Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000594.1 Hibiscus syriacus cultivar Beakdansim tig00001150_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: 61543
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3176 original size:17 final size:17
Alignment explanation
Indices: 3132--3177 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
3122 TCATAGGTAT
*
3132 TAAATGTTACAAGTTAC
1 TAAATGTTACAAGCTAC
*
3149 TAAACGTTACAAGCTAC
1 TAAATGTTACAAGCTAC
*
3166 TAAATGGTACAA
1 TAAATGTTACAA
3178 ACGTTTGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (17 bp):
TAAATGTTACAAGCTAC
Found at i:12210 original size:72 final size:70
Alignment explanation
Indices: 12088--12347 Score: 257
Period size: 72 Copynumber: 3.8 Consensus size: 70
12078 ATCACTTGGC
12088 AAATACAAACAATGGGAGTAGTTATGATGGCAGCTCACATGGGGTCTAAGAAGAAAATTATGATG
1 AAATACAAACAATGGGAGTAGTTATGATGGCAGCTCACATGGGGTCTAAGAAGAAAATTATGATG
12153 GTGCGGA
66 GT-C-GA
* * * * * * *
12160 AAATACAAACAATGAGAGTAGTTGTGATGGCAGCTTACATGGGGTATAAG-AGAGAATCACGA--
1 AAATACAAACAATGGGAGTAGTTATGATGGCAGCTCACATGGGGTCTAAGAAGAAAATTATGATG
12222 -T-G-
66 GTCGA
* * * * * *
12224 ATA-ACAATC-ATGGGAGTTGTTGTGATGGCAGCTCATATGGGGTCCAAGAAGAAAATTATGATG
1 AAATACAAACAATGGGAGTAGTTATGATGGCAGCTCACATGGGGTCTAAGAAGAAAATTATGATG
12287 GTACGA
66 GT-CGA
* * * ** *
12293 CAAATACAAAAAATGGGAGTAGTTATGATGACAACTCACATAAGGTCCAAGAAGA
1 -AAATACAAACAATGGGAGTAGTTATGATGGCAGCTCACATGGGGTCTAAGAAGA
12348 GAATCACGAT
Statistics
Matches: 150, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
62 33 0.22
63 14 0.09
64 2 0.01
65 1 0.01
66 1 0.01
68 2 0.01
70 2 0.01
71 13 0.09
72 82 0.55
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (70 bp):
AAATACAAACAATGGGAGTAGTTATGATGGCAGCTCACATGGGGTCTAAGAAGAAAATTATGATG
GTCGA
Found at i:17896 original size:15 final size:15
Alignment explanation
Indices: 17855--17897 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
17845 TTAGTACCTC
*
17855 TGAATGATTCAATGT
1 TGAATGATTCAGTGT
17870 TGAATGATTCAGTGT
1 TGAATGATTCAGTGT
*
17885 TGACTGATTCAGT
1 TGAATGATTCAGT
17898 AAAACAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (15 bp):
TGAATGATTCAGTGT
Found at i:17948 original size:27 final size:27
Alignment explanation
Indices: 17910--17972 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
17900 AACAATGCTG
*
17910 AATGATTCAACACAGAAGTATATTCTC
1 AATGATTCAACACAGAAGTACATTCTC
*
17937 AATGATTCAACACAGAAGTACATTCTG
1 AATGATTCAACACAGAAGTACATTCTC
17964 AATGATTCA
1 AATGATTCA
17973 GAATCATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (27 bp):
AATGATTCAACACAGAAGTACATTCTC
Found at i:30142 original size:23 final size:23
Alignment explanation
Indices: 30116--30202 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
30106 CAACTCATAT
**
30116 AATTACACCTAAGTGCCACGTAG
1 AATTACACCGGAGTGCCACGTAG
* *
30139 AATTACACCGGAGTACCGCGTAG
1 AATTACACCGGAGTGCCACGTAG
* *
30162 AATTGCACCGGAGTGCCACTTAG
1 AATTACACCGGAGTGCCACGTAG
*
30185 AATTGCACCGGAGTGCCA
1 AATTACACCGGAGTGCCA
30203 TATAATAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
AATTACACCGGAGTGCCACGTAG
Found at i:30389 original size:103 final size:103
Alignment explanation
Indices: 30224--30435 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
30214 CCATAAGGAA
*
30224 CACATATAATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCAGACCTC
1 CACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
*
30289 ACACATGTTCCAAAGAATACATATATGTCTCGAA-GAAC
66 ACACATGTTCCAAAGAATACATATATGTCCCGAATG-AC
*
30327 CACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
1 CACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
30392 ACACATGTTCCAAAGAATACATATATGTCCCGAATGAC
66 ACACATGTTCCAAAGAATACATATATGTCCCGAATGAC
30430 CACATA
1 CACATA
30436 GACCCTCTAC
Statistics
Matches: 105, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 104 0.99
104 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
CACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
ACACATGTTCCAAAGAATACATATATGTCCCGAATGAC
Found at i:30993 original size:64 final size:67
Alignment explanation
Indices: 30884--31011 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 67
30874 ATTTTCATCT
30884 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
30949 TA
66 TA
* * *
30951 TTTAATGG-GG-ATGCCTCGATGCACT-C-CTTATGTATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTT
31012 TCTTTTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 1 0.02
64 32 0.56
65 14 0.25
66 2 0.04
67 8 0.14
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
TA
Found at i:31034 original size:64 final size:64
Alignment explanation
Indices: 30896--31038 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
30886 TAATGGAGGT
* *
30896 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * * *
30961 ATGCCTCGATGCACT-C-CTTATGTATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATG
*
31023 TA
63 GA
31025 ATGCATCGATGCAC
1 ATGCATCGATGCAC
31039 ATTAAACAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
63 1 0.01
64 42 0.63
65 21 0.31
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:37170 original size:23 final size:23
Alignment explanation
Indices: 37144--37207 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
37134 CAGCTCATAT
*
37144 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * **
37167 AATTGCATCGGAGTGCCGTGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
37190 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
37208 TATAATAATG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:37339 original size:103 final size:103
Alignment explanation
Indices: 37215--37440 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
37205 CCATATAATA
* *
37215 ATGT-CCATAAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGT
*
37279 GTCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACATCACACATGTTCCAAAGAATACATAT
*
37318 ATGTCCCAAAGGACCATATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
37383 TCTCACCAGACATCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACATCACACATGTTCCAAAGAATACATAT
*
37421 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
37441 GACCCTCTAC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
103 113 0.97
104 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
TCTCACCAGACATCACACATGTTCCAAAGAATACATAT
Found at i:38033 original size:64 final size:63
Alignment explanation
Indices: 37900--38060 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
37890 TAATAGAGGT
* * * * *
37900 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATTGATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
37965 ATGCATTGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATTGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
38029 ATGCATTGATGCACTGCATGTGCATCGATGCA
1 ATGCATTGATGCACTCCATATGCATCGATGCA
38061 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 58 0.70
65 22 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (63 bp):
ATGCATTGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Done.