Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 43
Found at i:5837788 original size:25 final size:24
Alignment explanation
Indices: 5837671--5837786 Score: 78
Period size: 24 Copynumber: 4.7 Consensus size: 24
5837661 GATCAAAGAC
*
5837671 AAATATAAAAATAATAAACTA-A-AA
1 AAATAAAAAAATAA-AAA-TAGAGAA
* * *
5837695 AAATAATAAAATCAAAAGAGAAGAAAA
1 AAATAAAAAAAT-AAAA-A-TAGAGAA
*
5837722 AAATAAATAAATAAAAATAGAGAA
1 AAATAAAAAAATAAAAATAGAGAA
* *
5837746 AAATCGAAGAAAT-AAAAT-GAGATA
1 AAAT-AAAAAAATAAAAATAGAGA-A
5837770 AAATAAAAAAATAAAAA
1 AAATAAAAAAATAAAAA
5837787 ATAAAATACA
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
23 10 0.14
24 35 0.48
25 11 0.15
26 5 0.07
27 12 0.16
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (24 bp):
AAATAAAAAAATAAAAATAGAGAA
Found at i:5837804 original size:16 final size:16
Alignment explanation
Indices: 5837679--5837812 Score: 57
Period size: 16 Copynumber: 8.1 Consensus size: 16
5837669 ACAAATATAA
*
5837679 AAATAATAAACTAAAA-
1 AAATAA-AAAATAAAAT
*
5837695 AAATAATAAAATCAAAAG
1 AAATAA-AAAAT-AAAAT
*
5837713 AGAAGAAAAAA-ATAAAT
1 A-AATAAAAAATA-AAAT
5837730 AAAT-AAAAATAGAGAA-
1 AAATAAAAAATA-A-AAT
*
5837746 AAATCGAAGAAATAAAAT
1 AAAT--AAAAAATAAAAT
*
5837764 GAGAT--AAAATAAAA-
1 -AAATAAAAAATAAAAT
5837778 AAATAAAAAATAAAAT
1 AAATAAAAAATAAAAT
* *
5837794 ACATGAAAAATAAGAAT
1 AAATAAAAAATAA-AAT
5837811 AA
1 AA
5837813 TAATGCTAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
13 3 0.03
15 22 0.24
16 31 0.34
17 16 0.18
18 6 0.07
19 13 0.14
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (16 bp):
AAATAAAAAATAAAAT
Found at i:5838992 original size:17 final size:16
Alignment explanation
Indices: 5838954--5839004 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
5838944 TGGAAAAGAC
5838954 TAAAAGAATAAATAAACA
1 TAAAAGAAT-AATAAA-A
5838972 -AAAACGAATAATAAAA
1 TAAAA-GAATAATAAAA
*
5838988 TAAAATAAATAATAAAA
1 TAAAA-GAATAATAAAA
5839005 AACAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 24 0.83
18 4 0.14
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (16 bp):
TAAAAGAATAATAAAA
Found at i:5839148 original size:23 final size:23
Alignment explanation
Indices: 5839121--5839203 Score: 157
Period size: 23 Copynumber: 3.6 Consensus size: 23
5839111 TATTTCAAAA
*
5839121 ATATGTTTTCAAAACCAAATAAT
1 ATATGTTTTCAAAACCATATAAT
5839144 ATATGTTTTCAAAACCATATAAT
1 ATATGTTTTCAAAACCATATAAT
5839167 ATATGTTTTCAAAACCATATAAT
1 ATATGTTTTCAAAACCATATAAT
5839190 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
5839204 ATGTTTTCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.39
Consensus pattern (23 bp):
ATATGTTTTCAAAACCATATAAT
Found at i:5839209 original size:12 final size:12
Alignment explanation
Indices: 5839192--5839216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5839182 CATATAATAT
5839192 ATGTTTTCAAAA
1 ATGTTTTCAAAA
5839204 ATGTTTTCAAAA
1 ATGTTTTCAAAA
5839216 A
1 A
5839217 CTATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:5839291 original size:38 final size:40
Alignment explanation
Indices: 5839231--5839311 Score: 139
Period size: 38 Copynumber: 2.1 Consensus size: 40
5839221 ATTTTTTATA
*
5839231 TATATATATATATATATATTAAAAAAATGTTTTCAAACAC
1 TATATATATATATATATATTAAAAAAATGTTTTCAAAAAC
5839271 TATATAT-TATATATAT-TTAAAAAAATGTTTTCAAAAAC
1 TATATATATATATATATATTAAAAAAATGTTTTCAAAAAC
5839309 TAT
1 TAT
5839312 TTTTAAAACT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 24 0.60
39 9 0.22
40 7 0.17
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (40 bp):
TATATATATATATATATATTAAAAAAATGTTTTCAAAAAC
Found at i:5839331 original size:91 final size:88
Alignment explanation
Indices: 5839169--5839332 Score: 217
Period size: 91 Copynumber: 1.9 Consensus size: 88
5839159 CATATAATAT
* ** **
5839169 ATGTTTTCAAAACCATATAATATATGTTTTCAAAAATGTTTTCAAAAACTATATTTTTTATATAT
1 ATGTTTTCAAAACCATATAATATATATTTAAAAAAATGTTTTCAAAAACTATATTTTAAATATAT
5839234 ATATATATATATATATTAAAAAA
66 ATATATATATATATATTAAAAAA
*
5839257 ATGTTTTCAAACACTATATATTATATATATTTAAAAAAATGTTTTCAAAAACTAT-TTTTAAA-A
1 ATGTTTTCAAA-ACCATATA--ATATATATTTAAAAAAATGTTTTCAAAAACTATATTTTAAATA
5839320 CTATATA-ATATAT
63 -TATATATATATAT
5839333 GTTTTCAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
88 11 0.17
89 14 0.21
90 11 0.17
91 30 0.45
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (88 bp):
ATGTTTTCAAAACCATATAATATATATTTAAAAAAATGTTTTCAAAAACTATATTTTAAATATAT
ATATATATATATATATTAAAAAA
Found at i:5840242 original size:80 final size:80
Alignment explanation
Indices: 5840014--5840868 Score: 1154
Period size: 80 Copynumber: 10.6 Consensus size: 80
5840004 TTGTTGACAT
* * * * * * * *
5840014 ATAGCCCTTCTTGCCTTGAGCTATGTTGTAAGTTTGATTTGCCTCTGAGTTGAATGTAATCAAAC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAA--ATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
**
5840079 TCGAAGGTCTTAGATGATAG
64 TCGAAGGTCTT---TGGCAG
* ** * * * * * *
5840099 ATAACCCTTCTCACCTCGAGTTATGCTGTAAATTTGGTATGCCTTTGAGCTGAATGTAATCGAAC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
5840164 TCGCAGGTCTTTGGCAG
64 TCGAAGGTCTTTGGCAG
* *
5840181 ATAACCCTTCTTGCCTTGATCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
5840246 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * *
5840261 GTAGCCCTTCTTGTCTTGAGCTATGCTGCAAATTATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
5840326 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * *
5840341 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCCGAGTGAAATTGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
5840406 GAAGATCTTTGGCAG
66 GAAGGTCTTTGGCAG
* *
5840421 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
5840486 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * **
5840501 ATAGCCCTTTTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTCAAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
5840566 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * *
5840581 ATAGCCCTTCTTGCCTTGAGCTAAGCTACAAATGATGTGCCTTTGAGCTGAGTGT-ATTGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
5840645 GAAAGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * * * * * *
5840660 GTAGCCCTTATTTCCTTTAGCTATGCTGCAAATAATGTGTCTTTGAGCTGAGTGAAATCAAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
5840725 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
* * * * *
5840740 ATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCATTTGAGCTGAATGAAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
5840805 GAAGGTCTTTGGCAG
66 GAAGGTCTTTGGCAG
5840820 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCT
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCT
5840869 ATGCTGTAAA
Statistics
Matches: 683, Mismatches: 84, Indels: 11
0.88 0.11 0.01
Matches are distributed among these distances:
79 68 0.10
80 524 0.77
82 30 0.04
85 61 0.09
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (80 bp):
ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTGGCAG
Found at i:5840868 original size:27 final size:27
Alignment explanation
Indices: 5840831--5840893 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
5840821 TAGCCCTTCT
5840831 TGCC-TTGAGCTATGCTGCAAATGATG
1 TGCCTTTGAGCTATGCTGCAAATGATG
*
5840857 TGCCTTTGAGCTATGCTGTAAATGATG
1 TGCCTTTGAGCTATGCTGCAAATGATG
5840884 TGCCTTTGAG
1 TGCCTTTGAG
5840894 ATGAGTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (27 bp):
TGCCTTTGAGCTATGCTGCAAATGATG
Found at i:5840949 original size:107 final size:107
Alignment explanation
Indices: 5840758--5840975 Score: 330
Period size: 107 Copynumber: 2.0 Consensus size: 107
5840748 TCTAGCCTTA
*
5840758 AGCTATGCTGCAAATGATGTGCATTTGAGCTGAATGAAATCGAACTCGAAGGTCTTTGGCAGATA
1 AGCTATGCTGCAAATGATGTGCATTTGAGATGAATGAAATCGAACTCGAAGGTCTTTGGCAGATA
* *
5840823 GCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTG
66 ACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTACCTTTG
* * *
5840865 AGCTATGCTGTAAATGATGTGCCTTTGAGATGAGTGAAATCGAACTCGAAGGT-TTTAGGCAGAT
1 AGCTATGCTGCAAATGATGTGCATTTGAGATGAATGAAATCGAACTCGAAGGTCTTT-GGCAGAT
* * * *
5840929 AACCCTTCTTTCCTTTAGCTATTCTGCAAATGATTTACCTTTG
65 AACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTACCTTTG
5840972 AGCT
1 AGCT
5840976 GAGTGAAATC
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 3 0.03
107 97 0.97
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (107 bp):
AGCTATGCTGCAAATGATGTGCATTTGAGATGAATGAAATCGAACTCGAAGGTCTTTGGCAGATA
ACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTACCTTTG
Found at i:5840993 original size:187 final size:187
Alignment explanation
Indices: 5840673--5841055 Score: 554
Period size: 187 Copynumber: 2.1 Consensus size: 187
5840663 GCCCTTATTT
* *
5840673 CCTTT-AGCTATGCTGCAAATAATGTGTCTTTGAGCTGAGTGAAATCAAACTCGAAGGTCTTTGG
1 CCTTTGAGCTATGCTGCAAATAATGTGCCTTTGAGATGAGTGAAATCAAACTCGAAGGTCTTTGG
* *
5840737 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCATTTGAGCTGAATGAAATCGAA
66 CAGATAACCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTACATTTGAGCTGAATGAAATCGAA
* *
5840802 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
131 CTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTG
* * *
5840859 CCTTTGAGCTATGCTGTAAATGATGTGCCTTTGAGATGAGTGAAATCGAACTCGAAGGT-TTTAG
1 CCTTTGAGCTATGCTGCAAATAATGTGCCTTTGAGATGAGTGAAATCAAACTCGAAGGTCTTT-G
** * * * * *
5840923 GCAGATAACCCTTCTTTCCTTTAGCTATTCTGCAAATGATTTACCTTTGAGCTGAGTGAAATCGA
65 GCAGATAACCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTACATTTGAGCTGAATGAAATCGA
* * * * *
5840988 ACTCGAAGGTTTTTGGTAGATAACCTTTCTTGCCTTGAGCTATGCTACAAATGATTTT
