Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 41 of 168
Found at i:11298424 original size:5 final size:6
Alignment explanation
Indices: 11298371--11298490 Score: 57
Period size: 5 Copynumber: 21.3 Consensus size: 6
11298361 CTTAATCACC
*
11298371 TTAATA TTAA-A TTAATA -TAATA TTTATATA TTGATA --AATA TT-ATA
1 TTAATA TTAATA TTAATA TTAATA -TTA-ATA TTAATA TTAATA TTAATA
* *
11298416 TTAAT- TTAATA TTAA-A TCT--TA TTAA-A TTAATA -GAATA TTTATA
1 TTAATA TTAATA TTAATA T-TAATA TTAATA TTAATA TTAATA TTAATA
* * * *
11298459 TATAAGA TAAACA TTAA-A TTAATT TTAATA TT
1 T-TAATA TTAATA TTAATA TTAATA TTAATA TT
11298491 TAGATAGTCA
Statistics
Matches: 86, Mismatches: 12, Indels: 32
0.66 0.09 0.25
Matches are distributed among these distances:
4 4 0.05
5 38 0.44
6 33 0.38
7 8 0.09
8 3 0.03
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (6 bp):
TTAATA
Found at i:11298442 original size:60 final size:62
Alignment explanation
Indices: 11298375--11298490 Score: 182
Period size: 60 Copynumber: 1.9 Consensus size: 62
11298365 ATCACCTTAA
* * * *
11298375 TATTAAATTAATATAATATTTATATAT-TGATAAATATTATATTAA-TTTAATATTAAATCT
1 TATTAAATTAATAGAATATTTATATATAAGATAAACATTAAATTAATTTTAATATTAAATCT
11298435 TATTAAATTAATAGAATATTTATATATAAGATAAACATTAAATTAATTTTAATATT
1 TATTAAATTAATAGAATATTTATATATAAGATAAACATTAAATTAATTTTAATATT
11298491 TAGATAGTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 26 0.52
61 15 0.30
62 9 0.18
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (62 bp):
TATTAAATTAATAGAATATTTATATATAAGATAAACATTAAATTAATTTTAATATTAAATCT
Found at i:11298977 original size:10 final size:9
Alignment explanation
Indices: 11298962--11299004 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
11298952 AAAATATCAT
11298962 ATTAATTTTA
1 ATTAA-TTTA
*
11298972 ATTAATTTG
1 ATTAATTTA
11298981 ATTAATTTA
1 ATTAATTTA
*
11298990 ATTTAATTTG
1 A-TTAATTTA
11299000 ATTAA
1 ATTAA
11299005 AATTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 16 0.55
10 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (9 bp):
ATTAATTTA
Found at i:11298986 original size:19 final size:19
Alignment explanation
Indices: 11298962--11299004 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
11298952 AAAATATCAT
11298962 ATTAATTTTAA-TTAATTTG
1 ATTAA-TTTAATTTAATTTG
11298981 ATTAATTTAATTTAATTTG
1 ATTAATTTAATTTAATTTG
11299000 ATTAA
1 ATTAA
11299005 AATTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTAATTTAATTTAATTTG
Found at i:11301052 original size:25 final size:25
Alignment explanation
Indices: 11301024--11301112 Score: 142
Period size: 25 Copynumber: 3.6 Consensus size: 25
11301014 CAGACATACC
*
11301024 ACAGCTCATATGAGCTTCTCGATTT
1 ACAGCTCGTATGAGCTTCTCGATTT
*
11301049 ACAGATCGTATGAGCTTCTCGATTT
1 ACAGCTCGTATGAGCTTCTCGATTT
*
11301074 ACAGCTCGTATGAGCTTCCCGATTT
1 ACAGCTCGTATGAGCTTCTCGATTT
*
11301099 GCAGCTCGTATGAG
1 ACAGCTCGTATGAG
11301113 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCTCGATTT
Found at i:11301131 original size:25 final size:25
Alignment explanation
Indices: 11301054--11301132 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 25
11301044 GATTTACAGA
* * ** *
11301054 TCGTATGAGCTTCTCGATTTACAGC
1 TCGTATGAGCTTCCCAATTCGCAAC
* * *
11301079 TCGTATGAGCTTCCCGATTTGCAGC
1 TCGTATGAGCTTCCCAATTCGCAAC
*
11301104 TCGTATGAGTTTCCCAATTCGCAAC
1 TCGTATGAGCTTCCCAATTCGCAAC
11301129 TCGT
1 TCGT
11301133 GAGAGCATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
TCGTATGAGCTTCCCAATTCGCAAC
Found at i:11301132 original size:50 final size:50
Alignment explanation
Indices: 11301023--11301132 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
11301013 GCAGACATAC
* * * * *
11301023 CACAGCTCATATGAGCTTCTCGATTTACAGATCGTATGAGCTTCTCGATT
1 CACAACTCGTATGAGCTTCCCGATTTACAGATCGTATGAGCTTCCCAATT
* * * * *
11301073 TACAGCTCGTATGAGCTTCCCGATTTGCAGCTCGTATGAGTTTCCCAATT
1 CACAACTCGTATGAGCTTCCCGATTTACAGATCGTATGAGCTTCCCAATT
*
11301123 CGCAACTCGT
1 CACAACTCGT
11301133 GAGAGCATAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (50 bp):
CACAACTCGTATGAGCTTCCCGATTTACAGATCGTATGAGCTTCCCAATT
Found at i:11301936 original size:17 final size:17
Alignment explanation
Indices: 11301914--11301946 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11301904 ATAATAATTC
*
11301914 ATAAAAAAATTTTAAAA
1 ATAAAAAAATATTAAAA
11301931 ATAAAAAAATATTAAA
1 ATAAAAAAATATTAAA
11301947 CCGATTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAAAATATTAAAA
Found at i:11302550 original size:24 final size:24
Alignment explanation
Indices: 11302523--11302570 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
11302513 AAATTAGTAA
11302523 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
11302547 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
11302571 ACTAAACCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:11304477 original size:24 final size:24
Alignment explanation
Indices: 11304450--11304497 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
11304440 AGATTAGTAA
11304450 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
11304474 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
11304498 ATTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:11308347 original size:29 final size:30
Alignment explanation
Indices: 11308309--11308369 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
11308299 TATATTTTTT
11308309 ATAATATTTATA-CTTTTT-AATTTTCTAAA
1 ATAATATTTATATCTTTTTGAATTTT-TAAA
* *
11308338 ATAATTTTTATATTTTTTTGAATTTTTAAA
1 ATAATATTTATATCTTTTTGAATTTTTAAA
11308368 AT
1 AT
11308370 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (30 bp):
ATAATATTTATATCTTTTTGAATTTTTAAA
Found at i:11308913 original size:4 final size:4
Alignment explanation
Indices: 11308904--11308935 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
11308894 ATCATGTTGT
*
11308904 TTTA TTTA TTTA TTTA TTTA TTTA TCTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
11308936 CATTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:11310846 original size:2 final size:2
Alignment explanation
Indices: 11310841--11310870 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11310831 TACCAAGTAA
11310841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11310871 TTAAATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11328367 original size:19 final size:20
Alignment explanation
Indices: 11328332--11328374 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11328322 AAAAAAGTCA
* *
11328332 AAAAAATATTAATAATTTAT
1 AAAAAATATTAAAAATTAAT
11328352 AAAAAATA-TAAAAATTAAT
1 AAAAAATATTAAAAATTAAT
11328371 AAAA
1 AAAA
11328375 TGTACATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATATTAAAAATTAAT
Found at i:11328715 original size:17 final size:19
Alignment explanation
Indices: 11328693--11328735 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
11328683 GGGATTTTAA
11328693 TTTTTTAATAA-TTAT-TT
1 TTTTTTAATAATTTATATT
11328710 TTTTTT-ATAATTTATAATT
1 TTTTTTAATAATTTAT-ATT
11328729 TTTTTTA
1 TTTTTTA
11328736 TAGTTTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
19 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTAATAATTTATATT
Found at i:11328720 original size:19 final size:18
Alignment explanation
Indices: 11328693--11328737 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
11328683 GGGATTTTAA
*
11328693 TTTTTTAATAA-TTAT-T
1 TTTTTTTATAATTTATAT
11328709 TTTTTTTATAATTTATAAT
1 TTTTTTTATAATTTAT-AT
11328728 TTTTTTTATA
1 TTTTTTTATA
11328738 GTTTTGCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 10 0.40
17 4 0.16
19 11 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTATAATTTATAT
Found at i:11329848 original size:7 final size:8
Alignment explanation
Indices: 11329832--11329857 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11329822 AAAATATTTT
11329832 AAAATAAA
1 AAAATAAA
11329840 AAAATAAA
1 AAAATAAA
11329848 AAAATAAA
1 AAAATAAA
11329856 AA
1 AA
11329858 TTTATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:11331015 original size:15 final size:15
Alignment explanation
Indices: 11330995--11331028 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
11330985 TGTGTATGTG
11330995 ATGGTAGCTTGTTAA
1 ATGGTAGCTTGTTAA
11331010 ATGGTAGCTTGTTAA
1 ATGGTAGCTTGTTAA
11331025 ATGG
1 ATGG
11331029 CATATGCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (15 bp):
ATGGTAGCTTGTTAA
Found at i:11332912 original size:21 final size:21
Alignment explanation
Indices: 11332873--11332913 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11332863 AATCTCACCA
*
11332873 CTACAATACTCAATCTCATTT
1 CTACAATAATCAATCTCATTT
* *
11332894 CTACAATAATTAATTTCATT
1 CTACAATAATCAATCTCATT
11332914 GTAATTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (21 bp):
CTACAATAATCAATCTCATTT
Found at i:11335503 original size:19 final size:19
Alignment explanation
Indices: 11335474--11335525 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
11335464 TTTTTAATTA
11335474 TAAAAAA-TTTAAAATTTC
1 TAAAAAATTTTAAAATTTC
* *
11335492 TAAAAAATTTT-AGATTTG
1 TAAAAAATTTTAAAATTTC
*
11335510 TAAAATATTATTAAAA
1 TAAAAAATT-TTAAAA
11335526 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 20 0.74
19 5 0.19
20 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
TAAAAAATTTTAAAATTTC
Found at i:11336057 original size:17 final size:17
Alignment explanation
Indices: 11336004--11336057 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
11335994 GTGGACTAAA
* *
11336004 ATTTTTAAATGATTATTA
1 ATTTTTTAAT-ATTATTT
*
11336022 ATATTTTTAATATTGTTT
1 AT-TTTTTAATATTATTT
*
11336040 ATTTTTTAATTTTATTT
1 ATTTTTTAATATTATTT
11336057 A
1 A
