Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_pilon, 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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:2966512 original size:25 final size:24
Alignment explanation
Indices: 2966484--2966564 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 24
2966474 ACTACTTAGT
2966484 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * **
2966509 AGTTAAT-TTAAACTAAAC-TACTTGG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
2966534 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
2966560 AGTTA
1 AGTTA
2966565 GTGTTATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 2 0.05
25 21 0.51
26 16 0.39
27 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:2966537 original size:51 final size:51
Alignment explanation
Indices: 2966460--2966601 Score: 194
Period size: 51 Copynumber: 2.8 Consensus size: 51
2966450 GAACAAGTAT
2966460 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* *
2966511 TTAATTTAAACTAAACTACTTGGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * * *
2966562 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAACTAAACTACTTAGTAGTTATCCTTATCTA
2966602 TCGCATAACC
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 53 0.67
52 26 0.33
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:2972816 original size:38 final size:38
Alignment explanation
Indices: 2972774--2972846 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
2972764 AATGAAGGAC
*
2972774 TTGCTAAGGTGTT-TGATTGTTGATGGTTTAAATCTGAA
1 TTGCTAAGGTGTTAT-ATTGTTAATGGTTTAAATCTGAA
*
2972812 TTGCTAAGGTGTTATATTGTTAATGGTTTACATCT
1 TTGCTAAGGTGTTATATTGTTAATGGTTTAAATCT
2972847 TGGGTACTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (38 bp):
TTGCTAAGGTGTTATATTGTTAATGGTTTAAATCTGAA
Found at i:2980413 original size:19 final size:19
Alignment explanation
Indices: 2980389--2980442 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 19
2980379 AACAAAAATA
2980389 GTCAAGAAAATTTTATTAT
1 GTCAAGAAAATTTTATTAT
*
2980408 GTCAAG-AAAGTTTATTAT
1 GTCAAGAAAATTTTATTAT
*
2980426 TTCAAGAAAATTTTATT
1 GTCAAGAAAATTTTATT
2980443 TAAAATGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (19 bp):
GTCAAGAAAATTTTATTAT
Found at i:2983377 original size:31 final size:31
Alignment explanation
Indices: 2983341--2983400 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2983331 AACTTAAAAG
* *
2983341 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2983372 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
2983401 CATACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2983450 original size:22 final size:22
Alignment explanation
Indices: 2983424--2983468 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2983414 TAATAAATTA
*
2983424 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCAATAT
2983446 TTTAAAATAAATCAATCAATAT
1 TTTAAAATAAATCAATCAATAT
2983468 T
1 T
2983469 AATAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCAATAT
Found at i:2983475 original size:22 final size:22
Alignment explanation
Indices: 2983422--2983474 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
2983412 AATAATAAAT
*
2983422 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCAA
*
2983443 TATTTTAAAATAAATCAATCAA
1 TATTATAAAATAAATCAATCAA
2983465 TATTAATAAA
1 TATT-ATAAA
2983475 TTATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCAA
Found at i:2983478 original size:54 final size:54
Alignment explanation
Indices: 2983414--2983870 Score: 406
Period size: 54 Copynumber: 8.5 Consensus size: 54
2983404 ACAATTACAA
*
2983414 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAT
** *
2983468 TAATAAATTATTTAAAATAAATCAATATATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAT
*
2983522 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAT
** * **
2983576 TAATAAATTATTTAAAATAAATCAATTTATACAACTACAATAATAAATCAATCTATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCTATA--T
* * * * * *
2983636 TAAAATAAATCAATCTATACT-AATAAAT---TA-TTTAAAATAAATCAATCCATAT
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAT
* * ** * * **
2983688 T-TTAAAATAAAT-CAATCAATACTAATAAAT-TATTTAAAATAAATCAATCTATA-
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCTATAT
* * * *
2983741 TAACT--A-TA---ATAATAAATTAATCCATATTTTAAAATAAATCGATCTATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAT
* *
2983790 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAAT-TCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATAT
2983844 TAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
2983871 AATACAACTA
Statistics
Matches: 335, Mismatches: 39, Indels: 58
0.78 0.09 0.13
Matches are distributed among these distances:
47 2 0.01
48 31 0.09
49 8 0.02
50 10 0.03
51 2 0.01
52 4 0.01
53 4 0.01
54 227 0.68
55 4 0.01
56 1 0.00
57 4 0.01
58 16 0.05
59 1 0.00
60 2 0.01
62 13 0.04
63 6 0.02
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAT
Found at i:2983484 original size:32 final size:31
Alignment explanation
Indices: 2983446--2983743 Score: 142
Period size: 32 Copynumber: 10.8 Consensus size: 31
2983436 CAATCCATAT
2983446 TTTAAAATAAATCAATCAATATTAATAAATTA
1 TTTAAAATAAATCAATCAATA-TAATAAATTA
2983478 TTTAAAAT--A--AATCAATAT-AT--A-T-
1 TTTAAAATAAATCAATCAATATAATAAATTA
*
2983500 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCAATA-TAATAAATTA
2983532 TTTAAAATAAATCAATC----T-AT--A-T-
1 TTTAAAATAAATCAATCAATATAATAAATTA
*
2983554 TTTAAAATAAATCAATCTATATTAATAAATTA
1 TTTAAAATAAATCAATCAATA-TAATAAATTA
*
2983586 TTTAAAATAAATCAAT---T-T-ATACAACTA
1 TTTAAAATAAATCAATCAATATAATA-AATTA
* * **
2983613 --CAATAATAAATCAATCTATATTTTAAA--A
1 TTTAA-AATAAATCAATCAATATAATAAATTA
*
2983641 -------TAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCAATA-TAATAAATTA
*
2983666 TTTAAAATAAATCAATC-----CAT--A-T-
1 TTTAAAATAAATCAATCAATATAATAAATTA
2983688 TTTAAAATAAATCAATCAATACTAATAAATTA
1 TTTAAAATAAATCAATCAATA-TAATAAATTA
*
2983720 TTTAAAATAAATCAATCTATATAA
1 TTTAAAATAAATCAATCAATATAA
2983744 CTATAATAAT
Statistics
Matches: 210, Mismatches: 9, Indels: 95
0.67 0.03 0.30
Matches are distributed among these distances:
22 56 0.27
23 8 0.04
24 4 0.02
25 3 0.01
26 27 0.13
27 9 0.04
28 15 0.07
29 2 0.01
30 7 0.03
31 8 0.04
32 71 0.34
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTAAAATAAATCAATCAATATAATAAATTA
Found at i:2983494 original size:22 final size:22
Alignment explanation
Indices: 2983469--2983515 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2983459 AATCAATATT
2983469 AATAAAT-TATTTAAAATAAATC
1 AATAAATAT-TTTAAAATAAATC
*
2983491 AATATATATTTTAAAATAAATC
1 AATAAATATTTTAAAATAAATC
2983513 AAT
1 AAT
2983516 CTATACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAATATTTTAAAATAAATC
Found at i:2983520 original size:22 final size:22
Alignment explanation
Indices: 2983478--2983520 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2983468 TAATAAATTA
2983478 TTTAAAATAAATCAATATATAT
1 TTTAAAATAAATCAATATATAT
*
2983500 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATATATA
2983521 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATATATAT
Found at i:2983529 original size:22 final size:22
Alignment explanation
Indices: 2983480--2983528 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2983470 ATAAATTATT
**
2983480 TAAAATAAATCAATATATATTT
1 TAAAATAAATCAATATATATAA
*
2983502 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATATATA-TAA
2983525 TAAA
1 TAAA
2983529 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATATATATAA
Found at i:2983583 original size:22 final size:22
Alignment explanation
Indices: 2983530--2983582 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
2983520 ACTAATAAAT
2983530 TATT-TAAAATAAATCAATCTA
1 TATTATAAAATAAATCAATCTA
*
2983551 TATTTTAAAATAAATCAATCTA
1 TATTATAAAATAAATCAATCTA
2983573 TATTAATAAA
1 TATT-ATAAA
2983583 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCTA
Found at i:2983639 original size:134 final size:134
Alignment explanation
Indices: 2983483--2984008 Score: 864
Period size: 134 Copynumber: 3.9 Consensus size: 134
2983473 AATTATTTAA
*
2983483 AATAAATCAATATATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAA-
1 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
* *
2983547 TCTATATTTTAAAATAAATCAA-TCTATATTAATAAATTATTTAAAATAAATCAATTTATACAAC
66 TC-ATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCTATACAAC
2983611 TACAAT
129 TACAAT
2983617 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
* *
2983682 CCATATTTTAAAATAAATCAA-TCAATACTAATAAATTATTTAAAATAAATCAATCTATATAACT
66 TCATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCTATACAACT
*
2983746 ATAAT
130 ACAAT
* * *
2983751 AATAAATTAATCCATATTTTAAAATAAATCGATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
*
2983816 TCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCAATACAACTA
66 TCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTA
2983881 CAAT
131 CAAT
2983885 AATAAATCAAT-TAATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCA
1 AATAAATCAATCT-ATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCA
* *
2983948 ATTCCTATTTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAATCTATA
64 ATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATA
2984009 TTTTAAAATA
Statistics
Matches: 368, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
133 1 0.00
134 364 0.99
135 3 0.01
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (134 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
TCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTA
CAAT
Found at i:2983663 original size:22 final size:22
Alignment explanation
Indices: 2983588--2983662 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
2983578 ATAAATTATT
* *
2983588 TAAAATAAATCAATTTATACAA
1 TAAAATAAATCAATCTATATAA
**
2983610 CTACAATAATAAATCAATCTATATTT
1 -T--AA-AATAAATCAATCTATATAA
2983636 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
2983659 TAAA
1 TAAA
2983663 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:2983717 original size:22 final size:22
Alignment explanation
Indices: 2983668--2983716 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2983658 ATAAATTATT
* **
2983668 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCAATATAA
2983690 TAAAATAAATCAATCAATACTAA
1 TAAAATAAATCAATCAATA-TAA
2983713 TAAA
1 TAAA
2983717 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:2983717 original size:40 final size:39
Alignment explanation
Indices: 2983671--2983797 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 39
2983661 AATTATTTAA
2983671 AATAAATCAATCCATATTTTAAAATAAATCAATCAATACT
1 AATAAAT-AATCCATATTTTAAAATAAATCAATCAATACT
2983711 AAT--A-AAT---TA-TTTAAAATAAATCAATCTATATAACTATAAT
1 AATAAATAATCCATATTTTAAAATAAATCAATC-A-AT-AC-----T
* *
2983751 AATAAATTAATCCATATTTTAAAATAAATCGATCTATACT
