Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006602.1 Hibiscus syriacus cultivar Beakdansim tig00016194_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: 79189
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2157 original size:21 final size:21
Alignment explanation
Indices: 2133--2192 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2123 AAACCTTCTG
2133 GTGGTGGCATCTGAAATGGTT
1 GTGGTGGCATCTGAAATGGTT
2154 GTGGTGGCATC-GAAAATGGTT
1 GTGGTGGCATCTG-AAATGGTT
** * *
2175 ACGGTGCCATTTGAAATG
1 GTGGTGGCATCTGAAATG
2193 ATAGCAATGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.30
Consensus pattern (21 bp):
GTGGTGGCATCTGAAATGGTT
Found at i:3924 original size:19 final size:18
Alignment explanation
Indices: 3896--3932 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3886 GTAATAAAAA
*
3896 ATAATGTAATAAAATAATT
1 ATAATATAATAAAA-AATT
3915 ATAATATAATAAAAAATT
1 ATAATATAATAAAAAATT
3933 TACTTCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAATATAATAAAAAATT
Found at i:3957 original size:21 final size:21
Alignment explanation
Indices: 3929--3968 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3919 TATAATAAAA
3929 AATTTACTT-CTAAAAATGAT
1 AATTTACTTACTAAAAATGAT
*
3949 AATTATACTTACTTAAAATG
1 AATT-TACTTACTAAAAATG
3969 TAACCCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
AATTTACTTACTAAAAATGAT
Found at i:5416 original size:687 final size:687
Alignment explanation
Indices: 4103--5464 Score: 2652
Period size: 687 Copynumber: 2.0 Consensus size: 687
4093 GATATATCCA
4103 AAACGATAGCAAATACATGTCACCAAACATAACCGAAAAACATATAGAGATATTCGTTCGTACAA
1 AAACGATAGCAAATACATGTCACCAAACATAACCGAAAAACATATAGAGATATTCGTTCGTACAA
*
4168 AATAAGTAGTAGATCTCTCCTGATGCCAAATCTGCTAGCTTATGATGTGCTGTTATCTGAAAAAG
66 AATAAGTAGTAGATCTCTCCTGATGCCAAATCTGCTAGCTTATGATCTGCTGTTATCTGAAAAAG
*
4233 GGGAAAACTACAGAATGAGCTAAAAAGCTCATTGTGTTCCATACAGTGTATATAAAAATATATTG
131 GGGAAAACTACAGAATGAGCTAAAAAGCTCATTGTGTTCCATACAGTGTATATAAAAACATATTG
4298 ATAAAAATATTCCAGTAAAGTCGGTTTATGCAATCATGTCGTTAAAAAAATATGAACACTACCCC
196 ATAAAAATATTCCAGTAAAGTCGGTTTATGCAATCATGTCGTTAAAAAAATATGAACACTACCCC
4363 CAGCCCATCACATCAGAATGTGTAGGTTCCCCAGAACCATACACCCAGCCCACACATCAAATAAG
261 CAGCCCATCACATCAGAATGTGTAGGTTCCCCAGAACCATACACCCAGCCCACACATCAAATAAG
4428 GCCCTGAGCACAAAGCCGAGGAACCTGCGGATATACTTCCTTCAACAATACCCCCCAATGATTGT
326 GCCCTGAGCACAAAGCCGAGGAACCTGCGGATATACTTCCTTCAACAATACCCCCCAATGATTGT
4493 TCATGAATGTATTTGAATGAAAACAATGATTAATTCTTTAAAACATAAAAGAGTTCATGCTTAAA
391 TCATGAATGTATTTGAATGAAAACAATGATTAATTCTTTAAAACATAAAAGAGTTCATGCTTAAA
*
4558 AATCATATATAGAAATACGGAAATCAGAAGACAAATCAGTAGTATACAGAATTTCAGACATCGGA
456 AATCATATATAGAAATACGGAAATCAGAAGACAAATCAGTAGTATACAGAATTTCAGACATCGAA
4623 CAATCAATATTCAAAACATCGGTATAAAATACCGTAACCAGAAATCATATCAGAAATACGCGATA
521 CAATCAATATTCAAAACATCGGTATAAAATACCGTAACCAGAAATCATATCAGAAATACGCGATA
4688 AATCAGATATCATATACATAATATTCAGATATATATTTTAAAACATAAATAATTAACACTGTCGG
586 AATCAGATATCATATACATAATATTCAGATATATATTTTAAAACATAAATAATTAACACTGTCGG
4753 GAAACACACCTGTAACAGTCTGAGAAATCAGATAGGG
651 GAAACACACCTGTAACAGTCTGAGAAATCAGATAGGG
4790 AAACGATAGCAAATACATGTCACCAAACATAACCGAAAAACATATAGAGATATTCGTTCGTACAA
1 AAACGATAGCAAATACATGTCACCAAACATAACCGAAAAACATATAGAGATATTCGTTCGTACAA
*
4855 AATAAGTAGTAGATCTCTCCTGATGCCAAATCTGCTAGCTTATGATCTGTTGTTATCTGAAAAAG
