Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002408.1 Hibiscus syriacus cultivar Beakdansim tig00004926_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: 49979
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:823 original size:51 final size:47
Alignment explanation
Indices: 737--839 Score: 170
Period size: 51 Copynumber: 2.1 Consensus size: 47
727 GTCCGGATAT
737 TCCTCTCTGATTTTTATATCAAGAGTTCCCATCCCAGAGCCTGTTTCC
1 TCCTCTCTGATTTTTATATCAAGAGTTCCCATCCCAGAGCCTG-TTCC
785 TCCTCTCTGATTTTTTATATCAAGAGAGTTCCCATCCCAGAGCCTGTTCC
1 TCCTCTCTGA-TTTTTATATC-A-AGAGTTCCCATCCCAGAGCCTGTTCC
835 TCCTC
1 TCCTC
840 CTAGTGAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
48 10 0.19
49 10 0.19
50 10 0.19
51 22 0.42
ACGTcount: A:0.18, C:0.32, G:0.13, T:0.37
Consensus pattern (47 bp):
TCCTCTCTGATTTTTATATCAAGAGTTCCCATCCCAGAGCCTGTTCC
Found at i:856 original size:51 final size:51
Alignment explanation
Indices: 758--856 Score: 121
Period size: 51 Copynumber: 1.9 Consensus size: 51
748 TTTTATATCA
* ***
758 AGAGTTCCCATCCCAGAGCCTGTTTCCTCCTCTCTGATTTTTTATATCAAG
1 AGAGTTCCCATCCCAGAGCCTGTTTCCTCCTCTCTGATATGGCATATCAAG
*
809 AGAGTTCCCATCCCAGAGCCTG-TTCCTCCTCCTAGTGA-ATGGCATATC
1 AGAGTTCCCATCCCAGAGCCTGTTTCCTCCT-CT-CTGATATGGCATATC
857 TGGAACCCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 8 0.20
51 30 0.73
52 3 0.07
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.32
Consensus pattern (51 bp):
AGAGTTCCCATCCCAGAGCCTGTTTCCTCCTCTCTGATATGGCATATCAAG
Found at i:3869 original size:17 final size:19
Alignment explanation
Indices: 3829--3879 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3819 TTTCTATTTA
3829 GTAATTTATATTTTGAAAT
1 GTAATTTATATTTTGAAAT
*
3848 TTAATTTA-ATTTT-AAAT
1 GTAATTTATATTTTGAAAT
3865 GTAATTTGATATTTT
1 GTAATTT-ATATTTT
3880 TTAAGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
19 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
GTAATTTATATTTTGAAAT
Found at i:7411 original size:9 final size:9
Alignment explanation
Indices: 7397--7421 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7387 ACTGTCAATT
7397 TTTTTTTAA
1 TTTTTTTAA
7406 TTTTTTTAA
1 TTTTTTTAA
7415 TTTTTTT
1 TTTTTTT
7422 GGTATAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:12441 original size:2 final size:2
Alignment explanation
Indices: 12436--12474 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12426 ATAAAGAATC
12436 TA 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 TA T
12475 CTCTGTGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22855 original size:2 final size:2
Alignment explanation
Indices: 22848--22893 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
22838 TATAGATTTA
22848 AT AT AT AT AT AT 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 AT AT AT AT AT AT
22890 AT AT
1 AT AT
22894 CATAACAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22977 original size:24 final size:23
Alignment explanation
Indices: 22950--23003 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
22940 TATTCTGTAC
*
22950 TTAAATAATACATAA-ATAATATGA
1 TTAAAT-ATA-ATAACATAAAATGA
*
22974 TTAAAGTATAATAACTTAAAATGA
1 TTAAA-TATAATAACATAAAATGA
22998 TTAAAT
1 TTAAAT
23004 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 20 0.77
25 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (23 bp):
TTAAATATAATAACATAAAATGA
Found at i:23152 original size:17 final size:17
Alignment explanation
Indices: 23115--23152 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
23105 AGTCTTTATT
*
23115 TTTTTAAAATTTTGAAG
1 TTTTTAAAATTTCGAAG
23132 TTTTTAAAATATTCGAA-
1 TTTTTAAAAT-TTCGAAG
23149 TTTT
1 TTTT
23153 GTTGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (17 bp):
TTTTTAAAATTTCGAAG
Found at i:24788 original size:25 final size:25
Alignment explanation
Indices: 24754--24803 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
24744 TTCAGTTGAA
24754 ATCCTAATGCGCTAATTGATTTTAC
1 ATCCTAATGCGCTAATTGATTTTAC
24779 ATCCTAATGCGCTAATTGATTTTAC
1 ATCCTAATGCGCTAATTGATTTTAC
24804 TGATTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (25 bp):
ATCCTAATGCGCTAATTGATTTTAC
Found at i:25473 original size:75 final size:76
Alignment explanation
Indices: 25373--25520 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 76
25363 TAGAAAAAAA
*
25373 TAAAATAAATTAAAATAAAAAAATAAAGTCAAATTATTAATACCATTAATATTATGTT-AT-TTT
1 TAAAATAAATTAAAATAAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTTT
*
25436 TTTATAAACAT
66 TTCATAAACAT
25447 TAAAATAAATTTAAAATAAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTT
1 TAAAATAAA-TTAAAATAAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTT
25512 TTTCATAAA
65 TTTCATAAA
25521 TTTAAAGTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
74 9 0.13
75 48 0.70
76 2 0.03
77 10 0.14
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (76 bp):
TAAAATAAATTAAAATAAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTTT
TTCATAAACAT
Found at i:26151 original size:21 final size:21
Alignment explanation
