Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 25 of 172
Found at i:5958762 original size:30 final size:30
Alignment explanation
Indices: 5958722--5958823 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
5958712 ATTTAGGATT
*
5958722 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
5958752 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
5958782 AAAATGAAATTT-AGGAAAAGTTTGGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
5958812 AAAATGAAATTT
1 AAAATGAAATTT
5958824 TTATTTTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:5958844 original size:14 final size:15
Alignment explanation
Indices: 5958818--5958853 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
5958808 GGTCAAAATG
5958818 AAATTTTTATTTTTA
1 AAATTTTTATTTTTA
*
5958833 AAATTTTT-TTTTTG
1 AAATTTTTATTTTTA
5958847 AAATTTT
1 AAATTTT
5958854 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
AAATTTTTATTTTTA
Found at i:5960224 original size:38 final size:38
Alignment explanation
Indices: 5960182--5960259 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
5960172 TTTATTTTTT
* *
5960182 AATAATTTT-GAATATTTTAATAATTTTTCATTTTTAAA
1 AATAATTTTAGAATATTTTAA-AATTTTTAAATTTTAAA
* *
5960220 AATAATTTTATAATATTTTAAATTTTTTAAATTTTAAA
1 AATAATTTTAGAATATTTTAAAATTTTTAAATTTTAAA
5960258 AA
1 AA
5960260 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (38 bp):
AATAATTTTAGAATATTTTAAAATTTTTAAATTTTAAA
Found at i:5960245 original size:17 final size:16
Alignment explanation
Indices: 5960223--5960257 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5960213 TTTTAAAAAT
5960223 AATTTTATAATATTTTA
1 AATTTTATAA-ATTTTA
*
5960240 AATTTTTTAAATTTTA
1 AATTTTATAAATTTTA
5960256 AA
1 AA
5960258 AAATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTATAAATTTTA
Found at i:5960254 original size:39 final size:38
Alignment explanation
Indices: 5960182--5960266 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
5960172 TTTATTTTTT
* *
5960182 AATAATTTTGAATATTTTAATAATTTTTCATTTTTAAA
1 AATAATTTTGAATATTTTAATAATTTTTAATTTTAAAA
* *
5960220 AATAATTTTATAATATTTTAA-ATTTTTTAAATTTTAAAA
1 AATAATTTT-GAATATTTTAATAATTTTT-AATTTTAAAA
5960259 AATTAATT
1 AA-TAATT
5960267 AAATGTTGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 15 0.38
39 20 0.50
40 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (38 bp):
AATAATTTTGAATATTTTAATAATTTTTAATTTTAAAA
Found at i:5961059 original size:37 final size:36
Alignment explanation
Indices: 5961018--5961099 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
5961008 TTTTGTTTTT
5961018 AAACACGAGAACTTTGAAACAAAATAATAATTTTTGA
1 AAACACGAGAACTTTGAAACAAAA-AATAATTTTTGA
** ** **
5961055 AAACACGAAGATTTTTGAAACACGAAATTTTTTTTGA
1 AAACACG-AGAACTTTGAAACAAAAAATAATTTTTGA
5961092 AAACACGA
1 AAACACGA
5961100 AAACACAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
36 1 0.03
37 24 0.63
38 13 0.34
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (36 bp):
AAACACGAGAACTTTGAAACAAAAAATAATTTTTGA
Found at i:5961075 original size:17 final size:17
Alignment explanation
Indices: 5961046--5961101 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 17
5961036 ACAAAATAAT
5961046 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
5961063 AGATTTTTG-AAACACGA
1 A-ATTTTTGAAAACACGA
5961080 AATTTTTTTTGAAAACACGA
1 AA---TTTTTGAAAACACGA
5961100 AA
1 AA
5961102 ACACAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 10 0.29
18 7 0.21
19 6 0.18
20 10 0.29
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:5961165 original size:17 final size:18
Alignment explanation
Indices: 5961117--5961166 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
5961107 AAATTTTTTT
*
5961117 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
* *
5961135 AACACGACAGTTTTTG-A
1 AACACGAGAATTTTTGAA
*
5961152 AACATGAGAATTTTT
1 AACACGAGAATTTTT
5961167 TTAAAACACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (18 bp):
AACACGAGAATTTTTGAA
Found at i:5961193 original size:21 final size:22
Alignment explanation
Indices: 5961164--5961205 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5961154 CATGAGAATT
*
5961164 TTTTTAAAACAC-AAAATTTTA
1 TTTTGAAAACACAAAAATTTTA
5961185 TTTTGAAAACACAAAAATTTT
1 TTTTGAAAACACAAAAATTTT
5961206 GATAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTTGAAAACACAAAAATTTTA
Found at i:5961299 original size:17 final size:18
Alignment explanation
Indices: 5961268--5961760 Score: 228
Period size: 17 Copynumber: 27.2 Consensus size: 18
5961258 CAATGTCAAT
5961268 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
5961286 TTTTTGAAAGACGA-GAATT
1 TTTTTGAAA-AC-ACGAAAA
* *
5961305 TTTTTGAAAACACGGAGA
1 TTTTTGAAAACACGAAAA
* *
5961323 TTTAT-AAAACACGAAAGTTTT
1 TTTTTGAAAACACGAAA----A
*
5961344 TTTTTGAAAACAAGAAAA
1 TTTTTGAAAACACGAAAA
* * *
5961362 -TTTTCAAAATACGAGAA
1 TTTTTGAAAACACGAAAA
* *
5961379 TTTTTGAAAACAGGGGAAA
1 TTTTTGAAAACA-CGAAAA
*
5961398 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
5961416 ATTTT-AAAACACTAGAA
1 TTTTTGAAAACACGAAAA
*
5961433 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* * *
5961450 TTTTT-TAAACATGAGAA
1 TTTTTGAAAACACGAAAA
* *
5961467 TTTTTGAAAACACGAGGAT
1 TTTTTGAAAACACGA-AAA
*
5961486 TTTTTGAAATACA--AACA
1 TTTTTGAAA-ACACGAAAA
* *
5961503 TTTTAG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
* *
5961520 TTTTT-AAAACATGACAAT
1 TTTTTGAAAACACGA-AAA
5961538 TTTTTG-AAACACGAGAAATTTA
1 TTTTTGAAAACAC--GAAA---A
* **
5961560 TTTTTTAAAACATAAAAA
1 TTTTTGAAAACACGAAAA
* *
5961578 ATTTT-AAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* * *
5961595 TTTGTG-AAACTCGAGAA
1 TTTTTGAAAACACGAAAA
* * **
5961612 TTGTTGAAAAAAAATAAAAA
1 TTTTTG--AAAACACGAAAA
* *
5961632 ATTTTGAAAATACG-AAA
1 TTTTTGAAAACACGAAAA
**
5961649 TTTTTTTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * * * *
5961667 TTTTAG-AAATATGGACA
1 TTTTTGAAAACACGAAAA
5961684 TTTTTAGAAAACACGAAAA
1 TTTTT-GAAAACACGAAAA
* *
5961703 ATTTTGAAAA-A-TAAAA
1 TTTTTGAAAACACGAAAA
*
5961719 TTTTTTGAAAACACGAGAA
1 -TTTTTGAAAACACGAAAA
5961738 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACACG-AAAA
5961757 TTTT
1 TTTT
5961761 CTGATTTTTC
Statistics
Matches: 349, Mismatches: 89, Indels: 73
0.68 0.17 0.14
Matches are distributed among these distances:
15 3 0.01
16 10 0.03
17 134 0.38
18 96 0.28
19 63 0.18
20 16 0.05
21 7 0.02
22 15 0.04
23 5 0.01
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:5961308 original size:37 final size:37
Alignment explanation
Indices: 5961267--5961597 Score: 165
Period size: 35 Copynumber: 9.1 Consensus size: 37
5961257 ACAATGTCAA
* *
5961267 TTTTTTGAAAACACGAAAATTTTTGAAAGACGAGAAT
1 TTTTTTGAAAACACGAAAATTTTTAAAACACGAGAAT
* * *
5961304 TTTTTTGAAAACACGGAGATTTATAAAACACGA-AAGTTT
1 TTTTTTGAAAACACGAAAATTTTTAAAACACGAGAA---T
* * *
5961343 TTTTTTGAAAACAAGAAAATTTTCAAAATACGAGAA-
1 TTTTTTGAAAACACGAAAATTTTTAAAACACGAGAAT
* * *
5961379 -TTTTTGAAAACAGGGGAAATTTTTGAAAACATGA-AA-
1 TTTTTTGAAAACA-CGAAAATTTTT-AAAACACGAGAAT
** * * *
5961415 AATTTT-AAAACACTAGAATTTTGAAAACACGA-AGA-
1 TTTTTTGAAAACACGAAAATTTTTAAAACACGAGA-AT
* * *
5961450 TTTTTT--AAACATGAGAATTTTTGAAAACACGAGGA-
1 TTTTTTGAAAACACGAAAATTTTT-AAAACACGAGAAT
* *
5961485 TTTTTTGAAATACA--AACA-TTTTAGAAACATGA-AA-
1 TTTTTTGAAA-ACACGAAAATTTTTA-AAACACGAGAAT
* * * *
5961519 ATTTTT-AAAACATGACAATTTTTTGAAACACGAGAAATT
1 TTTTTTGAAAACACGA-AAATTTTTAAAACACGAG-AA-T
* ** *
5961558 TATTTTTTAAAACATAAAAAATTTTAAAACACGAGAAT
1 T-TTTTTGAAAACACGAAAATTTTTAAAACACGAGAAT
5961596 TT
1 TT
5961598 GTGAAACTCG
Statistics
Matches: 227, Mismatches: 43, Indels: 48
0.71 0.14 0.15
Matches are distributed among these distances:
32 3 0.01
33 3 0.01
34 30 0.13
35 58 0.26
36 24 0.11
37 44 0.19
38 5 0.02
39 30 0.13
40 22 0.10
41 8 0.04
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (37 bp):
TTTTTTGAAAACACGAAAATTTTTAAAACACGAGAAT
Found at i:5961333 original size:74 final size:76
Alignment explanation
Indices: 5961230--5961390 Score: 174
Period size: 76 Copynumber: 2.2 Consensus size: 76
5961220 CACGAGGATT
* * * * *
5961230 TTTTTTTG-AAACGCGGAAGTTTAT-GAA-AC-AATGTCAATTTTTTGAAAACACGAAAATTTTT
1 TTTTTTTGAAAACACGGAAGTTTATAAAACACGAAAGT-AATTTTTTGAAAACAAGAAAATTTTC
*
5961291 GAAAGACGAGAA
65 AAAAGACGAGAA
**
5961303 TTTTTTTGAAAACACGG-AGATTTATAAAACACGAAAGTTTTTTTTTGAAAACAAGAAAATTTTC
1 TTTTTTTGAAAACACGGAAG-TTTATAAAACACGAAAGTAATTTTTTGAAAACAAGAAAATTTTC
*
5961367 AAAATACGAGAA
65 AAAAGACGAGAA
5961379 --TTTTTGAAAACA
1 TTTTTTTGAAAACA
5961391 GGGGAAATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
73 10 0.14
74 24 0.32
75 2 0.03
76 34 0.46
77 4 0.05
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (76 bp):
TTTTTTTGAAAACACGGAAGTTTATAAAACACGAAAGTAATTTTTTGAAAACAAGAAAATTTTCA
AAAGACGAGAA
Found at i:5961408 original size:76 final size:75
Alignment explanation
Indices: 5961267--5961414 Score: 190
Period size: 76 Copynumber: 1.9 Consensus size: 75
5961257 ACAATGTCAA
* ** *
5961267 TTTTTTGAAAACACGAAAATTTTTGAAAGACGAGAATTTTTTTGAAAACACGGAGATTTATAAAA
1 TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAA-TTTTTTGAAAACACGGAAATTTATAAAA
5961332 CACGAAAGTTT
65 CACGAAAGTTT
* * *
5961343 TTTTTTGAAAACAAGAAAATTTTCAAAATACGAGAA-TTTTTGAAAACAGGGGAAATTTTTGAAA
1 TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAATTTTTTGAAAACA-CGGAAATTTAT-AAA
*
5961407 ACATGAAA
64 ACACGAAA
5961415 AATTTTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
74 12 0.19
75 8 0.13
76 42 0.68
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (75 bp):
TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAATTTTTTGAAAACACGGAAATTTATAAAAC
ACGAAAGTTT
Found at i:5961438 original size:34 final size:35
Alignment explanation
Indices: 5961396--5961749 Score: 144
Period size: 35 Copynumber: 9.9 Consensus size: 35
5961386 AAACAGGGGA
*
5961396 AATTTTTGAAAACATGAAAAATTTTAAAACACT-AG
1 AATTTTTGAAAACACGAAAAATTTTAAAACA-TGAG
* * *
5961431 AA-TTTTGAAAACACGAAGATTTTTTAAACATGAG
1 AATTTTTGAAAACACGAAAAATTTTAAAACATGAG
* **
5961465 AATTTTTGAAAACACGAGGATTTTTTGAAATACA--A-
1 AATTTTTGAAAACACGA-AAAATTTT-AAA-ACATGAG
* * * *
5961500 ACATTTTAG-AAACATGAAAATTTTTAAAACATGAC
1 A-ATTTTTGAAAACACGAAAAATTTTAAAACATGAG
* *
5961535 AATTTTTTG-AAACACGAGAAATTTATTTTTTAAAACATAAA
1 AA-TTTTTGAAAACACGA-AAA---A--TTTTAAAACATGAG
* * *
5961576 AAATTTT-AAAACACG-AGAATTTGTGAAAC-TCGAG
1 AATTTTTGAAAACACGAAAAATTT-TAAAACAT-GAG
* * ** * *
5961610 AATTGTTGAAAAAAAATAAAAAATTTTGAAAATACGA-
1 AATTTTTG--AAAACACGAAAAATTTT-AAAACATGAG
** *
5961647 AATTTTTTTAAACACG-AAAATTTTAGAAATATG-G
1 AATTTTTGAAAACACGAAAAATTTTA-AAACATGAG
*
5961681 ACATTTTTAGAAAACACGAAAAATTTTGAAAA-AT-AA
1 A-ATTTTT-GAAAACACGAAAAATTTT-AAAACATGAG
* *
5961717 AATTTTTTGAAAACACGAGAATTTTTGAAAACA
1 AA-TTTTTGAAAACACGAAAAATTTT-AAAACA
5961750 CGAAAAATTT
Statistics
Matches: 242, Mismatches: 43, Indels: 67
0.69 0.12 0.19
Matches are distributed among these distances:
