Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 8 of 20
Found at i:2639036 original size:14 final size:14
Alignment explanation
Indices: 2638988--2639045 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
2638978 TTATGATTTG
2638988 TATTTTTTAATTATT
1 TATTTTTTAA-TATT
*
2639003 TAAATTTTT-AT-TT
1 T-ATTTTTTAATATT
*
2639016 GTGTTTTTTAATATT
1 -TATTTTTTAATATT
2639031 TATTTTTTAATATT
1 TATTTTTTAATATT
2639045 T
1 T
2639046 TTAATTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
13 7 0.20
14 18 0.51
15 4 0.11
16 6 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TATTTTTTAATATT
Found at i:2639136 original size:24 final size:24
Alignment explanation
Indices: 2639106--2639154 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2639096 ATAAATTTAT
*
2639106 ATTTTTTCTTTATTTTCATCTTTTC
1 ATTTTTT-TTCATTTTCATCTTTTC
*
2639131 ATTTTTTTTCATTTTCTTCTTTTC
1 ATTTTTTTTCATTTTCATCTTTTC
2639155 TTTCCTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (24 bp):
ATTTTTTTTCATTTTCATCTTTTC
Found at i:2639139 original size:18 final size:17
Alignment explanation
Indices: 2639109--2639178 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 17
2639099 AATTTATATT
2639109 TTTTCTTTATTTTCATC
1 TTTTCTTTATTTTCATC
* *
2639126 TTTTCATTTTTTTTCATT
1 TTTTC-TTTATTTTCATC
2639144 TTCTTCTTT-TCTTTC--C
1 TT-TTCTTTAT-TTTCATC
2639160 TTTTCTTATATTTTTCATC
1 TTTTCTT-TA-TTTTCATC
2639179 ATATTTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
15 5 0.12
16 3 0.07
17 10 0.24
18 20 0.48
19 4 0.10
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTTTATTTTCATC
Found at i:2639163 original size:24 final size:24
Alignment explanation
Indices: 2639110--2639164 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
2639100 ATTTATATTT
2639110 TTTC-TTT-ATTTTCATCTTTTCA
1 TTTCTTTTCATTTTCATCTTTTCA
* *
2639132 TTTTTTTTCATTTTCTTCTTTTC-
1 TTTCTTTTCATTTTCATCTTTTCA
2639155 TTTCCTTTTC
1 TTT-CTTTTC
2639165 TTATATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.11
23 6 0.22
24 18 0.67
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTCTTTTCATTTTCATCTTTTCA
Found at i:2639691 original size:42 final size:42
Alignment explanation
Indices: 2639617--2639717 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
2639607 ATGGCCAGAT
* * *
2639617 TAGGCCACAACTAGTGCTAGATTGATCATCCAACAGCCAAATC
1 TAGG-CACAACTAGTGCTAAATTGAACATCCAACAACCAAATC
*
2639660 T-GGTCACAACTAGTGCTAAATT-AACGTTCCAACAACCAAATC
1 TAGG-CACAACTAGTGCTAAATTGAAC-ATCCAACAACCAAATC
*
2639702 TAGGCACAACCAGTGC
1 TAGGCACAACTAGTGC
2639718 CAGATCGGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.04
42 45 0.90
43 3 0.06
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (42 bp):
TAGGCACAACTAGTGCTAAATTGAACATCCAACAACCAAATC
Found at i:2640005 original size:17 final size:19
Alignment explanation
Indices: 2639985--2640020 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2639975 GAGGTAAATT
2639985 AAGAAAA-GAGA-AAAAAA
1 AAGAAAATGAGAGAAAAAA
2640002 AAGAAAATGAGAGAAAAAA
1 AAGAAAATGAGAGAAAAAA
2640021 CCCCTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (19 bp):
AAGAAAATGAGAGAAAAAA
Found at i:2641510 original size:12 final size:10
Alignment explanation
Indices: 2641484--2641522 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2641474 CGTTTTTCAT
2641484 TTTTTATTAA
1 TTTTTATTAA
2641494 TTTTTATTAA
1 TTTTTATTAA
* *
2641504 TTATT-TTAT
1 TTTTTATTAA
2641513 TTTTTATTAA
1 TTTTTATTAA
2641523 AATATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:2646532 original size:41 final size:41
Alignment explanation
Indices: 2646487--2646564 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
2646477 ATTTTGTTTT
*
2646487 ATTTTATGAGTTAAATTGTCATCTTTATATAGATTTAGGTA
1 ATTTTATGAGTTAAATCGTCATCTTTATATAGATTTAGGTA
* * * *
2646528 ATTTTTTGTGTTGAATCGTCATCTTTATGTAGATTTA
1 ATTTTATGAGTTAAATCGTCATCTTTATATAGATTTA
2646565 TATTTTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.51
Consensus pattern (41 bp):
ATTTTATGAGTTAAATCGTCATCTTTATATAGATTTAGGTA
Found at i:2665909 original size:14 final size:14
Alignment explanation
Indices: 2665890--2665929 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2665880 AACATATAAG
*
2665890 TAAATAAATAGAAA
1 TAAATAAATAAAAA
2665904 TAAATAAATAAAAA
1 TAAATAAATAAAAA
2665918 T-AATAATATAAA
1 TAAATAA-ATAAA
2665930 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAATAAATAAAAA
Found at i:2678679 original size:20 final size:21
Alignment explanation
Indices: 2678654--2678693 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2678644 ACCAATGAGA
2678654 GATAAA-CAACCATAAGAACT
1 GATAAACCAACCATAAGAACT
*
2678674 GATAAACCAACTATAAGAAC
1 GATAAACCAACCATAAGAAC
2678694 ATCAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.55, C:0.20, G:0.10, T:0.15
Consensus pattern (21 bp):
GATAAACCAACCATAAGAACT
Found at i:2680394 original size:17 final size:17
Alignment explanation
Indices: 2680372--2680407 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2680362 TTGTGACATC
2680372 TCAAATTAGTTATACCT
1 TCAAATTAGTTATACCT
2680389 TCAAATTAGTTATACCT
1 TCAAATTAGTTATACCT
2680406 TC
1 TC
2680408 TCTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (17 bp):
TCAAATTAGTTATACCT
Found at i:2695102 original size:21 final size:20
Alignment explanation
Indices: 2695053--2695105 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
2695043 TACCTATCTT
* * *
2695053 TTATTTGTAAATTTTTTTTA
1 TTATTTATAAATTTATATTA
2695073 TT-TTATATATAATTTATATTA
1 TTATT-TATA-AATTTATATTA
2695094 TTATTTATAAAT
1 TTATTTATAAAT
2695106 ACGTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.07
20 8 0.30
21 15 0.56
22 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATTTATAAATTTATATTA
Found at i:2695448 original size:21 final size:22
Alignment explanation
Indices: 2695424--2695464 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2695414 CAAAATTGAT
* *
2695424 AAAATAAATTTAAAA-GTATAG
1 AAAAAAAATATAAAATGTATAG
2695445 AAAAAAAATATAAAATGTAT
1 AAAAAAAATATAAAATGTAT
2695465 TAGGTGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAAAAAATATAAAATGTATAG
Found at i:2701694 original size:37 final size:38
Alignment explanation
Indices: 2701628--2701704 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
2701618 AAATAAAAAG
* * *
2701628 TTTAAAGTTTTGATTATAAATTAAAAAAAATTAATATT
1 TTTAAACTTTTAACTATAAATTAAAAAAAATTAATATT
*
2701666 TTTAAACTTTTAACTATAAATT-ATAAAAATTAATATT
1 TTTAAACTTTTAACTATAAATTAAAAAAAATTAATATT
2701703 TT
1 TT
2701705 AATTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
37 16 0.46
38 19 0.54
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTAAACTTTTAACTATAAATTAAAAAAAATTAATATT
Found at i:2701731 original size:25 final size:27
Alignment explanation
Indices: 2701688--2701738 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
2701678 ACTATAAATT
* *
2701688 ATAAAAATTAATATTTTAATT-TAAAA
1 ATAAAAATTAAAATATTAATTATAAAA
2701714 ATAAAAA-TAAAATATTAATTATAAA
1 ATAAAAATTAAAATATTAATTATAAA
2701739 TCATAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
ATAAAAATTAAAATATTAATTATAAAA
Found at i:2701738 original size:53 final size:54
Alignment explanation
Indices: 2701675--2701781 Score: 128
Period size: 53 Copynumber: 2.0 Consensus size: 54
2701665 TTTTAAACTT
* **
2701675 TTAACTATAAATTATAAAAATTAATA-TTTTAATTTAAA-AATAAAAATAAAATA
1 TTAACTATAAATCATAAAAATTAATATTTTTAAAATAAAGAAT-AAAATAAAATA
* * **
2701728 TTAATTATAAATCATAAATATTTTTATTTTTAAAATAAAGAATAAAATAAAATA
1 TTAACTATAAATCATAAAAATTAATATTTTTAAAATAAAGAATAAAATAAAATA
2701782 ATCATATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 21 0.47
54 21 0.47
55 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (54 bp):
TTAACTATAAATCATAAAAATTAATATTTTTAAAATAAAGAATAAAATAAAATA
Found at i:2701824 original size:60 final size:60
Alignment explanation
Indices: 2701711--2701826 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
2701701 TTTTAATTTA
* *
2701711 AAAATAAAAATAAAATATTAATTATAAATCATAAATATTTTTATTTTTAAAATAAAGAAT
1 AAAATAAAAATAAAATATTAATTATAAATCATAAATATGTTAATTTTTAAAATAAAGAAT
* * *
2701771 AAAAT-AAAATAATCATATTAATATTTAAATTATAAAT-TGTTAATATTTT-AAATAAA
1 AAAATAAAAATAA-AATATTAAT-TATAAATCATAAATATGTTAAT-TTTTAAAATAAA
2701827 CTTTAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
59 7 0.15
60 25 0.52
61 16 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (60 bp):
AAAATAAAAATAAAATATTAATTATAAATCATAAATATGTTAATTTTTAAAATAAAGAAT
Found at i:2702655 original size:17 final size:17
Alignment explanation
Indices: 2702633--2702666 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2702623 TTATAAAACT
2702633 CTTATGAAAAGTAATAA
1 CTTATGAAAAGTAATAA
2702650 CTTATGAAAAGTAATAA
1 CTTATGAAAAGTAATAA
2702667 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
CTTATGAAAAGTAATAA
Found at i:2702905 original size:22 final size:22
Alignment explanation
Indices: 2702880--2702923 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2702870 TTAAAACAAA
2702880 TTTT-TAGAAATATAAAAATTAT
1 TTTTATAGAAA-ATAAAAATTAT
* *
2702902 TTTTATATAAAATAAAATTTAT
1 TTTTATAGAAAATAAAAATTAT
