Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 24
Found at i:3287087 original size:20 final size:20
Alignment explanation
Indices: 3287022--3287193 Score: 76
Period size: 20 Copynumber: 8.6 Consensus size: 20
3287012 AATTTGACAA
*
3287022 TTTCGTAACACGAATTTCCTT
1 TTTCGCAACACGAATTTCC-T
* * ***
3287043 TTTCGCAACTCGATTTTTAA
1 TTTCGCAACACGAATTTCCT
* *
3287063 ATTCGCAACACGAGTTTCCT
1 TTTCGCAACACGAATTTCCT
* *
3287083 TTTCGCAACAAG-ATTTTCT
1 TTTCGCAACACGAATTTCCT
* * * * **
3287102 AATTCGTAACGCGAGTTTCAA
1 -TTTCGCAACACGAATTTCCT
* *
3287123 TTTCGCAACAGGAATTTCGT
1 TTTCGCAACACGAATTTCCT
* * **
3287143 TTTCGCAACTCGATTTTTGT
1 TTTCGCAACACGAATTTCCT
* * ***
3287163 ATTCGCAACGCGAATTTTAA
1 TTTCGCAACACGAATTTCCT
3287183 TTTCGCAACAC
1 TTTCGCAACAC
3287194 AAATGTTTTG
Statistics
Matches: 107, Mismatches: 42, Indels: 5
0.69 0.27 0.03
Matches are distributed among these distances:
19 5 0.05
20 85 0.79
21 17 0.16
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (20 bp):
TTTCGCAACACGAATTTCCT
Found at i:3287146 original size:60 final size:60
Alignment explanation
Indices: 3287044--3287193 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 60
3287034 AATTTCCTTT
* * * * *
3287044 TTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCCTTTTCGCAACAAGATTTTCT-AA
1 TTCGCAACGCGAATTTCAATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTT-TGAA
* * * * ** *
3287104 TTCGTAACGCGAGTTTCAATTTCGCAACAGGAATTTCGTTTTCGCAACTCGATTTTTGTA
1 TTCGCAACGCGAATTTCAATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTTGAA
*
3287164 TTCGCAACGCGAATTTTAATTTCGCAACAC
1 TTCGCAACGCGAATTTCAATTTCGCAACAC
3287194 AAATGTTTTG
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
59 1 0.01
60 73 0.99
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (60 bp):
TTCGCAACGCGAATTTCAATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTTGAA
Found at i:3287317 original size:22 final size:22
Alignment explanation
Indices: 3287292--3287349 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
3287282 CTCTTCGGCG
3287292 ACATCCGTCCCCATAT-CTGACA
1 ACATCCGTCCCCATATCCT-ACA
*
3287314 ACATCCGTCCCCATATCCTACG
1 ACATCCGTCCCCATATCCTACA
*
3287336 ACATCCTTCCCCAT
1 ACATCCGTCCCCAT
3287350 CTCTAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.24, C:0.45, G:0.07, T:0.24
Consensus pattern (22 bp):
ACATCCGTCCCCATATCCTACA
Found at i:3287377 original size:16 final size:16
Alignment explanation
Indices: 3287356--3287390 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3287346 CCATCTCTAA
3287356 TTTATTTTCACATAAT
1 TTTATTTTCACATAAT
* *
3287372 TTTATTTTTATATAAT
1 TTTATTTTCACATAAT
3287388 TTT
1 TTT
3287391 TCAATGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTTTCACATAAT
Found at i:3288220 original size:24 final size:24
Alignment explanation
Indices: 3288142--3288224 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
3288132 AGTCAGTATT
* *
3288142 CGAAATTTGATCTTGATCAATACC
1 CGAATTTTGATCTTGGTCAATACC
*
3288166 CGAACTTTGATCTTGGTCAATACC
1 CGAATTTTGATCTTGGTCAATACC
* *
3288190 CGTATTTTGATCTTGGTCAATACT
1 CGAATTTTGATCTTGGTCAATACC
*
3288214 CGGATTTTGAT
1 CGAATTTTGAT
3288225 GATGTTTCAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (24 bp):
CGAATTTTGATCTTGGTCAATACC
Found at i:3290821 original size:20 final size:20
Alignment explanation
Indices: 3290796--3290928 Score: 127
Period size: 20 Copynumber: 7.0 Consensus size: 20
3290786 TTTGCCTAGT
*
3290796 TCAAATTCTCAACTCGAAAA
1 TCAAATTCGCAACTCGAAAA
* * *
3290816 TCAAATTCGCAATTTGAAAC
1 TCAAATTCGCAACTCGAAAA
*
3290836 TCAAATTCGCAACACG---A
1 TCAAATTCGCAACTCGAAAA
*
3290853 --AAA-TCGCAACTCGATAA
1 TCAAATTCGCAACTCGAAAA
*
3290870 TAAAATTCGCAACTCGAAAA
1 TCAAATTCGCAACTCGAAAA
*
3290890 T-AGAATTCACAACTCGAAAA
1 TCA-AATTCGCAACTCGAAAA
*
3290910 TGAAATTCGCAACTCGAAA
1 TCAAATTCGCAACTCGAAA
3290929 TAGATTTTCA
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.10
15 3 0.03
17 1 0.01
19 4 0.04
20 75 0.81
21 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.22
Consensus pattern (20 bp):
TCAAATTCGCAACTCGAAAA
Found at i:3290897 original size:54 final size:54
Alignment explanation
Indices: 3290805--3290910 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 54
3290795 TTCAAATTCT
* * * * *
3290805 CAACTCGAAAATCAAATTCGCAATTTGAAACTCAAATTCGCAACACGAAAATCG
1 CAACTCGAAAATAAAATTCGCAACTCGAAAATCAAATTCACAACACGAAAATCG
* *
3290859 CAACTCGATAATAAAATTCGCAACTCGAAAAT-AGAATTCACAACTCGAAAAT
1 CAACTCGAAAATAAAATTCGCAACTCGAAAATCA-AATTCACAACACGAAAAT
3290911 GAAATTCGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.02
54 43 0.98
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (54 bp):
CAACTCGAAAATAAAATTCGCAACTCGAAAATCAAATTCACAACACGAAAATCG
Found at i:3291013 original size:20 final size:20
Alignment explanation
Indices: 3290990--3291043 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
3290980 TTTCGTGTTA
*
3290990 CGAATTTGAGTTTCGAATTG
1 CGAATTTGACTTTCGAATTG
* *
3291010 CGAATTCGACTTTCGAGTTG
1 CGAATTTGACTTTCGAATTG
* *
3291030 TGAATTTGATTTTC
1 CGAATTTGACTTTC
3291044 TTAAAGATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTTCGAATTG
Found at i:3293393 original size:21 final size:21
Alignment explanation
Indices: 3293367--3293478 Score: 118
Period size: 21 Copynumber: 5.3 Consensus size: 21
3293357 AGTATGGAAT
* *
3293367 GTGGATCTTAAACGATGCGAG
1 GTGGATCCTAAACGATGAGAG
*
3293388 GTGGATCCTAAACGATGGGAG
1 GTGGATCCTAAACGATGAGAG
*
3293409 GTGGATCCTGAACGATGAGAG
1 GTGGATCCTAAACGATGAGAG
* * *
3293430 GTGAATCCTAAACAATGTGAG
1 GTGGATCCTAAACGATGAGAG
* * *
3293451 GTAGATCCTGAACAATG-GTAG
1 GTGGATCCTAAACGATGAG-AG
3293472 GTGGATC
1 GTGGATC
3293479 AGGCTTCTTC
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 1 0.01
21 77 0.99
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.22
Consensus pattern (21 bp):
GTGGATCCTAAACGATGAGAG
Found at i:3293431 original size:42 final size:41
Alignment explanation
Indices: 3293367--3293478 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 41
3293357 AGTATGGAAT
* * *
3293367 GTGGATCTTAAACGATGCGAGGTGGATCCTAAACGATGGGAG
1 GTGGATCCTGAACGATG-GAGGTGGATCCTAAACAATGGGAG
* *
3293409 GTGGATCCTGAACGATGAGAGGTGAATCCTAAACAATGTGAG
1 GTGGATCCTGAACGATG-GAGGTGGATCCTAAACAATGGGAG
* *
3293451 GTAGATCCTGAACAATGGTAGGTGGATC
1 GTGGATCCTGAACGATGG-AGGTGGATC
3293479 AGGCTTCTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
41 1 0.02
42 59 0.98
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.22
Consensus pattern (41 bp):
GTGGATCCTGAACGATGGAGGTGGATCCTAAACAATGGGAG
Found at i:3293833 original size:21 final size:21
Alignment explanation
Indices: 3293809--3293978 Score: 184
Period size: 21 Copynumber: 8.1 Consensus size: 21
3293799 TGAAACAATC
*
3293809 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* *
3293830 TCACGTAAAGTAACTACCTCA
1 TCACGTAAAGCACCTACCTCA
*
3293851 CCACGTAAAGCACCATTA--TCA
1 TCACGTAAAGCACC--TACCTCA
* *
3293872 TCACGTAATGCAGCTACCTCA
1 TCACGTAAAGCACCTACCTCA
*
3293893 CCACGTAAAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
**
3293914 TCACGTAAAGCACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
3293935 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
* *
3293956 TCACGTAAAGCATCTATCTCA
1 TCACGTAAAGCACCTACCTCA
3293977 TC
1 TC
3293979 CCGTGGAGGT
Statistics
Matches: 123, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.02
20 1 0.01
21 117 0.95
22 1 0.01
23 2 0.02
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:3293977 original size:63 final size:63
Alignment explanation
Indices: 3293809--3293978 Score: 241
Period size: 63 Copynumber: 2.7 Consensus size: 63
3293799 TGAAACAATC
* * *
3293809 TCACGTAGAGCACCTACCTCATCACGTAAAGTAACTACCTCACCACGTAAAGCACCATTATCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCAACTACCTCATCACGTAAAGCACCATTATCA
* * * * *
3293872 TCACGTAATGCAGCTACCTCACCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCAACTACCTCATCACGTAAAGCACCATTATCA
* * *
3293935 TCACGTAAAGCACCGACCTCATCACGTAAAGCATCTATCTCATC
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCAACTACCTCATC
3293979 CCGTGGAGGT
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 93 1.00
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.21
Consensus pattern (63 bp):
TCACGTAAAGCACCTACCTCATCACGTAAAGCAACTACCTCATCACGTAAAGCACCATTATCA
Found at i:3294132 original size:42 final size:42
Alignment explanation
Indices: 3294078--3294246 Score: 239
Period size: 42 Copynumber: 4.0 Consensus size: 42
3294068 GCGATGGAAT
* * *
3294078 AGGTGATGGATCTCGGTGGCGAAGTGGATAATCAACTCGATG
1 AGGTGATAGATCTCGGTGTCGAAGTGGAGAATCAACTCGATG
** *
3294120 AGGTGATAGATCTCGGTGTCGAAGTGGAGAATCGGCTCGAAG
1 AGGTGATAGATCTCGGTGTCGAAGTGGAGAATCAACTCGATG
* * *
3294162 AGGTGATGGATCTCGGTGTCGAAGTGAAGAATCGACTCGATG
1 AGGTGATAGATCTCGGTGTCGAAGTGGAGAATCAACTCGATG
* *
3294204 AGGTGATAGATCTTGGTGTCGAAGTGGAGAATCAAGTCGATG
1 AGGTGATAGATCTCGGTGTCGAAGTGGAGAATCAACTCGATG
3294246 A
1 A
3294247 AAAAGTGGGG
Statistics
Matches: 112, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 112 1.00
ACGTcount: A:0.27, C:0.13, G:0.36, T:0.24
Consensus pattern (42 bp):
AGGTGATAGATCTCGGTGTCGAAGTGGAGAATCAACTCGATG
Found at i:3294222 original size:84 final size:84
Alignment explanation
Indices: 3294078--3294236 Score: 273
Period size: 84 Copynumber: 1.9 Consensus size: 84