11336058 ACATCTCTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 14 0.47
18 9 0.30
19 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
ATTTTTTAATATTATTT
Found at i:11336786 original size:5 final size:5
Alignment explanation
Indices: 11336776--11336807 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
11336766 ACTCACACTC
11336776 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT AC
1 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT AC
11336808 TTGAAAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (5 bp):
ACAAT
Found at i:11337116 original size:22 final size:22
Alignment explanation
Indices: 11337081--11337136 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
11337071 TGGAGCTGTG
* * *
11337081 GACTCAAGAAAATTTGCAATAT
1 GACTCGAGACAATTTGCAACAT
11337103 GACTCGAGACAATTTGCAACAT
1 GACTCGAGACAATTTGCAACAT
**
11337125 GTTTCGAGACAA
1 GACTCGAGACAA
11337137 ATACTTGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (22 bp):
GACTCGAGACAATTTGCAACAT
Found at i:11339359 original size:56 final size:50
Alignment explanation
Indices: 11339293--11339532 Score: 205
Period size: 50 Copynumber: 4.7 Consensus size: 50
11339283 ATTTGGGTAA
* * *
11339293 AGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGACATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACA-C--CGAG---ATG
*
11339349 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
** * * * * * *
11339399 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAATACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
** * * * * *
11339449 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCG-AGATG
* **
11339498 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
11339533 TTTGGCATGT
Statistics
Matches: 156, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
49 33 0.21
50 80 0.51
53 3 0.02
55 1 0.01
56 39 0.25
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
Found at i:11339401 original size:50 final size:50
Alignment explanation
Indices: 11339346--11339539 Score: 212
Period size: 50 Copynumber: 3.9 Consensus size: 50
11339336 CATTGAGATT
*
11339346 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * * * *
11339396 ATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* ** * *
11339446 ACGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** *
11339495 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
11339540 TGTTATTATC
Statistics
Matches: 119, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
49 39 0.33
50 80 0.67
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:11353171 original size:6 final size:6
Alignment explanation
Indices: 11353160--11353213 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
11353150 AAGTATATTC
11353160 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
11353208 ATGTAT
1 ATGTAT
11353214 GAATTCATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:11353913 original size:27 final size:28
Alignment explanation
Indices: 11353867--11353941 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
11353857 TAAAGGAAAC
* * * *
11353867 GCCTTTGTGACAATCACTGTA-ATGGAT
1 GCCTTTGTGACTATCTCTGTACAAGGAA
*
11353894 GCCTTTGTGGCTATCTCTGTACAAGGAA
1 GCCTTTGTGACTATCTCTGTACAAGGAA
* *
11353922 GCCTTTATGACTACCTCTGT
1 GCCTTTGTGACTATCTCTGT
11353942 TAAAATGATT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (28 bp):
GCCTTTGTGACTATCTCTGTACAAGGAA
Found at i:11363690 original size:16 final size:17
Alignment explanation
Indices: 11363658--11363690 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11363648 ATCGAACATG
11363658 ATTTTAGTAAGTTTGTA
1 ATTTTAGTAAGTTTGTA
*
11363675 ATTTTATTAA-TTTGTA
1 ATTTTAGTAAGTTTGTA
11363691 GAGTTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (17 bp):
ATTTTAGTAAGTTTGTA
Found at i:11364254 original size:4 final size:4
Alignment explanation
Indices: 11364236--11364275 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
11364226 CATTCCAATA
*
11364236 TCAT TCAT CCA- TCAT TCAT TCAT TCAT T-AT TCAT TC-T TCA
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCA
11364276 CTAGTTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 8 0.26
4 23 0.74
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (4 bp):
TCAT
Found at i:11364254 original size:15 final size:15
Alignment explanation
Indices: 11364236--11364271 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11364226 CATTCCAATA
11364236 TCATTCATCCATCAT
1 TCATTCATCCATCAT
* *
11364251 TCATTCATTCATTAT
1 TCATTCATCCATCAT
11364266 TCATTC
1 TCATTC
11364272 TTCACTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATTCATCCATCAT
Found at i:11364283 original size:15 final size:15
Alignment explanation
Indices: 11364236--11364285 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
11364226 CATTCCAATA
*
11364236 TCATTCATCCA-TCAT
1 TCATTCATTCACT-AT
*
11364251 TCATTCATTCATTAT
1 TCATTCATTCACTAT
11364266 TCATTC-TTCACTAGT
1 TCATTCATTCACTA-T
11364281 TCATT
1 TCATT
11364286 TTCTCTCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 6 0.19
15 24 0.77
16 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.02, T:0.48
Consensus pattern (15 bp):
TCATTCATTCACTAT
Found at i:11365147 original size:19 final size:19
Alignment explanation
Indices: 11365123--11365162 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
11365113 ATCTCATCTC
11365123 ATTCA-TTGCATTTAGATTA
1 ATTCATTTGCATTTAG-TTA
11365142 ATTCATTTGCATTTAGTTA
1 ATTCATTTGCATTTAGTTA
11365161 AT
1 AT
11365163 ATTAATGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTCATTTGCATTTAGTTA
Found at i:11368225 original size:79 final size:78
Alignment explanation
Indices: 11368081--11368337 Score: 324
Period size: 79 Copynumber: 3.3 Consensus size: 78
11368071 AAAGTATATA
*
11368081 AATTGAATTAAATGTATGAATTTTATATATGTATATGTGAGGTTCGAATATATATATGTATATAC
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTC-AA-ATATATATGTATATAC
11368146 ATGTATAAGTTATTG
64 ATGTATAAGTTATTG
*
11368161 AATTGAATTAAA-GTATGAAATATATATATATGTATATGTGAGGTTCAAATATATATGTATATAC
1 AATTGAATTAAAGGTATG-AAT-TTTATATATGTATATGTGAGGTTCAAATATATATGTATATAC
*
11368225 ATGTATAAGTTCTTG
64 ATGTATAAGTTATTG
* * * * * *
11368240 AATTGAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTC-GA-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCAAATATATATGTATATACAT
* *
11368303 ATACAAG-TACTTG
66 GTATAAGTTA-TTG
* *
11368316 AGTTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
11368338 GTAAATATTT
Statistics
Matches: 159, Mismatches: 14, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
75 1 0.01
76 43 0.27
77 1 0.01
78 19 0.12
79 50 0.31
80 22 0.14
81 23 0.14
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGAGGTTCAAATATATATGTATATACAT
GTATAAGTTATTG
Found at i:11368562 original size:40 final size:41
Alignment explanation
Indices: 11368486--11368584 Score: 155
Period size: 40 Copynumber: 2.4 Consensus size: 41
11368476 AGTTTTGTGC
11368486 CTAGCAGGCTTAATGCCAATGAAATTTTTCAAACTTAATGT
1 CTAGCAGGCTTAATGCCAATGAAATTTTTCAAACTTAATGT
* ** *
11368527 CTATCAGGCTTAATGCCGGTG-AATTTTTCAGACTTAATGT
1 CTAGCAGGCTTAATGCCAATGAAATTTTTCAAACTTAATGT
11368567 CTAGCAGGCTTAATGCCA
1 CTAGCAGGCTTAATGCCA
11368585 GTGTTCTGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 34 0.65
41 18 0.35
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCAATGAAATTTTTCAAACTTAATGT
Found at i:11368764 original size:35 final size:35
Alignment explanation
Indices: 11368725--11368897 Score: 102
Period size: 35 Copynumber: 5.2 Consensus size: 35
11368715 TTACATCTTA
11368725 TTTGATAAGTATATATATGCATTTAGTTATATACC
1 TTTGATAAGTATATATATGCATTTAGTTATATACC
* *
11368760 TTTG--AAGTGTATAT-T-CA-TTCGATTATAAGTA--
1 TTTGATAAGTATATATATGCATTTAG-TTAT-A-TACC
* **
11368791 TTTGATAGGTATATATATGCATTCGGTTATATACC
1 TTTGATAAGTATATATATGCATTTAGTTATATACC
* * **
11368826 TTTG--AAG--TGTATATGC-TTTCAATTATA-AGAA
1 TTTGATAAGTATATATATGCATTT-AGTTATATA-CC
* **
11368857 TTTGATAGGTATATATATGCATTCGGTTATATACC
1 TTTGATAAGTATATATATGCATTTAGTTATATACC
11368892 TTTGAT
1 TTTGAT
11368898 GTGTATATGC
Statistics
Matches: 100, Mismatches: 20, Indels: 36
0.64 0.13 0.23
Matches are distributed among these distances:
30 6 0.06
31 27 0.27
32 2 0.02
33 25 0.25
34 2 0.02
35 33 0.33
36 5 0.05
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.45
Consensus pattern (35 bp):
TTTGATAAGTATATATATGCATTTAGTTATATACC
Found at i:11368786 original size:31 final size:31
Alignment explanation
Indices: 11368751--11368974 Score: 118
Period size: 33 Copynumber: 6.9 Consensus size: 31
11368741 ATGCATTTAG
11368751 TTATATACCTTTGAAGTGTATATTCATTCGA
1 TTATATACCTTTGAAGTGTATATTCATTCGA
* *
11368782 TTATAAGTA--TTTGATAGGTATATATATGCATTCGG
1 TTAT-A-TACCTTTGA-A-GTGTATAT-T-CATTCGA
* * *
11368817 TTATATACCTTTGAAGTGTATATGCTTTCAA
1 TTATATACCTTTGAAGTGTATATTCATTCGA
** * *
11368848 TTATA-AGAATTTGATAGGTATATATATGCATTCGG
1 TTATATA-CCTTTGA-A-GTGTATAT-T-CATTCGA
* *
11368883 TTATATACCTTTGATGTGTATATGCATTCGA
1 TTATATACCTTTGAAGTGTATATTCATTCGA
*
11368914 TTATAAGTA--TTTGATAG-GTATATATGCATTCGG
1 TTAT-A-TACCTTTGA-AGTGTATAT-T-CATTCGA
* * * *
11368947 TTGTATACATTTGATGTGTATATGCATT
1 TTATATACCTTTGAAGTGTATATTCATT
11368975 TGGTTATAAG
Statistics
Matches: 145, Mismatches: 26, Indels: 44
0.67 0.12 0.20
Matches are distributed among these distances:
30 1 0.01
31 50 0.34
32 7 0.05
33 54 0.37
34 3 0.02
35 29 0.20
36 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.44
Consensus pattern (31 bp):
TTATATACCTTTGAAGTGTATATTCATTCGA
Found at i:11368804 original size:66 final size:66
Alignment explanation
Indices: 11368723--11369015 Score: 414
Period size: 66 Copynumber: 4.5 Consensus size: 66
