Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005122.1 Hibiscus syriacus cultivar Beakdansim tig00011521_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: 57674
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:6596 original size:2 final size:2
Alignment explanation
Indices: 6589--6657 Score: 92
Period size: 2 Copynumber: 36.5 Consensus size: 2
6579 CCTACCCGAT
6589 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
* *
6631 T- TA AA TA TA -A TG T- TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6658 TAAGATTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
1 4 0.07
2 56 0.93
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6742 original size:41 final size:41
Alignment explanation
Indices: 6691--6779 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
6681 TTGTAATGTT
* * *
6691 AATATATTA-TTTAATTATTATAAATATAATAAATTATTATA
1 AATATATTATTTTAATAATT-TAAAAATAATAAATGATTATA
*
6732 AATATTTTATTTTAATAATTTAAAAATAATAAATGATTATA
1 AATATATTATTTTAATAATTTAAAAATAATAAATGATTATA
6773 AATATAT
1 AATATAT
6780 ATTATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 33 0.79
42 9 0.21
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (41 bp):
AATATATTATTTTAATAATTTAAAAATAATAAATGATTATA
Found at i:9764 original size:23 final size:23
Alignment explanation
Indices: 9738--9798 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
9728 CACCACAGCT
*
9738 CATATAATTGCACCGAAGTGTCA
1 CATATAATTGCACCGAAGTGCCA
* *
9761 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
9784 CGTAGAATTGCACCG
1 CATATAATTGCACCG
9799 TGGTGCCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:9993 original size:103 final size:103
Alignment explanation
Indices: 9826--10039 Score: 365
Period size: 103 Copynumber: 2.1 Consensus size: 103
9816 GTCCATAAGG
* * *
9826 ACCACATATCATTCCTTAAGAATCGTATACATATACTAGGGATCAAGTAGGTATCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTATCTCACCAGACT
9891 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
* * *
9929 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTATCTCACCAGACT
*
9994 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
10032 ACCACATA
1 ACCACATA
10040 GACCCTCGAC
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTATCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
Found at i:17044 original size:18 final size:18
Alignment explanation
Indices: 17021--17084 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
17011 AACATTCCCA
*
17021 GTAATCTTATTTCCGCTG
1 GTAATCTTATTTCCGCCG
*
17039 GTAATCCTA-TTCTCGCCG
1 GTAATCTTATTTC-CGCCG
* *
17057 GTAATCATATTTTCGCCG
1 GTAATCTTATTTCCGCCG
*
17075 ATAATCTTAT
1 GTAATCTTAT
17085 ATTCTGCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 3 0.08
18 33 0.87
19 2 0.05
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (18 bp):
GTAATCTTATTTCCGCCG
Found at i:21248 original size:23 final size:24
Alignment explanation
Indices: 21221--21276 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
21211 ATTTGTTTAC
21221 GTTCGTTTATGTTC-ATTGATTGT
1 GTTCGTTTATGTTCGATTGATTGT
* *
21244 GTTCGTTTATGTTCGTTTGTTTGT
1 GTTCGTTTATGTTCGATTGATTGT
*
21268 GTGCGTTTA
1 GTTCGTTTA
21277 CATTTGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.09, C:0.09, G:0.25, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGATTGATTGT
Found at i:21285 original size:24 final size:24
Alignment explanation
Indices: 21240--21328 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 24
21230 TGTTCATTGA
**
21240 TTGTGTTCGTTTATGTTCGTTTGT
1 TTGTGTTCGTTTACATTCGTTTGT
* * *
21264 TTGTGTGCGTTTACATTTGTTT-A
