Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007897.1 Hibiscus syriacus cultivar Beakdansim tig00110283_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: 862109
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:713848 original size:50 final size:47
Alignment explanation
Indices: 713794--713916 Score: 133
Period size: 49 Copynumber: 2.5 Consensus size: 47
713784 AGATACCCAG
* *
713794 GTATAGCGCGGATCAGGGGGTGCGCTATACCTACGTGACG-CAAAATCACC
1 GTATA-CGCGGA-CA-GGGGCGCGCTATACCCACGTGACGTC-AAATCACC
*
713844 GTATATCGCGGGACAGGGGCGCGCTATACCCACGTGACGTCAAATCAGC
1 GTATA-CGC-GGACAGGGGCGCGCTATACCCACGTGACGTCAAATCACC
713893 GTATACGCGGTTA-AGGGGCGCGCT
1 GTATACGCGG--ACAGGGGCGCGCT
713917 TTACTGCTAC
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
47 2 0.03
48 14 0.22
49 35 0.54
50 11 0.17
51 3 0.05
ACGTcount: A:0.24, C:0.26, G:0.33, T:0.18
Consensus pattern (47 bp):
GTATACGCGGACAGGGGCGCGCTATACCCACGTGACGTCAAATCACC
Found at i:713872 original size:49 final size:48
Alignment explanation
Indices: 713810--713916 Score: 137
Period size: 49 Copynumber: 2.2 Consensus size: 48
713800 CGCGGATCAG
* *
713810 GGGGTGCGCTATACCTACGTGACG-CAAAATCACCGTATATCGCGG-GACA
1 GGGGCGCGCTATACCCACGTGACGTC-AAATCACCGTATA-CGCGGTGA-A
* *
713859 GGGGCGCGCTATACCCACGTGACGTCAAATCAGCGTATACGCGGTTAA
1 GGGGCGCGCTATACCCACGTGACGTCAAATCACCGTATACGCGGTGAA
713907 GGGGCGCGCT
1 GGGGCGCGCT
713917 TTACTGCTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
48 16 0.31
49 35 0.67
50 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.32, T:0.18
Consensus pattern (48 bp):
GGGGCGCGCTATACCCACGTGACGTCAAATCACCGTATACGCGGTGAA
Found at i:730675 original size:7 final size:7
Alignment explanation
Indices: 730665--730694 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
730655 TTAATTAATA
730665 ATTTATT
1 ATTTATT
730672 ATTTATT
1 ATTTATT
730679 ATTTATTT
1 ATTTA-TT
730687 ATTTATT
1 ATTTATT
730694 A
1 A
730695 AAAAAATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTATT
Found at i:733842 original size:35 final size:33
Alignment explanation
Indices: 733803--733869 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
733793 TATTTTTATC
733803 ATAATTAAAATAGTA-TTTATATATTATAATATTAA
1 ATAATTAAAATA-TATTTTA-AT-TTATAATATTAA
* *
733838 ATAATTTACATATATTTTAATTTATAATATTA
1 ATAATTAAAATATATTTTAATTTATAATATTA
733870 TGTTCAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 11 0.38
34 4 0.14
35 14 0.48
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
ATAATTAAAATATATTTTAATTTATAATATTAA
Found at i:737964 original size:19 final size:18
Alignment explanation
Indices: 737930--737971 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
737920 TTAGCATTGT
737930 GAAAAGAAAATAATGAAA
1 GAAAAGAAAATAATGAAA
737948 GAAAAGTAAAA-AGATGAAA
1 GAAAAG-AAAATA-ATGAAA
737967 GAAAA
1 GAAAA
737972 TTATAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (18 bp):
GAAAAGAAAATAATGAAA
Found at i:738104 original size:16 final size:18
Alignment explanation
Indices: 738064--738106 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
738054 AAATTCTAAG
738064 CAAATAAAATAATTAATT
1 CAAATAAAATAATTAATT
738082 CTTAAATAAAATAA-TAA-T
1 C--AAATAAAATAATTAATT
738100 CAAATAA
1 CAAATAA
738107 TCAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.26
18 3 0.13
19 3 0.13
20 11 0.48
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
CAAATAAAATAATTAATT
Found at i:740749 original size:30 final size:31
Alignment explanation
Indices: 740708--740782 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
740698 AAGCTCGAAC
* *
740708 CGACTCAAAAAGTTT-AATATGAGTTTGATT
1 CGACTCGAAAAGTTTAAATATGAGTTGGATT
*
740738 CGACTCGAAAAGTTTAAATCTGAGTTGGATT
1 CGACTCGAAAAGTTTAAATATGAGTTGGATT
*
740769 CAACTCG-AAAGTTT
1 CGACTCGAAAAGTTT
740783 GCGAGCATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 21 0.52
31 19 0.47
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (31 bp):
CGACTCGAAAAGTTTAAATATGAGTTGGATT
Found at i:741392 original size:2 final size:2
Alignment explanation
Indices: 741385--741411 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
741375 TTGTTCGGGC
741385 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
741412 GAGAAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:745867 original size:15 final size:14
Alignment explanation
Indices: 745813--745861 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
745803 TGATGTTTGA
745813 TTTTATGATTTAAGG
1 TTTTATGATTTAA-G
* *
745828 TTTTAGGGTTTTAAG
1 TTTTA-TGATTTAAG
745843 TTTTATGATTTATAG
1 TTTTATGATTTA-AG
745858 TTTT
1 TTTT
745862 TGGATTAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.18
15 17 0.61
16 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.18, T:0.59
Consensus pattern (14 bp):
TTTTATGATTTAAG
Found at i:755156 original size:31 final size:31
Alignment explanation
Indices: 755118--755188 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
755108 CGAACAGTGG
755118 GAAGCTGATCCAAAATCATAGAGAGATTGCA
1 GAAGCTGATCCAAAATCATAGAGAGATTGCA
755149 GAAGCTGATCCAAAATCATAGAGAGATTGCA
1 GAAGCTGATCCAAAATCATAGAGAGATTGCA
755180 GAAGCTGAT
1 GAAGCTGAT
755189 GGACTGTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (31 bp):
GAAGCTGATCCAAAATCATAGAGAGATTGCA
Found at i:757113 original size:64 final size:63
Alignment explanation
Indices: 757018--757159 Score: 196
Period size: 64 Copynumber: 2.2 Consensus size: 63
757008 CGACACAGGA
* * *
757018 AGTGCATCAATGCACCCCTTAAAATGGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-
1 AGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGT
* * * *
757081 AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 AGTGCATCGATGCA-CCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAGGT
757145 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
