Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 83 of 279
Found at i:27564239 original size:40 final size:40
Alignment explanation
Indices: 27564180--27565127 Score: 1581
Period size: 40 Copynumber: 23.7 Consensus size: 40
27564170 GAGCATTGGA
27564180 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564220 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564260 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564300 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564340 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564380 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564420 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564460 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564500 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564540 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564580 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564620 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564660 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564700 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564740 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564780 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564820 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564860 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564900 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27564940 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27564980 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27565020 ATATATCCGGGCTATGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
27565060 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
27565100 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
27565128 ATGTGTTTGC
Statistics
Matches: 843, Mismatches: 65, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 843 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:27565149 original size:80 final size:80
Alignment explanation
Indices: 27564180--27565127 Score: 1824
Period size: 80 Copynumber: 11.8 Consensus size: 80
27564170 GAGCATTGGA
*
27564180 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564245 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564260 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564325 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564340 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564405 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564420 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564485 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564500 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564565 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564580 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564645 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564660 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564725 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564740 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564805 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564820 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564885 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564900 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27564965 CAATTATGCGAGATG
66 CAATTATGCGAGATG
27564980 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
* *
27565045 CAATTATGCAAGTTG
66 CAATTATGCGAGATG
* * * * *
27565060 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATGTCCGGGTTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
27565125 CAA
66 CAA
27565128 ATGTGTTTGC
Statistics
Matches: 860, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 860 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (80 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTAAGCGAGTTGATATATCCGGGCTATGACCCGAAGG
CAATTATGCGAGATG
Found at i:27575874 original size:27 final size:27
Alignment explanation
Indices: 27575843--27575901 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
27575833 AAAAACATTA
27575843 TTCTAAAATAAAATAAAAGAAGTCTAG
1 TTCTAAAATAAAATAAAAGAAGTCTAG
27575870 TTCTAAAATAAAATAAAAGAAGTCTAG
1 TTCTAAAATAAAATAAAAGAAGTCTAG
27575897 TTCTA
1 TTCTA
27575902 TATAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (27 bp):
TTCTAAAATAAAATAAAAGAAGTCTAG
Found at i:27576338 original size:35 final size:34
Alignment explanation
Indices: 27576269--27576344 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
27576259 AAGAGGTCAT
* * *
27576269 TAAATT-GTTGTACCATATTGATGTGATGTGTCTC
1 TAAATTAG-TGTACCATATTGATGTCATATCTCTC
* *
27576303 TTAATTAGTGTACTATATTTGATGTCATATCTCTC
1 TAAATTAGTGTACCATA-TTGATGTCATATCTCTC
27576338 TAAATTA
1 TAAATTA
27576345 TTGCTAAAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (34 bp):
TAAATTAGTGTACCATATTGATGTCATATCTCTC
Found at i:27577007 original size:14 final size:14
Alignment explanation
Indices: 27576974--27577007 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
27576964 TATAATATCC
*
27576974 AAATAATAACAATA
1 AAATAGTAACAATA
27576988 AAATAGTAACAATA
1 AAATAGTAACAATA
*
27577002 TAATAG
1 AAATAG
27577008 CGAAATAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:27579347 original size:21 final size:20
Alignment explanation
Indices: 27579313--27579351 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
27579303 TTTATTCATA
27579313 TATATATGTATATTGTTTTG
1 TATATATGTATATTGTTTTG
*
27579333 TATATCATTTATATTGTTT
1 TATAT-ATGTATATTGTTT
27579352 CGTTACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (20 bp):
TATATATGTATATTGTTTTG
Found at i:27581491 original size:31 final size:31
Alignment explanation
Indices: 27581453--27581716 Score: 368
Period size: 31 Copynumber: 8.5 Consensus size: 31
27581443 AAATGACAAC
27581453 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
27581484 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
27581515 TGAAAAGTGGTAACTTCTA-CTACCTAATCAG
1 TGAAAAGTGGTAGCTTC-AGCTACCTGATCAG
*
27581546 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
27581577 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
27581608 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* * *
27581639 TGAAAAGTGGTAGCTCCGGCTACCTGATAAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* ** *
27581670 TGAAAAATGGTAGCACCAGTTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
27581701 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
27581717 TGGCTACAAG
Statistics
Matches: 208, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
31 207 1.00
32 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:27581823 original size:47 final size:48
Alignment explanation
Indices: 27581754--27581879 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 48
27581744 CAAGTGATTT
* *
27581754 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATG-CTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* * *
27581801 CTGTATAAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* ** *
27581849 C-GTGTAAGACCATAGATGGGCTATGGCATCA
1 CTGTATAAGACCATATCTGGGATATGGCATCA
27581880 TTATGTAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 65 0.96
48 3 0.04
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (48 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
Found at i:27582896 original size:29 final size:30
Alignment explanation
Indices: 27582864--27582925 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
27582854 ACTTAACAAG
*
27582864 CAAATGCTTTTAAAATAATAA-AAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
27582893 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
27582923 CAA
1 CAA
27582926 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAGAAAATTAA
Found at i:27587113 original size:3 final size:3
Alignment explanation
Indices: 27587105--27587158 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
27587095 TTTAAATATG
* * * *
27587105 ATA ATA ATA ATA ATG ATA ATG ATA ATA ATA ATA ATA AT- ATA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27587152 ATA ATA A
1 ATA ATA A
27587159 AAGTAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:27587560 original size:17 final size:17
Alignment explanation