66 AATAAGTAGTAGATCTCTCCTGATGCCAAATCTGCTAGCTTATGATCTGCTGTTATCTGAAAAAG
*
4920 GGGAAAACTACAGAATGAGCTAAAAAGCTCATTGTGTTCCATACATTGTATATAAAAACATATTG
131 GGGAAAACTACAGAATGAGCTAAAAAGCTCATTGTGTTCCATACAGTGTATATAAAAACATATTG
4985 ATAAAAATATTCCAGTAAAGTCGGTTTATGCAATCATGTCGTTAAAAAAATATGAACACTACCCC
196 ATAAAAATATTCCAGTAAAGTCGGTTTATGCAATCATGTCGTTAAAAAAATATGAACACTACCCC
5050 CAGCCCATCACATCAGAATGTGTAGGTTCCCCAGAACCATACACCCAGCCCACACATCAAATAAG
261 CAGCCCATCACATCAGAATGTGTAGGTTCCCCAGAACCATACACCCAGCCCACACATCAAATAAG
5115 GCCCTGAGCACAAAGCCGAGGAACCTGCGGATATACTTCCTTCAACAATACCCCCCAATGATTGT
326 GCCCTGAGCACAAAGCCGAGGAACCTGCGGATATACTTCCTTCAACAATACCCCCCAATGATTGT
5180 TCATGAATGTATTTGAATGAAAACAATGATTAATTCTTTAAAACATAAAAGAGTTCATGCTTAAA
391 TCATGAATGTATTTGAATGAAAACAATGATTAATTCTTTAAAACATAAAAGAGTTCATGCTTAAA
*
5245 AATCATATATAGAAATACGGAAATTAGAAGACAAATCAGTAGTATACAGAATTTCAGACATCGAA
456 AATCATATATAGAAATACGGAAATCAGAAGACAAATCAGTAGTATACAGAATTTCAGACATCGAA
* *
5310 CAATCAATATTCAAAACATTGGTATAAAATACCGTAACCAGAAATCATATCAGAAATACGCGGTA
521 CAATCAATATTCAAAACATCGGTATAAAATACCGTAACCAGAAATCATATCAGAAATACGCGATA
5375 AATCAGATATCATATACATAATATTCAGATATATATTTTAAAACATAAATAATTAACACTGTCGG
586 AATCAGATATCATATACATAATATTCAGATATATATTTTAAAACATAAATAATTAACACTGTCGG
5440 GAAACACACCTGTAACAGTCTGAGA
651 GAAACACACCTGTAACAGTCTGAGA
5465 GTTCAAATAG
Statistics
Matches: 667, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
687 667 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (687 bp):
AAACGATAGCAAATACATGTCACCAAACATAACCGAAAAACATATAGAGATATTCGTTCGTACAA
AATAAGTAGTAGATCTCTCCTGATGCCAAATCTGCTAGCTTATGATCTGCTGTTATCTGAAAAAG
GGGAAAACTACAGAATGAGCTAAAAAGCTCATTGTGTTCCATACAGTGTATATAAAAACATATTG
ATAAAAATATTCCAGTAAAGTCGGTTTATGCAATCATGTCGTTAAAAAAATATGAACACTACCCC
CAGCCCATCACATCAGAATGTGTAGGTTCCCCAGAACCATACACCCAGCCCACACATCAAATAAG
GCCCTGAGCACAAAGCCGAGGAACCTGCGGATATACTTCCTTCAACAATACCCCCCAATGATTGT
TCATGAATGTATTTGAATGAAAACAATGATTAATTCTTTAAAACATAAAAGAGTTCATGCTTAAA
AATCATATATAGAAATACGGAAATCAGAAGACAAATCAGTAGTATACAGAATTTCAGACATCGAA
CAATCAATATTCAAAACATCGGTATAAAATACCGTAACCAGAAATCATATCAGAAATACGCGATA
AATCAGATATCATATACATAATATTCAGATATATATTTTAAAACATAAATAATTAACACTGTCGG
GAAACACACCTGTAACAGTCTGAGAAATCAGATAGGG
Found at i:6200 original size:28 final size:28
Alignment explanation
Indices: 6168--6221 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
6158 TAAAATGTAA
* *
6168 TTTTTTT-CAAAATTACGAAAATAACAT
1 TTTTTTTAAAAAATTACAAAAATAACAT
6195 TTTTTTTAAAAAATTACAAAAATAACA
1 TTTTTTTAAAAAATTACAAAAATAACA
6222 CCCTTTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (28 bp):
TTTTTTTAAAAAATTACAAAAATAACAT
Found at i:13275 original size:29 final size:30
Alignment explanation
Indices: 13233--13290 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
13223 TTATTTACAA
* *
13233 AATTACGAAAATAGCACCAT-TTTAAAATT
1 AATTACCAAAATAGCACCATGTTCAAAATT
*
13262 AATTACCAATATAGCACCATGTTCAAAAT
1 AATTACCAAAATAGCACCATGTTCAAAAT
13291 ATTTACTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
AATTACCAAAATAGCACCATGTTCAAAATT
Found at i:13343 original size:26 final size:25
Alignment explanation
Indices: 13308--13357 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13298 GAAATGTCAT
* * *
13308 TTTTTCAAAAATTACGAAAATAGCA
1 TTTTTAAAAAAATACAAAAATAGCA
13333 TTTTTAAAAAAATACAAAAATAGCA
1 TTTTTAAAAAAATACAAAAATAGCA
