Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005432.1 Hibiscus syriacus cultivar Beakdansim tig00012453_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: 44303
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:1967 original size:30 final size:30
Alignment explanation
Indices: 1920--1984 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1910 TAAAATTTAT
* *
1920 TTTGG-GACTAAATTGAAATTTTAACTAAA
1 TTTGGAGACCAAAGTGAAATTTTAACTAAA
* *
1949 TTTGGAGACCAAAGTGAAATTTTGATTAAA
1 TTTGGAGACCAAAGTGAAATTTTAACTAAA
1979 TTTGGA
1 TTTGGA
1985 TCCAAATTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (30 bp):
TTTGGAGACCAAAGTGAAATTTTAACTAAA
Found at i:4952 original size:21 final size:21
Alignment explanation
Indices: 4935--4978 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4925 TGGCCTCTTG
*
4935 TATGTCCCGTAGGACCTCATA
1 TATGTCCCGAAGGACCTCATA
* *
4956 TATGTCTCGAAGGACCTAATA
1 TATGTCCCGAAGGACCTCATA
4977 TA
1 TA
4979 ATCCCTCGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (21 bp):
TATGTCCCGAAGGACCTCATA
Found at i:5923 original size:21 final size:21
Alignment explanation
Indices: 5882--5942 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
5872 GTAAGATTTA
* *
5882 TCCCGAATGACCTCATGTATG
1 TCCCGAAGGACCTCATATATG
5903 TCCCGAAGGACCTCGA-ATATG
1 TCCCGAAGGACCTC-ATATATG
*
5924 TCCTGAAAGG-CCTCATATA
1 TCCCG-AAGGACCTCATATA
5943 ATCCCTCGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 28 0.82
22 5 0.15
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGACCTCATATATG
Found at i:6091 original size:14 final size:14
Alignment explanation
Indices: 6069--6105 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6059 TTCTCTTATA
*
6069 ATCATATATTTCTT
1 ATCACATATTTCTT
6083 ATCACATATTTCTT
1 ATCACATATTTCTT
6097 ATCACATAT
1 ATCACATAT
6106 CATGTATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (14 bp):
ATCACATATTTCTT
Found at i:8693 original size:20 final size:20
Alignment explanation
Indices: 8670--8756 Score: 90
Period size: 20 Copynumber: 4.4 Consensus size: 20
8660 TCTTTTTTCA
8670 TTTCTCTTTTTTTTCTCTTT
1 TTTCTCTTTTTTTTCTCTTT
* * *
8690 TTTCTCTTTTCTCTCTTTTT
1 TTTCTCTTTTTTTTCTCTTT
* *
8710 TTTTTCTTTTCTCTTTC-ATTT
1 TTTCTCTTTT-T-TTTCTCTTT
8731 TTTCTCTTTTTTTT-TCTTT
1 TTTCTCTTTTTTTTCTCTTT
8750 TTT-TCTT
1 TTTCTCTT
8757 CAAGTAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
18 4 0.07
19 9 0.16
20 27 0.49
21 12 0.22
22 3 0.05
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTCTTTTTTTTCTCTTT
Found at i:8699 original size:18 final size:17
Alignment explanation
Indices: 8654--8756 Score: 79
Period size: 18 Copynumber: 6.1 Consensus size: 17
8644 TTTATTTTTA
8654 TTTTTTTCTTTTTTCAT-
1 TTTTTTTCTTTTTTC-TC
* *
8671 TTCTCTT-TTTTTTCTC
1 TTTTTTTCTTTTTTCTC
*
8687 TTTTTTCTCTTTTCTCTC
1 TTTTTT-TCTTTTTTCTC
*
8705 TTTTTTTTTTCTTTTCTC
1 TTTTTTTCTT-TTTTCTC
** * *
8723 TTTCATT-TTTTCTCTT
1 TTTTTTTCTTTTTTCTC
8739 TTTTTTTCTTTTTT-TC
1 TTTTTTTCTTTTTTCTC
8755 TT
1 TT
8757 CAAGTAAAAT
Statistics
Matches: 66, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
15 1 0.02
16 24 0.36
17 16 0.24
18 25 0.38
