Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 70 of 150
Found at i:20836384 original size:177 final size:177
Alignment explanation
Indices: 20836087--20836420 Score: 425
Period size: 177 Copynumber: 1.9 Consensus size: 177
20836077 CGGAGTAGGT
** * *
20836087 TGAAGATAGTGGATCTTGCCTTCCTGCACCAACAGCGAAGTAGATCGAAGACACTAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTACACCAACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
* * * * * * *
20836152 CCCTGGGTTACAGTGGAGCAGATTGAAGATGGCAGATATTGCCTTCCTGTACTGACAGCGAAGCA
66 CCATGGGTTACAGCGGAACAGATTAAAGATAGCAGATATTGCATTCCTATACTGACAGCGAAGCA
* *
20836217 AATCGAAGACACCAGTCTTGCCTTCCTCAACTGACAACGGAGCAGAC
131 AATCGAAGACACCAGCCTGGCCTTCCTCAACTGACAACGGAGCAGAC
* * * * *
20836264 TGAAGATAGCAGATCTTGCTTTCCTACACTAATAGTGAAGCAGATTGAAGACACTAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTACACCAACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
* * * * * *
20836329 CCATGGGTTGCAGCGGAATAGGTTAAAGATAGTAGATCTTGCATTCCTATACTGACAGTGAAGCA
66 CCATGGGTTACAGCGGAACAGATTAAAGATAGCAGATATTGCATTCCTATACTGACAGCGAAGCA
* * *
20836394 GATTGAAGACACTAGCCTGGCCTTCCT
131 AATCGAAGACACCAGCCTGGCCTTCCT
20836421 GGATTGCAGC
Statistics
Matches: 130, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
177 130 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (177 bp):
TGAAGATAGCAGATCTTGCCTTCCTACACCAACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
CCATGGGTTACAGCGGAACAGATTAAAGATAGCAGATATTGCATTCCTATACTGACAGCGAAGCA
AATCGAAGACACCAGCCTGGCCTTCCTCAACTGACAACGGAGCAGAC
Found at i:20836622 original size:131 final size:131
Alignment explanation
Indices: 20836436--20836815 Score: 591
Period size: 131 Copynumber: 2.9 Consensus size: 131
20836426 GCAGCAGAGC
* * *
20836436 AGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTAGAGTAGATCGAAGACGGCGAATCTT
1 AGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT
*
20836501 ATCTTCCTCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGAAA
66 ATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGAAA
20836566 T
131 T
*
20836567 AGGTTGGAAATTACAGATCTTATCTCCCTCAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT
1 AGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT
* *
20836632 ATCTTCCCCAGGAGTAGGAAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGGAA
66 ATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGAAA
20836697 T
131 T
** * * *
20836698 AGGTT-GAAGATTATGGATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGAATCT
1 AGGTTGGAA-ATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCT
* * * *
20836762 TATCTTCCCCAGGTAGTAAGGAAACAGATTTAAGCCACTAATCCTATTTCCCTG
65 TATCTTCCCCAGG-AGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTG
20836816 AAGTTGCAGT
Statistics
Matches: 229, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
130 3 0.01
131 191 0.83
132 35 0.15
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (131 bp):
AGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT
ATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGTCAGCAGTGAAA
T
Found at i:20836765 original size:44 final size:44
Alignment explanation
Indices: 20836452--20836766 Score: 117
Period size: 44 Copynumber: 7.2 Consensus size: 44
20836442 AAAATTACAG
* * * *
20836452 ATCTTATCTCCCTAAGCAGTAGTAGAGTAGATCGAAGACGGCGA
1 ATCTTATCTCCCTCAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * ** * *
20836496 ATCTTATCTTCCTCAGGAGTAG-GGAAGCAGATTTAAG-CCACTA
1 ATCTTATCTCCCTCAGCAGTAGTGG-AGCAGATCGAAGACGACGA
* * * * * ** * * **
20836539 GTCCTATCTCCCT-GGTCAGCAGTGAAATAGGTTGGAA-ATTAC-A
1 ATCTTATCTCCCTCAG-CAGTAGTGGAGCA-GATCGAAGACGACGA
*
20836582 GATCTTATCTCCCTCAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCTTATCTCCCTCAGCAGTAGTGGAGCAGATCGAAGACGACGA
* * ** * *
20836627 ATCTTATCTTCCC-CAGGAGTAG-GAAAGCAGATTTAAG-CCACTA
1 ATCTTATC-TCCCTCAGCAGTAGTG-GAGCAGATCGAAGACGACGA
* * * * ** * * ** * *
20836670 GTCCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTATGG
1 ATCTTATCTCCCTCAG-CAGTAGTGGAGCAGATCGAAGACGACGA
* * *
20836714 ATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGA
1 ATCTTATCTCCCTCAGCAGTAGTGGAGCAGATCGAAGACGACGA
20836758 ATCTTATCT
1 ATCTTATCT
20836767 TCCCCAGGTA
Statistics
Matches: 184, Mismatches: 71, Indels: 32
0.64 0.25 0.11
Matches are distributed among these distances:
42 6 0.03
43 48 0.26
44 123 0.67
45 7 0.04
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCTTATCTCCCTCAGCAGTAGTGGAGCAGATCGAAGACGACGA
Found at i:20840304 original size:19 final size:19
Alignment explanation
Indices: 20840280--20840317 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
20840270 AACCTAAGGG
20840280 TAAAATAGTAAA-TAAATAA
1 TAAAAT-GTAAATTAAATAA
20840299 TAAAATGTAAATTAAATAA
1 TAAAATGTAAATTAAATAA
20840318 AACTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAATGTAAATTAAATAA
Found at i:20842225 original size:75 final size:74
Alignment explanation
Indices: 20842092--20842230 Score: 190
Period size: 75 Copynumber: 1.9 Consensus size: 74
20842082 TACAAGTTGA
* * * * **
20842092 AAAAATTTGAATCAATATTTTAAAGAATTACAGAGTGATAAATTTAGAAATCTTTTTTAAAAAAA
1 AAAAATTTGAATCAATAGTTTAAAAAATTACAAAGTGATAAATTTAGAAAACGATTTTAAAAAAA
20842157 TGACAACTG
66 TGACAACTG
*
20842166 AAAAATTTCGAATCAATAGTTTAAAAAATTACAAAGTGATACATTCT-GAAAACGATTTTAAAAA
1 AAAAATTT-GAATCAATAGTTTAAAAAATTACAAAGTGATAAATT-TAGAAAACGATTTTAAAAA
20842230 A
64 A
20842231 TTTACAAACT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
74 8 0.14
75 47 0.84
76 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (74 bp):
AAAAATTTGAATCAATAGTTTAAAAAATTACAAAGTGATAAATTTAGAAAACGATTTTAAAAAAA
TGACAACTG
Found at i:20844433 original size:53 final size:53
Alignment explanation
Indices: 20844375--20844518 Score: 139
Period size: 53 Copynumber: 2.7 Consensus size: 53
20844365 TTGAACTAAT
*
20844375 AAAAAGGGTGTCGGTCATCAATGTCTTAGCACCCCAATTTTTTTTTTAATT-TGG
1 AAAAAGGGTGTCGGTCATCAATGTCTCAGCACCCCAA--TTTTTTTTAATTCTGG
* * * * * *
20844429 AAAAGGGGTGTCAGTTATCAGTGT-TCCAACACCCTAATTTTTTTTAATTCTGG
1 AAAAAGGGTGTCGGTCATCAATGTCT-CAGCACCCCAATTTTTTTTAATTCTGG
** * * *
20844482 AAAAAAAGTGTCGGCCATCACTGTCCCAGCACCCCAA
1 AAAAAGGGTGTCGGTCATCAATGTCTCAGCACCCCAA
20844519 AAAAATTAAT
Statistics
Matches: 70, Mismatches: 17, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
52 12 0.17
53 30 0.43
54 28 0.40
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (53 bp):
AAAAAGGGTGTCGGTCATCAATGTCTCAGCACCCCAATTTTTTTTAATTCTGG
Found at i:20844656 original size:56 final size:57
Alignment explanation
Indices: 20844547--20844668 Score: 174
Period size: 56 Copynumber: 2.1 Consensus size: 57
20844537 AATGTGACAG
* **
20844547 CCATCAGTGTCCCAGCACCCCAAAAAAACCTTTTTTTAATCAGATAAAGGGGTGCCGA
1 CCATCAGTGTCCCAACACCCCAAAAAAA-CAATTTTTAATCAGATAAAGGGGTGCCGA
* * *
20844605 CCATTAGTGTCCCAACACCCCAAAAAAA-AATTTTTAATCAGATAAGGGGGTGTCGA
1 CCATCAGTGTCCCAACACCCCAAAAAAACAATTTTTAATCAGATAAAGGGGTGCCGA
20844661 CCATCAGT
1 CCATCAGT
20844669 ATCATAACAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
56 31 0.54
58 26 0.46
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (57 bp):
CCATCAGTGTCCCAACACCCCAAAAAAACAATTTTTAATCAGATAAAGGGGTGCCGA
Found at i:20845292 original size:26 final size:26
Alignment explanation
Indices: 20845269--20845318 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
20845259 AGTGACTGGT
20845269 TTGACTAACTAATTCTATTAACTGAC
1 TTGACTAACTAATTCTATTAACTGAC
* *
20845295 TTGATTAACTGATTCTATTAACTG
1 TTGACTAACTAATTCTATTAACTG
20845319 TTTATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (26 bp):
TTGACTAACTAATTCTATTAACTGAC
Found at i:20845314 original size:13 final size:13
Alignment explanation
Indices: 20845274--20845318 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
20845264 CTGGTTTGAC
*
20845274 TAACTAATTCTAT
1 TAACTGATTCTAT
*
20845287 TAACTGACTT-GAT
1 TAACTGA-TTCTAT
20845300 TAACTGATTCTAT
1 TAACTGATTCTAT
20845313 TAACTG
1 TAACTG
20845319 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.07
13 23 0.85
14 2 0.07
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (13 bp):
TAACTGATTCTAT
Found at i:20848670 original size:63 final size:63
Alignment explanation
Indices: 20848571--20848713 Score: 189
Period size: 63 Copynumber: 2.3 Consensus size: 63
20848561 TAGTGTGGCT
* ** * * * *
20848571 CAAAATAGTGAGTTACATGGTCTGGACACACGCCTGTGTCTCTAG-CTCGTGTGTCCCTAATTC
1 CAAAATAGTGAGTTACACGACCTGCACACACGCCTGTGCCTCTAGCCT-ATATGTCCCTAATTC
* *
20848634 CAAAATAGTGAGTTACACGACCTGCACAGACGCCTGTGCCTCTAGCCTATATGTCTCTAATTC
1 CAAAATAGTGAGTTACACGACCTGCACACACGCCTGTGCCTCTAGCCTATATGTCCCTAATTC
20848697 CAAAATAGTGAGTTACA
1 CAAAATAGTGAGTTACA
20848714 TGGCTTACCA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
63 68 0.97
64 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (63 bp):
CAAAATAGTGAGTTACACGACCTGCACACACGCCTGTGCCTCTAGCCTATATGTCCCTAATTC
Found at i:20849304 original size:20 final size:20
Alignment explanation
Indices: 20849259--20849305 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20849249 CACGAGGGAG
20849259 GGAAAATAAGGAAGAAAGAA
1 GGAAAATAAGGAAGAAAGAA
**
20849279 AAAAAATAA-GAAGAAGAGAA
1 GGAAAATAAGGAAGAA-AGAA
20849299 GGAAAAT
1 GGAAAAT
20849306 GTTTCCTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (20 bp):
GGAAAATAAGGAAGAAAGAA
Found at i:20851116 original size:20 final size:21
Alignment explanation
Indices: 20851088--20851130 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
20851078 AAGTCCAAGT
20851088 AAAACTTAAAATAAAAA-TAA
1 AAAACTTAAAATAAAAATTAA
* **
20851108 AAAATTTAATTTAAAAATTAA
1 AAAACTTAAAATAAAAATTAA
20851129 AA
1 AA
20851131 GAATAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAACTTAAAATAAAAATTAA
Found at i:20853335 original size:16 final size:18
Alignment explanation
Indices: 20853296--20853335 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20853286 AATATTTATA
20853296 TTATTTTTATATAATATT
1 TTATTTTTATATAATATT
*
20853314 TAATTTTTATAT-AT-TT
1 TTATTTTTATATAATATT
20853330 TTATTT
1 TTATTT
20853336 ACTGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTTTATATAATATT
Found at i:20856639 original size:17 final size:17
Alignment explanation
Indices: 20856619--20856726 Score: 65
