Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_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: 2268343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1333443 original size:43 final size:42
Alignment explanation
Indices: 1333379--1333465 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 42
1333369 TCAGGCCAGG
1333379 TATATATATATATTTAAATTAAATATATAAATATTATATATA
1 TATATATATATATTTAAATTAAATATATAAATATTATATATA
* * *
1333421 TATATATATTTAATTTAAATTAAATTTATTAATATTATATATA
1 TATATATATAT-ATTTAAATTAAATATATAAATATTATATATA
1333464 TA
1 TA
1333466 ATAATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 10 0.24
43 31 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (42 bp):
TATATATATATATTTAAATTAAATATATAAATATTATATATA
Found at i:1333559 original size:30 final size:31
Alignment explanation
Indices: 1333523--1333598 Score: 82
Period size: 36 Copynumber: 2.3 Consensus size: 31
1333513 ACCAAATCCA
1333523 TCCCCGTCCCT-ATTTAGCATAAACGGTTTT
1 TCCCCGTCCCTCATTTAGCATAAACGGTTTT
1333553 TCCCCGTCCCCATCCTCATTTAGCATAAACGGTTTT
1 TCCCCGT---C--CCTCATTTAGCATAAACGGTTTT
**
1333589 TTTCCGTCCC
1 TCCCCGTCCC
1333599 CGTTTAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
30 7 0.18
31 2 0.05
33 2 0.05
35 3 0.08
36 24 0.63
ACGTcount: A:0.17, C:0.36, G:0.12, T:0.36
Consensus pattern (31 bp):
TCCCCGTCCCTCATTTAGCATAAACGGTTTT
Found at i:1338368 original size:474 final size:476
Alignment explanation
Indices: 1337136--1338498 Score: 1913
Period size: 474 Copynumber: 2.8 Consensus size: 476
1337126 TTCATTGGGA
*
1337136 CTAAGACCTCTATATAGCCCAAGGCACAAGGTGCAAAAAGGCGCTTGCCTGATTGAAATAAGTTG
1 CTAAGACCTCTATATAG-CTAA-GCACAAGGTGCAAAAA-GCGCTTGCCT-ATTGAAATAA----
* * * * **
1337201 GGTGCATACATATAAAAA-ATATATAATACACGTAGACGACAATAAACGATAATAACTAAGATAA
58 GGCGCATACATATAAAAATATATATCATACATGTAGACGATAATAAATAATAATAAC-AAGATAA
* * *
1337265 AGCCTTTGCTCGAAGCACATTTTAGGAAAAATAATGAGCAAAAAAGAAATACAATACAAACTTCA
122 AGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATG-GAAAAAAAGAAATACAACACAAACTTCA
1337330 AAGCCAAAAACGGAGCTCTA-TTTTTAACACTAAAACAGAGCAAC-T-T-CTCTGTTTTTAAACA
186 AAGCCAAAAACGGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTCTGTTTTTAAACA
* * *
1337391 ACAAAGTACAGTTTAAAGTCAGCCATAAAGGATAAAAGAACTAAAAGAAGAAAAAAATAGTAGAA
251 ACAAAGTACACTTTAAAATCAACCATAAAGGATAAAAGAACTAAAAGAAG-AAAAAATAGTAGAA
* * *
1337456 TAGATAGAGAGTCGAGGAAAAAAAAGTGAAGGTGACAGCGTTAAGGTTTAAAGAGAGTACGAAGT
315 TAGATAGAGAATCAAGG-AAAAAAAGTGAAGGTGACAGCGTTAAGGTTTAAAGAGAGTACGAAGG
1337521 TGAGTTAAATCTTTTAATTTATTAGAACTTAATATTGTTCTTCATTGGGATAGCTTATTTTAATC
379 TGAGTTAAATCTTTTAATTTATTAGAACTTAATATTGTTCTTCATTGGGATAGCTTATTTTAATC
1337586 AGTGTTATCAAGGGCGCCAGGTGCACTAGAGGCG
444 AGTGTTATCAAGGGCGCCAGGTG-ACTAGAGGCG
* * * * * ** *
1337620 CTAAGACATCTATATAGTCTAGGCACAAGGTGCGAAAAGCACTTGCCCGATTGAAATAAATCCCA
1 CTAAGACCTCTATATAG-CTAAGCACAAGGTGCAAAAAGCGCTTG-CCTATTGAAATAAGGCGCA
* * * *
1337685 TACATATAAAAATATATATCATATATGTAGGCGATAATAAATAATAATAAGTAAGATAAAGGCTT
64 TACATATAAAAATATATATCATACATGTAGACGATAATAAATAATAATAA-CAAGATAAAGCCTT
* *
1337750 TGCTCAAAGTACATTTTAGGAAAAATAATGGAATAAAAAAAAGAAATACAACACAAACTTTAAAG
128 TGCTCGAAGTACATTTTAGGAAAAATAATGG----AAAAAAAGAAATACAACACAAACTTCAAAG
* * * * *
1337815 CCAAAAATGGAGCTCTATTTTTTAACTCTAAAACAGAACAACTTCTCCTCTGTTATCAAACAACA
189 CCAAAAACGGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTCTGTTTTTAAACAACA
* * * *
1337880 AAGTACATTTTAAAATCAACCATAAAGGAGAAAAGAACTAAGATAAGAAAAAATAGTAGAATAGA
254 AAGTACACTTTAAAATCAACCATAAAGGATAAAAGAACTAAAAGAAGAAAAAATAGTAGAATAGA
* *
1337945 TAGAGAATCAAGGAAAAAAGGTGAAGGTGACAGCATTAAGGTTTAAAGAGAGTACGAAGGT-AGT
319 TAGAGAATCAAGGAAAAAAAGTGAAGGTGACAGCGTTAAGGTTTAAAGAGAGTACGAAGGTGAGT
* *
1338009 TAAATCTTTTAATTTATTAGAACTTAATATTGTTCTTTCATTGGTATAGCTTATTTTATTCAGTG
384 TAAATCTTTTAATTTATTAGAACTTAATATTGTTC-TTCATTGGGATAGCTTATTTTAATCAGTG
*
1338074 TTGTCAAGGGCGCCAGGTG-C-A-AGGCG
448 TTATCAAGGGCGCCAGGTGACTAGAGGCG
* *
1338100 CTAAGACCTCTATATAGCATGAAGCACAAGGTGCTAAAAAGTGCTTGACCTATTAAAATAAGGCG
1 CTAAGACCTCTATATAGC-T-AAGCACAAGGTGC-AAAAAGCGCTTG-CCTATTGAAATAAGGCG
1338165 CATACATATAAAAATATATATCATACATGTAGACGATAATAAATAATAATAACAAGATAAAGCCT
62 CATACATATAAAAATATATATCATACATGTAGACGATAATAAATAATAATAACAAGATAAAGCCT
* * *
1338230 TTGCTCGAAGTACATTTTAGG-AAAACAAT-G-AAAAAGGAAATACAACACTAACTTCAAAGCCA
127 TTGCTCGAAGTACATTTTAGGAAAAATAATGGAAAAAAAGAAATACAACACAAACTTCAAAGCCA
1338292 AAAACGGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTCTGTTTTTAAACAACAAAG
192 AAAACGGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTCTGTTTTTAAACAACAAAG
* * *
1338357 TACACTTTAAAAGCAACCATAAGGGATAAAAGAACTAAAAGAAGAAAAAATAGGAGAATAGATAG
257 TACACTTTAAAATCAACCATAAAGGATAAAAGAACTAAAAGAAGAAAAAATAGTAGAATAGATAG
*
1338422 AGACTCAAGGAGGAAAAAAAGTGAAGGTGACAGCGTTAAGGTTTAAAGAGAGTACGAAGGTGAGT
322 AGAATC-A--AGGAAAAAAAGTGAAGGTGACAGCGTTAAGGTTTAAAGAGAGTACGAAGGTGAGT
1338487 TAAATCTTTTAA
384 TAAATCTTTTAA
1338499 ATTTGCTTTG
Statistics
Matches: 781, Mismatches: 79, Indels: 44
0.86 0.09 0.05
Matches are distributed among these distances:
474 152 0.19
475 1 0.00
477 49 0.06
478 30 0.04
479 72 0.09
480 29 0.04
481 44 0.06
482 131 0.17
483 77 0.10
484 109 0.14
485 30 0.04
486 57 0.07
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.25
Consensus pattern (476 bp):
CTAAGACCTCTATATAGCTAAGCACAAGGTGCAAAAAGCGCTTGCCTATTGAAATAAGGCGCATA
CATATAAAAATATATATCATACATGTAGACGATAATAAATAATAATAACAAGATAAAGCCTTTGC
TCGAAGTACATTTTAGGAAAAATAATGGAAAAAAAGAAATACAACACAAACTTCAAAGCCAAAAA
CGGAGCTCTATTTTTTAACACTAAAACAGAGCAACTTCTCCTCTGTTTTTAAACAACAAAGTACA
CTTTAAAATCAACCATAAAGGATAAAAGAACTAAAAGAAGAAAAAATAGTAGAATAGATAGAGAA
TCAAGGAAAAAAAGTGAAGGTGACAGCGTTAAGGTTTAAAGAGAGTACGAAGGTGAGTTAAATCT
TTTAATTTATTAGAACTTAATATTGTTCTTCATTGGGATAGCTTATTTTAATCAGTGTTATCAAG
GGCGCCAGGTGACTAGAGGCG
Found at i:1344756 original size:16 final size:16
Alignment explanation
Indices: 1344737--1344767 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1344727 AAGTTAAGCT
1344737 TATTAAAAAGAAAATA
1 TATTAAAAAGAAAATA
*
1344753 TATTACAAAGAAAAT
1 TATTAAAAAGAAAAT
1344768 TCGATAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
TATTAAAAAGAAAATA
Found at i:1353401 original size:56 final size:55
Alignment explanation
Indices: 1353331--1353516 Score: 192
Period size: 56 Copynumber: 3.3 Consensus size: 55
1353321 CCCTATTTTC
* * * *
1353331 TAGATATATTCGATTTCTGGACCCCTATTTTTATGCTTCTTAATGGCAATAATTGG
1 TAGATATACTCGATTTC-GGACCCCTATTTTTATGCTTCTTAATGGCAACAACTGA
* **** * * *
1353387 TATATATACTCGATTTCGGAGTTTATATTTTTATGTTTCTTAATAGCAACAACTAA
1 TAGATATACTCGATTTCGGA-CCCCTATTTTTATGCTTCTTAATGGCAACAACTGA
** * * *
1353443 TAGATATACTCGATTTCGGGGGCCCTGTTTTTATGCTTATTAATGGCAACAACAGA
1 TAGATATACTCGATTTC-GGACCCCTATTTTTATGCTTCTTAATGGCAACAACTGA
1353499 TAGATATACTCGATTTCG
1 TAGATATACTCGATTTCG
1353517 AGGCCTGAGG
Statistics
Matches: 104, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
55 4 0.04
56 98 0.94
57 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (55 bp):
TAGATATACTCGATTTCGGACCCCTATTTTTATGCTTCTTAATGGCAACAACTGA
Found at i:1357448 original size:15 final size:15
Alignment explanation
Indices: 1357405--1357452 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1357395 CTTATTAAAA
*
1357405 TTAAAATTTTATAACT
1 TTAAAATTTTATTA-T
* *
1357421 TTTAATTTCTTATTAT
1 TTAAAATT-TTATTAT
1357437 TTAAAATTTTATTAT
1 TTAAAATTTTATTAT
1357452 T
1 T
1357453 AATAAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 8 0.31
16 13 0.50
17 5 0.19
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAAATTTTATTAT
Found at i:1369409 original size:31 final size:30
Alignment explanation
Indices: 1369369--1369457 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
1369359 ATAAATTTTA
*
1369369 ACAAGTTTAATGATTATTTTATAATCATTTG
1 ACAAATTTAATGATTATTTTATAAT-ATTTG
* * * *
1369400 ACAAATTTAATAATCATTTTGTAAATGTTTG
1 ACAAATTTAATGATTATTTTAT-AATATTTG
*
1369431 A-AAAGTTT-ATGACTATTTTATAATATT
1 ACAAA-TTTAATGATTATTTTATAATATT
1369458 AAATAATTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
29 5 0.11
30 12 0.26
31 26 0.57
32 3 0.07
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (30 bp):
ACAAATTTAATGATTATTTTATAATATTTG
Found at i:1372101 original size:10 final size:10
Alignment explanation
Indices: 1372086--1372125 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
1372076 ATTTATTTTT
1372086 TTAAAAATAA
1 TTAAAAATAA
