Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 159 of 235
Found at i:53601712 original size:22 final size:23
Alignment explanation
Indices: 53601687--53601733 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
53601677 ATTTAAACAT
53601687 AATCACCTATA-TTTGTTTTTGA
1 AATCACCTATATTTTGTTTTTGA
*
53601709 AATCACCTTTATTTTGTTTTTGA
1 AATCACCTATATTTTGTTTTTGA
53601732 AA
1 AA
53601734 ACTTTTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
AATCACCTATATTTTGTTTTTGA
Found at i:53604854 original size:19 final size:19
Alignment explanation
Indices: 53604805--53604854 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
53604795 TCCAAGAATT
53604805 TGATAGAGTTTTGAGAGGA
1 TGATAGAGTTTTGAGAGGA
*
53604824 TAATATGAGTTTTGAGAGGA
1 TGATA-GAGTTTTGAGAGGA
53604844 TGATAGAGTTT
1 TGATAGAGTTT
53604855 AGATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (19 bp):
TGATAGAGTTTTGAGAGGA
Found at i:53607023 original size:12 final size:12
Alignment explanation
Indices: 53607006--53607032 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53606996 CTGGTGATTG
53607006 GAATATCATAGA
1 GAATATCATAGA
53607018 GAATATCATAGA
1 GAATATCATAGA
53607030 GAA
1 GAA
53607033 AGAATAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (12 bp):
GAATATCATAGA
Found at i:53613120 original size:44 final size:42
Alignment explanation
Indices: 53613054--53613199 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 42
53613044 CATATATAAT
* *
53613054 GAAAATAATATTAGTATATAAATAGAAATAAAAATATAATAAATA
1 GAAAATAATAATAG--TATAAATAGAAATAATAA-ATAATAAATA
* *
53613099 GAAATATAATAATAGTATAAATATAAATAGATAAATAATAATTA
1 GAAA-ATAATAATAGTATAAATAGAAATA-ATAAATAATAAATA
*
53613143 GATAAATAATAATAGTATTAGAATAGCAA-AATAAAT-ATAAATA
1 GA-AAATAATAATAGTA-TA-AATAGAAATAATAAATAATAAATA
53613186 GAAACATAATAATA
1 GAAA-ATAATAATA
53613200 ATAGCAATAA
Statistics
Matches: 88, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 17 0.19
44 42 0.48
45 12 0.14
46 15 0.17
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (42 bp):
GAAAATAATAATAGTATAAATAGAAATAATAAATAATAAATA
Found at i:53613125 original size:29 final size:28
Alignment explanation
Indices: 53613092--53613199 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 28
53613082 TAAAAATATA
53613092 ATAAATAGAAATATAATAATAGTATAAAT
1 ATAAATAGAAATATAATAATAG-ATAAAT
53613121 ATAAATAGATAA-ATAATAATTAGATAAAT
1 ATAAATAGA-AATATAATAA-TAGATAAAT
* * * *
53613150 A-ATAATAGTATTAGAATAGCA-AAATAAAT
1 ATA-AATAGAAATATAATA--ATAGATAAAT
*
53613179 ATAAATAGAAACATAATAATA
1 ATAAATAGAAATATAATAATA
53613200 ATAGCAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
27 1 0.02
28 3 0.05
29 52 0.83
30 6 0.10
31 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (28 bp):
ATAAATAGAAATATAATAATAGATAAAT
Found at i:53613155 original size:15 final size:15
Alignment explanation
Indices: 53613089--53613154 Score: 84
Period size: 15 Copynumber: 4.5 Consensus size: 15
53613079 AAATAAAAAT
53613089 ATAATAAATAGA-AA
1 ATAATAAATAGATAA
53613103 TATAAT-AATAGTATAA
1 -ATAATAAATAG-ATAA
53613119 AT-ATAAATAGATAA
1 ATAATAAATAGATAA
*
53613133 ATAATAATTAGATAA
1 ATAATAAATAGATAA
53613148 ATAATAA
1 ATAATAA
53613155 TAGTATTAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
14 13 0.28
15 31 0.67
16 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (15 bp):
ATAATAAATAGATAA
Found at i:53614278 original size:44 final size:44
Alignment explanation
Indices: 53614227--53614549 Score: 155
Period size: 44 Copynumber: 7.3 Consensus size: 44
53614217 GTTACCTTAT
*
53614227 TGCTTAGGGAGTTAAGGCTCACTGTCTTCGATCTGCTCCACTAC
1 TGCTTAGGGAGATAAGGCTCACTGTCTTCGATCTGCTCCACTAC
* * * * ** * *
53614271 TGTTTAGGGAGATAAGATCTGTAAT-TCCCCG-CCTGTTACC-CTAC
1 TGCTTAGGGAGATAAG-GCT-CACTGTCTTCGATCTGCT-CCACTAC
* * * *
53614315 TGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGGTCCACTAC
1 TGCTTAGGGAGATAAGGCTCACTGTCTTCGATCTGCTCCACTAC
* ** * * *
53614359 TGCTTAAGGAGATAATATCTACAAT-T-TTC-AGCCTGTTACC-CTAC
1 TGCTTAGGGAGATAA-GGCT-CACTGTCTTCGA-TCTGCT-CCACTAC
* * * *
53614403 TGCTTAGGGGGTTAAGGCTCACCGTCTTCGATTTGCTCCACTAC
1 TGCTTAGGGAGATAAGGCTCACTGTCTTCGATCTGCTCCACTAC
* * * * * **
53614447 TGCTTAAGGAGATAAGATCTGTAAT-T-TTC-AGCCTATTACC-CTAC
1 TGCTTAGGGAGATAAG-GCT-CACTGTCTTCGA-TCTGCT-CCACTAC
* * * *
53614491 TACTTAGGGGGCTAAGGCTCACCGTCTTCGATCTGCTCCACTAC
1 TGCTTAGGGAGATAAGGCTCACTGTCTTCGATCTGCTCCACTAC
*
53614535 TGTTTAGGGAGATAA
1 TGCTTAGGGAGATAA
53614550 AATCTGTAAT
Statistics
Matches: 192, Mismatches: 65, Indels: 44
0.64 0.22 0.15
Matches are distributed among these distances:
42 4 0.02
43 20 0.10
44 143 0.74
45 20 0.10
46 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (44 bp):
TGCTTAGGGAGATAAGGCTCACTGTCTTCGATCTGCTCCACTAC
Found at i:53614329 original size:88 final size:88
Alignment explanation
Indices: 53614179--53614565 Score: 567
Period size: 88 Copynumber: 4.4 Consensus size: 88
53614169 GTTAGTTTCT
* * * * * *
53614179 CTACTACTTAGGGGGATAAGATCTGTAATTTTTAGCCTGTTACCTTATTGCTTAGGGAGTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
53614244 CTCACTGTCTTCGATCTGCTCCA
66 CTCACCGTCTTCGATCTGCTCCA
* ** *
53614267 CTACTGTTTAGGGAGATAAGATCTGTAATTCCCCGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
53614332 CTCACCGTCTTCGATCTGGTCCA
66 CTCACCGTCTTCGATCTGCTCCA
* * **
53614355 CTACTGCTTAAGGAGATAATATCTACAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
53614420 CTCACCGTCTTCGATTTGCTCCA
66 CTCACCGTCTTCGATCTGCTCCA
* * * *
53614443 CTACTGCTTAAGGAGATAAGATCTGTAATTTTCAGCCTATTACCCTACTACTTAGGGGGCTAAGG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
53614508 CTCACCGTCTTCGATCTGCTCCA
66 CTCACCGTCTTCGATCTGCTCCA
* *
53614531 CTACTGTTTAGGGAGATAAAATCTGTAATTTTCAG
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAG
53614566 TCTGCTTCCT
Statistics
Matches: 267, Mismatches: 32, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 267 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (88 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
CTCACCGTCTTCGATCTGCTCCA
Found at i:53614740 original size:45 final size:45
Alignment explanation
Indices: 53614652--53614742 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
53614642 CGATGGCTAA
* *
53614652 AATCTGCTCCATAGTCGATACATGGAGATAAGACTCTCCATTTTC
1 AATCTGCTCCATAGTCGATACAAGGAGATAAGACTCTCAATTTTC
* * *
53614697 AATCTGTTCCATAGTTGATACAAGGAGATAAGA-TCTGTAATTTTC
1 AATCTGCTCCATAGTCGATACAAGGAGATAAGACTCT-CAATTTTC
53614742 A
1 A
53614743 GTCTACTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 3 0.08
45 37 0.93
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (45 bp):
AATCTGCTCCATAGTCGATACAAGGAGATAAGACTCTCAATTTTC
Found at i:53614761 original size:178 final size:178
Alignment explanation
Indices: 53614542--53614862 Score: 489
Period size: 178 Copynumber: 1.8 Consensus size: 178
53614532 TACTGTTTAG
* * * * *
53614542 GGAGATAAAATCTGTAATTTTCAGTCTGCTTCCTTGCTATCTCAAGAAGATAAGGCTTGTATTTT
1 GGAGATAAAATCTGTAATTTTCAGTCTACTTCCTTGCTATCTCAAGAAAAGAAGACTTGTATCTT
* * * *
53614607 CGACCTGCTCTCTTGCTACCTCAGAAAGATAAGGCCGATGGCTAAAATCTGCTCCATAGTCGATA
66 CAACCTGCTCTCTTGCTACCTCAGAAAGATAAGACCGATGGCTAAAATCTGCTCCATAGCCAATA
*
53614672 CATGGAGATAAGACTCTCCATTTTCAATCTGTTCCATAGTTGATACAA
131 CATAGAGATAAGACTCTCCATTTTCAATCTGTTCCATAGTTGATACAA
* * *
53614720 GGAGATAAGATCTGTAATTTTCAGTCTACTTCTTTGCTATCTCAAGAAAAGAAGACTTTTATCTT
1 GGAGATAAAATCTGTAATTTTCAGTCTACTTCCTTGCTATCTCAAGAAAAGAAGACTTGTATCTT
* * * *
53614785 CAACCTGCTCTCTTGCTACTTCAGAGAGATAATACCGGTGGCTAAAATCTGCTCCATAGCCAATA
66 CAACCTGCTCTCTTGCTACCTCAGAAAGATAAGACCGATGGCTAAAATCTGCTCCATAGCCAATA
53614850 CATAGAGATAAGA
131 CATAGAGATAAGA
53614863 TCTATAATTT
Statistics
Matches: 126, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
178 126 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (178 bp):
GGAGATAAAATCTGTAATTTTCAGTCTACTTCCTTGCTATCTCAAGAAAAGAAGACTTGTATCTT
CAACCTGCTCTCTTGCTACCTCAGAAAGATAAGACCGATGGCTAAAATCTGCTCCATAGCCAATA
CATAGAGATAAGACTCTCCATTTTCAATCTGTTCCATAGTTGATACAA
Found at i:53615007 original size:133 final size:133
Alignment explanation
Indices: 53614697--53614995 Score: 420
Period size: 133 Copynumber: 2.2 Consensus size: 133
53614687 CTCCATTTTC
* ** * *
53614697 AATCTGTTCCATAGTTGATACAAGGAGATAAGATCTGTAATTTTCAGTCTACTTCTTTGCTATCT
1 AATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTACTTCTTTGCTACCT
* * *
53614762 CAAGAAAAGAAGACTTTTATCTTCAACCTGCTCTCTTGCTACTTCAGAGAGATAATACCGGTGGC
66 CAAGAAAAGAAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACCGGTGGC
53614827 TAA
131 TAA
* * * **
53614830 AATCTGCTCCATAGCCAATACATAGAGATAAGATCTATAATTTTCAGTCTGTTTCCTTT-CTACC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTACTT-CTTTGCTACC
* * * * *
53614894 TCAGGAAGATAAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGG
65 TCAAGAAAAGAAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACCGGTGG
53614959 CTAA
130 CTAA
53614963 AATCTGCTCCATAGCCGATACATGGAGATAAGA
1 AATCTGCTCCATAGCCGATACATGGAGATAAGA
53614996 CCCGCCATTT
Statistics
Matches: 145, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
133 141 0.97
134 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (133 bp):
AATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTACTTCTTTGCTACCT
CAAGAAAAGAAGACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACCGGTGGC
TAA
Found at i:53622176 original size:27 final size:27
Alignment explanation
Indices: 53622115--53622180 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
53622105 ATCACTATAC
*
53622115 AAACAATATAAAAACTTTAAAACAAGTA
