Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 89
Found at i:2004570 original size:45 final size:44
Alignment explanation
Indices: 2004462--2004571 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 44
2004452 CCAAACAAGG
* * *
2004462 TGTTGATGTTGTGTGACCCATACCTAAACTAAGGTATTGGGAGG
1 TGTTGATGTTGTGTGACCCAGACCTAAACTAAGATATTGGGAGA
* * * *** *
2004506 TGTCGATGCTATGTGACCCAGACCTCGCCTGAGATATTTGGGAGA
1 TGTTGATGTTGTGTGACCCAGACCTAAACTAAGATA-TTGGGAGA
*
2004551 TGTTGATGTTGTGTAACCCAG
1 TGTTGATGTTGTGTGACCCAG
2004572 GTCTACCCAA
Statistics
Matches: 51, Mismatches: 14, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
44 27 0.53
45 24 0.47
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (44 bp):
TGTTGATGTTGTGTGACCCAGACCTAAACTAAGATATTGGGAGA
Found at i:2005793 original size:7 final size:8
Alignment explanation
Indices: 2005750--2005792 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
2005740 AATTTGAAAT
2005750 AATATTAAA
1 AATATT-AA
2005759 AATATTGAA
1 AATATT-AA
* *
2005768 AAAAATAA
1 AATATTAA
2005776 AATATTAA
1 AATATTAA
2005784 AATATTAA
1 AATATTAA
2005792 A
1 A
2005793 TTAACATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
8 17 0.59
9 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (8 bp):
AATATTAA
Found at i:2007133 original size:23 final size:22
Alignment explanation
Indices: 2007085--2007134 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
2007075 GTATTATATT
*
2007085 ATATTTTAAAATATTAATTAAT
1 ATATTTTAAAATATTAATTAAA
* *
2007107 ATATTTTAAATATTTTTATTAAA
1 ATATTTTAAA-ATATTAATTAAA
2007130 ATATT
1 ATATT
2007135 ATTGGATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:2007264 original size:34 final size:36
Alignment explanation
Indices: 2007217--2007293 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 36
2007207 TCTAAAACTA
* * * * *
2007217 ATAAATAATATAAAATTTACTAA-TA-ATTTATTAT
1 ATAATTAAAATAAAATATAATAACTATATTTATAAT
2007251 ATAATTAAAATAAAATATAATAACTTATATTTATAAT
1 ATAATTAAAATAAAATATAATAAC-TATATTTATAAT
2007288 ATAATT
1 ATAATT
2007294 GAGTATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 19 0.54
36 2 0.06
37 14 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (36 bp):
ATAATTAAAATAAAATATAATAACTATATTTATAAT
Found at i:2007328 original size:23 final size:23
Alignment explanation
Indices: 2007302--2007349 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2007292 TTGAGTATTT
2007302 TATTATAATATTA-AAATATATAA
1 TATTATAATATTAGAAATAT-TAA
*
2007325 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAGAAATATTAA
2007348 TA
1 TA
2007350 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAATATTAGAAATATTAA
Found at i:2007380 original size:24 final size:23
Alignment explanation
Indices: 2007344--2007388 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2007334 ATTAGAAATA
2007344 TTAATAAATATATTTTAAATATT
1 TTAATAAATATATTTTAAATATT
* *
2007367 TTAATAATTAATATTTTGAATA
1 TTAATAAAT-ATATTTTAAATA
2007389 AAAGGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAATAAATATATTTTAAATATT
Found at i:2010089 original size:81 final size:81
Alignment explanation
Indices: 2009948--2010160 Score: 313
Period size: 81 Copynumber: 2.6 Consensus size: 81
2009938 TACATTTCTG
* * * *
2009948 TTCTTCAATTATG-CTGGATTTAC-GTTTAAGAAGTTGCTGTGTTTGTTGTTATGATCCTTCAGT
1 TTCTTCAATTATGATTGGATTTGCTG-TTAAGAAGTTGCTGAGTTTGTTGTTACGATCCTTCAGT
2010011 GACAATAGTTGTTCTTA
65 GACAATAGTTGTTCTTA
* * *
2010028 TTCTTCAATTACGATTGGATTTGCTGTTAAGAAGTTGTTGAGTTTGTTGTTACGATTCTTCAGTG
1 TTCTTCAATTATGATTGGATTTGCTGTTAAGAAGTTGCTGAGTTTGTTGTTACGATCCTTCAGTG
*
2010093 ACAATAGTTGTTCTTG
66 ACAATAGTTGTTCTTA
* *
2010109 TTCTTCAATTATGATTGGATTTGCTGTTAAGAAATTGCTGAGATTGTTGTTA
1 TTCTTCAATTATGATTGGATTTGCTGTTAAGAAGTTGCTGAGTTTGTTGTTA
2010161 TAATTGCTTT
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 12 0.10
81 106 0.89
82 1 0.01
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.46
Consensus pattern (81 bp):
TTCTTCAATTATGATTGGATTTGCTGTTAAGAAGTTGCTGAGTTTGTTGTTACGATCCTTCAGTG
ACAATAGTTGTTCTTA
Found at i:2010216 original size:65 final size:66
Alignment explanation
Indices: 2010107--2010231 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 66
2010097 TAGTTGTTCT
* *
2010107 TGTTCTTCAATTATGATTGGATTTGCTGTTAAGAAATTGCTGAGATTGTTG-TTATAATTGCTTT
1 TGTTCTTCAATTATGATTGGATTTACCGTTAAGAAATTGCTGAGATTGTTGTTTATAATTGCTTT
2010171 C
66 C
* * *
2010172 TGTTTTTCAATTATGCTTGGATTTACCGTCTAA-AAGTTGCTGAGATTGTTGTTTATAATT
1 TGTTCTTCAATTATGATTGGATTTACCGT-TAAGAAATTGCTGAGATTGTTGTTTATAATT
2010232 TTTTCAGCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 42 0.79
66 11 0.21
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (66 bp):
TGTTCTTCAATTATGATTGGATTTACCGTTAAGAAATTGCTGAGATTGTTGTTTATAATTGCTTT
C
Found at i:2016542 original size:43 final size:42
Alignment explanation
Indices: 2016486--2016710 Score: 204
Period size: 43 Copynumber: 5.3 Consensus size: 42
2016476 GGTAACAAAA
* *** *
2016486 AAACGCCGCAATAGATAACGATATATAGTGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGATAT-TAGCGGCGTTTGTCCAAC
* *
2016529 AAACGCCGTAATAGGTGTTGATATTGAGCGGCGTTTGTCCACC
1 AAACGCCGCAATAGGTGTTGATATT-AGCGGCGTTTGTCCAAC
2016572 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCCAAC
1 AAACGCCGCAATAGGTGTTGATA-TTAGCGGCGTTTGTCCAAC
** * * *
2016614 AAATACCGCAATAGGTATTGAGATTTAGCGGCGTGTT-T-GACAC
1 AAACGCCGCAATAGGTGTTGATA-TTAGCGGCGT-TTGTCCA-AC
* * ** * *
2016657 AAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATA-TTAGCGGCGTTTGTCCAAC
2016700 AAACGCCGCAA
1 AAACGCCGCAA
2016711 AAGATCTGGT
Statistics
Matches: 155, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
42 39 0.25
43 114 0.74
44 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAATAGGTGTTGATATTAGCGGCGTTTGTCCAAC
Found at i:2016640 original size:42 final size:43
Alignment explanation
Indices: 2016515--2016710 Score: 227
Period size: 43 Copynumber: 4.6 Consensus size: 43
2016505 GATATATAGT
* * *
2016515 GGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATTGAGC
1 GGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGC
* *
2016558 GGCGTTTGTCCACCAAACGCCGCAATAGGTGTTGATATTTAGC
1 GGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGC
** *
2016601 GGCGTTT-TCCAACAAATACCGCAATAGGTATTGAGATTTAGC
1 GGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGC
* *
2016643 GGCGTGTT-T-GACACAAACGCCGCAATAGGTCTTGAGATTTAGC
1 GGCGT-TTGTCCA-ACAAACGCCGCAATAGGTGTTGAGATTTAGC
** * *
2016686 GATGTTTTTCCCACAAACGCCGCAA
1 GGCGTTTGTCCAACAAACGCCGCAA
2016711 AAGATCTGGT
Statistics
Matches: 133, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
42 38 0.29
43 95 0.71
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGC
Found at i:2016660 original size:85 final size:86
Alignment explanation
Indices: 2016486--2016710 Score: 231
Period size: 85 Copynumber: 2.6 Consensus size: 86
2016476 GGTAACAAAA
* ** * * * * * *
2016486 AAACGCCGCAATAGATAACGATATATAGTGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGAT
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAACAAACACCGCAATAGGTATTGAG
*
2016551 ATTGAGCGGCGTTTGTCCACC
66 ATTGAGCGGCGTTTGTACACC
* *
2016572 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCCAACAAATACCGCAATAGGTATTGAG
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAACAAACACCGCAATAGGTATTGAG
*
2016636 ATTTAGCGGCGTGTT-TGACA-C
66 ATTGAGCGGCGT-TTGT-ACACC
* * ** * * *
2016657 AAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCCCACAAACGCCGCAA
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAACAAACACCGCAA
2016711 AAGATCTGGT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
85 68 0.59
86 48 0.41
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (86 bp):
AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAACAAACACCGCAATAGGTATTGAG
ATTGAGCGGCGTTTGTACACC
Found at i:2016959 original size:21 final size:21
Alignment explanation
Indices: 2016906--2016965 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
2016896 ATTTTCCAAT
*
2016906 AAAATTGACATCCATAAACAAC
1 AAAATTGAAATCCAT-AACAAC
* * *
2016928 AAACTTAAAATCCATAACAAG
1 AAAATTGAAATCCATAACAAC
2016949 AAAATTGAAATCCATAA
1 AAAATTGAAATCCATAA
2016966 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.57, C:0.18, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAATTGAAATCCATAACAAC
Found at i:2020562 original size:31 final size:31
Alignment explanation
Indices: 2020524--2020679 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
2020514 CCCGAAGGAC
* * *
2020524 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
2020555 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2020586 CAGTCCATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2020617 CAGTCCATATGTCCCCAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2020648 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2020679 C
1 C
2020680 CCTCTACCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2023231 original size:42 final size:41
Alignment explanation
Indices: 2022985--2023326 Score: 269
Period size: 41 Copynumber: 8.3 Consensus size: 41
2022975 GGTATATATA
* * * * * *
2022985 TAGCAGCGTTTGTATAAAAACACCACAAAAGAACGATTATT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * * * * *
2023026 TAGCGGTGTTTGTGCTTAAAACACCATTAAAGTAC-AGTATT
1 TAGCGGCGTTTGT-ATAAAAACGCCACTAAAGTACGAGTCTT
* * * * *
2023067 TAGTGGCGTTTATATAAAAGCGCCACTAAAGTATGAGTATT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
