Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008048.1 Hibiscus syriacus cultivar Beakdansim tig00110540_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: 541079
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:517223 original size:105 final size:105
Alignment explanation
Indices: 516916--517852 Score: 1479
Period size: 105 Copynumber: 9.0 Consensus size: 105
516906 CATTGTTCCA
* * * ** * * *
516916 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
516981 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
517022 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
517082 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
517122 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
517187 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
517227 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
517292 AGCGGTCCCTTCGTCGTGAATTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
517332 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
517397 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
517437 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
517502 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
517542 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
517607 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
517647 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGTTGACAGGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
517712 AGCAGTCCCTTCGTCGTGAAGTTAAAATTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
517752 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
517817 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
517853 CCTCGAGTGC
Statistics
Matches: 779, Mismatches: 46, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
100 84 0.11
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 609 0.78
106 74 0.09
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:518585 original size:68 final size:65
Alignment explanation
Indices: 518495--518652 Score: 199
Period size: 68 Copynumber: 2.4 Consensus size: 65
518485 AAGATATCTG
* * ** *
518495 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAG-G
518560 TT
64 TT
* * * *
518562 TGTGTTTCAAGAGTAACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
518627 T
65 T
*
518628 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
518653 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:518630 original size:67 final size:65
Alignment explanation
Indices: 518495--518889 Score: 233
Period size: 65 Copynumber: 5.8 Consensus size: 65
518485 AAGATATCTG
* * * * **
518495 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
518560 TT
64 TT
* * *
518562 TGTGTTTCAAGAGTAACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
518627 T
65 T
* * *
518628 TTGTTTCAAGGGAAACTGTCTCAAGAT-AGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAG-TGAGAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-
** *
518691 AGACAAA-ACT
55 ATTCAAAGATT
* * * * ** * * * * * *
518701 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * *
518766 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA-T-
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAA-----T-AA-ATTC
* *
518829 AGACGAAAT
59 A-AAG-ATT
* *
518838 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAAT
518890 TGTCTCAAGA
Statistics
Matches: 254, Mismatches: 50, Indels: 48
0.72 0.14 0.14
Matches are distributed among these distances:
64 5 0.02
65 81 0.32
66 9 0.04
67 24 0.09
68 31 0.12
70 2 0.01
71 3 0.01
72 55 0.22
73 39 0.15
74 5 0.02
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.29
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:518679 original size:36 final size:35
Alignment explanation
Indices: 518628--518908 Score: 263
Period size: 36 Copynumber: 8.0 Consensus size: 35
518618 TTCAAAGGTT
* *
518628 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
518664 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
518699 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
518737 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
518766 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
518801 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
518838 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
518873 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
518909 CTCTTCTAGT
Statistics
Matches: 203, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 133 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:518738 original size:138 final size:137
Alignment explanation
Indices: 518576--518889 Score: 423
Period size: 138 Copynumber: 2.3 Consensus size: 137
518566 TTTCAAGAGT
* * * *
518576 AACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
* *
518641 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
518705 TCCAAAAGA
129 TCCAAAAGA
* ** * * * * *
518714 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
518779 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
518844 CAAGAGA
131 CAAAAGA
518851 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAT
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAT
518890 TGTCTCAAGA
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
137 48 0.32
138 102 0.68
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:518787 original size:102 final size:102
Alignment explanation
Indices: 518664--518852 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
518654 TAGACGAAAA
*
518664 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGA
*
518729 GACGGAATTTGTTTCAA-AGAAAACATATTCAAATATT
65 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * ** *
518766 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
518831 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
518853 CTGTCTCAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 36 0.46
102 42 0.54
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:518950 original size:71 final size:72
Alignment explanation
Indices: 518770--518950 Score: 224
Period size: 72 Copynumber: 2.5 Consensus size: 72
518760 AATATTTTGT
* * *
518770 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
** *
518835 AATTTGT
66 AAACTGC
*
518842 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
518906 AAACT-C
66 AAACTGC
* * * *
518912 TTCTAGTGAAAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAAT-TTGTTT
518951 TAAGAAAAAC
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
70 10 0.10
71 27 0.28
72 59 0.61
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
AAACTGC
Found at i:519866 original size:22 final size:22
Alignment explanation
Indices: 519840--519888 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
519830 TTGTGTTTGG
* *
519840 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
519862 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
519884 TCAAA
1 TCAAA
519889 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:519895 original size:22 final size:22
Alignment explanation
Indices: 519852--519895 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
519842 AAAGGTTTGG
* * *
519852 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
519874 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
519896 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:520581 original size:22 final size:22
Alignment explanation
Indices: 520524--520595 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
520514 CTTTTTGTCC
*
520524 CTTTTTCTTTTTGATTTTTGTTTT
1 CTTTTTC-TTTTG-TTATTGTTTT
*
520548 TTTTTTCTTTTGTTATTGTTTCT
1 CTTTTTCTTTTGTTATTGTTT-T
*
520571 CTTTTTC-TTTGTT-TT-TTTG
1 CTTTTTCTTTTGTTATTGTTTT
520590 CTTTTT
1 CTTTTT
520596 TGCTTCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.14
20 3 0.07
21 2 0.05
22 14 0.33
23 12 0.28
24 6 0.14
ACGTcount: A:0.03, C:0.10, G:0.08, T:0.79
Consensus pattern (22 bp):
CTTTTTCTTTTGTTATTGTTTT
Found at i:520597 original size:16 final size:15
Alignment explanation
Indices: 520578--520618 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
520568 TCTCTTTTTC
*
520578 TTTGTTTTTTTGCTTT
1 TTTGTTCTTTT-CTTT
520594 TTTGCTTCTTTTCTTT
1 TTTG-TTCTTTTCTTT
520610 TTTGTTCTT
1 TTTGTTCTT
520619 GATTGGATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 6 0.26
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (15 bp):
TTTGTTCTTTTCTTT
Found at i:523826 original size:16 final size:18
Alignment explanation
Indices: 523794--523828 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
523784 ATATAAAAAC
523794 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
523812 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
523828 A
1 A
523829 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:523947 original size:2 final size:2
Alignment explanation
Indices: 523940--523972 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
523930 CAAAATAGGA
523940 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 A
523973 ATAACACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:534468 original size:9 final size:9
Alignment explanation
Indices: 534454--534484 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
534444 TGATCAAAGA
534454 ATTTAATTT
1 ATTTAATTT
534463 ATTTAATTT
1 ATTTAATTT
534472 ATTTAATTT
1 ATTTAATTT
534481 ATTT
1 ATTT
534485 GTTCGATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTAATTT
Done.