Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 9 of 199
Found at i:2911500 original size:19 final size:19
Alignment explanation
Indices: 2911473--2911542 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
2911463 TCAACTCATT
*
2911473 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
* *
2911492 TTTTAATTTAATAAAT-TG
1 TTTTAATTTAATAACTCTA
* *
2911510 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2911529 CTTTAATTTAATAA
1 TTTTAATTTAATAA
2911543 AATATTAAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
18 14 0.35
19 26 0.65
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2911792 original size:19 final size:19
Alignment explanation
Indices: 2911765--2911834 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
2911755 TCAACTCAAT
*
2911765 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
**
2911784 TTTTAATTTAATAA-AATA
1 TTTTAATTTAATAACTCTA
* *
2911802 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2911821 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2911835 AATATTAAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2911803 original size:18 final size:18
Alignment explanation
Indices: 2911782--2911840 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
2911772 TTAATAACTC
2911782 TATTTTAATTTAATAAAA
1 TATTTTAATTTAATAAAA
* * **
2911800 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAA-AA
2911819 TATTTTAATTTAATAAAA
1 TATTTTAATTTAATAAAA
2911837 TATT
1 TATT
2911841 AAGTAATACT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTAATTTAATAAAA
Found at i:2911815 original size:37 final size:37
Alignment explanation
Indices: 2911770--2911840 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2911760 TCAATTTTTT
2911770 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
2911807 ATTTAATAACTCTATTTTAATTTAATAAAATATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
2911841 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:2912152 original size:18 final size:19
Alignment explanation
Indices: 2912113--2912178 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 19
2912103 ACTTAATTTT
*
2912113 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
2912132 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
2912150 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
2912169 TTAAAT-AAAA
1 TTAAATGAAAA
2912179 AAATGAGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 19 0.47
19 21 0.52
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:2912179 original size:19 final size:19
Alignment explanation
Indices: 2912113--2912178 Score: 91
Period size: 18 Copynumber: 3.6 Consensus size: 19
2912103 ACTTAATTTT
2912113 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
2912132 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
2912150 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
2912169 TTAAA-TAAAA
1 TTAAATTAAAA
2912179 AAATGAGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 20 0.50
19 20 0.50
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:2912186 original size:20 final size:19
Alignment explanation
Indices: 2912113--2912187 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
2912103 ACTTAATTTT
* *
2912113 TTAAATTAAAATAGAGTTA
1 TTAAATAAAAAAAGAGTTA
* * * *
2912132 TTAAATGAGAATAG-TTTA
1 TTAAATAAAAAAAGAGTTA
* *
2912150 TTAAATTAAAATAGAGTTA
1 TTAAATAAAAAAAGAGTTA
2912169 TTAAATAAAAAAATGAGTT
1 TTAAATAAAAAAA-GAGTT
2912188 GAAGAGGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.33
19 26 0.57
20 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (19 bp):
TTAAATAAAAAAAGAGTTA
Found at i:2912304 original size:27 final size:27
Alignment explanation
Indices: 2912255--2912332 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
2912245 TTTTTTTTTC
2912255 CTTTGGCACCA-TGGTGCCGCCAATGA
1 CTTTGGCACCATTGGTGCCGCCAATGA
* *
2912281 CTTTGGCACCATTGGTGCCACCAATTTA
1 CTTTGGCACCATTGGTGCCGCCAA-TGA
*
2912309 -TTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
2912333 TTAATTGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.26
27 32 0.70
28 2 0.04
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATGA
Found at i:2912333 original size:27 final size:26
Alignment explanation
Indices: 2912256--2912341 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
2912246 TTTTTTTTCC
* *
2912256 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCTTGGTGCCGCCAATTTA
*
2912281 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACC-TTGGTGCCGCCAATTTA
2912309 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-TTGGTGCCGCCAATTTA
*
2912336 ATTGGC
1 TTTGGC
2912342 CTGATCAGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.17
27 41 0.79
28 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (26 bp):
TTTGGCACCTTGGTGCCGCCAATTTA
Found at i:2912860 original size:31 final size:31
Alignment explanation
Indices: 2912825--2912888 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2912815 AGGTATTCTT
2912825 TTGTTTTTAGCTTTTCTTATTCTATTACGCA
1 TTGTTTTTAGCTTTTCTTATTCTATTACGCA
2912856 TTGTTTTTAGCTTTTCTTATTCTATTACGCA
1 TTGTTTTTAGCTTTTCTTATTCTATTACGCA
2912887 TT
1 TT
2912889 CTAACACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.59
Consensus pattern (31 bp):
TTGTTTTTAGCTTTTCTTATTCTATTACGCA
Found at i:2916967 original size:5 final size:6
Alignment explanation
Indices: 2916950--2916974 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2916940 ATATGGCTAC
2916950 TGTTTT TGTTTT TGTTTT TGTTTT T
1 TGTTTT TGTTTT TGTTTT TGTTTT T
2916975 AAATAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TGTTTT
Found at i:2918294 original size:26 final size:27
Alignment explanation
Indices: 2918238--2918300 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
2918228 TAAAATTTAG
*
2918238 AAAATTTATTAAATTTTAATAAGAATAT
1 AAAATTT-TTAAATTTTAATAAAAATAT
*
2918266 AAAATATTTTAAA-TTTATTAAAAAT-T
1 AAAAT-TTTTAAATTTTAATAAAAATAT
2918292 AAAATTTTT
1 AAAATTTTT
2918301 TATAAAATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.12
26 6 0.19
27 10 0.31
28 10 0.31
29 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
AAAATTTTTAAATTTTAATAAAAATAT
Found at i:2918301 original size:26 final size:28
Alignment explanation
Indices: 2918238--2918302 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
2918228 TAAAATTTAG
* *
2918238 AAAATTTATTAAATTTTAATAAGAATAT
1 AAAATTTTTTAAATTTTAATAAAAATAT
* *
2918266 AAAATATTTTAAA-TTTATTAAAAAT-T
1 AAAATTTTTTAAATTTTAATAAAAATAT
2918292 AAAATTTTTTA
1 AAAATTTTTTA
2918303 TAAAATCGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 11 0.34
27 10 0.31
28 11 0.34
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AAAATTTTTTAAATTTTAATAAAAATAT
Found at i:2918575 original size:48 final size:49
Alignment explanation
Indices: 2918520--2918620 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 49
2918510 TTTTACGGAA
*
2918520 TTTATATTTCTTTACAT-TTTGTATAATTTTCTTACGA-CTTTATAAAAT
1 TTTATATTT-TTTACATATTTCTATAATTTTCTTACGATCTTTATAAAAT
** * * *
2918568 TTTATATTTTTTTTATATTTCTATTATTTTTTTACGATTTTTATAAAAT
1 TTTATATTTTTTACATATTTCTATAATTTTCTTACGATCTTTATAAAAT
2918617 TTTA
1 TTTA
2918621 CAGTATATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 5 0.11
48 26 0.58
49 14 0.31
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (49 bp):
TTTATATTTTTTACATATTTCTATAATTTTCTTACGATCTTTATAAAAT
Found at i:2918650 original size:19 final size:19
Alignment explanation
Indices: 2918567--2918674 Score: 76
Period size: 19 Copynumber: 5.5 Consensus size: 19
2918557 CTTTATAAAA
