Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 53 of 97
Found at i:21321439 original size:36 final size:36
Alignment explanation
Indices: 21321234--21321440 Score: 104
Period size: 36 Copynumber: 5.9 Consensus size: 36
21321224 CACACATATT
* * * *
21321234 TGTAAAGGTTCTAACTTAATCT--TG-AAAAGTTAG
1 TGTAAAGGTTATCACTTGATCTCATGAAAAAGCTAG
** * * * * *
21321267 TGTATGGGTTATCACTTGATTTCGTTAAAAAGTTGG
1 TGTAAAGGTTATCACTTGATCTCATGAAAAAGCTAG
* ** ** * *
21321303 TGTAAGGGTTAT-TTTTGATCTTGTGAAAAAGCAAT
1 TGTAAAGGTTATCACTTGATCTCATGAAAAAGCTAG
* * * * *
21321338 TGT-AAGTTTTATCTCTTGATCCCAT-AAAAAGCCAT
1 TGTAAAG-GTTATCACTTGATCTCATGAAAAAGCTAG
* * * *
21321373 TATAAGGGTTATCACTTAATC-CAATTAAAAAGCTAG
1 TGTAAAGGTTATCACTTGATCTC-ATGAAAAAGCTAG
21321409 TGTAAAGGTTATCACTTGATCTCATGAAAAAG
1 TGTAAAGGTTATCACTTGATCTCATGAAAAAG
21321441 TAAGAATCTT
Statistics
Matches: 129, Mismatches: 36, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
33 16 0.12
34 3 0.02
35 46 0.36
36 63 0.49
37 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (36 bp):
TGTAAAGGTTATCACTTGATCTCATGAAAAAGCTAG
Found at i:21321774 original size:17 final size:17
Alignment explanation
Indices: 21321752--21321785 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21321742 GTCTAACAAC
*
21321752 CTTGAGTGATCTGTTGT
1 CTTGAGTGATCCGTTGT
21321769 CTTGAGTGATCCGTTGT
1 CTTGAGTGATCCGTTGT
21321786 AGTAGCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.44
Consensus pattern (17 bp):
CTTGAGTGATCCGTTGT
Found at i:21324393 original size:25 final size:25
Alignment explanation
Indices: 21324359--21324408 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
21324349 AGTAGGCACA
21324359 ATGTCTATTTCGTTGTATAATGGTG
1 ATGTCTATTTCGTTGTATAATGGTG
*
21324384 ATGTCTATTTTGTTGTATAATGGTG
1 ATGTCTATTTCGTTGTATAATGGTG
21324409 TTACCTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.06, G:0.24, T:0.50
Consensus pattern (25 bp):
ATGTCTATTTCGTTGTATAATGGTG
Found at i:21324494 original size:38 final size:38
Alignment explanation
Indices: 21324451--21324570 Score: 152
Period size: 38 Copynumber: 3.2 Consensus size: 38
21324441 TGTACCATTG
21324451 TCAATGTGTCATCCAAGATAATGGGGACTATACCAATA
1 TCAATGTGTCATCCAAGATAATGGGGACTATACCAATA
** * * * *
21324489 TCAATGTGTTGTCCAAGATAGTGGGGATTCTACCATTA
1 TCAATGTGTCATCCAAGATAATGGGGACTATACCAATA
* *
21324527 TCAATGTGTCATCCAAGATAATGGAGACTGTA-CAATTA
1 TCAATGTGTCATCCAAGATAATGGGGACTATACCAA-TA
21324565 TCAATG
1 TCAATG
21324571 CATAGTCCAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
37 2 0.03
38 66 0.97
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (38 bp):
TCAATGTGTCATCCAAGATAATGGGGACTATACCAATA
Found at i:21324567 original size:76 final size:75
Alignment explanation
Indices: 21324426--21324684 Score: 245
Period size: 76 Copynumber: 3.4 Consensus size: 75
21324416 TAATTTCTTT
* * * *
21324426 CAAAATAGTGGGCATTGTACCATTGTCAATGTGTCATCCAAGATAATGGGGACTATACCAA-TAT
1 CAAAATAGTGGGGATTCTACCATTATCAATGTGTCATCCAAGATAATGGAGACTATA-CAATTAT
21324490 CAATGTGTTGTC
65 CAATGT-TTGTC
* *
21324502 CAAGATAGTGGGGATTCTACCATTATCAATGTGTCATCCAAGATAATGGAGACTGTACAATTATC
1 CAAAATAGTGGGGATTCTACCATTATCAATGTGTCATCCAAGATAATGGAGACTATACAATTATC
* *
21324567 AATGCATAGTC
66 AATG-TTTGTC
* * * * * * ** * * * *
21324578 CAAAATAGTGGAGACTGTATCATTATCAAAGAGTCATTTAAGATAGT-AAGACTATACCATTTTC
1 CAAAATAGTGGGGATTCTACCATTATCAATGTGTCATCCAAGATAATGGAGACTATACAATTATC
21324642 AATGTTCTGTC
66 AATGTT-TGTC
* * *
21324653 CAACATAATGGGGATTGC-ACCATTATTAATGT
1 CAAAATAGTGGGGATT-CTACCATTATCAATGT
21324685 TTGTCTTAGA
Statistics
Matches: 146, Mismatches: 33, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
74 1 0.01
75 45 0.31
76 100 0.68
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (75 bp):
CAAAATAGTGGGGATTCTACCATTATCAATGTGTCATCCAAGATAATGGAGACTATACAATTATC
AATGTTTGTC
Found at i:21324580 original size:38 final size:39
Alignment explanation
Indices: 21324441--21324606 Score: 148
Period size: 38 Copynumber: 4.4 Consensus size: 39
21324431 TAGTGGGCAT
* *
21324441 TGTACC-ATTGTCAATGTGTCA-TCCAAGATAATGGGGAC
1 TGTACCAATTATCAATGTGT-AGTCCAAGATAATGGAGAC
* * * * *
21324479 TATACCAA-TATCAATGTGTTGTCCAAGATAGTGGGGAT
1 TGTACCAATTATCAATGTGTAGTCCAAGATAATGGAGAC
*
21324517 TCTACC-ATTATCAATGTGTCA-TCCAAGATAATGGAGAC
1 TGTACCAATTATCAATGTGT-AGTCCAAGATAATGGAGAC
** * *
21324555 TGTA-CAATTATCAATGCATAGTCCAAAATAGTGGAGAC
1 TGTACCAATTATCAATGTGTAGTCCAAGATAATGGAGAC
*
21324593 TGTATC-ATTATCAA
1 TGTACCAATTATCAA
21324607 AGAGTCATTT
Statistics
Matches: 106, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
37 3 0.03
38 101 0.95
39 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (39 bp):
TGTACCAATTATCAATGTGTAGTCCAAGATAATGGAGAC
Found at i:21330117 original size:38 final size:40
Alignment explanation
Indices: 21330074--21330178 Score: 137
Period size: 38 Copynumber: 2.7 Consensus size: 40
21330064 ATAATGCTCG
* *
21330074 TGTGCATGATGTGGGGGGATGTACATGATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTACATGATGGCGACGGATA
* *
21330112 TGTGCACGATGTGGGGGGA--TACAATGATGGCGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTAC-ATGATGGCGACGGATA
21330151 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
21330179 GCTGGGTGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
36 3 0.05
37 8 0.14
38 21 0.36
39 19 0.33
40 4 0.07
41 3 0.05
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCGACGGATA
Found at i:21331464 original size:19 final size:19
Alignment explanation
Indices: 21331436--21331472 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21331426 GGTCATGACA
*
21331436 GCTCCTATGCCATTTTCAT
1 GCTCCCATGCCATTTTCAT
*
21331455 GCTCCCATGCTATTTTCA
1 GCTCCCATGCCATTTTCA
21331473 CGTTACCACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (19 bp):
GCTCCCATGCCATTTTCAT
Found at i:21332769 original size:35 final size:35
Alignment explanation
Indices: 21332741--21332881 Score: 219
Period size: 35 Copynumber: 4.0 Consensus size: 35
21332731 AGTGCATGTA
*
21332741 ATGATATTGCAATGTGCGTGTAGGGAGTGCACATG
1 ATGATATTGAAATGTGCGTGTAGGGAGTGCACATG
21332776 ATGATATTGAAATGTGCGTGTAGGGAGTGCACATG
1 ATGATATTGAAATGTGCGTGTAGGGAGTGCACATG
* *
21332811 ATGATATTGAAATGTGTGTGTAGGGAATGCACATG
1 ATGATATTGAAATGTGCGTGTAGGGAGTGCACATG
*** *
21332846 ATGATATTGCCTTGTGTGTGTAGGGAGTGCACATG
1 ATGATATTGAAATGTGCGTGTAGGGAGTGCACATG
21332881 A
1 A
21332882 GCTGAGTAAG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 99 1.00
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.30
Consensus pattern (35 bp):
ATGATATTGAAATGTGCGTGTAGGGAGTGCACATG
Found at i:21335966 original size:2 final size:2
Alignment explanation
Indices: 21335959--21335986 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21335949 CAAGATATGA
21335959 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
21335987 TTGAGGAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21337765 original size:56 final size:56
Alignment explanation
Indices: 21337724--21337833 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
21337714 AATTACTAAG
* * *
21337724 GCAATATTACGGGTATTCAACTCATGAGATAATGGTATTTCTGCCCCACTACTTAA
1 GCAATATTACGGGTATTCAACCCATAAGATAATGGTATTTCTGCCCAACTACTTAA
* * * * *
21337780 GCAATATTAGGGGTATTTAACCCATAAGATAGTGGTATTT-TGCCCCATTACTTA
1 GCAATATTACGGGTATTCAACCCATAAGATAATGGTATTTCTGCCCAACTACTTA
21337834 GGTAATATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
55 13 0.27
56 35 0.73
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (56 bp):
GCAATATTACGGGTATTCAACCCATAAGATAATGGTATTTCTGCCCAACTACTTAA
Found at i:21338774 original size:16 final size:16
Alignment explanation
Indices: 21338749--21338794 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
21338739 GAAACCAAAA
21338749 TTTG-GATTTTTATTT
1 TTTGAGATTTTTATTT
* *
21338764 TTTTAGATTTTGATTT
1 TTTGAGATTTTTATTT
*
21338780 TTTGATATTTTTATT
1 TTTGAGATTTTTATT
21338795 GAATTCAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (16 bp):
TTTGAGATTTTTATTT
Found at i:21343413 original size:38 final size:39
Alignment explanation
Indices: 21343323--21343425 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 39
21343313 ACCCGGCTCA
21343323 TGTACATCCCCCCACATCGTGCAC-ATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACAATAG-CGG-ACCATCG
* * *
21343363 TGTGCATGCCCCCACATCGTGCACAATGAG-TG-CCATCG
1 TGTACATCCCCCCACATCGTGCACAAT-AGCGGACCATCG
21343401 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
21343426 CGGGCACATC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 29 0.52
40 23 0.41
41 2 0.04
42 2 0.04
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.19
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACAATAGCGGACCATCG
Found at i:21348030 original size:11 final size:11
Alignment explanation
Indices: 21348014--21348044 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
21348004 TTATGCCATC
21348014 AAATAATATTA
1 AAATAATATTA
*
21348025 AAATAATAATA
1 AAATAATATTA
21348036 AAATAATAT
1 AAATAATAT
21348045 ATTTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATATTA
Found at i:21348160 original size:19 final size:19
Alignment explanation
Indices: 21348138--21348179 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