32 3 0.01
33 9 0.04
34 62 0.26
35 70 0.29
36 31 0.13
37 25 0.10
38 17 0.07
40 11 0.05
41 14 0.06
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.32
Consensus pattern (35 bp):
AATTTTTGAAAACACGAAAAATTTTAAAACATGAG
Found at i:5962088 original size:10 final size:10
Alignment explanation
Indices: 5962088--5962137 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
5962078 AATAAAATAA
*
5962088 AAATAAAAATT
1 AAATTAAAA-T
*
5962099 AAATTAAATT
1 AAATTAAAAT
*
5962109 AAATTAAATT
1 AAATTAAAAT
*
5962119 AAATTAAATT
1 AAATTAAAAT
5962129 AAATTAAAA
1 AAATTAAAA
5962138 ATATAAATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
10 29 0.81
11 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:5962095 original size:5 final size:5
Alignment explanation
Indices: 5962094--5962136 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
5962084 ATAAAAATAA
5962094 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAA
5962137 AATATAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:5962309 original size:17 final size:16
Alignment explanation
Indices: 5962287--5962345 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
5962277 AATTGAACCC
5962287 CTTTTTTCTTGTTTTTT
1 CTTTTTTCTT-TTTTTT
5962304 CTTTTTTCTTTTTTTCT
1 CTTTTTTCTTTTTTT-T
* *
5962321 CCTTTTTCTTCCTTTTT
1 CTTTTTTCTT-TTTTTT
5962338 -TTTTTTCT
1 CTTTTTTCT
5962346 GCTGGGCTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 12 0.32
17 21 0.57
18 4 0.11
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (16 bp):
CTTTTTTCTTTTTTTT
Found at i:5962320 original size:25 final size:25
Alignment explanation
Indices: 5962288--5962345 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
5962278 ATTGAACCCC
**
5962288 TTTTTTCTTGTTTTTTCTT-TTTTCT
1 TTTTTTCTTCCTTTTTCTTCTTTT-T
5962313 TTTTTTC-TCCTTTTTCTTCCTTTTT
1 TTTTTTCTTCCTTTTTCTT-CTTTTT
5962338 TTTTTTCT
1 TTTTTTCT
5962346 GCTGGGCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 9 0.32
25 15 0.54
26 4 0.14
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTTTCTTCCTTTTTCTTCTTTTT
Found at i:5962326 original size:24 final size:24
Alignment explanation
Indices: 5962299--5962345 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
5962289 TTTTTCTTGT
5962299 TTTTTCTT-TTTTCTTTTTTTCTCC
1 TTTTTCTTCTTTT-TTTTTTTCTCC
5962323 TTTTTCTTCCTTTTTTTTTTTCT
1 TTTTTCTT-CTTTTTTTTTTTCT
5962346 GCTGGGCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 9 0.43
26 4 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTCTTCTTTTTTTTTTTCTCC
Found at i:5962627 original size:3 final size:3
Alignment explanation
Indices: 5962621--5962679 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
5962611 TTTTCTTTTT
5962621 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
5962668 TTC TTC TTC TTC
1 TTC TTC TTC TTC
5962680 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:5962634 original size:10 final size:10
Alignment explanation
Indices: 5962613--5962679 Score: 74
Period size: 10 Copynumber: 7.3 Consensus size: 10
5962603 TAAAATTTTT
5962613 TTCTT-TTT-
1 TTCTTCTTTC
5962621 TTCTTCTTTC
1 TTCTTCTTTC
*
5962631 TTCTTCTCTC
1 TTCTTCTTTC
5962641 -T-TTCTTTC
1 TTCTTCTTTC
5962649 TTCTTC-TTC
1 TTCTTCTTTC
*
5962658 TTCTTCCTTC
1 TTCTTCTTTC
5962668 TTCTTC-TTC
1 TTCTTCTTTC
5962677 TTC
1 TTC
5962680 AAAACCGAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
8 11 0.21
9 20 0.38
10 21 0.40
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:5962667 original size:13 final size:13
Alignment explanation
Indices: 5962621--5962676 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
5962611 TTTTCTTTTT
*
5962621 TTCTTCTTTCTTC
1 TTCTTCCTTCTTC
*
5962634 TTCTCTCTTTC-T-
1 TTCT-TCCTTCTTC
5962646 TTCTT-CTTCTTC
1 TTCTTCCTTCTTC
5962658 TTCTTCCTTCTTC
1 TTCTTCCTTCTTC
5962671 TTCTTC
1 TTCTTC
5962677 TTCAAAACCG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 2 0.05
12 9 0.24
13 18 0.47
14 6 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTCCTTCTTC
Found at i:5963076 original size:29 final size:29
Alignment explanation
Indices: 5963043--5963159 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 29
5963033 TGTAATTTTT
*
5963043 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* *
5963072 TGAAAGTTTAGGGGTCT-AAATGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
5963102 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
5963131 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
5963160 TTATTTTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
29 14 0.19
30 58 0.78
31 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:5963095 original size:30 final size:30
Alignment explanation
Indices: 5963058--5963159 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
5963048 ATTTAGGATT
*
5963058 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
5963088 TAAATGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
5963118 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
5963148 AAAATGCAATTT
1 AAAATGAAATTT
5963160 TTATTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 2 0.03
30 62 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:5963617 original size:54 final size:55
Alignment explanation
Indices: 5963430--5963648 Score: 326
Period size: 54 Copynumber: 4.1 Consensus size: 55
5963420 CACGTGAGCC
* * *
5963430 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTG--AA
5963486 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAA
*
5963537 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
5963591 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
5963646 AAG
1 AAG
5963649 TAGAAATTGA
Statistics
Matches: 151, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 53 0.35
55 5 0.03
56 32 0.21
57 6 0.04
58 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
Found at i:5963646 original size:14 final size:14
Alignment explanation
Indices: 5963627--5963661 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5963617 GAGTTGATTT
5963627 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
*
5963641 TTGAAAAGTAGAAA
1 TTGAAAAATAGAAA
5963655 TTGAAAA
1 TTGAAAA
5963662 TACCTCAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:5963905 original size:85 final size:87
Alignment explanation
Indices: 5963761--5964008 Score: 299
Period size: 85 Copynumber: 2.8 Consensus size: 87
5963751 AACAGAAATT
* * *
5963761 AAAAACAGAATTTGAAAAGACCTCAGCTTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
5963826 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
5963848 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
*
5963911 TTGATTTTTGAGAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
5963937 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
5964001 GTTGATTT
64 GTTGATTT
5964009 TTGAAAAACA
Statistics
Matches: 137, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 31 0.23
88 3 0.02
89 31 0.23
91 33 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:5963996 original size:91 final size:88
Alignment explanation
Indices: 5963761--5964015 Score: 315
Period size: 91 Copynumber: 2.9 Consensus size: 88
5963751 AACAGAAATT
* * *
5963761 AAAAACAGAATTTGAAAAGACCTCAGCTTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
5963826 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* * * *
5963848 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
*
5963911 TTGATTTTTGAGAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
5963937 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
5964001 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
5964016 ACAAAAATTA
Statistics
Matches: 143, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 31 0.22
88 3 0.02
89 28 0.20
91 42 0.29
93 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:5974809 original size:37 final size:36
Alignment explanation
Indices: 5974768--5974849 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 36
5974758 TTTTGTTTTT
5974768 AAACACGAGAACTTTGAAACAAAATAATAATTTTTGA
1 AAACACGAGAACTTTGAAACAAAA-AATAATTTTTGA
** ** *
5974805 AAACACGAAGATTTTTGAAACACGAAATATTTTTTGA
1 AAACACG-AGAACTTTGAAACAAAAAATAATTTTTGA
5974842 AAACACGA
1 AAACACGA
5974850 AAACACAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 25 0.64
38 13 0.33
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (36 bp):
AAACACGAGAACTTTGAAACAAAAAATAATTTTTGA
Found at i:5974838 original size:19 final size:19
Alignment explanation
Indices: 5974797--5974851 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 19
5974787 CAAAATAATA
*
5974797 ATTTTTGAAAACACG-AAG
1 ATTTTTGAAAACACGAAAT
5974815 ATTTTTG-AAACACGAAAT
1 ATTTTTGAAAACACGAAAT
5974833 ATTTTTTGAAAACACGAAA
1 A-TTTTTGAAAACACGAAA
5974852 ACACAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 7 0.21
18 10 0.30
19 6 0.18
20 10 0.30
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (19 bp):
ATTTTTGAAAACACGAAAT
Found at i:5974915 original size:17 final size:18
Alignment explanation
Indices: 5974867--5974916 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
5974857 AAATTTTTTT
*
5974867 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
* *
5974885 AACACGACAGTTTTTG-A
1 AACACGAGAATTTTTGAA
*
5974902 AACATGAGAATTTTT
1 AACACGAGAATTTTT
5974917 TTAAAACACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (18 bp):
AACACGAGAATTTTTGAA
Found at i:5974943 original size:21 final size:22
Alignment explanation
Indices: 5974914--5974955 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5974904 CATGAGAATT
*
5974914 TTTTTAAAACAC-AAAATTTTA
1 TTTTGAAAACACAAAAATTTTA
5974935 TTTTGAAAACACAAAAATTTT
1 TTTTGAAAACACAAAAATTTT
5974956 GATAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTTGAAAACACAAAAATTTTA
Found at i:5975008 original size:37 final size:38
Alignment explanation
Indices: 5974962--5975085 Score: 123
Period size: 37 Copynumber: 3.3 Consensus size: 38
5974952 TTTTGATAAA
*
5974962 TTATGAAACACGAGGATTTTTTTTG-AAACGCGGAAAT
1 TTATGAAACACGAGGATTTTTTTTGAAAACACGGAAAT
* *
5974999 TTATGAAACA--AGG-TCAATTTTTTGAAAACACGAAAAT
1 TTATGAAACACGAGGAT--TTTTTTTGAAAACACGGAAAT
* * * *
5975036 TTTTGAAAGACGA-GAATTTTTTTGAAAACACGGAGAT
1 TTATGAAACACGAGGATTTTTTTTGAAAACACGGAAAT
*
5975073 TTATAAAACACGA
1 TTATGAAACACGA
5975086 AAGTTTTTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
34 1 0.01
35 3 0.04
36 7 0.10
37 56 0.81
38 1 0.01
39 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (38 bp):
TTATGAAACACGAGGATTTTTTTTGAAAACACGGAAAT
Found at i:5975048 original size:17 final size:18
Alignment explanation
Indices: 5975017--5975509 Score: 221
Period size: 17 Copynumber: 27.2 Consensus size: 18
5975007 CAAGGTCAAT
5975017 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
5975035 TTTTTGAAAGACGA-GAATT
1 TTTTTGAAA-AC-ACGAAAA
* *
5975054 TTTTTGAAAACACGGAGA
1 TTTTTGAAAACACGAAAA
* *
5975072 TTTAT-AAAACACGAAAGTTTTT
1 TTTTTGAAAACACGAAA-----A
*