*
2918567 TTTTATATTTTTTTTA-TAT
1 TTTTATA-TTTTTTTACAAT
* *
2918586 TTCTATTATTTTTTTACGAT
1 TTTTA-TATTTTTTTACAAT
*** *
2918606 TTTTATAAAATTTTACAGT
1 TTTTATATTTTTTTACAAT
*
2918625 ATATTATATTTTTTTACAAT
1 -TTTTATATTTTTTTACAAT
*
2918645 TTTTATAATTTTTT-CTAAT
1 TTTTATATTTTTTTAC-AAT
2918664 TTTTAATATTT
1 TTTT-ATATTT
2918675 GAATTTTTTA
Statistics
Matches: 68, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
18 1 0.01
19 40 0.59
20 27 0.40
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATATTTTTTTACAAT
Found at i:2918655 original size:20 final size:20
Alignment explanation
Indices: 2918567--2918658 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
2918557 CTTTATAAAA
* *
2918567 TTTTATATTTTTTTTA-TAT
1 TTTTATAATTTTTTTACAAT
* * *
2918586 TTCTATTATTTTTTTACGAT
1 TTTTATAATTTTTTTACAAT
** *
2918606 TTTTATAA-AATTTTACAGT
1 TTTTATAATTTTTTTACAAT
*
2918625 ATATTAT-ATTTTTTTACAAT
1 -TTTTATAATTTTTTTACAAT
2918645 TTTTATAATTTTTT
1 TTTTATAATTTTTT
2918659 CTAATTTTTA
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
19 26 0.48
20 28 0.52
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTATAATTTTTTTACAAT
Found at i:2918673 original size:39 final size:39
Alignment explanation
Indices: 2918567--2918674 Score: 96
Period size: 39 Copynumber: 2.8 Consensus size: 39
2918557 CTTTATAAAA
* * * *
2918567 TTTTAT-ATTTTTTTTATATTTCTATTATTTTTTTACGAT
1 TTTTATAATTTTTTCTA-ATTTTTAATATTTTTTTACAAT
* * * *
2918606 TTTTATAAAATTTTAC-AGTATATT-ATATTTTTTTACAAT
1 TTTTAT-AATTTTTTCTAAT-TTTTAATATTTTTTTACAAT
2918645 TTTTATAATTTTTTCTAATTTTTAATATTT
1 TTTTATAATTTTTTCTAATTTTTAATATTT
2918675 GAATTTTTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
38 10 0.19
39 34 0.65
40 3 0.06
41 5 0.10
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (39 bp):
TTTTATAATTTTTTCTAATTTTTAATATTTTTTTACAAT
Found at i:2918855 original size:85 final size:85
Alignment explanation
Indices: 2918752--2918973 Score: 259
Period size: 85 Copynumber: 2.6 Consensus size: 85
2918742 AATTTTTAAT
* * *
2918752 AAAATAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTT-ATGCATTTTAAAAGT
1 AAAAAAGGGGCCTAATTGCTTTTTTTGAAAAAGTTTGAGGG-CTTTTTTGATACATTTTAAAAGT
*
2918816 TCAAATACCCAATTGAATGCA
65 TCAAATACCCAAATGAATGCA
* *
2918837 AAAAAAGGGGCCTAATTGCTTTTTTTGAAAAGGTTTGAGGGCTTTTTTGATACATTTTGAAAGTT
1 AAAAAAGGGGCCTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTTTGATACATTTTAAAAGTT
* * *
2918902 CAAGTATCCAAATGAGTGCAAAAA
66 CAAATACCCAAATGAATGC----A
* * *
2918926 AAAAACAGGGGCTTAATTG-TATTTTTTCAAAAAATTTGAGGGCTTTTT
1 AAAAA-AGGGGCCTAATTGCT-TTTTTTGAAAAAGTTTGAGGGCTTTTT
2918974 GCACCCTTAA
Statistics
Matches: 117, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
84 7 0.06
85 67 0.57
89 7 0.06
90 36 0.31
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (85 bp):
AAAAAAGGGGCCTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTTTGATACATTTTAAAAGTT
CAAATACCCAAATGAATGCA
Found at i:2924409 original size:10 final size:10
Alignment explanation
Indices: 2924396--2924450 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
2924386 AAAAATTACA
2924396 AAAAAAATTT
1 AAAAAAATTT
*
2924406 -AAAATATTT
1 AAAAAAATTT
* *
2924415 ATAAAGA-TT
1 AAAAAAATTT
2924424 AAAAAAATTCT
1 AAAAAAATT-T
*
2924435 AAAAAAATAT
1 AAAAAAATTT
2924445 AAAAAA
1 AAAAAA
2924451 GGTAAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 15 0.42
10 12 0.33
11 9 0.25
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:2924540 original size:3 final size:3
Alignment explanation
Indices: 2924534--2924558 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2924524 TATACTAAAG
2924534 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2924559 TTGCTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2925044 original size:18 final size:19
Alignment explanation
Indices: 2925011--2925049 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2925001 ATGTTTTAAT
2925011 AAATAAAAATTATTTTGAA
1 AAATAAAAATTATTTTGAA
* *
2925030 AAATATAAA-TATTTTTAA
1 AAATAAAAATTATTTTGAA
2925048 AA
1 AA
2925050 GTTTTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATAAAAATTATTTTGAA
Found at i:2939382 original size:21 final size:21
Alignment explanation
Indices: 2939358--2939407 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2939348 CATTGTTTCT
*
2939358 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
2939379 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
2939400 AATCTCAC
1 AATCTCAC
2939408 TGGAGCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:2949185 original size:40 final size:41
Alignment explanation
Indices: 2949101--2949186 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 41
2949091 ACCCGCGATC
2949101 TTGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTG
1 TTGTTAGAATAAACTACCCCTTTAGTAC-CTGTCATTTATTG
*
2949143 TTGTTAGAATAAACTACCCCTTTGGTA-CTGTCATTTATTG
1 TTGTTAGAATAAACTACCCCTTTAGTACCTGTCATTTATTG
2949183 TTGT
1 TTGT
2949187 AATCTTAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 17 0.40
42 26 0.60
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.44
Consensus pattern (41 bp):
TTGTTAGAATAAACTACCCCTTTAGTACCTGTCATTTATTG
Found at i:2951957 original size:18 final size:18
Alignment explanation
Indices: 2951924--2951958 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2951914 ATTAATAGAT
*
2951924 ATAAAATTATATTTTAAA
1 ATAAAATTATAATTTAAA
*
2951942 ATAAAATTTTAATTTAA
1 ATAAAATTATAATTTAA
2951959 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAAATTATAATTTAAA
Found at i:2951984 original size:24 final size:22
Alignment explanation
Indices: 2951952--2952009 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
2951942 ATAAAATTTT
*
2951952 AATTTAATTTTTTAAAAATATAA
1 AATTAAATTTTTTAAAAA-ATAA
* *
2951975 AATATAAATTATTTAAATAATAA
1 AAT-TAAATTTTTTAAAAAATAA
*
2951998 AATTATATTTTT
1 AATTAAATTTTT
2952010 ACTATTATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 7 0.24
23 10 0.34
24 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTAAATTTTTTAAAAAATAA
Found at i:2953410 original size:29 final size:29
Alignment explanation
Indices: 2953368--2953425 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2953358 AAGAAGAAAG
2953368 AATGATGGAACACGTGGTATGTTAGGATT
1 AATGATGGAACACGTGGTATGTTAGGATT
2953397 AATGATGGAACACGTGGTATGTTAGGATT
1 AATGATGGAACACGTGGTATGTTAGGATT
2953426 CATATCATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (29 bp):
AATGATGGAACACGTGGTATGTTAGGATT
Found at i:2954885 original size:144 final size:145
Alignment explanation
Indices: 2954626--2954913 Score: 479
Period size: 144 Copynumber: 2.0 Consensus size: 145
2954616 TGTTCTTTAT
* *
2954626 ACACACTCGGGTAACCAGATCTCTTTTATTATTTTCAAGTGTTGTACTGTTATTGAGTGAGCTTT
1 ACACACTCGGGTAACCA-ATCTCTTTTATTATTTTCAAGTGTTGTACTGTCATTGAGCGAGCTTT
* *
2954691 ATCATTGTAATATCTTCCTTGAGAGGTGTCTTTAATCATTGTTATTATTTATCATATTTGTAAGG
65 ATCATTGTAATATCTTCCTTGAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAGG
2954756 GGTTGCTTAAGGTTAC
130 GGTTGCTTAAGGTTAC
* * * *
2954772 ACACACTTGGGTAACC-ATCTCTTTTATTCTTTTCAATTGTTGTATTGTCATTGAGCGAGCTTTA
1 ACACACTCGGGTAACCAATCTCTTTTATTATTTTCAAGTGTTGTACTGTCATTGAGCGAGCTTTA
2954836 TCATTGTAATATCTTCCTTGAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAGGG
66 TCATTGTAATATCTTCCTTGAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAGGG
*
2954901 TTTGCTTAAGGTT
131 GTTGCTTAAGGTT
2954914 TTTGAGTAGA
Statistics
Matches: 133, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
144 118 0.89
146 15 0.11
