Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 98 of 121
Found at i:16708774 original size:43 final size:43
Alignment explanation
Indices: 16708562--16708765 Score: 205
Period size: 43 Copynumber: 4.7 Consensus size: 43
16708552 ATTTAAAGTT
* * * *
16708562 TTTAAAGTTGTTTAGCCTCAGTATAAAAGAGCTTATTTTTTAA
1 TTTAAAGTTGTTTAGCCTCTGTATAGAGGAGCCTATTTTTTAA
* * * ** * *
16708605 TTTAAAATTGTTTTAGCCTTTATATAGAAAAACCCT-TTTCTTAA
1 TTTAAAGTTG-TTTAGCCTCTGTATAG-AGGAGCCTATTTTTTAA
* * * * * *
16708649 TTTTAAAGTTGTTTAACCTTTATATAGAGGAGCCCATTTCTTAT
1 -TTTAAAGTTGTTTAGCCTCTGTATAGAGGAGCCTATTTTTTAA
16708693 TTTAAAGTTGTTTAGCCTCTGTATAGAGGAGCCTATTTTTTAA
1 TTTAAAGTTGTTTAGCCTCTGTATAGAGGAGCCTATTTTTTAA
*
16708736 TTTAAATTTGTTT-GCCTCTGTATAGAGGAG
1 TTTAAAGTTGTTTAGCCTCTGTATAGAGGAG
16708766 TTTAATTTTG
Statistics
Matches: 134, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
42 17 0.13
43 62 0.46
44 41 0.31
45 14 0.10
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.45
Consensus pattern (43 bp):
TTTAAAGTTGTTTAGCCTCTGTATAGAGGAGCCTATTTTTTAA
Found at i:16714276 original size:2 final size:2
Alignment explanation
Indices: 16714269--16714304 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16714259 CGGCAATAGT
16714269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16714305 AAGGATTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16724501 original size:3 final size:3
Alignment explanation
Indices: 16724487--16724521 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
16724477 GAAAATAAAG
* *
16724487 GAA GAA GGA GAA GAA GAA GAA GAA GAA GAA AAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
16724522 GAATGAGAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:16724755 original size:26 final size:26
Alignment explanation
Indices: 16724684--16724864 Score: 91
Period size: 26 Copynumber: 6.5 Consensus size: 26
16724674 TTGAAAAGTT
*
16724684 AAAAG-AAAAAAAAAAAGGCAA-CTTTG
1 AAAAGTAAAAAAAAAAA--AAAGCTTTG
* *
16724710 AAAAGTCAAAACAAAAAAAAGCTTTG
1 AAAAGTAAAAAAAAAAAAAAGCTTTG
*
16724736 GAAAGTAAAAAAAAAAAAAAAGACAACTTTG
1 AAAAGT-AAAAAAAAAAAAAAG----CTTTG
* * * ** *
16724767 AAAAGT-CAACAAATAAAGGGTTTTG
1 AAAAGTAAAAAAAAAAAAAAGCTTTG
16724792 AAAAGTAAAAAAATAAAGAAAGGAAAAGCTTTG
1 AAAAGT---AAAA-AAA-AAA--AAAAGCTTTG
*
16724825 AAAAGTAAAAAAAAAAAAAAGGTTTG
1 AAAAGTAAAAAAAAAAAAAAGCTTTG
*
16724851 ACTAA-TAAAAAAAA
1 A-AAAGTAAAAAAAA
16724865 TATGCTTTGA
Statistics
Matches: 118, Mismatches: 21, Indels: 32
0.69 0.12 0.19
Matches are distributed among these distances:
25 12 0.10
26 34 0.29
27 24 0.20
28 3 0.03
29 14 0.12
30 6 0.05
31 12 0.10
33 13 0.11
ACGTcount: A:0.64, C:0.06, G:0.14, T:0.15
Consensus pattern (26 bp):
AAAAGTAAAAAAAAAAAAAAGCTTTG
Found at i:16724766 original size:57 final size:58
Alignment explanation
Indices: 16724656--16724864 Score: 212
Period size: 57 Copynumber: 3.6 Consensus size: 58
16724646 AAGAAAAAGA
*
16724656 AAAACAAAGAGAAAAGTTTTGAAAAGTTAAAAGAAAAAAAAAAAGGCAACTTTGAAAAGTC
1 AAAACAAAGA-AAAAGTTTTGAAAAG-TAAAA-AAAAAAAAAAAGACAACTTTGAAAAGTC
* *
16724717 AAAACAAA-AAAAAGCTTTGGAAAGTAAAAAAAAAAAAAAAGACAACTTTGAAAAGTC
1 AAAACAAAGAAAAAGTTTTGAAAAGTAAAAAAAAAAAAAAAGACAACTTTGAAAAGTC
* ** * * *
16724774 --AACAAATAAAGGGTTTTGAAAAGTAAAAAAATAAAGAAAGGAAAAGCTTTGAAAAGT-
1 AAAACAAAGAAAAAGTTTTGAAAAGTAAAAAAA-AAAAAAAAGACAA-CTTTGAAAAGTC
* * * *
16724831 AAAAAAAAAAAAAAGGTTTGACTAA-TAAAAAAAA
1 AAAACAAAGAAAAAGTTTTGA-AAAGTAAAAAAAA
16724865 TATGCTTTGA
Statistics
Matches: 126, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
55 6 0.05
56 20 0.16
57 37 0.29
58 17 0.13
59 35 0.28
60 3 0.02
61 8 0.06
ACGTcount: A:0.63, C:0.06, G:0.15, T:0.16
Consensus pattern (58 bp):
AAAACAAAGAAAAAGTTTTGAAAAGTAAAAAAAAAAAAAAAGACAACTTTGAAAAGTC
Found at i:16725736 original size:8 final size:8
Alignment explanation
Indices: 16725711--16725915 Score: 63
Period size: 8 Copynumber: 26.4 Consensus size: 8
16725701 TTTTTCTCAT
*
16725711 AAACCCTG
1 AAACCCTA
16725719 AAACCC-A
1 AAACCCTA
16725726 AAACCCTA
1 AAACCCTA
*
16725734 AAA-TCTCA
1 AAACCCT-A
*
16725742 AAACTCT-
1 AAACCCTA
**
16725749 AAAGTC-A
1 AAACCCTA
16725756 AAACCCTA
1 AAACCCTA
**
16725764 AAACTTTA
1 AAACCCTA
*
16725772 AAACTCTA
1 AAACCCTA
* *
16725780 AAA-CTTG
1 AAACCCTA
16725787 AAACCCTA
1 AAACCCTA
16725795 AAA-CCT-
1 AAACCCTA
16725801 AAA-CCTCA
1 AAACCCT-A
16725809 AAACCCTA
1 AAACCCTA
* *
16725817 AAACCTTG
1 AAACCCTA
* *
16725825 AAACCTTG
1 AAACCCTA
* *
16725833 AAACCTTG
1 AAACCCTA
*
16725841 AAA-CCTCG
1 AAACCCT-A
16725849 AAACCCTA
1 AAACCCTA
*
16725857 AAA-TCTCA
1 AAACCCT-A
* * *
16725865 GAATCTTA
1 AAACCCTA
16725873 AAACCC-A
1 AAACCCTA
***
16725880 AAATTTTA
1 AAACCCTA
16725888 AAACCCTA
1 AAACCCTA
*
16725896 AAACCTCAA
1 AAACC-CTA
16725905 AAACCCTA
1 AAACCCTA
16725913 AAA
1 AAA
16725916 TGAAACCTTG
Statistics
Matches: 150, Mismatches: 32, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
6 6 0.04
7 32 0.21
8 95 0.63
9 17 0.11
ACGTcount: A:0.48, C:0.29, G:0.04, T:0.19
Consensus pattern (8 bp):
AAACCCTA
Found at i:16725745 original size:16 final size:15
Alignment explanation
Indices: 16725706--16725798 Score: 80
Period size: 15 Copynumber: 6.1 Consensus size: 15
16725696 TTTATTTTTT
*
16725706 CTCATAAACCCTGAAA
1 CTCA-AAACCCTAAAA
*
16725722 CCCAAAACCCTAAAA
1 CTCAAAACCCTAAAA
*
16725737 TCTCAAAACTCT-AAA
1 -CTCAAAACCCTAAAA
*
16725752 GTCAAAACCCTAAAA
1 CTCAAAACCCTAAAA
* *
16725767 CTTTAAAACTCTAAAA
1 C-TCAAAACCCTAAAA
**
16725783 CTTGAAACCCTAAAA
1 CTCAAAACCCTAAAA
16725798 C
1 C
16725799 CTAAACCTCA
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
14 9 0.14
15 29 0.46
16 25 0.40
ACGTcount: A:0.48, C:0.29, G:0.03, T:0.19
Consensus pattern (15 bp):
CTCAAAACCCTAAAA
Found at i:16725758 original size:30 final size:30
Alignment explanation
Indices: 16725724--16725781 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
16725714 CCCTGAAACC
16725724 CAAAACCCTAAAA-TCTCAAAACTCTAAAGT
1 CAAAACCCTAAAACT-TCAAAACTCTAAAGT
*
16725754 CAAAACCCTAAAACTTTAAAACTCTAAA
1 CAAAACCCTAAAACTTCAAAACTCTAAA
16725782 ACTTGAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.21
Consensus pattern (30 bp):
CAAAACCCTAAAACTTCAAAACTCTAAAGT
Found at i:16725802 original size:38 final size:38
Alignment explanation
Indices: 16725771--16725859 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 38
16725761 CTAAAACTTT
*
16725771 AAAACTCTAAAA-CTTGAAACCCTAAAACCTAAACCTC
1 AAAACCCTAAAACCTTGAAACCCTAAAACCTAAACCTC
* *
16725808 AAAACCCTAAAACCTTGAAACCTTGAAACCTTGAAACCTC
1 AAAACCCTAAAACCTTGAAACCCTAAAACC-T-AAACCTC
*
16725848 GAAACCCTAAAA
1 AAAACCCTAAAA
16725860 TCTCAGAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
37 11 0.24
38 15 0.33
39 1 0.02
40 18 0.40
ACGTcount: A:0.47, C:0.29, G:0.06, T:0.18
Consensus pattern (38 bp):
AAAACCCTAAAACCTTGAAACCCTAAAACCTAAACCTC
Found at i:16725822 original size:16 final size:16
Alignment explanation
Indices: 16725706--16725882 Score: 84
Period size: 16 Copynumber: 11.4 Consensus size: 16
16725696 TTTATTTTTT
*
16725706 CTCATAAACCCTGAAAC
1 CTCA-AAACCCTAAAAC
*
16725723 C-CAAAACCCTAAAAT
1 CTCAAAACCCTAAAAC
*
16725738 CTCAAAACTCT-AAA-
1 CTCAAAACCCTAAAAC
*
16725752 GTCAAAACCCTAAAAC
1 CTCAAAACCCTAAAAC
* * *
16725768 TTTAAAACTCTAAAA-
1 CTCAAAACCCTAAAAC
**
16725783 CTTGAAACCCTAAAAC
1 CTCAAAACCCTAAAAC
16725799 CT--AAA-CCTCAAAAC
1 CTCAAAACCCT-AAAAC
* *
16725813 C-CTAAAACCTTGAAAC
1 CTC-AAAACCCTAAAAC
** * *
16725829 CTTGAAACCTTGAAAC
1 CTCAAAACCCTAAAAC
* *
16725845 CTCGAAACCCTAAAAT
1 CTCAAAACCCTAAAAC
* * *
16725861 CTCAGAATCTTAAAAC
1 CTCAAAACCCTAAAAC
16725877 C-CAAAA
1 CTCAAAA
16725883 TTTTAAAACC
Statistics
Matches: 125, Mismatches: 25, Indels: 22
0.73 0.15 0.13
Matches are distributed among these distances:
13 3 0.02
14 18 0.14
15 33 0.26
16 68 0.54
17 3 0.02
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.19
Consensus pattern (16 bp):
CTCAAAACCCTAAAAC
Found at i:16725836 original size:24 final size:24
Alignment explanation
Indices: 16725783--16725853 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
16725773 AACTCTAAAA
16725783 CTTGAAACCCTAAAACC-T-AAAC
1 CTTGAAACCCTAAAACCTTGAAAC
**
16725805 CTCAAAACCCTAAAACCTTGAAAC
1 CTTGAAACCCTAAAACCTTGAAAC
* * *
16725829 CTTGAAACCTTGAAACCTCGAAAC
1 CTTGAAACCCTAAAACCTTGAAAC
16725853 C
1 C
16725854 CTAAAATCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 15 0.38
23 1 0.03
24 24 0.60
ACGTcount: A:0.42, C:0.32, G:0.07, T:0.18
Consensus pattern (24 bp):
CTTGAAACCCTAAAACCTTGAAAC
Found at i:16730670 original size:12 final size:12
Alignment explanation
Indices: 16730653--16730682 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
16730643 TTAAAATAAT
16730653 TTATTATTTAAA
1 TTATTATTTAAA
16730665 TTATTATTTAAA
1 TTATTATTTAAA
16730677 TTATTA
1 TTATTA
16730683 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATTTAAA
Found at i:16730705 original size:17 final size:16
Alignment explanation
Indices: 16730674--16730722 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
16730664 ATTATTATTT
*
16730674 AAATTATTAATTTTAA
1 AAATAATTAATTTTAA
16730690 AAATAATTATATTTTAA
1 AAATAATTA-ATTTTAA
* * *
16730707 TAATATTTAATATTAA
1 AAATAATTAATTTTAA
16730723 GTATTGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATAATTAATTTTAA
