Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009258.1 Hibiscus syriacus cultivar Beakdansim tig00112907_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: 77151
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5259 original size:17 final size:17
Alignment explanation
Indices: 5234--5268 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5224 TATTCCAAGA
5234 CAAGACGGATCCCGAGG
1 CAAGACGGATCCCGAGG
* *
5251 CAAGTCGGATCTCGAGG
1 CAAGACGGATCCCGAGG
5268 C
1 C
5269 TTGCCTAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.34, T:0.11
Consensus pattern (17 bp):
CAAGACGGATCCCGAGG
Found at i:14795 original size:21 final size:20
Alignment explanation
Indices: 14770--14808 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
14760 CATCAAGGTC
14770 TTTGTAGACGCCATGAAATCT
1 TTTGTAGACGCCAT-AAATCT
* *
14791 TTTGTCGAGGCCATAAAT
1 TTTGTAGACGCCATAAAT
14809 TTCTGCAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
TTTGTAGACGCCATAAATCT
Found at i:24808 original size:87 final size:87
Alignment explanation
Indices: 24697--24859 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 87
24687 GAAAAATTAT
* *
24697 TTTATAAATTACAATAAAGGACAAAATT-TGTTATAAACTACAATAAAGTACAAAA-CTATTTAT
1 TTTATAAATTACAATAAAAGACAAAATTAT-TTATAAACTACAATAAAGGACAAAACCT-TTTAT
24760 AAATAACAATAAATTAAAAAACAA
64 AAATAACAATAAATTAAAAAACAA
* * *
24784 TTTATAAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGATAAAACCTTTTATAA
1 TTTATAAATTACAATAAAAGACAAAATTATTTATAAACTACAATAAAGGACAAAACCTTTTATAA
* *
24849 ATTATAATAAA
66 ATAACAATAAA
24860 AGGAGACATT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 64 0.96
88 3 0.04
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (87 bp):
TTTATAAATTACAATAAAAGACAAAATTATTTATAAACTACAATAAAGGACAAAACCTTTTATAA
ATAACAATAAATTAAAAAACAA
Found at i:24838 original size:29 final size:28
Alignment explanation
Indices: 24616--24859 Score: 177
Period size: 29 Copynumber: 8.5 Consensus size: 28
24606 AAGAATCATC
* *
24616 AAATTACAATAAAAGACAAAATGTTTTAG
1 AAATTACAATAAAGGACAAAAT-TTTTAT
* * *** * *
24645 AATTTATAATAAAAGTTTAAACTTTTTAG
1 AAATTACAAT-AAAGGACAAAATTTTTAT
*
24674 AATTTACAATAAA-GA-AAAATTATTTTAT
1 AAATTACAATAAAGGACAAAA-T-TTTTAT
24702 AAATTACAATAAAGGACAAAATTTGTTAT
1 AAATTACAATAAAGGACAAAATTT-TTAT
* * *
24731 AAACTACAATAAAGTACAAAACTATTTAT
1 AAATTACAATAAAGGACAAAA-TTTTTAT
* ** * **
24760 AAATAACAATAAATTAAAAAACAATTTAT
1 AAATTACAATAAAGGACAAAA-TTTTTAT
**
24789 AAATTACAATAAAATACAAAATTATTTAT
1 AAATTACAATAAAGGACAAAATT-TTTAT
* *
24818 AAATTACAATAAAGGATAAAACCTTTTAT
1 AAATTACAATAAAGGACAAAA-TTTTTAT
*
24847 AAATTATAATAAA
1 AAATTACAATAAA
24860 AGGAGACATT
Statistics
Matches: 175, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
26 3 0.02
27 1 0.01
28 22 0.13
29 135 0.77
30 14 0.08
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATTACAATAAAGGACAAAATTTTTAT
Found at i:24860 original size:58 final size:58
Alignment explanation
Indices: 24616--24860 Score: 219
Period size: 58 Copynumber: 4.2 Consensus size: 58
24606 AAGAATCATC
* * * * * *** * *
24616 AAATTACAATAAAAGACAAAATGT-TTTAGAATTTATAATAAAAGTTTAAACTTTTTAG
1 AAATTACAATAAAATACAAAAT-TATTTATAAATTACAATAAAGGAAAAAACATTTTAT
* * * *
24674 AATTTACAAT-AAAGA-AAAATTATTTTATAAATTACAATAAAGGACAAAA-TTTGTTAT
1 AAATTACAATAAAATACAAAATTA-TTTATAAATTACAATAAAGGAAAAAACATT-TTAT
* * * * ** *
24731 AAACTACAATAAAGTACAAAACTATTTATAAATAACAATAAATTAAAAAACAATTTAT
1 AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGAAAAAACATTTTAT
* *
24789 AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGATAAAACCTTTTAT
1 AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGAAAAAACATTTTAT
*
24847 AAATTATAATAAAA
1 AAATTACAATAAAA
24861 GGAGACATTT
Statistics
Matches: 151, Mismatches: 30, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
55 1 0.01
56 8 0.05
57 35 0.23
58 100 0.66
59 7 0.05
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (58 bp):
AAATTACAATAAAATACAAAATTATTTATAAATTACAATAAAGGAAAAAACATTTTAT
Found at i:34305 original size:23 final size:22
Alignment explanation
Indices: 34277--34319 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
34267 TAGGTACTAT
*
34277 AAACAAGGTAAACAACAAGATTA
1 AAACAAGATAAACAA-AAGATTA
34300 AAACAAGATAAACAAAAGAT
1 AAACAAGATAAACAAAAGAT
34320 ACAGAAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (22 bp):
AAACAAGATAAACAAAAGATTA
Found at i:48201 original size:51 final size:51
Alignment explanation
Indices: 48112--48226 Score: 149
Period size: 51 Copynumber: 2.2 Consensus size: 51
48102 AGCAACACAA
* * * *
48112 AACATGTGGAGCACCACAAGCATTGACTATATACAATAAAATTAAATAATAG
1 AACATGTGGAG-GCCACAAGCACTGACTATATAAAATAAAATTAAATAACAG
* * * *
48164 AACATGTGGAGGCCATAAGCACTGACTCTATAAAATAAAGTTATATAACAG
1 AACATGTGGAGGCCACAAGCACTGACTATATAAAATAAAATTAAATAACAG
48215 AACATGTGGAGG
1 AACATGTGGAGG
48227 GCACTAACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 44 0.80
52 11 0.20
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (51 bp):
AACATGTGGAGGCCACAAGCACTGACTATATAAAATAAAATTAAATAACAG
Found at i:59837 original size:49 final size:50
Alignment explanation
Indices: 59713--59841 Score: 161
Period size: 49 Copynumber: 2.5 Consensus size: 50
59703 TAGGTAAAGC
* *
59713 AAATTTCTAAGACCGAACATGCTCTAGCATTCCTTTTTTATGGAGGAGTAGAGA
1 AAATTTCTAAGACCGAATAAGCTCTA--ATTCCTTTTTTAT-G-GGAGTAGAGA
*
59767 AAATTTCTAAGACCGAATAAGCTCTAATTCCTTTTTTAT-GGAGTAGAGC
1 AAATTTCTAAGACCGAATAAGCTCTAATTCCTTTTTTATGGGAGTAGAGA
* * *
59816 AAATTTTTAAGATCGAGTAAGCTCTA
1 AAATTTCTAAGACCGAATAAGCTCTA
59842 GTGTTCGTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 32 0.46
52 13 0.19
54 24 0.35
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (50 bp):
AAATTTCTAAGACCGAATAAGCTCTAATTCCTTTTTTATGGGAGTAGAGA
Found at i:64614 original size:16 final size:16
Alignment explanation
Indices: 64595--64628 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
64585 CGTTGTGTTA
64595 ATATTTAT-TTACATTT
1 ATATTTATATT-CATTT
64611 ATATTTATATTCATTT
1 ATATTTATATTCATTT
64627 AT
1 AT
64629 TAAAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTTATATTCATTT
Found at i:71688 original size:29 final size:29
Alignment explanation
Indices: 71633--71719 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
71623 AATTCTATCC
*
71633 AGAAAAGAAAAGAAAAAAGAAAGGAAAAAG
1 AGAAAAAAAAAG-AAAAAGAAAGGAAAAAG
* * *
71663 GGAAAAATAAAAGAGATA-AAAGGAAAAAAG
1 AGAAAAA-AAAAGAAAAAGAAAGG-AAAAAG
71693 AGAAAAAAAAAGAAAAAGAAAGGAAAA
1 AGAAAAAAAAAGAAAAAGAAAGGAAAA
71720 TGAAAATGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
29 17 0.36
30 25 0.53
31 5 0.11
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (29 bp):
AGAAAAAAAAAGAAAAAGAAAGGAAAAAG
Found at i:72424 original size:19 final size:19
Alignment explanation
Indices: 72385--72424 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
72375 CCTGCTGATG
*
72385 AAGAAGAAAAAGTGAAAAA
1 AAGAAGAAAAAGTAAAAAA
72404 AAGAAGAAAAAGTAAAAAA
1 AAGAAGAAAAAGTAAAAAA
72423 AA
1 AA
72425 AAAAGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAGAAGAAAAAGTAAAAAA
Found at i:72488 original size:23 final size:24
Alignment explanation
Indices: 72457--72502 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
72447 TGAAATGAAA
72457 AGAAAAAGAAAC-AAAGAGAAAAT
