Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 49 of 100
Found at i:11937866 original size:166 final size:166
Alignment explanation
Indices: 11937556--11937909 Score: 392
Period size: 166 Copynumber: 2.1 Consensus size: 166
11937546 TCCTCTAAAT
* * * * * *
11937556 AGAGGCTCAATGACTTT-TAAAATTTAAAAGGCTTCTCTAAGTAGAGGCTTAATGACTTTTAAAA
1 AGAGGCTCAATAACTTTAAAAAATCTAAAAGGCTTCTCTAAGCAAAGACTTAATGACTTTTAAAA
* * ** * * *
11937620 ATTTAAAAGGGCTTTTCTAAGCGGAGGCTTGATAACTTTTAAAATTTTAAATGATTTTGCCCAAA
66 ATTTAAAA-GGATTCTCTAAGCAAAGGCTCGACAACTTTTAAAATTTTAAACGATTTTGCCCAAA
* * *
11937685 GGACTTATAAATCTTAATAATGAAAGCTCTTCTAAGC
130 GGACTTATAAATCTTAATAATAAAAACTCTTATAAGC
* * *
11937722 AGAGGCTCAATAACTTTAAAAAATCTAAAAGGCTTCTCTAAGCAAAGACTTGATGAGTTTTGAAA
1 AGAGGCTCAATAACTTTAAAAAATCTAAAAGGCTTCTCTAAGCAAAGACTTAATGACTTTTAAAA
* ** **
11937787 ATTTAAAA-GATTCCTCTAAGTAAAGGCTCGACAGTTTTTAAAAATTTT-AACGATTTTGTCTTA
66 ATTTAAAAGGATT-CTCTAAGCAAAGGCTCGACAACTTTT-AAAATTTTAAACGATTTTG-CCCA
* *
11937850 AA-GACTTATGAATCTTAATAATAAAAACTTTTATAAGC
128 AAGGACTTATAAATCTTAATAATAAAAACTCTTATAAGC
* *
11937888 AGAGACTCAACAACTTTAAAAA
1 AGAGGCTCAATAACTTTAAAAA
11937910 GCTCCTCTAA
Statistics
Matches: 156, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
165 3 0.02
166 94 0.60
167 59 0.38
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (166 bp):
AGAGGCTCAATAACTTTAAAAAATCTAAAAGGCTTCTCTAAGCAAAGACTTAATGACTTTTAAAA
ATTTAAAAGGATTCTCTAAGCAAAGGCTCGACAACTTTTAAAATTTTAAACGATTTTGCCCAAAG
GACTTATAAATCTTAATAATAAAAACTCTTATAAGC
Found at i:11938106 original size:43 final size:43
Alignment explanation
Indices: 11938061--11938858 Score: 403
Period size: 43 Copynumber: 18.8 Consensus size: 43
11938051 GCTTAACAAC
*
11938061 TTTAAAAAGTTTTAAAA-ACTCTTCTAAGTAAAGGCTCAATGACT
1 TTTAAAAA--TTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* ** *
11938105 TTTAAAAATTTTAAAAG-CTCCTCTAAACAAAGGCTCAATGACT
1 TTTAAAAA-TTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * * *
11938148 TTTGAAAGTTTAAAAGAATCATCTAAGTAGAGGCAT-AATTACT
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGC-TCAATGACT
* * * * *
11938191 TTTGAAAATTTAAAAGGCT-TATCTAAGCAGAGACTCAATGGCT
1 TTTAAAAATTTAAAAGACTCT-TCTAAGTAGAGGCTCAATGACT
* * *
11938234 TTTGAAAGTTTAAAAAACTCTTCTAAGTAGAGGCTCAATGACT
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * * *
11938277 TTTGAAAATTTAAAAGGCTCTTCTAGGTAGAGGCTTAATGAAT
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * *
11938320 TTTGAAAGTTTAAAAGACTCATT-TAAATATAGGCTCAATGACT
1 TTTAAAAATTTAAAAGACTC-TTCTAAGTAGAGGCTCAATGACT
* * *
11938363 TTTAAAAATTTAAAAGGCTCATCTAAGCAGAGGCTCAATGACT
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * **
11938406 TTTAAAAATTTTAAAAAGA-TCCTCTAAGCAAAGGCTTGATGACT
1 TTTAAAAA-TTT-AAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * * * * *
11938450 TTTGAAAATTTAAATGA-TTTTGCCTAA--A-AGACT-TACGAAT
1 TTTAAAAATTTAAAAGACTCTT--CTAAGTAGAGGCTCAATGACT
* * * * * * * ** *
11938490 CTTGATAA--TGATAG-CTCTTCTAAGTAGAAGCTTAAAAATT
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * *
11938530 TTTAAAAATTTAAAAAGACTCTTCTAAGCAGAGACTCAATAAAT
1 TTTAAAAATTT-AAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* ** * * * **
11938574 TTAAAAAATTTAAAAAGGTTCCTCTAAGTAGAGACTTAACAAC-
1 TTTAAAAATTT-AAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * *
11938617 TTTAAAAGGTTTATATAA-A-----C-AA--A-A-GCTAAACGACT
1 TTTAAAA-ATTTA-A-AAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * * *
11938652 TTTGAAAGTTTAAAAGACTCCTT-TAAGTAAAGCCTTAATGACT
1 TTTAAAAATTTAAAAGACT-CTTCTAAGTAGAGGCTCAATGACT
* * * * ** *
11938695 TTTGAAAATTTAAAAGGCTCCTCTAAGTAGAGGCTTAACAATT
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * ** *
11938738 TTTTAAAGTTT-AAAGACTCCGCTAAGTAGAGGCTCAATGATT
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
* * * *
11938780 TTTAAAAATTTAAAAGGCTTCTT-TAAGTAAAGGCTTAACGACT
1 TTTAAAAATTTAAAAGAC-TCTTCTAAGTAGAGGCTCAATGACT
* * * **
11938823 TTTGAAAGTTTAAAAGACTCCTCTAAACAGAGGCTC
1 TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTC
11938859 GTTAGAGGCT
Statistics
Matches: 582, Mismatches: 131, Indels: 83
0.73 0.16 0.10
Matches are distributed among these distances:
32 2 0.00
33 2 0.00
34 12 0.02
35 7 0.01
36 5 0.01
38 9 0.02
39 6 0.01
40 18 0.03
41 5 0.01
42 60 0.10
43 341 0.59
44 108 0.19
45 7 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (43 bp):
TTTAAAAATTTAAAAGACTCTTCTAAGTAGAGGCTCAATGACT
Found at i:11938157 original size:86 final size:86
Alignment explanation
Indices: 11938066--11938463 Score: 455
Period size: 86 Copynumber: 4.6 Consensus size: 86
11938056 ACAACTTTAA
* *
11938066 AAAGTTTTAAAAACTCTTCTAAGTAAAGGCTCAATGACTTTTAAAAATTTTAAAA-GCTCCTCTA
1 AAAGTTTTAAAAACTCTTCTAAGTAAAGGCTCAATGACTTTTGAAAA-TTTAAAAGGCTCATCTA
* *
11938130 AACAAAGGCTCAATGACTTTTG
65 AGCAGAGGCTCAATGACTTTTG
* * * * *
11938152 AAAG-TTTAAAAGAATCATCTAAGTAGAGGCAT-AATTACTTTTGAAAATTTAAAAGGCTTATCT
1 AAAGTTTTAAAA-ACTCTTCTAAGTAAAGGC-TCAATGACTTTTGAAAATTTAAAAGGCTCATCT
* *
11938215 AAGCAGAGACTCAATGGCTTTTG
64 AAGCAGAGGCTCAATGACTTTTG
* * * *
11938238 AAAGTTTAAAAAACTCTTCTAAGTAGAGGCTCAATGACTTTTGAAAATTTAAAAGGCTCTTCTAG
1 AAAGTTTTAAAAACTCTTCTAAGTAAAGGCTCAATGACTTTTGAAAATTTAAAAGGCTCATCTAA
* * *
11938303 GTAGAGGCTTAATGAATTTTG
66 GCAGAGGCTCAATGACTTTTG
* * *
11938324 AAAG-TTTAAAAGACTCATT-TAAATATAGGCTCAATGACTTTTAAAAATTTAAAAGGCTCATCT
1 AAAGTTTTAAAA-ACTC-TTCTAAGTAAAGGCTCAATGACTTTTGAAAATTTAAAAGGCTCATCT
*
11938387 AAGCAGAGGCTCAATGACTTTTA
64 AAGCAGAGGCTCAATGACTTTTG
* * * * **
11938410 AAAATTTTAAAAAGATCCTCTAAGCAAAGGCTTGATGACTTTTGAAAATTTAAA
1 AAAGTTTTAAAAA-CTCTTCTAAGTAAAGGCTCAATGACTTTTGAAAATTTAAA
11938464 TGATTTTGCC
Statistics
Matches: 260, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
85 21 0.08
86 193 0.74
87 46 0.18
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (86 bp):
AAAGTTTTAAAAACTCTTCTAAGTAAAGGCTCAATGACTTTTGAAAATTTAAAAGGCTCATCTAA
GCAGAGGCTCAATGACTTTTG
Found at i:11938554 original size:44 final size:45
Alignment explanation
Indices: 11938504--11938623 Score: 122
Period size: 44 Copynumber: 2.7 Consensus size: 45
11938494 ATAATGATAG
* *
11938504 CTCTTCTAAGTAGAAG-CTTAA-AAATTTTTAAAAATTTAAAAAGA
1 CTCTTCTAAGTAGAAGACTCAATAAA-TTTAAAAAATTTAAAAAGA
* *
11938548 CTCTTCTAAGCAG-AGACTCAATAAATTTAAAAAATTTAAAAAGG
1 CTCTTCTAAGTAGAAGACTCAATAAATTTAAAAAATTTAAAAAGA
* * * * *
11938592 TTCCTCTAAGTAG-AGACTTAACAACTTTAAAA
1 CTCTTCTAAGTAGAAGACTCAATAAATTTAAAA
11938624 GGTTTATATA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 2 0.03
44 59 0.92
45 3 0.05
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (45 bp):
CTCTTCTAAGTAGAAGACTCAATAAATTTAAAAAATTTAAAAAGA
Found at i:11938764 original size:85 final size:86
Alignment explanation
Indices: 11938649--11938848 Score: 276
Period size: 85 Copynumber: 2.3 Consensus size: 86
11938639 AAGCTAAACG
* * *
11938649 ACTTTTGAAAGTTTAAAAGACTCCTTTAAGTAAAGCCTTAATGACTTTTGAAAATTTAAAAGGCT
1 ACTTTTGAAAGTTTAAAAGACTCCTCTAAGTAAAGCCTCAATGACTTTTAAAAATTTAAAAGGCT
*
11938714 CCTCTAAGTAGAGGCTTAACA
66 CCTCTAAGTAAAGGCTTAACA
* * * * * *
11938735 ATTTTTTAAAGTTT-AAAGACTCCGCTAAGTAGAGGCTCAATGATTTTTAAAAATTTAAAAGGCT
1 ACTTTTGAAAGTTTAAAAGACTCCTCTAAGTAAAGCCTCAATGACTTTTAAAAATTTAAAAGGCT
* * *
11938799 TCTTTAAGTAAAGGCTTAACG
66 CCTCTAAGTAAAGGCTTAACA
11938820 ACTTTTGAAAGTTTAAAAGACTCCTCTAA
1 ACTTTTGAAAGTTTAAAAGACTCCTCTAA
11938849 ACAGAGGCTC
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 72 0.74
86 25 0.26
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (86 bp):
ACTTTTGAAAGTTTAAAAGACTCCTCTAAGTAAAGCCTCAATGACTTTTAAAAATTTAAAAGGCT
CCTCTAAGTAAAGGCTTAACA
Found at i:11939323 original size:147 final size:148
Alignment explanation
Indices: 11939056--11939355 Score: 548
Period size: 147 Copynumber: 2.0 Consensus size: 148
11939046 TTTGTTCTTG
11939056 TTACAACTTATAATCTTAACCTTTCATGGATGCATTTACCAAATGCTCTAAATACAATACATGCA
1 TTACAACTTATAATCTTAACCTTTCATGGATGCATTTACCAAATGCTCTAAATACAATACATGCA
11939121 ATGCAAACAAATTATTCCACTTCCAATTATGGTAGAAGGTTCTTAAAATCTCTCAC-TTTTTTTG
66 ATGCAAACAAATTATTCCACTTCCAATTATGGTAGAAGGTTCTTAAAATCTCTCACTTTTTTTTG
11939185 TTTTGGTCACCAAAATTT
131 TTTTGGTCACCAAAATTT
* * *
11939203 TTACAACTTGTAATCTTAACCTTTCATGGATGCATTTACCAAATGCTTTAAATACAATACATGTA
1 TTACAACTTATAATCTTAACCTTTCATGGATGCATTTACCAAATGCTCTAAATACAATACATGCA
11939268 ATGCAAACAAATTATTCCACTTCCAATTATGGTAGAAGGTTCTTAAAATCTCTCACTTTTTTTTT
66 ATGCAAACAAATTATTCCACTTCCAATTATGGTAGAAGGTTCTTAAAATCTCTCAC--TTTTTTT
11939333 TGTTTTGGTCACCAAAATTT
129 TGTTTTGGTCACCAAAATTT
11939353 TTA
1 TTA
11939356 ACAATTGCTA
Statistics
Matches: 147, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
147 118 0.80
150 29 0.20
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.39
Consensus pattern (148 bp):
TTACAACTTATAATCTTAACCTTTCATGGATGCATTTACCAAATGCTCTAAATACAATACATGCA
ATGCAAACAAATTATTCCACTTCCAATTATGGTAGAAGGTTCTTAAAATCTCTCACTTTTTTTTG
TTTTGGTCACCAAAATTT
Found at i:11950835 original size:3 final size:3
Alignment explanation
Indices: 11950827--11950883 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
11950817 CTAAAGTGAA
11950827 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11950875 TAT TAT TAT
1 TAT TAT TAT
11950884 GAAAAATTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11951381 original size:23 final size:24
Alignment explanation
Indices: 11951324--11951381 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
11951314 TTATATAAAA
11951324 ATAAAAAAAAATAATAGAAAAATC
1 ATAAAAAAAAATAATAGAAAAATC
** * *
11951348 AT-AAATTAAATAATGGAAATAT-
1 ATAAAAAAAAATAATAGAAAAATC
11951370 ATAAAAAAAAAT
1 ATAAAAAAAAAT
11951382 TGAACAAGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (24 bp):
ATAAAAAAAAATAATAGAAAAATC
Found at i:11952317 original size:4 final size:4
Alignment explanation
Indices: 11952310--11952338 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
11952300 CATATATATA
11952310 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
11952339 GTATGTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:11959839 original size:14 final size:13
Alignment explanation
Indices: 11959812--11959837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11959802 TTTAATATTT
11959812 TTAATATTAAAAA
1 TTAATATTAAAAA
11959825 TTAATATTAAAAA
1 TTAATATTAAAAA
11959838 ATATATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAATATTAAAAA
Found at i:11962553 original size:548 final size:543
Alignment explanation
Indices: 11961854--11962904 Score: 1689
Period size: 544 Copynumber: 1.9 Consensus size: 543
