Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004515.1 Hibiscus syriacus cultivar Beakdansim tig00009954_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: 75026
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:7331 original size:15 final size:15
Alignment explanation
Indices: 7308--7339 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7298 TGAAATGAAT
7308 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
7323 AATGCATGTATGCAA
1 AATGAATGTATGCAA
7338 AA
1 AA
7340 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:10081 original size:9 final size:9
Alignment explanation
Indices: 10067--10091 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10057 TAAACATGCT
10067 TTTAAATAA
1 TTTAAATAA
10076 TTTAAATAA
1 TTTAAATAA
10085 TTTAAAT
1 TTTAAAT
10092 TCACATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAATAA
Found at i:12686 original size:3 final size:3
Alignment explanation
Indices: 12657--12709 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
12647 TTGGGTTTTG
* *
12657 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
12704 TAA TAA
1 TAA TAA
12710 ATTTTAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:14557 original size:41 final size:41
Alignment explanation
Indices: 14512--14604 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
14502 TTAAAATCAA
* *
14512 TTGCGGCGTTTAC-AGAAAAACGCCTCTAATGTACAACCCAT
1 TTGCGGCGTTT-CTAGAAAAACGCCACTAAAGTACAACCCAT
* * * *
14553 TTGCGGCATTTCTTGTAAAACGCCACTAAAGTCCAACCCAT
1 TTGCGGCGTTTCTAGAAAAACGCCACTAAAGTACAACCCAT
*
14594 TTGCTGCGTTT
1 TTGCGGCGTTT
14605 TTTTACCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.98
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (41 bp):
TTGCGGCGTTTCTAGAAAAACGCCACTAAAGTACAACCCAT
Found at i:15908 original size:105 final size:105
Alignment explanation
Indices: 15702--16058 Score: 626
Period size: 105 Copynumber: 3.4 Consensus size: 105
15692 CACGTTTTGA
* * * *
15702 AAAGCTATTATTTTACCTATTCGAAAGCTATTATTTTTCTCCACGAAAGTAG-AAAACACTGCTG
1 AAAGTTATTATTTTGCCTATTCGAAAGCTATTATTTTTCTCCACGAAAGCAGAAAAACATTGCTG
*
15766 CCAAACAGTAAACCAGTAAAACAATATGTATAGATATTCG
66 CCAAGCAGTAAACCAGTAAAACAATATGTATAGATATTCG
*
15806 AAAGTTATTATTTTGCCTATTCGAAAGCTATTATTTTTCTCCACGAAAACAGAAAAACATTGCTG
1 AAAGTTATTATTTTGCCTATTCGAAAGCTATTATTTTTCTCCACGAAAGCAGAAAAACATTGCTG
15871 CCAAGCAGTAAACCAGTAAAACAATATGTATAGATATTCG
66 CCAAGCAGTAAACCAGTAAAACAATATGTATAGATATTCG
* * *
15911 AAAGTTATTATTTTTCCTATTCAAAAGCTATTATTTTTCTCCACGAAAGCAGAAAAACATTGCTA
1 AAAGTTATTATTTTGCCTATTCGAAAGCTATTATTTTTCTCCACGAAAGCAGAAAAACATTGCTG
15976 CCAAGCAGTAAACCAGTAAAACAATATGTATAGATATTCG
66 CCAAGCAGTAAACCAGTAAAACAATATGTATAGATATTCG
16016 AAAGTTATTATTTTGCCTATTCGAAAGCTATTATTTTTCTCCA
1 AAAGTTATTATTTTGCCTATTCGAAAGCTATTATTTTTCTCCA
16059 TTACGTTAGC
Statistics
Matches: 240, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
104 48 0.20
105 192 0.80
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (105 bp):
AAAGTTATTATTTTGCCTATTCGAAAGCTATTATTTTTCTCCACGAAAGCAGAAAAACATTGCTG
CCAAGCAGTAAACCAGTAAAACAATATGTATAGATATTCG
Found at i:15937 original size:23 final size:23
Alignment explanation
Indices: 15905--15949 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
15895 TATGTATAGA
* *
15905 TATTCGAAAGTTATTATTTTTCC
1 TATTCAAAAGCTATTATTTTTCC
15928 TATTCAAAAGCTATTATTTTTC
1 TATTCAAAAGCTATTATTTTTC
15950 TCCACGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (23 bp):
TATTCAAAAGCTATTATTTTTCC
Found at i:16746 original size:11 final size:12
Alignment explanation
Indices: 16720--16750 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
16710 CATTTTCTCC
16720 AAAACGCCGCTA
1 AAAACGCCGCTA
16732 AAAACGCCGCTA
1 AAAACGCCGCTA
16744 AAAACGC
1 AAAACGC
16751 TTTTGCTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.32, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:19831 original size:2 final size:2
Alignment explanation
Indices: 19824--19879 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
19814 CTTAAGATTA
19824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19866 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
19880 TTAATATAGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21878 original size:11 final size:11
Alignment explanation
Indices: 21862--21887 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21852 AACAATAGCT
21862 AGGTTTCTTTA
1 AGGTTTCTTTA
21873 AGGTTTCTTTA
1 AGGTTTCTTTA
21884 AGGT
1 AGGT
21888 GCTGGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.23, T:0.50
Consensus pattern (11 bp):
AGGTTTCTTTA
Found at i:24696 original size:2 final size:2
Alignment explanation
Indices: 24689--24761 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