130 ACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTG
5841046 CCTTTGAGCT
1 CCTTTGAGCT
5841056 GAGTGTAATC
Statistics
Matches: 174, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
186 8 0.05
187 166 0.95
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (187 bp):
CCTTTGAGCTATGCTGCAAATAATGTGCCTTTGAGATGAGTGAAATCAAACTCGAAGGTCTTTGG
CAGATAACCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTACATTTGAGCTGAATGAAATCGAA
CTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTG
Found at i:5840998 original size:80 final size:79
Alignment explanation
Indices: 5840859--5841162 Score: 374
Period size: 80 Copynumber: 3.8 Consensus size: 79
5840849 AAATGATGTG
* *
5840859 CCTTTGAGCTATGCTGTAAATGATGTGCCTTTGAGATGAGTGAAATCGAACTCGAAGGTTTTAGG
1 CCTTT-AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTTTT-GG
5840924 CAGATAACCCTTCTTT
64 CAGATAACCCTTCTTT
* * * *
5840940 CCTTTAGCTATTCTGCAAATGATTTACCTTTGAGCTGAGTGAAATCGAACTCGAAGGTTTTTGGT
1 CCTTTAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGG-TTTTGGC
* *
5841005 AGATAACCTTTCTTG
65 AGATAACCCTTCTTT
* * * * * *
5841020 CCTTGAGCTATGCTACAAATGATTTTCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGC
1 CCTTTAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGT-TTTGGC
*
5841085 AGATAGCCCTTCTTT
65 AGATAACCCTTCTTT
* ** * * *
5841100 CCTTAAGCTATATTGCAAATGATGTGCCTTTGAGCTGAATGTAATCGAACTCGTAGGTCTTTG
1 CCTTTAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGT-TTTG
5841163 AACATGTCAA
Statistics
Matches: 194, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
79 1 0.01
80 184 0.95
81 9 0.05
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (79 bp):
CCTTTAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGAAATCGAACTCGAAGGTTTTGGCA
GATAACCCTTCTTT
Found at i:5841132 original size:160 final size:161
Alignment explanation
Indices: 5840857--5841162 Score: 438
Period size: 160 Copynumber: 1.9 Consensus size: 161
5840847 GCAAATGATG
** *
5840857 TGCCTTTGAGCTATGCTGTAAATGATGTGCCTTTGAGATGAGTGAAATCGAACTCGAAGGTTTTA
1 TGCCTTTGAGCTATGCTACAAATGATGTGCCTTTGAGATGAGTGAAATCGAACTCAAAGGTTTTA
* * *
5840922 GGCAGATAACCCTTCTTTCCTTTAGCTATTCTGCAAATGATTTACCTTTGAGCTGAGTGAAATCG
66 GGCAGATAACCCTTCTTTCCTTAAGCTATTCTGCAAATGATGTACCTTTGAGCTGAATGAAATCG
*
5840987 AACTCGAAGGTTTTTGGTAGATAACCTTTCT
131 AACTCGAAGGTCTTTGGTAGATAACCTTTCT
* * * *
5841018 TGCC-TTGAGCTATGCTACAAATGATTTTCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTT
1 TGCCTTTGAGCTATGCTACAAATGATGTGCCTTTGAGATGAGTGAAATCGAACTCAAAGGT-TTT
* * *
5841082 -GGCAGATAGCCCTTCTTTCCTTAAGCTATAT-TGCAAATGATGTGCCTTTGAGCTGAATGTAAT
65 AGGCAGATAACCCTTCTTTCCTTAAGCTAT-TCTGCAAATGATGTACCTTTGAGCTGAATGAAAT
*
5841145 CGAACTCGTAGGTCTTTG
129 CGAACTCGAAGGTCTTTG
5841163 AACATGTCAA
Statistics
Matches: 128, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
160 120 0.94
161 8 0.06
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (161 bp):
TGCCTTTGAGCTATGCTACAAATGATGTGCCTTTGAGATGAGTGAAATCGAACTCAAAGGTTTTA
GGCAGATAACCCTTCTTTCCTTAAGCTATTCTGCAAATGATGTACCTTTGAGCTGAATGAAATCG
AACTCGAAGGTCTTTGGTAGATAACCTTTCT
Found at i:5842187 original size:95 final size:95
Alignment explanation
Indices: 5842002--5842258 Score: 275
Period size: 95 Copynumber: 2.7 Consensus size: 95
5841992 AGCTGGATCC
* * ** * * *
5842002 ATAAAGCCAGGGCGTTTAAAAAATTGCTCTAGAGGGACAACTCAATATCATTGTATAG-ATATTA
1 ATAAAGTCAGGGCATTTAACCAATTGCTCCAGAGGGACAACTC-A-AGC-TT-TATTGTATATTA
* *
5842066 TAATCACCTTTATCAGGCTAGCTGAATATTGTCC
62 TAATCACCTTTATCAGGCTAGCTGAATATTATCA
* * *
5842100 ATAAA-TCCGGGGCATTTAACCAATTGCTCCAGATGGACAACTCGAGCTTTATTGTATATTATAA
1 ATAAAGT-CAGGGCATTTAACCAATTGCTCCAGAGGGACAACTCAAGCTTTATTGTATATTATAA
* * *
5842164 TCGCCTTTATCAGGCTAGTTGAATCTTATCA
65 TCACCTTTATCAGGCTAGCTGAATATTATCA
* * * *
5842195 ATAAAGTTAGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATATATA
1 ATAAAGTCAGGGCATTTAACCAATTGCTCCAGAGGGACAACTCAAGCTTTATTGTATAT-TATA
5842259 TAATTATAAT
Statistics
Matches: 133, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
94 4 0.03
95 87 0.65
96 7 0.05
98 35 0.26
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
ATAAAGTCAGGGCATTTAACCAATTGCTCCAGAGGGACAACTCAAGCTTTATTGTATATTATAAT
CACCTTTATCAGGCTAGCTGAATATTATCA
Found at i:5845073 original size:28 final size:30
Alignment explanation
Indices: 5845028--5845083 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
5845018 GAAATCGAAG
*
5845028 AAATAAAATGAGAT-AAAATAA-AATAAAA
1 AAATAAAATGACATAAAAATAAGAATAAAA
5845056 AAATAAAAT-ACATGAAAAATAAGAATAA
1 AAATAAAATGACAT-AAAAATAAGAATAA
5845084 TAATGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.12
28 9 0.38
29 7 0.29
30 5 0.21
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (30 bp):
AAATAAAATGACATAAAAATAAGAATAAAA
Found at i:5846138 original size:18 final size:17
Alignment explanation
Indices: 5846111--5846167 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
5846101 GGAAAAGACC
5846111 AAAAGAATAAATAAATA
1 AAAAGAATAAATAAATA
5846128 AAAACGAAT-AATAAAATAA
1 AAAA-GAATAAAT-AAAT-A
*
5846147 AAATAAAATAAAT-AATA
1 AAA-AGAATAAATAAATA
5846164 AAAA
1 AAAA
5846168 ACAAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
16 1 0.03
17 11 0.32
18 11 0.32
19 7 0.21
20 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAAGAATAAATAAATA
Found at i:5846153 original size:11 final size:12
Alignment explanation
Indices: 5846116--5846166 Score: 61
Period size: 11 Copynumber: 4.2 Consensus size: 12
5846106 AGACCAAAAG
5846116 AATAAATAAATAA
1 AATAAAT-AATAA
5846129 AA-ACGAATAATAA
1 AATA--AATAATAA
5846142 AATAAA-AATAA
1 AATAAATAATAA
5846153 AATAAATAATAA
1 AATAAATAATAA
5846165 AA
1 AA
5846167 AACAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 11 0.32
12 10 0.29
13 9 0.26
14 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:5846173 original size:18 final size:18
Alignment explanation
Indices: 5846116--5846174 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
5846106 AGACCAAAAG
*
5846116 AATAAATAA-ATAAAAACG
1 AATAAATAATA-AAAAACA
*
5846134 AATAATAAAATAAAAATA-A
1 AATAA-ATAATAAAAA-ACA
5846153 AATAAATAATAAAAAACA
1 AATAAATAATAAAAAACA
5846171 AATA
1 AATA
5846175 TATATTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 1 0.03
18 19 0.56
19 12 0.35
20 2 0.06
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAATAATAAAAAACA
Found at i:5846272 original size:31 final size:31
Alignment explanation
Indices: 5846234--5846306 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
5846224 AACTATATAT
* *
5846234 TATATATATTT-AAAAATGTTTTCAAAAATTA
1 TATATATATTTCAAAAATATTTT-AAAAACTA
5846265 TATATATATTTTCAAAAATATTTTAAAAACTA
1 TATATATA-TTTCAAAAATATTTTAAAAACTA
5846297 TATATTATAT
1 TATA-TATAT
5846307 GTATGTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.22
32 15 0.41
33 14 0.38
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (31 bp):
TATATATATTTCAAAAATATTTTAAAAACTA
Found at i:5846282 original size:33 final size:34
Alignment explanation
Indices: 5846206--5846306 Score: 113
Period size: 33 Copynumber: 3.1 Consensus size: 34
5846196 TGTTTTCAAA
* *
5846206 ATTTCAAAAACATTTTC-AAACTATATATTATATAT
1 ATTTCAAAAATATTTTCAAAAAT-TATA-TATATAT
*
5846241 ATTT-AAAAATGTTTTCAAAAATTATATATATAT
1 ATTTCAAAAATATTTTCAAAAATTATATATATAT
*
5846274 -TTTCAAAAATATTTT-AAAAACTATATAT-TAT
1 ATTTCAAAAATATTTTCAAAAATTATATATATAT
5846305 AT
1 AT
5846307 GTATGTTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.05
32 16 0.28
33 17 0.29
34 14 0.24
35 8 0.14
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.45
Consensus pattern (34 bp):
ATTTCAAAAATATTTTCAAAAATTATATATATAT
Found at i:5846318 original size:60 final size:61
Alignment explanation
Indices: 5846249--5846368 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 61
5846239 ATATTTAAAA
* *
5846249 ATGTTTTCAAAA-AT-TATATATATATTTTCAAAAATATTTTAAAAACTATATATTATATGT
1 ATGTTTTCAAAACATATA-ATATATATTTTCAAAAAAAGTTTAAAAACTATATATTATATGT
*
5846309 ATGTTTTCAAAACCATATAATATATGTTTTCAAAAAAAGTTTAAAAACTATATATTATAT
1 ATGTTTTCAAAA-CATATAATATATATTTTCAAAAAAAGTTTAAAAACTATATATTATAT
5846369 ATATATATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
60 12 0.22
62 40 0.74
63 2 0.04
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (61 bp):
ATGTTTTCAAAACATATAATATATATTTTCAAAAAAAGTTTAAAAACTATATATTATATGT
Found at i:5846362 original size:35 final size:36
Alignment explanation
Indices: 5846317--5846455 Score: 106
Period size: 35 Copynumber: 3.8 Consensus size: 36
5846307 GTATGTTTTC
* *
5846317 AAAACCATATA-ATATATGTTTTCAAAAAAAGTTTA
1 AAAACTATATATATATATATTTTCAAAAAAAGTTTA
* * *
5846352 AAAACTATATATTATATATATATATTTTTAAAAAAA-ATCA
1 AAAAC----TA-TATATATATATATTTTCAAAAAAAGTTTA
* * *
5846392 AACACTATATATTATATATATTTT-AAAAAATGTTTTC
1 AAAACTATATA-TATATATATTTTCAAAAAAAG-TTTA
*
5846429 AAAACTATATA-ATATATGTTTTCAAAA
1 AAAACTATATATATATATATTTTCAAAA
5846456 CGTTTTCAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
35 25 0.30
36 18 0.22
37 11 0.13
39 1 0.01
40 10 0.12
41 17 0.21
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (36 bp):
AAAACTATATATATATATATTTTCAAAAAAAGTTTA
Found at i:5846363 original size:64 final size:62
Alignment explanation
Indices: 5846249--5846386 Score: 158
Period size: 62 Copynumber: 2.2 Consensus size: 62
5846239 ATATTTAAAA
* * *
5846249 ATGTTTTCAAAAATTATATATATATTTTCAAAAATATTTTAAAAACTATA-TAT-TATATGT
1 ATGTTTTCAAAAATTATATATATATTTTCAAAAAAAGTTTAAAAACTATATTATATATATAT
*
5846309 ATGTTTTCAAAACCA-TATAATATATGTTTTCAAAAAAAGTTTAAAAACTATATATTATATATAT
1 ATGTTTTCAAAA--ATTAT-ATATATATTTTCAAAAAAAGTTTAAAAAC--TATATTATATATAT
5846373 AT
61 AT
