Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 22 of 117
Found at i:2776653 original size:25 final size:25
Alignment explanation
Indices: 2776624--2776674 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2776614 ATATTGTATT
*
2776624 TAAAA-TTATTAAATTTAATTTTTAA
1 TAAAATTTA-TAAATATAATTTTTAA
*
2776649 TAAAATTTATATATATAATTTTTAA
1 TAAAATTTATAAATATAATTTTTAA
2776674 T
1 T
2776675 TTTATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TAAAATTTATAAATATAATTTTTAA
Found at i:2777482 original size:28 final size:28
Alignment explanation
Indices: 2777445--2777499 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2777435 TAGAATTATT
* *
2777445 AAAATTTAAATTTTAAT-AATTAAAATTA
1 AAAATCTAAAATTTAATCAA-TAAAATTA
*
2777473 AAAATCTAAAATTTCATCAATAAAATT
1 AAAATCTAAAATTTAATCAATAAAATT
2777500 GTTGGTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAATCTAAAATTTAATCAATAAAATTA
Found at i:2783731 original size:21 final size:20
Alignment explanation
Indices: 2783692--2783731 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
2783682 TGAAAATTTT
2783692 TTTTATGATGAAAAGAGTAA
1 TTTTATGATGAAAAGAGTAA
2783712 TTTTATGTTATGAAAA-AGTA
1 TTTTATG--ATGAAAAGAGTA
2783732 CGATTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTTATGATGAAAAGAGTAA
Found at i:2788209 original size:33 final size:33
Alignment explanation
Indices: 2788171--2788319 Score: 129
Period size: 33 Copynumber: 4.5 Consensus size: 33
2788161 TACCTTAGGT
* *
2788171 GGTTGTGGTTTGGGTGGAGGTGAAGTCTTTGGA
1 GGTTGTGGCTTGGGTGGAGGTGAATTCTTTGGA
* * * *
2788204 AGTTGTGGCTTGGGTGGAGGAGCATTGTTTGGA
1 GGTTGTGGCTTGGGTGGAGGTGAATTCTTTGGA
* * **
2788237 GGTTGT-GATTGGGATGGAGTTGGCTTCTTTGGA
1 GGTTGTGGCTTGGG-TGGAGGTGAATTCTTTGGA
* ** **
2788270 GGTTGTGGCTTGGGTGAAGGTGGGTTGATTGGA
1 GGTTGTGGCTTGGGTGGAGGTGAATTCTTTGGA
* *
2788303 GGTTGTGCCTTAGGTGG
1 GGTTGTGGCTTGGGTGG
2788320 TTGTGGTTTG
Statistics
Matches: 92, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
32 6 0.07
33 80 0.87
34 6 0.07
ACGTcount: A:0.12, C:0.05, G:0.47, T:0.36
Consensus pattern (33 bp):
GGTTGTGGCTTGGGTGGAGGTGAATTCTTTGGA
Found at i:2788220 original size:48 final size:46
Alignment explanation
Indices: 2788168--2788367 Score: 114
Period size: 48 Copynumber: 4.1 Consensus size: 46
2788158 TTCTACCTTA
2788168 GGTGGTTGTGGTTTGGGTGGAGGTGAAGTCTTTGGAAGTTGTGGCTTG
1 GGTGGTTGTGGTTTGGGTGGAGGTG-AGT-TTTGGAAGTTGTGGCTTG
** * ** ** * * * * *
2788216 GGTGGAGGAGCATTGTTTGGAGGTTGTGATTGGGATGGAGTTG-GCTTCTTT
1 GGTGGTTGTGGTTTGGGTGGAGG-TGAGTTTTGGA---AGTTGTG--GCTTG
* * * * * * *
2788267 GGAGGTTGTGGCTTGGGTGAAGGTGGGTTGATTGGAGGTTGTGCCTTA
1 GGTGGTTGTGGTTTGGGTGGAGGTGAGTT--TTGGAAGTTGTGGCTTG
2788315 GGTGGTTGTGGTTTGGGTGGAGGTGAAGTTTTTGGAAGTTGTGGCTTG
1 GGTGGTTGTGGTTTGGGTGGAGGTG-AG-TTTTGGAAGTTGTGGCTTG
2788363 GGTGG
1 GGTGG
2788368 AGGAGTATTG
Statistics
Matches: 107, Mismatches: 34, Indels: 22
0.66 0.21 0.13
Matches are distributed among these distances:
47 5 0.05
48 61 0.57
49 8 0.07
50 12 0.11
51 17 0.16
52 4 0.04
ACGTcount: A:0.12, C:0.04, G:0.47, T:0.36
Consensus pattern (46 bp):
GGTGGTTGTGGTTTGGGTGGAGGTGAGTTTTGGAAGTTGTGGCTTG
Found at i:2788255 original size:66 final size:65
Alignment explanation
Indices: 2788171--2788309 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 65
2788161 TACCTTAGGT
* * *
2788171 GGTTGTGGTTTGGGTGGAGGTGAAGTCTTTGGAAGTTGTGGCTTGGGTGGAGGAGCATTGTTTGG
1 GGTTGT-GATTGGGTGGAGGTGAAGTCTTTGGAAGTTGTGGCTTGGGTGAAGGAGCATTGATTGG
2788236 A
65 A
* *** * * **
2788237 GGTTGTGATTGGGATGGAGTTGGCTTCTTTGGAGGTTGTGGCTTGGGTGAAGGTGGGTTGATTGG
1 GGTTGTGATTGGG-TGGAGGTGAAGTCTTTGGAAGTTGTGGCTTGGGTGAAGGAGCATTGATTGG
2788302 A
65 A
2788303 GGTTGTG
1 GGTTGTG
2788310 CCTTAGGTGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 6 0.10
66 55 0.90
ACGTcount: A:0.12, C:0.04, G:0.47, T:0.36
Consensus pattern (65 bp):
GGTTGTGATTGGGTGGAGGTGAAGTCTTTGGAAGTTGTGGCTTGGGTGAAGGAGCATTGATTGGA
Found at i:2788285 original size:147 final size:150
Alignment explanation
Indices: 2788119--2788517 Score: 588
Period size: 147 Copynumber: 2.7 Consensus size: 150
2788109 GTGAGTTCAA
* * * * *
2788119 TGGAGGTTGTTGCTTGGGTGGAGGCGGGTTGACTGGAGGTTCTACCTTAGGTGGTTGTGGTTTGG
1 TGGAGGTTGTGGCTTGGGTGGAGGTGGGTTGATTGGAGGTTGTGCCTTAGGTGGTTGTGGTTTGG
*
2788184 GTGGAGGTGAAGTCTTTGGAAGTTGTGGCTTGGGTGGAGGAGCATTGTTTGGAGGTTGTGATT-G
66 GTGGAGGTGAAGTATTTGGAAGTTGTGGCTTGGGTGGAGGAGCATTGTTTGGAGGTTGTGATTGG
*
2788248 -GGA-TGGAGTTGGCTTCTT
131 TGGAGTGGAGGTGGCTTCTT
*
2788266 TGGAGGTTGTGGCTTGGGTGAAGGTGGGTTGATTGGAGGTTGTGCCTTAGGTGGTTGTGGTTTGG
1 TGGAGGTTGTGGCTTGGGTGGAGGTGGGTTGATTGGAGGTTGTGCCTTAGGTGGTTGTGGTTTGG
* * *
2788331 GTGGAGGTGAAGTTTTTGGAAGTTGTGGCTTGGGTGGAGGAGTATTGTTTGGAGGTTGTGGTTGG
66 GTGGAGGTGAAGTATTTGGAAGTTGTGGCTTGGGTGGAGGAGCATTGTTTGGAGGTTGTGATT--
*
2788396 GGTGGAGGTGGAGGTGGGTTCTT
129 GGTGGA-GTGGAGGTGGCTTCTT
*
2788419 TGGAGGTTGAGGCTTGGGTGGAGGTGGGTTGATTGGAGGTTGTGCCTTAGGTGGTTGTGGTTTGG
1 TGGAGGTTGTGGCTTGGGTGGAGGTGGGTTGATTGGAGGTTGTGCCTTAGGTGGTTGTGGTTTGG
* * * **
2788484 GTGGAAGTGAATTATTTGGAGGTTGAAGCTTGGG
66 GTGGAGGTGAAGTATTTGGAAGTTGTGGCTTGGG
2788518 GGGACGTGAA
Statistics
Matches: 227, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
147 119 0.52
150 1 0.00
151 3 0.01
153 104 0.46
ACGTcount: A:0.12, C:0.05, G:0.47, T:0.35
Consensus pattern (150 bp):
TGGAGGTTGTGGCTTGGGTGGAGGTGGGTTGATTGGAGGTTGTGCCTTAGGTGGTTGTGGTTTGG
GTGGAGGTGAAGTATTTGGAAGTTGTGGCTTGGGTGGAGGAGCATTGTTTGGAGGTTGTGATTGG
TGGAGTGGAGGTGGCTTCTT
Found at i:2788356 original size:33 final size:33
Alignment explanation
Indices: 2788319--2788405 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
2788309 GCCTTAGGTG
2788319 GTTGTGGTTTGGGTGGAGGTGAAGTT-TTTGGAA
1 GTTGTGGTTTGGGTGGAGGTGAA-TTGTTTGGAA
* * * *
2788352 GTTGTGGCTTGGGTGGAGGAGTATTGTTTGGAG
1 GTTGTGGTTTGGGTGGAGGTGAATTGTTTGGAA
*
2788385 GTTGTGGTTGGGGTGGAGGTG
1 GTTGTGGTTTGGGTGGAGGTG
2788406 GAGGTGGGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.11, C:0.01, G:0.51, T:0.37
Consensus pattern (33 bp):
GTTGTGGTTTGGGTGGAGGTGAATTGTTTGGAA
Found at i:2788472 original size:33 final size:33
Alignment explanation
Indices: 2788401--2788472 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
2788391 GTTGGGGTGG
* *
2788401 AGGTGGAGGTGGGTTCTTTGGAGGTTGAGGCTT
1 AGGTGGAGGTGGGTTCATTGGAGGTTGAGCCTT
* * *
2788434 GGGTGGAGGTGGGTTGATTGGAGGTTGTGCCTT
1 AGGTGGAGGTGGGTTCATTGGAGGTTGAGCCTT
2788467 AGGTGG
1 AGGTGG
2788473 TTGTGGTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.11, C:0.06, G:0.51, T:0.32
Consensus pattern (33 bp):
AGGTGGAGGTGGGTTCATTGGAGGTTGAGCCTT
Found at i:2788472 original size:72 final size:72
Alignment explanation
Indices: 2788330--2788472 Score: 173
Period size: 72 Copynumber: 2.0 Consensus size: 72
2788320 TTGTGGTTTG
* * * *
2788330 GGTGGAGGTGAAGTTTTTGGAAGTTGTGGCTTGGGTGGAGGAGTATTGTTTGGAGGTTGTGGTTG
1 GGTGGAGGTGAAGTTTTTGGAAGTTGAGGCTTGGGTGGAGGAGGATTGATTGGAGGTTGTGCTTG
*
2788395 GGGTGGA
66 AGGTGGA
* * * *
2788402 GGTGGAGGTG-GGTTCTTTGGAGGTTGAGGCTTGGGTGGAGGTGGGTTGATTGGAGGTTGTGCCT
1 GGTGGAGGTGAAGTT-TTTGGAAGTTGAGGCTTGGGTGGAGGAGGATTGATTGGAGGTTGTG-CT
2788466 T-AGGTGG
64 TGAGGTGG
2788473 TTGTGGTTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
71 3 0.05
72 55 0.92
73 2 0.03
ACGTcount: A:0.12, C:0.03, G:0.51, T:0.34
Consensus pattern (72 bp):
GGTGGAGGTGAAGTTTTTGGAAGTTGAGGCTTGGGTGGAGGAGGATTGATTGGAGGTTGTGCTTG
AGGTGGA
Found at i:2788508 original size:33 final size:33
Alignment explanation
Indices: 2788471--2789184 Score: 164
Period size: 33 Copynumber: 21.5 Consensus size: 33
2788461 TGCCTTAGGT
*
2788471 GGTTGTGGTTTGGGTGGAAGTGAATTATTTGGA
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
** * * * * *
2788504 GGTTGAAGCTTGGGGGGACGTGAATTTTTTGGT
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
** * * *
2788537 GG-T-TGGTTCACCGGAGGAGGTGGATTCTTTGGA
1 GGTTGTGGTT--TGGGTGGAAGTGAATTCTTTGGA
*
2788570 GGTTGTGGTTTGGCT-GAAGGTGAATTCTTTGGA
1 GGTTGTGGTTTGGGTGGAA-GTGAATTCTTTGGA
** * * * ****
2788603 GGTTGTGACTTGGATGGAGGT-AGGTTAACCGGA
1 GGTTGTGGTTTGGGTGGAAGTGA-ATTCTTTGGA
** ** * *
2788636 GGTTGTGACTTAAGTGG-AGATGAATTTTTTGGG
1 GGTTGTGGTTTGGGTGGAAG-TGAATTCTTTGGA
* * ** * **
2788669 GGCTGCGACTCGGGTGGAAGTGGGTTCTTTGGA
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
** ** * **
2788702 GGTTGTGACTTGGAAGG-TGTG--TTCACTGGA
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
* * * * *
2788732 AGTTGTGGGTTAGGT-GAAGGTGAATTATTAGGA
1 GGTTGTGGTTTGGGTGGAA-GTGAATTCTTTGGA
* * **
2788765 GGTTGCT-GCTTGGGTGGAAGGGGGTTCTTTGGA
1 GGTTG-TGGTTTGGGTGGAAGTGAATTCTTTGGA
** * * ** ***
2788798 GGTTGTGACTGGGGTGGAGGTGTGTTCACCGGA
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
* * * *
2788831 AGTTGTAGCTTGGGT-GAAGGTGAATTCATTGGA
1 GGTTGTGGTTTGGGTGGAA-GTGAATTCTTTGGA
* *
2788864 GGTTGTGGCTTGGGT-GAAGGTGAATTCATTGGA
1 GGTTGTGGTTTGGGTGGAA-GTGAATTCTTTGGA
** *
2788897 GGTTGTGGCTTT-GGTGGAAGTGGGTTGTTTGGA
1 GGTTGTGG-TTTGGGTGGAAGTGAATTCTTTGGA
* ** * * *
2788930 AGTTGTGACTTAGGTGGAGGTGAATTTTTTGGA
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
* * * * ** **
2788963 GGCTGTGGCTTAGATGGAAGTGTGTTCACTGGA
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
* *
2788996 GGTTGTGGAAGTTGTGGCTTGAGTGAAGGTGAATTCTTTGGG
1 GGTTGT-G--GTT-TGG---GTG-GAA-GTGAATTCTTTGGA
* * * ** *
2789038 GGTTGTGGCTCGGGTGAAAGTGGGTTCTTAGG-
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
** * * *
2789070 GAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGA
1 G-GTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
* * * * * **
2789104 GGTTGCGGCTTGGATGGAAATGTATTCACTGGA
1 GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
*
2789137 GGTTGTGG-CTGTGGT-GAAGGTGAATTCTTTGGA
1 GGTTGTGGTTTG-GGTGGAA-GTGAATTCTTTGGA
*
2789170 GGTTGTGGCTTGGGT
1 GGTTGTGGTTTGGGT
2789185 AGAGGTGTGT
Statistics
Matches: 483, Mismatches: 163, Indels: 70
0.67 0.23 0.10
Matches are distributed among these distances:
29 1 0.00
30 16 0.03
31 5 0.01
32 19 0.04
33 386 0.80
34 21 0.04
35 7 0.01
36 2 0.00
37 2 0.00
38 2 0.00
39 2 0.00
40 1 0.00
41 4 0.01
42 15 0.03
ACGTcount: A:0.17, C:0.07, G:0.42, T:0.34
Consensus pattern (33 bp):
GGTTGTGGTTTGGGTGGAAGTGAATTCTTTGGA
Found at i:2788622 original size:66 final size:65
Alignment explanation
Indices: 2788552--2789182 Score: 278
Period size: 66 Copynumber: 9.5 Consensus size: 65
