Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 25 of 195
Found at i:5767985 original size:19 final size:20
Alignment explanation
Indices: 5767942--5767986 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5767932 TAAGTTTAAT
* *
5767942 AATATTATTTTTTAATGAGTA
1 AATATTAATTTTTAA-GAATA
5767963 AATATTAATTTTTAA-AATA
1 AATATTAATTTTTAAGAATA
5767982 AATAT
1 AATAT
5767987 ATAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AATATTAATTTTTAAGAATA
Found at i:5768010 original size:17 final size:19
Alignment explanation
Indices: 5767986--5768040 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
5767976 AAAATAAATA
5767986 TATAAAAATTAATATTT-T
1 TATAAAAATTAATATTTAT
*
5768004 T-TAAAAATT-TTATTTAT
1 TATAAAAATTAATATTTAT
5768021 TAATAAAATATTAATATTTA
1 T-ATAAAA-ATTAATATTTA
5768041 ACTAACTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 5 0.17
17 10 0.33
18 1 0.03
19 5 0.17
20 3 0.10
21 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATAAAAATTAATATTTAT
Found at i:5770633 original size:2 final size:2
Alignment explanation
Indices: 5770626--5770652 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5770616 ATTCAAGTTT
5770626 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5770653 TTTATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5771989 original size:19 final size:19
Alignment explanation
Indices: 5771965--5772026 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 19
5771955 GTGAATTTTT
*
5771965 TTTAATAATTTAATAAAAA
1 TTTAATAAATTAATAAAAA
** *
5771984 TTTAATAAAGAAATATAAA
1 TTTAATAAATTAATAAAAA
*
5772003 -TTGATAAATTAAT-AAAA
1 TTTAATAAATTAATAAAAA
5772020 TTTAATA
1 TTTAATA
5772027 TGAAAATTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
17 3 0.09
18 15 0.45
19 15 0.45
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TTTAATAAATTAATAAAAA
Found at i:5773800 original size:2 final size:2
Alignment explanation
Indices: 5773793--5773817 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5773783 CAGATTTGTA
5773793 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5773818 ATTCTGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5774429 original size:11 final size:11
Alignment explanation
Indices: 5774413--5774452 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
5774403 TCTCATAAGA
5774413 GATTTGTTTAG
1 GATTTGTTTAG
5774424 GATTTG-TTAG
1 GATTTGTTTAG
*
5774434 AGATTTGTTTGG
1 -GATTTGTTTAG
5774446 GATTTGT
1 GATTTGT
5774453 CAGATATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 4 0.15
11 19 0.73
12 3 0.12
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (11 bp):
GATTTGTTTAG
Found at i:5774435 original size:22 final size:22
Alignment explanation
Indices: 5774410--5774452 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5774400 AAATCTCATA
5774410 AGAGATTTGTTTAGGATTTGTT
1 AGAGATTTGTTTAGGATTTGTT
*
5774432 AGAGATTTGTTTGGGATTTGT
1 AGAGATTTGTTTAGGATTTGT
5774453 CAGATATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTAGGATTTGTT
Found at i:5774542 original size:52 final size:51
Alignment explanation
Indices: 5774476--5774632 Score: 172
Period size: 52 Copynumber: 3.0 Consensus size: 51
5774466 TGGACAAAAA
* * * * *
5774476 GACTTGTAAAAGAAGAATTCTAAGAGAAAGATAATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTTTAAGAGGAA-ATAATTCTTAATAGGCAAGTTT
* *
5774528 GACTTGCAAGAGAAGAATTTTAAAAGGAAATAGATTCTTAATAGGCAAATTT
1 GACTTGCAAGAGAAGAATTTTAAGAGGAAATA-ATTCTTAATAGGCAAGTTT
* * * *
5774580 GATTTAC-AGAAGAAGAATTTTAGGAGGAAATGAATTCTTAATGGGCAAGTTT
1 GACTTGCAAG-AGAAGAATTTTAAGAGGAAAT-AATTCTTAATAGGCAAGTTT
5774632 G
1 G
5774633 TATATTTATA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 5 0.06
52 83 0.93
53 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (51 bp):
GACTTGCAAGAGAAGAATTTTAAGAGGAAATAATTCTTAATAGGCAAGTTT
Found at i:5774877 original size:76 final size:76
Alignment explanation
Indices: 5774745--5774895 Score: 248
Period size: 76 Copynumber: 2.0 Consensus size: 76
5774735 GCTCTATGTC
* * * * *
5774745 TTATGGGTGTGTATGTTTGTTTGTGAATGGATTAGAGGAGACTGAGAGGGTTCACATAAGTATGA
1 TTATGGGTGTATATGTTTATTTGTGAATGGATTAGAGGAGACTGAAAAGGTCCACATAAGTATGA
5774810 TATATGGGAGT
66 TATATGGGAGT
*
5774821 TTATGGGTGTATATGTTTATTTGTGAATGGATTAGAGGAGACTGAAAAGGTCCACATAGGTATGA
1 TTATGGGTGTATATGTTTATTTGTGAATGGATTAGAGGAGACTGAAAAGGTCCACATAAGTATGA
5774886 TATATGGGAG
66 TATATGGGAG
5774896 CATATGAGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.28, C:0.05, G:0.32, T:0.34
Consensus pattern (76 bp):
TTATGGGTGTATATGTTTATTTGTGAATGGATTAGAGGAGACTGAAAAGGTCCACATAAGTATGA
TATATGGGAGT
Found at i:5776745 original size:72 final size:72
Alignment explanation
Indices: 5776628--5776773 Score: 274
Period size: 72 Copynumber: 2.0 Consensus size: 72
5776618 TTTGGTACAA
5776628 GTCTATAATTGTTTCATAAAGAGTCCCAAAATATGAGCTGTCATAAAAAGAAAAAACAAAAGTAC
1 GTCTATAATTGTTTCATAAAGAGTCCCAAAATATGAGCTGTCATAAAAAGAAAAAACAAAAGTAC
5776693 GTTCGTT
66 GTTCGTT
* *
5776700 GTCTATGATTGTTTCATAAAGAGTCCCAAAATATGGGCTGTCATAAAAAGAAAAAACAAAAGTAC
1 GTCTATAATTGTTTCATAAAGAGTCCCAAAATATGAGCTGTCATAAAAAGAAAAAACAAAAGTAC
5776765 GTTCGTT
66 GTTCGTT
5776772 GT
1 GT
5776774 AACAACAATG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (72 bp):
GTCTATAATTGTTTCATAAAGAGTCCCAAAATATGAGCTGTCATAAAAAGAAAAAACAAAAGTAC
GTTCGTT
Found at i:5777660 original size:7 final size:7
Alignment explanation
Indices: 5777648--5777676 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5777638 AAATGGGGAT
5777648 GGAGAAG
1 GGAGAAG
5777655 GGAGAAG
1 GGAGAAG
5777662 GGAGAAG
1 GGAGAAG
5777669 GGAGAAG
1 GGAGAAG
5777676 G
1 G
5777677 TGGGGGAACT
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:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (7 bp):
GGAGAAG
Found at i:5778785 original size:9 final size:9
Alignment explanation
Indices: 5778768--5778825 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
5778758 TTGACTTTTC
*
5778768 TTATATCTG
1 TTATTTCTG
5778777 TTATTTCTG
1 TTATTTCTG
*
5778786 TTATAGTCTG
1 TTAT-TTCTG
5778796 TTA-TTCTG
1 TTATTTCTG
*
5778804 CTATTTCTG
1 TTATTTCTG
*
5778813 TTAGTTTCCG
1 TTA-TTTCTG
5778823 TTA
1 TTA
5778826 CAGAGGCAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 6 0.15
9 19 0.47
10 15 0.38
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (9 bp):
TTATTTCTG
Found at i:5778802 original size:18 final size:18
Alignment explanation
Indices: 5778768--5778825 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
5778758 TTGACTTTTC
5778768 TTATATCTGTTATTTCTG
1 TTATATCTGTTATTTCTG
5778786 TTATAGTCTGTTA-TTCTG
1 TTATA-TCTGTTATTTCTG
* * *
5778804 CTATTTCTGTTAGTTTCCG
1 TTATATCTGTTA-TTTCTG
5778823 TTA
1 TTA
5778826 CAGAGGCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 7 0.21
18 13 0.39
19 13 0.39
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (18 bp):
TTATATCTGTTATTTCTG
Found at i:5783423 original size:2 final size:2
Alignment explanation
Indices: 5783416--5783451 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5783406 TAGCAAAATT
5783416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5783452 GCTTCATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5784394 original size:10 final size:9
Alignment explanation
Indices: 5784371--5784395 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5784361 ATATCCCTCA
5784371 CAAAAAATC
1 CAAAAAATC
5784380 CAAAAAATC
1 CAAAAAATC
5784389 CAAAAAA
1 CAAAAAA
5784396 GTTTTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.20, G:0.00, T:0.08
Consensus pattern (9 bp):
CAAAAAATC
Found at i:5789802 original size:3 final size:3
Alignment explanation
Indices: 5789794--5789819 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5789784 ATCCAATATC
5789794 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5789820 AATTTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5790135 original size:18 final size:19
Alignment explanation
Indices: 5790114--5790153 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5790104 TATTTCAAAC
5790114 AAAATA-TTGATTTATGT-T
1 AAAATATTTG-TTTATGTAT
5790132 AAAATATTTGTTTATGTAT
1 AAAATATTTGTTTATGTAT
5790151 AAA
1 AAA
5790154 TTAAAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
AAAATATTTGTTTATGTAT
Found at i:5792260 original size:2 final size:2
Alignment explanation
Indices: 5792247--5792296 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
5792237 TTCAACTCAT
* *
5792247 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5792289 TA CA TA TA
1 TA TA TA TA
5792297 AAGTGTCCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5793794 original size:11 final size:11
Alignment explanation
Indices: 5793766--5793797 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
5793756 TATTGGAGAG
5793766 GAAGGGTATTA
1 GAAGGGTATTA
5793777 G-AGGGTATTA
1 GAAGGGTATTA
5793787 GAAGGGTATTA
1 GAAGGGTATTA
5793798 TTGTGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (11 bp):
GAAGGGTATTA
Found at i:5798339 original size:26 final size:27
Alignment explanation
Indices: 5798302--5798361 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
5798292 GAGATTGAAA
5798302 ATAATATAGAGA-TAAAATTAATTATT
1 ATAATATAGAGATTAAAATTAATTATT
5798328 ATAATGAT-GAGATTAAAATTAATTA-T
1 ATAAT-ATAGAGATTAAAATTAATTATT
*
5798354 AAAATATA
1 ATAATATA
5798362 TATTTAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 14 0.47
27 14 0.47
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (27 bp):
ATAATATAGAGATTAAAATTAATTATT
Found at i:5799998 original size:68 final size:69
Alignment explanation
