Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008737.1 Hibiscus syriacus cultivar Beakdansim tig00111812_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: 2791265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2773311 original size:2 final size:2
Alignment explanation
Indices: 2773306--2773356 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2773296 TCTCTCTCTC
2773306 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
2773348 TA TA TA TA T
1 TA TA TA TA T
2773357 CAAACATTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2774268 original size:59 final size:59
Alignment explanation
Indices: 2774183--2774309 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
2774173 ATTAATTTTA
* * * * *
2774183 CATCTTAACATTAAAAATATATTTTATTTTTATATTAACTTATTAAATATATTTTATTCT
1 CATCTTAACACTAAAAATATAGTTTATTCTTATATTAACTTA-AAAATATATTTTATACT
* *
2774243 CTTCTTAAC-CTAAAAATATAGTTTATTCTTATTTTAACTTAAAAATATATTTTATACT
1 CATCTTAACACTAAAAATATAGTTTATTCTTATATTAACTTAAAAATATATTTTATACT
2774301 CATCTTAAC
1 CATCTTAAC
2774310 TTATTACAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
58 23 0.39
59 28 0.47
60 8 0.14
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.50
Consensus pattern (59 bp):
CATCTTAACACTAAAAATATAGTTTATTCTTATATTAACTTAAAAATATATTTTATACT
Found at i:2774310 original size:29 final size:29
Alignment explanation
Indices: 2774183--2774312 Score: 152
Period size: 29 Copynumber: 4.4 Consensus size: 29
2774173 ATTAATTTTA
*
2774183 CATCTTAACATTAAAAATATATTTTATTTT
1 CATCTTAAC-TTAAAAATATATTTTATTCT
* * *
2774213 TATATTAACTTATTAAATATATTTTATTCT
1 CATCTTAACTTA-AAAATATATTTTATTCT
* * *
2774243 CTTCTTAACCTAAAAATATAGTTTATTCT
1 CATCTTAACTTAAAAATATATTTTATTCT
* * *
2774272 TATTTTAACTTAAAAATATATTTTATACT
1 CATCTTAACTTAAAAATATATTTTATTCT
2774301 CATCTTAACTTA
1 CATCTTAACTTA
2774313 TTACAGAAAT
Statistics
Matches: 81, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
29 51 0.63
30 30 0.37
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.50
Consensus pattern (29 bp):
CATCTTAACTTAAAAATATATTTTATTCT
Found at i:2774415 original size:24 final size:22
Alignment explanation
Indices: 2774412--2774504 Score: 60
Period size: 24 Copynumber: 3.9 Consensus size: 22
2774402 ACATATCTTT
* *
2774412 TATTATTATCTTAACTTAAAAATA
1 TATTTTTATTTTAACTT-AAAA-A
*
2774436 TATTTTTATTTTAATTATAAAATA
1 TATTTTTATTTTAACT-TAAAA-A
* *
2774460 TATTTTTATCTTAACTAAAAAAA
1 TATTTTTATTTTAACT-TAAAAA
* *
2774483 TATATTATATTTTTATCTTAAA
1 TAT-TTTTA-TTTTAACTTAAA
2774505 TTTAAGATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.07
24 45 0.80
25 7 0.12
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTTTATTTTAACTTAAAAA
Found at i:2774443 original size:30 final size:29
Alignment explanation
Indices: 2774184--2774503 Score: 170
Period size: 30 Copynumber: 11.2 Consensus size: 29
2774174 TTAATTTTAC
*
2774184 ATCTTAACATTAAAAATATATTTTATTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTATT
* * *
2774214 ATATTAACTTATTAAATATATTTTATTCTCT
1 ATCTTAACTTA-AAAATATATTTTATTAT-T
* * *
2774245 -TCTTAACCTAAAAATATAGTTTATTCTT
1 ATCTTAACTTAAAAATATATTTTATTATT
* *
2774273 ATTTTAACTTAAAAATATATTTTA-TACTC
