Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 126 of 133
Found at i:24389187 original size:60 final size:59
Alignment explanation
Indices: 24389116--24389232 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 59
24389106 GTTGCTTGGT
* *
24389116 GTGGATCGAACGATTTATGGCTGACTCTGATACCACTTGTCAC-GAGTTGAGACTTAAGC
1 GTGGATCGAACGATTTAGGGCTGACTCTGATACCACTTGTCACAG-GTCGAGACTTAAGC
* * *
24389175 GTGGATTCGAACGGTTTAGGGCTGACTTTGATACTACTTGTCACAGGTCGAGACTTAA
1 GTGGA-TCGAACGATTTAGGGCTGACTCTGATACCACTTGTCACAGGTCGAGACTTAA
24389233 ACTCTGAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 5 0.10
60 45 0.88
61 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (59 bp):
GTGGATCGAACGATTTAGGGCTGACTCTGATACCACTTGTCACAGGTCGAGACTTAAGC
Found at i:24390560 original size:39 final size:38
Alignment explanation
Indices: 24390506--24390632 Score: 191
Period size: 39 Copynumber: 3.3 Consensus size: 38
24390496 TTTCTGTTAC
24390506 ATCATGTTCCGAGCCTTCTGATCTTCGTCCTTGTATTTT
1 ATCATGTTCCGAGCCTTCTGA-CTTCGTCCTTGTATTTT
*
24390545 ATCATGTTCCGAGCCTTCTGCCCTTCGTCCTTGTATTTT
1 ATCATGTTCCGAGCCTTCTG-ACTTCGTCCTTGTATTTT
* *
24390584 ATCATGTTCCGAGCCTTCTGACCTCTGTCTTTGTATTTT
1 ATCATGTTCCGAGCCTTCTGACTTC-GTCCTTGTATTTT
*
24390623 ATCGTGTTCC
1 ATCATGTTCC
24390633 ATAGGTCGAA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
38 3 0.04
39 78 0.96
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.45
Consensus pattern (38 bp):
ATCATGTTCCGAGCCTTCTGACTTCGTCCTTGTATTTT
Found at i:24395550 original size:27 final size:27
Alignment explanation
Indices: 24395512--24395566 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
24395502 TGAAACCCTT
*
24395512 AACAGATTTTCCCGAGTCGACAGTATC
1 AACAGATTTTCCCGAGTCAACAGTATC
* *
24395539 AACAGATTTTCCTGAGTCAACCGTATC
1 AACAGATTTTCCCGAGTCAACAGTATC
24395566 A
1 A
24395567 GTGGACATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (27 bp):
AACAGATTTTCCCGAGTCAACAGTATC
Found at i:24396905 original size:26 final size:26
Alignment explanation
Indices: 24396869--24396921 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
24396859 GAAACCAGTA
* *
24396869 ATATAGATTATAACCAGTTACAAGCC
1 ATATAAATTATAACCAGTTAAAAGCC
24396895 ATATAAATTATAACCAGTTAAAAGCC
1 ATATAAATTATAACCAGTTAAAAGCC
24396921 A
1 A
24396922 ATAGCTTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (26 bp):
ATATAAATTATAACCAGTTAAAAGCC
Found at i:24398615 original size:6 final size:6
Alignment explanation
Indices: 24398604--24398634 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
24398594 TCACTAGAAA
*
24398604 AAAGCC AAAGCC AAAGCC AAAGCC AGAGCC A
1 AAAGCC AAAGCC AAAGCC AAAGCC AAAGCC A
24398635 GAGAAAGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGCC
Found at i:24401141 original size:24 final size:24
Alignment explanation
Indices: 24401083--24401141 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
24401073 TTAGCAATAA
* *
24401083 AAATTTTATAAATTTGATTTCAAT
1 AAATTTTTTAAATTTGATTTAAAT
24401107 ATAATTTTTTAAATTTG-TTTAAAT
1 A-AATTTTTTAAATTTGATTTAAAT
24401131 AAATTTATTTA
1 AAATTT-TTTA
24401142 TGTTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 12 0.39
25 14 0.45
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
AAATTTTTTAAATTTGATTTAAAT
Found at i:24405452 original size:20 final size:20
Alignment explanation
Indices: 24405415--24405452 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
24405405 CAATGAAAAT
*
24405415 ATCAATAAATGATTTTTTCA
1 ATCAATAAATGATGTTTTCA
24405435 ATCAAT-AATGATCGTTTT
1 ATCAATAAATGAT-GTTTT
24405453 TTTTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
ATCAATAAATGATGTTTTCA
Found at i:24406524 original size:19 final size:18
Alignment explanation
Indices: 24406500--24406545 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
24406490 ATATGATTTT
24406500 ATTAATTTTTATAAAATAA
1 ATTAATTTTTATAAAA-AA
*
24406519 ATTAATTATTTATATAAAA
1 ATTAATT-TTTATAAAAAA
*
24406538 ATTTATTT
1 ATTAATTT
24406546 AAATTATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 15 0.62
20 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTAATTTTTATAAAAAA
Found at i:24414896 original size:14 final size:15
Alignment explanation
Indices: 24414877--24414905 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24414867 GGCGAAATTA
24414877 ATTTAATA-AATTTT
1 ATTTAATATAATTTT
24414891 ATTTAATATAATTTT
1 ATTTAATATAATTTT
24414906 TATAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTAATATAATTTT
Found at i:24415009 original size:39 final size:39
Alignment explanation
Indices: 24414936--24415014 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 39
24414926 ACAAAATATA
24414936 TTTTAATTAAATATAAATATAATGTTTTATTTAAT-TAAT
1 TTTTAATTAAATATAAATATAA-GTTTTATTTAATATAAT
24414975 TTTTAATTAAATTATTAAATAATAA-TTTTA-TTAATATAAT
1 TTTTAATTAAA-TA-TAAAT-ATAAGTTTTATTTAATATAAT
24415015 ATATAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
39 16 0.44
40 11 0.31
41 5 0.14
42 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (39 bp):
TTTTAATTAAATATAAATATAAGTTTTATTTAATATAAT
Found at i:24417283 original size:15 final size:15
Alignment explanation
Indices: 24417256--24417288 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
24417246 CCTTTTAAAT
24417256 ATAAGTAAGATTTAA
1 ATAAGTAAGATTTAA
24417271 ATAAGATAA-ATTTAA
1 ATAAG-TAAGATTTAA
24417286 ATA
1 ATA
24417289 CAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (15 bp):
ATAAGTAAGATTTAA
Found at i:24417344 original size:62 final size:61
Alignment explanation
Indices: 24417215--24417345 Score: 144
Period size: 61 Copynumber: 2.1 Consensus size: 61
24417205 ATATTTCAAT
* *
24417215 GAAAGTTTAAATACAAATAAAAAATAAGACTCCTTTTAAATATAAGTAAGATTTAAATAAGA
1 GAAA-TTTAAATACAAATAAAAAATAAGACTCCTTTTAAATATAAGTAAAATATAAATAAGA
* *
24417277 TAAATTTAAATACAAATAAAAAAATAAGTCT-CTATTT-AATATAA-TAAAAATATAAA-AAGTC
1 GAAATTTAAATACAAAT-AAAAAATAAGACTCCT-TTTAAATATAAGT-AAAATATAAATAAG--
24417338 A
61 A
24417339 GAAATTT
1 GAAATTT
24417346 TTTTAGTATT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
60 4 0.07
61 30 0.51
62 25 0.42
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (61 bp):
GAAATTTAAATACAAATAAAAAATAAGACTCCTTTTAAATATAAGTAAAATATAAATAAGA
Found at i:24422245 original size:29 final size:27
Alignment explanation
Indices: 24422185--24422252 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 27
24422175 TATTATATTT
24422185 AAAACAAA-TTAAATAAAAATATCTAAC
1 AAAA-AAATTTAAATAAAAATATCTAAC
*
24422212 AAAAATATTTAAATACCAAAATAT-TAAGC
1 AAAAAAATTTAAATA--AAAATATCTAA-C
*
24422241 TAAAAAATTTAA
1 AAAAAAATTTAA
24422253 TAACTTCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.06
27 11 0.32
28 3 0.09
29 18 0.53
ACGTcount: A:0.63, C:0.09, G:0.01, T:0.26
Consensus pattern (27 bp):
AAAAAAATTTAAATAAAAATATCTAAC
Found at i:24423819 original size:17 final size:17
Alignment explanation
Indices: 24423782--24423819 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
24423772 GGATAAACTC
*
24423782 AATTTTTAAAAATTTAA
1 AATTTTTAAAAATTAAA
24423799 AATTTTT-AAAATTAAA
1 AATTTTTAAAAATTAAA
24423815 TAATT
1 -AATT
24423820 ATCAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTTAAAAATTAAA
Found at i:24425998 original size:21 final size:23
Alignment explanation
Indices: 24425957--24426000 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
24425947 TTAATTTTTT
*
24425957 ATTTTATATATTATTTTAATAAA
1 ATTTTATATATTATTTAAATAAA
24425980 ATTTTA-ATA-TATTTAAATAAA
1 ATTTTATATATTATTTAAATAAA
24426001 TTTCTATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 3 0.15
23 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTATATATTATTTAAATAAA
Found at i:24427682 original size:33 final size:33
Alignment explanation
Indices: 24427621--24427683 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
24427611 TATAAATTTT
* *
24427621 TAAAATTTAATTTAAATTTAAATTAATTTTTCA
1 TAAAATTTAATTCAAACTTAAATTAATTTTTCA
* *
24427654 TAAAATTTAATTCGAACTT-AATTAAATTTT
1 TAAAATTTAATTCAAACTTAAATTAATTTTT
24427684 ACTCTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (33 bp):
TAAAATTTAATTCAAACTTAAATTAATTTTTCA
Found at i:24430689 original size:4 final size:4
Alignment explanation
Indices: 24430674--24430704 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
24430664 GAGTAGTTAC
*
24430674 TGAG TAAG TGAG TGAG TGAG TGAG TGAG TGA
1 TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGA
24430705 CTCGGTGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (4 bp):
TGAG
Found at i:24437458 original size:14 final size:15
Alignment explanation
Indices: 24437426--24437459 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
24437416 AATTCGTTTA
24437426 TATTTGTTTAAAGTT
1 TATTTGTTTAAAGTT
24437441 TATTTGTTTAAA-TT
1 TATTTGTTTAAAGTT
24437455 TATTT
1 TATTT
24437460 TATTATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (15 bp):
TATTTGTTTAAAGTT
Found at i:24437517 original size:26 final size:27
Alignment explanation
Indices: 24437468--24437518 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
24437458 TTTATTATGA
*
24437468 TTTATTTATTGTTCATAAATATATTTG
1 TTTATTTATTGTTCATAAACATATTTG
*
24437495 TTTATTTA-TGTTCGTAAACATATT
1 TTTATTTATTGTTCATAAACATATT
24437519 CATTTAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (27 bp):
TTTATTTATTGTTCATAAACATATTTG
Found at i:24437524 original size:26 final size:27
Alignment explanation
Indices: 24437467--24437524 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
