Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008250.1 Hibiscus syriacus cultivar Beakdansim tig00110902_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: 31935
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:9231 original size:10 final size:9
Alignment explanation
Indices: 9194--9233 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
9184 AAAATGAGTG
*
9194 AAAATGAAA
1 AAAATAAAA
9203 AAAATAAAA
1 AAAATAAAA
9212 AATAATAAAA
1 AA-AATAAAA
9222 AAAATGAAAA
1 AAAAT-AAAA
9232 AA
1 AA
9234 TGGAAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 13 0.46
10 15 0.54
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (9 bp):
AAAATAAAA
Found at i:10781 original size:55 final size:55
Alignment explanation
Indices: 10243--10780 Score: 817
Period size: 55 Copynumber: 9.8 Consensus size: 55
10233 CCAACGATAA
* *
10243 TTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
10298 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
10353 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* *
10408 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * *
10463 ATGAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGACTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
10518 TTGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * * *
10573 ATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGGTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * *
10628 ATGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGAGTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTG
* * * * *
10684 TTGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAACAAACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * *
10739 ATGAAGATTGTTCGAGT-TCTATACTCCCTGAAGAAAGAGGGA
1 TTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGA
10781 ATGAACTCGT
Statistics
Matches: 442, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
54 1 0.00
55 392 0.89
56 49 0.11
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:11800 original size:1 final size:1
Alignment explanation
Indices: 11794--11819 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11784 GCAACCATCG
11794 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
11820 TAGAACGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15979 original size:18 final size:17
Alignment explanation
Indices: 15950--16098 Score: 74
Period size: 16 Copynumber: 8.6 Consensus size: 17
15940 ATAATTTAAG
15950 TTTATATATAAACTATA
1 TTTATATATAAACTATA
15967 TTTATATTATAAACTATA
1 TTTATA-TATAAACTATA
* *
15985 TATGCATAAACTATAAA-AAGTA
1 T-T---TATA-TATAAACTA-TA
* *
16007 TATAGTTTATAAACTATA
1 TTTA-TATATAAACTATA
* *
16025 TATATATATATA-TATA
1 TTTATATATAAACTATA
* *
16041 TATATATATATA-TATA
1 TTTATATATAAACTATA
* *
16057 TATATATATATA-TATA
1 TTTATATATAAACTATA
* *
16073 TATATATATATA-TATA
1 TTTATATATAAACTATA
*
16089 TATATATATA
1 TTTATATATA
16099 GTTTATAATT
Statistics
Matches: 115, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
16 62 0.54
17 12 0.10
18 26 0.23
19 2 0.02
21 1 0.01
22 12 0.10
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTATATATAAACTATA
Found at i:16026 original size:2 final size:2
Alignment explanation
Indices: 16021--16184 Score: 159
Period size: 2 Copynumber: 85.0 Consensus size: 2
16011 GTTTATAAAC
16021 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
*
16063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
16106 -A T- TA TA AA T- TA TA T- TA -A TA TGG TA TA TA TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
**
16144 TA -A CTA -A TA TA -A GTA -A CC TA TA T- 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
16183 TA
1 TA
16185 GTTTATAGAA
Statistics
