Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 183 of 206
Found at i:55829382 original size:27 final size:26
Alignment explanation
Indices: 55829279--55829388 Score: 127
Period size: 26 Copynumber: 4.2 Consensus size: 26
55829269 TTTAAAATTT
55829279 AAAATTAAAAA-AGTGAAAAAGCGGGG
1 AAAATTAAAAATAGTGAAAAAG-GGGG
* * *
55829305 -AAATTAAAAATATTGCAAAAGGGGA
1 AAAATTAAAAATAGTGAAAAAGGGGG
*
55829330 AAAATTAAAAATAATGGAAAAA-GGGG
1 AAAATTAAAAATAGT-GAAAAAGGGGG
55829356 AAAATTAAAAATAGTGAAAGAAGGGGG
1 AAAATTAAAAATAGTGAAA-AAGGGGG
*
55829383 GAAATT
1 AAAATT
55829389 TTAAAATGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
25 17 0.24
26 40 0.56
27 14 0.20
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.16
Consensus pattern (26 bp):
AAAATTAAAAATAGTGAAAAAGGGGG
Found at i:55829533 original size:23 final size:24
Alignment explanation
Indices: 55829492--55829547 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
55829482 AAACCGTTAA
55829492 AAAAATAAAAAGAGGGAAAAA-AAG
1 AAAAA-AAAAAGAGGGAAAAAGAAG
*
55829516 TAAAAAAAAAA-AGTGAAAAAGAAG
1 -AAAAAAAAAAGAGGGAAAAAGAAG
55829540 AAAAAAAA
1 AAAAAAAA
55829548 TTGAAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 16 0.55
24 8 0.28
25 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (24 bp):
AAAAAAAAAAGAGGGAAAAAGAAG
Found at i:55829534 original size:21 final size:20
Alignment explanation
Indices: 55829510--55829554 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
55829500 AAAGAGGGAA
55829510 AAAAAGTAAAAAAAAAAAGTG
1 AAAAAG-AAAAAAAAAAAGTG
* *
55829531 AAAAAGAAGAAAAAAAATTG
1 AAAAAGAAAAAAAAAAAGTG
55829551 AAAA
1 AAAA
55829555 TGATGATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (20 bp):
AAAAAGAAAAAAAAAAAGTG
Found at i:55829633 original size:28 final size:28
Alignment explanation
Indices: 55829567--55829628 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
55829557 ATGATTGGTG
* *
55829567 AAAATAAGGAAGGTGAAAAAAAAGAACA
1 AAAATAAGGAAGGTAAAAAAAAAAAACA
*
55829595 AAAATAAGGAAGGTAAAAAAAGAAAAAGA
1 AAAATAAGGAAGGTAAAAAAA-AAAAACA
55829624 AAAAT
1 AAAAT
55829629 CGGAATATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.08
Consensus pattern (28 bp):
AAAATAAGGAAGGTAAAAAAAAAAAACA
Found at i:55830625 original size:33 final size:31
Alignment explanation
Indices: 55830580--55830663 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 31
55830570 TTTTGTGAGA
*
55830580 TTAA-TAAGAATTTTCAAAAAAATTTAAAACAGT
1 TTAATTAA-AATTTTCAAAAAAAATT-AAA-AGT
55830613 TTAATTAAAATTTT-AAAAAAAATTAAAAGT
1 TTAATTAAAATTTTCAAAAAAAATTAAAAGT
* *
55830643 TATAATGAGAATTTTCAAAAA
1 T-TAATTAAAATTTTCAAAAA
55830664 TTTGAGGGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
30 4 0.09
31 14 0.31
32 14 0.31
33 10 0.22
34 3 0.07
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (31 bp):
TTAATTAAAATTTTCAAAAAAAATTAAAAGT
Found at i:55831563 original size:34 final size:34
Alignment explanation
Indices: 55831520--55831586 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
55831510 TTTATTCACT
55831520 TGTGTCTTGATCCGTAGAAATCTCTAAACTATGA
1 TGTGTCTTGATCCGTAGAAATCTCTAAACTATGA
*
55831554 TGTGTCTTGATCCGTAGAAATCTCTAAATTATG
1 TGTGTCTTGATCCGTAGAAATCTCTAAACTATG
55831587 TTAATATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (34 bp):
TGTGTCTTGATCCGTAGAAATCTCTAAACTATGA
Found at i:55837906 original size:27 final size:27
Alignment explanation
Indices: 55837875--55837930 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
55837865 TTATTGTTAA
55837875 TTTTGTTATTATTTTAAAGACATTTGT
1 TTTTGTTATTATTTTAAAGACATTTGT
* *
55837902 TTTTGTTATTATTTTAGAGGCATTTGT
1 TTTTGTTATTATTTTAAAGACATTTGT
55837929 TT
1 TT
55837931 GTTAAGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.14, T:0.61
Consensus pattern (27 bp):
TTTTGTTATTATTTTAAAGACATTTGT
Found at i:55839662 original size:2 final size:2
Alignment explanation
Indices: 55839655--55839682 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55839645 TATGCATTGA
55839655 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
55839683 GCATATAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55841848 original size:21 final size:21
Alignment explanation
Indices: 55841806--55841849 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55841796 TAATAAAATA
*
55841806 TATTATATATTATTTTTATAG
1 TATTATATATTATATTTATAG
55841827 TATTATATATTATGATTT-TAG
1 TATTATATATTAT-ATTTATAG
55841848 TA
1 TA
55841850 AATTCATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
TATTATATATTATATTTATAG
Found at i:55842102 original size:39 final size:39
Alignment explanation
Indices: 55842043--55842150 Score: 110
Period size: 44 Copynumber: 2.6 Consensus size: 39
55842033 TTTTTCCCTT
* *
55842043 ATACTATTACACCTCCATTCCATTCAACCAAACACA-AGA
1 ATACTATTACGCCTCTATTCCATTCAACCAAACA-ATAGA
*
55842082 ATACTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGA
1 ATACTATTACGCCTCTATT-C----CATTCAACCAAACAATAGA
*
55842126 ATTGCTATTACGCCTCTATTCCATT
1 A-TACTATTACGCCTCTATTCCATT
55842151 ACGCATCTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
39 17 0.29
40 5 0.09
43 1 0.02
44 18 0.31
45 17 0.29
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (39 bp):
ATACTATTACGCCTCTATTCCATTCAACCAAACAATAGA
Found at i:55842119 original size:44 final size:45
Alignment explanation
Indices: 55842056--55842152 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
55842046 CTATTACACC
*
55842056 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* *
55842100 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
55842145 TCCATTAC
1 TCCATTAC
55842153 GCATCTATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.48
45 24 0.50
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:55842153 original size:16 final size:16
Alignment explanation
Indices: 55842132--55842184 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
55842122 TTGAATTGCT
55842132 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
55842148 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
55842164 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
55842180 ATTAC
1 ATTAC
55842185 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:55843947 original size:45 final size:45
Alignment explanation
Indices: 55843883--55843973 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
55843873 ACTTACGGTG
55843883 AGCTAAGAACTTGGGTCATCTAAATCAAGACAAGTTTCAAATTCA
1 AGCTAAGAACTTGGGTCATCTAAATCAAGACAAGTTTCAAATTCA
55843928 AGCTAAGAACTTGGGTCATCTAAATCAAGACAAGTTTCAAATTCA
1 AGCTAAGAACTTGGGTCATCTAAATCAAGACAAGTTTCAAATTCA
55843973 A
1 A
55843974 TGGCTATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (45 bp):
AGCTAAGAACTTGGGTCATCTAAATCAAGACAAGTTTCAAATTCA
Found at i:55847813 original size:12 final size:12
Alignment explanation
Indices: 55847796--55847824 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
55847786 ATTTACAATT
55847796 CCATTACTTACA
1 CCATTACTTACA
55847808 CCATTACTTACA
1 CCATTACTTACA
55847820 CCATT
1 CCATT
55847825 TCTTCTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (12 bp):
CCATTACTTACA
Found at i:55849913 original size:18 final size:18
Alignment explanation
Indices: 55849890--55849927 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55849880 GTTTCCCAGG
55849890 TTAGGATTTTTAAGGTTT
1 TTAGGATTTTTAAGGTTT
*
55849908 TTAGGATTTTTAGGGTTT
1 TTAGGATTTTTAAGGTTT
55849926 TT
1 TT
55849928 GGAGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (18 bp):
TTAGGATTTTTAAGGTTT
Found at i:55849918 original size:10 final size:9
Alignment explanation
Indices: 55849890--55849927 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
55849880 GTTTCCCAGG
55849890 TTAGGATTT
1 TTAGGATTT
55849899 TTAAGG-TTT
1 TT-AGGATTT
55849908 TTAGGATTT
1 TTAGGATTT
*
55849917 TTAGGGTTT
1 TTAGGATTT
55849926 TT
1 TT
55849928 GGAGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 3 0.12
9 20 0.77
10 3 0.12
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (9 bp):
TTAGGATTT
Found at i:55850278 original size:127 final size:126
Alignment explanation
Indices: 55850085--55850489 Score: 629
Period size: 126 Copynumber: 3.2 Consensus size: 126
55850075 GTCTCGGTCA
* *
55850085 CGTGTACGCGCTTTTGCTACAGTAGGTTCT-AGAAAAATAATTTTGAGTTGACGTTTCTGAGCAA
1 CGTGGACGCGCTTTTGCTACAGTAGGTCCTGA-AAAAATAATTTTGAGTTGACGTTTCTGAGCAA
*
55850149 ATAGTTTAAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCTT
65 ATAGTTTAAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCT
* * *
55850211 CGTGGATGCGCTTTTGCTACAGTTA-GTCCTGAAAGAAATAATTTCGAGTTGATGTTTCTGAGCA
1 CGTGGACGCGCTTTTGCTACAG-TAGGTCCTGAAA-AAATAATTTTGAGTTGACGTTTCTGAGCA
*
55850275 AATAGTTT-AAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCA
64 AATAGTTTAAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCT
*
55850337 CGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATATTTTTGAGTTGACGTTTCTGAGCAAA
1 CGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAA
* * *
55850402 TAGTATAAAACAACGCTGCAAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCT
66 TAGTTTAAAAAAACGCTTCAAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCT
* *
55850463 CGTGGACGCACTTTCGCTACAGTAGGT
1 CGTGGACGCGCTTTTGCTACAGTAGGT
55850490 AGGGGTGTGC
Statistics
Matches: 256, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
125 35 0.14
126 181 0.71
127 40 0.16
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (126 bp):
CGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAA
TAGTTTAAAAAAACGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCT
Found at i:55850757 original size:18 final size:18
Alignment explanation
Indices: 55850731--55850815 Score: 125
Period size: 18 Copynumber: 4.7 Consensus size: 18
55850721 GTAGTGATTC
*
55850731 AATTTGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
55850749 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
55850767 AATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGGT
* *
55850785 AATTCGGTTAATTCAGTT
1 AATTCGGTTAATTCGGGT
*
55850803 AATTCTGTTAATT
1 AATTCGGTTAATT
55850816 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:55850803 original size:9 final size:9
Alignment explanation
Indices: 55850731--55850815 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
55850721 GTAGTGATTC
*
55850731 AATTTGGTT
1 AATTCGGTT
*
55850740 AATTCGGGT
1 AATTCGGTT
55850749 AATTCGGTT
1 AATTCGGTT
*
55850758 AATTCGGGT
1 AATTCGGTT
*
55850767 AATTCGGGT
1 AATTCGGTT
*
55850776 AATTCGGGT
1 AATTCGGTT
55850785 AATTCGGTT
1 AATTCGGTT
*
55850794 AATTCAGTT
1 AATTCGGTT
*
55850803 AATTCTGTT
1 AATTCGGTT
55850812 AATT
1 AATT
55850816 TTTAACCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55851589 original size:27 final size:27
Alignment explanation
Indices: 55851557--55851623 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
55851547 GTAGTGATTC
*
55851557 AATTTGGTTAATTCGGTTAATTCGGGT
1 AATTTGGTTAATTCGGGTAATTCGGGT
55851584 AATTTGGTTAATTCGGGTAATTCGGGT
1 AATTTGGTTAATTCGGGTAATTCGGGT
55851611 AATTTGGTTAATT
1 AATTTGGTTAATT
55851624 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.24, C:0.06, G:0.25, T:0.45
Consensus pattern (27 bp):
AATTTGGTTAATTCGGGTAATTCGGGT
Found at i:55851624 original size:9 final size:9
Alignment explanation
Indices: 55851557--55851623 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
55851547 GTAGTGATTC
*
55851557 AATTTGGTT
1 AATTCGGTT
55851566 AATTCGGTT
1 AATTCGGTT
*
55851575 AATTCGGGT
1 AATTCGGTT
*
55851584 AATTTGGTT
1 AATTCGGTT
*
55851593 AATTCGGGT
1 AATTCGGTT
*
55851602 AATTCGGGT
1 AATTCGGTT
*
55851611 AATTTGGTT
1 AATTCGGTT
55851620 AATT
1 AATT
55851624 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.24, C:0.06, G:0.25, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55851802 original size:12 final size:12
Alignment explanation
Indices: 55851785--55851809 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55851775 TGTTATTTTG
55851785 GGTCGGTTAACC
1 GGTCGGTTAACC
55851797 GGTCGGTTAACC
1 GGTCGGTTAACC
55851809 G
1 G
55851810 AATGAACATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:55852554 original size:7 final size:7
Alignment explanation
Indices: 55852542--55852567 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55852532 TTATATAAAT
55852542 AATACTA
1 AATACTA
55852549 AATACTA
1 AATACTA
55852556 AATACTA
1 AATACTA
55852563 AATAC
1 AATAC
55852568 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:55852761 original size:20 final size:20
Alignment explanation
Indices: 55852736--55852773 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55852726 TTTATTTTTA
55852736 AAAATCTAA-ATAATAATTGT
1 AAAATCTAATATAA-AATTGT
55852756 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
55852774 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:55853784 original size:11 final size:11
Alignment explanation
Indices: 55853770--55853846 Score: 79
Period size: 11 Copynumber: 6.9 Consensus size: 11
55853760 TTAAATATGG
55853770 ATTTGAGAGAA
1 ATTTGAGAGAA
* *
55853781 ATTTGAAAGGA
1 ATTTGAGAGAA
55853792 ATTTGAGAGTAA
1 ATTTGAGAG-AA
55853804 A-TTGAGAGGAA
1 ATTTGAGA-GAA
55853815 ATTT-AGAGGAA
1 ATTTGAGA-GAA
55853826 A-TTGAGAGGAA
1 ATTTGAGA-GAA
55853837 ATTTGAGAGA
1 ATTTGAGAGA
55853847 GGATTAGTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
10 2 0.04
11 44 0.77
12 11 0.19
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:55853795 original size:22 final size:22
Alignment explanation
Indices: 55853770--55853846 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
55853760 TTAAATATGG
*
55853770 ATTTGAGAGAAATTTGAAAGG-A
1 ATTTGAGAGAAA-TTGAGAGGAA
55853792 ATTTGAGAGTAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
55853815 ATTT-AGAGGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTGAGAGGAA
55853837 ATTTGAGAGA
1 ATTTGAGAGA
55853847 GGATTAGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
22 38 0.76
23 12 0.24
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:55853809 original size:33 final size:33
Alignment explanation
Indices: 55853770--55853846 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
55853760 TTAAATATGG
* *
55853770 ATTTGAGAGAAATTTGAAAGGAATTTGAGAGTAA
1 ATTTGAGAGAAATTT-AAAGGAAATTGAGAGGAA
*
55853804 A-TTGAGAGGAAATTTAGAGGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTTAAAGGAAATTGAGAGGAA
55853837 ATTTGAGAGA
1 ATTTGAGAGA
55853847 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 24 0.63
34 14 0.37
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAAAGGAAATTGAGAGGAA
Found at i:55857441 original size:12 final size:12
Alignment explanation
Indices: 55857424--55857451 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
55857414 CTCTTCACTT
55857424 TTTTTTATTTAA
1 TTTTTTATTTAA
55857436 TTTTTTATTTAA
1 TTTTTTATTTAA
55857448 TTTT
1 TTTT
55857452 ATTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTATTTAA
Found at i:55859277 original size:17 final size:18
Alignment explanation
Indices: 55859255--55859288 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
55859245 CAAGTGCTTT
55859255 TTTGACAAA-TTGGAACA
1 TTTGACAAATTTGGAACA
55859272 TTTGACAAATTTGGAAC
1 TTTGACAAATTTGGAAC
55859289 TGTATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (18 bp):
TTTGACAAATTTGGAACA
Found at i:55862363 original size:18 final size:17
Alignment explanation
Indices: 55862340--55862373 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55862330 TCAATGTTTA
*
55862340 TATAGCACAAATTATAAG
1 TATAGCA-AAAGTATAAG
55862358 TATAGCAAAAGTATAA
1 TATAGCAAAAGTATAA
55862374 ATATTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (17 bp):
TATAGCAAAAGTATAAG
Found at i:55862797 original size:18 final size:18
Alignment explanation
Indices: 55862778--55862810 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55862768 TTTTAAATTA
55862778 AAAAT-TAAAAATAAAGT
1 AAAATATAAAAATAAAGT
55862795 AAAATATAAAAA-AAAG
1 AAAATATAAAAATAAAG
55862811 AAGAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (18 bp):
AAAATATAAAAATAAAGT
Found at i:55864468 original size:30 final size:30
Alignment explanation
Indices: 55864432--55864491 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
55864422 CAAACTGTAA
55864432 GCAAACATCAGTAGTACCTTATAAGTATCT
1 GCAAACATCAGTAGTACCTTATAAGTATCT
*
55864462 GCAAACATCAGTAGTACTTTATAAGTATCT
1 GCAAACATCAGTAGTACCTTATAAGTATCT
55864492 TACAATCCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (30 bp):
GCAAACATCAGTAGTACCTTATAAGTATCT
Found at i:55876951 original size:19 final size:19
Alignment explanation
Indices: 55876905--55876955 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
55876895 CACTTACGCG
* **
55876905 CCAGGATGCACTTTGTGTG
1 CCAGGATGCGCTTTGTGCA
* *
55876924 CTAGTATGCGCTTTGTGCA
1 CCAGGATGCGCTTTGTGCA
55876943 CCAGGATGCGCTT
1 CCAGGATGCGCTT
55876956 CGAGCACCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (19 bp):
CCAGGATGCGCTTTGTGCA
Found at i:55876970 original size:19 final size:19
Alignment explanation
Indices: 55876928--55876970 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
55876918 TGTGTGCTAG
* * *
55876928 TATGCGCTTTGTGCACCAG
1 TATGCGCTTCGAGCACCAA
*
55876947 GATGCGCTTCGAGCACCAA
1 TATGCGCTTCGAGCACCAA
55876966 TATGC
1 TATGC
55876971 ACATTACGTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (19 bp):
TATGCGCTTCGAGCACCAA
Found at i:55879660 original size:43 final size:43
Alignment explanation
Indices: 55879514--55879669 Score: 126
Period size: 43 Copynumber: 3.6 Consensus size: 43
55879504 GTGATTTTGC
*
55879514 GTAAGACCATGTCTGGGACGTTGGCATCGATT-TGA-GATT-TACGT
1 GTAAGACCACGTCTGGGACGTTGGCATC-ATTAT-ATGATTATA--T
* * * * **
55879558 GTAAGACCAGGTCTGGGACATTGGCATC-GTATATGATCACGT
1 GTAAGACCACGTCTGGGACGTTGGCATCATTATATGATTATAT
* * *
55879600 GTAAGACC-CTATTTGGGACAG-TGGCATCATTATTTGATTATAT
1 GTAAGACCAC-GTCTGGGAC-GTTGGCATCATTATATGATTATAT
55879643 GTAAGACCACGTCTGGGACGTTGGCAT
1 GTAAGACCACGTCTGGGACGTTGGCAT
55879670 TGTACGAGCT
Statistics
Matches: 87, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
42 26 0.30
43 34 0.39
44 27 0.31
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
GTAAGACCACGTCTGGGACGTTGGCATCATTATATGATTATAT
Found at i:55881807 original size:14 final size:14
