Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 35 of 64
Found at i:5460342 original size:38 final size:34
Alignment explanation
Indices: 5460286--5460358 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 34
5460276 AATATGCATG
* *
5460286 AACATAATAATAATATATGACGTATGCATGATAATTA
1 AACATAATAATAAAATATGA---ATACATGATAATTA
*
5460323 AACATGAATGATAAAATATGAATACATGATAATTA
1 AACAT-AATAATAAAATATGAATACATGATAATTA
5460358 A
1 A
5460359 GGAATGCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 14 0.44
37 5 0.16
38 13 0.41
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (34 bp):
AACATAATAATAAAATATGAATACATGATAATTA
Found at i:5460440 original size:18 final size:18
Alignment explanation
Indices: 5460412--5460455 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5460402 ATCAAGTGGT
*
5460412 TTTAAGATTTAAGGGTTGG
1 TTTAAGGTTT-AGGGTTGG
5460431 -TTAAGGTTTAGGGTTGG
1 TTTAAGGTTTAGGGTTGG
5460448 TTTAAGGT
1 TTTAAGGT
5460456 CAAGGCTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (18 bp):
TTTAAGGTTTAGGGTTGG
Found at i:5460518 original size:14 final size:13
Alignment explanation
Indices: 5460475--5460708 Score: 160
Period size: 13 Copynumber: 17.8 Consensus size: 13
5460465 GGTTTATGAT
*
5460475 TTTAGGGTTTGGG
1 TTTAGGGTTTAGG
* * * *
5460488 GTTAAGGTTTTGA
1 TTTAGGGTTTAGG
5460501 TTTAGGGTTTAAGG
1 TTTAGGGTTT-AGG
*
5460515 TTTAGGGTTTAGT
1 TTTAGGGTTTAGG
*
5460528 TTTATGGTTTAGG
1 TTTAGGGTTTAGG
*
5460541 ATTTAGGGTCTAGG
1 -TTTAGGGTTTAGG
5460555 -TTAGGGTTTAGG
1 TTTAGGGTTTAGG
*
5460567 -TTA-GGTCTAAGG
1 TTTAGGGT-TTAGG
*
5460579 TTT-GGATTTAGG
1 TTTAGGGTTTAGG
*
5460591 GTTAGGGGTTTAGG
1 TTTA-GGGTTTAGG
*
5460605 ATCTA-GGTTTAGGG
1 -TTTAGGGTTTA-GG
5460619 TTTAGGGTTTAGG
1 TTTAGGGTTTAGG
*
5460632 TTTA-TGTTTAGGG
1 TTTAGGGTTTA-GG
*
5460645 TTTAAGGTTTAGGG
1 TTTAGGGTTTA-GG
*
5460659 TTTAGGGTTTAGA
1 TTTAGGGTTTAGG
*
5460672 TTT-GAGGTTT-GAT
1 TTTAG-GGTTTAG-G
* *
5460685 TTTAGGATTTACG
1 TTTAGGGTTTAGG
5460698 TTTAGGGTTTA
1 TTTAGGGTTTA
5460709 NNNNNNNNNN
Statistics
Matches: 174, Mismatches: 31, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
11 3 0.02
12 31 0.18
13 81 0.47
14 57 0.33
15 2 0.01
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.45
Consensus pattern (13 bp):
TTTAGGGTTTAGG
Found at i:5460523 original size:27 final size:27
Alignment explanation
Indices: 5460462--5460663 Score: 137
Period size: 27 Copynumber: 7.4 Consensus size: 27
5460452 AGGTCAAGGC
* *
5460462 TAGGGTTTATGATTTTAGGGTTT-GGGGT
1 TAGGGTTTA-GA-TTTAGGGTTTAAGGTT
* *
5460490 TAAGGTTTTGATTTAGGGTTTAAGGTT
1 TAGGGTTTAGATTTAGGGTTTAAGGTT
* *
5460517 TAGGGTTTAGTTTTATGGTTT-AGGATT
1 TAGGGTTTAGATTTAGGGTTTAAGG-TT
* * *
5460544 TAGGGTCTAG-GTTAGGGTTTAGGTTAGGTC
1 TAGGGTTTAGATTTAGGGTTTA----AGGTT
* * *
5460574 TAAGGTTTGGATTTAGGG-TTAGGGGTT
1 TAGGGTTTAGATTTAGGGTTTA-AGGTT
* * * *
5460601 TAGGATCTAGGTTTAGGGTTTAGGGTT
1 TAGGGTTTAGATTTAGGGTTTAAGGTT
5460628 TA-GGTTTATG-TTTAGGGTTTAAGGTT
1 TAGGGTTTA-GATTTAGGGTTTAAGGTT
5460654 TAGGGTTTAG
1 TAGGGTTTAG
5460664 GGTTTAGATT
Statistics
Matches: 136, Mismatches: 27, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
26 43 0.32
27 63 0.46
28 10 0.07
30 11 0.08
31 9 0.07
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.45
Consensus pattern (27 bp):
TAGGGTTTAGATTTAGGGTTTAAGGTT
Found at i:5460531 original size:20 final size:20
Alignment explanation
Indices: 5460475--5460708 Score: 140
Period size: 20 Copynumber: 11.6 Consensus size: 20
5460465 GGTTTATGAT
* *
5460475 TTTAGGGTTTGGGGTTAAGG
1 TTTAGGGTTTAGGTTTAAGG
* *
5460495 TTT-TGATTTAGGGTTTAAGG
1 TTTAGGGTTTA-GGTTTAAGG
* *
5460515 TTTAGGGTTTAGTTTTATGG
1 TTTAGGGTTTAGGTTTAAGG
* *
5460535 TTTAGGATTTAGGGTCT-AGG
1 TTTAGGGTTTA-GGTTTAAGG
5460555 -TTAGGGTTTAGGTTAGGTCTAAGG
1 TTTAGGGTTTAGG-T---T-TAAGG
* * *
5460579 TTT-GGATTTAGGGTTAGGGG
1 TTTAGGGTTTAGGTTTA-AGG
* * *
5460599 TTTAGGATCTAGGTTTAGGG
1 TTTAGGGTTTAGGTTTAAGG
*
5460619 TTTAGGGTTTAGGTTT-ATG
1 TTTAGGGTTTAGGTTTAAGG
*
5460638 TTTAGGGTTTAAGGTTTAGGG
1 TTTAGGGTTT-AGGTTTAAGG
* *
5460659 TTTAGGGTTTAGATTTGAGG
1 TTTAGGGTTTAGGTTTAAGG
** *
5460679 TTT-GATTTTAGGATTT-ACG
1 TTTAGGGTTTAGG-TTTAAGG
5460698 TTTAGGGTTTA
1 TTTAGGGTTTA
5460709 NNNNNNNNNN
Statistics
Matches: 164, Mismatches: 34, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
18 2 0.01
19 38 0.23
20 80 0.49
21 30 0.18
23 1 0.01
24 11 0.07
25 2 0.01
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.45
Consensus pattern (20 bp):
TTTAGGGTTTAGGTTTAAGG
Found at i:5460545 original size:7 final size:6
Alignment explanation
Indices: 5460487--5460708 Score: 110
Period size: 7 Copynumber: 34.0 Consensus size: 6
5460477 TAGGGTTTGG
* * * *
5460487 GGTTAA GGTTTT GATTTA GGGTTTAA GGTTTA GGGTTTA GTTTTA TGGTTTA
1 GGTTTA GGTTTA GGTTTA -GGTTT-A GGTTTA -GGTTTA GGTTTA -GGTTTA
* *
5460539 GGATTTA GGGTCTA GG-TTA GGGTTTA GG-TTA GGTCTAA GGTTT- GGATTTA
1 GG-TTTA -GGTTTA GGTTTA -GGTTTA GGTTTA GGT-TTA GGTTTA GG-TTTA
* * *
5460589 GGGTTA GGGGTTTA GGATCTA GGTTTA GGGTTTA GGGTTTA GGTTTA TGTTTA
1 GGTTTA --GGTTTA GG-TTTA GGTTTA -GGTTTA -GGTTTA GGTTTA GGTTTA
* *
5460642 GGGTTTAA GGTTTA GGGTTTA GGGTTTA GATTTGA GGTTT- GATTTTA
1 -GGTTT-A GGTTTA -GGTTTA -GGTTTA GGTTT-A GGTTTA G-GTTTA
*
5460689 GGATTTA CGTTTA GGGTTTA
1 GG-TTTA GGTTTA -GGTTTA
5460709 NNNNNNNNNN
Statistics
Matches: 169, Mismatches: 23, Indels: 47
0.71 0.10 0.20
Matches are distributed among these distances:
5 10 0.06
6 57 0.34
7 93 0.55
8 9 0.05
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (6 bp):
GGTTTA
Found at i:5460560 original size:12 final size:12
Alignment explanation
Indices: 5460543--5460580 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5460533 GGTTTAGGAT
5460543 TTAGGGTCTAGG
1 TTAGGGTCTAGG
*
5460555 TTAGGGTTTAGG
1 TTAGGGTCTAGG
5460567 TTA-GGTCTAAGG
1 TTAGGGTCT-AGG
5460579 TT
1 TT
5460581 TGGATTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.18, C:0.05, G:0.37, T:0.39
Consensus pattern (12 bp):
TTAGGGTCTAGG
Found at i:5460601 original size:84 final size:85
Alignment explanation
Indices: 5460490--5460708 Score: 214
Period size: 84 Copynumber: 2.6 Consensus size: 85
5460480 GGTTTGGGGT
* * * * *
5460490 TAAGGTTTTGATTTAGGGTTTAAGGTTTAGGGTTTAGTTTTATGGTTTAGGATTTAGGGTCTA-G
1 TAAGGTTTGGATTTAGGGTTTAAGGTTTAGGATCTAGGTTTAGGGTTTAGGATTTA-GGTCTATG
5460554 GTTAGGGTTT-AGGTTAGGTC
65 GTTAGGGTTTAAGGTTAGGTC
* * *
5460574 TAAGGTTTGGATTTAGGG-TTAGGGGTTTAGGATCTAGGTTTAGGGTTTAGGGTTTAGGTTTATG
1 TAAGGTTTGGATTTAGGGTTTA-AGGTTTAGGATCTAGGTTTAGGGTTTAGGATTTAGGTCTATG
* *
5460638 TTTAGGGTTTAAGGTTTAGGGTT
65 GTTAGGGTTTAAGG-TTA-GGTC
* * * * * *
5460661 TAGGGTTTAGATTT-GAGGTTTGA-TTTTAGGATTTACGTTTAGGGTTTA
1 TAAGGTTTGGATTTAG-GGTTTAAGGTTTAGGATCTAGGTTTAGGGTTTA
5460709 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
83 8 0.07
84 55 0.50
85 3 0.03
86 26 0.23
87 17 0.15
88 2 0.02
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (85 bp):
TAAGGTTTGGATTTAGGGTTTAAGGTTTAGGATCTAGGTTTAGGGTTTAGGATTTAGGTCTATGG
TTAGGGTTTAAGGTTAGGTC
Found at i:5461726 original size:11 final size:11
Alignment explanation
Indices: 5461710--5461749 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5461700 NNNNNNNNNT
5461710 TAGGTTAGGTC
1 TAGGTTAGGTC
*
5461721 TAGGTTAGGGTT
1 TAGGTTA-GGTC
5461733 TAGGTTAGGTC
1 TAGGTTAGGTC
*
5461744 CAGGTT
1 TAGGTT
5461750 TGGATTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.17, C:0.07, G:0.38, T:0.38
Consensus pattern (11 bp):
TAGGTTAGGTC
Found at i:5461739 original size:23 final size:23
Alignment explanation
Indices: 5461709--5461765 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
5461699 NNNNNNNNNN
* *
5461709 TTAGGTTAGGTCTAGGTTAGGGT
1 TTAGGTTAGGTCCAGGTTAGGAT
*
5461732 TTAGGTTAGGTCCAGGTTTGGAT
1 TTAGGTTAGGTCCAGGTTAGGAT
5461755 TTAGGGTTAGG
1 TTA-GGTTAGG
5461766 GGTTTAGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.18, C:0.05, G:0.39, T:0.39
Consensus pattern (23 bp):
TTAGGTTAGGTCCAGGTTAGGAT
Found at i:5461791 original size:7 final size:7
Alignment explanation
Indices: 5461754--5461861 Score: 63
Period size: 7 Copynumber: 16.4 Consensus size: 7
5461744 CAGGTTTGGA
5461754 TTTAGGG
1 TTTAGGG
5461761 -TTAGGGG
1 TTTA-GGG
*
5461768 TTTAGGA
1 TTTAGGG
*
5461775 TCTA-GG
1 TTTAGGG
5461781 -TTAGGG
1 TTTAGGG
5461787 TTTAGGG
1 TTTAGGG
5461794 TTTA-GG
1 TTTAGGG
5461800 TTTAGGG
1 TTTAGGG
*
5461807 TTTA-GA
1 TTTAGGG
5461813 TTT-GAGG
1 TTTAG-GG
**
5461820 TTT-GAT
1 TTTAGGG
*
5461826 TTTAGGA
1 TTTAGGG
*
5461833 TTTA-CG
1 TTTAGGG
5461839 TTTAGGG
1 TTTAGGG
5461846 TTTA-GG
1 TTTAGGG
*
5461852 TTGAGGG
1 TTTAGGG
5461859 TTT
1 TTT
5461862 TGGTTTGGAG
Statistics
Matches: 76, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
5 2 0.03
6 28 0.37
7 43 0.57
8 3 0.04
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:5461795 original size:13 final size:13
Alignment explanation
Indices: 5461723--5461811 Score: 62
Period size: 13 Copynumber: 7.0 Consensus size: 13
5461713 GTTAGGTCTA
5461723 GGTTAGGGTTTA-
1 GGTTAGGGTTTAG
**
5461735 GGTTA-GGTCCA-
1 GGTTAGGGTTTAG
* *
5461746 GGTTTGGATTTAG
1 GGTTAGGGTTTAG
5461759 GGTTAGGGGTTTAG
1 GGTTA-GGGTTTAG
*
5461773 GATCTA-GG-TTAG
1 GGT-TAGGGTTTAG
5461785 GGTTTAGGGTTTAG
1 GG-TTAGGGTTTAG
*
5461799 GTTTAGGGTTTAG
1 GGTTAGGGTTTAG
5461812 ATTTGAGGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
11 8 0.14
12 15 0.25
13 20 0.34
14 14 0.24
15 2 0.03
ACGTcount: A:0.17, C:0.03, G:0.40, T:0.39
Consensus pattern (13 bp):
GGTTAGGGTTTAG
Found at i:5461821 original size:13 final size:13
Alignment explanation
Indices: 5461787--5461861 Score: 66
Period size: 13 Copynumber: 5.8 Consensus size: 13
5461777 TAGGTTAGGG
*
5461787 TTTAGGGTTTAGG
1 TTTAGGGTTTAGA
5461800 TTTAGGGTTTAGA
1 TTTAGGGTTTAGA
5461813 TTT-GAGGTTT-GA
1 TTTAG-GGTTTAGA
*
5461825 TTTTAGGATTTACG-
1 -TTTAGGGTTTA-GA
*
5461839 TTTAGGGTTTAGG
1 TTTAGGGTTTAGA
*
5461852 TTGAGGGTTT
1 TTTAGGGTTT
5461862 TGGTTTGGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
12 4 0.08
13 46 0.88
14 1 0.02
15 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.33, T:0.48
Consensus pattern (13 bp):
TTTAGGGTTTAGA
Found at i:5461821 original size:26 final size:26
Alignment explanation
Indices: 5461786--5461861 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
5461776 CTAGGTTAGG
5461786 GTTTAGGGTTTAGGTTTAGGGTTTA-
1 GTTTAGGGTTTAGGTTTAGGGTTTAC
* *
5461811 GATTT-GAGGTTT-GATTTTAGGATTTAC
1 G-TTTAG-GGTTTAG-GTTTAGGGTTTAC
*
5461838 GTTTAGGGTTTAGGTTGAGGGTTT
1 GTTTAGGGTTTAGGTTTAGGGTTT
5461862 TGGTTTGGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
25 3 0.08
26 34 0.85
27 3 0.08
ACGTcount: A:0.17, C:0.01, G:0.34, T:0.47
Consensus pattern (26 bp):
GTTTAGGGTTTAGGTTTAGGGTTTAC
Found at i:5461821 original size:39 final size:38
Alignment explanation
Indices: 5461721--5461850 Score: 115