Period size: 17 Copynumber: 6.4 Consensus size: 17
20856609 CCAAACATCT
*
20856619 ATTCATATGAAATAACA
1 ATTCATACGAAATAACA
* * *
20856636 ATTCTTACCAAATGACA
1 ATTCATACGAAATAACA
** * * *
20856653 GCTCATGCAAAATAATA
1 ATTCATACGAAATAACA
* *
20856670 ATTCATATGAAATATCA
1 ATTCATACGAAATAACA
*
20856687 GTTCATACCG-AATAACA
1 ATTCATA-CGAAATAACA
* *
20856704 ATTCATGCAAAATAACA
1 ATTCATACGAAATAACA
*
20856721 GTTCAT
1 ATTCAT
20856727 GCTCCATCAT
Statistics
Matches: 64, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
16 1 0.02
17 62 0.97
18 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (17 bp):
ATTCATACGAAATAACA
Found at i:20856679 original size:51 final size:51
Alignment explanation
Indices: 20856619--20856718 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
20856609 CCAAACATCT
* * *
20856619 ATTCATATGAAATAACAATTCTTACCAAATGACAGCTCATGCAAAATAATA
1 ATTCATATGAAATAACAATTCATACCAAATAACAACTCATGCAAAATAATA
* * * *
20856670 ATTCATATGAAATATCAGTTCATACCGAATAACAATTCATGCAAAATAA
1 ATTCATATGAAATAACAATTCATACCAAATAACAACTCATGCAAAATAA
20856719 CAGTTCATGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (51 bp):
ATTCATATGAAATAACAATTCATACCAAATAACAACTCATGCAAAATAATA
Found at i:20873030 original size:21 final size:21
Alignment explanation
Indices: 20873004--20873055 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
20872994 TATTTTTAAA
20873004 ATTTTTA-AAAATATGTATATT
1 ATTTTTATAAAATATGTA-ATT
* *
20873025 ATTTTTATATAATATTTAATT
1 ATTTTTATAAAATATGTAATT
20873046 ATTTTATATA
1 ATTTT-TATA
20873056 TAATCATCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTTATAAAATATGTAATT
Found at i:20873038 original size:22 final size:21
Alignment explanation
Indices: 20873004--20873059 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
20872994 TATTTTTAAA
*
20873004 ATTTTTA-AAAATATGTATATT
1 ATTTTTATATAATATGTA-ATT
*
20873025 ATTTTTATATAATATTTAATT
1 ATTTTTATATAATATGTAATT
20873046 ATTTTATATATAAT
1 ATTTT-TATATAAT
20873060 CATCTGAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTTATATAATATGTAATT
Found at i:20873489 original size:15 final size:17
Alignment explanation
Indices: 20873468--20873508 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
20873458 AGACATTTTA
20873468 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
20873484 -AAATTATTAAAATGAT
1 AAAATTATAAAAATGAT
20873500 AAAATTATA
1 AAAATTATA
20873509 TTTTTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:20884763 original size:45 final size:45
Alignment explanation
Indices: 20884690--20884785 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
20884680 GAATGAATAG
20884690 AAAAT-GAGAAATGAGAAACATTTAGAAATG-AT-TATGGTTTTCTCC
1 AAAATGGAGAAATGAGAAACATTTAGAAATGAATGTA-GG-TTTC-CC
* * *
20884735 AAAATGGAGAAATGA-AATCTTTTGGAAATGAATGTAGGTTTCCC
1 AAAATGGAGAAATGAGAAACATTTAGAAATGAATGTAGGTTTCCC
20884779 AAAATGG
1 AAAATGG
20884786 TAATGGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
44 9 0.20
45 21 0.47
46 13 0.29
47 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (45 bp):
AAAATGGAGAAATGAGAAACATTTAGAAATGAATGTAGGTTTCCC
Found at i:20888574 original size:12 final size:12
Alignment explanation
Indices: 20888557--20888581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20888547 GTTACACCTC
20888557 ATTATTTATGTT
1 ATTATTTATGTT
20888569 ATTATTTATGTT
1 ATTATTTATGTT
20888581 A
1 A
20888582 ACTTGTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
ATTATTTATGTT
Found at i:20889521 original size:21 final size:21
Alignment explanation
Indices: 20889497--20889536 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20889487 ACGGTTTGTT
*
20889497 CACACGGCCATGTGACCCATC
1 CACAAGGCCATGTGACCCATC
*
20889518 CACAAGGCTATGTGACCCA
1 CACAAGGCCATGTGACCCA
20889537 CTCACATGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.15
Consensus pattern (21 bp):
CACAAGGCCATGTGACCCATC
Found at i:20889542 original size:21 final size:20
Alignment explanation
Indices: 20889496--20889542 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
20889486 CACGGTTTGT
*
20889496 TCACACGGCCATGTGACCCA
1 TCACAAGGCCATGTGACCCA
*
20889516 TCCACAAGGCTATGTGACCCA
1 T-CACAAGGCCATGTGACCCA
20889537 CTCACA
1 -TCACA
20889543 TGACCAAGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (20 bp):
TCACAAGGCCATGTGACCCA
Found at i:20890142 original size:90 final size:91
Alignment explanation
Indices: 20890027--20890194 Score: 259
Period size: 91 Copynumber: 1.9 Consensus size: 91
20890017 TGTTGTTAAA
* ** *
20890027 AAAATGTTATAAATTATATTTATAAA-AAAA-TAAAACATAACTTTAATAATAAAATAAAGTTAG
1 AAAATGTTATAAATTATATTAATAAAGAAAACT-AAACATAACTACAATAATAAAATAAAGCTAG
20890090 TGGAAGAAAACCAAAATAATTAACAAC
65 TGGAAGAAAACCAAAATAATTAACAAC
* *
20890117 AAAATGTTATAAATTATATTAATAAAGAAAACTAAACATAACTACAATAATATAATTAAGCTAGT
1 AAAATGTTATAAATTATATTAATAAAGAAAACTAAACATAACTACAATAATAAAATAAAGCTAGT
20890182 GGAAGAAAACCAA
66 GGAAGAAAACCAA
20890195 GAAAAAGCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
90 25 0.36
91 44 0.63
92 1 0.01
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (91 bp):
AAAATGTTATAAATTATATTAATAAAGAAAACTAAACATAACTACAATAATAAAATAAAGCTAGT
GGAAGAAAACCAAAATAATTAACAAC
Found at i:20895703 original size:18 final size:18
Alignment explanation
Indices: 20895680--20895722 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
20895670 CCCACGCCAG
20895680 AAAAAATAAAATATATGT
1 AAAAAATAAAATATATGT
* *
20895698 AAAAAATAAAATATTTTT
1 AAAAAATAAAATATATGT
20895716 AAAAAAT
1 AAAAAAT
20895723 TAATTCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAAATAAAATATATGT
Found at i:20896352 original size:19 final size:18
Alignment explanation
Indices: 20896312--20896353 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20896302 CTCATTTACT
*
20896312 TTTTTTATATTTTTATAG
1 TTTTTTATATTTTAATAG
20896330 TTTTTTATAATTATTAATA-
1 TTTTTTAT-ATT-TTAATAG
20896349 TTTTT
1 TTTTT
20896354 ATGATTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTTATATTTTAATAG
Found at i:20907111 original size:266 final size:266
Alignment explanation
Indices: 20906637--20907168 Score: 938
Period size: 266 Copynumber: 2.0 Consensus size: 266
20906627 ATTGGCCTAT
*
20906637 CCCGATCATCAAGCATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
1 CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
20906702 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
66 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
*
20906767 TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGTAGGAGTTCCTCTACGCATACAGC
131 TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGCAGGAGTTCCTCTACGCATACAGC
* *
20906832 TACTAATAGACCTATTGAGTTCACGAAACAAAAAAATTAGCAACTGAAACTATAAAAATTGTAAT
196 TACTAATAGACCTATTGAGATCACGAAACAAAAAAATTAGCAACTAAAACTATAAAAATTGTAAT
20906897 AACAAA
261 AACAAA
20906903 CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
1 CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
*
20906968 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTTCTCTTCTCCTTCTTAGCAA
66 TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
* * * * * *
20907033 TTTCCTTTCAATTTCTGGATCTAAAGGATAGAGGCCTTTAGCAGGAGTTCTTTTACGCATACAGC
131 TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGCAGGAGTTCCTCTACGCATACAGC
* * *
20907098 TAGTAATAGACCTATTGAGATCATGAAACAAAAAAATTAGCAATTAAAACTATAAAAATTGTAAT
196 TACTAATAGACCTATTGAGATCACGAAACAAAAAAATTAGCAACTAAAACTATAAAAATTGTAAT
20907163 AACAAA
261 AACAAA
20907169 AACTAAAGTT
Statistics
Matches: 252, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
266 252 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (266 bp):
CCCGATCATCAAACATCTGAGCAACAAGAGGATTAACATTCGGAGCTCCTAGATTAAGTTGCTCA
TTCATAGTAGGTGGATTGTTACCATCTTGATTCATTGCTTTTTGTCCTCTTCTCCTTCTTAGCAA
TGTCCTTTCAATTTCTGGACCTAAAGGATAGAGCCCTTCAGCAGGAGTTCCTCTACGCATACAGC
TACTAATAGACCTATTGAGATCACGAAACAAAAAAATTAGCAACTAAAACTATAAAAATTGTAAT
AACAAA
Found at i:20912019 original size:45 final size:45
Alignment explanation
Indices: 20911946--20912031 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
20911936 GCGTTTTCAT
* * *
20911946 ATGATGCCATAGCGTCTTTCACCAATGGTCTTATTCATTTTTATC
1 ATGACGCCATAACATCTTTCACCAATGGTCTTATTCATTTTTATC
* *
20911991 ATGACGCCATAACATCTTTCAGCTATGGTCTTATTCATTTT
1 ATGACGCCATAACATCTTTCACCAATGGTCTTATTCATTTT
20912032 CATAATAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
ATGACGCCATAACATCTTTCACCAATGGTCTTATTCATTTTTATC
Found at i:20913897 original size:21 final size:20
Alignment explanation
Indices: 20913869--20913907 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20913859 CTAACTGGCA
* *
20913869 AAATAAATGTTTAATTTTTC
1 AAATAAATGGTCAATTTTTC
20913889 AAATAAAATGGTCAATTTT
1 AAAT-AAATGGTCAATTTT
20913908 GATCCAAGTT
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:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
AAATAAATGGTCAATTTTTC
Found at i:20914121 original size:22 final size:19
Alignment explanation
Indices: 20914093--20914134 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
20914083 TTATAACAAC
20914093 TAATATATAATTATATTTATTA
1 TAATATAT-ATTA-A-TTATTA
20914115 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
20914134 T
1 T
20914135 CAACTTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:20914125 original size:16 final size:15
Alignment explanation
Indices: 20914093--20914131 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
20914083 TTATAACAAC
20914093 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
20914109 TTATTATAATATATAT
1 TAATTATAAT-TATAT
20914125 TAATTAT
1 TAATTAT
20914132 TATCAACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:20916306 original size:26 final size:27
Alignment explanation
Indices: 20916276--20916362 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
20916266 GCACAAATCA
*
20916276 GTCA-TTTACCCTCTAGGGGCATTACG
1 GTCATTTTACCCTCTAGGGGTATTACG
* *
20916302 GTCATTTTACCTTAC-AGGGGTATTTCG
1 GTCATTTTACCCT-CTAGGGGTATTACG
* * *
20916329 GTCATTTTAACCTATAAGGGTATTACG
1 GTCATTTTACCCTCTAGGGGTATTACG
20916356 GTCATTT
1 GTCATTT
20916363 AACAACCTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
26 4 0.08
27 45 0.90
28 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTCTAGGGGTATTACG
Found at i:20916320 original size:27 final size:28
Alignment explanation
Indices: 20916290--20916362 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
20916280 TTTACCCTCT
*
20916290 AGGGGCATTACGGTCATTTT-ACCT-TA
1 AGGGGTATTACGGTCATTTTAACCTATA
*
20916316 CAGGGGTATTTCGGTCATTTTAACCTATA
1 -AGGGGTATTACGGTCATTTTAACCTATA
20916345 A-GGGTATTACGGTCATTT
1 AGGGGTATTACGGTCATTT
20916363 AACAACCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 34 0.83
28 5 0.12
29 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (28 bp):
AGGGGTATTACGGTCATTTTAACCTATA
Found at i:20917781 original size:23 final size:24
Alignment explanation
Indices: 20917733--20917782 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
20917723 TTTTCGAATT
* * *
20917733 TCCTTGATTTTCTCCCCAATCTCC
1 TCCTTGATTTCCTCCACAAACTCC
20917757 TCCTTGATTTCCTCCACAAAC-CC
1 TCCTTGATTTCCTCCACAAACTCC
20917780 TCC
1 TCC
20917783 AAGACCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.16, C:0.44, G:0.04, T:0.36
Consensus pattern (24 bp):
TCCTTGATTTCCTCCACAAACTCC
Found at i:20924116 original size:23 final size:22
Alignment explanation
Indices: 20924091--20924133 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
20924081 GTTTAAATTT
20924091 TAATTAAT-TAA--AATTAACA
1 TAATTAATATAATTAATTAACA
20924110 TAATTAATCATAATTAATTAACA
1 TAATTAAT-ATAATTAATTAACA
20924133 T
1 T
20924134 TAAGTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.40
21 3 0.15
23 9 0.45
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATTAATATAATTAATTAACA
Found at i:20932366 original size:20 final size:20
Alignment explanation
Indices: 20932341--20932407 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
20932331 TCTTCCAAAA
20932341 TATCGATACCTGTGATGGTG
1 TATCGATACCTGTGATGGTG
* * ***
20932361 TATCGATATCT-TCCA--AAA
1 TATCGATACCTGT-GATGGTG
20932379 TATCGATACCTGTGATGGTG
1 TATCGATACCTGTGATGGTG
20932399 TATCGATAC
1 TATCGATAC
20932408 TTACATAGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
18 11 0.33
19 2 0.06
20 20 0.61
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
TATCGATACCTGTGATGGTG
Found at i:20932374 original size:38 final size:38
Alignment explanation
Indices: 20932329--20932406 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
20932319 TACCGATACT
20932329 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
1 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
20932367 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
1 TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
20932405 TA
1 TA
20932407 CTTACATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (38 bp):
TATCTTCCAAAATATCGATACCTGTGATGGTGTATCGA
Found at i:20936217 original size:33 final size:33
Alignment explanation
Indices: 20936174--20936271 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 33
20936164 TAGTCTATTG
* *
20936174 GGACAATAAACATAGAATGGAGATAGTCCACTA
1 GGACAATAAACAAAGAATAGAGATAGTCCACTA
* * * * * *
20936207 GGGCAGTAAACACATAACAGAGATAGCCCACTA
1 GGACAATAAACAAAGAATAGAGATAGTCCACTA
20936240 GGACAATAAACAAAGAATAGAGATAGTCCACT
1 GGACAATAAACAAAGAATAGAGATAGTCCACT
20936272 CTGAAAGTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
GGACAATAAACAAAGAATAGAGATAGTCCACTA
Found at i:20939654 original size:21 final size:20
Alignment explanation
Indices: 20939630--20939676 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
20939620 AGATGCAGGT
20939630 AGGATGAAAGAGATAAGAAGA
1 AGGATGAAAGAGA-AAGAAGA
*
20939651 AGGA--AAAGAGAACGAAGA
1 AGGATGAAAGAGAAAGAAGA
20939669 AGG-TGAAA
1 AGGATGAAA
20939677 CGTTGCCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 9 0.39
19 10 0.43
21 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.34, T:0.06
Consensus pattern (20 bp):
AGGATGAAAGAGAAAGAAGA
Found at i:20939667 original size:18 final size:19
Alignment explanation
Indices: 20939636--20939671 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20939626 AGGTAGGATG
20939636 AAAGAGATAAGAAGAAGGA
1 AAAGAGATAAGAAGAAGGA
*
20939655 AAAGAGA-ACGAAGAAGG
1 AAAGAGATAAGAAGAAGG
20939672 TGAAACGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.33, T:0.03
Consensus pattern (19 bp):
AAAGAGATAAGAAGAAGGA
Found at i:20941331 original size:11 final size:11
Alignment explanation
Indices: 20941315--20941339 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20941305 GTGATGCTAT
20941315 GTTCAATGGTG
1 GTTCAATGGTG
20941326 GTTCAATGGTG
1 GTTCAATGGTG
20941337 GTT
1 GTT
20941340 GAGTTTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (11 bp):
GTTCAATGGTG
Found at i:20942423 original size:21 final size:21
Alignment explanation
Indices: 20942399--20942440 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20942389 ACCATGATCG
20942399 TATGGTAATGATAATGAATTA
1 TATGGTAATGATAATGAATTA
*
20942420 TATGGTAATGATGATGAATTA
1 TATGGTAATGATAATGAATTA
20942441 AGTGTTACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (21 bp):
TATGGTAATGATAATGAATTA
Found at i:20946454 original size:51 final size:51
Alignment explanation
Indices: 20946387--20946517 Score: 147
Period size: 51 Copynumber: 2.6 Consensus size: 51
20946377 GTATGTCTAG
*** *
20946387 TACTATGTGCAGGCTACTATGTGTACCGGAT-AGCTTCGATCACGCATGTAA
1 TACTATGTGCAGGCTACTATGTGTACCGGATGAAAAT-GATCACACATGTAA
* * * ** *
20946438 TACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAG
1 TACTATGTGCAGGCTACTATGTGTACCGGATGAAAATGATCACACATGTAA
*
20946489 TACTATGTGCAGGCTACTATGTGAACCGG
1 TACTATGTGCAGGCTACTATGTGTACCGG
20946518 GTATCATTTA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
51 64 0.97
52 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (51 bp):
TACTATGTGCAGGCTACTATGTGTACCGGATGAAAATGATCACACATGTAA
Found at i:20946517 original size:102 final size:101
Alignment explanation
Indices: 20946332--20946517 Score: 266
Period size: 102 Copynumber: 1.8 Consensus size: 101
20946322 CGGTCACGTG
* * **
20946332 TGTAGTACTATGTCCAGGCTACTACGTGTACCAGAATGATAGGTCGTATGTCTAGTACTATGTGC
1 TGTAATACTATGTCCAGGCTACTACGTGTACCAGAATGAAAGGTCACATGTCTAGTACTATGTGC
*
20946397 AGGCTACTATGTGTACCGGATAGCTTCGATCACGCA
66 AGGCTACTATGTGAACCGGATAGCTTCGATCACGCA
* * * *
20946433 TGTAATACTATGTGCAGGCTACTACGTGTATC-GGATGAAAATGGTCACATGTGTAGTACTATGT
1 TGTAATACTATGTCCAGGCTACTACGTGTACCAGAATG-AAA-GGTCACATGTCTAGTACTATGT
20946497 GCAGGCTACTATGTGAACCGG
64 GCAGGCTACTATGTGAACCGG
20946518 GTATCATTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
100 4 0.05
101 31 0.42
102 39 0.53
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (101 bp):
TGTAATACTATGTCCAGGCTACTACGTGTACCAGAATGAAAGGTCACATGTCTAGTACTATGTGC
AGGCTACTATGTGAACCGGATAGCTTCGATCACGCA
Found at i:20947164 original size:17 final size:16
Alignment explanation
Indices: 20947142--20947175 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20947132 AGATAATTCA
*
20947142 TTTTAATTTTTCAAATT
1 TTTTAATATTT-AAATT
20947159 TTTTAATATTTAAATT
1 TTTTAATATTTAAATT
20947175 T
1 T
20947176 ACATTATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATATTTAAATT
Found at i:20957999 original size:7 final size:7
Alignment explanation
Indices: 20957988--20958022 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
20957978 TTGAGAGGTT
20957988 GGATGAG
1 GGATGAG
*
20957995 AGATGAG
1 GGATGAG
20958002 GGATGAG
1 GGATGAG
20958009 GGATGAG
1 GGATGAG
20958016 GGATGAG
1 GGATGAG
20958023 CTCTTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.14
Consensus pattern (7 bp):
GGATGAG
Found at i:20963524 original size:17 final size:17
Alignment explanation
Indices: 20963502--20963535 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20963492 ATACAACCTC
*
20963502 TTTTTTTTATGCACGAA
1 TTTTTTTAATGCACGAA
*
20963519 TTTTTTTAATTCACGAA
1 TTTTTTTAATGCACGAA
20963536 CCTAATTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (17 bp):
TTTTTTTAATGCACGAA
Found at i:20974972 original size:53 final size:53
Alignment explanation
Indices: 20974892--20974998 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
20974882 TTACAATTTT
*
20974892 TAATTATTTTCCAAAGTCAGAATAGGGGATTCCGAAATCAGTTCAACCCTGCC
1 TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
20974945 TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
1 TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
20974998 T
1 T
20974999 CACTAAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (53 bp):
TAATTATTTTCCAAAGTCAGAACAGGGGATTCCGAAATCAGTTCAACCCTGCC
Found at i:20975198 original size:16 final size:16
Alignment explanation
Indices: 20975177--20975208 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20975167 ATTTTGTTGC
*
20975177 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
20975193 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
20975209 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:20975396 original size:46 final size:43
Alignment explanation
Indices: 20975338--20975430 Score: 107
Period size: 46 Copynumber: 2.1 Consensus size: 43
20975328 GACAGATACA
* *
20975338 TGGTGGATTCAGCACACAGCAACCACCCTTTGTAATCAATGATAT
1 TGGTGGATTCAGCACACAACAACCA-CC-TTATAATCAATGATAT
* *
20975383 CTGGTGGGA-TCAGCACATAACAACCACCTTATAATTAATGATAT
1 -TGGT-GGATTCAGCACACAACAACCACCTTATAATCAATGATAT
20975427 TGGT
1 TGGT
20975431 TCACATAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.10
44 14 0.33
45 2 0.05
46 19 0.45
47 3 0.07
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (43 bp):
TGGTGGATTCAGCACACAACAACCACCTTATAATCAATGATAT
Found at i:20975494 original size:51 final size:50
Alignment explanation
Indices: 20975436--20975624 Score: 222
Period size: 51 Copynumber: 3.7 Consensus size: 50
20975426 TTGGTTCACA
* * *
20975436 TAGTAGCCTGCACATAGTACTACACATGTGACCATCATTATCCGATACAGG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA-TATCTGGTACAGG
* * * *
20975487 TAGTAGCCTGCACATAGTATTACACACGTGATCA-AAGCTATCTGGTAC-GCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA--TATCTGGTACAG-G
* * *
20975538 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCAT-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCATATCTGGTACAGG
20975588 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA
20975625 CTTTCACTAT
Statistics