11961844 TGACCATTGG
* * * * *
11961854 TCTTGTTTTGGGGAGGTAGCTCAAAAGCTCCATTTCTGTTTTTTTTTTTATTATTATTATTTTTT
1 TCTTGTTTTGGGGAGGTAGCCCAAAAGCTCCATTTCTGTATATTTTCTTACTATTATTATTTTTT
* *
11961919 ACTTATCTTGTCTTATTTACATTTAATTGTATTAATATTTATAGAGGTTGGATCATAAAATACAT
66 ACATATCTTATCTTATTTACATTTAATTGTATTAATATTTATAGAGGTTGGATCATAAAATACAT
*
11961984 AAATAAATATGTTAAAAATGATATATTTTTCATGGATGGTCATTTAAATTTTTTTTAAATATTAT
131 AAATAAATATGTGAAAAATGATAT-TTTTTCATGGATGGTCATTT-AATTTTTTTTAAATATTAT
* *
11962049 TATCATAA-AGGTCTAATAAAAAAATAATAATAATGATAAGAGACCTATCCAAATGATGAGATTT
194 TATCACAAGAGGT-TAATAAAAAAATAATAATAATGATAAGAGACC--TCCAAATGATAAGATTT
* * * * * * * *
11962113 TAAAGAAATTTGTATAGTAATTTTTATAATATTTTTAGGTGATAAGATTTATTAAATACTGCTAG
256 TAAAGAAATTGGTATAGTAATTCTTATAAAATCTCTAGGTAAGAAGATTTATTAAATACTACTAG
*
11962178 CATATT-AGAGTATTTATAAAAAATTTTAATACAATAAAAACTTTTATTTTCTCTTAAAAATAAT
321 CATATTGA-AGTATTTATAAAAAATTTTAATACAATAAAAACTTTTATTTTCCCTTAAAAATAAT
*
11962242 AAAAAGAAAAAAAATAAATAAACAAAATTTTCTTGAATAATGAATAAATGAAATATGTACACTAA
385 AAAAAG--AAAAAA-AAATAAACAAAATTTTCTCGAATAATGAATAAATGAAATATGTACACTAA
*
11962307 CATTTCATTATTTGCATTGTATACATGTAACTTAATTTTTGAAATATAAACATGAGCCTTTGATA
447 CATTTCATTATTTGCATTGTATACATGTAACTTAATTTTTGAAATATAAACACGAGCCTTTGATA
11962372 ATGAGATTTTAGAGAAGTTTGAGTATCAAGTA
512 ATGAGATTTTAGAGAAGTTTGAGTATCAAGTA
11962404 TCTTGTTTTGGGGAGGTAGCCCAAAAGCTCCATTTCTGGTATATTTTCTT-CT-TT-TTATTTTT
1 TCTTGTTTTGGGGAGGTAGCCCAAAAGCTCCATTTCT-GTATATTTTCTTACTATTATTATTTTT
11962466 TACATATCTTATCTTATTTACATTTAATTGTATTAATATTTATAGAGGTTGGATCATAAAATACA
65 TACATATCTTATCTTATTTACATTTAATTGTATTAATATTTATAGAGGTTGGATCATAAAATACA
*
11962531 TAAATAAATATGTGAAAAATGATATTTTTTCATGGATGGTCATTTTATTTTTTTTAAATATTATT
130 TAAATAAATATGTGAAAAATGATATTTTTTCATGGATGGTCATTTAATTTTTTTTAAATATTATT
*
11962596 ATCACAAGAGGTTAATAAAAAAATAATAATAATGATAAGAGACCTCCTAATGATAAGATTTTAAA
195 ATCACAAGAGGTTAATAAAAAAATAATAATAATGATAAGAGACCTCCAAATGATAAGATTTTAAA
* * *
11962661 GAAATTGGTATAGTGATTCTTATAAAATCTCTAGTTAAGAAGATTTATTAAATACTATTAGCATA
260 GAAATTGGTATAGTAATTCTTATAAAATCTCTAGGTAAGAAGATTTATTAAATACTACTAGCATA
** *
11962726 TTGAAGTATTTATAAAACTTTTTAATATAATAAAAACTTTTATTTTCCCTTAAAAATAATAAAAA
325 TTGAAGTATTTATAAAAAATTTTAATACAATAAAAACTTTTATTTTCCCTTAAAAATAATAAAAA
*
11962791 GAAAAAAAAATAAACAAAATTTTCTCGTATAATGAATAAATGAAATATGTACACTAACATTTCAT
390 GAAAAAAAAATAAACAAAATTTTCTCGAATAATGAATAAATGAAATATGTACACTAACATTTCAT
* *
11962856 TATTTGCATTGTATGCATGTAACTTAATTTTTGAAATGTAAACACGAGC
455 TATTTGCATTGTATACATGTAACTTAATTTTTGAAATATAAACACGAGC
11962905 TTTCAATGAT
Statistics
Matches: 466, Mismatches: 32, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
541 102 0.22
542 6 0.01
544 133 0.29
545 1 0.00
546 57 0.12
547 24 0.05
548 95 0.20
549 2 0.00
550 37 0.08
551 9 0.02
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (543 bp):
TCTTGTTTTGGGGAGGTAGCCCAAAAGCTCCATTTCTGTATATTTTCTTACTATTATTATTTTTT
ACATATCTTATCTTATTTACATTTAATTGTATTAATATTTATAGAGGTTGGATCATAAAATACAT
AAATAAATATGTGAAAAATGATATTTTTTCATGGATGGTCATTTAATTTTTTTTAAATATTATTA
TCACAAGAGGTTAATAAAAAAATAATAATAATGATAAGAGACCTCCAAATGATAAGATTTTAAAG
AAATTGGTATAGTAATTCTTATAAAATCTCTAGGTAAGAAGATTTATTAAATACTACTAGCATAT
TGAAGTATTTATAAAAAATTTTAATACAATAAAAACTTTTATTTTCCCTTAAAAATAATAAAAAG
AAAAAAAAATAAACAAAATTTTCTCGAATAATGAATAAATGAAATATGTACACTAACATTTCATT
ATTTGCATTGTATACATGTAACTTAATTTTTGAAATATAAACACGAGCCTTTGATAATGAGATTT
TAGAGAAGTTTGAGTATCAAGTA
Found at i:11971985 original size:16 final size:15
Alignment explanation
Indices: 11971960--11971993 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
11971950 AACCATTTGA
11971960 TTTTTTTTTTTCATT
1 TTTTTTTTTTTCATT
*
11971975 TTTTTTATTTTTTATT
1 TTTTTT-TTTTTCATT
11971991 TTT
1 TTT
11971994 ATTAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTCATT
Found at i:11972138 original size:12 final size:12
Alignment explanation
Indices: 11972121--11972146 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11972111 ACTCAACACA
11972121 TTTTTTCTTTTT
1 TTTTTTCTTTTT
11972133 TTTTTTCTTTTT
1 TTTTTTCTTTTT
11972145 TT
1 TT
11972147 AAGCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:11972277 original size:44 final size:44
Alignment explanation
Indices: 11972203--11972368 Score: 173
Period size: 44 Copynumber: 3.9 Consensus size: 44
11972193 AGGTTTAACA
* * * *
11972203 TTTTAAAAAATAGA-AAAGCTCCTCTCAATAGAGGCTCAATGAC
1 TTTTGAAAAATAAATAAAGCTCTTCTAAATAGAGGCTCAATGAC
*
11972246 TTTTGAAAAATAAATAAAGCTTTTCTAAATAGAGGCTCAATGA-
1 TTTTGAAAAATAAATAAAGCTCTTCTAAATAGAGGCTCAATGAC
* ** *
11972289 TTTTG---AA-AAATAAAGCTCATCTAAGCAGAGGCTCAAAGAC
1 TTTTGAAAAATAAATAAAGCTCTTCTAAATAGAGGCTCAATGAC
* * * *
11972329 TTTTGAAAAATAAATAAGGCTTTTCTAAGTAGAGACTCAA
1 TTTTGAAAAATAAATAAAGCTCTTCTAAATAGAGGCTCAA
11972369 CAACTCTGAG
Statistics
Matches: 102, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
39 27 0.26
40 7 0.07
43 19 0.19
44 49 0.48
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (44 bp):
TTTTGAAAAATAAATAAAGCTCTTCTAAATAGAGGCTCAATGAC
Found at i:11972312 original size:39 final size:40
Alignment explanation
Indices: 11972217--11972342 Score: 146
Period size: 39 Copynumber: 3.1 Consensus size: 40
11972207 AAAAAATAGA
* *
11972217 AAAGCTCCTCTCAATAGAGGCTCAATGACTTTTGAAAAATAAAT
1 AAAGCTCATCTAAATAGAGGCTCAATGACTTTTG---AA-AAAT
**
11972261 AAAGCTTTTCTAAATAGAGGCTCAATGA-TTTTGAAAAAT
1 AAAGCTCATCTAAATAGAGGCTCAATGACTTTTGAAAAAT
** *
11972300 AAAGCTCATCTAAGCAGAGGCTCAAAGACTTTTGAAAAAT
1 AAAGCTCATCTAAATAGAGGCTCAATGACTTTTGAAAAAT
11972340 AAA
1 AAA
11972343 TAAGGCTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
39 27 0.37
40 16 0.22
43 5 0.07
44 25 0.34
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (40 bp):
AAAGCTCATCTAAATAGAGGCTCAATGACTTTTGAAAAAT
Found at i:11978670 original size:2 final size:2
Alignment explanation
Indices: 11978663--11978717 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
11978653 TTTCTTCCAG
* *
11978663 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11978705 TA TA TA TA AA TA T
1 TA TA TA TA TA TA T
11978718 CTTTCTATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:11978689 original size:18 final size:18
Alignment explanation
Indices: 11978666--11978717 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
11978656 CTTCCAGTAT
11978666 ATATATATATATATATAA
1 ATATATATATATATATAA
11978684 ATATATATATATATATAA
1 ATATATATATATATATAA
*
11978702 ATATATATATAAATAT
1 ATATATATATATATAT
11978718 CTTTCTATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATATATATATATAA
Found at i:11981220 original size:199 final size:200
Alignment explanation
Indices: 11980882--11981242 Score: 448
Period size: 199 Copynumber: 1.8 Consensus size: 200
11980872 ATAGTTACTT
* * * *
11980882 TTATTGAAATTTCATCTAAAATTATTCCACAATTTGAGACAAATTTAGAAAAATTTTTCACTTAG
1 TTATTGAAATTTCATCTAAAATCACTCCACAATTTGAGACAAATTTAGAAAAATTTCTCACCTAG
* * *
11980947 AGATTTCTTAAAAAATTTACCATTTGAAATTTCTAAGAATCTCATCATTGGATAATTAGTATTTA
66 AGATTTCTTAAAAAATTAACCATTTGAAATTTCTAAAAATCTCATCATTGGATAATTAATATTTA
* *
11981012 AATTCAAAAATTTTTATTAA-ATTTGTGTTTTTTCTTATTTTTAAAAAATTAAAGATAAATATTA
131 AATTCAAAAA-ATTTATTAACATTT-TATTTTTTCTTATTTTTAAAAAATTAAAGATAAATATTA
11981076 ATTATTA
194 ATTATTA
* *
11981083 TTATTGAAACTTT-ATCT-AAATCACTCCACCATTTGGGACAAATTTAGAAAAATTTCTCACCTA
1 TTATTGAAA-TTTCATCTAAAATCACTCCACAATTTGAGACAAATTTAGAAAAATTTCTCACCTA
* ** ** * *
11981146 CGA-A-TT-TTATAGAAATTAACTTTTTTCAATTTCTAAAAATTTCATCATTTGATAATTAATAT
65 -GAGATTTCTTA-AAAAATTAACCATTTGAAATTTCTAAAAATCTCATCATTGGATAATTAATAT
*
11981208 TT-ATTCTCAAAAAATTTATTAACATTTTATTTTTT
128 TTAAAT-TCAAAAAATTTATTAACATTTTATTTTTT
11981243 TGTAATTTTT
Statistics
Matches: 136, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
198 20 0.15
199 57 0.42
200 41 0.30
201 15 0.11
202 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (200 bp):
TTATTGAAATTTCATCTAAAATCACTCCACAATTTGAGACAAATTTAGAAAAATTTCTCACCTAG
AGATTTCTTAAAAAATTAACCATTTGAAATTTCTAAAAATCTCATCATTGGATAATTAATATTTA
AATTCAAAAAATTTATTAACATTTTATTTTTTCTTATTTTTAAAAAATTAAAGATAAATATTAAT
TATTA
Found at i:11984034 original size:2 final size:2
Alignment explanation
Indices: 11984023--11984056 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11984013 CGATACAATC
11984023 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11984057 ATTGCTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11988256 original size:23 final size:24
Alignment explanation
Indices: 11988230--11988281 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
11988220 TAAAATTACA
*
11988230 AATATAA-AATTACTTACA-ATCAT
1 AATATAATAATTACATACATAT-AT
*
11988253 AATA-AATTATTACATACATATAT
1 AATATAATAATTACATACATATAT
11988276 AATATA
1 AATATA
11988282 TCAATAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 19 0.79
24 3 0.12
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (24 bp):
AATATAATAATTACATACATATAT
Found at i:11988277 original size:20 final size:21
Alignment explanation
Indices: 11988231--11988277 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
11988221 AAAATTACAA
11988231 ATATA-AAATTACTTACAATC
1 ATATATAAATTACTTACAATC
11988251 ATA-ATAAATTA-TTAC-ATAC
1 ATATATAAATTACTTACAAT-C
11988270 ATATATAA
1 ATATATAA
11988278 TATATCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 13 0.54
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATATAAATTACTTACAATC
Found at i:11991062 original size:19 final size:20
Alignment explanation
Indices: 11991033--11991070 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11991023 GATGGAATTT
11991033 TTTTTATAAAAATAATTAAA
1 TTTTTATAAAAATAATTAAA
*
11991053 TTTTTA-AAAAATTATTAA
1 TTTTTATAAAAATAATTAA
11991071 TGGATTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTTATAAAAATAATTAAA
Found at i:11992009 original size:29 final size:30
Alignment explanation
Indices: 11991973--11992073 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
11991963 TTAATAGTTT
*
11991973 TTTAAATATAAATTAAAAGTTAAAAATTTA
1 TTTAAATATAAATTAAAAATTAAAAATTTA
* *
11992003 TTT-AATATAAACTAAAAATTAAGAATTTA
1 TTTAAATATAAATTAAAAATTAAAAATTTA
11992032 TTTAAATATAAATTAAAAATT-AAAATCTTA
1 TTTAAATATAAATTAAAAATTAAAAAT-TTA
11992062 TTTAAATATAAA
1 TTTAAATATAAA
11992074 AATATATATA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
29 30 0.47
30 34 0.53
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
TTTAAATATAAATTAAAAATTAAAAATTTA
Found at i:11992676 original size:18 final size:19
Alignment explanation
Indices: 11992634--11992676 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