13358 CCCTTTTCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (25 bp):
TTTTTAAAAAAATACAAAAATAGCA
Found at i:14589 original size:29 final size:29
Alignment explanation
Indices: 14556--14611 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
14546 GCGCTTTATC
* *
14556 AGAAAATGTG-CTAGATCGATAATATTTGG
1 AGAAAAGGTGTCT-GATAGATAATATTTGG
*
14585 AGAAAGGGTGTCTGATAGATAATATTT
1 AGAAAAGGTGTCTGATAGATAATATTT
14612 CGTTGTTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (29 bp):
AGAAAAGGTGTCTGATAGATAATATTTGG
Found at i:15033 original size:33 final size:33
Alignment explanation
Indices: 14991--15056 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
14981 GGTGAGTTGG
14991 CATTCGGGTGTCT-TCTTCTTCTTCAGAATAATA
1 CATTCGGGTGT-TATCTTCTTCTTCAGAATAATA
15024 CATTCGGGTGTTATCTTCTTCTTCAGAATAATA
1 CATTCGGGTGTTATCTTCTTCTTCAGAATAATA
15057 GAGTCCATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (33 bp):
CATTCGGGTGTTATCTTCTTCTTCAGAATAATA
Found at i:15127 original size:3 final size:3
Alignment explanation
Indices: 15067--15113 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
15057 GAGTCCATGG
*
15067 CTT CTT CTT CTT CTT CTT CTT -TT C-T CTT CTT ATT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
15113 C
1 C
15114 CATTATTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:23410 original size:25 final size:26
Alignment explanation
Indices: 23365--23422 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
23355 TTAATTCTAT
23365 AAGACTTAAGAAGACTTCACTAGTAC
1 AAGACTTAAGAAGACTTCACTAGTAC
*
23391 AAGACTTAAG-AGACTTCACTAGTAT
1 AAGACTTAAGAAGACTTCACTAGTAC
23416 AA-ACTTA
1 AAGACTTA
23423 CCTCAACACG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 5 0.16
25 16 0.52
26 10 0.32
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (26 bp):
AAGACTTAAGAAGACTTCACTAGTAC
Found at i:24349 original size:15 final size:15
Alignment explanation
Indices: 24329--24363 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
24319 TTCTTCCCCG
*
24329 TAAAGAGGAGTTTTA
1 TAAAGAGGAGCTTTA
24344 TAAAGAGGAGCTTTA
1 TAAAGAGGAGCTTTA
24359 TAAAG
1 TAAAG
24364 TACAAACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.29
Consensus pattern (15 bp):
TAAAGAGGAGCTTTA
Found at i:24954 original size:31 final size:31
Alignment explanation
Indices: 24908--24991 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
24898 TTACTTGTAT
* *
24908 TTTATCAAAAT-TCTAATATGATACTTATAC
1 TTTAACAAAATATCTAATATGATACATATAC
* * * * *
24938 TTTGACAAACTATCTAATGTGGTACATATAT
1 TTTAACAAAATATCTAATATGATACATATAC
24969 TTTAACAAAATATAC-AATATGAT
1 TTTAACAAAATAT-CTAATATGAT
24992 GTTTGAACTA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 8 0.20
31 32 0.78
32 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTAACAAAATATCTAATATGATACATATAC
Found at i:27602 original size:20 final size:20
Alignment explanation
Indices: 27573--27622 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
27563 TTGGATAAGA
* *
27573 AGTATTGATATTGTTCTTAC
1 AGTATCGATAATGTTCTTAC
**
27593 AGTATCGATAATGTTCTTGT
1 AGTATCGATAATGTTCTTAC
27613 AGTATCGATA
1 AGTATCGATA
27623 CCCAAGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (20 bp):
AGTATCGATAATGTTCTTAC
Found at i:35982 original size:24 final size:24
Alignment explanation
Indices: 35952--35998 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
