: 85365--85400 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
85355 CCAACTTTTA
85365 ATATTATTTATATAC
1 ATATTATTTATATAC
85380 ATATATATTTATATAC
1 ATAT-TATTTATATAC
85396 -TATTA
1 ATATTA
85401 ATATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 7 0.35
16 11 0.55
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATTTATATAC
Found at i:85984 original size:13 final size:14
Alignment explanation
Indices: 85961--85998 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
85951 ATTATAATGT
*
85961 TTATAAAAATAATA
1 TTATTAAAATAATA
85975 TT-TTAAAAT-ATA
1 TTATTAAAATAATA
85987 TTATTAAAATAA
1 TTATTAAAATAA
85999 AATATACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.24
13 13 0.62
14 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTATTAAAATAATA
Found at i:87616 original size:16 final size:17
Alignment explanation
Indices: 87592--87624 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
87582 AACTTTTGTC
*
87592 GGTTCCTTCGTTTGTTT
1 GGTTCCTTCATTTGTTT
87609 GGTT-CTTCATTTGTTT
1 GGTTCCTTCATTTGTTT
87625 TTTAATTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.03, C:0.15, G:0.21, T:0.61
Consensus pattern (17 bp):
GGTTCCTTCATTTGTTT
Found at i:88042 original size:21 final size:21
Alignment explanation
Indices: 88018--88079 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
88008 GTTTCTCAAA
88018 TTAATAATTTAATTTATATTT
1 TTAATAATTTAATTTATATTT
*
88039 TTAATTATATTAATTTAT-TTT
1 TTAATAAT-TTAATTTATATTT
*
88060 TAAATTAATTTAA-TTATATT
1 TTAA-TAATTTAATTTATATT
88080 AATTCTATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 4 0.11
21 19 0.54
22 12 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAATAATTTAATTTATATTT
Found at i:89272 original size:16 final size:16
Alignment explanation
Indices: 89253--89284 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
89243 AATTTGCAAA
89253 AAATATTAAAAAATAT
1 AAATATTAAAAAATAT
*
89269 AAATATTAAAATATAT
1 AAATATTAAAAAATAT
89285 TTAAAAATTT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATTAAAAAATAT
Found at i:101123 original size:17 final size:17
Alignment explanation
Indices: 101092--101125 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
101082 ACGTGTATTT
**
101092 TATTGTTAATGTGATAA
1 TATTGTTAACATGATAA
101109 TATTGTTAACATGATAA
1 TATTGTTAACATGATAA
101126 CTTACACGGT
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:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TATTGTTAACATGATAA
Found at i:101330 original size:2 final size:2
Alignment explanation
Indices: 101323--101347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
101313 TCTTATTATT
101323 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
101348 ATGGTATTGT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:103615 original size:20 final size:21
Alignment explanation
Indices: 103590--103629 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
103580 TCTATTAGTT
*
103590 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
103610 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
103630 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:103652 original size:53 final size:52
Alignment explanation
Indices: 103537--103686 Score: 257
Period size: 53 Copynumber: 2.9 Consensus size: 52
103527 CTAAATTAAA
* * *
103537 TATTAGATAGGACCAGTTTTAATGAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
103589 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
103642 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
103687 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 10 0.11
52 33 0.35
53 51 0.54
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:103668 original size:20 final size:20
Alignment explanation
Indices: 103643--103682 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
103633 TCTATTAGTT
*
103643 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
103663 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
103683 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Done.