21348128 AAGTGAGAGG
21348138 AATATTTT-TGAAATAAAAT
1 AATATTTTAT-AAATAAAAT
*
21348157 AATATTTTATTAATAAAAT
1 AATATTTTATAAATAAAAT
21348176 AATA
1 AATA
21348180 CTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATTTTATAAATAAAAT
Found at i:21355234 original size:2 final size:2
Alignment explanation
Indices: 21355227--21355251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21355217 TCTATACATG
21355227 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21355252 TCATCATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21355340 original size:43 final size:43
Alignment explanation
Indices: 21355278--21355403 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 43
21355268 TCTCCCATCG
* * * * *
21355278 TCATCAACTCATGTGCACTCCCCACTAGCATATGGCTGGGTCA
1 TCATCGACTTATGTACACTCCCCACTAGCACATAGCTGGGTCA
* * *
21355321 TCATCGGCTTATGTACACT-CCCACTCGCACATAGTTGGGTCA
1 TCATCGACTTATGTACACTCCCCACTAGCACATAGCTGGGTCA
**
21355363 TCATCGACTTATGTACACT-CTTACTCA-CACATAGCTGGGTC
1 TCATCGACTTATGTACACTCCCCACT-AGCACATAGCTGGGTC
21355404 CACATCAACA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 54 0.78
43 15 0.22
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (43 bp):
TCATCGACTTATGTACACTCCCCACTAGCACATAGCTGGGTCA
Found at i:21355360 original size:42 final size:42
Alignment explanation
Indices: 21355312--21355403 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
21355302 CTAGCATATG
* *
21355312 GCTGGGTCATCATCGGCTTATGTACACTCCCACTCGCACATA
1 GCTGGGTCATCATCGACTTATGTACACTCCCACTCACACATA
* **
21355354 GTTGGGTCATCATCGACTTATGTACACTCTTACTCACACATA
1 GCTGGGTCATCATCGACTTATGTACACTCCCACTCACACATA
21355396 GCTGGGTC
1 GCTGGGTC
21355404 CACATCAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (42 bp):
GCTGGGTCATCATCGACTTATGTACACTCCCACTCACACATA
Found at i:21357361 original size:35 final size:33
Alignment explanation
Indices: 21357322--21357441 Score: 109
Period size: 35 Copynumber: 3.5 Consensus size: 33
21357312 AAGCCAAAGC
* *
21357322 GGTTTTTCAAAGGCTTAACCACAACTTTTCACAAT
1 GGTTTTTCAAAGGCTCAACCACAAC--TACACAAT
** * *
21357357 GGTTTTTCACGGGCTCAACCAAAAC-CCA-AAGT
1 GGTTTTTCAAAGGCTCAACCACAACTACACAA-T
21357389 GGTTTTTCAAAGGCTCAACCACAACCTACAACAAT
1 GGTTTTTCAAAGGCTCAACCACAA-CTAC-ACAAT
* *
21357424 GGTTTTTCACAGGATCAA
1 GGTTTTTCAAAGGCTCAA
21357442 TCAAAACCCA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
31 2 0.03
32 24 0.35
33 1 0.01
34 1 0.01
35 39 0.57
36 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (33 bp):
GGTTTTTCAAAGGCTCAACCACAACTACACAAT
Found at i:21357375 original size:67 final size:66
Alignment explanation
Indices: 21357265--21357452 Score: 225
Period size: 67 Copynumber: 2.8 Consensus size: 66
21357255 GGCTTTTACC
* * * * *
21357265 AGGCTTAGCCAAAACCTTTCACAATAGTTTTT-ACCGGGATCAACTAAAAGCCAAAGCGGTTTTT
1 AGGCTTAACCACAA-CTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGCGGTTTTT
21357329 CAA
64 CAA
* *
21357332 AGGCTTAACCACAACTTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTTAACCACAAC-TTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGCGGTTTTTC
21357397 AA
65 AA
* * * * *
21357399 AGGCTCAACCACAACCTACAACAATGGTTTTTCACAGGATCAATCAAAACCCAA
1 AGGCTTAACCACAACTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
21357453 CAACTAACTT
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
66 3 0.03
67 101 0.96
68 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (66 bp):
AGGCTTAACCACAACTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGCGGTTTTTCA
A
Found at i:21357397 original size:32 final size:33
Alignment explanation
Indices: 21357352--21357455 Score: 129
Period size: 32 Copynumber: 3.1 Consensus size: 33
21357342 ACAACTTTTC
*
21357352 ACAATGGTTTTTCACGGGCTCAACCAAAACCCA
1 ACAATGGTTTTTCACAGGCTCAACCAAAACCCA
* * *
21357385 A-AGTGGTTTTTCAAAGGCTCAACCACAACCTACA
1 ACAATGGTTTTTCACAGGCTCAACCAAAACC--CA
* *
21357419 ACAATGGTTTTTCACAGGATCAATCAAAACCCA
1 ACAATGGTTTTTCACAGGCTCAACCAAAACCCA
21357452 ACAA
1 ACAA
21357456 CTAACTTTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 25 0.42
33 7 0.12
34 3 0.05
35 24 0.41
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (33 bp):
ACAATGGTTTTTCACAGGCTCAACCAAAACCCA
Found at i:21366563 original size:32 final size:32
Alignment explanation
Indices: 21366527--21366655 Score: 127
Period size: 35 Copynumber: 3.8 Consensus size: 32
21366517 TTTACCGGGA
*
21366527 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* *
21366559 TCAACCACAACCTTTCACAA-TGGTTTTTC-ACGGAC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGG-C
21366594 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* *
21366626 TCAACCACAACCTACAACAATGGTTTTTCA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCA
21366656 CGAGATGAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
31 2 0.03
32 33 0.41
33 3 0.04
34 6 0.08
35 34 0.43
36 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:21366583 original size:35 final size:33
Alignment explanation
Indices: 21366544--21366655 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 33
21366534 AAACCCAAAG
21366544 TGGTTTTTCAAAGGCTCAACCACAACCTTTCACAA
1 TGGTTTTTCAAAGGCTCAACCACAACC--TCACAA
* *
21366579 TGGTTTTTC-ACGGACTCAACCAAAACC-CA-AA
1 TGGTTTTTCAAAGG-CTCAACCACAACCTCACAA
21366610 GTGGTTTTTCAAAGGCTCAACCACAACCTACAACAA
1 -TGGTTTTTCAAAGGCTCAACCACAACCT-C-ACAA
21366646 TGGTTTTTCA
1 TGGTTTTTCA
21366656 CGAGATGAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
31 2 0.03
32 23 0.35
33 3 0.05
34 4 0.06
35 32 0.48
36 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (33 bp):
TGGTTTTTCAAAGGCTCAACCACAACCTCACAA
Found at i:21366608 original size:67 final size:66
Alignment explanation
Indices: 21366500--21366675 Score: 257
Period size: 67 Copynumber: 2.6 Consensus size: 66
21366490 GCTTAGCCAA
* *
21366500 AACCTTTCACAATAGTTTTT-ACCGGGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-C-GGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
21366564 CAC
64 CAC
21366567 AACCTTTCACAATGGTTTTTCACGGACTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGA-TCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
21366632 AC
65 AC
* *
21366634 AACC-TACAACAATGGTTTTTCACGAGATGAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACG-GATCAACCAAAACCCAA
21366676 CAACTAACTT
Statistics
Matches: 101, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
66 5 0.05
67 93 0.92
68 3 0.03
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (66 bp):
AACCTTTCACAATGGTTTTTCACGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCA
C
Found at i:21366667 original size:35 final size:34
Alignment explanation
Indices: 21366508--21366678 Score: 101
Period size: 35 Copynumber: 5.1 Consensus size: 34
21366498 AAAACCTTTC
* * *
21366508 ACAATAGTTTTT-ACCGGGATCAACTAAAACC-CA
1 ACAATGGTTTTTCA-CGAGATCAACCAAAACCTCA
* * * *
21366541 A-AGTGGTTTTTCA-AAGGCTCAACCACAACCTTTC-
1 ACAATGGTTTTTCACGA-GATCAACCAAAACC--TCA
21366575 ACAATGGTTTTTCACG-GACTCAACCAAAACC-CA
1 ACAATGGTTTTTCACGAGA-TCAACCAAAACCTCA
* * * *
21366608 A-AGTGGTTTTTCA-AAGGCTCAACCACAACCTACA
1 ACAATGGTTTTTCACGA-GATCAACCAAAACCT-CA
*
21366642 ACAATGGTTTTTCACGAGATGAACCAAAACC-CA
1 ACAATGGTTTTTCACGAGATCAACCAAAACCTCA
21366675 ACAA
1 ACAA
21366679 CTAACTTTTC
Statistics
Matches: 103, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
32 42 0.41
33 10 0.10
34 5 0.05
35 45 0.44
36 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.23
Consensus pattern (34 bp):
ACAATGGTTTTTCACGAGATCAACCAAAACCTCA
Found at i:21373373 original size:216 final size:216
Alignment explanation
Indices: 21373111--21373568 Score: 623
Period size: 216 Copynumber: 2.1 Consensus size: 216
21373101 TAACTATTAT
* * *
21373111 ATATATTTAATTTATATATAAGTATTAATATAATTTATAATAAACTTTATTTATATGATTACATT
1 ATATATTTAATTTATATATAAGCATTAATATAACTTATAATAAACTTTATTTATATGATTACACT
** *
21373176 TAATAACCTTATTAATTATCACCTTTTTTTTTATAACATATTGTTTATAATTAGTTATTATTTAT
66 TAATAACCTTATTAATTATCACCTTAATTTTTATAACATATTATTTATAATTAGTTATTATTTAT
* *
21373241 ACAAACTTTG-CT-GTAAAATATTATAACATATAAATTGTATTATTAATGTCATATATACATAAT
131 ACAAACTTTGAATAGTAAAATATTATAACATATAAATTGTATCATTAATGTCATATAT--ATAAT
*
21373304 ATAGGAATATATTATACATATAC
194 AAAGGAATATATTATACATATAC
* *
21373327 ATATATTTAATTTATATATAAGCATTACTGTAACTTATAATAAACTTTATTTATATGATTACACT
1 ATATATTTAATTTATATATAAGCATTAATATAACTTATAATAAACTTTATTTATATGATTACACT
** * ** *
21373392 TAATAATTTTATTAGTTATCGTCTTAATTTTTATGACATATTATTTATAATTAGTTATTATTTAT
66 TAATAACCTTATTAATTATCACCTTAATTTTTATAACATATTATTTATAATTAGTTATTATTTAT
* * * *
21373457 ACAAACTTTGATATAAAAATTAAAATATTATAACATATAAGTTGTGTCATTAATTTCATATATAT
131 ACAAACTTTGA-AT----AGTAAAATATTATAACATATAAATTGTATCATTAATGTCATATATAT
* *
21373522 AATAAAGTAATATATTATATATATAC
191 AATAAAGGAATATATTATACATATAC
*
21373548 ATATATTTAATTTATACATAA
1 ATATATTTAATTTATATATAA
21373569 TTTTTACGTT
Statistics
Matches: 211, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
216 126 0.60
218 1 0.00
221 45 0.21
223 39 0.18
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (216 bp):
ATATATTTAATTTATATATAAGCATTAATATAACTTATAATAAACTTTATTTATATGATTACACT
TAATAACCTTATTAATTATCACCTTAATTTTTATAACATATTATTTATAATTAGTTATTATTTAT
