Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 117 of 335
Found at i:35709323 original size:72 final size:72
Alignment explanation
Indices: 35709231--35709396 Score: 287
Period size: 72 Copynumber: 2.3 Consensus size: 72
35709221 TGATATAGTG
* * *
35709231 TTAAAAATACTTACATAATATAATTATTAAAAATATATAAATAATATAATAAAGTATATAAATAA
1 TTAACAATACATACATAATATAATTATTAAAAATATATAAATAATATAATAAAATATATAAATAA
35709296 TATGATA
66 TATGATA
* *
35709303 TTAACAATGCATACATAATATAATTATTAAAAATATATACATAATATAATAAAATATATAAATAA
1 TTAACAATACATACATAATATAATTATTAAAAATATATAAATAATATAATAAAATATATAAATAA
35709368 TATGATA
66 TATGATA
35709375 TTAACAATACATACATAATATA
1 TTAACAATACATACATAATATA
35709397 GTTAAAAAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 88 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.35
Consensus pattern (72 bp):
TTAACAATACATACATAATATAATTATTAAAAATATATAAATAATATAATAAAATATATAAATAA
TATGATA
Found at i:35709434 original size:72 final size:70
Alignment explanation
Indices: 35709231--35709444 Score: 245
Period size: 72 Copynumber: 2.9 Consensus size: 70
35709221 TGATATAGTG
* * *
35709231 TTAAAAATACTTACATAATATAATTATTAAAAATATATAAATAATATAATAAAGTATATAAATAA
1 TTAACAATACATACATAATATAATTA-TAAAAATATATAAATAATATAATAATG-ATATAAATAA
35709296 TATGATA
64 TATGATA
* *
35709303 TTAACAATGCATACATAATATAATTATTAAAAATATATACATAATATAATAAAAT-ATATAAATA
1 TTAACAATACATACATAATATAATTA-TAAAAATATATAAATAATATAAT--AATGATATAAATA
35709367 ATATGATA
63 ATATGATA
* *
35709375 TTAACAATACATACATAATATAGTTA-AAAAATAATATTAAAAAATGAT-ATACATGATATAATA
1 TTAACAATACATACATAATATAATTATAAAAAT-ATA-TAAATAAT-ATAATA-ATGATATAA-A
35709438 TTAATAT
61 -TAATAT
35709445 ACATGTGCAT
Statistics
Matches: 124, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
70 7 0.06
71 5 0.04
72 101 0.81
73 3 0.02
74 8 0.06
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (70 bp):
TTAACAATACATACATAATATAATTATAAAAATATATAAATAATATAATAATGATATAAATAATA
TGATA
Found at i:35710309 original size:3 final size:3
Alignment explanation
Indices: 35710303--35710333 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
35710293 TTCGAAAAAA
35710303 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35710334 AACAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:35710320 original size:14 final size:14
Alignment explanation
Indices: 35710298--35710333 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
35710288 GTAGATTCGA
*
35710298 AAAAAAATAATAAT
1 AAAATAATAATAAT
35710312 AAAATAATAATAAT
1 AAAATAATAATAAT
35710326 AATAATAA
1 AA-AATAA
35710334 AACAAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:35710759 original size:21 final size:21
Alignment explanation
Indices: 35710733--35710797 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
35710723 ATTGGGTTTT
35710733 GGGTTTAATTTTGGTGGGTTA
1 GGGTTTAATTTTGGTGGGTTA
* * *
35710754 GGGTTTAGGTTATT-G-GGTTTT
1 GGGTTTA-ATT-TTGGTGGGTTA
35710775 GGGTTTAATTTTGGTGGGTTA
1 GGGTTTAATTTTGGTGGGTTA
35710796 GG
1 GG
35710798 TAAGGCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 24 0.71
22 3 0.09
23 2 0.06
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (21 bp):
GGGTTTAATTTTGGTGGGTTA
Found at i:35724106 original size:22 final size:24
Alignment explanation
Indices: 35724068--35724121 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
35724058 TAAATACTTT
35724068 AATTTTTAATATAATTTT-AGTTAA
1 AATTTTTAATATAATTTTGA-TTAA
*
35724092 TATTTTTAAT-T-ATTTTGATTAA
1 AATTTTTAATATAATTTTGATTAA
35724114 AATTTTTA
1 AATTTTTA
35724122 CACTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 16 0.59
23 2 0.07
24 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AATTTTTAATATAATTTTGATTAA
Found at i:35725695 original size:30 final size:30
Alignment explanation
Indices: 35725640--35725696 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35725630 ATTATAAAGG
*
35725640 TTTTTGTATTAAAAATTAGATTAAATTTTA
1 TTTTTGTATTAAAAATTAGAGTAAATTTTA
*
35725670 TTTTTTTATTTAAAAATTA-AGTAAATT
1 TTTTTGTA-TTAAAAATTAGAGTAAATT
35725697 AGTTCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (30 bp):
TTTTTGTATTAAAAATTAGAGTAAATTTTA
Found at i:35726813 original size:9 final size:8
Alignment explanation
Indices: 35726799--35726865 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 8
35726789 CCATGCTTTT
35726799 TTTTTATAA
1 TTTTT-TAA
35726808 TTTTTATGAA
1 TTTTT-T-AA
35726818 TTTTTT-A
1 TTTTTTAA
35726825 TATTTTTAA
1 T-TTTTTAA
35726834 --TTTTAA
1 TTTTTTAA
35726840 -TTTTTAA
1 TTTTTTAA
35726847 TTTTTATAA
1 TTTTT-TAA
*
35726856 TTTTTGAA
1 TTTTTTAA
35726864 TT
1 TT
35726866 ACTTATTGAC
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
6 6 0.12
7 8 0.16
8 13 0.25
9 17 0.33
10 7 0.14
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (8 bp):
TTTTTTAA
Found at i:35726836 original size:7 final size:7
Alignment explanation
Indices: 35726819--35726852 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
35726809 TTTTATGAAT
35726819 TTTTTATA
1 TTTTTA-A
35726827 TTTTTAA
1 TTTTTAA
35726834 -TTTTAA
1 TTTTTAA
35726840 TTTTTAA
1 TTTTTAA
35726847 TTTTTA
1 TTTTTA
35726853 TAATTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 13 0.52
8 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:35726841 original size:22 final size:22
Alignment explanation
Indices: 35726816--35726859 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
35726806 AATTTTTATG
*
35726816 AATTTTTTATATTTT-TAATTTT
1 AATTTTTAAT-TTTTATAATTTT
35726838 AATTTTTAATTTTTATAATTTT
1 AATTTTTAATTTTTATAATTTT
35726860 TGAATTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
AATTTTTAATTTTTATAATTTT
Found at i:35726844 original size:13 final size:14
Alignment explanation
Indices: 35726820--35726865 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
35726810 TTTATGAATT
35726820 TTTTATATTTTTAA
1 TTTTATATTTTTAA
35726834 TTTTA-ATTTTTAA
1 TTTTATATTTTTAA
35726847 TTTTTATAATTTTTGAA
1 -TTTTAT-ATTTTT-AA
35726864 TT
1 TT
35726866 ACTTATTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.29
14 10 0.36
16 8 0.29
17 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTATATTTTTAA
Found at i:35727405 original size:18 final size:18
Alignment explanation
Indices: 35727382--35727417 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
35727372 ATTGAACTAA
35727382 ATTTTTCTATTTT-TTAAT
1 ATTTTT-TATTTTATTAAT
35727400 ATTTTTTATTTTATTAAT
1 ATTTTTTATTTTATTAAT
35727418 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTTTATTTTATTAAT
Found at i:35727533 original size:2 final size:2
Alignment explanation
Indices: 35727526--35727564 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35727516 AAAGAAAAGA
35727526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35727565 AAAGATAACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35734673 original size:101 final size:100
Alignment explanation
Indices: 35734476--35734731 Score: 275
Period size: 101 Copynumber: 2.5 Consensus size: 100
35734466 CTTATTGTAT
* * * * ** *
35734476 CATAGTCCAACTATGGTCTTACATAT-GCATTGCCATGGCCCTGCCATGGTCTTATGTTCATAGT
1 CATAGTCCAACTATGATCTTACATATAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
* ** * * *
35734540 GCCATAACTCGGTTACGGTCTTATCATTAGAATGC
66 GCCATAACCCAATTACAGTCCTATCATCAGAATGC
* *
35734575 CATGGTCCAACCATGATCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACG-TCTATA
1 CATAGTCCAACTATGATCTTACATAT-AACACTGCCATGGTCCAACCATGGTCTTACGTTC-ATA
* *
35734639 GTGCCATAACCCAATTATAGTCCTGTCATCAGAATGC
64 GTGCCATAACCCAATTACAGTCCTATCATCAGAATGC
* * *
35734676 CATAGCCCAGCTAT-AGTCTTACATATATACACTGCCACGGTCCAACCATGGTCTTA
1 CATAGTCCAACTATGA-TCTTACATATA-ACACTGCCATGGTCCAACCATGGTCTTA
35734732 TGTTTGAATA
Statistics
Matches: 130, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
99 23 0.18
100 4 0.03
101 103 0.79
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (100 bp):
CATAGTCCAACTATGATCTTACATATAACACTGCCATGGTCCAACCATGGTCTTACGTTCATAGT
GCCATAACCCAATTACAGTCCTATCATCAGAATGC
Found at i:35738566 original size:16 final size:15
Alignment explanation
Indices: 35738545--35738592 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
35738535 GATGTGAATA
35738545 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
35738561 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
35738576 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
35738592 A
1 A
35738593 ATAATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:35738568 original size:24 final size:24
Alignment explanation
Indices: 35738541--35738596 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
35738531 TAATGATGTG
*
35738541 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
35738565 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
35738589 AATAATAA
1 AATAATAA
35738597 TTAATATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:35738575 original size:8 final size:8
Alignment explanation
Indices: 35738541--35738592 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
35738531 TAATGATGTG
*
35738541 AATAATAA
1 AATATTAA
35738549 AATATATAA
1 AATAT-TAA
35738558 AATA-TAA
1 AATATTAA
35738565 AATATTAA
1 AATATTAA
*
35738573 AATATCAA
1 AATATTAA
*
35738581 AATATTAG
1 AATATTAA
35738589 AATA
1 AATA
35738593 ATAATTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:35738806 original size:22 final size:24
Alignment explanation
Indices: 35738743--35738807 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
35738733 CGTGATAATA
*
35738743 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
35738768 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
35738791 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
35738808 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:35738855 original size:23 final size:22
Alignment explanation
Indices: 35738828--35738879 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
35738818 AAAAATATAT
* *
35738828 ATATATATTTATATATATACGTA
1 ATATATATTTA-AAATATACCTA
*
35738851 ATATAGAATTTAAAATATACCTA
1 ATATA-TATTTAAAATATACCTA
35738874 ATATAT
1 ATATAT
35738880 TAAAAGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATATATTTAAAATATACCTA
Found at i:35738919 original size:23 final size:25
Alignment explanation
Indices: 35738876--35738921 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35738866 TATACCTAAT
35738876 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
35738901 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
35738922 ACAAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:35739530 original size:37 final size:35
Alignment explanation
Indices: 35739475--35739563 Score: 124
Period size: 37 Copynumber: 2.5 Consensus size: 35
35739465 GTGGCTAGGG
* * *
35739475 TTTTTTATTTTTTATTTTTTTGGGTTAGGTTTTTTT
1 TTTTTTCTTTTTT-TTTTTTGGGGTTAGGTTTTTCT
35739511 CTTTTTTCTTCTTTTTTTTTTGGGGTTAGGTTTTTCT
1 -TTTTTTCTT-TTTTTTTTTTGGGGTTAGGTTTTTCT
35739548 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