Period size: 39 Copynumber: 3.4 Consensus size: 38
5461711 AGGTTAGGTC
* *
5461721 TAGG-TTAGGGTTTAGGT-TAGGTCCA-GGTTT-GGATT
1 TAGGTTTAGGGTTTAGATCTAGGT-TAGGGTTTAGGATT
* *
5461756 TAGGGTTAGGGGTTTAGGATCTAGGTTAGGGTTTAGGGTT
1 TAGGTTTA-GGGTTTA-GATCTAGGTTAGGGTTTAGGATT
* * **
5461796 TAGGTTTAGGGTTTAGATTTGAGGTTTGATTTTAGGATT
1 TAGGTTTAGGGTTTAGATCT-AGGTTAGGGTTTAGGATT
*
5461835 TACGTTTAGGGTTTAG
1 TAGGTTTAGGGTTTAG
5461851 GTTGAGGGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
35 4 0.05
36 3 0.04
37 7 0.09
38 7 0.09
39 46 0.59
40 11 0.14
ACGTcount: A:0.18, C:0.03, G:0.36, T:0.42
Consensus pattern (38 bp):
TAGGTTTAGGGTTTAGATCTAGGTTAGGGTTTAGGATT
Found at i:5464333 original size:50 final size:49
Alignment explanation
Indices: 5464266--5464422 Score: 160
Period size: 50 Copynumber: 3.2 Consensus size: 49
5464256 AGTCTTAAAA
* **
5464266 TTTGAAAAACTCATCTAAATAGAGGCTACAAAACTTTAAAAAGGT-AAGCT
1 TTTGAAAAACTCCTCTAAATAGAGGCTACAAAACTTTAAAAACCTCAA--T
* *
5464316 TTTGCAAAACTCCTCTAAATAGTA-GTTACAAATA-TTT-AAAACCTCAAT
1 TTTGAAAAACTCCTCTAAATAG-AGGCTACAAA-ACTTTAAAAACCTCAAT
* * * * *
5464364 TTAGAAAAACTCCTCTAAACAAAGGCTATAAAACTTTAAAAATCTCAAT
1 TTTGAAAAACTCCTCTAAATAGAGGCTACAAAACTTTAAAAACCTCAAT
5464413 TTTGAAAAAC
1 TTTGAAAAAC
5464423 ATCTTTAAAG
Statistics
Matches: 88, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
47 2 0.02
48 28 0.32
49 24 0.27
50 32 0.36
51 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (49 bp):
TTTGAAAAACTCCTCTAAATAGAGGCTACAAAACTTTAAAAACCTCAAT
Found at i:5464516 original size:49 final size:50
Alignment explanation
Indices: 5464399--5464585 Score: 145
Period size: 49 Copynumber: 3.8 Consensus size: 50
5464389 CTATAAAACT
* * * * *
5464399 TTAAAAATCTCAATTTTGAAAAA-CATCTT-TAAAGAAAAGCT-AGGAA-C
1 TTAAAAATCTCAACTTTGAAAAAGC-TCTTATAAAGATAGGCTAAGAAATA
* * *
5464446 TTCAAAATCTCAAATTATGAAAAAGCTCTTATAAAGATTGGCTAAGAAATA
1 TTAAAAATCTCAACTT-TGAAAAAGCTCTTATAAAGATAGGCTAAGAAATA
* * * * * *
5464497 TTAAAAATTTC-ATTTTGAAAAA-ATCCCTATAAAAATAGGCTAAGAAATT
1 TTAAAAATCTCAACTTTGAAAAAGCT-CTTATAAAGATAGGCTAAGAAATA
* *
5464546 TTAAAAGTCTCAACTTTG-AAAAGACTGTTATAAAGATAGG
1 TTAAAAATCTCAACTTTGAAAAAG-CTCTTATAAAGATAGG
5464586 AAAACTTTGA
Statistics
Matches: 109, Mismatches: 22, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
47 14 0.13
48 12 0.11
49 50 0.46
50 23 0.21
51 10 0.09
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (50 bp):
TTAAAAATCTCAACTTTGAAAAAGCTCTTATAAAGATAGGCTAAGAAATA
Found at i:5464674 original size:50 final size:48
Alignment explanation
Indices: 5464591--5464910 Score: 154
Period size: 50 Copynumber: 6.5 Consensus size: 48
5464581 ATAGGAAAAC
* *
5464591 TTTGAAAAA-CTGCTATAAAGAA-AAGCTAGGAAAC-TTCAAAATCTCAAA
1 TTTGAAAAAGCT-CTATAAA-AATAGGCTAAGAAACATT-AAAATCTCAAA
* * * *
5464639 TTATGAAAAAGCTCTTATAAATATTGGCTAAGAAACATTAAAATTTTC-AT
1 TT-TGAAAAAGCTC-TATAAAAATAGGCTAAGAAACATTAAAA-TCTCAAA
* * * ** *
5464689 TTTGAAAAAAACCCCTATAAAAATAGACTAAGAAATTTTAAAAATCTCAAC
1 TTTG--AAAAAGCTCTATAAAAATAGGCTAAGAAACATT-AAAATCTCAAA
* * *
5464740 TTTG-AAAAGACTCTATAAAGATAGGCTAAGAAACTTTGAAAATCTC-AT
1 TTTGAAAAAG-CTCTATAAAAATAGGCTAAGAAACATT-AAAATCTCAAA
* ** ** * **
5464788 TTTG-AAAATCTACTATAAGGATAACCTAAGAAACCTTAAAAATCTCATT
1 TTTGAAAAAGCT-CTATAAAAATAGGCTAAGAAACATT-AAAATCTCAAA
* * * * ** *
5464837 TTTTAAAAGGATCTTATAAAGATAGGCTAAGAAATTTTAAAAATCTC-AT
1 TTTGAAAAAGCTC-TATAAAAATAGGCTAAGAAACATT-AAAATCTCAAA
*
5464886 TTTGAAAAA-CTCTTATAAAGATAGG
1 TTTGAAAAAGCTC-TATAAAAATAGG
5464911 TTAAAAAATT
Statistics
Matches: 215, Mismatches: 42, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
47 2 0.01
48 59 0.27
49 55 0.26
50 78 0.36
51 21 0.10
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (48 bp):
TTTGAAAAAGCTCTATAAAAATAGGCTAAGAAACATTAAAATCTCAAA
Found at i:5464759 original size:179 final size:178
Alignment explanation
Indices: 5464413--5464764 Score: 591
Period size: 179 Copynumber: 2.0 Consensus size: 178
5464403 AAATCTCAAT
*
5464413 TTTGAAAAACATCTTTAAAGAAAAGCTAGGAACTTCAAAATCTCAAATTATGAAAAAGCTCTTAT
1 TTTGAAAAACATCTATAAAGAAAAGCTAGGAACTTCAAAATCTCAAATTATGAAAAAGCTCTTAT
* * *
5464478 AAAGATTGGCTAAGAAATATTAAAAATTTCATTTTGAAAAAATCCCTATAAAAATAGGCTAAGAA
66 AAAGATTGGCTAAGAAACATTAAAAATTTCATTTTGAAAAAACCCCTATAAAAATAGACTAAGAA
* *
5464543 ATTTTAAAAGTCTCAACTTTGAAAAGACTGTTATAAAGATAGGAAAAC
131 ATTTTAAAAATCTCAACTTTGAAAAGACTGCTATAAAGATAGGAAAAC
5464591 TTTGAAAAAC-TGCTATAAAGAAAAGCTAGGAAACTTCAAAATCTCAAATTATGAAAAAGCTCTT
1 TTTGAAAAACAT-CTATAAAGAAAAGCTAGG-AACTTCAAAATCTCAAATTATGAAAAAGCTCTT
* *
5464655 ATAAATATTGGCTAAGAAACATTAAAATTTTCATTTTGAAAAAAACCCCTATAAAAATAGACTAA
64 ATAAAGATTGGCTAAGAAACATTAAAAATTTCATTTTG-AAAAAACCCCTATAAAAATAGACTAA
5464720 GAAATTTTAAAAATCTCAACTTTGAAAAGACT-CTATAAAGATAGG
128 GAAATTTTAAAAATCTCAACTTTGAAAAGACTGCTATAAAGATAGG
5464765 CTAAGAAACT
Statistics
Matches: 163, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
177 1 0.01
178 27 0.17
179 80 0.49
180 55 0.34
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (178 bp):
TTTGAAAAACATCTATAAAGAAAAGCTAGGAACTTCAAAATCTCAAATTATGAAAAAGCTCTTAT
AAAGATTGGCTAAGAAACATTAAAAATTTCATTTTGAAAAAACCCCTATAAAAATAGACTAAGAA
ATTTTAAAAATCTCAACTTTGAAAAGACTGCTATAAAGATAGGAAAAC
Found at i:5464817 original size:48 final size:47
Alignment explanation
Indices: 5464591--5465022 Score: 289
Period size: 48 Copynumber: 8.9 Consensus size: 47
5464581 ATAGGAAAAC
* * * * *
5464591 TTTGAAAAACTGCTATAAAGAAAAGCTAGGAAAC-TTCAAAATCTCAAAT
1 TTTGAAAATCT-CTATAAAGATAGGCTAAGAAACTTTAAAAATCTC--AT
* * * * * * *
5464640 TATGAAAAAGCTCTTATAAATATTGGCTAAGAAACATTAAAATTTTCAT
1 TTTG-AAAATCTC-TATAAAGATAGGCTAAGAAACTTTAAAAATCTCAT
* * * * * *
5464689 TTTGAAAAAAACCCCTATAAAAATAGACTAAGAAATTTTAAAAATCTCAAC
1 TTTG---AAAATCTCTATAAAGATAGGCTAAGAAACTTTAAAAATCTC-AT
* *
5464740 TTTGAAAAGACTCTATAAAGATAGGCTAAGAAACTTTGAAAATCTCAT
1 TTTGAAAA-TCTCTATAAAGATAGGCTAAGAAACTTTAAAAATCTCAT
* ** *
5464788 TTTGAAAATCTACTATAAGGATAACCTAAGAAACCTTAAAAATCTCATTT
1 TTTGAAAATCT-CTATAAAGATAGGCTAAGAAACTTTAAAAATCTCA--T
* *
5464838 TTTAAAAGGATCT-TATAAAGATAGGCTAAGAAATTTTAAAAATCTCAT
1 TTTGAAA--ATCTCTATAAAGATAGGCTAAGAAACTTTAAAAATCTCAT
* * * * ** *
5464886 TTTGAAAAACTCTTATAAAGATAGGTTAA-AAAATTTTAGGATCTTATT
1 TTTGAAAATCTC-TATAAAGATAGGCTAAGAAACTTTAAAAATCTCA-T
* ** * * *
5464934 TTTGAAAGGGTC-CTATAAAGATATACGAAGAAATTTTAAAAATCTCAAC
1 TTTGAAA--ATCTCTATAAAGATAGGCTAAGAAACTTTAAAAATCTC-AT
5464983 TTTGAAAA-CTCTTATAAAGATAGGCTAAGAAACTTTAAAA
1 TTTGAAAATCTC-TATAAAGATAGGCTAAGAAACTTTAAAA
5465023 CCTTATTTAT
Statistics
Matches: 297, Mismatches: 65, Indels: 43
0.73 0.16 0.11
Matches are distributed among these distances:
46 4 0.01
47 15 0.05
48 109 0.37
49 59 0.20
50 86 0.29
51 20 0.07
52 4 0.01
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (47 bp):
TTTGAAAATCTCTATAAAGATAGGCTAAGAAACTTTAAAAATCTCAT
Found at i:5464886 original size:98 final size:96
Alignment explanation
Indices: 5464591--5465089 Score: 351
Period size: 96 Copynumber: 5.1 Consensus size: 96
5464581 ATAGGAAAAC
* * * * * * * * *
5464591 TTTGAAAAACTGC-TATAAAGAAAAGCTAGGAAACTTCAAAATCTCAAATTATGAAAAAGCTCTT
1 TTTG-AAAACT-CTTATAAAGATAGGCTAAGAAACTTAAAAATCTC-ATTTTTTAAAAGGATCTT
* * ** * *
5464655 ATAAATATTGGCTAAGAAACATTAAAATTTTCAT
63 ATAAAGATAGGCTAAGAAATTTTAAAAATCTCAT
* * * * * ** *
5464689 TTTGAAAAAAACCCCTATAAAAATAGACTAAGAAATTTTAAAAATCTCAACTTTGAAAA-GA-CT
1 TTTG---AAAACTCTTATAAAGATAGGCTAAGAAA-CTTAAAAATCTCATTTTTTAAAAGGATCT
* *
5464752 CTATAAAGATAGGCTAAGAAACTTTGAAAATCTCAT
62 -TATAAAGATAGGCTAAGAAATTTTAAAAATCTCAT
* **
5464788 TTTGAAAA-TCTACTATAAGGATAACCTAAGAAACCTTAAAAATCTCATTTTTTAAAAGGATCTT
1 TTTGAAAACTCT--TATAAAGATAGGCTAAGAAA-CTTAAAAATCTCATTTTTTAAAAGGATCTT
5464852 ATAAAGATAGGCTAAGAAATTTTAAAAATCTCAT
63 ATAAAGATAGGCTAAGAAATTTTAAAAATCTCAT
* * * * ** * * * *
5464886 TTTGAAAAACTCTTATAAAGATAGGTTAAAAAATTTTAGGATCTTA-TTTTTGAAAGGGTCCTAT
1 TTTG-AAAACTCTTATAAAGATAGGCTAAGAAACTTAAAAATCTCATTTTTTAAAAGGATCTTAT
** * *
5464950 AAAGATATACGAAGAAATTTTAAAAATCTCAAC
65 AAAGATAGGCTAAGAAATTTTAAAAATCTC-AT
* * * * *
5464983 TTTGAAAACTCTTATAAAGATAGGCTAAGAAACTTTAAAACCTTATTTATTTTGAAAAGGCTTTT
1 TTTGAAAACTCTTATAAAGATAGGCTAAGAAACTTAAAAATCTCA-TT-TTTT-AAAAGGATCTT
* * * * *
5465048 ACAAAAAAAGGCTAAAAAATTTTAAAAATCTTAT
63 ATAAAGATAGGCTAAGAAATTTTAAAAATCTCAT
5465082 TTTGAAAA
1 TTTGAAAA
5465090 GTTTGGTTGT
Statistics
Matches: 319, Mismatches: 66, Indels: 31
0.77 0.16 0.07
Matches are distributed among these distances:
95 1 0.00
96 81 0.25
97 48 0.15
98 61 0.19
99 54 0.17
100 64 0.20
101 10 0.03
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (96 bp):
TTTGAAAACTCTTATAAAGATAGGCTAAGAAACTTAAAAATCTCATTTTTTAAAAGGATCTTATA
AAGATAGGCTAAGAAATTTTAAAAATCTCAT
Found at i:5465804 original size:33 final size:33
Alignment explanation
Indices: 5465767--5465956 Score: 107
Period size: 33 Copynumber: 5.8 Consensus size: 33
5465757 AGCTCACCCG
**
5465767 AGTTTAAATCTCA-TCTTAGTGCCAACTAGTCTA
1 AGTTTAAATCTCATTC-TAGTGCCAACTAAACTA
* * *
5465800 AGTTTATATCTAATTCTAGTGTCAACTAAACTA
1 AGTTTAAATCTCATTCTAGTGCCAACTAAACTA
* * * * * **
5465833 GGCTTAAATCTCATTTTGGTTCCAGTTAAACATA
1 AGTTTAAATCTCATTCTAGTGCCAACTAAAC-TA
* * * * * *
5465867 A-CTTAAATCTTA-TCTAGGTGCTAGCTAGACTG
1 AGTTTAAATCTCATTCTA-GTGCCAACTAAACTA
* * * *
5465899 GGCTTAAATCTCATTCTGGTGCCAACTAAACTT
1 AGTTTAAATCTCATTCTAGTGCCAACTAAACTA
* * *
5465932 GGTTTAAATCTTATCCTAGTGCCAA
1 AGTTTAAATCTCATTCTAGTGCCAA
5465957 TTAGATTGGG
Statistics
Matches: 117, Mismatches: 35, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
32 3 0.03
33 107 0.91
34 7 0.06
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (33 bp):
AGTTTAAATCTCATTCTAGTGCCAACTAAACTA
Found at i:5465967 original size:66 final size:66
Alignment explanation
Indices: 5465814--5465974 Score: 155
Period size: 66 Copynumber: 2.5 Consensus size: 66
5465804 TATATCTAAT
* * * * * **
5465814 TCTA-GTGTCAACTAAACTAGGCTTAAATCTCATTTTGGTTCCAGTTAAACATAACTTAAATCTT
1 TCTAGGTGCCAACTAGACTGGGCTTAAATCTCATTCTGGTGCCAACTAAACATAACTTAAATCTT
5465878 A
66 A
* * * ***
5465879 TCTAGGTGCTAGCTAGACTGGGCTTAAATCTCATTCTGGTGCCAACTAAACTTGGTTTAAATCTT
1 TCTAGGTGCCAACTAGACTGGGCTTAAATCTCATTCTGGTGCCAACTAAACATAACTTAAATCTT
5465944 A
66 A
* * *
5465945 TCCTA-GTGCCAATTAGATTGGGCTTTAATC
1 T-CTAGGTGCCAACTAGACTGGGCTTAAATC
5465975 CTAATGGTGT
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
65 4 0.05
66 69 0.91
67 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (66 bp):
TCTAGGTGCCAACTAGACTGGGCTTAAATCTCATTCTGGTGCCAACTAAACATAACTTAAATCTT
A
Found at i:5466066 original size:31 final size:31
Alignment explanation
Indices: 5465992--5466067 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
5465982 TGTTAGTTAG
* *
5465992 ATTGGGCTTAATTCTCTTTAGTGCCACCTAA
1 ATTGGGCTTAATTCTCTCTAGTGCCAACTAA
* *
5466023 ACT-GGATGTAATTCTC-CTAGGTGCCAACTAA
1 ATTGGGCT-TAATTCTCTCTA-GTGCCAACTAA
