Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005694.1 Hibiscus syriacus cultivar Beakdansim tig00013320_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: 67050
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1866 original size:17 final size:16
Alignment explanation
Indices: 1844--1888 Score: 67
Period size: 14 Copynumber: 2.9 Consensus size: 16
1834 ATATAATAAT
1844 AATTATTATTATTAGA
1 AATTATTATTATTAGA
1860 AA--ATTATTATTAGAA
1 AATTATTATTATTAG-A
1875 AATTATTATTATTA
1 AATTATTATTATTA
1889 ATTACTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.42
15 3 0.12
16 2 0.08
17 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
AATTATTATTATTAGA
Found at i:1867 original size:14 final size:14
Alignment explanation
Indices: 1848--1885 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
1838 AATAATAATT
1848 ATTATTATTAGAAA
1 ATTATTATTAGAAA
1862 ATTATTATTAGAAA
1 ATTATTATTAGAAA
1876 ATTATTATTA
1 ATTATTATTA
1886 TTAATTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (14 bp):
ATTATTATTAGAAA
Found at i:4853 original size:14 final size:14
Alignment explanation
Indices: 4834--4865 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4824 CAAGGGGATA
4834 TTCATGAGAAAATC
1 TTCATGAGAAAATC
4848 TTCATGAGAAAATC
1 TTCATGAGAAAATC
4862 TTCA
1 TTCA
4866 CAAGAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (14 bp):
TTCATGAGAAAATC
Found at i:5578 original size:14 final size:14
Alignment explanation
Indices: 5559--5585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5549 AAGGCACTGA
5559 AGCACATTGCATAT
1 AGCACATTGCATAT
5573 AGCACATTGCATA
1 AGCACATTGCATA
5586 CAGTTACCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (14 bp):
AGCACATTGCATAT
Found at i:6575 original size:8 final size:8
Alignment explanation
Indices: 6537--6581 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
6527 ACAAAGAGCA
6537 AAAAAAAG
1 AAAAAAAG
6545 AAACAAAA-
1 AAA-AAAAG
6553 AAAACAAAG
1 AAAA-AAAG
6562 -AAAAAAG
1 AAAAAAAG
6569 AAAAAAAG
1 AAAAAAAG
6577 AAAAA
1 AAAAA
6582 GGGACGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 5 0.15
8 24 0.73
9 4 0.12
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:9326 original size:3 final size:3
Alignment explanation
Indices: 9320--9396 Score: 93
Period size: 3 Copynumber: 25.7 Consensus size: 3
9310 GTCAAAAAAA
* * * * *
9320 TAT TAT TAAA TAT TAT TAT TAC TAT TAT TAT TAT TAT TA- GAA AAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9365 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
9397 ATTACTTATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.02
3 61 0.95
4 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:18028 original size:18 final size:18
Alignment explanation
Indices: 18005--18050 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
17995 AGGCATTTGG
* *
18005 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
18023 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
18041 TCCTCGTGCT
1 TCCTC-TGCT
18051 GTTCTGGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.00, C:0.30, G:0.24, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:18060 original size:18 final size:19
Alignment explanation
Indices: 18015--18065 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
18005 TCCTCTGGTT
*
18015 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
18033 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
18051 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
18066 TGGAGTCCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:19663 original size:23 final size:23
Alignment explanation
Indices: 19633--19692 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
19623 TTCCCCTGTG
19633 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTCAAA
* *
19656 GGGGGAATTGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTCAAA
*
19679 -GGGGTATCGATTCC
1 GGGGGAATCGATTCC
19693 ATCTGCACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (23 bp):
GGGGGAATCGATTCCCCTTCAAA