* * ** ** * * *
2023108 TGGAGGATTTTGGGCTTAAAATGCCACTAAAGTATGAGTCTT
1 TAGCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTT
* * * *
2023150 TAGCAGCGTTTGTATAAAAATGCCACTAAAGTACTAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
*
2023191 TAGCGGCGTTTGTATAAACAACGCCACTAAA-TCACGAGTCTA
1 TAGCGGCGTTTGTATAAA-AACGCCACTAAAGT-ACGAGTCTT
* *
2023233 TAGCGGCGTTTGTATAAAAAACACCACTAAAGTAC-A-TTTT
1 TAGCGGCGTTTGTAT-AAAAACGCCACTAAAGTACGAGTCTT
* * * * *
2023273 TAGCGTCGTTTTTATAAAAACGACGCTATAGTACGAGTCTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
2023314 TAGCGGCGTTTGT
1 TAGCGGCGTTTGT
2023327 TCTAAAAATG
Statistics
Matches: 238, Mismatches: 54, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
39 15 0.06
40 31 0.13
41 96 0.40
42 92 0.39
43 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (41 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTT
Found at i:2023342 original size:42 final size:42
Alignment explanation
Indices: 2022985--2023334 Score: 243
Period size: 42 Copynumber: 8.5 Consensus size: 42
2022975 GGTATATATA
* * * * * *
2022985 TAGCAGCGTTTG-TATAAAAACACCACAAAAGAACGATTATT
1 TAGCGGCGTTTGTTATAAAAACGCCACTAAAGTACGAGTCTT
* ** * * * *
2023026 TAGCGGTGTTTGTGCTTAAAACACCATTAAAGTAC-AGTATT
1 TAGCGGCGTTTGTTATAAAAACGCCACTAAAGTACGAGTCTT
* * * * *
2023067 TAGTGGCGTTT-ATATAAAAGCGCCACTAAAGTATGAGTATT
1 TAGCGGCGTTTGTTATAAAAACGCCACTAAAGTACGAGTCTT
* * ** *** * * *
2023108 TGGAGGATTTTGGGCTTAAAATGCCACTAAAGTATGAGTCTT
1 TAGCGGCGTTTGTTATAAAAACGCCACTAAAGTACGAGTCTT
* * * *
2023150 TAGCAGCGTTTG-TATAAAAATGCCACTAAAGTACTAGTCTA
1 TAGCGGCGTTTGTTATAAAAACGCCACTAAAGTACGAGTCTT
*
2023191 TAGCGGCGTTTG-TATAAACAACGCCACTAAA-TCACGAGTCTA
1 TAGCGGCGTTTGTTATAAA-AACGCCACTAAAGT-ACGAGTCTT
* *
2023233 TAGCGGCGTTTG-TATAAAAAACACCACTAAAGTAC-A-TTTT
1 TAGCGGCGTTTGTTAT-AAAAACGCCACTAAAGTACGAGTCTT
* * * *
2023273 TAGCGTCGTTT-TTATAAAAACGACGCTATAGTACGAGTCTT
1 TAGCGGCGTTTGTTATAAAAACGCCACTAAAGTACGAGTCTT
*
2023314 TAGCGGCGTTTGTTCTAAAAA
1 TAGCGGCGTTTGTTATAAAAA
2023335 TGCCGCTACA
Statistics
Matches: 243, Mismatches: 55, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
39 15 0.06
40 31 0.13
41 92 0.38
42 101 0.42
43 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (42 bp):
TAGCGGCGTTTGTTATAAAAACGCCACTAAAGTACGAGTCTT
Found at i:2023482 original size:42 final size:41
Alignment explanation
Indices: 2023380--2023483 Score: 95
Period size: 42 Copynumber: 2.5 Consensus size: 41
2023370 GTAGTGATTG
*
2023380 CGGCGTTTGTTGAAAAAACGCCACTATAAACAACTCTATTA
1 CGGCGTTTGTTTAAAAAACGCCACTATAAACAACTCTATTA
* ** * ** *
2023421 CGACGTTTGAGCT-ATAAACGCCGTTA-AATTACCACTCTATTA
1 CGGCGTTTG-TTTAAAAAACGCCACTATAA--ACAACTCTATTA
2023463 CGGCGTTTGTTTAAAAAACGC
1 CGGCGTTTGTTTAAAAAACGC
2023484 TGCTAAAGTA
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
40 2 0.04
41 19 0.40
42 26 0.55
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (41 bp):
CGGCGTTTGTTTAAAAAACGCCACTATAAACAACTCTATTA
Found at i:2024416 original size:27 final size:27
Alignment explanation
Indices: 2024376--2024440 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
2024366 CTACCAATTT
*
2024376 TTTTATGAAGTATTGATTTATGAATTTTA
1 TTTTAT-AA-TATTGACTTATGAATTTTA
* *
2024405 TTTTATAATATTTACTTATGGATTTTA
1 TTTTATAATATTGACTTATGAATTTTA
*
2024432 TTTTCTAAT
1 TTTTATAAT
2024441 TTTCTGTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 24 0.75
28 2 0.06
29 6 0.19
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.58
Consensus pattern (27 bp):
TTTTATAATATTGACTTATGAATTTTA
Found at i:2029454 original size:23 final size:23
Alignment explanation
Indices: 2029424--2029476 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2029414 GTAGGCATGA
2029424 GGAAAAGTGAGAGA-TACTACACC
1 GGAAAAGTGAGAGAGTA-TACACC
*
2029447 GGAAAAGTGAGAGAGTATATACC
1 GGAAAAGTGAGAGAGTATACACC
2029470 GGAAAAG
1 GGAAAAG
2029477 AACCCAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.45, C:0.11, G:0.30, T:0.13
Consensus pattern (23 bp):
GGAAAAGTGAGAGAGTATACACC
Found at i:2034563 original size:24 final size:24
Alignment explanation
Indices: 2034536--2034611 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
2034526 ATATTTTTAT
2034536 TATAGTTTAAATTGATATAATTCA
1 TATAGTTTAAATTGATATAATTCA
** * *
2034560 TATA---TAATATTTTTTTGAATTTA
1 TATAGTTTAA-ATTGATAT-AATTCA
*
2034583 TTATAGTTTAAATTGATATGATTCA
1 -TATAGTTTAAATTGATATAATTCA
2034608 TATA
1 TATA
2034612 TAATTGTAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 12
0.64 0.16 0.21
Matches are distributed among these distances:
21 3 0.08
22 5 0.14
23 5 0.14
24 12 0.32
25 4 0.11
26 5 0.14
27 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (24 bp):
TATAGTTTAAATTGATATAATTCA
Found at i:2034565 original size:26 final size:25
Alignment explanation
Indices: 2034536--2034622 Score: 65
Period size: 26 Copynumber: 3.5 Consensus size: 25
2034526 ATATTTTTAT
*
2034536 TATAGTTTAAATTGATATAATTCATA
1 TATAATTTAAATTGATAT-ATTCATA
***
2034562 TATAATATTTTTTTGA-AT-TT-AT-
1 TATAAT-TTAAATTGATATATTCATA
*
2034584 TATAGTTTAAATTGATATGATTCATA
1 TATAATTTAAATTGATAT-ATTCATA
2034610 TATAATTGTAAAT
1 TATAATT-TAAAT
2034623 ATAATTTACA
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
21 6 0.13
22 7 0.16
23 2 0.04
24 4 0.09
25 2 0.04
26 13 0.29
27 11 0.24
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (25 bp):
TATAATTTAAATTGATATATTCATA
Found at i:2039105 original size:2 final size:2
Alignment explanation
Indices: 2039098--2039147 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2039088 CAACTTGTTA
2039098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2039140 AT AT AT AT
1 AT AT AT AT
2039148 TAAGGACAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2041528 original size:2 final size:2
Alignment explanation
Indices: 2041521--2041554 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2041511 CTCACAAAGA
* *
2041521 AT AT AT AT AT CT AT AT CT 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
2041555 CCCGACATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2043201 original size:27 final size:28
Alignment explanation
Indices: 2043171--2043224 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
2043161 TTAGTAATAA
*
2043171 TTTATTTATTTAATTTTT-T-ATTATTAG
1 TTTATATA-TTAATTTTTGTAATTATTAG
2043198 TTTATATATTAATTTTTGTAATTATTA
1 TTTATATATTAATTTTTGTAATTATTA
2043225 ATAATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 8 0.33
28 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTATATATTAATTTTTGTAATTATTAG
Found at i:2052733 original size:52 final size:53
Alignment explanation
Indices: 2052612--2052733 Score: 117
Period size: 52 Copynumber: 2.4 Consensus size: 53
2052602 AACATTAACA
* **
2052612 TATTACCATATCACT-AAAATAATAATAAACAATAACATTAATATAAATTCAT
1 TATTACCATATCACTAAAAATAATAATAAACAATAACATAAATATAAATAAAT
* * * * * * *
2052664 GA-TA-AATTTAAATTAAAAATAATAATAAACATTAACATAAATTTAAA-AAAT
1 TATTACCATAT-CACTAAAAATAATAATAAACAATAACATAAATATAAATAAAT
2052715 TATTACCATATCACTAAAA
1 TATTACCATATCACTAAAA
2052734 TGTTTTGAGA
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
50 3 0.06
51 7 0.14
52 38 0.75
53 3 0.06
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (53 bp):
TATTACCATATCACTAAAAATAATAATAAACAATAACATAAATATAAATAAAT
Found at i:2052852 original size:17 final size:16
Alignment explanation
Indices: 2052830--2052882 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
2052820 AATAATTAAT
2052830 TAATAAATTTAAATAAA
1 TAAT-AATTTAAATAAA
*
2052847 TAATAA-TTATATAAA
1 TAATAATTTAAATAAA
*
2052862 T-ATAATTTTAATAAA
1 TAATAATTTAAATAAA
*
2052877 AAATAA
1 TAATAA
2052883 AAAATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.13
15 16 0.53
16 6 0.20
17 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATTTAAATAAA
Found at i:2052860 original size:25 final size:24
Alignment explanation
Indices: 2052816--2052862 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
2052806 TAATTAGCAC
2052816 AAATAATAATTAATTAATAAATTT
1 AAATAATAATTAATTAATAAATTT
2052840 AAATAAATAA-TAATTATATAAAT
1 AAAT-AATAATTAATTA-ATAAAT
2052863 ATAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAATAATTAATTAATAAATTT
Found at i:2052872 original size:31 final size:27
Alignment explanation
Indices: 2052816--2052882 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 27
2052806 TAATTAGCAC
*
2052816 AAATAATAATTAATTAATAAATTTAAAT
1 AAATAATAATTAATAAATAAATTT-AAT
2052844 AAATAATAATTATATAAATATAATTTTAAT
1 AAATAATAATTA-ATAAATA-AA-TTTAAT
*
2052874 AAAAAATAA
1 AAATAATAA
2052883 AAAATTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 12 0.35
29 6 0.18
30 13 0.38
31 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AAATAATAATTAATAAATAAATTTAAT
Found at i:2052912 original size:13 final size:14
Alignment explanation
Indices: 2052879--2052914 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2052869 TTAATAAAAA
*
2052879 ATAAAAAATTATTT
1 ATAAAAAACTATTT
*
2052893 TTAAAAAACTATTT
1 ATAAAAAACTATTT
2052907 ATAAAAAA
1 ATAAAAAA
2052915 ATAACAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAAAAACTATTT
Found at i:2052923 original size:21 final size:21
Alignment explanation
Indices: 2052899--2052939 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2052889 ATTTTTAAAA
*
2052899 AACTATTTATAAAAAAATAAC
1 AACTATTTACAAAAAAATAAC
*
2052920 AACTATTTACAAAAATATAA
1 AACTATTTACAAAAAAATAA
