Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000490.1 Hibiscus syriacus cultivar Beakdansim tig00000934_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: 78149
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5607 original size:26 final size:26
Alignment explanation
Indices: 5571--5620 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
5561 GGAGACATCA
*
5571 ATAGATCTAATAATATTGTAATCTCG
1 ATAGATCTAATAAAATTGTAATCTCG
5597 ATAGATCTAATAAAATTGTAATCT
1 ATAGATCTAATAAAATTGTAATCT
5621 TTTCATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (26 bp):
ATAGATCTAATAAAATTGTAATCTCG
Found at i:9765 original size:32 final size:31
Alignment explanation
Indices: 9689--9765 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
9679 ATGATAGGTG
9689 TAAAAGTTTGAT-AAATTCAATGATCATTTTA
1 TAAAA-TTTGATAAAATTCAATGATCATTTTA
*
9720 TAACATTTGATAAAATAT-AATGATCATTTTA
1 TAAAATTTGATAAAAT-TCAATGATCATTTTA
9751 TAATAATTTGATAAA
1 TAA-AATTTGATAAA
9766 TTTAATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 6 0.15
31 24 0.59
32 11 0.27
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (31 bp):
TAAAATTTGATAAAATTCAATGATCATTTTA
Found at i:13810 original size:13 final size:14
Alignment explanation
Indices: 13773--13802 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13763 ATTATTGGAA
13773 TCAGAATATATGCT
1 TCAGAATATATGCT
13787 TCAGAATATATG-T
1 TCAGAATATATGCT
13800 TCA
1 TCA
13803 TGAAATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (14 bp):
TCAGAATATATGCT
Found at i:16099 original size:34 final size:34
Alignment explanation
Indices: 16056--16180 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
16046 TTCGTCCTAC
16056 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
16090 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
16125 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
16154 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
16181 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:16478 original size:22 final size:21
Alignment explanation
Indices: 16448--16509 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
16438 CTTTTCTTTT
16448 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
16470 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
16493 -TTTA-GTATATATTTTTT
1 TTTTATGTA-ATATTTTTT
16510 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 7 0.21
23 12 0.36
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:16505 original size:24 final size:23
Alignment explanation
Indices: 16462--16507 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
16452 CATGTAATAT
*
16462 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
16485 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
16508 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:16586 original size:46 final size:44
Alignment explanation
Indices: 16523--16654 Score: 137
Period size: 43 Copynumber: 3.0 Consensus size: 44
16513 TTTTTTAGAT
*
16523 TATATATATAAATATATTATTTTTTATTATCAGTTTTATTAATTTA
1 TATATATATATATATATTATTTTTTATTAT-A-TTTTATTAATTTA
* * *
16569 TATATATATATATATATTTACTTTTT-TTAT-TTTTTTTATTTTA
1 TATATATATATATATA-TTATTTTTTATTATATTTTATTAATTTA
* *
16612 TATATATAT-TAT-TTTTACTTTTTTATTATTATTTTATTTATTT
1 TATATATATATATATATTA-TTTTTTATTA-TATTTTATTAATTT
16655 GTTTTATTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
40 3 0.04
41 6 0.08
42 6 0.08
43 21 0.29
44 9 0.12
46 19 0.26
47 8 0.11
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (44 bp):
TATATATATATATATATTATTTTTTATTATATTTTATTAATTTA
Found at i:16602 original size:9 final size:9
Alignment explanation
Indices: 16585--16716 Score: 61
Period size: 9 Copynumber: 13.4 Consensus size: 9
16575 TATATATATA
*
16585 TTTACTTTT
1 TTTATTTTT
16594 TTTATTTTT
1 TTTATTTTT
16603 TTTATTTTAT
1 TTTATTTT-T
*
16613 ATATATATTATT
1 -T-T-TATTTTT
16625 TTTACTTTTT
1 TTTA-TTTTT
16635 TATTATTATTTT
1 T-TTA-T-TTTT
*
16647 ATTTATTTGT
1 -TTTATTTTT
*
16657 TTTA-TTTC
1 TTTATTTTT
*
16665 TATATTTTT
1 TTTATTTTT