Matches: 116, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
49 4 0.03
50 41 0.35
51 69 0.59
52 1 0.01
53 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCATATCTGGTACAGG
Found at i:20975617 original size:101 final size:102
Alignment explanation
Indices: 20975434--20975618 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
20975424 TATTGGTTCA
* *
20975434 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCATTATCCGATACAGGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCATTATCCGATACACGTAGTAGCCTGCA
*
20975499 CATAGTATTACACACGTGATCAAAGCTATCTGGTACG
66 CATAGTACTACACACGTGATCAAAGCTATCTGGTACG
* *
20975536 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCATTATCCGATACACGTAGTAGCCTGC
20975599 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
20975619 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 38 0.49
102 35 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCATTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCAAAGCTATCTGGTACG
Found at i:20975641 original size:101 final size:103
Alignment explanation
Indices: 20975431--20975652 Score: 274
Period size: 101 Copynumber: 2.2 Consensus size: 103
20975421 TGATATTGGT
* *
20975431 TCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCATTATCCGATACAGGTAGTAGCCT
1 TCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCATTATCCGATACACGTAGTAGCCT
* * **
20975496 GCACATAGTATTACACACGTGATCAAAGCTATCTGGTA
66 GCACATAGTACTACACACGTGACCAAAGCTATCTACTA
* * *
20975534 -CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCC
1 TCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCATTATCCGATACACGTAGTAGCC
* *
20975596 TGCACATAGTACTACACACGTGACCATCA-CTTTC-ACTA
65 TGCACATAGTACTACACACGTGACCA-AAGCTATCTACTA
* *
20975634 TCACATAGTGGCCTACACA
1 TCACATAGTAGCCTGCACA
20975653 CAGTCCATAC
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
100 2 0.02
101 59 0.58
102 37 0.36
103 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (103 bp):
TCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCATTATCCGATACACGTAGTAGCCT
GCACATAGTACTACACACGTGACCAAAGCTATCTACTA
Found at i:20994694 original size:66 final size:66
Alignment explanation
Indices: 20994588--20994715 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
20994578 TTATTACATT
*
20994588 AATGTCGCTGCATGAGTTAATTCCAGATTGCGTCCAGAATTGTCGCCGCACCTAACAGATGTCTG
1 AATGTCGCTGCATGAGTTAATTCCAGATTGCGTCCAGAATTGTCACCGCACCTAACAGATGTCTG
20994653 C
66 C
* * * *
20994654 AATGTCGCTGCAT-AGGTTAATTCCATATTGTGTCCAGAATTGTCATCGCACCTAATAGATGT
1 AATGTCGCTGCATGA-GTTAATTCCAGATTGCGTCCAGAATTGTCACCGCACCTAACAGATGT
20994716 TCGAATAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 1 0.02
66 55 0.98
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (66 bp):
AATGTCGCTGCATGAGTTAATTCCAGATTGCGTCCAGAATTGTCACCGCACCTAACAGATGTCTG
C
Found at i:20998055 original size:12 final size:13
Alignment explanation
Indices: 20998031--20998059 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20998021 GGGCTATAAC
20998031 TATTGCATTTATT
1 TATTGCATTTATT
20998044 TATTGC-TTTATT
1 TATTGCATTTATT
20998056 TATT
1 TATT
20998060 CATGTGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:21029513 original size:33 final size:33
Alignment explanation
Indices: 21029343--21029519 Score: 165
Period size: 33 Copynumber: 5.4 Consensus size: 33
21029333 TGTCCCGACA
* * * *
21029343 GACTTACCTTGTTCTGTATTTACTGTCCCAGCG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* * * *
21029376 GACTTACCCTATTTTATGTTTATTATCCCAGTG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* * * *
21029409 GACTTACTCTGTTTTGTGTTTACTATCCTAGCG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* ** *
21029442 AACTTACTTTGTTCTTTGTTTACTATCCCAGTG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* * *
21029475 GACTTACCCTATTCTGTGTTTACTGTCCCAATG
1 GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
* *
21029508 AACTTACTCTGT
1 GACTTACCCTGT
21029520 GGTTGCCATG
Statistics
Matches: 114, Mismatches: 30, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (33 bp):
GACTTACCCTGTTCTGTGTTTACTATCCCAGTG
Found at i:21029515 original size:66 final size:66
Alignment explanation
Indices: 21029343--21029517 Score: 208
Period size: 66 Copynumber: 2.7 Consensus size: 66
21029333 TGTCCCGACA
* * * * *
21029343 GACTTACCTTGTTCTGTATTTACTGTCCCAGCGGACTTACCCTATTTTATGTTTATTATCCCAGT
1 GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCTATTTTATGTTTACTATCCCAGT
21029408 G
66 G
* * * * * *
21029409 GACTTACTCTGTTTTGTGTTTACTATCCTAGCGAACTTACTTTGTTCTT-TGTTTACTATCCCAG
1 GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCTATT-TTATGTTTACTATCCCAG
21029473 TG
65 TG
* **
21029475 GACTTACCCTATTCTGTGTTTACTGTCCCAATGAACTTACTCT
1 GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCT
21029518 GTGGTTGCCA
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 87 0.98
67 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.43
Consensus pattern (66 bp):
GACTTACCCTGTTCTGTGTTTACTGTCCCAGCGAACTTACTCTATTTTATGTTTACTATCCCAGT
G
Found at i:21031284 original size:50 final size:50
Alignment explanation
Indices: 21031115--21031406 Score: 216
Period size: 50 Copynumber: 5.9 Consensus size: 50
21031105 GATAATAACA
* * *
21031115 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTT-TC-CTGTAC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTC-G--G
* * * * ** * * *
21031164 TGCCAATGCCATATCCCAGATATGGTCTTACATAGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * * ** * *
21031214 TGTCC-ATGTCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGC
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * *
21031264 TGCCAACGCCATATCCCAGACATGGTCCTACATGGGACCTCTTACCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * * * *
21031314 TGTCAATGCCATGTCCTAGACATGCTCTTACATGGGACCTCTTATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* ** * **
21031364 TGCCAACACCATGTTGCAGACACGGTCTTACATAAGACCTCTT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
21031407 TACCCAAATG
Statistics
Matches: 188, Mismatches: 49, Indels: 11
0.76 0.20 0.04
Matches are distributed among these distances:
49 35 0.19
50 147 0.78
51 4 0.02
52 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:21031290 original size:100 final size:100
Alignment explanation
Indices: 21031163--21031405 Score: 254
Period size: 100 Copynumber: 2.4 Consensus size: 100
21031153 GTTTCCTGTA
* * ** * * * *
21031163 CTGCCAATGCCATATCCCAGATATGGTCTTACATAGGAGTTCTCATATTGGTGTCCATGTCATGT
1 CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCTCACATCGGTGTCAATGCCATGT
* *
21031228 -CTCAGACATGGTCTTACGGGGGACCTCTCATCTCG
66 CCT-AGACATGCTCTTACAGGGGACCTCTCATCTCG
* * * *
21031263 CTGCCAACGCCATATCCCAGACATGGTCCTACATGGGACCTCTTACCTCGGTGTCAATGCCATGT
1 CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCTCACATCGGTGTCAATGCCATGT
* * *
21031328 CCTAGACATGCTCTTACATGGGACCTCTTATCTTG
66 CCTAGACATGCTCTTACAGGGGACCTCTCATCTCG
* * * ** * *
21031363 GTGCCAACACCATGTTGCAGACACGGTCTTACATAAGACCTCT
1 CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCT
21031406 TTACCCAAAT
Statistics
Matches: 116, Mismatches: 26, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
100 114 0.98
101 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (100 bp):
CTGCCAACGCCATATCCCAGACATGGTCTTACATAGGACCTCTCACATCGGTGTCAATGCCATGT
CCTAGACATGCTCTTACAGGGGACCTCTCATCTCG
Found at i:21038110 original size:50 final size:50
Alignment explanation
Indices: 21038035--21038276 Score: 247
Period size: 50 Copynumber: 4.8 Consensus size: 50
21038025 TTTCTTGTAC
* * * ** *
21038035 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
21038085 TGCCCATGCCATGTCCCAGACATGGTCTT--ATGGGGAACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGG-ACCTCTCATATCGG
* * *
21038135 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTC-CTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-ATATCGG
* * * * * *
21038185 TGCCAACGCCATGTCCTAGACATGGTATTACATGGGACCTCTTATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
** * *
21038235 TGCCAATGCCATGTTGCAGACACGGTCTTACATGAGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21038277 TTACCCAAAT
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
48 2 0.01
49 4 0.02
50 152 0.93
51 3 0.02
52 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:21038208 original size:100 final size:98
Alignment explanation
Indices: 21038035--21038268 Score: 274
Period size: 100 Copynumber: 2.3 Consensus size: 98
21038025 TTTCTTGTAC
* * * * *
21038035 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAG-TCTCATATTGGTGCCAACGCCATGTC
* *
21038100 CCAGACATGGTCTT-ATGGGGAACCTCTCATCTCGG
65 CCAGACATGGTATTAAT-GGG-ACCTCTCATCTCAG
* *
21038135 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCCTATCTCGGTGCCAACGCCATGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTCTCATAT-T-GGTGCCAACGCCATGT
* *
21038199 CCTAGACATGGTATTACATGGGACCTCTTATCTCAG
64 CCCAGACATGGTATTA-ATGGGACCTCTCATCTCAG
** *
21038235 TGCCAATGCCATGTTGCAGACACGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
21038269 AGACCTCTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
98 7 0.06
99 1 0.01
100 102 0.89
101 3 0.03
102 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (98 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTCTCATATTGGTGCCAACGCCATGTCC
CAGACATGGTATTAATGGGACCTCTCATCTCAG
Found at i:21058127 original size:16 final size:15
Alignment explanation
Indices: 21058093--21058133 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
21058083 GGTGATAATA
21058093 ATTAATATATAATTAT
1 ATTAAT-TATAATTAT
*
21058109 ATTTATTATAATGTAT
1 ATTAATTATAAT-TAT
21058125 ATTAATTAT
1 ATTAATTAT
21058134 TATCAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTAATTATAATTAT
Found at i:21058654 original size:41 final size:41
Alignment explanation
Indices: 21058591--21058677 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
21058581 CGACGAACCT
* * * **
21058591 GCTCGCACACTAGCCTTGCTGCCTTTGCACGCATCATACCA
1 GCTCGCACACCAGCCCTACTGCCCCTGCACGCATCATACCA
* * *
21058632 GCTCGCGCACCAGCCCTACTGCCCCTGCACGCATCATCCCT
1 GCTCGCACACCAGCCCTACTGCCCCTGCACGCATCATACCA
21058673 GCTCG
1 GCTCG
21058678 TGCCTTGCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.16, C:0.45, G:0.18, T:0.21