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (145 bp):
ACACACTCGGGTAACCAATCTCTTTTATTATTTTCAAGTGTTGTACTGTCATTGAGCGAGCTTTA
TCATTGTAATATCTTCCTTGAGAGATGTCTTCAATCATTGTTATTATTTATCATATTTGTAAGGG
GTTGCTTAAGGTTAC
Found at i:2956070 original size:31 final size:27
Alignment explanation
Indices: 2956002--2956070 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 27
2955992 TTTTTATATG
*
2956002 ATAATATAATTAATATAAATTTTTTTA
1 ATAATATATTTAATATAAATTTTTTTA
*
2956029 ATAA-ATTATTTAATATTGCAATTTTATGTTA
1 ATAATA-TATTTAATA-T-AAATTTT-T-TTA
2956060 ATAATATATTT
1 ATAATATATTT
2956071 TAGCATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.03
27 12 0.35
28 1 0.03
29 6 0.18
30 1 0.03
31 12 0.35
32 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (27 bp):
ATAATATATTTAATATAAATTTTTTTA
Found at i:2956100 original size:22 final size:23
Alignment explanation
Indices: 2956059--2956101 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2956049 ATTTTATGTT
*
2956059 AATAATATATTTTAGCATTTTTA
1 AATAATATATTTTAACATTTTTA
*
2956082 AATAATAT-TTTTAATATTTT
1 AATAATATATTTTAACATTTT
2956102 ATTGAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
AATAATATATTTTAACATTTTTA
Found at i:2956101 original size:21 final size:22
Alignment explanation
Indices: 2956059--2956102 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2956049 ATTTTATGTT
2956059 AATAATATATTTTAGCATTTTTA
1 AATAATATATTTTA-CATTTTTA
2956082 AATAATAT-TTTTA-ATATTTTA
1 AATAATATATTTTACAT-TTTTA
2956103 TTGAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 5 0.25
22 5 0.25
23 8 0.40
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
AATAATATATTTTACATTTTTA
Found at i:2958933 original size:13 final size:13
Alignment explanation
Indices: 2958915--2958941 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2958905 AAATATGTGC
2958915 ATGTTAGTTTGAA
1 ATGTTAGTTTGAA
2958928 ATGTTAGTTTGAA
1 ATGTTAGTTTGAA
2958941 A
1 A
2958942 AAAAAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (13 bp):
ATGTTAGTTTGAA
Found at i:2966923 original size:24 final size:24
Alignment explanation
Indices: 2966896--2966951 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2966886 TTCCTTCACA
2966896 GCCTCTGTAATTGCCATATACTCT
1 GCCTCTGTAATTGCCATATACTCT
2966920 GCCTCTGTAATTGCCATATACTCT
1 GCCTCTGTAATTGCCATATACTCT
2966944 GCCTCTGT
1 GCCTCTGT
2966952 TGTAGACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.38
Consensus pattern (24 bp):
GCCTCTGTAATTGCCATATACTCT
Found at i:2980788 original size:15 final size:15
Alignment explanation
Indices: 2980768--2980811 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 15
2980758 TCACCACTCT
2980768 TAATTATAAAAAAAA
1 TAATTATAAAAAAAA
2980783 TAATTATAATAAAAAA
1 TAATTATAA-AAAAAA
*
2980799 TAATAATAAAAAA
1 TAATTATAAAAAA
2980812 TCTTAGGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATTATAAAAAAAA
Found at i:2980806 original size:13 final size:13
Alignment explanation
Indices: 2980788--2980812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2980778 AAAAATAATT
2980788 ATAATAAAAAATA
1 ATAATAAAAAATA
2980801 ATAATAAAAAAT
1 ATAATAAAAAAT
2980813 CTTAGGAAGA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAATAAAAAATA
Found at i:2992043 original size:60 final size:60
Alignment explanation
Indices: 2991970--2992096 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
2991960 CTAAAACTAA
* * ** * *
2991970 AAAAAATCAATAAATTTAGC-CATTAATGTTTACAAAATTTGTCATTTGAGTTTGAATTCT
1 AAAAATTCAATAAATTTAGCGC-TCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
* *
2992030 AAAAATTCAATAAATTTAGCGCTCAACATTTACAAAATTTATCATTTTAATTTTAATTCT
1 AAAAATTCAATAAATTTAGCGCTCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
2992090 AAAAATT
1 AAAAATT
2992097 TTAAAAAAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (60 bp):
AAAAATTCAATAAATTTAGCGCTCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
Found at i:2992955 original size:60 final size:60
Alignment explanation
Indices: 2992823--2992939 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
2992813 TTAGAAACAA
* * * * *
2992823 AACTAAATTAACAAATTTTATAAATGTTGAGGGCTAAATCTATTGATTTTTTTGAATTAG
1 AACTAAATTGATAAATTTTATAAATATTGAGGGCTAAATCTATTGATATTTTTAAATTAG
* * *
2992883 AACTAAATTGATAAATTTTATAAATATTGAGGGCTAATTTTTTTGA-ATTTTTAAATT
1 AACTAAATTGATAAATTTTATAAATATTGAGGGCTAAATCTATTGATATTTTTAAATT
2992940 TAGGATCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 9 0.18
60 40 0.82
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (60 bp):
AACTAAATTGATAAATTTTATAAATATTGAGGGCTAAATCTATTGATATTTTTAAATTAG
Found at i:2996806 original size:18 final size:18
Alignment explanation
Indices: 2996780--2996816 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2996770 CTTAGATGGG
*
2996780 GGTGGTGGTGACGGTGGC
1 GGTGATGGTGACGGTGGC
*
2996798 GGTGATGGTGATGGTGGC
1 GGTGATGGTGACGGTGGC
2996816 G
1 G
2996817 ATGTTGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.59, T:0.24
Consensus pattern (18 bp):
GGTGATGGTGACGGTGGC
Found at i:2996824 original size:21 final size:20
Alignment explanation
Indices: 2996785--2996840 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
2996775 ATGGGGGTGG
2996785 TGGTGACGGTGGCG--GTGA
1 TGGTGACGGTGGCGATGTGA
*
2996803 TGGTGATGGTGGCGATGTTGA
1 TGGTGACGGTGGCGATG-TGA
**
2996824 TGGTGGGGGTGGCGATG
1 TGGTGACGGTGGCGATG
2996841 GAGTTGACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.41
20 1 0.03
21 18 0.56
ACGTcount: A:0.11, C:0.07, G:0.55, T:0.27
Consensus pattern (20 bp):
TGGTGACGGTGGCGATGTGA
Found at i:2996859 original size:3 final size:3
Alignment explanation
Indices: 2996851--2996903 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
2996841 GAGTTGACTC
* * *
2996851 TGG TGG TGG TGG TGG TGA TGG TGA TGG TGA TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
2996899 TGG TG
1 TGG TG
2996904 AAGAAGAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.06, C:0.00, G:0.60, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:3000450 original size:21 final size:21
Alignment explanation
Indices: 3000409--3000450 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3000399 TGTTGAAGTC
* *
3000409 GTAATTAGTTATTAGTTGATT
1 GTAATTAGTTATCAGTCGATT
3000430 GTAATTA-TTATCAGTACGATT
1 GTAATTAGTTATCAGT-CGATT
3000451 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (21 bp):
GTAATTAGTTATCAGTCGATT
Found at i:3001471 original size:42 final size:42
Alignment explanation
Indices: 3001412--3001497 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
3001402 TCAGGTATAT
3001412 ATATATATATACTGAATTTCTGAATTCTGTTTAAAACCATCA
1 ATATATATATACTGAATTTCTGAATTCTGTTTAAAACCATCA
3001454 ATATATATATACTGAATTTCTGAATTCTGTTTAAAACCATCA
1 ATATATATATACTGAATTTCTGAATTCTGTTTAAAACCATCA
3001496 AT
1 AT
3001498 CAAACCAGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (42 bp):
ATATATATATACTGAATTTCTGAATTCTGTTTAAAACCATCA
Found at i:3008821 original size:20 final size:20
Alignment explanation
Indices: 3008796--3008841 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 20
3008786 CTGTAGTAAG
3008796 ACATACCTGTTGAAAGAGCC
1 ACATACCTGTTGAAAGAGCC
3008816 ACATACCTGTTGAAAGAGCC
1 ACATACCTGTTGAAAGAGCC
3008836 ATCATA
1 A-CATA
3008842 AGGAAATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
ACATACCTGTTGAAAGAGCC
Found at i:3014153 original size:20 final size:20
Alignment explanation
Indices: 3014128--3014168 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3014118 AACTTGAGTA
*
3014128 CCAAACCCTAAATC-AAAACC
1 CCAAA-CCTAAACCTAAAACC
3014148 CCAAACCTAAACCTAAAACC
