Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 8 of 66
Found at i:2678421 original size:21 final size:24
Alignment explanation
Indices: 2678367--2678425 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 24
2678357 ATAATAACTT
*
2678367 ATATAATTA-TTAATAATTTATTT
1 ATATAATTATTTAATAATTTATTA
2678390 ATATACA-TATTTAA-AA-TT-TTA
1 ATATA-ATTATTTAATAATTTATTA
2678411 ATATAATTATTTAAT
1 ATATAATTATTTAAT
2678426 TATATCATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.03
21 14 0.45
22 2 0.06
23 9 0.29
24 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATAATTATTTAATAATTTATTA
Found at i:2678451 original size:81 final size:81
Alignment explanation
Indices: 2678303--2678487 Score: 192
Period size: 81 Copynumber: 2.2 Consensus size: 81
2678293 TTTATTTAAC
* * ** *
2678303 TTATTTACATACATGTTTAAGATTCTAACAAGATTATTTAATTATATTGTATTTATAATAACTTA
1 TTATTTACATACATATTTAAAATTCTAACAAGATTATTTAATTATATCATATTTATAATAACCTA
2678368 TATAATTATTAATAAT
66 TATAATTATTAATAAT
* * * ** *
2678384 TTATTTATATACATATTTAAAATTTTAATATA-ATTATTTAATTATATCATATTTATGTTCACCT
1 TTATTTACATACATATTTAAAATTCTAACA-AGATTATTTAATTATATCATATTTATAATAACCT
* *
2678448 ATATAATTGTTAACAACT
65 ATATAATTATTAATAA-T
* *
2678466 TATAATTACACGACATATTTAA
1 T-TATTTACA-TACATATTTAA
2678488 GACATGAAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 65 0.77
82 3 0.04
83 6 0.07
84 10 0.12
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.48
Consensus pattern (81 bp):
TTATTTACATACATATTTAAAATTCTAACAAGATTATTTAATTATATCATATTTATAATAACCTA
TATAATTATTAATAAT
Found at i:2680314 original size:3 final size:3
Alignment explanation
Indices: 2680306--2680331 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2680296 GGTTGGTGCT
2680306 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
2680332 TTAGAAGAGG
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:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:2680763 original size:29 final size:27
Alignment explanation
Indices: 2680709--2680775 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
2680699 TTAAAGATAT
*
2680709 ATTTAATTAAAAAATAAAATTATAAAA
1 ATTTAATTAAAAAATAAAATAATAAAA
2680736 ATTTAATTAAACATAATATAAA-AATAAAA
1 ATTTAATTAAA-A-AATA-AAATAATAAAA
*
2680765 ATTTATTTAAA
1 ATTTAATTAAA
2680776 TTTTTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.31
28 1 0.03
29 20 0.57
30 3 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (27 bp):
ATTTAATTAAAAAATAAAATAATAAAA
Found at i:2680792 original size:11 final size:11
Alignment explanation
Indices: 2680759--2680817 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
2680749 TAATATAAAA
2680759 ATAAAA-ATTT
1 ATAAAATATTT
* *
2680769 ATTTAAATTTTT
1 A-TAAAATATTT
2680781 ATAAAATATTT
1 ATAAAATATTT
*
2680792 AAAAAATATTT
1 ATAAAATATTT
*
2680803 -TCAAATATTT
1 ATAAAATATTT
2680813 ATAAA
1 ATAAA
2680818 CCAAAATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
10 9 0.24
11 25 0.66
12 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAAAATATTT
Found at i:2682515 original size:2 final size:2
Alignment explanation
Indices: 2682508--2682533 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2682498 TTTACTCTTC
2682508 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2682534 TTGCCCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2691076 original size:13 final size:13
Alignment explanation
Indices: 2691058--2691082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2691048 ATTTGCAAAA
2691058 ATTTTATAAAATT
1 ATTTTATAAAATT
2691071 ATTTTATAAAAT
1 ATTTTATAAAAT
2691083 CTCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:2692518 original size:2 final size:2
Alignment explanation
Indices: 2692511--2692548 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2692501 NNNNNNNNNN
2692511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2692549 GTTTTAATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2695252 original size:136 final size:136
Alignment explanation
Indices: 2695005--2695272 Score: 365
Period size: 136 Copynumber: 2.0 Consensus size: 136
2694995 CAATATTTGA
* **
2695005 TAGTACAAGATTAATTGAAGGTTCCGGAAGAGCCAATATTTCACTATCTAAAGGAACAAAGTTTA
1 TAGTACAAGATTAATTGAAGGCTCCAAAAGAGCCAATATTTCACTATCTAAAGGAACAAAGTTTA
* * * * *
2695070 TACTAAAATATGCATTATTTTCTACTAGGTCTCAAAGAAACCTATTAAATTTTAAAGATATTTGT
66 TAATAAAATATCCATTATTTTCTACTAGGTCTCAAAGAAACCTATTAAATTTAAAAAATATTCGT
2695135 CTCTAG
131 CTCTAG
* * * *** *
2695141 TAGTACAAGATTAATTGAAGGCTCTAAAAGTGCCAATTTTTCACTATCTGGGGGAACAAATTTTA
1 TAGTACAAGATTAATTGAAGGCTCCAAAAGAGCCAATATTTCACTATCTAAAGGAACAAAGTTTA
* * * *
2695206 TAATAAAATATCCATTATTTTCTATTAGGTCTCCAAGAAGCTTATTAAATTTAAAAAATATTCGT
66 TAATAAAATATCCATTATTTTCTACTAGGTCTCAAAGAAACCTATTAAATTTAAAAAATATTCGT
2695271 CT
131 CT
2695273 GAATGGATAT
Statistics
Matches: 113, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
136 113 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (136 bp):
TAGTACAAGATTAATTGAAGGCTCCAAAAGAGCCAATATTTCACTATCTAAAGGAACAAAGTTTA
TAATAAAATATCCATTATTTTCTACTAGGTCTCAAAGAAACCTATTAAATTTAAAAAATATTCGT
CTCTAG
Found at i:2697667 original size:19 final size:19
Alignment explanation
Indices: 2697643--2697680 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2697633 CTGCCAAACC
*
2697643 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
2697662 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
2697681 AGTTAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:2701430 original size:37 final size:37
Alignment explanation
Indices: 2701380--2701525 Score: 197
Period size: 37 Copynumber: 3.9 Consensus size: 37
2701370 TAATGTTGTG
*
2701380 TGATGATGCTGAAGTGTGCAAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACA
* *
2701417 TGATGATGTTGAAGTGTGCGAGTAAGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACA
*
2701454 TGATGATGTT-AGAGTATGCAAGTAGGGAGTGCACACA
1 TGATGATGTTGA-AGTGTGCAAGTAGGGAGTGCACACA
* * *
2701491 TGATGATGTTCAAATGTGCGAA-TAGGAAGTGCACA
1 TGATGATGTTGAAGTGTGC-AAGTAGGGAGTGCACA
2701526 TGACGATGAA
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
36 1 0.01
37 93 0.96
38 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.33, T:0.24
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACA
Found at i:2706573 original size:2 final size:2
Alignment explanation
Indices: 2706566--2706591 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2706556 TCACTAAGTG
2706566 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2706592 TTGTGCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2712887 original size:76 final size:75
Alignment explanation
Indices: 2712785--2713009 Score: 269
Period size: 76 Copynumber: 3.0 Consensus size: 75
2712775 CAGTTGGCAG
* * *
2712785 AAGCAGAAACCAGAAAAGGTGAGACCATGAGAGTGGAGATAGAAGTCAGGAGATGGCAATGACCA
1 AAGCAGAAACCA-AAAAGGTGAGACCATGAGAGTGGAGATGGAAGTCAGG-GACGGCAGTGACCA
2712850 G-TAGTC-AGCAA
64 GATAGTCGA-CAA
* * * *
2712861 AAGCAGAAATCAAAAAGGGTGAGACCATGAAAGTGGAGATGGAAGTCAGGGCACGACAGTGA-CT
1 AAGCAGAAACCAAAAA-GGTGAGACCATGAGAGTGGAGATGGAAGTCAGGG-ACGGCAGTGACCA
2712925 GATAGTCGACAA
64 GATAGTCGACAA
* *
2712937 AAGCAAAAACCAAAAAAGGTGAGACCGTGAGAGTGGAGATGGAAGTCAGGGGACGGCAGTGACC-
1 AAGCAGAAACC-AAAAAGGTGAGACCATGAGAGTGGAGATGGAAGTCA-GGGACGGCAGTGACCA
*
2713001 GACAGTCGA
64 GATAGTCGA
2713010 TAGAAACCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
75 7 0.05
76 112 0.87
77 10 0.08
ACGTcount: A:0.40, C:0.15, G:0.33, T:0.12
Consensus pattern (75 bp):
AAGCAGAAACCAAAAAGGTGAGACCATGAGAGTGGAGATGGAAGTCAGGGACGGCAGTGACCAGA
TAGTCGACAA
Found at i:2713209 original size:23 final size:21
Alignment explanation
Indices: 2713166--2713209 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2713156 AACTAAACCG
* *
2713166 AACTAATCGAAAAATCTAACT
1 AACTAATCGAAAAACCGAACT
2713187 AACTGAATCGAAAAAGCCGAACT
1 AACT-AATCGAAAAA-CCGAACT
2713210 CATTTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.18
Consensus pattern (21 bp):
AACTAATCGAAAAACCGAACT
Found at i:2715563 original size:45 final size:45
Alignment explanation
Indices: 2715513--2715640 Score: 170
Period size: 45 Copynumber: 2.8 Consensus size: 45
2715503 CACGCTATGA
*
2715513 TGTTACACGCCATGTACAAAAACT-TGTGACAAGCCATGGTTAG-T
1 TGTTACACGCCATGTACAAAAA-TATGTGACAAGCCATGATTAGCT
* ** *
2715557 GTGTTACACGCTATGTGTAAAAATATGTGACAAGCTATGATTAGCT
1 -TGTTACACGCCATGTACAAAAATATGTGACAAGCCATGATTAGCT
*
2715603 TGTTACATGCCATGTACAAAAATATGTGACAAGCCATG
1 TGTTACACGCCATGTACAAAAATATGTGACAAGCCATG
2715641 TACAAAAACC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
44 1 0.01
45 69 0.97
46 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAATATGTGACAAGCCATGATTAGCT
Found at i:2715643 original size:24 final size:24
Alignment explanation
Indices: 2715611--2715660 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2715601 CTTGTTACAT
*
2715611 GCCATGTACAAAAATATGTGACAA
1 GCCATGTACAAAAACATGTGACAA
*
2715635 GCCATGTACAAAAACCTGTGACAA
1 GCCATGTACAAAAACATGTGACAA
2715659 GC
1 GC
2715661 TACGGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (24 bp):
GCCATGTACAAAAACATGTGACAA
Found at i:2715699 original size:45 final size:45
Alignment explanation
Indices: 2715635--2715731 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
2715625 TATGTGACAA
*
2715635 GCCATGTACAAAAACCTGTGACAAGCTACGGTTAACTTGTTACAC
