Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000219.1 Hibiscus syriacus cultivar Beakdansim tig00000387_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: 169236
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:124885 original size:16 final size:16
Alignment explanation
Indices: 124864--124901 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
124854 GAAATGTGTC
124864 GATCCTCCAAGTGCTT
1 GATCCTCCAAGTGCTT
124880 GATCCTCCAAGTGCTT
1 GATCCTCCAAGTGCTT
124896 GATCCT
1 GATCCT
124902 GGGTATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (16 bp):
GATCCTCCAAGTGCTT
Found at i:132339 original size:24 final size:24
Alignment explanation
Indices: 132294--132344 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
132284 TTAATCATTG
*
132294 TAATCATATGCCAGTGAAAATCAA
1 TAATCATATGCCAGTCAAAATCAA
* *
132318 TAATCATATAG-CAGTCATAATCCA
1 TAATCATAT-GCCAGTCAAAATCAA
132342 TAA
1 TAA
132345 CCCATCACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (24 bp):
TAATCATATGCCAGTCAAAATCAA
Found at i:133054 original size:19 final size:20
Alignment explanation
Indices: 133012--133059 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
133002 CGGGTTGGGC
* * *
133012 GGTCGGGTCGAGTCGAACTG
1 GGTCGGGTTGAGTCAAACTA
133032 GGTCGGGTTG-GTCAAACTA
1 GGTCGGGTTGAGTCAAACTA
133051 GGTCGGGTT
1 GGTCGGGTT
133060 AAAAATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.15, C:0.17, G:0.44, T:0.25
Consensus pattern (20 bp):
GGTCGGGTTGAGTCAAACTA
Found at i:133881 original size:66 final size:67
Alignment explanation
Indices: 133811--133957 Score: 181
Period size: 67 Copynumber: 2.2 Consensus size: 67
133801 ACAAAATTCA
* * * *
133811 TTTCAAGGGAAAC-GATGTCAAAGA-TTGGTGTTTCAAGAGAAACTATCTAAAGGGAGACGAACT
1 TTTCAAGGGAAACAAAT-TCAAAGATTTGATGTTTCAAGAGAAACTATATAAAGGGAGACAAACT
133874 TTG
65 TTG
* * * * *
133877 TTTCAAGGGAAACAAATTCAAATATTTTATGTTTCAAGGGAAGCTGTATAAAGGGAGACAAACTT
1 TTTCAAGGGAAACAAATTCAAAGATTTGATGTTTCAAGAGAAACTATATAAAGGGAGACAAACTT
133942 TG
66 TG
*
133944 TTTTAAGGGAAACA
1 TTTCAAGGGAAACA
133958 GTCTCAAGAG
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
66 19 0.28
67 50 0.72
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (67 bp):
TTTCAAGGGAAACAAATTCAAAGATTTGATGTTTCAAGAGAAACTATATAAAGGGAGACAAACTT
TG
Found at i:133953 original size:36 final size:36
Alignment explanation
Indices: 133906--134236 Score: 308
Period size: 36 Copynumber: 9.4 Consensus size: 36
133896 AAATATTTTA
* * * *
133906 TGTTTCAAGGGAAGCTGTATAAAGGGAGAC-AAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA-TT
* *
133942 TGTTTTAAGGGAAACAGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
133978 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
* * * *
134014 TTTTTCAAGGGAAAAATGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGG-AAACTGTCTCAAGAGAGACGAAATT
* *
134051 TGTTTCAAAGGAAA-TCATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACT-GTCTCAAGAGAGACGAAATT
*
134087 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
** * * *
134123 AATTTCAAAGGAAAC-GATCTC---A-A-A--TATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACGAAATT
* * * * *
134152 TTTTTCAAGGGAATCTCTCTCAAGGGAGAC--AACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
* * *