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTCTTTTTTCTC
Found at i:8700 original size:32 final size:31
Alignment explanation
Indices: 8655--8756 Score: 108
Period size: 32 Copynumber: 3.4 Consensus size: 31
8645 TTATTTTTAT
*
8655 TTTTTTCTTTTTTCATTTCTCTTTTTTTTCTC
1 TTTTTTCTCTTTTCATTTCTCTTTTTTTT-TC
8687 TTTTTTCTCTTTTC---TCTCTTTTTTTTT-
1 TTTTTTCTCTTTTCATTTCTCTTTTTTTTTC
*
8714 TCTTTTCTC-TTTCATTTTTTCTCTTTTTTTTTC
1 TTTTTTCTCTTTTCA---TTTCTCTTTTTTTTTC
8747 TTTTTT-TCTT
1 TTTTTTCTCTT
8757 CAAGTAAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
26 4 0.07
27 8 0.14
28 1 0.02
29 12 0.20
32 28 0.47
33 6 0.10
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (31 bp):
TTTTTTCTCTTTTCATTTCTCTTTTTTTTTC
Found at i:8754 original size:34 final size:34
Alignment explanation
Indices: 8655--8755 Score: 98
Period size: 34 Copynumber: 2.8 Consensus size: 34
8645 TTATTTTTAT
**
8655 TTTTTTCT-TTTTTCATTTCTCTTTTTTTTCTCTTTTT
1 TTTTTTCTCTTTTT--TTT-TC-TTTTTTTCTCTTTCA
*
8692 TCTCTTTTCTCTCTTTTTTTT-TTCTTTTCTCTTTCA
1 T-T-TTTTCTCT-TTTTTTTTCTTTTTTTCTCTTTCA
8728 TTTTTTCTCTTTTTTTTTCTTTTTTTCT
1 TTTTTTCTCTTTTTTTTTCTTTTTTTCT
8756 TCAAGTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
33 8 0.15
34 16 0.29
35 1 0.02
36 13 0.24
37 1 0.02
38 2 0.04
39 9 0.16
40 1 0.02
41 4 0.07
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (34 bp):
TTTTTTCTCTTTTTTTTTCTTTTTTTCTCTTTCA
Found at i:14387 original size:15 final size:15
Alignment explanation
Indices: 14367--14399 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
14357 GCAATGAATT
14367 TTGGGCTATATTTGG
1 TTGGGCTATATTTGG
14382 TTGGGCTATATTTGG
1 TTGGGCTATATTTGG
14397 TTG
1 TTG
14400 TTCGCTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.06, G:0.33, T:0.48
Consensus pattern (15 bp):
TTGGGCTATATTTGG
Found at i:17606 original size:30 final size:30
Alignment explanation
Indices: 17565--17624 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
17555 TATTGAGTAA
* *
17565 ACATATTATTTCCATACTTTTATCACATAG
1 ACATATCATTTCCATACCTTTATCACATAG
17595 ACATATCATTTCCATACCTTTATCACATAG
1 ACATATCATTTCCATACCTTTATCACATAG
17625 CTCATATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (30 bp):
ACATATCATTTCCATACCTTTATCACATAG
Found at i:23731 original size:8 final size:8
Alignment explanation
Indices: 23718--23745 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
23708 CTACAATGTT
23718 GTGCTACA
1 GTGCTACA
23726 GTGCTACA
1 GTGCTACA
23734 GTGCTACA
1 GTGCTACA
23742 GTGC
1 GTGC
23746 ATCGATGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (8 bp):
GTGCTACA
Found at i:23764 original size:20 final size:20
Alignment explanation
Indices: 23735--23775 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
23725 AGTGCTACAG
23735 TGCTACAGTGCA-TCGATGCA
1 TGCTACAGTGCACT-GATGCA
*
23755 TGCTATAGTGCACTGATGCA
1 TGCTACAGTGCACTGATGCA
23775 T
1 T
23776 AAAAATTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
TGCTACAGTGCACTGATGCA
Found at i:24496 original size:23 final size:23
Alignment explanation
Indices: 24387--24496 Score: 125
Period size: 23 Copynumber: 4.7 Consensus size: 23
24377 TCGTATAAAT