5975094 TTTTTG-AAACAAGAAAA
1 TTTTTGAAAACACGAAAA
* * *
5975111 -TTTTCAAAATACGAGAA
1 TTTTTGAAAACACGAAAA
* *
5975128 TTTTTGAAAACAGGGGAAA
1 TTTTTGAAAACA-CGAAAA
*
5975147 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
5975165 CTTTT-AAAACACTAGAA
1 TTTTTGAAAACACGAAAA
*
5975182 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* * *
5975199 TTTTT-TAAACATGAGAA
1 TTTTTGAAAACACGAAAA
* *
5975216 TTTTTGAAAACACGAGGAT
1 TTTTTGAAAACACGA-AAA
*
5975235 TTTTTGAAATACA--AACA
1 TTTTTGAAA-ACACGAAAA
* *
5975252 TTTTAG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
* *
5975269 TTTTT-AAAACATGACAAT
1 TTTTTGAAAACACGA-AAA
5975287 TTTTTG-AAACACGAGTAATTTA
1 TTTTTGAAAACACGA--AA---A
* **
5975309 TTTTTTAAAACATAAAAA
1 TTTTTGAAAACACGAAAA
* *
5975327 ATTTT-AAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* * *
5975344 TTTGTG-AAACTCGAGAA
1 TTTTTGAAAACACGAAAA
* **
5975361 TTGTTGAAAAAACATAAAAA
1 TTTTTG--AAAACACGAAAA
* *
5975381 ATTTTGAAAATACG-AAA
1 TTTTTGAAAACACGAAAA
**
5975398 TTTTTTTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * * * *
5975416 TTTTAG-AAATATGGACA
1 TTTTTGAAAACACGAAAA
5975433 TTTTTAGAAAACACGAAAA
1 TTTTT-GAAAACACGAAAA
* *
5975452 ATTTTGAAAA-A-TAAAA
1 TTTTTGAAAACACGAAAA
*
5975468 TTTTTTGAAAACACGAGAA
1 -TTTTTGAAAACACGAAAA
5975487 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACACG-AAAA
5975506 TTTT
1 TTTT
5975510 CTGATTTTTC
Statistics
Matches: 348, Mismatches: 89, Indels: 75
0.68 0.17 0.15
Matches are distributed among these distances:
15 3 0.01
16 14 0.04
17 129 0.37
18 98 0.28
19 63 0.18
20 15 0.04
21 2 0.01
22 18 0.05
23 6 0.02
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:5975093 original size:37 final size:37
Alignment explanation
Indices: 5974962--5975139 Score: 111
Period size: 37 Copynumber: 4.8 Consensus size: 37
5974952 TTTTGATAAA
* * * *
5974962 TTATGAAACACGAGGATTTTTTTTG-AAACGCGGAAAT
1 TTATAAAACACGA-GAATTTTTTTGAAAACACGAAAAT
* *
5974999 TTATGAAACAAG-GTCAA-TTTTTTGAAAACACGAAAAT
1 TTATAAAACACGAG--AATTTTTTTGAAAACACGAAAAT
* * * * *
5975036 TTTTGAAAGACGAGAATTTTTTTGAAAACACGGAGAT
1 TTATAAAACACGAGAATTTTTTTGAAAACACGAAAAT
*
5975073 TTATAAAACACGA-AAGTTTTTTTTTTG-AAACAAGAAAAT
1 TTATAAAACACGAGAA----TTTTTTTGAAAACACGAAAAT
*
5975112 TT-TCAAAATACGAGAA--TTTTTGAAAACA
1 TTAT-AAAACACGAGAATTTTTTTGAAAACA
5975140 GGGGAAATTT
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
34 6 0.05
35 6 0.05
36 11 0.10
37 59 0.52
38 2 0.02
39 19 0.17
40 10 0.09
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (37 bp):
TTATAAAACACGAGAATTTTTTTGAAAACACGAAAAT
Found at i:5975157 original size:76 final size:76
Alignment explanation
Indices: 5975016--5975163 Score: 183
Period size: 76 Copynumber: 1.9 Consensus size: 76
5975006 ACAAGGTCAA
* ** *
5975016 TTTTTTGAAAACACGAAAATTTTTGAAAGACGAGAATTTTTTTGAAAACACGGAGATTTATAAAA
1 TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAA-TTTTTTGAAAACACGGAAATTTATAAAA
5975081 CACGAAAGTTTT
65 CACGAAAGTTTT
* * *
5975093 TTTTTTG-AAACAAGAAAATTTTCAAAATACGAGAA-TTTTTGAAAACAGGGGAAATTTTTGAAA
1 TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAATTTTTTGAAAACA-CGGAAATTTAT-AAA
*
5975156 ACATGAAA
64 ACACGAAA
5975164 ACTTTTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
74 12 0.20
75 8 0.13
76 34 0.56
77 7 0.11
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (76 bp):
TTTTTTGAAAACAAGAAAATTTTCAAAAGACGAGAATTTTTTGAAAACACGGAAATTTATAAAAC
ACGAAAGTTTT
Found at i:5975189 original size:34 final size:35
Alignment explanation
Indices: 5975145--5975498 Score: 126
Period size: 35 Copynumber: 9.9 Consensus size: 35
5975135 AAACAGGGGA
*
5975145 AATTTTTGAAAACATGAAAACTTTTAAAACACT-AG
1 AATTTTTGAAAACACGAAAACTTTTAAAACA-TGAG
* * *
5975180 AA-TTTTGAAAACACGAAGATTTTTTAAACATGAG
1 AATTTTTGAAAACACGAAAACTTTTAAAACATGAG
* **
5975214 AATTTTTGAAAACACGAGGATTTTTTGAAATACA--A-
1 AATTTTTGAAAACACGA-AAACTTTT-AAA-ACATGAG
* * * *
5975249 ACATTTTAG-AAACATGAAAATTTTTAAAACATGAC
1 A-ATTTTTGAAAACACGAAAACTTTTAAAACATGAG
* * *
5975284 AATTTTTTG-AAACACGAGTAATTTATTTTTTAAAACATAAA
1 AA-TTTTTGAAAACACGA--AA---A-CTTTTAAAACATGAG
* * *
5975325 AAATTTT-AAAACACGAGAA-TTTGTGAAAC-TCGAG
1 AATTTTTGAAAACACGAAAACTTT-TAAAACAT-GAG
* ** * * *
5975359 AATTGTTGAAAAAACATAAAAAATTTTGAAAATACGA-
1 AATTTTTG--AAAACACGAAAACTTTT-AAAACATGAG
** *
5975396 AATTTTTTTAAACACGAAAA-TTTTAGAAATATG-G
1 AATTTTTGAAAACACGAAAACTTTTA-AAACATGAG
* *
5975430 ACATTTTTAGAAAACACGAAAAATTTTGAAAA-AT-AA
1 A-ATTTTT-GAAAACACGAAAACTTTT-AAAACATGAG
* *
5975466 AATTTTTTGAAAACACGAGAATTTTTGAAAACA
1 AA-TTTTTGAAAACACGAAAACTTTT-AAAACA
5975499 CGAAAAATTT
Statistics
Matches: 245, Mismatches: 40, Indels: 67
0.70 0.11 0.19
Matches are distributed among these distances:
32 3 0.01
33 9 0.04
34 58 0.24
35 75 0.31
36 32 0.13
37 27 0.11
38 13 0.05
40 13 0.05
41 15 0.06
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.32
Consensus pattern (35 bp):
AATTTTTGAAAACACGAAAACTTTTAAAACATGAG
Found at i:5975337 original size:40 final size:40
Alignment explanation
Indices: 5975269--5975346 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
5975259 AACATGAAAA
* ** *
5975269 TTTTTAAAACATGACAATTTTTTGAAACACGAGTAATTTAT
1 TTTTTAAAACATGAAAAAATTTTAAAACACGAG-AATTTAT
5975310 TTTTTAAAACAT-AAAAAATTTTAAAACACGAGAATTT
1 TTTTTAAAACATGAAAAAATTTTAAAACACGAGAATTT
5975347 GTGAAACTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 5 0.15
40 16 0.48
41 12 0.36
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (40 bp):
TTTTTAAAACATGAAAAAATTTTAAAACACGAGAATTTAT
Found at i:5975641 original size:22 final size:21
Alignment explanation
Indices: 5975614--5975656 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
5975604 CGTTACCTTA
5975614 TTTTTGAAAACACGAGAAATTT
1 TTTTTGAAAACACGA-AAATTT
*
5975636 TTTTTGAAGACACGAAAATTT
1 TTTTTGAAAACACGAAAATTT
5975657 CGAAACGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (21 bp):
TTTTTGAAAACACGAAAATTT
Found at i:5975833 original size:5 final size:5
Alignment explanation
Indices: 5975823--5975904 Score: 74
Period size: 5 Copynumber: 16.0 Consensus size: 5
5975813 TAAAAGTATT
* * *
5975823 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAAA TTAAAT TAAAT TAAAT
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA -TAAAA TAAAA TAAAA
* * * * *
5975875 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
5975905 ATATAAATGC
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
5 65 0.89
6 7 0.10
7 1 0.01
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (5 bp):
TAAAA
Found at i:5975841 original size:15 final size:15
Alignment explanation
Indices: 5975822--5975904 Score: 94
Period size: 15 Copynumber: 5.4 Consensus size: 15
5975812 TTAAAAGTAT
*
5975822 TTAAAATAAAATAAA
1 TTAAAATAAATTAAA
* *
5975837 ATAAAATAAAATAAAA
1 TTAAAAT-AAATTAAA
*
5975853 TAAAAATTAAATTAAA
1 TTAAAA-TAAATTAAA
*
5975869 TTAAATTAAATTAAA
1 TTAAAATAAATTAAA
*
5975884 TTAAATTAAATTAAA
1 TTAAAATAAATTAAA
5975899 TTAAAA
1 TTAAAA
5975905 ATATAAATGC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
15 35 0.61
16 21 0.37
17 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAATAAATTAAA
Found at i:5976079 original size:17 final size:17
Alignment explanation
Indices: 5976057--5976098 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5976047 TTGAACCCCG
*
5976057 TTTTTCTTGTTTTT-TCT
1 TTTTTCTT-TTTTTCTCC
5976074 TTTTTCTTTTTTTCTCC
1 TTTTTCTTTTTTTCTCC
5976091 TTTTTCTT
1 TTTTTCTT
5976099 CCTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTTTTTCTCC
Found at i:5976396 original size:3 final size:3
Alignment explanation
Indices: 5976390--5976448 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
5976380 TTCTTTTTTT
5976390 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
5976437 TTC TTC TTC TTC
1 TTC TTC TTC TTC
5976449 AAAATCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:5976405 original size:10 final size:10
Alignment explanation
Indices: 5976380--5976448 Score: 74
Period size: 10 Copynumber: 7.3 Consensus size: 10
5976370 TAAAATTTTT
* *
5976380 TTCTTTTTTT
1 TTCTTCTTTC
5976390 TTCTTCTTTC
1 TTCTTCTTTC
*
5976400 TTCTTCTCTC
1 TTCTTCTTTC
5976410 -T-TTCTTTC
1 TTCTTCTTTC
5976418 TTCTTC-TTC
1 TTCTTCTTTC
*
5976427 TTCTTCCTTC
1 TTCTTCTTTC
5976437 TTCTTC-TTC
1 TTCTTCTTTC
5976446 TTC
1 TTC
5976449 AAAATCGAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
8 6 0.12
9 17 0.33
10 29 0.56
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:5976436 original size:13 final size:13
Alignment explanation
Indices: 5976390--5976445 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
5976380 TTCTTTTTTT
*
5976390 TTCTTCTTTCTTC
1 TTCTTCCTTCTTC
*
5976403 TTCTCTCTTTC-T-
1 TTCT-TCCTTCTTC
5976415 TTCTT-CTTCTTC
1 TTCTTCCTTCTTC
5976427 TTCTTCCTTCTTC
1 TTCTTCCTTCTTC
5976440 TTCTTC
1 TTCTTC
5976446 TTCAAAATCG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 3 0.08
11 2 0.05
12 9 0.24
13 18 0.47
14 6 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTCCTTCTTC
Found at i:5976843 original size:29 final size:29
Alignment explanation
Indices: 5976810--5976926 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 29
5976800 TGTAATTTTT
*
5976810 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* *
5976839 TGAAAGTTTAGGGGTCT-AAATGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
5976869 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
5976898 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
5976927 TTATTTTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
29 14 0.19
30 58 0.78
31 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:5976862 original size:30 final size:30
Alignment explanation
Indices: 5976825--5976926 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
5976815 ATTTAGGATT
*
5976825 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
5976855 TAAATGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
5976885 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
5976915 AAAATGCAATTT
1 AAAATGAAATTT
5976927 TTATTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 2 0.03
30 62 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:5978201 original size:26 final size:26
Alignment explanation
Indices: 5978165--5978274 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5978155 TGATACAAAT
5978165 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5978191 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5978217 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5978243 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5978269 TGATAA
1 TGATAA
5978275 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5980308 original size:137 final size:137
Alignment explanation
Indices: 5980062--5980348 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
5980052 GAGTAGTCTC
5980062 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