Indices: 27587502--27587564 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
27587492 AAAATAATAT
27587502 TAAAATATATATACGAGTAA
1 TAAAA-ATATATAC-A-TAA
* * * *
27587522 TAAAAAATGTATCCGTAT
1 T-AAAAATATATACATAA
27587540 TAAAAATATATACATAA
1 TAAAAATATATACATAA
27587557 TAAAAATA
1 TAAAAATA
27587565 CAATATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 20 0.59
18 3 0.09
20 7 0.21
21 4 0.12
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAATATATACATAA
Found at i:27587904 original size:15 final size:14
Alignment explanation
Indices: 27587879--27587914 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
27587869 TAATAATACT
27587879 ATATAATATATATA
1 ATATAATATATATA
27587893 ATATACATATATATA
1 ATATA-ATATATATA
27587908 AGTATAA
1 A-TATAA
27587915 CAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:27588615 original size:18 final size:20
Alignment explanation
Indices: 27588584--27588636 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
27588574 AAGCAAATTC
*
27588584 GAAAATAA-AATAA-A-AAG
1 GAAAATAATAATAATAGAAA
27588601 GAAAATAATAATAAATAGAAA
1 GAAAATAATAAT-AATAGAAA
27588622 GAAAATAATAATAAT
1 GAAAATAATAATAAT
27588637 GTAATATCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 8 0.26
18 3 0.10
19 2 0.06
20 4 0.13
21 14 0.45
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (20 bp):
GAAAATAATAATAATAGAAA
Found at i:27588627 original size:21 final size:22
Alignment explanation
Indices: 27588591--27588635 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
27588581 TTCGAAAATA
27588591 AAATAAAAAGGAAAATAATAAT
1 AAATAAAAAGGAAAATAATAAT
*
27588613 AAATAGAAA-GAAAATAATAAT
1 AAATAAAAAGGAAAATAATAAT
27588634 AA
1 AA
27588636 TGTAATATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (22 bp):
AAATAAAAAGGAAAATAATAAT
Found at i:27589612 original size:14 final size:14
Alignment explanation
Indices: 27589590--27589624 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
27589580 ACTATTAGCA
*
27589590 AGTTATTAAGAAGT
1 AGTTATTAAAAAGT
*
27589604 AGTTGTTAAAAAGT
1 AGTTATTAAAAAGT
27589618 AGTTATT
1 AGTTATT
27589625 CCATAAGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (14 bp):
AGTTATTAAAAAGT
Found at i:27601131 original size:4 final size:4
Alignment explanation
Indices: 27601122--27601160 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
27601112 AGATGCTCGT
*
27601122 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
27601161 AAAAGCATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:27601235 original size:4 final size:4
Alignment explanation
Indices: 27601226--27601275 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
27601216 TGCCTAAGAG
*
27601226 ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27601274 AT
1 AT
27601276 TTAGGGGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:27601522 original size:9 final size:9
Alignment explanation
Indices: 27601505--27601534 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27601495 TGAAGCAAAG
27601505 TTTTT-ATT
1 TTTTTAATT
27601513 TTTTTAATT
1 TTTTTAATT
27601522 TTTTTAATT
1 TTTTTAATT
27601531 TTTT
1 TTTT
27601535 ACGGCATCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTAATT
Found at i:27601888 original size:16 final size:17
Alignment explanation
Indices: 27601858--27601889 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27601848 GTTATCTGAT
27601858 AATTAAATATTTAAAAA
1 AATTAAATATTTAAAAA
27601875 AATTAAAT-TTTAAAA
1 AATTAAATATTTAAAA
27601890 TCTAAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATATTTAAAAA
Found at i:27610561 original size:5 final size:5
Alignment explanation
Indices: 27610551--27610575 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27610541 ATTATTATTT
27610551 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
27610576 GAAAAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:27610822 original size:17 final size:18
Alignment explanation
Indices: 27610800--27610833 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27610790 TATAAAAAAA
27610800 CTTTT-AAATTTTTTTAT
1 CTTTTAAAATTTTTTTAT
27610817 CTTTTAAAATTTTTTTA
1 CTTTTAAAATTTTTTTA
27610834 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTTAAAATTTTTTTAT
Found at i:27623796 original size:25 final size:26
Alignment explanation
Indices: 27623758--27623815 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
27623748 TGCATAATTG
*
27623758 TTTG-TTTTTATTTAACAGGTTCGT-
1 TTTGTTTTTTATTTAACAGGCTCGTC
*
27623782 TTTGTTTTTTGTTTAACAGGCTCGTCC
1 TTTGTTTTTTATTTAACAGGCTCGT-C
27623809 TTTGTTT
1 TTTGTTT
27623816 AAAGATAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 18 0.62
27 7 0.24
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (26 bp):
TTTGTTTTTTATTTAACAGGCTCGTC
Found at i:27627139 original size:14 final size:14
Alignment explanation
Indices: 27627122--27627151 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
27627112 AAAACTGAGC
27627122 AAGGAAAAATGGAA
1 AAGGAAAAATGGAA
27627136 AAGGAAAAATGGAA
1 AAGGAAAAATGGAA
27627150 AA
1 AA
27627152 AAAATGCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (14 bp):
AAGGAAAAATGGAA
Found at i:27642355 original size:16 final size:17
Alignment explanation
Indices: 27642316--27642354 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
27642306 TATGAAATAT
27642316 ATTTTTATTTAATTAAA
1 ATTTTTATTTAATTAAA
*
27642333 ATTTTTATTTAATTAAT
1 ATTTTTATTTAATTAAA
27642350 ATTTT
1 ATTTT
27642355 ACAATCACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTATTTAATTAAA
Found at i:27643616 original size:19 final size:19
Alignment explanation
Indices: 27643592--27643640 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
27643582 TTAGAATTTT
*
27643592 TTTAGAATTTCTATAAA-TA
1 TTTAGAATTT-TAAAAATTA
27643611 TTTAGAATTTTAAAAATTA
1 TTTAGAATTTTAAAAATTA
*
27643630 TTTTGAATTTT
1 TTTAGAATTTT
27643641 TTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTAGAATTTTAAAAATTA
Found at i:27651629 original size:15 final size:15
Alignment explanation
Indices: 27651609--27651638 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27651599 TTTAGCAAAA
*
27651609 GGATGGTGGGGGAAG
1 GGATGGTGGGAGAAG
27651624 GGATGGTGGGAGAAG
1 GGATGGTGGGAGAAG
27651639 AGGGGATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.63, T:0.13
Consensus pattern (15 bp):
GGATGGTGGGAGAAG
Found at i:27652085 original size:20 final size:20
Alignment explanation
Indices: 27652062--27652099 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27652052 AAAAAAAATT
*
27652062 AAATTCAAATTAAAATTTTA
1 AAATTCAAAATAAAATTTTA
27652082 AAATTCAAAATAAAATTT
1 AAATTCAAAATAAAATTT
27652100 CTAATATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTCAAAATAAAATTTTA
Found at i:27662261 original size:927 final size:927
Alignment explanation
Indices: 27660926--27662762 Score: 3334
Period size: 926 Copynumber: 2.0 Consensus size: 927
27660916 CTAAAGCCAA
*
27660926 TGCAACCTCCATACCCCAAATGGTATGACGCAAATGCCCAATGCGAATACCATGCGGGAGCCACA
1 TGCAACCTCCATACCCCAAATGGTATGACGCAAATGCCCAATGCAAATACCATGCGGGAGCCACA
*
27660991 GGACACTCGATAGAAAACTGCACCACTTTTAAGAAATTGGTTGAAAGACTCATCAACATGGGGAT
66 GGACACTCGATAGAAAACTGCACCACTTTCAAGAAATTGGTTGAAAGACTCATCAACATGGGGAT
*
27661056 TGTGAAATTTGATGATGCATCCAATACAGAGAATCCATTACCTAACCATGGGGATAAGGGAATAA
131 TGTGAAATTTGATGATACATCCAATACAGAGAATCCATTACCTAACCATGGGGATAAGGGAATAA
* * *
27661121 ATGCGATAATCGAGAGTTCGGGGAAAGAAATTAAGATGAATATTGCAGAAGTGAATACCCCGTTG
196 ATACAATAATCCAGAGTTCGGGGAAAGAAATTAAGATGAATATTGCAGAAGTGAATACCCCGTTG
*** *
27661186 AAAGAAGTATGGAAGAAAATGGTGGAAAGAGGTTTGATAGCACAGAATTTGGGGGTCAGGCCTCG
261 AAAGAAGTATGGAAGAAAATGGTGGAAAGAGGTTTGATAGCACAGAATTCAAGGGTCAGGCCCCG
* * *
27661251 AGAAGCGAAGAATTATTGTGAGTTCCACGATCAAGAGGATCACGAGATCCAAAAATGCAGCCAAT
326 AGAAGCAAAGAATTATTATGAGTTCCACGATCAAGAGGATCACGAGATCCAAAAATACAGCCAAT
* * * *
27661316 TCAGGGCTTTAATACAAGGATTGATGGATAATAAGGAGCTGGAATTCTTCGAATATGTCGGGAGC
391 TCAAGGCTTTAATACAAGGATTGATGGATAATAAGGAGATAGAATTCTTCGAATATAT-GGGAGC
* *
27661381 CCGGAAGAAGCAGATGTGTGTGCCTCCGAAGAGGGGTCGACGAAGGATGTTTACAAAGTCAACCA
455 CCAGAAGAAGCAGATGTGTGTGCCTCCGAAGAGAGGTCGACGAAGGATGTTTACAAAGTCAACCA
27661446 CCCAGTGGTTATCATATCACGTCCGAGAATGAATGAAGCCGGGGCACGAGTTGCGCCAAAGGTCG
520 CCCAGTGGTTATCATATCACGTCCGAGAATGAATGAAGCCGGGGCACGAGTTGCGCCAAAGGTCG
