Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004436.1 Hibiscus syriacus cultivar Beakdansim tig00009732_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: 66610
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Found at i:573 original size:186 final size:185
Alignment explanation
Indices: 368--708 Score: 503
Period size: 186 Copynumber: 1.8 Consensus size: 185
358 TATATAATCA
* *
368 GGTCGGGCCGGATTAAGTCACTGTTTTTTATTAAAT-AAAATATTTTTTTATTATTTCGGGTCGG
1 GGTCGGGCCGGATTAAGTCACTG-TTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTCGG
432 GTCGGGTTGGATTTCTAATT-CATATTCGGTCAGGTCAGATGAAACTTTATTTTGTTCGGGTC-G
65 GTC-----GGATTTCTAATTACATATTCGGTCAGGTCAGATGAAACTTTATTTTGTTCGGGTCAG
495 -GG-TTTTTAAGTGTGATATTCGGGTCGAGTTGGTCGGGTTTTTTTTAAGTGTGATATTCG
125 CGGATTTTTAAGTGTGATATTCGGGTCGAGTTGGTCGGGTTTTTTTTAAGTGTGATATTCG
*
554 GGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTCGGG
1 GGTCGGGCCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTCGGG
* * * *
619 TCGGATTTCTAATTAATATATTTGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCAGGTCGG
66 TCGGATTTCTAATT-ACATATTCGGTCAGGTCAGATGAAACTTTATTTTGTTCGGGTCA-G-CGG
684 ATTTTTAAGTGTGATATTCGGGTCG
128 ATTTTTAAGTGTGATATTCGGGTCG
709 GGTTCGGTTT
Statistics
Matches: 140, Mismatches: 7, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
181 12 0.09
183 38 0.27
185 13 0.09
186 51 0.36
187 2 0.01
188 24 0.17
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (185 bp):
GGTCGGGCCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGGTCGGG
TCGGATTTCTAATTACATATTCGGTCAGGTCAGATGAAACTTTATTTTGTTCGGGTCAGCGGATT
TTTAAGTGTGATATTCGGGTCGAGTTGGTCGGGTTTTTTTTAAGTGTGATATTCG
Found at i:892 original size:208 final size:203
Alignment explanation
Indices: 549--938 Score: 466
Period size: 208 Copynumber: 1.9 Consensus size: 203
539 TAAGTGTGAT
*
549 ATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGG
1 ATTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGG
* * ** ** *
614 TCGGGTCGGATTTCTAATTAATATATTTGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCAG
66 TCGGGTCGG--TTCGAATAAATATATTTGGTCGGG-CGGATGAAACTTTATTCGGGGCGAGTCAG
* *
679 GTCGGA-TTTTTAAGTGTGATATTCGGGTCGGGTTCGGTTTAGGGTTAAAAAAAACCGACCGACC
128 GTCGGATTTTTTAA--GTGAT-TTCGGGTCGGGTTCGGGTTAGGGTGAAAAAAAACCGACCGACC
743 CAACAATATATATA
190 CAACAATATATATA
757 ATTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAAAATAA-TTTTTATTATTTCAGG
1 ATTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGG
* * * ** *
821 TC-GGTCTGG-TCGAATGAAACTTTATTTGTTCGGG-GGTTTTTAAGTGTGATATTCGGGGCGAG
66 TCGGGTC-GGTTCGAAT-AAA-TATATTTGGTCGGGCGG-ATGAAACT-T--TATTCGGGGCGAG
*
883 TCGGGTCGGATTTTTTTAAGTGATTTCGGGTCGGGTTCGGGTTAGGGTGAAAAAAA
124 TCAGGTCGGA-TTTTTTAAGTGATTTCGGGTCGGGTTCGGGTTAGGGTGAAAAAAA
939 CCAGATCGAC
Statistics
Matches: 156, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
204 7 0.04
205 6 0.04
206 17 0.11
207 50 0.32
208 69 0.44
210 7 0.04
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.37
Consensus pattern (203 bp):
ATTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCAGG
TCGGGTCGGTTCGAATAAATATATTTGGTCGGGCGGATGAAACTTTATTCGGGGCGAGTCAGGTC
GGATTTTTTAAGTGATTTCGGGTCGGGTTCGGGTTAGGGTGAAAAAAAACCGACCGACCCAACAA
TATATATA
Found at i:4442 original size:16 final size:16
Alignment explanation
Indices: 4418--4448 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4408 GAGTATTATA
4418 AAAAATTAAATTTAAT
1 AAAAATTAAATTTAAT
*
4434 AAAATTTAAATTTAA
1 AAAAATTAAATTTAA
4449 ATTTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAAATTAAATTTAAT
Found at i:17121 original size:14 final size:14
Alignment explanation
Indices: 17092--17133 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
17082 GTCAACTTAA
*
17092 TATATTCTTTAAAAT
1 TATATT-TTAAAAAT
17107 TATATTTTAAAAAT
1 TATATTTTAAAAAT
*
17121 TAT-TTTAAAAAAT
1 TATATTTTAAAAAT
17134 AAAAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 9 0.36
14 10 0.40
15 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTTTAAAAAT
Found at i:17126 original size:12 final size:13
Alignment explanation
Indices: 17099--17131 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
17089 TAATATATTC
*
17099 TTTAAAATTATAT
1 TTTAAAAATATAT
17112 TTTAAAAAT-TAT
1 TTTAAAAATATAT
17124 TTTAAAAA
1 TTTAAAAA
17132 ATAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:17308 original size:73 final size:74
Alignment explanation
Indices: 17205--17342 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 74
17195 AGTTCTTTTT
* * * *
17205 CTCTCAACTCTCCCCTCTCCCTTTCTCCTCCCCTA-TATTTCATTGTCTGAAACAAAAAAAAAAT
1 CTCTCAACTCTCCCCTCCCCCCTCCTCCTCCCCGACT-TTTCATTGTCTGAAACAAAAAAAAAAT
17269 TCTGCTTTCA
65 TCTGCTTTCA
* * * *
17279 CTCTTAACTC-CCCCTCCCCCCTCCTCCTCCCCGACTTTTCATTTTTTGAAACAAAGAAAAAATT
1 CTCTCAACTCTCCCCTCCCCCCTCCTCCTCCCCGACTTTTCATTGTCTGAAACAAAAAAAAAATT
17343 GCAGTTAGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
73 45 0.82
74 10 0.18
ACGTcount: A:0.25, C:0.37, G:0.04, T:0.33
Consensus pattern (74 bp):
CTCTCAACTCTCCCCTCCCCCCTCCTCCTCCCCGACTTTTCATTGTCTGAAACAAAAAAAAAATT
CTGCTTTCA
Found at i:36991 original size:16 final size:16
Alignment explanation
Indices: 36941--36991 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
36931 AGAAGAAAAA
36941 AAAAAGAATAAAG-AAG
1 AAAAAGAA-AAAGAAAG
** * *
36957 ATGAAGAAAAACAAGG
1 AAAAAGAAAAAGAAAG
36973 AAAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAG
36989 AAA
1 AAA
36992 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAG
Found at i:37382 original size:18 final size:18
Alignment explanation
Indices: 37359--37395 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
37349 TCCAAGTTTA
37359 TCTTTTCAAAATTCAATT
1 TCTTTTCAAAATTCAATT
*
37377 TCTTTTCGAAATTCAATT
1 TCTTTTCAAAATTCAATT
37395 T
1 T
37396 ATTCTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (18 bp):
TCTTTTCAAAATTCAATT
Found at i:39739 original size:103 final size:103
Alignment explanation
Indices: 39555--39769 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 103
39545 GTCGAGGGTC
39555 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
39620 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
39658 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
39723 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
39761 TATGTGGTC
1 TATGTGGTC
39770 CTTATGGATA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:39848 original size:47 final size:46
Alignment explanation
Indices: 39792--39898 Score: 187
Period size: 47 Copynumber: 2.3 Consensus size: 46
39782 ATTACATGTT
39792 ACTACGGTGCAATTCTACGCGGCACTCCGGTGCAATTATTATATGGC
1 ACTACGGTGCAATTCTACGCGGCACTCCGGTGCAATTA-TATATGGC
*
39839 ACTACGGTGCAATTCTACGCGGCACTCCGGTGCAATTATATGTGGC
1 ACTACGGTGCAATTCTACGCGGCACTCCGGTGCAATTATATATGGC
*
39885 ACTTCGGTGCAATT
1 ACTACGGTGCAATT
39899 ATATGAGTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
46 20 0.34
47 38 0.66
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.28
Consensus pattern (46 bp):
ACTACGGTGCAATTCTACGCGGCACTCCGGTGCAATTATATATGGC
Found at i:39899 original size:23 final size:23
Alignment explanation