1 AATAAA-TAATCCATATTTTAAAATAAATCAATCAATACT
2983791 AATAAAT
1 AATAAAT
2983798 TATTTAAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 33
0.66 0.02 0.32
Matches are distributed among these distances:
32 17 0.25
33 3 0.04
34 2 0.03
35 2 0.03
36 3 0.04
38 1 0.01
39 1 0.01
40 14 0.20
42 1 0.01
44 3 0.04
45 2 0.03
46 2 0.03
47 2 0.03
48 16 0.23
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (39 bp):
AATAAATAATCCATATTTTAAAATAAATCAATCAATACT
Found at i:2983807 original size:32 final size:31
Alignment explanation
Indices: 2983768--2983871 Score: 118
Period size: 32 Copynumber: 3.6 Consensus size: 31
2983758 TAATCCATAT
*
2983768 TTTAAAATAAATCGATCTATACTAATAAATTA
1 TTTAAAATAAATCAATC-ATACTAATAAATTA
2983800 TTTAAAATAAATCAAT--T-C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
2983822 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAA-TCATACTAATAAATTA
2983854 TTTAAAATAAATCAATCA
1 TTTAAAATAAATCAATCA
2983872 ATACAACTAC
Statistics
Matches: 61, Mismatches: 1, Indels: 21
0.73 0.01 0.25
Matches are distributed among these distances:
22 15 0.25
23 2 0.03
24 1 0.02
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
30 1 0.02
31 4 0.07
32 30 0.49
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.38
Consensus pattern (31 bp):
TTTAAAATAAATCAATCATACTAATAAATTA
Found at i:2983811 original size:188 final size:186
Alignment explanation
Indices: 2983405--2984053 Score: 735
Period size: 188 Copynumber: 3.5 Consensus size: 186
2983395 ATAATTCATA
* * * * *
2983405 CAATTACAATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATATTA
1 CAATTATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATACTA
*
2983470 ATAAATTATTTAAAATAAATCAAT-ATATATTTTAAAATAAATCAATCTATACTAATAAATTATT
66 ATAAATTATTTAAAATAAATCAATCA-ATATTTTAAAATAAATCAATCAATACTAATAAATTATT
* * **
2983534 TAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATATTAATAAAT-TATTTAAAATAAAT
130 TAAAATAAATCAATCTATA---TAATAT-AAT-AA--TAAATTAATCCATAT-TTTAAAATAAAT
*
2983598 CAATTTATAC-AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAAATCAATCTATAC
1 CAA-TTATACTAA-TAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATAC
*
2983656 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTAT
64 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCAATACTAATAAATTAT
2983721 TTAAAATAAATCAATCTATATAACTATAATAATAAATTAATCCATATTTTAAAATAAAT
129 TTAAAATAAATCAATCTATATAA-TATAATAATAAATTAATCCATATTTTAAAATAAAT
*
2983780 CGATCTATACTAATAAATTATTTAAAATAAATCAAT-TCATATTTTAAAATAAATCAAT-TCATA
1 CAAT-TATACTAATAAATTATTTAAAATAAATCAATCT-ATATTTTAAAATAAATCAATCT-ATA
*** * *
2983843 CTAATAAATTATTTAAAATAAATCAATCAATACAACTACAAT-AATAAATCAAT--TAAT--A-T
63 CTAATAAATTATTTAAAATAAATCAATCAATA-TTTTAAAATAAATCAATCAATACTAATAAATT
*
2983902 -TTTAAAATAAATCAATTCATACTAATAAATTATTTAA-AATAAATCAATTCC-TATTTTAAAAT
127 ATTTAAAATAAATCAA-TC-TA-T-AT-AA-TA--TAATAATAAATTAA-TCCATATTTTAAAAT
2983964 AAAT
183 AAAT
* *
2983968 TAATTCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATACT
1 CAATT-ATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATACT
2984033 AATAAATTATTTAAAATAAAT
65 AATAAATTATTTAAAATAAAT
2984054 TATTTAAAAA
Statistics
Matches: 404, Mismatches: 25, Indels: 59
0.83 0.05 0.12
Matches are distributed among these distances:
181 1 0.00
182 47 0.12
183 6 0.01
184 6 0.01
185 7 0.02
186 9 0.02
187 7 0.02
188 295 0.73
189 12 0.03
190 1 0.00
192 1 0.00
193 5 0.01
194 7 0.02
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (186 bp):
CAATTATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATACTA
ATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCAATACTAATAAATTATTT
AAAATAAATCAATCTATATAATATAATAATAAATTAATCCATATTTTAAAATAAAT
Found at i:2983816 original size:18 final size:19
Alignment explanation
Indices: 2983795--2983838 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
2983785 TATACTAATA
2983795 AATTA-TTTAAAATAAATC
1 AATTATTTTAAAATAAATC
2983813 AATTCATATTTTAAAATAAATC
1 AA-T--TATTTTAAAATAAATC
2983835 AATT
1 AATT
2983839 CATACTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.09
19 2 0.09
21 3 0.14
22 15 0.68
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTATTTTAAAATAAATC
Found at i:2983826 original size:22 final size:22
Alignment explanation
Indices: 2983800--2983842 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2983790 TAATAAATTA
2983800 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
2983822 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
2983843 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:2983851 original size:22 final size:22
Alignment explanation
Indices: 2983802--2983850 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2983792 ATAAATTATT
**
2983802 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
2983824 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
2983847 TAAA
1 TAAA
2983851 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:2983851 original size:40 final size:39
Alignment explanation
Indices: 2983805--2984039 Score: 133
Period size: 40 Copynumber: 6.2 Consensus size: 39
2983795 AATTATTTAA
2983805 AATAAATCAATTCATATTTTAAAATAAATCAATTCATACT
1 AATAAATCAATT-ATATTTTAAAATAAATCAATTCATACT
* *** * *
2983845 AATAAAT-TATT-TAAAAT-AAATCAATCAATACAACTACAAT
1 AATAAATCAATTATATTTTAAAATAAATCAATTC-A-TAC--T
2983885 AATAAATCAATTAATATTTTAAAATAAATCAATTCATACT
1 AATAAATCAATT-ATATTTTAAAATAAATCAATTCATACT
*
2983925 AAT--A--AA-T-TA-TTTAAAATAAATCAATTCCTA-T
1 AATAAATCAATTATATTTTAAAATAAATCAATTCATACT
** * * * * *
2983956 TTTAAAATAAATTA-ATTCATACTAATAAAT-TATT--TA-A
1 AAT-AAATCAATTATATT-TTA-AAATAAATCAATTCATACT
*
2983993 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACT
1 AATAAATCAAT-TATATTTTAAAATAAATCAATTCATACT
2984033 AATAAAT
1 AATAAAT
2984040 TATTTAAAAT
Statistics
Matches: 144, Mismatches: 27, Indels: 48
0.66 0.12 0.22
Matches are distributed among these distances:
31 2 0.01
32 20 0.14
33 2 0.01
34 1 0.01
35 1 0.01
36 30 0.21
37 15 0.10
38 8 0.06
39 10 0.07
40 33 0.23
41 3 0.02
42 3 0.02
43 4 0.03
44 12 0.08
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (39 bp):
AATAAATCAATTATATTTTAAAATAAATCAATTCATACT
Found at i:2983910 original size:268 final size:268
Alignment explanation
Indices: 2983496--2984088 Score: 898
Period size: 268 Copynumber: 2.3 Consensus size: 268
2983486 AAATCAATAT
2983496 ATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAA
1 ATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAA
* **
2983561 TAAATCAATCTATATTAATAAATTATTTAAAATAAATCAATTTATACAACTACAATAATAAATCA
66 TAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCAATACAACTACAATAATAAATCA
2983626 ATCTATATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAAATAAATCAA-TCCATATT
131 ATCTATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATTCC-TATT
2983689 TTAAAATAAATCAA-TCAATACTAATAAATTATTTAAAATAAATCAATCTATATAACTATAATAA
194 TTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCTATATAACTATAATAA
2983753 TAAATTAATCC
258 TAAATTAATCC
*
2983764 ATATTTTAAAATAAATCGATCTATACTAATAAATTATTTAAAATAAATCAAT-TCATATTTTAAA
1 ATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCT-ATATTTTAAA
2983828 ATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCAATCAATACAACTACAATAATAAAT
65 ATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATCAATACAACTACAATAATAAAT
2983892 CAAT-TAATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATTCCTAT
129 CAATCT-ATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATTCCTAT
* *
2983956 TTTAAAATAAATTAATTCATACTAATAAATTATTTAAAATAAATCAATCTATAT---TTTAA-AA
193 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATATAACTATAATAA
*
2984017 TAAATCAATCC
258 TAAATTAATCC
* * * *
2984028 ATA--CT--AATAAAT-TAT-T-TA-AAATAAATTATTTAAAAATAAATCAATCTATATTTTATA
1 ATATTTTAAAATAAATCAATCTATACTAATAAATTATTT-AAAATAAATCAATCTATATTTTAAA
2984085 ATAA
65 ATAA
2984089 TTTATTTTAA
Statistics
Matches: 306, Mismatches: 11, Indels: 27
0.89 0.03 0.08
Matches are distributed among these distances:
256 12 0.04
257 28 0.09
258 2 0.01
259 2 0.01
260 7 0.02
262 1 0.00
264 15 0.05
265 4 0.01
267 3 0.01
268 225 0.74
269 7 0.02
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (268 bp):
ATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAA
TAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCAATACAACTACAATAATAAATCA
ATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATTCCTATTTT
AAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATATAACTATAATAATAA
ATTAATCC
Found at i:2983931 original size:22 final size:22
Alignment explanation
Indices: 2983885--2983930 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2983875 CAACTACAAT
* **
2983885 AATAAATCAATTAATATTTTAA
1 AATAAATCAATTCATATAATAA
2983907 AATAAATCAATTCATACTAATAA
1 AATAAATCAATTCATA-TAATAA
2983930 A
1 A
2983931 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAATCAATTCATATAATAA
Found at i:2983950 original size:18 final size:18
Alignment explanation
Indices: 2983929--2984025 Score: 51
Period size: 22 Copynumber: 5.2 Consensus size: 18
2983919 CATACTAATA
2983929 AATTATTTAAAATAAATC
1 AATTATTTAAAATAAATC
*
2983947 AATTCCTATTTTAAAATAAATT
1 AA-T--TA-TTTAAAATAAATC
* *
2983969 AATTCA--T--ACT-AATA
1 AATT-ATTTAAAATAAATC
2983983 AATTATTTAAAATAAATC
1 AATTATTTAAAATAAATC
2984001 AATCTATATTTTAAAATAAATC
1 AA--T-TA-TTTAAAATAAATC
2984023 AAT
1 AAT
2984026 CCATACTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 26
0.66 0.05 0.29
Matches are distributed among these distances:
13 1 0.02
14 7 0.12
15 3 0.05
17 3 0.05
18 7 0.12
19 2 0.03
20 3 0.05
21 5 0.08
22 29 0.48
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTATTTAAAATAAATC
Found at i:2983950 original size:54 final size:54
Alignment explanation
Indices: 2983617--2984053 Score: 338
Period size: 54 Copynumber: 8.1 Consensus size: 54
2983607 CAACTACAAT
2983617 AATAAATCAATCT-ATATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAA
1 AATAAATCAAT-TAATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAA
**
2983671 AATAAATCAATCCATATTTTAAAATAAATCAA-TCAATACTAATAAATTATTTAA
1 AATAAATCAATTAATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAA
* * * * * * * *
2983725 AATAAATCAATCTATATAACTATAATAATAAATTAATCCATATTTTAAAATAAATCGATCTAT
1 AATAAATCAAT-TA-AT-ATTTTAA-AATAAATCAATTCATA--CT--AATAAAT-TATTTAA
* * ** * ** *
2983788 ACT-AAT-AA--ATTA-TTTAAAATAAATCAATTCATA-TTTTAAAATAAAT-C
1 AATAAATCAATTAATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
** * *
2983835 AATTCATACTAATAAAT-TATTTAAAATAAATCAA-TCAATAC-AACTACA--A--T--
1 AATAAAT-C-AATTAATAT-TTTAAAATAAATCAATTC-ATACTAA-TAAATTATTTAA
2983885 AATAAATCAATTAATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATTAATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
** *
2983939 AATAAATCAATTCCTATTTTAAAATAAATTAATTCATACTAATAAATTATTTAA
1 AATAAATCAATTAATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
*
