Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001769.1 Hibiscus syriacus cultivar Beakdansim tig00003568_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: 98222
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:7497 original size:23 final size:23
Alignment explanation
Indices: 7467--7514 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
7457 TGTCGACGTA
7467 AGTCATGCCAACCTCCTACTCTT
1 AGTCATGCCAACCTCCTACTCTT
7490 AGTCATGCCAACCTCCTACTCTT
1 AGTCATGCCAACCTCCTACTCTT
7513 AG
1 AG
7515 AGGGTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.10, T:0.29
Consensus pattern (23 bp):
AGTCATGCCAACCTCCTACTCTT
Found at i:8153 original size:20 final size:20
Alignment explanation
Indices: 8117--8154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8107 ATCCTATTCC
**
8117 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
8137 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
8155 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:9362 original size:31 final size:31
Alignment explanation
Indices: 9324--9408 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
9314 TAAAATTTTA
*
9324 GGTACTAAAATGAAACGAAAAGTTAACGATG
1 GGTACTAAAATGAAACAAAAAGTTAACGATG
***
9355 GGTACTAAAATGAAACAAAAAGTTAATTTTG
1 GGTACTAAAATGAAACAAAAAGTTAACGATG
9386 GGTACTAAAATGAAACAAAAAGT
1 GGTACTAAAATGAAACAAAAAGT
9409 AAGCATTATG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (31 bp):
GGTACTAAAATGAAACAAAAAGTTAACGATG
Found at i:10987 original size:30 final size:29
Alignment explanation
Indices: 10941--11016 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 29
10931 GATATAACCA
*
10941 ATGATGGGTAATGATGTAATTGGTTCGTGAC
1 ATGAT-GGT-ATGATGTAATTGGTTCATGAC
10972 ATGATGGCTATGATGTAATTGGTTCATGAC
1 ATGATGG-TATGATGTAATTGGTTCATGAC
*
11002 GTGATGAGTATGATG
1 ATGATG-GTATGATG
11017 GTTGAGATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 34 0.83
31 7 0.17
ACGTcount: A:0.26, C:0.07, G:0.32, T:0.36
Consensus pattern (29 bp):
ATGATGGTATGATGTAATTGGTTCATGAC
Found at i:11016 original size:39 final size:39
Alignment explanation
Indices: 10972--11134 Score: 213
Period size: 39 Copynumber: 4.2 Consensus size: 39
10962 GGTTCGTGAC
10972 ATGATGGCTATGATGTAATTGGTTCATGACGTGATGAGT
1 ATGATGGCTATGATGTAATTGGTTCATGACGTGATGAGT
* * *
11011 ATGATGGTTGA-GATGTAATTGGTTCATGACTTGAGGAGT
1 ATGATGGCT-ATGATGTAATTGGTTCATGACGTGATGAGT
* * * *
11050 ATAATGGCTGTGATGTAATTGGTTTATGACGTGATGCGT
1 ATGATGGCTATGATGTAATTGGTTCATGACGTGATGAGT
* * *
11089 ATGATGGCAATGATGTAATTGGTTCATGACATGGT-AGT
1 ATGATGGCTATGATGTAATTGGTTCATGACGTGATGAGT
11127 ATGATGGC
1 ATGATGGC
11135 ATGTTCATGT
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
38 10 0.10
39 94 0.90
40 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.31, T:0.36
Consensus pattern (39 bp):
ATGATGGCTATGATGTAATTGGTTCATGACGTGATGAGT
Found at i:12811 original size:3 final size:3
Alignment explanation
Indices: 12798--12832 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
12788 CTGAGAGCTT
12798 GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
12833 GGGCTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29035 original size:21 final size:22
Alignment explanation
Indices: 29011--29056 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
29001 GCTGATGTGG
* *
29011 CAGTTC-ACAGTGTTGATATGA
1 CAGTTCAACAGTGTTAACATGA
29032 CAG-TCAACAGTGTTAACATGA
1 CAGTTCAACAGTGTTAACATGA
29053 CAGT
1 CAGT
29057 CTACGGTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (22 bp):
CAGTTCAACAGTGTTAACATGA
Found at i:29057 original size:21 final size:21
Alignment explanation
Indices: 29017--29057 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29007 GTGGCAGTTC
* *
29017 ACAGTGTTGATATGACAGTCA
1 ACAGTGTTAACATGACAGTCA
29038 ACAGTGTTAACATGACAGTC
1 ACAGTGTTAACATGACAGTC
29058 TACGGTGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (21 bp):
ACAGTGTTAACATGACAGTCA
Found at i:33063 original size:36 final size:36
Alignment explanation
Indices: 33012--33083 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
33002 CCTAGCATTC
* *
33012 GCCAAGAACCTGATTCGGATCCTGTTGCCTCTGAAA
1 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
33048 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
1 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
33084 CAGAAGGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (36 bp):
GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