35942 CCACATTTTT
35952 TTATAAATATAGAGTAAATATAAA
1 TTATAAATATAGAGTAAATATAAA
*
35976 TTATAAATCTAGAGTAAATATAA
1 TTATAAATATAGAGTAAATATAA
35999 TGTAATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (24 bp):
TTATAAATATAGAGTAAATATAAA
Found at i:37233 original size:31 final size:31
Alignment explanation
Indices: 37191--37250 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
37181 AACTTAAAAG
* * *
37191 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
37222 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
37251 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:37818 original size:24 final size:27
Alignment explanation
Indices: 37759--37853 Score: 83
Period size: 24 Copynumber: 3.6 Consensus size: 27
37749 AATTATATGG
37759 TATAAAATTAAATATTTATAATATAATAT
1 TATAAAATT-AATA-TTATAATATAATAT
* *
37788 TAAAAAATTAATATT-TAAT-TTAT-T
1 TATAAAATTAATATTATAATATAATAT
* *
37812 TATAAAAGTAATATTAAAAT-TAATAT
1 TATAAAATTAATATTATAATATAATAT
*
37838 CTATAATA-TAATATTA
1 -TATAAAATTAATATTA
37854 AAAAATTCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
24 14 0.25
25 9 0.16
26 13 0.23
27 8 0.14
28 4 0.07
29 8 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
TATAAAATTAATATTATAATATAATAT
Found at i:37837 original size:64 final size:64
Alignment explanation
Indices: 37761--37921 Score: 225
Period size: 64 Copynumber: 2.5 Consensus size: 64
37751 TTATATGGTA
*
37761 TAAAATTAAATATTTATAATATAATATTAAAAAATTAATATTTAATTTATTTATAAAAGTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTA-AAAAGTAATAT
* *
37826 TAAAATT-AATATCTATAATATAATATTAAAAAATTCATATTTAATTTATTTAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAGTAATAT
* ** *
37889 TAAAATAAAAATAAAATATAATATAAAATTAAA
1 TAAAAT-TAAAT-ATCTATAATATAATATTAAA
37922 TATAAAACCT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
63 16 0.19
64 43 0.50
65 10 0.12
66 17 0.20
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (64 bp):
TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAGTAATAT
Found at i:37916 original size:17 final size:16
Alignment explanation
Indices: 37892--37926 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
37882 TTAATATTAA
37892 AATAAAAATAAAATAT
1 AATAAAAATAAAATAT
*
37908 AATATAAAATTAAATAT
1 AATA-AAAATAAAATAT
37925 AA
1 AA
37927 AACCTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATAAAATAT
Found at i:37923 original size:12 final size:11
Alignment explanation
Indices: 37878--37928 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
37868 AATTTATTTA
*
37878 AAAATTAATATT
1 AAAATAAATA-T
*
37890 AAAATAAAAAT
1 AAAATAAATAT
37901 AAAATATAATAT
1 AAAATA-AATAT
37913 AAAATTAAATAT
1 AAAA-TAAATAT
37925 AAAA
1 AAAA
37929 CCTCTTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.21
12 25 0.74
13 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:39239 original size:15 final size:15
Alignment explanation
Indices: 39184--39233 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
39174 GTTAAGCATC
*
39184 TAATTTAAAATTTTAA
1 TAATTAAAAATTTT-A
39200 TAGATAATAAAAATTTTA
1 TA-AT--TAAAAATTTTA
39218 TAATTAAAAATTTTA
1 TAATTAAAAATTTTA
39233 T
1 T
39234 TTTTAATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 12 0.40
16 2 0.07
17 4 0.13
18 3 0.10
19 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TAATTAAAAATTTTA
