Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003823.1 Hibiscus syriacus cultivar Beakdansim tig00008198_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: 191471
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:165984 original size:177 final size:175
Alignment explanation
Indices: 165686--166035 Score: 592
Period size: 177 Copynumber: 2.0 Consensus size: 175
165676 TGTGTTGTAT
* *
165686 AAATGTTTTAAATACTTGTTTGAATTATCATGTGCACATGCTTGTTATATAAGTTTTGAAATATG
1 AAATGTTTTAAATACTTGTTTGAATTATCATGTGCACATGATTGTTATATAAGTTTTAAAATATG
* *
165751 ATTGTTTTATCAAATTTGACATATGAATGATTTATTTGGTTGAAATCCTGATTCCTGATTTACTA
66 ATTGTTTTATCAAATTTGACATATGAATGATTTATCTGGTTGAAATCCTAATTCCTGATTTACTA
* *
165816 ATTATAAATTATATTGTCTTATTCATGTTCTCTAGTTATTGATAC
131 ATTATAAAATATATTGTCTTATACATGTTCTCTAGTTATTGATAC
* * * *
165861 AAATGTTTTAAATACTTGTTTGAATTATCATGTGCACGTGATTGTTCTAATCTATTTTTAAAATA
1 AAATGTTTTAAATACTTGTTTGAATTATCATGTGCACATGATTGTTAT-AT-AAGTTTTAAAATA
165926 TGATTGTTTTATCAAATTTGACATATGAATGATTTATCTGGTTGAAATCCTAATTCCTGATTTAC
64 TGATTGTTTTATCAAATTTGACATATGAATGATTTATCTGGTTGAAATCCTAATTCCTGATTTAC
165991 TAATTATAAAATATATTGTCTTATACATGTTCTCTAGTTATTGAT
129 TAATTATAAAATATATTGTCTTATACATGTTCTCTAGTTATTGAT
166036 TTTAATGAAA
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
175 45 0.28
176 2 0.01
177 116 0.71
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (175 bp):
AAATGTTTTAAATACTTGTTTGAATTATCATGTGCACATGATTGTTATATAAGTTTTAAAATATG
ATTGTTTTATCAAATTTGACATATGAATGATTTATCTGGTTGAAATCCTAATTCCTGATTTACTA
ATTATAAAATATATTGTCTTATACATGTTCTCTAGTTATTGATAC
Found at i:167698 original size:18 final size:19
Alignment explanation
Indices: 167675--167723 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
167665 AATTTTGGTT
167675 TCGATACTCATGG-GAGTA
1 TCGATACTCATGGAGAGTA
* *
167693 TCGATACTGAGGGTAGAGTA
1 TCGATACTCATGG-AGAGTA
167713 TCGATACTCAT
1 TCGATACTCAT
167724 AGTATGGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 11 0.44
20 14 0.56
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (19 bp):
TCGATACTCATGGAGAGTA
Found at i:169196 original size:51 final size:51
Alignment explanation
Indices: 169120--169221 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
169110 GTGTATTTTG
*
169120 CACCACTTAACGTTAAACTTGTCATTTTTCTCACTTATTAACCACTTGTGA
1 CACCACTTAACGTTAAACTTGTCATTTTTCTCACTTATCAACCACTTGTGA
*
169171 CACCACTTAACGTTAAACTTGTCATTTTTCTCACTTGTCAACCACTTGTGA
1 CACCACTTAACGTTAAACTTGTCATTTTTCTCACTTATCAACCACTTGTGA
169222 AATGTTTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.38
Consensus pattern (51 bp):
CACCACTTAACGTTAAACTTGTCATTTTTCTCACTTATCAACCACTTGTGA
Found at i:169400 original size:42 final size:42
Alignment explanation
Indices: 169349--169624 Score: 171
Period size: 41 Copynumber: 6.7 Consensus size: 42
169339 CACCACAAAA
*
169349 TAGTAACTTTAGCGGCGTTTTTATACAAAATGTCGCAACAGAG
1 TAGT-ACTTTAGCGGCGTTTTTATACAAAATGCCGCAACAGAG
* * * **
169392 TAGTACTTTAGTGGCGTTTTTATAC-AAACGCCGCAATAGTT
1 TAGTACTTTAGCGGCGTTTTTATACAAAATGCCGCAACAGAG
** * * * * ** *
169433 TCA-T-CCATAGTGGCATTTTTTAAACAAACT-CCGTGACATAG
1 T-AGTACTTTAGCGGC-GTTTTTATACAAAATGCCGCAACAGAG
* * *
169474 TAGTACTTTAGCGGCGTTTTTATA-AAAATGCCGTAATAGGG
1 TAGTACTTTAGCGGCGTTTTTATACAAAATGCCGCAACAGAG