2702924 AATTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTATAGAAAATAAAAATTAT
Found at i:2709290 original size:16 final size:15
Alignment explanation
Indices: 2709257--2709293 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2709247 ATTGACTTTC
2709257 ATATTAATTAAAATA
1 ATATTAATTAAAATA
*
2709272 ATATTAATATAAGATA
1 ATATTAAT-TAAAATA
2709288 ATATTA
1 ATATTA
2709294 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATATTAATTAAAATA
Found at i:2709305 original size:31 final size:26
Alignment explanation
Indices: 2709275--2709324 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2709265 TAAAATAATA
*
2709275 TTAAT-ATAAGATAATATTATATTTT
1 TTAATAATTAGATAATATTATATTTT
2709300 TTAATAATTAGATAATATTATATTT
1 TTAATAATTAGATAATATTATATTT
2709325 AGTCTCTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
TTAATAATTAGATAATATTATATTTT
Found at i:2710872 original size:26 final size:27
Alignment explanation
Indices: 2710813--2710867 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2710803 TGCGTATCTA
*
2710813 TTTCTTTTT-TTTTCTAATTTTGAAGG
1 TTTCTTTTTCTTTTCTAATTTCGAAGG
*
2710839 TTTCTTTTTCTTTTCTGATTTCGAAGG
1 TTTCTTTTTCTTTTCTAATTTCGAAGG
2710866 TT
1 TT
2710868 GTTTTTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.64
Consensus pattern (27 bp):
TTTCTTTTTCTTTTCTAATTTCGAAGG
Found at i:2715304 original size:21 final size:21
Alignment explanation
Indices: 2715263--2715306 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2715253 CAAATAATGT
**
2715263 TTGTTACAAAATATATGAAAA
1 TTGTTACAAAATATACAAAAA
*
2715284 TTGTTATAAAATATACAAAAA
1 TTGTTACAAAATATACAAAAA
2715305 TT
1 TT
2715307 ATTCAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (21 bp):
TTGTTACAAAATATACAAAAA
Found at i:2735678 original size:20 final size:21
Alignment explanation
Indices: 2735632--2735683 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2735622 AAGAGCACAT
* * *
2735632 TCAAACAACTTCAAAGATGAT
1 TCAAACAAGTTCAAAAATGAC
2735653 TCAAACAAGTTCAAAAAT-AC
1 TCAAACAAGTTCAAAAATGAC
2735673 TCAAACAAGTT
1 TCAAACAAGTT
2735684 TGAAATTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (21 bp):
TCAAACAAGTTCAAAAATGAC
Found at i:2737819 original size:63 final size:63
Alignment explanation
Indices: 2737709--2737836 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 63
2737699 ATAGTCAACG
* * *
2737709 TTCAAATACATATTCAAAATAAATTTCAACTATGTCAACATAAGGTATATATCATGATCAAAC
1 TTCAAATACATATTCAAAATAAATTTCAACTATATCAACACAAGGTATAGATCATGATCAAAC
* * * * *
2737772 TTCAAATGCATATTCAAAATAAATTTCAACTATATCAACGCAGGGTATAGATTATGATCATAC
1 TTCAAATACATATTCAAAATAAATTTCAACTATATCAACACAAGGTATAGATCATGATCAAAC
2737835 TT
1 TT
2737837 GACTTAAGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (63 bp):
TTCAAATACATATTCAAAATAAATTTCAACTATATCAACACAAGGTATAGATCATGATCAAAC
Found at i:2741857 original size:99 final size:99
Alignment explanation
Indices: 2741731--2741930 Score: 330
Period size: 99 Copynumber: 2.0 Consensus size: 99
2741721 TTTTTCTATT
2741731 AAAGTGTGTCAAAAGTAATTTGAAGAGTAAATTAAAGAATAAACAAGTTAAGAAAAAATTTTCAA
1 AAAGTGTGTCAAAAGTAATTTGAAGAGTAAATTAAAGAATAAACAAGTTAAGAAAAAATTTTC-A
*
2741796 AACTCTTCAAAGTAAATAAAATGCACATCTATATC
65 AACTCTTCAAAGTAAATAAAATGCACAACTATATC
*
2741831 AAAGTGTGTCAAAA-TAATTTGAAGAGTAAATTAAAGAATAAACAAGTTAAGAACAAATTTTCAA
1 AAAGTGTGTCAAAAGTAATTTGAAGAGTAAATTAAAGAATAAACAAGTTAAGAAAAAATTTTCAA
* * * *
2741895 AGTTTTCAAAGTAAATGAAATGCACAAGTATATC
66 ACTCTTCAAAGTAAATAAAATGCACAACTATATC
2741929 AA
1 AA
2741931 GCGTAAATTA
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 33 0.35
99 47 0.50
100 14 0.15
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (99 bp):
AAAGTGTGTCAAAAGTAATTTGAAGAGTAAATTAAAGAATAAACAAGTTAAGAAAAAATTTTCAA
ACTCTTCAAAGTAAATAAAATGCACAACTATATC
Found at i:2742262 original size:66 final size:65
Alignment explanation
Indices: 2742153--2742278 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 65
2742143 GCATAACTAT
* ** *
2742153 TGCCTTTTCAAGGATCAAGAATAACCTTTGTATACTACTTTTTGAAGGCTAAAGTATAACCTCTA
1 TGCCTTTTCAAGGATCAAGAACAACCTTTAAATACTACATTTTGAAGGCTAAAGTATAACCTCTA
* * *
2742218 TGCCTTTT-AAGGATCAAGCACAACTTCTTTAAATACTACATTTTGAAGGTTAAGGTATAAC
1 TGCCTTTTCAAGGATCAAGAACAAC--CTTTAAATACTACATTTTGAAGGCTAAAGTATAAC
2742279 TTTTTTTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 14 0.27
65 8 0.15
66 30 0.58
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (65 bp):
TGCCTTTTCAAGGATCAAGAACAACCTTTAAATACTACATTTTGAAGGCTAAAGTATAACCTCTA
Found at i:2743328 original size:21 final size:21
Alignment explanation
Indices: 2743288--2743356 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
2743278 GGAAGCTTTT
2743288 AAGTTCAAGAGCA-CATTCAAAC
1 AAGTTCAA-AG-ATCATTCAAAC
*
2743310 AAGTTCAAAGATGATTCAAAC
1 AAGTTCAAAGATCATTCAAAC
* *
2743331 AAGTTCAAGGATCACTCAAAC
1 AAGTTCAAAGATCATTCAAAC
2743352 AAGTT
1 AAGTT
2743357 TGAAATTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 33 0.79
22 8 0.19
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (21 bp):
AAGTTCAAAGATCATTCAAAC
Found at i:2749659 original size:42 final size:42
Alignment explanation
Indices: 2749600--2749686 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
2749590 TTCAATGTAG
2749600 TAATAATTAATGGTTGATTCCGACTAAGAGAGACATGCCACT
1 TAATAATTAATGGTTGATTCCGACTAAGAGAGACATGCCACT
2749642 TAATAATTAATGGTTGATTCCGACTAAGAGAGACATGCCACT
1 TAATAATTAATGGTTGATTCCGACTAAGAGAGACATGCCACT
2749684 TAA
1 TAA
2749687 AATCTGCGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (42 bp):
TAATAATTAATGGTTGATTCCGACTAAGAGAGACATGCCACT
Found at i:2758389 original size:13 final size:16
Alignment explanation
Indices: 2758356--2758388 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2758346 TGTTTTCTTC
2758356 TTTTAATATATATTAT
1 TTTTAATATATATTAT
2758372 TTTTAAT-TATATT-T
1 TTTTAATATATATTAT
2758386 TTT
1 TTT
2758389 ATACTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTAATATATATTAT
Found at i:2779406 original size:2 final size:2
Alignment explanation
Indices: 2779399--2779428 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2779389 CTAATTATAG
2779399 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2779429 AGTAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2788731 original size:33 final size:33
Alignment explanation
Indices: 2788679--2788743 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
2788669 GTGACACTAA
* *
2788679 TGTGATATGTTAATGTATCATAATTCATGATAC
1 TGTGATATGTTAATATATCATAATTAATGATAC
* *
2788712 TGTGGTATTTTAATATATCATAATTAATGATA
1 TGTGATATGTTAATATATCATAATTAATGATA
2788744 ATATAACATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTGATATGTTAATATATCATAATTAATGATAC
Found at i:2795867 original size:29 final size:29
Alignment explanation
Indices: 2795811--2795867 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2795801 ACTATGTGAT
* **
2795811 ATATAATAATAAATAATATTTTTTTTAAA
1 ATATAATAATAAATAACATTTTAATTAAA
* *
2795840 ATATAATGATAAGTAACATTTTAATTAA
1 ATATAATAATAAATAACATTTTAATTAA
2795868 TATTAGTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (29 bp):
ATATAATAATAAATAACATTTTAATTAAA
Found at i:2797114 original size:31 final size:30
Alignment explanation
Indices: 2797061--2797135 Score: 114
Period size: 31 Copynumber: 2.5 Consensus size: 30
2797051 CTATTTAAGA
*
2797061 AAATAAACTTTTATATTTTTATTTTAAGTC
1 AAATAAATTTTTATATTTTTATTTTAAGTC
*
2797091 AAATAAATTTTTATACTTTTTATTTTGAGTC
1 AAATAAATTTTTATA-TTTTTATTTTAAGTC
*
2797122 AAATAAATCTTTAT
1 AAATAAATTTTTAT
2797136 TATTAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 14 0.34
31 27 0.66
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTTATTTTAAGTC
Found at i:2797927 original size:20 final size:21
Alignment explanation
Indices: 2797899--2797941 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2797889 GTAGTTAACT
2797899 AGTGCAGAGA-TTAAAAAAAA
1 AGTGCAGAGATTTAAAAAAAA
*
2797919 AGTGGAGAGATTTTAAAAAAAA
1 AGTGCAGAGA-TTTAAAAAAAA
2797941 A
1 A
2797942 AGGTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.58, C:0.02, G:0.21, T:0.19
Consensus pattern (21 bp):
AGTGCAGAGATTTAAAAAAAA
Found at i:2811310 original size:30 final size:30
Alignment explanation
Indices: 2811274--2811364 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
2811264 GTATTAAAGT
*
2811274 ATAATAAAATTTTTTTAAATATAACATGTA
1 ATAATAAAATTTTTTTAAACATAACATGTA
* * * **
2811304 ATAATAATATTTTTTTTAACATGATGTGTA
1 ATAATAAAATTTTTTTAAACATAACATGTA
* * *
2811334 ATAATAACATTTTTTTCAACATAACTTGTA
1 ATAATAAAATTTTTTTAAACATAACATGTA
2811364 A
1 A
2811365 CATATTTTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (30 bp):
ATAATAAAATTTTTTTAAACATAACATGTA
Found at i:2811335 original size:27 final size:27
Alignment explanation
Indices: 2811305--2811563 Score: 88
Period size: 29 Copynumber: 9.8 Consensus size: 27
2811295 TAACATGTAA
2811305 TAATAATATTTTTTTTAACATGATGTG
1 TAATAATATTTTTTTTAACATGATGTG
* *
2811332 TAATAATAACATTTTTTTCAACATAACT-TG
1 TAATAAT---ATTTTTTTTAACATGA-TGTG
* * *
2811362 TAA-CATA-TTTTTGT-ATATGATGTG
1 TAATAATATTTTTTTTAACATGATGTG
*
