Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003136.1 Hibiscus syriacus cultivar Beakdansim tig00006581_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: 56667
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:2294 original size:31 final size:32
Alignment explanation
Indices: 2242--2302 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
2232 TTTGATATTG
2242 ATTTTAATATTCAATGTGATACTT-AATTTTC
1 ATTTTAATATTCAATGTGATACTTGAATTTTC
2273 ATTTTAATA-TCTAAT-TAGATACTTGAATTT
1 ATTTTAATATTC-AATGT-GATACTTGAATTT
2303 AACTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 19 0.70
32 5 0.19
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (32 bp):
ATTTTAATATTCAATGTGATACTTGAATTTTC
Found at i:2734 original size:16 final size:16
Alignment explanation
Indices: 2710--2757 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
2700 TATAAATTAA
*
2710 ATTAATGATGCTCATC
1 ATTAGTGATGCTCATC
*
2726 ATTAGTGATGCTCGTC
1 ATTAGTGATGCTCATC
*
2742 ATTAGTGGTGCTCATC
1 ATTAGTGATGCTCATC
2758 GCTGCTCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (16 bp):
ATTAGTGATGCTCATC
Found at i:3319 original size:26 final size:26
Alignment explanation
Indices: 3285--3339 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
3275 TTAATATTTT
* *
3285 CCTTCTAAAATTTTATAAATTCAC-C
1 CCTTCTAAAAATTTAGAAATTCACTC
3310 CCTTCCTAAAAATTTAGAAATTCACTC
1 CCTT-CTAAAAATTTAGAAATTCACTC
3337 CCT
1 CCT
3340 CTGTGTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (26 bp):
CCTTCTAAAAATTTAGAAATTCACTC
Found at i:7722 original size:23 final size:24
Alignment explanation
Indices: 7677--7722 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
7667 CGTAAGTTAC
*
7677 CAAATGACAGAGAAAAATATGTCT
1 CAAATGACAGAGAAAAACATGTCT
* *
7701 CAAA-GACAGAGATAAACGTGTC
1 CAAATGACAGAGAAAAACATGTC
7723 ATAAAGCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (24 bp):
CAAATGACAGAGAAAAACATGTCT
Found at i:10072 original size:22 final size:23
Alignment explanation
Indices: 10026--10074 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
10016 CGTATAAGTA
10026 TAAATTAGTTAAAAATTTAAAGG
1 TAAATTAGTTAAAAATTTAAAGG
*
10049 TAAATTA-TTTAAAA-TTAAAGGG
1 TAAATTAGTTAAAAATTTAAA-GG
10071 TAAA
1 TAAA
10075 CTATATTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 5 0.21
22 12 0.50
23 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (23 bp):
TAAATTAGTTAAAAATTTAAAGG
Found at i:10824 original size:22 final size:22
Alignment explanation
Indices: 10796--10847 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
10786 GATCAGTGCT
10796 ATAATTTACCATTT-AATTTTAA
1 ATAATTTACC-TTTAAATTTTAA
10818 ATAATTTACCTTTAAATTTTAA
1 ATAATTTACCTTTAAATTTTAA
*
10840 CTAATTTA
1 ATAATTTA
10848 TAATTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTTACCTTTAAATTTTAA
Found at i:11789 original size:17 final size:16
Alignment explanation
Indices: 11763--11807 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
11753 AGAGAAAAAG
*
11763 ATAATAAAAATATATAA
1 ATAATTAAAATATAT-A
*
11780 ATAATTAAAATATATG
1 ATAATTAAAATATATA
11796 ATAATTTAAAAT
1 ATAA-TTAAAAT
11808 TTTTAATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
ATAATTAAAATATATA
Found at i:13177 original size:152 final size:143
Alignment explanation
Indices: 13045--13311 Score: 315
Period size: 142 Copynumber: 1.8 Consensus size: 143
13035 TTCCTATTTA
*
13045 AAATTTTAATTT-TATATAATTACTTTTAAGAAAAATAATCATATTTTAATATTTATTT-TTAAT
1 AAATATTAATTTAT-TATAATTA-TTTTAAGAAAAAT-AT--TATTTTAATATTTATTTATT--T
* * *
13108 ATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATTCTTAAATAAATAATAT
59 -TTAAGAAAAGAGATGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAATAAATAATAT
**
13173 -CATATTTTTATAAATTATAT
123 ACATATTAATATAAATTATAT
* * * * *
13193 ATATATTAATTTATTTTAATTATTTTTAGAAAGATGTTATTTTAATATTTATTTATTTTTAAGAA
1 AAATATTAATTTATTATAATTATTTTAAGAAAAATATTATTTTAATATTTATTTATTTTTAAGAA
* * *
13258 AAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTGATATTTTTAAATAAATAA
66 AAGAGATGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAATAAATAA
13312 ATATTTTATT
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
142 55 0.52
143 1 0.01
144 17 0.16
145 2 0.02
146 1 0.01
147 11 0.10
148 17 0.16
149 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (143 bp):
AAATATTAATTTATTATAATTATTTTAAGAAAAATATTATTTTAATATTTATTTATTTTTAAGAA
AAGAGATGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTCTTAAATAAATAATATACATATTA
ATATAAATTATAT
Found at i:13291 original size:142 final size:141
Alignment explanation
Indices: 13086--13342 Score: 367
Period size: 142 Copynumber: 1.8 Consensus size: 141
13076 AAAATAATCA
* * *
13086 TATTTTAATATTTATTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCCTTTTCT
1 TATTTTAATATTTATTTTT-ATATTAAGAAAAGAGATGTCTTAAAGCACCTAGAAGTCATTTTCT
*
13151 GATATTCTTAAATAAATAATATCATATT-TTTATAAATTATATATATATTAATTTATTTTAATTA
65 GATATTCTTAAATAAATAA-AT-ATATTATTTATAAA-TATATATAAATTAATTTATTTTAATTA
13215 TTTTTAGAAAGATGT
127 TTTTTAGAAAGATGT
* *
13230 TATTTTAATATTTATTTATT-T-TTAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCT
1 TATTTTAATATTTATTT-TTATATTAAGAAAAGAGATGTCTTAAAGCACCTAGAAGTCATTTTCT
* * *
13293 GATATTTTTAAATAAATAAATATTTTATTTATAAATATGTATAAATTAAT
65 GATATTCTTAAATAAATAAATATATTATTTATAAATATATATAAATTAAT
13343 AGATTTTCTT
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
140 17 0.17
141 10 0.10
142 55 0.54
143 1 0.01
144 17 0.17
145 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (141 bp):
TATTTTAATATTTATTTTTATATTAAGAAAAGAGATGTCTTAAAGCACCTAGAAGTCATTTTCTG
ATATTCTTAAATAAATAAATATATTATTTATAAATATATATAAATTAATTTATTTTAATTATTTT
TAGAAAGATGT
Found at i:15525 original size:12 final size:13
Alignment explanation
Indices: 15508--15536 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15498 ACATTCACAT
15508 ATTTACA-TTTGC
1 ATTTACATTTTGC
15520 ATTTACATTTTGC
1 ATTTACATTTTGC
15533 ATTT
1 ATTT
15537 TTACGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:17658 original size:2 final size:2
Alignment explanation
Indices: 17651--17680 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17641 TTATCCTTTA
17651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17681 CCTTTATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18012 original size:25 final size:26
Alignment explanation
Indices: 17977--18030 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
17967 TCCAGCAAAG
*
17977 AAAGAAGAAGGAAAAAAAGAAAAA-A
1 AAAGAAAAAGGAAAAAAAGAAAAATA
*
18002 AAAGAAAAAGGAAAAAAATAAAAATA
1 AAAGAAAAAGGAAAAAAAGAAAAATA
18028 AAA
1 AAA
18031 ATAAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (26 bp):
AAAGAAAAAGGAAAAAAAGAAAAATA
Found at i:18059 original size:33 final size:34
Alignment explanation
Indices: 17984--18059 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
17974 AAGAAAGAAG
* *
17984 AAGGAAAAAAAGAAAAAAAAAGAAAAAGGAAAAA
1 AAGGAAAATAAGAAAAAAAAACAAAAAGGAAAAA
** *
18018 AATAAAAATAA-AAATAAAAACAAAAAGGAAAAA
1 AAGGAAAATAAGAAAAAAAAACAAAAAGGAAAAA
18051 AAGGAAAAT
1 AAGGAAAAT
18060 TGAATCAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.05
Consensus pattern (34 bp):
AAGGAAAATAAGAAAAAAAAACAAAAAGGAAAAA
Found at i:23031 original size:22 final size:22
Alignment explanation
Indices: 23003--23081 Score: 149
Period size: 22 Copynumber: 3.6 Consensus size: 22
22993 ACATCTACAT