Consensus pattern (41 bp):
GCTCGCACACCAGCCCTACTGCCCCTGCACGCATCATACCA
Found at i:21062231 original size:27 final size:27
Alignment explanation
Indices: 21062179--21062264 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 27
21062169 ATAGTCATAC
* *
21062179 ATAACATA-GAGCAT-ACGGTCATTTT
1 ATAACATAGGGGCATAACAGTCATTTT
21062204 ATAACATAGGGGCATAACAGTCATTTT
1 ATAACATAGGGGCATAACAGTCATTTT
** * *
21062231 ACCACGTAGGAGGCATAACACTCATTTT
1 ATAACATAGG-GGCATAACAGTCATTTT
21062259 ATAACA
1 ATAACA
21062265 GAGGTCTACT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
25 8 0.16
26 5 0.10
27 17 0.35
28 19 0.39
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (27 bp):
ATAACATAGGGGCATAACAGTCATTTT
Found at i:21065466 original size:20 final size:20
Alignment explanation
Indices: 21065441--21065479 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21065431 AACTATTTCT
21065441 TTCAAATTAAGTTAAAAATA
1 TTCAAATTAAGTTAAAAATA
*
21065461 TTCAAATTAAGTTGAAAAT
1 TTCAAATTAAGTTAAAAAT
21065480 GATGATATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (20 bp):
TTCAAATTAAGTTAAAAATA
Found at i:21077669 original size:4 final size:4
Alignment explanation
Indices: 21077660--21077715 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
21077650 TATGAATGTG
21077660 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
21077708 ATAC ATAC
1 ATAC ATAC
21077716 CAACAGTGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:21088100 original size:27 final size:27
Alignment explanation
Indices: 21088070--21088125 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
21088060 CAAAATAATT
21088070 TTCAAAAT-TTGA-AAATAATTTTTAAAA
1 TTCAAAATATTGATAAA-AA-TTTTAAAA
*
21088097 TTCAAAATATTTATAAAAATTTTAAAA
1 TTCAAAATATTGATAAAAATTTTAAAA
21088124 TT
1 TT
21088126 TTCATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 18 0.69
28 5 0.19
29 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
TTCAAAATATTGATAAAAATTTTAAAA
Found at i:21088105 original size:19 final size:20
Alignment explanation
Indices: 21088059--21088124 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
21088049 TAACAAAAGA
*
21088059 TCAAAATAATTTTCAAAATT
1 TCAAAATAATTTTTAAAATT
*
21088079 TGAAAATAATTTTTAAAA-T
1 TCAAAATAATTTTTAAAATT
*
21088098 TCAAAAT-ATTTATAAAAATT
1 TCAAAATAATTT-TTAAAATT
*
21088118 TTAAAAT
1 TCAAAAT
21088125 TTTCATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 23 0.59
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAATT
Found at i:21088970 original size:14 final size:15
Alignment explanation
Indices: 21088940--21088972 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21088930 TTAAATCATC
21088940 TTATTTTTATATAAT
1 TTATTTTTATATAAT
*
21088955 TTATTTTTTTAT-AT
1 TTATTTTTATATAAT
21088969 TTAT
1 TTAT
21088973 GCAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTTTATATAAT
Found at i:21091791 original size:45 final size:45
Alignment explanation
Indices: 21091685--21091947 Score: 185
Period size: 45 Copynumber: 5.8 Consensus size: 45
21091675 TGGCTTGAAG
* * * * * **
21091685 GAAATGATTAAGACCATAGTTGAAAGATATTATGGCACTA-TACCG
1 GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCACCACGA-TT
* * * *
21091730 GGAAT-AGATAATACCATAGTTGAAAGACACTATGACACCA-TATT
1 GAAATGAG-TAAGACCATAGTTGAAAGACACTATGGCACCACGATT
* * * *
21091774 AGAAATGAGTAAGACCATAGCTGAAAGATATTATGGCATCACGATT
1 -GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCACCACGATT
** * * * * *
21091820 -CTATCGAGTAAGACTATAGCTGAAAGACGCTATGGCATCACGAAT
1 GAAAT-GAGTAAGACCATAGTTGAAAGACACTATGGCACCACGATT
* * * *
21091865 CAAA-GAAATAAGACCATAGTTGAAAGACACTATGGCAACACGATGG
1 GAAATG-AGTAAGACCATAGTTGAAAGACACTATGGCACCACGAT-T
* *
21091911 GAAATGAATAAGACCATGGTTGAAAGACACTATGGCA
1 GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
21091948 TCAAGACGAG
Statistics
Matches: 174, Mismatches: 35, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
44 4 0.02
45 130 0.75
46 39 0.22
47 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (45 bp):
GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCACCACGATT
Found at i:21091937 original size:46 final size:45
Alignment explanation
Indices: 21091870--21091992 Score: 156
Period size: 46 Copynumber: 2.7 Consensus size: 45
21091860 CGAATCAAAG
* * * *
21091870 AAATAAGACCATAGTTGAAAGACACTATGGCAACACGATGGGAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAG-AAT
* *
21091916 GAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACGAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAGAAT
* * *
21091961 AAATAAGACCGTGGTTGAAAGAGACCATGGCA
1 AAATAAGACCATGGTTGAAAGACACTATGGCA
21091993 CCCTCCGATC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
45 31 0.46
46 36 0.54
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.17
Consensus pattern (45 bp):
AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAGAAT
Found at i:21091981 original size:45 final size:45
Alignment explanation
Indices: 21091840--21091992 Score: 166
Period size: 45 Copynumber: 3.4 Consensus size: 45
21091830 AGACTATAGC
* * *
21091840 TGAAAGACGCTATGGCATCACGAATC-A-AAGAAATAAGACCATAGT
1 TGAAAGACACTATGGCATCACG-A-CGAGAATAAATAAGACCATGGT
* * * *
21091885 TGAAAGACACTATGGCAACACGATGGGAAATGAATAAGACCATGGT
1 TGAAAGACACTATGGCATCACGACGAG-AATAAATAAGACCATGGT
* *
21091931 TGAAAGACACTATGGCATCAAGACGAGAATAAATAAGACCGTGGT
1 TGAAAGACACTATGGCATCACGACGAGAATAAATAAGACCATGGT
* *
21091976 TGAAAGAGACCATGGCA
1 TGAAAGACACTATGGCA
21091993 CCCTCCGATC
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.01
45 51 0.57
46 38 0.42
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (45 bp):
TGAAAGACACTATGGCATCACGACGAGAATAAATAAGACCATGGT
Found at i:21095088 original size:15 final size:15
Alignment explanation
Indices: 21095068--21095096 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21095058 TAAACATCAA
21095068 GAATCATACAAAATG
1 GAATCATACAAAATG
21095083 GAATCATACAAAAT
1 GAATCATACAAAAT
21095097 CATGCATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (15 bp):
GAATCATACAAAATG
Found at i:21105656 original size:41 final size:40
Alignment explanation
Indices: 21105594--21105731 Score: 159
Period size: 41 Copynumber: 3.4 Consensus size: 40
21105584 AATGAGATAT
* * *
21105594 TAGCTAGCTTTGTGCCAGTGTATATTATCAGGTTTTGTGTC
1 TAGCAAGCTTTGTG-CAGTGTATATTATCAGGCTTTGTGCC
* *
21105635 TAGCAAGCTTTGTGTCGGTGTATATTATTAGGCTTTGTGCC
1 TAGCAAGCTTTGTG-CAGTGTATATTATCAGGCTTTGTGCC
* * * **
21105676 TAGCAGGCTTTGTGCTAGTGTATATTATCAAGCCTTAAGCC
1 TAGCAAGCTTTGTGC-AGTGTATATTATCAGGCTTTGTGCC
21105717 TAGCAAGCTTTGTGC
1 TAGCAAGCTTTGTGC
21105732 CGGTGAATTA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 81 0.99
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.39
Consensus pattern (40 bp):
TAGCAAGCTTTGTGCAGTGTATATTATCAGGCTTTGTGCC
Found at i:21108619 original size:2 final size:2
Alignment explanation
Indices: 21108612--21108648 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21108602 TGAAATGTAA
21108612 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
21108649 AGGATTTTGA
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:21111295 original size:21 final size:21
Alignment explanation
Indices: 21111269--21111311 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21111259 CTTAACGGGA
21111269 TAGCTGACGTGGCCAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
* *
21111290 TAGCTGATGTGGCTAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
21111311 T
1 T
21111312 TGCCACGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
TAGCTGACGTGGCCAGTTAAC
Found at i:21112420 original size:3 final size:3
Alignment explanation
Indices: 21112412--21112490 Score: 69
Period size: 3 Copynumber: 28.0 Consensus size: 3
21112402 CATTTTCTCA
* *
21112412 TCT TCT TCT TC- TCT TCT TCT T-T TCT TCT TCT TCT TCT CCA T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
21112457 TC- TCT TAT TCT TCT TTT TTT TC- TCT TCC TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
21112491 ACTACCCAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 9 0.15
3 52 0.85
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:21112426 original size:8 final size:8
Alignment explanation
Indices: 21112415--21112449 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
21112405 TTTCTCATCT
21112415 TCTTCTTC
1 TCTTCTTC
21112423 TCTTCTTC
1 TCTTCTTC
*
21112431 TTTTCTTC
1 TCTTCTTC
21112439 TTCTTCTTC
1 -TCTTCTTC
21112448 TC
1 TC
21112450 CATTTCTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
TCTTCTTC
Found at i:21112426 original size:11 final size:11
Alignment explanation
Indices: 21112412--21112490 Score: 72
Period size: 11 Copynumber: 7.1 Consensus size: 11
21112402 CATTTTCTCA
21112412 TCTTCTTCTTC
1 TCTTCTTCTTC
*
21112423 TCTTCTTCTTT
1 TCTTCTTCTTC
21112434 TCTTCTTCTTC
1 TCTTCTTCTTC
*
21112445 TTCTCCATTTCTTC
1 -TCTTC--TTCTTC
*
21112459 TCTTATTCTTC
1 TCTTCTTCTTC
*
21112470 T-TT-TTTTTC
1 TCTTCTTCTTC
*
21112479 TCTTCCTCTTC
1 TCTTCTTCTTC
21112490 T
1 T
21112491 ACTACCCAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
9 6 0.11
10 4 0.07
11 32 0.58
12 4 0.07
13 3 0.05
14 6 0.11
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:21112429 original size:14 final size:14
Alignment explanation
Indices: 21112406--21112490 Score: 68
Period size: 14 Copynumber: 6.1 Consensus size: 14
21112396 TCCTTCCATT
*
21112406 TTCTCATCTTCTTC
1 TTCTCTTCTTCTTC
21112420 TTCTCTTCTTCTT-
1 TTCTCTTCTTCTTC
21112433 TTCTTCTTCTTCTTC
1 TTC-TCTTCTTCTTC
*
21112448 TCCAT-TTCTTC-TC
1 TTC-TCTTCTTCTTC
* * *
21112461 TTATTCTTCTTTTTT
1 TT-CTCTTCTTCTTC
*
21112476 TTCTCTTCCTCTTC
1 TTCTCTTCTTCTTC
21112490 T
1 T
21112491 ACTACCCAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
13 7 0.13
14 42 0.76
15 6 0.11
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.65
Consensus pattern (14 bp):
TTCTCTTCTTCTTC
Found at i:21112446 original size:25 final size:25
Alignment explanation
Indices: 21112406--21112471 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
21112396 TCCTTCCATT
* *
21112406 TTCTCATCTTCTTCTTCT-CTTCTTC
1 TTCTCTTCTTCTTCTTCTCCAT-TTC
*
21112431 TTTTCTTCTTCTTCTTCTCCATTTC
1 TTCTCTTCTTCTTCTTCTCCATTTC