1 GCCATGTACAAAAACCTGTGACAAGCGACGGTTAACTTGTTACAC
* * **
2715680 GCCATGTACAAAAATCTGTGACAAGCGATGGTTAGGTTGTTACAC
1 GCCATGTACAAAAACCTGTGACAAGCGACGGTTAACTTGTTACAC
*
2715725 ACCATGT
1 GCCATGT
2715732 TGAAAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (45 bp):
GCCATGTACAAAAACCTGTGACAAGCGACGGTTAACTTGTTACAC
Found at i:2715738 original size:114 final size:114
Alignment explanation
Indices: 2715512--2715731 Score: 289
Period size: 114 Copynumber: 1.9 Consensus size: 114
2715502 ACACGCTATG
* * * * * * **
2715512 ATGTTACACGCCATGTACAAAAACTTGTGACAAGCCATGGTTAGTGTGTTACACGCTATGTGTAA
1 ATGTGACAAGCCATGTACAAAAACCTGTGACAAGCCACGGTTACTGTGTTACACGCCATGTACAA
* **
2715577 AAATATGTGACAAGCTATGATTAGCTTGTTACATGCCATGTACAAAAAT
66 AAATATGTGACAAGCGATGATTAGCTTGTTACACACCATGTACAAAAAT
*
2715626 ATGTGACAAGCCATGTACAAAAACCTGTGACAAGCTACGGTTAACT-TGTTACACGCCATGTACA
1 ATGTGACAAGCCATGTACAAAAACCTGTGACAAGCCACGGTT-ACTGTGTTACACGCCATGTACA
* * *
2715690 AAAATCTGTGACAAGCGATGGTTAGGTTGTTACACACCATGT
65 AAAATATGTGACAAGCGATGATTAGCTTGTTACACACCATGT
2715732 TGAAAAAAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
114 88 0.98
115 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (114 bp):
ATGTGACAAGCCATGTACAAAAACCTGTGACAAGCCACGGTTACTGTGTTACACGCCATGTACAA
AAATATGTGACAAGCGATGATTAGCTTGTTACACACCATGTACAAAAAT
Found at i:2715803 original size:26 final size:24
Alignment explanation
Indices: 2715746--2715820 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 24
2715736 AAAAAATACT
2715746 GTTGTTACACGCCATG-TACAAAAA
1 GTTGTTACACGCCATGTTA-AAAAA
*
2715770 -TATATTACACGCCATGGTTAAAAAA
1 GT-TGTTACACGCCAT-GTTAAAAAA
*
2715795 GGTTGTTACATGCCATGTTGAAAAAA
1 -GTTGTTACACGCCATGTT-AAAAAA
2715821 AATATATTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
23 1 0.02
24 12 0.29
25 9 0.21
26 19 0.45
27 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (24 bp):
GTTGTTACACGCCATGTTAAAAAA
Found at i:2715858 original size:29 final size:28
Alignment explanation
Indices: 2715818--2715894 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
2715808 CATGTTGAAA
* *
2715818 AAAAATATATTGTTGTTACACGTCATGTT
1 AAAAA-ATATTGTTGTTACACGACATATT
* *
2715847 GAAAAAATATTGTTATTACACGACCTATT
1 -AAAAAATATTGTTGTTACACGACATATT
*
2715876 CAAAAATATT-TTGTTACAC
1 AAAAAATATTGTTGTTACAC
2715895 TTTAATGCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.20
28 9 0.22
29 19 0.46
30 5 0.12
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (28 bp):
AAAAAATATTGTTGTTACACGACATATT
Found at i:2719593 original size:49 final size:49
Alignment explanation
Indices: 2719533--2719685 Score: 202
Period size: 49 Copynumber: 3.0 Consensus size: 49
2719523 AAAGCTTAGA
2719533 AGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATTACCAATTTC
1 AGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATTACCAATTTC
* * **
2719582 AGTAGCCAAATCTCGCCATTTTGGTATGTAATCCAT--TTCAGCCAAAGCTTAGA
1 AGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATT-A-CC-AA--TT-TC
2719635 AGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATTACCAATTTC
1 AGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATTACCAATTTC
2719684 AG
1 AG
2719686 CCGTTTGACT
Statistics
Matches: 88, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 38 0.43
50 4 0.05
52 4 0.05
53 36 0.41
54 1 0.01
55 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (49 bp):
AGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATTACCAATTTC
Found at i:2719659 original size:53 final size:53
Alignment explanation
Indices: 2719520--2719679 Score: 208
Period size: 53 Copynumber: 3.1 Consensus size: 53
2719510 GGATTCCATG
2719520 GCCAAAGCTTAGAAGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATTA
1 GCCAAAGCTTAGAAGGAGCCAAATCTCTCCATTTTGGTATGTAATCCAT-ATTA
** * *
2719574 -CC-AA--TT-TCAGTAGCCAAATCTCGCCATTTTGGTATGTAATCCAT-TTCA
1 GCCAAAGCTTAGAAGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATATT-A
2719622 GCCAAAGCTTAGAAGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATCATTA
1 GCCAAAGCTTAGAAGGAGCCAAATCTCTCCATTTTGGTATGTAATCCAT-ATTA
2719676 -CCAA
1 GCCAA
2719680 TTTCAGCCGT
Statistics
Matches: 90, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 36 0.40
50 4 0.04
52 4 0.04
53 40 0.44
54 1 0.01
55 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (53 bp):
GCCAAAGCTTAGAAGGAGCCAAATCTCTCCATTTTGGTATGTAATCCATATTA
Found at i:2722082 original size:4 final size:4
Alignment explanation
Indices: 2722068--2722113 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
2722058 TATCAAGATA
* * * *
2722068 ATAT CTAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
2722114 GAATTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:2722114 original size:6 final size:6
Alignment explanation
Indices: 2722068--2722113 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
2722058 TATCAAGATA
* * * *
2722068 ATATCT ATATAT ATATAT ATATAT ATATAT ATGTAT GTATGT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
2722114 GAATTTAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:2727665 original size:42 final size:42
Alignment explanation
Indices: 2727578--2727679 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 42
2727568 ACATAATTTA
**
2727578 ATATTAAATTGTAATTAATTAATAATATTCAAATAT-AAAGTT
1 ATATTAAATAATAATTAATTAATAATATTCAAATATAAAAG-T
*
2727620 ATATTAAATAATAATTAGA-TAATAATATTTCAAATATATCATA-T
1 ATATTAAATAATAATTA-ATTAATAATA-TTCAAATATA--AAAGT
2727664 ATATTAAATAA-AATTA
1 ATATTAAATAATAATTA
2727680 TCCATTGTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
42 23 0.44
43 15 0.29
44 12 0.23
46 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (42 bp):
ATATTAAATAATAATTAATTAATAATATTCAAATATAAAAGT
Found at i:2730088 original size:21 final size:21
Alignment explanation
Indices: 2730064--2730106 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2730054 AATTTTTTTA
* *
2730064 TATAATATTTTTTAAAAAAAT
1 TATAAAATTATTTAAAAAAAT
*
2730085 TATAAAATTATTTAAATAAAT
1 TATAAAATTATTTAAAAAAAT
2730106 T
1 T
2730107 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAAATTATTTAAAAAAAT
Found at i:2732595 original size:27 final size:25
Alignment explanation
Indices: 2732552--2732601 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
2732542 TGTATTTACT
* *
2732552 TATTTATATAATTATTAATATTTTA
1 TATTTACATAATTATTAAGATTTTA
2732577 TATTTACATAATATGATTAAGATTT
1 TATTTACATAAT-T-ATTAAGATTT
2732602 GAATACACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 1 0.05
27 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
TATTTACATAATTATTAAGATTTTA
Found at i:2735465 original size:18 final size:18
Alignment explanation
Indices: 2735442--2735482 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2735432 TAAAAATACG
*
2735442 ATTAAGACGTTTAACATC
1 ATTAAGACATTTAACATC
*
2735460 ATTAAGACATTTAACATT
1 ATTAAGACATTTAACATC
2735478 ATTAA
1 ATTAA
2735483 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (18 bp):
ATTAAGACATTTAACATC
Found at i:2735559 original size:16 final size:16
Alignment explanation
Indices: 2735539--2735573 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2735529 TAATAATTAT
*
2735539 AAAAATAATTATAATA
1 AAAAATAAATATAATA
2735555 AAAAATAAATATAATA
1 AAAAATAAATATAATA
2735571 AAA
1 AAA
2735574 TGATATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAATATAATA
Found at i:2737040 original size:2 final size:2
Alignment explanation
Indices: 2737033--2737058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2737023 TATTATATTC
2737033 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2737059 ATCCTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2737937 original size:3 final size:3
Alignment explanation
Indices: 2737931--2737960 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2737921 ATTATACTAC
2737931 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2737961 TTAAGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2743749 original size:21 final size:21
Alignment explanation
Indices: 2743723--2743763 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2743713 GACAATAATG
*
2743723 TGATAT-GTTGATATGACATAA
1 TGATATAGTT-ATATCACATAA
2743744 TGATATAGTTATATCACATA
1 TGATATAGTTATATCACATA
2743764 TTTCAATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (21 bp):
TGATATAGTTATATCACATAA
Found at i:2750397 original size:95 final size:95
Alignment explanation
Indices: 2750234--2750424 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
2750224 AAGTATGTTG
*
2750234 TTGATGTCAATGTTAAACAGATTGTATAGCTAAAGGAGATAAAAAATGAAACTGTACATAAAGGA
1 TTGATGTCAATGTTAAACAGATTGTAAAGCTAAAGGAGATAAAAAATGAAACTGTACATAAAGGA
2750299 TCAGTCTAACAGAGGACCTGATTGAAACTA
66 TCAGTCTAACAGAGGACCTGATTGAAACTA
*
2750329 TTGATGTCAATGTTAAACAGATTGTAAAGCTAAAGGAGATAAAAAATGAAACTTTACATAAAGGA
1 TTGATGTCAATGTTAAACAGATTGTAAAGCTAAAGGAGATAAAAAATGAAACTGTACATAAAGGA
2750394 TCAGTCTAACAGAGGACCTGATTGAAACTA
66 TCAGTCTAACAGAGGACCTGATTGAAACTA
2750424 T
1 T
2750425 GGAAGAGCTC
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (95 bp):
TTGATGTCAATGTTAAACAGATTGTAAAGCTAAAGGAGATAAAAAATGAAACTGTACATAAAGGA
TCAGTCTAACAGAGGACCTGATTGAAACTA
Found at i:2754871 original size:17 final size:17
Alignment explanation
Indices: 2754851--2754897 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2754841 TAATAAAGTA
*