Indices: 5799889--5800017 Score: 224
Period size: 68 Copynumber: 1.9 Consensus size: 69
5799879 TTTTTTAGAA
* * *
5799889 ATCAAGAGATCACTAGACAGTCCGATATTCGGAGAAATTCATGATAAAAAAAAAA-AAAAATAGA
1 ATCAAGAGATCACTAGACAGCCCAATATTCGGAGAAATTCATGAAAAAAAAAAAAGAAAAATAGA
5799953 AGAC
66 AGAC
5799957 ATCAAGAGATCACTAGACAGCCCAATATTCGGAGAAATTCATGAAAAAAAAAAAAGAAAAA
1 ATCAAGAGATCACTAGACAGCCCAATATTCGGAGAAATTCATGAAAAAAAAAAAAGAAAAA
5800018 AAAAAGGTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
68 52 0.91
69 5 0.09
ACGTcount: A:0.54, C:0.14, G:0.16, T:0.16
Consensus pattern (69 bp):
ATCAAGAGATCACTAGACAGCCCAATATTCGGAGAAATTCATGAAAAAAAAAAAAGAAAAATAGA
AGAC
Found at i:5804224 original size:2 final size:2
Alignment explanation
Indices: 5804217--5804265 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5804207 ATAAACCAAA
5804217 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5804259 AG AG AG A
1 AG AG AG A
5804266 ATGGAAAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5806272 original size:19 final size:18
Alignment explanation
Indices: 5806244--5806300 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
5806234 ATATATATAT
*
5806244 ATTTTTTATTATTTATTTA
1 ATTTTATATT-TTTATTTA
*
5806263 ATTTTATATTTTTATATA
1 ATTTTATATTTTTATTTA
* *
5806281 TTTTTTATATTTATATTTA
1 -ATTTTATATTTTTATTTA
5806300 A
1 A
5806301 AAAATAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTATATTTTTATTTA
Found at i:5806283 original size:17 final size:17
Alignment explanation
Indices: 5806239--5806296 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
5806229 ATCCAATATA
5806239 TATATATTTTTTATTATT
1 TATATATTTTTTATT-TT
* *
5806257 TATTTAATTTTATATTTT
1 TATAT-ATTTTTTATTTT
*
5806275 TATATATTTTTTATATT
1 TATATATTTTTTATTTT
5806292 TATAT
1 TATAT
5806297 TTAAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 15 0.44
18 10 0.29
19 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATATTTTTTATTTT
Found at i:5806287 original size:25 final size:26
Alignment explanation
Indices: 5806235--5806298 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
5806225 TTTGATCCAA
*
5806235 TATATATATATTTTTTATTATTTATT
1 TATATTTATATTTTTTATTATTTATT
5806261 TA-ATTT-TATATTTTTATATATTT-TT
1 TATATTTATAT-TTTTTAT-TATTTATT
5806286 TATATTTATATTT
1 TATATTTATATTT
5806299 AAAAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 3 0.09
25 14 0.42
26 13 0.39
27 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TATATTTATATTTTTTATTATTTATT
Found at i:5808432 original size:6 final size:6
Alignment explanation
Indices: 5808421--5808460 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
5808411 TTCAGTGTAA
*
5808421 AAAGCC AAAGCC AAAGCC AAAGCC AAAGCC AAAGCA AAAG
1 AAAGCC AAAGCC AAAGCC AAAGCC AAAGCC AAAGCC AAAG
5808461 GGCACCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.55, C:0.28, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGCC
Found at i:5815668 original size:19 final size:19
Alignment explanation
Indices: 5815631--5815674 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5815621 ATAGAAACAA
* *
5815631 TTCTTAAAACTCTTCATTT
1 TTCTTTAAACTCTACATTT
*
5815650 TTCTTTAAACTCTAGATTT
1 TTCTTTAAACTCTACATTT
5815669 TT-TTTA
1 TTCTTTA
5815675 TAAAAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.57
Consensus pattern (19 bp):
TTCTTTAAACTCTACATTT
Found at i:5828235 original size:187 final size:188
Alignment explanation
Indices: 5827919--5828289 Score: 690
Period size: 187 Copynumber: 2.0 Consensus size: 188
5827909 ATAAAAAACC
*
5827919 TCAAACTCAATTCAAAATTTGTTATTCAAAATTTGATTTGAATGCGATTGAATTTAAATTTTTTT
1 TCAAACTCAATTCAAAATTTGTTATTCAAAATTTGATTTGAATGCGATTGAATTTAAATTTTTTA
* *
5827984 ACTCGAGTTCAACTCGAGATAAATATCAAACTATTCAAACTCACTCAATTGATTCGTTTATTAAA
66 ACTCGAGCTCAACTCGAGATAAATATCAAAATATTCAAACTCACTCAATTGATTCGTTTATTAAA
*
5828049 TAAAAAATGAATTCAATTCTTAAACTCCACTTTAAGTTTGATTATTTGTGTTTGTTAT
131 TAAAAAATGAATTCAATTCCTAAACTCCACTTTAAGTTTGATTATTTGTGTTTGTTAT
*
5828107 TCAAACTCAATTCAAAATTTGTTATTCAAAATTTGATTTGAATGCGATTGAGTTTAAA-TTTTTA
1 TCAAACTCAATTCAAAATTTGTTATTCAAAATTTGATTTGAATGCGATTGAATTTAAATTTTTTA
5828171 ACTCGAGCTCAACTCGAGATAAATATCAAAATATTCAAACTCACTCAATTGATTCGTTTATTAAA
66 ACTCGAGCTCAACTCGAGATAAATATCAAAATATTCAAACTCACTCAATTGATTCGTTTATTAAA
5828236 TAAAAAATGAATTCAATTCCTAAACTCCACTTTAAGTTTGATTATTTGTGTTTG
131 TAAAAAATGAATTCAATTCCTAAACTCCACTTTAAGTTTGATTATTTGTGTTTG
5828290 AACTTGAGTT
Statistics
Matches: 178, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
187 121 0.68
188 57 0.32
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (188 bp):
TCAAACTCAATTCAAAATTTGTTATTCAAAATTTGATTTGAATGCGATTGAATTTAAATTTTTTA
ACTCGAGCTCAACTCGAGATAAATATCAAAATATTCAAACTCACTCAATTGATTCGTTTATTAAA
TAAAAAATGAATTCAATTCCTAAACTCCACTTTAAGTTTGATTATTTGTGTTTGTTAT
Found at i:5828377 original size:21 final size:20
Alignment explanation
Indices: 5828343--5828382 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5828333 GTAATTTTTA
5828343 ATTAAAATAAAAAAATATAT
1 ATTAAAATAAAAAAATATAT
5828363 ATTAAAATAAAAAAAT-TAT
1 ATTAAAATAAAAAAATATAT
5828382 A
1 A
5828383 CTAGACCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
ATTAAAATAAAAAAATATAT
Found at i:5832312 original size:19 final size:19
Alignment explanation
Indices: 5832242--5832316 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
5832232 CATTTTTAAA
5832242 TATTTATTTAATAAAAAATT
1 TATTTA-TTAATAAAAAATT
* * *
5832262 AATTAATCAATAAAAAATAATT
1 TATTTATTAAT--AAAA-AATT
*
5832284 TATTGATTAATAAAAAATT
1 TATTTATTAATAAAAAATT
*
5832303 TATTTTTTAA-AAAA
1 TATTTATTAATAAAA
5832317 TTATCTCATA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
18 4 0.09
19 16 0.36
20 8 0.18
21 4 0.09
22 12 0.27
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
TATTTATTAATAAAAAATT
Found at i:5832446 original size:42 final size:43
Alignment explanation
Indices: 5832400--5832489 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 43
5832390 TATTTTTTAA
5832400 TATAATTTTAC-CTATAAATAATATTACATTAA-TAAATAATAT
1 TATAATTTTACTC-ATAAATAATATTACATTAATTAAATAATAT
* * * *
5832442 TATAA-TTTATTCATAAATATTATTATATTAATTAATTAATAT
1 TATAATTTTACTCATAAATAATATTACATTAATTAAATAATAT
5832484 TATAAT
1 TATAAT
5832490 AATATATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 21 0.51
42 20 0.49
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (43 bp):
TATAATTTTACTCATAAATAATATTACATTAATTAAATAATAT
Found at i:5832447 original size:15 final size:17
Alignment explanation
Indices: 5832413--5832607 Score: 89
Period size: 15 Copynumber: 11.5 Consensus size: 17
5832403 AATTTTACCT
5832413 ATAAATAATATTACATTA
1 ATAAATAATATTA-ATTA
5832431 ATAAATAATATTATAATTTA
1 ATAAATAATA-T-TAA-TTA
*
5832451 TTCATAAATATTATTATATTA
1 ---ATAAATAATATTA-ATTA
*
5832472 ATTAATTAATATT-A-TA
1 A-TAAATAATATTAATTA
5832488 AT-AAT-ATATT-ATTA
1 ATAAATAATATTAATTA
*
5832502 ATACATAATA-TACTATTA
1 ATAAATAATATTA--ATTA
5832520 AT--ATAATA-T-ATTA
1 ATAAATAATATTAATTA
*
5832533 ATAAATAGTATT--TTA
1 ATAAATAATATTAATTA
5832548 ATAAAT-ATGATTAA-TA
1 ATAAATAAT-ATTAATTA
*
5832564 ATATTATAATA-T-ATTA
1 ATA-AATAATATTAATTA
*
5832580 ATAAATAATATAATAAATA
1 ATAAATAATAT--TAATTA
5832599 ATAAATAAT
1 ATAAATAAT
5832608 TTTATTTTAA
Statistics
Matches: 140, Mismatches: 10, Indels: 53
0.69 0.05 0.26
Matches are distributed among these distances:
13 12 0.09
14 7 0.05
15 28 0.20
16 25 0.18
17 4 0.03
18 20 0.14
19 23 0.16
20 5 0.04
21 5 0.04
22 2 0.01
23 9 0.06
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
ATAAATAATATTAATTA
Found at i:5832500 original size:16 final size:17
Alignment explanation
Indices: 5832481--5832532 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
5832471 AATTAATTAA
5832481 TATTATA-ATAATATAT
1 TATTATACATAATATAT
*
5832497 TATTAATACATAATATAC
1 TATT-ATACATAATATAT
*
5832515 TATTA-ATATAATATAT
1 TATTATACATAATATAT
5832531 TA
1 TA
5832533 ATAAATAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 15 0.48
17 4 0.13
18 12 0.39
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTATACATAATATAT
Found at i:5832600 original size:19 final size:20
Alignment explanation
Indices: 5832546--5832607 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
5832536 AATAGTATTT
*
5832546 TAATA-AATATGATTAAT-AA
1 TAATATAATAT-AATAATAAA
* *
5832565 TATTATAATATATTAATAAA
1 TAATATAATATAATAATAAA
5832585 TAATATAATA-AATAATAAA
1 TAATATAATATAATAATAAA
5832604 TAAT
1 TAAT
5832608 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TAATATAATATAATAATAAA
Found at i:5842034 original size:38 final size:39
Alignment explanation
Indices: 5841990--5842066 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
5841980 TTTAATATGA
*
5841990 TATTTAAATTTTAAAATATTTAA-TAAAAATTTAATTAT
1 TATTTAAATTTTAAAATATTTAATTAAAAATTAAATTAT
* *
5842028 TATTTAAATTTTAAAATTTTTAATTAATAATTAAATTAT
1 TATTTAAATTTTAAAATATTTAATTAAAAATTAAATTAT
5842067 AAATTTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 22 0.63
39 13 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTTAAATTTTAAAATATTTAATTAAAAATTAAATTAT
Found at i:5842049 original size:27 final size:26
Alignment explanation
Indices: 5842019--5842088 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
5842009 TTAATAAAAA
* * *
5842019 TTTAATTATTATTTAAATTTTAAAATT
1 TTTAATTAATAATTAAATTAT-AAATT
5842046 TTTAATTAATAATTAAATTATAAATT
1 TTTAATTAATAATTAAATTATAAATT
5842072 TATTAATTAATATATTA
1 T-TTAATTAATA-ATTA
5842089 TTTGAAAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.16
27 28 0.74
28 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAATTAATAATTAAATTATAAATT
Found at i:5842931 original size:2 final size:2
Alignment explanation
Indices: 5842920--5842952 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5842910 TAGTAACGTC
5842920 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5842953 TTGGATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5845797 original size:25 final size:27
Alignment explanation
Indices: 5845769--5845830 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
5845759 ATTTTTATTT
5845769 TATATATT-TAAATATTTTTT-ATAAA
1 TATATATTATAAATATTTTTTAATAAA
*
5845794 TATATATTAATATATATTTTTTAATAAA
1 TATATATT-ATAAATATTTTTTAATAAA
*
5845822 AATATATTA
1 TATATATTA
5845831 ATTCTAGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.25
27 12 0.38
28 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TATATATTATAAATATTTTTTAATAAA
Found at i:5845826 original size:28 final size:27
Alignment explanation
Indices: 5845780--5845832 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
5845770 ATATATTTAA
*
5845780 ATATTTTTTATAAATATATATTAATAT
1 ATATTTTTTATAAAAATATATTAATAT
5845807 ATATTTTTTAATAAAAATATATTAAT
1 ATATTTTTT-ATAAAAATATATTAAT
5845833 TCTAGTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATATTTTTTATAAAAATATATTAATAT
Found at i:5845831 original size:14 final size:14
Alignment explanation
Indices: 5845769--5845832 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 14
5845759 ATTTTTATTT
5845769 TATATATT--TAAA
1 TATATATTAATAAA
* *
5845781 TAT-TTTTTATAAA
1 TATATATTAATAAA
*
5845794 TATATATTAATATA
1 TATATATTAATAAA
* *
5845808 TATTTTTTAATAAA
1 TATATATTAATAAA
*
5845822 AATATATTAAT
1 TATATATTAAT
5845833 TCTAGTTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
11 3 0.08
12 3 0.08
13 7 0.18
14 26 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATATTAATAAA
Found at i:5856316 original size:10 final size:12
Alignment explanation
Indices: 5856285--5856334 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
5856275 TCTCAAAATT
5856285 TATATTAAAATAA
1 TATA-TAAAATAA
5856298 TATATAAAA-AA
1 TATATAAAATAA
5856309 TA-ATAAAATAA
1 TATATAAAATAA
* *
5856320 AATTTAAAACTAA
1 TATATAAAA-TAA
5856333 TA
1 TA
5856335 AGCTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 6 0.19
11 7 0.23
12 10 0.32
13 8 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
TATATAAAATAA
Found at i:5857512 original size:27 final size:27
Alignment explanation
Indices: 5857474--5857529 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5857464 TGTAAGTTTT
5857474 GTACTACTTGTCTCAATATTATACTTG
1 GTACTACTTGTCTCAATATTATACTTG
5857501 GTACTACTTGTCTCAATATTATACTTG
1 GTACTACTTGTCTCAATATTATACTTG
5857528 GT
1 GT
5857530 TGCCATCGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (27 bp):
GTACTACTTGTCTCAATATTATACTTG
Found at i:5859914 original size:254 final size:261
Alignment explanation
Indices: 5859442--5859918 Score: 664
Period size: 254 Copynumber: 1.8 Consensus size: 261
5859432 AAATGGATAA
* * * *
5859442 TATATTTAATGAAATATAAATGTATCAAATAATTAATTAGAGAATCAACAATTTTATATTTGTAA
1 TATATTTAATCAAATATAAATATATCAAATAATTAATTAGAAAATCAAC----TTATATTTATAA
* * *
5859507 TTGTACTATTTAGTAATTTATTAATTATATATTAATTGATTTAATTTGTTAAATTAAAAAAATTT
62 TTATAATATTTAGTAATTTATTAATTATATATTAATTGATTTAATTTGTCAAATTAAAAAAATTT
* * *
5859572 TAAAATTTAATACTTTTAATATGAATTGAATTGAGAGTAATTTAAAATCAATAATAAAAATATAA
127 T--AA--TAATACTTTTAATATGAATTGAATTAAAAGTAATTTAAAATCAATAATAAAAACATAA
*
5859637 ATATAATTAATTTAGTTTTTTGAATTATATTTGCTTTCTATGTTTATACATGAAATATAGCAATT
188 ATATAATTAATTTAATTTTTTGAATTATATTTGCTTTCTATGTTTATACATGAAATATAGCAATT
5859702 ACTGAATAC
253 ACTGAATAC
*
5859711 TATATTTAATCAAATATAAATATATCAAATAATTGATTAGAAAATCAAC-TAT-TTTATAATTAT
1 TATATTTAATCAAATATAAATATATCAAATAATTAATTAGAAAATCAACTTATATTTATAATTAT
* *
5859774 AAT-TTTAGT-ATTTATTTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAATTTT-A
66 AATATTTAGTAATTTA-TTAATTATATATTAATTGATTTAATTTGTCAAATTAAAAAAATTTTAA
* * *
5859836 -AA-A-TTTTAATATGAATTGAATTAAAAGTGATTTAAGATTAATAATAAAAACATAAATATAAT
130 TAATACTTTTAATATGAATTGAATTAAAAGTAATTTAAAATCAATAATAAAAACATAAATATAAT
5859898 TAATTTAATTTTTTGAATTAT
195 TAATTTAATTTTTTGAATTAT
5859919 TTTTAAATTA
Statistics
Matches: 190, Mismatches: 17, Indels: 17
0.85 0.08 0.08
Matches are distributed among these distances:
254 73 0.38
255 1 0.01
256 2 0.01
259 1 0.01
261 5 0.03
262 49 0.26
263 11 0.06
264 3 0.02
269 45 0.24
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (261 bp):
TATATTTAATCAAATATAAATATATCAAATAATTAATTAGAAAATCAACTTATATTTATAATTAT
AATATTTAGTAATTTATTAATTATATATTAATTGATTTAATTTGTCAAATTAAAAAAATTTTAAT
AATACTTTTAATATGAATTGAATTAAAAGTAATTTAAAATCAATAATAAAAACATAAATATAATT
AATTTAATTTTTTGAATTATATTTGCTTTCTATGTTTATACATGAAATATAGCAATTACTGAATA
C
Found at i:5866964 original size:3 final size:3
Alignment explanation
Indices: 5866958--5867003 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5866948 TTATACTTTT
5866958 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5867004 AATGCTAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5867125 original size:20 final size:21
Alignment explanation
Indices: 5867100--5867147 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5867090 ACCTCGATTA
5867100 AAAATTTCA-TAACTTTTGAT
1 AAAATTTCAGTAACTTTTGAT
* *
5867120 AAAATTTTAGTAATTTTTGAT
1 AAAATTTCAGTAACTTTTGAT
*
5867141 ATAATTT
1 AAAATTT
5867148 TAATCATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (21 bp):
AAAATTTCAGTAACTTTTGAT
Found at i:5867251 original size:22 final size:21
Alignment explanation
Indices: 5867226--5867276 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5867216 ATTTTTATAA
* *
5867226 AATTTTGGCAACCTCTTGATGT
1 AATTTTGGCAACCT-TTCATAT
* *
5867248 AATTTTTGTAACCTTTCATAT
1 AATTTTGGCAACCTTTCATAT
5867269 AATTTTGG
1 AATTTTGG
5867277 TAATTGAGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTTTGGCAACCTTTCATAT
Found at i:5867666 original size:22 final size:22
Alignment explanation
Indices: 5867639--5867682 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5867629 ATTAAATTAT
*
5867639 CTACTAAATTATTAATGATTTA
1 CTACTAAATTACTAATGATTTA
*
5867661 CTACTAAATTACTGATGATTTA
1 CTACTAAATTACTAATGATTTA
5867683 TTATAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
CTACTAAATTACTAATGATTTA
Found at i:5868033 original size:22 final size:22
Alignment explanation
Indices: 5868003--5868164 Score: 91
Period size: 22 Copynumber: 7.4 Consensus size: 22
5867993 TTTATCACAA
5868003 ATTTA-TATTAAATTATCTATT
1 ATTTACTATTAAATTATCTATT
* *
5868024 ATTTACTATTAAGTTATC-ACTA
1 ATTTACTATTAAATTATCTA-TT
* * *
5868046 ATTAACTGTTAAATTA-CTGATA
1 ATTTACTATTAAATTATCT-ATT
* * *
5868068 ATTTAATATTAAGTTATAT-TT
1 ATTTACTATTAAATTATCTATT
* * * *
5868089 ATTTACTTTTAAGTTTTCAATT
1 ATTTACTATTAAATTATCTATT
* * **
5868111 ATTAACTATTAAAGTATC-ACAG
1 ATTTACTATTAAATTATCTA-TT
*
5868133 ATTTACTATTAAATTTATCAATT
1 ATTTACTATTAAA-TTATCTATT
*
5868156 AATTACTAT
1 ATTTACTAT
5868165 CAAACGGAAG
Statistics
Matches: 104, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
21 23 0.22
22 66 0.63
23 14 0.13
24 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTACTATTAAATTATCTATT
Found at i:5868041 original size:43 final size:44
Alignment explanation
Indices: 5867935--5868164 Score: 157
Period size: 43 Copynumber: 5.3 Consensus size: 44
5867925 TCTTAGTTTG
* * *
5867935 ATTATTTACTA-TAACATTATCACATATTTA-TATTAAATTATCC
1 ATTATTTACTATTAA-GTTATCACAAATTTACTATTAAATTATCA
* * *** * *
5867978 ATAATATACTGCCAATTTATCACAAATTTA-TATTAAATTATCT
1 ATTATTTACTATTAAGTTATCACAAATTTACTATTAAATTATCA
* * * *
5868021 ATTATTTACTATTAAGTTATCACTAATTAACTGTTAAATTA-CTG
1 ATTATTTACTATTAAGTTATCACAAATTTACTATTAAATTATC-A
* * *** * * *
5868065 ATAATTTAATATTAAGTTAT-ATTTATTTACTTTTAAGTTTTCA
1 ATTATTTACTATTAAGTTATCACAAATTTACTATTAAATTATCA
* *
5868108 ATTATTAACTATTAAAG-TATCACAGATTTACTATTAAATTTATCA
1 ATTATTTACTATT-AAGTTATCACAAATTTACTATTAAA-TTATCA
*
5868153 ATTAATTACTAT
1 ATTATTTACTAT
5868165 CAAACGGAAG
Statistics
Matches: 143, Mismatches: 37, Indels: 12
0.74 0.19 0.06
Matches are distributed among these distances:
43 83 0.58
44 45 0.31
45 15 0.10
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (44 bp):
ATTATTTACTATTAAGTTATCACAAATTTACTATTAAATTATCA
Found at i:5868071 original size:65 final size:64
Alignment explanation
Indices: 5867995--5868164 Score: 171
Period size: 65 Copynumber: 2.6 Consensus size: 64
5867985 ACTGCCAATT
* * *
5867995 TATCACAAATTTATATTAAATTATCTATTATTTACTATTAAGTTATCACTAATTAACTGTTAAAT
1 TATCAC-AATTTATATTAAATTATCTATTATTTACTATTAAGTTATCAATAATTAACTATTAAAG
* * * * * * *
5868060 TACTGATAATTTAATATTAAGTTATAT-TTATTTACTTTTAAGTTTTCAATTATTAACTATTAAA
1 TA-TCACAATTT-ATATTAAATTATCTATTATTTACTATTAAGTTATCAATAATTAACTATTAAA
5868124 G
64 G
* *
5868125 TATCACAGATTTACTATTAAATTTATCAATTAATTACTAT
1 TATCACA-ATTTA-TATTAAA-TTATCTATTATTTACTAT
5868165 CAAACGGAAG
Statistics
Matches: 82, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
64 4 0.05
65 51 0.62
66 18 0.22
67 9 0.11
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (64 bp):
TATCACAATTTATATTAAATTATCTATTATTTACTATTAAGTTATCAATAATTAACTATTAAAG
Found at i:5868583 original size:22 final size:22
Alignment explanation
Indices: 5868558--5868656 Score: 81
Period size: 22 Copynumber: 4.5 Consensus size: 22
5868548 TTTTATGTTG
* *
5868558 TCAATGATTTGCTACTAAGCTA
1 TCAATGATTTACTACTAAACTA
* *
5868580 TCAATGATTTACTAATAAATTA
1 TCAATGATTTACTACTAAACTA
* **
5868602 TCTATGATTTACTACTAATTTA
1 TCAATGATTTACTACTAAACTA
* * * *
5868624 TGAATAATTTACTATTAAATTA
1 TCAATGATTTACTACTAAACTA