5980127 TGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
5980192 ACTGTTA
131 ACTGTTA
5980199 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
5980264 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
66 TGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
5980329 ACTGTTA
131 ACTGTTA
**
5980336 CCTGAATGGGCTT
1 CCCAAATGGGCTT
5980349 AGGCCCAATG
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAATACC
ACTGTTA
Found at i:5982528 original size:16 final size:16
Alignment explanation
Indices: 5982507--5982539 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5982497 TAAAAGATTA
5982507 AAAGTAA-ATAATACAC
1 AAAGTAATAT-ATACAC
5982523 AAAGTAATATATACAC
1 AAAGTAATATATACAC
5982539 A
1 A
5982540 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:5983791 original size:15 final size:16
Alignment explanation
Indices: 5983773--5983802 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5983763 GGTTTTGGGC
5983773 TGTTGGG-TTTTTAGA
1 TGTTGGGCTTTTTAGA
5983788 TGTTGGGCTTTTTAG
1 TGTTGGGCTTTTTAG
5983803 CCCGGGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.53
Consensus pattern (16 bp):
TGTTGGGCTTTTTAGA
Found at i:5984631 original size:205 final size:205
Alignment explanation
Indices: 5984174--5985130 Score: 1531
Period size: 205 Copynumber: 4.7 Consensus size: 205
5984164 AAATCTGCTT
* * *
5984174 CTTCGATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTACCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* *
5984239 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * *
5984304 GGATCTTGCTTCAGT-ATAAACATCTGAAGGCCAGATCTGCTATGTATCTACTCTCCGTCAAAAT
131 GGATC-TACTTCAGTGA-AATCATCTGAAGGCTAGATCTGCTATGTATCTACTCTCCATCAAAAT
5984368 GGAGATGCCAGA
194 GGAGATGCCAGA
5984380 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * *
5984445 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAATGATGTCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
** * * * * *
5984510 GGATCTACTTCAGTGCAAA-CATCTGAAGTTTGGATCTGCTATGTGTCTGCCCTCCGTCAAAATG
131 GGATCTACTTCAGTG-AAATCATCTGAAGGCTAGATCTGCTATGTATCTACTCTCCATCAAAATG
* *
5984574 GAGATTCCAGG
195 GAGATGCCAGA
*
5984585 CTTCGACTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* * *
5984650 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCTTTGTAAGCACAAGAATGCCAAATCATTTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* **
5984715 AGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTGCTATGTATCTACTCTCCATTGAAATGG
131 GGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTGCTATGTATCTACTCTCCATCAAAATGG
5984780 AGATGCCAGA
196 AGATGCCAGA
*
5984790 CTTCGATTTGTTCTCTGACAATACAAAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
5984855 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* * * *
5984920 AGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTTCTATGTATCTGCTCTCCATCGAAATGG
131 GGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTGCTATGTATCTACTCTCCATCAAAATGG
5984985 AGATGCCAGA
196 AGATGCCAGA
* * *
5984995 CTTCGACTTGTTATCTGACAATACAGAGTTGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
* *
5985060 ACGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
5985125 GGATCT
131 GGATCT
5985131 GCTTTAGCCA
Statistics
Matches: 696, Mismatches: 52, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
204 3 0.00
205 563 0.81
206 129 0.19
207 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAGCGTAAGCAC
GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTACTTCAGTGAAATCATCTGAAGGCTAGATCTGCTATGTATCTACTCTCCATCAAAATGG
AGATGCCAGA
Found at i:5993563 original size:16 final size:16
Alignment explanation
Indices: 5993542--5993574 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5993532 TAAAAGATTA
5993542 AAAGTAA-ATAATACAC
1 AAAGTAATAT-ATACAC
5993558 AAAGTAATATATACAC
1 AAAGTAATATATACAC
5993574 A
1 A
5993575 GGAAAAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAGTAATATATACAC
Found at i:5994798 original size:15 final size:16
Alignment explanation
Indices: 5994780--5994809 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5994770 GGTTTTGGGC
5994780 TGTTGGG-TTTTTAGA
1 TGTTGGGCTTTTTAGA
5994795 TGTTGGGCTTTTTAG
1 TGTTGGGCTTTTTAG
5994810 CCCGGGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.53
Consensus pattern (16 bp):
TGTTGGGCTTTTTAGA
Found at i:5995759 original size:10 final size:10
Alignment explanation
Indices: 5995744--5995776 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5995734 AGGTTACCAT
5995744 ATTTTATTTC
1 ATTTTATTTC
*
5995754 ATTTTATTTT
1 ATTTTATTTC
5995764 ATTTT-TTTC
1 ATTTTATTTC
5995773 ATTT
1 ATTT
5995777 ACAAATCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTATTTC
Found at i:5996489 original size:3 final size:3
Alignment explanation
Indices: 5996473--5996638 Score: 58
Period size: 3 Copynumber: 57.0 Consensus size: 3
5996463 TATTTATTCC
* ** * *
5996473 TAT TAT T-T TA- TAT TAT TGT CGT TAT TAA TAT ATAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * * * * **
5996517 CAT TAA TAT TAT TAT TAT TAT TAT TAC TAA TAT CAC TAT CAT CGT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
5996564 T-T TAT TAC TAT TAT TAT CAT CAT T-T TTT TAT CTAA TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* ** *
5996607 TAA CCT T-T TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5996639 ATTTTCTTTT
Statistics
Matches: 120, Mismatches: 35, Indels: 16
0.70 0.20 0.09
Matches are distributed among these distances:
2 14 0.12
3 102 0.85
4 4 0.03
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:5996604 original size:26 final size:25
Alignment explanation
Indices: 5996543--5996606 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
5996533 ATTATTATTA
*
5996543 CTAATATCACTATCATCGTTTTTTAT
1 CTAATAT-ATTATCATCGTTTTTTAT
* *
5996569 -TACTATTATTATCATCATTTTTTTAT
1 CTAATA-TATTATCATC-GTTTTTTAT
5996595 CTAATATATTAT
1 CTAATATATTAT
5996607 TAACCTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 12 0.39
26 15 0.48
27 4 0.13
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.55
Consensus pattern (25 bp):
CTAATATATTATCATCGTTTTTTAT
Found at i:5996830 original size:3 final size:3
Alignment explanation
Indices: 5996818--5997021 Score: 128
Period size: 3 Copynumber: 68.3 Consensus size: 3
5996808 ATTATTTGTG
* * ** *
5996818 TTA TTG TTA TTA TTA CTTT TTA TTA TTA CCA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
5996864 TTT TTA CTT- TTA TTA CTA TTA CTA -TA TTA TTA TTA TTA TTT TCTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* ** * * * * *
5996909 TTA CTA TTA TCG TTA TTA TTA ATA CTA ATA TTA ATA TTC TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** *
5996957 CTA TTA TTA TTA TCA TTA GTA TTA TTA TT- TT- TTA CCA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5997003 TTA TCA ATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
5997022 CGTTTTCATT
Statistics
Matches: 150, Mismatches: 45, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
2 8 0.05
3 136 0.91
4 6 0.04
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5997032 original size:18 final size:18
Alignment explanation
Indices: 5997011--5997045 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5997001 TATTATCAAT
*
5997011 ATTATTATTATCGTTTTC
1 ATTATCATTATCGTTTTC
*
5997029 ATTATCATTGTCGTTTT
1 ATTATCATTATCGTTTT
5997046 TATTTTTCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (18 bp):
ATTATCATTATCGTTTTC
Found at i:5998731 original size:25 final size:25
Alignment explanation
Indices: 5998697--5998745 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5998687 ACGGTGAAGG
*
5998697 TATAAATTGGGAGAAAATGTTTAAT
1 TATAAATTGGAAGAAAATGTTTAAT
5998722 TATAAATTGGAAGAAAATGTTTAA
1 TATAAATTGGAAGAAAATGTTTAA
5998746 AGCTTGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (25 bp):
TATAAATTGGAAGAAAATGTTTAAT
Found at i:6000136 original size:30 final size:28
Alignment explanation
Indices: 6000102--6000161 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
6000092 CATTTAATTC
6000102 ATTTCTAAACTATTAAAAATAATTTTTATA
1 ATTTCT-AACTATTAAAAATAA-TTTTATA
* *
6000132 ATTTCTAATTTTTAAAAATAATTTTATA
1 ATTTCTAACTATTAAAAATAATTTTATA
6000160 AT
1 AT
6000162 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.32
29 13 0.46
30 6 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTCTAACTATTAAAAATAATTTTATA
Found at i:6000174 original size:18 final size:17
Alignment explanation
Indices: 6000151--6000187 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
6000141 TTTTAAAAAT
6000151 AATTTTATAATATTTTAA
1 AATTTTATAA-ATTTTAA
*
6000169 AATTTTTTAAATTTTAA
1 AATTTTATAAATTTTAA
6000186 AA
1 AA
6000188 AATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTATAAATTTTAA
Found at i:6001253 original size:17 final size:17
Alignment explanation
Indices: 6001229--6001276 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
6001219 ATAGATACCT
*
6001229 AAATAATATTAAAATAT
1 AAATAATATTAAAATAA
* *
6001246 ACATAATA-TATACATAA
1 AAATAATATTA-AAATAA
6001263 AAATAATATTAAAA
1 AAATAATATTAAAA
6001277 ACTTATGTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAATATTAAAATAA
Found at i:6001554 original size:25 final size:22
Alignment explanation
Indices: 6001491--6001570 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 22
6001481 AATTAACACG
* * *
6001491 TAATAATAATAATAATGATA-A
1 TAATAAAAATAATGATGATATT
* * *
6001512 TAATAACAATATTAATGATATT
1 TAATAAAAATAATGATGATATT
6001534 ATAATTCAAAAATAATGATGATATT
1 -TAA-T-AAAAATAATGATGATATT
6001559 TAATAAAAATAA
1 TAATAAAAATAA
6001571 CAAAAGAGAC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 18 0.37
22 8 0.16
23 4 0.08
24 4 0.08
25 15 0.31
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (22 bp):
TAATAAAAATAATGATGATATT
Found at i:6003488 original size:73 final size:73
Alignment explanation
Indices: 6003333--6003585 Score: 386
Period size: 73 Copynumber: 3.5 Consensus size: 73
6003323 ACATGTGAAC
* *
6003333 TGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAA-CAGAAATTGAAATTACC
1 TGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--ATTTTGAAAAGCAGAAATTGAAATTACC
* *
6003396 TCAGCGTGTCC
63 TCAACGTGTCT
* *
6003407 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCTCA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAATTACCTCA
6003472 ACGTGTCT
66 ACGTGTCT
6003480 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAG-AGAAATTGAAATTACCTCA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAATTACCTCA
*
6003544 ATGTGTCT
66 ACGTGTCT
*
6003552 TGAGGCTCAACTCATTTCTCACAATATGAGTTGA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
6003586 TTCTTTCTAA
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
72 65 0.39
73 72 0.43
74 30 0.18
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (73 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAATTACCTCA
ACGTGTCT
Found at i:6004246 original size:144 final size:146
Alignment explanation