35739564 GGGTGTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 7 0.15
36 9 0.19
37 28 0.58
38 4 0.08
ACGTcount: A:0.04, C:0.06, G:0.12, T:0.78
Consensus pattern (35 bp):
TTTTTTCTTTTTTTTTTTTGGGGTTAGGTTTTTCT
Found at i:35740578 original size:72 final size:73
Alignment explanation
Indices: 35740339--35742857 Score: 2948
Period size: 72 Copynumber: 33.7 Consensus size: 73
35740329 AGTATGTGAT
*
35740339 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGACAGAAATTGAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAA-ACAGAAATTGAAAA
*
35740404 TACCTCAGCATGTGAAC
60 TACCTCAGC--GTG-TC
*
35740421 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAACAGAAATTGAAAAT
*
35740485 ACCTCAACGTGTC
61 ACCTCAGCGTGTC
* ** * *
35740498 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35740562 AGCGTGTC
66 AGCGTGTC
* * *
35740570 CCGTGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAACAGAAATTGAAAAT
*
35740635 ACCTCAACGTGTC
61 ACCTCAGCGTGTC
* ** * *
35740648 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35740712 AGCGTGTC
66 AGCGTGTC
* ** * * *
35740720 CCGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAATAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35740784 AGCGTGTC
66 AGCGTGTC
** *
35740792 CCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAAACAGAAATTGAAAATAC
*
35740857 CTCAACGTGTC
63 CTCAGCGTGTC
* * ** * * *
35740868 TTAAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACTTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
*
35740932 AACGTGTC
66 AGCGTGTC
* ** * *
35740940 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35741004 AGCGTGTC
66 AGCGTGTC
* * *
35741012 CCGAGGCTCAACTCACCTCTCGCAATATAAGTTGGTTTTTTTTTTTGAAAACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTT-G----ATTTTTTGAAAACAGAAATTGAAAAT
*
35741077 ACCTCAACGTGTC
61 ACCTCAGCGTGTC
* ** * * *
35741090 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACTTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35741154 AGCGTGTC
66 AGCGTGTC
* ** * *
35741162 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35741226 AGCGTGTC
66 AGCGTGTC
* *
35741234 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
35741299 TCAGCATGTC
64 TCAGCGTGTC
* ** * *
35741309 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCT
35741374 CAGCGTGTC
65 CAGCGTGTC
* ** * *
35741383 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35741447 AGCGTGTC
66 AGCGTGTC
* *
35741455 CCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAACAGAAATTGAAAAT
*
35741520 ACCTCAACGTGTC
61 ACCTCAGCGTGTC
* ** * * *
35741533 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACTTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35741597 AGCGTGTC
66 AGCGTGTC
* * *
35741605 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTAAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
35741670 TCAGCATGTC
64 TCAGCGTGTC
* ** * *
35741680 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAACAGAAATTGAAAATACC
35741745 TCAGCGTGTC
64 TCAGCGTGTC
** *
35741755 CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
35741820 TCAGCGTGTC
64 TCAGCGTGTC
* *
35741830 CCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAACAGAAATTGAAAATA
35741895 CCTCCA-CGTGTC
62 CCT-CAGCGTGTC
* ** * * *
35741907 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACTTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35741971 AGCGTGTC
66 AGCGTGTC
* *
35741979 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTCTTTGAAAGACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TTTGAAA-ACAGAAATTGAAAATACC
*
35742044 TCAGCATGTC
64 TCAGCGTGTC
* ** * *
35742054 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCT
35742119 CAGCGTGTC
65 CAGCGTGTC
* *
35742128 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
35742193 TCAGCATGTC
64 TCAGCGTGTC
* * * ** * * *
35742203 TTGAGTCTAAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAACAGAAATTGAAAATACC
35742268 TCAGCGTGTC
64 TCAGCGTGTC
* *
35742278 CTTAGGCTCCACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
35742343 TCAGCATGTGAAC
64 TCAGC--GTG-TC
*
35742356 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAACAGAAATTGAAAATA
* *
35742420 CCTCAACATGTC
62 CCTCAGCGTGTC
* *
35742432 TTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
35742497 TCAGCATGTC
64 TCAGCGTGTC
* ** * * *
35742507 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAATAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCT
*
35742572 CAGCATGTC
65 CAGCGTGTC
*
35742581 CTGAGGCTCCACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACC
*
35742646 TCAGCATGTGAAC
64 TCAGC--GTG-TC
*
35742659 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAACAGAAATTGAAAATA
*
35742723 CCTCAACGTGTC
62 CCTCAGCGTGTC
* ** * * *
35742735 TTGAGGCTCAACTCATTTCTCGTAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
35742799 AGCGTGTC
66 AGCGTGTC
* *
35742807 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-ATTTTG-AAACAGAAAT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAAT
35742858 AAAAACATCA
Statistics
Matches: 2145, Mismatches: 233, Indels: 129
0.86 0.09 0.05
Matches are distributed among these distances:
71 12 0.01
72 724 0.34
73 2 0.00
74 245 0.11
75 513 0.24
76 87 0.04
77 188 0.09
78 239 0.11
79 44 0.02
80 44 0.02
81 46 0.02
82 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (73 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
AGCGTGTC
Found at i:35740595 original size:150 final size:147
Alignment explanation
Indices: 35740344--35742857 Score: 3061
Period size: 150 Copynumber: 16.8 Consensus size: 147
35740334 GTGATCTGAA
35740344 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGACAGAAATTGAAAATACCT
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAA-ACAGAAATTGAAAATACCT
** *
35740409 CAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAG
60 CAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTTGAAAACAG
*
35740474 AAATTGAAAATACCTCAACGTGTCTTGAG
119 AAATTGAAAATACCTCAGCGTGTCTTGAG
** * *
35740503 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
* *
35740567 GTCCCGTGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAA
66 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTTGAAAACAGAAATTGAA
*
35740632 AATACCTCAACGTGTCTTGAG
127 AATACCTCAGCGTGTCTTGAG
** * *
35740653 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
** * * *
35740717 GTCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAATAGAAATTGAAATTA
66 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATA
***
35740780 CCTCAGCGTGTCCCAAG
131 CCTCAGCGTGTCTTGAG
* *
35740797 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAAACAGAAATTGAAAATACCTCAG
*** ** *
35740862 CGTGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAA
63 CGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAA
* * *
35740925 TTACTTCAACGTGTCTTGAG
128 ATACCTCAGCGTGTCTTGAG
** * *
35740945 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
* *
35741009 GTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGGTTTTTTTTTTTGAAAACAGAAATTGAA
66 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-G---ATTTTTTTGAAAACAGAAATTGAA
*
35741074 AATACCTCAACGTGTCTTGAG
127 AATACCTCAGCGTGTCTTGAG
** * * *
35741095 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACTTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
** ** * *
35741159 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTA
66 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATA
**
35741222 CCTCAGCGTGTCCCGAG
131 CCTCAGCGTGTCTTGAG
*
35741239 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
* ** ** * *
35741304 ATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAAT
64 GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAA
35741369 TACCTCAGCGTGTCTTGAG
129 TACCTCAGCGTGTCTTGAG
** * *
35741388 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
*
35741452 GTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAA
66 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTTGAAAACAGAAATTGAA
*
35741517 AATACCTCAACGTGTCTTGAG
127 AATACCTCAGCGTGTCTTGAG
** * * *
35741538 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACTTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
* *
35741602 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTAAAAAT
66 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAAT
*
35741667 ACCTCAGCATGTCTTGAG
130 ACCTCAGCGTGTCTTGAG
** * *
35741685 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAACAGAAATTGAAAATACCTCAGC
* *
35741750 GTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAA
64 GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAA
**
35741815 ATACCTCAGCGTGTCCCGAG
128 ATACCTCAGCGTGTCTTGAG
*
35741835 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATACCTCC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAACAGAAATTGAAAATACCT-C
** ** *
35741900 A-CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGA
61 AGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGA
* * **
35741962 AATTACTTCAGCGTGTCCCGAG
126 AAATACCTCAGCGTGTCTTGAG
*
35741984 GCTCAACTCACCTCTCGCAATATGAGTTGATTTCTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTT-TTTGAAA-ACAGAAATTGAAAATACCTCAGC
* ** ** * *
35742049 ATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAAT
64 GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAA
**
35742114 TACCTCAGCGTGTCCCGAG
129 TACCTCAGCGTGTCTTGAG
*
35742133 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
* ** * * ** * *
35742198 ATGTCTTGAGTCTAAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTACAACAGAAATTGAAA
64 GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAACAGAAATTGAAA
*
35742263 TTACCTCAGCGTGTCCTT-AG
128 ATACCTCAGCGTGT-CTTGAG
*
35742283 GCTCCACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
** *
35742348 ATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATT
64 --GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAACAGAAATT
* *
35742413 GAAAATACCTCAACATGTCTTGAG
124 GAAAATACCTCAGCGTGTCTTGAG
*
35742437 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
* ** ** * * *
35742502 ATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAATAGAAATTGAAAT
64 GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAA
* *
35742567 TACCTCAGCATGTCCTGAG
129 TACCTCAGCGTGTCTTGAG
*
35742586 GCTCCACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
** *
35742651 ATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATT
64 --GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAACAGAAATT
*
35742716 GAAAATACCTCAACGTGTCTTGAG
124 GAAAATACCTCAGCGTGTCTTGAG
** * * *
35742740 GCTCAACTCATTTCTCGTAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
*
35742804 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTG-AAACAGAAAT
66 GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAAT
35742858 AAAAACATCA
Statistics
Matches: 2128, Mismatches: 183, Indels: 104