ACAAACTTTGAATAGTAAAATATTATAACATATAAATTGTATCATTAATGTCATATATATAATAA
AGGAATATATTATACATATAC
Found at i:21373551 original size:17 final size:17
Alignment explanation
Indices: 21373513--21373571 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
21373503 TCATTAATTT
* *
21373513 CATATATATAATAAAGTA
1 CATATATTTAATATA-TA
21373531 -ATATA-TTATATATATA
1 CATATATTTA-ATATATA
*
21373547 CATATATTTAATTTATA
1 CATATATTTAATATATA
21373564 CATA-ATTT
1 CATATATTT
21373572 TTACGTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 8 0.23
17 24 0.69
18 3 0.09
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (17 bp):
CATATATTTAATATATA
Found at i:21376078 original size:24 final size:25
Alignment explanation
Indices: 21376026--21376081 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
21376016 ACATGTCGTG
* * *
21376026 TTAAATTTTATACGAAATGATATGG
1 TTAAAATTTATACGAAATGATAAGA
*
21376051 TTAAAATTTATAC-AATTGATAAGA
1 TTAAAATTTATACGAAATGATAAGA
21376075 TTAAAAT
1 TTAAAAT
21376082 GATTAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (25 bp):
TTAAAATTTATACGAAATGATAAGA
Found at i:21391263 original size:2 final size:2
Alignment explanation
Indices: 21391250--21391291 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
21391240 CACCATGGAA
*
21391250 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21391292 CTCACTACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21391413 original size:23 final size:22
Alignment explanation
Indices: 21391338--21391414 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
21391328 AATTTCGTTG
* *
21391338 GAAATTTTCAACGGATTTTCAAC
1 GAAATTTTCAAC-AAATTTCAAC
*
21391361 GAAATTTT-AACAAAAATTCAAC
1 GAAATTTTCAAC-AAATTTCAAC
* *
21391383 TAATATTTTCGACAAATTTCCAAC
1 GAA-ATTTTCAACAAATTT-CAAC
21391407 GAAATTTT
1 GAAATTTT
21391415 TCCGTTGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 12 0.28
23 23 0.53
24 8 0.19
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (22 bp):
GAAATTTTCAACAAATTTCAAC
Found at i:21394004 original size:49 final size:49
Alignment explanation
Indices: 21393951--21394061 Score: 177
Period size: 49 Copynumber: 2.3 Consensus size: 49
21393941 GTCATAATAT
* * *
21393951 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCTGATGATGATGA
1 TGACTCGGCTATGTACGAGTAGGGAGTGCGCATAAGCCGATGATGATAA
*
21394000 TGACTTGGCTATGTACGAGTAGGGAGTGCGCATAAGCCGATGATGATAA
1 TGACTCGGCTATGTACGAGTAGGGAGTGCGCATAAGCCGATGATGATAA
*
21394049 TGACCCGGCTATG
1 TGACTCGGCTATG
21394062 ATGATGAATG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 56 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.24
Consensus pattern (49 bp):
TGACTCGGCTATGTACGAGTAGGGAGTGCGCATAAGCCGATGATGATAA
Found at i:21394674 original size:21 final size:20
Alignment explanation
Indices: 21394650--21394723 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
21394640 CACCCGAATC
*
21394650 TCGCTGTAGCGAGAACGAACT
1 TCGCTGCAGCGAGAA-GAACT
21394671 TCGCTGCAGCGAG-A-AACT
1 TCGCTGCAGCGAGAAGAACT
* *
21394689 T-GCTGTAGCAAGAATGAACT
1 TCGCTGCAGCGAGAA-GAACT
*
21394709 TCGTTGCAGCGAGAA
1 TCGCTGCAGCGAGAA
21394724 ACTTGATGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 9 0.21
18 6 0.14
20 6 0.14
21 22 0.51
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (20 bp):
TCGCTGCAGCGAGAAGAACT
Found at i:21394697 original size:38 final size:38
Alignment explanation
Indices: 21394652--21394728 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
21394642 CCCGAATCTC
*
21394652 GCTGTAGCGAGAACGAACTTCGCTGCAGCGAGAAACTT
1 GCTGTAGCAAGAACGAACTTCGCTGCAGCGAGAAACTT
* *
21394690 GCTGTAGCAAGAATGAACTTCGTTGCAGCGAGAAACTT
1 GCTGTAGCAAGAACGAACTTCGCTGCAGCGAGAAACTT
21394728 G
1 G
21394729 ATGCCATGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.21
Consensus pattern (38 bp):
GCTGTAGCAAGAACGAACTTCGCTGCAGCGAGAAACTT
Found at i:21394702 original size:17 final size:18
Alignment explanation
Indices: 21394667--21394727 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
21394657 AGCGAGAACG
*
21394667 AACTTCGCTGCAGCGAGA
1 AACTTCGCTGCAGCAAGA
*
21394685 AACTT-GCTGTAGCAAGAA
1 AACTTCGCTGCAGCAAG-A
* *
21394703 TGAACTTCGTTGCAGCGAGA
1 --AACTTCGCTGCAGCAAGA
21394723 AACTT
1 AACTT
21394728 GATGCCATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 9 0.26
18 11 0.32
20 6 0.18
21 8 0.24
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (18 bp):
AACTTCGCTGCAGCAAGA
Found at i:21402835 original size:22 final size:22
Alignment explanation
Indices: 21402789--21402835 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
21402779 GTGAACGGTA
*
21402789 AAAGAAAGAAGAAAAAAGAGGG
1 AAAGAAAGAAGAAAAAAGAGAG
21402811 AAAGAAAGAAGAGAAAAAGA-AG
1 AAAGAAAGAAGA-AAAAAGAGAG
21402833 AAA
1 AAA
21402836 ATGGCTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGAAAAAAGAGAG
Found at i:21404073 original size:9 final size:9
Alignment explanation
Indices: 21404059--21404105 Score: 58
Period size: 9 Copynumber: 4.9 Consensus size: 9
21404049 GTATGTTATC
21404059 TTGTTATAT
1 TTGTTATAT
21404068 TTGTTATAT
1 TTGTTATAT
*
21404077 TTGTTAATGAAA
1 TTGTT-AT--AT
21404089 TTGTTATAT
1 TTGTTATAT
21404098 TTGTTATA
1 TTGTTATA
21404106 AATTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 23 0.70
10 2 0.06
11 2 0.06
12 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.60
Consensus pattern (9 bp):
TTGTTATAT
Found at i:21405519 original size:15 final size:16
Alignment explanation
Indices: 21405493--21405522 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21405483 AAGAGAATAA
21405493 AAGAAGAAGAAAGGAT
1 AAGAAGAAGAAAGGAT
21405509 AAGAA-AAGAAAGGA
1 AAGAAGAAGAAAGGA
21405523 AGAAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (16 bp):
AAGAAGAAGAAAGGAT
Found at i:21405525 original size:13 final size:14
Alignment explanation
Indices: 21405492--21405532 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
21405482 CAAGAGAATA
21405492 AAAGAAGAAGAAAGG
1 AAAGAA-AAGAAAGG
21405507 ATAAGAAAAGAAAGG
1 A-AAGAAAAGAAAGG
21405522 -AAG-AAAGAAAG
1 AAAGAAAAGAAAG
21405533 AGAGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.32
13 3 0.12
15 9 0.36
16 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAAGG
Found at i:21405612 original size:4 final size:4
Alignment explanation
Indices: 21405603--21405651 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
21405593 AACTAAAGAG
*
21405603 GAAA GAAA G-AA GAAA G-GA GAAA GAAA GGAAA GAAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA G-AAA GAAA GAAA GAAA
21405650 GA
1 GA
21405652 GAGAGGGAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 8 0.21
4 22 0.58
5 8 0.21
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:21405617 original size:11 final size:11
Alignment explanation
Indices: 21405597--21405651 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
21405587 TCTACCAACT
*
21405597 AAAGAGGAAAG
1 AAAGAAGAAAG
21405608 AAAGAAGAAAG
1 AAAGAAGAAAG
*
21405619 -GAGAAAGAAAGG
1 AAAG-AAGAAA-G
21405631 AAAG-A-AAAG
1 AAAGAAGAAAG
21405640 AAAGAAGAAAG
1 AAAGAAGAAAG
21405651 A
1 A
21405652 GAGAGGGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
9 5 0.14
10 6 0.17
11 22 0.61
12 1 0.03
13 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAG
Found at i:21405624 original size:18 final size:18
Alignment explanation
Indices: 21405603--21405655 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
21405593 AACTAAAGAG
21405603 GAAAGAAAGAAGAAAGGA
1 GAAAGAAAGAAGAAAGGA
21405621 GAAAGAAAG--GAAA-GA
1 GAAAGAAAGAAGAAAGGA
21405636 -AAAGAAAGAAGAAAGAGA
1 GAAAGAAAGAAGAAAG-GA
21405654 GA
1 GA
21405656 GGGAGAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 8 0.27
15 2 0.07
16 8 0.27
18 11 0.37
19 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAGAAAGGA
Found at i:21407041 original size:35 final size:35
Alignment explanation
Indices: 21406991--21407058 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
21406981 ATAATGGCAT
*
21406991 TTGATGTGTATGAGTAGGGAGTGCACACGATGATG
1 TTGATGTGTACGAGTAGGGAGTGCACACGATGATG
*
21407026 TTGATGTGTGCGAGTAGGGAGTGCACACGATGA
1 TTGATGTGTACGAGTAGGGAGTGCACACGATGA
21407059 CTCTGGCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.10, G:0.38, T:0.26
Consensus pattern (35 bp):
TTGATGTGTACGAGTAGGGAGTGCACACGATGATG
Found at i:21408476 original size:12 final size:12
Alignment explanation
Indices: 21408459--21408494 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
21408449 TGGGTAAGAC
21408459 ACGTGAGGAAAT
1 ACGTGAGGAAAT
21408471 ACGTGAGGAAAT
1 ACGTGAGGAAAT
* *
21408483 ATGTGAAGAAAT
1 ACGTGAGGAAAT
21408495 TAAGAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (12 bp):
ACGTGAGGAAAT
Found at i:21408997 original size:30 final size:30
Alignment explanation
Indices: 21408963--21409019 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
21408953 AATTCCGTTG
* *
21408963 GAAATGCTTTCCCAATGGAATTTTTCGTCA
1 GAAATGCTTTCCCAACGAAATTTTTCGTCA
* *
21408993 GAAATGTTTTTCCAACGAAATTTTTCG
1 GAAATGCTTTCCCAACGAAATTTTTCG
21409020 GTGGAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (30 bp):
GAAATGCTTTCCCAACGAAATTTTTCGTCA
Found at i:21409027 original size:30 final size:29
Alignment explanation
Indices: 21408961--21409027 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
