Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002718.1 Hibiscus syriacus cultivar Beakdansim tig00005609_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: 83648
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:15910 original size:29 final size:29
Alignment explanation
Indices: 15826--16193 Score: 233
Period size: 30 Copynumber: 12.6 Consensus size: 29
15816 ATTTTACATT
* *
15826 TTAACATTAAAAATATATTTTACTTTTATA
1 TTAAC-TTAAAAATATATTTTATTTTTATC
* *
15856 TTAACTTATTAAATATATTTTA-TTTTGTC
1 TTAACTTA-AAAATATATTTTATTTTTATC
* *
15885 TTAACCTAAAAATATATTTTATTTTTATT
1 TTAACTTAAAAATATATTTTATTTTTATC
* * *
15914 TTAAATTAAAAATATATTTTAGTATTAATC
1 TTAACTTAAAAATATATTTTA-TTTTTATC
* *
15944 TTAACTTAAAAATATATTTTATTGTTAAC
1 TTAACTTAAAAATATATTTTATTTTTATC
* * * * *
15973 TTAACTTATTACATAAATTATATTCTTAAT-
1 TTAACTTA-AAAATATATTTTATT-TTTATC
* ** * * * *
16003 TTAAATTGTTAAACATATTCTATTCTTACC
1 TTAACTT-AAAAATATATTTTATTTTTATC
* * * * * *
16033 TTAAATTATTAAATATAATTAATTCTTATT
1 TTAACTTA-AAAATATATTTTATTTTTATC
* * **
16063 TTAACTTAAACATATCTTTTATTCCTATC
1 TTAACTTAAAAATATATTTTATTTTTATC
** *
16092 TTAACTTAAAAA-A-A-AATATTTTTATT
1 TTAACTTAAAAATATATTTTATTTTTATC
* *
16118 TTAACTACAAAAATATATTTTATTTTTATA
1 TTAACT-TAAAAATATATTTTATTTTTATC
* * *
16148 TTAACTACAAAAATGTATTATATTTTTATC
1 TTAACT-TAAAAATATATTTTATTTTTATC
* *
16178 TTAAATTTAAAATATA
1 TTAACTTAAAAATATA
16194 GTCATAATAA
Statistics
Matches: 260, Mismatches: 66, Indels: 25
0.74 0.19 0.07
Matches are distributed among these distances:
26 13 0.05
27 5 0.02
28 14 0.05
29 86 0.33
30 140 0.54
31 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTTTTATC
Found at i:15963 original size:59 final size:58
Alignment explanation
Indices: 15826--16151 Score: 196
Period size: 59 Copynumber: 5.6 Consensus size: 58
15816 ATTTTACATT
* * * **
15826 TTAACATTAAAAATATATTTTACTTTTATATTAACTTATTAAATATATTTTATTTTGTC
1 TTAAC-TTAAAAATATATTTTATTTTTATATTAAATTATAAAATATATTTTATTTAATC
* *
15885 TTAACCTAAAAATATATTTTATTTTTATTTTAAATTA-AAAATATATTTTAGTATTAATC
1 TTAACTTAAAAATATATTTTATTTTTATATTAAATTATAAAATATATTTTA-T-TTAATC
* * * * * *
15944 TTAACTTAAAAATATATTTTATTGTTA-ACTTAACTTATTACATAAATTATATTCTTAAT-
1 TTAACTTAAAAATATATTTTATTTTTATA-TTAAATTATAAAATATATTTTA-T-TTAATC
* ** * * * ** * * * * *
16003 TTAAATTGTTAAACATATTCTATTCTTACCTTAAATTATTAAATATAATTAATTCTTATT
1 TTAACTT-AAAAATATATTTTATTTTTATATTAAATTATAAAATATATTTTATT-TAATC
* * ** * * * * * *
16063 TTAACTTAAACATATCTTTTATTCCTATCTTAACTTA-AAAAAAAATATT-TTT-ATT
1 TTAACTTAAAAATATATTTTATTTTTATATTAAATTATAAAATATATTTTATTTAATC
*
16118 TTAACTACAAAAATATATTTTATTTTTATATTAA
1 TTAACT-TAAAAATATATTTTATTTTTATATTAA
16152 CTACAAAAAT
Statistics
Matches: 205, Mismatches: 53, Indels: 21
0.73 0.19 0.08
Matches are distributed among these distances:
55 9 0.04
56 22 0.11
57 14 0.07
58 36 0.18
59 72 0.35
60 52 0.25
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.50
Consensus pattern (58 bp):
TTAACTTAAAAATATATTTTATTTTTATATTAAATTATAAAATATATTTTATTTAATC
Found at i:16135 original size:25 final size:25
Alignment explanation
Indices: 16092--16143 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
16082 TATTCCTATC
16092 TTAACTTAAAAAAAAATATTTTTATT
1 TTAACTTAAAAAAAAATA-TTTTATT
* *
16118 TTAAC-TACAAAAATATATTTTATT
1 TTAACTTAAAAAAAAATATTTTATT
16142 TT
1 TT