0.88 0.08 0.04
Matches are distributed among these distances:
143 10 0.00
144 193 0.09
145 4 0.00
146 83 0.04
147 184 0.09
148 129 0.06
149 403 0.19
150 706 0.33
151 55 0.03
152 157 0.07
153 13 0.01
154 163 0.08
159 28 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (147 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
GTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATA
CCTCAGCGTGTCTTGAG
Found at i:35740739 original size:222 final size:221
Alignment explanation
Indices: 35740344--35742846 Score: 3334
Period size: 222 Copynumber: 11.2 Consensus size: 221
35740334 GTGATCTGAA
35740344 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAGACAGAAATTGAAAATACCT
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTTGAAA-ACAGAAATTGAAAATACCT
* * * ** *
35740409 CAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACA
63 CA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-----TTTTTTGAAAACA
* *
35740473 GAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
120 GAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
*
35740538 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGTG
185 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
*
35740575 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAATACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTTGAAAACAGAAATTGAAAATACCTC
*
35740640 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAA
64 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAA
** *
35740704 ATTACCTCAGCGTGTCCCGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAATAGA
129 ATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGA
*
35740769 AATTGAAATTACCTCAGCGTGTCCCAAG
194 AATTGAAATTACCTCAGCGTGTCCCGAG
*
35740797 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
* *
35740862 CGTGTCTTAAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAAT
66 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAT
* *
35740926 TACTTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAA
131 TACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAA
35740991 TTGAAATTACCTCAGCGTGTCCCGAG
196 TTGAAATTACCTCAGCGTGTCCCGAG
* *
35741017 GCTCAACTCACCTCTCGCAATATAAGTTGGTTTTTTTTTTTGAAAACAGAAATTGAAAATACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTT-G-ATTTTTTTTTGAAAACAGAAATTGAAAATACCTC
*
35741082 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAA
64 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAA
*
35741146 ATTACTTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGA
129 ATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGA
35741211 AATTGAAATTACCTCAGCGTGTCCCGAG
194 AATTGAAATTACCTCAGCGTGTCCCGAG
*
35741239 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAAAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
* * *
35741302 GCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAA
65 ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAA
35741367 ATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGA
129 ATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGA
35741432 AATTGAAATTACCTCAGCGTGTCCCGAG
194 AATTGAAATTACCTCAGCGTGTCCCGAG
*
35741460 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTTGAAAACAGAAATTGAAAATACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTTGAAAACAGAAATTGAAAATACCTC
*
35741525 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAA
64 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAA
* ** ** *
35741589 ATTACTTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGAC
129 ATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-AC
* * * * **
35741654 AAAAATTAAAAATACCTCAGCATGTCTTGAG
191 AGAAATTGAAATTACCTCAGCGTGTCCCGAG
** * * *
35741685 GCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTTTGACAACAGAAATTGAAATTACCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
*** ** *
35741749 CGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAA
66 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAA
* ** ** * *
35741814 AATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAA
129 ATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-----ATTTTGAAA
* **
35741879 ACAGAAATTGAAAATACCTCCA-CGTGTCTTGAG
189 ACAGAAATTGAAATTACCT-CAGCGTGTCCCGAG
** * * * *
35741912 GCTCAACTCATTTCTCGCAATATGAGTTGA----ATTTTGAAAACAGAAATTGAAATTACTTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
** ** *
35741973 CGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTCTTTGAAAGACAAAAATTGAA
66 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT-TTTGAAA-ACAGAAATTGAA
* * * *
35742038 AATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACA
129 ATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACA
35742103 GAAATTGAAATTACCTCAGCGTGTCCCGAG
192 GAAATTGAAATTACCTCAGCGTGTCCCGAG
*
35742133 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAAAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
* * * * * *
35742196 GCATGTCTTGAGTCTAAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTACAACAGAAATTGA
65 ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--TTTTTTGAAAACAGAAATTGA
* ** *
35742261 AATTACCTCAGCGTGTCCTT-AGGCTCCACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAG
128 AATTACCTCAGCGTGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-
* **
35742325 ACAGAAATTGAAAATACCTCAGCATGTGAACCGAG
189 ACAGAAATTGAAATTACCTCAGC--GTGTCCCGAG
*
35742360 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTGAAAACAGAAATTGAAAATACCTCA
* ** *
35742425 ACATGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGA
65 ACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGA
* * * * *
35742490 AAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAAT
128 AATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAAC
* *
35742555 AGAAATTGAAATTACCTCAGCATGTCCTGAG
191 AGAAATTGAAATTACCTCAGCGTGTCCCGAG
*
35742586 GCTCCACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
* * * ** *
35742649 GCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAA
65 --ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----TTTTTTGAAAACAGAA
* * *
35742713 ATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGTAATATGAGTTGAATTTTGAA
123 ATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAA
35742778 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
188 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAG
*
35742812 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
35742847 GAAACAGAAA
Statistics
Matches: 2079, Mismatches: 148, Indels: 93
0.90 0.06 0.04
Matches are distributed among these distances:
218 11 0.01
219 60 0.03
220 213 0.10
221 207 0.10
222 483 0.23
223 22 0.01
224 346 0.17
225 154 0.07
226 138 0.07
227 96 0.05
228 142 0.07
229 131 0.06
230 32 0.02
231 44 0.02
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (221 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAT
TACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAA
TTGAAATTACCTCAGCGTGTCCCGAG
Found at i:35750885 original size:12 final size:12
Alignment explanation
Indices: 35750865--35750900 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
35750855 TGGGATATGC
*
35750865 AATGTATGAATG
1 AATGCATGAATG
35750877 AATGCATGAATG
1 AATGCATGAATG
35750889 AATGCATGAATG
1 AATGCATGAATG
35750901 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:35752519 original size:18 final size:18
Alignment explanation
Indices: 35752477--35752519 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35752467 ATTAATATTG
35752477 ACAAATAAAAAATAAAAT
1 ACAAATAAAAAATAAAAT
* *
35752495 AGAAATAAAAAA-AATAT
1 ACAAATAAAAAATAAAAT
35752512 ACATAATA
1 ACA-AATA
35752520 TATATATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (18 bp):
ACAAATAAAAAATAAAAT
Found at i:35752678 original size:22 final size:24
Alignment explanation
Indices: 35752615--35752679 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
35752605 CGTGATAATA
*
35752615 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
35752640 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
35752663 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
35752680 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:35752754 original size:57 final size:60
Alignment explanation
Indices: 35752665--35752775 Score: 158
Period size: 57 Copynumber: 1.9 Consensus size: 60
35752655 TAATATAGTT
35752665 AAGATATATACATAAGATAACATGTAAAAAATATATATATATATAAATAATATAATATTA
1 AAGATATATACATAAGATAACATGTAAAAAATATATATATATATAAATAATATAATATTA
* **
35752725 AAGATATATACAT-A-A-AATA-GTATAAAAATATATATATATATACGTAATATA
1 AAGATATATACATAAGATAACATGTA-AAAAATATATATATATATAAATAATATA
35752776 GAATTTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
56 3 0.06
57 29 0.62
58 1 0.02
59 1 0.02
60 13 0.28
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (60 bp):
AAGATATATACATAAGATAACATGTAAAAAATATATATATATATAAATAATATAATATTA
Found at i:35752789 original size:55 final size:56
Alignment explanation
Indices: 35752665--35752836 Score: 154
Period size: 57 Copynumber: 2.9 Consensus size: 56
35752655 TAATATAGTT
*
35752665 AAGATATATACATAAGATAACATGTAAAAAATATATATATATATAAATAATATAATATTA
1 AAGATATATACAT-A-A-AATA-GTAAAAAATATATATATATATAAATAATATAATATTA
** *
35752725 AAGATATATACATAAAATAGTATAAAAATATATATATATATACGTAATATAGA-ATTT
1 AAGATATATACATAAAATAGTA-AAAAATATATATATATATAAATAATATA-ATATTA
* * *
35752782 AA-A-ATATACCTAATATATTAAAAGAATATATAATATAATATTAAGA-AATATAATA
1 AAGATATATACATAAAATAGTAAAA-AATATAT-ATAT-ATA-TAA-ATAATATAATA
35752837 ATAATAAAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
54 3 0.03
55 21 0.22
56 8 0.08
57 38 0.40
58 11 0.12
59 1 0.01
60 13 0.14
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (56 bp):
AAGATATATACATAAAATAGTAAAAAATATATATATATATAAATAATATAATATTA
Found at i:35752817 original size:20 final size:20
Alignment explanation
Indices: 35752792--35752842 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
35752782 AAAATATACC
*
35752792 TAATATATTA-AAAGAATATA
1 TAATATAATATAAAGAA-ATA
*
35752812 TAATATAATATTAAGAAATA
1 TAATATAATATAAAGAAATA
35752832 TAATAATAATA
1 TAAT-ATAATA
35752843 AAAAATGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
TAATATAATATAAAGAAATA
Found at i:35752840 original size:21 final size:21
Alignment explanation
Indices: 35752803--35752842 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
35752793 AATATATTAA
35752803 AAGAATATATAATATAATATT
1 AAGAATATATAATATAATATT
35752824 AAGAA-ATATAATAATAATA
1 AAGAATATATAAT-ATAATA
35752843 AAAAATGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AAGAATATATAATATAATATT
Found at i:35753447 original size:36 final size:34
Alignment explanation
Indices: 35753400--35753501 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 34
35753390 GGCTAGGGTT
35753400 TTTTTATTTTTTATTTTTTTGGGTTAGGTTTTTTTC
1 TTTTT-TTTTTT-TTTTTTTGGGTTAGGTTTTTTTC
*
35753436 TTTTTTCTTTTTTTTTTTTTGGGTAAGG--TTTTTC
1 -TTTTT-TTTTTTTTTTTTTGGGTTAGGTTTTTTTC
