Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005106.1 Hibiscus syriacus cultivar Beakdansim tig00011478_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: 63058
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4322 original size:11 final size:11
Alignment explanation
Indices: 4306--4339 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
4296 AACATTTCAT
4306 AATATTTAAAA
1 AATATTTAAAA
*
4317 AATATTCAAAA
1 AATATTTAAAA
4328 AATATTTAAAA
1 AATATTTAAAA
4339 A
1 A
4340 TTAATACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:7993 original size:41 final size:41
Alignment explanation
Indices: 7919--8099 Score: 179
Period size: 41 Copynumber: 4.4 Consensus size: 41
7909 CATAAAATGA
* * *
7919 TACTTTAGCGTCGTTTTTTAAACAAACGCCGCAATAGAGTAG
1 TACTTTAGCGGCG-TTTTTATACAAACGACGCAATAGAGTAG
*
7961 TACTTTAGCGGCGTTTTTATATAAACGACGCAATAGAGTAG
1 TACTTTAGCGGCGTTTTTATACAAACGACGCAATAGAGTAG
* * *
8002 TACTTTAGCGGCGTTTTTATACAAAAGCCGTAATAG-GTCCA-
1 TACTTTAGCGGCGTTTTTATACAAACGACGCAATAGAGT--AG
* * * * * * *
8043 T-CTATAGTGGCGTTTTTAGACAAACGCCACAACAGATTAG
1 TACTTTAGCGGCGTTTTTATACAAACGACGCAATAGAGTAG
*
8083 TACTTTAGCGGCATTTT
1 TACTTTAGCGGCGTTTT
8100 GATAAAAAAT
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 30 0.26
41 71 0.62
42 13 0.11
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (41 bp):
TACTTTAGCGGCGTTTTTATACAAACGACGCAATAGAGTAG
Found at i:8084 original size:81 final size:83
Alignment explanation
Indices: 7970--8191 Score: 259
Period size: 81 Copynumber: 2.7 Consensus size: 83
7960 GTACTTTAGC
* * * * * * **
7970 GGCGTTTTTATATAAACGACGCAATAGAGTAGTACTTTAGCGGCGTTTTTATACAAAA-GCCGTA
1 GGCGTTTTTAAACAAACGCCGCAAAAGATTAGTACTTTAGCGGCATTTTTATACAAAATGCCACA
8034 ATA-GGTCCATCTATAGT
66 ATAGGGTCCATCTATAGT
* * * * *
8051 GGCGTTTTTAGACAAACGCCACAACAGATTAGTACTTTAGCGGCATTTTGATAAAAAATGCCACA
1 GGCGTTTTTAAACAAACGCCGCAAAAGATTAGTACTTTAGCGGCATTTTTATACAAAATGCCACA
*
8116 ATAGGGTTCATCTATAGT
66 ATAGGGTCCATCTATAGT
* * * *
8134 GGCGTTTTTCAAACAAACGCCGCAAAATATTAGAACTGTAGCGGCATTTTTACACAAA
1 GGCGTTTTT-AAACAAACGCCGCAAAAGATTAGTACTTTAGCGGCATTTTTATACAAA
8192 CGCTGCAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
81 49 0.42
82 7 0.06
83 22 0.19
84 39 0.33
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (83 bp):
GGCGTTTTTAAACAAACGCCGCAAAAGATTAGTACTTTAGCGGCATTTTTATACAAAATGCCACA
ATAGGGTCCATCTATAGT
Found at i:8371 original size:25 final size:25
Alignment explanation
Indices: 8312--8372 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
8302 CAAATCCCAT
*
8312 TCCCCTTTTCCATCTGTTCCCACGA
1 TCCCCTTTTTCATCTGTTCCCACGA
8337 TCCCCTTTTTCATCTGTTCCCACGA
1 TCCCCTTTTTCATCTGTTCCCACGA
*
8362 TTCCCTTTTTC
1 TCCCCTTTTTC
8373 CTCTTGCCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.10, C:0.41, G:0.07, T:0.43
Consensus pattern (25 bp):
TCCCCTTTTTCATCTGTTCCCACGA
Found at i:17001 original size:23 final size:23
Alignment explanation
Indices: 16975--17038 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
16965 CAGCTCGTAT
16975 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
16998 AATTGCACC-AGAGTGTCGCGTAG
1 AATTGCACCGA-AGTGCCACATAG
* *
17021 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
17039 TATAATAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:21336 original size:23 final size:23
Alignment explanation
Indices: 21310--21411 Score: 159
Period size: 23 Copynumber: 4.4 Consensus size: 23
21300 CAGCTCGTAT
*
21310 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGGAGTGCCACATAG
21333 AATTGCACCGGAGTGCCACATAG
1 AATTGCACCGGAGTGCCACATAG
*
21356 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACATAG
* *
21379 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACATAG
*
21402 AATTACACCG
1 AATTGCACCG
21412 TAGTACCATA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACATAG
Found at i:22802 original size:23 final size:23
Alignment explanation
Indices: 22776--22882 Score: 187
Period size: 23 Copynumber: 4.7 Consensus size: 23
22766 CACCACAGCT
* *
22776 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
22799 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
22822 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
22845 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
22868 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
22883 TAGTACCATA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:23929 original size:2 final size:2
Alignment explanation
Indices: 23922--23992 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
23912 CTTATATTCG
23922 TA 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 TA
23964 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 T
23993 GTCAATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28415 original size:72 final size:72
Alignment explanation
Indices: 28298--28441 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
28288 AAACCAATTC
*
28298 CAGTAATCGCTTTCATTGATACTGGAGCTGTAGAAACAATTATGAATCCATAAATACTTCCCCCA
1 CAGTAATCGCTTTCATTGATACTGGAGCTGCAGAAACAATTATGAATCCATAAATACTTCCCCCA
28363 GATTGGT
66 GATTGGT
28370 CAGTAATCGCTTTCATTGATACTGGAGCTGCAGAAACAATTATGAATCCATAAATACTTCCCCCA
1 CAGTAATCGCTTTCATTGATACTGGAGCTGCAGAAACAATTATGAATCCATAAATACTTCCCCCA
28435 GATTGGT
66 GATTGGT
28442 GGAGACCTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (72 bp):
CAGTAATCGCTTTCATTGATACTGGAGCTGCAGAAACAATTATGAATCCATAAATACTTCCCCCA
GATTGGT
Found at i:35510 original size:20 final size:20
Alignment explanation
Indices: 35485--35523 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35475 AGATTTTATA
35485 TTAGGGTGA-CGAACTTGAAC
1 TTAGGG-GAGCGAACTTGAAC
