Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001489.1 Hibiscus syriacus cultivar Beakdansim tig00002894_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: 93889
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:20428 original size:29 final size:31
Alignment explanation
Indices: 20378--20435 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
20368 TTAAAGTATA
** *
20378 ATATTGTGAATATATTTTATAATTTTATATT
1 ATATTGTGAATATATTAAATAATATTATATT
20409 ATATT-TG-ATATATTAAATAATATTATA
1 ATATTGTGAATATATTAAATAATATTATA
20436 ATGTGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 2 0.08
31 5 0.21
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (31 bp):
ATATTGTGAATATATTAAATAATATTATATT
Found at i:23829 original size:31 final size:29
Alignment explanation
Indices: 23794--23853 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
23784 ATAATAATAT
* *
23794 TTTATAATAATTTAATAAATTTAATGTCTAA
1 TTTATAAT-ATTTAA-AAAATTAATGACTAA
23825 TTTATAATATTTAAAAAATTAATGACTAA
1 TTTATAATATTTAAAAAATTAATGACTAA
23854 ATAATTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 13 0.48
30 6 0.22
31 8 0.30
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTATAATATTTAAAAAATTAATGACTAA
Found at i:34801 original size:12 final size:12
Alignment explanation
Indices: 34776--34808 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
34766 AGTTGATGCC
34776 ATTTTATA--AT
1 ATTTTATAGGAT
34786 ATTTTATAGGAT
1 ATTTTATAGGAT
34798 ATTTTATAGGA
1 ATTTTATAGGA
34809 CCACCTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
12 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (12 bp):
ATTTTATAGGAT
Found at i:43163 original size:2 final size:2
Alignment explanation
Indices: 43156--43196 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43146 TTAAAAGTTA
43156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43197 ACAACATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43465 original size:36 final size:36
Alignment explanation
Indices: 43388--43533 Score: 99
Period size: 38 Copynumber: 3.9 Consensus size: 36
43378 TAAAAAACGT
43388 TTTTGAAAACTTATATACAATATATAAGTTTTAAAAACA
1 TTTTGAAAA-TTATATACAATATAT-A-TTTTAAAAACA
*
43427 TTTTGAAAATTATATA-ACATATAT-TTTTGAAAATCA
1 TTTTGAAAATTATATACA-ATATATATTTT-AAAAACA
*
43463 TTTT-AAAA--ATAT--AATGTATAGTTTAAAATAAAAACA
1 TTTTGAAAATTATATACAATATATA-TTT----TAAAAACA
* *
43499 TTTTTGAAAATTTTATATAATATATAGTTTTAAAA
1 -TTTTGAAAATTATATACAATATATA-TTTTAAAA
43534 TATTTTGGAA
Statistics
Matches: 88, Mismatches: 5, Indels: 29
0.72 0.04 0.24
Matches are distributed among these distances:
31 5 0.06
32 1 0.01
33 7 0.08
35 8 0.09
36 16 0.18
37 6 0.07
38 22 0.25
39 9 0.10
40 3 0.03
42 11 0.12
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (36 bp):
TTTTGAAAATTATATACAATATATATTTTAAAAACA
Found at i:43553 original size:36 final size:35
Alignment explanation
Indices: 43387--43640 Score: 111
Period size: 36 Copynumber: 7.1 Consensus size: 35
43377 TTAAAAAACG
* *
43387 TTTTTGAAAACTTATATACAATATATAAGTTTTAAAAACA
1 TTTTGGAAAAC-TATAT--AATATAT-AGTTTT-AAAATA
* * *
43427 TTTT-GAAAATTATATAACATATATTTTTGAAAATCA
1 TTTTGGAAAACTATATAATATATAGTTTT-AAAAT-A
* *
43463 TTTT--AAAA--ATATAATGTATAGTTTAAAATAAAAACA
1 TTTTGGAAAACTATATAATATATAGTTT----T-AAAATA
* *
43499 TTTTTGAAAATTTTATATAATATATAGTTTTAAAATA
1 TTTTGGAAAA--CTATATAATATATAGTTTTAAAATA
*
43536 TTTTGGAAAACTCATATAATAT-T--TTTAAAAATCA
1 TTTTGGAAAACT-ATATAATATATAGTTTTAAAAT-A
* ** *
43570 TTTTTGAAAACTATATGGTATATAGTTTTGAAAACA
1 TTTTGGAAAACTATATAATATATAGTTTT-AAAATA
* *
43606 TTTT---TAA--ATATAATATATAGTTTAAAAAATA
1 TTTTGGAAAACTATATAATATATAGTTT-TAAAATA
43637 TTTT
1 TTTT
43641 TTGTGATATA
Statistics
Matches: 171, Mismatches: 25, Indels: 45
0.71 0.10 0.19
Matches are distributed among these distances:
31 23 0.13
33 30 0.18
34 13 0.08
35 15 0.09
36 33 0.19
37 23 0.13
38 10 0.06
39 5 0.03
40 4 0.02
42 15 0.09
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TTTTGGAAAACTATATAATATATAGTTTTAAAATA
Found at i:43570 original size:20 final size:21
Alignment explanation
Indices: 43532--43570 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
43522 ATAGTTTTAA
*
43532 AATATTTTGGAAAACTCATAT
1 AATATTTTGGAAAAATCATAT
*
43553 AATATTTT-TAAAAATCAT
1 AATATTTTGGAAAAATCAT
43571 TTTTGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (21 bp):
AATATTTTGGAAAAATCATAT
Found at i:43640 original size:31 final size:31
Alignment explanation
Indices: 43513--43641 Score: 100
Period size: 31 Copynumber: 3.9 Consensus size: 31
43503 TGAAAATTTT
*
43513 ATATAATATATAGTTTT-AAAATATTTTGGAA
1 ATATAATATATAGTTTTAAAAATATTTT-TAA
* *