*
35753470 TTTTTTTCTTTTTTTTTTGGGTT-GGTTTTTTT
1 TTTTTTTTTTTTTTTTTTGGGTTAGGTTTTTTT
35753502 TTGGGGGGGC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
31 2 0.03
32 16 0.27
33 10 0.17
34 6 0.10
36 14 0.24
37 11 0.19
ACGTcount: A:0.05, C:0.04, G:0.15, T:0.76
Consensus pattern (34 bp):
TTTTTTTTTTTTTTTTTTGGGTTAGGTTTTTTTC
Found at i:35753468 original size:35 final size:36
Alignment explanation
Indices: 35753398--35753487 Score: 130
Period size: 35 Copynumber: 2.5 Consensus size: 36
35753388 GTGGCTAGGG
* *
35753398 TTTTTTTATTTTTTATTTTTTTGGGTTAGGTTTTTT-
1 TTTTTTTCTTTTTT-TTTTTTTGGGTAAGGTTTTTTC
35753434 TCTTTTTTCTTTTTTTTTTTTTGGGTAAGG-TTTTTC
1 T-TTTTTTCTTTTTTTTTTTTTGGGTAAGGTTTTTTC
35753470 TTTTTTTCTTTTTTTTTT
1 TTTTTTTCTTTTTTTTTT
35753488 GGGTTGGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
35 22 0.44
36 16 0.32
37 12 0.24
ACGTcount: A:0.06, C:0.04, G:0.11, T:0.79
Consensus pattern (36 bp):
TTTTTTTCTTTTTTTTTTTTTGGGTAAGGTTTTTTC
Found at i:35753503 original size:35 final size:34
Alignment explanation
Indices: 35753398--35753503 Score: 128
Period size: 36 Copynumber: 3.1 Consensus size: 34
35753388 GTGGCTAGGG
*
35753398 TTTTTTTATTTTTTATTTTTTTGGGTTAGGTTTTTT
1 TTTTTTTCTTTTTT-TTTTTTTGGGTT-GGTTTTTT
* *
35753434 TCTTTTTTCTTTTTTTTTTTTTGGGTAAGGTTTTTC
1 T-TTTTTTCTTTTTTTTTTTTTGGGT-TGGTTTTTT
35753470 TTTTTTTC---TTTTTTTTTTGGGTTGGTTTTTT
1 TTTTTTTCTTTTTTTTTTTTTGGGTTGGTTTTTT
35753501 TTT
1 TTT
35753504 GGGGGGGCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
31 10 0.16
32 14 0.22
35 7 0.11
36 20 0.32
37 12 0.19
ACGTcount: A:0.05, C:0.04, G:0.14, T:0.77
Consensus pattern (34 bp):
TTTTTTTCTTTTTTTTTTTTTGGGTTGGTTTTTT
Found at i:35755220 original size:48 final size:46
Alignment explanation
Indices: 35755168--35755598 Score: 205
Period size: 48 Copynumber: 9.2 Consensus size: 46
35755158 GATAAATGGT
*
35755168 ATGAGAAAAAATTGAAAATTACATAGAAAGATAGATAATTTAAATGAA
1 ATGAGAAAAAATT-AAAATTAAATAGAAA-ATAGATAATTTAAATGAA
* *
35755216 ATGAG--AAAA--AAAATTGAAAT-GAACAA-ATATAATATAAATGAA
1 ATGAGAAAAAATTAAAATT-AAATAGAA-AATAGATAATTTAAATGAA
* * * * *
35755258 TTGAGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAA
1 ATGAGAAAAAATTAAAATTAAATAGAAA-ATAGAT-AATTTAAATGAA
** * *
35755306 ATGAGAAAAAAAATTATTTAAAAGATATGAGAAAA-A-ATTAAATTAAAATTGAA
1 ATGAG--AAAAAATTA---AAATTAAAT-AGAAAATAGA-T-AATTTAAA-TGAA
* * ** *
35755359 A-GA-AAGATAAATTTAAATGAAATGAGGAAAATATTTAAATTAAATG-A
1 ATGAGAA-A-AAATTAAAATTAAAT-A-GAAAATAGATAATTTAAATGAA
* ** *
35755406 ATGAGGAAAAAATTAAATTTGCATGGAAAGATAGATAATTTAAATGAA
1 ATGA-GAAAAAATTAAAATTAAATAGAAA-ATAGATAATTTAAATGAA
*
35755454 ATGAGAAAAAAATTAAATTTAAATA-AAAATA-AT-A--TAAATGAA
1 ATGAG-AAAAAATTAAAATTAAATAGAAAATAGATAATTTAAATGAA
* * *
35755496 ATGAGAAAAAAAATT-AAATTAAAATGGGAAGATAGATAAATTAAATGAA
1 ATGAG--AAAAAATTAAAATT-AAAT-AGAAAATAGATAATTTAAATGAA
* * * * * * *
35755545 ATGAGAAAAAAATAAATTTACAAGAAAAAAAATATAAATTAAATGAA
1 ATGAGAAAAAATTAAAATTA-AATAGAAAATAGATAATTTAAATGAA
35755592 ATG-GAAA
1 ATGAGAAA
35755599 TAGGAATGGA
Statistics
Matches: 300, Mismatches: 44, Indels: 80
0.71 0.10 0.19
Matches are distributed among these distances:
42 35 0.12
43 23 0.08
44 9 0.03
45 11 0.04
46 26 0.09
47 52 0.17
48 70 0.23
49 27 0.09
50 14 0.05
51 6 0.02
52 12 0.04
53 11 0.04
54 4 0.01
ACGTcount: A:0.61, C:0.01, G:0.13, T:0.25
Consensus pattern (46 bp):
ATGAGAAAAAATTAAAATTAAATAGAAAATAGATAATTTAAATGAA
Found at i:35755254 original size:42 final size:44
Alignment explanation
Indices: 35755200--35755320 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 44
35755190 ATAGAAAGAT
35755200 AGATAATTTAAATGAAATGAGAAAAAAAATTGAAAT-G-AACAA
1 AGATAATTTAAATGAAATGAGAAAAAAAATTGAAATGGAAACAA
* * * * * *
35755242 ATATAATATAAATGAATTGAGAAAAAATTAAATTTACATGGAAAGAA
1 AGATAATTTAAATGAAATGAG-AAAAA--AAATTGAAATGGAAACAA
35755289 AGATAAATTTAAATGAAATGAGAAAAAAAATT
1 AGAT-AATTTAAATGAAATGAGAAAAAAAATT
35755321 ATTTAAAAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
42 18 0.28
43 5 0.08
45 13 0.20
46 1 0.02
47 12 0.19
48 15 0.23
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.25
Consensus pattern (44 bp):
AGATAATTTAAATGAAATGAGAAAAAAAATTGAAATGGAAACAA
Found at i:35755413 original size:26 final size:26
Alignment explanation
Indices: 35755292--35755424 Score: 95
Period size: 26 Copynumber: 5.2 Consensus size: 26
35755282 GAAAGAAAGA
*
35755292 TAAATTTAAATGAAATGAGAAAAAAAAT
1 TAAA-TTAAATGAAATGAG-GAAAAAAT
* * *
35755320 T-ATTTAAAAGATATGA-GAAAAAAT
1 TAAATTAAATGAAATGAGGAAAAAAT
*
35755344 TAAATTAAAATTG-AA--A-G-AAAGA-
1 TAAATT-AAA-TGAAATGAGGAAAAAAT
*
35755366 TAAATTTAAATGAAATGAGGAAAATATT
1 TAAA-TTAAATGAAATGAGGAAAA-AAT
35755394 TAAATTAAATG-AATGAGGAAAAAAT
1 TAAATTAAATGAAATGAGGAAAAAAT
35755419 TAAATT
1 TAAATT
35755425 TGCATGGAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
21 2 0.02
22 9 0.11
23 6 0.07
24 11 0.13
25 12 0.14
26 29 0.35
27 9 0.11
28 5 0.06
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (26 bp):
TAAATTAAATGAAATGAGGAAAAAAT
Found at i:35755472 original size:27 final size:27
Alignment explanation
Indices: 35755366--35755477 Score: 87
Period size: 27 Copynumber: 4.4 Consensus size: 27
35755356 GAAAGAAAGA
* *
35755366 TAAATTTAAATGAAATGAGGAAAATATT
1 TAAATTTAAATGAAATGA-GAAAAAAAT
*
35755394 TAAA-TTAAATG-AATGAGGAAAAAAT
1 TAAATTTAAATGAAATGAGAAAAAAAT
** * * *
35755419 TAAATTTGCATGGAA--AG--ATAGA-
1 TAAATTTAAATGAAATGAGAAAAAAAT
35755441 T-AATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAATGAGAAAAAAAT
35755467 TAAATTTAAAT
1 TAAATTTAAAT
35755478 AAAAATAATA
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
21 10 0.16
22 1 0.02
23 5 0.08
25 15 0.23
26 11 0.17
27 18 0.28
28 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.14, T:0.29
Consensus pattern (27 bp):
TAAATTTAAATGAAATGAGAAAAAAAT
Found at i:35755476 original size:74 final size:74
Alignment explanation
Indices: 35755250--35755477 Score: 311
Period size: 74 Copynumber: 3.1 Consensus size: 74
35755240 AAATATAATA
35755250 TAAATGAATTGAGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAAA
1 TAAATGAA-TGAGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAG-AAA
35755315 AAAATT--ATT
64 AAAATTAAATT
* * * *
35755324 TAAAAGATATGAGAAAAAATTAAATTAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAAA
1 TAAATGA-ATGAGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGA-GAAA
* *
35755389 ATATTTAAA-T
64 AAAATTAAATT
* *
35755399 TAAATGAATGAGGAAAAAATTAAATTTGCATGGAAAGATAGAT-AATTTAAATGAAATGAGAAAA
1 TAAATGAATGA-GAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAAA
35755463 AAATTAAATT
65 AAATTAAATT
35755473 TAAAT
1 TAAAT
35755478 AAAAATAATA
Statistics
Matches: 134, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
73 11 0.08
74 87 0.65
75 35 0.26
76 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.14, T:0.27
Consensus pattern (74 bp):
TAAATGAATGAGAAAAAATTAAATTTACATGGAAAGAAAGATAAATTTAAATGAAATGAGAAAAA
AATTAAATT
Found at i:35755492 original size:42 final size:42
Alignment explanation
Indices: 35755440--35755590 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 42
35755430 GGAAAGATAG
*
35755440 ATAATTTAAATGAAATGAGAAAAAAATTAAATTTAAATAAAA
1 ATAATATAAATGAAATGAGAAAAAAATTAAATTTAAATAAAA
*
35755482 ATAATATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATA
1 ATAATATAAATGAAATGAG-AAAAAAATTAAATTTAAAT---AA-A-A
*
35755530 GATAA-ATTAAATGAAATGAGAAAAAAA-TAAATTTACAAGAAAA
1 -ATAATA-TAAATGAAATGAGAAAAAAATTAAATTTA-AATAAAA
* *
35755573 AAAATATAAATTAAATGA
1 ATAATATAAATGAAATGA
35755591 AATGGAAATA
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
42 32 0.34
43 20 0.22
44 1 0.01
45 2 0.02
46 2 0.02
47 8 0.09
48 11 0.12
49 17 0.18
ACGTcount: A:0.64, C:0.01, G:0.11, T:0.25
Consensus pattern (42 bp):
ATAATATAAATGAAATGAGAAAAAAATTAAATTTAAATAAAA
Found at i:35755528 original size:91 final size:90
Alignment explanation
Indices: 35755395--35755590 Score: 272
Period size: 91 Copynumber: 2.2 Consensus size: 90
35755385 GAAAATATTT
* *** *
35755395 AAAT-TAAATG-AATGAGGAAAAAATTAAATTTGCATGGAAAGATAGATAATTTAAATGAAATGA
1 AAATATAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATGA
*
35755458 GAAAAAAATTAAATTTA-AATAAAAA
66 GAAAAAAA-TAAATTTACAAGAAAAA
* *
35755483 TAATATAAATGAAATGAGAAAAAAAATTAAATTAAAATGGGAAGATAGATAAATTAAATGAAATG
1 AAATATAAATGAAATGAG-AAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATG
35755548 AGAAAAAAATAAATTTACAAGAAAAA
65 AGAAAAAAATAAATTTACAAGAAAAA
*
35755574 AAATATAAATTAAATGA
1 AAATATAAATGAAATGA
35755591 AATGGAAATA
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
88 3 0.03
89 6 0.06
90 14 0.15
91 71 0.76
ACGTcount: A:0.62, C:0.01, G:0.13, T:0.24
Consensus pattern (90 bp):
AAATATAAATGAAATGAGAAAAAAATTAAATTAAAATGGAAAGATAGATAAATTAAATGAAATGA
GAAAAAAATAAATTTACAAGAAAAA
Found at i:35755598 original size:6 final size:5
Alignment explanation
Indices: 35755580--35755663 Score: 69
Period size: 5 Copynumber: 15.6 Consensus size: 5
35755570 AAAAAAATAT
* * *
35755580 AAATT AAATG AAATGG AAATAG GAATGG AAATGG AAATA AAATG AAATG
1 AAATG AAATG AAAT-G AAAT-G AAAT-G AAAT-G AAATG AAATG AAATG
* *
35755629 AAATG AAATGG AAATG AAATTG GAATG ATATG AAA
1 AAATG AAAT-G AAATG AAA-TG AAATG AAATG AAA
35755664 AAAAAAATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
5 37 0.57
6 28 0.43
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:35755599 original size:11 final size:11
Alignment explanation
Indices: 35755585--35755653 Score: 79
Period size: 12 Copynumber: 6.2 Consensus size: 11
35755575 AATATAAATT
35755585 AAATGAAATGG
1 AAATGAAATGG
*
35755596 AAATAGGAATGG
1 AAAT-GAAATGG
*
35755608 AAATGGAAAT-A
1 AAAT-GAAATGG
35755619 AAATGAAAT-G
1 AAATGAAATGG
35755629 AAATGAAATGG
1 AAATGAAATGG
35755640 AAATGAAATTGG
1 AAATGAAA-TGG
35755652 AA
1 AA
35755654 TGATATGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
10 14 0.28
11 17 0.34
12 19 0.38
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.19
Consensus pattern (11 bp):
AAATGAAATGG
Found at i:35755655 original size:11 final size:10
Alignment explanation
Indices: 35755586--35755656 Score: 52
Period size: 11 Copynumber: 6.5 Consensus size: 10
35755576 ATATAAATTA
35755586 AATGAAATGG
1 AATGAAATGG
*
35755596 AAATAGGAATGG
1 -AAT-GAAATGG
**
35755608 AAATGGAAATAA
1 -AAT-GAAATGG
*
35755620 AATGAAATGA
1 AATGAAATGG
35755630 AATGAAATGG
1 AATGAAATGG
35755640 AAATGAAATTGG
1 -AATGAAA-TGG
35755652 AATGA
1 AATGA
35755657 TATGAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
10 15 0.30
11 18 0.36
12 17 0.34
ACGTcount: A:0.55, C:0.00, G:0.25, T:0.20
Consensus pattern (10 bp):
AATGAAATGG
Found at i:35755661 original size:16 final size:15
Alignment explanation
Indices: 35755580--35755663 Score: 69
Period size: 16 Copynumber: 5.2 Consensus size: 15
35755570 AAAAAAATAT
*
35755580 AAATTAAATGAAATGG
1 AAATGAAATGAAAT-G
*
35755596 AAATAGGAATGGAAATGG
1 AAAT-GAAAT-GAAAT-G
*
