Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005821.1 Hibiscus syriacus cultivar Beakdansim tig00013638_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: 71181
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4672 original size:19 final size:19
Alignment explanation
Indices: 4630--4666 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4620 TGATTTTGAA
4630 AAAAAATTAATTAGGCGAC
1 AAAAAATTAATTAGGCGAC
4649 AAAAAATTAATTAGGCGA
1 AAAAAATTAATTAGGCGA
4667 TTAAAATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (19 bp):
AAAAAATTAATTAGGCGAC
Found at i:6319 original size:23 final size:24
Alignment explanation
Indices: 6293--6343 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
6283 CCTTAATATG
*
6293 AATTATATTTATATACTTT-TTTT
1 AATTAGATTTATATACTTTATTTT
6316 AATT-GATTTATATACTTTATTTT
1 AATTAGATTTATATACTTTATTTT
6339 AATTA
1 AATTA
6344 AACTAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
AATTAGATTTATATACTTTATTTT
Found at i:6324 original size:22 final size:23
Alignment explanation
Indices: 6299--6342 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
6289 TATGAATTAT
6299 ATTTATATACTTT-TTTTAATTG
1 ATTTATATACTTTATTTTAATTG
6321 ATTTATATACTTTATTTTAATT
1 ATTTATATACTTTATTTTAATT
6343 AAACTAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTATATACTTTATTTTAATTG
Found at i:6816 original size:38 final size:39
Alignment explanation
Indices: 6752--6827 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
6742 TCATATTAAT
* *
6752 AAGTAGAAAATTAAAGTTTTACCTAGTTCTAAATAAATG
1 AAGTAGAAAACTAAAGCTTTACCTAGTTCTAAATAAATG
6791 AAGTAGAAAACTAAA-CTTTACCTAGTTCTAAATAAAT
1 AAGTAGAAAACTAAAGCTTTACCTAGTTCTAAATAAAT
6828 TAATTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 21 0.60
39 14 0.40
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (39 bp):
AAGTAGAAAACTAAAGCTTTACCTAGTTCTAAATAAATG
Found at i:8202 original size:20 final size:20
Alignment explanation
Indices: 8177--8215 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8167 ATGTTTTATT
*
8177 ATTTTTTTTAATAATGAAAC
1 ATTTTTTTTAAAAATGAAAC
8197 ATTTTTTTTAAAAATGAAA
1 ATTTTTTTTAAAAATGAAA
8216 AAATAAAAAA
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:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTTTTTTAAAAATGAAAC
Found at i:18395 original size:2 final size:2
Alignment explanation
Indices: 18388--18428 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
18378 AACATCTTGG
18388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18429 GTGTGAATTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19760 original size:30 final size:30
Alignment explanation
Indices: 19724--19786 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
19714 TAATATAACA
19724 TAAATATACTGATAATAAGTACGAATCAAG
1 TAAATATACTGATAATAAGTACGAATCAAG
* *
19754 TAAATATATTGATGATAAGTACGAATCAAG
1 TAAATATACTGATAATAAGTACGAATCAAG
19784 TAA
1 TAA