43544 A-ACTCATATAATATTTTTAAAAATCATTTTTGAAA
1 ATA-TAATAT-ATAGTTTTAAAAAT-ATTTTT--AA
* * *
43579 ACTATATGGTATATAGTTTTGAAAACATTTTTAA
1 A-TATA--ATATATAGTTTTAAAAATATTTTTAA
*
43613 ATATAATATATAGTTTAAAAAATATTTTT
1 ATATAATATATAGTTTTAAAAATATTTTT
43642 TGTGATATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
30 1 0.01
31 26 0.34
32 7 0.09
33 9 0.12
34 8 0.11
35 3 0.04
36 7 0.09
37 12 0.16
38 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (31 bp):
ATATAATATATAGTTTTAAAAATATTTTTAA
Found at i:43711 original size:18 final size:18
Alignment explanation
Indices: 43690--43728 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43680 ATTATTTCTT
*
43690 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
43708 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
43726 TTC
1 TTC
43729 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:44913 original size:25 final size:26
Alignment explanation
Indices: 44863--44923 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
44853 TACCTCTTAC
*
44863 TATTTCTTTATTTCATTTTTATTTAA
1 TATTTCTTTATATCATTTTTATTTAA
*
44889 TATTT-TTTATATCTATTTTTATTAAA
1 TATTTCTTTATATC-ATTTTTATTTAA
*
44915 AATTTCTTT
1 TATTTCTTT
44924 CATTTGTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 7 0.23
26 20 0.67
27 3 0.10
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTTCTTTATATCATTTTTATTTAA
Found at i:48619 original size:106 final size:106
Alignment explanation
Indices: 48429--49514 Score: 1766
Period size: 106 Copynumber: 10.4 Consensus size: 106
48419 TACAGCCTTT
* *
48429 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
* * * * *
48494 CGAAGGAACTGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
* * * * * *
48535 AGAGCCAATTTCAACTTCTCAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
* * * *
48600 CAAAGGGGCGGCTGATTGT---C--A-AA--T-TC-A-TTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
* * *
48630 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
48695 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
* *
48736 AGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
48801 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
*
48842 AGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
48907 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
* *
48948 AGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
49013 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
*
49054 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
49119 CGAA-GGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
49159 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
49224 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
*
49265 AGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
49330 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
49371 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
* * *
49436 CGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAGTTCC
66 CGAAGGGACCG-CTGGTTGTCAACAAACAATTTCTCAATTTC
* * * *
49477 AAAACCAATTTCAACTTCACGACGGAGGATATTGGACT
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
49515 TGGAACAATA
Statistics
Matches: 925, Mismatches: 42, Indels: 26
0.93 0.04 0.03
Matches are distributed among these distances:
95 76 0.08
96 1 0.00
97 1 0.00
98 2 0.00
100 3 0.00
101 3 0.00
103 1 0.00
104 2 0.00
105 107 0.12
106 729 0.79
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
Found at i:49275 original size:423 final size:424
Alignment explanation
Indices: 48433--49514 Score: 1760
Period size: 423 Copynumber: 2.6 Consensus size: 424
48423 GCCTTTAGAG
* *
48433 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAA
* * * * * * *
48498 GGAACTGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCTCAGCGAAGG
66 GGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* * * * * *
48563 ATATTGGAC-CCAAGACAACACAAGCTCAACTTCACGACAAAGGGGCGGCTGATTGT---C--A-
131 ATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * * *
48621 AA--T-TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACGCAA
195 AATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
48681 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
260 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATT
*
48746 TCAACTTCACAGCGAAGGATATTAGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
325 TCAACTTCACAACGAAGGATATTAGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
*
48811 GCTGGTTGTCAACAAACAATTTCTCAATTTCAGAG
390 GCTGGTTGTCAACAAACAATTTCTCAATTTCAGAA
*
48846 CCAATTTCAACTTCACAACGAAAGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAA
*
48911 GGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