16144 TATATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 10 0.42
26 5 0.21
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAACTTAAAAAAAAATATTTTATT
Found at i:16257 original size:30 final size:29
Alignment explanation
Indices: 16214--16350 Score: 107
Period size: 30 Copynumber: 4.6 Consensus size: 29
16204 AATACAAATA
* * *
16214 TTTAAGTTGAGATAAAAATAAATTATACTT
1 TTTAAATTAAGATAAAAATAAAATATA-TT
* * *
16244 TTTAATTTAAGATAATATTAAAATATATTT
1 TTTAAATTAAGATAAAAATAAAATATA-TT
* *
16274 TTTAAATTAAAATAAGAATAAAATATATT
1 TTTAAATTAAGATAAAAATAAAATATATT
*
16303 TTTAAGTTACA-A-AAATAATAAAATATATT
1 TTTAAATTA-AGATAAA-AATAAAATATATT
** *
16332 TAAAAAGTGAAGATAAAAA
1 TTTAAA-TTAAGATAAAAA
16351 ATATTTTTTA
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.02
29 28 0.33
30 53 0.62
31 3 0.03
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTAAATTAAGATAAAAATAAAATATATT
Found at i:18121 original size:21 final size:19
Alignment explanation
Indices: 18097--18139 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
18087 AATATGTGTT
18097 TATATGAAAAGTGATGAAAAA
1 TATATGAAAA-TGA-GAAAAA
*
18118 TATATGAAAATGAGAAATA
1 TATATGAAAATGAGAAAAA
18137 TAT
1 TAT
18140 TCATATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 3 0.14
21 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (19 bp):
TATATGAAAATGAGAAAAA
Found at i:18236 original size:18 final size:18
Alignment explanation
Indices: 18213--18247 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18203 AGGGATATAC
*
18213 AGTGGTCTTTCGGGACAT
1 AGTGGTCATTCGGGACAT
18231 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
18248 AATTTCAGTG
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:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:18876 original size:21 final size:21
Alignment explanation
Indices: 18850--18889 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18840 CGATATTTCT
18850 ATGCAT-CGATGCACTGTAGTA
1 ATGCATAC-ATGCACTGTAGTA
18871 ATGCATACATGCACTGTAG
1 ATGCATACATGCACTGTAG
18890 CACTATTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
ATGCATACATGCACTGTAGTA
Found at i:25123 original size:22 final size:22
Alignment explanation
Indices: 25098--25144 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
25088 GAGTCGAGGG
*
25098 ATATACAGTGGTCCTTCGGGAC
1 ATATACAATGGTCCTTCGGGAC
*
25120 ATATACAATGGTCCTTTGGGAC
1 ATATACAATGGTCCTTCGGGAC
25142 ATA
1 ATA
25145 GGGTTATTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (22 bp):
ATATACAATGGTCCTTCGGGAC
Found at i:33443 original size:11 final size:11
Alignment explanation
Indices: 33427--33455 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
33417 ACAGAAATGG
33427 AAATGAATATA
1 AAATGAATATA
33438 AAATGAATATA
1 AAATGAATATA
33449 AAATGAA
1 AAATGAA
33456 ATTGAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (11 bp):
AAATGAATATA
Found at i:33676 original size:12 final size:12
Alignment explanation
Indices: 33659--33684 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33649 AGTGTCTACT
33659 GATATTGTTTAA
1 GATATTGTTTAA
33671 GATATTGTTTAA
1 GATATTGTTTAA
33683 GA
1 GA
33685 AGGGTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (12 bp):
GATATTGTTTAA
Found at i:42612 original size:23 final size:23
Alignment explanation
Indices: 42586--42651 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
42576 AGATAGAGAA
*
