Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 4 of 138
Found at i:653728 original size:26 final size:26
Alignment explanation
Indices: 653639--653734 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 26
653629 TTTTCCATTC
*
653639 TTTCATTTTTTTTCATTTTT--TTTCCT
1 TTTCATCTTTTTTCATTTTTAATTT--T
* *
653665 TTTTATCTCTTTT--TTTTT-ATTTT
1 TTTCATCTTTTTTCATTTTTAATTTT
653688 TTTCATCTTTTTTCATTTTTAATTTT
1 TTTCATCTTTTTTCATTTTTAATTTT
* *
653714 TTTCCTTTTTTTTCATCTTTT
1 TTTCATCTTTTTTCAT-TTTT
653735 TCCACCCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
23 12 0.21
24 5 0.09
25 8 0.14
26 29 0.50
27 4 0.07
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTCATCTTTTTTCATTTTTAATTTT
Found at i:654139 original size:16 final size:15
Alignment explanation
Indices: 654102--654138 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
654092 TTTTTTTCTC
*
654102 TTTTTTCCTTTGTTT
1 TTTTTTTCTTTGTTT
*
654117 TATTTTTCTTTGTTT
1 TTTTTTTCTTTGTTT
654132 TTTTTTT
1 TTTTTTT
654139 TTTTATCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTGTTT
Found at i:657792 original size:50 final size:50
Alignment explanation
Indices: 657732--657826 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
657722 ATTATTTTTT
*
657732 ATTTCTAAATTTTTCACCATTTGAGTCAATTTAGAAATTTTTTTTTTGAA
1 ATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTTTTTTTTTGAA
** *
657782 ATTTCTAAATTTTTCATTATTTGAGCCTATTTAGAAATTTTTTTT
1 ATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTTTTTTT
657827 GCTTCTCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.55
Consensus pattern (50 bp):
ATTTCTAAATTTTTCACCATTTGAGCCAATTTAGAAATTTTTTTTTTGAA
Found at i:658426 original size:207 final size:205
Alignment explanation
Indices: 658031--658434 Score: 445
Period size: 207 Copynumber: 2.0 Consensus size: 205
658021 AAAAGAATAC
* *
658031 AATTACTTTTATTAAAATTTCATCTAAATTATTTCACCATTTGTGACAAATTTAGAGAACATTTC
1 AATTACTTTTATTAAAATTTCATCTAAATTATTTCACAATTTGTGACAAATTTAGAGAAAATTTC
* * ** * * *
658096 TTACCTAAAATTTTTTTAAAATTTTGTCATTTGAAATTTTTAAGAATCTCATCATTGGGTAATTT
66 TCACCTAAAATTTTTATAAAATTTTACCATTTGAAATTTCTAAGAATCTCATCATTGGATAATTA
* * *
658161 GTACTTAATTCTAAAATTTTTATCAATATTTTTTTATTTTTTATTTTTCTTCTTTTTTTGTTTTG
131 ATACTTAATTCTAAAATTTTTAT--ATATTTTTTTACTTTTTATTTTTCTTATTTTTTTGTTTTG
658226 AAAATAAATATT
194 AAAATAAATATT
*
658238 AATTA-TTATTATTAAAACTTT-ATCTAAATTATTTCACAATTTG-GAACAAATTTAGATAAAAT
1 AATTACTT-TTATTAAAA-TTTCATCTAAATTATTTCACAATTTGTG-ACAAATTTAGAGAAAAT
* *
658300 TTCTCACCTAGGAA-TTTTATAGAAA-TTTACCATTTGAAATTTCTATA-AATTTCAT-ATTTGG
63 TTCTCACCTA-AAATTTTTATA-AAATTTTACCATTTGAAATTTCTA-AGAATCTCATCA-TTGG
*
658361 ATAATTAATA-TTTATTCTCAAAATTTATT-T-TA-TTTTTTACCTTTTTATTTTTCTT-TTTAT
124 ATAATTAATACTTAATTCT-AAAATTT-TTATATATTTTTTTA-CTTTTTATTTTTCTTATTT-T
* *
658421 TTTTTTTTAAAAAT
185 TTTGTTTTGAAAAT
658435 TTAATCATGT
Statistics
Matches: 169, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
203 10 0.06
204 29 0.17
206 11 0.07
207 108 0.64
208 11 0.07
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.52
Consensus pattern (205 bp):
AATTACTTTTATTAAAATTTCATCTAAATTATTTCACAATTTGTGACAAATTTAGAGAAAATTTC
TCACCTAAAATTTTTATAAAATTTTACCATTTGAAATTTCTAAGAATCTCATCATTGGATAATTA
ATACTTAATTCTAAAATTTTTATATATTTTTTTACTTTTTATTTTTCTTATTTTTTTGTTTTGAA
AATAAATATT
Found at i:668221 original size:4 final size:4
Alignment explanation
Indices: 668212--668249 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
668202 GAAAGGGTAT
*
668212 TTAA TTAA TTAA TTAA CTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
668250 GAGAATAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:674683 original size:29 final size:29
Alignment explanation
Indices: 674632--674687 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
674622 ATAATAGGCT
674632 TTCGTTGGAGTAAAAAAAGATGTGCGGCC
1 TTCGTTGGAGTAAAAAAAGATGTGCGGCC
*
674661 TTCGTTGGAGTGAAAGAAA-ATGTGCGG
1 TTCGTTGGAGT-AAAAAAAGATGTGCGG
674688 AAAGATGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (29 bp):
TTCGTTGGAGTAAAAAAAGATGTGCGGCC
Found at i:683875 original size:22 final size:22
Alignment explanation
Indices: 683847--683890 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
683837 CTGCTAGGAT
683847 GTAGATTTGAACTTCTTTGGGC
1 GTAGATTTGAACTTCTTTGGGC
683869 GTAGATTTGAACTTCTTTGGGC
1 GTAGATTTGAACTTCTTTGGGC
683891 TTGCAATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (22 bp):
GTAGATTTGAACTTCTTTGGGC
Found at i:687076 original size:2 final size:2
Alignment explanation
Indices: 687069--687111 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
687059 CCTACTTGAA
687069 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
687111 A
1 A
687112 AGGCATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:696020 original size:22 final size:21
Alignment explanation
Indices: 695954--696020 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
695944 AGTATAAAAT
* *
695954 TTTTTAAATTTTATTAAATATA
1 TTTTTAAA-TTTATTTATTATA
* *
695976 TATTT-AA-TTA-TTATTAAA
1 TTTTTAAATTTATTTATTATA
*
695994 ATTTTAAATTATATTTATTATA
1 TTTTTAAATT-TATTTATTATA
696016 TTTTT
1 TTTTT
696021 TATTTTAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
18 8 0.24
19 5 0.15
20 1 0.03
21 4 0.12
22 15 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTAAATTTATTTATTATA
Found at i:698438 original size:19 final size:20
Alignment explanation
Indices: 698406--698443 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
698396 GAATCATACT
698406 AAAAATCATAAATT-ACTTC
1 AAAAATCATAAATTGACTTC
* *
698425 AAAAATGATTAATTGACTT
1 AAAAATCATAAATTGACTT
698444 GTAAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAATCATAAATTGACTTC
Found at i:699535 original size:2 final size:2
Alignment explanation
Indices: 699524--699559 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
699514 AAACAAAAGA
699524 AT AT -T AT 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 AT A
699560 GTTCTGTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:699827 original size:22 final size:21
Alignment explanation
Indices: 699802--699844 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
699792 GATGATGAGT
*
699802 ACATATATATATATATATAATG
1 ACATATATATATAAATA-AATG
* *
699824 ACATTTTTATATAAATAAATG
1 ACATATATATATAAATAAATG
699845 GACGAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
ACATATATATATAAATAAATG
Found at i:703067 original size:36 final size:36
Alignment explanation
Indices: 703026--703094 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
703016 ATGATCAGTT
* * *
703026 TTTAACTTAAA-ATGAATTTCATAATAAATTAAAAGA
1 TTTAACTTAAATATAAAATT-ATAAAAAATTAAAAGA
703062 TTTAACTTAAATATAAAATTATAAAAAATTAAA
1 TTTAACTTAAATATAAAATTATAAAAAATTAAA
703095 TATTTATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 23 0.79
37 6 0.21
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (36 bp):
TTTAACTTAAATATAAAATTATAAAAAATTAAAAGA
Found at i:703301 original size:35 final size:37
Alignment explanation
Indices: 703220--703318 Score: 113
Period size: 35 Copynumber: 2.9 Consensus size: 37
703210 TTGATATTAT
* *
703220 ATTAAATATTTAATTTAAA-AT-TAATTAATAATAAA
1 ATTAAATATTTAAATTAAATATAAAATTAATAATAAA
* *
703255 AATAAAAATTTAAATTAAATATAAAATT-ATAA-AAA
1 ATTAAATATTTAAATTAAATATAAAATTAATAATAAA
703290 ATTAAATATTT--ATTAAATATAAAA-TAATA
1 ATTAAATATTTAAATTAAATATAAAATTAATA
703319 CCATTTTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
32 1 0.02
33 16 0.29
35 28 0.51
36 6 0.11
37 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (37 bp):
ATTAAATATTTAAATTAAATATAAAATTAATAATAAA
Found at i:712417 original size:21 final size:22
Alignment explanation
Indices: 712393--712434 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
712383 AGCTTTAGAG
712393 TGGAA-ATTCAGAGTTTCAAAT
1 TGGAATATTCAGAGTTTCAAAT
* *
712414 TGGAATATTGAGATTTTCAAA
1 TGGAATATTCAGAGTTTCAAA
