Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006471.1 Hibiscus syriacus cultivar Beakdansim tig00015681_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: 68217
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:10580 original size:138 final size:138
Alignment explanation
Indices: 10327--10735 Score: 714
Period size: 138 Copynumber: 3.0 Consensus size: 138
10317 AAGGTCAATT
10327 GACCTTTCTGGTTGCAAGAGTCTAGTGG-AGATCCCTAATCTATCAGGAGCCATCAAGCTTCAAA
1 GACCTTTCTGGTTGCAAGAGTCTAG-GGAAGATCCCTAATCTATCAGGAGCCATCAAGCTTCAAA
*
10391 GCCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACTTTCCCTCAACCAGTTGGAATCTCTT
65 GCCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGAATCTCTT
10456 GAAAGCCTC
130 GAAAGCCTC
* * *
10465 GACCTTTCTGGTTGCAAGAGTCTTGGGAAGATCCCTAATCTATCAGAAGCCATAAAGCTTCAAAG
1 GACCTTTCTGGTTGCAAGAGTCTAGGGAAGATCCCTAATCTATCAGGAGCCATCAAGCTTCAAAG
*
10530 CCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACCTTCCCTTAACCAGTTGGAATCTCTTG
66 CCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGAATCTCTTG
*
10595 AAAGCCTT
131 AAAGCCTC
* *
10603 GACCTTTCTGGTTGCAAGAGTCTGGGGAAGATCCCCAATCTATCAGGAGCCATCAAGCTTCAAAG
1 GACCTTTCTGGTTGCAAGAGTCTAGGGAAGATCCCTAATCTATCAGGAGCCATCAAGCTTCAAAG
*
10668 CCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGCATCTCTT-
66 CCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGAATCTCTTG
10732 AAAG
131 AAAG
10736 AGCTTGGTCT
Statistics
Matches: 258, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
137 6 0.02
138 252 0.98
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (138 bp):
GACCTTTCTGGTTGCAAGAGTCTAGGGAAGATCCCTAATCTATCAGGAGCCATCAAGCTTCAAAG
CCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGAATCTCTTG
AAAGCCTC
Found at i:12384 original size:26 final size:26
Alignment explanation
Indices: 12351--12457 Score: 196
Period size: 26 Copynumber: 4.1 Consensus size: 26
12341 ATATGATTTG
12351 GACTTCAAATATTAATGTCATCCTTT
1 GACTTCAAATATTAATGTCATCCTTT
12377 GACTTCAAATATTAATGTCATCCTTT
1 GACTTCAAATATTAATGTCATCCTTT
12403 GACTTCAAATATTAATGTCATCCTTT
1 GACTTCAAATATTAATGTCATCCTTT
*
12429 GACTTCAAATATTACAAGTCATCCTTT
1 GACTTCAAATATTA-ATGTCATCCTTT
12456 GA
1 GA
12458 AATGTTGTTT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
26 66 0.84
27 13 0.16
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (26 bp):
GACTTCAAATATTAATGTCATCCTTT
Found at i:14412 original size:8 final size:7
Alignment explanation
Indices: 14384--14409 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
14374 TATATATATA
14384 TTTTTAT
1 TTTTTAT
14391 TTTTTAT
1 TTTTTAT
14398 TTTTTAT
1 TTTTTAT
14405 TTTTT
1 TTTTT
14410 TATACGGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:15191 original size:91 final size:91
Alignment explanation
Indices: 15080--15274 Score: 284
Period size: 91 Copynumber: 2.1 Consensus size: 91
15070 TTAAATGATC
15080 TTATCTTTATAAAAACCTTTCTTCATAGAATTAAATGCAAAAATATTATTAA-AAAATGAAGCGT
1 TTATCTTTAT-AAAACCTTTCTTCATAGAATTAAATGCAAAAATATTA-TAAGAAAATGAAGCGT
* *
15144 AGTTTACCAAGCAAACTTGACAATGTTA
64 AGTTTACCAAGCAAACTTGACAAAGCTA
** * *
15172 TTATCTTTATAAAACCTTTCTTCATAGAATTAAATTTAGATATATTATAAGAAAATGAAGCGTAG
1 TTATCTTTATAAAACCTTTCTTCATAGAATTAAATGCAAAAATATTATAAGAAAATGAAGCGTAG
* * *
15237 TTTAGCAAGTAAACTTGACAAAGCTC
