Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 55 of 141
Found at i:16467635 original size:21 final size:21
Alignment explanation
Indices: 16467600--16467654 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
16467590 AATCATATCT
16467600 TCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATATCATA
16467619 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
16467640 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
16467655 CCTCGAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.26
21 25 0.74
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:16468414 original size:44 final size:44
Alignment explanation
Indices: 16468349--16468892 Score: 487
Period size: 44 Copynumber: 12.4 Consensus size: 44
16468339 GCAGGAAGGT
* * * * *
16468349 AAGACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGAC
* *
16468393 AAGATCTGCTTTCTTCGATCTACTTTGC-CACCAGTAT-GGTAAGAC
1 AAGATCTGCTATCTTCGATCTAC-TT-CACACCAATATAGG-AAGAC
*
16468438 AAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGAC
* * * * * *
16468481 ATGACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGAC
* * * * *
16468525 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGAC
* *
16468570 AAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGAC
* * * ** * *
16468613 ATGACCTGCTATCTTTGATCTACTTCATGCCAATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGAC
* * * * *
16468657 AAGATCTTCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGAC
* *
16468702 AAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGAC
* * * * *
16468746 AGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGAC
* * * * *
16468790 AAGATCTAC-ATCTTCGATCTACTCCGCCACCAATATGGGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGAC
* *
16468834 AAGATCTGC-ATCTTCGATCCACCTC-CTACCAATATAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGAC
* *
16468877 AGGACCTGCTATCTTC
1 AAGATCTGCTATCTTC
16468893 ACTGATCTGA
Statistics
Matches: 401, Mismatches: 82, Indels: 34
0.78 0.16 0.07
Matches are distributed among these distances:
42 4 0.01
43 79 0.20
44 239 0.60
45 78 0.19
46 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
AAGATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGAC
Found at i:16468578 original size:132 final size:132
Alignment explanation
Indices: 16468351--16468888 Score: 873
Period size: 132 Copynumber: 4.1 Consensus size: 132
16468341 AGGAAGGTAA
16468351 GACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTAC
* *
16468416 TTTGCCACCAGTATGGTAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
66 TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
*
16468481 AT
131 AG
16468483 GACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTAC
* *
16468548 TTCGCCACCAGTATGGGAAGATAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAT
66 TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
*
16468613 AT
131 AG
* * *
16468615 GACCTGCTATCTTT-GATCTACTTCATGCCAATACATGAAGACAAGATCTTCTTTCTTCGATCTA
1 GACCTGCTAT-TTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTA
16468679 CTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAG
65 CTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAG
16468744 ACAG
129 ACAG
* * * * * *
16468748 GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTAC-ATCTTCGATCTAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTAC
* * * *
16468812 TCCGCCACCAATATGGGAAGATAAGATCTGCATCTTCGATCCACCTCCTACCAATATAGGAAGAC
66 TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
16468877 AG
131 AG
16468879 GACCTGCTAT
1 GACCTGCTAT
16468889 CTTCACTGAT
Statistics
Matches: 382, Mismatches: 21, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
131 29 0.08
132 289 0.76
133 64 0.17
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
GACCTGCTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTAC
TTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGAC
AG
Found at i:16476264 original size:22 final size:22
Alignment explanation
Indices: 16476244--16476297 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
16476234 ATATGTATAC
16476244 TAAAATAAAT-ATATACATATAGA
1 TAAAA-AAATAAT-TACATATAGA
*
16476267 TAAAAAAATAATTACATATAAA
1 TAAAAAAATAATTACATATAGA
16476289 TAAATAAAA
1 TAAA-AAAA
16476298 AAATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
TAAAAAAATAATTACATATAGA
Found at i:16476274 original size:26 final size:26
Alignment explanation
Indices: 16476245--16476309 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
16476235 TATGTATACT
* * *
16476245 AAAATAAATATATACATATAGATAAA
1 AAAATAATTATATACAAATAAATAAA
* *
16476271 AAAATAATTACATATAAATAAATAAA
1 AAAATAATTATATACAAATAAATAAA
16476297 AAAATAATTATAT
1 AAAATAATTATAT
16476310 TATACTACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAATAATTATATACAAATAAATAAA
Found at i:16480193 original size:15 final size:15
Alignment explanation
Indices: 16480173--16480202 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16480163 TTTTGGTGTT
16480173 TATATACAATTTATG
1 TATATACAATTTATG
*
16480188 TATATATAATTTATG
1 TATATACAATTTATG
16480203 CAGTTGTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (15 bp):
TATATACAATTTATG
Found at i:16487818 original size:21 final size:20
Alignment explanation
Indices: 16487794--16487835 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
16487784 ATTAATTAAT
16487794 ATAATAATAAAATTAAATATC
1 ATAATAATAAAATTAAA-ATC
* *
16487815 ATAATGATAAGATTAAAATC
1 ATAATAATAAAATTAAAATC
16487835 A
1 A
16487836 ATTGTGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAATAATAAAATTAAAATC
Found at i:16493738 original size:38 final size:38
Alignment explanation
Indices: 16493682--16493798 Score: 155
Period size: 38 Copynumber: 3.1 Consensus size: 38
16493672 AACTTTTAAT
* * *
16493682 ACACCGGCACTAAACCTGCTGGGCACAAAGCCTGAATA
1 ACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATA
*
16493720 ACACCGGCAATAAGCCTGCTAGGCACGAAGCCTGAATA
1 ACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATA
* * *
16493758 ACACCGGCACA-AAGCCTACTAGGTACAAAACCTGAATA
1 ACACCGGCA-ATAAGCCTGCTAGGCACAAAGCCTGAATA
16493796 ACA
1 ACA
16493799 ATATAATTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
38 69 0.99
39 1 0.01
ACGTcount: A:0.38, C:0.30, G:0.20, T:0.13
Consensus pattern (38 bp):
ACACCGGCAATAAGCCTGCTAGGCACAAAGCCTGAATA
Found at i:16493772 original size:22 final size:22
Alignment explanation
Indices: 16493703--16493774 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
16493693 AAACCTGCTG
16493703 GGCACAAAGCCTGAATAACACC
1 GGCACAAAGCCTGAATAACACC
*
16493725 GGCA-ATAAGCCTG-CT---A--
1 GGCACA-AAGCCTGAATAACACC
*
16493741 GGCACGAAGCCTGAATAACACC
1 GGCACAAAGCCTGAATAACACC
16493763 GGCACAAAGCCT
1 GGCACAAAGCCT
16493775 ACTAGGTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
16 11 0.29
17 1 0.03
18 1 0.03
20 1 0.03
21 2 0.05
22 22 0.58
ACGTcount: A:0.36, C:0.31, G:0.22, T:0.11
Consensus pattern (22 bp):
GGCACAAAGCCTGAATAACACC
Found at i:16495326 original size:3 final size:3
Alignment explanation
Indices: 16495260--16495309 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
16495250 TCCATATATA
* *
16495260 AAC AAT AAC ATC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16495308 AA
1 AA
16495310 AATTTTCATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.66, C:0.30, G:0.00, T:0.04
Consensus pattern (3 bp):
AAC
Found at i:16496950 original size:17 final size:17
Alignment explanation
Indices: 16496930--16496966 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
16496920 AATTCGTCTG
16496930 TTTATTTTTC-TTATTTA
1 TTTA-TTTTCGTTATTTA
16496947 TTTATTTTCGTTATTTA
1 TTTATTTTCGTTATTTA
16496964 TTT
1 TTT
16496967 TTATCTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTATTTTCGTTATTTA
Found at i:16496950 original size:30 final size:30
Alignment explanation
Indices: 16496910--16496968 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16496900 CCTCATTGGT
*
16496910 TTATTGATTTA-ATTCGTCTGTTTATTTTTC
1 TTATTGATTTATATTCGT-TATTTATTTTTC
* *
16496940 TTATTTATTTATTTTCGTTATTTATTTTT
1 TTATTGATTTATATTCGTTATTTATTTTT
16496969 ATCTCAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (30 bp):
TTATTGATTTATATTCGTTATTTATTTTTC
Found at i:16498519 original size:138 final size:137
Alignment explanation
Indices: 16498117--16498536 Score: 537
Period size: 137 Copynumber: 3.1 Consensus size: 137
16498107 GTTAAAAAAA
* * * * *
16498117 AATTATATTCTTTCCAACAGAATATTAATTT-TCATATCTTTTATATTTTGATTGAAATTATTTA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCT-ATTTCTTTTATATTTTGACTGAAATTAATTA
* *
16498181 ATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAAATGTTTATATTAATAAATTCGATAAAATATATACAATT-ATATTTTGTATGAATCAAAT
*
16498246 TCATATATT
129 CCATATATT
* * * * * *
16498255 AATTATACTCTTTCTAAAATAATATTAATTTCCATTT-TTTAAATATTTTGACCGAAATT-ATTA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCTATTTCTTT-TATATTTTGACTGAAATTAATTA
* * * *
16498318 ATATAAATGTTTATATTAATTAATT-TAGTAAACTATATACAACTAGTATTTTGTATGAATCAAA
65 ATATAAATGTTTATATTAATAAATTCGA-TAAAATATATACAATTA-TATTTTGTATGAATCAAA
16498382 TCCATATATT
128 TCCATATATT
* *
16498392 AATTGTATTTTTTCCAAAAAAATATTAATTTCTATTTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCTATTTCTTTTATATTTTGACTGAAATTAATTAA
*
16498457 TAT-AACGTTTTATATTAATAAATTCGATAAAATATATACAATTGATATTTTGTATGAATCAAA-
66 TATAAATG-TTTATATTAATAAATTCGATAAAATATATACAATT-ATATTTTGTATGAATCAAAT
16498520 CTCATATATT
129 C-CATATATT
16498530 AATTATA
1 AATTATA
16498537 CCTATGTTAT
Statistics
Matches: 241, Mismatches: 31, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
136 1 0.00
137 121 0.50
138 117 0.49
139 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.46
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAAAATATTAATTTCTATTTCTTTTATATTTTGACTGAAATTAATTAA
TATAAATGTTTATATTAATAAATTCGATAAAATATATACAATTATATTTTGTATGAATCAAATCC
ATATATT
Found at i:16501983 original size:24 final size:24
Alignment explanation
Indices: 16501920--16501971 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16501910 TTTCTAGAAG
* * *
16501920 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16501944 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
16501968 ATTT
1 ATTT
16501972 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:16506337 original size:24 final size:23
Alignment explanation
Indices: 16506281--16506325 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
16506271 AAGATTTAGT
* *
16506281 ATTTATGAGTATAATATATTTATC
1 ATTTATTAGCATAATATATTTA-C
16506305 ATTTATTAGCATAATATATTT
1 ATTTATTAGCATAATATATTT
16506326 GAATTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (23 bp):
ATTTATTAGCATAATATATTTAC
Found at i:16509697 original size:45 final size:45
Alignment explanation
Indices: 16509642--16509832 Score: 294
Period size: 45 Copynumber: 4.2 Consensus size: 45
16509632 TTCATTAAGA
*
16509642 CTACAAGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAAC
1 CTACGAGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAAC
*
16509687 CTACGAGCAGTGGGGCCGGTACATTCAGCTCTCAATTCATTCAAC
1 CTACGAGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAAC
* *
16509732 TTACGAGCAGTGGGGCTGGTACATTCAGCTCTCCATTCATTCAAC
1 CTACGAGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAAC
* * * *
16509777 TTACGAGCTGTGGGGCTGGTACATTCACCTCTCATTTCATT-AAGC
1 CTACGAGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAA-C
16509822 CTACGAGCAGT
1 CTACGAGCAGT
16509833 AGGACTACCA
Statistics
Matches: 134, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
44 2 0.01
45 132 0.99
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.28
