Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 11 of 125
Found at i:1646163 original size:24 final size:24
Alignment explanation
Indices: 1646087--1646170 Score: 93
Period size: 24 Copynumber: 3.5 Consensus size: 24
1646077 CTAATGGATG
*
1646087 AAAAATGAGAAAA-GAAAAAA-AATA
1 AAAAATGA-AAAATGAAAAAATGA-A
*
1646111 AAAAATGAAAAGGTGAAAAAATG-A
1 AAAAATGAAAA-ATGAAAAAATGAA
1646135 AAAAATGAAAAATGAAAAAATGAA
1 AAAAATGAAAAATGAAAAAATGAA
*
1646159 AAAAAAGAAAAA
1 AAAAATGAAAAA
1646171 ATAAAAAGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
23 13 0.25
24 32 0.62
25 7 0.13
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (24 bp):
AAAAATGAAAAATGAAAAAATGAA
Found at i:1646176 original size:24 final size:24
Alignment explanation
Indices: 1646103--1646187 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 24
1646093 GAGAAAAGAA
**
1646103 AAAAAAT-AAAAAATGAAAAGGTG
1 AAAAAATGAAAAAATGAAAAAATG
1646126 AAAAAATGAAAAAATG-AAAAATG
1 AAAAAATGAAAAAATGAAAAAATG
* *
1646149 AAAAAATGAAAAAAAAGAAAAAATA
1 AAAAAATG-AAAAAATGAAAAAATG
*
1646174 AAAAGAAGGAAAAA
1 AAAA-AATGAAAAA
1646188 GAAAGGCTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
23 20 0.38
24 15 0.28
25 15 0.28
26 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.09
Consensus pattern (24 bp):
AAAAAATGAAAAAATGAAAAAATG
Found at i:1646186 original size:16 final size:17
Alignment explanation
Indices: 1646087--1646191 Score: 73
Period size: 16 Copynumber: 6.6 Consensus size: 17
1646077 CTAATGGATG
*
1646087 AAAAATGAGAAAAGAA-A
1 AAAAATGA-AAAAAAAGA
*
1646104 AAAAAT--AAAAAATGA
1 AAAAATGAAAAAAAAGA
** *
1646119 AAAGGTG-AAAAAATGA
1 AAAAATGAAAAAAAAGA
*
1646135 AAAAATG--AAAAATGA
1 AAAAATGAAAAAAAAGA
1646150 AAAAATGAAAAAAAAGA
1 AAAAATGAAAAAAAAGA
* *
1646167 AAAAAT-AAAAAGAAGG
1 AAAAATGAAAAAAAAGA
1646183 AAAAA-GAAA
1 AAAAATGAAA
1646192 GGCTCAAATT
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
14 5 0.07
15 20 0.27
16 30 0.41
17 19 0.26
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (17 bp):
AAAAATGAAAAAAAAGA
Found at i:1646995 original size:63 final size:63
Alignment explanation
Indices: 1646875--1647038 Score: 175
Period size: 63 Copynumber: 2.6 Consensus size: 63
1646865 ATAGATCAAT
* *** *
1646875 GGATAAAATTTATTCTAAAATGGCTAGTGCTAAGAAACCTATGAGTGGTGACCAAGTGATGGA
1 GGATAAAATTTATTCTAAAATGGCTAGTACTAAGAAACCTATGAGCAATGACCAAGTGATCGA
* * * * * **
1646938 GGATGAAATTTGTTCTAAAATGGCTAGTACTGATAAGCCTATGAGCAATGATTAAGTGATCGA
1 GGATAAAATTTATTCTAAAATGGCTAGTACTAAGAAACCTATGAGCAATGACCAAGTGATCGA
* * * * *
1647001 AGACAGAATTTATTCTAAGATGGCTAGTGCTAAGAAAC
1 GGATAAAATTTATTCTAAAATGGCTAGTACTAAGAAAC
1647039 TCAAAATGGT
Statistics
Matches: 79, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
63 79 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (63 bp):
GGATAAAATTTATTCTAAAATGGCTAGTACTAAGAAACCTATGAGCAATGACCAAGTGATCGA
Found at i:1647554 original size:20 final size:20
Alignment explanation
Indices: 1647529--1647568 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1647519 CCAAATTTGA
*
1647529 CAAATGTGAACCTTTGAACT
1 CAAATGAGAACCTTTGAACT
*
1647549 CAAATGAGAAGCTTTGAACT
1 CAAATGAGAACCTTTGAACT
1647569 TTTGGATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (20 bp):
CAAATGAGAACCTTTGAACT
Found at i:1647957 original size:42 final size:42
Alignment explanation
Indices: 1647911--1648048 Score: 156
Period size: 42 Copynumber: 3.4 Consensus size: 42
1647901 CTATTTAGAT
*
1647911 GAGCATTTTGTTTTTTAAAAATTATAATGCCTCTGTTTAAAG
1 GAGCATTTTATTTTTTAAAAATTATAATGCCTCTGTTTAAAG
* *
1647953 GAGCATTTTATTTTTTAAAAGTTATAGTGCCTCTGTTTAAAG
1 GAGCATTTTATTTTTTAAAAATTATAATGCCTCTGTTTAAAG
* * * * ** * *
1647995 GATCA--TT-TTTTTCAAAAGTTGTGTTGCCTCTATTTAGAG
1 GAGCATTTTATTTTTTAAAAATTATAATGCCTCTGTTTAAAG
1648034 GAGCATTTTATTTTT
1 GAGCATTTTATTTTT
1648049 CAAAGTTGTG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 30 0.37
40 2 0.02
41 2 0.02
42 48 0.59
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (42 bp):
GAGCATTTTATTTTTTAAAAATTATAATGCCTCTGTTTAAAG
Found at i:1648046 original size:81 final size:80
Alignment explanation
Indices: 1647866--1648339 Score: 302
Period size: 81 Copynumber: 5.8 Consensus size: 80
1647856 CATAATTGTC
* * * * * * * *
1647866 GAGGAGCCTGTTATTTTTCAAAAGTTGTAGTGCTTCTATTTAGATGAGCATTTTGTTTTTTAAAA
1 GAGGAGCATTTTATTTTTC-AAAGTTATAGTGCCTCTGTTTAAAAGAGCA--TT-TTTTTCAAAA
* * ** *
1647931 ATTATAATGCCTCTGTTTA
62 GTTGTGTTGCCTCTATTTA
* * * *
1647950 AAGGAGCATTTTATTTTTTAAAAGTTATAGTGCCTCTGTTTAAAGGATCATTTTTTTCAAAAGTT
1 GAGGAGCATTTTA-TTTTTCAAAGTTATAGTGCCTCTGTTTAAAAGAGCATTTTTTTCAAAAGTT
1648015 GTGTTGCCTCTATTTA
65 GTGTTGCCTCTATTTA
* * * ** **
1648031 GAGGAGCATTTTATTTTTCAAAGTTGTGGTGCTTCTGTTTGGAAGAGCATTTATTTTTTAAAGTT
1 GAGGAGCATTTTATTTTTCAAAGTTATAGTGCCTCTGTTTAAAAGAGCATTT-TTTTCAAAAGTT
* * * *
1648096 GTAG-CGCTTTTGTTTA
65 GT-GTTGCCTCTATTTA
* * * * * * *
1648112 GAGAAGCATTTTATTTTTCAATGTTGTTA-AGCCTCTGTTTAGAGGAGAATTTTATTTTTC-AAA
1 GAGGAGCATTTTATTTTTCAAAGTT-ATAGTGCCTCTGTTTAAAAGAGCA--TT-TTTTTCAAAA
*
1648175 GTTGTGGTGCCTCTATTTA
62 GTTGTGTTGCCTCTATTTA
** * * * *
1648194 GATTAGCA-TTTATTTTTCGAAGTTATAGTCCCTTTATTTAAAAGAGCACTTATTTTTCAAAAGT
1 GAGGAGCATTTTATTTTTCAAAGTTATAGTGCCTCTGTTTAAAAGAGCA-TT-TTTTTCAAAAGT
* *
1648258 CGT-TAAGCCTCTATTTA
64 TGTGT-TGCCTCTATTTA
* *
1648275 GAAGAGCA-TTTATTTTTTGAAATTGTTA-A--GCCTCTGTTTAAAAGAGC-TTTATTTTCAAAA
1 GAGGAGCATTTTA-TTTTTCAAA--GTTATAGTGCCTCTGTTTAAAAGAGCATTT-TTTTCAAAA
1648335 GTTGT
62 GTTGT
1648340 TGAGCCTTTA
Statistics
Matches: 306, Mismatches: 69, Indels: 35
0.75 0.17 0.09
Matches are distributed among these distances:
78 1 0.00
79 15 0.05
80 42 0.14
81 164 0.54
82 33 0.11
83 7 0.02
84 39 0.13
85 5 0.02
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (80 bp):
GAGGAGCATTTTATTTTTCAAAGTTATAGTGCCTCTGTTTAAAAGAGCATTTTTTTCAAAAGTTG
TGTTGCCTCTATTTA
Found at i:1648079 original size:41 final size:41
Alignment explanation
Indices: 1647876--1648339 Score: 307
Period size: 41 Copynumber: 11.4 Consensus size: 41
1647866 GAGGAGCCTG
* * *
1647876 TTATTTTTCAAAAGTTGTAGTGCTTCTATTTAGATGAGCATT
1 TTATTTTTC-AAAGTTGTAGTGCCTCTGTTTAGAAGAGCATT
* * * * *
1647918 TTGTTTTTTAAAAATTATAATGCCTCTGTTTA-AAGGAGCATT
1 TT-ATTTTTCAAAGTTGTAGTGCCTCTGTTTAGAA-GAGCATT
* * *
1647960 TTATTTTTTAAAAGTTATAGTGCCTCTGTTTA-AAG-G-ATCA
1 TTA-TTTTTCAAAGTTGTAGTGCCTCTGTTTAGAAGAGCAT-T
* *
1648000 TT-TTTTTCAAAAGTTGT-GTTGCCTCTATTTAGAGGAGCATT
1 TTATTTTTC-AAAGTTGTAG-TGCCTCTGTTTAGAAGAGCATT
* * *
1648041 TTATTTTTCAAAGTTGTGGTGCTTCTGTTTGGAAGAGCA-T
1 TTATTTTTCAAAGTTGTAGTGCCTCTGTTTAGAAGAGCATT
* * * *
1648081 TTATTTTTTAAAGTTGTAGCGCTTTTGTTTAG-AGAAGCATT
1 TTATTTTTCAAAGTTGTAGTGCCTCTGTTTAGAAG-AGCATT
* * * *
1648122 TTATTTTTCAATGTTGTTA-AGCCTCTGTTTAGAGGAGAATT
1 TTATTTTTCAAAGTTG-TAGTGCCTCTGTTTAGAAGAGCATT
* * **
1648163 TTATTTTTCAAAGTTGTGGTGCCTCTATTTAGATTAGCA-T
1 TTATTTTTCAAAGTTGTAGTGCCTCTGTTTAGAAGAGCATT
* * * * * * *
1648203 TTATTTTTCGAAGTTATAGTCCCTTTATTTAAAAGAGCA-C
1 TTATTTTTCAAAGTTGTAGTGCCTCTGTTTAGAAGAGCATT
* * *
1648243 TTATTTTTCAAAAGTCGTTA-AGCCTCTATTTAGAAGAGCA-T
1 TTATTTTTC-AAAGTTG-TAGTGCCTCTGTTTAGAAGAGCATT
* * *
1648284 TTATTTTTTGAAA-TTGTTA-AGCCTCTGTTTAAAAGAGC--T
1 TTA-TTTTTCAAAGTTG-TAGTGCCTCTGTTTAGAAGAGCATT
1648323 TTA-TTTTCAAAAGTTGT
1 TTATTTTTC-AAAGTTGT
1648340 TGAGCCTTTA
Statistics
Matches: 339, Mismatches: 62, Indels: 46
0.76 0.14 0.10
Matches are distributed among these distances:
37 4 0.01
38 10 0.03
39 29 0.09
40 101 0.30
41 115 0.34
42 75 0.22
43 5 0.01
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.46
Consensus pattern (41 bp):
TTATTTTTCAAAGTTGTAGTGCCTCTGTTTAGAAGAGCATT
Found at i:1648146 original size:122 final size:122
Alignment explanation
Indices: 1647876--1648333 Score: 364
Period size: 122 Copynumber: 3.8 Consensus size: 122
1647866 GAGGAGCCTG
* * * * * * * * **
1647876 TTATTTTTCAAAAGTTG-TAGTGCTTCTATTTAGATGAGCATTTTGTTTTTTAAAAATTATAATG
1 TTATTTTTCAAAAGTCGTTA-AGCCTCTATTTAGAGGAGCATTTT-ATTTTTCAAAGTTGTGGTG
* * * * * * *
1647940 CCTCTGTTTA-AAGGAGCATTTTATTTTTTAAAAGTTATAGTGCCTCTGTTTAAAGGATCA-
64 CCTCTATTTAGAA-GAGCA-TTTA-TTTTTCAAAGTTATAGTCCCTTTATTTAAAAGAGCAC
* *
1648000 TT-TTTTTCAAAAGTTGTGT-TGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAGTTGTGGTGC
1 TTATTTTTCAAAAGTCGT-TAAGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAGTTGTGGTGC
* * * * * * * * *
1648063 TTCTGTTTGGAAGAGCATTTATTTTTTAAAGTTGTAG-CGCTTT-TGTTTAGAGAAGCATT
65 CTCTATTTAGAAGAGCATTTATTTTTCAAAGTTATAGTCCCTTTAT-TTAAAAG-AGCA-C
* * * *
1648122 TTATTTTTC-AATGTTGTTAAGCCTCTGTTTAGAGGAGAATTTTATTTTTCAAAGTTGTGGTGCC
1 TTATTTTTCAAAAGTCGTTAAGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAGTTGTGGTGCC
** *
1648186 TCTATTTAGATTAGCATTTATTTTTCGAAGTTATAGTCCCTTTATTTAAAAGAGCAC
66 TCTATTTAGAAGAGCATTTATTTTTCAAAGTTATAGTCCCTTTATTTAAAAGAGCAC
* * ***
1648243 TTATTTTTCAAAAGTCGTTAAGCCTCTATTTAGAAGAGCA-TTTATTTTTTGAAA-TTGTTAAGC
1 TTATTTTTCAAAAGTCGTTAAGCCTCTATTTAGAGGAGCATTTTA-TTTTTCAAAGTTGTGGTGC
* *
1648306 CTCTGTTTAAAAGAGC-TTTA-TTTTCAAA
65 CTCTATTTAGAAGAGCATTTATTTTTCAAA
1648334 AGTTGTTGAG
Statistics
Matches: 272, Mismatches: 49, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
118 1 0.00
119 14 0.05
120 21 0.08
121 36 0.13
122 142 0.52
123 54 0.20
124 3 0.01
125 1 0.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.46
Consensus pattern (122 bp):
TTATTTTTCAAAAGTCGTTAAGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAGTTGTGGTGCC
TCTATTTAGAAGAGCATTTATTTTTCAAAGTTATAGTCCCTTTATTTAAAAGAGCAC
Found at i:1649473 original size:50 final size:48
Alignment explanation
Indices: 1649418--1649586 Score: 177
Period size: 50 Copynumber: 3.5 Consensus size: 48
1649408 AATAAAAAGA
* *
1649418 ATTTCTAAATAGGCCTAAATGGTGAAAATTTTAAAAATTTCAAAAAAAAT
1 ATTTCTAAATAGGCCCAAATGGTGAAAA-TTTAGAAATTT-AAAAAAAAT
* *
1649468 ATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAA--T--AAAAAA-
1 ATTTCTAAATAGGCCCAAATGGTG-AAAATTTAGAAATTTAAAAAAAAT
*
1649512 ATTTCTAAATAGGCCCCAAATGGTGGAGAATTTAGAAATTTAAAAAAATAT
1 ATTTCTAAATAGG-CCCAAATGGT-GAAAATTTAGAAATTTAAAAAAA-AT
* * *
1649563 ATTTCTAATTTGACCCAAATGGTG
1 ATTTCTAAATAGGCCCAAATGGTG
1649587 GAATAATTAG
Statistics
Matches: 100, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
44 11 0.11
45 27 0.27
46 1 0.01
47 1 0.01
48 1 0.01
49 6 0.06
50 39 0.39
51 14 0.14
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (48 bp):
ATTTCTAAATAGGCCCAAATGGTGAAAATTTAGAAATTTAAAAAAAAT
Found at i:1649531 original size:45 final size:45
Alignment explanation
Indices: 1649461--1649560 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
1649451 AAAATTTCAA
*
1649461 AAAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAA-T
1 AAAAAA-ATTTCTAAATGGACCCAAATGGTGAAAAATTTAGAAATT
* * *
1649506 AAAAAAATTTCTAAATAGGCCCCAAATGGTGGAGAATTTAGAAATTT
1 AAAAAAATTTCTAAAT-GGACCCAAATGGTGAAAAATTTAGAAA-TT
1649553 AAAAAAAT
1 AAAAAAAT
1649561 ATATTTCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 10 0.21
45 29 0.60
47 9 0.19
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (45 bp):
AAAAAAATTTCTAAATGGACCCAAATGGTGAAAAATTTAGAAATT
Found at i:1649597 original size:95 final size:95
