Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 102 of 129
Found at i:16874356 original size:36 final size:37
Alignment explanation
Indices: 16874309--16874384 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 37
16874299 TGGGTGAAAG
*
16874309 AAAAAAAGAAAAAAGAA-A-AAATAAGA-GAAAAATAA
1 AAAAAAAGAAAAAAGAAGAGAAAAAAGATGAAAAA-AA
*
16874344 AAAAAAATGAAAAAATAAGAGAAAAAAGATGAAAAAAA
1 AAAAAAA-GAAAAAAGAAGAGAAAAAAGATGAAAAAAA
16874382 AAA
1 AAA
16874385 GACTCAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 7 0.20
36 9 0.26
37 1 0.03
38 12 0.34
39 6 0.17
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.07
Consensus pattern (37 bp):
AAAAAAAGAAAAAAGAAGAGAAAAAAGATGAAAAAAA
Found at i:16874377 original size:10 final size:9
Alignment explanation
Indices: 16874307--16874380 Score: 62
Period size: 10 Copynumber: 7.9 Consensus size: 9
16874297 AATGGGTGAA
16874307 AGAAAAAA-
1 AGAAAAAAG
16874315 AGAAAAAAG
1 AGAAAAAAG
*
16874324 AAAAAATAAG
1 AGAAAA-AAG
16874334 AGAAAAATA-
1 AGAAAAA-AG
*
16874343 AAAAAAAATG
1 AGAAAAAA-G
*
16874353 AAAAAATAAG
1 AGAAAA-AAG
16874363 AGAAAAAAG
1 AGAAAAAAG
16874372 ATGAAAAAA
1 A-GAAAAAA
16874381 AAAAGACTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
8 9 0.16
9 16 0.29
10 28 0.51
11 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:16874378 original size:29 final size:27
Alignment explanation
Indices: 16874307--16874384 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 27
16874297 AATGGGTGAA
16874307 AGAAAAAAAGAAAAAAGAAAAAATAAG
1 AGAAAAAAAGAAAAAAGAAAAAATAAG
*
16874334 AGAAAAATAAAAAAAAATGAAAAAATAAG
1 AGAAAAA-AAGAAAAAA-GAAAAAATAAG
16874363 AGAAAAAAGATGAAAAAA-AAAA
1 AGAAAAAA-A-GAAAAAAGAAAA
16874385 GACTCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 7 0.16
28 13 0.29
29 19 0.42
30 6 0.13
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (27 bp):
AGAAAAAAAGAAAAAAGAAAAAATAAG
Found at i:16875562 original size:21 final size:21
Alignment explanation
Indices: 16875492--16875566 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
16875482 TTAAGAAATC
*
16875492 TTCAAATGAGAATCTTTGAGT
1 TTCAAATGAGAATCTTTGAAT
* * * *
16875513 GTCGAGTGTGAATCTTTGAA-
1 TTCAAATGAGAATCTTTGAAT
*
16875533 CTCAAATGAGAATCTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
*
16875554 TTTAAATGAGAAT
1 TTCAAATGAGAAT
16875567 ATTTAAGGTG
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (21 bp):
TTCAAATGAGAATCTTTGAAT
Found at i:16875621 original size:79 final size:80
Alignment explanation
Indices: 16875519--16875687 Score: 232
Period size: 79 Copynumber: 2.1 Consensus size: 80
16875509 GAGTGTCGAG
** * * * *
16875519 TGTGAATCTTTGAACTCAAATGAGAATCTTTGAATTTTAAATGAGAATATTTAAGGTGTGAAACT
1 TGTGAATCTTAAAACTCAAATGAGAATATTTGAATTTCAAATGAGAATATTTAAGATGTGAAACC
16875584 C-AAAATTTATAGAA
66 CTAAAATTTATAGAA
* *
16875598 TGTGAATCTTAAAATTCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTAAGATGTGAAACC
1 TGTGAATCTTAAAACTCAAATGAGAATATTTGAATTTCAAATGAGAATATTTAAGATGTGAAACC
* * *
16875663 CTAAAGTTTATTGGA
66 CTAAAATTTATAGAA
16875678 TGTGAATCTT
1 TGTGAATCTT
16875688 CGAACTAATG
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 58 0.74
80 20 0.26
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (80 bp):
TGTGAATCTTAAAACTCAAATGAGAATATTTGAATTTCAAATGAGAATATTTAAGATGTGAAACC
CTAAAATTTATAGAA
Found at i:16875624 original size:20 final size:20
Alignment explanation
Indices: 16875596--16875648 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
16875586 AAATTTATAG
*
16875596 AATGTGAATCTTAAAATTCA
1 AATGAGAATCTTAAAATTCA
* * *
16875616 AATGAGAATATTTGAATTTCA
1 AATGAGAAT-CTTAAAATTCA
16875637 AATGAGAATCTT
1 AATGAGAATCTT
16875649 TAAGATGTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGAGAATCTTAAAATTCA
Found at i:16875849 original size:24 final size:24
Alignment explanation
Indices: 16875802--16875849 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16875792 AATCTTTGTA
* *
16875802 CTTAGATGTGAAACTCTAAGATTT
1 CTTAGATGTGAAACTCCAAAATTT
*
16875826 CTTAGATGTGAATCTCCAAAATTT
1 CTTAGATGTGAAACTCCAAAATTT
16875850 AAATGAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (24 bp):
CTTAGATGTGAAACTCCAAAATTT
Found at i:16875896 original size:114 final size:114
Alignment explanation
Indices: 16875720--16876063 Score: 518
Period size: 114 Copynumber: 3.0 Consensus size: 114
16875710 TTGTTGGATA
* * * *
16875720 TGAATCTCTAAAATTCAAACGAAAAGCTTTGAACTCAACTTTTAGATACAAATCTCTAAATTTTT
1 TGAATCTCCAAAATTTAAACGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTAAATTTTT
* *
16875785 GAGTGAGAATCTTTGTACTTAGATGTGAAACTCTAAGATTTCTTAGATG
66 GAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTCTTAGATG
*
16875834 TGAATCTCCAAAATTTAAATGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTAAATTTTT
1 TGAATCTCCAAAATTTAAACGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTAAATTTTT
16875899 GAGTGAGAACCTTT-ACACTTAGATGTGAAACTCTAAGATTTGC-TAGATG
66 GAGTGAGAACCTTTGA-ACTTAGATGTGAAACTCTAAGATTT-CTTAGATG
* * *
16875948 TGAATCTCCAAAA-TT-CACGAAAAGCTGTGAACTCAACTTTTGGATGCGAATCTCTAAATTTTT
1 TGAATCTCCAAAATTTAAACGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTAAATTTTT
* *
16876011 TAGTGAGAACCTTTGAACTTAGATGTGAAACTTTAAGATTTCTT-GAATG
66 GAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTCTTAG-ATG
16876060 TGAA
1 TGAA
16876064 CCTTTGAACT
Statistics
Matches: 212, Mismatches: 13, Indels: 12
0.89 0.05 0.05
Matches are distributed among these distances:
111 2 0.01
112 89 0.42
113 3 0.01
114 117 0.55
115 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (114 bp):
TGAATCTCCAAAATTTAAACGAAAAGCTTTGAACTCAACTTTTGGATACGAATCTCTAAATTTTT
GAGTGAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTCTTAGATG
Found at i:16876407 original size:41 final size:42
Alignment explanation
Indices: 16876341--16876452 Score: 163
Period size: 41 Copynumber: 2.7 Consensus size: 42
16876331 CAATGAGCAT
16876341 TTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAAGAACAA
1 TTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAAGAACAA
* * * * *
16876383 TTTA-TTTTTAAAAGTTATGATGCCTTTGTTTAGAGGAGCAA
1 TTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAAGAACAA
*
16876424 TTTATTTTTTCAAAGTTGTGGTGCCTCTG
1 TTTATTTTTTAAAAGTTGTGGTGCCTCTG
16876453 ATTAAAGGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
41 36 0.60
42 24 0.40
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (42 bp):
TTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAAGAACAA
Found at i:16876449 original size:42 final size:42
Alignment explanation
Indices: 16876335--16876470 Score: 170
Period size: 42 Copynumber: 3.3 Consensus size: 42
16876325 GATTGTCAAT
* *
16876335 GAGCATTTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAA
1 GAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAG
* * * *
16876377 GAACAATTTA-TTTTTAAAAGTTATGATGCCTTTGTTTAGAG
1 GAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAG
* * *
16876418 GAGCAATTTATTTTTTCAAAGTTGTGGTGCCTCTGATTAAAG
1 GAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAG
16876460 GAGC--TTTATTT
1 GAGCAATTTATTT
16876471 ATATTTTCAA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
40 7 0.09
41 36 0.45
42 37 0.46
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (42 bp):
GAGCAATTTATTTTTTAAAAGTTGTGGTGCCTCTGTTTAGAG
Found at i:16876547 original size:45 final size:44
Alignment explanation
Indices: 16876424--16876705 Score: 316
Period size: 45 Copynumber: 6.4 Consensus size: 44
16876414 AGAGGAGCAA
* * * * * *
16876424 TTTATTTTTTCAAAGTTGTGGTGCCTCTGATTAAAGGAGCTTTA
1 TTTATGTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
* *
16876468 TTTATATTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCTTTG
1 TTTATGTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
* * * *
16876512 TTTATGTTTTCTAAAGTCATTGACCCTTTGATTAGAAGAGCTTT-
1 TTTATGTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
* * *
16876556 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGCGAAGCTTTG
1 TTTATGTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
* *
16876600 TTTATGTTTTCCAAAGTCATTGAGCCTCTGATTAGAGGAGTTTTG
1 TTTATGTTTT-CAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
* * * * *