Found at i:24709 original size:55 final size:55
Alignment explanation
Indices: 24650--25130 Score: 624
Period size: 55 Copynumber: 8.8 Consensus size: 55
24640 AGCCTACTCC
**** * * *
24650 CTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATTTTATGTGTCTGCTCT
1 CTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGCTCT
*
24705 CTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
* ** *
24760 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAATGTATCTGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCT
* * *
24815 CTATTCATTCATAGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
24870 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
24925 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCT
* * *
24980 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAGACGGGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
* * *
25035 CTA-TCCATTCAGGGAGTATAGAACTCGAACAATCTTCATA-AATCGGGTCCGCTCC
1 CTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCT
*
25090 CTA-TCCGTTCAGGGAGTATAGAACT----CAATCTTCAACAAACG
1 CTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
25131 AGTTTGCTTC
Statistics
Matches: 387, Mismatches: 30, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
50 1 0.00
51 13 0.03
54 5 0.01
55 363 0.94
56 5 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
Found at i:26505 original size:23 final size:23
Alignment explanation
Indices: 26493--26618 Score: 98
Period size: 23 Copynumber: 5.3 Consensus size: 23
26483 ATTTCTCTTT
26493 TTTTTTCATTTTTCATTTTTTTC
1 TTTTTTCATTTTTCATTTTTTTC
26516 TTTTTTCATTTTTCA-TTTTTT-
1 TTTTTTCATTTTTCATTTTTTTC
* * *
26537 TTCTTCCATTTTCCATTTTTTCTTC
1 TTTTTTCATTTTTCA-TTTTT-TTC
* *
26562 TTTTTTC-CTTTTCGTTTTTTCCATC
1 TTTTTTCATTTTTCATTTTTT---TC
*
26587 ATTTTTCATTTTTC-TCATTTTTTC
1 TTTTTTCATTTTTCAT--TTTTTTC
26611 ATTTTTTC
1 -TTTTTTC
26619 TCTTTTATTT
Statistics
Matches: 81, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
21 12 0.15
22 7 0.09
23 24 0.30
24 8 0.10
25 20 0.25
26 5 0.06
27 5 0.06
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.72
Consensus pattern (23 bp):
TTTTTTCATTTTTCATTTTTTTC
Found at i:26511 original size:6 final size:7
Alignment explanation
Indices: 26494--26556 Score: 58
Period size: 7 Copynumber: 8.7 Consensus size: 7
26484 TTTCTCTTTT
26494 TTTTTCA
1 TTTTTCA
26501 TTTTTCA
1 TTTTTCA
*
26508 TTTTTTTCT
1 --TTTTTCA
26517 TTTTTCA
1 TTTTTCA
26524 TTTTTCA
1 TTTTTCA
26531 TTTTT--
1 TTTTTCA
26536 TTTCTTCCA
1 TTT-TT-CA
*
26545 TTTTCCA
1 TTTTTCA
26552 TTTTT
1 TTTTT
26557 TCTTCTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
5 3 0.07
6 2 0.04
7 31 0.67
8 1 0.02
9 9 0.20
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:26511 original size:16 final size:16
Alignment explanation
Indices: 26492--26617 Score: 69
Period size: 16 Copynumber: 7.4 Consensus size: 16
26482 TATTTCTCTT
26492 TTTTTTTCATTTTTCA
1 TTTTTTTCATTTTTCA
*
26508 TTTTTTTCTTTTTTCA
1 TTTTTTTCATTTTTCA
*
26524 TTTTTCATT-TTTTTTC-
1 TTTTT--TTCATTTTTCA
* *
26540 TTCCATTTTCCATTTTTTCT
1 TT---TTTTTCA-TTTTTCA
* *
26560 TCTTTTTTC-CTTTTCG
1 T-TTTTTTCATTTTTCA
26576 TTTTTTCCATCATTTTTCA
1 TTTTTT---TCATTTTTCA
*
26595 TTTTTCTCATTTTTTCA
1 TTTTTTTCA-TTTTTCA
26612 TTTTTT
1 TTTTTT
26618 CTCTTTTATT
Statistics
Matches: 86, Mismatches: 10, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
15 5 0.06
16 31 0.36
17 20 0.23
18 9 0.10
19 19 0.22
20 1 0.01
21 1 0.01
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.73
Consensus pattern (16 bp):
TTTTTTTCATTTTTCA
Found at i:26538 original size:43 final size:42
Alignment explanation
Indices: 26502--26616 Score: 115
Period size: 45 Copynumber: 2.6 Consensus size: 42
26492 TTTTTTTCAT
*
26502 TTTTCATTTTTTTCTTTTTTCATTTTTCATTTTTTTTCTTCCAT
1 TTTTCATTTTTTTCTTTTTTCATTTTTCGTTTTTTTT-TT-CAT
* * ***
26546 TTTCCATTTTTTCTTCTTTTTTC-CTTTTCGTTTTTTCCATCAT
1 TTTTCA-TTTTT-TTCTTTTTTCATTTTTCGTTTTTTTTTTCAT
*
26589 TTTTCATTTTTCTCATTTTTTCATTTTT
1 TTTTCATTTTTTTC-TTTTTTCATTTTT
