Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_228.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2969030
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 66526 characters in sequence are not A, C, G, or T
File 7 of 8
Found at i:2498746 original size:23 final size:23
Alignment explanation
Indices: 2498714--2498766 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
2498704 TGCTGTTGCA
*
2498714 TTGCATAATGCTATCACAATTCC
1 TTGCACAATGCTATCACAATTCC
*
2498737 TTGCACAATGCTGTCACAATTCC
1 TTGCACAATGCTATCACAATTCC
2498760 TTGCACA
1 TTGCACA
2498767 CGTAGTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (23 bp):
TTGCACAATGCTATCACAATTCC
Found at i:2502297 original size:30 final size:31
Alignment explanation
Indices: 2502263--2502331 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
2502253 TTTCTAGAAG
*
2502263 AGGTATAACCTTCGCACTACCTTTT-CATGC
1 AGGTATAACCTTCACACTACCTTTTACATGC
* *
2502293 AGGTATAACCTTTACACTACCTTTTACATGG
1 AGGTATAACCTTCACACTACCTTTTACATGC
2502324 AGGTATAA
1 AGGTATAA
2502332 TCACCAATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 23 0.66
31 12 0.34
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (31 bp):
AGGTATAACCTTCACACTACCTTTTACATGC
Found at i:2504403 original size:23 final size:23
Alignment explanation
Indices: 2504377--2504428 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
2504367 ATATTAAAAG
*
2504377 TTTAT-ATATAATAATTATATTCC
1 TTTATAATATAAT-ATAATATTCC
*
2504400 TTTATAATATGATATAATATTCC
1 TTTATAATATAATATAATATTCC
2504423 TATTAT
1 T-TTAT
2504429 TTAAACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTATAATATAATATAATATTCC
Found at i:2519084 original size:12 final size:11
Alignment explanation
Indices: 2519057--2519090 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2519047 ACTATAGTTG
2519057 ATATATAAACA
1 ATATATAAACA
2519068 ATATATGAAACA
1 ATATAT-AAACA
*
2519080 TTATATAAACA
1 ATATATAAACA
2519091 CTACTACTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATATAAACA
Found at i:2519925 original size:15 final size:14
Alignment explanation
Indices: 2519911--2520055 Score: 70
Period size: 15 Copynumber: 10.0 Consensus size: 14
2519901 TCATTTTTTA
2519911 AATATTAATAATTT
1 AATATTAATAATTT
*
2519925 ATTATTTAATTAAATTATT
1 AATA-TTAA-T-AA-T-TT
*
2519944 AATAATTAATAATGTA
1 AAT-ATTAATAAT-TT
2519960 AATATTAAT-ATTT
1 AATATTAATAATTT
2519973 --TATT-ATAATTT
1 AATATTAATAATTT
*
2519984 AATCATTAATATTTT
1 AAT-ATTAATAATTT
*
2519999 AAATACTAAT-ATTT
1 -AATATTAATAATTT
*
2520013 --TATTTATAATTT
1 AATATTAATAATTT
* *
2520025 AATATTATTATGATTAA
1 AATATTA--ATAATT-T
2520042 AATATTAATAATTT
1 AATATTAATAATTT
2520056 TAATTAATTT
Statistics
Matches: 98, Mismatches: 15, Indels: 36
0.66 0.10 0.24
Matches are distributed among these distances:
10 2 0.02
11 13 0.13
12 4 0.04
13 2 0.02
14 15 0.15
15 26 0.27
16 14 0.14
17 11 0.11
18 2 0.02
19 8 0.08
20 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (14 bp):
AATATTAATAATTT
Found at i:2519986 original size:40 final size:41
Alignment explanation
Indices: 2519942--2520028 Score: 131
Period size: 40 Copynumber: 2.1 Consensus size: 41
2519932 AATTAAATTA
*
2519942 TTAATAATTAATAATGTAAATATTAATATTTTA-TTATAAT
1 TTAATAATTAATAATGTAAATACTAATATTTTATTTATAAT
* * *
2519982 TTAATCATTAATATTTTAAATACTAATATTTTATTTATAAT
1 TTAATAATTAATAATGTAAATACTAATATTTTATTTATAAT
2520023 TTAATA
1 TTAATA
2520029 TTATTATGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 29 0.71
41 12 0.29
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (41 bp):
TTAATAATTAATAATGTAAATACTAATATTTTATTTATAAT
Found at i:2520326 original size:16 final size:16
Alignment explanation
Indices: 2520307--2520337 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2520297 TATTATGATT
2520307 AAAATATTAATATTTG
1 AAAATATTAATATTTG
2520323 AAAATATTAATATTT
1 AAAATATTAATATTT
2520338 TATAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAAATATTAATATTTG
Found at i:2521498 original size:13 final size:13
Alignment explanation
Indices: 2521482--2521508 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2521472 TTGTATAATA
2521482 AAATATTATATTC
1 AAATATTATATTC
2521495 AAATATTATATTC
1 AAATATTATATTC
2521508 A
1 A
2521509 TGTCAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATATTATATTC
Found at i:2524153 original size:2 final size:2
Alignment explanation
Indices: 2524146--2524188 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2524136 TTTCTTTACA
*
2524146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2524188 A
1 A
2524189 GACATATGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2524403 original size:24 final size:25
Alignment explanation
Indices: 2524357--2524411 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
2524347 CATAGTGTCG
*
2524357 AAAAT-TTA-ATTCTCCATGCAAAA
1 AAAATATTATATTCTCCACGCAAAA
*
2524380 ATAATATTATATTCT-CACGCAAAA
1 AAAATATTATATTCTCCACGCAAAA
2524404 AAAATATT
1 AAAATATT
2524412 TTATGCAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 18 0.67
25 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.33
Consensus pattern (25 bp):
AAAATATTATATTCTCCACGCAAAA
Found at i:2526835 original size:19 final size:20
Alignment explanation
Indices: 2526794--2526835 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2526784 CAAAATATTT
* * *
2526794 CAAAATGGAGAAAAAACTTA
1 CAAAATGGAAAAAAAAATCA
2526814 CAAAA-GGAAAAAAAAATCA
1 CAAAATGGAAAAAAAAATCA
2526833 CAA
1 CAA
2526836 TGTTTGCCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.67, C:0.12, G:0.12, T:0.10
Consensus pattern (20 bp):
CAAAATGGAAAAAAAAATCA
Found at i:2533434 original size:27 final size:27
Alignment explanation
Indices: 2533393--2533445 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2533383 ATAAAACAAG
2533393 TTACTTCCATGGGAACAAGTGGTAGGA
1 TTACTTCCATGGGAACAAGTGGTAGGA
*
2533420 TTACTTCCACT-GGAACAAGTTGTAGG
1 TTACTTCCA-TGGGAACAAGTGGTAGG
2533446 GTTATACTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (27 bp):
TTACTTCCATGGGAACAAGTGGTAGGA
Found at i:2550074 original size:33 final size:32
Alignment explanation
Indices: 2550037--2550098 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
2550027 ATATATATTA
2550037 TTAAT-AAAAATTAAATTAATAAA-TTAAAATTTG
1 TTAATCAAAAA-TAAATT--TAAATTTAAAATTTG
2550070 TTAATCAAAAATAAATTTAAATTTAAAAT
1 TTAATCAAAAATAAATTTAAATTTAAAAT
2550099 CATAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 4 0.15
32 7 0.26
33 11 0.41
34 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (32 bp):
TTAATCAAAAATAAATTTAAATTTAAAATTTG
Found at i:2550394 original size:2 final size:2
Alignment explanation
Indices: 2550387--2550417 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2550377 TGATAAAGAA
*
2550387 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2550418 ATCTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2558639 original size:2 final size:2
Alignment explanation
Indices: 2558600--2558626 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2558590 TATACTTTCC
2558600 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2558627 AGTTTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2559841 original size:30 final size:27
Alignment explanation
Indices: 2559805--2559873 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
2559795 TTATTAATTG
*
2559805 TAAAAATTTATTTAATTAAAAATAAAAATA
1 TAAAAATTTATTAAATT--AAATAAAAA-A
* *
2559835 TAAAAATTAAATTAAATTTAATAAAAAA
1 TAAAAATT-TATTAAATTAAATAAAAAA
2559863 TAAAAATTTAT
1 TAAAAATTTAT
2559874 ATACATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.06
28 9 0.26
29 8 0.24
30 8 0.24
31 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAAAATTTATTAAATTAAATAAAAAA
Found at i:2566933 original size:2 final size:2
Alignment explanation
Indices: 2566921--2566963 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2566911 TAATTTCTCT
*
2566921 TA TA AA 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 TA TA
2566963 T
1 T
2566964 TACTGAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2580426 original size:2 final size:2
Alignment explanation
Indices: 2580419--2580449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2580409 ATTCTTAAGT
2580419 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
2580450 GAGACTATAT
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:2580826 original size:79 final size:79
Alignment explanation
Indices: 2580685--2580842 Score: 221
Period size: 79 Copynumber: 2.0 Consensus size: 79
2580675 GCAATGATAG
* * *
2580685 TGTTGTATAATTAGGTGGGGTAGGCATAATTGAGTAAGATAGAATATCATGAATCTCTCATCAGC
1 TGTTATATAATTAGGTGGGGTAAGCATAATTGAGTAAGATAGAATATCACGAATCTCTCATCAGC
*
2580750 ACACATATTGCATA
66 ACACATATTACATA
* *
2580764 TGTTATATAATTGGGTGGGGTAAGCATAATTG-GATAGGATAGAATATCACGAATCT-TACATCA
1 TGTTATATAATTAGGTGGGGTAAGCATAATTGAG-TAAGATAGAATATCACGAATCTCT-CATCA
*
2580827 GCGCACATATTACATA
64 GCACACATATTACATA
2580843 ATTAGATGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 2 0.03
79 68 0.97
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (79 bp):
TGTTATATAATTAGGTGGGGTAAGCATAATTGAGTAAGATAGAATATCACGAATCTCTCATCAGC
ACACATATTACATA
Found at i:2580865 original size:51 final size:51