1 AAACGATAT-AAAACTTTAAAACAAGTA
* * * *
53622143 ATA-GATATAAAAGTTTAAAATAGGTA
1 AAACGATATAAAACTTTAAAACAAGTA
53622169 AAACGATA-AAAA
1 AAACGATATAAAA
53622181 TAAATAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 21 0.68
27 8 0.26
28 2 0.06
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.23
Consensus pattern (27 bp):
AAACGATATAAAACTTTAAAACAAGTA
Found at i:53622435 original size:15 final size:17
Alignment explanation
Indices: 53622415--53622456 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
53622405 TATAAATAGG
53622415 AATAGAAATACAAT-A-
1 AATAGAAATACAATAAT
*
53622430 AATAGAAATATAATAAT
1 AATAGAAATACAATAAT
53622447 AATAGAAATA
1 AATAGAAATA
53622457 TAATTAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 13 0.54
16 1 0.04
17 10 0.42
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (17 bp):
AATAGAAATACAATAAT
Found at i:53622457 original size:17 final size:15
Alignment explanation
Indices: 53622415--53622460 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 15
53622405 TATAAATAGG
*
53622415 AATAGAAATACAATA
1 AATAGAAATATAATA
53622430 AATAGAAATATAATAA
1 AATAGAAATATAAT-A
53622446 TAATAGAAATATAAT
1 -AATAGAAATATAAT
53622461 TAGATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 13 0.46
16 1 0.04
17 14 0.50
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (15 bp):
AATAGAAATATAATA
Found at i:53625701 original size:26 final size:26
Alignment explanation
Indices: 53625665--53625728 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
53625655 AGTTAAGAAA
53625665 TTATAT-A-AATAAAATGT-TTAAATT
1 TTATATAAGAATAAAAT-TATTAAATT
* *
53625689 TTATATAAGAATAATATTAGTTATATT
1 TTATATAAGAATAAAATTA-TTAAATT
53625716 TTAT-TAAGAATAA
1 TTATATAAGAATAA
53625729 TTTTTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 6 0.18
25 2 0.06
26 16 0.47
27 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
TTATATAAGAATAAAATTATTAAATT
Found at i:53627349 original size:21 final size:21
Alignment explanation
Indices: 53627302--53627349 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
53627292 AATTTATTCC
*
53627302 TTTAA-TATTTTAAATTTGTC
1 TTTAATTATTTTAAATTTGTA
* *
53627322 TTATAATTATTTTAATTTTTTA
1 TT-TAATTATTTTAAATTTGTA
53627344 TTTAAT
1 TTTAAT
53627350 ACAAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 7 0.30
22 14 0.61
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTAATTATTTTAAATTTGTA
Found at i:53633765 original size:25 final size:25
Alignment explanation
Indices: 53633748--53633874 Score: 141
Period size: 25 Copynumber: 5.1 Consensus size: 25
53633738 AGCTCTTGCA
*
53633748 AGCCAAATATCGGGAAGCT-AAGAG
1 AGCCAAATATCGGGAAGCTCATGAG
*
53633772 AGCC-ATTAATCGGGAAGCTCATGAG
1 AGCCAAAT-ATCGGGAAGCTCATGAG
* * * *
53633797 AGCTAAATAACGAGAAGCTCGTGAG
1 AGCCAAATATCGGGAAGCTCATGAG
* *
53633822 AGCCAAGTATCGGGAAGCTCGTGAG
1 AGCCAAATATCGGGAAGCTCATGAG
* *
53633847 AGCCAAATATCGGGACGCTCATAAG
1 AGCCAAATATCGGGAAGCTCATGAG
53633872 AGC
1 AGC
53633875 TGTGGTGTGT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
23 2 0.02
24 15 0.18
25 66 0.78
26 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (25 bp):
AGCCAAATATCGGGAAGCTCATGAG
Found at i:53640679 original size:43 final size:43
Alignment explanation
Indices: 53640595--53640680 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
53640585 AAGTCGTACA
*
53640595 ATGCCAATGTCCCAGACGTGGTCTAACATGTAACCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTAACATGTAAACACATATCG
* * *
53640638 ATGCCACTGTCCCAGACAG-GGTCTTAC-TCGTAAACATATATCG
1 ATGCCAATGTCCCAGAC-GTGGTCTAACAT-GTAAACACATATCG
53640681 GAATCCTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.03
43 35 0.95
44 1 0.03
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTAACATGTAAACACATATCG
Found at i:53645723 original size:18 final size:18
Alignment explanation
Indices: 53645700--53645738 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
53645690 GATGGAGGAT
53645700 AGCGAGGGCGATGAAGTA
1 AGCGAGGGCGATGAAGTA
53645718 AGCGAGGGCGATGAAGTA
1 AGCGAGGGCGATGAAGTA
53645736 AGC
1 AGC
53645739 AAGGTCGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.44, T:0.10
Consensus pattern (18 bp):
AGCGAGGGCGATGAAGTA
Found at i:53655151 original size:55 final size:55
Alignment explanation
Indices: 53655083--53655208 Score: 146
Period size: 55 Copynumber: 2.3 Consensus size: 55
53655073 AAGCCTGCCA
* * * *
53655083 AAAC-AACATGGGCGTGCGACACGCCCGTGTAGAAGACCCGTGGTTGAAACTGAG
1 AAACTAACACGGGCGTGAGACACGCCCGTGTAGAACACCCGTGGTCGAAACTGAG
* ** * **
53655137 AAACTAGCACGGGCGTGAGACACGCCCGTGTCTAACACCCGTGGTCGAACCTGTT
1 AAACTAACACGGGCGTGAGACACGCCCGTGTAGAACACCCGTGGTCGAAACTGAG
*
53655192 AAATTAACACGGGCGTG
1 AAACTAACACGGGCGTG
53655209 GGGCTTGCAT
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
54 4 0.07
55 55 0.93
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (55 bp):
AAACTAACACGGGCGTGAGACACGCCCGTGTAGAACACCCGTGGTCGAAACTGAG
Found at i:53660253 original size:14 final size:14
Alignment explanation
Indices: 53660236--53660262 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53660226 TATTAAAATA
53660236 AGAATTAAGAACAT
1 AGAATTAAGAACAT
53660250 AGAATTAAGAACA
1 AGAATTAAGAACA
53660263 AGTCAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.19
Consensus pattern (14 bp):
AGAATTAAGAACAT
Found at i:53667448 original size:13 final size:13
Alignment explanation
Indices: 53667432--53667456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53667422 CATTCACAAG
53667432 CCGAATACACATA
1 CCGAATACACATA
53667445 CCGAATACACAT
1 CCGAATACACAT
53667457 TCTCGGTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (13 bp):
CCGAATACACATA
Found at i:53684002 original size:42 final size:42
Alignment explanation
Indices: 53683956--53684040 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
53683946 ATACATATAG
* * *
53683956 TATCATTTCAATGCCATATCCCCGATATGGTCTTACATGAAA
1 TATCATATCAACGCCATATCCCCGACATGGTCTTACATGAAA
* ** *
53683998 TATCATATCAACGCCATGTCCTTGACATGGTCTTATATGAAA
1 TATCATATCAACGCCATATCCCCGACATGGTCTTACATGAAA
53684040 T
1 T
53684041 CACATACCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (42 bp):
TATCATATCAACGCCATATCCCCGACATGGTCTTACATGAAA
Found at i:53687263 original size:36 final size:36
Alignment explanation
Indices: 53687216--53687287 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
53687206 TTTATACAAA
*
53687216 CATGTAAACGGGAAGCTCTTCCAAGCCATATAACGG
1 CATGTAAACGGGAAGCTCTCCCAAGCCATATAACGG
*
53687252 CATGTAAACGGGAAGCTCTCCCGAGCCATATAACGG
1 CATGTAAACGGGAAGCTCTCCCAAGCCATATAACGG
53687288 GAAGCTCACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (36 bp):
CATGTAAACGGGAAGCTCTCCCAAGCCATATAACGG
Found at i:53687352 original size:25 final size:25
Alignment explanation
Indices: 53687324--53687427 Score: 109
Period size: 25 Copynumber: 4.2 Consensus size: 25
53687314 AAGCTCTTAC
*
53687324 GAGCCAAATATTGGGAAGCTCATGA
1 GAGCCAAATATCGGGAAGCTCATGA
* * *
53687349 GAGCTAAATAACGGGAAGCTCGTGA
1 GAGCCAAATATCGGGAAGCTCATGA
* * * *
53687374 GAACCAAGTATCAGGAAGCTCGTGA
1 GAGCCAAATATCGGGAAGCTCATGA
* * *
53687399 GAGCCTAATATCGGGATGCTCATAA
1 GAGCCAAATATCGGGAAGCTCATGA
53687424 GAGC
1 GAGC
53687428 TGTGTTGTGT
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (25 bp):
GAGCCAAATATCGGGAAGCTCATGA
Found at i:53692963 original size:21 final size:21
Alignment explanation
Indices: 53692947--53692999 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
53692937 TTAATGATTG
53692947 ATGATAGATTATGAATGTTTA
1 ATGATAGATTATGAATGTTTA
53692968 ATGATAGATTATGAATGTTTA
1 ATGATAGATTATGAATGTTTA
53692989 ATGATAG-TTAT
1 ATGATAGATTAT
53693000 ACAAGTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
ATGATAGATTATGAATGTTTA
Found at i:53698072 original size:13 final size:12
Alignment explanation
Indices: 53698053--53698090 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
53698043 TTTTGAAAAT
53698053 AATAATTAATTA
1 AATAATTAATTA
53698065 ACATAATTAATTA
1 A-ATAATTAATTA
53698078 TAAT-ATTAATTA
1 -AATAATTAATTA
53698090 A
1 A
53698091 GTGATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
AATAATTAATTA
Found at i:53698190 original size:25 final size:25
Alignment explanation
Indices: 53698144--53698193 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
53698134 ATTTTACATC
* *
53698144 AATAAAATTAGTATAACTTTTTTAA
1 AATAAAATTAGCACAACTTTTTTAA
53698169 AATAAAATTAGCACAA-TATTTTTAA
1 AATAAAATTAGCACAACT-TTTTTAA
53698194 CTAATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (25 bp):
AATAAAATTAGCACAACTTTTTTAA
Found at i:53709339 original size:17 final size:17
Alignment explanation
Indices: 53709319--53709359 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
53709309 CACATAAGAA
53709319 TCCTTGAAAAATAACAT
1 TCCTTGAAAAATAACAT
53709336 TCCTTGAAAAATAACAT
1 TCCTTGAAAAATAACAT
*
53709353 TTCTTGA
1 TCCTTGA
53709360 TTCCATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (17 bp):
TCCTTGAAAAATAACAT
Found at i:53711648 original size:25 final size:25
Alignment explanation
Indices: 53711592--53711648 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
53711582 GGACTCACCA
*
53711592 CAGCTCGTATGAGCTTACTGATTTG
1 CAGCTCGTATGAGCTTACTGATCTG
*
53711617 CAACTCGT-TAGAGCTTACTGATACT-
1 CAGCTCGTAT-GAGCTTACTGAT-CTG
53711642 CAGCTCG
1 CAGCTCG
53711649 GAGAAGCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.04
25 25 0.93
26 1 0.04
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACTGATCTG
Found at i:53724017 original size:36 final size:36
Alignment explanation
