Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 180 of 210
Found at i:53535428 original size:124 final size:125
Alignment explanation
Indices: 53535220--53535499 Score: 363
Period size: 124 Copynumber: 2.2 Consensus size: 125
53535210 TTATTTCGAA
** *
53535220 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTAT
* * * *
53535284 GAAATCATGCCTTCGTGGACGCGATTTCAGC-ACATTTGGTCATATAAGAAATTATT-TTTT
65 GAAATCACGCCCTCGTGGACGCGATTTC-GCTACAGTTGGTCATATAAGAAATAATTATTTT
53535344 TTGACGTTTTCTGAGCAAATAGTAT-AAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTA
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTA
* * *
53535407 TGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATCACGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATATAAGAAATAATTATTTT
* * * *
53535469 TTGACATTTCTGAGTAAATAGTGTCAAATCG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCG
53535500 TGCCCTCGTG
Statistics
Matches: 137, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
123 3 0.02
124 102 0.74
125 31 0.23
126 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTATG
AAATCACGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATATAAGAAATAATTATTTT
Found at i:53536061 original size:12 final size:12
Alignment explanation
Indices: 53536041--53536098 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
53536031 TGGAAGAAAA
53536041 TTGAGAGAATTT
1 TTGAGAGAATTT
*
53536053 TTGAAAGAA--T
1 TTGAGAGAATTT
*
53536063 TTGAGAGAGTTT
1 TTGAGAGAATTT
*
53536075 TTGAAAGAA--T
1 TTGAGAGAATTT
53536085 TTGAGAGAATTT
1 TTGAGAGAATTT
53536097 TT
1 TT
53536099 AAATGAAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
10 17 0.47
12 19 0.53
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
TTGAGAGAATTT
Found at i:53536112 original size:22 final size:22
Alignment explanation
Indices: 53536022--53536098 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
53536012 ACACTCGGTT
* *
53536022 AGAGAA-TTTTGGAAGAAAATTG
1 AGAGAATTTTTGAAAG-AATTTG
53536044 AGAGAATTTTTGAAAGAATTTG
1 AGAGAATTTTTGAAAGAATTTG
*
53536066 AGAGAGTTTTTGAAAGAATTTG
1 AGAGAATTTTTGAAAGAATTTG
53536088 AGAGAATTTTT
1 AGAGAATTTTT
53536099 AAATGAAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 42 0.84
23 8 0.16
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (22 bp):
AGAGAATTTTTGAAAGAATTTG
Found at i:53542708 original size:41 final size:41
Alignment explanation
Indices: 53542663--53542749 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
53542653 TTTAGCCTCC
* *
53542663 AATAA-CCAACCAAAATAATTAACAAATATAATTAATCATCA
1 AATAATCC-ACCAAAATAATTAACAAATATAACTAATAATCA
**
53542704 AATAATCCATTAAAATAATTAACAAATATAACTAATAATCA
1 AATAATCCACCAAAATAATTAACAAATATAACTAATAATCA
53542745 AATAA
1 AATAA
53542750 ACCATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (41 bp):
AATAATCCACCAAAATAATTAACAAATATAACTAATAATCA
Found at i:53542760 original size:41 final size:41
Alignment explanation
Indices: 53542674--53542761 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
53542664 ATAACCAACC
* * * *
53542674 AAAATAATTAACAAATATAATTAATCATCAAATAATCCATT
1 AAAATAATTAACAAATATAACTAATAATCAAATAAACCATA
53542715 AAAATAATTAACAAATATAACTAATAATCAAATAAACCATA
1 AAAATAATTAACAAATATAACTAATAATCAAATAAACCATA
53542756 AAAATA
1 AAAATA
53542762 TTAGATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (41 bp):
AAAATAATTAACAAATATAACTAATAATCAAATAAACCATA
Found at i:53545219 original size:32 final size:32
Alignment explanation
Indices: 53545180--53545247 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
53545170 AACAACTTAA
*
53545180 AAAAAACAAT-TCCATAATTCTCATCATCAATT
1 AAAAAACAATAT-CATAATTCTCATAATCAATT
53545212 AAAAAACAATATCATAATTCTCATAATCAATT
1 AAAAAACAATATCATAATTCTCATAATCAATT
53545244 AAAA
1 AAAA
53545248 TAACGTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (32 bp):
AAAAAACAATATCATAATTCTCATAATCAATT
Found at i:53552694 original size:88 final size:86
Alignment explanation
Indices: 53552543--53552717 Score: 201
Period size: 88 Copynumber: 2.0 Consensus size: 86
53552533 AAAATGGGTA
* **
53552543 AATTAGTTTTTTACATTAGATTAAATAATAAATTAGTCATTCCATTAAAAATTTATCTTTTTACG
1 AATTAGTTTTTTACATTAGATTAAAGAATAAATTAGTCATTCCATTAAAAATTTATCCATTTACG
*
53552608 CGGTTATAAATTGG-CTATTGT
66 CGGTTAAAAATTGGTC-ATTGT
* * * **
53552629 AATTAGTCTTTTATATATTAGATTAAAGAGTAAATT-GATCTTTCTTTTAAAAATTTATCCATTT
1 AATTAGT-TTTT-TACATTAGATTAAAGAATAAATTAG-TCATTCCATTAAAAATTTATCCATTT
**
53552693 ACGTTGTTAAAAATTGGTCATTGT
63 ACGCGGTTAAAAATTGGTCATTGT
53552717 A
1 A
53552718 TGTTAGCATA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
86 7 0.09
87 5 0.07
88 61 0.82
89 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (86 bp):
AATTAGTTTTTTACATTAGATTAAAGAATAAATTAGTCATTCCATTAAAAATTTATCCATTTACG
CGGTTAAAAATTGGTCATTGT
Found at i:53554117 original size:21 final size:21
Alignment explanation
Indices: 53554081--53554122 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53554071 CTCCAAAACA
*
53554081 AGGGAAAATGGGTTACATTTT
1 AGGGAAAATGGCTTACATTTT
* *
53554102 AGGGAAAATGTCTTACCTTTT
1 AGGGAAAATGGCTTACATTTT
53554123 CAATTTCCGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (21 bp):
AGGGAAAATGGCTTACATTTT
Found at i:53554975 original size:29 final size:29
Alignment explanation
Indices: 53554933--53554999 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
53554923 CACGGTTTTT
* *
53554933 TTACCAAAATAATATA-AAAAAATAATTAA
1 TTACGAAAAAAATATAGAAAAAA-AATTAA
*
53554962 TTACGAAAAAAATATAGAAAACAAATTAA
1 TTACGAAAAAAATATAGAAAAAAAATTAA
*
53554991 TTATGAAAA
1 TTACGAAAA
53555000 TAGGCATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.25
Consensus pattern (29 bp):
TTACGAAAAAAATATAGAAAAAAAATTAA
Found at i:53555536 original size:5 final size:5
Alignment explanation
Indices: 53555526--53555550 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53555516 ATTAAAAGAG
53555526 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
53555551 TAAACAAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:53562726 original size:32 final size:34
Alignment explanation
Indices: 53562690--53562765 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 34
53562680 TAAAATAAAT
*
53562690 TATGAAAAGTTAAG-AATGTAAAGAGACTTG-AG
1 TATGAAAAGTTAAGTAATGTAAAAAGACTTGAAG
*
53562722 TATGAAGAGTT-AGTAATGTAAAAAGACTTGAAG
1 TATGAAAAGTTAAGTAATGTAAAAAGACTTGAAG
53562755 -ATGAAAAGTTA
1 TATGAAAAGTTA
53562766 CACACATGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 2 0.05
32 34 0.89
33 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (34 bp):
TATGAAAAGTTAAGTAATGTAAAAAGACTTGAAG
Found at i:53562817 original size:38 final size:38
Alignment explanation
Indices: 53562775--53562862 Score: 149
Period size: 38 Copynumber: 2.3 Consensus size: 38
53562765 ACACACATGC
*
53562775 ATGAATAGTCACAACTCCTATAACATTTAGTTATGTAA
1 ATGAATAGTCACAACTCCTATAACATTTAGTGATGTAA
* *
53562813 ATGAATAGTCACAACTCCTATAGCATTTAGTGATGTAG
1 ATGAATAGTCACAACTCCTATAACATTTAGTGATGTAA
53562851 ATGAATAGTCAC
1 ATGAATAGTCAC
53562863 TTATAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (38 bp):
ATGAATAGTCACAACTCCTATAACATTTAGTGATGTAA
Found at i:53566716 original size:29 final size:29
Alignment explanation
Indices: 53566682--53566744 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
53566672 AAAAAAAATG
53566682 ATAAAAAATAAAA-AA-AATTAAATTTTA
1 ATAAAAAATAAAACAATAATTAAATTTTA
*
53566709 ATAAAAAATAAAACAATATTTAAATTTTA
1 ATAAAAAATAAAACAATAATTAAATTTTA
*
53566738 TTAAAAA
1 ATAAAAA
53566745 TTTTAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 13 0.41
28 2 0.06
29 17 0.53
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (29 bp):
ATAAAAAATAAAACAATAATTAAATTTTA
Found at i:53566755 original size:29 final size:28
Alignment explanation
Indices: 53566682--53566756 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
53566672 AAAAAAAATG
*
53566682 ATAAAAAA-TAAAAAAAATTAAATTTTA
1 ATAAAAAATTAAAAATAATTAAATTTTA
* *
53566709 ATAAAAAATAAAACAATATTTAAATTTTA
1 ATAAAAAATTAAA-AATAATTAAATTTTA
* *
53566738 TTAAAAATTTTAAAAATAA
1 ATAAAAA-ATTAAAAATAA
53566757 AAACCGCAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 8 0.21
28 3 0.08
29 23 0.61
30 4 0.11
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAAAAATTAAAAATAATTAAATTTTA
Found at i:53566831 original size:20 final size:19
Alignment explanation
Indices: 53566797--53566860 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
53566787 AAAATTTGAT
*
53566797 AAAATCATAAGAAAATTATTA
1 AAAATCGTAA-AAAATTA-TA
* *
53566818 AAAAT-GTAAAAAAATACA
1 AAAATCGTAAAAAATTATA
53566836 AAAATTCGTAAAAAATTATA
1 AAAA-TCGTAAAAAATTATA
53566856 AAAAT
1 AAAAT
53566861 TATCATACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 5 0.14
19 8 0.22
20 18 0.50
21 5 0.14
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAATCGTAAAAAATTATA
Found at i:53570223 original size:14 final size:15
Alignment explanation
Indices: 53570204--53570237 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
53570194 TTTACAAAAA
*
53570204 AAAAATAGAAT-AAT
1 AAAAATAAAATAAAT
53570218 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
53570233 AAAAA
1 AAAAA
53570238 AAGGTTCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:53571034 original size:26 final size:28
Alignment explanation
Indices: 53571004--53571081 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 28
53570994 GGATGGGAGG
*
53571004 GGAGTAAAAGTTTTGGGGGAAAGT-G-A
1 GGAGTAAAAGTTTTGGGGAAAAGTAGAA
*
53571030 GGAGTAAAGGTTTTGAGGGAAAAGTGAGAA
1 GGAGTAAAAGTTTTG-GGGAAAAGT-AGAA
*
53571060 GGAGTAAACGTTTTGGGGAAAA
1 GGAGTAAAAGTTTTGGGGAAAA
53571082 AGTAAAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.31
27 8 0.18
29 8 0.18
30 15 0.33
ACGTcount: A:0.37, C:0.01, G:0.40, T:0.22
Consensus pattern (28 bp):
GGAGTAAAAGTTTTGGGGAAAAGTAGAA
Found at i:53571430 original size:21 final size:20
Alignment explanation
Indices: 53571404--53571450 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
53571394 AAAAGGACCT
53571404 TTTTATACAT-TTTATAAATTA
1 TTTTATACATATTTATAAA--A
*
53571425 TTTTAT-GATATTTATAAAA
1 TTTTATACATATTTATAAAA
53571444 TTTTATA
1 TTTTATA
53571451 TTTTTATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 14 0.61