*
21112456 TTCTCTTATTCTTCTT
1 TTCTCTTCTTCTTCTT
21112472 TTTTTTCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTCTTCTTCTTCTTCTCCATTTC
Found at i:21125676 original size:24 final size:24
Alignment explanation
Indices: 21125631--21125688 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
21125621 GTTTAATTAC
** *
21125631 TTTTAATTTAATTTCATAAATTTA
1 TTTTAATTTAACATAATAAATTTA
* *
21125655 TTTTAATTTAACATAATGAATTTT
1 TTTTAATTTAACATAATAAATTTA
*
21125679 TTTTATTTTA
1 TTTTAATTTA
21125689 GTTTTTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTAATTTAACATAATAAATTTA
Found at i:21126020 original size:59 final size:59
Alignment explanation
Indices: 21125882--21126023 Score: 162
Period size: 59 Copynumber: 2.4 Consensus size: 59
21125872 ACAAGTTTAG
* *
21125882 GTATTAAATTGGACTAAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAGTTCAA
1 GTATCAAATTGGAC-AAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAATTCAA
* * * * * *
21125942 GTA-CTAATTTAGG-CAAAAAAAAGCTTAGGTGCCAAATTACGAAAAAGTGTCAAATTCAT
1 GTATC-AAATT-GGACAAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAATTCAA
21126001 GTATCAAATTGGACCAAAAAAAA
1 GTATCAAATTGGA-CAAAAAAAA
21126024 TTAAGTACCA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
58 2 0.03
59 46 0.68
60 18 0.26
61 2 0.03
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (59 bp):
GTATCAAATTGGACAAAAAAAAGCTTAGATACCAAATTAAGAAAAAGTATCAAATTCAA
Found at i:21145305 original size:22 final size:23
Alignment explanation
Indices: 21145266--21145312 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
21145256 CACGTTAGCT
21145266 AACAAATATATAAATAT-AAATA
1 AACAAATATATAAATATAAAATA
*
21145288 AACAAATAT-TCAAGTATAAAATA
1 AACAAATATAT-AAATATAAAATA
21145311 AA
1 AA
21145313 ATAAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 14 0.64
23 7 0.32
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (23 bp):
AACAAATATATAAATATAAAATA
Found at i:21152176 original size:2 final size:2
Alignment explanation
Indices: 21152169--21152202 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
21152159 AGACGGATCC
21152169 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21152203 TTATTATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21152857 original size:17 final size:18
Alignment explanation
Indices: 21152829--21152862 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21152819 TCATAAGCAA
21152829 TTAAACAATTCAATAACG
1 TTAAACAATTCAATAACG
21152847 TTAAA-AATTCAATAAC
1 TTAAACAATTCAATAAC
21152863 AAGCCGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (18 bp):
TTAAACAATTCAATAACG
Found at i:21158736 original size:30 final size:30
Alignment explanation
Indices: 21158700--21158759 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
21158690 CACGGTCTAG
*
21158700 CACATGGCCATGTGTCCAGACCGTGTGGCT
1 CACATGGCCATGTGTCCAGACCATGTGGCT
* * * *
21158730 CACATGGTCGTGTGTCTAGCCCATGTGGCT
1 CACATGGCCATGTGTCCAGACCATGTGGCT
21158760 TCTTAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (30 bp):
CACATGGCCATGTGTCCAGACCATGTGGCT
Found at i:21160686 original size:85 final size:85
Alignment explanation
Indices: 21160524--21160722 Score: 237
Period size: 85 Copynumber: 2.4 Consensus size: 85
21160514 GAATGTTGGA
* * * * *
21160524 AATAAATCCCGAAATAGAA-TTATTTGA--TTAAGTTTTCATTTGGAAACAAATCAAGATTAAAT
1 AATAAATCCCGAAACAGAATTTATTTAATTTTAAGTATTCATTTGGAAAAAAATCAAGATGAAAT
*
21160586 AAAATCTGTTAAACGAAAGT
66 AAAATCTGTTAAACGAAAGG
*
21160606 AATAAATCCCGAAACAGAATTTATTTAATTTTAA-TATTCGTTTGGAAAAAAATCAAAGATGAAA
1 AATAAATCCCGAAACAGAATTTATTTAATTTTAAGTATTCATTTGGAAAAAAATC-AAGATGAAA
* **
21160670 TAAAATCTGTTGAACGACGGG
65 TAAAATCTGTTAAACGAAAGG
* *
21160691 AATAAA-CCACGAAACAGATTTTATTCAATTTT
1 AATAAATCC-CGAAACAGAATTTATTTAATTTT
21160723 TATTTTTATT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
82 18 0.18
83 7 0.07
84 19 0.19
85 56 0.56
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (85 bp):
AATAAATCCCGAAACAGAATTTATTTAATTTTAAGTATTCATTTGGAAAAAAATCAAGATGAAAT
AAAATCTGTTAAACGAAAGG
Found at i:21161352 original size:20 final size:20
Alignment explanation
Indices: 21161327--21161364 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21161317 TTAAATGAGC
*
21161327 AATTAAATCAATTTGATTAA
1 AATTAAATCAAATTGATTAA
21161347 AATTAAATCAAATTGATT
1 AATTAAATCAAATTGATT
21161365 GGAATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
AATTAAATCAAATTGATTAA
Found at i:21161374 original size:20 final size:20
Alignment explanation
Indices: 21161331--21161380 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
21161321 ATGAGCAATT
* *
21161331 AAATCAATTTGATTAAAATT
1 AAATCAAATTGATTAAAATC
**
21161351 AAATCAAATTGATTGGAATC
1 AAATCAAATTGATTAAAATC
*
21161371 AAATAAAATT
1 AAATCAAATT
21161381 ATGATATATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATC
Found at i:21161590 original size:32 final size:34
Alignment explanation
Indices: 21161554--21161642 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 34
21161544 TTCAAATTTA
21161554 AAATTAAAATAGAGTTATTAAATGAGAA-A-ATT
1 AAATTAAAATAGAGTTATTAAATGAGAATATATT
21161586 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
1 AAATTAAAATAGAGTTATTAAATGAGAATA---TATT
21161623 AAATTAAAATAGAGTTATTA
1 AAATTAAAATAGAGTTATTA
21161643 CTTAATTAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
32 28 0.54
33 1 0.02
37 23 0.44
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (34 bp):
AAATTAAAATAGAGTTATTAAATGAGAATATATT
Found at i:21161647 original size:18 final size:19
Alignment explanation
Indices: 21161583--21161642 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
21161573 AAATGAGAAA
21161583 ATTAAATTAAAATAGAGTT
1 ATTAAATTAAAATAGAGTT
* * *
21161602 ATTAAATGAGAATAG-TTT
1 ATTAAATTAAAATAGAGTT
21161620 ATTAAATTAAAATAGAGTT
1 ATTAAATTAAAATAGAGTT
21161639 ATTA
1 ATTA
21161643 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (19 bp):
ATTAAATTAAAATAGAGTT
Found at i:21162232 original size:27 final size:27
Alignment explanation
Indices: 21162197--21162248 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
21162187 CATTTTAGTC
*
21162197 CTTTTGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
21162224 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
21162249 GTGATTCGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.21, T:0.33
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:21162323 original size:27 final size:26
Alignment explanation
Indices: 21162293--21162366 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 26
21162283 TTTTTGTTTT
21162293 TTTAGTATATTTTGGTAAATAAAAAAA
1 TTTA-TATATTTTGGTAAATAAAAAAA
21162320 TTTATATTATTTTGGTAAATAAAAAAA
1 TTTATA-TATTTTGGTAAATAAAAAAA
*
21162347 GTTATAATATTTTGGTAAAT
1 TTTAT-ATATTTTGGTAAAT
21162367 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 2 0.05
27 41 0.93
28 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (26 bp):
TTTATATATTTTGGTAAATAAAAAAA
Found at i:21162631 original size:12 final size:12
Alignment explanation
Indices: 21162601--21162633 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
21162591 TATATATTTT
21162601 AAAATT-ATATA
1 AAAATTAATATA
21162612 AAAA-TAATATA
1 AAAATTAATATA
21162623 AAAATTAATAT
1 AAAATTAATAT
21162634 TGACGGTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:21165320 original size:29 final size:29
Alignment explanation
Indices: 21165287--21165342 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
21165277 ACTCACTATA
* *
21165287 TTGTATTTAAATAAGTCCTTAACTTATTT
1 TTGTAGTTAAATAAGCCCTTAACTTATTT
21165316 TTGTAGTTAAATAAGCCCTTAACTTAT
1 TTGTAGTTAAATAAGCCCTTAACTTAT
21165343 GGTTTTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.46
Consensus pattern (29 bp):
TTGTAGTTAAATAAGCCCTTAACTTATTT
Found at i:21166740 original size:5 final size:6
Alignment explanation
Indices: 21166723--21166747 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21166713 AAAAACGAAT
21166723 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
21166748 CTTTTTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:21167560 original size:19 final size:20
Alignment explanation
Indices: 21167533--21167570 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
21167523 TAAATACATC
21167533 TATTCTATTT-TATCACATTA
1 TATTCTATTTAT-TCACATTA
21167553 TATT-TATTTATTCACATT
1 TATTCTATTTATTCACATT
21167571 CTTTTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTCTATTTATTCACATTA
Found at i:21172310 original size:50 final size:50
Alignment explanation
Indices: 21172194--21172437 Score: 249
Period size: 50 Copynumber: 4.9 Consensus size: 50
21172184 GAATATAACA
* * * * ** * * * *
21172194 TGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
* * * * * *
21172243 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAATTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
* * * *
21172293 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAA-CTCTCATCTAGG
* * *
21172343 TGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
*
21172393 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCAT
21172438 AATCTTAATT
Statistics
Matches: 164, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 40 0.24
50 120 0.73
51 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATCTAGG
Found at i:21172466 original size:56 final size:50
Alignment explanation
Indices: 21172243--21172437 Score: 257
Period size: 50 Copynumber: 3.9 Consensus size: 50
21172233 TTTCTTGTAC
* * * * ** * *
21172243 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAATTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* * *
21172293 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATCTTGG
* *
21172343 TGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
21172393 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
21172438 AATCTTAATT
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.02
50 123 0.96
51 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:21172472 original size:56 final size:50
Alignment explanation
Indices: 21172193--21172490 Score: 217
Period size: 50 Copynumber: 5.9 Consensus size: 50
21172183 TGAATATAAC
* * * * * *