2983993 AATAAATCAATCT-ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAAT-TAATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
2984047 AATAAAT
1 AATAAAT
2984054 TATTTAAAAA
Statistics
Matches: 311, Mismatches: 40, Indels: 64
0.75 0.10 0.15
Matches are distributed among these distances:
47 2 0.01
48 32 0.10
49 10 0.03
50 6 0.02
51 4 0.01
52 1 0.00
53 5 0.02
54 201 0.65
55 8 0.03
56 3 0.01
57 6 0.02
58 13 0.04
59 1 0.00
60 1 0.00
61 2 0.01
62 10 0.03
63 6 0.02
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (54 bp):
AATAAATCAATTAATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
Found at i:2983996 original size:32 final size:31
Alignment explanation
Indices: 2983956--2984055 Score: 101
Period size: 32 Copynumber: 3.5 Consensus size: 31
2983946 CAATTCCTAT
2983956 TTTAAAATAAATTAATTCATACTAATAAATTA
1 TTTAAAATAAATTAA-TCATACTAATAAATTA
*
2983988 TTTAAAATAAA-TCA--AT-CT-AT--A-T-
1 TTTAAAATAAATTAATCATACTAATAAATTA
*
2984010 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATTAAT-CATACTAATAAATTA
2984042 TTTAAAATAAATTA
1 TTTAAAATAAATTA
2984056 TTTAAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
22 11 0.20
23 2 0.04
24 1 0.02
26 4 0.07
27 4 0.07
28 4 0.07
30 1 0.02
31 3 0.06
32 24 0.44
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTAAAATAAATTAATCATACTAATAAATTA
Found at i:2984039 original size:22 final size:22
Alignment explanation
Indices: 2983990--2984038 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2983980 ATAAATTATT
* **
2983990 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
2984012 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2984035 TAAA
1 TAAA
2984039 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2984065 original size:15 final size:15
Alignment explanation
Indices: 2984033--2984150 Score: 121
Period size: 15 Copynumber: 7.5 Consensus size: 15
2984023 AATCCATACT
2984033 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
*
2984047 AATAAATTATTTAAA
1 AATAAATTATTTTAA
*
2984062 AATAAATCAATCTATATTTTAT
1 AAT--A--AA--T-TATTTTAA
*
2984084 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
2984099 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
2984114 AGTAAATTATTTTAA
1 AATAAATTATTTTAA
2984129 AATAAATTATTTTAA
1 AATAAATTATTTTAA
2984144 AATAAAT
1 AATAAAT
2984151 AATCTTATTA
Statistics
Matches: 86, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.10
15 61 0.71
16 1 0.01
17 1 0.01
18 1 0.01
19 2 0.02
20 1 0.01
21 1 0.01
22 9 0.10
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:2984127 original size:45 final size:43
Alignment explanation
Indices: 2984076--2984173 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 43
2984066 AATCAATCTA
* * * *
2984076 TATTTTATAATAATTTATTTTAAAATAAATTATTTTATAGTAAAT
1 TATTTTAAAATAAATTATTTTAAAATAAATAATCTTAT--TAAAT
2984121 TATTTTAAAATAAATTATTTTAAAATAAATAATCTTATTAAAT
1 TATTTTAAAATAAATTATTTTAAAATAAATAATCTTATTAAAT
2984164 TA-TTTAAAAT
1 TATTTTAAAAT
2984174 TATTTTAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 8 0.16
43 7 0.14
45 34 0.69
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (43 bp):
TATTTTAAAATAAATTATTTTAAAATAAATAATCTTATTAAAT
Found at i:2984903 original size:28 final size:30
Alignment explanation
Indices: 2984845--2984904 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 30
2984835 CTTATTTATC
*
2984845 TTTTCAATTTTGTAAAAAAAATTATATAAA
1 TTTTAAATTTTGTAAAAAAAATTATATAAA
*
2984875 TTTTAAATTTT-TAAAGAAAA-TATATAAA
1 TTTTAAATTTTGTAAAAAAAATTATATAAA
2984903 TT
1 TT
2984905 AATTATAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.36
29 8 0.29
30 10 0.36
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTAAATTTTGTAAAAAAAATTATATAAA
Found at i:2984942 original size:42 final size:41
Alignment explanation
Indices: 2984864--2984942 Score: 92
Period size: 42 Copynumber: 1.9 Consensus size: 41
2984854 TTGTAAAAAA
*
2984864 AATTATATAAATTTTAAATTTTTAAAGAAAATATATAAATT
1 AATTATATAAATTTTAAATTTTTAAAGAAAAAATATAAATT
2984905 AATTATAGTAGAA-TTT-AATTTGTTAAA-AAACAAATATA
1 AATTATA-TA-AATTTTAAATTT-TTAAAGAAA-AAATATA
2984943 TAATGAGGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
41 15 0.45
42 16 0.48
43 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (41 bp):
AATTATATAAATTTTAAATTTTTAAAGAAAAAATATAAATT
Found at i:2985092 original size:19 final size:19
Alignment explanation
Indices: 2985056--2985105 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
2985046 AACATTCACA
*
2985056 ATAATCTTA-TTCCCGCCG
1 ATAATCTTATTTCCAGCCG
2985074 ATAATCTTATTTCCAGCCG
1 ATAATCTTATTTCCAGCCG
*
2985093 ATAATTTTATTTC
1 ATAATCTTATTTC
2985106 TGTCGGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (19 bp):
ATAATCTTATTTCCAGCCG
Found at i:2985330 original size:20 final size:20
Alignment explanation
Indices: 2985298--2985338 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2985288 TGATAATAAA
2985298 ACAGACAACACGAAAACCCG
1 ACAGACAACACGAAAACCCG
*
2985318 ACAG-CAACGACGACAACCCG
1 ACAGACAAC-ACGAAAACCCG
2985338 A
1 A
2985339 GAAACAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.46, C:0.37, G:0.17, T:0.00
Consensus pattern (20 bp):
ACAGACAACACGAAAACCCG
Found at i:2991080 original size:2 final size:2
Alignment explanation
Indices: 2991073--2991117 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2991063 AATATGGGGT
2991073 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
2991115 TA T
1 TA T
2991118 TCTGACGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2991556 original size:37 final size:36
Alignment explanation
Indices: 2991515--2991622 Score: 98
Period size: 37 Copynumber: 3.0 Consensus size: 36
2991505 CATTAAATCT
2991515 TTTTATATTTTCAATTTTGTAAAAAAAAATATATAAA
1 TTTTATATTTTCAATTTT-TAAAAAAAAATATATAAA
* * * *
2991552 TTTTATGAATTTAAATTTTTTAAAGAAAATATATAAA
1 TTTTAT-ATTTTCAATTTTTAAAAAAAAATATATAAA
*
2991589 ---TAT-TTTTCAACTTGTTATAAAAACAAATATATAA
1 TTTTATATTTTCAA-TT-TT-TAAAAAAAAATATATAA
2991623 TAAAGATAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
32 5 0.09
33 2 0.03
34 5 0.09
35 14 0.24
37 22 0.38
38 10 0.17
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTATATTTTCAATTTTTAAAAAAAAATATATAAA
Found at i:2991764 original size:18 final size:19
Alignment explanation
Indices: 2991741--2991783 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2991731 CAGTAATCTT
2991741 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
*
2991759 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGATAATCTTAC
2991779 ATTCC
1 ATTCC
2991784 GTAAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:2994283 original size:6 final size:6
Alignment explanation
Indices: 2994272--2994314 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
2994262 GACACGTATT
2994272 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
2994315 GACGGCGGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2994976 original size:6 final size:6
Alignment explanation
Indices: 2994965--2995031 Score: 134
Period size: 6 Copynumber: 11.2 Consensus size: 6
2994955 AGGGGGACTC
2994965 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
2995013 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
2995032 AATACGTGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:2995130 original size:20 final size:20
Alignment explanation
Indices: 2995105--2995175 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
2995095 ATTTTCAACG
*
2995105 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
2995125 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
*
2995148 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
2995168 TTGCGATT
1 TTGCGATT
2995176 TTCTTCTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 22 0.52
21 3 0.07
22 3 0.07
23 14 0.33
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:2995151 original size:23 final size:23
Alignment explanation
Indices: 2995120--2995196 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
2995110 ATTCTCTCAG
2995120 TCGCATTGCGATTTTCTTCTAAA
1 TCGCATTGCGATTTTCTTCTAAA
*
2995143 TCGCGTTGCGA--TTCTATC--AA
1 TCGCATTGCGATTTTCT-TCTAAA
2995163 TCGCATTGCGATTTTCTTCTAAA
1 TCGCATTGCGATTTTCTTCTAAA
*
2995186 TCGCGTTGCGA
1 TCGCATTGCGA
2995197 ACTTGGAAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 12 0.26
21 6 0.13
22 6 0.13
23 22 0.48
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (23 bp):
TCGCATTGCGATTTTCTTCTAAA
Found at i:2995167 original size:43 final size:43
Alignment explanation
Indices: 2995103--2995196 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 43
2995093 TTATTTTCAA
* *
2995103 CGTTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
2995146 CGTTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
2995189 CGTTGCGA
1 CGTTGCGA
2995197 ACTTGGAAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.38
Consensus pattern (43 bp):
CGTTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
Found at i:2995235 original size:20 final size:20
Alignment explanation
Indices: 2995210--2995263 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
2995200 TGGAAGCTCG
*
2995210 CGTTGCGATTTT-TTTTTGAC
1 CGTTGCGATTTTCTTTTT-AA
2995230 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTTAA
2995250 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
2995264 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.11, C:0.17, G:0.19, T:0.54
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTTAA
Found at i:2995290 original size:19 final size:20
Alignment explanation
Indices: 2995250--2995300 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2995240 TTCTTTTTAA
*
2995250 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
2995270 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2995289 CGTTGCGATTTT
1 CGTTGCGATTTT
2995301 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:3004442 original size:31 final size:29
Alignment explanation
Indices: 3004388--3004460 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 29
3004378 GATGAATCAG
*
3004388 TGACTAAAATATAAAATCAATAACATAAA
1 TGACTAAAATATAAAATCAATAACACAAA
* *
3004417 TGACTAAAATTTAACAAATCGATAACACAAA
1 TGACTAAAATAT-A-AAATCAATAACACAAA
*
3004448 TGACTGAAATATA
1 TGACTAAAATATA
3004461 TTTGTTTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 11 0.30
30 2 0.05
31 24 0.65
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (29 bp):
TGACTAAAATATAAAATCAATAACACAAA
Found at i:3004785 original size:13 final size:13
Alignment explanation
Indices: 3004757--3004801 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
3004747 TCAAAACTAA
3004757 TAAAATTATAAAAT
1 TAAAA-TATAAAAT
* *
3004771 TAAACTATCAAAT
1 TAAAATATAAAAT
3004784 TAAAATATAAAGAT
1 TAAAATATAAA-AT
3004798 TAAA
1 TAAA
3004802 TAATAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (13 bp):
TAAAATATAAAAT
Found at i:3004802 original size:13 final size:12