** * *
169515 TTCA-TA-TATTA-TTGCGTTTTTA-AC-AAACGACGCAACAGAG
1 -T-AGTACT-TTAGCGGCGTTTTTATACAAAATGCCGCAACAGAG
*
169555 TAGTACTTTAGCGGCGTTTTTTATACAAACA--CCGCAAAAGAG
1 TAGTACTTTAGCGGCG-TTTTTATACAAA-ATGCCGCAACAGAG
* *
169597 TAGTAATTTAGCGGTGTTTTTATACAAA
1 TAGTACTTTAGCGGCGTTTTTATACAAA
169625 CGCCGTTATA
Statistics
Matches: 175, Mismatches: 41, Indels: 36
0.69 0.16 0.14
Matches are distributed among these distances:
38 1 0.01
39 6 0.03
40 29 0.17
41 70 0.40
42 61 0.35
43 7 0.04
44 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (42 bp):
TAGTACTTTAGCGGCGTTTTTATACAAAATGCCGCAACAGAG
Found at i:169476 original size:82 final size:81
Alignment explanation
Indices: 169362--169591 Score: 239
Period size: 82 Copynumber: 2.8 Consensus size: 81
169352 TAACTTTAGC
* * *
169362 GGCGTTTTTATACAAAATGTCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCA
1 GGCGTTTTTA-AC-AAACGACGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCA
* *
169427 ATA-GTTTCATCCA-TAGT
64 ATAGGGTTCATACATTA-T
* ** ** * * * *
169444 GGCATTTTTTAAACAAACTCCGTGACATAGTAGTACTTTAGCGGCGTTTTTATAAAAATGCCGTA
1 GGC-GTTTTT-AACAAACGACGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCA
*
169509 ATAGGGTTCATATATTAT
64 ATAGGGTTCATACATTAT
* *
169527 TGCGTTTTTAACAAACGACGCAACAGAGTAGTACTTTAGCGGCGTTTTTTATACAAACACCGCAA
1 GGCGTTTTTAACAAACGACGCAACAGAGTAGTACTTTAGCGGCG-TTTTTATACAAACGCCGCAA
169592 AAGAGTAGTA
Statistics
Matches: 118, Mismatches: 25, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
81 30 0.25
82 68 0.58
83 17 0.14
84 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (81 bp):
GGCGTTTTTAACAAACGACGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAAT
AGGGTTCATACATTAT
Found at i:169648 original size:41 final size:41
Alignment explanation
Indices: 169528--169719 Score: 176
Period size: 41 Copynumber: 4.7 Consensus size: 41
169518 ATATATTATT
* *
169528 GCGTTTTTA-ACAAACGA-CGCAACAGAGTA-GTACTTTAGCG
1 GCGTTTTTATACAAAC-ACCGCTATAGA-TACGTACTTTAGCG
* * *
169568 GCGTTTTTTATACAAACACCGCAAAAGAGTA-GTAATTTAGCG
1 GCG-TTTTTATACAAACACCGCTATAGA-TACGTACTTTAGCG
* * * * *
169610 GTGTTTTTATACAAACGCCGTTATAGACACGTACTTTAGTG
1 GCGTTTTTATACAAACACCGCTATAGATACGTACTTTAGCG
* * *
169651 GCGTTTTTATTCAAACACCGCTATAAATACGTTCTTTAGCG
1 GCGTTTTTATACAAACACCGCTATAGATACGTACTTTAGCG
** *
169692 GTATTTTTATACAAACGCCGCTATAGAT
1 GCGTTTTTATACAAACACCGCTATAGAT
169720 CTATAAGATT
Statistics
Matches: 125, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
40 4 0.03
41 92 0.74
42 29 0.23
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
GCGTTTTTATACAAACACCGCTATAGATACGTACTTTAGCG
Found at i:169689 original size:82 final size:83
Alignment explanation
Indices: 169557--169718 Score: 222
Period size: 82 Copynumber: 2.0 Consensus size: 83
169547 CAACAGAGTA
*
169557 GTACTTTAGCGGCGTTTTTTATACAAACACCGCAAAAGAGTAGTAATTTAGCGGTGTTTTTATAC
1 GTACTTTAGCGGCGTTTTTTATACAAACACCGCAAAAGAGTAGTAATTTAGCGGTATTTTTATAC
*
169622 AAACGCCGTTATAGACAC
66 AAACGCCGCTATAGACAC
* * * **
169640 GTACTTTAGTGGCG-TTTTTATTCAAACACCGCTATAA-A-TACGTTCTTTAGCGGTATTTTTAT
1 GTACTTTAGCGGCGTTTTTTATACAAACACCGC-AAAAGAGTA-GTAATTTAGCGGTATTTTTAT
169702 ACAAACGCCGCTATAGA
64 ACAAACGCCGCTATAGA