Found at i:16730989 original size:14 final size:14
Alignment explanation
Indices: 16730972--16731017 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
16730962 ATACCTTAAT
16730972 AAATAAAAATATTA
1 AAATAAAAATATTA
* *
16730986 AAATAATATATTTTA
1 AAATAA-AAATATTA
*
16731001 AACTAAAAATATTA
1 AAATAAAAATATTA
16731015 AAA
1 AAA
16731018 GTTATTTATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAAAATATTA
Found at i:16730990 original size:29 final size:29
Alignment explanation
Indices: 16730958--16731017 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
16730948 AAATAGTCAT
*
16730958 AATAATACCTTAATAAA-TAAAAATATTAA
1 AATAATACATT-ATAAACTAAAAATATTAA
* *
16730987 AATAATATATTTTAAACTAAAAATATTAA
1 AATAATACATTATAAACTAAAAATATTAA
16731016 AA
1 AA
16731018 GTTATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (29 bp):
AATAATACATTATAAACTAAAAATATTAA
Found at i:16732927 original size:20 final size:19
Alignment explanation
Indices: 16732901--16732944 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
16732891 ATTTTTATTT
16732901 TATAAAAATT-TAAAATATA
1 TATAAAAATTATAAAA-ATA
16732920 TATAAAAATTAATAAAAATA
1 TATAAAAATT-ATAAAAATA
16732940 TATAA
1 TATAA
16732945 TTTAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 8 0.35
21 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TATAAAAATTATAAAAATA
Found at i:16733278 original size:2 final size:2
Alignment explanation
Indices: 16733271--16733304 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16733261 TATCACTATC
16733271 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
16733305 TATTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16733641 original size:16 final size:16
Alignment explanation
Indices: 16733615--16733653 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16733605 TGTGAAAGGG
16733615 AGAATAAAAGCAAA-AA
1 AGAA-AAAAGCAAACAA
16733631 AGCAAAAAAGCAAACAA
1 AG-AAAAAAGCAAACAA
16733648 AGAAAA
1 AGAAAA
16733654 CTAACTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.74, C:0.10, G:0.13, T:0.03
Consensus pattern (16 bp):
AGAAAAAAGCAAACAA
Found at i:16733649 original size:9 final size:8
Alignment explanation
Indices: 16733620--16733653 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
16733610 AAGGGAGAAT
16733620 AAAAGCAA
1 AAAAGCAA
16733628 AAAAGCAA
1 AAAAGCAA
16733636 AAAAGCAA
1 AAAAGCAA
16733644 ACAAAG-AA
1 A-AAAGCAA
16733652 AA
1 AA
16733654 CTAACTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 1 0.04
8 20 0.80
9 4 0.16
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAGCAA
Found at i:16736117 original size:21 final size:21
Alignment explanation
Indices: 16736093--16736137 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16736083 TATTTGATAC
16736093 ATAAAAT-TATAATAAGATAAG
1 ATAAAATATATAATAA-ATAAG
*
16736114 ATAAAATGATATTATAAATAAG
1 ATAAAAT-ATATAATAAATAAG
16736136 AT
1 AT
16736138 TAGATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (21 bp):
ATAAAATATATAATAAATAAG
Found at i:16736136 original size:27 final size:26
Alignment explanation
Indices: 16736093--16736152 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
16736083 TATTTGATAC
*
16736093 ATAAAATTATAATAAGATAAGATAAA
1 ATAATATTATAATAAGATAAGATAAA
* * *
16736119 ATGATATTATAAATAAGATTAGATTAA
1 ATAATATTAT-AATAAGATAAGATAAA
16736146 ATAATAT
1 ATAATAT
16736153 CATCTTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (26 bp):
ATAATATTATAATAAGATAAGATAAA
Found at i:16736276 original size:63 final size:64
Alignment explanation
Indices: 16736208--16736358 Score: 232
Period size: 64 Copynumber: 2.4 Consensus size: 64
16736198 TGTTATATGC
* * *
16736208 AAAAATATAAAAAATATTATTTAAAGTGTTTT-TATACAAAAATATCTTAAATAATATATTTTT
1 AAAAATATAAAAAAAATTATTTAAAGTATTTTCTATACAAAAATATCTTAAATAATATATTTAT
* * * *
16736271 AAAAATATAAAAAAAATTATTTAAAGTATTTTCTATACATAAATGTTTTAAATAATCTATTTAT
1 AAAAATATAAAAAAAATTATTTAAAGTATTTTCTATACAAAAATATCTTAAATAATATATTTAT
16736335 AAAAATATAAAAAAAATTATTTAA
1 AAAAATATAAAAAAAATTATTTAA
16736359 GATGATTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 30 0.38
64 50 0.62
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (64 bp):
AAAAATATAAAAAAAATTATTTAAAGTATTTTCTATACAAAAATATCTTAAATAATATATTTAT
Found at i:16736385 original size:64 final size:62
Alignment explanation
Indices: 16736208--16736395 Score: 202
Period size: 64 Copynumber: 2.9 Consensus size: 62
16736198 TGTTATATGC
* * *
16736208 AAAAATATAAAAAATATTATTTAAAGTGTTTTT-ATACAAAAATATCTTAAATAATATATTTTT
1 AAAAATATAAAAAAAATTATTTAAA-TGTTTTTCATACCAAAATAT-TTAAATAATATATTTAT
* *
16736271 AAAAATATAAAAAAAATTATTTAAA-GTATTTTCTATA-CATAAATGTTTTAAATAATCTATTTA
1 AAAAATATAAAAAAAATTATTTAAATGT-TTTTC-ATACCA-AAAT-ATTTAAATAATATATTTA
16736334 T
62 T
* *
16736335 AAAAATATAAAAAAAATTATTTAAGATGATTTTTCATACCAAACTCTTTAATTATAATATA
1 AAAAATATAAAAAAAATTATTTAA-ATG-TTTTTCATACCAAAATATTTAA--ATAATATA
16736396 AAAAAACTTT
Statistics
Matches: 106, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
61 2 0.02
62 4 0.04
63 25 0.24
64 51 0.48
65 8 0.08
66 15 0.14
67 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (62 bp):
AAAAATATAAAAAAAATTATTTAAATGTTTTTCATACCAAAATATTTAAATAATATATTTAT
Found at i:16737001 original size:20 final size:21
Alignment explanation
Indices: 16736976--16737015 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
16736966 AAAATGTTAA
16736976 AATTTTAATT-TTAATAATTC
1 AATTTTAATTCTTAATAATTC
*
16736996 AATTTTAATTCTTGATAATT
1 AATTTTAATTCTTAATAATT
16737016 TTGAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
AATTTTAATTCTTAATAATTC
Found at i:16741243 original size:6 final size:6
Alignment explanation
Indices: 16741210--16741297 Score: 62
Period size: 6 Copynumber: 15.7 Consensus size: 6
16741200 TGACTATACA
* * *
16741210 TATATA TATATA TATATG --TATG TATATG TATATG --TATG TGTATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * * * *
16741254 TGTATG TGTATG TGTATG TATTTG TATATG TGTA-- TATATG TATA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATA
16741298 CACACATACA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
4 11 0.16
6 59 0.84
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:16741251 original size:18 final size:18
Alignment explanation
Indices: 16741216--16741270 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
16741206 TACATATATA
*
16741216 TATATATATATGTA--TG
1 TATATGTATATGTATGTG
16741232 TATATGTATATGTATGTG
1 TATATGTATATGTATGTG
* *
16741250 TATGTGTATGTGTATGTG
1 TATATGTATATGTATGTG
16741268 TAT
1 TAT
16741271 GTATTTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 13 0.38
18 21 0.62
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (18 bp):
TATATGTATATGTATGTG
Found at i:16741253 original size:16 final size:16
Alignment explanation
Indices: 16741222--16741296 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
16741212 TATATATATA
*
16741222 TATATGTATGTATATG
1 TATATGTATGTGTATG
16741238 TATATGTATGTGTATGTG
1 TATATGTATGTGTA--TG
*
16741256 TATGTGTATGTGTATG
1 TATATGTATGTGTATG
* * * *
16741272 TATTTGTATATGTGTA
1 TATATGTATGTGTATG
16741288 TATATGTAT
1 TATATGTAT
16741297 ACACACATAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
16 35 0.70
18 15 0.30
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (16 bp):
TATATGTATGTGTATG
Found at i:16741271 original size:18 final size:18
Alignment explanation
Indices: 16741230--16741288 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
16741220 TATATATGTA
* *
16741230 TGTATATGTATATGTATG
1 TGTATGTGTATGTGTATG
16741248 TGTATGTGTATGTGTATG
1 TGTATGTGTATGTGTATG
* * *
16741266 TGTATGTATTTGTATATG
1 TGTATGTGTATGTGTATG
16741284 TGTAT
1 TGTAT
16741289 ATATGTATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (18 bp):
TGTATGTGTATGTGTATG
Found at i:16741297 original size:16 final size:16
Alignment explanation
Indices: 16741209--16741297 Score: 65
Period size: 16 Copynumber: 5.7 Consensus size: 16
16741199 TTGACTATAC
* *
16741209 ATATATATATATATAT
1 ATATATGTATATGTAT
*
16741225 ATGTATGTATATGTAT
1 ATATATGTATATGTAT
* *
16741241 ATGTATGTGTATG--T
1 ATATATGTATATGTAT
* * *
16741255 GTATGTGTATGTGTAT
1 ATATATGTATATGTAT
* * *
16741271 GTATTTGTATATGTGT
1 ATATATGTATATGTAT
16741287 ATATATGTATA
1 ATATATGTATA
16741298 CACACATACA
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
14 9 0.16
16 48 0.84
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (16 bp):
ATATATGTATATGTAT
Found at i:16741357 original size:6 final size:6
Alignment explanation
Indices: 16741348--16741467 Score: 95
Period size: 6 Copynumber: 20.3 Consensus size: 6
16741338 TATGTATGTG
* * *
16741348 TACATA TACATA T--ATA TATATA CACATA TACATA TACATA CACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* * * * **
16741394 CACATA CACATA TACATA TACATA CACATATA TACACA TACGCA TACATA
1 TACATA TACATA TACATA TACATA TAC--ATA TACATA TACATA TACATA
* *
16741444 T--ATA TACATA TATATA TATATA TA
1 TACATA TACATA TACATA TACATA TA
16741468 TTATTTCAAT
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
4 8 0.08
6 83 0.86
8 5 0.05
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (6 bp):
TACATA
Found at i:16741467 original size:18 final size:18
Alignment explanation