Alignment explanation
Indices: 2580788--2580886 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
2580778 GTGGGGTAAG
* * *
2580788 CATAATTGGATAGGATAGAATATCACGAATCTTACATCAGCGCACATATTA
1 CATAATTAGATAGGATAGAATATCACGAATCTCACATCAGCACACATATTA
* * *
2580839 CATAATTAGATGGGATAGAATGTCACGAATCTCACATTAGCACACATA
1 CATAATTAGATAGGATAGAATATCACGAATCTCACATCAGCACACATA
2580887 AGGATTTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (51 bp):
CATAATTAGATAGGATAGAATATCACGAATCTCACATCAGCACACATATTA
Found at i:2584592 original size:45 final size:45
Alignment explanation
Indices: 2584543--2584640 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
2584533 CAACATGACG
* * * *
2584543 TGTAACAACCTAACCATGGTGTGTAACATATTTTTGTACATGGCA
1 TGTAACAACCTAACCATAGCGTATAACATATTTTTGTACATAGCA
* * ** * *
2584588 TGTAATAATCTAATTATAGCGTATAACATATTTTTGTATATAGCG
1 TGTAACAACCTAACCATAGCGTATAACATATTTTTGTACATAGCA
2584633 TGTAACAA
1 TGTAACAA
2584641 TAATATTTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (45 bp):
TGTAACAACCTAACCATAGCGTATAACATATTTTTGTACATAGCA
Found at i:2584639 original size:121 final size:121
Alignment explanation
Indices: 2584490--2584713 Score: 297
Period size: 121 Copynumber: 1.9 Consensus size: 121
2584480 TCATGACGTG
* * * *
2584490 TAACATGTTTTTATACATGGCGTATAACAA-AAGTATTTTTTTTCAACATGACGTGTAACAACCT
1 TAACATATTTTTATACATAGCGTATAACAATAA-TATTTTTCTTCAACATGACATGTAACAACCT
* * * *
2584554 AACCATGGTGTGTAACATATTTTTGTACATGGCATGTAATAATCTAATTATAGCGTA
65 AACCATAGCGTGTAACATATTTTTGCACATAGCATGTAATAATCTAATTATAGCGTA
* * * * * *
2584611 TAACATATTTTTGTATATAGCGTGTAACAATAATATTTTTCTTCAATATGGCATGTAACAACTTA
1 TAACATATTTTTATACATAGCGTATAACAATAATATTTTTCTTCAACATGACATGTAACAACCTA
*
2584676 ACCATAGCGTGTAACATATTTTTGCACATAGCGTGTAA
66 ACCATAGCGTGTAACATATTTTTGCACATAGCATGTAA
2584714 CATCATGGTG
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
121 85 0.98
122 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (121 bp):
TAACATATTTTTATACATAGCGTATAACAATAATATTTTTCTTCAACATGACATGTAACAACCTA
ACCATAGCGTGTAACATATTTTTGCACATAGCATGTAATAATCTAATTATAGCGTA
Found at i:2594415 original size:26 final size:27
Alignment explanation
Indices: 2594367--2594418 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2594357 GTAACAACTT
* *
2594367 TTTTCTTTAAAATGCTATGTAATAACA
1 TTTTCTTTAAAATGCCATCTAATAACA
*
2594394 TTTTC-TTAACATGCCATCTAATAAC
1 TTTTCTTTAAAATGCCATCTAATAAC
2594419 TTCTTGCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (27 bp):
TTTTCTTTAAAATGCCATCTAATAACA
Found at i:2597424 original size:30 final size:28
Alignment explanation
Indices: 2597390--2597465 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
2597380 AATTATAATC
*
2597390 ATAAAGATTTATTTGAATCAAAATAAAAA
1 ATAAAGATTTATTTAAAT-AAAATAAAAA
* *
2597419 TATAAAGATTTAATTAAATATAATAAAAA
1 -ATAAAGATTTATTTAAATAAAATAAAAA
*
2597448 ATAAAAATTTATTTAAAT
1 ATAAAGATTTATTTAAAT
2597466 TTTTTTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 16 0.39
29 9 0.22
30 16 0.39
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (28 bp):
ATAAAGATTTATTTAAATAAAATAAAAA
Found at i:2609110 original size:2 final size:2
Alignment explanation
Indices: 2609097--2609128 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2609087 ACAGATAGTT
*
2609097 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2609129 TACAGATGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2609848 original size:21 final size:20
Alignment explanation
Indices: 2609822--2609861 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2609812 GAAAGATTTG
2609822 AATTATGTTCTTTATCTTTTT
1 AATTATGTTCTTTAT-TTTTT
* *
2609843 AATTATTTTTTTTATTTTT
1 AATTATGTTCTTTATTTTT
2609862 CTTTAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (20 bp):
AATTATGTTCTTTATTTTTT
Found at i:2610551 original size:35 final size:35
Alignment explanation
Indices: 2610512--2610590 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
2610502 ATATTCTTGT
**
2610512 ATCACTATTGCATACATGAATTAGTAGATTCATGC
1 ATCACTATTGCATACATGAATTAACAGATTCATGC
* * *
2610547 ATCACTATTGCATGCATGAATTAACATATTCATGT
1 ATCACTATTGCATACATGAATTAACAGATTCATGC
2610582 ATCACTATT
1 ATCACTATT
2610591 AATTACATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (35 bp):
ATCACTATTGCATACATGAATTAACAGATTCATGC
Found at i:2611637 original size:22 final size:22
Alignment explanation
Indices: 2611609--2611654 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2611599 ATATATTAAC
2611609 TAGTCATGCAATAT-TTAAAAAT
1 TAGTCATGCAAT-TCTTAAAAAT
*
2611631 TAGTCATGTAATTCTTAAAAAT
1 TAGTCATGCAATTCTTAAAAAT
2611653 TA
1 TA
2611655 ATGATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
TAGTCATGCAATTCTTAAAAAT
Found at i:2611671 original size:22 final size:22
Alignment explanation
Indices: 2611646--2611687 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2611636 ATGTAATTCT
*
2611646 TAAAAATTAATGATAAAATGCC
1 TAAAAACTAATGATAAAATGCC
* *
2611668 TAAAAACTAATTATATAATG
1 TAAAAACTAATGATAAAATG
2611688 TTTGAACACT
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:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
TAAAAACTAATGATAAAATGCC
Found at i:2616313 original size:23 final size:23
Alignment explanation
Indices: 2616283--2616367 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
2616273 NNNNNNNNNN
2616283 AAGTTCGTGATAAAGCAACGGCG
1 AAGTTCGTGATAAAGCAACGGCG
2616306 AAGTTCGTGATAAAGCAACGGCG
1 AAGTTCGTGATAAAGCAACGGCG
* * * * *
2616329 AAGTTCGTAATCAAGCGATGACG
1 AAGTTCGTGATAAAGCAACGGCG
*
2616352 AAGTTCGTGATCAAGC
1 AAGTTCGTGATAAAGC
2616368 GACGACGTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (23 bp):
AAGTTCGTGATAAAGCAACGGCG
Found at i:2625058 original size:34 final size:34
Alignment explanation
Indices: 2625015--2625084 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2625005 ATCGGCATGA
2625015 AGAGAGTACCTTTCAACGTGTTTAAATTCTCCTT
1 AGAGAGTACCTTTCAACGTGTTTAAATTCTCCTT
2625049 AGAGAGTACCTTTCAACGTGTTTAAATTCTCCTT
1 AGAGAGTACCTTTCAACGTGTTTAAATTCTCCTT
2625083 AG
1 AG
2625085 CTTGATGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (34 bp):
AGAGAGTACCTTTCAACGTGTTTAAATTCTCCTT
Found at i:2631617 original size:13 final size:13
Alignment explanation
Indices: 2631599--2631629 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2631589 NNNNNNNCAC
2631599 TTATATGCTTTGA
1 TTATATGCTTTGA
2631612 TTATATGCTTTGA
1 TTATATGCTTTGA
2631625 TTATA
1 TTATA
2631630 GTGTGATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (13 bp):
TTATATGCTTTGA
Found at i:2634483 original size:26 final size:26
Alignment explanation
Indices: 2634445--2634494 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2634435 GTCTAGGTCT
*
2634445 AGATGTCAGCATGTTTGGTTGAGAAAG
1 AGATGGCAGCATGTTTGG-TGAGAAAG
2634472 AGATGGCA-CATGTTTGGTGAGAA
1 AGATGGCAGCATGTTTGGTGAGAA
2634495 TATATACTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 9 0.41
27 7 0.32
ACGTcount: A:0.30, C:0.08, G:0.34, T:0.28
Consensus pattern (26 bp):
AGATGGCAGCATGTTTGGTGAGAAAG
Found at i:2636842 original size:23 final size:23
Alignment explanation
Indices: 2636816--2636868 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
2636806 TTATTGCTAA
2636816 ATAATTTAGTTATCAAATGAATG
1 ATAATTTAGTTATCAAATGAATG
2636839 ATAATTTAGTTATCAAATGAATG
1 ATAATTTAGTTATCAAATGAATG
2636862 ATAATTT
1 ATAATTT
2636869 TTAAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (23 bp):
ATAATTTAGTTATCAAATGAATG
Found at i:2643140 original size:12 final size:12
Alignment explanation
Indices: 2643125--2643149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2643115 TAAATGACAC
2643125 AATACGATTAAT
1 AATACGATTAAT
2643137 AATACGATTAAT
1 AATACGATTAAT
2643149 A
1 A
2643150 CGAATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AATACGATTAAT
Found at i:2643862 original size:29 final size:29
Alignment explanation
Indices: 2643830--2643977 Score: 80
Period size: 32 Copynumber: 5.2 Consensus size: 29
2643820 GAATATGACA
*
2643830 TGTAACAATAATATTTTTTCAACATGGTG
1 TGTAACAATAATATTTTTTCAACATGGCG
* * *
2643859 TGTAATAACAGTATTTTTTTTTCAACATGGCG
1 TG---TAACAATAATATTTTTTCAACATGGCG
*
2643891 TGTAACAACT--T-TTTTTT-AACCATAGCG
1 TGTAACAA-TAATATTTTTTCAA-CATGGCG
* *
2643918 TGTAAC-AT-GT-TTTTGT--ACATGGCG
1 TGTAACAATAATATTTTTTCAACATGGCG
* * * * *
2643942 TGTAATAACAGTATTTTTTTAACATGGCA
1 TGTAACAATAATATTTTTTCAACATGGCG
2643971 TGTAACA
1 TGTAACA
2643978 CCCTAACCAT
Statistics
Matches: 95, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
24 11 0.12
25 3 0.03
26 11 0.12
27 23 0.24
28 1 0.01
29 20 0.21
30 1 0.01
32 25 0.26
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (29 bp):
TGTAACAATAATATTTTTTCAACATGGCG
Found at i:2643942 original size:24 final size:26
Alignment explanation
Indices: 2643873--2643977 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 26
2643863 ATAACAGTAT
*
2643873 TTTTTTTTCAACATGGCGTGTAACAAC
1 TTTTTTGT-AACATGGCGTGTAACAAC
* *
2643900 TTTTTTTTAACCATAGCGTGTAAC-A-
1 TTTTTTGTAA-CATGGCGTGTAACAAC
*
2643925 TGTTTTTGT-ACATGGCGTGTAATAAC
1 T-TTTTTGTAACATGGCGTGTAACAAC
* *
2643951 AGTATTTTTTTAACATGGCATGTAACA
1 --T-TTTTTGTAACATGGCGTGTAACA
2643978 CCCTAACCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
24 11 0.17