Indices: 53723970--53724040 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
53723960 ACACCGTTGG
* *
53723970 AATTTTAATAACAACTTTTCCTTTCTTTTTAAGATT
1 AATTTTAATAACAACTCTTCCTTTCTTTTCAAGATT
*
53724006 AATTTTAATAACAACTCTTCTTTTCTTTTCAAGAT
1 AATTTTAATAACAACTCTTCCTTTCTTTTCAAGAT
53724041 GGCCAATGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (36 bp):
AATTTTAATAACAACTCTTCCTTTCTTTTCAAGATT
Found at i:53732184 original size:27 final size:27
Alignment explanation
Indices: 53732145--53732279 Score: 146
Period size: 27 Copynumber: 5.0 Consensus size: 27
53732135 GGAAGAAACA
*
53732145 CCTTTGTGGCAATCTCTGTAAAGGAAG
1 CCTTTGTGACAATCTCTGTAAAGGAAG
* *
53732172 CCTTTGTGACAATATCT-AAAAGGGAAG
1 CCTTTGTGACAATCTCTGTAAA-GGAAG
* * *
53732199 TCTTTGTGACAATCTCTATAAAGGATG
1 CCTTTGTGACAATCTCTGTAAAGGAAG
* *
53732226 CCTTTGTGGCGATCTCTGTTAAAGGAAG
1 CCTTTGTGACAATCTCTG-TAAAGGAAG
* * *
53732254 CCTTTATGACTATCTCTGAAAAGGAA
1 CCTTTGTGACAATCTCTGTAAAGGAA
53732280 CATTTTCGTG
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
26 3 0.03
27 60 0.67
28 26 0.29
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (27 bp):
CCTTTGTGACAATCTCTGTAAAGGAAG
Found at i:53735602 original size:21 final size:21
Alignment explanation
Indices: 53735577--53735645 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
53735567 GTGTCCCTTG
53735577 TTATTCTAACATGTGTTTGTT
1 TTATTCTAACATGTGTTTGTT
* * *
53735598 TTATT-TAA-ATATATTTTCCTT
1 TTATTCTAACATGT-GTTT-GTT
53735619 GTTATTCTAACATGTGTTTGTT
1 -TTATTCTAACATGTGTTTGTT
53735641 TTATT
1 TTATT
53735646 TAAATACATT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 3 0.08
20 6 0.16
21 12 0.32
22 7 0.19
23 6 0.16
24 3 0.08
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (21 bp):
TTATTCTAACATGTGTTTGTT
Found at i:53735619 original size:43 final size:43
Alignment explanation
Indices: 53735572--53735660 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
53735562 AGTTGGTGTC
*
53735572 CCTTGTTATTCTAACATGTGTTTGTTTTATTTAAATATATTTT
1 CCTTGTTATTCTAACATGTGTTTGTTTTATTTAAATACATTTT
53735615 CCTTGTTATTCTAACATGTGTTTGTTTTATTTAAATACATTTT
1 CCTTGTTATTCTAACATGTGTTTGTTTTATTTAAATACATTTT
53735658 CCT
1 CCT
53735661 CTTAAGGTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.56
Consensus pattern (43 bp):
CCTTGTTATTCTAACATGTGTTTGTTTTATTTAAATACATTTT
Found at i:53735851 original size:84 final size:84
Alignment explanation
Indices: 53735710--53735879 Score: 313
Period size: 84 Copynumber: 2.0 Consensus size: 84
53735700 TTATTTGAGT
* *
53735710 TAGGTTGAATCGGTCGGTTGGACTAAGGGCAAGTCGAGATATTAGTTCAGAAGAGGATATTGAAT
1 TAGGTTGAATCGATCGGTTGGACTAAGGGCAAGTCGAGATATTAGTTCAAAAGAGGATATTGAAT
*
53735775 CGATTGACCCAAAAATCGG
66 CGATTGACCAAAAAATCGG
53735794 TAGGTTGAATCGATCGGTTGGACTAAGGGCAAGTCGAGATATTAGTTCAAAAGAGGATATTGAAT
1 TAGGTTGAATCGATCGGTTGGACTAAGGGCAAGTCGAGATATTAGTTCAAAAGAGGATATTGAAT
53735859 CGATTGACCAAAAAATCGG
66 CGATTGACCAAAAAATCGG
53735878 TA
1 TA
53735880 CATGTTGATT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (84 bp):
TAGGTTGAATCGATCGGTTGGACTAAGGGCAAGTCGAGATATTAGTTCAAAAGAGGATATTGAAT
CGATTGACCAAAAAATCGG
Found at i:53738977 original size:20 final size:20
Alignment explanation
Indices: 53738952--53738992 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
53738942 AAGTTTGCTG
53738952 AACTTAATATGCAAAAAGCA
1 AACTTAATATGCAAAAAGCA
*
53738972 AACTTAATATGCGAAAAGCA
1 AACTTAATATGCAAAAAGCA
53738992 A
1 A
53738993 GAGCATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (20 bp):
AACTTAATATGCAAAAAGCA
Found at i:53744594 original size:27 final size:26
Alignment explanation
Indices: 53744564--53744740 Score: 158
Period size: 27 Copynumber: 6.5 Consensus size: 26
53744554 AAATTGTACA
* *
53744564 GCACTAAGTGTGCGATTCGACTTTGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
* *
53744591 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCG-ATTGACTATG-TG
* *
53744618 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTG
*
53744645 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTG
* *
53744673 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTG
* * *
53744700 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGA-TTGACTATGTG
*
53744727 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
53744741 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 99 0.79
28 26 0.21
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:53744687 original size:82 final size:81
Alignment explanation
Indices: 53744564--53744719 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
53744554 AAATTGTACA
* * * *
53744564 GCACTAAGTGTGCGATTCGACTTTGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
53744628 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
53744645 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
53744710 TGCGAGTTGA
65 TGCGAATTGA
53744720 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:53744731 original size:82 final size:81
Alignment explanation
Indices: 53744560--53744740 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
53744550 GATTAAATTG
* * * *
53744560 TACAGCACTAAGTGTGCGATTCGACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
53744625 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
53744641 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
53744705 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
53744723 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
53744741 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 20 0.24
82 62 0.76
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:53746159 original size:47 final size:47
Alignment explanation
Indices: 53746090--53746275 Score: 318
Period size: 47 Copynumber: 4.0 Consensus size: 47
53746080 GGGTGTTACA
53746090 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGG
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGG
53746137 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGG
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGG
*
53746184 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGG
* * * * *
53746231 CTAATAGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
53746276 TCCCGAAGGG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGG
Found at i:53751174 original size:17 final size:18
Alignment explanation
Indices: 53751141--53751174 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53751131 TGTTAACACT
*
53751141 TAAAATAATATTATATAG
1 TAAAATAATAGTATATAG
53751159 TAAAATAAT-GTATATA
1 TAAAATAATAGTATATA
53751175 AAAAAATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAAATAATAGTATATAG
Found at i:53752622 original size:37 final size:37
Alignment explanation
Indices: 53752572--53752650 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
53752562 TTATTACGAA
* * *
53752572 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
53752609 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
53752646 GTCTT
1 GTCTT
53752651 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:53752895 original size:49 final size:49
Alignment explanation
Indices: 53752769--53753301 Score: 854
Period size: 49 Copynumber: 11.1 Consensus size: 49
53752759 CCCTTCGGGA
* * * * *
53752769 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53752815 CTCTGTCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CT-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53752863 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53752912 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53752961 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53753010 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53753059 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53753108 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53753157 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53753204 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53753251 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53753298 CTTA
1 CTTA
53753302 CTATCATTTC
Statistics
Matches: 468, Mismatches: 13, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
46 3 0.01
47 179 0.38
48 2 0.00
49 284 0.61
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53759781 original size:22 final size:21
Alignment explanation
Indices: 53759739--53759778 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53759729 ATACATAAAA
*
53759739 TTTTTAAAAGTACAAATTTAT
1 TTTTTAAAAGTAAAAATTTAT
*
53759760 TTTTTGAAAGTAAAAATTT
1 TTTTTAAAAGTAAAAATTT
53759779 TATCCTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTTTAAAAGTAAAAATTTAT
Found at i:53763875 original size:8 final size:8
Alignment explanation
Indices: 53763862--53763889 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
53763852 GGATTCAAAG
53763862 AAAGAAAT
1 AAAGAAAT
53763870 AAAGAAAT
1 AAAGAAAT
53763878 AAAGAAAT
1 AAAGAAAT
53763886 AAAG
1 AAAG
53763890 GTTTGTCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAGAAAT
Found at i:53769777 original size:13 final size:13
Alignment explanation
Indices: 53769759--53769784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53769749 CATAGGAAAA
53769759 ATTAGAGGGTAGT
1 ATTAGAGGGTAGT
53769772 ATTAGAGGGTAGT
1 ATTAGAGGGTAGT
53769785 GATTGAGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
ATTAGAGGGTAGT
Found at i:53776627 original size:9 final size:10
Alignment explanation
Indices: 53776582--53776628 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
53776572 TAACATGTTG
*
53776582 AATTTTAATT
1 AATTTTTATT