*
5846375 AT-TTTTAAAAAA
1 ATGTTTTCAAAAA
5846387 AATCAAACAC
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
60 12 0.18
61 3 0.05
62 27 0.41
63 1 0.02
64 4 0.06
65 11 0.17
66 8 0.12
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (62 bp):
ATGTTTTCAAAAATTATATATATATTTTCAAAAAAAGTTTAAAAACTATATTATATATATAT
Found at i:5846399 original size:40 final size:43
Alignment explanation
Indices: 5846323--5846412 Score: 125
Period size: 40 Copynumber: 2.2 Consensus size: 43
5846313 TTTCAAAACC
* *
5846323 ATATA-ATATATGTTTTCAAAAAAAGTTTAAAAACTATATATT
1 ATATATATATATGTTTTCAAAAAAAGATCAAAAACTATATATT
*
5846365 ATATATATATAT-TTTT-AAAAAAA-ATCAAACACTATATATT
1 ATATATATATATGTTTTCAAAAAAAGATCAAAAACTATATATT
5846405 ATATATAT
1 ATATATAT
5846413 TTTAAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 22 0.50
41 7 0.16
42 9 0.20
43 6 0.14
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (43 bp):
ATATATATATATGTTTTCAAAAAAAGATCAAAAACTATATATT
Found at i:5846466 original size:34 final size:34
Alignment explanation
Indices: 5846389--5846526 Score: 116
Period size: 34 Copynumber: 3.9 Consensus size: 34
5846379 TTAAAAAAAA
* *
5846389 TCAAACACTATATATTATATATATTTTAAAAAATGTTT
1 TCAAA-ACTATATA--ATATATATTTT-CAAAACGTTT
*
5846427 TCAAAACTATATAATATATGTTTTCAAAACGTTT
1 TCAAAACTATATAATATATATTTTCAAAACGTTT
* *
5846461 TCAAAACAATAAAATATATATTTTCGAAAACTGCTTT
1 TCAAAACTATATAATATATATTTTC-AAAAC-G-TTT
* * * *
5846498 CTAAAAATTATATATTATA-ATTTTTAAAA
1 -TCAAAACTATATAATATATATTTTCAAAA
5846527 ATATTTTCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
34 30 0.36
35 15 0.18
36 5 0.06
37 16 0.19
38 18 0.21
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (34 bp):
TCAAAACTATATAATATATATTTTCAAAACGTTT
Found at i:5846542 original size:35 final size:36
Alignment explanation
Indices: 5846399--5846543 Score: 120
Period size: 35 Copynumber: 4.1 Consensus size: 36
5846389 TCAAACACTA
* * *
5846399 TATATTATATATATTTTAAAAAATGTTTTC-AAAAC
1 TATATAATATATATTTTTAAAAATGTTTTCAAAAAT
* * *
5846434 TATATAATATAT-GTTTTCAAAACGTTTTCAAAACA-
1 TATATAATATATATTTTTAAAAATGTTTTCAAAA-AT
* * * *
5846469 -ATAAAATATATATTTTCGAAAACTGCTTTCTAAAAAT
1 TATATAATATATATTTT-TAAAAATGTTTTC-AAAAAT
* *
5846506 TATATATTATA-ATTTTTAAAAATATTTTCAAAAAT
1 TATATAATATATATTTTTAAAAATGTTTTCAAAAAT
5846541 TAT
1 TAT
5846544 GCTATATTAA
Statistics
Matches: 85, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
34 23 0.27
35 26 0.31
36 19 0.22
37 9 0.11
38 8 0.09
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATAATATATATTTTTAAAAATGTTTTCAAAAAT
Found at i:5854372 original size:23 final size:22
Alignment explanation
Indices: 5854340--5854423 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
5854330 TTGGTGCAGA
*
5854340 GGGAATCGATACCTCCCTTGAAG
1 GGGAACCGATACC-CCCTTGAAG
*
5854363 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* * *
5854386 GGGAGCCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
*
5854407 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
5854424 GGAGGTTCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 17 0.33
22 3 0.06
23 32 0.62
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:5866468 original size:32 final size:32
Alignment explanation
Indices: 5866425--5866503 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
5866415 TCAGGGTGAC
* * *
5866425 AATATCGATATTGTTCTT-GTAATATCGATACT
1 AATATCAATATTGTTCTTAG-AATACCGACACT
*
5866457 CATATCAATATTGTTCTTAGAATACCGACACT
1 AATATCAATATTGTTCTTAGAATACCGACACT
5866489 AATATCAATATTGTT
1 AATATCAATATTGTT
5866504 AGAGTACCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (32 bp):
AATATCAATATTGTTCTTAGAATACCGACACT
Found at i:5867815 original size:31 final size:31
Alignment explanation
Indices: 5867777--5867840 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
5867767 CTAGATACTA
*
5867777 GTCAGGTTTGCATTCAGATAATGC-TCAGTAT
1 GTCAGGTTCGCATTCAGATAATGCGT-AGTAT
*
5867808 GTCAGGTTCGCATTTAGATAATGCGTAGTAT
1 GTCAGGTTCGCATTCAGATAATGCGTAGTAT
5867839 GT
1 GT
5867841 TTAGTCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (31 bp):
GTCAGGTTCGCATTCAGATAATGCGTAGTAT
Found at i:5878550 original size:21 final size:21
Alignment explanation
Indices: 5878524--5878575 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
5878514 GGTCACTAGT
5878524 ATAATTTACCCTTT-ATTTTAA
1 ATAATTTA-CCTTTAATTTTAA
*
5878545 ATAATTTATCTTTAAATTTTAA
1 ATAATTTACCTTT-AATTTTAA
5878567 ACTAATTTA
1 A-TAATTTA
5878576 TAATTATACG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 8 0.30
22 8 0.30
23 7 0.26
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAATTTACCTTTAATTTTAA
Found at i:5879346 original size:7 final size:7
Alignment explanation
Indices: 5879334--5879378 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
5879324 ATTTGTAAAT
*
5879334 TTTACAA
1 TTTATAA
*
5879341 TTTACAA
1 TTTATAA
5879348 TTTATAA
1 TTTATAA
*
5879355 TTTATAC
1 TTTATAA
5879362 TTTATAA
1 TTTATAA
5879369 TTTATAA
1 TTTATAA
5879376 TTT
1 TTT
5879379 CAAGATCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTATAA
Found at i:5879494 original size:19 final size:19
Alignment explanation
Indices: 5879466--5879523 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
5879456 TTTTAAAAAT
5879466 AATTTAAAAATATATTTATA
1 AATTT-AAAATATATTTATA
*
5879486 AATTTAAAA-ATAAATTATGA
1 AATTTAAAATAT-ATTTAT-A
5879506 AA-TT-AAATATATTT-TA
1 AATTTAAAATATATTTATA
5879522 AA
1 AA
5879524 AAATATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 8 0.24
19 13 0.39
20 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTAAAATATATTTATA
Found at i:5879508 original size:20 final size:20
Alignment explanation
Indices: 5879466--5879509 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5879456 TTTTAAAAAT
*
5879466 AATTTAAAAATATATTTATA
1 AATTTAAAAATATAATTATA
5879486 AATTTAAAAATA-AATTATGA
1 AATTTAAAAATATAATTAT-A
5879506 AATT
1 AATT
5879510 AAATATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTTAAAAATATAATTATA
Found at i:5881398 original size:23 final size:23
Alignment explanation
Indices: 5881370--5881456 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 23
5881360 CACATATTTG
* *
5881370 TCCCGAAGGACCGCATAGTTTTA
1 TCCCGAAGGACCACATAGGTTTA
* *
5881393 TCCCGAATGACCACATAGGTTTG
1 TCCCGAAGGACCACATAGGTTTA
* ** * * *
5881416 TCCCAAAAAACCACACAGATTTG
1 TCCCGAAGGACCACATAGGTTTA
*
5881439 TCCCGAATGACCACATAG
1 TCCCGAAGGACCACATAG
5881457 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGGTTTA
Found at i:5883459 original size:27 final size:27
Alignment explanation
Indices: 5883421--5883485 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
5883411 GAGTATTACA
* *
5883421 AAACTATAAATTCTTACAATAATCAAT
1 AAACCATAAATTCTTAAAATAATCAAT
*
5883448 AAACCATAAATTCTTAAAATAGTCAAT
1 AAACCATAAATTCTTAAAATAATCAAT
*
5883475 AAATCATAAAT
1 AAACCATAAAT
5883486 CCTTTGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.31
Consensus pattern (27 bp):
AAACCATAAATTCTTAAAATAATCAAT
Found at i:5883959 original size:36 final size:36
Alignment explanation
Indices: 5883919--5883990 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
5883909 AGGGTAGCTA
5883919 AAAAATATTCTACTTGCATTTTTCCTTTTCCAAGTT
1 AAAAATATTCTACTTGCATTTTTCCTTTTCCAAGTT
5883955 AAAAATATTCTACTTGCATTTTTCCTTTTCCAAGTT
1 AAAAATATTCTACTTGCATTTTTCCTTTTCCAAGTT
5883991 GTTTACATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (36 bp):
AAAAATATTCTACTTGCATTTTTCCTTTTCCAAGTT
Found at i:5897859 original size:21 final size:21
Alignment explanation
Indices: 5897819--5897893 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
5897809 CATTCGGGAT
** *
5897819 ATATATGTAATCCTTGGGAAC
1 ATATATGTGGTCCTTTGGAAC
*
5897840 ATATATGTGGTTCTTTGGAAC
1 ATATATGTGGTCCTTTGGAAC
*
5897861 ACATAT-TGGTCCTTTGG-A-
1 ATATATGTGGTCCTTTGGAAC
*
5897879 ATATATGTGATCCTT
1 ATATATGTGGTCCTT
5897894 AAGGAGTGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 5 0.11
19 8 0.18
20 10 0.22
21 22 0.49
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (21 bp):
ATATATGTGGTCCTTTGGAAC
Found at i:5899417 original size:217 final size:216
Alignment explanation
Indices: 5898985--5899418 Score: 850
Period size: 217 Copynumber: 2.0 Consensus size: 216
5898975 TGGAAATAAA
5898985 TCCTAAAAGTTGTTAGTAATTATCAAATGAAGTAGAGGGCAAAATGGTCATTTGACTAATAATGA
1 TCCTAAAAGTTGTTAGTAATTATCAAATGAAGTAGAGGGCAAAATGGTCATTTGACTAATAATGA
5899050 ATTAAAAAGGATATGATAAGGATATATGTTAGAGGGGATAAGGAGAAGAGATATTCTCTTCATCT
66 ATTAAAAAGGATATGATAAGGATATATGTTAGAGGGGATAAGGAGAAGAGATATTCTCTTCATCT
5899115 TCTTCTTTCTTCATGTACGAGAGAGAGAAGAGCCAAGCTTGCAAAGGTAAGATTCTTGTTAGCTG
131 TCTTCTTTCTTCATGTACGAGAGAGAGAAGAGCCAAGCTTGCAAAGGTAAGATTCTTGTTAGCTG
5899180 ATTATTTGTTAATTTTAAGAG
196 ATTATTTGTTAATTTTAAGAG
5899201 TCCTAAAAGTTGTTAGTAATTATCAAATGAAGTAGAGGGCAAAATGGTCATTTGACTAATAATGA
1 TCCTAAAAGTTGTTAGTAATTATCAAATGAAGTAGAGGGCAAAATGGTCATTTGACTAATAATGA
*
5899266 ATTAAAATGGATATGATAAGGATATATGTTAGAGGGGATAAGGAAGAAGAGATATTCTCTTCATC
66 ATTAAAAAGGATATGATAAGGATATATGTTAGAGGGGATAAGG-AGAAGAGATATTCTCTTCATC
5899331 TTCTTCTTTCTTCATGTACGAGAGAGAGAAGAGCCAAGCTTGCAAAGGTAAGATTCTTGTTAGCT
130 TTCTTCTTTCTTCATGTACGAGAGAGAGAAGAGCCAAGCTTGCAAAGGTAAGATTCTTGTTAGCT
5899396 GATTATTTGTTAATTTTAAGAG
195 GATTATTTGTTAATTTTAAGAG
5899418 T
1 T
5899419 GGAGTAAGTG
Statistics
Matches: 216, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
216 107 0.50
217 109 0.50
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (216 bp):
TCCTAAAAGTTGTTAGTAATTATCAAATGAAGTAGAGGGCAAAATGGTCATTTGACTAATAATGA
ATTAAAAAGGATATGATAAGGATATATGTTAGAGGGGATAAGGAGAAGAGATATTCTCTTCATCT