5466054 ATTGGGCTTAATTC
1 ATTGGGCTTAATTC
5466068 ACCTTGGCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
30 5 0.14
31 28 0.78
32 3 0.08
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (31 bp):
ATTGGGCTTAATTCTCTCTAGTGCCAACTAA
Found at i:5466155 original size:31 final size:31
Alignment explanation
Indices: 5466120--5466191 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
5466110 GCTAGACTGA
* * *
5466120 GCTTAATTTTTCTTAATGCTAACTAAACTAG
1 GCTTAATTTTTCTCAATACCAACTAAACTAG
* * *
5466151 GCTTAAGTCTTCTCAATACCAACTAAACTTG
1 GCTTAATTTTTCTCAATACCAACTAAACTAG
5466182 GCTTAATTTT
1 GCTTAATTTT
5466192 CTTTTTCTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (31 bp):
GCTTAATTTTTCTCAATACCAACTAAACTAG
Found at i:5466263 original size:11 final size:11
Alignment explanation
Indices: 5466247--5466275 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5466237 ATATCTCATC
5466247 TTTTTCATTCA
1 TTTTTCATTCA
5466258 TTTTTCATTCA
1 TTTTTCATTCA
5466269 TTTTTCA
1 TTTTTCA
5466276 GCAACCCTTT
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:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTCATTCA
Found at i:5468011 original size:21 final size:21
Alignment explanation
Indices: 5467945--5468045 Score: 75
Period size: 22 Copynumber: 4.8 Consensus size: 21
5467935 TTATCATTTA
*
5467945 CTTTTTTTCTTTTCCTTCTTTT-
1 CTTTTTTTC-TTTCATT-TTTTC
* * *
5467967 CTTTTATTCTTCCCTTTTTATC
1 CTTTTTTTCTTTCATTTTT-TC
5467989 CTTTTTTTCTTTCATTTTTTC
1 CTTTTTTTCTTTCATTTTTTC
* *
5468010 CTTATTTTC-TT-ATTCTTTC
1 CTTTTTTTCTTTCATTTTTTC
*
5468029 ACTTTTTTT-TTCCATTT
1 -CTTTTTTTCTTTCATTT
5468046 CTTTGAATGG
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
19 7 0.11
20 13 0.20
21 20 0.31
22 24 0.38
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
CTTTTTTTCTTTCATTTTTTC
Found at i:5468496 original size:26 final size:27
Alignment explanation
Indices: 5468463--5468514 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5468453 TATTTCTCAT
5468463 TTTTTCTTTC-TTTTAATTTTTTTTCA
1 TTTTTCTTTCTTTTTAATTTTTTTTCA
5468489 TTTTTCTTTCTTTTTAATTTTTTTTC
1 TTTTTCTTTCTTTTTAATTTTTTTTC
5468515 TTTGCATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTTCTTTCTTTTTAATTTTTTTTCA
Found at i:5468502 original size:17 final size:16
Alignment explanation
Indices: 5468482--5468517 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5468472 CTTTTAATTT
*
5468482 TTTTTCATTTTTCTTTC
1 TTTTTAATTTTT-TTTC
5468499 TTTTTAATTTTTTTTC
1 TTTTTAATTTTTTTTC
5468515 TTT
1 TTT
5468518 GCATGTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTAATTTTTTTTC
Found at i:5470609 original size:20 final size:21
Alignment explanation
Indices: 5470586--5470632 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
5470576 TTTTGAAAAA
5470586 TTGACTTGAATTCAATC-AAT
1 TTGACTTGAATTCAATCAAAT
* **
5470606 TTGA-TTGATTTTGATCAAAT
1 TTGACTTGAATTCAATCAAAT
5470626 TTGACTT
1 TTGACTT
5470633 TATTTGACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.41
20 11 0.50
21 2 0.09
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (21 bp):
TTGACTTGAATTCAATCAAAT
Found at i:5471918 original size:3 final size:3
Alignment explanation
Indices: 5471910--5471945 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5471900 ATGCATGAAT
5471910 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5471946 TATGATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5472136 original size:26 final size:26
Alignment explanation
Indices: 5472107--5472220 Score: 83
Period size: 26 Copynumber: 4.3 Consensus size: 26
5472097 GGGTTTAGGT
5472107 TTTAGGGTCTAAGG-TTATGATTTTAG
1 TTTAGGGTCTAAGGTTTA-GATTTTAG
* *
5472133 TTTAGGGTCTAGGGATGGT-G-TTTT-G
1 TTTAGGGTCTAAGG-T-TTAGATTTTAG
* * *
5472158 ATTTAGGGTTTAGGGTTTAGGTTTTAGG
1 -TTTAGGGTCTAAGGTTTAGATTTTA-G
* *
5472186 TTTAAGGTCTAGGGTTTAGATTTTGAG
1 TTTAGGGTCTAAGGTTTAGATTTT-AG
5472213 TTTAGGGT
1 TTTAGGGT
5472221 TTAGGATTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
24 1 0.01
25 3 0.04
26 34 0.48
27 30 0.42
28 2 0.03
29 1 0.01
ACGTcount: A:0.18, C:0.03, G:0.33, T:0.46
Consensus pattern (26 bp):
TTTAGGGTCTAAGGTTTAGATTTTAG
Found at i:5472171 original size:7 final size:7
Alignment explanation
Indices: 5472159--5472297 Score: 72
Period size: 7 Copynumber: 20.6 Consensus size: 7
5472149 GGTGTTTTGA
5472159 TTTAGGG
1 TTTAGGG
5472166 TTTAGGG
1 TTTAGGG
*
5472173 TTTAGGT
1 TTTAGGG
5472180 TTTA-GG
1 TTTAGGG
*
5472186 TTTAAGG
1 TTTAGGG
*
5472193 TCTAGGG
1 TTTAGGG
*
5472200 TTTA-GA
1 TTTAGGG
* *
5472206 TTTTGAG
1 TTTAGGG
5472213 TTTAGGG
1 TTTAGGG
*
5472220 TTTAGGA
1 TTTAGGG
*
5472227 TTT-TGG
1 TTTAGGG
* *
5472233 ATTAAGG
1 TTTAGGG
*
5472240 TTTAGGT
1 TTTAGGG
*
5472247 TTTA-AG
1 TTTAGGG
*
5472253 TTTATGG
1 TTTAGGG
* *
5472260 TATAGGT
1 TTTAGGG
* *
5472267 TTTAAGT
1 TTTAGGG
*
5472274 TTTAGGT
1 TTTAGGG
5472281 TTTA-GG
1 TTTAGGG
*
5472287 TTTTGGG
1 TTTAGGG
5472294 TTTA
1 TTTA
5472298 AGGATGCATG
Statistics
Matches: 96, Mismatches: 31, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
6 20 0.21
7 76 0.79
ACGTcount: A:0.19, C:0.01, G:0.30, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:5472187 original size:20 final size:20
Alignment explanation
Indices: 5472159--5472297 Score: 111
Period size: 20 Copynumber: 6.8 Consensus size: 20
5472149 GGTGTTTTGA
* *
5472159 TTTAGGGTTTAGGGTTTAGGT
1 TTTAGGTTTTA-GGTTTAGGG
* *
5472180 TTTAGGTTTAAGGTCTAGGG
1 TTTAGGTTTTAGGTTTAGGG
*
5472200 TTTAGATTTT-GAGTTTAGGG
1 TTTAGGTTTTAG-GTTTAGGG
* *
5472220 TTTAGGATTTT-GGATTAAGG
1 TTTAGG-TTTTAGGTTTAGGG
* *
5472240 TTTAGGTTTTAAGTTTATGG
1 TTTAGGTTTTAGGTTTAGGG
* * *
5472260 TATAGGTTTTAAGTTTTAGGT
1 TTTAGGTTTT-AGGTTTAGGG
*
5472281 TTTAGGTTTTGGGTTTA
1 TTTAGGTTTTAGGTTTA
5472298 AGGATGCATG
Statistics
Matches: 93, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
19 5 0.05
20 59 0.63
21 29 0.31
ACGTcount: A:0.19, C:0.01, G:0.30, T:0.50
Consensus pattern (20 bp):
TTTAGGTTTTAGGTTTAGGG
Found at i:5472198 original size:27 final size:27
Alignment explanation
Indices: 5472159--5472300 Score: 103
Period size: 27 Copynumber: 5.3 Consensus size: 27
5472149 GGTGTTTTGA
*
5472159 TTTAGGGTTTAGGGTTTAGGTTTTAGG
1 TTTAAGGTTTAGGGTTTAGGTTTTAGG
* *
5472186 TTTAAGGTCTAGGGTTTAGATTTT-GAG
1 TTTAAGGTTTAGGGTTTAGGTTTTAG-G
* * * * *
5472213 TTTAGGGTTTAGGATTTTGGATTAAGG
1 TTTAAGGTTTAGGGTTTAGGTTTTAGG
* *
5472240 TTT-AGGTTTTA-AGTTTATGG-TATAGG
1 TTTAAGG-TTTAGGGTTTA-GGTTTTAGG
* * *
5472266 TTTTAAGTTTTAGGTTTTAGGTTTTGGG
1 -TTTAAGGTTTAGGGTTTAGGTTTTAGG
5472294 TTTAAGG
1 TTTAAGG
5472301 ATGCATGTAA
Statistics
Matches: 85, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
26 10 0.12
27 64 0.75
28 11 0.13
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.49
Consensus pattern (27 bp):
TTTAAGGTTTAGGGTTTAGGTTTTAGG
Found at i:5472377 original size:49 final size:49
Alignment explanation
Indices: 5472305--5472398 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
5472295 TTAAGGATGC
*
5472305 ATGTAACAAAATTACCAAAATGCCATTTATAAAAATGCAAACTTTGATT
1 ATGTAACAAAATTACCAAAATGCCATTGATAAAAATGCAAACTTTGATT
* *
5472354 ATGTAACAAAATTACTAAAATGCCATTGATAAAAATGCGAACTTT
1 ATGTAACAAAATTACCAAAATGCCATTGATAAAAATGCAAACTTT
5472399 CATGCATTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (49 bp):
ATGTAACAAAATTACCAAAATGCCATTGATAAAAATGCAAACTTTGATT
Found at i:5480487 original size:28 final size:29
Alignment explanation
Indices: 5480447--5480501 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
5480437 AAACCAAAAC
5480447 ATTTTTTCATTTT-ATTCCAATTTTTCAA
1 ATTTTTTCATTTTCATTCCAATTTTTCAA
** * *
5480475 ATTTTTTGTTTTTCTTTTCAATTTTTC
1 ATTTTTTCATTTTCATTCCAATTTTTC
5480502 CATTTTAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 11 0.50
29 11 0.50
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (29 bp):
ATTTTTTCATTTTCATTCCAATTTTTCAA
Found at i:5481406 original size:3 final size:3
Alignment explanation
Indices: 5481398--5481433 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5481388 ATGCTTGAAT
5481398 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5481434 TATGATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5481625 original size:19 final size:19
Alignment explanation
Indices: 5481601--5481648 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
5481591 TTGGCTTTAA
*
5481601 GGTTTAGGGTTAAGGTTTT
1 GGTTTAGGGTTAAGATTTT
*
5481620 GGTTTATGGTTAAGATTTT
1 GGTTTAGGGTTAAGATTTT
5481639 GGTTTAGGGT
1 GGTTTAGGGT
5481649 CTAGGGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (19 bp):
GGTTTAGGGTTAAGATTTT
Found at i:5481704 original size:27 final size:27
Alignment explanation
Indices: 5481639--5481705 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
5481629 TTAAGATTTT
* * *
5481639 GGTTTAGGGTCTAGGGTCTAGGTTTTA
1 GGTTTAGGGTTTAGGGTCTAAGTTTGA
**
5481666 GGTTTAAAGTTTAGGG-CTAAAGTTTGA
1 GGTTTAGGGTTTAGGGTCT-AAGTTTGA
5481693 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
5481706 CATTTTGCGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.40
Consensus pattern (27 bp):
GGTTTAGGGTTTAGGGTCTAAGTTTGA
Found at i:5481730 original size:13 final size:13
Alignment explanation
Indices: 5481568--5481750 Score: 86
Period size: 13 Copynumber: 13.9 Consensus size: 13
5481558 GTTTAGGGTT
*
5481568 GGTTTAAGGTCTA
1 GGTTTAAGGTTTA
* *
5481581 GG-TTAGGGTTTT
1 GGTTTAAGGTTTA
5481593 GGCTTTAAGGTTTA
1 GG-TTTAAGGTTTA
* *
5481607 GGGTTAAGGTTTT
1 GGTTTAAGGTTTA
* *
5481620 GGTTTATGGTTAA
1 GGTTTAAGGTTTA
* *
5481633 GATTT-TGGTTTA
1 GGTTTAAGGTTTA
* * *
5481645 GGGTCTAGGGTCTA
1 -GGTTTAAGGTTTA
*
5481659 GGTTTTAGGTTTAA
1 GGTTTAAGGTTT-A
* * * *
5481673 AGTTTAGGGCTAA
1 GGTTTAAGGTTTA
* *
5481686 AGTTTGAGGTTTA
1 GGTTTAAGGTTTA
*
5481699 GGGTTTACA--TTTT
1 -GGTTTA-AGGTTTA
5481712 GCGTTTAAGGTTTA
1 G-GTTTAAGGTTTA
*
5481726 GGTTTAAGGTTTG
1 GGTTTAAGGTTTA
*
5481739 GGTTTTAGGTTT
1 GGTTTAAGGTTT
5481751 TGTTTAGCGT
Statistics
Matches: 124, Mismatches: 36, Indels: 20
0.69 0.20 0.11
Matches are distributed among these distances:
12 17 0.14
13 75 0.60
14 31 0.25
15 1 0.01
ACGTcount: A:0.19, C:0.04, G:0.32, T:0.45
Consensus pattern (13 bp):
GGTTTAAGGTTTA
Found at i:5481737 original size:20 final size:20
Alignment explanation
Indices: 5481568--5481750 Score: 70
Period size: 20 Copynumber: 8.9 Consensus size: 20
5481558 GTTTAGGGTT
* *
5481568 GGTTTAAGGTCTAGG-TTAG
1 GGTTTAAGGTTTAGGTTTAA
*
5481587 GGTTT-TGGCTTTAAGGTTT-A
1 GGTTTAAGG-TTT-AGGTTTAA
* * *
5481607 GGGTTAAGGTTTTGGTTTAT
1 GGTTTAAGGTTTAGGTTTAA
* * *
5481627 GG-TTAAGATTTTGGTTTAG
1 GGTTTAAGGTTTAGGTTTAA
* * * *
5481646 GGTCTAGGGTCTAGGTTTTA
1 GGTTTAAGGTTTAGGTTTAA
* **
5481666 GGTTTAAAGTTTAGGGCTAA
1 GGTTTAAGGTTTAGGTTTAA
* *
5481686 AGTTTGAGGTTTAGGGTTTACA
1 GGTTTAAGGTTTA-GGTTTA-A
5481708 TTTTGCGTTTAAGGTTTAGGTTTAA
1 ----G-GTTTAAGGTTTAGGTTTAA
*