Alignment explanation
Indices: 3004763--3004819 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
3004753 CTAATAAAAT
3004763 TATAAAATTAAA
1 TATAAAATTAAA
*
3004775 CTATCAAATTAAAA
1 -TATAAAATT-AAA
3004789 TATAAAGATTAAA
1 TATAAA-ATTAAA
* *
3004802 TAATAAATTTAAG
1 T-ATAAAATTAAA
3004815 TATAA
1 TATAA
3004820 TAGGAGAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.11
13 22 0.59
14 11 0.30
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (12 bp):
TATAAAATTAAA
Found at i:3009929 original size:16 final size:19
Alignment explanation
Indices: 3009889--3009932 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3009879 TCACGGAATG
*
3009889 TAAGATTACCAGTGAGATG
1 TAAGATTACCAGTGAGATA
3009908 TAAGATTACCAG-G-GA-A
1 TAAGATTACCAGTGAGATA
3009924 TAAGATTAC
1 TAAGATTAC
3009933 TGGGAATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 1 0.04
19 12 0.50
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (19 bp):
TAAGATTACCAGTGAGATA
Found at i:3023287 original size:4 final size:4
Alignment explanation
Indices: 3023278--3025504 Score: 3921
Period size: 4 Copynumber: 558.8 Consensus size: 4
3023268 AGAAGATTTG
* * *
3023278 GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * *
3023326 GCAT GCAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GCAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
3023374 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GCAT GTAA GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
3023422 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GCAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
3023470 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * *
3023518 GCAT GTAT GTAT GTAT GTAT GCAT GCAT GCAT GTAT GTAT GCAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * *
3023566 GCAT GCAT GTAT GCAT GTAT GCAT GTAT GTAT GTAT GCAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
3023614 GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
3023662 GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
3023710 GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT G--T
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
3023756 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * *
3023804 GTAT GTAT GCAT GTAT GTAT GCAT GTAT GCAT GCAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
3023852 GTAT GCAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
3023900 GTAT GCAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
3023948 GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3023996 G--T GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024042 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024090 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024138 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024186 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024234 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024282 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024330 GTAT GTA- -TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024376 GTAT GTAT GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024423 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA- GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024470 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024518 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024566 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024614 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024662 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024710 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024758 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024806 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024854 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024902 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024950 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3024998 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025046 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025094 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025142 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025190 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025238 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025286 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025334 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025382 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025430 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
3025478 GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTA
3025505 ATTGGTTCTC
Statistics
Matches: 2133, Mismatches: 82, Indels: 16
0.96 0.04 0.01
Matches are distributed among these distances:
2 6 0.00
3 6 0.00
4 2121 0.99
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:3027682 original size:19 final size:19
Alignment explanation
Indices: 3027651--3027693 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3027641 TTTATTAAAA
3027651 ATAAAAAATATTT-TGAATT
1 ATAAAAAATATTTAT-AATT
3027670 ATAATAAAA-ATTTATAATT
1 ATAA-AAAATATTTATAATT
3027689 ATAAA
1 ATAAA
3027694 TTAAGCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAAAAAATATTTATAATT
Found at i:3046185 original size:20 final size:20
Alignment explanation
Indices: 3046162--3046237 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
3046152 CAACGCGAAC
*
3046162 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACAGTT
*
3046182 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCGCAACACAGTT
* * ** *
3046202 TCGAAAATCGCAATGCAATT
1 TCCAAATTCGCAACACAGTT
* *
3046222 TTCAAATTTGCAACAC
1 TCCAAATTCGCAACAC
3046238 TAATTACCGA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (20 bp):
TCCAAATTCGCAACACAGTT
Found at i:3046404 original size:57 final size:57
Alignment explanation
Indices: 3046208--3046386 Score: 295
Period size: 57 Copynumber: 3.1 Consensus size: 57
3046198 AGTTTCGAAA
* * *
3046208 ATCGCAATGCAATTTTCAAATTTGCAACACTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAACGCGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACT
*
3046265 ATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAACGCGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACT
* **
3046322 ATCGTAACGCGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACACAACT
1 ATCGCAACGCGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACT
3046379 ATCGCAAC
1 ATCGCAAC
3046387 ATGAATTTCG
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 113 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (57 bp):
ATCGCAACGCGATTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACAGTACT
Found at i:3046621 original size:14 final size:14
Alignment explanation
Indices: 3046602--3046631 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3046592 TTGTTGAATT
*
3046602 CGGATTTTTTTTAC
1 CGGATTTTTTGTAC
3046616 CGGATTTTTTGTAC
1 CGGATTTTTTGTAC
3046630 CG
1 CG
3046632 TGGTTACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.17, G:0.20, T:0.50
Consensus pattern (14 bp):
CGGATTTTTTGTAC
Found at i:3046719 original size:20 final size:20
Alignment explanation
Indices: 3046694--3046741 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3046684 CGGTAATTCG
3046694 CGTTGCGAATTTGAAAATCA
1 CGTTGCGAATTTGAAAATCA
* *
3046714 CGTTGCAAATTTGAAAATCG
1 CGTTGCGAATTTGAAAATCA
3046734 CGTTGCGA
1 CGTTGCGA
3046742 TAGTACTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCA
Found at i:3046783 original size:77 final size:77
Alignment explanation
Indices: 3046656--3046801 Score: 247
Period size: 77 Copynumber: 1.9 Consensus size: 77
3046646 GGTAATTGAG
* * *
3046656 GCGTTGCGATAGTAGTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTGAAAATCACGTTGCA
1 GCGTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCA
3046721 AATTTGAAAATC
66 AATTTGAAAATC
* *
3046733 GCGTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCG
1 GCGTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCA
3046798 AATT
66 AATT
3046802 CCGAAACTGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 64 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (77 bp):
GCGTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCA
AATTTGAAAATC
Found at i:3046795 original size:20 final size:19
Alignment explanation
Indices: 3046770--3046829 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
3046760 TCGGTAATTA
3046770 GCGTTGCGAATTTGAAAAT
1 GCGTTGCGAATTTGAAAAT
* *
3046789 CGCGTTGCGAATTCCGAAACT
1 -GCGTTGCGAATT-TGAAAAT
*
3046810 GAGTTGCGAATTTGTAAAAT
1 GCGTTGCGAATTTG-AAAAT
3046830 TCGCTTGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 27 0.82
21 5 0.15
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (19 bp):
GCGTTGCGAATTTGAAAAT
Found at i:3046816 original size:77 final size:77
Alignment explanation
Indices: 3046658--3046818 Score: 234
Period size: 77 Copynumber: 2.1 Consensus size: 77
3046648 TAATTGAGGC
* * *
3046658 GTTGCGATAGTAGTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTGAAAATCACGTTGCAAA
1 GTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCAAA
* *
3046723 TTTGAAAATCGC
66 TTCGAAAATCGA
* *
3046735 GTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAA
1 GTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCAAA
*
3046800 TTCCGAAACT-GA
66 TT-CGAAAATCGA
3046812 GTTGCGA
1 GTTGCGA
3046819 ATTTGTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
77 70 0.93
78 5 0.07
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (77 bp):
GTTGCGATAGTACTGTTTACCGATATCGGTAATTAGCGTTGCGAATTTGAAAATCACGTTGCAAA
TTCGAAAATCGA
Found at i:3053242 original size:36 final size:36
Alignment explanation
Indices: 3053175--3053247 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
3053165 CCTTAGGTCC
***
3053175 ATAAGGAATTATCAGCTCGATCGGTGCTGAACCTGT
1 ATAAGGAATTATCAGCTCGATCAAAGCTGAACCTGT
* * *
3053211 ATAAGGAATTATCAGTTTGATCAAAGTTGAACCTGT
1 ATAAGGAATTATCAGCTCGATCAAAGCTGAACCTGT
3053247 A
1 A
3053248 AAGACTTCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (36 bp):
ATAAGGAATTATCAGCTCGATCAAAGCTGAACCTGT
Found at i:3061520 original size:42 final size:43
Alignment explanation
Indices: 3061452--3061538 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
3061442 TAAAGAGGAT
*
3061452 TACAAGAACTCGGTAAATATGAT-AAAAAAAACAAAGTTCACA
1 TACAAGAACTCGATAAATATGATAAAAAAAAACAAAGTTCACA
* *
3061494 TACACGAACTCGATAAATATGGTAAAAAAAAACAAAGTTCACA
1 TACAAGAACTCGATAAATATGATAAAAAAAAACAAAGTTCACA
3061537 TA
1 TA
3061539 TACAGGTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 20 0.49
43 21 0.51
ACGTcount: A:0.54, C:0.15, G:0.11, T:0.20
Consensus pattern (43 bp):
TACAAGAACTCGATAAATATGATAAAAAAAAACAAAGTTCACA
Found at i:3062262 original size:18 final size:19
Alignment explanation
Indices: 3062227--3062263 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3062217 CACGGAATGT