2052940 TAATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (21 bp):
AACTATTTACAAAAAAATAAC
Found at i:2054082 original size:22 final size:22
Alignment explanation
Indices: 2054057--2054114 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2054047 TCACTCTCTA
*
2054057 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
2054079 CGACGAAATCCATCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
2054101 CGGCGAAATCCGTC
1 CGACGAAATCCGTC
2054115 TATCTCCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.45, G:0.16, T:0.17
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:2054585 original size:20 final size:20
Alignment explanation
Indices: 2054537--2054587 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2054527 CGATTATCTC
**
2054537 GTTGCGATAGTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
*
2054557 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
2054577 GTTGCGATTTT
1 GTTGCGATTTT
2054588 AAGTTTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:2054594 original size:20 final size:20
Alignment explanation
Indices: 2054551--2054595 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2054541 CGATAGTCAT
* *
2054551 TTTCATGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTTAAG
*
2054571 TTTCGTGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
2054591 TTTCA
1 TTTCA
2054596 GAAACTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:2054954 original size:42 final size:42
Alignment explanation
Indices: 2054906--2054999 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
2054896 CCTCTCCTAT
2054906 CATTCAAGAGGCCCCTATCATCCCTCAAGAG-TCCCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCCTCAAGAGAT-CCCTCCCAC
* * ** *
2054948 CGTTCAAGAGGCCCCTGTCATCGTTGAAGAGATCCCTCCCAC
1 CATTCAAGAGGCCCCTATCATCCCTCAAGAGATCCCTCCCAC
2054990 CATTCAAGAG
1 CATTCAAGAG
2055000 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.20
Consensus pattern (42 bp):
CATTCAAGAGGCCCCTATCATCCCTCAAGAGATCCCTCCCAC
Found at i:2054972 original size:21 final size:21
Alignment explanation
Indices: 2054877--2054978 Score: 89
Period size: 21 Copynumber: 4.9 Consensus size: 21
2054867 TTTCGACTCA
2054877 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
2054898 TCT-CCTATCATTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
2054919 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
2054940 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
*
2054961 CCTGTCATCGTTGAAGAG
1 CCTGTCATCGTTCAAGAG
2054979 ATCCCTCCCA
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 59 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:2054998 original size:21 final size:20
Alignment explanation
Indices: 2054930--2054999 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
2054920 CTATCATCCC
2054930 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGT-CCCTCCCACCGT
* ** *
2054951 TCAAGAGGCCCCTGTCATCGT
1 TCAAGA-GTCCCTCCCACCGT
* *
2054972 TGAAGAGATCCCTCCCACCAT
1 TCAAGAG-TCCCTCCCACCGT
2054993 TCAAGAG
1 TCAAGAG
2055000 CCCGATTCAC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (20 bp):
TCAAGAGTCCCTCCCACCGT
Found at i:2056563 original size:20 final size:20
Alignment explanation
Indices: 2056526--2056603 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
2056516 AGGTACACTT
* * *
2056526 TCGCAACGCTAAACTCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
2056546 TCGCATTGCGAAAGTCAAAA
1 TCGCAATGCGAAAGTCAAAA
*
2056566 TCGCAATGCGAAAGCCAAAA
1 TCGCAATGCGAAAGTCAAAA
* *
2056586 TCGCAACGCAAAAGTCAA
1 TCGCAATGCGAAAGTCAA
2056604 TTCGCGTTGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.44, C:0.26, G:0.17, T:0.14
Consensus pattern (20 bp):
TCGCAATGCGAAAGTCAAAA
Found at i:2056667 original size:20 final size:20
Alignment explanation
Indices: 2056642--2056730 Score: 151
Period size: 20 Copynumber: 4.5 Consensus size: 20
2056632 GCTATTTTCT
*
2056642 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
2056662 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
2056682 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
2056702 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
2056722 CGTTGCGAT
1 CGTTGCGAT
2056731 TTTTGCGTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:2056744 original size:34 final size:36
Alignment explanation
Indices: 2056657--2056752 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 36
2056647 CGATAGTCAA
*
2056657 ATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGT
1 ATTCGCGTTGCGATAATCAAATTCACGTTGCGATA-T
*
2056694 CAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT-T
1 ---ATTCGCGTTGCGATAATCAAATTCACGTTGCGATAT
* *
2056732 -TTTGCGTTGCGATATTCAAAT
1 ATTCGCGTTGCGATAATCAAAT
2056753 GAATGTGTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
34 19 0.37
38 1 0.02
40 32 0.62
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (36 bp):
ATTCGCGTTGCGATAATCAAATTCACGTTGCGATAT
Found at i:2056947 original size:19 final size:18
Alignment explanation
Indices: 2056923--2056958 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2056913 AAGCCGGTTG
*
2056923 TGATTGGGATTTTTGATTT
1 TGATTGCGA-TTTTGATTT
2056942 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
2056959 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2059025 original size:15 final size:14
Alignment explanation
Indices: 2058990--2059026 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2058980 TCCCGTGGCA
2058990 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
2059004 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
2059018 TCTTTCTTC
1 T-TTTCTTC
2059027 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:2059947 original size:17 final size:17
Alignment explanation
Indices: 2059921--2059958 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2059911 CGGATGGGGA
*
2059921 AGGATTTCGTTAGATAT
1 AGGATGTCGTTAGATAT
*
2059938 AGGATGTCGTTGGATAT
1 AGGATGTCGTTAGATAT
2059955 AGGA
1 AGGA
2059959 ACGGATGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (17 bp):
AGGATGTCGTTAGATAT
Found at i:2060134 original size:20 final size:20
Alignment explanation
Indices: 2060106--2060212 Score: 74
Period size: 20 Copynumber: 5.3 Consensus size: 20
2060096 AAATTCAGTG
*
2060106 TTGCAATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
* *
2060126 TTGCGATAGTCAGAATGGCG
1 TTGCGATAGTCAGAATCGCA
* **
2060146 TTGCGATTTTGT-ATTATCGCA
1 TTGCGA--TAGTCAGAATCGCA
* * *
2060167 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* *
2060187 TTGCGATAGTCAAAATCGCG
1 TTGCGATAGTCAGAATCGCA
2060207 TTGCGA
1 TTGCGA
2060213 ATATGGAAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 50 0.75
21 12 0.18
22 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:2060250 original size:20 final size:19
Alignment explanation
Indices: 2060227--2060272 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2060217 GGAAACTGAT
* *
2060227 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
2060247 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
2060266 TTGCGAT
1 TTGCGAT
2060273 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:2060262 original size:19 final size:19
Alignment explanation
Indices: 2060238--2060274 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2060228 TGCGATACTG
*
2060238 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2060257 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2060275 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2060898 original size:9 final size:9
Alignment explanation
Indices: 2060880--2060936 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
2060870 AAATATTAAA
2060880 TATTAATAT
1 TATTAATAT
*
2060889 TATTACTAT
1 TATTAATAT
*
2060898 TATTATTAT
1 TATTAATAT
2060907 TATTAATAT
1 TATTAATAT
* *
2060916 TAATTAGTTT
1 T-ATTAATAT
2060926 TATTACATAT
1 TATTA-ATAT
2060936 T
1 T
2060937 TTGCAGTCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
9 29 0.74
10 10 0.26
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (9 bp):
TATTAATAT
Found at i:2060901 original size:3 final size:3
Alignment explanation
Indices: 2060880--2060930 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
2060870 AAATATTAAA
* * *
2060880 TAT TAA TAT TAT TAC TAT TAT TAT TAT TAT TAA TAT TAAT TAGT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TA-T TAT
2060926 TAT TA
1 TAT TA
2060931 CATATTTTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2064540 original size:32 final size:32
Alignment explanation
Indices: 2064499--2064583 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
2064489 GTATTAAATG
* *
2064499 ATTTCTTTCCTTTTGTTTGTGAACATTAA-CT
1 ATTTATTTCCTTTTGTTTGTGAACACTAACCT
* * *
2064530 AATTTATTTCCTTTTATTTATGTACACTAACCT
1 -ATTTATTTCCTTTTGTTTGTGAACACTAACCT
* *
2064563 ATTTATTTTCTTTTGATTGTG
1 ATTTATTTCCTTTTGTTTGTG
2064584 TCATTTTCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
32 41 0.95
33 2 0.05
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.56
Consensus pattern (32 bp):
ATTTATTTCCTTTTGTTTGTGAACACTAACCT
Found at i:2065286 original size:13 final size:13
Alignment explanation
Indices: 2065268--2065293 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2065258 TGTCCAATAA
2065268 CAAAGGCAGTGAC
1 CAAAGGCAGTGAC
2065281 CAAAGGCAGTGAC
1 CAAAGGCAGTGAC
2065294 TAGTAGTAGT
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:0.38, C:0.23, G:0.31, T:0.08
Consensus pattern (13 bp):
CAAAGGCAGTGAC