66 TTTACCAAGCAAACTTGACAAAGCTA
15263 TTATCTTTATAA
1 TTATCTTTATAA
15275 TAAGAATTAA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
90 3 0.03
91 80 0.86
92 10 0.11
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (91 bp):
TTATCTTTATAAAACCTTTCTTCATAGAATTAAATGCAAAAATATTATAAGAAAATGAAGCGTAG
TTTACCAAGCAAACTTGACAAAGCTA
Found at i:15437 original size:59 final size:59
Alignment explanation
Indices: 15322--15441 Score: 147
Period size: 59 Copynumber: 2.0 Consensus size: 59
15312 ACTTATTTCA
* * * *
15322 AATTGGTCCCTAAACTTTTAAGTGTTTCAATTTCATTCCTAAACTATGATTATCATTCT
1 AATTAGTCCCTAAACTTTTAAGTATTTCAATTTCATTCATAAACTATGAATATCATTCT
*
15381 AATTAGTCCTTAAACTTTTGAA-TATTTCAATTTCA-TCATCAAACTATGACAT-TCATTCT
1 AATTAGTCCCTAAACTTTT-AAGTATTTCAATTTCATTCAT-AAACTATGA-ATATCATTCT
15440 AA
1 AA
15442 ATTGATCCTC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
58 3 0.06
59 47 0.89
60 3 0.06
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (59 bp):
AATTAGTCCCTAAACTTTTAAGTATTTCAATTTCATTCATAAACTATGAATATCATTCT
Found at i:19053 original size:138 final size:137
Alignment explanation
Indices: 18790--19109 Score: 391
Period size: 138 Copynumber: 2.3 Consensus size: 137
18780 ACTGTGCAAA
*
18790 TTTGGTTGAACTACCTTGCCTCAACCATTTGGCT-TCTCTTGAAAAGCTTGGCCTTTCTGACTGC
1 TTTGGTTGAACTACCTTGCCTCAACCATTTGG-TATCTCTTG-AAAGCTTGACCTTTCTGACTGC
* * * * *
18854 AAGAGTCTAGTGGAGATTCCTAATCTATCAGGAGCCATCAACCTTCAAATCCTTTGCTGCAATGG
64 AAGAATCTAGTGAAGATTCCTAATCCATCAGGAGCCATCAACCTTCAAATCCTTAGCTGCAATGA
* *
18919 GTGTGGAAG
129 CTGTAGAAG
* * * *
18928 TTTGGTTGAACTACCTTCCCTCAACCAGTTGGTATCTCTTGAAAGCCTTGACCTTTCTTATTGCA
1 TTTGGTTGAACTACCTTGCCTCAACCATTTGGTATCTCTTGAAAG-CTTGACCTTTCTGACTGCA
*
18993 AGAATTTACG-GAAGATTCCTAATCCATTC-GGAGCCATCAACCTT-AAATCACTTAAG-TGCAA
65 AGAATCTA-GTGAAGATTCCTAATCCA-TCAGGAGCCATCAACCTTCAAATC-CTT-AGCTGCAA
* *
19054 TTACTGTATAAG
126 TGACTGTAGAAG
*
19066 TTTGGTTGAACTACCTTGCCTCAACCATTTGGCATCTCTT-AAAG
1 TTTGGTTGAACTACCTTGCCTCAACCATTTGGTATCTCTTGAAAG
19110 GGCTTGGGCT
Statistics
Matches: 158, Mismatches: 18, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
137 14 0.09
138 140 0.89
139 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (137 bp):
TTTGGTTGAACTACCTTGCCTCAACCATTTGGTATCTCTTGAAAGCTTGACCTTTCTGACTGCAA
GAATCTAGTGAAGATTCCTAATCCATCAGGAGCCATCAACCTTCAAATCCTTAGCTGCAATGACT
GTAGAAG
Found at i:21460 original size:13 final size:13
Alignment explanation
Indices: 21442--21515 Score: 85
Period size: 13 Copynumber: 5.3 Consensus size: 13
21432 GTCACAACCC
21442 GACCCGACCCGTT
1 GACCCGACCCGTT
21455 GACCCGACCCGTT
1 GACCCGACCCGTT
21468 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
*
21486 TACCCGACCCGTT
1 GACCCGACCCGTT
*
21499 GACCCGACCTGTT
1 GACCCGACCCGTT
21512 GACC
1 GACC
21516 GTTGACCCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
13 40 0.75
18 13 0.25
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:21461 original size:18 final size:18
Alignment explanation
Indices: 21455--21496 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
21445 CCGACCCGTT
21455 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
21473 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
21491 GACCCG
1 GACCCG
21497 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:21474 original size:31 final size:31