25 3 0.05
26 9 0.14
27 20 0.32
28 7 0.11
29 13 0.21
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (26 bp):
TTTTTTGTAACATGGCGTGTAACAAC
Found at i:2644197 original size:45 final size:45
Alignment explanation
Indices: 2644102--2644200 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
2644092 TTATACATGA
* * ** * *
2644102 CGTGTAACAACTTAACCATGGTGTGTCGCACGTTTTTGTAAATGG
1 CGTGTAACAACCTAACCATGGCGTGTAACACGTTTCTGTAAACGG
* * *
2644147 CGTGTAACAACCTAACCATGGCGTGTAATATGTTTCTGTACACGG
1 CGTGTAACAACCTAACCATGGCGTGTAACACGTTTCTGTAAACGG
*
2644192 TGTGTAACA
1 CGTGTAACA
2644201 TCCTGGCGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
CGTGTAACAACCTAACCATGGCGTGTAACACGTTTCTGTAAACGG
Found at i:2645795 original size:16 final size:15
Alignment explanation
Indices: 2645754--2645809 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
2645744 AATTTTAAAC
*
2645754 TTTTATTTTGTTATA
1 TTTTATTTTATTATA
* *
2645769 TTTGATGTTATTATTA
1 TTTTATTTTATTA-TA
2645785 TTTTATTTTATTATA
1 TTTTATTTTATTATA
*
2645800 -ATTATTTTAT
1 TTTTATTTTAT
2645810 AATTATTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 9 0.26
15 12 0.35
16 13 0.38
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTTATTTTATTATA
Found at i:2646369 original size:22 final size:21
Alignment explanation
Indices: 2646344--2646385 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2646334 TATGATTTGG
*
2646344 TAAAAGATTAATATAATATTTT
1 TAAAAAATTAATAT-ATATTTT
*
2646366 TAAAAAATTTATATATATTT
1 TAAAAAATTAATATATATTT
2646386 ATTTTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAAAAATTAATATATATTTT
Found at i:2646660 original size:4 final size:4
Alignment explanation
Indices: 2646651--2646683 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2646641 AAAACTAATC
2646651 TTAT TTAT TTAT TTAT TTAT TTA- TTAT TT-T TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
2646684 GGAAAATGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:2648452 original size:26 final size:24
Alignment explanation
Indices: 2648423--2648477 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2648413 CTACTTTACC
2648423 TAATTACATATATTTTGTAACAACAA
1 TAATT-CATATATTTTGTAA-AACAA
* *
2648449 TAA-TGATATTTTTTGTAAAACAA
1 TAATTCATATATTTTGTAAAACAA
2648472 TCAATT
1 T-AATT
2648478 GTACAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 2 0.08
26 3 0.12
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (24 bp):
TAATTCATATATTTTGTAAAACAA
Found at i:2671275 original size:30 final size:31
Alignment explanation
Indices: 2671241--2671303 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
2671231 AAACAAAATG
* * **
2671241 AACCCAAA-CTCAAATATTAAAAGCCAAAAC
1 AACCCAAAGCTCAAAAATGAAAAGAAAAAAC
2671271 AACCCAAAGCTCAAAAATGAAAAGAAAAAAC
1 AACCCAAAGCTCAAAAATGAAAAGAAAAAAC
2671302 AA
1 AA
2671304 TAAAAAGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.62, C:0.22, G:0.06, T:0.10
Consensus pattern (31 bp):
AACCCAAAGCTCAAAAATGAAAAGAAAAAAC
Found at i:2672620 original size:24 final size:25
Alignment explanation
Indices: 2672584--2672631 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2672574 AATTTAATTT
2672584 TTTTTAAAATT-AAAATAATTTAAG
1 TTTTTAAAATTAAAAATAATTTAAG
** *
2672608 TTTTTAATTTTAAAAATATTTTAA
1 TTTTTAAAATTAAAAATAATTTAA
2672632 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTTAAAATTAAAAATAATTTAAG
Found at i:2680779 original size:7 final size:7
Alignment explanation
Indices: 2680779--2680902 Score: 54
Period size: 7 Copynumber: 18.3 Consensus size: 7
2680769 TTTAAATTTT
2680779 AATTATA
1 AATTATA
2680786 AATTATAAA
1 AATTAT--A
2680795 AATTA-A
1 AATTATA
2680801 AA-TA-A
1 AATTATA
*
2680806 AATT-TT
1 AATTATA
*
2680812 AA-TACA
1 AATTATA
2680818 AATTATA
1 AATTATA
*
2680825 AA-AACTA
1 AATTA-TA
*
2680832 ATATTTTA
1 A-ATTATA
*
2680840 AATTTAAA
1 AA-TTATA
2680848 AATTA--
1 AATTATA
2680853 AATTA-A
1 AATTATA
2680859 AATTATA
1 AATTATA
2680866 AATTATAAA
1 AATTAT--A
2680875 AATTA-A
1 AATTATA
*
2680881 AATT-TT
1 AATTATA
2680887 AATTATA
1 AATTATA
2680894 AATTATA
1 AATTATA
2680901 AA
1 AA
2680903 AGTTTAATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
5 11 0.12
6 23 0.26
7 35 0.39
8 9 0.10
9 12 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (7 bp):
AATTATA
Found at i:2680855 original size:13 final size:13
Alignment explanation
Indices: 2680837--2680881 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2680827 AACTAATATT
2680837 TTAAATTTAAAAA
1 TTAAATTTAAAAA
*
2680850 TTAAA-TTAAAAT
1 TTAAATTTAAAAA
2680862 TATAAATTATAAAAA
1 T-TAAATT-TAAAAA
2680877 TTAAA
1 TTAAA
2680882 ATTTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 5 0.19
15 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAATTTAAAAA
Found at i:2680887 original size:48 final size:52
Alignment explanation
Indices: 2680779--2680895 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 52
2680769 TTTAAATTTT
*
2680779 AATTATAAATTATAAAAATTAAAATAAAATTTTAATACAAATTATAAAAACTAA
1 AATTTTAAATTATAAAAATTAAAATAAAA-TTTAATA-AAATTATAAAAACTAA
* * *
2680833 TATTTTAAATT-TAAAAATTAAATTAAAA-TT-AT-AAATTATAAAAATTAA
1 AATTTTAAATTATAAAAATTAAAATAAAATTTAATAAAATTATAAAAACTAA
2680881 AATTTT-AATTATAAA
1 AATTTTAAATTATAAA
2680896 TTATAAAAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
47 4 0.07
48 24 0.42
50 2 0.04
51 2 0.04
53 16 0.28
54 9 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (52 bp):
AATTTTAAATTATAAAAATTAAAATAAAATTTAATAAAATTATAAAAACTAA
Found at i:2680903 original size:21 final size:21
Alignment explanation
Indices: 2680852--2680895 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
2680842 TTTAAAAATT
*
2680852 AAATTAAAATTATAAATTATAA
1 AAATTAAAATT-TTAATTATAA
2680874 AAATTAAAATTTTAATTATAA
1 AAATTAAAATTTTAATTATAA
2680895 A
1 A
2680896 TTATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTAAAATTTTAATTATAA
Found at i:2690276 original size:20 final size:20
Alignment explanation
Indices: 2690251--2690289 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2690241 CATGTCAGGT
*
2690251 TTAAAAAAATATTGTTACAA
1 TTAAAAAAAAATTGTTACAA
2690271 TTAAAAAAAAATTGTTACA
1 TTAAAAAAAAATTGTTACA
2690290 TGCTTTAACT
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:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
TTAAAAAAAAATTGTTACAA
Found at i:2690519 original size:34 final size:34
Alignment explanation
Indices: 2690444--2690519 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
2690434 TGTACCAAAC
* * * * * *
2690444 ATTACATATTAAGGTTAAAGTTTCAGCACTAGAT
1 ATTACATGTCAAGGTCAAAGCTTCAACACCAGAT
*
2690478 ATTACATGTCAAGGTCAAAGCTTCAACACCATAT
1 ATTACATGTCAAGGTCAAAGCTTCAACACCAGAT
2690512 ATTACATG
1 ATTACATG
2690520 CCAAACCTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (34 bp):
ATTACATGTCAAGGTCAAAGCTTCAACACCAGAT
Found at i:2706166 original size:33 final size:33
Alignment explanation
Indices: 2706128--2706195 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2706118 TTTATACTAT
2706128 TATAAT-TAA-AATAAAGAATATTAAAATAAAATA
1 TATAATATAAGAATAAA-AA-ATTAAAATAAAATA
*
2706161 TATAATATAAGAATCAAAAATTAAAATAAAATA
1 TATAATATAAGAATAAAAAATTAAAATAAAATA
2706194 TA
1 TA
2706196 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 22 0.69
34 5 0.16
35 5 0.16
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (33 bp):
TATAATATAAGAATAAAAAATTAAAATAAAATA
Found at i:2706232 original size:50 final size:47
Alignment explanation
Indices: 2706131--2706283 Score: 147
Period size: 50 Copynumber: 3.2 Consensus size: 47
2706121 ATACTATTAT
*
2706131 AATTAAAATAAAGA-ATATTAAAATAAAATATATAATATAAGAATCAAA
1 AATTAAAATAAA-ATATATAAAAATAAAATATATAATATAAGAA-CAAA
2706179 AATTAAAATAAAATATA-AAAAATTAAAATTTATATAATATAAGTAA-AACA
1 AATTAAAATAAAATATATAAAAA-TAAAA--TATATAATATAAG-AACAA-A
* * *
2706229 AATTAAAATAAAATATAT-AATATAAAAAATATATTA-AAGAA-ATAA
1 AATTAAAATAAAATATATAAAAATAAAATATATAATATAAGAACA-AA
*
2706274 AAATAAAATA
1 AATTAAAATA
2706284 TATAAGATTA
Statistics
Matches: 92, Mismatches: 5, Indels: 19
0.79 0.04 0.16
Matches are distributed among these distances:
45 13 0.14
46 4 0.04
47 12 0.13
48 20 0.22
49 7 0.08
50 34 0.37
51 2 0.02
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (47 bp):
AATTAAAATAAAATATATAAAAATAAAATATATAATATAAGAACAAA
Found at i:2706266 original size:26 final size:27
Alignment explanation
Indices: 2706138--2706266 Score: 90
Period size: 26 Copynumber: 4.7 Consensus size: 27
2706128 TATAATTAAA
*
2706138 ATAAAGAATATTAAAATAAAATATATAAT
1 ATAAA-AA-ATTAAATTAAAATATATAAT
2706167 ATAAGAATCAA--AAATTAAAATA-A-AAT
1 ATAA-AA--AATTAAATTAAAATATATAAT
* *
2706193 ATAAAAAATTAAAATTTATATAATATAAGT
1 ATAAAAAATT-AAATTAAAAT-ATATAA-T
*
2706223 A-AAACAAATTAAAATAAAATATATAAT
1 ATAAA-AAATTAAATTAAAATATATAAT
*
2706250 ATAAAAAA-TATATTAAA
1 ATAAAAAATTAAATTAAA
2706267 GAAATAAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 27
0.70 0.07 0.23
Matches are distributed among these distances:
23 2 0.03
25 2 0.03
26 22 0.28
27 7 0.09
28 20 0.25
29 17 0.21
30 9 0.11
31 1 0.01
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (27 bp):
ATAAAAAATTAAATTAAAATATATAAT
Found at i:2706284 original size:33 final size:33
Alignment explanation
