Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002691.1 Hibiscus syriacus cultivar Beakdansim tig00005556_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: 68839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7714 original size:46 final size:47
Alignment explanation
Indices: 7661--7751 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 47
7651 AATAATAATA
*
7661 TTATTTTAAG-AAATAATTAATATAATTAATAATATTT-TATTTTATT
1 TTATTTT-AGTAAATAATTAATATAATTAATAAAATTTGTATTTTATT
*
7707 TTATTTTAGTAAATAATTAATATAATTTATAAAATTTGTATTTTA
1 TTATTTTAGTAAATAATTAATATAATTAATAAAATTTGTATTTTA
7752 ATATAATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 2 0.05
46 32 0.78
47 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (47 bp):
TTATTTTAGTAAATAATTAATATAATTAATAAAATTTGTATTTTATT
Found at i:13228 original size:2 final size:2
Alignment explanation
Indices: 13221--13245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13211 CTGCCAATGA
13221 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 A
13246 ATTACTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20627 original size:13 final size:13
Alignment explanation
Indices: 20609--20635 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20599 TTACAGAATC
20609 GCATATGAAGACT
1 GCATATGAAGACT
20622 GCATATGAAGACT
1 GCATATGAAGACT
20635 G
1 G
20636 TTTAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:22590 original size:115 final size:114
Alignment explanation
Indices: 22405--22679 Score: 270
Period size: 116 Copynumber: 2.4 Consensus size: 114
22395 CTTAAGGTTA
* * * * * * *
22405 AATTTTAAAAAATTAAAAATTT-AGATACTAAAAAGAACCAAAATTGATAATTTAAGTATTAAAC
1 AATTTAAAAAAAAT-AAAATTTAAG-TATTAAAAAGAACCAAAACTGATAATTGAAATATAAAAC
* *
22469 GCGATAAAA-ACATTAGAGTATTAAAATGAATCAAAAACTAAAAGTT-AAGTAT
64 GCGATAAAAGA-ATTAGAGTAGT-AAATGAAACAAAAACTAAAAGTTGAA-TAT
*
22521 AATTTAAAAAAAATAAAAGTTTAAGTATTAAAATG-ACCAAAACTGATAATTGAAATATAAAACG
1 AATTTAAAAAAAATAAAA-TTTAAGTATTAAAAAGAACCAAAACTGATAATTGAAATATAAAACG
* * * * * *
22585 TGATAAAAGAATTATAGTAGTATATGAAACAAATACTAAAGGTTGCATAT
65 CGATAAAAGAATTAGAGTAGTAAATGAAACAAAAACTAAAAGTTGAATAT
* * *
22635 GATTTAAAAAAAAAATCAAAATTTAAGTATTAAAACGAACTAAAA
1 AATTT--AAAAAAAAT-AAAATTTAAGTATTAAAAAGAACCAAAA
22680 TTAATCATTT
Statistics
Matches: 132, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
114 26 0.20
115 46 0.35
116 48 0.36
117 12 0.09
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.28
Consensus pattern (114 bp):
AATTTAAAAAAAATAAAATTTAAGTATTAAAAAGAACCAAAACTGATAATTGAAATATAAAACGC
GATAAAAGAATTAGAGTAGTAAATGAAACAAAAACTAAAAGTTGAATAT
Found at i:26655 original size:2 final size:2
Alignment explanation
Indices: 26648--26673 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26638 TTAATATTTA
26648 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26674 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27804 original size:24 final size:24
Alignment explanation
Indices: 27777--27858 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
27767 ACGGAGATAT
*
27777 CAGAAATCAAAACAGATATCAGAA
1 CAGAAATCAAATCAGATATCAGAA
* * *
27801 CAG-AATCCATATCAAAAATCAGAA
1 CAGAAAT-CAAATCAGATATCAGAA
* *
27825 CAGAATTCAAGTCATG-TATCAGAA
1 CAGAAATCAAATCA-GATATCAGAA
*
27849 CAGAATTCAA
1 CAGAAATCAA
27859 GTCGAAAATC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 3 0.07
24 41 0.89
25 2 0.04
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
CAGAAATCAAATCAGATATCAGAA
Found at i:27869 original size:24 final size:23
Alignment explanation
Indices: 27794--27871 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
27784 CAAAACAGAT
*
27794 ATCAGAACAGAATCCATA-TCAAAA
1 ATCAGAACAGAATTCA-AGTC-AAA
**
27818 ATCAGAACAGAATTCAAGTCATGT
1 ATCAGAACAGAATTCAAGTCA-AA
27842 ATCAGAACAGAATTCAAGTCGAAA
1 ATCAGAACAGAATTCAAGTC-AAA
27866 ATCAGA
1 ATCAGA
27872 TAAAATATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
23 2 0.04
24 43 0.93
25 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (23 bp):
ATCAGAACAGAATTCAAGTCAAA
Found at i:31510 original size:2 final size:2
Alignment explanation