Alignment explanation
Indices: 1649407--1649586 Score: 276
Period size: 95 Copynumber: 1.9 Consensus size: 95
1649397 AAAAAATAAA
*
1649407 AAATAAAAAGAATTTCTAAATAGGCCTAAATGGTGAAAATTTTAAAAATTTCAAAAAAAATATTT
1 AAATAAAAAGAATTTCTAAATAGGCCCAAATGGTGAAAATTTTAAAAATTTCAAAAAAAATATTT
1649472 CTAAATTGACCCAAATGGTGAAAAATTTAG
66 CTAAATTGACCCAAATGGTGAAAAATTTAG
* *
1649502 AAATAAAAA-AATTTCTAAATAGGCCCCAAATGGTGGAGAA-TTTAGAAATTT-AAAAAAATATA
1 AAATAAAAAGAATTTCTAAATAGG-CCCAAATGGT-GAAAATTTTAAAAATTTCAAAAAAA-ATA
*
1649564 TTTCTAATTTGACCCAAATGGTG
63 TTTCTAAATTGACCCAAATGGTG
1649587 GAATAATTAG
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
94 21 0.27
95 53 0.68
96 4 0.05
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.29
Consensus pattern (95 bp):
AAATAAAAAGAATTTCTAAATAGGCCCAAATGGTGAAAATTTTAAAAATTTCAAAAAAAATATTT
CTAAATTGACCCAAATGGTGAAAAATTTAG
Found at i:1655881 original size:36 final size:36
Alignment explanation
Indices: 1655841--1655909 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1655831 TGATGGTACG
*
1655841 AATAAA-CATATCTAAATAGGAAAACATGATTATTTA
1 AATAAAGCATAT-TAAATAAGAAAACATGATTATTTA
** *
1655877 AATAAAGTTTATTAAATAATAAAACATGATTAT
1 AATAAAGCATATTAAATAAGAAAACATGATTAT
1655910 ACAGAATGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 25 0.89
37 3 0.11
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (36 bp):
AATAAAGCATATTAAATAAGAAAACATGATTATTTA
Found at i:1661616 original size:34 final size:34
Alignment explanation
Indices: 1661577--1661692 Score: 90
Period size: 34 Copynumber: 3.3 Consensus size: 34
1661567 ACTATACTAG
1661577 ATGCATTTTCAAAAAGTATTACATTTATCCGAAA
1 ATGCATTTTCAAAAAGTATTACATTTATCCGAAA
* * * * * *
1661611 ATGCATTAAT-GATAAGCATTGCAATTATATATCCGTAA
1 ATGCATT-TTCAAAAAGTATTAC-A-T-T-TATCCGAAA
* * *
1661649 ATGCATTTTCAAAAAGTATTATAATTATCTGAAA
1 ATGCATTTTCAAAAAGTATTACATTTATCCGAAA
*
1661683 ATTCATTTTC
1 ATGCATTTTC
1661693 GGAAGTAACT
Statistics
Matches: 60, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
34 31 0.52
35 3 0.05
36 1 0.02
37 3 0.05
38 22 0.37
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (34 bp):
ATGCATTTTCAAAAAGTATTACATTTATCCGAAA
Found at i:1670272 original size:14 final size:14
Alignment explanation
Indices: 1670253--1670282 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1670243 CCATTGTTTG
1670253 AATAAAAATTAAAA
1 AATAAAAATTAAAA
1670267 AATAAAAATTAAAA
1 AATAAAAATTAAAA
1670281 AA
1 AA
1670283 AGAAATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AATAAAAATTAAAA
Found at i:1680543 original size:18 final size:18
Alignment explanation
Indices: 1680520--1680555 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1680510 TTTAATTGAA
1680520 TTAATTA-ATTAAATCGAT
1 TTAATTATATT-AATCGAT
1680538 TTAATTATATTAATCGAT
1 TTAATTATATTAATCGAT
1680556 CAATCATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (18 bp):
TTAATTATATTAATCGAT
Found at i:1680580 original size:10 final size:11
Alignment explanation
Indices: 1680562--1680610 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
1680552 CGATCAATCA
1680562 TTAAATTAATT
1 TTAAATTAATT
1680573 TT-AATTAATT
1 TTAAATTAATT
*
1680583 ATTAAAAATAATT
1 -TT-AAATTAATT
*
1680596 TTAAATGAATT
1 TTAAATTAATT
1680607 TTAA
1 TTAA
1680611 TTTTCAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.25
11 15 0.47
12 2 0.06
13 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
TTAAATTAATT
Found at i:1680952 original size:15 final size:15
Alignment explanation
Indices: 1680928--1680957 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1680918 TATAATATAA
*
1680928 TTTGATTAATTCAAT
1 TTTGAATAATTCAAT
1680943 TTTGAATAATTCAAT
1 TTTGAATAATTCAAT
1680958 ATGAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (15 bp):
TTTGAATAATTCAAT
Found at i:1683938 original size:22 final size:22
Alignment explanation
Indices: 1683913--1683954 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1683903 AATTATTAAT
1683913 TAATAAAATGAATA-AAAATTCA
1 TAATAAAAT-AATATAAAATTCA
*
1683935 TAATAATATAATATAAAATT
1 TAATAAAATAATATAAAATT
1683955 AAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAAAATAATATAAAATTCA
Found at i:1683964 original size:18 final size:17
Alignment explanation
Indices: 1683939--1683972 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1683929 AATTCATAAT
1683939 AATATAATATAAAATTA
1 AATATAATATAAAATTA
*
1683956 AATATTAATATTAAATT
1 AATA-TAATATAAAATT
1683973 TATCATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAATATAAAATTA
Found at i:1684863 original size:21 final size:20
Alignment explanation
Indices: 1684837--1685072 Score: 114
Period size: 21 Copynumber: 11.5 Consensus size: 20
1684827 TATGTTAAAC
1684837 TAATAATATTATATATTAGTT
1 TAATAATATTATATATTA-TT
*
1684858 TAATAAGATT-TATTATTATTT
1 TAATAATATTATA-TATTA-TT
*
1684879 TAATAATATTTTCATATTATT
1 TAATAATATTAT-ATATTATT
*
1684900 T--TAATATTATATATTAAAT
1 TAATAATATTATATATT-ATT
**
1684919 TAATAATA-T-TATAGCATT
1 TAATAATATTATATATTATT
* *
1684937 TAATAATATTTTATTAATATT
1 TAATAATATTATA-TATTATT
*
1684958 TGA-AA-ATTATATATTAATT
1 TAATAATATTATATATT-ATT
*
1684977 TAA-AATTTTTAATATATTATAT
1 TAATAA-TATT-ATATATTAT-T
* *
1684999 TATTTAAATATTTAAAATATTAATT
1 TA-AT-AATA-TT-ATATATT-ATT
*
1685024 TAATAATATT-T-TAATATT
1 TAATAATATTATATATTATT
** *
1685042 TAATAATAAAAAATATTAGTT
1 TAATAATATTATATATTA-TT
*
1685063 TCATAATATT
1 TAATAATATT
1685073 TAAATACTTC
Statistics
Matches: 165, Mismatches: 28, Indels: 44
0.70 0.12 0.19
Matches are distributed among these distances:
18 29 0.18
19 31 0.19
20 11 0.07
21 53 0.32
22 18 0.11
23 5 0.03
24 2 0.01
25 14 0.08
26 2 0.01
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATAATATTATATATTATT
Found at i:1684888 original size:11 final size:11
Alignment explanation
Indices: 1684837--1684958 Score: 54
Period size: 11 Copynumber: 11.0 Consensus size: 11
1684827 TATGTTAAAC
*
1684837 TAATAATATTA
1 TAATAATATTT
* *
1684848 T-ATATTAGTT
1 TAATAATATTT
*
1684858 TAATAAGA-TT
1 TAATAATATTT
* *
1684868 TATTATTATTT
1 TAATAATATTT
1684879 TAATAATATTT
1 TAATAATATTT
* *
1684890 TCATATTATTT
1 TAATAATATTT
1684901 TAATATTATATATT
1 TAATA--ATAT-TT
* *
1684915 AAATTAATAATAT
1 TAA-TAAT-ATTT
**
1684928 T-ATAGCA-TT
1 TAATAATATTT
1684937 TAATAATATTT
1 TAATAATATTT
*
1684948 TATTAATATTT
1 TAATAATATTT
1684959 GAAAATTATA
Statistics
Matches: 79, Mismatches: 23, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
9 2 0.03
10 19 0.24
11 43 0.54
12 1 0.01
13 6 0.08
14 6 0.08
15 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TAATAATATTT
Found at i:1685013 original size:25 final size:27
Alignment explanation
Indices: 1684952--1685020 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
1684942 ATATTTTATT
1684952 AATATTTGAAAAT-TATATATTAATTTAA
1 AATATTT-AAAATAT-TATATTAATTTAA
* *
1684980 AATTTTTAATATATTATATT-ATTT-A
1 AATATTTAAAATATTATATTAATTTAA
1685005 AATATTTAAAATATTA
1 AATATTTAAAATATTA
1685021 ATTTAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 15 0.42
26 4 0.11
27 10 0.28
28 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
AATATTTAAAATATTATATTAATTTAA
Found at i:1685017 original size:27 final size:27
Alignment explanation
Indices: 1684952--1685018 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
1684942 ATATTTTATT
1684952 AATATTTGAAAAT-TATATATTAATTTA
1 AATATTT-AAAATATATATATTAATTTA
**
1684979 AA-ATTTTTAATATATTATATT-ATTTA
1 AATATTTAAAATATA-TATATTAATTTA
1685005 AATATTTAAAATAT
1 AATATTTAAAATAT
1685019 TAATTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 3 0.09
26 13 0.39
27 17 0.52
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
AATATTTAAAATATATATATTAATTTA
Found at i:1685044 original size:18 final size:18
Alignment explanation
Indices: 1684877--1685049 Score: 75
Period size: 18 Copynumber: 9.6 Consensus size: 18
1684867 TTATTATTAT
1684877 TTTAATAATATTTTCATATTA
1 TTTAATAATATTTT-A-A-TA
*
1684898 TTTTAATATTATATATTAA-A
1 -TTTAATA--ATATTTTAATA
* **
1684918 -TTAATAATATTATAGCA
1 TTTAATAATATTTTAATA
1684935 TTTAATAATATTTTATTAATA
1 TTTAATAATA--TT-TTAATA
1684956 TTTGAA-AATTATATATT-A-A
1 TTT-AATAA-TAT-T-TTAATA
1684975 TTTAA-AAT-TTTTAATA
1 TTTAATAATATTTTAATA
* *
1684991 TATT-ATATTATTTAAATA
1 T-TTAATAATATTTTAATA
1685009 TTTAA-AATA--TT-A-A
1 TTTAATAATATTTTAATA
1685022 TTTAATAATATTTTAATA
1 TTTAATAATATTTTAATA
1685040 TTTAATAATA
1 TTTAATAATA
1685050 AAAAATATTA
Statistics
Matches: 119, Mismatches: 11, Indels: 46
0.68 0.06 0.26
Matches are distributed among these distances:
13 6 0.05
14 7 0.06
15 3 0.03
16 12 0.10
17 12 0.10
18 39 0.33
19 4 0.03
20 5 0.04
21 12 0.10
22 12 0.10
23 1 0.01
24 6 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (18 bp):
TTTAATAATATTTTAATA
Found at i:1685204 original size:20 final size:20
Alignment explanation
Indices: 1685181--1685246 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1685171 ATATTTAATT
1685181 TAATAATTTAATATTTTTAA
1 TAATAATTTAATATTTTTAA
* *
1685201 TAATATTTTAATATTCTTT-T
1 TAATAATTTAATATT-TTTAA
* *
1685221 TTAT-ATTAAATA-TTTTAA
1 TAATAATTTAATATTTTTAA
1685239 TAATAATT
1 TAATAATT
1685247 ACATATACTA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 9 0.25
20 17 0.47
21 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TAATAATTTAATATTTTTAA
Found at i:1685230 original size:59 final size:60
Alignment explanation
Indices: 1685106--1685310 Score: 154
Period size: 59 Copynumber: 3.4 Consensus size: 60
1685096 AATTTATTAT
* * * *
1685106 TATTAAATA-TTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCA
1 TATTAAATATTTAATTTAATATATTATAATATTTTAATAAGATTTTAATATTATATTTCA
* * * * *
1685165 TCTTAAATATTTAATTTAATA-ATT-TAATATTTTTAATAATATTTTAATATTCTTTTTTA
1 TATTAAATATTTAATTTAATATATTATAATA-TTTTAATAAGATTTTAATATTATATTTCA
* * * *
1685224 TATTAAATATTTTAATAATAATTACATATACTATATTATTTTAGTAATATTTTAATA-T-TA-TT
1 TATTAAATA--TT--TAAT--TTA-ATATATTATAATATTTTAATAAGATTTTAATATTATATTT
1685286 CAA
59 C-A
1685289 TATTAAA-ATTTAAATTTAATAT
1 TATTAAATATTT-AATTTAATAT
1685311 GATTTTATTA
Statistics
Matches: 118, Mismatches: 15, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
58 8 0.07
59 44 0.37
60 12 0.10
61 5 0.04
62 2 0.02
63 4 0.03
64 3 0.03
65 12 0.10
66 4 0.03
67 20 0.17
68 4 0.03
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (60 bp):
TATTAAATATTTAATTTAATATATTATAATATTTTAATAAGATTTTAATATTATATTTCA
Found at i:1685353 original size:37 final size:40
Alignment explanation
Indices: 1685268--1685353 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 40
1685258 ATTATTTTAG
* * *
1685268 TAATATTTTAATATTATTCAATATTAAAATTTAAATTTAA
1 TAATATTTTAATATTAATCAATATTAAAAATTAAATGTAA
* *
1685308 T-ATGATTTTATTA-TAAT-AATATTAAAAATT-CATGTAA
1 TAAT-ATTTTAATATTAATCAATATTAAAAATTAAATGTAA
1685345 TAATATTTT
1 TAATATTTT
1685354 TAAAAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
37 11 0.28
38 14 0.36
39 5 0.13
40 9 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (40 bp):
TAATATTTTAATATTAATCAATATTAAAAATTAAATGTAA
Found at i:1685460 original size:29 final size:28
Alignment explanation
Indices: 1685424--1685572 Score: 117
Period size: 28 Copynumber: 5.2 Consensus size: 28
