Multiple sequence alignment - TraesCS3B01G219700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G219700 chr3B 100.000 4132 0 0 1 4132 264162578 264166709 0.000000e+00 7631.0
1 TraesCS3B01G219700 chr3B 96.094 128 4 1 1 128 443770745 443770619 1.510000e-49 207.0
2 TraesCS3B01G219700 chr3B 90.805 87 7 1 2694 2780 108832038 108831953 9.390000e-22 115.0
3 TraesCS3B01G219700 chr3A 94.516 3355 114 29 129 3457 244481552 244484862 0.000000e+00 5112.0
4 TraesCS3B01G219700 chr3A 93.952 711 37 4 3426 4132 244484866 244485574 0.000000e+00 1070.0
5 TraesCS3B01G219700 chr3D 92.963 1819 70 30 124 1918 185331596 185333380 0.000000e+00 2597.0
6 TraesCS3B01G219700 chr3D 91.580 1152 51 19 2778 3885 185334301 185335450 0.000000e+00 1548.0
7 TraesCS3B01G219700 chr3D 97.207 752 13 4 1948 2696 185333556 185334302 0.000000e+00 1266.0
8 TraesCS3B01G219700 chr3D 93.333 105 6 1 3838 3941 185335453 185335557 1.990000e-33 154.0
9 TraesCS3B01G219700 chr3D 90.323 93 9 0 2695 2787 446119060 446119152 5.610000e-24 122.0
10 TraesCS3B01G219700 chr3D 90.909 88 8 0 2695 2782 549330686 549330773 7.260000e-23 119.0
11 TraesCS3B01G219700 chr3D 88.043 92 11 0 2695 2786 84113329 84113420 4.370000e-20 110.0
12 TraesCS3B01G219700 chr2B 80.282 355 59 8 3758 4108 275307739 275308086 1.470000e-64 257.0
13 TraesCS3B01G219700 chr2B 95.349 129 6 0 1 129 256450667 256450539 5.410000e-49 206.0
14 TraesCS3B01G219700 chr2B 87.629 97 12 0 2684 2780 464873066 464873162 3.380000e-21 113.0
15 TraesCS3B01G219700 chr2B 100.000 29 0 0 4004 4032 637897331 637897359 2.000000e-03 54.7
16 TraesCS3B01G219700 chr2A 79.339 363 59 14 3754 4108 286423389 286423743 1.480000e-59 241.0
17 TraesCS3B01G219700 chr2A 93.878 49 2 1 1917 1964 672113324 672113372 5.730000e-09 73.1
18 TraesCS3B01G219700 chr2D 79.339 363 58 15 3754 4108 233386393 233386746 5.340000e-59 239.0
19 TraesCS3B01G219700 chr2D 97.656 128 2 1 2 129 314315742 314315616 6.950000e-53 219.0
20 TraesCS3B01G219700 chr2D 88.000 100 10 2 2688 2787 378043089 378043186 2.610000e-22 117.0
21 TraesCS3B01G219700 chr2D 97.561 41 1 0 1917 1957 428663689 428663729 2.060000e-08 71.3
22 TraesCS3B01G219700 chr2D 82.278 79 6 7 3966 4037 45052480 45052557 1.240000e-05 62.1
23 TraesCS3B01G219700 chr5D 96.124 129 4 1 2 130 48730640 48730767 4.190000e-50 209.0
24 TraesCS3B01G219700 chr5D 96.063 127 4 1 2 128 218908924 218908799 5.410000e-49 206.0
25 TraesCS3B01G219700 chr5D 84.337 83 7 5 4005 4084 513941442 513941363 4.430000e-10 76.8
26 TraesCS3B01G219700 chr5D 93.750 48 1 1 1916 1963 314704281 314704236 2.060000e-08 71.3
27 TraesCS3B01G219700 chr1D 95.455 132 5 1 2 133 204437030 204436900 4.190000e-50 209.0