24437457 TTTTATTATG
* *
24437467 ATTTATTTATTGTTCATAAATATATTT
1 ATTTATTTATTGTTCATAAACATATTC
* *
24437494 GTTTATTTA-TGTTCGTAAACATATTC
1 ATTTATTTATTGTTCATAAACATATTC
24437520 ATTTA
1 ATTTA
24437525 ATGTTTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (27 bp):
ATTTATTTATTGTTCATAAACATATTC
Found at i:24438095 original size:18 final size:19
Alignment explanation
Indices: 24438067--24438102 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
24438057 CTAATATAGT
24438067 TATATAATATATATTAAAA
1 TATATAATATATATTAAAA
24438086 TATA-AATATATATTAAA
1 TATATAATATATATTAAA
24438103 TACTTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATAATATATATTAAAA
Found at i:24454072 original size:2 final size:2
Alignment explanation
Indices: 24454065--24454089 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24454055 TGCTTACTAT
24454065 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
24454090 TTTATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24455198 original size:24 final size:24
Alignment explanation
Indices: 24455158--24455206 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
24455148 AAACAAATTT
* *
24455158 ATTTTATATCATTTTAATTTTTTA
1 ATTTTATATCATATTAATATTTTA
24455182 ATTTTATAT-ATAATTAATATTTTA
1 ATTTTATATCAT-ATTAATATTTTA
24455206 A
1 A
24455207 GACATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTTATATCATATTAATATTTTA
Found at i:24457392 original size:13 final size:13
Alignment explanation
Indices: 24457374--24457398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24457364 TTTTTTCTTA
24457374 TTTATATTATTAT
1 TTTATATTATTAT
24457387 TTTATATTATTA
1 TTTATATTATTA
24457399 ATTAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATATTATTAT
Found at i:24457745 original size:20 final size:21
Alignment explanation
Indices: 24457712--24457764 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
24457702 TAATATGCAT
* *
24457712 AAATATTAAGAATAATA-ATTA
1 AAATATAAAAAATAATATA-TA
24457733 AAATA-AAAAAATAATATATA
1 AAATATAAAAAATAATATATA
24457753 AAATATAAAAAA
1 AAATATAAAAAA
24457765 AATTCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAATATAAAAAATAATATATA
Found at i:24457763 original size:22 final size:20
Alignment explanation
Indices: 24457722--24457765 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
24457712 AAATATTAAG
*
24457722 AATAATAATTAAAATAAAAA
1 AATAATAATAAAAATAAAAA
24457742 AATAATATATAAAATATAAAAA
1 AATAATA-ATAAAA-ATAAAAA
24457764 AA
1 AA
24457766 ATTCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAATAATAAAAATAAAAA
Found at i:24457886 original size:30 final size:29
Alignment explanation
Indices: 24457840--24457904 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
24457830 GATGATTCAA
* *
24457840 CGGTTCGATCGCGTTCAATGGTTCAATTT
1 CGGTTCGATCGCGTTCAACGATTCAATTT
* * *
24457869 TGGTTCGGATCGGGTTCAGCGATTCAATTT
1 CGGTTC-GATCGCGTTCAACGATTCAATTT
24457899 CGGTTC
1 CGGTTC
24457905 AGTCAGACCG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37
Consensus pattern (29 bp):
CGGTTCGATCGCGTTCAACGATTCAATTT
Found at i:24458807 original size:18 final size:19
Alignment explanation
Indices: 24458768--24458817 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
24458758 TATTTTTTGT
24458768 ATTTTGTA-TTTT-TTTAC
1 ATTTTGTATTTTTGTTTAC
24458785 TATTTTGTATTTTTGTTTA-
1 -ATTTTGTATTTTTGTTTAC
*
24458804 ATTTT-TATTATTGT
1 ATTTTGTATTTTTGT
24458818 ATTTAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.28
18 13 0.45
19 4 0.14
20 4 0.14
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.72
Consensus pattern (19 bp):
ATTTTGTATTTTTGTTTAC
Found at i:24459548 original size:23 final size:24
Alignment explanation
Indices: 24459502--24459554 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
24459492 ATATGTGTAA
24459502 AAAAAAGTGAAAAAAAAAAGAAAG
1 AAAAAAGTGAAAAAAAAAAGAAAG
* *
24459526 AGAAAAG-GAAAAAGGAAAA-AAAG
1 AAAAAAGTGAAAAA-AAAAAGAAAG
24459549 AAAAAA
1 AAAAAA
24459555 AAAACTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (24 bp):
AAAAAAGTGAAAAAAAAAAGAAAG
Found at i:24460681 original size:44 final size:45
Alignment explanation
Indices: 24460548--24460803 Score: 200
Period size: 45 Copynumber: 5.7 Consensus size: 45
24460538 AAGCCTTTCA
* *
24460548 AATGAGAATTTTTGAAATTTTAGATGT-AAATCTTTAAAGTTTTTTTT
1 AATGAGAATTTTTGAAATTTTGGATGTGAAATC-TTAAAG--TTTTTG
* * * *
24460595 AAT-ATGAAATTTTGAAATTTTGGTTGTGAAATATTAATGTTTTTG
1 AATGA-GAATTTTTGAAATTTTGGATGTGAAATCTTAAAGTTTTTG
* * * *
24460640 AATGTGAATTTTTAAAATTTTCGATGTG-AATCTCT-AAGTTTTTTT
1 AATGAGAATTTTTGAAATTTTGGATGTGAAATCT-TAAAG-TTTTTG
* * * * *
24460685 AAGGAAAATCTTT-AACTTTTGGATGTGAAATCTTAAAATTTTTTG
1 AATGAGAATTTTTGAAATTTTGGATGTGAAATCTT-AAAGTTTTTG
* * * * *
24460730 GATAAGAATATTTGAAATTTTGGTTGTGAAATATTAAAGTTTTT-
1 AATGAGAATTTTTGAAATTTTGGATGTGAAATCTTAAAGTTTTTG
* * *
24460774 AATGTGAATTTTTAAAATTTTGAATGTGAA
1 AATGAGAATTTTTGAAATTTTGGATGTGAA
24460804 TCCCTAAGTT
Statistics
Matches: 162, Mismatches: 38, Indels: 21
0.73 0.17 0.10
Matches are distributed among these distances:
44 42 0.26
45 68 0.42
46 21 0.13
47 27 0.17
48 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (45 bp):
AATGAGAATTTTTGAAATTTTGGATGTGAAATCTTAAAGTTTTTG
Found at i:24460726 original size:22 final size:22
Alignment explanation
Indices: 24460599--24460803 Score: 83
Period size: 22 Copynumber: 9.2 Consensus size: 22
24460589 TTTTTTAATA
* * *
24460599 TGAAATTTTGAAATTTTGGTTG
1 TGAAATCTTAAAATTTTGGATG
* ** *
24460621 TGAAATATTAATGTTTTTGAATG
1 TGAAATCTTAA-AATTTTGGATG
* * *
24460644 TGAATTTTTAAAATTTTCGATG
1 TGAAATCTTAAAATTTTGGATG
** ** *
24460666 TG-AATCTCTAAGTTTTTTTAAG
1 TGAAATCT-TAAAATTTTGGATG
* *
24460688 -GAAAATCTTTAACTTTTGGATG
1 TG-AAATCTTAAAATTTTGGATG
*
24460710 TGAAATCTTAAAATTTTTTGGATA
1 TGAAATCTTAAAA--TTTTGGATG
* * *
24460734 AGAATAT-TTGAAATTTTGGTTG
1 TGAA-ATCTTAAAATTTTGGATG
* * **
24460756 TGAAATATTAAAGTTTTTAATG
1 TGAAATCTTAAAATTTTGGATG
* * *
24460778 TGAATTTTTAAAATTTTGAATG
1 TGAAATCTTAAAATTTTGGATG
24460800 TGAA
1 TGAA
24460804 TCCCTAAGTT
Statistics
Matches: 132, Mismatches: 42, Indels: 18
0.69 0.22 0.09
Matches are distributed among these distances:
21 6 0.05
22 86 0.65
23 22 0.17
24 16 0.12
25 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.47
Consensus pattern (22 bp):
TGAAATCTTAAAATTTTGGATG
Found at i:24461350 original size:16 final size:16
Alignment explanation
Indices: 24461329--24461403 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
24461319 ATGTGAAACT
24461329 TGAAATCTTACGAATC
1 TGAAATCTTACGAATC
* *
24461345 TGAAATTTTACGAATT
1 TGAAATCTTACGAATC
* * *
24461361 TGGAATCTCTGCGAAAC
1 TGAAATCT-TACGAATC
*
24461378 TTGAAATCTTACGAATT
1 -TGAAATCTTACGAATC
24461395 TGAAATCTT
1 TGAAATCTT
24461404 TGTGAATTTA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
16 29 0.63
17 10 0.22
18 7 0.15
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (16 bp):
TGAAATCTTACGAATC
Found at i:24462028 original size:14 final size:15
Alignment explanation
Indices: 24462009--24462056 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
24461999 TTAAAAAATT
*
24462009 AAAAGTTAATA-TAA
1 AAAAGTTAAAAGTAA
24462023 AAAAGTTAAAAGTAA
1 AAAAGTTAAAAGTAA
** *
24462038 AAAAGAAAAAAATAA
1 AAAAGTTAAAAGTAA
24462053 AAAA
1 AAAA
24462057 AAAGGAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (15 bp):
AAAAGTTAAAAGTAA
Found at i:24463859 original size:58 final size:56
Alignment explanation
Indices: 24463740--24463861 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 56
24463730 GTTGCACAAG
* *
24463740 AAAATTGATATTTTCAACTTTTCCTTAAAATATTTTTTTTGTATTTTTAATTTTGAGA
1 AAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGTATTTTTAATTTT--GA
24463798 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGATGATTTTT-ATTTT-A
1 AAAATTGATACTTTCAACTTTTCCT-AAAAATA-TTTTTTTTG-T-ATTTTTAATTTTGA
24463856 AAAATT
1 AAAATT
24463862 TTATTTTCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
58 31 0.53
59 6 0.10
60 9 0.16
61 6 0.10
62 6 0.10
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (56 bp):
AAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGTATTTTTAATTTTGA
Found at i:24463941 original size:26 final size:29
Alignment explanation
Indices: 24463912--24463965 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
24463902 AAATGTTTTT
24463912 ATTGATAATT-T-TTATTTT-TCAAAAAA
1 ATTGATAATTCTATTATTTTCTCAAAAAA
*
24463938 ATTGATAATTCTATTTTTTTCTCAAAAA
1 ATTGATAATTCTATTATTTTCTCAAAAA
24463966 GCCTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 1 0.04
28 6 0.25
29 7 0.29
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (29 bp):
ATTGATAATTCTATTATTTTCTCAAAAAA
Found at i:24464115 original size:121 final size:122
Alignment explanation
Indices: 24463851--24464156 Score: 358
Period size: 121 Copynumber: 2.5 Consensus size: 122
24463841 ATGATTTTTA
* *
24463851 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCT-TAAAAAT-GTTTTTAT
1 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAAATATTTTTTAT
* * * ** **
24463914 TGATAATTTTTATTTTTCAAAAAAATTGATAATTCTATTTTTTTCTCAAAAAGCCTT
66 TGATAAATTTTAGTTGTCAAAAAAATTGATAATTCTATACTTTTCTCAAAAAGAATT
* * * *
24463971 TTTCT-GAAATTTTAATTTCAAGAAAAATTGGTACTTTCAACTTTTTCTAAAAAAAATATTTTTT
1 TTT-TAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCT-AAAAAAATATTTTTT
* *
24464035 ATT-TTAAATTTT-GTTGTCAAGAAAAATTGATACTT-TCA-ACTTTTCTCAAAAA-AATAT
64 ATTGATAAATTTTAGTTGTCAA-AAAAATTGATAATTCT-ATACTTTTCTCAAAAAGAAT-T