757160 ATGTTAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
63 16 0.23
64 54 0.77
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (63 bp):
AGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAGGT
Found at i:757192 original size:20 final size:22
Alignment explanation
Indices: 757147--757204 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
757137 GCATGGGTAG
757147 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
757171 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
757191 TGCATCGATGCACT
1 TGCATCGATGCACT
757205 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:758741 original size:15 final size:15
Alignment explanation
Indices: 758721--758756 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
758711 TTTTGTCAAG
758721 AGTCAAAGTTTGAAA
1 AGTCAAAGTTTGAAA
758736 AGTCAAAGTTTGAAA
1 AGTCAAAGTTTGAAA
758751 AGTCAA
1 AGTCAA
758757 TGTGACACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (15 bp):
AGTCAAAGTTTGAAA
Found at i:759910 original size:483 final size:470
Alignment explanation
Indices: 758808--760077 Score: 1404
Period size: 473 Copynumber: 2.7 Consensus size: 470
758798 GGGTGTTACA
* ** * * * *
758808 ATGGATGTATATCTTAATACTCCCTGTACTGAAAAATTCACAGAAA-ATGGTGAG-ATGAT-GAG
1 ATGGGTGTATATCTTAATACTCCCAATACTGAAAAATTCA-AAAAAGATAGTAAGAAAGATAG-G
* * * * * *
758870 GTTTGGTCTAGAATCCATGGAAGGATGGCGTGTAACTATAGAAGATGTTGTTAGTAACGAATGAA
64 GTATGGTCTAGCATCCATGGAAGGATGGCGTGCAACTATAGAAGATGTTGTGAGTAACAAATGAC
*
758935 ACCTTCAATTTTCAAATGTCTCAAGCATTAGGACCCTATTTATTCTATTAGATTGGGGGAGATGC
129 ACCTTCAATTTTCAAATGTCTCAAGCATTATGACCCTATTTATTCTATTAGATTGGGGGAGATGC
* * * * * *
759000 TAAGATCAGGGATGG-TCGGGCGTCGACCGGGGGCAATC-GTCCTCCTAAAAATTTTAAATTATT
194 TAGGATCAGGGATGGATCGGG-GTCGA-CTGGGG-TATCAATCCT-CTGAAAATTTTAAATTATC
* * *** * *
759063 ATATATTTTAGATATTTTTTGTATTTTATAATGATAATTTGTTTCGTACTTCTATTTTTTTATAA
255 ATATATTTTAGATATTTTTTATATTTTCTAATGATAATTTGTTTCGTACTAAAATTTTATAATAA
**** * * *
759128 ATTCGTAATCACCTAAATTTTTTGAAGTTCGACCTTAATATAAATCTTACGTCTGTCTCCGCTGA
320 ATTCGTAATCACCTAAAAAAATTGAAGTTCGACCTAAATATAAATCATACGTCTATCTCCGCTGA
* ** * * *
759193 GGTGATATTTTAAAGTTTACGCCACTGATTACTTAAGAGAGAGTTTTATAATCCGAGTTAACATA
385 GGTGATATTTTAAAGTTTACACCACCAATTACTTAAGAAAGAGTTTTATAATCCAAATTAACATA
*
759258 GTTTATTCAATTGCAAATATAC
450 GTTTATTCAATTG-AAACATAC
* *
759280 ATGGGTGTATATCTTAATACTCCCAATACTGAAAAATTCAAAAAAGATAGTGAGAATGATAGGGT
1 ATGGGTGTATATCTTAATACTCCCAATACTGAAAAATTCAAAAAAGATAGTAAGAAAGATAGGGT
* * *
759345 ATGGTCTAGCATCCATGGAAGGATGGCGTGCAACTACATAAGATGTTGTGAGTTACAAATGACAC
66 ATGGTCTAGCATCCATGGAAGGATGGCGTGCAACTATAGAAGATGTTGTGAGTAACAAATGACAC
*
759410 CTTCAATTTTCAAATGTCTCAAGCATTATGACCCTATTTATTCTATT-GATTGGAGGAGATGCTA
131 CTTCAATTTTCAAATGTCTCAAGCATTATGACCCTATTTATTCTATTAGATTGGGGGAGATGCTA
* *
759474 GGATCGGGGATGGATCGGGAGTCGACTGGGCGTAGTCACTCCTCTGAAAATTTTAAATTATCATA
196 GGATCAGGGATGGATCGGG-GTCGACTGGG-GTA-TCAATCCTCTGAAAATTTTAAATTATCATA
759539 TATTTTAGATA-TTTTTATATTTTCTAATGATAATTTGTTTTTGCCAGT-CTAAAATTTTATAAT
258 TATTTTAGATATTTTTTATATTTTCTAATGATAATTTG--TTT--C-GTACTAAAATTTTATAA-
* * * * *
759602 TAAGTTCGTCATTACCTAAAAAAAATT-AAGTTCGCTCCTAACATA-AAATCATACGTCTATCTT
317 TAAATTCGTAATCACCT-AAAAAAATTGAAGTTCG-ACCTAA-ATATAAATCATACGTCTATCTC
* * *
759665 TGCTGAGGTG-TCATTTTAGAGTTTACATCACCAAGTT-CTTAAGAAAGAGTTTTATAATCCAAA
379 CGCTGAGGTGAT-ATTTTAAAGTTTACACCACCAA-TTACTTAAGAAAGAGTTTTATAATCCAAA
* *
759728 TTAACAT-GATTTATTCAATTTG-GACATAG
442 TTAACATAG-TTTATTCAA-TTGAAACATAC
* ** *
759757 ATGGGTGTATATCTTGATACTCCCAATACTGAAAAATT-AACTGAAGATGGTAAGAAAGATA-GG
1 ATGGGTGTATATCTTAATACTCCCAATACTGAAAAATTCAA-AAAAGATAGTAAGAAAGATAGGG
*
759820 TATGGTCTAGACTCTAGCGTCCATGGAAGGATGGCATGCAACTATAGAAGATGTTGTGAGTAACA
65 TATGGTCTAG---C-A---TCCATGGAAGGATGGCGTGCAACTATAGAAGATGTTGTGAGTAACA
* ** *
759885 AATGACACCTTCAATTTTCAAATGTCTCAAGCATTGTGACCAAATTTATTCTATTAGAATGGGGG
123 AATGACACCTTCAATTTTCAAATGTCTCAAGCATTATGACCCTATTTATTCTATTAGATTGGGGG
* * * * * * * *
759950 AGATGTTAGGATCAGAGATGGATTGGGGTTGATTAGGGATAT-AAGCCTCTTGAAAAATTTAAAT
188 AGATGCTAGGATCAGGGATGGATCGGGGTCGACT-GGGGTATCAATCCTC-TGAAAATTTTAAAT
* * *
760014 TATCATATATTTTAGATATTTTTTATATTTTCTAATGATAATTTATTCTTGTCCTAAAATTTTA
251 TATCATATATTTTAGATATTTTTTATATTTTCTAATGATAATTTGTT-TCGTACTAAAATTTTA
760078 AAAGTTTGTC
Statistics
Matches: 682, Mismatches: 82, Indels: 60
0.83 0.10 0.07
Matches are distributed among these distances:
471 4 0.01
472 100 0.15
473 154 0.23
474 8 0.01
476 24 0.04
477 81 0.12
478 89 0.13
479 11 0.02
480 12 0.02
481 7 0.01
482 33 0.05
483 126 0.18
484 33 0.05
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (470 bp):
ATGGGTGTATATCTTAATACTCCCAATACTGAAAAATTCAAAAAAGATAGTAAGAAAGATAGGGT
ATGGTCTAGCATCCATGGAAGGATGGCGTGCAACTATAGAAGATGTTGTGAGTAACAAATGACAC
CTTCAATTTTCAAATGTCTCAAGCATTATGACCCTATTTATTCTATTAGATTGGGGGAGATGCTA
GGATCAGGGATGGATCGGGGTCGACTGGGGTATCAATCCTCTGAAAATTTTAAATTATCATATAT
TTTAGATATTTTTTATATTTTCTAATGATAATTTGTTTCGTACTAAAATTTTATAATAAATTCGT
AATCACCTAAAAAAATTGAAGTTCGACCTAAATATAAATCATACGTCTATCTCCGCTGAGGTGAT
ATTTTAAAGTTTACACCACCAATTACTTAAGAAAGAGTTTTATAATCCAAATTAACATAGTTTAT
TCAATTGAAACATAC
Found at i:760116 original size:27 final size:27
Alignment explanation
Indices: 760069--760125 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
760059 TTCTTGTCCT
** *
760069 AAAATTTTAAAAGTTTGTCCTCACCTA
1 AAAATTTTAAAAGTTACTCCTAACCTA
*
760096 AAAATTTTAAAA-TTCACTCCTAACGTA
1 AAAATTTTAAAAGTT-ACTCCTAACCTA
760123 AAA
1 AAA
760126 TCCTATGTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (27 bp):
AAAATTTTAAAAGTTACTCCTAACCTA
Found at i:760180 original size:52 final size:52
Alignment explanation
Indices: 760121--760219 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
760111 ACTCCTAACG
* * * * *
760121 TAAAATCCTATGTCTGTCTCTACTTGATGATATTTTAAAGTTTAGATTAATA
1 TAAAATCCTACGTCTATCTATACTGGATAATATTTTAAAGTTTAGATTAATA
*