11992624 AATTTAAAAA
*
11992634 AATAAATTTAAATTCATTT
1 AATAAATTTAAATTCATAT
* *
11992653 ATTAAATTT-AATTTATAT
1 AATAAATTTAAATTCATAT
11992671 AATAAA
1 AATAAA
11992677 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAATTTAAATTCATAT
Found at i:11992752 original size:13 final size:13
Alignment explanation
Indices: 11992736--11992816 Score: 65
Period size: 13 Copynumber: 5.8 Consensus size: 13
11992726 TCACATATAT
11992736 ATAAAAATTAAAA
1 ATAAAAATTAAAA
* *
11992749 ATAAAAATTATAT
1 ATAAAAATTAAAA
11992762 AT-AAAATTAAAA
1 ATAAAAATTAAAA
*
11992774 GTAAAAATTATATAAA
1 ATAAAAA-T-TA-AAA
11992790 CATAAAAATTAAATTTA
1 -ATAAAAATTAAA---A
11992807 ATAAAAATTA
1 ATAAAAATTA
11992817 TACTTTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
12 9 0.17
13 17 0.31
14 3 0.06
15 4 0.07
16 14 0.26
17 7 0.13
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (13 bp):
ATAAAAATTAAAA
Found at i:11992773 original size:25 final size:24
Alignment explanation
Indices: 11992733--11992816 Score: 109
Period size: 25 Copynumber: 3.5 Consensus size: 24
11992723 AATTCACATA
11992733 TATATAAAAATTAAAAATAAAAAT
1 TATATAAAAATTAAAAATAAAAAT
*
11992757 TATATATAAAATTAAAAGTAAAAAT
1 TATATA-AAAATTAAAAATAAAAAT
* * *
11992782 TATATAAACA-TAAAAATTAAATT
1 TATATAAAAATTAAAAATAAAAAT
11992805 TA-ATAAAAATTA
1 TATATAAAAATTA
11992817 TACTTTTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
22 6 0.12
23 14 0.27
24 9 0.17
25 23 0.44
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (24 bp):
TATATAAAAATTAAAAATAAAAAT
Found at i:11992795 original size:17 final size:16
Alignment explanation
Indices: 11992769--11992818 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
11992759 TATATAAAAT
11992769 TAAAAGTAAAAATTATA
1 TAAAA-TAAAAATTATA
*
11992786 TAAACATAAAAATTAAA
1 TAAA-ATAAAAATTATA
**
11992803 TTTAATAAAAATTATA
1 TAAAATAAAAATTATA
11992819 CTTTTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 11 0.39
17 16 0.57
18 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
TAAAATAAAAATTATA
Found at i:11992873 original size:11 final size:11
Alignment explanation
Indices: 11992853--11992895 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
11992843 ATATGTGAAT
11992853 TAATTTATATA
1 TAATTTATATA
*
11992864 TAATTCATATA
1 TAATTTATATA
*
11992875 T--TATATATA
1 TAATTTATATA
11992884 TAATTTATATA
1 TAATTTATATA
11992895 T
1 T
11992896 GTGTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.27
11 19 0.73
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTTATATA
Found at i:11992881 original size:20 final size:20
Alignment explanation
Indices: 11992858--11992895 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11992848 TGAATTAATT
11992858 TATATATAATTCATATATTA
1 TATATATAATTCATATATTA
*
11992878 TATATATAATTTATATAT
1 TATATATAATTCATATAT
11992896 GTGTGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATAATTCATATATTA
Found at i:11993021 original size:14 final size:13
Alignment explanation
Indices: 11993002--11993043 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
11992992 ACAATTTTAA
11993002 ATATAATTAATTAT
1 ATATAATT-ATTAT
11993016 ATATAATTATTAT
1 ATATAATTATTAT
11993029 -TATAATT-TTAT
1 ATATAATTATTAT
11993040 ATAT
1 ATAT
11993044 GGTGATGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.15
12 10 0.37
13 5 0.19
14 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATAATTATTAT
Found at i:11995065 original size:21 final size:22
Alignment explanation
Indices: 11995018--11995068 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
11995008 AAATATTAGA
*
11995018 TATTGATTTAGTTTATTATAAG
1 TATTGATTTAGTTTATTATAAC
* **
11995040 AATTGATTTAG-TTATTATTTC
1 TATTGATTTAGTTTATTATAAC
11995061 TATTGATT
1 TATTGATT
11995069 GTATTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (22 bp):
TATTGATTTAGTTTATTATAAC
Found at i:12000768 original size:19 final size:20
Alignment explanation
Indices: 12000744--12000786 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12000734 TATATTTATA
12000744 TTATGTA-AAATATTATAAT
1 TTATGTATAAATATTATAAT
* *
12000763 TTATGTATTAATATTATATT
1 TTATGTATAAATATTATAAT
12000783 TTAT
1 TTAT
12000787 ACGAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTATGTATAAATATTATAAT
Found at i:12008315 original size:12 final size:12
Alignment explanation
Indices: 12008298--12008322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12008288 TTAAATTATA
12008298 AATAATATTTTT
1 AATAATATTTTT
12008310 AATAATATTTTT
1 AATAATATTTTT
12008322 A
1 A
12008323 TATATTACTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATAATATTTTT
Found at i:12010170 original size:74 final size:74
Alignment explanation
Indices: 12010088--12010272 Score: 232
Period size: 74 Copynumber: 2.5 Consensus size: 74
12010078 TAATCTTTAA
* * * *
12010088 AATTTAATAAAGATGATGTTTTTAAGATAAAAATATAATTTTTGTTAAAAATATGAAAA-ACTTT
1 AATTTAATAAAAATGATGTTTTTAAGATAAAAATACAATCTTTGTTAAAAATATGAAAATA-ATT
*
12010152 TATTTTTTAT
65 TATTTTTCAT
* *
12010162 GATTTAATAAAAATAATGTTTTTAAGAT-AAAATCACAATCTTTGTTAAAAATATGAAAATAATT
1 AATTTAATAAAAATGATGTTTTTAAGATAAAAAT-ACAATCTTTGTTAAAAATATGAAAATAATT
12010226 TATTTTTCAT
65 TATTTTTCAT
* *
12010236 AATTTAACAAAAATGACAT-TTTTTAACATAAAAATAC
1 AATTTAATAAAAATG--ATGTTTTTAAGATAAAAATAC
12010273 GGCTTTGTTG
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
73 5 0.05
74 71 0.75
75 12 0.13
76 7 0.07
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (74 bp):
AATTTAATAAAAATGATGTTTTTAAGATAAAAATACAATCTTTGTTAAAAATATGAAAATAATTT
ATTTTTCAT
Found at i:12011753 original size:27 final size:26
Alignment explanation
Indices: 12011723--12011782 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
12011713 AGATAAGATT
12011723 ATATTAT-TTAATCTAATTTTATTCATA
1 ATATTATCTTAATCT-ATTTTA-TCATA
* *
12011750 ATATCATCTTATTCTATTTTATCATA
1 ATATTATCTTAATCTATTTTATCATA
*
12011776 ATCTTAT
1 ATATTAT
12011783 GTACCAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 10 0.36
27 12 0.43
28 6 0.21
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATTATCTTAATCTATTTTATCATA
Found at i:12012328 original size:27 final size:27
Alignment explanation
Indices: 12012290--12012350 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
12012280 TATTATTGAT
12012290 GTGGGTTACTTGCTCAATTGTGAATTA
1 GTGGGTTACTTGCTCAATTGTGAATTA
12012317 GTGGGTTACTTGCTCAATTGTGAATTA
1 GTGGGTTACTTGCTCAATTGTGAATTA
12012344 GTGGGTT
1 GTGGGTT
12012351 GCTTTTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.20, C:0.10, G:0.30, T:0.41
Consensus pattern (27 bp):
GTGGGTTACTTGCTCAATTGTGAATTA
Found at i:12014745 original size:10 final size:10
Alignment explanation
Indices: 12014730--12014754 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12014720 TGTGCTCACA
12014730 ACACATATAT
1 ACACATATAT
12014740 ACACATATAT
1 ACACATATAT
12014750 ACACA
1 ACACA
12014755 CATACATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (10 bp):
ACACATATAT
Found at i:12014755 original size:12 final size:12
Alignment explanation
Indices: 12014730--12014774 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
12014720 TGTGCTCACA
12014730 ACACATATAT--
1 ACACATATATAC
12014740 ACACATATATAC
1 ACACATATATAC
*
12014752 ACACATACATAC
1 ACACATATATAC
*
12014764 ATACATATATA
1 ACACATATATA
12014775 TATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 10 0.33
12 20 0.67
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (12 bp):
ACACATATATAC
Found at i:12024257 original size:18 final size:18
Alignment explanation
Indices: 12024234--12024275 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12024224 GACATTGATC
12024234 ATTATTGCCTTTAATATG
1 ATTATTGCCTTTAATATG
*
12024252 ATTATTACCTTTAATATG
1 ATTATTGCCTTTAATATG
12024270 -TTATTG
1 ATTATTG
12024276 AAAACCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (18 bp):
ATTATTGCCTTTAATATG
Found at i:12036585 original size:12 final size:12
Alignment explanation
Indices: 12036568--12036607 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
12036558 CGGATGAAGA
12036568 GAAGGAGAGGAG
1 GAAGGAGAGGAG
12036580 GAA-G-GAGGA-
1 GAAGGAGAGGAG
12036589 GAAGGAGAGGAG
1 GAAGGAGAGGAG
12036601 GAAGGAG
1 GAAGGAG
12036608 GAGAAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 3 0.12
10 6 0.24
11 6 0.24
12 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
GAAGGAGAGGAG
Found at i:12036592 original size:21 final size:21
Alignment explanation
Indices: 12036566--12036655 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
12036556 TTCGGATGAA
12036566 GAGAAGGAGAGGAGGAAGGAG
1 GAGAAGGAGAGGAGGAAGGAG
12036587 GAGAAGGAGAGGAGGAAGGAG
1 GAGAAGGAGAGGAGGAAGGAG
* ** *
12036608 GAGAAAGAGAAAAGAAAGGAG
1 GAGAAGGAGAGGAGGAAGGAG
*
12036629 GAGAAAGAGAAGGA-GAAGGAG
1 GAGAAGGAG-AGGAGGAAGGAG
12036650 GAGAAG
1 GAGAAG
12036656 AAGGAGAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 58 0.97
22 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (21 bp):
GAGAAGGAGAGGAGGAAGGAG
Found at i:12036634 original size:15 final size:15
Alignment explanation
Indices: 12036564--12036663 Score: 61
Period size: 15 Copynumber: 7.1 Consensus size: 15
12036554 GATTCGGATG
12036564 AAGAGAAGGA-GAG-
1 AAGAGAAGGAGGAGA
*
12036577 GAG-GAAGGAGGAGA
1 AAGAGAAGGAGGAGA
* *
12036591 AGGAG-AGGAGGAAGG
1 AAGAGAAGGAGG-AGA
* *
12036606 AGGAGAAAGA-GA-A
1 AAGAGAAGGAGGAGA
12036619 AAGA-AAGGAGGAGA
1 AAGAGAAGGAGGAGA
* *
12036633 AAGAGAAGGAGAAGG
1 AAGAGAAGGAGGAGA
* *
12036648 AGGAGAAGAAGGAGA
1 AAGAGAAGGAGGAGA
12036663 A
1 A
12036664 GAAGAAGAAC
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
12 10 0.15
13 10 0.15
14 13 0.20
15 29 0.45
16 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (15 bp):
AAGAGAAGGAGGAGA
Found at i:12036644 original size:12 final size:11
Alignment explanation
Indices: 12036566--12036663 Score: 84
Period size: 10 Copynumber: 9.5 Consensus size: 11
12036556 TTCGGATGAA
*
12036566 GAGAAGGAGAG
1 GAGAAAGAGAG
*
12036577 GAGGAAG-GAG
1 GAGAAAGAGAG
*
12036587 GAGAAGGAGAG
1 GAGAAAGAGAG
*
12036598 GAGGAAG-GAG
1 GAGAAAGAGAG
*
12036608 GAGAAAGAGAA
1 GAGAAAGAGAG
*
12036619 AAGAAAG-GAG
1 GAGAAAGAGAG
12036629 GAGAAAGAGAAG
1 GAGAAAGAG-AG
12036641 GAG-AAG-GAG
1 GAGAAAGAGAG
12036650 GAG-AAGA-AG
1 GAGAAAGAGAG
12036659 GAGAA
1 GAGAA
12036664 GAAGAAGAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
9 13 0.19
10 27 0.39
11 25 0.36
12 5 0.07
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (11 bp):
GAGAAAGAGAG
Found at i:12036666 original size:12 final size:12
Alignment explanation
Indices: 12036563--12036670 Score: 58
