Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000238.1 Hibiscus syriacus cultivar Beakdansim tig00000412_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: 61305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5861 original size:19 final size:19
Alignment explanation
Indices: 5837--5874 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5827 TTAGGTATTT
*
5837 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
5856 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
5875 GATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:6639 original size:21 final size:22
Alignment explanation
Indices: 6604--6656 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
6594 TTTTAAATCA
* * *
6604 TTATTTATTATTTTATTATT-T
1 TTATTTTTTAATTTATAATTAT
*
6625 TTCTTTTTTAATTTATAATTAT
1 TTATTTTTTAATTTATAATTAT
6647 TTATTTTTTA
1 TTATTTTTTA
6657 TACATTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTTTTTAATTTATAATTAT
Found at i:9569 original size:11 final size:12
Alignment explanation
Indices: 9546--9574 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
9536 CATTTCGTTA
9546 TATTTTTGTTTT
1 TATTTTTGTTTT
9558 TATTTTTG-TTT
1 TATTTTTGTTTT
9569 TATTTT
1 TATTTT
9575 CAACGAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (12 bp):
TATTTTTGTTTT
Found at i:11406 original size:19 final size:19
Alignment explanation
Indices: 11382--11419 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11372 TTAGGTATTT
*
11382 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
11401 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
11420 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:11449 original size:32 final size:32
Alignment explanation
Indices: 11395--11456 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
11385 TTTAAATAGG
11395 TTTTAGTATTTTAATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTAATTAAGTTTTAGG-TATTAT
*
11428 TTTTA-TATTTTATATT-TGTTTTAGGTATT
1 TTTTAGTATTTTA-ATTAAGTTTTAGGTATT
11457 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTAATTAAGTTTTAGGTATTAT
Found at i:11457 original size:76 final size:74
Alignment explanation
Indices: 11354--11568 Score: 281
Period size: 76 Copynumber: 2.9 Consensus size: 74
11344 ATTTTAAACA
* * *
11354 TTATATTTTATCTTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTAT-TTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAAGATTTA
**
11419 GGATATTATTT
65 AAATATTA-TT
*
11430 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTA
1 TTATATTTTAT-TTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAAGATTTA
11495 AAATATTATT
65 AAATATTATT
* * * * *
11505 TAAAATATTATTATT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAATGTTTTAATTAGGATTTA
1 TTATATTTTATT-TTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAAGATTTA
11568 A
65 A
11569 GATGTTTTAG
Statistics
Matches: 127, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
73 25 0.20
74 24 0.19
75 12 0.09
76 66 0.52
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (74 bp):
TTATATTTTATTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAAGATTTAA
AATATTATT
Found at i:11505 original size:12 final size:12
Alignment explanation
Indices: 11490--11516 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11480 TTTAATTAGG
11490 ATTTAAAATATT
1 ATTTAAAATATT
11502 ATTTAAAATATT
1 ATTTAAAATATT
11514 ATT
1 ATT
11517 ATTTTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTAAAATATT
Found at i:12168 original size:11 final size:11
Alignment explanation
Indices: 12142--12182 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
12132 TTTATCCCAA
*
12142 TTTATTTATTTT
1 TTTATTTA-ATT
12154 TTTATTTAATT
1 TTTATTTAATT