2754851 ATATATTTTATATGTAC
1 ATATATTTTATATATAC
* *
2754868 ATATATTTAATTTATAC
1 ATATATTTTATATATAC
2754885 ATA-ATTTGTATAT
1 ATATATTT-TATAT
2754898 TTTATAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (17 bp):
ATATATTTTATATATAC
Found at i:2754922 original size:221 final size:213
Alignment explanation
Indices: 2754484--2754888 Score: 483
Period size: 216 Copynumber: 1.9 Consensus size: 213
2754474 ACTTTATTTT
* * * *
2754484 TATGATTACATTTAATAACTTTATTAATTATTATCTTAGTTTTTATAATATATTGTTTATAGTTA
1 TATGTTTACATTTAATAACTTTATTAATTATCATCTTAATTTTTATAATATATTGTTTATAATTA
* * *
2754549 GTAATTATTTAAACAAATTTTGAGATAAAACATTATAACGTATAAGTTGTATCATTAATTTCTTA
66 GTAATTATTTAAACAAATTTTAACATAAAACATTATAACATATAAGTTGTATCATTAATTTCTTA
*
2754614 TATACATAATAAAGTAATATATTATACATATACATATATTTAATTTATATATAAACAATACTGTA
131 TATACATAATAAAGTAATATATTATACATATACATATATTTAATTTATACAT--A-AATACTGTA
***
2754679 ACTTATAATAGATTTTGTTTA
193 ACTTATAATAGATAAAGTTTA
* * *
2754700 TATGTTTACCTTTAATAATTTTATTAGTTATCA-CTTTAATTTTTATAATATATTGTTTATAATT
1 TATGTTTACATTTAATAACTTTATTAATTATCATC-TTAATTTTTATAATATATTGTTTATAATT
* * * * *
2754764 AGTTATTATTTATATAAACTTTGATATAAACATTAAAATATTATAACATATAAGTTGTGTCATTA
65 AGTAATTATTTAAACAAA--TT--T-T-AACA-TAAAACATTATAACATATAAGTTGTATCATTA
* * * *
2754829 A-TT-TTATATATATAATAAAGTAATATATTTTATATGTACATATATTTAATTTATACATAA
123 ATTTCTTATATACATAATAAAGTAATATATTATACATATACATATATTTAATTTATACATAA
2754889 TTTGTATATT
Statistics
Matches: 161, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
215 1 0.01
216 70 0.43
218 3 0.02
219 1 0.01
220 1 0.01
221 51 0.32
222 4 0.02
223 30 0.19
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (213 bp):
TATGTTTACATTTAATAACTTTATTAATTATCATCTTAATTTTTATAATATATTGTTTATAATTA
GTAATTATTTAAACAAATTTTAACATAAAACATTATAACATATAAGTTGTATCATTAATTTCTTA
TATACATAATAAAGTAATATATTATACATATACATATATTTAATTTATACATAAATACTGTAACT
TATAATAGATAAAGTTTA
Found at i:2764538 original size:5 final size:5
Alignment explanation
Indices: 2764528--2764556 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2764518 CTTGAGGCTA
2764528 AAACT AAACT AAACT AAACT AAACT AAAC
1 AAACT AAACT AAACT AAACT AAACT AAAC
2764557 CCAACTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (5 bp):
AAACT
Found at i:2764562 original size:15 final size:15
Alignment explanation
Indices: 2764528--2764562 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2764518 CTTGAGGCTA
*
2764528 AAACTAAACTAAACT
1 AAACTAAACTAAACC
2764543 AAACTAAACTAAACC
1 AAACTAAACTAAACC
*
2764558 CAACT
1 AAACT
2764563 CGATGATGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACTAAACTAAACC
Found at i:2774998 original size:15 final size:15
Alignment explanation
Indices: 2774978--2775024 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2774968 GTCGTCGTCC
2774978 TCTTCATCATCATCA
1 TCTTCATCATCATCA
*
2774993 TCTTCATCATCGTCA
1 TCTTCATCATCATCA
* * *
2775008 TCGTCTTCATCAACA
1 TCTTCATCATCATCA
2775023 TC
1 TC
2775025 GTCACTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.23, C:0.34, G:0.04, T:0.38
Consensus pattern (15 bp):
TCTTCATCATCATCA
Found at i:2774999 original size:9 final size:9
Alignment explanation
Indices: 2774981--2775019 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2774971 GTCGTCCTCT
*
2774981 TCATCATCA
1 TCATCTTCA
2774990 TCATCTTCA
1 TCATCTTCA
*
2774999 TCATCGTCA
1 TCATCTTCA
*
2775008 TCGTCTTCA
1 TCATCTTCA
2775017 TCA
1 TCA
2775020 ACATCGTCAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.23, C:0.33, G:0.05, T:0.38
Consensus pattern (9 bp):
TCATCTTCA
Found at i:2775782 original size:2 final size:2
Alignment explanation
Indices: 2775775--2775801 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2775765 AGTGAGATTT
2775775 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
2775802 CACTGATAAA
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:2784664 original size:34 final size:34
Alignment explanation
Indices: 2784625--2784701 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
2784615 ACTTGGGGTT
*
2784625 TTAGGAATGTTGAAGAAAGTGAAAGTTTGTTTTA
1 TTAGGAATGTTGAAAAAAGTGAAAGTTTGTTTTA
*
2784659 TTAGGAATGTTGAAAAAAGTGAAAGTTTGTTTTG
1 TTAGGAATGTTGAAAAAAGTGAAAGTTTGTTTTA
2784693 TTAGGAATG
1 TTAGGAATG
2784702 ATGGCTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (34 bp):
TTAGGAATGTTGAAAAAAGTGAAAGTTTGTTTTA
Found at i:2788565 original size:25 final size:25
Alignment explanation
Indices: 2788520--2788570 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
2788510 AAAAAGCTCC
2788520 TCCTTAGAGCTTTTTTTTAAACTTT
1 TCCTTAGAGCTTTTTTTTAAACTTT
2788545 NTCCTTAGAGC-TTTTTTTAAACTTT
1 -TCCTTAGAGCTTTTTTTTAAACTTT
2788570 T
1 T
2788571 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 1 0.04
25 14 0.56
26 10 0.40
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.55
Consensus pattern (25 bp):
TCCTTAGAGCTTTTTTTTAAACTTT
Found at i:2804997 original size:2 final size:2
Alignment explanation
Indices: 2804990--2805020 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2804980 CAAAGATAAG
2804990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2805021 AGAGTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2805643 original size:15 final size:15
Alignment explanation
Indices: 2805618--2805658 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2805608 TAATCTTAAT
*
2805618 ATATAGGTATAGATA
1 ATATAGATATAGATA
* *
2805633 TTATAGATATATATA
1 ATATAGATATAGATA
2805648 ATATAGATATA
1 ATATAGATATA
2805659 AATTATAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (15 bp):
ATATAGATATAGATA
Found at i:2808596 original size:26 final size:24
Alignment explanation
Indices: 2808551--2808620 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
2808541 CCGCTGTATA
*
2808551 TTTCTTTTCTTTTTTTTTTTTACC
1 TTTCTTTTCTTTTTTATTTTTACC
* *
2808575 TTTCTCTTTGTTTATTTATTTTTA-A
1 TTTCT-TTTCTTT-TTTATTTTTACC
* * *
2808600 TTTATATTCTTTTTTGTTTTT
1 TTTCTTTTCTTTTTTATTTTT
2808621 TTTAATTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 8 0.22
24 10 0.27
25 10 0.27
26 9 0.24
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (24 bp):
TTTCTTTTCTTTTTTATTTTTACC
Found at i:2818313 original size:2 final size:2
Alignment explanation
Indices: 2818308--2818332 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2818298 ATATATTTCC
2818308 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2818333 ATCACTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2821165 original size:61 final size:61
Alignment explanation
Indices: 2821070--2821192 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
2821060 CTCAAATAAT
* * * *
2821070 TGACAAGTGCAGGGAGAAGGGAAGAGGAAGAGGAAGATCTTTCCTGCCCCAACTATAAATG
1 TGACAAATGCAGAGAGAAGGGAAGAGAAAGAGGAAGAACTTTCCTGCCCCAACTATAAATG
*
2821131 TGACAAATGCAGAGAGACGGGAAGAGAAAGAGGAAGAACTTTCCTGCCCCAACTATAAATG
1 TGACAAATGCAGAGAGAAGGGAAGAGAAAGAGGAAGAACTTTCCTGCCCCAACTATAAATG
2821192 T
1 T
2821193 AAAGGAATGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.16
Consensus pattern (61 bp):
TGACAAATGCAGAGAGAAGGGAAGAGAAAGAGGAAGAACTTTCCTGCCCCAACTATAAATG
Found at i:2828305 original size:100 final size:100
Alignment explanation
Indices: 2828128--2828329 Score: 395
Period size: 100 Copynumber: 2.0 Consensus size: 100
2828118 TTTTCTAGAT
2828128 ATGCAAGGTAGTTTTAAAATGGTAACAAGTATATAATATGGACAAAAATGTCAAATTATAAATAC
1 ATGCAAGGTAGTTTTAAAATGGTAACAAGTATATAATATGGACAAAAATGTCAAATTATAAATAC
2828193 TATAGGCATTTTTCTAAGGATAGTACTCAACTAAA
66 TATAGGCATTTTTCTAAGGATAGTACTCAACTAAA
2828228 ATGCAAGGTAGTTTTAAAATGGTAACAAGTATATAATATGGACAAAAATGTCAAATTATAAATAC
1 ATGCAAGGTAGTTTTAAAATGGTAACAAGTATATAATATGGACAAAAATGTCAAATTATAAATAC
*
2828293 TATAGGCCTTTTTCTAAGGATAGTACTCAACTAAA
66 TATAGGCATTTTTCTAAGGATAGTACTCAACTAAA
2828328 AT
1 AT
2828330 CCATAATTGA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (100 bp):
ATGCAAGGTAGTTTTAAAATGGTAACAAGTATATAATATGGACAAAAATGTCAAATTATAAATAC
TATAGGCATTTTTCTAAGGATAGTACTCAACTAAA
Found at i:2836197 original size:27 final size:27
Alignment explanation
Indices: 2836162--2836220 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2836152 TTATTTGATT
2836162 TTAAA-ATAA-AAAATATAAAAATTTAA
1 TTAAATATAATAAAA-ATAAAAATTTAA
* *
2836188 TTAAATATAATAAAAATAAATATTTAT
1 TTAAATATAATAAAAATAAAAATTTAA
2836215 TTAAAT
1 TTAAAT
2836221 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 20 0.69
28 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
TTAAATATAATAAAAATAAAAATTTAA
Found at i:2836956 original size:22 final size:22
Alignment explanation
Indices: 2836928--2836973 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2836918 TTGGTTTTAA
2836928 TTAAATTTA-AATAATTTACAAT
1 TTAAATTTACAATAATTTA-AAT
*
2836950 TTAAATTTACATTAATTTAAAT
1 TTAAATTTACAATAATTTAAAT
2836972 TT
1 TT
2836974 GATTAGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAATTTACAATAATTTAAAT
Found at i:2841294 original size:20 final size:20
Alignment explanation
Indices: 2841262--2841301 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2841252 AATTTTACTT
*
2841262 ATTTAAAATAAATAAGTAAA
1 ATTTAAAATAAATAAATAAA
2841282 ATTT-AAATAAAATAAATAAA
1 ATTTAAAAT-AAATAAATAAA
2841302 TAATATGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
ATTTAAAATAAATAAATAAA
Found at i:2841959 original size:22 final size:22
Alignment explanation