16876645 TTTTTGTTTTTCAAAGTCGTTGAGACTCTAATTAGAAGAGCCTTG
1 TTTATG-TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
16876690 TTTACT-TTTTCAAAGT
1 TTTA-TGTTTTCAAAGT
16876706 TGAAATTGTG
Statistics
Matches: 200, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
43 26 0.13
44 76 0.38
45 93 0.47
46 5 0.03
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.44
Consensus pattern (44 bp):
TTTATGTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
Found at i:16876567 original size:88 final size:88
Alignment explanation
Indices: 16876447--16876705 Score: 335
Period size: 88 Copynumber: 2.9 Consensus size: 88
16876437 AGTTGTGGTG
*
16876447 CCTCTGATTA-AAGGAGCTTTATTTATATTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCTTT
1 CCTCTGATTAGAA-GAGCTTTATTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCTTT
16876511 GTTTATGTTTTCTAAAGTCATTGAC
65 GTTTATGTTTTC-AAAGTCATTGAC
* * * *
16876536 CCTTTGATTAGAAGAGCTTT-TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGCGAAGCTTTG
1 CCTCTGATTAGAAGAGCTTTATTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCTTTG
*
16876600 TTTATGTTTTCCAAAGTCATTGAG
66 TTTATGTTTT-CAAAGTCATTGAC
* * * * * * *
16876624 CCTCTGATTAGAGGAGTTTTGTTTTTGTTTTTCAAAGTCGTTGAGACTCTAATTAGAAGAGCCTT
1 CCTCTGATTAGAAGAGCTTTATTTAT-TTTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCTTT
16876689 GTTTACT-TTTTCAAAGT
65 GTTTA-TGTTTTCAAAGT
16876706 TGAAATTGTG
Statistics
Matches: 149, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
88 78 0.52
89 27 0.18
90 43 0.29
91 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (88 bp):
CCTCTGATTAGAAGAGCTTTATTTATTTTTTCAAAGTCGTTGAGCCTCTAATTAGAGGAGCTTTG
TTTATGTTTTCAAAGTCATTGAC
Found at i:16876653 original size:133 final size:133
Alignment explanation
Indices: 16876424--16876705 Score: 361
Period size: 133 Copynumber: 2.1 Consensus size: 133
16876414 AGAGGAGCAA
* * * *
16876424 TTTATTTTTTCAAAGTTGTGGTGCCTCTGATTAAAGGAGCTTTATTTATATTTTCAAAGTCGTTG
1 TTTATTTTTTCAAAGTCGTGGAGCCTCTGATTAAAGAAGCTTTATTTATATTTTCAAAGTCATTG
* * *
16876489 AGCCTCTAATTAGAGGAGCTTTGTTTATG-TTTTCTAAAGTCATTGACCCTTTGATTAGAAGAG-
66 AGCCTCTAATTAGAGGAGCTTTGTTTATGTTTTTC-AAAGTCATTGACACTCTAATTAGAAGAGC
*
16876552 CTTT
130 CTTG
* ** * *
16876556 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGCGAAGCTTTGTTTATGTTTTCCAAAGTCATT
1 TTTATTTTTTCAAAGTCGTGGAGCCTCTGATTAAAGAAGCTTTATTTATATTTT-CAAAGTCATT
* * * * *
16876621 GAGCCTCTGATTAGAGGAGTTTTGTTTTTGTTTTTCAAAGTCGTTGAGACTCTAATTAGAAGAGC
65 GAGCCTCTAATTAGAGGAGCTTTGTTTATGTTTTTCAAAGTCATTGACACTCTAATTAGAAGAGC
16876686 CTTG
130 CTTG
*
16876690 TTTACTTTTTCAAAGT
1 TTTATTTTTTCAAAGT
16876706 TGAAATTGTG
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
132 46 0.36
133 59 0.46
134 23 0.18
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.44
Consensus pattern (133 bp):
TTTATTTTTTCAAAGTCGTGGAGCCTCTGATTAAAGAAGCTTTATTTATATTTTCAAAGTCATTG
AGCCTCTAATTAGAGGAGCTTTGTTTATGTTTTTCAAAGTCATTGACACTCTAATTAGAAGAGCC
TTG
Found at i:16878335 original size:3 final size:3
Alignment explanation
Indices: 16878309--16878364 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
16878299 TCGAGGTTTT
* *
16878309 TTA TT- TTA TT- TTA TTTA TTTA TTA TTA TTA TTA CTA TTA TCA TTA
1 TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
16878354 TTA TTA TTA TT
1 TTA TTA TTA TT
16878365 TTTAAATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 35 0.76
4 7 0.15
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16878530 original size:56 final size:56
Alignment explanation
Indices: 16878457--16878697 Score: 190
Period size: 59 Copynumber: 4.2 Consensus size: 56
16878447 TGATTTTCCT
* * *
16878457 AAAA-AAAATTTCAAAAAACATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTTTTT
1 AAAATAAAATTT-AAAAAAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTCTTTTG
* *
16878513 AAAATAAAATTTTAAAAAATATACTTTTGAAGGAAAA-TTGAATGTATCAATTTCTTTTG
1 AAAATAAAA-TTTAAAAAA-A-ATTTTTGAA-GAAAAGTTGAAAGTATCAATTTCTTTTG
* * * *
16878572 AATACAAAA-ATAAAAAATAAGTTTTTG-AGAAAAGTTGAAAGTATCAATTTCTCTTG
1 AAAATAAAATTTAAAAAA-AA-TTTTTGAAGAAAAGTTGAAAGTATCAATTTCTTTTG
* * *
16878628 AAAATAAAAAGGTTTAAAAATATATATTTTT-AGGGAAAAGTTGAAAATATCAAATTT-TCTT-
1 AAAAT-AAAA--TTTAAAAA-A-A-ATTTTTGA-AGAAAAGTTGAAAGTATC-AATTTCTTTTG
16878689 AAAATAAAA
1 AAAATAAAA
16878698 ATCTCCAAAT
Statistics
Matches: 153, Mismatches: 16, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
55 5 0.03
56 29 0.19
57 28 0.18
58 3 0.02
59 34 0.22
60 15 0.10
61 13 0.08
62 21 0.14
63 5 0.03
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.35
Consensus pattern (56 bp):
AAAATAAAATTTAAAAAAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTCTTTTG
Found at i:16879771 original size:2 final size:2
Alignment explanation
Indices: 16879760--16879795 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16879750 GAAGGTAAAC
16879760 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16879796 GAATCAGTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16881504 original size:8 final size:8
Alignment explanation
Indices: 16881491--16881516 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
16881481 AAATAATATT
16881491 TTTTTTTA
1 TTTTTTTA
16881499 TTTTTTTA
1 TTTTTTTA
16881507 TTTTTTTA
1 TTTTTTTA
16881515 TT
1 TT
16881517 AAACAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:16882743 original size:19 final size:19
Alignment explanation
Indices: 16882719--16882755 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16882709 TTATTATCAA
16882719 TTTAAACAAATTTGAATAT
1 TTTAAACAAATTTGAATAT
* *
16882738 TTTAAATAGATTTGAATA
1 TTTAAACAAATTTGAATA
16882756 ATATTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (19 bp):
TTTAAACAAATTTGAATAT
Found at i:16882764 original size:20 final size:19
Alignment explanation
Indices: 16882728--16882765 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
16882718 ATTTAAACAA
*
16882728 ATTTGAATATTTTAAATAG
1 ATTTGAATATATTAAATAG
16882747 ATTTGAATAATATTAAATA
1 ATTTGAAT-ATATTAAATA
16882766 AAGTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTTGAATATATTAAATAG
Found at i:16884701 original size:19 final size:19
Alignment explanation
Indices: 16884677--16884716 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
16884667 AAGTCTTATC
16884677 TATTTTAAATAAATTTGAA
1 TATTTTAAATAAATTTGAA
**
16884696 TATTTTAAATGGATTTGAA
1 TATTTTAAATAAATTTGAA
16884715 TA
1 TA
16884717 ATACTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
TATTTTAAATAAATTTGAA
Found at i:16884891 original size:25 final size:24
Alignment explanation
Indices: 16884853--16884911 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
16884843 ATTATTTATT
* *
16884853 ATTATCCTATGTGTCATCTAAAGAA
1 ATTAT-CTACGTGTCATCTAAAAAA
16884878 ATTACTCTACGTGTCATCTAAAAAA
1 ATTA-TCTACGTGTCATCTAAAAAA
16884903 ATTATCTAC
1 ATTATCTAC
16884912 TTAAATATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 5 0.16
25 25 0.81
26 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (24 bp):
ATTATCTACGTGTCATCTAAAAAA
Found at i:16885188 original size:17 final size:18
Alignment explanation
Indices: 16885148--16885188 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
16885138 CATTTAAAAC
*
16885148 ATTTATATATTAGTAAAT
1 ATTTATAAATTAGTAAAT
*
16885166 A-ATATAAATTA-TAAAT
1 ATTTATAAATTAGTAAAT
16885182 ATTTATA
1 ATTTATA
16885189 TTTTTTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.32
17 12 0.63
18 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTTATAAATTAGTAAAT
Found at i:16885718 original size:17 final size:16
Alignment explanation
Indices: 16885696--16885730 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
16885686 CAAATTGATG
*
16885696 AACTATAAGTAAATATA
1 AACTATAA-TAAAAATA
16885713 AACTATAATAAAAATA
1 AACTATAATAAAAATA
16885729 AA
1 AA
16885731 GATATAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
AACTATAATAAAAATA
Found at i:16888366 original size:52 final size:52
Alignment explanation
Indices: 16888283--16888387 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 52
16888273 TATAACTATA
16888283 CAAACTTGCCTATTAAAAATTTTTTTCCTCTTAAAATTCTTCTTCTGCAAGT
1 CAAACTTGCCTATTAAAAATTTTTTTCCTCTTAAAATTCTTCTTCTGCAAGT
* * *
