Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004311.1 Hibiscus syriacus cultivar Beakdansim tig00009455_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: 91106
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7427 original size:40 final size:35
Alignment explanation
Indices: 7336--7457 Score: 154
Period size: 35 Copynumber: 3.4 Consensus size: 35
7326 TAAAACTTGT
*
7336 AAAATAATCCTCAATTTCATTCTAAACCCCAATTTCC
1 AAAATAAT--TCAATTTCATTCTAAACCCCAAATTCC
* *
7373 AAAGTAATTCAATTTCATTCTAAACCCTAAATTCC
1 AAAATAATTCAATTTCATTCTAAACCCCAAATTCC
** * *
7408 AAAATAATTCAATTAAATTTTAAACCCCAAATTCT
1 AAAATAATTCAATTTCATTCTAAACCCCAAATTCC
*
7443 AAAATACTTCAATTT
1 AAAATAATTCAATTT
7458 AAGGTTTAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 67 0.91
37 7 0.09
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (35 bp):
AAAATAATTCAATTTCATTCTAAACCCCAAATTCC
Found at i:7521 original size:35 final size:35
Alignment explanation
Indices: 7453--7527 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
7443 AAAATACTTC
* * *
7453 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
7488 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
7523 AATTT
1 AATTT
7528 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:10868 original size:29 final size:28
Alignment explanation
Indices: 10805--10868 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
10795 AGCAACGAGT
*
10805 CGAGTCAAGCAACAAGTTTTTTTAACGAA
1 CGAGTCAAACAACAAG-TTTTTTAACGAA
*
10834 CAAGTCAAACAACAA-TTTTTTAACGAGCA
1 CGAGTCAAACAACAAGTTTTTTAACGA--A
10863 CGAGTC
1 CGAGTC
10869 GAGTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 11 0.37
29 19 0.63
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (28 bp):
CGAGTCAAACAACAAGTTTTTTAACGAA
Found at i:14737 original size:24 final size:24
Alignment explanation
Indices: 14677--14740 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 24
14667 GTTTGTTTAT
* * *
14677 TTAT-TGTTCACGAATATATTCAT
1 TTATATGTTCATGAATGTATTCAC
*
14700 TTA-ATGTTCGTGAATGTATTCAC
1 TTATATGTTCATGAATGTATTCAC
14723 TTATATGTTCATGAATGT
1 TTATATGTTCATGAATGT
14741 GTTTATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (24 bp):
TTATATGTTCATGAATGTATTCAC
Found at i:32236 original size:35 final size:35
Alignment explanation
Indices: 32185--32262 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
32175 GTATCAATGA
*
32185 GTAAGGGACATGTACAACTATTGAAATGATGCAAG
1 GTAAAGGACATGTACAACTATTGAAATGATGCAAG
32220 GTAAAGGACATGTACAACTATTGAAATGATGCAAG
1 GTAAAGGACATGTACAACTATTGAAATGATGCAAG
32255 GTAAAGGA
1 GTAAAGGA
32263 ATAGTTCTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (35 bp):
GTAAAGGACATGTACAACTATTGAAATGATGCAAG
Found at i:32840 original size:60 final size:59
Alignment explanation
Indices: 32703--32815 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
32693 AACATAATGA
* * * *
32703 ATAGTC-AAGTGAACATTTTGTAACTTTTAATAGTTGAGGACTCAACAAAGTAACACTCT
1 ATAGTCAAAG-GACCATTTTATAACTTTTAATAGTCGAGAACTCAACAAAGTAACACTCT
* * *
32762 ATAGTCAAAGGATCATTTTATAACTTTTAATAGTCGAAGAACTTAATAAAGTAA
1 ATAGTCAAAGGACCATTTTATAACTTTTAATAGTCG-AGAACTCAACAAAGTAA
32816 TATCTTATAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 29 0.63