Period size: 12 Copynumber: 9.8 Consensus size: 12
12036553 GGATTCGGAT
12036563 GAAG-AGAAGGA
1 GAAGAAGAAGGA
* *
12036574 GAGGAGGAAGGA
1 GAAGAAGAAGGA
12036586 G--G-AGAAGGA
1 GAAGAAGAAGGA
* *
12036595 GAGGAGGAAGGA
1 GAAGAAGAAGGA
*
12036607 G--G-AGAAAGA
1 GAAGAAGAAGGA
12036616 GAA-AAGAAAGGA
1 GAAGAAG-AAGGA
*
12036628 G--G-AGAAAGA
1 GAAGAAGAAGGA
*
12036637 GAAGGAGAAGGA
1 GAAGAAGAAGGA
*
12036649 GGAGAAGAAGGA
1 GAAGAAGAAGGA
12036661 GAAGAAGAAG
1 GAAGAAGAAG
12036671 AACTGCTCAG
Statistics
Matches: 73, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
9 18 0.25
10 4 0.05
11 7 0.10
12 44 0.60
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGGA
Found at i:12036666 original size:21 final size:21
Alignment explanation
Indices: 12036573--12036667 Score: 85
Period size: 21 Copynumber: 4.6 Consensus size: 21
12036563 GAAGAGAAGG
12036573 AGAGGAG--GAAGGAGGAGAA
1 AGAGGAGAAGAAGGAGGAGAA
12036592 GGAGAGGAG--GAAGGAGGAGAA
1 --AGAGGAGAAGAAGGAGGAGAA
*
12036613 AGA-GAAAAGAAAGGAGGAGAA
1 AGAGGAGAAG-AAGGAGGAGAA
* *
12036634 AGAGAAGGAGAAGGAGGAG-A
1 AGAGGAGAAGAAGGAGGAGAA
12036654 AGAAGGAGAAGAAG
1 AG-AGGAGAAGAAG
12036668 AAGAACTGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 4 0.06
21 51 0.81
22 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (21 bp):
AGAGGAGAAGAAGGAGGAGAA
Found at i:12036669 original size:15 final size:15
Alignment explanation
Indices: 12036588--12036672 Score: 55
Period size: 15 Copynumber: 5.3 Consensus size: 15
12036578 AGGAAGGAGG
* *
12036588 AGAAGGAGAGGAGGA
1 AGAAGGAGAAGAAGA
* *
12036603 AGGAGGAGAAAGAGAAA
1 AGAAGGAG-AAGA-AGA
*
12036620 AGAAAGGAGGAGAA-A
1 AG-AAGGAGAAGAAGA
12036635 GAGAAGGAGAAGGAGGAGA
1 -AGAAGGAGAA-GA--AGA
12036654 AGAAGGAGAAGAAGA
1 AGAAGGAGAAGAAGA
12036669 AGAA
1 AGAA
12036673 CTGCTCAGTG
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
15 22 0.40
16 8 0.15
17 8 0.15
18 16 0.29
19 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
AGAAGGAGAAGAAGA
Found at i:12037436 original size:28 final size:28
Alignment explanation
Indices: 12037404--12037463 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
12037394 ATAAGTTAAT
*
12037404 ATTAATCTTTAAAATAAATATA-TAAAAA
1 ATTAATATTTAAAA-AAATATACTAAAAA
* *
12037432 ATTAATATTTAAAAAAATTTACTCAAAA
1 ATTAATATTTAAAAAAATATACTAAAAA
12037460 ATTA
1 ATTA
12037464 TAATATGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (28 bp):
ATTAATATTTAAAAAAATATACTAAAAA
Found at i:12037450 original size:16 final size:15
Alignment explanation
Indices: 12037414--12037447 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12037404 ATTAATCTTT
*
12037414 AAAATAAATATATAA
1 AAAATTAATATATAA
*
12037429 AAAATTAATATTTAA
1 AAAATTAATATATAA
12037444 AAAA
1 AAAA
12037448 ATTTACTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTAATATATAA
Found at i:12043059 original size:3 final size:3
Alignment explanation
Indices: 12043051--12043089 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12043041 TTAATTCATA
12043051 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12043090 GTTCATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12048638 original size:26 final size:25
Alignment explanation
Indices: 12048584--12048638 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12048574 TCTCACCAAG
*
12048584 AATTTTATAAAAATTTATCATTTGA
1 AATTTTATAAAAATTTATCATTGGA
*
12048609 AATTTT-TATAAATTTCATCATTGGA
1 AATTTTATAAAAATTT-ATCATTGGA
12048634 TAATT
1 -AATT
12048639 AATATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.31
25 14 0.54
26 4 0.15
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (25 bp):
AATTTTATAAAAATTTATCATTGGA
Found at i:12048701 original size:19 final size:19
Alignment explanation
Indices: 12048677--12048713 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12048667 ATTTAATCAT
*
12048677 GAAAAAAAATACTAAGAAG
1 GAAAAAAAAAACTAAGAAG
12048696 GAAAAAAAAAACTAAGAA
1 GAAAAAAAAAACTAAGAA
12048714 AAATACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (19 bp):
GAAAAAAAAAACTAAGAAG
Found at i:12048728 original size:24 final size:23
Alignment explanation
Indices: 12048700--12048753 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
12048690 AAGAAGGAAA
* *
12048700 AAAAAAACTAAGAAAAATACTAAAT
1 AAAAAAA-TAA-AAAAATACCAAAG
12048725 AAAATAAATAAAAAAATACCAAAG
1 AAAA-AAATAAAAAAATACCAAAG
12048749 AAAAA
1 AAAAA
12048754 CAAAAAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 15 0.58
25 7 0.27
26 3 0.12
ACGTcount: A:0.76, C:0.07, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAAAAATAAAAAAATACCAAAG
Found at i:12049629 original size:3 final size:3
Alignment explanation
Indices: 12049621--12049645 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12049611 AAAACAAAAT
12049621 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
12049646 AAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12049964 original size:42 final size:41
Alignment explanation
Indices: 12049889--12051315 Score: 1089
Period size: 42 Copynumber: 34.3 Consensus size: 41
12049879 GTTTTTTTTT
* * *
12049889 TAAAAGCTCCTCTAATTAGAGGC-TCAATGACTTTGAGAAAAA
1 TAAATGCTCCTCTAAATAGAGGCAACAA--ACTTTGAGAAAAA
* *
12049931 TAAATTCTCCTCTAAATAGAGGCTTAAC-AACTTT-TGAAAAA
1 TAAATGCTCCTCTAAATAGAGGC--AACAAACTTTGAGAAAAA
** * ** ***
12049972 TAAAATGCTAATCTAAAAAGAGGCACCACAATTTTTTTTAAAAA
1 T-AAATGCTCCTCTAAATAGAGGCA--ACAAACTTTGAGAAAAA
* * * *
12050016 TAAATTGCTCCTTTAAACAGA-GCACCACAACTTT--GAAAAG
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* *
12050056 TAAAATGCTCTTTTAAATAGAGGCAACAAAACTTTGA-AAAAA
1 T-AAATGCTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
*
12050098 TAAATGGCTCATCTAAATAGAGGCAACATAACTTT-A-AAACAA
1 TAAAT-GCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAA-AA
* * *
12050140 TAAATGGCTCATCTAAATAAAGGCAACTTAACTTTG-GAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
* * * *
12050182 TAAATGGCTACTTTAAATAAAGGTAACAGAACTTTG-GAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
*
12050224 TAAATGGCTCTTCTAAATAGAGG---C--A-----A-AAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAACAAACTTTGAGAAAAA
* *
12050255 TAAATGGCTTCTCTAAATAGAGGTAACAGAACTTTG-GAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
*
12050297 TAAATGGCTCCTCTAAATGGAGGCAACAAAACTTTG-GAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
*
12050339 TAAATGGCTCCTATAAATAGAGGCAACAAAACTTT-AGAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
* * * ** * *
12050381 TAAATGCTCCTTTAAACAGAGGTATTATGACTTT-TGAAAAA
1 TAAATGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* * *
12050422 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* *
12050464 TAAATGTTTCCTTTAAATAGAGGCAAC-AACTTTG-GAAAAAA
1 TAAATG-CTCCTCTAAATAGAGGCAACAAACTTTGAG-AAAAA
* *
12050505 TAAATGGCTCCTCTGAATAAAGGCAACAAAACTTTG-GAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
* **
12050547 TAAATTGTTCCTCTAAATAGAATCAACAGAACTTTGA-AAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* *
12050589 TAAATGGCTCATCTAAATAGAGGCAATAAAACTTT-AGAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAA-CAAACTTTGAGAAAAA
* * * * *
12050631 TAAATGCTCCTTTAAACAGAGGTACCACAACTTT-AAAAAAA
1 TAAATGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* * *
12050672 TAAATGGCTCTTTTAAATATAGGCAAC-AACTTTG-GAAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAACAAACTTTGAGAAAAA
*
12050712 TAAATGACTCCTCTAAATAGAGGCAATAAAACTTTGA-AAAAA
1 TAAATG-CTCCTCTAAATAGAGGCAA-CAAACTTTGAGAAAAA
* *
12050754 TAAATTGCTCCTCTAAATAAAGGTAACAGAACTTTGA-AAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
*
12050796 TAAATGACTCCTCTAAA-AGAGGTAACAAAACTTTG-GAAAAA
1 TAAATG-CTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
* * *
12050837 TAAATGACCCCTCTAAATAGAGGCAACAAAATTTTG-GAAAAG
1 TAAATG-CTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
* *
12050879 TAAATTGCTCCTTTAAATGGAGGCAACAAAACTTTGA-AAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
* *
12050921 TAAATTGCTCATCTAAATAGAGGTAACAGAACTTTGAGAAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* * *
12050964 TAAATGATTCCTTTAAATAAAGGCAACAGAACTTTG-GAAAAA
1 TAAATG-CTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* * * *
12051006 TAAATGCTCCTTTAAATAGAGGCACCACGACTTT-TGAAAAA
1 TAAATGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* * * * *
12051047 TAAATTGCTCCTATAAACAGATGCACCATGACTTT--GAAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
* *
12051088 TAAATGGCTCCTTTAAATAGAGGTAACAAAACTTTGA-AAAAA
1 TAAAT-GCTCCTCTAAATAGAGGCAAC-AAACTTTGAGAAAAA
* *
12051130 TAAATTGCTCATATAAATAGAGGCAACAGAACTTTGAGAAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
12051173 TAAATTGCTCCTCTAAATAGAGGCAACAGAACTTTG-GAAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
*
12051215 TAAATTGCTTTCTCCTCTAAATAGACGCAACAGAACTTTGA-AAAAA
1 TAAA-TG----CTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
*
12051261 TAAATTGCTCCTCTAAATAGAGACAACAGAACTTTG-GAAAAA
1 TAAA-TGCTCCTCTAAATAGAGGCAACA-AACTTTGAGAAAAA
12051303 TAAATTGCTCCTC
1 TAAA-TGCTCCTC
12051316 AACAATCATG
Statistics
Matches: 1161, Mismatches: 139, Indels: 170
0.79 0.09 0.12
Matches are distributed among these distances:
31 26 0.02
34 1 0.00
36 1 0.00
37 1 0.00
39 2 0.00
40 61 0.05
41 230 0.20
42 677 0.58
43 101 0.09
44 20 0.02
45 1 0.00
46 40 0.03
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (41 bp):
TAAATGCTCCTCTAAATAGAGGCAACAAACTTTGAGAAAAA
Found at i:12050157 original size:84 final size:84
Alignment explanation
Indices: 12049894--12051315 Score: 1306
Period size: 83 Copynumber: 17.1 Consensus size: 84
12049884 TTTTTTAAAA
* * * *
12049894 GCTCCTCTAATTAGAGGC-TCAATGACTTTGAGAAAAATAAAT-TCTCCTCTAAATAGAGGCTTA
1 GCTCCTCTAAATAGAGGCAACAA-AACTTTGA-AAAAATAAATGGCTCCTCTAAATAGAGGC--A
*
12049957 AC--AACTTTTGAAAAATAAAAT-
62 ACAGAACTTTGGAAAAAT-AAATG
** * *** ** * * * *
12049978 GCTAATCTAAAAAGAGGCACCACAATTTTTTTTAAAAATAAATTGCTCCTTTAAACAGA-GCACC
1 GCTCCTCTAAATAGAGGCA--ACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAAC
* *
12050042 ACAACTTT-GAAAAGTAAAAT-
64 AGAACTTTGGAAAAAT-AAATG
* * * *
12050062 GCTCTTTTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAACAT
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
*
12050127 AACTTT-AAAACAATAAATG
66 AACTTTGGAAA-AATAAATG
* * ** * * * * *
12050146 GCTCATCTAAATAAAGGCAACTTAACTTTGGAAAAATAAATGGCTACTTTAAATAAAGGTAACAG
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
12050211 AACTTTGGAAAAATAAATG
66 AACTTTGGAAAAATAAATG
* * *