23003 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
23025 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
23047 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
23069 TTTTCAAAGATGA
1 TCTTCAAAGATGA
23082 AAACTTTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:23848 original size:113 final size:113
Alignment explanation
Indices: 23633--24403 Score: 1102
Period size: 113 Copynumber: 6.8 Consensus size: 113
23623 ATAGATCAGC
* * *
23633 ATCAACATTTCCAGA-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCA
1 ATCAGCATTTCCAGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
23697 TAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCATTCGATGG
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
* * *
23746 ATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCA
1 ATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * *
23810 TAATGAGAAGAACTTATTCAACTTTTTGCTCGAATTCATCATTCGATGG
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
* * *
23859 ATCAACATTACCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AAGGAAGTTC
1 ATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-GAAGTTC
* * *
23922 ATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGG
64 ATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
* * *
23972 ATCATCATTTCTAGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
24037 AATGAGAAGAGCTTGTTCAACCTTTTGCTTAAATCCATCACTT-GATGG
66 AATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCA-TTCGATGG
* *
24085 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
24150 AATGAAAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGG
66 AATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
* * * * *
24198 ATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCAT
1 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
24263 AATGAAAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGG
66 AATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
* * *
24311 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAAAAGAAGTTCAT
1 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
24376 AATAAGAAGAGCTTGTTCAACCTTTTGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGC
24404 ATAACTCTAT
Statistics
Matches: 615, Mismatches: 36, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
112 3 0.00
113 606 0.99
114 6 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (113 bp):
ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
Found at i:24178 original size:339 final size:339
Alignment explanation
Indices: 23526--24403 Score: 1158
Period size: 339 Copynumber: 2.6 Consensus size: 339
23516 AAAAGAAGAA
* *
23526 AGAGTTCATAATGAGAAGAACTCATCTGAAG-AGTAAGAAGAAGTTCATAATGAGAAGACCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
23590 TCAACCTTTTGCTCG-ACTCTATCGCAGAAAGAGATAGATCAGCATCAACATTTCCAGA-AGGAG
66 TCAACCTTTTGCTCGAATTC-AT--C------A-ATCGAT--GGATCAACATTTCCAGAGA-AAG
* *
23653 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAA
118 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAA
* * * *
23718 CTTTTTGCTCGAATTCATCATTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAAC
183 CCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTGCCAGGTAAAGTTCATAATGAGAAGAAC
* * * * * *
23783 TCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTATTCAACTTTTTGCTCGAATTCA
248 CCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAACTTATTCAACCTTTTGCTCAAATCCA
*
23848 TCATTCGATGGATCAACATTACCAG-G
313 TCACTCGATGGATCAACATTACCAGAG
23874 TAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AAGGAAGTTCATAATGAGAAGAACTT
1 -AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-GAAGTTCATAATGAGAAGAACTT