Indices: 2841934--2842040 Score: 60
Period size: 22 Copynumber: 4.8 Consensus size: 22
2841924 TGCATTCAAT
2841934 AATAATATTTTATTTTAAATCA
1 AATAATATTTTATTTTAAATCA
*
2841956 AATAA-ATTTTTATAATT-AAT-A
1 AATAATA-TTTTAT-TTTAAATCA
* * * *
2841977 ATTAATTATTTT-TATTAAGTAA
1 AATAA-TATTTTATTTTAAATCA
*
2841999 AATATTATTTATTATTTTAAATCA
1 AATAATA-TT-TTATTTTAAATCA
* *
2842023 TATAATATTAATATTTTA
1 AATAATATT-TTATTTTA
2842041 TATTAATATA
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
20 3 0.05
21 11 0.17
22 24 0.37
23 15 0.23
24 12 0.18
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (22 bp):
AATAATATTTTATTTTAAATCA
Found at i:2842045 original size:13 final size:13
Alignment explanation
Indices: 2842008--2842055 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2841998 AAATATTATT
*
2842008 TATTATTTTAAATCA
1 TATTATATT-AAT-A
*
2842023 TATAATATTAATA
1 TATTATATTAATA
*
2842036 TTTTATATTAATA
1 TATTATATTAATA
2842049 TATTATA
1 TATTATA
2842056 ATAAATTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 18 0.64
14 3 0.11
15 7 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTATATTAATA
Found at i:2842049 original size:24 final size:24
Alignment explanation
Indices: 2841931--2842058 Score: 60
Period size: 23 Copynumber: 5.4 Consensus size: 24
2841921 TAATGCATTC
* *
2841931 AATAATAATATTTTATTTTAA-AT
1 AATATTAATATTTTATATTAATAT
2841954 CAA-A-TAA-ATTTT-TA-TAAT-T
1 -AATATTAATATTTTATATTAATAT
*
2841973 AATAATTAATTATTTT-TATTAAGTAA
1 AAT-ATTAA-TATTTTATATTAA-TAT
* *
2841999 AATATTATTTATTATTTTA-AATCATAT
1 AATATTA---A-TATTTTATATTAATAT
2842026 AATATTAATATTTTATATTAATAT
1 AATATTAATATTTTATATTAATAT
*
2842050 ATTA-TAATA
1 AATATTAATA
2842059 AATTATGATA
Statistics
Matches: 82, Mismatches: 8, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 2 0.02
21 8 0.10
22 3 0.04
23 20 0.24
24 15 0.18
25 5 0.06
26 3 0.04
27 9 0.11
28 11 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (24 bp):
AATATTAATATTTTATATTAATAT
Found at i:2842329 original size:25 final size:23
Alignment explanation
Indices: 2842274--2842331 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
2842264 ATAATTCATA
*
2842274 AATTTTTAAAAATATTTTTATAT
1 AATTTTTAAAAATATTTTTAAAT
*
2842297 AATATTTTAAATATTATTTTTAGAAT
1 AAT-TTTTAAA-AATATTTTTA-AAT
*
2842323 AGTTTTTAA
1 AATTTTTAA
2842332 TATGACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 7 0.24
25 15 0.52
26 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
AATTTTTAAAAATATTTTTAAAT
Found at i:2845969 original size:25 final size:26
Alignment explanation
Indices: 2845910--2845975 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
2845900 ATAAATATTT
* *
2845910 TTATTTTTATTTTGAAA-TAATTAAG
1 TTATTTTTAATTAGAAATTAATTAAG
* *
2845935 CT-TTTGTAATTAGAAATTAATTAA-
1 TTATTTTTAATTAGAAATTAATTAAG
2845959 TTATTTTTAATTA-AAAT
1 TTATTTTTAATTAGAAAT
2845976 ATCAATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (26 bp):
TTATTTTTAATTAGAAATTAATTAAG
Found at i:2845982 original size:26 final size:26
Alignment explanation
Indices: 2845923--2845991 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
2845913 TTTTTATTTT
*
2845923 GAAA-TAATTAAGC-TTTTGTAATTA
1 GAAATTAATTAATCATTTTGTAATTA
*
2845947 GAAATTAATTAATTATTTT-TAATTA
1 GAAATTAATTAATCATTTTGTAATTA
*
2845972 -AAATATCAATTTATCATTTT
1 GAAAT-T-AATTAATCATTTT
2845992 ATGATCTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
24 8 0.22
25 14 0.38
26 15 0.41
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (26 bp):
GAAATTAATTAATCATTTTGTAATTA
Found at i:2849733 original size:25 final size:25
Alignment explanation
Indices: 2849705--2849755 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2849695 TATTACATAT
*
2849705 TAATATATC-ATATTATTATTTATTA
1 TAATATATCAATA-TATTAGTTATTA
*
2849730 TAATATGTCAATATATTAGTTATTA
1 TAATATATCAATATATTAGTTATTA
2849755 T
1 T
2849756 TGCATACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
TAATATATCAATATATTAGTTATTA
Found at i:2855114 original size:12 final size:13
Alignment explanation
Indices: 2855097--2855125 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2855087 TTACTTTAAT
2855097 TTATATTG-TATA
1 TTATATTGTTATA
2855109 TTATATTGTTATA
1 TTATATTGTTATA
2855122 TTAT
1 TTAT
2855126 CTTTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
TTATATTGTTATA
Found at i:2856525 original size:10 final size:10
Alignment explanation
Indices: 2856489--2856564 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 10
2856479 GAAATGAAAA
2856489 TATTTAAATAT
1 TATTT-AATAT
2856500 TATTTTAAT-T
1 TA-TTTAATAT
2856510 TA-TTAATAT
1 TATTTAATAT
2856519 TATTTAACTA-
1 TATTTAA-TAT
* *
2856529 TAATAAATAT
1 TATTTAATAT
*
2856539 TATAAATAATAT
1 TAT--TTAATAT
*
2856551 TATTTAATAA
1 TATTTAATAT
2856561 TATT
1 TATT
2856565 ATTTGAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
8 5 0.10
9 5 0.10
10 23 0.45
11 7 0.14
12 11 0.22
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTTAATAT
Found at i:2856532 original size:16 final size:14
Alignment explanation
Indices: 2856513--2856578 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 14
2856503 TTTAATTTAT
2856513 TAATATTATTTAACTA
1 TAATATTATTTAA--A
*
2856529 TAATAAATATTATAAA
1 TAAT-ATTATT-TAAA
2856545 TAATATTATTT-AA
1 TAATATTATTTAAA
2856558 TAATATTATTTGAATA
1 TAATATTATTT-AA-A
2856574 TAATA
1 TAATA
2856579 AATGTAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 13 0.30
14 1 0.02
15 6 0.14
16 15 0.35
17 5 0.12
18 3 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
TAATATTATTTAAA
Found at i:2856562 original size:45 final size:45
Alignment explanation
Indices: 2856507--2856601 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
2856497 TATTATTTTA
* * *
2856507 ATTTATTAATATTATTT-AACTATAATAAATATTATAAATAATATT
1 ATTTAATAATATTATTTGAA-TATAATAAATATAATAAAGAATATT
*
2856552 ATTTAATAATATTATTTGAATATAATAAATGTAATAAAGAATATT
1 ATTTAATAATATTATTTGAATATAATAAATATAATAAAGAATATT
2856597 ATTTA
1 ATTTA
2856602 GTATTATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (45 bp):
ATTTAATAATATTATTTGAATATAATAAATATAATAAAGAATATT
Found at i:2857784 original size:5 final size:5
Alignment explanation
Indices: 2857774--2857802 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2857764 CTTTTCATCC
2857774 ATTCA ATTCA ATTCA ATTCA ATTCA ATTC
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTC
2857803 CCCCCCCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCA
Found at i:2878478 original size:3 final size:3
Alignment explanation
Indices: 2878470--2878496 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2878460 ATAGGATTTT
2878470 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2878497 TCTACATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2880296 original size:16 final size:15
Alignment explanation
Indices: 2880271--2880310 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
2880261 AATTATAAAC
2880271 TTTTATTTTTTAAAATT
1 TTTTA-TTTTT-AAATT
2880288 TTTTATTTTTAAATT
1 TTTTATTTTTAAATT
2880303 TATTTATT
1 T-TTTATT
2880311 AACTAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTTTTAAATT
Found at i:2885067 original size:63 final size:63
Alignment explanation
Indices: 2885000--2885120 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
2884990 TTTTTTTATT
* * *
2885000 TTATATTAATAATTTAATAAAAAATTATTTAAGGGGCTCATTAAAAAATATAT-ATGTAACATA
1 TTATATTAATAATTTAACAAAAAATAATTT-AGGAGCTCATTAAAAAATATATAATGTAACATA
* * *
2885063 TTATATTAATAATTTAACAAAAAATAATTTTGTAGTTCATTAAAAAATATATAATGTA
1 TTATATTAATAATTTAACAAAAAATAATTTAGGAGCTCATTAAAAAATATATAATGTA
2885121 TAAAAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
62 18 0.35
63 33 0.65
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.40
Consensus pattern (63 bp):
TTATATTAATAATTTAACAAAAAATAATTTAGGAGCTCATTAAAAAATATATAATGTAACATA
Found at i:2885302 original size:132 final size:131
Alignment explanation
Indices: 2885065--2885328 Score: 519
Period size: 132 Copynumber: 2.0 Consensus size: 131
2885055 GTAACATATT
2885065 ATATTAATAATTTAACAAAAAATAATTTTGTAGTTCATTAAAAAATATATAATGTATAAAAAATT
1 ATATTAATAATTTAACAAAAAATAATTTTGTAGTTCATTAAAAAATATATAATGTATAAAAAATT
2885130 TTAAAATTTATGAGGGCCCATTAAGATTGTCAACAGATAGGGTATCTGTTAATTTCGAAATATTC
66 TTAAAATTTATGAGGGCCCATTAAGATTGTCAACAGATAGGGTATCTGTTAATTTCGAAATATTC
2885195 A
131 A
2885196 NATATTAATAATTTAACAAAAAATAATTTTGTAGTTCATTAAAAAATATATAATGTATAAAAAAT
1 -ATATTAATAATTTAACAAAAAATAATTTTGTAGTTCATTAAAAAATATATAATGTATAAAAAAT
2885261 TTTAAAATTTATGAGGGCCCATTAAGATTGTCAACAGATAGGGTATCTGTTAATTTCGAAATATT
65 TTTAAAATTTATGAGGGCCCATTAAGATTGTCAACAGATAGGGTATCTGTTAATTTCGAAATATT
2885326 CA
130 CA
2885328 A
1 A
2885329 ACCCTAACCC
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 1 0.01
132 131 0.99
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (131 bp):
ATATTAATAATTTAACAAAAAATAATTTTGTAGTTCATTAAAAAATATATAATGTATAAAAAATT
TTAAAATTTATGAGGGCCCATTAAGATTGTCAACAGATAGGGTATCTGTTAATTTCGAAATATTC
A
Found at i:2885591 original size:47 final size:45
Alignment explanation
Indices: 2885471--2885592 Score: 172
Period size: 45 Copynumber: 2.7 Consensus size: 45
2885461 AAGGAGCCGA
*
2885471 CGTGGTTGTGGCTGGGGAGAAAAGAAAGAAGAAATGAGTGTGGGG
1 CGTGGTTGTGGATGGGGAGAAAAGAAAGAAGAAATGAGTGTGGGG
* *
2885516 CATGGTTGTGGATGGGGAGAAAAGAAAGAAGAAATGAGTGATTTGGG