Indices: 6004023--6004336 Score: 415
Period size: 144 Copynumber: 2.2 Consensus size: 146
6004013 GTTGATTTTT
*
6004023 TTTTAAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATA
1 TTTTGAAAACAGAAATTGAAAATACCTCAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATA
* *
6004088 TAAGTTGATTTTTTTTGAA-AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAA-CA-T
65 TAAGTTGATTTTTTTT-AACAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACCACC
*
6004150 TCTCGCAATATAAGTTGAA
129 TCTAGCAATATAAGTTG-A
* * **
6004169 TTTTGAAAACAGAAATTGAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCATTTCTCGCAATA
1 TTTTGAAAACAGAAATTGAAAATACCTCAGCAGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
* * *
6004232 TGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACC
65 TAAGTTGATTTTTTTTAACAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAAC-CACC
*
6004297 TCTAGCAATATGAGTTGA
129 TCTAGCAATATAAGTTGA
*
6004315 TTTTGAAAAACAAAAATT-AAAA
1 TTTTG-AAAACAGAAATTGAAAA
6004337 GGCTTAACTC
Statistics
Matches: 148, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
143 4 0.03
144 78 0.53
146 40 0.27
147 26 0.18
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (146 bp):
TTTTGAAAACAGAAATTGAAAATACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATAT
AAGTTGATTTTTTTTAACAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACCACCTC
TAGCAATATAAGTTGA
Found at i:6004273 original size:75 final size:74
Alignment explanation
Indices: 6003983--6004318 Score: 441
Period size: 75 Copynumber: 4.5 Consensus size: 74
6003973 AGTGTGTAAT
*
6003983 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTT-AAAACAGAAATTGAAAATAC
*
6004048 CTCAGCATGTGAAC
64 CTCAGC--GTG-TC
*
6004062 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT-AAAACAGAAATTGAAAATACC
*
6004126 TCAACGTGTC
65 TCAGCGTGTC
* * * * * *
6004136 TTGAGGCTCAA--CA-TTCTCGCAATATAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAAATACCT
6004196 CAGCGTGTC
66 CAGCGTGTC
** *
6004205 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAA-AACAGAAATTGAAAATACC
6004270 TCAGCGTGTC
65 TCAGCGTGTC
*
6004280 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
6004319 GAAAAACAAA
Statistics
Matches: 232, Mismatches: 18, Indels: 18
0.87 0.07 0.07
Matches are distributed among these distances:
69 39 0.17
70 4 0.02
71 2 0.01
72 36 0.16
73 2 0.01
74 7 0.03
75 77 0.33
77 33 0.14
78 31 0.13
79 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (74 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAAATACCT
CAGCGTGTC
Found at i:6004483 original size:70 final size:70
Alignment explanation
Indices: 6004336--6004510 Score: 212
Period size: 70 Copynumber: 2.5 Consensus size: 70
6004326 AAAAATTAAA
* * * * * **
6004336 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
6004400 CCCCG
66 CCCCG
*
6004405 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
6004469 GTCTTG
65 GCCCCG
6004475 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
6004511 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
69 27 0.29
70 61 0.66
71 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:6016761 original size:3 final size:3
Alignment explanation
Indices: 6016753--6016789 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6016743 ACTAATGTAC
6016753 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
6016790 TTGAAATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6017411 original size:21 final size:21
Alignment explanation
Indices: 6017374--6017418 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6017364 AAAATTTATA
*
6017374 TTTTTATATATTTTTTTATTT
1 TTTTTATATATTTTTTTATGT
*
6017395 TTTTTGTAT-TTTCTTTTATGT
1 TTTTTATATATTT-TTTTATGT
6017416 TTT
1 TTT
6017419 AATATATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTTTATATATTTTTTTATGT
Found at i:6019410 original size:62 final size:60
Alignment explanation
Indices: 6019308--6019426 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 60
6019298 TTGACTTCAT
*
6019308 AACAAATTTAGCCCTCCAATATTTACGCATTCTATCAGTTTAATCCTAAAATTAAAAAAATC
1 AACAAATTTAGCCCTCCAATATTTACGAATTCTATCAGTTTAATCCT--AATTAAAAAAATC
* * * *
6019370 AACAAATTTAGCCCT-CAATATTTA-GAAATTTTTTTTAGTTTATTCCTAATTAAAAAA
1 AACAAATTTAGCCCTCCAATATTTACG-AA-TTCTATCAGTTTAATCCTAATTAAAAAA
6019427 TTATAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
60 11 0.22
61 10 0.20
62 29 0.58
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (60 bp):
AACAAATTTAGCCCTCCAATATTTACGAATTCTATCAGTTTAATCCTAATTAAAAAAATC
Found at i:6019589 original size:21 final size:21
Alignment explanation
Indices: 6019561--6019604 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6019551 TTGGGAACGA
*
6019561 TTAAAATCGTCTCTAA-AAAT
1 TTAAAATCGTCCCTAATAAAT
6019581 TTAAGAATCGTCCCTAATAAAT
1 TTAA-AATCGTCCCTAATAAAT
6019603 TT
1 TT
6019605 TAATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (21 bp):
TTAAAATCGTCCCTAATAAAT
Found at i:6025257 original size:24 final size:24
Alignment explanation
Indices: 6025221--6025270 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
6025211 GAAAAACCTA
*
6025221 ATTCTAATCAATG-TCAAATATATT
1 ATTCTAATAAATGCT-AAATATATT
6025245 ATTCTAATAAATGCTAAATATATT
1 ATTCTAATAAATGCTAAATATATT
6025269 AT
1 AT
6025271 GTCGAAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTCTAATAAATGCTAAATATATT
Found at i:6026234 original size:14 final size:15
Alignment explanation
Indices: 6026215--6026247 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
6026205 TAACATCAAC
6026215 AAAAAAATAAAAA-T
1 AAAAAAATAAAAACT
6026229 AAAAAAATAAAAACT
1 AAAAAAATAAAAACT
6026244 AAAA
1 AAAA
6026248 TGAGATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAATAAAAACT
Found at i:6028118 original size:44 final size:44
Alignment explanation
Indices: 6028045--6028169 Score: 130
Period size: 44 Copynumber: 2.8 Consensus size: 44
6028035 AAGATTCACC
* *
6028045 ATTGTAG-TTTCATTCTGACCCACCT-CAACTTCAGGGGTATAGGA
1 ATTGTAGCTTTCATTC-GATCCA-CTGCAACTTCAGGGATATAGGA
* *
6028089 ATTGTAGCTTTAATTCGATCCACTGCAACTTCAAGGATATAGGA
1 ATTGTAGCTTTCATTCGATCCACTGCAACTTCAGGGATATAGGA
* * * *
6028133 TTTGCAGC-TTCATCTTGCTCCACTGCAACTTCAGGGA
1 ATTGTAGCTTTCAT-TCGATCCACTGCAACTTCAGGGA
6028170 GATAAGATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 6 0.09
44 55 0.81
45 7 0.10
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
ATTGTAGCTTTCATTCGATCCACTGCAACTTCAGGGATATAGGA
Found at i:6028327 original size:44 final size:44
Alignment explanation
Indices: 6028256--6028404 Score: 140
Period size: 44 Copynumber: 3.4 Consensus size: 44
6028246 CCGCTACAAA
* * *
6028256 TTCAGTGAGATAATATTTATTA-CTTCAATCTGCTCCA-TTAAAAC
1 TTCAGAGAGATAAGATTT-TTAGCTTCAATATGCTCCAGTT-AAAC
* * * * *
6028300 TTTAGGGATATGAGATTTTTAGCTTCAATATGCTCCAGTTCAAC
1 TTCAGAGAGATAAGATTTTTAGCTTCAATATGCTCCAGTTAAAC
* * * **
6028344 TTCAGAGAGATAAGATTTGTAGCTTTAATATGCTCCACTGCAAC
1 TTCAGAGAGATAAGATTTTTAGCTTCAATATGCTCCAGTTAAAC
*
6028388 TTCAGGGAGATAAGATT
1 TTCAGAGAGATAAGATT
6028405 CGCTATGGTG
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
43 3 0.03
44 82 0.94
45 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (44 bp):
TTCAGAGAGATAAGATTTTTAGCTTCAATATGCTCCAGTTAAAC
Found at i:6035243 original size:126 final size:124
Alignment explanation
Indices: 6035014--6035257 Score: 328
Period size: 126 Copynumber: 2.0 Consensus size: 124
6035004 AGGATCATCA
* * ** * *
6035014 AACCATACAATCCCTATCTTGATGAACCTCTTGATCAACTTCGAATGCAGTGTAGTTCTCAATCG
1 AACCATACAATCCCCATCTTGATAAACCTCTCAATCAACTTCGAATGCAGTGCAGCTCTCAATCG
** * *
6035079 AGTGTCCCATTATTCCTGTGTGGTACTCGCATTGAGCATT-TGCATCATACCACTCATTG
66 AGTGTCCCATTATTCCTACGTGGCACTCGCATTAAGCATTGT-CATCATACCACTCATTG
* *
6035138 AACCTTACAATCCCCATCTTGATAAACCTCTCAATCAACTTCTAGAATGTAGTGCAGCTCTCAAT
1 AACCATACAATCCCCATCTTGATAAACCTCTCAATCAACTTC--GAATGCAGTGCAGCTCTCAAT
* *
6035203 CGAGTGTCCCATTTTTCCTACGTGGCATTCGCATTAAGCATTGTCATCATACCAC
64 CGAGTGTCCCATTATTCCTACGTGGCACTCGCATTAAGCATTGTCATCATACCAC
6035258 ATTGGAAACG
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
124 37 0.36
126 65 0.63
127 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (124 bp):
AACCATACAATCCCCATCTTGATAAACCTCTCAATCAACTTCGAATGCAGTGCAGCTCTCAATCG
AGTGTCCCATTATTCCTACGTGGCACTCGCATTAAGCATTGTCATCATACCACTCATTG
Found at i:6039220 original size:11 final size:11
Alignment explanation
Indices: 6039200--6039234 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6039190 ACGTGGTCAA
*
6039200 AAAATGATAAC
1 AAAATAATAAC
6039211 AAAATAATAAC
1 AAAATAATAAC
*
6039222 GAAATAATAAC
1 AAAATAATAAC
6039233 AA
1 AA
6039235 GTGGTAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAATAATAAC
Found at i:6052940 original size:29 final size:30
Alignment explanation
Indices: 6052898--6052971 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
6052888 GAATTGGATC
*
6052898 AAATCAAAATTTCATGTATAAAATTACACA-
1 AAATC-AAAGTTCATGTATAAAATTACACAT
* *
6052928 AAATCAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTACACA-T
*
6052959 AAATCATAGTTCA
1 AAATCAAAGTTCA
6052972 GGAATAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.55
30 5 0.13
31 12 0.32
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACACAT
Found at i:6053591 original size:29 final size:29
Alignment explanation
Indices: 6053557--6053613 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
6053547 TTCAAAATTA
*
6053557 TTAGAAAA-TACTAAAATATTATATAAAAT
1 TTAGAAAATTACTAAAA-ATTATAAAAAAT
*
6053586 TTAGAAAATTATTAAAAATTATAAAAAA
1 TTAGAAAATTACTAAAAATTATAAAAAA
6053614 AAAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (29 bp):
TTAGAAAATTACTAAAAATTATAAAAAAT
Found at i:6053603 original size:19 final size:19
Alignment explanation
Indices: 6053550--6053612 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
6053540 GAAAGTTTTC
*
6053550 AAAATTATTAGAAAATACTA
1 AAAATTATTAGAAAAT-TTA
*
6053570 AAATATTA-TATAAAATTTA
1 AAA-ATTATTAGAAAATTTA
6053589 GAAAATTATTA-AAAATTATA
1 -AAAATTATTAGAAAATT-TA
6053609 AAAA
1 AAAA
6053613 AAAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 16 0.43
20 17 0.46
21 4 0.11
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATTATTAGAAAATTTA
Found at i:6053612 original size:10 final size:10
Alignment explanation
Indices: 6053550--6053613 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
6053540 GAAAGTTTTC
*
6053550 AAAATTATTAG
1 AAAATTA-TAA
6053561 AAAA-TACTAA
1 AAAATTA-TAA
* *
6053571 AATATTATAT
1 AAAATTATAA
*
6053581 AAAATT-TAG
1 AAAATTATAA
*
6053590 AAAATTATTA
1 AAAATTATAA
6053600 AAAATTATAA
1 AAAATTATAA
6053610 AAAA
1 AAAA
6053614 AAAATTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
9 8 0.19
10 28 0.67
11 6 0.14
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAATTATAA
Found at i:6055403 original size:41 final size:41
Alignment explanation
Indices: 6055355--6055447 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
