Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006170.1 Hibiscus syriacus cultivar Beakdansim tig00014657_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: 53357
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4633 original size:2 final size:2
Alignment explanation
Indices: 4626--4661 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4616 ATACATTAGA
4626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4662 CATTTTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7158 original size:19 final size:20
Alignment explanation
Indices: 7134--7173 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7124 TTAATTTAAA
*
7134 TATTTTAAG-AATTATCTTT
1 TATTTTAAGAAATTATATTT
*
7153 TATTTTTAGAAATTATATTT
1 TATTTTAAGAAATTATATTT
7173 T
1 T
7174 CCTTGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (20 bp):
TATTTTAAGAAATTATATTT
Found at i:7984 original size:26 final size:26
Alignment explanation
Indices: 7954--8003 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
7944 TCCTTATCTT
7954 TTATTGCATCCTTATCTTTTATTTAA
1 TTATTGCATCCTTATCTTTTATTTAA
** *
7980 TTATTTTATCTTTATCTTTTATTT
1 TTATTGCATCCTTATCTTTTATTT
8004 TATTCTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (26 bp):
TTATTGCATCCTTATCTTTTATTTAA
Found at i:7989 original size:44 final size:43
Alignment explanation
Indices: 7928--8021 Score: 125
Period size: 44 Copynumber: 2.2 Consensus size: 43
7918 TTACTTTGAA
* *
7928 TTTATTTATTTTTTTATCCTTATCTTTTATTGCATCCTTATCT
1 TTTATTTATTATTTTATCCTTATCTTTTATTGCATCCTAATCT
* ** *
7971 TTTATTTAATTATTTTATCTTTATCTTTTATTTTATTCTAATCT
1 TTTATTT-ATTATTTTATCCTTATCTTTTATTGCATCCTAATCT
8015 TTTATTT
1 TTTATTT
8022 TAAAAACAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 7 0.16
44 37 0.84
ACGTcount: A:0.19, C:0.12, G:0.01, T:0.68
Consensus pattern (43 bp):
TTTATTTATTATTTTATCCTTATCTTTTATTGCATCCTAATCT
Found at i:8003 original size:18 final size:18
Alignment explanation
Indices: 7980--8023 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
7970 TTTTATTTAA
*
7980 TTATTTTA-TCTTTATCTT
1 TTATTTTATTC-TAATCTT
7998 TTATTTTATTCTAATCTT
1 TTATTTTATTCTAATCTT
8016 TTATTTTA
1 TTATTTTA
8024 AAAACAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTTATTCTAATCTT
Found at i:9881 original size:11 final size:11
Alignment explanation
Indices: 9865--9891 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9855 GTCCAACACC
9865 AACTCCTATGA
1 AACTCCTATGA
9876 AACTCCTATGA
1 AACTCCTATGA
9887 AACTC
1 AACTC
9892 TGCCACCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (11 bp):
AACTCCTATGA
Found at i:11036 original size:11 final size:12
Alignment explanation
Indices: 11016--11040 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11006 TCGATGGACC
11016 AAAATAAAAAAA
1 AAAATAAAAAAA
11028 AAAATAAAAAAA
1 AAAATAAAAAAA
11040 A
1 A
11041 CGTGGGATCA
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAATAAAAAAA
Found at i:13511 original size:2 final size:2
Alignment explanation
Indices: 13504--13533 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13494 CTAACTAGTA
13504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13534 GAAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22438 original size:19 final size:19
Alignment explanation
Indices: 22413--22457 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
22403 ATATACATGG
22413 ATAAAATACAATGCGAAAA
1 ATAAAATACAATGCGAAAA
* *
22432 GTAAAATACAGTGCGAAAA
1 ATAAAATACAATGCGAAAA
22451 ATAAAAT
1 ATAAAAT
22458 GCAAATGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.18