Indices: 31503--31539 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
31493 TATAACGACG
*
31503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31540 AAATAATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33202 original size:15 final size:15
Alignment explanation
Indices: 33179--33209 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33169 AAAGATGATA
*
33179 ACATGATATGACATG
1 ACATAATATGACATG
33194 ACATAATATGACATG
1 ACATAATATGACATG
33209 A
1 A
33210 GATGGTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (15 bp):
ACATAATATGACATG
Found at i:33461 original size:252 final size:248
Alignment explanation
Indices: 33014--33516 Score: 900
Period size: 252 Copynumber: 2.0 Consensus size: 248
33004 TGATTATAAT
33014 TAATATAATCGTACAACTCCAACAAAAATACATCATTACAATATACACAAACAGAGCACTAACAT
1 TAATATAATCGTACAACTCCAACAAAAATACATCATTACAATATACACAAACAGAGCACTAACAT
*
33079 TGTATCAAAAATCAATCCAATGTATAAGTGTATAATACAAATGTGTTATAAATGGTTAGATTTAT
66 TGTATCAAAAATCAATCCAATGTAT-AGTGTATAATACAAATGTGTTATAAATGGTTAAATTTAT
* *
33144 CTTGTGACATGCGACCATGACAATCAAAGATGATAACATGATATGACATGACATAATATGACATG
130 CTTGTGACATGCGACAATGACAATCAAAGATGATAACATGATATGACATGACATAACATGACAT-
33209 AGATGGTTGGTCCATAAATTTCTTAATTTAAAGTTTTATTCTACCATTTTATCTTGTCA
194 -GA---TTGGTCCATAAATTTCTTAATTTAAAGTTTTATTCTACCATTTTATCTTGTCA
33268 TAATATAATCGTACAACTCCAACAAAAATACATCATTACAATATACACAAACAGAGCACTAACAT
1 TAATATAATCGTACAACTCCAACAAAAATACATCATTACAATATACACAAACAGAGCACTAACAT
33333 TGTATCAAAAATCAATCCAATGTAT-GTGTATAATACAAATGTGTTATAAATGGTTAAATTTATC
66 TGTATCAAAAATCAATCCAATGTATAGTGTATAATACAAATGTGTTATAAATGGTTAAATTTATC
*
33397 TTGTGACATGCGACAATGACAATCAAAGATGATAACATGATATGATATGACATAACATGACATGA
131 TTGTGACATGCGACAATGACAATCAAAGATGATAACATGATATGACATGACATAACATGACATGA
*
33462 TTGGTCCATAAATTTCTTAATTTAAAGTTTTATTCTACTATTTTATCTTGTCA
196 TTGGTCCATAAATTTCTTAATTTAAAGTTTTATTCTACCATTTTATCTTGTCA
33515 TA
1 TA
33517 TGAAATAAGT
Statistics
Matches: 244, Mismatches: 5, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
247 54 0.22
250 2 0.01
252 98 0.40
254 90 0.37
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (248 bp):
TAATATAATCGTACAACTCCAACAAAAATACATCATTACAATATACACAAACAGAGCACTAACAT
TGTATCAAAAATCAATCCAATGTATAGTGTATAATACAAATGTGTTATAAATGGTTAAATTTATC
TTGTGACATGCGACAATGACAATCAAAGATGATAACATGATATGACATGACATAACATGACATGA
TTGGTCCATAAATTTCTTAATTTAAAGTTTTATTCTACCATTTTATCTTGTCA
Found at i:40526 original size:23 final size:23
Alignment explanation
Indices: 40500--40544 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40490 TTGTTCATTC
*
40500 AATTAAACTAATAGATGAAATAA
1 AATTAAACTAATAGATCAAATAA
* * *
40523 AATTTAATTAATCGATCAAATA
1 AATTAAACTAATAGATCAAATA
40545 CCAAAGTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (23 bp):
AATTAAACTAATAGATCAAATAA
Found at i:41694 original size:60 final size:60
Alignment explanation
Indices: 41553--41716 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 60
41543 GGATTTGGAA
** * * * *
41553 ATGAAATTAGAAGGTTTAAAAGTTTAGGGACTAATTTAAAATAAGGGTCATAGTTGGAGG
1 ATGAAATTAGAATATTTAAAAGTTTAAGGACCAATTTAAAATAAGGATAATAGTTGGAGG
* * * * * *
41613 ATGAAATTGGATTATTCAAAAGTTTAAGGACCAATTTAGAATGAGTATAATAG-TGTGAGG
1 ATGAAATTAGAATATTTAAAAGTTTAAGGACCAATTTAAAATAAGGATAATAGTTG-GAGG
* * * **
41673 ATGAAATTAAAATATTTAAAAGTTCAAAGATTAATTTAAAATAA
1 ATGAAATTAGAATATTTAAAAGTTTAAGGACCAATTTAAAATAA
41717 ATATCATAGT
Statistics
Matches: 81, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
59 2 0.02
60 79 0.98
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.32
Consensus pattern (60 bp):
ATGAAATTAGAATATTTAAAAGTTTAAGGACCAATTTAAAATAAGGATAATAGTTGGAGG
Found at i:42510 original size:2 final size:2
Alignment explanation
Indices: 42499--42555 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
42489 AATGTGTTGT
42499 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42540 TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA T
42556 TTACTGTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51706 original size:2 final size:2
Alignment explanation
Indices: 51701--51780 Score: 87
Period size: 2 Copynumber: 42.0 Consensus size: 2
51691 TTGGTCCAAT
* *