11368713 ATTTACATCT
* ** *
11368723 TATTTGATAAGTATATATATGCATTTAGTTATATACCTTTGAAGTGTATATTCATTCGATTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGAAGTGTATATGCATTCGATTATAA
11368788 G
66 G
* *
11368789 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGAAGTGTATATGCTTTCAATTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGAAGTGTATATGCATTCGATTATAA
11368854 G
66 G
* *
11368855 AATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTCGATTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGAAGTGTATATGCATTCGATTATAA
11368920 G
66 G
* * * * *
11368921 TATTTGATAGG--TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTTGGTTATAA
1 TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGAAGTGTATATGCATTCGATTATAA
11368984 G
66 G
* * *
11368985 TAGTTGATAAG--TATATATGCATTCGATTATA
1 TATTTGATAGGTATATATATGCATTCGGTTATA
11369016 ATTATTTGAT
Statistics
Matches: 208, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
64 76 0.37
66 132 0.63
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (66 bp):
TATTTGATAGGTATATATATGCATTCGGTTATATACCTTTGAAGTGTATATGCATTCGATTATAA
G
Found at i:11368992 original size:31 final size:32
Alignment explanation
Indices: 11368760--11369034 Score: 208
Period size: 31 Copynumber: 8.4 Consensus size: 32
11368750 GTTATATACC
* *
11368760 TTTGA-AGTGTATATTCATTCGATTATAAGTA
1 TTTGATAGTATATATGCATTCGATTATAAGTA
*
11368791 TTTGATAGGTATATATATGCATTCGGTTAT-A-TA
1 TTTGATA-G--TATATATGCATTCGATTATAAGTA
* * * *
11368824 CCTTTGA-AGTGTATATGCTTTCAATTATAAGAA
1 --TTTGATAGTATATATGCATTCGATTATAAGTA
*
11368857 TTTGATAGGTATATATATGCATTCGGTTAT-A-TA
1 TTTGATA-G--TATATATGCATTCGATTATAAGTA
*
11368890 CCTTTGAT-GTGTATATGCATTCGATTATAAGTA
1 --TTTGATAGTATATATGCATTCGATTATAAGTA
* * *
11368923 TTTGATAGGTATATATGCATTCGGTTGTATA-CA
1 TTTGATA-GTATATATGCATTCGATTATA-AGTA
* * *
11368956 TTTGAT-GTGTATATGCATTTGGTTATAAGTA
1 TTTGATAGTATATATGCATTCGATTATAAGTA
* *
11368987 GTTGATAAGTATATATGCATTCGATTATAATTA
1 TTTGAT-AGTATATATGCATTCGATTATAAGTA
11369020 TTTGATAAGTATATA
1 TTTGAT-AGTATATA
11369035 CATACATTTG
Statistics
Matches: 193, Mismatches: 29, Indels: 42
0.73 0.11 0.16
Matches are distributed among these distances:
30 1 0.01
31 72 0.37
32 4 0.02
33 70 0.36
34 4 0.02
35 42 0.22
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (32 bp):
TTTGATAGTATATATGCATTCGATTATAAGTA
Found at i:11380369 original size:21 final size:21
Alignment explanation
Indices: 11380306--11380369 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
11380296 TTTTTTACGT
**
11380306 AATTAATATTTAGATATTTTA
1 AATTAATATTTAGATATACTA
* ** *
11380327 ATTATTAAAATTTATTTTTACTA
1 A--ATTAATATTTAGATATACTA
11380350 AATTAATATTTAGATATACT
1 AATTAATATTTAGATATACT
11380370 CTTATTAATT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
21 16 0.52
23 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (21 bp):
AATTAATATTTAGATATACTA
Found at i:11385793 original size:26 final size:26
Alignment explanation
Indices: 11385763--11385842 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 26
11385753 AAAAAATTAT
11385763 TTAAAAGATTATAAAA-TA-TATAAAAG
1 TTAAAA-ATTA-AAAATTATTATAAAAG
*
11385789 TTAAAAATTAAAAATTATTATAAATG
1 TTAAAAATTAAAAATTATTATAAAAG
* *
11385815 -GAAAAA-TATAAATTATTA-AAAA-
1 TTAAAAATTAAAAATTATTATAAAAG
11385837 TTAAAA
1 TTAAAA
11385843 TAACAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 7 0.15
24 15 0.33
25 11 0.24
26 13 0.28
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
TTAAAAATTAAAAATTATTATAAAAG
Found at i:11385917 original size:16 final size:17
Alignment explanation
Indices: 11385887--11385921 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11385877 AATTTTTTTG
*
11385887 TAAAAATCATGGAAAAT
1 TAAAAATCATAGAAAAT
11385904 TAAAAAT-ATAGAAAAT
1 TAAAAATCATAGAAAAT
11385920 TA
1 TA
11385922 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (17 bp):
TAAAAATCATAGAAAAT
Found at i:11386412 original size:11 final size:10
Alignment explanation
Indices: 11386392--11386450 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
11386382 TTTGTAATTC
11386392 ATATACTTTTT
1 ATATA-TTTTT
11386403 ATATATTTTT
1 ATATATTTTT
11386413 A-ATATTTTT
1 ATATATTTTT
* *
11386422 AATAAAGTTTT
1 -ATATATTTTT
* *
11386433 AAATATTTTC
1 ATATATTTTT
11386443 ATA-ATTTT
1 ATATATTTT
11386451 AAATTTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 13 0.33
10 15 0.38
11 11 0.28
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (10 bp):
ATATATTTTT
Found at i:11386421 original size:20 final size:19
Alignment explanation
Indices: 11386398--11386543 Score: 54
Period size: 20 Copynumber: 7.7 Consensus size: 19
11386388 ATTCATATAC
11386398 TTTTTATATATTTTTAATAT
1 TTTTTATA-ATTTTTAATAT
* *
11386418 TTTTAATAAAGTTTTAA-AT
1 TTTTTAT-AATTTTTAATAT
*
11386437 ATTTTCATAA-TTTTAA-AT
1 -TTTTTATAATTTTTAATAT
* * *
11386455 TTTTT-TTATTTTTCATAA
1 TTTTTATAATTTTTAATAT
* * *
11386473 CTTATATAA-TTTT-ATGT
1 TTTTTATAATTTTTAATAT
* **
11386490 TATTTTATTAGTTTTTTTTAT
1 T-TTTTA-TAATTTTTAATAT
* *
11386511 TTTTT-TCATTTTTTAATAA
1 TTTTTAT-AATTTTTAATAT
*
11386530 TTTATATAATTTTT
1 TTTTTATAATTTTT
11386544 TGTAATTTAT
Statistics
Matches: 92, Mismatches: 23, Indels: 23
0.67 0.17 0.17
Matches are distributed among these distances:
16 2 0.02
17 11 0.12
18 21 0.23
19 26 0.28
20 28 0.30
21 4 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTATAATTTTTAATAT
Found at i:11386542 original size:19 final size:20
Alignment explanation
Indices: 11386520--11386567 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
11386510 TTTTTTTCAT
11386520 TTTTTAATAATTTAT-ATAA
1 TTTTTAATAATTTATAATAA
**
11386539 TTTTTTGTAATTTATAATAA
1 TTTTTAATAATTTATAATAA
11386559 TTTTATAAT
1 TTTT-TAAT
11386568 GTTTGTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 13 0.57
20 8 0.35
21 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTAATAATTTATAATAA
Found at i:11386544 original size:20 final size:21
Alignment explanation
Indices: 11386518--11386567 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
11386508 TATTTTTTTC
11386518 ATTTTTTAATAATTTAT-ATA
1 ATTTTTTAATAATTTATAATA
*
11386538 ATTTTTT-GTAATTTATAATA
1 ATTTTTTAATAATTTATAATA
*
11386558 ATTTTATAAT
1 ATTTTTTAAT
11386568 GTTTGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 16 0.64
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTTTAATAATTTATAATA
Found at i:11386552 original size:27 final size:27
Alignment explanation
Indices: 11386521--11386590 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
11386511 TTTTTTCATT
*
11386521 TTTTAATAATTTATATAATTTTTTGTAA
1 TTTTAATAATTTATATAA-TGTTTGTAA
11386549 TTTATAATAATTT-TATAATGTTTGT-A
1 TTT-TAATAATTTATATAATGTTTGTAA
*
11386575 TTTTATATATTTTATA
1 TTTTA-ATAATTTATA
11386591 GTTTTTAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 10 0.27
27 8 0.22
28 8 0.22
29 9 0.24
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTAATAATTTATATAATGTTTGTAA
Found at i:11386583 original size:29 final size:29
Alignment explanation
Indices: 11386524--11386590 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 29
11386514 TTTCATTTTT
*
11386524 TAATAATTTATATAATTTTTTGTAATTTA
1 TAATAATTTATATAATTGTTTGTAATTTA
*
11386553 TAATAATTT-TATAA-TGTTTGTATTTTA
1 TAATAATTTATATAATTGTTTGTAATTTA
*
11386580 T-ATATTTTATA
1 TAATAATTTATA
11386591 GTTTTTAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.18
27 14 0.41
28 5 0.15
29 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (29 bp):
TAATAATTTATATAATTGTTTGTAATTTA
Found at i:11386643 original size:12 final size:12
Alignment explanation
Indices: 11386628--11386652 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11386618 TTATGATTCT
11386628 TTTTTTTAATGA
1 TTTTTTTAATGA
11386640 TTTTTTTAATGA
1 TTTTTTTAATGA
11386652 T
1 T
11386653 ATTAAATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTTTTAATGA
Found at i:11387092 original size:12 final size:12
Alignment explanation
Indices: 11387046--11387100 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
11387036 ATGGTATTTT
*
11387046 AATTTT-AATAA
1 AATTTTAAATTA
11387057 AATATTTAAATTA
1 AAT-TTTAAATTA
11387070 ACA--TT-AATTA
1 A-ATTTTAAATTA
11387080 AATTTTAAATTA
1 AATTTTAAATTA
11387092 AATTTTAAA
1 AATTTTAAA
11387101 AAATTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
11 7 0.19
12 17 0.46
13 5 0.14
14 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
AATTTTAAATTA
Found at i:11387099 original size:23 final size:24
Alignment explanation
Indices: 11387046--11387104 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
11387036 ATGGTATTTT
11387046 AATTTTAATAAAATATTTAAATTA
1 AATTTTAATAAAATATTTAAATTA
*
11387070 ACA--TTAATTAAAT-TTTAAATTA
1 A-ATTTTAATAAAATATTTAAATTA
11387092 AATTTTAA-AAAAT
1 AATTTTAATAAAAT
11387105 TCTCTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 14 0.47
23 13 0.43
24 1 0.03
25 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTTTAATAAAATATTTAAATTA
Found at i:11387340 original size:29 final size:28
Alignment explanation
Indices: 11387281--11387340 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
11387271 TTTTTAAAAT
* *
11387281 AAAAAATGGGGGTTTATTTTTAATGGAA
1 AAAAAATGAGGGTTTATTTTAAATGGAA
*
11387309 AAAAAGATGAGGGTTTATTTTAATATTGAA
1 AAAAA-ATGAGGGTTTATTTTAA-ATGGAA
11387339 AA
1 AA
11387341 TGGGGGTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 5 0.19
29 15 0.56
30 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (28 bp):
AAAAAATGAGGGTTTATTTTAAATGGAA
Found at i:11389482 original size:42 final size:43
Alignment explanation
Indices: 11389383--11389533 Score: 180
Period size: 42 Copynumber: 3.5 Consensus size: 43