Indices: 2706234--2706318 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
2706224 AAACAAATTA
* *
2706234 AAATAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATAAAA-ATAAAATATAAAAAATTATAAT-AAG
* * *
2706268 AAATAAAAATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATAAAAAATTATAATAAG
*
2706301 AAATGAAAATAAAATATA
1 AAATAAAAATAAAATATA
2706319 TGACATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 31 0.70
34 13 0.30
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAAAATATAAAAAATTATAATAAG
Found at i:2706303 original size:29 final size:28
Alignment explanation
Indices: 2706269--2706417 Score: 82
Period size: 29 Copynumber: 5.2 Consensus size: 28
2706259 ATATTAAAGA
2706269 AATAAAAATAAAATATATAAGATTATAAT
1 AATAAAAATAAAATATATAA-ATTATAAT
*
2706298 AATAAATGAAAATAAAATATATGACATTA-AA-
1 AAT--A--AAAATAAAATATAT-AAATTATAAT
* ** *
2706329 AATATATTTAAGAGATGATATTAATTA-AA-
1 AATAAAAATAA-A-AT-ATATAAATTATAAT
2706358 AATATAAAATATAAA-ATATAAA-TAT-AT
1 AATA-AAAATA-AAATATATAAATTATAAT
2706385 --TAAAAATAAAATATATAAGATTATAAT
1 AATAAAAATAAAATATATAA-ATTATAAT
2706412 AATAAA
1 AATAAA
2706418 TGAAAATAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 36
0.67 0.07 0.26
Matches are distributed among these distances:
23 3 0.03
24 12 0.13
25 3 0.03
26 6 0.07
27 12 0.13
28 1 0.01
29 21 0.23
30 8 0.09
31 5 0.05
32 2 0.02
33 18 0.20
34 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.32
Consensus pattern (28 bp):
AATAAAAATAAAATATATAAATTATAAT
Found at i:2706319 original size:33 final size:34
Alignment explanation
Indices: 2706263--2706443 Score: 107
Period size: 33 Copynumber: 5.0 Consensus size: 34
2706253 AAAAATATAT
* * *
2706263 TAAAGAAATAAAAATAAAATATATAAGATTATAA
1 TAAATAAATGAAAATAAAATATATAAGATTAAAA
* *
2706297 T-AATAAATGAAAATAAAATATATGACATTAAAAA
1 TAAATAAATGAAAATAAAATATATAAGATT-AAAA
* *
2706331 TATATTTAAGAGATGATATTAATTAAAA-ATATAAAATATAAAATA
1 TA-A-AT-A-A-ATGA-A--AA-TAAAATATATAAGAT-T-AAA-A
* * *
2706376 TAAATATATTAAAAATAAAATATATAAGATTATAA
1 TAAATA-AATGAAAATAAAATATATAAGATTAAAA
* *
2706411 T-AATAAATGAAAATAAAATATATGACATTAAAA
1 TAAATAAATGAAAATAAAATATATAAGATTAAAA
2706444 ATATATTTAA
Statistics
Matches: 114, Mismatches: 19, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
33 47 0.41
34 9 0.08
35 2 0.02
36 3 0.03
37 7 0.06
38 11 0.10
39 1 0.01
40 5 0.04
41 3 0.03
42 2 0.02
43 10 0.09
44 11 0.10
45 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (34 bp):
TAAATAAATGAAAATAAAATATATAAGATTAAAA
Found at i:2706379 original size:22 final size:22
Alignment explanation
Indices: 2706354--2706399 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2706344 TGATATTAAT
2706354 TAAAAATA-TAAAATATAAAATA
1 TAAAAATATTAAAA-ATAAAATA
*
2706376 TAAATATATTAAAAATAAAATA
1 TAAAAATATTAAAAATAAAATA
2706398 TA
1 TA
2706400 TAAGATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATATTAAAAATAAAATA
Found at i:2706382 original size:6 final size:7
Alignment explanation
Indices: 2706356--2706399 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
2706346 ATATTAATTA
2706356 AAAATAT
1 AAAATAT
2706363 AAAATAT
1 AAAATAT
2706370 AAAATAT
1 AAAATAT
2706377 AAATATATT
1 AAA-ATA-T
2706386 AAAA-AT
1 AAAATAT
2706392 AAAATAT
1 AAAATAT
2706399 A
1 A
2706400 TAAGATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.15
7 21 0.62
8 4 0.12
9 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATAT
Found at i:2706400 original size:24 final size:23
Alignment explanation
Indices: 2706363--2706433 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 23
2706353 TTAAAAATAT
2706363 AAAATATAAAATATAAATATATTA
1 AAAATA-AAAATATAAATATATTA
*
2706387 AAAATAAAATATATAAGATTATAATA
1 AAAATAAAA-ATATAA-A-TATATTA
*
2706413 ATAAATGAAAATA-AAATATAT
1 A-AAATAAAAATATAAATATAT
2706434 GACATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 7 0.17
24 13 0.32
25 3 0.08
26 10 0.25
27 7 0.17
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (23 bp):
AAAATAAAAATATAAATATATTA
Found at i:2706408 original size:114 final size:114
Alignment explanation
Indices: 2706271--2706502 Score: 423
Period size: 114 Copynumber: 2.0 Consensus size: 114
2706261 ATTAAAGAAA
2706271 TAAAAATAAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATAT
*
2706336 TTAAGAGATGATATTA-ATTAAAAATATAA-AATATAAAATATAAATATAT
66 TTAAGAGATGATATTATA-TAAAAAT-TAATAATAAAAAATATAAATATAT
2706385 TAAAAATAAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATAT
2706450 TTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
66 TTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
2706499 TAAA
1 TAAA
2706503 TTTGTATTTT
Statistics
Matches: 115, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
113 3 0.03
114 111 0.97
115 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (114 bp):
TAAAAATAAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATAT
TTAAGAGATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
Found at i:2706418 original size:22 final size:23
Alignment explanation
Indices: 2706354--2706433 Score: 60
Period size: 23 Copynumber: 3.4 Consensus size: 23
2706344 TGATATTAAT
*
2706354 TAAAAATA-TAAAATATAAA-ATA
1 TAAATATATTAAAA-ATAAATATA
2706376 TAAATATATTAAAAATAAAATATA
1 TAAATATATTAAAAAT-AAATATA
*
2706400 TAAGATTATAATAATAAATGAAA-ATA
1 TAA-A-TATATTAA-AAAT-AAATATA
2706426 -AAATATAT
1 TAAATATAT
2706434 GACATTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
22 9 0.19
23 12 0.25
24 7 0.15
25 3 0.06
26 10 0.21
27 7 0.15
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (23 bp):
TAAATATATTAAAAATAAATATA
Found at i:2727636 original size:29 final size:29
Alignment explanation
Indices: 2727573--2727636 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2727563 ATTTATAATA
2727573 GATAAGATAAATCCTAATCAAATAGGAAT
1 GATAAGATAAATCCTAATCAAATAGGAAT
* *
2727602 GCTAAGATAAATCCTAATCAAATAGTAAT
1 GATAAGATAAATCCTAATCAAATAGGAAT
*
2727631 TATAAG
1 GATAAG
2727637 CCTAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (29 bp):
GATAAGATAAATCCTAATCAAATAGGAAT
Found at i:2740013 original size:63 final size:63
Alignment explanation
Indices: 2739914--2740039 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
2739904 CTATTGTAGG
2739914 CCGTCCTGCATAAAAGTCAAACATTTTGAGATTGAGGGAACATACTTTGCTGTGTTGAGTGTA
1 CCGTCCTGCATAAAAGTCAAACATTTTGAGATTGAGGGAACATACTTTGCTGTGTTGAGTGTA
* ** * *
2739977 CCGTCCTGCATAAAGGTCCCACATTTTGAGATTGAGGGAACATACTTTTCTGTTTTGAGTGTA
1 CCGTCCTGCATAAAAGTCAAACATTTTGAGATTGAGGGAACATACTTTGCTGTGTTGAGTGTA
2740040 AGTTAAGCAC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (63 bp):
CCGTCCTGCATAAAAGTCAAACATTTTGAGATTGAGGGAACATACTTTGCTGTGTTGAGTGTA
Found at i:2749055 original size:51 final size:51
Alignment explanation
Indices: 2748981--2749101 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 51
2748971 AATGTGTAAC
2748981 ACGATATGACACGATTAACACGTTAATTAAACATATCGAGTTAAATTTTAT
1 ACGATATGACACGATTAACACGTTAATTAAACATATCGAGTTAAATTTTAT
* * * *
2749032 ATGATGA-GACACGATTAATACGTTAATTAAATATATCGAGTTTAATTTTAT
1 ACGAT-ATGACACGATTAACACGTTAATTAAACATATCGAGTTAAATTTTAT
*
2749083 ACGATATGACACAATTAAC
1 ACGATATGACACGATTAAC
2749102 CTGATTAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
50 1 0.02
51 59 0.97
52 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (51 bp):
ACGATATGACACGATTAACACGTTAATTAAACATATCGAGTTAAATTTTAT
Found at i:2749298 original size:52 final size:52
Alignment explanation
Indices: 2749217--2749326 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
2749207 CCCCAAAAAT
* *
2749217 TTTTATAACAACTTTTATTTTTTAAAATTTTATAATTTTTCCCCA-ATAATAA
1 TTTTATAACAACTTTTATTTTTTAAAATTTTATAA-ATTTACCCATATAATAA
* *
2749269 TTTTATAGCATACTTTTATTTTTT-GAATTTTATAAATTTACCCATATAATAA
1 TTTTATAACA-ACTTTTATTTTTTAAAATTTTATAAATTTACCCATATAATAA
2749321 TTTTAT
1 TTTTAT
2749327 CTGTTATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
51 7 0.13
52 32 0.62
53 13 0.25
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.54
Consensus pattern (52 bp):
TTTTATAACAACTTTTATTTTTTAAAATTTTATAAATTTACCCATATAATAA
Found at i:2756125 original size:20 final size:20
Alignment explanation
Indices: 2756093--2756149 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
2756083 TTAAATATAT
*
2756093 AATTAATAAATAAAAAGGTGA
1 AATTAA-AAATAAAAAGGAGA
*
2756114 AATTAAAAATAAAAACTGAGA
1 AATTAAAAATAAAAA-GGAGA
2756135 AATTAAAAA-AAAAAG
1 AATTAAAAATAAAAAG
2756150 AAATAAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (20 bp):
AATTAAAAATAAAAAGGAGA
Found at i:2765413 original size:250 final size:248
Alignment explanation
Indices: 2764967--2766162 Score: 1081
Period size: 249 Copynumber: 4.8 Consensus size: 248
2764957 NNNNNNNNNN
* * ** *
2764967 AAAACTTATAAA-AGTGGAATAACTAAATTTTAAATCTTAACATAAATGTGTGAGTGTTAACGTA
1 AAAACTTATAAAGA-TGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAAAGTTAATGTA
* * * * * * * *
2765031 ACAAGTCAATCAAGTAAAAAAATATAATTTTAATGAAAAACAAACATTTATATTCATATTCTCGG
65 ACAAGTCAATTAAGTAAAAAAA-CTAATTTTAGT-AAAAAAAAACATTTAAATTTATATTTTTGG
* * * * * * *
2765096 ATTAAAAATGTTAACAATATACAAATTTGAAGTTTTAAATAAAAAATAATAAGAATAAAAATAAT
128 ATTAAAAGTATTAACGATATATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAAT
* * * * * * * *
