Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 180 of 190
Found at i:30400527 original size:31 final size:31
Alignment explanation
Indices: 30400426--30400530 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 31
30400416 TCATATTTAT
30400426 TAGATTCAATCTTTTAAAAGTAATTGAATGA
1 TAGATTCAATCTTTTAAAAGTAATTGAATGA
* *** * * *
30400457 TAGATAT-AA-CATTTGGACTTGGAATTCATATTTA
1 TAGAT-TCAATC-TTT-TAAAAGTAATTGA-A-TGA
30400491 TTAGATTCAATCTTTTAAAAGTAATTGAATGA
1 -TAGATTCAATCTTTTAAAAGTAATTGAATGA
30400523 TAGATTCA
1 TAGATTCA
30400531 TAAAAAATAT
Statistics
Matches: 52, Mismatches: 14, Indels: 16
0.63 0.17 0.20
Matches are distributed among these distances:
30 1 0.02
31 18 0.35
32 10 0.19
33 2 0.04
34 10 0.19
35 10 0.19
36 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (31 bp):
TAGATTCAATCTTTTAAAAGTAATTGAATGA
Found at i:30405052 original size:18 final size:19
Alignment explanation
Indices: 30405029--30405069 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
30405019 GTTAAAAATG
30405029 GCTGCCCAC-GCCACTGCC
1 GCTGCCCACTGCCACTGCC
30405047 GCTG-CCACTGCCACTGCC
1 GCTGCCCACTGCCACTGCC
*
30405065 ACTGC
1 GCTGC
30405070 ATCTTCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.12, C:0.51, G:0.22, T:0.15
Consensus pattern (19 bp):
GCTGCCCACTGCCACTGCC
Found at i:30405057 original size:6 final size:6
Alignment explanation
Indices: 30405034--30405069 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
30405024 AAATGGCTGC
*
30405034 CCAC-G CCACTG CCGCTG CCACTG CCACTG CCACTG C
1 CCACTG CCACTG CCACTG CCACTG CCACTG CCACTG C
30405070 ATCTTCTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.14, C:0.53, G:0.19, T:0.14
Consensus pattern (6 bp):
CCACTG
Found at i:30408134 original size:17 final size:18
Alignment explanation
Indices: 30408112--30408147 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
30408102 TGGGTGAGAA
30408112 AAAAATTGA-AAAAAATT
1 AAAAATTGATAAAAAATT
*
30408129 AAAAATTGATATAAAATT
1 AAAAATTGATAAAAAATT
30408147 A
1 A
30408148 TCGTTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
AAAAATTGATAAAAAATT
Found at i:30418087 original size:23 final size:23
Alignment explanation
Indices: 30418061--30418109 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
30418051 TAAAGGGCAG
30418061 AAAACCATGAATCTAACCAGATC
1 AAAACCATGAATCTAACCAGATC
* *
30418084 AAAACCATGAATCTTATCAGATC
1 AAAACCATGAATCTAACCAGATC
30418107 AAA
1 AAA
30418110 TCATTAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.20
Consensus pattern (23 bp):
AAAACCATGAATCTAACCAGATC
Found at i:30422512 original size:33 final size:33
Alignment explanation
Indices: 30422475--30422540 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
30422465 GATTATAATC
30422475 AAAACCAAATAAATCAAATCAATTCAACCGAAT
1 AAAACCAAATAAATCAAATCAATTCAACCGAAT
30422508 AAAACCAAATAAATCAAATCAATTCAACCGAAT
1 AAAACCAAATAAATCAAATCAATTCAACCGAAT
30422541 TCACTTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.58, C:0.21, G:0.03, T:0.18
Consensus pattern (33 bp):
AAAACCAAATAAATCAAATCAATTCAACCGAAT
Found at i:30424172 original size:36 final size:36
Alignment explanation
Indices: 30424121--30424304 Score: 165
Period size: 36 Copynumber: 5.1 Consensus size: 36
30424111 CTGACCAAAT
* * * *
30424121 CCAGAATTTGATCCTTGACCGTAATTCTGTCCATAG
1 CCAGGATTTGCTCCTTGCCCGAAATTCTGTCCATAG
* * * *
30424157 CCAGGAATTGCTCCTTGCCCGGAATTCTGCCCGTAG
1 CCAGGATTTGCTCCTTGCCCGAAATTCTGTCCATAG
* * * *
30424193 ACAGGATTTGCTCCTTGTCC-AGATTTCTCTCCATAG
1 CCAGGATTTGCTCCTTGCCCGA-AATTCTGTCCATAG
* *
30424229 CCAGGATTTGC-CCTTTGCCCAAAATTCTGCCCATAG
1 CCAGGATTTGCTCC-TTGCCCGAAATTCTGTCCATAG
* * * * *
30424265 CCAGGAGTTGCCCCTTGCCCAAAATTCCGTACATAG
1 CCAGGATTTGCTCCTTGCCCGAAATTCTGTCCATAG
30424301 CCAG
1 CCAG
30424305 AACTTGGTTC
Statistics
Matches: 120, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
35 2 0.02
36 115 0.96
37 3 0.03
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (36 bp):
CCAGGATTTGCTCCTTGCCCGAAATTCTGTCCATAG
Found at i:30425213 original size:25 final size:25
Alignment explanation
Indices: 30425179--30425236 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
30425169 TGAAACAAAT
*
30425179 TAACCCAAAATCAGCTTGCCTATTG
1 TAACCCAAAATCAGCATGCCTATTG
*
30425204 TAACCCAAAATCAGCATGCTTATTG
1 TAACCCAAAATCAGCATGCCTATTG
*
30425229 AAACCCAA
1 TAACCCAA
30425237 TAAAAACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (25 bp):
TAACCCAAAATCAGCATGCCTATTG
Found at i:30430901 original size:22 final size:22
Alignment explanation
Indices: 30430873--30430919 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
30430863 AATGCTATAC
30430873 AAAAGAAAGACTCATAAAATAG
1 AAAAGAAAGACTCATAAAATAG
30430895 AAAAGAAAGACTCATAAAATAG
1 AAAAGAAAGACTCATAAAATAG
30430917 AAA
1 AAA
30430920 TCATCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (22 bp):
AAAAGAAAGACTCATAAAATAG
Found at i:30434290 original size:2 final size:2
Alignment explanation
Indices: 30434283--30434309 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30434273 CTTAATTCTA
30434283 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
30434310 AAAGAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30436910 original size:22 final size:21
Alignment explanation
Indices: 30436885--30436950 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
30436875 GGGGTCTTTT
30436885 GATTTTATTTGCTTGGCC-AAAA
1 GATTTTATTT--TTGGCCAAAAA
* *
30436907 GATTTTGTTTTTGTCCAAAAA
1 GATTTTATTTTTGGCCAAAAA
* *
30436928 GATTTTGTTTTTGTCCAAAAA
1 GATTTTATTTTTGGCCAAAAA
30436949 GA
1 GA
30436951 ATTTGAACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.12
21 27 0.66
22 9 0.22
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44
Consensus pattern (21 bp):
GATTTTATTTTTGGCCAAAAA
Found at i:30436954 original size:22 final size:21
Alignment explanation
Indices: 30436903--30436955 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
30436893 TTGCTTGGCC
30436903 AAAAGATTTTGTTTTTGTCCA
1 AAAAGATTTTGTTTTTGTCCA
30436924 AAAAGATTTTGTTTTTGTCCA
1 AAAAGATTTTGTTTTTGTCCA
*
30436945 AAAAGAATTTG
1 AAAAGATTTTG
30436956 AACATAGCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (21 bp):
AAAAGATTTTGTTTTTGTCCA
Found at i:30437396 original size:17 final size:18
Alignment explanation
Indices: 30437374--30437407 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30437364 TTTAATCGAA
30437374 TTTTTA-TATTTAAATTT
1 TTTTTATTATTTAAATTT
*
30437391 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
30437408 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTATTTAAATTT
Found at i:30439219 original size:59 final size:60
Alignment explanation
Indices: 30439030--30439427 Score: 564
Period size: 59 Copynumber: 6.7 Consensus size: 60
30439020 TCTTGTGTAG
* *
30439030 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATATTTTTGAAAA-TTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTAT-TTTTTGAAAACTTTGATTTTCAA
* *
30439088 GGAAAATTGATACTTCCAACTTTTCCTCAAAAATATATTTTTTTG-AAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TA-TTTTTTGAAAACTTTGATTTTCAA
* *
30439149 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTCCTTTTTTGAAAA-TTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATT-ATTTTTTGAAAACTTTGATTTTCAA
* *
30439208 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTTGAAAACTTTGATTTTCAA
30439267 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTT-TTTTTTGAAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TTATTTTTTGAAAACTTTGATTTTCAA
* * *
30439328 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTGAAAACTTTTATTTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTTGAAAACTTTGATTTTCAA
*
30439387 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTT
30439428 TTAAAATCTT
Statistics
Matches: 309, Mismatches: 18, Indels: 25
0.88 0.05 0.07
Matches are distributed among these distances:
57 11 0.04
58 36 0.12
59 141 0.46
60 22 0.07
61 98 0.32
62 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.43
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTTGAAAACTTTGATTTTCAA
Found at i:30439331 original size:179 final size:176
Alignment explanation
Indices: 30439030--30439427 Score: 620
Period size: 179 Copynumber: 2.2 Consensus size: 176
30439020 TCTTGTGTAG
*
30439030 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATATTTTTGAAAATTTATTTTTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTGAAAATTTATTTTCAAGGAAAAT
*
30439095 TGATACTTCCAACTTTTCCTCAAAAATATATTTTTTTGAAACTTTGATTTCCAAGGAAAATTGAT
65 TGATACTTCCAACTTTTCCTCAAAAACATATTTTTTTGAAACTTTGATTTCCAAGGAAAATTGAT
* * *
30439160 ACTTTCAACTTTTCCTCAAAAATTCCTTTTTTGAAAA-TTTATTTTTAA
130 ACTTTCAACTTTTCCCCAAAAA-T-ATTTTTTGAAAACTTTATTTTCAA
30439208 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTTGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAA-TTT-ATTTTCAAGGAAAA
* * *
30439273 TTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAAACTTTGATTTTCAAGGAAAATTG
64 TTGATACTTCCAACTTTTCCTCAAAAACATATTTTTTTG-AAACTTTGATTTCCAAGGAAAATTG
*
30439337 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTTATTTTCGA
128 ATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAAC-TTTATTTTCAA
* *
30439387 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
30439428 TTAAAATCTT
Statistics
Matches: 204, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
177 21 0.10
178 48 0.24
179 135 0.66
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.43
Consensus pattern (176 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTCAAGGAAAATT
GATACTTCCAACTTTTCCTCAAAAACATATTTTTTTGAAACTTTGATTTCCAAGGAAAATTGATA
CTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTATTTTCAA
Found at i:30439426 original size:120 final size:118
Alignment explanation
Indices: 30439030--30439434 Score: 604
Period size: 120 Copynumber: 3.4 Consensus size: 118
30439020 TCTTGTGTAG
* *
30439030 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TATTTTTGAAAATTTATTTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGAAAA
* * * *
30439094 TTGATACTTCCAACTTTTCCTCAAAAATATATTTTTTTG-AAACTTTGATTTCCAA
66 TTGATACTTTCAACTTTTCC-CCAAAA-ATA-TTTTTTGAAAACTTTTATTTTCAA
*
30439149 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TCCTTTTTTGAAAATTTATTTTTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTTGAAAATTTATTTTTAAGGAAA