Alignment explanation
Indices: 55881772--55881808 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
55881762 TAGAATGAGG
55881772 GAAGGAGG-GAGAA
1 GAAGGAGGAGAGAA
55881785 G-AGGAAGGAGAGAA
1 GAAGG-AGGAGAGAA
55881799 GAAGGAGGAG
1 GAAGGAGGAG
55881809 GACTGATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 4 0.19
14 11 0.52
15 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (14 bp):
GAAGGAGGAGAGAA
Found at i:55883271 original size:16 final size:16
Alignment explanation
Indices: 55883250--55883285 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
55883240 TTTGGTTCAC
55883250 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
55883266 TGTATTGGATTAGAGT
1 TGTATTGGATTAGAGG
55883282 TGTA
1 TGTA
55883286 ATAGCTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:55883538 original size:16 final size:16
Alignment explanation
Indices: 55883501--55883555 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
55883491 TTAATCATAT
*
55883501 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
55883517 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
55883532 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
55883550 -TAAAAT
1 TTAAAAT
55883556 TCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:55883548 original size:18 final size:18
Alignment explanation
Indices: 55883507--55883555 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
55883497 ATATTTAAAC
55883507 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
55883525 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
55883541 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
55883556 TCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:55883692 original size:156 final size:156
Alignment explanation
Indices: 55883408--55883735 Score: 611
Period size: 156 Copynumber: 2.1 Consensus size: 156
55883398 TAGAATACCC
* *
55883408 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
55883473 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAACTAAATATATTTTAATTAAAA
55883538 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
55883564 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
*
55883629 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTACTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAACTAAATATATTTTAATTAAAA
55883694 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
55883720 TTAGCAGAAATTTGTT
1 TTAGCAGAAAATTGTT
55883736 ATTGTTATTT
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 167 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAACTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTATAA
Found at i:55883698 original size:18 final size:17
Alignment explanation
Indices: 55883677--55883711 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55883667 TTATTACTAA
*
55883677 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55883695 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55883712 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55883702 original size:137 final size:137
Alignment explanation
Indices: 55883413--55883853 Score: 297
Period size: 156 Copynumber: 3.1 Consensus size: 137
55883403 TACCCTTAGC
*
55883413 ATAAAATTGTT-TTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
1 ATAAAATTCTTATTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
*
55883477 CAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAATATA
66 CAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
55883542 TAATTTA
131 TAATTTA
* * * * * *
55883549 ATAAAATTCTTATAATTAGCAGAAAATTG-TT-TTGGTAAATGATTATTGTTAATGTTATTTAA-
1 ATAAAATTC-T-T-ATT-G--GTAAA-TGATTATT-GTTATTG-TTATT-TAAATTTTA-ATAAG
* * * * ** *
55883611 ATT-TTA--ATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTA
55 ATTATTATTATCAG-TAATAAATAT-TTTAAT-CATA---T--T--T----AAACATAATTATTA
*
55883673 CTAAATATATTTTAATTAAAATATATAATTTA
106 TTAAATATATTTTAATTAAAATATATAATTTA
*** * * *
55883705 ATAAAATTCTTATAATTAGCA-GA-AATTTGTTATTGTTATTTAAATTTTAATAAGATTATTAAT
1 ATAAAATTCTTATTGGTA-AATGATTA-TTGTTATTGTTATTTAAATTTTAATAAGATTATTATT
* * * * * ****
55883768 ATCAATAATAAATAATTTAATCATATTTAAACATAATTTTTATTAAATACATTATAATTTTGGTA
64 ATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATA
55883833 TATAATTTA
129 TATAATTTA
55883842 ATAAAATTCTTA
1 ATAAAATTCTTA
55883854 ATAATTCATA
Statistics
Matches: 227, Mismatches: 44, Indels: 67
0.67 0.13 0.20
Matches are distributed among these distances:
136 8 0.04
137 51 0.22
138 1 0.00
140 2 0.01
141 2 0.01
142 6 0.03
143 19 0.08
144 14 0.06
145 14 0.06
146 3 0.01
147 3 0.01
148 14 0.06
149 13 0.06
150 13 0.06
151 6 0.03
152 1 0.00
153 2 0.01
154 1 0.00
155 1 0.00
156 53 0.23
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (137 bp):
ATAAAATTCTTATTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTAT
CAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
TAATTTA
Found at i:55883893 original size:137 final size:135
Alignment explanation
Indices: 55883615--55883893 Score: 321
Period size: 137 Copynumber: 2.0 Consensus size: 135
55883605 ATTTAAATTT
* * *
55883615 TAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTACTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTACTAAATA
* * * *
55883680 TATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGAAATTTGTTATTGTTATT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTA-CA-AAATTTCTTATTGTTACT
* **
55883745 TAAATTT
129 CAAATCA
* *
55883752 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTTTTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTACTAAATA
**** *
55883817 CATTATAATTTTGGTATATAATTTAATAAAATTCTTAATAATT-C-ATA-TTCTTATATGAATTT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTT-ATAATTACAAAATTTCTTAT-TG---TT
55883879 ACTCAAATCA
126 ACTCAAATCA
55883889 TAATA
1 TAATA
55883894 TATGATAAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
133 6 0.05
134 4 0.03
136 1 0.01
137 103 0.86
138 6 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (135 bp):
TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTACTAAATA
CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTACAAAATTTCTTATTGTTACTCA
AATCA
Found at i:55890752 original size:54 final size:54
Alignment explanation
Indices: 55890687--55890835 Score: 214
Period size: 54 Copynumber: 2.8 Consensus size: 54
55890677 AAAGAAAAGA
*
55890687 AAAAGGTTGTGAAGCAGCTAAACTGAAACAGAAGAAAGAAACAGAAGGAACAGTT
1 AAAA-GTTGTGAAGCAGCTAAACTGAAACAGAAGAAAGAAACAGAAGGAACAGCT
* *
55890742 AAAAGTTGTGAAGCAGCTAAACTGAAACAGAA-AGAAGAAATAGAAGGAACGGCT
1 AAAAGTTGTGAAGCAGCTAAACTGAAACAGAAGA-AAGAAACAGAAGGAACAGCT
* *
55890796 --AAGTTGTGAAGTAGCTAAACTGAAACAGAAGGAAGAAACA
1 AAAAGTTGTGAAGCAGCTAAACTGAAACAGAAGAAAGAAACA
55890836 AAAGAAAAGG
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
52 36 0.42
53 1 0.01
54 45 0.52
55 4 0.05
ACGTcount: A:0.50, C:0.11, G:0.26, T:0.13
Consensus pattern (54 bp):
AAAAGTTGTGAAGCAGCTAAACTGAAACAGAAGAAAGAAACAGAAGGAACAGCT
Found at i:55891452 original size:4 final size:4
Alignment explanation
Indices: 55891443--55891470 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
55891433 TCTGTAAGCA
55891443 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
55891471 AATTGGATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:55897707 original size:13 final size:13
Alignment explanation
Indices: 55897689--55897713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55897679 ATATCTGGGA
55897689 AAACAAATAGCAT
1 AAACAAATAGCAT
55897702 AAACAAATAGCA
1 AAACAAATAGCA
55897714 ACCAAAAAAA
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:0.64, C:0.16, G:0.08, T:0.12
Consensus pattern (13 bp):
AAACAAATAGCAT
Found at i:55904624 original size:50 final size:49
Alignment explanation
Indices: 55904549--55904737 Score: 191
Period size: 51 Copynumber: 3.8 Consensus size: 49
55904539 AAGTGAAGTT
* *
55904549 GATAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAA
1 GATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACAGGAA
* * * *
55904598 CGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA
1 -GATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACAGGA-A
* * * * * * *
55904649 GCTTCGATCACGTGTGTAGTACTATATGCAAGCTACAACGTGTATCAGATGAA
1 G-ATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CAG--GAA
*
55904702 AAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 GATAGGTCACATGTGTAGTACTATGTGCAGGCTACTA
55904738 TGTCAACCGG
Statistics
Matches: 111, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
50 44 0.40
51 61 0.55
52 3 0.03
53 1 0.01
54 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
GATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACAGGAA
Found at i:55904739 original size:102 final size:101
Alignment explanation
Indices: 55904555--55904739 Score: 275
Period size: 102 Copynumber: 1.8 Consensus size: 101
55904545 AGTTGATAGG
* * * * * *
55904555 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAACGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATATGCAAGCTACAACGTGTACAGGAACAATAGGTCACATGTGTAGTAC
55904620 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