2811386 TAACAATAATATTTTTTTTAACATGATATAG
1 T---AATAATATTTTTTTTAACATGATGT-G
* * **
2811417 -AA-CA-ACTTTTTTTAACCAT-A-ACG
1 TAATAATATTTTTTTTAA-CATGATGTG
* *
2811440 T-ATAACATGTTTTTGT-ACATGATGTG
1 TAATAATAT-TTTTTTTAACATGATGTG
* * *
2811466 TAATAATATATTTTTTTCAATATGACGTA
1 TAATAATAT-TTTTTTT-AACATGATGTG
2811495 TAATAATA--TTTTTTAAC---ATGTG
1 TAATAATATTTTTTTTAACATGATGTG
* * * *
2811517 TAAT-ATA-TTTTTAT-ATATGATATA
1 TAATAATATTTTTTTTAACATGATGTG
2811541 TAATAATAATATTTTTTTAACAT
1 TAATAAT-AT-TTTTTTTAACAT
2811564 AACGTATAAC
Statistics
Matches: 167, Mismatches: 34, Indels: 60
0.64 0.13 0.23
Matches are distributed among these distances:
21 4 0.02
22 12 0.07
23 3 0.02
24 19 0.11
25 23 0.14
26 20 0.12
27 23 0.14
28 9 0.05
29 26 0.16
30 26 0.16
31 2 0.01
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (27 bp):
TAATAATATTTTTTTTAACATGATGTG
Found at i:2811462 original size:80 final size:83
Alignment explanation
Indices: 2811300--2811497 Score: 244
Period size: 80 Copynumber: 2.4 Consensus size: 83
2811290 AAATATAACA
* * * * *
2811300 TGTAATAATAATATTTTTTTTAACATGATGTGTAATAATAACATTTTTTTCAACATAACTTGTAA
1 TGTAATAATAATATTTTTTTTAACATGA-GTATAAGAACAACATTTTTTTCAACATAACGTATAA
*
2811365 CATATTTTTGTATATGATG
65 CATATTTTTGTACATGATG
*
2811384 TGTAACAATAATATTTTTTTTAACATGA-TAT-AGAACAAC-TTTTTTT-AACCATAACGTATAA
1 TGTAATAATAATATTTTTTTTAACATGAGTATAAGAACAACATTTTTTTCAA-CATAACGTATAA
*
2811445 CATGTTTTTGTACATGATG
65 CATATTTTTGTACATGATG
* *
2811464 TGTAATAAT-ATATTTTTTTCAATATGACGTATAA
1 TGTAATAATAATATTTTTTTTAACATGA-GTATAA
2811498 TAATATTTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
79 18 0.18
80 42 0.42
81 9 0.09
82 3 0.03
84 27 0.27
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (83 bp):
TGTAATAATAATATTTTTTTTAACATGAGTATAAGAACAACATTTTTTTCAACATAACGTATAAC
ATATTTTTGTACATGATG
Found at i:2811507 original size:80 final size:80
Alignment explanation
Indices: 2811300--2811572 Score: 256
Period size: 75 Copynumber: 3.4 Consensus size: 80
2811290 AAATATAACA
* *
2811300 TGTAATAATAATATTTTTTTTAACATGATGTGTAATAATAACATTTTTTTCAACATAACTTGTAA
1 TGTAATAATAATATTTTTTTTAACATGA--TGT-ATAATAA-ATTTTTTTCAACATAACGTATAA
*
2811365 CATATTTTTGTATATGATG
62 CATATTTTTGTACATGATG
* * * * *
2811384 TGTAACAATAATATTTTTTTTAACATGATATAGAACAACTTTTTTT-AACCATAACGTATAACAT
1 TGTAATAATAATATTTTTTTTAACATGATGTATAATAAATTTTTTTCAA-CATAACGTATAACAT
*
2811448 GTTTTTGTACATGATG
65 ATTTTTGTACATGATG
* * * * *
2811464 TGTAATAAT-ATATTTTTTTCAATATGACGTATAAT-AATATTTTTT-AACAT---GTGTAATAT
1 TGTAATAATAATATTTTTTTTAACATGATGTATAATAAAT-TTTTTTCAACATAACGTATAACAT
* * *
2811523 ATTTTTATATATGATA
65 ATTTTTGTACATGATG
* * *
2811539 TATAATAATAATA-TTTTTTTAACATAACGTATAA
1 TGTAATAATAATATTTTTTTTAACATGATGTATAA
2811573 CATCAACTGC
Statistics
Matches: 159, Mismatches: 27, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
75 45 0.28
76 3 0.02
78 5 0.03
79 30 0.19
80 42 0.26
81 5 0.03
82 2 0.01
84 27 0.17
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (80 bp):
TGTAATAATAATATTTTTTTTAACATGATGTATAATAAATTTTTTTCAACATAACGTATAACATA
TTTTTGTACATGATG
Found at i:2811806 original size:12 final size:12
Alignment explanation
Indices: 2811789--2811816 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2811779 GGTTTCAAAG
2811789 TGAACAATACCT
1 TGAACAATACCT
2811801 TGAACAATACCT
1 TGAACAATACCT
2811813 TGAA
1 TGAA
2811817 GTTTGAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (12 bp):
TGAACAATACCT
Found at i:2825287 original size:13 final size:13
Alignment explanation
Indices: 2825271--2825315 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
2825261 TTAATATTCA
2825271 ATTTTATTTTTTT
1 ATTTTATTTTTTT
2825284 A-TTTA-TTTTTT
1 ATTTTATTTTTTT
**
2825295 ATTTTATGATTTT
1 ATTTTATTTTTTT
2825308 ATTTTATT
1 ATTTTATT
2825316 AAAATATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 7 0.26
12 8 0.30
13 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (13 bp):
ATTTTATTTTTTT
Found at i:2825306 original size:19 final size:20
Alignment explanation
Indices: 2825272--2825312 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2825262 TAATATTCAA
* *
2825272 TTTTATTTTTTTA-TTTATT
1 TTTTATTTTATGATTTTATT
2825291 TTTTATTTTATGATTTTATT
1 TTTTATTTTATGATTTTATT
2825311 TT
1 TT
2825313 ATTAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTATTTTATGATTTTATT
Found at i:2832486 original size:16 final size:16
Alignment explanation
Indices: 2832461--2832502 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2832451 TAAATTAATA
*
2832461 AATT-ATTAATTTATC
1 AATTAATTAATGTATC
* *
2832476 GATTAATTAATGTGTC
1 AATTAATTAATGTATC
2832492 AATTAATTAAT
1 AATTAATTAAT
2832503 AAATTTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (16 bp):
AATTAATTAATGTATC
Found at i:2834349 original size:23 final size:23
Alignment explanation
Indices: 2834318--2834388 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
2834308 TAAGCAATGC
* *
2834318 CTAAGTCACACAATACTTTACTAA
1 CTAA-TCACGCAATACCTTACTAA
*
2834342 CTAATCACGCAATGCCTTACTAA
1 CTAATCACGCAATACCTTACTAA
* *
2834365 CTAGTAACGCAATACCTTACTAA
1 CTAATCACGCAATACCTTACTAA
2834388 C
1 C
2834389 AAGTAATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 37 0.90
24 4 0.10
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.27
Consensus pattern (23 bp):
CTAATCACGCAATACCTTACTAA
Found at i:2834393 original size:23 final size:23
Alignment explanation
Indices: 2834328--2834400 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2834318 CTAAGTCACA
* *
2834328 CAATACTTTACTAACTAA-TCACG
1 CAATACCTTACTAAC-AAGTAACG
* *
2834351 CAATGCCTTACTAACTAGTAACG
1 CAATACCTTACTAACAAGTAACG
*
2834374 CAATACCTTACTAACAAGTAATG
1 CAATACCTTACTAACAAGTAACG
2834397 CAAT
1 CAAT
2834401 GCCTATCAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 1 0.02
23 41 0.98
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (23 bp):
CAATACCTTACTAACAAGTAACG
Found at i:2847429 original size:19 final size:20
Alignment explanation
Indices: 2847397--2847443 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2847387 TCTATAAAAA
* *
2847397 AAATATAATTATTATTATAT
1 AAATATAATAATTATTAAAT
2847417 AAAT-TAATAATTATTAAAT
1 AAATATAATAATTATTAAAT
2847436 AATATATA
1 AA-ATATA
2847444 TACCTTGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATAATAATTATTAAAT
Found at i:2847885 original size:15 final size:15
Alignment explanation
Indices: 2847855--2847896 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2847845 TATTTTGAGT
2847855 TAACATTATAAAAATTA
1 TAAC-TTAT-AAAATTA
2847872 TAACTTATAAAATTA
1 TAACTTATAAAATTA
2847887 TCAA-TTATAA
1 T-AACTTATAA
2847897 TATATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TAACTTATAAAATTA
Found at i:2851472 original size:43 final size:42
Alignment explanation
Indices: 2851425--2851586 Score: 188
Period size: 43 Copynumber: 3.9 Consensus size: 42
2851415 TGTTTAAGAA
*
2851425 GTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTTTGTTGTT
1 GTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTATGTTG-T
2851468 GTTGTTTGGATATTTGTGTTTT-GTTATTTAAGTTTATGTTGT
1 GTTGTTTGGATATTTGT-TTTTAGTTATTTAAGTTTATGTTGT
* * *
2851510 -TTGTTTGGATCTTTGTGTTTAGTTATTTAAGTTTAT-AT-T
1 GTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTATGTTGT
* * * * * *
2851549 GTTATTTGGATATTTATGTATATTTATATAAGTTTATG
1 GTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTATG
2851587 CTTAAGATCT
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.01
40 34 0.32
41 30 0.29
42 1 0.01
43 35 0.33
44 4 0.04
ACGTcount: A:0.19, C:0.01, G:0.20, T:0.61
Consensus pattern (42 bp):
GTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTATGTTGT
Found at i:2851581 original size:40 final size:39
Alignment explanation
Indices: 2851425--2851585 Score: 151
Period size: 41 Copynumber: 3.9 Consensus size: 39
2851415 TGTTTAAGAA
* * * *
2851425 GTTGTTTGGATATTTGTTTTTAGTTATTTAAGTTTTTGTTGTT
1 GTTGTTTGGATATTTG-TGTTATTTATTTAAG--TTT-ATATT
* *
2851468 GTTGTTTGGATATTTGTGTTTTGTTATTTAAGTTTATGTT
1 GTTGTTTGGATATTTGTGTTAT-TTATTTAAGTTTATATT
* *
2851508 GTTTGTTTGGATCTTTGTGTTTAGTTATTTAAGTTTATATT
1 G-TTGTTTGGATATTTGTG-TTATTTATTTAAGTTTATATT
* * *
2851549 GTTATTTGGATATTTATGTATATTTATATAAGTTTAT
1 GTTGTTTGGATATTTGTGT-TATTTATTTAAGTTTAT
2851586 GCTTAAGATC
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.01
40 34 0.34
41 36 0.36
42 5 0.05
43 25 0.25
ACGTcount: A:0.19, C:0.01, G:0.19, T:0.61
Consensus pattern (39 bp):
GTTGTTTGGATATTTGTGTTATTTATTTAAGTTTATATT
Found at i:2856265 original size:69 final size:69
Alignment explanation
Indices: 2856191--2856326 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 69
2856181 ATAAATAACA
* * *
2856191 CTTAAATGCATAACAAACTTGTAAAAT-AACATG-TTGTCTCTAGTTTTCATTTCTCTTTCCCTT
1 CTTAAATACATAACAAACTTGT-AAATCAACATGCTT-TCTCTAGTTTCCATTTCTCCTTCCCTT
2856254 ACAGTG
64 ACAGTG
* *
2856260 CTTAAATACATAACAAACTTGTAAATCAATATGCTTTGTCTAGTTTCCATTTCTCCTTCCCTTAC
1 CTTAAATACATAACAAACTTGTAAATCAACATGCTTTCTCTAGTTTCCATTTCTCCTTCCCTTAC
2856325 AG
66 AG
2856327 ATACAACTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 4 0.07
69 54 0.90