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTATACATATTTATAAAA
Found at i:53571481 original size:9 final size:9
Alignment explanation
Indices: 53571403--53571511 Score: 53
Period size: 9 Copynumber: 11.6 Consensus size: 9
53571393 TAAAAGGACC
53571403 TTTTTATACA
1 TTTTTATA-A
53571413 -TTTTATAAA
1 TTTTTAT-AA
*
53571422 TTATTTTATGA
1 -T-TTTTATAA
*
53571433 TATTTATAAA
1 TTTTTAT-AA
*
53571443 ATTTTAT-A
1 TTTTTATAA
53571451 TTTTTATTCAA
1 TTTTTA-T-AA
* *
53571462 ATTTAATAA
1 TTTTTATAA
53571471 TTTTTATAA
1 TTTTTATAA
* *
53571480 TTTTTGTTTA
1 TTTTT-ATAA
*
53571490 TTTTT-TAT
1 TTTTTATAA
53571498 TTTTTATAA
1 TTTTTATAA
53571507 TTTTT
1 TTTTT
53571512 TTACCACATA
Statistics
Matches: 74, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
8 12 0.16
9 34 0.46
10 16 0.22
11 6 0.08
12 6 0.08
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:53574448 original size:21 final size:21
Alignment explanation
Indices: 53574422--53574474 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
53574412 CAGCAGTGGT
*
53574422 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGGTACTGTAGC
*
53574443 GGTGAGATTGGGTACTGTAGC
1 GGTGAGATTAGGTACTGTAGC
53574464 GGTGAGATTAG
1 GGTGAGATTAG
53574475 AAATAATGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.08, G:0.40, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGGTACTGTAGC
Found at i:53578574 original size:11 final size:12
Alignment explanation
Indices: 53578542--53578592 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 12
53578532 TCTTTTGTTT
53578542 TATATAT-AT-A
1 TATATATAATAA
53578552 TATATA-ATATAA
1 TATATATA-ATAA
53578564 TATAT-TAATAA
1 TATATATAATAA
53578575 TA-ATATAATAA
1 TATATATAATAA
53578586 TATATAT
1 TATATAT
53578593 TAACTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 8 0.23
11 16 0.46
12 11 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATATATAATAA
Found at i:53578581 original size:24 final size:24
Alignment explanation
Indices: 53578553--53578604 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
53578543 ATATATATAT
53578553 ATATAAT-ATAATATATTAA-TAATA
1 ATATAATAAT-ATATATTAACTAA-A
53578577 ATATAATAATATATATTAACTAAA
1 ATATAATAATATATATTAACTAAA
53578601 ATAT
1 ATAT
53578605 CTTTAACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAATAATATATATTAACTAAA
Found at i:53578604 original size:14 final size:13
Alignment explanation
Indices: 53578549--53578604 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
53578539 TTTTATATAT
*
53578549 ATATATATAATATA
1 ATATAT-TAATAAA
*
53578563 ATATATTAATAAT
1 ATATATTAATAAA
*
53578576 A-ATA-TAATAAT
1 ATATATTAATAAA
53578587 ATATATTAACTAAA
1 ATATATTAA-TAAA
53578601 ATAT
1 ATAT
53578605 CTTTAACATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 8 0.22
12 6 0.17
13 9 0.25
14 13 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATTAATAAA
Found at i:53585277 original size:21 final size:21
Alignment explanation
Indices: 53585251--53585308 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
53585241 CCTAAGGCTG
53585251 AACAGAAGCACATAAGTGG-TA
1 AACAGAAGCACATAAG-GGTTA
* *
53585272 AACAGAAACCCATAAGGGTTA
1 AACAGAAGCACATAAGGGTTA
* *
53585293 AACGGAAGCTCATAAG
1 AACAGAAGCACATAAG
53585309 AGCTGAACGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (21 bp):
AACAGAAGCACATAAGGGTTA
Found at i:53585301 original size:42 final size:42
Alignment explanation
Indices: 53585255--53585405 Score: 135
Period size: 42 Copynumber: 3.6 Consensus size: 42
53585245 AGGCTGAACA
* *
53585255 GAAGCACATAAGTGGTAAAC-AGAAACCCATAAGGGTTAAACG
1 GAAGCACATAAGAGCTAAACGA-AAACCCATAAGGGTTAAACG
* * * *
53585297 GAAGCTCATAAGAGCTGAACGAAAACCGATAAGGGTTAAACA
1 GAAGCACATAAGAGCTAAACGAAAACCCATAAGGGTTAAACG
* * * * * * *
53585339 GAAACTCAAAAGAGCTAAACGAAAACTCATAAGAGTTGAACA
1 GAAGCACATAAGAGCTAAACGAAAACCCATAAGGGTTAAACG
* *
53585381 GAAG-ATCATGAGAGCTAAATGAAAA
1 GAAGCA-CATAAGAGCTAAACGAAAA
53585406 GCAAACACGA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 88 0.99
43 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (42 bp):
GAAGCACATAAGAGCTAAACGAAAACCCATAAGGGTTAAACG
Found at i:53585317 original size:21 final size:21
Alignment explanation
Indices: 53585261--53585399 Score: 84
Period size: 21 Copynumber: 6.6 Consensus size: 21
53585251 AACAGAAGCA
* * * *
53585261 CATAAGTGGTAAACAGAAACC
1 CATAAGAGCTAAACGGAAACT
* * *
53585282 CATAAGGGTTAAACGGAAGCT
1 CATAAGAGCTAAACGGAAACT
* *
53585303 CATAAGAGCTGAACGAAAAC-
1 CATAAGAGCTAAACGGAAACT
* * *
53585323 CGATAAGGGTTAAACAGAAACT
1 C-ATAAGAGCTAAACGGAAACT
* *
53585345 CAAAAGAGCTAAACGAAAACT
1 CATAAGAGCTAAACGGAAACT
* * *
53585366 CATAAGAGTTGAACAGAAGA-T
1 CATAAGAGCTAAACGGAA-ACT
*
53585387 CATGAGAGCTAAA
1 CATAAGAGCTAAA
53585400 TGAAAAGCAA
Statistics
Matches: 87, Mismatches: 28, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
20 1 0.01
21 84 0.97
22 2 0.02
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (21 bp):
CATAAGAGCTAAACGGAAACT
Found at i:53587582 original size:22 final size:22
Alignment explanation
Indices: 53587557--53587599 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53587547 TCTCCCTATT
53587557 TTGCTACCATTTTATTATTATG
1 TTGCTACCATTTTATTATTATG
* *
53587579 TTGCTACTATTTTATTGTTAT
1 TTGCTACCATTTTATTATTAT
53587600 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTATTATTATG
Found at i:53589207 original size:27 final size:27
Alignment explanation
Indices: 53589173--53589241 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
53589163 GGAGTGGCTA
* *
53589173 CCACAGGCGGCACCAGTGGTGCCAGTG
1 CCACAGGCGGCACCAATGGTGCCACTG
* *
53589200 GCAGAGGCGGCACCAATGGTGCCACTG
1 CCACAGGCGGCACCAATGGTGCCACTG
*
53589227 CCACAGGTGGCACCA
1 CCACAGGCGGCACCA
53589242 CCCCCCTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.35, T:0.10
Consensus pattern (27 bp):
CCACAGGCGGCACCAATGGTGCCACTG
Found at i:53589314 original size:4 final size:4
Alignment explanation
Indices: 53589305--53589373 Score: 56
Period size: 4 Copynumber: 16.8 Consensus size: 4
53589295 GGGAAAGGAG
53589305 AAGA AAGA AAGA AAG- AA-A AAGA AAGA AAGAA AAGGA AAGGA GAAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AA-GA -AAGA
53589351 AAG- AA-A AAGA AAGGA AAGGA AAG
1 AAGA AAGA AAGA AA-GA AA-GA AAG
53589374 GAGAAGAAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
3 8 0.14
4 26 0.46
5 20 0.35
6 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:53589325 original size:14 final size:14
Alignment explanation
Indices: 53589303--53589420 Score: 73
Period size: 15 Copynumber: 8.0 Consensus size: 14
53589293 GAGGGAAAGG
53589303 AGAAGAAAGAAAGAA
1 AGAA-AAAGAAAGAA
53589318 AGAAAAAGAAAGAA
1 AGAAAAAGAAAGAA
53589332 AGAAAAGGAAAGGAGAAGAA
1 AG--AA--AAA-GA-AAGAA
53589352 AGAAAAAGAAAGGAA
1 AGAAAAAGAAA-GAA
* *
53589367 AGGAAAGGAGAAG-A
1 AGAAAAAGA-AAGAA
* *
53589381 AGAAAAGGGAAGGAA
1 AGAAAA-AGAAAGAA
*
53589396 GGAAAAA-AAA-AA
1 AGAAAAAGAAAGAA
53589408 AGAAAAA-AAAGAA
1 AGAAAAAGAAAGAA
53589421 GTAAAGGTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
12 11 0.13
13 4 0.05
14 22 0.26
15 26 0.31
16 7 0.08
18 5 0.06
19 2 0.02
20 7 0.08
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AGAAAAAGAAAGAA
Found at i:53589360 original size:30 final size:30
Alignment explanation
Indices: 53589317--53589386 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
53589307 GAAAGAAAGA
53589317 AAGAAA-AAGAAAGAAAGAAAAGGAAAGGAG
1 AAGAAAGAA-AAAGAAAGAAAAGGAAAGGAG
*
53589347 AAGAAAGAAAAAGAAAGGAAAGGAAAGGAG
1 AAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
53589377 AAG-AAGAAAA
1 AAGAAAGAAAA
53589387 GGGAAGGAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 7 0.18
30 29 0.76
31 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (30 bp):
AAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
Found at i:53589397 original size:23 final size:23
Alignment explanation
Indices: 53589287--53589409 Score: 90
Period size: 23 Copynumber: 5.2 Consensus size: 23
53589277 GTGGAGAAGA
*
53589287 AAAGGAGAGGGAAAGGAGAAGAAAG
1 AAAGGA-AAGGAAAGGAGAA-AAAG
* *
53589312 AAA-GAAAGAAAAAGA-AAGAAAG
1 AAAGGAAAGGAAAGGAGAA-AAAG
*
53589334 AAAAGGAAAGGAGAAGAAAGAAAAAG
1 -AAAGGAAAGGA-AAG-GAGAAAAAG
*
53589360 AAAGGAAAGGAAAGGAGAAGAAG
1 AAAGGAAAGGAAAGGAGAAAAAG
* * *
53589383 AAAAGGGAAGG-AAGGAAAAAAAA
1 -AAAGGAAAGGAAAGGAGAAAAAG
53589406 AAAG
1 AAAG
53589410 AAAAAAAAGA
Statistics
Matches: 80, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
22 11 0.14
23 26 0.32
24 20 0.25
25 16 0.20
26 5 0.06
27 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAAGGAAAGGAAAGGAGAAAAAG
Found at i:53590504 original size:156 final size:157
Alignment explanation
Indices: 53589732--53590610 Score: 1143
Period size: 155 Copynumber: 5.7 Consensus size: 157
53589722 AATAAAATTC
* * *
53589732 AAAAAAATGTAAAATAACACAAT-AAAAAAT-ATATATTTTTATTGAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* ** * * * * *
53589795 AAAAAATACAATTAAAGGGCCAAAATAAGAGTTATTTTT-TGAAATTTATTTAAAAAACACACTA
66 AAAAAATACGAGCAAAGGGCCGAAATAAGGGTTATTTTTCT-AAATTTATTTAAAAAACAGAATT
* * *
53589859 AATTAAAAAATTTGAAACATAATGTACT
130 AATTAATACATTTCAAACATAATGTACT
* * * *
53589887 AAAATAATGTAAAATAATAAAATTAGAAAATAGTATA-TTTT-TT-AAAGTAATAAAATCCGGAG
1 AAAATAATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGG-G
* *
53589949 AAAAAAATACGAACAAAGGGCCGAAATAAGGG-TATTTTACTAAATATT-TTTAAAAAACAGAAT
65 AAAAAAATACGAGCAAAGGGCCGAAATAAGGGTTATTTTTCTAAAT-TTATTTAAAAAACAGAAT
53590012 TAATTAATACATTTCAAACATAATGTACT
129 TAATTAATACATTTCAAACATAATGTACT
** * *
53590041 AAAATAATGTAAAATAATAAAATCCAAAAATAATATATTTTTATTGAAAGTAATAAAATCCGAG-
1 AAAATAATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
*
53590105 AAAAAATACGAGCAAAGGGGCGAAATAAGGGTTA-TTTTCTAAATTTATTTAAAAAACAGAATTA
66 AAAAAATACGAGCAAAGGGCCGAAATAAGGGTTATTTTTCTAAATTTATTTAAAAAACAGAATTA
*
53590169 ATTAATACATTTCAAACATAATGTAAT
131 ATTAATACATTTCAAACATAATGTACT
* ** * * *
53590196 AAAATAATATAAAATAATAAAATACGAAAATAACATATTTTTATTGAAAGTAATAATA-TC-CG-
1 AAAATAATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* * *
53590258 -AAAAATACGAGTAAAGGGCCGAAATAA-GGTT-TTTTTACTAAATTTTTTTAAAAAACA-CATT