16674 TTCT-TCTTTT
1 TT-TAT-TTTT
*
16684 TCTTCTTTTT
1 T-TTATTTTT
16694 CTTTATTTTT
1 -TTTATTTTT
* *
16704 TATATTTAT
1 TTTATTTTT
16713 TTTA
1 TTTA
16717 CTTACTATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 28
0.69 0.10 0.20
Matches are distributed among these distances:
8 5 0.05
9 37 0.39
10 28 0.29
11 10 0.11
12 9 0.09
13 6 0.06
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTATTTTT
Found at i:16627 original size:31 final size:33
Alignment explanation
Indices: 16579--16641 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
16569 TATATATATA
*
16579 TATATATTTACTTTTTTTA-TTTTTT-TTATTT
1 TATATATATACTTTTTTTACTTTTTTATTATTT
16610 TATATATATA-TTATTTTTACTTTTTTATTATT
1 TATATATATACTT-TTTTTACTTTTTTATTATT
16642 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 15 0.54
32 6 0.21
33 5 0.18
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (33 bp):
TATATATATACTTTTTTTACTTTTTTATTATTT
Found at i:16635 original size:25 final size:24
Alignment explanation
Indices: 16607--16683 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
16597 ATTTTTTTTA
16607 TTTTATATATATATTATTTTTACTT-
1 TTTTAT-TATATATT-TTTTTACTTC
* *
16632 TTTTATTAT-TATTTTATTTATTTG
1 TTTTATTATATATTTT-TTTACTTC
*
16656 TTTTATTTCTATATTTTTTT-CTTC
1 TTTTA-TTATATATTTTTTTACTTC
16680 TTTT
1 TTTT
16684 TCTTCTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.05
23 10 0.23
24 14 0.32
25 12 0.27
26 6 0.14
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTTATTATATATTTTTTTACTTC
Found at i:16683 original size:24 final size:21
Alignment explanation
Indices: 16591--16675 Score: 55
Period size: 24 Copynumber: 3.7 Consensus size: 21
16581 TATATTTACT
* *
16591 TTTTTTATTTTTTTTATTTTA
1 TTTTATATTTTTTTTTTTTTA
*
16612 TATATATATTATTTTTACTTTTTTA
1 T-TTTATATT-TTTTT--TTTTTTA
16637 TTATTAT-TTTATTTATTTGTTTTA
1 TT-TTATATTT-TTT-TTT-TTTTA
16661 TTTCTATATTTTTTT
1 TTT-TATATTTTTTT
16676 CTTCTTTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
21 1 0.02
22 6 0.12
23 10 0.20
24 19 0.38
25 14 0.28
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.76
Consensus pattern (21 bp):
TTTTATATTTTTTTTTTTTTA
Found at i:16821 original size:15 final size:15
Alignment explanation
Indices: 16803--16832 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16793 TATTTATTTC
16803 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
16818 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
16833 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:19800 original size:16 final size:16
Alignment explanation
Indices: 19774--19807 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
19764 AGATCCAATC
19774 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
19789 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
19806 AA
1 AA
19808 AAAACACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:19822 original size:23 final size:23
Alignment explanation
Indices: 19796--19869 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
19786 GAAAAGAAGC
19796 AAAAAAGCAAA-AAAAACACAAA-G
1 AAAAAAG-AAACAAAAACA-AAAGG
*
19819 AAAAAGAGAAACAAGAACAAAAGG
1 AAAAA-AGAAACAAAAACAAAAGG
*
19843 AAAAAAG-AGCAAAAATCAAAA-G
1 AAAAAAGAAACAAAAA-CAAAAGG
19865 AAAAA
1 AAAAA
19870 GGGACAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 12 0.27
23 18 0.41
24 14 0.32
ACGTcount: A:0.76, C:0.09, G:0.14, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAACAAAAACAAAAGG
Found at i:20533 original size:22 final size:22
Alignment explanation
Indices: 20505--20555 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
20495 CCCCATCAAT
20505 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
20527 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
20549 CCTTTGA
1 CCTTTGA
20556 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:21461 original size:36 final size:36
Alignment explanation
Indices: 21414--21518 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
21404 GTGCTCACTA
21414 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