2788542 GTTCACCGGA
* *
2788552 GGAGGTGGATTCTTTGGAGGTTGTGGTTTGGCTGAAGGTGAATTCTTTGGAGGTTGTGACTTGGA
1 GGAGGTGGATTCTTTGGAGGTTGTGGCTTGG-TGAAGGTGAATTCTTTGGAGGTTGTGACTTGGG
2788617 T
65 T
**** * * * * * * * * *
2788618 GGAGGTAGG-TTAACCGGAGGTTGTGACTTAAGTGGAGATGAATTTTTTGGGGGCTGCGACTCGG
1 GGAGGT-GGATTCTTTGGAGGTTGTGGCTT-GGTGAAGGTGAATTCTTTGGAGGTTGTGACTTGG
2788682 GT
64 GT
* * * ** ** * ** *
2788684 GGAAGTGGGTTCTTTGGAGGTTGTGACTT-G-GAAGGTGTGTTCACTGGAAGTTGTGGGTTAGGT
1 GGAGGTGGATTCTTTGGAGGTTGTGGCTTGGTGAAGGTGAATTCTTTGGAGGTTGTGACTTGGGT
* * * * ** *
2788747 GAAGGTGAATTATTAGGAGGTTGCT-GCTTGGGTGGAAGG-GGGTTCTTTGGAGGTTGTGACTGG
1 GGAGGTGGATTCTTTGGAGGTTG-TGGCTT-GGT-GAAGGTGAATTCTTTGGAGGTTGTGACTTG
2788810 GGT
63 GGT
*** * * * *
2788813 GGAGGTGTG-TTCACCGGAAGTTGTAGCTTGGGTGAAGGTGAATTCATTGGAGGTTGTGGCTTGG
1 GGAGGTG-GATTCTTTGGAGGTTGTGGCTT-GGTGAAGGTGAATTCTTTGGAGGTTGTGACTTGG
2788877 GT
64 GT
* * * ** * * *
2788879 GAAGGTGAATTCATTGGAGGTTGTGGCTTTGGTGGAA-GTGGGTTGTTTGGAAGTTGTGACTTAG
1 GGAGGTGGATTCTTTGGAGGTTGTGGC-TTGGT-GAAGGTGAATTCTTTGGAGGTTGTGACTTGG
2788943 GT
64 GT
* * * * ** *
2788945 GGAGGTGAATTTTTTGGAGGCTGTGGCTTAGATGGAAGTGTG--TTCACTGGAGGTTGTGGAAGT
1 GGAGGTGGATTCTTTGGAGGTTGTGGCTT-GGT-GAAG-GTGAATTCTTTGGAGGTTGT-G-ACT
2789008 TGTGGCTT
61 TG-GG--T
* * * * ** *
2789016 GAGTGAAGGTGAATTCTTTGGGGGTTGTGGCTCGGGTGAAAGTGGGTTCTTAGG-GAGTTGTGAC
1 --G-G-AGGTGGATTCTTTGGAGGTTGTGGCT-TGGTGAAGGTGAATTCTTTGGAG-GTTGTGAC
*
2789080 TTAGGT
60 TTGGGT
* * * * * ** *
2789086 GGAGGTGAATTTTTTGGAGGTTGCGGCTTGGATGGAA-ATGTATTCACTGGAGGTTGTGGC-TGT
1 GGAGGTGGATTCTTTGGAGGTTGTGGCTTGG-T-GAAGGTGAATTCTTTGGAGGTTGTGACTTG-
2789149 GGT
63 GGT
* *
2789152 GAAGGTGAATTCTTTGGAGGTTGTGGCTTGG
1 GGAGGTGGATTCTTTGGAGGTTGTGGCTTGG
2789183 GTAGAGGTGT
Statistics
Matches: 419, Mismatches: 112, Indels: 68
0.70 0.19 0.11
Matches are distributed among these distances:
63 38 0.09
64 2 0.00
65 14 0.03
66 285 0.68
67 19 0.05
68 7 0.02
69 2 0.00
70 1 0.00
71 1 0.00
72 2 0.00
73 7 0.02
74 6 0.01
75 35 0.08
ACGTcount: A:0.17, C:0.07, G:0.42, T:0.34
Consensus pattern (65 bp):
GGAGGTGGATTCTTTGGAGGTTGTGGCTTGGTGAAGGTGAATTCTTTGGAGGTTGTGACTTGGGT
Found at i:2788667 original size:99 final size:100
Alignment explanation
Indices: 2788554--2788982 Score: 385
Period size: 99 Copynumber: 4.4 Consensus size: 100
2788544 TCACCGGAGG
* * * *
2788554 AGGTGGATTCTTTGGAGGTTGTGGTTTGGCT-GAAGGTGAATTCTTTGGAGGTTGTGACTTGGAT
1 AGGTGAATTTTTTGGAGGTTGTGGCTTGGGTGGAAGGTGAATTCTTTGGAGGTTGTGACTTGGAT
* * * *
2788618 GGAGGTAG-GTTAACCGGAGGTTGTGACTTAAGTGG
66 GGAGGT-GTGTTCACCGGAAGTTGTGACTTAGGTGA
* * * * * * **
2788653 AGATGAATTTTTTGGGGGCTGCGACTCGGGTGGAA-GTGGGTTCTTTGGAGGTTGTGACTTGGA-
1 AGGTGAATTTTTTGGAGGTTGTGGCTTGGGTGGAAGGTGAATTCTTTGGAGGTTGTGACTTGGAT
* **
2788716 --AGGTGTGTTCACTGGAAGTTGTGGGTTAGGTGA
66 GGAGGTGTGTTCACCGGAAGTTGTGACTTAGGTGA
* * ** * *
2788749 AGGTGAATTATTAGGAGGTTGCT-GCTTGGGTGGAAGG-GGGTTCTTTGGAGGTTGTGACTGGGG
1 AGGTGAATTTTTTGGAGGTTG-TGGCTTGGGTGGAAGGTGAATTCTTTGGAGGTTGTGACTTGGA
*
2788812 TGGAGGTGTGTTCACCGGAAGTTGT-AGCTTGGGTGA
65 TGGAGGTGTGTTCACCGGAAGTTGTGA-CTTAGGTGA
** * *
2788848 AGGTGAATTCATTGGAGGTTGTGGCTTGGGT-GAAGGTGAATTCATTGGAGGTTGTGGCTTTGG-
1 AGGTGAATTTTTTGGAGGTTGTGGCTTGGGTGGAAGGTGAATTCTTTGGAGGTTGTGAC-TTGGA
* * **** *
2788911 TGGAAGTGGGTTGTTTGGAAGTTGTGACTTAGGTGG
65 TGGAGGTGTGTTCACCGGAAGTTGTGACTTAGGTGA
* * *
2788947 AGGTGAATTTTTTGGAGGCTGTGGCTTAGATGGAAG
1 AGGTGAATTTTTTGGAGGTTGTGGCTTGGGTGGAAG
2788983 TGTGTTCACT
Statistics
Matches: 263, Mismatches: 54, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
95 1 0.00
96 74 0.28
97 1 0.00
98 6 0.02
99 170 0.65
100 11 0.04
ACGTcount: A:0.17, C:0.07, G:0.42, T:0.34
Consensus pattern (100 bp):
AGGTGAATTTTTTGGAGGTTGTGGCTTGGGTGGAAGGTGAATTCTTTGGAGGTTGTGACTTGGAT
GGAGGTGTGTTCACCGGAAGTTGTGACTTAGGTGA
Found at i:2789059 original size:75 final size:75
Alignment explanation
Indices: 2788926--2789144 Score: 172
Period size: 75 Copynumber: 3.0 Consensus size: 75
2788916 GTGGGTTGTT
* * * * *
2788926 TGGAAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGCTGTGGCTTAGATGGAAGTGTGTTCA
1 TGGAAGTTGTGACTTAGGTGAAGGTGAATTCTTTGGAGGCTGTGGCTCAGATGAAAGTGGGTTCA
2788991 CTGGAGGTTG
66 CTGGAGGTTG
* * * * *
2789001 TGGAAGTTGTGGCTT-GAGTGAAGGTGAATTCTTTGGGGGTTGTGGCTCGGGTGAAAGTGGGTT-
1 TGGAAGTTGTGACTTAG-GTGAAGGTGAATTCTTTGGAGGCTGTGGCTCAGATGAAAGTGGGTTC
*
2789064 -CT-----TAG
65 ACTGGAGGTTG
* * * * ** **
2789069 -GG-AGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGTTGCGGCTTGGATGGAAA-TGTATTC
1 TGGAAGTTGTGACTTAGGTGAAGGTGAATTCTTTGGAGGCTGTGGCTCAGAT-GAAAGTGGGTTC
2789131 ACTGGAGGTTG
65 ACTGGAGGTTG
2789142 TGG
1 TGG
2789145 CTGTGGTGAA
Statistics
Matches: 112, Mismatches: 21, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
66 43 0.38
67 7 0.06
68 4 0.04
73 4 0.04
74 3 0.03
75 51 0.46
ACGTcount: A:0.18, C:0.07, G:0.41, T:0.34
Consensus pattern (75 bp):
TGGAAGTTGTGACTTAGGTGAAGGTGAATTCTTTGGAGGCTGTGGCTCAGATGAAAGTGGGTTCA
CTGGAGGTTG
Found at i:2789059 original size:141 final size:141
Alignment explanation
Indices: 2788860--2789144 Score: 435
Period size: 141 Copynumber: 2.0 Consensus size: 141
2788850 GTGAATTCAT
* * ** * *
2788860 TGGAGGTTGTGGCTTGGGTGAAGGTGAATTCATTGGAGGTTGTGGCTTTGGTGGAAGTGGGTTGT
1 TGGAAGTTGTGGCTTGAGTGAAGGTGAATTCATTGGAGGTTGTGGCTCGGGTGAAAGTGGGTTCT
* * * *
2788925 TTGGAAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGCTGTGGCTTAGATGGAAGTGTGTTC
66 TAGGAAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGCTGCGGCTTAGATGGAAATGTATTC
2788990 ACTGGAGGTTG
131 ACTGGAGGTTG
* *
2789001 TGGAAGTTGTGGCTTGAGTGAAGGTGAATTCTTTGGGGGTTGTGGCTCGGGTGAAAGTGGGTTCT
1 TGGAAGTTGTGGCTTGAGTGAAGGTGAATTCATTGGAGGTTGTGGCTCGGGTGAAAGTGGGTTCT
* * *
2789066 TAGGGAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGTTGCGGCTTGGATGGAAATGTATTC
66 TAGGAAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGCTGCGGCTTAGATGGAAATGTATTC
2789131 ACTGGAGGTTG
131 ACTGGAGGTTG
2789142 TGG
1 TGG
2789145 CTGTGGTGAA
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
141 129 1.00
ACGTcount: A:0.17, C:0.06, G:0.42, T:0.35
Consensus pattern (141 bp):
TGGAAGTTGTGGCTTGAGTGAAGGTGAATTCATTGGAGGTTGTGGCTCGGGTGAAAGTGGGTTCT
TAGGAAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGCTGCGGCTTAGATGGAAATGTATTC
ACTGGAGGTTG
Found at i:2789198 original size:66 final size:64
Alignment explanation
Indices: 2789001--2789205 Score: 207
Period size: 66 Copynumber: 3.1 Consensus size: 64
2788991 CTGGAGGTTG
* * * *
2789001 TGGAAGTTGTGGCTTGAGTGAAGGTGAATTCTTTGGGGGTTGTGGCTCGGGTGAAAGTGGGTTC-
1 TGGAGGTTGTGGCTTG-GTGAAGGTGAATTCTTTGGAGGTTGTGGCTTGGGTG-AAGTGTGTTCA
*
2789065 T
64 C
* * * * * * *
2789066 TAGG-GAGTTGTGACTTAGGTGGAGGTGAATTTTTTGGAGGTTGCGGCTTGGATGGAAATGTATT
1 T-GGAG-GTTGTGGCTT-GGTGAAGGTGAATTCTTTGGAGGTTGTGGCTTGGGT-GAAGTGTGTT
2789130 CAC
62 CAC
*
2789133 TGGAGGTTGTGGCTGTGGTGAAGGTGAATTCTTTGGAGGTTGTGGCTTGGGTAGAGGTGTGTTCA
1 TGGAGGTTGTGGCT-TGGTGAAGGTGAATTCTTTGGAGGTTGTGGCTTGGGT-GAAGTGTGTTCA
2789198 C
64 C
2789199 TGGAGGT
1 TGGAGGT
2789206 AGTGACATGG
Statistics
Matches: 112, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
65 1 0.01
66 106 0.95
67 5 0.04
ACGTcount: A:0.17, C:0.07, G:0.42, T:0.34
Consensus pattern (64 bp):
TGGAGGTTGTGGCTTGGTGAAGGTGAATTCTTTGGAGGTTGTGGCTTGGGTGAAGTGTGTTCAC
Found at i:2789203 original size:33 final size:32
Alignment explanation
Indices: 2789100--2789205 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 32
2789090 GTGAATTTTT
* * **
2789100 TGGAGGTTGCGGCTTGGATGGAAATGTATTCAC
1 TGGAGGTTGTGGCTTGGGT-GAGGTGTATTCAC
* **
2789133 TGGAGGTTGTGGC-TGTGGTGAAGGTGAATTCTT
1 TGGAGGTTGTGGCTTG-GGTG-AGGTGTATTCAC
*
2789166 TGGAGGTTGTGGCTTGGGTAGAGGTGTGTTCAC
1 TGGAGGTTGTGGCTTGGGT-GAGGTGTATTCAC
2789199 TGGAGGT
1 TGGAGGT
2789206 AGTGACATGG
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
32 3 0.05
33 52 0.90
34 3 0.05
ACGTcount: A:0.16, C:0.08, G:0.42, T:0.33
Consensus pattern (32 bp):
TGGAGGTTGTGGCTTGGGTGAGGTGTATTCAC
Found at i:2790153 original size:12 final size:12
Alignment explanation
Indices: 2790115--2790153 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2790105 GCTCCTTTCA
2790115 TTTCAACCAATG
1 TTTCAACCAATG
* * *
2790127 CTTAAACCAAAG
1 TTTCAACCAATG
2790139 TTTCAACCAATG
1 TTTCAACCAATG
2790151 TTT
1 TTT
2790154 AGAGGTGTAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (12 bp):
TTTCAACCAATG
Found at i:2796288 original size:25 final size:26
Alignment explanation
Indices: 2796223--2796288 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
2796213 AACATGAAAT
2796223 TTTTTTTATTTTATCAAATTCATATAA
1 TTTTTTTATTTT-TCAAATTCATATAA
* *
2796250 TTTTTTTAAATTTT-AAA-TCATATTA
1 TTTTTTT-ATTTTTCAAATTCATATAA
2796275 TTTTTTGTATTTTT
1 TTTTTT-TATTTTT
2796289 TTATCATACC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 18 0.53
26 4 0.12
27 8 0.24
28 4 0.12
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTTTATTTTTCAAATTCATATAA
Found at i:2799512 original size:20 final size:20
Alignment explanation
Indices: 2799474--2799514 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2799464 AAAAAGAGAG
** *
2799474 AGAGAGAGAGGTCATGCTGC
1 AGAGAGAGAGAACAAGCTGC
2799494 AGAGAGAGAGAACAAGCTGC
1 AGAGAGAGAGAACAAGCTGC
2799514 A
1 A
2799515 TTAGTACACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.37, T:0.10
Consensus pattern (20 bp):
AGAGAGAGAGAACAAGCTGC
Found at i:2801151 original size:2 final size:2
Alignment explanation
Indices: 2801144--2801174 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2801134 TTAATTCATG
2801144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2801175 ACACTAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2807110 original size:3 final size:3
Alignment explanation
Indices: 2807102--2807131 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2807092 TGAAAAAGTC
2807102 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2807132 TTCTTTACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2807295 original size:10 final size:11
Alignment explanation
Indices: 2807252--2807456 Score: 65
Period size: 11 Copynumber: 18.6 Consensus size: 11
2807242 TATTTAATTA
*
2807252 TAATATTTAAT
1 TAATATTAAAT
*
2807263 TAGATAATAAAT
1 TA-ATATTAAAT
2807275 TAATATT-AAT
1 TAATATTAAAT
2807285 TAA-ATTAAAT
1 TAATATTAAAT
*
2807295 T-ATAATAAA-
1 TAATATTAAAT