Alignment explanation
Indices: 21438--21507 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
21428 ACCGGTCACA
21438 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
*
21469 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
21500 ACCCGACC
1 ACCCGACC
21508 TGTTGACCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:22848 original size:18 final size:18
Alignment explanation
Indices: 22822--22857 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22812 TCGAAAGGAC
*
22822 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
22840 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
22858 CGGATGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:24029 original size:23 final size:24
Alignment explanation
Indices: 24002--24094 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 24
23992 CCGACTTTGA
* *
24002 ATTCTGTTATGAT-CCTGACTTGG
1 ATTCTGATATGATACTTGACTTGG
* *
24025 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACTTGG
* * *
24048 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACTTGG
24072 ATTCTGATATGATACTTGACTTG
1 ATTCTGATATGATACTTGACTTG
24095 AATTATGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 32 0.54
24 27 0.46
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACTTGG
Found at i:24072 original size:24 final size:24
Alignment explanation
Indices: 24017--24091 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
24007 GTTATGATCC
*
24017 TGACTTGGATTCTGATCTGATA-T
1 TGACATGGATTCTGATCTGATACT
*
24040 TGACATGGATTCTGATCTGATACA
1 TGACATGGATTCTGATCTGATACT
* *
24064 TGACCTGGATTCTGATATGATACT
1 TGACATGGATTCTGATCTGATACT
24088 TGAC
1 TGAC
24092 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
TGACATGGATTCTGATCTGATACT
Found at i:26295 original size:13 final size:13
Alignment explanation
Indices: 26277--26350 Score: 85
Period size: 13 Copynumber: 5.3 Consensus size: 13
26267 GTCACAACCC
26277 GACCCGACCCGTT
1 GACCCGACCCGTT
26290 GACCCGACCCGTT
1 GACCCGACCCGTT
26303 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
*
26321 TACCCGACCCGTT
1 GACCCGACCCGTT
*
26334 GACCCGACCTGTT
1 GACCCGACCCGTT
26347 GACC
1 GACC
26351 GTTGACCCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
13 40 0.75
18 13 0.25
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:26296 original size:18 final size:18
Alignment explanation
Indices: 26290--26331 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
26280 CCGACCCGTT
26290 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
26308 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
26326 GACCCG
1 GACCCG
26332 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:26309 original size:31 final size:31
Alignment explanation
Indices: 26273--26342 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
26263 ACCGGTCACA
26273 ACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
*
26304 ACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGTTG
26335 ACCCGACC
1 ACCCGACC
26343 TGTTGACCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (31 bp):
ACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:27685 original size:18 final size:18
Alignment explanation
Indices: 27659--27694 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27649 TCGAAAGGAC
*