35755614 AAATAAAATGAAATG
1 AAATGAAATGAAATG
35755629 AAATGAAATGGAAATG
1 AAATGAAAT-GAAATG
* *
35755645 AAATTGGAATGATATG
1 AAA-TGAAATGAAATG
35755661 AAA
1 AAA
35755664 AAAAAAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
15 9 0.16
16 26 0.46
17 11 0.19
18 11 0.19
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (15 bp):
AAATGAAATGAAATG
Found at i:35755893 original size:16 final size:16
Alignment explanation
Indices: 35755854--35755894 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
35755844 ACAAATTTAT
35755854 AAATTAAAT-TGACAA
1 AAATTAAATATGACAA
*
35755869 AAATAAAATATGA-AA
1 AAATTAAATATGACAA
35755884 AAATTTAAATA
1 AAA-TTAAATA
35755895 AAATATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (16 bp):
AAATTAAATATGACAA
Found at i:35755999 original size:14 final size:15
Alignment explanation
Indices: 35755942--35755996 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 15
35755932 GACTACTTCT
35755942 AATTAATATGAAAAA
1 AATTAATATGAAAAA
*
35755957 AATATGAAATGAATTAAAAA
1 AAT-T--AAT--ATGAAAAA
35755977 AATTAATATGAAAAA
1 AATTAATATGAAAAA
35755992 AATTA
1 AATTA
35755997 TATTAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 15 0.45
16 1 0.03
17 3 0.09
18 3 0.09
19 1 0.03
20 10 0.30
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
AATTAATATGAAAAA
Found at i:35756038 original size:5 final size:5
Alignment explanation
Indices: 35756030--35756151 Score: 59
Period size: 5 Copynumber: 22.4 Consensus size: 5
35756020 AAAAAAAATT
* * *
35756030 AATGA AATGA AATGTTA AAAGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
* *
35756082 AATGA ATATGA AATTA AATGA AATGTTA AATGA ATATAA AATGA AATG-
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
* *
35756130 -ATGA TTATGA AATGG AATGA AA
1 AATGA -AATGA AATGA AATGA AA
35756152 GTTTAAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
3 3 0.03
5 49 0.54
6 26 0.29
7 13 0.14
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:35756095 original size:28 final size:28
Alignment explanation
Indices: 35756055--35756130 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
35756045 TAAAAGAAAT
* *
35756055 ATGAATATGAAATGAAATGTAAT-TTGTA
1 ATGAATATGAAATGAAATGAAATGTT-AA
*
35756083 ATGAATATGAAATTAAATGAAATGTTAA
1 ATGAATATGAAATGAAATGAAATGTTAA
*
35756111 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
35756131 TGATTATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 40 0.95
29 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (28 bp):
ATGAATATGAAATGAAATGAAATGTTAA
Found at i:35756267 original size:5 final size:5
Alignment explanation
Indices: 35756257--35756324 Score: 64
Period size: 5 Copynumber: 12.6 Consensus size: 5
35756247 TAGATAATTT
* *
35756257 AAATG AAATG AAAATG AAAATG TAAATA AAATG AAATG AAATG CACATG
1 AAATG AAATG -AAATG -AAATG -AAATG AAATG AAATG AAATG -AAATG
*
35756306 AAATTG GAATG AAATG AAA
1 AAA-TG AAATG AAATG AAA
35756325 AAAAACAGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 30 0.57
6 23 0.43
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (5 bp):
AAATG
Found at i:35756273 original size:6 final size:6
Alignment explanation
Indices: 35756257--35756297 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
35756247 TAGATAATTT
*
35756257 AAATG- AAATGA AAATGA AAATGT AAAT-A AAATG- AAATGA AA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AA
35756298 TGCACATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 14 0.45
6 17 0.55
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.20
Consensus pattern (6 bp):
AAATGA
Found at i:35756273 original size:11 final size:10
Alignment explanation
Indices: 35756257--35756324 Score: 64
Period size: 11 Copynumber: 6.3 Consensus size: 10
35756247 TAGATAATTT
35756257 AAATGAAATG
1 AAATGAAATG
35756267 AAAATGAAAATG
1 -AAATG-AAATG
*
35756279 TAAATAAAATG
1 -AAATGAAATG
35756290 AAATGAAATG
1 AAATGAAATG
*
35756300 CACATGAAATTG
1 -AAATGAAA-TG
*
35756312 GAATGAAATG
1 AAATGAAATG
35756322 AAA
1 AAA
35756325 AAAAACAGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
10 13 0.28
11 23 0.49
12 11 0.23
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (10 bp):
AAATGAAATG
Found at i:35756287 original size:17 final size:17
Alignment explanation
Indices: 35756257--35756325 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
35756247 TAGATAATTT
35756257 AAATGAAATGAAAATGA
1 AAATGAAATGAAAATGA
35756274 AAATGTAAAT-AAAATG-
1 AAATG-AAATGAAAATGA
* *
35756290 AAATGAAATGCACATGA
1 AAATGAAATGAAAATGA
* *
35756307 AATTGGAATG-AAATGA
1 AAATGAAATGAAAATGA
35756323 AAA
1 AAA
35756326 AAAACAGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 4 0.09
16 16 0.37
17 19 0.44
18 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.17, T:0.20
Consensus pattern (17 bp):
AAATGAAATGAAAATGA
Found at i:35759944 original size:50 final size:49
Alignment explanation
Indices: 35759868--35760000 Score: 185
Period size: 50 Copynumber: 2.7 Consensus size: 49
35759858 AAAAAATAAT
* * *
35759868 TTTTTTTACTAGTCTGGTACCGGCCATTAGAAGACCAGAACCAAATTTTG
1 TTTTTTTACTAGCCTGGT-GCAGCCATTAGAAGACCAGAACCAAATTTTG
*
35759918 TTTTTTTACTAGCCTGGTGCAAGCCATTAGAAGGCCAGAACCAAATTTTG
1 TTTTTTTACTAGCCTGGTGC-AGCCATTAGAAGACCAGAACCAAATTTTG
* *
35759968 TTTTTTTACTAGCCTAGTGCCGACCATTAGAAG
1 TTTTTTTACTAGCCTGGTGCAG-CCATTAGAAG
35760001 CCCAAGACAA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
49 2 0.03
50 73 0.97
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (49 bp):
TTTTTTTACTAGCCTGGTGCAGCCATTAGAAGACCAGAACCAAATTTTG
Found at i:35762201 original size:3 final size:3
Alignment explanation
Indices: 35762193--35762217 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35762183 CATAATACTA
35762193 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
35762218 AAAACAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:35775619 original size:13 final size:13
Alignment explanation
Indices: 35775601--35775627 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35775591 GCTCGGCAGG
35775601 GACACGCCTGTGT
1 GACACGCCTGTGT
35775614 GACACGCCTGTGT
1 GACACGCCTGTGT
35775627 G
1 G
35775628 CGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (13 bp):
GACACGCCTGTGT
Found at i:35777939 original size:20 final size:20
Alignment explanation
Indices: 35777914--35777958 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
35777904 TGTTTTATGC
*
35777914 TTTAGAAAT-TTATCGAAAGT
1 TTTAGAAATCTT-TCAAAAGT
35777934 TTTAGAAATCTTTCAAAAGT
1 TTTAGAAATCTTTCAAAAGT
35777954 TTTAG
1 TTTAG
35777959 TCTCTAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (20 bp):
TTTAGAAATCTTTCAAAAGT
Found at i:35785061 original size:2 final size:2
Alignment explanation
Indices: 35785042--35785076 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
35785032 ATAATATAGG
* *
35785042 TA TA TG TA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35785077 GCAAATAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35788344 original size:22 final size:22
Alignment explanation
Indices: 35788316--35788366 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
35788306 TCAGAGAATT
**
35788316 TTTTTTTTTGCAAAATCTTAAA
1 TTTTTTTAAGCAAAATCTTAAA
35788338 TTTTTTTAAGCAAAATCTTAAA
1 TTTTTTTAAGCAAAATCTTAAA
35788360 TTTTTTT
1 TTTTTTT
35788367 CAAGATACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTTTTTAAGCAAAATCTTAAA
Found at i:35789799 original size:25 final size:25
Alignment explanation
Indices: 35789734--35789800 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
35789724 AGCTCTGAAG
* * *
35789734 AGCCATTAATTAGGAAACTCCGGAT
1 AGCCATTAATCAGGAAGCTCCGGAA
* *
35789759 AGCTA-TATATCGGGAAGCTCCGGAA
1 AGCCATTA-ATCAGGAAGCTCCGGAA
35789784 AGCCATTAATCAGGAAG
1 AGCCATTAATCAGGAAG
35789801 TTCACAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
24 2 0.06
25 29 0.88
26 2 0.06
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
AGCCATTAATCAGGAAGCTCCGGAA
Found at i:35789850 original size:26 final size:27
Alignment explanation
Indices: 35789762--35789850 Score: 80
Period size: 26 Copynumber: 3.4 Consensus size: 27
35789752 TCCGGATAGC
35789762 TATATATCGGGAAGCTC-CGGAA-AGCCA
1 TATA-ATCGGGAAGCTCAC-GAAGAGCCA
* * *
35789789 T-TAATCAGGAAGTTCACAAAGAGCC-
1 TATAATCGGGAAGCTCACGAAGAGCCA
* *
35789814 TTTAATTGGGAAGCTCACGAAGAGCCA
1 TATAATCGGGAAGCTCACGAAGAGCCA
35789841 TAT-ATCGGGA
1 TATAATCGGGA
35789851 CACTCATAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
25 13 0.27
26 33 0.67
27 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (27 bp):
TATAATCGGGAAGCTCACGAAGAGCCA
Found at i:35790345 original size:26 final size:26
Alignment explanation
Indices: 35790316--35790365 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
35790306 TACGAGTAAG
*
35790316 TTTAACTCAATTTAATACAATTCATA
1 TTTAACTCAATTCAATACAATTCATA
* *
35790342 TTTAATTCAATTCAATGCAATTCA
1 TTTAACTCAATTCAATACAATTCA
35790366 CATCTTAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTAACTCAATTCAATACAATTCATA
Found at i:35790346 original size:16 final size:16
Alignment explanation
Indices: 35790325--35790355 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35790315 GTTTAACTCA
35790325 ATTTAATACAATTCAT
1 ATTTAATACAATTCAT
*
35790341 ATTTAATTCAATTCA
1 ATTTAATACAATTCA
35790356 ATGCAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAATACAATTCAT
Found at i:35792272 original size:18 final size:18
Alignment explanation
Indices: 35792249--35792283 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35792239 ACAAAAAAAC
*
35792249 AGTAACATAATAATGAAT
1 AGTAACAAAATAATGAAT
*
35792267 AGTAACAAAATAGTGAA
1 AGTAACAAAATAATGAA
35792284 AAAAATAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.23
Consensus pattern (18 bp):
AGTAACAAAATAATGAAT
Found at i:35794760 original size:14 final size:14
Alignment explanation
Indices: 35794741--35794768 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35794731 TACAATACCC
35794741 AAACAATAGCAACA
1 AAACAATAGCAACA
35794755 AAACAATAGCAACA
1 AAACAATAGCAACA
35794769 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACAATAGCAACA
Found at i:35794851 original size:51 final size:51
Alignment explanation
Indices: 35794750--35794850 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
35794740 CAAACAATAG
* * ** *
35794750 CAACAAAACAATAGCAACATAATAGTGAAATAGTAGTAAAATAATGAAAAA
1 CAACAAAACAATAGCAACAAAATAGTGAAAAAACAGTAAAACAATGAAAAA
*
35794801 CAACAAGAA-AATAGCAACAAAATAGT-AAAAAACAGTAAAACAGTGAAAAA
1 CAACAA-AACAATAGCAACAAAATAGTGAAAAAACAGTAAAACAATGAAAAA
35794851 AAATTGCATA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 19 0.44
51 22 0.51
52 2 0.05
ACGTcount: A:0.63, C:0.11, G:0.12, T:0.14
Consensus pattern (51 bp):
CAACAAAACAATAGCAACAAAATAGTGAAAAAACAGTAAAACAATGAAAAA
Found at i:35799698 original size:3 final size:3
Alignment explanation
Indices: 35799680--35799728 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
35799670 TTTAATGATA
*
