Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003121.1 Hibiscus syriacus cultivar Beakdansim tig00006536_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: 67726
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3036 original size:19 final size:21
Alignment explanation
Indices: 2999--3041 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2989 TAACTTTTTC
2999 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
3019 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
3039 TTT
1 TTT
3042 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:3047 original size:19 final size:20
Alignment explanation
Indices: 2998--3047 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2988 TTAACTTTTT
*
2998 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
3018 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
3037 CTTTTACCTTT
1 CTTTTACCTTT
3048 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:6903 original size:17 final size:16
Alignment explanation
Indices: 6872--6905 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6862 CACGTGAGGA
6872 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
6888 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
6905 T
1 T
6906 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:19011 original size:20 final size:21
Alignment explanation
Indices: 18968--19020 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
18958 CAAAAATATT
*
18968 TATTTTAAATAACAAAATTAA
1 TATTTTAAATAACAAAACTAA
* *
18989 TATTTTTAATAA-AAAACTGA
1 TATTTTAAATAACAAAACTAA
19009 TATTTTAAATAA
1 TATTTTAAATAA
19021 TATTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
TATTTTAAATAACAAAACTAA
Found at i:26700 original size:2 final size:2
Alignment explanation
Indices: 26693--26722 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26683 AAAGACAAAA
26693 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
26723 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:26727 original size:2 final size:2
Alignment explanation
Indices: 26722--26758 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26712 TCTCTCTCTC
26722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26759 TTACAACGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27709 original size:43 final size:42
Alignment explanation
Indices: 27619--28022 Score: 207
Period size: 43 Copynumber: 9.3 Consensus size: 42
27609 TAGAGGGCTT
** * ** *
27619 AATTATAAAGGTAGAAAACGATATTGAAAAAAAAATAGAGGCATC
1 AATTATAAAGGTAGAAAGTGAGA-T-AAAAAAACTTAG-GGCCTC
* * *
27664 AATTATAAAGGTA-TAATTGTGATAAAAAAAACTTAGGGACCTC
1 AATTATAAAGGTAGAAAGTGAGAT-AAAAAAACTTAGGG-CCTC
* * *
27707 AATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAAAGGCCTC
1 AATTATAAAGGTAGAAAGTGAGA-TAAAAAAACTT-AGGGCCTC
** * * *
27751 AATTATAAAATTAAAAAAGTGGGATTAAAAAA-TTAGAGGCCTC
1 AATTATAAAGGT-AGAAAGTGAGATAAAAAAACTTAG-GGCCTC
*
27794 AATTATAAAGGTAGAAATTGAGATTGAAAAAAACTTAGGGGCCTC
1 AATTATAAAGGTAGAAAGTGAGA-T-AAAAAAACTTA-GGGCCTC
* * ** *