1 AGAAAAAGAAACGAAAGAGAAAAT
* *
72480 AGAAGAAGAAACGAAAGTGAAAA
1 AGAAAAAGAAACGAAAGAGAAAA
72503 CCCGAAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.70, C:0.04, G:0.22, T:0.04
Consensus pattern (24 bp):
AGAAAAAGAAACGAAAGAGAAAAT
Found at i:73269 original size:53 final size:53
Alignment explanation
Indices: 73106--73550 Score: 209
Period size: 53 Copynumber: 8.6 Consensus size: 53
73096 TAAGAAGCAC
* * * * * * *
73106 GCTCTAGCATTCCTTTCTTATGGATGAGTATAACAAAT-TTTAAAGATCAAGTAT
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTA-GAGAAATATTT-AAGACCCAGTAA
* * * * ** *
73160 GCTCTAGCGTTTC-TTGTTA--AAGGAGTAGAGAAAATTTTTAAGACTTAGCACA
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAG-AAATATTTAAGACCCAGTA-A
73212 -CTCTAGCATTCCTTTGTTATGGAGGAGTAGAGAAATATTTAAGACCCAGTAA
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAGAAATATTTAAGACCCAGTAA
* ** * * * * *
73264 GCTCTAGGATTCCTTT-ACATGGAGTAG-ATCA-AAAT-TTTAAGAACAAGAAA
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTA-GAGAAATATTTAAGACCCAGTAA
* * * * *
73314 GCTCTAGCGTTCATTT-CTATGGAGGAGTAGAGAAA-ATTTTAAGA-CTATATAA
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAGAAATA-TTTAAGACCCA-GTAA
* * *
73366 GCTCTAGCATTCCTTTCTTATTGAGGAGTAGAGAAA-ATTTTAAGACTACA-TAA
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAGAAATA-TTTAAGAC-CCAGTAA
*** * *
73419 GCTCTATTGTTTCTTTGTTATGGA-G-GTAGAGCAAA-ATTTTAAGA--CTGTAA
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAG-AAATA-TTTAAGACCCAGTAA
* * * * * *
73469 GCTCCAGC-GT--TTT-TT-TGGAGGAGTAGAGAAAATTTTTAAGATCGAGCAA
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAG-AAATATTTAAGACCCAGTAA
* * * *
73518 GCTCTAGCGTTCCTTGGTTATGGAAGTGTAGAG
1 GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAG
73551 CTCATAATTG
Statistics
Matches: 299, Mismatches: 64, Indels: 56
0.71 0.15 0.13
Matches are distributed among these distances:
45 4 0.01
46 3 0.01
47 19 0.06
49 12 0.04
50 44 0.15
51 44 0.15
52 57 0.19
53 83 0.28
54 32 0.11
55 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (53 bp):
GCTCTAGCATTCCTTTGTTATGGAGGAGTAGAGAAATATTTAAGACCCAGTAA
Found at i:73354 original size:155 final size:153
Alignment explanation
Indices: 73180--73550 Score: 420
Period size: 155 Copynumber: 2.4 Consensus size: 153
73170 TTCTTGTTAA
73180 AGGAGTAGAGAAAATTTTTAAGACT-TAGCACA-CTCTAGCATTCCTTTGTTATGGAGGAGTAGA
1 AGGAGTAGAGAAAATTTTTAAGACTATAGCA-AGCTCTAGCATTCCTTTGTTATGGAGGAGTAGA
* *
73243 G-AAATATTTAAGAC-CCAGTAAGCTCTA-GGATTCCTTT-ACATGGA-GTAGATCAAAATTTTA
65 GAAAAT-TTTAAGACTACA-TAAGCTCTATGG-TTCCTTTGACATGGAGGTAGAGCAAAATTTTA
*
73303 AGAACAAGAAAGCTCTAGCGTTCATTTCTATGG
127 AG-AC-AGAAAGCTCCAGCGTT--TTT-T-TGG
* * *
73336 AGGAGTAGAGAAAA-TTTTAAGACTATA-TAAGCTCTAGCATTCCTTTCTTATTGAGGAGTAGAG
1 AGGAGTAGAGAAAATTTTTAAGACTATAGCAAGCTCTAGCATTCCTTTGTTATGGAGGAGTAGAG
* * **
73399 AAAATTTTAAGACTACATAAGCTCTATTGTTTCTTTGTTATGGAGGTAGAGCAAAATTTTAAGAC
66 AAAATTTTAAGACTACATAAGCTCTATGGTTCCTTTGACATGGAGGTAGAGCAAAATTTTAAGAC
* *
73464 TGTAAGCTCCAGCGTTTTTTTGG
131 AGAAAGCTCCAGCGTTTTTTTGG
** * * * *
73487 AGGAGTAGAGAAAATTTTTAAGA-TCGAGCAAGCTCTAGCGTTCCTTGGTTATGGAAGTGTAGAG
1 AGGAGTAGAGAAAATTTTTAAGACTATAGCAAGCTCTAGCATTCCTTTGTTATGGAGGAGTAGAG
73551 CTCATAATTG
Statistics
Matches: 185, Mismatches: 21, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
151 19 0.10
152 38 0.21
153 3 0.02
154 1 0.01
155 77 0.42
156 30 0.16
157 17 0.09
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (153 bp):
AGGAGTAGAGAAAATTTTTAAGACTATAGCAAGCTCTAGCATTCCTTTGTTATGGAGGAGTAGAG
AAAATTTTAAGACTACATAAGCTCTATGGTTCCTTTGACATGGAGGTAGAGCAAAATTTTAAGAC
AGAAAGCTCCAGCGTTTTTTTGG
Done.