*
24464092 TTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATATTTTTTA
1 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCT-AAAAAAATATTTTTTA
24464157 AATTTTTATT
Statistics
Matches: 157, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
120 44 0.28
121 78 0.50
122 27 0.17
123 8 0.05
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (122 bp):
TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAAATATTTTTTAT
TGATAAATTTTAGTTGTCAAAAAAATTGATAATTCTATACTTTTCTCAAAAAGAATT
Found at i:24464178 original size:58 final size:58
Alignment explanation
Indices: 24463851--24464169 Score: 243
Period size: 59 Copynumber: 5.3 Consensus size: 58
24463841 ATGATTTTTA
* * ** *
24463851 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTC-CTTAAAAATGT
1 TTTTAAAAATTTTATTTTTAACAAAAATTGATACTTTCAACTTTTCTCAAAAAAATAT
* * ** **
24463908 TTTTATTGATAATTTTTATTTTTCAA-AAAAATTGATA-ATTCTATTTTTTTCTCAAAAAGCCT-
1 TTTTA---A-AAATTTTATTTTT-AACAAAAATTGATACTTTC-A-ACTTTTCTCAAAAA-AATA
24463970 T
58 T
* * * * * *
24463971 TTTCT-GAAATTTTAATTTCAAGAAAAATTGGTACTTTCAACTTTTTCTAAAAAAAATATT
1 TTT-TAAAAATTTTATTTTTAACAAAAATTGATACTTTCAAC-TTTTCTCAAAAAAATA-T
* * * * *
24464031 TTTTATTTTAAATTTTGTTGTCAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAAATAT
1 TTTTA---AAAATTTTATTTTTAACAAAAATTGATACTTTCAACTTTTCTCAAAAAAATAT
*
24464092 TTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAATAT
1 TTTTAAAAATTTTATTTTTAACAAAAATTGATACTTTCAACTTTT-CTCAAAAAAATAT
* *
24464151 TTTTTAAATTTTTATTTTT
1 TTTTAAAAATTTTATTTTT
24464170 TCTTAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
57 5 0.02
58 39 0.19
59 63 0.30
60 11 0.05
61 29 0.14
62 22 0.10
63 39 0.19
64 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48
Consensus pattern (58 bp):
TTTTAAAAATTTTATTTTTAACAAAAATTGATACTTTCAACTTTTCTCAAAAAAATAT
Found at i:24464211 original size:15 final size:16
Alignment explanation
Indices: 24464187--24464226 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
24464177 TTTAATCATA
*
24464187 AAAGAAAAAAAATACT
1 AAAGAAAAAAAATACC
24464203 AAA-AAAAAAAATACC
1 AAAGAAAAAAAATACC
24464218 AAAGAAAAA
1 AAAGAAAAA
24464227 TAAAAAACGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (16 bp):
AAAGAAAAAAAATACC
Found at i:24464507 original size:13 final size:13
Alignment explanation
Indices: 24464491--24464515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24464481 CTTCTTTTTT
24464491 CTTTTTTTTTTCC
1 CTTTTTTTTTTCC
24464504 CTTTTTTTTTTC
1 CTTTTTTTTTTC
24464516 TTTCTCTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
CTTTTTTTTTTCC
Found at i:24464512 original size:17 final size:18
Alignment explanation
Indices: 24464487--24464524 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
24464477 TTTTCTTCTT
*
24464487 TTTTCTTTTTTTTTTCCC
1 TTTTCTTTTTTCTTTCCC
*
24464505 TTTT-TTTTTTCTTTCTC
1 TTTTCTTTTTTCTTTCCC
24464522 TTT
1 TTT
24464525 CTCTAGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTCCC
Found at i:24465996 original size:40 final size:42
Alignment explanation
Indices: 24465911--24465998 Score: 144
Period size: 40 Copynumber: 2.1 Consensus size: 42
24465901 TTCTTCTATA
*
24465911 TGTATTAACGGTTGAAATTTTATTATTATAAAAAAATAGTAT
1 TGTATTAACGGTTGAAATCTTATTATTATAAAAAAATAGTAT
*
24465953 TGTATTAATGGTTG-AATCTTATTATTAT-AAAAAATAGTAT
1 TGTATTAACGGTTGAAATCTTATTATTATAAAAAAATAGTAT
24465993 TGTATT
1 TGTATT
24465999 TATTGAGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 18 0.41
41 13 0.30
42 13 0.30
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (42 bp):
TGTATTAACGGTTGAAATCTTATTATTATAAAAAAATAGTAT
Found at i:24467046 original size:12 final size:12
Alignment explanation
Indices: 24467031--24467087 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
24467021 AAATTATTTT
24467031 TTTAATTTTATA
1 TTTAATTTTATA
24467043 TTTAATTATATATA
1 TTTAATT-T-TATA
*
24467057 TTT-A-TATATA
1 TTTAATTTTATA
24467067 TTTAATTTTATA
1 TTTAATTTTATA
24467079 TTTATATTT
1 TTTA-ATTT
24467088 AAAATAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 7 0.18
11 1 0.03
12 17 0.45
13 6 0.16
14 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAATTTTATA
Found at i:24467066 original size:24 final size:22
Alignment explanation
Indices: 24467039--24467085 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 22
24467029 TTTTTAATTT
24467039 TATATTTAATTATATATATTTATA
1 TATATTTAATT-T-TATATTTATA
24467063 TATATTTAATTTTATATTTATA
1 TATATTTAATTTTATATTTATA
24467085 T
1 T
24467086 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.48
23 1 0.04
24 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATTTAATTTTATATTTATA
Found at i:24467067 original size:10 final size:10
Alignment explanation
Indices: 24467037--24467085 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
24467027 TTTTTTTAAT
*
24467037 TTTATATTTA
1 TTTATATATA
*
24467047 ATTATATATA
1 TTTATATATA
24467057 TTTATATATA
1 TTTATATATA
*
24467067 TTTAATTTTATA
1 TTT-A-TATATA
24467079 TTTATAT
1 TTTATAT
24467086 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 22 0.69
11 2 0.06
12 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTATATATA
Found at i:24470189 original size:30 final size:28
Alignment explanation
Indices: 24470148--24470217 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
24470138 AATTTGAAAA
*
24470148 AAAAATCTATTTGGATATAAAACAAAGAA-T
1 AAAAATTTATTT-GA-ATAAAACAAA-AAGT
*
24470178 AAAAATTTATTTGAATAAAATAAAAAGT
1 AAAAATTTATTTGAATAAAACAAAAAGT
*
24470206 ATAAATTTATTT
1 AAAAATTTATTT
24470218 TTAAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.06
28 21 0.58
29 2 0.06
30 11 0.31
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (28 bp):
AAAAATTTATTTGAATAAAACAAAAAGT
Found at i:24471925 original size:179 final size:179
Alignment explanation
Indices: 24471613--24471970 Score: 608
Period size: 179 Copynumber: 2.0 Consensus size: 179
24471603 TAAGGGTTCT
* * *
24471613 TAAAGAATAAGTTCTGACCTTTTGAACAAAATTAAGTTCAGGAGTTCGATTACGTGTGAAGAAGC
1 TAAAGAATAAGTTCTGACATTCTGAACAAAATTAAGTTCAGGAATTCGATTACGTGTGAAGAAGC
* * * * *
24471678 TTATAGCACCCCACAATATCTATTTTAAAATTGTATCATTTAATTTTAAATTTATTTTATGATCT
66 CTATAGCACCCCACAATACCCATTTTAAAATGGTATCATTTAATTTTAAATTTATTCTATGATCT
*
24471743 TAATTCTAATGGTTTTAAATTTTTATGTTGAATATTGAAATAATTCTTA
131 TAATTCTAATGATTTTAAATTTTTATGTTGAATATTGAAATAATTCTTA
* *
24471792 TAAAGAATAAGTTCTGACATTCTGAATAAAATTAGGTTCAGGAATTCGATTACGTGTGAAGAAGC
1 TAAAGAATAAGTTCTGACATTCTGAACAAAATTAAGTTCAGGAATTCGATTACGTGTGAAGAAGC
*
24471857 CTATAGCACCCCACAATACCCATTTTAAAATGGTATCATTTAATTTTAAATTTATTCTATGGTCT
66 CTATAGCACCCCACAATACCCATTTTAAAATGGTATCATTTAATTTTAAATTTATTCTATGATCT
24471922 TAATTCTAATGATTTTAAATTTTTATGTTGAATATTGAAATAATTCTTA
131 TAATTCTAATGATTTTAAATTTTTATGTTGAATATTGAAATAATTCTTA
24471971 AGATTTTTCA
Statistics
Matches: 167, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
179 167 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (179 bp):
TAAAGAATAAGTTCTGACATTCTGAACAAAATTAAGTTCAGGAATTCGATTACGTGTGAAGAAGC
CTATAGCACCCCACAATACCCATTTTAAAATGGTATCATTTAATTTTAAATTTATTCTATGATCT
TAATTCTAATGATTTTAAATTTTTATGTTGAATATTGAAATAATTCTTA
Found at i:24472246 original size:44 final size:44
Alignment explanation
Indices: 24472209--24472308 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 44
24472199 TTTATTTTTA
24472209 TTTTTATTTCTAAATTTTTCACTATTTGGGTCAATTTAGAATTT
1 TTTTTATTTCTAAATTTTTCACTATTTGGGTCAATTTAGAATTT
* **
24472253 TTTTTATTTCTAAATTTTTCATTATTTGGGTTTATTTAGAAATTACT
1 TTTTTATTTCTAAATTTTTCACTATTTGGGTCAATTTAG-AATT--T
24472300 TTTTTATTT
1 TTTTTATTT
24472309 TTTTGAAAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 36 0.72
45 4 0.08
47 10 0.20
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.61
Consensus pattern (44 bp):
TTTTTATTTCTAAATTTTTCACTATTTGGGTCAATTTAGAATTT
Found at i:24473046 original size:8 final size:8
Alignment explanation
Indices: 24473030--24473068 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
24473020 TTTTCTTAGA
24473030 TTTCTCTT
1 TTTCTCTT
*
24473038 TTTCCCTT
1 TTTCTCTT
*
24473046 TCTCTCTT
1 TTTCTCTT
*
24473054 CTTCTCTT
1 TTTCTCTT
24473062 TTTCTCT
1 TTTCTCT
24473069 CCATCTCTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTCTCTT
Found at i:24473652 original size:27 final size:29
Alignment explanation
Indices: 24473622--24473675 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
24473612 AAAAAACGAA
24473622 AAATCAA-AAACAAACAAAAAA-ATAAAT
1 AAATCAATAAACAAACAAAAAACATAAAT
* * *
24473649 AAATGAATAACCAACCAAAAAACATAA
1 AAATCAATAAACAAACAAAAAACATAA
24473676 CATTAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 12 0.55
29 4 0.18
ACGTcount: A:0.72, C:0.15, G:0.02, T:0.11
Consensus pattern (29 bp):
AAATCAATAAACAAACAAAAAACATAAAT
Found at i:24476485 original size:20 final size:20
Alignment explanation
Indices: 24476460--24476498 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24476450 AATCCTAAAT
24476460 TCAGAAACAATAAAATGAAC
1 TCAGAAACAATAAAATGAAC
* *
24476480 TCAGAAATATTAAAATGAA
1 TCAGAAACAATAAAATGAA
24476499 AACAGATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (20 bp):
TCAGAAACAATAAAATGAAC
Found at i:24476504 original size:20 final size:20
Alignment explanation
Indices: 24476470--24476509 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24476460 TCAGAAACAA
**
24476470 TAAAATGAACTCAGAAATAT
1 TAAAATGAAAACAGAAATAT
*
24476490 TAAAATGAAAACAGATATAT
1 TAAAATGAAAACAGAAATAT