Indices: 16741357--16741465 Score: 65
Period size: 20 Copynumber: 5.7 Consensus size: 18
16741347 GTACATATAC
16741357 ATATATATATATACACAT
1 ATATATATATATACACAT
* *
16741375 ATACATATACATACACAT
1 ATATATATATATACACAT
* * * *
16741393 ACACATACACATATACATAT
1 --ATATATATATATACACAT
* *
16741413 ACATACACATATATACACAT
1 --ATATATATATATACACAT
* * *
16741433 ACGCATACATATATATACAT
1 A--TATATATATATACACAT
16741453 ATATATATATATA
1 ATATATATATATA
16741466 TATTATTTCA
Statistics
Matches: 70, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
18 27 0.39
20 43 0.61
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (18 bp):
ATATATATATATACACAT
Found at i:16744528 original size:14 final size:16
Alignment explanation
Indices: 16744499--16744530 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
16744489 AATAAAGGAA
16744499 AAAAATAAAGAAAAAC
1 AAAAATAAAGAAAAAC
16744515 AAAAA-AAA-AAAAAC
1 AAAAATAAAGAAAAAC
16744529 AA
1 AA
16744531 TCACAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAATAAAGAAAAAC
Found at i:16747699 original size:2 final size:2
Alignment explanation
Indices: 16747646--16747682 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16747636 ACTCAAATTC
16747646 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 A
16747683 ATTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16753244 original size:14 final size:14
Alignment explanation
Indices: 16753225--16753253 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16753215 AACATACTTG
16753225 TAATAAATATTTGT
1 TAATAAATATTTGT
16753239 TAATAAATATTTGT
1 TAATAAATATTTGT
16753253 T
1 T
16753254 TTTCTAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAATAAATATTTGT
Found at i:16755037 original size:2 final size:2
Alignment explanation
Indices: 16755030--16755059 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16755020 TCCAAATAAG
16755030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16755060 ATCAATGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16757792 original size:130 final size:129
Alignment explanation
Indices: 16757623--16757974 Score: 469
Period size: 130 Copynumber: 2.7 Consensus size: 129
16757613 TTAAAAGCAA
* * *
16757623 TTGAAAA-TTTTTATTTTA-AAAGTTTTATTTTTTACGAAAAATTAATACTTTTAACTTTTTAC-
1 TTGAAAATTTTTTATTTTAGAAA-TTTTA-TTTTTAAGAAAAATTGATACTTTCAA-TTTTTACG
* *
16757685 TAAGAATATTTTTTAAAATTTTTATTTTCA-GAGAAATTGATACTTTCAACTTTCCCCCCAAAAT
63 TAAAAATATTTTTTAAAATTTTTATTTTCAGGA-AAATTGATACTTTCAACTTT-CCCACAAAAT
*
16757749 GTTT
126 GCTT
* *
16757753 TTGAAAATTTTTTATTTTAGAAATTTTATTTTTAAGAAAAATTGATACTTTCCATTTTTTCGTAA
1 TTGAAAATTTTTTATTTTAGAAATTTTATTTTTAAGAAAAATTGATACTTTCAATTTTTACGTAA
* *
16757818 AAATATTTTTTAAAACTTTTTATTTTCAGGAAAATTGATACTTTTAGCTTTCCCACAAAATGCTT
66 AAATATTTTTTAAAA-TTTTTATTTTCAGGAAAATTGATACTTTCAACTTTCCCACAAAATGCTT
* * * *
16757883 TTGGAAATTTTTTATTTTAGAAACTTTATTTTTAAGAAAAATTGATACTTTCAATTTTTCCTTAA
1 TTGAAAATTTTTTATTTTAGAAATTTTATTTTTAAGAAAAATTGATACTTTCAATTTTTACGT-A
*
16757948 AAATATATTTTTTGAAATTTTTATTTT
65 AAA-ATATTTTTTAAAATTTTTATTTT
16757975 ATAAAAATCA
Statistics
Matches: 199, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
129 6 0.03
130 116 0.58
131 60 0.30
132 17 0.09
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (129 bp):
TTGAAAATTTTTTATTTTAGAAATTTTATTTTTAAGAAAAATTGATACTTTCAATTTTTACGTAA
AAATATTTTTTAAAATTTTTATTTTCAGGAAAATTGATACTTTCAACTTTCCCACAAAATGCTT
Found at i:16758013 original size:5 final size:5
Alignment explanation
Indices: 16757996--16758027 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
16757986 TAAAAAAAAG
*
16757996 AAATT AAAAT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AAATT AA
16758028 GAAATACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AAATT
Found at i:16758072 original size:9 final size:9
Alignment explanation
Indices: 16758054--16758085 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
16758044 CTAATTCAAA
16758054 AATAACAAT
1 AATAACAAT
*
16758063 AATAATAAT
1 AATAACAAT
16758072 AATAACAAT
1 AATAACAAT
16758081 AATAA
1 AATAA
16758086 ATAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (9 bp):
AATAACAAT
Found at i:16758851 original size:15 final size:16
Alignment explanation
Indices: 16758825--16758926 Score: 68
Period size: 16 Copynumber: 6.2 Consensus size: 16
16758815 TCATTATCTC
16758825 ATAATTAATAAAAAATG
1 ATAA-TAATAAAAAATG
16758842 ATAA-AATAAAAAAATG
1 ATAATAAT-AAAAAATG
*
16758858 ATAATAATAATAATAA-A
1 ATAATAATAA-AA-AATG
* *
16758875 ATAAATAAT-AATAATA
1 AT-AATAATAAAAAATG
* *
16758891 ATAATAATAATAAATA
1 ATAATAATAAAAAATG
*
16758907 ATAATAA-AAACAAATA
1 ATAATAATAAA-AAATG
16758923 ATAA
1 ATAA
16758927 ATGAGAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
15 13 0.18
16 39 0.54
17 12 0.17
18 8 0.11
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (16 bp):
ATAATAATAAAAAATG
Found at i:16758883 original size:18 final size:18
Alignment explanation
Indices: 16758825--16758964 Score: 99
Period size: 18 Copynumber: 7.3 Consensus size: 18
16758815 TCATTATCTC
*
16758825 ATAATTAATAA-AAAAT-G
1 ATAA-TAATAATAAAATAA
*
16758842 ATAA-AATAAAAAAATGATA
1 ATAATAATAATAAAAT-A-A
16758861 ATAATAATAATAAAATAA
1 ATAATAATAATAAAATAA
16758879 ATAATAATAATAATAATAATA
1 ATAATAATAATAA-AAT-A-A
*
16758900 ATAAATAATAATAAAAACAA
1 AT-AATAATAAT-AAAATAA
* *
16758920 ATAATAAATGAGAAAA-AA
1 ATAAT-AATAATAAAATAA
16758938 ATAATAAATAAATAAAATAAA
1 ATAAT-AAT-AATAAAAT-AA
16758959 ATAATA
1 ATAATA
16758965 TGAGCTTATT
Statistics
Matches: 102, Mismatches: 7, Indels: 25
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.05
16 5 0.05
17 4 0.04
18 25 0.25
19 20 0.20
20 19 0.19
21 11 0.11
22 11 0.11
23 2 0.02
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (18 bp):
ATAATAATAATAAAATAA
Found at i:16758926 original size:3 final size:3
Alignment explanation
Indices: 16758825--16758913 Score: 89
Period size: 3 Copynumber: 30.3 Consensus size: 3
16758815 TCATTATCTC
* * *
16758825 ATA ATTA ATA A-A A-A ATG ATA A-A ATA A-A AAA ATG ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16758867 ATA ATA A-A ATAA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
16758913 A
1 A
16758914 AAACAAATAA
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
2 10 0.14
3 55 0.74
4 9 0.12
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:16758957 original size:9 final size:9
Alignment explanation
Indices: 16758842--16758958 Score: 65
Period size: 9 Copynumber: 13.1 Consensus size: 9
16758832 ATAAAAAATG
16758842 ATAAAATAA
1 ATAAAATAA
16758851 A-AAAATGATA
1 ATAAAAT-A-A
16758861 ATAATAAT-A
1 ATAA-AATAA
16758870 ATAAAATAA
1 ATAAAATAA
16758879 AT--AAT-A
1 ATAAAATAA
16758885 ATAATAAT-A
1 ATAA-AATAA
16758894 ATAATAATAA
1 ATAA-AATAA
16758904 ATAATAATAA
1 ATAA-AATAA
*
16758914 AAACAAAT-A
1 ATA-AAATAA
16758923 AT-AAATGAGA
1 ATAAAAT-A-A
*
16758933 AAAAAAT-A
1 ATAAAATAA
16758941 AT-AAATAA
1 ATAAAATAA
16758949 ATAAAATAA
1 ATAAAATAA
16758958 A
1 A
16758959 ATAATATGAG
Statistics
Matches: 88, Mismatches: 4, Indels: 32
0.71 0.03 0.26
Matches are distributed among these distances:
6 3 0.03
7 11 0.12
8 13 0.15
9 31 0.35
10 20 0.23
11 7 0.08
12 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.24
Consensus pattern (9 bp):
ATAAAATAA
Found at i:16759569 original size:20 final size:20
Alignment explanation
Indices: 16759519--16759592 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
16759509 TTGATTTTGA
*
16759519 TAAAATTAATAAT-ATAATAT
1 TAAAATT-ATAATAATAAAAT
* * * *
16759539 TAATTATTATAGTGATAAGAT
1 TAA-AATTATAATAATAAAAT
16759560 TAAAATTATAATAATAAAAT
1 TAAAATTATAATAATAAAAT
16759580 TAAAATTAATAAT
1 TAAAATT-ATAAT
16759593 TAAATATACG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
TAAAATTATAATAATAAAAT
Found at i:16759687 original size:30 final size:34
Alignment explanation
Indices: 16759652--16759728 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 34
16759642 AAATAATTAT
16759652 TAAAAATATT-A-TATTTAA-ATTTAT-AAGTAA
1 TAAAAATATTAATTATTTAATATTTATAAAGTAA
* *
16759682 TAAAAATTTTAAATTATTTAATATTTATAAATTAA
1 TAAAAATATT-AATTATTTAATATTTATAAAGTAA
16759717 TAAATAAT-TTAA
1 TAAA-AATATTAA
16759729 AAAATTAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 9 0.23
32 1 0.03
33 7 0.18
34 8 0.21
35 11 0.28
36 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
TAAAAATATTAATTATTTAATATTTATAAAGTAA
Found at i:16759722 original size:18 final size:18
Alignment explanation
Indices: 16759670--16759727 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
16759660 TTATATTTAA
* *
16759670 ATTTAT-AAGTAATAAAA
1 ATTTATAAATTAATAAAT
* *
16759687 ATTT-TAAATTATTTAAT
1 ATTTATAAATTAATAAAT
16759704 ATTTATAAATTAATAAAT
1 ATTTATAAATTAATAAAT
16759722 AATTTA
1 -ATTTA
16759728 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 1 0.03
17 15 0.47
18 11 0.34
19 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTATAAATTAATAAAT
Found at i:16764756 original size:2 final size:2
Alignment explanation
Indices: 16764751--16764806 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
16764741 ACACACACAC
* * * * *
16764751 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT GT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16764793 AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT
16764807 CTACATACAA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16769144 original size:43 final size:43
Alignment explanation
Indices: 16769080--16769180 Score: 175
Period size: 43 Copynumber: 2.3 Consensus size: 43
16769070 GAAGGAAAAG
16769080 AACACTCAAATTTATGATGCAAACTCAAACAACAGAACAATTC
1 AACACTCAAATTTATGATGCAAACTCAAACAACAGAACAATTC
* * *
16769123 AATACTCAAATTTATGATGCAATCTCAAACAACAGAATAATTC
1 AACACTCAAATTTATGATGCAAACTCAAACAACAGAACAATTC
16769166 AACACTCAAATTTAT
1 AACACTCAAATTTAT
16769181 CATTCCATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.26
Consensus pattern (43 bp):
AACACTCAAATTTATGATGCAAACTCAAACAACAGAACAATTC
Found at i:16772189 original size:21 final size:21
Alignment explanation
Indices: 16772141--16772182 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
16772131 GCTGTTTAAA
16772141 GATAATAATTTGTAAAATATT
1 GATAATAATTTGTAAAATATT
16772162 GATAATAATTTGTAAAATATT
1 GATAATAATTTGTAAAATATT
16772183 AGTAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (21 bp):
GATAATAATTTGTAAAATATT
Found at i:16773256 original size:26 final size:27
Alignment explanation
Indices: 16773220--16773275 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
16773210 CCAATTTCTC
*
16773220 CAATACCCATCAA-AAAGT-GAGGAAAT
1 CAATACCCATCAATAAA-TAGAGAAAAT
*
16773246 CAATAGCCATCAATAAATAGAGAAAAT
1 CAATACCCATCAATAAATAGAGAAAAT
16773273 CAA
1 CAA
16773276 GATGCGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (27 bp):
CAATACCCATCAATAAATAGAGAAAAT
Found at i:16778051 original size:52 final size:52
Alignment explanation
Indices: 16777965--16778121 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
16777955 TATAACCATA
* * * *
16777965 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
16778017 CAAACTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * **
16778069 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAAT-CTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
16778121 C
1 C
16778122 TTCTTGTCCA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 88 0.94
53 6 0.06
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:16779077 original size:52 final size:52
Alignment explanation
Indices: 16778991--16779147 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
16778981 TATAACCATA
* * *
16778991 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
16779043 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * **
16779095 CAAACTTACCTATTAAGAATCCTCTTT-CTCAT-GAAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-CTTTCCTCTTAG-AATTCTTCTCCTGCAAGT
16779147 C
1 C
16779148 TTCTTGTCCA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 1 0.01
52 89 0.95
53 4 0.04
ACGTcount: A:0.26, C:0.27, G:0.09, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:16779190 original size:11 final size:11
Alignment explanation
Indices: 16779174--16779202 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
16779164 AATATCTGAT
16779174 AAATCTCAAAC
1 AAATCTCAAAC
16779185 AAATCTCAAAC
1 AAATCTCAAAC
16779196 AAATCTC
1 AAATCTC
16779203 GTATGGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATCTCAAAC
Found at i:16779823 original size:61 final size:59
Alignment explanation
Indices: 16779695--16779918 Score: 261
Period size: 57 Copynumber: 3.8 Consensus size: 59
16779685 TTTTTGTTAG
16779695 GGAAAATTGAATAACTTTCAACTTTTCCC---AAATA---TTTTTGGAAATTTATTTTTCTTTAA
1 GGAAAATTG-AT-ACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTA--TTTC--TAA
* *
16779754 GGAAAATTGATACTTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATAC-TTTCAACTTTTCCCTAAAAATA-TTTTTTTTGGAAATTTATTTCTAA
16779815 GGAAAATTGATTACTTTCAACTTTTCACC--AAAATA--TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGA-TACTTTCAACTTTTC-CCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
*
16779872 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAA
16779919 TTTTTTTATT
Statistics
Matches: 147, Mismatches: 4, Indels: 28
0.82 0.02 0.16
Matches are distributed among these distances:
55 2 0.01
56 15 0.10
57 38 0.26
58 16 0.11
59 19 0.13
60 6 0.04
61 29 0.20
62 5 0.03
63 4 0.03
65 13 0.09
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
Found at i:16780404 original size:19 final size:20
Alignment explanation
Indices: 16780360--16780405 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
16780350 GAACACCGGT
*
16780360 GCCGGATTCTAGAAATTTTC
1 GCCGGAATCTAGAAATTTTC
* *
16780380 GTCGGAATCTGGAAA-TTTC
1 GCCGGAATCTAGAAATTTTC
16780399 GCCGGAA
1 GCCGGAA
16780406 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (20 bp):
GCCGGAATCTAGAAATTTTC
Found at i:16780492 original size:31 final size:31
Alignment explanation
Indices: 16780457--16780527 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
16780447 AACTGGACTG
*
16780457 GTTGCCGGAAACTTC-AATGTTCGCCGGAATT
1 GTTGCCGGAAAATTCAAAT-TTCGCCGGAATT
*
16780488 GTTGCCGGAAAATTCAAATTTCGCCTGAATT
1 GTTGCCGGAAAATTCAAATTTCGCCGGAATT
*
16780519 TTTGCCGGA
1 GTTGCCGGA
16780528 TTCTGGAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (31 bp):
GTTGCCGGAAAATTCAAATTTCGCCGGAATT
Found at i:16782000 original size:21 final size:20
Alignment explanation
Indices: 16781972--16782010 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16781962 GCATTAATGC
*
16781972 TAAAACTAACAGAAATAAGT
1 TAAAACTAACAAAAATAAGT
*
16781992 TAAATACTAATAAAAATAA
1 TAAA-ACTAACAAAAATAA
16782011 TGCACAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAAACTAACAAAAATAAGT
Found at i:16782591 original size:35 final size:36
Alignment explanation
Indices: 16782533--16782604 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
16782523 TTTTTTTGAC
16782533 TTATGATTTTCCAACTTCTTTTTTTTAAAAATGAGA
1 TTATGATTTTCCAACTTCTTTTTTTTAAAAATGAGA
* * *
16782569 TTATGGTTTTTCAACTTC-TTTTTTTAAACATGAGA
1 TTATGATTTTCCAACTTCTTTTTTTTAAAAATGAGA
16782604 T
1 T
16782605 GGTTATACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (36 bp):
TTATGATTTTCCAACTTCTTTTTTTTAAAAATGAGA
Found at i:16783012 original size:17 final size:17
Alignment explanation
Indices: 16782987--16783054 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
16782977 ATGAACGTAA
*
16782987 ATAAATTTATTTTTATT
1 ATAATTTTATTTTTATT
16783004 ATAATTTTATTTTTATT
1 ATAATTTTATTTTTATT
**
16783021 -TTTTGATTTA-TTTTATAT
1 ATAAT--TTTATTTTTAT-T
16783039 ATAATTTT-TTTTTATT
1 ATAATTTTATTTTTATT
16783055 TCATAGAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.07
17 31 0.76
18 5 0.12
19 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (17 bp):
ATAATTTTATTTTTATT
Found at i:16784772 original size:2 final size:2
Alignment explanation
Indices: 16784765--16784793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16784755 TTGATATAAG
16784765 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 A
16784794 GCACATGGGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16784968 original size:16 final size:17
Alignment explanation
Indices: 16784926--16784960 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16784916 TTTGCCTTCC
* *
16784926 TGAATTTATTTATTTGT
1 TGAATATATTAATTTGT
16784943 TGAATATATTAATTTGT
1 TGAATATATTAATTTGT
16784960 T
1 T
16784961 ATTATATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (17 bp):
TGAATATATTAATTTGT
Found at i:16785893 original size:19 final size:19
Alignment explanation
Indices: 16785869--16785905 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16785859 GGAAATAATT
16785869 AATTATAACATTCTTTTTC
1 AATTATAACATTCTTTTTC
*
16785888 AATTATAACCTTCTTTTT
1 AATTATAACATTCTTTTT
16785906 ATAAAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTATAACATTCTTTTTC
Found at i:16793164 original size:514 final size:514
Alignment explanation
Indices: 16792248--16793196 Score: 1605
Period size: 515 Copynumber: 1.8 Consensus size: 514
16792238 AGCATCCATA
* * *
16792248 AGTTATTGTGCTCAAGTTTTGTGGATTAAACAACAATTGAAGGATTTTGGAATTATCATAGATCA
1 AGTTATTGTACTCAAGTTTTATGGATTAAACAACAATTGAAGGATTTTGGAATTACCATAGATCA
* * *
16792313 TATTCCCATTAAATATGATAATATTAGAACTATCAATCTCACAAAAAATCCAATTCAATATTCAA
66 TATTCCCATTAAATACGATAATATTAGAACCATAAATCTCACAAAAAATCCAATTCAATATTCAA
* * *
16792378 GAACTAAATATATTGAAATTAGGTATCATTTTATTAGAGATCATGTTAAAAAAGGTGATCTTGTG
131 GAACTAAATATATTGAAATTAGGCATCATTTTATTAGAGATCATGTTAAAAAAGGTGATATTATG
* * *
16792443 CTTGAATATGTTGATACCTTACATCAATTAGTTGATATTTTTACAATACCTCTTGATAGAGATAG
196 CTTGAATATATTGATACCTTACATCAATTAGCTGATATTTTTACAAAACCTCTTGATAGAGATAG
*
16792508 ATTTCATACAATTAGAGGTGAACTTAGTATGATGAATGATCATTGAAATGAAATTCTTGATGGCA
261 ATTTCATACAATTAGAGGTGAACTTAATATGATGAATGATCATTGAAATGAAATTCTTGATGGCA
* *
16792573 CAATGAATGTTGATACCTTGTTTGACCAAATGTGTGTTTATCTTGACATATTTTTGAAATCTTAT
326 CAATGAATGTTGATACCTTGTCTGACCAAATGTATGTTTATCTTGACATATTTTTGAAATCTTAT
16792638 CTATGATTATATTTGTAATTATATAATGCATATTTGAATAGTTATATTGCTCATATCATGATTTT
391 CTATGATTATATTTGTAATTATATAATGCATATTTGAATAGTTATATTGCTCATATCATGATTTT
16792703 CTATGAAACAAAATAATGTTGTTCAATCCACAACTAAAACTGAATATGTAGTAGCTAGT
456 CTATGAAACAAAATAATGTTGTTCAATCCACAACTAAAACTGAATATGTAGTAGCTAGT
*
16792762 AGTTATTGTACTCAAGTTTTATGGATTAAACAATAATTTG-AGGATTTTGGAATTACCATAGATC
1 AGTTATTGTACTCAAGTTTTATGGATTAAACAACAA-TTGAAGGATTTTGGAATTACCATAGATC
* ** *
