Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007072.1 Hibiscus syriacus cultivar Beakdansim tig00018415_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: 290543
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:244984 original size:85 final size:83
Alignment explanation
Indices: 244763--245072 Score: 489
Period size: 83 Copynumber: 3.7 Consensus size: 83
244753 TTAACTAGAA
*
244763 GATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAAC
1 GATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
* *
244828 CAATCATTGAATTTAGAA
66 CAATCATTGAATTTGGAG
244846 GATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAA
1 GATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAA
244910 CCAATCATTGAATTTGGAG
65 CCAATCATTGAATTTGGAG
* *
244929 GATGAA-GAAGACTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GATGAATG-TG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
244993 AACCAATCATTGAATTTGGAG
63 AACCAATCATTGAATTTGGAG
* * * *
245014 GATGAATGTGCTCATAACATCTTCTGAAAGTGTTCTTTAAGTTATTTGATCTGGTTTGG
1 GATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
245073 TAGGAACTAC
Statistics
Matches: 210, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
82 5 0.02
83 123 0.59
84 6 0.03
85 71 0.34
86 5 0.02
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (83 bp):
GATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
CAATCATTGAATTTGGAG
Found at i:245888 original size:24 final size:23
Alignment explanation
Indices: 245845--245889 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
245835 GTTCATAATG
*
245845 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
245868 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
245890 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:246002 original size:24 final size:23
Alignment explanation
Indices: 245959--246003 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
245949 GTTCATAATG
*
245959 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
245982 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
246004 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:246107 original size:113 final size:114
Alignment explanation
Indices: 245796--246262 Score: 755
Period size: 114 Copynumber: 4.1 Consensus size: 114
245786 TAGCAAAGAT
* *
245796 TCAAATCTATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCTATCACTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
245861 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGC
*
245910 TCAAATCTATCACTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCTATCACTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
245975 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGC
**
246023 TCAAATCTATCACTTGATGGATT-ATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCTATCACTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
246087 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTTTTCAACCTTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGC
**
246137 TCAAATCTATCACTTGATGGATT-ATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCTATCACTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * *
246201 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGC
*
246250 AT-AATTCTATCAC
1 -TCAAATCTATCAC
246263 AGAAAGAGAT
Statistics
Matches: 340, Mismatches: 10, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
112 1 0.00
113 124 0.36
114 215 0.63
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (114 bp):
TCAAATCTATCACTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGC
Found at i:246191 original size:227 final size:228
Alignment explanation
Indices: 245796--246262 Score: 762
Period size: 227 Copynumber: 2.1 Consensus size: 228
245786 TAGCAAAGAT
* *
245796 TCAAATCTATCATTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCTATCACTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
245861 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTCAAATCTATCACTTG
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTCAAATCTATCACTTG
*
245926 ATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAAT
131 ATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
* *
245991 TCATAATGAGAAGAATTTGTTCAACCTTTTGC-