27661511 TGATCCAAAAGCCCGTTGCTTTTCCTTATAAAGATAGCAAAAGGGTACCGTGGAACTATAGCTGC
585 TGATCCAAAAGCCCGTTGCTTTTCCTTATAAAGATAGCAAAAGGGTACCGTGGAACTATAGCTGC
*
27661576 AATGTGACATTCCCGGGAGAGGAGACCCCGATTAATGCATCAGAAGAAGTTCAAGACGAAGGTTT
650 AATGTGACATTCCCGAGAGAGGAGACCCCGATTAATGCATCAGAAGAAGTTCAAGACGAAGGTTT
27661641 TTATACGCGCAGCGGAAGGCGTTATACCCCAAATACAAAAGTCGAGCAGGTTAAAGAAAAATCAT
715 TTATACGCGCAGCGGAAGGCGTTATACCCCAAATACAAAAGTCGAGCAGGTTAAAGAAAAATCAT
27661706 TAGCAATTGAGCAAAAGAAAGAGAAGCCGGCGGGGCCTGAACCAACTGTTAATGAATCAGTGACT
780 TAGCAATTGAGCAAAAGAAAGAGAAGCCGGCGGGGCCTGAACCAACTGTTAATGAATCAGTGACT
*
27661771 GAAAAAGAAGCCAAGGAATTCTTAAAATTCCTAAAGCACAGTGAATATAGTGTCGTAGAACAGTT
845 GAAAAAGAAGCCAAGGAATTCTTAAAATTCCTAAAGCACAGCGAATATAGTGTCGTAGAACAGTT
27661836 GTAGAAATAGCTAGCGTG
910 GTAGAAATAGCTAGCGTG
27661854 TGCAACCTCCATACCCCAAATGGTATGACGCAAATGCCCAATGCAAATACCATGCGGGAGCCACA
1 TGCAACCTCCATACCCCAAATGGTATGACGCAAATGCCCAATGCAAATACCATGCGGGAGCCACA
* * * * * *
27661919 GGACACTCGATAGAGAATTGTACTACTTTCAAGAAATTGGTTGAGAGACTCATCAA-ATGGGGGT
66 GGACACTCGATAGAAAACTGCACCACTTTCAAGAAATTGGTTGAAAGACTCATCAACATGGGGAT
* *
27661983 TGTGAAATTTGATGATACATCCAGTGCAGAGAATCCATTACCTAACCATGGGGATAAGGGAATAA
131 TGTGAAATTTGATGATACATCCAATACAGAGAATCCATTACCTAACCATGGGGATAAGGGAATAA
*
27662048 ATACAATAATCCAGAGTTCGGGGAAAGAAATTAAGATGAATGTTGCAGAAGTGAATACCCCGTTG
196 ATACAATAATCCAGAGTTCGGGGAAAGAAATTAAGATGAATATTGCAGAAGTGAATACCCCGTTG
27662113 AAAGAAGTATGGAAGAAAATGGTGGAAAGAGGTTTGATAGCACAGAATTCAAGGGTCAGGCCCCG
261 AAAGAAGTATGGAAGAAAATGGTGGAAAGAGGTTTGATAGCACAGAATTCAAGGGTCAGGCCCCG
* *
27662178 AGAAGCAAAGAATTATTATGAGTTCCACGATCAAGAGGATCACGAGATTCAGAAATACAGCCAAT
326 AGAAGCAAAGAATTATTATGAGTTCCACGATCAAGAGGATCACGAGATCCAAAAATACAGCCAAT
*
27662243 TCAAGGCTTTAGTACAAGGATTGATGGATAATAAGGAGATAGAATTCTTCGAATATATGGGAGCC
391 TCAAGGCTTTAATACAAGGATTGATGGATAATAAGGAGATAGAATTCTTCGAATATATGGGAGCC
*
27662308 TAGAAGAAGCAGATGTGTGTGCCTCCGAAGAGAGGTCGACGAAGGATGTTTACAAAGTCAACCAC
456 CAGAAGAAGCAGATGTGTGTGCCTCCGAAGAGAGGTCGACGAAGGATGTTTACAAAGTCAACCAC
*
27662373 CCAGTGGTTATCATATCACGTCCGAGAATGAATGAAGCTGGGGCACGAGTTGCGCCAAAGGTCGT
521 CCAGTGGTTATCATATCACGTCCGAGAATGAATGAAGCCGGGGCACGAGTTGCGCCAAAGGTCGT
27662438 GATCCAAAAGCCCGTTGCTTTTCCTTATAAAGATAGCAAAAGGGTACCGTGGAACTATAGCTGCA
586 GATCCAAAAGCCCGTTGCTTTTCCTTATAAAGATAGCAAAAGGGTACCGTGGAACTATAGCTGCA
*
27662503 ATGTGACATTCCCGAGAGAGGAGACCCCGATTAATGCATCAGAGGAAGTTCAAGACGAAGGTTTT
651 ATGTGACATTCCCGAGAGAGGAGACCCCGATTAATGCATCAGAAGAAGTTCAAGACGAAGGTTTT
27662568 TATACGCGCAGCGGAAGGCGTTATACCCCAAATACAAAAGTCGAGCAGGTTAAAGAAAAATCATT
716 TATACGCGCAGCGGAAGGCGTTATACCCCAAATACAAAAGTCGAGCAGGTTAAAGAAAAATCATT
27662633 AGCAATTGAGCAAAAGAAAGAGAAGCCGGCGGGGCCTGAACCAACTGTTAATGAATCAGTGACTG
781 AGCAATTGAGCAAAAGAAAGAGAAGCCGGCGGGGCCTGAACCAACTGTTAATGAATCAGTGACTG
27662698 AAAAAGAAGCCAAGGAATTCTTAAAATTCCTAAAGCACAGCGAATATAGTGTCGTAGAACAGTTG
846 AAAAAGAAGCCAAGGAATTCTTAAAATTCCTAAAGCACAGCGAATATAGTGTCGTAGAACAGTTG
27662763 CACAAACAGC
Statistics
Matches: 873, Mismatches: 36, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
926 455 0.52
927 304 0.35
928 114 0.13
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (927 bp):
TGCAACCTCCATACCCCAAATGGTATGACGCAAATGCCCAATGCAAATACCATGCGGGAGCCACA
GGACACTCGATAGAAAACTGCACCACTTTCAAGAAATTGGTTGAAAGACTCATCAACATGGGGAT
TGTGAAATTTGATGATACATCCAATACAGAGAATCCATTACCTAACCATGGGGATAAGGGAATAA
ATACAATAATCCAGAGTTCGGGGAAAGAAATTAAGATGAATATTGCAGAAGTGAATACCCCGTTG
AAAGAAGTATGGAAGAAAATGGTGGAAAGAGGTTTGATAGCACAGAATTCAAGGGTCAGGCCCCG
AGAAGCAAAGAATTATTATGAGTTCCACGATCAAGAGGATCACGAGATCCAAAAATACAGCCAAT
TCAAGGCTTTAATACAAGGATTGATGGATAATAAGGAGATAGAATTCTTCGAATATATGGGAGCC
CAGAAGAAGCAGATGTGTGTGCCTCCGAAGAGAGGTCGACGAAGGATGTTTACAAAGTCAACCAC
CCAGTGGTTATCATATCACGTCCGAGAATGAATGAAGCCGGGGCACGAGTTGCGCCAAAGGTCGT
GATCCAAAAGCCCGTTGCTTTTCCTTATAAAGATAGCAAAAGGGTACCGTGGAACTATAGCTGCA
ATGTGACATTCCCGAGAGAGGAGACCCCGATTAATGCATCAGAAGAAGTTCAAGACGAAGGTTTT
TATACGCGCAGCGGAAGGCGTTATACCCCAAATACAAAAGTCGAGCAGGTTAAAGAAAAATCATT
AGCAATTGAGCAAAAGAAAGAGAAGCCGGCGGGGCCTGAACCAACTGTTAATGAATCAGTGACTG
AAAAAGAAGCCAAGGAATTCTTAAAATTCCTAAAGCACAGCGAATATAGTGTCGTAGAACAGTTG
TAGAAATAGCTAGCGTG
Found at i:27668570 original size:43 final size:44
Alignment explanation
Indices: 27668509--27668595 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
27668499 ATTCACCAAG
* *
27668509 CCTTAAACCCCTAAGCAGTAGGGTAACAGG-TTAAATTTACAGA
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGA
* *
27668552 CCTTAACCCCCTAAGCAGTAGGGTAATAGGCTGAAAATTACAGA
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGA
27668596 TATTGTCTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (44 bp):
CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGA
Found at i:27669208 original size:41 final size:42
Alignment explanation
Indices: 27669111--27669226 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
27669101 GAGCAGCTAA
* * * *
27669111 AAGCCACAACAGATCTCCTTGAAGTTTCAGTGGAATTGATCG
1 AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTAAGCG
*
27669153 AAGCTACAGCAGATCTCCTTGAAGTTTTAGTGG-ATTAAGCG
1 AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTAAGCG
27669194 AAGCTACAGCAGATCTCCTTTGAAGTTTCAGTG
1 AAGCTACAGCAGATCTCC-TTGAAGTTTCAGTG
27669227 CAAAACCCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 24 0.36
42 43 0.64
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
AAGCTACAGCAGATCTCCTTGAAGTTTCAGTGGAATTAAGCG
Found at i:27670797 original size:3 final size:3
Alignment explanation
Indices: 27670791--27670860 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
27670781 CTATTATTCC
* * * * *
27670791 TAT TAT TTT TAT TAT TACC TAT TAT CAA TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
27670837 TGT TGT TGT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
27670861 GATTCTTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 54 0.96
4 2 0.04
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:27670822 original size:19 final size:19
Alignment explanation
Indices: 27670775--27670826 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
27670765 TATATTGTAG
*
27670775 TTATCACTATTATT-CCTA
1 TTATCAATATTATTACCTA
***
27670793 TTATTTTTATTATTACCTA
1 TTATCAATATTATTACCTA
27670812 TTATCAATATTATTA
1 TTATCAATATTATTA
27670827 TTATTATTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATCAATATTATTACCTA
Found at i:27671020 original size:3 final size:3
Alignment explanation
Indices: 27671012--27671039 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27671002 GCTCTATTTT
27671012 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27671040 CAATATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27671467 original size:16 final size:17
Alignment explanation
Indices: 27671448--27671485 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
27671438 AGGTACTAAT
27671448 ATTATATTTTAC-TATC
1 ATTATATTTTACTTATC
*
27671464 ATTATATTTTTCTTATC
1 ATTATATTTTACTTATC
27671481 ATTAT
1 ATTAT
27671486 CATCACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATTTTACTTATC
Found at i:27675518 original size:18 final size:16
Alignment explanation
Indices: 27675495--27675531 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
27675485 TCTAAAGTGT
27675495 AAAATAAATCTCAAAATA
1 AAAATAAAT-T-AAAATA
27675513 AAAATAAATTAAAATA
1 AAAATAAATTAAAATA
27675529 AAA
1 AAA
27675532 TAACTCCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 9 0.47
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAAATTAAAATA
Found at i:27679333 original size:25 final size:26
Alignment explanation
Indices: 27679305--27679364 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 26
27679295 TTATAATATT
*
27679305 AATTTAACATTAAAATT-AAATAAAA
1 AATTTAACAATAAAATTCAAATAAAA
* *
27679330 AA-TTAATAATAAAATTCAATTAAAA
1 AATTTAACAATAAAATTCAAATAAAA
*
27679355 CATTTAACAA
1 AATTTAACAA
27679365 CCGGCCACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 12 0.43
25 10 0.36
26 6 0.21
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.32
Consensus pattern (26 bp):
AATTTAACAATAAAATTCAAATAAAA
Found at i:27684584 original size:15 final size:16
Alignment explanation
Indices: 27684558--27684588 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
27684548 TCTAATATTG
27684558 TATTACATAAAATATC
1 TATTACATAAAATATC