16792826 ATATTCCCATTAAATGCGATAATATTAGTGCCATAAATCTCACCAAAAATCCAATTCAATATTCA
65 ATATTCCCATTAAATACGATAATATTAGAACCATAAATCTCACAAAAAATCCAATTCAATATTCA
* *
16792891 AGAACTAAATATATTGAAATTAGGCATCATTTTATTATAGATCATGTTCAAAAATGGTGATATTA
130 AGAACTAAATATATTGAAATTAGGCATCATTTTATTAGAGATCATGTT-AAAAAAGGTGATATTA
*
16792956 TGCTTGAATATATTGATACCTTACATCAATTAGCTGATATTTTTATAAAACCTCTTGATAGAGAT
194 TGCTTGAATATATTGATACCTTACATCAATTAGCTGATATTTTTACAAAACCTCTTGATAGAGAT
* *
16793021 AGATTTCATACAATTAGAGGTGAACTTAATATGATGAATGCTCCTTGAAATGAAATTCTTGATGG
259 AGATTTCATACAATTAGAGGTGAACTTAATATGATGAATGATCATTGAAATGAAATTCTTGATGG
* *
16793086 CACGATGAATGTTGATACCTTGTCTGATCAAATGTATGTTTATCTTGACATATTTTTGAAATCTT
324 CACAATGAATGTTGATACCTTGTCTGACCAAATGTATGTTTATCTTGACATATTTTTGAAATCTT
* *
16793151 GTCTATG-TTATATTTGTAATTATATGATGCATATTTGAATAGTTAT
389 ATCTATGATTATATTTGTAATTATATAATGCATATTTGAATAGTTAT
16793197 GTGGCATGTT
Statistics
Matches: 404, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
514 198 0.49
515 206 0.51
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (514 bp):
AGTTATTGTACTCAAGTTTTATGGATTAAACAACAATTGAAGGATTTTGGAATTACCATAGATCA
TATTCCCATTAAATACGATAATATTAGAACCATAAATCTCACAAAAAATCCAATTCAATATTCAA
GAACTAAATATATTGAAATTAGGCATCATTTTATTAGAGATCATGTTAAAAAAGGTGATATTATG
CTTGAATATATTGATACCTTACATCAATTAGCTGATATTTTTACAAAACCTCTTGATAGAGATAG
ATTTCATACAATTAGAGGTGAACTTAATATGATGAATGATCATTGAAATGAAATTCTTGATGGCA
CAATGAATGTTGATACCTTGTCTGACCAAATGTATGTTTATCTTGACATATTTTTGAAATCTTAT
CTATGATTATATTTGTAATTATATAATGCATATTTGAATAGTTATATTGCTCATATCATGATTTT
CTATGAAACAAAATAATGTTGTTCAATCCACAACTAAAACTGAATATGTAGTAGCTAGT
Found at i:16799079 original size:15 final size:15
Alignment explanation
Indices: 16799059--16799092 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
16799049 TCTATACAAT
*
16799059 ATTATCATATTAATG
1 ATTATCATACTAATG
16799074 ATTATCATACTAATG
1 ATTATCATACTAATG
16799089 ATTA
1 ATTA
16799093 ATATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTATCATACTAATG
Found at i:16799318 original size:14 final size:14
Alignment explanation
Indices: 16799301--16799343 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16799291 TTGAATATGA
16799301 TTATTTTAATTTTT
1 TTATTTTAATTTTT
*
16799315 TTA-TTTAAATTTT
1 TTATTTTAATTTTT
**
16799328 AAATTTTAATTTTT
1 TTATTTTAATTTTT
16799342 TT
1 TT
16799344 TTGTTTTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTTTAATTTTT
Found at i:16799576 original size:8 final size:8
Alignment explanation
Indices: 16799533--16799587 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 8
16799523 GATTTTTGTT
16799533 AAAAATAA
1 AAAAATAA
16799541 AAATAATAA
1 AAA-AATAA
* *
16799550 AAAGAGAA
1 AAAAATAA
* *
16799558 AAAATTGA
1 AAAAATAA
16799566 AAAAATAA
1 AAAAATAA
16799574 AAAAATAA
1 AAAAATAA
16799582 AAAAAT
1 AAAAAT
16799588 GGGGGTTGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
8 30 0.79
9 8 0.21
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (8 bp):
AAAAATAA
Found at i:16799585 original size:17 final size:18
Alignment explanation
Indices: 16799539--16799586 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
16799529 TGTTAAAAAT
*
16799539 AAAAATAATAAAAAGAGA
1 AAAAATAAAAAAAAGAGA
** *
16799557 AAAAATTGAAAAAATA-A
1 AAAAATAAAAAAAAGAGA
16799574 AAAAATAAAAAAA
1 AAAAATAAAAAAA
16799587 TGGGGGTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAAATAAAAAAAAGAGA
Found at i:16800217 original size:59 final size:58
Alignment explanation
Indices: 16800142--16800432 Score: 246
Period size: 59 Copynumber: 5.0 Consensus size: 58
16800132 AAAAGTAATA
16800142 TAAAATAAAAATTTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTT
1 TAAAAT-AAAA-TTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTT
* * * * * *
16800202 AAAAAAAAAGATTTCAAGAAGAA-ATTTTTGAGGAAAACTTGAAAATATCAATTTTT-TT
1 TAAAATAAA-ATTTCAA-AAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTT
* * * *
16800260 TAAAATAAAATTGT-TAAAAAATATTTTTGAGGAAAA-TATGGAAGTACCAA-TTTTCATT
1 TAAAATAAAATT-TCAAAAAAATATTTTTAAGGAAAAGT-TGAAAGTATCAATTTTTC-TT
* *
16800318 TAAAATAAATTTTTAAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAA-TTTTCTT
1 TAAAATAAA-ATTT-CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTT
* * *
16800377 TGAAAAATAAAACCTT----AAAATGA--TTTAAGAAAAAGTTAAAAGTATCAATTTTTCTT
1 T--AAAATAAAA-TTTCAAAAAAAT-ATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTT
16800433 ATATAAAAGC
Statistics
Matches: 193, Mismatches: 22, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
55 23 0.12
56 21 0.11
57 28 0.15
58 22 0.11
59 44 0.23
60 44 0.23
61 11 0.06
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (58 bp):
TAAAATAAAATTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTT
Found at i:16800279 original size:117 final size:118
Alignment explanation
Indices: 16800142--16800433 Score: 296
Period size: 116 Copynumber: 2.5 Consensus size: 118
16800132 AAAAGTAATA
16800142 TAAAATAAAAATTTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
1 TAAAAT-AAAATTTT--AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
* * * *
16800207 AAAAGATTTCAAGAAGAA-ATTTTTGAGGAAAACTTGAAAATATCAATTTT-TTT-
63 AAAAGATTTAAAAAAAAATATTTTTAAGGAAAACTTGAAAATATCAATTTTCTTTG
* * * *
16800260 TAAAATAAAATTGTTAAAAAATATTTTTGAGGAAAA-TATGGAAGTACCAA-TTTTCATTTAAAA
1 TAAAATAAAATT-TTAAAAAATATTTTTAAGGAAAAGT-TGAAAGTATCAATTTTTC-TTAAAAA
* ** * *
16800323 TAAATTTTTAAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTG
63 AAAAGATTTAAAAAAAAATATTTTTAAGGAAAACTTGAAAATATCAATTTTCTTTG
* ** * *
16800379 AAAAATAAAACCTT--AAAATGA--TTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTA
1 TAAAATAAAATTTTAAAAAAT-ATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTA
16800434 TATAAAAGCA
Statistics
Matches: 143, Mismatches: 22, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
115 26 0.18
116 59 0.41
117 36 0.25
118 13 0.09
119 9 0.06
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (118 bp):
TAAAATAAAATTTTAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAAA
AGATTTAAAAAAAAATATTTTTAAGGAAAACTTGAAAATATCAATTTTCTTTG
Found at i:16804086 original size:24 final size:24
Alignment explanation
Indices: 16804058--16804105 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
16804048 AAAAGGTCTC
* *
16804058 AAAGAGAGAAAGAAAAGTAAAATG
1 AAAGAAAGAAAGAAAAGAAAAATG
16804082 AAAGAAAGAAAGAAAAGAAAAATG
1 AAAGAAAGAAAGAAAAGAAAAATG
16804106 CCACACCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (24 bp):
AAAGAAAGAAAGAAAAGAAAAATG
Found at i:16804484 original size:15 final size:15
Alignment explanation
Indices: 16804463--16804513 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 15
16804453 AAAAGAGAAA
16804463 AAAAAGAAAAAAATGG
1 AAAAAGAAAAAAAT-G
16804479 AAAAGAGAAAAAAATG
1 AAAA-AGAAAAAAATG
* *
16804495 -AAAGGAAAAAAAAG
1 AAAAAGAAAAAAATG
16804509 AAAAA
1 AAAAA
16804514 AATGAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.30
15 6 0.20
16 5 0.17
17 10 0.33
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAAAATG
Found at i:16804486 original size:26 final size:26
Alignment explanation
Indices: 16804453--16804539 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 26
16804443 ACGAATGAAA
*
16804453 AAAAGAGAAAAAAAAGAAAAAAATGG
1 AAAAGAGAAAAAAATGAAAAAAATGG
*
16804479 AAAAGAGAAAAAAATGAAAGGAAA---
1 AAAAGAGAAAAAAATGAAA-AAAATGG
*
16804503 AAAA-AGAAAAAAATGAGAAAAATGG
1 AAAAGAGAAAAAAATGAAAAAAATGG
*
16804528 AAATGAGAAAAA
1 AAAAGAGAAAAA
16804540 GGAATACTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.06
23 13 0.25
24 4 0.08
25 3 0.06
26 25 0.49
27 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (26 bp):
AAAAGAGAAAAAAATGAAAAAAATGG
Found at i:16804533 original size:15 final size:14
Alignment explanation
Indices: 16804513--16804543 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
16804503 AAAAAGAAAA
16804513 AAATGAGAAAAATGG
1 AAATGAGAAAAA-GG
16804528 AAATGAGAAAAAGG
1 AAATGAGAAAAAGG
16804542 AA
1 AA
16804544 TACTCAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.10
Consensus pattern (14 bp):
AAATGAGAAAAAGG
Found at i:16805653 original size:21 final size:21
Alignment explanation
Indices: 16805629--16805669 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16805619 ATTGTTTAGG
* *
16805629 TTTCAAATGCGAATCTTTGAA
1 TTTCAAACGAGAATCTTTGAA
16805650 TTTCAAACGAGAATCTTTGA
1 TTTCAAACGAGAATCTTTGA
16805670 GATGTGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
TTTCAAACGAGAATCTTTGAA
Found at i:16805865 original size:15 final size:15
Alignment explanation
Indices: 16805845--16805892 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
16805835 TGCACATCTG
16805845 AAATTTTGTGAATCA
1 AAATTTTGTGAATCA
* *
16805860 AAATTTGGTGAAATTA
1 AAATTTTGTG-AATCA
* *
16805876 AAAATTTGAGAATCA
1 AAATTTTGTGAATCA
16805891 AA
1 AA
16805893 TTTCAGTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (15 bp):
AAATTTTGTGAATCA
Found at i:16806119 original size:43 final size:42
Alignment explanation
Indices: 16806033--16806383 Score: 367
Period size: 43 Copynumber: 8.3 Consensus size: 42
16806023 ATCGTTAAGA
* *
16806033 AGCATTT-TTATTTTCCAAAGTTATGGTTGCCTCTATTTAAAGG
1 AGCATTTATT-TTTT-CAAAGTTATGGTTGCCTCTGTTTAGAGG
* *
16806076 AGCAATTTATTTTTTCCAAAGTCATGG-TGCCTCTGTTTAAAGG