760173 TAAAATCCTACGTCTATCTATGCTGGATAATATTTTAAAGTTTAGAT
1 TAAAATCCTACGTCTATCTATACTGGATAATATTTTAAAGTTTAGAT
760220 CACTTAATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (52 bp):
TAAAATCCTACGTCTATCTATACTGGATAATATTTTAAAGTTTAGATTAATA
Found at i:767618 original size:14 final size:14
Alignment explanation
Indices: 767599--767629 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
767589 GAAACAATCT
767599 AAACCACTCATTAA
1 AAACCACTCATTAA
767613 AAACCACTCATTAA
1 AAACCACTCATTAA
767627 AAA
1 AAA
767630 AGTATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCACTCATTAA
Found at i:767734 original size:29 final size:29
Alignment explanation
Indices: 767691--767746 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
767681 TTTCCCTAAA
767691 TAAATTGATGTAAGCAATGACAATCAAAAC
1 TAAATTGATGTAAGCAATGAC-ATCAAAAC
767721 TAAA-TGATGTAAGCAATGACATCAAA
1 TAAATTGATGTAAGCAATGACATCAAA
767747 TTAATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (29 bp):
TAAATTGATGTAAGCAATGACATCAAAAC
Found at i:772326 original size:29 final size:29
Alignment explanation
Indices: 772284--772371 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
772274 ATTTTTACCT
772284 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
772313 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
772342 AATTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
772371 A
1 A
772372 TTAATTTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:772381 original size:23 final size:24
Alignment explanation
Indices: 772288--772381 Score: 64
Period size: 29 Copynumber: 3.5 Consensus size: 24
772278 TTACCTAACT
* *
772288 AAATTGATGTAAGCAATGACATCA
1 AAATTAATTTAAGCAATGACATCA
*
772312 AAACTAAATTGATGTAAGCAATGACATCA
1 AAA-TTAA-T--T-TAAGCAATGACATCA
772341 AAATTAAATTGATGTAAGCAATGACATC-
1 AAATT-AA-T--T-TAAGCAATGACATCA
772369 AAATTAATTTAAG
1 AAATTAATTTAAG
772382 TGTGAACTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
23 4 0.07
24 4 0.07
25 2 0.03
26 2 0.03
27 2 0.03
28 6 0.10
29 40 0.67
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.28
Consensus pattern (24 bp):
AAATTAATTTAAGCAATGACATCA
Found at i:774187 original size:24 final size:24
Alignment explanation
Indices: 774157--774211 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
774147 CAAATTAAAC
774157 CCGTCCGGACTAGGCGCACGAGAA
1 CCGTCCGGACTAGGCGCACGAGAA
*
774181 CCGTCCGGACTAGGCGTACGAGAA
1 CCGTCCGGACTAGGCGCACGAGAA
774205 CCGTCCG
1 CCGTCCG
774212 ACGCACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.35, G:0.33, T:0.11
Consensus pattern (24 bp):
CCGTCCGGACTAGGCGCACGAGAA
Found at i:776104 original size:21 final size:21
Alignment explanation
Indices: 776065--776104 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
776055 TTAACAAGTG
* **
776065 AAATTCTAAATATTTAAATGA
1 AAATTATAAATATAAAAATGA
776086 AAATTATAAATATAAAAAT
1 AAATTATAAATATAAAAAT
776105 TCATCGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
AAATTATAAATATAAAAATGA
Found at i:778380 original size:196 final size:197
Alignment explanation
Indices: 777897--778498 Score: 760
Period size: 197 Copynumber: 3.1 Consensus size: 197
777887 AACTTTTTAC
*
777897 TGTGACTAAATAAGTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
1 TGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
* * * * *
777962 AATGAGAAATTAATATTTGTTATAATTTTTTATTTTAATTAAATAAATTTATCACAATTTTCATT
66 AATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCACAATTTTTATT
* * * * * * **
778027 TTGATAAAATATTGGGACGAAATAAATTTGACATAATTTTTTACTATGATAAAACTTAATGGGTT
131 TTGATAAAATATTGTGACAAAATAAATTTGACATAAATTTTTATTTTGATAAAATTTAATATGTT
778092 AT
196 AT
* * * *
778094 TGTGACTAAATCATTTTATTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTTTTTAT
1 TGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
* *
778159 AATGAGAAATTAATATTTGTTATAAATTACTATTTTGATTAAATAAATTTGTTACAATTTTTTAT
66 AATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCACAA-TTTTTAT
* * *** * *
778224 TTCGATAAAATATTGTGACCAAATAAATTTGACA-AAAAAATTATTTTGATTAAATTTACTATGT
130 TTTGATAAAATATTGTGACAAAATAAATTTGACATAAATTTTTATTTTGATAAAATTTAATATGT
778288 TAT
195 TAT
* * * * * *
778291 TGTAACTAAATAAATTTGTTATACTTT-ATATTGTGAAAGAATATTATTTTTCATAATTTTTTAT
1 TGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
* * * * * * *
778355 -TTAGAGGAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTA
66 AAT-GAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCACAA-TTTTTA
* * **
778419 TTTTGAGAAAATATTGTGACAAAATAAATTTAACATAAATTTTTATTTTGACCAAATTTAATATG
129 TTTTGATAAAATATTGTGACAAAATAAATTTGACATAAATTTTTATTTTGATAAAATTTAATATG
778484 TTAT
194 TTAT
778488 TGTGACTAAAT
1 TGTGACTAAAT
778499 GCATGATTTA
Statistics
Matches: 346, Mismatches: 56, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
195 1 0.00
196 116 0.34
197 192 0.55
198 37 0.11
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (197 bp):
TGTGACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
AATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCACAATTTTTATT
TTGATAAAATATTGTGACAAAATAAATTTGACATAAATTTTTATTTTGATAAAATTTAATATGTT
AT
Found at i:781985 original size:178 final size:181
Alignment explanation
Indices: 781759--782082 Score: 421
Period size: 179 Copynumber: 1.8 Consensus size: 181
781749 TGTGAATACA
* * * **
781759 ATTATTTTTTTGTAACAATGTTTTTTGTAATAATTATTAACACTTATAGTTACAAAATTTGTCAA
1 ATTATTTTGTTGTAACAATGTTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCAA
* * *
781824 TATATTA-TTT-TTTATG-GCGCAAAAATATGGAGGGA-AATC-TTTGTGACAATATATTTTGTC
66 TATATGATTTTGTTTATGTAC-CAAAAAT-TGGA--GATAATCATTTGTGACAATACATTTTGTC
781884 ACTATAATTAAAACATATAACGACAACATTGTTTTTTACTAAAAACTTGAATCTC
127 ACTATAATTAAAACATATAACGACAACATTGTTTTTTACTAAAAACTTGAATCTC
* *
781939 ATTA-TTTGTTGTGACAAT-TTTTTTGTAACAATAATTATA-GCTTATAGTTACAAAACATGTCA
