Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009240.1 Hibiscus syriacus cultivar Beakdansim tig00112867_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: 51096
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3169 original size:31 final size:31
Alignment explanation
Indices: 3131--3192 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3121 TGCTCTTATT
*
3131 GATCTTCACTTAGTTTCTCTCAAACACTAAG
1 GATCTTCAATTAGTTTCTCTCAAACACTAAG
*
3162 GATCTTCAATTAGTTTCTCTCCAACACTAAG
1 GATCTTCAATTAGTTTCTCTCAAACACTAAG
3193 TAATTAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (31 bp):
GATCTTCAATTAGTTTCTCTCAAACACTAAG
Found at i:4449 original size:20 final size:20
Alignment explanation
Indices: 4426--4473 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
4416 ACAAGTTTAG
4426 AAAATCATTCATATATTACA
1 AAAATCATTCATATATTACA
4446 AAAATCATTCATATATTACA
1 AAAATCATTCATATATTACA
4466 AAAATCAT
1 AAAATCAT
4474 ACAACTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATCATTCATATATTACA
Found at i:7048 original size:22 final size:22
Alignment explanation
Indices: 7020--7080 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
7010 GGCTGTTTGG
7020 TCAAAGTCAAGGTCAACACTGA
1 TCAAAGTCAAGGTCAACACTGA
* * * *
7042 TCAAAGTTAAAGTCAACTCTGG
1 TCAAAGTCAAGGTCAACACTGA
*
7064 TCAAATTCAACGGTCAA
1 TCAAAGTCAA-GGTCAA
7081 GTCAATAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (22 bp):
TCAAAGTCAAGGTCAACACTGA
Found at i:7139 original size:13 final size:13
Alignment explanation
Indices: 7119--7153 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
7109 GACTGTGTTC
7119 GAGTTGACTCAAT
1 GAGTTGACTCAAT
7132 CG-GTTGACTCAAT
1 -GAGTTGACTCAAT
7145 GAGTTGACT
1 GAGTTGACT
7154 GAGCTTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (13 bp):
GAGTTGACTCAAT
Found at i:15165 original size:23 final size:23
Alignment explanation
Indices: 15135--15178 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15125 TTGACCCGAT
*
15135 TTGACCCGACCCGACCTGACTCG
1 TTGACCCGACCCGACCCGACTCG
15158 TTGACCCGACCCGACCCGACT
1 TTGACCCGACCCGACCCGACT
15179 GCCCGACCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.16
Consensus pattern (23 bp):
TTGACCCGACCCGACCCGACTCG
Found at i:15186 original size:23 final size:23
Alignment explanation
Indices: 15137--15197 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
15127 GACCCGATTT
* **
15137 GACCCGACCCGACCTGACTCGTT
1 GACCCGACCCGACCCGACTCGCC
15160 GACCCGACCCGACCCGACT-GCCC
1 GACCCGACCCGACCCGACTCG-CC
* *
15183 GACCCGTCCTGACCC
1 GACCCGACCCGACCC
15198 ATTGGCCGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.16, C:0.51, G:0.21, T:0.11
Consensus pattern (23 bp):
GACCCGACCCGACCCGACTCGCC
Found at i:17586 original size:22 final size:22
Alignment explanation
Indices: 17559--17603 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
17549 GCCTATATTA
17559 TGATCTGATACTTGACATGGAT
1 TGATCTGATACTTGACATGGAT
*
17581 TGATCTGATACTTGACCTGGAT
1 TGATCTGATACTTGACATGGAT
17603 T
1 T
17604 CTGTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
TGATCTGATACTTGACATGGAT
Found at i:19785 original size:17 final size:18
Alignment explanation
Indices: 19755--19788 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19745 TGACCTGACG
19755 CGTTGACCGACCGTTGAT
1 CGTTGACCGACCGTTGAT
*
19773 CGTTGATCG-CCGTTGA
1 CGTTGACCGACCGTTGA
19789 CAAGAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTTGACCGACCGTTGAT
Found at i:22167 original size:22 final size:22
Alignment explanation
Indices: 22141--22185 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
22131 GCCTATATTC
22141 TGATCTGATACTTGACATGGAT
1 TGATCTGATACTTGACATGGAT
*
22163 TGATCTGATACTTGACCTGGAT
1 TGATCTGATACTTGACATGGAT
22185 T
1 T
22186 CTGTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
TGATCTGATACTTGACATGGAT
Found at i:31579 original size:2 final size:2
Alignment explanation
Indices: 31572--31612 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
31562 CATTTTTAAA
* *
31572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AG AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31613 GCCAACGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:34237 original size:20 final size:21
Alignment explanation
Indices: 34214--34254 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
34204 TATTATATGT
**
34214 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
34234 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
34255 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:35663 original size:3 final size:3
Alignment explanation
Indices: 35655--35776 Score: 208
Period size: 3 Copynumber: 40.7 Consensus size: 3
35645 TTAATATATT
* *
35655 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
35703 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
35751 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
35777 TGGATAAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:36301 original size:113 final size:113
Alignment explanation
Indices: 36096--36986 Score: 1289
Period size: 113 Copynumber: 7.9 Consensus size: 113
36086 AGCATCAAAC
*
36096 AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *** * * * *
36161 TTGAACTTTCTCTGGAAAGGCTGATCCATCAATTGATGAATTCAGGTA
66 ATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAAGCA
36209 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
36274 ATGAACCTTCTCTGGAAAAAATAATCCATCCAGTGATGAATTC-AG-A
66 ATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAAGCA
*
36320 TTAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 --AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