35505 TTAGGGGAGCGAACTTGAA
1 TTAGGGGAGCGAACTTGAA
35524 TTCATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (20 bp):
TTAGGGGAGCGAACTTGAAC
Found at i:36939 original size:65 final size:65
Alignment explanation
Indices: 36779--36939 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
36769 TTGTTTAAGG
* * * **
36779 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
36842 A
65 A
*
36843 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
36907 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
36940 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:37452 original size:18 final size:18
Alignment explanation
Indices: 37429--37463 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
37419 CTAGGAGATT
37429 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
37447 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
37464 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:38798 original size:149 final size:147
Alignment explanation
Indices: 38374--38833 Score: 825
Period size: 147 Copynumber: 3.1 Consensus size: 147
38364 AGAGTCGAGG
* * **
38374 TCTACGCGGTCCTTCGGGATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA-
1 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
38438 TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
66 T-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
38503 ATGGCACTACGGTGCAAT
130 ATGGCACTACGGTGCAAT
38521 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
1 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
38586 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
38651 TGGCACTACGGTGCAAT
131 TGGCACTACGGTGCAAT
38668 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGG--ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
38733 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
64 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
38798 TATGGCACTACGGTGCAAT
129 TATGGCACTACGGTGCAAT
38817 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
38834 TGCAATTATA
Statistics
Matches: 304, Mismatches: 5, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
147 159 0.52
148 2 0.01
149 143 0.47
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
TGGCACTACGGTGCAAT
Found at i:38834 original size:23 final size:23
Alignment explanation
Indices: 38801--38845 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
38791 ATTATTATAT
*
38801 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
38824 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
38846 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:42107 original size:65 final size:65
Alignment explanation
Indices: 41947--42107 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
41937 TTGTTTAAGG
* * * **
41947 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
42010 A
65 A
*
42011 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
42075 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
42108 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:42619 original size:18 final size:18
Alignment explanation
Indices: 42596--42630 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42586 CTAGGAGATT
42596 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
42614 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
42631 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:43710 original size:149 final size:149
Alignment explanation
Indices: 43541--43850 Score: 534
Period size: 149 Copynumber: 2.1 Consensus size: 149
43531 GAGGGTTTAT
* **
43541 GCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA-TAT
1 GCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATACT-T
*
43605 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG
65 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATCATTATATG
43670 GCACTACGGTGCAATTCTAC
130 GCACTACGGTGCAATTCTAC
*
43690 GCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTG
1 GCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATACTTG
*
43755 ATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATTATTATATGG
66 ATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATCATTATATGG
43820 CACTACGGTGCAATTCTAC
131 CACTACGGTGCAATTCTAC
43839 GCGG-CACTTCGG
1 GCGGTC-CTTCGG
43851 TGCAATTATA
Statistics
Matches: 153, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
148 1 0.01
149 151 0.99
150 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (149 bp):
GCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATACTTG
ATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGCCCTTATGGACATCATTATATGG
CACTACGGTGCAATTCTAC
Found at i:43851 original size:23 final size:23
Alignment explanation
Indices: 43818--43862 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
43808 ATTATTATAT
*
43818 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
43841 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
43863 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:44971 original size:2 final size:2
Alignment explanation
Indices: 44964--45001 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
44954 ACTTAGATAA
44964 CT CT CT CT 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 CT CT CT CT
45002 GTAATTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:52594 original size:15 final size:15
Alignment explanation
Indices: 52574--52608 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
52564 CCGTAGGACC
52574 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
52589 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
52604 ACTAC
1 ACTAC
52609 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Done.