**
2807304 TAATTAATT-ACC
1 TAA-T-ATTAAAT
*
2807316 TAATATTAAAA
1 TAATATTAAAT
*
2807327 TATTATTAAAT
1 TAATATTAAAT
**
2807338 TAATATTTCAT
1 TAATATTAAAT
*
2807349 ATAA-AATAATATT
1 -TAATATTAA-A-T
2807362 ATAATATTATAA-
1 -TAATATTA-AAT
* *
2807374 TATTGTTTAAA-
1 TAAT-ATTAAAT
2807385 TAATATTAAGTAT
1 TAATATTAA--AT
2807398 TAAATATTAAA-
1 T-AATATTAAAT
* *
2807409 TATTATTAACT
1 TAATATTAAAT
2807420 TAATATT-AA-
1 TAATATTAAAT
* *
2807429 -AATTTTAAAA
1 TAATATTAAAT
*
2807439 TATTATTAAAT
1 TAATATTAAAT
2807450 TAATATT
1 TAATATT
2807457 GAGAATTTAG
Statistics
Matches: 142, Mismatches: 30, Indels: 44
0.66 0.14 0.20
Matches are distributed among these distances:
8 5 0.04
9 7 0.05
10 31 0.22
11 57 0.40
12 23 0.16
13 6 0.04
14 12 0.08
15 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (11 bp):
TAATATTAAAT
Found at i:2807299 original size:27 final size:27
Alignment explanation
Indices: 2807260--2807313 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2807250 TATAATATTT
* *
2807260 AATTAGATAATAAATTAAT-ATTAATTA
1 AATTAAATAAT-AATAAATAATTAATTA
*
2807287 AATTAAATTATAATAAATAATTAATTA
1 AATTAAATAATAATAAATAATTAATTA
2807314 CCTAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
AATTAAATAATAATAAATAATTAATTA
Found at i:2807342 original size:14 final size:14
Alignment explanation
Indices: 2807270--2807456 Score: 53
Period size: 14 Copynumber: 11.9 Consensus size: 14
2807260 AATTAGATAA
2807270 TAAATTAATATTAAT
1 TAAATTAATATT-AT
2807285 TAAATTAA-ATTAT
1 TAAATTAATATTAT
*
2807298 AATAAA-TAATTAATTACC
1 --TAAATTAA-T-ATTA-T
2807316 TAATATTAAAATATTAT
1 TAA-ATT--AATATTAT
2807333 TAAATTAATATTTCAT
1 TAAATTAATA-TT-AT
*
2807349 ATAAAATAATATTA-
1 -TAAATTAATATTAT
*
2807363 TAATATTATAATATTGTT
1 TAA-A-T-TAATATT-AT
2807381 TAAA-TAATATTAAGTAT
1 TAAATTAATA-T---TAT
2807398 TAAATATTAAATATTAT
1 T-AA-ATT-AATATTAT
*
2807415 TAACTTAATATTA-
1 TAAATTAATATTAT
2807428 -AAATTTTAAAATATTAT
1 TAAA--TT--AATATTAT
2807445 TAAATTAATATT
1 TAAATTAATATT
2807457 GAGAATTTAG
Statistics
Matches: 132, Mismatches: 8, Indels: 65
0.64 0.04 0.32
Matches are distributed among these distances:
12 2 0.02
13 5 0.04
14 31 0.23
15 18 0.14
16 28 0.21
17 24 0.18
18 14 0.11
19 2 0.02
20 4 0.03
21 4 0.03
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (14 bp):
TAAATTAATATTAT
Found at i:2807367 original size:8 final size:8
Alignment explanation
Indices: 2807354--2807444 Score: 52
Period size: 8 Copynumber: 12.2 Consensus size: 8
2807344 TTCATATAAA
2807354 ATAATATT
1 ATAATATT
2807362 ATAATATT
1 ATAATATT
2807370 ATAATATT
1 ATAATATT
* * *
2807378 GT-TTA-A
1 ATAATATT
2807384 ATAATATT
1 ATAATATT
*
2807392 A-AGTATT
1 ATAATATT
2807399 A-AATATT
1 ATAATATT
2807406 A-AATATT
1 ATAATATT
* *
2807413 ATTA-ACT
1 ATAATATT
2807420 -TAATATT
1 ATAATATT
* *
2807427 AAAATTTT
1 ATAATATT
*
2807435 AAAATATT
1 ATAATATT
2807443 AT
1 AT
2807445 TAAATTAATA
Statistics
Matches: 62, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
6 3 0.05
7 27 0.44
8 32 0.52
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (8 bp):
ATAATATT
Found at i:2807402 original size:17 final size:17
Alignment explanation
Indices: 2807330--2807403 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 17
2807320 ATTAAAATAT
*
2807330 TATTAAATTAATATTTCA-
1 TATTAAA-TAATA-TTAAG
* *
2807348 TATAAAATAATATTATAA
1 TATTAAATAATATTA-AG
2807366 TATT--ATAATATT--G
1 TATTAAATAATATTAAG
2807379 T-TTAAATAATATTAAG
1 TATTAAATAATATTAAG
2807395 TATTAAATA
1 TATTAAATA
2807404 TTAAATATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
12 2 0.04
13 1 0.02
14 8 0.18
16 12 0.27
17 13 0.29
18 9 0.20
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (17 bp):
TATTAAATAATATTAAG
Found at i:2807424 original size:35 final size:37
Alignment explanation
Indices: 2807358--2807428 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
2807348 TATAAAATAA
*
2807358 TATTATAATATTATAATATTGTTTAAATAATATTAAG
1 TATTATAATATTATAATATTGATTAAATAATATTAAG
*
2807395 TATTA-AATATTA-AATATT-ATTAACTTAATATTAA
1 TATTATAATATTATAATATTGATTAA-ATAATATTAA
2807429 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 4 0.13
35 15 0.48
36 7 0.23
37 5 0.16
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (37 bp):
TATTATAATATTATAATATTGATTAAATAATATTAAG
Found at i:2807442 original size:30 final size:28
Alignment explanation
Indices: 2807317--2807456 Score: 103
Period size: 30 Copynumber: 5.0 Consensus size: 28
2807307 TTAATTACCT
*
2807317 AATATTAAAATATTATTAAATTAATATTT
1 AATATT-AAATATTATTAAATTAATATTA
* * *
2807346 CATATAAAATAATATT--A-TAATATTA
1 AATATTAAATATTATTAAATTAATATTA
* *
2807371 TAATATT--GT-TTAAATAATATTAAGTATTA
1 -AATATTAAATATT-ATTAA-ATTAA-TATTA
*
2807400 AATATTAAATATTATTAACTTAATATTAA
1 AATATTAAATATTATTAAATTAATATT-A
*
2807429 AATTTTAAAATATTATTAAATTAATATT
1 AATATT-AAATATTATTAAATTAATATT
2807457 GAGAATTTAG
Statistics
Matches: 85, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
23 1 0.01
24 3 0.04
25 7 0.08
26 5 0.06
27 1 0.01
28 22 0.26
29 19 0.22
30 25 0.29
31 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
AATATTAAATATTATTAAATTAATATTA
Found at i:2809469 original size:84 final size:84
Alignment explanation
Indices: 2809355--2809509 Score: 197
Period size: 84 Copynumber: 1.8 Consensus size: 84
2809345 ATGAATTTAT
** *
2809355 TTTTAAAAAATTATTAAATATTTCAATAATTT-AGTAAAACTTAACTTTGGGATTTAAATTTTAT
1 TTTTAAAAAA-TATTAAATATTTCAATAATTTGA-TAAAACTTAA-TTTGAAATTTAAATCTTAT
2809419 AATAGTTTGGTATAATTAAAAA
63 AATAGTTTGGTATAATTAAAAA
* * * * *
2809441 TTTTAAAAAA-ATTAAATCTTTTAATAATTTGATAAGATTTAATTTGAAATTTAAATCTTCTAAT
1 TTTTAAAAAATATTAAATATTTCAATAATTTGATAAAACTTAATTTGAAATTTAAATCTTATAAT
2809505 AGTTT
66 AGTTT
2809510 TATAAGATTC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
83 23 0.38
84 26 0.43
85 1 0.02
86 10 0.17
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (84 bp):
TTTTAAAAAATATTAAATATTTCAATAATTTGATAAAACTTAATTTGAAATTTAAATCTTATAAT
AGTTTGGTATAATTAAAAA
Found at i:2809838 original size:2 final size:2
Alignment explanation
Indices: 2809829--2809866 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2809819 TTTTTAGATT
2809829 TC TC -C TC 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 TC TC TC TC T
2809867 TTTCTGCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2810559 original size:11 final size:11
Alignment explanation
Indices: 2810539--2810669 Score: 56
Period size: 11 Copynumber: 11.2 Consensus size: 11
2810529 AATAAACAAA
2810539 AAAAAGTAAAAT
1 AAAAA-TAAAAT
2810551 AAAAAT-AAA-
1 AAAAATAAAAT
*
2810560 AATAATACAAAT
1 AAAAATA-AAAT
2810572 -AAAATAAAGAT
1 AAAAATAAA-AT
2810583 AATGAAATAAAGAT
1 AA--AAATAAA-AT
*
2810597 AAATAAGATAAAT
1 AAA-AATA-AAAT
2810610 AAAAGAT-AAAT
1 AAAA-ATAAAAT
2810621 AACAAAATAAAGAT
1 -A-AAAATAAA-AT
* *
2810635 AAACATAAGAT
1 AAAAATAAAAT
* *
2810646 AAATATAAGAT
1 AAAAATAAAAT
2810657 -AAAATAAATAT
1 AAAAATAAA-AT
2810668 AA
1 AA
2810670 TGGTAAAGAT
Statistics
Matches: 94, Mismatches: 9, Indels: 32
0.70 0.07 0.24
Matches are distributed among these distances:
9 5 0.05
10 11 0.12
11 29 0.31
12 18 0.19
13 15 0.16
14 16 0.17
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2810575 original size:20 final size:19
Alignment explanation
Indices: 2810545--2810642 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 19
2810535 CAAAAAAAAG
2810545 TAAAATAAAAATAAAAATAA
1 TAAAAT-AAAATAAAAATAA
*
2810565 TACAAATAAAATAAAGATAA
1 TA-AAATAAAATAAAAATAA
*
2810585 TGAAATAAAGAT--AAATAA
1 TAAAATAAA-ATAAAAATAA
* * *
2810603 GATAAATAAAAGATAAATAA
1 TA-AAATAAAATAAAAATAA
* *
2810623 CAAAATAAAGATAAACATAA
1 TAAAATAAA-ATAAAAATAA
2810643 GATAAATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.10
19 21 0.34
20 31 0.50
21 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (19 bp):
TAAAATAAAATAAAAATAA
Found at i:2810610 original size:38 final size:38
Alignment explanation
Indices: 2810546--2810663 Score: 121
Period size: 38 Copynumber: 3.0 Consensus size: 38
2810536 AAAAAAAAGT
* * * *
2810546 AAAATAAAAATAAAAATAATACAAATAAAATAAAGATAAT
1 AAAATAAAGAT-AAAATAAGATAAATAAAATAAA-ATAAC
* *
2810586 GAAATAAAGAT-AAATAAGATAAATAAAAGATAAATAAC
1 AAAATAAAGATAAAATAAGATAAATAAAATA-AAATAAC
2810624 AAAATAAAGATAAACATAAGATAAATATAAGATAAAATAA
1 AAAATAAAGATAAA-ATAAGATAAATA-AA-ATAAAATAA
2810664 ATATAATGGT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
38 30 0.46
39 4 0.06
40 21 0.32
41 8 0.12
42 2 0.03
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (38 bp):
AAAATAAAGATAAAATAAGATAAATAAAATAAAATAAC
Found at i:2810633 original size:29 final size:28
Alignment explanation
Indices: 2810597--2810666 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
2810587 AAATAAAGAT
2810597 AAAT-AAGATAAATAAAAGATAAATAACA
1 AAATAAAGATAAATAAAAGATAAAT-ACA
* * *
2810625 AAATAAAGATAAACATAAGATAAATATA
1 AAATAAAGATAAATAAAAGATAAATACA
*
2810653 AGATAAA-ATAAATA
1 AAATAAAGATAAATA
2810667 TAATGGTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.17
28 12 0.33
29 18 0.50
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (28 bp):
AAATAAAGATAAATAAAAGATAAATACA
Found at i:2810636 original size:14 final size:13
Alignment explanation
Indices: 2810546--2810637 Score: 52
Period size: 14 Copynumber: 7.1 Consensus size: 13
2810536 AAAAAAAAGT
*
2810546 AAAATAAAAAT-A
1 AAAATAAAGATAA
*
2810558 AAAATAATACA-AA
1 AAAATAA-AGATAA
2810571 TAAAATAAAGATAA
1 -AAAATAAAGATAA
*
2810585 TGAAATAAAGATAA
1 -AAAATAAAGATAA
2810599 ATAAGAT-AA-ATAA
1 A-AA-ATAAAGATAA
*
2810612 AAGAT-AA-ATAA
1 AAAATAAAGATAA
2810623 CAAAATAAAGATAA
1 -AAAATAAAGATAA
2810637 A
1 A
2810638 CATAAGATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
11 8 0.12
12 12 0.18
13 13 0.20
14 30 0.46
15 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (13 bp):
AAAATAAAGATAA
Found at i:2810653 original size:6 final size:6
Alignment explanation
Indices: 2810570--2810681 Score: 53
Period size: 6 Copynumber: 19.7 Consensus size: 6
2810560 AATAATACAA
* *
2810570 ATAAA- ATAAAG ATAATGAA ATAAAG AT-AA- AT-AAG ATAAAT A-AAAG
1 ATAAAG ATAAAG ATAA--AG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG
* * * *
2810615 ATAAAT A-ACAAA ATAAAG ATAAAC AT-AAG ATAAAT AT-AAG ATAAA-
1 ATAAAG ATA-AAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG
* * *
2810660 ATAAAT ATAATG GTAAAG ATAA
1 ATAAAG ATAAAG ATAAAG ATAA
