Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003745.1 Hibiscus syriacus cultivar Beakdansim tig00008015_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: 54363
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:250 original size:30 final size:30
Alignment explanation
Indices: 214--321 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 30
204 TGTATTATTA
214 TGAAGAAGACGCCGAG-ACATCC-CCCTCATG
1 TGAAGAAGACGCCGAGTA-ATCCACCC-CATG
* * *
244 TGAAGAAAACGCCGAGTATTCCACCCCCAATA
1 TGAAGAAGACGCCGAGTAATCCA-CCCC-ATG
* *
276 TGCAA-AAGACGCCGAGTAATCCACCCAAAG
1 TG-AAGAAGACGCCGAGTAATCCACCCCATG
306 TGAAGAAGACGCCGAG
1 TGAAGAAGACGCCGAG
322 ACATCCTCTA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.03
30 32 0.50
31 5 0.08
32 23 0.36
33 2 0.03
ACGTcount: A:0.36, C:0.30, G:0.22, T:0.12
Consensus pattern (30 bp):
TGAAGAAGACGCCGAGTAATCCACCCCATG
Found at i:429 original size:20 final size:19
Alignment explanation
Indices: 384--430 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
374 TGCATCTTTA
*
384 TCTGCTCACCCCGTGAATT
1 TCTGCTCACCACGTGAATT
*
403 CCTTGCTCACCACGTGAATTT
1 TC-TGCTCACCACGTGAA-TT
424 TCTGCTC
1 TCTGCTC
431 TAGCCCTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.15, C:0.36, G:0.15, T:0.34
Consensus pattern (19 bp):
TCTGCTCACCACGTGAATT
Found at i:1551 original size:23 final size:21
Alignment explanation
Indices: 1507--1550 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1497 AAAAATTACT
1507 TAAAATATTATTATTTTTATA
1 TAAAATATTATTATTTTTATA
* *
1528 TAAAATATTAATATTTTTTTA
1 TAAAATATTATTATTTTTATA
1549 TA
1 TA
1551 TTTTTCGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAAATATTATTATTTTTATA
Found at i:1553 original size:31 final size:31
Alignment explanation
Indices: 1470--1564 Score: 77
Period size: 31 Copynumber: 3.0 Consensus size: 31
1460 TTTGTTTTAT
* * *
1470 TATTATTATTTTTTAATATTTTTAATAAAAAA
1 TATTAATATTTTTTTATATTTTT-ATATAAAA
* * *
1502 TTACTTAA-AATATTAT-TATTTTTATATAAAA
1 -TA-TTAATATTTTTTTATATTTTTATATAAAA
**
1533 TATTAATATTTTTTTATATTTTTCGATAAAA
1 TATTAATATTTTTTTATATTTTTATATAAAA
1564 T
1 T
1565 TTTCAATAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
29 4 0.08
30 7 0.15
31 21 0.44
32 7 0.15
33 6 0.12
34 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
TATTAATATTTTTTTATATTTTTATATAAAA
Found at i:8226 original size:24 final size:27
Alignment explanation
Indices: 8176--8237 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
8166 TCCCTTCCAT
*
8176 CCACCACCACCTCATTCTATTTCTCCG
1 CCACCACCACCTCATTCTATCTCTCCG
*
8203 CCATCACCACCTCATT-TA-CT-TCCG
1 CCACCACCACCTCATTCTATCTCTCCG
8227 CCACCACCACC
1 CCACCACCACC
8238 ACCACACCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.44
25 1 0.03
26 2 0.06
27 15 0.47
ACGTcount: A:0.21, C:0.52, G:0.03, T:0.24
Consensus pattern (27 bp):
CCACCACCACCTCATTCTATCTCTCCG
Found at i:11903 original size:30 final size:30
Alignment explanation
Indices: 11837--11958 Score: 129
Period size: 30 Copynumber: 4.0 Consensus size: 30
11827 ACCCAATCCG
* * * *
11837 AAAAT-AATTAATTGGATATTGATCTGACTCG
1 AAAATCAACTAATTCGAT-TTGATCCGAC-CC
* * *
11868 AAAATCAATTGATTCGATTTGATCCGACCT
1 AAAATCAACTAATTCGATTTGATCCGACCC
*
11898 AAAATCAACTGATTCGATTTGATCCGACCC
1 AAAATCAACTAATTCGATTTGATCCGACCC
*
11928 AAAATCAACTAATTCGATTTTGAACCGACCC
1 AAAATCAACTAATTCGA-TTTGATCCGACCC
11959 TATACCTGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 45 0.56
31 26 0.32
32 10 0.12
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (30 bp):
AAAATCAACTAATTCGATTTGATCCGACCC
Found at i:12087 original size:31 final size:31
Alignment explanation
Indices: 12049--12107 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
12039 ACTTACTAGA
**
12049 AACCCGAATAAAATTGAAACCAAAATAATCC
1 AACCCGAATAAAATACAAACCAAAATAATCC
* *
12080 AACCCGAATTAAATACAAACCGAAATAA
1 AACCCGAATAAAATACAAACCAAAATAA
12108 CATGAACTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (31 bp):
AACCCGAATAAAATACAAACCAAAATAATCC
Found at i:16481 original size:20 final size:20
