Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005404.1 Hibiscus syriacus cultivar Beakdansim tig00012392_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: 56966
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:3423 original size:15 final size:15
Alignment explanation
Indices: 3403--3439 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3393 AGAGTAAAAA
3403 GAAATAAAGATTATT
1 GAAATAAAGATTATT
3418 GAAATAAAGATTATT
1 GAAATAAAGATTATT
*
3433 GGAATAA
1 GAAATAA
3440 CTGTTAGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (15 bp):
GAAATAAAGATTATT
Found at i:3828 original size:19 final size:20
Alignment explanation
Indices: 3786--3837 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3776 TAACTGAGGA
3786 TTCCGTTAGCTAATGAATTC
1 TTCCGTTAGCTAATGAATTC
3806 TTCCGTTAGCTAATGAA-TC
1 TTCCGTTAGCTAATGAATTC
3825 TTCCGTTAG-TAAT
1 TTCCGTTAGCTAAT
3838 TCTAAATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.12
19 11 0.34
20 17 0.53
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (20 bp):
TTCCGTTAGCTAATGAATTC
Found at i:4931 original size:20 final size:22
Alignment explanation
Indices: 4889--4933 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
4879 ATCGAAATCT
*
4889 ATTTTATTTCTGAATATTGATAA
1 ATTTTATTTCTG-ATATTCATAA
4912 ATTTTATTT-TG-TATTCATAA
1 ATTTTATTTCTGATATTCATAA
4932 AT
1 AT
4934 CATTTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
22 2 0.10
23 9 0.43
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (22 bp):
ATTTTATTTCTGATATTCATAA
Found at i:8151 original size:13 final size:13
Alignment explanation
Indices: 8133--8157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8123 TCAGCTTTTC
8133 CTTTATTTTTAAG
1 CTTTATTTTTAAG
8146 CTTTATTTTTAA
1 CTTTATTTTTAA
8158 ATATACTAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (13 bp):
CTTTATTTTTAAG
Found at i:11947 original size:22 final size:23
Alignment explanation
Indices: 11904--11960 Score: 98
Period size: 22 Copynumber: 2.5 Consensus size: 23
11894 CCATTAAATG
11904 GTATTGATACTACTATATAGAGTA
1 GTATTGATACTAC-ATATAGAGTA
11928 GTATTGATACTAC-TATAGAGTA
1 GTATTGATACTACATATAGAGTA
11950 GTATTGATACT
1 GTATTGATACT
11961 CCTTTGATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 20 0.61
24 13 0.39
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (23 bp):
GTATTGATACTACATATAGAGTA
Found at i:14900 original size:18 final size:18
Alignment explanation
Indices: 14877--14944 Score: 127
Period size: 18 Copynumber: 3.8 Consensus size: 18
14867 CTGTGCTTAT
14877 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
*
14895 TTTTCAAAATCAAAACAA
1 TTTTCAAAATCAAAACAG
14913 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
14931 TTTTCAAAATCAAA
1 TTTTCAAAATCAAA
14945 GATTGACTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.29
Consensus pattern (18 bp):
TTTTCAAAATCAAAACAG
Found at i:15399 original size:21 final size:22
Alignment explanation
Indices: 15354--15400 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
15344 TAAAATCTTT
* *
15354 TTTTATTTTTACTTTAAATCGC
1 TTTTATTATTACTTTAAATAGC
*
15376 TTTTATTATTA-TTTAAATATC
1 TTTTATTATTACTTTAAATAGC
15397 TTTT
1 TTTT
15401 TACAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATTATTACTTTAAATAGC
Found at i:15401 original size:22 final size:23
Alignment explanation
Indices: 15353--15402 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
15343 TTAAAATCTT
* *
15353 TTTTTATTTTTACTTTAAATCGC
1 TTTTTATTATTACTTTAAATAGC
*
15376 -TTTTATTATTA-TTTAAATATC
1 TTTTTATTATTACTTTAAATAGC
15397 TTTTTA
1 TTTTTA
15403 CAAAAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTTATTATTACTTTAAATAGC
Found at i:17757 original size:3 final size:3
Alignment explanation
Indices: 17743--17779 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
17733 TTAAAAAGCA
17743 CTT CTCT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
17780 TTAATTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:22592 original size:19 final size:19
Alignment explanation
Indices: 22568--22610 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