6055345 ACTACACGGC
* * *
6055355 TTGCCACATGGTCGTGTCTTCCTTGTAGGTTGATTTTGCAT
1 TTGCCACATGGTCGTGTCTCCCTTATAGGTTGATTTTACAT
* * *
6055396 TTTCCACAAGGTCGTGTCTCCCTTATAGGTTGATTTTACGT
1 TTGCCACATGGTCGTGTCTCCCTTATAGGTTGATTTTACAT
6055437 TTGCCACATGG
1 TTGCCACATGG
6055448 CCACAGTCTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.41
Consensus pattern (41 bp):
TTGCCACATGGTCGTGTCTCCCTTATAGGTTGATTTTACAT
Found at i:6072288 original size:21 final size:21
Alignment explanation
Indices: 6072262--6072312 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6072252 CATTGTTTCT
* *
6072262 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
6072283 AATCTCACCGTTACAGTAACT
1 AATCTCACCGCTACAGTAACC
6072304 AATCTCACC
1 AATCTCACC
6072313 TCCACCGCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.27
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:6074090 original size:9 final size:9
Alignment explanation
Indices: 6074076--6074169 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
6074066 TTTGGTTAAA
6074076 AATTAACCG
1 AATTAACCG
6074085 AATTAACCG
1 AATTAACCG
*
6074094 AATTACCCG
1 AATTAACCG
* *
6074103 AATTACCCA
1 AATTAACCG
*
6074112 AATTACCCG
1 AATTAACCG
6074121 AATTAACCG
1 AATTAACCG
6074130 AATTAACCG
1 AATTAACCG
*
6074139 AATTACCCG
1 AATTAACCG
*
6074148 AATTAACCA
1 AATTAACCG
*
6074157 AATTAACCA
1 AATTAACCG
6074166 AATT
1 AATT
6074170 GAATCACTAC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 78 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:6074992 original size:5 final size:5
Alignment explanation
Indices: 6074982--6075011 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
6074972 GAGGATTTAG
6074982 ATTTT ATTTT ATTTT ATTTT ATTTT CATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT -ATTT
6075012 AGGCTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:6083404 original size:11 final size:12
Alignment explanation
Indices: 6083381--6083406 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6083371 CATTTGGTCC
6083381 TTTTACTATTTT
1 TTTTACTATTTT
6083393 TTTTACTATTTT
1 TTTTACTATTTT
6083405 TT
1 TT
6083407 CGGTCACTTT
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTACTATTTT
Found at i:6083798 original size:18 final size:17
Alignment explanation
Indices: 6083770--6083804 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6083760 ATTTTTAAGA
*
6083770 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
6083787 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
6083805 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:6084058 original size:16 final size:16
Alignment explanation
Indices: 6084037--6084075 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6084027 TTGATTTGCT
*
6084037 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
6084053 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
6084069 ATTACAC
1 ATTACAC
6084076 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:6084076 original size:16 final size:16
Alignment explanation
Indices: 6084049--6084090 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6084039 TACACAGCTT
6084049 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
6084065 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
* *
6084081 ATCCAATACA
1 TTCCATTACA
6084091 GCGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:6087845 original size:13 final size:12
Alignment explanation
Indices: 6087801--6087855 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
6087791 TAAAAAATAG
6087801 AAAATTCTATAT
1 AAAATTCTATAT
* *
6087813 AATAATTGTAGA-
1 AA-AATTCTATAT
6087825 AAAATTCTATAT
1 AAAATTCTATAT
*
6087837 AACAATTCTATAG
1 AA-AATTCTATAT
6087850 AAAATT
1 AAAATT
6087856 TAAATTGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 7 0.20
12 10 0.29
13 18 0.51
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (12 bp):
AAAATTCTATAT
Found at i:6104113 original size:42 final size:42
Alignment explanation
Indices: 6104054--6104155 Score: 188
Period size: 42 Copynumber: 2.5 Consensus size: 42
6104044 GCCCTTAATT
*
6104054 ATCGAGTT-GTATTCGAGTACAAAAATTGATAAATGAACTTA
1 ATCGAGTTCGAATTCGAGTACAAAAATTGATAAATGAACTTA
6104095 ATCGAGTTCGAATTCGAGTACAAAAATTGATAAATGAACTTA
1 ATCGAGTTCGAATTCGAGTACAAAAATTGATAAATGAACTTA
6104137 ATCGAGTTCGAATTCGAGT
1 ATCGAGTTCGAATTCGAGT
6104156 TCAAGTAGCT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
41 8 0.14
42 51 0.86
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (42 bp):
ATCGAGTTCGAATTCGAGTACAAAAATTGATAAATGAACTTA
Found at i:6108943 original size:50 final size:50
Alignment explanation
Indices: 6108872--6109264 Score: 432
Period size: 51 Copynumber: 7.8 Consensus size: 50
6108862 TTTTATCATT
*
6108872 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* * *
6108922 CGATTCACGTAGTAGCCTTCACATAGTCCTACACACGTGATCAAGTTTTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* **
6108972 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATTAAGTTTTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* * *
6109022 CGGTTCACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTA
* * * * * ***
6109073 TGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
* * *
6109123 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAG-CTTC
1 -CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGTTTTA
* * * * * ***
6109174 CTGGTCCACCTAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 C-GATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
*
6109225 TCGATACACGTAGTAGCCTT-AGCACAGTACTACACACGTG
1 -CGATACACGTAGTAGCCTTCA-CATAGTACTACACACGTG
6109265 TTTATCGATA
Statistics
Matches: 293, Mismatches: 41, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
49 3 0.01
50 138 0.47
51 146 0.50
52 6 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (50 bp):
CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA
Found at i:6109108 original size:26 final size:26
Alignment explanation
Indices: 6109076--6109158 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
6109066 AGCTTTTTGG
6109076 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
* *
6109102 TACACAT-GT-GACCATCATTTA-T-C
1 TACACATAGTAG-CCTTCACTTAGTAC
* **
6109125 GATACACGTAGTAGCCTTCACACAGTAC
1 --TACACATAGTAGCCTTCACTTAGTAC
6109153 TACACA
1 TACACA
6109159 CGTGACCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 1 0.02
24 2 0.05
25 16 0.38
26 20 0.48
27 2 0.05
28 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Found at i:6127647 original size:107 final size:108
Alignment explanation
Indices: 6127527--6127731 Score: 297
Period size: 107 Copynumber: 1.9 Consensus size: 108
6127517 TTTTTTTAAA
* *
6127527 ATTTTTTTCTTAAGAATGTATTGGCCCTTTTGACATGAAAAAGG-ATGACAACCCAAGCACCCCA
1 ATTTTTTTCTTAAGAATGTATTGACCCTTTTGACACG-AAAAGGAATGACAACCCAAGCACCCCA
*
6127591 CCTTGGTTACTCAACCCAACACACTCTT-ATTTTATTATTATAT
65 CCTTGATTACTCAACCCAACACACTCTTAATTTTATTATTATAT
* * * *
6127634 ATTTTTTTGTTAAGAATGTATTGACCCTTTTGACACGAAGAGGAATGACAACCCAAGTACCCTAC
1 ATTTTTTTCTTAAGAATGTATTGACCCTTTTGACACGAAAAGGAATGACAACCCAAGCACCCCAC
* * *
6127699 CTTGATTACTTAGCCTAACACACTCTTAATTTT
66 CTTGATTACTCAACCCAACACACTCTTAATTTT
6127732 TTTTTGTTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 5 0.06
107 76 0.88
108 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (108 bp):
ATTTTTTTCTTAAGAATGTATTGACCCTTTTGACACGAAAAGGAATGACAACCCAAGCACCCCAC
CTTGATTACTCAACCCAACACACTCTTAATTTTATTATTATAT
Found at i:6128873 original size:32 final size:33
Alignment explanation
Indices: 6128837--6128901 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
6128827 AAGAAGAGAG
*
6128837 AATAAAATTTATTAAAAT-GAAAT-AAAATAAAA
1 AATAAAATATA-TAAAATAGAAATAAAAATAAAA
*
6128869 AATAAAATATATAAAATATAAATAAAAATAAAA
1 AATAAAATATATAAAATAGAAATAAAAATAAAA
6128902 CTGGGTTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 6 0.21
32 14 0.48
33 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (33 bp):
AATAAAATATATAAAATAGAAATAAAAATAAAA
Found at i:6128884 original size:21 final size:21
Alignment explanation
Indices: 6128849--6128895 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
6128839 TAAAATTTAT
6128849 TAAAATGAAATAAAATAAAAAA
1 TAAAATGAAATAAAAT-AAAAA
* *
6128871 TAAAAT-ATATAAAATATAAA
1 TAAAATGAAATAAAATAAAAA
6128891 TAAAA
1 TAAAA
6128896 ATAAAACTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 8 0.35
22 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAAATGAAATAAAATAAAAA
Found at i:6138872 original size:72 final size:72
Alignment explanation
Indices: 6138775--6139091 Score: 580
Period size: 72 Copynumber: 4.4 Consensus size: 72
6138765 TTCCAATTTT
* *
6138775 GTTAACTGACCTAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6138840 CAAATTC
66 CAAATTC
*
6138847 GTTAACTGGCCCAGAAAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6138912 CAAATTC
66 CAAATTC
6138919 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6138984 CAAATTC
66 CAAATTC
*
6138991 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAAGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6139056 CAAATTC
66 CAAATTC
* *
6139063 GTTAAATGGCCCAGAGAGGAAGAGATGTG
1 GTTAACTGGCCCAGAGAGGAAGGGATGTG
6139092 CGAACAGAGG
Statistics
Matches: 238, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 238 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (72 bp):
GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
CAAATTC
Found at i:6145059 original size:72 final size:72
Alignment explanation
Indices: 6144966--6145257 Score: 521
Period size: 72 Copynumber: 4.1 Consensus size: 72
6144956 TTCCAATTTT
* *
6144966 GTTAACTGACCTAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6145031 CAAATTC
66 CAAATTC
6145038 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6145103 CAAATTC
66 CAAATTC
6145110 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6145175 CAAATTC
66 CAAATTC
* * * * *
6145182 GTTAAATGGCCCAGAGAGGAAGGGATGTGACCTAAAAGCCCATTGGAGGATAGTTTCAATTCAAC
1 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6145247 CAAATTC
66 CAAATTC
6145254 GTTA
1 GTTA
6145258 GTCCCCCAAT
Statistics
Matches: 213, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 213 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (72 bp):
GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
CAAATTC
Found at i:6145330 original size:144 final size:144
Alignment explanation
Indices: 6145182--6145503 Score: 405
Period size: 144 Copynumber: 2.2 Consensus size: 144
6145172 AACCAAATTC
* * * * * *
6145182 GTTAAATGGCCCAGAGAGGAAGGGA-TGTGACCTAA-AAGCCCATTGGAGGATAGTTTCAATTCA
1 GTTAAATGGCCCACAGAAGAAGGGATTG-GACC-AACAAGACAATTGGAGGATAGATTCAATGCA
*
6145245 ACCAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATTAAGTTGATTGCTTTGAAGGAA
64 ACCAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATCAAGTTGATTGCTTTGAAGGAA
6145310 CAAAGAGGAAAGATTG
129 CAAAGAGGAAAGATTG
* * ** *
