Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005826.1 Hibiscus syriacus cultivar Beakdansim tig00013654_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: 103771
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2230 original size:5 final size:5
Alignment explanation
Indices: 2172--2227 Score: 82
Period size: 5 Copynumber: 11.6 Consensus size: 5
2162 AAATTTTGGC
2172 TTTG- TTTGT TTTGT TTTGT TTTGT TTTGT TTTGTT TTTGT TTTGT TTT-T
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTG-T TTTGT TTTGT TTTGT
2221 TTT-T TTT
1 TTTGT TTT
2228 TTTGAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 12 0.24
5 33 0.66
6 5 0.10
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTTGT
Found at i:7688 original size:19 final size:19
Alignment explanation
Indices: 7666--7710 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
7656 ATGTAAAATT
7666 AAAAGAAAGGAATAAATAA
1 AAAAGAAAGGAATAAATAA
* *
7685 AAAAGAAAGGAATATATCA
1 AAAAGAAAGGAATAAATAA
7704 AAAAGAA
1 AAAAGAA
7711 TATTTTCCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAAGAAAGGAATAAATAA
Found at i:14463 original size:18 final size:18
Alignment explanation
Indices: 14423--14471 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
14413 TTTTATGAAA
* * *
14423 ACATTGAATGCATTTGAT
1 ACATCGAATGCACTTCAT
14441 ACATCGAATGCACTTCAT
1 ACATCGAATGCACTTCAT
*
14459 GCATCG-ATGCACT
1 ACATCGAATGCACT
14472 CTTAGTGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (18 bp):
ACATCGAATGCACTTCAT
Found at i:20276 original size:21 final size:21
Alignment explanation
Indices: 20209--20305 Score: 81
Period size: 23 Copynumber: 4.4 Consensus size: 21
20199 TTGTGCTTAA
*
20209 TGCATCGATACA-C-TAAATAG
1 TGCATCGATACACCTTGAAT-G
20229 TGCATCGATACATCCCTTTGAATG
1 TGCATCGATACA--CC-TTGAATG
* *
20253 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
20274 TGCACCGATGCACTCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
20297 TGCATCGAT
1 TGCATCGAT
20306 GCAACCATCG
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
20 12 0.19
21 13 0.21
22 2 0.03
23 18 0.29
24 13 0.21
25 4 0.06
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:23086 original size:65 final size:63
Alignment explanation
Indices: 23010--23169 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 63
23000 GAATAAATTG
* * * *
23010 AACATCAAATGCATTATATGCATCGATGCATAA-ACCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATT-TATGCATCGATGCACAAGA-CATACATCGATGCACTCAGGCTATTT-T-
23073 AA
62 AA
23075 AACATCGAATGCATTTGATGCATCGATGCACAAGACATACATCGATGCACTCAGGCTATTTTAA
1 AACATCGAATGCATTT-ATGCATCGATGCACAAGACATACATCGATGCACTCAGGCTATTTTAA
* * *
23139 AACATTGAGTGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
23170 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
64 28 0.33
65 51 0.61
66 5 0.06
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAAGACATACATCGATGCACTCAGGCTATTTTAA
Found at i:41708 original size:90 final size:89
Alignment explanation
Indices: 41555--41729 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 89
41545 CCTAACACAC
* *
41555 CCTTTTATAGCCAAGTTACCCTAGTCATAATAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATAATAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
41620 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
**
41645 CCTTTTATATTCAAGTTACCCTAATCAT-ATCAGGGATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATAAT-AGGGATTTTATTATTTCAAATTAATTAAATCTA
41709 TATTTAATTAATTGAAATTAA
65 TATTTAATTAATTGAAATTAA
41730 ATATTCGGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
89 9 0.11
90 70 0.89
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATAATAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:47674 original size:4 final size:4
Alignment explanation
Indices: 47665--48287 Score: 1160
Period size: 4 Copynumber: 156.2 Consensus size: 4
47655 CTGAAGGTTT
* * * *