27684574 TATTA-ATAAAATATC
1 TATTACATAAAATATC
27684589 GGAACTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (16 bp):
TATTACATAAAATATC
Found at i:27692507 original size:21 final size:22
Alignment explanation
Indices: 27692457--27692512 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
27692447 AATTTATGTA
**
27692457 ATTATATTTGTTTATATGATTT
1 ATTATATTACTTTATATGATTT
* *
27692479 -TTAAATTACTTTATAT-TTTT
1 ATTATATTACTTTATATGATTT
27692499 ATTATATTAGCTTT
1 ATTATATTA-CTTT
27692513 TAATGGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (22 bp):
ATTATATTACTTTATATGATTT
Found at i:27694842 original size:31 final size:30
Alignment explanation
Indices: 27694795--27694852 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
27694785 GAAATATGAG
* *
27694795 TTTAAAATTATTATTTAAGTTT-TTTTATA
1 TTTAAAATAATTATTTAAATTTATTTTATA
27694824 TTTATAAATAATTAATTTAAATTTATTTT
1 TTTA-AAATAATT-ATTTAAATTTATTTT
27694853 TGGCTAGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 7 0.29
31 9 0.38
32 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
TTTAAAATAATTATTTAAATTTATTTTATA
Found at i:27694908 original size:25 final size:22
Alignment explanation
Indices: 27694884--27694929 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
27694874 AAAAAATTTA
*
27694884 AAATTATATATTTATATTATTTTT
1 AAATTA-ATATTTA-ATGATTTTT
*
27694908 AATTTAATATTTAATGATTTTT
1 AAATTAATATTTAATGATTTTT
27694930 TATTCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
AAATTAATATTTAATGATTTTT
Found at i:27695046 original size:22 final size:22
Alignment explanation
Indices: 27695021--27695062 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27695011 TATTTTTATG
* *
27695021 TTTATAAATTACATAATATATT
1 TTTAAAAATAACATAATATATT
27695043 TTTAAAAATAACATAATATA
1 TTTAAAAATAACATAATATA
27695063 AAACCTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAAATAACATAATATATT
Found at i:27698890 original size:18 final size:18
Alignment explanation
Indices: 27698863--27698901 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
27698853 TACAGGCTGC
27698863 AATCACTTATATAAATGG
1 AATCACTTATATAAATGG
*
27698881 AATCAGTTATATAAATGG
1 AATCACTTATATAAATGG
27698899 AAT
1 AAT
27698902 TGATCGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (18 bp):
AATCACTTATATAAATGG
Found at i:27700015 original size:3 final size:3
Alignment explanation
Indices: 27700007--27700053 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
27699997 AAGAATATAG
27700007 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
27700054 GACACAGGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:27700447 original size:19 final size:19
Alignment explanation
Indices: 27700423--27700459 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
27700413 TATTAAAAAT
27700423 ATAAAAGC-TAAAACTTTAA
1 ATAAAAGCTTAAAA-TTTAA
27700442 ATAAAAGCTTAAAATTTA
1 ATAAAAGCTTAAAATTTA
27700460 GAAATTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAAAAGCTTAAAATTTAA
Found at i:27701816 original size:34 final size:34
Alignment explanation
Indices: 27701765--27701842 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
27701755 ATTTTCATCA
* * *
27701765 TAAT-AATTTTCTTTCAAAGTTGATCCATAATGT
1 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
27701798 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
1 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
27701832 TAATGAATCTT
1 TAATGAATCTT
27701843 TTACATGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 4 0.10
34 37 0.90
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (34 bp):
TAATGAATCTTCTTTCAAAATTGATCCATAATAT
Found at i:27707445 original size:14 final size:14
Alignment explanation
Indices: 27707422--27707465 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
27707412 TCATAAATCT
27707422 ATATTCAATATAATA
1 ATATT-AATATAATA
27707437 ATATTAATA-ATATA
1 ATATTAATATA-ATA
*
27707451 ATATTATTATAATA
1 ATATTAATATAATA
27707465 A
1 A
27707466 AATAACTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 19 0.73
15 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAATATAATA
Found at i:27708400 original size:22 final size:22
Alignment explanation
Indices: 27708374--27708416 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27708364 TAAACAAGTG
27708374 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
27708396 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
27708417 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:27712177 original size:22 final size:22
Alignment explanation
Indices: 27712149--27712191 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
27712139 AGGGGGAGTG
27712149 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
27712171 TAGGAATATTTTGTAGATATT
1 TAGGAATATTCTGTAAATATT
27712192 CTTTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:27712701 original size:20 final size:21
Alignment explanation
Indices: 27712670--27712717 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
27712660 TAATAAAAGA
*
27712670 AATAAT-AAAATAACAAGAAT
1 AATAATAAAAATAACAACAAT
*
27712690 AA-AATAAAAATAACGACAAT
1 AATAATAAAAATAACAACAAT
27712710 AATAATAA
1 AATAATAA
27712718 CTGAGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 16 0.67
21 5 0.21
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (21 bp):
AATAATAAAAATAACAACAAT
Found at i:27720545 original size:40 final size:40
Alignment explanation
Indices: 27720481--27720559 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
27720471 ACAGACCATG
* *
27720481 TGGGGATGAAATCGACTCACCCAGCCCTACACACCAAGTA
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
* *
27720521 TGGGGATAAAATTGACCCATCCAGCCCTACACACCAAGT
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGT
27720560 GGTACTGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.32, G:0.19, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
Found at i:27727634 original size:38 final size:38
Alignment explanation
Indices: 27727592--27727682 Score: 92
Period size: 40 Copynumber: 2.3 Consensus size: 38
27727582 GTCCAACCCA
* *
27727592 ACACACCATGTGGGGATAAAAACGACCCACCCAGCCCT
1 ACACACCATGTGGGAATAAAAACAACCCACCCAGCCCT
* * * * *
27727630 ACACACCAAGTGTGAGAATAAAATCAACCCATCTAGTCCT
1 ACACACC-A-TGTGGGAATAAAAACAACCCACCCAGCCCT
*
27727670 ACACACCAAGTGG
1 ACACACCATGTGG
27727683 TACTGTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
38 10 0.24
39 2 0.05
40 30 0.71
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.14
Consensus pattern (38 bp):
ACACACCATGTGGGAATAAAAACAACCCACCCAGCCCT
Found at i:27729209 original size:35 final size:35
Alignment explanation
Indices: 27729182--27729309 Score: 166
Period size: 35 Copynumber: 3.5 Consensus size: 35
27729172 CATGGCAAAG
*
27729182 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
27729217 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
27729252 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
**
27729292 TAAGAAATGTAGGTATGG
1 TGTGAAATGTAGGTATGG
27729310 CATTTCCCAT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
35 51 0.62
38 3 0.04
40 28 0.34
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:27729301 original size:75 final size:75
Alignment explanation
Indices: 27729182--27729352 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
27729172 CATGGCAAAG
** *
27729182 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
27729241 CCATACTGAGC
65 CCATACCGAGC
27729252 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
27729317 CATACCGAGT
66 CATACCGAGC
** *
27729327 TGAAAAATATAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
27729353 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:27729320 original size:35 final size:35
Alignment explanation
Indices: 27729185--27729350 Score: 158
Period size: 35 Copynumber: 4.6 Consensus size: 35
27729175 GGCAAAGTGT
* **
27729185 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
27729220 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
27729255 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
27729295 GAAATGTAGGTATGGCATTTCCCATACCGAGTTGAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
27729331 -AAATATAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
27729351 AATGAGGAAA
Statistics