16888335 CAAACTTGCCTATTAAGAATCTTTTTT-CTCTTAGAATTCTTCTTCTGTAAGT
1 CAAACTTGCCTATTAAAAAT-TTTTTTCCTCTTAAAATTCTTCTTCTGCAAGT
16888387 C
1 C
16888388 TTCTTATCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 43 0.88
53 6 0.12
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.45
Consensus pattern (52 bp):
CAAACTTGCCTATTAAAAATTTTTTTCCTCTTAAAATTCTTCTTCTGCAAGT
Found at i:16888734 original size:31 final size:30
Alignment explanation
Indices: 16888694--16888776 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
16888684 ATGAATCTTT
* *
16888694 AGCTTTGATACCATTTGTTGGAAATCACTAC
1 AGCTCTGATACCATTTGTTGG-AATCACCAC
* *
16888725 AGCTCTGATATCATTTGTTAGGAATCACCAT
1 AGCTCTGATACCATTTGTT-GGAATCACCAC
*
16888756 AGCTCTGATACCACTTGTTGG
1 AGCTCTGATACCATTTGTTGG
16888777 GCCAAATAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.04
31 41 0.91
32 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (30 bp):
AGCTCTGATACCATTTGTTGGAATCACCAC
Found at i:16889135 original size:16 final size:16
Alignment explanation
Indices: 16889114--16889156 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
16889104 TTGGTCCACT
16889114 CATAAACATACAAACA
1 CATAAACATACAAACA
* *
16889130 CATAAACATACACACT
1 CATAAACATACAAACA
16889146 CATAAGACATA
1 CATAA-ACATA
16889157 AATCTTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.56, C:0.26, G:0.02, T:0.16
Consensus pattern (16 bp):
CATAAACATACAAACA
Found at i:16889385 original size:3 final size:3
Alignment explanation
Indices: 16889377--16889451 Score: 111
Period size: 3 Copynumber: 25.3 Consensus size: 3
16889367 TTTATTGCTG
16889377 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16889425 TTA TGGTA -TA TTA -TA TTA -TA TTA TTA T
1 TTA T--TA TTA TTA TTA TTA TTA TTA TTA T
16889452 ACTATAGTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.09
3 59 0.88
5 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:16896424 original size:18 final size:18
Alignment explanation
Indices: 16896394--16896439 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
16896384 ACTAGACTTT
*
16896394 GAGA-AAAGGAAAAAAAA
1 GAGAGAAAGAAAAAAAAA
*
16896411 GAGAGAAAGAAAAATAAA
1 GAGAGAAAGAAAAAAAAA
16896429 G-GAAGAAAGAA
1 GAG-AGAAAGAA
16896440 GAAATCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (18 bp):
GAGAGAAAGAAAAAAAAA
Found at i:16896720 original size:8 final size:8
Alignment explanation
Indices: 16896707--16896754 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
16896697 TGTTTAGGTT
16896707 TTTTTTTA
1 TTTTTTTA
16896715 -TTTTTTA
1 TTTTTTTA
16896722 TTTTTTTA
1 TTTTTTTA
16896730 TTTGTTTTA
1 TTT-TTTTA
* **
16896739 ATTTAATA
1 TTTTTTTA
16896747 TTTTTTTA
1 TTTTTTTA
16896755 AATTAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
7 7 0.22
8 18 0.56
9 7 0.22
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:16896755 original size:16 final size:17
Alignment explanation
Indices: 16896728--16896760 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16896718 TTTATTTTTT
*
16896728 TATTTGTTTTAATTTAA
1 TATTTGTTTTAAATTAA
16896745 TATTT-TTTTAAATTAA
1 TATTTGTTTTAAATTAA
16896761 AAATGGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTGTTTTAAATTAA
Found at i:16899154 original size:25 final size:25
Alignment explanation
Indices: 16899106--16899154 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
16899096 GAAAAAAAAA
* * **
16899106 AGAGAGAAAGAAAAGATTTGGGAGG
1 AGAGAGAAAGAAAAAAATAAGGAGG
16899131 AGAGAGAAAGAAAAAAATAAGGAG
1 AGAGAGAAAGAAAAAAATAAGGAG
16899155 AAAGAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.08
Consensus pattern (25 bp):
AGAGAGAAAGAAAAAAATAAGGAGG
Found at i:16905132 original size:43 final size:42
Alignment explanation
Indices: 16905057--16905141 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 42
16905047 TAGAATATTA
16905057 TGATATTAGATTTGAAGTCATATTCTCGTCACAATGCCTATG
1 TGATATTAGATTTGAAGTCATATTCTCGTCACAATGCCTATG
* * *
16905099 TGATATTAGATTCTGAAGTTATTTTCTCTTCACAATGCCTATG
1 TGATATTAGATT-TGAAGTCATATTCTCGTCACAATGCCTATG
16905142 ATTTTGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 12 0.31
43 27 0.69
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.41
Consensus pattern (42 bp):
TGATATTAGATTTGAAGTCATATTCTCGTCACAATGCCTATG
Found at i:16906148 original size:2 final size:2
Alignment explanation
Indices: 16906141--16906165 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16906131 TGTTTTCACA
16906141 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16906166 AAATAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16916474 original size:2 final size:2
Alignment explanation
Indices: 16916469--16916509 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16916459 CAACTGCAAA
16916469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16916510 AAGACGGTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16917503 original size:19 final size:18
Alignment explanation
Indices: 16917461--16917505 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
16917451 AAATATGCTC
*
16917461 TTTTTTTTCCTTTTTTAT
1 TTTTTTTTCATTTTTTAT
* *
16917479 TCTTTTTTCATTTCTTTGT
1 TTTTTTTTCATTT-TTTAT
16917498 TTTTTTTT
1 TTTTTTTT
16917506 TTAATCAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTTTTTCATTTTTTAT
Found at i:16922806 original size:19 final size:21
Alignment explanation
Indices: 16922764--16922811 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
16922754 TATTAATAAA
16922764 ATAAATCAAATAATATTATTTT
1 ATAAAT-AAATAATATTATTTT
*
16922786 ATTAATAAATAAT-TT-TTTT
1 ATAAATAAATAATATTATTTT
16922805 ATAAATA
1 ATAAATA
16922812 TATTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 2 0.08
21 7 0.29
22 5 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAATAAATAATATTATTTT
Found at i:16922810 original size:15 final size:17
Alignment explanation
Indices: 16922790--16922852 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 17
16922780 TATTTTATTA
16922790 ATAAATA-ATTT-TTTT
1 ATAAATATATTTATTTT
16922805 ATAAATATATTTATTTT
1 ATAAATATATTTATTTT
16922822 -T--ATATATTTATTTT
1 ATAAATATATTTATTTT
*
16922836 AAAAATTAATATTTATT
1 ATAAA-T-ATATTTATT
16922853 AATTAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 13 0.32
15 7 0.17
16 5 0.12
17 5 0.12
18 1 0.03
19 9 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAAATATATTTATTTT
Found at i:16922847 original size:19 final size:20
Alignment explanation
Indices: 16922825--16922874 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
16922815 TTATTTTTAT
*
16922825 ATATTTATTTTAA-AAATTA
1 ATATTTATTTTAATAAAATA
16922844 ATATTTATTAATTAATAAAATA
1 ATATTTATT--TTAATAAAATA
16922866 ATA-TTATTT
1 ATATTTATTT
16922875 AATTTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
21 9 0.33
22 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTTATTTTAATAAAATA
Found at i:16926105 original size:9 final size:9
Alignment explanation
Indices: 16926091--16926115 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16926081 TATCGATAGC
16926091 AGCTATTGG
1 AGCTATTGG
16926100 AGCTATTGG
1 AGCTATTGG
16926109 AGCTATT
1 AGCTATT
16926116 TTCTTCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (9 bp):
AGCTATTGG
Found at i:16928008 original size:11 final size:12
Alignment explanation
Indices: 16927977--16928009 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16927967 TTAAATCATG
*
16927977 TTATTTTCGTAT
1 TTATTTTTGTAT
16927989 TTATTTTTGTAT
1 TTATTTTTGTAT
16928001 TT-TTTTTGT
1 TTATTTTTGT
16928010 TTCACCGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (12 bp):
TTATTTTTGTAT
Found at i:16939163 original size:20 final size:19
Alignment explanation
Indices: 16939111--16939165 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
16939101 GTCGGTTAAA
* *
16939111 TAATTATATTTTTTATTTT
1 TAATTATATATTTAATTTT
* *
16939130 TTATTATA-A-ATAATTATT
1 TAATTATATATTTAATT-TT
16939148 TAATTATATATTTAATTT
1 TAATTATATATTTAATTT
16939166 AATAAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 9 0.33
20 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTATATATTTAATTTT
Found at i:16939347 original size:25 final size:25
Alignment explanation
Indices: 16939319--16939373 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