Found at i:60230 original size:31 final size:31
Alignment explanation
Indices: 60171--60230 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
60161 AACTAAAAAA
* * *
60171 TTAAAAAATATAACAATAGATACTTAAAATT
1 TTAAAAAATATAACAATAAAAACCTAAAATT
60202 TTAAAAAATATAACAATAAAAACCTAAAA
1 TTAAAAAATATAACAATAAAAACCTAAAA
60231 GTATAACGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (31 bp):
TTAAAAAATATAACAATAAAAACCTAAAATT
Found at i:61093 original size:18 final size:18
Alignment explanation
Indices: 61070--61104 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61060 TAAAATGATA
61070 AACGAACACAAACGAACG
1 AACGAACACAAACGAACG
**
61088 AACGAACGTAAACGAAC
1 AACGAACACAAACGAAC
61105 AAAAAAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.26, G:0.17, T:0.03
Consensus pattern (18 bp):
AACGAACACAAACGAACG
Found at i:62359 original size:2 final size:2
Alignment explanation
Indices: 62352--62391 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
62342 TTATTATTAT
62352 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
62392 CGCGACTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62546 original size:30 final size:30
Alignment explanation
Indices: 62510--62629 Score: 152
Period size: 30 Copynumber: 4.0 Consensus size: 30
62500 ATTCTACATA
62510 GGATAAATTCCCTGTTCTAACATCTGCATG
1 GGATAAATTCCCTGTTCTAACATCTGCATG
* * *
62540 GGATAAACTTCCC-GTTCTGACATCTACATA
1 GGATAAA-TTCCCTGTTCTAACATCTGCATG
* * *
62570 AGATAAACTCCCCGTTCTAACATCTGCATG
1 GGATAAATTCCCTGTTCTAACATCTGCATG
* *
62600 GGATAAATCCCCTGTTCTGACATCTGCATG
1 GGATAAATTCCCTGTTCTAACATCTGCATG
62630 AGATTATATC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 4 0.05
30 66 0.88
31 5 0.07
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
GGATAAATTCCCTGTTCTAACATCTGCATG
Found at i:62595 original size:60 final size:60
Alignment explanation
Indices: 62502--62633 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 60
62492 CCGTCCTAAT
* * * *
62502 TCTACATAGGATAAATTCCCTGTTCTAACATCTGCATGGGATAAACTTCCC-GTTCTGACA
1 TCTACATAAGATAAACTCCCCGTTCTAACATCTGCATGGGATAAA-TCCCCTGTTCTGACA
62562 TCTACATAAGATAAACTCCCCGTTCTAACATCTGCATGGGATAAATCCCCTGTTCTGACA
1 TCTACATAAGATAAACTCCCCGTTCTAACATCTGCATGGGATAAATCCCCTGTTCTGACA
* *
62622 TCTGCATGAGAT
1 TCTACATAAGAT
62634 TATATCTCTG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.06
60 61 0.94
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (60 bp):
TCTACATAAGATAAACTCCCCGTTCTAACATCTGCATGGGATAAATCCCCTGTTCTGACA
Found at i:62650 original size:30 final size:30
Alignment explanation
Indices: 62511--62654 Score: 107
Period size: 30 Copynumber: 4.8 Consensus size: 30
62501 TTCTACATAG
* * * *
62511 GATAAATTCCCTGTTCTAACATCTGCATGG
1 GATAAATCCCCTGTCCTGACATCTGCATGA
* * * *
62541 GATAAACTTCCC-GTTCTGACATCTACATAA
1 GATAAA-TCCCCTGTCCTGACATCTGCATGA
* * *
62571 GATAAACTCCCC-GTTCTAACATCTGCATGG
1 GATAAA-TCCCCTGTCCTGACATCTGCATGA
*
62601 GATAAATCCCCTGTTCTGACATCTGCATGA
1 GATAAATCCCCTGTCCTGACATCTGCATGA
* *
62631 GATTATAT-CTCTGTCCTGAC-TCTG
1 GA-TAAATCCCCTGTCCTGACATCTG
62655 TTTGGGATGC
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.09
30 79 0.81
31 9 0.09
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (30 bp):
GATAAATCCCCTGTCCTGACATCTGCATGA
Found at i:63274 original size:23 final size:23
Alignment explanation
Indices: 63230--63274 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
63220 TTAATTGGAT
*
63230 TTTAAAATATTAATGGGTTTAAG
1 TTTAAAATATTAATAGGTTTAAG
*
63253 TTTAAAA-ATTATTAGGTATTAA
1 TTTAAAATATTAATAGGT-TTAA
63275 TATTTCGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (23 bp):
TTTAAAATATTAATAGGTTTAAG
Found at i:70945 original size:22 final size:23
Alignment explanation
Indices: 70910--70954 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
70900 AATTTGGTGA
** *
70910 TTTTAAAATTTATTTTTA-ATTT
1 TTTTAAAAAATATTATTATATTT
70932 TTTTAAAAAATATTATTATATTT
1 TTTTAAAAAATATTATTATATTT
70955 AAAAACATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAAAAAATATTATTATATTT
Found at i:72658 original size:22 final size:22
Alignment explanation
Indices: 72630--72673 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
72620 TAAGGGTTAA
*
72630 ATTGATGTGAAAATACGATATG
1 ATTGATGCGAAAATACGATATG
72652 ATTGATGCGAAAATACGATATG
1 ATTGATGCGAAAATACGATATG
72674 GGCGAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.30
Consensus pattern (22 bp):
ATTGATGCGAAAATACGATATG
Done.