3062227 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3062247 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
3062264 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3063823 original size:224 final size:224
Alignment explanation
Indices: 3063429--3063872 Score: 744
Period size: 224 Copynumber: 2.0 Consensus size: 224
3063419 GGGGGGGAAG
*
3063429 GGAAGAACTTTAATCATTATTTTTAATTGATTAAGAAGGAATTTGAACACACTGTTACTTTACTG
1 GGAAGAACTTTAATCATTATTTTTAATTGATTAAGAAGGAATTTGAACAAACTGTTACTTTACTG
* **
3063494 TGAATCTGAGCAATCCGGTTGATGAACATTCAGTCTTTCTTACATGATGTTCTTGGTTAAGTCGG
66 TGAATCTGAGCAATCCGGTTGATAAACATTCAGTCTTTCTTACATGATGTTCTCAGTTAAGTCGG
* ** *
3063559 CTAACTGATCGACTAAATCCGGTGCCGTTATTTTGGTTTCCAGCAAGGTTGATTCGGTTTTAGGT
131 CTAAATGATCGACTAAATCCGGTGCCACTATTTCGGTTTCCAGCAAGGTTGATTCGGTTTTAGGT
3063624 TATCATATTTATGAAGTCAATCAAAAAAT
196 TATCATATTTATGAAGTCAATCAAAAAAT
* * * *
3063653 GGAAGAACTTTAGTCATTATTTTTAGTTGATTGAGAAGGAATTTGAACAAAGTGTTACTTTACTG
1 GGAAGAACTTTAATCATTATTTTTAATTGATTAAGAAGGAATTTGAACAAACTGTTACTTTACTG
* * *
3063718 TGAATTTGAGCAATCCGGTTGATAAACATTCAGTCTTTCTTACATGATGTTCTCAGTTTAGTTGG
66 TGAATCTGAGCAATCCGGTTGATAAACATTCAGTCTTTCTTACATGATGTTCTCAGTTAAGTCGG
*
3063783 TTAAATGATCGACTAAATCCGGTGCCACTATTTCGGTTTCCAGCAAGGTTGATTCGGTTTTAGGT
131 CTAAATGATCGACTAAATCCGGTGCCACTATTTCGGTTTCCAGCAAGGTTGATTCGGTTTTAGGT
3063848 TATCATATTTATGAAGTCAATCAAA
196 TATCATATTTATGAAGTCAATCAAA
3063873 TCAATTTTCA
Statistics
Matches: 204, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
224 204 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (224 bp):
GGAAGAACTTTAATCATTATTTTTAATTGATTAAGAAGGAATTTGAACAAACTGTTACTTTACTG
TGAATCTGAGCAATCCGGTTGATAAACATTCAGTCTTTCTTACATGATGTTCTCAGTTAAGTCGG
CTAAATGATCGACTAAATCCGGTGCCACTATTTCGGTTTCCAGCAAGGTTGATTCGGTTTTAGGT
TATCATATTTATGAAGTCAATCAAAAAAT
Found at i:3068643 original size:18 final size:18
Alignment explanation
Indices: 3068620--3068659 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3068610 TTCCATCCGG
*
3068620 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
* *
3068638 TCTTATCATTTACTTCAG
1 TCTTATCATTTAATTCAA
3068656 TCTT
1 TCTT
3068660 TTCGAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:3071788 original size:21 final size:22
Alignment explanation
Indices: 3071750--3071802 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
3071740 GTACCCATAG
* *
3071750 TAAAAATGAAATTAAAAT-ATT
1 TAAAAATTAAATTAAAATGAAT
* *
3071771 TAAAAATTAATTTGAAATGAAT
1 TAAAAATTAAATTAAAATGAAT
*
3071793 TCAAAATTAA
1 TAAAAATTAA
3071803 GATACTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (22 bp):
TAAAAATTAAATTAAAATGAAT
Found at i:3072297 original size:17 final size:17
Alignment explanation
Indices: 3072275--3072308 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3072265 CCACATAAGC
3072275 TACTGCAAATTTATTCA
1 TACTGCAAATTTATTCA
*
3072292 TACTGCAAATTTGTTCA
1 TACTGCAAATTTATTCA
3072309 AGAAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (17 bp):
TACTGCAAATTTATTCA
Found at i:3073830 original size:26 final size:25
Alignment explanation
Indices: 3073801--3073849 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
3073791 TAAATTTGAT
3073801 AATAATTTATTATTATATATTTTTTA
1 AATAATTTATTATTAT-TATTTTTTA
3073827 AATAATTTATTATTATTATTTTT
1 AATAATTTATTATTATTATTTTT
3073850 ATATGTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
AATAATTTATTATTATTATTTTTTA
Found at i:3074307 original size:20 final size:20
Alignment explanation
Indices: 3074267--3074320 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3074257 GATGTGATTC
*
3074267 ATTATTAATTTTATATTTTT
1 ATTATTATTTTTATATTTTT
3074287 ATTATTATTTTTCATA-TTTT
1 ATTATTATTTTT-ATATTTTT
*
3074307 ATCATT-TTTTTATA
1 ATTATTATTTTTATA
3074321 CTTATAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.10
19 5 0.16
20 20 0.65
21 3 0.10
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTATTATTTTTATATTTTT
Found at i:3081406 original size:16 final size:16
Alignment explanation
Indices: 3081387--3081420 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3081377 TATATAATTC
3081387 TACATTTATTTAATAT
1 TACATTTATTTAATAT
3081403 TACATTTATTTAATAT
1 TACATTTATTTAATAT
3081419 TA
1 TA
3081421 AGATTATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TACATTTATTTAATAT
Found at i:3081678 original size:2 final size:2
Alignment explanation
Indices: 3081671--3081758 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
3081661 TGAATAGTTA
3081671 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3081713 AT AT AT AT AT AT 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 AT AT AT AT AT AT
3081755 AT AT
1 AT AT
3081759 TCATCGATAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3084907 original size:22 final size:22
Alignment explanation
Indices: 3084882--3084926 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3084872 ATCTATAAAG
*
3084882 TTAAATAGTATATTGGAGAAAT
1 TTAAATAGTATATTGGAAAAAT
3084904 TTAAATAGTATATTGGAAAAAT
1 TTAAATAGTATATTGGAAAAAT
3084926 T
1 T
3084927 AAAAGTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (22 bp):
TTAAATAGTATATTGGAAAAAT
Found at i:3088584 original size:5 final size:5
Alignment explanation
Indices: 3088574--3088598 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3088564 AAGGACGTCG
3088574 TTGAA TTGAA TTGAA TTGAA TTGAA
1 TTGAA TTGAA TTGAA TTGAA TTGAA
3088599 GAAACCGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TTGAA
Found at i:3097008 original size:21 final size:21
Alignment explanation
Indices: 3096947--3097076 Score: 119
Period size: 21 Copynumber: 6.3 Consensus size: 21
3096937 ACTATCGCAA
3096947 TGCGA-TT-TTCCAAATTCGT
1 TGCGATTTATTCCAAATTCGT
* * *
3096966 T--GATATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGT
3096987 TGCGATTTATTCCAAATTCGT
1 TGCGATTTATTCCAAATTCGT
3097008 TGCGATTTATTCCAAATTCGT
1 TGCGATTTATTCCAAATTCGT
* * *
3097029 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATT--CGT
*
3097050 TGCGATTTATTCTAAATTCGT
1 TGCGATTTATTCCAAATTCGT
3097071 TGCGAT
1 TGCGAT
3097077 AGTCCAAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.02
18 1 0.01
19 16 0.18
21 50 0.56
23 20 0.22
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (21 bp):
TGCGATTTATTCCAAATTCGT
Found at i:3097029 original size:63 final size:62
Alignment explanation
Indices: 3096947--3097076 Score: 208
Period size: 63 Copynumber: 2.1 Consensus size: 62
3096937 ACTATCGCAA
*
3096947 TGCGA-TTTTCCAAATTCGTTGATATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATTTTTCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGT
* * *
3097008 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGT
1 TGCGATTT-TTCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGT
3097071 TGCGAT
1 TGCGAT
3097077 AGTCCAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 5 0.08
62 2 0.03
63 56 0.89
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (62 bp):
TGCGATTTTTCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGT
Found at i:3097987 original size:21 final size:21
Alignment explanation
Indices: 3097963--3098046 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
3097953 TAAATCACAG
*
3097963 CGCGAACTTCGACTATCGCAA
1 CGCGAACTTGGACTATCGCAA
3097984 CGCGAACTTGGACTATCGCAA
1 CGCGAACTTGGACTATCGCAA
* * *
3098005 --CGAATTTGGAATAAATCGCAC
1 CGCGAACTTGGACT--ATCGCAA
3098026 CGCGAACTTGGACTATCGCAA
1 CGCGAACTTGGACTATCGCAA
3098047 TGAATTTGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 10 0.19
21 32 0.62
23 10 0.19
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (21 bp):
CGCGAACTTGGACTATCGCAA
Found at i:3098023 original size:42 final size:42
Alignment explanation
Indices: 3097977--3098057 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
3097967 AACTTCGACT
3097977 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
* *
3098019 ATCGCACCGCGAACTTGGACTATCGCAATGAATTTGGAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAA
3098058 AAGCGCATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:3098030 original size:63 final size:63
Alignment explanation
Indices: 3097928--3098046 Score: 202
Period size: 63 Copynumber: 1.9 Consensus size: 63
3097918 CGTTGCGATT
*
3097928 TTGGACTATCGCAACGAATTTAGAATAAATCACAGCGCGAACTTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTAGAATAAATCACACCGCGAACTTCGACTATCGCAACGCGAAC
* * *
3097991 TTGGACTATCGCAACGAATTTGGAATAAATCGCACCGCGAACTTGGACTATCGCAA
1 TTGGACTATCGCAACGAATTTAGAATAAATCACACCGCGAACTTCGACTATCGCAA
3098047 TGAATTTGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (63 bp):
TTGGACTATCGCAACGAATTTAGAATAAATCACACCGCGAACTTCGACTATCGCAACGCGAAC
Found at i:3098259 original size:17 final size:17
Alignment explanation
Indices: 3098237--3098275 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3098227 TATTTTCTCT
3098237 TATTTTAAATTCAAAAC
1 TATTTTAAATTCAAAAC
* *
3098254 TATTTTAAGTTTAAAAC
1 TATTTTAAATTCAAAAC
3098271 T-TTTT
1 TATTTT
3098276 GGACAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (17 bp):
TATTTTAAATTCAAAAC
Found at i:3100506 original size:24 final size:24
Alignment explanation
Indices: 3100471--3100525 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
3100461 CCCCAATTTA
*
3100471 CTTTC-CC-GAATCCATAACCCTT
1 CTTTCTCCAGAATCCATAACCCTC
*
3100493 CTTTCTCCAGAATCCCTAACCCTC
1 CTTTCTCCAGAATCCATAACCCTC
3100517 CTTTCTCCA
1 CTTTCTCCA
3100526 TTCCCAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 5 0.17
23 2 0.07
24 22 0.76
ACGTcount: A:0.20, C:0.44, G:0.04, T:0.33
Consensus pattern (24 bp):
CTTTCTCCAGAATCCATAACCCTC
Found at i:3104630 original size:16 final size:16
Alignment explanation
Indices: 3104609--3104640 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3104599 ATAGTAGCTA
3104609 CCTCTACTCTCTGCTC
1 CCTCTACTCTCTGCTC
3104625 CCTCTACTCTCTGCTC
1 CCTCTACTCTCTGCTC
3104641 AACAGGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.50, G:0.06, T:0.38
Consensus pattern (16 bp):
CCTCTACTCTCTGCTC
Found at i:3109433 original size:28 final size:28
Alignment explanation
Indices: 3109401--3109458 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3109391 GTTAAGTATG
3109401 AAAGAAGTTACTAGGTGACATTAAGCTA
1 AAAGAAGTTACTAGGTGACATTAAGCTA
3109429 AAAGAAGTTACTAGGTGACATTAAGCTA
1 AAAGAAGTTACTAGGTGACATTAAGCTA
3109457 AA
1 AA
3109459 CGAAATTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (28 bp):
AAAGAAGTTACTAGGTGACATTAAGCTA
Found at i:3117817 original size:14 final size:14
Alignment explanation
Indices: 3117798--3117826 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3117788 TCAATTTTCC
3117798 ATTAAATGAGGGAA
1 ATTAAATGAGGGAA
3117812 ATTAAATGAGGGAA
1 ATTAAATGAGGGAA
3117826 A
1 A
3117827 GCGAATTCCA
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:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (14 bp):
ATTAAATGAGGGAA
Found at i:3118338 original size:26 final size:27