Consensus pattern (19 bp):
ATAAAATACAATGCGAAAA
Found at i:24866 original size:2 final size:2
Alignment explanation
Indices: 24859--24897 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24849 CTTTAAACTT
24859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24898 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24902 original size:2 final size:2
Alignment explanation
Indices: 24897--24931 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24887 TATATATATA
24897 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
24932 ATGTATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:30007 original size:2 final size:2
Alignment explanation
Indices: 30000--30077 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
29990 TCAATCTACA
30000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30078 TTACGAAATA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30252 original size:13 final size:13
Alignment explanation
Indices: 30231--30269 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
30221 AATGACGCGC
*
30231 AATGAATGTCATA
1 AATGCATGTCATA
30244 AATGCATGTCATA
1 AATGCATGTCATA
*
30257 AATGCGTGTCATA
1 AATGCATGTCATA
30270 GATTTATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (13 bp):
AATGCATGTCATA
Found at i:30255 original size:84 final size:85
Alignment explanation
Indices: 30095--30259 Score: 260
Period size: 84 Copynumber: 2.0 Consensus size: 85
30085 ATACAATCAC
* * *
30095 GACACACGAATATGTGTCATCTTCATTTATGACGGGGACTTCAATGACACGCAATGTATGTTATA
1 GACACACAAATATGTGTCATCTTCATTTATGACGGGGACTTCAATGACACGCAATGAATGTCATA
*
30160 AATGCGTGTCATAAATTTAT
66 AATGCATGTCATAAATTTAT
* * *
30180 GACACACAAATGTGTGTCATCTTCATTTATGAC-GGGTCTTCAATGACGCGCAATGAATGTCATA
1 GACACACAAATATGTGTCATCTTCATTTATGACGGGGACTTCAATGACACGCAATGAATGTCATA
30244 AATGCATGTCATAAAT
66 AATGCATGTCATAAAT
30260 GCGTGTCATA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 42 0.58
85 31 0.42
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (85 bp):
GACACACAAATATGTGTCATCTTCATTTATGACGGGGACTTCAATGACACGCAATGAATGTCATA
AATGCATGTCATAAATTTAT
Found at i:33962 original size:436 final size:436
Alignment explanation
Indices: 33150--34021 Score: 1726
Period size: 436 Copynumber: 2.0 Consensus size: 436
33140 GTTTTGAGAG
33150 GTAACAAATGTAACAGATATTGTACATTTTTTATCCAGTGGAATTTTCTTCTCCTCTGCCCGTAA
1 GTAACAAATGTAACAGATATTGTACATTTTTTATCCAGTGGAATTTTCTTCTCCTCTGCCCGTAA
33215 TTCTTCTCTTTTGGATTTTTCAGGTAAATATTGATGTTTTATTTTTCTGTTCGATTGTATTCATT
66 TTCTTCTCTTTTGGATTTTTCAGGTAAATATTGATGTTTTATTTTTCTGTTCGATTGTATTCATT
33280 TGTCATTACTGTTTCGATAATTATAACATACAAGACATCTTTAGAAAAGAAAGAAGGAAGCTCTT
131 TGTCATTACTGTTTCGATAATTATAACATACAAGACATCTTTAGAAAAGAAAGAAGGAAGCTCTT
33345 GGACTGGAGTACAATCCTTCACAACACCTTTTAGCCAAGAGAATGGAAACACCAGGGTAGAGAAA
196 GGACTGGAGTACAATCCTTCACAACACCTTTTAGCCAAGAGAATGGAAACACCAGGGTAGAGAAA
33410 GGACTTGTGCTTGACTGGAATTCTTGTTTCTATCATTTGCTTTACAATACGCTCAATCTCATATT
261 GGACTTGTGCTTGACTGGAATTCTTGTTTCTATCATTTGCTTTACAATACGCTCAATCTCATATT
33475 TCTGGTAACGAAGATAATGATACGAGTGAATATTAGTAGACTGAGATCTTTCCTTGAGTCGGATA
326 TCTGGTAACGAAGATAATGATACGAGTGAATATTAGTAGACTGAGATCTTTCCTTGAGTCGGATA
33540 GGGTTATAGTTATTGGAACGATTAATAGAAATTTAATATGATCGAA
391 GGGTTATAGTTATTGGAACGATTAATAGAAATTTAATATGATCGAA
33586 GTAACAAATGTAACAGATATTGTACATTTTTTATCCAGTGGAATTTTCTTCTCCTCTGCCCGTAA
1 GTAACAAATGTAACAGATATTGTACATTTTTTATCCAGTGGAATTTTCTTCTCCTCTGCCCGTAA
33651 TTCTTCTCTTTTGGATTTTTCAGGTAAATATTGATGTTTTATTTTTCTGTTCGATTGTATTCATT
66 TTCTTCTCTTTTGGATTTTTCAGGTAAATATTGATGTTTTATTTTTCTGTTCGATTGTATTCATT