28 TraesCS3B01G219700 chr1D 90.000 90 9 0 2693 2782 6826291 6826202 2.610000e-22 117.0
29 TraesCS3B01G219700 chrUn 96.063 127 4 1 2 128 99493032 99493157 5.410000e-49 206.0
30 TraesCS3B01G219700 chrUn 91.837 49 4 0 1917 1965 103468140 103468092 7.410000e-08 69.4
31 TraesCS3B01G219700 chr4D 96.063 127 4 1 2 128 316576724 316576599 5.410000e-49 206.0
32 TraesCS3B01G219700 chr7D 94.574 129 7 0 2 130 635089188 635089316 2.520000e-47 200.0
33 TraesCS3B01G219700 chr7D 97.674 43 0 1 1917 1959 220311146 220311187 5.730000e-09 73.1
34 TraesCS3B01G219700 chr7D 93.617 47 3 0 1917 1963 467122926 467122880 2.060000e-08 71.3
35 TraesCS3B01G219700 chr5B 82.778 180 26 4 3888 4064 267431456 267431279 5.530000e-34 156.0
36 TraesCS3B01G219700 chr5B 89.130 92 9 1 2689 2779 405239979 405240070 3.380000e-21 113.0
37 TraesCS3B01G219700 chr7A 95.556 45 1 1 1917 1961 290919984 290919941 2.060000e-08 71.3
38 TraesCS3B01G219700 chr4A 90.385 52 4 1 1915 1965 637225137 637225086 2.670000e-07 67.6
39 TraesCS3B01G219700 chr4A 87.500 56 5 2 1909 1964 547197898 547197951 3.450000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G219700 chr3B 264162578 264166709 4131 False 7631.00 7631 100.00000 1 4132 1 chr3B.!!$F1 4131
1 TraesCS3B01G219700 chr3A 244481552 244485574 4022 False 3091.00 5112 94.23400 129 4132 2 chr3A.!!$F1 4003
2 TraesCS3B01G219700 chr3D 185331596 185335557 3961 False 1391.25 2597 93.77075 124 3941 4 chr3D.!!$F4 3817

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
303 304 0.176219 CCGCATCATGGCCAATGTTT 59.824 50.0 10.96 0.0 37.56 2.83 F
1062 1078 0.554305 TATACACGGCTCCCTCTCCA 59.446 55.0 0.00 0.0 0.00 3.86 F
1952 2115 0.257039 TGGGACGGAGGGAGTAGTAC 59.743 60.0 0.00 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2096 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.0 0.0 0.00 4.37 R
1997 2182 1.328680 CCTACACAGCACGAATCATGC 59.671 52.381 0.0 0.0 43.74 4.06 R
3739 3995 0.391263 CCGGCTTCTGGTAAGGTGAC 60.391 60.000 0.0 0.0 0.00 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.768046 AGGCTTTTACCTCCACCGA 58.232 52.632 0.00 0.00 33.62 4.69
19 20 0.613777 AGGCTTTTACCTCCACCGAG 59.386 55.000 0.00 0.00 33.62 4.63
20 21 0.323957 GGCTTTTACCTCCACCGAGT 59.676 55.000 0.00 0.00 33.93 4.18
21 22 1.439679 GCTTTTACCTCCACCGAGTG 58.560 55.000 0.00 0.00 33.93 3.51
22 23 1.001633 GCTTTTACCTCCACCGAGTGA 59.998 52.381 5.71 0.00 35.23 3.41
23 24 2.931320 GCTTTTACCTCCACCGAGTGAG 60.931 54.545 5.71 0.00 35.23 3.51
24 25 1.263356 TTTACCTCCACCGAGTGAGG 58.737 55.000 11.16 11.16 37.11 3.86
25 26 0.613853 TTACCTCCACCGAGTGAGGG 60.614 60.000 15.50 12.97 36.17 4.30
26 27 2.509931 TACCTCCACCGAGTGAGGGG 62.510 65.000 15.50 11.91 36.17 4.79
27 28 3.775654 CTCCACCGAGTGAGGGGC 61.776 72.222 5.71 0.00 35.23 5.80