3294068 GCGATGGAAT
* *
3294078 AGGTGATGGATCTCGGTGGCGAAGTGGATAATCAACTCGATGAGGTGATAGATCTCGGTGTCGAA
1 AGGTGATGGATCTCGGTGGCGAAGTGAAGAATCAACTCGATGAGGTGATAGATCTCGGTGTCGAA
3294143 GTGGAGAATCGGCTCGAAG
66 GTGGAGAATCGGCTCGAAG
* * *
3294162 AGGTGATGGATCTCGGTGTCGAAGTGAAGAATCGACTCGATGAGGTGATAGATCTTGGTGTCGAA
1 AGGTGATGGATCTCGGTGGCGAAGTGAAGAATCAACTCGATGAGGTGATAGATCTCGGTGTCGAA
3294227 GTGGAGAATC
66 GTGGAGAATC
3294237 AAGTCGATGA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.26, C:0.13, G:0.36, T:0.24
Consensus pattern (84 bp):
AGGTGATGGATCTCGGTGGCGAAGTGAAGAATCAACTCGATGAGGTGATAGATCTCGGTGTCGAA
GTGGAGAATCGGCTCGAAG
Found at i:3295648 original size:20 final size:20
Alignment explanation
Indices: 3295623--3295689 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
3295613 AAATTTTCAA
*
3295623 GAAAATCAAATTTGCAACTC
1 GAAAATCAAATTCGCAACTC
* *
3295643 GAAAATCGAATTCGCAATTC
1 GAAAATCAAATTCGCAACTC
* * *
3295663 GAAACTTAAATTCGCAACAC
1 GAAAATCAAATTCGCAACTC
3295683 GAAAATC
1 GAAAATC
3295690 GCAACACGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACTC
Found at i:3295693 original size:14 final size:14
Alignment explanation
Indices: 3295674--3295716 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
3295664 AAACTTAAAT
3295674 TCGCAACACGAAAA
1 TCGCAACACGAAAA
3295688 TCGCAACACGAAAA
1 TCGCAACACGAAAA
*
3295702 TCGCAACTCGAAAA
1 TCGCAACACGAAAA
3295716 T
1 T
3295717 GAAATTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.47, C:0.28, G:0.14, T:0.12
Consensus pattern (14 bp):
TCGCAACACGAAAA
Found at i:3295728 original size:34 final size:34
Alignment explanation
Indices: 3295683--3295762 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
3295673 TTCGCAACAC
* *
3295683 GAAAATCGCAACACGAAAATCGCAACTCGAAAAT
1 GAAATTCGCAACACGAAAATCGCAACTCAAAAAT
* *
3295717 GAAATTTGCAACACGAAAATTGCAACTCAAAAAT
1 GAAATTCGCAACACGAAAATCGCAACTCAAAAAT
3295751 GAAATTCGCAAC
1 GAAATTCGCAAC
3295763 TCAAATTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (34 bp):
GAAATTCGCAACACGAAAATCGCAACTCAAAAAT
Found at i:3295750 original size:48 final size:48
Alignment explanation
Indices: 3295654--3295750 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
3295644 AAAATCGAAT
* * * *
3295654 TCGCAATTCGAAACTTAAATTCGCAACACGAAAATCGCAACACGAAAA
1 TCGCAACTCGAAAATGAAATTCGCAACACGAAAATCGCAACACAAAAA
* * *
3295702 TCGCAACTCGAAAATGAAATTTGCAACACGAAAATTGCAACTCAAAAA
1 TCGCAACTCGAAAATGAAATTCGCAACACGAAAATCGCAACACAAAAA
3295750 T
1 T
3295751 GAAATTCGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.19
Consensus pattern (48 bp):
TCGCAACTCGAAAATGAAATTCGCAACACGAAAATCGCAACACAAAAA
Found at i:3296159 original size:16 final size:16
Alignment explanation
Indices: 3296126--3296172 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
3296116 AGCCGTGAAT
*
3296126 GGTTGTGAGAG--GGT
1 GGTTGTGAGAGATGGA
3296140 GGTTGTGAGAGATGGA
1 GGTTGTGAGAGATGGA
3296156 GGTTGTGAGAGATGGA
1 GGTTGTGAGAGATGGA
3296172 G
1 G
3296173 ATGGAGGGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 11 0.37
16 19 0.63
ACGTcount: A:0.21, C:0.00, G:0.53, T:0.26
Consensus pattern (16 bp):
GGTTGTGAGAGATGGA
Found at i:3296259 original size:37 final size:38
Alignment explanation
Indices: 3296201--3296279 Score: 133
Period size: 37 Copynumber: 2.1 Consensus size: 38
3296191 GATGGGAACG
*
3296201 GATGGGAACAGATGTCGCCGGAGAGAGTGAGAGATGGA
1 GATGGGAACAGATGTCACCGGAGAGAGTGAGAGATGGA
*
3296239 GATGGG-ACGGATGTCACCGGAGAGAGTGAGAGATGGA
1 GATGGGAACAGATGTCACCGGAGAGAGTGAGAGATGGA
3296276 GATG
1 GATG
3296280 AGATAGAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 33 0.85
38 6 0.15
ACGTcount: A:0.30, C:0.10, G:0.46, T:0.14
Consensus pattern (38 bp):
GATGGGAACAGATGTCACCGGAGAGAGTGAGAGATGGA
Found at i:3296403 original size:20 final size:20
Alignment explanation
Indices: 3296380--3296462 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
3296370 CTGCTAATTT
*
3296380 TAAATTCGCGTTGCGAATTC
1 TAAATTCGCGTTGCGAAATC
* *
3296400 TAAAATCGAGTTGCGAAAAT-
1 TAAATTCGCGTTGCG-AAATC
* * *
3296420 AAAATTCGCGTTGAGAAAGC
1 TAAATTCGCGTTGCGAAATC
* *
3296440 GAAATTCGCGTTGAGAAAT-
1 TAAATTCGCGTTGCGAAATC
3296459 TAAA
1 TAAA
3296463 ACTCACTTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
19 6 0.12
20 41 0.82
21 3 0.06
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (20 bp):
TAAATTCGCGTTGCGAAATC
Found at i:3296425 original size:40 final size:40
Alignment explanation
Indices: 3296381--3296556 Score: 140
Period size: 40 Copynumber: 4.4 Consensus size: 40
3296371 TGCTAATTTT
3296381 AAATTCGCGTTGCGAATTCTAAAATCGAGTTGCGAAAATA
1 AAATTCGCGTTGCGAATTCTAAAATCGAGTTGCGAAAATA
* ** * * * * *
3296421 AAATTCGCGTTGAGAAAGCGAAATTCGCGTTGAGAAATTA
1 AAATTCGCGTTGCGAATTCTAAAATCGAGTTGCGAAAATA
* * * * **
3296461 AAACTCACTTTGCGAATTATAAAATCGAGTTGCGAAAACG
1 AAATTCGCGTTGCGAATTCTAAAATCGAGTTGCGAAAATA
* * * *
3296501 AAACTCGTGTTGTGAATT-TAAAAATCGATTTGCGAAAA-A
1 AAATTCGCGTTGCGAATTCT-AAAATCGAGTTGCGAAAATA
* *
3296540 GAAATTTGTGTTGCGAA
1 -AAATTCGCGTTGCGAA
3296557 ATTGTCAAAT
Statistics
Matches: 103, Mismatches: 31, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
39 1 0.01
40 102 0.99
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (40 bp):
AAATTCGCGTTGCGAATTCTAAAATCGAGTTGCGAAAATA
Found at i:3296445 original size:60 final size:58
Alignment explanation
Indices: 3296381--3296538 Score: 165
Period size: 60 Copynumber: 2.6 Consensus size: 58
3296371 TGCTAATTTT
* * * *
3296381 AAATTCGCGTTGCGAATTCTAAAATCGAGTTGCGAAAATAAAATTCGCGTTGAGAAAGCG
1 AAATTCGCGTTGAGAATT-TAAAATCGATTTGCGAAAATAAAA-TCGAGTTGAGAAAACG
* * *
3296441 AAATTCGCGTTGAGAAATTAAAACTC-ACTTTGCGAATTATAAAATCGAGTTGCGAAAACG
1 AAATTCGCGTTGAGAATTTAAAA-TCGA-TTTGCGAA-AATAAAATCGAGTTGAGAAAACG
* * *
3296501 AAACTCGTGTTGTGAATTTAAAAATCGATTTGCGAAAA
1 AAATTCGCGTTGAGAATTT-AAAATCGATTTGCGAAAA
3296539 AGAAATTTGT
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
59 7 0.09
60 63 0.78
61 11 0.14
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (58 bp):
AAATTCGCGTTGAGAATTTAAAATCGATTTGCGAAAATAAAATCGAGTTGAGAAAACG
Found at i:3296553 original size:60 final size:59
Alignment explanation
Indices: 3296401--3296557 Score: 147
Period size: 60 Copynumber: 2.6 Consensus size: 59
3296391 TGCGAATTCT
* * * * *
3296401 AAAATCGAGTTGCGAAAATAAAATTCGCGTTGAGAAAGCGAAATTCGCGTTGAGAAATTA
1 AAAATCGATTTGCGAAAA-AAAATTCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTA
* * * * *
3296461 AAACTC-ACTTTGCGAATTATAAAA-TCGAGTTGCGAAAACGAAACTCGTGTTGTGAATTTA
1 AAAATCGA-TTTGCGAA--AAAAAATTCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTA
* *
3296521 AAAATCGATTTGCGAAAAAGAAATTTGTGTTGCGAAA
1 AAAATCGATTTGCGAAAAA-AAATTCGAGTTGCGAAA
3296558 TTGTCAAATT
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
58 2 0.03
59 4 0.05
60 65 0.84
61 5 0.06
62 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (59 bp):
AAAATCGATTTGCGAAAAAAAATTCGAGTTGCGAAAACGAAACTCGCGTTGAGAAATTA
Found at i:3296610 original size:20 final size:21
Alignment explanation
Indices: 3296585--3296627 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3296575 CGAATTCGTC
*
3296585 TTCTGTG-TGCGAATTCCAAA
1 TTCTGTGTTGCGAATTCAAAA
*
3296605 TTCTGTGTTGTGAATTCAAAA
1 TTCTGTGTTGCGAATTCAAAA
3296626 TT
1 TT
3296628 GAGTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (21 bp):
TTCTGTGTTGCGAATTCAAAA
Found at i:3300226 original size:18 final size:19
Alignment explanation
Indices: 3300194--3300230 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3300184 GGCAGCACGA
*
3300194 CCCCTCCCACGACCACCAG
1 CCCCTCCCACCACCACCAG
3300213 CCCCT-CCACCACCACCAG
1 CCCCTCCCACCACCACCAG
3300231 ATGCACCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.65, G:0.08, T:0.05
Consensus pattern (19 bp):
CCCCTCCCACCACCACCAG
Found at i:3301053 original size:2 final size:2
Alignment explanation
Indices: 3301046--3301089 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3301036 TTAACAACAC
3301046 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3301088 AG
1 AG
3301090 CTTAACCGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3302839 original size:19 final size:19
Alignment explanation
Indices: 3302815--3302862 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
3302805 TGTAGAATGG
3302815 GTATCGATACTGAAGTATA
1 GTATCGATACTGAAGTATA
3302834 GTATCGATACTGAAGTATA
1 GTATCGATACTGAAGTATA
3302853 GTATCGATAC
1 GTATCGATAC
3302863 CATAGTGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (19 bp):
GTATCGATACTGAAGTATA
Found at i:3303348 original size:45 final size:44
Alignment explanation
Indices: 3303286--3303399 Score: 156
Period size: 45 Copynumber: 2.6 Consensus size: 44
3303276 TATTTCATGT
*
3303286 TATGTGATATGATCTACGTGATTATATGAAAATGCGATACAAGC
1 TATGTGATATGAACTACGTGATTATATGAAAATGCGATACAAGC
* * *
3303330 TATGTGATATTGAACTACGTGATTATATGATAATGTGATATAAGC
1 TATGTGATA-TGAACTACGTGATTATATGAAAATGCGATACAAGC
* * *
3303375 TATGTGACATGACCTATGTGATTAT
1 TATGTGATATGAACTACGTGATTAT
3303400 TTATCTATGT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 23 0.37
45 39 0.63
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (44 bp):
TATGTGATATGAACTACGTGATTATATGAAAATGCGATACAAGC
Found at i:3303381 original size:14 final size:14
Alignment explanation
Indices: 3303321--3303425 Score: 68