1 CCAAACCTAAACCTAAAACC
3014168 C
1 C
3014169 TAAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.49, C:0.41, G:0.00, T:0.10
Consensus pattern (20 bp):
CCAAACCTAAACCTAAAACC
Found at i:3018647 original size:18 final size:18
Alignment explanation
Indices: 3018605--3018647 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3018595 TTAGGATTCA
3018605 ATGATTTTTGAGGTTTAGG
1 ATGA-TTTTGAGGTTTAGG
3018624 ATTGATTTTGA-GTTTAGGG
1 A-TGATTTTGAGGTTTA-GG
3018643 ATGAT
1 ATGAT
3018648 AATGGAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.41
19 10 0.45
20 3 0.14
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (18 bp):
ATGATTTTGAGGTTTAGG
Found at i:3022720 original size:35 final size:35
Alignment explanation
Indices: 3022630--3022720 Score: 80
Period size: 35 Copynumber: 2.6 Consensus size: 35
3022620 TTATAACATG
** *
3022630 TAAATTATTTTTTATAATA-AAATTTTTAAGATTTA
1 TAAATTA-TTTTTATAATATAAATTTAAAAGATGTA
* * *
3022665 AATAATATATTTTTGT--TATAAATTTAAAATATGTA
1 TA-AAT-TATTTTTATAATATAAATTTAAAAGATGTA
3022700 TAAATTATTTTTATAATATAA
1 TAAATTATTTTTATAATATAA
3022721 TTTTTTTGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
33 8 0.19
34 5 0.12
35 19 0.44
36 9 0.21
37 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
TAAATTATTTTTATAATATAAATTTAAAAGATGTA
Found at i:3023981 original size:3 final size:3
Alignment explanation
Indices: 3023973--3024002 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3023963 ACTCCTTGGC
3023973 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3024003 ATACCTATAC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3024043 original size:14 final size:14
Alignment explanation
Indices: 3024024--3024063 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3024014 TTGATTGTCA
3024024 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
3024038 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
3024052 GGAAAATGTTTT
1 GTAAAATGTTTT
3024064 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:3024072 original size:20 final size:20
Alignment explanation
Indices: 3024047--3024086 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3024037 CGTAAAATGA
*
3024047 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3024067 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3024087 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3024076 original size:34 final size:35
Alignment explanation
Indices: 3024032--3024098 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3024022 CAGTAAAATG
*
3024032 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3024066 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3024099 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3024102 original size:14 final size:15
Alignment explanation
Indices: 3024026--3024102 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3024016 GATTGTCAGT
* *
3024026 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
3024040 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
3024054 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
3024074 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
3024089 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3024103 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:3025472 original size:35 final size:36
Alignment explanation
Indices: 3025426--3025494 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
3025416 TGTCAATCAT
3025426 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
*
3025461 TTCAATATCCAACAAGGTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
3025495 TCTAACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:3025492 original size:27 final size:28
Alignment explanation
Indices: 3025462--3025531 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
3025452 AATAATAAAT
*
3025462 TCAATATCCAACAAGGTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
3025489 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
3025517 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
3025532 CTATAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:3028679 original size:7 final size:7
Alignment explanation
Indices: 3028667--3028692 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3028657 TCTACTTCAC
3028667 CAAAATG
1 CAAAATG
3028674 CAAAATG
1 CAAAATG
3028681 CAAAATG
1 CAAAATG
3028688 CAAAA
1 CAAAA
3028693 AAAAAAACAC
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:0.62, C:0.15, G:0.12, T:0.12
Consensus pattern (7 bp):
CAAAATG
Found at i:3038488 original size:22 final size:20
Alignment explanation
Indices: 3038459--3038498 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3038449 TTAAGAGGTT
*
3038459 TAATAGAAATTTTTAAAAAAG
1 TAATAG-AATTTTCAAAAAAG
3038480 TAATGAGAATTTTCAAAAA
1 TAAT-AGAATTTTCAAAAA
3038499 TTTTGAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
TAATAGAATTTTCAAAAAAG
Found at i:3038602 original size:60 final size:60
Alignment explanation
Indices: 3038487--3038602 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
3038477 AAGTAATGAG
* * * ** *
3038487 AATTTTCAAAAATTTTGAAGGTTTAATTAATATTTCAAAACTTTTGTAGAACTTAACTAA
1 AATTTTCAAAAAATTTGAAGGTTTAAGTAACATTTCAAAACAATTGAAGAACTTAACTAA
*
3038547 AATTTTCAAAAAATTT-AAGGGTTTAAGTAACATTTTCAAAA-AATTGAAGAGCTTAA
1 AATTTTCAAAAAATTTGAA-GGTTTAAGTAACA-TTTCAAAACAATTGAAGAACTTAA
3038603 GCCCCAAGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.04
60 37 0.79
61 8 0.17
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (60 bp):
AATTTTCAAAAAATTTGAAGGTTTAAGTAACATTTCAAAACAATTGAAGAACTTAACTAA
Found at i:3038603 original size:30 final size:30
Alignment explanation
Indices: 3038538--3038603 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
3038528 TTTTGTAGAA
* * *
3038538 CTTAACTAAAATTTTCAAAAAATTTAAGGG
1 CTTAAGTAAAATTTTCAAAAAATTGAAGAG
* *
3038568 TTTAAGTAACATTTTCAAAAAATTGAAGAG
1 CTTAAGTAAAATTTTCAAAAAATTGAAGAG
3038598 CTTAAG
1 CTTAAG
3038604 CCCCAAGCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (30 bp):
CTTAAGTAAAATTTTCAAAAAATTGAAGAG
Found at i:3044984 original size:34 final size:34
Alignment explanation
Indices: 3044909--3044986 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 34
3044899 ACAATAATAA
* *
3044909 ATATTTTATAAAACAAATTTATATTAATATTTAT
1 ATATTTTATAAAACAAATTTAAATAAATATTTAT
**
3044943 ATATTTTATAAATTAAATTTAAATAAA-ATATTAT
1 ATATTTTATAAAACAAATTTAAATAAATAT-TTAT
3044977 -TATTTT-TAAA
1 ATATTTTATAAA
3044987 CAATAGCTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 4 0.10
33 8 0.21
34 27 0.69
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (34 bp):
ATATTTTATAAAACAAATTTAAATAAATATTTAT
Found at i:3045824 original size:24 final size:23
Alignment explanation
Indices: 3045797--3045857 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
3045787 AATTTTAACA
3045797 AATAAAAAATATTAAGTT-AAAATT
1 AATAAAAAATATT--GTTAAAAATT
* *
3045821 AATATAAATATATTTTTAAAAATT
1 AATA-AAAAATATTGTTAAAAATT
3045845 AA-AAAAAATATTG
1 AATAAAAAATATTG
3045858 ACGGGTCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 8 0.26
23 3 0.10
24 12 0.39
25 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (23 bp):
AATAAAAAATATTGTTAAAAATT
Found at i:3048770 original size:16 final size:17
Alignment explanation
Indices: 3048741--3048787 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
3048731 TCCGCCTATA
3048741 TTAAT-TTTTAATTTT-T
1 TTAATATTTT-ATTTTAT
3048757 TTAATATTTTATTTTAT
1 TTAATATTTTATTTTAT
3048774 TT--TATTTTATTTTA
1 TTAATATTTTATTTTA
3048788 AAATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.41
