Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005348.1 Hibiscus syriacus cultivar Beakdansim tig00012128_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: 47761
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4235 original size:24 final size:24
Alignment explanation
Indices: 4208--4258 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
4198 AACGGATATA
*
4208 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
4232 TCAAGTATCAGATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
4256 TCA
1 TCA
4259 GTATTCGATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.20
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:4291 original size:24 final size:24
Alignment explanation
Indices: 4224--4310 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
4214 ATCAAAACAT
* *
4224 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCCGATCAG
*
4248 AATCCAGGTC-AGTATTCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
4271 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
4295 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
4311 TATAATAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:9317 original size:17 final size:17
Alignment explanation
Indices: 9287--9319 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9277 CATTACCATC
9287 ACTTGTTTTGTTGTCTA
1 ACTTGTTTTGTTGTCTA
9304 ACTT-TTTTGCTTGTCT
1 ACTTGTTTTG-TTGTCT
9320 TCTTCAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.61
Consensus pattern (17 bp):
ACTTGTTTTGTTGTCTA
Found at i:14231 original size:15 final size:16
Alignment explanation
Indices: 14211--14241 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
14201 AAACTTTGAA
14211 AAACATTTTT-CAAAG
1 AAACATTTTTCCAAAG
14226 AAACATTTTTCCAAAG
1 AAACATTTTTCCAAAG
14242 TTGGTTGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (16 bp):
AAACATTTTTCCAAAG
Found at i:18312 original size:16 final size:16
Alignment explanation
Indices: 18288--18320 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18278 TATCGCCGAC
*
18288 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
18304 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
18320 C
1 C
18321 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:18791 original size:15 final size:15
Alignment explanation
Indices: 18771--18800 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18761 AAACTTTGAA
*
18771 AAACATTTTTCAAAG
1 AAACATTTTCCAAAG
18786 AAACATTTTCCAAAG
1 AAACATTTTCCAAAG
18801 TTGGTTGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (15 bp):
AAACATTTTCCAAAG
Found at i:30419 original size:13 final size:13
Alignment explanation
Indices: 30401--30446 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
30391 TTATTTATTT
*
30401 TAAAAAATAAATA
1 TAAAAAATAAAAA
30414 TAAAAAATTAAAAA
1 TAAAAAA-TAAAAA
30428 T-AAAAATAAAAA
1 TAAAAAATAAAAA
30440 TAAAAAA
1 TAAAAAA
30447 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 7 0.23
13 17 0.57
14 6 0.20
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:30438 original size:5 final size:6
Alignment explanation
Indices: 30403--30445 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
30393 ATTTATTTTA
*
30403 AAAAAT AAATAT AAAAAATT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT -AAAAA-T AAAAAT AAAAAT AAAAAT AAAAA
30446 AATAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 23 0.70
7 9 0.27
8 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:30450 original size:20 final size:20
Alignment explanation
Indices: 30401--30446 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
30391 TTATTTATTT
*
30401 TAAAAAATAAATATAAAAAA
1 TAAAAAATAAAAATAAAAAA
*
30421 TTAAAAATAAAAAT-AAAAA
1 TAAAAAATAAAAATAAAAAA
30440 TAAAAAA
1 TAAAAAA
30447 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAAAAATAAAAATAAAAAA
Found at i:30495 original size:16 final size:17
Alignment explanation
Indices: 30469--30500 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
30459 CACAAACTAT
30469 AAAATGATATATTATAA
1 AAAATGATATATTATAA
30486 AAAATG-TATATTATA
1 AAAATGATATATTATA
30501 CATAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAAATGATATATTATAA
Found at i:30511 original size:16 final size:16
Alignment explanation
Indices: 30469--30511 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
30459 CACAAACTAT
30469 AAAATGATATATTATAA
1 AAAAT-ATATATTATAA
* *
30486 AAAATGTATATTATAC
1 AAAATATATATTATAA
*
30502 ATAATATATA
1 AAAATATATA
30512 CATGTAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
AAAATATATATTATAA
Found at i:38090 original size:26 final size:26
Alignment explanation
Indices: 38061--38119 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
38051 GTGAATTTAT
*
38061 AATATTTTAAAAAAAATAAAAATA-AA
1 AATATATTAAAAAAAA-AAAAATATAA
** *
38087 AATATATTATCAATAAAAAAATATAA
1 AATATATTAAAAAAAAAAAAATATAA
38113 AATATAT
1 AATATAT
38120 AATAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AATATATTAAAAAAAAAAAAATATAA
Found at i:38431 original size:20 final size:20
Alignment explanation
Indices: 38406--38458 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
38396 TAGTTCTTGT
38406 AATGTAAGATTACTAGTGAA
1 AATGTAAGATTACTAGTGAA
* * *
38426 AATGTAAGATTATTTGTGAG
1 AATGTAAGATTACTAGTGAA
38446 AATGTAAGATTAC
1 AATGTAAGATTAC
38459 CAGGGAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (20 bp):
AATGTAAGATTACTAGTGAA
Done.