Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003258.1 Hibiscus syriacus cultivar Beakdansim tig00006847_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: 81713
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:421 original size:139 final size:138
Alignment explanation
Indices: 169--421 Score: 325
Period size: 139 Copynumber: 1.8 Consensus size: 138
159 CACTTTAGTC
*
169 CATTACTTTAGGGGTAATCTGAATTGGTTCTCGTAGTAACATGCCCGAGGGACCATTTCGATTAT
1 CATTAATTTAGGGGTAATCTGAATTGGTTCTCGTAGTAACATGCCCGAGGGACCATTTCGATTAT
* * * **
234 TCGAAGTAATAATTGGTCAAATAAATTAGGATTAATATTAGAGTCTCCACTTTAGGTTTAATATC
66 TCGAAGTAATAATTCGTAAAATAAATTAGGATTAATATCAGAACCTCCACTTTAGGTTTAATATC
299 ATTTTAAA
131 ATTTTAAA
* * * *
307 CATTAATTTAGGGAGTAAT-TCGAATTGGCTT-TCGTATTAACATG-CTGATGGTCCATTTCGAT
1 CATTAATTTAGGG-GTAATCT-GAATTGG-TTCTCGTAGTAACATGCCCGAGGGACCATTTCGAT
* *
369 TATTCG-ATTCAATAATTTCTTAAAATAAATTAGGATTAATATCAGAACCTCCA
63 TATTCGAAGT-AATAA-TTCGTAAAATAAATTAGGATTAATATCAGAACCTCCA
422 TTTTTTACTT
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
137 2 0.02
138 39 0.40
139 55 0.56
140 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (138 bp):
CATTAATTTAGGGGTAATCTGAATTGGTTCTCGTAGTAACATGCCCGAGGGACCATTTCGATTAT
TCGAAGTAATAATTCGTAAAATAAATTAGGATTAATATCAGAACCTCCACTTTAGGTTTAATATC
ATTTTAAA
Found at i:2644 original size:6 final size:6
Alignment explanation
Indices: 2633--2671 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
2623 ATACTACTAC
2633 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAG
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAG
2672 CAAAAGCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:2677 original size:18 final size:18
Alignment explanation
Indices: 2638--2677 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2628 ACTACAAGGG
**
2638 AAAGGGAAAGGGAAAGGG
1 AAAGGGAAAGGGAAAGCA
2656 AAAGGGAAAGGGAAAGCA
1 AAAGGGAAAGGGAAAGCA
2674 AAAG
1 AAAG
2678 CCAAAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.42, T:0.00
Consensus pattern (18 bp):
AAAGGGAAAGGGAAAGCA
Found at i:8457 original size:3 final size:3
Alignment explanation
Indices: 8442--8473 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
8432 ATGATTGGAG
*
8442 TGA TGA AGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
8474 CACCACCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:10486 original size:12 final size:12
Alignment explanation
Indices: 10453--10487 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
10443 GACTCGATGA
10453 AAAATAAAAAAT
1 AAAATAAAAAAT
* *
10465 AACATGAAAAAT
1 AAAATAAAAAAT
10477 AAAATAAAAAA
1 AAAATAAAAAA
10488 ATCATATCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:20713 original size:44 final size:44
Alignment explanation
Indices: 20664--20795 Score: 248
Period size: 44 Copynumber: 3.0 Consensus size: 44
20654 AGAACAGGAG
20664 ATAACAAAAACATAGAAAACAACAACCTTGTTGCATGGGTAGAT
1 ATAACAAAAACATAGAAAACAACAACCTTGTTGCATGGGTAGAT
20708 ATAACAAAAACATAGAAAACAACAACCTTGTTGCATGGGTAGAT
1 ATAACAAAAACATAGAAAACAACAACCTTGTTGCATGGGTAGAT
*
20752 ATAACAAAAACATAGAAAACTACAACCTTGTTGCAT-GGTAGAT
1 ATAACAAAAACATAGAAAACAACAACCTTGTTGCATGGGTAGAT
20795 A
1 A
20796 GTTATCTCTC
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
43 8 0.09
44 79 0.91
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (44 bp):
ATAACAAAAACATAGAAAACAACAACCTTGTTGCATGGGTAGAT
Found at i:23229 original size:27 final size:28
Alignment explanation
Indices: 23198--23275 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
23188 CCTGTTTTGC
*
23198 TCAAAAATATTTTAAGTATTTAATTTAA
1 TCAAAAATATTTTAAGTATTTAATTAAA
**
23226 -C-AAAATAATAATAAGTATTT-ATTAAA