196 TCATAATAAGAAGAACTTGTTCAACCTTTTGCA
**
246023 TCAAATCTATCACTTGATGGATT-ATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCTATCACTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
246087 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTTTTCAACCTTTTTGCTCAAATCTATCACTT
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTCAAATCTATCACTT
**
246152 GATGGATT-ATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
130 GATGGATTGA-CATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
246216 GTTCATAATAAGAAGAACTTGTTCAACTTTTTGCA
194 ATTCATAATAAGAAGAACTTGTTCAACCTTTTGCA
*
246251 T-AATTCTATCAC
1 TCAAATCTATCAC
246263 AGAAAGAGAT
Statistics
Matches: 223, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
226 2 0.01
227 220 0.99
228 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (228 bp):
TCAAATCTATCACTTGATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTCAAATCTATCACTTG
ATGGATTGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
TCATAATAAGAAGAACTTGTTCAACCTTTTGCA
Found at i:246584 original size:3 final size:3
Alignment explanation
Indices: 246576--246656 Score: 121
Period size: 3 Copynumber: 27.3 Consensus size: 3
246566 ATTAATTTAT
* *
246576 TTA TTA TTA TTA -TA ATA TTA TTTA TTA TTA TAA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
246620 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
246657 ATATATATAT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.06
3 65 0.90
4 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:246586 original size:18 final size:17
Alignment explanation
Indices: 246565--246655 Score: 93
Period size: 15 Copynumber: 5.3 Consensus size: 17
246555 TTTTTACCCA
246565 TATTAATTTATTTATTAT
1 TATTAA-TTATTTATTAT
246583 TATTATAATATTATTTATTAT
1 TA-T-T-A-ATTATTTATTAT
246604 TA-TAATTATATTATTAT
1 TATTAATTAT-TTATTAT
246621 TATT-ATTA-TTATTAT
1 TATTAATTATTTATTAT
246636 TATT-ATTA-TTATTAT
1 TATTAATTATTTATTAT
246651 TATTA
1 TATTA
246656 TATATATATA
Statistics
Matches: 66, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
15 26 0.39
16 5 0.08
17 14 0.21
18 4 0.06
19 1 0.02
20 1 0.02
21 14 0.21
22 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTAATTATTTATTAT
Found at i:246661 original size:2 final size:2
Alignment explanation
Indices: 246654--246687 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
246644 TTATTATTAT
246654 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
246688 ATAATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:246808 original size:16 final size:16
Alignment explanation
Indices: 246787--246829 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
246777 ATCCCTAGCC
246787 GCCTCCAGCCGCCTCT
1 GCCTCCAGCCGCCTCT
246803 GCCTCCAGCCGCCTCT
1 GCCTCCAGCCGCCTCT
246819 GCCTCCA-CCGC
1 GCCTCCAGCCGC
246830 TGCCACGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.07, C:0.58, G:0.19, T:0.16
Consensus pattern (16 bp):
GCCTCCAGCCGCCTCT
Found at i:248166 original size:24 final size:22
Alignment explanation
Indices: 248138--248182 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
248128 TATTCTGGTA
248138 TTTTAAAATTTAATAATTAAATTT
1 TTTTAAAATTTAAT--TTAAATTT
**
248162 TTTTATTATTTAATTTAAATT
1 TTTTAAAATTTAATTTAAATT
248183 AACATTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAAATTTAATTTAAATTT
Found at i:250533 original size:37 final size:37
Alignment explanation
Indices: 250483--250599 Score: 216
Period size: 37 Copynumber: 3.1 Consensus size: 37
250473 TTTTGGGTTT
250483 GAAATATTAATTTAATAATTAAATTGGTTACAATTTA
1 GAAATATTAATTTAATAATTAAATTGGTTACAATTTA
250520 GAAATATTAATTTAATAATTAAATTGGTTACAATTTA
1 GAAATATTAATTTAATAATTAAATTGGTTACAATTTA
*
250557 GAAATATTAATTTAATAATTAAATTGGTTTCAATTATA
1 GAAATATTAATTTAATAATTAAATTGGTTACAATT-TA
250595 GAAAT
1 GAAAT
250600 CAGAAGTTAA
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
37 71 0.91
38 7 0.09
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (37 bp):
GAAATATTAATTTAATAATTAAATTGGTTACAATTTA
Found at i:251941 original size:97 final size:95
Alignment explanation
Indices: 251818--252009 Score: 269
Period size: 97 Copynumber: 2.0 Consensus size: 95
251808 CATTGAACTT
* * * *
