Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007947.1 Hibiscus syriacus cultivar Beakdansim tig00110369_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: 254465
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:243519 original size:23 final size:23
Alignment explanation
Indices: 243449--243521 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
243439 ATAGGTAAAC
* **
243449 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
243472 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
243495 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
243518 ATAT
1 ATAT
243522 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:243942 original size:23 final size:23
Alignment explanation
Indices: 243879--243943 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
243869 ATAGGTAAAC
* *
243879 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
243902 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
243925 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
243944 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:244168 original size:18 final size:18
Alignment explanation
Indices: 244147--244183 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
244137 GTAATTGGAG
244147 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
244165 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
244183 T
1 T
244184 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:248484 original size:2 final size:2
Alignment explanation
Indices: 248477--248511 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
248467 TATTAAAGAA
248477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
248512 AAATAGTACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:248594 original size:58 final size:58
Alignment explanation
Indices: 248485--248596 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 58
248475 AAATATATAT
* *
248485 ATATATATATATATATATATATATATAAAATAGTACAAAATCAAATGAAAATAATTTAAA
1 ATATATATATATATATATATACATATAAAATAG-ACAAAAT-AAATAAAAATAATTTAAA
* *
248545 ATATATATATATATATATATACGTATAATAATA-ACATGAAT-AATAAAAATAA
1 ATATATATATATATATATATACATATAA-AATAGACA-AAATAAATAAAAATAA
248597 ATGAATAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 10 0.22
59 3 0.07
60 29 0.63
61 4 0.09
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (58 bp):
ATATATATATATATATATATACATATAAAATAGACAAAATAAATAAAAATAATTTAAA
Found at i:248602 original size:17 final size:18
Alignment explanation
Indices: 248569--248604 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
248559 ATATATACGT
*
248569 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
248587 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
248604 A
1 A
248605 AATATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:250128 original size:104 final size:106
Alignment explanation
Indices: 249823--250326 Score: 704
Period size: 106 Copynumber: 4.8 Consensus size: 106
249813 AGTATTGTTA
* *
249823 TGAGTCC-ATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGAC
1 TGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGAC
** * * * *
249886 AGTCGGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
249928 CGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* *
249993 ACCAGCCGTCCCTTCGTTGTGAATTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
250034 TGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAA-T-GGAAATTGTTTGCTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
250097 ACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
250138 TGAGTCCAATAGCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACT-GAAAAGTGGTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAA-TTGTTTGTTGAC
250202 AACCAGCCGTCCC-T--TTGTGAAGTTGAACTTGTG-T-TCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
250239 TGAGTTCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
*
250304 AACCAGTCGTCCCTTCGTTGTGA
65 AACCAGCCGTCCCTTCGTTGTGA
250327 CTCTGAATGA
Statistics
Matches: 356, Mismatches: 34, Indels: 18
0.87 0.08 0.04
Matches are distributed among these distances:
101 47 0.13
102 26 0.07
103 19 0.05
104 96 0.27
105 18 0.05
106 149 0.42
107 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:250132 original size:210 final size:207
Alignment explanation
Indices: 249823--250324 Score: 699
Period size: 210 Copynumber: 2.4 Consensus size: 207
249813 AGTATTGTTA
*
249823 TGAGTCC-ATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGAC
1 TGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGAC
** * * * * * * *
249886 AGTCGGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTG
65 AACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATAGCCTTCGCTGTG
* * * *
249951 AAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGA
130 AAGTTGAAATTGACTCTGAAACT-GAAAAGTGGTTTGTTGACAACCAGCCGTCCC-T--TTGTGA
*
250015 ATTTGAACTTGTGTCGTCT
191 AGTTGAACTTGTGT--TCT
* *
250034 TGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAA-T-GGAAATTGTTTGCTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGACA
*
250097 ACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTTGAGTCCAATAGCCTTCGCTGTGA
66 ACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATAGCCTTCGCTGTGA
250162 AGTTGAAATTGACTCTGAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTTGTGAAGTTG
131 AGTTGAAATTGACTCTGAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTTGTGAAGTTG
250227 AACTTGTGTTCT
196 AACTTGTGTTCT
* * *
250239 TGAGTTCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTG-TTTGTTGAC
*
250304 AACCAGTCGTCCCTTCGTTGT
65 AACCAGCCGTCCCTTCGTTGT
250325 GACTCTGAAT
Statistics
Matches: 262, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
205 44 0.17
206 1 0.00
207 27 0.10
208 28 0.11
209 5 0.02
210 116 0.44
211 8 0.03
212 32 0.12
213 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (207 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTCGAGTCCAATAGCCTTCGCTGTGA
AGTTGAAATTGACTCTGAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTTGTGAAGTTG
AACTTGTGTTCT
Found at i:250443 original size:162 final size:157
Alignment explanation
Indices: 250177--250491 Score: 425
Period size: 162 Copynumber: 2.0 Consensus size: 157
250167 AAATTGACTC
* * * * *
250177 TGAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTTGTGAAGTTGAACTTGTGTTCTTGA
1 TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCCCGTTGTGAAGTTGAACTTGTGTTCTCGA
* * * ** * *
250242 GTTCAATATCCTTTGCTGTGAAGTTGAAATTGGCTC-TGAAACTGGGAAATTGTTTTGTTGACAA
66 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCATGAAACT-AAAAAGTGGTTTGTTGACAA
250306 CCAGTCGTCCCTTCGTTGTGACTCTGAA
130 CCAGTCGTCCCTTCGTTGTGACTCTGAA
250334 TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCCATTCGTTGTGAAGTTGAACTTGTGTTGC
1 TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCC---CGTTGTGAAGTTGAACTTGTGTT--
250399 CTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTGGTTTG
61 CTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC---ATGAAACTAAAAAGTGGTTTG
*
250464 TTGACAACCAGTCGTCCTTTCGTTGTGA
123 TTGACAACCAGTCGTCCCTTCGTTGTGA
250492 AGTTGAACTT
Statistics
Matches: 136, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
157 34 0.25
160 22 0.16
162 37 0.27
165 36 0.26
166 7 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (157 bp):
TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCCCGTTGTGAAGTTGAACTTGTGTTCTCGA
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCATGAAACTAAAAAGTGGTTTGTTGACAAC
CAGTCGTCCCTTCGTTGTGACTCTGAA
Found at i:251431 original size:36 final size:37
Alignment explanation
Indices: 251378--251453 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 37
251368 AGAAACAATT
251378 CAAAGGTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
251415 CAAA-GTTTGTTT-CAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTT-TTTCCAAGGGAAACTGTCTCAAGAGAGA
251451 CAA
1 CAA
251454 TGGTGAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 31 0.82
37 7 0.18
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (37 bp):
CAAAGGTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
Found at i:251972 original size:16 final size:18
Alignment explanation
Indices: 251941--251974 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
251931 TGTTGAATCC
251941 CCAAAGATGCCCCAATAT
1 CCAAAGATGCCCCAATAT
251959 CCAAA-ATG-CCCAATAT
1 CCAAAGATGCCCCAATAT
251975 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.41, C:0.32, G:0.09, T:0.18
Consensus pattern (18 bp):
CCAAAGATGCCCCAATAT
Found at i:253046 original size:22 final size:22
Alignment explanation
Indices: 253010--253061 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
253000 TTTTTGCTTC
*
253010 TTTCTTTTTTGTTC-TTGTTTTT
1 TTTC-TTTTTGTTCTTTCTTTTT
253032 TTTCTTTTTGCTTCTTTCTTTTT
1 TTTCTTTTTG-TTCTTTCTTTTT
253055 TGTTCTT
1 T-TTCTT
253062 GATTGAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 6 0.23
22 7 0.27
23 8 0.31
24 5 0.19
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTGTTCTTTCTTTTT
Done.