1372096 TTAAAAATACAA
1 TTAAAAAT--AA
*
1372108 TAAAAAATAA
1 TTAAAAATAA
1372118 TTAAAAAT
1 TTAAAAAT
1372126 GGATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 17 0.65
12 9 0.35
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:1373419 original size:29 final size:29
Alignment explanation
Indices: 1373387--1373443 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1373377 TTTTTAATTT
1373387 TTAATT-TTATTAAAAATGAATAAATAATA
1 TTAATTGTTATTAAAAAT-AATAAATAATA
* *
1373416 TTAATTGTTGTTAAAAATAATAATTAAT
1 TTAATTGTTATTAAAAATAATAAATAAT
1373444 GATGAGACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (29 bp):
TTAATTGTTATTAAAAATAATAAATAATA
Found at i:1373880 original size:12 final size:10
Alignment explanation
Indices: 1373834--1373890 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
1373824 TTACATTATG
*
1373834 TTTTTATTGA
1 TTTTTATTTA
* *
1373844 ATTTTATTCA
1 TTTTTATTTA
*
1373854 TTTTTAATTCA
1 TTTTT-ATTTA
1373865 TTTTTATTATA
1 TTTTTATT-TA
1373876 TTTTTATTTA
1 TTTTTATTTA
1373886 TTTTT
1 TTTTT
1373891 TAAAAAAGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 22 0.54
11 19 0.46
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:1373888 original size:21 final size:20
Alignment explanation
Indices: 1373828--1373890 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1373818 TTAGCTTTAC
* *
1373828 ATTATGTTTTTATTGAATTTT
1 ATTAT-TTTTTATTCATTTTT
*
1373849 ATTCATTTTTAATTCATTTTT
1 ATT-ATTTTTTATTCATTTTT
*
1373870 ATTATATTTTTATTTATTTTT
1 ATTAT-TTTTTATTCATTTTT
1373891 TAAAAAAGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (20 bp):
ATTATTTTTTATTCATTTTT
Found at i:1373891 original size:11 final size:11
Alignment explanation
Indices: 1373845--1373892 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1373835 TTTTATTGAA
1373845 TTTTATTCATT
1 TTTTATTCATT
*
1373856 TTTAATTCA-T
1 TTTTATTCATT
1373866 TTTTATT-ATAT
1 TTTTATTCAT-T
*
1373877 TTTTATTTATT
1 TTTTATTCATT
1373888 TTTTA
1 TTTTA
1373893 AAAAAGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 1 0.03
10 7 0.22
11 22 0.69
12 2 0.06
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTATTCATT
Found at i:1377857 original size:35 final size:35
Alignment explanation
Indices: 1377779--1377858 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
1377769 TTTTAAATGC
*
1377779 AACAAACTTACAATAAGTATTAAATGGTAAATGAT
1 AACAAAATTACAATAAGTATTAAATGGTAAATGAT
* *
1377814 AACCAAATTACAATAACTGATATTAAATTGT-AAT-A-
1 AACAAAATTACAATAA--G-TATTAAATGGTAAATGAT
1377849 AACAAAATTA
1 AACAAAATTA
1377859 ACTGAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
35 23 0.61
36 1 0.03
37 4 0.11
38 10 0.26
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (35 bp):
AACAAAATTACAATAAGTATTAAATGGTAAATGAT
Found at i:1380176 original size:17 final size:18
Alignment explanation
Indices: 1380156--1380194 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1380146 ATTATATAAG
1380156 TAAAATA-TTAAATAAAT
1 TAAAATATTTAAATAAAT
1380173 TAAAATATTTAAATAAAT
1 TAAAATATTTAAATAAAT
1380191 TAAA
1 TAAA
1380195 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATATTTAAATAAAT
Found at i:1387499 original size:2 final size:2
Alignment explanation
Indices: 1387492--1387526 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1387482 CTGTTTTTCT
1387492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1387527 GAGCAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1388394 original size:7 final size:7
Alignment explanation
Indices: 1388382--1388411 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1388372 TTTTAAAATC
1388382 ATTTTGA
1 ATTTTGA
1388389 ATTTTGA
1 ATTTTGA
1388396 ATTTTGA
1 ATTTTGA
1388403 ATTTTGA
1 ATTTTGA
1388410 AT
1 AT
1388412 CTTTCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (7 bp):
ATTTTGA
Found at i:1398107 original size:17 final size:18
Alignment explanation
Indices: 1398087--1398120 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1398077 TATTTTAACC
1398087 AAATTAATATT-TAATTT
1 AAATTAATATTATAATTT
*
1398104 AAATTATTATTATAATT
1 AAATTAATATTATAATT
1398121 GAAGACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTAATATTATAATTT
Found at i:1411851 original size:21 final size:21
Alignment explanation
Indices: 1411822--1411865 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1411812 GATAAAAAAA
* *
1411822 TTATCTAAATTATTAATATTT
1 TTATATAAAATATTAATATTT
1411843 TTATATAAAATATTAATATTT
1 TTATATAAAATATTAATATTT
1411864 TT
1 TT
1411866 TTAATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATATAAAATATTAATATTT
Found at i:1412272 original size:29 final size:30
Alignment explanation
Indices: 1412240--1412303 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1412230 TATTTTGACT
*
1412240 ACTAAACTATT-AATT-TTATCAATTAAATC
1 ACTAAACTATTAAATTATT-TCAATCAAATC
*
1412269 ACTAAATTATTAAAATTATTTCAATCAAATC
1 ACTAAACTATT-AAATTATTTCAATCAAATC
1412300 ACTA
1 ACTA
1412304 GCCGTCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.33
31 18 0.60
32 2 0.07
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (30 bp):
ACTAAACTATTAAATTATTTCAATCAAATC
Found at i:1420056 original size:16 final size:16
Alignment explanation
Indices: 1420035--1420067 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1420025 CTTCAACCTT
1420035 CTTGAAGTAAAGATAG
1 CTTGAAGTAAAGATAG
1420051 CTTGAAGTAAAGATAG
1 CTTGAAGTAAAGATAG
1420067 C
1 C
1420068 ACTTGAGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (16 bp):
CTTGAAGTAAAGATAG
Found at i:1420192 original size:35 final size:35
Alignment explanation
Indices: 1420129--1420351 Score: 115
Period size: 35 Copynumber: 6.0 Consensus size: 35
1420119 TGTCATCGAG
* *
1420129 AATCGAAAGTGCTATGCCTCTTTTCGTTCTACTTA
1 AATCGAAAGTGCTATGCCTCCTTCCGTTCTACTTA
*
1420164 AATCGAAAGTG-TAATGCTTCCTTCCGTTCTACTTTAGACGA
1 AATCGAAAGTGCT-ATGCCTCCTTCCGTTCTAC-TT-----A
* * * *
1420205 GAATCGAAAGTGCTATGCCTCCTTTCATTCTAGTTG
1 -AATCGAAAGTGCTATGCCTCCTTCCGTTCTACTTA
* * * * * *
1420241 AATTGAAAGTACGATGCTTCCTTCCATTATACTTTAGACGAA
1 AATCGAAAGTGCTATGCCTCCTTCCGTTCTAC-TT------A
* * * * *
1420283 AATTGAAAGTGTTATGCCTCCTTTCATTCTACTTG
1 AATCGAAAGTGCTATGCCTCCTTCCGTTCTACTTA
* * *
1420318 AATTGAAAGTGCAATGCTTCCTTCCGTTCTACTT
1 AATCGAAAGTGCTATGCCTCCTTCCGTTCTACTT
1420352 TAGACGAGAA
Statistics
Matches: 144, Mismatches: 28, Indels: 32
0.71 0.14 0.16
Matches are distributed among these distances:
34 1 0.01
35 81 0.56
36 4 0.03
41 5 0.03
42 52 0.36
43 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (35 bp):
AATCGAAAGTGCTATGCCTCCTTCCGTTCTACTTA
Found at i:1420217 original size:77 final size:77
Alignment explanation
Indices: 1420125--1420453 Score: 469
Period size: 77 Copynumber: 4.3 Consensus size: 77
1420115 ATTCTGTCAT
* * * * *
1420125 CGAGAATCGAAAGTGCTATGCCTCTTTTCGTTCTACTTAAATCGAAAGTGTAATGCTTCCTTCCG
1 CGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTGAATTGAAAGTGCAATGCTTCCTTCCG
*
1420190 TTCTACTTTAGA
66 TTATACTTTAGA
* * * *
1420202 CGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTAGTTGAATTGAAAGTACGATGCTTCCTTCCA
1 CGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTGAATTGAAAGTGCAATGCTTCCTTCCG
1420267 TTATACTTTAGA
66 TTATACTTTAGA
* * *
1420279 CGAAAATTGAAAGTGTTATGCCTCCTTTCATTCTACTTGAATTGAAAGTGCAATGCTTCCTTCCG
1 CGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTGAATTGAAAGTGCAATGCTTCCTTCCG
*
1420344 TTCTACTTTAGA
66 TTATACTTTAGA
* * * * *
1420356 CGAGAATCGAAAGTGTTATGCCTCCTTTCATTCTAGTTGAATTGAAAGTGCGATGCTTCATTTCG
1 CGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTGAATTGAAAGTGCAATGCTTCCTTCCG
1420421 TTATACTTTAGA
66 TTATACTTTAGA
* *
1420433 CAAGAATCGAAAGTGCGATGC
1 CGAGAATCGAAAGTGCTATGC
1420454 TTTCTTCCGT
Statistics
Matches: 224, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 224 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (77 bp):
CGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTGAATTGAAAGTGCAATGCTTCCTTCCG
TTATACTTTAGA
Found at i:1420228 original size:42 final size:41
Alignment explanation
Indices: 1420164--1420469 Score: 173
Period size: 42 Copynumber: 7.8 Consensus size: 41
1420154 GTTCTACTTA
*
1420164 AATCGAAAGTG-TAATGCTTCCTTCCGTTCTACTTTAGACGAG
1 AATCGAAAGTGCT-ATGCTTCCTTCCATTCTACTTTAGAC-AG
* * *
1420206 AATCGAAAGTGCTATGCCTCCTTTCATTCTA-GTT-----G
1 AATCGAAAGTGCTATGCTTCCTTCCATTCTACTTTAGACAG
* * * * *
1420241 AATTGAAAGTACGATGCTTCCTTCCATTATACTTTAGACGAA
