Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003284.1 Hibiscus syriacus cultivar Beakdansim tig00006912_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: 62335
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:9826 original size:65 final size:65
Alignment explanation
Indices: 9679--10136 Score: 488
Period size: 65 Copynumber: 7.0 Consensus size: 65
9669 ATGGGGGTTT
* * ** * * * * *
9679 GATTTTCACCCATGAACATGAAGCACCTTTCATGTTCAGTCATTTTACCTCTTCAGCAAACATCT
1 GATTTTCACCTATGAACATGAAACACCTTTCATGTTCAG-CCGTTTACCTCTTCGGCGATCACCC
9744 G
65 G
* * * * * *
9745 GATTTCCACCTATGAACACGAAACACTTTTCATGTTCAGCCGTTTATCTCTTCAGCGATCACTCG
1 GATTTTCACCTATGAACATGAAACACCTTTCATGTTCAGCCGTTTACCTCTTCGGCGATCACCCG
* * *
9810 GGTTTTCACCTTTGAACATGAAGCACCTTTCATGTTCAGCCGTTTACCTCTTCGGAC-ATCACCC
1 GATTTTCACCTATGAACATGAAACACCTTTCATGTTCAGCCGTTTACCTCTTCGG-CGATCACCC
9874 G
65 G
* * * * * *
9875 GATTTTCACTTATGAACATGAAATACCTTTCATGTTCAGTCGTTTATCTCTTCGGCGACCACCAG
1 GATTTTCACCTATGAACATGAAACACCTTTCATGTTCAGCCGTTTACCTCTTCGGCGATCACCCG
* ** * *
9940 AATTTTCACCTATGAACA-GAAAGCACCTTTCATGTTCAGTTGTTTACCTCTTTGGTGATCACCC
1 GATTTTCACCTATGAACATGAAA-CACCTTTCATGTTCAGCCGTTTACCTCTTCGGCGATCACCC
10004 G
65 G
** * * *
10005 GATTTTCACACCTATGAACATGAAGTACCTTTCATGTTCAGTCGTTTACCTCTTTGGTGATCACC
1 GATTTT--CACCTATGAACATGAAACACCTTTCATGTTCAGCCGTTTACCTCTTCGGCGATCACC
10070 CG
64 CG
** * * * *
10072 GATTTTCACCTATGAATGTGAAGCACCTTTTATTGTTCAGTCGTTTACCTCTTCGGTGATCACCC
1 GATTTTCACCTATGAACATGAAACACCTTTCA-TGTTCAGCCGTTTACCTCTTCGGCGATCACCC
10137 ACCGACCAAG
Statistics
Matches: 336, Mismatches: 49, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
64 5 0.01
65 204 0.61
66 66 0.20
67 58 0.17
68 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (65 bp):
GATTTTCACCTATGAACATGAAACACCTTTCATGTTCAGCCGTTTACCTCTTCGGCGATCACCCG
Found at i:10057 original size:197 final size:195
Alignment explanation
Indices: 9679--10127 Score: 567
Period size: 197 Copynumber: 2.3 Consensus size: 195
9669 ATGGGGGTTT
* * * * *
9679 GATTTTCACCCATGAACATGAAGCACCTTTCATGTTCAGTCATTTTACCTCTTCAGCAAACATCT
1 GATTTTCACCTATGAACATGAAGCACCTTTCATGTTCAGTC-GTTTACCTCTTCGGCAAACACCA
* * * *
9744 GGATTTCCACCTATGAACACGAAACACTTTTCATGTTCAGCCGTTTATCTCTTCAGCGATCACTC
65 GAATTTCCACCTATGAACACGAAACACCTTTCATGTTCAGCCGTTTACCTCTTCAGCGATCACCC
* *
9809 GGGTTTTCACCTTTGAACATGAAGCACCTTTCATGTTCAGCCGTTTACCTCTTCGGACATCACCC
130 GGATTTTCACCTATGAACATGAAGCACCTTTCATGTTCAGCCGTTTACCTCTTCGGACATCACCC
9874 G
195 G
* ** * * *
9875 GATTTTCACTTATGAACATGAAATACCTTTCATGTTCAGTCGTTTATCTCTTCGGCGACCACCAG
1 GATTTTCACCTATGAACATGAAGCACCTTTCATGTTCAGTCGTTTACCTCTTCGGCAAACACCAG
* ** ** *
9940 AATTTTCACCTATGAACA-GAAAGCACCTTTCATGTTCAGTTGTTTACCTCTTTGGTGATCACCC
66 AATTTCCACCTATGAACACGAAA-CACCTTTCATGTTCAGCCGTTTACCTCTTCAGCGATCACCC
* * * **