1 ATTATTTTGTTGTAACAATGTTTTTTGTAACAATAATTA-ACACTTATAGTTACAAAACATGTCA
* * *
782001 CTATATGATTTTGTTTTTGTACCAAAAATTGGAGATAATCATTTGTGACTATACATTTTGTCACT
65 ATATATGATTTTGTTTATGTACCAAAAATTGGAGATAATCATTTGTGACAATACATTTTGTCACT
*
782066 ATAATTAAAATATATAA
130 ATAATTAAAACATATAA
782083 TTATAAACAA
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
177 2 0.02
178 47 0.38
179 58 0.47
180 16 0.13
181 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (181 bp):
ATTATTTTGTTGTAACAATGTTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCAA
TATATGATTTTGTTTATGTACCAAAAATTGGAGATAATCATTTGTGACAATACATTTTGTCACTA
TAATTAAAACATATAACGACAACATTGTTTTTTACTAAAAACTTGAATCTC
Found at i:782135 original size:180 final size:177
Alignment explanation
Indices: 781759--782141 Score: 409
Period size: 179 Copynumber: 2.1 Consensus size: 177
781749 TGTGAATACA
* * * * **
781759 ATTATTTTTTTGTAACAATGTTTTTTGTAATAATTATTAACACTTATAGTTACAAAATTTGTCAA
1 ATTA-TTTCTTGTGACAAT-TTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCAA
* * *
781824 TATATTATTTTTTATGGCGCAAAAATATGGAGGGAAATCTTTGTGACAATATATTTTGTCACTAT
64 TATATGATTTTTTATGACGCAAAAATATGGA-GGAAATCTTTGTGACAATACATTTTGTCACTAT
* *** * *
781889 AATTAAAACATATAACGACAACATTGTTTTTTACTAAAAACTTGAATCTC
128 AATTAAAACATATAACGAAAACAAAATTTTTCACTAAAAACTTAAATCTC
* * *
781939 ATTATTTGTTGTGACAATTTTTTTGTAACAATAATTATA-GCTTATAGTTACAAAACATGTCACT
1 ATTATTTCTTGTGACAATTTTTTTGTAACAATAATTA-ACACTTATAGTTACAAAACATGTCAAT
* *
782003 ATATGATTTTGTTTTTGTAC-CAAAAAT-TGGA-GATAATCATTTGTGACTATACATTTTGTCAC
65 ATATGA-TTT-TTTATG-ACGCAAAAATATGGAGGA-AATC-TTTGTGACAATACATTTTGTCAC
* **
782065 TATAATTAAAATATATAATTATAAACAAAATTTTTCAC-AACAAA-TCTAAATCTC
125 TATAATTAAAACATATAACGA-AAACAAAATTTTTCACTAA-AAACT-TAAATCTC
782119 ATTATTTCTTGTGACAATTTTTT
1 ATTATTTCTTGTGACAATTTTTT
782142 GGGTCGTAAT
Statistics
Matches: 171, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
177 2 0.01
178 47 0.27
179 62 0.36
180 59 0.35
181 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (177 bp):
ATTATTTCTTGTGACAATTTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCAATA
TATGATTTTTTATGACGCAAAAATATGGAGGAAATCTTTGTGACAATACATTTTGTCACTATAAT
TAAAACATATAACGAAAACAAAATTTTTCACTAAAAACTTAAATCTC
Found at i:783969 original size:43 final size:41
Alignment explanation
Indices: 783901--783992 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
783891 CTTTGAAATT
* * *
783901 TCGTGTTTGTTTACGTAATTTATTTTTAGGAAAATATTTTTC
1 TCGTGTTTATTTACGTAATTCATTTTTAGAAAAATA-TTTTC
* *
783943 TCGTGTTTATTTCTCGTAATTCATTTTTTGAAAAATATTTTC
1 TCGTGTTTATTT-ACGTAATTCATTTTTAGAAAAATATTTTC
*
783985 TAGTGTTT
1 TCGTGTTT
783993 GGTTGGAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 23 0.53
43 20 0.47
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (41 bp):
TCGTGTTTATTTACGTAATTCATTTTTAGAAAAATATTTTC
Found at i:784250 original size:24 final size:22
Alignment explanation
Indices: 784205--784274 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 22
784195 CAAAATATTA
* *
784205 ATTATTAAAATATTTAAAAATAT
1 ATTATTAATAT-TTTAATAATAT
784228 ATTTATTAATATTTCTAATAATAT
1 A-TTATTAATATTT-TAATAATAT
* *
784252 AATATT-ATATTTTTAATATTAT
1 ATTATTAATA-TTTTAATAATAT
784274 A
1 A
784275 ATAAAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 12 0.30
23 10 0.25
24 18 0.45
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATTAATATTTTAATAATAT
Found at i:784251 original size:22 final size:22
Alignment explanation
Indices: 784231--784277 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
784221 AAAATATATT
784231 TATTAATATTTCTAATAATATAA
1 TATT-ATATTTCTAATAATATAA
* *
784254 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
784276 TA
1 TA
784278 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:784365 original size:17 final size:20
Alignment explanation
Indices: 784345--784384 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
784335 ATAATAAGTT
784345 ATAA-AAAT-AATT-TTTTA
1 ATAATAAATAAATTATTTTA
784362 ATAATAAATAAATTATTTTA
1 ATAATAAATAAATTATTTTA
784382 ATA
1 ATA
784385 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 4 0.20
19 4 0.20
20 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATAAATAAATTATTTTA
Found at i:784395 original size:21 final size:21
Alignment explanation
Indices: 784366--784424 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
784356 TTTTTAATAA
* *
784366 TAAATAAATTATTTTAATATTT
1 TAAATAAATAATATTAAT-TTT
784388 TAAA-AAATAATATTAATTTT
1 TAAATAAATAATATTAATTTT
*
784408 TATGATAAATAATATTA
1 TA-AATAAATAATATTA
784425 CCTATTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.16
21 12 0.38
22 15 0.47
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TAAATAAATAATATTAATTTT
Found at i:800942 original size:22 final size:23
Alignment explanation
Indices: 800900--800942 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
800890 TTTTTGAGAT
*
800900 TTTTTTTAAAATAATAGTTTTAA
1 TTTTTTTAAAATAATAATTTTAA
800923 TTTTTTTAAAATAA-AATTTT
1 TTTTTTTAAAATAATAATTTT
800943 CAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTTTTAAAATAATAATTTTAA
Found at i:815760 original size:29 final size:29
Alignment explanation
Indices: 815705--815760 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
815695 AGGAACCCTC
* *
815705 TTTTGAACCAGATGGTGAGAGAGTTTTTT
1 TTTTGAACCAGATCGTGAGAGACTTTTTT
* *
815734 TTTTGAACCAG-TCGTGTGAGACCTTTT
1 TTTTGAACCAGATCGTGAGAGACTTTTT
815761 AATGATTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.41
Consensus pattern (29 bp):
TTTTGAACCAGATCGTGAGAGACTTTTTT
Found at i:831603 original size:59 final size:59
Alignment explanation
Indices: 831510--831633 Score: 194
Period size: 59 Copynumber: 2.1 Consensus size: 59
831500 AGATTGTTGA
* * *
831510 TAAATAGTTTTAAAAGAATGACTAATATGTAATTAATTTATGTTATGGAGCTATTTTTG
1 TAAATAGTTTTAAAAGAATGACTAATACGAAATTAATTTAGGTTATGGAGCTATTTTTG
* * *