1685414 TGTTATTTAA
*
1685424 ATAATATTTGAATATTTAATATTAAATT
1 ATAATATTTAAATATTTAATATTAAATT
* *
1685452 AGTAGTATTTAAATATTTAAAATT--ATT
1 A-TAATATTTAAATATTTAATATTAAATT
1685479 ATAATATTTAAATAGTATTAATTATTAAATT
1 ATAATATTTAAATA-T-TTAA-TATTAAATT
* * **
1685510 AATAATATTT-AGTATGTAATATTATTTTT
1 -ATAATATTTAAATATTTAATATTA-AATT
* * *
1685539 AAAATATTTAAA-ATTAAATATTAATTT
1 ATAATATTTAAATATTTAATATTAAATT
1685566 AATAATA
1 -ATAATA
1685573 AACTATTATA
Statistics
Matches: 96, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
26 12 0.12
27 8 0.08
28 32 0.33
29 28 0.29
30 1 0.01
31 6 0.06
32 9 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (28 bp):
ATAATATTTAAATATTTAATATTAAATT
Found at i:1685504 original size:18 final size:18
Alignment explanation
Indices: 1685454--1685508 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1685444 ATTAAATTAG
1685454 TAGTATTTAAATATTTAAA
1 TAGTA-TTAAATATTTAAA
*
1685473 -ATTATTATAATATTTAAA
1 TAGTATTA-AATATTTAAA
*
1685491 TAGTATTAATTA-TTAAA
1 TAGTATTAAATATTTAAA
1685508 T
1 T
1685509 TAATAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.29
18 16 0.52
19 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TAGTATTAAATATTTAAA
Found at i:1685567 original size:18 final size:19
Alignment explanation
Indices: 1685544--1685580 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1685534 TTTTTAAAAT
1685544 ATTTAA-AATTAAA-TATTA
1 ATTTAATAA-TAAACTATTA
1685562 ATTTAATAATAAACTATTA
1 ATTTAATAATAAACTATTA
1685581 TATTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTAATAATAAACTATTA
Found at i:1685638 original size:16 final size:15
Alignment explanation
Indices: 1685598--1685640 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1685588 TTTTGTTCAT
1685598 AATATTTTAATATTA
1 AATATTTTAATATTA
1685613 AATA-TTTAAT-TTA
1 AATATTTTAATATTA
1685626 ATATGATTTTAATAT
1 A-AT-ATTTTAATAT
1685641 AGGATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 5 0.21
16 6 0.25
17 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AATATTTTAATATTA
Found at i:1685664 original size:11 final size:11
Alignment explanation
Indices: 1685648--1685679 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1685638 TATAGGATAT
1685648 TATTTAAATAA
1 TATTTAAATAA
1685659 TATTTAAATAA
1 TATTTAAATAA
*
1685670 TATTTGAATA
1 TATTTAAATA
1685680 TTAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TATTTAAATAA
Found at i:1685725 original size:24 final size:23
Alignment explanation
Indices: 1685695--1685767 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
1685685 TAAAAATTTA
1685695 ATATTATTTTTAAAATTTTTAAT
1 ATATTATTTTTAAAATTTTTAAT
* *
1685718 ATATTTATTATTT-AAATATTTAAA
1 ATA-TTATT-TTTAAAATTTTTAAT
*
1685742 ATATTA-ATTTAATAATATTTTAAT
1 ATATTATTTTTAA-AAT-TTTTAAT
1685766 AT
1 AT
1685768 TTAATAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 9 0.22
24 24 0.60
25 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTATTTTTAAAATTTTTAAT
Found at i:1685745 original size:26 final size:24
Alignment explanation
Indices: 1685698--1685745 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1685688 AAATTTAATA
**
1685698 TTATTTTTAAAATTTTTAATATAT
1 TTATTTTTAAAATTTAAAATATAT
1685722 TTATTATTTAAATATTTAAAATAT
1 TTATT-TTTAAA-ATTTAAAATAT
1685746 TAATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 6 0.30
26 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTTTTAAAATTTAAAATATAT
Found at i:1685771 original size:18 final size:18
Alignment explanation
Indices: 1685656--1685776 Score: 67
Period size: 18 Copynumber: 6.8 Consensus size: 18
1685646 ATTATTTAAA
1685656 TAATATTTAAATAATATTT
1 TAATATTT-AATAATATTT
* * * *
1685675 GAATATTAAATAAAAATT
1 TAATATTTAATAATATTT
** *
1685693 TAATATTATTTTTAAAATTTT
1 TAATA-T-TTAATAATA-TTT
*
1685714 TAATATATT--TATTATTT
1 TAATAT-TTAATAATATTT
*
1685731 AAATATTTAA-AATA--T
1 TAATATTTAATAATATTT
1685746 T-A-ATTTAATAATATTT
1 TAATATTTAATAATATTT
1685762 TAATATTTAATAATA
1 TAATATTTAATAATA
1685777 AATATTAGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
13 6 0.08
14 5 0.06
15 1 0.01
16 4 0.05
17 12 0.15
18 26 0.33
19 7 0.09
20 10 0.13
21 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
TAATATTTAATAATATTT
Found at i:1686075 original size:37 final size:39
Alignment explanation
Indices: 1685991--1686075 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 39
1685981 ATTATTTTAG
* *
1685991 TAATATTTTAATATTATTCAATATTAAAATTTAAATTAA
1 TAATATTTTAATATTAATCAATATTAAAAATTAAATTAA
* *
1686030 T-ATGATTTTATTA-TAAT-AATATTAAAAATT-CATGTAA
1 TAAT-ATTTTAATATTAATCAATATTAAAAATTAAAT-TAA
1686067 TAATATTTT
1 TAATATTTT
1686076 TAAAATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
36 2 0.05
37 21 0.54
38 7 0.18
39 9 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (39 bp):
TAATATTTTAATATTAATCAATATTAAAAATTAAATTAA
Found at i:1686180 original size:29 final size:28
Alignment explanation
Indices: 1686144--1686293 Score: 110
Period size: 29 Copynumber: 5.2 Consensus size: 28
1686134 TGTTATTTAA
*
1686144 ATAATATTTGAATATTTAATATTAAATT
1 ATAATATTTAAATATTTAATATTAAATT
* *
1686172 AGTAGTATTTAAATATTTAAAATT--ATT
1 A-TAATATTTAAATATTTAATATTAAATT
1686199 ATAATATTTAAATAGTATTAATTATTAAATT
1 ATAATATTTAAATA-T-TTAA-TATTAAATT
* * **
1686230 AATAATATTT-AGTATGTAATATTATTTTT
1 -ATAATATTTAAATATTTAATATTA-AATT
* * *
1686259 AAAATATTTTAAA-ATTAAATATTAATTT
1 ATAATA-TTTAAATATTTAATATTAAATT
1686287 AATAATA
1 -ATAATA
1686294 AACTATTATA
Statistics
Matches: 96, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
26 12 0.12
27 5 0.05
28 18 0.19
29 44 0.46
30 2 0.02
31 6 0.06
32 9 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
ATAATATTTAAATATTTAATATTAAATT
Found at i:1686224 original size:18 final size:18
Alignment explanation
Indices: 1686174--1686228 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1686164 ATTAAATTAG
1686174 TAGTATTTAAATATTTAAA
1 TAGTA-TTAAATATTTAAA
*
1686193 -ATTATTATAATATTTAAA
1 TAGTATTA-AATATTTAAA
*
1686211 TAGTATTAATTA-TTAAA
1 TAGTATTAAATATTTAAA
1686228 T
1 T
1686229 TAATAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.29
18 16 0.52
19 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TAGTATTAAATATTTAAA
Found at i:1686359 original size:16 final size:15
Alignment explanation
Indices: 1686319--1686361 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1686309 TTTTGTTCAT
1686319 AATATTTTAATATTA
1 AATATTTTAATATTA
1686334 AATA-TTTAAT-TTA
1 AATATTTTAATATTA
1686347 ATATGATTTTAATAT
1 A-AT-ATTTTAATAT
1686362 AGTATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 5 0.21
16 6 0.25
17 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
AATATTTTAATATTA
Found at i:1686379 original size:721 final size:726
Alignment explanation
Indices: 1684975--1686444 Score: 2817
Period size: 721 Copynumber: 2.0 Consensus size: 726
1684965 TATATATTAA
1684975 TTTAAAATTTTTAATATATTATATTATTTAAATATTTAAAATATTAATTTAATAATATTTTAATA
1 TTTAAAATTTTTAATATATTATATTATTTAAATATTTAAAATATTAATTTAATAATATTTTAATA
1685040 TTTAATAATAAAAAATATTAGTTTCATAATATTTAAATACTTCTTTTTATTTTAATAATTTATTA
66 TTTAATAAT--AAAATATTAGTTTCATAATATTTAAATACTTCTTTTTATTTTAATAATTTATTA
1685105 TTATTAAATATTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCATCTTA
129 TTATTAAATATTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCATCTTA
*
1685170 AATATTTAATTTAATAATTTAATATTTTTAATAATATTTTAATATTCTTTTTTATATTAAATATT
194 AATATTTAATTTAATAATTTAATATTTTTAATAATATTTTAATATTCTTTTTTATATTAAATATG
1685235 TTAATAATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTT
259 TTAATAATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTT
1685300 AAATTTAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTT
324 AAATTTAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTT
1685365 TAAAATTTTAAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATA
389 TAAAATTTTAAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATA
1685430 TTTGAATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGT
454 TTTGAATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGT
1685495 ATTAATTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTAAAATTAAATAT
519 ATTAATTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTAAAATTAAATAT
1685560 TAATTTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTT
584 TAATTTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTT
1685625 AATATGATTTTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAA
649 AATATGATTTTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAA
1685690 ATTTAATATTATT
714 ATTTAATATTATT
1685703 TTTAAAATTTTTAATATATT-TATTATTTAAATATTTAAAATATTAATTTAATAATATTTTAATA
1 TTTAAAATTTTTAATATATTATATTATTTAAATATTTAAAATATTAATTTAATAATATTTTAATA
1685767 TTTAATAAT-AAATATTAGTTTCATAATATTTAAATACTTCTTTTTATTTTAATAATTTATTATT
66 TTTAATAATAAAATATTAGTTTCATAATATTTAAATACTTCTTTTTATTTTAATAATTTATTATT
1685831 ATTAAATATTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCATCTTAAA
131 ATTAAATATTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCATCTTAAA
1685896 TATTTAATTTAATAATTTAATATTTTTAATAATATTTTAATATTC-TTTTTATATTAAATATGTT
196 TATTTAATTTAATAATTTAATATTTTTAATAATATTTTAATATTCTTTTTTATATTAAATATGTT
1685960 AATAATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTTAA
261 AATAATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTTAA
1686025 A-TTAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTT-AAAATATTTTA
326 ATTTAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTTTA
*
1686088 AAATTTTTAAATATTAAATATTATTTTAACAGTA-TTTTATATATTATGTTATTTAAATAATATT
391 AAATTTTAAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATATT
1686152 TGAATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGTAT
456 TGAATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGTAT
1686217 TAATTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTTAAAATTAAATATT
521 TAATTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATA-TTTAAAATTAAATATT
1686282 AATTTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTTA
585 AATTTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTTA
*
1686347 ATATGATTTTAATATAGTATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAAA
650 ATATGATTTTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAAA
1686412 TTTAATATTATT
715 TTTAATATTATT
* * *
1686424 TTTAAAGTTTTAAAAATATTA
1 TTTAAAATTTTTAATATATTA
1686445 AATATTAATT
Statistics
Matches: 734, Mismatches: 6, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
720 143 0.19
721 218 0.30
722 51 0.07
723 84 0.11
724 165 0.22
727 53 0.07
728 20 0.03
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (726 bp):
TTTAAAATTTTTAATATATTATATTATTTAAATATTTAAAATATTAATTTAATAATATTTTAATA
TTTAATAATAAAATATTAGTTTCATAATATTTAAATACTTCTTTTTATTTTAATAATTTATTATT
ATTAAATATTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCATCTTAAA
TATTTAATTTAATAATTTAATATTTTTAATAATATTTTAATATTCTTTTTTATATTAAATATGTT
AATAATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTTAA
ATTTAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTTTA
AAATTTTAAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATATT
TGAATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGTAT
TAATTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTAAAATTAAATATTA
ATTTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTTAA
TATGATTTTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAAAT
TTAATATTATT
Found at i:1686385 original size:11 final size:11
Alignment explanation
Indices: 1686369--1686400 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1686359 TATAGTATAT
1686369 TATTTAAATAA
1 TATTTAAATAA
1686380 TATTTAAATAA
1 TATTTAAATAA
*
1686391 TATTTGAATA
1 TATTTAAATA
1686401 TTAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TATTTAAATAA
Found at i:1686406 original size:18 final size:18
Alignment explanation
Indices: 1686377--1686421 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1686367 ATTATTTAAA
*
1686377 TAATATTTAAAT-AATATT
1 TAATA-TTAAATAAAAATT
1686395 TGAATATTAAATAAAAATT
1 T-AATATTAAATAAAAATT
1686414 TAATATTA
1 TAATATTA
1686422 TTTTTAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATATTAAATAAAAATT
Found at i:1686660 original size:721 final size:719
Alignment explanation
Indices: 1684975--1686662 Score: 2266
Period size: 721 Copynumber: 2.3 Consensus size: 719
1684965 TATATATTAA
* * *
1684975 TTTAAAATTTTTAATATATTATATTATTTAAATATTTAAAATATTAATTTAATAATATTTTAATA
1 TTTAAAATTTTAAAAATATT-TATTATTTAAATATGTAAAATATTAATTTAATAATATTTTAATA
* * * * * * * * *
1685040 TTTAATAATAAAAAATATTAGTTTCATAATATTTAAATACTTCTTTTTATTTTAATAATTTATTA
65 TTTAATAAT---AAATATTAGATTAATAAGAATTAAATACTTATATTAATGTTAATAATTAATTA
* ** * ** * * * ** *
1685105 TTATTAAATATTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCATCTTA
127 ATAAAAAATATTAATTTAATATAATATATTAAATTAATAAGATATGAAAGTCATA--TCATCTTA
* ** * ** *
1685170 AATATTTAATTTAATAATTTAATATTTTTAATAATATTTTAATATTCTTTTTTATATTAAATATT
190 AATATTTAATTAAATAAGATAAAATTTCAAATAATA--TTAATATTC-TTTTTATATTAAATATG
1685235 TTAATAATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTT
252 TTAATAATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTT
1685300 AAATTTAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTT
317 AAATTTAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTT
1685365 TAAAATTTTAAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATA
382 TAAAATTTTAAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATA
1685430 TTTGAATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGT
447 TTTGAATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGT
1685495 ATTAATTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTAAAATTAAATAT
512 ATTAATTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTAAAATTAAATAT
1685560 TAATTTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTT
577 TAATTTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTT
1685625 AATATGATTTTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAA
642 AATATGATTTTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAA
1685690 ATTTAATATTATT
707 ATTTAATATTATT
* * *
1685703 TTTAAAATTTTTAATATATTTATTATTTAAATATTTAAAATATTAATTTAATAATATTTTAATAT
1 TTTAAAATTTTAAAAATATTTATTATTTAAATATGTAAAATATTAATTTAATAATATTTTAATAT
* * * * * * * * * * *
1685768 TTAATAATAAATATTAGTTTCATAATATTTAAATACTTCTTTTTATTTTAATAATTTATTATTAT
66 TTAATAATAAATATTAGATTAATAAGAATTAAATACTTATATTAATGTTAATAATTAATTAATAA
* * ** * * * ** *
1685833 TAAATATTAATTTAATATATTATATTATTTTCATAAGATTTTAGTGTTATATTTCATCTTAAATA
131 AAAATATTAATTTAATATAATATATTAAATTAATAAGATATGAAAGTCATA--TCATCTTAAATA
* ** * **
1685898 TTTAATTTAATAATTTAATATTTTTAATAATATTTTAATATTCTTTTTATATTAAATATGTTAAT
194 TTTAATTAAATAAGATAAAATTTCAAATAATA--TTAATATTCTTTTTATATTAAATATGTTAAT
1685963 AATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTTAAA-T
257 AATAATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTTAAATT
1686027 TAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTT-AAAATATTTTAAAA
322 TAATATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTTTAAAA
*
1686091 TTTTTAAATATTAAATATTATTTTAACAGTA-TTTTATATATTATGTTATTTAAATAATATTTGA
387 TTTTAAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATATTTGA
1686155 ATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGTATTAA
452 ATATTTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGTATTAA
1686220 TTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTTAAAATTAAATATTAAT
517 TTATTAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATA-TTTAAAATTAAATATTAAT
1686285 TTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTTAATA
581 TTAATAATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTTAATA
*
1686350 TGATTTTAATATAGTATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAAATTT
646 TGATTTTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAAATTT
1686415 AATATTATT
711 AATATTATT
* ** *
1686424 TTTAAAGTTTTAAAAATATTAAATATTAATTT-AATA-GTAATTTATT-ATTTAATATTA-TTTA
1 TTTAAAATTTTAAAAATATT---TATT-ATTTAAATATGTAAAATATTAATTTAATAATATTTTA
* * *
1686485 AT-TGTATTAA-AGTAATATTA-ATTAATTACAGAATTAAATA-TTATAATTAATGTTATTTAAT
62 ATATTTAATAATA--AATATTAGATTAA-TA-AGAATTAAATACTTAT-ATTAATGTTA-ATAAT
1686546 TAATTCAAATAAAATAATATTAA-TTAATCATAATA-ATTAGAATTAATTAA-ATATGAAAG-CA
121 TAATT--AATAAAA-AATATTAATTTAAT-ATAATATATTA-AATTAA-TAAGATATGAAAGTCA
*
1686607 TA-CA-CTTGAA-A-TTAATTAAACATACAAGGATAAAATTGTCAAATAA-A-TAATATTCT
180 TATCATCTTAAATATTTAATT-AA-AT--AA-GATAAAATT-TCAAATAATATTAATATTCT
1686663 CAATTCCTGA
Statistics
Matches: 896, Mismatches: 41, Indels: 53
0.91 0.04 0.05
Matches are distributed among these distances:
719 7 0.01
720 154 0.17
721 252 0.28
722 79 0.09
723 101 0.11
724 180 0.20
725 26 0.03
726 21 0.02
727 56 0.06
728 20 0.02
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (719 bp):
TTTAAAATTTTAAAAATATTTATTATTTAAATATGTAAAATATTAATTTAATAATATTTTAATAT
TTAATAATAAATATTAGATTAATAAGAATTAAATACTTATATTAATGTTAATAATTAATTAATAA
AAAATATTAATTTAATATAATATATTAAATTAATAAGATATGAAAGTCATATCATCTTAAATATT
TAATTAAATAAGATAAAATTTCAAATAATATTAATATTCTTTTTATATTAAATATGTTAATAATA
ATTACATATACTATATTATTTTAGTAATATTTTAATATTATTCAATATTAAAATTTAAATTTAAT
ATGATTTTATTATAATAATATTAAAAATTCATGTAATAATATTTTTAAAAATATTTTAAAATTTT
AAAATATTAAATATTATTTTAACAGTATTTTTATATATTATGTTATTTAAATAATATTTGAATAT
TTAATATTAAATTAGTAGTATTTAAATATTTAAAATTATTATAATATTTAAATAGTATTAATTAT
TAAATTAATAATATTTAGTATGTAATATTATTTTTAAAATATTTAAAATTAAATATTAATTTAAT
AATAAACTATTATATTATATTTTGTTCATAATATTTTAATATTAAATATTTAATTTAATATGATT
TTAATATAGGATATTATTTAAATAATATTTAAATAATATTTGAATATTAAATAAAAATTTAATAT
TATT
Found at i:1689610 original size:22 final size:20
Alignment explanation
Indices: 1689583--1689623 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1689573 TGACACAAAT
1689583 AAATATGAAATATATTTTTTTA
1 AAATAT-AAATA-ATTTTTTTA
*
1689605 AAATATATATAATTTTTTT
1 AAATATAAATAATTTTTTT
1689624 GTATCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AAATATAAATAATTTTTTTA
Found at i:1690274 original size:11 final size:11
Alignment explanation
Indices: 1690258--1690292 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1690248 AAAATTTTAA
1690258 TTTATATTATT
1 TTTATATTATT
1690269 TTTATATTATT
1 TTTATATTATT
* *
1690280 TTAATGTTATT
1 TTTATATTATT
1690291 TT
1 TT
1690293 ATTGTATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTATATTATT
Found at i:1690486 original size:19 final size:20
Alignment explanation
Indices: 1690464--1690513 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1690454 AAATATTACA
1690464 TATTTATAAAATTATT-CTT
1 TATTTATAAAATTATTACTT
*
1690483 TATTT-TAAAATTTTTACTT
1 TATTTATAAAATTATTACTT
*
1690502 AATTTA-AAAATT
1 TATTTATAAAATT
1690514 TATAATGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTATAAAATTATTACTT
Found at i:1693762 original size:11 final size:12
Alignment explanation
Indices: 1693724--1693764 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1693714 ACAAATATAT
*
1693724 ATAAATAAATATA
1 ATAATTAAATA-A
1693737 A-AATTAAATAA
1 ATAATTAAATAA
1693748 ATAATTAAA-AA
1 ATAATTAAATAA
1693759 ATAATT
1 ATAATT
1693765 TTTTTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 10 0.38
12 15 0.58
13 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATTAAATAA
Found at i:1695206 original size:28 final size:28
Alignment explanation
Indices: 1695145--1695199 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1695135 ATTTCAAATC
* *
1695145 TTTAAATTGTAACTAAATTCTAAGGATA
1 TTTAAATTGAAACTAAATTCTAAGAATA
*
1695173 TTTAAATTGAAACTAAATTCTTAGAAT
1 TTTAAATTGAAACTAAATTCTAAGAAT
1695200 TCTTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (28 bp):
TTTAAATTGAAACTAAATTCTAAGAATA
Found at i:1702958 original size:16 final size:16
Alignment explanation
Indices: 1702933--1702972 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1702923 GAGAAGGGAA
*
1702933 AAAAAGAAAAGGAAAAT
1 AAAAA-AAAAGAAAAAT
*
1702950 AAAAAAAAATAAAAAT
1 AAAAAAAAAGAAAAAT
1702966 AAAAAAA
1 AAAAAAA
1702973 CTCATCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAT
Found at i:1703091 original size:13 final size:12
Alignment explanation
Indices: 1703072--1703101 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1703062 TCAATTTGAG
1703072 AAAAAAAATTAA
1 AAAAAAAATTAA
1703084 AGAAAAAAATTAA
1 A-AAAAAAATTAA
1703097 AAAAA
1 AAAAA
1703102 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTAA
Found at i:1703701 original size:15 final size:15
Alignment explanation
Indices: 1703681--1703719 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1703671 ATATATAAAT
*
1703681 AAAGAAAAGGAAAAG
1 AAAGAAAAAGAAAAG
1703696 AAAGAAAAAGAAAAG
1 AAAGAAAAAGAAAAG
1703711 AAAGGAAAA
1 AAA-GAAAA
1703720 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAAG
Found at i:1705525 original size:19 final size:19
Alignment explanation
Indices: 1705501--1705538 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1705491 TGATCTATAC
*
1705501 TAATTTGTAAGATATTATT
1 TAATTTGTAAGATACTATT
1705520 TAATTTGTAAGATACTATT
1 TAATTTGTAAGATACTATT
1705539 CTTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (19 bp):
TAATTTGTAAGATACTATT
Found at i:1709864 original size:23 final size:24
Alignment explanation
Indices: 1709810--1709864 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1709800 TTTAAATATA
* *
1709810 TTAAAAA-TTTATTAAAATAACAT
1 TTAAAAATTTTATAAAAATAAAAT
1709833 TTAAAAAATTTTA-AAAAATAAAAT
1 TT-AAAAATTTTATAAAAATAAAAT
1709857 TTAAAAAT
1 TTAAAAAT
1709865 CAATTAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 8 0.29
24 16 0.57
25 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAAAATTTTATAAAAATAAAAT
Found at i:1710216 original size:18 final size:17
Alignment explanation
Indices: 1710195--1710228 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1710185 ATTATATATA
1710195 TTTATATATATACTTAAT
1 TTTATATATATA-TTAAT
*
1710213 TTTATATTTATATTAA
1 TTTATATATATATTAA
1710229 AAAATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATATATATATTAAT
Found at i:1710242 original size:20 final size:20
Alignment explanation
Indices: 1710219--1710260 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1710209 TAATTTTATA
1710219 TTTATATTAAAAAATAATAT
1 TTTATATTAAAAAATAATAT
*
1710239 TTTATATTTAAAAATAATAT
1 TTTATATTAAAAAATAATAT
1710259 TT
1 TT
1710261 CATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATATTAAAAAATAATAT
Found at i:1713005 original size:22 final size:24
Alignment explanation
Indices: 1712960--1713009 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
1712950 TTTAATTTGG
1712960 TTAATCGATTAATTATCAAATTAAT
1 TTAATCGATTAATTA-CAAATTAAT
1712985 TTAATCGATTAA-TA-AAATTAAT
1 TTAATCGATTAATTACAAATTAAT
1713007 TTA
1 TTA
1713010 CAAAAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 11 0.44
24 2 0.08
25 12 0.48
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
TTAATCGATTAATTACAAATTAAT
Found at i:1719725 original size:14 final size:15
Alignment explanation
Indices: 1719690--1719727 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1719680 TTGATAATTA
1719690 CTTAATTTAAAAAAT
1 CTTAATTTAAAAAAT
*
1719705 CTAAATTTAAAAAAT
1 CTTAATTTAAAAAAT
1719720 -TTAATTTA
1 CTTAATTTA
1719728 TCCAAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (15 bp):
CTTAATTTAAAAAAT
Found at i:1719871 original size:660 final size:663
Alignment explanation
Indices: 1718896--1720217 Score: 2188
Period size: 660 Copynumber: 2.0 Consensus size: 663
1718886 ATAAACTAAT
1718896 ATTTACACATGTGATATATCATGAAAAACTTTTTCATATTTAATTTTGAAACTTTATCTAATCAA
1 ATTTACACATGTGATATATCATGAAAAACTTTTTCATATTTAATTTTGAAACTTTATCTAATCAA
1718961 ACTTTTATGATGAAAAAAAGAAAATATCGATTGTGAAAAAATCATAAATATATATTTGATAATTA
66 ACTTTTATGATGAAAAAAAGAAAATATCGATTGTGAAAAAATCATAAATATATATTTGATAATTA
* *
1719026 ATTAATTTTAAAAAATTATAAATTTTTAAAAATTTAGTTTATCCAAGTCTAATTTGAAATTAAGA
131 ATTAATTTTAAAAAATTATAAATTTTAAAAAATTTAATTTATCCAAGTCTAATTTGAAATTAAGA
* * *
1719091 TAAAAGAAGTTAGTATAATTTTAAATTTAGATAGGTGTGCAATTTTAAATTGAGATAAAATATTT
196 TAAAAGAAATTAGTATAATTTTAAATTTAGATAGATGTGCAATTTTAAATTAAGATAAAATATTT
* *
1719156 TTTATTTTAAATTATAAAAAAATAAAAACAAAAAATTGGTAAATAAGAATGGTTCAACCACAAAT
261 TTTATTTTAAATTATAAAAAAATAAAAACAAAAAATTAGTAAATAAGAATGGTTCAACCACAAAA
*
1719221 TTTATTTATTTAAATTTATATAAATATTAATTTAGACTGTGTATAATTTTTTATTCCT-AAAATT
326 TTTATTTATTTAAATTTATATAAATATTAATTTAGACAGTGTATAATTTTTTATT-CTAAAAATT
* *
1719285 TAAGGATTTAATTTTTAAAAATTATTTGAATTGGGTAAGAGTGAAATATGAGAAAATATATTTTA
390 TAAGGATTTAATCTTTAAAAACTATTTGAATTGGGTAAGAGTGAAATATGAGAAAATATATTTTA
* *
1719350 TTAGATTTAAATTAAGATAAATCTTATATATTTTTAAAGACTTTGATAAATATAAATTTTAAAAT
455 TTAGATTTAAATTAAAATAAATCTTATATATTTTTAAAGACTTTAATAAATATAAATTTTAAAAT
1719415 TTTAAAAAATTAAATAATTGATTGAATAAAATTATTTAAAAATATCTTACATGTCAATAATAT-A
520 TTTAAAAAATTAAATAATTGATTGAATAAAATTATTTAAAAATATCTTACATGTCAATAATATAA
* *
1719479 GATTTTTCACATAAGCATCAATATATGCAAATCTTATTAACTTTTTATGTATATTGTAATATAAT
585 G-TTGTTCACATAAGCATCAACATATGCAAATCTTATTAACTTTTTATGTATATTGTAATATAAT
*
1719544 ATTTTATATGATATG
649 ATTATATATGATATG
* ** * **
1719559 ATTTACACATGTGATATATTATGAAAATTTTTTTCATATTTAATTTTGAAACTTTATTTTGTCAA
1 ATTTACACATGTGATATATCATGAAAAACTTTTTCATATTTAATTTTGAAACTTTATCTAATCAA
* * * * *
1719624 TCTTTTATGATGAAAAGAAGAAAATATTGATTGTGAAAAAAATTATAGATATATATTTGATAATT
66 ACTTTTATGATGAAAAAAAGAAAATATCGATTGTG-AAAAAATCATAAATATATATTTGATAATT
* * *
1719689 ACTTAA-TTTAAAAAA-TCTAAA-TTTAAAAAATTTAATTTATCCAAGTTTAATTTGAAATTAAG
130 AATTAATTTTAAAAAATTATAAATTTTAAAAAATTTAATTTATCCAAGTCTAATTTGAAATTAAG
* * *
1719751 ATAAAA-AAATTAGTATTATTTTAAATTTAGATATATGTGTAATTTTAAATTAAGATAAAATATT
195 ATAAAAGAAATTAGTATAATTTTAAATTTAGATAGATGTGCAATTTTAAATTAAGATAAAATATT
* * *
1719815 TTTTATTTTAAATTATAAAAAAATAAAGACAAAATATTAGTAAATAAGAGTGGTTCAACCACAAA
260 TTTTATTTTAAATTATAAAAAAATAAAAACAAAAAATTAGTAAATAAGAATGGTTCAACCACAAA
1719880 ATTTATTTATTTAAATTTATATAAATATTAATTTAGACAGTGTATAATTTTTTATTCTAAAAATT
325 ATTTATTTATTTAAATTTATATAAATATTAATTTAGACAGTGTATAATTTTTTATTCTAAAAATT
1719945 TAAGGATTTAATCTTTAAAAACTATTTGAATTGGGTAAGAGTGAAATATGAGAAAATATATTTTA
390 TAAGGATTTAATCTTTAAAAACTATTTGAATTGGGTAAGAGTGAAATATGAGAAAATATATTTTA
*
1720010 TTAGATTTAAATTAAAATAAATCTTATATATTTTTAAAGACTTTAATAAATGTAAATTTTAAAAT
455 TTAGATTTAAATTAAAATAAATCTTATATATTTTTAAAGACTTTAATAAATATAAATTTTAAAAT
* *
1720075 TTTAAAAAATTAAATAATTGATTGAATAAAATTATTTGAAAATATCTTCCATGTCAATAATATAA
520 TTTAAAAAATTAAATAATTGATTGAATAAAATTATTTAAAAATATCTTACATGTCAATAATATAA
* * * * *
1720140 GTTGTTCACGTAAGTATCCACATATGCAAATTTTATTAATTTTTTATGTATATTGTAATATAATA
585 GTTGTTCACATAAGCATCAACATATGCAAATCTTATTAACTTTTTATGTATATTGTAATATAATA
1720205 TTATATATGATAT
650 TTATATATGATAT
1720218 AAGGTTTTTT
Statistics
Matches: 613, Mismatches: 43, Indels: 9
0.92 0.06 0.01
Matches are distributed among these distances:
659 2 0.00
660 428 0.70
661 46 0.08
662 5 0.01
663 100 0.16
664 32 0.05
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (663 bp):
ATTTACACATGTGATATATCATGAAAAACTTTTTCATATTTAATTTTGAAACTTTATCTAATCAA
ACTTTTATGATGAAAAAAAGAAAATATCGATTGTGAAAAAATCATAAATATATATTTGATAATTA
ATTAATTTTAAAAAATTATAAATTTTAAAAAATTTAATTTATCCAAGTCTAATTTGAAATTAAGA
TAAAAGAAATTAGTATAATTTTAAATTTAGATAGATGTGCAATTTTAAATTAAGATAAAATATTT
TTTATTTTAAATTATAAAAAAATAAAAACAAAAAATTAGTAAATAAGAATGGTTCAACCACAAAA
TTTATTTATTTAAATTTATATAAATATTAATTTAGACAGTGTATAATTTTTTATTCTAAAAATTT
AAGGATTTAATCTTTAAAAACTATTTGAATTGGGTAAGAGTGAAATATGAGAAAATATATTTTAT
TAGATTTAAATTAAAATAAATCTTATATATTTTTAAAGACTTTAATAAATATAAATTTTAAAATT
TTAAAAAATTAAATAATTGATTGAATAAAATTATTTAAAAATATCTTACATGTCAATAATATAAG
TTGTTCACATAAGCATCAACATATGCAAATCTTATTAACTTTTTATGTATATTGTAATATAATAT
TATATATGATATG
Found at i:1720084 original size:24 final size:24
Alignment explanation
Indices: 1720041--1720089 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1720031 TCTTATATAT
*
1720041 TTTTAAAGACTTTAATAAATGTAAA
1 TTTTAAAGACTTTAAAAAAT-TAAA
*
1720066 TTTTAAA-ATTTTAAAAAATTAAA
1 TTTTAAAGACTTTAAAAAATTAAA
1720089 T
1 T
1720090 AATTGATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
TTTTAAAGACTTTAAAAAATTAAA
Found at i:1732972 original size:10 final size:10
Alignment explanation
Indices: 1732953--1732986 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1732943 ATTATTATGT
*
1732953 AAAATATGAA
1 AAAATGTGAA
1732963 AAAATGTGAA
1 AAAATGTGAA
*
1732973 AATATGTGAA
1 AAAATGTGAA
1732983 AAAA
1 AAAA
1732987 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (10 bp):
AAAATGTGAA
Found at i:1746493 original size:15 final size:14
Alignment explanation
Indices: 1746473--1746502 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1746463 TATCATTGTG
1746473 TTTGATAATAGTATA
1 TTTGATAATA-TATA
1746488 TTTGATAATATATA
1 TTTGATAATATATA
1746502 T
1 T
1746503 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
TTTGATAATATATA
Found at i:1761515 original size:18 final size:18
Alignment explanation
Indices: 1761482--1761782 Score: 120
Period size: 19 Copynumber: 15.3 Consensus size: 18
1761472 AAAAAAAAGC
*
1761482 TAAAACATTTTAAAAATTT
1 TAAAA-ATTATAAAAATTT
*
1761501 TAAGAAATTCTAAAAATTT
1 TAA-AAATTATAAAAATTT
1761520 TAAAAATTATAAAATAATTT
1 TAAAAATTAT-AAA-AATTT
* ** *
1761540 TAACAAAATTTTTTGGAAATTG
1 T-A-AAAA--TTATAAAAATTT
* *
1761562 AAAAAATTGTAAAAATTTT
1 TAAAAATTATAAAAA-TTT
*
1761581 TAAAAAATTATAAAACAATCTA
1 T-AAAAATTAT-AAA-AAT-TT
* **
1761603 AAAAAATTATAAATTTTT
1 TAAAAATTATAAAAATTT
* *
1761621 TAAAAAAATTTTAACAATTTT
1 T--AAAAATTATAA-AAATTT
*
1761642 TAAAAATTCTAAAATAATTT
1 TAAAAATTAT-AAA-AATTT
*
1761662 TAGAAAACTT-TAAAAAATT
1 TA-AAAA-TTATAAAAATTT
* **
1761681 AAAAAATTCCGAAAAATTT
1 TAAAAATT-ATAAAAATTT
* *
1761700 TAAAAA-AATCCAAAACTTT
1 TAAAAATTAT--AAAAATTT
*
1761719 TAAAAATTTTAAAAAATTT
1 TAAAAATTAT-AAAAATTT
* *
1761738 TAAAAAATTCTGAAAACTTT
1 T-AAAAATTAT-AAAAATTT
*
1761758 TAAAAATTTTAAAAATTCT
1 TAAAAATTATAAAAATT-T
1761777 TAAAAA
1 TAAAAA
1761783 ATTTCTAAAA
Statistics
Matches: 215, Mismatches: 41, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
17 2 0.01
18 23 0.11
19 86 0.40
20 61 0.28
21 26 0.12
22 13 0.06
23 1 0.00
24 3 0.01
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (18 bp):
TAAAAATTATAAAAATTT
Found at i:1761539 original size:39 final size:38
Alignment explanation
Indices: 1761493--1761813 Score: 207
Period size: 39 Copynumber: 8.1 Consensus size: 38
1761483 AAAACATTTT
*
1761493 AAAAATTTTAAGAAATTCTAAAAATTTTAAAAATTATA
1 AAAAATTTTAAAAAATTCTAAAAATTTTAAAAATTATA
* ** ** *
1761531 AAATAATTTTAACAAAATTTTTTGGAAATTGAAAAAATTGTA
1 AAA-AATTTTAA-AAAA--TTCTAAAAATTTTAAAAATTATA
* * **
1761573 AAAATTTTTAAAAAATTATAAAACAATCTAAAAAAATTAT-
1 AAAAATTTTAAAAAATTCT-AAA-AAT-TTTAAAAATTATA
** * * *
1761613 AAATTTTTTAAAAAAATTTTAACAATTTTTAAAAATTCTA
1 AAAAATTTT-AAAAAATTCTAA-AAATTTTAAAAATTATA
* * * ***
1761653 AAATAATTTTAGAAAACTT-TAAAAAATTAAAAAATTCCG
1 AAA-AATTTTA-AAAAATTCTAAAAATTTTAAAAATTATA
* * * *
1761692 AAAAATTTTAAAAAAATCCAAAACTTTTAAAAATTTTA
1 AAAAATTTTAAAAAATTCTAAAAATTTTAAAAATTATA
* *
1761730 AAAAATTTTAAAAAATTCTGAAAACTTTTAAAAATT-TT
1 AAAAATTTTAAAAAATTCT-AAAAATTTTAAAAATTATA
* * *
1761768 AAAAATTCTTAAAAAATTTCTAAAAATTCTACAAATTTTTA
1 AAAAATT-TTAAAAAA-TTCTAAAAATTTTA-AAAATTATA
1761809 AAAAA
1 AAAAA
1761814 ATAAAAAAAA
Statistics
Matches: 222, Mismatches: 43, Indels: 33
0.74 0.14 0.11
Matches are distributed among these distances:
37 5 0.02
38 51 0.23
39 65 0.29
40 38 0.17
41 43 0.19
42 20 0.09
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (38 bp):
AAAAATTTTAAAAAATTCTAAAAATTTTAAAAATTATA
Found at i:1761549 original size:11 final size:10
Alignment explanation
Indices: 1761482--1761813 Score: 195
Period size: 10 Copynumber: 33.7 Consensus size: 10
1761472 AAAAAAAAGC
*
1761482 TAAAACATTT
1 TAAAAAATTT
1761492 T-AAAAATTT
1 TAAAAAATTT
* *
1761501 TAAGAAATTC
1 TAAAAAATTT
1761511 T-AAAAATTT
1 TAAAAAATTT
*
1761520 T-AAAAATTA
1 TAAAAAATTT
1761529 TAAAATAATTT
1 TAAAA-AATTT
1761540 TAACAAAATTTT
1 TAA-AAAA-TTT
***
1761552 TTGGAAA-TT
1 TAAAAAATTT
* *
1761561 GAAAAAATTG
1 TAAAAAATTT
*
1761571 TAAAAATTTT
1 TAAAAAATTT
*
1761581 TAAAAAATTA
1 TAAAAAATTT
*
1761591 TAAAACAATCT
1 TAAAA-AATTT
* *
1761602 AAAAAAATTA
1 TAAAAAATTT
**
1761612 T-AAATTTTT
1 TAAAAAATTT
1761621 TAAAAAAATTT
1 T-AAAAAATTT
*
1761632 T-AACAATTT
1 TAAAAAATTT
* *
1761641 TTAAAAATTC
1 TAAAAAATTT
1761651 TAAAATAATTT
1 TAAAA-AATTT
* *
1761662 TAGAAAACTT
1 TAAAAAATTT
1761672 TAAAAAA--T
1 TAAAAAATTT
*
1761680 TAAAAAATTC
1 TAAAAAATTT
**
1761690 CGAAAAATTT
1 TAAAAAATTT
*
1761700 TAAAAAA-AT
1 TAAAAAATTT
** *
1761709 CCAAAACTTT
1 TAAAAAATTT
1761719 T-AAAAATTT
1 TAAAAAATTT
1761728 TAAAAAATTT
1 TAAAAAATTT
*
1761738 TAAAAAATTC
1 TAAAAAATTT
* *
1761748 TGAAAACTTT
1 TAAAAAATTT
1761758 T-AAAAATTT
1 TAAAAAATTT
1761767 T-AAAAATTCT
1 TAAAAAATT-T
1761777 TAAAAAATTT
1 TAAAAAATTT
*
1761787 CT-AAAAATTC
1 -TAAAAAATTT
* *
1761797 TACAAATTTT
1 TAAAAAATTT
1761807 TAAAAAA
1 TAAAAAA
1761814 ATAAAAAAAA
Statistics
Matches: 240, Mismatches: 63, Indels: 38
0.70 0.18 0.11
Matches are distributed among these distances:
8 8 0.03
9 71 0.30
10 113 0.47
11 42 0.17
12 6 0.03
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:1761639 original size:22 final size:19
Alignment explanation
Indices: 1761574--1761647 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 19
1761564 AAAATTGTAA
1761574 AAATTTTT-AAAAAATTAT
1 AAATTTTTAAAAAAATTAT
** *
1761592 AAAACAATCTAAAAAAATTAT
1 -AAA-TTTTTAAAAAAATTAT
*
1761613 AAATTTTTTAAAAAAATTTT
1 AAA-TTTTTAAAAAAATTAT
1761633 AACAATTTTTAAAAA
1 -A-AATTTTTAAAAA