35799680 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
35799725 TAT T
1 TAT T
35799729 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:35799700 original size:11 final size:11
Alignment explanation
Indices: 35799684--35799722 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
35799674 ATGATATATT
35799684 TTATTATTTTA
1 TTATTATTTTA
*
35799695 TTATTATTTCA
1 TTATTATTTTA
35799706 TTATTATTTTA
1 TTATTATTTTA
35799717 TTATTA
1 TTATTA
35799723 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:35801410 original size:46 final size:46
Alignment explanation
Indices: 35801358--35801835 Score: 694
Period size: 46 Copynumber: 10.4 Consensus size: 46
35801348 GTGGAAAAGA
35801358 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
*
35801404 AAAGATACCATGGCAACATGATATGAAATGTGCAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
*
35801450 AAAGATACCATGGCAACATGAT-TAGAAATGTGTAAGACCATGATTG
1 AAAGATACCATGGCAACATGATAT-GAAATGTGTAAGACCATGGTTG
35801496 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* * **
35801542 AAAGATACCATGGCAACGTGACATGAAA-GAATAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* *
35801587 AAAGATACCATGGCAACCTTATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* * * * **
35801633 AAAGATACCATAGTAACGTGACATGAAA-GAATAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
*
35801678 AAAGATACCATAGCAACATGATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
** *
35801724 AAAGATACCACAGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
* * *
35801770 AAAGATACCATGGCAACATGACA-GAAATTGAGTAAGACCATAGTTG
1 AAAGATACCATGGCAACATGATATGAAA-TGTGTAAGACCATGGTTG
* * *
35801816 AAAGACACTATGGCATCATG
1 AAAGATACCATGGCAACATG
35801836 TCAAAGATAA
Statistics
Matches: 391, Mismatches: 36, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
45 85 0.22
46 305 0.78
47 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
AAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTG
Found at i:35809091 original size:26 final size:26
Alignment explanation
Indices: 35809054--35809137 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
35809044 TGATACAAAT
* *
35809054 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
35809080 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
35809106 TGATAATGCGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
35809132 TGATAA
1 TGATAA
35809138 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:35810801 original size:27 final size:27
Alignment explanation
Indices: 35810760--35810899 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 27
35810750 GAGGAAGTGT
*
35810760 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
35810787 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
35810814 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
35810841 TCTGGTGGCTCTACCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
35810869 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
35810895 TCTGG
1 TCTGG
35810900 CAGCCATGCT
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.05
27 81 0.81
28 14 0.14
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:35810845 original size:54 final size:55
Alignment explanation
Indices: 35810760--35810899 Score: 194
Period size: 54 Copynumber: 2.6 Consensus size: 55
35810750 GAGGAAGTGT
* * * *
35810760 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACAAATATCTGTA
* *
35810814 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACAAATATCTGTA
* *
35810869 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
35810900 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 59 0.77
55 18 0.23
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTACCACAAATATCTGTA
Found at i:35810985 original size:19 final size:22
Alignment explanation
Indices: 35810961--35811000 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
35810951 CTCCCCACAC
35810961 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
35810980 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
35811001 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:35824330 original size:24 final size:23
Alignment explanation
Indices: 35824285--35824366 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
35824275 TCTAGGCTGT
35824285 ATAACAGGAAGCTCATAAGAGCC
1 ATAACAGGAAGCTCATAAGAGCC
* **
35824308 ATAATCAGGAAGTTCATGCGAGCC
1 ATAA-CAGGAAGCTCATAAGAGCC
* *
35824332 AATAACGGGTAGCTC-TGAAGAGCC
1 -ATAACAGGAAGCTCAT-AAGAGCC
*
35824356 ATTAACGGGAA
1 A-TAACAGGAA
35824367 TCTCCGGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
23 6 0.13
24 36 0.78
25 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.17
Consensus pattern (23 bp):
ATAACAGGAAGCTCATAAGAGCC
Found at i:35824568 original size:24 final size:24
Alignment explanation
Indices: 35824541--35824595 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
35824531 CACAACTGAT
35824541 CGGGATGCTCCGA-AGAGCTATTAA
1 CGGGATGCT-CGAGAGAGCTATTAA
* *
35824565 CGGGAAGCTCGAGAGGGCTATTAA
1 CGGGATGCTCGAGAGAGCTATTAA
35824589 CGGGATG
1 CGGGATG
35824596 TTTTTTCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (24 bp):
CGGGATGCTCGAGAGAGCTATTAA
Found at i:35826680 original size:24 final size:23
Alignment explanation
Indices: 35826653--35826724 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
35826643 TATATTTAAA
*
35826653 AATTCAAATAATGAATAAAAAATT
1 AATT-AAATAATTAATAAAAAATT
**
35826677 AATTACAATAATTAA-AAATATTTT
1 AATTA-AATAATTAATAAA-AAATT
*
35826701 ATTTAAA-AATTAATAAAAAATT
1 AATTAAATAATTAATAAAAAATT
35826723 AA
1 AA
35826725 ACGCTTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 10 0.26
23 9 0.24
24 19 0.50
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (23 bp):
AATTAAATAATTAATAAAAAATT
Found at i:35829355 original size:24 final size:24
Alignment explanation
Indices: 35829324--35829372 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35829314 TAAGGGAAAT
35829324 TAAAAGATATTCAACTCCCTTTAC
1 TAAAAGATATTCAACTCCCTTTAC
35829348 TAAAAGATATTCAACTCCCTTTAC
1 TAAAAGATATTCAACTCCCTTTAC
35829372 T
1 T
35829373 TTCCCTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (24 bp):
TAAAAGATATTCAACTCCCTTTAC
Found at i:35831296 original size:13 final size:13
Alignment explanation
Indices: 35831278--35831302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35831268 CATGAGCAAA
35831278 ATTTTAAGTTGAT
1 ATTTTAAGTTGAT
35831291 ATTTTAAGTTGA
1 ATTTTAAGTTGA
35831303 ACTAAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
ATTTTAAGTTGAT
Found at i:35846943 original size:13 final size:14
Alignment explanation
Indices: 35846916--35846946 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
35846906 TTGAGATGAG
35846916 AATATTATCTTAAA
1 AATATTATCTTAAA
35846930 AATATTAT-TTAAA
1 AATATTATCTTAAA
35846943 AATA
1 AATA
35846947 AAATAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AATATTATCTTAAA
Found at i:35847574 original size:20 final size:21
Alignment explanation
Indices: 35847530--35847575 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
35847520 TAATGATAAC
35847530 AGCTTGTTCAACCAAATTAAA
1 AGCTTGTTCAACCAAATTAAA
*
35847551 AGCTTGTTTAACCAAATT-AA
1 AGCTTGTTCAACCAAATTAAA
35847571 AGCTT
1 AGCTT
35847576 TCCTAGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (21 bp):
AGCTTGTTCAACCAAATTAAA
Found at i:35854836 original size:21 final size:20
Alignment explanation
Indices: 35854802--35854854 Score: 83
Period size: 21 Copynumber: 2.7 Consensus size: 20
35854792 TAAGTGATAC
35854802 TTTAA-TTTATTTATGCAAA
1 TTTAATTTTATTTATGCAAA
35854821 TTTAATTTTCATTTATGCAAA
1 TTTAATTTT-ATTTATGCAAA
35854842 TTTAATTTT-TTTA
1 TTTAATTTTATTTA
35854855 ATTTAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.28
20 3 0.09
21 20 0.62
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTAATTTTATTTATGCAAA
Found at i:35854845 original size:35 final size:35
Alignment explanation
Indices: 35854805--35854872 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
35854795 GTGATACTTT
*
35854805 AATTT-ATTTATGCAAATTTAATTTTCATTTATGCA
1 AATTTAATTT-TGCAAATTTAATTTTCAATTATGCA
***
35854840 AATTTAATTTTTTTAATTTAATTTTCAATTATG
1 AATTTAATTTTGCAAATTTAATTTTCAATTATG
35854873 ATGTTTGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (35 bp):
AATTTAATTTTGCAAATTTAATTTTCAATTATGCA
Found at i:35855868 original size:7 final size:7
Alignment explanation
Indices: 35855856--35855880 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35855846 AGTCGTTTCA
35855856 TATTTAG
1 TATTTAG
35855863 TATTTAG
1 TATTTAG
35855870 TATTTAG
1 TATTTAG
35855877 TATT
1 TATT
35855881 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:35856416 original size:30 final size:30
Alignment explanation
Indices: 35856377--35856475 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
35856367 GGACGACGAT
35856377 GCAGGCCCATCAACAGCGCCCACACAATCA
1 GCAGGCCCATCAACAGCGCCCACACAATCA
* * *
35856407 GCTGGCCCATCAACAGCACCCATACAATCA
1 GCAGGCCCATCAACAGCGCCCACACAATCA
*
35856437 GCAAGCCCATCAACAGCGCCGC-CACAATCA
1 GCAGGCCCATCAACAGCGCC-CACACAATCA
* *
35856467 CCAAGCCCA
1 GCAGGCCCA
35856476 ACAGTTCAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 59 0.98
31 1 0.02
ACGTcount: A:0.33, C:0.43, G:0.15, T:0.08
Consensus pattern (30 bp):
GCAGGCCCATCAACAGCGCCCACACAATCA
Found at i:35856423 original size:15 final size:13
Alignment explanation
Indices: 35856381--35856456 Score: 62
Period size: 15 Copynumber: 5.2 Consensus size: 13
35856371 GACGATGCAG
35856381 GCCCATCAACAGC
1 GCCCATCAACAGC
*
35856394 GCCCACACAATCAGC
1 GCCCA-TCAA-CAGC
35856409 TGGCCCATCAACAGC
1 --GCCCATCAACAGC
*
35856424 ACCCATACAATCAGC
1 GCCCAT-CAA-CAGC
35856439 AAGCCCATCAACAGC
1 --GCCCATCAACAGC
35856454 GCC
1 GCC
35856457 GCCACAATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
13 13 0.25
14 6 0.12
15 16 0.31
16 6 0.12
17 10 0.20
ACGTcount: A:0.33, C:0.43, G:0.14, T:0.09
Consensus pattern (13 bp):
GCCCATCAACAGC
Found at i:35856553 original size:18 final size:18
Alignment explanation
Indices: 35856532--35856574 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35856522 TGTCAGGTAC
*
35856532 GTATCCTATCCCTTATAT
1 GTATCCTAACCCTTATAT
*
35856550 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
*
35856568 GTTTCCT
1 GTATCCT
35856575 TTTCCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:35860986 original size:126 final size:126
Alignment explanation
Indices: 35860761--35861761 Score: 1628
Period size: 126 Copynumber: 8.0 Consensus size: 126
35860751 ATAGCCTCAG
* *
35860761 TTTTTCTACAAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* *
35860826 CAGTGCATCCAGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* *
35860887 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCATGTGGGAGATTTTTTCCGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
35860952 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
*
