Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007318.1 Hibiscus syriacus cultivar Beakdansim tig00019525_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: 75587
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2201 original size:21 final size:19
Alignment explanation
Indices: 2168--2208 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2158 TGCATCAAGG
*
2168 TCTTTGTGGAAGCCATGAAA
1 TCTTTGTCGAAGCCAT-AAA
2188 TCTTTCGTCGAAGCCATAAA
1 TCTTT-GTCGAAGCCATAAA
2208 T
1 T
2209 TCCTACAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (19 bp):
TCTTTGTCGAAGCCATAAA
Found at i:2243 original size:12 final size:12
Alignment explanation
Indices: 2226--2261 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2216 ATAACTCCAA
*
2226 GGAATTAATATT
1 GGAATTAGTATT
2238 GGAATTAGTATT
1 GGAATTAGTATT
2250 GGAATTAGTATT
1 GGAATTAGTATT
2262 AAAGGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (12 bp):
GGAATTAGTATT
Found at i:8469 original size:13 final size:13
Alignment explanation
Indices: 8451--8475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8441 TCAGTTTTTC
8451 CTTTGTTTTTAAG
1 CTTTGTTTTTAAG
8464 CTTTGTTTTTAA
1 CTTTGTTTTTAA
8476 ACATGCTAAG
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:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (13 bp):
CTTTGTTTTTAAG
Found at i:10337 original size:18 final size:18
Alignment explanation
Indices: 10314--10358 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
10304 AATAGCTTTA
10314 TTAAATGAACCAATATGC
1 TTAAATGAACCAATATGC
***
10332 TTAAATGAA-TTGTATGC
1 TTAAATGAACCAATATGC
10349 TTAAATGAAC
1 TTAAATGAAC
10359 TAGCATGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (18 bp):
TTAAATGAACCAATATGC
Found at i:20572 original size:35 final size:37
Alignment explanation
Indices: 20526--20605 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
20516 TTTGAGAATT
*
20526 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
20561 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
20598 TGGTGATG
1 TGGTGATG
20606 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:32837 original size:27 final size:27
Alignment explanation
Indices: 32769--32829 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
32759 TGATTCATTA
* *
32769 CATTCATGAAATGGCAGCATGCTTAAT
1 CATTCATAAAATAGCAGCATGCTTAAT
32796 CATTCATAAAATAGCAGCATGCTTAAT
1 CATTCATAAAATAGCAGCATGCTTAAT
32823 CATTCAT
1 CATTCAT
32830 TTGTTAGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (27 bp):
CATTCATAAAATAGCAGCATGCTTAAT
Found at i:40618 original size:22 final size:20
Alignment explanation
Indices: 40593--40632 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40583 ATGTTTGTTT
40593 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
40615 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
40633 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:44897 original size:22 final size:20
Alignment explanation
Indices: 44872--44911 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44862 ATGTTTGTTT
44872 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
44894 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
44912 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:45145 original size:15 final size:15
Alignment explanation
Indices: 45122--45157 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
45112 ACTAATATTC
* *
45122 TTATCATAATATATA
1 TTATAATAACATATA
45137 TTATAATAACATATA
1 TTATAATAACATATA
45152 TTATAA
1 TTATAA
45158 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:46383 original size:23 final size:24
Alignment explanation
Indices: 46355--46407 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
46345 AAAATCAGCA
46355 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
46378 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
46402 AAGAAA
1 AAGAAA
46408 GAAAGAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:48614 original size:12 final size:13
Alignment explanation
Indices: 48591--48615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48581 ATGCACAACG
48591 AAAATACAAAAAA
1 AAAATACAAAAAA
48604 AAAATACAAAAA
1 AAAATACAAAAA
48616 GAAGTTCAAG
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:53276 original size:23 final size:24
Alignment explanation
Indices: 53248--53300 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
53238 AAAATCAGCA
53248 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
53271 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
53295 AAGAAA
1 AAGAAA
53301 GAAAGAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:58081 original size:15 final size:15
Alignment explanation
Indices: 58070--58098 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58060 ACTCAAAAAG
58070 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
58085 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
58099 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:59601 original size:80 final size:78
Alignment explanation
Indices: 59457--59606 Score: 180
Period size: 80 Copynumber: 1.9 Consensus size: 78
59447 AATTAACAAT
* *
59457 AAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-TT
1 AAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTT
59521 TAATGTTCATTTA
66 TAATGTTCATTTA
* * * *
59534 AAAAT-TTATTTAATT-ATTCTGAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTACAT
1 AAAATATTATTTAATTAATTC--AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACAA
59597 TCTTTTAATG
61 TCTTTTAATG
59607 CTTACTTACT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
75 4 0.07
76 10 0.16
77 15 0.25
78 1 0.02
79 3 0.05
80 21 0.34
81 7 0.11
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (78 bp):
AAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTT
TAATGTTCATTTA
Done.