Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007506.1 Hibiscus syriacus cultivar Beakdansim tig00020821_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: 60503
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:17757 original size:23 final size:23
Alignment explanation
Indices: 17731--17779 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
17721 TCAATAGTGT
17731 AGGTCACCATAGTTAAGACTGAG
1 AGGTCACCATAGTTAAGACTGAG
** * *
17754 AGGTTGCCATAGTTGAGGCTGAG
1 AGGTCACCATAGTTAAGACTGAG
17777 AGG
1 AGG
17780 AGATACGGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.35, T:0.22
Consensus pattern (23 bp):
AGGTCACCATAGTTAAGACTGAG
Found at i:21306 original size:13 final size:13
Alignment explanation
Indices: 21288--21334 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
21278 ACCCAACCCG
21288 ACCCGACCCGTTT
1 ACCCGACCCGTTT
21301 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* * *
21314 ACTCGACCAGTTG
1 ACCCGACCCGTTT
21327 ACCCGACC
1 ACCCGACC
21335 TGACCCGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.19, C:0.45, G:0.17, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:21344 original size:18 final size:18
Alignment explanation
Indices: 21318--21352 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21308 CCGTTTACTC
21318 GACCAGTTGACCCGACCT
1 GACCAGTTGACCCGACCT
*
21336 GACCCGTTGACCCGACC
1 GACCAGTTGACCCGACC
21353 CGTTGACTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.14
Consensus pattern (18 bp):
GACCAGTTGACCCGACCT
Found at i:21346 original size:8 final size:8
Alignment explanation
Indices: 21335--21382 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
21325 TGACCCGACC
21335 TGACCCGT
1 TGACCCGT
21343 TGACCC--
1 TGACCCGT
21349 -GACCCGT
1 TGACCCGT
*
21356 TGACTCGT
1 TGACCCGT
21364 TGA-CCGT
1 TGACCCGT
21371 TGACCCGT
1 TGACCCGT
21379 TGAC
1 TGAC
21383 TGTTGATCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
5 5 0.15
7 6 0.18
8 23 0.68
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (8 bp):
TGACCCGT
Found at i:21347 original size:13 final size:13
Alignment explanation
Indices: 21287--21359 Score: 65
Period size: 13 Copynumber: 5.2 Consensus size: 13
21277 AACCCAACCC
21287 GACCCGACCCGTT
1 GACCCGACCCGTT
*
21300 TACCCGACCCGTT
1 GACCCGACCCGTT
* * *
21313 TACTCGACCAGTT
1 GACCCGACCCGTT
21326 GACCCGACCTGACCCGTT
1 GA--C--CC-GACCCGTT
21344 GACCCGACCCGTT
1 GACCCGACCCGTT
21357 GAC
1 GAC
21360 TCGTTGACCG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
13 35 0.71
14 2 0.04
15 1 0.02
16 1 0.02
17 1 0.02
18 9 0.18
ACGTcount: A:0.18, C:0.42, G:0.21, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:21372 original size:15 final size:15
Alignment explanation
Indices: 21352--21388 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
21342 TTGACCCGAC
*
21352 CCGTTGACTCGTTGA
1 CCGTTGACCCGTTGA
21367 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
*
21382 CTGTTGA
1 CCGTTGA
21389 TCGGCGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.32
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:29881 original size:20 final size:20
Alignment explanation
Indices: 29851--29914 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
29841 AACCAATCCA
*
29851 TCTAGTATGGATAACAACCT
1 TCTAGTATGGATACCAACCT
29871 TCTAG-AGTGGATACCAACCT
1 TCTAGTA-TGGATACCAACCT
*
29891 TCTGGTATGGATACCAACCT
1 TCTAGTATGGATACCAACCT
29911 TCTA
1 TCTA
29915 ATATCAATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (20 bp):