1761648 TTCTAAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 17 0.40
21 21 0.49
22 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTTTAAAAAAATTAT
Found at i:1762187 original size:28 final size:28
Alignment explanation
Indices: 1762140--1762195 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1762130 AAGAATGTTT
*
1762140 AAAAATTTTGAAATTATTTAATTTTTTA
1 AAAAATTTTAAAATTATTTAATTTTTTA
1762168 AAAAATTTTAAAAGTT-TTTAATTTTTTA
1 AAAAATTTTAAAA-TTATTTAATTTTTTA
1762196 TTATTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
AAAAATTTTAAAATTATTTAATTTTTTA
Found at i:1762381 original size:19 final size:20
Alignment explanation
Indices: 1762357--1762396 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1762347 TCTTATTTCT
1762357 ATTTTTTATAAATTTT-AAA
1 ATTTTTTATAAATTTTCAAA
*
1762376 ATTTTTTATAATTTTTCAAA
1 ATTTTTTATAAATTTTCAAA
1762396 A
1 A
1762397 AAATTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTTATAAATTTTCAAA
Found at i:1762382 original size:10 final size:10
Alignment explanation
Indices: 1762357--1762450 Score: 59
Period size: 10 Copynumber: 9.5 Consensus size: 10
1762347 TCTTATTTCT
1762357 ATTTTTTATAA
1 ATTTTTTA-AA
1762368 A--TTTTAAA
1 ATTTTTTAAA
*
1762376 ATTTTTTATA
1 ATTTTTTAAA
*
1762386 ATTTTTCAAA
1 ATTTTTTAAA
*** *
1762396 AAAATTTAGA
1 ATTTTTTAAA
*
1762406 ATTTTTTAGA
1 ATTTTTTAAA
*
1762416 ATTGTTTT-GA
1 ATT-TTTTAAA
*
1762426 ATTTTTTAGA
1 ATTTTTTAAA
1762436 ATTTTTTAAA
1 ATTTTTTAAA
*
1762446 CTTTT
1 ATTTT
1762451 GGACAAAATT
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
8 3 0.05
9 9 0.14
10 49 0.74
11 5 0.08
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.57
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:1762427 original size:20 final size:19
Alignment explanation
Indices: 1762404--1762442 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1762394 AAAAAATTTA
1762404 GAATTTTTTAGAATTGTTTT
1 GAATTTTTTAGAATT-TTTT
1762424 GAATTTTTTAGAATTTTTT
1 GAATTTTTTAGAATTTTTT
1762443 AAACTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (19 bp):
GAATTTTTTAGAATTTTTT
Found at i:1762450 original size:20 final size:20
Alignment explanation
Indices: 1762400--1762450 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1762390 TTCAAAAAAA
1762400 TTTAGAATTTTTTAGAATTGT
1 TTTA-AATTTTTTAGAATTGT
*
1762421 TTTGAATTTTTTAGAATT-T
1 TTTAAATTTTTTAGAATTGT
*
1762440 TTTAAACTTTT
1 TTTAAATTTTT
1762451 GGACAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 10 0.37
20 14 0.52
21 3 0.11
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTTTAGAATTGT
Found at i:1762513 original size:19 final size:19
Alignment explanation
Indices: 1762460--1762513 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1762450 TGGACAAAAT
**
1762460 TTAAAATAATTTTGGAATA
1 TTAAAATAATTTTTTAATA
1762479 -TAAAATAATTTTTTTAATA
1 TTAAAATAA-TTTTTTAATA
1762498 TTAAAATAATTTTTTA
1 TTAAAATAATTTTTTA
1762514 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.26
19 15 0.48
20 8 0.26
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
TTAAAATAATTTTTTAATA
Found at i:1762524 original size:20 final size:20
Alignment explanation
Indices: 1762460--1762512 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1762450 TGGACAAAAT
**
1762460 TTAAAATAA-TTTTGGAATA
1 TTAAAATAATTTTTTTAATA
1762479 -TAAAATAATTTTTTTAATA
1 TTAAAATAATTTTTTTAATA
1762498 TTAAAATAATTTTTT
1 TTAAAATAATTTTTT
1762513 ATTTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 8 0.27
19 8 0.27
20 14 0.47
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTAAAATAATTTTTTTAATA
Found at i:1762535 original size:27 final size:26
Alignment explanation
Indices: 1762505--1762567 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
1762495 ATATTAAAAT
*
1762505 AATTTTTTATTTTTTAAAATT-TTTTAG
1 AATTTTTTAGTTTTT-AAATTGTTTT-G
1762532 AATTTTTTAAGTTTTTAAATTGTTTTG
1 AATTTTTT-AGTTTTTAAATTGTTTTG
*
1762559 AAGTTTTTA
1 AATTTTTTA
1762568 AAATTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 1 0.03
27 21 0.66
28 10 0.31
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (26 bp):
AATTTTTTAGTTTTTAAATTGTTTTG
Found at i:1762537 original size:19 final size:19
Alignment explanation
Indices: 1762515--1762656 Score: 89
Period size: 19 Copynumber: 7.5 Consensus size: 19
1762505 AATTTTTTAT
*
1762515 TTTTTAAAATTTTTTAGAA
1 TTTTTAAAATTTTTTAAAA
* *
1762534 TTTTT-TAAGTTTTT-AAA
1 TTTTTAAAATTTTTTAAAA
** *
1762551 TTGTTTTGAAGTTTTTAAAA
1 TT-TTTAAAATTTTTTAAAA
1762571 TTATTTAGAAA--TTTTAGAAA
1 TT-TTTA-AAATTTTTTA-AAA
*
1762591 -TTTTAAAATTTTTAAAAA
1 TTTTTAAAATTTTTTAAAA
** *
1762609 AATTTACAATTTTTTAAAA
1 TTTTTAAAATTTTTTAAAA
* *
1762628 TTTTTAATATTTTTTGAGAA
1 TTTTTAAAATTTTTT-AAAA
1762648 -TTTTAAAAT
1 TTTTTAAAAT
1762657 AAAAAATTTT
Statistics
Matches: 97, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
17 7 0.07
18 17 0.18
19 57 0.59
20 14 0.14
21 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (19 bp):
TTTTTAAAATTTTTTAAAA
Found at i:1762538 original size:11 final size:10
Alignment explanation
Indices: 1762513--1762642 Score: 73
Period size: 10 Copynumber: 13.7 Consensus size: 10
1762503 ATAATTTTTT
1762513 ATTTTTTAAA
1 ATTTTTTAAA
*
1762523 ATTTTTTAGA
1 ATTTTTTAAA
1762533 ATTTTTT--A
1 ATTTTTTAAA
*
1762541 AGTTTTT-AA
1 ATTTTTTAAA
*
1762550 ATTGTTTT-GA
1 ATT-TTTTAAA
*
1762560 AGTTTTTAAA
1 ATTTTTTAAA
*
1762570 ATTATTTAGAA
1 ATTTTTTA-AA
1762581 A--TTTTAGAA
1 ATTTTTTA-AA
1762590 A--TTTTAAA
1 ATTTTTTAAA
1762598 A-TTTTTAAA
1 ATTTTTTAAA
*** *
1762607 AAAATTTACA
1 ATTTTTTAAA
1762617 ATTTTTTAAA
1 ATTTTTTAAA
*
1762627 A-TTTTTAAT
1 ATTTTTTAAA
1762636 ATTTTTT
1 ATTTTTT
1762643 GAGAATTTTA
Statistics
Matches: 96, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
8 10 0.10
9 36 0.38
10 47 0.49
11 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:1762568 original size:27 final size:28
Alignment explanation
Indices: 1762515--1762651 Score: 77
Period size: 28 Copynumber: 4.9 Consensus size: 28
1762505 AATTTTTTAT
*
1762515 TTTTTAAAATTTTTTAGAATTTTTTAAG
1 TTTTTAAAATTTTTTAGAAGTTTTTAAG
*
1762543 TTTTT-AAATTGTTTT-GAAGTTTTTAAAA
1 TTTTTAAAATT-TTTTAGAAGTTTTT-AAG
* * *
1762571 TTATTTAGAAA--TTTTAGAAATTTTAAAA
1 TT-TTTA-AAATTTTTTAGAAGTTTTTAAG
*** * * *
1762599 TTTTTAAAAAAATTTACAATTTTTTAAAA
1 TTTTTAAAATTTTTTAGAAGTTTTT-AAG
*
1762628 TTTTTAATATTTTTTGAGAA-TTTT
1 TTTTTAAAATTTTTT-AGAAGTTTT
1762652 AAAATAAAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
26 3 0.03
27 17 0.20
28 32 0.37
29 28 0.33
30 3 0.03
31 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (28 bp):
TTTTTAAAATTTTTTAGAAGTTTTTAAG
Found at i:1762599 original size:8 final size:9
Alignment explanation
Indices: 1762515--1762641 Score: 87
Period size: 9 Copynumber: 13.6 Consensus size: 9
1762505 AATTTTTTAT
1762515 TTTTTAAAA
1 TTTTTAAAA
*
1762524 TTTTTTAGAA
1 -TTTTTAAAA
* *
1762534 TTTTTTAAG
1 TTTTTAAAA
*
1762543 TTTTTAAAT
1 TTTTTAAAA
* *
1762552 TGTTTTGAAG
1 T-TTTTAAAA
1762562 TTTTTAAAA
1 TTTTTAAAA
1762571 TTATTTAGAAA
1 TT-TTTA-AAA
1762582 -TTTTAGAAA
1 TTTTTA-AAA
1762591 -TTTTAAAA
1 TTTTTAAAA
1762599 TTTTTAAAAA
1 TTTTT-AAAA
** *
1762609 AATTTACAAT
1 TTTTTA-AAA
1762619 TTTTTAAAA
1 TTTTTAAAA
*
1762628 TTTTTAATA
1 TTTTTAAAA
1762637 TTTTT
1 TTTTT
1762642 TGAGAATTTT
Statistics
Matches: 94, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
8 3 0.03
9 55 0.59
10 33 0.35
11 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:1762614 original size:28 final size:29
Alignment explanation
Indices: 1762563--1762634 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
1762553 GTTTTGAAGT
* * *
1762563 TTTTAAAATTATTT-AGAAATTTTAGAA-A
1 TTTTAAAATT-TTTAAAAAAATTTACAATA
*
1762591 TTTTAAAATTTTTAAAAAAATTTACAATT
1 TTTTAAAATTTTTAAAAAAATTTACAATA
1762620 TTTTAAAATTTTTAA
1 TTTTAAAATTTTTAA
1762635 TATTTTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.08
28 20 0.53
29 15 0.39
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (29 bp):
TTTTAAAATTTTTAAAAAAATTTACAATA
Found at i:1762614 original size:37 final size:38
Alignment explanation
Indices: 1762544--1762641 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 38
1762534 TTTTTTAAGT
* * * ** *
1762544 TTTTAAATTGTTTTGAAGTTTTTAAAATTATTTAGAA-A
1 TTTTAAAAT-TTTTAAAATTTTTAAAAAAATTTACAATA
*
1762582 TTTTAGAAA-TTTTAAAATTTTTAAAAAAATTTACAATT
1 TTTTA-AAATTTTTAAAATTTTTAAAAAAATTTACAATA
*
1762620 TTTTAAAATTTTTAATATTTTT
1 TTTTAAAATTTTTAAAATTTTT
1762642 TGAGAATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
37 25 0.51
38 22 0.45
39 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (38 bp):
TTTTAAAATTTTTAAAATTTTTAAAAAAATTTACAATA
Found at i:1762691 original size:19 final size:19
Alignment explanation
Indices: 1762663--1762716 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1762653 AAATAAAAAA
1762663 TTTTAGAAAATTTTTGACTT
1 TTTTA-AAAATTTTTGACTT
*
1762683 TTTTAAAAACTTTTTGATTT
1 TTTTAAAAA-TTTTTGACTT
**
1762703 TTTTCTAAATTTTT
1 TTTTAAAAATTTTT
1762717 CTTTTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (19 bp):
TTTTAAAAATTTTTGACTT
Found at i:1771434 original size:2 final size:2
Alignment explanation
Indices: 1771427--1771451 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1771417 TGAAATGGTT
1771427 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1771452 GGAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1778744 original size:35 final size:35
Alignment explanation
Indices: 1778698--1778769 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
1778688 CATTAATACG
*
1778698 ATTTTAGTGCTTTATGATAGAAAATTAGACCAGGA
1 ATTTTAATGCTTTATGATAGAAAATTAGACCAGGA
1778733 ATTTTAATGCTTTATGATAGAAAATTAGACCAGGA
1 ATTTTAATGCTTTATGATAGAAAATTAGACCAGGA
1778768 AT
1 AT
1778770 GATGCTTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (35 bp):
ATTTTAATGCTTTATGATAGAAAATTAGACCAGGA
Found at i:1788603 original size:13 final size:13
Alignment explanation
Indices: 1788580--1788617 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
1788570 TATGTTATGC
1788580 TTTAA-ATTTTTT
1 TTTAATATTTTTT
1788592 TTTAATATTTTTT
1 TTTAATATTTTTT
1788605 TTTAATCATTTTT
1 TTTAAT-ATTTTT
1788618 AACATAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.21
13 13 0.54
14 6 0.25
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTAATATTTTTT
Found at i:1789406 original size:26 final size:25
Alignment explanation
Indices: 1789371--1789431 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
1789361 GTAGATATTG
1789371 ATTTCAATTTAAATAA-TTATCTAAAA
1 ATTT-AATTTAAATAATTTAT-TAAAA
1789397 TATTTAATTTAAATAATTTATTAAAA
1 -ATTTAATTTAAATAATTTATTAAAA
*
1789423 ATTTTATTT
1 ATTTAATTT
1789432 GATAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 8 0.25
26 16 0.50
27 8 0.25
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTAATTTAAATAATTTATTAAAA
Found at i:1791091 original size:114 final size:113
Alignment explanation
Indices: 1790923--1791149 Score: 391
Period size: 114 Copynumber: 2.0 Consensus size: 113
1790913 CAATTATTAC
* * *
1790923 CAATCTGTGTATTAATGGGATGGAAGTTGGTCTGGTTTCGCGTTGGCAGTTGCAACAATTGATTT
1 CAATCTGTGTATTAATGGAATGGAAGTTGGTCTGGTTGCGCGTTGGCAGTTGCAACAACTGATTT