1 CGTGGTTGTGGATGGGGAGAAAAGAAAGAAGAAATGAGTG--TGGGG
* * *
2885563 CGTGGCTGTGGTTAGGGAGAAAAGAAAGAA
1 CGTGGTTGTGGATGGGGAGAAAAGAAAGAA
2885593 TGATTGAAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 38 0.56
47 30 0.44
ACGTcount: A:0.34, C:0.04, G:0.43, T:0.19
Consensus pattern (45 bp):
CGTGGTTGTGGATGGGGAGAAAAGAAAGAAGAAATGAGTGTGGGG
Found at i:2886712 original size:18 final size:19
Alignment explanation
Indices: 2886673--2886712 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2886663 AAAAATATTA
*
2886673 CATAATTATATCATCATGT
1 CATAATTATATCATCATAT
*
2886692 CATATTTATAT-ATCATAT
1 CATAATTATATCATCATAT
2886710 CAT
1 CAT
2886713 CATCATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (19 bp):
CATAATTATATCATCATAT
Found at i:2886721 original size:21 final size:20
Alignment explanation
Indices: 2886673--2886722 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
2886663 AAAAATATTA
*
2886673 CATA-ATTATATCATCATGT
1 CATATATTATATCATCATAT
2886692 CATAT-TTATAT-ATCATAT
1 CATATATTATATCATCATAT
2886710 CATCATCATTATA
1 CAT-AT-ATTATA
2886723 AACGTGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.35
19 12 0.46
21 5 0.19
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (20 bp):
CATATATTATATCATCATAT
Found at i:2886795 original size:14 final size:15
Alignment explanation
Indices: 2886776--2886808 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
2886766 TAAATAAAAT
2886776 ATTAATTAA-TATTA
1 ATTAATTAATTATTA
2886790 ATTAATTAATTATTA
1 ATTAATTAATTATTA
2886805 ATTA
1 ATTA
2886809 TAAAAGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTAATTAATTATTA
Found at i:2888841 original size:22 final size:21
Alignment explanation
Indices: 2888802--2888846 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2888792 ATTTTTATTT
*
2888802 AAATTTAAAGTATTAAATATA
1 AAATTTAAAGTATAAAATATA
*
2888823 AAATTATAATGTATAAAATATA
1 AAATT-TAAAGTATAAAATATA
2888845 AA
1 AA
2888847 TAATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
AAATTTAAAGTATAAAATATA
Found at i:2888901 original size:16 final size:17
Alignment explanation
Indices: 2888882--2888914 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2888872 CACAAAATGA
2888882 TTAAATG-CATAAATAG
1 TTAAATGACATAAATAG
*
2888898 TTAAATGATATAAATAG
1 TTAAATGACATAAATAG
2888915 AAAGAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (17 bp):
TTAAATGACATAAATAG
Found at i:2889340 original size:48 final size:50
Alignment explanation
Indices: 2889235--2889364 Score: 133
Period size: 48 Copynumber: 2.6 Consensus size: 50
2889225 TTGAGGAAGC
* * *
2889235 CATTAAAAATTATATAATAAATAAATAATTTCATAAAATTTTGAAGGTAT
1 CATTAAAAATAATATAATAAATAAATAAATTCATAAAATTTTGAAAGTAT
*
2889285 TATTAAAAA-AATATAATAAATAAA-AAATTC-TAAAATTTTTGAAAG-AGT
1 CATTAAAAATAATATAATAAATAAATAAATTCATAAAA-TTTTGAAAGTA-T
* *
2889333 CATTAAAATATATTATATATATATACAATAAA
1 CATTAAAA-ATAATATA-ATAAATA-AATAAA
2889365 AATTTTCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
47 6 0.09
48 21 0.32
49 15 0.23
50 13 0.20
51 6 0.09
52 2 0.03
53 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (50 bp):
CATTAAAAATAATATAATAAATAAATAAATTCATAAAATTTTGAAAGTAT
Found at i:2894034 original size:31 final size:31
Alignment explanation
Indices: 2893954--2894027 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
2893944 CATTAGTAAT
* *
2893954 ATATATTTTAAATATTATAT-A-T-AATATA
1 ATATATTTTATATATAATATAATTAAATATA
*
2893982 ATATATTTTATATTTAATATAATTAAATATA
1 ATATATTTTATATATAATATAATTAAATATA
*
2894013 ATATTTTTTATATAT
1 ATATATTTTATATAT
2894028 GTTATAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 17 0.45
29 1 0.03
30 1 0.03
31 19 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATATATTTTATATATAATATAATTAAATATA
Found at i:2894279 original size:18 final size:17
Alignment explanation
Indices: 2894240--2894281 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2894230 CCGAACTTGA
*
2894240 AATAAAAAAATTAATAT
1 AATAAAAAAATTAAGAT
*
2894257 TATAATAAAAATTAAGAT
1 AATAA-AAAAATTAAGAT
2894275 AATAAAA
1 AATAAAA
2894282 TAAGTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AATAAAAAAATTAAGAT
Found at i:2899468 original size:21 final size:21
Alignment explanation
Indices: 2899442--2899485 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2899432 TGCCGAAGCT
*
2899442 AAAAAAAAAAGAAACAA-ACAA
1 AAAAAAAAAACAAA-AACACAA
2899463 AAAAAAAAAACAAAAACACAA
1 AAAAAAAAAACAAAAACACAA
2899484 AA
1 AA
2899486 TCAACGTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAAACACAA
Found at i:2899479 original size:19 final size:19
Alignment explanation
Indices: 2899442--2899485 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2899432 TGCCGAAGCT
*
2899442 AAAAAAAAAAGAAACAAAC
1 AAAAAAAAAAGAAAAAAAC
2899461 AAAAAAAAAA-AACAAAAAC
1 AAAAAAAAAAGAA-AAAAAC
2899480 ACAAAA
1 A-AAAA
2899486 TCAACGTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 16 0.73
20 4 0.18
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAAAAC
Found at i:2899485 original size:17 final size:18
Alignment explanation
Indices: 2899443--2899476 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2899433 GCCGAAGCTA
2899443 AAAAAAAAAGAAACAAAC
1 AAAAAAAAAGAAACAAAC
2899461 AAAAAAAAA-AAACAAA
1 AAAAAAAAAGAAACAAA
2899477 AACACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAACAAAC
Found at i:2900827 original size:12 final size:12
Alignment explanation
Indices: 2900812--2900838 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2900802 CTGCTGCTGC
2900812 TGCTGTTGTTGT
1 TGCTGTTGTTGT
2900824 TGCTGTTGTTGT
1 TGCTGTTGTTGT
2900836 TGC
1 TGC
2900839 ATTAGCTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.11, G:0.33, T:0.56
Consensus pattern (12 bp):
TGCTGTTGTTGT
Found at i:2903419 original size:23 final size:24
Alignment explanation
Indices: 2903378--2903427 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
2903368 AATAAAATAT
2903378 ACATAGCATAGATGAGAAGATCAA
1 ACATAGCATAGATGAGAAGATCAA
*
2903402 ACATAGC-TAGATGGGAAGATCAA
1 ACATAGCATAGATGAGAAGATCAA
2903425 ACA
1 ACA
2903428 GGGACTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.48, C:0.14, G:0.22, T:0.16
Consensus pattern (24 bp):
ACATAGCATAGATGAGAAGATCAA
Found at i:2911003 original size:521 final size:528
Alignment explanation
Indices: 2909960--2911003 Score: 1415
Period size: 547 Copynumber: 2.0 Consensus size: 528
2909950 ATATAATACG
* *
2909960 TATATATATAGATATAATGCTTAAAAATGTCTTTAAATTATTTCAAAATATTTAAATAATTTATT
1 TATATATATAGATATAATGCTTAAAAATCTCTTTAAATTATTTAAAAATATTTAAATAATTTATT
* *
2910025 ATTTTTTCGTTTTAGCTCTCATATATCTTTATTATTAAAATGGACAAACTGTGTCAATTAAAACA
66 ATTTTTTCATTTTAACTCTCATATATCTTTATTATTAAAATGGACAAACTGTGTCAATTAAAACA
* * *
2910090 TCATTTATTATTATTTTTACTCACATGATGTTAATATAAATATGAAATATATCATGTGATTATGT
131 TCATTTATTATTATTTTTACTCACATAATCTTAAGATAAATATGAAATATATCATGTGATTATGT
** * * * *
2910155 TATCATGTTACGTTAATACTTACTTTTAGATTTATTTGATTCAAAATAAAAATATAAAAAACTTG
196 TATCATGTTACGTTAATACTTACTTTTAGACCTACTTAACTCAAAATAAAAACATAAAAAACTTG
* ***** ** *
2910220 ATAATATAATAAAATAATAAAAATTTGTTTAAATTTTTTAAATAATTCCTGAATTTTTTAGGCAT
261 ATAATAAAATAAAATAAT--AAATTAAAAAAAAAATTTTAAATAATTCCTGAATTTTTAAGGCAT
*
2910285 TATGCTTTTTTATATTTTTTTTTATTTTGTTTCTTAAAATAAAGCCTACCTCATTCATAAAAAAA
324 TATGCTTTTTTATATTTTTTTTGATTTTGTTTCTTAAAATAAAG-C-ACCTCA-TC---------
*
2910350 ATAAAGTCCATTTCAAAAAAAAAAAAATTTGTGCTCAACAATTTTGATTGTTATTTTTATTCCTT
377 AT--A-TCCA-TACAAAAAAAAAAAAATTTGTGCTCAACAATTTTGATTGTTATTTTTATTCCTT
* *
2910415 GATTACACTTTTGAATTTTGATTTTCTAAATTTGAGACTGTACTCTCTTGTTTGCTTCCATTATT
438 GATTACACTTTTGAATTTTGATTTTCTAAATTTGAGACTGCACTCTCTTGTTTGCCTCCATTATT
2910480 TTTTTCCCTGTGTATGTCTGTGCTTT
503 TTTTTCCCTGTGTATGTCTGTGCTTT
* * *
2910506 TATATAATATATATATAATGGTTAAAAATCTTTTTAAATTATTTAAAAATATTTAAATAATTTAT
1 TATAT-ATATAGATATAATGCTTAAAAATCTCTTTAAATTATTTAAAAATATTTAAATAATTTAT
* * * * *
2910571 TATTTTTTCATTTTAACTCTTATATATCTTTATTATTAAAATTGACAAATTGTGTTAATTAAAAT
65 TATTTTTTCATTTTAACTCTCATATATCTTTATTATTAAAATGGACAAACTGTGTCAATTAAAAC
* *
2910636 ATCATTTATTATTATTTTTACTCACATAATCTTAAGATGAATATGAAATATGTCATGTGATTATG
130 ATCATTTATTATTATTTTTACTCACATAATCTTAAGATAAATATGAAATATATCATGTGATTATG
* * **
2910701 TTATTATGTTATGTTAATA-TGTGTTTTTAGACCTACTTAACTCAAAATAAAAACATAAAAAACT
195 TTATCATGTTACGTTAATACT-TACTTTTAGACCTACTTAACTCAAAATAAAAACATAAAAAACT
*
2910765 TGATAATAAAATAAAATAAT-AATTAAAAAAAAAATTTTAAATTATTCCTGAATTTTTAAGGCAT
259 TGATAATAAAATAAAATAATAAATTAAAAAAAAAATTTTAAATAATTCCTGAATTTTTAAGGCAT
2910829 TATGCTTTTTTATATTTTGTTTTGATTTTGTTTCTTAAAATAAAG-A-C-CA-C-T-T-CA-ACA
324 TATGCTTTTTTATATTTT-TTTTGATTTTGTTTCTTAAAATAAAGCACCTCATCATATCCATACA
* * * *
2910886 AAAAAAAAAAACTTTGTTCTCAACAATTTTGATTGTTATTTTTATTCCTTGATTCCATTTTTGAA
388 AAAAAAAAAAAATTTGTGCTCAACAATTTTGATTGTTATTTTTATTCCTTGATTACACTTTTGAA
*
2910951 TTTTGATTTTCTAAATTTGAGACTGCACTTTCTTGTTTGCCTCCATTATTTTT
453 TTTTGATTTTCTAAATTTGAGACTGCACTCTCTTGTTTGCCTCCATTATTTTT
2911004 CTGATCATGT
Statistics
Matches: 449, Mismatches: 46, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
521 113 0.25
523 2 0.00
524 1 0.00
528 1 0.00
538 1 0.00
540 2 0.00
541 1 0.00
542 1 0.00
544 53 0.12
545 25 0.06
546 6 0.01
547 243 0.54
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (528 bp):
TATATATATAGATATAATGCTTAAAAATCTCTTTAAATTATTTAAAAATATTTAAATAATTTATT
ATTTTTTCATTTTAACTCTCATATATCTTTATTATTAAAATGGACAAACTGTGTCAATTAAAACA