5481733 GGTTT-GGGTTTTAGGTTT
1 GGTTTAAGG-TTTAGGTTT
5481751 TGTTTAGCGT
Statistics
Matches: 119, Mismatches: 31, Indels: 27
0.67 0.18 0.15
Matches are distributed among these distances:
18 2 0.02
19 31 0.26
20 58 0.49
21 9 0.08
22 1 0.01
25 1 0.01
26 6 0.05
27 11 0.09
ACGTcount: A:0.19, C:0.04, G:0.32, T:0.45
Consensus pattern (20 bp):
GGTTTAAGGTTTAGGTTTAA
Found at i:5481812 original size:13 final size:13
Alignment explanation
Indices: 5481600--5481812 Score: 60
Period size: 13 Copynumber: 16.2 Consensus size: 13
5481590 TTTGGCTTTA
*
5481600 AGGTTTAGGGTTA
1 AGGTTTAGGGTTT
*
5481613 AGGTTT-TGGTTT
1 AGGTTTAGGGTTT
* *
5481625 ATGG-TTAAGATTT
1 A-GGTTTAGGGTTT
* *
5481638 TGGTTTAGGGTCT
1 AGGTTTAGGGTTT
* *
5481651 AGGGTCTAGGTTTT
1 A-GGTTTAGGGTTT
**
5481665 AGGTTTAAAGTTT
1 AGGTTTAGGGTTT
** **
5481678 AGGGCTAAAGTTT
1 AGGTTTAGGGTTT
5481691 GAGGTTTAGGGTTT
1 -AGGTTTAGGGTTT
** * *
5481705 ACATTTTGCGTTT
1 AGGTTTAGGGTTT
5481718 AAGGTTTA-GGTTT
1 -AGGTTTAGGGTTT
5481731 AAGGTTT-GGGTTTT
1 -AGGTTTAGGG-TTT
*
5481745 AGGTTT--TGTTT
1 AGGTTTAGGGTTT
***
5481756 AGCGTTTAAATTTT
1 AG-GTTTAGGGTTT
** *
5481770 AGGTCCAGGTTTT
1 AGGTTTAGGGTTT
* * *
5481783 GGGTTTTGGATTTT
1 AGGTTTAGG-GTTT
5481797 AGGTTTAGGGTTT
1 AGGTTTAGGGTTT
5481810 AGG
1 AGG
5481813 GATGCACATA
Statistics
Matches: 144, Mismatches: 44, Indels: 24
0.68 0.21 0.11
Matches are distributed among these distances:
11 5 0.03
12 14 0.10
13 83 0.58
14 42 0.29
ACGTcount: A:0.18, C:0.04, G:0.31, T:0.46
Consensus pattern (13 bp):
AGGTTTAGGGTTT
Found at i:5482591 original size:13 final size:13
Alignment explanation
Indices: 5482573--5482597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5482563 TTGTAGCAAG
5482573 GAAAACAACTAAA
1 GAAAACAACTAAA
5482586 GAAAACAACTAA
1 GAAAACAACTAA
5482598 TGGTTTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (13 bp):
GAAAACAACTAAA
Found at i:5488403 original size:21 final size:21
Alignment explanation
Indices: 5488374--5488420 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5488364 TAAAATCCAG
* *
5488374 ATTTTCTAAACTTCATGGGTA
1 ATTTCCTAAACTTCATAGGTA
*
5488395 ATTTCCTAAAGTTCATAGGTA
1 ATTTCCTAAACTTCATAGGTA
5488416 ATTTC
1 ATTTC
5488421 TATATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (21 bp):
ATTTCCTAAACTTCATAGGTA
Found at i:5492383 original size:21 final size:21
Alignment explanation
Indices: 5492357--5492457 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
5492347 TACAAGACCT
* * *
5492357 CACAACAAATTTCAGTTCAAA
1 CACAACAACTTCCAATTCAAA
*
5492378 CACAACAGCTTCCAATTCAAA
1 CACAACAACTTCCAATTCAAA
*
5492399 CACAACAACTTCCAATTCAGA
1 CACAACAACTTCCAATTCAAA
* ** *
5492420 CACAACAGCTTCCAGCTCAAT
1 CACAACAACTTCCAATTCAAA
* *
5492441 CACAACAGCTTTCAATT
1 CACAACAACTTCCAATT
5492458 AAAAAAATGT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.22
Consensus pattern (21 bp):
CACAACAACTTCCAATTCAAA
Found at i:5492423 original size:42 final size:42
Alignment explanation
Indices: 5492357--5492457 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
5492347 TACAAGACCT
* * *
5492357 CACAACAAATTTCAGTTCAAACACAACAGCTTCCAATTCAAA
1 CACAACAACTTTCAATTCAAACACAACAGCTTCCAACTCAAA
* * * *
5492399 CACAACAACTTCCAATTCAGACACAACAGCTTCCAGCTCAAT
1 CACAACAACTTTCAATTCAAACACAACAGCTTCCAACTCAAA
*
5492441 CACAACAGCTTTCAATT
1 CACAACAACTTTCAATT
5492458 AAAAAAATGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.22
Consensus pattern (42 bp):
CACAACAACTTTCAATTCAAACACAACAGCTTCCAACTCAAA
Found at i:5493133 original size:17 final size:15
Alignment explanation
Indices: 5493088--5493134 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 15
5493078 ATGAAATAAT
5493088 AAAATAT-TAACAA-
1 AAAATATATAACAAC
*
5493101 ATAATATATAACAAC
1 AAAATATATAACAAC
5493116 AAAATATAATAACTAAC
1 AAAATAT-ATAAC-AAC
5493133 AA
1 AA
5493135 TATGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 5 0.18
17 5 0.18
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATATATAACAAC
Found at i:5497901 original size:51 final size:51
Alignment explanation
Indices: 5497841--5497950 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 51
5497831 GCAGAGTTGA
* * * *
5497841 AGCTGAAGAATGATGTTAATATTGATGACTTAAAATTAATAAAAGACATTG
1 AGCTGAAGAATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTG
* *
5497892 AGCTGAAGAATGATGTTAATGTTAAGGACTTAAAATTAGCAAAAGACAGTG
1 AGCTGAAGAATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTG
5497943 AGCTGAAG
1 AGCTGAAG
5497951 CTAAAGAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (51 bp):
AGCTGAAGAATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTG
Found at i:5499105 original size:15 final size:15
Alignment explanation
Indices: 5499081--5499114 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5499071 TTCGAAGGAA
5499081 GAAAGCTAAATAGAT
1 GAAAGCTAAATAGAT
* *
5499096 GAAAGTTAAATGGAT
1 GAAAGCTAAATAGAT
5499111 GAAA
1 GAAA
5499115 ATAGGTGGGA
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:0.03, G:0.24, T:0.21
Consensus pattern (15 bp):
GAAAGCTAAATAGAT
Found at i:5500012 original size:26 final size:27
Alignment explanation
Indices: 5499980--5500044 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
5499970 GTTAATAATT
* *
5499980 TATTTTATTT-TTTAAATAAATTTTTA
1 TATTTTATTTACTCAAATAAATTTTTA
5500006 TATTTTATTATACTCAAATAAATTTTTA
1 TATTTTATT-TACTCAAATAAATTTTTA
*
5500034 TTTTTTGATTT
1 TATTTT-ATTT
5500045 GTATTTACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.27
27 1 0.03
28 20 0.61
29 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (27 bp):
TATTTTATTTACTCAAATAAATTTTTA
Found at i:5500121 original size:30 final size:30
Alignment explanation
Indices: 5500094--5500190 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
5500084 ATGTTAAGGG
5500094 TTTATTT-AGATAAAAATTAAAAGTTAAGAA
1 TTTATTTGA-ATAAAAATTAAAAGTTAAGAA
* * *
5500124 TTTATTTGAATATAAATTAAAAATTAAAAA
1 TTTATTTGAATAAAAATTAAAAGTTAAGAA
* * *
5500154 TTAATTT-AAAAATAAATTAAAAGTTAAAAA
1 TTTATTTGAATAA-AAATTAAAAGTTAAGAA
*
5500184 CTTATTT
1 TTTATTT
5500191 TAGTATAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 3 0.05
30 52 0.93
31 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTATTTGAATAAAAATTAAAAGTTAAGAA
Found at i:5500162 original size:12 final size:12
Alignment explanation
Indices: 5500144--5500181 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5500134 TATAAATTAA
5500144 AAATTAAAAATT
1 AAATTAAAAATT
*
5500156 AATTTAAAAA-T
1 AAATTAAAAATT
*
5500167 AAATTAAAAGTT
1 AAATTAAAAATT
5500179 AAA
1 AAA
5500182 AACTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AAATTAAAAATT
Found at i:5500213 original size:60 final size:60
Alignment explanation
Indices: 5500105--5500239 Score: 150
Period size: 60 Copynumber: 2.2 Consensus size: 60
5500095 TTATTTAGAT
* * *
5500105 AAAAATTAAAAGTTAAGAATTTATTTGAATATAAATTAAAAATTAAAAATTAATTTAA-A
1 AAAAATTAAAAGTTAAAAACTTATTTGAATATAAATTAAAAATAAAAAATTAATTTAACA
* * *
5500164 AATAAATTAAAAGTTAAAAACTTATTTTAGTAT-AA-TAAATATATAAAAAATTTATTTAACA
1 AA-AAATTAAAAGTTAAAAACTTATTTGAATATAAATTAAA-A-ATAAAAAATTAATTTAACA
*
5500225 AAAAATGATAAAGTT
1 AAAAATTA-AAAGTT
5500240 GAAAGGCTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 4 0.06
59 5 0.08
60 46 0.72
61 9 0.14
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (60 bp):
AAAAATTAAAAGTTAAAAACTTATTTGAATATAAATTAAAAATAAAAAATTAATTTAACA
Found at i:5502479 original size:43 final size:43
Alignment explanation
Indices: 5502431--5502513 Score: 141
Period size: 43 Copynumber: 1.9 Consensus size: 43
5502421 TTCTATAGGC
5502431 TACTGTTTCTGGAGCCAACTCTATGAATG-GTACTTCATACTGT
1 TACTGTTTCTGGAGCCAACTCTATGAA-GAGTACTTCATACTGT
*
5502474 TACTGTTTCTGGTGCCAACTCTATGAAGAGTACTTCATAC
1 TACTGTTTCTGGAGCCAACTCTATGAAGAGTACTTCATAC
5502514 CGGATGGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (43 bp):
TACTGTTTCTGGAGCCAACTCTATGAAGAGTACTTCATACTGT
Found at i:5504042 original size:13 final size:14
Alignment explanation
Indices: 5504016--5504044 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5504006 TTATTCTATA
5504016 GTTTTAATATAAAT
1 GTTTTAATATAAAT
5504030 GTTTTAA-ATAAAT
1 GTTTTAATATAAAT
5504043 GT
1 GT
5504045 AGGATATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
GTTTTAATATAAAT
Found at i:5509328 original size:18 final size:18
Alignment explanation
Indices: 5509258--5509326 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
5509248 CTTTTCTTAT
5509258 TTTTAATTTTGATTTTAA
1 TTTTAATTTTGATTTTAA
5509276 TTTTAATTTT-AGTTTTAA
1 TTTTAATTTTGA-TTTTAA
* *
5509294 TTTTAGTTTTGATTTTGA
1 TTTTAATTTTGATTTTAA
*
5509312 TTTTGATTTT-ATTTT
1 TTTTAATTTTGATTTT
5509327 TGTTTTTTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
17 6 0.13
18 38 0.84
19 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.70
Consensus pattern (18 bp):
TTTTAATTTTGATTTTAA
Found at i:5509333 original size:12 final size:12
Alignment explanation
Indices: 5509258--5509332 Score: 89
Period size: 12 Copynumber: 6.3 Consensus size: 12
5509248 CTTTTCTTAT
5509258 TTTTAATTTTGA
1 TTTTAATTTTGA
*
5509270 TTTTAATTTTAA
1 TTTTAATTTTGA
* *
5509282 TTTTAGTTTTAA
1 TTTTAATTTTGA
*
5509294 TTTTAGTTTTGA
1 TTTTAATTTTGA
*
5509306 TTTTGATTTTGA
1 TTTTAATTTTGA
*
5509318 TTTTATTTTTG-
1 TTTTAATTTTGA
5509329 TTTT
1 TTTT
5509333 TTGTTTAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
11 4 0.07
12 52 0.93
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (12 bp):
TTTTAATTTTGA
Found at i:5509345 original size:6 final size:6
Alignment explanation
Indices: 5509258--5509326 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
5509248 CTTTTCTTAT
* * * *
5509258 TTTTAA TTTTGA TTTTAA TTTTAA TTTTAG TTTTAA TTTTAG TTTTGA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
* *
5509306 TTTTGA TTTTGA TTTT-A TTTT
1 TTTTAA TTTTAA TTTTAA TTTT
5509327 TGTTTTTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
5 5 0.09
6 51 0.91
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:5510388 original size:24 final size:23
Alignment explanation
Indices: 5510362--5510405 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5510352 TTTTTTTCTT
5510362 TTTTTAATT-ATTTTATGTTTTGA
1 TTTTTAATTGATTTTAT-TTTTGA
*
5510385 TTTTTATTTGATTTTATTTTT
1 TTTTTAATTGATTTTATTTTT
5510406 CTATTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (23 bp):
TTTTTAATTGATTTTATTTTTGA
Found at i:5510394 original size:11 final size:10
Alignment explanation
Indices: 5510380--5510474 Score: 50
Period size: 10 Copynumber: 9.3 Consensus size: 10
5510370 TATTTTATGT
5510380 TTTGATTTTTA
1 TTTGA-TTTTA
5510391 TTTGATTTTA
1 TTTGATTTTA
**
5510401 TTTTTCTATTTA
1 -TTTGAT-TTTA
* *
5510413 GTTTGGTTTGA
1 -TTTGATTTTA
*
5510424 TTTGATTTTT
1 TTTGATTTTA
*
5510434 TTTG-TTTGA
1 TTTGATTTTA
* *
5510443 TTCGATTTAA
1 TTTGATTTTA
* *
5510453 TTT-TTTTTG
1 TTTGATTTTA