30439213 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAA-TTTTGATTTTCAA
65 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTT-ATTTTCAA
** *
30439267 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTGAAAACTTTGATTTTCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAA-TTT-ATTTTTAAGGAA
*
30439332 AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTTATTTTCGA
64 AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTTATTTTCAA
*
30439387 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT-AAAAT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAAT
30439435 CTTTTTATCT
Statistics
Matches: 264, Mismatches: 14, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
117 10 0.04
118 58 0.22
119 46 0.17
120 146 0.55
121 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.43
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGGAAAA
TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTTATTTTCAA
Found at i:30442471 original size:17 final size:16
Alignment explanation
Indices: 30442449--30442488 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
30442439 ACAGAGGTAA
* *
30442449 TTTTTTTGTTTTTTTT
1 TTTTTTTATTTTGTTT
30442465 GTTTTTTTATTTTGTTT
1 -TTTTTTTATTTTGTTT
30442482 TTTTTTT
1 TTTTTTT
30442489 CAAAGCTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (16 bp):
TTTTTTTATTTTGTTT
Found at i:30442479 original size:13 final size:13
Alignment explanation
Indices: 30442448--30442485 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
30442438 AACAGAGGTA
30442448 ATTTT-TTTGTTTT
1 ATTTTGTTT-TTTT
30442461 -TTTTGTTTTTTT
1 ATTTTGTTTTTTT
30442473 ATTTTGTTTTTTT
1 ATTTTGTTTTTTT
30442486 TTTCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (13 bp):
ATTTTGTTTTTTT
Found at i:30442594 original size:42 final size:41
Alignment explanation
Indices: 30442493--30442646 Score: 245
Period size: 41 Copynumber: 3.7 Consensus size: 41
30442483 TTTTTTCAAA
* *
30442493 GCTCCTCTAAACAGAGGCTCAACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* *
30442534 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
* *
30442576 GCTCCTCTAAGCAAAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
30442617 GCTCCTCTAAACAGAGGCACCACGACTTTG
1 GCTCCTCTAAACAGAGGCACCACGACTTTG
30442647 AAGAGGCACC
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 65 0.64
42 37 0.36
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
Found at i:30442632 original size:83 final size:83
Alignment explanation
Indices: 30442493--30442645 Score: 270
Period size: 83 Copynumber: 1.8 Consensus size: 83
30442483 TTTTTTCAAA
* *
30442493 GCTCCTCTAAACAGAGGCTCAACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAAAGGCACAACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
30442558 ACTTTTGAAAAATAAATT
66 ACTTTTGAAAAATAAATT
* *
30442576 GCTCCTCTAAGCAAAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAAAGGCACAACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
30442641 ACTTT
66 ACTTT
30442646 GAAGAGGCAC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (83 bp):
GCTCCTCTAAACAAAGGCACAACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTTGAAAAATAAATT
Found at i:30442653 original size:19 final size:19
Alignment explanation
Indices: 30442629--30442667 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30442619 TCCTCTAAAC
30442629 AGAGGCACCACGACTTTGA
1 AGAGGCACCACGACTTTGA
30442648 AGAGGCACCACGACTTTGA
1 AGAGGCACCACGACTTTGA
30442667 A
1 A
30442668 AAATAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (19 bp):
AGAGGCACCACGACTTTGA
Found at i:30442683 original size:60 final size:60
Alignment explanation
Indices: 30442590--30442705 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
30442580 CTCTAAGCAA
* *
30442590 AGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAG
1 AGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAG
30442650 AGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
1 AGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTT
30442706 TGGAAAGTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (60 bp):
AGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAG
Found at i:30442688 original size:143 final size:144
Alignment explanation
Indices: 30442505--30442792 Score: 497
Period size: 143 Copynumber: 2.0 Consensus size: 144
30442495 TCCTCTAAAC
* * *
30442505 AGAGGCTCAACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAA
1 AGAGGCACAACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAA
30442570 TAAATTGCTCCTCTAAGCAAAGGCACCACGACTTTG-GAAAGTAAATTGCTCCTCTAAACAGAGG
66 TAAATTGCTCCTCTAAGCAAAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGG
30442634 CACCACGACTTTGA
131 CACCACGACTTTGA
* * *
30442648 AGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAG
1 AGAGGCACAACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAA
*
30442713 TAAATTGCTCCTCTAAGCAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGG
66 TAAATTGCTCCTCTAAGCAAAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGG
*
30442778 CACCATGACTTTGA
131 CACCACGACTTTGA
30442792 A
1 A
30442793 AAGTAAATTG
Statistics
Matches: 136, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
143 94 0.69
144 42 0.31
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (144 bp):
AGAGGCACAACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAA
TAAATTGCTCCTCTAAGCAAAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGG
CACCACGACTTTGA
Found at i:30442726 original size:102 final size:102
Alignment explanation
Indices: 30442546--30442749 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
30442536 TCCTCTAAAC
*
30442546 AGAGGCACCACGACTTTTGAAAAATAAATTGCTCCTCTAAGCAAAGGCACCACGACTTTGGAAAG
1 AGAGGCACCACGACTTTTGAAAAATAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGGAAAG
30442611 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
66 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
*
30442648 AGAGGCACCACGAC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAA
1 AGAGGCACCACGACTTTTGAAAAATAAATTGCTCCTCTAAACAAAGGCACCACGAC-TTTGGAAA
*
30442712 GTAAATTGCTCCTCTAAGCAGAGGCACCACGACTTTGA
65 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
30442750 GAAAGTAAAT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 39 0.40
102 59 0.60
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (102 bp):
AGAGGCACCACGACTTTTGAAAAATAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGGAAAG
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
Found at i:30442734 original size:42 final size:41
Alignment explanation
Indices: 30442648--30443129 Score: 699
Period size: 41 Copynumber: 11.7 Consensus size: 41
30442638 ACGACTTTGA
* *
30442648 AGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
*
30442689 AGAGGCACCACGACTTTTGGAAAGTAAATTGCTCCTCTAAGC
1 AGAGGCACCACGAC-TTTGGAAAGTAAATTGCTCCTCTAAAC
30442731 AGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTG-GAAAGTAAATTGCTCCTCTAAAC
* *
30442773 AGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
* *
30442814 AAAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAAC
*
30442856 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAAC
*
30442898 AGAGGCATCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
* *
30442939 AAAGGCA--ACGAAACTTTGAAAAGTAAATTGCTCCTCTAAAC
1 AGAGGCACCACG--ACTTTGGAAAGTAAATTGCTCCTCTAAAC
*
30442980 AGAGGCACCATGACTTTGGAAAGTAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
30443021 AGAGGCA--ACGGAACTTTGGAAAGTAAATTGCTCCTCTAAAC
1 AGAGGCACCAC-G-ACTTTGGAAAGTAAATTGCTCCTCTAAAC
* *
30443062 AGAGGCACCATGACTTTGGAAAGTAAATTGCTCCCCTAAAC
1 AGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
30443103 AGAGGCA--ACGAAC-TTGGAAAAGTAAAT
1 AGAGGCACCACG-ACTTTGG-AAAGTAAAT
30443130 ACTCCTAGAC
Statistics
Matches: 406, Mismatches: 22, Indels: 27
0.89 0.05 0.06
Matches are distributed among these distances:
39 10 0.02
40 12 0.03
41 223 0.55
42 158 0.39
43 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (41 bp):
AGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
Found at i:30442870 original size:125 final size:123
Alignment explanation
Indices: 30442648--30443129 Score: 699
Period size: 125 Copynumber: 3.9 Consensus size: 123
30442638 ACGACTTTGA
* *
30442648 AGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAG
1 AGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGAC-TTTGGAAAG
*
30442713 TAAATTGCTCCTCTAAGCAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAAC
65 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATTGCTCCTCTAAAC
* *
30442773 AGAGGCACCATGACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGGAAAAA
1 AGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGG-AAAG
*
30442838 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAAC
65 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAAC
* * *
30442898 AGAGGCATCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAAAGGCA--ACGAAACTTTGAAAA
1 AGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCACG--ACTTTGGAAA
*
30442961 GTAAATTGCTCCTCTAAACAGAGGCACCATGACTTTGGAAAGTAAATTGCTCCTCTAAAC
64 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
* * *
30443021 AGAGGCA--ACGGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCATGACTTTGGAAA
1 AGAGGCACCAC-G-ACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGGAAA
*
30443084 GTAAATTGCTCCCCTAAACAGAGGCA--ACGAAC-TTGGAAAAGTAAAT
64 GTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGG-AAAGTAAAT
30443130 ACTCCTAGAC
Statistics
Matches: 329, Mismatches: 18, Indels: 23
0.89 0.05 0.06
Matches are distributed among these distances:
121 8 0.02
122 12 0.04
123 100 0.30
124 45 0.14
125 164 0.50
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (123 bp):
AGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAAAGGCACCACGACTTTGGAAAGT
AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAAC
Found at i:30444395 original size:7 final size:7
Alignment explanation
Indices: 30444350--30444417 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 7
30444340 TTTGAATCTC
30444350 CTTTTTT
1 CTTTTTT
*
30444357 ATTTTTT
1 CTTTTTT
30444364 CATTTTTT
1 C-TTTTTT
*
30444372 CATTTTTCCC
1 C-TTTTT--T
30444382 CTTTTTT
1 CTTTTTT
30444389 -TTCTTTT
1 CTT-TTTT
30444396 -TTTTTT
1 CTTTTTT
30444402 CTTTTTT
1 CTTTTTT
*