831569 TAAATAGTTTTAAAAGAATGACTAATACGAAATTAATTTCGGTTATGGTGGTATTTTTG
1 TAAATAGTTTTAAAAGAATGACTAATACGAAATTAATTTAGGTTATGGAGCTATTTTTG
831628 TAAATA
1 TAAATA
831634 TTGTTAAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (59 bp):
TAAATAGTTTTAAAAGAATGACTAATACGAAATTAATTTAGGTTATGGAGCTATTTTTG
Found at i:831660 original size:29 final size:29
Alignment explanation
Indices: 831627--831860 Score: 164
Period size: 29 Copynumber: 8.1 Consensus size: 29
831617 TGGTATTTTT
*
831627 GTAAATATTGTTAAGAATGTGTTAGTTCC
1 GTAAATATTGTTAAGAATGTGTTAGTTTC
*
831656 GTAAATATTGTTAAGAAGGTGTTAGTTTC
1 GTAAATATTGTTAAGAATGTGTTAGTTTC
* * *
831685 GTAAATATTGTTAAAAAATGTGTTATTTTT
1 GTAAATATTGTT-AAGAATGTGTTAGTTTC
* * *
831715 GTAAATATT-TCTAA-AAGGGTGTCATTTTC
1 GTAAATATTGT-TAAGAA-TGTGTTAGTTTC
* * *
831744 GTAAATATT-TCTAA-AAGGGTATTATTTTC
1 GTAAATATTGT-TAAGAA-TGTGTTAGTTTC
* *
831773 GTAAATATTTTTAA-AAGGGTGTTA-TTTAC
1 GTAAATATTGTTAAGAA-TGTGTTAGTTT-C
* * *
831802 GTAAATATT-TTAA-TA-GTGTTATTTTT
1 GTAAATATTGTTAAGAATGTGTTAGTTTC
* *
831828 GTAAATATTTTTAA-AAGGGTGTTAGTTTC
1 GTAAATATTGTTAAGAA-TGTGTTAGTTTC
831857 GTAA
1 GTAA
831861 TTAATTCTGT
Statistics
Matches: 179, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.08
27 8 0.04
28 10 0.06
29 122 0.68
30 24 0.13
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (29 bp):
GTAAATATTGTTAAGAATGTGTTAGTTTC
Found at i:831718 original size:88 final size:83
Alignment explanation
Indices: 831615--831860 Score: 269
Period size: 88 Copynumber: 2.8 Consensus size: 83
831605 TTTCGGTTAT
* * *
831615 GGTGGTATTTTTGTAAATATTGTTAAGAATGTGTTAGTTCCGTAAATATTGTTAAGAA-GGTGTT
1 GGTGTTATTTTTGTAAATATT-TTAA-AA-GTGTTATTTTCGTAAATATT-TTAA-AAGGGTGTT
831679 AGTTTCGTAAATATTGTTAAAAAA
61 AGTTTCGTAAATATT-TTAAAAAA
* * *
831703 TGTGTTATTTTTGTAAATATTTCTAAAAGGGTGTCATTTTCGTAAATATTTCTAAAAGGGTATTA
1 GGTGTTATTTTTGTAAATATTT-TAAAA--GTGTTATTTTCGTAAATATTT-TAAAAGGGTGTTA
* * *
831768 TTTTCGTAAATATTTTTAAAAG
62 GTTTCGTAAATATTTTAAAAAA
** * *
831790 GGTGTTATTTACGTAAATATTTTAATAGTGTTATTTTTGTAAATATTTTTAAAAGGGTGTTAGTT
1 GGTGTTATTTTTGTAAATATTTTAAAAGTGTTATTTTCGTAAATA-TTTTAAAAGGGTGTTAGTT
831855 TCGTAA
65 TCGTAA
831861 TTAATTCTGT
Statistics
Matches: 135, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
84 36 0.27
85 3 0.02
86 4 0.03
87 31 0.23
88 61 0.45
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (83 bp):
GGTGTTATTTTTGTAAATATTTTAAAAGTGTTATTTTCGTAAATATTTTAAAAGGGTGTTAGTTT
CGTAAATATTTTAAAAAA
Found at i:831719 original size:59 final size:57
Alignment explanation
Indices: 831627--831860 Score: 269
Period size: 58 Copynumber: 4.1 Consensus size: 57
831617 TGGTATTTTT
* * * *
831627 GTAAATATTGTTAAGAATGTGTTAGTTCCGTAAATATTGTTAAGAA-GGTGTTAGTTTC
1 GTAAATATT-TTAAAAATGTGTTATTTTCGTAAATATTTTTAA-AAGGGTGTTAGTTTC
* * * *
831685 GTAAATATTGTTAAAAAATGTGTTATTTTTGTAAATATTTCTAAAAGGGTGTCATTTTC
1 GTAAATATT-TT-AAAAATGTGTTATTTTCGTAAATATTTTTAAAAGGGTGTTAGTTTC
** *
831744 GTAAATATTTCTAAAAGGGTATTATTTTCGTAAATATTTTTAAAAGGGTGTTA-TTTAC
1 GTAAATATTT-TAAAAATGTGTTATTTTCGTAAATATTTTTAAAAGGGTGTTAGTTT-C
* *
831802 GTAAATATTTT-AATA-GTGTTATTTTTGTAAATATTTTTAAAAGGGTGTTAGTTTC
1 GTAAATATTTTAAAAATGTGTTATTTTCGTAAATATTTTTAAAAGGGTGTTAGTTTC
831857 GTAA
1 GTAA
831861 TTAATTCTGT
Statistics
Matches: 153, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
55 38 0.25
56 5 0.03
57 4 0.03
58 61 0.40
59 45 0.29
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (57 bp):
GTAAATATTTTAAAAATGTGTTATTTTCGTAAATATTTTTAAAAGGGTGTTAGTTTC
Found at i:831890 original size:113 final size:116
Alignment explanation
Indices: 831655--831868 Score: 294
Period size: 113 Copynumber: 1.9 Consensus size: 116
831645 GTGTTAGTTC
831655 CGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTTAAAAAATGTGTTATTTTTGTAAA
1 CGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTT-AAAAATGTGTTATTTTTGTAAA
* * *
831720 TATTTCTAAAAGGGTGTCATTTTCGTAAATATTTCTAAAAGGGTATTATTTT
65 TATTTCTAAAAGGGTGTCAGTTTCGTAAATAATTCTAAAAGGGTACTATTTT
* *
831772 CGTAAATATTTTTAA-AAGGGTGTTA-TTTACGTAAATATT-TT-AATA-GTGTTATTTTTGTAA
1 CGTAAATATTGTTAAGAA-GGTGTTAGTTT-CGTAAATATTGTTAAAAATGTGTTATTTTTGTAA
* * *
831832 ATATTTTTAAAAGGGTGTTAGTTTCGTAATTAATTCT
64 ATATTTCTAAAAGGGTGTCAGTTTCGTAAATAATTCT
831869 GTTAGGGTGC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
113 47 0.53
114 3 0.03
116 7 0.08
117 31 0.35
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (116 bp):
CGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTTAAAAATGTGTTATTTTTGTAAAT
ATTTCTAAAAGGGTGTCAGTTTCGTAAATAATTCTAAAAGGGTACTATTTT
Found at i:848494 original size:20 final size:21
Alignment explanation
Indices: 848471--848542 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 21
848461 ACCCAGTTTC
848471 CAAATTCGCAACAAAGAA-GT
1 CAAATTCGCAACAAAGAATGT
** *
848491 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAAAGAATGT
* *
848512 CAAATTCGCAAC--TGAATTT
1 CAAATTCGCAACAAAGAATGT
848531 CAAATTCGCAAC
1 CAAATTCGCAAC
848543 TCATTTTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 19 0.40
20 16 0.33
21 13 0.27
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.24
Consensus pattern (21 bp):
CAAATTCGCAACAAAGAATGT
Found at i:848527 original size:19 final size:19
Alignment explanation
Indices: 848490--848581 Score: 96
Period size: 19 Copynumber: 4.7 Consensus size: 19
848480 AACAAAGAAG
848490 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
848511 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
848530 TCAAATTCGCAACTCATTTT
1 TCAAATTCGCAACTGA-ATT
* *
848550 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
848570 T-AATTTCGCAAC
1 TCAAATTCGCAAC
848582 AGGTTTTAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 32 0.52
20 18 0.30
21 11 0.18
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:848556 original size:20 final size:19