27659 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
27677 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
27695 CGGATGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:28867 original size:23 final size:24
Alignment explanation
Indices: 28840--28932 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 24
28830 CCGACTTTGA
* *
28840 ATTCTGTTATGAT-CCTGACTTGG
1 ATTCTGATATGATACTTGACTTGG
* *
28863 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACTTGG
* * *
28886 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACTTGG
28910 ATTCTGATATGATACTTGACTTG
1 ATTCTGATATGATACTTGACTTG
28933 AATTATGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 32 0.54
24 27 0.46
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACTTGG
Found at i:28910 original size:24 final size:24
Alignment explanation
Indices: 28855--28929 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
28845 GTTATGATCC
*
28855 TGACTTGGATTCTGATCTGATA-T
1 TGACATGGATTCTGATCTGATACT
*
28878 TGACATGGATTCTGATCTGATACA
1 TGACATGGATTCTGATCTGATACT
* *
28902 TGACCTGGATTCTGATATGATACT
1 TGACATGGATTCTGATCTGATACT
28926 TGAC
1 TGAC
28930 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
TGACATGGATTCTGATCTGATACT
Found at i:30003 original size:91 final size:91
Alignment explanation
Indices: 29898--30113 Score: 249
Period size: 91 Copynumber: 2.4 Consensus size: 91
29888 TTTTTTATAC
* * **
29898 TTCTTCAT-GTAATTAAATGTAGAAATATTATAAAATAATGAAGTGTAATTTA-TTAGTAAACAT
1 TTCTTCATAG-AATTAAATGTAGAAATATTATAAAAAAAT-AAGCGTAATTTACCAAGTAAACAT
29961 GACAATAATATTATCTTTATAAAAACCT
64 GACAATAATATTATCTTTATAAAAACCT
* * *
29989 TTCTTCATAGAATTAAATGCA-AAATATTATTAAAAAAATAAGCGTAGTTTACCAAGTAAACTTG
1 TTCTTCATAGAATTAAATGTAGAAATATTA-TAAAAAAATAAGCGTAATTTACCAAGTAAACATG
** *
30053 ACAATGCTCTTATCTTTATAAAAACCT
65 ACAATAATATTATCTTTATAAAAACCT
* * * * *
30080 TTCTCCATAGAATTAGATCTAGAGATTTTATAAA
1 TTCTTCATAGAATTAAATGTAGAAATATTATAAA
30114 GAAAGGGTAA
Statistics
Matches: 105, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
90 18 0.17
91 80 0.76
92 7 0.07
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (91 bp):
TTCTTCATAGAATTAAATGTAGAAATATTATAAAAAAATAAGCGTAATTTACCAAGTAAACATGA
CAATAATATTATCTTTATAAAAACCT
Found at i:32156 original size:24 final size:24
Alignment explanation
Indices: 32129--32203 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
32119 TATATCAAAA
*
32129 ATCAAAACATAATCCAGATCAAGT
1 ATCAAAACAAAATCCAGATCAAGT
* * * *
32153 ATCAGATCAAAATCTAGGTCAAGT
1 ATCAAAACAAAATCCAGATCAAGT
* *
32177 ATCAGATAA-AAAATCGAGCTCAAGT
1 ATCA-A-AACAAAATCCAGATCAAGT
32202 AT
1 AT
32204 TCGATCAGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
24 23 0.57
25 16 0.40
26 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGATCAAGT
Found at i:32199 original size:25 final size:24
Alignment explanation
Indices: 32147--32203 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
32137 ATAATCCAGA
* * *
32147 TCAAGTATCAGATCAAAATCTAGG
1 TCAAGTATCAGATAAAAATCGAGC
32171 TCAAGTATCAGATAAAAAATCGAGC
1 TCAAGTATCAGAT-AAAAATCGAGC
32196 TCAAGTAT
1 TCAAGTAT
32204 TCGATCAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (24 bp):
TCAAGTATCAGATAAAAATCGAGC
Found at i:32223 original size:24 final size:25
Alignment explanation
Indices: 32147--32252 Score: 103