30 31 4.087892 CACCGAGTGAGGGGCCTG 62.088 72.222 0.84 0.00 35.23 4.85
31 32 4.316823 ACCGAGTGAGGGGCCTGA 62.317 66.667 0.84 0.00 35.02 3.86
32 33 3.003173 CCGAGTGAGGGGCCTGAA 61.003 66.667 0.84 0.00 0.00 3.02
33 34 2.266055 CGAGTGAGGGGCCTGAAC 59.734 66.667 0.84 0.00 0.00 3.18
34 35 2.286523 CGAGTGAGGGGCCTGAACT 61.287 63.158 0.84 4.20 0.00 3.01
35 36 1.599576 GAGTGAGGGGCCTGAACTC 59.400 63.158 0.84 10.20 32.68 3.01
36 37 2.232298 GAGTGAGGGGCCTGAACTCG 62.232 65.000 0.84 0.00 34.03 4.18
37 38 2.203788 TGAGGGGCCTGAACTCGT 60.204 61.111 0.84 0.00 34.03 4.18
38 39 1.841556 TGAGGGGCCTGAACTCGTT 60.842 57.895 0.84 0.00 34.03 3.85
39 40 0.543410 TGAGGGGCCTGAACTCGTTA 60.543 55.000 0.84 0.00 34.03 3.18
40 41 0.611714 GAGGGGCCTGAACTCGTTAA 59.388 55.000 0.84 0.00 0.00 2.01
41 42 1.002773 GAGGGGCCTGAACTCGTTAAA 59.997 52.381 0.84 0.00 0.00 1.52
42 43 1.162698 GGGGCCTGAACTCGTTAAAC 58.837 55.000 0.84 0.00 0.00 2.01
43 44 1.543871 GGGGCCTGAACTCGTTAAACA 60.544 52.381 0.84 0.00 0.00 2.83
44 45 1.534163 GGGCCTGAACTCGTTAAACAC 59.466 52.381 0.84 0.00 0.00 3.32
45 46 1.534163 GGCCTGAACTCGTTAAACACC 59.466 52.381 0.00 0.00 0.00 4.16
46 47 1.193874 GCCTGAACTCGTTAAACACCG 59.806 52.381 0.00 0.00 0.00 4.94
47 48 2.476821 CCTGAACTCGTTAAACACCGT 58.523 47.619 0.00 0.00 0.00 4.83
48 49 2.220133 CCTGAACTCGTTAAACACCGTG 59.780 50.000 0.00 0.00 0.00 4.94
49 50 2.861935 CTGAACTCGTTAAACACCGTGT 59.138 45.455 0.00 0.00 32.82 4.49
50 51 2.604011 TGAACTCGTTAAACACCGTGTG 59.396 45.455 4.57 0.00 39.75 3.82
61 62 3.034721 ACACCGTGTGTTACACCTATG 57.965 47.619 13.29 8.50 45.08 2.23
62 63 1.730064 CACCGTGTGTTACACCTATGC 59.270 52.381 13.29 0.00 45.93 3.14
63 64 1.338389 ACCGTGTGTTACACCTATGCC 60.338 52.381 13.29 0.00 45.93 4.40
64 65 0.996462 CGTGTGTTACACCTATGCCG 59.004 55.000 13.29 2.32 45.93 5.69
65 66 1.670674 CGTGTGTTACACCTATGCCGT 60.671 52.381 13.29 0.00 45.93 5.68
66 67 2.415759 CGTGTGTTACACCTATGCCGTA 60.416 50.000 13.29 0.00 45.93 4.02
67 68 3.184541 GTGTGTTACACCTATGCCGTAG 58.815 50.000 13.29 0.00 43.05 3.51
68 69 2.199236 GTGTTACACCTATGCCGTAGC 58.801 52.381 3.79 0.00 40.48 3.58
69 70 2.104967 TGTTACACCTATGCCGTAGCT 58.895 47.619 0.00 0.00 40.80 3.32
70 71 3.067180 GTGTTACACCTATGCCGTAGCTA 59.933 47.826 3.79 0.00 40.80 3.32
71 72 3.317149 TGTTACACCTATGCCGTAGCTAG 59.683 47.826 0.00 0.00 40.80 3.42
72 73 1.329256 ACACCTATGCCGTAGCTAGG 58.671 55.000 6.46 6.46 41.71 3.02
88 89 4.464262 GGCTCTGCCCCTTATTCG 57.536 61.111 0.00 0.00 44.06 3.34
89 90 1.527370 GGCTCTGCCCCTTATTCGT 59.473 57.895 0.00 0.00 44.06 3.85
90 91 0.756903 GGCTCTGCCCCTTATTCGTA 59.243 55.000 0.00 0.00 44.06 3.43
91 92 1.348036 GGCTCTGCCCCTTATTCGTAT 59.652 52.381 0.00 0.00 44.06 3.06