26617 TCTCTTTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.03
42 12 0.21
43 12 0.21
44 6 0.10
45 16 0.28
46 10 0.17
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.72
Consensus pattern (42 bp):
TTTTCATTTTTTTCTTTTTTCATTTTTCGTTTTTTTTTTCAT
Found at i:26567 original size:19 final size:18
Alignment explanation
Indices: 26533--26573 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
26523 ATTTTTCATT
26533 TTTTTTCTTCCATTTTCC
1 TTTTTTCTTCCATTTTCC
**
26551 ATTTTTTCTTCTTTTTTCC
1 -TTTTTTCTTCCATTTTCC
26570 TTTT
1 TTTT
26574 CGTTTTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTCTTCCATTTTCC
Found at i:26595 original size:7 final size:8
Alignment explanation
Indices: 26588--26618 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
26578 TTTTCCATCA
26588 TTTTTCAT
1 TTTTTCAT
26596 TTTTCTCAT
1 TTTT-TCAT
26605 TTTTTCAT
1 TTTTTCAT
26613 TTTTTC
1 TTTTTC
26619 TCTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:26618 original size:44 final size:43
Alignment explanation
Indices: 26498--26616 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 43
26488 TCTTTTTTTT
* * * *
26498 TCATTTTTCATTTTTTTCTTTTTTCATTTTTCATTTTTTTTCT
1 TCATTTTTCATTTTTCTCTTTTTTCATTTTTCAGTTTTTTCCA
* *
26541 TCCATTTTCCATTTTTTCTTCTTTTTTC-CTTTTC-GTTTTTTCCA
1 T-CATTTTTCA-TTTTTC-TCTTTTTTCATTTTTCAGTTTTTTCCA
26585 TCATTTTTCATTTTTCTCATTTTTTCATTTTT
1 TCATTTTTCATTTTTCTC-TTTTTTCATTTTT
26617 TCTCTTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 2 0.03
42 13 0.21
43 13 0.21
44 16 0.25
45 10 0.16
46 9 0.14
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.71
Consensus pattern (43 bp):
TCATTTTTCATTTTTCTCTTTTTTCATTTTTCAGTTTTTTCCA
Found at i:36398 original size:45 final size:45
Alignment explanation
Indices: 36277--36427 Score: 221
Period size: 45 Copynumber: 3.3 Consensus size: 45
36267 CCATGCTTTG
* *
36277 TTATTCACAAAAATAAATCCTAACCGCATGATATATAATTCGCATAC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATAC
36324 TTATTCAAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
1 TTATTC-AAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
* *
36370 TTATTCAAAAAATAAACCTAACCACATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
* *
36415 TTGTTCGAAAAAT
1 TTATTCAAAAAAT
36428 GAAAATAAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
45 48 0.49
46 33 0.34
47 15 0.15
48 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
Found at i:52849 original size:225 final size:225
Alignment explanation
Indices: 52458--52907 Score: 882
Period size: 225 Copynumber: 2.0 Consensus size: 225
52448 GTGTGACAAA
52458 AATGTGCCTTTAAAACTTAAGGGAAAATTTTATAGAATGACAATAAGACCAGTGCTGCTGTATGG
1 AATGTGCCTTTAAAACTTAAGGGAAAATTTTATAGAATGACAATAAGACCAGTGCTGCTGTATGG
52523 ATCAGAATGTTGGGCAATCAAGAAGGATCACGTAAGGAGGATGGAGGCCGCATAAATGAGAATAC
66 ATCAGAATGTTGGGCAATCAAGAAGGATCACGTAAGGAGGATGGAGGCCGCATAAATGAGAATAC
52588 TTCGATGGACATGTGGTAGGACTCTGTGGGACATGACACCAAACTCTGCTATTAGGATGTCCTTA
131 TTCGATGGACATGTGGTAGGACTCTGTGGGACATGACACCAAACTCTGCTATTAGGATGTCCTTA
52653 GGGGTGGTGTCTGTATCCGAAAAATTAAGG
196 GGGGTGGTGTCTGTATCCGAAAAATTAAGG
*
52683 AATGTGCCTTTAAAACTTAAGGGAAAATTTTATAGAATGATAATAAGACCAGTGCTGCTGTATGG
1 AATGTGCCTTTAAAACTTAAGGGAAAATTTTATAGAATGACAATAAGACCAGTGCTGCTGTATGG
*
52748 ATCAGAATGTTGGGCAATCAAGAAGGATCATGTAAGGAGGATGGAGGCCGCATAAATGAGAATAC
66 ATCAGAATGTTGGGCAATCAAGAAGGATCACGTAAGGAGGATGGAGGCCGCATAAATGAGAATAC
52813 TTCGATGGACATGTGGTAGGACTCTGTGGGACATGACACCAAACTCTGCTATTAGGATGTCCTTA
131 TTCGATGGACATGTGGTAGGACTCTGTGGGACATGACACCAAACTCTGCTATTAGGATGTCCTTA
52878 GGGGTGGTGTCTGTATCCGAAAAATTAAGG
196 GGGGTGGTGTCTGTATCCGAAAAATTAAGG
52908 GAGGGAAGAC
Statistics
Matches: 223, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
225 223 1.00
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (225 bp):
AATGTGCCTTTAAAACTTAAGGGAAAATTTTATAGAATGACAATAAGACCAGTGCTGCTGTATGG
ATCAGAATGTTGGGCAATCAAGAAGGATCACGTAAGGAGGATGGAGGCCGCATAAATGAGAATAC
TTCGATGGACATGTGGTAGGACTCTGTGGGACATGACACCAAACTCTGCTATTAGGATGTCCTTA
GGGGTGGTGTCTGTATCCGAAAAATTAAGG
Done.