Period size: 14 Copynumber: 7.1 Consensus size: 14
3303311 ATGAAAATGC
*
3303321 GATACAAGCTATGT
1 GATATAAGCTATGT
*
3303335 GATATTGAA-CTACGT
1 GATA-T-AAGCTATGT
* *
3303350 GATTATATGATAATGT
1 GA-TATAAGCT-ATGT
3303366 GATATAAGCTATGT
1 GATATAAGCTATGT
* * *
3303380 GACATGACCTATGT
1 GATATAAGCTATGT
* *
3303394 GATTATTTATCTATGT
1 GA-TA-TAAGCTATGT
3303410 GATATAAGCTATGT
1 GATATAAGCTATGT
3303424 GA
1 GA
3303426 AATGATATAA
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
14 32 0.46
15 18 0.26
16 19 0.28
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (14 bp):
GATATAAGCTATGT
Found at i:3303410 original size:44 final size:44
Alignment explanation
Indices: 3303286--3303430 Score: 166
Period size: 44 Copynumber: 3.3 Consensus size: 44
3303276 TATTTCATGT
* * * * *
3303286 TATGTGATATGATCTACGTGATTATATGAAAATGCGATACAAGC
1 TATGTGAAATGAACTACGTGATTATATGATAATGTGATATAAGC
*
3303330 TATGTGATATTGAACTACGTGATTATATGATAATGTGATATAAGC
1 TATGTGA-AATGAACTACGTGATTATATGATAATGTGATATAAGC
* * * * *
3303375 TATGTGACATGACCTATGTGATTAT-TTATCTATGTGATATAAGC
1 TATGTGAAATGAACTACGTGATTATATGAT-AATGTGATATAAGC
3303419 TATGTGAAATGA
1 TATGTGAAATGA
3303431 TATAAATGAT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 3 0.03
44 45 0.52
45 38 0.44
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (44 bp):
TATGTGAAATGAACTACGTGATTATATGATAATGTGATATAAGC
Found at i:3303563 original size:23 final size:23
Alignment explanation
Indices: 3303501--3303576 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
3303491 AGAGTCGAGG
*
3303501 TTCTACGCAGTCCTTCGGGACAA
1 TTCTACGCAGTCCTTCGAGACAA
* ** * * * *
3303524 TTCTGCGTGGTCTTTCGATATAT
1 TTCTACGCAGTCCTTCGAGACAA
* *
3303547 TTCTACGCAGTCCTTCGGGACAT
1 TTCTACGCAGTCCTTCGAGACAA
3303570 TTCTACG
1 TTCTACG
3303577 TGACACTTCA
Statistics
Matches: 38, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (23 bp):
TTCTACGCAGTCCTTCGAGACAA
Found at i:3304449 original size:23 final size:23
Alignment explanation
Indices: 3304416--3304480 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
3304406 CAGCTCGTAT
3304416 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* **
3304439 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCATGTAG
*
3304462 AAATGCACCAAAGTGCCAT
1 AAATGCACCGAAGTGCCAT
3304481 ATCAAATGTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:3305240 original size:35 final size:35
Alignment explanation
Indices: 3305182--3305249 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
3305172 TATGTTTCCA
*
3305182 GGTATCAATACATGCCTTCTGGTATCGATACTTAT
1 GGTATCAATACATGCCTTCTGGTATCAATACTTAT
* *
3305217 GGTATCGATACTAT-CCTTTTGGTATCAATACTT
1 GGTATCAATAC-ATGCCTTCTGGTATCAATACTT
3305250 CATGAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (35 bp):
GGTATCAATACATGCCTTCTGGTATCAATACTTAT
Found at i:3309068 original size:21 final size:20
Alignment explanation
Indices: 3309043--3309177 Score: 101
Period size: 21 Copynumber: 6.3 Consensus size: 20
3309033 CACCGAAGTG
3309043 CCACATAATTATCCCAAAAGA
1 CCACATAATT-TCCCAAAAGA
* *
3309064 CCACATAATTTGCACC-GAAGTG
1 CCACATAATTT-C-CCAAAAG-A
3309086 CCACATAATTGTCCCAAAAGA
1 CCACATAATT-TCCCAAAAGA
*
3309107 CCACATAATTTGCACCAAAATA
1 CCACATAATTT-C-CCAAAAGA
* ** *
3309129 CCACATATTTGTCCCGGATGA
1 CCACATAATT-TCCCAAAAGA
* *
3309150 CCACATAATTATCCCGAATGA
1 CCACATAATT-TCCCAAAAGA
3309171 CCACATA
1 CCACATA
3309178 TACCCTCGAC
Statistics
Matches: 93, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.02
21 56 0.60
22 33 0.35
23 2 0.02
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (20 bp):
CCACATAATTTCCCAAAAGA
Found at i:3309087 original size:43 final size:43
Alignment explanation
Indices: 3309026--3309159 Score: 196
Period size: 43 Copynumber: 3.1 Consensus size: 43
3309016 CTAAAGCTTG
*
3309026 TAATTTGCACCGAAGTGCCACATAATTATCCCAAAAGACCACA
1 TAATTTGCACCGAAGTGCCACATAATTGTCCCAAAAGACCACA
3309069 TAATTTGCACCGAAGTGCCACATAATTGTCCCAAAAGACCACA
1 TAATTTGCACCGAAGTGCCACATAATTGTCCCAAAAGACCACA
* * * * ** *
3309112 TAATTTGCACCAAAATACCACATATTTGTCCCGGATGACCACA
1 TAATTTGCACCGAAGTGCCACATAATTGTCCCAAAAGACCACA
3309155 TAATT
1 TAATT
3309160 ATCCCGAATG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (43 bp):
TAATTTGCACCGAAGTGCCACATAATTGTCCCAAAAGACCACA
Found at i:3309092 original size:22 final size:22
Alignment explanation
Indices: 3309026--3309095 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
3309016 CTAAAGCTTG
3309026 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
* *
3309048 TAATTAT-C-CCAAAAG-ACCACA
1 TAATT-TGCACC-GAAGTGCCACA
3309069 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTGCCACA
3309091 TAATT
1 TAATT
3309096 GTCCCAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 1 0.03
21 16 0.41
22 21 0.54
23 1 0.03
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (22 bp):
TAATTTGCACCGAAGTGCCACA
Found at i:3309131 original size:22 final size:22
Alignment explanation
Indices: 3309026--3309139 Score: 103
Period size: 21 Copynumber: 5.3 Consensus size: 22
3309016 CTAAAGCTTG
* * *
3309026 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCAAAATACCACA
*
3309048 TAATTAT-C-CCAAAAGACCACA
1 TAATT-TGCACCAAAATACCACA
* * *
3309069 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCAAAATACCACA
*
3309091 TAA-TTGTC-CCAAAAGACCACA
1 TAATTTG-CACCAAAATACCACA
3309112 TAATTTGCACCAAAATACCACA
1 TAATTTGCACCAAAATACCACA
3309134 T-ATTTG
1 TAATTTG
3309140 TCCCGGATGA
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 36 0.49
22 35 0.48
23 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (22 bp):
TAATTTGCACCAAAATACCACA
Found at i:3309154 original size:64 final size:64
Alignment explanation
Indices: 3309043--3309177 Score: 161
Period size: 64 Copynumber: 2.1 Consensus size: 64
3309033 CACCGAAGTG
*
3309043 CCACATAATTATCCCAAAAGACCACATAATTTGCACCGAAGTGCCACATAATTGTCCCAAAAGA
1 CCACATAATTATCCCAAAAGACCACATAATTTGCACCGAAGTGCCACATAATTATCCCAAAAGA
* * *
3309107 CCACATAATT-TGCACCAAAATACCACAT-ATTTGTC-CCGGA-TGACCACATAATTATCCCGAA
1 CCACATAATTAT-C-CCAAAAGACCACATAATTTG-CACCGAAGTG-CCACATAATTATCCCAAA
*
3309168 TGA
62 AGA
3309171 CCACATA
1 CCACATA
3309178 TACCCTCGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
63 3 0.05
64 45 0.73
65 14 0.23
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (64 bp):
CCACATAATTATCCCAAAAGACCACATAATTTGCACCGAAGTGCCACATAATTATCCCAAAAGA
Found at i:3315801 original size:21 final size:21
Alignment explanation
Indices: 3315775--3315814 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3315765 ACCCCTTTGA
*
3315775 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3315796 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3315815 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3317018 original size:15 final size:15
Alignment explanation
Indices: 3316998--3317045 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
3316988 CATTTTGAAT
3316998 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTTG
*
3317013 ATTTTGTGGATTGTTAG
1 A-TTT-TGGATTGTTTG
3317030 ATTTTGGATTTGTTTG
1 ATTTTGGA-TTGTTTG
3317046 GATGTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.18
16 12 0.43
17 11 0.39
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (15 bp):
ATTTTGGATTGTTTG
Found at i:3317024 original size:17 final size:17
Alignment explanation
Indices: 3317002--3317035 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3316992 TTGAATATTT
*
3317002 TGGATTGTTTGATTTTG
1 TGGATTGTTAGATTTTG
3317019 TGGATTGTTAGATTTTG
1 TGGATTGTTAGATTTTG
3317036 GATTTGTTTG
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:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (17 bp):
TGGATTGTTAGATTTTG
Found at i:3317631 original size:22 final size:23
Alignment explanation
Indices: 3317606--3317649 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3317596 AATTAAGTTT
3317606 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
3317628 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
3317650 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:3318729 original size:22 final size:20
Alignment explanation
Indices: 3318679--3318753 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 20
3318669 ATGTTTTAAG
*
3318679 GGTATCGATACCCTCCTGAA
1 GGTATCGATACCCTCCTCAA
*
3318699 GGTACCGATACCCATCCCTCAA
1 GGTATCGATACCC-T-CCTCAA
* *
3318721 GGTATCGATACCACTCTTAACA
1 GGTATCGATACC-CTCCTCA-A
3318743 GGTATCGATAC
1 GGTATCGATAC
3318754 ACCCTTATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
20 12 0.26
21 4 0.09
22 29 0.63
23 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCCTCCTCAA
Found at i:3320355 original size:3 final size:3
Alignment explanation
Indices: 3320299--3320344 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
3320289 TATATATATA
* *
3320299 TAT TAT AAT AAT TATT TAT TAT TAT TAT TAT TATT TAT TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
3320345 ATTCTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3320356 original size:22 final size:19
Alignment explanation
Indices: 3320299--3320344 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3320289 TATATATATA
* *
3320299 TATTATAATAATTATTTAT
1 TATTATTATTATTATTTAT
3320318 TATTATTATTATTATTTAT
1 TATTATTATTATTATTTAT
3320337 TATTATTA
1 TATTATTA