12165 TTTATTTAATT
1 TTTATTTAATT
12176 TTTATTT
1 TTTATTT
12183 CATTATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTATTTAATT
Found at i:12254 original size:38 final size:38
Alignment explanation
Indices: 12212--12295 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
12202 ATTAACCCCC
*
12212 TTTTATCT-TTATTACTATTTTTAATTCATTATTTATTA
1 TTTTAT-TATTATTACTATTTTTAATTCATAATTTATTA
* * * * *
12250 TTTTATTATTTTTTCTTTTTTTAATTTATAATTTTTTA
1 TTTTATTATTATTACTATTTTTAATTCATAATTTATTA
12288 TTTT-TTAT
1 TTTTATTAT
12296 ACCTTTTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
37 5 0.13
38 34 0.87
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (38 bp):
TTTTATTATTATTACTATTTTTAATTCATAATTTATTA
Found at i:12259 original size:15 final size:15
Alignment explanation
Indices: 12239--12295 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
12229 TTTTTAATTC
12239 ATTATTTATTATTTT
1 ATTATTTATTATTTT
* *
12254 ATTATTTTTTCTTTT
1 ATTATTTATTATTTT
* *
12269 TTTAATTTATAATTTT
1 ATT-ATTTATTATTTT
*
12285 -TTATTTTTTAT
1 ATTATTTATTAT
12296 ACCTTTTCAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
14 7 0.21
15 17 0.52
16 9 0.27
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTATTTATTATTTT
Found at i:21674 original size:19 final size:18
Alignment explanation
Indices: 21645--21695 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
21635 AACTTCAATT
*
21645 TTTTAACTTTTTTTAAT-
1 TTTTAATTTTTTTTAATG
*
21662 TTCATTAATTTTTTAT-ATG
1 TT--TTAATTTTTTTTAATG
21681 TTTTAATTTTTTTTA
1 TTTTAATTTTTTTTA
21696 TAAATATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
17 13 0.48
18 2 0.07
19 12 0.44
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTTTTTAATG
Found at i:22156 original size:163 final size:163
Alignment explanation
Indices: 21876--22187 Score: 441
Period size: 163 Copynumber: 1.9 Consensus size: 163
21866 TGTTCAGTTA
* * * *
21876 TTTTTTAATTTATTGATAATGTATATACATCATATAAATGTAATTTTTGGAATCTTAAACCTCTA
1 TTTTTTAATTTATTGATAATATATATACATCATATAAATATAATTATTCGAATCTTAAACCTCTA
* * * *
21941 AAATGAATAATACTCTTTTTTACCACTGGAATTATTTAGTAAAACATTTATGATGGTACGAGCAG
66 AAA-GAATAATACTCTTTTTTACCACTGAAATCATTTAGTAAAACATTTATGATGGTACAAGCAA
22006 GCAGATTAGTGAAGCGAGTTGTTTGTTCGATTGT
130 GCAGATTAGTGAAGCGAGTTGTTTGTTCGATTGT
* *
22040 TTTTTTATTTTATTGATAATATATATACATCATATAAATATAATTATTCGAATTTTAAACACT-T
1 TTTTTTAATTTATTGATAATATATATACATCATATAAATATAATTATTCGAATCTTAAAC-CTCT
* * *
22104 AACAA-AATAATACTCTTTTTTATC-GTGTAAATCATTTAGTAAAACCTTTATGATGGTACAAGC
65 AA-AAGAATAATACTCTTTTTTACCACTG-AAATCATTTAGTAAAACATTTATGATGGTACAAGC
*
22167 AAGCGGATTAGTGAAGCGAGT
128 AAGCAGATTAGTGAAGCGAGT
22188 GATGGTTATA
Statistics
Matches: 131, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
162 2 0.02
163 68 0.52
164 57 0.44
165 4 0.03
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (163 bp):
TTTTTTAATTTATTGATAATATATATACATCATATAAATATAATTATTCGAATCTTAAACCTCTA
AAAGAATAATACTCTTTTTTACCACTGAAATCATTTAGTAAAACATTTATGATGGTACAAGCAAG
CAGATTAGTGAAGCGAGTTGTTTGTTCGATTGT
Found at i:29375 original size:18 final size:19
Alignment explanation
Indices: 29352--29400 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
29342 GCCATTTTTT
29352 GTATCGATACTCAAGGG-A
1 GTATCGATACTCAAGGGTA
*
29370 GTATCGATA-TCTAGGGTA
1 GTATCGATACTCAAGGGTA
29388 GATTATCGATACT
1 G--TATCGATACT
29401 TTCAGTAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
20 8 0.31
21 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (19 bp):
GTATCGATACTCAAGGGTA
Found at i:32214 original size:14 final size:14
Alignment explanation
Indices: 32195--32224 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
32185 CATTGATCTA
32195 ATGTCGAACTTCTT