Consensus pattern (45 bp):
CTACGAGCAGTGGGGCTGGTACATTCAGCTCTCAATTCATTCAAC
Found at i:16516343 original size:41 final size:40
Alignment explanation
Indices: 16516280--16516369 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 40
16516270 TTTTTATACA
*
16516280 TATTA-TTATATGTTATTAAACTTTT-ATATCATTATATAT
1 TATTATTTATATATTATTAAACTTTTCATATCA-TATATAT
* *
16516319 TATTATTTATATTATTATTAAACTTTTCATTTTATATATAT
1 TATTATTTATA-TATTATTAAACTTTTCATATCATATATAT
16516360 TACTTATTTA
1 TA-TTATTTA
16516370 GACTAATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 5 0.11
40 5 0.11
41 23 0.52
42 11 0.25
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (40 bp):
TATTATTTATATATTATTAAACTTTTCATATCATATATAT
Found at i:16516361 original size:38 final size:35
Alignment explanation
Indices: 16516271--16516366 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 35
16516261 TATTTTGATT
* *
16516271 TTTTATACATATTATTATATGTTATTAAACTTTTA
1 TTTTATATATATTATTATATATTATTAAACTTTTA
16516306 TATCATTATATATTATTATTTATATTATTATTAAACTTTTCA
1 T-T--TTATATA-TATTA-TTATA-TATTATTAAACTTTT-A
16516348 TTTTATATATATTACTTAT
1 TTTTATATATATTA-TTAT
16516367 TTAGACTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
35 1 0.02
36 1 0.02
38 15 0.29
39 12 0.24
40 5 0.10
41 15 0.29
42 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTTATATATATTATTATATATTATTAAACTTTTA
Found at i:16521069 original size:12 final size:12
Alignment explanation
Indices: 16521052--16521089 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16521042 TAATTACTCA
16521052 ATTATT-TTCATT
1 ATTATTGTT-ATT
16521064 ATTATTGTTATT
1 ATTATTGTTATT
*
16521076 ATTAATGTTATT
1 ATTATTGTTATT
16521088 AT
1 AT
16521090 AACTATTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 22 0.92
13 2 0.08
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (12 bp):
ATTATTGTTATT
Found at i:16521505 original size:28 final size:27
Alignment explanation
Indices: 16521451--16521512 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
16521441 ACCGTATTTT
16521451 TAATTTATTTCAAATTTTCATTTATATA
1 TAATTTATTTCAAATTTT-ATTTATATA
* *
16521479 TTATTTATTTTAAA-TTTATTTTAATATA
1 TAATTTATTTCAAATTTTA-TTT-ATATA
16521507 TAATTT
1 TAATTT
16521513 CCTTTCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.21
28 22 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATTTATTTCAAATTTTATTTATATA
Found at i:16526483 original size:46 final size:45
Alignment explanation
Indices: 16526425--16526513 Score: 133
Period size: 46 Copynumber: 2.0 Consensus size: 45
16526415 AAAGAGAAAG
* *
16526425 GATCAAGGTGAAAACCCACAAAGAGCGCTTTGAGTCCAAAAAAAAA
1 GATCAAAGTGAAAACCCACAAAGAGCACTTTGAGT-CAAAAAAAAA
* *
16526471 GATCAAAGTGAAAACCCTCAAAGGGCACTTTGAGTCAAAAAAA
1 GATCAAAGTGAAAACCCACAAAGAGCACTTTGAGTCAAAAAAA
16526514 TAAAAAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 8 0.21
46 31 0.79
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (45 bp):
GATCAAAGTGAAAACCCACAAAGAGCACTTTGAGTCAAAAAAAAA
Found at i:16529038 original size:44 final size:44
Alignment explanation
Indices: 16527808--16529011 Score: 1640
Period size: 44 Copynumber: 27.4 Consensus size: 44
16527798 GGTGAAACTA
* * * *
16527808 TAAATCTTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGACTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
** *
16527852 -AAAGTCCTAGCTCCCTGAATAGCAGTGGAATAGGCAGAAGATTG
1 TAAA-TCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * *
16527896 TAAATCCTAGCTTCCTGACCAGCAGTGGAATAGGTGGAAGACT-
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * * *
16527939 AAAAGTCCTAGCTTCCTGAACAGTAGTGGAATAGGCGGAAGATTG
1 TAAA-TCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * *
16527984 TAAATACTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * *
16528028 -AAAGTTCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
1 TAAA-TCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * *
16528072 TAAATTCTAGCTCCCTGACCAGTAGTGGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * * *
16528116 TAAATCCTAGATCTCTGAACAGCAGTGGAATAGGCAGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
*
16528160 TAAATCCTAGCTCCTTGACCAGCAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* *
16528204 TAAATCCTAGCTCCCTGACCGGCAGTGGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * * * **
16528248 TAAGTCCTAGATCCCTCAACAGCAGTGGAATAGGTTGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * * * *
16528292 TAAGTCCTAGCTCCCTGAACAACAGTAGAATAGGCAGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
16528336 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* *
16528380 TAAATCCTAGCTCCCTGAACAACAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
*
16528424 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCAGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
*
16528468 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * * *
16528512 TAAATCCTAGCTCCCTGAACAGCAATGGAATAGGTGGAAGACTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * * **
16528556 TAAGTTCTAGCTCCCTGACCAGTAGTGGAATAGGTTGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* ** *
16528600 TAAGTCCTAGCTCCCTGAATAGCAGTGGAATAGGCGAAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* * *
16528644 TAAATCCTAGCTCCCTGAGCAGCAGTGGAATAGGTGAAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* ** *
16528688 TAAATCCTAGCTCCCTGAACAATAGTGGAATAGGCGGAAGGTTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* *
16528732 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGAAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
*
16528776 TAAATCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* *
16528820 TAAATCCTAGCTCCCTGACTAGCAGTGGAATAGGAGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* *
16528864 TAAATCCTAGCTCCCTGACCAGTAATGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* *
16528908 TAAATCCTAGCTCCTTGACTAGCAGTGGAATAGGCGGAAGATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* ** *
16528952 TAAATCCTAGCTCCCTGACCGGCAGTGGAATAGGCAAAAAATTG
1 TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
* *
16528996 TAAGTCCTATCTCCCT
1 TAAATCCTAGCTCCCT
16529012 ATGCAACAGT
Statistics
Matches: 1032, Mismatches: 122, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
43 9 0.01
44 1014 0.98
45 9 0.01
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (44 bp):
TAAATCCTAGCTCCCTGACCAGCAGTGGAATAGGCGGAAGATTG
Found at i:16529112 original size:87 final size:87
Alignment explanation
Indices: 16529014--16529223 Score: 303
Period size: 89 Copynumber: 2.4 Consensus size: 87
16529004 ATCTCCCTAT
* *
16529014 GCAACAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATTGAA
1 GCAACAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
16529079 GACCCCAGCCTTGTCTCCCAGA
66 GACCCCAGCCTTGTCTCCCAGA
* *
16529101 GCAACAGTGGAGTAGGTTAAAAAAATTACAGCTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
1 GCAACAGTGGAGTAGGTT--GAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
* * **
16529166 AAGACCTCAGTCTTGTCTCCGTGA
64 AAGACCCCAGCCTTGTCTCCCAGA
* * *
16529190 GCAGCAATGGAGTAGGTTGAAAATAACAGATCTT
1 GCAACAGTGGAGTAGGTTGAAAATTACAGATCTT
16529224 GTCTTCCTGT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
87 31 0.29
89 77 0.71
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (87 bp):
GCAACAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
GACCCCAGCCTTGTCTCCCAGA
Found at i:16530684 original size:12 final size:12
Alignment explanation
Indices: 16530667--16530704 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16530657 TAATTACTCA
16530667 ATTATT-TTCATT
1 ATTATTGTT-ATT
16530679 ATTATTGTTATT
1 ATTATTGTTATT
*
16530691 ATTAATGTTATT
1 ATTATTGTTATT
16530703 AT
1 AT
16530705 AACTATTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 22 0.92
13 2 0.08
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (12 bp):
ATTATTGTTATT
Found at i:16531120 original size:28 final size:27
Alignment explanation
Indices: 16531066--16531127 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
16531056 ACCGTATTTT
16531066 TAATTTATTTCAAATTTTCATTTATATA
1 TAATTTATTTCAAATTTT-ATTTATATA
* *
16531094 TTATTTATTTTAAA-TTTATTTTAATATA
1 TAATTTATTTCAAATTTTA-TTT-ATATA
16531122 TAATTT
1 TAATTT
16531128 CCTTTCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 6 0.21
28 22 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATTTATTTCAAATTTTATTTATATA
Found at i:16539693 original size:17 final size:20
Alignment explanation
Indices: 16539671--16539709 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
16539661 GCCCTACATC
16539671 AATAATT-GAT-TAGG-TAA
1 AATAATTGGATCTAGGCTAA
16539688 AATAATTGGATCTAGGCTAA
1 AATAATTGGATCTAGGCTAA
16539708 AA
1 AA
16539710 GAACTTGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 4 0.21
20 5 0.26
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (20 bp):
AATAATTGGATCTAGGCTAA
Found at i:16541802 original size:22 final size:23
Alignment explanation
Indices: 16541777--16541830 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
16541767 ATCAACACTT
** *
16541777 TTTCTTTTTCTTTTTATTT-ATA
1 TTTCTTTTTCAATATATTTCATA
* *
16541799 TTTCCTTTACAATATATTTCATA
1 TTTCTTTTTCAATATATTTCATA
16541822 TTTCTTTTT
1 TTTCTTTTT
16541831 TTAGAATTTC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTCTTTTTCAATATATTTCATA
Found at i:16550935 original size:32 final size:32
Alignment explanation
Indices: 16550892--16550963 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
16550882 TTTGATTCGT
*
16550892 TGTAATGGAATAGAGCTGTAATGGAATAGAGG
1 TGTAATAGAATAGAGCTGTAATGGAATAGAGG
*
16550924 TGTAATAGAATATAGCTGTAATGGAATAGAGG
1 TGTAATAGAATAGAGCTGTAATGGAATAGAGG
*
16550956 CGTAATAG
1 TGTAATAG
16550964 TATTCTTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.39, C:0.04, G:0.31, T:0.26
Consensus pattern (32 bp):
TGTAATAGAATAGAGCTGTAATGGAATAGAGG
Found at i:16550961 original size:16 final size:16
Alignment explanation
Indices: 16550892--16550954 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
16550882 TTTGATTCGT
16550892 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
*
16550908 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGC
* *
16550924 TGTAATAGAATATAGC
1 TGTAATGGAATAGAGC
16550940 TGTAATGGAATAGAG
1 TGTAATGGAATAGAG
16550955 GCGTAATAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.27
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:16551267 original size:120 final size:120
Alignment explanation
Indices: 16551130--16551713 Score: 820
Period size: 120 Copynumber: 5.0 Consensus size: 120
16551120 TTTATCATAT
*
16551130 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTGATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
16551195 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
16551250 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* * *
16551315 AAATATTCTTAAATGAATATAATAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
16551370 TTTAA-ATTAATTATTATTAAAATATAATTTAGTAAAAATATATAATTTAATAAAATTCTTAATA
1 TTTAACA-TAATTATTATT-AAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA
*
16551434 TTAAATATTC-T-TA-GAATTTACTAAAATCATAATATAGAATACTATAAAATATAA
64 TTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * * *
16551488 TTTAA-ATTAATTATTTTTAAATATAATTTAATAAAATTCT-TAATATT-A-AATATTCTTAA-A
1 TTTAACA-TAATTATTATTAAATATAATTTAATAAAAATATATAAT-TTAATAAAATTCTTAATA
* * *
16551548 -TGAATTTTC-TA-A--AA-TCA-T-AAA--AT-ATA-AT---ACTATAAAATATAA
64 TTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
16551590 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