Found at i:41173 original size:20 final size:21
Alignment explanation
Indices: 41148--41188 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
41138 TTCTGAATCA
41148 GAAAG-TGGATTATGAAATGT
1 GAAAGATGGATTATGAAATGT
*
41168 GAAAGTATTGATTATGAAATG
1 GAAAG-ATGGATTATGAAATG
41189 AAATGTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (21 bp):
GAAAGATGGATTATGAAATGT
Found at i:41216 original size:27 final size:27
Alignment explanation
Indices: 41158--41219 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
41148 GAAAGTGGAT
*
41158 TATGAAATGTGAAAGTATTGATTATGA
1 TATGAAATGTGAAAGTATTGATAATGA
*
41185 AATGAAATGTGAAAGTCA-TGA-AATGTA
1 TATGAAATGTGAAAGT-ATTGATAATG-A
41212 TATGAAAT
1 TATGAAAT
41220 AAAAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 26 0.87
28 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (27 bp):
TATGAAATGTGAAAGTATTGATAATGA
Found at i:45532 original size:2 final size:2
Alignment explanation
Indices: 45527--45595 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
45517 TGTGTGTGTG
45527 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
45569 TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45596 AAGTTGCTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48968 original size:33 final size:33
Alignment explanation
Indices: 48931--49004 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
48921 TTTTATTTAG
48931 ATATTTTCAGTTGGCAACCGAAAATGTTATGAA
1 ATATTTTCAGTTGGCAACCGAAAATGTTATGAA
48964 ATATTTTCAGTTGGCAACCGAAAATGTTATGAA
1 ATATTTTCAGTTGGCAACCGAAAATGTTATGAA
*
48997 ACATTTTC
1 ATATTTTC
49005 GGTTCAACCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (33 bp):
ATATTTTCAGTTGGCAACCGAAAATGTTATGAA
Found at i:49023 original size:31 final size:32
Alignment explanation
Indices: 48933--49023 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
48923 TTATTTAGAT
*
48933 ATTTTCAGTTGGCAACCGAAAATGTTATGAAAT
1 ATTTTCAGTT-GCAACCGAAAATGTTATGAAAC
48966 ATTTTCAGTTGGCAACCGAAAATGTTATGAAAC
1 ATTTTCAGTT-GCAACCGAAAATGTTATGAAAC
*
48999 ATTTTCGGTT-CAACC-AAAACTGTTA
1 ATTTTCAGTTGCAACCGAAAA-TGTTA
49024 AAATATTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.07
31 10 0.18
33 41 0.75
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
ATTTTCAGTTGCAACCGAAAATGTTATGAAAC
Found at i:49941 original size:54 final size:53
Alignment explanation
Indices: 49883--49990 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 53
49873 TATAAAATGA
*
49883 TCATCTAACTATTTATTATGTTCTAGACTCATCATTTTTCGTTAAAAAAATTGG
1 TCATCAAACTATTTATTATGTTCTAGACTCATCATTTTTCGTT-AAAAAATTGG
** *
49937 TCATCAAACTATTTATTATGTTCTAGACTTGTCCTTTTTCGTTAAAAAATTGG
1 TCATCAAACTATTTATTATGTTCTAGACTCATCATTTTTCGTTAAAAAATTGG
49990 T
1 T
49991 GGTTTTTAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 11 0.22
54 39 0.78
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (53 bp):
TCATCAAACTATTTATTATGTTCTAGACTCATCATTTTTCGTTAAAAAATTGG
Found at i:53840 original size:20 final size:21
Alignment explanation
Indices: 53801--53840 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53791 TTATGGGTCG
*
53801 AGTATCGATACTAGGATGAAC
1 AGTACCGATACTAGGATGAAC
53822 AGTACCGATACTA-GATGAA
1 AGTACCGATACTAGGATGAA
53841 TTCAGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
AGTACCGATACTAGGATGAAC