47665 TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGCA TGCA TGCA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
47713 TGTA TATA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47761 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
47809 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47857 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47905 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47953 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
48001 TATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
48049 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
48097 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
48145 TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
48191 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
48239 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
48287 T
1 T
48288 CCAAAAACGT
Statistics
Matches: 607, Mismatches: 10, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
2 2 0.00
4 605 1.00
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:49666 original size:19 final size:19
Alignment explanation
Indices: 49618--49666 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
49608 TCAACTCTGG
**
49618 TCAAAGTCAACGGGTCGGA
1 TCAAAGTCAATAGGTCGGA
*
49637 TCAAAGTCAATAGGTCGGT
1 TCAAAGTCAATAGGTCGGA
49656 TCAAAGTCAAT
1 TCAAAGTCAAT
49667 GCTTTGGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (19 bp):
TCAAAGTCAATAGGTCGGA
Found at i:49678 original size:19 final size:19
Alignment explanation
Indices: 49596--49679 Score: 50
Period size: 19 Copynumber: 4.6 Consensus size: 19
49586 ATTTTGAATT
49596 TTTGGGTCAAAGTCAA--C
1 TTTGGGTCAAAGTCAATGC
* * *
49613 TCT-GGTCAAAGTCAACGG
1 TTTGGGTCAAAGTCAATGC
* * *
49631 GTCGGATCAAAGTCAATAG-
1 TTTGGGTCAAAGTCAAT-GC
* * *
49650 GTCGGTTCAAAGTCAATGC
1 TTTGGGTCAAAGTCAATGC
49669 TTTGGGTCAAA
1 TTTGGGTCAAA
49680 TAGTTTGGGT
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
16 12 0.24
17 2 0.04
18 1 0.02
19 35 0.69
20 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (19 bp):
TTTGGGTCAAAGTCAATGC
Found at i:49714 original size:19 final size:19
Alignment explanation
Indices: 49670--49723 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
49660 AGTCAATGCT
* **
49670 TTGGGTCAAATAGTTTGGG
1 TTGGGTCAAACAGTTCAGG
49689 TCT-GGTCAAACAGTTCAGG
1 T-TGGGTCAAACAGTTCAGG
49708 TTGGGTCAAACAGTTC
1 TTGGGTCAAACAGTTC
49724 GGGTCAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (19 bp):
TTGGGTCAAACAGTTCAGG
Found at i:53982 original size:16 final size:18
Alignment explanation
Indices: 53959--54008 Score: 77
Period size: 16 Copynumber: 2.8 Consensus size: 18
53949 TTTGACTTTT
53959 TGGGTCAAAGTCAACT-C
1 TGGGTCAAAGTCAACTGC
53976 T-GGTCAAAGTCAACTGGC
1 TGGGTCAAAGTCAACT-GC
53994 TGGGTCAAAGTCAAC
1 TGGGTCAAAGTCAAC
54009 GGGTCAGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.47
17 1 0.03
18 2 0.07
19 13 0.43
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (18 bp):
TGGGTCAAAGTCAACTGC
Found at i:55995 original size:42 final size:42
Alignment explanation
Indices: 55968--56056 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
55958 TATATATCAC
*
55968 AACATTAGTGGCGCTTGTGCCTAAAATGCCACTATATAACCA
1 AACATTAGCGGCGCTTGTGCCTAAAATGCCACTATATAACCA
*
56010 AACATTAGCGGCGTTTGTGCCTAAAATGCCACTATATAACCA
1 AACATTAGCGGCGCTTGTGCCTAAAATGCCACTATATAACCA
56052 AACAT
1 AACAT
56057 GTTGCAGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
AACATTAGCGGCGCTTGTGCCTAAAATGCCACTATATAACCA
Found at i:65585 original size:16 final size:16
Alignment explanation
Indices: 65560--65591 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
65550 TATCGCAAAA
*
65560 AAATTTACTATTCATG
1 AAATTCACTATTCATG
65576 AAATTCACTATTCATG
1 AAATTCACTATTCATG
65592 TGAATAGTAA
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:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (16 bp):
AAATTCACTATTCATG