22558 TTGCAAAAAT
22568 ATTATTTCCACATTTTAAA
1 ATTATTTCCACATTTTAAA
22587 ATTATTTCCACATTTTAAA
1 ATTATTTCCACATTTTAAA
22606 ATTAT
1 ATTAT
22611 GGAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTTCCACATTTTAAA
Found at i:27045 original size:21 final size:22
Alignment explanation
Indices: 27006--27046 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
26996 TTTTATTTTA
*
27006 TTTATTTAAATTGAGAATTAGG
1 TTTATTTAAATTGACAATTAGG
*
27028 TTTATTT-ATTTGACAATTA
1 TTTATTTAAATTGACAATTA
27047 CGATGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTAGG
Found at i:31051 original size:14 final size:15
Alignment explanation
Indices: 31034--31067 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
31024 TTAAAAAACA
31034 AAAAAAT-GAAAAAG
1 AAAAAATGGAAAAAG
31048 AAAAAATGGAAAAAG
1 AAAAAATGGAAAAAG
31063 AAAAA
1 AAAAA
31068 GAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (15 bp):
AAAAAATGGAAAAAG
Found at i:31051 original size:15 final size:16
Alignment explanation
Indices: 31027--31067 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
31017 AGGAATTTTA
*
31027 AAAAACAAAAAAAT-G
1 AAAAAGAAAAAAATGG
31042 AAAAAG-AAAAAATGG
1 AAAAAGAAAAAAATGG
31057 AAAAAGAAAAA
1 AAAAAGAAAAA
31068 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 12 0.52
16 4 0.17
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAAAAATGG
Found at i:31075 original size:15 final size:15
Alignment explanation
Indices: 31027--31077 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
31017 AGGAATTTTA
* *
31027 AAAAACAAAAAAATG
1 AAAAAGAAAAAAAAG
**
31042 AAAAAGAAAAAATGG
1 AAAAAGAAAAAAAAG
*
31057 AAAAAGAAAAAGAA-
1 AAAAAGAAAAAAAAG
31071 AAAAAGA
1 AAAAAGA
31078 GAGATAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 7 0.23
15 23 0.77
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:38138 original size:54 final size:54
Alignment explanation
Indices: 38067--38181 Score: 158
Period size: 54 Copynumber: 2.1 Consensus size: 54
38057 TACCATATGA
** * * * * *
38067 GGGTATCGGTACCCTATTTCAATTATGTTTTCCCATGGTTCTAATACCATCAGG
1 GGGTATCAATACCCTATTGCAATTATGTTTTCACATGGTACCAATACAATCAGG
*
38121 GGGTATCAATACCCTATTGCAATTATGTTTTCACATGGTACCGATACAATCAGG
1 GGGTATCAATACCCTATTGCAATTATGTTTTCACATGGTACCAATACAATCAGG
38175 GGGTATC
1 GGGTATC
38182 GGTACCACAC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (54 bp):
GGGTATCAATACCCTATTGCAATTATGTTTTCACATGGTACCAATACAATCAGG
Found at i:43661 original size:18 final size:20
Alignment explanation
Indices: 43628--43669 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
43618 AATCTAGACC
43628 AAAATCTATCTTTGATTTTG
1 AAAATCTATCTTTGATTTTG
43648 AAAA-CTAT-TTTGATTTTG
1 AAAATCTATCTTTGATTTTG
43666 AAAA
1 AAAA
43670 AATAAGCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.64
19 4 0.18
20 4 0.18
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (20 bp):
AAAATCTATCTTTGATTTTG
Found at i:43670 original size:19 final size:20
Alignment explanation
Indices: 43628--43670 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
43618 AATCTAGACC
*
43628 AAAATCTATCTTTGATTTTG
1 AAAAACTATCTTTGATTTTG
43648 -AAAACTAT-TTTGATTTTG
1 AAAAACTATCTTTGATTTTG
43666 AAAAA
1 AAAAA
43671 ATAAGCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (20 bp):
AAAAACTATCTTTGATTTTG
Found at i:51572 original size:18 final size:17
Alignment explanation
Indices: 51550--51593 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
51540 GTTCTTTCTG
*
51550 TATTTTTATTATTTTCA
1 TATTTTTATTATTTTAA
* *
51567 TGATTTTCATTTTTTTAA
1 T-ATTTTTATTATTTTAA
51585 TATTTTTAT
1 TATTTTTAT
51594 GTATATTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTTATTATTTTAA
Found at i:51941 original size:23 final size:22
Alignment explanation
Indices: 51894--51942 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
51884 TTTATTAGGT
*
51894 ATTTTTTTCAAGTTAGTACTTA
1 ATTTTTTTCAAGTTAGTACTAA
*
51916 ATTTCTTTTC-AGTTGGTACCTAA
1 ATTT-TTTTCAAGTTAGTA-CTAA
51939 ATTT
1 ATTT
51943 GGCACATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (22 bp):
ATTTTTTTCAAGTTAGTACTAA
Done.