Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005448.1 Hibiscus syriacus cultivar Beakdansim tig00012482_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: 52188
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:661 original size:23 final size:23
Alignment explanation
Indices: 601--663 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
591 CATTTTATAT
* *
601 GGCACTTCGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACAC
* *
624 GGCACTACGGTGCATTTCTACCC
1 GGCACTTCGGTGCATTTCTACAC
647 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
664 ATACGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Found at i:4467 original size:24 final size:19
Alignment explanation
Indices: 4407--4456 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
4397 ATGCAATTAA
4407 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
4426 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
4445 TGCATCGATGCA
1 TGCATCGATGCA
4457 CATGTTAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:4472 original size:24 final size:22
Alignment explanation
Indices: 4405--4502 Score: 86
Period size: 19 Copynumber: 4.7 Consensus size: 22
4395 GAATGCAATT
4405 AATGCATCGATGCA---TAAGG
1 AATGCATCGATGCACTGTAAGG
*
4424 AGTGCATCGATGCA---TAAGG
1 AATGCATCGATGCACTGTAAGG
*
4443 AGTGCATCGATGCACATGTTAAGG
1 AATGCATCGATGCAC-TG-TAAGG
* *
4467 AATGCATCAATACACTGT-A-G
1 AATGCATCGATGCACTGTAAGG
4487 AATGCATCGATGCACT
1 AATGCATCGATGCACT
4503 TCAAGGGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 32 0.47
20 15 0.22
21 1 0.01
22 1 0.01
23 2 0.03
24 17 0.25
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (22 bp):
AATGCATCGATGCACTGTAAGG
Found at i:6073 original size:23 final size:23
Alignment explanation
Indices: 6039--6099 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
6029 ACATTTTATA
6039 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
6062 TGGCACTACGGTGTAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
6085 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
6100 TTTATACGAG
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:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:24288 original size:18 final size:17
Alignment explanation
Indices: 24258--24296 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
24248 TTTTGCATAT
*
24258 ATTATTATTTTTAATTA
1 ATTATTATATTTAATTA
*
24275 ATTATTAATATTTAATTT
1 ATTATT-ATATTTAATTA
24293 ATTA
1 ATTA
24297 ATCGATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATTATATTTAATTA
Found at i:24688 original size:19 final size:19
Alignment explanation
Indices: 24661--24697 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24651 GATAAAACAC
*
24661 TACCTAAAATATTATTTTT
1 TACCGAAAATATTATTTTT
24680 TACCGAAAATATTATTTT
1 TACCGAAAATATTATTTT
24698 CACTAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
TACCGAAAATATTATTTTT
Found at i:25927 original size:14 final size:14
Alignment explanation
Indices: 25908--25963 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
25898 CGTTCGTGAA
25908 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
25922 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
25935 --TT-GTTTATGTT
1 CGTTCGATTATGTT
25946 CGTTCGATTATGTT
1 CGTTCGATTATGTT
25960 CGTT
1 CGTT
25964 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:25942 original size:24 final size:24
Alignment explanation
Indices: 25915--25984 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
25905 GAACGTTCGA
*
25915 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
25939 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
25963 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
25985 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:26722 original size:10 final size:10
Alignment explanation
Indices: 26707--26781 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
26697 GGCTCTCCAA
26707 CGTTTATGTT
1 CGTTTATGTT
26717 CGTTTATGTT
1 CGTTTATGTT
26727 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
26738 ATGTTCGTGTT
1 -CGTTTATGTT
26749 CGTTTATGTT
1 CGTTTATGTT
26759 CG----TGTT
1 CGTTTATGTT
26765 CGTTTATGTT
1 CGTTTATGTT
26775 CGTTTAT
1 CGTTTAT
26782 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:26738 original size:16 final size:16
Alignment explanation
Indices: 26713--26777 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
26703 CCAACGTTTA
26713 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
26729 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
26745 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
26761 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
26777 T
1 T
26778 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:26868 original size:16 final size:16
Alignment explanation
Indices: 26847--26879 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
26837 AAAAAAATTT
26847 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
26863 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
26879 T
1 T
26880 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:43680 original size:140 final size:140
Alignment explanation
Indices: 43428--43690 Score: 386
Period size: 140 Copynumber: 1.9 Consensus size: 140
43418 TAATGAGAAG
* * * *
43428 AACTCATCAGATGAGGGAGAAGAAGTTCACATTGAGAAGAGCGTGTTCACCCTTTGTTCGATTCC
1 AACTCATCAGATAAGGGAGAAGAAGTTCAAATTGAGAAGAGCGTGTTCAACCTTTGCTCGATTCC
* * *
43493 ATCACATAATGAGGTGGATCAATATTTTCAATTGAGGATTTCATAATGAGAAGAACTCATTTGAT
66 ATCACATAAAGAGCTGGATCAATATTTTCAATTGAGGAGTTCATAATGAGAAGAACTCATTTGAT
43558 GAGGGAAAAT
131 GAGGGAAAAT
* * * *
43568 AACTCATCAGATAATGGAGAAGAAGTTCATAATT-AGAAGAGCTTGTTCAATCTTTGCTCTATTC
1 AACTCATCAGATAAGGGAGAAGAAGTTCA-AATTGAGAAGAGCGTGTTCAACCTTTGCTCGATTC
*
43632 CATCACA-AAAGAAGCTGGATCGATATTTTCAATTGAGGAGTTCATAATGAGAAGAACTC
65 CATCACATAAAG-AGCTGGATCAATATTTTCAATTGAGGAGTTCATAATGAGAAGAACTC
43691 GTCCAAACAG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
139 3 0.03
140 103 0.94
141 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (140 bp):
AACTCATCAGATAAGGGAGAAGAAGTTCAAATTGAGAAGAGCGTGTTCAACCTTTGCTCGATTCC
ATCACATAAAGAGCTGGATCAATATTTTCAATTGAGGAGTTCATAATGAGAAGAACTCATTTGAT
GAGGGAAAAT
Found at i:48099 original size:14 final size:15
Alignment explanation
Indices: 48080--48140 Score: 81
Period size: 15 Copynumber: 4.2 Consensus size: 15
48070 TAGTTTACCC
48080 CATA-TATACTTATG
1 CATATTATACTTATG
**
48094 CATA-TATACTTACA
1 CATATTATACTTATG
48108 CATATTATACTTATG
1 CATATTATACTTATG
*
48123 CGTATTATACTTATG
1 CATATTATACTTATG
48138 CAT
1 CAT
48141 GCATGTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
14 16 0.40
15 24 0.60
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (15 bp):
CATATTATACTTATG
Found at i:48116 original size:29 final size:29
Alignment explanation
Indices: 48080--48135 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
48070 TAGTTTACCC
48080 CATATATACTTATGCATA-TATACTTACA
1 CATATATACTTATGCATATTATACTTACA
*
48108 CATATTATACTTATGCGTATTATACTTA
1 CATA-TATACTTATGCATATTATACTTA
48136 TGCATGCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 4 0.16
29 13 0.52
30 8 0.32
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (29 bp):
CATATATACTTATGCATATTATACTTACA
Done.