Period size: 24 Copynumber: 4.4 Consensus size: 25
32137 ATAATCCAGA
32147 TCAAGTA-TCAGATCAAAATCTAGG
1 TCAAGTATTCAGATCAAAATCTAGG
* * *
32171 TCAAGTA-TCAGATAAAAAATCGAGC
1 TCAAGTATTCAGAT-CAAAATCTAGG
*
32196 TCAAGTATTC-GATCAGAATCTAGG
1 TCAAGTATTCAGATCAAAATCTAGG
* * *
32220 TCAAGTA-TCCGATCAGAATCTAAG
1 TCAAGTATTCAGATCAAAATCTAGG
*
32244 TCAGGTATT
1 TCAAGTATT
32253 ATAATAGAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
23 2 0.03
24 46 0.67
25 19 0.28
26 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (25 bp):
TCAAGTATTCAGATCAAAATCTAGG
Found at i:36835 original size:24 final size:24
Alignment explanation
Indices: 36808--36883 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
36798 TATATCAAAA
*
36808 ATCAAAACATAATCCAGATCAAGT
1 ATCAAAACAAAATCCAGATCAAGT
* * *
36832 ATCAGATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGATCAAGT
* * *
36856 ATCAGATAAAAAAATCTAGGTCAAGT
1 ATCA-A-AACAAAATCCAGATCAAGT
36882 AT
1 AT
36884 TCGATCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 24 0.57
26 18 0.43
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGATCAAGT
Found at i:36898 original size:24 final size:24
Alignment explanation
Indices: 36818--36926 Score: 130
Period size: 24 Copynumber: 4.5 Consensus size: 24
36808 ATCAAAACAT
*
36818 AATCCAGATCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
36842 AATCCAGGTCAAGTATCAGATAAAAA
1 AATCCAGGTCAAGTATCAGAT--CAA
*
36868 AATCTAGGTCAAGTATTC-GATCAA
1 AATCCAGGTCAAGTA-TCAGATCAA
* * *
36892 AATCTAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAA
36916 AATCCAGGTCA
1 AATCCAGGTCA
36927 GATATTATAA
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
23 2 0.03
24 52 0.69
26 19 0.25
27 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:39794 original size:26 final size:26
Alignment explanation
Indices: 39763--39814 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
39753 ATACCAAAGG
*
39763 TAAAAATAAAATGAAATAAAACAAAA
1 TAAAAATAAAACGAAATAAAACAAAA
* * *
39789 TAAAAATAGAACGAGATAAAATAAAA
1 TAAAAATAAAACGAAATAAAACAAAA
39815 AATGTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (26 bp):
TAAAAATAAAACGAAATAAAACAAAA
Found at i:40595 original size:32 final size:31
Alignment explanation
Indices: 40507--40631 Score: 119
Period size: 32 Copynumber: 3.9 Consensus size: 31
40497 TTAGTTTGTG
* *
40507 CAATAAAATAAAATGTTAGTAAGTTAGTAATAA
1 CAAT-AAATAAAA-GTTAGTATGTTAGTAAGAA
* * *
40540 CAATAAA-AAAAATTAATATGTTAGTAAGAT
1 CAATAAATAAAAGTTAGTATGTTAGTAAGAA
*
40570 CAAATAAATAAAAGTTAGTATGTTAGCT-CGAA
1 C-AATAAATAAAAGTTAGTATGTTAG-TAAGAA
* *
40602 CAATAAAATAAAGGTTAGAATGTTAGTAAG
1 CAAT-AAATAAAAGTTAGTATGTTAGTAAG
40632 TTAGTGACTA
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
30 15 0.20
31 14 0.19
32 41 0.55
33 5 0.07
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (31 bp):
CAATAAATAAAAGTTAGTATGTTAGTAAGAA
Found at i:40604 original size:62 final size:65
Alignment explanation
Indices: 40512--40631 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 65
40502 TTGTGCAATA
*
40512 AAATAAAATGTTAGTAAGTTAGTAATAACAATAAAA-AAA-ATTA-ATATGTTAGTAAGATCAAA
1 AAATAAAATGTTAGTAAGTTAGTAAGAACAATAAAATAAAGATTAGA-ATGTTAGTAAGATCAAA
40574 T
65 T
* * *
40575 AAATAAAA-GTTAGTATGTTAGCT-CGAACAATAAAATAAAGGTTAGAATGTTAGTAAG