134186 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
134222 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
134237 AAATTCAAAG
Statistics
Matches: 241, Mismatches: 40, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
29 18 0.07
31 1 0.00
32 1 0.00
33 2 0.01
34 28 0.12
35 2 0.01
36 154 0.64
37 35 0.15
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
Found at i:134072 original size:109 final size:109
Alignment explanation
Indices: 133927--134136 Score: 341
Period size: 109 Copynumber: 1.9 Consensus size: 109
133917 AAGCTGTATA
* * *
133927 AAGGGAGACAAACTTTGTTTTAAGGGAAACAGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAA
1 AAGGGAGACAAAATTTGTTTCAAAGGAAACAGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAA
* ** *
133992 CTGTCTCAAGAGAGACGAAATTTTTTTCAAGGGAAAAATGTCTC
66 CTGTCTCAAGAGAGACAAAATTAATTTCAAAGGAAAAATGTCTC
134036 AAGGGAGACAAAATTTGTTTCAAAGGAAATCA-TCTCAAGAGAGACGAAATTTGTTTCAAGGGAA
1 AAGGGAGACAAAATTTGTTTCAAAGGAAA-CAGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAA
134100 ACTGTCTCAAGAGAGACAAAATTAATTTCAAAGGAAA
65 ACTGTCTCAAGAGAGACAAAATTAATTTCAAAGGAAA
134137 CGATCTCAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 91 0.98
110 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (109 bp):
AAGGGAGACAAAATTTGTTTCAAAGGAAACAGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAA
CTGTCTCAAGAGAGACAAAATTAATTTCAAAGGAAAAATGTCTC
Found at i:134245 original size:99 final size:101
Alignment explanation
Indices: 133940--134313 Score: 301
Period size: 109 Copynumber: 3.6 Consensus size: 101
133930 GGAGACAAAC
* * ** * *
133940 TTTGTTTTAAGGGAAACAGTCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAATCTCTCTCAAGAGAGAC-AAACTTGTTTCAAGGGAAACAGTCTCAAGAGA
* ** * **
134005 GACGAAATTTTTTTCAAGGGAAA-AATGTCTCAAGGGAGACAAAA
65 GACAAAATTAATTTCAAAGGAAACAA--TCTCAA---AG---ATT
* * * *
134049 TTTGTTTCAAAGGAAATC-ATCTCAAGAGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTC-AAGGGAATCTCTCTCAAGAGAGAC-AAACTTGTTTCAAGGGAAACAGTCTCAAGAG
* *
134113 AGACAAAATTAATTTCAAAGGAAACGATCTCAAATATT
64 AGACAAAATTAATTTCAAAGGAAACAATCTCAAAGATT
*
134151 TTT-TTTCAAGGGAATCTCTCTCAAGGGAGAC-AACTTGTTTCAAGGGAAACAGTCTCAAGAGAG
1 TTTGTTTCAAGGGAATCTCTCTCAAGAGAGACAAACTTGTTTCAAGGGAAACAGTCTCAAGAGAG
* *
134214 ACAAAA-TATGTTTCAAGGGAAACAAAT-TCAAAGATT
66 ACAAAATTA-ATTTCAAAGGAAAC-AATCTCAAAGATT
*** * * * *
134250 TTTGTTTCGAAAAAAAACTGTCTCAAGAGAGAAAAAAACTTTGTTTCAAGGGAAACATTCTCAA
1 TTTGTTTC-AAGGGAATCTCTCTCAAGAGAG--ACAAAC-TTGTTTCAAGGGAAACAGTCTCAA
134314 AGTTTATCAA
Statistics
Matches: 225, Mismatches: 29, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
98 2 0.01
99 59 0.26
100 14 0.06
101 32 0.14
102 4 0.02
103 1 0.00
104 3 0.01
105 24 0.11
108 6 0.03
109 72 0.32
110 8 0.04
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (101 bp):
TTTGTTTCAAGGGAATCTCTCTCAAGAGAGACAAACTTGTTTCAAGGGAAACAGTCTCAAGAGAG
ACAAAATTAATTTCAAAGGAAACAATCTCAAAGATT
Found at i:134482 original size:36 final size:36
Alignment explanation
Indices: 134375--134733 Score: 154
Period size: 36 Copynumber: 9.6 Consensus size: 36
134365 TGAAATAATG
* * * * *
134375 TCTCAAGCGAGACAAAATTTGTTTTAGGAGGAAGA-TG
1 TCTCAAGTGAGATAAATTTTGTTTTA--AGGAAAACTA
* * * *
134412 TCTCAAGTGAGACAAAATTTGTTTTTTAGAGAAAACAA