21450 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
21487 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
21519 TAAACATTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
36 31 0.50
37 31 0.50
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:21508 original size:37 final size:37
Alignment explanation
Indices: 21414--21523 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
21404 GTGCTCACTA
21414 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
21450 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
21487 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
21524 ATTGAAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 30 0.46
37 32 0.49
38 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:21608 original size:102 final size:102
Alignment explanation
Indices: 21432--21888 Score: 772
Period size: 102 Copynumber: 4.5 Consensus size: 102
21422 CTTGAGACAG
** * * * *
21432 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
21497 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * * *
21534 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCATGAAACAAAATTTCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
21599 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
21636 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
21701 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
21738 TTTCCCTTGAAATGAATTTTGTCTCTC-TGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
21802 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
21839 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
21889 TAAACATTGA
Statistics
Matches: 332, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
101 98 0.30
102 234 0.70
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:21703 original size:37 final size:37
Alignment explanation
Indices: 21636--21722 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
21626 ATTGGAAACA
** * *
21636 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
21672 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
21709 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
21723 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:21794 original size:36 final size:37
Alignment explanation
Indices: 21752--21823 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
21742 CCTTGAAATG
* *
21752 AATTTTGTCTCTC-TGAGATAGTTTCCCTCGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
* *
21788 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACA
21824 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
Found at i:21878 original size:65 final size:65
Alignment explanation
Indices: 21788--21953 Score: 296
Period size: 65 Copynumber: 2.6 Consensus size: 65
21778 CTCGAAACAA
* *
21788 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
*
21853 AATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
*
21918 AATTTCGTCTCTCTTGAAACAGTTTCTCTTGAAACA
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
21954 AAATTTTGTC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 96 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (65 bp):
AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
Found at i:21884 original size:166 final size:169
Alignment explanation
Indices: 21672--21988 Score: 514
Period size: 166 Copynumber: 1.9 Consensus size: 169
21662 CTTGAGATAG
*
21672 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAA
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAA
* * *
21737 ATTTCCCTTGAAATGAATTTTGTCTCTC-TGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAAACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
21801 TTGAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** * * *
21839 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAA
* *
21903 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAAACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAAACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
21968 TTGAGACAGTTTTCTCTTGAA