12050230 GCTCTTCTAAATAGAGG---C---A-----AAAAAATAAATGGCTTCTCTAAATAGAGGTAACAG
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
12050284 AACTTTGGAAAAATAAATG
66 AACTTTGGAAAAATAAATG
* * * *
12050303 GCTCCTCTAAATGGAGGCAACAAAACTTTGGAAAAATAAATGGCTCCTATAAATAGAGGCAACAA
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
*
12050368 AACTTTAGAAAAATAAAT-
66 AACTTTGGAAAAATAAATG
* * * ** ** * * *
12050386 GCTCCTTTAAACAGAGGTATTATGACTTTTG-AAAAATAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAATAGAGGCAACAAAAC-TTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACA
*
12050450 CG-ACTTTGAAAAAATAAATG
65 -GAACTTTGGAAAAATAAATG
** * * *
12050470 TTTCCTTTAAATAGAGGCAAC--AACTTTGGAAAAAATAAATGGCTCCTCTGAATAAAGGCAACA
1 GCTCCTCTAAATAGAGGCAACAAAACTTT-GAAAAAATAAATGGCTCCTCTAAATAGAGGCAACA
* *
12050533 AAACTTTGGAAAAATAAATT
65 GAACTTTGGAAAAATAAATG
* ** * * * *
12050553 GTTCCTCTAAATAGAATCAACAGAACTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAATAA
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
*
12050618 AACTTTAGAAAAATAAAT-
66 AACTTTGGAAAAATAAATG
* * * * * * * * *
12050636 GCTCCTTTAAACAGAGGTACCACAACTTTAAAAAAATAAATGGCTCTTTTAAATATAGGCAAC--
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
12050699 AACTTTGGAAAAATAAATG
66 AACTTTGGAAAAATAAATG
* * * * *
12050718 ACTCCTCTAAATAGAGGCAATAAAACTTTGAAAAAATAAATTGCTCCTCTAAATAAAGGTAACAG
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
*
12050783 AACTTTGAAAAAATAAATG
66 AACTTTGGAAAAATAAATG
* * * * * *
12050802 ACTCCTCTAAA-AGAGGTAACAAAACTTTGGAAAAATAAATGACCCCTCTAAATAGAGGCAACAA
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
* * *
12050866 AATTTTGGAAAAGTAAATT
66 AACTTTGGAAAAATAAATG
* * * * *
12050885 GCTCCTTTAAATGGAGGCAACAAAACTTTGAAAAAATAAATTGCTCATCTAAATAGAGGTAACAG
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
12050950 AACTTTGAGAAAAATAAATG
66 AACTTTG-GAAAAATAAATG
** * * * * * *
12050970 ATTCCTTTAAATAAAGGCAACAGAACTTTGGAAAAATAAAT-GCTCCTTTAAATAGAGGCACCAC
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACA-
* *
12051034 G-ACTTTTGAAAAATAAATT
65 GAACTTTGGAAAAATAAATG
* * * * ** * * *
12051053 GCTCCTATAAACAGATGCACCATGACTTTG-AAAAATAAATGGCTCCTTTAAATAGAGGTAACAA
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
* *
12051117 AACTTTGAAAAAATAAATT
66 AACTTTGGAAAAATAAATG
* * * *
12051136 GCTCATATAAATAGAGGCAACAGAACTTTGAGAAAAATAAATTGCTCCTCTAAATAGAGGCAACA
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGA-AAAAATAAATGGCTCCTCTAAATAGAGGCAACA
12051201 GAACTTTGGAAAAATAAATTG
65 GAACTTTGGAAAAATAAA-TG
* * * * *
12051222 CTTTCTCCTCTAAATAGACGCAACAGAACTTTGAAAAAATAAATTGCTCCTCTAAATAGAGACAA
1 ---GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAA
*
12051287 CAGAACTTTGGAAAAATAAATT
63 CAGAACTTTGGAAAAATAAATG
12051309 GCTCCTC
1 GCTCCTC
12051316 AACAATCATG
Statistics
Matches: 1097, Mismatches: 198, Indels: 86
0.79 0.14 0.06
Matches are distributed among these distances:
73 65 0.06
76 1 0.00
78 1 0.00
79 1 0.00
81 21 0.02
82 92 0.08
83 353 0.32
84 347 0.32
85 119 0.11
86 16 0.01
87 4 0.00
88 50 0.05
89 27 0.02
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (84 bp):
GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATGGCTCCTCTAAATAGAGGCAACAG
AACTTTGGAAAAATAAATG
Found at i:12050257 original size:31 final size:31
Alignment explanation
Indices: 12050219--12050277 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
12050209 AGAACTTTGG
12050219 AAAAATAAATGGC-TCTTCTAAATAGAGGCAA
1 AAAAATAAATGGCTTC-TCTAAATAGAGGCAA
12050250 AAAAATAAATGGCTTCTCTAAATAGAGG
1 AAAAATAAATGGCTTCTCTAAATAGAGG
12050278 TAACAGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (31 bp):
AAAAATAAATGGCTTCTCTAAATAGAGGCAA
Found at i:12050272 original size:73 final size:73
Alignment explanation
Indices: 12050177--12050327 Score: 248
Period size: 73 Copynumber: 2.1 Consensus size: 73
12050167 TTAACTTTGG
* *
12050177 AAAAATAAATGGCTACTTTAAATAAAGGTAACAGAACTTTGGAAAAATAAATGGCTCTTCTAAAT
1 AAAAATAAATGGCTACTCTAAATAAAGGTAACAGAACTTTGGAAAAATAAATGGCTCCTCTAAAT
12050242 AGAGGCAA
66 AGAGGCAA
* *
12050250 AAAAATAAATGGCTTCTCTAAATAGAGGTAACAGAACTTTGGAAAAATAAATGGCTCCTCTAAAT
1 AAAAATAAATGGCTACTCTAAATAAAGGTAACAGAACTTTGGAAAAATAAATGGCTCCTCTAAAT
*
12050315 GGAGGCAA
66 AGAGGCAA
*
12050323 CAAAA
1 AAAAA
12050328 CTTTGGAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (73 bp):
AAAAATAAATGGCTACTCTAAATAAAGGTAACAGAACTTTGGAAAAATAAATGGCTCCTCTAAAT
AGAGGCAA
Found at i:12050421 original size:125 final size:124
Alignment explanation
Indices: 12050249--12051315 Score: 1091
Period size: 125 Copynumber: 8.5 Consensus size: 124
12050239 AATAGAGGCA
* * * *
12050249 AAAAAATAAATGGCTTCTCTAAATAGAGGTAACAGAACTTTGGAAAAATAAATGGCTCCTCTAAA
1 AAAAAATAAAT-GCTCCTCTAAATAGAGGCAACAG-ACTTTTGAAAAATAAATTGCTCCTCTAAA
* * * *
12050314 TGGAGGCAACAAAACTTTGGAAAAATAAATGGCTCCTATAAATAGAGGCAACAAAACTTT-
64 TAGAGGCAACAGAACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTTG
* * * **
12050374 AGAAAAATAAATGCTCCTTTAAACAGAGGTATTATGACTTTTGAAAAATAAATTGCTCCTCTAAA
1 A-AAAAATAAATGCTCCTCTAAATAGAGGCAACA-GACTTTTGAAAAATAAATTGCTCCTCTAAA
* * * ** *
12050439 CAGAGGCACCACG-ACTTTGAAAAAATAAATGTTTCCTTTAAATAGAGGCAAC--AACTTTGG
64 TAGAGGCAACA-GAACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTT-G
* * * * *
12050499 AAAAAATAAATGGCTCCTCTGAATAAAGGCAACAAAACTTTGGAAAAATAAATTGTTCCTCTAAA
1 AAAAAATAAAT-GCTCCTCTAAATAGAGGCAAC-AGACTTTTGAAAAATAAATTGCTCCTCTAAA
** * * * *
12050564 TAGAATCAACAGAACTTTGAAAAAATAAATGGCTCATCTAAATAGAGGCAATAAAACTTT-
64 TAGAGGCAACAGAACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTTG
* * * ** * * *
12050624 AGAAAAATAAATGCTCCTTTAAACAGAGGTACCACA-ACTTTAAAAAAATAAATGGCTCTTTTAA
1 A-AAAAATAAATGCTCCTCTAAATAGAGG--CAACAGACTTTTGAAAAATAAATTGCTCCTCTAA
* *
12050688 ATATAGGCAAC--AACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAATAAAACTTTG
63 ATAGAGGCAACAGAACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTTG
* *
12050748 AAAAAATAAATTGCTCCTCTAAATAAAGGTAACAGAAC-TTTGAAAAAATAAA-TGACTCCTCTA
1 AAAAAATAAA-TGCTCCTCTAAATAGAGGCAACAG-ACTTTTG-AAAAATAAATTG-CTCCTCTA
* * * *
12050811 AA-AGAGGTAACAAAACTTTGGAAAAATAAATGACCCCTCTAAATAGAGGCAACAAAATTTTG
62 AATAGAGGCAACAGAACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTTG
* * * * * *
12050873 GAAAAGTAAATTGCTCCTTTAAATGGAGGCAACAAAAC-TTTGAAAAAATAAATTGCTCATCTAA
1 AAAAAATAAA-TGCTCCTCTAAATAGAGGCAAC-AGACTTTTG-AAAAATAAATTGCTCCTCTAA
* * * * *
12050937 ATAGAGGTAACAGAACTTTGAGAAAAATAAATGATTCCTTTAAATAAAGGCAACAGAACTTTG
63 ATAGAGGCAACAGAACTTTG-GAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTTG
* * * * *
12051000 GAAAAATAAATGCTCCTTTAAATAGAGGCACCACGACTTTTGAAAAATAAATTGCTCCTATAAAC
1 AAAAAATAAATGCTCCTCTAAATAGAGGCAACA-GACTTTTGAAAAATAAATTGCTCCTCTAAAT
* * * * *
12051065 AGATGCACCATG-ACTTT-GAAAAATAAATGGCTCCTTTAAATAGAGGTAACAAAACTTTG
65 AGAGGCAACA-GAACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTTG
* * *
12051124 AAAAAATAAATTGCTCATATAAATAGAGGCAACAGAACTTTGAGAAAAATAAATTGCTCCTCTAA
1 AAAAAATAAA-TGCTCCTCTAAATAGAGGCAACAG-ACTTT-TGAAAAATAAATTGCTCCTCTAA
* * *
12051189 ATAGAGGCAACAGAACTTTGGAAAAATAAATTGCTTTCTCCTCTAAATAGACGCAACAGAACTTT
63 ATAGAGGCAACAGAACTTTGGAAAAATAAA-TG---ACTCCTCTAAATAGAGGCAACAAAACTTT
12051254 G
124 G
* *
12051255 AAAAAATAAATTGCTCCTCTAAATAGAGACAACAGAACTTTGGAAAAATAAATTGCTCCTC
1 AAAAAATAAA-TGCTCCTCTAAATAGAGGCAACAG-ACTTTTGAAAAATAAATTGCTCCTC
12051316 AACAATCATG
Statistics
Matches: 791, Mismatches: 114, Indels: 69
0.81 0.12 0.07
Matches are distributed among these distances:
122 3 0.00
123 70 0.09
124 93 0.12
125 340 0.43
126 132 0.17
127 69 0.09
128 2 0.00
130 19 0.02
131 63 0.08
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.25
Consensus pattern (124 bp):
AAAAAATAAATGCTCCTCTAAATAGAGGCAACAGACTTTTGAAAAATAAATTGCTCCTCTAAATA
GAGGCAACAGAACTTTGGAAAAATAAATGACTCCTCTAAATAGAGGCAACAAAACTTTG
Found at i:12052162 original size:64 final size:65
Alignment explanation
Indices: 12052091--12052241 Score: 157
Period size: 63 Copynumber: 2.4 Consensus size: 65
12052081 TTCGGAGGCT
* * * *
12052091 TCTCAGCACTAACAGATTTTAGAAA-AAGTTTCATCCA-CCATCACTAGGTCACTACTTATAGGT
1 TCTCAGCACTAACAAATTTTAGAAACAAATTTCAT-CATCCATCACTAGGTCACCACTCATAGGT
12052154 G
65 G
* * * * * *
12052155 TCTCAGCATTAGC-CATTTCA-AAACAAATTTCGTCATCCATCACTAGGTCACCACTCATAGGTT
1 TCTCAGCACTAACAAATTTTAGAAACAAATTTCATCATCCATCACTAGGTCACCACTCATAGGTG
* *
12052218 TCTCAACCCTAACAAATTTTAGAA
1 TCTCAGCACTAACAAATTTTAGAA
12052242 TAAACTTTGT
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
62 5 0.07
63 45 0.66
64 16 0.24
65 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (65 bp):
TCTCAGCACTAACAAATTTTAGAAACAAATTTCATCATCCATCACTAGGTCACCACTCATAGGTG
Found at i:12052912 original size:15 final size:14
Alignment explanation
Indices: 12052894--12052927 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
12052884 TGAGTTTTCC
*
12052894 TTTTCTTTTTTTTAT
1 TTTTCTCTTTTTT-T
12052909 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
12052923 TTTTC
1 TTTTC
12052928 CTTCATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTCTCTTTTTTT
Found at i:12057041 original size:56 final size:53
Alignment explanation
Indices: 12056954--12057122 Score: 166
Period size: 56 Copynumber: 3.2 Consensus size: 53
12056944 TTAGACTAAA
12056954 TTAGAAATATTTTTTCTTTTTG-AATTTCTAAATTTTTCATCATTTGGGCCTAT
1 TTAGAAATATTTTTT-TTTTTGAAATTTCTAAATTTTTCATCATTTGGGCCTAT
* *** * ** *
12057007 TTAGAAATCTTTTTTATTATTTTTTTATTTCTAAA-TTTTCTACCATTTGGTTCAAT
1 TTAGAAAT-ATTTTT-TT-TTTTGAAATTTCTAAATTTTTC-ATCATTTGGGCCTAT
* *
12057063 TTAAAAATATTTTTTTTTTTGAAATTT-TGAAATTTTT-ATTATTTGGGCCTAT
1 TTAGAAATATTTTTTTTTTTGAAATTTCT-AAATTTTTCATCATTTGGGCCTAT
12057115 TTAGAAAT
1 TTAGAAAT
12057123 TCCTCTTTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
52 18 0.20
53 19 0.21
54 12 0.13
55 15 0.16
56 27 0.30
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (53 bp):
TTAGAAATATTTTTTTTTTTGAAATTTCTAAATTTTTCATCATTTGGGCCTAT
Found at i:12058424 original size:21 final size:23
Alignment explanation
Indices: 12058398--12058439 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
12058388 CTACTTTCTG
12058398 TTTTTCCTAT-TTTT-TGTGTTC
1 TTTTTCCTATCTTTTCTGTGTTC
*
12058419 TTTTTCGTATCTTTTCTGTGT
1 TTTTTCCTATCTTTTCTGTGT
12058440 ATGATCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.05, C:0.14, G:0.12, T:0.69
Consensus pattern (23 bp):
TTTTTCCTATCTTTTCTGTGTTC
Found at i:12065335 original size:17 final size:17
Alignment explanation
Indices: 12065310--12065343 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12065300 GATTAGAATA
