Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007442.1 Hibiscus syriacus cultivar Beakdansim tig00020307_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: 76570
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7615 original size:19 final size:18
Alignment explanation
Indices: 7580--7622 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
7570 TATTAAAATG
*
7580 ATATTAAAATATTATATTA
1 ATATTAAAATATAATA-TA
7599 ATATTAAACA-ATAATATA
1 ATATTAAA-ATATAATATA
7617 ATATTA
1 ATATTA
7623 TTTGAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 13 0.59
20 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTAAAATATAATATA
Found at i:22298 original size:35 final size:35
Alignment explanation
Indices: 22259--22333 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
22249 CGTCACGAAC
* * *
22259 AGTAAGGCCCTGAGTACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
*
22294 AGTAAGGCCCTGAGCACACAGCCAAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
22329 AGTAA
1 AGTAA
22334 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
Found at i:22421 original size:24 final size:24
Alignment explanation
Indices: 22394--22445 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
22384 TATAGCAAAA
22394 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACATAATTCAAGTCAAGT
* * * *
22418 ATCATATCATAATTCAGGTCATGT
1 ATCAAAACATAATTCAAGTCAAGT
22442 ATCA
1 ATCA
22446 GATCAGAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (24 bp):
ATCAAAACATAATTCAAGTCAAGT
Found at i:22471 original size:23 final size:23
Alignment explanation
Indices: 22411--22500 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
22401 CATAATTCAA
* * *
22411 GTCAAGTATCATATCATAATTCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
22435 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
22459 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
* *
22482 GTCAATATCATAACAGAAT
1 GTCAATATCAGATCAGAAT
22501 TCAAATTTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
23 34 0.61
24 22 0.39
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:24956 original size:10 final size:9
Alignment explanation
Indices: 24943--24990 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
24933 GTCAAAGTTT
24943 TGGTCAACAG
1 TGGTCAAC-G
24953 TGGTCAACG
1 TGGTCAACG
24962 TGGGTCAAC-
1 T-GGTCAACG
24971 -GGTCAACG
1 TGGTCAACG
24979 -GGTCAACG
1 TGGTCAACG
24987 -GGTC
1 TGGTC
24991 GGGTCAACGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.19
8 12 0.33
9 2 0.06
10 15 0.42
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (9 bp):
TGGTCAACG
Found at i:24984 original size:8 final size:8
Alignment explanation
Indices: 24944--25003 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
24934 TCAAAGTTTT
24944 GGTCAACAG
1 GGTCAAC-G
24953 TGGTCAACGTG
1 -GGTCAAC--G
24964 GGTCAAC-
1 GGTCAACG
24971 GGTCAACG
1 GGTCAACG
24979 GGTCAACG
1 GGTCAACG
24987 GGT---CG
1 GGTCAACG
24992 GGTCAACG
1 GGTCAACG
25000 GGTC
1 GGTC
25004 GGGTCGGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 17 0.39
10 14 0.32
11 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.38, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:24995 original size:13 final size:13
Alignment explanation
Indices: 24977--25051 Score: 78
Period size: 13 Copynumber: 5.4 Consensus size: 13
24967 CAACGGTCAA
24977 CGGGTCAACGGGT
1 CGGGTCAACGGGT
24990 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
25008 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
25021 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
25034 CGGGTAAACGGGT
1 CGGGTCAACGGGT
25047 CGGGT
1 CGGGT
25052 TATGACCGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:25008 original size:18 final size:18
Alignment explanation
Indices: 24971--25026 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
24961 GTGGGTCAAC
24971 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
24992 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
25010 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
25027 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:25015 original size:31 final size:31
Alignment explanation
Indices: 24977--25038 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
24967 CAACGGTCAA
24977 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