Found at i:2065899 original size:20 final size:20
Alignment explanation
Indices: 2065874--2065942 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
2065864 GCGATTATCC
*
2065874 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
2065894 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
2065914 CGGTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
2065934 CGTTGCGAT
1 CGTTGCGAT
2065943 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:2065900 original size:34 final size:37
Alignment explanation
Indices: 2065856--2065943 Score: 92
Period size: 40 Copynumber: 2.4 Consensus size: 37
2065846 TGATTTTTAT
* *
2065856 TTCGCATTGCGATT-A-TCC-CGTTGCGATAGTCAAA
1 TTCGCGTTGCGATTCATTCCGCGGTGCGATAGTCAAA
**
2065890 TTCGCGTTGCGATAGTCATTTCCGCGGTGCGATAGTCATT
1 TTCGCGTTGCGAT--TCA-TTCCGCGGTGCGATAGTCAAA
2065930 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
2065944 TTAAGTTTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
34 12 0.27
36 1 0.02
37 1 0.02
38 1 0.02
39 3 0.07
40 26 0.59
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (37 bp):
TTCGCGTTGCGATTCATTCCGCGGTGCGATAGTCAAA
Found at i:2065952 original size:20 final size:20
Alignment explanation
Indices: 2065929--2065972 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2065919 CGATAGTCAT
2065929 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
* *
2065949 TTTCGTGTTGTGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
2065969 TTTC
1 TTTC
2065973 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:2066533 original size:21 final size:21
Alignment explanation
Indices: 2066456--2066570 Score: 70
Period size: 21 Copynumber: 5.5 Consensus size: 21
2066446 CACCTGTCAT
* * *
2066456 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
* * **
2066477 CGTTCAAGAGACCCGTATCATC
1 CGTTCAAGAGGCCCCTCCCA-C
* **
2066499 C-CTCAAGATTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
** *
2066519 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
2066540 CGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
2066561 CATTCAAGAG
1 CGTTCAAGAG
2066571 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 26, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
20 2 0.03
21 63 0.95
22 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:2066556 original size:42 final size:42
Alignment explanation
Indices: 2066448--2066570 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
2066438 GCCCGACTCA
* *
2066448 CCTGTCATCGTTCAAGAGG-CCTCTCCTATCGTTCAAGAGACC
1 CCTGTCATCGTTCAAGAGGTCC-CTCCCACCGTTCAAGAGACC
* * ** * *
2066490 CGTATCATCCCTCAAGA-TTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGT-CCCTCCCACCGTTCAAGAGACC
* *
2066532 CCTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
2066571 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGACC
Found at i:2068065 original size:20 final size:20
Alignment explanation
Indices: 2068042--2068080 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2068032 ATGATAAACT
*
2068042 CAAAATCGCAATGCGAAAGC
1 CAAAATCGCAACGCGAAAGC
2068062 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCGAAAG
2068081 TCAATTCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.21, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGC
Found at i:2068148 original size:20 final size:20
Alignment explanation
Indices: 2068125--2068273 Score: 166
Period size: 20 Copynumber: 7.8 Consensus size: 20
2068115 GATTTTCTCA
* *
2068125 TTGCGATAGTCAAATTCCCA
1 TTGCGATAGTCAAATTCGCG
* *
2068145 TTGCGATAATCAAATTCACG
1 TTGCGATAGTCAAATTCGCG
2068165 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
**
2068185 TTGATATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
2068205 TTGC-A-A-T---TTTTGCG
1 TTGCGATAGTCAAATTCGCG
*
2068219 TTGCGATAGTCAAATTCACG
1 TTGCGATAGTCAAATTCGCG
2068239 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
2068259 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
2068274 GAATGTGTAA
Statistics
Matches: 108, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 1 0.01
20 93 0.86
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:2068214 original size:94 final size:94
Alignment explanation
Indices: 2068074--2068273 Score: 251
Period size: 94 Copynumber: 2.1 Consensus size: 94
2068064 AAATCGCAAC
* * * * **
2068074 GCGAAAGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGTGATTTTCT-CATTGCGATAGTCA
1 GCGATAGTCAAATTCGCGTTGAGATAGTCAAATACGCGTTGCAATTTT-TGCATTGCGATAGTCA
*
2068137 AATTCCCATTGCGATAATCAAATTCACGTT
65 AATTCACATTGCGATAATCAAATTCACGTT
* * *
2068167 GCGATAGTCAAATTCGCGTTGATATAGTCAAATTCGCGTTGCAATTTTTGCGTTGCGATAGTCAA
1 GCGATAGTCAAATTCGCGTTGAGATAGTCAAATACGCGTTGCAATTTTTGCATTGCGATAGTCAA
* * *
2068232 ATTCACGTTGCGATAGTCAAATTCGCGTT
66 ATTCACATTGCGATAATCAAATTCACGTT
*
2068261 GCGATATTCAAAT
1 GCGATAGTCAAAT
2068274 GAATGTGTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
93 9 0.10
94 82 0.90
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (94 bp):
GCGATAGTCAAATTCGCGTTGAGATAGTCAAATACGCGTTGCAATTTTTGCATTGCGATAGTCAA
ATTCACATTGCGATAATCAAATTCACGTT
Found at i:2068459 original size:12 final size:12
Alignment explanation
Indices: 2068441--2068479 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2068431 GTGAAGCCAG
**
2068441 TTGTGATTGGGA
1 TTGTGATTTTGA
*
2068453 TTTTGATTTTGA
1 TTGTGATTTTGA
2068465 TTGTGATTTTGA
1 TTGTGATTTTGA
2068477 TTG
1 TTG
2068480 CCTTTTGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.56
Consensus pattern (12 bp):
TTGTGATTTTGA
Found at i:2068467 original size:18 final size:18
Alignment explanation
Indices: 2068444--2068478 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2068434 AAGCCAGTTG
2068444 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
*
2068462 TGATTGTGATTTTGATT
1 TGATTGGGATTTTGATT
2068479 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:2070833 original size:316 final size:316
Alignment explanation
Indices: 2070260--2070894 Score: 1225
Period size: 316 Copynumber: 2.0 Consensus size: 316
2070250 TAATTTCATG
2070260 TCCCCGATATACCCTGTCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTTGT
1 TCCCCGATATACCCTGTCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTTGT
2070325 TTGCCTGTCTATGGTGAGGAAAAACTTGGGTTCTTGAACATGTATGTTTATCAATAAAAGTCCTA
66 TTGCCTGTCTATGGTGAGGAAAAACTTGGGTTCTTGAACATGTATGTTTATCAATAAAAGTCCTA
*
2070390 ACTTGAAACATTTCACAATCTTTTATCCTCTTTGCAGTCATACGCCACGTACAGTTTTTGTCAAT
131 ACTTGAAACATTTCACAATCTTTTATCCTCTTTACAGTCATACGCCACGTACAGTTTTTGTCAAT
2070455 CATACACCTTGTTTCGAAACGATCTTTGCTTGATTTGTTAACTTTTAGTTGATAGCCATCTTCCA
196 CATACACCTTGTTTCGAAACGATCTTTGCTTGATTTGTTAACTTTTAGTTGATAGCCATCTTCCA
2070520 CACATTTCGTATACAAAGCTATCTTCAAGTCTTCCTTTGTATCAAAACAATCATCT
261 CACATTTCGTATACAAAGCTATCTTCAAGTCTTCCTTTGTATCAAAACAATCATCT
2070576 TCCCCGATATACCCTGTCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTTGT
1 TCCCCGATATACCCTGTCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTTGT
2070641 TTGCCTGTCTATGGTGAGGAAAAACTTGGGTTCTTGAACATGTATGTTTATCAATAAAAGTCCTA
66 TTGCCTGTCTATGGTGAGGAAAAACTTGGGTTCTTGAACATGTATGTTTATCAATAAAAGTCCTA
* *
2070706 ACTTGAAACATTTCGCAATCTTTTATCCTCTTTACAGTCATATGCCACGTACAGTTTTTGTCAAT
131 ACTTGAAACATTTCACAATCTTTTATCCTCTTTACAGTCATACGCCACGTACAGTTTTTGTCAAT
* *
2070771 CATACACTTTGTTTTGAAACGATCTTTGCTTGATTTGTTAACTTTTAGTTGATAGCCATCTTCCA
196 CATACACCTTGTTTCGAAACGATCTTTGCTTGATTTGTTAACTTTTAGTTGATAGCCATCTTCCA
2070836 CACATTTCGTATACAAAGCTATCTTCAAGTCTTCCTTTGTATCAAAACAATCATCT
261 CACATTTCGTATACAAAGCTATCTTCAAGTCTTCCTTTGTATCAAAACAATCATCT
2070892 TCC
1 TCC
2070895 AATCATCTTC
Statistics
Matches: 314, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
316 314 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (316 bp):
TCCCCGATATACCCTGTCATTCAAAAACATTAACTCAGCCAGAAAACCACCCAACACCTTTTTGT
TTGCCTGTCTATGGTGAGGAAAAACTTGGGTTCTTGAACATGTATGTTTATCAATAAAAGTCCTA
ACTTGAAACATTTCACAATCTTTTATCCTCTTTACAGTCATACGCCACGTACAGTTTTTGTCAAT
CATACACCTTGTTTCGAAACGATCTTTGCTTGATTTGTTAACTTTTAGTTGATAGCCATCTTCCA
CACATTTCGTATACAAAGCTATCTTCAAGTCTTCCTTTGTATCAAAACAATCATCT
Found at i:2080166 original size:17 final size:18
Alignment explanation
Indices: 2080133--2080169 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2080123 CACTAATATA
2080133 TTTTTTCATTTCCTTCTTT
1 TTTTTTCATTT-CTTCTTT
2080152 TTTTTTCATTT-TTCTTT
1 TTTTTTCATTTCTTCTTT
2080169 T
1 T
2080170 CTTGATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCATTTCTTCTTT
Found at i:2083215 original size:15 final size:15
Alignment explanation
Indices: 2083195--2083223 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2083185 TGCTCACAGC
2083195 AGCCCTCTTCCCAGT
1 AGCCCTCTTCCCAGT
2083210 AGCCCTCTTCCCAG
1 AGCCCTCTTCCCAG
2083224 CAGCATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.48, G:0.14, T:0.24
Consensus pattern (15 bp):
AGCCCTCTTCCCAGT
Found at i:2088814 original size:14 final size:14
Alignment explanation
Indices: 2088792--2088860 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
2088782 GATCCAGTCA
2088792 CTGAGTCAACCCGT
1 CTGAGTCAACCCGT
* ***
2088806 CTGAATCAATTTGGT
1 CTGAGTCAA-CCCGT
2088821 CTGAGTCAACCCGT
1 CTGAGTCAACCCGT
*
2088835 CTGAGTCAACTCGT
1 CTGAGTCAACCCGT
*
2088849 CTGAGTTAACCC
1 CTGAGTCAACCC
2088861 ATTGATTTTG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
14 33 0.77
15 10 0.23
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (14 bp):
CTGAGTCAACCCGT