24476510 CAAATCAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.25
Consensus pattern (20 bp):
TAAAATGAAAACAGAAATAT
Found at i:24477589 original size:30 final size:30
Alignment explanation
Indices: 24477553--24477655 Score: 109
Period size: 30 Copynumber: 3.3 Consensus size: 30
24477543 CAATTGAATG
* *
24477553 AAAATAAAAATTTAAAGATTTAATTAAGTA
1 AAAATAAATATTTAAAGACTTAATTAAGTA
* * *
24477583 AAAATAATTATTTAATGGCTTAATTGAA-TA
1 AAAATAAATATTTAAAGACTTAATT-AAGTA
*
24477613 AAAATAAATATTTAAAAACTTAATTAATGTA
1 AAAATAAATATTTAAAGACTTAATTAA-GTA
24477644 AATTAATAAATA
1 AA--AATAAATA
24477656 AAATAATTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
29 2 0.03
30 43 0.73
31 6 0.10
33 8 0.14
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (30 bp):
AAAATAAATATTTAAAGACTTAATTAAGTA
Found at i:24480920 original size:4 final size:4
Alignment explanation
Indices: 24480911--24480935 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
24480901 ATGCCGGTGT
24480911 TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA T
24480936 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCTA
Found at i:24484046 original size:50 final size:50
Alignment explanation
Indices: 24483971--24484070 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
24483961 TTGAATATTG
* *
24483971 TTACCTTTCATTTTCTAAACAAAAATTTCCGTCGTTGAACCCAAACTTTA
1 TTACCTTTCATTTTCTAAACAAAAATTTCCGTCGTTAAACCCAAAATTTA
24484021 TTACCTTTCATTTTCTAAACAAAAATTTCCGTCGTTAAACCCAAAATTTA
1 TTACCTTTCATTTTCTAAACAAAAATTTCCGTCGTTAAACCCAAAATTTA
24484071 ATTCAATTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (50 bp):
TTACCTTTCATTTTCTAAACAAAAATTTCCGTCGTTAAACCCAAAATTTA
Found at i:24492544 original size:17 final size:18
Alignment explanation
Indices: 24492510--24492552 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
24492500 TAACAATTTC
24492510 AAAAAACATAAATCAAATT
1 AAAAAA-ATAAATCAAATT
*
24492529 AAAAAAATAACT-AAATT
1 AAAAAAATAAATCAAATT
24492546 AAAAAAA
1 AAAAAAA
24492553 ACCATAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAAAAATAAATCAAATT
Found at i:24492553 original size:18 final size:19
Alignment explanation
Indices: 24492510--24492553 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
24492500 TAACAATTTC
*
24492510 AAAAAACATAAATCAAATT
1 AAAAAAAATAAATCAAATT
*
24492529 -AAAAAAATAACT-AAATT
1 AAAAAAAATAAATCAAATT
24492546 AAAAAAAA
1 AAAAAAAA
24492554 CCATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAAAATAAATCAAATT
Found at i:24495112 original size:66 final size:65
Alignment explanation
Indices: 24494862--24495113 Score: 208
Period size: 65 Copynumber: 3.9 Consensus size: 65
24494852 TTGAATAAAA
** * * * *
24494862 ATATTCACTCAATTAAGGCATTTATATTTAACAAACA-TCGTAAAT-AA-ATTTTTTTCAATGTT
1 ATATTCACTCAATTAAGGTGTTTATACTTAACAAA-AGTCGTAATTGAATAATTTTTTCAATTTT
24494924 T
65 T
* * * * *
24494925 ATATTCATTCAATTAAGGTGTTTATAGTTAACAAACGTCGTAATTGACTAATTTTTTCAATTCTT
1 ATATTCACTCAATTAAGGTGTTTATACTTAACAAAAGTCGTAATTGAATAATTTTTTCAATTTTT
* *** * * * **
24494990 ACATTCACTCAATTAAGACATTTATACTAAACAAACACT-GTAAATGAATTTTTTTTTTCAATTT
1 ATATTCACTCAATTAAGGTGTTTATACTTAACAAA-AGTCGTAATTGAA-TAATTTTTTCAATTT
24495054 TT
64 TT
* * **
24495056 ATATTTACTCAATTAAGGTGTTTAGT-TTTAACAAAATGTCGTAATTGAAGGATTTTTT
1 ATATTCACTCAATTAAGGTGTTTA-TACTTAACAAAA-GTCGTAATTGAATAATTTTTT
24495114 TAAAAGCCAA
Statistics
Matches: 145, Mismatches: 36, Indels: 13
0.75 0.19 0.07
Matches are distributed among these distances:
63 38 0.26
64 1 0.01
65 49 0.34
66 48 0.33
67 9 0.06
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (65 bp):
ATATTCACTCAATTAAGGTGTTTATACTTAACAAAAGTCGTAATTGAATAATTTTTTCAATTTTT
Found at i:24495112 original size:131 final size:128
Alignment explanation
Indices: 24494864--24495113 Score: 324
Period size: 131 Copynumber: 1.9 Consensus size: 128
24494854 GAATAAAAAT
* * *
24494864 ATTCACTCAATTAAGGCATTTATATTTAACAAACATCGTAAATAAATTTTTTTCAATGTTTATAT
1 ATTCACTCAATTAAGACATTTATACTAAACAAACATCGTAAATAAATTTTTTTCAATGTTTATAT
* **
24494929 TCATTCAATTAAGGTGTTTATAGTTAACAAACGTCGTAATTGACTAATTTTTTCAATTCTTAC
66 TCACTCAATTAAGGTGTTTATAGTTAACAAACGTCGTAATTGAAGAATTTTTTCAATTCTTAC
* *
24494992 ATTCACTCAATTAAGACATTTATACTAAACAAACA-CTGTAAATGAATTTTTTTTTTCAATTTTT
1 ATTCACTCAATTAAGACATTTATACTAAACAAACATC-GTAAAT-AA--ATTTTTTTCAATGTTT
* * * *
24495056 ATATTTACTCAATTAAGGTGTTTAGT-TTTAACAAAATGTCGTAATTGAAGGATTTTTT
62 ATATTCACTCAATTAAGGTGTTTA-TAGTTAAC-AAACGTCGTAATTGAAGAATTTTTT
24495114 TAAAAGCCAA
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
127 1 0.01
128 38 0.37
129 2 0.02
131 41 0.39
132 22 0.21
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (128 bp):
ATTCACTCAATTAAGACATTTATACTAAACAAACATCGTAAATAAATTTTTTTCAATGTTTATAT
TCACTCAATTAAGGTGTTTATAGTTAACAAACGTCGTAATTGAAGAATTTTTTCAATTCTTAC
Found at i:24502803 original size:29 final size:26
Alignment explanation
Indices: 24502768--24502836 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 26
24502758 TTTTTTATTT
*
24502768 AAAATAAAATTTAATTGAATATAAATTA
1 AAAATAAAATTTAATTAAATAT-AA-TA
*
24502796 AAGAATAAAATTTTATTAAATATAATA
1 AA-AATAAAATTTAATTAAATATAATA
24502823 AAATATAAAATTTA
1 AAA-ATAAAATTTA
24502837 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.03
27 13 0.36
28 4 0.11
29 18 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (26 bp):
AAAATAAAATTTAATTAAATATAATA
Found at i:24511256 original size:18 final size:18
Alignment explanation
Indices: 24511233--24511268 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24511223 TAAGCGCGCA
* *
24511233 GCAAAGATAAGAGGAAAC
1 GCAAAGAGAAGAGAAAAC
24511251 GCAAAGAGAAGAGAAAAC
1 GCAAAGAGAAGAGAAAAC
24511269 TGAGAGGAAA
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:0.58, C:0.11, G:0.28, T:0.03
Consensus pattern (18 bp):
GCAAAGAGAAGAGAAAAC
Found at i:24516756 original size:13 final size:13
Alignment explanation
Indices: 24516738--24516762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24516728 GAAATCAATT
24516738 TTAAATTTATAAC
1 TTAAATTTATAAC
24516751 TTAAATTTATAA
1 TTAAATTTATAA
24516763 ATGAATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTTATAAC
Found at i:24520058 original size:13 final size:13
Alignment explanation
Indices: 24520040--24520069 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24520030 CCTTTTTTTT
*
24520040 TTTTTATGTTATA
1 TTTTTATATTATA
24520053 TTTTTATATTATA
1 TTTTTATATTATA
24520066 TTTT
1 TTTT
24520070 AATTCTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTTATATTATA
Found at i:24521433 original size:101 final size:103
Alignment explanation
Indices: 24521258--24521473 Score: 328
Period size: 101 Copynumber: 2.1 Consensus size: 103
24521248 ACACACTCAA
* **
24521258 ATATATATACATGCATGATCATGTACATACATATACTTGTATACTTGTGTCTATCATATGTATGT
1 ATATATATACATGCATGATCATGTACATACATATACTTGTATACTTATGAATATCATATGTATGT
24521323 GTATGTGTA-TG-CCTTGGACAAAAGATTGTATACATC
66 GTATGTGTAGTGTCCTTGGACAAAAGATTGTATACATC
*
24521359 ATATATATACATGCATGATCTTGTACATACATATACTTGTATACTTATGAATATCATATGTATGT
1 ATATATATACATGCATGATCATGTACATACATATACTTGTATACTTATGAATATCATATGTATGT
*
24521424 GTATGTGTATGTGTATTTCTTGGACAAAAGATTGTATACATC
66 GTATGTGTA-GTG---TCCTTGGACAAAAGATTGTATACATC
*
24521466 ATACATAT
1 ATATATAT
24521474 GCATTATGCA
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
101 70 0.68
103 2 0.02
107 31 0.30
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (103 bp):
ATATATATACATGCATGATCATGTACATACATATACTTGTATACTTATGAATATCATATGTATGT
GTATGTGTAGTGTCCTTGGACAAAAGATTGTATACATC
Found at i:24521906 original size:114 final size:115
Alignment explanation
Indices: 24521763--24521990 Score: 413
Period size: 115 Copynumber: 2.0 Consensus size: 115
24521753 ATAAAATTTT
*
24521763 ATTAATTTGATCTTATCATCAAAATAAATTGTAAAATTTAAACGTTAACAAAAAA-AATTACTAG
1 ATTAATTTGATCTTATCATCAAAATAAATTGTAAAATTTAAAAGTTAACAAAAAATAATTACTAG
24521827 TTTTGATTTTAAAATGATACTAATGTCCACATATGTATTTTTAAGACCCA
66 TTTTGATTTTAAAATGATACTAATGTCCACATATGTATTTTTAAGACCCA
* *
24521877 ATTAATTTGATCTTATCATCAAAATAAATTGTAAAATTTAAAAGTTAACAAAAAATATTTATTAG
1 ATTAATTTGATCTTATCATCAAAATAAATTGTAAAATTTAAAAGTTAACAAAAAATAATTACTAG
*
24521942 TTTTGATTTTAAAATGATACTAATGTTCACATATGTATTTTTAAGACCC
66 TTTTGATTTTAAAATGATACTAATGTCCACATATGTATTTTTAAGACCC
24521991 TATAAGTAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
114 54 0.50
115 55 0.50
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (115 bp):
ATTAATTTGATCTTATCATCAAAATAAATTGTAAAATTTAAAAGTTAACAAAAAATAATTACTAG
TTTTGATTTTAAAATGATACTAATGTCCACATATGTATTTTTAAGACCCA
Found at i:24529316 original size:2 final size:2
Alignment explanation
Indices: 24529309--24529345 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24529299 AATATAATTT
24529309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24529346 GTAGACACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24531244 original size:14 final size:13
Alignment explanation
Indices: 24531186--24531247 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
24531176 GAAGTTTTTT
24531186 ATTAAAAATAAGTA
1 ATTAAAAATAA-TA
* *
24531200 AATAAAAATTATA
1 ATTAAAAATAATA
* *
24531213 ATAAAAAATTAAAA
1 ATTAAAAA-TAATA
24531227 ATTAAAAATAATA
1 ATTAAAAATAATA
24531240 GATTAAAA
1 -ATTAAAA
24531248 GATTTCATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 12 0.32
14 26 0.68
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
ATTAAAAATAATA
Found at i:24538390 original size:38 final size:39
Alignment explanation
