Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004074.1 Hibiscus syriacus cultivar Beakdansim tig00008919_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: 59977
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:263 original size:6 final size:6
Alignment explanation
Indices: 234--429 Score: 247
Period size: 6 Copynumber: 32.7 Consensus size: 6
224 GAAGAAGAGA
234 AGAAGAG AGAAGG AAGAGAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAG-G AGAAGG -AGA-AGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
285 AGAAGG AGAAGG AGAAGG AGAAGGG AGAAGG AGAAGG AG-AGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAA-GG AGAAGG AGAAGG AGAAGG AGAAGG
*
333 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AG-A-- AGAAGG AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * * * * * * *
378 AGGAGA AGAAGG AGAAGA AGGAGA AGAAGG AGAAGA AGAAGA AGAAGA
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
426 AGAA
1 AGAA
430 TTTTTTTAAT
Statistics
Matches: 173, Mismatches: 9, Indels: 15
0.88 0.05 0.08
Matches are distributed among these distances:
3 2 0.01
4 1 0.01
5 6 0.03
6 144 0.83
7 17 0.10
8 3 0.02
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:7244 original size:24 final size:24
Alignment explanation
Indices: 7216--7268 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
7206 TTGGATACTC
7216 AGCAGGTAAGTTCTGAAGGCTCAG
1 AGCAGGTAAGTTCTGAAGGCTCAG
7240 AGCAGGTAAGTTCTGAAGGCTCAG
1 AGCAGGTAAGTTCTGAAGGCTCAG
7264 AGCAG
1 AGCAG
7269 TTATCTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.34, T:0.19
Consensus pattern (24 bp):
AGCAGGTAAGTTCTGAAGGCTCAG
Found at i:15324 original size:19 final size:19
Alignment explanation
Indices: 15300--15336 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15290 AAAATCAAAG
15300 CAACA-TAATGGGGCGGCTT
1 CAACATTAAT-GGGCGGCTT
15319 CAACATTAATGGGCGGCT
1 CAACATTAATGGGCGGCT
15337 AATTTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (19 bp):
CAACATTAATGGGCGGCTT
Found at i:28963 original size:31 final size:31
Alignment explanation
Indices: 28925--29080 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
28915 CCCGAAGGAC
* *
28925 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
28956 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
28987 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
29018 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
29049 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
29080 C
1 C
29081 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:29506 original size:16 final size:18
Alignment explanation
Indices: 29485--29525 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29475 GCATGTTAAC
29485 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
29501 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
29519 TCATATA
1 ACATATA
29526 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:29909 original size:21 final size:21
Alignment explanation
Indices: 29879--29923 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29869 ATTCTGTCGT
* *
29879 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
29900 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
29921 TTG
1 TTG
29924 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:33006 original size:31 final size:31
Alignment explanation
Indices: 32971--33112 Score: 205
Period size: 31 Copynumber: 4.6 Consensus size: 31
32961 TCTATAGATT
* *
32971 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* ** *
33002 CCGAAGGACATAGGTAAACAGTCTGTATGTT
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
33033 CCGAAGAACATAGGTAAACAGTCCGTATGTT
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
33064 CCGAAGAACATAGGT-AACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
33094 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
33113 CCTCGACCCT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
30 28 0.28
31 72 0.72
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:33943 original size:21 final size:21
Alignment explanation
Indices: 33913--33957 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33903 ATTCTGTCGT
* *
33913 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
33934 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
33955 TTG
1 TTG
33958 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39982 original size:12 final size:12
Alignment explanation
Indices: 39965--39989 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39955 GTCAAATAAT
39965 TTAGGCACCAAA
1 TTAGGCACCAAA
39977 TTAGGCACCAAA
1 TTAGGCACCAAA
39989 T
1 T
39990 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:42231 original size:29 final size:29
Alignment explanation
Indices: 42197--42255 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42187 CCTAAATTAA
42197 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
42226 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
42255 T
1 T
42256 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:54610 original size:15 final size:17
Alignment explanation
Indices: 54579--54611 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
54569 ATGTATTTTT
54579 ATCTATCTTACAATTTA
1 ATCTATCTTACAATTTA
54596 ATCTA-CTTA-AATTTA
1 ATCTATCTTACAATTTA
54611 A
1 A
54612 AAAAAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (17 bp):
ATCTATCTTACAATTTA
Found at i:58087 original size:18 final size:18
Alignment explanation
Indices: 58064--58112 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
58054 TCATAAGGAA
58064 TTTTTTATGATTTATATT
1 TTTTTTATGATTTATATT
*
58082 TTTTTTATGTTTTATATT
1 TTTTTTATGATTTATATT
*
58100 TGTTTGTATGATT
1 T-TTTTTATGATT
58113 GTTTCTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.71
Consensus pattern (18 bp):
TTTTTTATGATTTATATT
Found at i:58493 original size:30 final size:30
Alignment explanation
Indices: 58457--58515 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
58447 TTTAATTTGA
58457 AATTTAGTCACCTAATTTTGAAGAATTATC
1 AATTTAGTCACCTAATTTTGAAGAATTATC
58487 AATTTAGTCACCTAATTTTGAAGAATTAT
1 AATTTAGTCACCTAATTTTGAAGAATTAT
58516 TTAAAGTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (30 bp):
AATTTAGTCACCTAATTTTGAAGAATTATC
Found at i:58889 original size:181 final size:179
Alignment explanation
Indices: 58517--58875 Score: 517
Period size: 181 Copynumber: 2.0 Consensus size: 179
58507 AAGAATTATT
* *
58517 TAAAGTATCGACA-CTTTTCAGGCGCTATAACTTCTTCTCTTTAAATTACAAAGTGTCGATACTA
1 TAAAGTATCGACACCTTTTCAGACGCTATAACTTCTTCTCTTTAAATTACAAAGTGTCGACACTA
** * ** * *
58581 TATTAATTTATCGACACTTTCAATATATCCGGTAGCTTTTTACTGATTTATCATTTCGAGACCTG
66 TATTAATTTATCGACACTTTCAATATATCCGGTAGCGCTTTACGGATTTATCATTAAGACACCGG
*
58646 TTTTGTCATATTATTACCTGTTATATTGCTATGAATCGATACATTTTTA
131 TTTTATCATATTATTACCTGTTATATTGCTATGAATCGATACATTTTTA
58695 TAAAGTATCGACACCTTTT-AGACGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGACAC
1 TAAAGTATCGACACCTTTTCAGACGCTATAACTTCTTCTC-TTTAAATTAC-AAAGTGTCGACAC
*
58759 TTATATTAATTTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCA-TAAGACA
64 -TATATTAATTTATCGACACTTTCAATATATCCGGTAGCGCTTTA-CGGATTTATCATTAAGACA
* * * * *
58823 TCGGTTTTATCATATTTTTACTTGTTATGTTGCTATGGATCGATACATTTTTA
127 CCGGTTTTATCATATTATTACCTGTTATATTGCTATGAATCGATACATTTTTA
58876 ATTTGTATCG
Statistics
Matches: 160, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
178 32 0.20
179 15 0.09
180 12 0.08
181 92 0.57
182 9 0.06
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (179 bp):
TAAAGTATCGACACCTTTTCAGACGCTATAACTTCTTCTCTTTAAATTACAAAGTGTCGACACTA
TATTAATTTATCGACACTTTCAATATATCCGGTAGCGCTTTACGGATTTATCATTAAGACACCGG
TTTTATCATATTATTACCTGTTATATTGCTATGAATCGATACATTTTTA
Done.