60 17 0.37
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (59 bp):
ATAGTCAAAGGACCATTTTATAACTTTTAATAGTCGAGAACTCAACAAAGTAACACTCT
Found at i:40906 original size:25 final size:23
Alignment explanation
Indices: 40854--40905 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
40844 AAACATTTCG
40854 TATATAAGAATGTGAGCTTTCAA
1 TATATAAGAATGTGAGCTTTCAA
40877 TATATAAGAATGTGAGCTTTCAA
1 TATATAAGAATGTGAGCTTTCAA
40900 TATATA
1 TATATA
40906 TATTTGTTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (23 bp):
TATATAAGAATGTGAGCTTTCAA
Found at i:40930 original size:13 final size:14
Alignment explanation
Indices: 40902--40934 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40892 GCTTTCAATA
*
40902 TATATATTTGTTCG
1 TATATATATGTTCG
40916 TATATATAT-TTCG
1 TATATATATGTTCG
40929 TATATA
1 TATATA
40935 AGAATGTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (14 bp):
TATATATATGTTCG
Found at i:47166 original size:13 final size:13
Alignment explanation
Indices: 47148--47181 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
47138 AATTTGCAAT
47148 TTTTTCAATTTTA
1 TTTTTCAATTTTA
47161 TTTTTCAATTTTA
1 TTTTTCAATTTTA
47174 TTTTTCAA
1 TTTTTCAA
47182 ACAACTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTCAATTTTA
Found at i:51872 original size:60 final size:60
Alignment explanation
Indices: 51801--51913 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
51791 ATAATCGAGT
* * *
51801 GATCATTTTGTAACTTTTAATAGTT-GAGGTACTCAATAAAGCAATGCCCTATAGTTGGGA
1 GATCATTTTGTAACTTTTAATAGTTGGATG-ACTCAACAAAGCAACGCCCTATAGTTGGGA
*
51861 GATCATTTTGTAACTTTTAATAGTTGGATGACTCAACAAAGCAACGTCCTATA
1 GATCATTTTGTAACTTTTAATAGTTGGATGACTCAACAAAGCAACGCCCTATA
51914 AGGCCATCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 45 0.94
61 3 0.06
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTTGGATGACTCAACAAAGCAACGCCCTATAGTTGGGA
Found at i:52757 original size:8 final size:9
Alignment explanation
Indices: 52726--52785 Score: 68
Period size: 9 Copynumber: 6.4 Consensus size: 9
52716 TTGAATTTAA
*
52726 AAAAAATCAT
1 AAAAAAT-AC
*
52736 AAAAAATAT
1 AAAAAATAC
52745 AAAAAATAC
1 AAAAAATAC
52754 AAAAAATAC
1 AAAAAATAC
52763 AAAAAAT-C
1 AAAAAATAC
52771 AGAAAAATTAC
1 A-AAAAA-TAC
52782 AAAA
1 AAAA
52786 CAATTAGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
8 2 0.04
9 31 0.67
10 11 0.24
11 2 0.04
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (9 bp):
AAAAAATAC
Found at i:52757 original size:18 final size:19
Alignment explanation
Indices: 52726--52785 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
52716 TTGAATTTAA
* *
52726 AAAAAATCATAAAAAATAT
1 AAAAAATCACAAAAAATAC
52745 AAAAAAT-ACAAAAAATAC
1 AAAAAATCACAAAAAATAC
* *
52763 AAAAAATCAGAAAAATTAC
1 AAAAAATCACAAAAAATAC
52782 AAAA
1 AAAA
52786 CAATTAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 16 0.44
19 20 0.56
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAAAATCACAAAAAATAC
Found at i:53069 original size:43 final size:43
Alignment explanation
Indices: 53021--53110 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
53011 ATGATAGAGA
*
53021 TAGCGCAGGATTGGAGCGCGCTACAATGAAAATATCTCCACTG
