Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002381.1 Hibiscus syriacus cultivar Beakdansim tig00004866_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: 57192
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:329 original size:134 final size:136
Alignment explanation
Indices: 1--370 Score: 546
Period size: 136 Copynumber: 2.7 Consensus size: 136
* * * *
1 GCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGTACTCTGT
1 GCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGT
* * * * * * * *
66 CCCCCTGCCTACTCTCAACGTTGAAGTGCTCGGCGTGATATTATAACACCCTGCCTACTCCACAC
66 CCCCCTTCCAACTCTTAACGTTGAAGCGCTCGGCGTGAAAATAGAACACCCTGCCTACCCCACAC
*
131 GTTAGA
131 GATAGA
* *
137 GCGCCCGGCGTAAGATCAAGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTAT
1 GCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGT
* * *
202 CCCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGTGAAAATAGAATACCCTGCCTACCCCATAC
66 CCCCCTTCCAACTCTTAACGTTGAAGCGCTCGGCGTGAAAATAGAACACCCTGCCTACCCCACAC
267 -ATAG-
131 GATAGA
*
271 GCGCCCGGCGTAAGATCAGGTCATCCGGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGT
1 GCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGT
*
336 CCCCCTTCCAACTCTTAATGTTGAAGCGCTCGGCG
66 CCCCCTTCCAACTCTTAACGTTGAAGCGCTCGGCG
371 AAATTCCTTA
Statistics
Matches: 211, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
134 95 0.45
135 3 0.01
136 113 0.54
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.22
Consensus pattern (136 bp):
GCGCCCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTGT
CCCCCTTCCAACTCTTAACGTTGAAGCGCTCGGCGTGAAAATAGAACACCCTGCCTACCCCACAC
GATAGA
Found at i:6554 original size:21 final size:21
Alignment explanation
Indices: 6530--6569 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6520 GGAACCTTGT
6530 AAAAG-AGGATGAAGAAGAAAG
1 AAAAGAAGG-TGAAGAAGAAAG
*
6551 AAAAGAAGGTGAATAAGAA
1 AAAAGAAGGTGAAGAAGAA
6570 GAACGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (21 bp):
AAAAGAAGGTGAAGAAGAAAG
Found at i:6616 original size:35 final size:35
Alignment explanation
Indices: 6570--6708 Score: 172
Period size: 35 Copynumber: 3.9 Consensus size: 35
6560 TGAATAAGAA
*
6570 GAACGAAAGGAATCATCGACACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
* * * *
6605 GAACGGAAGGAAACATCGGCACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAG-T
*
6641 GAACGAAAGGAAGCATCGTCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
** *
6676 GAACGGGAGGAAGCAT-AAGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGA-CACTTTCGATTCAA
6709 TTGTTCATCT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
35 59 0.66
36 31 0.34
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:6681 original size:71 final size:71
Alignment explanation
Indices: 6565--6708 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 71
6555 GAAGGTGAAT
* **
6565 AAGAAGAACGAAAGGAATCATCGACACTTTCGATTCAAGTGAACGGAAGGAAACATCGGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAACATAAGCACTTT
6630 CGATTC
66 CGATTC
* * *
6636 AAGAAGAACGAAAGGAAGCATCGTCACTTTCGATTCAAGTGAACGGGAGGAAGCATAAGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAACATAAGCACTTT
6701 CGATTC
66 CGATTC
6707 AA
1 AA
6709 TTGTTCATCT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGACACTTTCGATTCAAGTGAACGGAAGGAAACATAAGCACTTT
CGATTC
Found at i:26228 original size:37 final size:38
Alignment explanation
Indices: 26187--26261 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
26177 AATGTGGTTA
* * *