16939309 CAATTTGATT
16939319 ATTAATTTTAA-AAAATTAAAAATTA
1 ATTAA-TTTAATAAAATTAAAAATTA
** *
16939344 ATTAATTTAATCGATTTAAAAATTA
1 ATTAATTTAATAAAATTAAAAATTA
16939369 ATTAA
1 ATTAA
16939374 ATCAAAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTAATTTAATAAAATTAAAAATTA
Found at i:16939635 original size:21 final size:21
Alignment explanation
Indices: 16939594--16939635 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16939584 AATTTTGATT
** *
16939594 TTTAAAATTTTTCAAATAAAA
1 TTTAAAATTTTGAAAAAAAAA
16939615 TTTAAAATTTTGAAAAAAAAA
1 TTTAAAATTTTGAAAAAAAAA
16939636 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAAAATTTTGAAAAAAAAA
Found at i:16939701 original size:20 final size:20
Alignment explanation
Indices: 16939663--16939701 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16939653 TATATTTTTT
*
16939663 ATTTTCAGAAAAAATTTTAA
1 ATTTTCAGAAAAAAATTTAA
16939683 ATTTTCA-AAAATAAATTTA
1 ATTTTCAGAAAA-AAATTTA
16939702 TTTATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
ATTTTCAGAAAAAAATTTAA
Found at i:16939736 original size:14 final size:14
Alignment explanation
Indices: 16939717--16939755 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16939707 CAAATTTAGA
*
16939717 ATTATTTTTAAATT
1 ATTATTTTAAAATT
16939731 ATTATTTTAAAATT
1 ATTATTTTAAAATT
*
16939745 A-AATTTTAAAA
1 ATTATTTTAAAA
16939756 AATAGCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTATTTTAAAATT
Found at i:16943720 original size:16 final size:15
Alignment explanation
Indices: 16943698--16943738 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
16943688 TTTTATTTTT
16943698 TAATTAAAATAAAAA
1 TAATTAAAATAAAAA
*
16943713 TAAATTAAAATATAAA
1 T-AATTAAAATAAAAA
16943729 TAATTAAAAT
1 TAATTAAAAT
16943739 TTTTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATTAAAATAAAAA
Found at i:16944181 original size:19 final size:20
Alignment explanation
Indices: 16944144--16944189 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
16944134 TTTTTTTTTA
16944144 AAAACAAAAACAAATAACAT
1 AAAACAAAAACAAATAACAT
*
16944164 GAAACAAAATAC-AA-AACAT
1 AAAACAAAA-ACAAATAACAT
16944183 AAAACAA
1 AAAACAA
16944190 CAGTATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.48
20 10 0.43
21 2 0.09
ACGTcount: A:0.74, C:0.15, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAACAAAAACAAATAACAT
Found at i:16944896 original size:2 final size:2
Alignment explanation
Indices: 16944891--16944921 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16944881 TAGAAAAAAA
16944891 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16944922 AAATGGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16946686 original size:31 final size:31
Alignment explanation
Indices: 16946612--16946710 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 31
16946602 AATAAATTAT
* * * *
16946612 ATATCATTTCAAAAAATCAAATAAAAATTTC
1 ATATTATTTTAAAAAATTATATAAAAATTTC
*
16946643 A-ATTTCAATTTAAAAAATTATATAAAAATTTC
1 ATA-TT-ATTTTAAAAAATTATATAAAAATTTC
*
16946675 ATATTATTTTAAAATATT-TAGTAAAAATTTTC
1 ATATTATTTTAAAAAATTATA-TAAAAA-TTTC
16946707 ATAT
1 ATAT
16946711 CATTAAAGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
30 3 0.05
31 19 0.34
32 33 0.59
33 1 0.02
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (31 bp):
ATATTATTTTAAAAAATTATATAAAAATTTC
Found at i:16946949 original size:29 final size:29
Alignment explanation
Indices: 16946882--16946951 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
16946872 TTTTTAATTT
16946882 TTATAAATATAAAATTTTAATAAAAATAGA
1 TTATAAATA-AAAATTTTAATAAAAATAGA
*
16946912 TT-TAAAATAAAAATTTTCAATAAAAA-ATA
1 TTAT-AAATAAAAATTTT-AATAAAAATAGA
*
16946941 TTATGAATAAA
1 TTATAAATAAA
16946952 TTAGTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (29 bp):
TTATAAATAAAAATTTTAATAAAAATAGA
Found at i:16946989 original size:22 final size:21
Alignment explanation
Indices: 16946962--16947005 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
16946952 TTAGTAAATT
*
16946962 AATTTTTTA-AAATAATTTAA
1 AATTTTTTATTAATAATTTAA
16946982 AATTTTTTACTTAATAATTTAA
1 AATTTTTTA-TTAATAATTTAA
16947004 AA
1 AA
16947006 AGATGTGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTTTTATTAATAATTTAA
Found at i:16947953 original size:6 final size:6
Alignment explanation
Indices: 16947942--16947969 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
16947932 ATCCACTTAT
16947942 AATATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATA
16947970 AATAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:16962369 original size:19 final size:18
Alignment explanation
Indices: 16962334--16962371 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
16962324 TAAGTGATTT
*
16962334 TTTATTTTATTTTAAATA
1 TTTATTTTATATTAAATA
16962352 TTTATTTATATATTAAATA
1 TTTATTT-TATATTAAATA
16962371 T
1 T
16962372 ATTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTTTATATTAAATA
Found at i:16969320 original size:50 final size:50
Alignment explanation
Indices: 16969242--16969340 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 50
16969232 TTGTTTGTTG
* *
16969242 CCTTTCCTTCTTCTCTCTCGCATACCATTTTAT-TTTCTTGCTTTGCTTTTA
1 CCTTCCCTTCTTCTCTCTCGCATACCATTTT-TCTATCTTGCTTTG-TTTTA
*
16969293 CCTTCCCTTC-TCTCTCTCGCCA-GCCATTTTTCTATCTTGCTTTGTTTT
1 CCTTCCCTTCTTCTCTCTCG-CATACCATTTTTCTATCTTGCTTTGTTTT
16969341 CTTGCTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
49 5 0.12
50 27 0.63
51 11 0.26
ACGTcount: A:0.08, C:0.32, G:0.07, T:0.53
Consensus pattern (50 bp):
CCTTCCCTTCTTCTCTCTCGCATACCATTTTTCTATCTTGCTTTGTTTTA
Found at i:16969345 original size:13 final size:13
Alignment explanation
Indices: 16969327--16969352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16969317 CATTTTTCTA
16969327 TCTTGCTTTGTTT
1 TCTTGCTTTGTTT
16969340 TCTTGCTTTGTTT
1 TCTTGCTTTGTTT
16969353 CTTCCACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (13 bp):
TCTTGCTTTGTTT
Found at i:16970074 original size:2 final size:2
Alignment explanation
Indices: 16970067--16970097 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16970057 TGAGGTCATG
16970067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16970098 GTTTCATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16971818 original size:30 final size:31
Alignment explanation
Indices: 16971784--16971846 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
16971774 AAAAGGACTT
16971784 CAAGTATTG-AATTCTCTAAAAATTGACTAA
1 CAAGTATTGAAATTCTCTAAAAATTGACTAA
16971814 CAAGTATTGAAATTCTCTAAAAATTGACTAA
1 CAAGTATTGAAATTCTCTAAAAATTGACTAA
16971845 CA
1 CA
16971847 TCTTTCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGTATTGAAATTCTCTAAAAATTGACTAA
Found at i:16972553 original size:16 final size:17
Alignment explanation
Indices: 16972519--16972553 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16972509 ATAAATTTCC
*
16972519 AAAAACTATAATTTGTT
1 AAAAACTATAATTTATT
16972536 AAAAACTATAA-TTATT
1 AAAAACTATAATTTATT
16972552 AA
1 AA
16972554 TAAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAAACTATAATTTATT
Found at i:16974142 original size:28 final size:28
Alignment explanation
Indices: 16974110--16974167 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16974100 TCTTTGGGAG
16974110 GTAATTTGCAATTCATATTAGTGACTAT
1 GTAATTTGCAATTCATATTAGTGACTAT
16974138 GTAATTTGCAATTCATATTAGTGACTAT
1 GTAATTTGCAATTCATATTAGTGACTAT
16974166 GT
1 GT
16974168 TAAACAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (28 bp):
GTAATTTGCAATTCATATTAGTGACTAT
Found at i:16976296 original size:9 final size:10
Alignment explanation
Indices: 16976276--16976337 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
16976266 ATAAGGTTTA
*
16976276 TATAATTGTT
1 TATAATTATT
16976286 TA-AATTATT
1 TATAATTATT
16976295 TATAATTATT
1 TATAATTATT
*
16976305 TATATATTGTT
1 TATA-ATTATT
* *
16976316 TA-CATTATA
1 TATAATTATT
*
16976325 TATAATTGTT
1 TATAATTATT
16976335 TAT
1 TAT
16976338 TGTTTATATA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
9 14 0.34
10 20 0.49
11 7 0.17
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (10 bp):
TATAATTATT
Found at i:16976299 original size:33 final size:30
Alignment explanation
Indices: 16976261--16976330 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
