Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 126 of 141
Found at i:40280279 original size:12 final size:14
Alignment explanation
Indices: 40280253--40280284 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
40280243 ATTAATTAGG
40280253 ATTTTTTATATTTA
1 ATTTTTTATATTTA
40280267 ATTTTTT-TA-TTA
1 ATTTTTTATATTTA
40280279 ATTTTT
1 ATTTTT
40280285 CTCATGCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 2 0.11
14 7 0.39
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTTTATATTTA
Found at i:40281642 original size:9 final size:9
Alignment explanation
Indices: 40281628--40281695 Score: 93
Period size: 9 Copynumber: 7.4 Consensus size: 9
40281618 TTTGGTTAAA
40281628 AATTACCCG
1 AATTACCCG
40281637 AATTACCCG
1 AATTACCCG
40281646 AATTACCCG
1 AATTACCCG
*
40281655 AATTAACCG
1 AATTACCCG
40281664 AATTA-CCG
1 AATTACCCG
*
40281672 AAAAATACCCG
1 --AATTACCCG
40281683 AATTACCCG
1 AATTACCCG
40281692 AATT
1 AATT
40281696 TTTTTTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
8 3 0.06
9 43 0.81
10 4 0.08
11 3 0.06
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:40282401 original size:17 final size:19
Alignment explanation
Indices: 40282370--40282404 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
40282360 AAACCAAGAA
40282370 TTTAGAAAATAAATATATG
1 TTTAGAAAATAAATATATG
40282389 TTTA-AAAAT-AATATAT
1 TTTAGAAAATAAATATAT
40282405 AATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TTTAGAAAATAAATATATG
Found at i:40284700 original size:18 final size:18
Alignment explanation
Indices: 40284664--40284701 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40284654 TTATAATATA
* *
40284664 ATATATTATTTTATTTTT
1 ATATATTATTTAATGTTT
40284682 ATATATTATTTAATGTTT
1 ATATATTATTTAATGTTT
40284700 AT
1 AT
40284702 CACATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATATTATTTAATGTTT
Found at i:40285670 original size:151 final size:152
Alignment explanation
Indices: 40285469--40285780 Score: 590
Period size: 151 Copynumber: 2.1 Consensus size: 152
40285459 CCGTCTCGAT
*
40285469 TTAAAATATGACATTTAAATTTTGCTTAAATTCACTTATATTTTTATAAATGGCAAACCCAAATT
1 TTAATATATGACATTTAAATTTTGCTTAAATTCACTTATATTTTTATAAATGGCAAACCCAAATT
* *
40285534 GTTTAGGTCCATCTATATTTTTACTTTTTTAAATACATTAGCTGTATTCAATATTTTCTAGTTTT
66 GTTTAGGTCCATCTATATTTTTACTTTTTTAAATAAAATAGCTGTATTCAATATTTTCTAGTTTT
40285599 ATATAATTTTTTAAAATAAAAA
131 ATATAATTTTTTAAAATAAAAA
40285621 TTAATATATGACA-TTAAATTTTGCTTAAATTCACTTATATTTTTATAAATGGCAAACCCAAATT
1 TTAATATATGACATTTAAATTTTGCTTAAATTCACTTATATTTTTATAAATGGCAAACCCAAATT
40285685 GTTTAGGTCCATCTATATTTTTACTTTTTTAAATAAAATAGCTGTATTCAATATTTTCTAGTTTT
66 GTTTAGGTCCATCTATATTTTTACTTTTTTAAATAAAATAGCTGTATTCAATATTTTCTAGTTTT
40285750 ATATAATTTTTTAAAATAAAAA
131 ATATAATTTTTTAAAATAAAAA
40285772 TTAATATAT
1 TTAATATAT
40285781 ATTAATATTT
Statistics
Matches: 157, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
151 145 0.92
152 12 0.08
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (152 bp):
TTAATATATGACATTTAAATTTTGCTTAAATTCACTTATATTTTTATAAATGGCAAACCCAAATT
GTTTAGGTCCATCTATATTTTTACTTTTTTAAATAAAATAGCTGTATTCAATATTTTCTAGTTTT
ATATAATTTTTTAAAATAAAAA
Found at i:40288206 original size:9 final size:9
Alignment explanation
Indices: 40288192--40288225 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
40288182 ATTTTTCAAT
40288192 ATATTTTTA
1 ATATTTTTA
40288201 ATA-TTTTA
1 ATATTTTTA
*
40288209 ATATTTTTT
1 ATATTTTTA
40288218 ATATTTTT
1 ATATTTTT
40288226 TATGAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
ATATTTTTA
Found at i:40288214 original size:17 final size:17
Alignment explanation
Indices: 40288192--40288224 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40288182 ATTTTTCAAT
40288192 ATATTTTTAATATTTTA
1 ATATTTTTAATATTTTA
*
40288209 ATATTTTTTATATTTT
1 ATATTTTTAATATTTT
40288225 TTATGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTTTTAATATTTTA
Found at i:40288226 original size:9 final size:9
Alignment explanation
Indices: 40288164--40288228 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
40288154 ATTTTATACC
*
40288164 TTTTTATGT
1 TTTTTATAT
40288173 TTTCTTATAAT
1 TTT-TTAT-AT
*
40288184 TTTTCAATAT
1 TTTT-TATAT
40288194 ATTTTTA-AT
1 -TTTTTATAT
*
40288203 ATTTTAATAT
1 -TTTTTATAT
40288213 TTTTTATAT
1 TTTTTATAT
40288222 TTTTTAT
1 TTTTTAT
40288229 GAGAAAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
9 26 0.57
10 10 0.22
11 10 0.22
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (9 bp):
TTTTTATAT
Found at i:40288226 original size:19 final size:19
Alignment explanation
Indices: 40288172--40288227 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
40288162 CCTTTTTATG
*
40288172 TTTTCTTATAATTTTTCAATA
1 TTTT-TTAT-ATTTTTTAATA
*
40288193 TATTTTTA-ATATTTTAATA
1 T-TTTTTATATTTTTTAATA
40288212 TTTTTTATATTTTTTA
1 TTTTTTATATTTTTTA
40288228 TGAGAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.20
19 17 0.57
21 4 0.13
22 3 0.10
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTATATTTTTTAATA
Found at i:40288963 original size:25 final size:25
Alignment explanation
Indices: 40288908--40288963 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
40288898 TTTAGATTTT
*
40288908 TTTAAATTTTATAATTTTTAAAAAA
1 TTTAAATTTTAGAATTTTTAAAAAA
* *
40288933 TATAAATTTT-GAATTTTTATAAATA
1 TTTAAATTTTAGAATTTTTA-AAAAA
40288958 TTTAAA
1 TTTAAA
40288964 AATTGTTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTAAATTTTAGAATTTTTAAAAAA
Found at i:40288985 original size:21 final size:20
Alignment explanation
Indices: 40288953--40289000 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
40288943 GAATTTTTAT
*
40288953 AAATATTTAAAAATTGTTTTG
1 AAAT-TTTAAAAATTATTTTG
40288974 AAATTTTAAAAATTATTTTG
1 AAATTTTAAAAATTATTTTG
*
40288994 AACTTTT
1 AAATTTT
40289001 CTTTTGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (20 bp):
AAATTTTAAAAATTATTTTG
Found at i:40291586 original size:16 final size:16
Alignment explanation
Indices: 40291565--40291596 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40291555 TAGTTTTAGG
40291565 TGGGATGATTTGATCC
1 TGGGATGATTTGATCC
40291581 TGGGATGATTTGATCC
1 TGGGATGATTTGATCC
40291597 ATAATGGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (16 bp):
TGGGATGATTTGATCC
Found at i:40296444 original size:3 final size:3
Alignment explanation
Indices: 40296436--40296476 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
40296426 CCTCCGGCAC
40296436 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
40296477 CTCGAAACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:40299735 original size:25 final size:24
Alignment explanation
Indices: 40299698--40299749 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
40299688 ACTGTTATAA
* *
40299698 AAAATTATAAAAT-AAAAATTAATT
1 AAAATTACAAAATGAAAAAAT-ATT
40299722 AAAATTACATAAATGAAAAAATATT
1 AAAATTACA-AAATGAAAAAATATT
40299747 AAA
1 AAA
40299750 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAATATT
Found at i:40307421 original size:13 final size:13
Alignment explanation
Indices: 40307405--40307432 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40307395 GTAAAGACTT
40307405 ATACAAATTGTAG
1 ATACAAATTGTAG
40307418 ATACAAATTGTAG
1 ATACAAATTGTAG
40307431 AT
1 AT
40307433 TTGGAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (13 bp):
ATACAAATTGTAG
Found at i:40310007 original size:96 final size:97
Alignment explanation
Indices: 40309846--40310155 Score: 410
Period size: 96 Copynumber: 3.2 Consensus size: 97
40309836 CATTTTAGAT
* * * * * * *
40309846 TTTAGGG-TTTTAAGGGAAAAATTAAACAAATCAGGGTTTAGGATTTCTTAATTAAATTAACTAT
1 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
* * *
40309910 -AAGTTTTAAAAAACTAGATTAGGGTTTAGCG
66 AAAATTTTAAAAAATTAGATTAGGGTTTAGTG
* *
40309941 TTTATGATTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
* *
40310006 AAATTTTTAAAAAAATTAGATTAGCGTTTAGTG
66 AAAATTTT-AAAAAATTAGATTAGGGTTTAGTG
* * *
40310039 TTTAGGGTTTTTAAGG-AAAAATCAAATAAATTAGGATTTAGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
* * *
40310103 AAAATTTAAAAAAATTAGATTAGGTTTTAGTA
66 AAAATTTTAAAAAATTAGATTAGGGTTTAGTG
40310135 TTTAGGGTTTTTAAGGAAAAA
1 TTTAGGGTTTTTAAGGAAAAA
40310156 TCTAATAAAG
Statistics
Matches: 188, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
95 5 0.03
96 87 0.46
97 61 0.32
98 35 0.19
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.38
Consensus pattern (97 bp):
TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
AAAATTTTAAAAAATTAGATTAGGGTTTAGTG
Found at i:40310374 original size:2 final size:2
Alignment explanation
Indices: 40310367--40310392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40310357 GTTAAAAGTT
40310367 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
40310393 AGCATAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40315016 original size:12 final size:12
Alignment explanation
Indices: 40314999--40315023 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40314989 TCGGTCTTAC
40314999 TGTTTTGTTTTT
1 TGTTTTGTTTTT
40315011 TGTTTTGTTTTT
1 TGTTTTGTTTTT
40315023 T
1 T
40315024 CTTATCGACT
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TGTTTTGTTTTT
Found at i:40315904 original size:71 final size:71
Alignment explanation
Indices: 40315788--40316003 Score: 432
Period size: 71 Copynumber: 3.0 Consensus size: 71