131 TTGAGACAGTTTTCTCTTGAA
21989 GCATCATCTT
Statistics
Matches: 137, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
166 73 0.53
167 53 0.39
168 11 0.08
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAA
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAAACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:22102 original size:37 final size:37
Alignment explanation
Indices: 22061--22134 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
22051 TGGAACTAAG
* * **
22061 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
22098 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
22135 AATATCTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:22736 original size:105 final size:105
Alignment explanation
Indices: 22593--23480 Score: 862
Period size: 105 Copynumber: 8.5 Consensus size: 105
22583 GAAGCCAAAC
* *
22593 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
* * ** *
22658 CAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAAC
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
*
22698 TTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
*
22763 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * *
22803 TTC-CTAGTTTCAGGGCAAATTTCAACTTCACAGA-GAAGGATATTGGAC-CCAAGACAGCACAA
1 TTCTC-AATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGGACTCC-AGACAACACAA
* * * ** *
22865 GCTCAACTTCACAGCGAAGGGGCGGCTGACTGT---CGACAA-
63 GTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * * *
22904 ---GCAATTTCGGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
* *
22966 CAACTTCACAGCGAAGGGACGACTGGTTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAAT
* * * * * *
23007 TTCCCAATTCCAGAGCCGATTTCAACTCCACGAC-AGAGGATATCGTG-CTACCCGAGACAACAC
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGA-AGGATATTG-GACT--CC-AGACAACAC
23070 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACT
61 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAA-T
* ** * * * * * * *
23117 TT-TCAGTTTCA-TCCGCGATTTTAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACA
1 TTCTCAATTTCAGAGC-CAATTTCAACTTCACAACGAAGGATAT--TG-GACTCCAGACAACACA
*
23180 AGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAA-ACAT
62 AGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACA-AT
* * * *
23224 TTTTCAAATTTCAGAGCCAATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGT
1 TTCTC-AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGT
* * *
23289 TCAACTTCACAACGAAGGGACGACTGATTGTCAACAA-GA-
65 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
* * * * * * * *
23328 TT-TC--GTTCAGAGTCAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
* * **
23390 CAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAAT
66 CAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAAT
* * * * * *
23431 TTCCCAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
23481 GGAACAATAT
Statistics
Matches: 654, Mismatches: 94, Indels: 69
0.80 0.12 0.08
Matches are distributed among these distances:
98 74 0.11
99 2 0.00
100 81 0.12
101 3 0.00
102 9 0.01
103 4 0.01
104 6 0.01
105 177 0.27
106 122 0.19
107 7 0.01
108 7 0.01
109 154 0.24
110 5 0.01
111 1 0.00
112 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (105 bp):
TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTT
CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAAT
Found at i:23472 original size:424 final size:413
Alignment explanation
Indices: 22597--23480 Score: 1094
Period size: 424 Copynumber: 2.1 Consensus size: 413
22587 CCAAACTTCT
* * * *
22597 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAAC
1 CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCCAGACAACACAAATTCAAC
* * *
22662 TTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
66 TTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCACAGCCAATTTCAACTCC
* * *
22727 ACAATGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
131 ACAACGAAGGATATTGCACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTG
* * *