1 TCTCAAGTGAGATAAATTTTG-TTTTAAG-GAAAACTA
* * *
134450 TCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATTT
1 TCTCAAGTGAGATAAATTTTGTTTTAAGGAAAACTA
* * *
134486 TCTCCAA-TAAGACAAAATTTGTTCTT-AGGAAAACTA
1 TCT-CAAGTGAGATAAATTTTGTT-TTAAGGAAAACTA
* * * *
134522 TCTCATGTGAGATCAATTTTGTTTAAAATTTTGGAATAA-TG
1 TCTCAAGTGAGATAAATTTTGTTT-TAA----GGAA-AACTA
* * ** * *
134563 TCTCAAGCGAGATAAAATTTGTTTTGGGTGGAAGA-TG
1 TCTCAAGTGAGATAAATTTTGTTTT--AAGGAAAACTA
* * * *
134600 TCTCAAGTGAGACAAAATTTGTTTTTTTAGAGAAAACAA
1 TCTCAAGTGAGA-TAAATTT-TGTTTTAAG-GAAAACTA
* * *
134639 TCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATTG
1 TCTCAAGTGAGATAAATTTTGTTTTAAGGAAAACTA
* * * * *
134675 TTTCCAGCGAGACAAAATTTGTTATT-AGGAAAACTA
1 TCTCAAGTGAGATAAATTTTGTT-TTAAGGAAAACTA
* * *
134711 TATCATGTGAGATCAATTTTGTT
1 TCTCAAGTGAGATAAATTTTGTT
134734 CTAAATATTT
Statistics
Matches: 238, Mismatches: 64, Indels: 41
0.69 0.19 0.12
Matches are distributed among these distances:
35 3 0.01
36 91 0.38
37 60 0.25
38 40 0.17
39 17 0.07
41 25 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (36 bp):
TCTCAAGTGAGATAAATTTTGTTTTAAGGAAAACTA
Found at i:134697 original size:189 final size:190
Alignment explanation
Indices: 134368--134743 Score: 641
Period size: 189 Copynumber: 2.0 Consensus size: 190
134358 ATTTTAATGA
134368 AATAATGTCTCAAGCGAGACAAAATTTGTTTTAGGAGGAAGATGTCTCAAGTGAGACAAAATTTG
1 AATAATGTCTCAAGCGAGACAAAATTTGTTTTAGGAGGAAGATGTCTCAAGTGAGACAAAATTTG
*
134433 TTTTTTAGAGAAAACAATCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATTTTCTCCAATAAGA
66 TTTTTTAGAGAAAACAATCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATTTTCTCCAACAAGA
* *
134498 CAAAATTTGTTCTTAGGAAAACTATCTCATGTGAGATCAATTTTGTT-TAAA-ATTTTGG
131 CAAAATTTGTTATTAGGAAAACTATATCATGTGAGATCAATTTTGTTCTAAATATTTTGG
* * *
134556 AATAATGTCTCAAGCGAGATAAAATTTGTTTTGGGTGGAAGATGTCTCAAGTGAGACAAAATTTG
1 AATAATGTCTCAAGCGAGACAAAATTTGTTTTAGGAGGAAGATGTCTCAAGTGAGACAAAATTTG
* *
134621 TTTTTTTAGAGAAAACAATCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATTGTT-TCCAGCGA
66 -TTTTTTAGAGAAAACAATCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATT-TTCTCCAACAA
134685 GACAAAATTTGTTATTAGGAAAACTATATCATGTGAGATCAATTTTGTTCTAAATATTT
129 GACAAAATTTGTTATTAGGAAAACTATATCATGTGAGATCAATTTTGTTCTAAATATTT
134744 CAAAATTTTG
Statistics
Matches: 176, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
188 62 0.35
189 104 0.59
190 6 0.03
191 4 0.02
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (190 bp):
AATAATGTCTCAAGCGAGACAAAATTTGTTTTAGGAGGAAGATGTCTCAAGTGAGACAAAATTTG
TTTTTTAGAGAAAACAATCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATTTTCTCCAACAAGA
CAAAATTTGTTATTAGGAAAACTATATCATGTGAGATCAATTTTGTTCTAAATATTTTGG
Found at i:136938 original size:25 final size:25
Alignment explanation
Indices: 136910--136963 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
136900 ATTAACTTAG
136910 TATATAAATAATGTGAGATAAGTGA
1 TATATAAATAATGTGAGATAAGTGA
136935 TATATAAATAATGTGAGATAAGTGA
1 TATATAAATAATGTGAGATAAGTGA
136960 TATA
1 TATA
136964 AATTATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (25 bp):
TATATAAATAATGTGAGATAAGTGA
Found at i:137623 original size:23 final size:22
Alignment explanation
Indices: 137593--137677 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 22
