Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009421.1 Hibiscus syriacus cultivar Beakdansim tig00113394_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: 48393
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:479 original size:24 final size:24
Alignment explanation
Indices: 447--496 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
437 AAAACCAAGC
447 CATTAACCAGCTGCGTATCATCCA
1 CATTAACCAGCTGCGTATCATCCA
471 CATTAACCAGCTGCGTATCATCCA
1 CATTAACCAGCTGCGTATCATCCA
495 CA
1 CA
497 GTTCCCCCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (24 bp):
CATTAACCAGCTGCGTATCATCCA
Found at i:843 original size:22 final size:22
Alignment explanation
Indices: 818--864 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
808 ATTAAGCTTA
818 AAAAAAAAAAAGTTTAGGTACT
1 AAAAAAAAAAAGTTTAGGTACT
*** *
840 AAAAACGGATAGTTTAGGTACT
1 AAAAAAAAAAAGTTTAGGTACT
862 AAA
1 AAA
865 CGTATTAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.23
Consensus pattern (22 bp):
AAAAAAAAAAAGTTTAGGTACT
Found at i:12581 original size:27 final size:27
Alignment explanation
Indices: 12524--12600 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 27
12514 AATAAGCTAC
* *
12524 AAAAGAAAAACATAAAATTAAGGGATT
1 AAAATAAAAACATAAAATTAAAGGATT
*
12551 -AAATAAAAA-ATAAAATTTAAAGTATT
1 AAAATAAAAACATAAAA-TTAAAGGATT
* *
12577 AAAATAGCGAAACAGAAAATTAAA
1 AAAATA--AAAACATAAAATTAAA
12601 ATACCAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
25 6 0.15
26 16 0.40
27 5 0.12
29 8 0.20
30 5 0.12
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.21
Consensus pattern (27 bp):
AAAATAAAAACATAAAATTAAAGGATT
Found at i:14417 original size:151 final size:152
Alignment explanation
Indices: 14138--14440 Score: 581
Period size: 151 Copynumber: 2.0 Consensus size: 152
14128 TCCTTCGTCG
14138 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
14203 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
14268 TGAAATCCAATGTTG-TTGTGA
131 TGAAATCCAATGTTGTTTGTGA
14289 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
* *
14354 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
14419 TGAAATCCAATGTTGTTTGTGA
131 TGAAATCCAATGTTGTTTGTGA
14441 GCACGATATC
Statistics
Matches: 149, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
151 143 0.96
152 6 0.04
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (152 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
TGAAATCCAATGTTGTTTGTGA
Found at i:14571 original size:170 final size:170
Alignment explanation
Indices: 14289--14599 Score: 604
Period size: 170 Copynumber: 1.8 Consensus size: 170
14279 GTTGTTGTGA
14289 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
14354 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
14419 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
131 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
*
14459 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
*
14524 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTGAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
14589 TGAAATCCAAT
131 TGAAATCCAAT
14600 CTTCAGTAAA
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 139 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (170 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
Found at i:22263 original size:39 final size:39
Alignment explanation
Indices: 22198--22277 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
22188 TTAACAGTAG
* *
22198 ATGCAGCTTTCCCTTTGGTAGAGGATGAGTCAC-CGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTC-CTCGGGTA
* *
22237 ATGCAACTTTCCTTTTAGTAGCGGATGAGTCCTCGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
22276 AT
1 AT
22278 ACTCCGGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (39 bp):
ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
Found at i:25692 original size:12 final size:13
Alignment explanation
Indices: 25675--25703 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25665 CTTAATTACA
25675 AAAATTAAAA-TT
1 AAAATTAAAATTT
25687 AAAATTAAAATTT
1 AAAATTAAAATTT
25700 AAAA
1 AAAA
25704 ATTCGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:28127 original size:6 final size:6
Alignment explanation
Indices: 28096--28306 Score: 245
Period size: 6 Copynumber: 36.2 Consensus size: 6
28086 AAACAATGAT
* *
28096 TTTATA TCTA-A TTTATA -TCA-A TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
*
28141 TTTATA TTTATA TTTATA -TT-TA TTTATA -TTATA TTTATA CTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* * * * * * * *
28186 CTTATA CTTATA CTTATA CTTATA CTTATA CTTATA CTTATA CTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* * * *
28234 CTTATA CTTATA CTTATA CTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
28282 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
28307 GGCGTTGGTT
Statistics
Matches: 193, Mismatches: 6, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
4 3 0.02
5 17 0.09
6 173 0.90
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTATA
Found at i:37269 original size:39 final size:38
Alignment explanation
Indices: 37226--37332 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 38
37216 CGTGCACTCC
* *
37226 TGGGGTCTTCTCTATTTGCCTGAAGACGTCATGTAGTCG
1 TGGGGTCTTCT-TATTTGCCTGAAGACGCCATGTAATCG
* *
37265 TGGGGCCTTCTTCATTTTCCTGAAGACGCCATGTAATCG
1 TGGGGTCTTCTT-ATTTGCCTGAAGACGCCATGTAATCG
* * *
37304 TGGAGTCTTCATATTTAGCTTGAAGACGC
1 TGGGGTCTTCTTATTT-GCCTGAAGACGC
37333 GTGGAGCACC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 5 0.09
39 52 0.91
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (38 bp):
TGGGGTCTTCTTATTTGCCTGAAGACGCCATGTAATCG
Found at i:43912 original size:13 final size:13
Alignment explanation
Indices: 43894--43920 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43884 GTAAAGAAAA
43894 TTTGGTTAGCCAC
1 TTTGGTTAGCCAC
43907 TTTGGTTAGCCAC
1 TTTGGTTAGCCAC
43920 T
1 T
43921 ACGGTGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (13 bp):
TTTGGTTAGCCAC
Found at i:47149 original size:103 final size:100
Alignment explanation
Indices: 46965--47178 Score: 347
Period size: 103 Copynumber: 2.1 Consensus size: 100
46955 CAAAGAAAAA
* *
46965 TATCTGTTTAAATTTTTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCGA
1 TATCTGTTTAAAATATTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCGA
47030 ACTCTAAACCTCAAGGAATAACAACAACTTGCAGACG
66 ACTCTAAACCTCAAGGAAT-ACAA-AACTTGCAGACG
* *
47067 TATCTGGTTTAAAATATTTTTTAATCATTATCAACATACACATAGCCTGCAGATGTAACTGATCG
1 TATCT-GTTTAAAATATTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCG
*
47132 AACTCTAAACCTCAAGGAATATAAAACTTGCAGACG
65 AACTCTAAACCTCAAGGAATACAAAACTTGCAGACG
*
47168 TAACTGTTTAA
1 TATCTGTTTAA
47179 TTAAACGATA
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
100 6 0.06
101 16 0.15
102 8 0.08
103 75 0.71
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (100 bp):
TATCTGTTTAAAATATTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCGA
ACTCTAAACCTCAAGGAATACAAAACTTGCAGACG
Done.