712435 AGTTTAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (22 bp):
TGGAATATTCAGAGTTTCAAAT
Found at i:719811 original size:2 final size:2
Alignment explanation
Indices: 719804--719847 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
719794 AACCTTTCCA
719804 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
719846 TC
1 TC
719848 AAGCATCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:734972 original size:54 final size:53
Alignment explanation
Indices: 734858--734999 Score: 137
Period size: 53 Copynumber: 2.6 Consensus size: 53
734848 GCTTTTGCAC
* ** *
734858 AAGAAAAATTGATACTTTCAATTTTTCCTTAAAGCATTTGAGAGTTTTTATTTT
1 AAGAAAAATTGATACTTT-AACTTTTCCTTAAAATATATGAGAGTTTTTATTTT
* *
734912 ATGAAAAATTGATACCTTTAACTTTTCCTTAAAATATAT-ATA-TTTTTATTTTT
1 AAGAAAAATTGATA-CTTTAACTTTTCCTTAAAATATATGAGAGTTTTTA-TTTT
* * *
734965 AA-AGAAAATTGGTACTTCTAACTTTTTCTCAAAAT
1 AAGA-AAAATTGATACTT-TAACTTTTCCTTAAAAT
735000 GCTTTTTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
52 10 0.14
53 31 0.42
54 29 0.39
55 4 0.05
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.46
Consensus pattern (53 bp):
AAGAAAAATTGATACTTTAACTTTTCCTTAAAATATATGAGAGTTTTTATTTT
Found at i:735148 original size:14 final size:14
Alignment explanation
Indices: 735121--735154 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
735111 CCCAAAATGC
*
735121 TTTTGAAAATTTTTA
1 TTTT-AAAAATTTTA
735136 TTTTAAAAATTTTA
1 TTTTAAAAATTTTA
735150 TTTTA
1 TTTTA
735155 TTTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTTAAAAATTTTA
Found at i:735226 original size:15 final size:16
Alignment explanation
Indices: 735208--735242 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
735198 CTTTTCCTTT
735208 AAATTTT-TTTTAAAA
1 AAATTTTATTTTAAAA
*
735223 AAATTTTATTTTAGAA
1 AAATTTTATTTTAAAA
735239 AAAT
1 AAAT
735243 CATTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
AAATTTTATTTTAAAA
Found at i:736129 original size:24 final size:24
Alignment explanation
Indices: 736085--736141 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
736075 AAAGATAAAG
*
736085 TAAAAAAATAGTAATAATAATAGA
1 TAAAAATATAGTAATAATAATAGA
*
736109 TAAAAATATA-TATATATTAATAGA
1 TAAAAATATAGTA-ATAATAATAGA
736133 TAAATAATA
1 TAAA-AATA
736142 AAAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 23 0.79
25 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (24 bp):
TAAAAATATAGTAATAATAATAGA
Found at i:736138 original size:8 final size:7
Alignment explanation
Indices: 736096--736194 Score: 75
Period size: 6 Copynumber: 14.4 Consensus size: 7
736086 AAAAAAATAG
736096 TAAT-AA
1 TAATAAA
*
736102 TAATAGA
1 TAATAAA
736109 TAA-AAA
1 TAATAAA
*
736115 T-ATATA
1 TAATAAA
*
736121 TATATTAA
1 TA-ATAAA
736129 TAGATAAA
1 TA-ATAAA
736137 TAATAAA
1 TAATAAA
* *
736144 AAATATA
1 TAATAAA
736151 -AATAAA
1 TAATAAA
736157 TAAATAAA
1 T-AATAAA
736165 TAAATAAA
1 T-AATAAA
736173 TAATAAA
1 TAATAAA
736180 T-ATAAA
1 TAATAAA
736186 TAA-AAA
1 TAATAAA
736192 TAA
1 TAA
736195 AACTGTAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
5 1 0.01
6 27 0.36
7 22 0.29
8 26 0.34
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
TAATAAA
Found at i:736139 original size:4 final size:4
Alignment explanation
Indices: 736127--736189 Score: 71
Period size: 4 Copynumber: 16.5 Consensus size: 4
736117 TATATATATT
* *
736127 AATA GATA AAT- AATA AAAA ATATA AATA AATA AATA AATA AATA AAT-
1 AATA AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AATA AATA
736174 AATA AAT- -ATA AATA AA
1 AATA AATA AATA AATA AA
736190 AATAAAACTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 2 0.04
3 6 0.12
4 39 0.78
5 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:736148 original size:32 final size:33
Alignment explanation
Indices: 736110--736189 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 33
736100 AATAATAGAT
* * * *
736110 AAAAATATATATATATTAATAGATAAAT-AATA
1 AAAAATATAAATAAATAAATAAATAAATAAATA
736142 AAAAATATAAATAAATAAATAAATAAATAAATA
1 AAAAATATAAATAAATAAATAAATAAATAAATA
*
736175 ATAAATATAAATAAA
1 AAAAATATAAATAAA
736190 AATAAAACTG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 24 0.57
33 18 0.43
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAAATATAAATAAATAAATAAATAAATAAATA
Found at i:736153 original size:16 final size:17
Alignment explanation
Indices: 736132--736189 Score: 84
Period size: 16 Copynumber: 3.5 Consensus size: 17
736122 ATATTAATAG
736132 ATAAAT-AATAAAAAAT
1 ATAAATAAATAAAAAAT
*
736148 ATAAATAAATAAATAA-
1 ATAAATAAATAAAAAAT
*
736164 ATAAATAAATAATAAAT
1 ATAAATAAATAAAAAAT
736181 ATAAATAAA
1 ATAAATAAA
736190 AATAAAACTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 20 0.54
17 17 0.46
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAATAAATAAAAAAT
Found at i:736454 original size:44 final size:43
Alignment explanation
Indices: 736397--736497 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 43
736387 AAATTTTGAT
*
736397 CAAAGCTCCTCTAAGCAGAGACTCAATGACTTTTAAAAAATAAA
1 CAAAGCT-CTCTAAGCAGAGACCCAATGACTTTTAAAAAATAAA
* * * *
736441 CAAAGTTCTTCTAAGCAGAGGCCCGATGACTTTTGAAAAATAAA
1 CAAAGCTC-TCTAAGCAGAGACCCAATGACTTTTAAAAAATAAA
*
736485 TAAAGCTCTCTAA
1 CAAAGCTCTCTAA
736498 TCAAAGGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 6 0.12
44 43 0.88
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (43 bp):
CAAAGCTCTCTAAGCAGAGACCCAATGACTTTTAAAAAATAAA
Found at i:736547 original size:85 final size:82
Alignment explanation
Indices: 736450--736631 Score: 199
Period size: 84 Copynumber: 2.2 Consensus size: 82
736440 ACAAAGTTCT
* * * *
736450 TCTAAGCAGAGGC-CCGATGACTTTTGAAAAATAAATAAAGCTC-TCTAATCAAAGGTTTA-ACG
1 TCTAAACAGAGGCACC-ATAAC-TTTGAAAAAT-AA-AAAGCTCATCTAAACAAAGG-TAACACG
* *
736512 ACTTTGGGAAAGTAAATTGCTCC
61 ACTTTGAGAAA-TAAATTGCTCA
* *
736535 TCTAAACAGAGGCAACCATAACTTTGAAAAATAAAATGCTCATCTAAACAGAGGTAACTACGACT
1 TCTAAACAGAGGC-ACCATAACTTTGAAAAATAAAAAGCTCATCTAAACAAAGGTAAC-ACGACT
736600 TTGAGAAATAAATTGCTCA
64 TTGAGAAATAAATTGCTCA
736619 TCTAAACAGAGGC
1 TCTAAACAGAGGC
736632 TCGACAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
83 8 0.10
84 35 0.42
85 35 0.42
86 4 0.05
87 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (82 bp):
TCTAAACAGAGGCACCATAACTTTGAAAAATAAAAAGCTCATCTAAACAAAGGTAACACGACTTT
GAGAAATAAATTGCTCA
Found at i:736575 original size:42 final size:42
Alignment explanation
Indices: 736524--736631 Score: 153
Period size: 42 Copynumber: 2.6 Consensus size: 42
736514 TTTGGGAAAG
* *
736524 TAAATTGCTCCTCTAAACAGAGGCAACCATAACTTTGAAAAA
1 TAAATTGCTCATCTAAACAGAGGCAACCACAACTTTGAAAAA
* * * * *
736566 TAAAATGCTCATCTAAACAGAGGTAACTACGACTTTGAGAAA
1 TAAATTGCTCATCTAAACAGAGGCAACCACAACTTTGAAAAA
736608 TAAATTGCTCATCTAAACAGAGGC
1 TAAATTGCTCATCTAAACAGAGGC
736632 TCGACAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (42 bp):
TAAATTGCTCATCTAAACAGAGGCAACCACAACTTTGAAAAA
Found at i:738016 original size:15 final size:15
Alignment explanation
Indices: 737996--738025 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
737986 CTCGAATCCA
737996 TTCAACCTCTTTTAG
1 TTCAACCTCTTTTAG
*
738011 TTCAACTTCTTTTAG
1 TTCAACCTCTTTTAG
738026 CACTTTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.50
Consensus pattern (15 bp):
TTCAACCTCTTTTAG
Found at i:742464 original size:17 final size:17
Alignment explanation
Indices: 742442--742477 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
742432 TTTACCAGCA
742442 TTAAAAATTCACAAGCT
1 TTAAAAATTCACAAGCT
*
742459 TTAAAAATTCATAAGCT
1 TTAAAAATTCACAAGCT
742476 TT
1 TT
742478 TTTTTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (17 bp):
TTAAAAATTCACAAGCT
Found at i:748216 original size:51 final size:51
Alignment explanation
Indices: 748126--748222 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
748116 TTTGCACAAG
* *
748126 GAAAATTGATACTTTTAACTTTTTCTTAAAATATATTTTTTTATTTTTAAA