1790988 TTCCATTAATTTTGGTTTTGATGGGCCAATGAAAGTTGCAGGGATGAA
66 TTCCATTAATTTTGGTTTTGATGGGCCAATGAAAGTTGCAGGGATGAA
* * *
1791036 CAATCTGTGTGTTAATGGAATGGAAGTTGGGTCTGGTTGGGTGTTGGCAGTTGCAACAACTGATT
1 CAATCTGTGTATTAATGGAATGGAAGTT-GGTCTGGTTGCGCGTTGGCAGTTGCAACAACTGATT
1791101 TTTCCATTAATTTTGGTTTTGATGGGCCAATGAAAGTTGCAGGGATGAA
65 TTTCCATTAATTTTGGTTTTGATGGGCCAATGAAAGTTGCAGGGATGAA
1791150 GTAGATGATT
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 26 0.24
114 81 0.76
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.36
Consensus pattern (113 bp):
CAATCTGTGTATTAATGGAATGGAAGTTGGTCTGGTTGCGCGTTGGCAGTTGCAACAACTGATTT
TTCCATTAATTTTGGTTTTGATGGGCCAATGAAAGTTGCAGGGATGAA
Found at i:1792444 original size:21 final size:21
Alignment explanation
Indices: 1792420--1792482 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1792410 TATAAGACCT
* *
1792420 CACAACAGCTTCCAGTTCAAA
1 CACAACAGCTTTCAGCTCAAA
*
1792441 CACAACAGCTTTCAGCTCAAT
1 CACAACAGCTTTCAGCTCAAA
1792462 CACAACAGCTTTCAGCTCAAA
1 CACAACAGCTTTCAGCTCAAA
1792483 AAATATTGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.21
Consensus pattern (21 bp):
CACAACAGCTTTCAGCTCAAA
Found at i:1796906 original size:51 final size:51
Alignment explanation
Indices: 1796846--1796955 Score: 175
Period size: 51 Copynumber: 2.2 Consensus size: 51
1796836 GCAGAGCTGA
* * *
1796846 AGCTGAAGAATGATGTTAATATTGAGGACTTAAAATTAATAAAAGACATTG
1 AGCTGAAGAATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTG
* *
1796897 AGCTGAAGAATGATGTTAATGTTAAGGACTTAAAATTAGCAAAAGACAGTG
1 AGCTGAAGAATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTG
1796948 AGCTGAAG
1 AGCTGAAG
1796956 CTAAAAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (51 bp):
AGCTGAAGAATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTG
Found at i:1798075 original size:15 final size:15
Alignment explanation
Indices: 1798051--1798084 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1798041 TTTGAAGGAA
1798051 GAAAGCTAAATAGAT
1 GAAAGCTAAATAGAT
* *
1798066 GAAAGTTAAATCGAT
1 GAAAGCTAAATAGAT
1798081 GAAA
1 GAAA
1798085 ACATATGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21
Consensus pattern (15 bp):
GAAAGCTAAATAGAT
Found at i:1804054 original size:391 final size:390
Alignment explanation
Indices: 1803304--1804082 Score: 1326
Period size: 391 Copynumber: 2.0 Consensus size: 390
1803294 TTTAATGACA
** *
1803304 TGGTTTTATCTAGGCAGTTCTATGACTCCAGCACTGAGTTACCTGTACTTAAGCTGGTTCTTTTA
1 TGGTTTTATCTAGGCAGTTCTATGACTCCAGCACCAAGTTACCTGTACTTAAACTGGTTCTTTTA
*
1803369 ACCTACAGAGATGTGCAAGATCAAGTAGAAGTGTAACATGGGCATTTTAAACAAACCCTAGATGT
66 ACCTACAGAGATGTCCAAGATCAAGTAGAAGTGTAACATGGGCATTTTAAACAAACCCTAGATGT
1803434 TAGATTCAAACACATCTAAACCTAAATACTTTAAAGATCCAAGCCCAAAGTGAGTAGACTTTGGG
131 TAGATTCAAACACATCTAAACCTAAATACTTTAAAGATCCAAGCCCAAAGTGAGTAGACTTTGGG
*
1803499 AATGGAGTCATTTCTATGTGCACAATTGTGTGTTTTTGCACATGCTAGTGTATGCATTCATATTT
196 AATGGAGTCATTTCCATGTGCACAATTGTGTGTTTTTGCACATGCTAGTGTATGCATTCATATTT
** * * *
1803564 CAATATTGTATATTCTTGTGTTTGTGTCACAGAGACAGAGGTTGGAATATGGTCATCTGAGGCAA
261 CAATATTGTATATTCTTACGTTTGTGTCACAGAGACAAACGTTGGAATATGGGCATCTGAGGCAA
1803629 TTAATAGTATATATAGGCATACACTAGCGTACCCTTGTTAATTGGAACTTGACCTTTTGTTTGTT
326 TTAATAGTATATATAGGCATACACTAGCGTACCCTTGTTAATTGGAACTTGACCTTTTGTTTGTT
*
1803694 TGGTTTTATCTAGGCAGTTCTATGACTCCAGCACCAAGTTACCTGTACTTAAACTGGTTCTTTTT
1 TGGTTTTATCTAGGCAGTTCTATGACTCCAGCACCAAGTTACCTGTACTTAAACTGGTTCTTTTA
*
1803759 ACCTACAGAGATGTCCAAGATCAAGTAGAAGTGTAACATGGGTATTTTAAACAAACCCTAGATGT
66 ACCTACAGAGATGTCCAAGATCAAGTAGAAGTGTAACATGGGCATTTTAAACAAACCCTAGATGT
* *
1803824 TAGATTCAAACACATCTAAACTTAAATACTTTTAAAGATCCAAGGCCAAAGTGAGTAGAC-TTGG
131 TAGATTCAAACACATCTAAACCTAAATAC-TTTAAAGATCCAAGCCCAAAGTGAGTAGACTTTGG
*
1803888 AGAATGGAGTCATTTCCATGTGCATAATTGTGTGTTTTTGCACATGCTAGTGTATGCATTCATAT
195 -GAATGGAGTCATTTCCATGTGCACAATTGTGTGTTTTTGCACATGCTAGTGTATGCATTCATAT
* * * *
1803953 TTCAATATTGTATATTCTTACGTTTGTGTCGCCGAGACAAACTTTGGCATATGGGCATCTGAGGC
259 TTCAATATTGTATATTCTTACGTTTGTGTCACAGAGACAAACGTTGGAATATGGGCATCTGAGGC
* * * *
1804018 AATTAGTAGTGTATTTAGGCATACACTAGTGTACCCTTGTTAATTGGAACTTGACCTTTTGTTTG
324 AATTAATAGTATATATAGGCATACACTAGCGTACCCTTGTTAATTGGAACTTGACCTTTTGTTTG
1804083 GTATCTGTAT
Statistics
Matches: 364, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
390 156 0.43
391 208 0.57
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (390 bp):
TGGTTTTATCTAGGCAGTTCTATGACTCCAGCACCAAGTTACCTGTACTTAAACTGGTTCTTTTA
ACCTACAGAGATGTCCAAGATCAAGTAGAAGTGTAACATGGGCATTTTAAACAAACCCTAGATGT
TAGATTCAAACACATCTAAACCTAAATACTTTAAAGATCCAAGCCCAAAGTGAGTAGACTTTGGG
AATGGAGTCATTTCCATGTGCACAATTGTGTGTTTTTGCACATGCTAGTGTATGCATTCATATTT
CAATATTGTATATTCTTACGTTTGTGTCACAGAGACAAACGTTGGAATATGGGCATCTGAGGCAA
TTAATAGTATATATAGGCATACACTAGCGTACCCTTGTTAATTGGAACTTGACCTTTTGTTTGTT
Found at i:1807024 original size:179 final size:180
Alignment explanation
Indices: 1806715--1807043 Score: 534
Period size: 179 Copynumber: 1.8 Consensus size: 180
1806705 GAAGATTCAT
* *
1806715 TTTTTTGATGTTTGGCCTTTTTGTTCCTTCATCATAAGGCAAAAACCATTCATTCATTTATCTTT
1 TTTTTTGATGTTTGCCCTTTTTG---CTTCATCATAAGGCAAAAACCATTCATTCATTTACCTTT
* *
1806780 TAGGCGTAGGGGTCCTGATTTGATGCTTCATGGACAGATAACTACCACCCATATTTGGCGCCTTT
63 TAGGCATAGGGGTCCAGATTTGATGCTTCATGGACAGATAACTACCACCCATATTTGGCGCCTTT
1806845 TAAAAATTGAAAAGAAAAAACTTTTTATATGGATACTATAAAGGTGAGTTGCA
128 TAAAAATTGAAAAGAAAAAACTTTTTATATGGATACTATAAAGGTGAGTTGCA
* * *
1806898 TTTTTTGCTGTTTGCCCTTTTTG-TTCATCATAATGTAAAAACCATTCATTCATTTACCTTTTAG
1 TTTTTTGATGTTTGCCCTTTTTGCTTCATCATAAGGCAAAAACCATTCATTCATTTACCTTTTAG
* * *
1806962 GCATGGGGGTTCAGATTTGATGCTTCATGGACAGATAACTACCACCCATATTTGGTGCCTTTTAA
66 GCATAGGGGTCCAGATTTGATGCTTCATGGACAGATAACTACCACCCATATTTGGCGCCTTTTAA
1807027 AAATTGAAAAGAAAAAA
131 AAATTGAAAAGAAAAAA
1807044 AAAATATTTT
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
179 115 0.85
183 21 0.15
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (180 bp):
TTTTTTGATGTTTGCCCTTTTTGCTTCATCATAAGGCAAAAACCATTCATTCATTTACCTTTTAG
GCATAGGGGTCCAGATTTGATGCTTCATGGACAGATAACTACCACCCATATTTGGCGCCTTTTAA
AAATTGAAAAGAAAAAACTTTTTATATGGATACTATAAAGGTGAGTTGCA
Found at i:1816756 original size:3 final size:3
Alignment explanation
Indices: 1816748--1816779 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1816738 GGTTTTGATT
1816748 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1816780 ATGCCAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1819754 original size:19 final size:19
Alignment explanation
Indices: 1819716--1819754 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1819706 TATATATTTA
*
1819716 AAAAATAAAAAATTAAATC
1 AAAAATAAAAAAATAAATC
*
1819735 AAAAATAAAAAAATATATC
1 AAAAATAAAAAAATAAATC
1819754 A
1 A
1819755 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATAAAAAAATAAATC
Found at i:1820522 original size:22 final size:21
Alignment explanation
Indices: 1820472--1820522 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
1820462 ATCAACTCAC
1820472 TCACTTAA-TAATGCAAACAT
1 TCACTTAATTAATGCAAACAT
* *
1820492 T-A-TTCATTAATGCACACACT
1 TCACTTAATTAATGCAAACA-T
1820512 TCACTTAATTA
1 TCACTTAATTA
1820523 TATATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.12
19 11 0.46
20 3 0.12
21 1 0.04
22 6 0.25
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (21 bp):
TCACTTAATTAATGCAAACAT
Found at i:1826467 original size:105 final size:105
Alignment explanation
Indices: 1826206--1826536 Score: 357
Period size: 105 Copynumber: 3.1 Consensus size: 105
1826196 TTATGATTAT
* * * *
1826206 TTATTATGTTTCTTTGAACAAAAATGTAGTATTTAACAATTCGT-ATTTTTTTATTTGTTTGACT
1 TTATTGTGTTTCTTTGAACAAAAATGTAGTATTTGA-AATT--TAATTTTTTTATCTATTTGACT
* * *
1826270 TGATGATTTTTTATTTAATAAGCATTTATTAT-GGTTACGACAA
63 TGATGATTTTTGATTTAATAAACATTTATTATAGG-TATGACAA
** * *
1826313 TTATTGTGTTTCTTTGAACAAAAATGTAGTATTTGGCATGTAATATTTTTCATCTATTTGACTTG
1 TTATTGTGTTTCTTTGAACAAAAATGTAGTATTTGAAATTTAAT-TTTTTTATCTATTTGACTTG
* *
1826378 ATGACTTTTGATTTAATAAACATTT-TTATAGGTATGGCAA
65 ATGATTTTTGATTTAATAAACATTTATTATAGGTATGACAA
* * * * * * **
1826418 CTACTGTGTTTCTTTGAATAAAAATGCAGTATTTGATATTTAATTTTTTTATCTTATTT-TC-AA
1 TTATTGTGTTTCTTTGAACAAAAATGTAGTATTTGAAATTTAATTTTTTTATC-TATTTGACTTG
* *
1826481 ATGGTTTTTGATTTAATAAACATTTATTATAAGTATGACAA
65 ATGATTTTTGATTTAATAAACATTTATTATAGGTATGACAA
*
1826522 TTATTATGTTTCTTT
1 TTATTGTGTTTCTTT
1826537 AAAGTTAAAC
Statistics
Matches: 188, Mismatches: 31, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
103 23 0.12
104 35 0.19
105 54 0.29
106 43 0.23
107 33 0.18
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (105 bp):
TTATTGTGTTTCTTTGAACAAAAATGTAGTATTTGAAATTTAATTTTTTTATCTATTTGACTTGA
TGATTTTTGATTTAATAAACATTTATTATAGGTATGACAA
Found at i:1826804 original size:12 final size:12
Alignment explanation
Indices: 1826780--1826816 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1826770 CTTATATATA
1826780 TAATTATTT-TT
1 TAATTATTTATT
1826791 TAATTATTTATT
1 TAATTATTTATT
1826803 TAATT-TTATATT
1 TAATTATT-TATT
1826815 TA
1 TA
1826817 TATTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTATTTATT
Found at i:1826816 original size:16 final size:15
Alignment explanation
Indices: 1826783--1826856 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 15
1826773 ATATATATAA
* *
1826783 TTATTTTTTAATTAT
1 TTATTTTATATTTAT
* *
1826798 TTATTTAATTTTATAT
1 TTATTTTATATT-TAT
1826814 TTATATTTATA--TAT
1 TTAT-TTTATATTTAT
1826828 TT-TTTTATATTTAT
1 TTATTTTATATTTAT
*
1826842 TTAAGTTTATATTTA
1 TT-ATTTTATATTTA
1826857 CATTAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 6 0.13
13 1 0.02
14 10 0.22
15 8 0.17
16 17 0.37
17 4 0.09
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (15 bp):
TTATTTTATATTTAT
Found at i:1826842 original size:14 final size:14
Alignment explanation
Indices: 1826778--1826843 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 14
1826768 ACCTTATATA
*
1826778 TATAATTATTTTTT
1 TATATTTATTTTTT
*
1826792 AATTATTTATTTAATTT
1 TA-TATTTATTT--TTT
*
1826809 TATATTTA--TATT
1 TATATTTATTTTTT
1826821 TATA--TATTTTTT
1 TATATTTATTTTTT
1826833 TATATTTATTT
1 TATATTTATTT
1826844 AAGTTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
10 2 0.05
12 13 0.32
14 7 0.17
15 8 0.20
16 6 0.15
17 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATTTATTTTTT
Found at i:1826873 original size:18 final size:18
Alignment explanation
Indices: 1826850--1826892 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1826840 ATTTAAGTTT
1826850 ATATTTACA-TTAAAAATA
1 ATATTTACATTTAAAAA-A
*
1826868 ATATTTTATATTTAAAAAA
1 ATA-TTTACATTTAAAAAA
1826887 ATATTT
1 ATATTT
1826893 TATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTACATTTAAAAAA
Found at i:1826903 original size:22 final size:20
Alignment explanation
Indices: 1826859--1826895 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
1826849 TATATTTACA
1826859 TTAAAAATAATATTTTATAT
1 TTAAAAATAATATTTTATAT
1826879 TTAAAAA-AATATTTTAT
1 TTAAAAATAATATTTTAT
1826896 TAATTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAAAATAATATTTTATAT
Found at i:1827630 original size:27 final size:28