33716 TGTCATTACTGTTTCGATAATTATAACATACAAGACATCTTTAGAAAAGAAAGAAGGAAGCTCTT
131 TGTCATTACTGTTTCGATAATTATAACATACAAGACATCTTTAGAAAAGAAAGAAGGAAGCTCTT
*
33781 GGACTGGAGTAGAATCCTTCACAACACCTTTTAGCCAAGAGAATGGAAACACCAGGGTAGAGAAA
196 GGACTGGAGTACAATCCTTCACAACACCTTTTAGCCAAGAGAATGGAAACACCAGGGTAGAGAAA
33846 GGACTTGTGCTTGACTGGAATTCTTGTTTCTATCATTTGCTTTACAATACGCTCAATCTCATATT
261 GGACTTGTGCTTGACTGGAATTCTTGTTTCTATCATTTGCTTTACAATACGCTCAATCTCATATT
33911 TCTGGTAACGAAGATAATGATACGAGTGAATATTAGTAGACTGAGATCTTTCCTTGAGTCGGATA
326 TCTGGTAACGAAGATAATGATACGAGTGAATATTAGTAGACTGAGATCTTTCCTTGAGTCGGATA
*
33976 GTGTTATAGTTATTGGAACGATTAATAGAAATTTAATATGATCGAA
391 GGGTTATAGTTATTGGAACGATTAATAGAAATTTAATATGATCGAA
34022 CAGAAAAATA
Statistics
Matches: 434, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
436 434 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (436 bp):
GTAACAAATGTAACAGATATTGTACATTTTTTATCCAGTGGAATTTTCTTCTCCTCTGCCCGTAA
TTCTTCTCTTTTGGATTTTTCAGGTAAATATTGATGTTTTATTTTTCTGTTCGATTGTATTCATT
TGTCATTACTGTTTCGATAATTATAACATACAAGACATCTTTAGAAAAGAAAGAAGGAAGCTCTT
GGACTGGAGTACAATCCTTCACAACACCTTTTAGCCAAGAGAATGGAAACACCAGGGTAGAGAAA
GGACTTGTGCTTGACTGGAATTCTTGTTTCTATCATTTGCTTTACAATACGCTCAATCTCATATT
TCTGGTAACGAAGATAATGATACGAGTGAATATTAGTAGACTGAGATCTTTCCTTGAGTCGGATA
GGGTTATAGTTATTGGAACGATTAATAGAAATTTAATATGATCGAA
Found at i:53190 original size:128 final size:134
Alignment explanation
Indices: 52760--53323 Score: 372
Period size: 131 Copynumber: 4.3 Consensus size: 134
52750 TATGGGAATG
* * ** ** * * *
52760 TTGATTCATTGCACTATTC-TCAGGGAAGATTGAATTGAGG-GGACTTGTTTCAATGTTCCTCGG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCAAGGAACACTTGTTTCACTATTCCTC-A
** * * * * * * *
52823 GGAAGATCAAATGGGAAAACAGAAAAGAAGGACATGTTCCGCTGCTTCTTGAG-GGAAAATCAGA
65 GGAAGATCAAATCTG--AA-A-AAAAGATGGA-TTGTTCTGCTACTTATTGAGAGAAAAACCAGA
* *
52887 TCTGGAAATG
125 TCTAGAAATA
* * * * * *
52897 TTGATTCATTCCACTATTCTAT-AGAGAAGATTGAATCAAGGCATACTTGTTCCA-TATTACTCA
1 TTGATTCATTCCACTGTTCT-TCAGGGAAGATTGAATCAAGGAACACTTGTTTCACTATTCCTCA
* * * * ** * * * **
52960 GGGATATTAAATATGAATGATAG--GGATTTGTT-TCGCTTCTTATTGAG-GTAAATTCAGATCT
65 GGAAGATCAAATCTGAAAAAAAGATGGA-TTGTTCT-GCTACTTATTGAGAGAAAAACCAGATCT
* ** *
53021 GGGGACA
128 AGAAATA
*
53028 TTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCAAGGAACACTTG-TTC-C-ATTCCTC-G
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCAAGGAACACTTGTTTCACTATTCCTCAG
* * * *
53089 TAGAAGATCAAAT-TGGAGAAAAGATGGATTTGTT-TGCTACTT-TTTAG-G-AAAATCAGATCT
66 --GAAGATCAAATCTGAAAAAAAGATGGA-TTGTTCTGCTACTTATTGAGAGAAAAACCAGATCT
53149 AGAAATA
128 AGAAATA
* * * * * * *
53156 TTGATTCATTTCAGTGTTCTTCAAGGAAGATTGAATCTAGGCAGACTTGTTTCACTGTTCCTCAG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCAAGGAACACTTGTTTCACTATTCCTCAG
* * *
53221 GAATATCAAATCTGAAAAAAAGATGGATTGTTCTGCTGCTTATTGAGAGAAAAACCAGATCTGGA
66 GAAGATCAAATCTGAAAAAAAGATGGATTGTTCTGCTACTTATTGAGAGAAAAACCAGATCTAGA
*
53286 AATG
131 AATA
*
53290 TTGATTCATTCCACTGCTCTTCAGGGAAGATTGA
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGA
53324 TTCGAGGAGA
Statistics
Matches: 340, Mismatches: 68, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
128 57 0.17
129 20 0.06
130 33 0.10
131 113 0.33
132 5 0.01
133 4 0.01
134 46 0.14
135 2 0.01
137 28 0.08
138 22 0.06
139 10 0.03
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (134 bp):
TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCAAGGAACACTTGTTTCACTATTCCTCAG
GAAGATCAAATCTGAAAAAAAGATGGATTGTTCTGCTACTTATTGAGAGAAAAACCAGATCTAGA
AATA
Done.