* *
5868646 TAAATTATTTA
1 TCAATGATTTA
5868657 TCATTAAATT
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (22 bp):
TCAATGATTTACTACTAAACTA
Found at i:5868609 original size:44 final size:44
Alignment explanation
Indices: 5868561--5868646 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
5868551 TATGTTGTCA
* *
5868561 ATGATTTGCTACTAAGCTATCAATGATTTACTAATAAATTATCT
1 ATGATTTACTACTAAGCTATCAATAATTTACTAATAAATTATCT
** * *
5868605 ATGATTTACTACTAATTTATGAATAATTTACTATTAAATTAT
1 ATGATTTACTACTAAGCTATCAATAATTTACTAATAAATTAT
5868647 AAATTATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.44
Consensus pattern (44 bp):
ATGATTTACTACTAAGCTATCAATAATTTACTAATAAATTATCT
Found at i:5868662 original size:22 final size:22
Alignment explanation
Indices: 5868586--5868688 Score: 118
Period size: 22 Copynumber: 4.7 Consensus size: 22
5868576 GCTATCAATG
* ** *
5868586 ATTTACTAATAAATTATCTATG
1 ATTTACTATTAAATTATAAATA
* * *
5868608 ATTTACTACTAATTTATGAATA
1 ATTTACTATTAAATTATAAATA
*
5868630 ATTTACTATTAAATTATAAATT
1 ATTTACTATTAAATTATAAATA
5868652 ATTTA-TCATTAAATTATAAATA
1 ATTTACT-ATTAAATTATAAATA
5868674 ATTTACTATTAAATT
1 ATTTACTATTAAATT
5868689 GCTGATAATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
21 1 0.01
22 67 0.97
23 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAATTATAAATA
Found at i:5868716 original size:22 final size:22
Alignment explanation
Indices: 5868691--5868734 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5868681 ATTAAATTGC
5868691 TGATAATTTATTACT-AAGTTAT
1 TGATAATTTATTA-TAAAGTTAT
* *
5868713 TGATGATTTGTTATAAAGTTAT
1 TGATAATTTATTATAAAGTTAT
5868735 AACTATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (22 bp):
TGATAATTTATTATAAAGTTAT
Found at i:5868816 original size:22 final size:22
Alignment explanation
Indices: 5868791--5868949 Score: 103
Period size: 22 Copynumber: 7.4 Consensus size: 22
5868781 TAATTTACTA
*
5868791 ATTTATTATTAAATTATCATTG
1 ATTTACTATTAAATTATCATTG
** * * * *
5868813 ATTTAGAATTAAGTTATTAGTC
1 ATTTACTATTAAATTATCATTG
* *
5868835 ATTTACTATTATATTAT-TTGTG
1 ATTTACTATTAAATTATCAT-TG
* *
5868857 ATTTATTATTAAGTTATCA---
1 ATTTACTATTAAATTATCATTG
* *
5868876 ATTTACTACTAAATTATCAATG
1 ATTTACTATTAAATTATCATTG
* * *
5868898 ATTTATTATTATATTATTATGTG
1 ATTTACTATTAAATTATCAT-TG
**
5868921 -TTTACTATTATGTTATCATTG
1 ATTTACTATTAAATTATCATTG
5868942 ATTTACTA
1 ATTTACTA
5868950 CTTCATTTTT
Statistics
Matches: 102, Mismatches: 28, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
19 16 0.16
21 2 0.02
22 82 0.80
23 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (22 bp):
ATTTACTATTAAATTATCATTG
Found at i:5868830 original size:30 final size:30
Alignment explanation
Indices: 5868774--5868831 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5868764 TATGACAAAG
* *
5868774 TTATCATTAATTTACTAATTTATTATTAAA
1 TTATCATTAATTTACGAATTAATTATTAAA
*
5868804 TTATCATTGATTTA-GAATTAAGTTATTA
1 TTATCATTAATTTACGAATTAA-TTATTA
5868832 GTCATTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (30 bp):
TTATCATTAATTTACGAATTAATTATTAAA
Found at i:5868839 original size:44 final size:43
Alignment explanation
Indices: 5868791--5868946 Score: 149
Period size: 44 Copynumber: 3.6 Consensus size: 43
5868781 TAATTTACTA
* **
5868791 ATTTATTATTAAATTATCATTGATTTAGAATTAAGTTATTAGT
1 ATTTACTATTAAATTATCATTGATTTATTATTAAGTTATTAGT
* * *
5868834 CATTTACTATTATATTAT-TTGTGATTTATTATTAAGTTATCA--
1 -ATTTACTATTAAATTATCAT-TGATTTATTATTAAGTTATTAGT
* *
5868876 ATTTACTACTAAATTATCAATGATTTATTATTATA-TTATTATGT
1 ATTTACTATTAAATTATCATTGATTTATTATTA-AGTTATTA-GT
* **
5868920 GTTTACTATTATGTTATCATTGATTTA
1 ATTTACTATTAAATTATCATTGATTTA
5868947 CTACTTCATT
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
41 33 0.37
42 1 0.01
43 1 0.01
44 55 0.61
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (43 bp):
ATTTACTATTAAATTATCATTGATTTATTATTAAGTTATTAGT
Found at i:5868944 original size:85 final size:85
Alignment explanation
Indices: 5868790--5868946 Score: 194
Period size: 85 Copynumber: 1.8 Consensus size: 85
5868780 TTAATTTACT
* * * *
5868790 AATTTATTATTAAATTATCATTGATTTAGAATTAAGTTATTAGTCATTTACTATTATATTATTTG
1 AATTTACTACTAAATTATCAATGATTTAGAATTAAGTTATTAGTCATTTACTATTATATTATATG
5868855 TGATTTATTATTAAGTTATC
66 TGATTTATTATTAAGTTATC
** * *
5868875 AATTTACTACTAAATTATCAATGATTTATTATTATA-TTATTATGT-GTTTACTATTATGTTATC
1 AATTTACTACTAAATTATCAATGATTTAGAATTA-AGTTATTA-GTCATTTACTATTATATTAT-
5868938 AT-TGATTTA
63 ATGTGATTTA
5868947 CTACTTCATT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
85 57 0.93
86 4 0.07
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.53
Consensus pattern (85 bp):
AATTTACTACTAAATTATCAATGATTTAGAATTAAGTTATTAGTCATTTACTATTATATTATATG
TGATTTATTATTAAGTTATC
Found at i:5869081 original size:22 final size:22
Alignment explanation
Indices: 5869039--5869109 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
5869029 GATTAATTAT
*
5869039 CTACTAAATTATCAAAT-ATTTA
1 CTACTAAATTAT-AATTGATTTA
*
5869061 CTACTAAATTATAGTTGATTTA
1 CTACTAAATTATAATTGATTTA
* *
5869083 CCAC-AAATTAT-TTATGATTTA
1 CTACTAAATTATAAT-TGATTTA
5869104 CTACTA
1 CTACTA
5869110 TCAATTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 1 0.02
21 19 0.46
22 21 0.51
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.42
Consensus pattern (22 bp):
CTACTAAATTATAATTGATTTA
Found at i:5869369 original size:22 final size:21
Alignment explanation
Indices: 5869344--5869404 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 21
5869334 AATATTATTC
*
5869344 ATTTACTCTTAAGTTATCACTA
1 ATTTACTATTAAGTTATCA-TA
*
5869366 ATTTACTATTAAGTTGTTCATA
1 ATTTACTATTAAGTT-ATCATA
5869388 ATTTACTATTAAGTTAT
1 ATTTACTATTAAGTTAT
5869405 TAATGATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.03
22 31 0.89
23 3 0.09
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTTACTATTAAGTTATCATA
Found at i:5869486 original size:42 final size:42
Alignment explanation
Indices: 5869408--5869487 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
5869398 AAGTTATTAA
* *
5869408 TGATTAATTGTTAAGTTGTCGATAATTATTACTAAGTTGTTC
1 TGATTAATTGTTAAGTTGTCAATAATTATTAATAAGTTGTTC
* * *
5869450 TGATTACTT-TTAAGTTTTCAATGATTAATTAATAAGTT
1 TGATTAATTGTTAAGTTGTCAATAATT-ATTAATAAGTT
5869488 ATAATTTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 14 0.44
42 18 0.56
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (42 bp):
TGATTAATTGTTAAGTTGTCAATAATTATTAATAAGTTGTTC
Found at i:5869487 original size:22 final size:23
Alignment explanation
Indices: 5869372--5869489 Score: 72
Period size: 22 Copynumber: 5.5 Consensus size: 23
5869362 ACTAATTTAC
* * * *
5869372 TATTAAGTTGTTC-ATAATTTAC
1 TATTAAGTTATTCAATGATTAAT
5869394 TATTAAGTTATT-AATGATTAAT
1 TATTAAGTTATTCAATGATTAAT
* * * *
5869416 TGTTAAGTT-GTCGATAATT-AT
1 TATTAAGTTATTCAATGATTAAT
* * *
5869437 TACTAAGTTGTTC--TGATTACT
1 TATTAAGTTATTCAATGATTAAT
5869458 T-TTAAGTT-TTCAATGATTAAT
1 TATTAAGTTATTCAATGATTAAT
*
5869479 TAATAAGTTAT
1 TATTAAGTTAT
5869490 AATTTATCTA
Statistics
Matches: 72, Mismatches: 16, Indels: 15
0.70 0.16 0.15
Matches are distributed among these distances:
19 3 0.04
20 10 0.14
21 20 0.28
22 38 0.53
23 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (23 bp):
TATTAAGTTATTCAATGATTAAT
Found at i:5872843 original size:26 final size:29
Alignment explanation
Indices: 5872808--5872867 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
5872798 CATGAAAATC
*
5872808 AATAACAAAAT-T-ATTAA-AATAATAGT
1 AATAACAAAATATGATTAATAATAATAAT
* *
5872834 AATAAGAAAATATGTTTAATAATAATAAT
1 AATAACAAAATATGATTAATAATAATAAT
5872863 AATAA
1 AATAA
5872868 AAGTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.36
27 1 0.04
28 4 0.14
29 13 0.46
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (29 bp):
AATAACAAAATATGATTAATAATAATAAT
Found at i:5872859 original size:23 final size:23
Alignment explanation
Indices: 5872827--5872881 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5872817 ATTATTAAAA
* *
5872827 TAATAGTAATAAGAA-AATATGTT
1 TAATAATAATAAGAATAA-AAGTT
*
5872850 TAATAATAATAATAATAAAAGTT
1 TAATAATAATAAGAATAAAAGTT
5872873 TAATAATAA
1 TAATAATAA
5872882 AAAAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (23 bp):
TAATAATAATAAGAATAAAAGTT
Found at i:5872869 original size:26 final size:23
Alignment explanation
Indices: 5872825--5872881 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 23
5872815 AAATTATTAA
*
5872825 AATAATAGTAATAAGAAAATATGTTT
1 AATAATAATAATAAG-AAA-A-GTTT
*
5872851 AATAATAATAATAATAAAAGTTT
1 AATAATAATAATAAGAAAAGTTT
5872874 AATAATAA
1 AATAATAA
5872882 AAAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 12 0.41
24 1 0.03
25 3 0.10
26 13 0.45
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
AATAATAATAATAAGAAAAGTTT
Found at i:5872920 original size:26 final size:28
Alignment explanation
Indices: 5872891--5872948 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
5872881 AAAAAATATT
* *
5872891 TAAATTAAAATTT-AT-TAAAAATTTAA
1 TAAATGAAAATTTAATATAAAAAGTTAA
*
5872917 TAAATGAGAATTTAATAATAAAAAGTTAA
1 TAAATGAAAATTTAAT-ATAAAAAGTTAA
5872946 TAA
1 TAA
5872949 TAAAAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 11 0.42
27 2 0.08
29 13 0.50
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (28 bp):
TAAATGAAAATTTAATATAAAAAGTTAA
Found at i:5872947 original size:14 final size:14
Alignment explanation
Indices: 5872928--5872954 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5872918 AAATGAGAAT
5872928 TTAATAATAAAAAG
1 TTAATAATAAAAAG