1 TCAAAAAT-ATTTTAAGTATTTAATTAAA
* *
23252 TCAAAAAATACTTTAAATATTTAA
1 TC-AAAAATATTTTAAGTATTTAA
23276 ATGAAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
26 10 0.26
27 13 0.34
28 9 0.24
29 6 0.16
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (28 bp):
TCAAAAATATTTTAAGTATTTAATTAAA
Found at i:31075 original size:16 final size:16
Alignment explanation
Indices: 31051--31082 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31041 TATCGCCGAC
*
31051 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
31067 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
31083 AGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:34598 original size:13 final size:13
Alignment explanation
Indices: 34580--34606 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34570 CTACAGACGC
34580 GCATATGAAGACT
1 GCATATGAAGACT
34593 GCATATGAAGACT
1 GCATATGAAGACT
34606 G
1 G
34607 TTGAACTATG
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:34998 original size:13 final size:14
Alignment explanation
Indices: 34982--35013 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
34972 AAATGACATT
34982 TTAAAAAA-TATAA
1 TTAAAAAAGTATAA
34995 TTAAAAAAGTATAA
1 TTAAAAAAGTATAA
35009 TTAAA
1 TTAAA
35014 TATAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
TTAAAAAAGTATAA
Found at i:38384 original size:22 final size:22
Alignment explanation
Indices: 38359--38403 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38349 ATCATACACC
38359 ATATTGTTCACCCTTCGAGGTT
1 ATATTGTTCACCCTTCGAGGTT
* * *
38381 ATATTGTTTATCCTTTGAGGTT
1 ATATTGTTCACCCTTCGAGGTT
38403 A
1 A
38404 AATTATTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.47
Consensus pattern (22 bp):
ATATTGTTCACCCTTCGAGGTT
Found at i:39010 original size:23 final size:23
Alignment explanation
Indices: 38968--39011 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
38958 ACGTGGTAGC
**
38968 TGATGTGGTGATGATGTGGCAAT
1 TGATGTGGTGATGACATGGCAAT
38991 TGATGTGGTGATGACATGGCA
1 TGATGTGGTGATGACATGGCA
39012 GTCGACGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.32
Consensus pattern (23 bp):
TGATGTGGTGATGACATGGCAAT
Found at i:39021 original size:23 final size:23
Alignment explanation
Indices: 38972--39022 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
38962 GGTAGCTGAT
** * *
38972 GTGGTGATGATGTGGCAATTGAT
1 GTGGTGATGACATGGCAATCGAC
*
38995 GTGGTGATGACATGGCAGTCGAC
1 GTGGTGATGACATGGCAATCGAC
39018 GTGGT
1 GTGGT
39023 AGGTGTCGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.41, T:0.29
Consensus pattern (23 bp):
GTGGTGATGACATGGCAATCGAC
Found at i:47497 original size:18 final size:19
Alignment explanation
Indices: 47442--47505 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 19
47432 CGAAACCGGT
47442 TTTTTCGGTTCGGTTCGGG
1 TTTTTCGGTTCGGTTCGGG
*
47461 TTTTT---TAACGGTTCGGG
1 TTTTTCGGT-TCGGTTCGGG
47478 TTTTTCGGTTCGGTTC-GG
1 TTTTTCGGTTCGGTTCGGG
47496 TTTTTCGGTT
1 TTTTTCGGTT
47506 TTTCAATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.03
17 14 0.36
18 12 0.31
19 11 0.28
20 1 0.03
ACGTcount: A:0.03, C:0.14, G:0.31, T:0.52
Consensus pattern (19 bp):
TTTTTCGGTTCGGTTCGGG
Found at i:52527 original size:61 final size:60
Alignment explanation
Indices: 52414--52527 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 60
52404 ATAGTTGGGT
* *
52414 GATCATTTTGTAACTTTTAATAGTTGAGAGATTAAACAAAATAATATTATATAATCAAAA
1 GATCATTTAGTAACTTTTAATAGTTGAGAGATTAAACAAAATAATATCATATAATCAAAA
* * *
52474 GATCATTTAGTAATTTTTTAATAGTTGA-AGAACTT-AATAAAATAATGTCATATA
1 GATCATTTAGTAA-CTTTTAATAGTTGAGAG-A-TTAAACAAAATAATATCATATA
52528 GTCGATGGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
60 14 0.30
61 30 0.65