1 AGC-ATTTATTTTTT-CAAAGTTATGGTTGCCTCTGTTTAGAGG
*
16806119 AGCAATTTATTTTTTCAAAAGTTGT-GTTGCCTCTGTTTAGAGG
1 AGC-ATTTATTTTTTC-AAAGTTATGGTTGCCTCTGTTTAGAGG
* *
16806162 AGCAATTTA-TTTTTCAAAGTTATGGTTGCCTCTCTATTTAGAGA
1 AGC-ATTTATTTTTTCAAAGTTATGGTTG-C-CTCTGTTTAGAGG
* * * *
16806206 AGCAATTTATTTTTTCAAAATTAT-GTTGTCTCTGTTTAAAAG
1 AGC-ATTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGG
*
16806248 AGCATTT-TTATGTTTCAAAGTTATGGTTGCCTCTGTTTAGAGA
1 AGCATTTATT-T-TTTCAAAGTTATGGTTGCCTCTGTTTAGAGG
* * *
16806291 AGCATTTATTTTTTCAAAGTTGTGGTTGTCTCTATTTAGAGG
1 AGCATTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGG
* * * *
16806333 AACATTTATTTTTTCAAAGTCATTG-AGCCTCTGTTTAGAGG
1 AGCATTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGG
16806374 AGC-TTTATTT
1 AGCATTTATTT
16806384 ACTTTTTTCA
Statistics
Matches: 265, Mismatches: 31, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
40 9 0.03
41 27 0.10
42 83 0.31
43 86 0.32
44 45 0.17
45 15 0.06
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (42 bp):
AGCATTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGG
Found at i:16806190 original size:42 final size:43
Alignment explanation
Indices: 16806039--16806395 Score: 374
Period size: 42 Copynumber: 8.3 Consensus size: 43
16806029 AAGAAGCATT
* * *
16806039 TTTA-TTTTCCAAAGTTATGGTTGCCTCTATTTAAAGGAGCAA
1 TTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGGAGCAA
* *
16806081 TTTATTTTTTCCAAAGTCATGG-TGCCTCTGTTTAAAGGAGCAA
1 TTTATTTTTT-CAAAGTTATGGTTGCCTCTGTTTAGAGGAGCAA
*
16806124 TTTATTTTTTCAAAAGTTGT-GTTGCCTCTGTTTAGAGGAGCAA
1 TTTATTTTTTC-AAAGTTATGGTTGCCTCTGTTTAGAGGAGCAA
* *
16806167 TTTA-TTTTTCAAAGTTATGGTTGCCTCTCTATTTAGAGAAGCAA
1 TTTATTTTTTCAAAGTTATGGTTG-C-CTCTGTTTAGAGGAGCAA
* * * *
16806211 TTTATTTTTTCAAAATTAT-GTTGTCTCTGTTTAAAAGAGC-A
1 TTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGGAGCAA
*
16806252 TTT-TTATGTTTCAAAGTTATGGTTGCCTCTGTTTAGAGAAGC-A
1 TTTATT-T-TTTCAAAGTTATGGTTGCCTCTGTTTAGAGGAGCAA
* * * *
16806295 TTTATTTTTTCAAAGTTGTGGTTGTCTCTATTTAGAGGAAC-A
1 TTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGGAGCAA
* * * *
16806337 TTTATTTTTTCAAAGTCATTG-AGCCTCTGTTTAGAGGAGCTTTA
1 TTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGGAGC--AA
16806381 TTTACTTTTTTCAAA
1 TTTA-TTTTTTCAAA
16806396 AACAAAAAAA
Statistics
Matches: 267, Mismatches: 32, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
40 2 0.01
41 27 0.10
42 87 0.33
43 87 0.33
44 41 0.15
45 23 0.09
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (43 bp):
TTTATTTTTTCAAAGTTATGGTTGCCTCTGTTTAGAGGAGCAA
Found at i:16806393 original size:129 final size:127
Alignment explanation
Indices: 16806030--16806395 Score: 424
Period size: 129 Copynumber: 2.8 Consensus size: 127
16806020 ATGATCGTTA
* * *
16806030 AGAAGCATTT-TTATTTTCCAAAGTTATGGTTGCCTCTATTTAAAGGAGCAATTTATTTTTTCCA
1 AGAAGCATTTATT-TTTT-CAAAGTTATGGTTGTCTCTATTTAGAGGAACAATTTATTTTTT-CA
* * *
16806094 AAGTCATGGTGCCTCTGTTTAAAGGAGC-AATTTATTTTTTCAAAAGTTGTGTTGCCTCTGTTTA
63 AAGTCATTGTGCCTCTGTTTAAAGGAGCTTATTTATTTTTTC-AAAGTTATGTTGCCTCTGTTTA
16806158 G
127 G
*
16806159 AGGAGCAATTTA-TTTTTCAAAGTTATGGTTGCCTCTCTATTTAGA-GAAGCAATTTATTTTTTC
1 AGAAGC-ATTTATTTTTTCAAAGTTATGGTTG--TCTCTATTTAGAGGAA-CAATTTATTTTTTC
* * * * *
16806222 AAAATTA-TGTTGTCTCTGTTTAAAAGAGCATT-TTTA-TGTTTCAAAGTTATGGTTGCCTCTGT
62 AAAGTCATTG-TGCCTCTGTTTAAAGGAGC-TTATTTATTTTTTCAAAGTTAT-GTTGCCTCTGT
16806284 TTAG
124 TTAG
*
16806288 AGAAGCATTTATTTTTTCAAAGTTGTGGTTGTCTCTATTTAGAGGAAC-ATTTATTTTTTCAAAG
1 AGAAGCATTTATTTTTTCAAAGTTATGGTTGTCTCTATTTAGAGGAACAATTTATTTTTTCAAAG
* *
16806352 TCATTGAGCCTCTGTTTAGAGGAGCTTTATTTACTTTTTTCAAA
66 TCATTGTGCCTCTGTTTAAAGGAGC-TTATTTA-TTTTTTCAAA
16806396 AACAAAAAAA
Statistics
Matches: 200, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
126 34 0.17
127 19 0.09
128 30 0.15
129 85 0.43
130 32 0.16
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (127 bp):
AGAAGCATTTATTTTTTCAAAGTTATGGTTGTCTCTATTTAGAGGAACAATTTATTTTTTCAAAG
TCATTGTGCCTCTGTTTAAAGGAGCTTATTTATTTTTTCAAAGTTATGTTGCCTCTGTTTAG
Found at i:16806416 original size:15 final size:16
Alignment explanation
Indices: 16806396--16806425 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16806386 TTTTTTCAAA
16806396 AACAAAAA-AAAAAAC
1 AACAAAAACAAAAAAC
16806411 AACAAAAACAAAAAA
1 AACAAAAACAAAAAA
16806426 AAAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (16 bp):
AACAAAAACAAAAAAC
Found at i:16807074 original size:21 final size:21
Alignment explanation
Indices: 16807048--16807088 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16807038 ATCTTATTCT
* *
16807048 AAAGAGAAAGGGAGAGAAAAG
1 AAAGAGAAAGAGAAAGAAAAG
16807069 AAAGAGAAAGAGAAAGAAAA
1 AAAGAGAAAGAGAAAGAAAA
16807089 AATAAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (21 bp):
AAAGAGAAAGAGAAAGAAAAG
Found at i:16807527 original size:58 final size:58
Alignment explanation
Indices: 16807443--16807617 Score: 201
Period size: 58 Copynumber: 2.9 Consensus size: 58
16807433 AAATATATAT
* *
16807443 AAAATAAAAATTTTCAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATTAATTTTTCTTG
1 AAAAT-AAAATTTT-AAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTA
* * * * *
16807503 AAAATAAAATTATT-ACAAAATATTTCTAAGGAAAAGTTGGAAGTACCAATTTTTCTTA
1 AAAATAAAATT-TTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTA
*
16807561 AAAATAAAATTTTCAAAAAAATATATTTTTAAGGAAAAA-TTAAAAGTATCAATTTTT
1 AAAATAAAATTTT--AAAAAA-ATATTTTTAA-GAAAAAGTTGAAAGTATCAATTTTT
16807618 TTTGTATAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
57 2 0.02
58 48 0.50
59 6 0.06
60 11 0.11
61 24 0.25
62 5 0.05
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (58 bp):
AAAATAAAATTTTAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTA
Found at i:16815290 original size:125 final size:121
Alignment explanation
Indices: 16815122--16815372 Score: 448
Period size: 125 Copynumber: 2.0 Consensus size: 121
16815112 AACAAGGGTA
* *
16815122 GAATTGAAGGGTGGATGTGAAATTAGCTAGGCTAGAACCAATATTAATTTCATGTTCATTAATTA
1 GAATTGAAGGGCGGATGTGAAACTAGCTAGGCTAGAACCAATATTAATTTCATGTTCATTAATTA
16815187 ATTTCTTTCTTGTATATTATATATTATATATATATTTATAGAAAATAACTTTAATAGATT
66 ATTTCTTTCTTGTATATTATATA-TATAT-T-T-TTTATAGAAAATAACTTTAATAGATT
16815247 GAATTGAAGGGCGGATGTGAAACTAGCTAGGCTAGAACCAATATTAATTTCATGTTCATTAATTA
1 GAATTGAAGGGCGGATGTGAAACTAGCTAGGCTAGAACCAATATTAATTTCATGTTCATTAATTA
16815312 ATTTCTTTCTTGTATATTATATATATATTTTTTATAGAAAATAACTTTAATAGATT
66 ATTTCTTTCTTGTATATTATATATATATTTTTTATAGAAAATAACTTTAATAGATT
16815368 GAATT
1 GAATT
16815373 AATGGTATTC
Statistics
Matches: 124, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
121 31 0.25
122 1 0.01
123 1 0.01
124 5 0.04
125 86 0.69
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (121 bp):
GAATTGAAGGGCGGATGTGAAACTAGCTAGGCTAGAACCAATATTAATTTCATGTTCATTAATTA
ATTTCTTTCTTGTATATTATATATATATTTTTTATAGAAAATAACTTTAATAGATT
Found at i:16816326 original size:20 final size:21
Alignment explanation
Indices: 16816290--16816340 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
16816280 TCAGAAATTA
16816290 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
16816312 ATAAAATATTATTTTT-AAAT
1 ATAAAATATTATTTTTAAAAT
16816332 AT-AAATATT
1 ATAAAATATT
16816341 TAAAAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.24
20 6 0.21
21 5 0.17
22 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:16816337 original size:19 final size:21
Alignment explanation
Indices: 16816289--16816340 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
16816279 ATCAGAAATT
16816289 AATA-AAATATTATTTTTTAA
1 AATATAAATATTATTTTTTAA
16816309 AATATAAAATATTA-TTTTT-A
1 AATAT-AAATATTATTTTTTAA
16816329 AATATAAATATT
1 AATATAAATATT
16816341 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.23
20 10 0.33
21 5 0.17
22 8 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATAAATATTATTTTTTAA
Found at i:16819087 original size:22 final size:23
Alignment explanation
Indices: 16819049--16819092 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
16819039 TTAGAAAATA
16819049 AATTTTAAAAATATTTTAATATT
1 AATTTTAAAAATATTTTAATATT
*
16819072 AATTTT-AAAATTTTTTAATAT
1 AATTTTAAAAATATTTTAATAT
16819093 AGTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTTAAAAATATTTTAATATT
Found at i:16819783 original size:18 final size:17
Alignment explanation
Indices: 16819738--16819787 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
16819728 TTGGTTATTT
16819738 TAAAA-TAT-TATAA-A
1 TAAAATTATATATAATA
16819752 TAAAATTATATATAATA
1 TAAAATTATATATAATA
*
16819769 TAAATATTTTATATAATA
1 TAAA-ATTATATATAATA
16819787 T
1 T
16819788 TTTCTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 5 0.16
15 3 0.10
16 5 0.16
17 5 0.16
18 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTATATATAATA
Found at i:16819824 original size:18 final size:19
Alignment explanation
Indices: 16819801--16819838 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
16819791 CTTTAATCTG
*
16819801 ATAAA-TAATAAATTAAAA
1 ATAAATTAAGAAATTAAAA
*
16819819 ATAAATTAAGAACTTAAAA
1 ATAAATTAAGAAATTAAAA
16819838 A
1 A
16819839 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAAATTAAGAAATTAAAA
Found at i:16819897 original size:6 final size:6
Alignment explanation