2810682 TAAAATATAA
Statistics
Matches: 80, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
4 4 0.05
5 27 0.34
6 43 0.54
7 1 0.01
8 5 0.06
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (6 bp):
ATAAAG
Found at i:2810663 original size:16 final size:16
Alignment explanation
Indices: 2810624--2810669 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2810614 GATAAATAAC
*
2810624 AAAATAAAGATAAACAT
1 AAAATAAATAT-AACAT
* *
2810641 AAGATAAATATAAGAT
1 AAAATAAATATAACAT
2810657 AAAATAAATATAA
1 AAAATAAATATAA
2810670 TGGTAAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (16 bp):
AAAATAAATATAACAT
Found at i:2812715 original size:13 final size:13
Alignment explanation
Indices: 2812697--2812726 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2812687 TTATTTTCAG
*
2812697 AAAATGAAAATAA
1 AAAATGAAAACAA
2812710 AAAATGAAAACAA
1 AAAATGAAAACAA
2812723 AAAA
1 AAAA
2812727 GATTTTCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAATGAAAACAA
Found at i:2813534 original size:14 final size:14
Alignment explanation
Indices: 2813515--2813542 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2813505 TTTATCTTTA
2813515 CTAGCATATAATGC
1 CTAGCATATAATGC
2813529 CTAGCATATAATGC
1 CTAGCATATAATGC
2813543 GATGCGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
CTAGCATATAATGC
Found at i:2814041 original size:13 final size:13
Alignment explanation
Indices: 2814023--2814055 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2814013 GGTGCCTTTT
2814023 GTGAGACAAAACC
1 GTGAGACAAAACC
*
2814036 GTGAGACAAAACT
1 GTGAGACAAAACC
2814049 GTGAGAC
1 GTGAGAC
2814056 CTTCGGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.12
Consensus pattern (13 bp):
GTGAGACAAAACC
Found at i:2814829 original size:17 final size:18
Alignment explanation
Indices: 2814807--2814843 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2814797 TAAATAATAA
2814807 TATTTTTATTT-CA-TTTT
1 TATTTTT-TTTACACTTTT
2814824 TATTTTTTTTACACTTTT
1 TATTTTTTTTACACTTTT
2814842 TA
1 TA
2814844 GGATCAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 9 0.50
18 6 0.33
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTTTTTTTACACTTTT
Found at i:2817540 original size:6 final size:7
Alignment explanation
Indices: 2817509--2817550 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
2817499 ATATAATTTT
2817509 AAAAAA-
1 AAAAAAG
*
2817515 AATAAATG
1 AA-AAAAG
2817523 AAAAAAG
1 AAAAAAG
2817530 AAAAAAG
1 AAAAAAG
2817537 AAAAAAAG
1 -AAAAAAG
2817545 AAAAAA
1 AAAAAA
2817551 AATACCCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 20 0.65
8 9 0.29
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:2817541 original size:8 final size:8
Alignment explanation
Indices: 2817523--2817551 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2817513 AAAATAAATG
2817523 AAAAAAG-
1 AAAAAAGA
2817530 AAAAAAGA
1 AAAAAAGA
2817538 AAAAAAGA
1 AAAAAAGA
2817546 AAAAAA
1 AAAAAA
2817552 ATACCCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2818506 original size:15 final size:16
Alignment explanation
Indices: 2818488--2818524 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2818478 TAAAAATGGT
2818488 AAAAAATAAAAT-AAA
1 AAAAAATAAAATGAAA
*
2818503 AAAAAA-ACAATGAAA
1 AAAAAATAAAATGAAA
2818518 AAAAAAT
1 AAAAAAT
2818525 CTGCGATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAATAAAATGAAA
Found at i:2818936 original size:41 final size:42
Alignment explanation
Indices: 2818877--2818968 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 42
2818867 ACTTAGACCT
*
2818877 AAAAATTCAAACTCTCAATCCCAGAACTTTAAATCCAAACCC
1 AAAAATTCAAACTCTCAATCACAGAACTTTAAATCCAAACCC
* * * *
2818919 -AAAATTCAAACTTTCAATCATAGAATTTTGAATCCAAACCC
1 AAAAATTCAAACTCTCAATCACAGAACTTTAAATCCAAACCC
2818960 AAAAATTCA
1 AAAAATTCA
2818969 GACCACTCTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 36 0.82
42 8 0.18
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (42 bp):
AAAAATTCAAACTCTCAATCACAGAACTTTAAATCCAAACCC
Found at i:2819324 original size:3 final size:3
Alignment explanation
Indices: 2819316--2819383 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
2819306 TCAACATAGA
2819316 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
*
2819364 AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AA
2819384 ACACCAGTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2819829 original size:31 final size:31
Alignment explanation
Indices: 2819766--2819825 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
2819756 AAATTAATAA
*
2819766 AATATTAATTTTTAAATATAAAATATTATTT
1 AATATTAATTTTTAAATAAAAAATATTATTT
*
2819797 AATATT-ATTTTT-AATAAAAAATTTTATTT
1 AATATTAATTTTTAAATAAAAAATATTATTT
2819826 TTAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 15 0.56
30 6 0.22
31 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
AATATTAATTTTTAAATAAAAAATATTATTT
Found at i:2820585 original size:12 final size:12
Alignment explanation
Indices: 2820543--2820598 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
2820533 GTAACTTTAT
2820543 TAATATA-ATATA
1 TAATATATATA-A
*
2820555 TAAT-TATAAAA
1 TAATATATATAA
2820566 TCAA-ATATATAA
1 T-AATATATATAA
2820578 TAATATATAT-A
1 TAATATATATAA
2820589 T-ATATATATA
1 TAATATATATA
2820599 TGAGTTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 8 0.22
11 8 0.22
12 21 0.57
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATATATATAA
Found at i:2820979 original size:21 final size:19
Alignment explanation
Indices: 2820942--2820987 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2820932 AAAAAAATTA
**
2820942 AAAAAATTAAATGAAAAGCAG
1 AAAAAATTAAA--AAAAAAAG
2820963 AAAAAATTAAAAAAAAAAG
1 AAAAAATTAAAAAAAAAAG
2820982 AAAAAA
1 AAAAAA
2820988 GTTGAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 12 0.52
21 11 0.48
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAAATTAAAAAAAAAAG
Found at i:2821100 original size:20 final size:20
Alignment explanation
Indices: 2821067--2821107 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2821057 ACATTAAATA
* * *
2821067 TAAATTAAATAAAAGAAAAG
1 TAAATAAAAAAAAACAAAAG
2821087 TAAATAAAAAAAAACAAAAG
1 TAAATAAAAAAAAACAAAAG
2821107 T
1 T
2821108 TGAAGCTGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (20 bp):
TAAATAAAAAAAAACAAAAG
Found at i:2822065 original size:3 final size:3
Alignment explanation
Indices: 2822057--2822082 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2822047 ATTTACTAAA
2822057 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2822083 ATCCATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2822538 original size:103 final size:103
Alignment explanation
Indices: 2822359--2822567 Score: 382
Period size: 103 Copynumber: 2.0 Consensus size: 103
2822349 TCACACTCGA
2822359 TAAAGAAAAAGAGTTTCCATCCAAGGTCAGGTTTTCTTTGTCATCAATTTTCCATTGAAATTTAA
1 TAAAGAAAAAGAGTTTCCATCCAAGGTCAGGTTTTCTTTGTCATCAATTTTCCATTGAAATTTAA
*
2822424 GTAAATTTCCTTAGCTATTATAGTTTTGAGATAAAAAC
66 CTAAATTTCCTTAGCTATTATAGTTTTGAGATAAAAAC
* *
2822462 TAAAGAAAAAGAGTTTCCATCCAAGGTCAGGTTTTCTTTGTCATCATTTTTCCATTGAAATTTGA
1 TAAAGAAAAAGAGTTTCCATCCAAGGTCAGGTTTTCTTTGTCATCAATTTTCCATTGAAATTTAA
*
2822527 CTAAATTTCCTTAGGTATTATAGTTTTGAGATAAAAAC
66 CTAAATTTCCTTAGCTATTATAGTTTTGAGATAAAAAC
2822565 TAA
1 TAA
2822568 TGTGCTCGAT
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (103 bp):
TAAAGAAAAAGAGTTTCCATCCAAGGTCAGGTTTTCTTTGTCATCAATTTTCCATTGAAATTTAA
CTAAATTTCCTTAGCTATTATAGTTTTGAGATAAAAAC
Found at i:2823524 original size:16 final size:15
Alignment explanation
Indices: 2823503--2823676 Score: 74
Period size: 16 Copynumber: 11.0 Consensus size: 15
2823493 GCCCAATTCA
2823503 ATTTTTATATTGTATT
1 ATTTTTATATT-TATT
*
2823519 ATTTTTATTTTTATT
1 ATTTTTATATTTATT
*
2823534 -TTTTTGTATTT-TT
1 ATTTTTATATTTATT
*
2823547 GTATTTTATTATTTATT
1 AT-TTTTA-TATTTATT
* *
2823564 ATTATTATTATGTATT
1 ATTTTTA-TATTTATT
* *
2823580 AATATATGTATATCT-TT
1 -AT-T-TTTATATTTATT
2823597 ATTTATT-TATTTATT
1 ATTT-TTATATTTATT
2823612 -TTTGTTAATATTT-TT
1 ATTT-TT-ATATTTATT
2823627 ATGTATTT-TATTTATAT
1 AT-T-TTTATATTTAT-T
* *
2823644 AGTTATATATTTATT
1 ATTTTTATATTTATT
2823659 ATTATATTATAATTTATT
1 ATT-T-TTAT-ATTTATT
2823677 TATTATTCTT
Statistics
Matches: 121, Mismatches: 17, Indels: 38
0.69 0.10 0.22
Matches are distributed among these distances:
13 2 0.02
14 20 0.17
15 24 0.20
16 45 0.37
17 15 0.12
18 13 0.11
19 2 0.02
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.68
Consensus pattern (15 bp):
ATTTTTATATTTATT
Found at i:2823603 original size:4 final size:4
Alignment explanation
Indices: 2823594--2823680 Score: 52
Period size: 4 Copynumber: 20.5 Consensus size: 4
2823584 TATGTATATC
* *
2823594 TTTA TTTA TTTA TTTA TTTT TGTTAA TATT- TTTA TGTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA T-TT-A T-TTA TTTA TTTA -TTTA TTTA
* * *
2823641 TATA GTTA TATA TTTA -TTA TTATA TTATAA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA TT
2823681 ATTCTTTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
3 5 0.08
4 42 0.65
5 12 0.18
6 6 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:2824756 original size:20 final size:21
Alignment explanation
Indices: 2824711--2824771 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
2824701 TATCTTTATC
*
2824711 TTTATCTTATTTTTATTTTTTGT
1 TTTATCTT-TATTTA-TTTTTGT
*
2824734 TTTA-CTTTTCTTTATTTTT-T
1 TTTATC-TTTATTTATTTTTGT
2824754 TTTATCTTTATTTATTTT
1 TTTATCTTTATTTATTTT
2824772 CACTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 16 0.47
21 6 0.18
22 6 0.18
23 6 0.18
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATCTTTATTTATTTTTGT
Found at i:2824761 original size:16 final size:16
Alignment explanation
Indices: 2824705--2824771 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 16
2824695 ATTTTTTATC
*
2824705 TTTATCTTTATCTTATT
1 TTTATCTTTAT-TTTTT
2824722 TTTAT-TTT-TTGTTTT
1 TTTATCTTTATT-TTTT
2824737 ACTTT-TCTTTATTTTTT
1 --TTTATCTTTATTTTTT
2824754 TTTATCTTTATTTATTT
1 TTTATCTTTATTT-TTT
2824771 T
1 T
2824772 CACTTTTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
14 1 0.02
15 7 0.17
16 13 0.31
17 19 0.45
18 2 0.05
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTATCTTTATTTTTT
Found at i:2824791 original size:22 final size:22
Alignment explanation