Alignment explanation
Indices: 3118277--3118336 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
3118267 ATTTTGTTCA
3118277 GGTCGGGTTTTTTAAGTGCGATATTCG
1 GGTCGGGTTTTTTAAGTGCGATATTCG
*
3118304 GGTCGGGTTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTAAGTGCGATATTCG
3118331 GGTCGG
1 GGTCGG
3118337 TTCAGGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40
Consensus pattern (27 bp):
GGTCGGGTTTTTTAAGTGCGATATTCG
Found at i:3120215 original size:75 final size:74
Alignment explanation
Indices: 3120127--3120421 Score: 374
Period size: 75 Copynumber: 3.9 Consensus size: 74
3120117 GATAAGGATA
* * *
3120127 GAGAACGGCGTCGTTCCGAGATGGAGAAGAGCGGCGATTCCGATAGAGAAAAGGAAAGGGACAGA
1 GAGAACGGCGTCGTTCCGAGA-GGAGAAGAGCAGTGATTCCGATAGAGAAAAGGAAAGGGACAAA
3120192 GAAAAGCATC
65 GAAAAGCATC
* * * * * * *
3120202 GGGAACGGTGTCGTTCTGAGAGGGATAATAGCAGTGATTCGGATAGAGAAAAAGAAAGGGACAAA
1 GAGAACGGCGTCGTTCCGAGA-GGAGAAGAGCAGTGATTCCGATAGAGAAAAGGAAAGGGACAAA
3120267 GAAAAGCATC
65 GAAAAGCATC
* * * *
3120277 GAGAACGGCGTCGTTCTGAGAAGGAGAAGAGCAGTGATTCCGACAGAGAAAAGGAGAGGGAAAAA
1 GAGAACGGCGTCGTTCCGAG-AGGAGAAGAGCAGTGATTCCGATAGAGAAAAGGAAAGGGACAAA
** *
3120342 GAAAAATACC
65 GAAAAGCATC
* * *
3120352 GAGAACGGCGTCGTTCCGAGAGAGAGAAGAGCAGTGATTCCGATAGAGAGAAGGAGAGGGAGAAA
1 GAGAACGGCGTCGTTCCGAGAG-GAGAAGAGCAGTGATTCCGATAGAGAAAAGGAAAGGGACAAA
3120417 GAAAA
65 GAAAA
3120422 ACACCGTGAA
Statistics
Matches: 191, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
74 2 0.01
75 188 0.98
76 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.35, T:0.12
Consensus pattern (74 bp):
GAGAACGGCGTCGTTCCGAGAGGAGAAGAGCAGTGATTCCGATAGAGAAAAGGAAAGGGACAAAG
AAAAGCATC
Found at i:3120504 original size:12 final size:12
Alignment explanation
Indices: 3120489--3120668 Score: 79
Period size: 12 Copynumber: 14.8 Consensus size: 12
3120479 GGAAAGAGCT
3120489 AGGGAGAAGGAA
1 AGGGAGAAGGAA
3120501 AGGGAGAAGCGTGAA
1 AGGGAGAA--G-GAA
3120516 AGGGA-AAGAGAA
1 AGGGAGAAG-GAA
3120528 AGGGAGAA-G--
1 AGGGAGAAGGAA
*
3120537 AGAGA-AAGGGAA
1 AGGGAGAA-GGAA
3120549 AGGGA-AAGGCAA
1 AGGGAGAAGG-AA
* **
3120561 AGGGAAAAACAA
1 AGGGAGAAGGAA
* *
3120573 AGGGAGAGGGAG
1 AGGGAGAAGGAA
* *
3120585 AGGGAGAGGGAG
1 AGGGAGAAGGAA
* *
3120597 AGGGAGAGGGAG
1 AGGGAGAAGGAA
* *
3120609 AGGGAGAGGGAG
1 AGGGAGAAGGAA
3120621 AGGGA-AAGGGAA
1 AGGGAGAA-GGAA
*
3120633 AGAGA-AAGAGAA
1 AGGGAGAAG-GAA
*
3120645 AGGAAGTTAAGGGAA
1 AGGGAG--AA-GGAA
3120660 AGGGAGAAG
1 AGGGAGAAG
3120669 CGGAGGGAGT
Statistics
Matches: 136, Mismatches: 16, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.01
9 4 0.03
10 1 0.01
11 5 0.04
12 96 0.71
13 6 0.04
14 3 0.02
15 18 0.13
16 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.49, T:0.02
Consensus pattern (12 bp):
AGGGAGAAGGAA
Found at i:3120528 original size:27 final size:26
Alignment explanation
Indices: 3120489--3120557 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 26
3120479 GGAAAGAGCT
* *
3120489 AGGGAGAAGGAAAGGGAGAAGCGTGAA
1 AGGGA-AAGGAAAGGGAGAAGAGAGAA
3120516 AGGGAAAGAGAAAGGGAGAAGAGAGAA
1 AGGGAAAG-GAAAGGGAGAAGAGAGAA
3120543 AGGGAAAGGGAAAGG
1 AGGGAAA-GGAAAGG
3120558 CAAAGGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.48, T:0.01
Consensus pattern (26 bp):
AGGGAAAGGAAAGGGAGAAGAGAGAA
Found at i:3120664 original size:6 final size:6
Alignment explanation
Indices: 3120497--3120647 Score: 113
Period size: 6 Copynumber: 24.2 Consensus size: 6
3120487 CTAGGGAGAA
*
3120497 GGAAAG GGAGAAG CGTGAAAG GGAAAG AGAAAG GGAGAAG AGAGAAAG
1 GGAAAG GGA-AAG -G-GAAAG GGAAAG GGAAAG GGA-AAG -G-GAAAG
* * ** * * *
3120545 GGAAAG GGAAAG GCAAAG GGAAAA ACAAAG GGAGAG GGAGAG GGAGAG
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG
* * * * * *
3120593 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAAAG GGAAAG AGAAAG
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG
*
3120641 AGAAAG G
1 GGAAAG G
3120648 AAGTTAAGGG
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
6 105 0.84
7 8 0.06
8 8 0.06
9 4 0.03
ACGTcount: A:0.47, C:0.02, G:0.50, T:0.01
Consensus pattern (6 bp):
GGAAAG
Found at i:3128787 original size:128 final size:128
Alignment explanation
Indices: 3128559--3128790 Score: 455
Period size: 128 Copynumber: 1.8 Consensus size: 128
3128549 AAAAATAGCT
3128559 ATTTGTTGTTAGATTCAAGTTGAATTAATTTTATTTTTAAACTAAATAGAAGATACTGAGTTAAT
1 ATTTGTTGTTAGATTCAAGTTGAATTAATTTTATTTTTAAACTAAATAGAAGATACTGAGTTAAT
*
3128624 TACGTCACATGCCTCAAAGTATGAGTCTTATTTTAAATTGGTCCCTAATTTTTTGAATGTTCC
66 TACGCCACATGCCTCAAAGTATGAGTCTTATTTTAAATTGGTCCCTAATTTTTTGAATGTTCC
3128687 ATTTGTTGTTAGATTCAAGTTGAATTAATTTTATTTTTAAACTAAATAGAAGATACTGAGTTAAT
1 ATTTGTTGTTAGATTCAAGTTGAATTAATTTTATTTTTAAACTAAATAGAAGATACTGAGTTAAT
3128752 TACGCCACATGCCTCAAAGTATGAGTCTTATTTTAAATT
66 TACGCCACATGCCTCAAAGTATGAGTCTTATTTTAAATT
3128791 TGTGTAAACT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 103 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (128 bp):
ATTTGTTGTTAGATTCAAGTTGAATTAATTTTATTTTTAAACTAAATAGAAGATACTGAGTTAAT
TACGCCACATGCCTCAAAGTATGAGTCTTATTTTAAATTGGTCCCTAATTTTTTGAATGTTCC
Found at i:3130465 original size:260 final size:258
Alignment explanation
Indices: 3130008--3130762 Score: 900
Period size: 260 Copynumber: 2.9 Consensus size: 258
3129998 ATGACTATGT
* * * *
3130008 AGTAGCGCTTCTGTGCTTCACTA-TTTTTTTAATATTTAACTTTGATATACAATGTTTCATCTAA
1 AGTAGCGCTTCTGAGCTTCAATATTTTTTTTAATATTTAACTTTGGTATACAGTGTTTCATCTAA
* * * * *
3130072 TTTTAAC--AAGAGTTATATATATTTATTTTCCATTATAATCCACAAGCAC-TGATAGTTTAGTG
66 TTTTAACAAAAAAGTTATATAT-TTTATTTTCCATCATAATCAACAAGCACTTG-TGGTCTAGTG
* *
3130134 GTAGAATAGTA-CTCTGCCACGGTATAGACCCAGGTTAGATTCTCAGCTGGTGCACCCCATGAAG
129 GTAGAATAGTACCT-TGCCACGGTATAGAACCAGGTTAGATTCCCAGCTGGTGCACCCCATGAAG
* * *
3130198 CCATGATGATGATTGCGCTCAAGTGAAGTTAGGATTCTTCATAATCGTCTGATTACAAGACGACT
193 CCATGATGACGATTGCGCTCAAGTGAAGTCAGGATTCTTCATAATCGTCTGATTACAAGACGACG
3130263 C
258 C
*
3130264 AGTAGCGCTTCTGAGCTTCAATATTTTTTTTAATATTTAACTTTGGTATATAGTGTTTCATCTAA
1 AGTAGCGCTTCTGAGCTTCAATATTTTTTTTAATATTTAACTTTGGTATACAGTGTTTCATCTAA
3130329 TTTTAACAAACAAAGTTATATAGTTTTATTTTCCATCATAATCAACAAGCACTTGTGGTCTAGTG
66 TTTTAACAAA-AAAGTTATATA-TTTTATTTTCCATCATAATCAACAAGCACTTGTGGTCTAGTG
* * * * * * *
3130394 ATAGGATAGTACCTTGCCATGGT-TCA-AACCTGTGTTTGATTCCCTGCTGGTGCACTCCATGAA
129 GTAGAATAGTACCTTGCCACGGTAT-AGAACCAG-GTTAGATTCCCAGCTGGTGCACCCCATGAA
* * *
3130457 GCCATGATGACGATTGCGCTCAAGTGAAGTCAGGGTTTTTTATAATCGTCTGATTACAAGACGAC
192 GCCATGATGACGATTGCGCTCAAGTGAAGTCAGGATTCTTCATAATCGTCTGATTACAAGACGAC
3130522 GC
257 GC
* *
3130524 AGTAGCGCTTCTTAGCTTCAATATTTTTTTTTTTAAATATTTAACTTTGAG-AAACAGTGTTTCA
1 AGTAGCGCTTCTGAGCTTCAATA---TTTTTTTT-AATATTTAACTTTG-GTATACAGTGTTTCA
*
3130588 TCTAATTTTAACAAATATAGTTATATAATTTTATTTTCCATCATAATCAACAAGCA-TTAGTGGT
61 TCTAATTTTAACAAA-AAAGTTATAT-ATTTTATTTTCCATCATAATCAACAAGCACTT-GTGGT
** * * * * * *
3130652 CTAGTGGTAGAATAGTACCTTGCCACAATACAGACCCGAGGTTCA-ATTCCCGGTTGGTGGACTC
123 CTAGTGGTAGAATAGTACCTTGCCACGGTATAGAACC-AGGTT-AGATTCCCAGCTGGTGCACCC
** * * * *
3130716 CATGAAGATATGATGACCATCGCCCTCAAGTGAAGTTAGGAGTTCTT
186 CATGAAGCCATGATGACGATTGCGCTCAAGTGAAGTCAGGA-TTCTT
3130763 TAATGTTTTT
Statistics
Matches: 428, Mismatches: 50, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
256 21 0.05
257 45 0.11
259 6 0.01
260 171 0.40
261 5 0.01
263 10 0.02
264 107 0.25
265 58 0.14
266 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (258 bp):
AGTAGCGCTTCTGAGCTTCAATATTTTTTTTAATATTTAACTTTGGTATACAGTGTTTCATCTAA
TTTTAACAAAAAAGTTATATATTTTATTTTCCATCATAATCAACAAGCACTTGTGGTCTAGTGGT
AGAATAGTACCTTGCCACGGTATAGAACCAGGTTAGATTCCCAGCTGGTGCACCCCATGAAGCCA
TGATGACGATTGCGCTCAAGTGAAGTCAGGATTCTTCATAATCGTCTGATTACAAGACGACGC
Found at i:3141059 original size:285 final size:285
Alignment explanation
Indices: 3140549--3141399 Score: 1641
Period size: 285 Copynumber: 3.0 Consensus size: 285
3140539 CAAGGTAAAA
3140549 GGGATATCAATTGATTGCATAAACACATTGCAAACTGAAAAACCTGTTAAAGAACACTTACATGT
1 GGGATATCAATTGATTGCATAAACACATTGCAAACTGAAAAACCTGTTAAAGAACACTTACATGT
*
3140614 TTCCAAAGAGAAACGAGTCCGAAGTGTAGAAATTCATACTCCAGTTCTCTAGATCTGGTAAATAC
66 TTCCAAAGAGAAACGAGTCCGAAGTGTAGAAATTCATACTCCAGTTCTCCAGATCTGGTAAATAC
3140679 ACCAGACAATTTAGAATTTCTTGTGAACATCATTGTTTTTATTGCAAATCCAATTTAGAAAGAAT
131 ACCAGACAATTTAGAATTTCTTGTGAACATCATTGTTTTTATTGCAAATCCAATTTAGAAAGAAT
3140744 CCAATGATTCGACTACAAAGTGAAACATACTTCACAGCTAGCATAAACCCATTAACAACTTATGA
196 CCAATGATTCGACTACAAAGTGAAACATACTTCACAGCTAGCATAAACCCATTAACAACTTATGA
3140809 TTTTACCAGTAGAAACAGAAGTAAC
261 TTTTACCAGTAGAAACAGAAGTAAC
3140834 GGGATATCAATTGATTGCATAAACACATTGCAAACTGAAAAACCTGTTAAAGAACACTTACATGT
1 GGGATATCAATTGATTGCATAAACACATTGCAAACTGAAAAACCTGTTAAAGAACACTTACATGT
*
3140899 TTCCAAAGAGAAAAGAGTCCGAAGTGTAGAAATTCATACTCCAGTTCTCCAGATCTGGTAAATAC
66 TTCCAAAGAGAAACGAGTCCGAAGTGTAGAAATTCATACTCCAGTTCTCCAGATCTGGTAAATAC
3140964 ACCAGACAATTTAGAATTTCTTGTGAACATCATTGTTTTTATTGCAAATCCAATTTAGAAAGAAT
131 ACCAGACAATTTAGAATTTCTTGTGAACATCATTGTTTTTATTGCAAATCCAATTTAGAAAGAAT
3141029 CCAATGATTCGACTACAAAGTGAAACATACTTCACAGCTAGCATAAACCCATTAACAACTTATGA
196 CCAATGATTCGACTACAAAGTGAAACATACTTCACAGCTAGCATAAACCCATTAACAACTTATGA
3141094 TTTTACCAGTAGAAACAGAAGTAAC
261 TTTTACCAGTAGAAACAGAAGTAAC
3141119 GGGATATCAATTGATTGCATAAACACATTGCAAACTGAAAAACCTGTTAAAGAACACTTACATGT
1 GGGATATCAATTGATTGCATAAACACATTGCAAACTGAAAAACCTGTTAAAGAACACTTACATGT
**
3141184 TTCCAAAGAGAAACGAGTCCGAAGTGTAG-AATTCATACTTAAGTTCTCCAGATCTGGTAAATAC
66 TTCCAAAGAGAAACGAGTCCGAAGTGTAGAAATTCATACTCCAGTTCTCCAGATCTGGTAAATAC
*
3141248 ACCAGACAATTTAGAATTTCTTGTGAAAATCATTGTTTTTATTGCAAATCCAATTTAGAAAGAAT
131 ACCAGACAATTTAGAATTTCTTGTGAACATCATTGTTTTTATTGCAAATCCAATTTAGAAAGAAT
3141313 CCAATGATTTCGACTACAAAGTGAAACATACTTCACAGCTAGCATAAACCCATTAACAACTTATG
196 CCAATGA-TTCGACTACAAAGTGAAACATACTTCACAGCTAGCATAAACCCATTAACAACTTATG
3141378 ATTTTACCAGTAGAAACAGAAG
260 ATTTTACCAGTAGAAACAGAAG
3141400 GATCCTTTGG
Statistics
Matches: 559, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
284 104 0.19
285 455 0.81
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (285 bp):
GGGATATCAATTGATTGCATAAACACATTGCAAACTGAAAAACCTGTTAAAGAACACTTACATGT
TTCCAAAGAGAAACGAGTCCGAAGTGTAGAAATTCATACTCCAGTTCTCCAGATCTGGTAAATAC
ACCAGACAATTTAGAATTTCTTGTGAACATCATTGTTTTTATTGCAAATCCAATTTAGAAAGAAT
CCAATGATTCGACTACAAAGTGAAACATACTTCACAGCTAGCATAAACCCATTAACAACTTATGA
TTTTACCAGTAGAAACAGAAGTAAC
Found at i:3149995 original size:64 final size:64
Alignment explanation
Indices: 3149927--3150083 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
3149917 TTGAAGGTGT
** **
3149927 ATCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CTAGTAATAATA-AAACATCGAATGCATATTA-T
3149989 GC
63 GC
* * *
3149991 ATCGATGCATAAGTCATGCATCGATGCATCCTAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCTAGTAATAATAAAACATCGAATGCATATTATGC
* * *
3150055 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