21408951 AGAATTCCGT
* *
21408961 TGGAAATGCTTTCCCAATGGAATTTTTCG
1 TGGAAATGCTTTCCCAACGAAATTTTTCG
* * *
21408990 TCAGAAATGTTTTTCCAACGAAATTTTTCGG
1 T-GGAAATGCTTTCCCAACGAAATTTTTC-G
21409021 TGGAAAT
1 TGGAAAT
21409028 TTTCAATGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.03
30 27 0.90
31 2 0.07
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (29 bp):
TGGAAATGCTTTCCCAACGAAATTTTTCG
Found at i:21409068 original size:17 final size:17
Alignment explanation
Indices: 21409046--21409097 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
21409036 ATTTTTTGTT
21409046 GGAAAAGCATTTCCAAC
1 GGAAAAGCATTTCCAAC
**
21409063 GG-AAA--A-TTCCATT
1 GGAAAAGCATTTCCAAC
21409076 GGAAAAGCATTTCCAAC
1 GGAAAAGCATTTCCAAC
21409093 -GAAAA
1 GGAAAA
21409098 ATTCTGTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
16 9 0.33
17 7 0.26
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (17 bp):
GGAAAAGCATTTCCAAC
Found at i:21409078 original size:30 final size:30
Alignment explanation
Indices: 21409044--21409101 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
21409034 TGATTTTTTG
*
21409044 TTGGAAAAGCATTTCCAACGGAAAATTCCA
1 TTGGAAAAGCATTTCCAACGAAAAATTCCA
21409074 TTGGAAAAGCATTTCCAACGAAAAATTC
1 TTGGAAAAGCATTTCCAACGAAAAATTC
21409102 TGTTAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (30 bp):
TTGGAAAAGCATTTCCAACGAAAAATTCCA
Found at i:21409111 original size:30 final size:30
Alignment explanation
Indices: 21409042--21409121 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
21409032 AATGATTTTT
*
21409042 TGTTGGAAAAGCATTTCCAACGGAAAATTC
1 TGTTGGAAAAGCATTTCCAACGAAAAATTC
**
21409072 CATTGGAAAAGCATTTCCAACGAAAAATTC
1 TGTTGGAAAAGCATTTCCAACGAAAAATTC
* * *
21409102 TGTTAGAAAAACAATTCCAA
1 TGTTGGAAAAGCATTTCCAA
21409122 AGGAATTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (30 bp):
TGTTGGAAAAGCATTTCCAACGAAAAATTC
Found at i:21409274 original size:14 final size:14
Alignment explanation
Indices: 21409255--21409288 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
21409245 CAAAAATCAT
21409255 ATTTTTCCAACGAA
1 ATTTTTCCAACGAA
*
21409269 ATTTTT-CAACGGA
1 ATTTTTCCAACGAA
21409282 ATTTTTC
1 ATTTTTC
21409289 GTTGGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (14 bp):
ATTTTTCCAACGAA
Found at i:21410921 original size:67 final size:67
Alignment explanation
Indices: 21410809--21410967 Score: 185
Period size: 67 Copynumber: 2.4 Consensus size: 67
21410799 CGGAGCAATC
* * * * * ***
21410809 TCTTCACGGATGGCATCACAATCCTCGTCCGGGGCAATATGCCAACAAATGGCATCACTTGGAGT
1 TCTTCACGGATGGCATCACAATCATAGTCCAGGGCAATATCCCAACAAATGACATCACCCAGAGT
21410874 AT
66 AT
*
21410876 TCTTCACGGATGGCATCACAATCATAGTCCAAGGG-AATATCCCAACAGATGACATCACCCAGAG
1 TCTTCACGGATGGCATCACAATCATAGTCC-AGGGCAATATCCCAACAAATGACATCACCCAGAG
21410940 TAT
65 TAT
* ** *
21410943 TCTCCACAAATGGCATCATAATCAT
1 TCTTCACGGATGGCATCACAATCAT
21410968 CATCTTGAGT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
67 75 0.96
68 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (67 bp):
TCTTCACGGATGGCATCACAATCATAGTCCAGGGCAATATCCCAACAAATGACATCACCCAGAGT
AT
Found at i:21412776 original size:22 final size:22
Alignment explanation
Indices: 21412751--21412803 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
21412741 TGAATATTTT
*
21412751 TTAGGCATTGTGTCACTAGATG
1 TTAGGCATTGTGTCACTAGATA
* *
21412773 TTAGGTATTGTGTGACTAGATA
1 TTAGGCATTGTGTCACTAGATA
*
21412795 TTGGGCATT
1 TTAGGCATT
21412804 ACATGACTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (22 bp):
TTAGGCATTGTGTCACTAGATA
Found at i:21414278 original size:14 final size:14
Alignment explanation
Indices: 21414261--21414325 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
21414251 AGAAGAAAAG
21414261 AGAAAGGAGAAGAA
1 AGAAAGGAGAAGAA
* *
21414275 AGAAAGAAGAAAAA
1 AGAAAGGAGAAGAA
* *
21414289 AGAAAGGGGAGGAA
1 AGAAAGGAGAAGAA
21414303 AGAAA-GA-AAGAA
1 AGAAAGGAGAAGAA
21414315 A-AAAGAGAGAA
1 AGAAAG-GAGAA
21414326 AGGAATAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 3 0.08
12 5 0.12
13 3 0.08
14 29 0.73
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AGAAAGGAGAAGAA
Found at i:21414279 original size:4 final size:4
Alignment explanation
Indices: 21414270--21414327 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
21414260 GAGAAAGGAG
* *
21414270 AAGA AAGA AAG- AAGA AA-A AAGA AAGGGG AGGA AAGA AAGA AAGA AA-A
1 AAGA AAGA AAGA AAGA AAGA AAGA AA--GA AAGA AAGA AAGA AAGA AAGA
*
21414317 AAGA GAGA AAG
1 AAGA AAGA AAG
21414328 GAATAAAGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
3 9 0.21
4 32 0.74
6 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:21414292 original size:28 final size:28
Alignment explanation
Indices: 21414250--21414320 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
21414240 ACCCATAACC
*
21414250 AAGAAGAAAAGAGAAAGGAGAAGAAAGA
1 AAGAAGAAAAAAGAAAGGAGAAGAAAGA
* *
21414278 AAGAAGAAAAAAGAAAGGGGAGGAAAGA
1 AAGAAGAAAAAAGAAAGGAGAAGAAAGA
21414306 AAGAAAGAAAAAAGA
1 AAG-AAGAAAAAAGA
21414321 GAGAAAGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 28 0.72
29 11 0.28
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (28 bp):
AAGAAGAAAAAAGAAAGGAGAAGAAAGA
Found at i:21414329 original size:28 final size:28
Alignment explanation
Indices: 21414250--21414330 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
21414240 ACCCATAACC
*
21414250 AAGAAGAAAAGAGAAAGGAGAA-GAAAGA
1 AAGAAGAAAAAAGAAAGGA-AAGGAAAGA
**
21414278 AAGAAGAAAAAAGAAAGGGGAGGAAAGA
1 AAGAAGAAAAAAGAAAGGAAAGGAAAGA
*
21414306 AAGAAAGAAAAAAGAGA-GAAAGGAA
1 AAG-AAGAAAAAAGAAAGGAAAGGAA
21414331 TAAAGGTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.02
28 32 0.71
29 12 0.27
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (28 bp):
AAGAAGAAAAAAGAAAGGAAAGGAAAGA
Found at i:21417184 original size:22 final size:22
Alignment explanation
Indices: 21417145--21417203 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
21417135 CCAGCCCTGT
* * *
21417145 TTCTCATTGTAGCCAAAAAGAA
1 TTCTCACTGCAGCGAAAAAGAA
* *
21417167 TTCTCACTGCAGCGAAAATGGA
1 TTCTCACTGCAGCGAAAAAGAA
**
21417189 TTCTTGCTGCAGCGA
1 TTCTCACTGCAGCGA
21417204 GAAACTCTCG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (22 bp):
TTCTCACTGCAGCGAAAAAGAA
Found at i:21433301 original size:22 final size:23
Alignment explanation
Indices: 21433238--21433301 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
21433228 ACATGATTGA
21433238 ATATTAGGCAA-TGTG-TGACTAG
1 ATATTAGG-AATTGTGATGACTAG
*
21433260 ATATTAGGTATTGTGA-GACTAG
1 ATATTAGGAATTGTGATGACTAG
* *
21433282 CTTTTAGGAATTGT-ATGACT
1 ATATTAGGAATTGTGATGACT
21433302 TGTGCATTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.06
22 33 0.94
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (23 bp):
ATATTAGGAATTGTGATGACTAG
Found at i:21434193 original size:22 final size:22
Alignment explanation
Indices: 21434168--21434225 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
21434158 TATAATTTGG
* * *
21434168 TAGGCATTACGTGATTAGATTT
1 TAGGCATTGCGTGAATAGATAT
* *
21434190 TAGGCATTGTGTGAATGGATAT
1 TAGGCATTGCGTGAATAGATAT
21434212 TAGGCATTGCGTGA
1 TAGGCATTGCGTGA
21434226 CAAGTTGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (22 bp):
TAGGCATTGCGTGAATAGATAT
Found at i:21436694 original size:21 final size:19
Alignment explanation
Indices: 21436657--21436718 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
21436647 CATCTAGCTA
21436657 TTCTTTTTTCTTTTCCTGT
1 TTCTTTTTTCTTTTCCTGT
21436676 TTCTTTCTTTCTCTTTCCTG-
1 TTCTTT-TTTCT-TTTCCTGT
*
21436696 CTCTTTTTT-TTTT-CT-T
1 TTCTTTTTTCTTTTCCTGT
21436712 TTCTTTT
1 TTCTTTT
21436719 CTGTTTCTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 8 0.21
17 3 0.08
18 1 0.03
19 9 0.24
20 10 0.26
21 7 0.18
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (19 bp):
TTCTTTTTTCTTTTCCTGT
Found at i:21436725 original size:16 final size:16
Alignment explanation
Indices: 21436662--21436726 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
21436652 AGCTATTCTT
21436662 TTTTCTTTTCCTGTTTC
1 TTTTCTTTT-CTGTTTC
*
21436679 -TTTCTTTCTCT-TTCC
1 TTTTCTTT-TCTGTTTC
** * *
21436694 TGCTCTTTTTTTTTTC
1 TTTTCTTTTCTGTTTC
21436710 TTTTCTTTTCTGTTTC
1 TTTTCTTTTCTGTTTC
21436726 T
1 T
21436727 CTCCTTTCTC
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
15 5 0.14
16 30 0.83
17 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTTCTTTTCTGTTTC
Found at i:21436855 original size:7 final size:7
Alignment explanation
Indices: 21436836--21436882 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
21436826 CTCTTTCTCC
21436836 CTTC-TT
1 CTTCTTT
21436842 CTT-TTT
1 CTTCTTT
21436848 CTTCTTT
1 CTTCTTT
21436855 CTTCTTT
1 CTTCTTT
21436862 CTTCTCTCT
1 CTTCT-T-T
*
21436871 CTTGTTT
1 CTTCTTT
21436878 CTTCT
1 CTTCT
21436883 CCGACATGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
6 8 0.23
7 20 0.57
8 2 0.06
9 5 0.14
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (7 bp):
CTTCTTT
Found at i:21436873 original size:23 final size:23
Alignment explanation
Indices: 21436827--21436882 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
21436817 CTGCTCTCCC