1 ATCTTAACTTAAAAATATATTTTATTA-TT
* * * * *
2774302 ATCTTAACTTATTACAGAAATTATATTATT
1 ATCTTAACTTA-AAAATATATTTTATTATT
* * *
2774332 AACTTGAA-TTATTAAATATATTCTATTATT
1 ATCTT-AACTTA-AAAATATATTTTATTATT
* * * ** *
2774362 ACCTTAAATTATTAAATA-A-TAAATT-CT
1 ATCTTAACTTA-AAAATATATTTTATTATT
* *
2774389 ATTTTAACTTAAAACATATCTTTTATTATT
1 ATCTTAACTTAAAA-ATATATTTTATTATT
2774419 ATCTTAACTTAAAAATATA-TTT-TTA-T
1 ATCTTAACTTAAAAATATATTTTATTATT
2774445 -T-TTAA-TTATAAAATATA---T-TT-TT
1 ATCTTAACTTA-AAAATATATTTTATTATT
* * *
2774467 ATCTTAACTAAAAAAATATATTATATTTTT
1 ATCTTAACT-TAAAAATATATTTTATTATT
2774497 ATCTTAA
1 ATCTTAA
2774504 ATTTAAGATA
Statistics
Matches: 228, Mismatches: 39, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
22 4 0.02
23 4 0.02
24 16 0.07
25 10 0.04
26 4 0.02
27 15 0.07
28 10 0.04
29 62 0.27
30 98 0.43
31 5 0.02
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.50
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTATT
Found at i:2774457 original size:25 final size:25
Alignment explanation
Indices: 2774412--2774488 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 25
2774402 ACATATCTTT
*
2774412 TATTATTATCTTAACT-TAAAAATA
1 TATTTTTATCTTAACTATAAAAATA
* *
2774436 TATTTTTATTTTAATTAT-AAAATA
1 TATTTTTATCTTAACTATAAAAATA
*
2774460 TATTTTTATCTTAACTAAAAAAATA
1 TATTTTTATCTTAACTATAAAAATA
2774485 TATT
1 TATT
2774489 ATATTTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 34 0.76
25 11 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTTTTATCTTAACTATAAAAATA
Found at i:2774707 original size:18 final size:19
Alignment explanation
Indices: 2774671--2774723 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
2774661 AGATAAAAAA
2774671 AAAATTAATGTTAAGATGT
1 AAAATTAATGTTAAGATGT
* *
2774690 AAAATTAGT-TTAATATGT
1 AAAATTAATGTTAAGATGT
* *
2774708 -GAATTTATGTTAAGAT
1 AAAATTAATGTTAAGAT
2774724 ATATAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (19 bp):
AAAATTAATGTTAAGATGT
Found at i:2775005 original size:31 final size:31
Alignment explanation
Indices: 2774967--2775034 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
2774957 AAGGGGAATG
2774967 GTCCCTAACATTATCGATCCATTTGATTTTA
1 GTCCCTAACATTATCGATCCATTTGATTTTA
*
2774998 GTCCCTAATATTATCGATCCATTTGATTTTA
1 GTCCCTAACATTATCGATCCATTTGATTTTA
2775029 GTCCCT
1 GTCCCT
2775035 CGACTTAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (31 bp):
GTCCCTAACATTATCGATCCATTTGATTTTA
Found at i:2775233 original size:16 final size:16
Alignment explanation
Indices: 2775212--2775246 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2775202 TAGTTTACCC
* *
2775212 AAAAATATATTAAATT
1 AAAAATAAATTAAAAT
2775228 AAAAATAAATTAAAAT
1 AAAAATAAATTAAAAT
2775244 AAA
1 AAA
2775247 TTTAGTCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAAATTAAAAT
Found at i:2775860 original size:17 final size:16
Alignment explanation
Indices: 2775829--2775878 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 16
2775819 AAATATTTAA
2775829 TTATTTTTAAA-AATT
1 TTATTTTTAAATAATT
2775844 TTAATTTTTAAATAATT
1 TT-ATTTTTAAATAATT
2775861 TTATTTTATAAAATAATT
1 TTATTTT-T-AAATAATT
2775879 GACAAGTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.06