40315778 TAGGGGACAA
40315788 CTTAACTCATGTTTGTAATAACTGCGTAACGATGCTGTTTTTCCTTTTCTTCCCACCAAAGTCCA
1 CTTAACTCATGTTTGTAATAACTGCGTAACGATGCTGTTTTTCCTTTTCTTCCCACCAAAGTCCA
40315853 TTTTTC
66 TTTTTC
40315859 CTTAACTCATGTTTGTAATAACTGCGTAACGATGCTGTTTTTCCTTTTCTTCCCACCAAAGTCCA
1 CTTAACTCATGTTTGTAATAACTGCGTAACGATGCTGTTTTTCCTTTTCTTCCCACCAAAGTCCA
40315924 TTTTTC
66 TTTTTC
40315930 CTTAACTCATGTTTGTAATAACTGCGTAACGATGCTGTTTTTCCTTTTCTTCCCACCAAAGTCCA
1 CTTAACTCATGTTTGTAATAACTGCGTAACGATGCTGTTTTTCCTTTTCTTCCCACCAAAGTCCA
40315995 TTTTTC
66 TTTTTC
40316001 CTT
1 CTT
40316004 TTCTTCCCAC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 145 1.00
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (71 bp):
CTTAACTCATGTTTGTAATAACTGCGTAACGATGCTGTTTTTCCTTTTCTTCCCACCAAAGTCCA
TTTTTC
Found at i:40316007 original size:28 final size:28
Alignment explanation
Indices: 40315967--40316024 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
40315957 AACGATGCTG
40315967 TTTTTCCTTTTCTTCCCACCAAAGTCCA
1 TTTTTCCTTTTCTTCCCACCAAAGTCCA
40315995 TTTTTCCTTTTCTTCCCACCAAAGTCCA
1 TTTTTCCTTTTCTTCCCACCAAAGTCCA
40316023 TT
1 TT
40316025 ATAGGAAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.34, G:0.03, T:0.45
Consensus pattern (28 bp):
TTTTTCCTTTTCTTCCCACCAAAGTCCA
Found at i:40323175 original size:20 final size:21
Alignment explanation
Indices: 40323143--40323181 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40323133 TCACGTTAGC
*
40323143 AATTAATTATTTTTTTTTAAA
1 AATTAATTATTTTATTTTAAA
40323164 AATTAA-TATTTTATTTTA
1 AATTAATTATTTTATTTTA
40323182 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTAATTATTTTATTTTAAA
Found at i:40323673 original size:136 final size:137
Alignment explanation
Indices: 40323519--40323792 Score: 514
Period size: 136 Copynumber: 2.0 Consensus size: 137
40323509 AAGCATTTTC
40323519 CAAAATAATTTTTTTTTATTTATCAAAAGGATTAAAACCCAACTGGGATTACAGTGGCAAATTTA
1 CAAAATAA-TTTTTTTTATTTATCAAAAGGATTAAAACCCAACTGGGATTACAGTGGCAAATTTA
40323584 GGGGAGCTGGCAGGAGGTTAACCTCTTTAAAATAAAAAATTTTCTATTTAATCTTCTTTATAATA
65 GGGGAGCTGGCAGGAGGTTAACCTCTTTAAAATAAAAAATTTTCTATTTAATCTTCTTTATAATA
40323649 TATAAAAT
130 TATAAAAT
40323657 CAAAATAA-TTTTTTTATTTATCAAAAGGATTAAAACCCAACTGGGATTACAGTGGCAAATTTAG
1 CAAAATAATTTTTTTTATTTATCAAAAGGATTAAAACCCAACTGGGATTACAGTGGCAAATTTAG
**
40323721 GGGAGCTGGCAGGAGGTTAACCTCTTTTTAATAAAAAATTTTCTATTTAATCTTCTTTATAATAT
66 GGGAGCTGGCAGGAGGTTAACCTCTTTAAAATAAAAAATTTTCTATTTAATCTTCTTTATAATAT
40323786 ATAAAAT
131 ATAAAAT
40323793 TTTAAATTAT
Statistics
Matches: 134, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
136 126 0.94
138 8 0.06
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (137 bp):
CAAAATAATTTTTTTTATTTATCAAAAGGATTAAAACCCAACTGGGATTACAGTGGCAAATTTAG
GGGAGCTGGCAGGAGGTTAACCTCTTTAAAATAAAAAATTTTCTATTTAATCTTCTTTATAATAT
ATAAAAT
Found at i:40324788 original size:20 final size:21
Alignment explanation
Indices: 40324756--40324794 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40324746 TCACGTTAGC
*
40324756 AATTAATTATTTTTTTTTAAA
1 AATTAATTATTTTATTTTAAA
40324777 AATTAA-TATTTTATTTTA
1 AATTAATTATTTTATTTTA
40324795 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTAATTATTTTATTTTAAA
Found at i:40336551 original size:14 final size:14
Alignment explanation
Indices: 40336532--40336558 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40336522 TTGGTAACTT
40336532 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
40336546 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
40336559 AGGCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:40336720 original size:6 final size:6
Alignment explanation
Indices: 40336703--40336743 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
40336693 CGCCTTCTTC
*
40336703 TCCCCTT TCCCCT TCCCCT TCCCCT TCCCCT TCTCCT TCCC
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCC
40336744 TTTGGGTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCCT
Found at i:40346534 original size:24 final size:26
Alignment explanation
Indices: 40346507--40346558 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
40346497 TAAAAATTAT
*
40346507 TAAATTTTAATAAAAATAA-A-AAAA
1 TAAAATTTAATAAAAATAAGATAAAA
* *
40346531 TAAAATTTATTAAATATAAGATAAAA
1 TAAAATTTAATAAAAATAAGATAAAA
40346557 TA
1 TA
40346559 TGAAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 16 0.70
25 1 0.04
26 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
TAAAATTTAATAAAAATAAGATAAAA
Found at i:40346558 original size:34 final size:35
Alignment explanation
Indices: 40346482--40346556 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
40346472 AAAATTAACA
* *
40346482 AAAAATAAAAATCAATAAAAATTATTAAATTTTAAT
1 AAAAATAAAAA-CAATAAAAATTATTAAATATAAAT
*
40346518 AAAAATAAAAA-AATAAAATTTATTAAATATAAGAT
1 AAAAATAAAAACAATAAAAATTATTAAATATAA-AT
40346553 AAAA
1 AAAA
40346557 TATGAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 18 0.51
35 6 0.17
36 11 0.31
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (35 bp):
AAAAATAAAAACAATAAAAATTATTAAATATAAAT
Found at i:40346836 original size:10 final size:10
Alignment explanation
Indices: 40346780--40346937 Score: 51
Period size: 10 Copynumber: 16.1 Consensus size: 10
40346770 TTTTGGTACA
40346780 ATAA-TTTTT
1 ATAATTTTTT
*
40346789 ATATTTTTTT
1 ATAATTTTTT
* **
40346799 TTAAAATTTT
1 ATAATTTTTT
40346809 AT-ATTTCTTT
1 ATAATTT-TTT
* *
40346819 ACATTTTTTT
1 ATAATTTTTT
40346829 ATAATTTTCTT
1 ATAATTTT-TT
* *
40346840 ACAA--CTTT
1 ATAATTTTTT
**
40346848 ATAAAATTTT
1 ATAATTTTTT
40346858 ATAATTTTTT
1 ATAATTTTTT
* *
40346868 CT-ATATTTCT
1 ATAAT-TTTTT
**
40346878 AT-ATAGTTT
1 ATAATTTTTT
40346887 ATAATTTTTT
1 ATAATTTTTT
**
40346897 ACGA-TTTTT
1 ATAATTTTTT
**
40346906 ATAAAATTTT
1 ATAATTTTTT
* *
40346916 ACATTTTTTTT
1 ATA-ATTTTTT
40346927 ATAATTTTTT
1 ATAATTTTTT
40346937 A
1 A
40346938 CGAGTTTTAT
Statistics
Matches: 102, Mismatches: 37, Indels: 19
0.65 0.23 0.12
Matches are distributed among these distances:
8 5 0.05
9 19 0.19
10 64 0.63
11 14 0.14
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:40346908 original size:19 final size:19
Alignment explanation
Indices: 40346884--40346954 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
40346874 TTCTATATAG
40346884 TTTATAATTTTTTACGATT
1 TTTATAATTTTTTACGATT
**
40346903 TTTATAAAATTTTAC-ATTTTT
1 TTTATAATTTTTTACGA---TT
*
40346924 TTTATAATTTTTTACGAGT
1 TTTATAATTTTTTACGATT
40346943 TTTAT-ATTTTTT
1 TTTATAATTTTTT
40346955 TTCTAATTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.19
19 19 0.44
21 15 0.35
22 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTATAATTTTTTACGATT
Found at i:40346916 original size:29 final size:28
Alignment explanation
Indices: 40346825--40346925 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
40346815 CTTTACATTT
**
40346825 TTTTATAATTTTCTTACAACTTTATAAAA
1 TTTTATAATTTT-TTACATTTTTATAAAA
*
40346854 TTTTATAATTTTTT-CTATATTTCTAT-ATA
1 TTTTATAATTTTTTAC-AT-TTT-TATAAAA
*
40346883 GTTTATAATTTTTTACGATTTTTATAAAA
1 TTTTATAATTTTTTAC-ATTTTTATAAAA
* *
40346912 TTTTACATTTTTTT
1 TTTTATAATTTTTT
40346926 TATAATTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.02
28 6 0.10
29 45 0.78
30 6 0.10
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTATAATTTTTTACATTTTTATAAAA
Found at i:40346944 original size:58 final size:58
Alignment explanation
Indices: 40346825--40346955 Score: 142
Period size: 58 Copynumber: 2.2 Consensus size: 58
40346815 CTTTACATTT
*
40346825 TTTTATAATTTTCTTACAACTTTATAAAATTTTATAATTTTTTCTATATTTCTATATAG
1 TTTTATAATTTT-TTACAACTTTATAAAATTTTATAATTTTTTCTATATTTCTATAGAG
** * * *
40346884 -TTTATAATTTTTTACGATTTTTATAAAATTTTA-CATTTTTTTTATAATTT-TTTACGAG
1 TTTTATAATTTTTTAC-AACTTTATAAAATTTTATAATTTTTTCTAT-ATTTCTATA-GAG
*
40346942 TTTTATATTTTTTT
1 TTTTATAATTTTTT
40346956 TCTAATTCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
57 17 0.28
58 32 0.52
59 12 0.20
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (58 bp):
TTTTATAATTTTTTACAACTTTATAAAATTTTATAATTTTTTCTATATTTCTATAGAG
Found at i:40357860 original size:4 final size:4
Alignment explanation
Indices: 40357851--40357904 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
40357841 GTAGCTTACC
40357851 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
40357899 TGTA TG
1 TGTA TG
40357905 CTCTAAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:40366458 original size:16 final size:16
Alignment explanation
Indices: 40366433--40366466 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40366423 TTGTTTACGG
40366433 GAAAAAAAAAGAAAAA
1 GAAAAAAAAAGAAAAA
*
40366449 GAAAAGAAAAGAAAAA
1 GAAAAAAAAAGAAAAA
40366465 GA
1 GA
40366467 GAGAGTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAGAAAAA
Found at i:40371174 original size:17 final size:16
Alignment explanation
Indices: 40371128--40371177 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
40371118 TTCTACAATA
40371128 TTTTTCATAATTTTTGCAT
1 TTTTTCATAA-TTTT--AT
40371147 TTTTT-AT-ATTTTAT
1 TTTTTCATAATTTTAT
40371161 TATTTTCATAATTTTAT
1 T-TTTTCATAATTTTAT
40371178 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.11
15 4 0.14
16 6 0.21
17 8 0.29
18 2 0.07
19 5 0.18
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTTTCATAATTTTAT
Found at i:40376635 original size:25 final size:25
Alignment explanation