11389373 AATGTGATAT
* * *
11389383 CGTGTAAGACCACGTCTGGGACGTTTGCATCGATTTGA-GATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATAT-ATGA-TTA
*
11389427 CGTGTAAGACCATGTCTGGGACATTGGCATC-ATATATGATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGATTA
* * * * *
11389469 CGTGTAAGACCATGTCTGAGACAATGGCATCGTTATTTGATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGATTA
*
11389512 CATGTAAGACCACGTCTGGGAC
1 CGTGTAAGACCACGTCTGGGAC
11389534 TTTGACATTG
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.35
43 33 0.35
44 28 0.30
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGATTA
Found at i:11391790 original size:11 final size:10
Alignment explanation
Indices: 11391763--11391812 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
11391753 AAAAGAAATG
11391763 AAGAAAGAAA
1 AAGAAAGAAA
11391773 GATAGAAACGAAA
1 -A-AGAAA-GAAA
*
11391786 TAGAAAGAAGA
1 AAGAAAGAA-A
11391797 AAGAAAGAAA
1 AAGAAAGAAA
11391807 AAGAAA
1 AAGAAA
11391813 ATGGAGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 10 0.29
11 15 0.44
12 5 0.15
13 4 0.12
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:11392771 original size:40 final size:40
Alignment explanation
Indices: 11392650--11392789 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
11392640 GACTTCGAGT
* * * *
11392650 CGATGAGACACTAGGTGTCAATTTACTACTTTGGATTAATT
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGGATT-ATC
* * *
11392691 CGATGAGACACTAGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGGATTATC
* *
11392728 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTAGGTGTCAAATTATTACTTCGGATTATC
* * *
11392768 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTAGGTGTCAAA
11392790 CTGGTGTGTT
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
37 17 0.21
38 12 0.15
39 2 0.02
40 34 0.41
41 17 0.21
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTAGGTGTCAAATTATTACTTCGGATTATC
Found at i:11393658 original size:16 final size:15
Alignment explanation
Indices: 11393612--11393666 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
11393602 AAACACTTAT
*
11393612 ATATATATGTATAATA
1 ATATATAT-AATAATA
11393628 AGTATATA-AATAATA
1 A-TATATATAATAATA
11393643 GCATATATATAA-AATA
1 --ATATATATAATAATA
11393659 ATATATAT
1 ATATATAT
11393667 TTATGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 8 0.24
15 6 0.18
16 11 0.32
17 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATATATAATAATA
Found at i:11397786 original size:6 final size:6
Alignment explanation
Indices: 11397775--11397805 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
11397765 TGCAAGCAAC
*
11397775 CCCTCA CCCTCA CCCTCA CCCTCA CCGTCA C
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA C
11397806 TTCACTTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.65, G:0.03, T:0.16
Consensus pattern (6 bp):
CCCTCA
Found at i:11402174 original size:13 final size:14
Alignment explanation
Indices: 11402148--11402181 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
11402138 TTTCTTACAT
11402148 AAGAAAGCAAAGAA
1 AAGAAAGCAAAGAA
11402162 AAGAAAG-AAAGAA
1 AAGAAAGCAAAGAA
*
11402175 AAAAAAG
1 AAGAAAG
11402182 GACACTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (14 bp):
AAGAAAGCAAAGAA
Found at i:11438927 original size:85 final size:88
Alignment explanation
Indices: 11438779--11438978 Score: 254
Period size: 85 Copynumber: 2.3 Consensus size: 88
11438769 GTAAAAAGTC
* * * *
11438779 TCAAACTTTTTC---AAAAAAA-AATTAATTTCCTTTTTTTTGCAATCAGTTGGAGACTTGACCT
1 TCAAACTTTTTCAAAAAAAAAACAATTAAGTCCCTTTTTTTTGCAATCACTTGGAGACTTGAACT
*
11438840 TTCAAAATGCATAAAAAATGCC-
66 TTCAAAATGCATAAAAAAGGCCT
*
11438862 TCAAA-TTTTTCAAAAAAAAAACAATTAAGTCCCTTTTTTTT-CACTCACTT-GAGAACTTGAAC
1 TCAAACTTTTTCAAAAAAAAAACAATTAAGTCCCTTTTTTTTGCAATCACTTGGAG-ACTTGAAC
*
11438924 TTTCAAAATGTATAAAAAAGGCCT
65 TTTCAAAATGCATAAAAAAGGCCT
*
11438948 TCAAACTTTTTCAAAAAAAAAAGCAAATAAG
1 TCAAACTTTTTCAAAAAAAAAA-CAATTAAG
11438979 CACATGTTTT
Statistics
Matches: 101, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
82 6 0.06
83 5 0.05
84 3 0.03
85 42 0.42
86 22 0.22
87 16 0.16
88 7 0.07
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.33
Consensus pattern (88 bp):
TCAAACTTTTTCAAAAAAAAAACAATTAAGTCCCTTTTTTTTGCAATCACTTGGAGACTTGAACT
TTCAAAATGCATAAAAAAGGCCT
Found at i:11439023 original size:91 final size:85
Alignment explanation
Indices: 11438807--11439033 Score: 217
Period size: 85 Copynumber: 2.6 Consensus size: 85
11438797 AAATTAATTT
* * ** *
11438807 CCTTTTTTTTGCAATCAGTTG-GAGACTTGACCTTTCAAAATGCATAAAAAATGCCTCAAATTTT
1 CCTTTTTTTT-CACTCAATTGAGA-ACTTGAAATTTCAAAATGCATAAAAAAGGCCTCAAATTTT
*
11438871 TCAAAAAAAAAACAATTAAGTC
64 TCAAAAAAAAAACAAATAAGTC
* * *
11438893 CCTTTTTTTTCACTCACTTGAGAACTTGAACTTTCAAAATGTATAAAAAAGGCCTTCAAACTTTT
1 CCTTTTTTTTCACTCAATTGAGAACTTGAAATTTCAAAATGCATAAAAAAGGCC-TCAAA-TTTT
11438958 TCAAAAAAAAAAGCAAATAAG-C
64 TCAAAAAAAAAA-CAAATAAGTC
* * * * *
11438980 ACATGTTTTTTTTTCACTCAATTGAGTACTT-AAATTGTTAAAATACATTAAAAA
1 -C---CTTTTTTTTCACTCAATTGAGAACTTGAAATT-TCAAAATGCATAAAAAA
11439034 TGTCTTTTGA
Statistics
Matches: 118, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
85 36 0.31
86 17 0.14
87 17 0.14
88 8 0.07
90 4 0.03
91 36 0.31
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.34
Consensus pattern (85 bp):
CCTTTTTTTTCACTCAATTGAGAACTTGAAATTTCAAAATGCATAAAAAAGGCCTCAAATTTTTC
AAAAAAAAAACAAATAAGTC
Found at i:11439076 original size:20 final size:20
Alignment explanation
Indices: 11439040--11439077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11439030 AAAATGTCTT
**
11439040 TTGACCATTAACTTTAACAG
1 TTGACCATTAAAGTTAACAG
11439060 TTGACCATTAAAGTTAAC
1 TTGACCATTAAAGTTAAC
11439078 TTCATCCCAT
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:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
TTGACCATTAAAGTTAACAG
Found at i:11439212 original size:28 final size:28
Alignment explanation
Indices: 11439142--11439221 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
11439132 TAAAAATCAA
*
11439142 TAAAAGTTATGAAAAT-TATTAAATTTTAT
1 TAAAAATTA-GAAAATAT-TTAAATTTTAT
11439171 TAAAAATATA-AAAATATTTAAATTTTAT
1 TAAAAAT-TAGAAAATATTTAAATTTTAT
*
11439199 TAAAAATTAGAAAAAATTATAAA
1 TAAAAATTAGAAAATATT-TAAA
11439222 AATTGTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
27 2 0.04
28 30 0.67
29 11 0.24
30 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (28 bp):
TAAAAATTAGAAAATATTTAAATTTTAT
Found at i:11439233 original size:39 final size:36
Alignment explanation
Indices: 11439172--11439249 Score: 95
Period size: 39 Copynumber: 2.1 Consensus size: 36
11439162 AAATTTTATT
*
11439172 AAAAATATAAAAATATTTAAATTTTATTAAAAATTAGA
1 AAAAATATAAAAATATTAAAATTTTA-TAAAAATTA-A
*
11439210 AAAAATTATAAAAAT-TGTAAAATTTTATAAGAATTAA
1 AAAAA-TATAAAAATAT-TAAAATTTTATAAAAATTAA
11439247 AAA
1 AAA
11439250 TTACATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 4 0.11
38 14 0.39
39 18 0.50
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (36 bp):
AAAAATATAAAAATATTAAAATTTTATAAAAATTAA
Found at i:11439237 original size:19 final size:19
Alignment explanation
Indices: 11439177--11439244 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
11439167 TTATTAAAAA
*
11439177 TATAAAAATAT-TTAAATTT
1 TATAAAAAT-TGTAAAATTT
**
11439196 TATTAAAAATTAG-AAAAAAT
1 TA-TAAAAATT-GTAAAATTT
11439216 TATAAAAATTGTAAAATTT
1 TATAAAAATTGTAAAATTT
*
11439235 TATAAGAATT
1 TATAAAAATT
11439245 AAAAATTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 13 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TATAAAAATTGTAAAATTT
Found at i:11439500 original size:29 final size:29
Alignment explanation
Indices: 11439467--11439536 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
11439457 TCTTTACATT
11439467 TTTTATAATTTTCTTACGACTTTATAAAA
1 TTTTATAATTTTCTTACGACTTTATAAAA
11439496 TTTTATAATTTTCTTACGACTTTATAAAA
1 TTTTATAATTTTCTTACGACTTTATAAAA
11439525 TTTTATAATTTT
1 TTTTATAATTTT
11439537 TTTCTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTTATAATTTTCTTACGACTTTATAAAA
Found at i:11439556 original size:29 final size:27
Alignment explanation
Indices: 11439467--11439584 Score: 101
Period size: 29 Copynumber: 4.1 Consensus size: 27
11439457 TCTTTACATT
* * *
11439467 TTTTATAATTTTCTTACGACTTTATAAAA
1 TTTTATAATTTT-TTACTA-TTTCTATAA
* * *
11439496 TTTTATAATTTTCTTACGACTTTATAAAA
1 TTTTATAATTTT-TTACTA-TTTCTATAA
*
11439525 TTTTATAATTTTTTTCTATATTCTATATA
1 TTTTATAATTTTTTACTAT-TTCTATA-A
* *
11439554 TTTTATCATTTTTTACTATTTTTATAA
1 TTTTATAATTTTTTACTATTTCTATAA
11439581 TTTT
1 TTTT
11439585 TTTTCTAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
27 6 0.08
28 15 0.19
29 59 0.74
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTATAATTTTTTACTATTTCTATAA
Found at i:11439644 original size:9 final size:9
Alignment explanation
Indices: 11439584--11439672 Score: 67
Period size: 9 Copynumber: 9.8 Consensus size: 9
11439574 TTTATAATTT
*
11439584 TTTTTCTAA
1 TTTTTATAA
11439593 TTTTTAATAA
1 TTTTT-ATAA
**
11439603 AATTTA-AA
1 TTTTTATAA
*
11439611 TATTTT-TAT
1 T-TTTTATAA
11439620 TTTATTATAA
1 TTT-TTATAA
11439630 -TTTTATAA
1 TTTTTATAA
11439638 TTTTTATAA
1 TTTTTATAA
11439647 TTTTTATAA
1 TTTTTATAA
* *
11439656 CTTTTATTGA
1 TTTTTA-TAA
11439666 TTTTTAT
1 TTTTTAT
11439673 TTTTTTGTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
8 10 0.16
9 38 0.60
10 15 0.24
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11439923 original size:87 final size:89
Alignment explanation
Indices: 11439770--11440001 Score: 272
Period size: 91 Copynumber: 2.6 Consensus size: 89
11439760 ATTGTAGAAA