Alignment explanation
Indices: 848431--848581 Score: 88
Period size: 20 Copynumber: 7.6 Consensus size: 19
848421 AAATGACCAA
* * *
848431 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACTC-AATTT
* * *
848451 CAATTTCGCAACCCAGTTT
1 CAAATTCGCAACTCAATTT
** **
848470 CCAAATTCGCAACAAAGAAGT
1 -CAAATTCGCAACTCA-ATTT
*
848491 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTCAATTT
*
848512 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACTCAATTT
*
848531 CAAATTCGCAACTCATTTTT
1 CAAATTCGCAACTCA-ATTT
* *
848551 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACTC-AATTT
*
848571 -AATTTCGCAAC
1 CAAATTCGCAAC
848582 AGGTTTTAGT
Statistics
Matches: 103, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
19 34 0.33
20 52 0.50
21 14 0.14
22 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (19 bp):
CAAATTCGCAACTCAATTT
Found at i:848569 original size:40 final size:40
Alignment explanation
Indices: 848431--848582 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
848421 AAATGACCAA
* * * * * * *
848431 CAAATTCGCAACGCGAACTCCAATTTCGCAACCCAGTTTC
1 CAAATTCGCAACACGAATTTCAAATTCGCAACACATTTTT
* * *
848471 CAAATTCGCAACAAAGAA-GTCAAATTCGCAACAC-TGAATTT
1 CAAATTCGCAAC-ACGAATTTCAAATTCGCAACACAT--TTTT
* *
848512 CAAATTCGCAAC-TGAATTTCAAATTCGCAACTCATTTTT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACACATTTTT
* *
848551 CGAATTCGCAACACGAATTT-AATTTCGCAACA
1 CAAATTCGCAACACGAATTTCAAATTCGCAACA
848583 GGTTTTAGTT
Statistics
Matches: 89, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
39 27 0.30
40 44 0.49
41 18 0.20
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACACATTTTT
Found at i:848582 original size:19 final size:19
Alignment explanation
Indices: 848555--848601 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
848545 ATTTTTCGAA
848555 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
848574 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
848592 TTCGCAACAC
1 TTCGCAACAC
848602 AAATCTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:848731 original size:22 final size:22
Alignment explanation
Indices: 848688--848732 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
848678 ACTCTCTCCG
*
848688 ACGACATCCGTTCCTATATCTA
1 ACGACATCCGTTCCCATATCTA
*
848710 ACGACATCC-TTCCCCATCTCTA
1 ACGACATCCGTT-CCCATATCTA
848732 A
1 A
848733 TTTTTTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.27, C:0.38, G:0.07, T:0.29
Consensus pattern (22 bp):
ACGACATCCGTTCCCATATCTA
Found at i:848749 original size:14 final size:15
Alignment explanation
Indices: 848730--848767 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
848720 TCCCCATCTC
848730 TAATTTTTTT-TACA
1 TAATTTTTTTATACA
*
848744 TAATTTTATTTATATA
1 TAATTTT-TTTATACA
848760 TAATTTTT
1 TAATTTTT
848768 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTATACA
Found at i:848911 original size:43 final size:43
Alignment explanation
Indices: 848822--848977 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 43
848812 ATACATATTC
* * * * *
848822 TGCGGCG--TTTGTAAGAAAACGCCGGTAAAAATAAAAATCTAC
1 TGCGGCGTTTTTGT-AGAAAACGCCGCTAAAAATCAATACCTAT
*
848864 TGCGGCGTTTTTGTAGAAAACGCCGCTAAACATCAACTA-CTAT
1 TGCGGCGTTTTTGTAGAAAACGCCGCTAAAAATCAA-TACCTAT
** * *
848907 TGCGGCGTTTTAAT-GATAAACGCCGCTAAATATCAATACCTTT
1 TGCGGCGTTTTTGTAGA-AAACGCCGCTAAAAATCAATACCTAT
848950 TGCGGCGTTTGTTG-A-AAAATCGCCGCTA
1 TGCGGCGTTT-TTGTAGAAAA-CGCCGCTA
848978 TATGTTGTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
42 14 0.15
43 74 0.78
44 7 0.07
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (43 bp):
TGCGGCGTTTTTGTAGAAAACGCCGCTAAAAATCAATACCTAT
Found at i:851785 original size:20 final size:20
Alignment explanation
Indices: 851757--851800 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
851747 TTTTTGCGTT
* *
851757 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCACAAC
851777 GCGAAAGTCAAATTCACAAC
1 GCGAAAGTCAAATTCACAAC
851797 GCGA
1 GCGA
851801 TTATCGCGTT
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:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (20 bp):
GCGAAAGTCAAATTCACAAC
Found at i:851810 original size:54 final size:54
Alignment explanation
Indices: 851711--851815 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
851701 TAAGAAATGA
* * ** * * * *
851711 CAAATTCGCAACGCGGAAGTCAAATTCGCATTGTGATTTTTGCGTTGCGATAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCACAACGCGATTATCGCGTTACGATAGT
851765 CAAATTCGCAACGCGAAAGTCAAATTCACAACGCGATTATCGCGTTACGAT
1 CAAATTCGCAACGCGAAAGTCAAATTCACAACGCGATTATCGCGTTACGAT
851816 TGTTGCGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (54 bp):
CAAATTCGCAACGCGAAAGTCAAATTCACAACGCGATTATCGCGTTACGATAGT
Found at i:851893 original size:20 final size:20
Alignment explanation
Indices: 851870--851908 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
851860 TCGCAACGCG
851870 AATTTGACTTTCGCGTTGCA
1 AATTTGACTTTCGCGTTGCA
*
851890 AATTTGATTTTCGCGTTGC
1 AATTTGACTTTCGCGTTGC
851909 GAAAGTGTAC
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:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCA
Found at i:852024 original size:37 final size:37
Alignment explanation
Indices: 851982--852102 Score: 118
Period size: 37 Copynumber: 3.5 Consensus size: 37
851972 CAAATCAACT
851982 TTTACAAATCAATTAAACAAGCAAAAAACAATTCTTA
1 TTTACAAATCAATTAAACAAGCAAAAAACAATTCTTA
* *
852019 TTTACACATCAATT--A-AA-C--AAATCAA--C-T-
1 TTTACAAATCAATTAAACAAGCAAAAAACAATTCTTA
*
852046 TTTACAAATCAATTAAACAAGCAAAAAATAATTCTTA
1 TTTACAAATCAATTAAACAAGCAAAAAACAATTCTTA
* **
852083 TTTCCTCATCAATTAAACAA
1 TTTACAAATCAATTAAACAA
852103 ATCAACTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
27 13 0.20
28 1 0.02
29 2 0.03
30 2 0.03
31 7 0.11
33 6 0.09
34 2 0.03
35 2 0.03
36 1 0.02
37 30 0.45
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (37 bp):