Indices: 40376584--40376635 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
40376574 ATGCCTCTAA
* * *
40376584 AATAGTAACAAAATAATACGAACAT
1 AATAGTAACAAAATAACAAGAAAAT
40376609 AATAGTGAA-AAAATAACAAGAAAAT
1 AATAGT-AACAAAATAACAAGAAAAT
40376634 AA
1 AA
40376636 CCAAAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.65, C:0.08, G:0.10, T:0.17
Consensus pattern (25 bp):
AATAGTAACAAAATAACAAGAAAAT
Found at i:40377341 original size:2 final size:2
Alignment explanation
Indices: 40377334--40377373 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40377324 TGGTTTCACT
40377334 TA TA TA 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 TA TA TA
40377374 AATAAAAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40380549 original size:7 final size:7
Alignment explanation
Indices: 40380538--40380568 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
40380528 ATGTGGCAAA
40380538 AAAAAGAT
1 AAAAA-AT
40380546 AAAAAAT
1 AAAAAAT
40380553 AAAAAAT
1 AAAAAAT
40380560 AAAAAAT
1 AAAAAAT
40380567 AA
1 AA
40380569 TATAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.78
8 5 0.22
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:40380573 original size:19 final size:19
Alignment explanation
Indices: 40380535--40380614 Score: 55
Period size: 18 Copynumber: 4.4 Consensus size: 19
40380525 GAAATGTGGC
*
40380535 AAAAAA-AAGATAAAAAAT
1 AAAAAATAATATAAAAAAT
*
40380553 AAAAAATAA-A-AAATAAT
1 AAAAAATAATATAAAAAAT
**
40380570 ATAAAAAT-AT-TAAAATTT
1 A-AAAAATAATATAAAAAAT
40380588 AATAAAATAATAT-AAAAAT
1 AA-AAAATAATATAAAAAAT
40380607 ACAAAAAT
1 A-AAAAAT
40380615 CATAAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
17 9 0.19
18 23 0.48
19 14 0.29
20 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (19 bp):
AAAAAATAATATAAAAAAT
Found at i:40380578 original size:8 final size:8
Alignment explanation
Indices: 40380538--40380642 Score: 60
Period size: 8 Copynumber: 12.9 Consensus size: 8
40380528 ATGTGGCAAA
*
40380538 AAAAAGAT
1 AAAAATAT
40380546 AAAAA-AT
1 AAAAATAT
40380553 AAAAA-AT
1 AAAAATAT
40380560 AAAAA-AT
1 AAAAATAT
40380567 ---AATAT
1 AAAAATAT
40380572 AAAAATATT
1 AAAAATA-T
*
40380581 AAAATTTAAT
1 AAAA-AT-AT
40380591 AAAATAATAT
1 -AAA-AATAT
*
40380601 AAAAATAC
1 AAAAATAT
40380609 AAAAATCAT
1 AAAAAT-AT
40380618 AAAATATAT
1 AAAA-ATAT
*
40380627 AGAAATAT
1 AAAAATAT
40380635 AGAAAATA
1 A-AAAATA
40380643 ATTATAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 16 0.20
8 24 0.30
9 23 0.29
10 6 0.08
11 5 0.06
12 1 0.01
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATAT
Found at i:40384003 original size:37 final size:37
Alignment explanation
Indices: 40383962--40384033 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
40383952 ACATTAAGTA
* * *
40383962 ATGATAAATTCTGATGGTCATGTTAGAGGTGTTCACG
1 ATGATAAATTATGATAGTCATGTTAAAGGTGTTCACG
*
40383999 ATGATAAGTTATGATAGTCATGTTAAAGGTGTTCA
1 ATGATAAATTATGATAGTCATGTTAAAGGTGTTCA
40384034 TGGGTCAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (37 bp):
ATGATAAATTATGATAGTCATGTTAAAGGTGTTCACG
Found at i:40385112 original size:20 final size:19
Alignment explanation
Indices: 40385089--40385141 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
40385079 AAAATCATTA
40385089 AAAATCAATAAAAATATA-
1 AAAATCAATAAAAATATAG
*
40385107 ATAAAACAA-AAAAATATAG
1 A-AAATCAATAAAAATATAG
40385126 AAAAT-AATAAAAATAT
1 AAAATCAATAAAAATAT
40385142 TAAAGTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 2 0.07
18 21 0.70
19 7 0.23
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATCAATAAAAATATAG
Found at i:40388218 original size:30 final size:30
Alignment explanation
Indices: 40388179--40388245 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
40388169 ACTTTGTCTA
*
40388179 TTTTGGAAATTTAGATATATT-TTTTCGAAT
1 TTTTAGAAATTTAGATATATTGTTTT-GAAT
40388209 TTTTAGAAATTTAGATATATTGTTTTGAAT
1 TTTTAGAAATTTAGATATATTGTTTTGAAT
*
40388239 ATTTAGA
1 TTTTAGA
40388246 GTTTAGAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.52
Consensus pattern (30 bp):
TTTTAGAAATTTAGATATATTGTTTTGAAT
Found at i:40402311 original size:11 final size:11
Alignment explanation
Indices: 40402292--40402337 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
40402282 TTTTTTGTTA
*
40402292 TGCTGCTATTT
1 TGCTACTATTT
40402303 TGCTACTATTT
1 TGCTACTATTT
* * *
40402314 CGCTATTATAT
1 TGCTACTATTT
40402325 TGCTACTATTT
1 TGCTACTATTT
40402336 TG
1 TG
40402338 TTGTTGTTGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.52
Consensus pattern (11 bp):
TGCTACTATTT
Found at i:40418918 original size:74 final size:74
Alignment explanation
Indices: 40418797--40418939 Score: 250
Period size: 74 Copynumber: 1.9 Consensus size: 74
40418787 TATTACATCC
* * *
40418797 TTTCATTTATAATTATTTGAACACTGTAAATATTTGAAAATGTTCCAACAATAGTTTAGGTTAAA
1 TTTCATTTATAATTATTTGAACACTATAAATATTTGAAAATATTCCAACAATAATTTAGGTTAAA
40418862 CTACTGCAA
66 CTACTGCAA
*
40418871 TTTCATTTATAATTATTTGAACACTATAAATATTTGAAAATATTCCAACAATAATTTGGGTTAAA
1 TTTCATTTATAATTATTTGAACACTATAAATATTTGAAAATATTCCAACAATAATTTAGGTTAAA
40418936 CTAC
66 CTAC
40418940 AACAACCGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (74 bp):
TTTCATTTATAATTATTTGAACACTATAAATATTTGAAAATATTCCAACAATAATTTAGGTTAAA
CTACTGCAA
Found at i:40424120 original size:65 final size:65
Alignment explanation
Indices: 40424011--40424143 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
40424001 ATCTATTATA
* * * * * * *
40424011 ATAAGACCCTTCTAGAATGGTTTCTAATATATCTGACAATACTCTTACATTGGTAAATATCATAT
1 ATAAGACCCTTCTAGAACGATTTCTAATAGATCTAACAACACTCTTACATTAGCAAATATCATAT
* * * *
40424076 ATAAGATCCTTCTAGAACGATTTTTAATAGATCTAATAACACTCTTATATTAGCAAATATCATAT
1 ATAAGACCCTTCTAGAACGATTTCTAATAGATCTAACAACACTCTTACATTAGCAAATATCATAT
40424141 ATA
1 ATA
40424144 TATATATACA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (65 bp):
ATAAGACCCTTCTAGAACGATTTCTAATAGATCTAACAACACTCTTACATTAGCAAATATCATAT
Found at i:40426445 original size:156 final size:155
Alignment explanation
Indices: 40426176--40426954 Score: 1016
Period size: 156 Copynumber: 5.0 Consensus size: 155
40426166 CTACATGCAC
* * **
40426176 CCTTTTCAGGAAATTGTATC---GAAGCCATCTGAGGAATTACTCTTCAAGGAGAAAATGGTATG
1 CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCACAAGGAGAAAATGGTATG
* ** * * *
40426238 TTCTTGTGTACATATTTATATCTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAATGTCA
66 TTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCA
*
40426303 AATCAAGGATAACGAACTACGAACA
131 AATCAAGGATAATGAACTACGAACA
* *
40426328 CCTTTTTCAGGAAATTGAATCGAGGAAGCCATCTGAGAAATTACTCCACAAGGAGAAAATGGTAT
1 CC-TTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCACAAGGAGAAAATGGTAT
* * * *
40426393 GTTCTTGTGCATTTATTTATACTTTGAGTTGTGCGTTAGAGGATGGAGATAGGAACATAAAAGTC
65 GTTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTC
*
40426458 AAATCAAGGATAATGAACTAGGAACA
130 AAATCAAGGATAATGAACTACGAACA
* *
40426484 CCCTTTTCAGGAAACTGTATCGAGGAAGAAGCCATCTGGGAAATTACTCTACAAGGAGAAAATGG
1 -CCTTTTCAGGAAACTGTATCGA-G--GAAGCCATCTGAGAAATTACTCCACAAGGAGAAAATGG
* * * *
40426549 TATGTTCTTGTGC-TTGTATTTATATTTTGAGTTGTGTGTTTTAGGATTGAGATATGAACAT-AA
62 TATGTTCTTGTGCATT-TATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAA
* * *
40426612 GGTCAAATCAAGGGTGATGAACTA-GAAACA
126 AGTCAAATCAAGGATAATGAACTACG-AACA
* * *
40426642 CCCTTTCAGGAAACTGTATCGAGGAAGAAGCCATATGAGAAATTACTCCCCAAGGAGAAAATGGT
1 CCTTTTCAGGAAACTGTATCGA-G--GAAGCCATCTGAGAAATTACTCCACAAGGAGAAAATGGT
*
40426707 ATGTTCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAG
63 ATGTTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAG
* *
40426772 TCAAATCAAGGATAATAAACTACGAGCA
128 TCAAATCAAGGATAATGAACTACGAACA
* * *
40426800 TCCTTTTCAGGAAACTATATCAAGGAAGCCATCTGAGAAATTACTCC-CAAAGGAAAAAATGGTA
1 -CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCAC-AAGGAGAAAATGGTA
* * * *
40426864 TTTTCTTGTGC-TTGTATTTATAGTTTGAGTCGTGTGTTTGAGGATGGAGATAGGGATATAAAAG
64 TGTTCTTGTGCATT-TATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAG
*
40426928 TCAAATCAAGGATAATGAACTATGAAC
128 TCAAATCAAGGATAATGAACTACGAAC
40426955 TTTTCTTTTG
Statistics
Matches: 554, Mismatches: 57, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
152 2 0.00
153 17 0.03
155 2 0.00
156 252 0.45
157 117 0.21
158 56 0.10
159 108 0.19
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (155 bp):
CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCACAAGGAGAAAATGGTATG
TTCTTGTGCATTTATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCA
AATCAAGGATAATGAACTACGAACA
Found at i:40426741 original size:316 final size:312
Alignment explanation
Indices: 40426173--40426954 Score: 1051
Period size: 316 Copynumber: 2.5 Consensus size: 312
40426163 TAACTACATG
* * *
40426173 CACCCTTTTCAGGAAATTGTATC---GAAGCCATCTGAGG-AATTACTCTTCAAGGAGAAAATGG
1 CACCCTTTTCAGGAAACTATATCAAAGAAGCCATCTG-GGAAATTACTCTACAAGGAGAAAATGG
** *
40426234 TATGTTCTTGTG-TACATATTTATATCTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAA
65 TATGTTCTTGTGCT-TGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAA
* * * * *
40426298 TGTCAAATCAAGGATAACGAACTACGAACACCTTTTTCAGGAAATTGAATCGAGGAAGCCATCTG
129 AGTCAAATCAAGGATAATGAACTACGAACACCTCTTTCAGGAAACTGAATCGAGGAAGCCATATG
*
40426363 AGAAATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATTTATTTATACTTTGAGTTGTGCG