1 GAAAATTGATACTTCTAACTTTTTCTTAAAATATATTTTTTAATTTTTAAA
* *
748177 GAAAATTGGTACTTCTAACTTTTT-TTCAAAATGCT-TTTTTTAATTT
1 GAAAATTGATACTTCTAACTTTTTCTT-AAAAT-ATATTTTTTAATTT
748223 AATTTCAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 2 0.05
51 37 0.93
52 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (51 bp):
GAAAATTGATACTTCTAACTTTTTCTTAAAATATATTTTTTAATTTTTAAA
Found at i:748360 original size:14 final size:15
Alignment explanation
Indices: 748331--748364 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
748321 TTCAAAATGC
*
748331 TTTTGGAAATTTTTA
1 TTTTAGAAATTTTTA
748346 TTTTAGAAA-TTTTA
1 TTTTAGAAATTTTTA
748360 TTTTA
1 TTTTA
748365 TTTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (15 bp):
TTTTAGAAATTTTTA
Found at i:749281 original size:24 final size:24
Alignment explanation
Indices: 749254--749339 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
749244 CAAGAAAAAG
749254 ATAAAATAAAAAAAAATAGTAATA
1 ATAAAATAAAAAAAAATAGTAATA
* * * *
749278 ATAATAGATAAAAATATATATTGATA
1 ATAA-A-ATAAAAAAAAATAGTAATA
749304 GAT-AAATAAAAAAATTAATAGATAAGTA
1 -ATAAAATAAAAAAA--AATAG-TAA-TA
749332 ATAAAATA
1 ATAAAATA
749340 TATATTAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
24 12 0.26
25 2 0.04
26 19 0.41
27 6 0.13
28 7 0.15
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (24 bp):
ATAAAATAAAAAAAAATAGTAATA
Found at i:749312 original size:4 final size:4
Alignment explanation
Indices: 749305--749382 Score: 56
Period size: 4 Copynumber: 20.2 Consensus size: 4
749295 ATATTGATAG
* * * * * * *
749305 ATAA ATAA AAAA ATTA ATAG ATAA GT-A ATAA A-AT ATAT ATTA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
749351 ATAA ATAA ATAA AT-A AT-A ATAA ATAAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA A
749383 ACTGTAAATG
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
3 10 0.17
4 44 0.76
5 4 0.07
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:749350 original size:22 final size:22
Alignment explanation
Indices: 749274--749382 Score: 80
Period size: 22 Copynumber: 4.9 Consensus size: 22
749264 AAAAAATAGT
*
749274 AATAATAATAGAT-AA-AAATA
1 AATAATAATAAATAAATAAATA
* * * * *
749294 TATATTGATAGATAAATAAAAA
1 AATAATAATAAATAAATAAATA
*
749316 AATTAATAGATAAGT-AATAAAATA
1 AA-TAATA-ATAAATAAAT-AAATA
* *
749340 TATATTAATAAATAAATAAATA
1 AATAATAATAAATAAATAAATA
749362 AATAATAATAAATAAAATAAA
1 AATAATAATAAAT-AAATAAA
749383 ACTGTAAATG
Statistics
Matches: 67, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
20 10 0.15
21 2 0.03
22 26 0.39
23 20 0.30
24 9 0.13
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (22 bp):
AATAATAATAAATAAATAAATA
Found at i:749381 original size:46 final size:46
Alignment explanation
Indices: 749257--749383 Score: 145
Period size: 46 Copynumber: 2.8 Consensus size: 46
749247 GAAAAAGATA
* *
749257 AAATAAA-AAAAAATAGTAAT-AATAATAGATAAAAATATATATTGAT
1 AAATAAATAAAAAATAATAATAAATAATA-AT-AAAATATATATTAAT
* * *
749303 AGATAAATAAAAAA-ATTAATAGATAAGTAATAAAATATATATTAAT
1 AAATAAATAAAAAATAATAATAAATAA-TAATAAAATATATATTAAT
749349 AAATAAATAAATAAATAATAATAAATAA-AATAAAA
1 AAATAAATAAA-AAATAATAATAAATAATAATAAAA
749384 CTGTAAATGG
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
46 42 0.61
47 15 0.22
48 12 0.17
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (46 bp):
AAATAAATAAAAAATAATAATAAATAATAATAAAATATATATTAAT
Found at i:782440 original size:66 final size:66
Alignment explanation
Indices: 782331--782455 Score: 198
Period size: 66 Copynumber: 1.9 Consensus size: 66
782321 GAATAGGCTA
*
782331 GAAACTGATATGGTAGTTTCAGTTGGGTCTAATCCATTAGGCCTTGACTTTATCCAATTTTCACT
1 GAAACTGATATGATAGTTTCAGTTGGGTCTAATCCATTAGGCCTTGACTTTATCCAATTTTCACT
782396 T
66 T
* * *
782397 GAAACTGATATGATAGTTTGAGTTGGGTCTAA-CTTATTGGGCCTTGACTTTATCCAATT
1 GAAACTGATATGATAGTTTCAGTTGGGTCTAATC-CATTAGGCCTTGACTTTATCCAATT
782456 GTGACTTCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 1 0.02
66 53 0.98
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (66 bp):
GAAACTGATATGATAGTTTCAGTTGGGTCTAATCCATTAGGCCTTGACTTTATCCAATTTTCACT
T
Found at i:784495 original size:84 final size:84
Alignment explanation
Indices: 784393--784654 Score: 472
Period size: 84 Copynumber: 3.1 Consensus size: 84
784383 CGTGGTTTTC
* * *
784393 GTGGCCGTGGACGTGGAGGATTCAATGGAC-CTCAGTTTAATAGGCAGCAAGATGGAGGATACAA
1 GTGGCCGTGGACGCGGAGGATACAATGG-CTCTCAGTTTGATAGGCAGCAAGATGGAGGATACAA
784457 TTATGAAGCCCCTCCCCAAG
65 TTATGAAGCCCCTCCCCAAG
784477 GTGGCCGTGGACGCGGAGGATACAATGGCTCTCAGTTTGATAGGCAGCAAGATGGAGGATACAAT
1 GTGGCCGTGGACGCGGAGGATACAATGGCTCTCAGTTTGATAGGCAGCAAGATGGAGGATACAAT
784542 TATGAAGCCCCTCCCCAAG
66 TATGAAGCCCCTCCCCAAG
*
784561 GTGGCCGTGGACGCGGAGGATACAATGGCTCTCAGTTTGATAGGCAGCCAGATGGAGGATACAAT
1 GTGGCCGTGGACGCGGAGGATACAATGGCTCTCAGTTTGATAGGCAGCAAGATGGAGGATACAAT
784626 TATGAAGCCCCTCCCCAAG
66 TATGAAGCCCCTCCCCAAG
784645 GTGGCCGTGG
1 GTGGCCGTGG
784655 TGGGTTTTCT
Statistics
Matches: 173, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
83 1 0.01
84 172 0.99
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (84 bp):
GTGGCCGTGGACGCGGAGGATACAATGGCTCTCAGTTTGATAGGCAGCAAGATGGAGGATACAAT
TATGAAGCCCCTCCCCAAG
Found at i:786804 original size:13 final size:13
Alignment explanation
Indices: 786786--786814 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
786776 TATTGACATT
786786 ATATCATGTAGAA
1 ATATCATGTAGAA
786799 ATATCATGTAGAA
1 ATATCATGTAGAA
786812 ATA
1 ATA
786815 GAGAAAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (13 bp):
ATATCATGTAGAA
Found at i:800240 original size:3 final size:3
Alignment explanation
Indices: 800232--800286 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
800222 ATCCTAATAT
800232 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
800280 ATG ATG A
1 ATG ATG A
800287 ATTGACGATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:800533 original size:2 final size:2
Alignment explanation
Indices: 800526--800581 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
800516 ATTTCAATTT
* * * * *
800526 TA TA TA TA TA TA TA TA TA TC TA TA CA TA CA TA CA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
800568 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
800582 ACTGCTTTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:803259 original size:14 final size:13
Alignment explanation
Indices: 803224--803262 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
803214 TGAATTATAA
803224 TAAAATATTTAATT
1 TAAAAT-TTTAATT
*
803238 TAATATTTTAATAT
1 TAAAATTTTAAT-T
803252 TAAAATTTTAA
1 TAAAATTTTAA
803263 AATATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAAATTTTAATT
Found at i:819826 original size:20 final size:20
Alignment explanation
Indices: 819787--819828 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
819777 TTATGCAATA
*
819787 ATATAAAATACCATATAAAT
1 ATATAAAATACCATACAAAT
*
819807 ATATAAAATACCATGCAAAT
1 ATATAAAATACCATACAAAT
819827 AT
1 AT
819829 GTAATCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAAATACCATACAAAT
Found at i:819975 original size:25 final size:24
Alignment explanation
Indices: 819946--819994 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
819936 TAGAATATTA
*
819946 ATCATGTAATAACATATAATATCAT
1 ATCATGTAATAA-ATATAAAATCAT
819971 ATCATGTAATAAATATAAAATCAT
1 ATCATGTAATAAATATAAAATCAT
819995 GCAACAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (24 bp):
ATCATGTAATAAATATAAAATCAT
Found at i:820012 original size:24 final size:24
Alignment explanation
Indices: 819978--820064 Score: 58
Period size: 24 Copynumber: 3.6 Consensus size: 24
819968 CATATCATGT
819978 AATAAAT--ATAAAATCATGCAAC
1 AATAAATAAATAAAATCATGCAAC
*
820000 AATAAATAAATAAATAACTATGC-A-
1 AATAAATAAATAAA-ATC-ATGCAAC
* *
820024 AATAAATATATTAATAATCATACAATC
1 AATAAATA-AATAA-AATCATGCAA-C
820051 ACAT-AATAAATAAA
1 A-ATAAATAAATAAA