Found at i:53895 original size:21 final size:19
Alignment explanation
Indices: 53861--53904 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
53851 ATTTTGGGTT
53861 TTCTAAGGGAGTATCAATA
1 TTCTAAGGGAGTATCAATA
* *
53880 CTTCTAGGGAGAGTATCGATA
1 -TTCTAAGG-GAGTATCAATA
53901 TTCT
1 TTCT
53905 CCTATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (19 bp):
TTCTAAGGGAGTATCAATA
Found at i:54853 original size:3 final size:3
Alignment explanation
Indices: 54845--54879 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54835 ATACCACTCA
54845 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
54880 CAAGTTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:62783 original size:15 final size:16
Alignment explanation
Indices: 62763--62792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62753 TAAAATTTTT
62763 TGTTTC-ATTTTAAAA
1 TGTTTCTATTTTAAAA
62778 TGTTTCTATTTTAAA
1 TGTTTCTATTTTAAA
62793 TTTAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (16 bp):
TGTTTCTATTTTAAAA
Found at i:62981 original size:15 final size:15
Alignment explanation
Indices: 62949--62977 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62939 CATAAATACT
62949 GTAAAACTAAACTAA
1 GTAAAACTAAACTAA
62964 GTAAAA-TAAACTAA
1 GTAAAACTAAACTAA
62978 AGTAGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (15 bp):
GTAAAACTAAACTAA
Found at i:67371 original size:4 final size:4
Alignment explanation
Indices: 67355--67393 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
67345 AGCAACAATA
*
67355 AATT AAAT AATT AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AAT
67394 AAGATAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:71977 original size:18 final size:19
Alignment explanation
Indices: 71899--72006 Score: 85
Period size: 20 Copynumber: 5.5 Consensus size: 19
71889 GTTTTCAATT
71899 TCGCAACACGAATATGTAAA
1 TCGCAACACGAAT-TGTAAA
*** *
71919 TCGCATTGCG-ATTTTCCAAA
1 TCGCAACACGAATTGT--AAA
*
71939 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACACGAAT-TGTAAA
*
71960 TCGCAACATGAA-TGTAAA
1 TCGCAACACGAATTGTAAA
*
71978 TCGCAACGCGAATTTGTAAA
1 TCGCAACACGAA-TTGTAAA
71998 TCGCAACAC
1 TCGCAACAC
72007 AGAAGTCAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
18 18 0.26
19 2 0.03
20 34 0.49
21 11 0.16
22 2 0.03
23 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (19 bp):
TCGCAACACGAATTGTAAA
Found at i:72021 original size:20 final size:19
Alignment explanation
Indices: 71998--72143 Score: 98
Period size: 20 Copynumber: 7.4 Consensus size: 19
71988 AATTTGTAAA
*
71998 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
72018 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
*
72038 CCGCAACGCGATAGTCAAAT
1 TCGCAACGCGA-AGTCAAAT
* * *
72058 CCGCAACACAAAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
* *
72078 TCACAACGCGGAATTTCAAAT
1 TCGCAACGC-GAA-GTCAAAT
** *
72099 TCGCAA-TTGAATTTCAAAT
1 TCGCAACGCGAA-GTCAAAT
* *
72118 TCGCAAC-TGAATTTCAAAT
1 TCGCAACGCGAA-GTCAAAT
72137 TCGCAAC
1 TCGCAAC
72144 TAGATTTTCG
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
19 38 0.35
20 59 0.54
21 12 0.11
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:72043 original size:40 final size:38
Alignment explanation
Indices: 71935--72064 Score: 140
Period size: 38 Copynumber: 3.3 Consensus size: 38
71925 TGCGATTTTC
*