19787 CTAAATTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (30 bp):
TAAATATACTGATAATAAGTACGAATCAAG
Found at i:27904 original size:24 final size:24
Alignment explanation
Indices: 27811--27904 Score: 98
Period size: 24 Copynumber: 3.9 Consensus size: 24
27801 TATATCAAAA
* * * *
27811 ATCAAAACATAATTCAGTTCAGAT
1 ATCAGAACAGAATTCAGGTCAGGT
* * *
27835 ATCATAACATAATTCAGGTCAAGT
1 ATCAGAACAGAATTCAGGTCAGGT
* *
27859 ATTAGAACAGAATCCAGGTCAGGT
1 ATCAGAACAGAATTCAGGTCAGGT
*
27883 ATCAGATCAGAATTCAGGTCAG
1 ATCAGAACAGAATTCAGGTCAG
27905 AAATCAGGTA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGGTCAGGT
Found at i:30087 original size:25 final size:24
Alignment explanation
Indices: 30038--30087 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
30028 TAACAGTCAG
* *
30038 CGGGTCGGGTCAAATCGGGTTAAA
1 CGGGTCGAGTCAAATCGGGTCAAA
*
30062 CGGGTCGAGTCAAAATTGGGTCAAA
1 CGGGTCGAGTC-AAATCGGGTCAAA
30087 C
1 C
30088 TGCCCCAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (24 bp):
CGGGTCGAGTCAAATCGGGTCAAA
Found at i:46542 original size:24 final size:24
Alignment explanation
Indices: 46514--46561 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
46504 CTAGTGGGTT
46514 TAGAATCGGATGCACGAGCTTTAG
1 TAGAATCGGATGCACGAGCTTTAG
46538 TAGAATCGGATGCACGAGCTTTAG
1 TAGAATCGGATGCACGAGCTTTAG
46562 AATCAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (24 bp):
TAGAATCGGATGCACGAGCTTTAG
Found at i:46564 original size:21 final size:22
Alignment explanation
Indices: 46512--46570 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 22
46502 CTCTAGTGGG
46512 TTTAGAATCGGATGCACGAGCT
1 TTTAGAATCGGATGCACGAGCT
46534 TTAGTAGAATCGGATGCACGAGC-
1 TT--TAGAATCGGATGCACGAGCT
*
46557 TTTAGAATCAGATG
1 TTTAGAATCGGATG
46571 TGCTCGTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.32
22 2 0.06
23 2 0.06
24 19 0.56
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
TTTAGAATCGGATGCACGAGCT
Found at i:56255 original size:321 final size:321
Alignment explanation
Indices: 55617--56264 Score: 1007
Period size: 322 Copynumber: 2.0 Consensus size: 321
55607 TTGACAGACA
* *
55617 AAATTCAGGTCGGATCTTACCGGATACGAATTGAGTTCAGGTCGGATAATGTTTTGGATAATTAT
1 AAATTCAGGTCGGATCTTACCAGATACGAATTGACTTCAGGTCGGATAATGTTTTGGATAATTAT
* * *
55682 TTTTCGCATTTCAATGTTTAATGAATGTGAGTGAGAACATCGAATTGTAATTAATAATTTTATAT
66 TTTTCACATTTCAATGTTTAATGAACGTGAGTGAGAACATCGAATTGTAATTAATAATTGTATAT
* * * *
55747 AATTTAGAATAAATTACAAAAAATATTAGTAATTATGGGTCAATTTTGATAAAAATATAACTTGA
131 AATTTAAAATAAATTA-AAAAAATATTAATAATTATGGGTCAAATTTGATAAAAATATAACTTAA
* * * *
55812 ACTACCAAATTGAACAAACATGAAATTGGAAATAAAAAATTAAATAAATTAAACAACACATATTG
195 ACTACCAAATTGAACAAACATAAAATTGGAAATAAAAAAATAAAAAAATTAAACAACACACATTG
* *
55877 ACGAGAGATGAAATTGAATTAATTATAAAATGTGAAGCTAATATTAATATAAAAAATGGACT
260 ACGAGAGATGAAATGGAATTAATTATAAAATGTGAAGCTAATATTAATAAAAAAAATGGACT
* *
55939 AAATTCAGGTCAGG-TCTTACCAGATAC-ATATTGACTTCAGGTCGGATCACT-TTTTGGTTAAT