820065 TAAATAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
22 7 0.14
24 16 0.32
25 11 0.22
26 9 0.18
27 5 0.10
28 2 0.04
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.26
Consensus pattern (24 bp):
AATAAATAAATAAAATCATGCAAC
Found at i:820116 original size:20 final size:19
Alignment explanation
Indices: 820068--820131 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 19
820058 AAATAAATAA
*
820068 ATAATCATGTAATTAATAAT
1 ATAATCATGCAATTAA-AAT
*
820088 GTAAATCATGCAATTAAACAT
1 AT-AATCATGCAATTAAA-AT
*
820109 ATAATCATGCAAATAAAAAT
1 ATAATCATGC-AATTAAAAT
820129 ATA
1 ATA
820132 TAAACCATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (19 bp):
ATAATCATGCAATTAAAAT
Found at i:820232 original size:32 final size:32
Alignment explanation
Indices: 820181--820292 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 32
820171 AGCAAATAGT
* *
820181 AATATATAAACCATACAAATAAACATGTAATTA
1 AATATAT-AATCATGCAAATAAACATGTAATTA
*
820214 AATACATAATCATGCAAAT--A-A--TAA-TA
1 AATATATAATCATGCAAATAAACATGTAATTA
* * *
820240 TATATA-AATGATGCAAATAAACATGCAATTA
1 AATATATAATCATGCAAATAAACATGTAATTA
820271 AATATATAATCATGCAAATAAA
1 AATATATAATCATGCAAATAAA
820293 TATATTAAGC
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
25 11 0.17
26 6 0.10
27 4 0.06
28 1 0.02
29 1 0.02
30 3 0.05
31 7 0.11
32 24 0.38
33 6 0.10
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (32 bp):
AATATATAATCATGCAAATAAACATGTAATTA
Found at i:820266 original size:112 final size:109
Alignment explanation
Indices: 820089--820297 Score: 312
Period size: 112 Copynumber: 1.9 Consensus size: 109
820079 ATTAATAATG
* *
820089 TAAATCATGCAATTAAACATATAATCATGCAAATAAAAATATATAAACCATGCAAATAAATATGC
1 TAAATCATGCAATTAAACACATAATCATGCAAATAAAAATATATAAACCATGCAAATAAACATGC
820154 AATTAAATATATAATCAAGCAAATAGTAATATATAAACCATACAAA
66 AATTAAATATATAATCAAGCAAATA--AATATATAAACCATACAAA
* * **
820200 TAAA-CATGTAATTAAATACATAATCATGCAAATAATAATATATATAAATGATGCAAATAAACAT
1 TAAATCATGCAATTAAACACATAATCATGCAAATAA-AA-ATATATAAACCATGCAAATAAACAT
*
820264 GCAATTAAATATATAATCATGCAAATAAATATAT
64 GCAATTAAATATATAATCAAGCAAATAAATATAT
820298 TAAGCAAATA
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
110 35 0.39
111 6 0.07
112 48 0.54
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (109 bp):
TAAATCATGCAATTAAACACATAATCATGCAAATAAAAATATATAAACCATGCAAATAAACATGC
AATTAAATATATAATCAAGCAAATAAATATATAAACCATACAAA
Found at i:820270 original size:57 final size:56
Alignment explanation
Indices: 820089--820291 Score: 293
Period size: 55 Copynumber: 3.6 Consensus size: 56
820079 ATTAATAATG
*
820089 TAAATCATGCAATTAAACATATAATCATGCAAATAA-AAATATATAAACCATGCAAA
1 TAAA-CATGCAATTAAATATATAATCATGCAAATAATAAATATATAAACCATGCAAA
* * * *
820145 TAAATATGCAATTAAATATATAATCAAGCAAATAGT-AATATATAAACCATACAAA
1 TAAACATGCAATTAAATATATAATCATGCAAATAATAAATATATAAACCATGCAAA
* * **
820200 TAAACATGTAATTAAATACATAATCATGCAAATAATAATATATATAAATGATGCAAA
1 TAAACATGCAATTAAATATATAATCATGCAAATAATAA-ATATATAAACCATGCAAA
820257 TAAACATGCAATTAAATATATAATCATGCAAATAA
1 TAAACATGCAATTAAATATATAATCATGCAAATAA
820292 ATATATTAAG
Statistics
Matches: 129, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
55 76 0.59
56 5 0.04
57 48 0.37
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (56 bp):
TAAACATGCAATTAAATATATAATCATGCAAATAATAAATATATAAACCATGCAAA
Found at i:820284 original size:20 final size:20
Alignment explanation
Indices: 820256--820297 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
820246 AATGATGCAA
*
820256 ATAAACATGCAATTAAATAT
1 ATAAACATGCAAATAAATAT
*
820276 ATAATCATGCAAATAAATAT
1 ATAAACATGCAAATAAATAT
820296 AT
1 AT
820298 TAAGCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAAACATGCAAATAAATAT
Found at i:820289 original size:16 final size:16
Alignment explanation
Indices: 820270--820342 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 16
820260 ACATGCAATT
*
820270 AAATATATAATCATGC
1 AAATAAATAATCATGC
* *
820286 AAATAAATATATTAAGC
1 AAATAAATA-ATCATGC
* *
820303 AAATAAATTATCATAC
1 AAATAAATAATCATGC
820319 AAATATAATATTAGTCATGC
1 AAATA-AATA--A-TCATGC
820339 AAAT
1 AAAT
820343 TCATACAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
16 17 0.40
17 16 0.37
19 1 0.02
20 9 0.21
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (16 bp):
AAATAAATAATCATGC
Found at i:820341 original size:20 final size:18
Alignment explanation
Indices: 820261--820342 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 18
820251 TGCAAATAAA
*
820261 CATGCAATTAAATATATAAT
1 CATGCAAATAAATAT-T-AT
820281 CATGCAAATAAATA-TAT
1 CATGCAAATAAATATTAT
* *
820298 TAAGCAAAT-AA-ATTAT
1 CATGCAAATAAATATTAT
*
820314 CATACAAATATAATATTAGT
1 CATGCAAATA-AATATTA-T
820334 CATGCAAAT
1 CATGCAAAT
820343 TCATACAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 1 0.02
16 11 0.22
17 9 0.18
18 3 0.06
19 4 0.08
20 22 0.44
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (18 bp):
CATGCAAATAAATATTAT
Found at i:832576 original size:7 final size:7
Alignment explanation
Indices: 832564--832599 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
832554 GCACATAAGC
*
832564 CTACAGA
1 CTACAGG
832571 CTACAGG
1 CTACAGG
832578 CTACAGG
1 CTACAGG
832585 CTACAGG
1 CTACAGG
832592 CTACAGG
1 CTACAGG
832599 C
1 C
832600 ACCTGATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.14
Consensus pattern (7 bp):
CTACAGG
Found at i:835597 original size:27 final size:27
Alignment explanation
Indices: 835567--835635 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
835557 TACATTGTTT
*
835567 AAAATTCAAGTTTAGAAATTAAAACCA
1 AAAATTCAAGTTTAGAAATTAAAACAA
*
835594 AAAATTCAAGTTAAGAAATTAAAACAA
1 AAAATTCAAGTTTAGAAATTAAAACAA
835621 AAAATTC-AGTTTAGA
1 AAAATTCAAGTTTAGA
835636 TTAAACATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 7 0.18
27 32 0.82
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (27 bp):
AAAATTCAAGTTTAGAAATTAAAACAA
Found at i:837798 original size:5 final size:5
Alignment explanation
Indices: 837781--837813 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
837771 GTCGACGAAA
*
837781 AAAAT AAAGT AAAAT AAAAT AAAAT AAAA- AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
837814 GGAAATGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:841248 original size:12 final size:14
Alignment explanation
Indices: 841217--841245 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
841207 TTTAATTAAT
841217 TATTTAATTTTATA
1 TATTTAATTTTATA
841231 TATTTAATTTTATA
1 TATTTAATTTTATA
841245 T
1 T
841246 TTATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTAATTTTATA
Found at i:849772 original size:22 final size:22
Alignment explanation
Indices: 849744--849787 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
849734 CTAAATCTTC
*
849744 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
849766 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
849788 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:853464 original size:25 final size:23
Alignment explanation
Indices: 853430--853501 Score: 92
Period size: 25 Copynumber: 3.1 Consensus size: 23
853420 TTTGAAAGGG
*
853430 TTCGGCAATGAAGGCCTAAACAGGA
1 TTCGGCAATGAAGGCCTAAA-A-AA
853455 TTCGGCAATGAAGGCCTAAAAAA
1 TTCGGCAATGAAGGCCTAAAAAA
* *
853478 GTCGGCAATGAAGG-CTGAAAAA
1 TTCGGCAATGAAGGCCTAAAAAA
853500 TT
1 TT
853502 TTCTTCCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
22 8 0.19
23 14 0.33
24 1 0.02
25 20 0.47
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (23 bp):
TTCGGCAATGAAGGCCTAAAAAA
Found at i:853668 original size:22 final size:22
Alignment explanation
Indices: 853640--853683 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
853630 CTAAATCTTC
*
853640 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
853662 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
853684 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:864605 original size:20 final size:20