Found at i:2088825 original size:29 final size:28
Alignment explanation
Indices: 2088792--2088860 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
2088782 GATCCAGTCA
* *
2088792 CTGAGTCAACCCGTCTGAATCAATTTGGT
1 CTGAGTCAACCCGTCTGAATCAA-CTCGT
*
2088821 CTGAGTCAACCCGTCTGAGTCAACTCGT
1 CTGAGTCAACCCGTCTGAATCAACTCGT
*
2088849 CTGAGTTAACCC
1 CTGAGTCAACCC
2088861 ATTGATTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (28 bp):
CTGAGTCAACCCGTCTGAATCAACTCGT
Found at i:2091049 original size:19 final size:19
Alignment explanation
Indices: 2091012--2091050 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2091002 CTGGTAAATT
*
2091012 TTATTTTTGTATTTATAAA
1 TTATTTTTATATTTATAAA
2091031 TTATTTTTATGATTT-TAAA
1 TTATTTTTAT-ATTTATAAA
2091050 T
1 T
2091051 GTTTTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTATTTTTATATTTATAAA
Found at i:2095371 original size:5 final size:5
Alignment explanation
Indices: 2095361--2095400 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
2095351 CTTAATATAT
*
2095361 TAAAA TAAAA TAAAA TAAAA TAAATAA TAATA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA T-AA-AA TAAAA TAAAA TAA
2095401 TATTAGATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 24 0.77
6 4 0.13
7 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:2095429 original size:14 final size:13
Alignment explanation
Indices: 2095361--2095438 Score: 50
Period size: 13 Copynumber: 5.7 Consensus size: 13
2095351 CTTAATATAT
*
2095361 TAAAATAAAATAAAA
1 TAAAATAAAAT--TA
*
2095376 TAAAAT-AAATAA
1 TAAAATAAAATTA
*
2095388 TAATATAAAATAATA
1 TAAAATAAAAT--TA
* * *
2095403 TTAGATGAAATTA
1 TAAAATAAAATTA
2095416 TAAAAATAAAATTA
1 T-AAAATAAAATTA
2095430 TAAAATAAA
1 TAAAATAAA
2095439 TTTAAAAGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
12 7 0.14
13 15 0.29
14 14 0.27
15 15 0.29
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
TAAAATAAAATTA
Found at i:2095528 original size:27 final size:26
Alignment explanation
Indices: 2095477--2095528 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2095467 CTTATTGGAT
* *
2095477 AGAATTAATATATTAAATAAAATTAA
1 AGAAATAATATATAAAATAAAATTAA
*
2095503 AGAAATAATAATATAAAATAATATTA
1 AGAAATAAT-ATATAAAATAAAATTA
2095529 TATTAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AGAAATAATATATAAAATAAAATTAA
Found at i:2095784 original size:2 final size:2
Alignment explanation
Indices: 2095777--2095815 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2095767 AAGAGACTAT
2095777 TA TA TA TA TA T- 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 TA TA
2095816 GGGTTAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2099248 original size:5 final size:5
Alignment explanation
Indices: 2099144--2099247 Score: 181
Period size: 5 Copynumber: 20.8 Consensus size: 5
2099134 TATACGTATA
*
2099144 CAATA CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG
1 CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG
* *
2099194 CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATA CAATA
1 CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG
2099244 CAAT
1 CAAT
2099248 ATATAATGGC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 97 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (5 bp):
CAATG
Found at i:2099295 original size:10 final size:10
Alignment explanation
Indices: 2099280--2099308 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2099270 CACTATATCA
2099280 TATAGTATAT
1 TATAGTATAT
2099290 TATAGTATAT
1 TATAGTATAT
2099300 TAT-GTATAT
1 TATAGTATAT
2099309 ATTATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (10 bp):
TATAGTATAT
Found at i:2100163 original size:14 final size:15
Alignment explanation
Indices: 2100130--2100166 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2100120 TTTTGAAACA
2100130 CTTGATTTTATGATT
1 CTTGATTTTATGATT
2100145 CTTGATTTT-TGATAT
1 CTTGATTTTATGAT-T
2100160 -TTGATTT
1 CTTGATTT
2100167 GACACATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.62
Consensus pattern (15 bp):
CTTGATTTTATGATT
Found at i:2107194 original size:21 final size:21
Alignment explanation
Indices: 2107169--2107244 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
2107159 TCTTTCAGGT
2107169 ACATATATGTGGTTCTTTGGA
1 ACATATATGTGGTTCTTTGGA
** * *
2107190 ACATATATACGGTCCTTTGGG
1 ACATATATGTGGTTCTTTGGA
* * *
2107211 ACACATATTTAG-TCATTTGGA
1 ACATATATGTGGTTC-TTTGGA
*
2107232 ATATATATGTGGT
1 ACATATATGTGGT
2107245 CCTTCACGAC
Statistics
Matches: 39, Mismatches: 14, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (21 bp):
ACATATATGTGGTTCTTTGGA
Found at i:2114272 original size:21 final size:21
Alignment explanation
Indices: 2114246--2114328 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2114236 TTCTAAGCAG
*
2114246 TCCTTTGGGACATATATGTAT
1 TCCTTTGGGACATATATGTGT
*
2114267 TCCTTT-GGAGCATATATGCGT
1 TCCTTTGGGA-CATATATGTGT
* * * *
2114288 TCTTTTGGGTCATATATTTGG
1 TCCTTTGGGACATATATGTGT
* *
2114309 TCATTTGGAACATATATGTG
1 TCCTTTGGGACATATATGTG
2114329 GTCATATGGG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 3 0.06
21 44 0.90
22 2 0.04
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (21 bp):
TCCTTTGGGACATATATGTGT
Found at i:2114382 original size:21 final size:21
Alignment explanation
Indices: 2114298--2114386 Score: 74
Period size: 21 Copynumber: 4.1 Consensus size: 21
2114288 TCTTTTGGGT
* * *
2114298 CATATATTTGGTCATTTGGAA
1 CATATATGTGGTCATTCGGGA
2114319 CATATATGTGGTCATAT-GGGA
1 CATATATGTGGTCAT-TCGGGA
* *
2114340 CAATTCTATGAGGTTC-TTCGGGA
1 C-A-TATATGTGG-TCATTCGGGA
*
2114363 CATATATTTGGTCATTCGGGA
1 CATATATGTGGTCATTCGGGA
2114384 CAT
1 CAT
2114387 TTTATATGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
20 2 0.04
21 34 0.62
22 4 0.07
23 13 0.24
24 2 0.04
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (21 bp):
CATATATGTGGTCATTCGGGA
Found at i:2114409 original size:22 final size:22
Alignment explanation
Indices: 2114384--2114439 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2114374 TCATTCGGGA
* * *
2114384 CATTTTATATGGTACTTTGGTT
1 CATTTTATACGGTACTTCGGTG
**
2114406 CATTTCTACGCGGTACTTCGGTG
1 CATTT-TATACGGTACTTCGGTG
2114429 CATTTTATACG
1 CATTTTATACG
2114440 AGCTGTGGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.45
Consensus pattern (22 bp):
CATTTTATACGGTACTTCGGTG
Found at i:2115004 original size:90 final size:90
Alignment explanation
Indices: 2114850--2115027 Score: 320
Period size: 90 Copynumber: 2.0 Consensus size: 90
2114840 CCTAACACAC
* *
2114850 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAATTCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
2114915 ATTTAATTAATTGAAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
2114940 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
2115005 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
2115028 TTCGGGATTA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:2121224 original size:12 final size:12
Alignment explanation
Indices: 2121207--2121237 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2121197 TAGTGAGGAA
2121207 AAAATAATAATC
1 AAAATAATAATC
*
2121219 AAAATAATAATG
1 AAAATAATAATC
2121231 AAAATAA
1 AAAATAA
2121238 AAAGTGATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (12 bp):
AAAATAATAATC
Found at i:2122402 original size:38 final size:38
Alignment explanation
Indices: 2122360--2122449 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
2122350 ACACATGCCG
2122360 AGAAATAAATGGAAATAAAATTAAAAGAATATAACATA
1 AGAAATAAATGGAAATAAAATTAAAAGAATATAACATA
2122398 AGAAATAAATGGAAATAAAATTAAAAGAATATAACATA
1 AGAAATAAATGGAAATAAAATTAAAAGAATATAACATA
*
2122436 AAAAATAAATGGAA
1 AGAAATAAATGGAA
2122450 TAACTCCATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (38 bp):
AGAAATAAATGGAAATAAAATTAAAAGAATATAACATA
Found at i:2125240 original size:138 final size:135
Alignment explanation
Indices: 2124967--2125356 Score: 449
Period size: 138 Copynumber: 2.8 Consensus size: 135
2124957 AACTTGGAAA
* * * * * * *
2124967 TGGAGGCTCTATTATTAAACCTATTTGATTTATCCAATTATTGATTCGAATAATCGAAATAGA-C
1 TGGAGGCTATAATATTAATCCTAATTGTTTTAACCAATTATTGATTCGAATAATCGAAATGGACC
* * * * *
2125031 ATTCGAGCATTAAGGCGAGGGCTAAATTGAATTATCCCTTAAATTAGATGACTAAAGTGAAATTA
66 A-TCGA-CATTAAGGTGAGGGC-AAATCGAATTTTCCC-TAAATTAAAGGACTAAAGTGAAATTA
*
2125096 GGCCTAAGG
127 AGCCTAAGG
* *
2125105 TGGAGGCTTTAATATTAATCCTAATTAGTTTTAACCAATTAATGATTCGAATAATCGAAATGGAC
1 TGGAGGCTATAATATTAATCCTAATT-GTTTTAACCAATTATTGATTCGAATAATCGAAATGGAC
* * * *
2125170 CCTCAGACATTAAAGTGAGGGTCAAATCAAATTTTCCCTAAATTAAAGGACTAAATTGAAATTAA
65 CATC-GACATTAAGGTGAGGG-CAAATCGAATTTTCCCTAAATTAAAGGACTAAAGTGAAATTAA
2125235 GCCTAAGG
128 GCCTAAGG
* * *
2125243 TGTAGGCTATAATATTAATCCTAATTGATTTTAATCAATTATTTATTCGAATAATCGAAATGGAC
1 TGGAGGCTATAATATTAATCCTAATTG-TTTTAACCAATTATTGATTCGAATAATCGAAATGGAC
* * *
2125308 CATCTGGCATTAAGGTGAGAGACAAATCGAATTATTACCTAAATTAAAG
65 CATC-GACATTAAGGTGAG-GGCAAATCGAATT-TTCCCTAAATTAAAG
2125357 AAAGTTTGGG
Statistics
Matches: 215, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
137 1 0.00
138 136 0.63
139 74 0.34
140 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (135 bp):
TGGAGGCTATAATATTAATCCTAATTGTTTTAACCAATTATTGATTCGAATAATCGAAATGGACC
ATCGACATTAAGGTGAGGGCAAATCGAATTTTCCCTAAATTAAAGGACTAAAGTGAAATTAAGCC
TAAGG
Found at i:2127376 original size:18 final size:18
Alignment explanation