5872942 TTAATAATAAAAA
1 TTAATAATAAAAA
5872955 AATCATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
TTAATAATAAAAAG
Found at i:5879082 original size:17 final size:18
Alignment explanation
Indices: 5879052--5879085 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5879042 ATATATTTTT
5879052 ATATATTTAATAAATAAA
1 ATATATTTAATAAATAAA
*
5879070 ATAT-TTTATTAAATAA
1 ATATATTTAATAAATAA
5879086 TATAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTTAATAAATAAA
Found at i:5879096 original size:22 final size:23
Alignment explanation
Indices: 5879050--5879115 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
5879040 TTATATATTT
*
5879050 TTATATATTTAATAA-ATAAAATA
1 TTAT-TATTAAATAATATAAAATA
*
5879073 TT-TTATTAAATAATATAAATTA
1 TTATTATTAAATAATATAAAATA
5879095 TTATT-TTAAATTAAT-TAAAAT
1 TTATTATTAAA-TAATATAAAAT
5879116 TAATATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 9 0.24
22 20 0.54
23 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATTATTAAATAATATAAAATA
Found at i:5885181 original size:321 final size:319
Alignment explanation
Indices: 5884453--5885852 Score: 1240
Period size: 322 Copynumber: 4.3 Consensus size: 319
5884443 CAATTTTTTG
* * *
5884453 TCATTTATGTTGGTTTAGGACATTTTGTGTCATTAAAAGACAAAAATTTAAATTTGTATTTATTA
1 TCATTTATGTTTGTTTAGGAC-TTTT-TGTCATTAAAAGACAAAAATGTAAATTTGCATTTATTA
* * ** * * *
5884518 TTCTATTTTAAC-AGTTAAATAATTTTGATAAATAATATTAAATTTGTCTG-AATGATTGAACTT
64 TTCTATTTTAACTATTTAAATAACTTCAATACATGATATTAAACTTGT-TGAAATGATTGAACTT
* * * * **
5884581 AGTTTTCATAGTTGATATGTGTGAAAAAATTACCATTTGTGTCTTTTTAAGATTTTATTGTGTTG
128 AGTTTTCATAGTTGATATGTGTGAAAAAATTATCATTTATATCTTTTT-AGACTTTATTGTGCCG
* * *
5884646 TTAAAGGGTTAAAATATAATTTTATAGTTATATTTATATTTTAACAGTCTAGACAGCTTAAATAT
192 TTAAAGGG-TAAAATATAATTTTACAGTTATATTTATATTTTAACAGTTTAGATAGCTTAAATAT
* * * * * * *
5884711 ATGATATCAAATTGATCCAAATGATTGAACTTGG-TTTAATAGCTAT-ATATGTGTGAAAAAGTT
256 ATAATATTAAATTTATCTAAATGATTGAACTTGGTTTTCATA-AT-TGATATATGTGAAAAAGTT
5884774 A
319 A
* * * * * * * ** **
5884775 CCGTTTATATCTATTTAAGACTTTTGGTGTCGTTAAAAGGTAAAAATACAAATTTGCATTTATTA
1 TCATTTATGTTTGTTTAGGACTTTT--TGTCATTAAAAGACAAAAATGTAAATTTGCATTTATTA
* * * * *
5884840 TTCTATTTTAA-TAGTTTAGATAACTTCAATATATTATATT-AA-TTGTTGTAATAATTGAA-TA
64 TTCTATTTTAACTA-TTTAAATAACTTCAATACATGATATTAAACTTGTTGAAATGATTGAACT-
* * * * *
5884901 TAATTTTCACAGTTGATATGTGTGAAAAAGTTA-CTGTTTATATTTTTTTAAGACTTTATTGTGC
127 TAGTTTTCATAGTTGATATGTGTGAAAAAATTATC-ATTTATATCTTTTT-AGACTTTATTGTGC
* * *
5884965 CGTTAAAGGGTGAAAATATAATTTTACAGTTATATTTTTATTTTAACAGTTTATATAGTTTAAAT
190 CGTTAAAGGGT-AAAATATAATTTTACAGTTATATTTATATTTTAACAGTTTAGATAGCTTAAAT
* * * * * * * *
5885030 ACATGATATTAAATTTATCTGAATAATTAAATTTGATTTTCATAATTGATATACGTGAAAAAGTT
254 ATATAATATTAAATTTATCTAAATGATTGAACTTGGTTTTCATAATTGATATATGTGAAAAAGTT
5885095 A
319 A
* *
5885096 TCATTTATGTTTGTTTAGGACTTTTTGTACTATTAAAAGATAAAAATGTAAATTTACATTTATTA
1 TCATTTATGTTTGTTTAGGACTTTTTGT-C-ATTAAAAGACAAAAATGTAAATTTGCATTTATTA
* * * *
5885161 TTTTATTTTAACTATTTAGATAGCTTCAATATATGATATTAAACTTG-TGCAAATGATTGAACTT
64 TTCTATTTTAACTATTTAAATAACTTCAATACATGATATTAAACTTGTTG-AAATGATTGAACTT
* * ** * * *
5885225 AGTTTTCAT-GATTAATATATGTGAAAATGTTATCGTTTATCT-TTGTTTAG-CATTTTTTGTGC
128 AGTTTTCATAG-TTGATATGTGTGAAAAAATTATCATTTATATCTT-TTTAGAC-TTTATTGTGC
* *** * * * * * *
5885287 CATTAAAAGACAAAAATGTAATTTTGCAATTATATTTATGTTTTAATAATTTAGATAGCTTAAAT
190 CGTT-AAAGGGTAAAATATAATTTTACAGTTATATTTATATTTTAACAGTTTAGATAGCTTAAAT
* * * *
5885352 AAATAATATTAAATTTGTCTAAATGATTGAATTTGGTTTTTATAATTGATATGA-GTGAAAAAGT
254 ATATAATATTAAATTTATCTAAATGATTGAACTTGGTTTTCATAATTGATAT-ATGTGAAAAAGT
5885416 TA
318 TA
* * * * * *
5885418 TCATTTATGTCTATTTAGCACTTTTTTTGTCGTTAAAA-AGCAAAAATGTAAATTTGTATATATT
1 TCATTTATGTTTGTTTAGGAC--TTTTTGTCATTAAAAGA-CAAAAATGTAAATTTGCATTTATT
* * **
5885482 ATTCTGTTTTAA-TAGTTTAAATAACTTCAATACATGAAATTAAACTTGTCAAAATGATTGAACT
63 ATTCTATTTTAACTA-TTTAAATAACTTCAATACATGATATTAAACTTGTTGAAATGATTGAACT
* ** * *
5885546 TGGTTTTCATAGTTGATATGTGTGAAAAAATTATCATTTATATCTTTTTAGAACTTTGCTATGTC
127 TAGTTTTCATAGTTGATATGTGTGAAAAAATTATCATTTATATCTTTTTAG-ACTTTATTGTGCC
* * * * *
5885611 GTTAAAGGGTAAAATGT-ATTTTACAGTTATATTTATGTTCTAACAGTTTAAATAGCTTCAATAT
191 GTTAAAGGGTAAAATATAATTTTACAGTTATATTTATATTTTAACAGTTTAGATAGCTTAAATAT
* * * * * *
5885675 ATAATATTAAATTTGTATGAATGATTGAACTTGGTTTTCACAATTTA-ATATGTATGAATAAGTT
256 ATAATATTAAATTTATCTAAATGATTGAACTTGGTTTTCATAATTGATATATG--TGAAAAAGTT
5885739 A
319 A
* * * * * *
5885740 -CAGATTATGTTTGTTTAGGACTTTTTGTAACATCAAAATG-CAAAAATGCAAAATTACAGTTAT
1 TCA-TTTATGTTTGTTTAGGACTTTTTGT--CATTAAAA-GACAAAAATGTAAATTTGCATTTAT
* * * * * *
5885803 TATTTTGTTTTAACAATTTAAATAGC-TCTAATACATTATATTAAAGTTGT
62 TATTCTATTTTAACTATTTAAATAACTTC-AATACATGATATTAAACTTGT
5885853 CCAAATGTTT
Statistics
Matches: 879, Mismatches: 158, Indels: 82
0.79 0.14 0.07
Matches are distributed among these distances:
319 4 0.00
320 17 0.02
321 340 0.39
322 422 0.48
323 86 0.10
324 10 0.01
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (319 bp):
TCATTTATGTTTGTTTAGGACTTTTTGTCATTAAAAGACAAAAATGTAAATTTGCATTTATTATT
CTATTTTAACTATTTAAATAACTTCAATACATGATATTAAACTTGTTGAAATGATTGAACTTAGT
TTTCATAGTTGATATGTGTGAAAAAATTATCATTTATATCTTTTTAGACTTTATTGTGCCGTTAA
AGGGTAAAATATAATTTTACAGTTATATTTATATTTTAACAGTTTAGATAGCTTAAATATATAAT
ATTAAATTTATCTAAATGATTGAACTTGGTTTTCATAATTGATATATGTGAAAAAGTTA
Found at i:5885233 original size:161 final size:158
Alignment explanation
Indices: 5884453--5885868 Score: 861
Period size: 161 Copynumber: 8.8 Consensus size: 158
5884443 CAATTTTTTG
* * * * ** *
5884453 TCATTTATGTTGGTTTAGGACATTTTGTGTCATTAAAAGACAAAAATTTAAATTTGTATTTATTA
1 TCATTTATGTTTGTTTAGGAC-TTTT-TGTCGTTAAAAGATAAAAATGTAAATTTACAGTTATTA
* ** ** * * *
5884518 TTCTATTTTAACAG-TTAAATAATTTTGATAAATAATATTAAATTTGTCTGAATGATTGAACTTA
64 TTTTATTTTAACAGTTTAAATAGCTTCAATATATGATATTAAATTTGTC-AAATGATTGAACTTA
* * *
5884582 GTTTTCATAGTTGATATGTGTGAAAAAATTA
128 GTTTTCATAATTGATATATGTGAAAAAGTTA
* * * * * * * * * * *
5884613 CCATTTGTGTCTT-TTTAAGATTTTATTGTGTTGTTAAAGGGTTAAAATATAATTTTATAGTTA-
1 TCATTTATGT-TTGTTTAGGA-CTT-TT-TGTCGTTAAAAGATAAAAATGTAAATTTACAGTTAT
* * * * *
5884676 TATTTATATTTTAACAGTCTAGACAGCTTAAATATATGATATCAAA-TTGATCCAAATGATTGAA
62 TATTT-TATTTTAACAGTTTAAATAGCTTCAATATATGATATTAAATTTG-T-CAAATGATTGAA
* * * *
5884740 CTT-GGTTTAATAGCTAT-ATATGTGTGAAAAAGTTA
124 CTTAGTTTTCATA-AT-TGATATATGTGAAAAAGTTA
* * * * * * * ** * *
5884775 CCGTTTATATCTATTTAAGACTTTTGGTGTCGTTAAAAGGTAAAAATACAAATTTGCATTTATTA
1 TCATTTATGTTTGTTTAGGACTTTT--TGTCGTTAAAAGATAAAAATGTAAATTTACAGTTATTA
* * * * * * *
5884840 TTCTATTTTAATAGTTTAGATAACTTCAATATATTATATTAATTGTTGT--AATAATTGAA-TAT
64 TTTTATTTTAACAGTTTAAATAGCTTCAATATATGATATTAAAT-TTGTCAAATGATTGAACT-T
* * * *
5884902 AATTTTCACAGTTGATATGTGTGAAAAAGTTA
127 AGTTTTCATAATTGATATATGTGAAAAAGTTA
* * * * * * * * *
5884934 -CTGTTTATATTTTTTTAAGACTTTATTGTGCCGTTAAAGGGTGAAAATATAATTTTACAGTTA-
1 TC-ATTTATGTTTGTTTAGGACTTT-TTGT--CGTTAAAAGATAAAAATGTAAATTTACAGTTAT
* * * * * * * *
5884997 TATTTTTATTTTAACAGTTTATATAGTTTAAATACATGATATTAAATTTATCTGAATAATT-AAA
62 TA-TTTTATTTTAACAGTTTAAATAGCTTCAATATATGATATTAAATTTGTC-AAATGATTGAAC
* *
5885061 TTTGATTTTCATAATTGATATACGTGAAAAAGTTA
125 TTAG-TTTTCATAATTGATATATGTGAAAAAGTTA
* *
5885096 TCATTTATGTTTGTTTAGGACTTTTTGTACTATTAAAAGATAAAAATGTAAATTTACATTTATTA
1 TCATTTATGTTTGTTTAGGACTTTTTGT-C-GTTAAAAGATAAAAATGTAAATTTACAGTTATTA
* *
5885161 TTTTATTTTAACTA-TTTAGATAGCTTCAATATATGATATTAAACTTGTGCAAATGATTGAACTT
64 TTTTATTTTAAC-AGTTTAAATAGCTTCAATATATGATATTAAATTTGT-CAAATGATTGAACTT
* * *
5885225 AGTTTTCATGATTAATATATGTGAAAATGTTA
127 AGTTTTCATAATTGATATATGTGAAAAAGTTA
* * * * * * * * *
5885257 TCGTTTATCTTTGTTTAGCATTTTTTGTGCCATTAAAAGACAAAAATGTAATTTTGCAATTA-TA
1 TCATTTATGTTTGTTTAGGACTTTTTGT--CGTTAAAAGATAAAAATGTAAATTTACAGTTATTA
* * * * * * * *
5885321 TTTATGTTTTAATAATTTAGATAGCTTAAATAAATAATATTAAATTTGTCTAAATGATTGAATTT
64 TTT-TATTTTAACAGTTTAAATAGCTTCAATATATGATATTAAATTTGTC-AAATGATTGAACTT
* *
5885386 GGTTTTTATAATTGATATGA-GTGAAAAAGTTA
127 AGTTTTCATAATTGATAT-ATGTGAAAAAGTTA
* * * * **
5885418 TCATTTATGTCTATTTAGCACTTTTTTTGTCGTTAAAA-AGCAAAAATGTAAATTTGTA-TATAT
1 TCATTTATGTTTGTTTAGGAC--TTTTTGTCGTTAAAAGA-TAAAAATGTAAATTTACAGT-TAT
* * * * * * *
5885481 TATTCTGTTTTAATAGTTTAAATAACTTCAATACATGAAATTAAACTTGTCAAAATGATTGAACT
62 TATTTTATTTTAACAGTTTAAATAGCTTCAATATATGATATTAAATTTGTC-AAATGATTGAACT
* * * *
5885546 TGGTTTTCATAGTTGATATGTGTGAAAAAATTA
126 TAGTTTTCATAATTGATATATGTGAAAAAGTTA
* * * * *
5885579 TCATTTATATCTT-TTTAGAACTTTGCTATGTCGTTAAAGGGT-AAAATGT-ATTTTACAGTTA-
1 TCATTTATGT-TTGTTTAGGACTTT--T-TGTCGTTAAAAGATAAAAATGTAAATTTACAGTTAT
*
5885640 TA-TTTATGTTCTAACAGTTTAAATAGCTTCAATATATAATATTAAATTTGT-ATGAATGATTGA
62 TATTTTAT-TT-TAACAGTTTAAATAGCTTCAATATATGATATTAAATTTGTCA--AATGATTGA
* * * *
5885703 ACTTGGTTTTCACAATTTA-ATATGTATGAATAAGTTA
123 ACTTAGTTTTCATAATTGATATATG--TGAAAAAGTTA
* * * * * *
5885740 -CAGATTATGTTTGTTTAGGACTTTTTGTAACATCAAAATG-CAAAAATGCAAAATTACAGTTAT
1 TCA-TTTATGTTTGTTTAGGACTTTTTGT--CGTTAAAA-GATAAAAATGTAAATTTACAGTTAT
* * * * * * *
5885803 TATTTTGTTTTAACAATTTAAATAGC-TCTAATACATTATATTAAAGTTGTCCAAATGTTTGGAC
62 TATTTTATTTTAACAGTTTAAATAGCTTC-AATATATGATATTAAATTTGT-CAAATGATTGAAC
5885867 TT
125 TT
5885869 CATTATTGCC
Statistics
Matches: 995, Mismatches: 193, Indels: 134
0.75 0.15 0.10
Matches are distributed among these distances:
158 13 0.01
159 66 0.07
160 174 0.17
161 519 0.52
162 201 0.20
163 17 0.02
164 5 0.01
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (158 bp):
TCATTTATGTTTGTTTAGGACTTTTTGTCGTTAAAAGATAAAAATGTAAATTTACAGTTATTATT