** ** *** **
11439770 GGTCTTTTTTATGCATTTT-AGCATCTCAAGTACCCAATTGAGTGCCAAAAAAAAACTTGGGGCT
1 GGTCTTTTTTATGCATTTTGAAAAT-TCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCT
* *
11439834 TAATT-TTTTTTT-TAAAGTTTGAG
65 TAATTCTTTTTTTAAAAAGTTTAAG
11439857 GGTCTTTTTTATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTT
1 GGTCTTTTTTATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTT
11439922 AATTGCTTTTTTTGAAAAAGTTTAAG
66 AATT-CTTTTTTT-AAAAAGTTTAAG
* * * * *
11439948 GGCCTTTTTGATGCATTTTGAAAGTTCAAGTACTCAATTGAGTTAAAAAAAAAA
1 GGTCTTTTTTATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAA
11440002 GCAAGGGCTT
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
87 56 0.45
88 3 0.02
89 7 0.06
91 58 0.47
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (89 bp):
GGTCTTTTTTATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTT
AATTCTTTTTTTAAAAAGTTTAAG
Found at i:11440025 original size:91 final size:91
Alignment explanation
Indices: 11439773--11440030 Score: 258
Period size: 91 Copynumber: 2.9 Consensus size: 91
11439763 GTAGAAAGGT
* ** ** *** **
11439773 CTTTTTTATGCATTTT-AGCATCTCAAGTACCCAATTGAGTGCCAAAAAAAAACTTGGGGCTTAA
1 CTTTTTGATGCATTTTGAAAAT-TCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTTAA
* * *
11439837 TT--TTTTTTT--TAAAGTTTGAGGGT
65 TTACTTTTTTTGAAAAAGTTTAAGGGC
*
11439860 CTTTTTTATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTTAAT
1 CTTTTTGATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTTAAT
*
11439925 TGCTTTTTTTGAAAAAGTTTAAGGGC
66 TACTTTTTTTGAAAAAGTTTAAGGGC
* * * * **
11439951 CTTTTTGATGCATTTTGAAAGTTCAAGTACTCAATTGAGT-TAAAAAAAAAAGCAAGGGCTTAAT
1 CTTTTTGATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTTAAT
*
11440015 TACTTATTTTTTAAAA
66 TACTT-TTTTTGAAAA
11440031 TATTTGAGAA
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
87 53 0.37
88 3 0.02
89 7 0.05
90 24 0.17
91 57 0.40
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (91 bp):
CTTTTTGATGCATTTTGAAAATTCAAGTACCCAATTGAGTGAAAAAAAAAAACCAAGACCTTAAT
TACTTTTTTTGAAAAAGTTTAAGGGC
Found at i:11440940 original size:43 final size:41
Alignment explanation
Indices: 11440871--11441137 Score: 225
Period size: 42 Copynumber: 6.3 Consensus size: 41
11440861 TATGTGAAAA
* * * *
11440871 AAACGCCGTTAAAAAACATGACCTTTAGCGACGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGA-CTTTAGCGGCGCTTTA-TCAC
* * *
11440914 AAACGCCGCTAAAGAACGTGATCTTTAGTGGCTCTTTATCAC
1 AAACGCCGCTAAAGAACATGA-CTTTAGCGGCGCTTTATCAC
* * *
11440956 AAATGCCACTAAAGAACATGACTTTTAGCGGCGCTATATCAC
1 AAACGCCGCTAAAGAACATGAC-TTTAGCGGCGCTTTATCAC
* * *
11440998 AAACGCCGTTAAAGAGA-ATAACCTTTAGTGGCGCTTTTATCAC
1 AAACGCCGCTAAAGA-ACATGA-CTTTAGCGGCGC-TTTATCAC
* ** *
11441041 AAACGCCGCTATAGAGA-ATGACTTTAGCGGCTTTTTTTTCAC
1 AAACGCCGCTAAAGA-ACATGACTTTAGCGGC-GCTTTATCAC
* ** *
11441083 AAACGCCGCTATAGAGA-ATGACTTTAGCGGCTTTTTTTTCAC
1 AAACGCCGCTAAAGA-ACATGACTTTAGCGGC-GCTTTATCAC
11441125 AAACGCCGCTAAA
1 AAACGCCGCTAAA
11441138 AGTACCGTTC
Statistics
Matches: 191, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 132 0.69
43 58 0.30
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
AAACGCCGCTAAAGAACATGACTTTAGCGGCGCTTTATCAC
Found at i:11441089 original size:85 final size:84
Alignment explanation
Indices: 11440871--11441137 Score: 254
Period size: 85 Copynumber: 3.2 Consensus size: 84
11440861 TATGTGAAAA
* * * * * * *
11440871 AAACGCCGTTAAAAAACATGACCTTTAGCGACGCTTTACCCACAAACGCCGCTAAAGA-ACGTGA
1 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTATA-TCACAAACGCCGCTAAAGAGA-AT-A
*
11440935 TCTTTAGTGGCTC-TTTATCAC
63 ACTTTAGTGGCTCTTTTATCAC
* * *
11440956 AAATGCCACTAAAGAACATGACTTTTAGCGGCGCTATATCACAAACGCCGTTAAAGAGAATAACC
1 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTATATCACAAACGCCGCTAAAGAGAATAA-C
*
11441021 TTTAGTGGCGCTTTTATCAC
65 TTTAGTGGCTCTTTTATCAC
* ** * * * *
11441041 AAACGCCGCTATAGAGA-ATGAC-TTTAGCGGCTTTTTTTTCACAAACGCCGCTATAGAGAATGA
1 AAACGCCGCTAAAGA-ACATGACTTTTAGCGGC-GCTATATCACAAACGCCGCTAAAGAGAATAA
* * *
11441104 CTTTAGCGGCTTTTTTTTCAC
64 CTTTAGTGGCTCTTTTATCAC
11441125 AAACGCCGCTAAA
1 AAACGCCGCTAAA
11441138 AGTACCGTTC
Statistics
Matches: 150, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
83 1 0.01
84 67 0.45
85 81 0.54
86 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (84 bp):
AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTATATCACAAACGCCGCTAAAGAGAATAACT
TTAGTGGCTCTTTTATCAC
Found at i:11441104 original size:127 final size:125
Alignment explanation
Indices: 11440871--11441113 Score: 280
Period size: 127 Copynumber: 1.9 Consensus size: 125
11440861 TATGTGAAAA
*
11440871 AAACGCCGTTAAAAAACATGACCTTTAGCGACGCTTTACCCACAAACGCCGCTAAAGAACGTGAT
1 AAACGCCGTTAAAAAACATAACCTTTAGCGACGCTTTACCCACAAACGCCGCTAAAGAAC-TGAT
* *
11440936 CTTTAGTGGCTCTTTATCACAAATGCCACTAAAGAACATGACTTTTAGCGGCGCTATATCAC
65 CTTTAGCGGCTCTTTATCACAAACGCCACTAAAGAACATGAC-TTTAGCGGCGCTATATCAC
* * * *
11440998 AAACGCCGTTAAAGAGA-ATAACCTTTAGTGGCGCTTTTA-TCACAAACGCCGCTATAGAGAA-T
1 AAACGCCGTTAAA-AAACATAACCTTTAGCGACGC-TTTACCCACAAACGCCGCTA-A-AGAACT
* * * *
11441060 GA-CTTTAGCGGCTTTTTTTTCACAAACGCCGCTATAGAGA-ATGACTTTAGCGGC
62 GATCTTTAGCGGC-TCTTTATCACAAACGCCACTAAAGA-ACATGACTTTAGCGGC
11441114 TTTTTTTTCA
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
126 18 0.18
127 69 0.70
128 8 0.08
129 4 0.04
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (125 bp):
AAACGCCGTTAAAAAACATAACCTTTAGCGACGCTTTACCCACAAACGCCGCTAAAGAACTGATC
TTTAGCGGCTCTTTATCACAAACGCCACTAAAGAACATGACTTTAGCGGCGCTATATCAC
Found at i:11441505 original size:23 final size:23
Alignment explanation
Indices: 11441475--11441522 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
11441465 CATAAGTAAA
11441475 TAGATATATCAACCTATTGGCAC
1 TAGATATATCAACCTATTGGCAC
11441498 TAGATATATCAACCTATTGGCAC
1 TAGATATATCAACCTATTGGCAC
11441521 TA
1 TA
11441523 ATTCAGCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.31
Consensus pattern (23 bp):
TAGATATATCAACCTATTGGCAC
Found at i:11443150 original size:84 final size:84
Alignment explanation
Indices: 11443009--11443180 Score: 265
Period size: 84 Copynumber: 2.0 Consensus size: 84
11442999 TTTAGTGGCA
* *
11443009 TTTTTAAGAAAGTGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAA
1 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAA
*
11443074 CCTAAGCCCAACGACGCCG
66 CCTAAGCCCAAAGACGCCG
* * *
11443093 TTTTTAGGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTCGGGAAA-CGCCGCAAAAA
1 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT-GAGAAAGCGCCGCAAAAA
*
11443157 ACCTAAGCCTAAAGACGCCG
65 ACCTAAGCCCAAAGACGCCG
11443177 TTTT
1 TTTT
11443181 CTGAGCTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 75 0.94
85 5 0.06
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (84 bp):
TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAA
CCTAAGCCCAAAGACGCCG
Found at i:11443577 original size:114 final size:114
Alignment explanation
Indices: 11443091--11443576 Score: 706
Period size: 114 Copynumber: 4.3 Consensus size: 114
11443081 CCAACGACGC
*
11443091 CGTTTTTAGGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTCGGGAAA-CGCCGC-AA
1 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTT-GGGAAAGCGCCGCAAA
* * *
11443154 AAAACCTAAGCCTAAAGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGG
65 AAAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGG
* * *
11443204 CGTTTTTAAGAAAGCGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTTGGTAAAGCGCCACAAAA
1 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAA
* * * *
11443269 AAACCTAAGCCCAACGACGCCATTTTTTGAGCTTTCGGGGAATTAGCGG
66 AAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGG
* * * * * *
11443318 CGTTTTTAAGTAAGCGCTGCTAATTCTCAAGTCTTTAGCGGCGTTTTTGGGGAAGCGCTGCAAAA
1 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAA
* *
11443383 AAACCTAAGCCCAACGACGCCGTTCTCTAAGCTTTCGGAGATTTAGCGG
66 AAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGG
* * * *
11443432 CGTTTTCAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGTGTCGCAAAA
1 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAA
* *
11443497 AAACCTAAGCCCAACGACGCCGTTTTCTAAGATTTTGGGGATTTAGCGG
66 AAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGG
* *
11443546 CGCTTTTAGGAAAGCGCCGCTAATGCTCAGG
1 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGG
11443577 GATTTAAAAT
Statistics
Matches: 332, Mismatches: 39, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
112 5 0.02
113 51 0.15
114 276 0.83
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (114 bp):
CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAA
AAACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGATTTAGCGG
Found at i:11443813 original size:15 final size:15
Alignment explanation
Indices: 11443795--11443833 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
11443785 TACCATTTTA
11443795 AGGTTTATGGATTAT
1 AGGTTTATGGATTAT
* *
11443810 AGGTTTAGGGGTTAT
1 AGGTTTATGGATTAT
11443825 -GGTTTATGG
1 AGGTTTATGG
11443834 TTTAAAAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (15 bp):
AGGTTTATGGATTAT
Found at i:11443816 original size:22 final size:21
Alignment explanation
Indices: 11443791--11443838 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
11443781 GTGTTACCAT
*
11443791 TTTAAGGTTTATGGATTATAGG
1 TTTAAGGGTTATGGATTAT-GG
* *
11443813 TTTAGGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGATTATGG
11443834 TTTAA
1 TTTAA
11443839 AAGGCCGGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAAGGGTTATGGATTATGG
Found at i:11443895 original size:15 final size:15
Alignment explanation
Indices: 11443854--11443924 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