Indices: 24538348--24538422 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
24538338 AATTGCCTAT
* *
24538348 ATTAG-ACTTTGTTTTCTGATATAAACATGAAAGAAAAA
1 ATTAGTACTTTGTTTGCTGATATAAACATAAAAGAAAAA
** * *
24538386 ATTAGTTTTTTGTTTGCTGATGTAACCATAAAAGAAA
1 ATTAGTACTTTGTTTGCTGATATAAACATAAAAGAAA
24538423 CAGCAAATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
38 5 0.17
39 25 0.83
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (39 bp):
ATTAGTACTTTGTTTGCTGATATAAACATAAAAGAAAAA
Found at i:24539033 original size:27 final size:27
Alignment explanation
Indices: 24538974--24539033 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
24538964 TATGGCTTTA
* * * *
24538974 GCTGCAACTGTTGAAGCTGCTGGCTCT
1 GCTGCAACTGATGAAACAGCTGGCGCT
* *
24539001 GTTGCAACTGATGAAACAGCTGGGGCT
1 GCTGCAACTGATGAAACAGCTGGCGCT
24539028 GCTGCA
1 GCTGCA
24539034 GCTGTTGCTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (27 bp):
GCTGCAACTGATGAAACAGCTGGCGCT
Found at i:24540398 original size:15 final size:15
Alignment explanation
Indices: 24540378--24540419 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
24540368 TTTTTATTAA
24540378 AATTTTAAATTATTT
1 AATTTTAAATTATTT
24540393 AATTTTAAATT-TTT
1 AATTTTAAATTATTT
*
24540407 -A-TTTATATTATTT
1 AATTTTAAATTATTT
24540420 TTATATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 7 0.28
13 4 0.16
14 3 0.12
15 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTTTAAATTATTT
Found at i:24540421 original size:23 final size:23
Alignment explanation
Indices: 24540357--24540422 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
24540347 TTTTATAAAA
24540357 TTTATTTATGATT-TTTATTAAAATT
1 TTTATTTAT-ATTATTT-TT-AAATT
* * *
24540382 TTAAATTAT-TTAATTTTAAATT
1 TTTATTTATATTATTTTTAAATT
24540404 TTTATTTATATTATTTTTA
1 TTTATTTATATTATTTTTA
24540423 TATTATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
22 12 0.36
23 12 0.36
24 2 0.06
25 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTATTTATATTATTTTTAAATT
Found at i:24540428 original size:16 final size:15
Alignment explanation
Indices: 24540401--24540434 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
24540391 TTAATTTTAA
24540401 ATTTTTATTTATATT
1 ATTTTTATTTATATT
24540416 ATTTTTATATTATATT
1 ATTTTTAT-TTATATT
24540432 ATT
1 ATT
24540435 ATATCGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTTATTTATATT
Found at i:24542399 original size:17 final size:16
Alignment explanation
Indices: 24542348--24542400 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
24542338 ATGATATGAG
*
24542348 ATTTTAATTAATTTTAT
1 ATTTTAATT-ATTTTTT
24542365 ATTTTATATT-TTTGTTT
1 ATTTTA-ATTATTT-TTT
24542382 ATTTTAATGTATTTTTT
1 ATTTTAAT-TATTTTTT
24542399 AT
1 AT
24542401 AATTAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 5 0.16
17 20 0.65
18 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (16 bp):
ATTTTAATTATTTTTT
Found at i:24543438 original size:17 final size:19
Alignment explanation
Indices: 24543416--24543451 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
24543406 TAAAGTTTAC
24543416 TTATTT-TTTATTT-TATT
1 TTATTTATTTATTTATATT
24543433 TTATTTATTTATTTATATT
1 TTATTTATTTATTTATATT
24543452 AATAGTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTATTTATTTATTTATATT
Found at i:24543909 original size:13 final size:13
Alignment explanation
Indices: 24543891--24543935 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
24543881 AAACAGACAA
24543891 TAAAAAAAAAAAC
1 TAAAAAAAAAAAC
24543904 TAAAAAAAAAAATC
1 TAAAAAAAAAAA-C
*
24543918 CATAAAAAAAAAAC
1 TA-AAAAAAAAAAC
24543932 -AAAA
1 TAAAA
24543936 GTCTTCTCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 3 0.10
13 13 0.45
14 3 0.10
15 10 0.34
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (13 bp):
TAAAAAAAAAAAC
Found at i:24543912 original size:15 final size:16
Alignment explanation
Indices: 24543892--24543930 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
24543882 AACAGACAAT
24543892 AAAAAAAAAAAC-TAA
1 AAAAAAAAAAACATAA
**
24543907 AAAAAAAAATCCATAA
1 AAAAAAAAAAACATAA
24543923 AAAAAAAA
1 AAAAAAAA
24543931 CAAAAGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAAAAAAAAACATAA
Found at i:24543923 original size:16 final size:14
Alignment explanation
Indices: 24543890--24543930 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
24543880 TAAACAGACA
24543890 ATAAAAAAAAAAAC
1 ATAAAAAAAAAAAC
24543904 -TAAAAAAAAAAATCC
1 ATAAAAAAAAAAA--C
24543919 ATAAAAAAAAAA
1 ATAAAAAAAAAA
24543931 CAAAAGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
15 1 0.04
16 11 0.46
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (14 bp):
ATAAAAAAAAAAAC
Found at i:24545085 original size:31 final size:29
Alignment explanation
Indices: 24545050--24545113 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 29
24545040 TTAAAAATTC
24545050 AAACTTATAAA-CCTTCTAAATCCCAAAATCT
1 AAACTT-TAAATCCTTC-AAATCCCAAAA-CT
*
24545081 AAACTTTAAATCCTTCAAATCCTAAAACT
1 AAACTTTAAATCCTTCAAATCCCAAAACT
24545110 AAAC
1 AAAC
24545114 CCTAAACCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 6 0.19
30 14 0.45
31 11 0.35
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (29 bp):
AAACTTTAAATCCTTCAAATCCCAAAACT
Found at i:24545119 original size:29 final size:30
Alignment explanation
Indices: 24545057--24545121 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
24545047 TTCAAACTTA
**
24545057 TAAACCTTCTAAATCCCAAAATCTAAACTT
1 TAAACCTTCTAAATCCCAAAATCTAAACCC
*
24545087 TAAATCCTTC-AAATCCTAAAA-CTAAACCC
1 TAAA-CCTTCTAAATCCCAAAATCTAAACCC
24545116 TAAACC
1 TAAACC
24545122 CCAAAATCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 2 0.06
29 10 0.32
30 14 0.45
31 5 0.16
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (30 bp):
TAAACCTTCTAAATCCCAAAATCTAAACCC
Found at i:24545144 original size:20 final size:20
Alignment explanation
Indices: 24545104--24545148 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
24545094 TTCAAATCCT
24545104 AAAACTAAACCCTAAACCCC
1 AAAACTAAACCCTAAACCCC
*
24545124 AAAATCTAAACCTTAAA-CCC
1 AAAA-CTAAACCCTAAACCCC
24545144 AAAAC
1 AAAAC
24545149 CCTATAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 11 0.48
21 11 0.48
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAACTAAACCCTAAACCCC
Found at i:24545239 original size:60 final size:60
Alignment explanation
Indices: 24545109--24545396 Score: 195
Period size: 60 Copynumber: 4.8 Consensus size: 60
24545099 ATCCTAAAAC
* * * * *
24545109 TAAACCC--TAAACCCCAAAATCT-AAACCTTAAACCC--AAAACCCTATAATCAAAA-CT
1 TAAACCCTTTAAACCCTAAAA-CTAAAACCCTAAACCCTTTAAACCCTAAAAACAAAACCT
*** * * *
24545164 GTAAACCCCCAAAACTCTAAAACTAAAACCCTAAACCCTTTAAACCTTAAAAACAAAACCC
1 -TAAACCCTTTAAACCCTAAAACTAAAACCCTAAACCCTTTAAACCCTAAAAACAAAACCT
* ** * ***
24545225 TAAA-TCTTCTAAACTTTAAAA-TCAAAACCTTAAACCCCCCAAACCCT-AAAACTAAAACCT
1 TAAACCCTT-TAAACCCTAAAACT-AAAACCCTAAACCCTTTAAACCCTAAAAAC-AAAACCT
** ** *
24545285 TAAACCCTTTAAACCCTAAAAAC-AAAAGTCTAAA-CCTTGTAAACCCTAAAATTAGAACCT
1 TAAACCCTTTAAACCCT-AAAACTAAAACCCTAAACCCTT-TAAACCCTAAAAACAAAACCT
*
24545345 TAAACCCTTTAAACCCTAAAATCT-AAGCCCTAAAACCCTTTAAACCCTAAAA
1 TAAACCCTTTAAACCCTAAAA-CTAAAACCCT-AAACCCTTTAAACCCTAAAA
24545397 CTCTTAGAAC
Statistics
Matches: 179, Mismatches: 35, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
56 7 0.04
57 2 0.01
58 21 0.12
59 13 0.07
60 106 0.59
61 26 0.15
62 4 0.02
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (60 bp):
TAAACCCTTTAAACCCTAAAACTAAAACCCTAAACCCTTTAAACCCTAAAAACAAAACCT
Found at i:24545259 original size:90 final size:90
Alignment explanation
Indices: 24545108--24545396 Score: 311
Period size: 90 Copynumber: 3.2 Consensus size: 90
24545098 AATCCTAAAA
* * * * * *
24545108 CTAAACCC--TAAACCCCAAAATCTAAACCTTAAACC--CAAAACCCTATAATCAAAA-CTGTAA
1 CTAAACCCTTTAAACCCTAAAAACAAAACCCTAAACCTTCTAAACCCTAAAATCAAAACCT-TAA
*
24545168 ACCCCCAAAACTCTAAAACTAAAACC
65 ACCCCCAAAACCCTAAAACTAAAACC
* * **
24545194 CTAAACCCTTTAAACCTTAAAAACAAAACCCTAAATCTTCTAAACTTTAAAATCAAAACCTTAAA
1 CTAAACCCTTTAAACCCTAAAAACAAAACCCTAAACCTTCTAAACCCTAAAATCAAAACCTTAAA
*
24545259 CCCCCCAAACCCTAAAACTAAAACC
66 CCCCCAAAACCCTAAAACTAAAACC
* ** * * *
24545284 TTAAACCCTTTAAACCCTAAAAACAAAAGTCTAAACCTTGTAAACCCTAAAATTAGAACCTTAAA
1 CTAAACCCTTTAAACCCTAAAAACAAAACCCTAAACCTTCTAAACCCTAAAATCAAAACCTTAAA
*** *
24545349 CCCTTTAAACCCTAAAATCT-AAGCC
66 CCCCCAAAACCCTAAAA-CTAAAACC
24545374 CTAAAACCCTTTAAACCCTAAAA
1 CT-AAACCCTTTAAACCCTAAAA
24545397 CTCTTAGAAC
Statistics
Matches: 169, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
86 8 0.05
88 21 0.12
90 116 0.69
91 24 0.14
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (90 bp):
CTAAACCCTTTAAACCCTAAAAACAAAACCCTAAACCTTCTAAACCCTAAAATCAAAACCTTAAA
CCCCCAAAACCCTAAAACTAAAACC
Found at i:24545384 original size:31 final size:31
Alignment explanation
Indices: 24545109--24545411 Score: 172
Period size: 30 Copynumber: 10.1 Consensus size: 31
24545099 ATCCTAAAAC
*
24545109 TAAACCC--TAAACCCCAAAATCTAA-ACCT
1 TAAACCCTTTAAACCCTAAAATCTAAGACCT
* * *
24545137 TAAACCC--AAAACCCTATAATC-AA-AACT
1 TAAACCCTTTAAACCCTAAAATCTAAGACCT
*** * * *
24545164 GTAAACCCCCAAAACTCTAAAA-CTAAAACCC
1 -TAAACCCTTTAAACCCTAAAATCTAAGACCT
* * * *
24545195 TAAACCCTTTAAACCTTAAAAAC-AAAACCC
1 TAAACCCTTTAAACCCTAAAATCTAAGACCT
* ** *
24545225 TAAA-TCTTCTAAACTTTAAAATC-AAAACCT
1 TAAACCCTT-TAAACCCTAAAATCTAAGACCT
*** *
24545255 TAAACCCCCCAAACCCTAAAA-CTAAAACCT
1 TAAACCCTTTAAACCCTAAAATCTAAGACCT