Alignment explanation
Indices: 16464--16508 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
16454 ATAAATATTT
16464 TCTAGGATAGGTACATATGG
1 TCTAGGATAGGTACATATGG
*
16484 TCTAGGGTAGGTACATATGG
1 TCTAGGATAGGTACATATGG
*
16504 GCTAG
1 TCTAG
16509 CAACACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (20 bp):
TCTAGGATAGGTACATATGG
Found at i:17160 original size:3 final size:3
Alignment explanation
Indices: 17152--17182 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
17142 TGTCAATTAA
*
17152 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17183 TAAACTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20799 original size:21 final size:21
Alignment explanation
Indices: 20744--20793 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
20734 TCAGAACTCT
20744 CTGGTTCTTGTTCATCATGTG
1 CTGGTTCTTGTTCATCATGTG
*
20765 TTGGTTCTTGTTCATCATGTG
1 CTGGTTCTTGTTCATCATGTG
20786 CTGGTTCT
1 CTGGTTCT
20794 ACTTCAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.18, G:0.24, T:0.50
Consensus pattern (21 bp):
CTGGTTCTTGTTCATCATGTG
Found at i:24844 original size:30 final size:30
Alignment explanation
Indices: 24793--24859 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
24783 ACACTTTCGG
*
24793 TCACTTACGTTGCCATTTTATTAAGTTTTAA
1 TCACTTACATTGCCATTTTATTAAGTTTT-A
*
24824 TCACTTACATT-CCGTTTTATTAAGTTTTA
1 TCACTTACATTGCCATTTTATTAAGTTTTA
24853 TCACTTA
1 TCACTTA
24860 GACGTTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 8 0.24
30 16 0.47
31 10 0.29
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (30 bp):
TCACTTACATTGCCATTTTATTAAGTTTTA
Found at i:25824 original size:30 final size:31
Alignment explanation
Indices: 25773--25844 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
25763 TAATCTTCAA
* * *
25773 TGACCACATCTTAATTAAAACG-AACGAAAG
1 TGACCAAATCTCAATTAAAACGAAACAAAAG
*
25803 TGACCAAATCTCAATTGAAACGAAACAAAAG
1 TGACCAAATCTCAATTAAAACGAAACAAAAG
* *
25834 TAAACAAATCT
1 TGACCAAATCT
25845 TACATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 19 0.54
31 16 0.46
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.19
Consensus pattern (31 bp):
TGACCAAATCTCAATTAAAACGAAACAAAAG
Found at i:25842 original size:31 final size:30
Alignment explanation
Indices: 25780--25844 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
25770 CAATGACCAC
* * * *
25780 ATCTTAATTAAAACGAACGAAAGTGACCAA
1 ATCTCAATTAAAACGAACAAAAGTAAACAA
*
25810 ATCTCAATTGAAACGAAACAAAAGTAAACAA
1 ATCTCAATTAAAACG-AACAAAAGTAAACAA
25841 ATCT
1 ATCT
25845 TACATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (30 bp):
ATCTCAATTAAAACGAACAAAAGTAAACAA
Found at i:26446 original size:21 final size:21
Alignment explanation
Indices: 26422--26497 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
26412 CGGTTTAACC
26422 TAAATGTTTTTAGTTTTTTAT
1 TAAATGTTTTTAGTTTTTTAT
26443 TAAATGTTTTTAGTTTTTTAT
1 TAAATGTTTTTAGTTTTTTAT
*
26464 TAAATGTTTTTTTGTATTTTTAT
1 TAAATG-TTTTTAGT-TTTTTAT
*
26487 TTAAT-TTTTTA
1 TAAATGTTTTTA
26498 AATAATTATG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 32 0.64
22 7 0.14
23 11 0.22
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (21 bp):
TAAATGTTTTTAGTTTTTTAT
Found at i:27466 original size:17 final size:18
Alignment explanation
Indices: 27435--27468 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27425 AAATGTTACA
27435 ATGGTTAATAAAATTAAC
1 ATGGTTAATAAAATTAAC
*
27453 ATGG-TAATACAATTAA
1 ATGGTTAATAAAATTAA
27469 TCCTCGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (18 bp):
ATGGTTAATAAAATTAAC
Found at i:34878 original size:25 final size:25
Alignment explanation
Indices: 34831--34884 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
34821 CTCAAATTTT
* *
34831 ATTTTAATTTTAGTATTTCCTTTAA
1 ATTTTAATTTTAGTAGTTACTTTAA
*
34856 ATTTT-ATTTTAGTCAGTTACTTTAG
1 ATTTTAATTTTAGT-AGTTACTTTAA
34881 ATTT
1 ATTT
34885 CATAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (25 bp):
ATTTTAATTTTAGTAGTTACTTTAA
Found at i:38106 original size:12 final size:13