1 AATCGAAAGTGCTATGCTTCCTTCCATTCTACTTTAGAC-AG
* * * *
1420283 AATTGAAAGTGTTATGCCTCCTTTCATTCTAC-TT-----G
1 AATCGAAAGTGCTATGCTTCCTTCCATTCTACTTTAGACAG
* * *
1420318 AATTGAAAGTGCAATGCTTCCTTCCGTTCTACTTTAGACGAG
1 AATCGAAAGTGCTATGCTTCCTTCCATTCTACTTTAGAC-AG
* * * *
1420360 AATCGAAAGTGTTATGCCTCCTTTCATTCTA-GTT-----G
1 AATCGAAAGTGCTATGCTTCCTTCCATTCTACTTTAGACAG
* * * * * *
1420395 AATTGAAAGTGCGATGCTTCATTTCGTTATACTTTAGACAAG
1 AATCGAAAGTGCTATGCTTCCTTCCATTCTACTTTAGAC-AG
* * *
1420437 AATCGAAAGTGCGATGCTTTCTTCCGTTCTACT
1 AATCGAAAGTGCTATGCTTCCTTCCATTCTACT
1420470 CGAAAGTATG
Statistics
Matches: 198, Mismatches: 44, Indels: 44
0.69 0.15 0.15
Matches are distributed among these distances:
35 78 0.39
36 6 0.03
41 6 0.03
42 107 0.54
43 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (41 bp):
AATCGAAAGTGCTATGCTTCCTTCCATTCTACTTTAGACAG
Found at i:1420413 original size:154 final size:154
Alignment explanation
Indices: 1420127--1420453 Score: 521
Period size: 154 Copynumber: 2.1 Consensus size: 154
1420117 TCTGTCATCG
* * *
1420127 AGAATCGAAAGTGCTATGCCTCTTTTCGTTCTACTTAAATCGAAAGTGTAATGCTTCCTTCCGTT
1 AGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTAAATCGAAAGTGCAATGCTTCCTTCCGTT
1420192 CTACTTTAGACGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTAGTTGAATTGAAAGTACGATG
66 CTACTTTAGACGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTAGTTGAATTGAAAGTACGATG
*
1420257 CTTCCTTCCATTATACTTTAGACGA
131 CTTCATTCCATTATACTTTAGAC-A
* * * *
1420282 A-AATTGAAAGTGTTATGCCTCCTTTCATTCTACTTGAATTGAAAGTGCAATGCTTCCTTCCGTT
1 AGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTAAATCGAAAGTGCAATGCTTCCTTCCGTT
* *
1420346 CTACTTTAGACGAGAATCGAAAGTGTTATGCCTCCTTTCATTCTAGTTGAATTGAAAGTGCGATG
66 CTACTTTAGACGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTAGTTGAATTGAAAGTACGATG
* *
1420411 CTTCATTTCGTTATACTTTAGACA
131 CTTCATTCCATTATACTTTAGACA
*
1420435 AGAATCGAAAGTGCGATGC
1 AGAATCGAAAGTGCTATGC
1420454 TTTCTTCCGT
Statistics
Matches: 156, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
153 2 0.01
154 153 0.98
155 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (154 bp):
AGAATCGAAAGTGCTATGCCTCCTTTCATTCTACTTAAATCGAAAGTGCAATGCTTCCTTCCGTT
CTACTTTAGACGAGAATCGAAAGTGCTATGCCTCCTTTCATTCTAGTTGAATTGAAAGTACGATG
CTTCATTCCATTATACTTTAGACA
Found at i:1421032 original size:34 final size:35
Alignment explanation
Indices: 1420982--1421051 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
1420972 GTTAAAAACT
* *
1420982 ATATTAATATATTAAATTAAAAGCA-GGCACATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGCACATAA
*
1421016 ATATTAATAAACTAAATTAAAAGCAGGGCCCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGCACATAA
1421051 A
1 A
1421052 CTTATTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.26
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAGGGCACATAA
Found at i:1422469 original size:20 final size:21
Alignment explanation
Indices: 1422432--1422478 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1422422 AATGAACATC
1422432 TATATAAATAAATATTTAT-AA
1 TATA-AAATAAATATTTATAAA
* *
1422453 TATAAAATATATTTTTATAAA
1 TATAAAATAAATATTTATAAA
1422474 TATAA
1 TATAA
1422479 TCGAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAAAATAAATATTTATAAA
Found at i:1423081 original size:21 final size:25
Alignment explanation
Indices: 1423052--1423106 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
1423042 CAAAACCCTA
1423052 TTTT-TTCGTC-T-TTATC-TC-TC
1 TTTTCTTCGTCATATTATCTTCTTC
1423072 TTTTCTTCGTCTATATTATCTTCTTC
1 TTTTCTTCGTC-ATATTATCTTCTTC
1423098 TTTTCTTCG
1 TTTTCTTCG
1423107 AGAAGAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
23 1 0.03
24 5 0.17
25 2 0.07
26 11 0.38
ACGTcount: A:0.07, C:0.24, G:0.05, T:0.64
Consensus pattern (25 bp):
TTTTCTTCGTCATATTATCTTCTTC
Found at i:1428313 original size:30 final size:32
Alignment explanation
Indices: 1428279--1428346 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
1428269 ATAGTTTTTA
1428279 TATTTTATAGT-AAT-ATAATTATATAAATAT
1 TATTTTATAGTAAATAATAATTATATAAATAT
* * * *
1428309 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATAGT-AAATAATAATTATATAAATAT
1428342 TATTT
1 TATTT
1428347 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTTATAGTAAATAATAATTATATAAATAT
Found at i:1428348 original size:30 final size:28
Alignment explanation
Indices: 1428307--1428370 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
1428297 TTATATAAAT
* *
1428307 ATTATTTTTTATTAAAATAATATTTATATA
1 ATTATTATTTATTAAAAT-ATATTAAT-TA
* *
1428337 ATTATTATTTATTTAAATTTATTAATTA
1 ATTATTATTTATTAAAATATATTAATTA
1428365 ATTATT
1 ATTATT
1428371 TTTTTTGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.27
29 6 0.20
30 16 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTATTATTTATTAAAATATATTAATTA
Found at i:1428406 original size:20 final size:17
Alignment explanation
Indices: 1428363--1428394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1428353 ATTTATTAAT
1428363 TAATTAT-TTTTTTTGC
1 TAATTATATTTTTTTGC
1428379 TAATTATATTTTTTTG
1 TAATTATATTTTTTTG
1428395 TCTACAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (17 bp):
TAATTATATTTTTTTGC
Found at i:1428535 original size:17 final size:17
Alignment explanation
Indices: 1428515--1428553 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1428505 CTTTATTTTT
*
1428515 AATTTAAATTTATCATA
1 AATTTAAATTAATCATA
* *
1428532 AATTTATATTAATTATA
1 AATTTAAATTAATCATA
1428549 AATTT
1 AATTT
1428554 TTATAATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTAAATTAATCATA
Found at i:1430202 original size:21 final size:21
Alignment explanation
Indices: 1430150--1430189 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1430140 GTCATCTCCG
*
1430150 CAGGGTTATATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCT
1430171 CAGGGTTACATTCCTAGCC
1 CAGGGTTACATTCCTAGCC
1430190 TGCCAGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCT
Found at i:1430863 original size:23 final size:23
Alignment explanation
Indices: 1430837--1430900 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1430827 CAGCTATAAT
* *
1430837 AATTGCACCGAAGTGCCACGTAG
1 AATTACACCGAAGTGCCACATAG
*
1430860 AATTACACC-AGAGTGCCGCATAG
1 AATTACACCGA-AGTGCCACATAG
*
1430883 AATTACACCGTAGTGCCA
1 AATTACACCGAAGTGCCA
1430901 TATAATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.19
Consensus pattern (23 bp):
AATTACACCGAAGTGCCACATAG
Found at i:1431153 original size:30 final size:30
Alignment explanation
Indices: 1431112--1431178 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1431102 ATAATTTGTT
* * * *
1431112 TCACGTAGACATATTATTTTCTTACCTTTA
1 TCACATAGACATATCATTTCCATACCTTTA
1431142 TCACATAGACATATCATTTCCATACCTTTA
1 TCACATAGACATATCATTTCCATACCTTTA
1431172 TCACATA
1 TCACATA
1431179 ACTCATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (30 bp):
TCACATAGACATATCATTTCCATACCTTTA
Found at i:1437303 original size:59 final size:59
Alignment explanation
Indices: 1437211--1437329 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
1437201 ACCATAGCTC
* * *
1437211 TGATACCATTAAATGCAACACCCCCAACTCGTATCTGA-CTCGGATACTAGTTCGAGGTG
1 TGATACCATTAAATGCAACACCCCCAACCCGTATCCGATC-CGGATACTAGTCCGAGGTG
*
1437270 TGATACCATTAAATGTAACACCCCCAACCCGTATCCGATCCGGATACTAGTCCGAGGTG
1 TGATACCATTAAATGCAACACCCCCAACCCGTATCCGATCCGGATACTAGTCCGAGGTG
1437329 T
1 T
1437330 CACATTACCT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 54 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (59 bp):
TGATACCATTAAATGCAACACCCCCAACCCGTATCCGATCCGGATACTAGTCCGAGGTG
Found at i:1437885 original size:23 final size:22
Alignment explanation
Indices: 1437854--1437922 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
1437844 CACCACAGCT
* *
1437854 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCG-AGTGCCA
*
1437877 CGTAGAATTGCACCTGAGTGCCG
1 CGTAGAATTGCACC-GAGTGCCA
1437900 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCG-AGTGCCA
1437923 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (22 bp):
CGTAGAATTGCACCGAGTGCCA
Found at i:1440102 original size:34 final size:34
Alignment explanation
Indices: 1440018--1440090 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1440008 TTAAATGCTT
* *
1440018 TTAATATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATAATAGTATTCAAAATTTAAAA
* *
1440052 TTAAAATACAAATAATAGTATTCGAAATTTAACA