Found at i:66054 original size:36 final size:35
Alignment explanation
Indices: 65999--66080 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 35
65989 CCCATTCCTA
65999 TTTTCAAAAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAAAACATCTACCAAACTTTGAAAAACAT
* *
66034 TTTTCAAAGAAACATTTACCAAAGTTTGAAAAACAT
1 TTTTCAAA-AAACATCTACCAAACTTTGAAAAACAT
**
66070 TTAGCAAAAAA
1 TTTTCAAAAAA
66081 GAAAATGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 11 0.26
36 31 0.74
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (35 bp):
TTTTCAAAAAACATCTACCAAACTTTGAAAAACAT
Found at i:72245 original size:25 final size:25
Alignment explanation
Indices: 72215--72269 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
72205 TAGGACTAAA
72215 TTAAATAAAAATTAAAGTATAAATT
1 TTAAATAAAAATTAAAGTATAAATT
** *
72240 TTAAATAAGTATTAAATTATAAATT
1 TTAAATAAAAATTAAAGTATAAATT
*
72265 CTAAA
1 TTAAA
72270 AGGTGGGAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
TTAAATAAAAATTAAAGTATAAATT
Found at i:72255 original size:18 final size:17
Alignment explanation
Indices: 72229--72263 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
72219 ATAAAAATTA
*
72229 AAGTATAAATTTTAAAT
1 AAGTATAAATTATAAAT
72246 AAGTATTAAATTATAAAT
1 AAGTA-TAAATTATAAAT
72264 TCTAAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
AAGTATAAATTATAAAT
Found at i:73481 original size:8 final size:9
Alignment explanation
Indices: 73463--73500 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
73453 TCATAATTGT
73463 AATAGGAAA
1 AATAGGAAA
73472 AATA-GAAA
1 AATAGGAAA
*
73480 AAAAGAGAAA
1 AATAG-GAAA
73490 AATAGGAAA
1 AATAGGAAA
73499 AA
1 AA
73501 GGGATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 10 0.40
10 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (9 bp):
AATAGGAAA
Found at i:90686 original size:2 final size:2
Alignment explanation
Indices: 90650--90674 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90640 ACACACACAC
90650 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
90675 CTTTGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94889 original size:15 final size:15
Alignment explanation
Indices: 94864--94919 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
94854 AGACAACCCC
94864 TTTTA-TTTTATTAA
1 TTTTATTTTTATTAA
94878 TTTTATTTTTATTAA
1 TTTTATTTTTATTAA
94893 TTTTATTTTTATT-A
1 TTTTATTTTTATTAA
94907 -TTTATTTTTATTA
1 TTTTATTTTTATTA
94920 GGTATTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.30
14 6 0.15
15 22 0.55
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTTTTATTAA
Found at i:94933 original size:28 final size:29
Alignment explanation
Indices: 94864--94919 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
94854 AGACAACCCC
94864 TTTTATTTTATTAATTTTATTTTTATTAA
1 TTTTATTTTATTAATTTTATTTTTATTAA
94893 TTTTATTTTTATT-A-TTTATTTTTATTA
1 TTTTA-TTTTATTAATTTTATTTTTATTA
94920 GGTATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 13 0.50
29 6 0.23
30 7 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTTATTTTATTAATTTTATTTTTATTAA
Found at i:99164 original size:23 final size:23
Alignment explanation
Indices: 99132--99200 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
99122 AGTCATACTA
99132 GTCAACAGTCAATGGGTTGACTCG
1 GTCAA-AGTCAATGGGTTGACTCG
99156 GTCAAAGTCAATGGGTTGACTCG
1 GTCAAAGTCAATGGGTTGACTCG
* *
99179 ATCAAAGTCAATGAGTTGACTC
1 GTCAAAGTCAATGGGTTGACTC
99201 AGTCGAGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 38 0.88
24 5 0.12
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (23 bp):
GTCAAAGTCAATGGGTTGACTCG
Found at i:99210 original size:14 final size:14
Alignment explanation
Indices: 99191--99217 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
99181 CAAAGTCAAT
99191 GAGTTGACTCAGTC
1 GAGTTGACTCAGTC
99205 GAGTTGACTCAGT
1 GAGTTGACTCAGT
99218 GATTATATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (14 bp):
GAGTTGACTCAGTC
Done.