10004 GGATTTTCACACCTATGAACATGAAGTACCTTTCATGTTCAGTCGTTTACCTCTTTGGTGATCAC
130 GGATTTT--CACCTATGAACATGAAGCACCTTTCATGTTCAGCCGTTTACCTCTTCGGACATCAC
10069 CCG
193 CCG
** *
10072 GATTTTCACCTATGAATGTGAAGCACCTTTTATTGTTCAGTCGTTTACCTCTTCGG
1 GATTTTCACCTATGAACATGAAGCACCTTTCA-TGTTCAGTCGTTTACCTCTTCGG
10128 TGATCACCCA
Statistics
Matches: 214, Mismatches: 35, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
194 4 0.02
195 72 0.34
196 37 0.17
197 79 0.37
198 22 0.10
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.35
Consensus pattern (195 bp):
GATTTTCACCTATGAACATGAAGCACCTTTCATGTTCAGTCGTTTACCTCTTCGGCAAACACCAG
AATTTCCACCTATGAACACGAAACACCTTTCATGTTCAGCCGTTTACCTCTTCAGCGATCACCCG
GATTTTCACCTATGAACATGAAGCACCTTTCATGTTCAGCCGTTTACCTCTTCGGACATCACCCG
Found at i:18486 original size:13 final size:13
Alignment explanation
Indices: 18470--18498 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18460 GATTTAATTG
18470 AAAATAATAATAT
1 AAAATAATAATAT
18483 AAAATAATAATAT
1 AAAATAATAATAT
18496 AAA
1 AAA
18499 GGGGGCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATAATAATAT
Found at i:18756 original size:80 final size:80
Alignment explanation
Indices: 18623--18785 Score: 326
Period size: 80 Copynumber: 2.0 Consensus size: 80
18613 AAATGACCTA
18623 ATAAGGTTGGGTCAAAATCTGTCGGATTCGACTCTTGTATCCATTCCTAGGCATAGTTTACTTTA
1 ATAAGGTTGGGTCAAAATCTGTCGGATTCGACTCTTGTATCCATTCCTAGGCATAGTTTACTTTA
18688 GTTTCTTTTACATAC
66 GTTTCTTTTACATAC
18703 ATAAGGTTGGGTCAAAATCTGTCGGATTCGACTCTTGTATCCATTCCTAGGCATAGTTTACTTTA
1 ATAAGGTTGGGTCAAAATCTGTCGGATTCGACTCTTGTATCCATTCCTAGGCATAGTTTACTTTA
18768 GTTTCTTTTACATAC
66 GTTTCTTTTACATAC
18783 ATA
1 ATA
18786 CATGCATGCT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (80 bp):
ATAAGGTTGGGTCAAAATCTGTCGGATTCGACTCTTGTATCCATTCCTAGGCATAGTTTACTTTA
GTTTCTTTTACATAC
Found at i:22041 original size:17 final size:19
Alignment explanation
Indices: 22019--22053 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
22009 GCTTTTGTTC
22019 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
22036 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
22054 GAGATGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:29277 original size:2 final size:2
Alignment explanation
Indices: 29270--29295 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29260 ATTACCCACC
29270 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
29296 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:41988 original size:26 final size:24
Alignment explanation
Indices: 41959--42012 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
41949 AAAATGGAAG
41959 AAAAAATGA-GAAAGAAAAAAGAAAAT
1 AAAAAATGATG-AA-AAAAAAG-AAAT
41985 AAAAAATGATGAAAAAAAAGAAAT
1 AAAAAATGATGAAAAAAAAGAAAT
42009 AAAA
1 AAAA
42013 GGAGGGTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 8 0.30