TCTTCTTTCTTCATGTACGAGAGAGAGAAGAGCCAAGCTTGCAAAGGTAAGATTCTTGTTAGCTG
ATTATTTGTTAATTTTAAGAG
Found at i:5899872 original size:62 final size:63
Alignment explanation
Indices: 5899798--5899972 Score: 201
Period size: 64 Copynumber: 2.8 Consensus size: 63
5899788 TTAAAATAAG
**
5899798 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGT-ATCGATGCATCCCATTAATAATGA-A
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTCATCGATGCATCCCAACAATAAT-ACA
** * *
5899860 ACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCTCAACAATAATACA
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGT-CATCGATGCATCCCAACAATAATACA
* * * * * *
5899924 ACATCAAATACATTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGT-CATCGATGCAT
5899973 ACCTTCATTA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
62 34 0.35
63 1 0.01
64 61 0.64
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (63 bp):
ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTCATCGATGCATCCCAACAATAATACA
Found at i:5900682 original size:60 final size:61
Alignment explanation
Indices: 5900614--5900766 Score: 249
Period size: 61 Copynumber: 2.5 Consensus size: 61
5900604 AGGGTCGAGG
5900614 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTA-GTTCTT-GGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTG-TTACCTATGTTCTTCGGGACATATGGACT
5900674 GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGGACATATGGACT
* *
5900735 GTTTACCTAGGTTCTTCGGAATC-TATGGACTG
1 GTTTACCTATGTTCTTCGGGA-CATATGGACTG
5900767 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
59 7 0.08
60 38 0.43
61 42 0.48
62 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (61 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5900688 original size:30 final size:31
Alignment explanation
Indices: 5900614--5900766 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
5900604 AGGGTCGAGG
5900614 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5900645 GTTTACCTA-GTTCTT-GGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5900674 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5900705 G-TTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
5900735 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
5900766 G
1 G
5900767 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
29 23 0.20
30 42 0.36
31 50 0.43
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5901599 original size:16 final size:15
Alignment explanation
Indices: 5901578--5901608 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5901568 AACATATGCA
5901578 AATGACATGTATATAT
1 AATGACATGT-TATAT
5901594 AATGACATGTTATAT
1 AATGACATGTTATAT
5901609 GATATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (15 bp):
AATGACATGTTATAT
Found at i:5904421 original size:62 final size:62
Alignment explanation
Indices: 5904301--5904425 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 62
5904291 AGGGTCGAGG
* **
5904301 GTTTACCTATGTTCTTCGGGACATATGGACAGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACAGTTTACCTAGGTTCTTCGAAACATATGGACT
**
5904363 GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTAGGTTCTTCGAAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACAGTTTACCTAGGTTCTTCGAAA-CATATGGACT
5904425 G
1 G
5904426 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 56 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACAGTTTACCTAGGTTCTTCGAAACATATGGACT
Found at i:5904422 original size:31 final size:31
Alignment explanation
Indices: 5904301--5904411 Score: 195
Period size: 31 Copynumber: 3.6 Consensus size: 31
5904291 AGGGTCGAGG
*
5904301 GTTTACCTATGTTCTTCGGGACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5904332 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5904363 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5904394 GTTTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
5904412 AAATCTATGG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5907255 original size:64 final size:64
Alignment explanation
Indices: 5907177--5907395 Score: 219
Period size: 64 Copynumber: 3.4 Consensus size: 64
5907167 GAATGTGCAC
** **
5907177 CGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTCATGAA
1 CGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTCATGAA
5907240 T
64 T
* * ** *
5907241 CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGTAATTGGTGCAT
1 CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGAAT
* * ** * * * * *
5907305 CGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTTATGCA-
1 CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGAAT
*
5907368 CTGATGCATCAGTAGTGCATCGATGCAT
1 C-GATGCATAAGTAGTGCATCGATGCAT
5907396 ACCTTCATTA
Statistics
Matches: 130, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 123 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (64 bp):
CGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGAAT
Found at i:5908090 original size:31 final size:31
Alignment explanation
Indices: 5908052--5908163 Score: 206
Period size: 31 Copynumber: 3.6 Consensus size: 31
5908042 AGGGTCGAGG
5908052 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5908083 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5908114 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5908145 GTTTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
5908164 AATCTATGTA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5910687 original size:29 final size:29
Alignment explanation
Indices: 5910642--5910744 Score: 163
Period size: 29 Copynumber: 3.6 Consensus size: 29
5910632 TTTCATATGC
*
5910642 TCATGTA-CTCATATCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
5910670 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
* **
5910699 TCATATAGCTCATGTCATTTCTCTTGCAA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
5910728 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
5910745 CTTCATATCA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
28 7 0.10
29 62 0.90
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:5910794 original size:12 final size:12
Alignment explanation
Indices: 5910760--5910794 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5910750 TATCATGTTC
**
5910760 TCATATCACAGG
1 TCATATCACATA
5910772 TCATATCACATA
1 TCATATCACATA
5910784 TCATATCACAT
1 TCATATCACAT
5910795 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:5911214 original size:64 final size:64
Alignment explanation
Indices: 5911144--5911309 Score: 210
Period size: 64 Copynumber: 2.6 Consensus size: 64
5911134 GTATTATTGC
*
5911144 TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGTTGT-TTCACTATTAA
1 TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTCTTCA-TATTAA
* * * *
5911208 TGGGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTATTTTAA
1 TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTCTTCATATTAA
*** *
5911272 AAAGAGTGCATCGATGCACTACC-AATGCATCGATGCAC
1 TGGGA-TGCATCGATGCACT-CCTTATGCATCGATGCAC
5911310 ATTCATACAA
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
64 57 0.64
65 31 0.35
66 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (64 bp):
TGGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTCTTCATATTAA
Found at i:5917497 original size:15 final size:15
Alignment explanation
Indices: 5917474--5917521 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
5917464 CGTAGGACTC
*
5917474 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
* *
5917489 CTACGTCCCAAAAGA
1 CTACGTCCCGAAGGA
5917504 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
5917519 CTA
1 CTA
5917522 TTATACTCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (15 bp):
CTACGTCCCGAAGGA
Found at i:5917651 original size:29 final size:29
Alignment explanation
Indices: 5917606--5917737 Score: 230
Period size: 29 Copynumber: 4.6 Consensus size: 29
5917596 TTTCATATGC
*
5917606 TCATGTA-CTCATATCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
5917634 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
5917663 TCATGTAGCTCATGTCATTTCTCTTATGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
5917692 TCATGTAGCTCATGTCATTTCTCTTGCGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
5917721 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
5917738 CTTCATATCA
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 7 0.07
29 92 0.93
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:5918202 original size:64 final size:64
Alignment explanation
Indices: 5918094--5918270 Score: 187
Period size: 64 Copynumber: 2.8 Consensus size: 64
5918084 TAATGAAGGT
* * * ** ** * * **
5918094 ATGCATCGATGCACTACTAATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGT-GTCACTATTAATGGG
* * *
5918158 ATGCATCGATGCACTCCTTATACATCGATGCACCG-ATTGCATTCGTTGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATACATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
*
5918222 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGT
5918271 CTTTATTTTA
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
63 3 0.03
64 90 0.97
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATACATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:5918291 original size:64 final size:63
Alignment explanation
Indices: 5918157--5918318 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 63
5918147 TTATTGCTGG
* * * * *
5918157 GATGCATCGATGCACTCCTTATACATCGATGCACCGATTGCATTCGTTGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAAAGA
* *
5918221 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATTAAAGA
**
5918284 GAGTGCATCGATGCACTACCAATGCATCGATGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
5918319 ATTCATGCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 4 0.05
64 79 0.92
65 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:5920028 original size:16 final size:17
Alignment explanation
Indices: 5920001--5920033 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5919991 TTAGTGAGGC
5920001 ATAATAATAATGAAAAT
1 ATAATAATAATGAAAAT
5920018 ATAAT-ATAATGAAAAT
1 ATAATAATAATGAAAAT
5920034 GTCATAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
ATAATAATAATGAAAAT
Found at i:5920260 original size:24 final size:24
Alignment explanation
Indices: 5920232--5920306 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
5920222 TTGTCGTATA
5920232 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
* *
5920256 AATTT--ATCCTGAA-TGATCGCGTAG
1 AATTTGCA-CC-GAAGTG-CCACGTAG
*
5920280 AA-TTGCACTGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
5920303 AATT
1 AATT
5920307 ACACCGTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
22 1 0.03
23 17 0.44
24 20 0.51
25 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:5920301 original size:23 final size:23
Alignment explanation
Indices: 5920235--5920306 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
5920225 TCGTATAAAT
*
5920235 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACTGAAGTGCCACGTAGAA
* * *
5920258 TT-TATCCTGAA-TGATCGCGTAGAA
1 TTGCA--CTGAAGTG-CCACGTAGAA
5920282 TTGCACTGAAGTGCCACGTAGAA
1 TTGCACTGAAGTGCCACGTAGAA
5920305 TT
1 TT
5920307 ACACCGTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
22 1 0.03
23 19 0.51
24 16 0.43
25 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (23 bp):
TTGCACTGAAGTGCCACGTAGAA
Found at i:5920319 original size:23 final size:23
Alignment explanation
Indices: 5920238--5920320 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
5920228 TATAAATTTG
5920238 CACCGAAGTGCCACGTAGAATTTA
1 CACCGAAGTGCCACGTAGAA-TTA
* * * *
5920262 TC-CTGAA-TGATCGCGTAGAATTG
1 -CACCGAAGTG-CCACGTAGAATTA
*
5920285 CACTGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
5920308 CACCGTAA-TGCCA
1 CACCG-AAGTGCCA
5920321 TTAATATGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
22 1 0.02
23 28 0.61
24 16 0.35
25 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:5920465 original size:25 final size:26
Alignment explanation
Indices: 5920426--5920476 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
5920416 CAAAGAATAC
*
5920426 ATTTATGTCCTGAAGAACCACGTAGA
1 ATTTATGTCCCGAAGAACCACGTAGA
*
5920452 ATTT-TGTCCCGAAGGACCACGTAGA
1 ATTTATGTCCCGAAGAACCACGTAGA
5920477 CCCTCTACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (26 bp):
ATTTATGTCCCGAAGAACCACGTAGA
Found at i:5920598 original size:30 final size:31
Alignment explanation
Indices: 5920564--5920623 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
5920554 TATCTCGTAG
5920564 ACATATCA-TTTCCATACCTTTATCACATAT
1 ACATATCATTTTCCATACCTTTATCACATAT
5920594 ACATATCATTTTCCATACCTTTATCACATA
1 ACATATCATTTTCCATACCTTTATCACATA
5920624 GCTCATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (31 bp):
ACATATCATTTTCCATACCTTTATCACATAT
Found at i:5927426 original size:24 final size:23
Alignment explanation
Indices: 5927401--5927486 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
5927391 TCGTATAAAT
5927401 TTGCACCGAAGTGCCACATAGAA
1 TTGCACCGAAGTGCCACATAGAA
** *
5927424 TTTGTC-CCGAA-TGACTGCGTAGAA
1 -TTG-CACCGAAGTG-CCACATAGAA
* *
5927448 TTGTACTGAAGTGCCACATAGAA
1 TTGCACCGAAGTGCCACATAGAA
*
5927471 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
5927487 TATAATATGT
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
23 29 0.62
24 17 0.36
25 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACATAGAA
Found at i:5927762 original size:30 final size:31
Alignment explanation
Indices: 5927728--5927791 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
5927718 TTATATCGCG
*
5927728 TAGACATATCA-TTTCCATACCTTTATCACA
1 TAGACATATCATTTTCAATACCTTTATCACA
5927758 TAGACATATCATTTTCAATACCTTTATCACA
1 TAGACATATCATTTTCAATACCTTTATCACA
5927789 TAG
1 TAG
5927792 CTCATATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (31 bp):
TAGACATATCATTTTCAATACCTTTATCACA
Found at i:5931611 original size:19 final size:18
Alignment explanation
Indices: 5931567--5931612 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
5931557 TAAAAAATAT
5931567 AAAAAT-AGTTAAAATGA
1 AAAAATAAGTTAAAATGA
*
5931584 AAAAATAAGTTAAAGATTA
1 AAAAATAAGTTAAA-ATGA
*
5931603 AATAATAAGT
1 AAAAATAAGT
5931613 GGAAGGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAAATAAGTTAAAATGA
Found at i:5932120 original size:60 final size:60
Alignment explanation
Indices: 5932056--5932168 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
5932046 TATATTATAC
* ** * * *
5932056 TGTTTTATTAAGTATTTTGACTATTAAAAGTTATAAAATGGTCATTCGATTATATGAAGT
1 TGTTTTATTAAGTATCTCAACTATTAAAAGTTACAAAATGATCACTCGATTATATGAAGT
* *
5932116 TGTTTTATTGAGTCTCTCAACTATTAAAAGTTACAAAATGATCACTCGATTAT
1 TGTTTTATTAAGTATCTCAACTATTAAAAGTTACAAAATGATCACTCGATTAT
5932169 TCATTATGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (60 bp):
TGTTTTATTAAGTATCTCAACTATTAAAAGTTACAAAATGATCACTCGATTATATGAAGT
Found at i:5940186 original size:35 final size:34
Alignment explanation
Indices: 5940101--5940187 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
5940091 ATTTGGTATT
*
5940101 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
5940135 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
5940173 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
5940188 ATTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:5940403 original size:3 final size:3
Alignment explanation
Indices: 5940395--5940472 Score: 84
Period size: 3 Copynumber: 26.0 Consensus size: 3
5940385 CGCTGTCATT
** * *
5940395 GTC GTC GTC GTC GTC GTC ACC ATC GTC ATC GTC GTC GTC GTC GTC GTC
1 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC
** * *
5940443 ACC ATC GTC ATC GTC GTC GTC GTC GTC GTC
1 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC
5940473 ACCATCGTCA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.08, C:0.36, G:0.26, T:0.31
Consensus pattern (3 bp):
GTC
Found at i:5940429 original size:30 final size:30
Alignment explanation
Indices: 5940389--5940487 Score: 189
Period size: 30 Copynumber: 3.3 Consensus size: 30
5940379 ACTTCTCGCT
*
5940389 GTCATTGTCGTCGTCGTCGTCGTCACCATC
1 GTCATCGTCGTCGTCGTCGTCGTCACCATC
5940419 GTCATCGTCGTCGTCGTCGTCGTCACCATC
1 GTCATCGTCGTCGTCGTCGTCGTCACCATC
5940449 GTCATCGTCGTCGTCGTCGTCGTCACCATC
1 GTCATCGTCGTCGTCGTCGTCGTCACCATC
5940479 GTCATCGTC
1 GTCATCGTC
5940488 ATCCTCCGCA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.10, C:0.35, G:0.23, T:0.31
Consensus pattern (30 bp):
GTCATCGTCGTCGTCGTCGTCGTCACCATC
Found at i:5940484 original size:6 final size:6
Alignment explanation
Indices: 5940415--5940490 Score: 62
Period size: 6 Copynumber: 12.7 Consensus size: 6
5940405 TCGTCGTCAC
* * * ** *
5940415 CATCGT CATCGT CGTCGT CGTCGT CGTCAC CATCGT CATCGT CGTCGT
1 CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT CATCGT
* * **
5940463 CGTCGT CGTCAC CATCGT CATCGT CATC
1 CATCGT CATCGT CATCGT CATCGT CATC
5940491 CTCCGCAGGT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.12, C:0.37, G:0.21, T:0.30
Consensus pattern (6 bp):
CATCGT
Found at i:5940851 original size:27 final size:27
Alignment explanation
Indices: 5940789--5940844 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
5940779 AGATGAAGGC
*
5940789 GGCGACATCTGGTAATTGAAAGGCGAT
1 GGCGACATCTGGTAATGGAAAGGCGAT
*
5940816 GGCGGCATCTGGTAATGGAAAGGCGAT
1 GGCGACATCTGGTAATGGAAAGGCGAT
5940843 GG
1 GG
5940845 GCACATCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.39, T:0.20
Consensus pattern (27 bp):
GGCGACATCTGGTAATGGAAAGGCGAT
Found at i:5942507 original size:111 final size:111
Alignment explanation
Indices: 5942372--5942702 Score: 518
Period size: 111 Copynumber: 2.9 Consensus size: 111
5942362 AAAAAAATAA
5942372 TTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTAAA
1 TTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTAAA
*
5942437 ACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATATTTAATTC
66 ACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTC
5942483 TTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTAAA
1 TTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTAAA
* * * *
5942548 ACGTTAAAATATTACCGTATCAGCAAAATATCGAGATATTTAATTT
66 ACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTC
* * *
5942594 TTAATATAATAATCATGCATTAAATAAATCAACTAAATATTATTAATAATTTAAATTAAGTTAAA
1 TTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTT--A--AA-TTAAA
** *
5942659 TTAAAACGTTAAAATGTTATTGTATCAGCAAAGTGTAGAGATAT
61 TTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
5942703 ATGATTTCCA
Statistics
Matches: 201, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
111 155 0.77
113 1 0.00
115 2 0.01
116 43 0.21
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAATTAAA
ACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTC
Found at i:5943744 original size:133 final size:132
Alignment explanation
Indices: 5943550--5943813 Score: 465
Period size: 133 Copynumber: 2.0 Consensus size: 132
5943540 ACCATTAAGG
*
5943550 GATCATTTATAACTTTTACAATTGATGAACTAACAAAACAACGTTTTATAGTTGAAGAATTATTT
1 GATCATTTATAACTTTTACAATTGATGAACTAACAAAACAACGTTTTATAGTTAAAGAATTATTT
*
5943615 TGTAAGGGCATAATCAAGGACCATTAATGTACTTTGCCCAATAATTTATAAAATTATGAGATGAG
66 TGTAAGGGCATAATCAAGGACCATTAATGTACTTTACCCAATAATTTATAAAATTATGAGATGAG