1 TTAAAATACAAATAATAGTATTCAAAATTTAAAA
1440086 TTAAA
1 TTAAA
1440091 TTCAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATAATAGTATTCAAAATTTAAAA
Found at i:1442449 original size:17 final size:16
Alignment explanation
Indices: 1442429--1442489 Score: 63
Period size: 15 Copynumber: 3.9 Consensus size: 16
1442419 ATTAGCACAA
*
1442429 AAATAATTAATTAATTT
1 AAATAAATAA-TAATTT
1442446 AAATAAATAATAA-TT
1 AAATAAATAATAATTT
*
1442461 ATATAAATAAT-ATTT
1 AAATAAATAATAATTT
* *
1442476 TAATAAAAAATAAT
1 AAATAAATAATAAT
1442490 ATTTATAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 22 0.59
16 5 0.14
17 9 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAAATAATAATTT
Found at i:1442514 original size:32 final size:33
Alignment explanation
Indices: 1442433--1442520 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 33
1442423 GCACAAAAAT
*
1442433 AATTA-ATTAATTTAAATAAATAATAATTATATA
1 AATTATATTAATATAAA-AAATAATAATTATATA
* *
1442466 AATAATATT-TTAATAAAAAATAAT-ATT-TATA
1 AATTATATTAAT-ATAAAAAATAATAATTATATA
*
1442497 GAATTATATTAATATAAAATATAA
1 -AATTATATTAATATAAAAAATAA
1442521 AAACTATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
31 4 0.09
32 21 0.47
33 13 0.29
34 7 0.16
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (33 bp):
AATTATATTAATATAAAAAATAATAATTATATA
Found at i:1449021 original size:6 final size:6
Alignment explanation
Indices: 1449010--1449047 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
1449000 AGTTCCGCTT
1449010 AATTCA AATTCA AATTCA AATTCA AATTCA AATTCA AA
1 AATTCA AATTCA AATTCA AATTCA AATTCA AATTCA AA
1449048 GTGAGATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTCA
Found at i:1449948 original size:21 final size:22
Alignment explanation
Indices: 1449918--1449959 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1449908 TGTTTTCAAG
1449918 GTGAAGAATT-TGTTTGTTGAA
1 GTGAAGAATTGTGTTTGTTGAA
* *
1449939 GTGAATAATTGTTTTTGTTGA
1 GTGAAGAATTGTGTTTGTTGA
1449960 GTTTGAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (22 bp):
GTGAAGAATTGTGTTTGTTGAA
Found at i:1461468 original size:12 final size:13
Alignment explanation
Indices: 1461447--1461480 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1461437 TATGATCTAT
*
1461447 AATATTTAAC-AA
1 AATATATAACGAA
1461459 AATATATAACGAA
1 AATATATAACGAA
1461472 AATATATAA
1 AATATATAA
1461481 AAGAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (13 bp):
AATATATAACGAA
Found at i:1462355 original size:12 final size:12
Alignment explanation
Indices: 1462338--1462389 Score: 86
Period size: 13 Copynumber: 4.2 Consensus size: 12
1462328 ATTAACACCT
1462338 TTTGCATTTGCA
1 TTTGCATTTGCA
1462350 TTTGCATTTGCA
1 TTTGCATTTGCA
1462362 TTTTGCATTTGCA
1 -TTTGCATTTGCA
1462375 TTTGCATTTTGCA
1 TTTGCA-TTTGCA
1462388 TT
1 TT
1462390 GTATTTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
12 18 0.47
13 20 0.53
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:1462365 original size:25 final size:26
Alignment explanation
Indices: 1462337--1462389 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
1462327 AATTAACACC
1462337 TTTTGCATTTGCATTTGCA-TTTGCA
1 TTTTGCATTTGCATTTGCATTTTGCA
1462362 TTTTGCATTTGCATTTGCATTTTGCA
1 TTTTGCATTTGCATTTGCATTTTGCA
1462388 TT
1 TT
1462390 GTATTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (26 bp):
TTTTGCATTTGCATTTGCATTTTGCA
Found at i:1462368 original size:19 final size:19
Alignment explanation
Indices: 1462338--1462389 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1462328 ATTAACACCT
1462338 TTTGCA-TTTGCATTTGCA
1 TTTGCATTTTGCATTTGCA
1462356 TTTGCATTTTGCATTTGCA
1 TTTGCATTTTGCATTTGCA
1462375 TTTGCATTTTGCATT
1 TTTGCATTTTGCATT
1462390 GTATTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.18
19 27 0.82
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTGCATTTTGCATTTGCA
Found at i:1462397 original size:6 final size:6
Alignment explanation
Indices: 1462338--1462389 Score: 86
Period size: 6 Copynumber: 8.3 Consensus size: 6
1462328 ATTAACACCT
1462338 TTTGCA TTTGCA TTTGCA TTTGCA TTTTGCA TTTGCA TTTGCA TTTTGCA
1 TTTGCA TTTGCA TTTGCA TTTGCA -TTTGCA TTTGCA TTTGCA -TTTGCA
1462388 TT
1 TT
1462390 GTATTTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
6 32 0.73
7 12 0.27
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTGCA
Found at i:1463126 original size:31 final size:31
Alignment explanation
Indices: 1463088--1463149 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1463078 CCGAAAGACT
*
1463088 AGTCCATA-GATCCCGAAGAACCTAGGTAAAC
1 AGTCCATATG-TCCCGAAGAACATAGGTAAAC
*
1463119 AGTCCATATGTTCCGAAGAACATAGGTAAAC
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
1463150 CCTCGACCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
AGTCCATATGTCCCGAAGAACATAGGTAAAC
Found at i:1464008 original size:24 final size:24
Alignment explanation
Indices: 1463979--1464028 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1463969 GTGGGGTTGA
*
1463979 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1464003 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1464027 TT
1 TT
1464029 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1464526 original size:19 final size:19
Alignment explanation
Indices: 1464502--1464538 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1464492 TCACGTGAGG
1464502 ATTATTT-TCTTCTTATTTT
1 ATTATTTATCTT-TTATTTT
1464521 ATTATTTATCTTTTATTT
1 ATTATTTATCTTTTATTT
1464539 ACTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTATTTATCTTTTATTTT
Found at i:1474247 original size:24 final size:24
Alignment explanation
Indices: 1474218--1474267 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1474208 TGGTGGTTGA
*
1474218 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1474242 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1474266 TT
1 TT
1474268 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1479921 original size:64 final size:64
Alignment explanation
Indices: 1479813--1479934 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
1479803 TAATGAAGGT
* *
1479813 ATGCATCGATGAACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGAACTACTGATGCATCGATGCATAAAATGCATTCGATGTT-TCATTATTACTGGG
* * * * *
1479877 ATGCATCGATGCACTACTTATGTATCGATGCATGAATTGCATTCGATGTTTCATTATT
1 ATGCATCGATGAACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTCATTATT
1479935 TTAAAAGAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 1 0.02
64 49 0.98
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (64 bp):
ATGCATCGATGAACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTACTGGG
Found at i:1484949 original size:24 final size:24
Alignment explanation
Indices: 1484857--1484949 Score: 82
Period size: 24 Copynumber: 3.9 Consensus size: 24
1484847 ATCCGATTTT
* *
1484857 TGATTTGAATTCTGTTTTGACATC
1 TGATCTGAATTCTGTTTTGATATC
*
1484881 TGATCTGAAATT-TGTTCTGAT-TCC
1 TGATCTG-AATTCTGTTTTGATAT-C
* * * *
1484905 TAACCTGGATTCTGTTATGATATC
1 TGATCTGAATTCTGTTTTGATATC
*
1484929 TGATCTGAATTATGTTTTGAT
1 TGATCTGAATTCTGTTTTGAT
1484950 TTCCGATATC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
23 4 0.08
24 44 0.83
25 5 0.09
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATCTGAATTCTGTTTTGATATC
Found at i:1486044 original size:24 final size:24
Alignment explanation
Indices: 1486017--1486062 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1486007 ATACGTCTAG
*
1486017 ATTTAATACTT-TGATACATGATTC
1 ATTTAATA-TTATGAAACATGATTC
*
1486041 ATTTCATATTATGAAACATGAT
1 ATTTAATATTATGAAACATGAT
1486063 ATGAGTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (24 bp):
ATTTAATATTATGAAACATGATTC
Found at i:1487701 original size:12 final size:12
Alignment explanation
Indices: 1487686--1487711 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1487676 AAAGAGAGCT
1487686 AAAAAGAATAAG
1 AAAAAGAATAAG
1487698 AAAAAGAATAAG
1 AAAAAGAATAAG
1487710 AA
1 AA
1487712 GACACCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAAGAATAAG
Found at i:1489000 original size:30 final size:30
Alignment explanation
Indices: 1488934--1489006 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1488924 GATGATGTAA
* * * * *
1488934 ACGTCTTTTAGAAGTTATTACATAATCTAG
1 ACGTCTTTCAAAAGTTATTACACAATCCAC
* *
1488964 ATGTCTTTCAAAAGTTATTAGACAATCCAC
1 ACGTCTTTCAAAAGTTATTACACAATCCAC
1488994 ACGTCTTTTCAAA
1 ACGTC-TTTCAAA