16551655 AAATATTCTTATATGTATTTACTAAAATCATAATATATAATATTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
16551710 TTTA
1 TTTA
16551714 TAATCTACTT
Statistics
Matches: 412, Mismatches: 28, Indels: 48
0.84 0.06 0.10
Matches are distributed among these distances:
102 51 0.12
103 6 0.01
104 10 0.02
105 2 0.00
106 10 0.02
107 4 0.01
108 1 0.00
109 3 0.01
110 2 0.00
111 4 0.01
112 3 0.01
113 12 0.03
114 1 0.00
115 12 0.03
116 8 0.02
117 23 0.06
118 55 0.13
119 2 0.00
120 149 0.36
121 54 0.13
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:16551525 original size:99 final size:101
Alignment explanation
Indices: 16551409--16551625 Score: 359
Period size: 102 Copynumber: 2.2 Consensus size: 101
16551399 TAGTAAAAAT
*
16551409 ATATAATTTAATAAAATTCTTAATATTAAATATTCTT-A-GAATTTACTAAAATCATAATATAGA
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAATGAATTTACTAAAATCATAAAATAGA
*
16551472 ATACTATAAAATATAATTTAA-ATTAATTATTTTTAA
66 ATACTATAAAATATAATTTAACA-TAATTATTATTAA
* *
16551508 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTTCTAAAATCATAAAATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTT-AATGAATTTACTAAAATCATAAAATAG
16551573 AATACTATAAAATATAATTTAACATAATTATTATTAA
65 AATACTATAAAATATAATTTAACATAATTATTATTAA
16551610 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
16551626 ATATATAATT
Statistics
Matches: 110, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
99 37 0.34
101 1 0.01
102 71 0.65
103 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (101 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAATGAATTTACTAAAATCATAAAATAGA
ATACTATAAAATATAATTTAACATAATTATTATTAA
Found at i:16551526 original size:220 final size:222
Alignment explanation
Indices: 16551288--16551713 Score: 734
Period size: 220 Copynumber: 1.9 Consensus size: 222
16551278 TAATAAAAAT
*
16551288 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATATAATAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATATAATAAAATCATAAAATAT
*
16551353 AATACTATAAAATATAATTTAA-ATTAATTATTATTAAAATATAATTTAGTAAAAATATATAATT
66 AATACTATAAAATATAATTTAACA-TAATTATTATT-AAATATAATTTAATAAAAATATATAATT
16551417 TAATAAAATTCTTAATATTAAATATTC-T-TA-GAATTTACTAAAATCATAATATAGAATACTAT
129 TAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAGAATACTAT
16551479 AAAATATAATTTAAATTAATTATTTTTAA
194 AAAATATAATTTAAATTAATTATTTTTAA
* **
16551508 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTTCTAAAATCATAAAATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATATAATAAAATCATAAAATAT
16551573 AATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA
66 AATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA
* * *
16551638 ATAAAATTCTTAATATTAAATATTCTTATATGTATTTACTAAAATCATAATATATAATATTATAA
131 ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAGAATACTATAA
16551703 AATATAATTTA
196 AATATAATTTA
16551714 TAATCTACTT
Statistics
Matches: 194, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
219 54 0.28
220 95 0.49
221 3 0.02
222 42 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (222 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATATAATAAAATCATAAAATAT
AATACTATAAAATATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA
ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAGAATACTATAA
AATATAATTTAAATTAATTATTTTTAA
Found at i:16551691 original size:59 final size:59
Alignment explanation
Indices: 16551507--16551691 Score: 182
Period size: 59 Copynumber: 3.1 Consensus size: 59
16551497 ATTATTTTTA
* *
16551507 AATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTTCTAAAATCAT
1 AATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGTATTTACTAAAATCAT
* * * * * * *
16551566 AAAATATAATACT-ATAAAATATAATTTAACA-TAATTATTATTAAATATAATTTAATAAAA--A
1 --AATATAAT-TTAATAAAAT-T--CTTAATATTAAATATTCTTAAATGT-ATTTACTAAAATCA
16551627 T
59 T
*
16551628 -ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGTATTTACTAAAATCAT
1 AATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGTATTTACTAAAATCAT
16551686 AATATA
1 AATATA
16551692 TAATATTATA
Statistics
Matches: 97, Mismatches: 17, Indels: 22
0.71 0.12 0.16
Matches are distributed among these distances:
56 15 0.15
57 13 0.13
58 4 0.04
59 19 0.20
61 15 0.15
62 4 0.04
63 13 0.13
64 14 0.14
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (59 bp):
AATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGTATTTACTAAAATCAT
Found at i:16553171 original size:49 final size:49
Alignment explanation
Indices: 16553099--16553202 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
16553089 AGAAAAAAAC
* *
16553099 AAATTAAAATTAAGTTTAATATCATGAATCAAAA-AGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAATA-TCAACACTTTATA
16553148 AAATTAAAATTAAGTTCAATATCATGAATCAAAATATCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAATATCAACACTTTATA
16553197 AAATTA
1 AAATTA
16553203 TAACACATGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 51 0.98
50 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAATATCAACACTTTATA
Found at i:16553924 original size:134 final size:129
Alignment explanation
Indices: 16553681--16553948 Score: 464
Period size: 134 Copynumber: 2.0 Consensus size: 129
16553671 GTTTCATATT
16553681 AAAAAATTATTGCGGAGTACTTGCCTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGTC
1 AAAAAATTATTGCGGAGTACTTGCCTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGTC
16553746 CTCTAAAAGGTGCAAGAAATCCCTCACAATTTGTGTATCCAGCATCAACTAGATAATAACAACCT
66 CTCTAAAAGGTGCAAGAAATCCCTCACAATTTGTGTATCCAGCATCAACTAG----TAACAACCT
16553811 ATA
127 ATA
* *
16553814 AAANAAATTCTTGCGGAGTACTTGGCTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGT
1 AAA-AAATTATTGCGGAGTACTTGCCTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGT
*
16553879 CCTCTAAAAGGTGCAAGAAATCTCTCACAATTTGTGTATCCAGCATCAACTAGTAACAACCTATA
65 CCTCTAAAAGGTGCAAGAAATCCCTCACAATTTGTGTATCCAGCATCAACTAGTAACAACCTATA
16553944 AAAAA
1 AAAAA
16553949 CTTTTTTTAA
Statistics
Matches: 131, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
129 2 0.02
130 15 0.11
133 3 0.02
134 111 0.85
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (129 bp):
AAAAAATTATTGCGGAGTACTTGCCTGATAACCCTGACGCCACTCATTCAAATGATATCGTTGTC
CTCTAAAAGGTGCAAGAAATCCCTCACAATTTGTGTATCCAGCATCAACTAGTAACAACCTATA
Found at i:16555698 original size:16 final size:16
Alignment explanation
Indices: 16555677--16555713 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
16555667 AATAAATTGG
16555677 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
16555693 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
16555709 AATAT
1 AATAT
16555714 AATATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:16555863 original size:73 final size:75
Alignment explanation
Indices: 16555781--16555953 Score: 323
Period size: 73 Copynumber: 2.3 Consensus size: 75
16555771 TTTTTATTTT
*
16555781 AACAAATGCATTATTTAATAAATTGGAATATTAAAAATAAAAAAT-ATCCAAACTTTA-TTGAAT
1 AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
16555844 TACAAAAATA
66 TACAAAAATA
16555854 AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
1 AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
16555919 TACAAAAATA
66 TACAAAAATA
16555929 AACAAATGCATTATTTAGTAAATTG
1 AACAAATGCATTATTTAGTAAATTG
16555954 AAAAACAATT
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
73 44 0.45
74 12 0.12
75 41 0.42
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.32
Consensus pattern (75 bp):
AACAAATGCATTATTTAGTAAATTGGAATATTAAAAATAAAAAATAATCCAAACTTTACTTGAAT
TACAAAAATA
Found at i:16557114 original size:21 final size:21
Alignment explanation
Indices: 16557089--16557157 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 21
16557079 ACAGAAACGG
16557089 AAAACATCAACTTAATACAGA
1 AAAACATCAACTTAATACAGA
16557110 AAAACATCAACTTAATACAGAAA
1 AAAACATCAACTTAATACAG--A
*
16557133 CCAAAACATGAACTTAATACAGA
1 --AAAACATCAACTTAATACAGA
16557156 AA
1 AA
16557158 CCAAAACATG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
21 22 0.51
23 2 0.05
25 19 0.44
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (21 bp):
AAAACATCAACTTAATACAGA
Found at i:16557170 original size:25 final size:25
Alignment explanation
Indices: 16557079--16557166 Score: 121
Period size: 25 Copynumber: 3.6 Consensus size: 25
16557069 TAATCCATAA
*
16557079 ACAGAAACGGAAAACATCAACTTAAT
1 ACAGAAAC-CAAAACATCAACTTAAT
16557105 ACAG--A--AAAACATCAACTTAAT
1 ACAGAAACCAAAACATCAACTTAAT
*
16557126 ACAGAAACCAAAACATGAACTTAAT
1 ACAGAAACCAAAACATCAACTTAAT
16557151 ACAGAAACCAAAACAT
1 ACAGAAACCAAAACAT
16557167 GAACATTATA
Statistics
Matches: 57, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
21 20 0.35
23 1 0.02
24 1 0.02
25 31 0.54
26 4 0.07
ACGTcount: A:0.57, C:0.20, G:0.08, T:0.15
Consensus pattern (25 bp):
ACAGAAACCAAAACATCAACTTAAT
Found at i:16561535 original size:26 final size:26
Alignment explanation
Indices: 16561506--16561581 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
16561496 ACATATTTTC
* *
16561506 TCAAAATTTTATTATGGGCAAAATCG
1 TCAAAATTTTATTAAGGGTAAAATCG
* *
16561532 TCAAATTTTTACTAAGGGTAAAATCG
1 TCAAAATTTTATTAAGGGTAAAATCG
*
16561558 TCAAAAATTTT-TTAGGGGTAAAAT
1 TC-AAAATTTTATTAAGGGTAAAAT
16561582 AGGGATAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 35 0.83
27 7 0.17
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (26 bp):
TCAAAATTTTATTAAGGGTAAAATCG
Found at i:16567517 original size:10 final size:10
Alignment explanation
Indices: 16567502--16567557 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
16567492 TTTTAATTTT
16567502 ATATTTTTAA
1 ATATTTTTAA
**
16567512 ATATTTTTTG
1 ATATTTTTAA
16567522 AT-TTTTTAA
1 ATATTTTTAA
*
16567531 ATATTTTT-T
1 ATATTTTTAA
16567540 ATAATTTTTAA
1 AT-ATTTTTAA
*
16567551 ATGTTTT
1 ATATTTT
16567558 AAGGTTTTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
9 9 0.25
10 25 0.69
11 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:16567527 original size:19 final size:19
Alignment explanation
Indices: 16567498--16567557 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
16567488 ATTTTTTTAA
16567498 TTTTATATTTTTAAATATT
1 TTTTATATTTTTAAATATT
16567517 TTTTGAT-TTTTTAAATATT
1 TTTT-ATATTTTTAAATATT
*
16567536 TTTTATAATTTTTAAATGTT
1 TTTTAT-ATTTTTAAATATT
16567556 TT
1 TT
16567558 AAGGTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 2 0.05
19 20 0.54
20 15 0.41
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTATATTTTTAAATATT
Found at i:16568323 original size:20 final size:20
Alignment explanation
Indices: 16568298--16568337 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16568288 ATGGTACTTG
*
16568298 TTGCTAACACT-GTTAGTAAA
1 TTGCTAA-ACTAGTTAATAAA
16568318 TTGCTAAACTAGTTAATAAA
1 TTGCTAAACTAGTTAATAAA
16568338 AACTTGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
TTGCTAAACTAGTTAATAAA
Found at i:16569430 original size:23 final size:23
Alignment explanation
Indices: 16569395--16569445 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
16569385 GGATAGTGAG
*
16569395 TGTAATATACCGAAAATTACTAC
1 TGTAATACACCGAAAATTACTAC
*
16569418 TGTAATACCCCGAAAATTACTAC
1 TGTAATACACCGAAAATTACTAC
*
16569441 AGTAA
1 TGTAA
16569446 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACACCGAAAATTACTAC
Found at i:16572055 original size:32 final size:32
Alignment explanation
Indices: 16572019--16572160 Score: 169
Period size: 32 Copynumber: 4.4 Consensus size: 32
16572009 CGCGGTTCTA
* *
16572019 TGAAATGATAACAAATATCACCTTTCATTTTG
1 TGAAATGATAACAAATATCAACTTTAATTTTG
* * * * *
16572051 TGAAATAATAACAAGT-TACGACTTAAATTTTA
1 TGAAATGATAACAAATAT-CAACTTTAATTTTG
* * *
16572083 TGAAATAATAACAATTAACAACTTTAATTTTG