16976251 GCATTTGGTA
16976261 ATATAATAAGGTTTATATAATTGTTTAAATTAT
1 ATATAATAA--TTTATAT-ATTGTTTAAATTAT
* * *
16976294 TTATAATTATTTATATATTGTTTACATTAT
1 ATATAATAATTTATATATTGTTTAAATTAT
16976324 ATATAAT
1 ATATAAT
16976331 TGTTTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 19 0.58
31 7 0.21
33 7 0.21
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (30 bp):
ATATAATAATTTATATATTGTTTAAATTAT
Found at i:16976316 original size:30 final size:31
Alignment explanation
Indices: 16976272--16976374 Score: 100
Period size: 37 Copynumber: 3.2 Consensus size: 31
16976262 TATAATAAGG
*
16976272 TTTATATAATTGTTTAAATTATTTATAATTA
1 TTTATATAATTGTTTAAATTATATATAATTA
*
16976303 TTTATAT-ATTGTTTACATTATATATAATTGTTTA
1 TTTATATAATTGTTTAAATTATATATAA----TTA
* * *
16976337 TTGTTTATATATTGTTTAGATTATATATAATTG
1 TT-TATATA-ATTGTTTAAATTATATATAATTA
16976370 TTTAT
1 TTTAT
16976375 TGTTTGACTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
30 18 0.31
31 7 0.12
32 2 0.03
33 4 0.07
34 5 0.08
35 4 0.07
37 19 0.32
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (31 bp):
TTTATATAATTGTTTAAATTATATATAATTA
Found at i:16976325 original size:16 final size:16
Alignment explanation
Indices: 16976304--16976364 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 16
16976294 TTATAATTAT
*
16976304 TTATATATTGTTTACA
1 TTATATATTGTTTAGA
*
16976320 TTATATATAATTGTTTATTGT
1 -T-TATAT-ATTGTTTA--GA
16976341 TTATATATTGTTTAGA
1 TTATATATTGTTTAGA
16976357 TTATATAT
1 TTATATAT
16976365 AATTGTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 9 0.24
17 1 0.03
18 13 0.35
19 13 0.35
20 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (16 bp):
TTATATATTGTTTAGA
Found at i:16976326 original size:18 final size:18
Alignment explanation
Indices: 16976297--16976373 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 18
16976287 AAATTATTTA
*
16976297 TAATTATTTATATATTGTT
1 TAATTATATATA-ATTGTT
16976316 TACATTATATATAATTGTT
1 TA-ATTATATATAATTGTT
* *
16976335 T-ATTGTTTATATATTGTT
1 TAATTATATATA-ATTGTT
16976353 TAGATTATATATAATTGTT
1 TA-ATTATATATAATTGTT
16976372 TA
1 TA
16976374 TTGTTTGACT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 8 0.16
18 7 0.14
19 17 0.35
20 17 0.35
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.58
Consensus pattern (18 bp):
TAATTATATATAATTGTT
Found at i:16976346 original size:37 final size:37
Alignment explanation
Indices: 16976303--16976379 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
16976293 TTTATAATTA
16976303 TTTATATATTGTTTACATTATATATAATTGTTTATTG
1 TTTATATATTGTTTACATTATATATAATTGTTTATTG
*
16976340 TTTATATATTGTTTAGATTATATATAATTGTTTATTG
1 TTTATATATTGTTTACATTATATATAATTGTTTATTG
16976377 TTT
1 TTT
16976380 GACTTTTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.01, G:0.09, T:0.61
Consensus pattern (37 bp):
TTTATATATTGTTTACATTATATATAATTGTTTATTG
Found at i:16983645 original size:32 final size:32
Alignment explanation
Indices: 16983584--16983647 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
16983574 ATGATTTAAA
*
16983584 GCCTGTTTTTTTTCTCTTTAAAAGTCTTTCTT
1 GCCTGTTTTTTTTCTCTTGAAAAGTCTTTCTT
*
16983616 GCCTTTTTTTTTTC-CTTAGAAAA-TGCTTTCTT
1 GCCTGTTTTTTTTCTCTT-GAAAAGT-CTTTCTT
16983648 ATGATGTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.14, C:0.19, G:0.09, T:0.58
Consensus pattern (32 bp):
GCCTGTTTTTTTTCTCTTGAAAAGTCTTTCTT
Found at i:16984866 original size:55 final size:55
Alignment explanation
Indices: 16984726--16984902 Score: 185
Period size: 55 Copynumber: 3.2 Consensus size: 55
16984716 TAAAATATAA
* * * * * * * ** *
16984726 TAAAAAAATTAAAACATATAAGTTTATACTAATAATCTCTAACTGTCAGTATAAG
1 TAAAAAAATTAAAACATACAAGTATATACTGACAGTCTTTAACAGTTGGTATAGG
*
16984781 TAAGAAAATTAAAACATACAAGTATATACTGACAGTCTTTAACAGTTGGTATAGG
1 TAAAAAAATTAAAACATACAAGTATATACTGACAGTCTTTAACAGTTGGTATAGG
* * * * *
16984836 TAAAAAAATTAAAAAATACAAGTATATACTGACGGATGTTAAACA-TTGGTGTAGG
1 TAAAAAAATTAAAACATACAAGTATATACTGACAG-TCTTTAACAGTTGGTATAGG
16984891 TAAGAAAAATTA
1 TAA-AAAAATTA
16984903 CAAGTCTATA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
55 88 0.85
56 15 0.15
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (55 bp):
TAAAAAAATTAAAACATACAAGTATATACTGACAGTCTTTAACAGTTGGTATAGG
Found at i:16985006 original size:159 final size:160
Alignment explanation
Indices: 16984830--16985132 Score: 385
Period size: 159 Copynumber: 1.9 Consensus size: 160
16984820 TAACAGTTGG
* * ** *
16984830 TATAGGTAAAAAAATTAAAAAATACAAGTATATACTGA-CGGATGTTAAACATTGGTGTAGGTAA
1 TATAGGTAAAAAAATTAAAAAATACAAATATATACTGATAGGAT-TTAAACATCAGTATAGGTAA
* * *
16984894 GAAAAATTACAAGTCTATACTAATAAGCGTTAACTGTCGATATAGGTAAAAAAAATTAAAA-ATA
65 GAAAAATTACAAGTCTATACTAACAAGCATTAACTGTCGATATAGGCAAAAAAAATTAAAACATA
*
16984958 TAAGTCTATACTGATGGGCGCTAGCTATCGA
130 CAAGTCTATACTGATGGGCGCTAGCTATCGA
* * * * ** *
16984989 TATAGGTAAGAAAATTAAAACATACAAATCTATACTGATAGGCTTTAGGCGTCAGTATAGGTAAG
1 TATAGGTAAAAAAATTAAAAAATACAAATATATACTGATAGGATTTAAACATCAGTATAGGTAAG
* * * * *
16985054 AAAAATTACAAGTTTATGCTGACAGGCATTAACTGTTGATATAGGCAAAAAAAATTAAAACATAC
66 AAAAATTACAAGTCTATACTAACAAGCATTAACTGTCGATATAGGCAAAAAAAATTAAAACATAC
*
16985119 AAGTTTATACTGAT
131 AAGTCTATACTGAT
16985133 AGGTGTTAAC
Statistics
Matches: 120, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
159 101 0.84
160 19 0.16
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (160 bp):
TATAGGTAAAAAAATTAAAAAATACAAATATATACTGATAGGATTTAAACATCAGTATAGGTAAG
AAAAATTACAAGTCTATACTAACAAGCATTAACTGTCGATATAGGCAAAAAAAATTAAAACATAC
AAGTCTATACTGATGGGCGCTAGCTATCGA
Found at i:16986475 original size:19 final size:19
Alignment explanation
Indices: 16986428--16986475 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
16986418 ATAGGATCTG
**
16986428 CAATACTATTGTATGTGAT
1 CAATACTATTGTAAATGAT
* *
16986447 CAAAATTATTGTAAATGAT
1 CAATACTATTGTAAATGAT
16986466 CAATACTATT
1 CAATACTATT
16986476 AAAACATATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (19 bp):
CAATACTATTGTAAATGAT
Found at i:16990210 original size:3 final size:3
Alignment explanation
Indices: 16990202--16990241 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
16990192 ATTAATTAAT
16990202 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16990242 TAAAGATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16991798 original size:3 final size:3
Alignment explanation
Indices: 16991792--16991832 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
16991782 TAATAATAAT
*
16991792 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAT AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
16991833 TAATAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:16994772 original size:98 final size:99
Alignment explanation
Indices: 16994586--16994805 Score: 388
Period size: 98 Copynumber: 2.2 Consensus size: 99
16994576 ATTTTTATGT
16994586 AAATATTCTAATAGTTTGGTGAGACTTTATTATAAGATTTTTTTTTTTTTTAGAAAATATATTAA
1 AAATATTCTAATAGTTTGGTGAGACTTTATTATAAGA---TTTTTTTTTTTAGAAAATATATTAA
16994651 ATCTTACAATAGTTTAGTAAAATTTAATTTAAGATGC
63 ATCTTACAATAGTTTAGTAAAATTTAATTTAAGATGC
16994688 AAATATTCTAATAGTTTGGTGAGACTTTATTATAAGA-TTTTTTTTTTAGAAAATATATTAAATC
1 AAATATTCTAATAGTTTGGTGAGACTTTATTATAAGATTTTTTTTTTTAGAAAATATATTAAATC
* *
16994752 TTCCAATAGTTTAGTAAAATTTAATTTGAGATGC
66 TTACAATAGTTTAGTAAAATTTAATTTAAGATGC
16994786 AAATATTCTAATAGTTTGGT
1 AAATATTCTAATAGTTTGGT
16994806 AAGATAAAAT
Statistics
Matches: 116, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
98 79 0.68
102 37 0.32
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (99 bp):
AAATATTCTAATAGTTTGGTGAGACTTTATTATAAGATTTTTTTTTTTAGAAAATATATTAAATC
TTACAATAGTTTAGTAAAATTTAATTTAAGATGC
Found at i:16995086 original size:14 final size:13
Alignment explanation
Indices: 16995059--16995128 Score: 56
Period size: 14 Copynumber: 5.3 Consensus size: 13
16995049 AAAAAGAATC
*
16995059 TAAAACAATAAAAA
1 TAAAATAAT-AAAA
16995073 TAAAATAAATAAAA
1 TAAAAT-AATAAAA
* *
16995087 TGAAAT-AGAAAA
1 TAAAATAATAAAA
16995099 T-AAATAATAAAA
1 TAAAATAATAAAA
16995111 TCTAAAA-AATAAAA
1 --TAAAATAATAAAA
16995125 TAAA
1 TAAA
16995129 TGAAAATGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
11 4 0.09