1 AAATAAAATGTTAGTAAGTTAG-TAAGAACAATAAAATAAAGATTAGAATGTTAGTAAG
40632 TTAGTGACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
62 22 0.45
63 12 0.24
64 14 0.29
65 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (65 bp):
AAATAAAATGTTAGTAAGTTAGTAAGAACAATAAAATAAAGATTAGAATGTTAGTAAGATCAAAT
Found at i:50944 original size:30 final size:30
Alignment explanation
Indices: 50910--51093 Score: 257
Period size: 30 Copynumber: 6.1 Consensus size: 30
50900 AAAATATTTA
* *
50910 TTTACTTACTATACATATAATGATCAATGT
1 TTTACTTATTATACATATAATGACCAATGT
50940 TTTACTTATTATACATATAATGACCAATGT
1 TTTACTTATTATACATATAATGACCAATGT
50970 TTTACTTATTATACATATAATGACCAATGT
1 TTTACTTATTATACATATAATGACCAATGT
** ** *
51000 TTTAGGGTA-TA-ACATGGAATCTACTCAA-GT
1 TTTA-CTTATTATACATATAAT-GAC-CAATGT
51030 TTTACTTATTATACATATAATGACCAATGT
1 TTTACTTATTATACATATAATGACCAATGT
51060 TTTACTTATTATACATATAATGACCAATGT
1 TTTACTTATTATACATATAATGACCAATGT
51090 TTTA
1 TTTA
51094 GGGTATAACA
Statistics
Matches: 136, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
29 12 0.09
30 112 0.82
31 12 0.09
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (30 bp):
TTTACTTATTATACATATAATGACCAATGT
Found at i:51091 original size:90 final size:90
Alignment explanation
Indices: 50933--51125 Score: 377
Period size: 90 Copynumber: 2.1 Consensus size: 90
50923 CATATAATGA
50933 TCAATGTTTTACTTATTATACATATAATGACCAATGTTTTACTTATTATACATATAATGACCAAT
1 TCAA-GTTTTACTTATTATACATATAATGACCAATGTTTTACTTATTATACATATAATGACCAAT
50998 GTTTTAGGGTATAACATGGAATCTAC
65 GTTTTAGGGTATAACATGGAATCTAC
51024 TCAAGTTTTACTTATTATACATATAATGACCAATGTTTTACTTATTATACATATAATGACCAATG
1 TCAAGTTTTACTTATTATACATATAATGACCAATGTTTTACTTATTATACATATAATGACCAATG
51089 TTTTAGGGTATAACATGGAATCTAC
66 TTTTAGGGTATAACATGGAATCTAC
51114 TCAAGTTTTACT
1 TCAAGTTTTACT
51126 GTCTAAAACT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 98 0.96
91 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (90 bp):
TCAAGTTTTACTTATTATACATATAATGACCAATGTTTTACTTATTATACATATAATGACCAATG
TTTTAGGGTATAACATGGAATCTAC
Found at i:51903 original size:138 final size:138
Alignment explanation
Indices: 51652--51920 Score: 375
Period size: 138 Copynumber: 1.9 Consensus size: 138
51642 TTAAGGTCAA
* * *
51652 TTGACCTTTCTGGTTGCAAGAGTCTTGTGGAGATCCCTAATCTATCAGGAGCCATCAATCTTCAA
1 TTGACCTTTCTGATTGCAAGAGTCTAGTGGAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* **
51717 AGCCTTTGCTGCAATGGGTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGG-TATCTC
66 AGCCTTAGCTGCAATGACTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGCT-TCTC
51781 TTGAAAGCC
130 TTGAAAGCC
*
51790 TTGACCTTTCTTATTGCAAGAGTCTAGTGGAGATCCCTAATCTATCAGGAGCCATCAACCTT-AA
1 TTGACCTTTCTGATTGCAAGAGTCTAGTGGAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
* * * *
51854 ATCACTTAAG-TGCAATTACTGT-ATAAGTTTGGTTGAACTACCTTGCCTCAACCATTTGGCTTC
66 AGC-CTT-AGCTGCAATGACTGTGA-AAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGCTTC
51917 TCTT
128 TCTT
51921 ACAGAGCTTG
Statistics
Matches: 116, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
137 5 0.04
138 109 0.94
139 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (138 bp):
TTGACCTTTCTGATTGCAAGAGTCTAGTGGAGATCCCTAATCTATCAGGAGCCATCAACCTTCAA
AGCCTTAGCTGCAATGACTGTGAAAGTTTGGTTGAACTACCTTCCCTCAACCAGTTGGCTTCTCT
TGAAAGCC