* **
24545285 TAAACCCTTTAAACCCTAAAAAC-AA-AAGT
1 TAAACCCTTTAAACCCTAAAATCTAAGACCT
24545314 CTAAA-CCTTGTAAACCCTAAAAT-T-AGAACCT
1 -TAAACCCTT-TAAACCCTAAAATCTAAG-ACCT
*
24545345 TAAACCCTTTAAACCCTAAAATCTAAGCCCT
1 TAAACCCTTTAAACCCTAAAATCTAAGACCT
* * *
24545376 AAAACCCTTTAAACCCTAAAACTCTTAGAACT
1 TAAACCCTTTAAACCCTAAAA-TCTAAGACCT
24545408 TAAA
1 TAAA
24545412 GCTAAAACCT
Statistics
Matches: 219, Mismatches: 37, Indels: 34
0.76 0.13 0.12
Matches are distributed among these distances:
27 5 0.02
28 25 0.11
29 12 0.05
30 130 0.59
31 35 0.16
32 12 0.05
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (31 bp):
TAAACCCTTTAAACCCTAAAATCTAAGACCT
Found at i:24548138 original size:59 final size:59
Alignment explanation
Indices: 24548040--24548154 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 59
24548030 GATCTAGTGA
* * *
24548040 GTTTGACTCATGGACGATAATTTTAATAACTATCTCAATATAGTTCATATATCAATCTT
1 GTTTGACACATGGACGATAATTTTAATAACTAGCCCAATATAGTTCATATATCAATCTT
* *
24548099 GTTTGACACATGGACGATGATTTTAATAACTAGCCCAATATAGTTGATATATCAAT
1 GTTTGACACATGGACGATAATTTTAATAACTAGCCCAATATAGTTCATATATCAAT
24548155 GTTGGGCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (59 bp):
GTTTGACACATGGACGATAATTTTAATAACTAGCCCAATATAGTTCATATATCAATCTT
Found at i:24551220 original size:26 final size:26
Alignment explanation
Indices: 24551191--24551241 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
24551181 TGTGTCCAGA
*
24551191 CCCAAGT-GGACCCATTGGCGTTTAGG
1 CCCAAGTAGG-CCCATTAGCGTTTAGG
*
24551217 CCCAAGTAGGCCCATTAGTGTTTAG
1 CCCAAGTAGGCCCATTAGCGTTTAG
24551242 TGGGCTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (26 bp):
CCCAAGTAGGCCCATTAGCGTTTAGG
Found at i:24552412 original size:24 final size:23
Alignment explanation
Indices: 24552384--24552457 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
24552374 CCAAAAAAGA
24552384 AAAAAAAGTAAAAAAAAATGAAG
1 AAAAAAAGTAAAAAAAAATGAAG
* ** *
24552407 AGAAAAAAG-AGAAAAATAATTCTAC
1 A-AAAAAAGTA-AAAAA-AAATGAAG
24552432 AAAAAAAGTAAAAAAAAATGAA-
1 AAAAAAAGTAAAAAAAAATGAAG
24552454 AAAA
1 AAAA
24552458 TACATTCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
22 4 0.10
23 6 0.15
24 24 0.60
25 6 0.15
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.11
Consensus pattern (23 bp):
AAAAAAAGTAAAAAAAAATGAAG
Found at i:24558895 original size:152 final size:153
Alignment explanation
Indices: 24558516--24558961 Score: 804
Period size: 152 Copynumber: 2.9 Consensus size: 153
24558506 TTTACCAAGT
* *
24558516 AATTAGTTGTTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* *
24558581 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
24558646 TAAAGAAAAAAACAAAATCATCC
131 TAAAGAAAAAAACAAAATCATCC
*
24558669 AATTAATTATTGGAAATTATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
24558734 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
*
24558799 TAAA-AAAAATACAAAATCATCC
131 TAAAGAAAAAAACAAAATCATCC
24558821 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* * *
24558886 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGTAGAGGCTCTGTCGTCGGATTAAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
24558951 TAAAGAAAAAA
131 TAAAGAAAAAA
24558962 GAAAAAAAAA
Statistics
Matches: 281, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
152 147 0.52
153 134 0.48
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (153 bp):
AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
TAAAGAAAAAAACAAAATCATCC
Found at i:24559028 original size:13 final size:12
Alignment explanation
Indices: 24558996--24559027 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
24558986 AAAGTCAAAT
24558996 AAAAAAAATTCA
1 AAAAAAAATTCA
24559008 AAAAAAAATTCA
1 AAAAAAAATTCA
24559020 AAAAAAAA
1 AAAAAAAA
24559028 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:24559306 original size:20 final size:20
Alignment explanation
Indices: 24559277--24559322 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24559267 GGAAGATTCA
*
24559277 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCG
***
24559297 CCGGAATCTGGGTTTTTTCG
1 CCGGAATCTGGAAATTTTCG
24559317 CCGGAA
1 CCGGAA
24559323 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCG
Found at i:24559363 original size:19 final size:20
Alignment explanation
Indices: 24559339--24559381 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
24559329 CGGAAATTCA
24559339 CCGGTTTCTGGGATTCTT-G
1 CCGGTTTCTGGGATTCTTCG
24559358 CCGGTTTCTGGGATTCTTCG
1 CCGGTTTCTGGGATTCTTCG
24559378 CCGG
1 CCGG
24559382 AAACTGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.05, C:0.26, G:0.33, T:0.37
Consensus pattern (20 bp):
CCGGTTTCTGGGATTCTTCG
Found at i:24559378 original size:61 final size:63
Alignment explanation
Indices: 24559267--24559383 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 63
24559257 GAACTCCGGT
* *
24559267 GGAAGATTCACCGGATTCTGGAAATTTTCGCCGGAATCTGGGTTTTTTCGCCGGAAGTTGGCC
1 GGAAGATTCACCGGATTCTGGAAATTTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGCC
* * **
24559330 GGAA-ATTCACCGGTTTCTGG-GATTCTT-GCCGGTTTCTGGGATTCTTCGCCGGAA
1 GGAAGATTCACCGGATTCTGGAAATT-TTCGCCGGAATCTGGGATTCTTCGCCGGAA
24559384 ACTGGGCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 26 0.55
62 17 0.36
63 4 0.09
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (63 bp):
GGAAGATTCACCGGATTCTGGAAATTTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGCC
Found at i:24559388 original size:20 final size:19
Alignment explanation
Indices: 24559346--24559389 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
24559336 TCACCGGTTT
***
24559346 CTGGGATTCTTGCCGGTTT
1 CTGGGATTCTTGCCGGAAA
24559365 CTGGGATTCTTCGCCGGAAA
1 CTGGGATTCTT-GCCGGAAA
24559385 CTGGG
1 CTGGG
24559390 CAGTTCGCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.11, C:0.23, G:0.34, T:0.32
Consensus pattern (19 bp):
CTGGGATTCTTGCCGGAAA
Found at i:24559809 original size:12 final size:12
Alignment explanation
Indices: 24559792--24559825 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
24559782 CTAGCCCTCC
24559792 AAAATAAAAATT
1 AAAATAAAAATT
24559804 AAAAT-AAAATT
1 AAAATAAAAATT
*
24559815 AAAAAAAAAAT
1 AAAATAAAAAT
24559826 CTAGATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:24560077 original size:13 final size:13
Alignment explanation
Indices: 24560059--24560083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24560049 AAGAGAGAAA
24560059 AAAAAATAAAAAT
1 AAAAAATAAAAAT
24560072 AAAAAATAAAAA
1 AAAAAATAAAAA
24560084 ATACGGGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:24560141 original size:20 final size:20
Alignment explanation
Indices: 24560118--24560163 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
24560108 CTTGCCCATT
24560118 TGGGCCAGGCCCAAATGATC
1 TGGGCCAGGCCCAAATGATC
* *
24560138 TGGGTCAGGCCCAATTGATC
1 TGGGCCAGGCCCAAATGATC
*
24560158 CGGGCC
1 TGGGCC
24560164 CGGACCTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (20 bp):
TGGGCCAGGCCCAAATGATC
Found at i:24560384 original size:42 final size:42
Alignment explanation
Indices: 24560292--24560918 Score: 906
Period size: 42 Copynumber: 15.1 Consensus size: 42
24560282 TTTTTTTTTA
** * *
24560292 GCTCCTCTTGACAGAGGCTCTACGACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
24560333 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
24560375 GCTCCTCTAAACAGAGGCA--ACGAACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAATAAATT
* *
24560415 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
* *
24560457 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
* *
24560498 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
24560540 GCTCCTCTAAACAGAGGCA--ACGGAACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAAATAAATT
*
24560581 GCTCCTCTAAACAGAGGCA--ACGAACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAATAAATT
* *
24560621 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
24560663 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
* *
24560705 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
24560747 GCTCCTCTAAACAGAGGCAACACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
24560789 GCTCCTCTAAACAGAGGCAACACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
*
24560831 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
24560872 GCTCCTCTAAACAGAGGCA--ACGGAACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAAATAAATT
24560913 GCTCCT
1 GCTCCT
24560919 AGTCAATCAT
Statistics
Matches: 542, Mismatches: 30, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
39 2 0.00
40 64 0.12
41 173 0.32
42 303 0.56
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
Found at i:24562101 original size:8 final size:7
Alignment explanation
Indices: 24562088--24562141 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
24562078 TTGAATCTCT
24562088 TTTTTTC
1 TTTTTTC
24562095 ATTTTTTC
1 -TTTTTTC
*
24562103 -AT-TTC
1 TTTTTTC
*
24562108 TTTCTTC
1 TTTTTTC
24562115 TTTCTTTC
1 TTT-TTTC
24562123 -TTTTTC
1 TTTTTTC
24562129 TTTTTTC
1 TTTTTTC
24562136 TTTTTT
1 TTTTTT
24562142 TTTCCATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
5 3 0.08
6 6 0.15
7 20 0.51
8 10 0.26
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:24562128 original size:17 final size:17
Alignment explanation
Indices: 24562108--24562145 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
24562098 TTTTCATTTC
24562108 TTTCTTCTTTCTTTCTT
1 TTTCTTCTTTCTTTCTT
* *