92 93 2.613223 GGCTCTGCCCCTTATTCGTATC 60.613 54.545 0.00 0.00 44.06 2.24
93 94 2.613223 GCTCTGCCCCTTATTCGTATCC 60.613 54.545 0.00 0.00 0.00 2.59
94 95 1.975680 TCTGCCCCTTATTCGTATCCC 59.024 52.381 0.00 0.00 0.00 3.85
95 96 1.003233 CTGCCCCTTATTCGTATCCCC 59.997 57.143 0.00 0.00 0.00 4.81
96 97 1.359168 GCCCCTTATTCGTATCCCCT 58.641 55.000 0.00 0.00 0.00 4.79
97 98 2.158127 TGCCCCTTATTCGTATCCCCTA 60.158 50.000 0.00 0.00 0.00 3.53
98 99 2.500504 GCCCCTTATTCGTATCCCCTAG 59.499 54.545 0.00 0.00 0.00 3.02
99 100 3.787742 CCCCTTATTCGTATCCCCTAGT 58.212 50.000 0.00 0.00 0.00 2.57
100 101 4.815565 GCCCCTTATTCGTATCCCCTAGTA 60.816 50.000 0.00 0.00 0.00 1.82
101 102 4.708909 CCCCTTATTCGTATCCCCTAGTAC 59.291 50.000 0.00 0.00 0.00 2.73
102 103 5.327732 CCCTTATTCGTATCCCCTAGTACA 58.672 45.833 0.00 0.00 0.00 2.90
103 104 5.184671 CCCTTATTCGTATCCCCTAGTACAC 59.815 48.000 0.00 0.00 0.00 2.90
104 105 5.771666 CCTTATTCGTATCCCCTAGTACACA 59.228 44.000 0.00 0.00 0.00 3.72
105 106 6.436532 CCTTATTCGTATCCCCTAGTACACAT 59.563 42.308 0.00 0.00 0.00 3.21
106 107 7.039223 CCTTATTCGTATCCCCTAGTACACATT 60.039 40.741 0.00 0.00 0.00 2.71
107 108 5.524971 TTCGTATCCCCTAGTACACATTG 57.475 43.478 0.00 0.00 0.00 2.82
108 109 4.539726 TCGTATCCCCTAGTACACATTGT 58.460 43.478 0.00 0.00 0.00 2.71
109 110 4.581824 TCGTATCCCCTAGTACACATTGTC 59.418 45.833 0.00 0.00 0.00 3.18
110 111 4.340097 CGTATCCCCTAGTACACATTGTCA 59.660 45.833 0.00 0.00 0.00 3.58
111 112 5.507482 CGTATCCCCTAGTACACATTGTCAG 60.507 48.000 0.00 0.00 0.00 3.51
112 113 3.786553 TCCCCTAGTACACATTGTCAGT 58.213 45.455 0.00 0.00 0.00 3.41
113 114 4.938028 TCCCCTAGTACACATTGTCAGTA 58.062 43.478 0.00 0.00 0.00 2.74
114 115 5.525484 TCCCCTAGTACACATTGTCAGTAT 58.475 41.667 0.00 0.00 0.00 2.12
115 116 5.597182 TCCCCTAGTACACATTGTCAGTATC 59.403 44.000 0.00 0.00 0.00 2.24
116 117 5.362717 CCCCTAGTACACATTGTCAGTATCA 59.637 44.000 0.00 0.00 0.00 2.15
117 118 6.042093 CCCCTAGTACACATTGTCAGTATCAT 59.958 42.308 0.00 0.00 0.00 2.45
118 119 7.232737 CCCCTAGTACACATTGTCAGTATCATA 59.767 40.741 0.00 0.00 0.00 2.15
119 120 8.638873 CCCTAGTACACATTGTCAGTATCATAA 58.361 37.037 0.00 0.00 0.00 1.90
120 121 9.464714 CCTAGTACACATTGTCAGTATCATAAC 57.535 37.037 0.00 0.00 0.00 1.89
121 122 9.464714 CTAGTACACATTGTCAGTATCATAACC 57.535 37.037 0.00 0.00 0.00 2.85
122 123 7.272978 AGTACACATTGTCAGTATCATAACCC 58.727 38.462 0.00 0.00 0.00 4.11
123 124 5.437060 ACACATTGTCAGTATCATAACCCC 58.563 41.667 0.00 0.00 0.00 4.95
124 125 4.511454 CACATTGTCAGTATCATAACCCCG 59.489 45.833 0.00 0.00 0.00 5.73
125 126 4.407621 ACATTGTCAGTATCATAACCCCGA 59.592 41.667 0.00 0.00 0.00 5.14
126 127 4.395959 TTGTCAGTATCATAACCCCGAC 57.604 45.455 0.00 0.00 0.00 4.79
127 128 3.367321 TGTCAGTATCATAACCCCGACA 58.633 45.455 0.00 0.00 0.00 4.35