26187 TATTTTGATAAAATAT-TTAATATTATATTTTTATTTT
1 TATTTTGAGAAAATATCTTAATATAATATATTTATTTT
* *
26224 TATTTTGAGAAATTTTCTTAATATAATATATTTATTTT
1 TATTTTGAGAAAATATCTTAATATAATATATTTATTTT
26262 AAGTGTCTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (38 bp):
TATTTTGAGAAAATATCTTAATATAATATATTTATTTT
Found at i:29443 original size:28 final size:28
Alignment explanation
Indices: 29411--29466 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
29401 CAAAACGTAA
29411 AGTTATGTATGATTTTAAAAAAGATAGT
1 AGTTATGTATGATTTTAAAAAAGATAGT
29439 AGTTATGTATGATTTTAAAAAAGATAGT
1 AGTTATGTATGATTTTAAAAAAGATAGT
29467 TGAATAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (28 bp):
AGTTATGTATGATTTTAAAAAAGATAGT
Found at i:30165 original size:47 final size:48
Alignment explanation
Indices: 30069--30166 Score: 144
Period size: 47 Copynumber: 2.0 Consensus size: 48
30059 TGGATAAGAC
30069 TTTCATCCATCAACTTGTTGAGAAAAAAAAATAGGGATATTACTAAATAA
1 TTTCATCCATCAACTTGTTGAG--AAAAAAATAGGGATATTACTAAATAA
** *
30119 TTTCATCCATCAACTTGTTGAG-GTAAAATAGTGATATTACTAAATAA
1 TTTCATCCATCAACTTGTTGAGAAAAAAATAGGGATATTACTAAATAA
30166 T
1 T
30167 CTATTATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 23 0.51
50 22 0.49
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (48 bp):
TTTCATCCATCAACTTGTTGAGAAAAAAATAGGGATATTACTAAATAA
Found at i:34402 original size:13 final size:14
Alignment explanation
Indices: 34384--34413 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
34374 TACCCCGGAT
34384 TAATAATAAA-AAA
1 TAATAATAAAGAAA
34397 TAATAATAAAGAAA
1 TAATAATAAAGAAA
34411 TAA
1 TAA
34414 AACTTGCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
TAATAATAAAGAAA
Found at i:54222 original size:48 final size:48
Alignment explanation
Indices: 54151--54246 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
54141 TATTAATGCT
*
54151 CACCAAGATCATCCCATTTAGGGACGGGCATAGGATTCGTATCTTATG
1 CACCAAGATCATCCCATTTAGGGACGGGCATAGGATTAGTATCTTATG
*
54199 CACCAAGATCATCCCATTTAGGGACGGGTATAGGATTAGTATCTTATG
1 CACCAAGATCATCCCATTTAGGGACGGGCATAGGATTAGTATCTTATG
54247 AGTTTTGATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (48 bp):
CACCAAGATCATCCCATTTAGGGACGGGCATAGGATTAGTATCTTATG
Found at i:54362 original size:34 final size:33
Alignment explanation
Indices: 54314--54425 Score: 136
Period size: 33 Copynumber: 3.4 Consensus size: 33
54304 CTCATTGACC
* *
54314 CGGATCAGACTTTTTTAAAATATTATGTTTAGGT
1 CGGATCAGA-TTTTTTTAAAGATTATGTTTAGGT
*
54348 CGGATCAAATTTTTTTAAAGATTATGTTTAGGT
1 CGGATCAGATTTTTTTAAAGATTATGTTTAGGT
* * *
54381 CGAATCAGATTTTTTTTAAAGATTATATTTGGGT
1 CGGATCAGA-TTTTTTTAAAGATTATGTTTAGGT
*
54415 C-GATAAGATTT
1 CGGATCAGATTT
54426 GAGTTTAGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.04
33 34 0.50
34 31 0.46
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (33 bp):
CGGATCAGATTTTTTTAAAGATTATGTTTAGGT
Found at i:54372 original size:33 final size:34
Alignment explanation
Indices: 54314--54416 Score: 136
Period size: 34 Copynumber: 3.1 Consensus size: 34
54304 CTCATTGACC
* * *
54314 CGGATCAGACTTTTTTAAAATATTATGTTTAGGT
1 CGGATCAGAATTTTTTTAAAGATTATGTTTAGGT
54348 CGGATCA-AATTTTTTTAAAGATTATGTTTAGGT
1 CGGATCAGAATTTTTTTAAAGATTATGTTTAGGT
* * * *
54381 CGAATCAGATTTTTTTTAAAGATTATATTTGGGT
1 CGGATCAGAATTTTTTTAAAGATTATGTTTAGGT
54415 CG
1 CG
54417 ATAAGATTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.48
34 32 0.52
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (34 bp):
CGGATCAGAATTTTTTTAAAGATTATGTTTAGGT
Done.