TTATTTTAACAGTTTAAATAGCTTCAATATATGATATTAAATTTGTCAAATGATTGAACTTAGTT
TTCATAATTGATATATGTGAAAAAGTTA
Found at i:5886836 original size:9 final size:9
Alignment explanation
Indices: 5886808--5886839 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
5886798 ACAAATTGTG
5886808 TATTTAG-A
1 TATTTAGAA
5886816 TATTTA-AA
1 TATTTAGAA
5886824 TATTTAGAA
1 TATTTAGAA
5886833 TATTTAG
1 TATTTAG
5886840 TTTATGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 13 0.59
9 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (9 bp):
TATTTAGAA
Found at i:5892277 original size:150 final size:151
Alignment explanation
Indices: 5892120--5892417 Score: 490
Period size: 151 Copynumber: 2.0 Consensus size: 151
5892110 TTAAAAAAAA
* * * *
5892120 TAAAATGTACTCATATATTATTTTTAAAATAGATTTCTTGATTA-CTTCAAAAAATGGATTTTTT
1 TAAAATGTACTAAGATATTATCTTTAAAATAGATTTCTTGATTATCTTCAAAAAATGAATTTTTT
5892184 GATAATTTAAATATATATCTTTTAAATTTCAAATTCTCAAATGCAAATTTGATTTTTAGAGATTT
66 GATAATTTAAATATATATCTTTTAAATTTCAAATTCTCAAATGCAAATTTGATTTTTAGAGATTT
*
5892249 CATAATTATCCACTATTAAAC
131 CATAATAATCCACTATTAAAC
* * *
5892270 TAAAATGTACTAAGATATTATCTTTAAAATGGATTTCTTGATTATTTTTAAAAAATGAATTTTTT
1 TAAAATGTACTAAGATATTATCTTTAAAATAGATTTCTTGATTATCTTCAAAAAATGAATTTTTT
* *
5892335 GATAATTTAAATATATATCTTTTAAATTTTAAATTCTCAAATGCAATTTTGATTTTTAGAGATTT
66 GATAATTTAAATATATATCTTTTAAATTTCAAATTCTCAAATGCAAATTTGATTTTTAGAGATTT
*
5892400 CATAATAATCCTCTATTA
131 CATAATAATCCACTATTA
5892418 TTTGATTATT
Statistics
Matches: 136, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
150 40 0.29
151 96 0.71
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (151 bp):
TAAAATGTACTAAGATATTATCTTTAAAATAGATTTCTTGATTATCTTCAAAAAATGAATTTTTT
GATAATTTAAATATATATCTTTTAAATTTCAAATTCTCAAATGCAAATTTGATTTTTAGAGATTT
CATAATAATCCACTATTAAAC
Found at i:5893092 original size:11 final size:12
Alignment explanation
Indices: 5893076--5893104 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5893066 ATTTTTGAAA
5893076 TTTAAT-AAATT
1 TTTAATAAAATT
5893087 TTTAATAAAATT
1 TTTAATAAAATT
5893099 TTTAAT
1 TTTAAT
5893105 TTTATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTAATAAAATT
Found at i:5893833 original size:61 final size:63
Alignment explanation
Indices: 5893713--5893833 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 63
5893703 CCATTTCAAA
* * * *
5893713 GATTTAGAGTTTAATTGATTGGAAATATTAGCTTAATTGTCAAATCTGTTTTGAAGGCTGTAG
1 GATTTAGAGTTTAATTGATTCGAAAAATTAGCTTAATTATCAAATATGTTTTGAAGGCTGTAG
*
5893776 GATTTAGAGTTTAATTGA-TCGAAAAATTAGCTTAA-TATCAAATATGTTTTGGAGGCTG
1 GATTTAGAGTTTAATTGATTCGAAAAATTAGCTTAATTATCAAATATGTTTTGAAGGCTG
5893834 CCTCTTACCT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 20 0.38
62 15 0.28
63 18 0.34
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (63 bp):
GATTTAGAGTTTAATTGATTCGAAAAATTAGCTTAATTATCAAATATGTTTTGAAGGCTGTAG
Found at i:5894761 original size:16 final size:17
Alignment explanation
Indices: 5894740--5894774 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5894730 TATTTTATAT
*
5894740 TTAAAAAT-TAACAAAA
1 TTAAAAATATAAAAAAA
5894756 TTAAAAATATAAAAAAA
1 TTAAAAATATAAAAAAA
5894773 TT
1 TT
5894775 CAATGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAATATAAAAAAA
Found at i:5901069 original size:12 final size:12
Alignment explanation
Indices: 5901031--5901076 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
5901021 AAAATGAATT
5901031 TATTTTTATGAG
1 TATTTTTATGAG
*
5901043 T-TTTTTA-AAG
1 TATTTTTATGAG
5901053 TTATTTTTATGAG
1 -TATTTTTATGAG
5901066 TATTTTGTATG
1 TATTTT-TATG
5901077 TATTAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
10 2 0.07
11 7 0.25
12 13 0.46
13 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (12 bp):
TATTTTTATGAG
Found at i:5908658 original size:142 final size:142
Alignment explanation
Indices: 5908402--5908689 Score: 513
Period size: 142 Copynumber: 2.0 Consensus size: 142
5908392 CTGCAAGTTT
*
5908402 TCTTATCTATTAAGCAATATCTAATCAATTTCAAATAAATTTCTTATGAGATTTGAATCACTATT
1 TCTTATCTATCAAGCAATATCTAATCAATTTCAAATAAATTTCTTATGAGATTTGAATCACTATT
*
5908467 CCTAATAATTACCATATTGACTCAAATTTCATTAAATCATTAGCTTCACCTATAATGGAAGTCTC
66 CCTAATAATTACCATATTGACTCAAATTTCATTAAATCATTAGCTTCACCTACAATGGAAGTCTC
5908532 ACAATCATCTTC
131 ACAATCATCTTC
* *
5908544 TCTTATCTATCAAGCAATATCTAATTAATTTCAAATAAATTTTTTATGAGATTTGAATCACTATT
1 TCTTATCTATCAAGCAATATCTAATCAATTTCAAATAAATTTCTTATGAGATTTGAATCACTATT
* * *
5908609 CTTAATAATTACCATCTTGACTCAAATTTCATTAAATCATTGGCTTCACCTACAATGGAAGTCTC
66 CCTAATAATTACCATATTGACTCAAATTTCATTAAATCATTAGCTTCACCTACAATGGAAGTCTC
5908674 ACAATCATCTTC
131 ACAATCATCTTC
5908686 TCTT
1 TCTT
5908690 GTATATTTTT
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (142 bp):
TCTTATCTATCAAGCAATATCTAATCAATTTCAAATAAATTTCTTATGAGATTTGAATCACTATT
CCTAATAATTACCATATTGACTCAAATTTCATTAAATCATTAGCTTCACCTACAATGGAAGTCTC
ACAATCATCTTC
Found at i:5912031 original size:14 final size:14
Alignment explanation
Indices: 5911992--5912034 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5911982 TTTATTAAAA
5911992 TTATTTTAAA-TAT
1 TTATTTTAAATTAT
* *
5912005 ATAATTTATAATTAT
1 TTATTTTA-AATTAT
5912020 TTATTTTAAATTAT
1 TTATTTTAAATTAT
5912034 T
1 T
5912035 GATATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.25
14 9 0.38
15 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTTTAAATTAT
Found at i:5920565 original size:14 final size:12
Alignment explanation
Indices: 5920542--5920582 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
5920532 ATACTTCTTA
5920542 AAAAATAATAAT
1 AAAAATAATAAT
*
5920554 AAATAT-ATAAT
1 AAAAATAATAAT
5920565 AACAAA-AATAAT
1 AA-AAATAATAAT
5920577 AAAAAT
1 AAAAAT
5920583 TTGAAATCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:5920764 original size:8 final size:8
Alignment explanation
Indices: 5920751--5920776 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5920741 GAAAAAAGAG
5920751 AATATATA
1 AATATATA
5920759 AATATATA
1 AATATATA
5920767 AATATATA
1 AATATATA
5920775 AA
1 AA
5920777 ATTAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATATA
Found at i:5926631 original size:88 final size:88
Alignment explanation
Indices: 5926477--5926651 Score: 314
Period size: 88 Copynumber: 2.0 Consensus size: 88
5926467 AAATAATTAC
* * *
5926477 ATAATAAAAAATAATGCAAGTATAGGTAAAATTTGCTAAGAAATTCTTCATTTTTATTCATAATA
1 ATAACAAAAAATAATGCAAATATAGGCAAAATTTGCTAAGAAATTCTTCATTTTTATTCATAATA
5926542 ATCATGTACATACAAAGTAAAAT
66 ATCATGTACATACAAAGTAAAAT
*
5926565 ATAACAAAAAATAATGCAAATATAGGCAAAATTTGCTGAGAAATTCTTCATTTTTATTCATAATA
1 ATAACAAAAAATAATGCAAATATAGGCAAAATTTGCTAAGAAATTCTTCATTTTTATTCATAATA
5926630 ATCATGTACATACAAAGTAAAA
66 ATCATGTACATACAAAGTAAAA
5926652 ACAAATATAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (88 bp):
ATAACAAAAAATAATGCAAATATAGGCAAAATTTGCTAAGAAATTCTTCATTTTTATTCATAATA
ATCATGTACATACAAAGTAAAAT
Found at i:5931761 original size:19 final size:21
Alignment explanation
Indices: 5931718--5931761 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5931708 ATTTATCTTT
* *
5931718 TAAAAAATTAACAATTGTTTT
1 TAAAAAATTAACAATTATTTC
5931739 TAAAAAATTAA-AA-TATTTC
1 TAAAAAATTAACAATTATTTC
5931758 TAAA
1 TAAA
5931762 TAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAAATTAACAATTATTTC
Found at i:5931850 original size:19 final size:19
Alignment explanation
Indices: 5931828--5931869 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5931818 TATTTTTCTT
* *
5931828 TTTTCTTTTACTTTCTTTC
1 TTTTCATTTACTTTCATTC
*
5931847 TTTTCATTTGCTTTCATTC
1 TTTTCATTTACTTTCATTC
5931866 TTTT
1 TTTT
5931870 TATATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTCATTTACTTTCATTC
Found at i:5932139 original size:12 final size:13
Alignment explanation
Indices: 5932122--5932155 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5932112 CCCCTCATCG
5932122 AAAGGAAAAAA-A
1 AAAGGAAAAAAGA
5932134 AAAGGAAAAAAGA
1 AAAGGAAAAAAGA
*
5932147 AAAAGAAAA
1 AAAGGAAAA
5932156 GAGGAGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAGGAAAAAAGA
Found at i:5932201 original size:33 final size:32
Alignment explanation
Indices: 5932128--5932201 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
5932118 ATCGAAAGGA
*
5932128 AAAAAAAAAGGAAAAAAGAAAAAGAAAAGAGG
1 AAAAAAAAAGGAAAAAAGAAAAAGAAAAGAAG
* *
5932160 AGACAAAAAAGG-AAAATGAAACAAGAAGAAGAAG
1 A-AAAAAAAAGGAAAAAAGAAA-AAGAA-AAGAAG
5932194 AAAAAAAA
1 AAAAAAAA
5932202 TACTATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 9 0.26
33 20 0.57
34 6 0.17
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (32 bp):
AAAAAAAAAGGAAAAAAGAAAAAGAAAAGAAG
Found at i:5932488 original size:18 final size:17
Alignment explanation
Indices: 5932448--5932495 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
5932438 AAACAAAAAA
5932448 AAAG-GAAAAACTTTTAG
1 AAAGAGAAAAA-TTTTAG
5932465 AAAGAGAGAAAATTTTA-
1 AAAGAGA-AAAATTTTAG
5932482 AATAGAGAAAAATT
1 AA-AGAGAAAAATT
5932496 CAAAAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 12 0.43
18 12 0.43
19 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.17, T:0.23
Consensus pattern (17 bp):
AAAGAGAAAAATTTTAG
Found at i:5935360 original size:3 final size:3
Alignment explanation
Indices: 5935352--5935376 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5935342 TGCTTTTGAA
5935352 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5935377 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5944076 original size:15 final size:16
Alignment explanation