169719 TCTATAAGAT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
81 2 0.03
82 52 0.74
83 16 0.23
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (83 bp):
GTACTTTAGCGGCGTTTTTTATACAAACACCGCAAAAGAGTAGTAATTTAGCGGTATTTTTATAC
AAACGCCGCTATAGACAC
Found at i:172048 original size:43 final size:42
Alignment explanation
Indices: 171967--172344 Score: 371
Period size: 42 Copynumber: 9.0 Consensus size: 42
171957 GGCGTTTGCA
** *
171967 TCCAAAAACGCCGCTATAGATCT-GAATTTTTACGGCGTTTAT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTT-T
* * * *
172009 TCCAAAAACGTCGCTATATATCTCGACCTTCTGCAGCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTT-T
* * *
172052 TCCTAAAACGCCACTATAGATCT-GACCTTTTGCGGCATTTT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTT
** * *
172093 T---GGAACGCCGCTATAGATC-CGACATTTTGTGGCGTTTT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTT
** * *
172131 CTATAAAAACGCCGTTATAGATCTCGACCTATTGCGGCGTTTGT
1 -TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTT-T
172175 TCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTT
*
172216 CTCCAAAAACGCCGCTATAGAGCTCGA-CTTATTGCGGCGTTTGT
1 -TCCAAAAACGCCGCTATAGATCTCGACCTT-TTGCGGCGTTT-T
* * *
172260 TCCGAAAAACGCC-ATATAGATC-AGACCTTTTGCGGTGTTTT
1 TCC-AAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTT
* * * *
172301 CTCAAAAAATGCCGCTATAGATTTCGACCTATTGCGGCGTTTT
1 -TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTT
172344 T
1 T
172345 TTTTTCACAA
Statistics
Matches: 276, Mismatches: 43, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
38 30 0.11
39 1 0.00
41 12 0.04
42 113 0.41
43 109 0.39
44 11 0.04
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (42 bp):
TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTT
Found at i:172101 original size:38 final size:38
Alignment explanation
Indices: 172058--172130 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
172048 TTGTTCCTAA
* *
172058 AACGCCACTATAGATCTGACCTTTTGCGGCATTTTTGG
1 AACGCCACTATAGATCCGACATTTTGCGGCATTTTTGG
* * *
172096 AACGCCGCTATAGATCCGACATTTTGTGGCGTTTT
1 AACGCCACTATAGATCCGACATTTTGCGGCATTTT
172131 CTATAAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (38 bp):
AACGCCACTATAGATCCGACATTTTGCGGCATTTTTGG
Found at i:172192 original size:123 final size:122
Alignment explanation
Indices: 171973--172215 Score: 330
Period size: 123 Copynumber: 2.0 Consensus size: 122
171963 TGCATCCAAA
* * * *
171973 AACGCCGCTATAGATCTGAATTTTTACGGCGTTTATTCCAAAAACGTCGCTATATATCTCGACCT
1 AACGCCGCTATAGATCCGAATTTTTA-GGCGTTTATTACAAAAACGCCGCTATAGATCTCGACCT
*
172038 TCTGCAGCGTTTGTTCCTAAAACGCCACTATAGATCTGACCTTTTGCGGCATTTTTGG
65 TCTGCAGCGTTTGTTCCAAAAACGCCACTATAGATCTGACCTTTTGCGGCATTTTTGG
* *
172096 AACGCCGCTATAGATCCGACATTTTGT-GGCGTTT-TCTATAAAAACGCCGTTATAGATCTCGAC
1 AACGCCGCTATAGATCCGA-ATTTT-TAGGCGTTTAT-TACAAAAACGCCGCTATAGATCTCGAC
* * *
172159 CTAT-TGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
63 CT-TCTGCAGCGTTTGTTCCAAAAACGCCACTATAGATCTGACCTTTTGCGGCATTTT
172216 CTCCAAAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
122 1 0.01
123 98 0.92
124 6 0.06
125 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (122 bp):
AACGCCGCTATAGATCCGAATTTTTAGGCGTTTATTACAAAAACGCCGCTATAGATCTCGACCTT