Matches: 115, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
35 82 0.71
36 2 0.02
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:27730530 original size:30 final size:30
Alignment explanation
Indices: 27730494--27730562 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
27730484 ACACCTACAC
* *
27730494 GCTCGTGTCG-TTCA-CTCGTGTGACCCGCAA
1 GCTCGTG-CGATTCACCT-GTGTAACCCACAA
27730524 GCTCGTGCGATTCACCTGTGTAACCCACAA
1 GCTCGTGCGATTCACCTGTGTAACCCACAA
*
27730554 GCCCGTGCG
1 GCTCGTGCG
27730563 GTTTACACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 30 0.88
31 2 0.06
ACGTcount: A:0.16, C:0.35, G:0.26, T:0.23
Consensus pattern (30 bp):
GCTCGTGCGATTCACCTGTGTAACCCACAA
Found at i:27731578 original size:40 final size:40
Alignment explanation
Indices: 27731523--27731598 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
27731513 GGCCATGTAG
*
27731523 GGATAAAATCGACCCACCCAGCCTTACACACCAAGTATGA
1 GGATAAAATCGACCCACCCAGCCCTACACACCAAGTATGA
* *
27731563 GGATAAAATCGACCCATCTAGCCCTACACACCAAGT
1 GGATAAAATCGACCCACCCAGCCCTACACACCAAGT
27731599 GGTACAGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.37, C:0.33, G:0.14, T:0.16
Consensus pattern (40 bp):
GGATAAAATCGACCCACCCAGCCCTACACACCAAGTATGA
Found at i:27735836 original size:47 final size:47
Alignment explanation
Indices: 27735710--27735839 Score: 161
Period size: 47 Copynumber: 2.8 Consensus size: 47
27735700 ACAATCGATA
* * * *
27735710 AATACCTATACCATGGCTTGTAGTCAAATCAAAGTAACTTATCCCGG
1 AATACCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGG
* * * * * *
27735757 AGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCCTCTCTG
1 AATACCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGG
*
27735804 AATACTTATACCATGACCTGTAGTCAAATCAAGGTA
1 AATACCTATACCATGACCTGTAGTCAAATCAAGGTA
27735840 TCATTCGTAC
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (47 bp):
AATACCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGG
Found at i:27736561 original size:19 final size:19
Alignment explanation
Indices: 27736522--27736559 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
27736512 ACATGAATTC
27736522 ATCAATGAAAACTTTCAAA
1 ATCAATGAAAACTTTCAAA
*
27736541 ATCAAT-AATACTTTCAAA
1 ATCAATGAAAACTTTCAAA
27736559 A
1 A
27736560 ATTGAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (19 bp):
ATCAATGAAAACTTTCAAA
Found at i:27739253 original size:29 final size:29
Alignment explanation
Indices: 27739220--27739288 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
27739210 TGTGTGTACC
*
27739220 ATGTGAAAAGGGATATCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
27739249 ATGTGAAAAGGGATAGCTTCGGCTATCGA
1 ATGTGAAAAGGGATAGCTTCGGCTATCGA
*
27739278 ATATGAAAAGG
1 ATGTGAAAAGG
27739289 AAATGTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.25
Consensus pattern (29 bp):
ATGTGAAAAGGGATAGCTTCGGCTATCGA
Found at i:27742331 original size:11 final size:11
Alignment explanation
Indices: 27742315--27742342 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
27742305 TTGTTTTATA
27742315 TTCTTTCAACT
1 TTCTTTCAACT
27742326 TTCTTTCAACT
1 TTCTTTCAACT
27742337 TTCTTT
1 TTCTTT
27742343 ATTTTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (11 bp):
TTCTTTCAACT
Found at i:27743267 original size:30 final size:30
Alignment explanation
Indices: 27743233--27743291 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
27743223 AAGGAGAAGC
*
27743233 AAAAGAGAATGAAAAAAAAAGAAAAAAAAG
1 AAAAGAGAAAGAAAAAAAAAGAAAAAAAAG
** * *
27743263 AAAAGTTAAAGAACATAAAAGAAAAAAAA
1 AAAAGAGAAAGAAAAAAAAAGAAAAAAAA
27743292 TTAAATTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.07
Consensus pattern (30 bp):
AAAAGAGAAAGAAAAAAAAAGAAAAAAAAG
Found at i:27744722 original size:3 final size:3
Alignment explanation
Indices: 27744714--27744752 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
27744704 ACTAAATTTG
27744714 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27744753 TGGTAAACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27750972 original size:31 final size:31
Alignment explanation
Indices: 27750934--27750994 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
27750924 AAATGAAGAG
27750934 AGTGGGTGTAACATCCCAAAAATTATGTTAT
1 AGTGGGTGTAACATCCCAAAAATTATGTTAT
27750965 AGTGGGTGTAACATCCCAAAAATTATGTTA
1 AGTGGGTGTAACATCCCAAAAATTATGTTA
27750995 GAAGAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (31 bp):
AGTGGGTGTAACATCCCAAAAATTATGTTAT
Found at i:27752800 original size:7 final size:7
Alignment explanation
Indices: 27752788--27752816 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
27752778 GGTTACTCGA
27752788 CGACTTT
1 CGACTTT
27752795 CGACTTT
1 CGACTTT
27752802 CGACTTT
1 CGACTTT
27752809 CGACTTT
1 CGACTTT
27752816 C
1 C
27752817 CCCGATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (7 bp):
CGACTTT
Found at i:27754542 original size:12 final size:12
Alignment explanation
Indices: 27754522--27754560 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
27754512 CACACGGGCA
*
27754522 TGTGCTAGGCCG
1 TGTGATAGGCCG
*
27754534 TGTGATAGGCTG
1 TGTGATAGGCCG
27754546 TGTGATAGGCCG
1 TGTGATAGGCCG
27754558 TGT
1 TGT
27754561 AACCCATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.41, T:0.31
Consensus pattern (12 bp):
TGTGATAGGCCG
Found at i:27762184 original size:13 final size:13
Alignment explanation
Indices: 27762166--27762191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27762156 CTGTGCATTC
27762166 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
27762179 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
27762192 AACAAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:27763982 original size:30 final size:30
Alignment explanation
Indices: 27763948--27764006 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
27763938 CAGTTAATCG
27763948 AACGAATTCGGTTAATCGGTCGGTTAACCA
1 AACGAATTCGGTTAATCGGTCGGTTAACCA
*
27763978 AACGAATTCGGTTAATTGGTCGGTTAACC
1 AACGAATTCGGTTAATCGGTCGGTTAACC
27764007 GAATTAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (30 bp):
AACGAATTCGGTTAATCGGTCGGTTAACCA
Found at i:27764226 original size:18 final size:18
Alignment explanation
Indices: 27764203--27764240 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27764193 AATATAGATT
27764203 AACCCAAGTACCCAACCC
1 AACCCAAGTACCCAACCC
* *
27764221 AACCCAATTTCCCAACCC
1 AACCCAAGTACCCAACCC
27764239 AA
1 AA
27764241 TTATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.47, G:0.03, T:0.11
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:27764234 original size:13 final size:13
Alignment explanation
Indices: 27764218--27764242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27764208 AAGTACCCAA
27764218 CCCAACCCAATTT
1 CCCAACCCAATTT
27764231 CCCAACCCAATT
1 CCCAACCCAATT
27764243 ATAAAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (13 bp):
CCCAACCCAATTT
Found at i:27764305 original size:5 final size:6
Alignment explanation
Indices: 27764269--27764312 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
27764259 AATTAATAAG
*
27764269 TAAAAA TAAAAA TCTAAAAC TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA --TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
27764313 ACATATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 29 0.85
8 5 0.15
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:27764313 original size:20 final size:20
Alignment explanation
Indices: 27764269--27764306 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27764259 AATTAATAAG
**
27764269 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATAAAAAAC
27764289 TAAAAATAAAAATAAAAA
1 TAAAAATAAAAATAAAAA
27764307 TAAAAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAC
Found at i:27764346 original size:9 final size:9
Alignment explanation
Indices: 27764332--27764390 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
27764322 TTTATACAAA
27764332 TAATTCGGT
1 TAATTCGGT
27764341 TAATTCGGT
1 TAATTCGGT
* *
27764350 TAATTTGGG
1 TAATTCGGT
27764359 TAATTCAGG-
1 TAATTC-GGT
**
27764368 TAATTCAAT
1 TAATTCGGT
*
27764377 TAATTCTGT
1 TAATTCGGT
27764386 TAATT
1 TAATT
27764391 TTATACTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 39 0.95
10 2 0.05