27839 AATT-GAAAGTGTAGAAAGTGAGATTGAAAAAACTTAAAAGCTTC
1 AATTATAAAG-GTAGAAAGTGAGA-TAAAAAAACTT-AGGGCCTC
* * *
27883 AATTATAAAGTTA-ATAA-TGAGATTACAAAA-TTAGGGGCCTC
1 AATTATAAAGGTAGA-AAGTGAGATAAAAAAACTTA-GGGCCTC
* * * * *
27924 AATTATAAAAGTAACAAAAG-G-GATTGAAAAAA-TTAGAGACTTC
1 AATTATAAAGGT-A-GAAAGTGAGA-TAAAAAAACTTAG-GGCCTC
* * * * *
27967 AATTATAAAGATAAAAAGTGAGATTGAATAATA-TTAGGACCTC
1 AATTATAAAGGTAGAAAGTGAGA-T-AAAAAAACTTAGGGCCTC
28010 AATTATAAAGGTA
1 AATTATAAAGGTA
28023 AAAAATAAGA
Statistics
Matches: 282, Mismatches: 53, Indels: 50
0.73 0.14 0.13
Matches are distributed among these distances:
40 1 0.00
41 21 0.07
42 23 0.08
43 97 0.34
44 81 0.29
45 58 0.21
46 1 0.00
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (42 bp):
AATTATAAAGGTAGAAAGTGAGATAAAAAAACTTAGGGCCTC
Found at i:27737 original size:45 final size:43
Alignment explanation
Indices: 27688--28019 Score: 218
Period size: 44 Copynumber: 7.7 Consensus size: 43
27678 AATTGTGATA
27688 AAAAAAACTTAGGGACCTCAATTAGAAAGTTAGAAAGTGAGATT
1 AAAAAAACTTAGGG-CCTCAATTAGAAAGTTAGAAAGTGAGATT
* * * * *
27732 AAAAAAACTTAAAGGCCTCAATTATAAAATTAAAAAAGTGGGATT
1 AAAAAAACTT-AGGGCCTCAATTAGAAAGTT-AGAAAGTGAGATT
* * *
27777 -AAAAAA-TTAGAGGCCTCAATTATAAAGGTAGAAATTGAGATT
1 AAAAAAACTTAG-GGCCTCAATTAGAAAGTTAGAAAGTGAGATT
27819 GAAAAAAACTTAGGGGCCTCAATT-GAAAGTGTAGAAAGTGAGATT
1 -AAAAAAACTTA-GGGCCTCAATTAGAAAGT-TAGAAAGTGAGATT
* ** * *
27864 GAAAAAACTTAAAAGCTTCAATTATAAAGTTA-ATAA-TGAGATT
1 AAAAAAACTT-AGGGCCTCAATTAGAAAGTTAGA-AAGTGAGATT
* * * *
27907 -ACAAAA-TTAGGGGCCTCAATTATAAAAGTAACAAAAG-G-GATT
1 AAAAAAACTTA-GGGCCTCAATTA-GAAAGTTA-GAAAGTGAGATT
* * * * * *
27949 GAAAAAA-TTAGAGACTTCAATTATAAAGATAAAAAGTGAGATT
1 AAAAAAACTTAG-GGCCTCAATTAGAAAGTTAGAAAGTGAGATT
* * * *
27992 GAATAATA-TTAGGACCTCAATTATAAAG
1 -AAAAAAACTTAGGGCCTCAATTAGAAAG
28020 GTAAAAAATA
Statistics
Matches: 232, Mismatches: 35, Indels: 43
0.75 0.11 0.14
Matches are distributed among these distances:
40 1 0.00
41 16 0.07
42 33 0.14
43 65 0.28
44 70 0.30
45 46 0.20
46 1 0.00
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (43 bp):
AAAAAAACTTAGGGCCTCAATTAGAAAGTTAGAAAGTGAGATT
Found at i:27757 original size:87 final size:87
Alignment explanation
Indices: 27601--28026 Score: 259
Period size: 87 Copynumber: 4.9 Consensus size: 87
27591 TATGAAATTG
* * * ** * ** * *
27601 TAAAAAAA-TAGAGGGCTTAATTATAAAGGTAGAAAACGATATTGAAAAAAAAATAGAGGCATCA
1 TAAAAAAATTAGAGGCCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAAACTTAAAGGCCTCA
* * * *
27665 ATTATAAAGGT-ATAATTGTGA
66 ATTATAAAAGTAAAAAGTGGGA
*
27686 TAAAAAAAACTTAG-GGACCTCAATTAGAAAGTTAGAAAGTGAGATT-AAAAAAACTTAAAGGCC
1 T-AAAAAAA-TTAGAGG-CCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAAACTTAAAGGCC
*
27749 TCAATTATAAAATTAAAAAAGTGGGA
63 TCAATTATAAAAGT-AAAAAGTGGGA
* * * **
27775 TTAAAAAATTAGAGGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAAACTTAGGGGCCTCA
1 TAAAAAAATTAGAGGCCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAAACTTAAAGGCCTCA
** * *
27840 ATTGA-AAGTGTAGAAAGTGAGA
66 ATT-ATAAAAGTAAAAAGTGGGA
* * * * * * * **
27862 TTGAAAAAACTTAAAAGCTTCAATTATAAAGTTA-ATAA-TGAGATT--ACAAAA-TTAGGGGCC
1 -T-AAAAAAATTAGAGGCCTCAATTAGAAAGGTAGA-AAGTGAGATTGAAAAAAACTTAAAGGCC
*
27922 TCAATTATAAAAGTAACAAA-AGGGA
63 TCAATTATAAAAGTAA-AAAGTGGGA
* * * * * * * *
27947 TTGAAAAAATTAGAGACTTCAATTATAAAGATAAAAAGTGAGATTGAATAATA-TT--AGGACCT
1 -TAAAAAAATTAGAGGCCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAAACTTAAAGG-CCT
*
28009 CAATTATAAAGGTAAAAA
64 CAATTATAAAAGTAAAAA
28027 ATAAGATTTA
Statistics
Matches: 273, Mismatches: 49, Indels: 38
0.76 0.14 0.11
Matches are distributed among these distances:
84 28 0.10
85 39 0.14
86 32 0.12
87 72 0.26
88 66 0.24
89 36 0.13
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.25
Consensus pattern (87 bp):
TAAAAAAATTAGAGGCCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAAACTTAAAGGCCTCA
ATTATAAAAGTAAAAAGTGGGA
Found at i:27841 original size:132 final size:128
Alignment explanation
Indices: 27647--27937 Score: 395
Period size: 132 Copynumber: 2.2 Consensus size: 128
27637 CGATATTGAA
* * * *
27647 AAAAAAATAGAGGCATCAATTATAAAGGTATAATTGTGATAAAAAAAACTTAGGGACCTCAATTA
1 AAAAAATTAGAGGCCTCAATTATAAAGGTAAAATTGAGATAAAAAAAACTTAGGGACCTCAATT-
* *
27712 GAAAGT-TAGAAAGTGAGATTAAAAAAACTTAAAGGCCTCAATTATAAAATTAAAAAAGTGGGAT
65 GAAAGTGTAGAAAGTGAGATTAAAAAAACTTAAAAGCCTCAATTATAAAATT-AAAAA-TGAGAT
27776 T
128 T
* *
27777 AAAAAATTAGAGGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAAACTTAGGGGCCTCAAT
1 AAAAAATTAGAGGCCTCAATTATAAAGGTA-AAATTGAGA-TAAAAAAAACTTAGGGACCTCAAT
* * * *
27842 TGAAAGTGTAGAAAGTGAGATTGAAAAAACTTAAAAGCTTCAATTATAAAGTTAATAATGAGATT
64 TGAAAGTGTAGAAAGTGAGATTAAAAAAACTTAAAAGCCTCAATTATAAAATTAAAAATGAGATT
* * *
27907 ACAAAATTAGGGGCCTCAATTATAAAAGTAA
1 AAAAAATTAGAGGCCTCAATTATAAAGGTAA
27938 CAAAAGGGAT
Statistics
Matches: 143, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
129 1 0.01
130 61 0.43
131 17 0.12
132 64 0.45
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (128 bp):
AAAAAATTAGAGGCCTCAATTATAAAGGTAAAATTGAGATAAAAAAAACTTAGGGACCTCAATTG
AAAGTGTAGAAAGTGAGATTAAAAAAACTTAAAAGCCTCAATTATAAAATTAAAAATGAGATT
Found at i:28025 original size:43 final size:42
Alignment explanation
Indices: 27662--28044 Score: 260
Period size: 43 Copynumber: 8.9 Consensus size: 42
27652 AATAGAGGCA
* * * **
27662 TCAATTATAAAGGT-ATAATTGTGATAAAAAAAACTTAGGGACC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAA-TTA-GGACC
* * * *
27705 TCAATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAAAGG-CC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAA-TT--AGGACC
** * *
27749 TCAATTATAAAATTAAAAAAGTGGGATT-AAAAAATTAGAGGCC
1 TCAATTATAAAGGT-AAAAAGTGAGATTGAAAAAATTAG-GACC
* * *
27792 TCAATTATAAAGGTAGAAATTGAGATTGAAAAAAACTTAGGGGCC
1 TCAATTATAAAGGTAAAAAGTGAGATTG-AAAAAA-TTA-GGACC
* * ** *
27837 TCAATT-GAAAGTGTAGAAAGTGAGATTGAAAAAACTTAAAAGCT
1 TCAATTATAAAG-GTAAAAAGTGAGATTGAAAAAA-TTAGGA-CC
* * * *