16 10 0.34
17 7 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTAATATTTTATTTTAT
Found at i:3048771 original size:5 final size:5
Alignment explanation
Indices: 3048761--3048787 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3048751 ATTTTTTTAA
3048761 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
3048788 AAATTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:3048820 original size:17 final size:17
Alignment explanation
Indices: 3048798--3048840 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3048788 AAATTTATAT
*
3048798 TTTTTATTTATTGGAAG
1 TTTTTATTTATTAGAAG
* *
3048815 TTTTTATATATTATAAG
1 TTTTTATTTATTAGAAG
3048832 TTTTT-TTTA
1 TTTTTATTTA
3048841 ATGTGTTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
TTTTTATTTATTAGAAG
Found at i:3055000 original size:20 final size:19
Alignment explanation
Indices: 3054975--3055018 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
3054965 TATAATTATT
3054975 TTTAA-GTTCTTTCTTTTTAA
1 TTTAAGGTT-TTT-TTTTTAA
3054995 TTTAAGGGTTTTTTTTTTAA
1 TTTAA-GGTTTTTTTTTTAA
3055015 TTTA
1 TTTA
3055019 GTCTTAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 16 0.73
21 3 0.14
22 3 0.14
ACGTcount: A:0.20, C:0.05, G:0.09, T:0.66
Consensus pattern (19 bp):
TTTAAGGTTTTTTTTTTAA
Found at i:3055687 original size:13 final size:13
Alignment explanation
Indices: 3055671--3055710 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3055661 TTTAAACCAA
3055671 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
3055684 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
3055697 ATTTTTCAAAAGC
1 ACTTTTCAAAAGC
3055710 A
1 A
3055711 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3056149 original size:15 final size:16
Alignment explanation
Indices: 3056118--3056151 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3056108 TTCCAAAACA
3056118 TAAAATGTGAATCAAG
1 TAAAATGTGAATCAAG
*
3056134 TAAAATGT-ATTCAAG
1 TAAAATGTGAATCAAG
3056149 TAA
1 TAA
3056152 GCTCATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (16 bp):
TAAAATGTGAATCAAG
Found at i:3093106 original size:21 final size:21
Alignment explanation
Indices: 3093077--3093116 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3093067 ACGGAAATTG
*
3093077 AAAAGGTAATACATTTTCCTT
1 AAAAGGTAACACATTTTCCTT
* *
3093098 AAAATGTAACCCATTTTCC
1 AAAAGGTAACACATTTTCC
3093117 CTTGTTTTGG
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:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAAGGTAACACATTTTCCTT
Found at i:3114560 original size:17 final size:17
Alignment explanation
Indices: 3114538--3114571 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3114528 ATTAAATATT
*
3114538 AAATTATTTAAAAAATA
1 AAATTATGTAAAAAATA
*
3114555 AAATTATGTAACAAATA
1 AAATTATGTAAAAAATA
3114572 TATCTATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATTATGTAAAAAATA
Found at i:3115543 original size:21 final size:22
Alignment explanation
Indices: 3115519--3115568 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
3115509 CATTATTTTT
*
3115519 AATCTCACT-GCTACAGTATCC
1 AATCTCACTAGCTACAGTAACC
*
3115540 AATCTCA-TAGCTACAGTAACT
1 AATCTCACTAGCTACAGTAACC
3115561 AATCTCAC
1 AATCTCAC
3115569 CGTCACCGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.34, C:0.30, G:0.08, T:0.28
Consensus pattern (22 bp):
AATCTCACTAGCTACAGTAACC
Found at i:3125814 original size:23 final size:23
Alignment explanation
Indices: 3125788--3125860 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
3125778 AGTGCCACAC
*
3125788 TGATATGTAGCCGAAGTTACCAT
1 TGATATGTAGCCGAAGCTACCAT
* *
3125811 TGATATGTAGCCGTAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAT
* * *
3125834 TGAAATTTAACCGAAGCTACCAT
1 TGATATGTAGCCGAAGCTACCAT
3125857 TGAT
1 TGAT
3125861 CAATAACATT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAT
Found at i:3127762 original size:21 final size:21
Alignment explanation
Indices: 3127738--3127779 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3127728 CTTTTTGTTC
*
3127738 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
3127759 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
3127780 TACTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:3129784 original size:21 final size:21
Alignment explanation
Indices: 3129743--3129785 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3129733 AAACTTTCAT
*
3129743 TGTACAAATTAATTTTTTTTA
1 TGTACAAATTAATTTTATTTA
*
3129764 TGTATAAATTTAA-TTTATTTA
1 TGTACAAA-TTAATTTTATTTA
3129785 T
1 T
3129786 TGAATAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (21 bp):
TGTACAAATTAATTTTATTTA
Found at i:3130694 original size:2 final size:2
Alignment explanation
Indices: 3130687--3130721 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3130677 CTTTCAACGC
3130687 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3130722 AATATAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3130990 original size:2 final size:2
Alignment explanation
Indices: 3130983--3131014 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3130973 AAATCTTTGA
3130983 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
3131015 CTCAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3143546 original size:30 final size:30
Alignment explanation
Indices: 3143512--3143572 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3143502 TTAATTTCTG
* * *
3143512 AGTTTTGGGGTAAAAGTGTAAATATGCAAA
1 AGTTTAGGGGCAAAACTGTAAATATGCAAA
* *
3143542 AGTTTAGGGGCAAAACTGTAATTTTGCAAA
1 AGTTTAGGGGCAAAACTGTAAATATGCAAA
3143572 A
1 A
3143573 ATCGAGTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
AGTTTAGGGGCAAAACTGTAAATATGCAAA
Found at i:3144023 original size:50 final size:50
Alignment explanation
Indices: 3143965--3144158 Score: 178
Period size: 50 Copynumber: 3.9 Consensus size: 50
3143955 CATTGAGATT
*
3143965 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCAAG
** * * * * * *
3144015 ATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATAGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCAAG
** * * *
3144065 ATGAGAACTCCCATGTAAGACCATATATGGGATATGGCATTGGCAGTACAAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA--CCAAG
** * * *
3144117 A--A-ACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
3144159 TGTTATTATC
Statistics
Matches: 114, Mismatches: 28, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
49 33 0.29
50 78 0.68
52 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCAAG
Found at i:3150768 original size:2 final size:2
Alignment explanation
Indices: 3150761--3150789 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3150751 CAATAATAGA
3150761 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3150790 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3152592 original size:19 final size:20
Alignment explanation
Indices: 3152543--3152592 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
3152533 TAAAATATAA
* *
3152543 ATTTTGGAATTTTTATAAAT
1 ATTTTAGAATTTTGATAAAT
*
3152563 ATTTTAAAATTTTGA-AAATT
1 ATTTTAGAATTTTGATAAA-T
3152583 ATTTT-GAATT
1 ATTTTAGAATT
3152593 ATTTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTTTAGAATTTTGATAAAT
Found at i:3153598 original size:33 final size:33
Alignment explanation
Indices: 3153561--3153634 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 33
3153551 TTATGTTAGT
*
3153561 GTTTTATAAAATTAAATCAAATATATTTATAAA
1 GTTTTATAAAATTAAATCAAAAATATTTATAAA
** *
3153594 G-TTT-TAAAATTGTATTAAAAATATTTATAAA
1 GTTTTATAAAATTAAATCAAAAATATTTATAAA