51701 TA TA TA TA TA TA TA TG TA TA TA TA TA -A T- TG T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
51739 TT TT TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51781 AATTATTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
1 4 0.06
2 64 0.94
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:53429 original size:2 final size:2
Alignment explanation
Indices: 53418--53498 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
53408 TCTTTCACTT
53418 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53499 AAGTTTGAGA
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:58070 original size:60 final size:60
Alignment explanation
Indices: 57947--58075 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
57937 TCTGGTGACT
* * * *
57947 ATTTTATAACTTTTAATAGTCGAGAGACTTAACAAAGTAATATTATATAGTTAAAGGATC
1 ATTTTATAACTTTTAATAGTCGAGAGACTTAACAAAATAATATTATATAATGAAAGGACC
* * * * * *
58007 ATTTTATAATTTTTAATAGTTGAGAGACTTAATAAAATATTATCT-TATAATGGAGGGACC
1 ATTTTATAACTTTTAATAGTCGAGAGACTTAACAAAATAATAT-TATATAATGAAAGGACC
58067 ATTTATATA
1 ATTT-TATA
58076 CTTCACTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
60 52 0.91
61 5 0.09
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGAGAGACTTAACAAAATAATATTATATAATGAAAGGACC
Found at i:58798 original size:29 final size:29
Alignment explanation
Indices: 58747--58804 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
58737 GTGTTGGCCG
* * *
58747 TAGGTCGTCATGCCTTTCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
58776 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
58805 AAGAGATTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.26
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:58883 original size:23 final size:23
Alignment explanation
Indices: 58855--58907 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
58845 ATCTGAGGCC
58855 ATCCGAACGAGCTATGCGAGGGCA
1 ATCCGAACGAGCTATGCGAGGG-A
*
58879 A-CCGAGCGAGCTATGCGAGGGA
1 ATCCGAACGAGCTATGCGAGGGA
58901 ATCCGAA
1 ATCCGAA
58908 GGAAGCCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 23 0.88
24 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.34, T:0.11
Consensus pattern (23 bp):
ATCCGAACGAGCTATGCGAGGGA
Found at i:58971 original size:29 final size:29
Alignment explanation
Indices: 58925--58980 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
58915 GAGCGAGGGT
* *
58925 AGGTCTCCCGGAGTGCATGGCAACCTACA
1 AGGTCGCCCGGAGGGCATGGCAACCTACA
*
58954 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCAACCTA
58981 TGTGTTGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.30, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCAACCTACA
Found at i:59081 original size:29 final size:29
Alignment explanation
Indices: 59039--59126 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
59029 GAGCAAGGGT
* *
59039 AGGTCGCCCGGAGTGTATGACGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
59068 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
59097 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
59126 A
1 A
59127 CCAACACTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.23, C:0.30, G:0.33, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:65546 original size:18 final size:17
Alignment explanation
Indices: 65520--65553 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
65510 CTAATAGTTT
65520 ATTTATAATTGTTTTAAG
1 ATTTATAA-TGTTTTAAG
*
65538 ATTTTTAATGTTTTAA
1 ATTTATAATGTTTTAA
65554 AACTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
ATTTATAATGTTTTAAG
Found at i:68697 original size:22 final size:22
Alignment explanation
Indices: 68632--68699 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
68622 ATCTCCGACA
68632 AATTCACAGTGTATGACAAATT
1 AATTCACAGTGTATGACAAATT
68654 AATT-AC-GT-TCACGTGACAAATT
1 AATTCACAGTGT-A--TGACAAATT
68676 AATGTCACAGTGTATGAC-AATT
1 AAT-TCACAGTGTATGACAAATT
68698 AA
1 AA
68700 ATTAGCCCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 2 0.05
22 22 0.56
23 5 0.13
24 2 0.05
25 3 0.08
26 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (22 bp):
AATTCACAGTGTATGACAAATT
Done.