251818 TGTTTGATGTTCATATTAGTGTCTTCAATTTTGACCAGGTGTCTTGTTGTTCCATAGTTCATTTG
1 TGTTTGATGTTCATATTAGTGTCTTCAATTTTGACCAGGTGTCTTATTCTTCCATAGTCCACTTG
*
251883 TCCTTCATTCATGGATTCATCCATAGTCCATA
66 TCCTTCATTCATGGATGCATCCA-A-TCCATA
* * *
251915 TGTTTGATGTTCATCTTA-TCGTCTTCAATTTTTATCAGGTGTCTTATTCTTCCATAGTCCACTT
1 TGTTTGATGTTCATATTAGT-GTCTTCAATTTTGACCAGGTGTCTTATTCTTCCATAGTCCACTT
*
251979 GTCTTTCATTCATGGATGCATCCAATCCATA
65 GTCCTTCATTCATGGATGCATCCAATCCATA
252010 GTCCATTTGA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 6 0.07
96 2 0.02
97 77 0.91
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (95 bp):
TGTTTGATGTTCATATTAGTGTCTTCAATTTTGACCAGGTGTCTTATTCTTCCATAGTCCACTTG
TCCTTCATTCATGGATGCATCCAATCCATA
Found at i:261976 original size:29 final size:29
Alignment explanation
Indices: 261939--261997 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
261929 CCAATTTCAC
*
261939 CCCTGACTATTTGTATATACTAATCACAT
1 CCCTAACTATTTGTATATACTAATCACAT
261968 CCCTAACTATTTGTATATACTAATCACAT
1 CCCTAACTATTTGTATATACTAATCACAT
261997 C
1 C
261998 ACTTCTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
CCCTAACTATTTGTATATACTAATCACAT
Found at i:262917 original size:16 final size:16
Alignment explanation
Indices: 262898--262928 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
262888 AGATTTGATA
262898 TGATATATTCATTTGG
1 TGATATATTCATTTGG
262914 TGATATATTCATTTG
1 TGATATATTCATTTG
262929 TTTAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (16 bp):
TGATATATTCATTTGG
Found at i:266825 original size:60 final size:60
Alignment explanation
Indices: 266732--266914 Score: 262
Period size: 59 Copynumber: 3.1 Consensus size: 60
266722 GACGCAAGTC
* *
266732 CTTAAACTTTATCT-TTTTTTGTTTTAAGTCCCTAAACTATTTTTTGGTCAAAATAAGCA
1 CTTAAACTATGTCTCTTTTTTGTTTTAAGTCCCTAAACTATTTTTTGGTCAAAATAAGCA
* * * *
266791 TTTAAATTATGTCTCTTTTTTGTTTTAAGTCCCTAAACTATTTTCTGGTC-AAATAAGCC
1 CTTAAACTATGTCTCTTTTTTGTTTTAAGTCCCTAAACTATTTTTTGGTCAAAATAAGCA
* * * *
266850 CTTAAACTATGTCTCTTTTTTGTTTTAAGTCCCTACACTATTCTTTGGTCAAAACAAGTA
1 CTTAAACTATGTCTCTTTTTTGTTTTAAGTCCCTAAACTATTTTTTGGTCAAAATAAGCA
266910 CTTAA
1 CTTAA
266915 TTTTATGTGA
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
59 63 0.58
60 45 0.42
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.46
Consensus pattern (60 bp):
CTTAAACTATGTCTCTTTTTTGTTTTAAGTCCCTAAACTATTTTTTGGTCAAAATAAGCA
Found at i:283160 original size:22 final size:22
Alignment explanation
Indices: 283134--283178 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
283124 TAAATTGCCT
283134 AAAAGATCGGTCGAAAAGGCCG
1 AAAAGATCGGTCGAAAAGGCCG
283156 AAAAGATCGGTCGAAAAGGCCG
1 AAAAGATCGGTCGAAAAGGCCG
283178 A
1 A
283179 GCGAGTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.31, T:0.09
Consensus pattern (22 bp):
AAAAGATCGGTCGAAAAGGCCG
Found at i:287548 original size:180 final size:180
Alignment explanation
Indices: 287230--287573 Score: 399
Period size: 180 Copynumber: 1.9 Consensus size: 180
287220 TCACTCTTCC
* * * *
287230 ATGAAATAACTGATATTTTAGGATCTGTTGAATTAACTCCAGATGAAACCAAATCAGGGTTTTCA
1 ATGAAATAACTGACATTTTAGGAGCTGTTAAAGTAACTCCAGATGAAACCAAATCAGGGTTTTCA
* * * *
287295 ATAACTCCACAAACCACTGGCAGGGAGCTTGAATTCATGGAACAATCGTTGTCTAGAAGGCCGGG
66 ATAACCCCACAAACCAATGCCAGGGAGCTTGAATTCATGGAACAACCGTTGTCTAGAAGGCCGGG
* *
287360 TGTTTGTCAAAATGCCCAGCAGAGGAGTGAATTGGTGGAAAAGAAGCGGA
131 TGTTTGTCAAAATGCCCAGAAGAAGAGTGAATTGGTGGAAAAGAAGCGGA
* * * *
287410 ATGAAATAACTGACATTTTTGGAGCTGTTAAAGTAA-TCTCAGGTGAAATCC-CATCTGGGTTTT
1 ATGAAATAACTGACATTTTAGGAGCTGTTAAAGTAACTC-CAGATGAAA-CCAAATCAGGGTTTT
** * * * * * *
287473 CAATAACCCCAGGAACCAATGCCAGTGAGCTTGAGTTTATTGAGCAACCGTTGTC-AGGCAGGCC
64 CAATAACCCCACAAACCAATGCCAGGGAGCTTGAATTCATGGAACAACCGTTGTCTA-GAAGGCC
* * *
287537 -AGTGGTTTGTCAAAATTCCCAGAAGAAGAGTGGATTG
128 GGGT-GTTTGTCAAAATGCCCAGAAGAAGAGTGAATTG
287574 CTGGGAACAG
Statistics
Matches: 135, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
179 5 0.04
180 128 0.95
181 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (180 bp):
ATGAAATAACTGACATTTTAGGAGCTGTTAAAGTAACTCCAGATGAAACCAAATCAGGGTTTTCA
ATAACCCCACAAACCAATGCCAGGGAGCTTGAATTCATGGAACAACCGTTGTCTAGAAGGCCGGG
TGTTTGTCAAAATGCCCAGAAGAAGAGTGAATTGGTGGAAAAGAAGCGGA
Done.