Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006221.1 Hibiscus syriacus cultivar Beakdansim tig00014821_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: 62157
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2577 original size:24 final size:22
Alignment explanation
Indices: 2532--2592 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
2522 CAAATGGCAA
*
2532 TCATTCTTTATACTTCACATTTT
1 TCATTCTTTATA-TTCACATTTC
* *
2555 TACATTATTTATATTCATTATTTC
1 T-CATTCTTTATATTCA-CATTTC
2579 TCATTCTTTATATT
1 TCATTCTTTATATT
2593 TATTTCATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (22 bp):
TCATTCTTTATATTCACATTTC
Found at i:6535 original size:18 final size:18
Alignment explanation
Indices: 6514--6565 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
6504 TATCTTTTTG
*
6514 AAATTCAATTTATTTTCA
1 AAATTCAATTTATTATCA
*
6532 AAATTCAAGTTATTATCA
1 AAATTCAATTTATTATCA
6550 AAATTCAATTTATTAT
1 AAATTCAATTTATTAT
6566 TTTATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (18 bp):
AAATTCAATTTATTATCA
Found at i:7706 original size:122 final size:123
Alignment explanation
Indices: 7487--8065 Score: 793
Period size: 122 Copynumber: 4.7 Consensus size: 123
7477 TACTCGATGG
7487 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAA-GAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * * * * *
7551 ATAAGAAGAACTTATTTAACTTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAAC
7609 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAA-AAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * **
7673 ATGAGAAGAACTTGTTCAACTTTTTGCTTGATTCTATCACAGAAGAAGATAGATCAGT
66 ATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAAC
* *
7731 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
7795 ATGAGAAGAACTTGTTCAACCTTTTGCATGATTCTATCACAGAAGGAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAAC
*
7853 AT--ACATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTT-ATCTGAAG-AGGAAGAAGAAGTT
1 ATCAACA--TTTCCAGA-AGAGTTCATAATGAGAAGAA-TTCATCTGAAGAAGGAAGAAGAAGTT
* * *
7914 CATAAT---AAGAACTTGTTCAACCTTTTGCGTAACTCTATCACAGAAGGAGATAGATCAAC
62 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAAC
* * * *
7973 ATCAACATTCATTTCCCAAAGAGAGTTTATAATGAGAAGAACTCATCTGAAGAAGG-AGAACAAG
1 ATC-A-A--CATTT-CCAGA-AGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAG
*
8037 TTCATAATGAGAAGAATTTGTTCAACCTT
60 TTCATAATGAGAAGAACTTGTTCAACCTT
8066 GCCTTAATTC
Statistics
Matches: 414, Mismatches: 25, Indels: 30
0.88 0.05 0.06
Matches are distributed among these distances:
120 55 0.13
121 5 0.01
122 231 0.56
123 49 0.12
124 6 0.01
125 46 0.11
126 5 0.01
128 17 0.04
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGAGATAGATCAAC
Found at i:8425 original size:3 final size:3
Alignment explanation
Indices: 8410--8479 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
8400 TCATTTGGGT
*
8410 TTA TTA ATA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8456 TT- TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA
8480 CAAGCCCAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
2 6 0.10
3 53 0.85
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:8442 original size:29 final size:29
Alignment explanation
Indices: 8411--8479 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
8401 CATTTGGGTT
*
8411 TATTAATATTATTATTTTATTATTATTA-T
1 TATTATTATTATTATTTT-TTATTATTATT
8440 TATTATTATTATTATTTTTTATTATTATT
1 TATTATTATTATTATTTTTTATTATTATT
8469 TATTATTATTA
1 TATTATTATTA
8480 CAAGCCCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 9 0.24
29 29 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTATTATTATTATTTTTTATTATTATT
Found at i:10190 original size:144 final size:141
Alignment explanation
Indices: 9973--10279 Score: 449
Period size: 146 Copynumber: 2.1 Consensus size: 141
9963 TCCTTTTCTG
* *
9973 ATATTTTTATAAATAT-TAATTTAATTTATTTTTTAATTATTTTTAGAGAAATGTTTTATTAATA