5943680 GT
131 GT
* *
5943682 GATCATTTATAACTTTTATAATTGATGAACTTAACAAAACAATGTTTTATAGTTAAAGAATTATT
1 GATCATTTATAACTTTTACAATTGATGAAC-TAACAAAACAACGTTTTATAGTTAAAGAATTATT
* *
5943747 TTGTAAGGGCATAATTAGGGACCATTAATGTACTTTACCCAATAATTTATAAAATTATGAGATGA
65 TTGTAAGGGCATAATCAAGGACCATTAATGTACTTTACCCAATAATTTATAAAATTATGAGATGA
5943812 GG
130 GG
5943814 AGGAGGTTCA
Statistics
Matches: 125, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
132 29 0.23
133 96 0.77
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (132 bp):
GATCATTTATAACTTTTACAATTGATGAACTAACAAAACAACGTTTTATAGTTAAAGAATTATTT
TGTAAGGGCATAATCAAGGACCATTAATGTACTTTACCCAATAATTTATAAAATTATGAGATGAG
GT
Found at i:5947026 original size:310 final size:309
Alignment explanation
Indices: 5946451--5947069 Score: 1157
Period size: 310 Copynumber: 2.0 Consensus size: 309
5946441 GTGGAAGCTT
*
5946451 TTGCAGAAAATTGAAAATATTTGCACATCGATTTAGAGTGGTTCGACTTTCTCAACCAAAGTCTA
1 TTGCAGAAAATTAAAAATATTTGCACATCGATTTAGAGTGGTTCGACTTTCTCAACCAAAGTCTA
*
5946516 CGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTTTCTTTCTTTTA
66 CGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTA
5946581 AGGACAAATAGTAACCTTACAACTCCCTCAAGAATTATACCCCCAAATTCTTGAGAACACTCTCT
131 AGGACAAATAGTAACCTTACAACTCCCTCAAGAATTATACCCCCAAATTCTTGAGAACACTCTCT
*
5946646 CCCAAAGAGAAAATTACAAATTTCGCAAACTTACAGAAAATCTCACAAGGCTAGATGTTTGCACA
196 CCCAAAGAGAAAATTACAAATTTCGCAAACTTACAGAAAACCTCACAAGGCTAGATGTTTGCACA
5946711 ATTCTAGAACAAAGAAAGAACACTCAAGAATAAATACAATTGAGCACAA
261 ATTCTAGAACAAAGAAAGAACACTCAAGAATAAATACAATTGAGCACAA
5946760 TTGCAGAAAAATTAAAAATATTTGCACATCGATTTAGAGTGGTTCGACTTTCTCAACCAAAGTCT
1 TTGCAG-AAAATTAAAAATATTTGCACATCGATTTAGAGTGGTTCGACTTTCTCAACCAAAGTCT
*
5946825 ACGTCCACTACCTTAGTTATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTT
65 ACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTT
*
5946890 AAGGACAAATAGTAACCTTATAACTCCCTCAAGAATTATACCCCCAAATTCTTGAGAACACTCTC
130 AAGGACAAATAGTAACCTTACAACTCCCTCAAGAATTATACCCCCAAATTCTTGAGAACACTCTC
5946955 TCCCAAAGAGAAAATTACAAATTTCGCAAACTTACAGAAAACCTCACAAGGCTAGATGTTTGCAC
195 TCCCAAAGAGAAAATTACAAATTTCGCAAACTTACAGAAAACCTCACAAGGCTAGATGTTTGCAC
* * *
5947020 AATTCTAGAACAAAGAAATAACACTCAAGAATGAATACAATTGAGTACAA
260 AATTCTAGAACAAAGAAAGAACACTCAAGAATAAATACAATTGAGCACAA
5947070 GTAGTGTTCT
Statistics
Matches: 301, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
309 6 0.02
310 295 0.98
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.28
Consensus pattern (309 bp):
TTGCAGAAAATTAAAAATATTTGCACATCGATTTAGAGTGGTTCGACTTTCTCAACCAAAGTCTA
CGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTATCTTTCTTTTA
AGGACAAATAGTAACCTTACAACTCCCTCAAGAATTATACCCCCAAATTCTTGAGAACACTCTCT
CCCAAAGAGAAAATTACAAATTTCGCAAACTTACAGAAAACCTCACAAGGCTAGATGTTTGCACA
ATTCTAGAACAAAGAAAGAACACTCAAGAATAAATACAATTGAGCACAA
Found at i:5949810 original size:23 final size:22
Alignment explanation
Indices: 5949755--5949835 Score: 94
Period size: 23 Copynumber: 3.7 Consensus size: 22
5949745 TATAAATTAT
5949755 CCGAATGACCACATAGA-TGTC
1 CCGAATGACCACATAGATTGTC
*
5949776 CC-AAAGACCACATAGGATTGTC
1 CCGAATGACCACATA-GATTGTC
*
5949798 CCGAATGACCACATATAATTGTC
1 CCGAATGACCACATA-GATTGTC
* *
5949821 CCTAAGGACCACATA
1 CCGAATGACCACATA
5949836 TATATTCCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
20 11 0.22
21 4 0.08
22 6 0.12
23 30 0.59
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (22 bp):
CCGAATGACCACATAGATTGTC
Found at i:5949857 original size:21 final size:21
Alignment explanation
Indices: 5949758--5949901 Score: 87
Period size: 21 Copynumber: 6.7 Consensus size: 21
5949748 AAATTATCCG
* * *
5949758 AATGACCACATAGATGTCCCA
1 AATGACCACATATATATTCCA
* *
5949779 AA-GACCACATAGGAT-TGTCCCG
1 AATGACCACATA-TATAT-T-CCA
*
5949801 AATGACCACATATA-ATTGTCCCT
1 AATGACCACATATATA-T-T-CCA
*
5949824 AAGGACCACATATATATTCCA
1 AATGACCACATATATATTCCA
* *
5949845 AATGACCAAATATATATCCCA
1 AATGACCACATATATATTCCA
* * *
5949866 AATGATCGCATAGATATTCCA
1 AATGACCACATATATATTCCA
* *
5949887 AAGGATCACATATAT
1 AATGACCACATATAT
5949902 GTTTCGAAGG
Statistics
Matches: 99, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.10
21 53 0.54
22 6 0.06
23 29 0.29
24 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (21 bp):
AATGACCACATATATATTCCA
Found at i:5954996 original size:23 final size:25
Alignment explanation
Indices: 5954970--5955016 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
5954960 AAAATATTAA
5954970 TTTAATT-TTTAAAATAA-TATTTT
1 TTTAATTATTTAAAATAATTATTTT
*
5954993 TTTAATTATTTGAAATAATTATTT
1 TTTAATTATTTAAAATAATTATTT
5955017 AATCATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTAATTATTTAAAATAATTATTTT
Found at i:5957599 original size:20 final size:21
Alignment explanation
Indices: 5957574--5957616 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5957564 TAAAATTGTA
*
5957574 AAAAAT-ATGATGTTTTAAAT
1 AAAAATAATAATGTTTTAAAT
*
5957594 AAAAATAATAATTTTTTAAAT
1 AAAAATAATAATGTTTTAAAT
5957615 AA
1 AA
5957617 TTTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAAAT
Found at i:5957617 original size:12 final size:12
Alignment explanation
Indices: 5957600--5957644 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
5957590 AAATAAAAAT
5957600 AATAATTTTTTA
1 AATAATTTTTTA
5957612 AATAATTTTTTA
1 AATAATTTTTTA
*
5957624 AATAATTTTTTT
1 AATAATTTTTTA
*
5957636 ATTAATTTT
1 AATAATTTT
5957645 ATTATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATAATTTTTTA
Found at i:5958114 original size:9 final size:9
Alignment explanation
Indices: 5958086--5958120 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5958076 AATCTTATTA
5958086 TTAATAAAT
1 TTAATAAAT
*
5958095 TAAATATAAT
1 TTAATA-AAT
5958105 TTAATAAAT
1 TTAATAAAT
5958114 TTAATAA
1 TTAATAA
5958121 TGTGTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TTAATAAAT
Found at i:5958602 original size:31 final size:31
Alignment explanation
Indices: 5958491--5958649 Score: 149
Period size: 31 Copynumber: 5.0 Consensus size: 31
5958481 TATGTTAAAA
* * *
5958491 ATATTATTAAATTAAGAATTAAAATAAAATAT
1 ATATTTTTAAGTTAAG-ATAAAAATAAAATAT
*
5958523 A-ATTTTTGAATTTAAGATAAAAATATATATATAT
1 ATATTTTT-AAGTTAAGATAAAAATA-A-A-ATAT
* * *
5958557 ATATATATTAAGTTAAGTTAAAAATAAAACAT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAATAT
*
5958589 ATATTTTTAAGTTAAAATAAAAATAAAATAT
1 ATATTTTTAAGTTAAGATAAAAATAAAATAT
* ** *
5958620 ACATTTTTAAGTTCTGATAAGAATAAAATA
1 ATATTTTTAAGTTAAGATAAAAATAAAATA
5958650 AAATATATTA
Statistics
Matches: 105, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
31 61 0.58
32 16 0.15
33 2 0.02
34 6 0.06
35 17 0.16
36 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (31 bp):
ATATTTTTAAGTTAAGATAAAAATAAAATAT
Found at i:5958685 original size:30 final size:30
Alignment explanation
Indices: 5958644--5958745 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
5958634 TGATAAGAAT
*
5958644 AAAATAAAATATATTAAATAATTTAAAATA
1 AAAATAAAATATATTAAATAAATTAAAATA
* * *
5958674 AAAATATAATATATTTAATAAATTAAGAT-
1 AAAATAAAATATATTAAATAAATTAAAATA
* *
5958703 AAAAT-ATATACT-TTAAA-AAGTTAAAATA
1 AAAATAAAATA-TATTAAATAAATTAAAATA
*
5958731 ATAATAAAATATATT
1 AAAATAAAATATATT
5958746 TTTAAAATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
27 8 0.14
28 12 0.21
29 12 0.21
30 25 0.44
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATAAAATATATTAAATAAATTAAAATA
Found at i:5958695 original size:25 final size:26
Alignment explanation
Indices: 5958641--5958695 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
5958631 TTCTGATAAG
5958641 AATAAAATAAAATATATTAAATAATT
1 AATAAAATAAAATATATTAAATAATT
*
5958667 --TAAAATAAAA-ATA-TAATATATTT
1 AATAAAATAAAATATATTAA-ATAATT
5958690 AATAAA
1 AATAAA
5958696 TTAAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 3 0.12
23 8 0.32
24 10 0.40
25 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AATAAAATAAAATATATTAAATAATT
Found at i:5958717 original size:27 final size:27
Alignment explanation
Indices: 5958646--5958736 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
5958636 ATAAGAATAA
* *
5958646 AATAAAATATA-TTAAATAATTTAAAAT
1 AATAATATATATTTAAA-AAGTTAAAAT
* *
5958673 AAAAATATAATATATTTAATAAA-TTAAGAT
1 -AATA-AT-ATATATTTAA-AAAGTTAAAAT
5958703 AA-AATATATACTTTAAAAAGTTAAAAT
1 AATAATATATA-TTTAAAAAGTTAAAAT
5958730 AATAATA
1 AATAATA
5958737 AAATATATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
26 8 0.15
27 15 0.29
28 8 0.15
29 3 0.06
30 11 0.21
31 6 0.12
32 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (27 bp):
AATAATATATATTTAAAAAGTTAAAAT
Found at i:5958740 original size:33 final size:30
Alignment explanation
Indices: 5958641--5958795 Score: 119
Period size: 31 Copynumber: 5.2 Consensus size: 30
5958631 TTCTGATAAG
5958641 AATAA-AATAAAATATA--TTAAATAATTTAA
1 AATAATAATAAAATATATTTTAAA-AA-TTAA
* *
5958670 AATAAAAATATAATATA-TTTAATAAATTAA
1 AATAATAATAAAATATATTTTAA-AAATTAA
* *
5958700 GATAA-AAT---ATATACTTTAAAAAGTTAA
1 AATAATAATAAAATATATTTTAAAAA-TTAA
* *
5958727 AATAATAATAAAATATATTTTTAAAATTTTA
1 AATAATAATAAAATATA-TTTTAAAAATTAA
* * *
5958758 TATGAGAATAAAATATATTTTATAAAATTAA
1 AATAATAATAAAATATATTTTA-AAAATTAA
5958789 AATAATA
1 AATAATA
5958796 GTATAATAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
26 8 0.08
27 13 0.13
28 3 0.03
29 8 0.08
30 23 0.23
31 38 0.38
32 8 0.08
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (30 bp):
AATAATAATAAAATATATTTTAAAAATTAA
Found at i:5959316 original size:10 final size:9
Alignment explanation
Indices: 5959293--5959327 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5959283 TTTGATTCAA