Indices: 39796--39903 Score: 126
Period size: 23 Copynumber: 4.7 Consensus size: 23
39786 CATGTTACTA
* *
39796 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTATATGCGGCACTC
** *
39819 CGGTGCAATTATTATATGGCACTA
1 CGGTGCAATTA-TATGCGGCACTC
* *
39843 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTATATGCGGCACTC
* *
39866 CGGTGCAATTATATGTGGCACTT
1 CGGTGCAATTATATGCGGCACTC
39889 CGGTGCAATTATATG
1 CGGTGCAATTATATG
39904 AGTTGTGGTG
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
23 52 0.74
24 18 0.26
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTATATGCGGCACTC
Found at i:45564 original size:103 final size:103
Alignment explanation
Indices: 45381--45701 Score: 581
Period size: 103 Copynumber: 3.1 Consensus size: 103
45371 GTCGAGGGTC
*
45381 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGCCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
45446 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
* *
45484 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
45549 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
45587 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
45652 TTGATCCCTAGT-ATATGTATATGATTCTTAAGGAATGA
66 TTGAT-CCTTGTCATATGTATATGATTCTTAAGGAATGA
45690 TATGTGGTCCTT
1 TATGTGGTCCTT
45702 ATGGACATTA
Statistics
Matches: 210, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 205 0.98
104 5 0.02
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGTCATATGTATATGATTCTTAAGGAATGA
Found at i:45753 original size:23 final size:23
Alignment explanation
Indices: 45718--45793 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
45708 ATTATTACAT
*
45718 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* ***
45741 GGCACTCCGGTGCAATGAT-TATAT
1 GGCACTACGGTGCAAT--TCTACGC
45765 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
45788 GGCACT
1 GGCACT
45794 CAAGTGCAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 1 0.02
23 22 0.54
24 17 0.41
25 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:45780 original size:47 final size:47
Alignment explanation
Indices: 45711--45827 Score: 155
Period size: 47 Copynumber: 2.5 Consensus size: 47
45701 TATGGACATT
* * **
45711 ATTACATGGCACTACAGTGCAATTCTACGCGGCACTCCGGTGCAATG
1 ATTATATGGCACTACGGTGCAATTCTACGCGGCACTCAAGTGCAATG
*
45758 ATTATATGGCACTACGGTGCAATTCTACGCGGCACTCAAGTGCAATT
1 ATTATATGGCACTACGGTGCAATTCTACGCGGCACTCAAGTGCAATG
* **
45805 A-TATGTGGCACTTTGGTGCAATT
1 ATTATATGGCACTACGGTGCAATT
45828 ATATGAGTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
46 19 0.31
47 43 0.69
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
ATTATATGGCACTACGGTGCAATTCTACGCGGCACTCAAGTGCAATG
Found at i:45800 original size:23 final size:23
Alignment explanation
Indices: 45718--45804 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
45708 ATTATTACAT
45718 GGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
* * ***
45741 GGCACTCCGGTGCAATGAT-TATAT
1 GGCACTACAGTGCAAT--TCTACGC
*
45765 GGCACTACGGTGCAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
45788 GGCACT-CAAGTGCAATT
1 GGCACTAC-AGTGCAATT
45805 ATATGTGGCA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
22 2 0.04
23 30 0.60
24 17 0.34
25 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Found at i:45814 original size:23 final size:22
Alignment explanation
Indices: 45717--45832 Score: 70
Period size: 23 Copynumber: 5.0 Consensus size: 22
45707 CATTATTACA
* * *
45717 TGGCACTACAGTGCAATTCTACG
1 TGGCACTA-GGTGCAATTATATG
* * * *
45740 CGGCACTCCGGTGCAATGATTATA
1 TGGCACT-AGGTGCAATTA-TATG