*
53776592 AATTTTATATCA
1 AATTTT-TAT-T
53776604 AATTTTTATT
1 AATTTTTATT
53776614 AATTTTTATT
1 AATTTTTATT
53776624 -ATTTT
1 AATTTT
53776629 CGATAGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 5 0.16
10 16 0.50
11 5 0.16
12 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTTTTATT
Found at i:53776784 original size:16 final size:16
Alignment explanation
Indices: 53776765--53776797 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53776755 TAATTCATAA
53776765 TATAAT-TAATTTTAAT
1 TATAATCTAA-TTTAAT
53776781 TATAATCTAATTTAAT
1 TATAATCTAATTTAAT
53776797 T
1 T
53776798 TGGGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAATCTAATTTAAT
Found at i:53776798 original size:22 final size:22
Alignment explanation
Indices: 53776754--53776798 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
53776744 AGTTTTTGTA
53776754 TTAATTCATAATATAATTAATT
1 TTAATTCATAATATAATTAATT
*
53776776 TTAATT-ATAATCTAATTTAATT
1 TTAATTCATAATATAA-TTAATT
53776798 T
1 T
53776799 GGGTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTCATAATATAATTAATT
Found at i:53785618 original size:41 final size:40
Alignment explanation
Indices: 53785567--53785800 Score: 279
Period size: 41 Copynumber: 5.6 Consensus size: 40
53785557 GGATCCCGGT
*
53785567 GGAATTAGCACTTAGCAACCACCTTATAATCAATGATACGG
1 GGAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGG
* * *
53785608 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACTTAGCAACCCC-TT-ATAATCAATGATACGG
53785650 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGG
1 -GGAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGG
* * * *
53785692 GGAATCGGCACATAGCAACCCCTTTCACAATCAATAATACGG
1 GGAATCAGCACTTAGCAACCCC-TT-ATAATCAATGATACGG
* * *
53785734 TGGAATCAGCACTTCGAAACCACCTTATAATCAATGACACGG
1 -GGAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGG
*
53785776 GGAATCTGCACTTAGCAACCCCTTA
1 GGAATCAGCACTTAGCAACCCCTTA
53785801 CATTCAAAGA
Statistics
Matches: 164, Mismatches: 21, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
40 9 0.05
41 57 0.35
42 55 0.34
43 39 0.24
44 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCCTTATAATCAATGATACGG
Found at i:53785665 original size:84 final size:84
Alignment explanation
Indices: 53785563--53785799 Score: 393
Period size: 84 Copynumber: 2.8 Consensus size: 84
53785553 CAAAGGATCC
*
53785563 CGGTGGAATTAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*
53785628 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGAATA
*
53785647 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCGGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*
53785712 CCTTTCACAATCAATAATA
66 CCTTTCACAATCAAGAATA
* * * * *
53785731 CGGTGGAATCAGCACTTCGAAACCACCTTATAATCAATGACACGGGGAATCTGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
53785796 CCTT
66 CCTT
53785800 ACATTCAAAG
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 144 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAGAATA
Found at i:53789438 original size:24 final size:26
Alignment explanation
Indices: 53789402--53789457 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
53789392 TGCAAAAAAG
* *
53789402 TAAAGAAAATTTT-TAAAAT-TATTA
1 TAAATAAAATTTTAAAAAATATATTA
*
53789426 TAAATAAATTTTTAAAAAATATATTA
1 TAAATAAAATTTTAAAAAATATATTA
*
53789452 AAAATA
1 TAAATA
53789458 GAAAAAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 11 0.42
25 5 0.19
26 10 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAATAAAATTTTAAAAAATATATTA
Found at i:53789481 original size:9 final size:9
Alignment explanation
Indices: 53789440--53789524 Score: 59
Period size: 9 Copynumber: 9.4 Consensus size: 9
53789430 TAAATTTTTA
53789440 AAAAATATATT
1 AAAAATA-A-T
*
53789451 AAAAATAGAA
1 AAAAATA-AT
* *
53789461 AAAAACATT
1 AAAAATAAT
53789470 AAAAATAAT
1 AAAAATAAT
53789479 AAAAAT--T
1 AAAAATAAT
* *
53789486 GAAAATTAT
1 AAAAATAAT
* *
53789495 TAAAATTAT
1 AAAAATAAT
53789504 AAAAATAAT
1 AAAAATAAT
53789513 AAAAAT-AT
1 AAAAATAAT
53789521 AAAA
1 AAAA
53789525 TATAGAAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.10
8 6 0.10
9 35 0.57
10 6 0.10
11 8 0.13
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAAATAAT
Found at i:53789490 original size:17 final size:18
Alignment explanation
Indices: 53789470--53789518 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
53789460 AAAAAACATT
53789470 AAAAATAATAAAAATT-G
1 AAAAATAATAAAAATTAG
* * *
53789487 -AAAATTATTAAAATTAT
1 AAAAATAATAAAAATTAG
53789504 AAAAATAATAAAAAT
1 AAAAATAATAAAAAT
53789519 ATAAAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 13 0.52
18 12 0.48
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAATAATAAAAATTAG
Found at i:53789521 original size:17 final size:17
Alignment explanation
Indices: 53789450--53789524 Score: 71
Period size: 17 Copynumber: 4.3 Consensus size: 17
53789440 AAAAATATAT
* *
53789450 TAAAAATAGAAAAAAACA
1 TAAAAATA-ATAAAAATA
53789468 TTAAAAATAATAAAAAT-
1 -TAAAAATAATAAAAATA
* * *
53789485 TGAAAATTATTAAAATTA
1 T-AAAAATAATAAAAATA
53789503 TAAAAATAATAAAAATA
1 TAAAAATAATAAAAATA
53789520 TAAAA
1 TAAAA
53789525 TATAGAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.02
17 30 0.65
18 7 0.15
19 8 0.17
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (17 bp):
TAAAAATAATAAAAATA
Found at i:53789533 original size:8 final size:8
Alignment explanation
Indices: 53789469--53789533 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 8
53789459 AAAAAAACAT
53789469 TAAAAATAA
1 TAAAAAT-A
53789478 TAAAAAT-
1 TAAAAATA
*
53789485 TGAAAATTA
1 T-AAAAATA
*
53789494 TTAAAATTA
1 -TAAAAATA
53789503 TAAAAATAA
1 TAAAAAT-A
53789512 TAAAAATA
1 TAAAAATA
53789520 T-AAAATA
1 TAAAAATA
*
53789527 TAGAAAT
1 TAAAAAT
53789534 TCTTAAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
7 8 0.17
8 17 0.35
9 22 0.46
10 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (8 bp):
TAAAAATA
Found at i:53789540 original size:42 final size:43
Alignment explanation
Indices: 53789469--53789559 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 43
53789459 AAAAAAACAT
*
53789469 TAAAAATAATAAAAATTGAAAATTATTAAAATTATA-AAAATAA
1 TAAAAATAATAAAAATAGAAAATTATTAAAATTATATAAAAT-A
* *
53789512 TAAAAAT-ATAAAATATAG-AAATTCTTAAAATTTTATAAAATA
1 TAAAAATAATAAAA-ATAGAAAATTATTAAAATTATATAAAATA
53789554 TAAAAA
1 TAAAAA
53789560 ATTGCAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (43 bp):
TAAAAATAATAAAAATAGAAAATTATTAAAATTATATAAAATA
Found at i:53789541 original size:34 final size:34
Alignment explanation
Indices: 53789468--53789558 Score: 91
Period size: 34 Copynumber: 2.7 Consensus size: 34
53789458 GAAAAAAACA
53789468 TTAAAAATAATAAAAAT-TGAAAATTATTAAAATT
1 TTAAAAATAATAAAAATAT-AAAATTATTAAAATT
*
53789502 ATAAAAATAATAAAAATATAAAA-TA-TAGAAATT
1 TTAAAAATAATAAAAATATAAAATTATTA-AAATT
**
53789535 CTT-AAAATTTTATAAAATATAAAA
1 -TTAAAAATAATA-AAAATATAAAA
53789559 AATTGCAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 2 0.04
33 14 0.29
34 32 0.65
35 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (34 bp):
TTAAAAATAATAAAAATATAAAATTATTAAAATT
Found at i:53789888 original size:174 final size:172
Alignment explanation
Indices: 53789600--53789950 Score: 605
Period size: 174 Copynumber: 2.0 Consensus size: 172
53789590 AAAAATATTA
*
53789600 TTACAAATTATTCAAAAAATAATATTAAATTCCAAAAATATAAAAAAAAATCTACAATTTTATAT
1 TTACAAATTATTCAAAAAATAATATTAAATTACAAAAATATAAAAAAAAATCTACAATTTTATAT
53789665 ACACAGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACA
66 ACACAGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACA
* *
53789730 CTCTACTATCACCAAGTTTTAGAGAGATCCGTAGTGGACAAG
131 CTCCACTATCACCAAGCTTTAGAGAGATCCGTAGTGGACAAG
*
53789772 TTACAAATTATTCAAATAATAATATTAAATTACAAAAATATAAAAAAGAAAATCTACAATTTTAT
1 TTACAAATTATTCAAAAAATAATATTAAATTACAAAAATAT-AAAAA-AAAATCTACAATTTTAT
* **
53789837 ATACACAGTTTCGATTGTCACTTATGTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAA
64 ATACACAGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAA
*
53789902 CACTCCACTATCACCAAGCTTTAGAGAGATTCGTAGTGGACAAG
129 CACTCCACTATCACCAAGCTTTAGAGAGATCCGTAGTGGACAAG
53789946 -TACAA
1 TTACAA
53789951 CAAATTGCCA
Statistics
Matches: 169, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
172 39 0.23
173 10 0.06
174 120 0.71
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (172 bp):
TTACAAATTATTCAAAAAATAATATTAAATTACAAAAATATAAAAAAAAATCTACAATTTTATAT
ACACAGTCTCGATTGTCACTTACCTTCTCTATTTATTTCCTCACCTTAGTTTACATCTCAAAACA
CTCCACTATCACCAAGCTTTAGAGAGATCCGTAGTGGACAAG
Found at i:53790270 original size:28 final size:28
Alignment explanation
Indices: 53790233--53790319 Score: 106
Period size: 27 Copynumber: 3.1 Consensus size: 28
53790223 TTATTGATTT
* *
53790233 TTTTAAATATTTTTAATAAATTTCTA-TA
1 TTTTAAATATTTTTCATAAATTT-TACAA
*
53790261 TTTTAAATATTTTTCATAACTTTTACAA
1 TTTTAAATATTTTTCATAAATTTTACAA
* *
53790289 TTTT-AATATTTTTCATAAATTATATAA
1 TTTTAAATATTTTTCATAAATTTTACAA
53790316 TTTT
1 TTTT
53790320 TATTTTGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 26 0.50
28 26 0.50
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTAAATATTTTTCATAAATTTTACAA
Found at i:53790317 original size:27 final size:27
Alignment explanation
Indices: 53790233--53790319 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 27
53790223 TTATTGATTT
* *
53790233 TTTTAAATATTTTTAATAAATTTCTATA
1 TTTTAAATATTTTTCATAAATTTATA-A
* *
53790261 TTTTAAATATTTTTCATAACTTTTACAA
1 TTTTAAATATTTTTCATAA-ATTTATAA
53790289 TTTT-AATATTTTTCATAAATTATATAA