48976 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
49041 ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
196 ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
49106 TTCAACTTCACGACGAA-GGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTT
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTT
*
49170 CAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
326 CAACTTCACAACGAAGGATATTAGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
49235 CTGGTTGTCAACAAACAATTTCTCAATTTCAGAA
391 CTGGTTGTCAACAAACAATTTCTCAATTTCAGAA
49269 CCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAA
49334 GGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
49399 ATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGACTGGTTGTCAACAAAC
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAAC
* * * * * * *
49463 AATTTCCCAGTTCCAAAACCAATTTCAACTTCACGACGGAGGATATTGGACT
195 AATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
49515 TGGAACAATA
Statistics
Matches: 622, Mismatches: 34, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
413 166 0.27
414 2 0.00
416 1 0.00
418 1 0.00
419 2 0.00
421 1 0.00
422 4 0.01
423 377 0.61
424 68 0.11
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (424 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTAGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAACAAACAATTTCTCAATTTCAGAA
Found at i:50606 original size:38 final size:36
Alignment explanation
Indices: 50545--50798 Score: 146
Period size: 38 Copynumber: 7.1 Consensus size: 36
50535 AAAAAAACGT
50545 TTTTGAAAACTTATATACAATATATAAGTTTTAAAAACA
1 TTTTGAAAA-TTATATA-AATATAT-AGTTTTAAAAACA
*
50584 TTTTGAAAATTATATAACATATAT--TTTTGAAAATCA
1 TTTTGAAAATTATATAA-ATATATAGTTTT-AAAAACA
*
50620 TTTT-AAAA--ATAT-AATGTATAGTTTAAAATAAAAACA
1 TTTTGAAAATTATATAAATATATAGTTT----TAAAAACA
* *
50656 TTTTTGAAAATTTTATATAATATATAGTTTTAAAAATA
1 -TTTTGAAAATTATATA-AATATATAGTTTTAAAAACA
*
50694 TTTTGGAAAACTCATAT--A-ATAT--TTTTAAAAATCA
1 TTTT-GAAAA-TTATATAAATATATAGTTTTAAAAA-CA
* ** *
50728 TTTTTGAAAACTATAT-GGTATATAGTTTTGAAAACA
1 -TTTTGAAAATTATATAAATATATAGTTTTAAAAACA
* * *
50764 TTTT--TAA--ATAT-AATATATAGTTTAAAAAATA
1 TTTTGAAAATTATATAAATATATAGTTTTAAAAACA
50795 TTTT
1 TTTT
50799 TTGGGATATA
Statistics
Matches: 174, Mismatches: 19, Indels: 52
0.71 0.08 0.21
Matches are distributed among these distances:
31 28 0.16
32 1 0.01
33 22 0.13
34 6 0.03
35 24 0.14
36 19 0.11
37 18 0.10
38 29 0.17
39 13 0.07
40 3 0.02
42 11 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATTATATAAATATATAGTTTTAAAAACA
Found at i:50725 original size:33 final size:32
Alignment explanation
Indices: 50675--50743 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
50665 ATTTTATATA
50675 ATATATAGTTTTAAAAAT-ATTTTGGAAAACT
1 ATATATAGTTTTAAAAATCATTTTGGAAAACT
* *
50706 CATATAATATTTTTAAAAATCATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAATCATTTTGGAAAACT
50740 ATAT
1 ATAT
50744 GGTATATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 4 0.12
33 17 0.52
34 12 0.36
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (32 bp):
ATATATAGTTTTAAAAATCATTTTGGAAAACT
Found at i:50728 original size:20 final size:21
Alignment explanation
Indices: 50690--50728 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
50680 TAGTTTTAAA
*
50690 AATATTTTGGAAAACTCATAT
1 AATATTTTGGAAAAATCATAT
*
50711 AATATTTT-TAAAAATCAT
1 AATATTTTGGAAAAATCAT
50729 TTTTGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (21 bp):
AATATTTTGGAAAAATCATAT
Found at i:50869 original size:18 final size:18
Alignment explanation
Indices: 50848--50886 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50838 ATTATTTCTT
*
50848 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
50866 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
50884 TTC
1 TTC
50887 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:52066 original size:25 final size:26
Alignment explanation
Indices: 52016--52076 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
52006 TACCTCTTAC
*
52016 TATTTCTTTATTTCATTTTTATTTAA
1 TATTTCTTTATATCATTTTTATTTAA
*
52042 TATTT-TTTATATCTATTTTTATTAAA
1 TATTTCTTTATATC-ATTTTTATTTAA
*
52068 AATTTCTTT
1 TATTTCTTT
52077 CATTTGTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 7 0.23
26 20 0.67
27 3 0.10
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTTCTTTATATCATTTTTATTTAA
Found at i:61478 original size:2 final size:2
Alignment explanation
Indices: 61471--61496 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61461 ATTTTTGAAG
61471 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