TCATTTATTATTATTTTTACTCACATAATCTTAAGATAAATATGAAATATATCATGTGATTATGT
TATCATGTTACGTTAATACTTACTTTTAGACCTACTTAACTCAAAATAAAAACATAAAAAACTTG
ATAATAAAATAAAATAATAAATTAAAAAAAAAATTTTAAATAATTCCTGAATTTTTAAGGCATTA
TGCTTTTTTATATTTTTTTTGATTTTGTTTCTTAAAATAAAGCACCTCATCATATCCATACAAAA
AAAAAAAAATTTGTGCTCAACAATTTTGATTGTTATTTTTATTCCTTGATTACACTTTTGAATTT
TGATTTTCTAAATTTGAGACTGCACTCTCTTGTTTGCCTCCATTATTTTTTTCCCTGTGTATGTC
TGTGCTTT
Found at i:2927159 original size:7 final size:7
Alignment explanation
Indices: 2927147--2927172 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2927137 ACAATATTAT
2927147 TAAATAA
1 TAAATAA
2927154 TAAATAA
1 TAAATAA
2927161 TAAATAA
1 TAAATAA
2927168 TAAAT
1 TAAAT
2927173 CAATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAATAA
Found at i:2927200 original size:22 final size:23
Alignment explanation
Indices: 2927166--2927220 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
2927156 AATAATAAAT
* * *
2927166 AATAAATCAATTTTATTAAATTA
1 AATAAATAAATTTTATAAAATGA
2927189 AAT-AATAAA-TTTATAAAATGA
1 AATAAATAAATTTTATAAAATGA
2927210 AATAAATAAAT
1 AATAAATAAAT
2927221 AAAATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.48
22 11 0.41
23 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AATAAATAAATTTTATAAAATGA
Found at i:2930803 original size:23 final size:24
Alignment explanation
Indices: 2930770--2930815 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
2930760 TCAAATAAAC
2930770 ATAGCATAGATGGGAAGATCAAAT
1 ATAGCATAGATGGGAAGATCAAAT
2930794 ATAGC-TAGATGGGAAGATCAAA
1 ATAGCATAGATGGGAAGATCAAA
2930816 CAGGGACTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.20
Consensus pattern (24 bp):
ATAGCATAGATGGGAAGATCAAAT
Found at i:2932431 original size:15 final size:16
Alignment explanation
Indices: 2932411--2932451 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2932401 TCCCATTACG
2932411 TGTGGCTGCTGG-GGC
1 TGTGGCTGCTGGAGGC
2932426 TGTGGCTG-TGGAGGC
1 TGTGGCTGCTGGAGGC
2932441 TGCTGG-TGCTG
1 TG-TGGCTGCTG
2932452 CTGAGGCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 15 0.65
16 5 0.22
ACGTcount: A:0.02, C:0.17, G:0.51, T:0.29
Consensus pattern (16 bp):
TGTGGCTGCTGGAGGC
Found at i:2934632 original size:14 final size:15
Alignment explanation
Indices: 2934613--2934641 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2934603 GTCCACATAC
2934613 TGCAAAC-ACCTGAG
1 TGCAAACTACCTGAG
2934627 TGCAAACTACCTGAG
1 TGCAAACTACCTGAG
2934642 AAAAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (15 bp):
TGCAAACTACCTGAG
Found at i:2937917 original size:138 final size:138
Alignment explanation
Indices: 2937664--2937924 Score: 355
Period size: 138 Copynumber: 1.9 Consensus size: 138
2937654 AGATCCAGCC
* ** *
2937664 AGATTTGGTCGCGGGAAGCACCGAATTTGGTGCTTTCCGATCAGATCCCACAATTGGATCTAACA
1 AGATCTGGTCGCGGGAAGCACCGAATCAGGTGATTTCCGATCAGATCCCACAATTGGATCTAACA
*
2937729 CTCCACGACCAGATCCAGCCATGGAGAAGCGCTGATCTAGCGTCGTAGTGGCCAGATCTGGCTCT
66 CTCCACGACCAGATCCAGCCACGGAGAAGCGCTGATCTAGCGTCGTAGTGGCCAGATCTGGCTCT
2937794 CAATAGTT
131 CAATAGTT
* * * **
2937802 AGATCTGGTCGCGGGAAGCACCGGATCAGGT-ATTTCTCGATCGGATCCCACAGTTGGATCTGGC
1 AGATCTGGTCGCGGGAAGCACCGAATCAGGTGATTTC-CGATCAGATCCCACAATTGGATCTAAC
* * * * *
2937866 ACTCCACGGCCAGATCCAGCCGCGGGGAAGC-ATCGATCTAGCGTCGTAGTGGCTAGATC
65 ACTCCACGACCAGATCCAGCCACGGAGAAGCGCT-GATCTAGCGTCGTAGTGGCCAGATC
2937925 CGACCACATG
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
137 5 0.05
138 101 0.95
ACGTcount: A:0.23, C:0.27, G:0.28, T:0.22
Consensus pattern (138 bp):
AGATCTGGTCGCGGGAAGCACCGAATCAGGTGATTTCCGATCAGATCCCACAATTGGATCTAACA
CTCCACGACCAGATCCAGCCACGGAGAAGCGCTGATCTAGCGTCGTAGTGGCCAGATCTGGCTCT
CAATAGTT
Found at i:2944642 original size:30 final size:30
Alignment explanation
Indices: 2944606--2944662 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2944596 GGTGCCTTTG
*
2944606 AGTGTGAGAGACTAGTTGCACATATTCTTA
1 AGTGTGAGAGACCAGTTGCACATATTCTTA
*
2944636 AGTGTGAGGGACCAGTTGCACATATTC
1 AGTGTGAGAGACCAGTTGCACATATTC
2944663 CAGCAGGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (30 bp):
AGTGTGAGAGACCAGTTGCACATATTCTTA
Found at i:2946694 original size:111 final size:109
Alignment explanation
Indices: 2946507--2946897 Score: 408
Period size: 111 Copynumber: 3.5 Consensus size: 109
2946497 TATTGTTCAA
* * * *
2946507 TAGTTTTTTAGGCAGTGCGTGACTGGTTTTTATATATTGCATTACCTGTTGTAGTTAGAGTGGTG
1 TAGTTTTTTAGGC-TTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGTAGGT-GAGTGGTG
** * *
2946572 GTGTGTGACTTGTGCAATTCATGTGTTGTTTTGAGGCCTTTGTTTAG
64 G-ACGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAG
* *
2946619 TAGTTTTTTAGGCTTGCGTGACTGGTTTTTATATATTGCGTTACTTGTTGTAGCGTGAGTGGTGG
1 TAGTTTTTTAGGCTTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGTAG-GTGAGTGGTGG
* * *
2946684 CACGTGACTTGTGCAATCCATGTGTTGTTTAGGGGCTTTTGTTTAA
65 -ACGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAG
* * ** *
2946730 TAG-TTTTTAGGGTTACGTGACCT-AATTTTATATATTGCGTGACGTGTTGTTATGTATTGTGAG
1 TAGTTTTTTAGGCTTGCGTGA-CTGGTTTTTATATATTGCGTGACCTGTTG-TA-G----GT--G
*
2946793 AGTGGTTGAGCGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAG
57 AGTGGTGGA-CGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAG
* * * * * *
2946847 TAGTTTTTTAGGATTGCATTACTGGTTTCTATGTATTACGTGACCTGTTGT
1 TAGTTTTTTAGGCTTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGT
2946898 TATATATTGC
Statistics
Matches: 234, Mismatches: 33, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
110 37 0.16
111 91 0.39
112 15 0.06
115 2 0.01
116 1 0.00
117 55 0.24
118 33 0.14
ACGTcount: A:0.17, C:0.10, G:0.28, T:0.45
Consensus pattern (109 bp):
TAGTTTTTTAGGCTTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGTAGGTGAGTGGTGGA
CGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAG
Found at i:2946947 original size:118 final size:117
Alignment explanation
Indices: 2946679--2946985 Score: 346
Period size: 118 Copynumber: 2.6 Consensus size: 117
2946669 TAGCGTGAGT
* * *
2946679 GGTGGCACGTGACTTGTGCAATCCATGTGTTGTTTAGGGGCTTTTGTTTAATAGTTTTTAGGGTT
1 GGTGGCGCGTGACTTGTGCAATTCATGTGTTGTTTAGGGGCTTTTGTTTAATAGTTTTTAGGATT
* * * * * * * *
2946744 ACGTGACCTAATTTTATATATTGCGTGACGTGTTGTTATGTATTGTGAGAGT
66 GCATTACCTAATTTTATATATTACGTGACCTGTTGTTATATATTGCGAGAGC
* * * *
2946796 GGTTGAGCGTGACTTGTGCAATTCATGTGTTGTTTAGAGGCTTTTGTTTAGTAGTTTTTTAGGAT
1 GGTGGCGCGTGACTTGTGCAATTCATGTGTTGTTTAGGGGCTTTTGTTTAATAG-TTTTTAGGAT
** *
2946861 TGCATTA-CTGGTTTCTATGTATTACGTGACCTGTTGTTATATATTGCGAGAGC
65 TGCATTACCTAATTT-TATATATTACGTGACCTGTTGTTATATATTGCGAGAGC
*** * * * * *
2946914 GGTGGCGCGTGACTTGTGCAATTCGCCTCTTGTTTAGGGGCGTTTGTTCACTAGTTATTAGGCAT
1 GGTGGCGCGTGACTTGTGCAATTCATGTGTTGTTTAGGGGCTTTTGTTTAATAGTTTTTAGG-AT
2946979 TGCATTA
65 TGCATTA
2946986 ATGTGTATTA
Statistics
Matches: 158, Mismatches: 29, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
117 60 0.38
118 98 0.62
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (117 bp):
GGTGGCGCGTGACTTGTGCAATTCATGTGTTGTTTAGGGGCTTTTGTTTAATAGTTTTTAGGATT
GCATTACCTAATTTTATATATTACGTGACCTGTTGTTATATATTGCGAGAGC
Found at i:2953790 original size:26 final size:26
Alignment explanation
Indices: 2953754--2953803 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2953744 GAATGAATAT
* * *
2953754 AAAGAGTAATATGTAAATTATACAAC
1 AAAGAATAATATGGAAATGATACAAC
2953780 AAAGAATAATATGGAAATGATACA
1 AAAGAATAATATGGAAATGATACA
2953804 GAATAATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (26 bp):
AAAGAATAATATGGAAATGATACAAC
Found at i:2955407 original size:24 final size:24
Alignment explanation
Indices: 2955380--2955493 Score: 103
Period size: 24 Copynumber: 4.9 Consensus size: 24
2955370 TCAGCCACTG
2955380 GATCTCCAACTGCATTGACTGTTA
1 GATCTCCAACTGCATTGACTGTTA
*
2955404 GATCTCCAATTGCATTGAC---TA
1 GATCTCCAACTGCATTGACTGTTA
* * ** * *
2955425 CATCTGCATTTGCA-TCACTTGCT-
1 GATCTCCAACTGCATTGAC-TGTTA
*
2955448 GAATCTCCAACTGCATTGACTGTTG
1 G-ATCTCCAACTGCATTGACTGTTA
2955473 GATCTCCAACTGCATTGACTG
1 GATCTCCAACTGCATTGACTG
2955494 CATTTGCATT
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
20 3 0.04
21 13 0.18
24 52 0.72
25 4 0.06
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (24 bp):
GATCTCCAACTGCATTGACTGTTA
Found at i:2958058 original size:19 final size:20
Alignment explanation
Indices: 2958034--2958071 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2958024 GCGAATAATA
2958034 ACCACT-CCAAAAGGCTCCT
1 ACCACTGCCAAAAGGCTCCT
*
2958053 ACCACTGCCAAAATGCTCC
1 ACCACTGCCAAAAGGCTCC
2958072 GAAGTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.42, G:0.11, T:0.16
Consensus pattern (20 bp):
ACCACTGCCAAAAGGCTCCT
Found at i:2971466 original size:57 final size:57
Alignment explanation
Indices: 2971398--2971512 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
2971388 AAAGGGGGAG
*
2971398 AAGTATGGCAGAGATCTTAGGGGAGAATTTAAGAGAGATAGGAAGTAGAAGCTGTCT
1 AAGTATGGCAGAGATCTTAAGGGAGAATTTAAGAGAGATAGGAAGTAGAAGCTGTCT
*
2971455 AAGTATGGCAGAGATCTTAAGGGAGAATTTAGGAGAGATAGGAAGTAGAAGCTGTCT
1 AAGTATGGCAGAGATCTTAAGGGAGAATTTAAGAGAGATAGGAAGTAGAAGCTGTCT
2971512 A
1 A
2971513 GGGGCAGTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (57 bp):
AAGTATGGCAGAGATCTTAAGGGAGAATTTAAGAGAGATAGGAAGTAGAAGCTGTCT
Found at i:2975594 original size:73 final size:74