Alignment explanation
Indices: 38076--38112 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
38066 ATAAATCATC
38076 ATAAATTTTTTAA
1 ATAAATTTTTTAA
38089 ATAAATTTTTTAA
1 ATAAATTTTTTAA
*
38102 A-AAATTATTTA
1 ATAAATTTTTTA
38113 GGTGTACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATAAATTTTTTAA
Found at i:41505 original size:138 final size:138
Alignment explanation
Indices: 41255--41618 Score: 568
Period size: 138 Copynumber: 2.6 Consensus size: 138
41245 TGTCAGTACC
*
41255 CAAAGTGGTGAAAGA-GCGTTCCCGGGGGCGCGCCTTTGATTATTTTGTCAGAGAATATGTTATC
1 CAAAGTGGT-AAAAACGCGTTCCCGGGGGCGCGCCTTTGATTATTTTGTCAGAGAATATGTTATC
* * *
41319 ATTGCACTATTATGTCTCTCATATCCCCTGGAGAACTATTCATATCAGTACCTATTATTTATGAG
65 ATTGCCCTATTATGTCACTCATATCCCCCGGAGAACTATTCATATCAGTACCTATTATTTATGAG
41384 GGGACTTGA
130 GGGACTTGA
* *
41393 CAAAGTGGTAAAAACGCGTTCTCGGGGGCGCGCCTTTGATTATTTTGTCAAAGAATATGTTATCA
1 CAAAGTGGTAAAAACGCGTTCCCGGGGGCGCGCCTTTGATTATTTTGTCAGAGAATATGTTATCA
* * *
41458 TTGCCCTATTATGTCACTCATGTCCCCCGGAGAACTATTCATGTCAGTACCTATTATTTCTGAGG
66 TTGCCCTATTATGTCACTCATATCCCCCGGAGAACTATTCATATCAGTACCTATTATTTATGAGG
*
41523 GGACTTGG
131 GGACTTGA
* * ** *
41531 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTCTCA
1 CAAAGTGGTAAAAACGCGTTCCCGGGGGCGCGCCTTTGATTATTTTGTCAGAGAATATGTTATCA
*
41596 TTGCCCTATTTTGTCACTCATAT
66 TTGCCCTATTATGTCACTCATAT
41619 GAAATTGGAT
Statistics
Matches: 206, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
137 4 0.02
138 202 0.98
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (138 bp):
CAAAGTGGTAAAAACGCGTTCCCGGGGGCGCGCCTTTGATTATTTTGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATATCCCCCGGAGAACTATTCATATCAGTACCTATTATTTATGAGG
GGACTTGA
Found at i:41739 original size:61 final size:62
Alignment explanation
Indices: 41660--41784 Score: 216
Period size: 61 Copynumber: 2.0 Consensus size: 62
41650 ATTATGTGAA
*
41660 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATCAGTTGGTT
1 GTTTGAAT-AATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
*
41723 GTTTGAAT-ATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1 GTTTGAATAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
41784 G
1 G
41785 AGACATTGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 52 0.87
63 8 0.13
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (62 bp):
GTTTGAATAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:41870 original size:14 final size:14
Alignment explanation
Indices: 41851--41881 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
41841 TGATAAGTTG
41851 GTTTTAATGTATAT
1 GTTTTAATGTATAT
41865 GTTTTAATGTATAT
1 GTTTTAATGTATAT
41879 GTT
1 GTT
41882 AAGGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:42028 original size:34 final size:34
Alignment explanation
Indices: 41989--42061 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
41979 TTAAGTTGAA
41989 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
* *
42023 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
*
42057 ATTAA
1 TTTAA
42062 AAACATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACCATAATTTGTAT
Found at i:42603 original size:21 final size:20
Alignment explanation
Indices: 42579--42635 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
42569 AACCCTGCGA
* *
42579 GCTAAGCATGTAACCTGGTGG
1 GCTAAGAATGTAACCT-GAGG
*
42600 GCTAGGAATGTAACCCTGAGG
1 GCTAAGAATGTAA-CCTGAGG
42621 GCTAAGAATGTAACC
1 GCTAAGAATGTAACC
42636 ATGCGAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (20 bp):
GCTAAGAATGTAACCTGAGG
Found at i:44260 original size:22 final size:22
Alignment explanation
Indices: 44229--44281 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
44219 TAAATTCATT
44229 ATAAAT-TTAA-ATTAAATAATA
1 ATAAATATTAACATT-AATAATA
*
44250 ATAAATATTAACATTAATTATA
1 ATAAATATTAACATTAATAATA
*
44272 AAAAATATTA
1 ATAAATATTA
44282 CCATATCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 19 0.68
23 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAATATTAACATTAATAATA
Done.