Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007414.1 Hibiscus syriacus cultivar Beakdansim tig00020039_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: 60632
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:8448 original size:21 final size:19
Alignment explanation
Indices: 8423--8474 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
8413 ATTGGAGTGC
8423 AAAAAGAAGAGAAAAATCAGA
1 AAAAAGAAGAGAAAAA--AGA
*
8444 AAAAAGAAGA-AGAAAAGA
1 AAAAAGAAGAGAAAAAAGA
*
8462 AAAAAAAAGAGAA
1 AAAAAGAAGAGAA
8475 GTTCAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.44
19 1 0.04
20 4 0.15
21 10 0.37
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAGAAAAAAGA
Found at i:14162 original size:23 final size:23
Alignment explanation
Indices: 14134--14190 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
14124 AAAATCAGCA
14134 AAGAAAATAAAAGCACTCAAAAG
1 AAGAAAATAAAAGCACTCAAAAG
* * *
14157 AAGAAATTGAAAGCACTCGAAAG
1 AAGAAAATAAAAGCACTCAAAAG
14180 AAGAAAATAAA
1 AAGAAAATAAA
14191 GAAAGAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.11
Consensus pattern (23 bp):
AAGAAAATAAAAGCACTCAAAAG
Found at i:23739 original size:90 final size:91
Alignment explanation
Indices: 23596--23766 Score: 272
Period size: 90 Copynumber: 1.9 Consensus size: 91
23586 CATGTGCCTT
* *
23596 GCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGTTCTCT
1 GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGCTCTCT
23661 CCCTATTCGGCCAAGCCATGTGTTTA
66 CCCTATTCGGCCAAGCCATGTGTTTA
* * * * *
23687 GCATATGAACAG-CCCCATGTGCCTTGTATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCTCT
1 GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGCTCTCT
23751 CCCTATTCGGCCAAGC
66 CCCTATTCGGCCAAGC
23767 ATCATTTCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 62 0.85
91 11 0.15
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (91 bp):
GCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAAGCGCCAAGATGAAGAGCTCTCT
CCCTATTCGGCCAAGCCATGTGTTTA
Found at i:28334 original size:6 final size:6
Alignment explanation
Indices: 28323--28361 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
28313 GATGTAGGAG
28323 TCTTTT TCTTTT CTCTTTT TCTTTT TCTTCTT TCTTTT T
1 TCTTTT TCTTTT -TCTTTT TCTTTT TCTT-TT TCTTTT T
28362 GTTGCATCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 19 0.61
7 12 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:28341 original size:13 final size:12
Alignment explanation
Indices: 28323--28361 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 12
28313 GATGTAGGAG
28323 TCTTTTTCTTTT
1 TCTTTTTCTTTT
28335 CTCTTTTTCTTTT
1 -TCTTTTTCTTTT
28348 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
28361 T
1 T
28362 GTTGCATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:28347 original size:19 final size:19
Alignment explanation
Indices: 28323--28361 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28313 GATGTAGGAG
28323 TCTTTTTCTT-TTCTCTTTT
1 TCTTTTTCTTCTT-TCTTTT
28342 TCTTTTTCTTCTTTCTTTT
1 TCTTTTTCTTCTTTCTTTT
28361 T
1 T
28362 GTTGCATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTTTTTCTTCTTTCTTTT
Found at i:28564 original size:13 final size:14
Alignment explanation
Indices: 28546--28590 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 14
28536 TTAAATGTAG
28546 AAGAAATG-AATGA
1 AAGAAATGAAATGA
28559 AAGAAATGAAATGAA
1 AAGAAATGAAATG-A
28574 AATGAAAATGAAATGA
1 AA-G-AAATGAAATGA
28590 A
1 A
28591 GGATTAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 3 0.11
16 3 0.11
17 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (14 bp):
AAGAAATGAAATGA
Found at i:28571 original size:5 final size:5
Alignment explanation
Indices: 28548--28590 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
28538 AAATGTAGAA
28548 GAAAT G-AAT GAAA- GAAAT GAAAT GAAAAT GAAAAT GAAAT GAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT G-AAAT G-AAAT GAAAT GAA
28591 GGATTAGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 8 0.23
5 16 0.46
6 11 0.31
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (5 bp):
GAAAT
Found at i:28578 original size:11 final size:10
Alignment explanation
Indices: 28548--28590 Score: 54
Period size: 9 Copynumber: 4.3 Consensus size: 10
28538 AAATGTAGAA
28548 GAAATG-AAT
1 GAAATGAAAT
28557 GAAA-GAAAT
1 GAAATGAAAT
28566 GAAATGAAAAT
1 GAAATG-AAAT
28577 GAAAATGAAAT
1 G-AAATGAAAT
28588 GAA
1 GAA
28591 GGATTAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 11 0.37
10 3 0.10
11 10 0.33
12 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (10 bp):
GAAATGAAAT
Found at i:42170 original size:22 final size:22
Alignment explanation
Indices: 42138--42179 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42128 TCCATTTCAA
42138 CATCAACACCATCAACATCCTC
1 CATCAACACCATCAACATCCTC
* *
42160 CATCAAGACCATCATCATCC
1 CATCAACACCATCAACATCC
42180 ACTTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (22 bp):
CATCAACACCATCAACATCCTC
Found at i:47911 original size:35 final size:35
Alignment explanation
Indices: 47828--47939 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
47818 TACTATATGT
*
47828 TCATCA-ACATCTTCCACCACCATTTTCACGCCTATA
1 TCATCACA-ATCTTCCATCACCA-TTTCACGCCTATA
* * * *
47864 TAATCACTATCTTCCATCACCATTGCATGCCTATA
1 TCATCACAATCTTCCATCACCATTTCACGCCTATA
* * * *
47899 TCATCGCAATCTTCTATCACCGTTTCACACCTATA
1 TCATCACAATCTTCCATCACCATTTCACGCCTATA
47934 TCATCA
1 TCATCA
47940 TCATTCCCTT
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