70 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (69 bp):
CTTAAATACATAACAAACTTGTAAATCAACATGCTTTCTCTAGTTTCCATTTCTCCTTCCCTTAC
AGTG
Found at i:2857335 original size:21 final size:21
Alignment explanation
Indices: 2857311--2857356 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2857301 TAAATTCAAG
*
2857311 AATTAAGGTTAAGGTTTTGGA
1 AATTAAGGTTAAGGTATTGGA
2857332 AATTAAGGTTAAGGTATTGGA
1 AATTAAGGTTAAGGTATTGGA
2857353 AATT
1 AATT
2857357 GGGATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (21 bp):
AATTAAGGTTAAGGTATTGGA
Found at i:2859327 original size:202 final size:202
Alignment explanation
Indices: 2858842--2859352 Score: 627
Period size: 204 Copynumber: 2.5 Consensus size: 202
2858832 AGATCTCCCC
* * * *
2858842 ATATTACGCATTGAGTGAGTTATAATTATTGGGTATTGCGAGAGTGGAGATGCGTGACTTGTGCA
1 ATATTACGCATTGAGTGA-CT-T-ATTATTAGGTATTGCGAGACTGCAG-TGCGTGACTTGTGCA
* * * * *
2858907 ATTTATCTCTTATTTTGAGGCTTTTTTTCACTCA-TTTGTAGATACTGCATGACTGGTTTTTATG
62 ATTCATCTCTTGTTTTGAGGCTTTTGTTCACT-AGTTTTTAGACACTGCATGACTGGTTTTTATG
* * *
2858971 TATTGCGTGACTATTGTTATGTTTTGCATTACATTAGGCCGTTACGTGACTGGTTATGTTTGCAT
126 TATTGCGTAACTATTGTTATGTTTTGCATGACATTAGGCCGTTACGTGACTGGTTATGATTGCAT
*
2859036 AATGCGTGGGTGG
191 AAT-CGTGAGTGG
* * * * * *
2859049 ATGTTAAGCATTGAGTGACTTATTATTAGGTATTGCTAGACTGGCGGTGCGTGATTTGTGAAATT
1 ATATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACT-GCAGTGCGTGACTTGTGCAATT
* * * **
2859114 CATCACTTGTTTTGAGGCTTTTGTTAACTAGTTTTTAGACGCTGTGTGACT-GTTTTTATGTATT
65 CATCTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGACACTGCATGACTGGTTTTTATGTATT
* * *
2859178 GCGTAACCTGTTGTTATGTTTTGCGTGACATT-GAGCTGTTACGTGACTGGTTAT-ATTGACATA
130 GCGTAA-CTATTGTTATGTTTTGCATGACATTAG-GCCGTTACGTGACTGGTTATGATTG-CATA
2859241 AT-GTGAGTGG
192 ATCGTGAGTGG
*
2859251 ATATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTGACAGTGCGTGGCTTGTGCAATT
1 ATATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTG-CAGTGCGTGACTTGTGCAATT
*
2859316 CATCTCTTGTTTAGAGGCTTTTGTTCACTAGTTTTTA
65 CATCTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTA
2859353 AGGTCTGCAT
Statistics
Matches: 261, Mismatches: 37, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
201 1 0.00
202 97 0.37
203 23 0.09
204 120 0.46
205 3 0.01
206 1 0.00
207 16 0.06
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (202 bp):
ATATTACGCATTGAGTGACTTATTATTAGGTATTGCGAGACTGCAGTGCGTGACTTGTGCAATTC
ATCTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGACACTGCATGACTGGTTTTTATGTATTG
CGTAACTATTGTTATGTTTTGCATGACATTAGGCCGTTACGTGACTGGTTATGATTGCATAATCG
TGAGTGG
Found at i:2866339 original size:137 final size:137
Alignment explanation
Indices: 2866087--2866339 Score: 348
Period size: 137 Copynumber: 1.8 Consensus size: 137
2866077 TTGAGTGACT
2866087 TATTACTCACGAGATATGATATTAACTACTCACGTGATTCAAAATTTAGTACTCGTGTGATTCCA
1 TATTACTCACGAGATATGATATTAACTACTCACGTGATTCAAAATTTAGTACTCGTGTGATTCCA
* * * *
2866152 TATATAAGGATGCCTGATTCCATATCAAATACTAGCGTAATTCCATATTTACTATTAACGCGACT
66 TATAAAACGATGCCTGATTCCATATCAAATACTAGCGTAATTCAAAATTTACTATTAACGCGACT
2866217 CCAATTC
131 CCAATTC
* * * * *
2866224 TATTACTCACGTGA-CTGCATATTAACTACTCATGTGATTCAAAATTTTGTACTCGTGTGATTTC
1 TATTACTCACGAGATATG-ATATTAACTACTCACGTGATTCAAAATTTAGTACTCGTGTGATTCC
* * * * *
2866288 ATATAAATACTAT-CGTGATTCCGTATCAAATACTCGCGTTATTCAAAATTTA
65 ATATAAA-ACGATGCCTGATTCCATATCAAATACTAGCGTAATTCAAAATTTA
2866340 GTACTCGCTT
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
136 2 0.02
137 95 0.95
138 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (137 bp):
TATTACTCACGAGATATGATATTAACTACTCACGTGATTCAAAATTTAGTACTCGTGTGATTCCA
TATAAAACGATGCCTGATTCCATATCAAATACTAGCGTAATTCAAAATTTACTATTAACGCGACT
CCAATTC
Found at i:2866367 original size:23 final size:23
Alignment explanation
Indices: 2866273--2866367 Score: 54
Period size: 23 Copynumber: 4.2 Consensus size: 23
2866263 CAAAATTTTG
2866273 TACTCG-TGTGATTTCATAT-AAA
1 TACTCGCT-TGATTTCATATCAAA
** * * *
2866295 TACTATCGTGATTCCGTATCAAA
1 TACTCGCTTGATTTCATATCAAA
* ** *
2866318 TACTCGCGTT-A-TTCAAAATTTAG
1 TACTCGC-TTGATTTC-ATATCAAA
2866341 TACTCGCTTGATTTCATATCAAA
1 TACTCGCTTGATTTCATATCAAA
2866364 TACT
1 TACT
2866368 AAAGGCAATC
Statistics
Matches: 49, Mismatches: 18, Indels: 11
0.63 0.23 0.14
Matches are distributed among these distances:
22 17 0.35
23 28 0.57
24 4 0.08
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (23 bp):
TACTCGCTTGATTTCATATCAAA
Found at i:2869513 original size:23 final size:23
Alignment explanation
Indices: 2869470--2869526 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2869460 GTAGTCACCC
* *
2869470 TGTCATGCAATGACCTTTCAATA
1 TGTCATGCAATGACATATCAATA
*
2869493 TGTCATGTAATGACATATCAACTA
1 TGTCATGCAATGACATATCAA-TA
*
2869517 -GTCAAGCAAT
1 TGTCATGCAAT
2869527 TTTAAACTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (23 bp):
TGTCATGCAATGACATATCAATA
Found at i:2873881 original size:55 final size:55
Alignment explanation
Indices: 2873807--2873954 Score: 165
Period size: 55 Copynumber: 2.7 Consensus size: 55
2873797 GTTGACTTGG
* * *
2873807 CATGTTGAAAATTTAGTTGTTACATGTCATGTCGGAAAATAAAGTTGTTACACGTT
1 CATGTTGAAAATTTCGTTGTTACATGTCATGTCGAAAAATAAAGTTGCTACAC-TT
* * *
2873863 -ATGTTGAAAATTTCGTTGTTACATGTCATATTGAAAAATATAGTTGCTACACTT
1 CATGTTGAAAATTTCGTTGTTACATGTCATGTCGAAAAATAAAGTTGCTACACTT
* * * * *
2873917 CATATTGAAGA-TTCAATTATTACATGTCATGTTGAAAA
1 CATGTTGAAAATTTC-GTTGTTACATGTCATGTCGAAAA
2873955 TTTAGTAGTT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
54 5 0.06
55 74 0.94
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (55 bp):
CATGTTGAAAATTTCGTTGTTACATGTCATGTCGAAAAATAAAGTTGCTACACTT
Found at i:2873949 original size:82 final size:82
Alignment explanation
Indices: 2873854--2874064 Score: 217
Period size: 82 Copynumber: 2.6 Consensus size: 82
2873844 AATAAAGTTG
* * * **
2873854 TTACACGTTATGTTGAAAATTTCGTTGTTACATGTCATATTGAAAAATATAGTTGCTACACTTCA
1 TTACACGTCATGTTGAAAATTTAGTTGTTACATGTCATATTGAAAAATATAGTTACTACACGCCA
*
2873919 TATTGAAGATTCAATTA
66 TATAGAAGATTCAATTA
* * * * * * * *
2873936 TTACATGTCATGTTGAAAATTTAGTAGTTATACGCCATGTTGAAAAATGTAGTTATTACACGCCA
1 TTACACGTCATGTTGAAAATTTAGTTGTTACATGTCATATTGAAAAATATAGTTACTACACGCCA
* * * *
2874001 TGTAGAAGATTTAGTTT
66 TATAGAAGATTCAATTA
* *
2874018 TTACACATCATATTGAAAAATTTAGTTGTTACATGTCATGA-TGAAAA
1 TTACACGTCATGTTG-AAAATTTAGTTGTTACATGTCAT-ATTGAAAA
2874065 TGTTGTTACA
Statistics
Matches: 101, Mismatches: 26, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
82 76 0.75
83 25 0.25
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (82 bp):
TTACACGTCATGTTGAAAATTTAGTTGTTACATGTCATATTGAAAAATATAGTTACTACACGCCA
TATAGAAGATTCAATTA
Found at i:2873992 original size:55 final size:55
Alignment explanation
Indices: 2873814--2874065 Score: 150
Period size: 55 Copynumber: 4.6 Consensus size: 55
2873804 TGGCATGTTG
* * * ** * *** *
2873814 AAAATTTAGTTGTTACATGTCATGTCGGAAAATAAAGTTGTTACACGTTATGTTG-
1 AAAATGTAGTTATTACATGTCATGT-TGAAAATTTAGTAGTTACACACCATATTGA
* * * * * * * **
2873869 AAAATTTCGTTGTTACATGTCATATTGAAAAATATAGTTGCTACACTTCATATTG-
1 AAAATGTAGTTATTACATGTCATGTTG-AAAATTTAGTAGTTACACACCATATTGA
* * * * *
2873924 AAGAT-TCAATTATTACATGTCATGTTGAAAATTTAGTAGTTATACGCCATGTTGA
1 AAAATGT-AGTTATTACATGTCATGTTGAAAATTTAGTAGTTACACACCATATTGA
* * * * ** *
2873979 AAAATGTAGTTATTACACGCCATGTAGAAGATTTAGTTTTTACACATCATATTGA
1 AAAATGTAGTTATTACATGTCATGTTGAAAATTTAGTAGTTACACACCATATTGA
* * *
2874034 AAAATTTAGTTGTTACATGTCATGATGAAAAT
1 AAAATGTAGTTATTACATGTCATGTTGAAAAT
2874066 GTTGTTACAT
Statistics
Matches: 154, Mismatches: 39, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
54 22 0.14
55 131 0.85
56 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (55 bp):
AAAATGTAGTTATTACATGTCATGTTGAAAATTTAGTAGTTACACACCATATTGA
Found at i:2874069 original size:24 final size:24
Alignment explanation
Indices: 2874042--2874105 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
2874032 GAAAAATTTA
2874042 GTTGTTACATGTCATGATGAAAAT
1 GTTGTTACATGTCATGATGAAAAT
2874066 GTTGTTACATGTCATGATGAAAAT
1 GTTGTTACATGTCATGATGAAAAT
*
2874090 GTTGTTACACGTCATG
1 GTTGTTACATGTCATG
2874106 CCATAATTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (24 bp):
GTTGTTACATGTCATGATGAAAAT
Found at i:2875380 original size:38 final size:38
Alignment explanation
Indices: 2875334--2875414 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
2875324 TGTGTACTTG
* *
2875334 AGAA-TTCTAATATGTGATTAGTTGTTAAGATAATTCT
1 AGAATTTCTAATACGTGATTAGTTGTTAAAATAATTCT
*
2875371 GGAATTTCTAATACGTGATTAGTTGTTAAAATAATTCT
1 AGAATTTCTAATACGTGATTAGTTGTTAAAATAATTCT
2875409 AGAATT
1 AGAATT
2875415 CTATGTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (38 bp):
AGAATTTCTAATACGTGATTAGTTGTTAAAATAATTCT
Found at i:2882328 original size:22 final size:22
Alignment explanation
Indices: 2882300--2882341 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2882290 GTATCTCTGA
2882300 TTTTTAGGCATTGCATGATTGG
1 TTTTTAGGCATTGCATGATTGG
*
2882322 TTTTTAGGTATTGCATGATT
1 TTTTTAGGCATTGCATGATT