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:27767971 original size:13 final size:13
Alignment explanation
Indices: 27767953--27767978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27767943 CTGTGCATTC
27767953 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
27767966 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
27767979 AACAAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:27768890 original size:22 final size:23
Alignment explanation
Indices: 27768847--27768891 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
27768837 ATGATGTGTT
* *
27768847 GGGTTGGACGGAGATGGTATGCA
1 GGGTTGGACGGAGATAGCATGCA
*
27768870 GGGTTGGA-TGAGATAGCATGCA
1 GGGTTGGACGGAGATAGCATGCA
27768892 TCCATGCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.24, C:0.09, G:0.44, T:0.22
Consensus pattern (23 bp):
GGGTTGGACGGAGATAGCATGCA
Found at i:27771832 original size:40 final size:39
Alignment explanation
Indices: 27771782--27771880 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
27771772 TTACGGTACC
* * *
27771782 ATTGGATGTGTAGGGTTGGATAGGTTGATTTTATCCCTAT
1 ATTGG-TGTGTAGGGTTGGATAGGTCGATTCTATCCCCAT
* * *
27771822 ACTTGGTGTGTAAGGCTGGGTAGGTCGATTCTATCCCCAT
1 A-TTGGTGTGTAGGGTTGGATAGGTCGATTCTATCCCCAT
*
27771862 A-TGGTGTGTTGGGTTGGAT
1 ATTGGTGTGTAGGGTTGGAT
27771881 GAATATAGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
38 14 0.29
40 30 0.62
41 4 0.08
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.38
Consensus pattern (39 bp):
ATTGGTGTGTAGGGTTGGATAGGTCGATTCTATCCCCAT
Found at i:27773775 original size:20 final size:20
Alignment explanation
Indices: 27773750--27773812 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
27773740 TAGATTTTAG
27773750 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
*
27773770 ATGCCAACTTGGATTTCTAG
1 ATGCCAACTTGGATTTCTAA
*
27773790 ATGCCAACCTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
27773810 ATG
1 ATG
27773813 GGATGAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGCCAACTTGGATTTCTAA
Found at i:27773846 original size:13 final size:14
Alignment explanation
Indices: 27773828--27773884 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
27773818 AAAATAGATT
27773828 TTTAATTAA-AAAA
1 TTTAATTAATAAAA
27773841 TTTAATTAATTAAAA
1 TTTAATTAA-TAAAA
27773856 TTT--TTAAACCTAAAA
1 TTTAATT-AA--TAAAA
27773871 TTTAATTAA-AAAA
1 TTTAATTAATAAAA
27773884 T
1 T
27773885 ATGTTCATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 16 0.43
14 2 0.05
15 15 0.41
16 2 0.05
17 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAATTAATAAAA
Found at i:27774100 original size:20 final size:20
Alignment explanation
Indices: 27774075--27774137 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
27774065 TAGATTTTAG
27774075 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
27774095 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
27774115 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
27774135 ATG
1 ATG
27774138 GGATGAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGCCAACTTGGATTTCTAA
Found at i:27774171 original size:13 final size:14
Alignment explanation
Indices: 27774153--27774209 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
27774143 AAAATAGATT
27774153 TTTAATTAA-AAAA
1 TTTAATTAATAAAA
27774166 TTTAATTAATTAAAA
1 TTTAATTAA-TAAAA
27774181 TTT--TTAAACCTAAAA
1 TTTAATT-AA--TAAAA
27774196 TTTAATTAA-AAAA
1 TTTAATTAATAAAA
27774209 T
1 T
27774210 ATGTTCATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 16 0.43
14 2 0.05
15 15 0.41
16 2 0.05
17 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAATTAATAAAA
Found at i:27774201 original size:325 final size:325
Alignment explanation
Indices: 27773611--27774260 Score: 1264
Period size: 325 Copynumber: 2.0 Consensus size: 325
27773601 TTGCTTCGGG
27773611 TTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGATACTATTTTGTTACG
1 TTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGATACTATTTTGTTACG
27773676 AAGTGATCACTCTACTGTTAAGTTCTGTTATCTTTCTAACGGTAATCCTACGTGGCAGTCCAACT
66 AAGTGATCACTCTACTGTTAAGTTCTGTTATCTTTCTAACGGTAATCCTACGTGGCAGTCCAACT
*
27773741 AGATTTTAGATGCCAACTTGGATTTCTAAATGCCAACTTGGATTTCTAGATGCCAACCTGGATTT
131 AGATTTTAGATGCCAACTTGGATTTCTAAATGCCAACTTGGATTTCTAAATGCCAACCTGGATTT
27773806 CTAAATGGGATGAAAATAGATTTTTAATTAAAAAATTTAATTAATTAAAATTTTTAAACCTAAAA
196 CTAAATGGGATGAAAATAGATTTTTAATTAAAAAATTTAATTAATTAAAATTTTTAAACCTAAAA
* *
27773871 TTTAATTAAAAAATATGTTCATCTCTTCTTTTTAATTTTTCTTCAGTTTCTTCTTTTTTTCAATA
261 TTTAATTAAAAAATATGTTCATCTCTTCTTCTTAATTATTCTTCAGTTTCTTCTTTTTTTCAATA
27773936 TTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGATACTATTTTGTTACG
1 TTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGATACTATTTTGTTACG
27774001 AAGTGATCACTCTACTGTTAAGTTCTGTTATCTTTCTAACGGTAATCCTACGTGGCAGTCCAACT
66 AAGTGATCACTCTACTGTTAAGTTCTGTTATCTTTCTAACGGTAATCCTACGTGGCAGTCCAACT
*
27774066 AGATTTTAGATGCCAACTTGGATTTCTAAATGCCAACTTGGATTTCTAAATGCCAACTTGGATTT
131 AGATTTTAGATGCCAACTTGGATTTCTAAATGCCAACTTGGATTTCTAAATGCCAACCTGGATTT
27774131 CTAAATGGGATGAAAATAGATTTTTAATTAAAAAATTTAATTAATTAAAATTTTTAAACCTAAAA
196 CTAAATGGGATGAAAATAGATTTTTAATTAAAAAATTTAATTAATTAAAATTTTTAAACCTAAAA
27774196 TTTAATTAAAAAATATGTTCATCTCTTCTTCTTAATTATTCTTCAGTTTCTTCTTTTTTTCAATA
261 TTTAATTAAAAAATATGTTCATCTCTTCTTCTTAATTATTCTTCAGTTTCTTCTTTTTTTCAATA
27774261 GTTTTTTTTT
Statistics
Matches: 321, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
325 321 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (325 bp):
TTACATTTTAGTCACTTATGTTTGAAATGTTACGTTTTAGTCACTTATGATACTATTTTGTTACG
AAGTGATCACTCTACTGTTAAGTTCTGTTATCTTTCTAACGGTAATCCTACGTGGCAGTCCAACT
AGATTTTAGATGCCAACTTGGATTTCTAAATGCCAACTTGGATTTCTAAATGCCAACCTGGATTT
CTAAATGGGATGAAAATAGATTTTTAATTAAAAAATTTAATTAATTAAAATTTTTAAACCTAAAA
TTTAATTAAAAAATATGTTCATCTCTTCTTCTTAATTATTCTTCAGTTTCTTCTTTTTTTCAATA
Found at i:27775871 original size:21 final size:20
Alignment explanation
Indices: 27775838--27775881 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
27775828 AAAATTAATT
* *
27775838 AAAAATTCTAAAAGTAAAAA
1 AAAAATTATAAAAGCAAAAA
27775858 AAAAATTATCAAAAGCATAAAA
1 AAAAATTAT-AAAAGCA-AAAA
27775880 AA
1 AA
27775882 GTTATAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAATTATAAAAGCAAAAA
Found at i:27778044 original size:8 final size:8
Alignment explanation
Indices: 27778033--27778065 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
27778023 TTTAAAATGC
27778033 AAAAA-AA
1 AAAAAGAA
27778040 AAAAAGAA
1 AAAAAGAA
27778048 AAAAAGAA
1 AAAAAGAA
27778056 AAAAGAGAA
1 AAAA-AGAA
27778065 A
1 A
27778066 GTAATAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 5 0.21
8 14 0.58
9 5 0.21
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:27779195 original size:18 final size:18
Alignment explanation
Indices: 27779164--27779198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27779154 ATAACTCAAT
**
27779164 TATTTTATTTTATTTTTA
1 TATTTTATAATATTTTTA
27779182 TATTTTATAATATTTTT
1 TATTTTATAATATTTTT
27779199 TTTATCTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTATAATATTTTTA
Found at i:27782029 original size:23 final size:23
Alignment explanation
Indices: 27782002--27782045 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
27781992 TACAAAAAAT
*
27782002 TTTAAAACAAGTAAATATAAAGG
1 TTTAAAACAAGTAAAAATAAAGG
* *
27782025 TTTAAAATAGGTAAAAATAAA
1 TTTAAAACAAGTAAAAATAAA
27782046 TAATATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.27
Consensus pattern (23 bp):
TTTAAAACAAGTAAAAATAAAGG
Found at i:27783393 original size:44 final size:43
Alignment explanation
Indices: 27783301--27783391 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
27783291 CAACTTTCCG
*
27783301 AAAATTTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
1 AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
27783344 AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
1 AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
27783387 AAAAA
1 AAAAA
27783392 ATAAAATACC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.22, C:0.29, G:0.04, T:0.45
Consensus pattern (43 bp):
AAAAATTCCTTTGCACTAGATTCCTCCCTCTTTTTCTCCTTTT
Found at i:27783478 original size:4 final size:5
Alignment explanation