Indices: 2824753--2824794 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2824743 CTTTATTTTT
2824753 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
2824775 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
2824795 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:2824860 original size:56 final size:56
Alignment explanation
Indices: 2824790--2824904 Score: 187
Period size: 57 Copynumber: 2.1 Consensus size: 56
2824780 TTTTGTTCTA
*
2824790 TTTTCTTTAAATAAAAAT-CAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAATAAAAATCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
**
2824845 TTTTCTTAGAAATAAATTTCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTT-GAAATAAAAATCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
2824902 TTT
1 TTT
2824905 CAGTATCAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 7 0.13
56 8 0.15
57 40 0.73
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (56 bp):
TTTTCTTGAAATAAAAATCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:2824911 original size:13 final size:13
Alignment explanation
Indices: 2824893--2824918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2824883 AAAAGTTGAA
2824893 AGTATCAATTTTC
1 AGTATCAATTTTC
2824906 AGTATCAATTTTC
1 AGTATCAATTTTC
2824919 CTTAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
AGTATCAATTTTC
Found at i:2824967 original size:73 final size:70
Alignment explanation
Indices: 2824836--2824978 Score: 214
Period size: 73 Copynumber: 2.0 Consensus size: 70
2824826 AAAAGTTGAA
* * * *
2824836 AGTATCAATTTTTCTTAGAAATAAATTTCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA
1 AGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA
2824901 TTTTC
66 TTTTC
*
2824906 AGTATCAATTTTCCTTAAAAATAAATTTTTTAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTAT
1 AGTATCAATTTTCCTTAAAAATAAA--TTTCAAAAAAA-GATTTTTGAGGAAAAGTTGAAAGTAT
2824971 CAATTTTC
63 CAATTTTC
2824979 CTTAAAAATC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
70 23 0.35
72 9 0.14
73 33 0.51
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (70 bp):
AGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA
TTTTC
Found at i:2825117 original size:58 final size:58
Alignment explanation
Indices: 2824906--2825269 Score: 515
Period size: 60 Copynumber: 6.2 Consensus size: 58
2824896 ATCAATTTTC
* *
2824906 AGTATCAATTTTCCTTAAAAATAAATTTTTTAAAAAAAGGATTTTTGAGGAAAAGTTGAA
1 AGTATCAATTTTCCTTAAAAATAAA-TTTTTCAAAAAA-TATTTTTGAGGAAAAGTTGAA
*
2824966 AGTATCAATTTTCCTTAAAAATCAAAATTTTT-GAAAAATATTTTTGAGGAAAAGTTGAA
1 AGTATCAATTTTCCTTAAAAAT--AAATTTTTCAAAAAATATTTTTGAGGAAAAGTTGAA
* *
2825025 AGTATCAATTTTCCTTATAAATAAA-TTTTCAAAAAATATTTTTGGGGGAAAAGTTGAA
1 AGTATCAATTTTCCTTAAAAATAAATTTTTCAAAAAATATTTTT-GAGGAAAAGTTGAA
*
2825083 AGTATCAATTTTCCTT-AAAA-AAATTTTTCGAAAAAAAGATTTTTGAGGAAAAGTTGAA
1 AGTATCAATTTTCCTTAAAAATAAATTTTTC--AAAAAATATTTTTGAGGAAAAGTTGAA
* *
2825141 AGTATCAATTTTCCTTGAAAATCAAA-GTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAA
1 AGTATCAATTTTCCTTAAAAAT-AAATTTTTC--AAAAAATATTTTTGAGGAAAAGTTGAA
*
2825201 AGTATCAATTTTCCTTAAAAATAAA-TTTTCAAAAAATATTTTTGGGGAAAAGTTGAA
1 AGTATCAATTTTCCTTAAAAATAAATTTTTCAAAAAATATTTTTGAGGAAAAGTTGAA
2825258 AGTATCAATTTT
1 AGTATCAATTTT
2825270 TCCTACACAA
Statistics
Matches: 280, Mismatches: 14, Indels: 23
0.88 0.04 0.07
Matches are distributed among these distances:
56 7 0.03
57 61 0.22
58 58 0.21
59 64 0.23
60 79 0.28
61 8 0.03
62 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (58 bp):
AGTATCAATTTTCCTTAAAAATAAATTTTTCAAAAAATATTTTTGAGGAAAAGTTGAA
Found at i:2825175 original size:117 final size:113
Alignment explanation
Indices: 2824906--2825269 Score: 500
Period size: 117 Copynumber: 3.1 Consensus size: 113
2824896 ATCAATTTTC
* *
2824906 AGTATCAATTTTCCTTAAAAATAAATTTTTTAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTAT
1 AGTATCAATTTTCCTT-AAAATAAA--TTTTCAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTAT
2824971 CAATTTTCCTTAAAAATCAAAATTTTT-G-AAAAATATTTTTGAGGAAAAGTTGAA
62 CAATTTTCCTT--AAA--AAAATTTTTCGAAAAAATATTTTTGAGGAAAAGTTGAA
*
2825025 AGTATCAATTTTCCTTATAAATAAATTTTCAAAAAATATTTTTGGGGGAAAAGTTGAAAGTATCA
1 AGTATCAATTTTCCTTA-AAATAAATTTTCAAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCA
*
2825090 ATTTTCCTTAAAAAAATTTTTCGAAAAAAAGATTTTTGAGGAAAAGTTGAA
64 ATTTTCCTTAAAAAAATTTTTCG-AAAAAATATTTTTGAGGAAAAGTTGAA
*
2825141 AGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTAT
1 AGTATCAATTTTCCTT-AAAAT-AAATTTTC--AAAAAATATTTTTGAGGAAAAGTTGAAAGTAT
* *
2825206 CAATTTTCCTTAAAAATAAATTTTC-AAAAAATATTTTTGGGGAAAAGTTGAA
62 CAATTTTCCTTAAAAA-AATTTTTCGAAAAAATATTTTTGAGGAAAAGTTGAA
2825258 AGTATCAATTTT
1 AGTATCAATTTT
2825270 TCCTACACAA
Statistics
Matches: 226, Mismatches: 9, Indels: 22
0.88 0.04 0.09
Matches are distributed among these distances:
113 9 0.04
114 1 0.00
115 3 0.01
116 51 0.23
117 84 0.37
118 35 0.15
119 43 0.19
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (113 bp):
AGTATCAATTTTCCTTAAAATAAATTTTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
TTTCCTTAAAAAAATTTTTCGAAAAAATATTTTTGAGGAAAAGTTGAA
Found at i:2825273 original size:176 final size:177
Alignment explanation
Indices: 2824906--2825269 Score: 619
Period size: 175 Copynumber: 2.1 Consensus size: 177
2824896 ATCAATTTTC
*
2824906 AGTATCAATTTTCCTTAAAAATAAATTTTTTAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTAT
1 AGTATCAATTTTCCTTAAAAATAAATTTTTGAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTAT
***
2824971 CAATTTTCCTTAAAAATCAAAATTTTTGAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTT
66 CAATTTTCCTTAAAAATCAAAATTTAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTT
*
2825036 TCCTTATAAATAAATTTTCAAAAAATATTTTTGGGGGAAAAGTTGAA
131 TCCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGGAAAAGTTGAA
2825083 AGTATCAATTTTCCTT-AAAA-AAATTTTTCGAAAAAAA-GATTTTTGAGGAAAAGTTGAAAGTA
1 AGTATCAATTTTCCTTAAAAATAAATTTTT-GAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTA
* *
2825145 TCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
65 TCAATTTTCCTTAAAAATCAAAATTT-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
2825210 TTTCCTTAAAAATAAATTTTCAAAAAATATTTTT-GGGGAAAAGTTGAA
129 TTTCCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGGAAAAGTTGAA
2825258 AGTATCAATTTT
1 AGTATCAATTTT
2825270 TCCTACACAA
Statistics
Matches: 178, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
175 83 0.47
176 79 0.44
177 16 0.09
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (177 bp):
AGTATCAATTTTCCTTAAAAATAAATTTTTGAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTAT
CAATTTTCCTTAAAAATCAAAATTTAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTT
TCCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGGAAAAGTTGAA
Found at i:2827150 original size:3 final size:3
Alignment explanation
Indices: 2827129--2827315 Score: 104
Period size: 3 Copynumber: 60.3 Consensus size: 3
2827119 TCTTCTTTTG
2827129 TAT T-T TAT GTAT T-T TAT TAT TAT TAT TAT TAT GTAT ATATT TATT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TA-T TA-T
* *
2827174 TAT T-T TTT TAT TA- TAT TA- GAT T-T ATAT GTAT ATAGT TAT ATATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TA-T TAT -TA-T
* * *
2827218 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TTT GTAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
** *
2827264 TAT ATACT TGGG T-T TA- TCT TAT T-T TAT TAT TAT TAT TAT TAT TAT
1 TAT -TA-T T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2827309 TAT TAT T
1 TAT TAT T
2827316 TTTAATTATC
Statistics
Matches: 149, Mismatches: 15, Indels: 40
0.73 0.07 0.20
Matches are distributed among these distances:
2 14 0.09
3 100 0.67
4 31 0.21
5 4 0.03
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2827716 original size:25 final size:25
Alignment explanation
Indices: 2827680--2827727 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2827670 TGAGGAGAAT
2827680 TTTTTCTAGAAATTT-TGGCGAAAAA
1 TTTTTCTAGAAATTTCTGG-GAAAAA
*
2827705 TTTTTCTGGAAATTTCTGGGAAA
1 TTTTTCTAGAAATTTCTGGGAAA
2827728 TTTCCAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTTTCTAGAAATTTCTGGGAAAAA
Found at i:2827770 original size:30 final size:31
Alignment explanation
Indices: 2827736--2827801 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
2827726 AATTTCCAGA
2827736 TTCCGACGAAAATTCCGGCGAAAC-TTGAA-T
1 TTCCGACGAAAATTCCGGC-AAACTTTGAAGT
* * * *
2827766 TTCCGGCTACAATTCCGGCCAACTTTGAAGT
1 TTCCGACGAAAATTCCGGCAAACTTTGAAGT
2827797 TTCCG
1 TTCCG
2827802 GCGACCTACC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.10
30 21 0.70
31 6 0.20
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (31 bp):
TTCCGACGAAAATTCCGGCAAACTTTGAAGT
Found at i:2828144 original size:5 final size:5
Alignment explanation
Indices: 2828112--2828143 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2828102 CAACCCCCCT
*
2828112 CCGAG CCGAG CCGAG CCGAG CCGAG CCAAG CC
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CC
2828144 ACCAAGCCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.22, C:0.44, G:0.34, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:2828236 original size:20 final size:19
Alignment explanation
Indices: 2828208--2828256 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
2828198 CAGGTTTTTT
2828208 TTTTTTATTTCT-TTGTTTA
1 TTTTTTATTT-TATTGTTTA
*
2828227 TTTGTTTATTTTATTTTTTA
1 TTT-TTTATTTTATTGTTTA
2828247 TTTTTTATTT
1 TTTTTTATTT
2828257 ATTAGATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTATTTTATTGTTTA
Found at i:2828246 original size:12 final size:12
Alignment explanation
Indices: 2828203--2828259 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
2828193 CGCACCAGGT
*
2828203 TTTTTTTTTTTA
1 TTTTTTATTTTA
*
2828215 TTTCTTT-GTTTA
1 TTT-TTTATTTTA
2828227 TTTGTTTATTTTA
1 TTT-TTTATTTTA
2828240 TTTTTTATTTT-
1 TTTTTTATTTTA
*
2828251 TTATTTATT
1 TTTTTTATT
2828260 AGATTAGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 8 0.21
12 21 0.54
13 10 0.26
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:2828272 original size:32 final size:32
Alignment explanation
Indices: 2828208--2828272 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
2828198 CAGGTTTTTT
* * * *
2828208 TTTTTTATTTCTTTGTTTATTTGTTTATTTTA
1 TTTTTTATTTCTTTATTTATTAGATTAGTTTA