12 15 0.32
14 22 0.47
15 6 0.13
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:16996495 original size:65 final size:64
Alignment explanation
Indices: 16996366--16996509 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
16996356 TACAAGTTAG
* **
16996366 AAAAAATAAAATGATCTGGATCAAATCGAGATCAAAACAGGTGACCGAAGTTGAACCATAAGTC
1 AAAAAATAAAATGATCTAGATCAAATCGAGATCAAAACAGGTGACCGAAGACGAACCATAAGTC
** * * * * *
16996430 AAAAAAATAAAATGATCTAGATTGAGTCGAGATCAAAATAGGTGACCG-AGACGAAATCGTGAGT
1 -AAAAAATAAAATGATCTAGATCAAATCGAGATCAAAACAGGTGACCGAAGACG-AACCATAAGT
16996494 C
64 C
16996495 AAAAAATAAAATGAT
1 AAAAAATAAAATGAT
16996510 TTGGACCGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 18 0.26
65 50 0.74
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.19
Consensus pattern (64 bp):
AAAAAATAAAATGATCTAGATCAAATCGAGATCAAAACAGGTGACCGAAGACGAACCATAAGTC
Found at i:17001180 original size:16 final size:16
Alignment explanation
Indices: 17001156--17001190 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17001146 ACTACATCCT
17001156 TTTTCTTTTCCTGTCA
1 TTTTCTTTTCCTGTCA
* *
17001172 TTTTGTTTTCCTTTCA
1 TTTTCTTTTCCTGTCA
17001188 TTT
1 TTT
17001191 CATATTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTCTTTTCCTGTCA
Found at i:17002605 original size:20 final size:21
Alignment explanation
Indices: 17002569--17002620 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
17002559 CCCGAAATTA
17002569 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
17002591 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
17002612 AT-AAATATT
1 ATAAAATATT
17002621 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:17002611 original size:21 final size:22
Alignment explanation
Indices: 17002569--17002620 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
17002559 CCCGAAATTA
17002569 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
17002591 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
17002612 AT-AAATATT
1 ATAAAATATT
17002621 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:17002703 original size:10 final size:10
Alignment explanation
Indices: 17002690--17002715 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
17002680 TTATATAATG
17002690 TCGGGTCGGC
1 TCGGGTCGGC
17002700 TCGGGTCGGC
1 TCGGGTCGGC
17002710 TCGGGT
1 TCGGGT
17002716 TTTAGGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.50, T:0.23
Consensus pattern (10 bp):
TCGGGTCGGC
Found at i:17002741 original size:11 final size:11
Alignment explanation
Indices: 17002725--17002753 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
17002715 TTTTAGGCAT
17002725 ACCCGACCCCG
1 ACCCGACCCCG
17002736 ACCCGACCCCG
1 ACCCGACCCCG
17002747 ACCCGAC
1 ACCCGAC
17002754 TTCGATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.62, G:0.17, T:0.00
Consensus pattern (11 bp):
ACCCGACCCCG
Found at i:17008026 original size:37 final size:38
Alignment explanation
Indices: 17007985--17008081 Score: 126
Period size: 37 Copynumber: 2.6 Consensus size: 38
17007975 ATAATTAGTA
* * *
17007985 AAATCTTCCAATAGTTTGGTAAGATTTACGTT-GATGC
1 AAATCTTCCAATAGTTTAGTAAGATTTAAGTTAGATAC
*
17008022 AAATC-TCTCAATAGTTTAGTAAGATTTAATTTAAGATAC
1 AAATCTTC-CAATAGTTTAGTAAGATTTAAGTT-AGATAC
17008061 AAATCTTCCAATAGTTTAGTA
1 AAATCTTCCAATAGTTTAGTA
17008082 GGATAAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
36 2 0.04
37 26 0.50
39 22 0.42
40 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (38 bp):
AAATCTTCCAATAGTTTAGTAAGATTTAAGTTAGATAC
Found at i:17008251 original size:3 final size:3
Alignment explanation
Indices: 17008230--17008303 Score: 121
Period size: 3 Copynumber: 24.3 Consensus size: 3
17008220 TCTTTAGAAA
* *
17008230 TAT TTT TAT TAT ATCT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17008276 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17008304 TAGAAGAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
3 64 0.97
4 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17008914 original size:3 final size:3
Alignment explanation
Indices: 17008906--17008937 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17008896 CTTCTTGTTT
17008906 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
17008938 CTTAGACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:17009021 original size:111 final size:111
Alignment explanation
Indices: 17008827--17009042 Score: 432
Period size: 111 Copynumber: 1.9 Consensus size: 111
17008817 GGTGATTTAT
17008827 CTTAGACTTAAATCCCAATCAATTTGATCCCTAACTTTATGCAAATAGATCTTTATTCCAAAAAA
1 CTTAGACTTAAATCCCAATCAATTTGATCCCTAACTTTATGCAAATAGATCTTTATTCCAAAAAA
17008892 TACCCTTCTTGTTTTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTA
66 TACCCTTCTTGTTTTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTA
17008938 CTTAGACTTAAATCCCAATCAATTTGATCCCTAACTTTATGCAAATAGATCTTTATTCCAAAAAA
1 CTTAGACTTAAATCCCAATCAATTTGATCCCTAACTTTATGCAAATAGATCTTTATTCCAAAAAA
17009003 TACCCTTCTTGTTTTAGTAGTAGTAGTAGTAGTAGTAGTA
66 TACCCTTCTTGTTTTAGTAGTAGTAGTAGTAGTAGTAGTA
17009043 AAGACAATAC
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (111 bp):
CTTAGACTTAAATCCCAATCAATTTGATCCCTAACTTTATGCAAATAGATCTTTATTCCAAAAAA
TACCCTTCTTGTTTTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTA
Found at i:17009025 original size:3 final size:3
Alignment explanation
Indices: 17009017--17009042 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17009007 CTTCTTGTTT
17009017 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
17009043 AAGACAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:17022145 original size:8 final size:8
Alignment explanation
Indices: 17022132--17022158 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17022122 TTTTTCAAAT
17022132 AATTCATA
1 AATTCATA
17022140 AATTCATA
1 AATTCATA
17022148 AATTCATA
1 AATTCATA
17022156 AAT
1 AAT
17022159 CAATGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
AATTCATA
Found at i:17024567 original size:5 final size:5
Alignment explanation
Indices: 17024558--17024597 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
17024548 GAGAAAGAAA
* *
17024558 AAAAT GAAAT AAAAT GAAAT AAAAT AAAAT AAAAT GAAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAA
17024598 AATAAAGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:17024573 original size:10 final size:10
Alignment explanation
Indices: 17024554--17024596 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
17024544 AAAGGAGAAA
17024554 GAAA-AAAAT
1 GAAATAAAAT
17024563 GAAATAAAAT
1 GAAATAAAAT
17024573 GAAATAAAAT
1 GAAATAAAAT
*
17024583 AAAATAAAAT
1 GAAATAAAAT
17024593 GAAA
1 GAAA
17024597 AAATAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 4 0.13
10 27 0.87
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.16
Consensus pattern (10 bp):
GAAATAAAAT
Found at i:17024581 original size:20 final size:19
Alignment explanation
Indices: 17024554--17024603 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
17024544 AAAGGAGAAA
*
17024554 GAAAAAAATGAAATAAAAT
1 GAAAAAAATAAAATAAAAT
17024573 GAAATAAAATAAAATAAAAT
1 GAAA-AAAATAAAATAAAAT
17024593 G-AAAAAATAAA
1 GAAAAAAATAAA
17024604 GAAGCACTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.28
19 6 0.21
20 15 0.52
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (19 bp):
GAAAAAAATAAAATAAAAT
Found at i:17025669 original size:50 final size:50
Alignment explanation
Indices: 17025518--17025693 Score: 246
Period size: 50 Copynumber: 3.5 Consensus size: 50
17025508 GTCACGGAGC
* * * * *
17025518 ATTTTCATATAAGATTTTTAAAGTTTCAAAGCCTCTGTTTATGATAAGCC
1 ATTTTCAGACAAGATTTTTAAAGTTTCAAAGTCTCTGTTTATGAGAAGCT
17025568 ATTTTCAGACAAGATTTTTAAAAGTTTCAAA-TCCTCTGTTTATGAGAAGCT
1 ATTTTCAGACAAGATTTTT-AAAGTTTCAAAGT-CTCTGTTTATGAGAAGCT
* * *
17025619 ATTTTTAGACAAGATTTTTAAAGTTTCAAAGTCTCTGTTTATGGGGAGCT
1 ATTTTCAGACAAGATTTTTAAAGTTTCAAAGTCTCTGTTTATGAGAAGCT
*
17025669 ATTTTCAAACAAGATTTTTAAAGTT
1 ATTTTCAGACAAGATTTTTAAAGTT
17025694 CTAAAGCCTC
Statistics
Matches: 113, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
50 67 0.59
51 46 0.41
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (50 bp):
ATTTTCAGACAAGATTTTTAAAGTTTCAAAGTCTCTGTTTATGAGAAGCT