194 AGAAATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATACTTTGAGTTGTGCG
* *
40426428 TTAGAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATGAACTAGGAA
259 TTAGAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATAAACTACGAA
*
40426482 CACCCTTTTCAGGAAACTGTATCGAGGAAGAAGCCATCTGGGAAATTACTCTACAAGGAGAAAAT
1 CACCCTTTTCAGGAAACTATATC-A--AAGAAGCCATCTGGGAAATTACTCTACAAGGAGAAAAT
* * * *
40426547 GGTATGTTCTTGTGCTTGTATTTATATTTTGAGTTGTGTGTTTTAGGATTGAGATATGAACAT-A
63 GGTATGTTCTTGTGCTTGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAA
* * * *
40426611 AGGTCAAATCAAGGGTGATGAACTA-GAAACACC-CTTTCAGGAAACTGTATCGAGGAAGAAGCC
128 AAGTCAAATCAAGGATAATGAACTACG-AACACCTCTTTCAGGAAACTGAATCGA-G--GAAGCC
* *
40426674 ATATGAGAAATTACTCCCCAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATATTTTGAGTT
189 ATATGAGAAATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATACTTTGAGTT
* * * *
40426739 GTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCAAATCAAGGATAATAAACTACGAG
254 GTGCGTTAGAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATAAACTACGAA
* * * * *
40426798 CATCCTTTTCAGGAAACTATATCAAGGAAGCCATCTGAGAAATTACTC-CCAAAGGAAAAAATGG
1 CACCCTTTTCAGGAAACTATATCAAAGAAGCCATCTGGGAAATTACTCTAC-AAGGAGAAAATGG
* * * * *
40426862 TATTTTCTTGTGCTTGTATTTATAGTTTGAGTCGTGTGTTTGAGGATGGAGATAGGGATATAAAA
65 TATGTTCTTGTGCTTGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAAA
*
40426927 GTCAAATCAAGGATAATGAACTATGAAC
130 GTCAAATCAAGGATAATGAACTACGAAC
40426955 TTTTCTTTTG
Statistics
Matches: 415, Mismatches: 43, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
309 22 0.05
312 1 0.00
313 105 0.25
314 57 0.14
315 88 0.21
316 142 0.34
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (312 bp):
CACCCTTTTCAGGAAACTATATCAAAGAAGCCATCTGGGAAATTACTCTACAAGGAGAAAATGGT
ATGTTCTTGTGCTTGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAAAG
TCAAATCAAGGATAATGAACTACGAACACCTCTTTCAGGAAACTGAATCGAGGAAGCCATATGAG
AAATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATACTTTGAGTTGTGCGTT
AGAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATAAACTACGAA
Found at i:40438416 original size:28 final size:26
Alignment explanation
Indices: 40438365--40438422 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
40438355 ACAGATAAAA
* *
40438365 TTAATTTTTTTATTAAATAGATTAAT
1 TTAATTTTTTTATTAAAAAAATTAAT
40438391 TTAATTTTTATATATTAAAAAAATTAAT
1 TTAATTTTT-T-TATTAAAAAAATTAAT
40438419 TTAA
1 TTAA
40438423 GTCAATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 9 0.32
27 1 0.04
28 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TTAATTTTTTTATTAAAAAAATTAAT
Found at i:40442618 original size:60 final size:59
Alignment explanation
Indices: 40442524--40442657 Score: 137
Period size: 60 Copynumber: 2.3 Consensus size: 59
40442514 TTTTTTAAAT
* * * * *
40442524 AATTTTT-AATTTTTAGAGTTAGGATTAAATTGACATA-TTTTGGAAATATTGAGGGCCA
1 AATTTTTGAATTTTTAGAATTAGAACTAAAATGACA-ACTTTTGGAAACATTGAGGGCCA
* * * *
40442582 AATTTATTGAATTTTTAGAATTATAACTAAAATGACAACTTTTGTAAACATTGATGGCTA
1 AATTT-TTGAATTTTTAGAATTAGAACTAAAATGACAACTTTTGGAAACATTGAGGGCCA
*
40442642 AATTTGTTGATTTTTT
1 AATTT-TTGAATTTTT
40442658 TATATATTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 5 0.08
59 3 0.05
60 54 0.87
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (59 bp):
AATTTTTGAATTTTTAGAATTAGAACTAAAATGACAACTTTTGGAAACATTGAGGGCCA
Found at i:40445431 original size:29 final size:27
Alignment explanation
Indices: 40445361--40445428 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
40445351 AATATTTTTA
*
40445361 TATTTAAAATATTATATAGAACTTAAT
1 TATTAAAAATATTATATAGAACTTAAT
*
40445388 TTTTAAAAATATTATATAGAACTT-AT
1 TATTAAAAATATTATATAGAACTTAAT
40445414 TGAATTAAAAATATT
1 T--ATTAAAAATATT
40445429 TATTGAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.08
27 22 0.61
28 11 0.31
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (27 bp):
TATTAAAAATATTATATAGAACTTAAT
Found at i:40445968 original size:20 final size:20
Alignment explanation
Indices: 40445926--40446025 Score: 76
Period size: 19 Copynumber: 5.5 Consensus size: 20
40445916 AAGTTTATGA
* *
40445926 AAATGTACGTATTT-ATTAT
1 AAATGTACATATTTAATTAC
40445945 AAATGTACATATTTAATTAC
1 AAATGTACATATTTAATTAC
** *
40445965 AAATGTACA-AAGTAAAT-C
1 AAATGTACATATTTAATTAC
40445983 -AA--T---TATTTAATTAC
1 AAATGTACATATTTAATTAC
40445997 AAAATGTACATATTT-ATTAC
1 -AAATGTACATATTTAATTAC
40446017 AAATGTACA
1 AAATGTACA
40446026 AAGTAAACCA
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
13 5 0.08
14 1 0.02
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 27 0.43
20 18 0.29
21 5 0.08
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (20 bp):
AAATGTACATATTTAATTAC
Found at i:40446026 original size:52 final size:51
Alignment explanation
Indices: 40445935--40446064 Score: 190
Period size: 52 Copynumber: 2.5 Consensus size: 51
40445925 AAAATGTACG
* *
40445935 TATTT-ATTATAAATGTACATATTTAATTACAAATGTACAAAGTAAATCAAT
1 TATTTAATTAAAAATGTACATATTT-ATTACAAATGTACAAAGTAAACCAAT
40445986 TATTTAATTACAAAATGTACATATTTATTACAAATGTACAAAGTAAACCAAT
1 TATTTAATTA-AAAATGTACATATTTATTACAAATGTACAAAGTAAACCAAT
* **
40446038 TATTTAATTATATTTGTACATATTTAT
1 TATTTAATTAAAAATGTACATATTTAT
40446065 ATTATTACAC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
51 19 0.26
52 39 0.54
53 14 0.19
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (51 bp):
TATTTAATTAAAAATGTACATATTTATTACAAATGTACAAAGTAAACCAAT
Found at i:40458884 original size:21 final size:20
Alignment explanation
Indices: 40458848--40458901 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
40458838 AATTTTAATT
* *
40458848 ATTTTTAAAATATTTATACA
1 ATTTTTAATATTTTTATACA
*
40458868 ATTTTTAATGATTTTTATATA
1 ATTTTTAAT-ATTTTTATACA
*
40458889 TTTTTTAATATTT
1 ATTTTTAATATTT
40458902 ATAGATGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTTAATATTTTTATACA
Found at i:40464498 original size:20 final size:20
Alignment explanation
Indices: 40464473--40464512 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40464463 TAAACTTGAA
40464473 TTCCGTTAAAGTATAATGAC
1 TTCCGTTAAAGTATAATGAC
40464493 TTCCGTTAAAGTATAATGAC
1 TTCCGTTAAAGTATAATGAC
40464513 ATGACACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TTCCGTTAAAGTATAATGAC
Found at i:40466938 original size:36 final size:36
Alignment explanation
Indices: 40466882--40466951 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
40466872 CTGTTAACTA
* *
40466882 CACTGCTTCTTTGGTTACTTATGGTGAACCCACTTT
1 CACTGCTTCTATGGTAACTTATGGTGAACCCACTTT
*
40466918 CACTGCTTCTATGGTAACTTATGGTGAATCCACT
1 CACTGCTTCTATGGTAACTTATGGTGAACCCACT
40466952 GCATCTATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (36 bp):
CACTGCTTCTATGGTAACTTATGGTGAACCCACTTT
Found at i:40469759 original size:30 final size:32
Alignment explanation
Indices: 40469723--40469787 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 32
40469713 AATTCAACTA
40469723 TAAATAGAGGCA-T-TCTCATTAGTTATCCTC
1 TAAATAGAGGCATTCTCTCATTAGTTATCCTC
40469753 TAAATAGAGGCATTCCCTCTCATTAGTTATCCTC
1 TAAATAGAGGCATT--CTCTCATTAGTTATCCTC
40469787 T
1 T
40469788 CAGGATACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 12 0.39
31 1 0.03
34 18 0.58
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (32 bp):
TAAATAGAGGCATTCTCTCATTAGTTATCCTC
Found at i:40472130 original size:11 final size:10
Alignment explanation
Indices: 40472114--40472264 Score: 61
Period size: 10 Copynumber: 15.4 Consensus size: 10
40472104 AGAAAGAAAG
40472114 AAAAATTAATA
1 AAAAATT-ATA
40472125 AAAAATTATA
1 AAAAATTATA
*
40472135 AAAAAGTAT-
1 AAAAATTATA
* *
40472144 -TAAATTGTA
1 AAAAATTATA
40472153 ATAAAA-TATA
1 A-AAAATTATA
***
40472163 AAATGGTA-A
1 AAAAATTATA
40472172 AAAAATTATAA
1 AAAAATTAT-A
*
40472183 AAAAATTGTA
1 AAAAATTATA
**
40472193 AAATTTTAT-
1 AAAAATTATA
40472202 AAAAATTAT-
1 AAAAATTATA
40472211 --AAATTATA
1 AAAAATTATA
* *
40472219 TAGAAATATAGAA
1 -AAAAAT-TA-TA
40472232 AAAAATTATA
1 AAAAATTATA
40472242 AAAAATGTA-A
1 AAAAAT-TATA
*
40472252 AGAAA-TATA
1 AAAAATTATA
40472261 AAAA
1 AAAA
40472265 TCGTAAAATT
Statistics
Matches: 104, Mismatches: 22, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
7 7 0.07
8 7 0.07
9 19 0.18
10 36 0.35
11 27 0.26
12 7 0.07
13 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:40472166 original size:18 final size:18
Alignment explanation
Indices: 40472126--40472175 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
40472116 AAATTAATAA
*
40472126 AAAATTATAAAAAAGTAT
1 AAAATTGTAAAAAAGTAT
*
40472144 TAAATTGTAATAAAA-TAT
1 AAAATTGTAA-AAAAGTAT
*
40472162 AAAATGGTAAAAAA
1 AAAATTGTAAAAAA
40472176 ATTATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
AAAATTGTAAAAAAGTAT
Found at i:40472176 original size:18 final size:18
Alignment explanation
Indices: 40472133--40472184 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
40472123 TAAAAAATTA
* * *
40472133 TAAAAAAGTATTAAATTG
1 TAAAAAAATATAAAATGG
*
40472151 TAATAAAATATAAAATGG
1 TAAAAAAATATAAAATGG
40472169 TAAAAAAATTATAAAA
1 TAAAAAAA-TATAAAA
40472185 AAATTGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (18 bp):
TAAAAAAATATAAAATGG
Found at i:40472214 original size:18 final size:19
Alignment explanation
Indices: 40472173--40472225 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
40472163 AAATGGTAAA
* *
40472173 AAAATTATAAAAAAATTGT
1 AAAATTATATAAAAATTAT
