Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005375.1 Hibiscus syriacus cultivar Beakdansim tig00012252_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: 101603
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:2093 original size:2 final size:2
Alignment explanation
Indices: 2086--2133 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2076 CCTCGACCCC
2086 TA TA TA TA TA TA TA TA T- 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
*
2127 GA TA TA T
1 TA TA TA T
2134 GTAAAACCCG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2299 original size:19 final size:19
Alignment explanation
Indices: 2234--2302 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
2224 TCTATCCGAA
*
2234 TAAAATATATTTTAAAATAAT
1 TAAATTATA-TTT-AAATAAT
* *
2255 TAAAATAATATTT-TATAAT
1 T-AAATTATATTTAAATAAT
**
2274 TTTATTATATTTAAATAAT
1 TAAATTATATTTAAATAAT
2293 TAAATTATAT
1 TAAATTATAT
2303 AATTATATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 8 0.22
19 19 0.51
21 4 0.11
22 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTATATTTAAATAAT
Found at i:2309 original size:38 final size:37
Alignment explanation
Indices: 2239--2342 Score: 94
Period size: 38 Copynumber: 2.9 Consensus size: 37
2229 CCGAATAAAA
* *
2239 TATATTTTAAAATAATTAAAATA-ATATTTTATAATTTTAT
1 TATA-TTT-AAATAATTAAATTATATA-ATTATAATTTT-T
2279 TATATTTAAATAATTAAATTATATAATTAT-ATTTTT
1 TATATTTAAATAATTAAATTATATAATTATAATTTTT
* *
2315 AATA-TTAAATAA-TATATT-T-TAATTATAA
1 TATATTTAAATAATTAAATTATATAATTATAA
2343 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
32 7 0.12
33 2 0.03
34 5 0.09
35 8 0.14
36 4 0.07
37 5 0.09
38 17 0.29
39 6 0.10
40 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATATTTAAATAATTAAATTATATAATTATAATTTTT
Found at i:2316 original size:21 final size:19
Alignment explanation
Indices: 2292--2346 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
2282 ATTTAAATAA
2292 TTAAATTATATAATTATATTT
1 TTAAATTATATAA-TATA-TT
*
2313 TTAATATTAAATAATATATT
1 TTAA-ATTATATAATATATT
*
2333 TT-AATTATAAAATA
1 TTAAATTATATAATA
2347 AAAAATCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 9 0.30
19 1 0.03
20 4 0.13
21 8 0.27
22 8 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATTATATAATATATT
Found at i:2321 original size:27 final size:27
Alignment explanation
Indices: 2277--2330 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2267 TTATAATTTT
*
2277 ATTATATTTAAATAATTAAATTATATA
1 ATTATATTTAAATAATTAAATAATATA
*
2304 ATTATATTTTTAAT-ATTAAATAATATA
1 ATTATA-TTTAAATAATTAAATAATATA
2331 TTTTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTATATTTAAATAATTAAATAATATA
Found at i:2347 original size:21 final size:20
Alignment explanation
Indices: 2295--2347 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2285 TAAATAATTA
* *
2295 AATTATATAATTATATTTTT
1 AATTATAAAATAATATTTTT
*
2315 AA-TATTAAATAATATATTTT
1 AATTATAAAATAATAT-TTTT
2335 AATTATAAAATAA
1 AATTATAAAATAA
2348 AAAATCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 10 0.37
20 8 0.30
21 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTATAAAATAATATTTTT
Found at i:15217 original size:2 final size:2
Alignment explanation
Indices: 15210--15247 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15200 AAACACCATA
15210 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
15248 CTAAACATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19231 original size:48 final size:49
Alignment explanation
Indices: 19175--19271 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
19165 TCAACTTTTG
19175 ATACTTGCAATACAATCATTGAA-TTTTAGTTCGTTTTCAATAAGGTTA
1 ATACTTGCAATACAATCATTGAATTTTTAGTTCGTTTTCAATAAGGTTA
19223 ATACTTGCAATACAATCATTGAATTTTTAGTTCGTTTTCAATAAGGTTA
1 ATACTTGCAATACAATCATTGAATTTTTAGTTCGTTTTCAATAAGGTTA
19272 CTATCGTTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 23 0.48
49 25 0.52
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (49 bp):
ATACTTGCAATACAATCATTGAATTTTTAGTTCGTTTTCAATAAGGTTA
Found at i:19318 original size:3 final size:3
Alignment explanation
Indices: 19310--19345 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
19300 GACGTGGCAG
*
19310 CTT CTT CTT -TT CTT CTT CTT CCT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
19346 AAAACTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:30420 original size:2 final size:2
Alignment explanation
Indices: 30413--30452 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30403 CTCGACCCAA
30413 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
30453 GTAAAACCCG
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):
AT
Found at i:30641 original size:23 final size:21
Alignment explanation
Indices: 30615--30659 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
30605 TTTAAAATAA
30615 TTAA-ATTAATATAATTAATATTT
1 TTAATATTAA-ATAA-T-ATATTT
30638 TTAATATTAAATAATATATTT
1 TTAATATTAAATAATATATTT
30659 T
1 T
30660 AATTATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 8 0.38
24 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATATTAAATAATATATTT
Found at i:30674 original size:21 final size:19
Alignment explanation
Indices: 30620--30662 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
30610 AATAATTAAA
*
30620 TTAATA-TAATTAATATTT
1 TTAATATTAAATAATATTT
30638 TTAATATTAAATAATATATT
1 TTAATATTAAATAATAT-TT
30658 TTAAT
1 TTAAT
30663 TATATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATATTAAATAATATTT
Found at i:43633 original size:2 final size:2
Alignment explanation
Indices: 43626--43681 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
43616 AAACACCATA
43626 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
* *
43668 AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT
43682 CTAAACATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50411 original size:17 final size:17
Alignment explanation
Indices: 50389--50422 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
50379 TCACGCGAGG
50389 AAGAAGTTGCAAAAAGA
1 AAGAAGTTGCAAAAAGA
*
50406 AAGAAGTTGCAAGAAGA
1 AAGAAGTTGCAAAAAGA
50423 GGAACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.26, T:0.12
Consensus pattern (17 bp):
AAGAAGTTGCAAAAAGA
Found at i:71890 original size:23 final size:23
Alignment explanation
Indices: 71841--71888 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
71831 TTTAAATGAT
* *
71841 AAACGAACATAAACGAACACAAT
1 AAACGAACATAAACAAACACAAA
*
71864 AAACGAACA-ACACAAACACAAA
1 AAACGAACATAAACAAACACAAA
71886 AAA
1 AAA
71889 ACAAACTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.67, C:0.23, G:0.06, T:0.04
Consensus pattern (23 bp):
AAACGAACATAAACAAACACAAA
Found at i:80815 original size:2 final size:2
Alignment explanation
Indices: 80808--80837 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80798 GCTTTATTTC
80808 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
80838 GAGCAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.