Matches: 135, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
1 10 0.07
2 121 0.90
3 4 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16369 original size:2 final size:2
Alignment explanation
Indices: 16364--16407 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
16354 AATATGCACA
*
16364 AT AT AT AT AA ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16407 A
1 A
16408 AAAATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 38 0.97
3 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16670 original size:35 final size:36
Alignment explanation
Indices: 16600--16673 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
16590 ACAATAGTTA
* *
16600 ATATATGTAACATATAGTATATGTATACATGTAAACT
1 ATATATGTAACATATAGTACATGTATA-ATATAAACT
* *
16637 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACATATAGTACATGTATAATATAAACT
16672 AT
1 AT
16674 GTATAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (36 bp):
ATATATGTAACATATAGTACATGTATAATATAAACT
Found at i:16687 original size:18 final size:18
Alignment explanation
Indices: 16664--16734 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
16654 TACATGTATG
*
16664 TATAAACTATGTATA-ATA
1 TATAAA-TATATATATATA
16682 TATAAACTATATATATATA
1 TATAAA-TATATATATATA
*
16701 TATATATATATATATATA
1 TATAAATATATATATATA
* *
16719 TATATATATGTATATA
1 TATAAATATATATATA
16735 CAATCTATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
18 41 0.84
19 8 0.16
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
TATAAATATATATATATA
Found at i:16694 original size:2 final size:2
Alignment explanation
Indices: 16675--16734 Score: 86
Period size: 2 Copynumber: 30.0 Consensus size: 2
16665 ATAAACTATG
*
16675 TA TA -A TA TA TA AA CTA 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
*
16717 TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA
16735 CAATCTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:16796 original size:21 final size:20
Alignment explanation
Indices: 16772--16862 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 20
16762 ATATGTAACC
16772 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACAATAGTT
**
16793 TATA-TTAGTGTACTATATAGTT
1 TATATTTA-TAAAC-A-ATAGTT
* * *
16815 TATACTTTATAACCTATAGTA
1 TATA-TTTATAAACAATAGTT
*
16836 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACAATAGTT
16857 TATATT
1 TATATT
16863 AATGTACTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.05
20 6 0.11
21 30 0.55
22 11 0.20
23 2 0.04
24 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATTTATAAACAATAGTT
Found at i:16886 original size:22 final size:21
Alignment explanation
Indices: 16787--16889 Score: 84
Period size: 22 Copynumber: 4.8 Consensus size: 21
16777 TTTATAAACA
*
16787 ATAGTTTATATTAGTGTACTAT
1 ATAGTTTATATTAATGTAC-AT
* * *
16809 ATAGTTTATACTTTAT-AACCT
1 ATAGTTTATA-TTAATGTACAT
* * **
16830 ATAGTATATAATTTATAAAC-T
1 ATAGTTTAT-ATTAATGTACAT
16851 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
16873 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
16890 TAATTATCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.10
21 23 0.34
22 34 0.51
23 3 0.04
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (21 bp):
ATAGTTTATATTAATGTACAT
Found at i:16938 original size:12 final size:11
Alignment explanation
Indices: 16834--17104 Score: 68
Period size: 12 Copynumber: 23.3 Consensus size: 11
16824 TAACCTATAG
16834 TATATAATTTA
1 TATATAATTTA
*
16845 TAAACTATAGTTTA
1 T--A-TATAATTTA
*
16859 TAT-TAATGTA
1 TATATAATTTA
*
16869 CTATATAGTTTA
1 -TATATAATTTA
16881 TAT-TAATGTTA
1 TATATAAT-TTA
16892 -AT-T-ATCTTA
1 TATATAAT-TTA
16901 -ACTATAATTTA
1 TA-TATAATTTA
*
16912 TAT-TAATATA
1 TATATAATTTA