21172193 ATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGA--TGT-TTCTTG
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * * * * ** * *
21172240 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGAGAATTCTCATATAG
1 -A-TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * * * * *
21172292 GTGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTTG
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGG-ACCTCTCATCTCG
* *
21172342 GTGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
* * **
21172392 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTTAATT
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTC---ATC-T--CG
* * *
21172448 ATGCCAATGCCATGTCCCAAACATGGTCTTACATTGGATCTCT
1 ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
21172491 TTACCCAAAT
Statistics
Matches: 204, Mismatches: 34, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
48 1 0.00
49 32 0.16
50 121 0.59
51 5 0.02
52 3 0.01
53 3 0.01
54 1 0.00
56 38 0.19
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:21180274 original size:44 final size:44
Alignment explanation
Indices: 21180225--21180770 Score: 471
Period size: 44 Copynumber: 12.4 Consensus size: 44
21180215 ATCATATTCT
* * * * *
21180225 TGAAGTTGCAGCGGAGTATATTGAAGTTGTAAATCTTATCTTCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* ** *
21180269 TGAAGTTGCAATGGAGCAGATTGAAGACATAAATCTTATCTCCT
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * * * *
21180313 TAAAATTACAATGGAGCAGATTTAAGTTATAGATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * ** * *
21180357 TGAGGTCGTAGTGGAGCAGATTGAAGACACAAATCTTATCTCCT
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * *
21180401 TGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTATTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * *
21180445 TGAAGTTGCAGTGGAGCAGACTGAAAATTACAAATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTG-AAGTTATAAATCTTATCTCCC
* * *
21180490 TGAAGTTACATTGGAGCAGATTGAAGTTATAGATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * ** * * *
21180534 TGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * * *
21180578 TGAAGTTACAGTGAAGCAGATTGAAATTACAAGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * * * * *
21180622 TAAAGTTGCAATGGAGCAGACTGAAAGTTACAAATATTGTCTCCC
1 TGAAGTTGCAGTGGAGCAGATTG-AAGTTATAAATCTTATCTCCC
* * * * * *
21180667 TAAAGTTGTAGTGGAGCAGATTGAAGCTATAAGTCTTGTCTCCT
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
* * *** * * * **
21180711 TGAAATTACAGTGGAATGGATCGAAGCTACACGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
*
21180755 TAAAGTTGCAGTGGAG
1 TGAAGTTGCAGTGGAG
21180771 TGGGTCGAAG
Statistics
Matches: 397, Mismatches: 103, Indels: 4
0.79 0.20 0.01
Matches are distributed among these distances:
44 322 0.81
45 75 0.19
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAGATTGAAGTTATAAATCTTATCTCCC
Found at i:21180528 original size:177 final size:177
Alignment explanation
Indices: 21180223--21180697 Score: 646
Period size: 177 Copynumber: 2.7 Consensus size: 177
21180213 ATATCATATT
* * ** * *
21180223 CTTGAAGTTGCAGCGGAGTATATTGAAGTTGTAAATCTTATCTTCCTGAAGTTGCAATGGAGCAG
1 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
* * * * * * *
21180288 ATTGAAGA-CATAAATCTTATCTCCTTAAAATTACAATGGAGCAGATTTAAGTTATAGATCTTAT
66 ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATAGATCTTAT
* * *
21180352 CTCCCTGAGGTCGTAGTGGAGCAGATTGAAGACACAAATCTTATCTC
131 CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
* *
21180399 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTATTATCTCCCTGAAGTTGCAGTGGAGCAG
1 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
* *
21180464 ACTGAAAATTACAAATCTTATCTCCCTGAAGTTACATTGGAGCAGATTGAAGTTATAGATCTTAT
66 ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATAGATCTTAT
21180529 CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
131 CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
* * * * * *
21180576 CCTGAAGTTACAGTGAAGCAGATTGAAATTACAAGTCTTATCTCCCTAAAGTTGCAATGGAGCAG
1 CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
* * * ** * *
21180641 ACTGAAAGTTACAAATATTGTCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTATA
66 ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATA
21180698 AGTCTTGTCT
Statistics
Matches: 262, Mismatches: 36, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
176 63 0.24
177 199 0.76
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (177 bp):
CTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAG
ACTGAAAATTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGTTATAGATCTTAT
CTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAAACCTCATCTC
Found at i:21180754 original size:177 final size:177
Alignment explanation
Indices: 21180260--21180767 Score: 536
Period size: 177 Copynumber: 2.9 Consensus size: 177
21180250 GTTGTAAATC
* * * * * * * * * *
21180260 TTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAGA-CATAAATCTTATCTCCTTAAAATTACAA
1 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
* * ** ** * *
21180324 TGGAGCAGATTTAAGTTATAGATCTTATCTCCCTGAGGTCGTAGTGGAGCAGATTGAAGACACAA
66 TGGAGCAGATTGAAGCTATAGATCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGACACAA
* * * *
21180389 ATCTTATCTCCTTGAAGTTGCAGCGGAGCAGATTGAAGTTACAAGTA
131 ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAATTACAAGTA
* * * * *
21180436 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAATTACAAATCTTATCTCCCTGAAGTTACAT
1 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
* ** * * *
21180501 TGGAGCAGATTGAAGTTATAGATCTTATCTCCCTGAGGTCGCAGTGGAGCAGATTGAAGACACAA
66 TGGAGCAGATTGAAGCTATAGATCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGACACAA
* * * *
21180566 ACCTCATCTCCCTGAAGTTACAGTGAAGCAGATTGAAATTACAAGTC
131 ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAATTACAAGTA
* * **
21180613 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAGTTACAAATATTGTCTCCCTAAAGTTGTAG
1 TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
* * * **
21180678 TGGAGCAGATTGAAGCTATA-AGTCTTGTCTCCTTGAAATTACAGTGGAATGGATCGAAG-CTAC
66 TGGAGCAGATTGAAGCTATAGA-TCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGAC-AC
** *
21180741 ACGTCTTATCTCCCTAAAGTTGCAGTG
129 AAATCTTATCTCCCTGAAGTTGCAGTG
21180768 GAGTGGGTCG
Statistics
Matches: 283, Mismatches: 46, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
176 34 0.12
177 249 0.88
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (177 bp):
TTATCTCCCTAAAGTTGCAATGGAGCAGACTGAAAATTACAAATATTATCTCCCTAAAGTTACAG
TGGAGCAGATTGAAGCTATAGATCTTATCTCCCTGAAATCACAGTGGAACAGATCGAAGACACAA
ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAATTACAAGTA
Found at i:21181006 original size:16 final size:18
Alignment explanation
Indices: 21180975--21181010 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
21180965 GCCCAAACAG
21180975 AAACCTAAAGACAAAAAA
1 AAACCTAAAGACAAAAAA
21180993 AAACC-AAA-ACAAAAAA
1 AAACCTAAAGACAAAAAA
21181009 AA
1 AA
21181011 TTATAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.78, C:0.17, G:0.03, T:0.03
Consensus pattern (18 bp):
AAACCTAAAGACAAAAAA
Found at i:21182186 original size:3 final size:3
Alignment explanation
Indices: 21182159--21182223 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
21182149 TAAACCTTAG
* * * *
21182159 ATT ATT CATT ATTT ATT ATT TTT ATT ATC ATT CA-T ATT ATT CTC ATT
1 ATT ATT -ATT A-TT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
*
21182206 ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
21182224 TTTAAAACCA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 1 0.02
3 40 0.83
4 7 0.15
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:21185714 original size:19 final size:18
Alignment explanation
Indices: 21185672--21185714 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
21185662 AATTTTTTAT
21185672 ATAAAAATATTTAAAATA
1 ATAAAAATATTTAAAATA
*
21185690 ACAAAAACTATTTTAAAA-A
1 ATAAAAA-TA-TTTAAAATA
21185709 ATAAAA
1 ATAAAA
21185715 TAAAACTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 8 0.38
20 7 0.33
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAATATTTAAAATA
Found at i:21187996 original size:14 final size:14
Alignment explanation
Indices: 21187958--21188000 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
21187948 CAAAATGTAC
21187958 AATATAATTAAA-T
1 AATATAATTAAATT
21187971 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
21187986 AA-ATAATTTAATT
1 AATATAATTAAATT
21187999 AA
1 AA
21188001 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:21190708 original size:54 final size:54
Alignment explanation
Indices: 21190636--21190748 Score: 199
Period size: 54 Copynumber: 2.1 Consensus size: 54
21190626 CCAATATGAG
*
21190636 TTTATAAATATTTAGGTCATGCAAAATTCTTCTTTAAATTTTTGGGCTCTTTCA
1 TTTATAAATATTTAGGTCATGCAAAATTCTTCTTTAAATTTTTGGGCACTTTCA
* *
21190690 TTTATAAATATTTGGGTCATGCAAGATTCTTCTTTAAATTTTTGGGCACTTTCA
1 TTTATAAATATTTAGGTCATGCAAAATTCTTCTTTAAATTTTTGGGCACTTTCA
21190744 TTTAT
1 TTTAT
21190749 TGTTTCTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (54 bp):
TTTATAAATATTTAGGTCATGCAAAATTCTTCTTTAAATTTTTGGGCACTTTCA
Found at i:21190734 original size:30 final size:29
Alignment explanation
Indices: 21190640--21190735 Score: 78
Period size: 30 Copynumber: 3.4 Consensus size: 29
21190630 TATGAGTTTA
*
21190640 TAAATATTTAGGTCATGCAAAATTCTTCTT
1 TAAATATTTGGGTCATGC-AAATTCTTCTT
* * *
21190670 TAAATTTTTGGG-C-T-C--TTTCATT-TA
1 TAAATATTTGGGTCATGCAAATTC-TTCTT
21190694 TAAATATTTGGGTCATGCAAGATTCTTCTT
1 TAAATATTTGGGTCATGCAA-ATTCTTCTT
*
21190724 TAAATTTTTGGG
1 TAAATATTTGGG
21190736 CACTTTCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
24 15 0.30
25 3 0.06
26 1 0.02
27 2 0.04
28 1 0.02
29 3 0.06
30 25 0.50
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (29 bp):
TAAATATTTGGGTCATGCAAATTCTTCTT
Found at i:21195332 original size:54 final size:53
Alignment explanation
Indices: 21195237--21195339 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 53
21195227 AGTGATTATC
* * * *
21195237 TTAATATTAAATTTAATTTAATCTTTATCTACAATTCTATTATTTTAATAAGAT
1 TTAAGATTAAATTTAATTTAATATTTATCTACAA-TATATTATATTAATAAGAT
*