Indices: 2127353--2127405 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
2127343 ATTTTTCGGT
2127353 TCTTCCTTCTTCGGCTCC
1 TCTTCCTTCTTCGGCTCC
*
2127371 TCTTCCTTCTTGGGCTCC
1 TCTTCCTTCTTCGGCTCC
* *
2127389 TCTTCTTTCTTTGGCTC
1 TCTTCCTTCTTCGGCTC
2127406 TTCCTTCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.00, C:0.38, G:0.13, T:0.49
Consensus pattern (18 bp):
TCTTCCTTCTTCGGCTCC
Found at i:2127416 original size:18 final size:17
Alignment explanation
Indices: 2127353--2127421 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 17
2127343 ATTTTTCGGT
2127353 TCTTCCTTCTTCGGCTCC
1 TCTT-CTTCTTCGGCTCC
*
2127371 TCTTCCTTCTTGGGCTCC
1 TCTT-CTTCTTCGGCTCC
* *
2127389 TCTTCTTTCTTTGGCTCT
1 TCTTC-TTCTTCGGCTCC
*
2127407 TCCTTCTTCTCCGGC
1 T-CTTCTTCTTCGGC
2127422 ACCTTCGCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
17 1 0.02
18 39 0.89
19 4 0.09
ACGTcount: A:0.00, C:0.39, G:0.13, T:0.48
Consensus pattern (17 bp):
TCTTCTTCTTCGGCTCC
Found at i:2128583 original size:12 final size:11
Alignment explanation
Indices: 2128521--2128594 Score: 60
Period size: 12 Copynumber: 6.5 Consensus size: 11
2128511 ATCCTGAAAT
2128521 AAATAAAATAA
1 AAATAAAATAA
*
2128532 AATTAATAATAA
1 AAATAA-AATAA
* *
2128544 TAATAATAACAA
1 AAATAA-AATAA
2128556 AAA-AAAATAA
1 AAATAAAATAA
*
2128566 AGATAAAGATAA
1 AAATAAA-ATAA
*
2128578 AAATAATATAA
1 AAATAAAATAA
2128589 ATAATA
1 A-AATA
2128595 CACTACTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
10 6 0.12
11 15 0.30
12 29 0.58
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:2128614 original size:28 final size:29
Alignment explanation
Indices: 2128578--2128637 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2128568 ATAAAGATAA
2128578 AAATAATAT-AAATA-ATACACTACTTTTC
1 AAATAATATAAAATATATACACTA-TTTTC
* *
2128606 AAATTATATAAAATATATATACTATTTTC
1 AAATAATATAAAATATATACACTATTTTC
2128635 AAA
1 AAA
2128638 ACTTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.29
29 13 0.46
30 7 0.25
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATAATATAAAATATATACACTATTTTC
Found at i:2128645 original size:21 final size:21
Alignment explanation
Indices: 2128621--2128729 Score: 87
Period size: 21 Copynumber: 4.9 Consensus size: 21
2128611 ATATAAAATA
2128621 TATATACTATTTTCAAAACTT
1 TATATACTATTTTCAAAACTT
*
2128642 TATATACATTATTTATTTTCAAAACTA
1 TATATAC------TATTTTCAAAACTT
* *
2128669 TATAAACTATTTTTAAAACTT
1 TATATACTATTTTCAAAACTT
*
2128690 TATATACATTATTTATTAAAA--T
1 TATATAC--TATTT-TCAAAACTT
2128712 TATATACTATTTTCAAAA
1 TATATACTATTTTCAAAA
2128730 TTATAATATA
Statistics
Matches: 73, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
19 5 0.07
20 5 0.07
21 25 0.34
22 8 0.11
23 5 0.07
24 6 0.08
27 19 0.26
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATACTATTTTCAAAACTT
Found at i:2128645 original size:23 final size:21
Alignment explanation
Indices: 2128615--2128739 Score: 85
Period size: 21 Copynumber: 5.6 Consensus size: 21
2128605 CAAATTATAT
2128615 AAAA-TATATATACTATTTTC
1 AAAACTATATATACTATTTTC
*
2128635 AAAACTTTATATACATTATTTATTTTC
1 AAAAC--TATAT--A-TA-CTATTTTC
* *
2128662 AAAACTATATAAACTATTTTT
1 AAAACTATATATACTATTTTC
* *
2128683 AAAACTTTATATACATTATTTATT
1 AAAACTATATATAC--TATTT-TC
2128707 AAAA-T-TATATACTATTTTC
1 AAAACTATATATACTATTTTC
*
2128726 AAAATTATAATATA
1 AAAACTAT-ATATA
2128740 TATATATATA
Statistics
Matches: 85, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.06
20 10 0.12
21 19 0.22
22 13 0.15
23 12 0.14
24 6 0.07
25 6 0.07
26 2 0.02
27 12 0.14
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAACTATATATACTATTTTC
Found at i:2128662 original size:27 final size:27
Alignment explanation
Indices: 2128628--2128706 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
2128618 ATATATATAC
2128628 TATTTTCAAAACTTTATATACATTATT
1 TATTTTCAAAACTTTATATACATTATT
*
2128655 TATTTTCAAAAC--TATATA-A--A-C
1 TATTTTCAAAACTTTATATACATTATT
*
2128676 TATTTTTAAAACTTTATATACATTATT
1 TATTTTCAAAACTTTATATACATTATT
2128703 TATT
1 TATT
2128707 AAAATTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
21 11 0.26
22 1 0.02
23 6 0.14
24 2 0.05
25 6 0.14
26 1 0.02
27 16 0.37
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTTTCAAAACTTTATATACATTATT
Found at i:2128678 original size:48 final size:44
Alignment explanation
Indices: 2128609--2128729 Score: 172
Period size: 48 Copynumber: 2.7 Consensus size: 44
2128599 ACTTTTCAAA
2128609 TTATATAAAATATATATACTATTTTCAAAACTTTATATACATTAT
1 TTAT-TAAAATATATATACTATTTTCAAAACTTTATATACATTAT
* *
2128654 TTATTTTCAAAACTATATAAACTATTTTTAAAACTTTATATACATTAT
1 TTA--TT-AAAA-TATATATACTATTTTCAAAACTTTATATACATTAT
2128702 TTATTAAAAT-TATATACTATTTTCAAAA
1 TTATTAAAATATATATACTATTTTCAAAA
2128730 TTATAATATA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
43 16 0.24
44 1 0.01
45 7 0.10
46 3 0.04
47 5 0.07
48 36 0.53
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (44 bp):
TTATTAAAATATATATACTATTTTCAAAACTTTATATACATTAT
Found at i:2133319 original size:417 final size:417
Alignment explanation
Indices: 2132545--2133382 Score: 1534
Period size: 417 Copynumber: 2.0 Consensus size: 417
2132535 TGCACTTTGT
*
2132545 CCGTTAACTTGGACACTTCAACCTGCGTGTTAGTGTGAAATGTGTTATACACAAACATAGAAAAG
1 CCGTTAACTTGGACACTTCAACCTGCATGTTAGTGTGAAATGTGTTATACACAAACATAGAAAAG
*
2132610 AAACATAGCTCACATAGCTTGGAAACTCTCACATGGGCAACCTTAATATACAGTTAAGGAAATGT
66 AAACATAGCTCACATAGCTTGGAAACTCTCACATGGGCAACCTTAATATACAGTTAAGGAAATAT
2132675 GCGAACGATTTTGTTATTATTTTTTTAACAAAACCGATAAAAAATTACTGGAAACATTATTATTT
131 GCGAACGATTTTGTTATTATTTTTTTAACAAAACCGATAAAAAATTACTGGAAACATTATTATTT
* *
2132740 TTACAGGTTTTGTTATTATTGAGCGTTTTACCGGTTTTGTTAACATATCTGGTAAAGCGCTATTA
196 TTACAGGTTTTGTTACTATTGAGCGTTTTACCGGTTTTGTTAACATATCTGGTAAAGCGCTACTA
* *
2132805 GTTTTGTTATTTTTTCTACAGGTTTTGTTATTATTAGGCACTTTACTGGAAATGTCAAAAAACAT
261 GTTTTGTTATTTTTTCTACAGGTTTTGTTATTATTAGGCAATTTACCGGAAATGTCAAAAAACAT
2132870 TAATGTTTTAAGTATAAATAATAATGTATTATATAATTTTTTATCGGTTTTATTAAAAAAATAAT
326 TAATGTTTTAAGTATAAATAATAATGTATTATATAATTTTTTATCGGTTTTATTAAAAAAATAAT
2132935 AACAACACCGATAGCGCTTTTCCTTAA
391 AACAACACCGATAGCGCTTTTCCTTAA
2132962 CCGTTAACTTGGACACTTCAACCTGCATGTTAGTGTGAAATGTGTTATACACAAACATAGAAAAG
1 CCGTTAACTTGGACACTTCAACCTGCATGTTAGTGTGAAATGTGTTATACACAAACATAGAAAAG
* *
2133027 AAACATAGCTCCCATAGCTTGGAAACTCTCACATGGGCAACCTTAATATACAGTTAATGAAATAT
66 AAACATAGCTCACATAGCTTGGAAACTCTCACATGGGCAACCTTAATATACAGTTAAGGAAATAT
*
2133092 GCTAACGATTTTGTTATTA-TTTTTTAACAAAACCGATAAAAAATTACTGGAAACATTATTATTT
131 GCGAACGATTTTGTTATTATTTTTTTAACAAAACCGATAAAAAATTACTGGAAACATTATTATTT
* *
2133156 TTACCGGTTTTGTTACTATTGAGCGTTTTACCGGTTTTGTTAACATATTTGGTAAAGCGCTACTA
196 TTACAGGTTTTGTTACTATTGAGCGTTTTACCGGTTTTGTTAACATATCTGGTAAAGCGCTACTA
*
2133221 GTTTTGTTATTTTTTTCTACCGGTTTTGTTATTATTAGGCAATTTACCGGAAATGTCAAAAAACA
261 GTTTTGTTA-TTTTTTCTACAGGTTTTGTTATTATTAGGCAATTTACCGGAAATGTCAAAAAACA
* *
2133286 TTAATGTTTTAGGTATAAATAATAATGTATTATATATTTTTTTATCGGTTTTATTAAAAAAATAA
325 TTAATGTTTTAAGTATAAATAATAATGTATTATATAATTTTTTATCGGTTTTATTAAAAAAATAA
2133351 TAACAACACCGATAGCGCTTTTCCTTAA
390 TAACAACACCGATAGCGCTTTTCCTTAA
2133379 CCGT
1 CCGT
2133383 ATATTAAGAC
Statistics
Matches: 406, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
416 115 0.28
417 291 0.72
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (417 bp):
CCGTTAACTTGGACACTTCAACCTGCATGTTAGTGTGAAATGTGTTATACACAAACATAGAAAAG
AAACATAGCTCACATAGCTTGGAAACTCTCACATGGGCAACCTTAATATACAGTTAAGGAAATAT
GCGAACGATTTTGTTATTATTTTTTTAACAAAACCGATAAAAAATTACTGGAAACATTATTATTT
TTACAGGTTTTGTTACTATTGAGCGTTTTACCGGTTTTGTTAACATATCTGGTAAAGCGCTACTA
GTTTTGTTATTTTTTCTACAGGTTTTGTTATTATTAGGCAATTTACCGGAAATGTCAAAAAACAT
TAATGTTTTAAGTATAAATAATAATGTATTATATAATTTTTTATCGGTTTTATTAAAAAAATAAT
AACAACACCGATAGCGCTTTTCCTTAA
Found at i:2140969 original size:6 final size:6
Alignment explanation
Indices: 2140958--2140992 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2140948 TATAGTCAAG
*
2140958 AGAAAT AGAAAT AGAATT GAGAAAT AGAAAT AGAA
1 AGAAAT AGAAAT AGAAAT -AGAAAT AGAAAT AGAA
2140993 TCGAGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AGAAAT
Found at i:2140979 original size:19 final size:19
Alignment explanation
Indices: 2140957--2141010 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
2140947 TTATAGTCAA
*
2140957 GAGAAATAGAAATAGAATT
1 GAGAAATAGAAATAGAATC
2140976 GAGAAATAGAAATAGAATC
1 GAGAAATAGAAATAGAATC
2140995 GAGAAGA-AGAAATAGA
1 GAGAA-ATAGAAATAGA
2141011 GAATTTAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 32 0.97
20 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.15
Consensus pattern (19 bp):
GAGAAATAGAAATAGAATC
Found at i:2146181 original size:6 final size:6
Alignment explanation
Indices: 2146170--2146204 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2146160 TATAGTCAAG
*
2146170 AGAAAT AGAAAT AGAATT GAGAAAT AGAAAT AGAA
1 AGAAAT AGAAAT AGAAAT -AGAAAT AGAAAT AGAA
2146205 TCGAGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (6 bp):
AGAAAT
Found at i:2146191 original size:19 final size:19
Alignment explanation
Indices: 2146169--2146222 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
2146159 TTATAGTCAA
*
2146169 GAGAAATAGAAATAGAATT
1 GAGAAATAGAAATAGAATC
2146188 GAGAAATAGAAATAGAATC
1 GAGAAATAGAAATAGAATC
2146207 GAGAAGA-AGAAATAGA
1 GAGAA-ATAGAAATAGA
2146223 GAATTTAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 32 0.97
20 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.15
