Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007025.1 Hibiscus syriacus cultivar Beakdansim tig00018181_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: 76408
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9044 original size:138 final size:138
Alignment explanation
Indices: 8796--9075 Score: 380
Period size: 138 Copynumber: 2.0 Consensus size: 138
8786 ACCCCTTTCT
* ** * ** * **
8796 GATTTGTATGATGAGTTTATATGTTAGGTCTAAGATCATGATAATTTCTTGTAGATTATTTGGGC
1 GATTTGTATGACGAGTTTATATGTTAAATCTAAGATCATGATAATTACTCATAGATTAGTAAGGC
* * *
8861 AAATGGATATTTTCGTTTAATAATAGATTTGACTTTGATAGATTACGCGAGTTTACCAAATATCA
66 AAATGGATATTGTCGTTTAATAATAGATTTGACTTTGATAGATTACGCGAGTTCACCAAATATAA
8926 CGTGAAAG
131 CGTGAAAG
* * * * *
8934 GATTTGTATGGCGAGTTTATATGTTAAATTTAAGATCGTGATAATTACTCATAGATTGGTAAGGT
1 GATTTGTATGACGAGTTTATATGTTAAATCTAAGATCATGATAATTACTCATAGATTAGTAAGGC
**
8999 AAATGGATATTGTCGTTTAATAATAGATTTGACTTTGATAGATTACTTGAGTTCACCAAATATAA
66 AAATGGATATTGTCGTTTAATAATAGATTTGACTTTGATAGATTACGCGAGTTCACCAAATATAA
*
9064 TGTGAAAG
131 CGTGAAAG
9072 GATT
1 GATT
9076 GCAGCTTATA
Statistics
Matches: 122, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
138 122 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (138 bp):
GATTTGTATGACGAGTTTATATGTTAAATCTAAGATCATGATAATTACTCATAGATTAGTAAGGC
AAATGGATATTGTCGTTTAATAATAGATTTGACTTTGATAGATTACGCGAGTTCACCAAATATAA
CGTGAAAG
Found at i:11209 original size:24 final size:23
Alignment explanation
Indices: 11169--11213 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
11159 CTGCACATAA
11169 ACAATAAAAGTGGGTAAATTAATT
1 ACAATAAAAGTGGGT-AATTAATT
*
11193 ACAATGAAAAGT-TGTAATTAA
1 ACAAT-AAAAGTGGGTAATTAA
11214 GTAAAACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 7 0.37
25 6 0.32
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (23 bp):
ACAATAAAAGTGGGTAATTAATT
Found at i:12506 original size:21 final size:20
Alignment explanation
Indices: 12477--12546 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
12467 GGATGCTAAT
12477 ATAAAAAGATATAATGTTAAC
1 ATAAAAAGATAT-ATGTTAAC
* ** *
12498 ATGAAAAGACGTATCGTTAAT
1 ATAAAAAGATATAT-GTTAAC
*
12519 ATAAAAAGATACGATGTTAAC
1 ATAAAAAGATA-TATGTTAAC
12540 ATAAAAA
1 ATAAAAA
12547 AACGATTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAAAAAGATATATGTTAAC
Found at i:13049 original size:26 final size:26
Alignment explanation
Indices: 13016--13066 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13006 GCACTTCAAA
* *
13016 ATTTTAATATTTTAGATTTTCCATAT
1 ATTTTAATATTTTAAAATTTCCATAT
*
13042 ATTTTAATTTTTTAAAATTTCCATA
1 ATTTTAATATTTTAAAATTTCCATA
13067 ATCATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTTTAATATTTTAAAATTTCCATAT
Found at i:18163 original size:15 final size:15
Alignment explanation
Indices: 18145--18180 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
18135 AATATATTTT
18145 AAATAATTAAAAAAC
1 AAATAATTAAAAAAC
*
18160 AAAT-ATTAAGAAAC
1 AAATAATTAAAAAAC
18174 AAATAAT
1 AAATAAT
18181 CAAATAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (15 bp):
AAATAATTAAAAAAC
Found at i:20920 original size:8 final size:8
Alignment explanation
Indices: 20907--20932 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20897 GAAGCTTCTT
20907 TCCCAGAA
1 TCCCAGAA
20915 TCCCAGAA
1 TCCCAGAA
20923 TCCCAGAA
1 TCCCAGAA
20931 TC
1 TC
20933 AGCTTCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (8 bp):
TCCCAGAA
Found at i:27460 original size:20 final size:20
Alignment explanation
Indices: 27435--27476 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
27425 GCGCTCCACT
27435 CCTCTTTCTGTTCTAAATCC
1 CCTCTTTCTGTTCTAAATCC
27455 CCTCTTTCTGTTCTAAATCC
1 CCTCTTTCTGTTCTAAATCC
27475 CC
1 CC
27477 AAACTCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.38, G:0.05, T:0.43
Consensus pattern (20 bp):
CCTCTTTCTGTTCTAAATCC
Found at i:35107 original size:12 final size:12
Alignment explanation
Indices: 35090--35125 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35080 TATCATGTTC
*
35090 TCATATAACATG
1 TCATATCACATG
*
35102 TCATATCACATA
1 TCATATCACATG
35114 TCATATCACATG
1 TCATATCACATG
35126 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:35109 original size:25 final size:24
Alignment explanation
Indices: 35057--35109 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
35047 TTCTCTTGTG
*
35057 ATCATGTATCTCATATCACTTCAT
1 ATCATGTATCTCATATAACTTCAT
35081 ATCATGT-TCTCATATAACATGTCAT
1 ATCATGTATCTCATATAAC-T-TCAT
35106 ATCA
1 ATCA
35110 CATATCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (24 bp):
ATCATGTATCTCATATAACTTCAT
Found at i:35565 original size:64 final size:64
Alignment explanation
Indices: 35427--35588 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 64
35417 TCTTTTAATG
* * *
35427 AAGGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTTTCATTATTAA
1 AAGG-ATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAA
* * * * ** *