*
40472192 AAAATTTTATAAAAATTAT
1 AAAATTATATAAAAATTAT
*
40472211 -AAATTATATAGAAAT
1 AAAATTATATAAAAAT
40472226 ATAGAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
AAAATTATATAAAAATTAT
Found at i:40472264 original size:30 final size:30
Alignment explanation
Indices: 40472169--40472264 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
40472159 TATAAAATGG
* *
40472169 TAAAAAAATTATAAAAAAATTGT-AA-AATTT
1 TAAAAAAATTAT-AAAAAA-TGTAAAGAAATA
* * * *
40472199 TATAAAAATTAT--AAATTATATAGAAATA
1 TAAAAAAATTATAAAAAATGTAAAGAAATA
40472227 TAGAAAAAAATTATAAAAAATGTAAAGAAATA
1 T--AAAAAAATTATAAAAAATGTAAAGAAATA
40472259 TAAAAA
1 TAAAAA
40472265 TCGTAAAATT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
26 2 0.04
27 4 0.08
28 4 0.08
30 26 0.52
32 14 0.28
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (30 bp):
TAAAAAAATTATAAAAAATGTAAAGAAATA
Found at i:40472491 original size:18 final size:19
Alignment explanation
Indices: 40472459--40472495 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40472449 ACTAAAGGTT
40472459 TTTTTTATGTATTTTATAA
1 TTTTTTATGTATTTTATAA
*
40472478 TTTTTTAT-TTTTTTATAA
1 TTTTTTATGTATTTTATAA
40472496 AAATTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTTTTATGTATTTTATAA
Found at i:40472546 original size:17 final size:17
Alignment explanation
Indices: 40472524--40472582 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
40472514 ATTTTCTTAC
40472524 TAATTTAATAATTTTAA
1 TAATTTAATAATTTTAA
*
40472541 TAATTTAATATTTTTATTA
1 TAATTTAATAATTTTA--A
* * *
40472560 AAAATTAATAATTTTTA
1 TAATTTAATAATTTTAA
40472577 TAATTT
1 TAATTT
40472583 TTTTGCTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 20 0.61
19 13 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTTAATAATTTTAA
Found at i:40480281 original size:11 final size:11
Alignment explanation
Indices: 40480239--40480289 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
40480229 TCACAACTTC
40480239 AATTA-AATTA
1 AATTATAATTA
**
40480249 TAATTATTTTTA
1 -AATTATAATTA
40480261 AATGTATAATTA
1 AAT-TATAATTA
40480273 AATTATAATTA
1 AATTATAATTA
*
40480284 TATTAT
1 AATTAT
40480290 TTCAACTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 21 0.64
12 12 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
AATTATAATTA
Found at i:40480328 original size:103 final size:102
Alignment explanation
Indices: 40480137--40480332 Score: 236
Period size: 103 Copynumber: 1.9 Consensus size: 102
40480127 CCTAATTTAT
* *
40480137 ATTAAATTATAATTGTTTTTAAATCTATAATTATCACAACTTCTATTTTATTTCAACTTTTTTAC
1 ATTAAATTATAATTATTTTTAAATCTATAATTATCACAAC-TCTATATTATTTCAACTTTTTTAC
** **
40480202 TTCTAATTATTTTTAAATATGTAATTATCACAACTTCA
65 TAATAATTATAATTAAATATGTAATTATCACAACTTCA
* * *
40480240 ATTAAATTATAATTATTTTTAAATGTATAATTAAATTATAA-T-TATATTATTTCAAC-TTTTTA
1 ATTAAATTATAATTATTTTTAAATCTATAATT--ATCACAACTCTATATTATTTCAACTTTTTTA
*
40480302 CTAATAATTCTAAATTAAATATTGTAATTAT
64 CTAATAATTAT-AATTAAATA-TGTAATTAT
40480333 TTTTAAATAT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
101 14 0.18
102 20 0.25
103 40 0.51
105 5 0.06
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.51
Consensus pattern (102 bp):
ATTAAATTATAATTATTTTTAAATCTATAATTATCACAACTCTATATTATTTCAACTTTTTTACT
AATAATTATAATTAAATATGTAATTATCACAACTTCA
Found at i:40487276 original size:17 final size:18
Alignment explanation
Indices: 40487250--40487286 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40487240 AATTTGGGGC
*
40487250 TTAAAGTTTT-ATAAATA
1 TTAAAATTTTCATAAATA
40487267 TTAAAATTTTCATAAATA
1 TTAAAATTTTCATAAATA
40487285 TT
1 TT
40487287 TTACTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TTAAAATTTTCATAAATA
Found at i:40489957 original size:19 final size:19
Alignment explanation
Indices: 40489918--40489976 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
40489908 TGTAAAAAAA
40489918 TATAAA-ATTTTGAATTCTTT
1 TATAAATATTTTGAA-T-TTT
40489938 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
40489957 T-GAAATATTTTGTAATTTT
1 TATAAATATTTTG-AATTTT
40489976 T
1 T
40489977 GTTGAGAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 10 0.28
19 11 0.31
20 7 0.19
21 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:40489962 original size:18 final size:19
Alignment explanation
Indices: 40489941--40489977 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
40489931 ATTCTTTTAT
40489941 AAATATTTTG-AATTTTTG
1 AAATATTTTGTAATTTTTG
40489959 AAATATTTTGTAATTTTTG
1 AAATATTTTGTAATTTTTG
40489978 TTGAGAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
AAATATTTTGTAATTTTTG
Found at i:40490447 original size:31 final size:31
Alignment explanation
Indices: 40490412--40490477 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
40490402 TAAAATGAGT
* *
40490412 TTTTAGGTTCCTTAAAAGTTGGAAAAAAAAA
1 TTTTAAGTCCCTTAAAAGTTGGAAAAAAAAA
* *
40490443 TTTTAAGTCCCTTAAAAGTTGGTAAAAGAAA
1 TTTTAAGTCCCTTAAAAGTTGGAAAAAAAAA
40490474 TTTT
1 TTTT
40490478 GGGGCCCCTC
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:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (31 bp):
TTTTAAGTCCCTTAAAAGTTGGAAAAAAAAA
Found at i:40490495 original size:32 final size:31
Alignment explanation
Indices: 40490425--40490500 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
40490415 TAGGTTCCTT
* * *
40490425 AAAAGTTGGAAAAAAAAATTTTAAGTCCCTT
1 AAAAGTTGGTAAAAAAAATTTTAAGCCCCTC
* **
40490456 AAAAGTTGGTAAAAGAAATTTTGGGGCCCCTC
1 AAAAGTTGGTAAAAAAAATTTT-AAGCCCCTC
40490488 AAAAGTTGGTAAA
1 AAAAGTTGGTAAA
40490501 TAATTTTTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 20 0.53
32 18 0.47
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (31 bp):
AAAAGTTGGTAAAAAAAATTTTAAGCCCCTC
Found at i:40495629 original size:4 final size:4
Alignment explanation
Indices: 40495620--40495693 Score: 148
Period size: 4 Copynumber: 18.5 Consensus size: 4
40495610 AACAATGTTG
40495620 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
40495668 TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TG
40495694 CATGCATGCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 70 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:40496114 original size:24 final size:24
Alignment explanation
Indices: 40496064--40496115 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
40496054 TAACTTATAT
* ** *
40496064 AAAAAGTATTATTAAATCTATTCA
1 AAAAAATATTATTAAATAAATTAA
40496088 AAAAAATATTATTAAATAAATTAA
1 AAAAAATATTATTAAATAAATTAA
40496112 AAAA
1 AAAA
40496116 TAAATTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAAATATTATTAAATAAATTAA
Found at i:40496122 original size:24 final size:24
Alignment explanation
Indices: 40496071--40496122 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
40496061 TATAAAAAGT
** *
40496071 ATTATTAAATCTATTCAAAAAAAT
1 ATTATTAAATAAATTCAAAAAAAA
40496095 ATTATTAAATAAATT-AAAAAATAA
1 ATTATTAAATAAATTCAAAAAA-AA
40496119 ATTA
1 ATTA
40496123 AGAGTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTATTAAATAAATTCAAAAAAAA
Found at i:40501147 original size:41 final size:41
Alignment explanation
Indices: 40501080--40501235 Score: 143
Period size: 41 Copynumber: 3.8 Consensus size: 41
40501070 TTCAGAGGGC
** * * *
40501080 TTTAGTGGCGTTTTTAAACAAACGCCGCTAATGTTATGGTT
1 TTTAGTGGCGTTTTTTTATAAGCGCCGCTAATGTTAAGGTT
* * * * * *
40501121 TTTAGTGGTGTTTTTTTCTGAGCGCCGCTAATTTTAGGGCT
1 TTTAGTGGCGTTTTTTTATAAGCGCCGCTAATGTTAAGGTT
* ** *
40501162 TTTAGCGGCG-TTTTCGATAATGCGCCGCTAAAGTTAAGGTT
1 TTTAGTGGCGTTTTTTTATAA-GCGCCGCTAATGTTAAGGTT
*
40501203 TTTAGTGGCGTTTTTTTGTAAAGCGCCGCTAAT
1 TTTAGTGGCGTTTTTTTAT-AAGCGCCGCTAAT
40501236 ATTGGAGTTT
Statistics
Matches: 87, Mismatches: 25, Indels: 5
0.74 0.21 0.04
Matches are distributed among these distances:
40 6 0.07
41 64 0.74
42 15 0.17
43 2 0.02
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.40
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTTTATAAGCGCCGCTAATGTTAAGGTT
Found at i:40501217 original size:82 final size:82
Alignment explanation
Indices: 40501102--40501257 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 82
40501092 TTTAAACAAA
* * * * *
40501102 CGCCGCTAATGTTATGGTTTTTAGTGGTGTTTTTTTCT-GAGCGCCGCTAATTTTAGG-GCTTTT
1 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTCTAAAGCGCCGCTAATATT-GGAG-TTTT
40501165 AGCGGCGTTTTCGATAATG
64 AGCGGCGTTTTCGATAATG
*
40501184 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTGTAAAGCGCCGCTAATATTGGAGTTTTAG
1 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTCTAAAGCGCCGCTAATATTGGAGTTTTAG
40501249 CGGCGTTTT
66 CGGCGTTTT
40501258 GATGGAAACG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 51 0.77
83 15 0.23
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.41
Consensus pattern (82 bp):
CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTCTAAAGCGCCGCTAATATTGGAGTTTTAG
CGGCGTTTTCGATAATG
Found at i:40501246 original size:42 final size:42
Alignment explanation
Indices: 40501118--40501257 Score: 105
Period size: 41 Copynumber: 3.4 Consensus size: 42
40501108 TAATGTTATG
* * * * *
40501118 GTTTTTAGTGGTGTTTTTTTCT-GAGCGCCGCTAATTTTAGG-
1 GTTTTTAGCGGCGTTTTTTTGTAAAGCGCCGCTAATATT-GGA
* * * *
40501159 GCTTTTAGCGGCG--TTTTCGATAATGCGCCGCTAA-AGTT-AA
1 GTTTTTAGCGGCGTTTTTTTG-TAAAGCGCCGCTAATA-TTGGA
*
40501199 GGTTTTTAGTGGCGTTTTTTTGTAAAGCGCCGCTAATATTGGA
1 -GTTTTTAGCGGCGTTTTTTTGTAAAGCGCCGCTAATATTGGA