66 AAAAAATACGAGCAAAGGGCCGAAATAAGGGTTATTTTT-CTAAATTTATTTAAAAAACAGAATT
* *
53590319 AAATTAGTAAATTTCAAACATAATGTACT
130 -AATTAATACATTTCAAACATAATGTACT
53590348 AAAATAATGTAAAATAATAAAATAAAAAAATAATATA-TTTTATTGAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
53590412 AAAAAATACGAGCAAAGGGCCGAAATAAGGGTTATTTTTCTAAATTTATTTAAAAAACAGAATTA
66 AAAAAATACGAGCAAAGGGCCGAAATAAGGGTTATTTTTCTAAATTTATTTAAAAAACAGAATTA
*
53590477 ATTAATACATTTCTAACATAATGTACT
131 ATTAATACATTTCAAACATAATGTACT
* ** *
53590504 AAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAA-TC-CGA
1 AAAATAATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* **
53590567 AAAACAGTACGAATAAAGGGCCGAAATAAGGGTT-TTTTTACTAA
66 AAAA-AATACGAGCAAAGGGCCGAAATAAGGGTTATTTTT-CTAA
53590611 TTTTTTTTGA
Statistics
Matches: 641, Mismatches: 60, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
151 30 0.05
152 104 0.16
153 2 0.00
154 100 0.16
155 228 0.36
156 129 0.20
157 48 0.07
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (157 bp):
AAAATAATGTAAAATAATAAAATAAAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
AAAAAATACGAGCAAAGGGCCGAAATAAGGGTTATTTTTCTAAATTTATTTAAAAAACAGAATTA
ATTAATACATTTCAAACATAATGTACT
Found at i:53590519 original size:463 final size:466
Alignment explanation
Indices: 53589764--53590610 Score: 1327
Period size: 463 Copynumber: 1.8 Consensus size: 466
53589754 TAAAAAATAT
* *
53589764 ATATTTTTATTGAAAGTAATAAAATTCGGGAAAAAAATACAATTAAAGGGCCAAAATAAGAGTTA
1 ATATTTTTATTGAAAGTAATAAAATTCGCG-AAAAAATACAAGTAAAGGGCCAAAATAAGAGTTA
*
53589829 TTTTTTGAAATTTATTTAAAAAACACACTAAATTAAAAAATTTGAAACATAATGTACTAAAATAA
65 TTTTTTGAAATTTATTTAAAAAACACACTAAATTAAAAAATTTCAAACATAATGTACTAAAATAA
* * *
53589894 TGTAAAATAATAAAATTAGAAAATAGTATATTTTTTAAAGTAATAAAATCCGGAGAAAAAAATAC
130 TGTAAAATAATAAAATAAAAAAATAATATATTTTTTAAAGTAATAAAATCCGGAGAAAAAAATAC
53589959 GAACAAAGGGCCGAAATAAGGGTATTTTACTAAATATTTTTAAAAAACAGAATTAATTAATACAT
195 GAACAAAGGGCCGAAATAAGGGTATTTTACTAAATATTTTTAAAAAACAGAATTAATTAATACAT
* *
53590024 TTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATCCAAAAATAATATATTTTTATTGAA
260 TTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAA
* *
53590089 AGTAATAAAATCCGAGAAAA-AATACGAGCAAAGGGGCGAAATAAGGGTTATTTT-CTAAATTTA
325 AGTAATAAAATCCGA-AAAACAATACGAACAAAGGGCCGAAATAAGGGTTATTTTACTAAATTTA
53590152 TTTAAAAAACAGAATTAATTAATACATTTCAAACATAATGTAATAAAATAATATAAAATAATAAA
389 TTTAAAAAACAGAATTAATTAATACATTTCAAACATAATGTAATAAAATAATATAAAATAATAAA
53590217 ATACGAAAATAAC
454 ATACGAAAATAAC
* * *
53590230 ATATTTTTATTGAAAGTAATAATA-TC-CG-AAAAATACGAGTAAAGGGCCGAAATAAG-GTT-T
1 ATATTTTTATTGAAAGTAATAAAATTCGCGAAAAAATACAAGTAAAGGGCCAAAATAAGAGTTAT
* * **
53590290 TTTTACT-AAATTTTTTTAAAAAACACATTAAATTAGTAAATTTCAAACATAATGTACTAAAATA
66 TTTT--TGAAATTTATTTAAAAAACACACTAAATTAAAAAATTTCAAACATAATGTACTAAAATA
*
53590354 ATGTAAAATAATAAAATAAAAAAATAATATATTTTATTGAAAGTAATAAAATTCGG-GAAAAAAA
129 ATGTAAAATAATAAAATAAAAAAATAATATATTTT-TT-AAAGTAATAAAATCCGGAGAAAAAAA
* *
53590418 TACGAGCAAAGGGCCGAAATAAGGGTTATTTTTCTAAAT-TTATTTAAAAAACAGAATTAATTAA
192 TACGAACAAAGGGCCGAAATAAGGG-TATTTTACTAAATATT-TTTAAAAAACAGAATTAATTAA
* *
53590482 TACATTTCTAACATAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTA
255 TACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTA
* * *
53590547 TTGAAAGTAATAAAATCCGAAAAACAGTACGAATAAAGGGCCGAAATAAGGGTTTTTTTACTAA
320 TTGAAAGTAATAAAATCCGAAAAACAATACGAACAAAGGGCCGAAATAAGGGTTATTTTACTAA
53590611 TTTTTTTTGA
Statistics
Matches: 348, Mismatches: 25, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
460 5 0.01
461 87 0.25
462 66 0.19
463 160 0.46
464 5 0.01
465 2 0.01
466 23 0.07
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (466 bp):
ATATTTTTATTGAAAGTAATAAAATTCGCGAAAAAATACAAGTAAAGGGCCAAAATAAGAGTTAT
TTTTTGAAATTTATTTAAAAAACACACTAAATTAAAAAATTTCAAACATAATGTACTAAAATAAT
GTAAAATAATAAAATAAAAAAATAATATATTTTTTAAAGTAATAAAATCCGGAGAAAAAAATACG
AACAAAGGGCCGAAATAAGGGTATTTTACTAAATATTTTTAAAAAACAGAATTAATTAATACATT
TCAAACATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAA
GTAATAAAATCCGAAAAACAATACGAACAAAGGGCCGAAATAAGGGTTATTTTACTAAATTTATT
TAAAAAACAGAATTAATTAATACATTTCAAACATAATGTAATAAAATAATATAAAATAATAAAAT
ACGAAAATAAC
Found at i:53596377 original size:11 final size:11
Alignment explanation
Indices: 53596351--53596384 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
53596341 TAAACTAACA
53596351 ACAAAAAATA-
1 ACAAAAAATAT
*
53596361 ATAAAAAATAT
1 ACAAAAAATAT
53596372 ACAAAAAATAT
1 ACAAAAAATAT
53596383 AC
1 AC
53596385 TAACAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
ACAAAAAATAT
Found at i:53596859 original size:23 final size:26
Alignment explanation
Indices: 53596815--53596861 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
53596805 TAAGATATGA
53596815 AAATAATAAAGTATATATAATTTAAT
1 AAATAATAAAGTATATATAATTTAAT
*
53596841 AAATTATAAA-TAT-TA-AATTTA
1 AAATAATAAAGTATATATAATTTA
53596862 TTAGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 3 0.15
26 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
AAATAATAAAGTATATATAATTTAAT
Found at i:53611443 original size:113 final size:114
Alignment explanation
Indices: 53611289--53611560 Score: 349
Period size: 113 Copynumber: 2.4 Consensus size: 114
53611279 CGTCTCCCGA
* *
53611289 GCTTTC-AGGGATTTAGCGGCGCTTTTACAGAAAGCGCCGCTAATGCTGAAGTCTTTAGCGGCG-
1 GCTTTCGAGGGATTTAGCGGCGTTTTTAGA-AAAGCGCCGCTAATG-TGAAGTCTTTAGCGGCGT
* *
53611352 TTTTTGTTAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCT-G
64 TTTTTG-GAAAGCGCCGCAAAAAAAACTAAGCCCAACGACGCCGTTTTCTAG
* **
53611402 GCTTTCG-GGGATTTTAGCGGCGTTTTT-GTTAAAGCGCCGCTAATGTTCAGTCTTTAGCGGCGT
1 GCTTTCGAGGGA-TTTAGCGGCGTTTTTAG-AAAAGCGCCGCTAATGTGAAGTCTTTAGCGGCGT
* * * *
53611465 TTTTTGGAAAGCGCCGCAAAAAAAACTAAGCGCAACGTCGTCGTTTTCTAT
64 TTTTTGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGACGCCGTTTTCTAG
*
53611516 GCTTTTGAGGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATG
1 GCTTTCGAGGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATG
53611561 ATCAGGGATT
Statistics
Matches: 138, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
112 25 0.18
113 58 0.42
114 50 0.36
115 5 0.04
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (114 bp):
GCTTTCGAGGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGTGAAGTCTTTAGCGGCGTTT
TTTGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGACGCCGTTTTCTAG
Found at i:53611481 original size:112 final size:114
Alignment explanation
Indices: 53611289--53611565 Score: 350
Period size: 114 Copynumber: 2.4 Consensus size: 114
53611279 CGTCTCCCGA
* * **
53611289 GCTTTC-AGGGATTTAGCGGCGCTTTTACAGAAAGCGCCGCTAATGCTGAAGTCTTTAGCGGCGT
1 GCTTTCGAGGGATTTAGCGGCGTTTTTAGA-AAAGCGCCGCTAATG-TTCAGTCTTTAGCGGCGT
* *
53611353 TTTTGTTAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCT-G
64 TTTTGTGAAAGCGCCGCAAAAAAAACTAAGCCCAACGACGCCGTTTTCTAG
*
53611402 GCTTTCG-GGGATTTTAGCGGCGTTTTT-GTTAAAGCGCCGCTAATGTTCAGTCTTTAGCGGCGT
1 GCTTTCGAGGGA-TTTAGCGGCGTTTTTAG-AAAAGCGCCGCTAATGTTCAGTCTTTAGCGGCGT
* * * *
53611465 TTTT-TGGAAAGCGCCGCAAAAAAAACTAAGCGCAACGTCGTCGTTTTCTAT
64 TTTTGT-GAAAGCGCCGCAAAAAAAACTAAGCCCAACGACGCCGTTTTCTAG
* *
53611516 GCTTTTGAGGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGATCAG
1 GCTTTCGAGGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGTTCAG
53611566 GGATTTAAAA
Statistics
Matches: 142, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
111 1 0.01
112 30 0.21
113 52 0.37
114 54 0.38
115 5 0.04
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (114 bp):
GCTTTCGAGGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGTTCAGTCTTTAGCGGCGTTT
TTGTGAAAGCGCCGCAAAAAAAACTAAGCCCAACGACGCCGTTTTCTAG
Found at i:53612943 original size:39 final size:39
Alignment explanation
Indices: 53612889--53612978 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 39
53612879 TAATTGGAAT
*
53612889 GGTTTAGGGGTTATGCTTT-AGGGGTTAGGGAGATTTAGG
1 GGTTTATGGGTTATGCTTTAAGGGGTTAGGG-GATTTAGG
* *
53612928 GGTTTATGGTTTATGCTTTAAGGGTTTAGGGGATTTAGG
1 GGTTTATGGGTTATGCTTTAAGGGGTTAGGGGATTTAGG
53612967 GG-TTATGGGTTA
1 GGTTTATGGGTTA
53612979 GGAATTTGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 9 0.20
39 27 0.59
40 10 0.22
ACGTcount: A:0.18, C:0.02, G:0.40, T:0.40
Consensus pattern (39 bp):
GGTTTATGGGTTATGCTTTAAGGGGTTAGGGGATTTAGG
Found at i:53615823 original size:22 final size:23
Alignment explanation
Indices: 53615798--53615860 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
53615788 AATAAAATTA
53615798 TATTAAAATTATTATTA-AATAT
1 TATTAAAATTATTATTAGAATAT
*
53615820 TATTAATAATTA-TATTAGTAATGT
1 TATTAA-AATTATTATTAG-AATAT
53615844 TATT-AAATTATATATTA
1 TATTAAAATTAT-TATTA
53615861 TTTTATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 16 0.46
23 6 0.17
24 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
TATTAAAATTATTATTAGAATAT
Found at i:53615859 original size:12 final size:11
Alignment explanation
Indices: 53615792--53615872 Score: 50
Period size: 12 Copynumber: 7.5 Consensus size: 11
53615782 CTTAATAATA
53615792 AAATTA-TATT
1 AAATTATTATT
53615802 AAAATTATTATT
1 -AAATTATTATT
53615814 AAA-TATTATT
1 AAATTATTATT
53615824 AATAATTA-TATT
1 -A-AATTATTATT
*
53615836 AGTAA-TGTTATT
1 A--AATTATTATT
53615848 AAATTATATATT
1 AAATTAT-TATT
53615860 --ATT-TTATT
1 AAATTATTATT
53615868 AAATT
1 AAATT
53615873 GTACTTAACA
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
8 4 0.07
9 1 0.02
10 15 0.26
11 14 0.24
12 22 0.38
13 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
AAATTATTATT
Found at i:53616029 original size:9 final size:9
Alignment explanation
Indices: 53615995--53616447 Score: 180
Period size: 9 Copynumber: 52.8 Consensus size: 9
53615985 AACAACTCAA
53615995 AACTTACAT
1 AACTTACAT
* *
53616004 AACCTAAAT
1 AACTTACAT
*
53616013 AACCTACAT
1 AACTTACAT
53616022 AACTTACAT
1 AACTTACAT
*
53616031 AA--TACAA
1 AACTTACAT
*
53616038 AACTCACAT
1 AACTTACAT
*
53616047 AACTTAAAT
1 AACTTACAT
** *
53616056 CTCTTACAC
1 AACTTACAT
*
53616065 AACTTAAAT
1 AACTTACAT
53616074 AACCTT-CAT
1 AA-CTTACAT
*
53616083 AA--TACTTTT
1 AACTTAC--AT
53616092 AACTTACAT
1 AACTTACAT
53616101 AACTTACAT
1 AACTTACAT
*