1489007 GTATTGTAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 27 0.79
31 7 0.21
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (30 bp):
ACGTCTTTCAAAAGTTATTACACAATCCAC
Found at i:1489511 original size:37 final size:37
Alignment explanation
Indices: 1489438--1489512 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1489428 ACTATAAGAT
*
1489438 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
1489475 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
1489512 A
1 A
1489513 AGGTTAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:1497999 original size:3 final size:3
Alignment explanation
Indices: 1497991--1498015 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1497981 ACATAAACTT
1497991 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
1498016 AAAAGGAAAG
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:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1503392 original size:21 final size:20
Alignment explanation
Indices: 1503361--1503402 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
1503351 AAGATAAACT
1503361 TATTTTTTTATATTAT-ATTA
1 TATTTTTTTATA-TATGATTA
1503381 TATTTATTTTATATATGATTA
1 TATTT-TTTTATATATGATTA
1503402 T
1 T
1503403 TTGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTTTTATATATGATTA
Found at i:1514751 original size:29 final size:30
Alignment explanation
Indices: 1514708--1514783 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
1514698 TCTCAGTTTC
1514708 GATTTCTCTTTTCTTTTGATTA-AAAAAAA
1 GATTTCTCTTTTCTTTTGATTAGAAAAAAA
*
1514737 TATTTCTCTTTTCTTTTGATTAGAAAAAAA
1 GATTTCTCTTTTCTTTTGATTAGAAAAAAA
1514767 GATTTCTCTTTTCTTTT
1 GATTTCTCTTTTCTTTT
1514784 TGGTCAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 21 0.48
30 23 0.52
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.54
Consensus pattern (30 bp):
GATTTCTCTTTTCTTTTGATTAGAAAAAAA
Found at i:1518750 original size:20 final size:21
Alignment explanation
Indices: 1518727--1518804 Score: 87
Period size: 20 Copynumber: 3.9 Consensus size: 21
1518717 TTCCAATTTG
1518727 GCAACGCGAATATGT-AAA-TC
1 GCAACGCGAATA-GTCAAATTC
*
1518747 GCAACAC-AGA-AGTCAAATTC
1 GCAACGCGA-ATAGTCAAATTC
1518767 GCAACGCG-ATAGTCAAATTC
1 GCAACGCGAATAGTCAAATTC
1518787 GCAACGCGAA-AGTCAAAT
1 GCAACGCGAATAGTCAAAT
1518805 GTTTTTACGC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.04
19 6 0.12
20 41 0.82
21 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (21 bp):
GCAACGCGAATAGTCAAATTC
Found at i:1518771 original size:40 final size:40
Alignment explanation
Indices: 1518680--1518804 Score: 100
Period size: 40 Copynumber: 3.1 Consensus size: 40
1518670 AAATGACCAA
* **
1518680 CAAATTCGCAACGCG--AGCTCAAATTTCGCAAC-CCAATTT
1 CAAATTCGCAACGCGATAG-TCAAA-TTCGCAACACGAAAGT
* *
1518719 CCAATTTGGCAACGCGAATATGT-AAA-TCGCAACAC-AGAAGT
1 -CAAATTCGCAACGCG-ATA-GTCAAATTCGCAACACGA-AAGT
*
1518760 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
1518800 CAAAT
1 CAAAT
1518805 GTTTTTACGC
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
38 2 0.03
39 6 0.09
40 51 0.74
41 4 0.06
42 3 0.04
43 2 0.03
44 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
Found at i:1519274 original size:20 final size:19
Alignment explanation
Indices: 1519246--1519284 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1519236 ACCAAATTCA
1519246 CAACACGAAAATGAAAATCG
1 CAACACGAAAAT-AAAATCG
* *
1519266 CAACGCGAAACTAAAATCG
1 CAACACGAAAATAAAATCG
1519285 AGTTGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.10
Consensus pattern (19 bp):
CAACACGAAAATAAAATCG
Found at i:1521446 original size:21 final size:21
Alignment explanation
Indices: 1521427--1521525 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
1521417 GATGCACCTA
* *
1521427 TCATCATTCAAGAGGCACCTC
1 TCATCGTTCAAGAGGCCCCTC
1521448 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
1521469 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
1521490 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
1521511 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
1521526 TCCCACCCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1521474 original size:42 final size:42
Alignment explanation
Indices: 1521427--1521545 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
1521417 GATGCACCTA
* *
1521427 TCATCATTCAAGAGGCACCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
* * *
1521469 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
* * *
1521511 TCATCGTTCAAGAGGTC-CCACCCGCCGTTCAAGAG
1 TCATCATTCAAGAGG-CACCTCCCACCGTTCAAGAG
1521546 CCCGATTCAT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.03
42 60 0.92
43 3 0.05
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (42 bp):
TCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCCTC
Found at i:1522994 original size:61 final size:62
Alignment explanation
Indices: 1522893--1523032 Score: 176
Period size: 66 Copynumber: 2.2 Consensus size: 62
1522883 TTTTACATTG
*
1522893 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTAGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTAGTA
** * * *
1522953 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTAGT
1523018 A
62 A
1523019 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1523033 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 17 0.25
61 17 0.25
64 4 0.06
66 30 0.44
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTAGTA
Found at i:1523722 original size:24 final size:24
Alignment explanation
Indices: 1523695--1523758 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1523685 AGTGGAGCTG
1523695 AAATTTATATTGAAATTCAAACTC
1 AAATTTATATTGAAATTCAAACTC
* * *
1523719 AAATTGAAATTTAAATTCAAACTC
1 AAATTTATATTGAAATTCAAACTC
*
1523743 CAA-TTATATATGAAAT
1 AAATTTATAT-TGAAAT
1523759 GAATTTGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATTTATATTGAAATTCAAACTC
Found at i:1523726 original size:18 final size:18
Alignment explanation
Indices: 1523703--1523739 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1523693 TGAAATTTAT
1523703 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1523721 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1523739 A
1 A
1523740 CTCCAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1524160 original size:25 final size:25
Alignment explanation
Indices: 1524126--1524175 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1524116 ATTATTTTTC
*
1524126 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1524151 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1524176 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1524289 original size:20 final size:20
Alignment explanation
Indices: 1524266--1524340 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1524256 AATAAGCGTT
* *
1524266 GCGATAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
1524286 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
1524306 ACGAAAGTCAAATTCACAAC
1 GCGAAAGTCAAATTCGCAAC
*
1524326 GTGAAAGTCAAATTC
1 GCGAAAGTCAAATTC
1524341 AGTTTGCGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1524667 original size:18 final size:18
Alignment explanation
Indices: 1524641--1524681 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1524631 AGGTGAAGCC
*
1524641 GATTGTGATTGGGATTTT
1 GATTTTGATTGGGATTTT
*
1524659 GATTTTGATTGTGATTTT
1 GATTTTGATTGGGATTTT
1524677 GATTT
1 GATTT
1524682 CCTTTGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (18 bp):
GATTTTGATTGGGATTTT
Found at i:1524675 original size:12 final size:12
Alignment explanation
Indices: 1524641--1524680 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1524631 AGGTGAAGCC
**
1524641 GATTGTGATTGG
1 GATTGTGATTTT
*
1524653 GATTTTGATTTT
1 GATTGTGATTTT
1524665 GATTGTGATTTT
1 GATTGTGATTTT
1524677 GATT
1 GATT
1524681 TCCTTTGGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (12 bp):
GATTGTGATTTT
Found at i:1526963 original size:24 final size:24
Alignment explanation
Indices: 1526936--1526989 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1526926 CCATCACATC
*
1526936 ATCAAAATCC-GAGTATTCCCCAAG
1 ATCAAAATCCAG-GTATTCACCAAG
* *
1526960 ATCAAAGTCCAGGTATTGACCAAG
1 ATCAAAATCCAGGTATTCACCAAG
1526984 ATCAAA
1 ATCAAA
1526990 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCAGGTATTCACCAAG
Found at i:1527923 original size:20 final size:19
Alignment explanation
Indices: 1527887--1527976 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
