Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006181.1 Hibiscus syriacus cultivar Beakdansim tig00014701_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: 96297
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:9307 original size:81 final size:81
Alignment explanation
Indices: 9172--9330 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 81
9162 GAGTACTATC
* * *
9172 TGCCCATGTCATAGTAATTAAGTATAATAAAGAGTATCTAACTACAAACCATCCATCTTAATTAT
1 TGCCCATCTCATAGTAATTAAGTATAATAAAGAGTATCCAACTACAAACCATCCATCTCAATTAT
9237 AAACTTTTAAAAAAAT
66 AAACTTTTAAAAAAAT
* *
9253 TGCCCATCTCATAGTAATTAAGTATAATAAATAGTATCCAACTACAAACTATCCATCTCAATTAT
1 TGCCCATCTCATAGTAATTAAGTATAATAAAGAGTATCCAACTACAAACCATCCATCTCAATTAT
*
9318 AAATTTTTAAAAA
66 AAACTTTTAAAAA
9331 TATTACATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (81 bp):
TGCCCATCTCATAGTAATTAAGTATAATAAAGAGTATCCAACTACAAACCATCCATCTCAATTAT
AAACTTTTAAAAAAAT
Found at i:17533 original size:24 final size:24
Alignment explanation
Indices: 17488--17533 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
17478 AATTTCATAT
* *
17488 TGTTTATATATGAATTTTTAAAAA
1 TGTTTAAATATGAATTTCTAAAAA
17512 TGTTTAAATAT-AATCTTCTAAA
1 TGTTTAAATATGAAT-TTCTAAA
17534 CATGCATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
TGTTTAAATATGAATTTCTAAAAA
Found at i:19896 original size:26 final size:26
Alignment explanation
Indices: 19860--19911 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
19850 CAAAAATCAA
19860 GTTATATAGTGACATTAAACTTACGG
1 GTTATATAGTGACATTAAACTTACGG
* *
19886 GTTATATAGTGATATTTAACTTACGG
1 GTTATATAGTGACATTAAACTTACGG
19912 AACTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (26 bp):
GTTATATAGTGACATTAAACTTACGG
Found at i:25977 original size:42 final size:43
Alignment explanation
Indices: 25929--26011 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
25919 AAAGAATGTT
*
25929 TTTAATATGTTAGTTTAATGTA-TTGTGGATTTTTACTTTAAC
1 TTTAATATGTTAGTTTAATGTATTTATGGATTTTTACTTTAAC
** *
25971 TTTAATATGTTAGTTTGGTGTATTTATGGATTTTTATTTTA
1 TTTAATATGTTAGTTTAATGTATTTATGGATTTTTACTTTA
26012 GAGTTTAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 20 0.56
43 16 0.44
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.58
Consensus pattern (43 bp):
TTTAATATGTTAGTTTAATGTATTTATGGATTTTTACTTTAAC
Found at i:30940 original size:19 final size:20
Alignment explanation
Indices: 30901--30940 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30891 TGGTTCACGG
*
30901 AATATAAGATTACCAGTGGA
1 AATAAAAGATTACCAGTGGA
30921 AATAAAAGATTACCAG-GGA
1 AATAAAAGATTACCAGTGGA
30940 A
1 A
30941 TAGGATTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (20 bp):
AATAAAAGATTACCAGTGGA
Found at i:32508 original size:15 final size:15
Alignment explanation
Indices: 32483--32521 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
32473 AATTATATTA
*
32483 AAAAACAAACAAAAAG
1 AAAAAC-AACAAAAAC
*
32499 AAAAACAACAACAAC
1 AAAAACAACAAAAAC
32514 AAAAACAA
1 AAAAACAA
32522 ATGTGTAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAACAACAAAAAC
Found at i:37260 original size:31 final size:31
Alignment explanation
Indices: 37222--37293 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
37212 ATACACATGT
*
37222 TATTACGAGGGAGAAAATCTGTGTCATTTCA
1 TATTACGAAGGAGAAAATCTGTGTCATTTCA
37253 TATTACGAAGGAGAAAATCTGTGTCATTTCA
1 TATTACGAAGGAGAAAATCTGTGTCATTTCA
37284 TATTACGAAG
1 TATTACGAAG
37294 CTAGGATCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (31 bp):
TATTACGAAGGAGAAAATCTGTGTCATTTCA
Found at i:38647 original size:13 final size:13
Alignment explanation
Indices: 38618--38670 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
38608 AATAATAAAT
*
38618 AATAAAAAATTTAC
1 AATAAAAAA-GTAC
*
38632 AATAAAAAAGTCC
1 AATAAAAAAGTAC
* *
38645 AATAAACAACTAC
1 AATAAAAAAGTAC
38658 AATAAAAAAGTAC
1 AATAAAAAAGTAC
38671 TAAATACAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 23 0.72
14 9 0.28
ACGTcount: A:0.64, C:0.13, G:0.04, T:0.19
Consensus pattern (13 bp):
AATAAAAAAGTAC
Found at i:43199 original size:2 final size:2
Alignment explanation
Indices: 43192--43236 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
43182 GATGAAATTC
43192 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
43234 TA T
1 TA T
43237 GGATAGGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52764 original size:16 final size:17
Alignment explanation
Indices: 52734--52766 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52724 TAGGTTAAAT
52734 TATAAAATTATTTTTTA
1 TATAAAATTATTTTTTA
*
52751 TATAAATTTATTTTTT
1 TATAAAATTATTTTTT
52767 GAAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATAAAATTATTTTTTA
Found at i:53801 original size:24 final size:24
Alignment explanation
Indices: 53768--53818 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
53758 ATAGAATTGT
* *
53768 TACATATATACATACATACCTACG
1 TACATATATACACACATACATACG
* *
53792 TACATGTATACACGCATACATACG
1 TACATATATACACACATACATACG
53816 TAC
1 TAC
53819 GTACATGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.27
Consensus pattern (24 bp):
TACATATATACACACATACATACG
Found at i:53832 original size:24 final size:25
Alignment explanation
Indices: 53778--53835 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
53768 TACATATATA
53778 CATACATACCTACGTACATGTATACACG
1 CATACATACCTACGTACATG---ACACG
* *
53806 CATACATACGTACGTACATG-CATG
1 CATACATACCTACGTACATGACACG
53830 CATACA
1 CATACA
53836 CATACATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 9 0.32
28 19 0.68
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (25 bp):
CATACATACCTACGTACATGACACG
Found at i:55633 original size:29 final size:31
Alignment explanation
Indices: 55601--55658 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
55591 CTAAAAAAAA
* *
55601 ATAAACACT-AAATTAATTA-AAAAAAACTC
1 ATAAACAATAAAAATAATTAGAAAAAAACTC
*
55630 ATAATCAATAAAAATAATTAGAAAAAAAC
1 ATAAACAATAAAAATAATTAGAAAAAAAC
55659 AGATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (31 bp):
ATAAACAATAAAAATAATTAGAAAAAAACTC
Found at i:65760 original size:40 final size:40
Alignment explanation
Indices: 65705--65789 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
65695 CTAGCATTGT
65705 GATGGGTCTAGGCTCAATGGTGATCTCACTAGGTCAAATG
1 GATGGGTCTAGGCTCAATGGTGATCTCACTAGGTCAAATG
65745 GATGGGTCTAGGCTCAATGGTGATCTCACTAGGTCAAATG
1 GATGGGTCTAGGCTCAATGGTGATCTCACTAGGTCAAATG
65785 GATGG
1 GATGG
65790 AGGTGTTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (40 bp):
GATGGGTCTAGGCTCAATGGTGATCTCACTAGGTCAAATG
Found at i:65763 original size:19 final size:19
Alignment explanation
Indices: 65705--65764 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
65695 CTAGCATTGT
65705 GATGGGTCTAGGCTCAATG
1 GATGGGTCTAGGCTCAATG
**
65724 G-TGATCTCACTAGG-TCAAATG
1 GATG-GGT--CTAGGCTC-AATG
65745 GATGGGTCTAGGCTCAATG
1 GATGGGTCTAGGCTCAATG
65764 G
1 G
65765 TGATCTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
18 2 0.06
19 12 0.39
20 4 0.13
21 11 0.35
22 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (19 bp):
GATGGGTCTAGGCTCAATG
Found at i:65785 original size:21 final size:21
Alignment explanation
Indices: 65712--65781 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
65702 TGTGATGGGT
65712 CTAGGCTCAATGGTGATCTCA
1 CTAGGCTCAATGGTGATCTCA
**
65733 CTAGG-TCAAATGGATG-GGT--
1 CTAGGCTC-AATGG-TGATCTCA
65752 CTAGGCTCAATGGTGATCTCA
1 CTAGGCTCAATGGTGATCTCA
65773 CTAGG-TCAA
1 CTAGGCTCAA
65782 ATGGATGGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
18 2 0.05
19 11 0.28
20 8 0.21
21 16 0.41
22 2 0.05
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
CTAGGCTCAATGGTGATCTCA
Found at i:67365 original size:23 final size:23
Alignment explanation
Indices: 67312--67365 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
67302 TACAAATATG
*
67312 TTCACGAAAATTAAATGAACATG
1 TTCACGAAAATTAAATGAACATA
* * *
67335 TCCGCGAATATTAAATGAACATA
1 TTCACGAAAATTAAATGAACATA
67358 TTCACGAA
1 TTCACGAA
67366 CGAACACTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (23 bp):
TTCACGAAAATTAAATGAACATA
Found at i:70336 original size:29 final size:29
Alignment explanation
Indices: 70303--70360 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
70293 TATTGCAAAT
*
70303 ATCTATTAAAATGAAATAAATAATCTCAG
1 ATCTATTAAAATGAAATAAATAATATCAG
*
70332 ATCTATTAAAATGAGATAAATAATATCAG
1 ATCTATTAAAATGAAATAAATAATATCAG
70361 TTTGCGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (29 bp):
ATCTATTAAAATGAAATAAATAATATCAG
Found at i:72387 original size:22 final size:22
Alignment explanation
Indices: 72359--72407 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
72349 TGATATAATA
72359 TATAAGTAATAAGGACTAAATG
1 TATAAGTAATAAGGACTAAATG
72381 TATAAGTAATAAGGACTAAATG
1 TATAAGTAATAAGGACTAAATG
72403 TATAA
1 TATAA
72408 TTATAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (22 bp):
TATAAGTAATAAGGACTAAATG
Found at i:93855 original size:37 final size:37
Alignment explanation
Indices: 93805--93879 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
93795 CCATCTCCCC
93805 CTAATCCATAGTTATGAACTCTCTATTACGGTCACCA
1 CTAATCCATAGTTATGAACTCTCTATTACGGTCACCA
* * * * *
93842 CTAATCCGTAGTTATTAACTCTTTGTTCCGGTCACCA
1 CTAATCCATAGTTATGAACTCTCTATTACGGTCACCA
93879 C
1 C
93880 CAACACCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (37 bp):
CTAATCCATAGTTATGAACTCTCTATTACGGTCACCA
Done.