Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003796.1 Hibiscus syriacus cultivar Beakdansim tig00008120_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: 32781
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:580 original size:181 final size:182
Alignment explanation
Indices: 197--683 Score: 831
Period size: 181 Copynumber: 2.7 Consensus size: 182
187 CTAAAATTAC
*
197 CGACACTTTTTAAATGGTATCGACACA-TTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
1 CGACACTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
* * *
261 TTAGAAAGTGTCG--ATAGGTTGTAAACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
66 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
*
324 TATTACAAAATTATATATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 TATTACAAAATTATATATTACATTATAAATATGGGTTCCGATGTGTAAATGT
376 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
441 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
506 ATATTACAAAA-TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATATATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
558 CGACACTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
622 ATTAAAAAGTGTCGATATAGTTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
684 ATAGCATTGC
Statistics
Matches: 292, Mismatches: 11, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
179 6 0.02
180 20 0.07
181 162 0.55
182 47 0.16
183 57 0.20
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (182 bp):
CGACACTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATATATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:2056 original size:14 final size:14
Alignment explanation
Indices: 2037--2073 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2027 AAGGGCAACA
2037 ACAAAATTGTCGAC
1 ACAAAATTGTCGAC
2051 ACAAAATTGTCGAC
1 ACAAAATTGTCGAC
2065 ACAAAATTG
1 ACAAAATTG
2074 CATAAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (14 bp):
ACAAAATTGTCGAC
Found at i:2293 original size:9 final size:9
Alignment explanation
Indices: 2278--2355 Score: 75
Period size: 9 Copynumber: 8.7 Consensus size: 9
2268 TACTGTTTGG
2278 ATCATCATC
1 ATCATCATC
*
2287 TTCATCATC
1 ATCATCATC
2296 ATCATCATC
1 ATCATCATC
*
2305 GTCATCATC
1 ATCATCATC
* *
2314 TTCATCGTC
1 ATCATCATC
* *
2323 AGCTTCATC
1 ATCATCATC
*
2332 GTCATCATC
1 ATCATCATC
*
2341 ATCGTCATC
1 ATCATCATC
*
2350 TTCATC
1 ATCATC
2356 GTCAGCTTAT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (9 bp):
ATCATCATC
Found at i:2297 original size:6 final size:6
Alignment explanation
Indices: 2278--2355 Score: 75
Period size: 6 Copynumber: 13.0 Consensus size: 6
2268 TACTGTTTGG
* * * * *
2278 ATCATC ATCTTC ATCATC ATCATC ATCGTC ATCATC TTCATC GTCAGC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* * * *
2326 TTCATC GTCATC ATCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC
2356 GTCAGCTTAT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.37
Consensus pattern (6 bp):
ATCATC
Found at i:2331 original size:36 final size:36
Alignment explanation
Indices: 2291--2363 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
2281 ATCATCTTCA
*
2291 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
2327 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
2363 T
1 T
2364 ATCTTCTGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.37
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:2356 original size:12 final size:12
Alignment explanation
Indices: 2282--2359 Score: 93
Period size: 12 Copynumber: 6.2 Consensus size: 12
2272 GTTTGGATCA
*
2282 TCATCTTCATCA
1 TCATCTTCATCG
*
2294 TCATCATCATCG
1 TCATCTTCATCG
2306 TCATCATCTTCATCG
1 ---TCATCTTCATCG
*
2321 TCAGCTTCATCG
1 TCATCTTCATCG
*
2333 TCATCATCATCG
1 TCATCTTCATCG
2345 TCATCTTCATCG
1 TCATCTTCATCG
2357 TCA
1 TCA
2360 GCTTATCTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
12 45 0.80
15 11 0.20
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:4422 original size:193 final size:197
Alignment explanation
Indices: 3804--4744 Score: 1522
Period size: 194 Copynumber: 4.9 Consensus size: 197
3794 TTTAAATTAG
3804 TATCGACACAAACT-AAA-AGTGTCGA-ACATTATTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAC
3866 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* *
3931 GACACTTTTT-TATATGGATCG--ACTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACAAA
131 GACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGATTTCCATTCATTCTGGAACAAA
3993 AA
196 AA
**
3995 TATCGACACAAACTAAAATAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATTT
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAC
4060 TTGTACCGGTTAGATTG-AAAATTAC--ATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* * *
4122 GACACTTTTTATATATGGATCGACACTTTATGGGTGCA-CCTGTTTTTCATTCATTCTGGAACAA
131 GACACTTTTTATATATGGATCGACAC-TTATGGTTGCACCCTGATTTCCATTCATTCTGGAACAA
4186 AAA
195 AAA
4189 TATCGACACAAACTAAAATAGTGTCGACACATTATTAGACATA-TCTCTCATAAAACCGGTATA-
1 TATCGACACAAACTAAAATAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAC
4252 TTGTA-CGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
4315 GACACTTTTTATATATGGATCGACACTTATGGTTGCACCCT-ATTTCCATTCATTCTGGAACAAA
131 GACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGATTTCCATTCATTCTGGAACAAA
4379 AA
196 AA
4381 TATCGACACAAACTAAAATAGTGTCGACACATTATTTAGACATATTTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTAAAATAGTGTCGACACATTA-TTAGACATA-TTCTCTCATAAAACCGGTAT
*
4446 ACTTGTACCGGTTAGATTGAAAAA-TACATATTACATTATAC--TTGGTTTTCGATGTTTTTGGG
64 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGG
4508 ATCGACAC--TTT-TATATGGATCGACACTTATGGTTGCACCCT-ATTTTCCATTCATTCTGGAA
128 ATCGACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGA-TTTCCATTCATTCTGGAA
4569 C-AAAA
192 CAAAAA
* *
4574 -ATCGACACAAAATAAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTAAAATAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
*
4638 CTTGTACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGTTTTCGATGTTTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGTTTTTGGGA
4702 TCGACACTTTTTATATATGGATC--CACTTTATGGTTGCACCCTG
129 TCGACACTTTTTATATATGGATCGACAC-TTATGGTTGCACCCTG
4745 TTGCCATATT
Statistics
Matches: 714, Mismatches: 10, Indels: 47
0.93 0.01 0.06
Matches are distributed among these distances:
191 120 0.17
192 147 0.21
193 161 0.23
194 162 0.23
195 53 0.07
196 55 0.08
197 16 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
TATCGACACAAACTAAAATAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTATGGTTGCACCCTGATTTCCATTCATTCTGGAACAAA
AA
Found at i:4909 original size:19 final size:19
Alignment explanation
Indices: 4863--4911 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
4853 TTATATTCAC
*
4863 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
4882 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
4901 ATACAAAATTA
1 ATACAAAATTA
4912 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:6806 original size:21 final size:21
Alignment explanation
Indices: 6781--6824 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
6771 CCCCTTATGC
6781 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
6802 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
6823 CT
1 CT
6825 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:9078 original size:20 final size:20
Alignment explanation
Indices: 9046--9102 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
9036 ATCCGGTATC
*
9046 ATTT-TACCGGTTTTATCAT
1 ATTTATACCTGTTTTATCAT
9065 -TTTGATACCTGTTTTATCAT
1 ATTT-ATACCTGTTTTATCAT
* *
9085 ATTTTTACCTGTTATATC
1 ATTTATACCTGTTTTATC
9103 GTTGTGGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (20 bp):
ATTTATACCTGTTTTATCAT
Found at i:9255 original size:20 final size:20
Alignment explanation
Indices: 9228--9274 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
9218 TCCGGTAACG
9228 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
9247 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
9268 TTTTACC
1 TTTTACC
9275 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:16630 original size:17 final size:16
Alignment explanation
Indices: 16577--16626 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
16567 CATCTGTTAG
*
16577 TCTTGTTAAAAGAATA
1 TCTTGTTAAAATAATA
*
16593 TCTT-TTAACCAATGATA
1 TCTTGTTAA--AATAATA
16610 TCTTGTTAAAATAATA
1 TCTTGTTAAAATAATA
16626 T
1 T