Indices: 16819886--16819911 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16819876 TAGGCTGGAG
16819886 GCAACA GCAACA GCAACA GCAACA GC
1 GCAACA GCAACA GCAACA GCAACA GC
16819912 TATCGATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.35, G:0.19, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:16820289 original size:28 final size:30
Alignment explanation
Indices: 16820244--16820305 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
16820234 AATCATATGA
* *
16820244 TTTATTAATAAATTATTAA-AATT-TTAAT
1 TTTATTAATAAATAATTAATAATTAATAAT
16820272 TTTATTAATTAAA-AATTAATAATTAATAAT
1 TTTATTAA-TAAATAATTAATAATTAATAAT
16820302 TTTA
1 TTTA
16820306 AGTATCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 13 0.45
29 8 0.28
30 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTATTAATAAATAATTAATAATTAATAAT
Found at i:16832145 original size:29 final size:30
Alignment explanation
Indices: 16832112--16832170 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
16832102 GCCATCAATG
16832112 AAGTAATTTAATTAACTAT-TTAATCTCAT
1 AAGTAATTTAATTAACTATGTTAATCTCAT
*
16832141 AAGTAATTTAATTGACTATGTTAATCTCAT
1 AAGTAATTTAATTAACTATGTTAATCTCAT
16832171 GGTGTCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (30 bp):
AAGTAATTTAATTAACTATGTTAATCTCAT
Found at i:16833476 original size:22 final size:22
Alignment explanation
Indices: 16833428--16833480 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
16833418 AAATTATATA
*
16833428 TTTAAAA-AAAGTTATATATTT
1 TTTAAAATAAAGTTATAAATTT
*
16833449 TGTAAAATAAAGTT-TAAATTAT
1 TTTAAAATAAAGTTATAAATT-T
16833471 TTTAAAATAA
1 TTTAAAATAA
16833481 TTTTAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
TTTAAAATAAAGTTATAAATTT
Found at i:16835009 original size:66 final size:66
Alignment explanation
Indices: 16834927--16835073 Score: 276
Period size: 66 Copynumber: 2.2 Consensus size: 66
16834917 TTAAAGTAGA
16834927 TCTCCCAATAGTTTGGTGAAATTTTATTATAAAAAGATTTGTAAAAAAATTGTGAATTTCATTAA
1 TCTCCCAATAGTTTGGTGAAATTTTATTATAAAAAGATTTGTAAAAAAATTGTGAATTTCATTAA
16834992 G
66 G
*
16834993 TCTCCCAATAGTTTGGTGAAATTTTATTATAAAGAGATTTGTAAAAAAATTGTGAATTTCATTAA
1 TCTCCCAATAGTTTGGTGAAATTTTATTATAAAAAGATTTGTAAAAAAATTGTGAATTTCATTAA
16835058 G
66 G
*
16835059 TCTCTCAATAGTTTG
1 TCTCCCAATAGTTTG
16835074 ATAGGACTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 79 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (66 bp):
TCTCCCAATAGTTTGGTGAAATTTTATTATAAAAAGATTTGTAAAAAAATTGTGAATTTCATTAA
G
Found at i:16835273 original size:18 final size:19
Alignment explanation
Indices: 16835244--16835284 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
16835234 TTTTATAAGG
16835244 TTTTTATCTGAAAAGATTT
1 TTTTTATCTGAAAAGATTT
*
16835263 TTTTTAT-TGAAAGGATTT
1 TTTTTATCTGAAAAGATTT
16835281 TTTT
1 TTTT
16835285 GTTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (19 bp):
TTTTTATCTGAAAAGATTT
Found at i:16835471 original size:9 final size:10
Alignment explanation
Indices: 16835446--16835470 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16835436 ATAGAAACTT
16835446 AAAAAATAAA
1 AAAAAATAAA
16835456 AAAAAATAAA
1 AAAAAATAAA
16835466 AAAAA
1 AAAAA
16835471 TGAAATCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:16836338 original size:15 final size:17
Alignment explanation
Indices: 16836318--16836357 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
16836308 GATTGGAGCC
16836318 AAAAG-AAAG-AAAAAA
1 AAAAGAAAAGCAAAAAA
16836333 AAAAGAAAAGCAAAAAA
1 AAAAGAAAAGCAAAAAA
16836350 AAAA-AAAA
1 AAAAGAAAA
16836358 TTATAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.22
16 8 0.35
17 10 0.43
ACGTcount: A:0.88, C:0.03, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGCAAAAAA
Found at i:16836350 original size:20 final size:20
Alignment explanation
Indices: 16836318--16836356 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
16836308 GATTGGAGCC
16836318 AAAAGAAAGAAAAAAAAAAG
1 AAAAGAAAGAAAAAAAAAAG
16836338 AAAAGCAAA-AAAAAAAAAA
1 AAAAG-AAAGAAAAAAAAAA
16836357 ATTATAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGAAAAAAAAAAG
Found at i:16836790 original size:117 final size:118
Alignment explanation
Indices: 16836569--16836790 Score: 268
Period size: 117 Copynumber: 1.9 Consensus size: 118
16836559 TTGAAAAATG
* * * *
16836569 ATCTAGATTGAGCCAAGATCGAGTGACCGGGATGAAACCACAGGTCAAAAAATGAAGTGACCAGA
1 ATCTAGATTGAACCAAGATAGAGTGACCGGGATGAAACCACAAGTC-AAAAATGAAGCGACCAGA
* * * * * * *
16836634 ACCGAGTTGAGGTTAAAGATAAATGATCGGGACAAAATCACAAGTCAGGAAGTT
65 ACCGAGTCGAAGTAAAAAATAAATAACCAGGACAAAATCACAAGTCAGGAAGTT
* ** *
16836688 ATCTGGATTGAACCAAGACTAG-GTGACCGGGATGAAATTACAAGTC-AAAATGAAGCGACCAGG
1 ATCTAGATTGAACCAAGA-TAGAGTGACCGGGATGAAACCACAAGTCAAAAATGAAGCGACCAGA
*
16836751 ACCGAGTCGAAGTAAAAAATAAATAACCAGGACAGAATCA
65 ACCGAGTCGAAGTAAAAAATAAATAACCAGGACAAAATCA
16836791 TGAAGCATAA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
117 47 0.55
119 37 0.43
120 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (118 bp):
ATCTAGATTGAACCAAGATAGAGTGACCGGGATGAAACCACAAGTCAAAAATGAAGCGACCAGAA
CCGAGTCGAAGTAAAAAATAAATAACCAGGACAAAATCACAAGTCAGGAAGTT
Found at i:16837036 original size:120 final size:120
Alignment explanation
Indices: 16836882--16837183 Score: 286
Period size: 120 Copynumber: 2.5 Consensus size: 120
16836872 AGTCAAGGTT
* * * * *
16836882 AAAAATAAAT-AATCGAGATAAAACCATGAATCATAAAAAATGATTTGGATTAAGTCAAGATCAG
1 AAAAATAAATGACT-GAGATGAAACCACGAGTCATAAAAAATGATCTGGATTAAGTCAAGATCAG
* * * * *** *
16836946 GTGATTGGGATAAAATCACGA-GTCAAAAATGAAACGACCTGGATTAAGTCGAGATC
65 GTGACTAGGACAAAACCAC-ATGTCAAAAATGAAACGACAAAGATCAAGTCGAGATC
* * * * * * * * *
16837002 GAAGATAAATGATTTG-GATGAAACTACGAGTCATAAAAAATGGTCTAGATTGAGCCAAGATTAG
1 AAAAATAAATGA-CTGAGATGAAACCACGAGTCATAAAAAATGATCTGGATTAAGTCAAGATCAG
* * * * *
16837066 GTGACTAGGACGAAACCACATGTCAAATATGAAGCGACAAAGATCGAGTCGAGGTC
65 GTGACTAGGACAAAACCACATGTCAAAAATGAAACGACAAAGATCAAGTCGAGATC
* * *
16837122 AAAAATAAATGACTGAGATGAAACCATGAGTCATAAGAAATGATCTGGACTAAGTCAAGATC
1 AAAAATAAATGACTGAGATGAAACCACGAGTCATAAAAAATGATCTGGATTAAGTCAAGATC
16837184 GAGTGAGTGA
Statistics
Matches: 140, Mismatches: 38, Indels: 8
0.75 0.20 0.04
Matches are distributed among these distances:
119 3 0.02
120 134 0.96
121 2 0.01
122 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (120 bp):
AAAAATAAATGACTGAGATGAAACCACGAGTCATAAAAAATGATCTGGATTAAGTCAAGATCAGG
TGACTAGGACAAAACCACATGTCAAAAATGAAACGACAAAGATCAAGTCGAGATC
Found at i:16844699 original size:14 final size:15
Alignment explanation
Indices: 16844680--16844710 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
16844670 ATGAGGTATC
16844680 TTCCTTTA-TTGCCT
1 TTCCTTTATTTGCCT
16844694 TTCCTTTATTTGCCT
1 TTCCTTTATTTGCCT
16844709 TT
1 TT
16844711 TTCAGAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.06, C:0.26, G:0.06, T:0.61
Consensus pattern (15 bp):
TTCCTTTATTTGCCT
Found at i:16849453 original size:3 final size:3
Alignment explanation
Indices: 16849447--16849481 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16849437 AATAATAGTA
16849447 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
16849482 ATTGTAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16850638 original size:30 final size:29
Alignment explanation
Indices: 16850604--16850660 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
16850594 TTTTATCTAA
* *
16850604 TTAAAGAGTCCATTGATTAAAAATAAAAAT
1 TTAAAGACTCAATTGATT-AAAATAAAAAT
* *
16850634 TTAAATACTCAATTGATTATAATAAAA
1 TTAAAGACTCAATTGATTAAAATAAAA
16850661 TGATAGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 8 0.35
30 15 0.65
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (29 bp):
TTAAAGACTCAATTGATTAAAATAAAAAT
Found at i:16853083 original size:3 final size:3
Alignment explanation
Indices: 16853075--16853100 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16853065 ATTCCGTGGG
16853075 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
16853101 TTTCATCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16853704 original size:18 final size:19
Alignment explanation
Indices: 16853669--16853711 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
16853659 AAGTTTTTAA
* *
16853669 ATTTTAATATATATTTATT
1 ATTTTAATATAAAATTATT
16853688 ATTTTAATA-AAAATTATT
1 ATTTTAATATAAAATTATT
16853706 ATTTTA
1 ATTTTA
16853712 TTCTTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTAATATAAAATTATT
Found at i:16855617 original size:17 final size:17
Alignment explanation
Indices: 16855590--16855623 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16855580 AAACCCAAAA
16855590 TTATTAAACTT-AATTT
1 TTATTAAACTTCAATTT
16855606 TTATTCAAACTTCAATTT
1 TTATT-AAACTTCAATTT
16855624 ATTTATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTAAACTTCAATTT
Found at i:16858692 original size:25 final size:25
Alignment explanation
Indices: 16858658--16858708 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
16858648 CAATGAGAGA
* *
16858658 TTAGTAATTTGATACGTAGTTAATT
1 TTAGTAATTTAATACATAGTTAATT
*
16858683 TTAGTAATTTAATATATAGTTAATT
1 TTAGTAATTTAATACATAGTTAATT
16858708 T
1 T
16858709 ATATTATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (25 bp):
TTAGTAATTTAATACATAGTTAATT