* * * *
23938 GTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCATCATTTCTAGAGAAAATTCATAATGAG
64 GTTCAACCTTTTGCTCGAATTCATCAATCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAG
*
24003 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTTA
129 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCA
* *
24068 AATCCATCACTT-GATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACCCATCTGAA
194 AATCCATCA-TTCGATGGATCAGCATTGCCAG-GTAAAGTTCATAATGAGAAGAACCCATCTGAA
* *
24131 GAAGGAAGAAGAAGTTCATAATGAAAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGAT
257 GAAGGAAGAAGAAGTTCATAATGAAAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTCGAT
* * *
24196 GGATCAACTTTTCTAGAG
322 GGATCAACATTACCAGAG
* * * * *
24214 AAAGTTCATAATGAGAAGAACTTATCTGAAGAATGAAGAAGAAGTTCATAATGAAAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * *
24279 TCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
66 TCAACCTTTTGCTCGAATTCATCAATCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAA
* * *
24344 GAACTTATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTTGC
131 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
24404 ATAACTCTAT
Statistics
Matches: 475, Mismatches: 46, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
339 381 0.80
340 7 0.01
341 4 0.01
342 1 0.00
348 1 0.00
349 33 0.07
350 45 0.09
351 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (339 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTCGAATTCATCAATCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAA
GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
TCCATCATTCGATGGATCAGCATTGCCAGGTAAAGTTCATAATGAGAAGAACCCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAAAAGAACTTATTCAACCTTTTGCTCAAATCCATCACTCGATGGAT
CAACATTACCAGAG
Found at i:24609 original size:39 final size:39
Alignment explanation
Indices: 24566--24707 Score: 207
Period size: 39 Copynumber: 3.6 Consensus size: 39
24556 ATCCCCAGTG
*
24566 GAAG-AGTTCATAATGAGAAAAACTCATCTGAAGAATGAA
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAA
* *
24605 GAAGAAATTCATAATGAGAAGAACTCATCTAAAGAAGAA
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
* *
24644 GAATAAGTTCATAATGAGAAGAACTCATCTTG-AGAGGAA
1 GAAGAAGTTCATAATGAGAAGAACTCATC-TGAAGAAGAA
24683 GAAGAAGTTCATAATGAGAAGAACT
1 GAAGAAGTTCATAATGAGAAGAACT
24708 TGTTTGACCT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
39 64 0.69
40 29 0.31
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.20
Consensus pattern (39 bp):
GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
Found at i:24618 original size:121 final size:121
Alignment explanation
Indices: 24328--24629 Score: 314
Period size: 121 Copynumber: 2.5 Consensus size: 121
24318 TTTCCAGAGA
* * * *
24328 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAAAACTCATCTGAAGAA-GAAGAAGAA-TTCATAATAAGAAGAACTTGTT
* * * *
24393 CAACCTTTTGCATAACTCTATCACAGAAGGATATATATCATCATCAGCATTTCCAGAAG
64 CAACCTTTTACATAACTCTATCACAGAAGGAGATATATCATCATCACCATGT-CAGAAG
* *
24452 AAGTTCATAATGAGAAAAACTCATCTGACGAAGAAGAAG--TTCATAATTAGAAGAACTTGTTCA
1 AAGTTCATAATGAGAAAAACTCATCTGAAGAAGAAGAAGAATTCATAATAAGAAGAACTTGTTC-
* * ** * *
24515 AACTTTTTAC-TAGATTAC-ATCACAGAAGGAGATGA-ATTGTCATCCCCA-GT-GGAAG
65 AACCTTTTACATA-ACT-CTATCACAGAAGGAGAT-ATATCATCATCACCATGTCAGAAG
*
24570 -AGTTCATAATGAGAAAAACTCATCTGAAGAATGAAGAAGAAATTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAAAACTCATCTGAAGAA-GAAGAAG-AATTCATAATAAGAAGAACT
24630 CATCTAAAGA
Statistics
Matches: 152, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
117 30 0.20
118 11 0.07
120 24 0.16
121 50 0.33
122 2 0.01
123 6 0.04
124 29 0.19