36385 TTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAAACA
64 TTATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAAGCA
*
36435 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*** * *
36500 ATGAACTTTCTCTGGAAATGTTGATCCATCCAA-TGATGAATTCAAACA
66 ATGAACTTTCTCTGGAAAAAATAATCCAT-CAAGTGATGAATTCAAGCA
* *
36548 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
**
36613 ATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGAT-AGATTTGAGCA
66 ATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGA-ATTCAAGCA
36661 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-C--CTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *** *
36723 ATGAACTCTAC-CTGGCAATGTTGATCCATC-AGATGATGAATTCAAGCA
66 ATGAACT-TTCTCTGGAAAAAATAATCCATCAAG-TGATGAATTCAAGCA
* * *
36771 AAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
**
36836 ATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGAT-AGATTTGAGCA
66 ATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGA-ATTCAAGCA
36884 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** *
36949 ATGAACTTTCTCTTCAAAAAAATAATCCATCAATTGAT
66 ATGAACTTTCTC-TGGAAAAAATAATCCATCAAGTGAT
36987 AGATTTGAAT
Statistics
Matches: 703, Mismatches: 58, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
109 2 0.00
110 91 0.13
111 5 0.01
112 9 0.01
113 567 0.81
114 28 0.04
115 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAAGCA
Found at i:37797 original size:83 final size:83
Alignment explanation
Indices: 37605--38035 Score: 785
Period size: 83 Copynumber: 5.2 Consensus size: 83
37595 TTCATCTTTT
* * *
37605 AATTCCAACGATTGGTTCTGTCC-AACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATT-CAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
37669 ATTGAGCAAATTCATCTTCCA
64 ATTG-GCAAATTCATCTTCCA
37690 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
37755 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
37773 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
37838 TGAGCAAATTCATCTTCCA
66 TG-GCAAATTCATCTTCCA
37857 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
37922 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
37940 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
38004 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
38022 AATTCAATGATTGG
1 AATTCAATGATTGG
38036 ACTAAGATAT
Statistics
Matches: 341, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
82 32 0.09
83 165 0.48
84 140 0.41
85 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (83 bp):
AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGGCAAATTCATCTTCCA
Found at i:37871 original size:167 final size:167
Alignment explanation
Indices: 37605--38035 Score: 796
Period size: 167 Copynumber: 2.6 Consensus size: 167
37595 TTCATCTTTT
* * *
37605 AATTCCAACGATTGGTTCTGTCC-AACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATT-CAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
37669 ATTGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAG
64 ATTGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAG
37734 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
129 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
37773 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
37838 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
66 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
37903 CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
131 CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
37940 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
38004 TG-GCAAATTCATCTTCCAAATTCAATGATTGG
66 TGAGCAAATTCATCTTCCAAATTCAATGATTGG
38036 ACTAAGATAT
Statistics
Matches: 259, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
165 30 0.12
166 4 0.02
167 221 0.85
168 4 0.02
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (167 bp):
AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
Found at i:39179 original size:11 final size:10
Alignment explanation
Indices: 39154--39212 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
39144 TTGACCCCTT
39154 TTTTTTCTTCTC
1 TTTTTT-TT-TC
39166 TTTTTTTTTCC
1 TTTTTTTTT-C
*
39177 TTTTCATTTTC
1 TTTT-TTTTTC
39188 TATTTTTTTTC
1 T-TTTTTTTTC
*
39199 TTCTTTTTTC
1 TTTTTTTTTC
39209 TTTT
1 TTTT
39213 CTCTTCAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 12 0.30
11 15 0.38
12 13 0.32
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:39206 original size:26 final size:25
Alignment explanation
Indices: 39166--39214 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
39156 TTTTCTTCTC
39166 TTTTTTTTTC-CTTTTCATTTTCTAT
1 TTTTTTTTTCTCTTTTC-TTTTCTAT
*
39191 TTTTTTTCTTCTTTTTTCTTTTCT
1 TTTTTTT-TTCTCTTTTCTTTTCT
39215 CTTCAAGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 9 0.43
27 5 0.24
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTCTCTTTTCTTTTCTAT
Found at i:49544 original size:13 final size:15
Alignment explanation
Indices: 49522--49558 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
49512 TTTGACAGAA
49522 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
49534 AAATAAAATACTTGC
1 AAATAAAATACTTGC
49549 AAATAAAATA
1 AAATAAAATA
49559 AACATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:50389 original size:21 final size:23
Alignment explanation
Indices: 50354--50396 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
50344 GAAAACATAT
50354 AAAATAAATAACTAAATATAATA
1 AAAATAAATAACTAAATATAATA
*
50377 AAAAT-AA-AACTAAATCTAAT
1 AAAATAAATAACTAAATATAAT
50397 TCCTAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAATAAATAACTAAATATAATA
Done.