1 TTTTAAATATTTTTCATAAATT-TATAA
53790316 TTTT
1 TTTT
53790320 TATTTTGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.04
27 22 0.43
28 23 0.45
29 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAAATATTTTTCATAAATTTATAA
Found at i:53790361 original size:19 final size:20
Alignment explanation
Indices: 53790325--53790363 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53790315 ATTTTTATTT
*
53790325 TGTTTTTTTAATAATTTTTAG
1 TGTTTTTGTAAT-ATTTTTAG
53790346 TGTTTTTGTAAT-TTTTTA
1 TGTTTTTGTAATATTTTTA
53790364 ATGAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (20 bp):
TGTTTTTGTAATATTTTTAG
Found at i:53790387 original size:9 final size:9
Alignment explanation
Indices: 53790184--53790446 Score: 75
Period size: 9 Copynumber: 28.9 Consensus size: 9
53790174 TTTTAATTTG
*
53790184 TTTTATCAT
1 TTTTATAAT
**
53790193 TTTTATGCT
1 TTTTATAAT
53790202 TTTTATAAT
1 TTTTATAAT
*
53790211 ATTTTATAAA
1 -TTTTATAAT
*
53790221 TTTTATTGATTT
1 TTTTA-T-A-AT
*
53790233 TTTTAAATAT
1 TTTTATA-AT
53790243 TTTTAATAAAT
1 TTTT-AT-AAT
*
53790254 TTCTAT-A-
1 TTTTATAAT
*
53790261 TTTTAAATAT
1 TTTTATA-AT
*
53790271 TTTTCATAAC
1 TTTT-ATAAT
*
53790281 TTTTACAAT
1 TTTTATAAT
*
53790290 TTTAAT-AT
1 TTTTATAAT
*
53790298 TTTTCATAAA
1 TTTT-ATAAT
*
53790308 TTATATAAT
1 TTTTATAAT
53790317 TTTTAT--T
1 TTTTATAAT
53790324 TTGTT-T--T
1 TT-TTATAAT
*
53790331 TTTAATAAT
1 TTTTATAAT
*
53790340 TTTTAGT-GT
1 TTTTA-TAAT
*
53790349 TTTTGTAAT
1 TTTTATAAT
53790358 TTTT-TAAT
1 TTTTATAAT
** *
53790366 GAATTATATT
1 -TTTTATAAT
53790376 TTTTATAAT
1 TTTTATAAT
* *
53790385 TTTTTTCAT
1 TTTTATAAT
*
53790394 TTATAATAA-
1 TT-TTATAAT
53790403 TTTTATATAT
1 TTTTATA-AT
* *
53790413 TTTCCAT-TT
1 TTT-TATAAT
53790422 TTTTATAA-
1 TTTTATAAT
53790430 TTTTATAAT
1 TTTTATAAT
53790439 TTTTATAA
1 TTTTATAA
53790447 ATTTAATCAT
Statistics
Matches: 183, Mismatches: 45, Indels: 52
0.65 0.16 0.19
Matches are distributed among these distances:
6 1 0.01
7 12 0.07
8 27 0.15
9 85 0.46
10 41 0.22
11 11 0.06
12 6 0.03
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:53790406 original size:27 final size:28
Alignment explanation
Indices: 53790376--53790442 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
53790366 GAATTATATT
*
53790376 TTTTATAATTTTTTTCA-TTTATAATAA
1 TTTTATAATTTTTTCCATTTTATAATAA
* * *
53790403 TTTTAT-ATATTTTCCATTTTTTTATAA
1 TTTTATAATTTTTTCCATTTTATAATAA
53790430 TTTTATAATTTTT
1 TTTTATAATTTTT
53790443 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 8 0.24
27 20 0.61
28 5 0.15
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTATAATTTTTTCCATTTTATAATAA
Found at i:53790440 original size:19 final size:19
Alignment explanation
Indices: 53790376--53790442 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 19
53790366 GAATTATATT
*
53790376 TTTTATAA-TTTTTT-TCA
1 TTTTATAATTTTTTTATAA
**
53790393 -TTTATAATAATTTTATATA
1 TTTTATAATTTTTTTATA-A
**
53790412 TTTT-CCATTTTTTTATAA
1 TTTTATAATTTTTTTATAA
53790430 TTTTATAATTTTT
1 TTTTATAATTTTT
53790443 ATAAATTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
16 7 0.19
17 4 0.11
18 6 0.17
19 16 0.44
20 3 0.08
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTTTATAA
Found at i:53790897 original size:49 final size:49
Alignment explanation
Indices: 53790844--53790942 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
53790834 ATTAGTTGTA
53790844 GAGTTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATT
1 GAGTTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATT
53790893 GAGTTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATT
1 GAGTTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATT
53790942 G
1 G
53790943 TAATCGTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.44
Consensus pattern (49 bp):
GAGTTCATTGTGATGATGGATTATAAATTTAAGGATTTTAATATATATT
Found at i:53794317 original size:29 final size:28
Alignment explanation
Indices: 53794250--53794318 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
53794240 TTATAGCATG
* *
53794250 TTTATT-TTTATTTTAAAAATAGGAATT
1 TTTATTATTTTTTTTAAAAATAGGAACT
*
53794277 TTTATAGTATTTTTTTTAAACATAGGAAACT
1 TTTAT--TATTTTTTTTAAAAATAGG-AACT
53794308 TTTATTATTTT
1 TTTATTATTTT
53794319 ATTAGTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 5 0.14
29 7 0.20
30 15 0.43
31 8 0.23
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (28 bp):
TTTATTATTTTTTTTAAAAATAGGAACT
Found at i:53795868 original size:108 final size:106
Alignment explanation
Indices: 53795648--53795851 Score: 310
Period size: 108 Copynumber: 1.9 Consensus size: 106
53795638 AATAAAGTAG
53795648 ATTA-TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
1 ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
53795712 TAATAAATTCATATAAGAATAAAAATTTTATTAAATTATATATT
66 TAATAAATTCATATAAGAAT---AATTTTATTAAATTATATATT
53795756 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATA-TTT-TAGTATTATATATTATGATT
1 ATTATTAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGATT
53795819 TTATTAGTAAATTCATATAAGAAT-A-TTTATTAA
65 TTA--A-TAAATTCATATAAGAATAATTTTATTAA
53795852 CAATTTTATT
Statistics
Matches: 91, Mismatches: 0, Indels: 12
0.88 0.00 0.12
Matches are distributed among these distances:
106 8 0.09
107 1 0.01
108 27 0.30
109 26 0.29
110 12 0.13
111 17 0.19
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (106 bp):
ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
TAATAAATTCATATAAGAATAATTTTATTAAATTATATATT
Found at i:53795874 original size:17 final size:17
Alignment explanation
Indices: 53795854--53795887 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53795844 TTTATTAACA
53795854 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53795871 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53795888 TCTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:53796107 original size:44 final size:46
Alignment explanation
Indices: 53796044--53796141 Score: 155
Period size: 44 Copynumber: 2.2 Consensus size: 46
53796034 CTATTATACC
* *
53796044 TCTATTTCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTAT
1 TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
53796088 TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
*
53796134 TCCATTAC
1 TCTATTAC
53796142 GCATCTATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
44 25 0.51
45 4 0.08
46 20 0.41
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (46 bp):
TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
Found at i:53796141 original size:46 final size:44
Alignment explanation
Indices: 53796051--53796141 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 44
53796041 ACCTCTATTT
* *
53796051 CATTCAACCAAACACAAGAATACCATTACGCCTCTATTCTATTA
1 CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTA
53796095 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAA-TACC-ATTACGCCTCTATTCCATTA
53796141 C
1 C
53796142 GCATCTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.44
45 4 0.09
46 20 0.47
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.27
Consensus pattern (44 bp):
CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTA
Found at i:53796142 original size:16 final size:16
Alignment explanation
Indices: 53796121--53796157 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
53796111 AGAATTACCT
*
53796121 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
53796137 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
53796153 ATTAC
1 ATTAC
53796158 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:53797691 original size:18 final size:18
Alignment explanation
Indices: 53797647--53797691 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
53797637 ACCAATACGA
53797647 TATAAATAAATTAAAATT
1 TATAAATAAATTAAAATT
* *
53797665 TATATATAAATTATTAATT
1 TATAAATAAATTA-AAATT
53797684 TA-AAATAA
1 TATAAATAA
53797692 TTGAAATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAAATAAATTAAAATT
Found at i:53807054 original size:20 final size:20
Alignment explanation
Indices: 53807011--53807057 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
53807001 ATGGGATTTG
* * * *
53807011 CACTTGGGTGCCCTTGTTTG
1 CACTTCGGTGCCCCTGTATA
53807031 CACTTCGGTGCCCCTGTATA
1 CACTTCGGTGCCCCTGTATA
53807051 CACTTCG
1 CACTTCG
53807058 ATGTCTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.32, G:0.23, T:0.34
Consensus pattern (20 bp):
CACTTCGGTGCCCCTGTATA
Found at i:53807236 original size:7 final size:7
Alignment explanation
Indices: 53807224--53807259 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
53807214 AAGATATTAG
53807224 TAAATGT
1 TAAATGT
53807231 TAAATGT
1 TAAATGT
53807238 TAAATGT
1 TAAATGT
53807245 TAAATGT
1 TAAATGT
53807252 TAAATGT
1 TAAATGT
53807259 T
1 T
53807260 CGATGAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (7 bp):
TAAATGT
Found at i:53807539 original size:15 final size:15
Alignment explanation
Indices: 53807519--53807555 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
53807509 AGTTTGAGAC
53807519 GAATGATGAACTACA
1 GAATGATGAACTACA
*
53807534 GAATGATGAATTACA
1 GAATGATGAACTACA
*
53807549 TAATGAT
1 GAATGAT
53807556 TATTAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (15 bp):
GAATGATGAACTACA
Found at i:53809198 original size:34 final size:35
Alignment explanation
Indices: 53809131--53809203 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
53809121 AATGATGTTA
* **
53809131 AATTGTATGTATTTATTTTGTACATAGCAGAATTG
1 AATTGTATGTATGTATAATGTACATAGCAGAATTG
* *
53809166 AATTGTATGTATGTATAAT-TACATTGCCGAATTG