137583 AGTTGAGGGT
*
137593 TACATAGGTCCTTCGGGATATAG
1 TACATAGGTCCTTCGGGA-ACAG
* *
137616 TACATAGGTCTTTCAGGACACAG
1 TACATAGGTCCTTCGGGA-ACAG
* **
137639 TACACAGGTTTTTCGGG-ACA-
1 TACATAGGTCCTTCGGGAACAG
137659 TACATGAGGTCCTTCGGGA
1 TACAT-AGGTCCTTCGGGA
137678 CAAATTTCAC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.08
21 13 0.26
23 33 0.66
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGAACAG
Found at i:137892 original size:17 final size:19
Alignment explanation
Indices: 137845--137893 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
137835 TGTGAAATGA
*
137845 TATACGTATTAT-ATGATG
1 TATATGTATTATGATGATG
*
137863 TATATGTTGTTATGAT-ATG
1 TATATG-TATTATGATGATG
137882 TA-ATGTATTATG
1 TATATGTATTATG
137894 GGAATCATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 10 0.38
20 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (19 bp):
TATATGTATTATGATGATG
Found at i:146534 original size:17 final size:17
Alignment explanation
Indices: 146508--146542 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
146498 TCGAGAGATC
*
146508 AAGCAGATTTTAGAGAA
1 AAGCAAATTTTAGAGAA
146525 AAGCAAATTTTAGAGAA
1 AAGCAAATTTTAGAGAA
146542 A
1 A
146543 GTGGTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (17 bp):
AAGCAAATTTTAGAGAA
Found at i:147500 original size:25 final size:25
Alignment explanation
Indices: 147466--147528 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
147456 CCTATCACCA
* *
147466 ATTTATCTCTCATTTTTTA-CTTTTT
1 ATTTTTCTCTCA-TTTGTAGCTTTTT
147491 ATTTTTCTCTTTCATTTGTAGCTTTTT
1 ATTTTTCTC--TCATTTGTAGCTTTTT
*
147518 CTTTTTCTCTC
1 ATTTTTCTCTC
147529 TCATTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 10 0.31
26 5 0.16
27 17 0.53
ACGTcount: A:0.11, C:0.19, G:0.03, T:0.67
Consensus pattern (25 bp):
ATTTTTCTCTCATTTGTAGCTTTTT
Found at i:148259 original size:34 final size:30
Alignment explanation
Indices: 148221--148289 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
148211 TCGATATAAC
*
148221 AATTTAAGGAAAAATGGTTTTTGGACTTGAACTG
1 AATTTAA--AAAAAT-GTATTTGGACTT-AACTG
*
148255 AATTT-AAAAAATGTATTTGGACTTAATTG
1 AATTTAAAAAAATGTATTTGGACTTAACTG
148284 AATTTA
1 AATTTA
148290 TTCAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 11 0.34
31 6 0.19
33 1 0.03
34 5 0.16
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (30 bp):
AATTTAAAAAAATGTATTTGGACTTAACTG
Found at i:148297 original size:31 final size:31
Alignment explanation
Indices: 148230--148289 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
148220 CAATTTAAGG
*
148230 AAAAATGGTTTTTGGACTTGAACTGAATTTA
1 AAAAATGGTATTTGGACTTGAACTGAATTTA
*
148261 AAAAAT-GTATTTGGACTT-AATTGAATTTA
1 AAAAATGGTATTTGGACTTGAACTGAATTTA
148290 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (31 bp):
AAAAATGGTATTTGGACTTGAACTGAATTTA
Found at i:157580 original size:21 final size:22
Alignment explanation
Indices: 157541--157591 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
157531 TTGAGATTGT
*
157541 TTCAAGTTTAAGTTTTTTTGAA
1 TTCAAGTCTAAGTTTTTTTGAA
157563 TTCAAGTCTAAG-TTTTTTGAA
1 TTCAAGTCTAAGTTTTTTTGAA
157584 TTCAAGTC
1 TTCAAGTC
157592 GAGTTTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (22 bp):
TTCAAGTCTAAGTTTTTTTGAA
Done.