* * * *
21436827 TCTTTCTCCCTTCTTCTTTTTCT
1 TCTTTCTTCTTTCTTCTCTCTCT
21436850 TCTTTCTTCTTTCTTCTCTCTCT
1 TCTTTCTTCTTTCTTCTCTCTCT
*
21436873 TGTTTCTTCT
1 TCTTTCTTCT
21436883 CCGACATGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (23 bp):
TCTTTCTTCTTTCTTCTCTCTCT
Found at i:21436883 original size:16 final size:14
Alignment explanation
Indices: 21436838--21436883 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
21436828 CTTTCTCCCT
21436838 TCTTCTTTTTCTTC
1 TCTTCTTTTTCTTC
21436852 T-TTCTTCTTTCTTC
1 TCTTCTT-TTTCTTC
21436866 TCTCTCTTGTTTCTTC
1 TCT-TCTT-TTTCTTC
21436882 TC
1 TC
21436884 CGACATGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 1 0.04
16 13 0.46
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.67
Consensus pattern (14 bp):
TCTTCTTTTTCTTC
Found at i:21436950 original size:70 final size:67
Alignment explanation
Indices: 21436831--21437005 Score: 201
Period size: 70 Copynumber: 2.6 Consensus size: 67
21436821 TCTCCCTCTT
* *
21436831 TCTCCCTTCTTC-TTTTTCTTCTTTCTTCTTTCTT-CTCTCTCTTGTTTCTTCTCCGACATGCCG
1 TCTCCC-TCTTCTTTTTTCTTCTTT-TTCTTTTTTCCTCTCTCTTCTTTCTTCTCCGACATGCCG
*
21436894 TTAC
64 CTAC
** *
21436898 TCTCCCTCTATCTTTTTTCTTCTTTTTCTTTTTTCCTCTCTCTCCTCTTTCTTCTCCGGTATGTC
1 TCTCCCTCT-TCTTTTTTCTTCTTTTTCTTTTTTCCTCTCTCT--TCTTTCTTCTCCGACATGCC
21436963 GCTAC
63 GCTAC
** *
21436968 TCTCCCTCTCTCTTCCTTCTTCTTTTTCTTATTTCCTC
1 TCTCCCTCT-TCTTTTTTCTTCTTTTTCTTTTTTCCTC
21437006 ACTCGGGTAC
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
66 3 0.03
67 16 0.17
68 20 0.22
70 54 0.58
ACGTcount: A:0.04, C:0.35, G:0.05, T:0.56
Consensus pattern (67 bp):
TCTCCCTCTTCTTTTTTCTTCTTTTTCTTTTTTCCTCTCTCTTCTTTCTTCTCCGACATGCCGCT
AC
Found at i:21450085 original size:42 final size:42
Alignment explanation
Indices: 21450025--21450113 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
21450015 TGTTGATGTG
* *
21450025 GACCCGGCTATGTGCGAGTAGGAGTGCACAAAAGCCGTTGCT
1 GACCCGACTATGTACGAGTAGGAGTGCACAAAAGCCGTTGCT
*
21450067 GACCCGACTATGTACGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGACTATGTACGAGTAGGAGTGCACAAAAGCCGTTGCT
*
21450109 AACCC
1 GACCC
21450114 AGTTATATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (42 bp):
GACCCGACTATGTACGAGTAGGAGTGCACAAAAGCCGTTGCT
Found at i:21450127 original size:42 final size:42
Alignment explanation
Indices: 21450026--21450149 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 42
21450016 GTTGATGTGG
* * * *
21450026 ACCCGGCTATGTGCGAGTAGGAGTGCACAAAAGCCGTTGCTG
1 ACCCGACTATATGCGAGTAGGAGTGCACATAAGCCGTTGCTA
* *
21450068 ACCCGACTATGTACGAGTAGGAGTGCACATAAGCCGTTGCTA
1 ACCCGACTATATGCGAGTAGGAGTGCACATAAGCCGTTGCTA
* * * *
21450110 ACCC-AGTTATATGCGAGT-GAGAGTACGCATAAGTCGTTGC
1 ACCCGA-CTATATGCGAGTAG-GAGTGCACATAAGCCGTTGC
21450150 ATATGAGATG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.03
42 68 0.97
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (42 bp):
ACCCGACTATATGCGAGTAGGAGTGCACATAAGCCGTTGCTA
Found at i:21450197 original size:2 final size:2
Alignment explanation
Indices: 21450190--21450221 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21450180 ATGATGATTG
*
21450190 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21450222 GGTATATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21458829 original size:42 final size:42
Alignment explanation
Indices: 21458731--21458865 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
21458721 CATTCATTGT
*
21458731 CATAGCCGGGTCATCATCATCAGCTTATGCGCACTCCCTACTCGCA
1 CATAGCCGGGTCAACATC--CA-CTTATGCGCACT-CCTACTCGCA
* * * **
21458777 TATAGCCGGGTCAGCATCCACTTATGCGCACTTCTACTCATA
1 CATAGCCGGGTCAACATCCACTTATGCGCACTCCTACTCGCA
* ** *
21458819 CATAGTCGGGTCAACATCGGCTTATACGCACTCCTACTCGCA
1 CATAGCCGGGTCAACATCCACTTATGCGCACTCCTACTCGCA
21458861 CATAG
1 CATAG
21458866 TTAGCTCATC
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 45 0.60
43 12 0.16
44 2 0.03
46 16 0.21
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (42 bp):
CATAGCCGGGTCAACATCCACTTATGCGCACTCCTACTCGCA
Found at i:21458889 original size:24 final size:24
Alignment explanation
Indices: 21458859--21458910 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
21458849 CTCCTACTCG
21458859 CACATAGTTAGCTCATCATTATCA
1 CACATAGTTAGCTCATCATTATCA
21458883 CACATAGTTAGCTCATCATTATCA
1 CACATAGTTAGCTCATCATTATCA
21458907 CACA
1 CACA
21458911 ACATTATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (24 bp):
CACATAGTTAGCTCATCATTATCA
Found at i:21461714 original size:12 final size:12
Alignment explanation
Indices: 21461697--21461722 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21461687 TGCTAGAAAA
21461697 TGATAAGTGATT
1 TGATAAGTGATT
21461709 TGATAAGTGATT
1 TGATAAGTGATT
21461721 TG
1 TG
21461723 TGATTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (12 bp):
TGATAAGTGATT
Found at i:21462276 original size:28 final size:26
Alignment explanation
Indices: 21462240--21462328 Score: 87
Period size: 25 Copynumber: 3.4 Consensus size: 26
21462230 CCGATAGGCT
* *
21462240 ATTAGACGTGGCTAGGCCAT-GGTCTATG
1 ATTATACGTGGCAAGGCCATAGG--T-TG
21462268 ATTATACGTGGCAAGGCCATAGGTTG
1 ATTATACGTGGCAAGGCCATAGGTTG
*
21462294 -TTATACGTGGCAAGGCCA-CGAGTTG
1 ATTATACGTGGCAAGGCCATAG-GTTG
21462319 A-TATACGTGG
1 ATTATACGTGG
21462329 TTGCGACCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
24 1 0.02
25 31 0.56
26 2 0.04
27 1 0.02
28 18 0.33
29 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (26 bp):
ATTATACGTGGCAAGGCCATAGGTTG
Found at i:21462963 original size:18 final size:19
Alignment explanation
Indices: 21462940--21462979 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
21462930 TAAGTGGAGA
21462940 ATTTTAT-AATAAAATAAT
1 ATTTTATGAATAAAATAAT
21462958 ATTTTATGAATAAAATAAT
1 ATTTTATGAATAAAATAAT
21462977 ATT
1 ATT
21462980 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:21464596 original size:35 final size:35
Alignment explanation
Indices: 21464569--21464824 Score: 223
Period size: 35 Copynumber: 7.3 Consensus size: 35
21464559 TTAATTGTTT
21464569 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * * *
21464604 AATTTAATTAAATAAGCCCAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
21464639 AATTTTAATCAACTAAGCCCAATGACTTACTTAAAC
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ****
21464675 AAATTTAAT-AAGTTAGGCCCAATAACTTAGTTGTTT
1 -AATTTAATCAA-TTAGGCCCAATAACTTAATTAAAC
* * * *
21464711 AATTTAATTAATTAGGTCGAATGACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
21464746 AATTTAATTAATTAGGCTCAATGATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
21464781 AATTTAGTTAATTAGG--C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
21464813 AATTTTAATCAA
1 AA-TTTAATCAA
21464825 GTGCTTGAGA
Statistics
Matches: 179, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
32 14 0.08
33 8 0.04
35 104 0.58
36 51 0.28
37 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:21464646 original size:71 final size:70
Alignment explanation
Indices: 21464569--21464817 Score: 245
Period size: 71 Copynumber: 3.6 Consensus size: 70
21464559 TTAATTGTTT
* * *
21464569 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAAATAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGGCCCAATAATTTAAT
21464634 TAAAC
66 TAAAC
* * * * *
21464639 AATTTTAATCAACTAAGCCCAATGACTTACTTAAACAAATTTAA-TAAGTTAGGCCCAATAACTT
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC-AATTTAATTAA-TTAGGCCCAATAATTT
* ****
21464703 AGTTGTTT
63 AATTAAAC
* * * * * *
21464711 AATTTAATTAATTAGGTCGAATGACTTAATTAAACAATTTAATTAATTAGGCTCAATGATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGGCCCAATAATTTAAT
21464776 TAAAC
66 TAAAC
* * *
21464781 AATTTAGTTAATTAGG--C-ACAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
21464818 TAATCAAGTG
Statistics
Matches: 144, Mismatches: 31, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
67 18 0.12
70 40 0.28
71 62 0.43
72 24 0.17
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (70 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAGGCCCAATAATTTAAT
TAAAC
Found at i:21466320 original size:2 final size:2
Alignment explanation
Indices: 21466310--21466346 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
21466300 ACATATTTAC
*
21466310 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21466347 CGCATATACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21466476 original size:43 final size:43
Alignment explanation
Indices: 21466400--21466517 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
21466390 TCACCAGCTC
* * * * * *
21466400 ATGCGCAGTCCCTACTCACACATGGCTGGGTCAT-CATCGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCCGAGTCATAC-TCGGCTT
*
21466443 ATGCGCACTCCCTACTCGCACATAACCGAGTCATACTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAGCCGAGTCATACTCGGCTT
21466486 ATGCGCACTCCCTACTCGCA-ATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
21466518 ATATAATTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 11 0.17
43 54 0.82
44 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAGCCGAGTCATACTCGGCTT
Found at i:21473829 original size:51 final size:52
Alignment explanation
Indices: 21473755--21473867 Score: 187