1 TAGCGCAGGATTGGAGCGAGCTACAATGAAAATATCTCCACTG
* *
53064 TAGCGCAGGGTTGGAGCGAGCTACAGTGAAAATATCTCCACTG
1 TAGCGCAGGATTGGAGCGAGCTACAATGAAAATATCTCCACTG
53107 TAGC
1 TAGC
53111 ATAGCGTTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (43 bp):
TAGCGCAGGATTGGAGCGAGCTACAATGAAAATATCTCCACTG
Found at i:53120 original size:43 final size:43
Alignment explanation
Indices: 53031--53122 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
53021 TAGCGCAGGA
* * *
53031 TTGGAGCGCGCTACAATGAAAATATCTCCACTGTAGCGCAGGG
1 TTGGAGCGAGCTACAATGAAAATATCTCCACTGTAGCACAGCG
* *
53074 TTGGAGCGAGCTACAGTGAAAATATCTCCACTGTAGCATAGCG
1 TTGGAGCGAGCTACAATGAAAATATCTCCACTGTAGCACAGCG
53117 TTGGAG
1 TTGGAG
53123 ATGGTCTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (43 bp):
TTGGAGCGAGCTACAATGAAAATATCTCCACTGTAGCACAGCG
Found at i:55947 original size:37 final size:37
Alignment explanation
Indices: 55897--55972 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
55887 CTGTTATGAA
*
55897 AGTACACACAATATGAATGAGAAAATATGTAAAAGAG
1 AGTACACACAATATGAACGAGAAAATATGTAAAAGAG
*
55934 AGTACACATAATATGAACGAGAAAATATGTAAAAGAG
1 AGTACACACAATATGAACGAGAAAATATGTAAAAGAG
55971 AG
1 AG
55973 GAGTTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (37 bp):
AGTACACACAATATGAACGAGAAAATATGTAAAAGAG
Found at i:64320 original size:23 final size:21
Alignment explanation
Indices: 64294--64343 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 21
64284 GAATGCCAAT
*
64294 CTTTTCTTTATCTTTCTTTTACC
1 CTTTTCTTCAT-TTTCTTTT-CC
64317 CTTTTTCTTCATTTTCTTTTCC
1 C-TTTTCTTCATTTTCTTTTCC
64339 CTTTT
1 CTTTT
64344 TCTCTTGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 3 0.12
23 9 0.36
24 9 0.36
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (21 bp):
CTTTTCTTCATTTTCTTTTCC
Found at i:64344 original size:23 final size:24
Alignment explanation
Indices: 64295--64346 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
64285 AATGCCAATC
*
64295 TTTTCTTTATCTTTCTTTTACCCT
1 TTTTCTTCATCTTTCTTTTACCCT
64319 TTTTCTTCAT-TTTCTTTT-CCCT
1 TTTTCTTCATCTTTCTTTTACCCT
64341 TTTTCT
1 TTTTCT
64347 CTTGCTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.37
23 8 0.30
24 9 0.33
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTCTTCATCTTTCTTTTACCCT
Found at i:75396 original size:16 final size:16
Alignment explanation
Indices: 75375--75405 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
75365 TAAACTCTTA
75375 TTTTAATTTTAAATAC
1 TTTTAATTTTAAATAC
*
75391 TTTTAATTTTTAATA
1 TTTTAATTTTAAATA
75406 AGACTAGCGA
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:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAATTTTAAATAC
Found at i:81993 original size:22 final size:22
Alignment explanation
Indices: 81951--81993 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
81941 AAATAATAAT
*
81951 ATTATAAAAAAATATTGATTTG
1 ATTATAAAAAAATATTAATTTG
*
81973 ATTATAATATAAAT-TTAATTT
1 ATTATAA-AAAAATATTAATTT
81994 TTTGGTACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTATAAAAAAATATTAATTTG
Found at i:88376 original size:15 final size:15
Alignment explanation
Indices: 88337--88365 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88327 TGGTTTTCAG