2882342 AAGTTGTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.50
Consensus pattern (22 bp):
TTTTTAGGCATTGCATGATTGG
Found at i:2882351 original size:22 final size:22
Alignment explanation
Indices: 2882304--2882355 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2882294 CTCTGATTTT
* * *
2882304 TAGGCATTGCATGATTGGTTTT
1 TAGGTATTGCATGATTAGTTTG
2882326 TAGGTATTGCATGATTAAG-TTG
1 TAGGTATTGCATGATT-AGTTTG
2882348 TAGGTATT
1 TAGGTATT
2882356 ACATAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.23, C:0.06, G:0.27, T:0.44
Consensus pattern (22 bp):
TAGGTATTGCATGATTAGTTTG
Found at i:2882373 original size:22 final size:22
Alignment explanation
Indices: 2882323--2882375 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2882313 CATGATTGGT
* * *
2882323 TTTTAGGTATTGCATGATTAAG
1 TTTTAGGTATTACATAATTAAC
* *
2882345 TTGTAGGTATTACATAATTGAC
1 TTTTAGGTATTACATAATTAAC
2882367 TTTTAGGTA
1 TTTTAGGTA
2882376 ATGCCTAAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
TTTTAGGTATTACATAATTAAC
Found at i:2882475 original size:22 final size:22
Alignment explanation
Indices: 2882447--2882557 Score: 98
Period size: 22 Copynumber: 5.0 Consensus size: 22
2882437 ATGTCATATC
2882447 AATTAGTTACGCAATACTTAAA
1 AATTAGTTACGCAATACTTAAA
* * *
2882469 AATTAGTTACGTAATGCCTAAA
1 AATTAGTTACGCAATACTTAAA
* ***
2882491 AATTAGTCATATAATACTTAAA
1 AATTAGTTACGCAATACTTAAA
* * *
2882513 AATTAATCACGCAATATCTAAAA
1 AATTAGTTACGCAATA-CTTAAA
**
2882536 AACGA-TTACGCAATACTTAAA
1 AATTAGTTACGCAATACTTAAA
2882557 A
1 A
2882558 CTATTGAATT
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
21 6 0.08
22 57 0.80
23 8 0.11
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (22 bp):
AATTAGTTACGCAATACTTAAA
Found at i:2882497 original size:44 final size:44
Alignment explanation
Indices: 2882447--2882557 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 44
2882437 ATGTCATATC
* * * *
2882447 AATTAGTTACGCAATACTTAAAAATTAGTTACGTAATGCCTAAA
1 AATTAGTTACGCAATACTTAAAAATTAATCACGCAATACCTAAA
* *** *
2882491 AATTAGTCATATAATACTTAAAAATTAATCACGCAATATCTAAA
1 AATTAGTTACGCAATACTTAAAAATTAATCACGCAATACCTAAA
2882535 AA--ACGATTACGCAATACTTAAAA
1 AATTA-G-TTACGCAATACTTAAAA
2882558 CTATTGAATT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
42 1 0.02
43 1 0.02
44 50 0.96
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (44 bp):
AATTAGTTACGCAATACTTAAAAATTAATCACGCAATACCTAAA
Found at i:2882754 original size:60 final size:60
Alignment explanation
Indices: 2882655--2882773 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
2882645 GAGAAGAATG
* * * *
2882655 CTCAAAATGCTTAAAGGTTTTTCTTCATATATTAGAAATCACTCCAAAATACTTAAAATA
1 CTCAAAATGCTTAAAGATTTTTCTTCATATATCAAAAATCACTCCAAAATACTCAAAATA
* * * *
2882715 CTCAAAATGCTTAATGATTTTTTTTCGTATATCAAAAATCACTCCAAAATTCTCAAAAT
1 CTCAAAATGCTTAAAGATTTTTCTTCATATATCAAAAATCACTCCAAAATACTCAAAAT
2882774 GCTTAAGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (60 bp):
CTCAAAATGCTTAAAGATTTTTCTTCATATATCAAAAATCACTCCAAAATACTCAAAATA
Found at i:2884595 original size:27 final size:27
Alignment explanation
Indices: 2884546--2884604 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2884536 CTAATTTTAA
* *
2884546 GGATAACTTTAGCTACTAAAAGTGGAT
1 GGATAACTTTACCTACTAAAAGTAGAT
*
2884573 GGATAACTTTACCCT-CTAGAAGTAGAT
1 GGATAACTTTA-CCTACTAAAAGTAGAT
2884600 GGATA
1 GGATA
2884605 CCCTAACCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (27 bp):
GGATAACTTTACCTACTAAAAGTAGAT
Found at i:2886892 original size:37 final size:37
Alignment explanation
Indices: 2886833--2886915 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 37
2886823 TAAGATCTTC
* *
2886833 TTTCTCTTTCTAAACTCTTTCTTTTATAGTTAT-TTTT
1 TTTCTCTTTCTAAACTCTTTCTTTCA-AGTTATCTTTA
**
2886870 TTTCTCTTTCTTTACT-TGTTCTTTCAAGTTATCTTTA
1 TTTCTCTTTCTAAACTCT-TTCTTTCAAGTTATCTTTA
*
2886907 TTTGTCTTT
1 TTTCTCTTT
2886916 TTAAGTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
36 7 0.18
37 32 0.82
ACGTcount: A:0.13, C:0.17, G:0.05, T:0.65
Consensus pattern (37 bp):
TTTCTCTTTCTAAACTCTTTCTTTCAAGTTATCTTTA
Found at i:2886911 original size:23 final size:23
Alignment explanation
Indices: 2886878--2886924 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2886868 TTTTTCTCTT
2886878 TCTTTACTTGT-TCTTTCAAGTTA
1 TCTTTACTTGTCT-TTTCAAGTTA
* *
2886901 TCTTTATTTGTCTTTTTAAGTTA
1 TCTTTACTTGTCTTTTCAAGTTA
2886924 T
1 T
2886925 ATTTCATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.17, C:0.13, G:0.09, T:0.62
Consensus pattern (23 bp):
TCTTTACTTGTCTTTTCAAGTTA
Found at i:2887804 original size:30 final size:30
Alignment explanation
Indices: 2887761--2887818 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2887751 CCTTCATATT
*
2887761 TTTTTAAGACTAAGATAGAACCTCTCTACC
1 TTTTCAAGACTAAGATAGAACCTCTCTACC
* * *
2887791 TTTTCAAGGCTAAGGTAGAACCTTTCTA
1 TTTTCAAGACTAAGATAGAACCTCTCTA
2887819 TATTTCAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (30 bp):
TTTTCAAGACTAAGATAGAACCTCTCTACC
Found at i:2895707 original size:5 final size:5
Alignment explanation
Indices: 2895697--2895721 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2895687 CTGGCTTTTA
2895697 AAGGG AAGGG AAGGG AAGGG AAGGG
1 AAGGG AAGGG AAGGG AAGGG AAGGG
2895722 TAAATTCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AAGGG
Found at i:2896354 original size:27 final size:27
Alignment explanation
Indices: 2896323--2896374 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2896313 ATTATTTTTA
* *
2896323 TTAATATATAATATATTTCAATATAAT
1 TTAATATAAAATATATTTAAATATAAT
* *
2896350 TTAATTTAAAATTTATTTAAATATA
1 TTAATATAAAATATATTTAAATATA
2896375 TTAAAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATATAAAATATATTTAAATATAAT
Found at i:2896392 original size:20 final size:19
Alignment explanation
Indices: 2896364--2896403 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2896354 TTTAAAATTT
2896364 ATTTAAATATATTAA-AATA
1 ATTTAAATAT-TTAATAATA
2896383 ATTTATAATATTTAATAATA
1 ATTTA-AATATTTAATAATA
2896403 A
1 A
2896404 AAAATAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATATTTAATAATA
Found at i:2896796 original size:38 final size:38
Alignment explanation
Indices: 2896744--2896827 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
2896734 AAAAATCAAA
* *
2896744 TTTAGTATATTTAAATTAGCCTATTTGGCCTAGGTTTTT
1 TTTAGT-TATTTAAATTAGCCTATTGGGCCTAGCTTTTT
* * *
2896783 TTTAGTTATTTAAATTAGCTTGTTGGGCCTATCTTTTT
1 TTTAGTTATTTAAATTAGCCTATTGGGCCTAGCTTTTT
2896821 TTTAGTT
1 TTTAGTT
2896828 TAAAAGTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 34 0.85
39 6 0.15
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (38 bp):
TTTAGTTATTTAAATTAGCCTATTGGGCCTAGCTTTTT
Found at i:2901369 original size:53 final size:53
Alignment explanation
Indices: 2901312--2901573 Score: 205
Period size: 53 Copynumber: 5.0 Consensus size: 53
2901302 CAAAACACTT
* *
2901312 TTGGGCGTTTCTATACTTGGAACACCCTAGGCGCTTCTACATTTGGAACGCCC
1 TTGGGCGCTTCTATACTTGGAACACCCTAGGCGCTTCTACACTTGGAACGCCC
* * * * * *
2901365 TTGGGCGCTT-TAGCACTTGGAACGCCACTAGACGTTTCTACGCTTGGAAC-ACC
1 TTGGGCGCTTCTA-TACTTGGAACACC-CTAGGCGCTTCTACACTTGGAACGCCC
* * * ** ** *
2901418 TTGGACGCTTCTACACTTGGAACGCCCT-GATGCTTCTGTACTTGGAACACCC
1 TTGGGCGCTTCTATACTTGGAACACCCTAGGCGCTTCTACACTTGGAACGCCC
* * * * *
2901470 -TGGGTGCTTTTATAC-TGGAACA-CCTTGGTCG-TTCTGCACTTGGAACGTCC
1 TTGGGCGCTTCTATACTTGGAACACCCTAGG-CGCTTCTACACTTGGAACGCCC
* * * * * *
2901520 TTGGGAGCTTCTATACTTGGAACACCCTAGGTGTTTCTGCGCTTGGAACACCC
1 TTGGGCGCTTCTATACTTGGAACACCCTAGGCGCTTCTACACTTGGAACGCCC
2901573 T
1 T
2901574 GAGCACTTTT
Statistics
Matches: 167, Mismatches: 32, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
49 3 0.02
50 23 0.14
51 40 0.24
52 14 0.08
53 66 0.40
54 21 0.13
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (53 bp):
TTGGGCGCTTCTATACTTGGAACACCCTAGGCGCTTCTACACTTGGAACGCCC
Found at i:2901485 original size:26 final size:26
Alignment explanation
Indices: 2901320--2901574 Score: 151
Period size: 26 Copynumber: 9.8 Consensus size: 26
2901310 TTTTGGGCGT
* * *
2901320 TTCTATACTTGGAACACCCTAGGCGC
1 TTCTACACTTGGAACACCCTGGGTGC
* * *
2901346 TTCTACATTTGGAACGCCCTTGGGCGC
1 TTCTACACTTGGAACACCC-TGGGTGC
* * ** *
2901373 TT-TAGCACTTGGAACGCCACTAGACGT
1 TTCTA-CACTTGGAACACC-CTGGGTGC
* * **
2901400 TTCTACGCTTGGAACACCTTGGACGC
1 TTCTACACTTGGAACACCCTGGGTGC
* *
2901426 TTCTACACTTGGAACGCCCT-GATGC
1 TTCTACACTTGGAACACCCTGGGTGC
**
2901451 TTCTGTACTTGGAACACCCTGGGTGC
1 TTCTACACTTGGAACACCCTGGGTGC
* * *
2901477 TTTTATAC-TGGAACA-CCTTGGT-C
1 TTCTACACTTGGAACACCCTGGGTGC
* * * *
2901500 GTTCTGCACTTGGAACGTCCTTGGGAGC
1 -TTCTACACTTGGAAC-ACCCTGGGTGC
* * *
2901528 TTCTATACTTGGAACACCCTAGGTGT
1 TTCTACACTTGGAACACCCTGGGTGC
* *
2901554 TTCTGCGCTTGGAACACCCTG
1 TTCTACACTTGGAACACCCTG
2901575 AGCACTTTTG
Statistics
Matches: 177, Mismatches: 42, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
23 1 0.01
24 11 0.06
25 34 0.19
26 73 0.41
27 54 0.31
28 4 0.02
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (26 bp):
TTCTACACTTGGAACACCCTGGGTGC