40501242 G-TTTTAGCGGCGTTTT
1 GTTTTTAGCGGCGTTTT
40501258 GATGGAAACG
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
39 4 0.05
40 1 0.01
41 47 0.63
42 16 0.21
43 7 0.09
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.42
Consensus pattern (42 bp):
GTTTTTAGCGGCGTTTTTTTGTAAAGCGCCGCTAATATTGGA
Found at i:40501886 original size:8 final size:7
Alignment explanation
Indices: 40501866--40501973 Score: 63
Period size: 7 Copynumber: 14.4 Consensus size: 7
40501856 GATATAAGGT
40501866 TTAGGGG
1 TTAGGGG
40501873 TTAGGGG
1 TTAGGGG
*
40501880 TTAAGGG
1 TTAGGGG
**
40501887 TTAGGAAT
1 TTAGG-GG
*
40501895 TTAGGGC
1 TTAGGGG
*
40501902 TTAGAGG
1 TTAGGGG
*
40501909 TTAAGGG
1 TTAGGGG
**
40501916 TTAGTGAT
1 TTAG-GGG
40501924 TTAGGGGG
1 TTA-GGGG
*
40501932 TTAGGGT
1 TTAGGGG
40501939 TTAAGGGG
1 TT-AGGGG
40501947 ATTTAGGGG
1 --TTAGGGG
*
40501956 TTAGGGAT
1 TTAGGG-G
40501964 TTAGGGG
1 TTAGGGG
40501971 TTA
1 TTA
40501974 AGGTGTCAAG
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
7 44 0.59
8 23 0.31
9 6 0.08
10 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.44, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:40501886 original size:15 final size:15
Alignment explanation
Indices: 40501863--40501976 Score: 72
Period size: 15 Copynumber: 7.5 Consensus size: 15
40501853 TGGGATATAA
*
40501863 GGTTTAGGGGTTAGG
1 GGTTAAGGGGTTAGG
40501878 GGTTAA-GGGTTAGG
1 GGTTAAGGGGTTAGG
** * * *
40501892 AATTTAGGGCTTAGA
1 GGTTAAGGGGTTAGG
40501907 GGTTAA-GGGTTAGTG
1 GGTTAAGGGGTTAG-G
** *
40501922 ATTTAGGGGGTTAGG
1 GGTTAAGGGGTTAGG
*
40501937 GTTTAAGGGGATTTAGG
1 GGTTAAGGGG--TTAGG
*
40501954 GGTT-AGGGATTTAGG
1 GGTTAAGGG-GTTAGG
40501969 GGTTAAGG
1 GGTTAAGG
40501977 TGTCAAGGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 13
0.70 0.17 0.12
Matches are distributed among these distances:
14 17 0.23
15 35 0.47
16 14 0.19
17 8 0.11
ACGTcount: A:0.22, C:0.01, G:0.45, T:0.32
Consensus pattern (15 bp):
GGTTAAGGGGTTAGG
Found at i:40501897 original size:29 final size:29
Alignment explanation
Indices: 40501865--40501945 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
40501855 GGATATAAGG
40501865 TTTAGGGGTTAGGGGTTAAGGGTTAG-GAA
1 TTTAGGGGTTAGGGGTTAAGGGTTAGTG-A
* *
40501894 TTTAGGGCTTAGAGGTTAAGGGTTAGTGA
1 TTTAGGGGTTAGGGGTTAAGGGTTAGTGA
*
40501923 TTTAGGGGGTTAGGGTTTAAGGG
1 TTTA-GGGGTTAGGGGTTAAGGG
40501946 GATTTAGGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 29 0.64
30 16 0.36
ACGTcount: A:0.22, C:0.01, G:0.43, T:0.33
Consensus pattern (29 bp):
TTTAGGGGTTAGGGGTTAAGGGTTAGTGA
Found at i:40501960 original size:24 final size:25
Alignment explanation
Indices: 40501921--40501970 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
40501911 AAGGGTTAGT
40501921 GATTTAGGGGGTTAGGG-TTTAAGGG
1 GATTTAGGGGGTTAGGGATTT-AGGG
40501946 GATTTA-GGGGTTAGGGATTTAGGG
1 GATTTAGGGGGTTAGGGATTTAGGG
40501970 G
1 G
40501971 TTAAGGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.32
Consensus pattern (25 bp):
GATTTAGGGGGTTAGGGATTTAGGG
Found at i:40504311 original size:26 final size:26
Alignment explanation
Indices: 40504282--40504339 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
40504272 CTCGTTGCAT
*
40504282 AATAATTCTTACTCTATAGCTTATGA
1 AATAATTCTTACTCTATAGCTTATAA
40504308 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTTACTCTATAGCTTATAA
40504334 AATAAT
1 AATAAT
40504340 ATAAATCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (26 bp):
AATAATTCTTACTCTATAGCTTATAA
Found at i:40504826 original size:16 final size:16
Alignment explanation
Indices: 40504805--40504835 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40504795 CCAATTCAAA
40504805 TAGTATTATTTAATAC
1 TAGTATTATTTAATAC
40504821 TAGTATTATTTAATA
1 TAGTATTATTTAATA
40504836 TGGTTCCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TAGTATTATTTAATAC
Found at i:40505814 original size:31 final size:31
Alignment explanation
Indices: 40505776--40505843 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
40505766 GCCTTTAGCG
*
40505776 GCGCTTTTTAACGCCACTAAAGGCATTTGCT
1 GCGCTTTTTAACGCCACTAAAGGCATTTGCA
40505807 GCGCTTTTTAACGCCACTAAAGGCATTTGCA
1 GCGCTTTTTAACGCCACTAAAGGCATTTGCA
40505838 GCGCTT
1 GCGCTT
40505844 GAGGAAGCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (31 bp):
GCGCTTTTTAACGCCACTAAAGGCATTTGCA
Found at i:40505943 original size:44 final size:43
Alignment explanation
Indices: 40505894--40505987 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 43
40505884 TAACTTTTGT
40505894 GGCGCTTACAGAAAAAAACGCCGCT-AAAGATCA-TGTTCTTTAGC
1 GGCGCTTA-AGAAAAAAACGCCGCTAAAAG-T-AGTGTTCTTTAGC
**
40505938 GGCGCTT-AGTTAAAAACGCCGCTAAAAGTAGTGTTCTTTAGC
1 GGCGCTTAAGAAAAAAACGCCGCTAAAAGTAGTGTTCTTTAGC
40505980 GGCGCTTA
1 GGCGCTTA
40505988 TTTCACAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
41 1 0.02
42 33 0.73
43 4 0.09
44 7 0.16
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
GGCGCTTAAGAAAAAAACGCCGCTAAAAGTAGTGTTCTTTAGC
Found at i:40505961 original size:42 final size:42
Alignment explanation
Indices: 40505907--40505987 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 42
40505897 GCTTACAGAA
40505907 AAAAACGCCGCT-AAAGATCA-TGTTCTTTAGCGGCGCTTAGTT
1 AAAAACGCCGCTAAAAG-T-AGTGTTCTTTAGCGGCGCTTAGTT
40505949 AAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTA
1 AAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTA
40505988 TTTCACAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
41 1 0.03
42 32 0.86
43 4 0.11
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTAGTT
Found at i:40506452 original size:12 final size:12
Alignment explanation
Indices: 40506435--40506483 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
40506425 TTTTGAACCT
40506435 CTGCTTCTCTCG
1 CTGCTTCTCTCG
*
40506447 CTGCTTCTCTTG
1 CTGCTTCTCTCG
**
40506459 CTGCGGC-CT--
1 CTGCTTCTCTCG
40506468 CTGCTTCTCTCG
1 CTGCTTCTCTCG
40506480 CTGC
1 CTGC
40506484 AGCCTCTGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.17
10 2 0.07
11 2 0.07
12 20 0.69
ACGTcount: A:0.00, C:0.41, G:0.20, T:0.39
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:40506471 original size:21 final size:21
Alignment explanation
Indices: 40506447--40506515 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
40506437 GCTTCTCTCG
* *
40506447 CTGCTTCTCTTGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
40506468 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
40506489 CTGCTTCCCTCGCTGCTGCGT
1 CTGCTTCTCTCGCTGCAGCCT
40506510 CTGCTT
1 CTGCTT
40506516 TAAGTTGTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.01, C:0.41, G:0.22, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:40508746 original size:15 final size:15
Alignment explanation
Indices: 40508726--40508754 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40508716 CTATTCCACA
40508726 ATTTTCACGAAGTTT
1 ATTTTCACGAAGTTT
40508741 ATTTTCACGAAGTT
1 ATTTTCACGAAGTT
40508755 AACTAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
ATTTTCACGAAGTTT
Found at i:40510221 original size:9 final size:9
Alignment explanation
Indices: 40510207--40510237 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40510197 GTTAAACGAA
40510207 TCGAGTTAT
1 TCGAGTTAT
*
40510216 TCGAGTTAA
1 TCGAGTTAT
40510225 TCGAGTTAT
1 TCGAGTTAT
40510234 TCGA
1 TCGA
40510238 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40510403 original size:29 final size:30
Alignment explanation
Indices: 40510370--40510426 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
40510360 CTTTTTTACT
40510370 TTTCCCTCAAAACTTTTACTCCT-TCCCAC
1 TTTCCCTCAAAACTTTTACTCCTCTCCCAC
40510399 TTTCCCTCAAAACTTTTACTCCTCTCCC
1 TTTCCCTCAAAACTTTTACTCCTCTCCC
40510427 CTCCCAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTCCCTCAAAACTTTTACTCCTCTCCCAC
Found at i:40510564 original size:30 final size:31
Alignment explanation
Indices: 40510530--40510589 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40510520 AAACCTTTTA
*
40510530 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
40510560 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
40510590 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:40511658 original size:115 final size:114
Alignment explanation
Indices: 40511372--40511871 Score: 468
Period size: 115 Copynumber: 4.4 Consensus size: 114
40511362 CGGTCAACAC
* ** * * * * *
40511372 AAAATCCAACAAAACGGCAACGTTTTTTATT-ATAACCCATTGAAATTTTGCGGCGTTTTCAACG
1 AAAATCCTACAAAACGGCAACG-TTTTTATTGA-AACAAAATCACATTTTGCGGCGTTTTTAACA
* * * * * *
40511436 CAGCGCCGCTAAAGGCTGACATTTTTCGGCGTTTTACAAAAAATGCCACTAA
64 TAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTAC-AAAAACGCCAGTAA
* ** * * * *
40511488 TAAATCCTACACCACGGCAGCG-TTTTATTAAAACAGAATCACATTTTGCTGCGTTTTTAATC-T
1 AAAATCCTACAAAACGGCAACGTTTTTATTGAAACAAAATCACATTTTGCGGCGTTTTTAA-CAT
*
40511551 AGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTGGCAAAAACGCCAGTAA
65 AGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTT-ACAAAAACGCCAGTAA
* *
40511602 AAAATCCCACAAAACGGCAA-GATTTTTATTGAAACAAAATCACATTTTGCGGCGTTTTTGACAT
1 AAAATCCTACAAAACGGCAACG-TTTTTATTGAAACAAAATCACATTTTGCGGCGTTTTTAACAT
* *
40511666 AGCGCCGCTAAAGGATGATCTTTTGCGGCATTTTACCAAAAACGCCAGTAA
65 AGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTA-CAAAAACGCCAGTAA
* * * * * *