62 2 0.04
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (60 bp):
GATCATTTAGTAACTTTTAATAGTTGAGAGATTAAACAAAATAATATCATATAATCAAAA
Found at i:62641 original size:20 final size:20
Alignment explanation
Indices: 62616--62653 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62606 TATGAGTATA
62616 TTGTATAATATAGTATAGTT
1 TTGTATAATATAGTATAGTT
**
62636 TTGTATTGTATAGTATAG
1 TTGTATAATATAGTATAG
62654 AATTGTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
TTGTATAATATAGTATAGTT
Found at i:65965 original size:31 final size:31
Alignment explanation
Indices: 65917--66039 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
65907 CCCGAAGGAC
* * *
65917 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
65948 CAGCCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
65979 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
66010 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
66040 CCCTCGACCC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:66873 original size:21 final size:21
Alignment explanation
Indices: 66843--66887 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
66833 ATTCTGGCGT
66843 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
66864 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
66885 TTG
1 TTG
66888 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:69788 original size:20 final size:19
Alignment explanation
Indices: 69763--69800 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
69753 ATTGTTATGT
69763 AGAGAAAAAAATGGGAAAAA
1 AGAGAAAAAAAT-GGAAAAA
*
69783 AGAGAAAATAATGGAAAA
1 AGAGAAAAAAATGGAAAA
69801 GGCAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
AGAGAAAAAAATGGAAAAA
Found at i:72262 original size:30 final size:30
Alignment explanation
Indices: 72226--72312 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
72216 TTGGTTTTTA
*
72226 AAAAAATAATTTACATAAAATTAATTACTT
1 AAAAAATAATTTACATAAAATAAATTACTT
* * *
72256 AAAAAATATTTTACGTAAAATAAATTACAT
1 AAAAAATAATTTACATAAAATAAATTACTT
* * * **
72286 ACAAATTATTTTATGTAAAATAAATTA
1 AAAAAATAATTTACATAAAATAAATTA
72313 TATCTTCTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAAATAATTTACATAAAATAAATTACTT
Found at i:73652 original size:2 final size:2
Alignment explanation
Indices: 73645--73684 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
73635 TTACATAAAC
73645 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
73685 GTGTGGATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74188 original size:8 final size:10
Alignment explanation
Indices: 74176--74239 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 10
74166 TTAAAATTTT
74176 TATATT-TAA
1 TATATTATAA
74185 -ATATTATAA
1 TATATTATAA
74194 TATATTACTAA
1 TATATTA-TAA
* *
74205 TAAAATATAA
1 TATATTATAA
*
74215 TATTATTAAAA
1 TA-TATTATAA
74226 TAT-TTA-AA
1 TATATTATAA
74234 TATATT
1 TATATT
74240 CATTAAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 10 0.22
9 8 0.18
10 12 0.27
11 15 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (10 bp):
TATATTATAA
Found at i:74260 original size:22 final size:20
Alignment explanation
Indices: 74178--74263 Score: 59
Period size: 22 Copynumber: 4.2 Consensus size: 20
74168 AAAATTTTTA
* *
74178 TATTTAAATATTATAATATAT
1 TATTAAAATA-TATAAAATAT
* *
74199 TACTAATAA-A-ATATAATAT
1 TATTAA-AATATATAAAATAT
*
74218 TATTAAAATATTTAAATATAT
1 TATTAAAATATATAAA-ATAT
*
74239 TCATTAAAATTATATCAAATAT
1 T-ATTAAAA-TATATAAAATAT
74261 TAT
1 TAT
74264 ATTAATATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.04
19 13 0.26
20 3 0.06
21 12 0.24
22 14 0.28
23 6 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAAAATATATAAAATAT
Done.