TTTACAAATCAATTAAACAAGCAAAAAACAATTCTTA
Found at i:852069 original size:64 final size:64
Alignment explanation
Indices: 851970--852127 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
851960 ATAAATAAAC
851970 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAACAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAACAATTCTTATTTACACATCAATTA
* * *
852034 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAACAATTCTTATTTACACATCAATTA
852098 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
852128 ATTCAATTAA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 86 0.96
65 4 0.04
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAACAATTCTTATTTACACATCAATTA
Found at i:853556 original size:42 final size:42
Alignment explanation
Indices: 853490--853618 Score: 170
Period size: 42 Copynumber: 3.1 Consensus size: 42
853480 GTGAATCGGG
*
853490 ATCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGAC
1 ATCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGG-C
*
853533 A-CTTGAACGGTGGGAGGGGCCTCTTGAACGATGATAGGGGC
1 ATCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* * *** *
853574 ATCTTGAACGATAGGATATGCCTCTTGAACGATGACAGGTGC
1 ATCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
853616 ATC
1 ATC
853619 GGGCTTCTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
41 2 0.03
42 73 0.96
43 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.22
Consensus pattern (42 bp):
ATCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
Found at i:853571 original size:21 final size:21
Alignment explanation
Indices: 853491--853608 Score: 103
Period size: 21 Copynumber: 5.6 Consensus size: 21
853481 TGAATCGGGA
* * *
853491 TCTTGAACGGTGGGAGGGACC
1 TCTTGAACGATGAGAGGGGCC
* *
853512 TCTTGAACGATGACAGGGGAC
1 TCTTGAACGATGAGAGGGGCC
* * *
853533 ACTTGAACGGTGGGAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
* *
853554 TCTTGAACGATGATAGGGGCA
1 TCTTGAACGATGAGAGGGGCC
***
853575 TCTTGAACGAT-AGGATATGCC
1 TCTTGAACGATGA-GAGGGGCC
853596 TCTTGAACGATGA
1 TCTTGAACGATGA
853609 CAGGTGCATC
Statistics
Matches: 75, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
20 1 0.01
21 73 0.97
22 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGAGAGGGGCC
Found at i:853971 original size:63 final size:63
Alignment explanation
Indices: 853904--854023 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
853894 TAGAGCGGCT
* * *
853904 ACCTCATCACGTAAAGTA-TATACCTCACCACGTAGCGCACCATTGTCATCGCGTAAAACATCC
1 ACCTCACCACGTAAAG-ACCATACCTCACCACGTAGCGCACCATTGTCATCACGTAAAACATCC
* * *
853967 ACCTCACCACGTAAAGACCGTACCTCATCACGTAGCGCACCATTGTCTTCACGTAAA
1 ACCTCACCACGTAAAGACCATACCTCACCACGTAGCGCACCATTGTCATCACGTAAA
854024 GTACCAACCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
62 1 0.02
63 49 0.98
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.22
Consensus pattern (63 bp):
ACCTCACCACGTAAAGACCATACCTCACCACGTAGCGCACCATTGTCATCACGTAAAACATCC
Found at i:854034 original size:63 final size:64
Alignment explanation
Indices: 853924--854063 Score: 178
Period size: 63 Copynumber: 2.2 Consensus size: 64
853914 GTAAAGTATA
* * *
853924 TACCTCACCACGTAGCGCACCATTGTCATCGCGTAAAACATCCACCTCACCACGTAAAG-ACCG
1 TACCTCATCACGTAGCGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGTACCG
* ** **
853987 TACCTCATCACGTAGCGCACCATTGTCTTCACGTAAAGTA-CCAACCTCATGACGCAAAGTACCG
1 TACCTCATCACGTAGCGCACCATTGTCATCACGTAAAACATCC-ACCTCACCACGCAAAGTACCG
854051 -ACCTCATCACGTA
1 TACCTCATCACGTA
854064 ACTCTCCTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
62 2 0.03
63 61 0.91
64 4 0.06
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (64 bp):
TACCTCATCACGTAGCGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGTACCG
Found at i:855772 original size:20 final size:20
Alignment explanation
Indices: 855747--855819 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
855737 AAACTTAAAT
*
855747 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
855767 TTGCAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
855787 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
855807 TCGCAACGCGAAA
1 TCGCAACGCGAAA
855820 CTAAATTTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:855881 original size:20 final size:20
Alignment explanation
Indices: 855838--855881 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
855828 GCGTTGTGAT
* * *
855838 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGAATTTAAG
855858 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
855878 TTTC
1 TTTC
855882 AAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:856236 original size:22 final size:22
Alignment explanation
Indices: 856206--856252 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
856196 GAGATAGACA
*
856206 GATTTCGTCGGAGATGGGGACG
1 GATTACGTCGGAGATGGGGACG
*
856228 GATTACGTCGGAGATGGGGATG
1 GATTACGTCGGAGATGGGGACG
856250 GAT
1 GAT
856253 GTCGTCGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.11, G:0.45, T:0.23
Consensus pattern (22 bp):
GATTACGTCGGAGATGGGGACG
Found at i:856258 original size:22 final size:21
Alignment explanation
Indices: 856209--856259 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
856199 ATAGACAGAT
856209 TTCGTCGGAGATGGGGACGGA
1 TTCGTCGGAGATGGGGACGGA
*
856230 TTACGTCGGAGATGGGGATGGA
1 TT-CGTCGGAGATGGGGACGGA
856252 TGTCGTCG
1 T-TCGTCG
856260 TAGAGAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.07
22 24 0.89
23 1 0.04
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.24
Consensus pattern (21 bp):
TTCGTCGGAGATGGGGACGGA
Found at i:856400 original size:20 final size:20
Alignment explanation
Indices: 856375--856436 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
856365 ATAAACGCGC
856375 TTTGACTTATGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
*