174 175 9.627395 TTTTTCGTTCAAAGAAAAACTATGTGA 57.373 25.926 16.96 0.00 46.34 3.58
210 211 8.547894 GGTTTCTCACATTTATTTTTCAACCAC 58.452 33.333 0.00 0.00 31.05 4.16
284 285 5.474532 TGATAATTCATGGCCAGATACTTGC 59.525 40.000 13.05 0.00 0.00 4.01
303 304 0.176219 CCGCATCATGGCCAATGTTT 59.824 50.000 10.96 0.00 37.56 2.83
419 420 9.927668 ATCGATTTGTCCATAAAAGAAAATTGT 57.072 25.926 0.00 0.00 0.00 2.71
421 422 8.977505 CGATTTGTCCATAAAAGAAAATTGTGT 58.022 29.630 0.00 0.00 0.00 3.72
424 425 6.815089 TGTCCATAAAAGAAAATTGTGTGCT 58.185 32.000 0.00 0.00 0.00 4.40
432 433 5.248870 AGAAAATTGTGTGCTTCTCGTTT 57.751 34.783 0.00 0.00 0.00 3.60
433 434 5.036737 AGAAAATTGTGTGCTTCTCGTTTG 58.963 37.500 0.00 0.00 0.00 2.93
444 445 4.856487 TGCTTCTCGTTTGTTTGTTTTCAG 59.144 37.500 0.00 0.00 0.00 3.02
445 446 4.259411 GCTTCTCGTTTGTTTGTTTTCAGC 60.259 41.667 0.00 0.00 0.00 4.26
467 468 4.159879 GCTATATTACCCCGCTGACTACAT 59.840 45.833 0.00 0.00 0.00 2.29
536 537 6.745907 GGTTCGATTGCAACTAAAAAGATACC 59.254 38.462 0.00 0.00 0.00 2.73
551 552 8.454570 AAAAAGATACCTTGTTTCCTCGTAAA 57.545 30.769 0.00 0.00 31.91 2.01
554 555 7.430992 AGATACCTTGTTTCCTCGTAAAAAC 57.569 36.000 0.00 0.00 36.21 2.43
557 558 4.701171 ACCTTGTTTCCTCGTAAAAACACA 59.299 37.500 10.10 4.19 43.11 3.72
599 603 9.710900 TTAGCCATCAAGATGTTACACTATATG 57.289 33.333 9.04 0.00 37.11 1.78
600 604 6.652481 AGCCATCAAGATGTTACACTATATGC 59.348 38.462 9.04 1.45 37.11 3.14
639 643 5.300792 TCCATCCAGTTGGTTAACAAGAAAC 59.699 40.000 8.10 6.31 40.38 2.78
661 665 3.346315 TGATTGCATATAGCCAATCGGG 58.654 45.455 16.84 0.00 44.83 5.14
726 731 5.105392 TGTTGCTTTGTTCTTCTGTGGATTT 60.105 36.000 0.00 0.00 0.00 2.17
737 742 7.801893 TCTTCTGTGGATTTTTACCCTAGTA 57.198 36.000 0.00 0.00 0.00 1.82
746 751 9.841295 TGGATTTTTACCCTAGTATAATCACAC 57.159 33.333 0.00 0.00 34.59 3.82
827 839 1.474855 GCAAAAGGGCCTTGCAAGAAA 60.475 47.619 28.05 0.00 46.78 2.52
838 850 6.401394 GGCCTTGCAAGAAAAAGAAGATAAT 58.599 36.000 28.05 0.00 0.00 1.28
840 852 7.388776 GGCCTTGCAAGAAAAAGAAGATAATTT 59.611 33.333 28.05 0.00 0.00 1.82
841 853 8.777413 GCCTTGCAAGAAAAAGAAGATAATTTT 58.223 29.630 28.05 0.00 0.00 1.82
998 1014 0.824109 TCGCACCACCCTATCTCTTG 59.176 55.000 0.00 0.00 0.00 3.02
1011 1027 2.381725 TCTCTTGCATGTCAGCTCTG 57.618 50.000 0.00 0.00 34.99 3.35
1050 1066 1.791204 CTGCTCTGCTGCATATACACG 59.209 52.381 1.31 0.00 42.48 4.49
1062 1078 0.554305 TATACACGGCTCCCTCTCCA 59.446 55.000 0.00 0.00 0.00 3.86
1103 1119 1.374252 GTTCCGCGGTGTCAGTCAT 60.374 57.895 27.15 0.00 0.00 3.06
1398 1414 3.624861 CCGAGATTAACAAGCAGCTCAAT 59.375 43.478 0.00 0.00 0.00 2.57
1784 1807 2.066262 TGTACTTGCTTGCGCTCTTAC 58.934 47.619 9.73 1.18 36.97 2.34