30444409 CTCTTTT
1 CTTTTTT
30444416 CT
1 CT
30444418 CATTTTTCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
6 6 0.12
7 26 0.51
8 13 0.25
9 5 0.10
10 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (7 bp):
CTTTTTT
Found at i:30444397 original size:11 final size:11
Alignment explanation
Indices: 30444383--30444408 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30444373 ATTTTTCCCC
30444383 TTTTTTTTCTT
1 TTTTTTTTCTT
30444394 TTTTTTTTCTT
1 TTTTTTTTCTT
30444405 TTTT
1 TTTT
30444409 CTCTTTTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:30448332 original size:59 final size:59
Alignment explanation
Indices: 30448199--30448481 Score: 349
Period size: 59 Copynumber: 4.7 Consensus size: 59
30448189 TTGTGTAGGA
* *
30448199 AAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTTG-AAACTTTGATTTCCAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAA-ATA--TTTTTTGAAAATTTTGATTTTCAAGG
* * *
30448261 AAAATTGATACTTTCAATTTTTCCTCAAAAATCCCTTTTTTGAAAA-TTT-ATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT--ATTTTTTGAAAATTTTGATTTTCAAGG
* *
30448320 AAAATTGCTACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTGATTTTCAAGG
* * * *
30448379 AAAATTGATACTTTCAACTTTTCCCCAAAAATGTTTTTTGAAAACTTTT-ATTTTCGAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAA-TTTTGATTTTCAAGG
* * *
30448438 AAAATTGATATTTTCAACTTTTTCTCAAAAATATTTTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAA
30448482 ATCTTTTTAT
Statistics
Matches: 197, Mismatches: 18, Indels: 15
0.86 0.08 0.07
Matches are distributed among these distances:
57 11 0.06
58 3 0.02
59 135 0.69
60 16 0.08
61 7 0.04
62 25 0.13
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTGATTTTCAAGG
Found at i:30452359 original size:24 final size:25
Alignment explanation
Indices: 30452332--30452379 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
30452322 TGAGTTATGG
30452332 TTTGAT-AAAATAAAGTTTTCATGA
1 TTTGATAAAAATAAAGTTTTCATGA
**
30452356 TTTGATAAAAATCGAGTTTTCATG
1 TTTGATAAAAATAAAGTTTTCATG
30452380 GTGCCTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (25 bp):
TTTGATAAAAATAAAGTTTTCATGA
Found at i:30458041 original size:2 final size:2
Alignment explanation
Indices: 30458034--30458062 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30458024 AAATAAGAAT
30458034 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30458063 CTGGAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30468454 original size:2 final size:2
Alignment explanation
Indices: 30468449--30468477 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30468439 TCTCTCTATG
30468449 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 T
30468478 GTTGGCCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30470068 original size:33 final size:32
Alignment explanation
Indices: 30470017--30470083 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
30470007 GGATGCCAAG
* *
30470017 AATAACATTTGAATTGCAATGTGCTTGAAACCC
1 AATAACATCTGAACTGCAATGTGC-TGAAACCC
*
30470050 AATAACATCTGAACTGCAATGTGCTGAAATCC
1 AATAACATCTGAACTGCAATGTGCTGAAACCC
30470082 AA
1 AA
30470084 ATTTTCACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (32 bp):
AATAACATCTGAACTGCAATGTGCTGAAACCC
Found at i:30472807 original size:75 final size:75
Alignment explanation
Indices: 30472684--30472832 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
30472674 TATCTATAAT
*
30472684 ATAAACATGTAAATACTGAAAACTCAACTAACCATGAGTATGGACAACCAAATGGTTAAGCAAAA
1 ATAAACATGTAAATACTGAAAACTCAACTAACCATGAGAATGGACAACCAAATGGTTAAGCAAAA
30472749 AAGGACTTGA
66 AAGGACTTGA
* * * * **
30472759 ATAAACATGTAAATGCTGGAAATTCTACTAACCATGAGAATGGACAACCAAATGGTTAAGTGAAA
1 ATAAACATGTAAATACTGAAAACTCAACTAACCATGAGAATGGACAACCAAATGGTTAAGCAAAA
30472824 AAGGACTTG
66 AAGGACTTG
30472833 GAAGACTTAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (75 bp):
ATAAACATGTAAATACTGAAAACTCAACTAACCATGAGAATGGACAACCAAATGGTTAAGCAAAA
AAGGACTTGA
Found at i:30473619 original size:41 final size:41
Alignment explanation
Indices: 30473553--30473634 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
30473543 AGACAGCCAT
* * *
30473553 AATATATACAAGAAAATGAAGGCATAAACATGTCAGCACAA
1 AATAAATACAAGAAAAAGAAAGCATAAACATGTCAGCACAA
30473594 AATAAATACAAGAAAAAGAAAGCATAAACATGTCAGCACAA
1 AATAAATACAAGAAAAAGAAAGCATAAACATGTCAGCACAA
30473635 GAATCTCTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.15
Consensus pattern (41 bp):
AATAAATACAAGAAAAAGAAAGCATAAACATGTCAGCACAA
Found at i:30476235 original size:159 final size:159
Alignment explanation
Indices: 30475946--30476257 Score: 572
Period size: 159 Copynumber: 2.0 Consensus size: 159
30475936 CCTTGGCCTA
30475946 AGCACATATCTCTCTCCATCTCCCAATTAGACTTTCTATTCACAAGCACCACATTCTAGACATAA
1 AGCACATATCTCTCTCCATCTCCCAATTAGACTTTCTATTCACAAGCACCACATTCTAGACATAA
30476011 CCGATACTGCAAATATTGACTCACTACGAGATTTAGTACAATGCAATTACAATATGCATGCTTTA
66 CCGATACTGCAAATATTGACTCACTACGAGATTTAGTACAATGCAATTACAATATGCATGCTTTA
30476076 GTATGTTCTCATGCATCTCTTTCAGCATG
131 GTATGTTCTCATGCATCTCTTTCAGCATG
* * *
30476105 AGCACATATCTCTCTCCATTTCCCAATTAGACTTTCTATTCACAAGCACCGCATTCTAGACATGA
1 AGCACATATCTCTCTCCATCTCCCAATTAGACTTTCTATTCACAAGCACCACATTCTAGACATAA
*
30476170 -CGAATACTGCAAATATTGACTCACTACGAGATTTAGTACAATGCAATTACAATATGTATGCTTT
66 CCG-ATACTGCAAATATTGACTCACTACGAGATTTAGTACAATGCAATTACAATATGCATGCTTT
30476234 AGTATGTTCTCATGCATCTCTTTC
130 AGTATGTTCTCATGCATCTCTTTC
30476258 CTGAACAATT
Statistics
Matches: 148, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
158 2 0.01
159 146 0.99
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (159 bp):
AGCACATATCTCTCTCCATCTCCCAATTAGACTTTCTATTCACAAGCACCACATTCTAGACATAA
CCGATACTGCAAATATTGACTCACTACGAGATTTAGTACAATGCAATTACAATATGCATGCTTTA
GTATGTTCTCATGCATCTCTTTCAGCATG
Found at i:30481105 original size:2 final size:2
Alignment explanation
Indices: 30481100--30481127 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30481090 TGCAATAAAT
30481100 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
30481128 TCAAATCATC
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:30483696 original size:28 final size:27
Alignment explanation
Indices: 30483657--30483712 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
30483647 AGAGAAAGAC
* *
30483657 TTTTTGGTTTAAGTTTATTCATTTAGA
1 TTTTTGGTTTAAATTGATTCATTTAGA
30483684 TTTTGTGGTTTAAATTGATTCATTTAGA
1 TTTT-TGGTTTAAATTGATTCATTTAGA
30483712 T
1 T
30483713 ATATGTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.23, C:0.04, G:0.16, T:0.57
Consensus pattern (27 bp):
TTTTTGGTTTAAATTGATTCATTTAGA
Found at i:30490855 original size:27 final size:28
Alignment explanation
Indices: 30490823--30490905 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
30490813 ATTTGACATA
*
30490823 TTAATATAAATTATAATACAATA-AAAT
1 TTAATATAAATTATAATACAAAATAAAT
* *
30490850 TTAATATATATT-TAATATAAAATAAAT
1 TTAATATAAATTATAATACAAAATAAAT
* *
30490877 ATAATATAAATATATAA-AAAAAATAAAT
1 TTAATATAAAT-TATAATACAAAATAAAT
30490905 T
1 T
30490906 ATTTGAAAGG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 8 0.17
27 24 0.52
28 11 0.24
29 3 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
TTAATATAAATTATAATACAAAATAAAT
Found at i:30492114 original size:10 final size:8
Alignment explanation
Indices: 30492058--30492123 Score: 59
Period size: 8 Copynumber: 8.6 Consensus size: 8
30492048 TTTGACCTCG
*
30492058 TATATATA
1 TATATATT
*
30492066 TATA-AAT
1 TATATATT
*
30492073 TATTTATT
1 TATATATT
30492081 TA-AT-TT
1 TATATATT
30492087 TATATATT
1 TATATATT
30492095 TATATATT
1 TATATATT
*
30492103 TATTTAATT
1 TATAT-ATT
30492112 T-TATATT
1 TATATATT
30492119 TATAT
1 TATAT
30492124 TAAAAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
6 4 0.09
7 11 0.24
8 27 0.59
9 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:30492149 original size:23 final size:25
Alignment explanation
Indices: 30492109--30492163 Score: 96
Period size: 23 Copynumber: 2.3 Consensus size: 25
30492099 TATTTATTTA
30492109 ATTTTATATTTATATTAAAAATAAT
1 ATTTTATATTTATATTAAAAATAAT
30492134 ATTTTATATTT-T-TTAAAAATAAT
1 ATTTTATATTTATATTAAAAATAAT
30492157 ATTTTAT
1 ATTTTAT
30492164 TAATTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 18 0.60
24 1 0.03
25 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTTATATTTATATTAAAAATAAT
Found at i:30501738 original size:35 final size:34
Alignment explanation
Indices: 30501710--30501779 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
30501700 AAGTTAAATT
30501710 TTTTATACTTTATTTTTTCAAATCAAAGTTTATAA
1 TTTTATACTTTATTTTTTCAAATCAAAG-TTATAA
*
30501745 TTTTATATTTTATTTTTTCAAATCAAAGTTTATAA
1 TTTTATACTTTATTTTTTCAAATCAAAG-TTATAA
30501780 GTATTTCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (34 bp):
TTTTATACTTTATTTTTTCAAATCAAAGTTATAA
Found at i:30502064 original size:18 final size:18
Alignment explanation
Indices: 30502041--30502075 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30502031 ATTATAATAG
*
30502041 ATAAATTTATGTATGTTT
1 ATAAATATATGTATGTTT
*
30502059 ATAAATATATTTATGTT
1 ATAAATATATGTATGTT
30502076 AAATCAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
ATAAATATATGTATGTTT
Found at i:30519672 original size:30 final size:30
Alignment explanation
Indices: 30519608--30519915 Score: 97
Period size: 30 Copynumber: 10.0 Consensus size: 30
30519598 TCTTCACCAA
** * * * *
30519608 CACCACCACCACCACCAACACCAACACCAA
1 CACCACCACCACCACCCTCATCATCATCAT
30519638 CACCACCACCACCACCCTCATCATCATCAT
1 CACCACCACCACCACCCTCATCATCATCAT
* *
30519668 CACCATCACCATCACCACCACCAC-CACCCTCATCAT
1 CA-C--CA-C--CACCACCACC-CTCATCATCATCAT
* * * * *
30519704 CACCATCACCACCACCAC-CAACACCACCCT
1 CACCACCACCACCACC-CTCATCATCATCAT
** * * * *
30519734 CGTCATCACCACCACCAC-CACCTTCGTCAT
1 CACCACCACCACCACC-CTCATCATCATCAT
* *
30519764 CACCACCACCACCA---ACGTCATCATCAT
1 CACCACCACCACCACCCTCATCATCATCAT
* * ** * *
30519791 CGCCACCAACACCACTTTCGTCATCAACAT
1 CACCACCACCACCACCCTCATCATCATCAT
* * * *
30519821 CGCCACCAACACCACCCTCGTCATCATCCT
1 CACCACCACCACCACCCTCATCATCATCAT
* * * *
30519851 CACCAACAACACCTTCTTCATCATCAGAATCATCAT
1 CACCACCACCACC-AC--CCTCATC---ATCATCAT
* * *
30519887 CACCACCAACACCACCTTCGTCATCATCA
1 CACCACCACCACCACCCTCATCATCATCA
30519916 GAATCGTCAC
Statistics
Matches: 214, Mismatches: 47, Indels: 34
0.73 0.16 0.12