1 AAATTCAGGTC-GGATCTTACCAGATACGA-ATTGACTTCAGGTCGGAT-AATGTTTTGGATAAT
* *
56001 TATTTTTCACATTTCAATGTTTAATGAACGTGAGTGAGAACGTCGAATTGTAATTAGTAATTGTA
63 TATTTTTCACATTTCAATGTTTAATGAACGTGAGTGAGAACATCGAATTGTAATTAATAATTGTA
* *
56066 TATGATTTAAAATAAATT-AAAAAATATTAATAATTATGGGTCAAATTTGATAAAAATATAATTT
128 TATAATTTAAAATAAATTAAAAAAATATTAATAATTATGGGTCAAATTTGATAAAAATATAACTT
56130 AAACTACCAAAATTGAACAAACATAAAATTGGAAATAAAAAAATAAAAAAATTAAACAACACACA
193 AAACTACC-AAATTGAACAAACATAAAATTGGAAATAAAAAAATAAAAAAATTAAACAACACACA
* * *
56195 TTGACGAGGGATGAAATGGAATTAATTATAAAATGTGAAGTTGATATTAATAAAAAAAATGGACT
257 TTGACGAGAGATGAAATGGAATTAATTATAAAATGTGAAGCTAATATTAATAAAAAAAATGGACT
56260 AAATT
1 AAATT
56265 GCATACATTT
Statistics
Matches: 298, Mismatches: 24, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
320 50 0.17
321 118 0.40
322 126 0.42
323 4 0.01
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (321 bp):
AAATTCAGGTCGGATCTTACCAGATACGAATTGACTTCAGGTCGGATAATGTTTTGGATAATTAT
TTTTCACATTTCAATGTTTAATGAACGTGAGTGAGAACATCGAATTGTAATTAATAATTGTATAT
AATTTAAAATAAATTAAAAAAATATTAATAATTATGGGTCAAATTTGATAAAAATATAACTTAAA
CTACCAAATTGAACAAACATAAAATTGGAAATAAAAAAATAAAAAAATTAAACAACACACATTGA
CGAGAGATGAAATGGAATTAATTATAAAATGTGAAGCTAATATTAATAAAAAAAATGGACT
Found at i:56866 original size:2 final size:2
Alignment explanation
Indices: 56548--56856 Score: 137
Period size: 2 Copynumber: 154.0 Consensus size: 2
56538 TTAAAACAAT
56548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTGA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA
* * * * * * *
56591 TA TGA TA CA TG CA TA TA TA -A TG TA CA T- TA TA CT- TA TG CA TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
56632 GA T- TA -A TA CA T- TA -A TA CA T- TA TA -A GTA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
56669 TA -A TA TA AA GTA TA TA -A GTA TA TA AA GTA TA TA TA CA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
56710 AA GTA TA -A GTG TA TA TA TA TA TA TA TA AA T- TA AA AA GTA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
56751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA GT- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
56793 GTA TA TA TA TA TA TA TA TA TA AA CTA TA TA GTA TA TA TA CA TA
1 -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
*
56836 TA AA GTA TA -A GTA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA
56857 CAATTATATA
Statistics
Matches: 229, Mismatches: 45, Indels: 66
0.67 0.13 0.19
Matches are distributed among these distances:
1 16 0.07
2 194 0.85
3 18 0.08
4 1 0.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:56880 original size:14 final size:15
Alignment explanation
Indices: 56863--57244 Score: 204
Period size: 14 Copynumber: 25.9 Consensus size: 15
56853 TATACAATTA
*
56863 TATAAACTATA-AAG
1 TATAAAGTATATAAG
56877 TAT-AAGTATATAAG
1 TATAAAGTATATAAG
* *
56891 TATATA-TATA-AAC
1 TATAAAGTATATAAG
56904 TATAAAGTATATAA-