1 ATATTTTTATATATATAT-A-TTAATTTATTTTTTAATTATTTTTAGAGAAATGATTTATTAATA
*
10037 TTTATTTATTTTTTTTATATTAAGAAAGGGCTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
64 TTTATTTA-TTTTTTAATATTAAGAAAGGG-TTGTCTTAAAGCAACTAGAAGT-ATTTTCTGATA
*
10102 TTTTTAAATAAATAAAT
126 TTTCTAAATAAAT-AAT
*
10119 ATCTTTTTATATATATATATTAATTTTATTTTTTAATT-TTTTTAGAGAAAT-ATTTATTAATAT
1 ATATTTTTATATATATATATTAA-TTTATTTTTTAATTATTTTTAGAGAAATGATTTATTAATAT
*
10182 TTATTTATTTTTTAATATTAAGAAAGGGTTGTCTTAAAGCAACTAGAAGTTTTTTCTGATATTTC
65 TTATTTATTTTTTAATATTAAGAAAGGGTTGTCTTAAAGCAACTAGAAGTATTTTCTGATATTTC
*
10247 TAAATAAATTAT
130 TAAATAAATAAT
* *
10259 ATATATATATATATATATATT
1 ATATTTTTATATATATATATT
10280 TATTAAAAAT
Statistics
Matches: 149, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
140 20 0.13
141 22 0.15
142 22 0.15
143 20 0.13
144 18 0.12
145 17 0.11
146 29 0.19
147 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (141 bp):
ATATTTTTATATATATATATTAATTTATTTTTTAATTATTTTTAGAGAAATGATTTATTAATATT
TATTTATTTTTTAATATTAAGAAAGGGTTGTCTTAAAGCAACTAGAAGTATTTTCTGATATTTCT
AAATAAATAAT
Found at i:10285 original size:144 final size:145
Alignment explanation
Indices: 9993--10279 Score: 451
Period size: 141 Copynumber: 2.0 Consensus size: 145
9983 AAATATTAAT
* *
9993 TTAATTTATTTTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTATTTATTTTTTTTATATT
1 TTAATTTATTTTTTAATTATTTTTAGAGAAATGATTTATTAATATTTATTTATTTTTTTAATATT
* *
10058 AAGAAAGGGCTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATATTTTTAAATAAATAAATATCT
66 AAGAAAGGGCTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATATTTCTAAATAAATAAATATAT
* *
10123 TTTTATATATATATA
131 ATATATATATATATA
10138 TTAATTTTATTTTTTAATT-TTTTTAGAGAAAT-ATTTATTAATATTTATTTA-TTTTTTAATAT
1 TTAA-TTTATTTTTTAATTATTTTTAGAGAAATGATTTATTAATATTTATTTATTTTTTTAATAT
* *
10200 TAAGAAAGGG-TTGTCTTAAAGCAACTAGAAGT-TTTTTCTGATATTTCTAAATAAAT-TATATA
65 TAAGAAAGGGCTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATATTTCTAAATAAATAAATATA
10262 TATATATATATATATA
130 TATATATATATATATA
10278 TT
1 TT
10280 TATTAAAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
140 20 0.15
141 22 0.17
142 22 0.17
143 20 0.15
144 18 0.14
145 17 0.13
146 14 0.11
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (145 bp):
TTAATTTATTTTTTAATTATTTTTAGAGAAATGATTTATTAATATTTATTTATTTTTTTAATATT
AAGAAAGGGCTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATATTTCTAAATAAATAAATATAT
ATATATATATATATA
Found at i:11507 original size:22 final size:23
Alignment explanation
Indices: 11474--11525 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
11464 GAATAAAATT
* *
11474 TTAACATAAATACTATTAATAAAA
1 TTAA-ATAAATAATATTAAAAAAA
*
11498 -TAAATAAATAATTTTAAAAAAA
1 TTAAATAAATAATATTAAAAAAA
11520 TTAAAT
1 TTAAAT
11526 TTCAAGATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
TTAAATAAATAATATTAAAAAAA
Found at i:23816 original size:31 final size:31
Alignment explanation
Indices: 23737--23809 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
23727 CCCAATAGTT
23737 ATGTT-GGGGACCATATTGCAAATAGACTAA
1 ATGTTAGGGGACCATATTGCAAATAGACTAA
* *
23767 ATGTTAGGGGGCCATATTGCAAATGGACTAA
1 ATGTTAGGGGACCATATTGCAAATAGACTAA
23798 ATGTTAGGGGAC
1 ATGTTAGGGGAC
23810 TGTATTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 5 0.13
31 34 0.87
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (31 bp):
ATGTTAGGGGACCATATTGCAAATAGACTAA
Found at i:28437 original size:60 final size:59
Alignment explanation
Indices: 28335--28449 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 59
28325 TGACATGATC
** * *
28335 CCTTCAAGTTCCAGGGGAAGCATTCAACTGCGAGCTTCTTCGACCTCAAA-GTCGAGATG
1 CCTTCAAGTTAAAGGGGAAGCATTCAACTACCAGCTTCTTCGACCT-AAATGTCGAGATG
* *
28394 CCTTCAAGTTAAATGGGAAGGCATTCAACTACCAGCTTGTTCGACCTAAATGTCGA
1 CCTTCAAGTTAAAGGGGAA-GCATTCAACTACCAGCTTCTTCGACCTAAATGTCGA