Found at i:17025782 original size:44 final size:44
Alignment explanation
Indices: 17025682--17025811 Score: 145
Period size: 44 Copynumber: 3.0 Consensus size: 44
17025672 TTCAAACAAG
* * * * * *
17025682 ATTTTTAAAGTTCTAAAGCCTCTATATAGATAAACTTTTTCAAA
1 ATTTTTAAAGTTTTAAGGCCTCTATTTAGAGAAGCTTTTTTAAA
* *
17025726 ATCTTTAAAGTTTTAAGGTCTCTATTTAGAGAAGCTTTTTTAAA
1 ATTTTTAAAGTTTTAAGGCCTCTATTTAGAGAAGCTTTTTTAAA
* * *
17025770 ATTTTTAAAGTTTCAAGGCCTTTGTTTAGATG-AGCTTTTTTA
1 ATTTTTAAAGTTTTAAGGCCTCTATTTAGA-GAAGCTTTTTTA
17025812 GCATTGAAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 71 0.99
45 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (44 bp):
ATTTTTAAAGTTTTAAGGCCTCTATTTAGAGAAGCTTTTTTAAA
Found at i:17029063 original size:3 final size:3
Alignment explanation
Indices: 17029055--17029084 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17029045 TTTTCATATC
17029055 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17029085 GATGATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17029319 original size:16 final size:16
Alignment explanation
Indices: 17029285--17029319 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17029275 ATAAAATAAT
**
17029285 AATAATAAAAAGGGGA
1 AATAATAAAAAGGAAA
17029301 AATAATAAAAAGGAAA
1 AATAATAAAAAGGAAA
17029317 AAT
1 AAT
17029320 GACTCTCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (16 bp):
AATAATAAAAAGGAAA
Found at i:17033029 original size:34 final size:35
Alignment explanation
Indices: 17032969--17033039 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 35
17032959 ACCATCACAA
* *
17032969 GCATTATTATTTTTTATAGTCGTGAAATTATGAGT
1 GCATTATTATTATTTATAGCCGTGAAATTATGAGT
* *
17033004 GCATTATTA-TATTTATAGCCTTGAAATTATTAGT
1 GCATTATTATTATTTATAGCCGTGAAATTATGAGT
17033038 GC
1 GC
17033040 CATTCTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.46
Consensus pattern (35 bp):
GCATTATTATTATTTATAGCCGTGAAATTATGAGT
Found at i:17039035 original size:21 final size:22
Alignment explanation
Indices: 17038965--17039047 Score: 84
Period size: 21 Copynumber: 3.9 Consensus size: 22
17038955 TTTACTTATA
*
17038965 AATATTATATTAAT-AACAA-T
1 AATATTATATTAATAAATAAGT
* * *
17038985 -GTATTATAATATATTAATAAGT
1 AATATTATATTA-ATAAATAAGT
17039007 AATATTATATTAATAAATAA-T
1 AATATTATATTAATAAATAAGT
*
17039028 AATGTTATATTAATAAATAA
1 AATATTATATTAATAAATAA
17039048 AATAATAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.17
20 2 0.04
21 24 0.46
22 8 0.15
23 9 0.17
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (22 bp):
AATATTATATTAATAAATAAGT
Found at i:17039124 original size:18 final size:18
Alignment explanation
Indices: 17038996--17039144 Score: 57
Period size: 18 Copynumber: 9.1 Consensus size: 18
17038986 TATTATAATA
*
17038996 TATTAATAAGTAATAT-T
1 TATTAATAAATAATATAT
17039013 ATATTAATAAATAATA-A-
1 -TATTAATAAATAATATAT
* *
17039030 TGTTATATTAATAA-ATA-
1 TATTA-ATAAATAATATAT
* *
17039047 AAATAATAAAT-AT-TAT
1 TATTAATAAATAATATAT
*
17039063 TACTTTAATTAATAA-ATAT
1 TA--TTAATAAATAATATAT
17039082 TA-TAAT-AAT-ATAT-T
1 TATTAATAAATAATATAT
17039096 T-TT-AT---TAATATAT
1 TATTAATAAATAATATAT
*
17039109 TATTAATAAATAATATAC
1 TATTAATAAATAATATAT
*
17039127 TGTTAAT--ATAATATAT
1 TATTAATAAATAATATAT
17039143 TA
1 TA
17039145 ATGAATATTA
Statistics
Matches: 99, Mismatches: 14, Indels: 38
0.66 0.09 0.25
Matches are distributed among these distances:
11 1 0.01
12 4 0.04
13 4 0.04
14 6 0.06
15 10 0.10
16 24 0.24
17 10 0.10
18 34 0.34
19 6 0.06
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (18 bp):
TATTAATAAATAATATAT
Found at i:17039143 original size:34 final size:32
Alignment explanation
Indices: 17039006--17039144 Score: 110
Period size: 33 Copynumber: 4.3 Consensus size: 32
17038996 TATTAATAAG
17039006 TAATAT-TATATTAATAAATAATA-ATGTTATAT
1 TAATATAT-TATTAATAAATAATATATGTTA-AT
* * * *
17039038 TAATAAATAAAATAATAAATATTATTACT-TTAAT
1 TAATATAT-TATTAATAAATAATA-TA-TGTTAAT
* * *
17039072 TAATA-AATATT-AT-AATAATATATTTTTAT
1 TAATATATTATTAATAAATAATATATGTTAAT
17039101 TAATATATTATTAATAAATAATATACTGTTAAT
1 TAATATATTATTAATAAATAATATA-TGTTAAT
17039134 ATAATATATTA
1 -TAATATATTA
17039145 ATGAATATTA
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
28 1 0.01
29 11 0.13
30 11 0.13
31 4 0.05
32 16 0.19
33 20 0.24
34 17 0.20
35 4 0.05
36 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (32 bp):
TAATATATTATTAATAAATAATATATGTTAAT
Found at i:17039274 original size:15 final size:15
Alignment explanation
Indices: 17039254--17039305 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
17039244 ATATTATTAA
17039254 AATATAATTATTTTT
1 AATATAATTATTTTT
* *
17039269 AATATAAATAATTTT
1 AATATAATTATTTTT
*
17039284 AATAATAAATAATTTTT
1 AAT-AT-AATTATTTTT
17039301 AATAT
1 AATAT
17039306 TTTAATAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 16 0.53
16 4 0.13
17 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATAATTATTTTT
Found at i:17039299 original size:32 final size:32
Alignment explanation
Indices: 17039233--17039305 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 32
17039223 AATATTTTAA
*
17039233 TTTAATATTAAATATTATTAAAATATAATTATT
1 TTTAATA-TAAATATTATTAAAATATAATAATT
17039266 TTTAATATAAATAATT-TTAATAATA-AATAATT
1 TTTAATATAAAT-ATTATTAA-AATATAATAATT
17039298 TTTAATAT
1 TTTAATAT
17039306 TTTAATAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
32 23 0.62
33 14 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAATATAAATATTATTAAAATATAATAATT
Found at i:17039303 original size:17 final size:17
Alignment explanation
Indices: 17039233--17039304 Score: 80
Period size: 16 Copynumber: 4.4 Consensus size: 17
17039223 AATATTTTAA
*
17039233 TTTAATATTAAAT-ATT
1 TTTAATAATAAATAATT
* *
17039249 ATTAA-AATATAATTATT
1 TTTAATAATA-AATAATT
17039266 TTTAAT-ATAAATAA-T
1 TTTAATAATAAATAATT
17039281 TTTAATAATAAATAATT
1 TTTAATAATAAATAATT
17039298 TTTAATA
1 TTTAATA
17039305 TTTTAATAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
15 10 0.21
16 19 0.40
17 18 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATAATAAATAATT
Found at i:17039456 original size:15 final size:14
Alignment explanation
Indices: 17039432--17039469 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17039422 CAAAAAATAT
17039432 AAAT-ATTTTTTAA
1 AAATCATTTTTTAA
* *
17039445 AAATCAATTTTTAT
1 AAATCATTTTTTAA
17039459 AAATCATTTTT
1 AAATCATTTTT
17039470 CGGAGCCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATCATTTTTTAA
Found at i:17043031 original size:22 final size:22
Alignment explanation
Indices: 17043006--17043053 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
17042996 TTACTGTATC
*
17043006 AATTCGATTCGATTACAACTCT
1 AATTCGACTCGATTACAACTCT
*
17043028 AATTCGACTCGATTTCAACTCT
1 AATTCGACTCGATTACAACTCT
17043050 AATT
1 AATT
17043054 GTGACCGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (22 bp):
AATTCGACTCGATTACAACTCT
Found at i:17044732 original size:17 final size:17
Alignment explanation
Indices: 17044712--17044744 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17044702 TAATATTTAT
17044712 AAATTAATAAATTATTA
1 AAATTAATAAATTATTA
*
17044729 AAATTATTAAATTATT
1 AAATTAATAAATTATT
17044745 TTTATGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTAATAAATTATTA
Found at i:17044743 original size:8 final size:8
Alignment explanation
Indices: 17044711--17044744 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
17044701 TTAATATTTA
*
17044711 TAAATTAA
1 TAAATTAT
17044719 TAAATTAT
1 TAAATTAT
17044727 TAAAATTAT
1 T-AAATTAT
17044736 TAAATTAT
1 TAAATTAT
17044744 T
1 T
17044745 TTTATGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAAATTAT
Found at i:17046744 original size:2 final size:2
Alignment explanation
Indices: 17046717--17046762 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
17046707 TCCTTTTAGA
17046717 AT AT A- AT AT A- AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17046755 AT AT AT AT
1 AT AT AT AT
17046763 TAATACAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17047871 original size:21 final size:21
Alignment explanation
Indices: 17047832--17047871 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17047822 GTTACTTTAT
*
17047832 AAAAAAATATATTATAATTGA
1 AAAAAAATATATAATAATTGA