Period size: 52 Copynumber: 2.2 Consensus size: 52
21473745 GGATTAGAAT
21473755 TAAAC-TTTTA-TTACAAATTACAAATTAAAACA-TTTTTAATTTGTGCTCC
1 TAAACATTTTACTTACAAATTACAAATTAAAACATTTTTTAATTTGTGCTCC
*
21473804 TAAACATTTTACTTACAAATTACAAATTAAAACATTTTTTAATTTGTGCTTC
1 TAAACATTTTACTTACAAATTACAAATTAAAACATTTTTTAATTTGTGCTCC
*
21473856 TAAGCATTTTAC
1 TAAACATTTTAC
21473868 ACAACCTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
49 5 0.08
50 5 0.08
51 22 0.37
52 27 0.46
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.43
Consensus pattern (52 bp):
TAAACATTTTACTTACAAATTACAAATTAAAACATTTTTTAATTTGTGCTCC
Found at i:21483199 original size:2 final size:2
Alignment explanation
Indices: 21483192--21483256 Score: 58
Period size: 2 Copynumber: 31.0 Consensus size: 2
21483182 CTATACTATG
* * * * *
21483192 TA TA TA TA TA TA TA TA TA TA TA GTGG TT TA TT TN TA TA CTA TG
1 TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA -TA TA
21483235 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
21483257 GGTGGTTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 48 0.92
3 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21483231 original size:43 final size:43
Alignment explanation
Indices: 21483183--21483268 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
21483173 TCAAAATTCC
21483183 TATACTATGTATATATATATATATATATATA-GTGGTTTATTT
1 TATACTATGTATATATATATATATATATATAGGTGGTTTATTT
21483225 NTATACTATGTATATATATATATATATATATAGGTGGTTTATTT
1 -TATACTATGTATATATATATATATATATATAGGTGGTTTATTT
21483269 GAAATGCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 31 0.74
44 11 0.26
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.51
Consensus pattern (43 bp):
TATACTATGTATATATATATATATATATATAGGTGGTTTATTT
Found at i:21487288 original size:22 final size:22
Alignment explanation
Indices: 21487263--21487315 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
21487253 ATTTTAGATA
*
21487263 TCCTTAATTTAAGGAATTAAAT
1 TCCTTAATTTAAGGAACTAAAT
*
21487285 TCCTTAATTTAAGGAACTAGAT
1 TCCTTAATTTAAGGAACTAAAT
21487307 TCCTTAATT
1 TCCTTAATT
21487316 CAAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (22 bp):
TCCTTAATTTAAGGAACTAAAT
Found at i:21500768 original size:20 final size:20
Alignment explanation
Indices: 21500743--21500780 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21500733 AATTAGCTAG
*
21500743 GGATGTATAGATAGATTTGT
1 GGATGTATAGATACATTTGT
*
21500763 GGATGTATCGATACATTT
1 GGATGTATAGATACATTT
21500781 TCATGGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.39
Consensus pattern (20 bp):
GGATGTATAGATACATTTGT
Found at i:21502712 original size:25 final size:23
Alignment explanation
Indices: 21502651--21502714 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 23
21502641 ATGTGTTGTC
*
21502651 TTAA-TTAAGACAAGA-ATAGTT
1 TTAATTTAAGACAAGAGATAGTG
*
21502672 TTAATTT-AGATAAGAGTATATGTG
1 TTAATTTAAGACAAGAG-ATA-GTG
*
21502696 TTGATTTAAGACAAGAGAT
1 TTAATTTAAGACAAGAGAT
21502715 GTCTTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 11 0.32
22 2 0.06
23 3 0.09
24 10 0.29
25 8 0.24
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (23 bp):
TTAATTTAAGACAAGAGATAGTG
Found at i:21504809 original size:20 final size:20
Alignment explanation
Indices: 21504776--21504828 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
21504766 CAGAAAAGAC
* *
21504776 TTAGTCAACCAAGAAATGAG
1 TTAGTCAACTAAGAAATAAG
* *
21504796 TTAGTCCACTAAGAAGTAAG
1 TTAGTCAACTAAGAAATAAG
21504816 TTAGTCAACTAAG
1 TTAGTCAACTAAG
21504829 TGCTCACTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (20 bp):
TTAGTCAACTAAGAAATAAG
Found at i:21510291 original size:21 final size:22
Alignment explanation
Indices: 21510266--21510306 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21510256 CCTAGGTGGA
*
21510266 AAAATTCAAGGGAA-AAGTGCG
1 AAAATTCAAGGAAACAAGTGCG
21510287 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
21510307 AAAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.15
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGCG
Found at i:21510312 original size:22 final size:21
Alignment explanation
Indices: 21510265--21510312 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21510255 CCCTAGGTGG
* *
21510265 AAAAATTCAAGGGAAAAGTGC
1 AAAAATTCAAGGAAAAAGTGA
*
21510286 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGA
21510308 AAAAA
1 AAAAA
21510313 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.58, C:0.08, G:0.21, T:0.12
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGA
Found at i:21515974 original size:10 final size:10
Alignment explanation
Indices: 21515946--21515984 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
21515936 CCTCACCAAA
21515946 CATCAAATAT
1 CATCAAATAT
*
21515956 CACCAAAATAT
1 CATC-AAATAT
*
21515967 CATGAAATAT
1 CATCAAATAT
21515977 CATCAAAT
1 CATCAAAT
21515985 TCAGCCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (10 bp):
CATCAAATAT
Found at i:21526243 original size:28 final size:28
Alignment explanation
Indices: 21526213--21526383 Score: 198
Period size: 29 Copynumber: 5.9 Consensus size: 28
21526203 TACTTTTAAC
*
21526213 ATGTTTGTCTTAATTTAGACAAGAAAAC
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
21526241 ATGTTTCGTCTTAATTTAGACAAGAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAT
*
21526270 ATGTTTGTATTAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAG-AAAAT
*
21526300 ATTTTTTGTCTTAATTTAGACAAGAAAAT
1 A-TGTTTGTCTTAATTTAGACAAGAAAAT
* * * *
21526329 ATATTTTTCTCAATTTACACAAGATAAAAT
1 ATGTTTGTCTTAATTTAGACAAG--AAAAT
* *
21526359 ATTTTTGTCTTAATTAAAGACAAGA
1 ATGTTTGTCTTAATT-TAGACAAGA
21526384 GTTGTCTGAA
Statistics
Matches: 123, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
28 33 0.27
29 41 0.33
30 30 0.24
31 19 0.15
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAT
Found at i:21526322 original size:59 final size:58
Alignment explanation
Indices: 21526213--21526383 Score: 220
Period size: 59 Copynumber: 2.9 Consensus size: 58
21526203 TACTTTTAAC
* * *
21526213 ATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTCGTCTTAATTTAGACAAGAAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAAT
*
21526270 ATGTTTGTATTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAAT
1 ATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAAT
* * * * *
21526329 ATATTTTTCTCAATTTACACAAGATAAAATA-TTTTTGTCTTAATTAAAGACAAGA
1 ATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAATT-TAGACAAGA
21526384 GTTGTCTGAA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
57 15 0.15
58 28 0.28
59 57 0.57
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (58 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAAAT
Found at i:21545027 original size:43 final size:42
Alignment explanation
Indices: 21544939--21545070 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 42
21544929 GTAATTATAT
* * *
21544939 TGACTCGGTTATGTGCGAGTAGGGAGTGCACATAAGTCGAG-GA
1 TGACTCGATTATGTGCGAGTAGGGAGTGCGCATAACT-G-GTGA
* *
21544982 TGACTCGATTATGTGTGAGTAGGGAGTGCGCCTAACCTGGTGA
1 TGACTCGATTATGTGCGAGTAGGGAGTGCGCATAA-CTGGTGA
* * ** * *
21545025 TGACCCAACCATGTGCAAGTAGGGAGTGCGCATGAGCTGGTGA
1 TGACTCGATTATGTGCGAGTAGGGAGTGCGCAT-AACTGGTGA
21545068 TGA
1 TGA
21545071 TGATGATGTG
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.01
43 70 0.96
44 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (42 bp):
TGACTCGATTATGTGCGAGTAGGGAGTGCGCATAACTGGTGA
Found at i:21564985 original size:27 final size:28
Alignment explanation
Indices: 21564955--21565007 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
21564945 TCGAAGTATA
* *
21564955 GGGGCAAAATC-GTAATTTTTTCACCTC
1 GGGGCAAAATCAATAAATTTTTCACCTC
*
21564982 GGGGCTAAATCAATAAATTTTTCACC
1 GGGGCAAAATCAATAAATTTTTCACC
21565008 CTAGCACTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (28 bp):
GGGGCAAAATCAATAAATTTTTCACCTC
Found at i:21566660 original size:60 final size:60
Alignment explanation
Indices: 21566536--21566663 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
21566526 CTGTAGCTTT
* * * * * * *
21566536 TCGCTGCAGCGAAATTCATTCTCGTTGCAGCGAGAAACTTTCTGTTTATGGGTTACAATT
1 TCGCTGCAGCAAAATTCATTCTCGCTGCAGCGAAAAACTTTCTGTTTATGGATCAAAATC
* * * *
21566596 TCGCTGCAGCAAAATTTATTCTTGCTGTAGTGAAAAACTTTCTGTTTTAT-GATCAAAATC
1 TCGCTGCAGCAAAATTCATTCTCGCTGCAGCGAAAAACTTTCTG-TTTATGGATCAAAATC
21566656 TCGCTGCA
1 TCGCTGCA
21566664 ATGAAAAACT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 51 0.91
61 5 0.09
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (60 bp):
TCGCTGCAGCAAAATTCATTCTCGCTGCAGCGAAAAACTTTCTGTTTATGGATCAAAATC
Found at i:21568180 original size:21 final size:19
Alignment explanation
Indices: 21568144--21568184 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
21568134 ACATGTCGAG
21568144 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
21568163 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
21568184 T
1 T
21568185 GTTTTAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:21572103 original size:19 final size:20
Alignment explanation
Indices: 21572067--21572105 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
21572057 TCGTATAGCT