Found at i:2901586 original size:26 final size:26
Alignment explanation
Indices: 2901535--2901589 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2901525 AGCTTCTATA
***
2901535 CTTGGAACACCCTAGGTGTTTCTGCG
1 CTTGGAACACCCTAGCACTTTCTGCG
2901561 CTTGGAACACCCTGAGCACTTT-TGCG
1 CTTGGAACACCCT-AGCACTTTCTGCG
2901587 CTT
1 CTT
2901590 TGAATACTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (26 bp):
CTTGGAACACCCTAGCACTTTCTGCG
Found at i:2902544 original size:26 final size:26
Alignment explanation
Indices: 2902513--2902650 Score: 129
Period size: 26 Copynumber: 5.3 Consensus size: 26
2902503 TTAGGCCACT
2902513 TAGAAGCACCCAAGGGCGTT-TAGGTG
1 TAGAAGCACCCAAGGGCGTTCTA-GTG
* * *
2902539 CAGAAGCACCC-AGGGTGTTCTAGTA
1 TAGAAGCACCCAAGGGCGTTCTAGTG
* *
2902564 TAGAAGCACCCAAAGGCGTTCCAAGTG
1 TAGAAGCACCCAAGGGCGTT-CTAGTG
* *
2902591 TAGAAGCGCCCAA-GGTGTTCTAAGTG
1 TAGAAGCACCCAAGGGCGTTCT-AGTG
* *
2902617 TTGAAGCGCCCAAGGGCGTTCCTAGTG
1 TAGAAGCACCCAAGGGCGTT-CTAGTG
*
2902644 CAGAAGC
1 TAGAAGC
2902651 GCCTAGGGTA
Statistics
Matches: 91, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
25 20 0.22
26 39 0.43
27 30 0.33
28 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (26 bp):
TAGAAGCACCCAAGGGCGTTCTAGTG
Found at i:2902673 original size:26 final size:26
Alignment explanation
Indices: 2902539--2903065 Score: 337
Period size: 26 Copynumber: 20.3 Consensus size: 26
2902529 CGTTTAGGTG
* *
2902539 CAGAAGCACCCAGGGTGTT-CTAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * * *
2902564 TAGAAGCACCCAAAGGCGTTCCAAGTG
1 CAGAAGCGCCC-AGGGTGTTCCAAGTA
* * * *
2902591 TAGAAGCGCCCAAGGTGTTCTAAGTG
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
** * * *
2902617 TTGAAGCGCCCAAGGGCGTTCCTAGTG
1 CAGAAGCGCCC-AGGGTGTTCCAAGTA
* * *
2902644 CAGAAGCGCCTAGGGTATTTCAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
*
2902670 CAGAAGTGCCCAGGGTGTTCCAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * *
2902696 CAAAAGC-ACCAGGGCGTTCCAAGTG
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * *
2902721 CAGAAACGCCCAGGGTATTCTAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* *
2902747 TAGAAGTGCCCAGGGTGTTCCAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * *
2902773 CAAAAGC-ACCAGGGCGTTCCAAGTG
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * * *
2902798 TAGAAGCGTCCAAGTTGTTCCAAGTG
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * *
2902824 CAAAAGCGCCCAAGGTATTCCAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * *
2902850 CAAAAGTGCCCAGGGTGTTCTAAGTG
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
** * *
2902876 CAGAAGCATCCAAGGTATTCCAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
*
2902902 CAGAAGTGCCCAGGGTGTTCCAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * * *
2902928 CAGAAGC-ACTATGGCGTTCCAAGTG
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * **
2902953 TAGAAGCGCCTAAGGTGTTCCAAGGG
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
* * * *
2902979 CAAAAACGCCCAGTGGCGTTCCAAGTG
1 CAGAAGCGCCCAG-GGTGTTCCAAGTA
* *
2903006 CTA-AAACGCCCAAGGGCT-TTCCAAGTG
1 C-AGAAGCGCCC-AGGG-TGTTCCAAGTA
* * *
2903033 CAGAAGCACCCAGGATGTTTCAAGTA
1 CAGAAGCGCCCAGGGTGTTCCAAGTA
2903059 CAGAAGC
1 CAGAAGC
2903066 TCCCTAAAGT
Statistics
Matches: 388, Mismatches: 102, Indels: 23
0.76 0.20 0.04
Matches are distributed among these distances:
25 70 0.18
26 244 0.63
27 71 0.18
28 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (26 bp):
CAGAAGCGCCCAGGGTGTTCCAAGTA
Found at i:2902736 original size:77 final size:77
Alignment explanation
Indices: 2902629--2903064 Score: 446
Period size: 77 Copynumber: 5.6 Consensus size: 77
2902619 GAAGCGCCCA
* * * *
2902629 AGGGCGTTCCTAGTGCAGAAGCGCCTAGGGTATTTCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
1 AGGGCGTTCCAAGTGCAGAAGCGCCCAAGGTATTCCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
2902694 TACAAAAGCACC
66 TACAAAAGCACC
* * * *
2902706 AGGGCGTTCCAAGTGCAGAAACGCCCAGGGTATTCTAAGTATAGAAGTGCCCAGGGTGTTCCAAG
1 AGGGCGTTCCAAGTGCAGAAGCGCCCAAGGTATTCCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
2902771 TACAAAAGCACC
66 TACAAAAGCACC
* * * * * * * * *
2902783 AGGGCGTTCCAAGTGTAGAAGCGTCCAAGTTGTTCCAAGTGCAAAAGCGCCCAAGGTATTCCAAG
1 AGGGCGTTCCAAGTGCAGAAGCGCCCAAGGTATTCCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
2902848 TACAAAAGTGC-CC
66 TACAAAA--GCACC
* * **
2902861 AGGGTGTTCTAAGTGCAGAAGCATCCAAGGTATTCCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
1 AGGGCGTTCCAAGTGCAGAAGCGCCCAAGGTATTCCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
* *
2902926 TACAGAAGCACT
66 TACAAAAGCACC
* * * * ** * ** *
2902938 ATGGCGTTCCAAGTGTAGAAGCGCCTAAGGTGTTCCAAGGGCAAAAACGCCCAGTGGCGTTCCAA
1 AGGGCGTTCCAAGTGCAGAAGCGCCCAAGGTATTCCAAGTACAGAAGTGCCCAG-GGTGTTCCAA
*
2903003 GTGCTAAAACGC-CC
65 GTAC-AAAA-GCACC
* * * *
2903017 AAGGGCTTTCCAAGTGCAGAAGCACCC-AGGATGTTTCAAGTACAGAAG
1 -AGGGCGTTCCAAGTGCAGAAGCGCCCAAGG-TATTCCAAGTACAGAAG
2903065 CTCCCTAAAG
Statistics
Matches: 292, Mismatches: 59, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
76 2 0.01
77 172 0.59
78 74 0.25
79 9 0.03
80 35 0.12
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.19
Consensus pattern (77 bp):
AGGGCGTTCCAAGTGCAGAAGCGCCCAAGGTATTCCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
TACAAAAGCACC
Found at i:2902916 original size:155 final size:152
Alignment explanation
Indices: 2902629--2903064 Score: 473
Period size: 155 Copynumber: 2.8 Consensus size: 152
2902619 GAAGCGCCCA
* * * * * ** * ** *
2902629 AGGGCGTTCCTAGTGCAGAAGCGCCTAGGGTATTTCAAGTACAGAAGTGCCCAGGGTGTTCCAAG
1 AGGGCGTTCCAAGTGTAGAAGCGCCTAAGGTGTTCCAAGGGCAAAAACGCCCAAGGTGTTCCAAG
* * * *
2902694 TACAAAAGCACCAGGGCGTTCCAAGTGCAGAAACGC-CCAGGGTATTCTAAGTATAGAAGTGCCC
66 TACAAAAGC-CCAGGGTGTTCCAAGTGCAG-AA-GCACCAAGGTATTCCAAGTACAGAAGTGCCC
2902758 AGGGTGTTCCAAGTACAAAAGCACC
128 AGGGTGTTCCAAGTACAAAAGCACC
* * * *
2902783 AGGGCGTTCCAAGTGTAGAAGCGTCC-AAGTTGTTCCAAGTGCAAAAGCGCCCAAGGTATTCCAA
1 AGGGCGTTCCAAGTGTAGAAGCG-CCTAAGGTGTTCCAAGGGCAAAAACGCCCAAGGTGTTCCAA
*
2902847 GTACAAAAGTGCCCAGGGTGTTCTAAGTGCAGAAGCATCCAAGGTATTCCAAGTACAGAAGTGCC
65 GTACAAAA--GCCCAGGGTGTTCCAAGTGCAGAAGCA-CCAAGGTATTCCAAGTACAGAAGTGCC
* *
2902912 CAGGGTGTTCCAAGTACAGAAGCACT
127 CAGGGTGTTCCAAGTACAAAAGCACC
* * *
2902938 ATGGCGTTCCAAGTGTAGAAGCGCCTAAGGTGTTCCAAGGGCAAAAACGCCCAGTGGCGTTCCAA
1 AGGGCGTTCCAAGTGTAGAAGCGCCTAAGGTGTTCCAAGGGCAAAAACGCCCA-AGGTGTTCCAA
* * * *
2903003 GTGCTAAAACGCCCAAGGGCT-TTCCAAGTGCAGAAGCACCCAGGATGTTTCAAGTACAGAAG
65 GTAC-AAAA-GCCC-AGGG-TGTTCCAAGTGCAGAAGCACCAAGG-TATTCCAAGTACAGAAG
2903065 CTCCCTAAAG
Statistics
Matches: 240, Mismatches: 31, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
153 2 0.01
154 62 0.26
155 114 0.47
156 22 0.09
157 39 0.16
158 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.19
Consensus pattern (152 bp):
AGGGCGTTCCAAGTGTAGAAGCGCCTAAGGTGTTCCAAGGGCAAAAACGCCCAAGGTGTTCCAAG
TACAAAAGCCCAGGGTGTTCCAAGTGCAGAAGCACCAAGGTATTCCAAGTACAGAAGTGCCCAGG
GTGTTCCAAGTACAAAAGCACC
Found at i:2905758 original size:34 final size:33
Alignment explanation
Indices: 2905686--2905772 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 33
2905676 TTTGAATGTC
* *
2905686 ATATATTTTATTTTCATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
* *
2905719 ATATATTTTATTTTTATTTCTTTAATATAATTTT
1 ATATATTTTATTTTTATTT-ATTAATATAATCTT
* *
2905753 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
2905773 TTATTTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 18 0.39
34 20 0.43
35 8 0.17
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTAATATAATCTT
Found at i:2905768 original size:74 final size:72
Alignment explanation
Indices: 2905686--2905845 Score: 182
Period size: 74 Copynumber: 2.2 Consensus size: 72
2905676 TTTGAATGTC
*
2905686 ATATATTTTATTTTCATTTATTATTATAATCTTATAT-ATTTT-ATTTTTATTT-CTTTAATATA
1 ATATATTTTATTTTCATTTATTATTATAATCTTATATAATTTTAATTTTT-TTTAATTT--T-TA
*
2905748 ATTTTTTATATT
62 A-TTCTTATATT
* * * * * *
2905760 ATATATTTTATTTTTATTTATTTTTCTTATGTTATATAATTTTAATTTTTTTTAATTTTTGATTC
1 ATATATTTTATTTTCATTTATTATTATAATCTTATATAATTTTAATTTTTTTTAATTTTTAATTC
2905825 TTATATT
66 TTATATT
2905832 ATATATTTTATTTT
1 ATATATTTTATTTT
2905846 AATATTTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
72 23 0.31
73 2 0.03
74 33 0.44
75 8 0.11
76 9 0.12
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (72 bp):
ATATATTTTATTTTCATTTATTATTATAATCTTATATAATTTTAATTTTTTTTAATTTTTAATTC
TTATATT
Found at i:2905818 original size:35 final size:32
Alignment explanation
Indices: 2905749--2905866 Score: 98
Period size: 39 Copynumber: 3.4 Consensus size: 32
2905739 TTTAATATAA
2905749 TTTTTTATATTATATATTTTATTTTTATTTAT
1 TTTTTTATATTATATATTTTATTTTTATTTAT
*
2905781 TTTTCTTATGTTATATAATTTTAATTTTT-TTTAATTT
1 TTTT-TTATATTATAT-ATTTT-ATTTTTATTT-A--T
2905818 TTGATTCTTATATTATATATTTTATTTTAATATTT-T
1 TT--TT-TTATATTATATATTTTATTTT--TATTTAT
*
2905854 TATTTTA-ATTATA
1 TTTTTTATATTATA
2905867 ACATTATAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
32 10 0.14
33 13 0.18
34 10 0.14
35 7 0.10
36 2 0.03
