Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002048.1 Hibiscus syriacus cultivar Beakdansim tig00004172_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: 60253
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:8805 original size:5 final size:5
Alignment explanation
Indices: 8795--8841 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
8785 TTAACCCATT
8795 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
8842 GCATGTGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:9082 original size:25 final size:25
Alignment explanation
Indices: 9045--9094 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9035 TCATATTTTT
9045 TAATTAAAATAAAATATT-TTAATTA
1 TAATTAAAATAAAAT-TTATTAATTA
* *
9070 TAATTATAGTAAAATTTATTAATTA
1 TAATTAAAATAAAATTTATTAATTA
9095 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TAATTAAAATAAAATTTATTAATTA
Found at i:10903 original size:2 final size:2
Alignment explanation
Indices: 10896--10925 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10886 TAAATTGTGC
10896 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10926 TTTACGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12495 original size:2 final size:2
Alignment explanation
Indices: 12488--12535 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12478 TCGTATCTAG
12488 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
12530 AT AT AT
1 AT AT AT
12536 GAGTATTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14215 original size:2 final size:2
Alignment explanation
Indices: 14208--14233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14198 ATATCAATCC
14208 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
14234 CTGAAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15758 original size:2 final size:2
Alignment explanation
Indices: 15751--15787 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
15741 CAAGGTGACA
15751 AT AT AT 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 AT AT AT A
15788 AGATTACATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16234 original size:2 final size:2
Alignment explanation
Indices: 16227--16251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16217 AATATGAATG
16227 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 A
16252 CGTATGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40465 original size:15 final size:15
Alignment explanation
Indices: 40447--40488 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
40437 ATATTTATAT
40447 ATATATATATTATTA
1 ATATATATATTATTA
40462 ATAT-TATATT-TTA
1 ATATATATATTATTA
* *
40475 AAATATAGATTATT
1 ATATATATATTATT
40489 TTTTAATCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.26
14 11 0.48
15 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATATATATTATTA
Found at i:43637 original size:2 final size:2
Alignment explanation
Indices: 43630--43655 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43620 TTATAATAGA
43630 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
43656 CGCACACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44107 original size:74 final size:74
Alignment explanation
Indices: 43987--44138 Score: 241
Period size: 74 Copynumber: 2.1 Consensus size: 74
43977 AAACGCCATA
*
43987 CATGCATGCATGGATGCTGACATAACATCCAATGATTCAGGAGTATAACATAATTGATGCAACAT
1 CATGCATGCATGGATGCTGACATAACATCCAATGATTCAAGAGTATAACATAATTGATGCAACAT
*
44052 GCCATGCAG
66 GCCAAGCAG
* * * * *
44061 CATGCATGTATGTATGCTGACGTAACATCCAATTATTCAAGAGTATAACATAATTGATGCAATAT
1 CATGCATGCATGGATGCTGACATAACATCCAATGATTCAAGAGTATAACATAATTGATGCAACAT
44126 GCCAAGCAG
66 GCCAAGCAG
44135 CATG
1 CATG
44139 AATTCACATG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (74 bp):
CATGCATGCATGGATGCTGACATAACATCCAATGATTCAAGAGTATAACATAATTGATGCAACAT
GCCAAGCAG
Found at i:46376 original size:60 final size:60
Alignment explanation
Indices: 46310--46435 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
46300 TTGGGGAACC
* * * *
46310 AATTTAGAAAGAGGGTCATAATTTAGG-GATGAAATT-AGAATGTTCAAAAGTTTAAGGACT
1 AATTTAGAAAGAGAGTCATAATTT-GGAGATGAAATTGA-AATATGCAAAAGTTTAAAGACT
* * *
46370 AGTTTAGAATGAGAGTCATAGTTTGGAGATGAAATTGAAATATGCAAAAGTTTAAAGACT
1 AATTTAGAAAGAGAGTCATAATTTGGAGATGAAATTGAAATATGCAAAAGTTTAAAGACT
46430 AATTTA
1 AATTTA
46436 AAATAAATGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.04
60 53 0.95
61 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (60 bp):
AATTTAGAAAGAGAGTCATAATTTGGAGATGAAATTGAAATATGCAAAAGTTTAAAGACT
Found at i:46451 original size:60 final size:60
Alignment explanation
Indices: 46324--46455 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
46314 TAGAAAGAGG
* * * * * * *
46324 GTCATAATTTAGG-GATGAAATTAGAATGTTCAAAAGTTTAAGGACTAGTTTAGAATGAGA
1 GTCATAGTTT-GGAGATGAAATTAGAATATGCAAAAGTTTAAAGACTAATTTAAAATGAAA
46384 GTCATAGTTTGGAGATGAAATT-GAAATATGCAAAAGTTTAAAGACTAATTTAAAAT-AAA
1 GTCATAGTTTGGAGATGAAATTAG-AATATGCAAAAGTTTAAAGACTAATTTAAAATGAAA
*
46443 TGTTATAGTTTGG
1 -GTCATAGTTTGG
46456 GGATATATGG
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 5 0.08
60 56 0.92
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (60 bp):
GTCATAGTTTGGAGATGAAATTAGAATATGCAAAAGTTTAAAGACTAATTTAAAATGAAA
Found at i:46688 original size:19 final size:20
Alignment explanation
Indices: 46650--46689 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
46640 TGGTTCACGG
46650 AATGTAAGATTATCAGTGGA
1 AATGTAAGATTATCAGTGGA
46670 AATGTAAGATTATCA-TGGA
1 AATGTAAGATTATCAGTGGA
46689 A
1 A
46690 TATAATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (20 bp):
AATGTAAGATTATCAGTGGA
Found at i:52837 original size:21 final size:21
Alignment explanation
Indices: 52787--52843 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
52777 AAACGATAAA
*
52787 AAAATGTCA-AAAGACAGAAG
1 AAAATATCATAAAGACAGAAG
52807 AAACATATCATAAAGACAGAA-
1 AAA-ATATCATAAAGACAGAAG
52828 ATAAATATCATAAAGA
1 A-AAATATCATAAAGA
52844 TAAAAAATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 18 0.55
22 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.12, T:0.16
Consensus pattern (21 bp):
AAAATATCATAAAGACAGAAG
Found at i:54156 original size:18 final size:18
Alignment explanation
Indices: 54133--54175 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
54123 CCGGTTCGAA
54133 TGGTTCAACGGTTCTAGC
1 TGGTTCAACGGTTCTAGC
54151 TGGTTCAACGGTTCTAGC
1 TGGTTCAACGGTTCTAGC
54169 TGGTTCA
1 TGGTTCA
54176 CTAGTAACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (18 bp):
TGGTTCAACGGTTCTAGC
Done.