53616110 AATACATA-AT
1 -A-ACTTACAT
53616120 AACTTAC--
1 AACTTACAT
53616127 AACTTACAT
1 AACTTACAT
53616136 AA--TACATCT
1 AACTTACA--T
53616145 AACTTAC--
1 AACTTACAT
53616152 AACTTACAT
1 AACTTACAT
53616161 AA--TACATCT
1 AACTTACA--T
53616170 AACTTAC--
1 AACTTACAT
*
53616177 AACTTACGT
1 AACTTACAT
53616186 AA--TACATTT
1 AACTTACA--T
53616195 AACTTAC--
1 AACTTACAT
53616202 AACTTACAT
1 AACTTACAT
53616211 AA--TACATTT
1 AACTTACA--T
53616220 AACTTACAT
1 AACTTACAT
*
53616229 AACTTACGT
1 AACTTACAT
* *
53616238 AA-TCCATCTT
1 AACT-TA-CAT
53616248 AACTTACAT
1 AACTTACAT
*
53616257 AATACATA-AT
1 -A-ACTTACAT
53616267 AACTTAC--
1 AACTTACAT
53616274 AACTTACAT
1 AACTTACAT
*
53616283 AACATACAT
1 AACTTACAT
* **
53616292 TACTTTGAT
1 AACTTACAT
53616301 AACTTACAT
1 AACTTACAT
53616310 AAC-T---T
1 AACTTACAT
53616315 -ACTTACAT
1 AACTTACAT
53616323 AACTTACAT
1 AACTTACAT
53616332 AACTTACAT
1 AACTTACAT
*
53616341 AACTAACAT
1 AACTTACAT
* *
53616350 TA--TACAC
1 AACTTACAT
53616357 AACTTACAT
1 AACTTACAT
53616366 AA--TACAT
1 AACTTACAT
*
53616373 TACTTACAT
1 AACTTACAT
53616382 AACTTAAAGCAT
1 AACTT--A-CAT
53616394 AA--TA-AT
1 AACTTACAT
53616400 AACTTACAT
1 AACTTACAT
*
53616409 AA--TACAC
1 AACTTACAT
53616416 AACTTACAT
1 AACTTACAT
* *
53616425 AGCTTACAC
1 AACTTACAT
53616434 AA--TACAT
1 AACTTACAT
53616441 AACTTAC
1 AACTTAC
53616448 CCGTGCAATT
Statistics
Matches: 330, Mismatches: 52, Indels: 124
0.65 0.10 0.25
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
6 5 0.02
7 79 0.24
8 14 0.04
9 182 0.55
10 15 0.05
11 26 0.08
12 5 0.02
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:53616069 original size:43 final size:43
Alignment explanation
Indices: 53615992--53616075 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
53615982 CTGAACAACT
* * *
53615992 CAAAACTTACATAACCTAAATAACCTACATAACTTACATAATA
1 CAAAACTCACATAACCTAAATAACCTACACAACTTAAATAATA
* ** *
53616035 CAAAACTCACATAACTTAAATCTCTTACACAACTTAAATAA
1 CAAAACTCACATAACCTAAATAACCTACACAACTTAAATAA
53616076 CCTTCATAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (43 bp):
CAAAACTCACATAACCTAAATAACCTACACAACTTAAATAATA
Found at i:53616252 original size:19 final size:19
Alignment explanation
Indices: 53616227--53616274 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
53616217 TTTAACTTAC
* * *
53616227 ATAACTTACGTAATCCATC
1 ATAACTTACATAATACATA
*
53616246 TTAACTTACATAATACATA
1 ATAACTTACATAATACATA
53616265 ATAACTTACA
1 ATAACTTACA
53616275 ACTTACATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:53616318 original size:13 final size:13
Alignment explanation
Indices: 53616302--53616329 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53616292 TACTTTGATA
53616302 ACTTACATAACTT
1 ACTTACATAACTT
53616315 ACTTACATAACTT
1 ACTTACATAACTT
53616328 AC
1 AC
53616330 ATAACTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTTACATAACTT
Found at i:53616385 original size:25 final size:26
Alignment explanation
Indices: 53616065--53616410 Score: 263
Period size: 25 Copynumber: 13.4 Consensus size: 26
53616055 TCTCTTACAC
* *
53616065 AACTTAAATAACCTT-CATAATACTTTT
1 AACTTACATAA-CTTACATAATAC-ATT
53616092 AACTTACATAACTTACATAATACATAAT
1 AACTTACATAACTTACATAATACAT--T
53616120 AACTTAC--AACTTACATAATACATCT
1 AACTTACATAACTTACATAATACAT-T
53616145 AACTTAC--AACTTACATAATACATCT
1 AACTTACATAACTTACATAATACAT-T
*
53616170 AACTTAC--AACTTACGTAATACATTT
1 AACTTACATAACTTACATAATACA-TT
53616195 AACTTAC--AACTTACATAATACATTT
1 AACTTACATAACTTACATAATACA-TT
* *
53616220 AACTTACATAACTTACGTAATCCATCTT
1 AACTTACATAACTTACATAATACA--TT
53616248 AACTTACATAA--TACATAATA-ACTT
1 AACTTACATAACTTACATAATACA-TT
* *
53616272 ACAACTTACATAACATACAT--TACTTTGAT
1 --AACTTACATAACTTACATAATAC-AT--T
53616301 AACTTACATAACTTAC-T--TACA-T
1 AACTTACATAACTTACATAATACATT
53616323 AACTTACATAACTTACATAACTAACATT
1 AACTTACATAACTTACATAA-T-ACATT
*
53616351 -A--TACACAACTTACATAATACATT
1 AACTTACATAACTTACATAATACATT
53616374 -ACTTACATAACTTAAAGCATAATA-A-T
1 AACTTACATAACTT--A-CATAATACATT
53616400 AACTTACATAA
1 AACTTACATAA
53616411 TACACAACTT
Statistics
Matches: 277, Mismatches: 15, Indels: 54
0.80 0.04 0.16
Matches are distributed among these distances:
22 17 0.06
23 7 0.03
24 4 0.01
25 104 0.38
26 47 0.17
27 63 0.23
28 34 0.12
29 1 0.00
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.34
Consensus pattern (26 bp):
AACTTACATAACTTACATAATACATT
Found at i:53616402 original size:59 final size:56
Alignment explanation
Indices: 53616301--53616425 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 56
53616291 TTACTTTGAT
*
53616301 AACTTACAT-AACTTACTTACATAACTTACATAACTTACATAACTAACATTATACAC
1 AACTTACATAAACTTACTTACATAACTTACATAAC-TACATAACTAACATAATACAC
*
53616357 AACTTACATAATACATTACTTACATAACTTAAAGCATAA-TA-ATAACTTACATAATACAC
1 AACTTACATAA-AC-TTACTTACATAACTT--A-CATAACTACATAACTAACATAATACAC
53616416 AACTTACATA
1 AACTTACATA
53616426 GCTTACACAA
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
56 9 0.15
57 1 0.02
58 2 0.03
59 41 0.67
60 2 0.03
61 1 0.02
62 5 0.08
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (56 bp):
AACTTACATAAACTTACTTACATAACTTACATAACTACATAACTAACATAATACAC
Found at i:53616404 original size:43 final size:43
Alignment explanation
Indices: 53616315--53616447 Score: 141
Period size: 43 Copynumber: 3.1 Consensus size: 43
53616305 TACATAACTT
*
53616315 ACTTACATAACTTACATAACTTACATAAC-T-AACATTATACACA
1 ACTTACATAA--TACATAACTTACATAACTTAAACATAATACACA
* *
53616358 ACTTACATAATACATTACTTACATAACTTAAAGCATAATA-ATA
1 ACTTACATAATACATAACTTACATAACTTAAA-CATAATACACA
* * * *
53616401 ACTTACATAATACACAACTTACATAGCTT--ACACAATACATA
1 ACTTACATAATACATAACTTACATAACTTAAACATAATACACA
53616442 ACTTAC
1 ACTTAC
53616448 CCGTGCAATT
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
40 6 0.08
41 26 0.33
42 1 0.01
43 40 0.51
44 6 0.08
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (43 bp):
ACTTACATAATACATAACTTACATAACTTAAACATAATACACA
Found at i:53621942 original size:66 final size:65
Alignment explanation
Indices: 53621834--53622004 Score: 200
Period size: 66 Copynumber: 2.6 Consensus size: 65
53621824 GAGCAAATTA
* * * * *
53621834 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAAAG-AAGATATGAAGAAATCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAG-TATGAAGAAATCCA
53621898 G
65 G
* *
53621899 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAAATCCA
53621964 G
65 G
* * * * *
53621965 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
53622005 CGGCAGCGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 86 0.95
67 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAAATCCAG
Found at i:53622002 original size:21 final size:21
Alignment explanation
Indices: 53621976--53622019 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
53621966 AGCAGCTTAG
*
53621976 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
*
53621997 AGCAGAGGCGGCAGCGAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
53622018 AG
1 AG
53622020 TACAGGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.43, T:0.02
Consensus pattern (21 bp):
AGCAGAGGCGGCAGCAAGAGA
Found at i:53622026 original size:21 final size:21
Alignment explanation
Indices: 53621983--53622026 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
53621973 TAGAGCAGAT
*
53621983 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAGCAAGAGAAGCACAG
* *
53622004 GCGGCAGCGAGAGAAGTACAG
1 GCGGCAGCAAGAGAAGCACAG
53622025 GC
1 GC
53622027 TGCTAAGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.43, T:0.02
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGCACAG
Found at i:53622046 original size:42 final size:42
Alignment explanation
Indices: 53621995--53622087 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
53621985 GGCAGCAAGA
**
53621995 GAAGCAGAGGCGGCAGCGAGAGAAGTACAGGCTGCTA-AGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTGC-AGAGAGG
* * * *
53622037 GAAGCAGAGGCTAAAGCGAGGGAAGTAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTGCAGAGAGG
53622079 GAAGCAGAG
1 GAAGCAGAG
53622088 CAGCGTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.06
Consensus pattern (42 bp):
GAAGCAGAGGCGAAAGCGAGAGAAGTACAGGCTGCAGAGAGG
Found at i:53622047 original size:21 final size:20
Alignment explanation
Indices: 53621995--53622087 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 20
53621985 GGCAGCAAGA
* * *
53621995 GAAGCAGAGGCGGCAGCGAGA
1 GAAGCAGAGGCTGCA-AGAGG
* *
53622016 GAAGTACAGGCTGCTAAGAGG
1 GAAGCAGAGGCTGC-AAGAGG
*
53622037 GAAGCAGAGGCT-AAAGCGAGG
1 GAAGCAGAGGCTGCAA--GAGG
* *
53622058 GAAGTAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTGCA-AGAGG
53622079 GAAGCAGAG
1 GAAGCAGAG
53622088 CAGCGTCAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
19 2 0.04
21 51 0.93
22 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.06
Consensus pattern (20 bp):
GAAGCAGAGGCTGCAAGAGG
Found at i:53622443 original size:43 final size:43
Alignment explanation
Indices: 53622382--53622470 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
53622372 NNNNNTTTAC
*
53622382 AAGACCCTGATCTATAGCGGCACTTTTACCAAAAACGCCGCTA
1 AAGACCCTGATCTATAGCGGCACTTATACCAAAAACGCCGCTA
* *
53622425 AAGACCCT-AGTCTATAGCGGCGCTTATACCAAAAACGCCGTTA
1 AAGACCCTGA-TCTATAGCGGCACTTATACCAAAAACGCCGCTA
53622468 AAG
1 AAG
53622471 GTATTACTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 41 0.98
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (43 bp):
AAGACCCTGATCTATAGCGGCACTTATACCAAAAACGCCGCTA
Found at i:53622487 original size:43 final size:42
Alignment explanation
Indices: 53622440--53622531 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
53622430 CCTAGTCTAT
* *
53622440 AGCGGCGCTTATACCAAAAACGCCGTTAAAGGTATTACTCTTC
1 AGCGGCGCTTATA-CAAAAACGCCGGTAAAGCTATTACTCTTC
* * * *
53622483 AGCGGCGCTTCTACTAAAGCGCCGGTAAAGCTCTTACTCTTC
1 AGCGGCGCTTATACAAAAACGCCGGTAAAGCTATTACTCTTC
53622525 AGCGGCG
1 AGCGGCG
53622532 TTTGTGATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 31 0.72
43 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (42 bp):
AGCGGCGCTTATACAAAAACGCCGGTAAAGCTATTACTCTTC
Found at i:53622520 original size:42 final size:43
Alignment explanation