25008 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
25039 AAACGGGTCG
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:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:27066 original size:35 final size:35
Alignment explanation
Indices: 27020--27094 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
27010 CGTCACGAAC
* *
27020 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
*
27055 AGTAAGGCCCTGAGCACACAGCCAAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
27090 AGTAA
1 AGTAA
27095 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCAAGGAGCCTCCA
Found at i:27182 original size:24 final size:24
Alignment explanation
Indices: 27155--27206 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
27145 TATAGCAAAA
27155 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACATAATTCAAGTCAAGT
* * * *
27179 ATCATATCATAATTCAGGTCATGT
1 ATCAAAACATAATTCAAGTCAAGT
27203 ATCA
1 ATCA
27207 GATCAGAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (24 bp):
ATCAAAACATAATTCAAGTCAAGT
Found at i:27232 original size:23 final size:23
Alignment explanation
Indices: 27172--27261 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
27162 CATAATTCAA
* * *
27172 GTCAAGTATCATATCATAATTCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
27196 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
27220 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
* *
27243 GTCAATATCATAACAGAAT
1 GTCAATATCAGATCAGAAT
27262 TCAAATTTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
23 34 0.61
24 22 0.39
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:29717 original size:10 final size:9
Alignment explanation
Indices: 29704--29751 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
29694 GTCAAAGTTT
29704 TGGTCAACAG
1 TGGTCAAC-G
29714 TGGTCAACG
1 TGGTCAACG
29723 TGGGTCAAC-
1 T-GGTCAACG
29732 -GGTCAACG
1 TGGTCAACG
29740 -GGTCAACG
1 TGGTCAACG
29748 -GGTC
1 TGGTC
29752 GGGTCAACGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.19
8 12 0.33
9 2 0.06
10 15 0.42
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (9 bp):
TGGTCAACG
Found at i:29745 original size:8 final size:8
Alignment explanation
Indices: 29705--29764 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
29695 TCAAAGTTTT
29705 GGTCAACAG
1 GGTCAAC-G
29714 TGGTCAACGTG
1 -GGTCAAC--G
29725 GGTCAAC-
1 GGTCAACG
29732 GGTCAACG
1 GGTCAACG
29740 GGTCAACG
1 GGTCAACG
29748 GGT---CG
1 GGTCAACG
29753 GGTCAACG
1 GGTCAACG
29761 GGTC
1 GGTC
29765 GGGTCGGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 17 0.39
10 14 0.32
11 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.38, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:29756 original size:13 final size:13
Alignment explanation
Indices: 29738--29812 Score: 78
Period size: 13 Copynumber: 5.4 Consensus size: 13
29728 CAACGGTCAA
29738 CGGGTCAACGGGT
1 CGGGTCAACGGGT
29751 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
29769 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
29782 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
29795 CGGGTAAACGGGT
1 CGGGTCAACGGGT
29808 CGGGT
1 CGGGT
29813 TATGACCGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:29769 original size:18 final size:18
Alignment explanation
Indices: 29732--29787 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
29722 GTGGGTCAAC
29732 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
29753 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
29771 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
29788 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:29776 original size:31 final size:31
Alignment explanation
Indices: 29738--29799 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
29728 CAACGGTCAA
29738 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
29769 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
29800 AAACGGGTCG
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:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:36699 original size:66 final size:63
Alignment explanation
Indices: 36592--36714 Score: 149
Period size: 66 Copynumber: 1.9 Consensus size: 63
36582 TTTGTTGAAG
* * * *
36592 GTGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATAAACATCGAATGCCATT
1 GTGCATCGATGCACAAGGAGTGCATCGATACACTCA-TTAAAAT--ACAAACATCGAATGCCATT
36657 A
63 A
*
36658 GTGCATCGATGCATAAGGAGTGCATCGATACACCTGC-TTAAAATACAAACATCGAAT
1 GTGCATCGATGCACAAGGAGTGCATCGATACA-CT-CATTAAAATACAAACATCGAAT
36715 AGGATTTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
64 12 0.24
66 35 0.70
67 2 0.04
68 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (63 bp):
GTGCATCGATGCACAAGGAGTGCATCGATACACTCATTAAAATACAAACATCGAATGCCATTA
Found at i:48757 original size:21 final size:21
Alignment explanation
Indices: 48727--48787 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
48717 TCGAAGCTAA
* *
48727 AGCGAGAGAAGCAAAGAGAGC
1 AGCGATAGAAGCAGAGAGAGC
*
48748 AGCGATAGAATCAGAGAGAGC
1 AGCGATAGAAGCAGAGAGAGC
*
48769 AACGATAGAAGCAGAGAGA
1 AGCGATAGAAGCAGAGAGA
48788 AAAACATCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.34, T:0.05
Consensus pattern (21 bp):
AGCGATAGAAGCAGAGAGAGC
Found at i:49193 original size:42 final size:43
Alignment explanation
Indices: 49125--49227 Score: 104
Period size: 42 Copynumber: 2.4 Consensus size: 43
49115 TTTTTAGGAA
* *
49125 AAAACGCCGCTAAATGA-CCAACCTATTGCAGCGTTTGTG-C-CC
1 AAAA-GCCGCTAAAT-ATCAAACCTATTGCAGCGTTTGTGACTAC
* * **
49167 GACAAGCCGCTAAATATCAAATCTATTGTGGCGTTTGTGACTAC
1 -AAAAGCCGCTAAATATCAAACCTATTGCAGCGTTTGTGACTAC
49211 AAAAGCCGCTAAATATC
1 AAAAGCCGCTAAATATC
49228 GAACTTGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.02
42 28 0.56
43 20 0.40
44 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAAGCCGCTAAATATCAAACCTATTGCAGCGTTTGTGACTAC
Found at i:49609 original size:19 final size:17
Alignment explanation
Indices: 49587--49624 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
49577 ATACAAACAC
49587 AACAAC-AATATATAAA
1 AACAACAAATATATAAA
49603 AACAACAAATATATAAA
1 AACAACAAATATATAAA
*
49620 GACAA
1 AACAA
49625 AAGAAAGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.68, C:0.13, G:0.03, T:0.16
Consensus pattern (17 bp):
AACAACAAATATATAAA
Found at i:54740 original size:140 final size:139
Alignment explanation
Indices: 54487--54740 Score: 327
Period size: 140 Copynumber: 1.8 Consensus size: 139
54477 GACTAAATGT
*
54487 AAAAATGGAGGCTCTAATATTAATCCTAATTGATTTCAACCAATTATTGAATCAAATAACAGATA
1 AAAAATGGAGGCTCTAATATAAATCCTAATTGATTTCAACCAATTATTGAATCAAATAACAGATA
*
54552 TGGACCCTCGAGCATTTAATGCGAGGACTAAATCAAATACTCCCTAAATCAAGGGACTAAAGTGA
66 TGGACCCTCGAGCATTTAATGCGAGGACTAAATCAAATAATCCCTAAATCAAGGGACTAAAGTGA
54617 AATTAAATA
131 AATTAAATA
* * * * * *
54626 AAAAATGGAGGCTCTAAT-TAACGATCTTAATT-ATTTTTAACCGATTATTTAATCGAATATTCA
1 AAAAATGGAGGCTCTAATATAA--ATCCTAATTGA-TTTCAACCAATTATTGAATCAAATA-ACA
* * * *
54689 -ATATTGACCCTC-AGTCATTTAATGCGAGGGCTAAATCGAATAATCCTTAAAT
62 GATATGGACCCTCGAG-CATTTAATGCGAGGACTAAATCAAATAATCCCTAAAT
54741 TAAGAAGTTT
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
138 2 0.02
139 21 0.21
140 73 0.74
141 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (139 bp):
AAAAATGGAGGCTCTAATATAAATCCTAATTGATTTCAACCAATTATTGAATCAAATAACAGATA
TGGACCCTCGAGCATTTAATGCGAGGACTAAATCAAATAATCCCTAAATCAAGGGACTAAAGTGA
AATTAAATA
Found at i:65409 original size:18 final size:19
Alignment explanation
Indices: 65388--65423 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
65378 ATAAAAACTC
65388 TAAAATATAT-GATAATTT
1 TAAAATATATGGATAATTT
*
65406 TAAAATTTATGGATAATT
1 TAAAATATATGGATAATT
65424 GCCCCGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
TAAAATATATGGATAATTT
Found at i:67650 original size:31 final size:32
Alignment explanation
Indices: 67612--67673 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
67602 GAAGAATATG
67612 TTATCGTCGAACGATTGTTGTTTT-AATAGTT
1 TTATCGTCGAACGATTGTTGTTTTAAATAGTT
*
67643 TTATCGTCGAATGATTGTTGTTTTAAATAGT
1 TTATCGTCGAACGATTGTTGTTTTAAATAGT
67674 GTCATCTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.48
Consensus pattern (32 bp):
TTATCGTCGAACGATTGTTGTTTTAAATAGTT
Found at i:67752 original size:22 final size:23
Alignment explanation
Indices: 67724--67771 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
67714 ACTGTGTTGA
67724 ACCATGCTTTGAGATTTCG-TAT
1 ACCATGCTTTGAGATTTCGATAT
*
67746 ACCATGCTTTGAGATTTTGATAT
1 ACCATGCTTTGAGATTTCGATAT
67769 ACC
1 ACC
67772 GAAAGTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (23 bp):
ACCATGCTTTGAGATTTCGATAT
Done.