Alignment explanation
Indices: 864580--864635 Score: 96
Period size: 20 Copynumber: 2.8 Consensus size: 20
864570 CATACAGCAC
864580 AAAAATAGAATATATTATCT
1 AAAAATAGAATATATTATCT
864600 AAAAATAGAAGT-TATTATCT
1 AAAAATAGAA-TATATTATCT
864620 AAAAATAGAATATATT
1 AAAAATAGAATATATT
864636 CAATGCTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (20 bp):
AAAAATAGAATATATTATCT
Found at i:866307 original size:16 final size:16
Alignment explanation
Indices: 866282--866319 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
866272 TAATTTTATT
*
866282 TAATTAAATTAAAATA
1 TAATTTAATTAAAATA
*
866298 TAATTTAATTTAAATA
1 TAATTTAATTAAAATA
866314 T-ATTTA
1 TAATTTA
866320 TAGTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAATTAAAATA
Found at i:870934 original size:13 final size:13
Alignment explanation
Indices: 870916--870945 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
870906 TATAATTCGA
*
870916 ATTAAATTTATAT
1 ATTAAATATATAT
870929 ATTAAATATATAT
1 ATTAAATATATAT
870942 ATTA
1 ATTA
870946 TTAGAATACA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAAATATATAT
Found at i:871408 original size:18 final size:18
Alignment explanation
Indices: 871385--871423 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
871375 AAAATAATTT
871385 AATAAAATTTC-TTAAGTA
1 AATAAAATTTCATTAA-TA
*
871403 AATAAATTTTCATTAATA
1 AATAAAATTTCATTAATA
871421 AAT
1 AAT
871424 TTGATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
AATAAAATTTCATTAATA
Found at i:883153 original size:18 final size:19
Alignment explanation
Indices: 883118--883159 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
883108 TAAATTGAAT
*
883118 TATATATTTTATTTATTTTC
1 TATATATTTTA-TAATTTTC
*
883138 TATATATTTTA-AATTTTT
1 TATATATTTTATAATTTTC
883156 TATA
1 TATA
883160 AAATAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATATTTTATAATTTTC
Found at i:883795 original size:2 final size:2
Alignment explanation
Indices: 883790--883829 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
883780 AGAAACATTG
*
883790 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CG CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
883830 AAGCTGGTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:896938 original size:31 final size:28
Alignment explanation
Indices: 896903--896975 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 28
896893 AATATCATAA
*
896903 ATGATTTATAAATTATAATAAAATATTTAAT
1 ATGATTT-TAAATTATAA-AAAA-ATTGAAT
*
896934 ATGATATTTAAATTTTAAAAAAATTGAAT
1 ATGAT-TTTAAATTATAAAAAAATTGAAT
* *
896963 GTGATTTTGAATT
1 ATGATTTTAAATT
896976 GTATAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.19
29 10 0.27
30 4 0.11
31 14 0.38
32 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (28 bp):
ATGATTTTAAATTATAAAAAAATTGAAT
Found at i:905341 original size:21 final size:21
Alignment explanation
Indices: 905300--905341 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
905290 CTTGTCGTCC
*
905300 CTGTTGTGCCCGTCGTCGTTG
1 CTGTTGTGCCCGGCGTCGTTG
* *
905321 CTGTTGTGCCTGGCGTTGTTG
1 CTGTTGTGCCCGGCGTCGTTG
905342 GGGTCGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.36, T:0.40
Consensus pattern (21 bp):
CTGTTGTGCCCGGCGTCGTTG
Found at i:909688 original size:14 final size:14
Alignment explanation
Indices: 909671--909704 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
909661 ATATATATAT
909671 ATATATACACACAC
1 ATATATACACACAC
* *
909685 ATATATACATACAT
1 ATATATACACACAC
909699 ATATAT
1 ATATAT
909705 GATCAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATATACACACAC
Found at i:909702 original size:12 final size:12
Alignment explanation
Indices: 909661--909703 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
909651 ATATTATAAT
* *
909661 ATATATATATAT
1 ATATATACATAC
* *
909673 ATATACACACAC
1 ATATATACATAC
909685 ATATATACATAC
1 ATATATACATAC
909697 ATATATA
1 ATATATA
909704 TGATCAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATATACATAC
Found at i:911956 original size:21 final size:21
Alignment explanation
Indices: 911932--911993 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
911922 AAAATATAAA
*
911932 AAATATATTTTTAATTTTATT
1 AAATATATTTTAAATTTTATT
*
911953 AAATTTATTTATAAATTTTA-T
1 AAATATATTT-TAAATTTTATT
*
911974 AAA-A-ATTTTAAATTATATT
1 AAATATATTTTAAATTTTATT
911993 A
1 A
911994 TTTTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
21 13 0.37
22 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATATATTTTAAATTTTATT
Found at i:912000 original size:40 final size:40
Alignment explanation
Indices: 911938--912054 Score: 94
Period size: 40 Copynumber: 2.9 Consensus size: 40
911928 TAAAAAATAT
* * **
911938 ATTTTTAATTTTATTAAATTTAT-TTATAAATTTTATAAAA
1 ATTTTAAATTATATTATTTTTATATTATAAA-TTTATAAAA
* ** *
911978 ATTTTAAATTATATTATTTTTATATTTTTTATTTATATAA
1 ATTTTAAATTATATTATTTTTATATTATAAATTTATAAAA
** *
912018 ATTTTGTATTATATTATTATATTATATT-TAAAATTAT
1 ATTTTAAATTATATTATT-T-TTATATTATAAATTTAT
912055 TAAATCTACT
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
40 43 0.70
41 11 0.18
42 7 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (40 bp):
ATTTTAAATTATATTATTTTTATATTATAAATTTATAAAA
Found at i:912042 original size:13 final size:13
Alignment explanation
Indices: 911985--912045 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
911975 AAAATTTTAA
911985 ATTATATTAT-TT
1 ATTATATTATATT
*
911997 -TTATATT-TTTT
1 ATTATATTATATT
*
912008 ATT-TATATAAATT
1 ATTATAT-TATATT
*
912021 -TTGTATTATATT
1 ATTATATTATATT
912033 ATTATATTATATT
1 ATTATATTATATT
912046 TAAAATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
10 1 0.03
11 12 0.31
12 10 0.26
13 16 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (13 bp):
ATTATATTATATT
Found at i:915236 original size:13 final size:13
Alignment explanation
Indices: 915205--915239 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
915195 ATTTATTTAC
*
915205 TTTTAATTTTATA
1 TTTTAATTTAATA
915218 -TTTAATTTAATA
1 TTTTAATTTAATA
915230 TTTTAATTTA
1 TTTTAATTTA
915240 TTCTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTAATTTAATA
Found at i:915330 original size:13 final size:12
Alignment explanation
Indices: 915278--915342 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 12
915268 AGTTAAAAAA
915278 TTAT-AAAATAT
1 TTATAAAAATAT
*
915289 TTATAAATTATGAT
1 TTATAAA-AAT-AT
915303 ATTATATAAAATAT
1 -TTATA-AAAATAT
915317 TTATAAAAATTAT
1 TTATAAAAA-TAT
*
915330 TTTTATAAAATAT
1 TTATA-AAAATAT
915343 GTCAATTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 4 0.09
12 6 0.14
13 17 0.39
14 8 0.18
15 7 0.16
16 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TTATAAAAATAT
Found at i:918892 original size:33 final size:30
Alignment explanation
Indices: 918855--918944 Score: 83
Period size: 33 Copynumber: 2.8 Consensus size: 30
918845 ACAAGTGATC
*
918855 AAATTATATCCAAACAATAAAAAATAAATAATT
1 AAATTATAT-CAAA-AATAAAAAATAAA-AATA
* *
918888 AAATTATAT-TAAAATAATAAATAAAAATA
1 AAATTATATCAAAAATAAAAAATAAAAATA
*
918917 AAATTATATTCAAATAATGAAACAATAA
1 AAATTATA-TCAAA-AAT-AAAAAATAA
918945 TAAAGTAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 11 0.23
30 13 0.28
31 4 0.09
32 3 0.06
33 16 0.34
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (30 bp):
AAATTATATCAAAAATAAAAAATAAAAATA
Found at i:918909 original size:26 final size:27
Alignment explanation
Indices: 918872--918934 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
918862 ATCCAAACAA
*
918872 TAAAA-AATAAAT-AATTAAATTATAT
1 TAAAATAATAAATAAATAAAATTATAT
918897 TAAAATAATAAATAAAAATAAAATTATAT
1 TAAAATAATAAAT--AAATAAAATTATAT
*
918926 TCAAATAAT
1 TAAAATAAT
918935 GAAACAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 5 0.16
26 7 0.22
29 20 0.62
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAAATAATAAATAAATAAAATTATAT
Found at i:918931 original size:29 final size:29
Alignment explanation
Indices: 918870--918948 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
918860 ATATCCAAAC
* *
918870 AATAAAAAATAAATAATTAAATTATATTAA
1 AATAATAAATAAA-AATAAAATTATATTAA
*
918900 AATAATAAATAAAAATAAAATTATATTCA
1 AATAATAAATAAAAATAAAATTATATTAA
* *
918929 AATAATGAAACAATAATAAA
1 AATAAT-AAATAAAAATAAA
918949 GTAGTGGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (29 bp):
AATAATAAATAAAAATAAAATTATATTAA
Found at i:920449 original size:37 final size:37
Alignment explanation
Indices: 920398--920475 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
920388 CAAATTAGAA
* *
920398 GGAGCAAGAGGGAAGCAGTTAAGCAAGAGAGTAAGAG
1 GGAGCAAGAAGGAAGCAGTCAAGCAAGAGAGTAAGAG
* *
920435 GGAGTAAGAAGGAAGCAGTCGAGCAAGAGAGTAAGAG
1 GGAGCAAGAAGGAAGCAGTCAAGCAAGAGAGTAAGAG
920472 GGAG
1 GGAG
920476 GCAAAGATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.42, C:0.08, G:0.42, T:0.08
Consensus pattern (37 bp):
GGAGCAAGAAGGAAGCAGTCAAGCAAGAGAGTAAGAG
Found at i:921173 original size:2 final size:2
Alignment explanation
Indices: 921166--921200 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
921156 TTTTCATGTT
921166 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 T
921201 CTTTTAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:922135 original size:2 final size:2
Alignment explanation
Indices: 922128--922168 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
922118 ATTAGAGAAC
922128 AT AT AT AT AT AT 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 AT AT AT A
922169 AGCAAGATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:922197 original size:2 final size:2
Alignment explanation
Indices: 922190--922219 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
922180 ATTAGAGAAC
922190 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
922220 AACAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:923158 original size:2 final size:2
Alignment explanation
Indices: 923151--923190 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
923141 CAGAAAGTTC
923151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
923191 TAGACATAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:928962 original size:52 final size:52
Alignment explanation
Indices: 928901--929009 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
928891 TTTTTTCTGT
* *
928901 AAGTCAAACTTGCCTATTAAGAATC-CCTTTCCTTTTAAAATTCTTCTCTTAC
1 AAGTCAAACTTACCTATTAAGAATCACCTTT-CTCTTAAAATTCTTCTCTTAC
* * *
928953 AAGTCAAACTTACCTATTAAGAATCATCTTTCTCTTAGAATTTTTCTCTTAC
1 AAGTCAAACTTACCTATTAAGAATCACCTTTCTCTTAAAATTCTTCTCTTAC
929005 AAGTC
1 AAGTC
929010 TTCTTATCCA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 47 0.92
53 4 0.08
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (52 bp):
AAGTCAAACTTACCTATTAAGAATCACCTTTCTCTTAAAATTCTTCTCTTAC
Found at i:929341 original size:25 final size:25
Alignment explanation
Indices: 929312--929359 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
929302 ATGCACTTCT
929312 CACATCTTAAACCTTTAGCTCTTTC
1 CACATCTTAAACCTTTAGCTCTTTC
* *
929337 CACATCTTGAACTTTTAGCTCTT
1 CACATCTTAAACCTTTAGCTCTT
929360 CTACGTCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (25 bp):
CACATCTTAAACCTTTAGCTCTTTC
Found at i:929372 original size:24 final size:25
Alignment explanation
Indices: 929325--929372 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
929315 ATCTTAAACC
*
929325 TTTAGCTCTTTCCACATCTTGAACT
1 TTTAGCTCTTTCCACATCTCGAACT
* *
929350 TTTAGCTC-TTCTACGTCTCGAAC
1 TTTAGCTCTTTCCACATCTCGAAC
929373 CTTCGACTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (25 bp):
TTTAGCTCTTTCCACATCTCGAACT
Found at i:930049 original size:52 final size:52
Alignment explanation
Indices: 929963--930119 Score: 226
Period size: 52 Copynumber: 3.0 Consensus size: 52
929953 TATAACCATA
* * * *
929963 CAAACTTGCCCATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGT
* *
930015 CAAACTTGCCTATTAAGAATCCCTTTTCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGT
* *
930067 CAAACTTACCTATTAAGAATCATCTTTT-TCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-TCTTTTCTCTTAGAATTCTTCTCTTGCAAGT
930119 C
1 C
930120 TTCTTATCCA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 89 0.95
53 5 0.05
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:930156 original size:11 final size:11
Alignment explanation
Indices: 930140--930175 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
930130 TCTAGCAATA
930140 TCTAACAAATC
1 TCTAACAAATC
930151 TCTAACAAATC
1 TCTAACAAATC
* *
930162 CCAAACAAATC
1 TCTAACAAATC
930173 TCT
1 TCT
930176 TATGAGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:958498 original size:14 final size:16
Alignment explanation
Indices: 958479--958513 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
958469 AATTTATGGG
958479 TTTTAAATTT-TATT-
1 TTTTAAATTTATATTA
958493 TTTTAAATTTATATTA
1 TTTTAAATTTATATTA
958509 TTTTA
1 TTTTA
958514 TTAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 4 0.21
16 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAAATTTATATTA
Found at i:958602 original size:18 final size:18
Alignment explanation
Indices: 958579--958613 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
958569 ATAAAAATTT
958579 AAAATATATAAATTAATA
1 AAAATATATAAATTAATA
*
958597 AAAATATATAATTTAAT
1 AAAATATATAAATTAAT
958614 TCGATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATATATAAATTAATA
Found at i:958614 original size:56 final size:55
Alignment explanation
Indices: 958501--958604 Score: 131
Period size: 56 Copynumber: 1.9 Consensus size: 55
958491 TTTTTTAAAT
* **
958501 TTATATTATTTTATTAAAAATTTTAATATACTTAAATTAATTTATATATAAAATAA
1 TTATATTATTTTATTAAAAATTTAAATATAC-TAAATTAATAAATATATAAAATAA
* *
958557 TTATTTTATTTTA-TAAAAATTTAAAATATA-TAAATTAATAAAAATATA
1 TTATATTATTTTATTAAAAATTT-AAATATACTAAATTAATAAATATATA
958605 TAATTTAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
54 15 0.36
55 9 0.21
56 18 0.43
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (55 bp):
TTATATTATTTTATTAAAAATTTAAATATACTAAATTAATAAATATATAAAATAA
Found at i:958682 original size:12 final size:12
Alignment explanation
Indices: 958649--958696 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
958639 TATTTTAATC
958649 TAAATTTAATAT
1 TAAATTTAATAT
*
958661 ATATATTTAATAT
1 -TAAATTTAATAT
958674 TAAATTTAA-ATT
1 TAAATTTAATA-T
*
958686 TAAATTAAATA
1 TAAATTTAATA
958697 AAAAAAATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 1 0.03
12 17 0.57
13 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATTTAATAT
Found at i:960190 original size:24 final size:24
Alignment explanation
Indices: 960161--960208 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
960151 TAAGTATATA
960161 GCAAGATAAAAATAAAAATTAGTT
1 GCAAGATAAAAATAAAAATTAGTT
960185 GCAAGATAAAAATAAAAATTAGTT
1 GCAAGATAAAAATAAAAATTAGTT
960209 ATGTAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.25
Consensus pattern (24 bp):
GCAAGATAAAAATAAAAATTAGTT
Found at i:962352 original size:18 final size:17
Alignment explanation
Indices: 962303--962359 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
962293 TTTATATTTG
962303 ATTTAAATAATTTATTA-
1 ATTTAAATAATTT-TTAT
962320 ATTT-AATCAATTTTTAT
1 ATTTAAAT-AATTTTTAT
962337 ATTTAAATATATTTTTATT
1 ATTTAAATA-ATTTTTA-T
962356 ATTT
1 ATTT
962360 TAATTAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.17
17 14 0.40
18 10 0.29
19 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAATAATTTTTAT
Found at i:962456 original size:23 final size:24
Alignment explanation
Indices: 962379--962456 Score: 88
Period size: 23 Copynumber: 3.2 Consensus size: 24
962369 AAATATATCG
*
962379 AATTTAAATTTAAGTATAAATAATTA
1 AATTTATATTTAA-TAT-AATAATTA
*
962405 AATTT-TATTTAATATAAAAATTA
1 AATTTATATTTAATATAATAATTA
* *
962428 AATTTAT-TTTTATATATTAATTA