Found at i:53314 original size:3 final size:3
Alignment explanation
Indices: 53306--53362 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
53296 TTGTTCGGAT
53306 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53354 TTA TTA TTA
1 TTA TTA TTA
53363 CAGGCCAAGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53825 original size:2 final size:2
Alignment explanation
Indices: 53818--53852 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53808 TTTCATTTTC
53818 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 A
53853 AAAGAAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54026 original size:6 final size:6
Alignment explanation
Indices: 54008--54038 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
53998 GACACGTATT
*
54008 ACCACG ACAACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
54039 GACGGCGGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.39, C:0.45, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:54708 original size:40 final size:40
Alignment explanation
Indices: 54630--54846 Score: 344
Period size: 40 Copynumber: 5.3 Consensus size: 40
54620 TGCGATTTTG
*
54630 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
54672 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
* *
54712 GACTATCGCAACGAATTTGGAATAAATCACAACGCAAACTTC
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
**
54754 GACTATCATAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
54794 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
*
54834 GATTATCGCAACG
1 GACTATCGCAACG
54847 CGAACTTGGA
Statistics
Matches: 163, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
40 105 0.64
41 3 0.02
42 55 0.34
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
Found at i:54871 original size:82 final size:82
Alignment explanation
Indices: 54630--54846 Score: 375
Period size: 82 Copynumber: 2.7 Consensus size: 82
54620 TGCGATTTTG
54630 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
54695 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
* **
54712 GACTATCGCAACGAATTTGGAATAAATCACAACGCAAACTTCGACTATCATAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
54777 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
* *
54794 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGATTATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACG
54847 CGAACTTGGA
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
80 27 0.21
81 1 0.01
82 99 0.78
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
ATCGCAACGCGAACTTC
Found at i:54905 original size:21 final size:21
Alignment explanation
Indices: 54880--54932 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
54870 AATATGTAAA
54880 TCGCGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
54901 TCGCGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
54922 TCGCGTTGCGA
1 TCGCGTTGCGA
54933 ATCTGGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:55011 original size:19 final size:19
Alignment explanation
Indices: 54960--55014 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
54950 CGATACCGGA
* *
54960 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGATTTATC
54979 GATCGCATTGCGATTTATC
1 GATCGCATTGCGATTTATC
54998 GATCGCATTGCGATTTA
1 GATCGCATTGCGATTTA