Indices: 26125--26175 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
26115 TACTAAAAAC
*
26125 ATTATTATTTCTATCGGTTTT
1 ATTATTATTTCTATCGATTTT
* *
26146 ATTATTTTTTCTATTGATTTT
1 ATTATTATTTCTATCGATTTT
26167 ATTATTATT
1 ATTATTATT
26176 GGGTACTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (21 bp):
ATTATTATTTCTATCGATTTT
Found at i:28139 original size:30 final size:32
Alignment explanation
Indices: 28105--28172 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
28095 ATAGTTTTTA
28105 TATTTTATAGT-AAT-ATAATTATATAAATAT
1 TATTTTATAGTAAATAATAATTATATAAATAT
* * * *
28135 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATAGT-AAATAATAATTATATAAATAT
28168 TATTT
1 TATTT
28173 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTTATAGTAAATAATAATTATATAAATAT
Found at i:32696 original size:21 final size:21
Alignment explanation
Indices: 32670--32711 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32660 AATAATTAAT
*
32670 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
32691 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
32712 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:38068 original size:25 final size:22
Alignment explanation
Indices: 38039--38106 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 22
38029 AATAAATCAA
38039 AATAAAAAAATAAATAAAAATAG
1 AATAAAAAAATAAATAAAAAT-G
* *
38062 ATCATAAAAATATTAAATAAATATG
1 A--ATAAAAA-AATAAATAAAAATG
38087 AA-AACAAAAATAAATAAAAA
1 AATAA-AAAAATAAATAAAAA
38107 ATATTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
22 12 0.32
23 5 0.14
25 9 0.24
26 11 0.30
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (22 bp):
AATAAAAAAATAAATAAAAATG
Found at i:38071 original size:26 final size:22
Alignment explanation
Indices: 38042--38106 Score: 58
Period size: 26 Copynumber: 2.8 Consensus size: 22
38032 AAATCAAAAT
38042 AAAAAAATAAATAAAAATAGATCATA
1 AAAAAAATAAATAAAAAT-GA--A-A
* * *
38068 AAAATATTAAATAAATATGAAA
1 AAAAAAATAAATAAAAATGAAA
*
38090 ACAAAAATAAATAAAAA
1 AAAAAAATAAATAAAAA
38107 ATATTAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 14 0.44
23 1 0.03
25 2 0.06
26 15 0.47
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (22 bp):
AAAAAAATAAATAAAAATGAAA
Found at i:38108 original size:25 final size:25
Alignment explanation
Indices: 38044--38110 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
38034 ATCAAAATAA
** *
38044 AAAAATAAAT-AAAAATA-GATCAT
1 AAAAATAAATAAAAAATATGAAAAC
*
38067 AAAAAT-ATTAAATAAATATGAAAAC
1 AAAAATAAATAAA-AAATATGAAAAC
38092 AAAAATAAATAAAAAATAT
1 AAAAATAAATAAAAAATAT
38111 TAATATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
22 2 0.06
23 8 0.23
24 5 0.14
25 15 0.43
26 5 0.14
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (25 bp):
AAAAATAAATAAAAAATATGAAAAC
Found at i:38139 original size:36 final size:35
Alignment explanation
Indices: 38054--38142 Score: 87
Period size: 36 Copynumber: 2.5 Consensus size: 35
38044 AAAAATAAAT
*
38054 AAAAATAGATCAT-AAAAATATTAAATAAATATGA
1 AAAAATAGATAATAAAAAATATTAAATAAATATGA
*
38088 AAACAA-AAATAAATAAAAAATATT-AATATAATAAT-A
1 AAA-AATAGAT-AATAAAAAATATTAAATA-AAT-ATGA
38124 AAAAATAGATGAATAAAAA
1 AAAAATAGAT-AATAAAAA
38143 GACGGGGCGT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
34 6 0.13
35 10 0.22
36 27 0.60
37 2 0.04
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (35 bp):
AAAAATAGATAATAAAAAATATTAAATAAATATGA
Found at i:38322 original size:95 final size:95
Alignment explanation
Indices: 38145--38394 Score: 340
Period size: 95 Copynumber: 2.6 Consensus size: 95
38135 AATAAAAAGA
* * *
38145 CGGGGCGTTTAACAAATTGCTCTAGAGGGACAACTCAATGTCATTGTATAG-ATATTATAATCAC
1 CGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAA-G-C-TT-TATTGTATATTATAATCAC
38209 CTTTATCAGGCTAGCTGAATATTATCCATAAAAT
62 CTTTATCAGGCTAGCTGAATATTATCCATAAAAT
* * *
38243 CGGGGTGTTTAACCAATTACTCTAGAGGAACAACTCAAGCCTTATTGTATATTATAATCACCTTT
1 CGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
* * * *
38308 ATCAGGCTATCTGAATCTTATCTATAAAGT
66 ATCAGGCTAGCTGAATATTATCCATAAAAT
* *
38338 CAGGGTATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATATATA
1 CGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATA
38395 TAATATTATA
Statistics
Matches: 135, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
94 4 0.03
95 91 0.67
96 5 0.04
97 1 0.01
98 34 0.25
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (95 bp):
CGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
ATCAGGCTAGCTGAATATTATCCATAAAAT
Found at i:45583 original size:44 final size:47
Alignment explanation
Indices: 45517--45614 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 47
45507 TTTATTTTTG
45517 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
45564 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
45609 TTTTTG
1 TTTTTG
45615 TGAATAACTA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
44 28 0.57
45 12 0.24
46 4 0.08
47 5 0.10
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Done.