TCTAGTATGGATACCAACCT
Found at i:29924 original size:20 final size:20
Alignment explanation
Indices: 29881--29927 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29871 TCTAGAGTGG
** **
29881 ATACCAACCTTCTGGTATGG
1 ATACCAACCTTCTAATATCA
29901 ATACCAACCTTCTAATATCA
1 ATACCAACCTTCTAATATCA
29921 ATACCAA
1 ATACCAA
29928 ACATTCAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.28
Consensus pattern (20 bp):
ATACCAACCTTCTAATATCA
Found at i:38740 original size:23 final size:21
Alignment explanation
Indices: 38714--38758 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
38704 TTCATACCTG
38714 AAATATCATTCATGATAAATATC
1 AAATAT-ATTCATGATAAA-ATC
*
38737 AAATATGTTCATGATAAAATC
1 AAATATATTCATGATAAAATC
38758 A
1 A
38759 TATGTAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 11 0.52
23 6 0.29
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (21 bp):
AAATATATTCATGATAAAATC
Found at i:38763 original size:19 final size:21
Alignment explanation
Indices: 38722--38763 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
38712 TGAAATATCA
38722 TTCATGATAAATATCAAATATG
1 TTCATGATAAATATC-AATATG
38744 TTCATGATAAA-ATC-ATATG
1 TTCATGATAAATATCAATATG
38763 T
1 T
38764 AACAATCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
21 3 0.15
22 11 0.55
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCATGATAAATATCAATATG
Found at i:43532 original size:44 final size:43
Alignment explanation
Indices: 43480--43594 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 43
43470 TGTAGAAAGC
* * **
43480 TATAAGGTCTTACCCTTGCACATAGTAGAGGAGCATGCGCAAA
1 TATAAGGTCTTACCCTTGCACATAGCAGAGAAGCATGCAAAAA
* *
43523 TGATAAGGTCTTACCC-TGTCACATAGCAGAGAAGCCTTCAAAAA
1 T-ATAAGGTCTTACCCTTG-CACATAGCAGAGAAGCATGCAAAAA
*
43567 TAGTAAGGTCTTACCCTTGTACATAGCA
1 TA-TAAGGTCTTACCCTTGCACATAGCA
43595 AATGAGCCTT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
43 4 0.07
44 55 0.90
45 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (43 bp):
TATAAGGTCTTACCCTTGCACATAGCAGAGAAGCATGCAAAAA
Found at i:47556 original size:22 final size:22
Alignment explanation
Indices: 47526--47575 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
47516 CAAAGAGAAT
*
47526 TGGGCTCCCCACGGTGATACAC
1 TGGGTTCCCCACGGTGATACAC
*
47548 TGGGTTCCCTACGGTGATACAC
1 TGGGTTCCCCACGGTGATACAC
47570 TGGGTT
1 TGGGTT
47576 GAATAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (22 bp):
TGGGTTCCCCACGGTGATACAC
Found at i:48094 original size:13 final size:13
Alignment explanation
Indices: 48076--48106 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
48066 TAGGACATCC
48076 TCTAAAAATACGA
1 TCTAAAAATACGA
48089 TCTAAAAATACGA
1 TCTAAAAATACGA
48102 TCTAA
1 TCTAA
48107 CTCTATGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (13 bp):
TCTAAAAATACGA
Found at i:49323 original size:15 final size:15
Alignment explanation
Indices: 49303--49334 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
49293 ATAGCAGACA
49303 TATTACCAGGGACTC
1 TATTACCAGGGACTC
49318 TATTACCAGGGACTC
1 TATTACCAGGGACTC
49333 TA
1 TA
49335 GCAGCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (15 bp):
TATTACCAGGGACTC
Found at i:49957 original size:2 final size:2
Alignment explanation
Indices: 49950--50017 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
49940 TCGATAATAC
49950 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
49992 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