Matches are distributed among these distances:
27 20 0.09
30 133 0.62
31 2 0.01
33 14 0.07
34 1 0.00
35 2 0.01
36 41 0.19
37 1 0.00
ACGTcount: A:0.31, C:0.50, G:0.03, T:0.15
Consensus pattern (30 bp):
CACCACCACCACCACCCTCATCATCATCAT
Found at i:30519732 original size:36 final size:36
Alignment explanation
Indices: 30519601--30519755 Score: 168
Period size: 36 Copynumber: 4.3 Consensus size: 36
30519591 TTTATCTTCT
* * * * *
30519601 TCACCAACACCACCACCACCACCAACACCAACACCA
1 TCACCACCACCACCAACACCACCATCATCATCACCA
* * *
30519637 ACACCACCACCACC-ACCCTCATCATCATCATCACCA
1 TCACCACCACCACCAACAC-CACCATCATCATCACCA
* * *
30519673 TCACCATCACCACCACCACCACCCTCATCATCACCA
1 TCACCACCACCACCAACACCACCATCATCATCACCA
* *
30519709 TCACCACCACCACCAACACCACCCTCGTCATCACCA
1 TCACCACCACCACCAACACCACCATCATCATCACCA
*
30519745 CCACCACCACC
1 TCACCACCACC
30519756 TTCGTCATCA
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
35 2 0.02
36 95 0.96
37 2 0.02
ACGTcount: A:0.34, C:0.56, G:0.01, T:0.10
Consensus pattern (36 bp):
TCACCACCACCACCAACACCACCATCATCATCACCA
Found at i:30519775 original size:3 final size:3
Alignment explanation
Indices: 30519602--30519755 Score: 107
Period size: 3 Copynumber: 51.3 Consensus size: 3
30519592 TTATCTTCTT
* * * *
30519602 CAC CAA CAC CAC CAC CAC CAC CAA CAC CAA CAC CAA CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
* * * * * *
30519650 CAC C-C TCAT CAT CAT CAT CAC CAT CAC CAT CAC CAC CAC CAC CAC
1 CAC CAC -CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
* * * * ** *
30519695 C-C TCAT CAT CAC CAT CAC CAC CAC CAC CAA CAC CAC C-C TCGT CAT
1 CAC -CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC -CAC CAC
30519740 CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC C
30519756 TTCGTCATCA
Statistics
Matches: 122, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
2 3 0.02
3 119 0.98
ACGTcount: A:0.34, C:0.56, G:0.01, T:0.09
Consensus pattern (3 bp):
CAC
Found at i:30519796 original size:21 final size:21
Alignment explanation
Indices: 30519617--30519800 Score: 104
Period size: 21 Copynumber: 8.8 Consensus size: 21
30519607 ACACCACCAC
* ** *
30519617 CACCACCAACACCAACACCAA
1 CACCACCACCACCAACGTCAT
* *
30519638 CACCACCACCACCACCCTCAT
1 CACCACCACCACCAACGTCAT
* * * * **
30519659 CATCATCATCACCATCACCAT
1 CACCACCACCACCAACGTCAT
* *
30519680 CACCACCACCACCACCCTCAT
1 CACCACCACCACCAACGTCAT
* * *
30519701 CATCACCATCACC-AC--CAC
1 CACCACCACCACCAACGTCAT
* **
30519719 CACCAACACCACCCTCGTCAT
1 CACCACCACCACCAACGTCAT
*
30519740 CACCACCACCACCACCTTCGTCAT
1 CACCACCACCACCA---ACGTCAT
30519764 CACCACCACCACCAACGTCAT
1 CACCACCACCACCAACGTCAT
* * *
30519785 CATCATCGCCACCAAC
1 CACCACCACCACCAAC
30519801 ACCACTTTCG
Statistics
Matches: 125, Mismatches: 32, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
18 12 0.10
19 1 0.01
20 1 0.01
21 90 0.72
24 21 0.17
ACGTcount: A:0.32, C:0.54, G:0.02, T:0.12
Consensus pattern (21 bp):
CACCACCACCACCAACGTCAT
Found at i:30519884 original size:39 final size:39
Alignment explanation
Indices: 30519841--30519930 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
30519831 ACCACCCTCG
*
30519841 TCATCATC-CTCACCAACAACACCTTCTTCATCATCAGAA
1 TCATCATCAC-CACCAACAACACCTTCGTCATCATCAGAA
*
30519880 TCATCATCACCACCAACACCACCTTCGTCATCATCAGAA
1 TCATCATCACCACCAACAACACCTTCGTCATCATCAGAA
* *
30519919 TCGTCACCACCA
1 TCATCATCACCA
30519931 TCTCCATCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.32, C:0.41, G:0.04, T:0.22
Consensus pattern (39 bp):
TCATCATCACCACCAACAACACCTTCGTCATCATCAGAA
Found at i:30529845 original size:127 final size:124
Alignment explanation
Indices: 30529625--30529875 Score: 396
Period size: 127 Copynumber: 2.0 Consensus size: 124
30529615 GACTGTAGCT
* *
30529625 AGTGGCTAGGTTGTTAATTCATTTTTCTTTTTTTTTTTATTTTATTTTATTATAATTTTGCCTCT
1 AGTGGCTAGGTTGTCAATTAATTTTTCTTTTTTTTTTTATTTTATTTTATTATAATTTTGCCTCT
* * *
30529690 AATCCGGCTTCTATATATGTTGTGGTTTTATATGAGATCGGAATTAAATGGCTGTAGAA
66 AATCCGGCTTCTATAGATGTTCTGGTTTTATATGAGATCGGAATTAAAGGGCTGTAGAA
*
30529749 AGTGGCTAGGTTGTCAATTAATTTTTCTTTTTCTTTTCTTTTATTTA-TTTATTTATAATTTTGC
1 AGTGGCTAGGTTGTCAATTAATTTTTCTTTTT-TTTT-TTAT-TTTATTTTA-TTATAATTTTGC
*
30529813 CTCTAATCCGGCTTCTATAGATGTTCTTGTTTTATATGAGATCGGAATTAAAGGGCTGTAGAA
62 CTCTAATCCGGCTTCTATAGATGTTCTGGTTTTATATGAGATCGGAATTAAAGGGCTGTAGAA
30529876 TCTTGAAAAG
Statistics
Matches: 116, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
124 30 0.26
125 4 0.03
126 7 0.06
127 75 0.65
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.50
Consensus pattern (124 bp):
AGTGGCTAGGTTGTCAATTAATTTTTCTTTTTTTTTTTATTTTATTTTATTATAATTTTGCCTCT
AATCCGGCTTCTATAGATGTTCTGGTTTTATATGAGATCGGAATTAAAGGGCTGTAGAA
Found at i:30531292 original size:69 final size:69
Alignment explanation
Indices: 30531210--30531344 Score: 270
Period size: 69 Copynumber: 2.0 Consensus size: 69
30531200 AAGTAGGCAG
30531210 GGTTGGTTTTCATTTCTACAAGTTGCAAATGCATTTGATAAAATGACAACATAGACTAACCTTGA
1 GGTTGGTTTTCATTTCTACAAGTTGCAAATGCATTTGATAAAATGACAACATAGACTAACCTTGA
30531275 GATA
66 GATA
30531279 GGTTGGTTTTCATTTCTACAAGTTGCAAATGCATTTGATAAAATGACAACATAGACTAACCTTGA
1 GGTTGGTTTTCATTTCTACAAGTTGCAAATGCATTTGATAAAATGACAACATAGACTAACCTTGA
30531344 G
66 G
30531345 GTTTGTATCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (69 bp):
GGTTGGTTTTCATTTCTACAAGTTGCAAATGCATTTGATAAAATGACAACATAGACTAACCTTGA
GATA
Found at i:30535068 original size:2 final size:2
Alignment explanation
Indices: 30535063--30535088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30535053 ATATATATAT
30535063 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
30535089 GATAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30535267 original size:21 final size:21
Alignment explanation
Indices: 30535241--30535280 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
30535231 TATATACTAT
30535241 ATTTAAAAAT-TAAATAAATAA
1 ATTTAAAAATATAAA-AAATAA
30535262 ATTTAAAAATATAAAAAAT
1 ATTTAAAAATATAAAAAAT
30535281 TAATATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTTAAAAATATAAAAAATAA
Found at i:30535601 original size:7 final size:7
Alignment explanation
Indices: 30535591--30535617 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30535581 ATAATTAAAT
30535591 AATATAA
1 AATATAA
30535598 AATATAA
1 AATATAA
30535605 AATATAA
1 AATATAA
30535612 AATATA
1 AATATA
30535618 TTTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATATAA
Found at i:30545726 original size:51 final size:51
Alignment explanation
Indices: 30545664--30545773 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
30545654 AGGATATGGA
* * *
30545664 AGGTTTAGGGTTTTGATTTTAGAGTTTAGAGATTTT-AGG-GTTTGGGTTTTG
1 AGGTTTGGGGTTTTGATTTAAGAGTTT-G-GATTTTAAGGAGTTTGGATTTTG
* *
30545715 TGGTTTGGGGTTTTGATTTAAGAGTTTGGATTTTAAGGATTTTGGATTTTG
1 AGGTTTGGGGTTTTGATTTAAGAGTTTGGATTTTAAGGAGTTTGGATTTTG
30545766 AGGTTTGG
1 AGGTTTGG
30545774 ATTTAAGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
49 6 0.12
50 4 0.08
51 41 0.80
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (51 bp):
AGGTTTGGGGTTTTGATTTAAGAGTTTGGATTTTAAGGAGTTTGGATTTTG
Found at i:30545741 original size:14 final size:14
Alignment explanation
Indices: 30545724--30545785 Score: 63
Period size: 14 Copynumber: 4.3 Consensus size: 14
30545714 GTGGTTTGGG
*
30545724 GTTTTGATTTAAGA
1 GTTTGGATTTAAGA
30545738 GTTTGGATTTTAAGGA
1 GTTTGGA-TTTAA-GA
* *
30545754 TTTTGGATTT-TGA
1 GTTTGGATTTAAGA
30545767 GGTTTGGATTTAAGA
1 -GTTTGGATTTAAGA
30545782 GTTT
1 GTTT
30545786 AAAGGTTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 2 0.05
14 19 0.49
15 10 0.26
16 8 0.21
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (14 bp):
GTTTGGATTTAAGA
Found at i:30545751 original size:15 final size:15
Alignment explanation
Indices: 30545731--30545785 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
30545721 GGGGTTTTGA
30545731 TTTAAGAGTTTGGAT
1 TTTAAGAGTTTGGAT
*
30545746 TTTAAGGATTTTGGAT
1 TTTAA-GAGTTTGGAT
*
30545762 TTTGAG-GTTTGGA-
1 TTTAAGAGTTTGGAT
30545775 TTTAAGAGTTT
1 TTTAAGAGTTT
30545786 AAAGGTTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.15
14 10 0.29
15 6 0.18
16 13 0.38
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (15 bp):
TTTAAGAGTTTGGAT
Found at i:30545760 original size:16 final size:16
Alignment explanation
Indices: 30545739--30545859 Score: 63
Period size: 16 Copynumber: 7.6 Consensus size: 16
30545729 GATTTAAGAG
30545739 TTTGGATTTTAAGGAT
1 TTTGGATTTTAAGGAT
*
30545755 TTTGGATTTTGAGG--
1 TTTGGATTTTAAGGAT
*
30545769 TTTGGA-TTTAA-GAG
1 TTTGGATTTTAAGGAT
** * **
30545783 TTTAAAGGTTTGGGGAT
1 TTTGGA-TTTTAAGGAT
* *
30545800 TTTGGATTTTTGAGGGT
1 TTTGGA-TTTTAAGGAT
30545817 TTTGGATTTT-AGGAGT
1 TTTGGATTTTAAGGA-T
* * *
30545833 TTTTGATTTTATGGGGT
1 TTTGGATTTTA-AGGAT
30545850 TTTGGATTTT
1 TTTGGATTTT
30545860 TAGGGGTTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
12 1 0.01
13 4 0.05
14 10 0.13
15 3 0.04
16 30 0.38
17 29 0.37
18 2 0.03
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTGGATTTTAAGGAT
Found at i:30545819 original size:17 final size:16
Alignment explanation
Indices: 30545799--30545869 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 16
30545789 GGTTTGGGGA
30545799 TTTTGGATTTTTGAGGG
1 TTTTGGATTTTT-AGGG
30545816 TTTTGGA-TTTTAGGAG
1 TTTTGGATTTTTAGG-G
* *
30545832 TTTTTGATTTTATGGGG
1 TTTTGGATTTT-TAGGG
30545849 TTTTGGATTTTTAGGGG
1 TTTTGGATTTTTA-GGG
30545866 TTTT
1 TTTT
30545870 AAAAACTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.07
16 12 0.26
17 28 0.61
18 3 0.07
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (16 bp):
TTTTGGATTTTTAGGG
Found at i:30545842 original size:33 final size:34
Alignment explanation
Indices: 30545799--30545869 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
30545789 GGTTTGGGGA
30545799 TTTTGGATTTT-TGAGGGTTTTGGA-TTTTAGGAG
1 TTTTGGATTTTATG-GGGTTTTGGATTTTTAGGAG
* *
30545832 TTTTTGATTTTATGGGGTTTTGGATTTTTAGGGG
1 TTTTGGATTTTATGGGGTTTTGGATTTTTAGGAG
30545866 TTTT
1 TTTT
30545870 AAAAACTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 20 0.59
34 14 0.41
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (34 bp):
TTTTGGATTTTATGGGGTTTTGGATTTTTAGGAG
Found at i:30546196 original size:16 final size:16
Alignment explanation
Indices: 30546165--30546206 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