16922 GTATATAATTTA
1 -TATATAATTTA
16934 CTATATAATTTA
1 -TATATAATTTA
*
16946 TAAAATATAGTTTA
1 T---ATATAATTTA
16960 TAT-TAATATTA
1 TATATAAT-TTA
16971 -ATATTAATTTTA
1 TATA-TAA-TTTA
*
16983 TAGACTATATTT-
1 TATA-TA-ATTTA
16995 TATATTAATATTA
1 TATA-TAAT-TTA
* *
17008 -ATTACAAATTA
1 TA-TATAATTTA
*
17019 TAAACT-ATATTA
1 TATA-TAAT-TTA
*
17031 TAT-TAATATA
1 TATATAATTTA
*
17041 AAT-TAATATTA
1 TATATAAT-TTA
17052 -ATAATAATTATA
1 TAT-ATAATT-TA
17064 TTAATATTAATTATAA
1 -T-ATA-TAATT-T-A
17080 TATATAATTTA
1 TATATAATTTA
17091 TATATAATTTA
1 TATATAATTTA
17102 TAT
1 TAT
17105 TAAGGGCGGG
Statistics
Matches: 198, Mismatches: 25, Indels: 74
0.67 0.08 0.25
Matches are distributed among these distances:
9 6 0.03
10 34 0.17
11 52 0.26
12 55 0.28
13 16 0.08
14 24 0.12
15 10 0.05
16 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (11 bp):
TATATAATTTA
Found at i:16970 original size:6 final size:6
Alignment explanation
Indices: 16959--17107 Score: 59
Period size: 6 Copynumber: 25.2 Consensus size: 6
16949 AATATAGTTT
* * * *
16959 ATATTA ATATTA ATATTA ATTTTA TAGACT- ATATTTT ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA -ATATTA ATA-TTA ATATTA ATATTA
** * * *
17008 ATTACAA ATTATAA ACTATATT ATATTA ATA-TA A-ATTA ATATTA ATAAT-
1 A-TATTA A-TATTA A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA
17057 A-ATT- ATATTA ATATTA AT-TATA ATATATA AT-TT- ATATATA AT-TT-
1 ATATTA ATATTA ATATTA ATAT-TA ATAT-TA ATATTA ATAT-TA ATATTA
17101 ATATTA A
1 ATATTA A
17108 GGGCGGGAAC
Statistics
Matches: 111, Mismatches: 16, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
4 8 0.07
5 18 0.16
6 55 0.50
7 29 0.26
8 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:16979 original size:48 final size:47
Alignment explanation
Indices: 16834--16980 Score: 134
Period size: 48 Copynumber: 3.0 Consensus size: 47
16824 TAACCTATAG
*
16834 TATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAA
1 TATATAATTTATAAACTATAGTTTATATTAA--TA-TA-ATA-TTAAT-TTAA
* * * * * *
16887 TGT-TAATTATCTTAACTATAATTTATATTAATATAGTATATAATTTAC
1 TATATAATT-TATAAACTATAGTTTATATTAATATAATAT-TAATTTAA
*
16935 TATATAATTTATAAAATATAGTTTATATTAATATTAATATTAATTT
1 TATATAATTTATAAACTATAGTTTATATTAATA-TAATATTAATTT
16981 TATAGACTAT
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
48 32 0.42
49 15 0.19
50 2 0.03
51 2 0.03
52 5 0.06
53 21 0.27
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (47 bp):
TATATAATTTATAAACTATAGTTTATATTAATATAATATTAATTTAA
Found at i:17051 original size:21 final size:21
Alignment explanation
Indices: 17017--17076 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
17007 AATTACAAAT
*
17017 TATAAACT-ATATTATATTAA
1 TATAAATTAATATTATATTAA
*
17037 TATAAATTAATATTAATAATAA
1 TATAAATTAATATT-ATATTAA
*
17059 T-TATATTAATATTA-ATTA
1 TATAAATTAATATTATATTA
17077 TAATATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.09
20 8 0.24
21 16 0.47
22 7 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAATTAATATTATATTAA
Found at i:17079 original size:21 final size:21
Alignment explanation
Indices: 17042--17107 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
17032 ATTAATATAA
*
17042 ATTAATATTAATAATAATTAT
1 ATTAATATTAATTATAATTAT
17063 ATTAATATTAATTATAA-TAT
1 ATTAATATTAATTATAATTAT
17083 A-TAAT-TT-ATATATAATTTAT
1 ATTAATATTAAT-TATAA-TTAT
17103 ATTAA
1 ATTAA
17108 GGGCGGGAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 2 0.05
18 7 0.17
19 4 0.10
20 8 0.20
21 19 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAATATTAATTATAATTAT
Found at i:17086 original size:65 final size:65
Alignment explanation
Indices: 16892--17086 Score: 161
Period size: 65 Copynumber: 2.9 Consensus size: 65
16882 ATTAATGTTA