* *
45764 TGGCACTACGGTGCAATTCTACG
1 TGGCACTA-GGTGCAATTATATG
* *
45787 CGGCACTCAAGTGCAATTATATG
1 TGGCACT-AGGTGCAATTATATG
*
45810 TGGCACTTTGGTGCAATTATATG
1 TGGCAC-TAGGTGCAATTATATG
45833 AGTTGTGGTG
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
23 50 0.74
24 18 0.26
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28
Consensus pattern (22 bp):
TGGCACTAGGTGCAATTATATG
Found at i:47018 original size:137 final size:137
Alignment explanation
Indices: 46739--47079 Score: 386
Period size: 137 Copynumber: 2.5 Consensus size: 137
46729 GGGGTGTTAC
46739 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
46804 AACCTTAGATTGATTCAGCATCTACGAAAATGAATAAAAGAATAACCTCACTTGAGGATCAACAT
66 AACCTTAGATTAATTCAGCATCTACGAAAATGAATAAAACAATAACCTCACTTGAGGATCAACAT
*
46869 TTAGAGG
131 TTAGAAG
* * * *
46876 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAAAAGAAGCTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* ** * * ** * * * *
46941 GACCTTATCTTAATTCATCA-CATATGAAGTTGAAT-CAACAA-CATCTC-TTTCGAGGATCAAC
66 AACCTTAGATTAATTCAGCATC-TACGAAAATGAATAAAACAATAACCTCACTT-GAGGATCAAC
47002 ATTTCCAGATAG
129 ATTT--AGA-AG
* * * ** *
47014 -AGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAACAAGTTCATAATCTGAAGAACTTATTC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
47078 AA
66 AA
47080 TCTTTTGCTC
Statistics
Matches: 170, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
134 2 0.01
135 18 0.11
136 5 0.03
137 144 0.85
138 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (137 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTAGATTAATTCAGCATCTACGAAAATGAATAAAACAATAACCTCACTTGAGGATCAACAT
TTAGAAG
Found at i:47514 original size:21 final size:20
Alignment explanation
Indices: 47485--47523 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
47475 TGGGGTTATA
* *
47485 AAAACCACATAACAAAATGT
1 AAAACCACAGAAAAAAATGT
47505 AAAACACACAGAAAAAAAT
1 AAAAC-CACAGAAAAAAAT
47524 CAAGAGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAACCACAGAAAAAAATGT
Found at i:50282 original size:30 final size:32
Alignment explanation
Indices: 50233--50293 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
50223 TAATATCGGA
* *
50233 TCGGTTAGCTTTGGGTCGGGTCAAT-ATTAGT
1 TCGGTTAGATTTGGGTCGGGCCAATCATTAGT
*
50264 TCGGTT-GATTTGGTTCGGGCCAATCATTAG
1 TCGGTTAGATTTGGGTCGGGCCAATCATTAG
50294 ATTTTTTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.16, C:0.15, G:0.31, T:0.38
Consensus pattern (32 bp):
TCGGTTAGATTTGGGTCGGGCCAATCATTAGT
Found at i:51100 original size:2 final size:2
Alignment explanation
Indices: 51093--51118 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51083 ACAGAAGCAA
51093 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
51119 TAGGATACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51433 original size:20 final size:19
Alignment explanation
Indices: 51410--51453 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
51400 CAAGTAAGAT
51410 TTATAATATTATTTA-ATAAA
1 TTAT-ATATT-TTTACATAAA
51430 TTATATATTTTTACGATAAA
1 TTATATATTTTTAC-ATAAA
51450 TTAT
1 TTAT
51454 TGATGTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 5 0.23
20 13 0.59
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATATATTTTTACATAAA
Found at i:58657 original size:14 final size:14
Alignment explanation
Indices: 58640--58666 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58630 TATAGCCATC
58640 TTTTTTCCTTTTCT
1 TTTTTTCCTTTTCT
58654 TTTTTTCCTTTTC
1 TTTTTTCCTTTTC
58667 CATCTCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCCTTTTCT
Done.