42586 AAACATGTCATAAAAACATATAT
1 AAACATGTCATAAAAACATAGAT
* **
42609 AAACGTGTCATAAATGCATAGAT
1 AAACATGTCATAAAAACATAGAT
*
42632 AAACATGTCACAAAAACATA
1 AAACATGTCATAAAAACATA
42652 ATTATTCTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.23
Consensus pattern (23 bp):
AAACATGTCATAAAAACATAGAT
Found at i:51422 original size:27 final size:27
Alignment explanation
Indices: 51384--51436 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
51374 TATCTTAATA
*
51384 AAGTTGCTCGAATCATACCCTGCTATC
1 AAGTTGCTCGAACCATACCCTGCTATC
* *
51411 AAGTTGTTCGAACCATGCCCTGCTAT
1 AAGTTGCTCGAACCATACCCTGCTAT
51437 TCTGACACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (27 bp):
AAGTTGCTCGAACCATACCCTGCTATC
Found at i:51565 original size:27 final size:27
Alignment explanation
Indices: 51532--51686 Score: 98
Period size: 27 Copynumber: 6.0 Consensus size: 27
51522 TTACCTTGAT
*
51532 CAAGTTG-TTCGAACCATACCTTGTTAC
1 CAAGTTGCTT-GAACCATACCCTGTTAC
*
51559 CAAGTTGCTTGAACCATGCCCTGTTATC
1 CAAGTTGCTTGAACCATACCCTGTTA-C
** * *
51587 C---TACCTTG----TTACCCTG--AT
1 CAAGTTGCTTGAACCATACCCTGTTAC
**
51605 CAAGTTG-TTCGAACCATGTCCTGTTAC
1 CAAGTTGCTT-GAACCATACCCTGTTAC
* * *
51632 CAAATTGCTTGAACCATGCCCTATTAC
1 CAAGTTGCTTGAACCATACCCTGTTAC
*
51659 CAAGTTGCTTGAACCATGCCCTGTTAC
1 CAAGTTGCTTGAACCATACCCTGTTAC
51686 C
1 C
51687 CTAACATCTC
Statistics
Matches: 97, Mismatches: 18, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 2 0.02
21 8 0.08
25 10 0.10
27 69 0.71
28 6 0.06
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.32
Consensus pattern (27 bp):
CAAGTTGCTTGAACCATACCCTGTTAC
Found at i:51933 original size:27 final size:27
Alignment explanation
Indices: 51865--51945 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
51855 GTAGTGTCAG
* *
51865 AGTAACATGACATGATTCAAGCAACTT
1 AGTAGCATGACATGATTCGAGCAACTT
* ** *
51892 -GATAGCAGGGTATGATTCGAGTAACTT
1 AG-TAGCATGACATGATTCGAGCAACTT
*
51919 AGTAGCATGACATGATTCGAACAACTT
1 AGTAGCATGACATGATTCGAGCAACTT
51946 TATCAGCATA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (27 bp):
AGTAGCATGACATGATTCGAGCAACTT
Found at i:52272 original size:16 final size:16
Alignment explanation
Indices: 52232--52273 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
52222 GTAATCAATG
*
52232 TATAATTAAAAATTAAA
1 TATAATT-AAAATAAAA
*
52249 T-TATTTAAAATAAAA
1 TATAATTAAAATAAAA
52264 TATAATTAAA
1 TATAATTAAA
52274 TTATTTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.43
16 11 0.52
17 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAATTAAAATAAAA
Found at i:63893 original size:36 final size:36
Alignment explanation
Indices: 63811--63893 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
63801 TGGTGGAGCC
* * *
63811 GGTGGTGGCGCTGGAGGAGGTCTTGGTGGCGGTCTG
1 GGTGGTGGAGCAGGAGGAGGTCTTGGTGGCGGTCTA
* * *
63847 GGAGGCGGAGCAGGAGGAGGTCTTGGTGGCGGTTTA
1 GGTGGTGGAGCAGGAGGAGGTCTTGGTGGCGGTCTA
63883 GGTGGTGGAGC
1 GGTGGTGGAGC
63894 TGGCGGTGGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.11, C:0.12, G:0.55, T:0.22
Consensus pattern (36 bp):
GGTGGTGGAGCAGGAGGAGGTCTTGGTGGCGGTCTA
Found at i:63937 original size:24 final size:24
Alignment explanation
Indices: 63910--63986 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
63900 TGGAGAAGGC
*
63910 GGAGGTTTCGGAGGTGGTGCTGGT
1 GGAGGTTTCGGAGGCGGTGCTGGT
*** *
63934 GGAGGAGCCGGAGGCGGTGCAGGT