88337 AAAATGAATTACTGA
1 AAAATGAATTACTGA
88352 AAAATGAATTACTG
1 AAAATGAATTACTG
88366 TAATTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (15 bp):
AAAATGAATTACTGA
Found at i:88776 original size:22 final size:23
Alignment explanation
Indices: 88718--88858 Score: 81
Period size: 24 Copynumber: 5.6 Consensus size: 23
88708 TTATTTAAAT
88718 ATAAAAATAATATTATTCATTATTAAA
1 ATAAAAAT-ATATTA-T-ATTATT-AA
*
88745 TATATAAAAAATTATTATATTATTAA
1 -ATA-AAAATA-TATTATATTATTAA
88771 ATAAAATATAATATCTTATATTA-TATA
1 ATAAAA-AT-ATA--TTATATTATTA-A
*
88798 AT-ATAAT-TGATTATATTATTAA
1 ATAAAAATAT-ATTATATTATTAA
*
88820 CTAAAAAATATATTATATTATTAA
1 AT-AAAAATATATTATATTATTAA
*
88844 TATTAATAATATATT
1 -A-TAAAAATATATT
88859 TTAAATATTT
Statistics
Matches: 92, Mismatches: 7, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
22 10 0.11
23 3 0.03
24 21 0.23
25 19 0.21
26 8 0.09
27 17 0.18
28 5 0.05
29 9 0.10
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (23 bp):
ATAAAAATATATTATATTATTAA
Found at i:88780 original size:30 final size:32
Alignment explanation
Indices: 88713--88781 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
88703 AAATATTATT
88713 TAAATATAAAAATAATATTATTCATTATTAAA
1 TAAATATAAAAATAATATTATTCATTATTAAA
*
88745 T--ATATAAAAA-ATTATTA-T-ATTATTAAA
1 TAAATATAAAAATAATATTATTCATTATTAAA
88772 TAAAATATAA
1 T-AAATATAA
88782 TATCTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 10 0.30
28 1 0.03
29 6 0.18
30 15 0.45
32 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAATATAAAAATAATATTATTCATTATTAAA
Found at i:88811 original size:49 final size:45
Alignment explanation
Indices: 88745--88865 Score: 133
Period size: 46 Copynumber: 2.7 Consensus size: 45
88735 CATTATTAAA
* *
88745 TATATAA-AAAATTATTATATTATTAAATAAAATATAATATCTTATAT
1 TATATAATATAATTATTATATTATTAAAT-AAA-A-AATATATTATAT
*
88792 TATATAATATAATTGATTATATTATTAACTAAAAAATATATTATAT
1 TATATAATATAATT-ATTATATTATTAAATAAAAAATATATTATAT
*
88838 TAT-TAATATTAA-TAATATATT-TTAAATA
1 TATATAATA-TAATTATTATATTATTAAATA
88866 TTTTAATAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
43 6 0.09
44 7 0.11
45 6 0.09
46 17 0.26
47 8 0.12
48 8 0.12
49 14 0.21
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (45 bp):
TATATAATATAATTATTATATTATTAAATAAAAAATATATTATAT
Found at i:89115 original size:42 final size:42
Alignment explanation
Indices: 89056--89170 Score: 185
Period size: 42 Copynumber: 2.7 Consensus size: 42
89046 ATAAATTACG
** *
89056 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAACATT
89098 TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAACATT
* *
89140 TTCCGAAAAACGAATTACATGAAACAAACAC
1 TTCCGGAAAACGAATTACGTGAAACAAACAC
89171 AGTATTTCGG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGAAAAAACATT
Found at i:90020 original size:24 final size:23
Alignment explanation
Indices: 89988--90043 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
89978 TGTAAATTAT
89988 AATTAATTATTGTAATCAATATAA
1 AATT-ATTATTGTAATCAATATAA
* * *
90012 AATTGATTATTTTATTTAATATAA
1 AATT-ATTATTGTAATCAATATAA
90036 AATTATTA
1 AATTATTA
90044 CTACGAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTATTATTGTAATCAATATAA
Done.