1818 1851 2.012937 AACAATTCGATCGGGCGTAA 57.987 45.000 16.41 1.49 0.00 3.18
1867 1900 4.775236 ACTATGACCAGAAATGCCTTCTC 58.225 43.478 0.00 0.00 42.84 2.87
1949 2112 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
1952 2115 0.257039 TGGGACGGAGGGAGTAGTAC 59.743 60.000 0.00 0.00 0.00 2.73
1953 2116 0.550432 GGGACGGAGGGAGTAGTACT 59.450 60.000 1.37 1.37 0.00 2.73
1954 2117 1.677942 GGACGGAGGGAGTAGTACTG 58.322 60.000 7.76 0.00 0.00 2.74
1955 2118 1.064832 GGACGGAGGGAGTAGTACTGT 60.065 57.143 7.76 0.00 0.00 3.55
1956 2119 2.171448 GGACGGAGGGAGTAGTACTGTA 59.829 54.545 7.76 0.00 0.00 2.74
1957 2120 3.465871 GACGGAGGGAGTAGTACTGTAG 58.534 54.545 7.76 0.00 0.00 2.74
1958 2121 2.843113 ACGGAGGGAGTAGTACTGTAGT 59.157 50.000 7.76 0.22 0.00 2.73
1959 2122 3.265479 ACGGAGGGAGTAGTACTGTAGTT 59.735 47.826 7.76 0.00 0.00 2.24
1960 2123 3.626670 CGGAGGGAGTAGTACTGTAGTTG 59.373 52.174 7.76 0.00 0.00 3.16
1961 2124 4.598022 GGAGGGAGTAGTACTGTAGTTGT 58.402 47.826 7.76 0.00 0.00 3.32
1962 2125 5.015515 GGAGGGAGTAGTACTGTAGTTGTT 58.984 45.833 7.76 0.00 0.00 2.83
1963 2126 5.125257 GGAGGGAGTAGTACTGTAGTTGTTC 59.875 48.000 7.76 0.00 0.00 3.18
1964 2127 5.890049 AGGGAGTAGTACTGTAGTTGTTCT 58.110 41.667 7.76 0.00 0.00 3.01
1965 2128 5.945191 AGGGAGTAGTACTGTAGTTGTTCTC 59.055 44.000 7.76 4.91 0.00 2.87
1966 2129 5.709164 GGGAGTAGTACTGTAGTTGTTCTCA 59.291 44.000 7.76 0.00 0.00 3.27
1967 2130 6.127952 GGGAGTAGTACTGTAGTTGTTCTCAG 60.128 46.154 7.76 0.00 0.00 3.35
1969 2132 5.768662 AGTAGTACTGTAGTTGTTCTCAGCA 59.231 40.000 5.39 0.00 0.00 4.41
1970 2133 5.730296 AGTACTGTAGTTGTTCTCAGCAT 57.270 39.130 0.00 0.00 0.00 3.79
1971 2134 6.835819 AGTACTGTAGTTGTTCTCAGCATA 57.164 37.500 0.00 0.00 0.00 3.14
1972 2135 7.411486 AGTACTGTAGTTGTTCTCAGCATAT 57.589 36.000 0.00 0.00 0.00 1.78
2355 2540 0.685097 TGCCTCTCGGTAAAGCAAGT 59.315 50.000 0.00 0.00 0.00 3.16
2655 2842 5.124297 TGCTCAACATGACAATAATGACCTG 59.876 40.000 0.00 0.00 0.00 4.00
2706 2893 6.377912 AGCATTATACTCTACTCCCTCTGTT 58.622 40.000 0.00 0.00 0.00 3.16
2721 2908 7.939588 ACTCCCTCTGTTCCATAATATAAAAGC 59.060 37.037 0.00 0.00 0.00 3.51
2771 2958 5.623956 ATGTTCTTGTATTATGGGACGGA 57.376 39.130 0.00 0.00 0.00 4.69
2825 3012 7.219535 TGACAATATTAGAGCTTCGACGTAAAC 59.780 37.037 0.00 0.00 0.00 2.01
3075 3262 2.903357 CTGCGTACCTCATGCCCT 59.097 61.111 0.00 0.00 38.50 5.19
3166 3353 3.136260 AGGATCCATCTCTGCCTTTCTTC 59.864 47.826 15.82 0.00 0.00 2.87
3183 3370 6.766944 CCTTTCTTCTCAGACATAATCATGCT 59.233 38.462 0.00 0.00 35.39 3.79
3184 3371 7.041916 CCTTTCTTCTCAGACATAATCATGCTC 60.042 40.741 0.00 0.00 35.39 4.26
3186 3373 5.601729 TCTTCTCAGACATAATCATGCTCCT 59.398 40.000 0.00 0.00 35.39 3.69
3187 3374 5.465532 TCTCAGACATAATCATGCTCCTC 57.534 43.478 0.00 0.00 35.39 3.71