2828240 TTTTTTATTT-TTTATTTATTAGATTAGGTTTA
1 TTTTTTATTTCTTTATTTATTAGATTA-GTTTA
2828272 T
1 T
2828273 GTAATATTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.74
Consensus pattern (32 bp):
TTTTTTATTTCTTTATTTATTAGATTAGTTTA
Found at i:2828477 original size:57 final size:57
Alignment explanation
Indices: 2828336--2828702 Score: 352
Period size: 57 Copynumber: 6.1 Consensus size: 57
2828326 AAAAATTCTA
*
2828336 AAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTAAAAGAAAAATAAATTTCC
1 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-CCT--TAG--AAATAAATTTCC
*
2828399 AAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 --AA-AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* * *
2828459 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATC-ATTTTCCTCAGAAGTAAATTTCAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC-C
*
2828516 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTT-CTTAAAAGAAGAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-A-AATAAATTTCC
* * *
2828577 ---AAATATTTTAGGGAAAAAGTTGAAAAGTATCAATTTTCCTTAAAGAAA-AATAATTCC
1 AAAAAATATTTTTGGGGAAAAGTTG-AAAGTATCAATTTTCCTT--AGAAATAA-ATTTCC
* *
2828634 AAAAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTT-TTCTAGAAATAAATTTTTC
1 ----AAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT-TAGAAATAAA-TTTCC
2828697 AAAAAA
1 AAAAAA
2828703 AGGATTTTGA
Statistics
Matches: 261, Mismatches: 19, Indels: 50
0.79 0.06 0.15
Matches are distributed among these distances:
56 22 0.08
57 71 0.27
58 27 0.10
59 24 0.09
60 17 0.07
61 1 0.00
62 17 0.07
63 6 0.02
64 23 0.09
65 50 0.19
66 3 0.01
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:2832094 original size:11 final size:11
Alignment explanation
Indices: 2832080--2832117 Score: 53
Period size: 9 Copynumber: 3.5 Consensus size: 11
2832070 AAAAGGTCTC
2832080 AAAAATAAAAA
1 AAAAATAAAAA
2832091 AAAAAT--AAA
1 AAAAATAAAAA
2832100 AAAAATAAAAGA
1 AAAAATAAAA-A
2832112 AAAAAT
1 AAAAAT
2832118 GCCACACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.38
11 8 0.33
12 7 0.29
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.11
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:2832451 original size:13 final size:13
Alignment explanation
Indices: 2832433--2832457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2832423 ATCAACAATG
2832433 GATGAAAAAAAAT
1 GATGAAAAAAAAT
2832446 GATGAAAAAAAA
1 GATGAAAAAAAA
2832458 AGAAAAAAAA
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:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
GATGAAAAAAAAT
Found at i:2832462 original size:10 final size:10
Alignment explanation
Indices: 2832449--2832507 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
2832439 AAAAAATGAT
2832449 GAAAAAAAAA
1 GAAAAAAAAA
2832459 GAAAAAAAAA
1 GAAAAAAAAA
*
2832469 -AGGAAAAAAA
1 GA-AAAAAAAA
**
2832479 GAAAAAATGA
1 GAAAAAAAAA
2832489 GAAAAAAAGAA
1 GAAAAAAA-AA
2832500 GGAAAAAA
1 -GAAAAAA
2832508 TGAGAAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 2 0.05
12 7 0.18
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:2832465 original size:12 final size:12
Alignment explanation
Indices: 2832450--2832483 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2832440 AAAAATGATG
2832450 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
2832462 AAAAAAAAGGAA
1 AAAAAAAAAGAA
2832474 AAAAAGAAAA
1 AAAAA-AAAA
2832484 AATGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:2832465 original size:22 final size:21
Alignment explanation
Indices: 2832438--2832515 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
2832428 CAATGGATGA
2832438 AAAAAAATGATGAAAAAAAAAG
1 AAAAAAATGA-GAAAAAAAAAG
** *
2832460 AAAAAAAAAAG-GAAAAAAAG
1 AAAAAAATGAGAAAAAAAAAG
2832480 -AAAAAATGAGAAAAAAAGAAG
1 AAAAAAATGAGAAAAAAA-AAG
*
2832501 GAAAAAATGAGAAAA
1 AAAAAAATGAGAAAA
2832516 TGAAAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.17
20 13 0.28
21 4 0.09
22 22 0.47
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (21 bp):
AAAAAAATGAGAAAAAAAAAG
Found at i:2832496 original size:12 final size:12
Alignment explanation
Indices: 2832436--2832478 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
2832426 AACAATGGAT
*
2832436 GAAAAAAAATGA
1 GAAAAAAAAAGA
2832448 TGAAAAAAAAAGA
1 -GAAAAAAAAAGA
2832461 -AAAAAAAAAG-
1 GAAAAAAAAAGA
2832471 GAAAAAAA
1 GAAAAAAA
2832479 GAAAAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 17 0.61
13 11 0.39
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:2832506 original size:38 final size:38
Alignment explanation
Indices: 2832447--2832523 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
2832437 AAAAAAAATG
2832447 ATGAAAAAAAAAGAAAAAAAAAAGGAAAAAAAGAAAAA
1 ATGAAAAAAAAAGAAAAAAAAAAGGAAAAAAAGAAAAA
* ** * * *
2832485 ATGAGAAAAAAAGAAGGAAAAAATGAGAAAATGAAAAA
1 ATGAAAAAAAAAGAAAAAAAAAAGGAAAAAAAGAAAAA
2832523 A
1 A
2832524 AAAGATTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (38 bp):
ATGAAAAAAAAAGAAAAAAAAAAGGAAAAAAAGAAAAA
Found at i:2832514 original size:10 final size:10
Alignment explanation
Indices: 2832434--2832515 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 10
2832424 TCAACAATGG
*
2832434 ATGAAAAAAA
1 ATGAGAAAAA
2832444 ATGATGAAAAA
1 ATGA-GAAAAA
**
2832455 AAAAGAAAAAA
1 ATGAG-AAAAA
**
2832466 AAAAGGAAAAA
1 ATGA-GAAAAA
2832477 A--AGAAAAA
1 ATGAGAAAAA
2832485 ATGAGAAAAA
1 ATGAGAAAAA
*
2832495 AAGAAGGAAAAA
1 ATG-A-GAAAAA
2832507 ATGAGAAAA
1 ATGAGAAAA
2832516 TGAAAAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
8 7 0.12
9 1 0.02
10 19 0.32
11 24 0.40
12 9 0.15
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (10 bp):
ATGAGAAAAA
Found at i:2832516 original size:30 final size:30
Alignment explanation
Indices: 2832449--2832528 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
2832439 AAAAAATGAT
** *
2832449 GAAAAAAAAAGAAAAAAAAAAGGAAAAAAA
1 GAAAAAATGAGAAAAAAAGAAGGAAAAAAA
*
2832479 GAAAAAATGAGAAAAAAAGAAGGAAAAAAT
1 GAAAAAATGAGAAAAAAAGAAGGAAAAAAA
* *
2832509 GAGAAAATGAAAAAAAAAGA
1 GAAAAAATGAGAAAAAAAGA
2832529 TTCAAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (30 bp):
GAAAAAATGAGAAAAAAAGAAGGAAAAAAA
Found at i:2832523 original size:8 final size:8
Alignment explanation
Indices: 2832464--2832523 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
2832454 AAAAAGAAAA
*
2832464 AAAAAAGG
1 AAAAAATG
*
2832472 AAAAAAAG
1 AAAAAATG
2832480 AAAAAATG
1 AAAAAATG
*
2832488 AGAAAA--
1 AAAAAATG
* *
2832494 AAAGAAGG
1 AAAAAATG
2832502 AAAAAATG
1 AAAAAATG
*
2832510 AGAAAATG
1 AAAAAATG
2832518 AAAAAA
1 AAAAAA
2832524 AAAGATTCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
6 4 0.10
8 37 0.90
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (8 bp):
AAAAAATG
Found at i:2833827 original size:42 final size:41
Alignment explanation
Indices: 2833741--2834486 Score: 1109
Period size: 42 Copynumber: 18.1 Consensus size: 41
2833731 ATGATCGTCT
2833741 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
*
2833781 AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* *
2833823 AGGAGCAATTTATTTTTCCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
*
2833865 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
2833906 AGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
2833948 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
*
2833988 AGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
2834029 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
*
2834069 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2834110 AGGAGCAATTTATTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
*
2834150 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2834191 AGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
*
2834233 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
2834275 AGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
* *
2834317 AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
2834358 AGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
*
2834400 AGGAGCAATTTACTTTCCAAAGTCCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGT-CGTGGTGCCTCTGTTTAG
* * *
2834440 AGGAGCAATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
2834481 AGGAGC
1 AGGAGC
2834487 TTCGGCCAAA
Statistics
Matches: 649, Mismatches: 36, Indels: 41
0.89 0.05 0.06
Matches are distributed among these distances:
39 18 0.03
40 152 0.23
41 208 0.32
42 267 0.41
43 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:2834038 original size:81 final size:81
Alignment explanation
Indices: 2833741--2834486 Score: 1085
Period size: 81 Copynumber: 9.1 Consensus size: 81
2833731 ATGATCGTCT
2833741 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAG
*
2833804 TCGTGGTGCCTCTGTTGAG
64 TCGT-GTGCCTCTGTTTAG
* *
2833823 AGGAGCAATTTATTTTTCCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
*
2833888 CGTGGTGCCTCTGTTGAG
65 CGT-GTGCCTCTGTTTAG
* *
2833906 AGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-
2833971 TCGT-TGCCTCTGTTTAG
64 TCGTGTGCCTCTGTTTAG
*
2833988 AGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T
2834053 CGT-TGCCTCTGTTTAG
65 CGTGTGCCTCTGTTTAG
* *
2834069 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCAAAGTT
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T
2834134 CGT-TGCCTCTGTTTAG
65 CGTGTGCCTCTGTTTAG
* *
2834150 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCCAAAGT
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGT
2834215 CGTGGTGCCTCTGTTTAG
65 CGT-GTGCCTCTGTTTAG
* *
2834233 AGGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCCAAAG
1 AGGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAG
2834298 TCGTGGTGCCTCTGTTTAG
64 TCGT-GTGCCTCTGTTTAG
* * *
2834317 AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCCAAAGT
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGT
*
2834382 CGTGGTGCCTCTGTTGAG
65 CGT-GTGCCTCTGTTTAG
*
2834400 AGGAGCAATTTACTTTCCAAAGTCCGT--TGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAAG
1 AGGAGCAATTTACTTTTCAAAGT-CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAG
* *
2834462 TCGTTGAGTCTCTGTTTAG
64 TCG-TGTGCCTCTGTTTAG
2834481 AGGAGC
1 AGGAGC
2834487 TTCGGCCAAA
Statistics
Matches: 635, Mismatches: 18, Indels: 23
0.94 0.03 0.03