11443844 CGGGGTTTAA
* *
11443854 GGTTTAAAGGTTATG
1 GGTTTAGAGTTTATG
* * *
11443869 TGTTAAGGGTTTATG
1 GGTTTAGAGTTTATG
11443884 GGTTTAGAGTTT-TAG
1 GGTTTAGAGTTTAT-G
11443899 GGTTTA-AGTTTAT-
1 GGTTTAGAGTTTATG
*
11443912 GGTTTAGGGTTTA
1 GGTTTAGAGTTTA
11443925 GATTAACTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
13 6 0.14
14 11 0.25
15 27 0.61
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (15 bp):
GGTTTAGAGTTTATG
Found at i:11443925 original size:7 final size:7
Alignment explanation
Indices: 11443874--11443925 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
11443864 TTATGTGTTA
11443874 AGGGTTT
1 AGGGTTT
11443881 ATGGGTTT
1 A-GGGTTT
*
11443889 AGAGTTTT
1 AG-GGTTT
11443897 AGGGTTT
1 AGGGTTT
*
11443904 A-AGTTT
1 AGGGTTT
*
11443910 ATGGTTT
1 AGGGTTT
11443917 AGGGTTT
1 AGGGTTT
11443924 AG
1 AG
11443926 ATTAACTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
6 5 0.14
7 19 0.51
8 13 0.35
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:11444205 original size:21 final size:21
Alignment explanation
Indices: 11444176--11444253 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
11444166 TTATGGTTAA
* *
11444176 TTTAAGGGTTAGGATTTAAGG
1 TTTAGGGGTTAGGAGTTAAGG
* *
11444197 TTTAGGGGTTAGTAGTTAGGG
1 TTTAGGGGTTAGGAGTTAAGG
* *
11444218 GTTAGGGGTTAAGAGTT-AGTG
1 TTTAGGGGTTAGGAGTTAAG-G
11444239 ATTTAGGGGTTAGGA
1 -TTTAGGGGTTAGGA
11444254 TTTAGGGATT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.02
21 32 0.71
22 12 0.27
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (21 bp):
TTTAGGGGTTAGGAGTTAAGG
Found at i:11444255 original size:14 final size:14
Alignment explanation
Indices: 11444197--11444260 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
11444187 GGATTTAAGG
*
11444197 TTTAGGGGTTAGTA
1 TTTAGGGGTTAGGA
* *
11444211 GTTAGGGGTTAGGG
1 TTTAGGGGTTAGGA
* * *
11444225 GTTAAGAGTTAGTGA
1 TTTAGGGGTTAG-GA
11444240 TTTAGGGGTTAGGA
1 TTTAGGGGTTAGGA
11444254 TTTAGGG
1 TTTAGGG
11444261 ATTCAAGGGT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 30 0.75
15 10 0.25
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (14 bp):
TTTAGGGGTTAGGA
Found at i:11445047 original size:147 final size:147
Alignment explanation
Indices: 11444722--11445124 Score: 618
Period size: 147 Copynumber: 2.7 Consensus size: 147
11444712 ATTATTTTTT
* *
11444722 GCGGCGTTTTTATAAAAAACTCCCCAAAAAATAATTTTACTTTAAAAAATAGCGAGATTTTTAGC
1 GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGCGAGATTTTTAGC
*
11444787 ATAGCAAAACTA-TGTCGTTTTATTCCAAATGAAATATTTTTTTGCTGCGTTTTATATAAAAACG
66 ATAGCAAAAC-AGTGTCGTTTTATTCCAAATGAAATA-TTTTTTGCGGCGTTTTATATAAAAACG
11444851 CCGCAAAAGGTGAGCAATA
129 CCGCAAAAGGTGAGCAATA
*
11444870 GCGGCGTTTTTTATAAAAAATGCCAC--AAAATAATTTTACTTTAAAAAATAGCGAGATTTTTAG
1 GCGGCG-TTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGCGAGATTTTTAG
11444933 CATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATATTTTTTGCGGCGTTTTATATAAAAACGC
65 CATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATATTTTTTGCGGCGTTTTATATAAAAACGC
11444998 CGCAAAAGGTGAGCAATA
130 CGCAAAAGGTGAGCAATA
* * **
11445016 GCGGCGTTTTAATAAAAAACGCCACAAAAAATAATTTTAGTTTAAAAAATTAGCGCCA-TTTTA-
1 GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAA-TAGCGAGATTTTTAG
* * * *
11445079 TATAGCAAAACAGTGTTGTTTTATTCAAAATAAAATAATTTTTTGC
65 CATAGCAAAACAGTGTCGTTTTATTCCAAATGAAAT-ATTTTTTGC
11445125 AATCAAAAAA
Statistics
Matches: 236, Mismatches: 13, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
145 17 0.07
146 84 0.36
147 107 0.45
148 12 0.05
149 16 0.07
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (147 bp):
GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGCGAGATTTTTAGC
ATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATATTTTTTGCGGCGTTTTATATAAAAACGCC
GCAAAAGGTGAGCAATA
Found at i:11453747 original size:43 final size:43
Alignment explanation
Indices: 11453661--11453886 Score: 226
Period size: 43 Copynumber: 5.3 Consensus size: 43
11453651 TTTGCGGCGT
* * * *
11453661 AACGCCGTTAAAAAACATGACCTTTAGCGACGC-TTTACCCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCACA
* *
11453704 AACGCCGCTAAAGAACGTGATCTTTAGCGGCGCTTTTATCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACA
*** * * *
11453747 AACATTGCTAAAGAACATGACCTTTAACGGTGTTTTTATCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACA
* * *
11453790 AACGCCGTTAAAGAGA-ATAACCTTTAGTGGCGCTTTTATCACA
1 AACGCCGCTAAAGA-ACATGACCTTTAGCGGCGCTTTTATCACA
* ** *
11453833 AACGCCGCTATAGAGA-ATGA-CTTTAGCGGCTTTTTTTTCACA
1 AACGCCGCTAAAGA-ACATGACCTTTAGCGGCGCTTTTATCACA
11453875 AACGCCGCTAAA
1 AACGCCGCTAAA
11453887 AGTACCGTTC
Statistics
Matches: 150, Mismatches: 31, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
42 29 0.19
43 116 0.77
44 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACA
Found at i:11458514 original size:43 final size:42
Alignment explanation
Indices: 11458432--11458563 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 42
11458422 AATCAGACCC
11458432 TAAACATTAAACCATAAACCTAAGCCCCTAAACCATAAACCA
1 TAAACATTAAACCATAAACCTAAGCCCCTAAACCATAAACCA
* * *
11458474 TAAACTTTAAA-CACTAAACCCTAAGCCCCTAAGCCCTAAACCA
1 TAAACATTAAACCA-TAAA-CCTAAGCCCCTAAACCATAAACCA
* * *
11458517 TAAACCATT-AACCTTAAACACTAA-ACACTAAA-CACTAAACCA
1 TAAA-CATTAAACCATAAAC-CTAAGCCCCTAAACCA-TAAACCA
11458559 TAAAC
1 TAAAC
11458564 CTACACCCTA
Statistics
Matches: 75, Mismatches: 9, Indels: 13
0.77 0.09 0.13
Matches are distributed among these distances:
41 4 0.05
42 31 0.41
43 36 0.48
44 4 0.05
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.18
Consensus pattern (42 bp):
TAAACATTAAACCATAAACCTAAGCCCCTAAACCATAAACCA
Found at i:11458518 original size:50 final size:49
Alignment explanation
Indices: 11458432--11458590 Score: 171
Period size: 50 Copynumber: 3.2 Consensus size: 49
11458422 AATCAGACCC
*
11458432 TAAACATTAAAC-CATAAA-CCTAAGCCCCTAAACCATAAACCATAAACTT
1 TAAACACTAAACAC-TAAACCCTAAG-CCCTAAACCATAAACCATAAACTT
* * * *
11458481 TAAACACTAAACCCTAAGCCCCTAAGCCCTAAACCATAAACCATTAACCT
1 TAAACACTAAACACTAA-ACCCTAAGCCCTAAACCATAAACCATAAACTT
* * * * * *
11458531 TAAACACTAAACACTAAACACTAAACCATAAACC-TACACCCTAAACTA
1 TAAACACTAAACACTAAACCCTAAGCCCTAAACCATAAACCATAAACTT
11458579 TAAACACTAAAC
1 TAAACACTAAAC
11458591 TCTTAACACT
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
48 21 0.23
49 27 0.29
50 39 0.42
51 6 0.06
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.18
Consensus pattern (49 bp):
TAAACACTAAACACTAAACCCTAAGCCCTAAACCATAAACCATAAACTT
Found at i:11458583 original size:34 final size:35
Alignment explanation
Indices: 11458509--11458590 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
11458499 CCCCTAAGCC
*
11458509 CTAAAC-CATAAACCATTAACCTTAAACACTAAACA
1 CTAAACAC-TAAACCATAAACCTTAAACACTAAACA
* *
11458544 CTAAACACTAAACCATAAACC-TACACCCTAAACTA
1 CTAAACACTAAACCATAAACCTTAAACACTAAAC-A
11458579 -TAAACACTAAAC
1 CTAAACACTAAAC
11458591 TCTTAACACT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 22 0.52
35 19 0.45
36 1 0.02
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.18
Consensus pattern (35 bp):
CTAAACACTAAACCATAAACCTTAAACACTAAACA
Found at i:11458599 original size:62 final size:63
Alignment explanation
Indices: 11458481--11458630 Score: 166
Period size: 62 Copynumber: 2.4 Consensus size: 63
11458471 CCATAAACTT
* * *
11458481 TAAACACTAAACCCTAAGCCCCTA-AGCCCTAAACCATAAACCATTAACCTTAAACACTAAA-CA
1 TAAACACTAAACCATAA--ACCTACAGCCCTAAACCATAAACCATAAACCTTAAACACTAAATCA
*
11458544 CTAAACACTAAACCATAAACCTACA-CCCTAAACTATAAA-CACTAAACTCTT-AACACTAAATC
1 -TAAACACTAAACCATAAACCTACAGCCCTAAACCATAAACCA-TAAAC-CTTAAACACTAAATC
11458606 A
63 A
* *
11458607 TAAACCCTAAACCTTAAACCTACA
1 TAAACACTAAACCATAAACCTACA
11458631 TCTTAAACCC
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
61 2 0.03
62 52 0.68
63 6 0.08
64 16 0.21
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.19
Consensus pattern (63 bp):
TAAACACTAAACCATAAACCTACAGCCCTAAACCATAAACCATAAACCTTAAACACTAAATCA
Found at i:11458644 original size:7 final size:7
Alignment explanation
Indices: 11458428--11458644 Score: 107
Period size: 7 Copynumber: 31.1 Consensus size: 7
11458418 TTAAAATCAG
11458428 ACCCTAA
1 ACCCTAA
**
11458435 ACATTAA
1 ACCCTAA
*
11458442 ACCATAA
1 ACCCTAA
11458449 A-CCTAA
1 ACCCTAA
*
11458455 GCCCCTAA
1 -ACCCTAA
*
11458463 ACCATAA
1 ACCCTAA
*
11458470 ACCATAA
1 ACCCTAA
**
11458477 ACTTTAA
1 ACCCTAA
*
11458484 ACACTAA
1 ACCCTAA
11458491 ACCCTAA
1 ACCCTAA
*
11458498 GCCCCTAA
1 -ACCCTAA
*
11458506 GCCCTAA
1 ACCCTAA
*
11458513 ACCATAA
1 ACCCTAA
* *
11458520 ACCATTA
1 ACCCTAA
*
11458527 ACCTTAA
1 ACCCTAA
*
11458534 ACACTAA
1 ACCCTAA
*
11458541 ACACTAA
1 ACCCTAA
*
11458548 ACACTAA
1 ACCCTAA
*
11458555 ACCATAA
1 ACCCTAA
*
11458562 A-CCTAC
1 ACCCTAA
11458568 ACCCTAA
1 ACCCTAA
**
11458575 ACTATAA
1 ACCCTAA
*
11458582 ACACTAA
1 ACCCTAA
* *
11458589 ACTCTTA
1 ACCCTAA
*
11458596 ACACTAA
1 ACCCTAA
* *
11458603 ATCATAA
1 ACCCTAA
11458610 ACCCTAA
1 ACCCTAA
*
11458617 ACCTTAA
1 ACCCTAA
*
11458624 A-CCTAC
1 ACCCTAA
* *
11458630 ATCTTAA
1 ACCCTAA
11458637 ACCCTAA
1 ACCCTAA
11458644 A
1 A
11458645 TATATATTAC
Statistics
Matches: 158, Mismatches: 47, Indels: 10
0.73 0.22 0.05
Matches are distributed among these distances:
6 12 0.08
7 135 0.85
8 11 0.07
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:11458917 original size:14 final size:14
Alignment explanation
Indices: 11458898--11458932 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11458888 TCCTAAACCC
11458898 TTAAACCATAAACA
1 TTAAACCATAAACA
* *
11458912 TTAAACCTTAAATA
1 TTAAACCATAAACA