50018 CAAGACGATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50430 original size:44 final size:42
Alignment explanation
Indices: 50316--50484 Score: 135
Period size: 44 Copynumber: 3.8 Consensus size: 42
50306 TGTACACCCA
* * * *
50316 GTAAGGACTTACCCTGAGCACAAAGCCGAGAAGCCTGTGGAAAG
1 GTAAGGTCTTACCCT-TGCACATAGCAGAG-AGCCTGTGGAAAG
* *
50360 TTGTAAGGTATTACCCTTGCAAATAGCAGATGAGCCTGTGGAAACG
1 --GTAAGGTCTTACCCTTGCACATAGCAGA-GAGCCTGTGGAAA-G
* * *
50406 GTTAGGTCTTACCC-TGACACATAGCAGAAGAGCCT-TCAGAAATA
1 GTAAGGTCTTACCCTTG-CACATAGCAG-AGAGCCTGT-GGAAA-G
*
50450 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCT
1 GTAAGGTCTTACCCTTGCACATAGCAGA-GAGCCT
50485 TCAGAAACTT
Statistics
Matches: 102, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 4 0.04
44 59 0.58
45 24 0.24
46 15 0.15
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (42 bp):
GTAAGGTCTTACCCTTGCACATAGCAGAGAGCCTGTGGAAAG
Found at i:50485 original size:44 final size:43
Alignment explanation
Indices: 50362--50492 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 43
50352 GTGGAAAGTT
* * * * *
50362 GTAAGGTATTACCCTTGCAAATAGCAGATGAGCCTGT-GGAAACG
1 GTAAGGTCTTACCCTTGCACATAGCA-AAGAGCCT-TCAGAAACA
* *
50406 GTTAGGTCTTACCC-TGACACATAGCAGAAGAGCCTTCAGAAATA
1 GTAAGGTCTTACCCTTG-CACATAGCA-AAGAGCCTTCAGAAACA
50450 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAC
1 GTAAGGTCTTACCCTTGCACATAGCAAA-GAGCCTTCAGAAAC
50493 TTCCTCCAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
43 5 0.07
44 67 0.91
45 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (43 bp):
GTAAGGTCTTACCCTTGCACATAGCAAAGAGCCTTCAGAAACA
Found at i:52479 original size:17 final size:19
Alignment explanation
Indices: 52444--52484 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
52434 ATTGAATACT
52444 TTTAATAATATACTAACAA
1 TTTAATAATATACTAACAA
52463 TTTAATAAT-TA-TAACAA
1 TTTAATAATATACTAACAA
*
52480 ATTAA
1 TTTAA
52485 AAGGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTAATAATATACTAACAA
Found at i:57270 original size:26 final size:24
Alignment explanation
Indices: 57221--57305 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 24
57211 TTTAATTCAT
57221 AATATTTTTATATATTAATT-TTAA
1 AATATTTTT-TATATTAATTATTAA
57245 AAGTATTTTTTATATTAACTTATT-A
1 AA-TATTTTTTATATTAA-TTATTAA
*
57270 AATATATTTTATCATTAAATTAATTTAA
1 AATATTTTTTAT-ATT-AATT-A-TTAA
57298 AATATTTT
1 AATATTTT
57306 ATCTTTATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
24 19 0.37
25 17 0.33
26 5 0.10
27 2 0.04
28 8 0.16
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (24 bp):
AATATTTTTTATATTAATTATTAA
Found at i:58427 original size:4 final size:4
Alignment explanation
Indices: 58420--58496 Score: 100
Period size: 4 Copynumber: 18.8 Consensus size: 4
58410 ATATATATAT
* *
58420 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAG
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
58468 ATAC ATGC ATAC ATAT ATTTAC ATAC ATA
1 ATAC ATAC ATAC ATAC A--TAC ATAC ATA
58497 TATCAGAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
4 60 0.95
6 3 0.05
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:60324 original size:14 final size:16
Alignment explanation
Indices: 60305--60336 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60295 ATACTTTGTC
60305 ACTATAC-T-ATCGAT
1 ACTATACTTCATCGAT
60319 ACTATACTTCATCGAT
1 ACTATACTTCATCGAT
60335 AC
1 AC
60337 CTATTCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
ACTATACTTCATCGAT
Done.