1 ATGTCGAACTTCTT
32209 ATGTCGAACTTCTT
1 ATGTCGAACTTCTT
32223 AT
1 AT
32225 CAATTGATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.43
Consensus pattern (14 bp):
ATGTCGAACTTCTT
Found at i:34614 original size:18 final size:18
Alignment explanation
Indices: 34583--34621 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
34573 TCAATTGGCG
*
34583 ACCCTAATGCTATTGACA
1 ACCCTAATACTATTGACA
* *
34601 ACCCTAATATTATTGGCA
1 ACCCTAATACTATTGACA
34619 ACC
1 ACC
34622 AAATAGTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (18 bp):
ACCCTAATACTATTGACA
Found at i:36107 original size:18 final size:18
Alignment explanation
Indices: 36079--36121 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
36069 TGCCCGGGCT
* * *
36079 AGTCCACATACCTCGGTA
1 AGTCCATATACATCGATA
*
36097 ATTCCATATACATCGATA
1 AGTCCATATACATCGATA
36115 AGTCCAT
1 AGTCCAT
36122 CAATCAGATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (18 bp):
AGTCCATATACATCGATA
Found at i:39866 original size:14 final size:13
Alignment explanation
Indices: 39817--39872 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
39807 AGAGATGAAT
*
39817 AAATAATTATTAA
1 AAATTATTATTAA
39830 ATAATTA-TATTAA
1 A-AATTATTATTAA
*
39843 AATATAATTATTAA
1 AA-ATTATTATTAA
39857 AAATTCATTATATAA
1 AAATT-ATTAT-TAA
39872 A
1 A
39873 TTTAATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.03
13 13 0.37
14 17 0.49
15 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTATTATTAA
Found at i:41534 original size:19 final size:17
Alignment explanation
Indices: 41495--41529 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41485 TTTTAAAACT
*
41495 AAATATTAGATATATTA
1 AAATATTAGATATATAA
41512 AAATATTAGATATATAA
1 AAATATTAGATATATAA
41529 A
1 A
41530 GAAATTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
AAATATTAGATATATAA
Found at i:48096 original size:6 final size:5
Alignment explanation
Indices: 48071--48122 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 5
48061 GGTGAGCATT
*
48071 GAAAA -AAAA GGAAAA GAAAA GAAAAA GAAGA GAAAA GGAAAA GGAAAA
1 GAAAA GAAAA -GAAAA GAAAA G-AAAA GAAAA GAAAA -GAAAA -GAAAA
48119 GAAA
1 GAAA
48123 GTAAAAATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.10
5 17 0.41
6 20 0.49
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:48096 original size:11 final size:11
Alignment explanation
Indices: 48072--48122 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
48062 GTGAGCATTG
*
48072 AAAA-AAAAGG
1 AAAAGAAAAGA
48082 AAAAGAAAAGA
1 AAAAGAAAAGA
*
48093 AAAAGAAGAGA
1 AAAAGAAAAGA
* *
48104 AAAGGAAAAGG
1 AAAAGAAAAGA
48115 AAAAGAAA
1 AAAAGAAA
48123 GTAAAAATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 4 0.12
11 30 0.88
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:48104 original size:16 final size:16
Alignment explanation
Indices: 48071--48122 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
48061 GGTGAGCATT
*
48071 GAAAA-AAAAGGAAAA
1 GAAAAGAAAAAGAAAA
*
48086 GAAAAGAAAAAGAAGA
1 GAAAAGAAAAAGAAAA
*
48102 GAAAAGGAAAAGGAAAA
1 GAAAA-GAAAAAGAAAA
48119 GAAA
1 GAAA
48123 GTAAAAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 5 0.16
16 13 0.42
17 13 0.42
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAAGAAAA
Found at i:53746 original size:26 final size:25
Alignment explanation
Indices: 53716--53780 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 25
53706 ATGTTCACAA
* * *
53716 GATTTTAAGATTTTGGATAATTTAT
1 GATTTTAAGATTTTAGAAAATTAAT
*
53741 GAATTTTAAGAGTTTAGAAAATTAAT
1 G-ATTTTAAGATTTTAGAAAATTAAT
53767 GATTTTAAGATTTT
1 GATTTTAAGATTTT
53781 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (25 bp):
GATTTTAAGATTTTAGAAAATTAAT
Done.