Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003288.1 Hibiscus syriacus cultivar Beakdansim tig00006918_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: 186948
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:162653 original size:23 final size:22
Alignment explanation
Indices: 162627--162675 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
162617 ATTAAATTTC
162627 AAAAAAG-TAAAATAATAAAATA
1 AAAAAAGATAAAA-AATAAAATA
* *
162649 TAAAAATGATAAAAGATAAAATA
1 -AAAAAAGATAAAAAATAAAATA
162672 AAAA
1 AAAA
162676 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.61
24 5 0.22
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAAAGATAAAAAATAAAATA
Found at i:162655 original size:52 final size:52
Alignment explanation
Indices: 162544--162648 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 52
162534 AATTAAATTA
* * * * *
162544 AAAT-AAATCAAAGAAGGAAATATTAAATTTTAAAAATGTTATATAAAAAAT
1 AAATAAAATCAAAGAAGAAAATATTAAATTTCAAAAAAGTAAAATAAAAAAT
162595 AAATAAAAT-AAATGAAGAAAATATTAAATTTCAAAAAAGTAAAATAATAAAAT
1 AAATAAAATCAAA-GAAGAAAATATTAAATTTCAAAAAAGTAAAATAA-AAAAT
162648 A
1 A
162649 TAAAAATGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 7 0.15
52 33 0.72
53 6 0.13
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.27
Consensus pattern (52 bp):
AAATAAAATCAAAGAAGAAAATATTAAATTTCAAAAAAGTAAAATAAAAAAT
Found at i:162674 original size:5 final size:5
Alignment explanation
Indices: 162664--162728 Score: 51
Period size: 5 Copynumber: 12.2 Consensus size: 5
162654 ATGATAAAAG
* *
162664 ATAAA ATAAAA ATAAA ACAAA ATAAA A-AAA GTGGGAAA ATAAAA ATAAA
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA AT---AAA AT-AAA ATAAA
*
162713 ACAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA A
162729 AAGAAGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.06
5 31 0.65
6 10 0.21
8 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (5 bp):
ATAAA
Found at i:162729 original size:16 final size:16
Alignment explanation
Indices: 162666--162728 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
162656 GATAAAAGAT
162666 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
***
162682 AAAATAAAAA-AAGTGGG
1 AAAATAAAAATAA--AAC
162699 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
162715 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
162729 AAGAAGTGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 11 0.29
16 15 0.39
17 10 0.26
18 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.13
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:164401 original size:200 final size:200
Alignment explanation
Indices: 163854--164525 Score: 945
Period size: 200 Copynumber: 3.4 Consensus size: 200
163844 ACCATATGGC
** * * * *
163854 TCGAGCTTTATGGAATAGAACTCG-AAGTTTTTTGTTGACAGGTAGCCCTTCTCGTCTTGAGCTA
1 TCGAGCTGAATGGAATTGAACTCGAAAG--TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTA
* * * * * * *
163918 TGCTGTAAATTCGACTAGGAGATAGTTTCTTGTTGCTAAATCGCAGTCAATCTAGGTCATATTCT
64 TGCTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCT
* *
163983 TGACTTAAAGACCTCAGTTTAAACTTCAACCGAAAAGTATTTCCTCATTGCTACCATGCAATTGA
129 TGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCAATTGA
164048 TATGCCT
194 TATGCCT
* * * * *
164055 TCGATCTGAATGGAATTGAACTCAAAAGTTTTGTTGACAGAT-AGCTTTCTCACCTTGAGCTATG
1 TCGAGCTGAATGGAATTGAACTCGAAAGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * *
164119 TTGTAAATTCGGCTGGGAGATAGTTCCTCT-TTGCTAAATCTCAACCAACCTAGGTCTTCTTCTT
66 CTGTAAATTCGGCTGGGAGATAGTTCCT-TGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTT
* * ** *
164183 GACTTAAAAACCTCAGTTTAAACTTTAACCGGAAAGTAGTTCCTTGTTGCTACCATGCAGTTGAT
130 GACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCAATTGAT
164248 ATGCCT
195 ATGCCT
* *
164254 TCGAGCTGAATGGAATTGAACTCGAAAGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGATATA
1 TCGAGCTGAATGGAATTGAACTCGAAAGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
164319 CTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAGCCAACCTAGGTTTTCTTCTTG
66 CTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTG
*
164384 ACTTAAAGACCTCAGTTTAAACTTCAACTGGAAAGTAGTTCCTCATTGCTACCATGCAATTGATA
131 ACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCAATTGATA
*
164449 TACCT
196 TGCCT
* * * * * *
164454 TCAAGCTTAATGAAATCGAACTCGAAAGTTTTGTTGACAAATAACCCTTCCCGCCTTGAGCTATG
1 TCGAGCTGAATGGAATTGAACTCGAAAGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
164519 CTGTAAA
66 CTGTAAA
164526 CGGTTCCTCT
Statistics
Matches: 413, Mismatches: 54, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
199 174 0.42
200 217 0.53
201 19 0.05
202 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (200 bp):