1 TATAAAGTATATAAG
56918 TATAAAGTAT-TAAAG
1 TATAAAGTATAT-AAG
56933 TATATAA-TATA-AAG
1 TATA-AAGTATATAAG
56947 TAATAAACTGTTTGGATATAAG
1 T-ATAAA--G--T--ATATAAG
* *
56969 TATAAAAGTACATAAA
1 TAT-AAAGTATATAAG
*
56985 TATAAAGTATATAAA
1 TATAAAGTATATAAG
57000 TAT-AAGTATATAAG
1 TATAAAGTATATAAG
* *
57014 TATATACTATA-AAG
1 TATAAAGTATATAAG
*
57028 TATTAAACTATAT-A-
1 TA-TAAAGTATATAAG
*
57042 TATAAAGTATATAAA
1 TATAAAGTATATAAG
57057 TAT-AAGTATATAAG
1 TATAAAGTATATAAG
* *
57071 TATATACTATA-AAG
1 TATAAAGTATATAAG
*
57085 TATTAAACTATATAA-
1 TA-TAAAGTATATAAG
*
57100 TAT-AAGTAT-TAAA
1 TATAAAGTATATAAG
57113 TATAAAGTATATAAG
1 TATAAAGTATATAAG
*
57128 TATTAAAGCATATAA-
1 TA-TAAAGTATATAAG
* *
57143 TATAAAATAT-TAAAC
1 TATAAAGTATAT-AAG
* *
57158 CATATA--ATATAAG
1 TATAAAGTATATAAG
*
57171 TATTAAA-TATA-AAT
1 TA-TAAAGTATATAAG
57185 TATTAAAGTAT-TAAAG
1 TA-TAAAGTATAT-AAG
57201 TATATAA--ATATAAG
1 TATA-AAGTATATAAG
*
57215 TATTAAAGTATATAAA
1 TA-TAAAGTATATAAG
*
57231 TATATAGTTATATA
1 TATAAAG-TATATA
57245 TATTAATTTA
Statistics
Matches: 294, Mismatches: 30, Indels: 86
0.72 0.07 0.21
Matches are distributed among these distances:
12 3 0.01
13 37 0.13
14 111 0.38
15 85 0.29
16 43 0.15
18 1 0.00
19 1 0.00
20 1 0.00
21 5 0.02
22 7 0.02
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (15 bp):
TATAAAGTATATAAG
Found at i:56886 original size:22 final size:21
Alignment explanation
Indices: 56861--57244 Score: 165
Period size: 22 Copynumber: 17.3 Consensus size: 21
56851 TATATACAAT
*
56861 TATATAAACTATAAAGTATAAG
1 TATATAAAGTATAAA-TATAAG
*
56883 TATAT-AAGTATATATATAA-
1 TATATAAAGTATAAATATAAG
56902 -ACTATAAAGTATATAATATAAAG
1 TA-TATAAAGTATA-AATAT-AAG
56925 TAT-TAAAGTATATAATATAAAG
1 TATATAAAGTATA-AATAT-AAG
* **
56947 TA-ATAAACTGTTTGGATATAAG
1 TATATAAA--GTATAAATATAAG
56969 TATA-AAAGTACATAAATATAAAG
1 TATATAAAGT--ATAAATAT-AAG
56992 TATATAAA-TATAAGTATATAAG
1 TATATAAAGTATAA--ATATAAG
* **
57014 TATATACTATAAAGTATTAA-ACTATA
1 ----TA-TATAAAGTATAAATA-TAAG
57040 TATATAAAGTATATAAATATAAG
1 TATATAAAG--TATAAATATAAG
*
57063 TATAT-AAGTATATACTATAAAG
1 TATATAAAGTATA-AATAT-AAG
*
57085 TAT-TAAACTATATAATATAAG
1 TATATAAAGTATA-AATATAAG
57106 TAT-TAAA-TATAAAGTATATAAG
1 TATATAAAGTAT-AA--ATATAAG
*
57128 TAT-TAAAGCATATAATATAA-
1 TATATAAAGTATA-AATATAAG
* **
57148 AATATTAAACCATATAATATAAG
1 TATA-TAAAGTATA-AATATAAG
57171 TAT-TAAA-TATAAATTATTAAAG
1 TATATAAAGTATAAA-TA-T-AAG
57193 TAT-TAAAGTATATAAATATAAG
1 TATATAAAG--TATAAATATAAG
57215 TAT-TAAAGTATATAAATATATAG
1 TATATAAAG--TATAAATATA-AG
57238 TTATATA
1 -TATATA
57245 TATTAATTTA
Statistics
Matches: 293, Mismatches: 23, Indels: 89
0.72 0.06 0.22
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 29 0.10
21 49 0.17
22 134 0.46
23 38 0.13
24 13 0.04
25 9 0.03
26 5 0.02
27 6 0.02
28 4 0.01
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (21 bp):
TATATAAAGTATAAATATAAG
Found at i:57057 original size:57 final size:57