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (121 bp):
AAGTTCATAATGAGAAAAACTCATCTGAAGAAGAAGAAGAATTCATAATAAGAAGAACTTGTTCA
ACCTTTTACATAACTCTATCACAGAAGGAGATATATCATCATCACCATGTCAGAAG
Found at i:39322 original size:6 final size:6
Alignment explanation
Indices: 39313--39351 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
39303 AAAAATGAAA
* * *
39313 AAAAGT AAAAGC AAAAGT AAAAGG AAAAGG AAAAGT AAA
1 AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAA
39352 GAAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.03, G:0.21, T:0.08
Consensus pattern (6 bp):
AAAAGT
Found at i:39334 original size:18 final size:18
Alignment explanation
Indices: 39313--39351 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
39303 AAAAATGAAA
*
39313 AAAAGTAAAAGCAAAAGT
1 AAAAGGAAAAGCAAAAGT
*
39331 AAAAGGAAAAGGAAAAGT
1 AAAAGGAAAAGCAAAAGT
39349 AAA
1 AAA
39352 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.21, T:0.08
Consensus pattern (18 bp):
AAAAGGAAAAGCAAAAGT
Found at i:39358 original size:18 final size:18
Alignment explanation
Indices: 39313--39357 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
39303 AAAAATGAAA
*
39313 AAAAGTAAAAGCAAAAGT
1 AAAAGAAAAAGCAAAAGT
* *
39331 AAAAGGAAAAGGAAAAGT
1 AAAAGAAAAAGCAAAAGT
39349 -AAAGAAAAA
1 AAAAGAAAAA
39358 AAATTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGCAAAAGT
Found at i:45187 original size:22 final size:22
Alignment explanation
Indices: 45157--45201 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
45147 AACATAAAAA
45157 ATTATTTTTTATTAAATATTTTT
1 ATTATTTTTTATTAAAT-TTTTT
*
45180 ATTA-TTTTTATTTAATTTTTT
1 ATTATTTTTTATTAAATTTTTT
45201 A
1 A
45202 AATAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTATTTTTTATTAAATTTTTT
Found at i:45497 original size:21 final size:23
Alignment explanation
Indices: 45460--45513 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
45450 ATTCGCATCG
*
45460 TCCACGCCGACCGGGGCA-TTCC
1 TCCAAGCCGACCGGGGCATTTCC
45482 TCCAAGCCGACC-GGGCATTTCC
1 TCCAAGCCGACCGGGGCATTTCC
45504 TCCAAGCCGA
1 TCCAAGCCGA
45514 AGGCAATGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.15
Consensus pattern (23 bp):
TCCAAGCCGACCGGGGCATTTCC
Found at i:48438 original size:21 final size:21
Alignment explanation
Indices: 48382--48479 Score: 62
Period size: 20 Copynumber: 4.9 Consensus size: 21
48372 AAATGACCAA
*
48382 CAAATTCGCAACGCGAATATG
1 CAAATTCGCAACGCGAATATC
* ** * *
48403 TAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGAATATC
48423 CAAATTCGCAACGCGAA-AGT-
1 CAAATTCGCAACGCGAATA-TC
* * *
48443 CAAATTTGCAAC-TGAAT-TT
1 CAAATTCGCAACGCGAATATC
*
48462 CAAATTCGCAACGTGAAT
1 CAAATTCGCAACGCGAAT
48480 TTAATTTCGT
Statistics
Matches: 58, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.02
19 14 0.24
20 30 0.52
21 13 0.22
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (21 bp):
CAAATTCGCAACGCGAATATC
Found at i:48446 original size:20 final size:20
Alignment explanation
Indices: 48423--48474 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
48413 TGCGATTTTC
48423 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * **
48443 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
48462 CAAATTCGCAACG
1 CAAATTCGCAACG
48475 TGAATTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:48480 original size:20 final size:20
Alignment explanation
Indices: 48423--48481 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
48413 TGCGATTTTC
* **
48423 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGTGAATTT
*
48443 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACGTGAATTT
48462 CAAATTCGCAACGTGAATTT
1 CAAATTCGCAACGTGAATTT