55904656 TCACGTGTGTAGTACTATATGCAAGCTACAACGTGTATCAGATGAA-AAT-GGTCACATGTGTAG
1 TCACGTGTGTAGTACTATATGCAAGCTACAACGTGTA-CAG--GAACAATAGGTCACATGTGTAG
55904719 TACTATGTGCAGGCTACTATG
63 TACTATGTGCAGGCTACTATG
55904740 TCAACCGGGT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
101 34 0.45
102 36 0.48
103 2 0.03
104 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATATGCAAGCTACAACGTGTACAGGAACAATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:55909154 original size:27 final size:28
Alignment explanation
Indices: 55909106--55909173 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
55909096 AAATAAAAAA
*
55909106 TTACCAAAATGT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
*
55909133 TTACTAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
55909160 TTACCAAAATATAT
1 TTACCAAAATATAT
55909174 CAAAAAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:55909188 original size:9 final size:9
Alignment explanation
Indices: 55909174--55909217 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
55909164 CAAAATATAT
55909174 CAAAAAAAA
1 CAAAAAAAA
55909183 C-AAAAAAA
1 CAAAAAAAA
55909191 CAAAAAAAA
1 CAAAAAAAA
* *
55909200 TAAAAAACA
1 CAAAAAAAA
*
55909209 GAAAAAAAA
1 CAAAAAAAA
55909218 ACTTGAACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.86, C:0.09, G:0.02, T:0.02
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:55909189 original size:8 final size:8
Alignment explanation
Indices: 55909176--55909215 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
55909166 AAATATATCA
55909176 AAAAAAAC
1 AAAAAAAC
55909184 AAAAAAAC
1 AAAAAAAC
55909192 AAAAAAA-
1 AAAAAAAC
55909199 ATAAAAAAC
1 A-AAAAAAC
55909208 AGAAAAAA
1 A-AAAAAA
55909216 AAACTTGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 1 0.03
8 21 0.72
9 7 0.24
ACGTcount: A:0.88, C:0.07, G:0.03, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:55909196 original size:17 final size:16
Alignment explanation
Indices: 55909174--55909218 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
55909164 CAAAATATAT
55909174 CAAAAAAAACAAAAAAA
1 CAAAAAAAA-AAAAAAA
*
55909191 CAAAAAAAATAAAAAA
1 CAAAAAAAAAAAAAAA
55909207 CAGAAAAAAAAA
1 CA-AAAAAAAAA
55909219 CTTGAACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAA
Found at i:55909289 original size:27 final size:27
Alignment explanation
Indices: 55909259--55909325 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
55909249 AGGGAAGCAA
55909259 GTTGGCGGCACCAAACAAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
****
55909286 GTTGGCGGCACCAGTGGAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
55909313 GTTGGCGGCACCA
1 GTTGGCGGCACCA
55909326 CCCTTGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.16
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGATCCCT
Found at i:55909405 original size:10 final size:10
Alignment explanation
Indices: 55909374--55909507 Score: 58
Period size: 10 Copynumber: 13.1 Consensus size: 10
55909364 AGGAGAGGGG
*
55909374 AAGAAGAAGA
1 AAGAAAAAGA
55909384 AAGAAAGGAAGA
1 AAGAAA--AAGA
55909396 AAGAAAAAGA
1 AAGAAAAAGA
* *
55909406 AGGAAAAGGA
1 AAGAAAAAGA
* * *
55909416 AAGGAGAGGA
1 AAGAAAAAGA
55909426 AAG--AAAGA
1 AAGAAAAAGA
*
55909434 AA-AAGAAGGA
1 AAGAA-AAAGA
*
55909444 AAGAAAAGGA
1 AAGAAAAAGA
** *
55909454 AAGAGGAGGA
1 AAGAAAAAGA
*
55909464 AAGAAAAGGA
1 AAGAAAAAGA
*
55909474 AAGGAGAAGAGAA
1 AA-GA-AAAAG-A
*
55909487 AAAAAAAAGA
1 AAGAAAAAGA
*
55909497 AAGAAGAAGA
1 AAGAAAAAGA
55909507 A
1 A
55909508 GAGGGAAGGA
Statistics
Matches: 96, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
8 5 0.05
10 66 0.69
11 8 0.08
12 14 0.15
13 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:55909411 original size:14 final size:13
Alignment explanation
Indices: 55909377--55909450 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
55909367 AGAGGGGAAG
55909377 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
55909389 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
55909402 AAGAAGGAAAAGGAAA
1 AAGAA-G-AAA-GAAA
55909418 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
55909436 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
55909450 A
1 A
55909451 GGAAAGAGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 4 0.08
16 5 0.10
18 5 0.10
19 4 0.08
20 2 0.04
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:55909431 original size:20 final size:20
Alignment explanation
Indices: 55909408--55909480 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
55909398 GAAAAAGAAG
55909408 GAAAAGGAAAGGAGAGGAAA
1 GAAAAGGAAAGGAGAGGAAA
* *
55909428 G-AAAGAAAAAGA-AGGAAA
1 GAAAAGGAAAGGAGAGGAAA
55909446 GAAAAGGAAA-GAGGAGGAAA
1 GAAAAGGAAAGGA-GAGGAAA
55909466 GAAAAGGAAAGGAGA
1 GAAAAGGAAAGGAGA
55909481 AGAGAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 9 0.20
19 16 0.35
20 19 0.41
21 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAAAGGAAAGGAGAGGAAA
Found at i:55909433 original size:34 final size:33
Alignment explanation
Indices: 55909389--55909470 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 33
55909379 GAAGAAAGAA
*
55909389 AGGAAGAAAGAAAAAGAAGGAAAAGGAAAGG-AG
1 AGGAAGAAAGAAAAAGAAGG-AAAGAAAAGGAAG
55909422 AGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
1 AGG-AAGAAAGAAAAAGAAGGAAAGAAAAGG-AAG
*
55909457 AGGAGGAAAGAAAA
1 AGGAAGAAAGAAAA
55909471 GGAAAGGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 12 0.27
34 27 0.61
35 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (33 bp):
AGGAAGAAAGAAAAAGAAGGAAAGAAAAGGAAG
Found at i:55909487 original size:38 final size:38
Alignment explanation
Indices: 55909386--55909488 Score: 106
Period size: 38 Copynumber: 2.7 Consensus size: 38
55909376 GAAGAAGAAA
* *
55909386 GAAAGGAAGAAAGAAAAAGAAG-GAAAAGGAAAGGAGAG
1 GAAAGAAAGAAA-AAGAAGAAGAGAAAAGGAAAGGAGAG
55909424 GAAAGAAAGAAAAAGAAGGAA-AGAAAAGGAAA-GAGGAG
1 GAAAGAAAGAAAAAGAA-GAAGAGAAAAGGAAAGGA-GAG
* *
55909462 GAAAGAAA-AGGAAAGGAGAAGAGAAAA
1 GAAAGAAAGA-AAAAGAAGAAGAGAAAA
55909489 AAAAAAGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
37 10 0.18
38 46 0.82
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (38 bp):
GAAAGAAAGAAAAAGAAGAAGAGAAAAGGAAAGGAGAG
Found at i:55909490 original size:20 final size:20
Alignment explanation
Indices: 55909394--55909528 Score: 97
Period size: 20 Copynumber: 7.0 Consensus size: 20
55909384 AAGAAAGGAA
* * *
55909394 GAAAGAAAAAGAAGGAAAAG
1 GAAAGAGAAGGAAAGAAAAG
55909414 GAAAG-GAGAGGAAAG-AAA-
1 GAAAGAGA-AGGAAAGAAAAG
*
55909432 GAAAAAGAAGGAAAGAAAAG
1 GAAAGAGAAGGAAAGAAAAG
*
55909452 GAAAGAGGAGGAAAGAAAAG
1 GAAAGAGAAGGAAAGAAAAG
55909472 GAAAGGAGAAGAGAAA-AAAA-
1 GAAA-GAGAAG-GAAAGAAAAG
* *
55909492 -AAAGA-AAGAAGAAGAAGAG
1 GAAAGAGAAGGA-AAGAAAAG
* *
55909511 GGAAG-GAAGGAAGGAAAA
1 GAAAGAGAAGGAAAGAAAA
55909529 AAAAGAAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
16 1 0.01
17 5 0.05
18 16 0.18
19 17 0.19
20 39 0.43
21 9 0.10
22 4 0.04
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
GAAAGAGAAGGAAAGAAAAG
Found at i:55911742 original size:17 final size:17
Alignment explanation
Indices: 55911720--55911756 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
55911710 ATGGGGTAAG
55911720 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
55911737 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
55911754 ATG
1 ATG
55911757 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:55912762 original size:15 final size:14
Alignment explanation
Indices: 55912722--55912750 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55912712 TTTTTGTATC
55912722 AATTTAATTATTCT
1 AATTTAATTATTCT
55912736 AATTTAATTATTCT
1 AATTTAATTATTCT
55912750 A
1 A
55912751 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:55915154 original size:18 final size:18
Alignment explanation
Indices: 55915128--55915165 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55915118 GTCCCAATGA
*
55915128 TCGCCACCACATTCTTCT
1 TCGCAACCACATTCTTCT
55915146 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
55915164 TC
1 TC
55915166 ACCACCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.42, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:55915172 original size:18 final size:18
Alignment explanation
Indices: 55915131--55915172 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
55915121 CCAATGATCG
*
55915131 CCACCACATTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
55915149 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
55915167 CCACCA
1 CCACCA
55915173 ACCATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:55915909 original size:3 final size:3
Alignment explanation
Indices: 55915901--55915959 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
55915891 AGTAACATCT
55915901 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55915949 TAA TAA TAA TA
1 TAA TAA TAA TA
55915960 CTATAAAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55927742 original size:20 final size:21
Alignment explanation
Indices: 55927695--55927742 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