35861013 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTACTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
35861078 CGGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * * **
35861139 TTTTTCTACGAACTACTGTAGCAAAAGTGCGTCCATGTAGGAGCTTTTTTCTAAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* * * * *
35861204 CGGTGCATCCTGCTTGAAGTGTTTTTAACACTATTTGTTCAAAAACGTCTACTCAAAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* *
35861265 TTTTTCTACTAACTACTGTAGCAAAAGCGCGTCCACGTGGGATC-TTTTTCCGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
35861329 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * * * * * *
35861390 TTTTTCTATGAACTACTGTAGCAAAAGTGCGTCTACATGGTAGCTTTTTTCTGAAATTTTGCTGG
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* *
35861455 CAGTGCATCCTGCTTGATGTGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* * *
35861516 TTTTTCTACTAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCTAAATTTTACTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
35861581 CAGTGCATACTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA-AGATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGA-ATTA
* * **
35861642 TTTTTCTACGAACTATTGTAGCAAAAGGGCGTCCACGTGGGAGCTTTTTTCTAAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
* *
35861707 CAGTGCATCTTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA
35861762 ATTAACCTAA
Statistics
Matches: 808, Mismatches: 65, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
125 112 0.14
126 696 0.86
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (126 bp):
TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
Found at i:35861760 original size:503 final size:504
Alignment explanation
Indices: 35860761--35861762 Score: 1711
Period size: 503 Copynumber: 2.0 Consensus size: 504
35860751 ATAGCCTCAG
35860761 TTTTTCTACAAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTGA
1 TTTTTCTACAAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTGA
*
35860826 CAGTGCATCCAGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTT
66 CAGTGCATCCAGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTT
**
35860891 TCTACGAACTACTGTAGCAAAAGCGCGTCCATGTGGGAGATTTTTTCCGAAATTTTGCTGACAGT
131 TCTACGAACTACTGTAGCAAAAGCGCGTCCACATGGGAGATTTTTTCCGAAATTTTGCTGACAGT
35860956 GCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTA
196 GCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTA
*
35861021 CGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTACTGACGGTGCAT
261 CGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTACTGACAGTGCAT
*
35861086 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTACGAA
326 ACTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTACGAA
* * * *
35861151 CTACTGTAGCAAAAGTGCGTCCATGTAGGAGCTTTTTTCTAAAATTTTGCTGACGGTGCATCCTG
391 CTACTGTAGCAAAAGGGCGTCCACGTAGGAGCTTTTTTCTAAAATTTTGCTGACAGTGCATCCTA
*
35861216 CTTGAAGTGTTTTTAACACTATTTGTTCAAAAACGTCTACTCAAAATTA
456 CTTGAAGCGTTTTTAACACTATTTGTTCAAAAACGTCTACTCAAAATTA
* * *
35861265 TTTTTCTACTAACTACTGTAGCAAAAGCGCGTCCACGTGGGATC-TTTTTCCGAAATTTTGCTGA
1 TTTTTCTACAAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTGA
*
35861329 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTT
66 CAGTGCATCCAGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTT
* * * * * * *
35861394 TCTATGAACTACTGTAGCAAAAGTGCGTCTACATGGTAGCTTTTTTCTGAAATTTTGCTGGCAGT
131 TCTACGAACTACTGTAGCAAAAGCGCGTCCACATGGGAGATTTTTTCCGAAATTTTGCTGACAGT
* *
35861459 GCATCCTGCTTGATGTGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTA
196 GCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTA
* *
35861524 CTAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCTAAATTTTACTGACAGTGCAT
261 CGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTACTGACAGTGCAT
35861589 ACTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA-AGATTATTTTTCTACGA
326 ACTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGA-ATTATTTTTCTACGA
* * *
35861653 ACTATTGTAGCAAAAGGGCGTCCACGTGGGAGCTTTTTTCTAAAATTTTGCTGACAGTGCATCTT
390 ACTACTGTAGCAAAAGGGCGTCCACGTAGGAGCTTTTTTCTAAAATTTTGCTGACAGTGCATCCT
* *
35861718 ACTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAA
455 ACTTGAAGCGTTTTTAACACTATTTGTTCAAAAACGTCTACTCAA
35861763 TTAACCTAAA
Statistics
Matches: 467, Mismatches: 30, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
502 1 0.00
503 424 0.91
504 42 0.09
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (504 bp):
TTTTTCTACAAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCAGAAATTTTGCTGA
CAGTGCATCCAGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTT
TCTACGAACTACTGTAGCAAAAGCGCGTCCACATGGGAGATTTTTTCCGAAATTTTGCTGACAGT
GCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTA
CGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTACTGACAGTGCAT
ACTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTATTTTTCTACGAA
CTACTGTAGCAAAAGGGCGTCCACGTAGGAGCTTTTTTCTAAAATTTTGCTGACAGTGCATCCTA
CTTGAAGCGTTTTTAACACTATTTGTTCAAAAACGTCTACTCAAAATTA
Found at i:35861907 original size:19 final size:19
Alignment explanation
Indices: 35861883--35861955 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
35861873 ACCATTATGT
35861883 ATCAATTAACCCTAAATTA
1 ATCAATTAACCCTAAATTA
* * *
35861902 ATCAATTAACGCTCATTTA
1 ATCAATTAACCCTAAATTA
*
35861921 ATCGAA-TAACCCTAATTTA
1 ATC-AATTAACCCTAAATTA
* * *
35861940 ATTAACTAACCATAAA
1 ATCAATTAACCCTAAA
35861956 CCCTAAAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 2 0.05
19 40 0.91
20 2 0.05
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (19 bp):
ATCAATTAACCCTAAATTA
Found at i:35862050 original size:21 final size:21
Alignment explanation
Indices: 35862024--35862069 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
35862014 CCTAAAATCA
35862024 TAAACCACTAACCATAAACCC
1 TAAACCACTAACCATAAACCC
*
35862045 TAAACCACTAACTATAAACCC
1 TAAACCACTAACCATAAACCC
35862066 TAAA
1 TAAA
35862070 ATAACTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACCACTAACCATAAACCC
Found at i:35862573 original size:16 final size:17
Alignment explanation
Indices: 35862549--35862591 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
35862539 CTTAATTTAG
35862549 TATTATTTTTC-TAAAA
1 TATTATTTTTCGTAAAA
*
35862565 TATTTTTTTTCGTAAAA
1 TATTATTTTTCGTAAAA
*
35862582 TAATATTTTT
1 TATTATTTTT
35862592 GTATAGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTTTTCGTAAAA
Found at i:35862685 original size:15 final size:16
Alignment explanation
Indices: 35862661--35862705 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
35862651 TTTTGAAAGG
35862661 CTTAAAAATATTTTAT
1 CTTAAAAATATTTTAT
*
35862677 -TTAACAATATTTTAT
1 CTTAAAAATATTTTAT
*
35862692 CTCAAAAATATTTT
1 CTTAAAAATATTTT
35862706 TTTGTCCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
CTTAAAAATATTTTAT
Found at i:35864824 original size:16 final size:17
Alignment explanation
Indices: 35864785--35864828 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
35864775 AACTCGAATA
35864785 ATTTCACTC-AA-TTCG
1 ATTTCACTCGAATTTCG
35864800 ACTTT-ACTCGAATTTC-
1 A-TTTCACTCGAATTTCG
35864816 ATTTCACTCGAAT
1 ATTTCACTCGAAT
35864829 CGATTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.32
16 14 0.56
17 3 0.12
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (17 bp):
ATTTCACTCGAATTTCG
Found at i:35865935 original size:102 final size:102
Alignment explanation
Indices: 35865759--35865989 Score: 428
Period size: 102 Copynumber: 2.3 Consensus size: 102
35865749 AAGTATTTAA
* * *
35865759 TTAAATCGAGTAAAAATGTTTTGAGTTATTGACGAGTCTTATTTTATCATCCTATATTTATTTGA
1 TTAAATCGAATAAATATGTTTTGAGTTATTAACGAGTCTTATTTTATCATCCTATATTTATTTGA
35865824 ATTTTTTCGACCTTAATCTAGTGAAATGAAATTCAAG
66 ATTTTTTCGACCTTAATCTAGTGAAATGAAATTCAAG
35865861 TTAAATCGAATAAATATGTTTTGAGTTATTAACGAGTCTTATTTTATCATCCTATATTTATTTGA
1 TTAAATCGAATAAATATGTTTTGAGTTATTAACGAGTCTTATTTTATCATCCTATATTTATTTGA
35865926 ATTTTTTCGACCTTAATCTAGTGAAATGAAATTCAAG
66 ATTTTTTCGACCTTAATCTAGTGAAATGAAATTCAAG
35865963 TTAAATCGAATAAATATG-TTTGAGTTA
1 TTAAATCGAATAAATATGTTTTGAGTTA
35865990 AATTAAAAAA
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
101 9 0.07
102 117 0.93
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (102 bp):
TTAAATCGAATAAATATGTTTTGAGTTATTAACGAGTCTTATTTTATCATCCTATATTTATTTGA
ATTTTTTCGACCTTAATCTAGTGAAATGAAATTCAAG
Found at i:35866871 original size:17 final size:18
Alignment explanation
Indices: 35866851--35866884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35866841 GAAAGAGAGT
35866851 AAAAA-ATGAAAAAAAAC
1 AAAAATATGAAAAAAAAC
*
35866868 AAAAATCTGAAAAAAAA
1 AAAAATATGAAAAAAAA
35866885 AGGGTGGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAAATATGAAAAAAAAC
Found at i:35867029 original size:3 final size:3
Alignment explanation
Indices: 35867021--35867094 Score: 84
Period size: 3 Copynumber: 25.3 Consensus size: 3
35867011 TCCATTTCGG
* *
35867021 GAA GAA GAAA GAA GGA GAA GAA G-A GAA GAAA GAA GAA -AA GAA GGA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA
35867066 GAA GAA GAA -AA GAA GAA -AA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
35867095 GAGAGGAAGG
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.13
3 47 0.77
4 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35867048 original size:8 final size:8
Alignment explanation
Indices: 35867021--35867092 Score: 76
Period size: 8 Copynumber: 9.0 Consensus size: 8
35867011 TCCATTTCGG
35867021 GAAGAAGA
1 GAAGAAGA
35867029 -AAGAAGGA
1 GAAGAA-GA
35867037 GAAGAAGA
1 GAAGAAGA
35867045 GAAGAA-A
1 GAAGAAGA
*
35867052 GAAGAAAA
1 GAAGAAGA
*
35867060 GAAGGAGAA
1 GAAGAAG-A
*
35867069 GAAGAAAA
1 GAAGAAGA
*
35867077 GAAGAAAA
1 GAAGAAGA
35867085 GAAGAAGA
1 GAAGAAGA
35867093 AGGAGAGGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
7 12 0.22
8 32 0.58
9 11 0.20
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (8 bp):
GAAGAAGA
Found at i:35867077 original size:25 final size:29
Alignment explanation
Indices: 35867022--35867103 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
35867012 CCATTTCGGG
35867022 AAGAAG-AAAGAAGGAGAAGAAGAGAAGA
1 AAGAAGAAAAGAAGGAGAAGAAGAGAAGA
*
35867050 AAGAAGAAAAGAAGGAGAAGAAGAAAAGA
1 AAGAAGAAAAGAAGGAGAAGAAGAGAAGA
* *
35867079 AGAAAAGAAGAAGAAGGAGAGGAAG
1 A-AGAAGAA-AAGAAGGAGAAGAAG
35867104 GAGGCGGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
28 6 0.12
29 22 0.46
30 6 0.12
31 14 0.29
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (29 bp):
AAGAAGAAAAGAAGGAGAAGAAGAGAAGA
Found at i:35867174 original size:20 final size:20
Alignment explanation
Indices: 35867118--35867175 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
35867108 CGGCATCAGT
* *
35867118 GAGGGAAGAAAAAAGAAAAA
1 GAGGGAAGGAAAAAGAAGAA
* **
35867138 GA-GAAAGAGAAGGAGAAGAA
1 GAGGGAAG-GAAAAAGAAGAA
35867158 GAGGGAAGGAAAAAGAAG
1 GAGGGAAGGAAAAAGAAG
35867176 GAAAAAAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 4 0.14
20 20 0.71