24387 TTGCACCGAAGTGCCATGTAGAA
1 TTGCACCGAAGTGCCATGTAGAA
* *
24410 TTTGTC-CCGAAG-GACAGCGTAGAA
1 -TTG-CACCGAAGTGCCA-TGTAGAA
* *
24434 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCATGTAGAA
24457 TTGCACCGAAGTGCCATGTAGAA
1 TTGCACCGAAGTGCCATGTAGAA
* *
24480 TTGTACCGTAGTGCCAT
1 TTGCACCGAAGTGCCAT
24497 ATAATATGTC
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
22 1 0.01
23 54 0.73
24 18 0.24
25 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (23 bp):
TTGCACCGAAGTGCCATGTAGAA
Found at i:24734 original size:30 final size:30
Alignment explanation
Indices: 24700--24762 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
24690 TCATATCGCG
* * * *
24700 TAGACATATTATTTCCATACTTTTATCACA
1 TAGACACATCATTTCCACACCTTTATCACA
24730 TAGACACATCATTTCCACACCTTTATCACA
1 TAGACACATCATTTCCACACCTTTATCACA
24760 TAG
1 TAG
24763 CTCATATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
TAGACACATCATTTCCACACCTTTATCACA
Found at i:29707 original size:15 final size:16
Alignment explanation
Indices: 29687--29719 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29677 TAACATGCAT
29687 ATTAAAATGAAA-CTA
1 ATTAAAATGAAACCTA
*
29702 ATTAAAATTAAACCTA
1 ATTAAAATGAAACCTA
29718 AT
1 AT
29720 ATTTATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (16 bp):
ATTAAAATGAAACCTA
Found at i:33139 original size:14 final size:14
Alignment explanation
Indices: 33120--33148 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33110 CGATCACGCA
33120 CTACTCCTTTTAGT
1 CTACTCCTTTTAGT
33134 CTACTCCTTTTAGT
1 CTACTCCTTTTAGT
33148 C
1 C
33149 AACTGAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (14 bp):
CTACTCCTTTTAGT
Found at i:34049 original size:23 final size:23
Alignment explanation
Indices: 34023--34068 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
34013 CACCACAGCT
*
34023 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
34046 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
34069 TATAATGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:34790 original size:64 final size:62
Alignment explanation
Indices: 34655--34810 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 62
34645 TAATGAAGGT
* * * ** *
34655 ATGCATCGATGCACTACTGATGCATCGGTGCATAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAATGCATTCGATGTTCTATTATTAAAGAG
* *
34718 ATGCATCGATGCATGACTTATGCATCGATGCACTAATTGCATTCGATGTTTCTATT-TTAAA-AG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAATGCATTCGATG-TTCTATTATTAAAGAG
*
34781 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
34811 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 30 0.38
64 41 0.52
65 7 0.09
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:36909 original size:23 final size:22
Alignment explanation
Indices: 36879--36922 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
36869 AAATGGGTTG
* *
36879 AACCGACTCGTTTACTCGATCC
1 AACCGACTCGCTTACCCGATCC
36901 AACCTGACTCGCTTACCCGATC
1 AACC-GACTCGCTTACCCGATC
36923 AGACCCGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.23, C:0.39, G:0.14, T:0.25
Consensus pattern (22 bp):
AACCGACTCGCTTACCCGATCC
Done.