71935 CAAATTCGCAACGCGAATCTGTAAATCGCAACATGAATGT
1 CAAATTCGCAACGCGAAT-TGTAAATCGCAACACGAA-GT
71975 -AAA-TCGCAACGCGAATTTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAA-TTGTAAATCGCAACAC-GAAGT
* *
72013 CAAATTCGCAACGCG-ATAGTCAAATCCGCAACGCGATAGT
1 CAAATTCGCAACGCGAATTGT-AAAT-CGCAACACGA-AGT
*
72053 CAAATCCGCAAC
1 CAAATTCGCAAC
72065 ACAAAAGTCA
Statistics
Matches: 79, Mismatches: 4, Indels: 14
0.81 0.04 0.14
Matches are distributed among these distances:
38 31 0.39
39 17 0.22
40 31 0.39
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (38 bp):
CAAATTCGCAACGCGAATTGTAAATCGCAACACGAAGT
Found at i:72136 original size:38 final size:40
Alignment explanation
Indices: 72072--72182 Score: 129
Period size: 39 Copynumber: 2.8 Consensus size: 40
72062 AACACAAAAG
* * *
72072 TCAAATTCACAACGCGGAATTTCAAATTCGCAA-TTGAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCGCAACTAGAATT
* *
72112 TCAAATTCGCAAC-TGAATTTCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACTAGAATT
* *
72151 TCGAATTCGCAACACGAATTT-AATTTCGCAAC
1 TCAAATTCGCAACACGAATTTCAAATTCGCAAC
72183 AGGTTTTAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 17 0.27
39 27 0.44
40 18 0.29
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (40 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACTAGAATT
Found at i:72157 original size:20 final size:19
Alignment explanation
Indices: 72088--72182 Score: 120
Period size: 19 Copynumber: 4.9 Consensus size: 19
72078 TCACAACGCG
*
72088 GAATTTCAAATTCGCAATT
1 GAATTTCAAATTCGCAACT
72107 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
72126 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* * *
72145 AGATTTTCGAATTCGCAACAC
1 -GAATTTCAAATTCGCAAC-T
*
72166 GAATTT-AATTTCGCAAC
1 GAATTTCAAATTCGCAAC
72183 AGGTTTTAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
19 46 0.69
20 21 0.31
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:72180 original size:19 final size:19
Alignment explanation
Indices: 72156--72202 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
72146 GATTTTCGAA
72156 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
72175 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
72193 TTCGCAACAC
1 TTCGCAACAC
72203 AAATGTTTTG
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:72374 original size:16 final size:15
Alignment explanation
Indices: 72339--72377 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
72329 TTCCCATCTC
*
72339 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
72354 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
72370 TAATTTTT
1 TAATTTTT
72378 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:72984 original size:12 final size:12
Alignment explanation
Indices: 72963--72996 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
72953 ACCACATTTC
*
72963 CAATACCAAACA
1 CAATATCAAACA
72975 CAATATCAAACA
1 CAATATCAAACA
*
72987 CAATCTCAAA
1 CAATATCAAA
72997 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:73137 original size:24 final size:24
Alignment explanation
Indices: 73108--73163 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
73098 GTGAGTACTA
**
73108 GTCAATATTCAAAATTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
* *
73132 GTCAATACCCAGACTTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