37 8 0.11
38 5 0.07
39 14 0.19
40 3 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (32 bp):
TTTTTTATATTATATATTTTATTTTTATTTAT
Found at i:2905829 original size:34 final size:33
Alignment explanation
Indices: 2905758--2905830 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
2905748 ATTTTTTATA
* *
2905758 TTATATATTTTATTTTTATTTATTTTTCTTATG
1 TTATATATTTTATTTTTATTTATTTTTCATATC
*
2905791 TTATATAATTTTAATTTTT-TTTAATTTTTGAT-TC
1 TTATAT-ATTTT-ATTTTTATTT-ATTTTTCATATC
2905825 TTATAT
1 TTATAT
2905831 TATATATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 6 0.18
34 15 0.44
35 13 0.38
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (33 bp):
TTATATATTTTATTTTTATTTATTTTTCATATC
Found at i:2905834 original size:39 final size:33
Alignment explanation
Indices: 2905749--2905845 Score: 108
Period size: 39 Copynumber: 2.8 Consensus size: 33
2905739 TTTAATATAA
2905749 TTTT-TTATATTATATATTTTATTTTTATTTAT
1 TTTTCTTATATTATATATTTTATTTTTATTTAT
*
2905781 TTTTCTTATGTTATATAATTTTAATTTTT-TTTAATTT
1 TTTTCTTATATTATAT-ATTTT-ATTTTTATTT-A--T
2905818 TTGATTCTTATATTATATATTTTATTTT
1 TT--TTCTTATATTATATATTTTATTTT
2905846 AATATTTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
32 4 0.07
33 10 0.18
34 8 0.15
35 7 0.13
37 8 0.15
38 5 0.09
39 13 0.24
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (33 bp):
TTTTCTTATATTATATATTTTATTTTTATTTAT
Found at i:2905854 original size:14 final size:15
Alignment explanation
Indices: 2905832--2905862 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2905822 TTCTTATATT
2905832 ATATATTTTATTTTA
1 ATATATTTTATTTTA
2905847 ATAT-TTTTATTTTA
1 ATATATTTTATTTTA
2905861 AT
1 AT
2905863 TATAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:2905884 original size:72 final size:72
Alignment explanation
Indices: 2905753--2905887 Score: 161
Period size: 72 Copynumber: 1.9 Consensus size: 72
2905743 ATATAATTTT
* * * * *
2905753 TTATATTATATATTTTATTTTTATTTATTTTTCTTATGTTATATAATTTTAATTTTTTTTAATTT
1 TTATATTATATATTTTATTTTTATTTATTATTCTTATATTATATAATTTAAAATATTTTTAATTT
2905818 TTGATTC
66 TTGATTC
2905825 TTATATTATATATTTTATTTTAATATTT-TTATT-TTA-ATTATA-ACATTATAAAATATTTTTA
1 TTATATTATATATTTTATTTT--TATTTATTATTCTTATATTATATA-ATT-TAAAATATTTTTA
2905886 AT
62 AT
2905888 AAGGTAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
70 1 0.02
71 8 0.15
72 36 0.67
73 4 0.07
74 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (72 bp):
TTATATTATATATTTTATTTTTATTTATTATTCTTATATTATATAATTTAAAATATTTTTAATTT
TTGATTC
Found at i:2920738 original size:12 final size:13
Alignment explanation
Indices: 2920721--2920753 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2920711 TACCTCTTTC
2920721 TCTCTTTTTCT-T
1 TCTCTTTTTCTAT
*
2920733 TTTCTTTTTCTAT
1 TCTCTTTTTCTAT
2920746 TCTCTTTT
1 TCTCTTTT
2920754 GTATTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTCTTTTTCTAT
Found at i:2921008 original size:21 final size:22
Alignment explanation
Indices: 2920963--2921004 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2920953 CTTATTCAAT
2920963 GTTTTATACTTTATGTATTTTA
1 GTTTTATACTTTATGTATTTTA
2920985 GTTTTATA-TTTAT-TATTTTA
1 GTTTTATACTTTATGTATTTTA
2921005 AGTTCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (22 bp):
GTTTTATACTTTATGTATTTTA
Found at i:2927700 original size:21 final size:21
Alignment explanation
Indices: 2927676--2927715 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2927666 ATTAGTAAGA
* *
2927676 AAATGTCATTTCAACATAATC
1 AAATATCATATCAACATAATC
*
2927697 AAATATCATATCAATATAA
1 AAATATCATATCAACATAA
2927716 ATAACAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATATCATATCAACATAATC
Found at i:2939346 original size:15 final size:15
Alignment explanation
Indices: 2939316--2939363 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2939306 TCTCTCTCTA
2939316 TATATATATATATATAT
1 TATAT-TATAT-TATAT
2939333 TATATTATATTATAT
1 TATATTATATTATAT
* *
2939348 TGTAGTATATTATAT
1 TATATTATATTATAT
2939363 T
1 T
2939364 TAGTATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 19 0.66
16 5 0.17
17 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
TATATTATATTATAT
Found at i:2939348 original size:10 final size:10
Alignment explanation
Indices: 2939316--2939363 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
2939306 TCTCTCTCTA
2939316 TATATATATAT
1 TATAT-TATAT
2939327 ATATATTATAT
1 -TATATTATAT
2939338 TATATTATAT
1 TATATTATAT
* *
2939348 TGTAGTATAT
1 TATATTATAT
2939358 TATATT
1 TATATT
2939364 TAGTATGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 22 0.69
11 5 0.16
12 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (10 bp):
TATATTATAT
Found at i:2946115 original size:16 final size:15
Alignment explanation
Indices: 2946094--2946123 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2946084 AAAAAAGTAT
2946094 AACAAAAAACCAAAAA
1 AACAAAAAA-CAAAAA
2946110 AACAAAAAACAAAA
1 AACAAAAAACAAAA
2946124 GAAGATAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (15 bp):
AACAAAAAACAAAAA
Found at i:2948492 original size:17 final size:17
Alignment explanation
Indices: 2948457--2948493 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2948447 TTTGTGTAAT
**
2948457 TTTTAGACATTTTTTAA
1 TTTTAGACATTTTCAAA
2948474 TTTTAGACATTTTCAAA
1 TTTTAGACATTTTCAAA
2948491 TTT
1 TTT
2948494 CACATATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTTAGACATTTTCAAA
Found at i:2949197 original size:20 final size:20
Alignment explanation
Indices: 2949160--2949197 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2949150 ATATAATGTT
*
2949160 ATTTTGTTTTCTTTTAGTTA
1 ATTTTGTTTTCTTCTAGTTA
2949180 ATTTTGATTTT-TTCTAGT
1 ATTTTG-TTTTCTTCTAGT
2949198 GAATGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (20 bp):
ATTTTGTTTTCTTCTAGTTA
Found at i:2953679 original size:57 final size:57
Alignment explanation
Indices: 2953604--2953719 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
2953594 TTTAACTAAA
* * *
2953604 TATAAAACGTAAAGCACATTAAAAACATACACTCAAAATAGTTTTTTCTTATATAAT
1 TATAAAACATAAAACACATTAAAAACATACACTCAAAATAATTTTTTCTTATATAAT
* *
2953661 TATAAAACATAAAACACATTAAAAATATATACTCAAAATAATTTTTTCTTATATAAT
1 TATAAAACATAAAACACATTAAAAACATACACTCAAAATAATTTTTTCTTATATAAT
2953718 TA
1 TA
2953720 GGGTAATAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (57 bp):
TATAAAACATAAAACACATTAAAAACATACACTCAAAATAATTTTTTCTTATATAAT
Found at i:2954032 original size:4 final size:4
Alignment explanation
Indices: 2954025--2954049 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2954015 TAATAATATT
2954025 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
2954050 AAACTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:2956073 original size:21 final size:22
Alignment explanation
Indices: 2956038--2956081 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2956028 CTCTTAAAGC
2956038 AATTTAAAACAAAATAACATAA
1 AATTTAAAACAAAATAACATAA
* *
2956060 AATTT-AACCAAAATAACTTAA
1 AATTTAAAACAAAATAACATAA
2956081 A
1 A
2956082 TTAACTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (22 bp):
AATTTAAAACAAAATAACATAA
Found at i:2957636 original size:42 final size:40
Alignment explanation
Indices: 2957570--2957816 Score: 158
Period size: 40 Copynumber: 5.8 Consensus size: 40
2957560 ATTGAAAATT
* * *
2957570 CTAATATAAATTAATTTTACAT-TTATTAATTTACAAGTTTGA
1 CTAATATAAA--AATTTTATATATT-TAAATTTACAAGTTCGA
* *
2957612 CTAATATAAAAATTTTATATATTTAAATTTGCATCATAGTACAA
1 CTAATATAAAAATTTTATATATTTAAATTT--A-CA-AGTTCGA
* * *
2957656 GTAATATAAATTAATTTTATAT-TTATTAGTTTACAAGTTCGA
1 CTAATATAAA--AATTTTATATATT-TAAATTTACAAGTTCGA
* * *
2957698 CTAATATAAAAGTTTTATATATTTAAGTTGGCATCATAGTTCGA
1 CTAATATAAAAATTTTATATATTTAAATT--TA-CA-AGTTCGA
* * * * * *
2957742 GTAATATAAATTAATTTTACAT-TTATTAGTTTATAAGTTCAA
1 CTAATATAAA--AATTTTATATATT-TAAATTTACAAGTTCGA
*
2957784 CTAATATAAAATTTTTATATATTTAAATTTACA
1 CTAATATAAAAATTTTATATATTTAAATTTACA
2957817 TCATAGTTAT
Statistics
Matches: 161, Mismatches: 27, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
40 44 0.27
41 6 0.04
42 41 0.25
43 7 0.04
44 31 0.19
45 4 0.02
46 28 0.17
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (40 bp):
CTAATATAAAAATTTTATATATTTAAATTTACAAGTTCGA
Found at i:2957663 original size:44 final size:43
Alignment explanation
Indices: 2957611--2957824 Score: 174
Period size: 44 Copynumber: 5.0 Consensus size: 43
2957601 TACAAGTTTG
* *
2957611 ACTAATATAAAAATTTTATATATTTAAATTTGCATCATAGTACA
1 ACTAATATAAAAATTTTATATATTTAAGTTT-CATCATAGTTCA
* * *
2957655 AGTAATATAAATTAATTTTATAT-TTATTAGTTT-A-CA-AGTTCG
1 ACTAATATAAA--AATTTTATATATT-TAAGTTTCATCATAGTTCA
* * *
2957697 ACTAATATAAAAGTTTTATATATTTAAGTTGGCATCATAGTTCG
1 ACTAATATAAAAATTTTATATATTTAAGTT-TCATCATAGTTCA
* * *
2957741 AGTAATATAAATTAATTTTACAT-TTATTAGTTT-AT-A-AGTTCA
1 ACTAATATAAA--AATTTTATATATT-TAAGTTTCATCATAGTTCA
* *
2957783 ACTAATATAAAATTTTTATATATTTAAATTTACATCATAGTT
1 ACTAATATAAAAATTTTATATATTTAAGTTT-CATCATAGTT
2957825 ATATATATAT
Statistics
Matches: 134, Mismatches: 20, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
40 27 0.20