Alignment explanation
Indices: 2975489--2975631 Score: 234
Period size: 73 Copynumber: 1.9 Consensus size: 74
2975479 ACATTCAAAT
* *
2975489 TCAAATTTTCAAATAGTGAGCTTTTAGCTGGCTAACCATTCTTCTTAGTCGATTAAGTCTTCTCT
1 TCAAATTTTCAAACAGTGAGCTTTTAGCTGGCTAACCATACTTCTTAGTCGATTAAGTCTTCTCT
*
2975554 GTCTCGTAA
66 ATCTCGTAA
* *
2975563 TCAAATTTT-TAACAGTGAGCTTTTAGTTGGCTAACCATACTTCTTAGTCGATTAAGTCTTCTCT
1 TCAAATTTTCAAACAGTGAGCTTTTAGCTGGCTAACCATACTTCTTAGTCGATTAAGTCTTCTCT
2975627 ATCTC
66 ATCTC
2975632 ACAATCTACT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
73 55 0.86
74 9 0.14
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (74 bp):
TCAAATTTTCAAACAGTGAGCTTTTAGCTGGCTAACCATACTTCTTAGTCGATTAAGTCTTCTCT
ATCTCGTAA
Found at i:2983266 original size:18 final size:18
Alignment explanation
Indices: 2983243--2983278 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2983233 CTCTTTAACT
*
2983243 TGTGAAGTCCCTTCATGA
1 TGTGAAGTCACTTCATGA
2983261 TGTGAAGTCACTTCATGA
1 TGTGAAGTCACTTCATGA
2983279 ATGATTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (18 bp):
TGTGAAGTCACTTCATGA
Found at i:2986397 original size:74 final size:73
Alignment explanation
Indices: 2986314--2986548 Score: 303
Period size: 74 Copynumber: 3.2 Consensus size: 73
2986304 AGAGATCTCT
*
2986314 TAATCGGTTAAAGCCTCTTGTAATAAGTTAAAGTAGAGAACACAATAACAAGACAGTGAAAGTCA
1 TAATCGGTTAAAGCCT-TTGTAATAAGTTAAAGTAGAGAACACAATAGCAAGACAGTGAAAGTCA
2986379 GAGAAGCTA
65 GAGAAGCTA
*
2986388 TAATCGGTTAGAGCCTTTTGTAATAAGTTAAAGTAGAGAACACAATAGCAAGACAGTGAAAGTCA
1 TAATCGGTTAAAGCC-TTTGTAATAAGTTAAAGTAGAGAACACAATAGCAAGACAGTGAAAGTCA
*
2986453 GAGAAGTTA
65 GAGAAGCTA
* * * * * **
2986462 TAATCGGTTAGAGCCTTCTATAATCAGTTAGAGCAGAGAACACAGCAGCAAGACAGT-ACAA-TG
1 TAATCGGTTAAAGCCTT-TGTAATAAGTTAAAGTAGAGAACACAATAGCAAGACAGTGA-AAGT-
* *
2986525 CAGAAAAGCTG
63 CAGAGAAGCTA
2986536 TAATCGGTTAAAG
1 TAATCGGTTAAAG
2986549 TTGTCTATAA
Statistics
Matches: 144, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
73 4 0.03
74 139 0.97
75 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (73 bp):
TAATCGGTTAAAGCCTTTGTAATAAGTTAAAGTAGAGAACACAATAGCAAGACAGTGAAAGTCAG
AGAAGCTA
Found at i:2990493 original size:45 final size:45
Alignment explanation
Indices: 2990395--2990520 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 45
2990385 GACTTAGGGT
* * *
2990395 TTACGTGACTAGTTGATAGGAG-ATTGCGTACCTGATTTTTATGTA
1 TTACGTGACTAGTTGATA-GAGCATTGCATAACTGGTTTTTATGTA
**
2990440 TTGTGTGACT-GATTGATAGAGCATTGCATAACTGGTTTTTA-GTAA
1 TTACGTGACTAG-TTGATAGAGCATTGCATAACTGGTTTTTATGT-A
* * *
2990485 TTACGTGACTAGTGGATAG-GCATTACATGACTGGTT
1 TTACGTGACTAGTTGATAGAGCATTGCATAACTGGTT
2990521 GATAGGCATT
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
44 21 0.31
45 45 0.67
46 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (45 bp):
TTACGTGACTAGTTGATAGAGCATTGCATAACTGGTTTTTATGTA
Found at i:2990600 original size:23 final size:23
Alignment explanation
Indices: 2990574--2990655 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
2990564 TTGCAAGGCG
2990574 TTGCGTGACTGGTTGATATGGCA
1 TTGCGTGACTGGTTGATATGGCA
* **
2990597 TTGCGTGACTGATTGATATGATA
1 TTGCGTGACTGGTTGATATGGCA
* **
2990620 TTGCGTTACTGGTTTTTA-GGCA
1 TTGCGTGACTGGTTGATATGGCA
*
2990642 TTACGTGACTGGTT
1 TTGCGTGACTGGTT
2990656 TTTAAACTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 14 0.29
23 34 0.71
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.40
Consensus pattern (23 bp):
TTGCGTGACTGGTTGATATGGCA
Found at i:2990659 original size:22 final size:22
Alignment explanation
Indices: 2990470--2990656 Score: 88
Period size: 22 Copynumber: 8.4 Consensus size: 22
2990460 GCATTGCATA
* **
2990470 ACTGGTTTTTAGTAATTACGTG
1 ACTGGTTTATAGGCATTACGTG
* ** *
2990492 ACTAGTGGATAGGCATTACATG
1 ACTGGTTTATAGGCATTACGTG
*
2990514 ACTGGTTGATAGGCATTACGTG
1 ACTGGTTTATAGGCATTACGTG
* * * ** * *
2990536 ATTAGTTTTTAGTTATTGCATG
1 ACTGGTTTATAGGCATTACGTG
* * *
2990558 AGTGGTTTGCA-AGGCGTTGCGTG
1 ACTGGTTT--ATAGGCATTACGTG
* *
2990581 ACTGGTTGATATGGCATTGCGTG
1 ACTGGTTTATA-GGCATTACGTG
* * ** * *
2990604 ACTGATTGATATGATATTGCGTT
1 ACTGGTTTATA-GGCATTACGTG
*
2990627 ACTGGTTTTTAGGCATTACGTG
1 ACTGGTTTATAGGCATTACGTG
2990649 ACTGGTTT
1 ACTGGTTT
2990657 TTAAACTTTG
Statistics
Matches: 122, Mismatches: 39, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
21 1 0.01
22 70 0.57
23 51 0.42
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.39
Consensus pattern (22 bp):
ACTGGTTTATAGGCATTACGTG
Found at i:2992084 original size:16 final size:16
Alignment explanation
Indices: 2992065--2992147 Score: 50
Period size: 16 Copynumber: 5.1 Consensus size: 16
2992055 TAAAAATTAA
2992065 TAAATAATAACTAAAT
1 TAAATAATAACTAAAT
2992081 TAAAATAAATAAACATAAAAT
1 T-AAAT-AAT-AAC-T-AAAT
*
2992102 TAAAT--TAACTTAA-
1 TAAATAATAACTAAAT
2992115 TAAA-AATAAACTAAA-
1 TAAATAAT-AACTAAAT
*
2992130 TAGAAAAATAACTAAAT
1 TA-AATAATAACTAAAT
2992147 T
1 T
2992148 CTAACCTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 21
0.70 0.03 0.27
Matches are distributed among these distances:
13 4 0.07
14 3 0.06
15 9 0.17
16 13 0.24
17 9 0.17
18 3 0.06
19 3 0.06
20 5 0.09
21 5 0.09
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (16 bp):
TAAATAATAACTAAAT
Found at i:2992086 original size:25 final size:25
Alignment explanation
Indices: 2992057--2992130 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
2992047 CAAAAATATA
2992057 AAAATTAATAAATAATAACTAAATT
1 AAAATTAATAAATAATAACTAAATT
* *
2992082 AAAATAAATAAACATAA-AATTAAATT
1 AAAATTAAT-AA-ATAATAACTAAATT
*
2992108 -AACTTAATAAA-AATAAACTAAAT
1 AAAATTAATAAATAAT-AACTAAAT
2992131 AGAAAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 2 0.05
23 1 0.03
24 9 0.22
25 14 0.35
26 10 0.25
27 4 0.10
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATTAATAAATAATAACTAAATT
Found at i:2992099 original size:31 final size:32
Alignment explanation
Indices: 2992064--2992147 Score: 82
Period size: 35 Copynumber: 2.6 Consensus size: 32
2992054 ATAAAAATTA
2992064 ATAAATAATAACTAAATTAAAATAAA-TAAAC
1 ATAAATAATAACTAAATTAAAATAAACTAAAC
* * *
2992095 ATAAAATTAAATTAACTTAATAAAAATAAACTAAAT
1 AT-AAA-T-AA-TAACTAAATTAAAATAAACTAAAC
*
2992131 AGAAA-AATAACTAAATT
1 ATAAATAATAACTAAATT
2992148 CTAACCTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
31 10 0.24
32 5 0.12
33 1 0.02
34 2 0.05
35 19 0.45
36 5 0.12
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.27
Consensus pattern (32 bp):
ATAAATAATAACTAAATTAAAATAAACTAAAC
Found at i:2992101 original size:15 final size:14
Alignment explanation
Indices: 2992070--2992129 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
2992060 ATTAATAAAT
* *
2992070 AATAACTAAATTAA
1 AATAAATAAACTAA
2992084 AATAAATAAACATAA
1 AATAAATAAAC-TAA
*
2992099 AATTAAATTAACTTAA
1 AA-TAAATAAAC-TAA
2992115 TAA-AAATAAACTAA
1 -AATAAATAAACTAA
2992129 A
1 A
2992130 TAGAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 1 0.03
14 12 0.32
15 12 0.32
16 11 0.29
17 2 0.05
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAATAAACTAA
Found at i:2999218 original size:23 final size:23
Alignment explanation
Indices: 2999185--2999241 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
2999175 ACGTATCATG
*
2999185 CAATG-CTTAAACACCAGTTACA
1 CAATGCCTTAAAAACCAGTTACA
* **
2999207 CAATGCCTTAAAAATCAGTTAGG
1 CAATGCCTTAAAAACCAGTTACA
2999230 CAATGCC-TAAAA
1 CAATGCCTTAAAA
2999242 TTAGTCATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (23 bp):
CAATGCCTTAAAAACCAGTTACA
Found at i:2999484 original size:38 final size:38
Alignment explanation
Indices: 2999420--2999498 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
2999410 TCAAAGATGT
* *
2999420 AATGATTAAGTCATGCAATACCTAAAAGCCAATCTCGC
1 AATGATTAAGTCACGCAATACCTAAAAACCAATCTCGC
* * * * *
2999458 AATGCTTAAGTCACGCAATGCTTAAAAATCAGTCTCGC
1 AATGATTAAGTCACGCAATACCTAAAAACCAATCTCGC
2999496 AAT
1 AAT
2999499 ACCTAAAAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (38 bp):
AATGATTAAGTCACGCAATACCTAAAAACCAATCTCGC
Found at i:2999511 original size:21 final size:22
Alignment explanation
Indices: 2999466--2999591 Score: 94
Period size: 22 Copynumber: 5.8 Consensus size: 22
2999456 GCAATGCTTA
* *
2999466 AGTCACGCAATGCTTAAAAATC
1 AGTCACGCAATACCTAAAAATC
*
2999488 AGTCTCGCAATACCTAAAAA-C
1 AGTCACGCAATACCTAAAAATC
* * *
2999509 AGTAACGTAATACCTAAAAATT
1 AGTCACGCAATACCTAAAAATC
* *
2999531 AGTCTCGCAATAACTAAAAA-C
1 AGTCACGCAATACCTAAAAATC
* ** * *
2999552 TAGTGACATAATGCCTAAAAACC
1 -AGTCACGCAATACCTAAAAATC
* *
2999575 AGTAACACAATACCTAA
1 AGTCACGCAATACCTAA
2999592 TAACTAATTG
Statistics
Matches: 80, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
21 18 0.22
22 61 0.76
23 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.21
Consensus pattern (22 bp):
AGTCACGCAATACCTAAAAATC
Found at i:2999541 original size:43 final size:44
Alignment explanation
Indices: 2999480--2999577 Score: 135
Period size: 43 Copynumber: 2.2 Consensus size: 44
2999470 ACGCAATGCT
* *
2999480 TAAAAATCAGTCTCGCAATACCTAAAAAC-AGTAACGTAATACC
1 TAAAAATCAGTCTCGCAATAACTAAAAACTAGTAACATAATACC
* * *
2999523 TAAAAATTAGTCTCGCAATAACTAAAAACTAGTGACATAATGCC
1 TAAAAATCAGTCTCGCAATAACTAAAAACTAGTAACATAATACC
*
2999567 TAAAAACCAGT
1 TAAAAATCAGT