6145326 GTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGACAATTGGAGGATAGATTCAATGCAAC
1 GTTAAATGGCCCACAGAAGAAGGGATTGGACCAACAAGACAATTGGAGGATAGATTCAATGCAAC
* * *
6145391 CAAATTCGTTAGTCTCCCAATATCTTTTGGAATGGATCCATCAAGTTGGTTGCTTTGAAGGAACA
66 CAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATCAAGTTGATTGCTTTGAAGGAACA
* **
6145456 ACGAGTCAAGATTG
131 AAGAGGAAAGATTG
* * ** *
6145470 GTTAAGTTGCTGACAGAAGATGGGATTGGACCAA
1 GTTAAATGGCCCACAGAAGAAGGGATTGGACCAA
6145504 TAAACCAATT
Statistics
Matches: 158, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
143 2 0.01
144 154 0.97
145 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (144 bp):
GTTAAATGGCCCACAGAAGAAGGGATTGGACCAACAAGACAATTGGAGGATAGATTCAATGCAAC
CAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATCAAGTTGATTGCTTTGAAGGAACA
AAGAGGAAAGATTG
Found at i:6145514 original size:144 final size:144
Alignment explanation
Indices: 6145223--6145503 Score: 481
Period size: 144 Copynumber: 2.0 Consensus size: 144
6145213 CTAAAAGCCC
* *
6145223 ATTGGAGGATAGTTTCAATTCAACCAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
1 ATTGGAGGATAGATTCAATGCAACCAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
*
6145288 TAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
66 CAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
6145353 GGACCAACAAGACA
131 GGACCAACAAGACA
* *
6145367 ATTGGAGGATAGATTCAATGCAACCAAATTCGTTAGTCTCCCAATATCTTTTGGAATGGATCCAT
1 ATTGGAGGATAGATTCAATGCAACCAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
* * **
6145432 CAAGTTGGTTGCTTTGAAGGAACAACGAGTCAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
66 CAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
6145497 GGACCAA
131 GGACCAA
6145504 TAAACCAATT
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 128 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (144 bp):
ATTGGAGGATAGATTCAATGCAACCAAATTCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
CAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
GGACCAACAAGACA
Found at i:6147402 original size:27 final size:28
Alignment explanation
Indices: 6147368--6147420 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6147358 CCATTTTCTC
*
6147368 TCACTCTAT-TTATTTTTT-ATTTTTAT
1 TCACTCTATATGATTTTTTAATTTTTAT
6147394 TCACTTCTATATGATTTTTTAATTTTT
1 TCAC-TCTATATGATTTTTTAATTTTT
6147421 TGAATTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 5 0.22
28 8 0.35
29 6 0.26
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (28 bp):
TCACTCTATATGATTTTTTAATTTTTAT
Found at i:6148809 original size:15 final size:17
Alignment explanation
Indices: 6148780--6148812 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
6148770 GTTCCATCAC
6148780 TTTTTTCTAATTTTATT
1 TTTTTTCTAATTTTATT
6148797 TTTTTTC-AA-TTTATT
1 TTTTTTCTAATTTTATT
6148812 T
1 T
6148813 AAAAAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCTAATTTTATT
Found at i:6152893 original size:25 final size:24
Alignment explanation
Indices: 6152865--6152922 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
6152855 AATTTGGTGT
* * *
6152865 TCAAATTTGCAAATTAAAAAAATAA
1 TCAAATTT-AAAAATAAAAAAAAAA
*
6152890 TCAAAATATAAAAATAAAAAAAAAA
1 TC-AAATTTAAAAATAAAAAAAAAA
6152915 TCAAATTT
1 TCAAATTT
6152923 TCCCCTTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 5 0.19
25 17 0.63
26 5 0.19
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (24 bp):
TCAAATTTAAAAATAAAAAAAAAA
Found at i:6154405 original size:22 final size:22
Alignment explanation
Indices: 6154378--6154428 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
6154368 CTCTCTAATC
6154378 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
6154400 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
6154422 CTCTCAA
1 CTCTCAA
6154429 ACCCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:6154504 original size:28 final size:30
Alignment explanation
Indices: 6154472--6154535 Score: 105
Period size: 28 Copynumber: 2.2 Consensus size: 30
6154462 CTCTCAAATC
6154472 TATTTTTTAAAATAATTAT-AA-TTTTTTA
1 TATTTTTTAAAATAATTATAAATTTTTTTA
*
6154500 TATTTTTTAAAATAATTTTAAATTTTTTTA
1 TATTTTTTAAAATAATTATAAATTTTTTTA
6154530 TATTTT
1 TATTTT
6154536 CATCAATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 18 0.55
29 2 0.06
30 13 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTTTTAAAATAATTATAAATTTTTTTA
Found at i:6155629 original size:7 final size:7
Alignment explanation
Indices: 6155617--6155641 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6155607 AGTCGATTGA
6155617 TATTTAG
1 TATTTAG
6155624 TATTTAG
1 TATTTAG
6155631 TATTTAG
1 TATTTAG
6155638 TATT
1 TATT
6155642 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:6156314 original size:18 final size:18
Alignment explanation
Indices: 6156293--6156327 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6156283 AGGTATGTTT
* *
6156293 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
6156311 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
6156328 TCCTTTTTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:6156862 original size:34 final size:33
Alignment explanation
Indices: 6156824--6158541 Score: 1740
Period size: 29 Copynumber: 55.7 Consensus size: 33
6156814 AAATAAAAAC
* *
6156824 CCTAATTTAATTGAAAACCCTAACCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6156858 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6156887 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6156916 CCTAAATTAATTAAAAA-CC---CTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6156945 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6156979 CCTACCTTAATTAAAAACCCTAAC--A--CTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
* ** *
6157008 CATAGCTTAATTAAAAA---T-CCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157037 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
* *
6157071 CCTAACTTAATTAAAAACCCTAATCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6157105 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6157134 CCTAAATTAATTAAAAA-CCT---TAGCCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6157163 CCTAAATTAGTTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157192 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6157226 CCTAGCTTAATTAAAAA-CC---CTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6157255 CCTAAATTAATTAAAAACCCTAATCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6157289 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6157318 CCTAAATTAATTAAAAA-CC---CTAACCTTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157347 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157376 CCTAAATTAATTAAAAA-CC---CTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
**
6157405 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6157439 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
** *
6157473 CCTAGCTTAATTAAAAACCCTAATCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6157507 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157536 CCTAAATTAATTAAAAA-CC---CTAA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6157564 CTTAAATTAATT-AAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157592 CCTAAATTAATTAAAAACCCTAAC--A--CTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
* ** *
6157621 CATAGCTTAATTAAAAA---T-CCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157650 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
* *
6157684 CCTAACTTAATTAAAAACCCTAATCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6157718 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6157747 CCTAAATTAATTAAAAA-CCT---TAGCCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
* *
6157776 CCTAAATTAGTTTAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157805 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6157839 CCTAGCTTAATTAAAAA-CC---CTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6157868 CCTAAATTAATTAAAAACCCTAATCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6157902 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157931 CCTAAATTAATT-AAAA-CCT---TAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157959 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6157988 CCTAAATTAATTAAAAA-CC---CTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
**
6158017 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6158051 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
** *
6158085 CCTAGCTTAATTAAAAACCCTAATCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6158119 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6158148 CCTAAATTAATTAAAAA-CC---CTAA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6158176 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6158205 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6158239 CCTACCTTAATTAAAAA-CC---CTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
**
6158268 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6158302 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
** *
6158336 CCTAGCTTAATTAAAAACCCTAATCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
6158370 CCTAAATTAATTAAAAACCCT-A--AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6158399 CCTAAATTAATT-AAAA-CC---CTAA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
*
6158426 CCTAAATTAATTAAAAACCCT-A--AA-CCTAG
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
6158455 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CTAACCCTAA
**
6158489 CCTAGCTTAATTAAAAA-CC---CTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACTAACCCTAA
**
6158518 CCTAGCTTAATTAAAAACCCTAAC
1 CCTAAATTAATTAAAAACCCTAAC
6158542 CATTAAATTT
Statistics
Matches: 1496, Mismatches: 69, Indels: 239
0.83 0.04 0.13
Matches are distributed among these distances:
25 2 0.00
26 2 0.00
27 32 0.02
28 119 0.08
29 658 0.44
30 53 0.04
31 1 0.00
32 2 0.00
33 26 0.02
34 601 0.40
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (33 bp):
CCTAAATTAATTAAAAACCCTAACTAACCCTAA
Found at i:6156920 original size:63 final size:60
Alignment explanation
Indices: 6156824--6158540 Score: 1871
Period size: 63 Copynumber: 27.9 Consensus size: 60
6156814 AAATAAAAAC
* *
6156824 CCTAATTTAATTGAAAACCCTAACCTAACCCTAACCTAAATTAATTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-C-AA-CCTAACCTAAATTAATTAAAAACCCTAAACCTAA
*
6156887 CCTAAATTAATTAAAAACCCT-A-AACCTAACCTAAATTAATTAAAAACCCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
**
6156945 CCTAAATTAATTAAAAACCCTAATCTAACCCTAACCTACCTTAATTAAAAACCCT-AACACTAA
1 CCTAAATTAATTAAAAACCCTAA-C-AA-CCTAACCTAAATTAATTAAAAACCCTAAAC-CTAA
* ** *
6157008 CATAGCTTAATTAAAAATCCTAAC--CCTAACCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCT-A---AA-CCTAA
*
6157071 CCTAACTTAATTAAAAACCCTAATCTAAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-C--AACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