1527877 ACAAAAACCT
*
1527887 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTC-C
* *
1527906 GTTGCTAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCC
**
1527925 GTTGCGAATTTGACTTTCAC
1 GTTGCGAATTTGAAATTC-C
* *
1527945 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGA-AATTCC
*
1527965 GTTACGAATTTG
1 GTTGCGAATTTG
1527977 GAAAATCGCA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
19 24 0.42
20 31 0.54
21 2 0.04
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCC
Found at i:1527928 original size:19 final size:20
Alignment explanation
Indices: 1527887--1527957 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
1527877 ACAAAAACCT
* *
1527887 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCAC
*
1527906 GTTGCTAATTTGAAATTCA-
1 GTTGCGAATTTGAAATTCAC
**
1527925 GTTGCGAATTTGACTTTCAC
1 GTTGCGAATTTGAAATTCAC
1527945 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1527958 CTATTGCGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 25 0.57
20 19 0.43
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCAC
Found at i:1530928 original size:32 final size:33
Alignment explanation
Indices: 1530828--1530930 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
1530818 ACAAAGTTTA
* *
1530828 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
* *
1530860 TGATAAATTTAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1530893 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1530925 CGATAA
1 CGATAA
1530931 TTGAAACAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.23
33 50 0.77
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.33
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:1530949 original size:21 final size:21
Alignment explanation
Indices: 1530925--1530966 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1530915 ACTTCAAGTT
1530925 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1530946 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1530967 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1547536 original size:23 final size:23
Alignment explanation
Indices: 1547479--1547536 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1547469 CAACTGAAAG
*
1547479 CGTGTCATAGAGGCAGAGAAAAA
1 CGTGTCATAAAGGCAGAGAAAAA
* *
1547502 CGTATCATAAAGGCAGA-AGAATA
1 CGTGTCATAAAGGCAGAGA-AAAA
*
1547525 CGTGTCAAAAAG
1 CGTGTCATAAAG
1547537 TTGGATTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.16
Consensus pattern (23 bp):
CGTGTCATAAAGGCAGAGAAAAA
Found at i:1552106 original size:8 final size:8
Alignment explanation
Indices: 1552075--1552199 Score: 88
Period size: 8 Copynumber: 14.9 Consensus size: 8
1552065 TTTTTCTATA
*
1552075 TATATATA
1 TATATATG
1552083 TATATATG
1 TATATATG
*
1552091 TATGTATG
1 TATATATG
1552099 TATATATG
1 TATATATG
*
1552107 TATGTATG
1 TATATATG
1552115 TATGTATATG
1 TA--TATATG
*
1552125 TACGTACGTATA
1 TA--TA--TATG
*
1552137 TATGTATG
1 TATATATG
*
1552145 TATGTATG
1 TATATATG
*
1552153 TATATACG
1 TATATATG
*
1552161 TATGTATG
1 TATATATG
**
1552169 TACGTATG
1 TATATATG
1552177 TATATATG
1 TATATATG
* *
1552185 TATGTATT
1 TATATATG
1552193 TATATAT
1 TATATAT
1552200 CTGAATAGGA
Statistics
Matches: 94, Mismatches: 19, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
8 78 0.83
10 11 0.12
12 5 0.05
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (8 bp):
TATATATG
Found at i:1552106 original size:12 final size:12
Alignment explanation
Indices: 1552071--1552191 Score: 111
Period size: 12 Copynumber: 10.2 Consensus size: 12
1552061 TTATTTTTTC
* *
1552071 TATATATATATA
1 TATATATGTATG
1552083 TATATATGTATG
1 TATATATGTATG
* *
1552095 TATGTATATATG
1 TATATATGTATG
*
1552107 TATGTATGTATG
1 TATATATGTATG
*
1552119 --TATATGTACG
1 TATATATGTATG
** *
1552129 TACGTATATATG
1 TATATATGTATG
*
1552141 TATGTATGTATG
1 TATATATGTATG
*
1552153 TATATACGTATG
1 TATATATGTATG
* *
1552165 TATGTACGTATG
1 TATATATGTATG
1552177 TATATATGTATG
1 TATATATGTATG
1552189 TAT
1 TAT
1552192 TTATATATCT
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
10 8 0.09
12 81 0.91
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.47
Consensus pattern (12 bp):
TATATATGTATG
Found at i:1552110 original size:4 final size:4
Alignment explanation
Indices: 1552087--1552191 Score: 124
Period size: 4 Copynumber: 26.8 Consensus size: 4
1552077 TATATATATA
* * *
1552087 TATG TATG TATG TATA TATG TATG TATG TATG TA-- TATG TACG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
1552133 TATA TATG TATG TATG TATG TATA TACG TATG TATG TACG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1552181 TATG TATG TAT
1 TATG TATG TAT
1552192 TTATATATCT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
2 2 0.02
4 83 0.98
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:1556583 original size:16 final size:17
Alignment explanation
Indices: 1556558--1556602 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1556548 CTGGTCTGTA
1556558 ATTATATATTT-TTTTT
1 ATTATATATTTATTTTT
*
1556574 ATTATTTATTTATTTTT
1 ATTATATATTTATTTTT
*
1556591 AATA-ATATTTAT
1 ATTATATATTTAT
1556603 ATGTATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTATATATTTATTTTT
Found at i:1556599 original size:20 final size:19
Alignment explanation
Indices: 1556576--1556620 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1556566 TTTTTTTTAT
* *
1556576 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
1556596 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
1556615 TATTTA
1 TATTTA
1556621 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:1556610 original size:26 final size:30
Alignment explanation
Indices: 1556571--1556626 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1556561 ATATATTTTT
*
1556571 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1556598 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1556627 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:1556627 original size:3 final size:3
Alignment explanation
Indices: 1556619--1556713 Score: 145
Period size: 3 Copynumber: 31.7 Consensus size: 3
1556609 TTAATATATT
* *
1556619 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1556667 TAG TAG TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1556714 TGGATAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1557673 original size:113 final size:113
Alignment explanation
Indices: 1557033--1557673 Score: 1104
Period size: 113 Copynumber: 5.7 Consensus size: 113
1557023 GAATTATGCC
* * *
1557033 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* **** * **
1557097 TATGGACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
* *
1557145 AAATGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * *
1557210 TATGAACTTTAACTGGAAAAGCTGATCCATCAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
1557258 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1557323 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
1557371 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1557436 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
*
1557484 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1557549 TATGAATTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
66 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
1557597 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1557662 TATGAACTCGAA
66 TATGAACTCGAA
1557674 AAGCTGATCC
Statistics
Matches: 510, Mismatches: 18, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
112 3 0.01
113 507 0.99
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCATAT
Found at i:1558626 original size:81 final size:82
Alignment explanation
Indices: 1558341--1558788 Score: 792
Period size: 82 Copynumber: 5.5 Consensus size: 82
1558331 CCTACTGAAT
*
1558341 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1558406 ATTGGTTTTTATCAAAC
66 ATTGGTTTTTATCAAAC
*
1558423 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1558488 ATTGGTTTTTATCAAAC
66 ATTGGTTTTTATCAAAC
1558505 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
* * *
1558570 ATTGG-TTCTGTCTAAC
66 ATTGGTTTTTATCAAAC
1558586 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
* * *
1558651 ATTGG-TTCTGTCTAAC
66 ATTGGTTTTTATCAAAC
* *
1558667 CAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1558732 ATTGGTTTTTATCAAAC
66 ATTGGTTTTTATCAAAC