11458926 TTAAACC
1 TTAAACC
11458933 CTAACCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAACCATAAACA
Found at i:11459110 original size:40 final size:40
Alignment explanation
Indices: 11459048--11459123 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
11459038 ATTTTGCGAA
* **
11459048 AAGCGCTGCTAATGCTTGATCTATAGCGGCGTTTTTCAAC
1 AAGCGCCGCTAATGCTCAATCTATAGCGGCGTTTTTCAAC
* * *
11459088 AAGCGCCGCTAATTCTCAATCTATTGCGGCTTTTTT
1 AAGCGCCGCTAATGCTCAATCTATAGCGGCGTTTTT
11459124 TTAAAAAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (40 bp):
AAGCGCCGCTAATGCTCAATCTATAGCGGCGTTTTTCAAC
Found at i:11459236 original size:41 final size:41
Alignment explanation
Indices: 11459195--11459293 Score: 191
Period size: 41 Copynumber: 2.4 Consensus size: 41
11459185 TTTGTCGTGT
11459195 TTTTTTGA-AAAGCGCCGTTAATGCTCGATCTATAGCGGTG
1 TTTTTTGACAAAGCGCCGTTAATGCTCGATCTATAGCGGTG
11459235 TTTTTTGACAAAGCGCCGTTAATGCTCGATCTATAGCGGTG
1 TTTTTTGACAAAGCGCCGTTAATGCTCGATCTATAGCGGTG
11459276 TTTTTTGACAAAGCGCCG
1 TTTTTTGACAAAGCGCCG
11459294 CTATTTCTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 8 0.14
41 50 0.86
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTTTTGACAAAGCGCCGTTAATGCTCGATCTATAGCGGTG
Found at i:11459308 original size:41 final size:41
Alignment explanation
Indices: 11459195--11459339 Score: 186
Period size: 41 Copynumber: 3.6 Consensus size: 41
11459185 TTTGTCGTGT
*
11459195 TTTTTTGA-AAAGCGCCGTTAATGCTCGATCTATAGCGGTG
1 TTTTTTGACAAAGCGCCGCTAATGCTCGATCTATAGCGGTG
*
11459235 TTTTTTGACAAAGCGCCGTTAATGCTCGATCTATAGCGGTG
1 TTTTTTGACAAAGCGCCGCTAATGCTCGATCTATAGCGGTG
* * * * **
11459276 TTTTTTGACAAAGCGCCGCTATTTCTCAATCTATTGCGACG
1 TTTTTTGACAAAGCGCCGCTAATGCTCGATCTATAGCGGTG
* *
11459317 CTTTTT-AAAAAGCGCCGCTAATG
1 TTTTTTGACAAAGCGCCGCTAATG
11459340 TCACTAAAGC
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 22 0.24
41 71 0.76
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTTTTGACAAAGCGCCGCTAATGCTCGATCTATAGCGGTG
Found at i:11459405 original size:197 final size:197
Alignment explanation
Indices: 11459047--11459493 Score: 528
Period size: 197 Copynumber: 2.3 Consensus size: 197
11459037 CATTTTGCGA
* *
11459047 AAAGCGCTGCTAATGCTTGATCTATAGCGGCGTTTTTCAACAAGCGCCGCTAATTCTCAATCTAT
1 AAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAACAAGCGCCGCTAATTCTCAATCTAT
* ** * * *
11459112 TGCGGCTTTTTTTTAAAAAGTGTCGCTAATGCCACTAAAGCTCAACAACAAATGACGTCGTTTTG
66 TGCGACTGCTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTTG
* *** ***
11459177 CTCAACTTTTTGTCGTGTTTTTTTGAAAAGCGCCGTTAATGCTCGATCTATAGCGGTGTTTTTTG
131 CTCAACTTTTTGTCGTGATTTTCCAAAAAGCGCAACTAATGCTCGATCTATAGCGGTGTTTTTTG
11459242 AC
196 AC
* * ** *
11459244 AAAGCGCCGTTAATGCTCGATCTATAGCGGTGTTTTTTGACAAAGCGCCGCTATTTCTCAATCTA
1 AAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAC-AAGCGCCGCTAATTCTCAATCTA
*
11459309 TTGCGAC-GCTTTTTAAAAAGCGCCGCTAATGTCACTAAAGCTCAACAACAAACGACGTCGTTTT
65 TTGCGACTGCTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTT
* *
11459373 GCTCAACTTTTT-T-GTGGCATTTTCCAAAAAGCGCAACTAATGCTCGATCTATAGTGGCG-TTT
130 GCTCAACTTTTTGTCGT-G-ATTTTCCAAAAAGCGCAACTAATGCTCGATCTATAGCGGTGTTTT
* *
11459435 CTCA-
193 TTGAC
*** * * *
11459439 AATATTTCCGCTAATGCTCGATCTATTGTGGCGCTTTTT-AAAAAGCGCCGCTAAT
1 AA-AGCGCCGCTAATGCTCGATCTATAGCGGCG-TTTTTCAACAAGCGCCGCTAAT
11459494 GCCACTAAAG
Statistics
Matches: 210, Mismatches: 35, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
195 16 0.08
196 31 0.15
197 135 0.64
198 28 0.13
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (197 bp):
AAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAACAAGCGCCGCTAATTCTCAATCTAT
TGCGACTGCTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTTG
CTCAACTTTTTGTCGTGATTTTCCAAAAAGCGCAACTAATGCTCGATCTATAGCGGTGTTTTTTG
AC
Found at i:11459490 original size:40 final size:40
Alignment explanation
Indices: 11459393--11459495 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
11459383 TTTGTGGCAT
**
11459393 TTTC-CAAAAAGCGCAACTAATGCTCGATCTATAGTGGCG
1 TTTCTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCG
* *** *
11459432 TTTCTCAAATATTTCCGCTAATGCTCGATCTATTGTGGCG
1 TTTCTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCG
*
11459472 CTTT-TTAAAAAGCGCCGCTAATGC
1 -TTTCTCAAAAAGCGCCGCTAATGC
11459496 CACTAAAGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
39 4 0.08
40 43 0.86
41 3 0.06
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (40 bp):
TTTCTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCG
Found at i:11459609 original size:155 final size:154
Alignment explanation
Indices: 11459235--11459611 Score: 443
Period size: 155 Copynumber: 2.4 Consensus size: 154
11459225 TATAGCGGTG
* * * * * * *
11459235 TTTTTTGACAAAGCGCCGTTAATGCTCGATCTATAGCGGTGTTTTTTGACAAAGCGCCGCTATTT
1 TTTTCTGA-AAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTT--CAAAACGTCGCTAATG
*
11459300 CTCAATCTATTGCGACGCTTTTTAAAAAGCGCCGCTAATGTCACTAAAGCTCAACAACAAACGAC
63 CTCAATCTATTGCGACGCTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAACAAACGAC
11459365 GTCGTTTTGCTCAACTTTTTTGTGGCA
128 GTCGTTTTGCTCAACTTTTTTGTGGCA
** ** * * **
11459392 TTTTCCAAAAAGCGCAACTAATGCTCGATCTATAGTGGCG-TTTCTCAAATATTTCCGCTAATGC
1 TTTTCTGAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTTCAAA-ACGT-CGCTAATGC
* * * * *
11459456 TCGATCTATTGTGGCGCTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATCAAACTACG
64 TCAATCTATTGCGACGCTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAACAAACGACG
* *
11459521 T-GTTTTGCTCAATTTTTTTGTGTCA
129 TCGTTTTGCTCAACTTTTTTGTGGCA
* * *
11459546 TTTTCTGAAAAGTGCCGCTAATGCTCGATCTATAGCGACGTTTGTTTCAGAAACGTCGTTAATGC
1 TTTTCTGAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTT-TTTCA-AAACGTCGCTAATGC
11459611 T
64 T
11459612 TGACCTTTTA
Statistics
Matches: 181, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
153 4 0.02
154 55 0.30
155 82 0.45
156 33 0.18
157 7 0.04
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (154 bp):
TTTTCTGAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTTCAAAACGTCGCTAATGCTC
AATCTATTGCGACGCTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAACAAACGACGTC
GTTTTGCTCAACTTTTTTGTGGCA
Found at i:11461712 original size:25 final size:25
Alignment explanation
Indices: 11461638--11461715 Score: 111
Period size: 25 Copynumber: 3.1 Consensus size: 25
11461628 ATGTGGTGCT
*
11461638 TTTGTGGCAAATTCTCTGAAAAGCT
1 TTTGTGGCAAATTCTCTGAAAAGCC
*
11461663 TTTGTGGCGAATTCTCTGAAAAGCC
1 TTTGTGGCAAATTCTCTGAAAAGCC
* * *
11461688 TTTGTGACAAACTCTCTAAAAAGCC
1 TTTGTGGCAAATTCTCTGAAAAGCC
11461713 TTT
1 TTT
11461716 ATGGTGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (25 bp):
TTTGTGGCAAATTCTCTGAAAAGCC
Found at i:11470629 original size:11 final size:11
Alignment explanation
Indices: 11470583--11470634 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
11470573 ACACTAATAA
11470583 CAAAATAGTAG
1 CAAAATAGTAG
* *
11470594 CAATATAATAG
1 CAAAATAGTAG
* *
11470605 CGAAATGGTAG
1 CAAAATAGTAG
*
11470616 CAAAATAGTGG
1 CAAAATAGTAG
11470627 CAAAATAG
1 CAAAATAG
11470635 CTTATTCAAG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:11470632 original size:22 final size:22
Alignment explanation
Indices: 11470577--11470634 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
11470567 ATCCTAACAC
* *
11470577 TAATAACAAAATAGTAGCAATA
1 TAATAGCAAAATAGTAGCAAAA
* *
11470599 TAATAGCGAAATGGTAGCAAAA
1 TAATAGCAAAATAGTAGCAAAA
* *
11470621 TAGTGGCAAAATAG
1 TAATAGCAAAATAG
11470635 CTTATTCAAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.21
Consensus pattern (22 bp):
TAATAGCAAAATAGTAGCAAAA
Found at i:11471586 original size:21 final size:21
Alignment explanation
Indices: 11471562--11471601 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11471552 TTGTTTTTTT
**
11471562 TTTTGAAAAATTTAAAAATTA
1 TTTTGAAAAAAATAAAAATTA
*
11471583 TTTTTAAAAAAATAAAAAT
1 TTTTGAAAAAAATAAAAAT
11471602 ATGTGAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TTTTGAAAAAAATAAAAATTA
Found at i:11472237 original size:20 final size:19
Alignment explanation
Indices: 11472212--11472268 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
11472202 AATATTTGAA
*
11472212 AATTTAACATAAATTTTGT
1 AATTTAACATAAATTTTAT
*
11472231 AATTTTAAC-TATATTTTAT
1 AA-TTTAACATAAATTTTAT
* *
11472250 TATTTAATATAAATTTTAT
1 AATTTAACATAAATTTTAT
11472269 TACTATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 5 0.16
19 20 0.65
20 6 0.19
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
AATTTAACATAAATTTTAT
Found at i:11475552 original size:2 final size:2
Alignment explanation
Indices: 11475545--11475587 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11475535 TATGGACTGC
11475545 TA TA 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 TA TA
11475587 T
1 T
11475588 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11477377 original size:2 final size:2
Alignment explanation
Indices: 11477370--11477432 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
11477360 NNNNNNNNNN
11477370 TA TA 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 TA TA
11477412 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
11477433 CAGTTGCATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11480914 original size:16 final size:16
Alignment explanation
Indices: 11480881--11480914 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11480871 AAATTAGCAC
*
11480881 TTGATTCTCTATAATT
1 TTGATTCTCCATAATT
*
11480897 TTGATTCTCCATAGTT
1 TTGATTCTCCATAATT
11480913 TT
1 TT
11480915 TATTTTAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.56