24679 ATCACCAAAT
24689 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
24731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24762 TAATTAACTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26885 original size:3 final size:3
Alignment explanation
Indices: 26877--26939 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
26867 TGACTGTTTT
* * * *
26877 GAA GAA GAA GAA GAA GAAA GAA GGGA GAA GAA GAA AAA GCA GAA GAG
1 GAA GAA GAA GAA GAA G-AA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
*
26924 GAG GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA G
26940 CTGCCATGTC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
3 45 0.90
4 5 0.10
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:34356 original size:15 final size:15
Alignment explanation
Indices: 34336--34370 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34326 TGTAAACAAA
* *
34336 TTCTTAGCTTAGTCT
1 TTCTTACCTGAGTCT
34351 TTCTTACCTGAGTCT
1 TTCTTACCTGAGTCT
34366 TTCTT
1 TTCTT
34371 CTCTTGATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.11, C:0.23, G:0.11, T:0.54
Consensus pattern (15 bp):
TTCTTACCTGAGTCT
Found at i:37859 original size:14 final size:14
Alignment explanation
Indices: 37840--37867 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37830 CATTCTGTCA
37840 TGCAACCACTATCC
1 TGCAACCACTATCC
37854 TGCAACCACTATCC
1 TGCAACCACTATCC
37868 ACTTGTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.43, G:0.07, T:0.21
Consensus pattern (14 bp):
TGCAACCACTATCC
Found at i:44783 original size:24 final size:23
Alignment explanation
Indices: 44756--44855 Score: 59
Period size: 24 Copynumber: 4.4 Consensus size: 23
44746 TTAATTACAT
44756 TTTTATATAAATAATTTAATATA
1 TTTTATATAAATAATTTAATATA
* *
44779 GTTTTCTAT---TATTTATAATATA
1 -TTTTATATAAATAATT-TAATATA
* * *
44801 -TATATATATAT-ATTTAATAAAA
1 TTTTATATAAATAATTTAAT-ATA
44823 TTTGTATA-AAATAATTTAATATA
1 TTT-TATATAAATAATTTAATATA
*
44846 TATATATATA
1 T-TTTATATA
44856 TCATTTTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
20 5 0.09
21 8 0.14
22 11 0.20
23 12 0.21
24 20 0.36
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTATATAAATAATTTAATATA
Found at i:46461 original size:4 final size:4
Alignment explanation
Indices: 46454--46479 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
46444 ATTTCTTTCT
46454 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
46480 ATTCTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:62844 original size:24 final size:24
Alignment explanation
Indices: 62797--62883 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
62787 TCTTATATGT
* *
62797 CACTACGGTGC-ATTTCTACATGG
1 CACTACGGTGCAAATTCTACGTGG
*
62820 CACTTCGGTGCAAATTCTACGTGG
1 CACTACGGTGCAAATTCTACGTGG
*
62844 CACTTCGGTGCAAATTCTACGTGG
1 CACTACGGTGCAAATTCTACGTGG
62868 CACTACGGTGCAAATT
1 CACTACGGTGCAAATT
62884 TATACGAGCT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 10 0.17
24 49 0.83
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (24 bp):
CACTACGGTGCAAATTCTACGTGG
Found at i:64486 original size:24 final size:24
Alignment explanation
Indices: 64459--64516 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
64449 AACGGTTAAC
*
64459 GAGTTGACTCGGTCAACTTGGTCT
1 GAGTTGACTCGGTCAACTTAGTCT
*
64483 GAGTTAACTCGGTCAACTTAGTCT
1 GAGTTGACTCGGTCAACTTAGTCT
*
64507 AAGTTGACTC
1 GAGTTGACTC
64517 AGCTTCTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (24 bp):
GAGTTGACTCGGTCAACTTAGTCT
Found at i:68730 original size:21 final size:21
Alignment explanation
Indices: 68678--68733 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
68668 AAACCCTACG
* * **
68678 GCGGTGGCACCTGATATTGTT
1 GCGGTGGCATCTGATATGGAA
* *
68699 GCAGTGCCATCTGATATGGAA
1 GCGGTGGCATCTGATATGGAA
68720 GCGGTGGCATCTGA
1 GCGGTGGCATCTGA
68734 CTCGACTAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.27
Consensus pattern (21 bp):
GCGGTGGCATCTGATATGGAA
Found at i:71505 original size:27 final size:27
Alignment explanation
Indices: 71467--71519 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
71457 GATGAAGATT
* *
71467 TGATGCTGTGGACTTTTAAGTTTAAAA
1 TGATGCTATGGACTTTCAAGTTTAAAA
*
71494 TGATGCTATGGAGTTTCAAGTTTAAA
1 TGATGCTATGGACTTTCAAGTTTAAA
71520 GTGGTGATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.40
Consensus pattern (27 bp):
TGATGCTATGGACTTTCAAGTTTAAAA
Found at i:71799 original size:2 final size:2
Alignment explanation
Indices: 71792--71816 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71782 AAAAGAGTAT
71792 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
71817 CTATTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.