1558749 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1558789 TGACATTTCA
Statistics
Matches: 353, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
81 157 0.44
82 196 0.56
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
ATTGGTTTTTATCAAAC
Found at i:1559967 original size:10 final size:10
Alignment explanation
Indices: 1559942--1560015 Score: 69
Period size: 10 Copynumber: 7.1 Consensus size: 10
1559932 GACCCCCTTT
1559942 TTCTTTTTTC
1 TTCTTTTTTC
*
1559952 CT-TTTTTTC
1 TTCTTTTTTC
*
1559961 TTCTTTTTTT
1 TTCTTTTTTC
*
1559971 TTCTTTTTCATT
1 TTCTTTTT--TC
*
1559983 TTCTATTTTTTT
1 TTC--TTTTTTC
1559995 TTCTTTTTTC
1 TTCTTTTTTC
1560005 TTCTTTTTTC
1 TTCTTTTTTC
1560015 T
1 T
1560016 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
9 8 0.15
10 32 0.58
12 10 0.18
14 5 0.09
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:1559985 original size:34 final size:35
Alignment explanation
Indices: 1559938--1560012 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
1559928 CCTTGACCCC
* *
1559938 CTTTTTCTTTTTTCCT-TTTTTTCTTCTTTTTTTTT
1 CTTTTTCTATTTT-CTATTTTTTCTTCTTTTTTCTT
*
1559973 CTTTTTC-ATTTTCTATTTTTTTTTCTTTTTTCTT
1 CTTTTTCTATTTTCTATTTTTTCTTCTTTTTTCTT
1560007 CTTTTT
1 CTTTTT
1560013 TCTCTTCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 2 0.06
34 27 0.75
35 7 0.19
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (35 bp):
CTTTTTCTATTTTCTATTTTTTCTTCTTTTTTCTT
Found at i:1560015 original size:7 final size:7
Alignment explanation
Indices: 1559939--1560011 Score: 57
Period size: 6 Copynumber: 10.7 Consensus size: 7
1559929 CTTGACCCCC
1559939 TTTTTCT
1 TTTTTCT
1559946 TTTTTCCTT
1 TTTTT-C-T
1559955 TTTTTCT
1 TTTTTCT
*
1559962 TCTTT-T
1 TTTTTCT
1559968 TTTTTC-
1 TTTTTCT
1559974 TTTTTC-
1 TTTTTCT
*
1559980 ATTTTC-
1 TTTTTCT
*
1559986 TATTT-T
1 TTTTTCT
1559992 TTTTTCT
1 TTTTTCT
1559999 TTTTTCT
1 TTTTTCT
1560006 TCTTTT
1 T-TTTT
1560012 TTCTCTTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
6 23 0.43
7 19 0.35
8 6 0.11
9 6 0.11
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:1570615 original size:13 final size:15
Alignment explanation
Indices: 1570593--1570629 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1570583 TTTGACATAA
1570593 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
1570605 AAATAAAATACTTGC
1 AAATAAAATACTTGC
1570620 AAATAAAATA
1 AAATAAAATA
1570630 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:1570668 original size:18 final size:17
Alignment explanation
Indices: 1570620--1570670 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
1570610 AAATACTTGC
*
1570620 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
1570638 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
1570656 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
1570671 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:1572812 original size:20 final size:19
Alignment explanation
Indices: 1572789--1572833 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1572779 TTTTTTTTAT
* *
1572789 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
1572809 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
1572828 TATTTA
1 TATTTA
1572834 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:1572823 original size:26 final size:30
Alignment explanation
Indices: 1572784--1572839 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1572774 TATATTTTTT
*
1572784 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1572811 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1572840 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:1572840 original size:3 final size:3
Alignment explanation
Indices: 1572832--1572929 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
1572822 TTAATATATT
* *
1572832 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1572880 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1572928 TA
1 TA
1572930 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1573049 original size:23 final size:22
Alignment explanation
Indices: 1573023--1573072 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1573013 TTGTACAATT
1573023 ATTTATTAATAAAAATATGTGGC
1 ATTTATTAAT-AAAATATGTGGC
* *
1573046 ATTTATTGATGAAATATGTGGC
1 ATTTATTAATAAAATATGTGGC
1573068 ATTTA
1 ATTTA
1573073 ATTGATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (22 bp):
ATTTATTAATAAAATATGTGGC
Found at i:1573063 original size:22 final size:23
Alignment explanation
Indices: 1573035--1573078 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
1573025 TTATTAATAA
1573035 AAATATGTGGCATTT-ATTGATG
1 AAATATGTGGCATTTAATTGATG
1573057 AAATATGTGGCATTTAATTGAT
1 AAATATGTGGCATTTAATTGAT
1573079 TTGCAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (23 bp):
AAATATGTGGCATTTAATTGATG
Found at i:1573202 original size:2 final size:2
Alignment explanation
Indices: 1573195--1573223 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1573185 CAGTGTTAAG
1573195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1573224 TTTTCTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1578531 original size:5 final size:5
Alignment explanation
Indices: 1578521--1578550 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1578511 TACTCATCAC
*
1578521 AAACA AAACA AAACT AAACA AAACA AAACA
1 AAACA AAACA AAACA AAACA AAACA AAACA
1578551 GACTAGCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.20, G:0.00, T:0.03
Consensus pattern (5 bp):
AAACA
Found at i:1578541 original size:15 final size:15
Alignment explanation
Indices: 1578521--1578549 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1578511 TACTCATCAC
1578521 AAACAAAACAAAACT
1 AAACAAAACAAAACT
1578536 AAACAAAACAAAAC
1 AAACAAAACAAAAC
1578550 AGACTAGCAG
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:0.76, C:0.21, G:0.00, T:0.03
Consensus pattern (15 bp):
AAACAAAACAAAACT
Found at i:1583566 original size:2 final size:2
Alignment explanation
Indices: 1583559--1583588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1583549 TTTTAGCCTA
1583559 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
1583589 TTCATCTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1583905 original size:17 final size:17
Alignment explanation
Indices: 1583875--1583908 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1583865 AATTTTAAAT
1583875 TTAAACTTTTTATTCAA
1 TTAAACTTTTTATTCAA
1583892 TTAAA-TTTTATATTCAA
1 TTAAACTTTT-TATTCAA
1583909 ATTCAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAACTTTTTATTCAA
Found at i:1588311 original size:16 final size:16
Alignment explanation
Indices: 1588290--1588323 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1588280 TTACTATTCA
*
1588290 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1588306 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1588322 CG
1 CG
1588324 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1589094 original size:15 final size:16
Alignment explanation
Indices: 1589074--1589105 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1589064 TGGCAGATCC
1589074 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
1589089 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
1589105 A
1 A
1589106 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:1593281 original size:25 final size:25
Alignment explanation
Indices: 1593228--1593289 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
1593218 TTTTTATCAT
* **
1593228 CATAAAATTTTATAAATTTACTTTT
1 CATAAAATTTTATAAATTCACTTAA
1593253 CATAAAATTTTATAAATTC-CATTAA
1 CATAAAATTTTATAAATTCAC-TTAA
1593278 CATAAAATTTTA
1 CATAAAATTTTA
1593290 CATCCCGTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (25 bp):
CATAAAATTTTATAAATTCACTTAA
Found at i:1599001 original size:29 final size:29
Alignment explanation
Indices: 1598966--1599047 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1598956 AAACTAAATT
*
1598966 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1598995 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1599024 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1599048 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1600359 original size:15 final size:15
Alignment explanation
Indices: 1600336--1600365 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1600326 ACGAGGCTGG
1600336 AATTACAACAATAAC
1 AATTACAACAATAAC
*
1600351 AATTCCAACAATAAC