1 AATTGTATGTATGTATAATGTACATAGCAGAATTG
53809200 AATT
1 AATT
53809204 TAGCATGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (35 bp):
AATTGTATGTATGTATAATGTACATAGCAGAATTG
Found at i:53809440 original size:43 final size:42
Alignment explanation
Indices: 53809320--53809441 Score: 97
Period size: 43 Copynumber: 2.8 Consensus size: 42
53809310 TCTGATATGT
* * *
53809320 GATTTCATGTAAGACCACGTCTGGAACGTTGGCATTGATTTGA
1 GATTACATGTAAGACC-CGTCTGGGACGTTGGCATCGATTTGA
** * *
53809363 GATTTATGTGTAAGACCCTGTCTGAGATAG-TGGCATCGATATTTG-
1 GA-TTACATGTAAGACCC-GTCTGGGA-CGTTGGCATCG--ATTTGA
53809408 G-TTACATGTAAGACCTCGTCTGGGACGTTGGCAT
1 GATTACATGTAAGACC-CGTCTGGGACGTTGGCAT
53809442 TGTACGAGCT
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
42 1 0.02
43 28 0.46
44 25 0.41
45 2 0.03
46 5 0.08
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
GATTACATGTAAGACCCGTCTGGGACGTTGGCATCGATTTGA
Found at i:53809645 original size:68 final size:68
Alignment explanation
Indices: 53809536--53809674 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
53809526 ATTGAGCTAA
53809536 ATAGTTCAGGTACGTGTGAAGTTAAGTGTTCATGAAAATAAGGTAAGTATATTATTTGAGTTGAT
1 ATAGTTCAGGTACGTGTGAAGTTAAGTGTTCATGAAAATAAGGTAAGTATATTATTTGAGTTGAT
53809601 GAT
66 GAT
53809604 ATAGTTCAGGTACGTGTGAAGTTAAGTGTTCATGAAAATAAGGTAAGTATATTATTTGAGTTGAT
1 ATAGTTCAGGTACGTGTGAAGTTAAGTGTTCATGAAAATAAGGTAAGTATATTATTTGAGTTGAT
53809669 GAT
66 GAT
53809672 ATA
1 ATA
53809675 ATTATGCATA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (68 bp):
ATAGTTCAGGTACGTGTGAAGTTAAGTGTTCATGAAAATAAGGTAAGTATATTATTTGAGTTGAT
GAT
Found at i:53820141 original size:13 final size:13
Alignment explanation
Indices: 53820123--53820151 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53820113 ATGAATAAAT
53820123 AGGGTTTGTATGA
1 AGGGTTTGTATGA
53820136 AGGGTTTGTATGA
1 AGGGTTTGTATGA
53820149 AGG
1 AGG
53820152 TTCATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (13 bp):
AGGGTTTGTATGA
Found at i:53820194 original size:81 final size:81
Alignment explanation
Indices: 53820059--53820210 Score: 277
Period size: 81 Copynumber: 1.9 Consensus size: 81
53820049 GGGGTCGGGT
* * *
53820059 TTTGTATGAAGGTTCATCAAGAAGTGTATTCTGACTGAAATATAGGTACTAAAGATGAATAAATA
1 TTTGTATGAAGGTTCATCAAGAAGTGTATTCTGACTCAAATATAAGTAATAAAGATGAATAAATA
53820124 GGGTTTGTATGAAGGG
66 GGGTTTGTATGAAGGG
53820140 TTTGTATGAAGGTTCATCAAGAAGTGTATTCTGACTCAAATATAAGTAATAAAGATGAATAAATA
1 TTTGTATGAAGGTTCATCAAGAAGTGTATTCTGACTCAAATATAAGTAATAAAGATGAATAAATA
53820205 GGGTTT
66 GGGTTT
53820211 TTTTTTACTC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (81 bp):
TTTGTATGAAGGTTCATCAAGAAGTGTATTCTGACTCAAATATAAGTAATAAAGATGAATAAATA
GGGTTTGTATGAAGGG
Found at i:53824972 original size:15 final size:16
Alignment explanation
Indices: 53824924--53824972 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
53824914 TCTTATATAA
53824924 TGAAACTCTAGAAT-G
1 TGAAACTCTAGAATAG
*
53824939 TGAAACTCTAGATTA-
1 TGAAACTCTAGAATAG
*
53824954 TGAAACTATA-AATAG
1 TGAAACTCTAGAATAG
53824969 TGAA
1 TGAA
53824973 GCTGCAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 26 0.90
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (16 bp):
TGAAACTCTAGAATAG
Found at i:53860190 original size:28 final size:27
Alignment explanation
Indices: 53860126--53860277 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
53860116 ATATTAAGTC
* *
53860126 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
53860153 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
53860181 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
53860208 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
53860236 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
53860263 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53860278 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:53860210 original size:55 final size:55
Alignment explanation
Indices: 53860126--53860302 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
53860116 ATATTAAGTC
* * *
53860126 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
53860181 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
53860236 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
53860292 CGCACACTTAG
1 CGCACACTTAG
53860303 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:53865038 original size:22 final size:23
Alignment explanation
Indices: 53864984--53865042 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
53864974 ATGTAATCTT
* *
53864984 AGATATGATATGTAATCTTTAGA
1 AGATACGATTTGTAATCTTTAGA
53865007 AGATACGATTCTGTAATC-TT-GA
1 AGATACGATT-TGTAATCTTTAGA
**
53865029 AGATTTGATTTGTA
1 AGATACGATTTGTA
53865043 GATAGCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 10 0.32
23 10 0.32
24 7 0.23
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.41
Consensus pattern (23 bp):
AGATACGATTTGTAATCTTTAGA
Found at i:53871793 original size:23 final size:20
Alignment explanation
Indices: 53871737--53871794 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
53871727 ATCTTCAAAT
53871737 ATATGTAATCTTAG-ATATG
1 ATATGTAATCTTAGAATATG
53871756 ATATGTAATCTTTAGAATATATG
1 ATATGTAATC-TTAG-A-ATATG
*
53871779 ATTCTGTAATCTTAGA
1 A-TATGTAATCTTAGA
53871795 GATTTGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 10 0.30
20 4 0.12
22 1 0.03
23 10 0.30
24 8 0.24
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (20 bp):
ATATGTAATCTTAGAATATG
Found at i:53875965 original size:23 final size:23
Alignment explanation
Indices: 53875921--53875965 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
53875911 ATAATAAGTT
**
53875921 TAAAAATAATATTAAGCCAATAA
1 TAAAAATAATATTAAAACAATAA
* *
53875944 TAAAAATAATGTTAAAATAATA
1 TAAAAATAATATTAAAACAATA
53875966 TATGAACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAATAATATTAAAACAATAA
Found at i:53877834 original size:41 final size:41
Alignment explanation
Indices: 53877709--53877838 Score: 113
Period size: 41 Copynumber: 3.1 Consensus size: 41
53877699 TCCACTTGGC
*
53877709 AAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
1 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
* * * * * * *
53877750 AAGATCGGTCT-CTTCTG-TCCATTCCAATGTAA-TCTCAGGGAGAT
1 AAGA-C---CTGATGC-GATCTACTCTACTGTAACT-TCAGAGAGAT
53877794 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
1 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
53877835 AAGA
1 AAGA
53877839 TCCTTTATCT
Statistics
Matches: 65, Mismatches: 15, Indels: 18
0.66 0.15 0.18
Matches are distributed among these distances:
40 3 0.05
41 30 0.46
42 2 0.03
43 2 0.03
44 26 0.40
45 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (41 bp):
AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
Found at i:53877866 original size:85 final size:84
Alignment explanation
Indices: 53877709--53877879 Score: 236
Period size: 85 Copynumber: 2.0 Consensus size: 84
53877699 TCCACTTGGC
* * * *
53877709 AAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCGGTCTCTTCTGTCCATTC
1 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCGGTATCTTATCTCCA-TC
53877774 CAATGTAATCTCAGGGAGAT
65 CAATGTAATCTCAGGGAGAT
** *
53877794 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCTGC-T
1 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CGGTATCTT-ATCTCCAT
*
53877858 CCACTGTAATCTCAGGGAGAT
64 CCAATGTAATCTCAGGGAGAT
53877879 A
1 A
53877880 GGATTACTAG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
85 67 0.88
86 6 0.08
87 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (84 bp):
AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCGGTATCTTATCTCCATCC
AATGTAATCTCAGGGAGAT
Found at i:53878067 original size:142 final size:142
Alignment explanation
Indices: 53877799--53878212 Score: 711
Period size: 142 Copynumber: 2.9 Consensus size: 142
53877789 GAGATAAGAC
* *
53877799 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATCTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * *
53877864 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGTTATAATATCAGGGAAATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
53877929 TCTGGTTTCAAT
131 TCTGGTTTCAAT
*
53877941 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
53878006 TAATATCAGGGAGACAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
53878071 TCTGGTTTCAAT
131 TCTGGTTTCAAT
* *
53878083 CTGATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTGTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
53878148 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAGGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
53878213 ACTAGCTTCG
Statistics
Matches: 255, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 255 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGTTTCAAT
Found at i:53878290 original size:142 final size:141
Alignment explanation
Indices: 53878178--53878510 Score: 531
Period size: 142 Copynumber: 2.3 Consensus size: 141
53878168 TACTAGCTTC
*
53878178 AATCTGCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCTACTCCGCTGTAATCTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCTACTCCGCTGTAATCTC
* *
53878243 GGGGAGATAAGATTTCTGGCTTCAATCTAATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG
66 AGGGAGATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
53878308 ATCCTTTATTTT
131 AT-CTTTATTTT
* * * *
53878320 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATATGCTCTGCTGTAATCTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCTACTCCGCTGTAATCTC
* * *
53878385 AGGGAGATAAGATTTCTGGCTTCAATTTGATGCGATCTACTCTACTATAACTTCAGAGAGATAAG
66 AGGGAGATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
53878450 ATGCTTTATTTT
131 AT-CTTTATTTT
* * *
53878462 AATCTGCTCCACTGTAATCTTAGGGAGATAAGATTACTAGCTTCAATCT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCT
53878511 GCTTCATTAC
Statistics
Matches: 175, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 175 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (141 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCTACTCCGCTGTAATCTC
AGGGAGATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
ATCTTTATTTT
Found at i:53878380 original size:186 final size:186
Alignment explanation
Indices: 53877998--53878410 Score: 664
Period size: 186 Copynumber: 2.2 Consensus size: 186
53877988 TTTTAATCCA
* * * *
53877998 CTCCACTGTAATATCAGGGAGACAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGAGAG
1 CTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
* *
53878063 ATAAGATTTCTGGTTTCAATCTGATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTG
66 ATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTG
*
53878128 TATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
131 TATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATATG
* * *
53878184 CTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCTACTCCGCTGTAATCTCGGGGAG
1 CTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
* * *
53878249 ATAAGATTTCTGGCTTCAATCTAATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTT
66 ATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTG
*
53878314 TATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATATG
131 TATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATATG
* * * *
53878370 CTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAAT
1 CTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAAT
53878411 TTGATGCGAT
Statistics
Matches: 208, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
186 208 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (186 bp):
CTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGAGAG
ATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTG
TATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATATG
Found at i:53878418 original size:328 final size:328
Alignment explanation
Indices: 53877850--53878513 Score: 1103
Period size: 328 Copynumber: 2.0 Consensus size: 328
53877840 CCTTTATCTT
* *
53877850 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGTTATAATATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTATAATATC
* *
53877915 AGGGAAATAAGATTTCTGGTTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
66 AGGGAAATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
*
53877980 ATCCTTTATTTTAATCCACTCCACTGTAATATCAGGGAGACAGGATTACTAGCTTCAATCTGCTC
131 ATCCTTTATTTTAATCCACTCCACTGTAATATCAGGGAGACAGGATTACTAGCTTCAATATGCTC
*
53878045 CGCTGTAATCTCAGAGAGATAAGATTTCTGGTTTCAATCTGATGCGATCTACTCTACTATAACTT
196 CGCTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTATAACTT
*
53878110 CAGAGAGATAAGATCCTGTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
261 CAGAGAGATAAGATCCTGTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGC
53878175 TTC
326 TTC
* * * *
53878178 AATCTGCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATCTACTCCGCTGTAATCTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTATAATATC
* * *
53878243 GGGGAGATAAGATTTCTGGCTTCAATCTAATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG
66 AGGGAAATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
* * * *
53878308 ATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCGATATGCTC
131 ATCCTTTATTTTAATCCACTCCACTGTAATATCAGGGAGACAGGATTACTAGCTTCAATATGCTC
* * *
53878373 TGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATTTGATGCGATCTACTCTACTATAACTT
196 CGCTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTATAACTT
* * * *
53878438 CAGAGAGATAAGATGCTTTATTTTAATCTGCTCCACTGTAATCTTAGGGAGATAAGATTACTAGC
261 CAGAGAGATAAGATCCTGTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGC
53878503 TTC
326 TTC
53878506 AATCTGCT
1 AATCTGCT
53878514 TCATTACACT
Statistics
Matches: 311, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
328 311 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (328 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTATAATATC
AGGGAAATAAGATTTCTGGCTTCAATCTAATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
ATCCTTTATTTTAATCCACTCCACTGTAATATCAGGGAGACAGGATTACTAGCTTCAATATGCTC
CGCTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTATAACTT
CAGAGAGATAAGATCCTGTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGC
TTC
Found at i:53890610 original size:27 final size:26
Alignment explanation
Indices: 53890580--53890630 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
53890570 ATGAAATTCT
*
53890580 TACAAA-CAACATGATTGATTAACAATA
1 TACAAAGCAA-ATGA-TGAATAACAATA
53890607 TACAAAGCAAATGATGAATAACAA
1 TACAAAGCAAATGATGAATAACAA
53890631 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.22
Consensus pattern (26 bp):
TACAAAGCAAATGATGAATAACAATA
Found at i:53896423 original size:17 final size:17
Alignment explanation
Indices: 53896401--53896433 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53896391 AAACAACATA
53896401 ACTCTTGACCTTTCATG
1 ACTCTTGACCTTTCATG
53896418 ACTCTTGACCTTTCAT
1 ACTCTTGACCTTTCAT
53896434 ATAACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCTTGACCTTTCATG
Found at i:53900702 original size:17 final size:17
Alignment explanation
Indices: 53900680--53900712 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53900670 AAACAACATA
53900680 ACTCTTGACCTTTCATG
1 ACTCTTGACCTTTCATG
53900697 ACTCTTGACCTTTCAT
1 ACTCTTGACCTTTCAT
53900713 ATAACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCTTGACCTTTCATG
Found at i:53902759 original size:22 final size:21
Alignment explanation
Indices: 53902703--53902746 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53902693 CCAAGAATAG
53902703 AATGCTTCAAAATCTTGGAGA
1 AATGCTTCAAAATCTTGGAGA
53902724 AATGCTTCAAAATCTTGGAGA
1 AATGCTTCAAAATCTTGGAGA
53902745 AA
1 AA
53902747 ATTTTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
AATGCTTCAAAATCTTGGAGA
Found at i:53903373 original size:22 final size:22
Alignment explanation
Indices: 53903345--53903392 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
53903335 TCTAATCCTT
53903345 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
53903367 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
53903389 TCAA
1 TCAA
53903393 ATCCATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTTCCTTCCAAAATTCTC
Found at i:53903467 original size:28 final size:30
Alignment explanation
Indices: 53903426--53903488 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 30
53903416 CCTCAATTTC
53903426 ATTTTTGAAAATAATTTT-AATTTTTTTAT
1 ATTTTTGAAAATAATTTTAAATTTTTTTAT
53903455 ATTTTT-AAAATAATTTTAAATTTTTTTAT
1 ATTTTTGAAAATAATTTTAAATTTTTTTAT
53903484 ATTTT
1 ATTTT
53903489 CATCAATGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
ATTTTTGAAAATAATTTTAAATTTTTTTAT
Found at i:53905268 original size:25 final size:25
Alignment explanation
Indices: 53905240--53905308 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
53905230 TTTAAATTTA
*
53905240 TTATCTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
53905265 TTATTTAATATAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
53905290 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
53905309 ACCCTAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:53905326 original size:17 final size:18
Alignment explanation
Indices: 53905301--53905335 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53905291 CTATTTGATG
53905301 TAAT-AAAAACCCTAACT
1 TAATAAAAAACCCTAACT
*
53905318 TAATTAAAAACCCTAACT
1 TAATAAAAAACCCTAACT
53905336 CTAACCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAAAAAACCCTAACT
Found at i:53905353 original size:29 final size:29
Alignment explanation
Indices: 53905311--53905456 Score: 256
Period size: 29 Copynumber: 5.0 Consensus size: 29
53905301 TAATAAAAAC
* *
53905311 CCTAACTTAATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
53905340 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
53905369 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
53905398 CCTAATTTAATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
53905427 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
53905456 C
1 C
53905457 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 111 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.29
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:53905595 original size:55 final size:55
Alignment explanation
Indices: 53905511--53905746 Score: 445
Period size: 55 Copynumber: 4.3 Consensus size: 55
53905501 NNNNNNNNNN
53905511 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
53905566 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
*
53905621 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTCGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
* *
53905676 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
53905731 TAATTTTACATAATTT
1 TAATTTTACATAATTT
53905747 TACATAATGT
Statistics
Matches: 178, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 178 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.44
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:53905745 original size:10 final size:10
Alignment explanation