17047853 AAAAAAAT-TATAATGAATT
1 AAAAAAATATATAAT-AATT
17047872 ATTTTCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAAAATATATAATAATTGA
Found at i:17049745 original size:16 final size:16
Alignment explanation
Indices: 17049724--17049769 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
17049714 GAAATTTCAT
17049724 TTAGAAACGTAACATA
1 TTAGAAACGTAACATA
17049740 TTAGAAACGTAACATA
1 TTAGAAACGTAACATA
17049756 TTAGAAACGTAACA
1 TTAGAAACGTAACA
17049770 GACATACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (16 bp):
TTAGAAACGTAACATA
Found at i:17056335 original size:89 final size:89
Alignment explanation
Indices: 17056111--17056363 Score: 312
Period size: 89 Copynumber: 2.8 Consensus size: 89
17056101 CATAAAATAG
* * *
17056111 GAAAAAGATAACTAAAATAAGAACAATCTTTAATATCCTATTATTTATATTATTTCATAAAATAA
1 GAAAAA-ATAAATAAAATAAGAACAATATTAAATATCCTATTATTTATATTATTTCATAAAATAA
* * * *
17056176 AAACAATTAGAAGATAACAACATTGA
65 GAACAATGAGAAAATAAAAACATT-A
* *
17056202 GACAAAAACAAATAAAATAAGAACAA-ATTTAGAATATCTTATTATTTATATTATTTCATAAAAT
1 GA-AAAAATAAATAAAATAAGAACAATA-TTA-AATATCCTATTATTTATATTATTTCATAAAAT
*
17056266 AAGAATAATGAGAAAATAAAAACATT-
63 AAGAACAATGAGAAAATAAAAACATTA
* * * *
17056292 TAAAAAATAAATAAAATAAAAACAATATTCAAATATCCTATTATTTACATTGTTTCATAAAATAA
1 GAAAAAATAAATAAAATAAGAACAATATT-AAATATCCTATTATTTATATTATTTCATAAAATAA
17056357 GAACAAT
65 GAACAAT
17056364 AACAAAATGA
Statistics
Matches: 140, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
89 60 0.43
90 3 0.02
91 21 0.15
92 56 0.40
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.31
Consensus pattern (89 bp):
GAAAAAATAAATAAAATAAGAACAATATTAAATATCCTATTATTTATATTATTTCATAAAATAAG
AACAATGAGAAAATAAAAACATTA
Found at i:17057550 original size:29 final size:29
Alignment explanation
Indices: 17057518--17057577 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
17057508 AAATTATATA
17057518 TTTTTA-TTATACAT-AAATAAATTTTCAT
1 TTTTTATTTATA-ATCAAATAAATTTTCAT
* *
17057546 TTTTTATTTATATTCAAATAAATTTTTAT
1 TTTTTATTTATAATCAAATAAATTTTCAT
17057575 TTT
1 TTT
17057578 AAACAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTATTTATAATCAAATAAATTTTCAT
Found at i:17057586 original size:22 final size:22
Alignment explanation
Indices: 17057561--17057602 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17057551 ATTTATATTC
*
17057561 AAATAAATT-TTTATTTTAAACA
1 AAAT-AATTATTTATATTAAACA
17057583 AAATAATTATTTATATTAAA
1 AAATAATTATTTATATTAAA
17057603 ATTCAATTTA
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:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATAATTATTTATATTAAACA
Found at i:17059173 original size:2 final size:2
Alignment explanation
Indices: 17059166--17059197 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17059156 CTCCTTCCTA
17059166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17059198 TAATAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17068253 original size:29 final size:28
Alignment explanation
Indices: 17068221--17068310 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
17068211 AATTTTTATC
*
17068221 ATTTTATTATAATCAAAACATTTATTTTT
1 ATTTAATTATAATCAAAA-ATTTATTTTT
*
17068250 ATTTAATTGAGTAATCAAAATTTTA-TTTT
1 ATTTAATT-A-TAATCAAAAATTTATTTTT
*
17068279 ATTTAATTA-AATTCTTAAATATTTATTTTT
1 ATTTAATTATAA-TC--AAAAATTTATTTTT
17068309 AT
1 AT
17068311 CTACTTAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 1 0.02
29 26 0.51
30 11 0.22
31 9 0.18
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTTAATTATAATCAAAAATTTATTTTT
Found at i:17074060 original size:12 final size:12
Alignment explanation
Indices: 17074036--17074079 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
17074026 GGTCCTGGCA
17074036 GTGGAA-GAGGTG
1 GTGGAAGGA-GTG
*
17074048 GTGGGAGGAGTG
1 GTGGAAGGAGTG
17074060 GTGGAAGGAGTG
1 GTGGAAGGAGTG
*
17074072 GAGGAAGG
1 GTGGAAGG
17074080 GATGGTAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 26 0.93
13 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.61, T:0.14
Consensus pattern (12 bp):
GTGGAAGGAGTG
Found at i:17074097 original size:36 final size:36
Alignment explanation
Indices: 17074057--17074132 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
17074047 GGTGGGAGGA
17074057 GTGGTGGAAGGAGTGGAGGAAGGGATGGTAGTGGCC
1 GTGGTGGAAGGAGTGGAGGAAGGGATGGTAGTGGCC
* * * *
17074093 GTGGTGGATGGAGTGGGGGAAGGGATGGTGGTGGTC
1 GTGGTGGAAGGAGTGGAGGAAGGGATGGTAGTGGCC
17074129 GTGG
1 GTGG
17074133 AGGTAGGCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.04, G:0.59, T:0.20
Consensus pattern (36 bp):
GTGGTGGAAGGAGTGGAGGAAGGGATGGTAGTGGCC
Found at i:17079322 original size:17 final size:18
Alignment explanation
Indices: 17079290--17079323 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17079280 CGATCCTTCC
*
17079290 TTTATTTTTCATTATTTT
1 TTTAATTTTCATTATTTT
17079308 TTTAATTTT-ATTATTT
1 TTTAATTTTCATTATTT
17079324 GATTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTAATTTTCATTATTTT
Found at i:17079331 original size:22 final size:22
Alignment explanation
Indices: 17079303--17079344 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17079293 ATTTTTCATT
17079303 ATTTTTTTAATTTTATTATTTG
1 ATTTTTTTAATTTTATTATTTG
*
17079325 ATTTTTTTAATTTTTTTATT
1 ATTTTTTTAATTTTATTATT
17079345 AAAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
ATTTTTTTAATTTTATTATTTG
Found at i:17079607 original size:25 final size:25
Alignment explanation
Indices: 17079579--17079627 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
17079569 TTTTTTTCAA
* * *
17079579 TTATTTTTTAAAGTTTTTGCTTTTT
1 TTATGTTTAAAAGTTTTTACTTTTT
*
17079604 TTATGTTTAAAATTTTTTACTTTT
1 TTATGTTTAAAAGTTTTTACTTTT
17079628 ATTTTTCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATGTTTAAAAGTTTTTACTTTTT
Found at i:17080315 original size:20 final size:20
Alignment explanation
Indices: 17080265--17080315 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
17080255 ATTTAATAAA
*
17080265 AAATTATATTTATATATAATT
1 AAATTATA-ATATATATAATT
* *
17080286 AAGTTGTAATATATATAATT
1 AAATTATAATATATATAATT
17080306 AAATTATAAT
1 AAATTATAAT
17080316 TTACATTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
AAATTATAATATATATAATT
Found at i:17086539 original size:126 final size:126
Alignment explanation
Indices: 17086308--17086559 Score: 479
Period size: 126 Copynumber: 2.0 Consensus size: 126
17086298 GAAAGAAAAG
17086308 AAGAAAGGTAAGCATGTTAGCTTTGCAGATATATTGAAGTGTTTGGAGATTCAAGTCAATGGAGG
1 AAGAAAGGTAAGCATGTTAGCTTTGCAGATATATTGAAGTGTTTGGAGATTCAAGTCAATGGAGG
17086373 ATTTGTTGGGATTTGCCTTGAATCTCAGAATCTCACATCGAAAGTTAAGTAAGTTGGAATT
66 ATTTGTTGGGATTTGCCTTGAATCTCAGAATCTCACATCGAAAGTTAAGTAAGTTGGAATT
17086434 AAGAAAGGTAAGCATGTTAGCTTTGCAGATACTATTGAAGTGTTTGGAGATTCAAGTCAATGGAG
1 AAGAAAGGTAAGCATGTTAGCTTTGCAGATA-TATTGAAGTGTTTGGAGATTCAAGTCAATGGAG
*
17086499 GATTTGTTGGGATTTGCCTT-AATCTCAGAATCTCACATCGAAAGTTAAGTAAGTTTGAATT
65 GATTTGTTGGGATTTGCCTTGAATCTCAGAATCTCACATCGAAAGTTAAGTAAGTTGGAATT
17086560 TGTCTTGTAT
Statistics
Matches: 124, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
126 71 0.57
127 53 0.43
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33
Consensus pattern (126 bp):
AAGAAAGGTAAGCATGTTAGCTTTGCAGATATATTGAAGTGTTTGGAGATTCAAGTCAATGGAGG
ATTTGTTGGGATTTGCCTTGAATCTCAGAATCTCACATCGAAAGTTAAGTAAGTTGGAATT
Found at i:17088881 original size:10 final size:10
Alignment explanation
Indices: 17088866--17088902 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
17088856 ATTCAAATTA
17088866 TTTAAATAAT
1 TTTAAATAAT
17088876 TTTAAATAAT
1 TTTAAATAAT
**
17088886 TTTATTTAAT
1 TTTAAATAAT
17088896 TTTAAAT
1 TTTAAAT
17088903 TATTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTAAATAAT
Found at i:17088912 original size:20 final size:20
Alignment explanation
Indices: 17088860--17088912 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
17088850 ATATTTATTC
17088860 AAATTATTTAAA--TAATTTT
1 AAATTA-TTAAATTTAATTTT
* **
17088879 AAATAATTTTATTTAATTTT
1 AAATTATTAAATTTAATTTT
17088899 AAATTATTAAATTT
1 AAATTATTAAATTT
17088913 TAATCATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 18 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATTATTAAATTTAATTTT
Done.