35492 TAGGATGCATCAATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA
1 AAGGATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATG-TTTCATTATTAA
35556 AA-GAGTGCATCGATGCACTAAC-AATGCATCGAT
1 AAGGA-TGCATCGATGCACT-ACTAATGCATCGAT
35589 ACACCTTCAA
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 2 0.02
64 69 0.84
65 11 0.13
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (64 bp):
AAGGATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAA
Found at i:41951 original size:12 final size:12
Alignment explanation
Indices: 41934--41969 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41924 TATCATGTTC
*
41934 TCATATAACATG
1 TCATATCACATG
*
41946 TCATATCACATA
1 TCATATCACATG
41958 TCATATCACATG
1 TCATATCACATG
41970 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:41953 original size:25 final size:24
Alignment explanation
Indices: 41901--41953 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
41891 TTCTCTTGTG
*
41901 ATCATGTATCTCATATCACTTCAT
1 ATCATGTATCTCATATAACTTCAT
41925 ATCATGT-TCTCATATAACATGTCAT
1 ATCATGTATCTCATATAAC-T-TCAT
41950 ATCA
1 ATCA
41954 CATATCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (24 bp):
ATCATGTATCTCATATAACTTCAT
Found at i:42349 original size:64 final size:63
Alignment explanation
Indices: 42276--42432 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 63
42266 TAATGAAGGT
* * * **
42276 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATG-TTTCATTATTAATGGG
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATT-TTAA-AAG
* * ** *
42340 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATTTTAAAAG
*
42403 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTAATGCATCGAT
42433 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.03
64 72 0.90
65 6 0.08
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATTTTAAAAG
Found at i:54095 original size:13 final size:13
Alignment explanation
Indices: 54077--54101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54067 CCACTTAAAA
54077 CGGGTTTGGAGCT
1 CGGGTTTGGAGCT
54090 CGGGTTTGGAGC
1 CGGGTTTGGAGC
54102 CTTAGATGAA
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:0.08, C:0.16, G:0.48, T:0.28
Consensus pattern (13 bp):
CGGGTTTGGAGCT
Found at i:54801 original size:11 final size:11
Alignment explanation
Indices: 54785--54827 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
54775 AATAATGAGG
54785 AAAAATACAAA
1 AAAAATACAAA
54796 AAAAATAC-AA
1 AAAAATACAAA
*
54806 AAAAATGAAAAA
1 AAAAAT-ACAAA
54818 AAAAATACAA
1 AAAAATACAA
54828 TCACATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.29
11 12 0.43
12 8 0.29
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.09
Consensus pattern (11 bp):
AAAAATACAAA
Found at i:54810 original size:22 final size:22
Alignment explanation
Indices: 54785--54827 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
54775 AATAATGAGG
*
54785 AAAAAT-ACAAAAAAAAT-ACAA
1 AAAAATGA-AAAAAAAAATACAA
54806 AAAAATGAAAAAAAAAATACAA
1 AAAAATGAAAAAAAAAATACAA
54828 TCACATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.09
Consensus pattern (22 bp):
AAAAATGAAAAAAAAAATACAA
Found at i:54816 original size:9 final size:10
Alignment explanation
Indices: 54785--54827 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
54775 AATAATGAGG
54785 AAAAATACAAA
1 AAAAATAC-AA
54796 AAAAATACAA
1 AAAAATACAA
*
54806 AAAAATGAAAAA
1 AAAAAT--ACAA
54818 AAAAATACAA
1 AAAAATACAA
54828 TCACATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 11 0.39
11 8 0.29
12 9 0.32
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.09
Consensus pattern (10 bp):
AAAAATACAA
Found at i:55029 original size:23 final size:23
Alignment explanation
Indices: 54999--55046 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
54989 AAATAATAGT
*
54999 AATAATAAGTATTAA-AATAAAAA
1 AATAATAA-TAGTAAGAATAAAAA
55022 AATAATAATAGTAATGAATAAAAA
1 AATAATAATAGTAA-GAATAAAAA
55046 A
1 A
55047 CAAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 8 0.36
24 9 0.41
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (23 bp):
AATAATAATAGTAAGAATAAAAA
Found at i:55095 original size:2 final size:2
Alignment explanation
Indices: 55088--55118 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55078 AATCAAAGTA
55088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55119 AAATAAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59770 original size:39 final size:40
Alignment explanation
Indices: 59724--59803 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
59714 AAATTAAGTC
* *
59724 AAATATAT-TTATAAAATCGTATACAATATTAAAAAT-TAA
1 AAATATATGCTATAAAATCGTATAAAAT-TTAAAAATATAA
*
59763 AAATATATGCTATAAAATCTTATAAAATTTAAAAATATAA
1 AAATATATGCTATAAAATCGTATAAAATTTAAAAATATAA
59803 A
1 A
59804 CGATAGTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 16 0.44
40 20 0.56
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (40 bp):
AAATATATGCTATAAAATCGTATAAAATTTAAAAATATAA
Done.