35 43 0.70
36 18 0.30
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.33
Consensus pattern (35 bp):
TCATCACAATCTTCCATCACCATTTCACGCCTATA
Found at i:49255 original size:22 final size:22
Alignment explanation
Indices: 49230--49271 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
49220 CAATTTATTT
49230 ATCTT-TTATTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
49252 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
49272 CCAACACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:49606 original size:11 final size:10
Alignment explanation
Indices: 49590--49643 Score: 58
Period size: 9 Copynumber: 5.5 Consensus size: 10
49580 CTTTTTTTTC
*
49590 AAAAAATAC-
1 AAAAAAAACA
49599 AAAAAAAACA
1 AAAAAAAACA
**
49609 CAAAAAAGGCA
1 -AAAAAAAACA
49620 AAAAAAAA-A
1 AAAAAAAACA
49629 AAAAAAAACA
1 AAAAAAAACA
49639 AAAAA
1 AAAAA
49644 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
9 17 0.46
10 12 0.32
11 8 0.22
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:49659 original size:28 final size:28
Alignment explanation
Indices: 49589--49650 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
49579 GCTTTTTTTT
* *
49589 CAAAAAATACAAAAAAAACACAAAAAAGG
1 CAAAAAA-ACAAAAAAAAAACAAAAAAGC
*
49618 CAAAAAAAAAAAAAAAAAACAAAAAAGC
1 CAAAAAAACAAAAAAAAAACAAAAAAGC
49646 CAAAA
1 CAAAA
49651 TTTCAAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.81, C:0.13, G:0.05, T:0.02
Consensus pattern (28 bp):
CAAAAAAACAAAAAAAAAACAAAAAAGC
Found at i:53714 original size:403 final size:403
Alignment explanation
Indices: 52895--54005 Score: 2079
Period size: 403 Copynumber: 2.8 Consensus size: 403
52885 CAAAATACAT
* *
52895 GCTTCTTTGGACAAATGTTTATACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAACA
1 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
52960 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
66 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
*
53025 TTCAGATTCGAGGTCGAATCTTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
131 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
* *
53090 CAAA-G--GAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAAGATCAGA
196 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
* * *
53152 ACAGAAGAAGACTTACGACGACTTTTTAAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
261 ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
* *
53217 GAAGATACGACCTTCTGTCTCTTATCTTTCTAACGGTTCTTGAATCGCATCAATCTGATATCAGG
326 GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
53282 AACTCAAGATATG
391 AACTCAAGATATG
53295 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
1 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
53360 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
66 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
53425 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
131 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
53490 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
196 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
* *
53555 ACAGAAGCAGACTGACAACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
261 ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
53620 GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
326 GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
53685 AACTCAAGATATG
391 AACTCAAGATATG
53698 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAG-A
1 GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
53762 TATCTATTCGGTAAGTAT-ATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
66 TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
53826 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
131 TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
53891 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
196 CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
53956 ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTA
261 ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTA
54006 CTGAAGACAT
Statistics
Matches: 695, Mismatches: 13, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
400 196 0.28
401 225 0.32
402 19 0.03
403 255 0.37
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (403 bp):
GCTTCTTTGGACAAATGTTTCTACTCGAACCTATTAGAAGAACAAAGTCTCGAAGATTCAAAGCA
TATCTATTCGGTAAGTATAATGTGAATGAATCATTAAACGATTCTAATGTTGCTCCCTTTAATGT
TTCAGATTCGAGGTCGAATATTTTTGAAGAAAGGGAGGATGATACATGCATCACAAGGCTCACAT
CAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACTCGTCCAAGCATTGGAAAAGAATATCATA
ACAGAAGCAGACTAACGACGACTTTTTGAATGGGATCCTGATCTTATTTAGTCAAGATGTCTTCT
GAAGATACGACCTTCTGTCTCTTATCTTTCCAACGGTTCTTGAATCGCATCAATCCGATATCAGG
AACTCAAGATATG
Found at i:54651 original size:11 final size:11
Alignment explanation
Indices: 54637--54677 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
54627 TTGCAATTCA
54637 TTTATCTT-TT
1 TTTATCTTATT
54647 CTTTATCTTATT
1 -TTTATCTTATT
*
54659 TTAATCTTATT
1 TTTATCTTATT
54670 TTTATCTT
1 TTTATCTT
54678 GTTTCCAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 25 0.93
12 2 0.07
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:58319 original size:24 final size:25
Alignment explanation
Indices: 58292--58338 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
58282 TGATGTAATG
*
58292 TATG-TATATATATATG-AATATATC
1 TATGTTATA-ATAAATGAAATATATC
58316 TATGTTATAATAAATGAAATATA
1 TATGTTATAATAAATGAAATATA
58339 AATCATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (25 bp):
TATGTTATAATAAATGAAATATATC
Done.