1 GGAGGTTTCGGAGGCGGTGCTGGT
* * *
63958 GGTGGTTTCGGAGGCGGCGCTGGC
1 GGAGGTTTCGGAGGCGGTGCTGGT
63982 GGAGG
1 GGAGG
63987 AATTGGGGGA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.10, C:0.14, G:0.57, T:0.18
Consensus pattern (24 bp):
GGAGGTTTCGGAGGCGGTGCTGGT
Found at i:72370 original size:50 final size:49
Alignment explanation
Indices: 72261--72372 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 49
72251 TCAATTTTAT
* *
72261 CCTTAAAATTGTTTAATTGCATCATTTATACCCTAACCCTAACTTATAAC
1 CCTT-AAATTATTTAATTGCATCATTTATACCCTAACCCTAACTTATAAA
* * * *
72311 CCTCAAAATTATTTAATTGCATCATTTTATACCTTAGTCCTTAACTTA-AAA
1 CCT-TAAATTATTTAATTGCATCA-TTTATACCCTA-ACCCTAACTTATAAA
72362 CCTTAAATTAT
1 CCTTAAATTAT
72373 AAATTATAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
50 28 0.54
51 15 0.29
52 9 0.17
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (49 bp):
CCTTAAATTATTTAATTGCATCATTTATACCCTAACCCTAACTTATAAA
Found at i:72884 original size:22 final size:22
Alignment explanation
Indices: 72856--72901 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
72846 ACACGCACGT
72856 TCATATATTAGATGACAATAGA
1 TCATATATTAGATGACAATAGA
72878 TCATATATTAGATGACAATAGA
1 TCATATATTAGATGACAATAGA
72900 TC
1 TC
72902 GGATTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATATATTAGATGACAATAGA
Found at i:73555 original size:28 final size:28
Alignment explanation
Indices: 73507--73561 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
73497 TCGTCATTGC
*
73507 TTTCAAGCAATGACTCGACAACATAATA
1 TTTCAAGCAATGACTAGACAACATAATA
* *
73535 TTTCAAGCAATGACTATACAATATAAT
1 TTTCAAGCAATGACTAGACAACATAAT
73562 GTGAACGGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (28 bp):
TTTCAAGCAATGACTAGACAACATAATA
Found at i:78620 original size:33 final size:33
Alignment explanation
Indices: 78578--78640 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
78568 GGCTACCAAG
78578 TAATCCCCACGTGAGCTATAACGACAAGTCCAT
1 TAATCCCCACGTGAGCTATAACGACAAGTCCAT
*
78611 TAATCCCCACGTGAGCTATAACGTCAAGTC
1 TAATCCCCACGTGAGCTATAACGACAAGTC
78641 TACAACCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (33 bp):
TAATCCCCACGTGAGCTATAACGACAAGTCCAT
Found at i:81165 original size:44 final size:42
Alignment explanation
Indices: 81102--81201 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 42
81092 CTATATGCAA
*
81102 TATCTTCTTTTACATTTTTTTTGCTAGTTTCCTGTCCTCAAAGG
1 TATCTTCTTTTGCA--TTTTTTGCTAGTTTCCTGTCCTCAAAGG
* * *
81146 TATCTTATTTTGCATTTTTTGCTAGTTTCTTGTCCTCCAAGG
1 TATCTTCTTTTGCATTTTTTGCTAGTTTCCTGTCCTCAAAGG
*
81188 TATCCTCTTTTGCA
1 TATCTTCTTTTGCA
81202 CGTTCTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 38 0.76
44 12 0.24
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.52
Consensus pattern (42 bp):
TATCTTCTTTTGCATTTTTTGCTAGTTTCCTGTCCTCAAAGG
Found at i:81494 original size:36 final size:36
Alignment explanation
Indices: 81447--81520 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
81437 TTCGACGAGT
81447 TCTTTCGATTCTGTGCTTCCAGCTTTGTCATTCTCA
1 TCTTTCGATTCTGTGCTTCCAGCTTTGTCATTCTCA
81483 TCTTTCGATTCTGTGCTTCCAGCTTTGTCATTCTCA
1 TCTTTCGATTCTGTGCTTCCAGCTTTGTCATTCTCA
81519 TC
1 TC
81521 ATAGACAGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.11, C:0.28, G:0.14, T:0.47
Consensus pattern (36 bp):
TCTTTCGATTCTGTGCTTCCAGCTTTGTCATTCTCA
Done.