2999578 AACACAATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 27 0.57
44 20 0.43
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.22
Consensus pattern (44 bp):
TAAAAATCAGTCTCGCAATAACTAAAAACTAGTAACATAATACC
Found at i:3003609 original size:2 final size:2
Alignment explanation
Indices: 3003602--3003669 Score: 104
Period size: 2 Copynumber: 34.0 Consensus size: 2
3003592 CCAAAAGTTT
3003602 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A CTA -A NTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA
3003644 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3003670 ACTGACAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.03
2 58 0.94
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3006768 original size:31 final size:30
Alignment explanation
Indices: 3006708--3006808 Score: 150
Period size: 30 Copynumber: 3.4 Consensus size: 30
3006698 TTGAATATGT
*
3006708 CGTGTAACAACAATATCTTTTT-AACATGG
1 CGTGTAACAACAATATTTTTTTCAACATGG
* *
3006737 CGTGTAATAATAATATTTTTTTTCAACATGG
1 CGTGTAACAACAATA-TTTTTTTCAACATGG
*
3006768 CGTGTAACAACAGTATTTTTTTCAACATGG
1 CGTGTAACAACAATATTTTTTTCAACATGG
3006798 CGTGTAACAAC
1 CGTGTAACAAC
3006809 CTGGCTTGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
29 13 0.20
30 32 0.50
31 19 0.30
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (30 bp):
CGTGTAACAACAATATTTTTTTCAACATGG
Found at i:3006883 original size:69 final size:68
Alignment explanation
Indices: 3006810--3007020 Score: 273
Period size: 69 Copynumber: 3.1 Consensus size: 68
3006800 TGTAACAACC
* * * * * *
3006810 TGGCTTGTCATAGATTTTTGTACCTGGCGTGTAACAAGCTAATCATAGCTTGTCACAGGTTTTTG
1 TGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCAT-GCTTGTCACAGGTTTTTG
3006875 TACT
65 TACT
* *
3006879 TGGCTTGTCACATATTTTTATACATAGTGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTG
1 TGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCAT-GCTTGTCACAGGTTTTTG
3006944 TA-T
65 TACT
*
3006947 ATGG-TATGTCACATATTTTTGTACATAACGTGTAACACGCTAACCATGACTTGTCACAGGTTTT
1 -TGGCT-TGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATG-CTTGTCACAGGTTTT
*
3007011 TGTACA
63 TGTACT
3007017 TGGC
1 TGGC
3007021 GTGTAACAAG
Statistics
Matches: 124, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
68 3 0.02
69 121 0.98
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (68 bp):
TGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATGCTTGTCACAGGTTTTTGT
ACT
Found at i:3007017 original size:45 final size:44
Alignment explanation
Indices: 3006953--3007059 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 44
3006943 GTATATGGTA
* *
3006953 TGTCACATA-TTTTTGTACATAACGTGTAACACGCTAACCATGAC
1 TGTCACA-AGTTTTTGTACATAACGTGTAACAAGCTAACCATAAC
* **
3006997 TTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAAC
1 -TGTCACAAGTTTTTGTACATAACGTGTAACAAGCTAACCATAAC
3007042 TGTCACAAGTTTTTGTAC
1 TGTCACAAGTTTTTGTAC
3007060 TAGGCTTGTC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 17 0.31
45 38 0.69
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (44 bp):
TGTCACAAGTTTTTGTACATAACGTGTAACAAGCTAACCATAAC
Found at i:3007083 original size:68 final size:69
Alignment explanation
Indices: 3006991--3007200 Score: 280
Period size: 69 Copynumber: 3.1 Consensus size: 69
3006981 ACACGCTAAC
* ** *
3006991 CATGACTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAAC-TGTCACAAGTTTT
1 CATGGCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATAACTTGTCACAAGTTTT
3007055 TGTA
66 TGTA
* * *
3007059 C-TAGGCTTGTCACATATTTTTGTACATAGCATGTAACATGCTAACCATAGCTTGTCACAAGTTT
1 CAT-GGCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATAACTTGTCACAAGTTT
3007123 TTGTA
65 TTGTA
* * * * *
3007128 CATGGCGTGTCACATATTTTTGAACATAGCGTGTAACACGCTAACCATGACTTGTCACAGGTTTT
1 CATGGCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATAACTTGTCACAAGTTTT
*
3007193 TATA
66 TGTA
3007197 CATG
1 CATG
3007201 ACGTGTAAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
67 1 0.01
68 42 0.34
69 80 0.65
70 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (69 bp):
CATGGCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATAACTTGTCACAAGTTTT
TGTA
Found at i:3007085 original size:113 final size:114
Alignment explanation
Indices: 3006881--3007137 Score: 344
Period size: 113 Copynumber: 2.3 Consensus size: 114
3006871 TTTGTACTTG
* * * * ** *
3006881 GCTTGTCACATA-TTTTTATACATAGTGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGT
1 GCTTGTCACA-AGTTTTTGTACATGGCGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGT
*
3006945 ATATGGTATGTCACATATTTTTGTACATAACGTGTAACACGCTAACCAT-
65 ATATGGTATGTCACATATTTTTGTACATAACATGTAACACGCTAACCATA
*
3006994 GACTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAAC-TGTCACAAGTTTTTGT
1 G-CTTGTCACAAGTTTTTGTACATGGCGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGT
* *
3007058 ACTA-GGCT-TGTCACATATTTTTGTACATAGCATGTAACATGCTAACCATA
65 A-TATGG-TATGTCACATATTTTTGTACATAACATGTAACACGCTAACCATA
3007108 GCTTGTCACAAGTTTTTGTACATGGCGTGT
1 GCTTGTCACAAGTTTTTGTACATGGCGTGT
3007138 CACATATTTT
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
113 85 0.67
114 42 0.33
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (114 bp):
GCTTGTCACAAGTTTTTGTACATGGCGTGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTA
TATGGTATGTCACATATTTTTGTACATAACATGTAACACGCTAACCATA
Found at i:3007097 original size:24 final size:24
Alignment explanation
Indices: 3007051--3007097 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3007041 CTGTCACAAG
* *
3007051 TTTTTGTACTAGGCTTGTCACATA
1 TTTTTGTACTAGGCATGTAACATA
3007075 TTTTTGTACATA-GCATGTAACAT
1 TTTTTGTAC-TAGGCATGTAACAT
3007098 GCTAACCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45
Consensus pattern (24 bp):
TTTTTGTACTAGGCATGTAACATA
Found at i:3007125 original size:182 final size:183
Alignment explanation
Indices: 3006813--3007313 Score: 695
Period size: 182 Copynumber: 2.7 Consensus size: 183
3006803 AACAACCTGG
* * * * *
3006813 CTTGTCATAGATTTTTGTACCTGGCGTGTAACAAGCTAATCATAGCTTGTCACAGGTTTTTGTAC
1 CTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAGCTTGTCACAAGTTTTTGTAC
* * ** * *
3006878 TTGGCTTGTCACATATTTTTATACATAGTGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTT
66 TAGGCTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGGCTTGTCACAAGTTTTT
* * *
3006943 GTATATGGTATGTCACATATTTTTGTACATAACGTGTAACACGCTAACCATGA
131 GTACATGGCATGTCACATATTTTTGAACATAACGTGTAACACGCTAACCATGA
*
3006996 CTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAAC-TGTCACAAGTTTTTGTAC
1 CTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAGCTTGTCACAAGTTTTTGTAC
* *
3007060 TAGGCTTGTCACATATTTTTGTACATAGCATGTAACATGCTAACCATAGCTTGTCACAAGTTTTT
66 TAGGCTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGGCTTGTCACAAGTTTTT
* *
3007125 GTACATGGCGTGTCACATATTTTTGAACATAGCGTGTAACACGCTAACCATGA
131 GTACATGGCATGTCACATATTTTTGAACATAACGTGTAACACGCTAACCATGA
* * * * *
3007178 CTTGTCACAGGTTTTTATACATGACGTGTAAAAAACTAACCATAGCTTGTCAC-AGATTTGTGTA
1 CTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAGCTTGTCACAAG-TTTTTGTA
* * * *
3007242 C-ATGGCTTGTCACATATTTTTGTACATGGCATGTAATAAGCTAATCATGGATTGTCACATA-TT
65 CTA-GGCTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGGCTTGTCACA-AGTT
3007305 TTTGTACAT
128 TTTGTACAT
3007314 AGCGTGTAAC
Statistics
Matches: 284, Mismatches: 30, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
182 167 0.59
183 116 0.41
184 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (183 bp):
CTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAACCATAGCTTGTCACAAGTTTTTGTAC
TAGGCTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGGCTTGTCACAAGTTTTT
GTACATGGCATGTCACATATTTTTGAACATAACGTGTAACACGCTAACCATGA
Found at i:3007147 original size:24 final size:24
Alignment explanation
Indices: 3007104--3007161 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
3007094 ACATGCTAAC
* *
3007104 CATAGCTTGTCACAAGTTTTTGTA
1 CATAGCGTGTCACAAGTTTTTGAA
*
3007128 CATGGCGTGTCACATA-TTTTTGAA
1 CATAGCGTGTCACA-AGTTTTTGAA
3007152 CATAGCGTGT
1 CATAGCGTGT
3007162 AACACGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
CATAGCGTGTCACAAGTTTTTGAA
Found at i:3007251 original size:69 final size:69
Alignment explanation
Indices: 3007173--3007313 Score: 165
Period size: 69 Copynumber: 2.0 Consensus size: 69
3007163 ACACGCTAAC
* * *
3007173 CATGACTTGTCACAGGTTTTTATACATGACGTGTAAAAAACTAACCATAGCTTGTCACAGATTTG
1 CATGACTTGTCACAGATTTTTATACATGACATGTAAAAAACTAACCATAGATTGTCACAGATTTG
3007238 TGTA
66 TGTA
* * * * * * * * * *
3007242 CATGGCTTGTCACATATTTTTGTACATGGCATGTAATAAGCTAATCATGGATTGTCACATATTTT
1 CATGACTTGTCACAGATTTTTATACATGACATGTAAAAAACTAACCATAGATTGTCACAGATTTG
3007307 TGTA
66 TGTA
3007311 CAT
1 CAT
3007314 AGCGTGTAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (69 bp):
CATGACTTGTCACAGATTTTTATACATGACATGTAAAAAACTAACCATAGATTGTCACAGATTTG
TGTA
Found at i:3007254 original size:24 final size:24
Alignment explanation
Indices: 3007222--3007271 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
3007212 ACTAACCATA
3007222 GCTTGTCACAGATTTGTGTACATG
1 GCTTGTCACAGATTTGTGTACATG
* *
3007246 GCTTGTCACATATTTTTGTACATG
1 GCTTGTCACAGATTTGTGTACATG
3007270 GC
1 GC
3007272 ATGTAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (24 bp):
GCTTGTCACAGATTTGTGTACATG
Done.