2765161 TATAATTCAAAAATAACACAGAAAAGCTATAACATAAAATTGTAAAAATTGACGTA
193 TATAGTTCAAAATTAACATAGAAAAGCTTTAACGTAAAACTATAAGAATTGACGTA
* * * * *
2765217 AAAATTTATAAAGACGAAATAATTAAATTTTAAATCTTAACGTAAACGTGTTAAAGTTAATGTAA
1 AAAACTTATAAAGATGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAAAGTTAATGTAA
* *
2765282 CAAGTCCATTAAGTAAAAAAACTAATTTTAGTAAAAAATAAATATTTAAATTTATATTTTTGGAT
66 CAAGTCAATTAAGTAAAAAAACTAATTTTAGTAAAAAA-AAACATTTAAATTTATATTTTTGGAT
* * *
2765347 TAAAAGTATTAAACGATATATAAATTTTAATTTTTAAACAAAGAATAATAAGGATAAAATTAATT
130 TAAAAGTATT-AACGATATATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAATT
* * * ** * *
2765412 ATAGTTCAAAATTGACATAGATAAGTTTTAACGT-AAACGGTAACAATTGACATA
194 ATAGTTCAAAATTAACATAGAAAAGCTTTAACGTAAAACTATAAGAATTGACGTA
* *
2765466 AAAACTTATAAAGATAAAATAACTAAATTTTAAATCTTAACATAAATGTGTGAGAA-TTAATGTA
1 AAAACTTATAAAGATGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTGA-AAGTTAATGTA
* ** *
2765530 ATAAGTCAATTAAGTAAAAAAAATCTAATTTTA-T-TGAAAAAA-ATTTAAATTTATATTATTAG
65 ACAAGTCAATTAAGT-AAAAAAA-CTAATTTTAGTAAAAAAAAACATTTAAATTTATATT-TTTG
* * *
2765592 GA-TAAAAGTGGTTAATGATATATAAATTTTAATTTTTAAATAAAAAA-AATAATG--AAAAA-A
127 GATTAAAAGT-ATTAACGATATATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATA
* * * *
2765652 ATTATAGTTTAAAATTGACATAG-ATAGACTTTGAA-GTAAAAACTATAAGAATTGATGTA
191 ATTATAGTTCAAAATTAACATAGAAAAG-CTTT-AACGT-AAAACTATAAGAATTGACGTA
* * * * *
2765711 AAAATTTATAAA-AGTGGAATAACTAAATTTTAAATCTTAACGTAAATATGTAAAAATTAATGTA
1 AAAACTTATAAAGA-TGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAAAGTTAATGTA
* * * * * * *
2765775 ATAAATTAATTAAGTAACAAAATCTAATTTTAGTGAAAAAAGAACATTTATATTTATATTATTGG
65 ACAAGTCAATTAAGTAA-AAAAACTAATTTTAGT-AAAAAAAAACATTTAAATTTATATTTTTGG
********** * * *
2765840 NNNNNNNNNNTGTAATGATAT-TCAAATTTTTATTTTTAAATAAAAAATAATAAAGATAAAAATA
128 ATTAAAAGTAT-TAACGATATAT-AAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATA
* * * * *
2765904 ATTATAGTTCAAAATTAACATAAAAAACCCTTAATGTAAAATTATAAGAATTGACGT-
191 ATTATAGTTCAAAATTAACATAGAAAAGCTTTAACGTAAAACTATAAGAATTGACGTA
* * * * * *
2765961 AAAACTTATAAAGGTGGAATAA-TTAATTTTAAATCTTAATGTGAACT-TGTGAAAGTTAACGTA
1 AAAACTTATAAAGATGAAATAACTAAATTTTAAATCTTAACGT-AAATGTGTGAAAGTTAATGTA
* ** * *
2766024 ACAAGTCAATTAAGTAAAAAAAACTAACTTTAGTGAAAAATGAATATTTAAATTTATAATTTTGG
65 ACAAGTCAATTAAGT-AAAAAAACTAATTTTAGT-AAAAAAAAACATTTAAATTTATATTTTTGG
* * * * * *
2766089 ATTAAAAGTATTTAACCATATACAAATCTTAACTTTTAAGT---AAATAAT-A--ATAATAATAA
128 ATTAAAAGTA-TTAACGATATATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAA
2766148 TTATAGTTCAAAATT
192 TTATAGTTCAAAATT
2766163 GATATAAATA
Statistics
Matches: 774, Mismatches: 139, Indels: 73
0.78 0.14 0.07
Matches are distributed among these distances:
242 2 0.00
243 52 0.07
244 20 0.03
245 87 0.11
246 13 0.02
247 63 0.08
248 61 0.08
249 234 0.30
250 179 0.23
251 35 0.05
252 26 0.03
253 2 0.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (248 bp):
AAAACTTATAAAGATGAAATAACTAAATTTTAAATCTTAACGTAAATGTGTGAAAGTTAATGTAA
CAAGTCAATTAAGTAAAAAAACTAATTTTAGTAAAAAAAAACATTTAAATTTATATTTTTGGATT
AAAAGTATTAACGATATATAAATTTTAATTTTTAAATAAAAAATAATAAGGATAAAAATAATTAT
AGTTCAAAATTAACATAGAAAAGCTTTAACGTAAAACTATAAGAATTGACGTA
Found at i:2765571 original size:20 final size:20
Alignment explanation
Indices: 2765546--2765583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2765536 CAATTAAGTA
*
2765546 AAAAAAATCTAATTTTATTG
1 AAAAAAATCTAAATTTATTG
*
2765566 AAAAAAATTTAAATTTAT
1 AAAAAAATCTAAATTTAT
2765584 ATTATTAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAAAAATCTAAATTTATTG
Found at i:2765969 original size:495 final size:493
Alignment explanation
Indices: 2764967--2766164 Score: 1203
Period size: 495 Copynumber: 2.4 Consensus size: 493
2764957 NNNNNNNNNN
**
2764967 AAAACTTATAAA-AGTGGAATAACTAAATTTTAAATCTTAACATAAATGTGTGAGTGTTAACGTA
1 AAAACTTATAAAGA-TGGAATAACTAAATTTTAAATCTTAACATAAATGTGTGAGAATTAACGTA
* * * * *
2765031 ACAAGTCAATCAAGT-AAAAAAATATAATTTTAATGAAAAACAAACATTTATATTCATATTCTCG
65 ACAAGTCAATTAAGTAAAAAAAATCTAATTTTAATG-AAAA-AAACATTTAAATTTATATT-TTG
* * *
2765095 GATTAAAAATGTTAACAATATACAAATTTGAAGTTTTAAATAAAAAATAATAA-GAATAAAAATA
127 GATTAAAAGTGTTAACAATATACAAATTTTAACTTTTAAATAAAAAA-AATAATG---AAAAA-A
* * * * *
2765159 ATTATAATTCAAAAATAACACAGAAAAGCTATAACATAAAATTGTAAAAATTGACGTAAAAATTT
187 ATTATAGTTCAAAATTGACACAGAAAAGCTATAACATAAAACTATAAAAATTGACGTAAAAATTT
* * * * * *
2765224 ATAAAGACGAAATAATTAAATTTTAAATCTTAACGTAAACGTGTTAAAGTTAATGTAACAAGTCC
252 ATAAAGACGAAATAACTAAATTTTAAATCTTAACGTAAACATGTAAAAATTAATGTAACAAATCA
* *
2765289 ATTAAGTAAAAAAACTAATTTTAGTAAAAAATAAATATTTAAATTTATATTTTTGGATTAAAAGT
317 ATTAAGTAAAAAAACTAATTTTAGTAAAAAATAAACATTTAAATTTATATTATTGGATTAAAAGT
* * *
2765354 ATTAAACGATATATAAATTTTAATTTTTAAACAAAGAATAATAAGGATAAAATTAATTATAGTTC
382 ATTAAACGATATATAAATTTTAATTTTTAAACAAAAAATAATAAAGATAAAAATAATTATAGTTC
* * * *** *
2765419 AAAATTGACATAGATAAGTTTTAACGTAAACGGTAACAATTGACATA
447 AAAATTAACATAAAAAACCCTTAACGTAAACGATAACAATTGACATA
** *
2765466 AAAACTTATAAAGATAAAATAACTAAATTTTAAATCTTAACATAAATGTGTGAGAATTAATGTAA
1 AAAACTTATAAAGATGGAATAACTAAATTTTAAATCTTAACATAAATGTGTGAGAATTAACGTAA
* *
2765531 TAAGTCAATTAAGTAAAAAAAATCTAATTTTATTG-AAAAAA-ATTTAAATTTATATTATTAGGA
66 CAAGTCAATTAAGTAAAAAAAATCTAATTTTAATGAAAAAAACATTTAAATTTATATT-TT-GGA
** * *
2765594 -TAAAAGTGGTTAATGATATATAAATTTTAATTTTTAAATAAAAAAAATAATGAAAAAAATTATA
129 TTAAAAGT-GTTAACAATATACAAATTTTAACTTTTAAATAAAAAAAATAATGAAAAAAATTATA
* * * * * * *
2765658 GTTTAAAATTGACATAG-ATAGACTTTGAA-GTAAAAACTATAAGAATTGATGTAAAAATTTATA
193 GTTCAAAATTGACACAGAAAAG-CTAT-AACAT-AAAACTATAAAAATTGACGTAAAAATTTATA
* * * * *
2765721 AA-AGTGGAATAACTAAATTTTAAATCTTAACGTAAATATGTAAAAATTAATGTAATAAATTAAT
255 AAGA-CGAAATAACTAAATTTTAAATCTTAACGTAAACATGTAAAAATTAATGTAACAAATCAAT
* * * *********
2765785 TAAGTAACAAAATCTAATTTTAGTGAAAAAA-GAACATTTATATTTATATTATTGGNNNNNNNNN
319 TAAGTAA-AAAAACTAATTTTAGT-AAAAAATAAACATTTAAATTTATATTATTGGATTAAAAGT
* * * *
2765849 NTGT-AATGATAT-TCAAATTTTTATTTTTAAATAAAAAATAATAAAGATAAAAATAATTATAGT
382 AT-TAAACGATATAT-AAATTTTAATTTTTAAACAAAAAATAATAAAGATAAAAATAATTATAGT
* ** * *
2765912 TCAAAATTAACATAAAAAACCCTTAATGTAAAATTATAAGAATTGACGT-
445 TCAAAATTAACATAAAAAACCCTTAACGT-AAACGATAACAATTGACATA
* * ** *
2765961 AAAACTTATAAAGGTGGAATAA-TTAATTTTAAATCTTAATGTGAACT-TGTGA-AAGTTAACGT
1 AAAACTTATAAAGATGGAATAACTAAATTTTAAATCTTAACAT-AAATGTGTGAGAA-TTAACGT
* * *
2766023 AACAAGTCAATTAAGTAAAAAAAA-CTAACTTTAGTGAAAAATGAATATTTAAATTTATAATTTT
64 AACAAGTCAATTAAGTAAAAAAAATCTAATTTTAATGAAAAA--AACATTTAAATTTAT-ATTTT
* * * * * *
2766087 GGATTAAAAGTATTTAACCATATACAAATCTTAACTTTTAAGT--AAATAATAAT-AATAATAAT
126 GGATTAAAAGT-GTTAACAATATACAAATTTTAACTTTTAAATAAAAAAAATAATGAA-AAAAAT
2766149 TATAGTTCAAAATTGA
189 TATAGTTCAAAATTGA
2766165 TATAAATAAA
Statistics
Matches: 579, Mismatches: 97, Indels: 50
0.80 0.13 0.07
Matches are distributed among these distances:
492 3 0.01
493 36 0.06
494 150 0.26
495 160 0.28
496 51 0.09
497 84 0.15
498 6 0.01
499 70 0.12
500 19 0.03
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (493 bp):
AAAACTTATAAAGATGGAATAACTAAATTTTAAATCTTAACATAAATGTGTGAGAATTAACGTAA
CAAGTCAATTAAGTAAAAAAAATCTAATTTTAATGAAAAAAACATTTAAATTTATATTTTGGATT
AAAAGTGTTAACAATATACAAATTTTAACTTTTAAATAAAAAAAATAATGAAAAAAATTATAGTT
CAAAATTGACACAGAAAAGCTATAACATAAAACTATAAAAATTGACGTAAAAATTTATAAAGACG
AAATAACTAAATTTTAAATCTTAACGTAAACATGTAAAAATTAATGTAACAAATCAATTAAGTAA
AAAAACTAATTTTAGTAAAAAATAAACATTTAAATTTATATTATTGGATTAAAAGTATTAAACGA
TATATAAATTTTAATTTTTAAACAAAAAATAATAAAGATAAAAATAATTATAGTTCAAAATTAAC
ATAAAAAACCCTTAACGTAAACGATAACAATTGACATA
Found at i:2766993 original size:14 final size:14
Alignment explanation
Indices: 2766974--2767004 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2766964 TACAATATAT
2766974 ATAAGAATTATACG
1 ATAAGAATTATACG
2766988 ATAAGAATTATACG
1 ATAAGAATTATACG
2767002 ATA
1 ATA
2767005 TATATCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:2775665 original size:30 final size:29
Alignment explanation
Indices: 2775606--2775747 Score: 137
Period size: 28 Copynumber: 4.8 Consensus size: 29
2775596 CAACTTGAAC
*
2775606 ATGTTTATCTTAATTTAGACAAG-AAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAAT
* *
2775634 ATGTTTGTCTTAATTTCAAATAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAGAAAAAT
* * *
2775664 ATTTTTTATCTTAATCTAGACAAGAAAACAT
1 A-TGTTTGTCTTAATTTAGACAAGAAAA-AT
*
2775695 A--TTTGTCTCAATTTAGACAAGATAAAAT
1 ATGTTTGTCTTAATTTAGACAAGA-AAAAT
* *
2775723 ATTTTTGTCTTAATTAAAGACAAGA
1 ATGTTTGTCTTAATT-TAGACAAGA
2775748 GTTGTCTTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
28 36 0.39
29 8 0.09
30 26 0.28
31 23 0.25
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (29 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAAT
Found at i:2775684 original size:59 final size:58
Alignment explanation
Indices: 2775609--2775736 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 58
2775599 CTTGAACATG
* * * * *
2775609 TTTATCTTAATTTAGACAAGAAAATATGTTTGTCTTAATTTCAAATAAGA-AAAATATTT
1 TTTATCTTAATCTAGACAAGAAAACATATTTGTCTCAATTT-AAACAAGATAAAATA-TT
*
2775668 TTTATCTTAATCTAGACAAGAAAACATATTTGTCTCAATTTAGACAAGATAAAATATT
1 TTTATCTTAATCTAGACAAGAAAACATATTTGTCTCAATTTAAACAAGATAAAATATT