3320345 ATTCTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATTATTATTATTTAT
Found at i:3321827 original size:29 final size:28
Alignment explanation
Indices: 3321782--3321921 Score: 83
Period size: 28 Copynumber: 4.9 Consensus size: 28
3321772 TTTTTATATA
*
3321782 TTTATTTCATTCA-TTTTATTACTCTTTAT
1 TTTATTTTATT-ATTTTTATT-CTCTTTAT
*
3321811 TTTATTTTATTATTTTTTTTCTCTTT-T
1 TTTATTTTATTATTTTTATTCTCTTTAT
* * *
3321838 GATTTA-TTTAATATTTTTTATTTTATTTAT
1 --TTTATTTTATTA-TTTTTATTCTCTTTAT
* * *
3321868 TTTCTTATTATT-TTTTTCTTTTCTTTAT
1 TTTATT-TTATTATTTTTATTCTCTTTAT
* * *
3321896 TTTCTTATTATT-TTTTTCTTTTCTTT
1 TTTATT-TTATTATTTTTATTCTCTTT
3321922 CCTTTCATTT
Statistics
Matches: 94, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.01
28 56 0.60
29 32 0.34
30 5 0.05
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTATTTTATTATTTTTATTCTCTTTAT
Found at i:3321880 original size:11 final size:10
Alignment explanation
Indices: 3321806--3321921 Score: 54
Period size: 9 Copynumber: 12.2 Consensus size: 10
3321796 TTTATTACTC
*
3321806 TTTATTTTAT
1 TTTATTTTCT
3321816 TTTATTATT-T
1 TTTATT-TTCT
*
3321826 TTT-TTCTCT
1 TTTATTTTCT
*
3321835 TTTGA-TTTAT
1 TTT-ATTTTCT
* *
3321845 TTAATATT-T
1 TTTATTTTCT
*
3321854 TTTATTTT-A
1 TTTATTTTCT
3321863 TTTATTTTCT
1 TTTATTTTCT
3321873 TATTA-TTT-T
1 T-TTATTTTCT
*
3321882 TTTCTTTTC-
1 TTTATTTTCT
3321891 TTTATTTTCT
1 TTTATTTTCT
3321901 TATTA-TTT-T
1 T-TTATTTTCT
*
3321910 TTTCTTTTCT
1 TTTATTTTCT
3321920 TT
1 TT
3321922 CCTTTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
8 5 0.06
9 40 0.49
10 28 0.35
11 8 0.10
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.78
Consensus pattern (10 bp):
TTTATTTTCT
Found at i:3321880 original size:20 final size:21
Alignment explanation
Indices: 3321812--3321909 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 21
3321802 ACTCTTTATT
3321812 TTATTTTA-TTATTTT-TTT-
1 TTATTTTATTTATTTTCTTTA
* * *
3321830 TCTCTTTTGATTTATTTAATATTTT
1 T-TATTTT-ATTTATTT--TCTTTA
3321855 TTATTTTATTTATTTTC-TTA
1 TTATTTTATTTATTTTCTTTA
*
3321875 TTATTTT-TTTCTTTTCTTTA
1 TTATTTTATTTATTTTCTTTA
3321895 TT-TTCTTA-TTATTTT
1 TTATT-TTATTTATTTT
3321910 TTTCTTTTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
18 1 0.02
19 15 0.23
20 23 0.36
21 7 0.11
23 9 0.14
24 8 0.12
25 1 0.02
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (21 bp):
TTATTTTATTTATTTTCTTTA
Found at i:3321912 original size:28 final size:28
Alignment explanation
Indices: 3321804--3321921 Score: 127
Period size: 28 Copynumber: 4.2 Consensus size: 28
3321794 ATTTTATTAC
*
3321804 TCTTTATTTTATT-TTATTATTTTT-TTT
1 TCTTTATTTTCTTATTATT-TTTTTCTTT
* *
3321831 CTCTTTTGATTTAT-TTAATA-TTTTTTATTT
1 -TC-TTT-ATTT-TCTTATTATTTTTTTCTTT
*
3321861 TATTTATTTTCTTATTATTTTTTTCTTT
1 TCTTTATTTTCTTATTATTTTTTTCTTT
3321889 TCTTTATTTTCTTATTATTTTTTTCTTT
1 TCTTTATTTTCTTATTATTTTTTTCTTT
3321917 TCTTT
1 TCTTT
3321922 CCTTTCATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 14
0.80 0.05 0.14
Matches are distributed among these distances:
26 1 0.01
27 9 0.12
28 46 0.59
29 9 0.12
30 10 0.13
31 3 0.04
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.77
Consensus pattern (28 bp):
TCTTTATTTTCTTATTATTTTTTTCTTT
Found at i:3321927 original size:28 final size:28
Alignment explanation
Indices: 3321851--3321935 Score: 109
Period size: 28 Copynumber: 3.1 Consensus size: 28
3321841 TTATTTAATA
* * *
3321851 TTTTTTATTTTATTTATTTTCTTATTAT
1 TTTTTTCTTTTCTTTACTTTCTTATTAT
*
3321879 TTTTTTCTTTTCTTTATTTTCTTATTAT
1 TTTTTTCTTTTCTTTACTTTCTTATTAT
* *
3321907 TTTTTTCTTTTCTTTCCTTTCAT-TTAT
1 TTTTTTCTTTTCTTTACTTTCTTATTAT
3321934 TT
1 TT
3321936 AATATTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
27 6 0.12
28 46 0.88
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTTTCTTTTCTTTACTTTCTTATTAT
Found at i:3326928 original size:21 final size:21
Alignment explanation
Indices: 3326904--3326995 Score: 98
Period size: 21 Copynumber: 4.3 Consensus size: 21
3326894 CACAGAAGTG
3326904 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
* *
3326925 CCACATAATT-TACACCTAATTG-
1 CCACATAATTGT-C-CCGAA-GGA
* **
3326947 CCACATATTTGTCCCGAAAAA
1 CCACATAATTGTCCCGAAGGA
3326968 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
3326989 CCACATA
1 CCACATA
3326996 GACCCTTGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
20 1 0.02
21 40 0.70
22 14 0.25
23 2 0.04
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:3326935 original size:43 final size:43
Alignment explanation
Indices: 3326887--3326977 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
3326877 CTACAGCTCG
* **
3326887 TAATTTGCACAGAAGTGCCACATAATTGTCCCGAAGGACCACA
1 TAATTTACACAGAAGTGCCACATAATTGTCCCGAAAAACCACA
** * *
3326930 TAATTTACACCTAATTGCCACATATTTGTCCCGAAAAACCACA
1 TAATTTACACAGAAGTGCCACATAATTGTCCCGAAAAACCACA
3326973 TAATT
1 TAATT
3326978 GTCCCGAAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (43 bp):
TAATTTACACAGAAGTGCCACATAATTGTCCCGAAAAACCACA
Found at i:3327524 original size:20 final size:22
Alignment explanation
Indices: 3327493--3327546 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3327483 CATGCTTGGA
3327493 GGTATCAG-TACCA-CC-TTAAG
1 GGTAT-AGATACCACCCTTTAAG
*
3327513 GGTATAGATACCACCCTTTAGG
1 GGTATAGATACCACCCTTTAAG
*
3327535 GGTATCGATACC
1 GGTATAGATACC
3327547 TATACATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 10 0.34
21 2 0.07
22 15 0.52
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (22 bp):
GGTATAGATACCACCCTTTAAG
Found at i:3331241 original size:13 final size:14
Alignment explanation
Indices: 3331223--3331253 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3331213 TTAGTGAGCC
3331223 ATAATAATAATA-T
1 ATAATAATAATATT
3331236 ATAATAATAATATT
1 ATAATAATAATATT
3331250 ATAA
1 ATAA
3331254 GGAAATGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATAATAATATT
Found at i:3334583 original size:25 final size:24
Alignment explanation
Indices: 3334537--3334593 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
3334527 TATAATAATG
*
3334537 ATAAATAAAATAAATAACAAAACA
1 ATAAATAAAATAAATAAAAAAACA
* *
3334561 ATAAATAAAAGTTAATAAAAAAAGA
1 ATAAATAAAA-TAAATAAAAAAACA
*
3334586 AAAAATAA
1 ATAAATAA
3334594 TTAAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (24 bp):
ATAAATAAAATAAATAAAAAAACA
Found at i:3335840 original size:3 final size:3
Alignment explanation
Indices: 3335832--3335904 Score: 83
Period size: 3 Copynumber: 23.3 Consensus size: 3
3335822 CTGCATAAAT
*
3335832 ATA ATA ATA ATA ATTA ATTA ATA ATA AGTA ATA ATA ATA ATA ATA TTA
1 ATA ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * *
3335880 ATA ATA ATT CTA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3335905 ATAAATGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 50 0.83
4 10 0.17
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3335868 original size:30 final size:29
Alignment explanation
Indices: 3335832--3335904 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 29
3335822 CTGCATAAAT
*
3335832 ATAATAATAATAATTAATTAATAATAA-GTA
1 ATAATAATAATAA-T-ATTAATAATAATCTA
3335862 ATAATAATAATAATATTAATAATAATTCTA
1 ATAATAATAATAATATTAATAATAA-TCTA
*
3335892 ATAATAAAAATAA
1 ATAATAATAATAA
3335905 ATAAATGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 11 0.28
29 1 0.03
30 27 0.69
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (29 bp):
ATAATAATAATAATATTAATAATAATCTA
Found at i:3336853 original size:106 final size:106
Alignment explanation
Indices: 3336673--3337077 Score: 567
Period size: 106 Copynumber: 3.7 Consensus size: 106
3336663 CCACTTCGTC
* * * * * *
3336673 GTGAAGTTAAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGCTGGGAAGTTAAAATTGACTCTGA
1 GTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
* *
3336738 AATTGGGAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCT
66 AATTAGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCT
* *
3336779 ATGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
*
3336844 AATTAGGAAGTTGTTTATTGACAGTCAGCCGCCCCTTCGCT
66 AATTAGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCT
* * *
3336885 GTGAAGTTTAGCTTGTGCTGTATAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
3336950 AATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCT
66 AA-----T-T---A---GGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCT
3337003 GTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
*
3337068 AATTGGGAAG
66 AATTAGGAAG
3337078 CCCCTTCGTC
Statistics
Matches: 268, Mismatches: 19, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
106 164 0.61
111 1 0.00
112 2 0.01
113 1 0.00
115 1 0.00
118 99 0.37
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
AATTAGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCT
Found at i:3336952 original size:12 final size:12
Alignment explanation
Indices: 3336935--3336967 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3336925 GCTGTGAAGT
3336935 TGAAATTGGCTC
1 TGAAATTGGCTC
3336947 TGAAATTGGCTC
1 TGAAATTGGCTC
3336959 TGAAATTGG
1 TGAAATTGG
3336968 GAAGTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (12 bp):
TGAAATTGGCTC
Found at i:3337037 original size:118 final size:118
Alignment explanation
Indices: 3336829--3337073 Score: 445
Period size: 118 Copynumber: 2.1 Consensus size: 118