Consensus pattern (19 bp):
GAGAAATAGAAATAGAATC
Found at i:2153668 original size:18 final size:19
Alignment explanation
Indices: 2153645--2153680 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2153635 ACAAAATGTC
2153645 AAAATG-GTATCGATACCG
1 AAAATGAGTATCGATACCG
*
2153663 AAAATGAGTATCGGTACC
1 AAAATGAGTATCGATACC
2153681 ATGGTAAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (19 bp):
AAAATGAGTATCGATACCG
Found at i:2154145 original size:44 final size:44
Alignment explanation
Indices: 2154097--2154507 Score: 552
Period size: 44 Copynumber: 9.3 Consensus size: 44
2154087 TAAAACGAAT
*
2154097 CCATAAATGAAATGCATAACGGTGCATTAAGGTATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* * *
2154141 CCATAAATGAAATGCATAATGATGCATTAAGGCATGAAAGGATT
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* * **
2154185 TCATAAATGAAATGCATAACGATGCATTAAGGCATGAAATAATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
*
2154229 CCATAAATGAAATGCATAACGGTGTATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* *
2154273 CCATAAATGAAATGCATAACGGTACATTAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* * * ** * *
2154317 TCATAAATGGAATGCATAACGATATATTAAAGGCATGAGATGATG
1 CCATAAATGAAATGCATAACGGTGCATT-AAGGCATGAAAGGATG
*
2154362 CCATAAATGAAATGCATCACGGTGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
* * * **
2154406 CCATAACTGAAATGCATAATGTTAAATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATT-AAGGCATGAAAGGATG
* * *
2154451 CCATAAATGAAATGCATAAAGGTTCATTAAAGGAATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATT-AAGGCATGAAAGGATG
2154496 CCATAAATGAAA
1 CCATAAATGAAA
2154508 ATAATGAATG
Statistics
Matches: 323, Mismatches: 42, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
44 219 0.68
45 104 0.32
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (44 bp):
CCATAAATGAAATGCATAACGGTGCATTAAGGCATGAAAGGATG
Found at i:2156229 original size:32 final size:31
Alignment explanation
Indices: 2156171--2156237 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 31
2156161 GGTTGACCTA
2156171 AACCGAAAATCAACCAATTCAATATTG-TCCC
1 AACCGAAAATCAACCAATTCAATATTGAT-CC
**
2156202 AACCGAAAAATCAACCAA-TCTGGTATTGATCC
1 AACCG-AAAATCAACCAATTC-AATATTGATCC
2156234 AACC
1 AACC
2156238 CGATATTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 7 0.23
32 23 0.74
33 1 0.03
ACGTcount: A:0.42, C:0.28, G:0.09, T:0.21
Consensus pattern (31 bp):
AACCGAAAATCAACCAATTCAATATTGATCC
Found at i:2156440 original size:15 final size:15
Alignment explanation
Indices: 2156420--2156454 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2156410 AATCTAGACT
*
2156420 CGAAATTACCCGACC
1 CGAAATAACCCGACC
2156435 CGAAATAACCCGACC
1 CGAAATAACCCGACC
2156450 CGAAA
1 CGAAA
2156455 CCAATTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09
Consensus pattern (15 bp):
CGAAATAACCCGACC
Found at i:2158490 original size:26 final size:25
Alignment explanation
Indices: 2158460--2158517 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
2158450 CAGGGAAAAG
2158460 TAAAAATTAGGACAATCATGTGGTT
1 TAAAAATTAGGACAATCATGTGGTT
2158485 TAAAAATTAGGACAATCATGTGGTT
1 TAAAAATTAGGACAATCATGTGGTT
2158510 TAAAAATT
1 TAAAAATT
2158518 TTAGCCCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (25 bp):
TAAAAATTAGGACAATCATGTGGTT
Found at i:2158547 original size:18 final size:19
Alignment explanation
Indices: 2158511--2158548 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2158501 CATGTGGTTT
* *
2158511 AAAAATTTTAGCCCTCAAC
1 AAAAAGTTTAGCCCACAAC
2158530 AAAAAGTTTAG-CCACAAC
1 AAAAAGTTTAGCCCACAAC
2158548 A
1 A
2158549 TGCTAGACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (19 bp):
AAAAAGTTTAGCCCACAAC
Found at i:2159377 original size:22 final size:21
Alignment explanation
Indices: 2159330--2159371 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2159320 ATCAGATTAT
2159330 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
2159351 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
2159372 TGCAGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:2159451 original size:21 final size:19
Alignment explanation
Indices: 2159417--2159485 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 19
2159407 GTGGGTATAT
2159417 ATTCCCCCCAGGGGATATCG
1 ATTCCCCCCAGGGGATA-CG
2159437 ATTCCCCCCAGGGGGA-ACAG
1 ATTCCCCCCA-GGGGATAC-G
2159457 ATTCCCCCCCAAGGGG-TACCG
1 ATT-CCCCCC-AGGGGATA-CG
2159478 ATTCCCCC
1 ATTCCCCC
2159486 ATGTCTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.02
20 20 0.47
21 20 0.47
22 2 0.05
ACGTcount: A:0.20, C:0.41, G:0.23, T:0.16
Consensus pattern (19 bp):
ATTCCCCCCAGGGGATACG
Found at i:2159465 original size:22 final size:21
Alignment explanation
Indices: 2159420--2159485 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
2159410 GGTATATATT
2159420 CCCCCC-AGGGGATATC-GATT-
1 CCCCCCAAGGGGA-A-CAGATTC
*
2159440 CCCCCCAGGGGGAACAGATTC
1 CCCCCCAAGGGGAACAGATTC
* *
2159461 CCCCCCAAGGGGTACCGATTC
1 CCCCCCAAGGGGAACAGATTC
2159482 CCCC
1 CCCC
2159486 ATGTCTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 11 0.28
21 27 0.69
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.14
Consensus pattern (21 bp):
CCCCCCAAGGGGAACAGATTC
Found at i:2165353 original size:33 final size:33
Alignment explanation
Indices: 2165311--2165380 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2165301 CCTTTACAAC
*
2165311 TCCCTAGTTTTTCACGGGCTAAACTAAAACCTT
1 TCCCTAGTTTTTCACGGGATAAACTAAAACCTT
* * *
2165344 TCCCTAGTTTTTCACGGGATCAGCTAGAACCTT
1 TCCCTAGTTTTTCACGGGATAAACTAAAACCTT
2165377 TCCC
1 TCCC
2165381 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (33 bp):
TCCCTAGTTTTTCACGGGATAAACTAAAACCTT
Found at i:2165816 original size:19 final size:19
Alignment explanation
Indices: 2165792--2165828 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2165782 TCCTTTGCAC
2165792 TATGGTATCGATACCCTTG
1 TATGGTATCGATACCCTTG
*
2165811 TATGGTATCGGTACCCTT
1 TATGGTATCGATACCCTT
2165829 TTACTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
TATGGTATCGATACCCTTG
Found at i:2165877 original size:22 final size:22
Alignment explanation
Indices: 2165849--2165890 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2165839 AGTTTGAGCC
*
2165849 TTCATAGGGGTATCGGTACCCA
1 TTCATAGGGGTATCGATACCCA
2165871 TTCATAGGGGTATCGATACC
1 TTCATAGGGGTATCGATACC
2165891 TCTTTGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (22 bp):
TTCATAGGGGTATCGATACCCA
Found at i:2169279 original size:22 final size:22
Alignment explanation
Indices: 2169251--2169292 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2169241 AGTTTGAGCC
2169251 TTCATAGGGATATCGGTACCCA
1 TTCATAGGGATATCGGTACCCA
*
2169273 TTCATAGGGGTATCGGTACC
1 TTCATAGGGATATCGGTACC
2169293 TCTTTGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (22 bp):
TTCATAGGGATATCGGTACCCA
Found at i:2171651 original size:22 final size:21
Alignment explanation
Indices: 2171610--2171659 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
2171600 CACATACATG
2171610 TGATATGTGACAGAAGAGAAGA
1 TGATATGTGACAGAAGAGAA-A
*
2171632 -GATATGTGATCATAAGAGAAA
1 TGATATGTGA-CAGAAGAGAAA
2171653 TGATATG
1 TGATATG
2171660 AATATATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.44, C:0.04, G:0.28, T:0.24
Consensus pattern (21 bp):
TGATATGTGACAGAAGAGAAA
Found at i:2179252 original size:541 final size:540
Alignment explanation
Indices: 2178145--2179764 Score: 2744
Period size: 541 Copynumber: 3.0 Consensus size: 540
2178135 CCACATATGC
*
2178145 ATTAAAATCTAAAATAAATCCAAGTATTATGCATGACCAAAATGGAATGTAGAATATGGCATCTC
1 ATTAAAATCTAAAATAAATCCAAGTATTATGCATGACCAAAATGGTATGTAGAATATGGCATCTC
2178210 GTATACAAGGCAATTAAAATATTAAAATAATAACATATAATATAGAATGACTAAATTAAAAGAAA
66 GTATACAAGGCAATTAAAATATTAAAATAATAACATATAATATAGAATGACTAAATTAAAAGAAA
2178275 CAATAATTAAAAACCCAAAACATAAAGGTACGAACTTAATTTAGTGACTAAAATGAAAATAAATA
131 CAATAATTAAAAACCCAAAACATAAAGGTACGAACTTAATTTAGTGACTAAAATGAAAATAAATA
* * *
2178340 AAATAAAAATACCAAATT-AAATGCTCAATAGCCTATTTCGTGACCGAATTGTGAGAATAGAGTG
196 AAATAAAAATACCAAATTAAAATGCTCAATAACCTGTTTCGTGACCGAATTGTGAGATTAGAGTG
2178404 ACCACGCGTATAATTTTCCCATCCCCAAATTACACAGACACCC-CCTCTTGAAACGACGTAGTTT
261 ACCACGCGTATAATTTTCCCATCCCCAAATTACACAGACACCCTCCTCTTGAAACGACGTAGTTT
2178468 CAATTTGGGTATAAATACCCTTAAATGGCCGAAAATGGTCAAAAATGGCCTTTGTTCTCTCATTT
326 CAATTT-GGTATAAATACCCTTAAATGG-C---------CAAAAATGGCCTTTGTTCTCTCATTT
* *
2178533 CTTCAAATTTCTTTCTCTCTCTAAAAATGAGAGAATCCATTATTTATGTCCTCTCTCTAAACATC
380 CTTCAAATTTCTTTCTCTCTCTAAAAATGAGAGAATCCATTCTTTCTGTCCTCTCTCTAAACATC
*
2178598 CCACCGGTGGGATGGCCGGCCGACAGCCGTTTGCCCCTTTTCTTCTAAACCCAAATCTATGCCCC
445 CCACCGGTGGGATGGCCGGCCGACAGCCGTTCGCCCCTTTTCTTCTAAACCCAAATCTATGCCCC
2178663 TTTCGTCCTAAAAGCGAATAAATAGGGCTAA
510 TTTCGTCCTAAAAGCGAATAAATAGGGCTAA
*
2178694 ATTAAAATCTAAAATAAATCCAAGTATTATGTATGACCAAAATGGTATGTAGAATATGGCATCTC
1 ATTAAAATCTAAAATAAATCCAAGTATTATGCATGACCAAAATGGTATGTAGAATATGGCATCTC
*
2178759 GTATACAAGGCAATTAAAATATTAAAATAATAACATATAATATAGAATGACTAAATTAAAAGAAG
66 GTATACAAGGCAATTAAAATATTAAAATAATAACATATAATATAGAATGACTAAATTAAAAGAAA
* *
2178824 CAATAATTAAAAACCCTAAACATAAATGTACGAACTTAATTTAGTGACTAAAATGAAAATAAATA
131 CAATAATTAAAAACCCAAAACATAAAGGTACGAACTTAATTTAGTGACTAAAATGAAAATAAATA
* *
2178889 AAATAAAAATACCAAATTAAAATGCTCAATAACCTGTTTCGTGACCAAATTATGAGATTAGAGTG
196 AAATAAAAATACCAAATTAAAATGCTCAATAACCTGTTTCGTGACCGAATTGTGAGATTAGAGTG