22792 TCAACAATAATTTCCTAGTTTCAGGGCAAATTTCAACTTCACAGAGAAGGATATTGGACCCAAGA
196 TCAACAATAATTTCCAAATTTCAGAGCAAATTTCAACTTCACAGAGAAGGATATTGGACCCAAGA
* * * * *
22857 CAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTCGGAGCCAATC
261 CAACACAAGCTCAACTTCACAACGAAGGGACGACTGACTGTCAACAAG-AATTTCGGAGCCAATC
* *
22922 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACG
325 TCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACG
**
22987 ACTGGTTGTCAACAAACAATTTCC
390 ACTGACTGTCAACAAACAATTTCC
* * * * *
23011 CAATTCCAGAGCCGATTTCAACTCCAC-GACAGAGGATATCGTG-CTACCCGAGACAACACAAGT
1 CAATTCCAGAGCCAATTTCAACTTCACAG-CGGAGGATATTG-GACT--CC-AGACAACACAAAT
* ** * * * *
23074 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCATCCG-CGATTT
61 TCAACTTCACAACGAAGGGACCGCTGCCTGTCAAC-AACAACTTCTCAATTTCA-CAGCCAATTT
* * * *
23138 TAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA
124 CAACTCCACAACGAAGGATAT--TG-CACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGA
* * * *
23203 CAGCTGGTTGTCAACAA-ACATTTTTCAAATTTCAGAGCCAATTTCAACTTCGCAGCGAAGGATA
186 CAGCTGGTTGTCAACAATA-A-TTTCCAAATTTCAGAGCAAATTTCAACTTCACAGAGAAGGATA
* * * *
23267 TTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAG-ATTT
249 TTGGACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGACTGTCAACAAGAATTT
* * * *
23331 CGTTCAGAGTCAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTT
314 CG----GAGCCAATCTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTT
* *
23396 CACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCC
375 CACAGCGAAGGGACGACTGACTGTCAACAAACAATTTCC
* *
23435 CAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTC
23481 GGAACAATAT
Statistics
Matches: 394, Mismatches: 58, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
414 35 0.09
415 1 0.00
416 2 0.01
417 42 0.11
418 37 0.09
419 1 0.00
420 9 0.02
421 54 0.14
422 88 0.22
423 1 0.00
424 123 0.31
425 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (413 bp):
CAATTCCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCCAGACAACACAAATTCAAC
TTCACAACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCACAGCCAATTTCAACTCC
ACAACGAAGGATATTGCACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTG
TCAACAATAATTTCCAAATTTCAGAGCAAATTTCAACTTCACAGAGAAGGATATTGGACCCAAGA
CAACACAAGCTCAACTTCACAACGAAGGGACGACTGACTGTCAACAAGAATTTCGGAGCCAATCT
CAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACGA
CTGACTGTCAACAAACAATTTCC
Found at i:23986 original size:34 final size:34
Alignment explanation
Indices: 23943--24011 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
23933 TTCGTCCTAC
23943 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
23977 TAGGATTCAAACTCCTAAAGATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
24011 T
1 T
24012 GCTAGGATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:24391 original size:24 final size:23
Alignment explanation
Indices: 24346--24398 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
24336 TTTCATGTAA
*
24346 TATTTTTTACATTTTATGTATTT
1 TATTTTTTACATTTTATATATTT
*
24369 TCTTTTTTAC-TTTAGTATATATTT
1 TATTTTTTACATTT--TATATATTT
24393 TATTTT
1 TATTTT
24399 ATTTTTAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 3 0.12
23 9 0.36
24 13 0.52
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.70
Consensus pattern (23 bp):
TATTTTTTACATTTTATATATTT
Found at i:24488 original size:9 final size:9
Alignment explanation
Indices: 24470--24591 Score: 52
Period size: 9 Copynumber: 12.8 Consensus size: 9
24460 ATATATTTAC
24470 TTTTTT-TT
1 TTTTTTATT
24478 TTTTTTATT
1 TTTTTTATT
24487 TTATATATATATT
1 TT-T-T-T-TATT
*
24500 ATTTTTACTT
1 TTTTTTA-TT
24510 TTTTATTA-T
1 TTTT-TTATT
*
24519 TATTTTATT
1 TTTTTTATT
24528 TATTTGTT-TT
1 T-TTT-TTATT
* *
24538 ATTTCTATAT
1 TTTTTTAT-T
*
24548 TTTTTTCTT
1 TTTTTTATT
* *
24557 TTTCTTCTT
1 TTTTTTATT
24566 TTTCTTTATT
1 TTT-TTTATT
*
24576 TTTTATATT
1 TTTTTTATT
*
24585 TATTTTA
1 TTTTTTA
24592 CTTACTATTT
Statistics
Matches: 86, Mismatches: 15, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