16627 TCTTTATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.14
16 11 0.39
17 9 0.32
18 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (16 bp):
TCTTGTTAAAATAATA
Found at i:16646 original size:14 final size:14
Alignment explanation
Indices: 16623--16667 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
16613 TGTTAAAATA
*
16623 ATATTCTTTATTGT
1 ATATTTTTTATTGT
*
16637 ATATTTTTTATTTT
1 ATATTTTTTATTGT
16651 AATATTATTTTATTGT
1 -ATATT-TTTTATTGT
16667 A
1 A
16668 AAATAATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 12 0.46
15 6 0.23
16 8 0.31
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (14 bp):
ATATTTTTTATTGT
Found at i:16814 original size:244 final size:245
Alignment explanation
Indices: 16384--16864 Score: 919
Period size: 244 Copynumber: 2.0 Consensus size: 245
16374 ACTTAAATTT
16384 TTTATTGTATACTTTTTATTTTAATATTATTTTATAGTAAAATAATTAGATATGTAGAATAAATA
1 TTTATTGTATACTTTTTATTTTAATATTATTTTATAGTAAAATAATTAGATATGTAGAATAAATA
16449 AAAAGGCTTAAATGAAAAAGCAACCCTCAAACTATGCTATTTTTTTAGTTTTAAGTACCTAAACT
66 AAAAGGCTTAAATGAAAAAGCAACCCTCAAACTATGCTATTTTTTTAGTTTTAAGTACCTAAACT
16514 AATTTTTAATCAAACCAGGTACCTAAACTATTCTTCTGTCATTATTTTAAACTCATCTGTTAGTC
131 AATTTTTAATCAAACCAGGTACCTAAACTATTCTTCTGTCATTATTTTAAACTCATCTGTTAGTC
16579 TTGTTAAAAGAATATCTTTTAACCAATGATATCTTGTTAAAATAATATTC
196 TTGTTAAAAGAATATCTTTTAACCAATGATATCTTGTTAAAATAATATTC
* *
16629 TTTATTGTATATTTTTTATTTTAATATTATTTTATTGTAAAATAATTAGATATGTAGAATAAAT-
1 TTTATTGTATACTTTTTATTTTAATATTATTTTATAGTAAAATAATTAGATATGTAGAATAAATA
* *
16693 AAAAGGCTTAAATGAAAAAGCAGCCCTCAAACTATGCTATTTTTTTTGTTTTAAGTACCTAAACT
66 AAAAGGCTTAAATGAAAAAGCAACCCTCAAACTATGCTATTTTTTTAGTTTTAAGTACCTAAACT
16758 AATTTTTAATCAAACCAGGTACCTAAACTATTCTTCTGTCATTATTTTAAACTCATCTGTTAGTC
131 AATTTTTAATCAAACCAGGTACCTAAACTATTCTTCTGTCATTATTTTAAACTCATCTGTTAGTC
16823 TTGTTAAAAGAATATCTTTTAACCAATGATATCTTGTTAAAA
196 TTGTTAAAAGAATATCTTTTAACCAATGATATCTTGTTAAAA
16865 CAATTATGAA
Statistics
Matches: 232, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
244 170 0.73
245 62 0.27
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (245 bp):
TTTATTGTATACTTTTTATTTTAATATTATTTTATAGTAAAATAATTAGATATGTAGAATAAATA
AAAAGGCTTAAATGAAAAAGCAACCCTCAAACTATGCTATTTTTTTAGTTTTAAGTACCTAAACT
AATTTTTAATCAAACCAGGTACCTAAACTATTCTTCTGTCATTATTTTAAACTCATCTGTTAGTC
TTGTTAAAAGAATATCTTTTAACCAATGATATCTTGTTAAAATAATATTC
Found at i:22446 original size:12 final size:13
Alignment explanation
Indices: 22418--22458 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
22408 ATAGGCAGTA
*
22418 ATATTCATATTA-
1 ATATTCATATCAC
*
22430 TTATTCAT-TCAC
1 ATATTCATATCAC
22442 ATATTCATATCAC
1 ATATTCATATCAC
22455 ATAT
1 ATAT
22459 ACACATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.08
12 14 0.58
13 8 0.33
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTCATATCAC
Found at i:29721 original size:67 final size:66
Alignment explanation
Indices: 29664--29790 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 66
29654 TTAATTTTTC
29664 ATTAGAAAATTAGA-A-TAGTAATTTATCATTTTT-TAT-CTATTAATAATTATTAATTTTTTTA
1 ATTA-AAAATTAGATATTAGTAATTTATCATTTTTAT-TGCTATTAATAATTATTAATTTTTTTA
29725 TCT
64 TCT
* * *
29728 ATTAAAAATTATATATTAGTAATTTATTATTTTTATTGGCTATTAATAAATTAGTAATTTTTT
1 ATTAAAAATTAGATATTAGTAATTTATCATTTTTATT-GCTATTAAT-AATTATTAATTTTTT
29791 GAATGAAGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
63 8 0.15
64 5 0.09
65 18 0.33
66 1 0.02
67 8 0.15
68 14 0.26
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (66 bp):
ATTAAAAATTAGATATTAGTAATTTATCATTTTTATTGCTATTAATAATTATTAATTTTTTTATC
T
Found at i:29751 original size:40 final size:42
Alignment explanation
Indices: 29696--29780 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 42
29686 TTATCATTTT
* *
29696 TTATCTATTAATAA-TTATTAATTTTT-TTATCTATTAA-AAA
1 TTATATATTAATAATTTATT-ATTTTTATTAGCTATTAATAAA
* *
29736 TTATATATTAGTAATTTATTATTTTTATTGGCTATTAATAAA
1 TTATATATTAATAATTTATTATTTTTATTAGCTATTAATAAA
29778 TTA
1 TTA
29781 GTAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 18 0.47
41 14 0.37
42 6 0.16
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (42 bp):
TTATATATTAATAATTTATTATTTTTATTAGCTATTAATAAA
Done.