* *
3153625 ATCTTATAAA
1 GTTTTATAAA
3153635 GTTGAGAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 23 0.70
32 5 0.15
33 5 0.15
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (33 bp):
GTTTTATAAAATTAAATCAAAAATATTTATAAA
Found at i:3154456 original size:21 final size:21
Alignment explanation
Indices: 3154432--3154471 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3154422 TTTTTTTAAA
3154432 AAGAATAAAAAAT-TAAAATTC
1 AAGAA-AAAAAATATAAAATTC
*
3154453 AAGAAAAAATATATAAAAT
1 AAGAAAAAAAATATAAAAT
3154472 GTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AAGAAAAAAAATATAAAATTC
Found at i:3155423 original size:26 final size:26
Alignment explanation
Indices: 3155394--3155443 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3155384 CAGTGGTTGG
* * *
3155394 TTTGATTAATTAATTCTATTAATTAA
1 TTTGATCAACTAATTCCATTAATTAA
*
3155420 TTTGATCAACTGATTCCATTAATT
1 TTTGATCAACTAATTCCATTAATT
3155444 GTTTATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (26 bp):
TTTGATCAACTAATTCCATTAATTAA
Found at i:3157158 original size:36 final size:36
Alignment explanation
Indices: 3157117--3157189 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
3157107 TTAATGCACT
* *
3157117 TTAATTCACCTCATTTTATATTTATAACGATACCAA
1 TTAATTCACCTCATTTTACATTCATAACGATACCAA
*
3157153 TTAATTCACGTCATTTTACATTCATAACGATACCAA
1 TTAATTCACCTCATTTTACATTCATAACGATACCAA
3157189 T
1 T
3157190 ATCAATCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.40
Consensus pattern (36 bp):
TTAATTCACCTCATTTTACATTCATAACGATACCAA
Found at i:3159408 original size:29 final size:29
Alignment explanation
Indices: 3159375--3159433 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3159365 ATCACTCAAT
3159375 TTAAAAGTTATAAAAGAATCATTAAACTA
1 TTAAAAGTTATAAAAGAATCATTAAACTA
3159404 TTAAAAGTTATAAAAGAATCATTAAACTA
1 TTAAAAGTTATAAAAGAATCATTAAACTA
3159433 T
1 T
3159434 CCTATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (29 bp):
TTAAAAGTTATAAAAGAATCATTAAACTA
Found at i:3159919 original size:14 final size:14
Alignment explanation
Indices: 3159896--3159925 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3159886 TGGGTGTAGT
3159896 TTACCCTTGAAATA
1 TTACCCTTGAAATA
*
3159910 TTACCTTTGAAATA
1 TTACCCTTGAAATA
3159924 TT
1 TT
3159926 TCATAATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (14 bp):
TTACCCTTGAAATA
Found at i:3161969 original size:16 final size:16
Alignment explanation
Indices: 3161945--3162009 Score: 105
Period size: 16 Copynumber: 4.1 Consensus size: 16
3161935 TTCGCTGTAT
3161945 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
3161961 TGGATTAGAGGCGTAA
1 TGGAATAGAGGCGTAA
3161977 T-GAATTAGAGGCGTAA
1 TGGAA-TAGAGGCGTAA
3161993 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
3162009 T
1 T
3162010 AGCAAATCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.04
16 40 0.89
17 3 0.07
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.23
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:3162050 original size:45 final size:44
Alignment explanation
Indices: 3161989--3162078 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
3161979 AATTAGAGGC
3161989 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
3162034 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
3162078 G
1 G
3162079 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 23 0.55
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:3162260 original size:16 final size:16
Alignment explanation
Indices: 3162223--3162264 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3162213 TTAATCATAT
*
3162223 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3162239 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3162254 TTAAAATATAT
1 TTAAAATATAT
3162265 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3162271 original size:14 final size:15
Alignment explanation
Indices: 3162232--3162273 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3162222 TTTAAACATA
*
3162232 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3162247 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3162261 A-TATAATTTAATA
1 ATTATAATTAAATA
3162274 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3162323 original size:61 final size:61
Alignment explanation
Indices: 3162258--3162445 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
3162248 TTATAATTAA
3162258 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
* * * * * * * * *
3162319 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATAAATTTACTCA-AATCAT
* *
3162378 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
3162439 AATATAT
1 AATATAT
3162446 GATACTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 31 0.32
60 23 0.24
61 37 0.38
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
Found at i:3162369 original size:120 final size:121
Alignment explanation
Indices: 3162226--3162518 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 121
3162216 ATCATATTTA
3162226 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
3162291 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
*
3162346 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
3162411 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* * *
3162467 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
3162519 TAAAATAATT
Statistics
Matches: 165, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 163 0.99
121 2 0.01
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:3162382 original size:59 final size:59
Alignment explanation
Indices: 3162226--3162522 Score: 184
Period size: 59 Copynumber: 5.0 Consensus size: 59
3162216 ATCATATTTA
* * * *
3162226 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAAT
* * * * *
3162285 AATCA-ATATTCTTATATAAATTTACTCA-AATCATAATATATGATACT-ATAAAA-TATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATGAT-CTAATAAAATTATAAA-T
* * * *
3162346 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAAT
* * * * * * *
3162405 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAA-GATAATT
1 AACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATGAT-CTAATAAAATTATAA-A
3162465 T
59 T
* * *
3162466 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT-TAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAA
3162523 ATAATTATAA
Statistics
Matches: 177, Mismatches: 39, Indels: 45
0.68 0.15 0.17
Matches are distributed among these distances:
57 10 0.06
58 11 0.06
59 56 0.32
60 28 0.16
61 51 0.29
62 12 0.07
63 9 0.05
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (59 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAAT
Found at i:3162391 original size:14 final size:15
Alignment explanation
Indices: 3162342--3162393 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3162332 ATAAAATATA
3162342 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3162357 TATTAAATATATTAT
1 AATTAAATATATTAT
3162372 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3162385 AATTTAATA
1 AATTAAATA
3162394 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3162566 original size:47 final size:46
Alignment explanation
Indices: 3162500--3162666 Score: 146
Period size: 47 Copynumber: 3.6 Consensus size: 46
3162490 TTAATTAAAA
*
3162500 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTATCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTATCT
* * * * * *
3162547 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
* * * *
3162592 TA-AT-AATAATATATAATTTCATAA-AATTCTTAATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTATCT
*
3162638 TATATGAATTTATACAATTTAAAATAATT
1 TATATGAATTTATATAATTTAAAATAATT
3162667 CGGATCAATC
Statistics
Matches: 92, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
43 3 0.03
44 15 0.16
45 14 0.15
46 13 0.14
47 40 0.43
48 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
Found at i:3162588 original size:26 final size:28
Alignment explanation
Indices: 3162559--3162630 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
3162549 TATGAATTTG
*
3162559 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
3162585 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
3162613 TAAAATTCTTAATAATAA
1 TATAA-T-TTAATAATAA
3162631 ATTTTCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 12 0.31
29 1 0.03
30 10 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:3162827 original size:22 final size:22
Alignment explanation
Indices: 3162799--3162843 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3162789 ACTAAGCTTG
3162799 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
3162821 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
3162843 A
1 A
3162844 GTTAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTCATTAAATTACTTTCAA
Found at i:3177412 original size:17 final size:16
Alignment explanation
Indices: 3177386--3177434 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
3177376 AATATTTTTT
3177386 AAAT-TTTTTTTATAA
1 AAATATTTTTTTATAA
3177401 AGAATATTTTTTTA-AA
1 A-AATATTTTTTTATAA
3177417 AAATATATCTTTTTATAA
1 AAATAT-T-TTTTTATAA
3177435 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.21
16 7 0.24
17 14 0.48
18 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
AAATATTTTTTTATAA
Found at i:3177439 original size:17 final size:17
Alignment explanation
Indices: 3177392--3177441 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
3177382 TTTTAAATTT
3177392 TTTTTATAAAGAATAT-T-
1 TTTTTA-AAA-AATATATC
3177409 TTTTTAAAAAATATATC
1 TTTTTAAAAAATATATC
* *
3177426 TTTTTATAATATATAT
1 TTTTTAAAAAATATAT
3177442 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 5 0.17
16 4 0.14
17 20 0.69
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTTTAAAAAATATATC
Found at i:3180088 original size:170 final size:171
Alignment explanation
Indices: 3179793--3180108 Score: 483
Period size: 170 Copynumber: 1.9 Consensus size: 171
3179783 GACCATCAGG
* *
3179793 AACAGTGAGCGGCAGCAACAGAAAGTTCACATCAAAGATAAATGAAATCCATATACGGTAAGTAT
1 AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
*
3179858 AATCATAATTAAAAATGAAATCCAAATATGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
66 AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
*
3179923 AAGATTTAATC-TAAATCCAATTAATCTTAAATTGGAAATGC
131 AA-AGTTAATCTTAAATCCAATTAATCTTAAATTGGAAATGC
* * * *
3179964 AACAG-GAGTGGCAGCAACAGAAAGTTAATATCAAAGAAAAATGAAATCCATATATGGTGAGTAT
1 AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
* ** ** *
3180028 AATCATAATTAAAACTGAAATCCGTATACGCTTTTTTGAATGACCAAACCTCACTAAAAGGGAAA
66 AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
3180093 AAAGTTAATCTTAAAT
131 AAAGTTAATCTTAAAT
3180109 TAAGATGTAG
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
169 7 0.05
170 118 0.91
171 5 0.04
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (171 bp):
AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
AAAGTTAATCTTAAATCCAATTAATCTTAAATTGGAAATGC
Found at i:3181704 original size:143 final size:143
Alignment explanation
Indices: 3181439--3181708 Score: 344
Period size: 143 Copynumber: 1.9 Consensus size: 143
3181429 CTCAGATGTA
* ** * * *
3181439 GTTCTTCATCTTAGTTTCCTTGAGTAAATCTTTATCTTTGATTAAACCACGCACCAAATTAGTAT
1 GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
* * *** * * * *
3181504 TAGAGCCTCCTTTTTGGCACTTGTGATGGCGGATAACAATCATTCACATGGTATTAGAAGGTATT
66 CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACATGATATTAGAAGGTATT
3181569 ACTCTGAATTGTT
131 ACTCTGAATTGTT
* * *
3181582 GTTCTTCATCTCAACTTCCTT-AGTAATTTCTTTATCTTTAATTAAACCGCACACCAAATTGGCA
1 GTTCTTCATCTCAACTTCCTTGAGTAA-ATCTTTATCTTTAATTAAACCACACACCAAATTAGCA
* *
3181646 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCCTTCACATGATCTTAGAAGGT
65 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACATGATATTAGAAGGT
3181709 TGGAAGAGTT
Statistics
Matches: 106, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
142 5 0.05
143 101 0.95
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (143 bp):
GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACATGATATTAGAAGGTATT
ACTCTGAATTGTT
Found at i:3192489 original size:26 final size:29
Alignment explanation
Indices: 3192446--3192502 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 29
3192436 CATAAAACCC
3192446 AATTACAACCCAAACCC-AAGACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
* *
3192474 AATTA-AA-CCAAGCCCAAATACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
3192501 AA
1 AA
3192503 CCCAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 14 0.54
28 5 0.19
ACGTcount: A:0.53, C:0.35, G:0.04, T:0.09
Consensus pattern (29 bp):
AATTACAACCCAAACCCAAAGACCCAACA
Found at i:3192842 original size:11 final size:11
Alignment explanation
Indices: 3192814--3192861 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
3192804 AAAGGTCTTT
*
3192814 TTTTA-TTTCA
1 TTTTATTTTTA
*
3192824 TTTATATTTTTG
1 TTT-TATTTTTA
3192836 TTTTATTTTTA
1 TTTTATTTTTA
3192847 TTTTATTTTTTA
1 TTTTA-TTTTTA
3192859 TTT
1 TTT
3192862 CGAAATAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 3 0.09
11 14 0.44
12 15 0.47
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:3192843 original size:17 final size:17
Alignment explanation
Indices: 3192813--3192861 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3192803 AAAAGGTCTT
*
3192813 TTTTTATTTCATTTATA
1 TTTTTATTTTATTTATA
* *
3192830 TTTTTGTTTTATTTTTA
1 TTTTTATTTTATTTATA
*
3192847 TTTTATTTTTTATTT
1 TTTT-TATTTTATTT
3192862 CGAAATAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTATTTTATTTATA
Found at i:3192856 original size:12 final size:12
Alignment explanation
Indices: 3192824--3192861 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3192814 TTTTATTTCA
*
3192824 TTTATATTTTTGT
1 TTTAT-TTTTTAT
3192837 TTTA-TTTTTAT
1 TTTATTTTTTAT
3192848 TTTATTTTTTAT
1 TTTATTTTTTAT
3192860 TT
1 TT
3192862 CGAAATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 9 0.39
13 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:3193708 original size:3 final size:3
Alignment explanation
Indices: 3193559--3193693 Score: 125
Period size: 3 Copynumber: 45.3 Consensus size: 3
3193549 TTAGCAGCAA
* * * * * *
3193559 TAT TAT T-T ATAT TAT TAA TAG TAT TAT TAT TAT TAA TGT CAT CAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** *
3193604 TGC TA- TAG TAT TAT TAT CT-T TAT TACT T-T TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
3193648 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3193694 GTTGCATTTA
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
2 6 0.05
3 100 0.91
4 4 0.04
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3193991 original size:2 final size:2
Alignment explanation
Indices: 3193984--3194008 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3193974 TTTTTATAAG
3193984 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3194009 TTGTACGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3197098 original size:24 final size:24
Alignment explanation
Indices: 3197066--3197118 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3197056 ACTAAGGTTT