48482 AATTTCGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGTGAATTT
Found at i:48488 original size:19 final size:19
Alignment explanation
Indices: 48445--48488 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
48435 GCGAAAGTCA
48445 AATTT-GCAACTGAATTTC
1 AATTTCGCAACTGAATTTC
*
48463 AAATTCGCAACGTGAATTT-
1 AATTTCGCAAC-TGAATTTC
48482 AATTTCG
1 AATTTCG
48489 TAACAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 11 0.50
20 7 0.32
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (19 bp):
AATTTCGCAACTGAATTTC
Found at i:49256 original size:12 final size:12
Alignment explanation
Indices: 49235--49268 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
49225 ACCAAATTTC
*
49235 CAATACCAAACA
1 CAATATCAAACA
49247 CAATATCAAACA
1 CAATATCAAACA
*
49259 CAATCTCAAA
1 CAATATCAAA
49269 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:49442 original size:24 final size:23
Alignment explanation
Indices: 49392--49444 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
49382 GTATTCGAAA
*
49392 TTTGATCTGGTCAATACCCGGAC
1 TTTGATCTGGTCAATACCCAGAC
* *
49415 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATC-TGGTCAATACCCAGAC
49439 TTTGAT
1 TTTGAT
49445 GATGTGATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (23 bp):
TTTGATCTGGTCAATACCCAGAC
Found at i:52080 original size:20 final size:20
Alignment explanation
Indices: 52052--52093 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
52042 GCAACGCTTA
52052 TTTCACGTTGCGAATTTACC
1 TTTCACGTTGCGAATTTACC
*
52072 TTTCGCGTTGCGAATTTACC
1 TTTCACGTTGCGAATTTACC
52092 TT
1 TT
52094 CAACATGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
TTTCACGTTGCGAATTTACC
Found at i:52192 original size:25 final size:25
Alignment explanation
Indices: 52154--52203 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
52144 AAATCAATTA
* *
52154 AACATTGTTGTGGGTACATTATTTG
1 AACATTGATATGGGTACATTATTTG
52179 AACATTGATATGGGTACATTATTTG
1 AACATTGATATGGGTACATTATTTG
52204 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (25 bp):
AACATTGATATGGGTACATTATTTG
Found at i:52317 original size:23 final size:23
Alignment explanation
Indices: 52285--52343 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
52275 ATATTTGAAC
52285 ATTGTTATGTATAAATTTG-TTAT
1 ATTG-TATGTATAAATTTGATTAT
* * **
52308 GTATGTATGTTTTGATTTGATTAT
1 AT-TGTATGTATAAATTTGATTAT
52332 ATTGTATGTATA
1 ATTGTATGTATA
52344 TTTTCATTCA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (23 bp):
ATTGTATGTATAAATTTGATTAT
Found at i:52590 original size:24 final size:25
Alignment explanation
Indices: 52563--52614 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
52553 TTTCAAATTC
*
52563 ATTTTATATGT-AATTGGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
* *
52587 A-TTTAAATTTCAATTTGAGTTTGA
1 ATTTTAAATGTCAATTGGAGTTTGA
52611 ATTT
1 ATTT
52615 CAATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (25 bp):
ATTTTAAATGTCAATTGGAGTTTGA
Found at i:52603 original size:18 final size:18
Alignment explanation
Indices: 52582--52618 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52572 GTAATTGGAG
52582 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
52600 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
52618 T
1 T
52619 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:52625 original size:24 final size:24
Alignment explanation
Indices: 52574--52626 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
52564 TTTTATATGT
* * *
52574 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
52598 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
52622 AATTT
1 AATTT
52627 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Done.