* * *
2178954 ACCACGCGTATAATTTTTCCATCCCCAAATTACACAGACACCCTTCTCTTGAAACGATGTAGTTT
261 ACCACGCGTATAATTTTCCCATCCCCAAATTACACAGACACCCTCCTCTTGAAACGACGTAGTTT
*
2179019 CAATTTGGATATAAATACCCTTAAATGGCCAAAAATGGCCTTTGTTCTCTCTTTTCTTCAAATTT
326 CAATTTGG-TATAAATACCCTTAAATGGCCAAAAATGGCCTTTGTTCTCTCATTTCTTCAAATTT
*
2179084 CTTTCTCTCTCTAAAAATGGGAGAATCCATTCTTTCTGTCCTCTCTCTAAACATCCCACCGGTGG
390 CTTTCTCTCTCTAAAAATGAGAGAATCCATTCTTTCTGTCCTCTCTCTAAACATCCCACCGGTGG
2179149 GATGGCCGGCCGACAGCCGTTCGCCCCTTTTCTTCTAAACCCAAATCTATGCCCCTTTCGTCCTA
455 GATGGCCGGCCGACAGCCGTTCGCCCCTTTTCTTCTAAACCCAAATCTATGCCCCTTTCGTCCTA
2179214 AAAGCGAATAAATAGGGCTAA
520 AAAGCGAATAAATAGGGCTAA
2179235 ATTAAAATCTAAAATAAATCCAAGTATTATGCATGACCAAAATGGTATGTAGAATATGGCATCTC
1 ATTAAAATCTAAAATAAATCCAAGTATTATGCATGACCAAAATGGTATGTAGAATATGGCATCTC
2179300 GTATACAAGGCAATTAAAATATTAAAATAATAACATATAATATAGAATGACTAAATTAAAAGAAA
66 GTATACAAGGCAATTAAAATATTAAAATAATAACATATAATATAGAATGACTAAATTAAAAGAAA
2179365 CAATAATTAAAAACCCAAAACATAAAGGTACGAACTTAATTTAGTGACTAAAATGAAAATAAATA
131 CAATAATTAAAAACCCAAAACATAAAGGTACGAACTTAATTTAGTGACTAAAATGAAAATAAATA
*
2179430 AAATAAAAATACCAAATTAAAATGCTCAATAACCTGTTTCGTGACTGAATTGTGAGATTAGAGTG
196 AAATAAAAATACCAAATTAAAATGCTCAATAACCTGTTTCGTGACCGAATTGTGAGATTAGAGTG
* * *
2179495 ACCACACGTATAATTTTCCCATCCCCAAATTACACAGACA-CCTCCACCTTAAAACGACGTAGTT
261 ACCACGCGTATAATTTTCCCATCCCCAAATTACACAGACACCCTCC-TCTTGAAACGACGTAGTT
* *
2179559 TCAATTTAGG------TA----TAAATGGTCGAAAATGGCCTTTGTTCTCTCATTTCTTCAAATT
325 TCAATTT-GGTATAAATACCCTTAAATGGCCAAAAATGGCCTTTGTTCTCTCATTTCTTCAAATT
* * *
2179614 TCTTTCTCTCTCTAAAAATGAGAGAATTCATTCTTTCTGCCCTCTCTCTAAAAATCCCACCGGTG
389 TCTTTCTCTCTCTAAAAATGAGAGAATCCATTCTTTCTGTCCTCTCTCTAAACATCCCACCGGTG
** * *
2179679 GGATGGTTGGCCGACAGCCATTCGCCCTTTTTCTTCTAAACCCAAATCTATGCCCCTTTCGTCCT
454 GGATGGCCGGCCGACAGCCGTTCGCCCCTTTTCTTCTAAACCCAAATCTATGCCCCTTTCGTCCT
2179744 AAAAGCGAATAAATAGGGCTA
519 AAAAGCGAATAAATAGGGCTA
2179765 GATCTAATTT
Statistics
Matches: 1024, Mismatches: 42, Indels: 28
0.94 0.04 0.03
Matches are distributed among these distances:
531 183 0.18
535 2 0.00
540 4 0.00
541 495 0.48
542 2 0.00
549 208 0.20
550 86 0.08
551 44 0.04
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (540 bp):
ATTAAAATCTAAAATAAATCCAAGTATTATGCATGACCAAAATGGTATGTAGAATATGGCATCTC
GTATACAAGGCAATTAAAATATTAAAATAATAACATATAATATAGAATGACTAAATTAAAAGAAA
CAATAATTAAAAACCCAAAACATAAAGGTACGAACTTAATTTAGTGACTAAAATGAAAATAAATA
AAATAAAAATACCAAATTAAAATGCTCAATAACCTGTTTCGTGACCGAATTGTGAGATTAGAGTG
ACCACGCGTATAATTTTCCCATCCCCAAATTACACAGACACCCTCCTCTTGAAACGACGTAGTTT
CAATTTGGTATAAATACCCTTAAATGGCCAAAAATGGCCTTTGTTCTCTCATTTCTTCAAATTTC
TTTCTCTCTCTAAAAATGAGAGAATCCATTCTTTCTGTCCTCTCTCTAAACATCCCACCGGTGGG
ATGGCCGGCCGACAGCCGTTCGCCCCTTTTCTTCTAAACCCAAATCTATGCCCCTTTCGTCCTAA
AAGCGAATAAATAGGGCTAA
Found at i:2183878 original size:22 final size:22
Alignment explanation
Indices: 2183853--2183896 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2183843 AAAAGAATCG
2183853 TGATGAATGTTTTC-TAAA-GTTT
1 TGATG-AT-TTTTCATAAATGTTT
2183875 TGATGATTTTTCATAAATGTTT
1 TGATGATTTTTCATAAATGTTT
2183897 GTTCATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
TGATGATTTTTCATAAATGTTT
Found at i:2184089 original size:22 final size:22
Alignment explanation
Indices: 2184064--2184107 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2184054 ATAGCTTTAT
2184064 GCACATGCACTTAAATATAACA
1 GCACATGCACTTAAATATAACA
2184086 GCACATGCACTTAAATATAACA
1 GCACATGCACTTAAATATAACA
2184108 ATTAGTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (22 bp):
GCACATGCACTTAAATATAACA
Found at i:2188614 original size:50 final size:50
Alignment explanation
Indices: 2188548--2188648 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
2188538 CCAACATATC
** * *
2188548 TTTATCAGTAGAATCCAGTAAGTCGGTTGGATTTGTGGTTTCAACAGCAG
1 TTTATCAGTAGAATCCAACAAGTCGGTTGGATTAGTGGTTTCAACAACAG
2188598 TTTATCAGTAGAATCCAACAAGTCGGTTGGATTAGTGGTTTCAACAACAG
1 TTTATCAGTAGAATCCAACAAGTCGGTTGGATTAGTGGTTTCAACAACAG
2188648 T
1 T
2188649 GGTTTCAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (50 bp):
TTTATCAGTAGAATCCAACAAGTCGGTTGGATTAGTGGTTTCAACAACAG
Found at i:2188820 original size:50 final size:50
Alignment explanation
Indices: 2188765--2188883 Score: 141
Period size: 50 Copynumber: 2.4 Consensus size: 50
2188755 AGAAAGTGCG
* * *
2188765 CCCCCTGCATCGCGCTATATGCTGATTTGGCGTCACGTGAGTATAGCGCA
1 CCCCCTGCATCGCGCTATATGCTGATCTGACGCCACGTGAGTATAGCGCA
** * * * *
2188815 CCCCCTGCCCCGCGATATATGGTGATCTGACGCCACGTGGGTATAGCGCG
1 CCCCCTGCATCGCGCTATATGCTGATCTGACGCCACGTGAGTATAGCGCA
2188865 CCCCCTG-ATCCGCGCTATA
1 CCCCCTGCAT-CGCGCTATA
2188884 CGCCACGTAG
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.17, C:0.34, G:0.26, T:0.23
Consensus pattern (50 bp):
CCCCCTGCATCGCGCTATATGCTGATCTGACGCCACGTGAGTATAGCGCA
Found at i:2189804 original size:35 final size:34
Alignment explanation
Indices: 2189719--2189805 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2189709 ATTTGATATT
*
2189719 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2189753 TAAATGATAACTAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2189791 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2189806 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2190035 original size:6 final size:6
Alignment explanation
Indices: 2190019--2190081 Score: 57
Period size: 6 Copynumber: 11.5 Consensus size: 6
2190009 ACTCCTCGCT
* **
2190019 GTCATC ATCATC GTCATC G---TC GTCATC ACCATC GTCATC G---TC
1 GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC
2190061 GTCATC GTCATC GTCATC GTC
1 GTCATC GTCATC GTCATC GTC
2190082 CTGAGCAGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
3 6 0.13
6 39 0.87
ACGTcount: A:0.17, C:0.35, G:0.16, T:0.32
Consensus pattern (6 bp):
GTCATC
Found at i:2190045 original size:21 final size:21
Alignment explanation
Indices: 2190019--2190081 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
2190009 ACTCCTCGCT
2190019 GTCATCATCATCGTCATCGTC
1 GTCATCATCATCGTCATCGTC
*
2190040 GTCATCACCATCGTCATCGTC
1 GTCATCATCATCGTCATCGTC
*
2190061 GTCATCGTCATCGTCATCGTC
1 GTCATCATCATCGTCATCGTC
2190082 CTGAGCAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.17, C:0.35, G:0.16, T:0.32
Consensus pattern (21 bp):
GTCATCATCATCGTCATCGTC
Found at i:2192065 original size:111 final size:111
Alignment explanation
Indices: 2191927--2192148 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
2191917 ATTACAAAAA
* * *
2191927 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
2191992 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2192038 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
2192103 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2192149 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2192470 original size:50 final size:48
Alignment explanation
Indices: 2192416--2192549 Score: 142
Period size: 50 Copynumber: 2.7 Consensus size: 48
2192406 CACGTGTCAG
*
2192416 ATATCCAGGTATAGCACGGATCAGGGGGCACGCTATACCCACGTGGCGCC
1 ATAT-CAGGTATAGCGCGG-TCAGGGGGCACGCTATACCCACGTGGCGCC
* * * * *
2192466 ATATCACCGTATATCGCGGGGCAGGGGGCGCGCTATACCCACGTGGTGCC
1 ATATCA-GGTATAGCGC-GGTCAGGGGGCACGCTATACCCACGTGGCGCC
* *
2192516 AAATCAGCATATAGCGCGGTGCAGGGGGCACGCT
1 ATATCAG-GTATAGCGCGGT-CAGGGGGCACGCT
2192550 TTCCTGCTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
49 4 0.06
50 62 0.91
51 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.16
Consensus pattern (48 bp):
ATATCAGGTATAGCGCGGTCAGGGGGCACGCTATACCCACGTGGCGCC
Found at i:2193335 original size:21 final size:21
Alignment explanation
Indices: 2193311--2193352 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2193301 TCCATCCCTG
2193311 CATAGGAGGATCACCTCTTTT
1 CATAGGAGGATCACCTCTTTT
2193332 CATAGGAGGATCACCTCTTTT
1 CATAGGAGGATCACCTCTTTT
2193353 AGTGTGGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
CATAGGAGGATCACCTCTTTT
Found at i:2203041 original size:28 final size:30
Alignment explanation
Indices: 2203010--2203066 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
2203000 TGAGATACTA
2203010 ATTTG-AAAAAAAA-ATGATATCAATTGAT
1 ATTTGAAAAAAAAATATGATATCAATTGAT
2203038 ATTTGAAAAAAAAAATATGATATCAATTG
1 ATTTG-AAAAAAAAATATGATATCAATTG
2203067 TAGGTGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
30 8 0.31
31 13 0.50
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (30 bp):
ATTTGAAAAAAAAATATGATATCAATTGAT
Found at i:2205084 original size:20 final size:21
Alignment explanation
Indices: 2205059--2205132 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 21
2205049 CTTGCACATG
* *
2205059 AAGTTTCAAAACTTTGGA-GC
1 AAGTTTCAAAACTTTAGATGA
*
2205079 AAGTTTCGAAAC-TTAGATGA
1 AAGTTTCAAAACTTTAGATGA
2205099 AAGTTTCAAAACTATT-G-TGA
1 AAGTTTCAAAACT-TTAGATGA
* *
2205119 AAGTATCGAAACTT
1 AAGTTTCAAAACTT
2205133 CTAAACACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.11
20 37 0.82
21 1 0.02
22 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (21 bp):
AAGTTTCAAAACTTTAGATGA
Found at i:2205774 original size:15 final size:14
Alignment explanation
Indices: 2205739--2205773 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2205729 TTTACCCTTA
*
2205739 AAATTTTAAACTTT
1 AAATTTTAAACATT
*
2205753 AAATTTTAGACATT
1 AAATTTTAAACATT
2205767 AAATTTT
1 AAATTTT
2205774 TTATGTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (14 bp):
AAATTTTAAACATT
Done.