3150084 ACCTTCTGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCTAGTAATAATAAAACATCGAATGCATATTATGC
Found at i:3150733 original size:23 final size:23
Alignment explanation
Indices: 3150689--3150733 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3150679 ATTATTATAT
*
3150689 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
3150712 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
3150734 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:3153695 original size:6 final size:6
Alignment explanation
Indices: 3153684--3153711 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3153674 AAAACAATAA
3153684 AATTAT AATTAT AATTAT AATTAT AATT
1 AATTAT AATTAT AATTAT AATTAT AATT
3153712 GACAGGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:3154588 original size:31 final size:32
Alignment explanation
Indices: 3154523--3154610 Score: 160
Period size: 31 Copynumber: 2.8 Consensus size: 32
3154513 GATCACATGT
3154523 AAACTCTTAAATTTTAAGTTAAGATTAAAAAA
1 AAACTCTTAAATTTTAAGTTAAGATTAAAAAA
3154555 AAACTCTTAAATTTTAAGTTAAGATT-AAAAA
1 AAACTCTTAAATTTTAAGTTAAGATTAAAAAA
*
3154586 AAACTCTTAAATTTTAAATTAAGAT
1 AAACTCTTAAATTTTAAGTTAAGAT
3154611 CAGAACGGCC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 29 0.53
32 26 0.47
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (32 bp):
AAACTCTTAAATTTTAAGTTAAGATTAAAAAA
Found at i:3156038 original size:3 final size:3
Alignment explanation
Indices: 3156030--3156055 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3156020 GCTTGCTTGC
3156030 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3156056 GTGCAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3156377 original size:73 final size:73
Alignment explanation
Indices: 3156288--3156433 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 73
3156278 TCTGGCTTTC
* * *
3156288 TGTAGGAATTTGACTTACCATTGATCTCATTTCACTCTGTAGATGAATCCTTTCATTCTTTCTAA
1 TGTAGGAATTTAACTTACCATTGATCTCATTTCACTCTGTAGACGAATCCTTTCATTCTTTCCAA
3156353 AGCTTTTG
66 AGCTTTTG
*
3156361 TGTAGGAATTTAACTTACCATTGATCTCATTTCACTTTGTAGACGAATCCTTTCATTCTTTCCAA
1 TGTAGGAATTTAACTTACCATTGATCTCATTTCACTCTGTAGACGAATCCTTTCATTCTTTCCAA
3156426 AGCTTTTG
66 AGCTTTTG
3156434 CAATTTGACC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (73 bp):
TGTAGGAATTTAACTTACCATTGATCTCATTTCACTCTGTAGACGAATCCTTTCATTCTTTCCAA
AGCTTTTG
Found at i:3164601 original size:23 final size:23
Alignment explanation
Indices: 3164563--3164606 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3164553 TATATGTTCC
*
3164563 ATTTTTATGTGCTGTAAATTTAG
1 ATTTTTAGGTGCTGTAAATTTAG
*
3164586 ATTTTTAGGTGTTGTAAATTT
1 ATTTTTAGGTGCTGTAAATTT
3164607 GGCTCATAGG
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:0.25, C:0.02, G:0.18, T:0.55
Consensus pattern (23 bp):
ATTTTTAGGTGCTGTAAATTTAG
Found at i:3169367 original size:10 final size:10
Alignment explanation
Indices: 3169352--3169390 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
3169342 ATTTTAAAAC
*
3169352 TATAAATGTA
1 TATAAATATA
3169362 TATAAATATA
1 TATAAATATA
*
3169372 TATATATATA
1 TATAAATATA
*
3169382 TATATATAT
1 TATAAATAT
3169391 TAATGAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (10 bp):
TATAAATATA
Found at i:3169372 original size:2 final size:2
Alignment explanation
Indices: 3169360--3169390 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3169350 ACTATAAATG
*
3169360 TA TA TA AA 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
3169391 TAATGAAATG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3169668 original size:2 final size:2
Alignment explanation
Indices: 3169661--3169699 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3169651 TTATTCGAGT
3169661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3169700 CTTATTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3186900 original size:19 final size:20
Alignment explanation
Indices: 3186876--3186931 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
3186866 AATGTCAAGG
3186876 CAATAAAAAATAG-TAAA-AA
1 CAATAAAAAA-AGATAAATAA
3186895 CAATAAATAAAAGATAAATAA
1 CAATAAA-AAAAGATAAATAA
3186916 -AATAAAAAGAAGATAA
1 CAATAAAAA-AAGATAA
3186932 TCCTCACGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
19 11 0.33
20 20 0.61
21 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (20 bp):
CAATAAAAAAAGATAAATAA
Found at i:3196982 original size:20 final size:21
Alignment explanation
Indices: 3196957--3197004 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3196947 TTTTTTTTTC
3196957 TTTTTCTTTCAAACAT-C-ATT
1 TTTTTCTTTCAAAC-TGCTATT
* *
3196977 TTTTTCGTTCGAACTGCTATT
1 TTTTTCTTTCAAACTGCTATT
3196998 TTTTTCT
1 TTTTTCT
3197005 CACATTCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.57
21 9 0.39
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (21 bp):
TTTTTCTTTCAAACTGCTATT
Found at i:3200997 original size:18 final size:18
Alignment explanation
Indices: 3200962--3201004 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3200952 AAATATATTA
*
3200962 AAAT-AATAAAAGCGATT
1 AAATAAATAAAAGCAATT
*
3200979 AAATAAATAAAAGTAATT
1 AAATAAATAAAAGCAATT
3200997 AAAGTAAA
1 AAA-TAAA
3201005 AATAAGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAGCAATT
Found at i:3206140 original size:23 final size:23
Alignment explanation
Indices: 3206098--3206165 Score: 100
Period size: 23 Copynumber: 2.8 Consensus size: 23
3206088 GAATGATATT
3206098 TTAACATTAAAGAGTATAAAAACTAA
1 TTAA-ATTAAA-A-TATAAAAACTAA
3206124 TTAAATTAAAATATAAAAACTAA
1 TTAAATTAAAATATAAAAACTAA
*
3206147 TTAAGTTAAAATATAAAAA
1 TTAAATTAAAATATAAAAA
3206166 ATAAATTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 30 0.73
24 1 0.02
25 6 0.15
26 4 0.10
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TTAAATTAAAATATAAAAACTAA
Found at i:3207970 original size:2 final size:2
Alignment explanation
Indices: 3207963--3208006 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3207953 AAGTCAGGAT
3207963 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
3208005 TA
1 TA
3208007 AATCTGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3218665 original size:31 final size:31
Alignment explanation
Indices: 3218567--3218680 Score: 102
Period size: 31 Copynumber: 3.6 Consensus size: 31
3218557 AAAATGTTAC
* * * * * *
3218567 AAAATGGTCATTGAATTTTTCAAATGATTAC
1 AAAATGATCATTAAACTTATCAAATTATTAA
* * * *
3218598 AAAATGATAATTAAACTTTACCAAACTATTAT
1 AAAATGATCATTAAAC-TTATCAAATTATTAA
*
3218630 AAAATAATCATTAAACTTATCAAATTATTAA
1 AAAATGATCATTAAACTTATCAAATTATTAA
* *
3218661 AAAATGATCTTTAATCTTAT
1 AAAATGATCATTAAACTTAT
3218681 AAAAAAACTA
Statistics
Matches: 65, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
31 41 0.63
32 24 0.37
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (31 bp):
AAAATGATCATTAAACTTATCAAATTATTAA
Found at i:3219460 original size:21 final size:20
Alignment explanation
Indices: 3219434--3219531 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
3219424 ATCAGTTTCC
3219434 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
3219455 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
3219474 ACAAATTCGCATTGCG-TTTTG
1 A-AAA-TCGCAACGCGATTTTG
* *
3219495 CCAAAATCGCAACGCGAATATG
1 --AAAATCGCAACGCGATTTTG
3219517 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
3219532 ACACATAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.02
20 21 0.34
21 32 0.52
22 6 0.10
23 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:3219560 original size:20 final size:20
Alignment explanation
Indices: 3219498--3219691 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3219488 CGTTTTGCCA
* ** *
3219498 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3219518 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3219538 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3219558 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3219578 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3219598 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3219618 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
3219638 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
3219658 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
3219679 AAATCGCAACGCG
1 AAATCGCAACGCG
3219692 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3219582 original size:60 final size:60
Alignment explanation
Indices: 3219498--3219691 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3219488 CGTTTTGCCA
* ** * *
3219498 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
3219558 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
3219618 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
3219679 AAATCGCAACGCG
1 AAATCGCAACGCG
3219692 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:3220791 original size:6 final size:6
Alignment explanation
Indices: 3220780--3220806 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3220770 AATATTGATC
3220780 TGGATT TGGATT TGGATT TGGATT TGG
1 TGGATT TGGATT TGGATT TGGATT TGG
3220807 CAGTTTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (6 bp):
TGGATT
Found at i:3222150 original size:75 final size:75
Alignment explanation
Indices: 3221978--3222145 Score: 218
Period size: 75 Copynumber: 2.3 Consensus size: 75
3221968 ATTTGAATAC
* * *
3221978 AATTTACAATATTTTTATATATTTTAAATTTCTGTTAATGGAATAAATAATTCTTAATTTTTATT
1 AATTTATAATATTTTTATATATTTTAAATTTCTGTTAATGAAAGAAATAATTCTTAATTTTTATT
3222043 TATTAACTAT
66 TATTAACTAT
* * *
3222053 AATTTATAATATTTTTATATATTTTTAATGTT-TGTTAGTGAAAGAAATAATT-TTTATTTTTAT
1 AATTTATAATATTTTTATATATTTTAAAT-TTCTGTTAATGAAAGAAATAATTCTTAATTTTTAT
**
3222116 TTATTAGTTAT
65 TTATTAACTAT
*
3222127 AA-TT-TAATATTTATATATA
1 AATTTATAATATTTTTATATA
3222146 ATATTAGAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
72 14 0.17
73 2 0.02
74 21 0.25
75 44 0.53
76 2 0.02
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.55
Consensus pattern (75 bp):
AATTTATAATATTTTTATATATTTTAAATTTCTGTTAATGAAAGAAATAATTCTTAATTTTTATT
TATTAACTAT
Found at i:3222278 original size:70 final size:72
Alignment explanation
Indices: 3222199--3222491 Score: 302
Period size: 70 Copynumber: 4.1 Consensus size: 72
3222189 TAAAATTATA
*
3222199 AAATTATAATAAATAAATAAAATTAAGAATTATTT-TT-ATTAACAAAAATTAAAAATATATAAA
1 AAATTATAATTAATAAATAAAATTAAGAATTATTTCTTCATTAACAAAAATTAAAAATATATAAA
3222262 ATATTGT
66 ATATTGT
* * * * *
3222269 AAATTATAATTAATAAATAAAAATTAAAAACTAATTCTTTCATTGACAAAGATTAAAAATATGTA
1 AAATTATAATTAATAAAT-AAAATTAAGAATTATTTC-TTCATTAACAAAAATTAAAAATA--TA
* *
3222334 AAAAAAATTGT
62 TAAAATATTGT
*
3222345 AAATTATAGTTAATAAAT-AAA--AA-AATTATTTCTTCCATTAACAAAAA-TAAAAATATATAA
1 AAATTATAATTAATAAATAAAATTAAGAATTATTTCTT-CATTAACAAAAATTAAAAATATATAA
* *
3222405 ACTATTAT
65 AATATTGT
* * * *
3222413 AAATTATAGTTAAT-AA-AAAATTAAGACTTGTTTCTTCCATTAA-AACAATCT-AAAATATATA