1 TGAAATGATAACAAATATCAACTTTAATTTTG
16572115 TGAAATGATAACAAATATCAACTTTAATTTTG
1 TGAAATGATAACAAATATCAACTTTAATTTTG
*
16572147 TTAAATGATAACAA
1 TGAAATGATAACAA
16572161 TATTCCTCTA
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.01
32 91 0.99
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (32 bp):
TGAAATGATAACAAATATCAACTTTAATTTTG
Found at i:16574522 original size:20 final size:20
Alignment explanation
Indices: 16574480--16574524 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16574470 AAATTTAGGA
* *
16574480 GAGAATTTTGAGAGTGGTTT
1 GAGAATTTTGAAAGTGATTT
16574500 GAGAATTTTGAAAGT-ATTGT
1 GAGAATTTTGAAAGTGATT-T
16574520 GAGAA
1 GAGAA
16574525 ATTAATAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (20 bp):
GAGAATTTTGAAAGTGATTT
Found at i:16580693 original size:230 final size:226
Alignment explanation
Indices: 16580291--16580928 Score: 644
Period size: 230 Copynumber: 2.8 Consensus size: 226
16580281 ATTAAAGCAG
* * * * * *
16580291 AACGCAGGGTTCGGTGTTGATCAATTGTTGCTTTAGCGGCGCTAATC-TAGAAACGCCGCCAAAG
1 AACGCAGCGTTCGGTGTTAATCAATTGTCGCTTTAGCGGCGC-AAACATAAAAACGCTGCCAAAG
* * *
16580355 ATCGGTATTAACGGCGCTTA-TATACTAAATGCCACAGAAAGTTTAACCAAAATGCATCATTTGG
65 ATCGATATTAACGGCGCTTACGA-A-TAAACGCCACAGAAAG-TTAACCAAAATGCATC-TTTGG
* * * * *
16580419 CCTCGAGGTATAGTGGCATTTAGCGGCGCTTTAGTTA-CAACGCCACTAAAGATCTTCATTAGCA
126 CCTTGATGTATGGTGGCATTTAGCGGCGCTTT--TAACCAACGCCACTAAAGATCTTCATTAAC-
* *
16580483 G-CGATTTCACCATAGCGCCGCAAAAG-AAGTTAAAACTA
188 GTCGATTTCACCAAAACGCCGC-AAAGTAAGTTAAAACTA
* * * * *
16580521 AACGCAGTGTTCGGTGTTCATCAATTGTGGCTTTAGCGGCGCAAACATAAAAACGCTGCTAAAAA
1 AACGCAGCGTTCGGTGTTAATCAATTGTCGCTTTAGCGGCGCAAACATAAAAACGCTGCCAAAGA
* * * *
16580586 TCGATATTAACGGTGCTTACCGGATAAACGCCTCAGAAAGCTAACCAAAATGCATCGTTTGGCCT
66 TCGATATTAACGGCGCTTA-CGAATAAACGCCACAGAAAGTTAACCAAAATGCATC-TTTGGCCT
16580651 TGATGTATGGTGGCATTTAGCGGCGCTTTTAACCTGAACGCCACTAAAGATCTTCATTAACGTCG
129 TGATGTATGGTGGCATTTAGCGGCGCTTTTAACC--AACGCCACTAAAGATCTTCATTAACGTCG
* *** ** **
16580716 TTTTCGTTAAAACGCCGCCGAGTCTGTTAAAACTA
192 ATTTCACCAAAACGCCGCAAAGTAAGTTAAAACTA
* * * * * * * * *
16580751 AATGTAGCGTTTGGTTTTAATCAATTG-CGATTCCAGCGGCGCTAATA-AAAAATCGCTGCGAAA
1 AACGCAGCGTTCGGTGTTAATCAATTGTCGCTT-TAGCGGCGCAAACATAAAAA-CGCTGCCAAA
* *
16580814 GATCAGA-ATTAACGGCGCTTAACGAATAAACGCCGCAGAAAGTTAACCAAAACGCATCTTTGGC
64 GATC-GATATTAACGGCGCTT-ACGAATAAACGCCACAGAAAGTTAACCAAAATGCATCTTTGGC
* *
16580878 CTTGATTTATGGTGGCATTTAGCGGCGCTTTAAACCAAACGCCACTAAAGA
127 CTTGATGTATGGTGGCATTTAGCGGCGCTTTTAACC-AACGCCACTAAAGA
16580929 AAACGCCGCA
Statistics
Matches: 344, Mismatches: 52, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
227 2 0.01
228 15 0.04
229 103 0.30
230 220 0.64
231 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (226 bp):
AACGCAGCGTTCGGTGTTAATCAATTGTCGCTTTAGCGGCGCAAACATAAAAACGCTGCCAAAGA
TCGATATTAACGGCGCTTACGAATAAACGCCACAGAAAGTTAACCAAAATGCATCTTTGGCCTTG
ATGTATGGTGGCATTTAGCGGCGCTTTTAACCAACGCCACTAAAGATCTTCATTAACGTCGATTT
CACCAAAACGCCGCAAAGTAAGTTAAAACTA
Found at i:16581282 original size:190 final size:191
Alignment explanation
Indices: 16580943--16581291 Score: 440
Period size: 190 Copynumber: 1.8 Consensus size: 191
16580933 GCCGCAAAAT
*
16580943 ATGTTAAAACTAAACACAACGTTCGATTTTGATAAATTCTGGATTTCACGGCGCTAATTGAAAAA
1 ATGTTAAAACTAAACACAACGTTCGATTTTGATAAATTCTGGATTTCACGGCGCTAAATGAAAAA
**
16581008 CGCCGCTAAAGATCGGTATTAACGACGCTTAACTAGTAAACGCCGCAAAAAGTTAACCAAAACGC
66 CGCCGCTAAAGATCGGTATTAACGACGCTTAACTAAAAAACGCCGCAAAAAGTTAACCAAAACGC
*
16581073 ATCGTTTGGCCGTGAGGTATAGTGG-CATTTAGCGGCGCTTTGCCTAAAAATGCCACTAGAG
131 ATCGTTTGGCCGAGAGGTATA-TGGTCATTTAGCGGCGCTTTGCCTAAAAATGCCACTAGAG
* * * * *
16581134 ATGTTAAAACTAAACGCATCGTTCG-TTGTTGAT-CATTGTGGCA-TTCGCGGCGCTAACAT-AA
1 ATGTTAAAACTAAACACAACGTTCGATT-TTGATAAATTCTGG-ATTTCACGGCGCTAA-ATGAA
* * * * ** * **
16581195 AATCGCCGCTAAATATCGGTATTAACGGCGCTTGAC-AAAAAACGCCGCAAGTATTTAACCAAGG
63 AAACGCCGCTAAAGATCGGTATTAACGACGCTTAACTAAAAAACGCCGCAAAAAGTTAACCAAAA
*
16581259 CGCATCGTTTTGGCGGAGAGGTATATGGTCATT
128 CGCATCG-TTTGGCCGAGAGGTATATGGTCATT
16581292 AGTGGTGCTT
Statistics
Matches: 134, Mismatches: 19, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
189 31 0.23
190 73 0.54
191 30 0.22
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (191 bp):
ATGTTAAAACTAAACACAACGTTCGATTTTGATAAATTCTGGATTTCACGGCGCTAAATGAAAAA
CGCCGCTAAAGATCGGTATTAACGACGCTTAACTAAAAAACGCCGCAAAAAGTTAACCAAAACGC
ATCGTTTGGCCGAGAGGTATATGGTCATTTAGCGGCGCTTTGCCTAAAAATGCCACTAGAG
Found at i:16581805 original size:15 final size:16
Alignment explanation
Indices: 16581771--16581807 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
16581761 AAGGATTTAG
16581771 GGTATATTTGGGGATT
1 GGTATATTTGGGGATT
*
16581787 -GTAT-TTTGGGGTTT
1 GGTATATTTGGGGATT
16581801 GGTATAT
1 GGTATAT
16581808 ATTGTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 9 0.50
15 8 0.44
16 1 0.06
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (16 bp):
GGTATATTTGGGGATT
Found at i:16581924 original size:15 final size:15
Alignment explanation
Indices: 16581900--16581933 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16581890 GGACTTGGAT
16581900 TTTAGGGTTTGGTGG
1 TTTAGGGTTTGGTGG
* *
16581915 TTTAGTGTTTTGTGG
1 TTTAGGGTTTGGTGG
16581930 TTTA
1 TTTA
16581934 TGAGTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.35, T:0.56
Consensus pattern (15 bp):
TTTAGGGTTTGGTGG
Found at i:16583666 original size:16 final size:15
Alignment explanation
Indices: 16583645--16583680 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
16583635 TTTAAATTTT
16583645 CTTTTTTTGGTCAATG
1 CTTTTTTTGGT-AATG
16583661 CTTTTTTTGGTAATG
1 CTTTTTTTGGTAATG
16583676 -TTTTT
1 CTTTTT
16583681 CCTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 4 0.20
16 11 0.55
ACGTcount: A:0.11, C:0.08, G:0.17, T:0.64
Consensus pattern (15 bp):
CTTTTTTTGGTAATG
Found at i:16584119 original size:15 final size:15
Alignment explanation
Indices: 16584099--16584134 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
16584089 ACCACCAATT
*
16584099 TGTTTTCATTTGTAC
1 TGTTTTCATTTCTAC
16584114 TGTTTTCATTTCTAC
1 TGTTTTCATTTCTAC
16584129 T-TTTTC
1 TGTTTTC
16584135 CTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (15 bp):
TGTTTTCATTTCTAC
Found at i:16584794 original size:9 final size:9
Alignment explanation
Indices: 16584780--16584835 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
16584770 ATTAAAATGA
16584780 TACATAACT
1 TACATAACT
16584789 TACATAACT
1 TACATAACT
*
16584798 TA-TTAA--
1 TACATAACT
16584804 TACATAACT
1 TACATAACT
*
16584813 TATATAA--
1 TACATAACT
*
16584820 TATATAACT
1 TACATAACT
16584829 TACATAA
1 TACATAA
16584836 TACGACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.05
7 10 0.26
8 3 0.08
9 23 0.61
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:16584795 original size:41 final size:40
Alignment explanation
Indices: 16584735--16584835 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 40
16584725 TTACCCATTT
*
16584735 ATAATACAT-ACATTACATAACTTATTAATATATATA-TTAAA
1 ATAATACATAAC-TTACATAACTTATTAATACATA-ACTT-AA
* *
16584776 ATGATACATAACTTACATAACTTATTAATACATAACTTAT
1 ATAATACATAACTTACATAACTTATTAATACATAACTTAA
*
16584816 ATAATATATAACTTACATAA
1 ATAATACATAACTTACATAA
16584836 TACGACATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 20 0.38
41 31 0.58
42 2 0.04
ACGTcount: A:0.50, C:0.12, G:0.01, T:0.38
Consensus pattern (40 bp):
ATAATACATAACTTACATAACTTATTAATACATAACTTAA
Found at i:16584826 original size:16 final size:16
Alignment explanation
Indices: 16584789--16584838 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
16584779 ATACATAACT
16584789 TACATAACTTAT-TAA
1 TACATAACTTATATAA
16584804 TACATAACTTATATAA
1 TACATAACTTATATAA
* *
16584820 TATATAACTTACATAA
1 TACATAACTTATATAA
16584836 TAC
1 TAC
16584839 GACATAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (16 bp):
TACATAACTTATATAA
Found at i:16585057 original size:9 final size:9
Alignment explanation
Indices: 16585036--16585109 Score: 85
Period size: 9 Copynumber: 8.2 Consensus size: 9
16585026 TTGCATTTCA
*
16585036 ATAAATTAA
1 ATAAATTAC
*
16585045 ATAATTTAC
1 ATAAATTAC
*
16585054 ATAAATTAA
1 ATAAATTAC
*
16585063 ATAACTTAC
1 ATAAATTAC
*
16585072 ATAACTTAC
1 ATAAATTAC
*
16585081 ATAAATTAA
1 ATAAATTAC
16585090 ATAAATTAC
1 ATAAATTAC
*
16585099 ATAACTTAC
1 ATAAATTAC
16585108 AT
1 AT
16585110 TACATAATAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAAATTAC
Found at i:16585057 original size:18 final size:18
Alignment explanation
Indices: 16585036--16585109 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
16585026 TTGCATTTCA
*
16585036 ATAAATTAAATAATTTAC
1 ATAAATTAAATAACTTAC
16585054 ATAAATTAAATAACTTAC
1 ATAAATTAAATAACTTAC
* * * *
16585072 ATAACTTACATAAATTAA
1 ATAAATTAAATAACTTAC
*
16585090 ATAAATTACATAACTTAC
1 ATAAATTAAATAACTTAC
16585108 AT
1 AT
16585110 TACATAATAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAATTAAATAACTTAC
Found at i:16585066 original size:27 final size:27
Alignment explanation
Indices: 16585035--16585109 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
16585025 TTTGCATTTC
* *
16585035 AATAAATTAAATAATTTACATAAATTA
1 AATAAATTACATAACTTACATAAATTA
*
16585062 AATAACTTACATAACTTACATAAATTA
1 AATAAATTACATAACTTACATAAATTA
16585089 AATAAATTACATAACTTACAT
1 AATAAATTACATAACTTACAT
16585110 TACATAATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (27 bp):
AATAAATTACATAACTTACATAAATTA
Found at i:16585128 original size:36 final size:36
Alignment explanation
Indices: 16585054--16585125 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
16585044 AATAATTTAC
* *
16585054 ATAAATTAAATAACTTACATAACTTACATAAATTAA
1 ATAAATTAAATAACTTACATAACATACATAAATAAA
* * *
16585090 ATAAATTACATAACTTACATTACATA-ATACATAAA
1 ATAAATTAAATAACTTACATAACATACATAAATAAA
16585125 A
1 A
16585126 ATATATCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (36 bp):
ATAAATTAAATAACTTACATAACATACATAAATAAA
Found at i:16587395 original size:21 final size:21
Alignment explanation
Indices: 16587369--16587438 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
16587359 CTACAACTTA
* *
16587369 AAGCAGACGCGGCATCGAGGG
1 AAGCAGACGCGGCAACGAGAG
* *
16587390 AAGCAGAGGCTGCAACGAGAG
1 AAGCAGACGCGGCAACGAGAG
* ** *
16587411 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGACGCGGCAACGAGAG
16587432 AAGCAGA
1 AAGCAGA
16587439 GGTTCAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.37, C:0.20, G:0.39, T:0.04
Consensus pattern (21 bp):
AAGCAGACGCGGCAACGAGAG
Found at i:16587439 original size:21 final size:21
Alignment explanation
Indices: 16587384--16587440 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
16587374 GACGCGGCAT
* *
16587384 CGAGGGAAGCAGAGGCTGCAA
1 CGAGAGAAGCAGAGGCTACAA
*
16587405 CGAGAGAAGCAGAGGCTACAG
1 CGAGAGAAGCAGAGGCTACAA
16587426 CGAGAGAAGCAGAGG
1 CGAGAGAAGCAGAGG
16587441 TTCAAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.42, T:0.04
Consensus pattern (21 bp):
CGAGAGAAGCAGAGGCTACAA
Found at i:16588135 original size:126 final size:127
Alignment explanation
Indices: 16587823--16588153 Score: 371
Period size: 126 Copynumber: 2.6 Consensus size: 127
16587813 GTTTTTGTAC
* * * *
16587823 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCATTTGTAAACAAAGCGCCGCTGAAGAACATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT-TTAACAAAGCGCCGCTAAAGAACATG
* * * * * * *
16587888 TTCTTTAACAGCGTTTTTATACAAAACGTCGTTAAAGAACATGTTCTTTAGCGGCGCTTAATA
65 TTCTTTAGCGGCGCTTATATAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAATA
* * * * * * * *