5510462 TTTGATTTTA
1 TTTGATTTTA
5510472 TTT
1 TTT
5510475 TTATACTTTT
Statistics
Matches: 61, Mismatches: 19, Indels: 9
0.69 0.21 0.10
Matches are distributed among these distances:
9 12 0.20
10 29 0.48
11 12 0.20
12 8 0.13
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.71
Consensus pattern (10 bp):
TTTGATTTTA
Found at i:5510411 original size:24 final size:23
Alignment explanation
Indices: 5510354--5510411 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
5510344 CACAAAATTT
*
5510354 TTTTTCTTTTTTTAATTATTTTA
1 TTTTTCTATTTTTAATTATTTTA
* *
5510377 TGTTTT-GATTTTTATTTGATTTTA
1 T-TTTTCTATTTTTAATT-ATTTTA
5510401 TTTTTCTATTT
1 TTTTTCTATTT
5510412 AGTTTGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTTTCTATTTTTAATTATTTTA
Found at i:5510440 original size:24 final size:24
Alignment explanation
Indices: 5510390--5510474 Score: 89
Period size: 24 Copynumber: 3.4 Consensus size: 24
5510380 TTTGATTTTT
*
5510390 ATTTGATTTTATTTTTCTATTTAGTTTG
1 ATTTGA-TTTAATTTT-T-TTT-GTTTG
* *
5510418 GTTTGATTTGATTTTTTTTGTTTG
1 ATTTGATTTAATTTTTTTTGTTTG
*
5510442 ATTCGATTTAATTTTTTTTGTTTG
1 ATTTGATTTAATTTTTTTTGTTTG
*
5510466 ATTTTATTT
1 ATTTGATTT
5510475 TTATACTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 33 0.67
25 3 0.06
26 1 0.02
27 7 0.14
28 5 0.10
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.69
Consensus pattern (24 bp):
ATTTGATTTAATTTTTTTTGTTTG
Found at i:5510476 original size:19 final size:20
Alignment explanation
Indices: 5510419--5510476 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
5510409 TTTAGTTTGG
*
5510419 TTTGATTTGATTTT-TTTTG
1 TTTGATTTGATTTTATTTTT
* *
5510438 TTTGATTCGATTTAATTTTT
1 TTTGATTTGATTTTATTTTT
5510458 TTTG-TTTGATTTTATTTTT
1 TTTGATTTGATTTTATTTTT
5510477 ATACTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 25 0.76
20 8 0.24
ACGTcount: A:0.14, C:0.02, G:0.12, T:0.72
Consensus pattern (20 bp):
TTTGATTTGATTTTATTTTT
Found at i:5510589 original size:14 final size:15
Alignment explanation
Indices: 5510570--5510612 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
5510560 TTTTATATTT
*
5510570 TTATATTTGTTTG-A
1 TTATATTTATTTGCA
5510584 TTATATTTATTTGCA
1 TTATATTTATTTGCA
*
5510599 TGATATTTTATTTG
1 TTATA-TTTATTTG
5510613 TACAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 5 0.20
16 8 0.32
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (15 bp):
TTATATTTATTTGCA
Found at i:5510806 original size:24 final size:24
Alignment explanation
Indices: 5510778--5511091 Score: 105
Period size: 24 Copynumber: 12.8 Consensus size: 24
5510768 ATATTGATTT
5510778 ATATATTTATTTGCATGATTATTA
1 ATATATTTATTTGCATGATTATTA
* *
5510802 ATATATTTATTTGCATGAATACCTAA
1 ATATATTTATTTGCATGATTA--TTA
* *
5510828 TATACTTATGTGTGTGATTGCATGATTACTA
1 -ATA--TAT-T-TAT--TTGCATGATTATTA
* *
5510859 ATATATTTATTTGCATGTTTACCTA
1 ATATATTTATTTGCATGATTA-TTA
* ** * *
5510884 ATATATTTATGTGTGTGGTTGCATGTT
1 ATATATTTATTTGCATGATT--AT-TA
* *
5510911 AT-TATTTATGTGCATGATTATTG
1 ATATATTTATTTGCATGATTATTA
**
5510934 ATATA-TTATTTGTGTGATTTATTA
1 ATATATTTATTTGCATGA-TTATTA
*** *
5510958 ATATATTTGCATGAAT-ATTATTA
1 ATATATTTATTTGCATGATTATTA
* *
5510981 ATATA-TTATTTGTATG-GTATT-
1 ATATATTTATTTGCATGATTATTA
* * *
5511002 TTATA-CTA-TTGCATGATTATTG
1 ATATATTTATTTGCATGATTATTA
* *
5511024 ATATTATTGCA-TTGTATGATATGATT-
1 ATA-TATT-TATTTGCATGAT-T-ATTA
* *
5511050 TTATATTTA-TTGCATGATATGATTT
1 ATATATTTATTTGCATGAT-T-ATTA
5511075 A-ATATTTA-TTGCATGAT
1 ATATATTTATTTGCATGAT
5511092 ATTGGCATGA
Statistics
Matches: 221, Mismatches: 44, Indels: 50
0.70 0.14 0.16
Matches are distributed among these distances:
20 6 0.03
21 10 0.05
22 12 0.05
23 25 0.11
24 76 0.34
25 37 0.17
26 21 0.10
27 11 0.05
28 3 0.01
29 3 0.01
30 4 0.02
31 3 0.01
33 10 0.05
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.51
Consensus pattern (24 bp):
ATATATTTATTTGCATGATTATTA
Found at i:5510850 original size:57 final size:57
Alignment explanation
Indices: 5510788--5510914 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 57
5510778 ATATATTTAT
5510788 TTGCATGATTATTAATATATTTATTTGCATGAATACCTAATATACTTATGTGTGTGA
1 TTGCATGATTATTAATATATTTATTTGCATGAATACCTAATATACTTATGTGTGTGA
* ** * *
5510845 TTGCATGATTACTAATATATTTATTTGCATGTTTACCTAATATATTTATGTGTGTGG
1 TTGCATGATTATTAATATATTTATTTGCATGAATACCTAATATACTTATGTGTGTGA
5510902 TTGCATG-TTATTA
1 TTGCATGATTATTA
5510915 TTTATGTGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
56 5 0.08
57 59 0.92
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (57 bp):
TTGCATGATTATTAATATATTTATTTGCATGAATACCTAATATACTTATGTGTGTGA
Found at i:5511101 original size:11 final size:10
Alignment explanation
Indices: 5511081--5511121 Score: 57
Period size: 11 Copynumber: 4.1 Consensus size: 10
5511071 ATTTAATATT
5511081 TATTGCATGA
1 TATTGCATGA
5511091 TATTGGCATGA
1 TATT-GCATGA
*
5511102 TATT-TATGA
1 TATTGCATGA
5511111 TATTGCATGA
1 TATTGCATGA
5511121 T
1 T
5511122 TGCATGGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.30
10 9 0.33
11 10 0.37
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (10 bp):
TATTGCATGA
Found at i:5520763 original size:23 final size:23
Alignment explanation
Indices: 5520721--5520768 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5520711 GATTACTTGT
** *
5520721 TAGTGCATGATGTCCCATGTGGA
1 TAGTGCATGATAACCAATGTGGA
*
5520744 TAGTGCATGATAACCAATGTTGA
1 TAGTGCATGATAACCAATGTGGA
5520767 TA
1 TA
5520769 AGAAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (23 bp):
TAGTGCATGATAACCAATGTGGA
Found at i:5521475 original size:137 final size:137
Alignment explanation
Indices: 5521202--5521460 Score: 448
Period size: 137 Copynumber: 1.9 Consensus size: 137
5521192 ATTTAAGGTA
**
5521202 AGATTTTAAGTTTCAATGTCTCGATCAAGAAGAAGCCTTTTCAATAGTAAGAATGATCTATAAAA
1 AGATTTTAAGTTTCAATACCTCGATCAAGAAGAAGCCTTTTCAATAGTAAGAATGATCTATAAAA
5521267 CCTTGAGGCATGATTTTCAAAATTAGATATCTCATTTTATTTTTCAAAAGTTTCAAAATGTCAGT
66 CCTTGAGGCATGATTTTCAAAATTAGATATCTCATTTTATTTTTCAAAAGTTTCAAAATGTCAGT
5521332 TGTGGGG
131 TGTGGGG
* * * *
5521339 AGATTTTAAGTTTTAATACCTCTATTAAGGAAG-AGCCTTTTCAATGGTAAGAATGATCTATAAA
1 AGATTTTAAGTTTCAATACCTCGATCAA-GAAGAAGCCTTTTCAATAGTAAGAATGATCTATAAA
5521403 ACCTTGAGGCATGATTTTCAAAATTAGATATCTCATTTTATTTTTCAAAAGTTTCAAA
65 ACCTTGAGGCATGATTTTCAAAATTAGATATCTCATTTTATTTTTCAAAAGTTTCAAA
5521461 GCTTTAGTTG
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
137 111 0.97
138 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (137 bp):
AGATTTTAAGTTTCAATACCTCGATCAAGAAGAAGCCTTTTCAATAGTAAGAATGATCTATAAAA
CCTTGAGGCATGATTTTCAAAATTAGATATCTCATTTTATTTTTCAAAAGTTTCAAAATGTCAGT
TGTGGGG
Found at i:5521518 original size:48 final size:47
Alignment explanation
Indices: 5521439--5521623 Score: 156
Period size: 48 Copynumber: 4.1 Consensus size: 47
5521429 GATATCTCAT
* *
5521439 TTTATTTTTCAAAAGTT----TCAAAGCTTTAGTTGTGGGGGAGCAC
1 TTTATTTTTCAAAAGTTCAAATCAAAGCCTCAGTTGTGGGGGAGCAC
* *
5521482 TTTATTTTTCAAAAGCTTCAAATCAAAGCCTCAGTTGTGGTGGAGCAT
1 TTTATTTTTCAAAAG-TTCAAATCAAAGCCTCAGTTGTGGGGGAGCAC
* * * ** *
5521530 TTTATTTTT-TAAAGTT----TCAAAGTCTCAGTAGTAAGGGAGAAC
1 TTTATTTTTCAAAAGTTCAAATCAAAGCCTCAGTTGTGGGGGAGCAC
* * *
5521572 TTTATTTTCCAAAAGTTTCAAATCAAAGCCTC-GATTGTGGGAGAGCAT
1 TTTATTTTTCAAAAG-TTCAAATCAAAGCCTCAG-TTGTGGGGGAGCAC
5521620 TTTA
1 TTTA
5521624 AAATTTCAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
42 27 0.25
43 19 0.17
44 4 0.04
46 2 0.02
47 5 0.05
48 52 0.48
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (47 bp):
TTTATTTTTCAAAAGTTCAAATCAAAGCCTCAGTTGTGGGGGAGCAC
Found at i:5521592 original size:90 final size:91
Alignment explanation
Indices: 5521436--5521623 Score: 249
Period size: 90 Copynumber: 2.1 Consensus size: 91
5521426 TTAGATATCT
* * ** * *
5521436 CATTTTATTTTTCAAAAGTTTCAAAGCTTTAGTTGTGGGGGAGCACTTTATTTTTCAAAAGCTTC
1 CATTTTATTTTTCAAAAGTTTCAAAGCTTCAGTAGTAAGGGAGAACTTTATTTTCCAAAAGCTTC
5521501 AAATCAAAGCCTC-AGTTGTGGTG-GAG
66 AAATCAAAGCCTCGA-TTGTGG-GAGAG
* *
5521527 CATTTTATTTTT-TAAAGTTTCAAAG-TCTCAGTAGTAAGGGAGAACTTTATTTTCCAAAAGTTT
1 CATTTTATTTTTCAAAAGTTTCAAAGCT-TCAGTAGTAAGGGAGAACTTTATTTTCCAAAAGCTT
5521590 CAAATCAAAGCCTCGATTGTGGGAGAG
65 CAAATCAAAGCCTCGATTGTGGGAGAG
5521617 CATTTTA
1 CATTTTA
5521624 AAATTTCAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
89 2 0.02
90 71 0.83
91 13 0.15
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (91 bp):
CATTTTATTTTTCAAAAGTTTCAAAGCTTCAGTAGTAAGGGAGAACTTTATTTTCCAAAAGCTTC
AAATCAAAGCCTCGATTGTGGGAGAG
Found at i:5521672 original size:41 final size:41
Alignment explanation
Indices: 5521618--5521712 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
5521608 GTGGGAGAGC
* * *
5521618 ATTTT-AAAATTTCAAAATCTTAGTTGTGGGG-AGTATTTT
1 ATTTTCAAAATTTCAAAATCTCAGCTGTGGGGAAGCATTTT
5521657 ATTTTCAAAAGTTTCAAAATCTCAGCTGTGGGGAAGCATTTT
1 ATTTTCAAAA-TTTCAAAATCTCAGCTGTGGGGAAGCATTTT
5521699 ATTTTTCAAAATTT
1 A-TTTTCAAAATTT
5521713 TTAATGCCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
39 5 0.10
40 4 0.08
41 20 0.41
42 11 0.22
43 9 0.18
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (41 bp):
ATTTTCAAAATTTCAAAATCTCAGCTGTGGGGAAGCATTTT
Found at i:5521994 original size:6 final size:6
Alignment explanation
Indices: 5521983--5522055 Score: 85
Period size: 6 Copynumber: 12.3 Consensus size: 6
5521973 AAATCTTATC
* *
5521983 TTAATT TTAATT TTAATT TTAA-T TTGATT TTAATT TTAATT TTGATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
* * * *
5522030 TTAGTC TTAATT TTAGTT TTGATT TT
1 TTAATT TTAATT TTAATT TTAATT TT
5522056 GTTTTAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
5 4 0.07
6 51 0.93
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:5522014 original size:17 final size:17
Alignment explanation
Indices: 5521992--5522042 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
5521982 CTTAATTTTA
5521992 ATTTTAATTTTAATTTG
1 ATTTTAATTTTAATTTG
5522009 ATTTTAATTTTAATTTTG
1 ATTTTAATTTTAA-TTTG
* *
5522027 ATTTTAGTCTTAATTT
1 ATTTTAATTTTAATTT
5522043 TAGTTTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (17 bp):
ATTTTAATTTTAATTTG
Found at i:5522016 original size:23 final size:23
Alignment explanation
Indices: 5521986--5522067 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
5521976 TCTTATCTTA
5521986 ATTTTAATTTTAATTTTAATTTG
1 ATTTTAATTTTAATTTTAATTTG
* *
5522009 ATTTTAATTTTAATTTTGATTTT
1 ATTTTAATTTTAATTTTAATTTG
* * *
5522032 AGTCTTAATTTTAGTTTTGATTTTG
1 A-TTTTAATTTTAATTTT-AATTTG
5522057 -TTTTAAATTTT
1 ATTTT-AATTTT
5522068 TTTGATTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
23 25 0.52
24 20 0.42
25 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.66
Consensus pattern (23 bp):
ATTTTAATTTTAATTTTAATTTG
Found at i:5522066 original size:12 final size:11
Alignment explanation
Indices: 5521987--5522089 Score: 66
