Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003443.1 Hibiscus syriacus cultivar Beakdansim tig00007260_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: 55135
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3435 original size:35 final size:36
Alignment explanation
Indices: 3379--3446 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
3369 ATACAATCTG
*
3379 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTAAATCATCACCATAT
*
3415 TCCATCACCA-TATCACGCCTAAATTATCACCA
1 TCCATCACCATTATCACGCCTAAATCATCACCA
3447 ACTTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.32, C:0.37, G:0.03, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTAAATCATCACCATAT
Found at i:7803 original size:22 final size:23
Alignment explanation
Indices: 7769--7821 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
7759 ACAATCTATC
* *
7769 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACACCTAAAT
7792 CATCACCA-TATCACACCTAAAT
1 CATCACCATTATCACACCTAAAT
*
7814 TATCACCA
1 CATCACCA
7822 ACTTCTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (23 bp):
CATCACCATTATCACACCTAAAT
Found at i:9506 original size:13 final size:13
Alignment explanation
Indices: 9488--9513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9478 GTTAAGGATT
9488 GATGGTGATGGAA
1 GATGGTGATGGAA
9501 GATGGTGATGGAA
1 GATGGTGATGGAA
9514 ATAGTATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (13 bp):
GATGGTGATGGAA
Found at i:9866 original size:20 final size:19
Alignment explanation
Indices: 9841--9883 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
9831 GAAACCCCTT
9841 TGAAAACACA-AGATTTGTAA
1 TGAAAACACATA-ATTT-TAA
*
9861 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
9880 TGAA
1 TGAA
9884 GATAAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 13 0.62
21 1 0.05
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:14537 original size:23 final size:22
Alignment explanation
Indices: 14502--14557 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
14492 TGAGATACAA
* * *
14502 CAACAACACCATCTCCATTTCAT
1 CAACACCATCATCTCCA-TCCAT
*
14525 CAACACCATCATCTTCATCCAT
1 CAACACCATCATCTCCATCCAT
*
14547 CAAAACCATCA
1 CAACACCATCA
14558 ATTCCGCAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.23
Consensus pattern (22 bp):
CAACACCATCATCTCCATCCAT
Found at i:14921 original size:22 final size:22
Alignment explanation
Indices: 14896--14937 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
14886 AGAAAAGAAT
*
14896 AAATGAAAAAGAAAAAGAAAAA
1 AAATCAAAAAGAAAAAGAAAAA
*
14918 AAATCAAAAAGAGAAAGAAA
1 AAATCAAAAAGAAAAAGAAA
14938 GCCAAGGAAA
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:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (22 bp):
AAATCAAAAAGAAAAAGAAAAA
Found at i:24445 original size:21 final size:21
Alignment explanation
Indices: 24406--24449 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
24396 TCCATCTCTA
24406 TCCTTTCTTTATTTCATTTCAT
1 TCCTTTCTTTA-TTCATTTCAT
24428 TCCTTATCTTTA-TCATTTCAT
1 TCCTT-TCTTTATTCATTTCAT
24449 T
1 T
24450 AATCTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCTTTCTTTATTCATTTCAT
Found at i:24672 original size:14 final size:14
Alignment explanation
Indices: 24653--24682 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24643 AGGATTCAGC
24653 CATGAAGATACATT
1 CATGAAGATACATT
*
24667 CATGAAGATATATT
1 CATGAAGATACATT
24681 CA
1 CA
24683 GTATATCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
CATGAAGATACATT
Found at i:27631 original size:19 final size:20
Alignment explanation
Indices: 27607--27657 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
27597 CAGCCAAGAG
* *
27607 CATGTATATTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
27626 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
27646 CATGTATTTTCA
1 CATGTATTTTCA
27658 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:28509 original size:11 final size:11
Alignment explanation
Indices: 28493--28539 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
28483 GTGCAAAAAG
28493 AAAGAAAAGAA
1 AAAGAAAAGAA
**
28504 AAAGAAGAATCA
1 AAAGAA-AAGAA
28516 AAAGAAAAGAA
1 AAAGAAAAGAA
*
28527 AAAGAGAAGAA
1 AAAGAAAAGAA
28538 AA
1 AA
28540 GTTGCAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:29849 original size:24 final size:24