16587951 AAAAACGCCACTAAAGATCATATTCTTTAGCGGCGCTTATAGA-AAAACGCCACTAAAGATCATG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTA-ACAAAGCGCCGCTAAAGAACATG
* *
16588015 TTCTTTAGTGGCGCTTATA-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA-A
65 TTCTTTAGCGGCGCTTATATAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-ATA
* * * ** *
16588077 AAAAACGCCGCTAAAGACCATGTTCTTCAGTGGCGTTTTTCTCAAAGCGCCGCTAAAGAACATGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAACAAAGCGCCGCTAAAGAACATGT
16588142 TCTTTAGCGGCG
66 TCTTTAGCGGCG
16588154 TTTTTGGTTG
Statistics
Matches: 165, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
126 99 0.60
127 33 0.20
128 33 0.20
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (127 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAACAAAGCGCCGCTAAAGAACATGT
TCTTTAGCGGCGCTTATATAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAATA
Found at i:16588154 original size:42 final size:42
Alignment explanation
Indices: 16587823--16588158 Score: 323
Period size: 42 Copynumber: 8.0 Consensus size: 42
16587813 GTTTTTGTAC
* * *
16587823 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCATTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAA
* * * *
16587865 ACAAAGCGCCGCTGAAGAACATGTTCTTTAACAGCGTTTTTATA
1 A-AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTA-A
* * * * *
16587909 CAAAACGTCGTTAAAGAACATGTTCTTTAGCGGCG-CTTAATA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTA-A
* * * * * *
16587951 AAAAACGCCACTAAAGATCATATTCTTTAGCGGCGCTTATAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAA
* * * * *
16587993 AAAAACGCCACTAAAGATCATGTTCTTTAGTGGCGCTTATAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAA
* * **
16588035 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAA
* * * **
16588077 AAAAACGCCGCTAAAGACCATGTTCTTCAGTGGCGTTTTTCT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAA
* * *
16588119 CAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
16588159 GGTTGTAAAC
Statistics
Matches: 247, Mismatches: 44, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
42 181 0.73
43 65 0.26
44 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTAA
Found at i:16589873 original size:5 final size:5
Alignment explanation
Indices: 16589858--16589887 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
16589848 TTCTATATGG
16589858 ATTTT ATTTTT ATTTT ATTTT ATTTT ATTT
1 ATTTT A-TTTT ATTTT ATTTT ATTTT ATTT
16589888 AAATAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:16594412 original size:29 final size:29
Alignment explanation
Indices: 16594370--16594426 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
16594360 TGTCTAAGAA
16594370 TGAAACACTATCATTTTTGTGCAAAACTG
1 TGAAACACTATCATTTTTGTGCAAAACTG
16594399 TGAAACACTATCATTTTTGTGCAAAACT
1 TGAAACACTATCATTTTTGTGCAAAACT
16594427 ATGTCACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (29 bp):
TGAAACACTATCATTTTTGTGCAAAACTG
Found at i:16595885 original size:18 final size:18
Alignment explanation
Indices: 16595842--16595885 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
16595832 ACCCAATCCA
* *
16595842 AACCCAAGTATTCAACCC
1 AACCCAATTACTCAACCC
16595860 AACCCAATTACTCAACCC
1 AACCCAATTACTCAACCC
16595878 AACCCAAT
1 AACCCAAT
16595886 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.41, G:0.02, T:0.16
Consensus pattern (18 bp):
AACCCAATTACTCAACCC
Found at i:16599101 original size:16 final size:16
Alignment explanation
Indices: 16599057--16599106 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
16599047 CATGTTTTCG
16599057 TAAAATTTT-AATTTA
1 TAAAATTTTAAATTTA
* *
16599072 -GACATTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
16599088 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
16599104 TAA
1 TAA
16599107 TAAAATTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:16602112 original size:261 final size:261
Alignment explanation
Indices: 16601585--16602369 Score: 970
Period size: 261 Copynumber: 3.0 Consensus size: 261
16601575 CGAGTGGCCC
16601585 TAGAGAATATATATTATGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
1 TAGAGAATATATATTATGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
* * *
16601650 TGCGGGAAAAGTATGCAGTGTATAATAATTGGTTGAACTATCTTATGTTAATTTATCGTCAGCCA
66 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTT-ATTTATCGCCTG-CA
* * * * * * * *
16601715 ATTTATCAAATCCCTATGAGGA-TACTAAGACTTGAGGAGTTTCATTTCACTACTTTGCAA-TTA
129 GTTTATCAAATCTCTAT-AAGATTAATGAGATTTAAGGAGTTTCGTTTCACTA-TTT-CAAGTTA
* * * *
16601778 TA-TACTTGATATATAATGTTGCATCCT-G-CAAATCTGAAAAATTCAAAT--TTTTTTTAATAT
191 TACT-CTTGATAAATAATGTTGCATCCTAGTAAAAT-TG-AAAA-TAAAATCAATTTTTTAATAT
16601838 GATACACTCT
252 GATACACTCT
* * * * *
16601848 TAGAGAATATATATAACGTAACGGCGAGGTGAGGTGGCTCCACGTTGT-GACAGTTGCTTTTGAT
1 TAGAGAATATATATTATGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGA-AGTTGCTTTTGCT
* * * * *
16601912 GTGCTGGAAGA-TACACAGTGTATAATAATTGGTTGAACTATCTTATATTATTTATTGCCTGTCA
65 GTGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTG-CA
*
16601976 GTTTATCAAATCTCTATAAGATTAATGAGATTTAAGGAGTTTCGTTTCACTATTTCACAGTTACA
129 GTTTATCAAATCTCTATAAGATTAATGAGATTTAAGGAGTTTCGTTTCACTATTTCA-AGTTATA
* * * * *
16602041 CTCTTGATAAATAATGCTGTAT-CTAGTAAAATTGAAAATAAAATCAGTTTTTTAATATAATATA
193 CTCTTGATAAATAATGTTGCATCCTAGTAAAATTGAAAATAAAATCAATTTTTTAATATGATACA
16602105 CTCT
258 CTCT
*
16602109 TAGAGAATATATATTATGTAACGGCAAGGTGAGGTGGCCCCACGCTGTGGAAGTTGCTTTTGCTG
1 TAGAGAATATATATTATGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
16602174 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTGCTAG
66 TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTGC-AG
* * * * *
16602239 TTTTTCAAATCTCTATAA-AGTTAATGAGATTTAAGAAGTTTTGTTTCATTACTTCAGAGTTATA
130 TTTATCAAATCTCTATAAGA-TTAATGAGATTTAAGGAGTTTCGTTTCACTATTTCA-AGTTATA
* *
16602303 CTCTTGATAAAATAATATTGCATCCCA-TAAAATT--AAA-AAAATCAATTTTTTAATATGATAC
193 CTCTTGAT-AAATAATGTTGCATCCTAGTAAAATTGAAAATAAAATCAATTTTTTAATATGATAC
16602364 ACTCT
257 ACTCT
16602369 T
1 T
16602370 TGTGAAAGTT
Statistics
Matches: 451, Mismatches: 56, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
259 7 0.02
260 40 0.09
261 163 0.36
262 156 0.35
263 83 0.18
264 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (261 bp):
TAGAGAATATATATTATGTAACGGCAAGGTGAGGTGGCCCCACGTTGTGGAAGTTGCTTTTGCTG
TGCGGGAAAAGTACGCAGTGTATAATAATTGGTTGAACTATCTTATGTTATTTATCGCCTGCAGT
TTATCAAATCTCTATAAGATTAATGAGATTTAAGGAGTTTCGTTTCACTATTTCAAGTTATACTC
TTGATAAATAATGTTGCATCCTAGTAAAATTGAAAATAAAATCAATTTTTTAATATGATACACTC
T
Found at i:16603377 original size:64 final size:63
Alignment explanation
Indices: 16603274--16603402 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 63
16603264 TTATCAAACT
*
16603274 CTCAACTTTTGTCAGTTCTAATCCTTACAATAGTACCAATGTTACTACTTTTCTCATTCATTAG
1 CTCAACTTTTGTCACTTCTAATCCTTACAATAGTACCAATGTTACTAC-TTTCTCATTCATTAG
* *
16603338 CTCAACTTTTGTCACTTGTAATCCTTACAATAGTGCCAATGTTACTACTTTCTCATTCATTAG
1 CTCAACTTTTGTCACTTCTAATCCTTACAATAGTACCAATGTTACTACTTTCTCATTCATTAG
16603401 CT
1 CT
16603403 TTCTGCATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 17 0.27
64 45 0.73
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.42
Consensus pattern (63 bp):
CTCAACTTTTGTCACTTCTAATCCTTACAATAGTACCAATGTTACTACTTTCTCATTCATTAG
Found at i:16605615 original size:27 final size:27
Alignment explanation
Indices: 16605563--16605615 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
16605553 ACCACTAAAA
*
16605563 ATAATAGAAAATATAAATTTTAAAATT
1 ATAATAGAAAATATAAATTATAAAATT
* *
16605590 ATAATATATAATA-AAATTATATAAAT
1 ATAATAGAAAATATAAATTATA-AAAT
16605616 AATTTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
ATAATAGAAAATATAAATTATAAAATT
Found at i:16608152 original size:22 final size:22
Alignment explanation
Indices: 16608127--16608179 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
16608117 GGTAAAGACA
* *
16608127 GTAAATGAGGAGGAAAAAAAGG
1 GTAAATGAGAAAGAAAAAAAGG
*
16608149 GT-AATGAGAAAGAAAAGAAGG
1 GTAAATGAGAAAGAAAAAAAGG
*
16608170 GGAATATGAG
1 GTAA-ATGAG
16608180 TGCCTGCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 17 0.68
22 3 0.12
23 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.36, T:0.11
Consensus pattern (22 bp):
GTAAATGAGAAAGAAAAAAAGG
Found at i:16608154 original size:21 final size:21
Alignment explanation
Indices: 16608130--16608170 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16608120 AAAGACAGTA
* *
16608130 AATGAGGAGGAAAAAAAGGGT
1 AATGAGAAAGAAAAAAAGGGT
*
16608151 AATGAGAAAGAAAAGAAGGG
1 AATGAGAAAGAAAAAAAGGG
16608171 GAATATGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (21 bp):
AATGAGAAAGAAAAAAAGGGT
Found at i:16608779 original size:275 final size:269
Alignment explanation
Indices: 16608285--16608833 Score: 814
Period size: 275 Copynumber: 2.0 Consensus size: 269
16608275 AGTATAATAA
* *
16608285 AAATATGTGAGACCCATTATAATAAGAATATATACAATATTTGTCCTGTTAATGTATTTATTAGA
1 AAATATGTGAGACCCATTATAATAAGAATATATACAATATTTATCCTGTTAATGTACTTATTAGA
* *
16608350 TTAAAAATACTTTTTAAAAAAATTAATTTTAATTATAAATTAATAAATATATGTGTGACCCAAAT
66 TTAAAAATACTTTTTAAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGACCCAAAT
* * * * * *
16608415 TCTTATTAAATAAAATAAGACATTGTCTGCAAGTTAAGTTAAATAAAATATATTTTCTTTCTAGA
131 ACTTATTAAATAAAATAAGACATTATCTGCAAATCAAGTTAAACAAAATATATTTTCTTTCTAAA
* **
16608480 AGATTTAGTATTTATTAGTATAATATATTTTGCATTTATTAGCATAATTTATTTGACCTATGAAT
196 AGATTTAGTATTTATTAATATAATATATTTTGCATTTATTAGCATAATTTATTTGACCTACAAAT
16608545 TTAATCTAT
261 TTAATCTAT
*
16608554 AAATATGTGAGACCCATTATAATAAGAATATATATATGTAATATTTAT-CTAGTTAATGTACTTA
1 AAATATGTGAGACCCATTATAATAAG-A-ATATATA--CAATATTTATCCT-GTTAATGTACTTA
* *
16608618 TTAGATTAAAAAAATATTTTTTTAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGA
61 TTAGATT--AAAAATACTTTTTAAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGA
* * *
16608683 CTCAAATACTTATTAAATAAAATAAGAGATTATTTGCAAATCAAGTTAAACAAAATATATTTTCT
124 CCCAAATACTTATTAAATAAAATAAGACATTATCTGCAAATCAAGTTAAACAAAATATATTTTCT
* *
16608748 TTCTAAAAGATTTAGT-TTATATTAATATAATATATTTTGTATTTATTAGTATAATTTATTTGAC
189 TTCTAAAAGATTTAGTATT-TATTAATATAATATATTTTGCATTTATTAGCATAATTTATTTGAC
*
16608812 CTACAAATTTAGTCTAT
253 CTACAAATTTAATCTAT
16608829 AAATA
1 AAATA
16608834 GACACTTTTA
Statistics
Matches: 250, Mismatches: 22, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
269 26 0.10
270 1 0.00
271 7 0.03
272 2 0.01
273 27 0.11
274 2 0.01
275 185 0.74
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (269 bp):
AAATATGTGAGACCCATTATAATAAGAATATATACAATATTTATCCTGTTAATGTACTTATTAGA
TTAAAAATACTTTTTAAAAAAATTAAATTAAATTATAAATTAATAAATATATGTGTGACCCAAAT
ACTTATTAAATAAAATAAGACATTATCTGCAAATCAAGTTAAACAAAATATATTTTCTTTCTAAA
AGATTTAGTATTTATTAATATAATATATTTTGCATTTATTAGCATAATTTATTTGACCTACAAAT
TTAATCTAT
Found at i:16611212 original size:6 final size:6
Alignment explanation
Indices: 16611201--16611227 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16611191 GTATTGCATA
16611201 TCCGTG TCCGTG TCCGTG TCCGTG TCC
1 TCCGTG TCCGTG TCCGTG TCCGTG TCC
16611228 ATGCTTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.37, G:0.30, T:0.33
Consensus pattern (6 bp):
TCCGTG
Found at i:16615040 original size:13 final size:12
Alignment explanation
Indices: 16615016--16615058 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
16615006 TTAAAAATTA
16615016 AAAAATAGAAAAT
1 AAAAA-AGAAAAT
16615029 AAAAAAGTAAAAT
1 AAAAAAG-AAAAT
* *
16615042 TAAAAAGAAAAG
1 AAAAAAGAAAAT
16615054 AAAAA
1 AAAAA
16615059 GGAATTCTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAGAAAAT
Found at i:16615753 original size:11 final size:11
Alignment explanation
Indices: 16615739--16615786 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
16615729 ATTGCTGTTA
16615739 TGTTGCTATTT
1 TGTTGCTATTT
*
16615750 TGTTGCTATTA
1 TGTTGCTATTT
*
16615761 TGTTGCTCTTT
1 TGTTGCTATTT
** *
16615772 TACTACTATTT
1 TGTTGCTATTT
16615783 TGTT
1 TGTT
16615787 ATTATATTGC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (11 bp):
TGTTGCTATTT
Found at i:16615756 original size:22 final size:22
Alignment explanation
Indices: 16615730--16615772 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16615720 TTGTTGTTTA
*
16615730 TTGCTGTTATGTTGCTATTTTG
1 TTGCTATTATGTTGCTATTTTG
*
16615752 TTGCTATTATGTTGCTCTTTT
1 TTGCTATTATGTTGCTATTTT
16615773 ACTACTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.12, G:0.19, T:0.60
Consensus pattern (22 bp):
TTGCTATTATGTTGCTATTTTG
Found at i:16615780 original size:22 final size:22
Alignment explanation
Indices: 16615736--16615786 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
16615726 TTTATTGCTG
** *
16615736 TTATGTTGCTATTTTGTTGCTA
1 TTATGTTGCTATTTTACTACTA
*
16615758 TTATGTTGCTCTTTTACTACTA
1 TTATGTTGCTATTTTACTACTA
*
16615780 TTTTGTT
1 TTATGTT
16615787 ATTATATTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.61
Consensus pattern (22 bp):
TTATGTTGCTATTTTACTACTA
Found at i:16620525 original size:37 final size:37
Alignment explanation
Indices: 16620474--16620566 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
16620464 TACACAAGTT
* ** *
16620474 ATCCAACCGA-AACACGCTAGTTGCTCATAAGGGCTA
1 ATCCAACCGATAACACGCCAAATGCTCATAAGAGCTA
*
16620510 ATCCACCCGATAACACGCCAAATGCTCATAAGAGCTA
1 ATCCAACCGATAACACGCCAAATGCTCATAAGAGCTA
* *
16620547 ATCCATCCGATAACATGCCA
1 ATCCAACCGATAACACGCCA
16620567 GATCAAGATA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 9 0.18
37 40 0.82
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.18
Consensus pattern (37 bp):
ATCCAACCGATAACACGCCAAATGCTCATAAGAGCTA
Found at i:16624748 original size:27 final size:27
Alignment explanation
Indices: 16624718--16624781 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
16624708 CATTACCAAA
16624718 TTTGCCACGAA-GGCTTCCATCTCTTAG
1 TTTGCCAC-AAGGGCTTCCATCTCTTAG
* * *
16624745 TTTGCCACAAGGGCTTCTATTTTTTAG
1 TTTGCCACAAGGGCTTCCATCTCTTAG
*
16624772 ATTGCCACAA
1 TTTGCCACAA
16624782 ATAATTCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TTTGCCACAAGGGCTTCCATCTCTTAG
Found at i:16624869 original size:27 final size:26
Alignment explanation
Indices: 16624803--16624893 Score: 112
Period size: 26 Copynumber: 3.5 Consensus size: 26
16624793 TTTGAGATCC
* * **
16624803 CTACAAAGGCTTTCATTTTAAATACA
1 CTACAAAGGCTTCCATTTCAAATATG
16624829 CTACAAAGGCTTCCATTTCATAA-ATGG
1 CTACAAAGGCTTCCATTTCA-AATAT-G
*
16624856 CTACAAAGGTTTCCATTTCAAATATG
1 CTACAAAGGCTTCCATTTCAAATATG
16624882 CTACAAAGGCTT
1 CTACAAAGGCTT
16624894 TTATTTCTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 33 0.59
27 23 0.41
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
CTACAAAGGCTTCCATTTCAAATATG
Found at i:16625072 original size:23 final size:23
Alignment explanation
Indices: 16625040--16625092 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
16625030 ACCCACCAGT
*
16625040 CATGGTCTTAAAGGATATAGTGC
1 CATGGCCTTAAAGGATATAGTGC
* * *
16625063 CATGGCCTTACATGATATGGTGC
1 CATGGCCTTAAAGGATATAGTGC
16625086 CATGGCC
1 CATGGCC
16625093 ATGGGCTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (23 bp):
CATGGCCTTAAAGGATATAGTGC
Found at i:16629650 original size:37 final size:37
Alignment explanation
Indices: 16629609--16629694 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
16629599 GAGAATGAGA
* *
16629609 ACAACATGCTTTTCAAATCAGTAATAAACATAGCCAT
1 ACAACATGCTTTTCAAATCAGTAATAAAAATAACCAT
*
16629646 ACAACATGCTTTTCAAATTAGTAATAAAAATAACCAT
1 ACAACATGCTTTTCAAATCAGTAATAAAAATAACCAT
16629683 ACAACATGCTTT
1 ACAACATGCTTT
16629695 CACAAAGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (37 bp):
ACAACATGCTTTTCAAATCAGTAATAAAAATAACCAT
Found at i:16640308 original size:44 final size:43
Alignment explanation
Indices: 16640211--16640332 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 43
16640201 ACTTGATGCG
* * * *
16640211 ATCTGCTCTACTGCAACATCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATGACTTTA
* * *
16640255 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGA-TTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-GACTTT-A
* *
16640299 ATCTGCTCCACTGTAACTTCAAGGAGATAAGATT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
16640333 TGCCCTCTTC
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 6 0.09
44 58 0.91
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATGACTTTA
Found at i:16640475 original size:128 final size:128
Alignment explanation
Indices: 16640323--16641961 Score: 2391
Period size: 128 Copynumber: 12.8 Consensus size: 128
16640313 AACTTCAAGG
* * * * *
16640323 AGATAAGATTTGCCCTCTTCGATCTGCTCCGCTACTGTTTAGGGAGACAAGAGCTATAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
*
16640388 ACCTATTCCACTGCTGAGCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
*
16640451 AGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * * **
16640516 ACCTACTCCACTGCTGGCTAGGGATATTGGACTTGTGGCTTAAATCTATTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * * *
16640579 AGATAAGATTTGACG-CTTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTTC
1 AGATAAGATTCGCCGTC-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCC
* * ** * *
16640643 AACCTATTCCACTACTGACTAGGGACGTAGGACTTGTGGCTTGAATCTGCTTCCTTACATTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * *
16640707 AGATAAGATTCGCCGTCTTCAATCTGCTCCGCTATTGTTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* *
16640772 ACCTACTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* *
16640835 AGATAAGATTCGCCGTCTTCGATCTACTCCGCTACTGCTTAGGAAGACAAGATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * *
16640900 ACCTACTCCACCGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * * *
16640963 AGATAAGATTCGCCGTCTTAGATCTGTTCCGCTACTGCTTAGAGAGACAAGATCTATAATATCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* *
16641028 ACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATTTGCTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * * *
16641091 AGATAAGATTCGCCGTCTTCAATCTGCTCTGCTACTACTTAGGGAGACAATATCTGTAATTTTCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * * * * *
16641156 ACTTACTCCACTACTGGCTAGGGATATAGGATTTGTGGCTTAAATCTGTTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * * *
16641219 AGATAAGATTTGCCG-CTTTTGATCTGCTCCGCTACTGGTTAGGGAGACAAGATCTATAATTTTC
1 AGATAAGATTCGCCGTC-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCC
* * * * *
16641283 AACCTATTCCACTACTGACTAGGGACATAGGACTTGTGGCTTGAATCTGCTTCCTTACATTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * *
16641347 AAATAACATTCGCCGTCTTCAATCTGCTCCGCTACTGTTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * *
16641412 ACCTACTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATTTGCTTCCTTACAATTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* *
16641475 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTCTAATTTCAA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* *
16641540 ACCTATTCCACTACTGACTAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * **
16641603 AGATAAGATTCGCCATCTTCAATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAATTTCCC
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CC
* *
16641668 AACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATTTGCTTCCTTACACTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * **
16641732 AGATAAGATTCGCCATCTTCAATCTGCTCTACTACTGCTTAGGGAGACAAGATCTGTAATTTCCC
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CC
16641797 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * * *
16641861 AGATAAGATTTGCCATCTTCGATCTGCTCCGCTACTACTTAGGGAGGCAAGATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * *
16641926 ACCTACTCCATTGCTGACTAGGGAGATAGGACTTGT
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGT
16641962 AATCTTCAAC
Statistics
Matches: 1364, Mismatches: 142, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
127 2 0.00
128 1116 0.82
129 246 0.18
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (128 bp):
AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
Found at i:16641993 original size:44 final size:44
Alignment explanation
Indices: 16641915--16642043 Score: 154
Period size: 44 Copynumber: 2.9 Consensus size: 44
16641905 AGGCAAGATC
* * * *
16641915 TGTAAT-TTCCAACCTACTCCATTGCT-GACTAGGGAGATAGGACT
1 TGTAATCTT-CAACCTATTCCACTGCTGGTC-AGGGAGCTAGGACT
* **
16641959 TGTAATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAAGTTT
1 TGTAATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGGACT
*
16642003 TGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGG
1 TGTAATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGG
16642044 TTTTGTGGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 70 0.95
45 4 0.05
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (44 bp):
TGTAATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGGACT
Found at i:16642047 original size:44 final size:44
Alignment explanation
Indices: 16641962--16642048 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
16641952 TAGGACTTGT
16641962 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAAGTTTTGC
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAAGTTTTGC
*
16642006 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGGTTTTG
1 AATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAAGTTTTG
16642049 TGGTTTCACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAAGTTTTGC
Found at i:16644181 original size:6 final size:6
Alignment explanation
Indices: 16644172--16644283 Score: 87
Period size: 6 Copynumber: 19.7 Consensus size: 6
16644162 TTTTTCTCCT
*
16644172 TTTTGA TTTTGA TTTTGA TTTTGA --TTGA TTTTGA -TTT-- TTTTGC
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* * * * * *
16644215 TTTTGC TTTTGA CTTTGA TTTTTA TTTTTA -TTT-- TTTTGTT TTTTGCT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTG-A TTTTG-A
16644262 TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTT
16644284 TTTTATTGAA
Statistics
Matches: 91, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
4 10 0.11
5 6 0.07
6 64 0.70
7 11 0.12
ACGTcount: A:0.12, C:0.04, G:0.13, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:16644219 original size:31 final size:32
Alignment explanation
Indices: 16644178--16644243 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
16644168 TCCTTTTTGA
16644178 TTTTGATTTTGATTTTGA-TTGATTTTGATTT
1 TTTTGATTTTGATTTTGACTTGATTTTGATTT
* * *
16644209 TTTTGCTTTTGCTTTTGACTTTGATTTTTATTT
1 TTTTGATTTTGATTTTGAC-TTGATTTTGATTT
16644242 TT
1 TT
16644244 ATTTTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 16 0.53
33 14 0.47
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.70
Consensus pattern (32 bp):
TTTTGATTTTGATTTTGACTTGATTTTGATTT
Found at i:16645573 original size:37 final size:38
Alignment explanation
Indices: 16645520--16645593 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
16645510 CAATTAAAAA
*
16645520 TGTAAAAAGATATATATATATATATAAAAATA-AAGTG
1 TGTAAAAAGATATATATACATATATAAAAATACAAGTG
* * *
16645557 TGTAAACAGATGTATATACATATATAAATATACAAGT
1 TGTAAAAAGATATATATACATATATAAAAATACAAGT
16645594 ATATGTATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (38 bp):
TGTAAAAAGATATATATACATATATAAAAATACAAGTG
Found at i:16645991 original size:3 final size:3