21 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
GAGGGAAGGAAAAAGAAGAA
Found at i:35867655 original size:15 final size:15
Alignment explanation
Indices: 35867609--35867677 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
35867599 AAATAGTATA
35867609 AAAAAATAAAATACT-
1 AAAAAATAAAATA-TG
***
35867624 AAAAAATATCTTAATG
1 AAAAAATAAAAT-ATG
35867640 AAAAAATAAAATATG
1 AAAAAATAAAATATG
*
35867655 AAAAGAAATAAAAGATG
1 -AAA-AAATAAAATATG
35867672 AAAAAA
1 AAAAAA
35867678 GACTTTTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 16 0.37
16 16 0.37
17 11 0.26
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAATATG
Found at i:35867663 original size:17 final size:17
Alignment explanation
Indices: 35867643--35867675 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35867633 CTTAATGAAA
*
35867643 AAATAAAATATGAAAAG
1 AAATAAAAGATGAAAAG
35867660 AAATAAAAGATGAAAA
1 AAATAAAAGATGAAAA
35867676 AAGACTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
AAATAAAAGATGAAAAG
Found at i:35867733 original size:11 final size:12
Alignment explanation
Indices: 35867717--35867751 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
35867707 TTTTTTTACT
35867717 AAAATAATATA-
1 AAAATAATATAG
35867728 AAAATAATATATG
1 AAAATAATATA-G
35867741 AAAATAATATA
1 AAAATAATATA
35867752 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
AAAATAATATAG
Found at i:35867744 original size:13 final size:12
Alignment explanation
Indices: 35867716--35867752 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
35867706 ATTTTTTTAC
35867716 TAAAATAATATA
1 TAAAATAATATA
35867728 -AAAATAATATA
1 TAAAATAATATA
35867739 TGAAAATAATATA
1 T-AAAATAATATA
35867752 T
1 T
35867753 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
13 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
TAAAATAATATA
Found at i:35867947 original size:118 final size:119
Alignment explanation
Indices: 35867755--35868017 Score: 384
Period size: 119 Copynumber: 2.2 Consensus size: 119
35867745 TAATATATTT
*
35867755 TAAAAAATAAAATCTGAAAATTTAAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTACTAA
1 TAAAAAATAAAATCCGAAAA--TAAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTACTAA
*
35867820 ATTACTAT-AAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATA
64 ATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATA
* * * * * * *
35867875 TAAAAAATAAAATCCGAAAATAAAAACTACCAATAAAGTGTCAAAATCAGGGTTATTTATTAAAT
1 TAAAAAATAAAATCCGAAAATAAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTACTAAAT
* *
35867940 TAATATAAAAAACACTTAAATAATACATTTGAAATATTATGTACTAAAATAATA
66 TAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATA
*
35867994 TAAAAAAATAAAATACGAAAATAA
1 T-AAAAAATAAAATCCGAAAATAA
35868018 TATATATTAA
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
118 43 0.33
119 46 0.36
120 40 0.31
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (119 bp):
TAAAAAATAAAATCCGAAAATAAAAAATACAAACAAAGGGCCAAAATCAGAGTTATTTACTAAAT
TAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATA
Found at i:35868003 original size:13 final size:13
Alignment explanation
Indices: 35867985--35868049 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
35867975 ATTATGTACT
*
35867985 AAAATAATATAAA
1 AAAATAAAATAAA
35867998 AAAATAAAATACGAA
1 AAAATAAAATA--AA
* *
35868013 AATAATATATATTAA
1 AA-AATA-AAATAAA
*
35868028 AAAATAAAATAAG
1 AAAATAAAATAAA
35868041 AAAATAAAA
1 AAAATAAAA
35868050 ATTTACCAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 23 0.55
14 4 0.10
15 8 0.19
16 4 0.10
17 3 0.07
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:35868032 original size:30 final size:29
Alignment explanation
Indices: 35867987--35868047 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
35867977 TATGTACTAA
*
35867987 AATAATATAAAAAAATAAAATACGAAAAT
1 AATAATATAAAAAAATAAAATAAGAAAAT
*
35868016 AATATATATTAAAAAATAAAATAAGAAAAT
1 AATA-ATATAAAAAAATAAAATAAGAAAAT
35868046 AA
1 AA
35868048 AAATTTACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (29 bp):
AATAATATAAAAAAATAAAATAAGAAAAT
Found at i:35870803 original size:21 final size:20
Alignment explanation
Indices: 35870779--35870852 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 20
35870769 TTAAATACAT
35870779 TACAACATTAATCTAATTAA
1 TACAACATTAATCTAATTAA
*
35870799 -A-TACATTAATCTAA-T--
1 TACAACATTAATCTAATTAA
* *
35870814 TAGAACATTAAT-TAAATACA
1 TACAACATTAATCTAATTA-A
35870834 TTACAACATTAATCTAATT
1 -TACAACATTAATCTAATT
35870853 GGAACAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
16 4 0.10
17 10 0.24
18 12 0.29
19 1 0.02
21 11 0.26
22 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (20 bp):
TACAACATTAATCTAATTAA
Found at i:35870805 original size:26 final size:26
Alignment explanation
Indices: 35870769--35870852 Score: 98
Period size: 26 Copynumber: 3.1 Consensus size: 26
35870759 GGAACAAACT
35870769 TTAAATACATTACAACATTAATCTAA
1 TTAAATACATTACAACATTAATCTAA
* *
35870795 TTAAATACATTA-ATCTAATTAGAACATTAA
1 TTAAATACATTACAAC--ATTA-ATC--TAA
35870825 TTAAATACATTACAACATTAATCTAA
1 TTAAATACATTACAACATTAATCTAA
35870851 TT
1 TT
35870853 GGAACAAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
25 2 0.04
26 17 0.35
27 4 0.08
28 4 0.08
29 4 0.08
30 15 0.31
31 2 0.04
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (26 bp):
TTAAATACATTACAACATTAATCTAA
Found at i:35870806 original size:18 final size:17
Alignment explanation
Indices: 35870777--35870825 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
35870767 CTTTAAATAC
*
35870777 ATTACAACATTAATCTA
1 ATTAAAACATTAATCTA
35870794 ATTAAATACATTAATCTA
1 ATTAAA-ACATTAATCTA
*
35870812 ATTAGAACATTAAT
1 ATTAAAACATTAAT
35870826 TAAATACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTAAAACATTAATCTA
Found at i:35874572 original size:39 final size:39
Alignment explanation
Indices: 35874503--35874623 Score: 122
Period size: 42 Copynumber: 3.1 Consensus size: 39
35874493 GGTTTTTTTT
* *
35874503 ATAACTAACAATAAT--TAAG-GTTTTTTACTAACAATA
1 ATAACCAACAATAATAATAAGAATTTTTTACTAACAATA
** * *
35874539 ATAACCAACAATCCTAATAATAATTTTTTACTAACAACAACA
1 ATAACCAACAATAATAATAAGAATTTTTTACT---AACAATA
* *
35874581 ATAACTAACAATAATAATAAGAGTTTTTTACTAACAATA
1 ATAACCAACAATAATAATAAGAATTTTTTACTAACAATA
35874620 ATAA
1 ATAA
35874624 TAATATTTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
36 12 0.18
38 3 0.04
39 19 0.28
42 33 0.49
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.32
Consensus pattern (39 bp):
ATAACCAACAATAATAATAAGAATTTTTTACTAACAATA
Found at i:35874578 original size:42 final size:42
Alignment explanation
Indices: 35874532--35874626 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
35874522 GTTTTTTACT
** *
35874532 AACAATAATAACCAACAATCCTAATAATAATTTTTTACTAAC
1 AACAATAATAACCAACAATAATAATAAGAATTTTTTACTAAC
* * *
35874574 AACAACAATAACTAACAATAATAATAAGAGTTTTTTACTAAC
1 AACAATAATAACCAACAATAATAATAAGAATTTTTTACTAAC
*
35874616 AATAATAATAA
1 AACAATAATAA
35874627 TATTTTTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (42 bp):
AACAATAATAACCAACAATAATAATAAGAATTTTTTACTAAC
Found at i:35874620 original size:26 final size:25
Alignment explanation
Indices: 35874584--35874649 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
35874574 AACAACAATA
35874584 ACTAACAATAATAATAAGAGTTTTTT
1 ACTAACAATAATAATAAGA-TTTTTT
*
35874610 ACTAACAATAATAATAATATTTTTT
1 ACTAACAATAATAATAAGATTTTTT
* *
35874635 TCTAATAATAATAAT
1 ACTAACAATAATAAT
35874650 TACTAACAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
25 19 0.51
26 18 0.49
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ACTAACAATAATAATAAGATTTTTT
Found at i:35874682 original size:13 final size:12
Alignment explanation
Indices: 35874664--35874693 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
35874654 AACAACAACA
35874664 AACAATAATAAT
1 AACAATAATAAT
35874676 CAACAATAATAAT
1 -AACAATAATAAT
35874689 AACAA
1 AACAA
35874694 CGAAAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (12 bp):
AACAATAATAAT
Found at i:35874784 original size:33 final size:33
Alignment explanation
Indices: 35874747--35874809 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
35874737 ATAATACCTT
* **
35874747 CTCTTTTCTATTTTTTTTTCCTTCTCTTTCTTC
1 CTCTTCTCTATTCCTTTTTCCTTCTCTTTCTTC
* *
35874780 CTCTTCTCTATTCCTTTTTCTTTCTTTTTC
1 CTCTTCTCTATTCCTTTTTCCTTCTCTTTC
35874810 AATCTTCTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (33 bp):
CTCTTCTCTATTCCTTTTTCCTTCTCTTTCTTC
Found at i:35877576 original size:10 final size:11
Alignment explanation
Indices: 35877555--35877600 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
35877545 AAGTAATACA
35877555 AATATAACATG
1 AATATAACATG
35877566 AATAT-ACATG
1 AATATAACATG
*
35877576 ACATATAATATG
1 A-ATATAACATG
35877588 AA-ATAACATG
1 AATATAACATG
35877598 AAT
1 AAT
35877601 TATTGATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 15 0.50
11 10 0.33
12 5 0.17
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (11 bp):
AATATAACATG
Found at i:35877582 original size:22 final size:22
Alignment explanation
Indices: 35877556--35877598 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35877546 AGTAATACAA
35877556 ATATAACATG-AATATACATGAC
1 ATATAACATGAAATA-ACATGAC
*
35877578 ATATAATATGAAATAACATGA
1 ATATAACATGAAATAACATGA
35877599 ATTATTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (22 bp):
ATATAACATGAAATAACATGAC
Found at i:35889182 original size:17 final size:18
Alignment explanation
Indices: 35889151--35889184 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35889141 TAAACACAGA
35889151 AATTAAAACTGAGTAAGC
1 AATTAAAACTGAGTAAGC
*
35889169 AATT-AAACTTAGTAAG
1 AATTAAAACTGAGTAAG
35889185 TTCGTATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (18 bp):
AATTAAAACTGAGTAAGC
Found at i:35891995 original size:25 final size:25
Alignment explanation
Indices: 35891967--35892019 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
35891957 AGTACATAAA
* *
35891967 TAATGATAACAATGGACAATA-ATAG
1 TAATAATAACAA-GAACAATATATAG
*
35891992 TAATAATAATAAGAACAATATATAG
1 TAATAATAACAAGAACAATATATAG
35892017 TAA
1 TAA
35892020 AAAAACATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (25 bp):
TAATAATAACAAGAACAATATATAG
Found at i:35892054 original size:2 final size:2
Alignment explanation
Indices: 35892047--35892075 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35892037 AATTCTTTTA
35892047 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 A
35892076 AATGATAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35896863 original size:22 final size:23
Alignment explanation
Indices: 35896821--35896864 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
35896811 TACAAAGTTT
35896821 TGTTTATGAGAGGACTTAAAAGG
1 TGTTTATGAGAGGACTTAAAAGG
* *
35896844 TGTTTATG-GATGCCTTAAAAG
1 TGTTTATGAGAGGACTTAAAAG
35896865 CTTAATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (23 bp):
TGTTTATGAGAGGACTTAAAAGG
Done.