*
2775726 TTTGTCTTAAT
1 TTTATCTTAAT
2775737 TAAAGACAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 18 0.30
59 43 0.70
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (58 bp):
TTTATCTTAATCTAGACAAGAAAACATATTTGTCTCAATTTAAACAAGATAAAATATT
Found at i:2776104 original size:8 final size:8
Alignment explanation
Indices: 2776091--2776118 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2776081 AGAAGAGATT
2776091 GAAAAGAA
1 GAAAAGAA
2776099 GAAAAGAA
1 GAAAAGAA
2776107 GAAAAGAA
1 GAAAAGAA
2776115 GAAA
1 GAAA
2776119 GAATGTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
GAAAAGAA
Found at i:2777539 original size:3 final size:3
Alignment explanation
Indices: 2777531--2777580 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
2777521 TTAATGCGGC
*
2777531 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA -TA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
2777576 TTA TT
1 TTA TT
2777581 TGTATGCTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2783441 original size:29 final size:28
Alignment explanation
Indices: 2783398--2783477 Score: 108
Period size: 29 Copynumber: 2.9 Consensus size: 28
2783388 CAGCTTTAAC
* * *
2783398 ATGTTTGTCTTAATTTAGATAAGAAAAT
1 ATGTTTGTTTTAATTTAAACAAGAAAAT
*
2783426 ATGTTTAGTTTTAATTTAAACAAGAATAT
1 ATGTTT-GTTTTAATTTAAACAAGAAAAT
2783455 ATGTTTGTTTTAATTTAAA-AAGA
1 ATGTTTGTTTTAATTTAAACAAGA
2783478 GAACAAGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
27 4 0.09
28 19 0.40
29 24 0.51
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (28 bp):
ATGTTTGTTTTAATTTAAACAAGAAAAT
Found at i:2783526 original size:28 final size:30
Alignment explanation
Indices: 2783495--2783563 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
2783485 AAAAATATTT
2783495 TTTGTCTTAATCTAGACAA-A-AAAACATA
1 TTTGTCTTAATCTAGACAAGATAAAACATA
* * * * *
2783523 TTTGTCTCAATTTAGATAAGATAAAATATT
1 TTTGTCTTAATCTAGACAAGATAAAACATA
2783553 TTTGTCTTAAT
1 TTTGTCTTAAT
2783564 TAAAGACAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 16 0.48
29 1 0.03
30 16 0.48
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (30 bp):
TTTGTCTTAATCTAGACAAGATAAAACATA
Found at i:2783559 original size:30 final size:29
Alignment explanation
Indices: 2783480--2783574 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
2783470 TAAAAAGAGA
*
2783480 ACAAGAAAAATATTTTTTGTCTTAATCTAG
1 ACAAGAAAAATA-TTTTTGTCTTAATTTAG
* * *
2783510 ACAA-AAAAACATATTTGTCTCAATTTAG
1 ACAAGAAAAATATTTTTGTCTTAATTTAG
* *
2783538 ATAAGATAAAATATTTTTGTCTTAATTAAAG
1 ACAAGA-AAAATATTTTTGTCTTAATT-TAG
2783569 ACAAGA
1 ACAAGA
2783575 GTTGTCTTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 17 0.33
29 7 0.13
30 21 0.40
31 7 0.13
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (29 bp):
ACAAGAAAAATATTTTTGTCTTAATTTAG
Found at i:2787626 original size:116 final size:116
Alignment explanation
Indices: 2787428--2787644 Score: 263
Period size: 116 Copynumber: 1.9 Consensus size: 116
2787418 ACTGTCACCA
* * * * * *
2787428 TCTCTCTTTGTCTATCTCTTGCCATCTCGTCATATCGTCGTTGATTTATAAACCAAAAAGCATGA
1 TCTCTCTTTGTCTATCTCTTGCCATCTCGCCATATCATCGTCGATCTACAAACAAAAAAGCATGA
*
2787493 CATGGCAAGGAACAATATGTTCTTGGGTTTATTGGTTTACATTCACAAAAC
66 CATGGCAAGGAACAATATATTCTTGGGTTTATTGGTTTACATTCACAAAAC
* ** * * * *
2787544 TCTCTCTTTGTCTATCTTTTGTTATCTCGCCATATTATCGTCGATCTACAGACAAAAAAGTATGG
1 TCTCTCTTTGTCTATCTCTTGCCATCTCGCCATATCATCGTCGATCTACAAACAAAAAAGCATGA
** * * *
2787609 CATGGTGAGTAATAATATATTTTTGGGTTTATTGGT
66 CATGGCAAGGAACAATATATTCTTGGGTTTATTGGT
2787645 ATTGAGTTTT
Statistics
Matches: 82, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
116 82 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (116 bp):
TCTCTCTTTGTCTATCTCTTGCCATCTCGCCATATCATCGTCGATCTACAAACAAAAAAGCATGA
CATGGCAAGGAACAATATATTCTTGGGTTTATTGGTTTACATTCACAAAAC
Found at i:2793570 original size:2 final size:2
Alignment explanation
Indices: 2793563--2793601 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2793553 GCATTCAAAT
2793563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2793602 GAGGCATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2793749 original size:16 final size:16
Alignment explanation
Indices: 2793724--2793775 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
2793714 TCATTACATT
*
2793724 TATTAATTAATTAAAA
1 TATTATTTAATTAAAA
2793740 TATTATTTAATTAAAA
1 TATTATTTAATTAAAA
2793756 TATTATTTAATTAAAA
1 TATTATTTAATTAAAA
2793772 -ATTA
1 TATTA
2793776 AAGATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTATTTAATTAAAA
Found at i:2800362 original size:16 final size:16
Alignment explanation
Indices: 2800341--2800371 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2800331 TTGTGACGGT
2800341 TTGAAGAAGAGGTTGG
1 TTGAAGAAGAGGTTGG
*
2800357 TTGAAGAAGATGTTG
1 TTGAAGAAGAGGTTG
2800372 ACAAAGTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (16 bp):
TTGAAGAAGAGGTTGG
Found at i:2805161 original size:126 final size:125
Alignment explanation
Indices: 2804933--2805261 Score: 348
Period size: 126 Copynumber: 2.6 Consensus size: 125
2804923 TCCTTGTCAG
* * *
2804933 CTAATTTTGGAAAGATCCCAAAATCACCACCATCTCCTAATCCAGCACCATCAAAACA-CCAGGG
1 CTAA-TTTGGAAAGACCCCAAAATCACCACC-TCTCCTAAGCCAGCACCATCAAAACATCAAGGG
* * * * * ** * * **
2804997 AGACCTTGAGCAACC-AGTACAACAAAGGTCATCTCCAGAATTTCAGCTCATCTCCATGTTTA
64 ATA-ATCGAGCAGCCGAGCACAACAAAAATCATCACCAGAATTTCAGCTCATATCCACATTTA
2805059 CTAATTTCGGAAAGACCCCAAAATCACCACCTTCTCCTAAGCCAGCACCATCAAAACATCAAGGG
1 CTAATTT-GGAAAGACCCCAAAATCACCACC-TCTCCTAAGCCAGCACCATCAAAACATCAAGGG
* * * *
2805124 ATAATCAAGCAGCCGA-CACAACAAAAATCA-CGACCAGATTTTCAGTTGATATCCACATTTA
64 ATAATCGAGCAGCCGAGCACAACAAAAATCATC-ACCAGAATTTCAGCTCATATCCACATTTA
* * * *
2805185 CTAATCTTGGAAAGACCCC-AATTCACCA--TCTCCTAAGCCAGCACCACCAAAAGATCAAGGCA
1 CTAAT-TTGGAAAGACCCCAAAATCACCACCTCTCCTAAGCCAGCACCATCAAAACATCAAGGGA
2805247 TAATCGAGCAGCCGA
65 TAATCGAGCAGCCGA
2805262 TGCAACGACA
Statistics
Matches: 174, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
122 45 0.26
125 12 0.07
126 107 0.61
127 10 0.06
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (125 bp):
CTAATTTGGAAAGACCCCAAAATCACCACCTCTCCTAAGCCAGCACCATCAAAACATCAAGGGAT
AATCGAGCAGCCGAGCACAACAAAAATCATCACCAGAATTTCAGCTCATATCCACATTTA
Found at i:2805286 original size:122 final size:124
Alignment explanation
Indices: 2805055--2805289 Score: 314
Period size: 122 Copynumber: 1.9 Consensus size: 124
2805045 CATCTCCATG
*
2805055 TTTACTAATTTCGGAAAGACCCCAAAATCACCACCTTCTCCTAAGCCAGCACCATCAAAACATCA
1 TTTACTAATTTCGGAAAGACCCCAAAATCACCA-C-TCTCCTAAGCCAGCACCACCAAAACATCA
* *
2805120 AGGGATAATCAAGCAGCCGACACAACAAAAATCACGACCAGATTTTCAGTTGATATCCACA
64 AGGCATAATCAAGCAGCCGACACAACAAAAATCACCACCAGATTTTCAGTTGATATCCACA
* *
2805181 TTTACTAATCTT-GGAAAGACCCC-AATTCACCA-TCTCCTAAGCCAGCACCACCAAAAGATCAA
1 TTTACTAAT-TTCGGAAAGACCCCAAAATCACCACTCTCCTAAGCCAGCACCACCAAAACATCAA
* ** * * * *
2805243 GGCATAATCGAGCAGCCGATGCAACGACAATCACCTCCCGATTTTCA
65 GGCATAATCAAGCAGCCGACACAACAAAAATCACCACCAGATTTTCA
2805290 TTTTGCTTCA
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
122 66 0.69
125 8 0.08
126 20 0.21
127 2 0.02
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.20
Consensus pattern (124 bp):
TTTACTAATTTCGGAAAGACCCCAAAATCACCACTCTCCTAAGCCAGCACCACCAAAACATCAAG
GCATAATCAAGCAGCCGACACAACAAAAATCACCACCAGATTTTCAGTTGATATCCACA
Found at i:2806392 original size:2 final size:2
Alignment explanation
Indices: 2806385--2806413 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2806375 AAAGAATAAG
2806385 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 T
2806414 TGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2810263 original size:2 final size:2
Alignment explanation
Indices: 2810256--2810293 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2810246 TACTCTTTAA
* *
2810256 GT GT GT GT AT GC GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2810294 ATGCTTATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.03, G:0.47, T:0.47
Consensus pattern (2 bp):
GT
Found at i:2812485 original size:125 final size:125
Alignment explanation
Indices: 2812263--2812515 Score: 434
Period size: 125 Copynumber: 2.0 Consensus size: 125
2812253 TAATTTTATT
* *
2812263 TTTTACCTTACCTTGACTTAGTCTTTTTATTGTGAAGAAAGAATTAGTCTTTGATCCACATTCTG
1 TTTTACATTACCTTGACTTAGTCTTTTTATTGTGAAGAAAGAATCAGTCTTTGATCCACATTCTG
* *
2812328 ACGTTATAAATATTTTGTAACGTTAGATAGAATATTTCATCCTGATTTAGTCTTTAATTC
66 ACGTTATAAATATTTTGTAACGTTAGACAGAATATTTAATCCTGATTTAGTCTTTAATTC
*
2812388 TTTTACATTACCTTGACTTAGTCTTTTTATTGTGAAGAAAGAATCAGTCTTTGATTCACATTCTG
1 TTTTACATTACCTTGACTTAGTCTTTTTATTGTGAAGAAAGAATCAGTCTTTGATCCACATTCTG
* * *
2812453 CCTTTATAAATATTTTGTAATGTTAGACAGAATATTTAATCCTGATTTAGTCTTTAATTC
66 ACGTTATAAATATTTTGTAACGTTAGACAGAATATTTAATCCTGATTTAGTCTTTAATTC
2812513 TTT
1 TTT
2812516 CAGGATATTT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (125 bp):
TTTTACATTACCTTGACTTAGTCTTTTTATTGTGAAGAAAGAATCAGTCTTTGATCCACATTCTG
ACGTTATAAATATTTTGTAACGTTAGACAGAATATTTAATCCTGATTTAGTCTTTAATTC
Found at i:2816008 original size:14 final size:14
Alignment explanation
Indices: 2815989--2816023 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2815979 TGTTTTATTA