Alignment explanation
Indices: 29791--29856 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
29781 GACCTTTGGT
* * * *
29791 AAAGACATGTCCTTTGATATTCCA
1 AAAGATATGTCCCTTGAAATTCAA
*
29815 AAAGTTATGTCCCTTGAAATTCAA
1 AAAGATATGTCCCTTGAAATTCAA
* *
29839 AAAGATGTGTCACTTGAA
1 AAAGATATGTCCCTTGAA
29857 GTGCCAAGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (24 bp):
AAAGATATGTCCCTTGAAATTCAA
Found at i:33143 original size:21 final size:22
Alignment explanation
Indices: 33102--33144 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
33092 TGGACTAAAG
*
33102 GTAGCTAGAGGTAGTTGGAAGA
1 GTAGCTAGAGGTAGCTGGAAGA
33124 GTAGCT-GAGG-AGCTGAGAAGA
1 GTAGCTAGAGGTAGCTG-GAAGA
33145 CCAAAACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.33, C:0.07, G:0.42, T:0.19
Consensus pattern (22 bp):
GTAGCTAGAGGTAGCTGGAAGA
Found at i:33529 original size:19 final size:20
Alignment explanation
Indices: 33505--33550 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33495 TGACCAAGAG
*
33505 CATGTATCATCAT-TAAAAT
1 CATGTATCATCATCAAAAAT
**
33524 CATGTATTTTCATCAAAAAT
1 CATGTATCATCATCAAAAAT
33544 CATGTAT
1 CATGTAT
33551 TTTCAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (20 bp):
CATGTATCATCATCAAAAAT
Found at i:33931 original size:17 final size:17
Alignment explanation
Indices: 33909--33949 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
33899 ACATCATCAA
33909 CTTCCATATCATGCCAT
1 CTTCCATATCATGCCAT
33926 CTTCCATATCATGCCAT
1 CTTCCATATCATGCCAT
33943 CTTCCAT
1 CTTCCAT
33950 CTCCATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.05, T:0.37
Consensus pattern (17 bp):
CTTCCATATCATGCCAT
Found at i:34348 original size:13 final size:13
Alignment explanation
Indices: 34330--34354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34320 TTGATAAAAA
34330 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
34343 AAGAAAAAGAAA
1 AAGAAAAAGAAA
34355 AGACTCCTAC
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAG
Found at i:34425 original size:11 final size:11
Alignment explanation
Indices: 34409--34433 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34399 AAGAAGAATC
34409 AAAAGAAAAGA
1 AAAAGAAAAGA
34420 AAAAGAAAAGA
1 AAAAGAAAAGA
34431 AAA
1 AAA
34434 GTTACAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:36657 original size:19 final size:20
Alignment explanation
Indices: 36619--36657 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36609 ATCATTCACT
*
36619 TGCATACTATATGATTTTCA
1 TGCATAATATATGATTTTCA
36639 TGCATAATATATG-TTTTCA
1 TGCATAATATATGATTTTCA
36658 CATCTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (20 bp):
TGCATAATATATGATTTTCA
Found at i:37650 original size:19 final size:20
Alignment explanation
Indices: 37626--37676 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
37616 CGGCCAAGAG
* *
37626 CATGTATCTTCATTAAA-AT
1 CATGTATTTTCATCAAACAT
37645 CATGTATTTTCATCAAACAT
1 CATGTATTTTCATCAAACAT
37665 CATGTATTTTCA
1 CATGTATTTTCA
37677 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAACAT
Found at i:38052 original size:17 final size:17
Alignment explanation
Indices: 38030--38070 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
38020 ACATCACCAA
38030 CTTCCATATCACGCCAT
1 CTTCCATATCACGCCAT
*
38047 CTTCCATATCATGCCAT
1 CTTCCATATCACGCCAT
*
38064 ATTCCAT
1 CTTCCAT
38071 CTTCATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.37, G:0.05, T:0.34
Consensus pattern (17 bp):
CTTCCATATCACGCCAT
Found at i:38089 original size:24 final size:24
Alignment explanation
Indices: 38043--38089 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38033 CCATATCACG
*
38043 CCATCTTCCATATCATGCCATATT
1 CCATCTTCCATATCACGCCATATT
*
38067 CCATCTT-CATTTCACGCCTATAT
1 CCATCTTCCATATCACGCC-ATAT
38090 AATCAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.23, C:0.34, G:0.04, T:0.38
Consensus pattern (24 bp):
CCATCTTCCATATCACGCCATATT
Found at i:46988 original size:24 final size:25
Alignment explanation
Indices: 46953--47006 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
46943 ACTTGGAGCC
*
46953 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
46977 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
47001 TCAAGT
1 TCAAGT
47007 TGCATAACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Done.