21572067 ATCTATCGATAAAGATTACAG
1 ATCTATCGAT-AAGATTACAG
21572088 ATCTATCGAT-AGATTACA
1 ATCTATCGATAAGATTACA
21572106 TTCTAGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (20 bp):
ATCTATCGATAAGATTACAG
Found at i:21584357 original size:21 final size:20
Alignment explanation
Indices: 21584333--21584380 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
21584323 ATCTTACCTT
*
21584333 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
21584354 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
21584375 TTTTTC
1 TTTTTC
21584381 TACCTAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:21584380 original size:22 final size:22
Alignment explanation
Indices: 21584338--21584378 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21584328 ACCTTTTTTT
*
21584338 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
21584360 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
21584379 TCTACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:21585189 original size:17 final size:19
Alignment explanation
Indices: 21585148--21585189 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
21585138 ATGTATATAT
21585148 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
21585169 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
21585186 ATGA
1 ATGA
21585190 TGATGACTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:21585315 original size:46 final size:46
Alignment explanation
Indices: 21585184--21585316 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 46
21585174 TAATGTTGTG
* * * *
21585184 TGATGATGATGACTC-GGCTATGTGCCAGTAAGGAGTGCGCATAAGC
1 TGATGATGATGAC-CAGGCTATGTGCGAGTAGGGAGTGCACATGAGC
* * *
21585230 TGATGATGA--CCCA-GCTATGTGCGAGGAGGGACTGCACATGAGC
1 TGATGATGATGACCAGGCTATGTGCGAGTAGGGAGTGCACATGAGC
* *
21585273 TGATGATGATGACCAGGCTATGTACGAGTAGGGAGTGAACATGA
1 TGATGATGATGACCAGGCTATGTGCGAGTAGGGAGTGCACATGA
21585317 CTGTCACGAC
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
43 34 0.48
44 1 0.01
45 3 0.04
46 33 0.46
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.22
Consensus pattern (46 bp):
TGATGATGATGACCAGGCTATGTGCGAGTAGGGAGTGCACATGAGC
Found at i:21586354 original size:38 final size:40
Alignment explanation
Indices: 21586268--21586370 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 40
21586258 ACCCGGCTCA
*
21586268 TGTACATCCCCCAACATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCAACATCGTGCACATAGCCAGCACCATCG
* * * *
21586308 TGTGCATCCCCTC-ACATCGTGCACA-A-TCAGTATCATCG
1 TGTACATCCCC-CAACATCGTGCACATAGCCAGCACCATCG
*
21586346 TGTACATCCCCCTACATCGTGCACA
1 TGTACATCCCCCAACATCGTGCACA
21586371 CGGGCACTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
37 1 0.02
38 30 0.55
39 1 0.02
40 22 0.40
41 1 0.02
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (40 bp):
TGTACATCCCCCAACATCGTGCACATAGCCAGCACCATCG
Found at i:21607361 original size:29 final size:28
Alignment explanation
Indices: 21607283--21607469 Score: 205
Period size: 28 Copynumber: 6.5 Consensus size: 28
21607273 TAGCTTAAAC
*
21607283 ATGTTTGTCTTAATTTAGACAAGAAAAC
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
*
21607311 ATGTTTGTCTTAATTTATACAAGAAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
21607339 ATGTTTGGTCTTAATTTAGACAAGAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAT
*
21607368 ATATTTGTCTTAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAG-AAAAT
* * * *
21607398 ACGTTTTTTCTTAATCTAGACAAGAAAAC
1 ATG-TTTGTCTTAATTTAGACAAGAAAAT
* * *
21607427 ATATTTGT-TTCAATTTAGAAAATATAATAT
1 ATGTTTGTCTT-AATTTAGACAAGA-AA-AT
*
21607457 ATTTTTGTCTTAA
1 ATGTTTGTCTTAA
21607470 ATTAAAATAA
Statistics
Matches: 134, Mismatches: 17, Indels: 14
0.81 0.10 0.08
Matches are distributed among these distances:
27 2 0.01
28 56 0.42
29 40 0.30
30 23 0.17
31 13 0.10
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAT
Found at i:21607375 original size:57 final size:57
Alignment explanation
Indices: 21607283--21607469 Score: 225
Period size: 59 Copynumber: 3.2 Consensus size: 57
21607273 TAGCTTAAAC
* *
21607283 ATGTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTATACAAG-AAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGAAAAAT
*
21607339 ATGTTTGGTCTTAATTTAGACAAGAAAATATATTTGTCTTAATTTAAGACAAGAAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTT-AGACAAGAAAAAT
* * * * * *
21607398 ACGTTTTTTCTTAATCTAGACAAGAAAACATATTTGT-TTCAATTTAGAAAATATAATAT
1 ATG-TTTGTCTTAATTTAGACAAGAAAACATATTTGTCTT-AATTTAGACAAGA-AAAAT
*
21607457 ATTTTTGTCTTAA
1 ATGTTTGTCTTAA
21607470 ATTAAAATAA
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
56 6 0.05
57 36 0.32
58 23 0.21
59 44 0.39
60 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (57 bp):
ATGTTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGAAAAAT
Found at i:21615186 original size:16 final size:17
Alignment explanation
Indices: 21615154--21615186 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21615144 CACATTTAAC
21615154 TAACTAAAACTATCAAAT
1 TAACTAAAAC-ATCAAAT
21615172 TAACTAAAA-ATCAAA
1 TAACTAAAACATCAAA
21615187 ACCTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
TAACTAAAACATCAAAT
Found at i:21635936 original size:11 final size:11
Alignment explanation
Indices: 21635916--21635945 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21635906 TCCGATTAAA
21635916 TATTAATATTT
1 TATTAATATTT
*
21635927 TATTATTATTT
1 TATTAATATTT
21635938 TATTAATA
1 TATTAATA
21635946 AAATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTAATATTT
Found at i:21642542 original size:42 final size:42
Alignment explanation
Indices: 21642494--21642576 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
21642484 ACATGGCTGG
*
21642494 GTCATCATCAGCTTATGTTCACTCCTACTCACACATAGTCGA
1 GTCATCATCAGCTTATGTACACTCCTACTCACACATAGTCGA
* *
21642536 GTCATCATCGGCTTATGTACACTCCTACTCGCACATAGTCG
1 GTCATCATCAGCTTATGTACACTCCTACTCACACATAGTCG
21642577 GGTCCACATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.30
Consensus pattern (42 bp):
GTCATCATCAGCTTATGTACACTCCTACTCACACATAGTCGA
Found at i:21644173 original size:42 final size:42
Alignment explanation
Indices: 21644124--21644275 Score: 146
Period size: 42 Copynumber: 3.6 Consensus size: 42
21644114 TGTAGACACA
*
21644124 ACTATGTGCGAGTAGGAGTGCTCATACA-CCGATGATGACCCG
1 ACTATGTGCGAGTAGGAGTGCACATA-AGCCGATGATGACCCG
* * * *
21644166 GCTATGTGCGAGTAGAAGTGCACATAAGTC-ATTGATGACTCG
1 ACTATGTGCGAGTAGGAGTGCACATAAGCCGA-TGATGACCCG
* * * * *
21644208 ACGATATGCGAGTAGGAGTGCGCATAAGCCGATGCTGACCCA
1 ACTATGTGCGAGTAGGAGTGCACATAAGCCGATGATGACCCG
* * *
21644250 ACCATGTGCTAATAGGGAGTGCACAT
1 ACTATGTGCGAGTA-GGAGTGCACAT
21644276 GAACTGACGA
Statistics
Matches: 87, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.02
42 74 0.85
43 11 0.13
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (42 bp):
ACTATGTGCGAGTAGGAGTGCACATAAGCCGATGATGACCCG
Found at i:21646359 original size:54 final size:54
Alignment explanation
Indices: 21646144--21646359 Score: 263
Period size: 54 Copynumber: 4.0 Consensus size: 54
21646134 ATTAGTATAC
* * * * *
21646144 CACCACATCTCATCC-AGCTCATGTGCATCCCCACACATTGTGCACATGGCCGAA
1 CACCCCATCTCA-CCTAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGA
* * *
21646198 CACCCCATCTCACCTAGCTCATGTTCATCCCCCCACATCGTCCACATAGCCAGA
1 CACCCCATCTCACCTAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGA
* * * * * *
21646252 CACCCTATCTCACCCAACTCATGTGCATCCCCCCATATCATGCACATAACCGGA
1 CACCCCATCTCACCTAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGA
* * *
21646306 CACCCCATCTCACCTAGCTCATGTGCATCCCCCTATATCGTGGACATAGCCGGA
1 CACCCCATCTCACCTAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGA
21646360 GTTATCGTGT
Statistics
Matches: 137, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 2 0.01
54 135 0.99
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (54 bp):
CACCCCATCTCACCTAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCGGA
Found at i:21647571 original size:35 final size:35
Alignment explanation
Indices: 21647532--21647640 Score: 103
Period size: 35 Copynumber: 2.9 Consensus size: 35
21647522 TCAAATTTGT
*
21647532 AACAAAACTCTTTCTTTTACCTTCTCAAAATTTCC
1 AACAAAACTCTTTCTTTTACCTTCTCAAAATTTAC
*
21647567 AACAAAACTCTTTCTATTTCTATTTCCTTCTAAAAATTTAC
1 AACAAAACTCTTTC--TTT-TA---CCTTCTCAAAATTTAC
** *
21647608 AGTAAAACTCTTTCTATTT-CCCTCTCAAAATTT
1 AACAAAACTCTTTCT-TTTACCTTCTCAAAATTT
21647641 TGCAGCATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
35 26 0.43
37 3 0.05
38 2 0.03
39 2 0.03
40 2 0.03
41 26 0.43
ACGTcount: A:0.32, C:0.25, G:0.01, T:0.42
Consensus pattern (35 bp):
AACAAAACTCTTTCTTTTACCTTCTCAAAATTTAC
Found at i:21647587 original size:41 final size:41
Alignment explanation
Indices: 21647542--21647627 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
21647532 AACAAAACTC
* *
21647542 TTTCT-TTTACCTTCTCAAAATTTCCAACAAAACTCTTTCTA
1 TTTCTATTT-CCTTCTAAAAATTTACAACAAAACTCTTTCTA
**
21647583 TTTCTATTTCCTTCTAAAAATTTACAGTAAAACTCTTTCTA
1 TTTCTATTTCCTTCTAAAAATTTACAACAAAACTCTTTCTA
21647624 TTTC
1 TTTC
21647628 CCTCTCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 37 0.93
42 3 0.08
ACGTcount: A:0.29, C:0.23, G:0.01, T:0.47