5959293 TTATTAAAT
1 TTATTAAAT
5959302 TTATTAAATT
1 TTATTAAA-T
*
5959312 TTATTTAAT
1 TTATTAAAT
5959321 TTATTAA
1 TTATTAA
5959328 TAGTAGGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATTAAAT
Found at i:5961925 original size:34 final size:34
Alignment explanation
Indices: 5961886--5961955 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
5961876 AATTCAAGAG
5961886 AGAAGGTTAATGATTTGTGCATTTAACTAGGGAA
1 AGAAGGTTAATGATTTGTGCATTTAACTAGGGAA
5961920 AGAAGGTTAATGATTTGTGCATTTAACTAGGGAA
1 AGAAGGTTAATGATTTGTGCATTTAACTAGGGAA
5961954 AG
1 AG
5961956 TTACCACCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (34 bp):
AGAAGGTTAATGATTTGTGCATTTAACTAGGGAA
Found at i:5969003 original size:256 final size:252
Alignment explanation
Indices: 5968609--5969095 Score: 780
Period size: 257 Copynumber: 1.9 Consensus size: 252
5968599 TTTGGTCGGG
*
5968609 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTAT
1 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTAT
* * * *
5968674 ATATTTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTTCAATTAAGTCACTGTTT
66 ATATTTAGGAATAATTACAATAATACCCCTATATATATAATATATTTCCAATTAAGTCACTATTT
*
5968739 TTATTGAATAAAAATAA-TTTTTTTATTATTTCAGGTCGGATTTCTAATTCATATATTCGGGTCG
131 TTATTGAATAAAAATAATTTTTTTTATTATTTCAGGTCGGATATCTAATTCATATATTCGGGTCG
5968803 GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCTGTTTTTTTTTAAGTGTGATAT
196 GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCTGTTTTTTTTTAAGTGTGATAT
* * *
5968860 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCAAAAAAATATATAATTTTACG
1 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCG----AAAAAATATATAATTTTACC
*
5968925 TTATATATTTAGGAATAATTACAATAATACACCTCTCTATATAT-ATATATTTCCAATTAAGTCA
62 TTATATATTTAGGAATAATTACAATAATAC-CC-CTATATATATAATATATTTCCAATTAAGTCA
** * *
5968989 CTATTTTTATTGAATAAAAATAATTTTTTTTATTATTTTGGGTCGGGTATCTAATTCATATATTT
125 CTATTTTTATTGAATAAAAATAATTTTTTTTATTATTTCAGGTCGGATATCTAATTCATATATTC
5969054 GGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCT
190 GGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCT
5969096 CGGATGGAGG
Statistics
Matches: 215, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
251 39 0.18
255 48 0.22
256 41 0.19
257 87 0.40
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (252 bp):
TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTAT
ATATTTAGGAATAATTACAATAATACCCCTATATATATAATATATTTCCAATTAAGTCACTATTT
TTATTGAATAAAAATAATTTTTTTTATTATTTCAGGTCGGATATCTAATTCATATATTCGGGTCG
GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCTGTTTTTTTTTAAGTGTGATAT
Found at i:5969525 original size:61 final size:61
Alignment explanation
Indices: 5969416--5969533 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
5969406 TATGGAATTG
* * *
5969416 GATTTCAATTCAATTTCCTGCCAACCAAACAGAATATGGAATTAGATTCTAATTCCTGATA
1 GATTCCAATTCAATTTCCTGCCAACCAAACAGAATATGAAATTAGATTCCAATTCCTGATA
*
5969477 GATTCCAATTCAATTTCCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCCT
1 GATTCCAATTCAATTTCCTGCCAACCAAACAGAATATGAAATTAGATTCCAATTCCT
5969534 TCACAGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (61 bp):
GATTCCAATTCAATTTCCTGCCAACCAAACAGAATATGAAATTAGATTCCAATTCCTGATA
Found at i:5970101 original size:2 final size:2
Alignment explanation
Indices: 5970085--5970121 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
5970075 GCATATTAGC
5970085 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5970122 GCATATGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5971391 original size:19 final size:18
Alignment explanation
Indices: 5971294--5971383 Score: 53
Period size: 16 Copynumber: 4.9 Consensus size: 18
5971284 CTAGAAATTA
5971294 TATATATTTTT-AAAAAC
1 TATATATTTTTCAAAAAC
**
5971311 TATA-GGTTTT-AAAAAC
1 TATATATTTTTCAAAAAC
* *
5971327 TATATATTATATACACTATAA-
1 TATATATT-T-TTCA--AAAAC
* *
5971348 TACATATTTTTTAAAAAC
1 TATATATTTTTCAAAAAC
5971366 TATATATGTTTTCAAAAA
1 TATATAT-TTTTCAAAAA
5971384 TATTATATAT
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
16 14 0.26
17 8 0.15
18 7 0.13
19 12 0.23
20 2 0.04
21 7 0.13
22 3 0.06
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (18 bp):
TATATATTTTTCAAAAAC
Found at i:5972135 original size:14 final size:13
Alignment explanation
Indices: 5972111--5972144 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5972101 TTGAAAAAGG
*
5972111 AAGAGAAAAGAAA
1 AAGAAAAAAGAAA
5972124 AATGAAAAAAGAAA
1 AA-GAAAAAAGAAA
5972138 AAGAAAA
1 AAGAAAA
5972145 GGGGGATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:5974078 original size:25 final size:24
Alignment explanation
Indices: 5974023--5974078 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
5974013 TCAGGATCAT
5974023 AAAAAA-ATAGCAAAGAAAAAATG
1 AAAAAAGATAGCAAAGAAAAAATG
5974046 AAAAAAGATAGCAAA-AAGAAAATG
1 AAAAAAGATAGCAAAGAA-AAAATG
5974070 AAAACAAGA
1 AAAA-AAGA
5974079 GATTAAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.27
24 18 0.60
25 4 0.13
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.07
Consensus pattern (24 bp):
AAAAAAGATAGCAAAGAAAAAATG
Found at i:5975059 original size:29 final size:29
Alignment explanation
Indices: 5975004--5975059 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
5974994 TGCCTTAATT
* *
5975004 TTTTTAAAAAATTAAATAAGTCTTCAAAC
1 TTTTTAAAAAATTAAATAAGACCTCAAAC
* * *
5975033 TTTTTAAAATATTAATTAGGACCTCAA
1 TTTTTAAAAAATTAAATAAGACCTCAA
5975060 GCTTAGTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTTTAAAAAATTAAATAAGACCTCAAAC
Found at i:5977150 original size:11 final size:11
Alignment explanation
Indices: 5977136--5977164 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5977126 TAAAACAATA
5977136 TTAAAATTTCT
1 TTAAAATTTCT
5977147 TTAAAATTTCT
1 TTAAAATTTCT
5977158 TTAAAAT
1 TTAAAAT
5977165 AATATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAAAATTTCT
Found at i:5977241 original size:13 final size:13
Alignment explanation
Indices: 5977220--5977249 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5977210 CTACTTTCTA
*
5977220 AAAATAAAAACAT
1 AAAACAAAAACAT
5977233 AAAACAAAAACAT
1 AAAACAAAAACAT
5977246 AAAA
1 AAAA
5977250 TACTTTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAACAAAAACAT
Found at i:5981607 original size:20 final size:21
Alignment explanation
Indices: 5981568--5981609 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5981558 GGTACTCGGG
5981568 GTAGTATCGATACCCTCCCATA
1 GTAGTATCGATA-CCTCCCATA
*
5981590 GTAGTATTGATA-CTCCCATA
1 GTAGTATCGATACCTCCCATA
5981610 AAAGTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (21 bp):
GTAGTATCGATACCTCCCATA
Found at i:5981615 original size:20 final size:20
Alignment explanation
Indices: 5981582--5981622 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5981572 TATCGATACC
** *
5981582 CTCCCATAGTAGTATTGATA
1 CTCCCATAAAAGTATTAATA
5981602 CTCCCATAAAAGTATTAATA
1 CTCCCATAAAAGTATTAATA
5981622 C
1 C
5981623 CGTAGATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (20 bp):
CTCCCATAAAAGTATTAATA
Found at i:5985117 original size:20 final size:20
Alignment explanation
Indices: 5985079--5985119 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5985069 AGGGCACCCA
*
5985079 GTAACAATAATATTAATATT
1 GTAACAATAATATCAATATT
* *
5985099 GTAAGAATAATATCGATATT
1 GTAACAATAATATCAATATT
5985119 G
1 G
5985120 GGTAGAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (20 bp):
GTAACAATAATATCAATATT
Found at i:5985334 original size:20 final size:20
Alignment explanation
Indices: 5985292--5985345 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
5985282 CCATAACACC
* *
5985292 AGAGTATTGATACTCATTAT
1 AGAGTATCGATACTCACTAT
*
5985312 AGAGTATCGATACTCACTCT
1 AGAGTATCGATACTCACTAT
*
5985332 AGAGCATCGATACT
1 AGAGTATCGATACT
5985346 GCCTTAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (20 bp):
AGAGTATCGATACTCACTAT
Found at i:5987018 original size:6 final size:6
Alignment explanation
Indices: 5987007--5987034 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5986997 CTAAAACATA
5987007 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
5987035 GGAGGCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:5989497 original size:25 final size:26
Alignment explanation
Indices: 5989465--5989513 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5989455 ACTAATAATT
5989465 TAATAATGATTACAAAT-ATGATTAA
1 TAATAATGATTACAAATAATGATTAA
*
5989490 TAATAATGATTACTAATAATGATT
1 TAATAATGATTACAAATAATGATT
5989514 TACTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (26 bp):
TAATAATGATTACAAATAATGATTAA
Found at i:5989547 original size:15 final size:15
Alignment explanation
Indices: 5989529--5989574 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
5989519 ATTATTATTA
*
5989529 ATTTAATGATTTGAT
1 ATTTAATGATTTAAT
*
5989544 ATTTAATTATTTAAT
1 ATTTAATGATTTAAT
5989559 ATTTAATGATTTAAT
1 ATTTAATGATTTAAT
5989574 A
1 A
5989575 ATGATATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (15 bp):
ATTTAATGATTTAAT
Found at i:5989554 original size:8 final size:8
Alignment explanation
Indices: 5989517--5989573 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
5989507 AATGATTTAC
5989517 TAATTA-T
1 TAATTATT
5989524 T-ATTAATT
1 TAATT-ATT
*
5989532 TAATGATT
1 TAATTATT
*
5989540 TGA-TATT
1 TAATTATT
5989547 TAATTATT
1 TAATTATT
5989555 TAA-TATT
1 TAATTATT
*
5989562 TAATGATT
1 TAATTATT
5989570 TAAT
1 TAAT
5989574 AATGATATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
6 3 0.08
7 14 0.35
8 21 0.52
9 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (8 bp):