*
12065310 TTATCATATTTATTTAT
1 TTATCATATTAATTTAT
*
12065327 TTATTATATTAATTTAT
1 TTATCATATTAATTTAT
12065344 GAATTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATCATATTAATTTAT
Found at i:12065722 original size:25 final size:26
Alignment explanation
Indices: 12065694--12065743 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
12065684 TAATATAATT
*
12065694 TTTTCATTTTATTTTC-TTTCTTTTC
1 TTTTCATTTTAGTTTCTTTTCTTTTC
* *
12065719 TTTTCCTTTTCGTTTCTTTTCTTTT
1 TTTTCATTTTAGTTTCTTTTCTTTT
12065744 TCCCTTCCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (26 bp):
TTTTCATTTTAGTTTCTTTTCTTTTC
Found at i:12065734 original size:16 final size:16
Alignment explanation
Indices: 12065710--12065745 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12065700 TTTTATTTTC
*
12065710 TTTCTTTTCTTTTCCT
1 TTTCGTTTCTTTTCCT
*
12065726 TTTCGTTTCTTTTCTT
1 TTTCGTTTCTTTTCCT
12065742 TTTC
1 TTTC
12065746 CCTTCCCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTCGTTTCTTTTCCT
Found at i:12065739 original size:21 final size:20
Alignment explanation
Indices: 12065705--12065743 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
12065695 TTTCATTTTA
12065705 TTTTCTTTCTTTTCTTTTCC
1 TTTTCTTTCTTTTCTTTTCC
12065725 TTTTCGTTTCTTTTCTTTT
1 TTTTC-TTTCTTTTCTTTT
12065744 TCCCTTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTCTTTCTTTTCTTTTCC
Found at i:12065740 original size:5 final size:5
Alignment explanation
Indices: 12065694--12065743 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
12065684 TAATATAATT
* *
12065694 TTTTC ATTTTA TTTTC -TTTC TTTTC TTTTCC TTTTC GTTTC TTTTC TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC TTTTC TTTT
12065744 TCCCTTCCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
4 4 0.11
5 25 0.66
6 9 0.24
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:12066750 original size:20 final size:19
Alignment explanation
Indices: 12066725--12066767 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
12066715 AGGTGCATTT
12066725 TTTATTTATTTTTATAATTA
1 TTTATTTATTTTT-TAATTA
*
12066745 TTTATTTATTTTTTAATTT
1 TTTATTTATTTTTTAATTA
12066764 TTTA
1 TTTA
12066768 ATATATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTATTTTTTAATTA
Found at i:12066785 original size:27 final size:27
Alignment explanation
Indices: 12066723--12066820 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 27
12066713 CTAGGTGCAT
*
12066723 TTTTTA-TTTATTTTTATAATTATTTA
1 TTTTTATTTTATTTTTATAATTATTAA
12066749 TTTATT-TTTTAATTTTT-TAA-TATATAA
1 TTT-TTATTTT-ATTTTTATAATTAT-TAA
* * *
12066776 TTTTTATTTTCTTTCTATTATT-TCT-A
1 TTTTTATTTTATTTTTATAATTAT-TAA
12066802 TATTTTATTTTATTTTTAT
1 T-TTTTATTTTATTTTTAT
12066821 GTGAACTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
26 14 0.25
27 36 0.63
28 7 0.12
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTTATTTTATTTTTATAATTATTAA
Found at i:12066951 original size:15 final size:16
Alignment explanation
Indices: 12066918--12066957 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
12066908 AAAATAAAAT
12066918 AAAATAAA-TATAAAC
1 AAAATAAACTATAAAC
*
12066933 AAAATAAACTTTAAA-
1 AAAATAAACTATAAAC
12066948 AAAA-AAACTA
1 AAAATAAACTA
12066958 AGCAAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 5 0.23
15 12 0.55
16 5 0.23
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAATAAACTATAAAC
Found at i:12068582 original size:16 final size:16
Alignment explanation
Indices: 12068563--12068598 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12068553 TTTTCTTCAC
*
12068563 TTTTTTTCTTTCTTTT
1 TTTTTTTCTTACTTTT
*
12068579 TTTTTTTGTTACTTTT
1 TTTTTTTCTTACTTTT
12068595 TTTT
1 TTTT
12068599 CCCTCAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTTCTTACTTTT
Found at i:12073592 original size:20 final size:20
Alignment explanation
Indices: 12073560--12073598 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12073550 GTAATTATTT
*
12073560 TTTGTTTATTTGCT-TTGTG
1 TTTGTTTAATTGCTCTTGTG
12073579 TTTGCTTTAATTGCTCTTGT
1 TTTG-TTTAATTGCTCTTGT
12073599 TTACTTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.08, C:0.10, G:0.18, T:0.64
Consensus pattern (20 bp):
TTTGTTTAATTGCTCTTGTG
Found at i:12077737 original size:41 final size:41
Alignment explanation
Indices: 12077680--12077766 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
12077670 AAAAAGGATA
* *
12077680 ATTAAAACCAATAATTAATTAATTTCCTTTTTTTTGGTACT
1 ATTAAAACCAATAATTAATTAATTGCCTATTTTTTGGTACT
*
12077721 ATTAAAGCCAATAATTAATTAATTGCCTATTTTTTGGTACT
1 ATTAAAACCAATAATTAATTAATTGCCTATTTTTTGGTACT
12077762 ATTAA
1 ATTAA
12077767 TTAATTGCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (41 bp):
ATTAAAACCAATAATTAATTAATTGCCTATTTTTTGGTACT
Found at i:12080872 original size:26 final size:29
Alignment explanation
Indices: 12080818--12080899 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
12080808 AATAATTGTG
* *
12080818 TGAATATTACTTT-ATTATTTTTTCATTATT
1 TGAATA-TAATTTAATTATTTATT-ATTATT
*
12080848 TGAATATAATTTTATT-TTTATTTATTATT
1 TGAATATAATTTAATTATTTA-TTATTATT
*
12080877 TTAATATAATTTAATTATTTATT
1 TGAATATAATTTAATTATTTATT
12080900 TTTTATTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 30 0.67
30 15 0.33
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (29 bp):
TGAATATAATTTAATTATTTATTATTATT
Found at i:12080884 original size:29 final size:30
Alignment explanation
Indices: 12080818--12080906 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
12080808 AATAATTGTG
* *
12080818 TGAATATTACTTTATTATTT-TTTCATTATT
1 TGAATATAATTTTATTATTTATTT-ATTATT
12080848 TGAATATAATTTTATT-TTTATTTATTATT
1 TGAATATAATTTTATTATTTATTTATTATT
* * *
12080877 TTAATATAATTTAATTATTTATTTTTTATT
1 TGAATATAATTTTATTATTTATTTATTATT
12080907 GTTTGGATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 23 0.44
30 29 0.56
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
TGAATATAATTTTATTATTTATTTATTATT
Found at i:12080917 original size:33 final size:31
Alignment explanation
Indices: 12080832--12080921 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 31
12080822 TATTACTTTA
*
12080832 TTATTTTTTCATTATTTGAATATAATTTTATTT
1 TTATTTTTT-ATT-TTTGAATATAATTTAATTT
*
12080865 TTATTTATTA-TTTT-AATATAATTTAATTAT
1 TTATTTTTTATTTTTGAATATAATTTAATT-T
*
12080895 TTATTTTTTATTGTTTGGATATAATTT
1 TTATTTTTTATT-TTTGAATATAATTT
12080922 GATCACTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 13 0.27
30 13 0.27
31 2 0.04
32 4 0.08
33 17 0.35
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (31 bp):
TTATTTTTTATTTTTGAATATAATTTAATTT
Found at i:12084246 original size:12 final size:10
Alignment explanation
Indices: 12084218--12084242 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12084208 ATGCATATTG
12084218 AAAAATTCCT
1 AAAAATTCCT
12084228 AAAAATTCCT
1 AAAAATTCCT
12084238 AAAAA
1 AAAAA
12084243 AATTTCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTCCT
Found at i:12087378 original size:39 final size:39
Alignment explanation
Indices: 12087335--12087413 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 39
12087325 ATTTCAATGA
*
12087335 TAGTTTTTC-ACTACAGAATAGTGTATTATTCAACTGCTC
1 TAGTTTTTCAAC-ACAGAATAGTATATTATTCAACTGCTC
12087374 TAGTTTTTCAACACAGAATAGTATATTATTCAACTGCTC
1 TAGTTTTTCAACACAGAATAGTATATTATTCAACTGCTC
12087413 T
1 T
12087414 TCTATTGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (39 bp):
TAGTTTTTCAACACAGAATAGTATATTATTCAACTGCTC
Found at i:12087732 original size:34 final size:34
Alignment explanation
Indices: 12087686--12087751 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
12087676 TCATACTTAG
*
12087686 ACTTCATTTTGATCATACTGTTTCTCATTTATAA
1 ACTTCATCTTGATCATACTGTTTCTCATTTATAA
**
12087720 ACTTCATCTTGATGGTACTGTTTCTCATTTAT
1 ACTTCATCTTGATCATACTGTTTCTCATTTAT
12087752 GATATTGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (34 bp):
ACTTCATCTTGATCATACTGTTTCTCATTTATAA
Found at i:12088430 original size:19 final size:19
Alignment explanation
Indices: 12088406--12088443 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12088396 AAAAACGATT
*
12088406 AAATAAAAATTAAAATTGA
1 AAATAAAAATAAAAATTGA
12088425 AAATAAAAATAAAAATTGA
1 AAATAAAAATAAAAATTGA
12088444 TAGATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AAATAAAAATAAAAATTGA
Found at i:12089137 original size:12 final size:12
Alignment explanation
Indices: 12089117--12089153 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
12089107 ATTTCTAGTT
12089117 TAATATTAATAA
1 TAATATTAATAA
*
12089129 TAATTTTAATAA
1 TAATATTAATAA
12089141 TAATATTAATAA
1 TAATATTAATAA
12089153 T
1 T
12089154 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:12089138 original size:18 final size:18
Alignment explanation
Indices: 12089115--12089150 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12089105 TCATTTCTAG
*
12089115 TTTAATATTAATAATAAT
1 TTTAATAATAATAATAAT
*
12089133 TTTAATAATAATATTAAT
1 TTTAATAATAATAATAAT
12089151 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATAATAATAATAAT
Found at i:12089795 original size:22 final size:23
Alignment explanation
Indices: 12089767--12089815 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
12089757 CTGGATCGTC
12089767 GAAAATTGGGAAGGAGAAAG-AA
1 GAAAATTGGGAAGGAGAAAGAAA
** *
12089789 GAAAATTTTGAAGGAGAGAGAAA
1 GAAAATTGGGAAGGAGAAAGAAA
12089812 GAAA
1 GAAA
12089816 GAAGAGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (23 bp):
GAAAATTGGGAAGGAGAAAGAAA
Found at i:12094138 original size:12 final size:12
Alignment explanation
Indices: 12094121--12094157 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
12094111 TTTTTTTTTA
12094121 ATTATTAATATT
1 ATTATTAATATT
*
12094133 ATTATTAAAATT
1 ATTATTAATATT
12094145 ATTATTAATATT
1 ATTATTAATATT
12094157 A
1 A
12094158 AACTGGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTATTAATATT
Found at i:12094150 original size:18 final size:18
Alignment explanation
Indices: 12094124--12094159 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12094114 TTTTTTAATT
*
12094124 ATTAATATTATTATTAAA
1 ATTAATATTAATATTAAA
*
12094142 ATTATTATTAATATTAAA
1 ATTAATATTAATATTAAA
12094160 CTGGAAACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAATATTAATATTAAA
Found at i:12096011 original size:49 final size:49
Alignment explanation
Indices: 12095878--12096089 Score: 324
Period size: 47 Copynumber: 4.4 Consensus size: 49
12095868 TTTGAAAAAA
* *
12095878 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTT-TAG
1 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAAG
* *
12095926 ATGA-AATTTTAAAGTTGTTGAGCCTCTACTGGAAGGAGCTTTTCCAAG
1 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAAG
* *
12095974 ATGAGAATTTTAAAGTTGTTGAGCCTTTGCTGAAAGGAGCTTTTTC-AG
1 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAAG
* *
12096022 ATGA-AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
1 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAAG
12096070 ATGAGAATTTTAAAGTTGTT
1 ATGAGAATTTTAAAGTTGTT
12096090 CCAAGATGAG
Statistics
Matches: 150, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
47 76 0.51
48 22 0.15
49 52 0.35
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (49 bp):
ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAAG
Found at i:12096042 original size:96 final size:96
Alignment explanation
Indices: 12095878--12096089 Score: 354
Period size: 96 Copynumber: 2.2 Consensus size: 96
12095868 TTTGAAAAAA
* *
12095878 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTTAGATGAAATTTTAAAGTTG
1 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAGATGAAATTTTAAAGTTG
12095943 TTGAGCCTCTACTG-GAAGGAGCTTTTCCAAG
66 TTGAGCCTCTACTGAG-AGGAGCTTTTCCAAG
* *
12095974 ATGAGAATTTTAAAGTTGTTGAGCCTTTGCTGAAAGGAGCTTTTTCAGATGAAATTTTAAAGTTG
1 ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAGATGAAATTTTAAAGTTG
* *
12096039 TTGAGCCTCTGCTGAGAGGAGCTTTTTCAAG
66 TTGAGCCTCTACTGAGAGGAGCTTTTCCAAG
12096070 ATGAGAATTTTAAAGTTGTT
1 ATGAGAATTTTAAAGTTGTT
12096090 CCAAGATGAG
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 108 0.99
97 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (96 bp):
ATGAGAATTTTAAAGTTGTTGAGCCTCTACTGAAAGGAGCTTTTTCAGATGAAATTTTAAAGTTG
TTGAGCCTCTACTGAGAGGAGCTTTTCCAAG
Found at i:12096100 original size:25 final size:25
Alignment explanation
Indices: 12096066--12096114 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
12096056 GGAGCTTTTT
12096066 CAAGATGAGAATTTTAAAGTTGTTC
1 CAAGATGAGAATTTTAAAGTTGTTC
12096091 CAAGATGAGAATTTTAAAGTTGTT
1 CAAGATGAGAATTTTAAAGTTGTT
12096115 GAGCCTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (25 bp):
CAAGATGAGAATTTTAAAGTTGTTC
Found at i:12096114 original size:74 final size:70
Alignment explanation
Indices: 12096020--12096160 Score: 219
Period size: 74 Copynumber: 2.0 Consensus size: 70
12096010 GAGCTTTTTC
*
12096020 AGATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAGAATTTTAAAG
1 AGATGAAATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTC-A-A-GAGAATTTTAAAG
12096085 TTGTTCCA
63 TTGTTCCA
* *
12096093 AGATGAGAATTTTAAAGTTGTTGAGCCTTTACTGAGATGAGCTTTTTCAAGAGAATTTTAAAGTT
1 AGATGA-AATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTT
12096158 GTT
65 GTT
12096161 GAGCCTCTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
71 18 0.28
72 1 0.02
73 7 0.11
74 38 0.59
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (70 bp):
AGATGAAATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTG
TTCCA
Found at i:12096161 original size:46 final size:46
Alignment explanation
Indices: 12096097--12096184 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
12096087 GTTCCAAGAT
* *
12096097 GAGAATTTTAAAGTTGTTGAGCCTTTACTGAGATGAGCTTTTTCAA
1 GAGAATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAA
*
12096143 GAGAATTTTAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTT
1 GAGAATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTT
12096185 CAATAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (46 bp):
GAGAATTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAA
Found at i:12096382 original size:18 final size:18
Alignment explanation
Indices: 12096359--12096395 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12096349 TCATTTCTAG
*
12096359 TTTAATATTAATAATAAT
1 TTTAATAATAATAATAAT
*
12096377 TTTAATAATATTAATAAT
1 TTTAATAATAATAATAAT
12096395 T
1 T
12096396 AAAAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAATAATAATAATAAT
Found at i:12099447 original size:20 final size:19
Alignment explanation
Indices: 12099419--12099466 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
12099409 AATTATTTTA
* *
12099419 AAAACAAATTTAAAATAAAT
1 AAAATAAATTGAAAA-AAAT
*
12099439 AAAATAAATTGAAAAAATT
1 AAAATAAATTGAAAAAAAT
12099458 ATAAATAAA
1 A-AAATAAA
12099467 ATGTAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATAAATTGAAAAAAAT
Found at i:12099510 original size:19 final size:17
Alignment explanation
Indices: 12099474--12099512 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
12099464 AAAATGTAAT
*
12099474 TAAATATTATTGAAAAA
1 TAAATATTATGGAAAAA
12099491 TAAATATTATCGGCAAAAA
1 TAAATATTAT-GG-AAAAA
12099510 TAA
1 TAA
12099513 TAATTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (17 bp):
TAAATATTATGGAAAAA
Found at i:12101433 original size:26 final size:26
Alignment explanation
Indices: 12101399--12101450 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
12101389 ATCAATAGTT
*
12101399 TTACCTACGAAATTTTTCATTGATAA
1 TTACCTACGAAAATTTTCATTGATAA
* *
12101425 TTACTTACGAAAATTTTCTTTGATAA
1 TTACCTACGAAAATTTTCATTGATAA
12101451 ACCATCGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (26 bp):
TTACCTACGAAAATTTTCATTGATAA
Found at i:12101492 original size:1 final size:1
Alignment explanation
Indices: 12101488--12101514 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
12101478 CACAAAAGAG
12101488 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
12101515 CAGTTGGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12108841 original size:22 final size:22
Alignment explanation
Indices: 12108806--12108870 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 22
12108796 CAAAACTTTC
*
12108806 ACAAATAAAAAATAAATTACT-TA
1 ACAAAT-AAAAATAAATT-CTCCA
12108829 ACAAATAAAAATAAATTCTCCA
1 ACAAATAAAAATAAATTCTCCA
12108851 ACAATACTAAAAATAAATTC
1 ACAA-A-TAAAAATAAATTC
12108871 AAAAAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 2 0.05
22 16 0.42
23 7 0.18
24 13 0.34
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.25
Consensus pattern (22 bp):
ACAAATAAAAATAAATTCTCCA
Found at i:12108976 original size:33 final size:32
Alignment explanation
Indices: 12108934--12109052 Score: 99
Period size: 33 Copynumber: 3.8 Consensus size: 32
12108924 ATATAACTAG
12108934 CAAATTTCAACAAATATATAACCAAAACCTAAA
1 CAAATTTCAACAAATATATAACCAAAACC-AAA
* *
12108967 CAAATTTCAACATATATAAAACC--AA-C-AA
1 CAAATTTCAACAAATATATAACCAAAACCAAA
* * *
12108995 -AAA-CTCAACAAAT-TGGTAACTAAAACCCAAA
1 CAAATTTCAACAAATAT-ATAACCAAAA-CCAAA
* *
12109026 CAAATTTCAACAAATTTATAACAAAAA
1 CAAATTTCAACAAATATATAACCAAAA
12109053 ATTAAACCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
25 1 0.01
26 11 0.16
27 3 0.04
28 4 0.06
30 2 0.03
31 4 0.06
32 3 0.04
33 38 0.57
34 1 0.01
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.21
Consensus pattern (32 bp):
CAAATTTCAACAAATATATAACCAAAACCAAA
Found at i:12109399 original size:63 final size:63
Alignment explanation
Indices: 12109320--12109441 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
12109310 AAATTTACTG
** *
12109320 ATGGAATTTCTCTTGGTAATGTGTTATTTTTTTTTT-CAAATTCTTTTACCGATAGATTTAGCA
1 ATGGAATTTCTCTTGGTAATGT-CAATTTTTTTTTTGCAAATTCTTTTACCAATAGATTTAGCA
* * * *
12109383 ATGGAATTTTTGTTGGTAATGTCAATTTTTTTTTTGTAAATTTTTTTACCAATAGATTT
1 ATGGAATTTCTCTTGGTAATGTCAATTTTTTTTTTGCAAATTCTTTTACCAATAGATTT
12109442 TTTTGTTGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 11 0.22
63 40 0.78
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (63 bp):
ATGGAATTTCTCTTGGTAATGTCAATTTTTTTTTTGCAAATTCTTTTACCAATAGATTTAGCA
Found at i:12109839 original size:2 final size:2
Alignment explanation
Indices: 12109834--12109867 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12109824 TGTGTGTGTG
12109834 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
12109868 AACAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12110413 original size:22 final size:22
Alignment explanation
Indices: 12110365--12110417 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
12110355 CTAAAAAAAT
* *
12110365 AAATAAAATAAATATTAGAATT
1 AAATATAATAAATATTAGAATA
12110387 AAATATAATAAATA-TAGAATA
1 AAATATAATAAATATTAGAATA
12110408 ACAATATAAT
1 A-AATATAAT
12110418 TTTAATCCTN
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATATAATAAATATTAGAATA
Found at i:12116848 original size:19 final size:20
Alignment explanation
Indices: 12116826--12116867 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
12116816 ATTTTTCCTT
12116826 AAAAATTAT-ATTTTTTTAA
1 AAAAATTATCATTTTTTTAA
*
12116845 AAAAATTATCCCTTTTTTTAA
1 AAAAATTAT-CATTTTTTTAA
12116866 AA
1 AA
12116868 GACATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAATTATCATTTTTTTAA
Found at i:12117985 original size:16 final size:17
Alignment explanation
Indices: 12117924--12117985 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
12117914 AAAGATAAAG
12117924 AATAGGATAAATAAAAT
1 AATAGGATAAATAAAAT
*
12117941 AA-AAGATAAATAAAGAT
1 AATAGGATAAATAAA-AT
*
12117958 AAATAGG-CAAAT-AAAT
1 -AATAGGATAAATAAAAT
12117974 AATAGGATAAAT
1 AATAGGATAAAT
12117986 TAAGGTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.16
16 17 0.46
17 6 0.16
18 6 0.16
19 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.13, T:0.21
Consensus pattern (17 bp):
AATAGGATAAATAAAAT
Found at i:12120562 original size:30 final size:31
Alignment explanation
Indices: 12120528--12120585 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
12120518 AACTTGTTGA
*
12120528 AAAATT-AAACTTTGCCTAAAAACTCATTGG
1 AAAATTCAAACTTTGCCGAAAAACTCATTGG
* *
12120558 AAAATTCAACCTTTGTCGAAAAACTCAT
1 AAAATTCAAACTTTGCCGAAAAACTCAT
12120586 CAAAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (31 bp):
AAAATTCAAACTTTGCCGAAAAACTCATTGG
Found at i:12121146 original size:16 final size:17
Alignment explanation
Indices: 12121127--12121159 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12121117 TAAAGAATAG
12121127 GATAAATAAA-ATAAAT
1 GATAAATAAAGATAAAT
12121143 GATAAATAAAGATAAAT
1 GATAAATAAAGATAAAT
12121160 AGAGAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
GATAAATAAAGATAAAT
Found at i:12121158 original size:10 final size:10
Alignment explanation
Indices: 12121135--12121192 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 10
12121125 AGGATAAATA
12121135 AAATAAATGAT
1 AAATAAA-GAT
12121146 AAATAAAGAT
1 AAATAAAGAT
12121156 AAATAGAGAGAT
1 AAATA-A-AGAT
12121168 AAATAATAGGAT
1 AAATAA-A-GAT
*
12121180 AAATTAAGAT
1 AAATAAAGAT
12121190 AAA
1 AAA