Alignment explanation
Indices: 56984--57130 Score: 262
Period size: 57 Copynumber: 2.6 Consensus size: 57
56974 AAGTACATAA
56984 ATATAAAGTATATAAATATAAGTATATAAGTATATACTATAAAGTATTAAACTATAT
1 ATATAAAGTATATAAATATAAGTATATAAGTATATACTATAAAGTATTAAACTATAT
57041 ATATAAAGTATATAAATATAAGTATATAAGTATATACTATAAAGTATTAAACTATAT
1 ATATAAAGTATATAAATATAAGTATATAAGTATATACTATAAAGTATTAAACTATAT
57098 A-ATATAAGTAT-TAAATATAAAGTATATAAGTAT
1 ATATA-AAGTATATAAATAT-AAGTATATAAGTAT
57131 TAAAGCATAT
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
56 10 0.11
57 78 0.89
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (57 bp):
ATATAAAGTATATAAATATAAGTATATAAGTATATACTATAAAGTATTAAACTATAT
Found at i:57068 original size:65 final size:63
Alignment explanation
Indices: 56993--57234 Score: 263
Period size: 65 Copynumber: 3.9 Consensus size: 63
56983 AATATAAAGT
*
56993 ATATAA-ATATAAGTA-TATAAGTATATACTATAAAGTATTAAACTATAT-ATATAA--AGT--
1 ATATAATATATAAGTATTA-AAGTATATACTATAAAGTATTAAACTATATAATATAAGTATTAA
57050 ATATAA-ATATAAGTA-TATAAGTATATACTATAAAGTATTAAACTATATAATATAAGTATTAA
1 ATATAATATATAAGTATTA-AAGTATATACTATAAAGTATTAAACTATATAATATAAGTATTAA
* * * *
57112 ATATAAAGTATATAAGTATTAAAGCATATAATATAAAATATTAAACCATATAATATAAGTATTAA
1 ATAT-AA-TATATAAGTATTAAAGTATATACTATAAAGTATTAAACTATATAATATAAGTATTAA
* *
57177 ATATAA-ATTATTAAAGTATTAAAGTATATA-AATATAAGTATTAAAGTATATAAATATA
1 ATATAATA-TA-T-AAGTATTAAAGTATATACTATA-AAGTATTAAACTATAT-AATATA
57235 TAGTTATATA
Statistics
Matches: 161, Mismatches: 10, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
57 48 0.30
58 6 0.04
60 2 0.01
62 5 0.03
63 4 0.02
64 6 0.04
65 82 0.51
66 8 0.05
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (63 bp):
ATATAATATATAAGTATTAAAGTATATACTATAAAGTATTAAACTATATAATATAAGTATTAA
Found at i:57246 original size:65 final size:60
Alignment explanation
Indices: 56870--57246 Score: 251
Period size: 65 Copynumber: 6.1 Consensus size: 60
56860 TTATATAAAC
* * *
56870 TATAAAGTATAAGTATATAAGTATAT-ATATAAACTA-TAAAGTATATAATATAAAGTATTAAA
1 TATAAA-TATAAGTATATAAGTATATAATATAAAGTATTAAACTATATAATAT-AAG--TTATA
* * * * * * *
56932 GTATATAATATAAAGTA-ATAAACTGTTTGGATAT-AAGTATAAAAGTACATAAATATAA---AG
1 -TATA-AATAT-AAGTATAT-AAGTATAT-AATATAAAGTATTAAACTATAT-AATATAAGTTA-
56992 TA
59 TA
*
56994 TATAAATATAAGTATATAAGTATATACTATAAAGTATTAAACTATAT-ATATAA---AGTA
1 TATAAATATAAGTATATAAGTATATAATATAAAGTATTAAACTATATAATATAAGTTA-TA
* *
57051 TATAAATATAAGTATATAAGTATATACTATAAAGTATTAAACTATATAATATAAGTATTAAA
1 TATAAATATAAGTATATAAGTATATAATATAAAGTATTAAACTATATAATATAAG--TTATA
* * * *
57113 TATAAAGTATATAAGTAT-TAAAGCATATAATATAAAATATTAAACCATATAATATAAGTATTAA
1 TAT-AA--ATATAAGTATAT-AAGTATATAATATAAAGTATTAAACTATATAATATAAG--TTAT
57177 A
60 A
*
57178 TATAAATTATTAAAGTAT-TAAAGTATATAA-ATATAAGTATTAAAGTATATAAATATATAGTTA
1 TATAAA-TA-T-AAGTATAT-AAGTATATAATATA-AAGTATTAAACTATAT-AATATA-AGTTA
57241 TA
59 TA
57243 TATA
1 TATA
57247 TTAATTTATA
Statistics