28450 CATTGTGGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 19 0.40
60 29 0.60
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (59 bp):
CCTTCAAGTTAAAGGGGAAGCATTCAACTACCAGCTTCTTCGACCTAAATGTCGAGATG
Found at i:38103 original size:22 final size:22
Alignment explanation
Indices: 38077--38158 Score: 67
Period size: 23 Copynumber: 3.7 Consensus size: 22
38067 ATAGGGCAGA
* *
38077 GGGAATCGATACCCCCATGAAG
1 GGGAACCGATACCCCCATGAAC
* * *
38099 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATACCCCC-ATGAAC
* * *
38122 GGGAACCGATTCCCCCCT-TAC
1 GGGAACCGATACCCCCATGAAC
*
38143 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
38159 CAAGGGTTCT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
21 15 0.30
22 15 0.30
23 20 0.40
ACGTcount: A:0.24, C:0.34, G:0.23, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCATGAAC
Found at i:38120 original size:23 final size:22
Alignment explanation
Indices: 38077--38137 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
38067 ATAGGGCAGA
* *
38077 GGGAATCGATACCCCCATGAAG
1 GGGAACCGATTCCCCCATGAAG
* *
38099 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCC-ATGAAG
38122 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
38138 CTTACGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCATGAAG
Found at i:38152 original size:21 final size:22
Alignment explanation
Indices: 38099--38159 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
38089 CCCCATGAAG
* *
38099 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCCTT-AAC
38122 GGGAACCGATTCCCCCCTT-AC
1 GGGAACCGATTCCCCCCTTAAC
* *
38143 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
38160 AAGGGTTCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.47
23 18 0.53
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTAAC
Found at i:49889 original size:2 final size:2
Alignment explanation
Indices: 49882--49910 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49872 CTTTAAACAA
49882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49911 AAACTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50580 original size:75 final size:69
Alignment explanation
Indices: 50501--50650 Score: 156
Period size: 69 Copynumber: 2.1 Consensus size: 69
50491 AAATCATTGC
* * * * *
50501 AATTAAGTCGTTGTCCCTCACAAAATATTTTGGTATAATTACTTTTTAGGACACTATTAATTTTA
1 AATTAAGT-GTTGACCC-CA-AAAATA-TCTAGTATAATTACTTTTTAAGAC-CTA-CAATTTTA
50566 AAATTAATGA
60 AAATTAATGA
* ** * *
50576 AATTAAGTTTTGACCCCAAATTTATCTAGTTTAATTACTTTTTAAGACCTACAATTTTAAAGTTA
1 AATTAAGTGTTGACCCCAAAAATATCTAGTATAATTACTTTTTAAGACCTACAATTTTAAAATTA
50641 ATGA
66 ATGA
50645 AATTAA
1 AATTAA
50651 ACCCTTAATC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
69 22 0.34
70 3 0.05
71 20 0.31
72 4 0.06
73 2 0.03
74 6 0.09
75 8 0.12
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (69 bp):
AATTAAGTGTTGACCCCAAAAATATCTAGTATAATTACTTTTTAAGACCTACAATTTTAAAATTA
ATGA
Found at i:59270 original size:18 final size:18
Alignment explanation
Indices: 59244--59286 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
59234 GAGGACGATA
* **
59244 ATGAAGAAGAAGATTATG
1 ATGATGAAGAAGAGAATG
59262 ATGATGAAGAAGAGAATG
1 ATGATGAAGAAGAGAATG
59280 ATGATGA
1 ATGATGA
59287 CGATGGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (18 bp):
ATGATGAAGAAGAGAATG
Found at i:59286 original size:24 final size:23
Alignment explanation
Indices: 59237--59298 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
59227 TAACCTAGAG
*
59237 GACGAT-AATGAAGAAGAAGATTAT
1 GACGATGAA-GAAG-AGAAGATGAT
*
59261 GATGATGAAGAAGAGAATGATGAT
1 GACGATGAAGAAGAGAA-GATGAT
*
59285 GACGATGGAGAAGA
1 GACGATGAAGAAGA
59299 ACCCGAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 4 0.12
24 26 0.81
25 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.32, T:0.18
Consensus pattern (23 bp):
GACGATGAAGAAGAGAAGATGAT
Done.