Indices: 27783450--27783495 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
27783440 CTAATTTAAT
*
27783450 AATAA AATAA AATAA AATAA AAT-A AATAAA AACAAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AA-TAA AATAA AATAA
27783496 TATCTTCCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
5 25 0.69
6 7 0.19
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:27785794 original size:30 final size:29
Alignment explanation
Indices: 27785742--27785798 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
27785732 CCACATCTTC
*
27785742 ACTCAATCGATTACTATCTTTAAATTAAAA
1 ACTCAATCGATTACAATCTTT-AATTAAAA
*
27785772 ACTCAATCGATTGCAAAT-TTTAATTAA
1 ACTCAATCGATTAC-AATCTTTAATTAA
27785799 GAGTTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 16 0.67
31 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (29 bp):
ACTCAATCGATTACAATCTTTAATTAAAA
Found at i:27786718 original size:43 final size:43
Alignment explanation
Indices: 27786669--27786757 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
27786659 TTACCCAAAA
27786669 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
1 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
27786712 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
1 TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
27786755 TAC
1 TAC
27786758 TTTTATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (43 bp):
TACAAACATTAATATTATCCCACCAATTTGAATGTCGAGTTCT
Found at i:27794674 original size:22 final size:22
Alignment explanation
Indices: 27794649--27794702 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
27794639 ATCCTAGTCT
*
27794649 CGTCGTGACGACCATCGCTTGA
1 CGTCGTGACGACCATCACTTGA
* * * *
27794671 CGTCGCGATGATCATCATTTGA
1 CGTCGTGACGACCATCACTTGA
*
27794693 CATCGTGACG
1 CGTCGTGACG
27794703 TGGACTTTGT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CGTCGTGACGACCATCACTTGA
Found at i:27795106 original size:22 final size:24
Alignment explanation
Indices: 27795081--27795124 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
27795071 GGCACGTTAT
27795081 TTTTTGTTC-TGT-TTCTTCTTGG
1 TTTTTGTTCTTGTGTTCTTCTTGG
27795103 TTTTTGTTCTTGTGTTCTTCTT
1 TTTTTGTTCTTGTGTTCTTCTT
27795125 TTTGCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (24 bp):
TTTTTGTTCTTGTGTTCTTCTTGG
Found at i:27799512 original size:20 final size:19
Alignment explanation
Indices: 27799487--27799536 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
27799477 GATATACATT
*
27799487 ATTAATTCATTAATCATTTA
1 ATTAATTAATTAATC-TTTA
27799507 ATTAATCTAATTAATCTTTA
1 ATTAAT-TAATTAATCTTTA
27799527 ATTAATTAAT
1 ATTAATTAAT
27799537 CTTAATCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAATTAATTAATCTTTA
Found at i:27799534 original size:15 final size:16
Alignment explanation
Indices: 27799508--27799544 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
27799498 AATCATTTAA
27799508 TTAATCTAATTAATCT
1 TTAATCTAATTAATCT
27799524 TTAAT-TAATTAATC-
1 TTAATCTAATTAATCT
27799538 TTAATCT
1 TTAATCT
27799545 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATCTAATTAATCT
Found at i:27799949 original size:20 final size:20
Alignment explanation
Indices: 27799887--27799950 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
27799877 ATGAGCATTT
*
27799887 TTAAATT-ATGTTTAATATATA
1 TTAAATTAATCTTTAAT-TA-A
* *
27799908 TT-AATTAATTCATTAA-TCA
1 TTAAATTAA-TCTTTAATTAA
27799927 TTAAATTAATCTTTAATTAA
1 TTAAATTAATCTTTAATTAA
27799947 TTAA
1 TTAA
27799951 CCTTAATCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
19 9 0.26
20 17 0.50
21 3 0.09
22 5 0.15
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAAATTAATCTTTAATTAA
Found at i:27800306 original size:16 final size:15
Alignment explanation
Indices: 27800285--27800329 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
27800275 ATTAAATTTT
27800285 ATTAATTGAGATTAAG
1 ATTAATT-AGATTAAG
27800301 ATTAATTA-ATTAAAG
1 ATTAATTAGATT-AAG
*
27800316 ATTTATTAGATTAA
1 ATTAATTAGATTAA
27800330 TTAAATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 13 0.50
16 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (15 bp):
ATTAATTAGATTAAG
Found at i:27800328 original size:20 final size:19
Alignment explanation
Indices: 27800301--27800355 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
27800291 TGAGATTAAG
*
27800301 ATTAATTAATTAAAGATTT
1 ATTAATTAATTAAAGATTA
27800320 ATTAGATTAATTAAATGATTA
1 ATTA-ATTAATTAAA-GATTA
*
27800341 ATGAATTAATTAAAG
1 ATTAATTAATTAAAG
27800356 TATATACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 20 0.62
21 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (19 bp):
ATTAATTAATTAAAGATTA
Found at i:27804449 original size:71 final size:71
Alignment explanation
Indices: 27804367--27804512 Score: 238
Period size: 71 Copynumber: 2.1 Consensus size: 71
27804357 CCATCAGAGT
* * **
27804367 ATCGATAAAAGTGCAGGGGATGTTGAACTTTGGCTACTGGCTTGACTTGTTTCAGTAGAAGTCCT
1 ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
27804432 CAAGGA
66 CAAGGA
*
27804438 ATCGATAAAAGTACAGGAGATGTTGAACTTTTGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
1 ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
*
27804503 CAAGGT
66 CAAGGA
27804509 ATCG
1 ATCG
27804513 GTAGCACTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (71 bp):
ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
CAAGGA
Found at i:27806712 original size:22 final size:20
Alignment explanation
Indices: 27806687--27806749 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
27806677 TCCAAACAAT
27806687 AACAACAAAATAGTGAAATGAC
1 AACAACAAAATAGTGAAA--AC
* *
27806709 AACAA-ACAAT-GAGAAAAC
1 AACAACAAAATAGTGAAAAC
*
27806727 AACAGCAAAATAGTGGAAAAC
1 AACAACAAAATAGT-GAAAAC
27806748 AA
1 AA
27806750 TAGTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 6 0.18
21 12 0.36
22 5 0.15
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (20 bp):
AACAACAAAATAGTGAAAAC
Found at i:27807192 original size:24 final size:24
Alignment explanation
Indices: 27807164--27807220 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
27807154 ATATATTTAA
*
27807164 ATAATATTTAAATTTGTTAATATT
1 ATAATATTTAAATTAGTTAATATT
27807188 ATAATATTTAAATTAGTTAATATT
1 ATAATATTTAAATTAGTTAATATT
*
27807212 ATTATATTT
1 ATAATATTT
27807221 TAGTAAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
ATAATATTTAAATTAGTTAATATT
Found at i:27812745 original size:16 final size:16
Alignment explanation
Indices: 27812696--27812748 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
27812686 AAAAATTATG
*
27812696 TTTTCCATCATTCTAA
1 TTTTCCATCCTTCTAA
*
27812712 TTTTCTATCCCTT-TAA
1 TTTTCCAT-CCTTCTAA
*
27812728 TTTTCCATCCTTCCAA
1 TTTTCCATCCTTCTAA
27812744 TTTTC
1 TTTTC
27812749 TTTCCACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.13
16 24 0.77
17 3 0.10
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTCCATCCTTCTAA
Found at i:27814418 original size:17 final size:17
Alignment explanation
Indices: 27814396--27814432 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
27814386 GCACATGGCC
27814396 GTGTGG-ACACAGCCCAT
1 GTGTGGCACAC-GCCCAT
27814413 GTGTGGCACACGCCCAT
1 GTGTGGCACACGCCCAT
27814430 GTG
1 GTG
27814433 GCCATTCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.19
Consensus pattern (17 bp):
GTGTGGCACACGCCCAT
Found at i:27816663 original size:43 final size:39
Alignment explanation
Indices: 27816586--27816688 Score: 102
Period size: 43 Copynumber: 2.5 Consensus size: 39
27816576 TTTTATATTC
*
27816586 TTTAGAATTTTTTTAATAAATTATATTTTTTTAAAATATCAAT
1 TTTAGAATTTTTTT-AT-AATTATATTTTATTAAAA-AT-AAT
*
27816629 TTTAGAATTTTTTTATAATTAT-TTTGAATATTAAAAATTAT
1 TTTAGAATTTTTTTATAATTATATTT---TATTAAAAATAAT
*
27816670 TTT-GAATTTTTTTGTAATT
1 TTTAGAATTTTTTTATAATT
27816689 TTTGTTGAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
40 18 0.33
41 11 0.20
42 4 0.07
43 21 0.39
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (39 bp):
TTTAGAATTTTTTTATAATTATATTTTATTAAAAATAAT
Found at i:27819961 original size:14 final size:13
Alignment explanation
Indices: 27819942--27819980 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
27819932 ATTTAATGTT
27819942 TAATTATATTAGGA
1 TAATTAT-TTAGGA
*
27819956 TAATTATTAAGGA
1 TAATTATTTAGGA
*