2815989 TTATTTATATTTAT
1 TTATTTATATTTAT
*
2816003 TTATTTATTTTTAT
1 TTATTTATATTTAT
2816017 TCTATTT
1 T-TATTT
2816024 TCTCATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATATTTAT
Found at i:2831468 original size:14 final size:14
Alignment explanation
Indices: 2831428--2831476 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2831418 TTAAGTTAGA
*
2831428 ATTTAGTCATTTTT
1 ATTTAGTTATTTTT
*
2831442 AGTTA-TT-TTTTT
1 ATTTAGTTATTTTT
2831454 ATTTAGTTATTTTT
1 ATTTAGTTATTTTT
*
2831468 ATTAAGTTA
1 ATTTAGTTA
2831477 AGTTAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 9 0.31
13 3 0.10
14 17 0.59
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.65
Consensus pattern (14 bp):
ATTTAGTTATTTTT
Found at i:2846039 original size:21 final size:21
Alignment explanation
Indices: 2846006--2846046 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2845996 TTAAAGTCAT
*
2846006 TTAAAATAGAATAACTTAAAA
1 TTAAAATAAAATAACTTAAAA
*
2846027 TTAAAGTAAAATAACTTAAA
1 TTAAAATAAAATAACTTAAA
2846047 CTAAACTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
TTAAAATAAAATAACTTAAAA
Found at i:2847295 original size:30 final size:31
Alignment explanation
Indices: 2847259--2847324 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2847249 ATAACATGGT
* *
2847259 CACATGGCAT-TTCATCCTCTATGTCAATGC
1 CACATGGCATATTCAACCTCCATGTCAATGC
*
2847289 CACATGGCATATTCAACTTCCATGTCAATGC
1 CACATGGCATATTCAACCTCCATGTCAATGC
2847320 CACAT
1 CACAT
2847325 TGTATAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (31 bp):
CACATGGCATATTCAACCTCCATGTCAATGC
Found at i:2847812 original size:3 final size:3
Alignment explanation
Indices: 2847804--2847855 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
2847794 TACACACATC
* * * *
2847804 ATA ATA ATA ATA ATA ACA ACA ACA ACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2847852 ATA A
1 ATA A
2847856 CAATTAGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:2848853 original size:24 final size:23
Alignment explanation
Indices: 2848800--2848845 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2848790 AATTTATGAA
*
2848800 AATAATAATTTT--TTTTTATTT
1 AATAAAAATTTTAATTTTTATTT
2848821 AATAAAAATATTTAATTTTTATTT
1 AATAAAAAT-TTTAATTTTTATTT
2848845 A
1 A
2848846 TTCTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
24 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATAAAAATTTTAATTTTTATTT
Found at i:2863406 original size:2 final size:2
Alignment explanation
Indices: 2863399--2863425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2863389 TTTTAAACAA
2863399 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2863426 AAAACTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2865929 original size:150 final size:151
Alignment explanation
Indices: 2865657--2865959 Score: 545
Period size: 150 Copynumber: 2.0 Consensus size: 151
2865647 GCATAACCAC
* * *
2865657 AACTTTGATATAATCATGAATTTATCAGTGATCATCAATCTTCCTTCAAATATTTGAAATACTGT
1 AACTTTGATATAATCATGAATTTATCAGTAATCATCAATCTTCCTTCAAATACTTGAAATACAGT
2865722 TGTTTTCAAACTCATGCAATTGATTTTAATTGAAATCAAAGTCACGTAAGAGTTTGAAATGAAAA
66 TGTTTTCAAACTCATGCAATTGATTTTAATTGAAATCAAAGTCACGTAAGAGTTTGAAATGAAAA
*
2865787 AGGAACTTAAAAACAAGTGAA
131 AGGAACTTAAAAACAAGCGAA
* *
2865808 AACTTTGATATAATCATGAATTTATCAGTAATCATCAATCTTCTTTCAAATCCTTGAAATA-AGT
1 AACTTTGATATAATCATGAATTTATCAGTAATCATCAATCTTCCTTCAAATACTTGAAATACAGT
2865872 TGTTTTCAAACTCATGCAATTGATTTTAATTGAAATCAAAGTCACGTAAGAGTTTGAAATGAAAA
66 TGTTTTCAAACTCATGCAATTGATTTTAATTGAAATCAAAGTCACGTAAGAGTTTGAAATGAAAA
2865937 AGGAACTTAAAAACAAGCGAA
131 AGGAACTTAAAAACAAGCGAA
2865958 AA
1 AA
2865960 ACCATTTACA
Statistics
Matches: 146, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
150 89 0.61
151 57 0.39
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (151 bp):
AACTTTGATATAATCATGAATTTATCAGTAATCATCAATCTTCCTTCAAATACTTGAAATACAGT
TGTTTTCAAACTCATGCAATTGATTTTAATTGAAATCAAAGTCACGTAAGAGTTTGAAATGAAAA
AGGAACTTAAAAACAAGCGAA
Found at i:2875554 original size:61 final size:62
Alignment explanation
Indices: 2875399--2875556 Score: 139
Period size: 61 Copynumber: 2.6 Consensus size: 62
2875389 AGCCCTGATC
* * *
2875399 TATAT-TGGATGGTGTGGGCAATTCCCACGACTAGG-AAAAAGGGGGGCCTAAAGCCCCAATT
1 TATATATGG-TGGCGTGGGCAATTCCCACGAGTAGGTAAAAAGGGGGACCTAAAGCCCCAATT
** * * * * *
2875460 CGTACTA-GGTGGCATGGGCAGTTCCTA-GTAGTAGGTAAAAA-GGGGACTTGAAGCTCCC-ATT
1 TATA-TATGGTGGCGTGGGCAATTCCCACG-AGTAGGTAAAAAGGGGGACCTAAAGC-CCCAATT
*
2875521 TATATATGGTGGGGTGGGCAATTCCCACGAGTAGGT
1 TATATATGGTGGCGTGGGCAATTCCCACGAGTAGGT
2875557 GATGNNNNNN
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
60 3 0.04
61 59 0.80
62 12 0.16
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (62 bp):
TATATATGGTGGCGTGGGCAATTCCCACGAGTAGGTAAAAAGGGGGACCTAAAGCCCCAATT
Found at i:2877305 original size:27 final size:27
Alignment explanation
Indices: 2877267--2877321 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
2877257 CTTGTGACCA
*
2877267 ACAAAGTCCAAATGTGCTAAGGCACCT
1 ACAAAGTCCAAAGGTGCTAAGGCACCT
*
2877294 ACAAAGTCCAAAGGTGCTAATGCACCT
1 ACAAAGTCCAAAGGTGCTAAGGCACCT
2877321 A
1 A
2877322 ACCAATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (27 bp):
ACAAAGTCCAAAGGTGCTAAGGCACCT
Found at i:2881467 original size:22 final size:20
Alignment explanation
Indices: 2881428--2881467 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2881418 TTAACCTTTC
2881428 AATAGCAAATTCATAATTTG
1 AATAGCAAATTCATAATTTG
2881448 AATAGCACAATTCCATAATT
1 AATAGCA-AATT-CATAATT
2881468 AAGTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (20 bp):
AATAGCAAATTCATAATTTG
Found at i:2881578 original size:46 final size:46
Alignment explanation
Indices: 2881487--2881588 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
2881477 ACCTTAATCT
* * * *
2881487 ACAATTTAAAAACACAATTCAATAATTAATTAATCTACCTTAGTCC
1 ACAATTTAACAACACAATTCAACAATTAATTAATCAACCTCAGTCC
* **
2881533 ACAATTTAACAACACAGTTCAACAATTAATTGTTCAACCTCAGTCC
1 ACAATTTAACAACACAATTCAACAATTAATTAATCAACCTCAGTCC
2881579 ACAATTTAAC
1 ACAATTTAAC
2881589 TAATAATCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.43, C:0.23, G:0.04, T:0.30
Consensus pattern (46 bp):
ACAATTTAACAACACAATTCAACAATTAATTAATCAACCTCAGTCC
Found at i:2883327 original size:21 final size:20
Alignment explanation
Indices: 2883285--2883328 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2883275 GATGAACATC
*
2883285 TATTGATACATGGCCAAATG
1 TATTGATACATGACCAAATG
*
2883305 TATTGATACATGAACCCAATG
1 TATTGATACATG-ACCAAATG
2883326 TAT
1 TAT
2883329 CAATACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
TATTGATACATGACCAAATG
Found at i:2892526 original size:38 final size:39
Alignment explanation
Indices: 2892453--2892540 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 39
2892443 AATCACTAAG
2892453 TTTTATTTGAATTACTCACAAATGATTATAAACACTCAT
1 TTTTATTTGAATTACTCACAAATGATTATAAACACTCAT
* * **
2892492 TTTTACTTGAATTACTCAC-ATTGATTATAAACACTTGT
1 TTTTATTTGAATTACTCACAAATGATTATAAACACTCAT
2892530 TTTTATTTGAA
1 TTTTATTTGAA
2892541 AGGTTCAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 26 0.59
39 18 0.41
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (39 bp):
TTTTATTTGAATTACTCACAAATGATTATAAACACTCAT
Found at i:2893199 original size:22 final size:22
Alignment explanation
Indices: 2893174--2893219 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2893164 ACATCAAATA
2893174 TGCTTAAA-CCGATGGCTCAATG
1 TGCTTAAACCCG-TGGCTCAATG
2893196 TGCTTAAACCCGTGGCTCAATG
1 TGCTTAAACCCGTGGCTCAATG
2893218 TG
1 TG
2893220 AAATGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCTTAAACCCGTGGCTCAATG
Found at i:2900511 original size:35 final size:35
Alignment explanation
Indices: 2900471--2900544 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
2900461 TTGATAAAGG
** * * *
2900471 TTGATCCTGTAAAAGGCACGTTGTAGAGGTTATGC
1 TTGATCCTACAAAAGGCACATTGTAAAGGTTATAC
*
2900506 TTGATCCTACAAAAGGCATATTGTAAAGGTTATAC
1 TTGATCCTACAAAAGGCACATTGTAAAGGTTATAC
2900541 TTGA
1 TTGA
2900545 CCTTATTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (35 bp):
TTGATCCTACAAAAGGCACATTGTAAAGGTTATAC
Found at i:2903737 original size:70 final size:72
Alignment explanation
Indices: 2903588--2903747 Score: 227
Period size: 71 Copynumber: 2.2 Consensus size: 72
2903578 TTTATACTCT
* * *
2903588 ACACATAAGTATCAATACCTGTAAGTCAAATATCGATACTTTGAACATAAATTGTTTTCCCAAGG
1 ACAC-TAAGTATCAATACCTATAAGTCAAATATCGATACTTTGAAAACAAATTGTTTTCCCAAGG
*
2903653 CATTTTGA
65 CATTCTGA
*
2903661 ACACTAAGTAT-GATACCTATAAGT-AAGATATCGATACTTTGAAAACAAA-TGTTTTCCCAAGG
1 ACACTAAGTATCAATACCTATAAGTCAA-ATATCGATACTTTGAAAACAAATTGTTTTCCCAAGG
2903723 CATTCTGA
65 CATTCTGA
*
2903731 ACACTAAGTATTAATAC
1 ACACTAAGTATCAATAC
2903748 TTCTTTTTGA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
70 33 0.42
71 35 0.44
72 7 0.09
73 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (72 bp):
ACACTAAGTATCAATACCTATAAGTCAAATATCGATACTTTGAAAACAAATTGTTTTCCCAAGGC
ATTCTGA
Found at i:2909040 original size:48 final size:48
Alignment explanation
Indices: 2908969--2909075 Score: 178
Period size: 48 Copynumber: 2.2 Consensus size: 48
2908959 TTCACAGCGT