Alignment explanation
Indices: 16645983--16646016 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
16645973 ACAATGAAAC
*
16645983 TAA TAA TAA TTAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
16646017 CACTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16647773 original size:41 final size:43
Alignment explanation
Indices: 16647659--16647774 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 43
16647649 ATGCGATCTG
** *
16647659 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATTCG
1 CTCTACTGCAACTTCAGAGAGATAAGATCTA-TACTGCAATTCA
* * ** * *
16647703 CTCCACTACTGCTT-AGGGAGATAAGATCTA-A-TGCGATTCA
1 CTCTACTGCAACTTCAGAGAGATAAGATCTATACTGCAATTCA
16647743 CTCTACTGCAACTTCAGAGAGATAAGATCTAT
1 CTCTACTGCAACTTCAGAGAGATAAGATCTAT
16647775 TACTTTAATC
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
40 15 0.27
41 16 0.29
43 15 0.27
44 10 0.18
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (43 bp):
CTCTACTGCAACTTCAGAGAGATAAGATCTATACTGCAATTCA
Found at i:16647809 original size:44 final size:44
Alignment explanation
Indices: 16647654--16647832 Score: 149
Period size: 44 Copynumber: 4.2 Consensus size: 44
16647644 ACTTGATGCG
* *
16647654 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTA
** * * * * *
16647698 AT-TCGCTCCACTACTGCTT-AGGGAGATAAGATCTAATGCGATTC
1 ATCT-GCTCCACTACAACTTCAGAGAGATAAGATCTATTAC-TTTA
*
16647742 A-CT-CT--ACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTA
* * *
16647782 ATCTGCTCCACTACAACTTCA-AGGAGATAGGAT-TATCGACTTCA
1 ATCTGCTCCACTACAACTTCAGA-GAGATAAGATCTAT-TACTTTA
16647826 ATCTGCT
1 ATCTGCT
16647833 TCCTTACACT
Statistics
Matches: 104, Mismatches: 21, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
40 10 0.10
41 19 0.18
42 4 0.04
43 22 0.21
44 49 0.47
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTA
Found at i:16648229 original size:129 final size:129
Alignment explanation
Indices: 16647825--16649060 Score: 1925
Period size: 129 Copynumber: 9.6 Consensus size: 129
16647815 TATCGACTTC
*
16647825 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTT-GATGTGCTCCGCTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCG-CTTTCGATCTGCTCCGCTACTGCTTAGG
* *
16647889 GAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTAACCAGGGACATAGGACTTGTGGCTTA
65 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * * *
16647953 AATCTGATTCCTTACACTTGAAGATAAGATTCGCTG-TCTCCGATATGCTCCGCTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCT-TTCGATCTGCTCCGCTACTGCTTAGG
* ** * *
16648017 GAGACCAA-ATCTATAATTT-CCAACCTATTCCACTATTAACCAGGGAGATAGGACTTGTGGCTT
65 GAGA-CAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTT
16648080 A
129 A
* *
16648081 AATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGCTTTCGATCTGCTCTGCTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGG
* *
16648146 AGACAAGTTCTGTAATTTCCCAACCTATTCCAGTGCTGACCAGGGATATAGGACTTGTGGCTTA
66 AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* *
16648210 AATCTGCTTCCTTAGACTTGAAGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGG
*
16648275 AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGTGATATAGGACTTGTGGCTTA
66 AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* *
16648339 AATCTTCTTCCTTACACTTGAAGATAAGATTTC-CCG-TCTTCGATCTGCTCCGCTATTGCTTAG
1 AATCTGCTTCCTTACACTTGAAGATAAGA-TTCGCCGCT-TTCGATCTGCTCCGCTACTGCTTAG
16648402 GGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTT
64 GGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTT
16648467 A
129 A
* * *
16648468 AATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGCTTTCGATCTACTCTGCTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGG
* * * *
16648533 AGATAAGATCTGTAATTTCCCAACTTATTCCACTGCTGACCAGTGATATAGGGCTTGTGGCTTA
66 AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
*
16648597 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCG-TCTTCGATCTGCTCCGCTATTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCT-TTCGATCTGCTCCGCTACTGCTTAGG
* * *
16648661 GAGACAAGCTCTGTAATTTCCCAACCTATTTCACTGCTGACCAGGGATATAGGACTTGTGGTTTA
65 GAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * *
16648726 AATCTGCTTCCTTACACTTGAAGATAAGATTCACCGCTTTCGATTTCCTCCGCTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGG
* *
16648791 AGACAAGATCTGTAATTTCACAACCTATTCCACTGCTGACTAGGGATATAGGACTTGTGGCTTA
66 AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
* * * * *
16648855 AATCTGTTTCCTTACACTTGAAGATAAGATTTGTCGCTTTCGATCTACTCCGCTACTGCTTAAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGG
**
16648920 AGACAAGATCTGTAATTTCCCAACCTATTCCACTTTTGACCAGGGATATA-GAGCTTGTGGCTTA
66 AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGA-CTTGTGGCTTA
*
16648984 AATATGCTTCCTTACACTTGAAGATAAGATTCGCCG-TATTCGATCTGCTCCGCTACTGCTTAGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCT-TTCGATCTGCTCCGCTACTGCTTAGG
16649048 GAGACAAGATCTG
65 GAGACAAGATCTG
16649061 CTATATTCAC
Statistics
Matches: 1017, Mismatches: 77, Indels: 27
0.91 0.07 0.02
Matches are distributed among these distances:
126 1 0.00
127 4 0.00
128 188 0.18
129 820 0.81
130 4 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (129 bp):
AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGG
AGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTA
Found at i:16650848 original size:129 final size:129
Alignment explanation
Indices: 16650613--16651115 Score: 787
Period size: 129 Copynumber: 3.9 Consensus size: 129
16650603 TGATGAATAG
* *
16650613 TATTCCACTGCTGACCAGTGATATAGGGCTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATA
1 TATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATA
* *
16650678 AGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACC
66 AGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACC
* *
16650742 TATTTCACTGCTGACCAGGGATATAGGACTTGTGGTTTAAATCTGCTTCCTTACACTTGAAGATA
1 TATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATA
* * * *
16650807 AGATTCACCGCT-TTCGATTTCCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCACAACC
66 AGATTCGCCG-TATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACC
* *
16650871 TATTCCACTGCTGACTAGGGATATAGGACTTGTGGCTTAAATCTGTTTCCTTACACTTGAAGATA
1 TATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATA
* * * *
16650936 AGATTTGTCGCT-TTCGATCTACTCCGCTACTGCTTAAGGAGACAAGATCTGTAATTTCCCAACC
66 AGATTCGCCG-TATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACC
** *
16651000 TATTCCACTTTTGACCAGGGATATA-GAGCTTGTGGCTTAAATATGCTTCCTTACACTTGAAGAT
1 TATTCCACTGCTGACCAGGGATATAGGA-CTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGAT
16651064 AAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTG
65 AAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTG
16651116 CTATATTCAC
Statistics
Matches: 342, Mismatches: 29, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
128 3 0.01
129 338 0.99
130 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (129 bp):
TATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATA
AGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACC
Found at i:16653268 original size:22 final size:23
Alignment explanation
Indices: 16653213--16653268 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
16653203 TTTTCCTTCT
* *
16653213 TTTTTCATTTTTGATTTGGATGAC
1 TTTTTC-TTTTTGACTTGGATCAC
*
16653237 TTTTT-ATTTTGACTTGGATCA-
1 TTTTTCTTTTTGACTTGGATCAC
16653258 TTTTTCTTTTT
1 TTTTTCTTTTT
16653269 TTTTTTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
24 5 0.19
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.64
Consensus pattern (23 bp):
TTTTTCTTTTTGACTTGGATCAC
Found at i:16657884 original size:3 final size:3
Alignment explanation
Indices: 16657862--16657907 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
16657852 AAGATGAAAC
* *
16657862 TAA TAA TGAT TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16657908 CACTAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:16677100 original size:80 final size:80
Alignment explanation
Indices: 16676967--16677126 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
16676957 AGTCTTTGAT
16676967 GGAGTTCTCGATAATAGTATGGTGGAACAAACCGTTTTCGCAAGATGCGCTTCATTTCAACCCAA
1 GGAGTTCTCGATAATAGTATGGTGGAACAAACCGTTTTCGCAAGATGCGCTTCATTTCAACCCAA
*
16677032 GTAGTAACAGGTTGC
66 ATAGTAACAGGTTGC
*
16677047 GGAGTTCTCGATAATAGTATGGTGGAACAAACCGTTTTCGTAAGATGCGCTTCATTTCAACCCAA
1 GGAGTTCTCGATAATAGTATGGTGGAACAAACCGTTTTCGCAAGATGCGCTTCATTTCAACCCAA
16677112 ATAGTAACAGGTTGC
66 ATAGTAACAGGTTGC
16677127 TCTCGATAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (80 bp):
GGAGTTCTCGATAATAGTATGGTGGAACAAACCGTTTTCGCAAGATGCGCTTCATTTCAACCCAA
ATAGTAACAGGTTGC
Found at i:16681468 original size:46 final size:46
Alignment explanation
Indices: 16681416--16681505 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
16681406 ATAAAAGACA
16681416 TCGACCCACTATC-AGGAATGATAGGAACCTTGGTATATGATGAACC
1 TCGACCCACTATCAAGG-ATGATAGGAACCTTGGTATATGATGAACC
16681462 TCGACCCACTATCAAGGATGATAGGAACCTTGGTATATGATGAA
1 TCGACCCACTATCAAGGATGATAGGAACCTTGGTATATGATGAA
16681506 TGCCACACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 40 0.93
47 3 0.07
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (46 bp):
TCGACCCACTATCAAGGATGATAGGAACCTTGGTATATGATGAACC
Found at i:16685682 original size:27 final size:27
Alignment explanation
Indices: 16685642--16685710 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
16685632 TTTAAGAGAT
* *
16685642 CGCCATAAATGCTTTCATTTCATGATT-
1 CGCCACAAAGGCTTTCATTTCAT-ATTA
*
16685669 TGCCACAAAGGCTTTCATTTCATATTA
1 CGCCACAAAGGCTTTCATTTCATATTA
*
16685696 CGTCACAAAGGCTTT
1 CGCCACAAAGGCTTT
16685711 TTTTCTCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (27 bp):
CGCCACAAAGGCTTTCATTTCATATTA
Found at i:16688606 original size:10 final size:10
Alignment explanation
Indices: 16688591--16688628 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
16688581 AGCTGCTGCC
16688591 AGAAAAAGAG
1 AGAAAAAGAG
16688601 AGAAAAAGAG
1 AGAAAAAGAG
*
16688611 AGAAAGAGAAG
1 AGAAAAAG-AG
16688622 AGAAAAA
1 AGAAAAA
16688629 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAG
Found at i:16688850 original size:39 final size:38
Alignment explanation
Indices: 16688788--16688921 Score: 119
Period size: 39 Copynumber: 3.2 Consensus size: 38
16688778 TAGATGTTAC
*
16688788 TTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGG
1 TTAGTATTATT-TTAGT--AAAACTAATATTATTGTTATGG
16688829 TTAGTTATTATTTTAGTAAAACCCTAATTATTATTGTTA--G
1 TTAG-TATTATTTTAGTAAAA--CTAA-TATTATTGTTATGG
*
16688869 TTAGTATTATTTTGAGTATAAAACTATTATTATTGTTATTGTG
1 TTAGTATTATTTT-AG--TAAAACTAATATTATTGTTA-TG-G
16688912 TTAGTTATTA
1 TTAG-TATTA
16688922 AGATTAGTGG
Statistics
Matches: 79, Mismatches: 2, Indels: 21
0.77 0.02 0.21
Matches are distributed among these distances:
39 24 0.30
40 10 0.13
41 13 0.16
42 22 0.28
43 5 0.06
44 5 0.06
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.51
Consensus pattern (38 bp):
TTAGTATTATTTTAGTAAAACTAATATTATTGTTATGG
Found at i:16691673 original size:95 final size:94
Alignment explanation
Indices: 16691486--16691674 Score: 242
Period size: 95 Copynumber: 2.0 Consensus size: 94
16691476 CTTTTTTCTA
*
16691486 AAAAAATTTAGTAAAAAACTCTTATTTCGGCCATTTGTTCGTATTTTTCTCGAATTTTATTACTT
1 AAAAAATTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTCTCGAATTTTATTACTT
* *
16691551 TCAATAAAAATATATTATTTTTGAATTTTT
66 T-AATAAAAATATATAATTTCTGAATTTTT
* * *
16691581 AAAAAATTTAGTAAAAGAC-CTTTACTTCGGCCCTTTGTTCGTATTTTTTTCTTCGCATTTTATT
1 AAAAAATTTAGTAAAAAACTC-TTACTTCGGCCATTTGTTCGTA--TTTTTC-TCGAATTTTATT