856395 TTTGACTTATGTGTTGTGAA
1 TTTGACTTATGTGTTGCGAA
856415 TTTGACTTCA-GTG-TGCGAA
1 TTTGACTT-ATGTGTTGCGAA
856434 TTT
1 TTT
856437 AGAAAATCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 8 0.21
20 30 0.77
21 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (20 bp):
TTTGACTTATGTGTTGCGAA
Found at i:856455 original size:21 final size:21
Alignment explanation
Indices: 856429--856474 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
856419 ACTTCAGTGT
856429 GCGAATTTAGAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
*
856450 GCGAATTTAGAAAATCGCAAT
1 GCGAATTTAGAAAATCGCAAC
856471 GCGA
1 GCGA
856475 TTCACATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:859340 original size:21 final size:21
Alignment explanation
Indices: 859310--859472 Score: 115
Period size: 21 Copynumber: 7.9 Consensus size: 21
859300 GATTTACATA
*
859310 TTCGCATTGCGATAGTCTAAG
1 TTCGCGTTGCGATAGTCTAAG
*
859331 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCTAAG
* * * *
859352 TTCGCATTGCGAT-TTTTCAAA
1 TTCGCGTTGCGATAGTCT-AAG
* *
859373 TT--CGTTGTGATAGTCCAAG
1 TTCGCGTTGCGATAGTCTAAG
* * * *
859392 TTTGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCTAAG
*
859415 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCTAAG
859434 TTCGCGTTGCGATAGTCTCCAAG
1 TTCGCGTTGCGATAGTCT--AAG
859457 TT--CGTTGCGATAGTCT
1 TTCGCGTTGCGATAGTCT
859473 CCAAATTCGT
Statistics
Matches: 113, Mismatches: 19, Indels: 20
0.74 0.12 0.13
Matches are distributed among these distances:
19 20 0.18
20 2 0.02
21 77 0.68
23 14 0.12
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCTAAG
Found at i:859362 original size:42 final size:41
Alignment explanation
Indices: 859310--859516 Score: 190
Period size: 42 Copynumber: 5.0 Consensus size: 41
859300 GATTTACATA
* *
859310 TTCGCATTGCGATAGTCT-AAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCTCAAATT--CGTTGCGATAGTCCAAG
* * *
859352 TTCGCATTGCGAT-TTTTCAAATTCGTTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCTCAAATTCGTTGCGATAGTCCAAG
* * *
859392 TTTGCGTTGCGATTTATTC-CAAATTCGTTGCGATAGTCCAAG
1 TTCGCATTGCGA--TAGTCTCAAATTCGTTGCGATAGTCCAAG
* * *
859434 TTCGCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAA
1 TTCGCATTGCGATAGTCT-CAAATTCGTTGCGATAG--TCCAAG
* *
859478 TTCG--TTGCGGTAGTCTCCAAATTCGTTACGATAGTCCAA
1 TTCGCATTGCGATAGTCT-CAAATTCGTTGCGATAGTCCAA
859517 AATCGCAACG
Statistics
Matches: 141, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
40 34 0.24
41 2 0.01
42 94 0.67
43 2 0.01
44 9 0.06
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCTCAAATTCGTTGCGATAGTCCAAG
Found at i:859473 original size:21 final size:21
Alignment explanation
Indices: 859409--859513 Score: 142
Period size: 21 Copynumber: 5.0 Consensus size: 21
859399 TGCGATTTAT
859409 TCCAAATTCGTTGCGATAG--
1 TCCAAATTCGTTGCGATAGTC
*
859428 TCCAAGTTCGCGTTGCGATAGTC
1 TCCAAATT--CGTTGCGATAGTC
*
859451 TCCAAGTTCGTTGCGATAGTC
1 TCCAAATTCGTTGCGATAGTC
*
859472 TCCAAATTCGTTGCGGTAGTC
1 TCCAAATTCGTTGCGATAGTC
*
859493 TCCAAATTCGTTACGATAGTC
1 TCCAAATTCGTTGCGATAGTC
859514 CAAAATCGCA
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
19 7 0.09
21 62 0.81
23 8 0.10
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
TCCAAATTCGTTGCGATAGTC
Found at i:860664 original size:21 final size:21
Alignment explanation
Indices: 860634--860780 Score: 103
Period size: 21 Copynumber: 7.0 Consensus size: 21
860624 TGCGATTTTG
860634 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
* *
860655 GACTACCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
* *
860676 GACTATCGTAACGAATTTGTA
1 GACTATCGCAACGAATTTGGA
*
860697 -A-TAAATCGCAACGCGAACTT-GA
1 GACT--ATCGCAA--CGAATTTGGA
*
860719 -ACTATCGCAATGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
860739 -A-TAAATCGCAACGCAAACTT--A
1 GACT--ATCGCAACG--AATTTGGA
860760 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
860781 AAATCGCAAC
Statistics
Matches: 98, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
19 11 0.11
20 4 0.04
21 68 0.69
22 3 0.03
23 12 0.12
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
GACTATCGCAACGAATTTGGA
Found at i:860707 original size:42 final size:40
Alignment explanation
Indices: 860634--860812 Score: 168
Period size: 42 Copynumber: 4.3 Consensus size: 40
860624 TGCGATTTTG
* * * *
860634 GACTATCGCAACGAATTTGGAGACTACCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGAATA-AATCGCAACGAACTT-GA
*
860676 GACTATCGTAACGAATTTGTAATAAATCGCAACGCGAACTTGA
1 GACTATCGCAACGAATTTG-AATAAATCGCAA--CGAACTTGA
*
860719 -ACTATCGCAATGAATTTGGAATAAATCGCAACGCAAACTT-A
1 GACTATCGCAACGAATTT-GAATAAATCGCAACG--AACTTGA
* *
860760 GACTATCGCAACGAATTTGGA-AAATCGCAACGCGAACTT-C
1 GACTATCGCAACGAATTTGAATAAATCGCAA--CGAACTTGA
860800 GACTATCGCAACG
1 GACTATCGCAACG
860813 CGAACTTTGA
Statistics
Matches: 118, Mismatches: 10, Indels: 20
0.80 0.07 0.14
Matches are distributed among these distances:
40 29 0.25
41 3 0.03
42 74 0.63
43 5 0.04
44 7 0.06
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGAATAAATCGCAACGAACTTGA
Found at i:860807 original size:21 final size:21
Alignment explanation
Indices: 860701--860837 Score: 120
Period size: 21 Copynumber: 6.6 Consensus size: 21
860691 TTTGTAATAA
*
860701 ATCGCAACGCGAACTTGAACT
1 ATCGCAACGCGAACTTGGACT
* * *
860722 ATCGCAA--TGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
860741 AAATCGCAACGCAAACTTAGACT
1 --ATCGCAACGCGAACTTGGACT
* **
860764 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
860783 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
860804 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTGGACT
*
860825 ATCGCAATGCGAA
1 ATCGCAACGCGAA
860838 TATGTAAATC
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
19 22 0.24
21 61 0.68
23 7 0.08
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Done.