3336819 GCTGTGAAGT
*
3336829 TGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTT
1 TGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTG
3336894 AGCTTGTGCTGTATAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 AGCTTGTGCTGTATAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* *
3336947 TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTG
1 TGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTG
* *
3337012 AGCTTGTGCTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 AGCTTGTGCTGTATAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
3337065 TGAAATTGG
1 TGAAATTGG
3337074 GAAGCCCCTT
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 122 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (118 bp):
TGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTG
AGCTTGTGCTGTATAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
Found at i:3341152 original size:12 final size:12
Alignment explanation
Indices: 3341135--3341160 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3341125 TAATTGTGAA
3341135 AATTTGAAATTT
1 AATTTGAAATTT
3341147 AATTTGAAATTT
1 AATTTGAAATTT
3341159 AA
1 AA
3341161 AAACCCGATT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTTGAAATTT
Found at i:3341337 original size:10 final size:10
Alignment explanation
Indices: 3341235--3341350 Score: 53
Period size: 10 Copynumber: 11.6 Consensus size: 10
3341225 TTTAGATTAT
*
3341235 AAAATAAAAA
1 AAAATAATAA
**
3341245 ATAAATACGAA
1 A-AAATAATAA
*
3341256 AAAATATTAA
1 AAAATAATAA
* *
3341266 TATAATAATGA
1 -AAAATAATAA
*
3341277 TAAATAA-AA
1 AAAATAATAA
* *
3341286 TAAATAACAA
1 AAAATAATAA
3341296 AACAATAA-AA
1 AA-AATAATAA
3341306 AAAAGTTAAT-A
1 AAAA--TAATAA
*
3341317 AAAA-AA-GA
1 AAAATAATAA
*
3341325 AAAATAATTA
1 AAAATAATAA
3341335 AAAATAATAA
1 AAAATAATAA
3341345 AAAATA
1 AAAATA
3341351 TGATGTAAGT
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.08
9 12 0.14
10 36 0.43
11 28 0.34
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (10 bp):
AAAATAATAA
Found at i:3342391 original size:3 final size:3
Alignment explanation
Indices: 3342383--3342444 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
3342373 TGCACAAATG
* **
3342383 TAA TAA TAA TAA TTAA TTAA TAA TAA TAA TAA TAT TAA TAA TAA TTC
1 TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3342430 TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA
3342445 ATAAATGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
3 43 0.86
4 7 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3343004 original size:125 final size:123
Alignment explanation
Indices: 3342769--3343006 Score: 325
Period size: 123 Copynumber: 1.9 Consensus size: 123
3342759 GCCTTGAGCT
** ** *
3342769 ATGTTGCAAATGAACATGATATCCTTCGTCGTGAAGTTGAAATTGTGGAGGCCCCTTAGTCGTGA
1 ATGTTGCAAATGAACATGATATCCTTCGTCGTGAAGTTGAAATAATAAAGGCCCCTTAGTAGTGA
*
3342834 AGTTGAGCCTGAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGGTTA
66 AGTTGAACCTGAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGGTTA
* * * * *
3342892 ATGTTGCTAGTGAGCATGAT-TCCATTCGTCGTGAAGTTGAAATAATAAATGGTCCCTTCGTAGT
1 ATGTTGCAAATGAACATGATATCC-TTCGTCGTGAAGTTGAAATAATAAA-GGCCCCTTAGTAGT
* *
3342956 GAAGTTGAACCTTGGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT
64 GAAGTTGAACC-TGAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT
3343007 GTAAGTTGTG
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
122 3 0.03
123 38 0.38
124 21 0.21
125 37 0.37
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (123 bp):
ATGTTGCAAATGAACATGATATCCTTCGTCGTGAAGTTGAAATAATAAAGGCCCCTTAGTAGTGA
AGTTGAACCTGAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGGTTA
Found at i:3343838 original size:3 final size:3
Alignment explanation
Indices: 3343830--3343883 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
3343820 TGCACAAATG
*
3343830 TAA TAA TAA TAA TTAA TTAA TAA TAA GTAA TAA TAC TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA -TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
*
3343878 AAA TAA
1 TAA TAA
3343884 ATAAATGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 35 0.78
4 10 0.22
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3345071 original size:53 final size:52
Alignment explanation
Indices: 3344999--3345106 Score: 162
Period size: 53 Copynumber: 2.1 Consensus size: 52
3344989 CGATTACTAT
* *
3344999 TTATAAGTAGACAAGATAATTTGGTTGTCAAATAGTAAACTTAGTTGGTAGA
1 TTATAAGTAGACAAGATAATTTGGTTGTCAAATAATAAAATTAGTTGGTAGA
* **
3345051 TTATGAAGTTGACAAGATAATTTGGTTGTCATTTAATAAAATTAGTTGGTAGA
1 TTAT-AAGTAGACAAGATAATTTGGTTGTCAAATAATAAAATTAGTTGGTAGA
3345104 TTA
1 TTA
3345107 CACGAGTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 4 0.08
53 46 0.92
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (52 bp):
TTATAAGTAGACAAGATAATTTGGTTGTCAAATAATAAAATTAGTTGGTAGA
Found at i:3349104 original size:2 final size:2
Alignment explanation
Indices: 3349097--3349129 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3349087 AATTGATGTT
3349097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3349130 TACAATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3349391 original size:2 final size:2
Alignment explanation
Indices: 3349386--3349420 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3349376 TATAAAAAAT
3349386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3349421 GTATTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3349787 original size:23 final size:23
Alignment explanation
Indices: 3349755--3349799 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3349745 TATTACATGT
*
3349755 TCTCTATCTTTTTGACATGTTTA
1 TCTCTATCTTTGTGACATGTTTA
* *
3349778 TCTCTGTCTTTGTGATATGTTT
1 TCTCTATCTTTGTGACATGTTT
3349800 TTATCTACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (23 bp):
TCTCTATCTTTGTGACATGTTTA
Found at i:3350247 original size:19 final size:19
Alignment explanation
Indices: 3350225--3350271 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3350215 TAGGTTTACA
*
3350225 ATTATATTTATAAATCTTT
1 ATTATATTTATAAATATTT
3350244 ATTATAATTT-TAAATATTT
1 ATTAT-ATTTATAAATATTT
*
3350263 -TTATTTTTA
1 ATTATATTTA
3350272 ATATTCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 4 0.17
19 13 0.54
20 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATATTTATAAATATTT
Found at i:3350976 original size:21 final size:21
Alignment explanation
Indices: 3350950--3350994 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
3350940 GAGAGATTAC
3350950 AGATACTTACAGAACCACCGG
1 AGATACTTACAGAACCACCGG
3350971 AGATACTTACAGAACCACCGG
1 AGATACTTACAGAACCACCGG
3350992 AGA
1 AGA
3350995 AGATTCTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (21 bp):
AGATACTTACAGAACCACCGG
Found at i:3352747 original size:13 final size:14
Alignment explanation
Indices: 3352718--3352770 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
3352708 TAAACTGAAA
*
3352718 AAGAAAAGAAAATG
1 AAGAAAAGAATATG
3352732 AA-AAAAG--TATG
1 AAGAAAAGAATATG
3352743 -AGAAAAGAATATG
1 AAGAAAAGAATATG
*
3352756 AAGAAACGAA-ATG
1 AAGAAAAGAATATG
3352769 AA
1 AA
3352771 TGAACAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 8 0.24
13 14 0.42
14 10 0.30
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (14 bp):
AAGAAAAGAATATG
Found at i:3359032 original size:29 final size:29
Alignment explanation
Indices: 3358968--3359024 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3358958 CAATAGACTG
3358968 AAATAAATACAACATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
3358997 AAATAAATACAAGATACAAATTAGAAAC
1 AAATAAATACAACATACAAATTAGAAAC
3359025 TGATTAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.63, C:0.14, G:0.05, T:0.18
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Found at i:3360550 original size:18 final size:18
Alignment explanation
Indices: 3360523--3360571 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
3360513 TGTCATCACT
3360523 ACGAAGGACCACTATGTC
1 ACGAAGGACCACTATGTC
*
3360541 ACGAATGACCACTATGTC
1 ACGAAGGACCACTATGTC
*
3360559 CCGAAGGACCACT
1 ACGAAGGACCACT
3360572 CCTTAAGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (18 bp):
ACGAAGGACCACTATGTC
Found at i:3366577 original size:21 final size:22
Alignment explanation
Indices: 3366542--3366597 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
3366532 TAAGCATGTG
3366542 TTTATATGAGTATATGTGATAT-A
1 TTTATAT--GTATATGTGATATGA
*
3366565 TGTTAT-TGTATATGTTATATGA
1 T-TTATATGTATATGTGATATGA
3366587 TTTATATGTAT
1 TTTATATGTAT
3366598 TCATGTTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 16 0.55
22 7 0.24
23 2 0.07
24 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (22 bp):
TTTATATGTATATGTGATATGA
Found at i:3367010 original size:21 final size:21
Alignment explanation
Indices: 3366984--3367024 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3366974 GTTCTACGTG
*
3366984 ATCCTTCGGGACATATATGTA
1 ATCCTTCGGAACATATATGTA
*
3367005 ATCCTTTGGAACATATATGT
1 ATCCTTCGGAACATATATGT
3367025 GGTACTTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
ATCCTTCGGAACATATATGTA
Found at i:3367154 original size:18 final size:18
Alignment explanation
Indices: 3367105--3367156 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
3367095 TATGTGATAT
* * *
3367105 GTGGTTCTTCGAGATATA