Indices: 53622397--53622531 Score: 123
Period size: 43 Copynumber: 3.2 Consensus size: 43
53622387 CCTGATCTAT
* * * ** *
53622397 AGCGGCACTTTTACCAAAAACGCCGCTAAAGAC-CCTAGTCTAT-
1 AGCGGCGCTTATACCAAAAACGCCGGTAAAG-CTATTACTCT-TC
* *
53622440 AGCGGCGCTTATACCAAAAACGCCGTTAAAGGTATTACTCTTC
1 AGCGGCGCTTATACCAAAAACGCCGGTAAAGCTATTACTCTTC
* * * *
53622483 AGCGGCGCTTCTA-CTAAAGCGCCGGTAAAGCTCTTACTCTTC
1 AGCGGCGCTTATACCAAAAACGCCGGTAAAGCTATTACTCTTC
53622525 AGCGGCG
1 AGCGGCG
53622532 TTTGTGATAT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
42 32 0.42
43 45 0.58
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (43 bp):
AGCGGCGCTTATACCAAAAACGCCGGTAAAGCTATTACTCTTC
Found at i:53622656 original size:22 final size:22
Alignment explanation
Indices: 53622624--53622666 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53622614 CTGCGACGCT
*
53622624 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
53622646 AAAAAGTGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
53622667 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:53627821 original size:83 final size:83
Alignment explanation
Indices: 53627682--53627842 Score: 313
Period size: 83 Copynumber: 1.9 Consensus size: 83
53627672 CTTCGCATAT
53627682 ACAACTCCCACCCCAAACACAGATACAAAATTAATAGATTTAACATGCTTAACATGCTCGTATAC
1 ACAACTCCCACCCCAAACACAGATACAAAATTAATAGATTTAACATGCTTAACATGCTCGTATAC
53627747 AGATAACATAATACTTAC
66 AGATAACATAATACTTAC
*
53627765 ACAACTCCCACCCCAAACACAGATACAGAATTAATAGATTTAACATGCTTAACATGCTCGTATAC
1 ACAACTCCCACCCCAAACACAGATACAAAATTAATAGATTTAACATGCTTAACATGCTCGTATAC
53627830 AGATAACATAATA
66 AGATAACATAATA
53627843 TTTAAATAGT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.24
Consensus pattern (83 bp):
ACAACTCCCACCCCAAACACAGATACAAAATTAATAGATTTAACATGCTTAACATGCTCGTATAC
AGATAACATAATACTTAC
Found at i:53632262 original size:2 final size:2
Alignment explanation
Indices: 53632255--53632285 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53632245 TCCCTTTCAC
53632255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53632286 GTAAGTGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53634692 original size:26 final size:26
Alignment explanation
Indices: 53634656--53634706 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
53634646 ACATATTTTC
* *
53634656 TCAAAATTTTACCAGTGGTAAAATTA
1 TCAAAAATTTACCAGAGGTAAAATTA
* *
53634682 TCAAAAATTTATCGGAGGTAAAATT
1 TCAAAAATTTACCAGAGGTAAAATT
53634707 GTTAAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (26 bp):
TCAAAAATTTACCAGAGGTAAAATTA
Found at i:53634713 original size:26 final size:26
Alignment explanation
Indices: 53634672--53634731 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
53634662 TTTTACCAGT
53634672 GGTAAAATTATCAAAAATTTATCGGA
1 GGTAAAATTATCAAAAATTTATCGGA
* * * * *
53634698 GGTAAAATTGTTAAAATTTTATTGGG
1 GGTAAAATTATCAAAAATTTATCGGA
53634724 GGTAAAAT
1 GGTAAAAT
53634732 AGGGATGAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (26 bp):
GGTAAAATTATCAAAAATTTATCGGA
Found at i:53642404 original size:18 final size:18
Alignment explanation
Indices: 53642371--53642423 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
53642361 ATTCACCTAA
*
53642371 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
53642390 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
*
53642408 ACCCAACCCAATCCAA
1 ACCCAACCCAACCCAA
53642424 TCAAGACTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:53642411 original size:13 final size:13
Alignment explanation
Indices: 53642395--53642419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53642385 CAAGTATCCA
53642395 ACCCAACCCAATT
1 ACCCAACCCAATT
53642408 ACCCAACCCAAT
1 ACCCAACCCAAT
53642420 CCAATCAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:53642453 original size:17 final size:17
Alignment explanation
Indices: 53642431--53642491 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
53642421 CAATCAAGAC
53642431 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
53642448 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
53642467 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
53642485 TTATGTA
1 TTATGTA
53642492 GTGATTCAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 16 0.48
18 4 0.12
19 4 0.12
20 9 0.27
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:53642476 original size:37 final size:37
Alignment explanation
Indices: 53642426--53642500 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
53642416 CAATCCAATC
53642426 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
53642463 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
53642500 A
1 A
53642501 TTCGGTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.45
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:53642513 original size:9 final size:9
Alignment explanation
Indices: 53642499--53642538 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
53642489 GTAGTGATTC
53642499 AATTCGGTT
1 AATTCGGTT
*
53642508 AATTCGGGT
1 AATTCGGTT
53642517 AATTCGGTT
1 AATTCGGTT
53642526 AATTCGGTT
1 AATTCGGTT
53642535 AATT
1 AATT
53642539 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:53660294 original size:41 final size:41
Alignment explanation
Indices: 53660228--53660422 Score: 189
Period size: 41 Copynumber: 4.8 Consensus size: 41
53660218 TTTTAAACCT
** *
53660228 TTAGCGGTATTTTTATCTAAGCGCCGCTAATTCTCGGATCC
1 TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATCC
* * * *
53660269 TTCGCAGCGTTTTTATCTAAGCGCCGCTAATGCTCGGGTCT
1 TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATCC
* * *
53660310 TTAGCGGTGTTTTTATCTGAA-CGCTGCTAGTGCTCTGG--CC
1 TTAGCGGCGTTTTTATCT-AAGCGCCGCTAATGCTC-GGATCC
* * * *
53660350 TTTGGCGGCATTTTTATATAAGCGCCGCTAATGCTCGGATCT
1 -TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATCC
* * *
53660392 TTAGCGGCGTTTTTAACTGAGCGCCACTAAT
1 TTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
53660423 TCTCTTGTCT
Statistics
Matches: 122, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
40 5 0.04
41 112 0.92
42 5 0.04
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (41 bp):
TTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGATCC
Found at i:53660453 original size:82 final size:82
Alignment explanation
Indices: 53660286--53660464 Score: 214
Period size: 82 Copynumber: 2.2 Consensus size: 82
53660276 CGTTTTTATC
* * * ** *
53660286 TAAGCGCCGCTAATGCTCGGGTCTTTAGCGGTGTTTTTATCTGAACGCTGCTAGTGCTCTGGCCT
1 TAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAACGCCACTAATGCTCTGGCCT
** * *
53660351 TTGGCGGCATTTTTATA
66 TCAGCGGCATTTGTAGA
* * * *
53660368 TAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAGCGCCACTAATTCTCTTGTCT
1 TAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAACGCCACTAATGCTCTGGCCT
* *
53660433 TCAGTGGCGTTTGTAGA
66 TCAGCGGCATTTGTAGA
53660450 TAAGCGCCGCTAATG
1 TAAGCGCCGCTAATG
53660465 TATTTACCTT
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (82 bp):
TAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGAACGCCACTAATGCTCTGGCCT
TCAGCGGCATTTGTAGA
Found at i:53660475 original size:123 final size:123
Alignment explanation
Indices: 53660224--53660487 Score: 280
Period size: 123 Copynumber: 2.1 Consensus size: 123
53660214 GATTTTTTAA
* * * * *
53660224 ACCTTTAGCGGTATTTTTATCTAAGCGCCGCTAATTCTCGGATCCTTCGCAGCGTTTTTATCTAA
1 ACCTTTAGCGGCATTTTTATATAAGCGCCGCTAATGCTCGGATCCTTAGCAGCGTTTTTAACTAA
* * * * ** * *
53660289 GCGCCGCTAATGCTCGGGTCTTTAGCGGTGTTTTTATCTGAACGCTGCTAGTGCTCTG
66 GCGCCACTAATGCTCGGGTCTTCAGCGGCGTTTGTAGATGAACGCCGCTAATGCTCTG
* * * * *
53660347 GCCTTTGGCGGCATTTTTATATAAGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAACTGA
1 ACCTTTAGCGGCATTTTTATATAAGCGCCGCTAATGCTCGGATCCTTAGCAGCGTTTTTAACTAA
* ** * * *
53660412 GCGCCACTAATTCTCTTGTCTTCAGTGGCGTTTGTAGAT-AAGCGCCGCTAATG-TATTT
66 GCGCCACTAATGCTCGGGTCTTCAGCGGCGTTTGTAGATGAA-CGCCGCTAATGCT-CTG
53660470 ACCTTTAGCGGCATTTTT
1 ACCTTTAGCGGCATTTTT
53660488 GCCGAAGCGC
Statistics
Matches: 113, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
122 3 0.03
123 110 0.97
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (123 bp):
ACCTTTAGCGGCATTTTTATATAAGCGCCGCTAATGCTCGGATCCTTAGCAGCGTTTTTAACTAA
GCGCCACTAATGCTCGGGTCTTCAGCGGCGTTTGTAGATGAACGCCGCTAATGCTCTG
Found at i:53661816 original size:37 final size:37
Alignment explanation
Indices: 53661761--53661831 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
53661751 AAATTTAATG
* *
53661761 TTTAGGGGTTAGGGGATTTAGGGGTTAAGGGTTATGC
1 TTTAAGGGTTAGGGGATTTAGGGGTAAAGGGTTATGC
*
53661798 TTTAAGGGTTATGGGATTTAGGGGTAAAGGGTTA
1 TTTAAGGGTTAGGGGATTTAGGGGTAAAGGGTTA
53661832 GGGGGTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.01, G:0.41, T:0.35
Consensus pattern (37 bp):
TTTAAGGGTTAGGGGATTTAGGGGTAAAGGGTTATGC
Found at i:53664247 original size:14 final size:14
Alignment explanation
Indices: 53664228--53664254 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53664218 CATGATTTCT
53664228 TACATGTCTGTTCC
1 TACATGTCTGTTCC
53664242 TACATGTCTGTTC
1 TACATGTCTGTTC
53664255 TGCTTTGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (14 bp):
TACATGTCTGTTCC
Found at i:53669373 original size:66 final size:65
Alignment explanation
Indices: 53669267--53669436 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
53669257 GAGCAAATTA
* * * *
53669267 CACAACTTAAAGCAGAGGCAACA-TGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACCCCA
53669330 G
65 G
*
53669331 CTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACCCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACCCCA
53669396 G
65 G
* * * *
53669397 CAGCAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
53669437 CGGCAGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
64 1 0.01
65 21 0.23
66 67 0.72
67 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.12
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACCCCAG
Found at i:53669464 original size:42 final size:42
Alignment explanation
Indices: 53669418--53669519 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
53669408 AGCAGATGCG
* * * *
53669418 GCAGCAAGAGAAGCAGAGGCGGCAGCGAGAGAAGTATAGGCT