TCGAGCTGAATGGAATTGAACTCGAAAGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
CTGTAAATTCGGCTGGGAGATAGTTCCTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTG
ACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCAATTGATA
TGCCT
Found at i:171197 original size:60 final size:59
Alignment explanation
Indices: 171079--171198 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 59
171069 AAATTAAATT
* * ** *
171079 AAAATAAATCAAAGAAGGAAATATTAAATTTTAAAAATGTTATATAAAAAATATTAAAA
1 AAAATAAATCAAAGAAGAAAATATTAAATTTCAAAAATGAAAAATAAAAAATATTAAAA
171138 AAAATAAAAT-AAATGAAGAAAATATTAAATTTCAGAAAA-GAAAAATAATAAAATA-TAAAA
1 AAAAT-AAATCAAA-GAAGAAAATATTAAATTTCA-AAAATGAAAAATAA-AAAATATTAAAA
171198 A
1 A
171199 TGTTAAAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
59 8 0.15
60 34 0.65
61 10 0.19
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.25
Consensus pattern (59 bp):
AAAATAAATCAAAGAAGAAAATATTAAATTTCAAAAATGAAAAATAAAAAATATTAAAA
Found at i:171386 original size:18 final size:18
Alignment explanation
Indices: 171365--171407 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
171355 GTTGTTTTTA
*
171365 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
171383 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
171401 AAATAAA
1 AAATAAA
171408 TAATATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:173102 original size:75 final size:77
Alignment explanation
Indices: 173002--173154 Score: 256
Period size: 75 Copynumber: 2.0 Consensus size: 77
172992 ACCTCTTTTG
* * *
173002 ACTAATATAAAGAGAAAAAAATACAAGATAATTTTATAGAAACAAATTTTGATTTCTGATCCTAA
1 ACTAATATAAAGAGAAAAAAATACAAGATAATTTTAGAGAAACAAAATTTGATTTATGATCCTAA
173067 CCCCTAGTATCT
66 CCCCTAGTATCT
*
173079 ACTAATAT-AA-AGAAATAAATACAAGATAATTTTAGAGAAACAAAATTTGATTTATGATCCTAA
1 ACTAATATAAAGAGAAAAAAATACAAGATAATTTTAGAGAAACAAAATTTGATTTATGATCCTAA
173142 CCCCTAGTATCT
66 CCCCTAGTATCT
173154 A
1 A
173155 TTTATTAAGT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 62 0.86
76 2 0.03
77 8 0.11
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (77 bp):
ACTAATATAAAGAGAAAAAAATACAAGATAATTTTAGAGAAACAAAATTTGATTTATGATCCTAA
CCCCTAGTATCT
Found at i:175259 original size:6 final size:6
Alignment explanation
Indices: 175250--175388 Score: 211
Period size: 6 Copynumber: 24.3 Consensus size: 6
175240 ATAATAATTT
*
175250 AATAAA AATAAT AAT-AA AATAAA AAT-AA AAT-AA AATAAA AAT-AA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
175294 AAT-AA AAT-AA AA-AAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
175339 AATAAA AATTAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
175387 AA
1 AA
175389 GGGTCAAAAA
Statistics
Matches: 125, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
5 32 0.26
6 93 0.74
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:175398 original size:1 final size:1
Alignment explanation
Indices: 175265--175388 Score: 59
Period size: 1 Copynumber: 124.0 Consensus size: 1
175255 AAATAATAAT
* * * * * * * * * * *
175265 AAAATAAAAATAAAATAAAATAAAAATAAAATAAAATAAAAAAAAATAAAAATAAAAATAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * * * * * *
175330 AAAAATAAAAATAAAAATTAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
175389 GGGTCAAAAA
Statistics
Matches: 83, Mismatches: 40, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (1 bp):
A
Found at i:176758 original size:21 final size:21
Alignment explanation
Indices: 176732--176785 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
176722 TGGATTCAAC
176732 TGAAAGCACATTCCTCTTTAA
1 TGAAAGCACATTCCTCTTTAA
*
176753 TGAAAGCATATTCCTCTTTAA
1 TGAAAGCACATTCCTCTTTAA
*
176774 TGAAAGAACATT
1 TGAAAGCACATT
176786 TCCCTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
TGAAAGCACATTCCTCTTTAA
Found at i:176792 original size:21 final size:21
Alignment explanation
Indices: 176732--176792 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
176722 TGGATTCAAC
176732 TGAAAGCACA-TTCCTCTTTAA
1 TGAAAG-ACATTTCCTCTTTAA
176753 TGAAAG-CATATTCCTCTTTAA
1 TGAAAGACAT-TTCCTCTTTAA
176774 TGAAAGAACATTTCC-CTTT
1 TGAAAG-ACATTTCCTCTTT
176793 GTTTGGCGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.06
21 27 0.75
22 4 0.11
23 3 0.08
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (21 bp):
TGAAAGACATTTCCTCTTTAA
Found at i:185800 original size:12 final size:12
Alignment explanation
Indices: 185783--185809 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
185773 AGCCATAGAA
185783 AGGTTTGGTACC
1 AGGTTTGGTACC
185795 AGGTTTGGTACC
1 AGGTTTGGTACC
185807 AGG
1 AGG
185810 GTAAACCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.15, G:0.37, T:0.30
Consensus pattern (12 bp):
AGGTTTGGTACC
Done.