Period size: 12 Copynumber: 9.0 Consensus size: 11
5521977 CTTATCTTAA
*
5521987 TTTTAATTTTAA
1 TTTTAATTTT-G
5521999 TTTTAA-TTTG
1 TTTTAATTTTG
*
5522009 ATTTTAATTTTAA
1 -TTTTAATTTT-G
*
5522022 TTTTGATTTTAG
1 TTTTAATTTT-G
*
5522034 TCTTAATTTTAG
1 TTTTAATTTT-G
*
5522046 TTTTGATTTTG
1 TTTTAATTTTG
*
5522057 TTTTAAATTT-
1 TTTTAATTTTG
* *
5522067 TTTTGATTTTT
1 TTTTAATTTTG
5522078 TTTTAAATTTTG
1 TTTT-AATTTTG
5522090 GGTCAAAGTC
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
10 8 0.11
11 22 0.31
12 42 0.58
ACGTcount: A:0.23, C:0.01, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTAATTTTG
Found at i:5522757 original size:20 final size:18
Alignment explanation
Indices: 5522720--5522762 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5522710 GTTGAGGTTT
5522720 TTTTTAGGTTTGAGTTGAA
1 TTTTTAGGTTTGAGTTG-A
* *
5522739 TTTTTGGGTTTTAGTTTGA
1 TTTTTAGGTTTGAG-TTGA
5522758 TTTTT
1 TTTTT
5522763 CCAATGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (18 bp):
TTTTTAGGTTTGAGTTGA
Found at i:5523170 original size:15 final size:14
Alignment explanation
Indices: 5523146--5523208 Score: 58
Period size: 15 Copynumber: 4.4 Consensus size: 14
5523136 TTCATTTTGA
5523146 TTTTTATTTGATTT
1 TTTTTATTTGATTT
5523160 TTTTCTATTTGATTT
1 TTTT-TATTTGATTT
* *
5523175 GATTTGATTT--TTT
1 -TTTTTATTTGATTT
5523188 TGTTTTATTTGATTT
1 T-TTTTATTTGATTT
5523203 TATTTT
1 T-TTTT
5523209 TATACTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
13 10 0.26
14 4 0.10
15 22 0.56
16 3 0.08
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.75
Consensus pattern (14 bp):
TTTTTATTTGATTT
Found at i:5523179 original size:10 final size:10
Alignment explanation
Indices: 5523165--5523207 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
5523155 GATTTTTTTC
5523165 TATTTGATTT
1 TATTTGATTT
*
5523175 GATTTGATTT
1 TATTTGATTT
5523185 T-TTTG-TTT
1 TATTTGATTT
5523193 TATTTGATTT
1 TATTTGATTT
5523203 TATTT
1 TATTT
5523208 TTATACTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 4 0.14
9 8 0.28
10 17 0.59
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (10 bp):
TATTTGATTT
Found at i:5523209 original size:23 final size:25
Alignment explanation
Indices: 5523133--5523218 Score: 88
Period size: 25 Copynumber: 3.4 Consensus size: 25
5523123 TTTTTTATTA
*
5523133 TTTTTC-ATTTTGATTTTTATTTGATT
1 TTTTTCTA-TTTGA-TTTGATTTGATT
5523159 TTTTTCTATTTGATTTGATTTGATT
1 TTTTTCTATTTGATTTGATTTGATT
* *
5523184 TTTTTGT-TTT-ATTTGATTTTATT
1 TTTTTCTATTTGATTTGATTTGATT
*
5523207 TTTATACTATTT
1 TTT-TTCTATTT
5523219 TTTGTTTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 15 0.29
24 5 0.10
25 20 0.38
26 11 0.21
27 1 0.02
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.72
Consensus pattern (25 bp):
TTTTTCTATTTGATTTGATTTGATT
Found at i:5523323 original size:14 final size:15
Alignment explanation
Indices: 5523304--5523346 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
5523294 TTTTATATTT
*
5523304 TTATATTTGTTTG-A
1 TTATATTTATTTGCA
5523318 TTATATTTATTTGCA
1 TTATATTTATTTGCA
*
5523333 TGATATTTTATTTG
1 TTATA-TTTATTTG
5523347 TACGATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 5 0.20
16 8 0.32
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (15 bp):
TTATATTTATTTGCA
Found at i:5523526 original size:24 final size:24
Alignment explanation
Indices: 5523497--5523734 Score: 146
Period size: 24 Copynumber: 9.6 Consensus size: 24
5523487 TTTATGATTT
5523497 ATATATTTATTTGCATGATTATTA
1 ATATATTTATTTGCATGATTATTA
*
5523521 ATATATTTACTTGCATGATTATTA
1 ATATATTTATTTGCATGATTATTA
*
5523545 ATATATTTATTTGCATGATTACCTA
1 ATATATTTATTTGCATGATTA-TTA
5523570 ATATACTTGTATGTGTAATTGCATGATTATTA
1 ATATA-TT-TA----T--TTGCATGATTATTA
* * * *
5523602 TTATATTTATTTGTATGATCACCTA
1 ATATATTTATTTGCATGATTA-TTA
*
5523627 ATATATTTA--TG--TGATTATTGC
1 ATATATTTATTTGCATGATTATT-A
* * * *
5523648 ATGTTATTAATGTGCATAATTATTA
1 AT-ATATTTATTTGCATGATTATTA
** * *
5523673 ATATA-TTATTTTTATAATTTACTA
1 ATATATTTATTTGCATGA-TTATTA
*** *
5523697 ATATATTTGCATGAATGATTATTA
1 ATATATTTATTTGCATGATTATTA
5523721 ATATA-TTATTTGCA
1 ATATATTTATTTGCA
5523735 CAGTATTTTA
Statistics
Matches: 163, Mismatches: 33, Indels: 37
0.70 0.14 0.16
Matches are distributed among these distances:
20 1 0.01
21 7 0.04
22 5 0.03
23 15 0.09
24 76 0.47
25 25 0.15
26 10 0.06
27 2 0.01
30 2 0.01
31 3 0.02
32 6 0.04
33 11 0.07
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (24 bp):
ATATATTTATTTGCATGATTATTA
Found at i:5523596 original size:57 final size:56
Alignment explanation
Indices: 5523531--5523658 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 56
5523521 ATATATTTAC
*
5523531 TTGCATGATTATTAATATATTTATTTGCATGATTACCTAATATACTTGTATGTG-TAA
1 TTGCATGATTATTAATATATTTATTTGCATGATCACCTAATATA-TT-TATGTGATAA
* * *
5523588 TTGCATGATTATTATTATATTTATTTGTATGATCACCTAATATATTTATGTGATTA
1 TTGCATGATTATTAATATATTTATTTGCATGATCACCTAATATATTTATGTGATAA
5523644 TTGCATG-TTATTAAT
1 TTGCATGATTATTAAT
5523659 GTGCATAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
55 13 0.20
56 11 0.17
57 41 0.63
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (56 bp):
TTGCATGATTATTAATATATTTATTTGCATGATCACCTAATATATTTATGTGATAA
Found at i:5524724 original size:29 final size:29
Alignment explanation
Indices: 5524689--5524759 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
5524679 GTTTTTTGTA
* * * *
5524689 TATATTCATATTAGTTGTGTCTATTCATG
1 TATATTCATATTAATTATATCTATTAATG
5524718 TATATTCATATTAATTATATCTATTAATG
1 TATATTCATATTAATTATATCTATTAATG
5524747 TATA-TCTATATTA
1 TATATTC-ATATTA
5524760 TTCGTGTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 2 0.05
29 35 0.95
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.52
Consensus pattern (29 bp):
TATATTCATATTAATTATATCTATTAATG
Found at i:5524744 original size:13 final size:14
Alignment explanation
Indices: 5524708--5524755 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
5524698 ATTAGTTGTG
*
5524708 TCTATTCATGTATA
1 TCTATTAATGTATA
5524722 TTCATATTAAT-TATA
1 -TC-TATTAATGTATA
5524737 TCTATTAATGTATA
1 TCTATTAATGTATA
5524751 TCTAT
1 TCTAT
5524756 ATTATTCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.23
14 11 0.37
15 6 0.20
16 6 0.20
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.52
Consensus pattern (14 bp):
TCTATTAATGTATA
Found at i:5525591 original size:12 final size:12
Alignment explanation
Indices: 5525576--5525620 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
5525566 TTTTTTTAAT
5525576 TATTTATTTATA
1 TATTTATTTATA
5525588 TATTTATTTATATA
1 TATTTA-TT-TATA
5525602 TATTTAATTT-TA
1 TATTT-ATTTATA
5525614 TATTTAT
1 TATTTAT
5525621 ATTAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
12 13 0.43
13 3 0.10
14 11 0.37
15 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTATTTATA
Found at i:5530605 original size:19 final size:19
Alignment explanation
Indices: 5530553--5530605 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
5530543 TAAAATTTTT
*
5530553 TTTTATTTTAATACA-TTA
1 TTTTATTTTAATATATTTA
* *
5530571 TTTTCTTTT-TTATATTTA
1 TTTTATTTTAATATATTTA
5530589 TTTTATTTTAATATATT
1 TTTTATTTTAATATATT
5530606 CTTATGCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 3 0.11
18 19 0.68
19 6 0.21
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTTTAATATATTTA
Found at i:5530723 original size:23 final size:21
Alignment explanation
Indices: 5530680--5530723 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
5530670 ATTGATCATA
**
5530680 TTATTTTTTATACTTTTAAAT
1 TTATTTTTTATACTTAAAAAT
5530701 TTATTTATTTGATACTTAAAAAT
1 TTATTT-TTT-ATACTTAAAAAT
5530724 ATTACATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATTTTTTATACTTAAAAAT
Found at i:5532151 original size:14 final size:15
Alignment explanation
Indices: 5532123--5532151 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5532113 TATCAATTTG
5532123 TTTTTAAGAATAAAC
1 TTTTTAAGAATAAAC
5532138 TTTTTAAGAA-AAAC
1 TTTTTAAGAATAAAC
5532152 AAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
TTTTTAAGAATAAAC
Found at i:5532518 original size:49 final size:50
Alignment explanation
Indices: 5532416--5532518 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
5532406 CATAAGATAT
* * **
5532416 AAATTACAATAGTGATAAACTATATCTTGAAAAAAAGTTTTAAACAAAAA
1 AAATTACAATAGTAATAAACTATAACTTGAAAAAAAGTTGCAAACAAAAA
* *
5532466 AAATTATAATAGTAATAGAA-TATAACTTG-AAAAAAGTTGCAAACCAAAA
1 AAATTACAATAGTAATA-AACTATAACTTGAAAAAAAGTTGCAAACAAAAA
5532515 AAAT
1 AAAT
5532519 AAAAAAATTG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 21 0.46
50 23 0.50
51 2 0.04
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (50 bp):
AAATTACAATAGTAATAAACTATAACTTGAAAAAAAGTTGCAAACAAAAA
Found at i:5533213 original size:12 final size:12
Alignment explanation
Indices: 5533196--5533220 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5533186 ATGTTTTAAC
5533196 ACATATATATAT
1 ACATATATATAT
5533208 ACATATATATAT
1 ACATATATATAT
5533220 A
1 A
5533221 TAATGTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:5534486 original size:63 final size:64
Alignment explanation
Indices: 5534419--5534572 Score: 147
Period size: 63 Copynumber: 2.4 Consensus size: 64
5534409 CAAATACGTG
* * *
5534419 TTCAATAATCCATACAAAAAATTTTGGAT-AGGATTATTGAAGGCATTTT-TAGCCAGAAACTCC
1 TTCAATAATCCAT-CAAAAAATTTTGGATAAGGATTATTCAAGGCATTTTCTAGCCAAAAACACC
* * * * * *
5534482 TTCAATAA-CC-TCATTCAACATTTT-GTTAAGGATTATTCAATGCGTTTTCTAGCTAAAAACAC
1 TTCAATAATCCATCA--AAAAATTTTGGATAAGGATTATTCAAGGCATTTTCTAGCCAAAAACAC
5534544 C
64 C
5534545 TTCAATAATGCCATCAAAAAAATTTTGG
1 TTCAATAAT-CCATC-AAAAAATTTTGG
5534573 TTTAATTATA
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
60 2 0.03
61 3 0.04
62 26 0.37
63 27 0.38
65 9 0.13
66 3 0.04
67 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (64 bp):
TTCAATAATCCATCAAAAAATTTTGGATAAGGATTATTCAAGGCATTTTCTAGCCAAAAACACC
Found at i:5534638 original size:35 final size:35
Alignment explanation
Indices: 5534589--5534658 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
5534579 TATATTTGTA
* *
5534589 AAGTCAATTGTAGGTTTATGTCCAGAAAACATTTG
1 AAGTCAATTATAGGTTTATGCCCAGAAAACATTTG
*
5534624 AAGTCAGTTATAGGTTTATGCCCAGAAAACATTTG
1 AAGTCAATTATAGGTTTATGCCCAGAAAACATTTG
5534659 GTTTATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (35 bp):
AAGTCAATTATAGGTTTATGCCCAGAAAACATTTG
Found at i:5537648 original size:19 final size:18
Alignment explanation
Indices: 5537620--5537655 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5537610 TCTGGTCGAA
5537620 AAACTCGTCGAAAAATTC
1 AAACTCGTCGAAAAATTC
5537638 AAACTTCGTCGAAAAATT
1 AAAC-TCGTCGAAAAATT
5537656 TCGTCGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (18 bp):
AAACTCGTCGAAAAATTC
Found at i:5538036 original size:15 final size:14
Alignment explanation