* * * * *
16892 ATTATCTTAACTAT-AATTTATATTAAT-AT-AGTATA-TAAT-TTACTATATAATTTATAAAAT
1 ATTATATTAA-TATAAATTAATATTAATAATAATTATATTAATATTAAT-TATAATATATAAAAT
16952 AT
64 AT
* *
16954 AGTTTATATTAATATTAATATTAAT-TTTATAGACTATATTTTATATTAATATTAATTACAA-AT
1 A--TTATATTAATA-TAA-ATTAATATTAATA-A-TA-A--TTATATTAATATTAATTATAATA-
*
17017 TATAAACTAT
56 TATAAAATAT
17027 ATTATATTAATATAAATTAATATTAATAATAATTATATTAATATTAATTATAATATATAA
1 ATTATATTAATATAAATTAATATTAATAATAATTATATTAATATTAATTATAATATATAA
17087 TTTATATATA
Statistics
Matches: 106, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 9 0.08
65 30 0.28
66 6 0.06
67 2 0.02
68 3 0.03
69 7 0.07
70 9 0.08
71 11 0.10
72 4 0.04
73 18 0.17
74 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (65 bp):
ATTATATTAATATAAATTAATATTAATAATAATTATATTAATATTAATTATAATATATAAAATAT
Found at i:17095 original size:11 final size:11
Alignment explanation
Indices: 17079--17104 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17069 ATTAATTATA
17079 ATATATAATTT
1 ATATATAATTT
17090 ATATATAATTT
1 ATATATAATTT
17101 ATAT
1 ATAT
17105 TAAGGGCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATATAATTT
Found at i:17540 original size:14 final size:13
Alignment explanation
Indices: 17517--17586 Score: 83
Period size: 14 Copynumber: 5.3 Consensus size: 13
17507 CGTTCGTGAA
17517 CGTTCGGTTATGTT
1 CGTTC-GTTATGTT
17531 CGTTCAGTTATGTT
1 CGTTC-GTTATGTT
17545 CG-T--TTATGTT
1 CGTTCGTTATGTT
17555 CGTTCGATTATGTT
1 CGTTCG-TTATGTT
17569 CGTTCGATTATGTT
1 CGTTCG-TTATGTT
17583 CGTT
1 CGTT
17587 TATGTTCATT
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
10 9 0.18
11 1 0.02
13 1 0.02
14 40 0.78
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.51
Consensus pattern (13 bp):
CGTTCGTTATGTT
Found at i:17568 original size:38 final size:38
Alignment explanation
Indices: 17517--17606 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 38
17507 CGTTCGTGAA
*
17517 CGTTCGGTTATGTTCGTTC-AGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTCGA-TTATGTTCGTTTATGTT
17555 CGTTCGATTATGTTCGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTCGATTATGTTCGTTTATGTT
*
17593 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
17607 TAACCCAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
37 1 0.02
38 46 0.96
39 1 0.02
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (38 bp):
CGTTCGATTATGTTCGTTCGATTATGTTCGTTTATGTT
Found at i:17571 original size:24 final size:24
Alignment explanation
Indices: 17493--17572 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 24
17483 ACATAGGTCT
*
17493 TGTTCGTTTAT-TTACGTTCG-TGAA
1 TGTTCGTTTATGTT-CGTTCGAT-TA
* *
17517 CGTTCGGTTATGTTCGTTC-AGTTA
1 TGTTCGTTTATGTTCGTTCGA-TTA
17541 TGTTCGTTTATGTTCGTTCGATTA
1 TGTTCGTTTATGTTCGTTCGATTA
17565 TGTTCGTT
1 TGTTCGTT
17573 CGATTATGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 43 0.91
25 4 0.09
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.51
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCGATTA
Found at i:17583 original size:24 final size:24
Alignment explanation
Indices: 17556--17606 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
17546 GTTTATGTTC
*
17556 GTTCGATTATGTTCGTTCGA-TTAT
1 GTTCGATTATGTTCATTC-ATTTAT
*
17580 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCATTCATTTAT
17604 GTT
1 GTT
17607 TAACCCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.55
Consensus pattern (24 bp):
GTTCGATTATGTTCATTCATTTAT
Found at i:18706 original size:16 final size:16
Alignment explanation
Indices: 18685--18723 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
18675 GGGTCTCCAA
18685 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