30546155 GTTTTTAATA
30546165 TATTTTTAACTATTATT
1 TATTTTTAACTATTA-T
*
30546182 TATTTTTAA-TTTTAT
1 TATTTTTAACTATTAT
30546197 TATTATTTAA
1 TATT-TTTAA
30546207 ACAATTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTTAACTATTAT
Found at i:30546874 original size:29 final size:28
Alignment explanation
Indices: 30546842--30546897 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
30546832 TTATTTTTTG
*
30546842 TTTTT-ATATTTTTATATAATTAATAATTA
1 TTTTTAATATTATTAT-T-ATTAATAATTA
30546871 TTTTTAAATATTATTATTATTAATAAT
1 TTTTT-AATATTATTATTATTAATAAT
30546898 ATTATCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 14 0.58
30 1 0.04
31 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTAATATTATTATTATTAATAATTA
Found at i:30546900 original size:15 final size:15
Alignment explanation
Indices: 30546847--30546908 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
30546837 TTTTGTTTTT
*
30546847 ATATTTTTATATAATTA
1 ATATTATTAT-TAA-TA
*
30546864 ATAATTATTTTTAAATA
1 AT-ATTATTATT-AATA
*
30546881 TTATTATTATTAATA
1 ATATTATTATTAATA
*
30546896 ATATTATCATTAA
1 ATATTATTATTAA
30546909 AATTAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 15 0.41
16 8 0.22
17 6 0.16
18 8 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATTATTAATA
Found at i:30547264 original size:109 final size:109
Alignment explanation
Indices: 30547120--30547478 Score: 495
Period size: 109 Copynumber: 3.3 Consensus size: 109
30547110 TTTATTCCCA
* * * *
30547120 GAGGTCTTACAAATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAAACCGTAAGTTAAAAAA
1 GAGGTCTTACAAATCATGCCCGGAAGTCTTACAGAATTGATTGGGATAAACCGCAAGTTAAAAAA
*
30547185 TAAAGAATCGATCGAGATAACATCGCGAATCAAATTTATGCTTG
66 TAAAGAATCGATCGGGATAACATCGCGAATCAAATTTATGCTTG
* * *
30547229 AAGGTCTTACAAATCATGCCCGGAAGTCTTGCAGAATTGATTGGGATAAACTGCAAGTTAAAAAA
1 GAGGTCTTACAAATCATGCCCGGAAGTCTTACAGAATTGATTGGGATAAACCGCAAGTTAAAAAA
*
30547294 TAAAGAATCGATCGGGATAACATCGCGAATCGAATTTATGCTTG
66 TAAAGAATCGATCGGGATAACATCGCGAATCAAATTTATGCTTG
* * * * * *
30547338 GAGATCTTAGACATCATGCTC-GAAGGTCTTACAGAATTGATTGAGATAACACCACAAGTTAAAA
1 GAGGTCTTACAAATCATGCCCGGAA-GTCTTACAGAATTGATTGGGATAA-ACCGCAAGTTAAAA
* ** *
30547402 GATAAAGAATCGATCGGGATAACATCGTAAATCAAATTTATGCTCG
64 AATAAAGAATCGATCGGGATAACATCGCGAATCAAATTTATGCTTG
* * *
30547448 GAGGTCTTAAAAATCATGCCCAGAGGTCTTA
1 GAGGTCTTACAAATCATGCCCGGAAGTCTTA
30547479 GAAATCATGC
Statistics
Matches: 219, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
108 3 0.01
109 138 0.63
110 76 0.35
111 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (109 bp):
GAGGTCTTACAAATCATGCCCGGAAGTCTTACAGAATTGATTGGGATAAACCGCAAGTTAAAAAA
TAAAGAATCGATCGGGATAACATCGCGAATCAAATTTATGCTTG
Found at i:30547466 original size:22 final size:23
Alignment explanation
Indices: 30547441--30547546 Score: 94
Period size: 22 Copynumber: 4.8 Consensus size: 23
30547431 AATCAAATTT
*
30547441 ATGCTCGGAGGTCTTA-AAAATC
1 ATGCCCGGAGGTCTTACAAAATC
* *
30547463 ATGCCCAGAGGTCTTA-GAAATC
1 ATGCCCGGAGGTCTTACAAAATC
* * *
30547485 ATGCTCGAAGGTCTTACAGAATC
1 ATGCCCGGAGGTCTTACAAAATC
* * * *
30547508 ATGCCCTGAGGTCTTATAGAATT
1 ATGCCCGGAGGTCTTACAAAATC
30547531 AT--CCGGAGGTCTTACA
1 ATGCCCGGAGGTCTTACA
30547547 GAATTGACTG
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
21 12 0.18
22 32 0.47
23 24 0.35
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (23 bp):
ATGCCCGGAGGTCTTACAAAATC
Found at i:30547511 original size:23 final size:22
Alignment explanation
Indices: 30547449--30547550 Score: 86
Period size: 23 Copynumber: 4.6 Consensus size: 22
30547439 TTATGCTCGG
* *
30547449 AGGTCTTA-AAAATCATGCCCA
1 AGGTCTTACAGAATCATGCCGA
*
30547470 GAGGTCTTAGA-AATCATGCTCGA
1 -AGGTCTTACAGAATCATGC-CGA
30547493 AGGTCTTACAGAATCATGCCCTG-
1 AGGTCTTACAGAATCATG-CC-GA
* * *
30547516 AGGTCTTATAGAATTAT-CCGG
1 AGGTCTTACAGAATCATGCCGA
30547537 AGGTCTTACAGAAT
1 AGGTCTTACAGAAT
30547551 TGACTGGGAT
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.01
21 15 0.22
22 25 0.36
23 26 0.38
24 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (22 bp):
AGGTCTTACAGAATCATGCCGA
Found at i:30547541 original size:44 final size:45
Alignment explanation
Indices: 30547441--30547550 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 45
30547431 AATCAAATTT
*
30547441 ATGCTCGGAGGTCTTA-AAAATCATGCCCAGAGGTCTTAGAAATC
1 ATGCTCGGAGGTCTTACAGAATCATGCCCAGAGGTCTTAGAAATC
* * * *
30547485 ATGCTCGAAGGTCTTACAGAATCATGCCCTGAGGTCTTATAGAATT
1 ATGCTCGGAGGTCTTACAGAATCATGCCCAGAGGTCTTAGA-AATC
30547531 AT-C-CGGAGGTCTTACAGAAT
1 ATGCTCGGAGGTCTTACAGAAT
30547551 TGACTGGGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 31 0.53
45 22 0.38
46 5 0.09
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
ATGCTCGGAGGTCTTACAGAATCATGCCCAGAGGTCTTAGAAATC
Found at i:30547637 original size:24 final size:24
Alignment explanation
Indices: 30547610--30547661 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
30547600 ATCGCGAATC
* *
30547610 GAATTTATACCCGAAGATTTTACA
1 GAATTCATACCCGAAGATCTTACA
* *
30547634 GAA-TCATGCCCGGAGATCTTACA
1 GAATTCATACCCGAAGATCTTACA
30547657 GAATT
1 GAATT
30547662 GACTGGGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (24 bp):
GAATTCATACCCGAAGATCTTACA
Found at i:30547749 original size:110 final size:110
Alignment explanation
Indices: 30547533--30547770 Score: 327
Period size: 110 Copynumber: 2.2 Consensus size: 110
30547523 ATAGAATTAT
* *
30547533 CCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAAATAAAGAATCGATTGGGACA
1 CCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAAATAAAAAATCGATCGGGACA
* * *
30547598 ACATCGCGAATCGAATTTATACCCGAAGATTTTACAGAATCATGC
66 ACACCGCGAATCGAAATTATACCCGAAGATCTTACAGAATCATGC
* * *
30547643 CCGGAGATCTTACAGAATTGACTGGGATAACACCGCAAGTCGAAAGATAAAAAATCGATCGGGAT
1 CCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTC-AAAAATAAAAAATCGATCGGGAC
* * * *
30547708 AACACCGTGAATCGAAATTATGCCCGAA-AGTCTTAGA-AATCATGT
65 AACACCGCGAATCGAAATTATACCCGAAGA-TCTTACAGAATCATGC
*
30547753 TCGGAGGTCTTACAGAAT
1 CCGGAGGTCTTACAGAAT
30547771 CATACTCAGA
Statistics
Matches: 112, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
110 64 0.57
111 48 0.43
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (110 bp):
CCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAAATAAAAAATCGATCGGGACA
ACACCGCGAATCGAAATTATACCCGAAGATCTTACAGAATCATGC
Found at i:30547750 original size:286 final size:285
Alignment explanation
Indices: 30547230--30548053 Score: 896
Period size: 286 Copynumber: 2.9 Consensus size: 285
30547220 TTATGCTTGA
* * * * * *
30547230 AGGTCTTACAAATCATGCCCGGAAGTCTTGCAGAATTGATTGGGATAA-ACTGCAAGTTAAAAAA
1 AGGTCCTAGAAATCAT-CCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAG-TAAAAAA
* ** *
30547294 TAAAGAATCGATCGGGATAACATCGCGAATCGAATTTATGCTTGGAGATCTT--AGACATCATGC
64 TAAAGAATCGATCGGGACAACATCGCGAATCGAATTTATGCCCGAAGATCTTACAGA-ATCATGC
* * * * *
30547357 TCGAAGGTCTTACAGAATTGATTGAGATAACACCACAAGTTAAAAGATAAAGAATCGATCGGGAT
128 CCGAAGGTCTTACAGAATTGACTGGGATAACACCACAAGTCAAAAGATAAAAAATCGATCGGGAT
* * * * * *
30547422 AACATCGTAAATCAAATTTATGCTCGGAGGTCTTAAAAATCATGCCCAGAGGTCTTAGA-AATCA
193 AACACCGTGAATCAAATTTATGCCCGAAGGTCTTAAAAATCATGCCCGGAGGTCTTACAGAATCA
* * * *
30547486 TGCTC-GAAGGTCTTACAGAATCATGCCCTG
258 TACTCAG-AGGTCTCACAGAAT--TACCCGG
* * * *
30547516 AGGTCTTATAGAATTAT-CCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAAAT
1 AGGTCCTAGA-AATCATCCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTAAAAAAT
* * *
30547580 AAAGAATCGATTGGGACAACATCGCGAATCGAATTTATACCCGAAGATTTTACAGAATCATGCCC
65 AAAGAATCGATCGGGACAACATCGCGAATCGAATTTATGCCCGAAGATCTTACAGAATCATGCCC
* * * *
30547645 GGAGATCTTACAGAATTGACTGGGATAACACCGCAAGTCGAAAGATAAAAAATCGATCGGGATAA
130 GAAGGTCTTACAGAATTGACTGGGATAACACCACAAGTCAAAAGATAAAAAATCGATCGGGATAA
* * **
30547710 CACCGTGAATCGAAA-TTATGCCCGAAAGTCTTAGAAATCATGTTCGGAGGTCTTACAGAATCAT
195 CACCGTGAATC-AAATTTATGCCCGAAGGTCTTAAAAATCATGCCCGGAGGTCTTACAGAATCAT
30547774 ACTCAGAGGTCTCACAGAATTACCCGG
259 ACTCAGAGGTCTCACAGAATTACCCGG
* * * * *
30547801 AGGTCCTAGAAATCATGCCCGGAGGTCTTATAGAATTGACTGGGATAACATCGTAAGTTAGAAAT
1 AGGTCCTAGAAATCAT-CCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTAAAAAAT
** * * * * * * *
30547866 AAAGAATCGATCAAGACAATACCGCGAATCAAAATTATGCCC-AGAGGTCTTACAAAAT--TACC
65 AAAGAATCGATCGGGACAACATCGCGAATCGAATTTATGCCCGA-AGATCTTACAGAATCATGCC
** * * *
30547928 TAAAGGTCTTACAGAATTGACT-GGATAACACTATAAGTCAAAAGATAAAAAATCGATTGGGATA
129 CGAAGGTCTTACAGAATTGACTGGGATAACACCACAAGTCAAAAGATAAAAAATCGATCGGGATA
* * * ** *
30547992 ACACCGCGAATTAAATTTATGTCTTAAGGTCTTACAAATCATGCCCGGAGGTCTTACAGAAT
194 ACACCGTGAATCAAATTTATGCCCGAAGGTCTTAAAAATCATGCCCGGAGGTCTTACAGAAT
30548054 TGACTGGGAT
Statistics
Matches: 452, Mismatches: 75, Indels: 25
0.82 0.14 0.05
Matches are distributed among these distances:
282 3 0.01
283 86 0.19
284 26 0.06
285 92 0.20
286 211 0.47
287 33 0.07
288 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (285 bp):
AGGTCCTAGAAATCATCCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTAAAAAATA
AAGAATCGATCGGGACAACATCGCGAATCGAATTTATGCCCGAAGATCTTACAGAATCATGCCCG
AAGGTCTTACAGAATTGACTGGGATAACACCACAAGTCAAAAGATAAAAAATCGATCGGGATAAC
ACCGTGAATCAAATTTATGCCCGAAGGTCTTAAAAATCATGCCCGGAGGTCTTACAGAATCATAC
TCAGAGGTCTCACAGAATTACCCGG
Found at i:30547805 original size:21 final size:22
Alignment explanation
Indices: 30547754--30547805 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
30547744 AAATCATGTT
* *
30547754 CGGAGGTCTTACAGAATCATACT
1 CGGAGGTCTCACAGAAT-ATACC
*
30547777 CAGAGGTCTCACAGAAT-TACC
1 CGGAGGTCTCACAGAATATACC
30547798 CGGAGGTC
1 CGGAGGTC
30547806 CTAGAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 10 0.40
23 15 0.60
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (22 bp):
CGGAGGTCTCACAGAATATACC
Found at i:30547982 original size:108 final size:108
Alignment explanation
Indices: 30547823--30548141 Score: 358
Period size: 109 Copynumber: 2.9 Consensus size: 108
30547813 TCATGCCCGG
* * * *** *
30547823 AGGTCTTATAGAATTGACTGGGATAACA-TCGTAAGTTAGAAATAAAGAATCGATCAAGACAATA
1 AGGTCTTACAGAATTGACTGGGATAACACT-GTAAGTCAAAAATAAAGAATCGATTGGGACAACA
* * *
30547887 CCGCGAATCAAAATTATGCCCAGAGGTCTTACAAAATTACCTAA
65 CCGCGAATCAAATTTATGCCTAGAGGTCTTACAAAATTACCCAA
* * *