Indices: 5538013--5538112 Score: 91
Period size: 14 Copynumber: 7.2 Consensus size: 14
5538003 ATAAATATAT
5538013 TAATAGATAAAAAA
1 TAATAGATAAAAAA
5538027 TAATTAGATAAATAAA
1 TAA-TAGATAAA-AAA
* *
5538043 AAATAGATAAATAA
1 TAATAGATAAAAAA
5538057 TAATA-ATAAAAAA
1 TAATAGATAAAAAA
* *
5538070 TAAAAG-TAGATAAA
1 TAATAGATA-AAAAA
* *
5538084 TAATA-A-AAATAT
1 TAATAGATAAAAAA
5538096 TAATAGATAAAAAA
1 TAATAGATAAAAAA
5538110 TAA
1 TAA
5538113 AAAATATATT
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
12 7 0.10
13 15 0.22
14 24 0.36
15 16 0.24
16 5 0.07
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
TAATAGATAAAAAA
Found at i:5538050 original size:30 final size:29
Alignment explanation
Indices: 5538014--5538094 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 29
5538004 TAAATATATT
* *
5538014 AATAGATAAAAAATAATTAGATAAATAA-AA
1 AATAGATAAATAATAA-TA-ATAAAAAATAA
5538044 AATAGATAAATAATAATAATAAAAAATAA
1 AATAGATAAATAATAATAATAAAAAATAA
*
5538073 AAGTAGATAAATAATAAAAATA
1 AA-TAGATAAATAATAATAATA
5538095 TTAATAGATA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 7 0.15
29 6 0.13
30 33 0.72
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (29 bp):
AATAGATAAATAATAATAATAAAAAATAA
Found at i:5538069 original size:24 final size:23
Alignment explanation
Indices: 5538019--5538127 Score: 80
Period size: 24 Copynumber: 4.5 Consensus size: 23
5538009 ATATTAATAG
*
5538019 ATAAAAAATAATTAGATAAATAAAAA
1 ATAATAAATAA-TA-AT-AATAAAAA
5538045 ATAGATAAATAATAATAATAAAAA
1 ATA-ATAAATAATAATAATAAAAA
*
5538069 ATAA-AAGTAGATAAATAATAAAAA
1 ATAATAAATA-AT-AATAATAAAAA
*
5538093 TATTAATAGATAA-AA-AATAAAAA
1 -A-TAATAAATAATAATAATAAAAA
*
5538116 ATATATTAATAA
1 ATA-ATAAATAA
5538128 ATAGACAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
21 2 0.03
22 11 0.16
23 11 0.16
24 24 0.34
25 3 0.04
26 9 0.13
27 10 0.14
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (23 bp):
ATAATAAATAATAATAATAAAAA
Found at i:5538082 original size:23 final size:23
Alignment explanation
Indices: 5537993--5538118 Score: 77
Period size: 23 Copynumber: 5.5 Consensus size: 23
5537983 AATTAATCAA
* * *
5537993 AATAAAAAAGATAAATATATTAAT
1 AATAAAAAATAGAAATAGA-TAAT
*
5538017 AGATAAAAAAT--AATTAGAT-A-
1 A-ATAAAAAATAGAAATAGATAAT
5538037 AATAAAAAATAGATAAATA-ATAAT
1 AATAAAAAATAG--AAATAGATAAT
5538061 AATAAAAAATA-AAAGTAGATAAAT
1 AATAAAAAATAGAAA-TAGAT-AAT
** *
5538085 AAT-AAAAATATTAATAGATAAAA
1 AATAAAAAATAGAAATAGAT-AAT
5538108 AATAAAAAATA
1 AATAAAAAATA
5538119 TATTAATAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
19 9 0.11
20 1 0.01
21 4 0.05
22 5 0.06
23 30 0.36
24 27 0.32
25 8 0.10
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (23 bp):
AATAAAAAATAGAAATAGATAAT
Found at i:5538113 original size:30 final size:30
Alignment explanation
Indices: 5538022--5538118 Score: 86
Period size: 33 Copynumber: 3.0 Consensus size: 30
5538012 TTAATAGATA
*
5538022 AAAAATAATTAGATAAATAAAAAATAGATAAAT
1 AAAAAT-ATTA-ATAAATAAAAAATAAAT-AAT
* * *
5538055 AATAATAATAAAAAATAAAAGTAGATAAATAAT
1 AAAAATATTAATAAATAAAA--A-ATAAATAAT
* *
5538088 AAAAATATTAATAGATAAAAAATAAAAAAT
1 AAAAATATTAATAAATAAAAAATAAATAAT
5538118 A
1 A
5538119 TATTAATAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 9 0.17
31 10 0.19
32 3 0.06
33 25 0.48
34 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (30 bp):
AAAAATATTAATAAATAAAAAATAAATAAT
Found at i:5538518 original size:41 final size:41
Alignment explanation
Indices: 5538383--5538750 Score: 329
Period size: 41 Copynumber: 9.0 Consensus size: 41
5538373 TTTTATCAAA
* *
5538383 GCTCCTCTAAGT-AGAGGCTCTACGACTTTGAAAAAATAAACG
1 GCTCCTCTAA-TCAGAGGCTCCACGACTTTG-AAAAATAAATG
* * *
5538425 AAGCTCATCTAAACAAAGGCTCCACGACTTTG-AAAATAAATG
1 --GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAATG
*
5538467 GCTTCC-CTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
1 GC-TCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAATG
* * * *
5538508 GCTTCTCTAATCAGAGGCTCAACGACTTTAAAAAATAAATA
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAATG
* * *
5538549 GCTCCTC-AATCAAAGGCTCAACGACTTTGAAAAATAAATA
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAATG
** * * * * * *
5538589 AATCCTCTCAGCAGAAGCACCATGAC-TTCAAAAATAAAT-
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAATG
* * * *
5538628 GCTCCTCTAAAT-AGAGGCACCACAACTTTGAAAAGTAAATT
1 GCTCCTCT-AATCAGAGGCTCCACGACTTTGAAAAATAAATG
* * *
5538669 GCTCCTCTAAAT-AGAGGCAACCACAACTTTGAAAAATAAATT
1 GCTCCTCT-AATCAGAGGC-TCCACGACTTTGAAAAATAAATG
* * *
5538711 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAT
1 GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAAT
5538751 AAATTACTCC
Statistics
Matches: 278, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
39 17 0.06
40 85 0.31
41 106 0.38
42 45 0.16
44 25 0.09
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCCACGACTTTGAAAAATAAATG
Found at i:5538560 original size:81 final size:81
Alignment explanation
Indices: 5538382--5538750 Score: 327
Period size: 81 Copynumber: 4.5 Consensus size: 81
5538372 TTTTTATCAA
* * * * * *
5538382 AGCTCCTCTAAGT-AGAGGCTCTACGACTTTGAAAAAATAAACGAAGCTCATCTAAACAAAGGCT
1 AGCTCCTCTAA-TCAGAGGCTCAACGACTTTG-AAAAATAAATG--GCTCCTCTAATCAGAGGCA
*
5538446 CCACGACTTTGAAAATAAAT
62 CCACGACTTTAAAAATAAAT
* * * *
5538466 GGCTTCC-CTAATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTTCTCTAATCAGAGGCTCAA
1 AGC-TCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCACCA
5538530 CGACTTTAAAAAATAAAT
65 CGACTTT-AAAAATAAAT
* *** * * * *
5538548 AGCTCCTC-AATCAAAGGCTCAACGACTTTGAAAAATAAATAAATCCTCTCAGCAGAAGCACCAT
1 AGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCACCAC
*
5538612 GACTTCAAAAATAAAT
66 GACTTTAAAAATAAAT
* * * * *
5538628 -GCTCCTCTAAAT-AGAGGCACCACAACTTTGAAAAGTAAATTGCTCCTCTAAAT-AGAGGCAAC
1 AGCTCCTCT-AATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCT-AATCAGAGGC-AC
*
5538690 CACAACTTTGAAAAATAAAT
63 CACGACTTT-AAAAATAAAT
* * * * *
5538710 TGCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAT
1 AGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAT
5538751 AAATTACTCC
Statistics
Matches: 236, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
79 7 0.03
80 44 0.19
81 89 0.38
82 24 0.10
83 46 0.19
84 23 0.10
85 3 0.01
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (81 bp):
AGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCACCAC
GACTTTAAAAATAAAT
Found at i:5539081 original size:44 final size:44
Alignment explanation
Indices: 5539020--5539124 Score: 119
Period size: 43 Copynumber: 2.4 Consensus size: 44
5539010 TTTAAGGCTT
* *
5539020 TTCAAAGGTTCTCATTTGGCAAACTT-GGA-ATTCATATCCAAAAA
1 TTCAAAGCTTCTCATTTGG--AACTTGGGAGATTCACATCCAAAAA
* *
5539064 -TCTAAAGCTTTTCATTT-GAATTTGGGAGATTCACATCCAAAAA
1 TTC-AAAGCTTCTCATTTGGAACTTGGGAGATTCACATCCAAAAA
5539107 TTCAAAGCTTCTCATTTG
1 TTCAAAGCTTCTCATTTG
5539125 AGTTTAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
41 4 0.08
42 3 0.06
43 30 0.59
44 14 0.27
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (44 bp):
TTCAAAGCTTCTCATTTGGAACTTGGGAGATTCACATCCAAAAA
Found at i:5540422 original size:16 final size:16
Alignment explanation
Indices: 5540401--5540439 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5540391 AGCTTTGAAG
5540401 GATCTTTAGATGCATT
1 GATCTTTAGATGCATT
*
5540417 GATCTTTAGATGTATT
1 GATCTTTAGATGCATT
5540433 GATCTTT
1 GATCTTT
5540440 TATATATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (16 bp):
GATCTTTAGATGCATT
Found at i:5540564 original size:33 final size:31
Alignment explanation
Indices: 5540522--5540637 Score: 124
Period size: 34 Copynumber: 3.6 Consensus size: 31
5540512 AATTTGAGTC
* *
5540522 TTTTTTTTTCCTTATTTCATCTTTTTTTTCTCT
1 TTTTTTTTTCATT-TTTCACCTTTTTTTTCT-T
* * *
5540555 TTTTTTTTTCATTTTCCCCCCTTTTTTTCTT
1 TTTTTTTTTCATTTTTCACCTTTTTTTTCTT
**
5540586 TTTTTTTTTCACCTTTCACCATTTTCTTTTCTTT
1 TTTTTTTTTCATTTTTCACC-TTTT-TTTTC-TT
5540620 TTTTTTTTTCATTTTTCA
1 TTTTTTTTTCATTTTTCA
5540638 TCCATTGTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
31 17 0.25
32 16 0.24
33 17 0.25
34 18 0.26
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTTTTTTCATTTTTCACCTTTTTTTTCTT
Found at i:5540580 original size:32 final size:31
Alignment explanation
Indices: 5540544--5540634 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 31
5540534 TATTTCATCT
* *
5540544 TTTTTTTCTCTTTTTTTTTTCATTTTCCCCCC
1 TTTTTTTCT-TTTTTTTTTTCATTTTCACCAC
* *
5540576 TTTTTTTCTTTTTTTTTTTCACCTTTCACCAT
1 TTTTTTTCTTTTTTTTTTTCA-TTTTCACCAC
5540608 TTTCTTTTCTTTTTTTTTTTTCATTTT
1 TTT-TTTTC-TTTTTTTTTTTCATTTT
5540635 TCATCCATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.24
32 18 0.35
33 8 0.16
34 13 0.25
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (31 bp):
TTTTTTTCTTTTTTTTTTTCATTTTCACCAC
Found at i:5547314 original size:13 final size:13
Alignment explanation
Indices: 5547289--5547334 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
5547279 ATTTTTGATA
*
5547289 AAATAAAATAAAT
1 AAATAAAACAAAT
*
5547302 AAGTAAAACAAAT
1 AAATAAAACAAAT
*
5547315 AAATAAAATAAAAT
1 AAATAAAA-CAAAT
5547329 AAATAA
1 AAATAA
5547335 GAAAATACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (13 bp):
AAATAAAACAAAT
Found at i:5547637 original size:10 final size:10
Alignment explanation
Indices: 5547604--5547646 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
5547594 TTTTTCAGAA
5547604 TTCCCTTCTT
1 TTCCCTTCTT
*
5547614 TTCTTCTCTCTT
1 TTC-CCT-TCTT
5547626 TTCCCTTCTT
1 TTCCCTTCTT
5547636 TTCCCCTTCTT
1 TT-CCCTTCTT
5547647 CTCTCTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 9 0.32
11 12 0.43
12 7 0.25
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (10 bp):
TTCCCTTCTT
Found at i:5548127 original size:16 final size:17
Alignment explanation
Indices: 5548106--5548170 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
5548096 AAAATAAAAA
* *
5548106 AGATAAATATATTAA-T
1 AGATAAATAAAATAATT
5548122 AGATAAA-AAAATAATT
1 AGATAAATAAAATAATT
* *
5548138 AGATAAATAAAAGAAAT
1 AGATAAATAAAATAATT
5548155 AGATAAATAATAATAA
1 AGATAAATAA-AATAA
5548171 AAAAATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 5 0.12
16 15 0.37
17 17 0.41
18 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (17 bp):
AGATAAATAAAATAATT
Found at i:5548146 original size:45 final size:42
Alignment explanation
Indices: 5548097--5548220 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 42
5548087 AAATTAATCA
* *
5548097 AAATAAAAAAGATAAATATATTAATAGATAAAAAAATAATTAGAT
1 AAATAAAAAA-ATAAATATATTAATAGATAAAAAAATAA--AAAC
* *
5548142 AAATAAAAGAAATAGATA-AATAATA-ATAAAAAAATAAAAAC
1 AAATAAAA-AAATAAATATATTAATAGATAAAAAAATAAAAAC
* * *
5548183 AGAT-AAATAATAAAAATATTAATAGATAAAAAAATAAA
1 AAATAAAAAAATAAATATATTAATAGATAAAAAAATAAA