55927685 TTCTGTAGTG
*
55927695 AAGAATATGAGAAGAGAGAAA
1 AAGAAAATGAGAAGAGAGAAA
* *
55927716 AA-TAAATGGGAAGA-AGAAA
1 AAGAAAATGAGAAGAGAGAAA
55927735 AAGAAAAT
1 AAGAAAAT
55927743 AAAAAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.32
20 13 0.59
21 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (21 bp):
AAGAAAATGAGAAGAGAGAAA
Found at i:55931087 original size:57 final size:61
Alignment explanation
Indices: 55930975--55931122 Score: 182
Period size: 57 Copynumber: 2.5 Consensus size: 61
55930965 AATTGACGGT
*
55930975 AAAAAGGATCTAGCCTGGACGGGTGATCCTATTCTGATATAGCCCTCTCGAAGAATATGTGTG
1 AAAAAGGATCTAGCCTGGACGGGTGATCC--TTCTGATATAGCCCTCCCGAAGAATATGTGTG
*
55931038 AAAAA-GATCTAGCCTGGATGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATA--TGTG
1 AAAAAGGATCTAGCCTGGACGGGTGATCCTTCTGATATAGCCCTCCCGAAGAATATGTGTG
* * *
55931093 AAAAATGGATTTAGCCCGGACGGGTAATCC
1 AAAAA-GGATCTAGCCTGGACGGGTGATCC
55931123 GAATTAGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
55 9 0.12
57 39 0.51
58 2 0.03
61 1 0.01
62 20 0.26
63 5 0.07
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (61 bp):
AAAAAGGATCTAGCCTGGACGGGTGATCCTTCTGATATAGCCCTCCCGAAGAATATGTGTG
Found at i:55936541 original size:18 final size:19
Alignment explanation
Indices: 55936506--55936542 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55936496 AGCCTGCTTC
55936506 AACTTCAACAACAGCTTTA
1 AACTTCAACAACAGCTTTA
*
55936525 AACTTCAAGAACA-CTTTA
1 AACTTCAACAACAGCTTTA
55936543 GACACCTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.27
Consensus pattern (19 bp):
AACTTCAACAACAGCTTTA
Found at i:55940519 original size:33 final size:33
Alignment explanation
Indices: 55940477--55940540 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
55940467 TGTCATTTTT
* *
55940477 TTTTAATTTCAAATTTCATTTAATTACATTTCA
1 TTTTAATTTCAAACTTCATTTAATTAAATTTCA
* *
55940510 TTTTCATTTCAAACTTCATTTCATTAAATTT
1 TTTTAATTTCAAACTTCATTTAATTAAATTT
55940541 TTTTTCCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTTAATTTCAAACTTCATTTAATTAAATTTCA
Found at i:55940577 original size:21 final size:21
Alignment explanation
Indices: 55940525--55940577 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
55940515 ATTTCAAACT
*
55940525 TCATTTC-ATTAAATTTTTTT
1 TCATTTCAATTAAATTTTTTC
* * *
55940545 TCCATCTAAATTTAATTTTTTC
1 T-CATTTCAATTAAATTTTTTC
55940567 TCATTTCAATT
1 TCATTTCAATT
55940578 CTTTTTTCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 1 0.04
21 12 0.48
22 12 0.48
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.58
Consensus pattern (21 bp):
TCATTTCAATTAAATTTTTTC
Found at i:55940627 original size:17 final size:18
Alignment explanation
Indices: 55940605--55940644 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
55940595 ACAAGTAGTC
55940605 TCATTTCAATTT-TATTT
1 TCATTTCAATTTATATTT
55940622 TCATTTCAATTTATATTT
1 TCATTTCAATTTATATTT
55940640 T-ATTT
1 TCATTT
55940645 TCATCTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (18 bp):
TCATTTCAATTTATATTT
Found at i:55940681 original size:28 final size:28
Alignment explanation
Indices: 55940643--55940825 Score: 130
Period size: 28 Copynumber: 6.6 Consensus size: 28
55940633 TATATTTTAT
*
55940643 TTTCATCTCATATTCATTTCAACTTTCA
1 TTTCATTTCATATTCATTTCAACTTTCA
* * * *
55940671 TTTGATTTCATATTCATTTCAAATTACG
1 TTTCATTTCATATTCATTTCAACTTTCA
*
55940699 TTTCATTTCATATTTATTT-AACGTTTCA
1 TTTCATTTCATATTCATTTCAAC-TTTCA
* ***
55940727 TTTCATTT-AAATTTC-TTT-TTTTTTCA
1 TTTCATTTCATA-TTCATTTCAACTTTCA
*
55940753 TTTCAATTT-ATATTTTAATTTC-A-TTTCA
1 TTTC-ATTTCATA--TTCATTTCAACTTTCA
* *
55940781 TATTCATTTCATATTCATTTCAAATATCA
1 T-TTCATTTCATATTCATTTCAACTTTCA
55940810 TTTCATATTCAT-TTCA
1 TTTCAT-TTCATATTCA
55940826 AATTTTGTCT
Statistics
Matches: 124, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
26 9 0.07
27 20 0.16
28 76 0.61
29 19 0.15
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTCATTTCATATTCATTTCAACTTTCA
Found at i:55940702 original size:23 final size:23
Alignment explanation
Indices: 55940675--55940829 Score: 110
Period size: 23 Copynumber: 6.9 Consensus size: 23
55940665 CTTTCATTTG
55940675 ATTTCATATTCATTTCAAATTAC
1 ATTTCATATTCATTTCAAATTAC
* * *
55940698 GTTTCAT-TTCATATT-TATTTAAC
1 ATTTCATATTCAT-TTCAAATT-AC
* *
55940721 GTTTCAT-TTCATTT-AAATTTC
1 ATTTCATATTCATTTCAAATTAC
** * * *
55940742 -TTTTTTTTTCATTTCAATTTAT
1 ATTTCATATTCATTTCAAATTAC
* *
55940764 ATTTTA-ATTTCATTTCATATT-C
1 ATTTCATA-TTCATTTCAAATTAC
55940786 ATTTCATATTCATTTCAAA-TATC
1 ATTTCATATTCATTTCAAATTA-C
55940809 ATTTCATATTCATTTCAAATT
1 ATTTCATATTCATTTCAAATT
55940830 TTGTCTTATT
Statistics
Matches: 104, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.04
21 9 0.09
22 32 0.31
23 58 0.56
24 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.01, T:0.56
Consensus pattern (23 bp):
ATTTCATATTCATTTCAAATTAC
Found at i:55940773 original size:18 final size:18
Alignment explanation
Indices: 55940747--55940818 Score: 53
Period size: 18 Copynumber: 4.1 Consensus size: 18
55940737 ATTTCTTTTT
*
55940747 TTTTCATTTCAATTT-ATA
1 TTTTAATTTC-ATTTCATA
55940765 TTTTAATTTCATTTCATA
1 TTTTAATTTCATTTCATA
*
55940783 --TTCATTTCATATTCAT-
1 TTTTAATTTCAT-TTCATA
** *
55940799 TTCAAATATCATTTCATA
1 TTTTAATTTCATTTCATA
55940817 TT
1 TT
55940819 CATTTCAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 9 0.21
17 14 0.33
18 20 0.47
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATTTCATTTCATA
Found at i:55940786 original size:11 final size:11
Alignment explanation
Indices: 55940772--55940825 Score: 90
Period size: 11 Copynumber: 4.8 Consensus size: 11
55940762 ATATTTTAAT
55940772 TTCATTTCATA
1 TTCATTTCATA
55940783 TTCATTTCATA
1 TTCATTTCATA
*
55940794 TTCATTTCAAA
1 TTCATTTCATA
55940805 TATCATTTCATA
1 T-TCATTTCATA
55940817 TTCATTTCA
1 TTCATTTCA
55940826 AATTTTGTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 30 0.75
12 10 0.25
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (11 bp):
TTCATTTCATA
Found at i:55940878 original size:17 final size:17
Alignment explanation
Indices: 55940858--55940897 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
55940848 TTTTACTTTA
*
55940858 TTTAAATTT-TTTCTCAT
1 TTTAAATTTCATTC-CAT
55940875 TTTAAATTTCATTCCAT
1 TTTAAATTTCATTCCAT
55940892 TTTAAA
1 TTTAAA
55940898 ATGTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTCATTCCAT
Found at i:55940923 original size:25 final size:25
Alignment explanation
Indices: 55940876--55940924 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55940866 TTTTCTCATT
* * *
55940876 TTAAATTTCATTCCATTTTAAAATG
1 TTAAATTTCATTCAAATTCAAAATG
*
55940901 TTAAATTTCATTTAAATTCAAAAT
1 TTAAATTTCATTCAAATTCAAAAT
55940925 TTTTCTCATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (25 bp):
TTAAATTTCATTCAAATTCAAAATG
Found at i:55941083 original size:17 final size:17
Alignment explanation
Indices: 55941053--55941104 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
55941043 TTTATTTTTT
55941053 TCATTTCAATTTTCATTTC
1 TCATTTC-A-TTTCATTTC
55941072 TCATTTCATTTCATTTC
1 TCATTTCATTTCATTTC
** *
55941089 AGATTTCAATTCATTT
1 TCATTTCATTTCATTT
55941105 AAATTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 22 0.73
18 1 0.03
19 7 0.23
ACGTcount: A:0.23, C:0.19, G:0.02, T:0.56
Consensus pattern (17 bp):
TCATTTCATTTCATTTC
Found at i:55941132 original size:19 final size:18
Alignment explanation
Indices: 55941097--55941145 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
55941087 TCAGATTTCA
55941097 ATTCATTTAAATTTATAT
1 ATTCATTTAAATTTATAT
*
55941115 ATTCATTTTAA-TTATAT
1 ATTCATTTAAATTTATAT
* *
55941132 ATACATTTCAATTT
1 ATTCATTTAAATTT
55941146 CTATTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTCATTTAAATTTATAT
Found at i:55941215 original size:24 final size:24
Alignment explanation
Indices: 55941180--55941232 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
55941170 TTCCAATTTT
*
55941180 AATTTAATTTCAACTTCTTTTTAA
1 AATTTAAATTCAACTTCTTTTTAA
*
55941204 AATTTAAATTCAATTTCTTTTTAA
1 AATTTAAATTCAACTTCTTTTTAA
55941228 AATTT
1 AATTT
55941233 TACTCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTTAAATTCAACTTCTTTTTAA
Found at i:55941246 original size:24 final size:24
Alignment explanation
Indices: 55941195--55941254 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
55941185 AATTTCAACT
* *
55941195 TCTTTTTAAAATTTAAATTCAATT
1 TCTTTTTAAAATTTAAACTCAATA
*
55941219 TCTTTTTAAAATTT-TACTCATATA
1 TCTTTTTAAAATTTAAACTCA-ATA
*
55941243 TCTTTTTTAAAT
1 TCTTTTTAAAAT
55941255 ATATTTTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (24 bp):
TCTTTTTAAAATTTAAACTCAATA
Found at i:55942337 original size:5 final size:5
Alignment explanation
Indices: 55942322--55942350 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
55942312 CTATCCGGGC
55942322 CCAAA -CAAA CCAAA CCAAA CCAAA CCAAA
1 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA
55942351 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:55943825 original size:13 final size:13
Alignment explanation