30547931 AGGTCTTACAGAATTGACT-GGATAACACTATAAGTCAAAAGATAAAAAATCGATTGGGATAACA
1 AGGTCTTACAGAATTGACTGGGATAACACTGTAAGTCAAAA-ATAAAGAATCGATTGGGACAACA
* * * **
30547995 CCGCGAATTAAATTTATGTCTTA-AGGTCTTAC-AAATCATGCCCGG
65 CCGCGAATCAAATTTATG-CCTAGAGGTCTTACAAAAT--TACCCAA
*
30548040 AGGTCTTACAGAATTGACTGGGATAACACTGCAAGTCAAAAATAAAGAATCGATTGGGACAACAC
1 AGGTCTTACAGAATTGACTGGGATAACACTGTAAGTCAAAAATAAAGAATCGATTGGGACAACAC
* * * *
30548105 CGCGAATCGAATTTATGCCTGGAGATCTTACAGAATT
66 CGCGAATCAAATTTATGCCTAGAGGTCTTACAAAATT
30548142 GACTGGGATA
Statistics
Matches: 175, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
107 20 0.11
108 64 0.37
109 69 0.39
110 22 0.13
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (108 bp):
AGGTCTTACAGAATTGACTGGGATAACACTGTAAGTCAAAAATAAAGAATCGATTGGGACAACAC
CGCGAATCAAATTTATGCCTAGAGGTCTTACAAAATTACCCAA
Found at i:30548210 original size:88 final size:87
Alignment explanation
Indices: 30548027--30548222 Score: 293
Period size: 88 Copynumber: 2.2 Consensus size: 87
30548017 AAGGTCTTAC
* *
30548027 AAATCATGCCCGGAGGTCTTACAGAATTGACTGGGATAACACTGCAAGTCAAAAATAAAGAATCG
1 AAATTATGCCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAAATAAAGAATCG
* *
30548092 ATTGGGACAACACCGCGAATCG
66 ATTGGAACAACACCGCGAATCA
* * * *
30548114 AATTTATGCCTGGAGATCTTACAGAATTGACTGGGATAACACCGCAAGTCGAAAGATAAAGAATC
1 AAATTATGCCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTC-AAAAATAAAGAATC
* *
30548179 GATTGGAATAACACTGCGAATCA
65 GATTGGAACAACACCGCGAATCA
30548202 AAATTATGCCCGGAGGTCTTA
1 AAATTATGCCCGGAGGTCTTA
30548223 GAAATCATGC
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
87 45 0.47
88 50 0.53
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (87 bp):
AAATTATGCCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAAATAAAGAATCG
ATTGGAACAACACCGCGAATCA
Found at i:30548232 original size:22 final size:22
Alignment explanation
Indices: 30548202--30548269 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
30548192 CTGCGAATCA
* * *
30548202 AAATTATGCCCGGAGGTCTTAG
1 AAATCATGCCCGAAGGTCTTAC
**
30548224 AAATCATGCCCGAAAATCTTAC
1 AAATCATGCCCGAAGGTCTTAC
30548246 AGAATCATGCCCGAAGGTCTTAC
1 A-AATCATGCCCGAAGGTCTTAC
30548269 A
1 A
30548270 GAATTGACTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (22 bp):
AAATCATGCCCGAAGGTCTTAC
Found at i:30548357 original size:133 final size:133
Alignment explanation
Indices: 30548130--30548383 Score: 454
Period size: 133 Copynumber: 1.9 Consensus size: 133
30548120 TGCCTGGAGA
* *
30548130 TCTTACAGAATTGACTGGGATAACACCGCAAGTCGAAAGATAAAGAATCGATTGGAATAACACTG
1 TCTTACAGAATTGACTGGGATAACACCGCAAGTCGAAAGATAAAGAATCGATCGGAATAACACCG
30548195 CGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCGAAAATCTTACAGAATCATGCCCGA
66 CGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCGAAAATCTTACAGAATCATGCCCGA
30548260 AGG
131 AGG
* *
30548263 TCTTACAGAATTGACTGGGATAGCACCGCAAGTCGAAAGATAAAGAATCGATCGGGATAACACCG
1 TCTTACAGAATTGACTGGGATAACACCGCAAGTCGAAAGATAAAGAATCGATCGGAATAACACCG
**
30548328 CGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTTACAGAAT
66 CGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCGAAAATCTTACAGAAT
30548384 TGACTGGGAT
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 115 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (133 bp):
TCTTACAGAATTGACTGGGATAACACCGCAAGTCGAAAGATAAAGAATCGATCGGAATAACACCG
CGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCGAAAATCTTACAGAATCATGCCCGA
AGG
Found at i:30548365 original size:22 final size:22
Alignment explanation
Indices: 30548335--30548377 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
30548325 CCGCGAATCA
* *
30548335 AAATTATGCCCGGAGGTCTTAG
1 AAATCATGCCCGAAGGTCTTAG
30548357 AAATCATGCCCGAAGGTCTTA
1 AAATCATGCCCGAAGGTCTTA
30548378 CAGAATTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (22 bp):
AAATCATGCCCGAAGGTCTTAG
Found at i:30548390 original size:110 final size:110
Alignment explanation
Indices: 30547796--30548495 Score: 533
Period size: 110 Copynumber: 6.4 Consensus size: 110
30547786 CACAGAATTA
* * * * * *
30547796 CCCGGAGGTCCTAGAAATCATGCCCGGAGGTCTTATAGAATTGACTGGGATAACATCGTAAGT-T
1 CCCGGAGGTCTTACAAATCATGCCCGAAGGTCTTACAGAATTGACTGGGATAACACCGTAAGTCG
** * *
30547860 AGAA-ATAAAGAATCGATCAAGACAATACCGCGAATCAAAATTATG
66 A-AAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
* * ** **
30547905 CCCAGAGGTCTTACAAA--ATTACCTAAAGGTCTTACAGAATTGACT-GGATAACACTATAAGTC
1 CCCGGAGGTCTTACAAATCA-TGCCCGAAGGTCTTACAGAATTGACTGGGATAACACCGTAAGTC
* * * * *
30547967 AAAAGATAAAAAATCGATTGGGATAACACCGCGAATTAAATTTATG
65 GAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
* *** * * *
30548013 TCTTAAGGTCTTACAAATCATGCCCGGAGGTCTTACAGAATTGACTGGGATAACACTGCAAGTC-
1 CCCGGAGGTCTTACAAATCATGCCCGAAGGTCTTACAGAATTGACTGGGATAACACCGTAAGTCG
* * * * *
30548077 AAAAATAAAGAATCGATTGGGACAACACCGCGAATCGAATTTATG
66 AAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
* * * * * * * **
30548122 CCTGGAGATCTTACAGAAT--TGACTG--GG-ATAACACCGCAAGTCGA--AAGATAA-A--G-A
1 CCCGGAGGTCTTACA-AATCATGCCCGAAGGTCTTACA--G-AA-TTGACTGGGATAACACCGTA
** * * *** * * *
30548176 A-TCGATTGGA-ATAACACTGCGAATCAAAATTATGC-CCG-GAGGTCTTAGAAATCATG
61 AGTCGA-AAGATA-AAGAAT-CG-ATCGGGA-TA-ACACCGCGA-ATC--A-AAATTATG
* ** * *
30548232 CCCGAAAATCTTACAGAATCATGCCCGAAGGTCTTACAGAATTGACTGGGATAGCACCGCAAGTC
1 CCCGGAGGTCTTACA-AATCATGCCCGAAGGTCTTACAGAATTGACTGGGATAACACCGTAAGTC
30548297 GAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
65 GAAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
* *
30548343 CCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTTACAGAATTGACTGGGATAACATCGTAAGTCG
1 CCCGGAGGTCTTACAAATCATGCCCGAAGGTCTTACAGAATTGACTGGGATAACACCGTAAGTCG
30548408 AAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
66 AAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
* *
30548453 CCCGGAGGTCTTACAGAATCATGTCCGGAGGTCTTACAGAATT
1 CCCGGAGGTCTTACA-AATCATGCCCGAAGGTCTTACAGAATT
30548496 ACCCGAAGGT
Statistics
Matches: 461, Mismatches: 92, Indels: 74
0.74 0.15 0.12
Matches are distributed among these distances:
102 2 0.00
103 4 0.01
104 6 0.01
105 6 0.01
106 8 0.02
107 28 0.06
108 75 0.16
109 90 0.20
110 147 0.32
111 46 0.10
112 7 0.02
113 6 0.01
114 10 0.02
115 10 0.02
116 3 0.01
117 8 0.02
118 5 0.01
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (110 bp):
CCCGGAGGTCTTACAAATCATGCCCGAAGGTCTTACAGAATTGACTGGGATAACACCGTAAGTCG
AAAGATAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG
Found at i:30548507 original size:21 final size:21
Alignment explanation
Indices: 30548453--30548516 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
30548443 CAAAATTATG
*
30548453 CCCGGAGGTCTTACAGAATCATG
1 CCCGGAGGTCTTACAGAAT--TA
*
30548476 TCCGGAGGTCTTACAGAATTA
1 CCCGGAGGTCTTACAGAATTA
*
30548497 CCCGAAGGTCTTACAGAATT
1 CCCGGAGGTCTTACAGAATT
30548517 GATTGAGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.51
23 18 0.49
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
CCCGGAGGTCTTACAGAATTA
Found at i:30548584 original size:131 final size:130
Alignment explanation
Indices: 30548365--30548624 Score: 371
Period size: 131 Copynumber: 2.0 Consensus size: 130
30548355 AGAAATCATG
* * * * *
30548365 CCCGAAGGTCTTACAGAATTGACTGGGATAACATCGTAAGTCGAAAGATAAAGAATCGATCGGGA
1 CCCGAAGGTCTTACAGAATTGACTGAGATAACATCATAAGTCAAAAAATAAAGAATCGATCGAGA
* *
30548430 TAACACCGCGAATCAAAATTATGCCCGGAGGTCTTACAGAATCATGTCCGGAGGTCTTACAGAAT
66 CAACACCGCGAATCAAAATTATGCCCGAAGGTCTTACAGAAT--TGTCCGGAGGTCTTACAGAAT
30548495 TA
129 TA
*
30548497 CCCGAAGGTCTTACAGAATTGATTGAGATAACA-CATCAAGT-AAAAAATAAAGAATCGATCGAG
1 CCCGAAGGTCTTACAGAATTGACTGAGATAACATCAT-AAGTCAAAAAATAAAGAATCGATCGAG
* * * *
30548560 ACAATACCGTGAATCGAAATTATGCTCGAAGGTCTTACAGAATTGTCCGGAGGTCTTACAGAATT
65 ACAACACCGCGAATCAAAATTATGCCCGAAGGTCTTACAGAATTGTCCGGAGGTCTTACAGAATT
30548625 GACTGGATAA
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
129 22 0.19
131 58 0.50
132 35 0.30
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (130 bp):
CCCGAAGGTCTTACAGAATTGACTGAGATAACATCATAAGTCAAAAAATAAAGAATCGATCGAGA
CAACACCGCGAATCAAAATTATGCCCGAAGGTCTTACAGAATTGTCCGGAGGTCTTACAGAATTA
Found at i:30548682 original size:108 final size:108
Alignment explanation
Indices: 30548481--30548691 Score: 300
Period size: 108 Copynumber: 2.0 Consensus size: 108
30548471 TCATGTCCGG
*
30548481 AGGTCTTACAGAATTACCCGAAGGTCTTACAGAATTGATTGAGATAACACATCAAGTAAAAAATA
1 AGGTCTTACAGAATTACCCGAAGGTCTTACAGAATTGACTGAGATAACACATCAAGTAAAAAATA
*
30548546 AAGAATCGATCGAGACAATACCGTGAATCGAAATTATGCTCGA
66 AAGAATCGATCGAGACAATACCGCGAATCGAAATTATGCTCGA
** * *
30548589 AGGTCTTACAGAATTGTCCGGAGGTCTTACAGAATTGACTG-GATAACACTAT-AAGTCAAAAGA
1 AGGTCTTACAGAATTACCCGAAGGTCTTACAGAATTGACTGAGATAACAC-ATCAAGT-AAAAAA
* * * *
30548652 TAAAGAATCGATCGGGATAATATCGCGAATCGAATTTATG
64 TAAAGAATCGATCGAGACAATACCGCGAATCGAAATTATG
30548692 GCCTAAGATT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
107 12 0.13
108 79 0.87
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (108 bp):
AGGTCTTACAGAATTACCCGAAGGTCTTACAGAATTGACTGAGATAACACATCAAGTAAAAAATA
AAGAATCGATCGAGACAATACCGCGAATCGAAATTATGCTCGA
Found at i:30548706 original size:108 final size:108
Alignment explanation
Indices: 30548484--30548726 Score: 296
Period size: 108 Copynumber: 2.2 Consensus size: 108
30548474 TGTCCGGAGG
* * *
30548484 TCTTACAGAATTACCCGAAGGTCTTACAGAATTGATTGAGATAACACATCAAGTAAAAAATAAAG
1 TCTTACAGAATTGCCCGGAGGTCTTACAGAATTGACTGAGATAACACATCAAGTAAAAAATAAAG
* *
30548549 AATCGATCGAGACAATACCGTGAATCGAAATTATGCTCGAAGG
66 AATCGATCGAGACAATACCGCGAATCGAAATTATGCTCGAAGA
* *
30548592 TCTTACAGAATTGTCCGGAGGTCTTACAGAATTGACTG-GATAACACTAT-AAGTCAAAAGATAA
1 TCTTACAGAATTGCCCGGAGGTCTTACAGAATTGACTGAGATAACAC-ATCAAGT-AAAAAATAA
* * * * *
30548655 AGAATCGATCGGGATAATATCGCGAATCGAATTTATGGC-CTAAGA
64 AGAATCGATCGAGACAATACCGCGAATCGAAATTAT-GCTCGAAGA
*
30548700 TTTTACA-AATCATGCCCGGAGGTCTTA
1 TCTTACAGAAT--TGCCCGGAGGTCTTA
30548727 TAAAATCATG
Statistics
Matches: 116, Mismatches: 14, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
107 15 0.13
108 85 0.73
109 16 0.14
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (108 bp):
TCTTACAGAATTGCCCGGAGGTCTTACAGAATTGACTGAGATAACACATCAAGTAAAAAATAAAG
AATCGATCGAGACAATACCGCGAATCGAAATTATGCTCGAAGA
Found at i:30548787 original size:132 final size:132