55015 GTTGGTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (19 bp):
GATCGCATTGCGATTTATC
Found at i:55474 original size:49 final size:49
Alignment explanation
Indices: 55421--55516 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
55411 TGATTAGATA
*
55421 AAACCAATTAATAACTTCGTTTTTAAACAATATAGGGTGATTATAATGT
1 AAACCAATTAATAACTTCGTTTTTAAACAATATAGAGTGATTATAATGT
*
55470 AAACCAATTAATAACTTCGTTTTTAAATAATATAGAGTGATTATAAT
1 AAACCAATTAATAACTTCGTTTTTAAACAATATAGAGTGATTATAAT
55517 ATAGCATGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (49 bp):
AAACCAATTAATAACTTCGTTTTTAAACAATATAGAGTGATTATAATGT
Found at i:57634 original size:26 final size:26
Alignment explanation
Indices: 57598--57647 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
57588 TGGTGGAACT
57598 GAATTTGAAAAAAATATTAAATTCAA
1 GAATTTGAAAAAAATATTAAATTCAA
**
57624 GAATTTGAAAACGATATTAAATTC
1 GAATTTGAAAAAAATATTAAATTC
57648 GAGTTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (26 bp):
GAATTTGAAAAAAATATTAAATTCAA
Found at i:57654 original size:24 final size:25
Alignment explanation
Indices: 57598--57662 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
57588 TGGTGGAACT
57598 GAATTTGAAAAAAATATTAAATTCAA
1 GAATTTGAAAAAAATATTAAATTC-A
**
57624 GAATTTGAAAACGATATTAAATTC-
1 GAATTTGAAAAAAATATTAAATTCA
* *
57648 GAGTTTGAACAAAAT
1 GAATTTGAAAAAAAT
57663 CTGTGTCGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 11 0.33
26 22 0.67
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (25 bp):
GAATTTGAAAAAAATATTAAATTCA
Found at i:60838 original size:2 final size:2
Alignment explanation
Indices: 60826--60873 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
60816 AAAAATTGCA
* * *
60826 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60867 AT AT AT A
1 AT AT AT A
60874 ACTTAGATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:62945 original size:83 final size:82
Alignment explanation
Indices: 62787--62983 Score: 233
Period size: 83 Copynumber: 2.4 Consensus size: 82
62777 TGTGCCAACA
*
62787 GTATCGATACT-GACCCCTTGGGTATCGATACTCATCTGAGTATTGATACCAAATTGGGCTTCGA
1 GTATCGATACTCGACCCC-TGGGTATCGATACTCATCTGAGTATTGATACCAAATTGGACTTCGA
62851 TGTTTTGAAAAATACCT-T
65 TGTTTTGAAAAA-ACCTCT
* ** *
62869 GGTATCGATACTCTACCCCTGGGTATCGATACTC-TCGTGAGTATTGATACCGGATTTGACTTCG
1 -GTATCGATACTCGACCCCTGGGTATCGATACTCATC-TGAGTATTGATACCAAATTGGACTTCG
*
62933 ATGTTTCT-AAAAAGCCTCT
64 ATGTTT-TGAAAAAACCTCT
* *
62952 GTATCGATAC-CGACCCTCTGAGTATTGATACT
1 GTATCGATACTCGACCC-CTGGGTATCGATACT
62984 GGGCCCCGAG
Statistics
Matches: 100, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
81 5 0.05
82 28 0.28
83 61 0.61
84 6 0.06
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (82 bp):
GTATCGATACTCGACCCCTGGGTATCGATACTCATCTGAGTATTGATACCAAATTGGACTTCGAT
GTTTTGAAAAAACCTCT
Found at i:62981 original size:21 final size:19
Alignment explanation
Indices: 62952--63003 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
62942 AAAAGCCTCT
*
62952 GTATCGATACCGACCCTCTGA
1 GTATTGATACCGACCC-C-GA
* *
62973 GTATTGATACTGGGCCCCGA
1 GTATTGATAC-CGACCCCGA
62993 GTATTGATACC
1 GTATTGATACC
63004 CCTGCATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 12 0.46
21 10 0.38
22 4 0.15
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (19 bp):
GTATTGATACCGACCCCGA
Done.