40511717 GAAATCTTACAGAACGGCAACGTTTTTATTGAAACAAAATCACATTTTGCGGCGTTTTCAGCTTA
1 AAAATCCTACAAAACGGCAACGTTTTTATTGAAACAAAATCACATTTTGCGGCGTTTTTAACATA
* ** * ** * * * * *
40511782 GTGCCGGGAAAGCCCAAACTTTTACGGCGTTTTACCCAAAACGCCACTAA
66 GCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTA-CAAAAACGCCAGTAA
* * * * *
40511832 TATATCCTATAAAACGCCACCGTTTTTATTGAAACAAAAT
1 AAAATCCTACAAAACGGCAACGTTTTTATTGAAACAAAAT
40511872 TCCTTTAAAT
Statistics
Matches: 318, Mismatches: 58, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
113 1 0.00
114 88 0.28
115 211 0.66
116 18 0.06
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (114 bp):
AAAATCCTACAAAACGGCAACGTTTTTATTGAAACAAAATCACATTTTGCGGCGTTTTTAACATA
GCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTACAAAAACGCCAGTAA
Found at i:40512434 original size:21 final size:21
Alignment explanation
Indices: 40512392--40512441 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
40512382 CCTAGCCTAG
40512392 ACCCTAAACCCCAACCCATAA
1 ACCCTAAACCCCAACCCATAA
* ***
40512413 ACCTTAAACCCCAACTTGTAA
1 ACCCTAAACCCCAACCCATAA
40512434 ACCCTAAA
1 ACCCTAAA
40512442 TTGTAAATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (21 bp):
ACCCTAAACCCCAACCCATAA
Found at i:40512470 original size:15 final size:17
Alignment explanation
Indices: 40512450--40512481 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40512440 AATTGTAAAT
40512450 CATAA-TCAC-TAAACC
1 CATAATTCACATAAACC
40512465 CATAATTCACATAAACC
1 CATAATTCACATAAACC
40512482 TTAATTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (17 bp):
CATAATTCACATAAACC
Found at i:40512771 original size:9 final size:10
Alignment explanation
Indices: 40512745--40512774 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
40512735 TTTTTAATAA
*
40512745 ATATTTTTAT
1 ATATTTTTAC
40512755 ATATTTTTAC
1 ATATTTTTAC
40512765 ATATTTTTAC
1 ATATTTTTAC
40512775 TTTCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTTTAC
Found at i:40513157 original size:113 final size:114
Alignment explanation
Indices: 40512945--40513271 Score: 489
Period size: 113 Copynumber: 2.9 Consensus size: 114
40512935 TAGGTTTTTT
** **
40512945 GCGGCGCTTTTACAAAAACGCCACCAAAGCCTCCCAAACTAAGAAAAACGACGTCGTTGGGCTTA
1 GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCAAAAACTAAGAAAAACGACGTCGTTGGGCTTA
* * * *
40513010 GGTTTTTTGCAGCGATTTTTAAAAAACGCTGCTAAAACCCTGAGCATTA
66 GGTTTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTA
*
40513059 GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCAAAAACTAAG-AAAACGATGTCGTTGGGCTTA
1 GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCAAAAACTAAGAAAAACGACGTCGTTGGGCTTA
* *
40513123 GGTCTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCTGAGAATTA
66 GGTTTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTA
* * *
40513172 -CTTGCGC-TTCTCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTTGGCT
1 GC-GGCGCTTTC-CCAAAAACGCCACCAAAGCCTCAAAAACTAAGAAAAACGACGTCGTTGGGCT
40513235 TAGGTTTTTTGCGGCGCTTTTTAAAAAACGCCGCTAA
64 TAGGTTTTTTGCGGCGCTTTTTAAAAAACGCCGCTAA
40513272 TGCTCATTGT
Statistics
Matches: 194, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
112 4 0.02
113 98 0.51
114 92 0.47
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (114 bp):
GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCAAAAACTAAGAAAAACGACGTCGTTGGGCTTA
GGTTTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTA
Found at i:40513306 original size:39 final size:38
Alignment explanation
Indices: 40513240--40513390 Score: 115
Period size: 39 Copynumber: 3.8 Consensus size: 38
40513230 TGGCTTAGGT
* * * *
40513240 TTTTTGCGGCGCTTTTT-AAAAAACGCCGCTAATGCTCA
1 TTTTAGCGGCG-TTTTTGTAAAATCGCCGCTAATGCTAA
* * * * * *
40513278 TTGTTAACGGCGTTTTTGTAGAAGCGCCGGTAATACTGA
1 TT-TTAGCGGCGTTTTTGTAAAATCGCCGCTAATGCTAA
* *
40513317 TATTTAGCGGCGTTTTTTTAAAATCGCCGCTACTGCTTAA
1 T-TTTAGCGGCGTTTTTGTAAAATCGCCGCTAATGC-TAA
**
40513357 TTTTTAGCGGCGTTTGTTGTCCAATCGCCGCTAA
1 -TTTTAGCGGCGTTT-TTGTAAAATCGCCGCTAA
40513391 AAGCGCCGCT
Statistics
Matches: 87, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
38 7 0.08
39 49 0.56
40 16 0.18
41 15 0.17
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (38 bp):
TTTTAGCGGCGTTTTTGTAAAATCGCCGCTAATGCTAA
Found at i:40515158 original size:21 final size:21
Alignment explanation
Indices: 40515132--40515199 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
40515122 CAACAACTTA
* *
40515132 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
**
40515153 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
*
40515174 AAGCAGAGGCCGCAGTGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
40515195 AAGCA
1 AAGCA
40515200 ACGAGAGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.43, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:40515224 original size:12 final size:12
Alignment explanation
Indices: 40515165--40515224 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
40515155 GCAGAGGCTA
40515165 CAGCGAGAGAAG
1 CAGCGAGAGAAG
**
40515177 CA--GAG-GCCG
1 CAGCGAGAGAAG
*
40515186 CAGTGAGAGAAG
1 CAGCGAGAGAAG
*
40515198 CAACGAGAGAAG
1 CAGCGAGAGAAG
*
40515210 CAGCGATAGAAG
1 CAGCGAGAGAAG
40515222 CAG
1 CAG
40515225 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 4 0.11
10 3 0.08
11 3 0.08
12 27 0.73
ACGTcount: A:0.40, C:0.18, G:0.38, T:0.03
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:40519992 original size:20 final size:20
Alignment explanation
Indices: 40519955--40519998 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
40519945 AAAATTACAA
* *
40519955 TTTTTATACTTTTTAAATTAT
1 TTTTTATAC-TTTAAAAATAT
40519976 TTTTTAT-CTTTAAAAATAT
1 TTTTTATACTTTAAAAATAT
40519995 TTTT
1 TTTT
40519999 AAAATTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 1 0.05
21 7 0.33
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTATACTTTAAAAATAT
Found at i:40523352 original size:79 final size:80
Alignment explanation
Indices: 40523257--40523416 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 80
40523247 ATATGAAATT
40523257 TTAATTTTGATTCAATCATACATATTTAAAGAAATAAATACAATCATTTATTTTTAGATTTAGAT
1 TTAATTTTGATTCAATCATACATATTTAAAGAAATAAATACAATCATTTATTTTTAGATTTAGAT
40523322 AAATATAATTATTTG
66 AAATATAATTATTTG
40523337 TTAATTTTGA-TCAATCATACATATTTAAAGAAATAAATACAATCATTTATTTTTAGATTTAGAT
1 TTAATTTTGATTCAATCATACATATTTAAAGAAATAAATACAATCATTTATTTTTAGATTTAGAT
40523401 AAATATAATTATTTG
66 AAATATAATTATTTG
40523416 T
1 T
40523417 GTACAATATA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 70 0.88
80 10 0.12
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (80 bp):
TTAATTTTGATTCAATCATACATATTTAAAGAAATAAATACAATCATTTATTTTTAGATTTAGAT
AAATATAATTATTTG
Found at i:40524611 original size:31 final size:32
Alignment explanation
Indices: 40524567--40524641 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
40524557 TCGAGCAGGA
* *
40524567 TGGGTTAAGTTTTGA-TCTGGGTCACTCCA-GTT
1 TGGGTCAA-TTTTGACTCCGGGTCA-TCCAGGTT
*
40524599 TGGGTCAATTTTGACTCCGGGTCATTCAGGTT
1 TGGGTCAATTTTGACTCCGGGTCATCCAGGTT
40524631 TGGGTCAATTT
1 TGGGTCAATTT
40524642 CAAGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 9 0.24
32 29 0.76
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (32 bp):
TGGGTCAATTTTGACTCCGGGTCATCCAGGTT
Found at i:40540486 original size:18 final size:20
Alignment explanation
Indices: 40540445--40540486 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
40540435 CTGAAAATGG
* *
40540445 TTTTTGAAAAATGATTTATT
1 TTTTTGAAAAATGATTAATA
40540465 TTTTTGAAAAA-G-TTAATA
1 TTTTTGAAAAATGATTAATA
40540483 TTTT
1 TTTT
40540487 CTGGTGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTTTGAAAAATGATTAATA
Found at i:40540546 original size:32 final size:33
Alignment explanation
Indices: 40540479--40540550 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
40540469 TGAAAAAGTT
*
40540479 AATATTTTCTGGTGTTTGGATAAATTTGTGTAA
1 AATATTTTCTGGTGTTTGGACAAATTTGTGTAA
* *
40540512 AATATTTTCTGTTGTTT-GACAAATTT-TTTAAA
1 AATATTTTCTGGTGTTTGGACAAATTTGTGT-AA
40540544 AATATTT
1 AATATTT
40540551 CATAAAAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 2 0.06
32 17 0.49
33 16 0.46
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (33 bp):
AATATTTTCTGGTGTTTGGACAAATTTGTGTAA
Found at i:40540921 original size:13 final size:13
Alignment explanation
Indices: 40540903--40540969 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
40540893 ATGCGAAGAA
40540903 TATTATTTAAAAT
1 TATTATTTAAAAT
*
40540916 TATTATTTTTAAAT
1 TATTA-TTTAAAAT
40540930 T-TTA-TTATAAAT
1 TATTATTTA-AAAT
*
40540942 TATTGTTTTTAAAATT
1 TA-T-TATTTAAAA-T
40540958 TATTA-TTAAAAT
1 TATTATTTAAAAT
40540970 AAAATTGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
11 2 0.05
12 6 0.14
13 14 0.33
14 10 0.23
15 5 0.12
16 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
TATTATTTAAAAT
Found at i:40540941 original size:26 final size:26
Alignment explanation
Indices: 40540912--40540963 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
40540902 ATATTATTTA
*
40540912 AAATTATTATTTTTAAATTTTATTAT
1 AAATTATTATTTTTAAAATTTATTAT
*
40540938 AAATTATTGTTTTTAAAATTTATTAT
1 AAATTATTATTTTTAAAATTTATTAT
40540964 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
AAATTATTATTTTTAAAATTTATTAT
Found at i:40541495 original size:22 final size:23
Alignment explanation