25 7 0.26
26 11 0.41
27 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (24 bp):
AAAAAATGATGAAAAAAAAGAAAT
Found at i:42006 original size:46 final size:46
Alignment explanation
Indices: 41874--42007 Score: 112
Period size: 47 Copynumber: 2.8 Consensus size: 46
41864 ATTTCGCTTG
* * * * **
41874 AAGAAGAAAAGAAAAATGGAAAAAATGAAAAATGATGGAAAAAATGAA
1 AAGAAAAAAAGAAACA--GAAAAAATGGAAAATAAAAGAAAAAATGAA
**
41922 AAGAAAAAAAAGAAACAGAAAAAATGGAAAATGGAAGAAAAAATGAGA
1 AAG-AAAAAAAGAAACAGAAAAAATGGAAAATAAAAGAAAAAATGA-A
*
41970 AAG-AAAAAAGAAA-ATAAAAAATGATGAAAA-AAAAGAAA
1 AAGAAAAAAAGAAACAGAAAAAATG--GAAAATAAAAGAAA
42008 TAAAAGGAGG
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
45 9 0.12
46 16 0.22
47 30 0.41
48 7 0.10
49 11 0.15
ACGTcount: A:0.72, C:0.01, G:0.19, T:0.08
Consensus pattern (46 bp):
AAGAAAAAAAGAAACAGAAAAAATGGAAAATAAAAGAAAAAATGAA
Found at i:43339 original size:37 final size:37
Alignment explanation
Indices: 43288--43358 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
43278 GAAACAGTTT
*
43288 AATCTTAAGTCTTCACGGAAGAGTAGTGAAGCAAGTC
1 AATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAGTC
43325 AATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
1 AATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
43359 ACTTATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (37 bp):
AATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAGTC
Found at i:43450 original size:55 final size:55
Alignment explanation
Indices: 43376--43741 Score: 279
Period size: 55 Copynumber: 6.8 Consensus size: 55
43366 TTTATGAAGG
* *
43376 TCGAGTCCTATACTCTCTAAAGGAATAGGGAGCGGACACGTTTGTTGAAGATCGT
1 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACACGTTTGTTGAAGATCGT
* * *
43431 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCAGACACGTTTGTTAAAGATTGT
1 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACACGTTTGTTGAAGATCGT
* * *
43486 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCAGATC-CGTTTGTTGAA-AACTAT
1 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGA-CACGTTTGTTGAAGATC-GT
* * * * * * *
43541 TCGAGTCCTATACTCTCTCATGGAATAGGGAGTGAACCCGTTTGTTGAAGATC--
1 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACACGTTTGTTGAAGATCGT
* * * * * * *
43594 T--A-TACTCT-CTCTCTGAAGGAATATAGAGAGGAC-C-TATTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACACGT-TTGT-TGAAGATCGT
* * * * * * *
43645 TCGAGTTCTATACTCTCTGATA-GAATAGAGAGGGGGCCCGTTTATTGAAAATTGT
1 TCGAGTTCTATACTCTCT-AAAGGAATAGAGAGCGGACACGTTTGTTGAAGATCGT
* * * * * *
43700 TAGAATAT-TATACTCTCTGAATGAATAGGGAGCAGACACGTT
1 TCGAGT-TCTATACTCTCTAAAGGAATAGAGAGCGGACACGTT
43742 GGCCGAAGAT
Statistics
Matches: 249, Mismatches: 45, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
47 1 0.00
48 4 0.02
49 26 0.10
50 4 0.02
51 2 0.01