73156 GTCAATAC
1 GTCAATAC
73164 TCGGATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (24 bp):
GTCAATACCCAAAATTTGATCTTG
Found at i:73387 original size:23 final size:24
Alignment explanation
Indices: 73346--73391 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
73336 ATTCATATAA
73346 CCCTAAAGAAGAAGAAAAAGAAGT
1 CCCTAAAGAAGAAGAAAAAGAAGT
*
73370 CCCTGAAGAA-AAGAAAAAGAAG
1 CCCTAAAGAAGAAGAAAAAGAAG
73392 AAAATGCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.59, C:0.13, G:0.22, T:0.07
Consensus pattern (24 bp):
CCCTAAAGAAGAAGAAAAAGAAGT
Found at i:75451 original size:18 final size:18
Alignment explanation
Indices: 75413--75453 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
75403 AGCAAAAGGA
**
75413 AATCAAAATCAAAATTGC
1 AATCAAAATCAAAATCCC
75431 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
75449 AATCA
1 AATCA
75454 CAACAGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:75847 original size:20 final size:20
Alignment explanation
Indices: 75822--75870 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
75812 AAATCGCAAC
*
75822 GCGAATTTGACTTTCACGTT
1 GCGAATTTGACTTTCACATT
*
75842 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTCACATT
75862 GCGAATTTG
1 GCGAATTTG
75871 TACCTTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
GCGAATTTGACTTTCACATT
Found at i:76063 original size:68 final size:67
Alignment explanation
Indices: 75924--76068 Score: 226
Period size: 68 Copynumber: 2.2 Consensus size: 67
75914 AATTTAAAAC
75924 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATAATTCTTATTTACACATCAAC
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAATAATAATTCTTATTTACACATCAAC
75989 TTA
65 TTA
* *
75992 AACAAATCAACTTTTACAAATCAA-TAAACAAGC-AAAA-AATAATTCTTATTTCCTCATCAA-T
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAATAATAATTCTTATTTACACATCAACT
76053 TA
66 TA
*
76055 AACAAAACAACTTT
1 AACAAATCAACTTT
76069 CAATGTAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
63 16 0.22
64 21 0.28
65 4 0.05
67 9 0.12
68 24 0.32
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.29
Consensus pattern (67 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAATAATAATTCTTATTTACACATCAACT
TA
Found at i:77472 original size:21 final size:21
Alignment explanation
Indices: 77412--77474 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
77402 ATGAATCAGA
* * *
77412 CTCTTGAACGGCGGGCGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
77433 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
77454 CTCTTAAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
77475 TTTTACGATA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:77694 original size:4 final size:4
Alignment explanation
Indices: 77673--77713 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
77663 GGGCCGCTGA
* *
77673 AAAT AAAT TAAT ACAT AAAT AAA- AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
77714 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:77704 original size:19 final size:19
Alignment explanation
Indices: 77677--77713 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
77667 CGCTGAAAAT
* *
77677 AAATTAATACATAAATAAA
1 AAATAAATAAATAAATAAA
77696 AAATAAATAAATAAATAA
1 AAATAAATAAATAAATAA
77714 TGCCGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAATAAATAAATAAA
Done.