1 GTGGTCCTTCGGGACATA
3367123 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
3367141 GTGGTCCTTTGGGACA
1 GTGGTCCTTCGGGACA
3367157 AATTCTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:3368941 original size:39 final size:39
Alignment explanation
Indices: 3368890--3368985 Score: 174
Period size: 39 Copynumber: 2.5 Consensus size: 39
3368880 CCAAGAGAAG
3368890 GAAGGAAGGAAGATTTTGGGGGAAAAAGGGTAATCAAGA
1 GAAGGAAGGAAGATTTTGGGGGAAAAAGGGTAATCAAGA
* *
3368929 GAAGGAAAGAAGATTTTGGGGGAAAAAGGGTAATTAAGA
1 GAAGGAAGGAAGATTTTGGGGGAAAAAGGGTAATCAAGA
3368968 GAAGGAAGGAAGATTTTG
1 GAAGGAAGGAAGATTTTG
3368986 TTGCTGGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.44, C:0.01, G:0.38, T:0.18
Consensus pattern (39 bp):
GAAGGAAGGAAGATTTTGGGGGAAAAAGGGTAATCAAGA
Found at i:3369103 original size:10 final size:11
Alignment explanation
Indices: 3369077--3369103 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3369067 AAAGTGGAGG
3369077 ATTTTTTAATT
1 ATTTTTTAATT
3369088 ATTTTTTAATT
1 ATTTTTTAATT
3369099 ATTTT
1 ATTTT
3369104 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTTAATT
Found at i:3369673 original size:2 final size:2
Alignment explanation
Indices: 3369666--3369705 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3369656 GAGTCACTCA
3369666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3369706 TGTTTATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3370112 original size:38 final size:39
Alignment explanation
Indices: 3370022--3370134 Score: 124
Period size: 39 Copynumber: 2.9 Consensus size: 39
3370012 TTATCATCTC
*
3370022 AATAAATGAATTGTAATTA-TTCTTCCTTAAAAAACCCAA
1 AATAAATGAATTGTAATCATTTCTTCCTT-AAAAACCCAA
* * *
3370061 AATAAATTAATTGTAATCATTTCTT-CTT-AAAACTTCAT
1 AATAAATGAATTGTAATCATTTCTTCCTTAAAAAC-CCAA
* *
3370099 AATAAATGAATTGTAATCATTTTTTTTCTTAAAAAC
1 AATAAATGAATTGTAATCA-TTTCTTCCTTAAAAAC
3370135 TCCCATTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
37 5 0.08
38 20 0.32
39 25 0.40
40 8 0.13
41 5 0.08
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.41
Consensus pattern (39 bp):
AATAAATGAATTGTAATCATTTCTTCCTTAAAAACCCAA
Found at i:3370581 original size:30 final size:31
Alignment explanation
Indices: 3370523--3370581 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
3370513 AGCAGCTCGA
* *
3370523 AAATATAATATATTAAGATATTATTATTTTT
1 AAATATAATATATTAAAATATTAATATTTTT
3370554 AAATA-AAT-TATTAATAATATTAATATTT
1 AAATATAATATATTAA-AATATTAATATTT
3370582 ATGTATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
AAATATAATATATTAAAATATTAATATTTTT
Found at i:3372984 original size:42 final size:42
Alignment explanation
Indices: 3372923--3373007 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
3372913 ACTAAAATCC
* * *
3372923 GTGTATGGGTGATGTCTAAGACAAGATTTTGAACTTAGAACT
1 GTGTATGGGTGAAGGCTAAGACAAGATTTTGAACCTAGAACT
3372965 GTGTATGGGTGAAGGCTAAGACAAGATTTTGAACCTAGAACT
1 GTGTATGGGTGAAGGCTAAGACAAGATTTTGAACCTAGAACT
3373007 G
1 G
3373008 CATGGAGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (42 bp):
GTGTATGGGTGAAGGCTAAGACAAGATTTTGAACCTAGAACT
Found at i:3376873 original size:43 final size:42
Alignment explanation
Indices: 3376820--3376942 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
3376810 TTTTTTTATT
* * *
3376820 TTTACAATTGAGATCTTTAATTTTTTCAAT-TCCACTTTTTACA
1 TTTATAATTGAGAACCTTAATTTTTT-AATCT-CACTTTTTACA
* * *
3376863 TTTATAATTGAGAACCTTGATTTTTTAATCTCGCTTTTTACC
1 TTTATAATTGAGAACCTTAATTTTTTAATCTCACTTTTTACA
* * *
3376905 TTTATAATTGAG-GCTCGTGATTTTTTCAATCTCACTTT
1 TTTATAATTGAGAAC-CTTAATTTTTT-AATCTCACTTT
3376943 CTATCTTTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 34 0.50
43 33 0.49
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.50
Consensus pattern (42 bp):
TTTATAATTGAGAACCTTAATTTTTTAATCTCACTTTTTACA
Found at i:3376901 original size:42 final size:43
Alignment explanation
Indices: 3376839--3376942 Score: 133
Period size: 42 Copynumber: 2.4 Consensus size: 43
3376829 GAGATCTTTA
*
3376839 ATTTTTTCAAT-TCCACTTTTTACATTTATAATTGAGAAC-CTTG
1 ATTTTTTCAATCT-CACTTTTTACATTTATAATTGAG-ACTCGTG
* * *
3376882 ATTTTTT-AATCTCGCTTTTTACCTTTATAATTGAGGCTCGTG
1 ATTTTTTCAATCTCACTTTTTACATTTATAATTGAGACTCGTG
3376924 ATTTTTTCAATCTCACTTT
1 ATTTTTTCAATCTCACTTT
3376943 CTATCTTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.02
42 34 0.64
43 18 0.34
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (43 bp):
ATTTTTTCAATCTCACTTTTTACATTTATAATTGAGACTCGTG
Found at i:3376966 original size:108 final size:109
Alignment explanation
Indices: 3376864--3377061 Score: 260
Period size: 108 Copynumber: 1.8 Consensus size: 109
3376854 CTTTTTACAT
* * * *
3376864 TTATAATTGAGAACCTTGATTTTTT-AATCTCGC-TTTTTACCTTTATAATTGAGG-CTCGTGA-
1 TTATAATTAAG-ACCCT-ATTTTTTCAATCTCGCTTTTTTACCTTTATAATTGAGGTC-CCTAAT
* *
3376925 TTTTTTCAATCTCACTTTCTATCTTTATTTAATCTCACTTTTAACCA
63 TTTTTTCAATCTAACTTTCTACCTTTATTTAATCTCACTTTTAACCA
* * *
3376972 TTATAATTAAGGCCCTATTTTTTCAATCTCGCTTTTTTACTTTTATAATTTAGGTCCCTAATTTT
1 TTATAATTAAGACCCTATTTTTTCAATCTCGCTTTTTTACCTTTATAATTGAGGTCCCTAATTTT
3377037 TTTCAATCTAACTTTCTACCTTTAT
66 TTTCAATCTAACTTTCTACCTTTAT
3377062 AATTGAAGCT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
106 7 0.09
107 11 0.14
108 32 0.42
109 27 0.35
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.51
Consensus pattern (109 bp):
TTATAATTAAGACCCTATTTTTTCAATCTCGCTTTTTTACCTTTATAATTGAGGTCCCTAATTTT
TTTCAATCTAACTTTCTACCTTTATTTAATCTCACTTTTAACCA
Found at i:3376975 original size:23 final size:23
Alignment explanation
Indices: 3376932--3376975 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3376922 TGATTTTTTC
* *
3376932 AATCTCACTTTCTATCTTTATTT
1 AATCTCACTTTCTACCATTATTT
3376955 AATCTCACTTT-TAACCATTAT
1 AATCTCACTTTCT-ACCATTAT
3376976 AATTAAGGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (23 bp):
AATCTCACTTTCTACCATTATTT
Found at i:3377061 original size:44 final size:40
Alignment explanation
Indices: 3376955--3377107 Score: 118
Period size: 44 Copynumber: 3.7 Consensus size: 40
3376945 ATCTTTATTT
*
3376955 AATCTCACTTTTAACCATTATAATTAAGGCCCTATTTTTTC
1 AATCTCACTTTT-ACCTTTATAATTAAGGCCCTATTTTTTC
* * *
3376996 AATCTCGCTTTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTC
1 AATCTCAC--TTTTACCTTTATAATTAAGG-CCCT-A-TTTTTTC
*
3377041 AATCTAACTTTCTACCTTTATAATTGAA-GCTCCTAATCTTTTT-
1 AATCTCACTTT-TACCTTTATAATT-AAGGC-CCT-AT-TTTTTC
*
3377084 AATCTCAATTTT---TTTATAATTAAG
1 AATCTCACTTTTACCTTTATAATTAAG
3377108 ACCCCTAATT
Statistics
Matches: 92, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
38 2 0.02
39 9 0.10
41 7 0.08
42 14 0.15
43 22 0.24
44 24 0.26
45 14 0.15
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.49
Consensus pattern (40 bp):
AATCTCACTTTTACCTTTATAATTAAGGCCCTATTTTTTC
Found at i:3387226 original size:24 final size:24
Alignment explanation
Indices: 3387199--3387289 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
3387189 ATTTGAATTC
*
3387199 TGATCTGATACTTGACATGGATTT
1 TGATATGATACTTGACATGGATTT
* ** *
3387223 TGATCTGATA-TCTGATTTGGATTC
1 TGATATGATACT-TGACATGGATTT
*
3387247 TGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTT
3387271 TGATATGATACTTGACATG
1 TGATATGATACTTGACATG
3387290 AATTATGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
23 1 0.02
24 55 0.96
25 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTT
Found at i:3387240 original size:48 final size:49
Alignment explanation
Indices: 3387164--3387280 Score: 157
Period size: 48 Copynumber: 2.4 Consensus size: 49
3387154 TTCCCTACCC
* * *
3387164 ACATGGATATTTTATCTGAT-TTTCGATTTGAATTCTGATCTGATACTTG
1 ACATGGAT-TTTGATCTGATATCTCGATTTGAATTCTGATATGATACTTG
*
3387213 ACATGGATTTTGATCTGATATCT-GATTTGGATTCTGATATGATACTTG
1 ACATGGATTTTGATCTGATATCTCGATTTGAATTCTGATATGATACTTG
* *
3387261 ACCTGGATTTTGATATGATA
1 ACATGGATTTTGATCTGATA
3387281 CTTGACATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
48 51 0.84
49 10 0.16
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (49 bp):
ACATGGATTTTGATCTGATATCTCGATTTGAATTCTGATATGATACTTG
Found at i:3387303 original size:24 final size:24
Alignment explanation
Indices: 3387192--3387296 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 24
3387182 ATTTTCGATT
* *
3387192 TGAATTCTGATCTGATACTTGACA
1 TGAATTATGATATGATACTTGACA
* * * **
3387216 TGGATTTTGATCTGATA-TCTGATT
1 TGAATTATGATATGATACT-TGACA
* * *
3387240 TGGATTCTGATATGATACTTGACC
1 TGAATTATGATATGATACTTGACA
* *
3387264 TGGATTTTGATATGATACTTGACA
1 TGAATTATGATATGATACTTGACA
3387288 TGAATTATG
1 TGAATTATG
3387297 TTTTGATTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 1 0.01
24 65 0.97
25 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (24 bp):
TGAATTATGATATGATACTTGACA
Found at i:3387471 original size:43 final size:43
Alignment explanation
Indices: 3387405--3387499 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
3387395 GGGCCTTAAT
* *
3387405 TGGTATGTTGGTGGGTGTATGGTT-TGGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCT-GGGAAACCTACACATTA
3387448 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
3387491 TGGTGTGTT
1 TGGTGTGTT
3387500 CGGTTGGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 48 0.98
44 1 0.02
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:3395860 original size:18 final size:18