Matches are distributed among these distances:
80 1 0.00
81 231 0.36
82 77 0.12
83 207 0.33
84 119 0.19
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (81 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
GTGTGCCTCTGTTTAG
Found at i:2834510 original size:9 final size:9
Alignment explanation
Indices: 2834496--2834594 Score: 94
Period size: 9 Copynumber: 10.6 Consensus size: 9
2834486 CTTCGGCCAA
2834496 AAAAAAAAC
1 AAAAAAAAC
2834505 AAAAAAAA-
1 AAAAAAAAC
2834513 AAAACAAAA-
1 AAAA-AAAAC
2834522 AAACAAAAAC
1 AAA-AAAAAC
2834532 AAAAAAAATC
1 AAAAAAAA-C
*
2834542 AAAAAAATC
1 AAAAAAAAC
*
2834551 AAAAAAATC
1 AAAAAAAAC
*
2834560 AAAAAAATC
1 AAAAAAAAC
*
2834569 AAAACAAAAAT
1 -AAA-AAAAAC
2834580 AAAAAAAATC
1 AAAAAAAA-C
2834590 AAAAA
1 AAAAA
2834595 TAAAAATGTT
Statistics
Matches: 79, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
8 4 0.05
9 48 0.61
10 23 0.29
11 4 0.05
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:2834546 original size:48 final size:49
Alignment explanation
Indices: 2834493--2834600 Score: 134
Period size: 48 Copynumber: 2.2 Consensus size: 49
2834483 GAGCTTCGGC
2834493 CAAAAAAAAAACAAAAAAA-AAAAACAA-AAAAACAAAAACAAAAAAAAT
1 CAAAAAAAAAACAAAAAAACAAAAA-AATAAAAACAAAAACAAAAAAAAT
* * *
2834541 C--AAAAAAATCAAAAAAATCAAAAAAATCAAAACAAAAATAAAAAAAAT
1 CAAAAAAAAAACAAAAAAA-CAAAAAAATAAAAACAAAAACAAAAAAAAT
2834589 CAAAAATAAAAA
1 CAAAAA-AAAAA
2834601 TGTTGAGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
46 15 0.30
47 2 0.04
48 26 0.52
50 3 0.06
51 4 0.08
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.06
Consensus pattern (49 bp):
CAAAAAAAAAACAAAAAAACAAAAAAATAAAAACAAAAACAAAAAAAAT
Found at i:2834600 original size:1 final size:1
Alignment explanation
Indices: 2834494--2834587 Score: 62
Period size: 1 Copynumber: 94.0 Consensus size: 1
2834484 AGCTTCGGCC
* * * * ** ** *
2834494 AAAAAAAAAACAAAAAAAAAAAACAAAAAAACAAAAACAAAAAAAATCAAAAAAATCAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * *
2834559 CAAAAAAATCAAAACAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2834588 TCAAAAATAA
Statistics
Matches: 69, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:2834800 original size:3 final size:3
Alignment explanation
Indices: 2834779--2834892 Score: 60
Period size: 3 Copynumber: 36.3 Consensus size: 3
2834769 TCTTCTTTTG
2834779 TAT T-T TAT GTAT T-T TAT TAT TAT TAT TAT TAT TAT GTAT ATATT TATT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TA-T TA-T
* * *
2834827 TAT T-T TTT TAT TA- GAT TA- GAT T-T ATAT GTAT ATAGT TAT ATATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TA-T TAT -TA-T
2834871 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
2834893 TTTTTTTTTG
Statistics
Matches: 90, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
2 9 0.10
3 52 0.58
4 26 0.29
5 3 0.03
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2834937 original size:3 final size:3
Alignment explanation
Indices: 2834924--2834954 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2834914 TGGGTTTATC
2834924 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2834955 TTTAATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2835043 original size:43 final size:45
Alignment explanation
Indices: 2834937--2835045 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 45
2834927 TTTTATTATT
* * *
2834937 ATTATTATTATTATTATTTTTAATTATCTGTTCTGATTTTTCCTG
1 ATTATTATTATTATTTTTTTTAAATATCTGTTCTGATTTATCCTG
* * *
2834982 ATTATCAGATATTTTTTTTTTTAAATATCT-TT-TGATTTAT-CTG
1 ATTATTA-TTATTATTTTTTTTAAATATCTGTTCTGATTTATCCTG
*
2835025 ATTATTATCTAGTATTTTTTT
1 ATTATTAT-TATTATTTTTTT
2835046 ATTTTTGATT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
43 19 0.37
44 7 0.13
45 8 0.15
46 18 0.35
ACGTcount: A:0.24, C:0.07, G:0.06, T:0.62
Consensus pattern (45 bp):
ATTATTATTATTATTTTTTTTAAATATCTGTTCTGATTTATCCTG
Found at i:2835352 original size:25 final size:25
Alignment explanation
Indices: 2835316--2835363 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2835306 TGAGGAGAAT
2835316 TTTTTCTAGAAATTT-TGGCGAAAAA
1 TTTTTCTAGAAATTTCTGG-GAAAAA
*
2835341 TTTTTCTGGAAATTTCTGGGAAA
1 TTTTTCTAGAAATTTCTGGGAAA
2835364 TTTCCAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTTTCTAGAAATTTCTGGGAAAAA
Found at i:2835406 original size:30 final size:31
Alignment explanation
Indices: 2835372--2835437 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
2835362 AATTTCCAGA
2835372 TTCCGACGAAAATTCCGGCGAAAC-TTGAA-T
1 TTCCGACGAAAATTCCGGC-AAACTTTGAAGT
* * * *
2835402 TTCCGGCTACAATTCCGGCCAACTTTGAAGT
1 TTCCGACGAAAATTCCGGCAAACTTTGAAGT
2835433 TTCCG
1 TTCCG
2835438 GCGACCTACC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.10
30 21 0.70
31 6 0.20
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (31 bp):
TTCCGACGAAAATTCCGGCAAACTTTGAAGT
Found at i:2835866 original size:8 final size:8
Alignment explanation
Indices: 2835853--2835912 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
2835843 CACCAGGTTT
2835853 TTTTTTTA
1 TTTTTTTA
2835861 TTTTTTTTA
1 -TTTTTTTA
* *
2835870 TTTCTTTG
1 TTTTTTTA
* *
2835878 TTTATTTG
1 TTTTTTTA
2835886 TTTATTTTA
1 TTT-TTTTA
*
2835895 TTTGTTTA
1 TTTTTTTA
2835903 -TTTTTTA
1 TTTTTTTA
2835910 TTT
1 TTT
2835913 ATTAGATTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
7 6 0.14
8 22 0.52
9 14 0.33
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2835868 original size:13 final size:13
Alignment explanation
Indices: 2835850--2835908 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
2835840 CCGCACCAGG
2835850 TTTTTTTTTTATT
1 TTTTTTTTTTATT
* *
2835863 TTTTTTATTTCTT
1 TTTTTTTTTTATT
2835876 TGTTTATTTGTTTATT
1 T-TTT-TTT-TTTATT
* *
2835892 TTATTTGTTTATT
1 TTTTTTTTTTATT
2835905 TTTT
1 TTTT
2835909 ATTTATTAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 21 0.58
14 5 0.14
15 4 0.11
16 6 0.17
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:2836046 original size:59 final size:57
Alignment explanation
Indices: 2835982--2836410 Score: 355
Period size: 59 Copynumber: 7.1 Consensus size: 57
2835972 ATAAAAATAA
2835982 AAAAATTCTAAAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTGCCTAAAAG
1 AAAAATTCTAAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-CCTAAAAG
* * *
2836041 AAAAATAAATTTCCAAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA-
1 ---AA-AAA-TT-CTAAA-AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-TAAAAG
* * *
2836105 ATAAATT-TCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAG
1 AAAAATTCT-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT-AAAAG
* * * *
2836163 TAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAG
1 AAAAATTC-TAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-TAAAAG
* * *
2836222 AAAAATAAATTTCCAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAA
1 ---AA-AAA-TT-C--TAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTCCTAAAA
2836287 -
57 G
* * ** *
2836287 ATAAATTTTCAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCG
1 AAAAATTCT-AAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC-T-AAAA--G
* * * *
2836350 -AAATTTC-CAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCCTAAAAA
1 AAAAATTCTAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTCCTAAAAG
2836406 AAAAA
1 AAAAA
2836411 GTCATTCTTT
Statistics
Matches: 302, Mismatches: 37, Indels: 61
0.75 0.09 0.15
Matches are distributed among these distances:
56 1 0.00
57 45 0.15
58 22 0.07
59 99 0.33
60 21 0.07
61 4 0.01
62 8 0.03
63 5 0.02
64 6 0.02
65 42 0.14
66 44 0.15
67 5 0.02
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (57 bp):
AAAAATTCTAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAAAG
Found at i:2836275 original size:125 final size:117
Alignment explanation
Indices: 2835992--2836402 Score: 533
Period size: 125 Copynumber: 3.4 Consensus size: 117
2835982 AAAAATTCTA
2835992 AAAAATATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTGCCTAAAAGAAAAATAAATTTCCAA
1 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-CCT--AAG--AAATAAATTT-CAA
*
2836057 AATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAATTTCC
59 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
* *
2836115 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAGTAAATTTCAAAAAAAAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAATAAATTTCAAAAAAAAA
2836180 TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
66 TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-AAAATAAATTTCC
* *
2836236 AAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAATTTTC-AAA
1 ----AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAATAAA-TTTCAAAA
***
2836300 AAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
61 AAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AAATTTCC
*
2836358 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCCTAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTCCTAA
2836403 AAAAAAAAGT
Statistics
Matches: 262, Mismatches: 12, Indels: 32
0.86 0.04 0.10
Matches are distributed among these distances:
116 46 0.18
117 9 0.03
118 34 0.13
119 11 0.04
120 5 0.02
121 16 0.06
122 42 0.16
123 5 0.02
124 1 0.00
125 89 0.34
126 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (117 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTAAGAAATAAATTTCAAAAAAAAA
TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTTCC
Found at i:2840647 original size:16 final size:15
Alignment explanation
Indices: 2840609--2840638 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2840599 TAGAAATGCT
2840609 AGAGAAAGCTAGAAG
1 AGAGAAAGCTAGAAG
2840624 AGAGAAAGCTA-AAG
1 AGAGAAAGCTAGAAG
2840638 A
1 A
2840639 AGGAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.07, G:0.30, T:0.07
Consensus pattern (15 bp):
AGAGAAAGCTAGAAG
Found at i:2842775 original size:57 final size:57
Alignment explanation
Indices: 2842702--2843016 Score: 477
Period size: 57 Copynumber: 5.4 Consensus size: 57
2842692 AAATAGCTGT
*
2842702 AAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGA
* *
2842759 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAAGATTTTTGAGGA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC----AAAAAATATTTTTGGGGA
* * * *
2842820 AAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCTGAAAAATATTTTTGAGAA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC-AAAAAATATTTTTGGGGA