* * *
6157134 CCTAAATTAATTAAAAACCTTAGC--CCTAACCTAAATTAGTTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
** *
6157192 CCTAAATTAATTAAAAACCCTAATCTAACCCTAACCTAGCTTAATTAAAAACCCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-C-AA-CCTAACCTAAATTAATTAAAAACCCTAAACCTAA
6157255 CCTAAATTAATTAAAAACCCTAATCTAAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-C--AACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
*
6157318 CCTAAATTAATTAAAAACCCTAAC--CTTAACCTAAATTAATTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
**
6157376 CCTAAATTAATTAAAAACCCTAAC--CCTAACCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCT-A---AA-CCTAA
** **
6157439 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAACCTAGCTTAATTAAAAACCCTAATCTAAACC
1 CCTAAATTAATTAAAAACCCTAA-C-AA-CCTAACCTAAATTAATTAAAAA-CC----CTAAACC
6157504 TAA
58 TAA
6157507 CCTAAATTAATTAAAAACCCT-A-AACCTAACCTAAATTAATTAAAAACCCT-AACCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
*
6157564 CTTAAATTAATT-AAAACCCT-A-AACCTAACCTAAATTAATTAAAAACCCT-AACACTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAAC-CTAA
* ** *
6157621 CATAGCTTAATTAAAAATCCTAAC--CCTAACCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCT-A---AA-CCTAA
*
6157684 CCTAACTTAATTAAAAACCCTAATCTAAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-C--AACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
* * * *
6157747 CCTAAATTAATTAAAAACCTTAGC--CCTAACCTAAATTAGTTTAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
** *
6157805 CCTAAATTAATTAAAAACCCTAATCTAACCCTAACCTAGCTTAATTAAAAACCCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-C-AA-CCTAACCTAAATTAATTAAAAACCCTAAACCTAA
6157868 CCTAAATTAATTAAAAACCCTAATCTAAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAA-C--AACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
*
6157931 CCTAAATTAATT-AAAACCTTAAC--CCTAACCTAAATTAATTAAAAACCCTAAACCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
**
6157988 CCTAAATTAATTAAAAACCCTAAC--CCTAACCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCT-A---AA-CCTAA
** **
6158051 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAACCTAGCTTAATTAAAAACCCTAATCTAAACC
1 CCTAAATTAATTAAAAACCCTAA-C-AA-CCTAACCTAAATTAATTAAAAA-CC----CTAAACC
6158116 TAA
58 TAA
6158119 CCTAAATTAATTAAAAACCCT-A-AACCTAACCTAAATTAATTAAAAACCCT-AACCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
6158176 CCTAAATTAATTAAAAACCCT-A-AACCTAACCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCT-A---AA-CCTAA
** **
6158239 CCTACCTTAATTAAAAACCCTAAC--CCTAACCTAGCTTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCT-A---AA-CCTAA
** **
6158302 CCTAGCTTAATTAAAAACCCTAATCTAACCCTAACCTAGCTTAATTAAAAACCCTAATCTAAACC
1 CCTAAATTAATTAAAAACCCTAA-C-AA-CCTAACCTAAATTAATTAAAAA-CC----CTAAACC
6158367 TAA
58 TAA
6158370 CCTAAATTAATTAAAAACCCT-A-AACCTAACCTAAATTAATT-AAAACCCT-AACCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
*
6158426 CCTAAATTAATTAAAAACCCT-A-AACCTAGCCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCT-A---AA-CCTAA
** **
6158489 CCTAGCTTAATTAAAAACCCTAAC--CCTAACCTAGCTTAATTAAAAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAA
6158541 CCATTAAATT
Statistics
Matches: 1464, Mismatches: 88, Indels: 208
0.83 0.05 0.12
Matches are distributed among these distances:
56 87 0.06
57 144 0.10
58 336 0.23
59 9 0.01
61 3 0.00
62 35 0.02
63 611 0.42
64 23 0.02
67 5 0.00
68 190 0.13
69 12 0.01
72 3 0.00
73 6 0.00
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (60 bp):
CCTAAATTAATTAAAAACCCTAACAACCTAACCTAAATTAATTAAAAACCCTAAACCTAA
Found at i:6158701 original size:10 final size:10
Alignment explanation
Indices: 6158686--6158710 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6158676 TTTTGGCTTA
6158686 ATAATTTTAC
1 ATAATTTTAC
6158696 ATAATTTTAC
1 ATAATTTTAC
6158706 ATAAT
1 ATAAT
6158711 GTTAGATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:6162262 original size:128 final size:126
Alignment explanation
Indices: 6161821--6162296 Score: 803
Period size: 125 Copynumber: 3.8 Consensus size: 126
6161811 CCCAAACTTG
* * *
6161821 CTACTATAGCAAAATCGCGTCCACGAGGACGCGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCG
* *
6161886 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAGAAAAAAATTTATTTCTTACATGAC
66 TAGAAACGATTTTATACTATTTGCTCAGAAACATCAGAAAAAAAATTATTTCTTACATGAC
*
6161947 CTACTGTAGCAAAATCGCGTCCAGGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCG
6162012 TAGAAACGATTTTATACTATTTGCTCAGAAACATCAG-AAAAAAATTATTTCTTACATGAC
66 TAGAAACGATTTTATACTATTTGCTCAGAAACATCAGAAAAAAAATTATTTCTTACATGAC
* *
6162072 CTATTGTAGCAAAATCGCATCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCG
*
6162137 TAGAAACAATTTTATACTATTTGCTCAGAAACATCAGAAAAAAAAAATTATTTCTTACATGAC
66 TAGAAACGATTTTATACTATTTGCTCAGAAACATCAG--AAAAAAAATTATTTCTTACATGAC
*
6162200 CTACTGTAGCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCG
**
6162265 TAGAATGGATTTTATACTATTTGAC-CAGAAAC
66 TAGAAACGATTTTATACTATTTG-CTCAGAAAC
6162297 GTCAACTCGA
Statistics
Matches: 330, Mismatches: 16, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
125 120 0.36
126 97 0.29
128 112 0.34
129 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCG
TAGAAACGATTTTATACTATTTGCTCAGAAACATCAGAAAAAAAATTATTTCTTACATGAC
Found at i:6162281 original size:253 final size:251
Alignment explanation
Indices: 6161827--6162296 Score: 816
Period size: 253 Copynumber: 1.9 Consensus size: 251
6161817 CTTGCTACTA
* * *
6161827 TAGCAAAATCGCGTCCACGAGGACGCGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAG
1 TAGCAAAATCGCATCCACGAGGACGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAA
* *
6161892 CGATTTTATACTATTTGCTCAGAAACATCAGAAAAAAATTTATTTCTTACATGACCTACTGTAGC
66 CAATTTTATACTATTTGCTCAGAAACATCAGAAAAAAAATTATTTCTTACATGACCTACTGTAGC
*
6161957 AAAATCGCGTCCAGGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAACGAT
131 AAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAACGAT
6162022 TTTATACTATTTG-CTCAGAAACATCAGAAAAAAATTATTTCTTACATGACCTATTG
196 TTTATACTATTTGAC-CAGAAACATCAGAAAAAAATTATTTCTTACATGACCTATTG
*
6162078 TAGCAAAATCGCATCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAA
1 TAGCAAAATCGCATCCACGAGGACGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAA
6162143 CAATTTTATACTATTTGCTCAGAAACATCAGAAAAAAAAAATTATTTCTTACATGACCTACTGTA
66 CAATTTTATACTATTTGCTCAGAAACATCAG--AAAAAAAATTATTTCTTACATGACCTACTGTA
* **
6162208 GCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAATGG
129 GCAAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAACG
6162273 ATTTTATACTATTTGACCAGAAAC
194 ATTTTATACTATTTGACCAGAAAC
6162297 GTCAACTCGA
Statistics
Matches: 206, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
251 91 0.44
253 114 0.55
254 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (251 bp):
TAGCAAAATCGCATCCACGAGGACGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAA
CAATTTTATACTATTTGCTCAGAAACATCAGAAAAAAAATTATTTCTTACATGACCTACTGTAGC
AAAATCGCGTCCACGAGGGCGAGATTTCACAATTTCTTCTCAAATAGCATCCTCGTAGAAACGAT
TTTATACTATTTGACCAGAAACATCAGAAAAAAATTATTTCTTACATGACCTATTG
Found at i:6165742 original size:71 final size:72
Alignment explanation
Indices: 6165616--6165762 Score: 260
Period size: 71 Copynumber: 2.1 Consensus size: 72
6165606 TTCTAATTTT
6165616 GTTAACTGGCCCAGAGAAGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAAGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6165681 CAAATTC
66 CAAATTC
** *
6165688 GTTAACTGGCTGAGAGAGGAAGGGATGTG-CCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGGCCCAGAGAAGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
6165752 CAAATTC
66 CAAATTC
6165759 GTTA
1 GTTA
6165763 GTCCCCCAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 46 0.64
72 26 0.36
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (72 bp):
GTTAACTGGCCCAGAGAAGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
CAAATTC
Found at i:6168909 original size:13 final size:13
Alignment explanation
Indices: 6168877--6168927 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
6168867 ATATGTTCTT
*
6168877 TATATTTTAAAATA
1 TATATTTT-ATATA
*
6168891 TATATTTTATATG
1 TATATTTTATATA
*
6168904 TATATTTTTTATA
1 TATATTTTATATA
6168917 TATATTTTATA
1 TATATTTTATA
6168928 ATTCACATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 24 0.75
14 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATATTTTATATA
Found at i:6168913 original size:15 final size:15
Alignment explanation
Indices: 6168889--6168927 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 15
6168879 TATTTTAAAA
6168889 TATATATTTTATATG
1 TATATATTTTATATG
6168904 TATAT-TTTT-TA--
1 TATATATTTTATATG
6168915 TATATATTTTATA
1 TATATATTTTATA
6168928 ATTCACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.23
12 4 0.18
13 4 0.18
14 4 0.18
15 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TATATATTTTATATG
Found at i:6168968 original size:25 final size:26
Alignment explanation
Indices: 6168913--6168972 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
6168903 GTATATTTTT
*
6168913 TATATATATTTTATAATTCACATATA
1 TATACATATTTTATAATTCACATATA
* * * *
6168939 CATACATATTTT-TAATTTATATCTA
1 TATACATATTTTATAATTCACATATA
6168964 TATACATAT
1 TATACATAT
6168973 ATATATATCT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (26 bp):
TATACATATTTTATAATTCACATATA
Found at i:6171377 original size:12 final size:12
Alignment explanation
Indices: 6171361--6171394 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6171351 TTGCAAAAGG
6171361 AGATGCAAGATC
1 AGATGCAAGATC
* *
6171373 GGATGCAAGATT
1 AGATGCAAGATC
6171385 AGATGCAAGA
1 AGATGCAAGA
6171395 AAAACTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (12 bp):
AGATGCAAGATC
Found at i:6174111 original size:20 final size:19
Alignment explanation
Indices: 6174086--6174162 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 19
6174076 TAGATTCAAT
*
6174086 AAAAAATATAAAAAAAGAA
1 AAAAAAAATAAAAAAAGAA
*
6174105 AAAAAAAAGAAAAAAAAGAA
1 AAAAAAAA-TAAAAAAAGAA
*
6174125 GAAAAAAGAA-AGAAGAAGAGAAA
1 -AAAAAA-AATA-AA-AAAAG-AA
6174148 AGAAAAAAATAAAAA
1 A-AAAAAAATAAAAA
6174163 GGAGAGGCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
19 7 0.15
20 11 0.23
21 10 0.21
22 11 0.23
23 8 0.17
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAAAATAAAAAAAGAA
Found at i:6174117 original size:17 final size:17
Alignment explanation
Indices: 6174097--6174154 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
6174087 AAAAATATAA
6174097 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
*
6174114 AAAAAAAAGAAGAAAAAAG
1 AAAAAGAA-AA-AAAAAAG
* *
6174133 AAAGAAG-AAGAGAAAAG
1 AAA-AAGAAAAAAAAAAG
6174150 AAAAA
1 AAAAA
6174155 AATAAAAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 3 0.09
19 11 0.32
20 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Done.