TAATTATT
Found at i:5989585 original size:16 final size:17
Alignment explanation
Indices: 5989564--5989596 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5989554 TTAATATTTA
5989564 ATGA-TTTAATAATGAT
1 ATGATTTTAATAATGAT
*
5989580 ATGATTTTAGTAATGAT
1 ATGATTTTAATAATGAT
5989597 TACTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (17 bp):
ATGATTTTAATAATGAT
Found at i:5989645 original size:21 final size:23
Alignment explanation
Indices: 5989590--5989679 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 23
5989580 ATGATTTTAG
* *
5989590 TAATGATTACTAATAATATTTTATTAT
1 TAATGATT--TAATAATA--TTACTAA
5989617 TAAT-ATTTAATAA-A-TACTAA
1 TAATGATTTAATAATATTACTAA
*
5989637 TAATGATTTTATAATTATTACTAA
1 TAATGATTTAATAA-TATTACTAA
*
5989661 TAATGATTTCATAATATTA
1 TAATGATTTAATAATATTA
5989680 AATAACATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
20 8 0.15
21 8 0.15
23 7 0.13
24 25 0.45
26 3 0.05
27 4 0.07
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (23 bp):
TAATGATTTAATAATATTACTAA
Found at i:5989651 original size:24 final size:24
Alignment explanation
Indices: 5989624--5989676 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5989614 TATTAATATT
*
5989624 TAATAAATACTAATAATGATTTTA
1 TAATAAATACTAATAATGATTTCA
* *
5989648 TAATTATTACTAATAATGATTTCA
1 TAATAAATACTAATAATGATTTCA
5989672 TAATA
1 TAATA
5989677 TTAAATAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
TAATAAATACTAATAATGATTTCA
Found at i:5989662 original size:34 final size:34
Alignment explanation
Indices: 5989597--5989663 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
5989587 TAGTAATGAT
* *
5989597 TACTAATAATATTTTATTATTAATATTTAATAAA
1 TACTAATAATATTTTATAATTAATATCTAATAAA
*
5989631 TACTAATAATGATTTTATAATTATTA-CTAATAA
1 TACTAATAAT-ATTTTATAATTAATATCTAATAA
5989664 TGATTTCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (34 bp):
TACTAATAATATTTTATAATTAATATCTAATAAA
Found at i:5989846 original size:13 final size:13
Alignment explanation
Indices: 5989822--5989880 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
5989812 ATTACTAATG
5989822 AATAAT-ATGATT
1 AATAATAATGATT
5989834 AATAATAATGATT
1 AATAATAATGATT
* *
5989847 ACTAATAGTGATTT
1 AATAATAATGA-TT
*
5989861 ACTAATAATGATT
1 AATAATAATGATT
*
5989874 ATTAATA
1 AATAATA
5989881 TTGCGTTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
12 6 0.15
13 23 0.56
14 12 0.29
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
AATAATAATGATT
Found at i:5989868 original size:27 final size:25
Alignment explanation
Indices: 5989824--5989881 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
5989814 TACTAATGAA
5989824 TAATATGATTAATAATAATGATTAC
1 TAATATGATTAATAATAATGATTAC
* *
5989849 TAATAGTGATTTACTAATAATGATTAT
1 TAATA-TGA-TTAATAATAATGATTAC
5989876 TAATAT
1 TAATAT
5989882 TGCGTTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 4 0.14
27 20 0.69
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (25 bp):
TAATATGATTAATAATAATGATTAC
Found at i:5991396 original size:13 final size:13
Alignment explanation
Indices: 5991371--5991426 Score: 87
Period size: 13 Copynumber: 4.3 Consensus size: 13
5991361 ATTAATAATA
5991371 ATTAGTAAATCATT
1 ATTAGT-AATCATT
5991385 ATTAGTAATCATT
1 ATTAGTAATCATT
*
5991398 ATTATTAATCA-T
1 ATTAGTAATCATT
5991410 ATTAGTAATCATT
1 ATTAGTAATCATT
5991423 ATTA
1 ATTA
5991427 AATTATTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
12 11 0.28
13 22 0.56
14 6 0.15
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (13 bp):
ATTAGTAATCATT
Found at i:5991416 original size:25 final size:26
Alignment explanation
Indices: 5991378--5991426 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
5991368 ATAATTAGTA
5991378 AATCATTATTAGTAATCATTATTATT
1 AATCATTATTAGTAATCATTATTATT
5991404 AATCA-TATTAGTAATCATTATTA
1 AATCATTATTAGTAATCATTATTA
5991427 AATTATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (26 bp):
AATCATTATTAGTAATCATTATTATT
Found at i:5998669 original size:21 final size:21
Alignment explanation
Indices: 5998645--5998692 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
5998635 TAACATTTAT
5998645 AATGCTATTTTTCTCTCTAAA
1 AATGCTATTTTTCTCTCTAAA
5998666 AATGCTATTTTTCTCTCTAAA
1 AATGCTATTTTTCTCTCTAAA
5998687 AATGCT
1 AATGCT
5998693 TAGTATAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (21 bp):
AATGCTATTTTTCTCTCTAAA
Found at i:6001419 original size:19 final size:19
Alignment explanation
Indices: 6001397--6001435 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6001387 CCACTATGGC
6001397 ATTTTGTTTAGCAATGATT
1 ATTTTGTTTAGCAATGATT
6001416 ATTTTGTTTAGCAATGATT
1 ATTTTGTTTAGCAATGATT
6001435 A
1 A
6001436 ATGCACATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.51
Consensus pattern (19 bp):
ATTTTGTTTAGCAATGATT
Found at i:6001508 original size:31 final size:31
Alignment explanation
Indices: 6001470--6001576 Score: 187
Period size: 31 Copynumber: 3.5 Consensus size: 31
6001460 AACTACGTAA
*
6001470 TTAGTACTTAAACTATTAATTTCGTTTCATT
1 TTAGTACTTAAACTATCAATTTCGTTTCATT
*
6001501 TTAGTACTTAAATTATCAATTTCGTTTCATT
1 TTAGTACTTAAACTATCAATTTCGTTTCATT
6001532 TTAGTACTTAAACTATCAATTTCGTTTCATT
1 TTAGTACTTAAACTATCAATTTCGTTTCATT
*
6001563 TTAATACTTAAACT
1 TTAGTACTTAAACT
6001577 TTAATTTTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (31 bp):
TTAGTACTTAAACTATCAATTTCGTTTCATT
Found at i:6003033 original size:7 final size:7
Alignment explanation
Indices: 6003021--6003106 Score: 59
Period size: 7 Copynumber: 12.3 Consensus size: 7
6003011 GCAATGAACT
6003021 CTAAACC
1 CTAAACC
6003028 CTAAACC
1 CTAAACC
*
6003035 TTAAA-C
1 CTAAACC
*
6003041 CTCAAACT
1 CT-AAACC
6003049 CTAAA-C
1 CTAAACC
6003055 CTCAAACC
1 CT-AAACC
6003063 CTAAACC
1 CTAAACC
* *
6003070 TTAAATC
1 CTAAACC
* *
6003077 TTAAACT
1 CTAAACC
* *
6003084 ATAAATC
1 CTAAACC
*
6003091 ATAAACC
1 CTAAACC
6003098 CTAAACC
1 CTAAACC
6003105 CT
1 CT
6003107 TAATTTGATT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
6 4 0.06
7 53 0.85
8 5 0.08
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:6003041 original size:14 final size:14
Alignment explanation
Indices: 6003021--6003106 Score: 66
Period size: 14 Copynumber: 6.1 Consensus size: 14
6003011 GCAATGAACT
*
6003021 CTAAACCCTAAACC
1 CTAAACCTTAAACC
* * *
6003035 TTAAACCTCAAACT
1 CTAAACCTTAAACC
*
6003049 CTAAACCTCAAACC
1 CTAAACCTTAAACC
*
6003063 CTAAACCTTAAATC
1 CTAAACCTTAAACC
* *
6003077 TTAAA-CTATAAATC
1 CTAAACCT-TAAACC
* *
6003091 ATAAACCCTAAACC
1 CTAAACCTTAAACC
6003105 CT
1 CT
6003107 TAATTTGATT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
13 2 0.04
14 54 0.95
15 1 0.02
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAACCTTAAACC
Found at i:6003049 original size:28 final size:28
Alignment explanation
Indices: 6003017--6003070 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
6003007 CTTTGCAATG
*
6003017 AACTCTAAACC-CTAAACCTTAAACCTCA
1 AACTCTAAACCTC-AAACCCTAAACCTCA
6003045 AACTCTAAACCTCAAACCCTAAACCT
1 AACTCTAAACCTCAAACCCTAAACCT
6003071 TAAATCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (28 bp):
AACTCTAAACCTCAAACCCTAAACCTCA
Found at i:6003062 original size:35 final size:35
Alignment explanation
Indices: 6003022--6003109 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
6003012 CAATGAACTC
* *
6003022 TAAACCCTAAACCTTAAACCTCAAACTCTAAA-CC
1 TAAACCCTAAACCTTAAACCTCAAACTATAAATCA
* *
6003056 TCAAACCCTAAACCTTAAATCTTAAACTATAAATCA
1 T-AAACCCTAAACCTTAAACCTCAAACTATAAATCA
6003092 TAAACCCTAAACCCTTAA
1 TAAACCCTAAA-CCTTAA
6003110 TTTGATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
34 1 0.02
35 38 0.81
36 8 0.17
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (35 bp):
TAAACCCTAAACCTTAAACCTCAAACTATAAATCA
Found at i:6003082 original size:21 final size:21
Alignment explanation
Indices: 6003019--6003104 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
6003009 TTGCAATGAA
6003019 CTCTAAACCCTAAACCTTAAAC
1 CTCTAAA-CCTAAACCTTAAAC
*
6003041 CTC-AAACTCTAAACCTCAAAC
1 CTCTAAAC-CTAAACCTTAAAC
*
6003062 C-CTAAACCTTAAATCTTAAA-
1 CTCTAAACC-TAAACCTTAAAC
* * *
6003082 CTATAAATCATAAACCCTAAAC
1 CTCTAAA-CCTAAACCTTAAAC
6003104 C
1 C
6003105 CTTAATTTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.08
21 42 0.82
22 5 0.10
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (21 bp):
CTCTAAACCTAAACCTTAAAC
Found at i:6004331 original size:23 final size:23
Alignment explanation
Indices: 6004299--6004352 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
6004289 CTCTTAGGCC
6004299 TTGAGCTTGAATCGAGCTCAAAA
1 TTGAGCTTGAATCGAGCTCAAAA
* * *
6004322 TTGAGTTTGAATTGAGCTCAAAT
1 TTGAGCTTGAATCGAGCTCAAAA
6004345 TTGAGCTT
1 TTGAGCTT
6004353 AAAATCAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (23 bp):
TTGAGCTTGAATCGAGCTCAAAA
Found at i:6004427 original size:18 final size:16
Alignment explanation
Indices: 6004406--6004436 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6004396 CTTTTGAATT
6004406 TTTTTTGAGTTCGAGC
1 TTTTTTGAGTTCGAGC
6004422 TTTTTTGAGTTCGAG
1 TTTTTTGAGTTCGAG
6004437 TCGAGTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.26, T:0.52
Consensus pattern (16 bp):
TTTTTTGAGTTCGAGC
Found at i:6005004 original size:19 final size:19
Alignment explanation
Indices: 6004966--6005005 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6004956 CGAATAATTG
* * *
6004966 AATCGAATATAATATTTTA
1 AATCAAATATAAAATCTTA
6004985 AATCAAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
6005004 AA
1 AA
6005006 ATTACTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Done.