Alignment explanation
Indices: 3395837--3395878 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3395827 ATACTCATAA
3395837 CTTCCCCAAGAAATCAAC
1 CTTCCCCAAGAAATCAAC
**
3395855 CTTCCCTGAGAAATCAAC
1 CTTCCCCAAGAAATCAAC
3395873 CTTCCC
1 CTTCCC
3395879 TAACTACCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.40, G:0.07, T:0.21
Consensus pattern (18 bp):
CTTCCCCAAGAAATCAAC
Found at i:3395879 original size:18 final size:18
Alignment explanation
Indices: 3395845--3395879 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3395835 AACTTCCCCA
3395845 AGAAATCAACCTTCCCTG
1 AGAAATCAACCTTCCCTG
3395863 AGAAATCAACCTTCCCT
1 AGAAATCAACCTTCCCT
3395880 AACTACCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (18 bp):
AGAAATCAACCTTCCCTG
Found at i:3401982 original size:26 final size:26
Alignment explanation
Indices: 3401960--3402049 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 26
3401950 TAGTTATACT
3401960 TTTAATAAATTAAAATAAATTATATA
1 TTTAATAAATTAAAATAAATTATATA
** ** *
3401986 TTTTTTAAATTAAAATAAAAAATATT
1 TTTAATAAATTAAAATAAATTATATA
* *
3402012 TTTAATTTAAGTCAATAATAAA--ATATA
1 TTTAA--TAAATTAA-AATAAATTATATA
3402039 TTTAATAAATT
1 TTTAATAAATT
3402050 GATATAAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
25 4 0.08
26 24 0.49
27 9 0.18
28 6 0.12
29 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
TTTAATAAATTAAAATAAATTATATA
Found at i:3402759 original size:27 final size:25
Alignment explanation
Indices: 3402718--3402799 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 25
3402708 ATACTTTTAA
* *
3402718 TAAATTAAAATAAATTATATATTTT
1 TAAATTAAAATAAATAAAATATTTT
*
3402743 TCAATTAAAATAAAAATAAAATATTTT
1 TAAATTAAAAT--AAATAAAATATTTT
*
3402770 TAAATTAAGTTAAT-AATAAAATATATT
1 TAAATTAA---AATAAATAAAATATTTT
3402797 TAA
1 TAA
3402800 TAATTTGATA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
25 10 0.21
27 34 0.72
30 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (25 bp):
TAAATTAAAATAAATAAAATATTTT
Found at i:3402823 original size:25 final size:26
Alignment explanation
Indices: 3402736--3402828 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 26
3402726 AATAAATTAT
** *
3402736 ATATTTTTCAATTAAAATAAAAATAAA
1 ATATTTTT-AATTAAGTTAATAATAAA
3402763 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTT-AATTAAGTTAATAATAAA
* * *
3402790 ATATATTTAA-TAATTTGAT-ATAAAA
1 ATATTTTTAATTAAGTTAATAAT-AAA
*
3402815 ATATTTTTAGTTAA
1 ATATTTTTAATTAA
3402829 TATATATAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
24 2 0.04
25 18 0.33
26 5 0.09
27 30 0.55
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (26 bp):
ATATTTTTAATTAAGTTAATAATAAA
Found at i:3402854 original size:756 final size:731
Alignment explanation
Indices: 3401576--3403079 Score: 2201
Period size: 756 Copynumber: 2.0 Consensus size: 731
3401566 ATAAATATTT
* *
3401576 AATTAAATATTTTTAATTATCGATAATATATTACGTTTTATAAATACAATTATTGAAACTCATAA
1 AATTAAATATTTTTAATTATCGATAATATATCACATTTTATAAATACAATTATTGAAACTCATAA
*
3401641 AATTTATAAAAGATAATATCTTTTATCATTAAAATTATTCGATGAATTCGTTCAAAAATAATATT
66 AATTTATAAAAGATAATATCTTTTATCATTAAAATTATTAGATGAATTCGTTCAAAAATAATATT
* * * *
3401706 TTTATCTGGGATAAACAGGGTATCATTTTTCGCAAATTTTTATTTTGCGTTAACTACATGCATGA
131 ATTATCAGGGATAAACAGGATATCATTTTTCGCAAATTTTTATTTTGCGTTAACTACATGCATAA
* * *
3401771 TAATTTATCTTTGTGTTTTGTCCATTTTTTATTACTAATTTCAAAAAACATAATATATGGTCACT
196 TAACTTATCTTTGTGTTTTGTCCATTTTTTATCACTAATTTCAAAAAACATAAGATATGGTCACT
*
3401836 TTTATTTTTATTTAATTAAGATATGGCTACCTCGAGCTAACTGACGTTAAAATCAGTTAAATATT
261 TTTATTTTTATTTAATTAAGATATGGCTACCTCGAG---ACTGACGTTAAAATCAGCTAAATATT
* * *
3401901 TTAATATATTCACACATTTAGTCCCTGATATTTATATATTATCTCAATTTAGTTATACTTTTAAT
323 TTAATATATTAACACATTTAGTCCCTGATATTTACATATTATCTCAATTTAGTCATACTTTTAAT
*
3401966 AAATTAAAATAAATTATATATTTTTTAAATTAAAATAAAAAATATTTTTAATTTAAGTCAATAAT
388 AAATTAAAATAAATTATATATTTTTTAAATTAAAATAAAAAATATTTTTAAATTAAGTCAATAAT
3402031 AAAATATATTTAATAAATTGATATAAAAATATTTTTAGTTAATATATATAAAATTATATGATATA
453 AAAATATATTTAATAAATTGATATAAAAATATTTTTAGTTAATATATATAAAATTATATGATATA
* ***
3402096 TAATTCATATCACAGGTACCTGGTTCATAATTTTTTATTTTTTATTTAAATTATATTA-TTTTAA
518 TAATTCAGATCACAGGTACCCAATTCATAA-----T-TTTTTTATTTAAATTATATTATTTTTAA
* * *
3402160 AAAAATTATATAAAAAATTCTAAAATTTAAAATTTAAAAG-TATAATATATCTAATCTATACATA
577 AAAAATTATAT-AAAAATTCTAAAATTTAAAATTTAAAAGCTATAATATATATAATCCACACATA
3402224 AAGTTTAAAAATTCAAATTACATAATTGAAATAAAATTTATTAAAATTTAAAATAAAGAAGTATA
641 AAGTTTAAAAATTCAAATTACATAATTGAAATAAAATTTATTAAAATTTAAAATAAAGAAGTATA
3402289 ATTAAATTTCAAATATTTTGAAGTTA
706 ATTAAATTTCAAATATTTTGAAGTTA
* *
3402315 AATTAAATATTTTTAATTATCGATAATATATCACATTTTGTAAATACAATTATTGAAGCTCATAA
1 AATTAAATATTTTTAATTATCGATAATATATCACATTTTATAAATACAATTATTGAAACTCATAA
* *
3402380 AATTTATAAAAGATAATATCTTTTATCATTAAAATGGTTTTAGATGAATTTGTTCAAGAACAATA
66 AATTTATAAAAGATAATATCTTTTATCATTAAAAT--TATTAGATGAATTCGTTC-A-AA-AATA
* *
3402445 TTTATAGAGAACAATATATTATCAGGGATAAAGAGGATATCATTTTTCGCAAATTTTTATTTTGG
126 ---AT--------AT-TATTATCAGGGATAAACAGGATATCATTTTTCGCAAATTTTTATTTTGC
* *
3402510 GTTAACTACATGCATAATAACTTATCTTTGTGTTTTGTCCATTTTTTGTCATTAATTTCAAAAAA
179 GTTAACTACATGCATAATAACTTATCTTTGTGTTTTGTCCATTTTTTATCACTAATTTC-AAAAA
* * * * *
3402575 ACATAAGATATGGTGACTTTTGTTTTTATTTATTTAAGATATGG-TCACCTCGAG-CTGTCTTTA
243 ACATAAGATATGGTCACTTTTATTTTTATTTAATTAAGATATGGCT-ACCTCGAGACTGACGTTA
* * * *
3402638 ACATCAGCTAAATATTTTGATATATTAACACATTT-GATCCCTGTTATTTACATATTCTCTCAAT
307 AAATCAGCTAAATATTTTAATATATTAACACATTTAG-TCCCTGATATTTACATATTATCTCAAT
*
3402702 TTAGTCATACTTTTAATAAATTAAAATAAATTATATA-TTTTTCAATTAAAATAAAAATAAAATA
371 TTAGTCATACTTTTAATAAATTAAAATAAATTATATATTTTTTAAATTAAAAT---AA-AAAATA
* *
3402766 TTTTTAAATTAAGTTAATAATAAAATATATTTAATAATTTGATATAAAAATATTTTTAGTTAATA
432 TTTTTAAATTAAGTCAATAATAAAATATATTTAATAAATTGATATAAAAATATTTTTAGTTAATA
*
3402831 TATATAAAATTATATGATATATAATTCAGATCACGGGTACCCAATTCATAATTTTTTTATTTAAA
497 TATATAAAATTATATGATATATAATTCAGATCACAGGTACCCAATTCATAATTTTTTTATTTAAA
* * *
3402896 TTATATTATTTTTTAAAAAATTATATAAAAATTTTAAATTTTAAAATTTAAAAGTCTATAATATA
562 TTATATTATTTTTAAAAAAATTATATAAAAATTCTAAAATTTAAAATTTAAAAG-CTATAATATA
3402961 TATAATCCACACATAAAGTTTAAAAATTCAAATTACATAATTGAAATAAAATTTATTAAAATTTA
626 TATAATCCACACATAAAGTTTAAAAATTCAAATTACATAATTGAAATAAAATTTATTAAAATTTA
* *
3403026 AAATAAAGATGTATAATTAAATTTCAAATGTTTTGAAGTTA
691 AAATAAAGAAGTATAATTAAATTTCAAATATTTTGAAGTTA
**
3403067 AAAGAAATATTTT
1 AATTAAATATTTT
3403080 AAAAAATATT
Statistics
Matches: 688, Mismatches: 50, Indels: 41
0.88 0.06 0.05
Matches are distributed among these distances:
739 96 0.14
741 15 0.02
742 1 0.00
743 2 0.00
744 4 0.01
747 2 0.00
750 47 0.07
751 17 0.02
752 136 0.20
753 98 0.14
755 4 0.01
756 213 0.31
757 53 0.08
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (731 bp):
AATTAAATATTTTTAATTATCGATAATATATCACATTTTATAAATACAATTATTGAAACTCATAA
AATTTATAAAAGATAATATCTTTTATCATTAAAATTATTAGATGAATTCGTTCAAAAATAATATT
ATTATCAGGGATAAACAGGATATCATTTTTCGCAAATTTTTATTTTGCGTTAACTACATGCATAA
TAACTTATCTTTGTGTTTTGTCCATTTTTTATCACTAATTTCAAAAAACATAAGATATGGTCACT
TTTATTTTTATTTAATTAAGATATGGCTACCTCGAGACTGACGTTAAAATCAGCTAAATATTTTA
ATATATTAACACATTTAGTCCCTGATATTTACATATTATCTCAATTTAGTCATACTTTTAATAAA
TTAAAATAAATTATATATTTTTTAAATTAAAATAAAAAATATTTTTAAATTAAGTCAATAATAAA
ATATATTTAATAAATTGATATAAAAATATTTTTAGTTAATATATATAAAATTATATGATATATAA
TTCAGATCACAGGTACCCAATTCATAATTTTTTTATTTAAATTATATTATTTTTAAAAAAATTAT
ATAAAAATTCTAAAATTTAAAATTTAAAAGCTATAATATATATAATCCACACATAAAGTTTAAAA
ATTCAAATTACATAATTGAAATAAAATTTATTAAAATTTAAAATAAAGAAGTATAATTAAATTTC
AAATATTTTGAAGTTA
Found at i:3403192 original size:39 final size:39
Alignment explanation
Indices: 3403084--3403192 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 39
3403074 TATTTTAAAA
*
3403084 AATATTTTACAATGTTA-ACGTGAAATAATTTAAGAAATT
1 AATATTTTAGAATGTTAGA-GTGAAATAATTTAAGAAATT
* * * * *
3403123 AAGAATTTAGAACGTTTTGA-TGTCAA-AATTTAAGAAATT
1 AATATTTTAGAATG-TTAGAGTG-AAATAATTTAAGAAATT
*
3403162 TATATTTTAGAATGTTAGAGTGAAATAATTT
1 AATATTTTAGAATGTTAGAGTGAAATAATTT
3403193 GAGGATTATG
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
38 6 0.11
39 42 0.79
40 4 0.08
41 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (39 bp):
AATATTTTAGAATGTTAGAGTGAAATAATTTAAGAAATT
Found at i:3405399 original size:13 final size:13
Alignment explanation
Indices: 3405381--3405407 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3405371 TTGGTCCATA
3405381 TATATTTTTATTT
1 TATATTTTTATTT
3405394 TATATTTTTATTT
1 TATATTTTTATTT
3405407 T
1 T
3405408 TTTATTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATATTTTTATTT
Found at i:3408356 original size:27 final size:27
Alignment explanation
Indices: 3408326--3408391 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
3408316 AAAACAATGA
3408326 TGAATGATTCAGCACAGAAATACATTC
1 TGAATGATTCAGCACAGAAATACATTC
*
3408353 TGAATGATTCAGCACAGAAGTACATTC
1 TGAATGATTCAGCACAGAAATACATTC
*
3408380 TGAATAATTCAG
1 TGAATGATTCAG
3408392 AGCCATTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (27 bp):
TGAATGATTCAGCACAGAAATACATTC
Found at i:3416141 original size:38 final size:39
Alignment explanation
Indices: 3416035--3416209 Score: 232
Period size: 38 Copynumber: 4.6 Consensus size: 39
3416025 AGAGAAATTG
* *