12121193 AAAACAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 14 0.33
11 11 0.26
12 17 0.40
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (10 bp):
AAATAAAGAT
Found at i:12123385 original size:12 final size:12
Alignment explanation
Indices: 12123370--12123421 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12123360 GTTCTTGTTT
12123370 TTCTTGTCCTTA
1 TTCTTGTCCTTA
* * *
12123382 TTCTTATTCTTG
1 TTCTTGTCCTTA
*
12123394 TTCTTGTTCTTA
1 TTCTTGTCCTTA
* *
12123406 TTATTTTCCTTA
1 TTCTTGTCCTTA
12123418 TTCT
1 TTCT
12123422 CATTCTCCTT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (12 bp):
TTCTTGTCCTTA
Found at i:12123393 original size:18 final size:18
Alignment explanation
Indices: 12123370--12123427 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
12123360 GTTCTTGTTT
12123370 TTCTTGTCCTTATTCTTA
1 TTCTTGTCCTTATTCTTA
* *
12123388 TTCTTGTTCTTGTTCTTA
1 TTCTTGTCCTTATTCTTA
* * *
12123406 TTATTTTCCTTATTCTCA
1 TTCTTGTCCTTATTCTTA
12123424 TTCT
1 TTCT
12123428 CCTTTTTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.10, C:0.21, G:0.05, T:0.64
Consensus pattern (18 bp):
TTCTTGTCCTTATTCTTA
Found at i:12123447 original size:8 final size:8
Alignment explanation
Indices: 12123430--12123471 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
12123420 CTCATTCTCC
12123430 TTTTTT-T
1 TTTTTTCT
12123437 TTTTTTCT
1 TTTTTTCT
12123445 TTTTTTCT
1 TTTTTTCT
*
12123453 TTTTATTAT
1 TTTT-TTCT
12123462 TTTTTTCT
1 TTTTTTCT
12123470 TT
1 TT
12123472 AATTGAAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 6 0.19
8 18 0.58
9 7 0.23
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTCT
Found at i:12123448 original size:14 final size:14
Alignment explanation
Indices: 12123429--12123467 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12123419 TCTCATTCTC
12123429 CTTTTTTTTTTTTT
1 CTTTTTTTTTTTTT
*
12123443 CTTTTTTTCTTTTT
1 CTTTTTTTTTTTTT
*
12123457 ATTATTTTTTT
1 CTT-TTTTTTT
12123468 CTTTAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (14 bp):
CTTTTTTTTTTTTT
Found at i:12123450 original size:17 final size:17
Alignment explanation
Indices: 12123430--12123471 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
12123420 CTCATTCTCC
*
12123430 TTTTTT-TTTTT-TTCT
1 TTTTTTCTTTTTATTAT
12123445 TTTTTTCTTTTTATTAT
1 TTTTTTCTTTTTATTAT
12123462 TTTTTTCTTT
1 TTTTTTCTTT
12123472 AATTGAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 6 0.25
16 5 0.21
17 13 0.54
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTCTTTTTATTAT
Found at i:12126712 original size:3 final size:3
Alignment explanation
Indices: 12126704--12126756 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
12126694 CATAATCAAG
12126704 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12126751 TAA TAA
1 TAA TAA
12126757 AAGTATAGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12127602 original size:29 final size:29
Alignment explanation
Indices: 12127559--12127617 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
12127549 TGCATACTTA
12127559 ATAAGTTTCAGCTAAGATTCAATGCCAAG
1 ATAAGTTTCAGCTAAGATTCAATGCCAAG
*
12127588 ATAAGTTTC-GACTAAGATTCAATTCCAAG
1 ATAAGTTTCAG-CTAAGATTCAATGCCAAG
12127617 A
1 A
12127618 CCATGTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (29 bp):
ATAAGTTTCAGCTAAGATTCAATGCCAAG
Found at i:12129923 original size:49 final size:49
Alignment explanation
Indices: 12129866--12129962 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
12129856 ATGTTTCAGA
*
12129866 ATACCACACCTTAGCTACATGACAACATTTATAAGCATCAGATTTATAT
1 ATACCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATAT
* * *
12129915 ATACCACACTTTAGCTGCATGACAACATTTATAAACGTCAGATTTATA
1 ATACCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATA
12129963 CTAGATCCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (49 bp):
ATACCACACCTTAGCTACATGACAACATTTATAAACATCAGATTTATAT
Found at i:12134746 original size:57 final size:58
Alignment explanation
Indices: 12134672--12135078 Score: 155
Period size: 57 Copynumber: 6.6 Consensus size: 58
12134662 AAAATTTTTC
* **
12134672 AAAAATATTTTACGAAAAAGTCAAAAGTATCAATTTTCTTTGAAAAT-CCAA-TTAAAA
1 AAAAATATTTGA-GAAAAAGTCAAAAGTATCAATTTTCTTTGAAAATAAAAATTTAAAA
* ** * *
12134729 AAAAATACTTTGAGAAAAAATTGAAAGTATTAATTTT-TCATGAAAATAAAAATTTCAAAA
1 AAAAATA-TTTGAGAAAAAGTCAAAAGTATCAATTTTCT-TTGAAAATAAAAATTT-AAAA
* * * * * **
12134789 AATATATTTTTGAGGAAAAGTTGAAAA-TATCAATTTTCCTTGAAAATATTAATTTTTCTTGAAA
1 AA-AAATATTTGAGAAAAAG-TCAAAAGTATCAATTTTCTTTGAAAATA--AA--AAT-TT-AAA
12134853 A
58 A
* * **
12134854 TAAAAATTTTAAAAACATTTTAAGGAAAAGTTGAAAGTATCAATTTT-TCTTGAAAATAAAAATT
1 -AAAAA---T------A-TTTGAGAAAAAGTCAAAAGTATCAATTTTCT-TTGAAAATAAAAATT
**
12134918 TCCAA
54 TAAAA
* * * ** * *
12134923 AAACAT-TTTAAGGAAAAGTTGAAAGTATCAATTTT-TCTTAAAAATAAAATTTTCAAAA
1 AAAAATATTTGAGAAAAAGTCAAAAGTATCAATTTTCT-TTGAAAATAAAAATTT-AAAA
* * ** *
12134981 AAGATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-TCTTGAAAATAAAAATTAAAAA
1 AA-AAATATTTGAGAAAAAGTCAAAAGTATCAATTTTCT-TTGAAAATAAAAATTTAAAA
* **
12135040 AAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1 AAAAA-TA--TTTGAGAAAAAGTCAAAAGTATCAATTTT
12135079 TCTTATTTAA
Statistics
Matches: 274, Mismatches: 44, Indels: 60
0.72 0.12 0.16
Matches are distributed among these distances:
56 1 0.00
57 79 0.29
58 12 0.04
59 12 0.04
60 75 0.27
61 35 0.13
62 2 0.01
64 1 0.00
65 9 0.03
66 2 0.01
68 5 0.02
69 2 0.01
70 2 0.01
71 1 0.00
73 2 0.01
74 4 0.01
75 30 0.11
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (58 bp):
AAAAATATTTGAGAAAAAGTCAAAAGTATCAATTTTCTTTGAAAATAAAAATTTAAAA
Found at i:12134824 original size:60 final size:60
Alignment explanation
Indices: 12134695--12135082 Score: 340
Period size: 60 Copynumber: 6.3 Consensus size: 60
12134685 GAAAAAGTCA
** * * * * *
12134695 AAAGTATCAA-TTTTCTTTGAAAAT-CCAA-TTAAAAAAAAATA-CTTTGAGAAAAAATTG
1 AAAGTATCAATTTTTC-TTGAAAATAAAAATTTCAAAAAATATATTTTTGAGGAAAAGTTG
* *
12134752 AAAGTATTAATTTTTCATGAAAATAAAAATTTCAAAAAATATATTTTTGAGGAAAAGTTG
1 AAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAATATATTTTTGAGGAAAAGTTG
* * ** * * *
12134812 AAAATATCAATTTTCCTTGAAAATATTAATTTTTCTTGAAAATAAAAATTTTAAAAACATTTTAA
1 AAAGTATCAATTTTTCTTGAAAATA--AAAATTTC------A-AAAAA---T--ATA-TTTTTGA
12134877 GGAAAAGTTG
51 GGAAAAGTTG
* * *
12134887 AAAGTATCAATTTTTCTTGAAAATAAAAATTTC-CAAAA-ACA-TTTTAAGGAAAAGTTG
1 AAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAATATATTTTTGAGGAAAAGTTG
* * * *
12134944 AAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAGATATTTTTGAGAAAAAGTTG
1 AAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAATATATTTTTGAGGAAAAGTTG
** *
12135004 AAAGTATCAATTTTTCTTGAAAATAAAAATTAAAAAAAAAAGTATTTTTGAGGAAAAGTTG
1 AAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAATA-TATTTTTGAGGAAAAGTTG
12135065 AAAGTATCAATTTTTCTT
1 AAAGTATCAATTTTTCTT
12135083 ATTTAAAGGC
Statistics
Matches: 272, Mismatches: 36, Indels: 42
0.78 0.10 0.12
Matches are distributed among these distances:
57 63 0.23
58 11 0.04
59 15 0.06
60 84 0.31
61 36 0.13
62 6 0.02
65 4 0.01
68 1 0.00
69 5 0.02
72 1 0.00
73 6 0.02
74 2 0.01
75 38 0.14
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (60 bp):
AAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAATATATTTTTGAGGAAAAGTTG
Found at i:12134833 original size:19 final size:19
Alignment explanation
Indices: 12134809--12134855 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
12134799 TGAGGAAAAG
12134809 TTGAAAATATCAATTTTCC
1 TTGAAAATATCAATTTTCC
* *
12134828 TTGAAAATATTAATTTTTC
1 TTGAAAATATCAATTTTCC
12134847 TTGAAAATA
1 TTGAAAATA
12134856 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (19 bp):
TTGAAAATATCAATTTTCC
Found at i:12134840 original size:79 final size:75
Alignment explanation
Indices: 12134749--12134911 Score: 227
Period size: 75 Copynumber: 2.1 Consensus size: 75
12134739 TGAGAAAAAA
* * *
12134749 TTGAAAGTATTAATTTTTCATGAAAATAAAAATTTCAAAAAATATATTTTTGAGGAAAAGTTGAA
1 TTGAAAATATTAATTTTTCATGAAAATAAAAATTT--AAAAA-ACA-TTTTAAGGAAAAGTTGAA
12134814 AATATCAATTTTCC
62 AATATCAATTTTCC
* * *
12134828 TTGAAAATATTAATTTTTCTTGAAAATAAAAATTTTAAAAACATTTTAAGGAAAAGTTGAAAGTA
1 TTGAAAATATTAATTTTTCATGAAAATAAAAATTTAAAAAACATTTTAAGGAAAAGTTGAAAATA
*
12134893 TCAATTTTTC
66 TCAATTTTCC
12134903 TTGAAAATA
1 TTGAAAATA
12134912 AAAATTTCCA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
75 38 0.49
76 2 0.03
77 4 0.05
79 33 0.43
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (75 bp):
TTGAAAATATTAATTTTTCATGAAAATAAAAATTTAAAAAACATTTTAAGGAAAAGTTGAAAATA
TCAATTTTCC
Found at i:12134861 original size:19 final size:19
Alignment explanation
Indices: 12134809--12134863 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
12134799 TGAGGAAAAG
*
12134809 TTGAAAATATCAATTTTCC
1 TTGAAAATATAAATTTTCC
* *
12134828 TTGAAAATATTAATTTTTC
1 TTGAAAATATAAATTTTCC
*
12134847 TTGAAAATAAAAATTTT
1 TTGAAAATATAAATTTT
12134864 AAAAACATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (19 bp):
TTGAAAATATAAATTTTCC
Found at i:12135050 original size:61 final size:58
Alignment explanation
Indices: 12134828--12135082 Score: 309
Period size: 57 Copynumber: 4.4 Consensus size: 58
12134818 TCAATTTTCC
* * ** * *
12134828 TTGAAAATATTAATTTTTCTTGAAAATAAAAATT-TTAAAAACA-TTTTAAGGAAAAG
1 TTGAAAGTATCAATTTTTCTTGAAAATAAAAATTAAAAAAAATATTTTTGAGGAAAAG
*** * *
12134884 TTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCCAAAAACA-TTTTAAGGAAAAG
1 TTGAAAGTATCAATTTTTCTTGAAAATAAAAATTAAAAAAAATATTTTTGAGGAAAAG
* * * *
12134941 TTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAGATATTTTTGAGAAAAAG
1 TTGAAAGTATCAATTTTTCTTGAAAATAAAA-ATT-AAAAAAAATATTTTTGAGGAAAAG
12135001 TTGAAAGTATCAATTTTTCTTGAAAATAAAAATTAAAAAAAAAAGTATTTTTGAGGAAAAG
1 TTGAAAGTATCAATTTTTCTTGAAAATAAAAATT--AAAAAAAA-TATTTTTGAGGAAAAG
12135062 TTGAAAGTATCAATTTTTCTT
1 TTGAAAGTATCAATTTTTCTT
12135083 ATTTAAAGGC
Statistics
Matches: 175, Mismatches: 18, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
56 32 0.18
57 50 0.29
58 2 0.01
59 7 0.04
60 48 0.27
61 36 0.21
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.36
Consensus pattern (58 bp):
TTGAAAGTATCAATTTTTCTTGAAAATAAAAATTAAAAAAAATATTTTTGAGGAAAAG
Found at i:12137508 original size:2 final size:2
Alignment explanation
Indices: 12137501--12137527 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12137491 CTTCTAATAT
12137501 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
12137528 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.