16 14 0.45
17 7 0.23
18 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTTTTAAATAATT
Found at i:2776920 original size:16 final size:18
Alignment explanation
Indices: 2776898--2776939 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
2776888 GTAAAATATA
*
2776898 AAATATAATCGAT-CATT
1 AAATATAATCAATACATT
*
2776915 -AATATATTCAATACATT
1 AAATATAATCAATACATT
2776932 AAATATAA
1 AAATATAA
2776940 AAATACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 10 0.50
17 4 0.20
18 6 0.30
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATATAATCAATACATT
Found at i:2780719 original size:17 final size:18
Alignment explanation
Indices: 2780680--2780718 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2780670 AATTAGAAAG
2780680 AAAATAAATAAACAAGAT
1 AAAATAAATAAACAAGAT
*
2780698 AAAATAAA-AATCAAGACT
1 AAAATAAATAAACAAGA-T
2780716 AAA
1 AAA
2780719 TTGTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAATAAATAAACAAGAT
Found at i:2782125 original size:14 final size:13
Alignment explanation
Indices: 2782108--2782157 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
2782098 AAAATAAAAT
*
2782108 AAAAATAAAGAGA
1 AAAAAAAAAGAGA
2782121 AAAAAGAAAAGAGA
1 AAAAA-AAAAGAGA
*
2782135 AAAGAGAAAAGAGA
1 AAA-AAAAAAGAGA
2782149 AAAAGAAAA
1 AAAA-AAAA
2782158 TAATAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.19
14 24 0.77
15 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAGAGA
Found at i:2782130 original size:7 final size:7
Alignment explanation
Indices: 2782114--2782157 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
2782104 AAATAAAAAT
2782114 AAAGAGA
1 AAAGAGA
*
2782121 AAAAAGA
1 AAAGAGA
2782128 AAAGAGA
1 AAAGAGA
2782135 AAAGAGA
1 AAAGAGA
2782142 AAAGAGA
1 AAAGAGA
2782149 AAA-AGA
1 AAAGAGA
2782155 AAA
1 AAA
2782158 TAATAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAGAGA
Found at i:2782196 original size:29 final size:29
Alignment explanation
Indices: 2782163--2782250 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 29
2782153 GAAAATAATA
* *
2782163 ATAATATGTA-TATATTTATTAAAAACTAT
1 ATAATATATATTATATTT-TCAAAAACTAT
2782192 ATAATATATATTATATTTTCAAAAACTAT
1 ATAATATATATTATATTTTCAAAAACTAT
2782221 ATAATATATATTATATTTTCAAAAACTAT
1 ATAATATATATTATATTTTCAAAAACTAT
2782250 A
1 A
2782251 ATATGTTTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 49 0.88
30 7 0.12
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (29 bp):
ATAATATATATTATATTTTCAAAAACTAT
Found at i:2782263 original size:49 final size:48
Alignment explanation
Indices: 2782198--2782298 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 48
2782188 CTATATAATA
* *
2782198 TATATTATATTTTCAAAAACTATATA-ATATATATTATATTTTCAAAAAC
1 TATAATATATTTTCAAAAACTATATATAT-TATA-AATATTTTCAAAAAC
* * * *
2782247 TATAATATGTTTTCAAAAATTATATATGTTATAAATGTTTTCAAAAAC
1 TATAATATATTTTCAAAAACTATATATATTATAAATATTTTCAAAAAC
2782295 TATA
1 TATA
2782299 TATTCTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 17 0.38
49 27 0.60
50 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (48 bp):
TATAATATATTTTCAAAAACTATATATATTATAAATATTTTCAAAAAC
Found at i:2782273 original size:19 final size:20