1 TTGTGTTCGTTTACATTCGTTTGT
* * *
21287 TTATGTTCGTTTACATCCGTTCGT
1 TTGTGTTCGTTTACATTCGTTTGT
*
21311 TTATGTTCGTTTATCATT
1 TTGTGTTCGTTTA-CATT
21329 TAACTAAATG
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
23 17 0.33
24 31 0.61
25 3 0.06
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.57
Consensus pattern (24 bp):
TTGTGTTCGTTTACATTCGTTTGT
Found at i:22650 original size:30 final size:33
Alignment explanation
Indices: 22591--22653 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
22581 AGTTGTTGAT
22591 GTTTATTTATATTTTTAAGATTGTATTTGTGTTC
1 GTTTATTTATATTTTTAAGATTG-ATTTGTGTTC
*
22625 GTTTATTTAT-TTTTTAATA-TG-TTTGTGTT
1 GTTTATTTATATTTTTAAGATTGATTTGTGTT
22654 TGATTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.29
32 2 0.07
33 8 0.29
34 10 0.36
ACGTcount: A:0.19, C:0.02, G:0.14, T:0.65
Consensus pattern (33 bp):
GTTTATTTATATTTTTAAGATTGATTTGTGTTC
Found at i:22737 original size:23 final size:24
Alignment explanation
Indices: 22707--22762 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
22697 AATATGCCCG
* *
22707 TTATATGTTATTCAACATGTTTGT
1 TTATATGTTAGTCAACATGTTTAT
* *
22731 TTA-ATGTTCGTGAACATGTTTAT
1 TTATATGTTAGTCAACATGTTTAT
22754 TTATATGTT
1 TTATATGTT
22763 TAGAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (24 bp):
TTATATGTTAGTCAACATGTTTAT
Found at i:24912 original size:17 final size:17
Alignment explanation
Indices: 24887--24926 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
24877 AAGTCCTTTA
* *
24887 AAAAATAATAAAAATTT
1 AAAATTAATAAAAAGTT
*
24904 AAAATTAATATAAAGTT
1 AAAATTAATAAAAAGTT
24921 AAAATT
1 AAAATT
24927 TCCATTTGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTAATAAAAAGTT
Found at i:43812 original size:20 final size:20
Alignment explanation
Indices: 43787--43836 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
43777 GTGCCAAAGA
43787 ACTTTAACCAGTGATTTGAC
1 ACTTTAACCAGTGATTTGAC
* *
43807 ACTTTAACCAGTGGTTTGTC
1 ACTTTAACCAGTGATTTGAC
43827 ACTTTAACCA
1 ACTTTAACCA
43837 ATAGAATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (20 bp):
ACTTTAACCAGTGATTTGAC
Found at i:54026 original size:22 final size:21
Alignment explanation
Indices: 53992--54036 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
53982 ATCAATTATC
* *
53992 TATTTTTTTTCAATTAGAAAT
1 TATTTTTTATCAATAAGAAAT
*
54013 TATTTTTCTATCAATAAGATAT
1 TATTTTT-TATCAATAAGAAAT
54035 TA
1 TA
54037 ACACGTCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (21 bp):
TATTTTTTATCAATAAGAAAT
Found at i:54994 original size:23 final size:26
Alignment explanation
Indices: 54939--54988 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
54929 CATTTAAATG
*
54939 ATAAACGAACACAAACGAACGAACATA
1 ATAAATGAACACAAACGAAC-AACATA
*
54966 ATAAATGAACATAAACGAA-AACA
1 ATAAATGAACACAAACGAACAACA
54989 AAAAATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
27 17 0.81
ACGTcount: A:0.62, C:0.18, G:0.10, T:0.10
Consensus pattern (26 bp):
ATAAATGAACACAAACGAACAACATA
Found at i:55351 original size:39 final size:39
Alignment explanation
Indices: 55322--55401 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
55312 AACGAGCCCT
* *
55322 TTGTTCGTGTTCGTTCATTTAATTAAACGAACGTAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACGTAAACC
*
55361 TTGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAAC
1 TTGTTCATGTTCGTTCATTTAAT---TAAACGAACGTAAAC
55402 GAACTTTCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 22 0.63
42 13 0.37
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (39 bp):
TTGTTCATGTTCGTTCATTTAATTAAACGAACGTAAACC
Done.