Matches: 263, Mismatches: 25, Indels: 50
0.78 0.07 0.15
Matches are distributed among these distances:
57 57 0.22
58 9 0.03
59 23 0.09
60 7 0.03
61 5 0.02
62 6 0.02
63 14 0.05
64 19 0.07
65 96 0.37
66 20 0.08
67 7 0.03
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (60 bp):
TATAAATATAAGTATATAAGTATATAATATAAAGTATTAAACTATATAATATAAGTTATA
Found at i:58065 original size:162 final size:162
Alignment explanation
Indices: 57794--58108 Score: 400
Period size: 162 Copynumber: 1.9 Consensus size: 162
57784 ATATGTTCCT
* * * *
57794 TGTTTGATCCTTACAAACACCAAACACTTTTTCTCAACCTGTTTTGAAGATCAAAACCCCCAAAC
1 TGTTTGATCCTTACAAACACCAAACACATTTCCTCAACCTGTTTTAAAGATCAAAAACCCCAAAC
* * *
57859 TGAAGCACTGTTCATCTTCTTCCCTAACCCTAAATCCTAAATCCCACCATTCA-CCCCCTTCCAT
66 TGAAGCACTATTCATCTTCTTCCCTAACCCTAAATCCCAAATCCCACCATTCATCCCCCTTCCAC
57923 TTCTTCAACCGAGACTATTCCTCTTCCCCTTC
131 TTCTTCAACCGAGACTATTCCTCTTCCCCTTC
* * * ***
57955 TGTTTGATCCTTACAAACACCAAACACATTTCCTCTACCTTTTTTTAAAGATTAAAAATGTCAAA
1 TGTTTGATCCTTACAAACACCAAACACATTTCCTCAACC-TGTTTTAAAGATCAAAAACCCCAAA
* * * * * *
58020 -TAGAAGTACTATTCATTTTCTTCCCTAACCCTAAATCCCAAATCCCACTATTTATTTCCCTTTC
65 CT-GAAGCACTATTCATCTTCTTCCCTAACCCTAAATCCCAAATCCCACCATTCA-TCCCCCTTC
* *
58084 CCCTTCTTCAACCGAGACTCTTCCT
128 CACTTCTTCAACCGAGACTATTCCT
58109 ATTCTAATTA
Statistics
Matches: 129, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
161 37 0.29
162 64 0.50
164 28 0.22
ACGTcount: A:0.28, C:0.33, G:0.06, T:0.34
Consensus pattern (162 bp):
TGTTTGATCCTTACAAACACCAAACACATTTCCTCAACCTGTTTTAAAGATCAAAAACCCCAAAC
TGAAGCACTATTCATCTTCTTCCCTAACCCTAAATCCCAAATCCCACCATTCATCCCCCTTCCAC
TTCTTCAACCGAGACTATTCCTCTTCCCCTTC
Found at i:58248 original size:3 final size:3
Alignment explanation
Indices: 58240--58265 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58230 TCCCCTCTCC
58240 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
58266 ATTCTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:60296 original size:22 final size:22
Alignment explanation
Indices: 60254--60294 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
60244 TTATTTATTT
*
60254 TAATTTATTTTATTATGTTTCA
1 TAATTTATATTATTATGTTTCA
*
60276 TAATTTA-ATTATTTTGTTT
1 TAATTTATATTATTATGTTT
60295 TCTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (22 bp):
TAATTTATATTATTATGTTTCA
Found at i:65002 original size:54 final size:54
Alignment explanation
Indices: 64915--65033 Score: 193
Period size: 54 Copynumber: 2.2 Consensus size: 54
64905 TGTAGCGCGA
* *
64915 AAATCGATTACTACAGCTTGGCGACTCAACTGGGAACAATGATGGTCAAGCCCT
1 AAATCGATTACGACAACTTGGCGACTCAACTGGGAACAATGATGGTCAAGCCCT
** *
64969 AAATCGATTACGACAACTTGGCGACTCCGCTGGGAACAATGATGGTCAAGCCTT
1 AAATCGATTACGACAACTTGGCGACTCAACTGGGAACAATGATGGTCAAGCCCT
65023 AAATCGATTAC
1 AAATCGATTAC
65034 ATATTGTCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (54 bp):
AAATCGATTACGACAACTTGGCGACTCAACTGGGAACAATGATGGTCAAGCCCT
Done.