Consensus pattern (16 bp):
TTGATTCTCCATAATT
Found at i:11482428 original size:26 final size:26
Alignment explanation
Indices: 11482399--11482458 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
11482389 CCCCCAGCTT
* *
11482399 AATTTTGACGATTTTACCCTTGGTAA
1 AATTTTGACGATTTTACCCCTAGTAA
*
11482425 AATTTTGACGATTTTGCCCCTAGTAA
1 AATTTTGACGATTTTACCCCTAGTAA
11482451 AATTTTGA
1 AATTTTGA
11482459 GAAAATATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (26 bp):
AATTTTGACGATTTTACCCCTAGTAA
Found at i:11484314 original size:14 final size:14
Alignment explanation
Indices: 11484295--11484325 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11484285 TGCATTTAAT
11484295 AAATTCAATCAAAC
1 AAATTCAATCAAAC
*
11484309 AAATTCAATCAACC
1 AAATTCAATCAAAC
11484323 AAA
1 AAA
11484326 CAGACATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATTCAATCAAAC
Found at i:11484977 original size:29 final size:29
Alignment explanation
Indices: 11484931--11485003 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
11484921 GATTTTTATG
*
11484931 TTATGTATATTATTTTAT-TATATAATATA
1 TTATGTATATTATATTATAT-TATAATATA
*
11484960 TTATGTTATATTA-ATTATATTATATTATA
1 TTATG-TATATTATATTATATTATAATATA
11484989 TTAT-TATA-TATATTA
1 TTATGTATATTATATTA
11485004 ATAAAGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.05
27 8 0.21
29 21 0.54
30 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTATGTATATTATATTATATTATAATATA
Found at i:11484981 original size:5 final size:5
Alignment explanation
Indices: 11484936--11485003 Score: 70
Period size: 5 Copynumber: 13.4 Consensus size: 5
11484926 TTATGTTATG
*
11484936 TATAT TAT-T T-TAT TATAT AATATAT TATGT TATAT TA-AT TATAT TATAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATAT
11484985 TATAT TATTAT ATATAT TA
1 TATAT TA-TAT -TATAT TA
11485004 ATAAAGTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 32 0.59
6 6 0.11
7 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:11486301 original size:2 final size:2
Alignment explanation
Indices: 11486294--11486320 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11486284 TAGTATGTAA
11486294 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
11486321 AATTTAAAAT
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:11488111 original size:23 final size:24
Alignment explanation
Indices: 11488083--11488132 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
11488073 AACTTCATTC
11488083 ATATATCAATTT-CATA-CTCAAGT
1 ATATAT-AATTTGCATATCTCAAGT
*
11488106 ATATATAATTTGCATATCTCAATT
1 ATATATAATTTGCATATCTCAAGT
11488130 ATA
1 ATA
11488133 CAACACTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (24 bp):
ATATATAATTTGCATATCTCAAGT
Found at i:11490663 original size:57 final size:57
Alignment explanation
Indices: 11490547--11490692 Score: 140
Period size: 57 Copynumber: 2.5 Consensus size: 57
11490537 AACAGGAAAA
* * *
11490547 TTGGGTTATGGGA-ACTAGATGGCCGGCA-ACACTATTTTTTCTATTAAAAAATGATTT
1 TTGGGTT-TTGGACACTAGATGGCCGGCACCCACTATTTTTTCTATTAAAAAA-GAATT
* *
11490604 TTGGGTTTTGGACACTAGATGGCCGGCACCCATGTATTTTTT-TTTTCAAAAAA-AATT
1 TTGGGTTTTGGACACTAGATGGCCGGCACCCA-CTATTTTTTCTATT-AAAAAAGAATT
**
11490661 TTGGGGTGCTGGCACACT-GATGGCCGGCACCC
1 TT-GGGTTTTGG-ACACTAGATGGCCGGCACCC
11490693 CTTTATCTGA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
56 4 0.05
57 27 0.36
58 26 0.34
59 19 0.25
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (57 bp):
TTGGGTTTTGGACACTAGATGGCCGGCACCCACTATTTTTTCTATTAAAAAAGAATT
Found at i:11502165 original size:166 final size:166
Alignment explanation
Indices: 11501829--11502189 Score: 498
Period size: 166 Copynumber: 2.2 Consensus size: 166
11501819 TAGCATAAAT
* *
11501829 TAAATAATGAAATGTAAGCCTTGAAACTAAGTAACGATAATAACACAAAATATGCACAATATTAA
1 TAAA-AATGAAATATAAGGCTTGAAACTAAGTAACGATAATAACACAAAATATGCACAATATTAA
* *
11501894 AAATAAAAAAATTAGATTAAATTATGAGTAAACGAAATACAAACACATAAATACATTAGATAAAG
65 AAATAAAAAAATTAGATTAAATTATGAGTAAACGAAATACAAACACACAAATACATTAGATAAAC
*
11501959 AATACTAAATGCACTACAATTATTTTTAAACACACAA
130 AATACTAAATCCACTACAATTATTTTTAAACACACAA
** * **
11501996 TAAAAATGAAATATAAGGCTTGAAACTAAGTAATTATAATAACACAATAAATATGTATGATATTA
1 TAAAAATGAAATATAAGGCTTGAAACTAAGTAACGATAATAACAC-A-AAATATGCACAATATTA
* * **
11502061 AAATTTTAAAAAA-TAGATTAAATTA-GAAGTAAAACGAAATTTAAACACACAAATACATT-GAT
64 AAA-ATAAAAAAATTAGATTAAATTATG-AGT-AAACGAAATACAAACACACAAATACATTAGAT
11502123 AAACAATACTAAATCCACTACAATTATTTTT-AA-ACACAA
126 AAACAATACTAAATCCACTACAATTATTTTTAAACACACAA
*
11502162 TAAAAATGAAACATAAGGCTTGAAACTA
1 TAAAAATGAAATATAAGGCTTGAAACTA
11502190 GAGGTATTCA
Statistics
Matches: 174, Mismatches: 15, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
166 70 0.40
167 8 0.05
168 64 0.37
169 32 0.18
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (166 bp):
TAAAAATGAAATATAAGGCTTGAAACTAAGTAACGATAATAACACAAAATATGCACAATATTAAA
AATAAAAAAATTAGATTAAATTATGAGTAAACGAAATACAAACACACAAATACATTAGATAAACA
ATACTAAATCCACTACAATTATTTTTAAACACACAA
Found at i:11502342 original size:11 final size:11
Alignment explanation
Indices: 11502322--11502358 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
11502312 GACTCGACCC
11502322 ATATTAAATAT
1 ATATTAAATAT
*
11502333 ATATTTAATAT
1 ATATTAAATAT
*
11502344 ATATAAAATAT
1 ATATTAAATAT
11502355 ATAT
1 ATAT
11502359 ATTTGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:11502381 original size:25 final size:25
Alignment explanation
Indices: 11502327--11502408 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
11502317 GACCCATATT
* * *
11502327 AAATATATATTT-AATATATATAAA
1 AAATATATATTTGATTAAAAATAAA
*
11502351 ATATATATATTTGATTAAAAATAAA
1 AAATATATATTTGATTAAAAATAAA
*
11502376 AAATATATATTTGATTAAAATTAAA
1 AAATATATATTTGATTAAAAATAAA
11502401 AAATATAT
1 AAATATAT
11502409 TTAATATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 11 0.22
25 40 0.78
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATATATATTTGATTAAAAATAAA
Found at i:11504507 original size:3 final size:3
Alignment explanation
Indices: 11504499--11504533 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11504489 TAAATGTCAG
11504499 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11504534 GTTTGTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11508505 original size:3 final size:3
Alignment explanation
Indices: 11508465--11508492 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11508455 TAACAAAATC
11508465 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11508493 TATTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11508549 original size:19 final size:19
Alignment explanation
Indices: 11508481--11508550 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 19
11508471 AATAATAATA
*
11508481 ATAATAATAATATATTTTA-
1 ATAATATTAA-ATATTTTAT
*
11508500 ATAATATTCAATTATTTTATT
1 ATAATATT-AAATATTTTA-T
11508521 ATTAACATATTAAATATTTTAT
1 A-T-A-ATATTAAATATTTTAT
11508543 ATAATATT
1 ATAATATT
11508551 TTTCAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 19 0.45
20 3 0.07
21 2 0.05
22 3 0.07
23 10 0.24
24 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATATTAAATATTTTAT
Found at i:11509590 original size:11 final size:10
Alignment explanation
Indices: 11509551--11509596 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
11509541 TCTAAATCCT
*
11509551 TTCTCTCAAT
1 TTCTCTCAAA
11509561 TTCTCTCCAATA
1 TTCTCT-CAA-A
11509573 TTCTCTCAAA
1 TTCTCTCAAA
11509583 TTCGTCTCAAA
1 TTC-TCTCAAA
11509594 TTC
1 TTC
11509597 CTCTTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 10 0.31
11 16 0.50
12 6 0.19
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.43
Consensus pattern (10 bp):
TTCTCTCAAA
Found at i:11509617 original size:22 final size:21
Alignment explanation
Indices: 11509592--11509638 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11509582 ATTCGTCTCA
11509592 AATTCCTCTTAAAAAAAGCTTT
1 AATT-CTCTTAAAAAAAGCTTT
* *
11509614 AATTTTTTTAAAAAAAGCTTT
1 AATTCTCTTAAAAAAAGCTTT
11509635 AATT
1 AATT
11509639 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (21 bp):
AATTCTCTTAAAAAAAGCTTT
Found at i:11509624 original size:21 final size:21
Alignment explanation
Indices: 11509600--11509640 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11509590 CAAATTCCTC
11509600 TTAAAAAAAGCTTTAATTTTT
1 TTAAAAAAAGCTTTAATTTTT
11509621 TTAAAAAAAGCTTTAATTTT
1 TTAAAAAAAGCTTTAATTTT
11509641 ATTTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
TTAAAAAAAGCTTTAATTTTT
Found at i:11511328 original size:29 final size:29
Alignment explanation
Indices: 11511276--11511368 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 29
11511266 ACGACGCAGA
11511276 CCCATCAACAGCACCCACACAATCACTCA-G
1 CCCATCAACAG-ACCCACACAATCAC-CAGG
*
11511306 CCCATCAACATG-CCCATACAATCACCAGG
1 CCCATCAACA-GACCCACACAATCACCAGG
* **
11511335 CCCAGCAACAGCACTGACACAATCATCC-GG
1 CCCATCAACAG-ACCCACACAATCA-CCAGG
11511365 CCCA
1 CCCA
11511369 GCACTTCAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
28 3 0.06
29 22 0.42
30 25 0.47
31 3 0.06
ACGTcount: A:0.34, C:0.44, G:0.11, T:0.11
Consensus pattern (29 bp):
CCCATCAACAGACCCACACAATCACCAGG
Found at i:11511884 original size:10 final size:11
Alignment explanation
Indices: 11511841--11511881 Score: 54
Period size: 9 Copynumber: 4.1 Consensus size: 11
11511831 GGCACGGAGA
11511841 TTGATATTA-T
1 TTGATATTATT
11511851 TTGAT-TTATT
1 TTGATATTATT
11511861 TTGA-A-TATT
1 TTGATATTATT
11511870 TTGATATTATT
1 TTGATATTATT
11511881 T
1 T
11511882 GATGTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 11 0.41
10 11 0.41
11 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (11 bp):
TTGATATTATT
Done.