24562125 TTTCTTTTTTCTTTTTT
1 TTTCTTCTTTCTTTCTT
24562142 TTTC
1 TTTC
24562146 CATCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTCTTTCTTTCTT
Found at i:24566209 original size:152 final size:153
Alignment explanation
Indices: 24565830--24566275 Score: 804
Period size: 152 Copynumber: 2.9 Consensus size: 153
24565820 TTTACCAAGT
* *
24565830 AATTAGTTGTTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* *
24565895 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
24565960 TAAAGAAAAAAACAAAATCATCC
131 TAAAGAAAAAAACAAAATCATCC
*
24565983 AATTAATTATTGGAAATTATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
24566048 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
*
24566113 TAAA-AAAAATACAAAATCATCC
131 TAAAGAAAAAAACAAAATCATCC
24566135 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* * *
24566200 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGTAGAGGCTCTGTCGTCGGATTAAT
66 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
24566265 TAAAGAAAAAA
131 TAAAGAAAAAA
24566276 GAAAAAAAAA
Statistics
Matches: 281, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
152 147 0.52
153 134 0.48
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (153 bp):
AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTTAT
TAAAGAAAAAAACAAAATCATCC
Found at i:24566324 original size:17 final size:16
Alignment explanation
Indices: 24566277--24566346 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
24566267 AAGAAAAAAG
24566277 AAAAAAAAATCAAGATCA
1 AAAAAAAAATCAA-AT-A
** *
24566295 AAATCAAAGTCAAATA
1 AAAAAAAAATCAAATA
24566311 AAAAAAAAATTCAAA-A
1 AAAAAAAAA-TCAAATA
24566327 AAAAAAAAA--AAA-A
1 AAAAAAAAATCAAATA
24566340 AAAAAAA
1 AAAAAAA
24566347 CCTGGAGCGG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 11 0.24
16 17 0.38
17 7 0.16
18 10 0.22
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAAAAAAATCAAATA
Found at i:24566711 original size:20 final size:20
Alignment explanation
Indices: 24566682--24566727 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24566672 GGAAGATTCA
*
24566682 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCG
***
24566702 CCGGAATCTGGGTTTTTTCG
1 CCGGAATCTGGAAATTTTCG
24566722 CCGGAA
1 CCGGAA
24566728 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCG
Found at i:24566768 original size:19 final size:20
Alignment explanation
Indices: 24566744--24566786 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
24566734 CGGAAATTCA
24566744 CCGGTTTCTGGGATTCTT-G
1 CCGGTTTCTGGGATTCTTCG
24566763 CCGGTTTCTGGGATTCTTCG
1 CCGGTTTCTGGGATTCTTCG
24566783 CCGG
1 CCGG
24566787 AAACTGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.05, C:0.26, G:0.33, T:0.37
Consensus pattern (20 bp):
CCGGTTTCTGGGATTCTTCG
Found at i:24566783 original size:61 final size:63
Alignment explanation
Indices: 24566672--24566788 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 63
24566662 GAACTCCGGT
* *
24566672 GGAAGATTCACCGGATTCTGGAAATTTTCGCCGGAATCTGGGTTTTTTCGCCGGAAGTTGGCC
1 GGAAGATTCACCGGATTCTGGAAATTTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGCC
* * **
24566735 GGAA-ATTCACCGGTTTCTGG-GATTCTT-GCCGGTTTCTGGGATTCTTCGCCGGAA
1 GGAAGATTCACCGGATTCTGGAAATT-TTCGCCGGAATCTGGGATTCTTCGCCGGAA
24566789 ACTGGGCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 26 0.55
62 17 0.36
63 4 0.09
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (63 bp):
GGAAGATTCACCGGATTCTGGAAATTTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGCC
Found at i:24566793 original size:20 final size:19
Alignment explanation
Indices: 24566751--24566794 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
24566741 TCACCGGTTT
***
24566751 CTGGGATTCTTGCCGGTTT
1 CTGGGATTCTTGCCGGAAA
24566770 CTGGGATTCTTCGCCGGAAA
1 CTGGGATTCTT-GCCGGAAA
24566790 CTGGG
1 CTGGG
24566795 CAGTTCGCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.11, C:0.23, G:0.34, T:0.32
Consensus pattern (19 bp):
CTGGGATTCTTGCCGGAAA
Found at i:24567213 original size:12 final size:12
Alignment explanation
Indices: 24567196--24567227 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
24567186 CTAGCCCTCC
24567196 AAAATAAAAATT
1 AAAATAAAAATT
24567208 AAAAT-AAAATT
1 AAAATAAAAATT
24567219 AAAA-AAAAA
1 AAAATAAAAA
24567228 AATCTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:24567432 original size:12 final size:14
Alignment explanation
Indices: 24567399--24567435 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
24567389 GAAAAAAAAA
*
24567399 ATATATATATATAT
1 ATATATACATATAT
24567413 ATATATACATATAT
1 ATATATACATATAT
24567427 -TA-ATACATA
1 ATATATACATA
24567436 ATAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.32
13 2 0.09
14 13 0.59
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:24567445 original size:44 final size:46
Alignment explanation
Indices: 24567344--24567449 Score: 109
Period size: 44 Copynumber: 2.4 Consensus size: 46
24567334 ATAATAATAT
*
24567344 AATAATAATAAATATATAACTATATACATATAAATCTATTCTAATG
1 AATAATAATAAATATATAACTATATACATATAAATATATTCTAATG
* * *
24567390 AA-AA-AAAAAATATATATA-TATATATATATACATATA-T-TAAT-
1 AATAATAATAAATATATA-ACTATATACATATAAATATATTCTAATG
24567431 ACATAATAATAAATA-ATAA
1 A-ATAATAATAAATATATAA
24567450 AATACACAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
41 1 0.02
42 6 0.12
43 6 0.12
44 33 0.65
45 3 0.06
46 2 0.04
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (46 bp):
AATAATAATAAATATATAACTATATACATATAAATATATTCTAATG
Found at i:24567483 original size:7 final size:7
Alignment explanation
Indices: 24567466--24567500 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
24567456 CAAGAGAGAA
24567466 AAAAAAT
1 AAAAAAT
24567473 -AAAAAT
1 AAAAAAT
24567479 AAAAAAT
1 AAAAAAT
24567486 AAAAAAT
1 AAAAAAT
24567493 AAAAAAT
1 AAAAAAT
24567500 A
1 A
24567501 CGGGTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:24567484 original size:14 final size:15
Alignment explanation
Indices: 24567465--24567498 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
24567455 ACAAGAGAGA
24567465 AAAAAAAT-AAAAAT
1 AAAAAAATAAAAAAT
24567479 -AAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
24567493 AAAAAA
1 AAAAAA
24567499 TACGGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:24567555 original size:20 final size:20
Alignment explanation
Indices: 24567532--24567577 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
24567522 CTTGCCCATT
24567532 TGGGCCAGGCCCAAATGATC
1 TGGGCCAGGCCCAAATGATC
* *
24567552 TGGGTCAGGCCCAATTGATC
1 TGGGCCAGGCCCAAATGATC
*
24567572 CGGGCC
1 TGGGCC
24567578 CGGACCTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (20 bp):
TGGGCCAGGCCCAAATGATC
Found at i:24572514 original size:178 final size:178
Alignment explanation
Indices: 24572185--24573061 Score: 730
Period size: 178 Copynumber: 4.9 Consensus size: 178
24572175 TATTTCTCAT
* * * * *
24572185 GATTTGTGGTTTCGTCTCGATCATTTATTTTTGACCTCGACTTGGTCCTAGTCACTTTTGTTTTG
1 GATTCGTGGTTTCGTCTCGATCATTTATTTTTGATCTCGACTAGGTCTTAGTCA-TTTTATTTTG
* ** * *
24572250 ACTTGTGATTTTATC-CCAGTCACATGATTCGTGATTTTATCTCGATCATTTATTTAT-AACTTC
65 ACTTGTGGTTTCGTCTCCA-TCACATGATTCATGATTTTATCTCGATCATTTATTT-TCAACCTC
*** * * * * * *
24572313 GACTCAATCTT-GATCGTTTTATTTTGACTTGTGATTTTATCCCTATCACAT
128 GACTTGGTCTTAG-TCATTTTATTTTGACTCGTGATTTCATCCCGATCATAC
* *
24572364 GATTCGTGGTTTCGTCTCGATCATTTATTTTTGA-CTTCAACTAGGTTTTAGTCATTTTATTTTG
1 GATTCGTGGTTTCGTCTCGATCATTTATTTTTGATC-TCGACTAGGTCTTAGTCATTTTATTTTG
* * * * * * ** *
24572428 ACTTATGGTTTCGTCTCGATCATACGATTCATGATTTTGTTTCGATCATTTATTTTTTACCTCAA
65 ACTTGTGGTTTCGTCTCCATCACATGATTCATGATTTTATCTCGATCATTTATTTTCAACCTCGA
* ** * *
24572493 CTTGGTCTTATTCGCTTTATTTTGACTCGTGAATTCATCACGATCATAC
130 CTTGGTCTTAGTCATTTTATTTTGACTCGTGATTTCATCCCGATCATAC
* * * * * * * *
24572542 AATTCGTGATTTCATCTCGATCATTTATTTTTTATCTCAACTCA-ATCTTGGTCGTTTTATTTTG
1 GATTCGTGGTTTCGTCTCGATCATTTATTTTTGATCTCGACT-AGGTCTTAGTCATTTTATTTTG
* * * * * * * * * * *
24572606 ACTTGTGATTTCGTTTCGATCACATAATTTACGGTTTCATCCCGATCATTTATTTTCGATCTCGA
65 ACTTGTGGTTTCGTCTCCATCACATGATTCATGATTTTATCTCGATCATTTATTTTCAACCTCGA
* * * * ** *
24572671 CTTGGTCCTGGTCATTTTATTTTGACTCATGGTTTTGTCTCGATCATAC
130 CTTGGTCTTAGTCATTTTATTTTGACTCGTGATTTCATCCCGATCATAC
* * * ** ** * * * *
24572720 AATTCATAGTTTTATCTCGATCATTTATTTTCAATCTCGACTCGATCCTGGTCATTTTATTTTGA
1 GATTCGTGGTTTCGTCTCGATCATTTATTTTTGATCTCGACTAGGTCTTAGTCATTTTATTTTGA
* * * * * *
24572785 CTTGTGGTTTCGTCTCAATCAAATGATTCATGGTTTTATC-CTGATCATTTA-CTCCAACCTCAA
66 CTTGTGGTTTCGTCTCCATCACATGATTCATGATTTTATCTC-GATCATTTATTTTCAACCTCGA
* *
24572848 CTCGATCTTAGTCATTTTATTTTGACTCGTGATTTCATCCC-AGTCATAC
130 CTTGGTCTTAGTCATTTTATTTTGACTCGTGATTTCATCCCGA-TCATAC
* * * * * * *
24572897 GATTCGTGATTTCGTCTTGATCATTTATTTTCGATCTCGACTCGGTCTTAATCACTTTATTTGGA
1 GATTCGTGGTTTCGTCTCGATCATTTATTTTTGATCTCGACTAGGTCTTAGTCATTTTATTTTGA
* * * * *
24572962 CTCGTGGTTTCATC-CCAGTCATACGATTCATGATTTCATCAT-GATCATTTATTTTCAACCTCG
66 CTTGTGGTTTCGTCTCCA-TCACATGATTCATGATTTTATC-TCGATCATTTATTTTCAACCTCG
* * * *
24573025 ACTTGGTCCTAGTCACTTTATTTTGACTTGTGGTTTC
129 ACTTGGTCTTAGTCATTTTATTTTGACTCGTGATTTC
24573062 GTCTCAGTCA
Statistics
Matches: 556, Mismatches: 129, Indels: 27
0.78 0.18 0.04
Matches are distributed among these distances:
176 3 0.01
177 137 0.25
178 365 0.66
179 51 0.09
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (178 bp):
GATTCGTGGTTTCGTCTCGATCATTTATTTTTGATCTCGACTAGGTCTTAGTCATTTTATTTTGA