Indices: 5944051--5944081 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5944041 GTCCAATTAG
5944051 ATTTATTATTTTTTTT
1 ATTTATTATTTTTTTT
5944067 ATTT-TTATTTTTTTT
1 ATTTATTATTTTTTTT
5944082 GTTTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
ATTTATTATTTTTTTT
Found at i:5944919 original size:19 final size:19
Alignment explanation
Indices: 5944897--5944957 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
5944887 AGGTTTTTCC
5944897 TTTTTCATTTTCT-TTTTAT
1 TTTTTCA-TTTCTATTTTAT
*
5944916 TTTTTGATTTCTATTTTATT
1 TTTTTCATTTCTATTTTA-T
*
5944936 TTATTTTATTT-TATTTTAT
1 TT-TTTCATTTCTATTTTAT
5944955 TTT
1 TTT
5944958 CACCCATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 6 0.16
19 14 0.38
20 10 0.27
21 7 0.19
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTCATTTCTATTTTAT
Found at i:5944975 original size:5 final size:5
Alignment explanation
Indices: 5944910--5944957 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
5944900 TTCATTTTCT
*
5944910 TTTTA -TTT- TTTGA TTTCTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5944958 CACCCATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 5 0.13
5 29 0.76
6 4 0.11
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5956503 original size:119 final size:117
Alignment explanation
Indices: 5956098--5956544 Score: 411
Period size: 118 Copynumber: 3.8 Consensus size: 117
5956088 TCACTTAATT
* * * * * * * *
5956098 TTGGCTCAGTCTAAATAATTTCTTATGATTTGTGGTTT-AGTCCTGATCATTTATTTTTAACC-T
1 TTGGCTCAGTCCAGATCATTTATTATGATTCGTGGTTTCA-TCCCGATCATTTATTCTTGACCTT
* * * * * * * * * * *
5956161 CAGCTCGGTCTTGGTCGTCTCATTTGACTCGTGGTTCTGTCCCAGTCATTTAATC
65 GA-CTCGGTCCTGATCATTTTATTTGACTTGTGGTTTTGT-CCAGTTACTTAGTC
* * * * * *
5956216 TTGGCTCAATCCAGATCATTTCTTATGATTCGTGATTCCATCTCGATCATTTATTCTCGACCTTG
1 TTGGCTCAGTCCAGATCATTTATTATGATTCGTGGTTTCATCCCGATCATTTATTCTTGACCTTG
* * * * *
5956281 ACTTGGTCCTGGTCACTTTATTTTGACTTGTGGTTTCGTCCCGTTCACTT-GAT-
66 ACTCGGTCCTGATCATTTTA-TTTGACTTGTGGTTTTGTCCAGTT-ACTTAG-TC
* * *
5956334 TTGGCTCAGTCCAGATCATTTATTATGATTCATAGTTTCGTCCCGATCATTTATTCTTGA-CTCT
1 TTGGCTCAGTCCAGATCATTTATTATGATTCGTGGTTTCATCCCGATCATTTATTCTTGACCT-T
* *
5956398 GACTCGGTCCTGATCGTTTTATTTTGACTTATGGTTTTGTCCTAGTTACTTAGTC
65 GACTCGGTCCTGATCATTTTA-TTTGACTTGTGGTTTTGTCC-AGTTACTTAGTC
** *
5956453 TTGGCTCAGTTTAGATCATTTATTATGATTCGTGGTTTCATCCCGATCATTCATT-TTCGACCTT
1 TTGGCTCAGTCCAGATCATTTATTATGATTCGTGGTTTCATCCCGATCATTTATTCTT-GACCTT
*
5956517 GACTCGATCCTGATCATTTTATTTGACT
65 GACTCGGTCCTGATCATTTTATTTGACT
5956545 CATGTTTAAT
Statistics
Matches: 268, Mismatches: 50, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
117 2 0.01
118 167 0.62
119 97 0.36
120 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (117 bp):
TTGGCTCAGTCCAGATCATTTATTATGATTCGTGGTTTCATCCCGATCATTTATTCTTGACCTTG
ACTCGGTCCTGATCATTTTATTTGACTTGTGGTTTTGTCCAGTTACTTAGTC
Found at i:5956515 original size:237 final size:236
Alignment explanation
Indices: 5956088--5956544 Score: 540
Period size: 237 Copynumber: 1.9 Consensus size: 236
5956078 TTGCATTATC
* * ** * *
5956088 TCACTTAATTTTGGCTCAGTCTAAATAATTTCTTATGATTTGTGGTTTAGTCCTGATCATTTATT
1 TCACTTAATTTTGGCTCAGTCCAAATAATTTATTATGATTCATAGTTTAGTCCCGATCATTTATT
* * * * *
5956153 TTTAACCTCAGCTCGGTCTTGGTCGTCTCATTTGACTCGTGGTTCTGTCCCAGTCATTTAATCTT
66 CTTAACCTCAGCTCGGTCCTGATCGTCTCATTTGACTCATGGTTCTGTCCCAGTCACTTAATCTT
* * *
5956218 GGCTCAATCCAGATCATTTCTTATGATTCGTGATTCCATCTCGATCATTTATTCTCGACCTTGAC
131 GGCTCAATCCAGATCATTTATTATGATTCGTGATTCCATCCCGATCATTCATTCTCGACCTTGAC
* * *
5956283 TTGGTCCTGGTCACTTTATTTTGACTTGTGGTTTCGTCCCGT
196 TCGATCCTGATCACTTTA-TTTGACTTGTGGTTTCGTCCCGT
* * * *
5956325 TCACTTGA-TTTGGCTCAGTCCAGATCATTTATTATGATTCATAGTTTCGTCCCGATCATTTATT
1 TCACTTAATTTTGGCTCAGTCCAAATAATTTATTATGATTCATAGTTTAGTCCCGATCATTTATT
* * * * * * * * *
5956389 CTTGA-CTCTGACTCGGTCCTGATCGTTTTATTTTGACTTATGGTTTTGTCCTAGTTACTTAGTC
66 CTTAACCTCAG-CTCGGTCCTGATCGTCTCA-TTTGACTCATGGTTCTGTCCCAGTCACTTAATC
* ** * * *
5956453 TTGGCTCAGTTTAGATCATTTATTATGATTCGTGGTTTCATCCCGATCATTCATTTTCGACCTTG
129 TTGGCTCAATCCAGATCATTTATTATGATTCGTGATTCCATCCCGATCATTCATTCTCGACCTTG
*
5956518 ACTCGATCCTGATCATTTTATTTGACT
194 ACTCGATCCTGATCACTTTATTTGACT
5956545 CATGTTTAAT
Statistics
Matches: 181, Mismatches: 37, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
235 4 0.02
236 72 0.40
237 105 0.58
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.44
Consensus pattern (236 bp):
TCACTTAATTTTGGCTCAGTCCAAATAATTTATTATGATTCATAGTTTAGTCCCGATCATTTATT
CTTAACCTCAGCTCGGTCCTGATCGTCTCATTTGACTCATGGTTCTGTCCCAGTCACTTAATCTT
GGCTCAATCCAGATCATTTATTATGATTCGTGATTCCATCCCGATCATTCATTCTCGACCTTGAC
TCGATCCTGATCACTTTATTTGACTTGTGGTTTCGTCCCGT
Found at i:5956739 original size:25 final size:26
Alignment explanation
Indices: 5956695--5956748 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
5956685 ATCTAGGCCC
*
5956695 ATTTTGGTTCAGGCCCAACTAAGCCT
1 ATTTTGGTTCAAGCCCAACTAAGCCT
*
5956721 ATTTTGG-TCAAGCCCAACTAGGCCT
1 ATTTTGGTTCAAGCCCAACTAAGCCT
5956746 ATT
1 ATT
5956749 ACAGCCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (26 bp):
ATTTTGGTTCAAGCCCAACTAAGCCT
Found at i:5957639 original size:11 final size:11
Alignment explanation
Indices: 5957619--5957668 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
5957609 GATCATAAGT
*
5957619 TTTTTTTTTTCA
1 TTTTTATTTT-A
*
5957631 TTTTATTTTTTA
1 TTTT-TATTTTA
5957643 TTTTTATTTTA
1 TTTTTATTTTA
5957654 TTTTTATTTTA
1 TTTTTATTTTA
5957665 TTTT
1 TTTT
5957669 CACCCATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
11 21 0.58
12 9 0.25
13 6 0.17
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:5957639 original size:13 final size:13
Alignment explanation
Indices: 5957618--5957663 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
5957608 CGATCATAAG
5957618 TTTTT-TTTTTTCA
1 TTTTTATTTTTT-A
5957631 -TTTTATTTTTTA
1 TTTTTATTTTTTA
5957643 TTTTTA--TTTTA
1 TTTTTATTTTTTA
5957654 TTTTTATTTT
1 TTTTTATTTT
5957664 ATTTTCACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 11 0.38
12 5 0.17
13 13 0.45
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:5957641 original size:18 final size:17
Alignment explanation
Indices: 5957618--5957668 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
5957608 CGATCATAAG
5957618 TTTTTTTTTTTCATTTTA
1 TTTTTTTTTTT-ATTTTA
5957636 TTTTTTATTTTTATTTTA
1 TTTTTT-TTTTTATTTTA
*
5957654 -TTTTTATTTTATTTT
1 TTTTTTTTTTTATTTT
5957669 CACCCATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 12 0.39
19 5 0.16
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTTTTTATTTTA
Found at i:5957686 original size:6 final size:6
Alignment explanation
Indices: 5957618--5957668 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
5957608 CGATCATAAG
*
5957618 TTTTTT TTTTTCA -TTTTA TTTTTTA TTTTTA -TTTTA TTTTTA -TTTTA
1 TTTTTA TTTTT-A TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
5957665 TTTT
1 TTTT
5957669 CACCCATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
5 11 0.28
6 23 0.59
7 5 0.13
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:5959189 original size:7 final size:7
Alignment explanation
Indices: 5959177--5959201 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5959167 GCAGTGATGG
5959177 TTTCAAT
1 TTTCAAT
5959184 TTTCAAT
1 TTTCAAT
5959191 TTTCAAT
1 TTTCAAT
5959198 TTTC
1 TTTC
5959202 CACGAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTCAAT
Found at i:5968492 original size:35 final size:35
Alignment explanation
Indices: 5968446--5968516 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
5968436 GATGATTCCG
5968446 CATTAACAAAGGTACCAAGAGAATCCGACTATGTA
1 CATTAACAAAGGTACCAAGAGAATCCGACTATGTA
5968481 CATTAACAAAGGTACCAAGAGAATCCGACTATGTA
1 CATTAACAAAGGTACCAAGAGAATCCGACTATGTA
5968516 C
1 C
5968517 CAAACTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (35 bp):
CATTAACAAAGGTACCAAGAGAATCCGACTATGTA
Found at i:5968741 original size:138 final size:138
Alignment explanation
Indices: 5968493--5968768 Score: 516
Period size: 138 Copynumber: 2.0 Consensus size: 138
5968483 TTAACAAAGG
*
5968493 TACCAAGAGAATCCGACTATGTACCAAACTTATATTCTCCAGATAGACGGCTCATCTCCAATTAC
1 TACCAAGAGAATCCGACTATGTACCAAACTTATATTCTCCAGATAGACGGCTCACCTCCAATTAC
5968558 AAATAAAAATCCTTGCAATGCCACCTATAGGCAACGCCCTAGGCCAAGGAGCCAAAACCAACCTC
66 AAATAAAAATCCTTGCAATGCCACCTATAGGCAACGCCCTAGGCCAAGGAGCCAAAACCAACCTC
*
5968623 TCCTCAGC
131 TCCGCAGC
*
5968631 TACCAAGAGAATCCGACTATGTACCAAACTTATATTCTCCAGATAGACGTCTCACCTCCAATTAC
1 TACCAAGAGAATCCGACTATGTACCAAACTTATATTCTCCAGATAGACGGCTCACCTCCAATTAC
*
5968696 AAATAAAAATCCTTGCAATGCTACCTATAGGCAACGCCCTAGGCCAAGGAGCCAAAACCAACCTC
66 AAATAAAAATCCTTGCAATGCCACCTATAGGCAACGCCCTAGGCCAAGGAGCCAAAACCAACCTC
5968761 TCCGCAGC
131 TCCGCAGC
5968769 CACTCACAAT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 134 1.00
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (138 bp):
TACCAAGAGAATCCGACTATGTACCAAACTTATATTCTCCAGATAGACGGCTCACCTCCAATTAC
AAATAAAAATCCTTGCAATGCCACCTATAGGCAACGCCCTAGGCCAAGGAGCCAAAACCAACCTC
TCCGCAGC
Found at i:5973882 original size:28 final size:30
Alignment explanation
Indices: 5973827--5973884 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
5973817 AAAATTGGTC
* * *
5973827 ACTTAACTTTTTAAAATTTTCTATTTTGAT
1 ACTTAACTTTTAAAAATTTACTAATTTGAT
5973857 ACTTAA-TTTTAAAAATTTAC-AATTTGAT
1 ACTTAACTTTTAAAAATTTACTAATTTGAT
5973885 CATAAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 12 0.48
30 6 0.24
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (30 bp):
ACTTAACTTTTAAAAATTTACTAATTTGAT