18701 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
18717 CGTTTAT
1 CGTTTAT
18724 TAAATGAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:19610 original size:40 final size:40
Alignment explanation
Indices: 19559--19670 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
19549 AAGTTACATT
*
19559 GAATCACTTAACATCATATAACCATTAATATTAGTATCT-A
1 GAATCAGTTAACATCATATAACCATTAATATTAGTAT-TGA
* * *
19599 GTATCAGTTAACATCATATAACAATTAACATTAGTATTGA
1 GAATCAGTTAACATCATATAACCATTAATATTAGTATTGA
*
19639 GAATCACG-TAACATCAGATAATCCATATAATA
1 GAATCA-GTTAACATCATATAA-CCAT-TAATA
19671 AAGATAATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.02
40 51 0.85
41 4 0.07
42 4 0.07
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (40 bp):
GAATCAGTTAACATCATATAACCATTAATATTAGTATTGA
Found at i:23706 original size:5 final size:5
Alignment explanation
Indices: 23693--23753 Score: 59
Period size: 5 Copynumber: 12.2 Consensus size: 5
23683 AATAATTTTC
* * * * *
23693 ATAAT ATAAA ATAAT ATAAT ATAAT ACAAT ATAAT ACAAT ACAAT ACAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
23743 ACAGT ATAAT A
1 ATAAT ATAAT A
23754 CAGTACAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.30
Consensus pattern (5 bp):
ATAAT
Found at i:23795 original size:15 final size:15
Alignment explanation
Indices: 23725--23895 Score: 126
Period size: 15 Copynumber: 11.4 Consensus size: 15
23715 AATACAATAT
* *
23725 AATACAATACAATAC
1 AATACAGTACAGTAC
* *
23740 AATACAGTATAATAC
1 AATACAGTACAGTAC
* *
23755 AGTACAATACAGTAC
1 AATACAGTACAGTAC
* * *
23770 AATATAATATAGTAC
1 AATACAGTACAGTAC
*
23785 AATACAGTATAGTAC
1 AATACAGTACAGTAC
* * *
23800 AATATATTATAGTAC
1 AATACAGTACAGTAC
* * * *
23815 AGTATAGTATAGCAC
1 AATACAGTACAGTAC
*
23830 AGTACAGTACAGTAC
1 AATACAGTACAGTAC
* *
23845 AGTACAATACAGTAC
1 AATACAGTACAGTAC
* *
23860 AATATAGTACAGTAT
1 AATACAGTACAGTAC
* *
23875 AGTACAGTACAATAC
1 AATACAGTACAGTAC
23890 AATACA
1 AATACA
23896 ATTTTAAATA
Statistics
Matches: 127, Mismatches: 29, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 127 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (15 bp):
AATACAGTACAGTAC
Found at i:23897 original size:5 final size:5
Alignment explanation
Indices: 23727--23895 Score: 113
Period size: 5 Copynumber: 33.8 Consensus size: 5
23717 TACAATATAA
* * * * * * * * *
23727 TACAA TACAA TACAA TACAG TATAA TACAG TACAA TACAG TACAA TATAA
1 TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG
* * * * * * * * *
23777 TATAG TACAA TACAG TATAG TACAA TATAT TATAG TACAG TATAG TATAG
1 TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG
* * * * *
23827 CACAG TACAG TACAG TACAG TACAA TACAG TACAA TATAG TACAG TATAG
1 TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG TACAG
* *
23877 TACAG TACAA TACAA TACA
1 TACAG TACAG TACAG TACA
23896 ATTTTAAATA
Statistics
Matches: 131, Mismatches: 33, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 131 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (5 bp):
TACAG
Found at i:30202 original size:65 final size:64
Alignment explanation
Indices: 30095--30229 Score: 200
Period size: 65 Copynumber: 2.1 Consensus size: 64
30085 ACACCCTAAT
* * *
30095 TCGAATGCATTTTGTGTACCGATTCACAACCATGCATCGATGCACTCCT-GATTTTATTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGGATCTT-TTGAAACA
* *
30159 TCGAATGCATTTTATGTATCGATGCACAGATCATGCATCGATGCACTCCTGGATCTTTTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACA-ACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
30224 TCGAAT
1 TCGAAT
30230 ATAATTAGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
64 25 0.39
65 34 0.53
66 5 0.08
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
Done.