27881 TCAATTATAAAGTTAATAA-TGAGATT-ACAAAATTAGGGGCC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTA-GGACC
* *
27922 TCAATTATAAAAGTAACAAAAG-G-GATTGAAAAAATTAGAGACT
1 TCAATTATAAAGGT-A-AAAAGTGAGATTGAAAAAATTAG-GACC
* *
27965 TCAATTATAAAGATAAAAAGTGAGATTGAATAATATTAGGACC
1 TCAATTATAAAGGTAAAAAGTGAGATTGAA-AAAATTAGGACC
* * *
28008 TCAATTATAAAGGTAAAAAATAAGATTTAAAAAATTA
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTA
28045 AGATGAAAAA
Statistics
Matches: 272, Mismatches: 46, Indels: 45
0.75 0.13 0.12
Matches are distributed among these distances:
41 23 0.08
42 30 0.11
43 97 0.36
44 75 0.28
45 45 0.17
46 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (42 bp):
TCAATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGACC
Found at i:44447 original size:14 final size:14
Alignment explanation
Indices: 44428--44458 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44418 TTGTGTTATT
44428 TATATATATGTATG
1 TATATATATGTATG
*
44442 TATATATATGTGTG
1 TATATATATGTATG
44456 TAT
1 TAT
44459 GTATGTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:45125 original size:35 final size:35
Alignment explanation
Indices: 45086--45161 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
45076 ACCAATCAAA
45086 TAGTCTTTCTTCCCCTATAATAAGAAGATCAAGTG
1 TAGTCTTTCTTCCCCTATAATAAGAAGATCAAGTG
45121 TAGTCTTTCTTCCCCTATAATAAGAAGATCAAGTG
1 TAGTCTTTCTTCCCCTATAATAAGAAGATCAAGTG
*
45156 TTGTCT
1 TAGTCT
45162 AAACATAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (35 bp):
TAGTCTTTCTTCCCCTATAATAAGAAGATCAAGTG
Found at i:45236 original size:2 final size:2
Alignment explanation
Indices: 45229--45258 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45219 ATTCAAAACA
45229 AT AT 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 AT AT
45259 GCTTATACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59531 original size:18 final size:18
Alignment explanation
Indices: 59505--59543 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
59495 GTGGGATCCA
*
59505 ATTAGAAATAATATATTT
1 ATTAAAAATAATATATTT
* *
59523 ATTAAAAATATTATTTTT
1 ATTAAAAATAATATATTT
59541 ATT
1 ATT
59544 TAATAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTAAAAATAATATATTT
Found at i:65606 original size:14 final size:13
Alignment explanation
Indices: 65566--65608 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
65556 GTAATCTTGA
65566 AAAAATAT-TTTT
1 AAAAATATATTTT
*
65578 AAAAA-ATACTTT
1 AAAAATATATTTT
65590 AAAATATATATTTT
1 AAAA-ATATATTTT
65604 AAAAA
1 AAAAA
65609 ACCTAAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.08
12 12 0.46
13 2 0.08
14 10 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATATATTTT
Found at i:65864 original size:18 final size:18
Alignment explanation
Indices: 65843--65877 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65833 CCCTTATTCT
*
65843 GGAAGTAAACCTTAATAC
1 GGAAATAAACCTTAATAC
*
65861 GGAAATAAAGCTTAATA
1 GGAAATAAACCTTAATA
65878 ATCGGCCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (18 bp):
GGAAATAAACCTTAATAC
Done.