27819969 TTATTATTTAGG
1 TAATTATTTAGG
27819981 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TAATTATTTAGGA
Found at i:27820258 original size:39 final size:39
Alignment explanation
Indices: 27820214--27820291 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
27820204 ATTTATTTGT
27820214 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
1 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
27820253 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
1 TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
27820292 GAAGGTTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (39 bp):
TTTTCCCCAAAAATCATGAGCCACTAAATCTATCTAGCC
Found at i:27825634 original size:20 final size:20
Alignment explanation
Indices: 27825595--27825634 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27825585 ATTTATTTTC
* *
27825595 ATTTATTTTTAATTATCTTT
1 ATTTATTTGTAATTACCTTT
*
27825615 ATTTATTTGTATTTACCTTT
1 ATTTATTTGTAATTACCTTT
27825635 TAGAATTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTATTTGTAATTACCTTT
Found at i:27829334 original size:22 final size:20
Alignment explanation
Indices: 27829309--27829351 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
27829299 AAACACAATA
27829309 ACAAGTCAATATTCTAATATTC
1 ACAA-TCAA-ATTCTAATATTC
* *
27829331 ACAATCAAATTTTATTATTC
1 ACAATCAAATTCTAATATTC
27829351 A
1 A
27829352 TTCCTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (20 bp):
ACAATCAAATTCTAATATTC
Found at i:27830431 original size:18 final size:18
Alignment explanation
Indices: 27830405--27830442 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27830395 ATTTTTATAC
*
27830405 ATATTTTTTAATCTTATT
1 ATATATTTTAATCTTATT
*
27830423 ATATATTTTAATTTTATT
1 ATATATTTTAATCTTATT
27830441 AT
1 AT
27830443 GCACGCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATATTTTAATCTTATT
Found at i:27835826 original size:13 final size:13
Alignment explanation
Indices: 27835808--27835840 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
27835798 TTTAATATTC
27835808 AAAATT-TTTTATA
1 AAAATTATTTT-TA
27835821 AAAATTATTTTTA
1 AAAATTATTTTTA
27835834 AAAATTA
1 AAAATTA
27835841 AAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTATTTTTA
Found at i:27836371 original size:12 final size:12
Alignment explanation
Indices: 27836354--27836387 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
27836344 CGACCAGCCC
27836354 ATATTAATTTTT
1 ATATTAATTTTT
*
27836366 ATATTATTTTTT
1 ATATTAATTTTT
27836378 ATA-TAATTTT
1 ATATTAATTTT
27836388 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:27836545 original size:30 final size:30
Alignment explanation
Indices: 27836509--27836569 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
27836499 CAATTTAACA
*
27836509 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
*
27836539 AGCAAATGCCTTTAAAATAATAAAAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
27836569 A
1 A
27836570 ACAATAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.25
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:27837314 original size:7 final size:7
Alignment explanation
Indices: 27837302--27837329 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
27837292 TAATGTTAGA
27837302 CTGCCTC
1 CTGCCTC
27837309 CTGCCTC
1 CTGCCTC
27837316 CTGCCTC
1 CTGCCTC
27837323 CTGCCTC
1 CTGCCTC
27837330 GGAGTCTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.14, T:0.29
Consensus pattern (7 bp):
CTGCCTC
Found at i:27844254 original size:36 final size:36
Alignment explanation
Indices: 27844209--27844277 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
27844199 ATATTAATAT
27844209 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAATTAA
1 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAATTAA
27844245 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAAT
1 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAAT
27844278 CCAAAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (36 bp):
ATTTTTAAAAAATTTGAAAAGTCAAATCAAAATTAA
Found at i:27844600 original size:29 final size:29
Alignment explanation
Indices: 27844558--27844616 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
27844548 ACTAATGCAA
27844558 AGAATGAACTATGTTATGTATATTTTCCT
1 AGAATGAACTATGTTATGTATATTTTCCT
27844587 AGAATGAACTATGTTATGTATATTTTCCT
1 AGAATGAACTATGTTATGTATATTTTCCT
27844616 A
1 A
27844617 CTAACTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (29 bp):
AGAATGAACTATGTTATGTATATTTTCCT
Found at i:27849278 original size:10 final size:10
Alignment explanation
Indices: 27849265--27849306 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
27849255 AAAATTATAG
27849265 AATTTCTTTT
1 AATTTCTTTT
*
27849275 AATTCCTTTT
1 AATTTCTTTT
* *
27849285 ATTTTATTTT
1 AATTTCTTTT
27849295 -ATTTCTTTT
1 AATTTCTTTT
27849304 AAT
1 AAT
27849307 ATTATCCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTCTTTT
Found at i:27850143 original size:38 final size:36
Alignment explanation
Indices: 27850101--27850171 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 36
27850091 TTTCACAATG
*
27850101 AGTTTT-AAATCCATCATTCTTTTTCATTCAATAATTTA
1 AGTTTTGAAAT-CATCA-TCATTTT-ATTCAATAATTTA
27850139 AGTTTTGAAATCATCATCATTTTATTCAATAAT
1 AGTTTTGAAATCATCATCATTTTATTCAATAAT
27850172 CTACATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 10 0.32
37 6 0.19
38 11 0.35
39 4 0.13
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (36 bp):
AGTTTTGAAATCATCATCATTTTATTCAATAATTTA
Found at i:27855798 original size:15 final size:16
Alignment explanation
Indices: 27855780--27855826 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
27855770 TGATAATGTA
27855780 AATAAC-AATAATACT
1 AATAACGAATAATACT
* *
27855795 AAT-ACTAATAATAAT
1 AATAACGAATAATACT
27855810 AATAACGAATAAT-CT
1 AATAACGAATAATACT
27855825 AA
1 AA
27855827 ATTTTCGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 17 0.63
16 8 0.30
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (16 bp):
AATAACGAATAATACT
Found at i:27856030 original size:3 final size:3
Alignment explanation
Indices: 27856022--27856049 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27856012 TAAAATGGTT
27856022 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
27856050 TGTACAAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:27857210 original size:11 final size:11
Alignment explanation
Indices: 27857149--27857220 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
27857139 CTTTTTAAAC
*
27857149 ATTATATATAT
1 ATTATGTATAT
27857160 ATT-T-T-TAT
1 ATTATGTATAT
*
27857168 ATTATGTCTAT
1 ATTATGTATAT
*
27857179 ATT-T-TATGT
1 ATTATGTATAT
* *
27857188 ATTTTTTA-AT
1 ATTATGTATAT
27857198 ATTATGTATAT
1 ATTATGTATAT
27857209 ATTATGTATAT
1 ATTATGTATAT
27857220 A
1 A
27857221 CTTTTAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
8 6 0.12
9 8 0.16
10 11 0.22
11 25 0.50
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (11 bp):
ATTATGTATAT
Found at i:27857248 original size:23 final size:22
Alignment explanation
Indices: 27857205--27857254 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
27857195 AATATTATGT
*
27857205 ATATATTATGTATATACTTTTA
1 ATATATTATATATATACTTTTA
* *
27857227 ATATCATTATATATTTATTTTTA
1 ATAT-ATTATATATATACTTTTA
27857250 ATATA
1 ATATA
27857255 AACGTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTATATATATACTTTTA
Found at i:27857671 original size:13 final size:13
Alignment explanation
Indices: 27857653--27857677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27857643 ATTATTATTA
27857653 TATATATTTCTTT
1 TATATATTTCTTT
27857666 TATATATTTCTT
1 TATATATTTCTT
27857678 ATTACTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTCTTT
Found at i:27861570 original size:9 final size:9
Alignment explanation
Indices: 27861554--27861612 Score: 93
Period size: 9 Copynumber: 6.7 Consensus size: 9
27861544 ATCAACGCTT
27861554 TTGCATTCA
1 TTGCATTCA
*
27861563 TCGCATTCA
1 TTGCATTCA
27861572 TTGCATTCA
1 TTGCATTCA
*
27861581 TCGCATTCA
1 TTGCATTCA
27861590 TTGCATTCA
1 TTGCATTCA
27861599 TTGCATTCA
1 TTGCATTCA
27861608 -TGCAT
1 TTGCAT
27861613 CAGCATTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
8 5 0.11
9 41 0.89
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (9 bp):
TTGCATTCA
Done.