1 GCAGCGAGGGAAGCAGAGGCGACAGCGAGAGAAGTAGAGGCT
* * *
53669460 GCAGCGAGGGAAGCAGAGGCTATAGCGAGCGAAGTAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCGACAGCGAGAGAAGTAGAGGCT
53669502 GCAGCGAGGGAAGCAGAG
1 GCAGCGAGGGAAGCAGAG
53669520 CAGCGTCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.43, T:0.07
Consensus pattern (42 bp):
GCAGCGAGGGAAGCAGAGGCGACAGCGAGAGAAGTAGAGGCT
Found at i:53669480 original size:21 final size:21
Alignment explanation
Indices: 53669407--53669519 Score: 118
Period size: 21 Copynumber: 5.4 Consensus size: 21
53669397 CAGCAGCTTA
* * *
53669407 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGAG
*
53669428 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
* * *
53669449 AAGTATAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
** *
53669470 AAGCAGAGGCTATAGCGAGCG
1 AAGCAGAGGCTGCAGCGAGAG
* *
53669491 AAGTAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
53669512 AAGCAGAG
1 AAGCAGAG
53669520 CAGCGTCAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.34, C:0.17, G:0.42, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:53669880 original size:43 final size:43
Alignment explanation
Indices: 53669827--53670031 Score: 214
Period size: 43 Copynumber: 4.8 Consensus size: 43
53669817 ATCTGCCAAA
* * * ** *
53669827 TTTAGTGGCGTTTTTGGTAAAAGCATCGCTAAATATAAGGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATAAGGGTC
* * * *
53669870 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATAAGGGTC
* * * *
53669913 TTTAGCAGCGTTTGTGGGGAAAGCGCCGCTAAAGATTAGGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATAAGGGTC
* *** *
53669956 TTTAGTGGCGTTTGTGGTCGAAGCGCCGCTAGAGATCAA-GGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAT-AAGGGTC
*
53669999 TTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
53670032 TACCCTAATC
Statistics
Matches: 131, Mismatches: 30, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
43 130 0.99
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATAAGGGTC
Found at i:53669972 original size:86 final size:86
Alignment explanation
Indices: 53669834--53670031 Score: 243
Period size: 86 Copynumber: 2.3 Consensus size: 86
53669824 AAATTTAGTG
* * ** *
53669834 GCGTTTTTGGTAAAAGCATCGCTAAATATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCAC
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCAC
*
53669899 TAAAGATCATGGTCTTTAGCA
66 TAAAGATCAAGGTCTTTAGCA
* * * * *** *
53669920 GCGTTTGTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCGAAGCGCCGC
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCAC
* * *
53669985 TAGAGATCAAGGTCTTTTGCG
66 TAAAGATCAAGGTCTTTAGCA
53670006 GCGTTTGTGGGAAAAGCGCCGCTAAA
1 GCGTTTGTGGGAAAAGCGCCGCTAAA
53670032 TACCCTAATC
Statistics
Matches: 94, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 94 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (86 bp):
GCGTTTGTGGGAAAAGCGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCAC
TAAAGATCAAGGTCTTTAGCA
Found at i:53670044 original size:43 final size:43
Alignment explanation
Indices: 53669997--53670140 Score: 182
Period size: 43 Copynumber: 3.3 Consensus size: 43
53669987 GAGATCAAGG
* * * * * *
53669997 TCTTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAATACCCTAA
1 TCTTTAGCGGCGCTTGTCGCAAAAACGCCGCTAAATACCCTGA
* *
53670040 TCTTTCGCGGCGCTTGTCGCAAAAACGCAGCTAAATACCCTGA
1 TCTTTAGCGGCGCTTGTCGCAAAAACGCCGCTAAATACCCTGA
* *
53670083 TCTTTAGCAGCGCTTCTCGCAAAAACGCCGCTAAAGT-CCCTGA
1 TCTTTAGCGGCGCTTGTCGCAAAAACGCCGCTAAA-TACCCTGA
53670126 TCTTTAGCGGCGCTT
1 TCTTTAGCGGCGCTT
53670141 CCACTAAAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 87 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTGTCGCAAAAACGCCGCTAAATACCCTGA
Found at i:53670141 original size:43 final size:43
Alignment explanation
Indices: 53670017--53670159 Score: 182
Period size: 43 Copynumber: 3.3 Consensus size: 43
53670007 CGTTTGTGGG
* * * *
53670017 AAAAGCGCCGCTAAATACCCTAATCTTTCGCGGCGCTTGTCGC
1 AAAAACGCCGCTAAATACCCTGATCTTTAGCGGCGCTTCTCGC
* *
53670060 AAAAACGCAGCTAAATACCCTGATCTTTAGCAGCGCTTCTCGC
1 AAAAACGCCGCTAAATACCCTGATCTTTAGCGGCGCTTCTCGC
*
53670103 AAAAACGCCGCTAAAGT-CCCTGATCTTTAGCGGCGCTTC-CAC
1 AAAAACGCCGCTAAA-TACCCTGATCTTTAGCGGCGCTTCTCGC
* *
53670145 TAAAGCGCCGCTAAA
1 AAAAACGCCGCTAAA
53670160 GGTCTTAGTC
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 15 0.17
43 72 0.82
44 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAATACCCTGATCTTTAGCGGCGCTTCTCGC
Found at i:53670358 original size:31 final size:29
Alignment explanation
Indices: 53670290--53670362 Score: 112
Period size: 28 Copynumber: 2.5 Consensus size: 29
53670280 GGCGCTTTTC
53670290 AAAGCGCCGCTAAAAGTATTTGCGGCGCT
1 AAAGCGCCGCTAAAAGTATTTGCGGCGCT
*
53670319 -TAGCGCCGCTAAAAGTATTTGCGGCGCT
1 AAAGCGCCGCTAAAAGTATTTGCGGCGCT
53670347 AAAAAGCGCCGCTAAA
1 --AAAGCGCCGCTAAA
53670363 GGCCTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 27 0.69
31 12 0.31
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (29 bp):
AAAGCGCCGCTAAAAGTATTTGCGGCGCT
Found at i:53670973 original size:23 final size:23
Alignment explanation
Indices: 53670943--53670986 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53670933 AGAATGATTA
53670943 TCCCATCTTGGGTCGTACTATTC
1 TCCCATCTTGGGTCGTACTATTC
* *
53670966 TCCCATCTTGGTTCTTACTAT
1 TCCCATCTTGGGTCGTACTAT
53670987 AATCTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.43
Consensus pattern (23 bp):
TCCCATCTTGGGTCGTACTATTC
Found at i:53680311 original size:18 final size:19
Alignment explanation
Indices: 53680288--53680329 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
53680278 TATTTTCAAA
53680288 TTAATTATA-AATAATTTT
1 TTAATTATATAATAATTTT
* *
53680306 TTAATTTTATTATAATTTT
1 TTAATTATATAATAATTTT
53680325 TTAAT
1 TTAAT
53680330 AAGTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATTATATAATAATTTT
Found at i:53685474 original size:24 final size:24
Alignment explanation
Indices: 53685446--53685518 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
53685436 AGTATAAAAG
53685446 TATATTGATGTTTGACCCATCAAT
1 TATATTGATGTTTGACCCATCAAT
* *
53685470 TATATTGATGTTTGACTCAACAAT
1 TATATTGATGTTTGACCCATCAAT
53685494 TATATTGATGTTTGACCCATCAAT
1 TATATTGATGTTTGACCCATCAAT
53685518 T
1 T
53685519 TTTTATACTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (24 bp):
TATATTGATGTTTGACCCATCAAT
Found at i:53687933 original size:35 final size:35
Alignment explanation
Indices: 53687887--53687962 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
53687877 GAAACGGAAG
53687887 AAACAAGAAGAAAAAAAAGTACAATTGTTCAAAAA
1 AAACAAGAAGAAAAAAAAGTACAATTGTTCAAAAA
*
53687922 AAACAAGAAGAAACAAAAGTACAATTGTTCAAAAA
1 AAACAAGAAGAAAAAAAAGTACAATTGTTCAAAAA
53687957 AAACAA
1 AAACAA
53687963 AAAAACGAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.13
Consensus pattern (35 bp):
AAACAAGAAGAAAAAAAAGTACAATTGTTCAAAAA
Found at i:53690453 original size:100 final size:99
Alignment explanation
Indices: 53690280--53690995 Score: 861
Period size: 100 Copynumber: 7.2 Consensus size: 99
53690270 TAACCATAGT
* * * * *
53690280 TTGCAATTTAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCC-AGGCGGTGCAGTGGGATAG
1 TTGCAA-TTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACAG
* * *
53690344 ATTGAAGCTACAACGGCGAATCTTATTTCCCTGACA
64 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
53690380 TTGCAATTAAGAAGATAGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAA-AAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
53690445 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
53690480 TTGCAATTAAAAGATTGAAGCTAAAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGAT
1 TTGCAATTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGAT
*
53690545 TGAAGCTACAACAGCAGATCTTACTTCCCTGACA
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
53690579 TTGCAATTAAGAAGATTGAAGCTACAACAGCAGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAA-AAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
53690644 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * *
53690679 TTGCAATTCAAAATATTGAAGCTACAACAGCGGATCTTATTTTCCTAGTGATGCAATGGAACAGA
1 TTGCAATT-AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* * *
53690744 TTGAAGTTACAACAGCGGATTTTGCTTCCC---C-
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * *
53690775 -GGCAGTTAAAAAGATTGAAGCTACAACAACAGATCTTACTTTCCTAGCTTTGCAGTGGAACAGA
1 TTGCAATT-AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* ** *
53690839 TTGAAGCTACAACAGCAGATCTCGCTTCCCCGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
** * * * ** * * ** *
53690874 TCACAACTCAAAACATTGAAGCCACAATGGCGAATCTTAC-TTCCCAGGCAATGCAGCGGAACAG
1 TTGCAA-TTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACAG
* * * * * * *
53690938 ATTGAAGCTACGATAGTGAATCTCATTTCCCCGACA
64 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
53690974 TTGCAAGTAAATAGATTGAAGC
1 TTGCAATTAAA-AGATTGAAGC
53690996 CACGATGGCG
Statistics
Matches: 538, Mismatches: 66, Indels: 24
0.86 0.11 0.04
Matches are distributed among these distances:
95 79 0.15
97 1 0.00
98 1 0.00
99 108 0.20
100 345 0.64
101 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (99 bp):
TTGCAATTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGAT
TGAAGCTACAACAGCGGATCTTACTTCCCTGACA
Found at i:53690627 original size:199 final size:200
Alignment explanation
Indices: 53690280--53690995 Score: 880
Period size: 199 Copynumber: 3.6 Consensus size: 200
53690270 TAACCATAGT
* * * * *
53690280 TTGCAATTTAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCC-AGGCGGTGCAGTGGGATAG
1 TTGCAACTTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGGCGATGCAGTGGAACAG
* * *
53690344 ATTGAAGCTACAACGGCGAATCTTATTTCCCTGACATTGCAATTAAGAAGATAGAAGCTACAACA
66 ATTGAAGCTACAACAGCG-ATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCTACAACA
*
53690409 GCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCC
130 GCAGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCC
53690474 CTGACA
195 CTGACA
* * *
53690480 TTGCAA-TTAAAAGATTGAAGCTAAAACAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAACAG
1 TTGCAACTTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGGCGATGCAGTGGAACAG
53690543 ATTGAAGCTACAACAGCAGATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCTACAACA
66 ATTGAAGCTACAACAGC-GATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCTACAACA
53690608 GCAGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCC
130 GCAGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCC
53690673 CTGACA
195 CTGACA
* * * * *
53690679 TTGCAA-TTCAAAATATTGAAGCTACAACAGCGGATCTTATTTTCCTA-GTGATGCAATGGAACA
1 TTGCAACTT-AAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGGCGATGCAGTGGAACA
* * * * * *
53690742 GATTGAAGTTACAACAGCGGATTTTGCTTCCC---C--GGCAGTTAAAAAGATTGAAGCTACAAC
65 GATTGAAGCTACAACAGC-GATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCTACAAC
* * * **
53690802 AACAGATCTTACTTTCCTAGCTTTGCAGTGGAACAGATTGAAGCTACAACAGCAGATCTCGCTTC
129 AGCAGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTC
*
53690867 CCCGACA
194 CCTGACA
** * * * ** * * *
53690874 TCACAACTCAAAACATTGAAGCCACAATGGCGAATCTTAC-TTCCCAGGCAATGCAGCGGAACAG
1 TTGCAACTTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGGCGATGCAGTGGAACAG
* * * * * * *
53690938 ATTGAAGCTACGATAGTGAATCTCATTTCCCCGACATTGCAAGTAA-ATAGATTGAAGC
66 ATTGAAGCTACAACAGCG-ATCTTACTTCCCTGACATTGCAATTAAGA-AGATTGAAGC
53690996 CACGATGGCG
Statistics
Matches: 450, Mismatches: 54, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
194 6 0.01
195 153 0.34
196 1 0.00
197 1 0.00
198 1 0.00
199 188 0.42
200 100 0.22
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (200 bp):
TTGCAACTTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGGCGATGCAGTGGAACAG
ATTGAAGCTACAACAGCGATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCTACAACAG
CAGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCC
TGACA
Found at i:53690858 original size:50 final size:50
Alignment explanation
Indices: 53690289--53690860 Score: 535
Period size: 50 Copynumber: 11.6 Consensus size: 50
53690279 TTTGCAATTT
* * **
53690289 AAAAGATTGAAGCTACAACGGCGAATCTTACTTTCC-AGGCGGTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTA-GCATTGCAGTGG
* * * * * *
53690339 GATAGATTGAAGCTACAACGGCGAATCTTA-TTTCCCT-GACATTGCAAT-T
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTT-CCTAG-CATTGCAGTGG
* *
53690388 AAGAAGATAGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGG
1 AA-AAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGG
* * * *
53690439 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAAT-T
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGG
* *
53690488 AAAAGATTGAAGCTAAAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGG
* * * * *
53690538 AACAGATTGAAGCTACAACAGCAGATCTTACTTCCCT-GACATTGCAAT-T
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGG
* *
53690587 AAGAAGATTGAAGCTACAACAGCAGATCTTACTTTCCTAGCGTTGCAGTGG
1 AA-AAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGG
* * * **
53690638 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAATTC
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGG
* * * *
53690688 AAAATATTGAAGCTACAACAGCGGATCTTATTTTCCTAGTGA-TGCAATGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGG
* * * * ** **
53690738 AACAGATTGAAGTTACAACAGCGGATTTTGC-TTCC---C-CGGCAGTTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGG
* * *
53690783 AAAAGATTGAAGCTACAACAACAGATCTTACTTTCCTAGCTTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGG
* *
53690833 AACAGATTGAAGCTACAACAGCAGATCT
1 AAAAGATTGAAGCTACAACAGCGGATCT
53690861 CGCTTCCCCG
Statistics
Matches: 424, Mismatches: 76, Indels: 44
0.78 0.14 0.08
Matches are distributed among these distances:
45 29 0.07
46 4 0.01
49 56 0.13
50 324 0.76
51 11 0.03
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (50 bp):
AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGG
Found at i:53690942 original size:50 final size:50
Alignment explanation
Indices: 53690888--53691017 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 50
53690878 AACTCAAAAC
* * *
53690888 ATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCAATGC-AGCGGAACAG
1 ATTGAAGCCACGATGGCGAATCTTACTTCCCAGACAATGCAAG-GAAACAG
* * * * * * * * *
53690938 ATTGAAGCTACGATAGTGAATCTCATTTCCCCGACATTGCAAGTAAATAG
1 ATTGAAGCCACGATGGCGAATCTTACTTCCCAGACAATGCAAGGAAACAG
53690988 ATTGAAGCCACGATGGCGAATCTTACTTCC
1 ATTGAAGCCACGATGGCGAATCTTACTTCC
53691018 TGAAATTGCA
Statistics
Matches: 62, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
50 60 0.97
51 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (50 bp):
ATTGAAGCCACGATGGCGAATCTTACTTCCCAGACAATGCAAGGAAACAG
Found at i:53691971 original size:5 final size:5
Alignment explanation
Indices: 53691961--53691994 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
53691951 TGCTTACTGT
53691961 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
53691995 TTAAAGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:53692018 original size:20 final size:19
Alignment explanation
Indices: 53691962--53692008 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
53691952 GCTTACTGTT
** *
53691962 TTTATTTTATTTTATTTTAT
1 TTTATTTTATTTT-TTAAAG
53691982 TTTATTTTATTTTTTAAAG
1 TTTATTTTATTTTTTAAAG
53692001 TTTATTTT
1 TTTATTTT
53692009 TCTTTGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTATTTTATTTTTTAAAG
Found at i:53695745 original size:10 final size:11
Alignment explanation
Indices: 53695725--53695749 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53695715 CCATGGTACC
53695725 TTTCTTTTTTT
1 TTTCTTTTTTT
53695736 TTTCTTTTTTT
1 TTTCTTTTTTT
53695747 TTT
1 TTT
53695750 ATTAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:53696238 original size:264 final size:263
Alignment explanation
Indices: 53695753--53696248 Score: 569
Period size: 264 Copynumber: 1.9 Consensus size: 263
53695743 TTTTTTTATT
* *
53695753 AAAATGATTAAATTTCAATGTTGATGTCTCTAATTTATCTAAATTTGAGATTTAATCTCAATACT
1 AAAATGATTAAATTTCAATGTTGA-GTCTCTAATTTATCTAAATTTGAAATTTAATCTCAACACT
** * * *
53695818 TTGATTTTTAACGTAATTTGGTCCCTATATTCTTATAATGTTATTAATCAGTCTAAATAGTTAAT
65 TCAATTTCTAACGTAATTTGATCACTATATTCTTATAATGTTATTAATCAGTCTAAATAGTTAAT
* *
53695883 ATCATCAACTTTTTGATTAAAACATTACGTTGTTATATATAATCTTAATACATTAAGAGTCTTAG
130 ATCATCAACTTTTTGATTAAAACATTACGTGGTTATATATAATCTTAATACACTAAGAGTCTTAG
* *
53695948 AAACTAACACGTGGTTTCCAATTTCTTTTAAGTTTGCGTACGTCTTACCTTTCTTTATGCAGTTT
195 AAACTAACAAGTGCTTTCCAATTTCTTTTAAGTTTGCGTACGTCTTACCTTTCTTTATGCAGTTT
53696013 TGGA
260 TGGA
* * *
53696017 AAAATGATTAAATTTCAATTTTG-GTCTC-ACTCTTATGCCTAAATTTGAAATTTAA-CTTCTAC
1 AAAATGATTAAATTTCAATGTTGAGTCTCTAAT-TTAT--CTAAATTTGAAATTTAATC-TCAAC
* * * * * *
53696079 ACTTCAATTTCTAATGTAATTTGATCATTGTATTTTTATATTGTTATTAATTAGT-TCAAATAGT
62 ACTTCAATTTCTAACGTAATTTGATCACTATATTCTTATAATGTTATTAATCAGTCT-AAATAGT
* * * * *
53696143 TAATATCATTAA-TTTTTCGATTAAAATATTATGTGGTTATATATAAT-TTGAATGTC-CTAAGG
126 TAATATCATCAACTTTTT-GATTAAAACATTACGTGGTTATATATAATCTT-AAT-ACACTAAGA
* * * *
53696205 GTCTTAGAGAC-AGATAAGTAGCTTT-CTATTTCTTTTAGGTTTGC
188 GTCTTAGAAACTA-ACAAGT-GCTTTCCAATTTCTTTTAAGTTTGC
53696249 CTTGCTGTAT
Statistics
Matches: 193, Mismatches: 29, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
261 2 0.01
262 9 0.05
263 10 0.05
264 167 0.87
265 5 0.03
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (263 bp):
AAAATGATTAAATTTCAATGTTGAGTCTCTAATTTATCTAAATTTGAAATTTAATCTCAACACTT
CAATTTCTAACGTAATTTGATCACTATATTCTTATAATGTTATTAATCAGTCTAAATAGTTAATA
TCATCAACTTTTTGATTAAAACATTACGTGGTTATATATAATCTTAATACACTAAGAGTCTTAGA
AACTAACAAGTGCTTTCCAATTTCTTTTAAGTTTGCGTACGTCTTACCTTTCTTTATGCAGTTTT
GGA
Found at i:53697732 original size:57 final size:57
Alignment explanation
Indices: 53697625--53697757 Score: 151
Period size: 56 Copynumber: 2.3 Consensus size: 57
53697615 GGTTTAATAA
* * * * * **
53697625 TTTTTTTAATTTAAATTAGACTCTGAATTTAATAATTATTCCGTATTGAGA-TTAAAC
1 TTTTTTT-ATTCAAGTTAGACTCTAAACTTAACAATTATTCCACATTGAGACTTAAAC
*
53697682 TTTTTTTATTCAAGTTAGACTCTAAACTTAACAATTGTTCTCACATTGAGACTTAAAC
1 TTTTTTTATTCAAGTTAGACTCTAAACTTAACAATTATTC-CACATTGAGACTTAAAC
* *
53697740 TTTTTTTGTCCAAGTTAG
1 TTTTTTTATTCAAGTTAG
53697758 TCCTTGGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 27 0.42
57 15 0.23
58 22 0.34
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (57 bp):
TTTTTTTATTCAAGTTAGACTCTAAACTTAACAATTATTCCACATTGAGACTTAAAC
Found at i:53697902 original size:31 final size:31
Alignment explanation
Indices: 53697838--53697904 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
53697828 CAATAAAAAA
* * **
53697838 TTCAAACCCCAATGTGGGAACAGTTGCTTAG
1 TTCAAACCCCAATGTGAGAACAATTGCCAAG
* *
53697869 TTCAAACCTCAATGTGAGAATAATTGCCAAG
1 TTCAAACCCCAATGTGAGAACAATTGCCAAG
53697900 TTCAA
1 TTCAA
53697905 GCCTTATTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (31 bp):
TTCAAACCCCAATGTGAGAACAATTGCCAAG
Found at i:53698220 original size:19 final size:19
Alignment explanation
Indices: 53698196--53698233 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53698186 TTATCAGTAT
53698196 TTATTTATAAATTTATTTA
1 TTATTTATAAATTTATTTA
* *
53698215 TTATTTATTATTTTATTTA
1 TTATTTATAAATTTATTTA
53698234 ATAATAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTATAAATTTATTTA
Found at i:53703451 original size:30 final size:29
Alignment explanation
Indices: 53703394--53703451 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
53703384 CCTTTTTACT
* *
53703394 TTTCCCTCAAAACTTTTACTCCTTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTCCCAC
53703423 TTTCCCCCAAAACTTTTACTCCCCTCCCA
1 TTTCCCCCAAAACTTTTACT-CCCTCCCA
53703452 ACCCCCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:53703458 original size:29 final size:28
Alignment explanation
Indices: 53703401--53703460 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
53703391 ACTTTTCCCT
* *
53703401 CAAAACTTTTACTCCTTCCCACTTTCCCC
1 CAAAACTTTTACTCCCTCCCAC-TCCCCC
*
53703430 CAAAACTTTTACTCCCCTCCCA-ACCCCC
1 CAAAACTTTTACT-CCCTCCCACTCCCCC
53703458 CAA
1 CAA
53703461 TCTACCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 13 0.48
30 7 0.26
ACGTcount: A:0.25, C:0.48, G:0.00, T:0.27
Consensus pattern (28 bp):
CAAAACTTTTACTCCCTCCCACTCCCCC
Found at i:53711145 original size:23 final size:23