1 AATTACAACAATAAC
1600366 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:1603769 original size:29 final size:29
Alignment explanation
Indices: 1603734--1603815 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1603724 AAACTAAATT
*
1603734 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1603763 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1603792 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1603816 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1606193 original size:14 final size:14
Alignment explanation
Indices: 1606150--1606197 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
1606140 ACTAAAAGTT
1606150 TTAATAATTTTAATAA
1 TTAATAA-TTT-ATAA
1606166 TTTAA-AATTATATAA
1 -TTAATAATT-TATAA
1606181 TTAATAATTTATAA
1 TTAATAATTTATAA
1606195 TTA
1 TTA
1606198 TCTAAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.41
15 10 0.34
16 3 0.10
17 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATAATTTATAA
Found at i:1611205 original size:111 final size:111
Alignment explanation
Indices: 1611066--1611287 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
1611056 ATTACAAAAA
* * *
1611066 TTAATTCTTAATCTAATAATCATTCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1611131 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
1611177 TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1611242 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
1611288 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTCAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:1611631 original size:50 final size:50
Alignment explanation
Indices: 1611573--1611681 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
1611563 TGTCATATAT
* * * *
1611573 TCAG-GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAGA
1 TCAGCGTATAGCGCGGAGCAGGAGGCGCGCTATACCCACGTGACGCCAAA
* * * *
1611622 TCATCGTATATCGCGGGGCAGGAGGCGCGCTATACCCACGTGACGTCAAA
1 TCAGCGTATAGCGCGGAGCAGGAGGCGCGCTATACCCACGTGACGCCAAA
1611672 TCAGCGTATA
1 TCAGCGTATA
1611682 ACGTGATTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 3 0.06
50 47 0.94
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (50 bp):
TCAGCGTATAGCGCGGAGCAGGAGGCGCGCTATACCCACGTGACGCCAAA
Found at i:1633834 original size:346 final size:346
Alignment explanation
Indices: 1633201--1633883 Score: 1321
Period size: 346 Copynumber: 2.0 Consensus size: 346
1633191 GATACTGAAT
*
1633201 TTTTGGACCTATAAATCCCATTTATGTTGAGAATATTGATGTGTTGTCTGGATTTTACCTTAGTT
1 TTTTGGACCTATAAATCCCATTTAAGTTGAGAATATTGATGTGTTGTCTGGATTTTACCTTAGTT
1633266 TCCTTGGTTCAACCTCTTCAGGTTTTGCCGTGATTGATGCATGTTCCATCATGCATGACCTTGCA
66 TCCTTGGTTCAACCTCTTCAGGTTTTGCCGTGATTGATGCATGTTCCATCATGCATGACCTTGCA
*
1633331 GCTCAATCATGGTTTCTAACTTTTTATGAAAACCATATCATGATAGACTTTTATAGGACATGATC
131 GCTCAATCATGGTTTCTAACTTTTTATGAAAACCATATCACGATAGACTTTTATAGGACATGATC
1633396 ATGGAGCAAAAGTTGATGTTATTGTTGACTAAAGGCTTTGAAATGCCATGGTTTTGTTGAGGTTT
196 ATGGAGCAAAAGTTGATGTTATTGTTGACTAAAGGCTTTGAAATGCCATGGTTTTGTTGAGGTTT
1633461 CAATTTGTAGGTGGATTTGGTTGGGTGGGGAAGGCACTGTTTCTTTATTATGCATTTAAAGTGAG
261 CAATTTGTAGGTGGATTTGGTTGGGTGGGGAAGGCACTGTTTCTTTATTATGCATTTAAAGTGAG
1633526 CTTCTCCACATCATGCTATAC
326 CTTCTCCACATCATGCTATAC
1633547 TTTTGGACCTATAAATCCCATTTAAGTTGAGAATATTGATGTGTTGTCTGGATTTTACCTTAGTT
1 TTTTGGACCTATAAATCCCATTTAAGTTGAGAATATTGATGTGTTGTCTGGATTTTACCTTAGTT
*
1633612 TCCTTGGTTCAACCTCTTCAGGTTTTGCCGTGATTGATGCATGTTCCATCATGCATGGCCTTGCA
66 TCCTTGGTTCAACCTCTTCAGGTTTTGCCGTGATTGATGCATGTTCCATCATGCATGACCTTGCA
*
1633677 GCTCAATCATGGTTTCTAACTTTTTATGAAAACCATATCACGCTAGACTTTTATAGGACATGATC
131 GCTCAATCATGGTTTCTAACTTTTTATGAAAACCATATCACGATAGACTTTTATAGGACATGATC
*
1633742 ATGGAGCATAAGTTGATGTTATTGTTGACTAAAGGCTTTGAAATGCCATGGTTTTGTTGAGGTTT
196 ATGGAGCAAAAGTTGATGTTATTGTTGACTAAAGGCTTTGAAATGCCATGGTTTTGTTGAGGTTT
1633807 CAATTTGTAGGTGGATTTGGTTGGGTGGGGAAGGCACTGTTTCTTTATTATGCATTTAAAGTGAG
261 CAATTTGTAGGTGGATTTGGTTGGGTGGGGAAGGCACTGTTTCTTTATTATGCATTTAAAGTGAG
1633872 CTTCTCCACATC
326 CTTCTCCACATC
1633884 CCCCACCATT
Statistics
Matches: 332, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
346 332 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (346 bp):
TTTTGGACCTATAAATCCCATTTAAGTTGAGAATATTGATGTGTTGTCTGGATTTTACCTTAGTT
TCCTTGGTTCAACCTCTTCAGGTTTTGCCGTGATTGATGCATGTTCCATCATGCATGACCTTGCA
GCTCAATCATGGTTTCTAACTTTTTATGAAAACCATATCACGATAGACTTTTATAGGACATGATC
ATGGAGCAAAAGTTGATGTTATTGTTGACTAAAGGCTTTGAAATGCCATGGTTTTGTTGAGGTTT
CAATTTGTAGGTGGATTTGGTTGGGTGGGGAAGGCACTGTTTCTTTATTATGCATTTAAAGTGAG
CTTCTCCACATCATGCTATAC
Found at i:1634257 original size:3 final size:3
Alignment explanation
Indices: 1634249--1634282 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1634239 TTTTAAATTA
1634249 AAT AAT AAT AA- AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1634283 TTAGAGTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1634271 original size:17 final size:17
Alignment explanation
Indices: 1634249--1634282 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1634239 TTTTAAATTA
1634249 AATAATAATAAAATAAT
1 AATAATAATAAAATAAT
1634266 AATAATAATAAAATAAT
1 AATAATAATAAAATAAT
1634283 TTAGAGTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAATAAAATAAT
Found at i:1634282 original size:11 final size:11
Alignment explanation
Indices: 1634248--1634281 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1634238 ATTTTAAATT
1634248 AAATAATAATA
1 AAATAATAATA
1634259 AAATAATAATA
1 AAATAATAATA
1634270 ATAATAA-AATA
1 A-AATAATAATA
1634281 A
1 A
1634282 TTTAGAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAATAATA
Found at i:1635726 original size:36 final size:32
Alignment explanation
Indices: 1635641--1635731 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 32
1635631 AAAAAATTAT
*
1635641 ATAATTTATAATATTTTTAATTATAATAAAAA
1 ATAATTTATAATAATTTTAATTATAATAAAAA
* * *
1635673 ATCATATTATGACAATTTTAGAGTTTATAATAAAAAA
1 ATAAT-TTATAATAATTTTA-A--TTATAAT-AAAAA
1635710 ATAATTTATAATAATTTTAATT
1 ATAATTTATAATAATTTTAATT
1635732 TTAACTTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
32 4 0.09
33 13 0.28
34 1 0.02
35 1 0.02
36 19 0.40
37 9 0.19
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (32 bp):
ATAATTTATAATAATTTTAATTATAATAAAAA
Found at i:1638884 original size:19 final size:19
Alignment explanation
Indices: 1638860--1638897 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1638850 AGATTATGCA
1638860 GGGGGTA-CAGATTCCCCCT
1 GGGGGTATC-GATTCCCCCT
1638879 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
1638898 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGGGTATCGATTCCCCCT
Found at i:1639123 original size:2 final size:2
Alignment explanation
Indices: 1639118--1639202 Score: 145
Period size: 2 Copynumber: 42.5 Consensus size: 2
1639108 TGTGTATTAG
*
1639118 TA TA TA TA AA T- TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1639160 TA TA TA 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 TA TA TA
1639202 T
1 T
1639203 CTTATATGTT
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.01
2 77 0.97
3 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1639685 original size:23 final size:23
Alignment explanation
Indices: 1639658--1639701 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1639648 GAGTCGAGGG
1639658 TCTACGCGGTCCTTCGAGACAAT
1 TCTACGCGGTCCTTCGAGACAAT
* *
1639681 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGAGACA
1639702 TATATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGAGACAAT
Found at i:1639833 original size:18 final size:17
Alignment explanation
Indices: 1639805--1639841 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1639795 GGACATATGT
*
1639805 GATATGTGGTCCTTCGG
1 GATATGTGGTCATTCGG
1639822 GATATAGTGGTCATTCGG
1 GATAT-GTGGTCATTCGG
1639840 GA
1 GA
1639842 CATTTCTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.19, C:0.14, G:0.35, T:0.32
Consensus pattern (17 bp):
GATATGTGGTCATTCGG
Found at i:1644545 original size:23 final size:22
Alignment explanation
Indices: 1644501--1644546 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1644491 GTACTGTAGC
**
1644501 AGGGAATCGGTACCCTGTAGCA
1 AGGGAATCGGTACCCTCAAGCA
*
1644523 AGGGAATCGGTTCCCCTCAAGCA
1 AGGGAATCGG-TACCCTCAAGCA
1644546 A
1 A
1644547 TCTGGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.17
Consensus pattern (22 bp):
AGGGAATCGGTACCCTCAAGCA
Done.