8 10 0.12
9 38 0.44
10 24 0.28
11 7 0.08
12 2 0.02
13 5 0.06
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTTTTATT
Found at i:24511 original size:23 final size:19
Alignment explanation
Indices: 24425--24552 Score: 77
Period size: 19 Copynumber: 6.5 Consensus size: 19
24415 TATAAATATA
* *
24425 TTATTTTTTATTATCAGTT
1 TTATTTTTTATTATTATTT
* *
24444 TTATTAATTTATATATATATAT
1 TTATT-TTTTAT-TAT-TATTT
*
24466 TTACTTTTT-TT-TT-TTT
1 TTATTTTTTATTATTATTT
24482 TTATTTTATATATATATTATTT
1 TTATTTT-T-TAT-TATTATTT
24504 TTACTTTTTTATTATTA-TT
1 TTA-TTTTTTATTATTATTT
*
24523 TTATTTATTTGTT-TTATTT
1 TTATTT-TTTATTATTATTT
24542 CTATATTTTTT
1 -T-TATTTTTT
24553 TCTTTTTCTT
Statistics
Matches: 86, Mismatches: 9, Indels: 27
0.70 0.07 0.22
Matches are distributed among these distances:
16 8 0.09
17 2 0.02
18 8 0.09
19 19 0.22
20 16 0.19
21 16 0.19
22 13 0.15
23 4 0.05
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATTTTTTATTATTATTT
Found at i:24513 original size:25 final size:23
Alignment explanation
Indices: 24477--24559 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 23
24467 TACTTTTTTT
*
24477 TTTTTTTA-TTTTATA-TATATA
1 TTTTTTTACTTTTTTATTATATA
24498 TTATTTTTACTTTTTTATTAT-TA
1 TT-TTTTTACTTTTTTATTATATA
* *
24521 TTTTATTTATTTGTTTTATTTCTATA
1 TTTT-TTTACTT-TTTTA-TTATATA
24547 TTTTTTT-CTTTTT
1 TTTTTTTACTTTTT
24560 CTTCTTTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.04
22 8 0.16
23 19 0.37
24 10 0.20
25 6 0.12
26 6 0.12
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (23 bp):
TTTTTTTACTTTTTTATTATATA
Found at i:24540 original size:38 final size:38
Alignment explanation
Indices: 24428--24541 Score: 99
Period size: 38 Copynumber: 2.9 Consensus size: 38
24418 AAATATATTA
* * *
24428 TTTTTTATTATCAGTTTTATTAATTTATATATATATATTTAC
1 TTTTTTATTATTA-TTTTATTTATTTAT-T-T-TATTTTTAC
*
24470 TTTTTT-TT-TT-TTTTATTTTATATATATATTATTTTTAC
1 TTTTTTATTATTATTTTA-TTTAT-T-TATTTTATTTTTAC
*
24508 TTTTTTATTATTATTTTATTTATTTGTTTTATTT
1 TTTTTTATTATTATTTTATTTATTTATTTTATTT
24542 CTATATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
38 27 0.45
39 8 0.13
40 9 0.15
41 10 0.17
42 6 0.10
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.72
Consensus pattern (38 bp):
TTTTTTATTATTATTTTATTTATTTATTTTATTTTTAC
Found at i:24696 original size:15 final size:15
Alignment explanation
Indices: 24678--24707 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24668 TATTTATTTC
24678 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
24693 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
24708 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:29230 original size:14 final size:14
Alignment explanation
Indices: 29211--29264 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
29201 CGTTCGTGAA
29211 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
29225 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
29239 CG-T---TTATATT
1 CGTTCGGTTATGTT
29249 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
29263 CG
1 CG
29265 CTTATGTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 24 0.71
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:29286 original size:24 final size:24
Alignment explanation
Indices: 29212--29273 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
29202 GTTCGTGAAC
*
29212 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGCTTATGTTCGTTCGGTTAT
* *
29236 GTTCGTTTATATTCGTTCGGTTAT
1 GTTCGCTTATGTTCGTTCGGTTAT
29260 GTTCGCTTATGTTC
1 GTTCGCTTATGTTC
29274 ATTCATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.52
Consensus pattern (24 bp):
GTTCGCTTATGTTCGTTCGGTTAT
Found at i:30383 original size:16 final size:16
Alignment explanation
Indices: 30362--30428 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
30352 GTCTCCAGCG
*
30362 TTTATGTTCGTGTTCA
1 TTTATATTCGTGTTCA
* * *
30378 TTTATGTTTGTGTTCG
1 TTTATATTCGTGTTCA
*
30394 TTTATATTCGTGTTCG
1 TTTATATTCGTGTTCA
30410 TTTATATTCGT-TT-A
1 TTTATATTCGTGTTCA
30424 TTTAT