3188 3375 4.897670 TCTCAGACATAATCATGCTCCTCA 59.102 41.667 0.00 0.00 35.39 3.86
3229 3423 7.288389 AGCACATGATCCATGGTTAATTAACAT 59.712 33.333 25.59 15.73 45.16 2.71
3388 3582 8.500753 TCTGAAGTTGTTATGTAACTTGTGTT 57.499 30.769 7.74 0.00 45.52 3.32
3475 3710 1.909700 AGGTCAACAACGGCATTGAT 58.090 45.000 0.00 0.00 41.23 2.57
3576 3832 2.423577 ACGATGCCCTTACACAAAGTC 58.576 47.619 0.00 0.00 32.89 3.01
3601 3857 4.258702 AGAAACTACATATGGCTAGGCG 57.741 45.455 12.19 0.00 0.00 5.52
3605 3861 4.891992 ACTACATATGGCTAGGCGAAAT 57.108 40.909 12.19 2.29 0.00 2.17
3637 3893 7.568199 AAACTACACTTTTATGTGCAACTCT 57.432 32.000 0.00 0.00 41.30 3.24
3644 3900 7.013274 ACACTTTTATGTGCAACTCTGTAACAT 59.987 33.333 0.00 0.00 41.30 2.71
3724 3980 0.179032 TTGTGACGTTGTCATGCCCT 60.179 50.000 2.62 0.00 44.63 5.19
3737 3993 0.983378 ATGCCCTAGGGGTGTCTCAC 60.983 60.000 29.57 10.31 46.51 3.51
3739 3995 1.617947 GCCCTAGGGGTGTCTCACTG 61.618 65.000 29.57 0.00 46.51 3.66
3783 4057 1.134907 CCTAGGTCGGTTACGCAATGT 60.135 52.381 0.00 0.00 40.69 2.71
3815 4089 2.829914 CCATGGCCCCACGACATG 60.830 66.667 0.00 0.00 41.15 3.21
3825 4099 2.173669 CACGACATGATGGTCCCGC 61.174 63.158 0.00 0.00 34.24 6.13
3941 4266 0.038709 GAGGCTAGGCTAGTCGCATG 60.039 60.000 22.54 0.00 41.67 4.06
3968 4294 4.516698 ACAACACAAAACCATAGAGCTCTG 59.483 41.667 26.78 12.23 0.00 3.35
3969 4295 4.357918 ACACAAAACCATAGAGCTCTGT 57.642 40.909 26.78 17.59 0.00 3.41
4012 4338 8.719596 TGTAACCCCTACACAATCAATATACAT 58.280 33.333 0.00 0.00 35.50 2.29
4039 4365 3.153130 GGAGTAGGGTATTACCTCGTCC 58.847 54.545 12.54 9.71 42.09 4.79
4043 4369 1.007479 AGGGTATTACCTCGTCCACCA 59.993 52.381 12.54 0.00 38.64 4.17
4044 4370 1.411612 GGGTATTACCTCGTCCACCAG 59.588 57.143 12.54 0.00 38.64 4.00
4046 4372 1.411612 GTATTACCTCGTCCACCAGGG 59.588 57.143 0.00 0.00 33.57 4.45
4092 4418 5.600069 TGCTCATGTTACCATCTGATCTACT 59.400 40.000 0.00 0.00 0.00 2.57
4094 4420 6.015519 GCTCATGTTACCATCTGATCTACTCT 60.016 42.308 0.00 0.00 0.00 3.24
4099 4425 8.183104 TGTTACCATCTGATCTACTCTTATGG 57.817 38.462 0.00 0.00 40.18 2.74
4100 4426 7.785028 TGTTACCATCTGATCTACTCTTATGGT 59.215 37.037 8.91 8.91 44.88 3.55
4102 4428 5.475220 ACCATCTGATCTACTCTTATGGTCG 59.525 44.000 0.00 0.00 41.97 4.79
4114 4440 9.917872 CTACTCTTATGGTCGTATACAATATCG 57.082 37.037 3.32 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.613777 CTCGGTGGAGGTAAAAGCCT 59.386 55.000 0.00 0.00 42.53 4.58
2 3 1.001633 TCACTCGGTGGAGGTAAAAGC 59.998 52.381 4.52 0.00 44.93 3.51
4 5 1.621814 CCTCACTCGGTGGAGGTAAAA 59.378 52.381 8.45 0.00 44.93 1.52
5 6 1.263356 CCTCACTCGGTGGAGGTAAA 58.737 55.000 8.45 0.00 44.93 2.01
6 7 0.613853 CCCTCACTCGGTGGAGGTAA 60.614 60.000 13.59 0.00 44.93 2.85