Alignment explanation
Indices: 53711118--53711163 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
53711108 GAACTTCACA
*
53711118 ATTTTTCT-TAATTTGGTACTTT
1 ATTTTTTTATAATTTGGTACTTT
53711140 ATTTTTTTATAATTTGGTACTTT
1 ATTTTTTTATAATTTGGTACTTT
53711163 A
1 A
53711164 ACTTGATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.63
Consensus pattern (23 bp):
ATTTTTTTATAATTTGGTACTTT
Found at i:53711227 original size:60 final size:55
Alignment explanation
Indices: 53711120--53711251 Score: 133
Period size: 60 Copynumber: 2.3 Consensus size: 55
53711110 ACTTCACAAT
* * *
53711120 TTTTCTTAATTTGGTACTTTATTTTTTTATAATTTGGTACTTTAACTTGATGCTG
1 TTTTCTTAATTTGGTACTTAATTTTTTTATAATTTGATACTTGAACTTGATGCTG
**
53711175 TTTTC-TAATTTGGTACTTCAAATTTTTTTGAGTCCAATTTGATACTTGAACTTGACACT-
1 TTTTCTTAATTTGGTACTT--AATTTTTTT-A-T--AATTTGATACTTGAACTTGATGCTG
* *
53711234 CTTTCTTAATTTTGTACT
1 TTTTCTTAATTTGGTACT
53711252 AAACTTGTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
54 13 0.21
55 5 0.08
56 8 0.13
57 1 0.02
58 1 0.02
59 4 0.06
60 31 0.49
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (55 bp):
TTTTCTTAATTTGGTACTTAATTTTTTTATAATTTGATACTTGAACTTGATGCTG
Found at i:53721783 original size:22 final size:22
Alignment explanation
Indices: 53721748--53721789 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53721738 TCCAAAACAC
*
53721748 GGGAAAATGCCTTACATTTTTA
1 GGGAAAATACCTTACATTTTTA
* *
53721770 GGGAAAATATCTTACCTTTT
1 GGGAAAATACCTTACATTTT
53721790 CAATTTCCGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (22 bp):
GGGAAAATACCTTACATTTTTA
Found at i:53724242 original size:18 final size:18
Alignment explanation
Indices: 53724219--53724254 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53724209 CAATTAAACC
53724219 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
53724237 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
53724255 TAAATAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:53724311 original size:16 final size:18
Alignment explanation
Indices: 53724288--53724339 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
53724278 TCTAAACAAT
* *
53724288 TTAAAATATAAAAATTTA
1 TTAATATATATAAATTTA
53724306 TTAATATGTATATAAATTTA
1 TTAATA--TATATAAATTTA
*
53724326 TTAATATATGTAAA
1 TTAATATATATAAA
53724340 AACAACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.41
20 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTAATATATATAAATTTA
Found at i:53724337 original size:22 final size:20
Alignment explanation
Indices: 53724294--53724332 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53724284 CAATTTAAAA
53724294 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
53724314 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
53724333 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:53724453 original size:20 final size:20
Alignment explanation
Indices: 53724428--53724467 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53724418 AAATATTTTC
*
53724428 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTCCAGAAA
53724448 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
53724468 TCATTTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:53724469 original size:34 final size:33
Alignment explanation
Indices: 53724418--53724482 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
53724408 AAACACCAGA
53724418 AAATATTTTCAGTAAATCATTTTTCAGAAAAGT
1 AAATATTTTCAGTAAATCATTTTTCAGAAAAGT
*
53724451 AAATCATTTTCCAG-AAATCATTTTTCGGAAAA
1 AAAT-ATTTT-CAGTAAATCATTTTTCAGAAAA
53724483 CATTTTACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 22 0.76
35 3 0.10
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (33 bp):
AAATATTTTCAGTAAATCATTTTTCAGAAAAGT
Found at i:53728183 original size:3 final size:3
Alignment explanation
Indices: 53728169--53728228 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
53728159 TTTGCATTGC
* * * * *
53728169 CAT CAC CAT CAT CAT CAT CAT TAT CAC CAT CAC CAT CTT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
*
53728217 CAT CAT CTT CAT
1 CAT CAT CAT CAT
53728229 GTGAGAACCC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:53728198 original size:27 final size:27
Alignment explanation
Indices: 53728168--53728221 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
53728158 CTTTGCATTG
*
53728168 CCATCACCATCATCATCATCATTATCA
1 CCATCACCATCATCATCATCATCATCA
*
53728195 CCATCACCATCTTCATCATCATCATCA
1 CCATCACCATCATCATCATCATCATCA
53728222 TCTTCATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.30
Consensus pattern (27 bp):
CCATCACCATCATCATCATCATCATCA
Found at i:53732571 original size:13 final size:13
Alignment explanation
Indices: 53732553--53732578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53732543 AATATCTTTG
53732553 GTTTTTGTTGTTT
1 GTTTTTGTTGTTT
53732566 GTTTTTGTTGTTT
1 GTTTTTGTTGTTT
53732579 TTAATGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (13 bp):
GTTTTTGTTGTTT
Found at i:53735833 original size:2 final size:2
Alignment explanation
Indices: 53735826--53735860 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53735816 AATAAATGCG
53735826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53735861 GCATAGGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53736022 original size:2 final size:2
Alignment explanation
Indices: 53736015--53736093 Score: 88
Period size: 2 Copynumber: 40.0 Consensus size: 2
53736005 AATTCCAAGC
* * * * * * *
53736015 TA TA TA TA AA TA TA TA TG TA TA TA AA AA TA TA GA -A TA CA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53736056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53736094 AGTATACATG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (2 bp):
TA
Found at i:53740928 original size:16 final size:16
Alignment explanation
Indices: 53740907--53740938 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53740897 AGCGATTGGA
53740907 CTTTTACAATTTAGTC
1 CTTTTACAATTTAGTC
53740923 CTTTTACAATTTAGTC
1 CTTTTACAATTTAGTC
53740939 TCTGTACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (16 bp):
CTTTTACAATTTAGTC
Found at i:53741875 original size:16 final size:16
Alignment explanation
Indices: 53741856--53741889 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
53741846 TAAGGTTATG
53741856 AGAATTTAGGGTTCTT
1 AGAATTTAGGGTTCTT
*
53741872 AGAATTTAGGGTTTTT
1 AGAATTTAGGGTTCTT
53741888 AG
1 AG
53741890 GTCCGAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44
Consensus pattern (16 bp):
AGAATTTAGGGTTCTT
Found at i:53742243 original size:17 final size:18
Alignment explanation
Indices: 53742205--53742243 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
53742195 AAAAAATAAT
* *
53742205 AAAATTTTTATACACATT
1 AAAATTTTTATACAAATA
53742223 AAAATTTTT-TACAAATA
1 AAAATTTTTATACAAATA
53742240 AAAA
1 AAAA
53742244 GGTGAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTTTTATACAAATA
Found at i:53742887 original size:2 final size:2
Alignment explanation
Indices: 53742880--53742904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53742870 TTCTTAACTT
53742880 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
53742905 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:53752139 original size:4 final size:4
Alignment explanation
Indices: 53752132--53752161 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
53752122 ATATATATAT
*
53752132 ATAG ATAG ATAG ATAG ATAG ATAG AAAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
53752162 TTTAATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (4 bp):
ATAG
Found at i:53755728 original size:3 final size:3
Alignment explanation
Indices: 53755720--53755757 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
53755710 AATTGAGTCT
53755720 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53755758 TGAAGTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53759761 original size:4 final size:4
Alignment explanation
Indices: 53759752--53759797 Score: 67
Period size: 4 Copynumber: 11.5 Consensus size: 4
53759742 ATTAAAACTA
*
53759752 AAAT AAAT AAAT AAAT AAAAT AGA- AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
53759798 TAACAAGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 2 0.05
4 32 0.84
5 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:53768212 original size:20 final size:20
Alignment explanation
Indices: 53768184--53768227 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53768174 TTATTTGAAA
*
53768184 TTTAAATATCTTTTTTAA-TT
1 TTTAAATAT-TATTTTAACTT
*
53768204 TTTATATATTATTTTAACTT
1 TTTAAATATTATTTTAACTT
53768224 TTTA
1 TTTA
53768228 GATAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTAAATATTATTTTAACTT
Found at i:53768235 original size:21 final size:19
Alignment explanation
Indices: 53768196--53768236 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
53768186 TAAATATCTT
*
53768196 TTTTAATTTTTATATATTA
1 TTTTAATTTTTAGATATTA
53768215 TTTTAACTTTTTAGATAATTA
1 TTTTAA-TTTTTAGAT-ATTA
53768236 T
1 T
53768237 ATATATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTAATTTTTAGATATTA
Found at i:53770324 original size:25 final size:25
Alignment explanation
Indices: 53770268--53770329 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
53770258 ATTGAACTAA
*
53770268 TTAAATAA-TTAAATTTTATTAATT
1 TTAAATAATTTAAATTTTATGAATT
* *
53770292 TTATAATAATTTTAATTTTATGCATT
1 TTA-AATAATTTAAATTTTATGAATT
53770318 TTAAATAATTTA
1 TTAAATAATTTA
53770330 TTTAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 3 0.09
25 13 0.41
26 16 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAAATAATTTAAATTTTATGAATT
Found at i:53793823 original size:23 final size:23
Alignment explanation
Indices: 53793780--53793834 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
53793770 CCGGCCCGAT
*
53793780 TTTTAATAAAT-ACAAAAAAAATA
1 TTTTAA-AAATAAAAAAAAAAATA
53793803 TTTTAAAAATAAAAAATAAAAATA
1 TTTTAAAAATAAAAAA-AAAAATA
53793827 TTTTAAAA
1 TTTTAAAA
53793835 GTATTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 4 0.14
23 10 0.34
24 15 0.52
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TTTTAAAAATAAAAAAAAAAATA
Done.