Indices: 53905730--53905754 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53905720 TTGGGACTTA
53905730 ATAATTTTAC
1 ATAATTTTAC
53905740 ATAATTTTAC
1 ATAATTTTAC
53905750 ATAAT
1 ATAAT
53905755 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:53905998 original size:7 final size:7
Alignment explanation
Indices: 53905986--53906025 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
53905976 CCATATTGTT
53905986 TAAACCC
1 TAAACCC
53905993 TAAACCC
1 TAAACCC
*
53906000 TAAGCCC
1 TAAACCC
53906007 TAAAACCC
1 T-AAACCC
53906015 TAAAACCC
1 T-AAACCC
53906023 TAA
1 TAA
53906026 CTTAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:53906017 original size:8 final size:8
Alignment explanation
Indices: 53905987--53906025 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
53905977 CATATTGTTT
53905987 AAACCCT-
1 AAACCCTA
53905994 AAACCCT-
1 AAACCCTA
*
53906001 AAGCCCTA
1 AAACCCTA
53906009 AAACCCTA
1 AAACCCTA
53906017 AAACCCTA
1 AAACCCTA
53906025 A
1 A
53906026 CTTAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 13 0.45
8 16 0.55
ACGTcount: A:0.46, C:0.38, G:0.03, T:0.13
Consensus pattern (8 bp):
AAACCCTA
Found at i:53906039 original size:18 final size:18
Alignment explanation
Indices: 53906016--53906086 Score: 88
Period size: 18 Copynumber: 3.7 Consensus size: 18
53906006 CTAAAACCCT
53906016 AAAACCCTAACTTAATTA
1 AAAACCCTAACTTAATTA
53906034 AAAACCCTAACCTAACTTAATTA
1 AAAA--C---CCTAACTTAATTA
*
53906057 AAAACCTTAACTTAATTA
1 AAAACCCTAACTTAATTA
53906075 AAAACCCTAACT
1 AAAACCCTAACT
53906087 CTAACCTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 27 0.59
20 1 0.02
21 1 0.02
23 17 0.37
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAACCCTAACTTAATTA
Found at i:53906102 original size:29 final size:29
Alignment explanation
Indices: 53906059--53906202 Score: 252
Period size: 29 Copynumber: 4.9 Consensus size: 29
53906049 CTTAATTAAA
*
53906059 AACCTTAACTTAATTAAAAACCCTAACTCT
1 AACC-TAATTTAATTAAAAACCCTAACTCT
53906089 AACCTAATTTAATTAAAAACCCTAACTCT
1 AACCTAATTTAATTAAAAACCCTAACTCT
*
53906118 AACCTAATTTAATTAAAAACCCTAACCCT
1 AACCTAATTTAATTAAAAACCCTAACTCT
53906147 AACCTAATTTAATTAAAAACCCTAACTCT
1 AACCTAATTTAATTAAAAACCCTAACTCT
*
53906176 AAGCTAATTTAATTAAAAACCCTAACT
1 AACCTAATTTAATTAAAAACCCTAACT
53906203 TAATTAAAAA
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 106 0.96
30 4 0.04
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.30
Consensus pattern (29 bp):
AACCTAATTTAATTAAAAACCCTAACTCT
Found at i:53906205 original size:18 final size:18
Alignment explanation
Indices: 53906179--53906219 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
53906169 TAACTCTAAG
*
53906179 CTAATTTAATTAAAAACC
1 CTAACTTAATTAAAAACC
53906197 CTAACTTAATTAAAAACC
1 CTAACTTAATTAAAAACC
53906215 CTAAC
1 CTAAC
53906220 CCAAACCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (18 bp):
CTAACTTAATTAAAAACC
Found at i:53906296 original size:10 final size:10
Alignment explanation
Indices: 53906281--53906305 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53906271 TTGGGACTTA
53906281 ATAATTTTAC
1 ATAATTTTAC
53906291 ATAATTTTAC
1 ATAATTTTAC
53906301 ATAAT
1 ATAAT
53906306 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:53906802 original size:160 final size:161
Alignment explanation
Indices: 53906538--53906855 Score: 539
Period size: 160 Copynumber: 2.0 Consensus size: 161
53906528 CATATTGTTC
* *
53906538 CGTATTCTAGTGGAGAAAGGTCGACCCTTTGATTTGCGACGCAATTTTCTATCCGGTAACAGTTT
1 CGTATTCTAGTGGAGAAAGGTCGACCCTTTGATTTGCGACGCAATTCTCTATCCGGTAACAGCTT
* * *
53906603 AAAAGGAGTAAGAGATACGGGCGGCCACTTACGTTCATCT-GGACCGGTGGGAAAACGTGTCTCC
66 AAAAGGAGCAAGAGATACGGGCGACCACTTACGTTCATCTGGGACCGGTGGGAAAACATGTCTCC
53906667 ATACGTTGTACATGTTTTCTAATTTGTACAT
131 ATACGTTGTACATGTTTTCTAATTTGTACAT
* * *
53906698 CGTATTCTAGTGGAGCAAGGTCGACCCTTTGGTTTGCGACGCAATTCTCTATCTGGTAACAGCTT
1 CGTATTCTAGTGGAGAAAGGTCGACCCTTTGATTTGCGACGCAATTCTCTATCCGGTAACAGCTT
53906763 AAAAGGAGCAAGAGATACGGGCGACCACTTACGTTCATCTGGGACCGGTGGGAAAACATGTCTCC
66 AAAAGGAGCAAGAGATACGGGCGACCACTTACGTTCATCTGGGACCGGTGGGAAAACATGTCTCC
* *
53906828 ATATGTTGTACATGTTTTCTAGTTTGTA
131 ATACGTTGTACATGTTTTCTAATTTGTA
53906856 GACTTCGTCC
Statistics
Matches: 147, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
160 98 0.67
161 49 0.33
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (161 bp):
CGTATTCTAGTGGAGAAAGGTCGACCCTTTGATTTGCGACGCAATTCTCTATCCGGTAACAGCTT
AAAAGGAGCAAGAGATACGGGCGACCACTTACGTTCATCTGGGACCGGTGGGAAAACATGTCTCC
ATACGTTGTACATGTTTTCTAATTTGTACAT
Found at i:53911075 original size:55 final size:55
Alignment explanation
Indices: 53910991--53911139 Score: 271
Period size: 55 Copynumber: 2.7 Consensus size: 55
53910981 NNNNNNNNNN
*
53910991 ATTAACACAATTTTTGGACTTAATAATTTTACATAATTTGATAATTTTACTAACC
1 ATTAACACAATTTTCGGACTTAATAATTTTACATAATTTGATAATTTTACTAACC
53911046 ATTAACACAATTTTCGGACTTAATAATTTTACATAATTTGATAATTTTACTAACC
1 ATTAACACAATTTTCGGACTTAATAATTTTACATAATTTGATAATTTTACTAACC
* *
53911101 ATTAACAAAATTTTGGGACTTAATAATTTTACATAATTT
1 ATTAACACAATTTTCGGACTTAATAATTTTACATAATTT
53911140 TACATAATGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (55 bp):
ATTAACACAATTTTCGGACTTAATAATTTTACATAATTTGATAATTTTACTAACC
Found at i:53911138 original size:10 final size:10
Alignment explanation
Indices: 53911123--53911147 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53911113 TTGGGACTTA
53911123 ATAATTTTAC
1 ATAATTTTAC
53911133 ATAATTTTAC
1 ATAATTTTAC
53911143 ATAAT
1 ATAAT
53911148 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:53914143 original size:123 final size:123
Alignment explanation
Indices: 53913924--53914148 Score: 380
Period size: 123 Copynumber: 1.8 Consensus size: 123
53913914 CCCAAACTTG
53913924 CTACTGTAGCAAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* * *
53913989 TATAAGTGATTTTATACTATTTGCTTAGAAACGTCAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
* * *
53914047 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGG
1 CTACTGTAGCAAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
53914112 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
53914149 CTCGAAATAT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 94 0.99
124 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (123 bp):
CTACTGTAGCAAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
Found at i:53914377 original size:61 final size:61
Alignment explanation
Indices: 53914295--53914414 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
53914285 CAGTCAGCGC
* **
53914295 GACCTACTGACGTGGACGCGATGTCCTGTTACGTACCCTGACATCACGCTGACGTGGACGT
1 GACCTACTGACATGGACGCGATGTCCTGCCACGTACCCTGACATCACGCTGACGTGGACGT
* *
53914356 GACCTGCTGACATGGATGCGATGTCCTGCCACGTACCCTGACATCACGCTGACGTGGAC
1 GACCTACTGACATGGACGCGATGTCCTGCCACGTACCCTGACATCACGCTGACGTGGAC
53914415 ACGATTTCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.22
Consensus pattern (61 bp):
GACCTACTGACATGGACGCGATGTCCTGCCACGTACCCTGACATCACGCTGACGTGGACGT
Found at i:53916788 original size:12 final size:12
Alignment explanation
Indices: 53916757--53916782 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53916747 TGCAACAACA
53916757 TTAGAGATGATC
1 TTAGAGATGATC
53916769 TTAGAGATGATC
1 TTAGAGATGATC
53916781 TT
1 TT
53916783 GTAGATAAAC
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:0.08, G:0.23, T:0.38
Consensus pattern (12 bp):
TTAGAGATGATC
Found at i:53917228 original size:52 final size:52
Alignment explanation
Indices: 53917150--53917253 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
53917140 TAGTCTTTAA
*
53917150 TTAGCCATATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
1 TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
53917202 TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
1 TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
53917254 CTTTAAGCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (52 bp):
TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
Found at i:53917844 original size:22 final size:22
Alignment explanation
Indices: 53917819--53917863 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53917809 TGCTTCCACC
53917819 ACTCCTATTCTTAACCCAAGTG
1 ACTCCTATTCTTAACCCAAGTG
53917841 ACTCCTATTCTTAACCCAAGTG
1 ACTCCTATTCTTAACCCAAGTG
53917863 A
1 A
53917864 ACCATCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (22 bp):
ACTCCTATTCTTAACCCAAGTG
Found at i:53920051 original size:40 final size:39
Alignment explanation
Indices: 53919861--53920044 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
53919851 CGAATGATGT
* * * *
53919861 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
53919901 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
53919941 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53919979 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53920020 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
53920045 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53920067 original size:79 final size:79
Alignment explanation
Indices: 53919913--53920077 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
53919903 GGACTAAGAT
* **
53919913 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
53919978 ATCCGAGTTAAGTC
66 ATCCGAGTTAAATC
* * *
53919992 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
53920055 TATATCCG-GTTAAATT
63 TAAATCCGAGTTAAATC
53920071 CCGAAGG
1 CCGAAGG
53920078 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGAGTTAAATC
Done.