Alignment explanation
Indices: 1827570--1827634 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
1827560 AAAAAGTTGA
1827570 AAATT-TTTTTAAAAAAAATTAATATTT
1 AAATTATTTTTAAAAAAAATTAATATTT
* *
1827597 TAA-TATTTTTAAATAAACATTAA-A-TT
1 AAATTATTTTTAAA-AAAAATTAATATTT
1827623 AAATTATTTTTA
1 AAATTATTTTTA
1827635 TTAATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 5 0.16
27 19 0.59
28 8 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
AAATTATTTTTAAAAAAAATTAATATTT
Found at i:1835523 original size:18 final size:18
Alignment explanation
Indices: 1835500--1835540 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1835490 TAACCTTCGA
1835500 CCTTAGCTTGGCAACTCC
1 CCTTAGCTTGGCAACTCC
*
1835518 CCTTAGCTTGGTAACTCC
1 CCTTAGCTTGGCAACTCC
*
1835536 ACTTA
1 CCTTA
1835541 AGCCTCATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.34, G:0.15, T:0.32
Consensus pattern (18 bp):
CCTTAGCTTGGCAACTCC
Found at i:1840739 original size:54 final size:54
Alignment explanation
Indices: 1840647--1840757 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
1840637 GAAAATAAGA
* * * *
1840647 AGTATGTGCAACAGGTTATGGATTTGTTAAATCCAAAGAGAGCATCGCAAGCTC
1 AGTATGTGCAACAGGTTATAGATTTGTTAAATCCAAAGAAAACATCACAAGCTC
* *
1840701 AGTATGTGCAACAGGTTATAGATTTGTTGAATCTAAAGAAAACATCACAAGCTC
1 AGTATGTGCAACAGGTTATAGATTTGTTAAATCCAAAGAAAACATCACAAGCTC
1840755 AGT
1 AGT
1840758 CGAAGCCAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (54 bp):
AGTATGTGCAACAGGTTATAGATTTGTTAAATCCAAAGAAAACATCACAAGCTC
Found at i:1841968 original size:13 final size:13
Alignment explanation
Indices: 1841950--1841976 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1841940 CTTTCCATCA
1841950 CTATCCATTTTAT
1 CTATCCATTTTAT
1841963 CTATCCATTTTAT
1 CTATCCATTTTAT
1841976 C
1 C
1841977 GCAAATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (13 bp):
CTATCCATTTTAT
Found at i:1849450 original size:24 final size:24
Alignment explanation
Indices: 1849418--1849487 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
1849408 TTAATCATAG
*
1849418 AAAATAATATTTTTTAATATA-AA
1 AAAATAATATTTTTTAAAATACAA
*
1849441 AAATATAATATTTGTTGAAAATACAA
1 AAA-ATAATATTT-TTTAAAATACAA
*
1849467 AAAAAATATATTTTTTAAAAT
1 AAAATA-ATATTTTTTAAAAT
1849488 TCAACAACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.08
24 9 0.23
25 16 0.41
26 11 0.28
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (24 bp):
AAAATAATATTTTTTAAAATACAA
Found at i:1849463 original size:27 final size:25
Alignment explanation
Indices: 1849433--1849487 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
1849423 AATATTTTTT
* *
1849433 AATATAAAAAATATAATATTTGTTGAA
1 AATACAAAAAAAAT-ATATTT-TTGAA
*
1849460 AATACAAAAAAAATATATTTTTTAA
1 AATACAAAAAAAATATATTTTTGAA
1849485 AAT
1 AAT
1849488 TCAACAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
27 12 0.48
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (25 bp):
AATACAAAAAAAATATATTTTTGAA
Found at i:1849598 original size:20 final size:20
Alignment explanation
Indices: 1849573--1849645 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
1849563 TTAGAATTTA
1849573 ATAAAAACAATGTTTATAAG
1 ATAAAAACAATGTTTATAAG
* * *
1849593 ATAAAAAACATAATCTTTGT-TG
1 AT-AAAAAC--AATGTTTATAAG
*
1849615 A-AAAAATAATGTTTATAAG
1 ATAAAAACAATGTTTATAAG
1849634 ATAAAAGACAAT
1 ATAAAA-ACAAT
1849646 CTTTGTTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
18 7 0.18
19 2 0.05
20 11 0.28
21 10 0.26
22 2 0.05
23 7 0.18
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (20 bp):
ATAAAAACAATGTTTATAAG
Found at i:1849601 original size:21 final size:21
Alignment explanation
Indices: 1849575--1849645 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1849565 AGAATTTAAT
1849575 AAAAACAATGTTTATAAGATA
1 AAAAACAATGTTTATAAGATA
* * *
1849596 AAAAACATAATCTTTGT-TG--A
1 AAAAAC--AATGTTTATAAGATA
*
1849616 AAAAATAATGTTTATAAGATA
1 AAAAACAATGTTTATAAGATA
*
1849637 AAAGACAAT
1 AAAAACAAT
1849646 CTTTGTTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 6 0.17
21 14 0.39
22 1 0.03
23 7 0.19
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAACAATGTTTATAAGATA
Found at i:1849626 original size:41 final size:39
Alignment explanation
Indices: 1849575--1849735 Score: 139
Period size: 39 Copynumber: 4.1 Consensus size: 39
1849565 AGAATTTAAT
1849575 AAAAACAATGTTTATAAGATAAAAAACATAATCTTTGTTGA
1 AAAAACAATGTTTATAAGAT-AAAAACATAATCTTTGTT-A
*
1849616 AAAAATAATGTTTATAAGATAAAAGAC--AATCTTTGTTTA
1 AAAAACAATGTTTATAAGATAAAA-ACATAATCTTTG-TTA
* * * * * * * *
1849655 AACAACAATGTTTCTCATATGAAAACATAGTTTTTATTA
1 AAAAACAATGTTTATAAGATAAAAACATAATCTTTGTTA
* * * *
1849694 AAAAGATAATATTTTTAAGATAAAAATATAAT-TTTGTTA
1 AAAA-ACAATGTTTATAAGATAAAAACATAATCTTTGTTA
1849733 AAA
1 AAA
1849736 GTATAAAAAT
Statistics
Matches: 95, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
38 2 0.02
39 42 0.44
40 30 0.32
41 21 0.22
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (39 bp):
AAAAACAATGTTTATAAGATAAAAACATAATCTTTGTTA
Found at i:1849665 original size:39 final size:39
Alignment explanation
Indices: 1849574--1849667 Score: 127
Period size: 41 Copynumber: 2.4 Consensus size: 39
1849564 TAGAATTTAA
1849574 TAAAAACAATGTTTATAAGATAAAAAACATAATCTTTGTT
1 TAAAAACAATGTTTATAAGATAAAAAACA-AATCTTTGTT
* * *
1849614 GAAAAAATAATGTTTATAAGATAAAAGAC-AATCTTTGTT
1 -TAAAAACAATGTTTATAAGATAAAAAACAAATCTTTGTT
1849653 TAAACAACAATGTTT
1 TAAA-AACAATGTTT
1849668 CTCATATGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.06
39 19 0.40
41 25 0.53
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (39 bp):
TAAAAACAATGTTTATAAGATAAAAAACAAATCTTTGTT
Found at i:1849724 original size:22 final size:24
Alignment explanation
Indices: 1849692--1849748 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 24
1849682 TAGTTTTTAT
*
1849692 TAAAAAGATAATATTT-TT-AAG-A
1 TAAAAATATAAT-TTTGTTAAAGTA
1849714 TAAAAATATAATTTTGTTAAAAGTA
1 TAAAAATATAATTTTGTT-AAAGTA
1849739 TAAAAATATA
1 TAAAAATATA
1849749 TGTTTTTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.10
22 13 0.43
24 3 0.10
25 11 0.37
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (24 bp):
TAAAAATATAATTTTGTTAAAGTA
Found at i:1855109 original size:25 final size:25
Alignment explanation
Indices: 1855075--1855125 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1855065 AATTCTACCA
1855075 AACCAAGAAGGAAAAATAATCAATT
1 AACCAAGAAGGAAAAATAATCAATT
1855100 AACCAAGAAGGAAAAATAATCAATT
1 AACCAAGAAGGAAAAATAATCAATT
1855125 A
1 A
1855126 GCAGACTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.16
Consensus pattern (25 bp):
AACCAAGAAGGAAAAATAATCAATT
Found at i:1856638 original size:24 final size:24
Alignment explanation
Indices: 1856611--1856656 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1856601 TCAAATTATC
1856611 ATGTATATTTAAATTTTTATAATT
1 ATGTATATTTAAATTTTTATAATT
*
1856635 ATGTATATTTGAATTTTTATAA
1 ATGTATATTTAAATTTTTATAA
1856657 ATTTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (24 bp):
ATGTATATTTAAATTTTTATAATT
Found at i:1856666 original size:24 final size:23
Alignment explanation
Indices: 1856615--1856675 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
1856605 ATTATCATGT
**
1856615 ATATTTAAATTTTTATAATTATGT
1 ATATTT-AATTTTTATAATTATAA
1856639 ATATTTGAATTTTTATAAATT-TAA
1 ATATTT-AATTTTTAT-AATTATAA
1856663 ATATTT-ATTTTTA
1 ATATTTAATTTTTA
1856676 ATTGATAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 7 0.21
24 22 0.67
25 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (23 bp):
ATATTTAATTTTTATAATTATAA
Found at i:1857836 original size:18 final size:18
Alignment explanation
Indices: 1857815--1857849 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1857805 AGATTGCAGG
1857815 TGAT-AAACCTCAATGATA
1 TGATAAAACCT-AATGATA
1857833 TGATAAAACCTAATGAT
1 TGATAAAACCTAATGAT
1857850 GATTGTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
TGATAAAACCTAATGATA
Found at i:1858931 original size:44 final size:46
Alignment explanation
Indices: 1858868--1858971 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 46
1858858 ATATTTTAAT
*
1858868 ATAAAATATAAATATTTTAATAATAA-ATGCTACTA-TTTAAATATTC
1 ATAAAATATAAATATTTTAAGAATAATAT--TACTATTTTAAATATTC
1858914 ATAAAA-AT-AATATTTTAAGAATAATATTACTATTTTAAATATT-
1 ATAAAATATAAATATTTTAAGAATAATATTACTATTTTAAATATTC
* *
1858957 TTAAAATATTAATAT
1 ATAAAATATAAATAT
1858972 AAAGAGTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
43 10 0.19
44 27 0.52
45 9 0.17
46 6 0.12
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (46 bp):
ATAAAATATAAATATTTTAAGAATAATATTACTATTTTAAATATTC
Found at i:1859036 original size:18 final size:19
Alignment explanation
Indices: 1859000--1859037 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1858990 TTATTTTAAG
*
1859000 TATTTTTATATTAATATAA
1 TATTTTAATATTAATATAA
1859019 TATTTTAATATTAA-ATAA
1 TATTTTAATATTAATATAA
1859037 T
1 T
1859038 TTCAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTAATATTAATATAA
Found at i:1859336 original size:74 final size:73
Alignment explanation
Indices: 1859253--1859411 Score: 178
Period size: 74 Copynumber: 2.2 Consensus size: 73
1859243 CAAATGGATC
* * * * * *
1859253 CTAAGATAGAAAACGAAATTTTTACTGAAAACATGAAAATAGTATTTTTCATAATTCAATAAAGA
1 CTAAAATAGAAAAAGAAACTTTTACTAAAAACATGAAAA-AATATTTTTCAAAATTCAATAAAGA
*
1859318 CAACATTTT
65 AAACATTTT
* ** *
1859327 CTAAAATAGAAAAAGCAACTTTTGTTAAAAACATGAAAAAATATTTTTTAAAATTCAATAAAGAA
1 CTAAAATAGAAAAAGAAACTTTTACTAAAAACATGAAAAAATATTTTTCAAAATTCAATAAAGAA
*
1859392 AACGTTTT
66 AACATTTT
*
1859400 -TAAGATA-AAAAA
1 CTAAAATAGAAAAA
1859412 TACAATCTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
71 5 0.07
72 6 0.08
73 29 0.40
74 32 0.44
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (73 bp):
CTAAAATAGAAAAAGAAACTTTTACTAAAAACATGAAAAAATATTTTTCAAAATTCAATAAAGAA
AACATTTT
Found at i:1859422 original size:73 final size:74
Alignment explanation
Indices: 1859280--1859435 Score: 192
Period size: 73 Copynumber: 2.1 Consensus size: 74
1859270 ATTTTTACTG
* * * *
1859280 AAAACATGAAAATAGTATTTTTCATAATTCAATAAAGACAACATTTTCTAAAATAGAAAAAGCAA
1 AAAACATGAAAATAATATTTTTCAAAATTCAATAAAGAAAACATTTTCTAAAATAGAAAAAACAA
1859345 CTTTTGTTA
66 CTTTTGTTA
* * *
1859354 AAAACATGAAAA-AATATTTTTTAAAATTCAATAAAGAAAACGTTTT-TAAGATA-AAAAATACA
1 AAAACATGAAAATAATATTTTTCAAAATTCAATAAAGAAAACATTTTCTAAAATAGAAAAA-ACA
*
1859416 ATCTTTTGTTG
65 A-CTTTTGTTA
*
1859427 AAAAGATGA
1 AAAACATGA
1859436 CGTATATAAG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
71 5 0.07
72 9 0.13
73 45 0.63
74 12 0.17
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (74 bp):
AAAACATGAAAATAATATTTTTCAAAATTCAATAAAGAAAACATTTTCTAAAATAGAAAAAACAA
CTTTTGTTA
Found at i:1859929 original size:28 final size:27
Alignment explanation
Indices: 1859897--1859951 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1859887 TTTAGAAAAC
*
1859897 AAAAAATAGAAAATAAAAATTATTTTCT
1 AAAAAATA-AAAATAAAAAATATTTTCT
1859925 AAAAAATAAAAATAAAAAATATTTTCT
1 AAAAAATAAAAATAAAAAATATTTTCT
1859952 CAAACCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAAAATAAAAATAAAAAATATTTTCT
Done.