CTGCAGCGTTTGTTCCAAAAACGCCACTATAGATCTGACCTTTTGCGGCATTTTTGG
Found at i:172212 original size:85 final size:86
Alignment explanation
Indices: 171970--172342 Score: 392
Period size: 85 Copynumber: 4.4 Consensus size: 86
171960 GTTTGCATCC
** * * * * *
171970 AAAAACGCCGCTATAGATCT-GAATTTTTACGGCGTTTATTCCAAAAACGTCGCTATATATCTCG
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-G
* * *
172034 ACCTTCTGCAGCGTTTGT-TCCT
65 ACCTTTTGCGGCGTTT-TCTCAT
* * * ** *
172056 -AAAACGCCACTATAGATCT-GACCTTTTGCGGCATTT-TT---GGAACGCCGCTATAGATCCGA
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
* *
172115 CATTTTGTGGCGTTTTCT-AT
66 CCTTTTGCGGCGTTTTCTCAT
*
172135 AAAAACGCCGTTATAGATCTCGACCTATTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
*
172200 CCTTTTGCGGCGTTTTCTC-C
66 CCTTTTGCGGCGTTTTCTCAT
* * * *
172220 AAAAACGCCGCTATAGAGCTCGACTTATTGCGGCGTTTGTTCCGAAAAACGCC-ATATAGATCAG
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTTCC-AAAAACGCCGCTATAGATCTG
*
172284 ACCTTTTGCGGTGTTTTCTCA-
65 ACCTTTTGCGGCGTTTTCTCAT
* *
172305 AAAAATGCCGCTATAGATTTCGACCTATTGCGGCGTTT
1 AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTT
172343 TTTTTTTCAC
Statistics
Matches: 242, Mismatches: 35, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
79 2 0.01
80 31 0.13
81 29 0.12
82 2 0.01
84 2 0.01
85 167 0.69
86 9 0.04
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (86 bp):
AAAAACGCCGCTATAGATCTCGACCTATTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA
CCTTTTGCGGCGTTTTCTCAT
Found at i:179632 original size:2 final size:2
Alignment explanation
Indices: 179627--179651 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
179617 AAATTAAAAT
179627 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 T
179652 TAAAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:185089 original size:43 final size:43
Alignment explanation
Indices: 185042--185179 Score: 222
Period size: 43 Copynumber: 3.2 Consensus size: 43
185032 TGTTCACTTA
* * **
185042 TGGTTGTTCGCGGGGTCATAGTTGATCGACACATGATCATGGG
1 TGGTTGCTCGCTGGGTTGTAGTTGATCGACACATGATCATGGG
185085 TGGTTGCTCGCTGGGTTGTAGTTGATCGACACATGATCATGGG
1 TGGTTGCTCGCTGGGTTGTAGTTGATCGACACATGATCATGGG
* *
185128 TGGTTGCTCGCTGGGTTGTAGTTGATCGACACATGATCTTTGG
1 TGGTTGCTCGCTGGGTTGTAGTTGATCGACACATGATCATGGG
185171 TGGTTGCTC
1 TGGTTGCTC
185180 ACCTGAAACA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (43 bp):
TGGTTGCTCGCTGGGTTGTAGTTGATCGACACATGATCATGGG
Found at i:187387 original size:30 final size:31
Alignment explanation
Indices: 187344--187426 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 31
187334 AATAAATGTT
*
187344 TAAAA-TTACAAGGACCAAAATGAG-AAGAA-
1 TAAAACTTA-AAGGACCAAAATGAGAAAAAAC
*
187373 TAGCAACTTAAAGGACCAAAAT-AGAAAAAAC
1 TA-AAACTTAAAGGACCAAAATGAGAAAAAAC
*
187404 TAAAACTTAAAGGACTAAAATGA
1 TAAAACTTAAAGGACCAAAATGA
187427 CACACACAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.09
30 35 0.78
31 6 0.13
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (31 bp):
TAAAACTTAAAGGACCAAAATGAGAAAAAAC
Found at i:187473 original size:30 final size:29
Alignment explanation
Indices: 187380--187484 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
187370 GAATAGCAAC
* * *