21195291 TTAAGATTAAATTTAATTTAATATTTATCTTGATAA-ATATTATATTAAT
1 TTAAGATTAAATTTAATTTAATATTTATC-T-ACAATATATTATATTAAT
21195340 TTAATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
54 38 0.90
55 1 0.02
56 3 0.07
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (53 bp):
TTAAGATTAAATTTAATTTAATATTTATCTACAATATATTATATTAATAAGAT
Found at i:21200302 original size:9 final size:9
Alignment explanation
Indices: 21200290--21200314 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21200280 TAGTAAAAAG
21200290 TTGAAAATT
1 TTGAAAATT
21200299 TTGAAAATT
1 TTGAAAATT
21200308 TTGAAAA
1 TTGAAAA
21200315 CAGGGGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (9 bp):
TTGAAAATT
Found at i:21201715 original size:50 final size:50
Alignment explanation
Indices: 21201610--21201742 Score: 167
Period size: 50 Copynumber: 2.7 Consensus size: 50
21201600 TTACTGAGGT
* * * *
21201610 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGTACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
* *
21201660 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
** * * *
21201710 TATGAGAACTCTCATGTAAGACCATATCTGGGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGA
21201743 TATGACATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATGGGCACCAA
Found at i:21208577 original size:22 final size:22
Alignment explanation
Indices: 21208560--21208604 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21208550 CATGAATGAT
21208560 TTTAATTGGAAGCATGAACAAC
1 TTTAATTGGAAGCATGAACAAC
21208582 TTTAATTGGAAGCATGAACAAC
1 TTTAATTGGAAGCATGAACAAC
21208604 T
1 T
21208605 GAGGCACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (22 bp):
TTTAATTGGAAGCATGAACAAC
Found at i:21221691 original size:23 final size:22
Alignment explanation
Indices: 21221634--21221683 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
21221624 TTCTCTCTTA
21221634 TAGGGTTAAGGTTTTTAATTTT
1 TAGGGTTAAGGTTTTTAATTTT
* *
21221656 TAAGGTTATGGTTTTTAATATTT
1 TAGGGTTAAGGTTTTTAAT-TTT
21221679 TAGGG
1 TAGGG
21221684 GTAGGGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (22 bp):
TAGGGTTAAGGTTTTTAATTTT
Found at i:21227994 original size:20 final size:20
Alignment explanation
Indices: 21227969--21228009 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
21227959 TTACGTATCC
21227969 TCCACTCTTGCTACTGGTGG
1 TCCACTCTTGCTACTGGTGG
21227989 TCCACTCTTGCTACTGGTGG
1 TCCACTCTTGCTACTGGTGG
21228009 T
1 T
21228010 TGAGCCGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.29, G:0.24, T:0.37
Consensus pattern (20 bp):
TCCACTCTTGCTACTGGTGG
Found at i:21234246 original size:16 final size:16
Alignment explanation
Indices: 21234225--21234272 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
21234215 AAGATTAGAG
21234225 AAAGAAGTGAAGATGA
1 AAAGAAGTGAAGATGA
21234241 AAAGAAGTGAAGATGA
1 AAAGAAGTGAAGATGA
*
21234257 AAGGAA--GAAGATGA
1 AAAGAAGTGAAGATGA
21234271 AA
1 AA
21234273 TAGGGGATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 10 0.32
16 21 0.68
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.10
Consensus pattern (16 bp):
AAAGAAGTGAAGATGA
Found at i:21241392 original size:51 final size:50
Alignment explanation
Indices: 21241219--21241655 Score: 436
Period size: 51 Copynumber: 8.6 Consensus size: 50
21241209 TTCGATACAT
* *
21241219 GTAGTAGCATTCACATAGTACTACACACGTGATCAAG-TTTTACGGTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTTCAC
*
21241269 GTAGTAGCCTTCACATAGTACTACACACGTGATCAAG-TTTTACGGTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTTCAC
* * *
21241319 ATAGTAGCCTTCACATAGTACTACACACGTGGCCAAAGCTTTTCGGTACAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTTCAC
* * * * * *
21241370 ATAGTAGCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATTCAT
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTTCAC
* * *
21241421 GTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTTCGGTACAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTTCAC
* * * * * * *
21241472 ATAGTAGCCTTTACTTAGTACAACACATGTGACC-ATCATTTATCGATTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTTCAC
* * *
21241523 GTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTT-AGTACAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTT-TTCGGTTCAC
* * ** * *
21241574 GTTGTAGCCTTCACTTAGTACTACACATTTGACC-ATCATTTATCGATTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTTCAC
*
21241625 GTAGTAGCCTTCACACAGTACTACACACGTG
1 GTAGTAGCCTTCACATAGTACTACACACGTG
21241656 TTCATCGATA
Statistics
Matches: 320, Mismatches: 53, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
49 7 0.02
50 89 0.28
51 209 0.65
52 10 0.03
53 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
GTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTTCGGTTCAC
Found at i:21241447 original size:102 final size:102
Alignment explanation
Indices: 21241210--21241655 Score: 621
Period size: 102 Copynumber: 4.4 Consensus size: 102
21241200 CTTTTATCAT
* * * * * * *
21241210 TCGATACATGTAGTAGCATTCACATAGTACTACACACGTGATC-AAG-TTTTACGGTTCACGTAG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAG
* * * ***
21241273 TAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * *
21241311 -CGGTTCACATAGTAGCCTTCACATAGTACTACACACGTGGCCAAAGCTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
21241375 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* *
21241412 TCGATTCATGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
* *
21241477 AGCCTTTACTTAGTACAACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * *
21241514 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTT-AGTACACGTTG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT-TTCGGTACACATAG
*
21241578 TAGCCTTCACTTAGTACTACACATTTGACCATCATTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
21241616 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTG
21241656 TTCATCGATA
Statistics
Matches: 310, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
100 35 0.11
101 45 0.15
102 228 0.74
103 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:21242837 original size:11 final size:12
Alignment explanation
Indices: 21242809--21242841 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
21242799 GCCCAAACGT
21242809 CGAAATTTTCGAA
1 CGAAATTTTC-AA
21242822 CGAAATTTTC-A
1 CGAAATTTTCAA
21242833 CGAAATTTT
1 CGAAATTTT
21242842 TCTGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:21250042 original size:551 final size:551
Alignment explanation
Indices: 21249002--21250097 Score: 1836
Period size: 551 Copynumber: 2.0 Consensus size: 551
21248992 AATTTTTTAA
*
21249002 ATTATAATTTAACATAACAAATCATGCAGAAGAGAAAAACCCCAAAACATTATCCAAAGTTCACA
1 ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAAGTTCACA
*** *
21249067 AATCAAAAATTTGAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACACAAACTAAAATGT
66 AATCAAAAATCCAAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACAAAAACTAAAATGT
*
21249132 CCAATACCACTACTTGTAAGGTTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCATC
131 CCAATACCACTACTTGCAAGGTTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCATC
* * * * *
21249197 CTAGTCTCGATTATCTGAAATCAAAGTTTAAGGGCGTGAGCTTAAAAATGCTCAATGTAGGTCTT
196 CTAGTCCCGATTATCTAAAATCAAAGTTTAAGGGCGTAAGATTAAAAAGGCTCAATGTAGGTCTT
* *
21249262 AAATAACAATTATTTCACAAAAATAATTCATTATAACATCATATTAATCAGCCCATAACATATAT
261 AAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGCCCATAACATATAT
*
21249327 AAATTACTCAATTATAAATCAAATATGGCAGATTGTGTAATGACGTAATTAATACAACATTTTTA
326 AAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTAATTAATACAACATTTTTA
** * *
21249392 GAATACAATACAGTTATTAGAACTTAAATCCTACCTAACTCCGCTACACGCCACATAGAGTTCCC
391 GAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGCTACACGCCACACAGAGTTCCC
* * *
21249457 TATAACTCATCCAACCAATAACACACCAAAATGTGATCTAACCACCAGAAATTGTAGATTTACTG
456 CATAACTCATCCAACCAATAACACACCAAAATGTGATCCAACCACCAGAAATTATAGATTTACTG
*
21249522 CCAAATACATAATATTGT-GACAAGAAAAAC
521 CCAAATACATAATATTATGGACAAGAAAAAC
* *
21249552 ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAATTTCGCA
1 ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAAGTTCACA
* *
21249617 AATCAAAAATCCAAACCAAAGTCCCAAAATTAAAGTCCATAAAGCATGAACAAAAACTAAAATTT
66 AATCAAAAATCCAAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACAAAAACTAAAATGT
* *
21249682 CCAATACCACTACTTGCAAGGTTTTTTCAAAAAATAATCAAGAGTACCTTCGTAGCCAAGCCCAT
131 CCAATACCACTACTTGCAAGG-TTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCAT
21249747 CCTAGTCCCGATTATCTAAAATCAAAGTTTAAGGAG-GTAAGATTAAAAAGGCTCAATGTAGGTC
195 CCTAGTCCCGATTATCTAAAATCAAAGTTTAAGG-GCGTAAGATTAAAAAGGCTCAATGTAGGTC
*
21249811 TTAAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGTCCATAACATAT
259 TTAAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGCCCATAACATAT
*
21249876 ATAAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTATTTAATACAACATTTT
324 ATAAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTAATTAATACAACATTTT
* *
21249941 TAGAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGTTACACGCCATACAGAGTTC
389 TAGAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGCTACACGCCACACAGAGTTC
* * *
21250006 CCCATAACTCATCCAACTAATAACACACCAAAATGTGGTCCAACCACCAGAAATTATGGATTTAC
454 CCCATAACTCATCCAACCAATAACACACCAAAATGTGATCCAACCACCAGAAATTATAGATTTAC
*
21250071 TGCCAGATACATAATATTATGGACAAG
519 TGCCAAATACATAATATTATGGACAAG
21250098 CCACCAGAAA
Statistics
Matches: 507, Mismatches: 36, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
550 141 0.28
551 359 0.71
552 7 0.01
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.26
Consensus pattern (551 bp):
ATTATAATTTAACATAACAAATCATGCAGAAAAGAAAAACCCCAAAACATTATCCAAAGTTCACA
AATCAAAAATCCAAACCAAAGTCCCAAAAATAAAGTCCATAAAGCATGAACAAAAACTAAAATGT
CCAATACCACTACTTGCAAGGTTTTCCAAAAAATAACCAAGAGTACCTTCGTAGCCAAGCCCATC
CTAGTCCCGATTATCTAAAATCAAAGTTTAAGGGCGTAAGATTAAAAAGGCTCAATGTAGGTCTT
AAATAACAATTAGTTCACAAAAACAATTCATTATAACATCATATTAATCAGCCCATAACATATAT
AAATTACTCAATTATAAATCAAATATGGCAAATTGTGTAATGACGTAATTAATACAACATTTTTA
GAATACAATACAAATATTAGAACTTAAATCCTACCCAACTCCGCTACACGCCACACAGAGTTCCC
CATAACTCATCCAACCAATAACACACCAAAATGTGATCCAACCACCAGAAATTATAGATTTACTG
CCAAATACATAATATTATGGACAAGAAAAAC
Done.