1 AAATTATAATTAATAAATAAAATTAAGAATTATTTCTT-CATTAACAAAAAT-TAAAAATATAT-
3222474 AAAATATTGT
63 AAAATATTGT
3222484 AAATTATA
1 AAATTATA
3222492 TTCAAATATG
Statistics
Matches: 187, Mismatches: 22, Indels: 27
0.79 0.09 0.11
Matches are distributed among these distances:
67 5 0.03
68 23 0.12
69 6 0.03
70 52 0.28
71 48 0.26
72 2 0.01
73 2 0.01
74 21 0.11
76 28 0.15
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (72 bp):
AAATTATAATTAATAAATAAAATTAAGAATTATTTCTTCATTAACAAAAATTAAAAATATATAAA
ATATTGT
Found at i:3222363 original size:76 final size:71
Alignment explanation
Indices: 3222180--3222429 Score: 217
Period size: 71 Copynumber: 3.5 Consensus size: 71
3222170 ACTATAATTT
* * * * *
3222180 AATATAATATAAAATTATAAAATTATAATAAATAAAT-AAAATTAAGAATTATTTTTATTAACAA
1 AATATAA-AAAAAATTGT-AAATTATAATTAATAAATAAAAATTAAAAATAATTTTTATTAACAA
3222244 AAATTAAA
64 AAATTAAA
* * *
3222252 AATATATAAAATATTGTAAATTATAATTAATAAATAAAAATTAAAAACTAATTCTTTCATTGACA
1 AATATAAAAAAAATTGTAAATTATAATTAATAAATAAAAATTAAAAA-TAATT-TTT-ATTAACA
*
3222317 AAGATTAAA
63 AAAATTAAA
* *
3222326 AATATGTAAAAAAAATTGTAAATTATAGTTAATAAAT---AA--AAAAATTATTTCTTCCATTAA
1 AATA--TAAAAAAAATTGTAAATTATAATTAATAAATAAAAATTAAAAATAATTT-TT--ATTAA
3222386 CAAAAA-TAAA
61 CAAAAATTAAA
* ** * *
3222396 AATATATAAACTATTATAAATTATAGTTAATAAA
1 AATATAAAAAAAATTGTAAATTATAATTAATAAA
3222430 AAATTAAGAC
Statistics
Matches: 151, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
68 26 0.17
69 1 0.01
70 31 0.21
71 32 0.21
72 10 0.07
73 5 0.03
74 18 0.12
76 28 0.19
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (71 bp):
AATATAAAAAAAATTGTAAATTATAATTAATAAATAAAAATTAAAAATAATTTTTATTAACAAAA
ATTAAA
Found at i:3225822 original size:2 final size:2
Alignment explanation
Indices: 3225815--3225898 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
3225805 TTGTGGCGTG
3225815 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
3225857 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
3225899 ATTTGATCCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3236031 original size:2 final size:2
Alignment explanation
Indices: 3236024--3236054 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3236014 CATGTGAGAC
3236024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3236055 ACAATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3236892 original size:30 final size:29
Alignment explanation
Indices: 3236856--3236922 Score: 102
Period size: 27 Copynumber: 2.3 Consensus size: 29
3236846 TCTCTTTGAA
*
3236856 AATCATTTAAAAATGTGAGGAGTCGCCATC
1 AATCATTT-AAAAGGTGAGGAGTCGCCATC
3236886 AATCATTT--AAGGTGAGGAGTCGCCATC
1 AATCATTTAAAAGGTGAGGAGTCGCCATC
3236913 AATCATTTAA
1 AATCATTTAA
3236923 GGTGAGATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 26 0.76
30 8 0.24
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (29 bp):
AATCATTTAAAAGGTGAGGAGTCGCCATC
Found at i:3236906 original size:27 final size:27
Alignment explanation
Indices: 3236870--3236928 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
3236860 ATTTAAAAAT
3236870 GTGAGGAGTCGCCATCAATCATTTAAG
1 GTGAGGAGTCGCCATCAATCATTTAAG
3236897 GTGAGGAGTCGCCATCAATCATTTAAG
1 GTGAGGAGTCGCCATCAATCATTTAAG
3236924 GTGAG
1 GTGAG
3236929 ATTGGAACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (27 bp):
GTGAGGAGTCGCCATCAATCATTTAAG
Found at i:3239381 original size:44 final size:44
Alignment explanation
Indices: 3239193--3240055 Score: 269
Period size: 44 Copynumber: 19.6 Consensus size: 44
3239183 AGTTGACGCT
* * * * * *
3239193 GATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATATC
1 GATCCACCTCCTTCTGTGATGGAATCGAGCG-AAATAAAGATGTC
* * ***
3239238 GATCCACTTCCTTCTGTGATGGAAATCGAAC-AATATGTCGATG-C
1 GATCCACCTCCTTCTGTGATGG-AATCGAGCGAA-ATAAAGATGTC
* * * ** *
3239282 TGATCTACCTCATTCTGTGATAGAATCGAGC-AAA-AGTTGACG-C
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATA-AAGATGTC
* * * * *
3239325 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTC
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
* ***
3239370 GATCCACCTCCTTCTGTGATGGAATCGAAC-AAGATGTCGATG-C
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAA-ATAAAGATGTC
* * * * * *
3239413 TGATCTATCTCCTTCTGTGATAGAATCGAGC-AAA-AAGTTGACGTT
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAA--AGATGTC
* * * * * *
3239458 GATCCAACTCCTTCTGCGATGGATTTGAGCAAAATAAAAATGTC
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
* ** * **** * *
3239502 GATCCACCTCATTCTGTGATGGAATCGAATGAGACGTTGGTGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
* * * * * * *
3239546 GATCTACCTCATTCTGTGATAGAAACTAGC--AA-AAAGTTGACGC
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATG--TC
* * * ** *
3239589 TGATCCAACTCCTTCTGCGATGGATTTAAGCGAAATAAAAATGTC
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
* * * *** *
3239634 GATTCACCTCCTTCTGTGATGGAATTGAAC-AAGATGTCGATGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAA-ATAAAGATGTC
* * * * ** *
3239678 GATCTACCTCCTTCTGTGATAGAATCAAGCTAAA-AGTTGACG-C
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATA-AAGATGTC
* * * * * *
3239721 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATATC
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
* ** * *** *
3239766 GATCCACCTCCTTCTGCGATGGAATCGAATGAGATGTTGGTG-C
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
** * * * *
3239809 TGATTTACCTTCTTCTGTGATAGAAACGAGC--AA-AAAGTTAACG-C
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAG---ATGTC
* * * * *
3239853 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTC
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
* * *** *
3239898 GATCCATCTCCTTCTGTGATGGAATCGAAC-AAGATGTTGATGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAA-ATAAAGATGTC
* * * * ** *
3239942 GATCTACCTCCTTCTGTGATAGAATCAAGCTAAA-AGCTGACG-C
1 GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATA-AAGATGTC
* * * * * *
3239985 TGATCCAACTCCTTCTGTGATGGATTTGAGCGAAATAAAAATATT
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
*
3240030 GATCCACCTCCTTCTGCGATGGAATC
1 GATCCACCTCCTTCTGTGATGGAATC
3240056 AAATGAGATG
Statistics
Matches: 572, Mismatches: 206, Indels: 81
0.67 0.24 0.09
Matches are distributed among these distances:
41 4 0.01
42 2 0.00
43 39 0.07
44 453 0.79
45 55 0.10
46 11 0.02
47 8 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATGGAATCGAGCGAAATAAAGATGTC
Found at i:3239461 original size:132 final size:132
Alignment explanation
Indices: 3239164--3240113 Score: 1418
Period size: 132 Copynumber: 7.2 Consensus size: 132
3239154 CAACTCCATA
*
3239164 TGTGAT-GAATCGAGCAAGAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA
1 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCG-AAA
* * * *
3239228 TAAAAATATCGATCCACTTCCTTCTGTGATGGAAATCGAACAATATGTCGATGCTGATCTACCTC
65 TAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACAAGATGTTGATGCTGATCTACCTC
*
3239293 ATTC
129 CTTC
3239297 TGTGATAGAATCGAGC-AAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
1 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
* *
3239361 AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTCGATGCTGATCTATCTCCT
66 AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGCTGATCTACCTCCT
3239426 TC
131 TC
* *
3239428 TGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCCTTCTGCGATGGATTTGAGCAAAAT
1 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
* ** * * * *
3239493 AAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAATGAGACGTTGGTGTTGATCTACCTCAT
66 AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGCTGATCTACCTCCT
3239558 TC
131 TC
* * *
3239560 TGTGATAGAAACTAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTAAGCGAAAT
1 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
* * * *
3239625 AAAAATGTCGATTCACCTCCTTCTGTGATGGAATTGAACAAGATGTCGATGTTGATCTACCTCCT
66 AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGCTGATCTACCTCCT
3239690 TC
131 TC
* *
3239692 TGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
1 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
* * ** * * *
3239757 AAAAATATCGATCCACCTCCTTCTGCGATGGAATCGAATGAGATGTTGGTGCTGATTTACCTTCT
66 AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGCTGATCTACCTCCT
3239822 TC
131 TC
* *
3239824 TGTGATAGAAACGAGCAAAAAGTTAACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
1 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
* *
3239889 AAAAATGTCGATCCATCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGTTGATCTACCTCCT
66 AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGCTGATCTACCTCCT
3239954 TC
131 TC
* * * *
3239956 TGTGATAGAATCAAGCTAAAAGCTGACGCTGATCCAACTCCTTCTGTGATGGATTTGAGCGAAAT
1 TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
* * * * ** * *
3240021 AAAAATATTGATCCACCTCCTTCTGCGATGGAATCAAATGAGATGTTGGTGCTGATCTACCTTCT
66 AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGCTGATCTACCTCCT
3240086 TC
131 TC
*
3240088 TGTGATAGAATCGAGCAAACAGTTGA
1 TGTGATAGAATCGAGCAAAAAGTTGA
3240114 ACAATCTCTT
Statistics
Matches: 736, Mismatches: 79, Indels: 5
0.90 0.10 0.01
Matches are distributed among these distances:
131 49 0.07
132 629 0.85
133 49 0.07
134 9 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (132 bp):
TGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT
AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGATGCTGATCTACCTCCT
TC
Found at i:3240494 original size:37 final size:37
Alignment explanation
Indices: 3240442--3240563 Score: 178
Period size: 36 Copynumber: 3.4 Consensus size: 37
3240432 CAAGTGAGAT
* *
3240442 TTGTTTCGAGGGAAACTGTCTCTAA-AGAGACAAAAC
1 TTGTTTCAAGAGAAACTGTCTCTAAGAGAGACAAAAC
3240478 TTTGTTTCAAGAGAAACTGTCT-TAAGAGAGACAAAAC
1 -TTGTTTCAAGAGAAACTGTCTCTAAGAGAGACAAAAC
* *
3240515 TTGTTTCAAGAGAAAATGTCTC-AAGGGAGACAAAAC
1 TTGTTTCAAGAGAAACTGTCTCTAAGAGAGACAAAAC
3240551 TTGTTTCAAGAGA
1 TTGTTTCAAGAGA
3240564 GACAAAATTC
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
36 49 0.62
37 30 0.38
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TTGTTTCAAGAGAAACTGTCTCTAAGAGAGACAAAAC
Found at i:3240526 original size:21 final size:21
Alignment explanation
Indices: 3240467--3240580 Score: 85
Period size: 21 Copynumber: 6.0 Consensus size: 21
3240457 CTGTCTCTAA
3240467 AGAGACAAAACTTTGTTTC-A-
1 AGAGACAAAAC-TTGTTTCAAG
3240487 AGAG---AAAC-TGTCTT-AAG
1 AGAGACAAAACTTGT-TTCAAG
3240504 AGAGACAAAACTTGTTTC-A-
1 AGAGACAAAACTTGTTTCAAG
*
3240523 AGAG--AAAA--TGTCTCAAG
1 AGAGACAAAACTTGTTTCAAG
*
3240540 GGAGACAAAACTTGTTTCAAG
1 AGAGACAAAACTTGTTTCAAG
3240561 AGAGACAAAA-TTCGTTTCAA
1 AGAGACAAAACTT-GTTTCAA
3240581 TTGAAACGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 29
0.69 0.04 0.27
Matches are distributed among these distances:
15 8 0.11
16 4 0.05
17 15 0.20
19 8 0.11
20 13 0.17
21 27 0.36
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (21 bp):
AGAGACAAAACTTGTTTCAAG
Done.