Found at i:5974542 original size:14 final size:15
Alignment explanation
Indices: 5974523--5974551 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5974513 AATTGCCAAA
5974523 ATTA-TTAAAATATT
1 ATTATTTAAAATATT
5974537 ATTATTTAAAATATT
1 ATTATTTAAAATATT
5974552 TTTTGTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTATTTAAAATATT
Found at i:5991894 original size:21 final size:20
Alignment explanation
Indices: 5991857--5991897 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5991847 TTTAAATTCA
* *
5991857 TTTTTATTTTTTTTAATAAT
1 TTTTTATTTATTATAATAAT
5991877 TTTTTATTTAATTATAATAAT
1 TTTTTATTT-ATTATAATAAT
5991898 AAATATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATTTATTATAATAAT
Found at i:5992156 original size:21 final size:22
Alignment explanation
Indices: 5992132--5992176 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
5992122 AAAATTATGC
5992132 ATAAATATCGTTAAATT-TAAA
1 ATAAATATCGTTAAATTGTAAA
*
5992153 ATAAATATTGTTAAATTGTAAA
1 ATAAATATCGTTAAATTGTAAA
5992175 AT
1 AT
5992177 TAACAGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
ATAAATATCGTTAAATTGTAAA
Found at i:5992172 original size:126 final size:125
Alignment explanation
Indices: 5992029--5992277 Score: 435
Period size: 126 Copynumber: 2.0 Consensus size: 125
5992019 TTTTGTACAC
*
5992029 AAATATTGTTAAATTGTAAAATTAGCAACTTTTGTGTCAAAAAATATTATTAAATTTAATTATTG
1 AAATATTGTTAAATTGTAAAATTAACAACTTTTGTGTCAAAAAATATTATTAAATTTAATTA-TG
* *
5992094 TTTTTTTGACACAAACGTTGCTAATTAAAAAATTATGCATAAATATCGTTAAATTTAAAAT
65 TTTTTTTGACACAAACGTCGCTAATTAAAAAATTACGCATAAATATCGTTAAATTTAAAAT
*
5992155 AAATATTGTTAAATTGTAAAATTAACAGCTTTTGTGTCAAAAAATATTATTAAATTTAATTATGT
1 AAATATTGTTAAATTGTAAAATTAACAACTTTTGTGTCAAAAAATATTATTAAATTTAATTATGT
* *
5992220 TTTTTTGATACAAACGTCGTTAATTAAAAAATTACGCATAAATATCGTTAAATTTAAA
66 TTTTTTGACACAAACGTCGCTAATTAAAAAATTACGCATAAATATCGTTAAATTTAAA
5992278 GATATTTTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 57 0.49
126 60 0.51
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (125 bp):
AAATATTGTTAAATTGTAAAATTAACAACTTTTGTGTCAAAAAATATTATTAAATTTAATTATGT
TTTTTTGACACAAACGTCGCTAATTAAAAAATTACGCATAAATATCGTTAAATTTAAAAT
Found at i:5993677 original size:17 final size:17
Alignment explanation
Indices: 5993636--5993677 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5993626 TATCAAATAG
5993636 TATTTTT-ATTATATTA
1 TATTTTTAATTATATTA
* * *
5993652 AATTATTAATTATTTTA
1 TATTTTTAATTATATTA
5993669 TATTTTTAA
1 TATTTTTAA
5993678 ATAAAAATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTTAATTATATTA
Found at i:5999493 original size:24 final size:22
Alignment explanation
Indices: 5999453--5999519 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 22
5999443 ATAAAATTAT
*
5999453 AATTTTTAATATCAAAAAATAAAA
1 AATTTTAAATAT-AAAAAAT-AAA
5999477 AATTTTAAAATATAAAAAATAAA
1 AATTTT-AAATATAAAAAATAAA
5999500 AATTTTAAATATTAAAAAAT
1 AATTTTAAATA-TAAAAAAT
5999520 GACATAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 5 0.12
23 17 0.43
24 13 0.32
25 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (22 bp):
AATTTTAAATATAAAAAATAAA
Found at i:6002075 original size:58 final size:58
Alignment explanation
Indices: 6001984--6002095 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
6001974 ATTATATAAT
* **
6001984 ACTTTAATTTAGTTATACAGGCACTAACGTTGTTGGATAGTGTCATGAAGGTTACTTA
1 ACTTTAATTTAGTTATACAGACACTAACGTTGTTGGATAGCATCATGAAGGTTACTTA
* * *
6002042 ACTTTGATTTAGTTATACAGATACTAACTTTGTTGGATAGCATCATGAAGGTTA
1 ACTTTAATTTAGTTATACAGACACTAACGTTGTTGGATAGCATCATGAAGGTTA
6002096 GCTGGAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (58 bp):
ACTTTAATTTAGTTATACAGACACTAACGTTGTTGGATAGCATCATGAAGGTTACTTA
Found at i:6030833 original size:4 final size:4
Alignment explanation
Indices: 6030811--6030884 Score: 58
Period size: 4 Copynumber: 17.2 Consensus size: 4
6030801 AATATTTTTT
* * ** *
6030811 TTAA ATAA TTGAA TGAA TTAA TTGAA TTAA TTAA TTTT TTAA ATAA TTAAA
1 TTAA TTAA TT-AA TTAA TTAA TT-AA TTAA TTAA TTAA TTAA TTAA TT-AA
6030862 TTAA TTAA TTAAA TTAAA TTAA T
1 TTAA TTAA TT-AA TT-AA TTAA T
6030885 CAACTTTAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
4 36 0.64
5 20 0.36
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (4 bp):
TTAA
Found at i:6030836 original size:9 final size:8
Alignment explanation
Indices: 6030811--6030884 Score: 58
Period size: 9 Copynumber: 8.6 Consensus size: 8
6030801 AATATTTTTT
*
6030811 TTAAATAA
1 TTAATTAA
*
6030819 TTGAATGAA
1 TT-AATTAA
6030828 TTAATTGAA
1 TTAATT-AA
6030837 TTAATTAA
1 TTAATTAA
**
6030845 TTTTTTAA
1 TTAATTAA
*
6030853 ATAATTAAA
1 TTAATT-AA
6030862 TTAATTAA
1 TTAATTAA
6030870 TTAAATTAAA
1 TT-AATT-AA
6030880 TTAAT
1 TTAAT
6030885 CAACTTTAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
8 20 0.38
9 28 0.54
10 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (8 bp):
TTAATTAA
Found at i:6030857 original size:38 final size:39
Alignment explanation
Indices: 6030807--6030884 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
6030797 AAGTAATATT
* *
6030807 TTTTTTAAATAATTGAATGAATTAATTGAATT-AATTAA
1 TTTTTTAAATAATTAAATGAATTAATTAAATTAAATTAA
*
6030845 TTTTTTAAATAATTAAATTAATTAATTAAATTAAATTAA
1 TTTTTTAAATAATTAAATGAATTAATTAAATTAAATTAA
6030884 T
1 T
6030885 CAACTTTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (39 bp):
TTTTTTAAATAATTAAATGAATTAATTAAATTAAATTAA
Found at i:6030865 original size:13 final size:13
Alignment explanation
Indices: 6030811--6030880 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
6030801 AATATTTTTT
*
6030811 TTAAATAATTGAA
1 TTAAATAATTAAA
* * *
6030824 TGAATTAATTGAA
1 TTAAATAATTAAA
* **
6030837 TTAATTAATT-TT
1 TTAAATAATTAAA
6030849 TTAAATAATTAAA
1 TTAAATAATTAAA
*
6030862 TTAATTAATTAAA
1 TTAAATAATTAAA
6030875 TTAAAT
1 TTAAAT
6030881 TAATCAACTT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
12 9 0.20
13 37 0.80
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (13 bp):
TTAAATAATTAAA
Found at i:6032262 original size:19 final size:18
Alignment explanation
Indices: 6032233--6032269 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6032223 ATATCACTTA
6032233 TAATTATTATAATATAAT
1 TAATTATTATAATATAAT
*
6032251 TAATTAATTATAATTTAAT
1 TAATT-ATTATAATATAAT
6032270 ATTATGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTATTATAATATAAT
Found at i:6032571 original size:24 final size:26
Alignment explanation
Indices: 6032530--6032578 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
6032520 TTAGTAACTT
6032530 TATTTGTGAATATAATATA-ATATAA
1 TATTTGTGAATATAATATATATATAA
* *
6032555 TATTT-TGCATATCATATATATATA
1 TATTTGTGAATATAATATATATATA
6032579 TACAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (26 bp):
TATTTGTGAATATAATATATATATAA
Found at i:6033399 original size:114 final size:114
Alignment explanation
Indices: 6033269--6033499 Score: 365
Period size: 114 Copynumber: 2.0 Consensus size: 114
6033259 TTATTTGATT
6033269 TTTTGTTATATATCTTTGCATCCCTTTATTTAATTAATTATTTATAATTAATACTATTTATAGGT
1 TTTTGTTATATATCTTTGCATCCCTTTATTTAATTAATTATTTATAATTAATACTATTTATAGGT
*
6033334 TTCATTCTATTTTAGAAATTGTAGTAACTAAAACAAATAAGGCGACAAG
66 TTCATTCTATTTTAGAAATTGTAGTAACTAAAACAAATAAGGCAACAAG
* * * *
6033383 TTTTG-TACTATATCTTTGCTTCCTTTTATTTATTTAATTGTTTATAATTAATACTATTTATAGG
1 TTTTGTTA-TATATCTTTGCATCCCTTTATTTAATTAATTATTTATAATTAATACTATTTATAGG
* * * *
6033447 TTTTATTCTGTTTTAGAAATTGTTGTGACTAAAACAAATAAGGCAACAAG
65 TTTCATTCTATTTTAGAAATTGTAGTAACTAAAACAAATAAGGCAACAAG
6033497 TTT
1 TTT
6033500 GTAAAGAAAC
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
113 2 0.02
114 105 0.98
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (114 bp):
TTTTGTTATATATCTTTGCATCCCTTTATTTAATTAATTATTTATAATTAATACTATTTATAGGT
TTCATTCTATTTTAGAAATTGTAGTAACTAAAACAAATAAGGCAACAAG
Found at i:6034798 original size:18 final size:18
Alignment explanation
Indices: 6034775--6034809 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6034765 ATTTATGTTT
6034775 TTATGGTTATCATCATCG
1 TTATGGTTATCATCATCG
6034793 TTATGGTTATCATCATC
1 TTATGGTTATCATCATC
6034810 ATGTATGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (18 bp):
TTATGGTTATCATCATCG
Found at i:6043996 original size:10 final size:10
Alignment explanation
Indices: 6043983--6044021 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
6043973 AAAATTTAAA
6043983 AATTATTTAG
1 AATTATTTAG
6043993 AATTATTT-G
1 AATTATTTAG
6044002 AAATTATTTAG
1 -AATTATTTAG
6044013 AATTATTTA
1 AATTATTTA
6044022 TTTTTGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 25 0.93
11 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (10 bp):
AATTATTTAG
Found at i:6044005 original size:20 final size:20
Alignment explanation
Indices: 6043982--6044020 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
6043972 TAAAATTTAA
6043982 AAATTATTTAGAATTATTTG
1 AAATTATTTAGAATTATTTG
6044002 AAATTATTTAGAATTATTT
1 AAATTATTTAGAATTATTT
6044021 ATTTTTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
AAATTATTTAGAATTATTTG
Found at i:6044412 original size:19 final size:19
Alignment explanation
Indices: 6044388--6044430 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
6044378 TTATTAGTTA
6044388 ATACTTTAATTAAAAATATT
1 ATACTTTAA-TAAAAATATT
*
6044408 A-AC-TTGATAAAAATATT
1 ATACTTTAATAAAAATATT
6044425 ATACTT
1 ATACTT
6044431 ATGTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
17 11 0.55
18 5 0.25
19 3 0.15
20 1 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (19 bp):
ATACTTTAATAAAAATATT
Done.