Indices: 55943807--55943837 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
55943797 ATTGCATATA
*
55943807 TTATTTTATTTAT
1 TTATTTTATCTAT
55943820 TTATTTTATCTAT
1 TTATTTTATCTAT
55943833 TTATT
1 TTATT
55943838 ATCTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTATCTAT
Found at i:55950897 original size:44 final size:44
Alignment explanation
Indices: 55950847--55951248 Score: 298
Period size: 44 Copynumber: 9.0 Consensus size: 44
55950837 CATCATAACG
* * *
55950847 AATCTTATCTCCCTGAAGTTGTAGTGGAGCATATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
55950891 AATCTTATCTCCTTGAAGTTACAGTGGAGTAGATTAAAACTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
*
55950935 AATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTTAAA-CTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCTACA
* * *
55950979 AATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCTACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * * * *
55951023 AGTCTCATCTCCTTAAAGTTGTAGTGGAGCAGATTGAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CA
* * * * *
55951068 AATTTTATTTCCCTGAAATTGCAGTGGAACATATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG---C----TACA
* * * *
55951119 AATCTTATCTCTCC-GAAGTTGCGGTGAAGTAGATTGAAA-ATAACA
1 AATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATT-AAAGCT-ACA
* * * * *
55951164 AATCTTATCCCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CA
* * *
55951209 AATCTTAT-TTCC---ACTT-CAGTGGAACAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
55951248 A
1 A
55951249 GTTGCAGTGG
Statistics
Matches: 283, Mismatches: 59, Indels: 37
0.75 0.16 0.10
Matches are distributed among these distances:
39 2 0.01
40 17 0.06
41 3 0.01
43 5 0.02
44 146 0.52
45 78 0.28
51 25 0.09
52 7 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACA
Found at i:55951105 original size:132 final size:133
Alignment explanation
Indices: 55950847--55951551 Score: 320
Period size: 132 Copynumber: 5.4 Consensus size: 133
55950837 CATCATAACG
* * * *
55950847 AATCTTATCTCCCTGAAGTTGTAGTGGAGCATATTAAAGCCACAAATCTTATCTCCTTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTCATCTCCTTAAAGTTA
* * * *
55950912 CAGTGGAGTAGATTAAAACTATAAATCTTATATCCCTGAAGTTGCAGTGGAGCAGATTTAAA-CT
66 CAGTGGAGCAGATTAAAACTACAAATCTTATATCCCTGAAATTGCAGTGGAACAGATTTAAAGCT
55950976 ACA
131 ACA
* * * * * *
55950979 AATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCTACGAGTCTCATCTCCTTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTCATCTCCTTAAAGTTA
* * * * * *
55951044 TAGTGGAGCAGATTGAAGA-TAGCGAATTTTATTTCCCTGAAATTGCAGTGGAACATATTAAAGC
66 CAGTGGAGCAGATT-AAAACTA-CAAATCTTATATCCCTGAAATTGCAGTGGAACAGATT-----
*
55951108 TACAAGTTACA
124 TA-AAGCTACA
* * * *** * * * *
55951119 AATCTTATCTCTCC-GAAGTTGCGGTGAAGTAGATTGAAAATAACAAATCTTATCCCCCTGAAGT
1 AATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATT-AAAGCCACAAATCTCATCTCCTTAAAGT
* * * * * *
55951183 TGCAGTGGAGTAGATTGAAGA-TAGCTAATCTTAT-TTCC---ACTT-CAGTGGAACAGA-TTAA
64 TACAGTGGAGCAGATT-AAAACTA-CAAATCTTATATCCCTGAAATTGCAGTGGAACAGATTTAA
55951241 AG-----
127 AGCTACA
*** * *
55951243 ---C-TA-----C--AAGTTGCAGTGGAGCAGATTGAAAATAACAAATCTTATCTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCACAAATCTCATCTCCTTAAAGTT
* * * * * * * *
55951297 GCAATGGAGTAGATTGAAGAC-AGCTAATCTTAT-TTCCTTAAAGTTGCAGTGGAATAGATTAAA
65 ACAGTGGAGCAGATT-AAAACTA-CAAATCTTATATCCCTGAAA-TTGCAGTGGAACAGATT---
*
55951360 GCTATAAGTTACA
124 --TA-AAGCTACA
* * * * ** ** *
55951373 AATCTTATCTCTCTGAAGTTGCGGTGGAGTAGATTGAAGTTACAAATCTTGTCTTCC-TGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTCATC-TCCTTAAAGTT
* ** * * * * *
55951437 GCAGTGGAGCAGATTAAAGTTACAAATTTTATCTCCCT-AAAGTTGCAGTGGAGCA-AATTGAAG
65 ACAGTGGAGCAGATTAAAACTACAAATCTTATATCCCTGAAA-TTGCAGTGGAACAGATTTAAAG
55951500 CTACA
129 CTACA
* * * * *
55951505 AGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCAACAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAAT
55951552 TTTATACCTC
Statistics
Matches: 456, Mismatches: 74, Indels: 86
0.74 0.12 0.14
Matches are distributed among these distances:
113 80 0.18
114 1 0.00
116 1 0.00
117 2 0.00
118 11 0.02
119 1 0.00
120 2 0.00
121 1 0.00
124 2 0.00
125 3 0.01
129 3 0.01
130 2 0.00
132 117 0.26
133 35 0.08
134 2 0.00
135 1 0.00
136 11 0.02
137 3 0.01
138 4 0.01
139 28 0.06
140 75 0.16
141 71 0.16
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (133 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTCATCTCCTTAAAGTTA
CAGTGGAGCAGATTAAAACTACAAATCTTATATCCCTGAAATTGCAGTGGAACAGATTTAAAGCT
ACA
Found at i:55951311 original size:45 final size:45
Alignment explanation
Indices: 55951247--55951542 Score: 249
Period size: 44 Copynumber: 6.5 Consensus size: 45
55951237 TTAAAGCTAC
*
55951247 AAGTTGCAGTGGAGCAGATTGAAAATAACAAATCTTATCTCCCTA
1 AAGTTGCAGTGGAGTAGATTGAAAATAACAAATCTTATCTCCCTA
* * * * * * *
55951292 AAGTTGCAATGGAGTAGATTGAAGACAGCTAATCTTATTTCCTTA
1 AAGTTGCAGTGGAGTAGATTGAAAATAACAAATCTTATCTCCCTA
* * *
55951337 AAGTTGCAGTGGAATAGATT-AAAGCTATAAGTTACAAATCTTATCTCTCTG
1 AAGTTGCAGTGGAGTAGATTGAAA---AT-A---ACAAATCTTATCTCCCTA
* * * * * *
55951388 AAGTTGCGGTGGAGTAGATTG-AAGTTACAAATCTTGTCTTCCTG
1 AAGTTGCAGTGGAGTAGATTGAAAATAACAAATCTTATCTCCCTA
* * * *
55951432 AAGTTGCAGTGGAGCAGATT-AAAGTTACAAATTTTATCTCCCTA
1 AAGTTGCAGTGGAGTAGATTGAAAATAACAAATCTTATCTCCCTA
* * ** * *
55951476 AAGTTGCAGTGGAGCAAATTGAAGCT-ACAAGTCTTATCTCCCTG
1 AAGTTGCAGTGGAGTAGATTGAAAATAACAAATCTTATCTCCCTA
*
55951520 AAGTTGTAGTGGAGTAGATTGAA
1 AAGTTGCAGTGGAGTAGATTGAA
55951543 GCAACAAATT
Statistics
Matches: 201, Mismatches: 40, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
44 108 0.54
45 58 0.29
47 1 0.00
48 2 0.01
51 32 0.16
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (45 bp):
AAGTTGCAGTGGAGTAGATTGAAAATAACAAATCTTATCTCCCTA
Found at i:55951332 original size:113 final size:115
Alignment explanation
Indices: 55951134--55951369 Score: 341
Period size: 113 Copynumber: 2.0 Consensus size: 115
55951124 TATCTCTCCG
* * * *
55951134 AAGTTGCGGTGAAGTAGATTGAAAATAACAAATCTTATCCCCCTGAAGTTGCAGTGGAGTAGATT
1 AAGTTGCAGTGAAGCAGATTGAAAATAACAAATCTTATCCCCCTAAAGTTGCAATGGAGTAGATT
*
55951199 GAAGATAGCTAATCTTATTTCC-ACTT-CAGTGGAACAGATTAAAGCTAC
66 GAAGACAGCTAATCTTATTTCCAACTTGCAGTGGAACAGATTAAAGCTAC
* *
55951247 AAGTTGCAGTGGAGCAGATTGAAAATAACAAATCTTATCTCCCTAAAGTTGCAATGGAGTAGATT
1 AAGTTGCAGTGAAGCAGATTGAAAATAACAAATCTTATCCCCCTAAAGTTGCAATGGAGTAGATT
* * *
55951312 GAAGACAGCTAATCTTATTTCCTTAAAGTTGCAGTGGAATAGATTAAAGCTAT
66 GAAGACAGCTAATCTTATTTCC---AACTTGCAGTGGAACAGATTAAAGCTAC
55951365 AAGTT
1 AAGTT
55951370 ACAAATCTTA
Statistics
Matches: 108, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
113 80 0.74
117 3 0.03
118 25 0.23
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (115 bp):
AAGTTGCAGTGAAGCAGATTGAAAATAACAAATCTTATCCCCCTAAAGTTGCAATGGAGTAGATT
GAAGACAGCTAATCTTATTTCCAACTTGCAGTGGAACAGATTAAAGCTAC
Found at i:55951433 original size:44 final size:44
Alignment explanation
Indices: 55951365--55951591 Score: 244
Period size: 44 Copynumber: 5.2 Consensus size: 44
55951355 TTAAAGCTAT
*
55951365 AAGTTACAAATCTTATC-TCTCTGAAGTTGCGGTGGAGTAGATTG
1 AAGTTACAAATCTTATCTTC-CTGAAGTTGCAGTGGAGTAGATTG
* * *
55951409 AAGTTACAAATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTA
1 AAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTG
* * * * *
55951453 AAGTTACAAATTTTATCTCCCTAAAGTTGCAGTGGAGCAAATTG
1 AAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTG
* * * *
55951497 AAGCTACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTG
1 AAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTG
** * * *
55951541 AAGCAACAAATTTTATACCT-CTGAAGTTGCAGTGG-GATAGAATG
1 AAGTTACAAATCTTAT-CTTCCTGAAGTTGCAGTGGAG-TAGATTG
55951585 AAGTTAC
1 AAGTTAC
55951592 TTCAAAAAGA
Statistics
Matches: 154, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.01
44 150 0.97
45 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (44 bp):
AAGTTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTG
Found at i:55951520 original size:88 final size:88
Alignment explanation
Indices: 55951365--55951575 Score: 271
Period size: 88 Copynumber: 2.4 Consensus size: 88
55951355 TTAAAGCTAT
* * * * * * *
55951365 AAGTTACAAATCTTATCTCTCTGAAGTTGCGGTGGAGTAGATTGAAGTTACAAATCTTGTCTTCC
1 AAGTTACAAATTTTATCTCTCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCTTATCTCCC
55951430 TGAAGTTGCAGTGGAGCAGATTA
66 TGAAGTTGCAGTGGAGCAGATTA
* * *
55951453 AAGTTACAAATTTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGCTACAAGTCTTATCTCCC
1 AAGTTACAAATTTTATCTCTCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCTTATCTCCC
* * *
55951518 TGAAGTTGTAGTGGAGTAGATTG
66 TGAAGTTGCAGTGGAGCAGATTA
**
55951541 AAGCAACAAATTTTATAC-CTCTGAAGTTGCAGTGG
1 AAGTTACAAATTTTAT-CTCTCTGAAGTTGCAGTGG
55951576 GATAGAATGA
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
88 104 0.99
89 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (88 bp):
AAGTTACAAATTTTATCTCTCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCTTATCTCCC
TGAAGTTGCAGTGGAGCAGATTA