Found at i:16858708 original size:16 final size:17
Alignment explanation
Indices: 16858687--16858732 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
16858677 TTAATTTTAG
*
16858687 TAATTTAATATATA-GT
1 TAATTTAATATATATGA
16858703 TAATTT-ATATTATATGA
1 TAATTTAATA-TATATGA
*
16858720 AAATTTAATATAT
1 TAATTTAATATAT
16858733 GTAGTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 10 0.40
17 9 0.36
18 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TAATTTAATATATATGA
Found at i:16859032 original size:62 final size:63
Alignment explanation
Indices: 16858958--16859102 Score: 170
Period size: 62 Copynumber: 2.3 Consensus size: 63
16858948 GATTATGACA
*
16858958 AGAATATTATAGTAATTTTGACCAATTATGGTAAG-AAGGTCATTTCTATAATTATGATAAGAG-
1 AGAA-ATTATAGTAATTTTGACCAATTATGGTAAGAAAGAT-ATTTCTATAATTATGATAAGAGT
* * * * * *
16859021 AGAAATTATAGTAATTTTAACTAATTATGGTATGAAAGATATTTTTGTAATTATGGTAAGAGT
1 AGAAATTATAGTAATTTTGACCAATTATGGTAAGAAAGATATTTCTATAATTATGATAAGAGT
* *
16859084 AG-TATTATAATAATTTTGA
1 AGAAATTATAGTAATTTTGA
16859103 TCCTTTATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 60 0.86
63 10 0.14
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (63 bp):
AGAAATTATAGTAATTTTGACCAATTATGGTAAGAAAGATATTTCTATAATTATGATAAGAGT
Found at i:16860844 original size:21 final size:22
Alignment explanation
Indices: 16860820--16860872 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
16860810 TTACTTAGTG
16860820 ATTTATTTCATATA-TATCTTT
1 ATTTATTTCATATATTATCTTT
* *
16860841 ATTTATGTCTTA-ATTATCTTT
1 ATTTATTTCATATATTATCTTT
16860862 ATTT-TTT-ATAT
1 ATTTATTTCATAT
16860873 CTTTGTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 21 0.81
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTATTTCATATATTATCTTT
Found at i:16864289 original size:15 final size:14
Alignment explanation
Indices: 16864269--16864318 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
16864259 TAAAATTACC
16864269 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
* *
16864283 AAGAAAAAAAAGCA
1 AAAAAAAAAAAACA
16864297 AAAAAATAAAAAACA
1 AAAAAA-AAAAAACA
*
16864312 ACAAAAA
1 AAAAAAA
16864319 TCAGTAGCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:16864307 original size:18 final size:17
Alignment explanation
Indices: 16864269--16864318 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
16864259 TAAAATTACC
16864269 AAAAAAAA-AAAACAAAG
1 AAAAAAAACAAAA-AAAG
*
16864286 AAAAAAAAGCAAAAAAAT
1 AAAAAAAA-CAAAAAAAG
16864304 AAAAAACAACAAAAA
1 AAAAAA-AACAAAAA
16864319 TCAGTAGCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.28
18 15 0.52
19 6 0.21
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (17 bp):
AAAAAAAACAAAAAAAG
Found at i:16866311 original size:22 final size:21
Alignment explanation
Indices: 16866286--16866344 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
16866276 AAAAAATAGT
*
16866286 AAAATAAGATAAAAAACAACTG
1 AAAATAA-ATAAAAAAAAACTG
*
16866308 AAAATAAAATAAAATAAAAACTT
1 AAAAT-AAATAAAA-AAAAACTG
*
16866331 AAAACAAATAAAAA
1 AAAATAAATAAAAA
16866345 TGGTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 19 0.59
23 12 0.38
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (21 bp):
AAAATAAATAAAAAAAAACTG
Found at i:16866796 original size:21 final size:22
Alignment explanation
Indices: 16866736--16866796 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
16866726 AGATTTTTCT
*
16866736 AGAAATTCAAACT-TCAATCCA
1 AGAAATTCAAACTCTAAATCCA
** *
16866757 AGAGCTTCAAA-TCCAAATCCA
1 AGAAATTCAAACTCTAAATCCA
*
16866778 A-AAATTCAAACTCTGAATC
1 AGAAATTCAAACTCTAAATC
16866797 TTTAAACCCG
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.23
Consensus pattern (22 bp):
AGAAATTCAAACTCTAAATCCA
Found at i:16867218 original size:3 final size:3
Alignment explanation
Indices: 16867199--16867278 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
16867189 GGGAAAGAAC
* *
16867199 AAT AAA AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16867247 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16867279 ACACTAGTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16867642 original size:54 final size:54
Alignment explanation
Indices: 16867562--16867668 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 54
16867552 CCATTTGTCA
* * * *
16867562 AAAAAATAATTTGGACTGAGTTGAGATCAAACAACTAGGATTGAACTGCAAGTC
1 AAAAAATAATTTAGACTGAGTCGAGATCAAACAACTAGAATTGAAATGCAAGTC
* * ** *
16867616 AAAAAATTATTTAGATTGAGTCGAGATTGAACGACTAGAATTGAAATGCAAGT
1 AAAAAATAATTTAGACTGAGTCGAGATCAAACAACTAGAATTGAAATGCAAGT
16867669 AAGAAAAACG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (54 bp):
AAAAAATAATTTAGACTGAGTCGAGATCAAACAACTAGAATTGAAATGCAAGTC
Found at i:16867899 original size:61 final size:61
Alignment explanation
Indices: 16867820--16868016 Score: 183
Period size: 61 Copynumber: 3.2 Consensus size: 61
16867810 AGTCAAAATC
* *
16867820 AAAAGCAAGTGATCGGGATCAAATCGCAT-A-TCAAATAGATGACTTGGACTGACCTGAGATCT-
1 AAAA-CAAGTGAT-GGGATCAAATC-CATGAGTCAAACAGATGACTTAGACTGACCTGAGAT-TG
*
16867882 AAAACAAGTGACTGGGATCAAA-CCATGAGTCAAACAGATGACTTAGACTGAGCTGAGATTG
1 AAAACAAGTGA-TGGGATCAAATCCATGAGTCAAACAGATGACTTAGACTGACCTGAGATTG
* * * * * * *
16867943 AAAGCAAGTGATTGAGATCAAAT-CATGAGTAAAAAAGATGA-TCTGGATTGA-GTCGAGATTG
1 AAAACAAGTGA-TGGGATCAAATCCATGAGTCAAACAGATGACT-TAGACTGACCT-GAGATTG
16868004 AAAACAAGTGATG
1 AAAACAAGTGATG
16868017 ATGTAACGAT
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
59 3 0.03
60 7 0.06
61 101 0.87
62 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (61 bp):
AAAACAAGTGATGGGATCAAATCCATGAGTCAAACAGATGACTTAGACTGACCTGAGATTG
Found at i:16872919 original size:3 final size:3
Alignment explanation
Indices: 16872905--16873067 Score: 113
Period size: 3 Copynumber: 59.0 Consensus size: 3
16872895 ACCAATTTTC
* *
16872905 ATT ATT AGT ATT ATT TTT A-T ATT A-T ATT A-T ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * *
16872949 ATT A-T ATT -TT A-T ATT ATT ATT ATT AAA ACT A-T AGT A-T AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
16872992 -GT ATT A-T ATT -TT A-T ACT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
16873036 ATT AGGT ATT A-T ATT -TT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16873068 TTTTTCCTTT
Statistics
Matches: 128, Mismatches: 16, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
2 29 0.23
3 97 0.76
4 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:16873981 original size:4 final size:4
Alignment explanation
Indices: 16873958--16874005 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
16873948 TCATTTTCAT
* *
16873958 TTTA TTTT TTTGA TTTTA TTTA TTTA TTTA TTTA TTT- TTTA GTTA TTT
1 TTTA TTTA TTT-A -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
16874006 TTTTGTGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
4 30 0.81
5 1 0.03
6 3 0.08
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:16881495 original size:17 final size:16
Alignment explanation
Indices: 16881457--16881522 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
16881447 ATGGAACATA
*
16881457 AAAATAAAATAAAAACTT
1 AAAAT-AAATAAAAA-TG
16881475 AAAATAAATAAAAATGG
1 AAAATAAATAAAAAT-G
16881492 AAAA-AAA-AAAAAT-
1 AAAATAAATAAAAATG
*
16881505 -AAA-AAATGAAAATG
1 AAAATAAATAAAAATG
16881519 AAAA
1 AAAA
16881523 AAAGAAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 6 0.14
13 5 0.12
15 9 0.21
16 4 0.10
17 13 0.31
18 5 0.12
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATAAATAAAAATG
Found at i:16881512 original size:22 final size:22
Alignment explanation
Indices: 16881431--16881510 Score: 52
Period size: 25 Copynumber: 3.3 Consensus size: 22
16881421 AAAAAATTAG
*
16881431 TAAAATAAAATAAAAAATGGAACA
1 TAAAA-AAAATAAAAAAT-GAAAA
* *
16881455 TAAAAATAAAATAAAAACTTAAAA
1 T-AAAA-AAAATAAAAAATGAAAA
**
16881479 TAAATAAAAATGGAAAAAAAAAAAA
1 TAAA-AAAAAT--AAAAAATGAAAA
16881504 TAAAAAA
1 TAAAAAA
16881511 TGAAAATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 8 0.17
24 9 0.20
25 29 0.63
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (22 bp):
TAAAAAAAATAAAAAATGAAAA
Found at i:16881517 original size:38 final size:41
Alignment explanation
Indices: 16881432--16881525 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 41
16881422 AAAAATTAGT
* *
16881432 AAAATAAAATAAAAAATGGAACATAAAAATAAAATAAAAACTT
1 AAAAT-AAAT-AAAAATGGAACATAAAAATAAAATAAAAAATG
16881475 AAAATAAATAAAAATGGAA-A-AAAAA-AAAATAAAAAATG
1 AAAATAAATAAAAATGGAACATAAAAATAAAATAAAAAATG
*
16881513 AAAATGAA-AAAAA
1 AAAATAAATAAAAA
16881526 GAAAACCTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
37 5 0.10
38 18 0.38
39 5 0.10
40 1 0.02
41 10 0.21
42 4 0.08
43 5 0.10
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (41 bp):
AAAATAAATAAAAATGGAACATAAAAATAAAATAAAAAATG
Found at i:16881522 original size:22 final size:22
Alignment explanation
Indices: 16881475--16881530 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
16881465 ATAAAAACTT
*
16881475 AAAATAAAT-AAAAATGGAAAA
1 AAAAAAAATAAAAAATGGAAAA
16881496 AAAAAAAATAAAAAAT-GAAAA
1 AAAAAAAATAAAAAATGGAAAA
* *
16881517 TGAAAAAAAGAAAA
1 -AAAAAAAATAAAA
16881531 CCTATGATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAAAAAATAAAAAATGGAAAA
Done.