Consensus pattern (41 bp):
TTTCTATTTCCTTCTAAAAATTTACAACAAAACTCTTTCTA
Found at i:21647809 original size:45 final size:48
Alignment explanation
Indices: 21647734--21647826 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 48
21647724 CCTCGACTAG
*
21647734 CGACTTTCCCCTTTGCTCTCTCTCACACCGACTTCTTTCTTT-CTTCTT
1 CGACTTTCCCCTTTGC-CTCTCTCACACCGACTTCTCTCTTTCCTTCTT
21647782 CGACTTT-CCCTTTG-CTCTCTCACACCGACTTCTCTCTTTCCTTCT
1 CGACTTTCCCCTTTGCCTCTCTCACACCGACTTCTCTCTTTCCTTCT
21647827 CCAAATAGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 24 0.56
46 5 0.12
47 7 0.16
48 7 0.16
ACGTcount: A:0.09, C:0.41, G:0.06, T:0.44
Consensus pattern (48 bp):
CGACTTTCCCCTTTGCCTCTCTCACACCGACTTCTCTCTTTCCTTCTT
Found at i:21652211 original size:2 final size:2
Alignment explanation
Indices: 21652204--21652240 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21652194 TTTCTTTGAC
21652204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21652241 CATTATCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21652341 original size:43 final size:42
Alignment explanation
Indices: 21652294--21652397 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 42
21652284 TCCCCACTCG
*
21652294 CACATAGCTGGGTCATCATCAGCTTATGTGCACTCCAATGC-CA
1 CACATAGCTGGGTCATCATCAGCTCATGTGCACTCCAA--CACA
* * * * *
21652337 CACATAGTTGGGTCATCCTCAGCTCATGTTCACTCCCACACG
1 CACATAGCTGGGTCATCATCAGCTCATGTGCACTCCAACACA
*
21652379 CACATAACTGGGTCATCAT
1 CACATAGCTGGGTCATCAT
21652398 TATCACACAA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 17 0.33
43 33 0.65
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (42 bp):
CACATAGCTGGGTCATCATCAGCTCATGTGCACTCCAACACA
Found at i:21661122 original size:26 final size:26
Alignment explanation
Indices: 21661062--21661123 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
21661052 ACCATATACC
*
21661062 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
21661088 CATCATCATCATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
21661114 CATCATCATC
1 CATCATCATC
21661124 TCATATGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.23
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:21663060 original size:42 final size:42
Alignment explanation
Indices: 21662988--21663070 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
21662978 GGGTCTCACA
* * *
21662988 AGCATAGCTCATGTGCATTCATACATCGCACATGGCTGGGTC
1 AGCACAGCTCATGTGCACTCATACAACGCACATGGCTGGGTC
*
21663030 AGCACAGCTCATGTGCACTCTTACAACGCACATGGCTGGGT
1 AGCACAGCTCATGTGCACTCATACAACGCACATGGCTGGGT
21663071 TGTAATTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (42 bp):
AGCACAGCTCATGTGCACTCATACAACGCACATGGCTGGGTC
Found at i:21668760 original size:159 final size:160
Alignment explanation
Indices: 21668469--21668766 Score: 481
Period size: 159 Copynumber: 1.9 Consensus size: 160
21668459 TATATAAAAA
* * *
21668469 AGAGATTTTCACCTTAGGGGTAAAATGGTAATTTTACATCTCGAGTCTAAATTTTTAAGTTTTCA
1 AGAGATTTTAACCTTAAGGGTAAAATGATAATTTTACATCTCGAGTCTAAATTTTTAAGTTTTCA
* * * * *
21668534 TCAACTTGAGTACCTTTAATCTATTTTGGACCTTTTCTCAATGTCAAAAAAGTAAAAAGATTGCA
66 TAAACTCGAGTACCTCTAATCTATTGTGGACCTTTGCTCAATGTCAAAAAAGTAAAAAGATTGCA
21668599 CAA-AAAAAGAACAAGAAGACAAAGAAGAG
131 CAAGAAAAAGAACAAGAAGACAAAGAAGAG
* *
21668628 AGAGATTTTAATCTTAAGGGTAAAATGATAATTTTACATCTCGAGTCTAAATTTTTAAGTTTTCC
1 AGAGATTTTAACCTTAAGGGTAAAATGATAATTTTACATCTCGAGTCTAAATTTTTAAGTTTTCA
* *
21668693 TAAACTCGAGTACCTCTAATCTATTGTGGACCTTTGCTCAATGTCAAAAGAGTAAAAAGATTTCA
66 TAAACTCGAGTACCTCTAATCTATTGTGGACCTTTGCTCAATGTCAAAAAAGTAAAAAGATTGCA
21668758 CAAGAAAAA
131 CAAGAAAAA
21668767 AAAAATAAGG
Statistics
Matches: 126, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
159 121 0.96
160 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (160 bp):
AGAGATTTTAACCTTAAGGGTAAAATGATAATTTTACATCTCGAGTCTAAATTTTTAAGTTTTCA
TAAACTCGAGTACCTCTAATCTATTGTGGACCTTTGCTCAATGTCAAAAAAGTAAAAAGATTGCA
CAAGAAAAAGAACAAGAAGACAAAGAAGAG
Found at i:21686549 original size:37 final size:37
Alignment explanation
Indices: 21686442--21686552 Score: 114
Period size: 37 Copynumber: 3.0 Consensus size: 37
21686432 CCTCAACCCT
* * *** * * *
21686442 TGTGCACTCCTTACACGCACAAGGCAATACCACCATA
1 TGTGCACTCCCTACTCGCACACCTCAATATCATCATG
** *
21686479 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCGCACACCTCAATATCATCATG
*
21686516 TGTGCACTCCCTACTCGCACACCTCATTATCATCATG
1 TGTGCACTCCCTACTCGCACACCTCAATATCATCATG
21686553 CAACATTATT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.25, C:0.35, G:0.13, T:0.27
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACACCTCAATATCATCATG
Found at i:21687652 original size:199 final size:198
Alignment explanation
Indices: 21687311--21687708 Score: 753
Period size: 199 Copynumber: 2.0 Consensus size: 198
21687301 AGGAAATATA
21687311 TGGAAGTTTCAAAGCAAGCTTCCATGGGGGGTGCAAAAAATGTGGGCAAAGAAGAAGAAGAAGAA
1 TGGAAGTTTCAAAGCAAGCTTCCATGGGGGGTGCAAAAAATGTGGGCAAAGAAGAAGAAGAAGAA
*
21687376 GAAGTGCTGGAAATTTGAAGCACCTCCTAGAAACTTAGATATTTATGCTATATGTTTATCCATTT
66 GAAGTGCTGGAAATTTGAAGCACCTCCTAGAAACTTAGATATTTATGCTATATGCTTATCCATTT
21687441 TCTCATGAAATTACCAAAATGTCCTTAACAAGGTCATTTTATCTTTCCATTGCCTTTATGCAATC
131 TCTCATGAAATTACCAAAATGTCCTTAACAAGGTCATTTTATCTTTCCATTGCCTTTATGCAATC
21687506 TTT
196 TTT
21687509 TNGGAAGTTTCAAAGCAAGCTTCCATGGGGGGTGCAAAAAATGT-GGCAAAAGAAGAAGAAGAAG
1 T-GGAAGTTTCAAAGCAAGCTTCCATGGGGGGTGCAAAAAATGTGGGC-AAAGAAGAAGAAGAAG
*
21687573 AAGAAGTGCTGGAAATTTGAAGCACCTCCTAGAAACTTAGATATTTATGCTTTATGCTTATCCAT
64 AAGAAGTGCTGGAAATTTGAAGCACCTCCTAGAAACTTAGATATTTATGCTATATGCTTATCCAT
21687638 TTTCTCATGAAATTACCAAAATGTCCTTAACAAGGTCATTTTATCTTTCCATTGCCTTTATGCAA
129 TTTCTCATGAAATTACCAAAATGTCCTTAACAAGGTCATTTTATCTTTCCATTGCCTTTATGCAA
21687703 TCTTT
194 TCTTT
21687708 T
1 T
21687709 TACTTCTTTG
Statistics
Matches: 196, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
198 4 0.02
199 192 0.98
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (198 bp):
TGGAAGTTTCAAAGCAAGCTTCCATGGGGGGTGCAAAAAATGTGGGCAAAGAAGAAGAAGAAGAA
GAAGTGCTGGAAATTTGAAGCACCTCCTAGAAACTTAGATATTTATGCTATATGCTTATCCATTT
TCTCATGAAATTACCAAAATGTCCTTAACAAGGTCATTTTATCTTTCCATTGCCTTTATGCAATC
TTT
Found at i:21688368 original size:36 final size:37
Alignment explanation
Indices: 21688237--21688370 Score: 173
Period size: 36 Copynumber: 3.6 Consensus size: 37
21688227 TAACCGTGTG
* *
21688237 TGTGCAGTGTGGGAGTGCACATGCTGATGATATATGCCA
1 TGTGCGGTGTGGGAGTGCACATGATGAT-AT-TATGCCA
* * *
21688276 TATGCGGTGTGGGAGTGCACGTAATGATA-TATGCCA
1 TGTGCGGTGTGGGAGTGCACATGATGATATTATGCCA
* *
21688312 TGTGCGGTGTGGGAGTGCACATGAGGATATTAT-CTA
1 TGTGCGGTGTGGGAGTGCACATGATGATATTATGCCA
21688348 TGTGCGGTGTGGGAGTGCACATG
1 TGTGCGGTGTGGGAGTGCACATG
21688371 TGCTGAGTTG
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
36 57 0.68
37 3 0.04
38 1 0.01
39 23 0.27
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.28
Consensus pattern (37 bp):
TGTGCGGTGTGGGAGTGCACATGATGATATTATGCCA
Found at i:21689407 original size:15 final size:16
Alignment explanation
Indices: 21689387--21689418 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21689377 TGTTATTATG
21689387 ATTA-TTTATTTTTAA
1 ATTATTTTATTTTTAA
21689402 ATTATTTTATTTTTAA
1 ATTATTTTATTTTTAA
21689418 A
1 A
21689419 CATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATTTTATTTTTAA
Found at i:21690274 original size:27 final size:28
Alignment explanation
Indices: 21690244--21690318 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 28
21690234 AGACATTAAA
* *
21690244 GTGTAACAA-AATGTTTTTGAATATGGC
1 GTGTAACAACAATATTTTTCAATATGGC
* * *
21690271 GTGTAACAATGATTTTTTTTCAATATGGC
1 GTGTAACAA-CAATATTTTTCAATATGGC
21690300 GTGTAACAACAATATTTTT
1 GTGTAACAACAATATTTTT
21690319 TTTCAACATG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.22
28 7 0.17
29 24 0.60
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.41
Consensus pattern (28 bp):
GTGTAACAACAATATTTTTCAATATGGC
Found at i:21690299 original size:29 final size:28
Alignment explanation
Indices: 21690244--21690339 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 28
21690234 AGACATTAAA
* * *
21690244 GTGTAACAA-AATGTTTTTGAATATGGC
1 GTGTAACAATATTTTTTTTCAATATGGC
21690271 GTGTAACAATGATTTTTTTTCAATATGGC
1 GTGTAACAAT-ATTTTTTTTCAATATGGC
* *
21690300 GTGTAACAACAATATTTTTTTTCAACATGGT
1 GTGT---AACAATATTTTTTTTCAATATGGC
21690331 GTGTAACAA
1 GTGTAACAA
21690340 CTTTTTGTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.15
28 5 0.08
29 19 0.32
31 20 0.34
32 6 0.10
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (28 bp):
GTGTAACAATATTTTTTTTCAATATGGC
Found at i:21690320 original size:31 final size:32
Alignment explanation
Indices: 21690257--21690340 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 32
21690247 TAACAAAATG
*
21690257 TTTTTGAATATGGCGTGT---AACAATGATTT
1 TTTTTCAATATGGCGTGTAACAACAATGATTT
21690286 TTTTTCAATATGGCGTGTAACAACAAT-ATTT
1 TTTTTCAATATGGCGTGTAACAACAATGATTT
* *
21690317 TTTTTCAACATGGTGTGTAACAAC
1 TTTTTCAATATGGCGTGTAACAAC
21690341 TTTTTGTAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 17 0.35
31 26 0.53
32 6 0.12
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (32 bp):
TTTTTCAATATGGCGTGTAACAACAATGATTT
Done.