16691645 ACTTT-A-AAAAATATCATAATTTCT-AATTTT
62 ACTTTAATAAAAATAT-ATAATTTCTGAATTTT
16691675 ATAATTTTAC
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
94 1 0.01
95 52 0.63
96 8 0.10
97 6 0.07
98 16 0.19
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (94 bp):
AAAAAATTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTCTCGAATTTTATTACTT
TAATAAAAATATATAATTTCTGAATTTTT
Found at i:16691782 original size:157 final size:152
Alignment explanation
Indices: 16691576--16692051 Score: 518
Period size: 159 Copynumber: 3.1 Consensus size: 152
16691566 TATTTTTGAA
* * *
16691576 TTTTTAAA-AAATTTAGTAAAAGACCTTTACTTCGGCCCTTTGTTCGTATTTTTTTCTTCGCATT
1 TTTTTAAATAACTTTAGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTTC-TCGCATT
* *
16691640 TTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTGTGT
65 TTATTACTTTAAAAAATATCATAATTTCTAATTTTATTATTTTACATTATTTCAGTACATT-TGT
16691705 TTGAAATTTATTAATTTAGTGTGT
129 TTGAAATTTATTAATTTAGTGTGT
* * *
16691729 TTTTTAAATTAA-TTTAGTGTAAAAAAACCCTTA-TTCCTGCCCTTTGCTCGTATTATTTTCTCG
1 TTTTTAAA-TAACTTTA--GT-AAAAAACCCTTACTT-CGGCCCTTTGTTCGTATTTTTTTCTCG
* * * * *
16691792 AATTTTATTACTTTCAATAAAAATAT-ATTATTTTTGTATTTTATTATTTTATATTATTTCAGTA
61 CATTTTATTACTTT--A-AAAAATATCATAATTTCT-AATTTTATTATTTTACATTATTTCAGTA
* * * *
16691856 CATTTTTTTGAAATATTTGTATTAA-TTATTTCTGAA
122 CATTTGTTTG-AA-A-TT-TATTAATTTA-GTGTG-T
* * * * * *
16691892 TTTTTAAA-AACTTTAGTAAAACACTCTTACTTCGGCCATTAGTTCGTATTTTTTTC-CAC-GTT
1 TTTTTAAATAACTTTAGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCGCATTT
*
16691954 TATTACTTTAAAAAATATCATAATTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTT
66 TATTACTTTAAAAAATATCATAATTTCTAATTTTATTATTTTACATTATTTCAGTACATT-TGTT
16692019 TGAAATTTATTAATTTAGTGTGT
130 TGAAATTTATTAATTTAGTGTGT
16692042 TTTTTAAATA
1 TTTTTAAATA
16692052 TACCATTTTT
Statistics
Matches: 266, Mismatches: 35, Indels: 46
0.77 0.10 0.13
Matches are distributed among these distances:
150 8 0.03
151 10 0.04
152 5 0.02
153 9 0.03
154 43 0.16
155 15 0.06
156 20 0.08
157 42 0.16
158 14 0.05
159 67 0.25
160 5 0.02
161 7 0.03
162 13 0.05
163 8 0.03
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (152 bp):
TTTTTAAATAACTTTAGTAAAAAACCCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCGCATTT
TATTACTTTAAAAAATATCATAATTTCTAATTTTATTATTTTACATTATTTCAGTACATTTGTTT
GAAATTTATTAATTTAGTGTGT
Found at i:16692353 original size:38 final size:37
Alignment explanation
Indices: 16692303--16692446 Score: 108
Period size: 38 Copynumber: 4.0 Consensus size: 37
16692293 CTTATCTTTT
16692303 TTTCTTTCTTTTTCCTTCCTTCCCTCTTCTTCTTCTTC
1 TTTCTTTCTTTTTCCTTCC-TCCCTCTTCTTCTTCTTC
* *
16692341 TTTCTTTTTTTTTTCTT-CT-CCT-TTC--CTT-TTC
1 TTTCTTTCTTTTTCCTTCCTCCCTCTTCTTCTTCTTC
* * *
16692372 TTTCCTTC--TTTCCTCTCCTCTCCTTTTCTTTCTTTTTC
1 TTTCTTTCTTTTTCCT-TCCTC-CCTCTTC-TTCTTCTTC
* * *
16692410 TTTCTTTCTTTCTCCTTCTTTCCCTCTCCTTC-TCTTC
1 TTTCTTTCTTTTTCCTTC-CTCCCTCTTCTTCTTCTTC
16692447 CCCCCACCCA
Statistics
Matches: 83, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
29 5 0.06
30 1 0.01
31 11 0.13
32 3 0.04
33 3 0.04
34 6 0.07
35 3 0.04
36 1 0.01
37 8 0.10
38 28 0.34
39 7 0.08
40 7 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (37 bp):
TTTCTTTCTTTTTCCTTCCTCCCTCTTCTTCTTCTTC
Found at i:16692358 original size:21 final size:21
Alignment explanation
Indices: 16692327--16692381 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
16692317 CTTCCTTCCC
*
16692327 TCTTCTTCTTCTTCTTTCTTTT
1 TCTT-TTCTTCTTCTTTCCTTT
* *
16692349 TTTTTTCTTCTCCTTTCCTTT
1 TCTTTTCTTCTTCTTTCCTTT
*
16692370 TCTTTCCTTCTT
1 TCTTTTCTTCTT
16692382 TCCTCTCCTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTCTTCTTCTTTCCTTT
Found at i:16692388 original size:28 final size:28
Alignment explanation
Indices: 16692352--16692440 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 28
16692342 TTCTTTTTTT
*
16692352 TTTCTTCTCCTTTCCTTTTCTTTCCTTC
1 TTTCCTCTCCTTTCCTTTTCTTTCCTTC
*
16692380 TTTCCTCTCCTCTCCTTTTCTTT-CTT-
1 TTTCCTCTCCTTTCCTTTTCTTTCCTTC
*
16692406 TTT-CT-TTCTTT-C-TTTC--TCCTTC
1 TTTCCTCTCCTTTCCTTTTCTTTCCTTC
16692428 TTTCCCTCTCCTT
1 TTT-CCTCTCCTT
16692441 CTCTTCCCCC
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.02
21 3 0.06
22 7 0.14
23 1 0.02
24 6 0.12
25 6 0.12
26 3 0.06
27 3 0.06
28 21 0.41
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTCCTCTCCTTTCCTTTTCTTTCCTTC
Found at i:16692415 original size:14 final size:14
Alignment explanation
Indices: 16692396--16692431 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16692386 CTCCTCTCCT
*
16692396 TTTCTTTCTTTTTC
1 TTTCTTTCTTTCTC
16692410 TTTCTTTCTTTCTC
1 TTTCTTTCTTTCTC
*
16692424 CTTCTTTC
1 TTTCTTTC
16692432 CCTCTCCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCTTTCTTTCTC
Found at i:16692437 original size:14 final size:15
Alignment explanation
Indices: 16692420--16692448 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16692410 TTTCTTTCTT
16692420 TCTCCTTCT-TTCCC
1 TCTCCTTCTCTTCCC
16692434 TCTCCTTCTCTTCCC
1 TCTCCTTCTCTTCCC
16692449 CCCACCCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (15 bp):
TCTCCTTCTCTTCCC
Found at i:16697015 original size:51 final size:51
Alignment explanation
Indices: 16696939--16697053 Score: 212
Period size: 51 Copynumber: 2.3 Consensus size: 51
16696929 ACTTCTGATC
*
16696939 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACA
*
16696990 AGTGACAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACA
16697041 AGTGACAAGTGAT
1 AGTGACAAGTGAT
16697054 TAATGTGATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACA
Found at i:16698580 original size:44 final size:43
Alignment explanation
Indices: 16698439--16698605 Score: 169
Period size: 43 Copynumber: 3.9 Consensus size: 43
16698429 AGTTTGTACA
* * *
16698439 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCAAATAAT-G
1 ATGCCAACGTCCCAAACATGGTCTTACACGTAATCATA-AATCG
* *
16698482 ATGCC-ACTGTCCCAAACAAGGTCTTACACGTAATCATATA-CG
1 ATGCCAAC-GTCCCAAACATGGTCTTACACGTAATCATAAATCG
* * * *
16698524 ATGCCAATGTCCCAGACATGGTCTTACACCTAAATCTTAAATCG
1 ATGCCAACGTCCCAAACATGGTCTTACACGT-AATCATAAATCG
* * **
16698568 ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCATA
1 ATGCCAACGTCCCAAACATGGTCTTACACGTAATCATA
16698606 TATCAGAATC
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 29 0.28
43 45 0.44
44 29 0.28
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAAACATGGTCTTACACGTAATCATAAATCG
Found at i:16699240 original size:15 final size:13
Alignment explanation
Indices: 16699212--16699238 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16699202 CACAAACTAT
16699212 AAAATTTTCACAC
1 AAAATTTTCACAC
16699225 AAAATTTTCACAC
1 AAAATTTTCACAC
16699238 A
1 A
16699239 CACAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:16708110 original size:21 final size:23
Alignment explanation
Indices: 16708084--16708125 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
16708074 TTATATCGGT
16708084 ATAAATGGATAC-A-ACAAATAA
1 ATAAATGGATACTACACAAATAA
*
16708105 ATAAATGTATACTACACAAAT
1 ATAAATGGATACTACACAAAT
16708126 TAGACACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (23 bp):
ATAAATGGATACTACACAAATAA
Found at i:16709849 original size:125 final size:125
Alignment explanation
Indices: 16709627--16710039 Score: 655
Period size: 125 Copynumber: 3.3 Consensus size: 125
16709617 ATTTATTAAG
* * *
16709627 GAAATCGCTCCCACGTGGACTCGTTTTTGATACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * * * *
16709692 GTTTCTAAGCAAAGAGTATAAAAAACGCTTCAAGCAGGATGTTTTATAAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
* *
16709752 GAAATCGCTCCCATGTGGACGCGCTTTTGCTACAGTAGGTCCTAAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
*
16709817 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
* *
16709877 GAAATCGCTCCCACGTGGACGCGATTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * *
16709942 GTTTTTGAGAAAATAGTATAAAAAACGCTTCAAGCAGGGTGCTTTATCAGAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
* * *
16710002 GAAATCACTCTCACGTGGACGTGCTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
16710040 CATGTTTGGG
Statistics
Matches: 265, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 265 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
Found at i:16711136 original size:49 final size:49
Alignment explanation
Indices: 16710995--16711112 Score: 227
Period size: 49 Copynumber: 2.4 Consensus size: 49
16710985 GAATATTAAT
*
16710995 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAAC
1 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAATTAAAC
16711044 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAATTAAAC
1 TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAATTAAAC
16711093 TATTTTGTATTTTATTACAT
1 TATTTTGTATTTTATTACAT
16711113 TAATATAAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (49 bp):
TATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAATTAAAC
Found at i:16711276 original size:21 final size:21
Alignment explanation
Indices: 16711235--16711292 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
16711225 CCAACTTCCA
* *
16711235 GCGGGGGTTGTGGTTGCTCCG
1 GCGGGGATTCTGGTTGCTCCG
16711256 GCGGGGATTCTGGTT-CATCCG
1 GCGGGGATTCTGGTTGC-TCCG
*
16711277 GTAGGGGA-TCTGGTTG
1 G-CGGGGATTCTGGTTG
16711293 TCAATGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 25 0.81
22 5 0.16
ACGTcount: A:0.07, C:0.17, G:0.47, T:0.29
Consensus pattern (21 bp):
GCGGGGATTCTGGTTGCTCCG
Found at i:16711559 original size:18 final size:18
Alignment explanation
Indices: 16711533--16711575 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16711523 GACTAAAAAA
* * *
16711533 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
16711551 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
16711569 AGGATAC
1 AGGATAC
16711576 GCACTTGGCA
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:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:16713445 original size:11 final size:12
Alignment explanation
Indices: 16713431--16713493 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 12
16713421 TTAAATATGG
16713431 ATTTGAGA-GAA
1 ATTTGAGAGGAA
*
16713442 ATTTGAAAGGAA
1 ATTTGAGAGGAA
16713454 A-TTGAGA--ACA
1 ATTTGAGAGGA-A
16713464 ATTTGAGAGGAA
1 ATTTGAGAGGAA
*
16713476 A-TTGAAAGGAA
1 ATTTGAGAGGAA
16713487 A-TTGAGA
1 ATTTGAGA
16713494 AAGGATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 1 0.02
10 2 0.05
11 33 0.77
12 6 0.14
13 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.27, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:16713458 original size:22 final size:22
Alignment explanation
Indices: 16713433--16713498 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
16713423 AAATATGGAT
16713433 TTGAGAGAAATTTGAAAGGAAA
1 TTGAGAGAAATTTGAAAGGAAA
*
16713455 TTGAGA-ACAATTTGAGAGGAAA
1 TTGAGAGA-AATTTGAAAGGAAA
* *
16713477 TTGAAAGGAAATTGAGAAAGGA
1 TTGAGA-GAAATT-TGAAAGGA
16713499 TTAATTTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 1 0.03
22 24 0.67
23 4 0.11
24 7 0.19
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (22 bp):
TTGAGAGAAATTTGAAAGGAAA
Found at i:16713481 original size:33 final size:33
Alignment explanation
Indices: 16713431--16713494 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
16713421 TTAAATATGG
16713431 ATTTGAGAGAAATTTGAAAGGAAATTGAGAACA
1 ATTTGAGAGAAATTTGAAAGGAAATTGAGAACA
16713464 ATTTGAGAGGAAA-TTGAAAGGAAATTGAGAA
1 ATTTGAGA-GAAATTTGAAAGGAAATTGAGAA
16713495 AGGATTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.27, T:0.23
Consensus pattern (33 bp):
ATTTGAGAGAAATTTGAAAGGAAATTGAGAACA
Done.