* *
2842879 AAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGGGGA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAATATTTTT-GGGGA
*
2842937 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAATATTTTTGGAGA
1 AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGA
2842994 AAAGTTGAAAGTATCAATTTTCC
1 AAAGTTGAAAGTATCAATTTTCC
2843017 CTACACAAGA
Statistics
Matches: 235, Mismatches: 17, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
57 77 0.33
58 59 0.25
59 45 0.19
61 47 0.20
62 7 0.03
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.36
Consensus pattern (57 bp):
AAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAATATTTTTGGGGA
Found at i:2849978 original size:24 final size:25
Alignment explanation
Indices: 2849950--2850003 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
2849940 TTAAATGTAA
* *
2849950 ATAAAAAG-AACAAAGAAATAAAAT
1 ATAAAAAGTAAAAAAAAAATAAAAT
*
2849974 ATAAAAAGTAAAAAAAAAATTAAAT
1 ATAAAAAGTAAAAAAAAAATAAAAT
2849999 ATAAA
1 ATAAA
2850004 TTAAATAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (25 bp):
ATAAAAAGTAAAAAAAAAATAAAAT
Found at i:2852554 original size:4 final size:4
Alignment explanation
Indices: 2852545--2852575 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2852535 ATTGCTTGAA
*
2852545 AAAT AAAT AAAT AAAT AAAT AAAA AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2852576 AACCATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:2852576 original size:8 final size:8
Alignment explanation
Indices: 2852543--2852577 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2852533 CAATTGCTTG
2852543 AAAAATAA
1 AAAAATAA
*
2852551 ATAAATAA
1 AAAAATAA
*
2852559 ATAAATAA
1 AAAAATAA
2852567 AAAAATAA
1 AAAAATAA
2852575 AAA
1 AAA
2852578 CCATAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:2855546 original size:3 final size:3
Alignment explanation
Indices: 2855538--2855581 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2855528 AATGCAAATG
2855538 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2855582 CGTTAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2856551 original size:8 final size:8
Alignment explanation
Indices: 2856538--2856576 Score: 60
Period size: 8 Copynumber: 4.6 Consensus size: 8
2856528 TTAAAATCCT
2856538 TTTTTTTA
1 TTTTTTTA
2856546 TTTTTTTA
1 TTTTTTTA
2856554 TTTTTTTA
1 TTTTTTTA
2856562 TTTATTTTTA
1 -TT-TTTTTA
2856572 TTTTT
1 TTTTT
2856577 AATTATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 19 0.66
9 4 0.14
10 6 0.21
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2856582 original size:20 final size:18
Alignment explanation
Indices: 2856538--2856586 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
2856528 TTAAAATCCT
2856538 TTTTTTTA-TT-TTTTTA
1 TTTTTTTATTTATTTTTA
2856554 TTTTTTTATTTATTTTTA
1 TTTTTTTATTTATTTTTA
2856572 TTTTTAATTATTTAT
1 TTTTT--TTATTTAT
2856587 ATAAAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.28
17 2 0.07
18 11 0.38
20 8 0.28
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTATTTATTTTTA
Found at i:2858254 original size:34 final size:34
Alignment explanation
Indices: 2858216--2858283 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
2858206 ATCAAATAAG
* *
2858216 GATGCGACGTAGATTTATTAAATT-AAGTTATTAA
1 GATGCAACATAGATTTATTAAATTAAAG-TATTAA
2858250 GATGCAACATAGATTTATTAAATTAAAGTATTAA
1 GATGCAACATAGATTTATTAAATTAAAGTATTAA
2858284 ATAATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 28 0.90
35 3 0.10
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.37
Consensus pattern (34 bp):
GATGCAACATAGATTTATTAAATTAAAGTATTAA
Found at i:2858759 original size:17 final size:17
Alignment explanation
Indices: 2858738--2858829 Score: 62
Period size: 18 Copynumber: 5.0 Consensus size: 17
2858728 ATTATTAAAT
2858738 GTAAATAAAAAGAACAAA
1 GTAAATAAAAAGAA-AAA
2858756 -TAAATAAAATAGAAAAA
1 GTAAATAAAA-AGAAAAA
* *
2858773 GTAAAAAAAAACATTAAATA
1 GTAAATAAAAAGA--AAA-A
*
2858793 -TAAATTAAATAAAAGAAAA
1 GTAAA-TAAA-AAGA-AAAA
2858812 GTAAATAAAAAGGAAAAA
1 GTAAATAAAAA-GAAAAA
2858830 AACAGAGGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
17 14 0.24
18 18 0.31
19 13 0.22
20 11 0.19
21 3 0.05
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (17 bp):
GTAAATAAAAAGAAAAA
Found at i:2858777 original size:18 final size:18
Alignment explanation
Indices: 2858738--2858782 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2858728 ATTATTAAAT
2858738 GTAAATAAAAAGAACAAA
1 GTAAATAAAAAGAACAAA
2858756 -TAAATAAAATAGAA-AAA
1 GTAAATAAAA-AGAACAAA
2858773 GTAAA-AAAAA
1 GTAAATAAAAA
2858783 ACATTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 16 0.64
18 8 0.32
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (18 bp):
GTAAATAAAAAGAACAAA
Found at i:2859621 original size:3 final size:3
Alignment explanation
Indices: 2859613--2859638 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2859603 ATTTACTAAA
2859613 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2859639 ATCCATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2859849 original size:22 final size:22
Alignment explanation
Indices: 2859824--2859892 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
2859814 ATTTAAAGAT
2859824 TTAAAGATTTATATTTGATGCA
1 TTAAAGATTTATATTTGATGCA
** ** * * *
2859846 TTAACTATGAACATTTAAAG-A
1 TTAAAGATTTATATTTGATGCA
2859867 TTTAAAGATTTATATTTGATGCA
1 -TTAAAGATTTATATTTGATGCA
2859890 TTA
1 TTA
2859893 TGTGTATAAA
Statistics
Matches: 31, Mismatches: 14, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (22 bp):
TTAAAGATTTATATTTGATGCA
Found at i:2859867 original size:44 final size:44
Alignment explanation
Indices: 2859804--2859892 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2859794 AACCAGCAAC
2859804 AACTATGAACATTTAAAGATTTAAAGATTTATATTTGATGCATT
1 AACTATGAACATTTAAAGATTTAAAGATTTATATTTGATGCATT
2859848 AACTATGAACATTTAAAGATTTAAAGATTTATATTTGATGCATT
1 AACTATGAACATTTAAAGATTTAAAGATTTATATTTGATGCATT
2859892 A
1 A
2859893 TGTGTATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (44 bp):
AACTATGAACATTTAAAGATTTAAAGATTTATATTTGATGCATT
Found at i:2860675 original size:23 final size:21
Alignment explanation
Indices: 2860648--2860691 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
2860638 TAGTAATTAG
2860648 TTTTATTTGAATTGATATTTTAA
1 TTTTATTT-AATTGA-ATTTTAA
*
2860671 TTTTATTTAATTTAATTTTAA
1 TTTTATTTAATTGAATTTTAA
2860692 ATATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTTATTTAATTGAATTTTAA
Found at i:2860862 original size:22 final size:21
Alignment explanation
Indices: 2860823--2860863 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2860813 TTTTATATAT
* *
2860823 AAATTTATTTAAATATATTAA
1 AAATTTATTAAAAAATATTAA
2860844 AAATTATATTAAAAAATATT
1 AAATT-TATTAAAAAATATT
2860864 TACACAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTATTAAAAAATATTAA
Found at i:2862183 original size:2 final size:2
Alignment explanation
Indices: 2862178--2862209 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2862168 GTCAGCAACC
2862178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2862210 CACTGATGTG
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):
TA
Found at i:2864318 original size:13 final size:13
Alignment explanation
Indices: 2864296--2864328 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2864286 AGCAAACTTG
*
2864296 TGGCATAGGAGGC
1 TGGCACAGGAGGC
2864309 TGGCACAGGAGGC
1 TGGCACAGGAGGC
2864322 TGGCACA
1 TGGCACA
2864329 CATGAGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.42, T:0.12
Consensus pattern (13 bp):
TGGCACAGGAGGC
Found at i:2876281 original size:17 final size:18
Alignment explanation
Indices: 2876256--2876289 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2876246 TTAAAATTTT
*
2876256 ATTTTATAA-TATATAAA
1 ATTTCATAATTATATAAA
2876273 ATTTCATAATTATATAA
1 ATTTCATAATTATATAA
2876290 GAAAAAATTT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTCATAATTATATAAA
Found at i:2877423 original size:14 final size:12
Alignment explanation
Indices: 2877403--2877445 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
2877393 TAAATTTTAA
2877403 TTTTAATAAAAT
1 TTTTAATAAAAT
2877415 TCATTTAATATAAAT
1 T--TTTAATA-AAAT
*
2877430 TTTTAATTAAAT
1 TTTTAATAAAAT
2877442 TTTT
1 TTTT
2877446 TTATTCACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
14 7 0.26
15 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTAATAAAAT
Found at i:2877501 original size:24 final size:24
Alignment explanation
Indices: 2877439--2877493 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2877429 TTTTTAATTA
*
2877439 AATTTTTTT-ATTCACAATTATAAT
1 AATTTTTTTAATT-ATAATTATAAT
2877463 AATTTTTTTAATTATAATTATAAT
1 AATTTTTTTAATTATAATTATAAT
2877487 AATTTTT
1 AATTTTT
2877494 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTTTTTTAATTATAATTATAAT
Found at i:2877826 original size:7 final size:6
Alignment explanation
Indices: 2877763--2877822 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
2877753 CAATTTTTTA
* * * * *
2877763 TTAAAT TTAGA- TGAAAT TTAGAT ATTAAAT GTATAT ATTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT -TTAAAT TTAAAT
2877812 TTAAAT TTAAA
1 TTAAAT TTAAA
2877823 ATTTGAATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
5 3 0.07
6 29 0.71
7 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:2877939 original size:22 final size:24
Alignment explanation
Indices: 2877913--2877956 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
2877903 ATATAAATTT
2877913 ATTAAAAT-ATAT-TAAAAATTAG
1 ATTAAAATAATATATAAAAATTAG
2877935 ATTAAAATAATATATAAAAATT
1 ATTAAAATAATATATAAAAATT
2877957 TTAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
ATTAAAATAATATATAAAAATTAG
Found at i:2879345 original size:13 final size:14
Alignment explanation
Indices: 2879328--2879376 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
2879318 TAATAAATTT
2879328 TTTTAATTTATTAA
1 TTTTAATTTATTAA
* *
2879342 TTTAAAATT-TTAA
1 TTTTAATTTATTAA
*
2879355 TTTTAATTTAATTAT
1 TTTTAATTT-ATTAA
2879370 TTTTAAT
1 TTTTAAT
2879377 AAAAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 11 0.39
14 7 0.25
15 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTAATTTATTAA
Done.