CTTGTGGTTTCGTCTCCATCACATGATTCATGATTTTATCTCGATCATTTATTTTCAACCTCGAC
TTGGTCTTAGTCATTTTATTTTGACTCGTGATTTCATCCCGATCATAC
Found at i:24572742 original size:267 final size:268
Alignment explanation
Indices: 24572199--24573052 Score: 719
Period size: 267 Copynumber: 3.2 Consensus size: 268
24572189 TGTGGTTTCG
* * * * *
24572199 TCTCGATCATTTATTTTTGACCTCGACTTGGTCCTAGTCACTTTTGTTTTGACTTGTGATTTTAT
1 TCTCGATCATTTATTTTTGACCTCAACTTGGTCCTAGTCACTTTTATTTTGACTCGTGAATTCAT
** * *
24572264 CCCAGTCACATGATTCGTGATTTTATCTCGATCATTTATTTATAACTTCGACTCAATCTTGATCG
66 CCCAGTCACACAATTCGTGATTTCATCTCGATCATTTATTTATAACTTCAACTCAATCTTGATCG
* * * ** * *
24572329 TTTTATTTTGACTTGTGATTTTATCCCTATCACATGATTCGTGGTTTCGTCTCGATCATTTATTT
131 TTTTATTTTGACTTGTGATTTCATCCCGATCACATAATTCACGGTTTCATCCCGATCATTTATTT
* ** * *
24572394 TTGACTTCAACTAGGTTTTAGTCATTTTATTTTGACTTATGGTTTCGTCTCGATCATACGATTCA
196 TCGACTTCAACTAGGTCCTAGTCATTTTATTTTGACTCATGGTTTCGTCTCGATCATACAATTCA
*
24572459 TGATTTTG
261 TGATTTTA
* * * * *
24572467 TTTCGATCATTTATTTTTTACCTCAACTTGGTCTTATTCGC-TTTATTTTGACTCGTGAATTCAT
1 TCTCGATCATTTATTTTTGACCTCAACTTGGTCCTAGTCACTTTTATTTTGACTCGTGAATTCAT
* * * * *
24572531 CAC-GATCATACAATTCGTGATTTCATCTCGATCATTTATTTTTTA-TCTCAACTCAATCTTGGT
66 CCCAG-TCACACAATTCGTGATTTCATCTCGATCATTTATTTATAACT-TCAACTCAATCTTGAT
* ** *
24572594 CGTTTTATTTTGACTTGTGATTTCGTTTCGATCACATAATTTACGGTTTCATCCCGATCATTTAT
129 CGTTTTATTTTGACTTGTGATTTCATCCCGATCACATAATTCACGGTTTCATCCCGATCATTTAT
* * * *
24572659 TTTCGA-TCTCGACTTGGTCCTGGTCATTTTATTTTGACTCATGGTTTTGTCTCGATCATACAAT
194 TTTCGACT-TCAACTAGGTCCTAGTCATTTTATTTTGACTCATGGTTTCGTCTCGATCATACAAT
24572723 TCAT-AGTTTTA
258 TCATGA-TTTTA
** * * * * * * ** *
24572734 TCTCGATCATTTATTTTCAATCTCGACTCGATCCTGGTCA-TTTTATTTTGACTTGTGGTTTCGT
1 TCTCGATCATTTATTTTTGACCTCAACTTGGTCCTAGTCACTTTTATTTTGACTCGTGAATTCAT
* * * ** * * * * ** * *
24572798 CTCAATCAAATGATTCATGGTTTTATC-CTGATCATTTA-CTCCAACCTCAACTCGATCTT-AGT
66 CCCAGTCACACAATTCGTGATTTCATCTC-GATCATTTATTTATAACTTCAACTCAATCTTGA-T
* * * ** ** * * **
24572860 CATTTTATTTTGACTCGTGATTTCATCCC-AGTCATACGATTCGTGATTTCGTCTTGATCATTTA
129 CGTTTTATTTTGACTTGTGATTTCATCCCGA-TCACATAATTCACGGTTTCATCCCGATCATTTA
* * * * * * * * * *
24572924 TTTTCGA-TCTCGACTCGGTCTTAATCACTTTATTTGGACTCGTGGTTTCATC-CCAGTCATACG
193 TTTTCGACT-TCAACTAGGTCCTAGTCATTTTATTTTGACTCATGGTTTCGTCTCGA-TCATACA
*
24572987 ATTCATGATTTCA
256 ATTCATGATTTTA
** *
24573000 TCAT-GATCATTTATTTTCAACCTCGACTTGGTCCTAGTCAC-TTTATTTTGACT
1 TC-TCGATCATTTATTTTTGACCTCAACTTGGTCCTAGTCACTTTTATTTTGACT
24573053 TGTGGTTTCG
Statistics
Matches: 471, Mismatches: 101, Indels: 30
0.78 0.17 0.05
Matches are distributed among these distances:
265 3 0.01
266 172 0.37
267 261 0.55
268 35 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (268 bp):
TCTCGATCATTTATTTTTGACCTCAACTTGGTCCTAGTCACTTTTATTTTGACTCGTGAATTCAT
CCCAGTCACACAATTCGTGATTTCATCTCGATCATTTATTTATAACTTCAACTCAATCTTGATCG
TTTTATTTTGACTTGTGATTTCATCCCGATCACATAATTCACGGTTTCATCCCGATCATTTATTT
TCGACTTCAACTAGGTCCTAGTCATTTTATTTTGACTCATGGTTTCGTCTCGATCATACAATTCA
TGATTTTA
Found at i:24573085 original size:89 final size:89
Alignment explanation
Indices: 24572185--24573116 Score: 594
Period size: 89 Copynumber: 10.5 Consensus size: 89
24572175 TATTTCTCAT
* * * * * *
24572185 GATTTGTGGTTTCGTCTCGATCATTTATTTTTGACCTCGACTTGGTCCTAGTCACTTTTGTTTTG
1 GATTCGTGATTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCA-TTTTATTTTG
* ** * * *
24572250 ACTTGTGATTTTATCCCAGTCACAT
65 ACTTGTGGTTTCGTCTCAGTCATAC
* * * ** * *
24572275 GATTCGTGATTTTATCTCGATCATTTATTTAT-AACTTCGACTCAAT-CTTGATCGTTTTATTTT
1 GATTCGTGATTTCATCTCGATCATTTATTT-TCGACCTCGACTCGGTCCTAG-TCATTTTATTTT
* ** * * *
24572338 GACTTGTGATTTTATCCCTA-TCACAT
64 GACTTGTGGTTTCGTCTC-AGTCATAC
* * * * * * **
24572364 GATTCGTGGTTTCGTCTCGATCATTTATTTTTGACTTCAACTAGGTTTTAGTCATTTTATTTTGA
1 GATTCGTGATTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTGA
*
24572429 CTTATGGTTTCGTCTC-GATCATAC
66 CTTGTGGTTTCGTCTCAG-TCATAC
* ** * ** * * * * **
24572453 GATTCATGATTTTGTTTCGATCATTTATTTTTTACCTCAACTTGGTCTTATTCGCTTTATTTTGA
1 GATTCGTGATTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTGA
* ** * *
24572518 CTCGTGAATTCATCAC-GATCATAC
66 CTTGTGGTTTCGTCTCAG-TCATAC
* ** * * ** * * *
24572542 AATTCGTGATTTCATCTCGATCATTTATTTTTTATCTCAACTCAATCTTGGTCGTTTTATTTTGA
1 GATTCGTGATTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTGA
* * * *
24572607 CTTGTGATTTCGTTTC-GATCACAT
66 CTTGTGGTTTCGTCTCAG-TCATAC
* * * * *
24572631 AATTTACG-G-TTTCATCCCGATCATTTATTTTCGATCTCGACTTGGTCCTGGTCATTTTATTTT
1 GA-TT-CGTGATTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTT
** *
24572694 GACTCATGGTTTTGTCTC-GATCATAC
64 GACTTGTGGTTTCGTCTCAG-TCATAC
* * * * * * *
24572720 AATTCAT-AGTTTTATCTCGATCATTTATTTTCAATCTCGACTCGATCCTGGTCATTTTATTTTG
1 GATTCGTGA-TTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTG
* * *
24572784 ACTTGTGGTTTCGTCTCAATCAAAT
65 ACTTGTGGTTTCGTCTCAGTCATAC
* * * * * * * * *
24572809 GATTCATGGTTTTATC-CTGATCATTTA-CTCCAACCTCAACTCGATCTTAGTCATTTTATTTTG
1 GATTCGTGATTTCATCTC-GATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTG
* * * *
24572872 ACTCGTGATTTCATCCCAGTCATAC
65 ACTTGTGGTTTCGTCTCAGTCATAC
* * * * * * *
24572897 GATTCGTGATTTCGTCTTGATCATTTATTTTCGATCTCGACTCGGTCTTAATCACTTTATTTGGA
1 GATTCGTGATTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTGA
* * *
24572962 CTCGTGGTTTCATCCCAGTCATAC
66 CTTGTGGTTTCGTCTCAGTCATAC
* * * *
24572986 GATTCATGATTTCATCAT-GATCATTTATTTTCAACCTCGACTTGGTCCTAGTCACTTTATTTTG
1 GATTCGTGATTTCATC-TCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTG
* *
24573050 ACTTGTGGTTTCGTCTCAGTCACAT
65 ACTTGTGGTTTCGTCTCAGTCATAC
* * ** * *
24573075 TACTCGTGATTTTGTCTCGATTATTTTTTTTCGACCTCGACT
1 GATTCGTGATTTCATCTCGATCATTTATTTTCGACCTCGACT
24573117 TGATCTTGAT
Statistics
Matches: 678, Mismatches: 145, Indels: 39
0.79 0.17 0.05
Matches are distributed among these distances:
87 1 0.00
88 74 0.11
89 556 0.82
90 44 0.06
91 3 0.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (89 bp):
GATTCGTGATTTCATCTCGATCATTTATTTTCGACCTCGACTCGGTCCTAGTCATTTTATTTTGA
CTTGTGGTTTCGTCTCAGTCATAC
Found at i:24573540 original size:26 final size:26
Alignment explanation
Indices: 24573511--24573578 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
24573501 CCAACTAGGC
24573511 CCATTTGTGTCTAGGCTCGATT-GTGT
1 CCATTTGTGTCTAGGCTCGATTAGT-T
* *
24573537 CCA-TTGACGTCCAGGCTCGATTAGTT
1 CCATTTG-TGTCTAGGCTCGATTAGTT
*
24573563 CCATTGGTGTCTAGGC
1 CCATTTGTGTCTAGGC
24573579 CAAATTAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.09
26 27 0.79
27 4 0.12
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (26 bp):
CCATTTGTGTCTAGGCTCGATTAGTT
Found at i:24573664 original size:13 final size:14
Alignment explanation
Indices: 24573640--24573668 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24573630 ATCATCATCA
24573640 TTATTATTATTATT
1 TTATTATTATTATT
24573654 TTATT-TTATTATT
1 TTATTATTATTATT
24573667 TT
1 TT
24573669 TCTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:24573674 original size:19 final size:18
Alignment explanation
Indices: 24573640--24573678 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
24573630 ATCATCATCA
24573640 TTATTATTATTATTTTATT
1 TTATTATTATTATTTT-TT
* *
24573659 TTATTATTTTTCTTTTTT
1 TTATTATTATTATTTTTT
24573677 TT
1 TT
24573679 TTTTTACTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTATTATTATTATTTTTT
Found at i:24573683 original size:23 final size:22
Alignment explanation
Indices: 24573652--24573697 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
24573642 ATTATTATTA
* *
24573652 TTTTATTTTATTATTTTTCTTTT
1 TTTTATTTTACTA-CTTTCTTTT
*
24573675 TTTTTTTTTACTACTTTCTTTT
1 TTTTATTTTACTACTTTCTTTT
24573697 T
1 T
24573698 CTGTTCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTATTTTACTACTTTCTTTT
Found at i:24579123 original size:1 final size:1
Alignment explanation
Indices: 24579119--24579143 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
24579109 TTAAAAACCC
24579119 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
24579144 GACCCAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24580148 original size:14 final size:15
Alignment explanation
Indices: 24580123--24580151 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24580113 ATCATTAAAT
24580123 TATAATTAATTATAA
1 TATAATTAATTATAA
24580138 TATAA-TAATTATAA
1 TATAATTAATTATAA
24580152 ATGATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATTAATTATAA
Found at i:24580366 original size:25 final size:24
Alignment explanation
Indices: 24580332--24580381 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
24580322 GATGGTGATA
*
24580332 ACTTTGTCCTTATTCTGGAAGCCCT
1 ACTTTGTCCTTATTCT-GAAACCCT
* *
24580357 ACTTTTTCCTTGTTCTGAAACCCT
1 ACTTTGTCCTTATTCTGAAACCCT
24580381 A
1 A
24580382 TTCTGATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.42
Consensus pattern (24 bp):
ACTTTGTCCTTATTCTGAAACCCT
Found at i:24582062 original size:27 final size:27
Alignment explanation
Indices: 24582031--24582095 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
24582021 AGGCTTTAGA
*
24582031 TGCAACTGTTGAAGCTGCTGAGG-CTGC
1 TGCAACTGTTGAAGCAGCTG-GGTCTGC
*
24582058 TGCAACTGATGAAGCAGCTGGGTCTGC
1 TGCAACTGTTGAAGCAGCTGGGTCTGC
*
24582085 TGCAGCTGTTG
1 TGCAACTGTTG
24582096 TTGCACCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.18, C:0.22, G:0.34, T:0.26
Consensus pattern (27 bp):
TGCAACTGTTGAAGCAGCTGGGTCTGC
Done.