2908969 AGTGCAGAATGCAGGTGAATCATCCAATGTGAGTGCATTTGCTGGTAC
1 AGTGCAGAATGCAGGTGAATCATCCAATGTGAGTGCATTTGCTGGTAC
* * *
2909017 AGTGCAGAATGCTGGTGAATCATCTAATGTGAGTGCATTTGCTGGTCC
1 AGTGCAGAATGCAGGTGAATCATCCAATGTGAGTGCATTTGCTGGTAC
*
2909065 AATGCAGAATG
1 AGTGCAGAATG
2909076 TAGACAGTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (48 bp):
AGTGCAGAATGCAGGTGAATCATCCAATGTGAGTGCATTTGCTGGTAC
Found at i:2909386 original size:72 final size:74
Alignment explanation
Indices: 2909246--2909452 Score: 215
Period size: 72 Copynumber: 2.8 Consensus size: 74
2909236 TATTGATCCA
* *
2909246 TTTCATGGTCTTTCTGGTGTATCTCCAAACATAGTGCATATTAGCAACCAATCTGGACTGCCTTC
1 TTTCATGGTCTTTCTGGTGTATCTCC-AACATAGTGCATAGTAGCAACCAATCTGGACTGCCTCC
2909311 TAATCAAAGC
65 TAATCAAAGC
* * * * * *
2909321 TTTCTTGGTCTTTCTGGTGTATCTCC-A-ATAGTTCATGGTAGTAGCCAATTTGGACTGCCTCCT
1 TTTCATGGTCTTTCTGGTGTATCTCCAACATAGTGCATAGTAGCAACCAATCTGGACTGCCTCCT
* * *
2909384 AATGAAGGG
66 AATCAAAGC
* * * * * **
2909393 TTTCATAGTCTTTGTTGTGAATC-ACAA-ATAGTGCATAGTAGCAGGCAATCTGGACTGCCT
1 TTTCATGGTCTTTCTGGTGTATCTCCAACATAGTGCATAGTAGCAACCAATCTGGACTGCCT
2909453 GTTCAAGCAC
Statistics
Matches: 109, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
71 1 0.01
72 82 0.75
73 1 0.01
75 25 0.23
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (74 bp):
TTTCATGGTCTTTCTGGTGTATCTCCAACATAGTGCATAGTAGCAACCAATCTGGACTGCCTCCT
AATCAAAGC
Found at i:2916333 original size:2 final size:2
Alignment explanation
Indices: 2916326--2916353 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2916316 CTCACTGCAT
2916326 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
2916354 GGAACACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2921253 original size:20 final size:19
Alignment explanation
Indices: 2921215--2921253 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2921205 GAAAAAGAAA
*
2921215 ATTCATTTGTAGTTTGTTT
1 ATTCATTTGTAGGTTGTTT
*
2921234 ATTCTTTTGTAGAGTTGTTT
1 ATTCATTTGTAG-GTTGTTT
2921254 GAAAAGAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.15, C:0.05, G:0.18, T:0.62
Consensus pattern (19 bp):
ATTCATTTGTAGGTTGTTT
Found at i:2924096 original size:25 final size:26
Alignment explanation
Indices: 2924047--2924096 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2924037 GAATTTAAAA
*
2924047 ATAATTTTATCACTAAAAGTAGATAG
1 ATAATTTTATCACTAAAAATAGATAG
*
2924073 ATAATTTTATCA-TAAAAATGGATA
1 ATAATTTTATCACTAAAAATAGATA
2924097 CATGCCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (26 bp):
ATAATTTTATCACTAAAAATAGATAG
Found at i:2927102 original size:14 final size:14
Alignment explanation
Indices: 2927085--2927113 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2927075 ATATAAATAT
2927085 GTATATAGATTAAA
1 GTATATAGATTAAA
2927099 GTATATAGATTAAA
1 GTATATAGATTAAA
2927113 G
1 G
2927114 GATTAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (14 bp):
GTATATAGATTAAA
Found at i:2928874 original size:23 final size:23
Alignment explanation
Indices: 2928847--2928890 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2928837 AAAAAAAATC
* *
2928847 AATAACAATGGGTAATTACCATA
1 AATAACAATGCGTAATCACCATA
2928870 AATAACAATGCGTAATCACCA
1 AATAACAATGCGTAATCACCA
2928891 CGAAAATAAA
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:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (23 bp):
AATAACAATGCGTAATCACCATA
Found at i:2930001 original size:13 final size:13
Alignment explanation
Indices: 2929965--2930007 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2929955 TAAACTAATT
*
2929965 AATACATAAATTAA
1 AATAAATAAA-TAA
2929979 AATCAAATAAATAA
1 AAT-AAATAAATAA
*
2929993 AATAAATAATTAA
1 AATAAATAAATAA
2930006 AA
1 AA
2930008 AGTAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 11 0.42
14 9 0.35
15 6 0.23
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:2934330 original size:2 final size:2
Alignment explanation
Indices: 2934323--2934355 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2934313 CATTTAAACA
2934323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2934356 AAATGAGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2935464 original size:14 final size:14
Alignment explanation
Indices: 2935445--2935472 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2935435 CTCAAGCAAT
2935445 TCAAACTCAACAGG
1 TCAAACTCAACAGG
2935459 TCAAACTCAACAGG
1 TCAAACTCAACAGG
2935473 AAAAACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (14 bp):
TCAAACTCAACAGG
Found at i:2938411 original size:28 final size:27
Alignment explanation
Indices: 2938335--2938448 Score: 120
Period size: 28 Copynumber: 4.1 Consensus size: 27
2938325 AAAATATTTC
2938335 TTTTGTTACATGCCCTTTATAATTTCTA
1 TTTTGTTACATG-CCTTTATAATTTCTA
* * ** *
2938363 TTTTATAACACACACTTTATAATTTATA
1 TTTTGTTACATGC-CTTTATAATTTCTA
*
2938391 TTTTGTTACATGCCTTGTATAATTTTTA
1 TTTTGTTACATGCCTT-TATAATTTCTA
* *
2938419 TTTTGTTGCATGCCTTGACTAATTTCTA
1 TTTTGTTACATGCCTTTA-TAATTTCTA
2938447 TT
1 TT
2938449 CTATTATACG
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
27 5 0.07
28 65 0.93
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.53
Consensus pattern (27 bp):
TTTTGTTACATGCCTTTATAATTTCTA
Found at i:2938847 original size:56 final size:56
Alignment explanation
Indices: 2938755--2938861 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
2938745 TTATATGCCT
* * * * *
2938755 TGTATAATCTCTATTTTGTTCCACGCACTTTATAACTTTTGTTTTGTTACATATCC
1 TGTATAATCTCTATTTTGTTACACGCACCTAATAACTTTTATTTTCTTACATATCC
* *
2938811 TGTATAATTTTTATTTTGTTACACGC-CCTAAGTAACTTTTATTTTCTTACA
1 TGTATAATCTCTATTTTGTTACACGCACCTAA-TAACTTTTATTTTCTTACA
2938862 CGCCCTGACT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 3 0.07
56 40 0.93
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.50
Consensus pattern (56 bp):
TGTATAATCTCTATTTTGTTACACGCACCTAATAACTTTTATTTTCTTACATATCC
Found at i:2938850 original size:28 final size:27
Alignment explanation
Indices: 2938819--2938899 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 27
2938809 CCTGTATAAT
* *
2938819 TTTTATTTTGTTACACGCCCTAAGTAA
1 TTTTATTTTCTTACACGCCCTAACTAA
*
2938846 CTTTTATTTTCTTACACGCCCTGACTAA
1 -TTTTATTTTCTTACACGCCCTAACTAA
* *
2938874 TTTCTATTTTCTTACATGCCATAACT
1 TTT-TATTTTCTTACACGCCCTAACT
2938900 TTAATCCACT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.46
Consensus pattern (27 bp):
TTTTATTTTCTTACACGCCCTAACTAA
Found at i:2939955 original size:34 final size:33
Alignment explanation
Indices: 2939894--2939981 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
2939884 AAAAAAATTA
* * *
2939894 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAA-ATAAAATATATAAAATTATAAT-AAG
* *
2939929 AAATAAAAATAAAATATATAAGATTATAATAAT
1 AAATAAAAATAAAATATATAAAATTATAATAAG
2939962 AAATAAAAATAAAAATATAT
1 AAATAAAAAT-AAAATATAT
2939982 GACATTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
33 12 0.26
34 27 0.57
35 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
AAATAAAAATAAAATATATAAAATTATAATAAG
Found at i:2940171 original size:54 final size:54
Alignment explanation
Indices: 2940106--2940250 Score: 238
Period size: 54 Copynumber: 2.7 Consensus size: 54
2940096 TAGCAAAGTA
* * *
2940106 CTTGTAAACCAAACACTGTAATATTATCTTCTCTGCATTTTAATCATTATTTTG
1 CTTGTATACCAAACACTGTAATATTATTTTTTCTGCATTTTAATCATTATTTTG
2940160 CTTGTATACCAAACACTGTAATGA-TATTTTTTCTGCATTTTAATCATTATTTTG
1 CTTGTATACCAAACACTGTAAT-ATTATTTTTTCTGCATTTTAATCATTATTTTG
*
2940214 CTTGTATACCAAACACTGTAATGTTATTTTTTCTGCA
1 CTTGTATACCAAACACTGTAATATTATTTTTTCTGCA
2940251 ATAACATTGC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
54 84 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (54 bp):
CTTGTATACCAAACACTGTAATATTATTTTTTCTGCATTTTAATCATTATTTTG
Found at i:2944353 original size:38 final size:40
Alignment explanation
Indices: 2944296--2944397 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 40
2944286 TATTTAACTT
*
2944296 AAAATATTAAAAAAATAAAAAATATTAATACTTAATT-TTAA
1 AAAATATT--AAAATTAAAAAATATTAATACTTAATTATTAA
* * * *
2944337 AAAAT-TTTAACTT--AAAATATTAATATTTAATTATTCA
1 AAAATATTAAAATTAAAAAATATTAATACTTAATTATTAA
*
2944374 ATAATATTAAAATTAAAAAATATT
1 AAAATATTAAAATTAAAAAATATT
2944398 TTTAAATGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
36 18 0.37
37 7 0.14
38 9 0.18
40 10 0.20
41 5 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (40 bp):
AAAATATTAAAATTAAAAAATATTAATACTTAATTATTAA
Found at i:2945215 original size:86 final size:86
Alignment explanation
Indices: 2945121--2945279 Score: 300
Period size: 86 Copynumber: 1.8 Consensus size: 86
2945111 AATAATTAAA
* *
2945121 ATGTAACAACAATTATAAAATAATTAGTCTATATAAAAGTAGGATAATGTATTTTTCCATCTGAA
1 ATGTAACAACAATTATAAAATAATTAGTCTATATAAAAGTAGAATAATGTATTTTTCCATATGAA
2945186 AAAATTACACAATTTGTGTAG
66 AAAATTACACAATTTGTGTAG
2945207 ATGTAACAACAATTATAAAATAATTAGTCTATATAAAAGTAGAATAATGTATTTTTCCATATGAA
1 ATGTAACAACAATTATAAAATAATTAGTCTATATAAAAGTAGAATAATGTATTTTTCCATATGAA
2945272 AAAATTAC
66 AAAATTAC
2945280 GCATAATTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.35
Consensus pattern (86 bp):
ATGTAACAACAATTATAAAATAATTAGTCTATATAAAAGTAGAATAATGTATTTTTCCATATGAA
AAAATTACACAATTTGTGTAG
Done.