Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004084.1 Hibiscus syriacus cultivar Beakdansim tig00008935_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: 57911
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3253 original size:22 final size:22
Alignment explanation
Indices: 3228--3272 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3218 AAGCAGTTAT
*
3228 ACTCTCCAGACAAGATTATTAC
1 ACTCTCCAGACAAGAGTATTAC
3250 ACTCTCCAGACAAGAGTATTAC
1 ACTCTCCAGACAAGAGTATTAC
3272 A
1 A
3273 ATATGGGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (22 bp):
ACTCTCCAGACAAGAGTATTAC
Found at i:7267 original size:12 final size:12
Alignment explanation
Indices: 7250--7276 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7240 AAAATATTAA
7250 TTTAATTATATT
1 TTTAATTATATT
7262 TTTAATTATATT
1 TTTAATTATATT
7274 TTT
1 TTT
7277 GTGGTTAGGA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTAATTATATT
Found at i:13921 original size:60 final size:60
Alignment explanation
Indices: 13827--13985 Score: 171
Period size: 60 Copynumber: 2.7 Consensus size: 60
13817 ATTCTTATTA
* * * *
13827 TAAATTA-TCCCTAAA-TATTTTAATATTCTAATTTTATCCTCAAACTAT-AATACTCATTC
1 TAAATTAGTCCCTAAACT-TTTAAATATTCCAATTTTATCCTCAAAATATGAAT-CCCATTC
* * *
13886 TAAATTAGTCCTTAAACTTTTAAATATTCCAATTTTATCTTCAAAATATGAGTCCCATTC
1 TAAATTAGTCCCTAAACTTTTAAATATTCCAATTTTATCCTCAAAATATGAATCCCATTC
* * * * *
13946 TAAATTGGTCCCCAAACTTTAAAATCTTCCAATTTAATCC
1 TAAATTAGTCCCTAAACTTTTAAATATTCCAATTTTATCC
13986 CTAAATTCAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 7 0.08
60 73 0.88
61 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (60 bp):
TAAATTAGTCCCTAAACTTTTAAATATTCCAATTTTATCCTCAAAATATGAATCCCATTC
Found at i:14342 original size:20 final size:20
Alignment explanation
Indices: 14317--14354 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
14307 TGATGTGATT
14317 CACTCCAAAAGAATTAAATC
1 CACTCCAAAAGAATTAAATC
14337 CACTCCAAAAGAATTAAA
1 CACTCCAAAAGAATTAAA
14355 ATCACGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.24, G:0.05, T:0.18
Consensus pattern (20 bp):
CACTCCAAAAGAATTAAATC
Found at i:23861 original size:125 final size:125
Alignment explanation
Indices: 23639--23889 Score: 466
Period size: 125 Copynumber: 2.0 Consensus size: 125
23629 TAAATCATCT
* * *
23639 TTGTCACTCTTGTGCAACCCGGATGAGCTTCCTTCATTTTCTTCATCAAGATAAGAAACTTCGTA
1 TTGTCACTCTAGTGCAACCCGGATGAGCTACCTTCACTTTCTTCATCAAGATAAGAAACTTCGTA
23704 TTCAGAATCTGATCCTCTCATCGATAAGTTGTCACCTTTTGAGTCATCTTCAGTTTCCGA
66 TTCAGAATCTGATCCTCTCATCGATAAGTTGTCACCTTTTGAGTCATCTTCAGTTTCCGA
*
23764 TTGTCACTCTAGTGCAACCCGGATGAGCTACCTTCACTTTCTTCATCAAGATACGAAACTTCGTA
1 TTGTCACTCTAGTGCAACCCGGATGAGCTACCTTCACTTTCTTCATCAAGATAAGAAACTTCGTA
23829 TTCAGAATCTGATCCTCTCATCGATAAGTTGTCACCTTTTGAGTCATCTTCAGTTTCCGA
66 TTCAGAATCTGATCCTCTCATCGATAAGTTGTCACCTTTTGAGTCATCTTCAGTTTCCGA
23889 T
1 T
23890 AGTTCTTCGT
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 122 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (125 bp):
TTGTCACTCTAGTGCAACCCGGATGAGCTACCTTCACTTTCTTCATCAAGATAAGAAACTTCGTA
TTCAGAATCTGATCCTCTCATCGATAAGTTGTCACCTTTTGAGTCATCTTCAGTTTCCGA
Found at i:24932 original size:40 final size:40
Alignment explanation
Indices: 24888--24964 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
24878 CCGACGTTAT
24888 TCTAGTTTAGACACTGCTAAAGAGGACTATTTCCAATTAG
1 TCTAGTTTAGACACTGCTAAAGAGGACTATTTCCAATTAG
*
24928 TCTAGTTTAGACACTGCTAAAGATGACTATTTCCAAT
1 TCTAGTTTAGACACTGCTAAAGAGGACTATTTCCAAT
24965 ATGTCCTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (40 bp):
TCTAGTTTAGACACTGCTAAAGAGGACTATTTCCAATTAG
Found at i:37655 original size:23 final size:24
Alignment explanation
Indices: 37621--37666 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
37611 TGTAATATGT
37621 TCTATGTCTTTATGACAC-ATTTA
1 TCTATGTCTTTATGACACGATTTA
37644 TCTATG-CATTTATGACACGATTT
1 TCTATGTC-TTTATGACACGATTT
37667 TCTTTGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.05
23 16 0.76
24 4 0.19
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (24 bp):
TCTATGTCTTTATGACACGATTTA
Found at i:38400 original size:17 final size:17
Alignment explanation
Indices: 38378--38413 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
38368 AAAAATTGTG
*
38378 TAAAATCATTTTTATCA
1 TAAAATCATTTTAATCA
38395 TAAAATCATTTTAATCA
1 TAAAATCATTTTAATCA
38412 TA
1 TA
38414 TTTTACAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATCATTTTAATCA
Found at i:39541 original size:30 final size:30
Alignment explanation
Indices: 39505--39564 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
39495 GTTCGAACCA
39505 TAAATTCTTCATTTGATGTAAGGACATTGT
1 TAAATTCTTCATTTGATGTAAGGACATTGT
39535 TAAATTCTTCATTTGATGTAAGGACATTGT
1 TAAATTCTTCATTTGATGTAAGGACATTGT
39565 GGTAGAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (30 bp):
TAAATTCTTCATTTGATGTAAGGACATTGT
Found at i:51620 original size:4 final size:4
Alignment explanation
Indices: 51613--51659 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
51603 CACATACGCA
* * *
51613 TACG TACG TATG TACG TATG TATG TACG TACG TACG TACG TACG TAC
1 TACG TACG TACG TACG TACG TACG TACG TACG TACG TACG TACG TAC
51660 ATTTACAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (4 bp):
TACG
Found at i:51630 original size:12 final size:12
Alignment explanation
Indices: 51613--51658 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
51603 CACATACGCA
51613 TACGTACGTATG
1 TACGTACGTATG
*
51625 TACGTATGTATG
1 TACGTACGTATG
*
51637 TACGTACGTACG
1 TACGTACGTATG
51649 TACGTACGTA
1 TACGTACGTA
51659 CATTTACAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (12 bp):
TACGTACGTATG
Found at i:51731 original size:2 final size:2
Alignment explanation
Indices: 51724--51748 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51714 CATACTAATA
51724 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
51749 CACACGTGTG
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
Done.