Found at i:55951917 original size:22 final size:22
Alignment explanation
Indices: 55951883--55951941 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
55951873 ACCCTAAATC
* *
55951883 CCTAGCTTGTGCCACCG-CAGCT
1 CCTAGCCTCTGCCACCGTC-GCT
*
55951905 CCTTGCCTCTGCCACCGTCGCT
1 CCTAGCCTCTGCCACCGTCGCT
55951927 CCTAGCCTCTGCCAC
1 CCTAGCCTCTGCCAC
55951942 ATTATTGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.10, C:0.47, G:0.19, T:0.24
Consensus pattern (22 bp):
CCTAGCCTCTGCCACCGTCGCT
Found at i:55953098 original size:3 final size:3
Alignment explanation
Indices: 55953090--55953136 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
55953080 CTAGCCCATT
55953090 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55953137 TACTGTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55955757 original size:37 final size:37
Alignment explanation
Indices: 55955714--55955786 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
55955704 CATCTACCGA
*
55955714 TGTTTGGATTTTTGGGAGTTGGCATTGACCCTCCACG
1 TGTTTGGATTTTCGGGAGTTGGCATTGACCCTCCACG
55955751 TGTTTGGATTTTCGGGAGTTGGCATTGACCCTCCAC
1 TGTTTGGATTTTCGGGAGTTGGCATTGACCCTCCAC
55955787 AACCCGGCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.37
Consensus pattern (37 bp):
TGTTTGGATTTTCGGGAGTTGGCATTGACCCTCCACG
Found at i:55956316 original size:12 final size:12
Alignment explanation
Indices: 55956285--55956310 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55956275 TTCAACTAAT
55956285 AAAGCAAACAAA
1 AAAGCAAACAAA
55956297 AAAGCAAACAAA
1 AAAGCAAACAAA
55956309 AA
1 AA
55956311 CTCAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAGCAAACAAA
Found at i:55956522 original size:53 final size:54
Alignment explanation
Indices: 55956411--55956542 Score: 137
Period size: 53 Copynumber: 2.5 Consensus size: 54
55956401 GTTGGTGCCG
* * *
55956411 GCCATCAGTGT-CCAAAAGAAAAAAAAATTCAAGACCCGAAAACGGTGGTACTA
1 GCCATCAATGTCCCAAAACAAAAAAAAATTCAAGACCCGAAAAAGGTGGTACTA
* * *
55956464 GCCATCAAT-TCCCAAAACAAAAATAAAA-TCGAGACCCGAAAAAGGT-GTAGTC
1 GCCATCAATGTCCCAAAACAAAAA-AAAATTCAAGACCCGAAAAAGGTGGTACTA
* **
55956516 GACCATCAGTGTCCCAAAGGAAAAAAA
1 G-CCATCAATGTCCCAAAACAAAAAAA
55956543 TTTTGTCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
52 6 0.09
53 44 0.67
54 16 0.24
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.14
Consensus pattern (54 bp):
GCCATCAATGTCCCAAAACAAAAAAAAATTCAAGACCCGAAAAAGGTGGTACTA
Found at i:55968305 original size:11 final size:13
Alignment explanation
Indices: 55968285--55968316 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55968275 AATAAATTAA
55968285 TAAAATATCAT-T
1 TAAAATATCATAT
55968297 TAAAA-ATCATAT
1 TAAAATATCATAT
55968309 TAAAATAT
1 TAAAATAT
55968317 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:55977705 original size:6 final size:6
Alignment explanation
Indices: 55977694--55977767 Score: 148
Period size: 6 Copynumber: 12.3 Consensus size: 6
55977684 TGATTAATAT
55977694 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
55977742 ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC AT
55977768 GTGTGTGTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:55983291 original size:12 final size:12
Alignment explanation
Indices: 55983274--55983298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55983264 GGTGTTCATT
55983274 CGGTTAACCGAC
1 CGGTTAACCGAC
55983286 CGGTTAACCGAC
1 CGGTTAACCGAC
55983298 C
1 C
55983299 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:55983473 original size:9 final size:9
Alignment explanation
Indices: 55983459--55983544 Score: 102
Period size: 9 Copynumber: 9.4 Consensus size: 9
55983449 TTTGGTTAAA
55983459 AATTACCCG
1 AATTACCCG
55983468 AATTACCCG
1 AATTACCCG
*
55983477 AATTAACCG
1 AATTACCCG
55983486 AATTACCCG
1 AATTACCCG
*
55983495 AATTAACCG
1 AATTACCCG
*
55983504 AATTAACCG
1 AATTACCCG
55983513 AATTA-CCG
1 AATTACCCG
**
55983521 AAAAACACCCG
1 --AATTACCCG
55983532 AATTACCCG
1 AATTACCCG
55983541 AATT
1 AATT
55983545 TTTTTTATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
8 3 0.04
9 58 0.87
10 3 0.04
11 3 0.04
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:55983491 original size:27 final size:27
Alignment explanation
Indices: 55983459--55983519 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
55983449 TTTGGTTAAA
*
55983459 AATTACCCGAATTACCCGAATTAACCG
1 AATTACCCGAATTAACCGAATTAACCG
55983486 AATTACCCGAATTAACCGAATTAACCG
1 AATTACCCGAATTAACCGAATTAACCG
55983513 AATTACC
1 AATTACC
55983520 GAAAAACACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.28, G:0.10, T:0.23
Consensus pattern (27 bp):
AATTACCCGAATTAACCGAATTAACCG
Found at i:55984451 original size:26 final size:26
Alignment explanation
Indices: 55984422--55984478 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
55984412 CTGATGTCGA
*
55984422 ATCCCCTTCTATTATTACTGATGCAT
1 ATCCCCTTCTATTATTACTAATGCAT
*
55984448 ATCCCCTTCTGTTATTACTAATGCAT
1 ATCCCCTTCTATTATTACTAATGCAT
55984474 ATCCC
1 ATCCC
55984479 ATCTGTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (26 bp):
ATCCCCTTCTATTATTACTAATGCAT
Found at i:55999032 original size:43 final size:41
Alignment explanation
Indices: 55998979--55999082 Score: 153
Period size: 39 Copynumber: 2.6 Consensus size: 41
55998969 CAACTCTTTA
*
55998979 TATAGAAGTTGTAAGTGACTATTCATCTACATCACTTAAATGC
1 TATAGGAGTTGT--GTGACTATTCATCTACATCACTTAAATGC
55999022 TATAGGAG-T-TGTGACTATTCATCTACATCACTTAAATGC
1 TATAGGAGTTGTGTGACTATTCATCTACATCACTTAAATGC
55999061 TATAGGAG-T-TGTGACTATTCAT
1 TATAGGAGTTGTGTGACTATTCAT
55999083 GCATGTGTGT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
39 51 0.85
41 1 0.02
42 1 0.02
43 7 0.12
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (41 bp):
TATAGGAGTTGTGTGACTATTCATCTACATCACTTAAATGC
Found at i:55999042 original size:39 final size:39
Alignment explanation
Indices: 55998993--55999082 Score: 180
Period size: 39 Copynumber: 2.3 Consensus size: 39
55998983 GAAGTTGTAA
55998993 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
55999032 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
1 GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
55999071 GTGACTATTCAT
1 GTGACTATTCAT
55999083 GCATGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (39 bp):
GTGACTATTCATCTACATCACTTAAATGCTATAGGAGTT
Found at i:55999137 original size:32 final size:32
Alignment explanation
Indices: 55999092--55999166 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
55999082 TGCATGTGTG
55999092 TAACTCTTCATCTTCAAGTCTCTTAACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTAACATTTC
* * *
55999124 TAACTCTTGATCTTCAAGTTTCTTCACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTAACATTTC
*
55999156 CAACTCTTCAT
1 TAACTCTTCAT
55999167 AATTTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.04, T:0.44
Consensus pattern (32 bp):
TAACTCTTCATCTTCAAGTCTCTTAACATTTC
Found at i:56003592 original size:38 final size:38
Alignment explanation
Indices: 56003497--56003592 Score: 87
Period size: 38 Copynumber: 2.6 Consensus size: 38
56003487 TGTCTATTCA
* *
56003497 ATTTCATTACAAT-CCTATTCCATTTCTACAGAATGGCT
1 ATTTCATTACAATACTTATTCCATTTCTACA-AATGCCT
56003535 ATTTCATT---ATAGCTCTATTCCATTTCATTAC-AAT-CCT
1 ATTTCATTACAATA-CT-TATTCCATTTC--TACAAATGCCT
56003572 ATTTCATTACAATACTTATTC
1 ATTTCATTACAATACTTATTC
56003593 AATTCCATCC
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
35 2 0.04
37 11 0.23
38 27 0.56
39 2 0.04
40 6 0.12
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (38 bp):
ATTTCATTACAATACTTATTCCATTTCTACAAATGCCT
Found at i:56008339 original size:2 final size:2
Alignment explanation
Indices: 56008332--56008362 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
56008322 TGTTTAATGA
56008332 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
56008363 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:56008367 original size:2 final size:2
Alignment explanation
Indices: 56008362--56008392 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
56008352 TCTCTCTCTC
*
56008362 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56008393 TTCAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:56012322 original size:3 final size:3
Alignment explanation
Indices: 56012314--56012398 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
56012304 TATTAACATG
56012314 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56012362 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
56012399 CTAAGGGCGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56014019 original size:47 final size:47
Alignment explanation
Indices: 56013904--56014063 Score: 196
Period size: 47 Copynumber: 3.4 Consensus size: 47
56013894 GGATAGCAGT
* * *
56013904 AACAACATTCGGACAGCATTGATTTG-TACAAAAATGAACAGCATTTA
1 AACAACATTCGGACAGCATTAATATGCTA-AAAAATGGACAGCATTTA
* * * * *
56013951 AGCACCAATTTGGACAACATTAATATGCTAAAAAACGGACAGCATTTA
1 AACAAC-ATTCGGACAGCATTAATATGCTAAAAAATGGACAGCATTTA
* * *
56013999 ACCAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATCTA
1 AACAACATTCGGACAGCATTAATATGCTAAAAAATGGACAGCATTTA