41 4 0.03
42 32 0.24
43 6 0.04
44 33 0.25
45 4 0.03
46 28 0.21
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (43 bp):
ACTAATATAAAAATTTTATATATTTAAGTTTCATCATAGTTCA
Found at i:2957824 original size:86 final size:86
Alignment explanation
Indices: 2957571--2957824 Score: 400
Period size: 86 Copynumber: 3.0 Consensus size: 86
2957561 TTGAAAATTC
* *
2957571 TAATATAAATTAATTTTACATTTATTAATTTACAAGTTTGACTAATATAAAAATTTTATATATTT
1 TAATATAAATTAATTTTACATTTATTAGTTTACAAGTTCGACTAATATAAAAATTTTATATATTT
*
2957636 AAATTTGCATCATAGTACAAG
66 AAATTTGCATCATAGTTCAAG
* *
2957657 TAATATAAATTAATTTTATATTTATTAGTTTACAAGTTCGACTAATATAAAAGTTTTATATATTT
1 TAATATAAATTAATTTTACATTTATTAGTTTACAAGTTCGACTAATATAAAAATTTTATATATTT
* * *
2957722 AAGTTGGCATCATAGTTCGAG
66 AAATTTGCATCATAGTTCAAG
* * *
2957743 TAATATAAATTAATTTTACATTTATTAGTTTATAAGTTCAACTAATATAAAATTTTTATATATTT
1 TAATATAAATTAATTTTACATTTATTAGTTTACAAGTTCGACTAATATAAAAATTTTATATATTT
*
2957808 AAATTTACATCATAGTT
66 AAATTTGCATCATAGTT
2957825 ATATATATAT
Statistics
Matches: 153, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 153 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (86 bp):
TAATATAAATTAATTTTACATTTATTAGTTTACAAGTTCGACTAATATAAAAATTTTATATATTT
AAATTTGCATCATAGTTCAAG
Found at i:2957831 original size:2 final size:2
Alignment explanation
Indices: 2957824--2957850 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2957814 ACATCATAGT
2957824 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2957851 TTAGGGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2958060 original size:44 final size:44
Alignment explanation
Indices: 2957942--2958060 Score: 104
Period size: 44 Copynumber: 2.8 Consensus size: 44
2957932 TTTGCGACAT
* * **
2957942 AGTTCAAGTAATATAAATTAATTTTACATTT--ATTAGTTTATA
1 AGTTCAAATAATATAAATTAATTTTACTTTTAAATTACATTATA
* * *
2957984 AGTTCAACTGATATAAA--AATTTTATATATTTAAATTTACATTAT-
1 AGTTCAAATAATATAAATTAATTTTA-CT-TTTAAA-TTACATTATA
*
2958028 TGTTCAAATAATATAAATTAATTTTACTTTTAA
1 AGTTCAAATAATATAAATTAATTTTACTTTTAA
2958061 TAATTCAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
40 7 0.12
42 18 0.30
44 20 0.33
45 8 0.13
46 7 0.12
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (44 bp):
AGTTCAAATAATATAAATTAATTTTACTTTTAAATTACATTATA
Found at i:2964370 original size:3 final size:3
Alignment explanation
Indices: 2964362--2964387 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2964352 TCTTCATGGA
2964362 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
2964388 AGGAGATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:2964619 original size:2 final size:2
Alignment explanation
Indices: 2964612--2964642 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2964602 ACAAACATGA
2964612 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2964643 TATATTCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2966882 original size:2 final size:2
Alignment explanation
Indices: 2966875--2966905 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2966865 ACCAACACTT
*
2966875 TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2966906 ATAGCTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:2971624 original size:2 final size:2
Alignment explanation
Indices: 2971619--2971655 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2971609 TCAGGATGAC
2971619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2971656 AAAGAGAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2972455 original size:25 final size:23
Alignment explanation
Indices: 2972400--2972455 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
2972390 TTACAAAAAA
2972400 AATTTTTAAAAAATTATTTTTAT
1 AATTTTTAAAAAATTATTTTTAT
* *
2972423 TATATTTAAATAAACTT-TTATTTAT
1 AATTTTTAAA-AAA-TTATT-TTTAT
2972448 AATTTTTA
1 AATTTTTA
2972456 TTCAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 8 0.31
24 5 0.19
25 13 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTTTTAAAAAATTATTTTTAT
Found at i:2994174 original size:14 final size:14
Alignment explanation
Indices: 2994155--2994187 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
2994145 ATAATTTTTT
2994155 AATTTTATAAAAAA
1 AATTTTATAAAAAA
2994169 AA-TTT-TAAAAAA
1 AATTTTATAAAAAA
2994181 AATTTTA
1 AATTTTA
2994188 AATTTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.53
13 6 0.35
14 2 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTATAAAAAA
Found at i:2994180 original size:11 final size:12
Alignment explanation
Indices: 2994162--2994189 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2994152 TTTAATTTTA
2994162 TAAAAAAAATTT
1 TAAAAAAAATTT
2994174 TAAAAAAAATTT
1 TAAAAAAAATTT
2994186 TAAA
1 TAAA
2994190 TTTAATTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAAAATTT
Found at i:2997310 original size:19 final size:19
Alignment explanation
Indices: 2997242--2997302 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
2997232 CATAAATATG
* * *
2997242 TACATTAAATATGAGGAAG
1 TACATTAGATATGAAGAAA
*
2997261 TACATTAGATATGAAGAGA
1 TACATTAGATATGAAGAAA
* *
2997280 TACATTGGATATGACGAAA
1 TACATTAGATATGAAGAAA
2997299 TACA
1 TACA
2997303 ATTGATATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (19 bp):
TACATTAGATATGAAGAAA
Found at i:3000631 original size:8 final size:8
Alignment explanation
Indices: 3000620--3000645 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3000610 GTAATATTAA
3000620 AACAAACT
1 AACAAACT
3000628 AACAAACT
1 AACAAACT
3000636 AACAAACT
1 AACAAACT
3000644 AA
1 AA
3000646 TTAATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.12
Consensus pattern (8 bp):
AACAAACT
Found at i:3002096 original size:19 final size:19
Alignment explanation
Indices: 3002072--3002108 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3002062 AAGGAGAATA
3002072 AATTTACATAAATAGGAAG
1 AATTTACATAAATAGGAAG
*
3002091 AATTTACATAGATAGGAA
1 AATTTACATAAATAGGAA
3002109 TGTGCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (19 bp):
AATTTACATAAATAGGAAG
Found at i:3012704 original size:29 final size:29
Alignment explanation
Indices: 3012655--3012805 Score: 141
Period size: 29 Copynumber: 5.4 Consensus size: 29
3012645 GTTGTAGATC
* *
3012655 ATGTTG-AAAATTTAATTGTTATACTTTT
1 ATGTTGAAAAATGTAATTGTTATACTGTT
* * *
3012683 ATGTTGAAATATGTAATTGTTATATTCTT
1 ATGTTGAAAAATGTAATTGTTATACTGTT
* *
3012712 ATGTTGAAATATGTAATTGTTACA-TGTT
1 ATGTTGAAAAATGTAATTGTTATACTGTT
* ** *
3012740 ATGTT-AAAAATTTAATTGTTGCAC-GTC
1 ATGTTGAAAAATGTAATTGTTATACTGTT
* *
3012767 ATGTTGAAAAATGTAATTATTATAC-ATT
1 ATGTTGAAAAATGTAATTGTTATACTGTT
*
3012795 ATGATGAAAAA
1 ATGTTGAAAAA
3012806 AATGTTACAT
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 22 0.21
28 40 0.39
29 41 0.40
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (29 bp):
ATGTTGAAAAATGTAATTGTTATACTGTT
Found at i:3012732 original size:16 final size:16
Alignment explanation
Indices: 3012684--3012732 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3012674 TATACTTTTA
3012684 TGTTGAAATATGTAAT
1 TGTTGAAATATGTAAT
* * *
3012700 TGTT-ATAT-TCTTA-
1 TGTTGAAATATGTAAT
3012713 TGTTGAAATATGTAAT
1 TGTTGAAATATGTAAT
3012729 TGTT
1 TGTT
3012733 ACATGTTATG
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 4 0.17
14 6 0.25
15 6 0.25
16 8 0.33
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (16 bp):
TGTTGAAATATGTAAT
Found at i:3013140 original size:15 final size:17
Alignment explanation
Indices: 3013112--3013146 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3013102 GAAAGTAAGC
3013112 AAAGAAAATCTTTTC-A
1 AAAGAAAATCTTTTCTA
3013128 AAAGAAAAT-TTTTCTA
1 AAAGAAAATCTTTTCTA
3013144 AAA
1 AAA
3013147 TTGAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAGAAAATCTTTTCTA
Found at i:3023687 original size:20 final size:20
Alignment explanation
Indices: 3023662--3023702 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3023652 TGTGAGTTGG
3023662 TATATGTTTTGATTTTTTTT
1 TATATGTTTTGATTTTTTTT
3023682 TATATGTTTTGATTTTTTTT
1 TATATGTTTTGATTTTTTTT
3023702 T
1 T
3023703 TGGTTAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.76
Consensus pattern (20 bp):
TATATGTTTTGATTTTTTTT
Found at i:3023928 original size:26 final size:26
Alignment explanation
Indices: 3023878--3023935 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
3023868 TTAATATAGT
*
3023878 TATTTTATTTAATTTTAAAATATTAA
1 TATTTTATTTAATTTTAAAACATTAA
3023904 TATTTTACTTATAA-TTT-AAACATTAA
1 TATTTTA-TT-TAATTTTAAAACATTAA
*
3023930 CATTTT
1 TATTTT
3023936 CAAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 20 0.71
27 5 0.18
28 3 0.11
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTTATTTAATTTTAAAACATTAA
Found at i:3023968 original size:26 final size:26
Alignment explanation
Indices: 3023939--3023991 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3023929 ACATTTTCAA
* *
3023939 AAATATTAAT-ATTTTATTTATAATTT
1 AAATAATAATAATTTTACTT-TAATTT
*
3023965 AAATAATCATAATTTTACTTTAATTT
1 AAATAATAATAATTTTACTTTAATTT
3023991 A
1 A
3023992 TAAATTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
AAATAATAATAATTTTACTTTAATTT
Done.