187380 TTAAAGGACCAAAATAGAAAAAACTAAAAC
1 TTAAAGGACTAAAATAG-AAAAACAAAAAT
* * *
187410 TTAAAGGACTAAAAT-GACACACACAGAATT
1 TTAAAGGACTAAAATAGA-A-AAACAAAAAT
*
187440 TTAAAGGGCTAAAATAGTAAAAACAAAAAT
1 TTAAAGGACTAAAATAG-AAAAACAAAAAT
* *
187470 TTAAGGGTCTAAAAT
1 TTAAAGGACTAAAAT
187485 GGTATTAACA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
28 1 0.02
29 2 0.03
30 53 0.90
31 2 0.03
32 1 0.02
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.20
Consensus pattern (29 bp):
TTAAAGGACTAAAATAGAAAAACAAAAAT
Found at i:188905 original size:3 final size:3
Alignment explanation
Indices: 188891--188927 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
188881 ATATTTATGT
188891 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
188928 TATTTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:189506 original size:28 final size:28
Alignment explanation
Indices: 189466--189562 Score: 117
Period size: 28 Copynumber: 3.4 Consensus size: 28
189456 AGGAATTATG
*
189466 GTTTCAAGAGAAATC-GACTCAAAGATTT
1 GTTTCAAAAGAAA-CAGACTCAAAGATTT
189494 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
*
189522 GTTTCAAGAA-AAACAAACTCAAAGATGATGT
1 GTTTCAA-AAGAAACAGACTCAAAGAT--T-T
189553 GTTTCAAAAG
1 GTTTCAAAAG
189563 CAACTGTCTT
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
27 1 0.02
28 47 0.77
29 2 0.03
30 3 0.05
31 8 0.13
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:189660 original size:64 final size:65
Alignment explanation
Indices: 189513--189738 Score: 189
Period size: 65 Copynumber: 3.5 Consensus size: 65
189503 GAAACAGACT
** ** * * *
189513 CAAAGATTTGTTTCAAGAAAAACAAACTCAAAGAT-GATGTGTTTCAAAAGCAACTGTCTTAAA-
1 CAAA-ATTTGTTTCAAGGGAAACGTACTCAAAGATCGA--TGTTT-AAAGGGAACTGTCTCAAAC
189576 GAGA
62 GAGA
* * * *
189580 CAAAA-TCGTTTCAAGGGAAACG-ACTCAAATAT-GATGTTTAAAGGGAAATTGTCTCAAGCGAG
1 CAAAATTTGTTTCAAGGGAAACGTACTCAAAGATCGATGTTTAAAGGG-AACTGTCTCAAACGAG
189642 A
65 A
* ** * * * *
189643 CAAAATTTGTTTTAAGGGAAACGTTTTCAAAGATCGGTGTTTCATGGGAACTGTCTCAAATGAGA
1 CAAAATTTGTTTCAAGGGAAACGTACTCAAAGATCGATGTTTAAAGGGAACTGTCTCAAACGAGA
189708 CAAAATTTG-TTCAAGGGAAACGT--TCAAAGAT
1 CAAAATTTGTTTCAAGGGAAACGTACTCAAAGAT
189739 GTTTGTTTGT
Statistics
Matches: 132, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
61 4 0.03
62 22 0.17
63 9 0.07
64 39 0.30
65 43 0.33
66 11 0.08
67 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (65 bp):
CAAAATTTGTTTCAAGGGAAACGTACTCAAAGATCGATGTTTAAAGGGAACTGTCTCAAACGAGA
Found at i:190874 original size:14 final size:15
Alignment explanation
Indices: 190848--190879 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
190838 TGTAAATTTC
190848 ATGTGTCATGTATGT
1 ATGTGTCATGTATGT
190863 ATGTGT-ATGTATGT
1 ATGTGTCATGTATGT
190877 ATG
1 ATG
190880 ATTTCTCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (15 bp):
ATGTGTCATGTATGT
Found at i:191019 original size:21 final size:21
Alignment explanation
Indices: 190989--191030 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
190979 GACCTGAGAC
190989 AATTTGTTT-CCGTGCCCCAA
1 AATTTGTTTCCCGTGCCCCAA
*
191009 AATTTAGTTTCCCTTGCCCCAA
1 AATTT-GTTTCCCGTGCCCCAA
191031 CTTCTATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (21 bp):
AATTTGTTTCCCGTGCCCCAA
Done.