56014046 AACAACATTCGGACAGCA
1 AACAACATTCGGACAGCA
56014064 CCTTGTCATC
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
47 57 0.60
48 36 0.38
49 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (47 bp):
AACAACATTCGGACAGCATTAATATGCTAAAAAATGGACAGCATTTA
Found at i:56014718 original size:43 final size:42
Alignment explanation
Indices: 56014642--56014767 Score: 137
Period size: 43 Copynumber: 3.0 Consensus size: 42
56014632 GAAACACATA
* * * *
56014642 TATCACATA-CAATGCCATATCCCAGATATGGTCTTACATGT
1 TATCACATATCGATGCCATATCCCAGACAAGGTCTTACACGT
*
56014683 TATCACATATCGATGCCACTATCCTAGACAAGGTCTTACACGT
1 TATCACATATCGATGCCA-TATCCCAGACAAGGTCTTACACGT
* * * * *
56014726 AATCTCATATCGATGCCAATGTCCCAGACATGGTTTTACACG
1 TATCACATATCGATGCC-ATATCCCAGACAAGGTCTTACACG
56014768 AAATCGTTCC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
41 9 0.13
42 7 0.10
43 54 0.76
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (42 bp):
TATCACATATCGATGCCATATCCCAGACAAGGTCTTACACGT
Found at i:56018008 original size:9 final size:9
Alignment explanation
Indices: 56017994--56018043 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
56017984 TTTTGGTTAA
56017994 AAATTAACC
1 AAATTAACC
56018003 AAATTAACC
1 AAATTAACC
* *
56018012 GAATTACCC
1 AAATTAACC
*
56018021 GAATTAACC
1 AAATTAACC
* *
56018030 GAATTACCC
1 AAATTAACC
56018039 AAATT
1 AAATT
56018044 GAATCACTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (9 bp):
AAATTAACC
Found at i:56018025 original size:18 final size:18
Alignment explanation
Indices: 56017995--56018043 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
56017985 TTTGGTTAAA
*
56017995 AATTAACCAAATTAACCG
1 AATTACCCAAATTAACCG
*
56018013 AATTACCCGAATTAACCG
1 AATTACCCAAATTAACCG
56018031 AATTACCCAAATT
1 AATTACCCAAATT
56018044 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (18 bp):
AATTACCCAAATTAACCG
Found at i:56018189 original size:18 final size:18
Alignment explanation
Indices: 56018153--56018192 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56018143 TTTTATGATT
**
56018153 GGTTGGGTTGGGTAATTG
1 GGTTGGGTTGAATAATTG
*
56018171 GGTTGGGTTGAATACTTG
1 GGTTGGGTTGAATAATTG
56018189 GGTT
1 GGTT
56018193 TAGATTGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.45, T:0.40
Consensus pattern (18 bp):
GGTTGGGTTGAATAATTG
Found at i:56028817 original size:3 final size:3
Alignment explanation
Indices: 56028802--56028854 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
56028792 ATGAATGGAA
* *
56028802 AAG AAG AAA AAG AAG AAG AAG AAG AAG TAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
56028850 AAG AA
1 AAG AA
56028855 AAACTATATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:56029256 original size:25 final size:25
Alignment explanation
Indices: 56029226--56029296 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
56029216 CTTTTCTTAA
56029226 ACTTTTGATTTTTAATATTTT-AAAT
1 ACTTTT-ATTTTTAATATTTTAAAAT
*
56029251 ACTTTT-TTTTGAATATTTTTAAAAT
1 ACTTTTATTTTTAATA-TTTTAAAAT
*
56029276 AATTTTATTTCTTAATATTTT
1 ACTTTTATTT-TTAATATTTT
56029297 TATAATATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 8 0.21
24 4 0.10
25 15 0.38
26 7 0.18
27 5 0.13
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (25 bp):
ACTTTTATTTTTAATATTTTAAAAT
Found at i:56031644 original size:33 final size:33
Alignment explanation
Indices: 56031596--56031664 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
56031586 GGCTCCCAAG
56031596 TAGCTTGAGCCGAGTATCATTT-AGCTCAAATGA
1 TAGCTTGAGCCGAGTAT-ATTTCAGCTCAAATGA
** * *
56031629 TAGCTTGAGTTGAGTATTTTTCAGCTCGAATGA
1 TAGCTTGAGCCGAGTATATTTCAGCTCAAATGA
56031662 TAG
1 TAG
56031665 TTCGAGCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (33 bp):
TAGCTTGAGCCGAGTATATTTCAGCTCAAATGA
Found at i:56033421 original size:25 final size:23
Alignment explanation
Indices: 56033393--56033438 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
56033383 GCATTATTAA
*
56033393 GATAATTAATCCTGTTTTATAATAC
1 GATAATTAAACC--TTTTATAATAC
*
56033418 GATATTTAAACCTTTTATAAT
1 GATAATTAAACCTTTTATAAT
56033439 CAAGGTCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
25 10 0.53
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (23 bp):
GATAATTAAACCTTTTATAATAC
Found at i:56039200 original size:17 final size:18
Alignment explanation
Indices: 56039169--56039202 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
56039159 TTAATGGGAT
*
56039169 AAAAAATGTTTCAATTAG
1 AAAAAATGTTCCAATTAG
56039187 AAAAAAT-TTCCAATTA
1 AAAAAATGTTCCAATTA
56039203 ATGAACCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (18 bp):
AAAAAATGTTCCAATTAG
Found at i:56039687 original size:10 final size:11
Alignment explanation
Indices: 56039668--56039699 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
56039658 CGACCCTAAT
56039668 AAAACAAAAAA
1 AAAACAAAAAA
56039679 AAAACAAAAAA
1 AAAACAAAAAA
56039690 AAAACCAAAA
1 AAAA-CAAAA
56039700 CAAATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:56041881 original size:221 final size:219
Alignment explanation
Indices: 56041498--56041935 Score: 716
Period size: 221 Copynumber: 2.0 Consensus size: 219
56041488 TTCTATCTTG
*
56041498 AGATAACAAGATGTCACATCCAGTAAGTTAGGATACAACACCTCGAATCCTCGAGAATAAACTTT
1 AGATAACAAGATGCCACATCCAGTAAGTTAGGATACAACACCTCGAATCCTCGAGAATAAACTTT
56041563 TTTTATTTTTTTATTCCAAAACTCACATATTTTAATTTTAAAAGGATATTCAGTCATTCAGGTTC
66 TTTTATTTTTTTATTCCAAAACTCACATATTTTAATTTTAAAAGGATATTCAGTCATTCAGGTTC
* ** *
56041628 AATGGAAAAAAATTGAAACCCAGTAAGTTAGGGCACGACTTCTCGCATTTCTAAATACCGAACAT
131 AACGGAAAAAAATCAAAACCCAGTAAGTTAGGGCACGACTTCTCGCATTTCGAAATACCGAACAT
*
56041693 TGCCTTATTTTGGAAATTTTCTCT
196 TGCATTATTTTGGAAATTTTCTCT
*
56041717 AGATAACAAGATGCCACGTCCAGTAAGTTAGGATACAACACCTCGAATCCTCGAGAATAAACTTT
1 AGATAACAAGATGCCACATCCAGTAAGTTAGGATACAACACCTCGAATCCTCGAGAATAAACTTT
* * ** *
56041782 TCTTTCATTTTTTTATTCCAATACTCACGTATTTTAATTTTAAAAGGATATTTGGTCATTTAGGT
66 T-TTT-ATTTTTTTATTCCAAAACTCACATATTTTAATTTTAAAAGGATATTCAGTCATTCAGGT
* *
56041847 TCAAC-GAGAAAAAATCAAAACCTAGTTAGTTAGGGCACGACTTCTCGCATTTCGAAATACCGAA
129 TCAACGGA-AAAAAATCAAAACCCAGTAAGTTAGGGCACGACTTCTCGCATTTCGAAATACCGAA
56041911 CATTGCATTATTTTGGAAATTTTCT
193 CATTGCATTATTTTGGAAATTTTCT
56041936 TTATTATAAA
Statistics
Matches: 202, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
219 64 0.32
220 5 0.02
221 133 0.66
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (219 bp):
AGATAACAAGATGCCACATCCAGTAAGTTAGGATACAACACCTCGAATCCTCGAGAATAAACTTT
TTTTATTTTTTTATTCCAAAACTCACATATTTTAATTTTAAAAGGATATTCAGTCATTCAGGTTC
AACGGAAAAAAATCAAAACCCAGTAAGTTAGGGCACGACTTCTCGCATTTCGAAATACCGAACAT
TGCATTATTTTGGAAATTTTCTCT
Found at i:56042216 original size:18 final size:17
Alignment explanation
Indices: 56042190--56042252 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
56042180 TTTAATAATG
*
56042190 ATAATAATAAACAAATAA
1 ATAAAAATAAA-AAATAA
*
56042208 ATAAAAATATAGAAATGAA
1 ATAAAAATA-AAAAAT-AA
*
56042227 ATGAAAATAAAAAATATA
1 ATAAAAATAAAAAATA-A
56042245 A-AAAAATA
1 ATAAAAATA
56042253 CGATAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 7 0.19
18 19 0.51
19 11 0.30
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.21
Consensus pattern (17 bp):
ATAAAAATAAAAAATAA
Found at i:56043998 original size:44 final size:44
Alignment explanation
Indices: 56043911--56044430 Score: 348
Period size: 44 Copynumber: 11.5 Consensus size: 44
56043901 AATCCGACCT
* * * * * * *
56043911 ACTGCAACTTCAGAGATATAAGATTCATCGTTTTAATCCGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTGCTCC
* *
56043955 ACTGCAACTTCAGAGAGATAGGATTAATAGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTGCTCC
* * ** * *
56043999 ACTGCAACTTTAGGGAGATAATATTGGTTATCTTCAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAATCTGCTCC
* * * * *
56044044 AGTGCAACTTCAGGAAGATAAGACTTGTTATGGTAGACTT-AATCCGCTCT
1 ACTGCAACTTCAGGGAGATAAGA----TTA--ATAG-CTTCAATCTGCTCC
* *
56044094 ACTGCAACTTTAGGGAGATAGGATTAATAGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTGCTCC
* ** * *
56044138 ACTGCAACTTCAAGGAGATAAGATTGGTATCTTCAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTGCTCC
* * ** * *
56044182 ACTGCAACTTTAGGGAGATAAGGTTGTTTATCTTCAATCTGCTTC
1 ACTGCAACTTCAGGGAGATAAGATT-AATAGCTTCAATCTGCTCC
* * * *
56044227 ACTACAACTTCAGGGAGATAAGACTTGTTATGGTAGACTT-AATCCGAC-CT
1 ACTGCAACTTCAGGGAGATAAGA----TTA--ATAG-CTTCAATCTG-CTCC
* * * * * * * * *
56044277 ACTACAACTTTAGAGG-TATAGGATTCATCGTTTTAATCCGCTCC
1 ACTGCAACTTCAG-GGAGATAAGATTAATAGCTTCAATCTGCTCC
*
56044321 ACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTGCTCC
* ** ** *
56044365 ACTGCAACTTTAGAAAGATAAGATTGGTATCTTCAA-CTTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATC-TGCTCC
*
56044409 ACTGCAACTTTAGGGAGATAAG
1 ACTGCAACTTCAGGGAGATAAG
56044431 GTTTGTTATC
Statistics
Matches: 373, Mismatches: 80, Indels: 46
0.75 0.16 0.09
Matches are distributed among these distances:
43 9 0.02
44 225 0.60
45 69 0.18
46 5 0.01
49 4 0.01
50 52 0.14
51 9 0.02
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTAATAGCTTCAATCTGCTCC
Done.