Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009501.1 Hibiscus syriacus cultivar Beakdansim tig00115052_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: 13916
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Found at i:777 original size:2 final size:2
Alignment explanation
Indices: 770--804 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
760 TATTTCTTGG
770 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 A
805 AGATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2529 original size:37 final size:39
Alignment explanation
Indices: 2488--2561 Score: 100
Period size: 37 Copynumber: 1.9 Consensus size: 39
2478 CATAATTCTA
2488 ATAATATGATA-TTATATCTTTAAT-AT-TATAATGATAT
1 ATAATATGATACTTATAT-TTTAATAATATATAATGATAT
* *
2525 ATAATATTATACTTTTATTTTAATAATATATAATGAT
1 ATAATATGATACTTATATTTTAATAATATATAATGAT
2562 TTTTCAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 16 0.50
38 7 0.22
39 9 0.28
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (39 bp):
ATAATATGATACTTATATTTTAATAATATATAATGATAT
Found at i:2548 original size:29 final size:31
Alignment explanation
Indices: 2486--2558 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
2476 CTCATAATTC
*
2486 TAATAATATGATATTATATCTTTAATATTATAA
1 TAAT-ATATAATATTATATCTTT-ATATTATAA
* *
2519 TGATATATAATATTATA-CTTT-TATTTTAA
1 TAATATATAATATTATATCTTTATATTATAA
2548 TAATATATAAT
1 TAATATATAAT
2559 GATTTTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 17 0.47
31 4 0.11
32 12 0.33
33 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (31 bp):
TAATATATAATATTATATCTTTATATTATAA
Found at i:5529 original size:22 final size:22
Alignment explanation
Indices: 5499--5540 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5489 TTGTCAATCA
*
5499 CTAAGTTGCTAAAGTAAAACAT
1 CTAAATTGCTAAAGTAAAACAT
5521 CTAAATTGCTAAAGTAAAAC
1 CTAAATTGCTAAAGTAAAAC
5541 CTATTATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (22 bp):
CTAAATTGCTAAAGTAAAACAT
Found at i:5647 original size:29 final size:27
Alignment explanation
Indices: 5605--5671 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
5595 ATCATAATTC
*
5605 TAATAATATGATATAAT-CTTTATATTATAA
1 TAAT-ATATAATATAATACTTT-T-TT-TAA
* *
5635 TGATATATAATATTATACTTTTTTTAA
1 TAATATATAATATAATACTTTTTTTAA
5662 TAATATATAA
1 TAATATATAA
5672 GATTTTTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 12 0.38
28 2 0.06
29 11 0.34
30 7 0.22
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (27 bp):
TAATATATAATATAATACTTTTTTTAA
Found at i:6310 original size:140 final size:137
Alignment explanation
Indices: 6060--6337 Score: 468
Period size: 140 Copynumber: 2.0 Consensus size: 137
6050 CCTATGATAG
6060 CTACATTAACACTTTGAACTTCCATCTCCACATTAGAATCACCTTGTAAGTATCGAGCATGGGAC
1 CTACATTAACACTTTGAACTTCCATCTCCACATTAGAATCACCTTGTAAGTATCGAGCATGGGAC
*
6125 ATGATAATATCTTTATTTAAGGGCTAAATTGTGAGTAAAAATGGTTTAGAGACTAAAAATAT-TT
66 ATGATAATATCTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATATATT
6189 TTTTTGA
131 TTTTTGA
* *
6196 CTACATTAACACTTTGAACTTCCATCTCCACATTTAGGATCACCTTGTAAGTATCGAGCAATGGT
1 CTACATTAACACTTTGAACTTCCATCTCCACA-TTAGAATCACCTTGTAAGTATCGAGC-ATGGG
*
6261 ACATGATAATTATATTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATA
64 ACATGATAA-TAT-CTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATA
6326 TAATTTTTTTGA
127 T-ATTTTTTTGA
6338 ATTGTTAGAG
Statistics
Matches: 132, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
136 32 0.24
137 25 0.19
138 13 0.10
139 3 0.02
140 50 0.38
142 9 0.07
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (137 bp):
CTACATTAACACTTTGAACTTCCATCTCCACATTAGAATCACCTTGTAAGTATCGAGCATGGGAC
ATGATAATATCTTTATTTAAGGGCTAAATTGTGAGCAAAAATGGTTTAGAGACTAAAAATATATT
TTTTTGA
Found at i:12643 original size:121 final size:126
Alignment explanation
Indices: 12397--12645 Score: 361
Period size: 130 Copynumber: 2.0 Consensus size: 126
12387 TAGCTACATT
12397 AACACTTTGAACTTCCATCTCCACATTTAGGATCACTTGTAAGTATCGAGCAATGGGACATGATA
1 AACACTTTGAACTTCCATCT---CATTTAGGATCACTTGTAAGTATCGAGCAATGGGACAT-ATA
*
12462 ATTATATTTTATTTAAGGGCTAAATGTGAGTAAAAATGGTTTAGAGACTAAAAATATTTTTTTGA
62 ATTATATTTTA-TTAAGGGCTAAA--TGAGCAAAAATGGTTTAGAGACTAAAAATATTTTTTTGA
12527 CTA
124 CTA
12530 AACACTTTGAACTTCCATCT-ATTTAGGATCACCTTGTAAGTATCGAGCAATGGGACAT-TAA-T
1 AACACTTTGAACTTCCATCTCATTTAGGATCA-CTTGTAAGTATCGAGCAATGGGACATATAATT
12592 ATATTTTA-T-AGGGCTAAA-GAGCAAAAATGGTTTAGAGACT--AAATATTTTTTTGA
65 ATATTTTATTAAGGGCTAAATGAGCAAAAATGGTTTAGAGACTAAAAATATTTTTTTGA
12646 ATTGTTAGAG
Statistics
Matches: 114, Mismatches: 1, Indels: 16
0.87 0.01 0.12
Matches are distributed among these distances:
119 14 0.12
121 21 0.18
124 9 0.08
125 1 0.01
127 9 0.08
128 3 0.03
129 11 0.10
130 26 0.23
133 20 0.18
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (126 bp):
AACACTTTGAACTTCCATCTCATTTAGGATCACTTGTAAGTATCGAGCAATGGGACATATAATTA
TATTTTATTAAGGGCTAAATGAGCAAAAATGGTTTAGAGACTAAAAATATTTTTTTGACTA
Done.