Indices: 40541464--40541509 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
40541454 GACCCATCCG
40541464 TATTATTTTTTAAAATATATTTA
1 TATTATTTTTTAAAATATATTTA
**
40541487 TATTA-TTTTTAATTTATATTTA
1 TATTATTTTTTAAAATATATTTA
40541509 T
1 T
40541510 TAATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATTTTTTAAAATATATTTA
Found at i:40541983 original size:23 final size:23
Alignment explanation
Indices: 40541953--40542000 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
40541943 ATTGACGAAG
*
40541953 TTAGTTGTATAGTTAATTAGGTT
1 TTAGTTGTATAGTTAATTAAGTT
40541976 TTAGTTGTATAGTTAATTAAGTT
1 TTAGTTGTATAGTTAATTAAGTT
40541999 TT
1 TT
40542001 GGTTAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (23 bp):
TTAGTTGTATAGTTAATTAAGTT
Found at i:40542269 original size:4 final size:4
Alignment explanation
Indices: 40542252--40542304 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
40542242 TAAGTAATAA
* *
40542252 AAAG AAAT AAAG AAAG AAAG ATAG AAATG AAACAG AAAG -AAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG
40542302 AAA
1 AAA
40542305 AAGAAAATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 3 0.07
4 31 0.76
5 3 0.07
6 3 0.07
7 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.06
Consensus pattern (4 bp):
AAAG
Found at i:40543207 original size:41 final size:40
Alignment explanation
Indices: 40543150--40543240 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 40
40543140 CTTCGAGTCG
* * * *
40543150 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCA
1 ATGAGGCACTGAGTGTCAATTTACTACTTTGAATT-ATCCA
* *
40543191 ATGAGGCACTGAGTGTCAATTTATTACTTTGAATTATCCG
1 ATGAGGCACTGAGTGTCAATTTACTACTTTGAATTATCCA
40543231 ATGAGGCACT
1 ATGAGGCACT
40543241 AGGTGCCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 13 0.30
41 31 0.70
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (40 bp):
ATGAGGCACTGAGTGTCAATTTACTACTTTGAATTATCCA
Found at i:40545445 original size:88 final size:88
Alignment explanation
Indices: 40545327--40545502 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
40545317 AAAATTTGAA
40545327 TTTTTTATCGAATTTTTCGAATCGAATCCTGCTCACCCCTAAATGAAAGTTAGAAATAATAAACT
1 TTTTTTATCGAATTTTTCGAATCGAATCCTGCTCACCCCTAAATGAAAGTTAGAAATAATAAACT
40545392 AACCTTTTTAAATATTAAATGGG
66 AACCTTTTTAAATATTAAATGGG
40545415 TTTTTTATCGAATTTTTCGAATCGAATCCTGCTCACCCCTAAATGAAAGTTAGAAATAATAAACT
1 TTTTTTATCGAATTTTTCGAATCGAATCCTGCTCACCCCTAAATGAAAGTTAGAAATAATAAACT
40545480 AACCTTTTTAAATATTAAATGGG
66 AACCTTTTTAAATATTAAATGGG
40545503 ATTTCGATCT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (88 bp):
TTTTTTATCGAATTTTTCGAATCGAATCCTGCTCACCCCTAAATGAAAGTTAGAAATAATAAACT
AACCTTTTTAAATATTAAATGGG
Found at i:40549398 original size:74 final size:75
Alignment explanation
Indices: 40549310--40549458 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
40549300 ATAAATATTT
40549310 TCTAACAAATTGAAAATAGTTTTTTTTAAAGTCTTTATACTTAAATAACATTAAGACAAGTACAA
1 TCTAACAAATTGAAAATAGTTTTTTTTAAAGTCTTTATACTTAAATAACATTAAGACAAGTACAA
40549375 CTTAACAAGC
66 CTTAACAAGC
40549385 TCTAACAAA-TGAAAATAGTTTTTTTTAAAGTCTTTATACTTAAATAACATTAAGACAAGTACAA
1 TCTAACAAATTGAAAATAGTTTTTTTTAAAGTCTTTATACTTAAATAACATTAAGACAAGTACAA
40549449 CTTAACAAGC
66 CTTAACAAGC
40549459 AAATACCTCT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 65 0.88
75 9 0.12
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (75 bp):
TCTAACAAATTGAAAATAGTTTTTTTTAAAGTCTTTATACTTAAATAACATTAAGACAAGTACAA
CTTAACAAGC
Found at i:40553340 original size:40 final size:40
Alignment explanation
Indices: 40553207--40553346 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
40553197 GACTTCGAGT
* *
40553207 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATATATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGAT-TATC
* * * * *
40553248 CGATGAGGCATTGGGTG-CCAA-T-TTACTTCAGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
* * *
40553285 CGATGAGACATTGGGTGTCAAATTATTATTTCAAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
* *
40553325 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
40553347 CTGGTATGTT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
37 18 0.22
38 12 0.15
39 2 0.03
40 33 0.41
41 15 0.19
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
Found at i:40558202 original size:14 final size:14
Alignment explanation
Indices: 40558183--40558211 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40558173 TTAGACTGAG
40558183 CTAGAATACCCATA
1 CTAGAATACCCATA
40558197 CTAGAATACCCATA
1 CTAGAATACCCATA
40558211 C
1 C
40558212 ACTTATCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.21
Consensus pattern (14 bp):
CTAGAATACCCATA
Found at i:40559919 original size:52 final size:52
Alignment explanation
Indices: 40559863--40559963 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
40559853 TAAATAGCTC
* *
40559863 ATTCAGATTCAGAAGCTTGTCATACAATCTCATTCATATACATACTCCCATA
1 ATTCAGATTCAGAAGCATATCATACAATCTCATTCATATACATACTCCCATA
*
40559915 ATTCAGATTCAGAAGCATATCATACAATCTCATTCATATACATGCTCCC
1 ATTCAGATTCAGAAGCATATCATACAATCTCATTCATATACATACTCCC
40559964 CCTTAACTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.32
Consensus pattern (52 bp):
ATTCAGATTCAGAAGCATATCATACAATCTCATTCATATACATACTCCCATA
Found at i:40562066 original size:21 final size:23
Alignment explanation
Indices: 40562033--40562075 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
40562023 TCCTTTTAAC
40562033 TTTTACATATAATTAAAAATATT
1 TTTTACATATAATTAAAAATATT
*
40562056 TTTTA-AT-TAATTGAAAATAT
1 TTTTACATATAATTAAAAATAT
40562076 AATCTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTACATATAATTAAAAATATT
Found at i:40562772 original size:274 final size:274
Alignment explanation
Indices: 40562283--40562836 Score: 1099
Period size: 274 Copynumber: 2.0 Consensus size: 274
40562273 AAATTCATAA
40562283 GACCTAAAATATAATCTGAAAAGTTTAAGGGCATCGGAGGCTTACTCACCCCTTTAAATTTGCCC
1 GACCTAAAATATAATCTGAAAAGTTTAAGGGCATCGGAGGCTTACTCACCCCTTTAAATTTGCCC
40562348 TTATTTCAGGATAAGTCCTCCAAGTAATGATGAAATTTGATTGAAAACCAAATCCTAATATTCAT
66 TTATTTCAGGATAAGTCCTCCAAGTAATGATGAAATTTGATTGAAAACCAAATCCTAATATTCAT
40562413 TTCATAATCTCAAAATAAATAACAAATAATAAAACATATAACTCAAATTTGTCAACTTTTAAATT
131 TTCATAATCTCAAAATAAATAACAAATAATAAAACATATAACTCAAATTTGTCAACTTTTAAATT
40562478 AATACTCGTAATATTACAACAATAGTTAAGATAATACCACAACACCAAAGCAGAACATTATCAAC
196 AATACTCGTAATATTACAACAATAGTTAAGATAATACCACAACACCAAAGCAGAACATTATCAAC
40562543 ATGTAAACTAATCC
261 ATGTAAACTAATCC
40562557 GACCTAAAATATAATCTGAAAAGTTTAAGGGCATCGGAGGCTTACTCACCCCTTTAAATTTGCCC
1 GACCTAAAATATAATCTGAAAAGTTTAAGGGCATCGGAGGCTTACTCACCCCTTTAAATTTGCCC
40562622 TTATTTCAGGATAAGTCCTCCAAGTAATGATGAAATTTGATTGAAAACCAAATCCTAATATTCAT
66 TTATTTCAGGATAAGTCCTCCAAGTAATGATGAAATTTGATTGAAAACCAAATCCTAATATTCAT
40562687 TTCATAATCTCAAAATAAATAACAAATAATAAAACATATAACTCAAATTTGTCAACTTTTAAATT
131 TTCATAATCTCAAAATAAATAACAAATAATAAAACATATAACTCAAATTTGTCAACTTTTAAATT
40562752 AATACTCGTAATATTACAACAATAGTTAAGATAATACCACAACACCAAAGCAGAACATTATCAAC
196 AATACTCGTAATATTACAACAATAGTTAAGATAATACCACAACACCAAAGCAGAACATTATCAAC
40562817 ATGTAAACTAATCC
261 ATGTAAACTAATCC
*
40562831 GGCCTA
1 GACCTA
40562837 CAAGTCTACC
Statistics
Matches: 279, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
274 279 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (274 bp):
GACCTAAAATATAATCTGAAAAGTTTAAGGGCATCGGAGGCTTACTCACCCCTTTAAATTTGCCC
TTATTTCAGGATAAGTCCTCCAAGTAATGATGAAATTTGATTGAAAACCAAATCCTAATATTCAT
TTCATAATCTCAAAATAAATAACAAATAATAAAACATATAACTCAAATTTGTCAACTTTTAAATT
AATACTCGTAATATTACAACAATAGTTAAGATAATACCACAACACCAAAGCAGAACATTATCAAC
ATGTAAACTAATCC
Found at i:40563559 original size:22 final size:22
Alignment explanation
Indices: 40563533--40563586 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
40563523 TTTAATTTTG
*
40563533 ATATAATTTAATTTATTTATTT
1 ATATAATTTAATTAATTTATTT
* * *
40563555 TTATAATTTCATTAATTTGTTT
1 ATATAATTTAATTAATTTATTT
*
40563577 ATATATTTTA
1 ATATAATTTA
40563587 CACCATTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
ATATAATTTAATTAATTTATTT
Found at i:40567923 original size:74 final size:75
Alignment explanation
Indices: 40567818--40567966 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
40567808 TTACTTATAG
40567818 ATATGAATTTTTTTTAAAAAAAAGTATATTTTACAAAAAAGATTATATTAGTTATTTATTTACAT
1 ATATGAATTTTTTTTAAAAAAAAGTATATTTTACAAAAAAGATTATATTAGTTATTTATTTACAT
40567883 TATTTTTTTA
66 TATTTTTTTA
40567893 ATATGAA-TTTTTTTAAAAAAAAGTATATTTTACAAAAAAGATTATATTAGTTATTTATTTACAT
1 ATATGAATTTTTTTTAAAAAAAAGTATATTTTACAAAAAAGATTATATTAGTTATTTATTTACAT
40567957 TATTTTTTTA
66 TATTTTTTTA
40567967 TTCAACATTA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 67 0.91
75 7 0.09
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (75 bp):
ATATGAATTTTTTTTAAAAAAAAGTATATTTTACAAAAAAGATTATATTAGTTATTTATTTACAT
TATTTTTTTA
Found at i:40569600 original size:19 final size:19
Alignment explanation
Indices: 40569561--40569621 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
40569551 TTTAACTTTC
* *
40569561 TTTATATATGTTTTAGAATT
1 TTTATAAATATTTT-GAATT
40569581 TTTATAAATATTTTGAA-T
1 TTTATAAATATTTTGAATT
*
40569599 TTTAAAAATTATTTTGAATT
1 TTTATAAA-TATTTTGAATT
40569619 TTT
1 TTT
40569622 TGTAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 8 0.22
19 12 0.33
20 16 0.44
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTATAAATATTTTGAATT
Done.