Alignment explanation
Indices: 30548610--30548858 Score: 340
Period size: 132 Copynumber: 1.9 Consensus size: 132
30548600 AATTGTCCGG
* * *
30548610 AGGTCTTACAGAATTGACTGGATAACACTATAAGTCAAAAGATAAAGAATCGATCGGGATAATA-
1 AGGTCTTACAGAATTGACTGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGGGATAACAC
* * * * * *
30548674 TCGCGAATCGAATTTATGGCCTAAGATTTTACAAATCATGCCCGGAGGTCTTATAAAATCATGTT
66 T-ACGAATCAAAATTATGCCCGAAGATCTTACAAATCATGCCCGGAGGTCTTATAAAATCATGTT
30548739 CGA
130 CGA
* *
30548742 AGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAA-ATAAAGAATCGATTGGGATAACA
1 AGGTCTTACAGAATTGACT-GGATAACACCACAAGTCAAAAGATAAAGAATCGATCGGGATAACA
* * *
30548806 CTACGAATCAAAATTATGCCCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTA
65 CTACGAATCAAAATTATGCCCGAAGATCTTACAAATCATGCCCGGAGGTCTTA
30548859 GAGATTATGC
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
132 82 0.81
133 19 0.19
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (132 bp):
AGGTCTTACAGAATTGACTGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGGGATAACAC
TACGAATCAAAATTATGCCCGAAGATCTTACAAATCATGCCCGGAGGTCTTATAAAATCATGTTC
GA
Found at i:30548846 original size:22 final size:22
Alignment explanation
Indices: 30548816--30548886 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
30548806 CTACGAATCA
*
30548816 AAATTATGCCCGGAGGTCTTAG
1 AAATCATGCCCGGAGGTCTTAG
30548838 AAATCATGCCCGGAGGTCTTAG
1 AAATCATGCCCGGAGGTCTTAG
* * * *
30548860 AGATTATGCCCAGAGGTCTTAC
1 AAATCATGCCCGGAGGTCTTAG
30548882 AAATC
1 AAATC
30548887 TTAAAATCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (22 bp):
AAATCATGCCCGGAGGTCTTAG
Found at i:30550950 original size:18 final size:17
Alignment explanation
Indices: 30550923--30550978 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
30550913 AATATGTCTA
30550923 TTTTGTTTGTTTTTTTTT
1 TTTTG-TTGTTTTTTTTT
*
30550941 TTTTGCTTGTTTTATTTT
1 TTTTG-TTGTTTTTTTTT
30550959 TTTTGTT-TTTTGTTTTT
1 TTTTGTTGTTTT-TTTTT
30550976 TTT
1 TTT
30550979 ATGCCCCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.12
17 9 0.26
18 21 0.62
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (17 bp):
TTTTGTTGTTTTTTTTT
Found at i:30550967 original size:25 final size:24
Alignment explanation
Indices: 30550932--30550980 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
30550922 ATTTTGTTTG
30550932 TTTTTTTTTTTTTGCTTGTTTTAT
1 TTTTTTTTTTTTTGCTTGTTTTAT
* *
30550956 TTTTTTTGTTTTTTGTTTTTTTTAT
1 TTTTTTT-TTTTTTGCTTGTTTTAT
30550981 GCCCCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.04, C:0.02, G:0.08, T:0.86
Consensus pattern (24 bp):
TTTTTTTTTTTTTGCTTGTTTTAT
Found at i:30555480 original size:15 final size:15
Alignment explanation
Indices: 30555460--30555497 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
30555450 TTATCAAGAA
30555460 GTGCATGAGATGCAT
1 GTGCATGAGATGCAT
*
30555475 GTGCATGGGATGCAT
1 GTGCATGAGATGCAT
30555490 GTGCATGA
1 GTGCATGA
30555498 AAAATACGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (15 bp):
GTGCATGAGATGCAT
Found at i:30557086 original size:14 final size:15
Alignment explanation
Indices: 30557067--30557095 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30557057 GTATTATTCT
30557067 TTTTATTAT-AAATA
1 TTTTATTATCAAATA
30557081 TTTTATTATCAAATA
1 TTTTATTATCAAATA
30557096 GTAAATTAAA
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:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTATTATCAAATA
Found at i:30557600 original size:51 final size:51
Alignment explanation
Indices: 30557535--30557648 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 51
30557525 AGGATATGAA
* *
30557535 AGGTTTAGGG-TTTTGATTTTAGAGTTTAGAGATTTT-AGG-GTTTGGGTTTTG
1 AGGTTT-GGGATTTTGATTTAAGAGTTT-G-GATTTTAAGGAGTTTGGATTTTG
* *
30557586 TGGTTTGGGATTTTGATTTAAGAGTTTGGATTTTAAGGATTTTGGATTTTG
1 AGGTTTGGGATTTTGATTTAAGAGTTTGGATTTTAAGGAGTTTGGATTTTG
30557637 AGGTTT-GGATTT
1 AGGTTTGGGATTT
30557649 AAGAGTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
49 6 0.11
50 13 0.24
51 36 0.65
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (51 bp):
AGGTTTGGGATTTTGATTTAAGAGTTTGGATTTTAAGGAGTTTGGATTTTG
Found at i:30557622 original size:15 final size:15
Alignment explanation
Indices: 30557602--30557656 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
30557592 GGGATTTTGA
30557602 TTTAAGAGTTTGGAT
1 TTTAAGAGTTTGGAT
*
30557617 TTTAAGGATTTTGGAT
1 TTTAA-GAGTTTGGAT
*
30557633 TTTGAG-GTTTGGA-
1 TTTAAGAGTTTGGAT
30557646 TTTAAGAGTTT
1 TTTAAGAGTTT
30557657 AAAGGTTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.15
14 10 0.29
15 6 0.18
16 13 0.38
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (15 bp):
TTTAAGAGTTTGGAT
Found at i:30557631 original size:16 final size:16
Alignment explanation
Indices: 30557593--30557714 Score: 62
Period size: 16 Copynumber: 7.9 Consensus size: 16
30557583 TTGTGGTTTG
30557593 GGATTTT-GA-TTTAA
1 GGATTTTGGATTTTAA
*
30557607 -GAGTTTGGATTTTAA
1 GGATTTTGGATTTTAA
*
30557622 GGATTTTGGATTTTGA
1 GGATTTTGGATTTTAA
30557638 GG--TTTGGA-TTTAA
1 GGATTTTGGATTTTAA
* ** * **
30557651 -GAGTTTAAAGGTTTGG
1 GGATTTTGGA-TTTTAA
*
30557667 GGATTTTGGATTTTTGA
1 GGATTTTGGA-TTTTAA
*
30557684 GGGTTTTGGATTTT-A
1 GGATTTTGGATTTTAA
*
30557699 GGAGTTTCGGATTTTA
1 GGA-TTTTGGATTTTA
30557715 TGAGGTTTCG
Statistics
Matches: 81, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
12 1 0.01
13 9 0.11
14 12 0.15
15 8 0.10
16 32 0.40
17 19 0.23
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (16 bp):
GGATTTTGGATTTTAA
Found at i:30557656 original size:14 final size:14
Alignment explanation
Indices: 30557600--30557656 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
30557590 TTGGGATTTT
30557600 GATTTAAGAGTTTG
1 GATTTAAGAGTTTG
*
30557614 GATTTTAAGGATTTTG
1 GA-TTTAA-GAGTTTG
*
30557630 GATTT-TGAGGTTTG
1 GATTTAAGA-GTTTG
30557644 GATTTAAGAGTTT
1 GATTTAAGAGTTT
30557657 AAAGGTTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 2 0.06
14 15 0.43
15 10 0.29
16 8 0.23
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (14 bp):
GATTTAAGAGTTTG
Found at i:30557690 original size:17 final size:16
Alignment explanation
Indices: 30557670--30557740 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 16
30557660 GGTTTGGGGA
30557670 TTTTGGATTTTTGAGGG
1 TTTTGGATTTTT-AGGG
30557687 TTTTGGA-TTTTAGGAG
1 TTTTGGATTTTTAGG-G
*
30557703 TTTCGGA-TTTTATGAGG
1 TTTTGGATTTTTA-G-GG
* *
30557720 TTTCGAATTTTTAGGGG
1 TTTTGGATTTTTA-GGG
30557737 TTTT
1 TTTT
30557741 AAAAACTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.07
16 16 0.35
17 20 0.43
18 7 0.15
ACGTcount: A:0.15, C:0.03, G:0.30, T:0.52
Consensus pattern (16 bp):
TTTTGGATTTTTAGGG
Found at i:30562066 original size:25 final size:24
Alignment explanation
Indices: 30562028--30562082 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
30562018 ATATCTTTCT
*
30562028 TTAAAAGGGTTCGACAATGAAGGC
1 TTAAAAGGATTCGACAATGAAGGC
30562052 TTAAACAGGATTCGACAATGAAGGC
1 TTAAA-AGGATTCGACAATGAAGGC
*
30562077 CTAAAA
1 TTAAAA
30562083 TAGAAGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.20
Consensus pattern (24 bp):
TTAAAAGGATTCGACAATGAAGGC
Found at i:30562319 original size:22 final size:22
Alignment explanation
Indices: 30562288--30562329 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30562278 TTGTCTATCC
* *
30562288 TAATTTTAGAGATACAAATACT
1 TAATTCTAGAAATACAAATACT
30562310 TAATTCTAGAAATACAAATA
1 TAATTCTAGAAATACAAATA
30562330 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAAATACAAATACT
Found at i:30565648 original size:12 final size:12
Alignment explanation
Indices: 30565632--30565661 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30565622 AAATGAAGGG
30565632 AGAGGAGGAGGA
1 AGAGGAGGAGGA
*
30565644 CGAGGAGGAGGA
1 AGAGGAGGAGGA
30565656 AGAGGA
1 AGAGGA
30565662 AGAGAGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.57, T:0.00
Consensus pattern (12 bp):
AGAGGAGGAGGA
Found at i:30572655 original size:14 final size:13
Alignment explanation
Indices: 30572635--30572682 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
30572625 TAAATATTAA
30572635 TTTTAATGAAATT
1 TTTTAATGAAATT
*
30572648 TATTTAATATAAATT
1 T-TTTAAT-GAAATT
*
30572663 TTTTAGTGAAATT
1 TTTTAATGAAATT
30572676 TTTTAAT
1 TTTTAAT
30572683 TTTAGTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 12 0.41
14 11 0.38
15 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
TTTTAATGAAATT
Found at i:30572665 original size:27 final size:27
Alignment explanation
Indices: 30572622--30572682 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
30572612 TATAAGTAAA
*
30572622 ATTTAAATATTAA-TTTTAATGAAATTT
1 ATTT-AATATAAATTTTTAATGAAATTT
*
30572649 ATTTAATATAAATTTTTTAGTGAAATTT
1 ATTTAATATAAA-TTTTTAATGAAATTT
30572677 -TTTAAT
1 ATTTAAT
30572683 TTTAGTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.23
27 10 0.33
28 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (27 bp):
ATTTAATATAAATTTTTAATGAAATTT
Found at i:30578868 original size:16 final size:17
Alignment explanation
Indices: 30578842--30578883 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
30578832 GTTTTTAAAT
* *
30578842 TATTTTAATATATACTA
1 TATTATAATATATAATA
30578859 TA-TATAATATATAATA
1 TATTATAATATATAATA
30578875 TATTATAAT
1 TATTATAAT
30578884 TATTTCACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTATAATATATAATA
Found at i:30581865 original size:15 final size:16
Alignment explanation
Indices: 30581845--30581878 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
30581835 TTAGTTTGAA
*
30581845 AATATAAAA-ACTTAC
1 AATATAAAATAATTAC
30581860 AATATAAAATAATTAC
1 AATATAAAATAATTAC
30581876 AAT
1 AAT
30581879 TTTAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATAAAATAATTAC
Found at i:30588728 original size:14 final size:12
Alignment explanation
Indices: 30588709--30588765 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
30588699 TTTAAAGCAT
30588709 TTTTAATATATATA
1 TTTTAAT-TAT-TA
30588723 TTTTAATTATTA
1 TTTTAATTATTA
*
30588735 TTTTACTT-TTA
1 TTTTAATTATTA
*
30588746 TTATTATTTATTA
1 TT-TTAATTATTA
30588759 TTATTAA
1 TT-TTAA
30588766 AAATAATTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
11 5 0.13
12 14 0.37
13 12 0.32
14 7 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTAATTATTA
Found at i:30589001 original size:14 final size:15
Alignment explanation
Indices: 30588976--30589004 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30588966 TAGTTCGATC
30588976 CAATTCAGATCGGTT
1 CAATTCAGATCGGTT
30588991 CAATT-AGATCGGTT
1 CAATTCAGATCGGTT
30589005 AGTAGCTATT
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:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (15 bp):
CAATTCAGATCGGTT
Found at i:30589112 original size:28 final size:28
Alignment explanation
Indices: 30589061--30589114 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
30589051 TCTACGCTTG
* **
30589061 AAACGACGTTGTTTTGGTCATATGCTCA
1 AAACGACGTCGTTTTGCCCATATGCTCA
*
30589089 AAACGACGTCGTTTTGCCCTTATGCT
1 AAACGACGTCGTTTTGCCCATATGCT
30589115 TTATATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (28 bp):
AAACGACGTCGTTTTGCCCATATGCTCA
Found at i:30595745 original size:24 final size:24
Alignment explanation
Indices: 30595713--30595761 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
30595703 CTGATATCAA
*
30595713 TTCATTTTTTGATTATTGCTAGCG
1 TTCATTTTTTGATTATAGCTAGCG
* *
30595737 TTCATTTTTTTATTGTAGCTAGCG
1 TTCATTTTTTGATTATAGCTAGCG
30595761 T
1 T
30595762 CTTTCTGCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.55
Consensus pattern (24 bp):
TTCATTTTTTGATTATAGCTAGCG
Found at i:30597132 original size:22 final size:23
Alignment explanation
Indices: 30597102--30597152 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
30597092 CTTATTAATT
**
30597102 TTAA-AATTTATTATTTTATCAA
1 TTAATAATTTATTATTACATCAA
*
30597124 -TAATAATTTTTTATTACATCAA
1 TTAATAATTTATTATTACATCAA
30597146 TTAATAA
1 TTAATAA
30597153 AAATCTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 15 0.62
23 6 0.25
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATAATTTATTATTACATCAA
Found at i:30597288 original size:34 final size:34
Alignment explanation
Indices: 30597250--30597314 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
30597240 TAATATTCCG
* *
30597250 AAAATTCATTTTTGGTAAATTATAAAATTTACTC
1 AAAATTCATTTTTAGTAAACTATAAAATTTACTC
* *
30597284 AAAATTTATTTTTAGTAAGCTATAAAATTTA
1 AAAATTCATTTTTAGTAAACTATAAAATTTA
30597315 TCGGATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (34 bp):
AAAATTCATTTTTAGTAAACTATAAAATTTACTC
Found at i:30597438 original size:27 final size:27
Alignment explanation
Indices: 30597370--30597445 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 27
30597360 TTTTATTTAC
* *
30597370 AAAAATTTTAAATATATAAATGAAACA
1 AAAAATTTAAAATATATATATGAAACA
30597397 AAAAATTGTAAAATATATATATGAAACA
1 AAAAATT-TAAAATATATATATGAAACA
**
30597425 AAAAATTTCCAATATATATAT
1 AAAAATTTAAAATATATATAT
30597446 TTAAAGCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (27 bp):
AAAAATTTAAAATATATATATGAAACA
Found at i:30597494 original size:28 final size:27
Alignment explanation
Indices: 30597436--30597500 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 27
30597426 AAAATTTCCA
***
30597436 ATATATATATTTAAAGCTTTTTGTTTC
1 ATATATATATTTAAAAAATTTTGTTTC
*
30597463 ATATATATATTTAAAAAAATTTTGTTTT
1 ATATATATATTT-AAAAAATTTTGTTTC
30597491 ATATATATAT
1 ATATATATAT
30597501 ATATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 12 0.36
28 21 0.64
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
ATATATATATTTAAAAAATTTTGTTTC
Found at i:30597495 original size:2 final size:2
Alignment explanation
Indices: 30597490--30597520 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30597480 AATTTTGTTT
30597490 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 T
30597521 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30598418 original size:15 final size:16
Alignment explanation
Indices: 30598398--30598431 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
30598388 TTAGTTTGAA
*
30598398 AATATAAAA-ACTTAC
1 AATATAAAATAATTAC
30598413 AATATAAAATAATTAC
1 AATATAAAATAATTAC
30598429 AAT
1 AAT
30598432 TTTAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATAAAATAATTAC
Found at i:30606163 original size:75 final size:75
Alignment explanation
Indices: 30606078--30606228 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
30606068 TACTGCAGAG
*
30606078 CTCAAGCTTCTTCCTAGGAAGTTTCTTAGTCAACATATCTGCTATATTCTTATCAGTGTGAACTT
1 CTCAAGCTTCTTCCTAGGAAGTTTCTTAGTCAACATATCTGCTATATTCCTATCAGTGTGAACTT
30606143 TCTTCAATAA
66 TCTTCAATAA
*
30606153 CTCAAGCTTCTTCCTAGGAAGTTTCTTAGTCAACATATCTGTTATATTCCTATCAGTGTGAACTT
1 CTCAAGCTTCTTCCTAGGAAGTTTCTTAGTCAACATATCTGCTATATTCCTATCAGTGTGAACTT
30606218 TCTTCAATAA
66 TCTTCAATAA
30606228 C
1 C
30606229 ATTTGATGTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (75 bp):
CTCAAGCTTCTTCCTAGGAAGTTTCTTAGTCAACATATCTGCTATATTCCTATCAGTGTGAACTT
TCTTCAATAA
Found at i:30611323 original size:22 final size:23
Alignment explanation
Indices: 30611293--30611343 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
30611283 CTTATTAATT
**
30611293 TTAA-AATTTATTATTTTATCAA
1 TTAATAATTTATTATTACATCAA
*
30611315 -TAATAATTTTTTATTACATCAA
1 TTAATAATTTATTATTACATCAA
30611337 TTAATAA
1 TTAATAA
30611344 AAATCTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 15 0.62
23 6 0.25
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATAATTTATTATTACATCAA
Found at i:30611637 original size:27 final size:26
Alignment explanation
Indices: 30611562--30611637 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 26
30611552 TTTAATTACA
*
30611562 AAAAAATTTAAATATATAAATGAAAC
1 AAAAAATTTAAATATATATATGAAAC
30611588 AAAAAATTGTAAAATATATATATGAAAC
1 AAAAAATT-T-AAATATATATATGAAAC
*
30611616 AAAAAATTTCTAATATATATAT
1 AAAAAATTT-AAATATATATAT
30611638 TTAAAACTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.18
27 13 0.29
28 24 0.53
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (26 bp):
AAAAAATTTAAATATATATATGAAAC
Found at i:30611658 original size:27 final size:28
Alignment explanation
Indices: 30611628--30611692 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
30611618 AAAATTTCTA
30611628 ATATATATATTT-AAAACTTTTTGTTTC
1 ATATATATATTTAAAAACTTTTTGTTTC
* *
30611655 ATATATATATTTAAAAATTTTTTGTTTT
1 ATATATATATTTAAAAACTTTTTGTTTC
30611683 ATATATATAT
1 ATATATATAT
30611693 ATATGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 12 0.34
28 23 0.66
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (28 bp):
ATATATATATTTAAAAACTTTTTGTTTC
Found at i:30612078 original size:18 final size:19
Alignment explanation
Indices: 30612052--30612095 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
30612042 AAAATATGAA
* *
30612052 AATAATTATGTAAATT-AT
1 AATATTTATATAAATTAAT
30612070 AATATTTATATAAATTAAT
1 AATATTTATATAAATTAAT
30612089 AAT-TTTA
1 AATATTTA
30612096 AGGTTGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AATATTTATATAAATTAAT
Found at i:30612250 original size:26 final size:27
Alignment explanation
Indices: 30612221--30612286 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
30612211 AGATCATTGG
*
30612221 ATTTGATTT-TACTAAAATCAATTATT
1 ATTTTATTTGTACTAAAATCAATTATT
30612247 ATTTTATTTAAATGTACTAAAATCAATTATT
1 ATTTTA-TT---TGTACTAAAATCAATTATT
30612278 ATTTTATTT
1 ATTTTATTT
30612287 AAATGTACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
26 5 0.15
27 3 0.09
30 3 0.09
31 23 0.68
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTTTATTTGTACTAAAATCAATTATT
Found at i:30612265 original size:31 final size:31
Alignment explanation
Indices: 30612230--30612298 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
30612220 GATTTGATTT
30612230 TACTAAAATCAATTATTATTTTATTTAAATG
1 TACTAAAATCAATTATTATTTTATTTAAATG
30612261 TACTAAAATCAATTATTATTTTATTTAAATG
1 TACTAAAATCAATTATTATTTTATTTAAATG
30612292 TACTAAA
1 TACTAAA
30612299 TAACCATGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (31 bp):
TACTAAAATCAATTATTATTTTATTTAAATG
Found at i:30612629 original size:15 final size:16
Alignment explanation
Indices: 30612609--30612642 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
30612599 TTAGTTTGAA
*
30612609 AATATAAAA-ACTTAC
1 AATATAAAATAATTAC
30612624 AATATAAAATAATTAC
1 AATATAAAATAATTAC
30612640 AAT
1 AAT
30612643 TTTAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AATATAAAATAATTAC
Found at i:30625055 original size:25 final size:27
Alignment explanation
Indices: 30625018--30625075 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
30625008 TAAATTAAGG
*
30625018 ATAAAATAGTAAATGTAATT-TTGTTT-
1 ATAAATTAGTAAAT-TAATTATTGTTTA
*
30625044 ATAAATTA-TAAATTAATTATTTTTTA
1 ATAAATTAGTAAATTAATTATTGTTTA
30625070 ATAAAT
1 ATAAAT
30625076 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.18
25 10 0.36
26 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (27 bp):
ATAAATTAGTAAATTAATTATTGTTTA
Found at i:30625577 original size:34 final size:34
Alignment explanation
Indices: 30625539--30625603 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
30625529 TAATATTCCG
* *
30625539 AAAATTCATTTTTGGTAAATTATAAAATTTACTC
1 AAAATTCATTTTTAGTAAACTATAAAATTTACTC
* *
30625573 AAAATTTATTTTTAGTAAGCTATAAAATTTA
1 AAAATTCATTTTTAGTAAACTATAAAATTTA
30625604 TCAGATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (34 bp):
AAAATTCATTTTTAGTAAACTATAAAATTTACTC
Found at i:30625727 original size:27 final size:27
Alignment explanation
Indices: 30625659--30625734 Score: 107
Period size: 28 Copynumber: 2.8 Consensus size: 27
30625649 TTTTATTTAC
* *
30625659 AAAAATTTTAAATATATAAATGAAACA
1 AAAAATTTAAAATATATATATGAAACA
30625686 AAAAATTGTAAAATATATATATGAAACA
1 AAAAATT-TAAAATATATATATGAAACA
**
30625714 AAAAATTTCCAATATATATAT
1 AAAAATTTAAAATATATATAT
30625735 ATATTTAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.43
28 25 0.57
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (27 bp):
AAAAATTTAAAATATATATATGAAACA
Found at i:30625778 original size:28 final size:29
Alignment explanation
Indices: 30625726--30625795 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 29
30625716 AAATTTCCAA
**
30625726 TATATATATATATTTAAAGCTTTTTGTT-
1 TATATATATATATTTAAAAATTTTTGTTC
30625754 TCATATATATAT-TTTAAAAATTTTTGTTC
1 T-ATATATATATATTTAAAAATTTTTGTTC
30625783 TATATATATATAT
1 TATATATATATAT
30625796 ATATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 25 0.68
29 12 0.32
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (29 bp):
TATATATATATATTTAAAAATTTTTGTTC
Done.