53 2 0.01
54 7 0.03
55 193 0.78
56 9 0.04
57 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACACGTTTGTTGAAGATCGT
Found at i:43686 original size:159 final size:163
Alignment explanation
Indices: 43376--43741 Score: 383
Period size: 159 Copynumber: 2.3 Consensus size: 163
43366 TTTATGAAGG
* *
43376 TCGAGTCCTATACTCTCTAAAGGAATAGGGAGCGGACACGTTTGTTGAAGATCGTTCGAGTTCTA
1 TCGAGTCCTATACTCTCTAAAGGAATAGGGAGCGAACACGTTTGTTGAAGATCG-TC-AGTACTA
43441 TACTCTCTAAAGGAATAGAGAGCAGACACGTTTGTTAAAGATTGTTCGAGTTCTATACTCTCTAA
64 TACTCTCTAAAGGAATAGAGAGCAGACACGTTTGTTAAAGATTGTTCGAGTTCTATACTCTCTAA
* *
43506 AGGAATAGAGAGCAGATCCGTTTGTTGAAAACTAT
129 AGGAATAGAGAGCAGACCCGTTTATTGAAAACTAT
* * * * *
43541 TCGAGTCCTATACTCTCTCATGGAATAGGGAGTGAACCCGTTTGTTGAAGATC-T-A-TACTCT-
1 TCGAGTCCTATACTCTCTAAAGGAATAGGGAGCGAACACGTTTGTTGAAGATCGTCAGTACTATA
* *
43602 CTCTCTGAAGGAATATAGAG-AGGAC-C-TATT-TTATGAAGATTGTTCGAGTTCTATACTCTCT
66 CTCTCTAAAGGAATAGAGAGCA-GACACGT-TTGTTA--AAGATTGTTCGAGTTCTATACTCTCT
* ** * * *
43663 GATA-GAATAGAGAGGGGGCCCGTTTATTGAAAATTGT
127 -AAAGGAATAGAGAGCAGACCCGTTTATTGAAAACTAT
* * ** * *
43700 TAGAATATTATACTCTCTGAATGAATAGGGAGC-AGACACGTT
1 TCGAGTCCTATACTCTCTAAAGGAATAGGGAGCGA-ACACGTT
43742 GGCCGAAGAT
Statistics
Matches: 169, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
157 4 0.02
158 5 0.03
159 104 0.62
160 6 0.04
161 1 0.01
163 1 0.01
165 48 0.28
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (163 bp):
TCGAGTCCTATACTCTCTAAAGGAATAGGGAGCGAACACGTTTGTTGAAGATCGTCAGTACTATA
CTCTCTAAAGGAATAGAGAGCAGACACGTTTGTTAAAGATTGTTCGAGTTCTATACTCTCTAAAG
GAATAGAGAGCAGACCCGTTTATTGAAAACTAT
Found at i:44046 original size:23 final size:23
Alignment explanation
Indices: 43998--44050 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
43988 TTTTTATATT
*
43998 TTAG-TAATTATATTTATATTAG
1 TTAGTTAATTATATTAATATTAG
44020 TTAGATTAATTA-ATTAATATT-G
1 TTAG-TTAATTATATTAATATTAG
44042 TTTAGTTAA
1 -TTAGTTAA
44051 ATAAATTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 9 0.33
23 12 0.44
24 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (23 bp):
TTAGTTAATTATATTAATATTAG
Found at i:55760 original size:11 final size:11
Alignment explanation
Indices: 55744--55768 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55734 ATTAAAAATA
55744 TTAATATTTTT
1 TTAATATTTTT
55755 TTAATATTTTT
1 TTAATATTTTT
55766 TTA
1 TTA
55769 GAACGCTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTAATATTTTT
Found at i:60844 original size:13 final size:13
Alignment explanation
Indices: 60826--60851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60816 TTGTTCTACG
60826 GCTGTGTGGATTC
1 GCTGTGTGGATTC
60839 GCTGTGTGGATTC
1 GCTGTGTGGATTC
60852 AGTTGGGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.38, T:0.38
Consensus pattern (13 bp):
GCTGTGTGGATTC
Done.