1 AATTTATATTTAATATAATAATTA
962451 AATTTA
1 AATTTA
962457 ATGGAATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 31 0.67
24 4 0.09
25 6 0.13
26 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (24 bp):
AATTTATATTTAATATAATAATTA
Found at i:962587 original size:24 final size:23
Alignment explanation
Indices: 962526--962592 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 23
962516 AAATTCAATC
*
962526 AAATTTAAATTAAATATGAAATCTT
1 AAATTTAAATTAAAT-T-AAAGCTT
962551 AAATTTTAAATTAAATTAAAGCTT
1 AAA-TTTAAATTAAATTAAAGCTT
*
962575 AAATTTAATATTATATTA
1 AAATTTAA-ATTAAATTA
962593 GTTTGACTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
23 5 0.13
24 17 0.45
25 4 0.11
26 12 0.32
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
AAATTTAAATTAAATTAAAGCTT
Found at i:973430 original size:19 final size:19
Alignment explanation
Indices: 973406--973443 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
973396 CTCAAAATTT
973406 GCCAGCACAGAAGCTATAA
1 GCCAGCACAGAAGCTATAA
973425 GCCAGCACAGAAGCTATAA
1 GCCAGCACAGAAGCTATAA
973444 AATCGAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.11
Consensus pattern (19 bp):
GCCAGCACAGAAGCTATAA
Found at i:976124 original size:82 final size:81
Alignment explanation
Indices: 975967--976129 Score: 236
Period size: 82 Copynumber: 2.0 Consensus size: 81
975957 TATTTAATTA
* * * * *
975967 ACATAAGTAATTTCTTTTAATCACATATAAATGATCTTTTTACTGAATGTGGGATACACTACATT
1 ACATAAGTAATTTCTTTTAAACACATATAAATGATCCTTCTACTCAATATGGGATACACTACATT
* *
976032 TTAAATTACCAACAAT
66 CTAAACTACCAACAAT
* *
976048 ACATAAGTAATTTCTTTTAAACTATATATAAATGATCCTTCTACTCAATATGGGATACACTATAT
1 ACATAAGTAATTTCTTTTAAAC-ACATATAAATGATCCTTCTACTCAATATGGGATACACTACAT
976113 TCTAAACTACCAACAAT
65 TCTAAACTACCAACAAT
976130 CCCGTACTAG
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 21 0.29
82 51 0.71
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (81 bp):
ACATAAGTAATTTCTTTTAAACACATATAAATGATCCTTCTACTCAATATGGGATACACTACATT
CTAAACTACCAACAAT
Found at i:981289 original size:82 final size:81
Alignment explanation
Indices: 981180--981338 Score: 212
Period size: 82 Copynumber: 2.0 Consensus size: 81
981170 CTTAATTAAT
* * * * *
981180 ATAAGTAATTTCTTTAAATCATATATAAATTATCTTTCT-TCTCAACGAGAGATACACTACGTTC
1 ATAAGTAATTTCTTTAAATCACATATAAATAATCTTTATAT-TCAACGAGAGATACACCACATTC
981244 TAAACTACCAACAGTAC
65 TAAACTACCAACAGTAC
* * * *
981261 ATAAGTAATTTCTTTTAAATCACATATAAATAATCTTTATATTTAATGTGGGATACACCACATTC
1 ATAAGTAATTTC-TTTAAATCACATATAAATAATCTTTATATTCAACGAGAGATACACCACATTC
981326 TAAACTACCAACA
65 TAAACTACCAACA
981339 ATAAAAGTGG
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 12 0.18
82 54 0.81
83 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (81 bp):
ATAAGTAATTTCTTTAAATCACATATAAATAATCTTTATATTCAACGAGAGATACACCACATTCT
AAACTACCAACAGTAC
Found at i:981624 original size:21 final size:21
Alignment explanation
Indices: 981594--981636 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
981584 GAGAAGAGAG
981594 TATGCGAATGGCAAATTTCCT
1 TATGCGAATGGCAAATTTCCT
*
981615 TATGCTAATGGCAAATTTCCT
1 TATGCGAATGGCAAATTTCCT
981636 T
1 T
981637 TCTTCTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (21 bp):
TATGCGAATGGCAAATTTCCT
Found at i:996692 original size:15 final size:12
Alignment explanation
Indices: 996658--996698 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
996648 ATTAATTAGT
*
996658 TTAATTTTTTTA
1 TTAAATTTTTTA
996670 TTAAATTTTTTA
1 TTAAATTTTTTA
996682 TTAAATTATTTT-
1 TTAAATT-TTTTA
996694 TTAAA
1 TTAAA
996699 AAATAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTAAATTTTTTA
Found at i:996740 original size:24 final size:23
Alignment explanation
Indices: 996703--996750 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
996693 TTTAAAAAAT
996703 AATTTCATAAATTTT-ACCTAAA
1 AATTTCATAAATTTTCACCTAAA
*
996725 AATTTCATATATATTTTCTCCTAAA
1 AATTTCATA-A-ATTTTCACCTAAA
996750 A
1 A
996751 CAATCATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 5 0.23
25 7 0.32
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTCATAAATTTTCACCTAAA
Found at i:1009796 original size:2 final size:2
Alignment explanation
Indices: 1009789--1009813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1009779 GTCAATTAAG
1009789 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 A
1009814 CACACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1013171 original size:2 final size:2
Alignment explanation
Indices: 1013164--1013191 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1013154 ATCATCAGAT
1013164 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1013192 TATCATCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1019856 original size:41 final size:42
Alignment explanation
Indices: 1019777--1019870 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 42
1019767 ATCGAAATTT
* *
1019777 ATTTTTATTTCTAAATTTTTCACTATTTACGTCAATTTA-AA
1 ATTTTTTTTTCTAAATTTTTCACCATTTACGTCAATTTAGAA
* * *
1019818 ATTTTTTTTTCTAAATTTTTTACCATTT-GGATCTATTTAGAA
1 ATTTTTTTTTCTAAATTTTTCACCATTTACG-TCAATTTAGAA
1019860 ATTTTCTTTTT
1 ATTTT-TTTTT
1019871 TTTTTTGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
40 1 0.02
41 32 0.71
42 7 0.16
43 5 0.11
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.59
Consensus pattern (42 bp):
ATTTTTTTTTCTAAATTTTTCACCATTTACGTCAATTTAGAA
Found at i:1019997 original size:25 final size:24
Alignment explanation
Indices: 1019951--1020011 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1019941 CATTTGAGAC
* * *
1019951 AAATTTTAAAAAATTTACCATTTG
1 AAATTTTTAAAAATTCACCATTGG
*
1019975 AAATTTTTAAAAATCTCATCATTGG
1 AAATTTTTAAAAAT-TCACCATTGG
*
1020000 ATAATTGTTAAA
1 A-AATTTTTAAA
1020012 TATTTTTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 13 0.43
25 8 0.27
26 9 0.30
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (24 bp):
AAATTTTTAAAAATTCACCATTGG
Found at i:1020284 original size:4 final size:4
Alignment explanation
Indices: 1020275--1020319 Score: 58
Period size: 4 Copynumber: 11.2 Consensus size: 4
1020265 ATAATCACTT
1020275 AATA AATA AATA AATA AATA AATA AGATA TAA-A AATA AA-A AATA A
1 AATA AATA AATA AATA AATA AATA A-ATA -AATA AATA AATA AATA A
1020320 TACCAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 5 0.14
4 27 0.73
5 4 0.11
6 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:1021390 original size:43 final size:43
Alignment explanation
Indices: 1021299--1021549 Score: 263
Period size: 43 Copynumber: 5.8 Consensus size: 43
1021289 TAAAAACTCC
* * *
1021299 TCTAAACAAAGGCTCCACAACTTTCAAGAAATAAATAAGGCTCC
1 TCTAAACAAAGGCTCAACAACTTT-AAAAAATAAATAAGGCTCT
** *
1021343 TCTAAGTAAAGGCTTAACAACTTTAAAAAATAAATAAGGCTCT
1 TCTAAACAAAGGCTCAACAACTTTAAAAAATAAATAAGGCTCT
* * * * **
1021386 TCTAAGCAGAGGCTCAACAACTTTGAAAAATAAAAAAAAACTCCT
1 TCTAAACAAAGGCTCAACAACTTTAAAAAAT-AAATAAGGCT-CT
** *
1021431 T-TAAACAAAGGCTCAATGACTTTGAAAAATAAATAAGGCTCT
1 TCTAAACAAAGGCTCAACAACTTTAAAAAATAAATAAGGCTCT
* * *
1021473 TTTAAACAGAA-GCTCAACGACTTTAAAAAATAAATAAAGCTCT
1 TCTAAACA-AAGGCTCAACAACTTTAAAAAATAAATAAGGCTCT
* * *
1021516 TCTAAATAGAGGCTCAATAACTTTAAAAAATAAA
1 TCTAAACAAAGGCTCAACAACTTTAAAAAATAAA
1021550 GCTTATTGAC
Statistics
Matches: 174, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
42 4 0.02
43 113 0.65
44 54 0.31
45 3 0.02
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.24
Consensus pattern (43 bp):
TCTAAACAAAGGCTCAACAACTTTAAAAAATAAATAAGGCTCT
Found at i:1021453 original size:87 final size:86
Alignment explanation
Indices: 1021299--1021549 Score: 263
Period size: 87 Copynumber: 2.9 Consensus size: 86
1021289 TAAAAACTCC
* * * ** * ** * *
1021299 TCTAAACA-AAGGCTCCACAACTTTCAAGAAATAAATAAGGCTCCTCTAAGTAAAGGCTTAACAA
1 TCTAAACAGAA-GCTCAACAACTTT-AAAAAATAAAAAAAACTCTTCTAAACAAAGGCTCAATAA
1021363 CTTTAAAAAATAAATAAGGCTCT
64 CTTTAAAAAATAAATAAGGCTCT