3197066 AACA-TATACTTCAAGAGTATGTA
1 AACATTATACTTCAAGAGTATGTA
3197089 AACATTATACTTCAAGAGTATGTA
1 AACATTATACTTCAAGAGTATGTA
3197113 AACATT
1 AACATT
3197119 CTCTTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (24 bp):
AACATTATACTTCAAGAGTATGTA
Found at i:3198980 original size:2 final size:2
Alignment explanation
Indices: 3198973--3198997 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3198963 AAGTGTGCTT
3198973 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3198998 TATTTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3209170 original size:21 final size:20
Alignment explanation
Indices: 3209146--3209190 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3209136 AAGAATATTA
*
3209146 TATTAATAATAATAATAATTT
1 TATTAATAAT-ATAATAATAT
*
3209167 TATTTAATAATTTAATAATAT
1 TA-TTAATAATATAATAATAT
3209188 TAT
1 TAT
3209191 CTTATACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.05
21 12 0.57
22 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAATAATATAATAATAT
Found at i:3213112 original size:16 final size:15
Alignment explanation
Indices: 3213087--3213116 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3213077 AAAAAATAAC
3213087 AAAATTTGAGGGAAT
1 AAAATTTGAGGGAAT
3213102 AAAAGTTTGAGGGAA
1 AAAA-TTTGAGGGAA
3213117 AGTAAATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (15 bp):
AAAATTTGAGGGAAT
Found at i:3213235 original size:31 final size:29
Alignment explanation
Indices: 3213200--3213258 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3213190 GGAGGTGGGA
*
3213200 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTT-GGGGAAAAG
* *
3213231 TGGGAGGGAGTAAAAATTTTGGGGAAAA
1 TGGGAGAGAATAAAAATTTTGGGGAAAA
3213259 ATAAAAGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 13 0.52
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.20
Consensus pattern (29 bp):
TGGGAGAGAATAAAAATTTTGGGGAAAAG
Found at i:3213486 original size:9 final size:9
Alignment explanation
Indices: 3213472--3213508 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3213462 TATAGTTTGA
3213472 TATTCGAAT
1 TATTCGAAT
3213481 TATTCGAAT
1 TATTCGAAT
*
3213490 TATTCGAGT
1 TATTCGAAT
3213499 TATTCGAAT
1 TATTCGAAT
3213508 T
1 T
3213509 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3213899 original size:19 final size:17
Alignment explanation
Indices: 3213875--3213909 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3213865 TATTATATGA
3213875 TGAATTGACGAATTGATGT
1 TGAATTGA-GAA-TGATGT
3213894 TGAATTGAGAATGATG
1 TGAATTGAGAATGATG
3213910 GAATGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (17 bp):
TGAATTGAGAATGATGT
Found at i:3216657 original size:61 final size:59
Alignment explanation
Indices: 3216548--3216664 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 59
3216538 ATCACTCTAA
3216548 TATTAAAATAGTATAATACTTATTAAAGATAAATATTAGAATAAATTTAATATTAAATC
1 TATTAAAATAGTATAATACTTATTAAAGATAAATATTAGAATAAATTTAATATTAAATC
* *
3216607 TATTAAATTAGTATAATATTTATATATAAGATAAATATTA-AACTAAATTTAATATTAA
1 TATTAAAATAGTATAATACTTAT-TA-AAGATAAATATTAGAA-TAAATTTAATATTAA
3216665 GATAATCACT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
59 21 0.40
60 4 0.08
61 28 0.53
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (59 bp):
TATTAAAATAGTATAATACTTATTAAAGATAAATATTAGAATAAATTTAATATTAAATC
Found at i:3225333 original size:3 final size:3
Alignment explanation
Indices: 3225325--3225360 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3225315 CCGTCATGGA
*
3225325 GAT GAT GAT GTT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3225361 TGGTTCAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (3 bp):
GAT
Found at i:3233186 original size:40 final size:40
Alignment explanation
Indices: 3233122--3233212 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
3233112 ATAGTTGGGG
* * * **
3233122 AAAACGTGTCCAGCGAGGCGCGCTTTCCTGCACAGTTTGC
1 AAAACGCGTCCAGCGAGGCACGCTTTCCTGCACAATCAGC
* * *
3233162 AAAACGCGTCCAGTGAGGTACGCTTTCTTGCACAATCAGC
1 AAAACGCGTCCAGCGAGGCACGCTTTCCTGCACAATCAGC
3233202 AAAACGC-TCCA
1 AAAACGCGTCCA
3233213 ATAGGACACG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (40 bp):
AAAACGCGTCCAGCGAGGCACGCTTTCCTGCACAATCAGC
Found at i:3234455 original size:24 final size:24
Alignment explanation
Indices: 3234417--3234498 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
3234407 AATCTTCCAG
**
3234417 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTACTTATTTGTTTCAA
*
3234441 TTTAACTCTACTTATTTGTTTCAA
1 TTAAACTCTACTTATTTGTTTCAA
** *
3234465 TTAAACTCCGCTTATTTATTTCAA
1 TTAAACTCTACTTATTTGTTTCAA
*
3234489 TCAAACTCTA
1 TTAAACTCTA
3234499 ATTAGTCTAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (24 bp):
TTAAACTCTACTTATTTGTTTCAA
Found at i:3235351 original size:14 final size:14
Alignment explanation
Indices: 3235332--3235358 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3235322 TGTGTTGTTT
3235332 ACACCATTATCAAA
1 ACACCATTATCAAA
3235346 ACACCATTATCAA
1 ACACCATTATCAA
3235359 GCCACTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (14 bp):
ACACCATTATCAAA
Found at i:3236402 original size:2 final size:2
Alignment explanation
Indices: 3236395--3236423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3236385 AAAAACATTC
3236395 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 A
3236424 CCACTGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3237878 original size:15 final size:15
Alignment explanation
Indices: 3237858--3237888 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3237848 CATCAATGAA
3237858 AAAATGCACATGTTT
1 AAAATGCACATGTTT
3237873 AAAATGCACATGTTT
1 AAAATGCACATGTTT
3237888 A
1 A
3237889 TGCCAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
AAAATGCACATGTTT
Found at i:3244285 original size:74 final size:72
Alignment explanation
Indices: 3244132--3244276 Score: 236
Period size: 72 Copynumber: 2.0 Consensus size: 72
3244122 TCTCGGATTT
* * *
3244132 AAAAAATGGATCATGCCTAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCATTTAAAA
1 AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCAAGATCATTTAAAA
3244197 CTTGAGA
66 CTTGAGA
*
3244204 AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTCTCTTCTTAATTCCCAAGATCGTTTAA
1 AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCT-T-TTCTTAATTCCCAAGATCATTTAA
3244269 AACTTGAG
64 AACTTGAG
3244277 TTTGAAAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 36 0.54
73 1 0.01
74 30 0.45
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (72 bp):
AAAAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCAAGATCATTTAAAA
CTTGAGA
Found at i:3244523 original size:13 final size:13
Alignment explanation
Indices: 3244505--3244529 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3244495 ATAGCAACAA
3244505 AAATAAATAAAAT
1 AAATAAATAAAAT
3244518 AAATAAATAAAA
1 AAATAAATAAAA
3244530 GGGATAAATC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:3244751 original size:20 final size:21
Alignment explanation
Indices: 3244681--3244751 Score: 63
Period size: 26 Copynumber: 3.2 Consensus size: 21
3244671 ACATATATAT
*
3244681 ATAAATTATAAAATATAATAA
1 ATAAATTATAAAGTATAATAA
* *
3244702 ATATATATATACAAGTATGTATATAT
1 ATAAAT-TATA-AAGTA--TA-ATAA
3244728 ATAAATTATAAAGTATAA-AA
1 ATAAATTATAAAGTATAATAA
3244748 ATAA
1 ATAA
3244752 GTAAGTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 5 0.12
21 6 0.15
22 6 0.15
23 4 0.10
24 5 0.12
25 6 0.15
26 8 0.20
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAAATTATAAAGTATAATAA
Done.