3416035 TCTCAAGGGAGACAAAAT-TT-TGTTTCAAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* *
3416072 TCTCAAGCGAGAAAAAATCTTCTGTTTCGAGGGAAACTG
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
*
3416111 TCTCAAGAGAGACAAAA-CTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* * *
3416149 TCTCAAGCGAGATAAAATATTTTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
* *
3416188 TCT-AAGCGAGATAAAATATTCT
1 TCTCAAGCGAGACAAAATCTTCT
3416210 TTAAAAACAG
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
37 16 0.13
38 55 0.45
39 52 0.42
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (39 bp):
TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
Found at i:3416156 original size:77 final size:76
Alignment explanation
Indices: 3416018--3416204 Score: 250
Period size: 77 Copynumber: 2.5 Consensus size: 76
3416008 TCAAAGTTTA
* * * * *
3416018 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCGAGGGAAACTGTCTCAAGAGAGACAAAATTCTGTTTCAAGGGAAACTATCTCAAGCGAG
*
3416083 AAAAAATCTTC
66 AAAAAATATTC
*
3416094 TGTTTCGAGGGAAACTGTCTCAAGAGAGACAAAACTTCTGTTTCGAGGGAAACTATCTCAAGCGA
1 TGTTTCGAGGGAAACTGTCTCAAGAGAGACAAAA-TTCTGTTTCAAGGGAAACTATCTCAAGCGA
* *
3416159 GATAAAATATTT
65 GAAAAAATATTC
* * *
3416171 TGTTTCGAGGGAAACTATCT-AAGCGAGATAAAAT
1 TGTTTCGAGGGAAACTGTCTCAAGAGAGACAAAAT
3416205 ATTCTTTAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
75 1 0.01
76 41 0.42
77 56 0.57
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (76 bp):
TGTTTCGAGGGAAACTGTCTCAAGAGAGACAAAATTCTGTTTCAAGGGAAACTATCTCAAGCGAG
AAAAAATATTC
Found at i:3418192 original size:32 final size:31
Alignment explanation
Indices: 3418154--3418230 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
3418144 CGGGGCCGTG
* *
3418154 GGGCCTACCTAAGAACACATCTTAGGGTCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
3418186 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3418217 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3418231 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3418213 original size:63 final size:63
Alignment explanation
Indices: 3418107--3418230 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
3418097 CCATAAGGGA
* * ** *
3418107 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* * *
3418170 ACATCTTAGGGTC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3418231 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:3419139 original size:17 final size:17
Alignment explanation
Indices: 3419119--3419158 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3419109 CAACGGTCCA
*
3419119 GTCAACGGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
* *
3419136 GTCAACAGTCTGGTTGG
1 GTCAACAGTCGGGTCGG
3419153 GTCAAC
1 GTCAAC
3419159 CCGGTTCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.23
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGG
Found at i:3419176 original size:19 final size:19
Alignment explanation
Indices: 3419152--3419219 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
3419142 AGTCTGGTTG
*
3419152 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
3419171 GGTCAAATCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* * *
3419190 GGTCAAATCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
3419210 GGTCAAACCG
1 GGTCAAACCG
3419220 ATTTTTCCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 31 0.72
20 12 0.28
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:3421041 original size:13 final size:13
Alignment explanation
Indices: 3421023--3421048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3421013 GCAAGCCAGT
3421023 AACAAAATCCATA
1 AACAAAATCCATA
3421036 AACAAAATCCATA
1 AACAAAATCCATA
3421049 GTAATACGCT
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:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
AACAAAATCCATA
Found at i:3426449 original size:19 final size:19
Alignment explanation
Indices: 3426425--3426461 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3426415 GGTCAAAGAA
3426425 AGTCAACGGTCAACGGTCC
1 AGTCAACGGTCAACGGTCC
3426444 AGTCAACGGTCAACGGTC
1 AGTCAACGGTCAACGGTC
3426462 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
AGTCAACGGTCAACGGTCC
Found at i:3426473 original size:17 final size:17
Alignment explanation
Indices: 3426451--3426491 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3426441 TCCAGTCAAC
*
3426451 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
* *
3426468 GGTCAATAGTCTGGTCG
1 GGTCAACAGTCGGGTCG
3426485 GGTCAAC
1 GGTCAAC
3426492 CCGGTTCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.39, T:0.22
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:3426519 original size:10 final size:10
Alignment explanation
Indices: 3426487--3426536 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
3426477 TCTGGTCGGG
*
3426487 TCAACCCGGT
1 TCAAACCGGT
*
3426497 TCAGACCGG-
1 TCAAACCGGT
3426506 TCAAACCGGT
1 TCAAACCGGT
*
3426516 TCAAAACTGG-
1 TC-AAACCGGT
3426526 TCAAACCGGT
1 TCAAACCGGT
3426536 T
1 T
3426537 TTTCCAGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:3426527 original size:20 final size:19
Alignment explanation
Indices: 3426485--3426536 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
3426475 AGTCTGGTCG
* *
3426485 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
3426504 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
3426524 GGTCAAACCGGTT
1 GGTCAAACCGGTT
3426537 TTTCCAGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:3431490 original size:6 final size:6
Alignment explanation
Indices: 3431481--3431509 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3431471 AAAAAAAAAT
3431481 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
3431510 TGAATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:3431625 original size:14 final size:14
Alignment explanation
Indices: 3431606--3431648 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3431596 GTTACAATAA
3431606 AAATAAATAAAAAT
1 AAATAAATAAAAAT
3431620 AAATAAATAATAAA-
1 AAATAAATAA-AAAT
*
3431634 AAAT-AGTAAAAAT
1 AAATAAATAAAAAT
3431647 AA
1 AA
3431649 TAAGAACGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 6 0.23
14 14 0.54
15 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:3431637 original size:10 final size:11
Alignment explanation
Indices: 3431601--3431651 Score: 58
Period size: 10 Copynumber: 5.1 Consensus size: 11
3431591 TAATAGTTAC
3431601 AATAAA-AATA
1 AATAAATAATA
3431611 AATAAA-AATA
1 AATAAATAATA
3431621 AATAAATAATA
1 AATAAATAATA
*
3431632 AA-AAATAGT-
1 AATAAATAATA
3431641 AA-AAATAATA
1 AATAAATAATA
3431651 A
1 A
3431652 GAACGAGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 8 0.22
10 23 0.62
11 6 0.16
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (11 bp):
AATAAATAATA
Found at i:3434801 original size:23 final size:23
Alignment explanation
Indices: 3434774--3434830 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
3434764 TGTGACATGT
3434774 TCTCTACCTTTATGACACGTTTA
1 TCTCTACCTTTATGACACGTTTA
** * * *
3434797 TCTCTGTCTTTGTGACATGTTTT
1 TCTCTACCTTTATGACACGTTTA
3434820 TCTCTACCTTT
1 TCTCTACCTTT
3434831 TGGTAGCTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.14, C:0.25, G:0.11, T:0.51
Consensus pattern (23 bp):
TCTCTACCTTTATGACACGTTTA
Found at i:3437432 original size:126 final size:126
Alignment explanation
Indices: 3437207--3437441 Score: 434
Period size: 126 Copynumber: 1.9 Consensus size: 126
3437197 GTAATCGACT
3437207 CTCGAACTCGAAATTTTGGTAATGCATATCAAAATGTTGTTTTAATATAATTAAAATTTAATTTT
1 CTCGAACTCGAAATTTTGGTAATGCATATCAAAATGTTGTTTTAATATAATTAAAATTTAATTTT
* *
3437272 ATTAAAATAAAAAATGTATTTTGGGTGTCTAATCATACCCTAATAAAAAATTGGTGACGAA
66 ATTAAAATAAAAAATGTATTTTGGGTGCCTAATCACACCCTAATAAAAAATTGGTGACGAA
*
3437333 CTCGAACTCGAAATTTTGGTAATGCATATCAAAATGTTGTTTTAATATGATTAAAATTTAATTTT
1 CTCGAACTCGAAATTTTGGTAATGCATATCAAAATGTTGTTTTAATATAATTAAAATTTAATTTT
*
3437398 ATTAAAATAACAAATGTATTTTGGGTGCCTAATCACACCCTAAT
66 ATTAAAATAAAAAATGTATTTTGGGTGCCTAATCACACCCTAAT
3437442 TAAAGATGGG
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 105 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (126 bp):
CTCGAACTCGAAATTTTGGTAATGCATATCAAAATGTTGTTTTAATATAATTAAAATTTAATTTT
ATTAAAATAAAAAATGTATTTTGGGTGCCTAATCACACCCTAATAAAAAATTGGTGACGAA
Found at i:3440244 original size:41 final size:42
Alignment explanation
Indices: 3440188--3440284 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 42
3440178 TCATTTTATG
* * * *
3440188 TTATAAAA-ATATTATTTAATTATTAAAAATATAA-AAATTA
1 TTATAAAATATATTATTTAATCATTAAAAAGAAAATAAATAA
*
3440228 TTATAAAATATATTA-TTAATCGTTAAAAAGAAAATAAATAA
1 TTATAAAATATATTATTTAATCATTAAAAAGAAAATAAATAA
*
3440269 TTAT-AAATGTATTATT
1 TTATAAAATATATTATT
3440285 ATAAAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
40 32 0.67
41 16 0.33
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (42 bp):
TTATAAAATATATTATTTAATCATTAAAAAGAAAATAAATAA
Found at i:3440296 original size:15 final size:15
Alignment explanation
Indices: 3440258--3440299 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3440248 CGTTAAAAAG
* *
3440258 AAAATAAATAATTAT
1 AAAATATATTATTAT
*
3440273 -AAATGTATTATTAT
1 AAAATATATTATTAT
3440287 AAAATATATTATT
1 AAAATATATTATT
3440300 TTAGTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
AAAATATATTATTAT
Done.