5548221 TATATATATT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
39 6 0.09
40 9 0.13
41 18 0.27
43 12 0.18
44 6 0.09
45 14 0.21
46 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.23
Consensus pattern (42 bp):
AAATAAAAAAATAAATATATTAATAGATAAAAAAATAAAAAC
Found at i:5548164 original size:4 final size:4
Alignment explanation
Indices: 5548097--5548257 Score: 60
Period size: 4 Copynumber: 39.8 Consensus size: 4
5548087 AAATTAATCA
* * * * * * *
5548097 AAAT AAAA AAGAT AAAT ATAT TAAT AGAT AAAA AAAT AATT AGAT AAAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
5548146 AAAAG AAAT AGAT AAAT -AAT -AAT AAAA AAAT AAAA ACAGAT AAAT -AAT
1 -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT
* * * * * * * *
5548194 AAA- AATAT TAAT AGAT AAAA AAAT AAAT ATAT ATAT TAAT AAAT AGAC
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
5548242 AAAT AATAA AAAT AAA
1 AAAT AA-AT AAAT AAA
5548258 AATAAAAGCC
Statistics
Matches: 110, Mismatches: 38, Indels: 18
0.66 0.23 0.11
Matches are distributed among these distances:
3 11 0.10
4 85 0.77
5 12 0.11
6 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5548214 original size:17 final size:17
Alignment explanation
Indices: 5548096--5548222 Score: 88
Period size: 16 Copynumber: 7.7 Consensus size: 17
5548086 AAAATTAATC
*
5548096 AAAATA-AAAAAGAT-A
1 AAAATATAAATAGATAA
* *
5548111 AATATATTAATAGATAA
1 AAAATATAAATAGATAA
*
5548128 AAAA-ATAATTAGATAA
1 AAAATATAAATAGATAA
*
5548144 ATAAA-AGAAATAGATAA
1 A-AAATATAAATAGATAA
* * *
5548161 ATAATAATAAAAAAATAA
1 AAAAT-ATAAATAGATAA
*
5548179 AAACAGATAAATA-AT-A
1 AAA-ATATAAATAGATAA
*
5548195 AAAATATTAATAGATAA
1 AAAATATAAATAGATAA
5548212 AAAA-ATAAATA
1 AAAATATAAATA
5548223 TATATATTAA
Statistics
Matches: 86, Mismatches: 18, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
15 12 0.14
16 31 0.36
17 25 0.29
18 17 0.20
19 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAATATAAATAGATAA
Found at i:5548222 original size:45 final size:41
Alignment explanation
Indices: 5548086--5548222 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 41
5548076 ATCTTAATTG
*
5548086 AAAATTAATCAAAATAAA-AAAGATAAATATATTAATAGATAAA
1 AAAATAAAT-AAAA-AAATAAA-ATAAATATATTAATAGATAAA
* * * * * * *
5548129 AAAATAATTAGATAAATAAAAGAAATAGATAAATA-ATAAT
1 AAAATAAATAAAAAAATAAAATAAATATATTAATAGATAAA
*
5548169 AAAA-AAATAAAAACAGATAAATAATAAAAATATTAATAGATAAA
1 AAAATAAATAAAAA-A-AT-AA-AATAAATATATTAATAGATAAA
5548213 AAAATAAATA
1 AAAATAAATA
5548223 TATATATTAA
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
39 6 0.08
40 9 0.13
41 17 0.24
42 7 0.10
43 19 0.27
44 8 0.11
45 5 0.07
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (41 bp):
AAAATAAATAAAAAAATAAAATAAATATATTAATAGATAAA
Found at i:5548249 original size:43 final size:41
Alignment explanation
Indices: 5548118--5548263 Score: 118
Period size: 43 Copynumber: 3.4 Consensus size: 41
5548108 ATAAATATAT
* * *
5548118 TAATAGATAAAAAAATAATTAGATAAATAAAAGAAATAGATAAA
1 TAATA-ATAAAAAAATAAATA-ATAAAT-AAATAAATAGAAAAA
* *
5548162 TAATAATAAAAAAATAAA-AACAGATAAAT-AATA-AAAATA
1 TAATAATAAAAAAATAAATAATAAATAAATAAATAGAAAA-A
* * *
5548201 TTAATAGATAAAAAAATAAATATATATATTAATAAATAGACAAA
1 -TAATA-ATAAAAAAATAAATA-ATAAATAAATAAATAGAAAAA
*
5548245 TAATAAAAATAAAAATAAA
1 TAATAATAA-AAAAATAAA
5548264 AGCCAATTAG
Statistics
Matches: 84, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
38 3 0.04
39 5 0.06
40 8 0.10
41 17 0.20
42 5 0.06
43 33 0.39
44 10 0.12
45 3 0.04
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (41 bp):
TAATAATAAAAAAATAAATAATAAATAAATAAATAGAAAAA
Found at i:5548259 original size:84 final size:84
Alignment explanation
Indices: 5548108--5548264 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 84
5548098 AATAAAAAAG
* * * *
5548108 ATAAATATATTAATAGATAAAAAAATAATTAGATAAATAAAAGAAATAGATAAATAATAATAAAA
1 ATAAAAATATTAATAGATAAAAAAATAAATAGATAAATAAAAGAAATAGACAAATAATAAAAAAA
5548173 AAATAAAAACAGATAAATA
66 AAATAAAAACAGATAAATA
* * * *
5548192 ATAAAAATATTAATAGATAAAAAAATAAATATATATAT-TAATAAATAGACAAATAATAAAAATA
1 ATAAAAATATTAATAGATAAAAAAATAAATAGATAAATAAAAGAAATAGACAAATAATAAAAA-A
5548256 AAAATAAAA
65 AAAATAAAA
5548265 GCCAATTAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 20 0.31
84 44 0.69
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (84 bp):
ATAAAAATATTAATAGATAAAAAAATAAATAGATAAATAAAAGAAATAGACAAATAATAAAAAAA
AAATAAAAACAGATAAATA
Found at i:5550706 original size:64 final size:63
Alignment explanation
Indices: 5550638--5550759 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
5550628 TGTTGGCCCA
* * *
5550638 AAAAAAAGGCCTTCAAT-AATCTCCTGACAAAAACTTGAAAGGGATTATTGAAGGCGTTTTCAGT
1 AAAAAAAGGCCTTCAATAAAT-TACTGA-AAAAAATTGAAAGCGATTATTGAAGGCGTTTTCAGT
* * **
5550702 AAAAAAATGCCTTCAATAAATTACTTAAAAAAATTTTAAGCGATTATTGAAGGCGTTT
1 AAAAAAAGGCCTTCAATAAATTACTGAAAAAAATTGAAAGCGATTATTGAAGGCGTTT
5550760 ATGACTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 27 0.54
64 20 0.40
65 3 0.06
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (63 bp):
AAAAAAAGGCCTTCAATAAATTACTGAAAAAAATTGAAAGCGATTATTGAAGGCGTTTTCAGT
Found at i:5550964 original size:63 final size:62
Alignment explanation
Indices: 5550897--5551078 Score: 154
Period size: 63 Copynumber: 2.9 Consensus size: 62
5550887 TTTTTAGTTT
**
5550897 AAAAACGCATTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGTGTTTTATG-C-A
1 AAAAAC-C-TTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAG-CATTTATGACTA
* ** ** * * * *
5550960 AAAAATTTCTTCAATAAT-TTCTTTTAAAATATTTGAGGGGATTATTGAAAGCATTTGTGACTA
1 AAAAA--CCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTATGACTA
* * * *
5551023 AAAATACCTTAAATAATCCCCTGATAAAAAATTAGAGTTGCTTATTGAAGGCATTT
1 AAAA-ACCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTT
5551079 TCTACAAAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
61 5 0.06
62 36 0.40
63 47 0.52
64 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (62 bp):
AAAAACCTTCAATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTATGACTA
Found at i:5551089 original size:63 final size:62
Alignment explanation
Indices: 5550909--5551089 Score: 166
Period size: 62 Copynumber: 2.9 Consensus size: 62
5550899 AAACGCATTC
** * ** *
5550909 AATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGTGTTTTATGCAAAAAATTTCTTC
1 AATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTT-TACAAAAAATACCTTA
** ** * * * * *
5550972 AATAAT-TTCTTTTAAAATATTTGAGGGGATTATTGAAAGCATTTGTGACTAAAAATACCTTA
1 AATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTT-TTACAAAAAATACCTTA
* * *
5551034 AATAATCCCCTGATAAAAAATTAGAGTTGCTTATTGAAGGCATTTTCTACAAAAAA
1 AATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTT-TACAAAAAA
5551090 AATGCCTTCA
Statistics
Matches: 88, Mismatches: 27, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
62 46 0.52
63 42 0.48
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (62 bp):
AATAATCCCCTGATAAAAAATTAGAGTGGATTATTGAAAGCATTTTTACAAAAAATACCTTA
Found at i:5551267 original size:263 final size:252
Alignment explanation
Indices: 5551220--5551709 Score: 555
Period size: 252 Copynumber: 1.9 Consensus size: 252
5551210 TGCAAAAAAA
* *
5551220 AAAAAAAATACCTTCAATAATTTCCTTTAAAATATTTAAAGGGATTATTGAAGGCGTTTGTGACT
1 AAAAAAAATATCTTCAATAATTTCATTTAAAATATTT-AAGGGATTATTGAAGGCGTTTGTGACT
* * * *
5551285 AAAAATACCCTCAATAATGCCTTGATAAAAAATTGGAG-TGAATTATTGAAAGCATTTTTTACAA
65 AAAAATACCTTCAATAATCCCTTGATAAAAAATTAGAGTTG-ATTATTGAAGGCATTTTTTACAA
*
5551349 AAAAAATACCTTCAATAATTTTCTTTACAATTTTTTATGGGATTGTTAAAGGCA-TTTTTAGTCT
129 AAAAAAT-CCTTCAATAATTTTCTTTAC-ATTTTTTATGGGATTATTAAAGGCATTTTTTAGTCT
* * * * *
5551413 AAAAATGCCTT-AATAATCTCCTGA-TAAAAAATTAGAGTGGATTATTGAAAGTATTTTTTG
192 AAAAATGCCTTCAATAATCCCCT-ATTAAAAAATTGGAATGGATTATTGAAAGGATTTTCTG
* * * * *
5551473 TAAAAAAATATCTTCAATAATTTCATTTAAAATATTTGAGTGATTATTGAAGGTGTTTGTGACTT
1 AAAAAAAATATCTTCAATAATTTCATTTAAAATATTTAAGGGATTATTGAAGGCGTTTGTGACTA
** ** * * * *
5551538 AAAATATTTTCAATAATCTTTTGATAAAAAATTACAGTTGATTATTAAAGGTATTTTTTGCAAAA
66 AAAATACCTTCAATAATCCCTTGATAAAAAATTAGAGTTGATTATTGAAGGCATTTTTTACAAAA
* * * * *
5551603 AAACA-CCTTCAATAATTTAT-TTTAAAATTTTTGTGAGATTATTGAA-G-ATATTTTTAGTCTA
131 AAA-ATCCTTCAATAATTT-TCTTTACATTTTTTATGGGATTATTAAAGGCAT-TTTTTAGTCTA
* * *
5551664 AAAACGCCTTCAATAATCCCCTGTTAAAAAATTGAAATGGATTATT
193 AAAATGCCTTCAATAATCCCCTATTAAAAAATTGGAATGGATTATT
5551710 AAATGCGTTT
Statistics
Matches: 199, Mismatches: 31, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
248 1 0.01
249 1 0.01
250 36 0.18
251 46 0.23
252 78 0.39
253 37 0.19
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (252 bp):
AAAAAAAATATCTTCAATAATTTCATTTAAAATATTTAAGGGATTATTGAAGGCGTTTGTGACTA
AAAATACCTTCAATAATCCCTTGATAAAAAATTAGAGTTGATTATTGAAGGCATTTTTTACAAAA
AAAATCCTTCAATAATTTTCTTTACATTTTTTATGGGATTATTAAAGGCATTTTTTAGTCTAAAA
ATGCCTTCAATAATCCCCTATTAAAAAATTGGAATGGATTATTGAAAGGATTTTCTG
Found at i:5551291 original size:62 final size:62
Alignment explanation
Indices: 5551223--5551743 Score: 222
Period size: 63 Copynumber: 8.3 Consensus size: 62
5551213 AAAAAAAAAA
* * *
5551223 AAAAATACCTTCAATAATTTCCTTTAAAATATTTAAAGGGATTATTGAAGGCGTTTGTGACT
1 AAAAATACCTTCAATAATTTCCTTTAAAATATTTAGAGGGATTATTGAAGGCATTTTTGACT
* * * * * * *
5551285 AAAAATACCCTCAATAA-TGCCTTGATAAAA-AATTGGAGTGAATTATTGAAAGCATTTTTTACA
1 AAAAATACCTTCAATAATTTCCTT--TAAAATATTTAGAG-GGATTATTGAAGGCATTTTTGAC-
*
5551348 AA
62 -T
* * * * * * *
5551350 AAAAATACCTTCAATAATTTTCTTTACAATTTTTTA-TGGGATTGTTAAAGGCATTTTTAGTCT
1 AAAAATACCTTCAATAATTTCCTTTA-AAATATTTAGAGGGATTATTGAAGGCATTTTT-GACT
* * * * * *
5551413 AAAAATGCCTT-AATAATCTCCTGATAAAA-AATTAGAGTGGATTATTGAAAGTATTTTTTGTA-
1 AAAAATACCTTCAATAATTTCCT-TTAAAATATTTAGAG-GGATTATTGAAGGCA-TTTTTG-AC
*
5551475 A
62 T
* * * ** *
5551476 AAAAATATCTTCAATAATTTCATTTAAAATATTT-GAGTGATTATTGAAGGTGTTTGTGACT
1 AAAAATACCTTCAATAATTTCCTTTAAAATATTTAGAGGGATTATTGAAGGCATTTTTGACT
* ** * * * * *
5551537 TAAAATATTTTCAATAATCTT--TTGATAAAA-AATTACAGTTGATTATTAAAGGTATTTTTTG-
1 AAAAATACCTTCAATAAT-TTCCTT--TAAAATATTTAGAG-GGATTATTGAAGGCA-TTTTTGA
*
5551598 CAA
61 C-T
* ** * * * ** *
5551601 AAAAACACCTTCAATAATTTATTTTAAAAT-TTTTGTGAGATTATTGAAGATATTTTTAGTCT
1 AAAAATACCTTCAATAATTTCCTTTAAAATATTTAGAGGGATTATTGAAGGCATTTTT-GACT
** ** * * * * * * * *
5551663 AAAAACGCCTTCAATAATCCCCTGTTAAAAAATTGAAATGGATTATTAAATGCGTTTTT-AGT
1 AAAAATACCTTCAATAATTTCCT-TTAAAATATTTAGAGGGATTATTGAAGGCATTTTTGACT
5551725 AAAAAATACCTTCAATAAT
1 -AAAAATACCTTCAATAAT
5551744 GTTAAATGTT
Statistics
Matches: 335, Mismatches: 92, Indels: 63
0.68 0.19 0.13
Matches are distributed among these distances:
60 3 0.01
61 37 0.11
62 86 0.26
63 111 0.33
64 70 0.21
65 22 0.07
66 6 0.02
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (62 bp):
AAAAATACCTTCAATAATTTCCTTTAAAATATTTAGAGGGATTATTGAAGGCATTTTTGACT
Done.