61497 TAACAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66243 original size:2 final size:2
Alignment explanation
Indices: 66236--66279 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
66226 TATCACGTGA
66236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66278 AT
1 AT
66280 TTCTGACTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66721 original size:22 final size:22
Alignment explanation
Indices: 66679--66727 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
66669 GATTTATTCC
66679 CAAAATTTTAGTATTTACTTTT
1 CAAAATTTTAGTATTTACTTTT
*
66701 -AAAATTTT-TTATTTAATCTTTT
1 CAAAATTTTAGTATTT-A-CTTTT
66723 CAAAA
1 CAAAA
66728 GAAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 5 0.22
23 4 0.17
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (22 bp):
CAAAATTTTAGTATTTACTTTT
Found at i:77130 original size:3 final size:3
Alignment explanation
Indices: 77122--77199 Score: 147
Period size: 3 Copynumber: 25.7 Consensus size: 3
77112 TCTCTCTCCC
77122 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
77168 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
77200 GAAAATAACC
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 71 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:77369 original size:21 final size:21
Alignment explanation
Indices: 77343--77396 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
77333 GTTTCCAGAT
*
77343 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
77364 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
77385 TCGCAATGCGAA
1 TCGCAATGCGAA
77397 TTTGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:77409 original size:20 final size:21
Alignment explanation
Indices: 77343--77415 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
77333 GTTTCCAGAT
* * *
77343 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACAA
*
77364 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACAA
* *
77385 TCGCAATGCGAATTTGTA-AA
1 TCGCAATGCGAACTTGGACAA
77405 TCGCAATGCGA
1 TCGCAATGCGA
77416 TAGTCCAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 12 0.26
21 35 0.74
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACAA
Found at i:77435 original size:21 final size:19
Alignment explanation
Indices: 77411--77466 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
77401 TAAATCGCAA
*
77411 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAATT--CGT
*
77432 TGCGATTTATTCCAAATTCGT
1 TGCGA--TAGTCCAAATTCGT
77453 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
77467 ATCGCAACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.27
21 13 0.43
23 9 0.30
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
TGCGATAGTCCAAATTCGT
Found at i:78222 original size:21 final size:21
Alignment explanation
Indices: 78196--78267 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
78186 ATTGAAATAA
78196 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * *
78217 ATCGCAA--TGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
78236 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
78259 ATCGCAACG
1 ATCGCAACG
78268 AACAATCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 9 0.22
21 23 0.56
23 9 0.22
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:78223 original size:37 final size:38
Alignment explanation
Indices: 78173--78265 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 38
78163 CGTTGTGATT
78173 TTGGACTATCGCAA-TTGAAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAATTTGAAATAAATCGCAACGCGAAC
*
78210 TTGGACTATCGCAATGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGC----AATTTGAAATAAATCGCAACGCGAAC
78252 TTGGACTATCGCAA
1 TTGGACTATCGCAA
78266 CGAACAATCA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
37 12 0.24
38 2 0.04
41 2 0.04
42 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (38 bp):
TTGGACTATCGCAATTTGAAATAAATCGCAACGCGAAC
Found at i:78623 original size:58 final size:58
Alignment explanation
Indices: 78561--78713 Score: 161
Period size: 58 Copynumber: 2.6 Consensus size: 58
78551 TGATGTATTT
* *
78561 TAAATTAGTCATTGAACTTTTGAATATTTCAATTTCAC-CCTCAAACTATGACTC-ATTC
1 TAAATTAGTCCTTGAACTTTTGAATATTTCAATTTCACATC-CAAACTATGACTCGA-TC
* * *
78619 TAAATTAATCCTTGAACTTTTGAATATCAT-AATTTCATATCCAAACTATGACTCGATC
1 TAAATTAGTCCTTGAACTTTTGAATAT-TTCAATTTCACATCCAAACTATGACTCGATC
* * * *
78677 TAAATTGGTCCCTAAACTTTTGAGTA-TTCTAATTTCA
1 TAAATTAGTCCTTGAACTTTTGAATATTTC-AATTTCA
78714 TTCTCAAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
56 1 0.01
58 75 0.95
59 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (58 bp):
TAAATTAGTCCTTGAACTTTTGAATATTTCAATTTCACATCCAAACTATGACTCGATC
Done.