1 TTTAT
30429 TAAATGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 39 0.85
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.61
Consensus pattern (16 bp):
TTTATATTCGTGTTCA
Found at i:40085 original size:24 final size:25
Alignment explanation
Indices: 40064--40125 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
40054 AAAAAATAGT
40064 TTTTA-CATTAACTTATTAAATATA
1 TTTTATCATTAACTTATTAAATATA
*
40088 TTTTATTATTAACTTAATTTTAAA-ATA
1 TTTTATCATTAACTT-A--TTAAATATA
*
40115 TTTTATTATTA
1 TTTTATCATTA
40126 TTTTAACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 5 0.15
25 8 0.24
26 1 0.03
27 14 0.42
28 5 0.15
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTATCATTAACTTATTAAATATA
Found at i:40131 original size:27 final size:29
Alignment explanation
Indices: 40071--40146 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 29
40061 AGTTTTTACA
40071 TTAACTTATTAAATATATTTTATTATTAAC
1 TTAACTT-TTAAATATATTTTATTATTAAC
**
40101 TTAA-TTTTAAA-ATATTTTATTATTATT
1 TTAACTTTTAAATATATTTTATTATTAAC
40128 TTAACTTTTCAAAGTATAT
1 TTAACTTTT-AAA-TATAT
40147 ATTTTATCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 18 0.45
28 9 0.22
29 5 0.12
30 4 0.10
31 4 0.10
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (29 bp):
TTAACTTTTAAATATATTTTATTATTAAC
Found at i:41392 original size:23 final size:23
Alignment explanation
Indices: 41345--41393 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
41335 AAAGATATAA
* *
41345 AAATGTGTCACAAATGTATAAAT
1 AAATGTGTCACAAAGGTAGAAAT
*
41368 AAATGTGTCACAAAGGTAGAGAT
1 AAATGTGTCACAAAGGTAGAAAT
41391 AAA
1 AAA
41394 CATGTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.24
Consensus pattern (23 bp):
AAATGTGTCACAAAGGTAGAAAT
Found at i:41399 original size:23 final size:23
Alignment explanation
Indices: 41350--41400 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
41340 TATAAAAATG
* * **
41350 TGTCACAAATGTATAAATAAATG
1 TGTCACAAAGGTAGAAATAAACA
*
41373 TGTCACAAAGGTAGAGATAAACA
1 TGTCACAAAGGTAGAAATAAACA
41396 TGTCA
1 TGTCA
41401 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (23 bp):
TGTCACAAAGGTAGAAATAAACA
Found at i:53042 original size:12 final size:12
Alignment explanation
Indices: 53025--53049 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53015 AACGGTCCGC
53025 GACCGCGATTTT
1 GACCGCGATTTT
53037 GACCGCGATTTT
1 GACCGCGATTTT
53049 G
1 G
53050 TGGTTTCGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (12 bp):
GACCGCGATTTT
Found at i:53111 original size:21 final size:21
Alignment explanation
Indices: 53087--53131 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
53077 GGACGGCCAT
53087 AATAGCGTCC-GCGACGACCGC
1 AATAGCG-CCAGCGACGACCGC
*
53108 AATAGCGCCAGCGACGGCCGC
1 AATAGCGCCAGCGACGACCGC
53129 AAT
1 AAT
53132 CACGGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.27, C:0.36, G:0.29, T:0.09
Consensus pattern (21 bp):
AATAGCGCCAGCGACGACCGC
Found at i:64419 original size:2 final size:2
Alignment explanation
Indices: 64414--64443 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
64404 GAAAAAATAC
*
64414 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64444 GAATCATCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:78019 original size:18 final size:18
Alignment explanation
Indices: 77998--78044 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
77988 CTCGTGGTCG
*
77998 TGGTCGTGGTATTGGTAT
1 TGGTAGTGGTATTGGTAT
*
78016 TGGTATTGGTATTGGTAT
1 TGGTAGTGGTATTGGTAT
*
78034 TGGTAATGGTA
1 TGGTAGTGGTA
78045 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.02, G:0.36, T:0.45
Consensus pattern (18 bp):
TGGTAGTGGTATTGGTAT
Found at i:78046 original size:6 final size:6
Alignment explanation
Indices: 78004--78044 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
77994 GTCGTGGTCG
*
78004 TGGTAT TGGTAT TGGTAT TGGTAT TGGTAT TGGTAA TGGTA
1 TGGTAT TGGTAT TGGTAT TGGTAT TGGTAT TGGTAT TGGTA
78045 ATACGTGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (6 bp):
TGGTAT
Done.