* * * *
1021386 TCTAAGCAGAGGCTCAACAACTTTGAAAAATAAAAAAAAACTCCTT-TAAACAAAGGCTCAATGA
1 TCTAAACAGAAGCTCAACAACTTTAAAAAAT-AAAAAAAACT-CTTCTAAACAAAGGCTCAATAA
*
1021450 CTTTGAAAAATAAATAAGGCTCT
64 CTTTAAAAAATAAATAAGGCTCT
* * * * * *
1021473 TTTAAACAGAAGCTCAACGACTTTAAAAAATAAATAAAGCTCTTCTAAATAGAGGCTCAATAACT
1 TCTAAACAGAAGCTCAACAACTTTAAAAAATAAAAAAAACTCTTCTAAACAAAGGCTCAATAACT
1021538 TTAAAAAATAAA
66 TTAAAAAATAAA
1021550 GCTTATTGAC
Statistics
Matches: 134, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
85 3 0.02
86 41 0.31
87 87 0.65
88 3 0.02
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.24
Consensus pattern (86 bp):
TCTAAACAGAAGCTCAACAACTTTAAAAAATAAAAAAAACTCTTCTAAACAAAGGCTCAATAACT
TTAAAAAATAAATAAGGCTCT
Found at i:1021509 original size:130 final size:131
Alignment explanation
Indices: 1021290--1021549 Score: 353
Period size: 130 Copynumber: 2.0 Consensus size: 131
1021280 TTAATAATAT
* **
1021290 AAAAACTCCTCTAAACAAAGGCTCCACAACTTTCAAGAAATAAATAAGGCTCCTCTAAGTAAAGG
1 AAAAACTCCTCTAAACAAAGGCTCAACAACTTTCAAGAAATAAATAAGGCTCCTCTAAACAAAGG
* * * *
1021355 CTTAACAACTTTAAAAAATAAATAAGGCTCTTCTAAGCAGAGGCTCAACAACTTTGAAAAATAAA
66 CTCAACAACTTTAAAAAATAAATAAAGCTCTTCTAAACAGAGGCTCAACAACTTTAAAAAATAAA
1021420 A
131 A
* ** * * *
1021421 AAAAACTCCTTTAAACAAAGGCTCAATGACTTTGAA-AAATAAATAAGGCTCTTTTAAACAGAA-
1 AAAAACTCCTCTAAACAAAGGCTCAACAACTTTCAAGAAATAAATAAGGCTCCTCTAAACA-AAG
* * *
1021484 GCTCAACGACTTTAAAAAATAAATAAAGCTCTTCTAAATAGAGGCTCAATAACTTTAAAAAATAA
65 GCTCAACAACTTTAAAAAATAAATAAAGCTCTTCTAAACAGAGGCTCAACAACTTTAAAAAATAA
1021549 A
130 A
1021550 GCTTATTGAC
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
130 79 0.71
131 33 0.29
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.24
Consensus pattern (131 bp):
AAAAACTCCTCTAAACAAAGGCTCAACAACTTTCAAGAAATAAATAAGGCTCCTCTAAACAAAGG
CTCAACAACTTTAAAAAATAAATAAAGCTCTTCTAAACAGAGGCTCAACAACTTTAAAAAATAAA
A
Found at i:1021821 original size:33 final size:33
Alignment explanation
Indices: 1021784--1021846 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1021774 TCATGCACCG
* * *
1021784 AACATTCTCACATACAATGCATGTTATGCACTA
1 AACATTCACAAATACAATGCATGCTATGCACTA
* *
1021817 AACATTCAGAAATGCAATGCATGCTATGCA
1 AACATTCACAAATACAATGCATGCTATGCA
1021847 AATGTCAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (33 bp):
AACATTCACAAATACAATGCATGCTATGCACTA
Found at i:1023032 original size:8 final size:8
Alignment explanation
Indices: 1023021--1023050 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1023011 ATTTTTTCTC
1023021 TTTTTACA
1 TTTTTACA
1023029 TTTTTACA
1 TTTTTACA
*
1023037 TTTTTTCA
1 TTTTTACA
1023045 TTTTTA
1 TTTTTA
1023051 TTTTTTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTTACA
Found at i:1023056 original size:16 final size:15
Alignment explanation
Indices: 1023008--1023115 Score: 51
Period size: 16 Copynumber: 6.7 Consensus size: 15
1022998 AATTTAAGTC
1023008 TTCATTTTTTCTCTTTT
1 TTCATTTTTT-T-TTTT
* **
1023025 TACATTTTTACATTTT
1 TTCATTTTT-TTTTTT
1023041 TTCATTTTTATTTTTT
1 TTCATTTTT-TTTTTT
1023057 TATC-TCTTTTTTTTTT
1 T-TCAT-TTTTTTTTTT
*
1023073 TT--TTTCTTTTGTTT
1 TTCATTT-TTTTTTTT
*
1023087 TCCATTTTCTCTTTTTTTT
1 TTCA--TT-T-TTTTTTTT
1023106 TTCATTTTTT
1 TTCATTTTTT
1023116 ATCCATTATT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
13 2 0.03
14 9 0.12
15 4 0.06
16 27 0.38
17 16 0.22
18 2 0.03
19 12 0.17
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (15 bp):
TTCATTTTTTTTTTT
Found at i:1023073 original size:19 final size:18
Alignment explanation
Indices: 1023045--1023107 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
1023035 CATTTTTTCA
* *
1023045 TTTTTATTTTTTTATCTC
1 TTTTTTTTTTTTTTTCTC
1023063 TTTTTTTTTTTTTTTCT-
1 TTTTTTTTTTTTTTTCTC
* ***
1023080 TTTGTTTTCCATTTTCTC
1 TTTTTTTTTTTTTTTCTC
1023098 TTTTTTTTTT
1 TTTTTTTTTT
1023108 CATTTTTTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.37
18 22 0.63
ACGTcount: A:0.05, C:0.11, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTCTC
Found at i:1023121 original size:30 final size:27
Alignment explanation
Indices: 1023035--1023122 Score: 81
Period size: 30 Copynumber: 3.1 Consensus size: 27
1023025 TACATTTTTA
** *
1023035 CATTTTTTCATTTTTAT-TTTTTTATC
1 CATTTTTTTTTTTTTTTCTTTTTTATC
*
1023061 TC-TTTTTTTTTTTTTTTCTTTTGTTTTC
1 -CATTTTTTTTTTTTTTTCTTTT-TTATC
1023089 CATTTTCTCTTTTTTTTTTCATTTTTTATC
1 CATTTT-T-TTTTTTTTTTC-TTTTTTATC
1023119 CATT
1 CATT
1023123 ATTAATTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
26 12 0.24
27 6 0.12
28 8 0.16
29 1 0.02
30 19 0.38
31 4 0.08
ACGTcount: A:0.09, C:0.14, G:0.01, T:0.76
Consensus pattern (27 bp):
CATTTTTTTTTTTTTTTCTTTTTTATC
Found at i:1025142 original size:31 final size:31
Alignment explanation
Indices: 1025095--1025169 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1025085 AACTGGGTAG
* * *
1025095 GTTGCCGGAAACTTC-AATGTTCGCCGGAATT
1 GTTGCCGAAAAATTCAAAT-TTCGCCGAAATT
1025126 GTTGCCGAAAAATTCAAATTTCGCCGAAATT
1 GTTGCCGAAAAATTCAAATTTCGCCGAAATT
1025157 -TTCGCC-AAAAATT
1 GTT-GCCGAAAAATT
1025170 TCTAAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 9 0.23
31 27 0.69
32 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (31 bp):
GTTGCCGAAAAATTCAAATTTCGCCGAAATT
Found at i:1025587 original size:15 final size:17
Alignment explanation
Indices: 1025550--1025589 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1025540 ATTAGATAAG
1025550 TAAAAATACAAAAATGA
1 TAAAAATACAAAAATGA
1025567 -ATAAAATA-AAAAA-GA
1 TA-AAAATACAAAAATGA
1025582 TAAAAATA
1 TAAAAATA
1025590 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (17 bp):
TAAAAATACAAAAATGA
Found at i:1027611 original size:10 final size:10
Alignment explanation
Indices: 1027591--1027629 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1027581 TGATTTTCCT
1027591 TTTTAATTTGA
1 TTTT-ATTTGA
*
1027602 TTTGATTTGA
1 TTTTATTTGA
*
1027612 TTTTATTTTA
1 TTTTATTTGA
1027622 TTTTATTT
1 TTTTATTT
1027630 CTAACCCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 22 0.88
11 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
TTTTATTTGA
Found at i:1028656 original size:9 final size:9
Alignment explanation
Indices: 1028640--1028685 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
1028630 TTTGGTATTT
*
1028640 TTTAATTTA
1 TTTATTTTA
1028649 TTTTATTTTA
1 -TTTATTTTA
1028659 TTTA-TTTA
1 TTTATTTTA
*
1028667 TTTATTATA
1 TTTATTTTA
1028676 TTTATTTTA
1 TTTATTTTA
1028685 T
1 T
1028686 AAGTATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 8 0.25
9 16 0.50
10 8 0.25
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1028660 original size:22 final size:20
Alignment explanation
Indices: 1028635--1028683 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
1028625 ATTTTTTTGG
*
1028635 TATTTTTTAATTTATTTTATTT
1 TATTTTTT-ATTTATTATA-TT
1028657 TATTTATTTATTTATTATATT
1 TATTT-TTTATTTATTATATT
1028678 TATTTT
1 TATTTT
1028684 ATAAGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 7 0.28
22 14 0.56
23 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTTTATTTATTATATT
Found at i:1028662 original size:4 final size:4
Alignment explanation
Indices: 1028635--1028682 Score: 53
Period size: 4 Copynumber: 11.2 Consensus size: 4
1028625 ATTTTTTTGG
1028635 TATT T-TT TAATT TATTT TATTT TATT TATT TATT TATT ATATT TATT
1 TATT TATT T-ATT TA-TT TA-TT TATT TATT TATT TATT -TATT TATT
1028682 T
1 T
1028683 TATAAGTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.08
4 21 0.52
5 16 0.40
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:1029386 original size:13 final size:13
Alignment explanation
Indices: 1029370--1029395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1029360 AAAAATTTAG
1029370 AAATAAAAATAAA
1 AAATAAAAATAAA
1029383 AAATAAAAATAAA
1 AAATAAAAATAAA
1029396 TTTTGATGAT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAAATAAA
Done.