Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007783.1 Hibiscus syriacus cultivar Beakdansim tig00110067_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: 35085
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:2248 original size:24 final size:21
Alignment explanation
Indices: 2214--2256 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 21
2204 TCCACAAGAC
2214 ATGTCCTTTGAAATTTCAAAGG
1 ATGTCCTTTGAAA-TTCAAAGG
2236 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
2257 AGAATGTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:2258 original size:24 final size:22
Alignment explanation
Indices: 2209--2263 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
2199 GGTGATCCAC
2209 AAGACATGTCCTTTGAAATTTCA
1 AAGA-ATGTCCTTTGAAATTTCA
*
2232 AAGGATGTACCTCTTGAAA-TTCAA
1 AAGAATGT-CCT-TTGAAATTTC-A
2256 AAGAATGT
1 AAGAATGT
2264 TCCAATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 9 0.33
24 14 0.52
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (22 bp):
AAGAATGTCCTTTGAAATTTCA
Found at i:7358 original size:90 final size:90
Alignment explanation
Indices: 7205--7382 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
7195 GACTAACACA
* * **
7205 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTAATATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGAATTTTAATATTTCAAATTAATTAAATCTAT
* *
7270 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
7295 CCTTTTATATCCAAGTTACCCTAATCATATCAGGAATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGAATTTTAATATTTCAAATTAATTAAATCTAT
7360 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
7383 TTCGAGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGAATTTTAATATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:12243 original size:27 final size:28
Alignment explanation
Indices: 12191--12255 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
12181 AAAAAAAATC
*
12191 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
12219 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
12246 AGAAAAGAAA
1 AGAAAAGAAA
12256 AGAAAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:12275 original size:4 final size:5
Alignment explanation
Indices: 12245--12274 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
12235 ATTCAAAAAG
12245 AAGAA AAGAA AAGAA AAGAA AAG-A AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
12275 GTTGAAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:14348 original size:13 final size:15
Alignment explanation
Indices: 14324--14355 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
14314 CAAGTGAAGA
14324 AAAACTAAAGAAAT-
1 AAAACTAAAGAAATG
14338 AAAAC-AAAGAAATG
1 AAAACTAAAGAAATG
14352 AAAA
1 AAAA
14356 TGCAAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.75, C:0.06, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAACTAAAGAAATG
Found at i:26575 original size:14 final size:13
Alignment explanation
Indices: 26549--26578 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
26539 ACTCAAAAAG
26549 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
26562 AAGAAAAGAAAGAA
1 AAGAAAA-AAAGAA
26576 AAG
1 AAG
26579 TTGGAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:29330 original size:11 final size:13
Alignment explanation
Indices: 29298--29327 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29288 TGGCCAAAGA
29298 TGAAAAGGTATGT
1 TGAAAAGGTATGT
29311 TGAAAAGGTATG-
1 TGAAAAGGTATGT
29323 TGAAA
1 TGAAA
29328 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:33857 original size:33 final size:33
Alignment explanation
Indices: 33813--33881 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
33803 CATCACCATA
*
33813 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
33846 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
33879 TTC
1 TTC
33882 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Done.