Alignment explanation
Indices: 2782236--2782276 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2782226 ATATATTATA
2782236 TTTTCAAAAACTATAATATG
1 TTTTCAAAAACTATAATATG
*
2782256 TTTTCAAAAATTAT-ATATG
1 TTTTCAAAAACTATAATATG
2782275 TT
1 TT
2782277 ATAAATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTTCAAAAACTATAATATG
Found at i:2782307 original size:28 final size:30
Alignment explanation
Indices: 2782246--2782311 Score: 95
Period size: 28 Copynumber: 2.3 Consensus size: 30
2782236 TTTTCAAAAA
*
2782246 CTATAATATGTTTTCAAAAATTATATATGT
1 CTATAATATGTTTTCAAAAACTATATATGT
2782276 -TATAA-ATGTTTTCAAAAACTATATAT-T
1 CTATAATATGTTTTCAAAAACTATATATGT
2782303 CTAT-ATATG
1 CTATAATATG
2782312 CCATATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.06
28 26 0.79
29 5 0.15
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (30 bp):
CTATAATATGTTTTCAAAAACTATATATGT
Found at i:2783094 original size:224 final size:225
Alignment explanation
Indices: 2782687--2783161 Score: 528
Period size: 224 Copynumber: 2.1 Consensus size: 225
2782677 CCGACTTTAG
* * * * * *
2782687 AAGATGTGACTGAAAGATGGCTCCTCGTCACTGAGTTAAGCCAAATTGCAATCAATTTGTGGATG
1 AAGATTTGACTGAAA-ATGGCTCCTTGTCACTGAGTTAAGCCAAAATACAATCAATTAGTGGATA
* * * * * ** *
2782752 TGTTTTTTAGATAATAATCCTCCATCATTAAGTTGAAATTTTGCCTGAAAACTTTAACTGGAAAA
65 AGTTTCTGAGATAAGAATCCTCCATCATGAAGTTGAAATCCTGCCTGAAAACTTTAACTGAAAAA
* * * ** * *
2782817 TAGCTCAACGCCACTAAGTTAAGGTAGACTGCAGTCTATTCTAGATTGGTTTTCGAACCTAATAT
130 TAGCTCAACACCACTAAGTTAAGCTAGAATGCAACCAATTCTAGATTGGTTTTCAAACCTAATAT
* *
2782882 TCTAT-ATCATGGAGTTGAGAATGACTTCAAA
195 CCT-TCATCATGGAATTGAGAATGACTTCAAA
*
2782913 AAGATTT-ACTGGAAAATGGCTCCTTGTCACTGAGTTAAGCCAAAATACAGTCAA-TAGTGGATA
1 AAGATTTGACT-GAAAATGGCTCCTTGTCACTGAGTTAAGCCAAAATACAATCAATTAGTGGATA
* * * * *
2782976 AGTTTCTGAGTTAAGAATCCTCCGTCGTGAAGTTGAGA-CCTGACTTGAAAACTTTAACT-AAAA
65 AGTTTCTGAGATAAGAATCCTCCATCATGAAGTTGAAATCCTG-CCTGAAAACTTTAACTGAAAA
** * *
2783039 AGTAGCTCCTCACCACTGAGTTAAGCTAGAATGCAACCAATTCTGGATTGGTTTTCAAACCTAAT
129 A-TAGCTCAACACCACTAAGTTAAGCTAGAATGCAACCAATTCTAGATTGGTTTTCAAACCTAAT
* * *
2783104 ATCCTTCGTCGTGGAATTGAGAATGACTTCGAA
193 ATCCTTCATCATGGAATTGAGAATGACTTCAAA
* *
2783137 TAGATTTGACTGAAAGTGGCTCCTT
1 AAGATTTGACTGAAAATGGCTCCTT
2783162 TCTGCTATGC
Statistics
Matches: 206, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
223 7 0.03
224 148 0.72
225 41 0.20
226 10 0.05
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (225 bp):
AAGATTTGACTGAAAATGGCTCCTTGTCACTGAGTTAAGCCAAAATACAATCAATTAGTGGATAA
GTTTCTGAGATAAGAATCCTCCATCATGAAGTTGAAATCCTGCCTGAAAACTTTAACTGAAAAAT
AGCTCAACACCACTAAGTTAAGCTAGAATGCAACCAATTCTAGATTGGTTTTCAAACCTAATATC
CTTCATCATGGAATTGAGAATGACTTCAAA
Found at i:2783251 original size:19 final size:19
Alignment explanation
Indices: 2783227--2783267 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2783217 TCTCCGTCAT
2783227 AAAGTTGAGAACTGGCCTG
1 AAAGTTGAGAACTGGCCTG
**
2783246 AAAGTTGAGGCCTGGCCTG
1 AAAGTTGAGAACTGGCCTG
2783265 AAA
1 AAA
2783268 ACTTTAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.20
Consensus pattern (19 bp):
AAAGTTGAGAACTGGCCTG
Done.