7 8 1.000019 CCCTCACTCGGTGGAGGTA 60.000 63.158 13.59 0.00 44.93 3.08
8 9 2.283966 CCCTCACTCGGTGGAGGT 60.284 66.667 13.59 0.00 44.93 3.85
9 10 3.077556 CCCCTCACTCGGTGGAGG 61.078 72.222 9.38 9.38 44.93 4.30
10 11 3.775654 GCCCCTCACTCGGTGGAG 61.776 72.222 4.52 0.00 46.13 3.86
13 14 4.087892 CAGGCCCCTCACTCGGTG 62.088 72.222 0.00 0.00 34.45 4.94
14 15 3.846405 TTCAGGCCCCTCACTCGGT 62.846 63.158 0.00 0.00 0.00 4.69
15 16 3.003173 TTCAGGCCCCTCACTCGG 61.003 66.667 0.00 0.00 0.00 4.63
16 17 2.232298 GAGTTCAGGCCCCTCACTCG 62.232 65.000 0.00 0.00 0.00 4.18
17 18 1.599576 GAGTTCAGGCCCCTCACTC 59.400 63.158 0.00 2.32 0.00 3.51
18 19 2.286523 CGAGTTCAGGCCCCTCACT 61.287 63.158 0.00 0.00 0.00 3.41
19 20 2.113243 AACGAGTTCAGGCCCCTCAC 62.113 60.000 0.00 0.00 0.00 3.51
20 21 0.543410 TAACGAGTTCAGGCCCCTCA 60.543 55.000 0.00 0.00 0.00 3.86
21 22 0.611714 TTAACGAGTTCAGGCCCCTC 59.388 55.000 0.00 0.00 0.00 4.30
22 23 1.061546 TTTAACGAGTTCAGGCCCCT 58.938 50.000 0.00 0.00 0.00 4.79
23 24 1.162698 GTTTAACGAGTTCAGGCCCC 58.837 55.000 0.00 0.00 0.00 5.80
24 25 1.534163 GTGTTTAACGAGTTCAGGCCC 59.466 52.381 0.00 0.00 0.00 5.80
25 26 1.534163 GGTGTTTAACGAGTTCAGGCC 59.466 52.381 0.00 0.00 0.00 5.19
26 27 1.193874 CGGTGTTTAACGAGTTCAGGC 59.806 52.381 0.00 0.00 0.00 4.85
27 28 2.220133 CACGGTGTTTAACGAGTTCAGG 59.780 50.000 0.00 0.00 0.00 3.86
28 29 2.861935 ACACGGTGTTTAACGAGTTCAG 59.138 45.455 8.21 0.00 30.02 3.02
29 30 2.604011 CACACGGTGTTTAACGAGTTCA 59.396 45.455 11.82 0.00 31.85 3.18
30 31 2.604462 ACACACGGTGTTTAACGAGTTC 59.396 45.455 11.82 0.00 45.08 3.01
31 32 2.620242 ACACACGGTGTTTAACGAGTT 58.380 42.857 11.82 0.00 45.08 3.01
32 33 2.298411 ACACACGGTGTTTAACGAGT 57.702 45.000 11.82 1.52 45.08 4.18
46 47 4.524855 GCTACGGCATAGGTGTAACACAC 61.525 52.174 7.44 7.44 42.22 3.82
47 48 2.417651 GCTACGGCATAGGTGTAACACA 60.418 50.000 0.00 0.00 37.13 3.72
48 49 2.159142 AGCTACGGCATAGGTGTAACAC 60.159 50.000 0.00 0.00 40.21 3.32
49 50 2.104967 AGCTACGGCATAGGTGTAACA 58.895 47.619 0.00 0.00 40.21 2.41
50 51 2.884894 AGCTACGGCATAGGTGTAAC 57.115 50.000 0.00 0.00 40.21 2.50
51 52 2.889045 CCTAGCTACGGCATAGGTGTAA 59.111 50.000 2.09 0.00 41.79 2.41
52 53 2.511659 CCTAGCTACGGCATAGGTGTA 58.488 52.381 2.09 0.00 41.79 2.90
53 54 1.329256 CCTAGCTACGGCATAGGTGT 58.671 55.000 2.09 0.00 41.79 4.16
54 55 0.038159 GCCTAGCTACGGCATAGGTG 60.038 60.000 22.05 0.00 46.77 4.00
55 56 2.352817 GCCTAGCTACGGCATAGGT 58.647 57.895 22.05 0.00 46.77 3.08
61 62 3.507597 GGCAGAGCCTAGCTACGGC 62.508 68.421 20.37 20.37 46.69 5.68
62 63 2.731374 GGCAGAGCCTAGCTACGG 59.269 66.667 0.00 0.00 46.69 4.02
72 73 2.613223 GGATACGAATAAGGGGCAGAGC 60.613 54.545 0.00 0.00 0.00 4.09
73 74 2.028020 GGGATACGAATAAGGGGCAGAG 60.028 54.545 0.00 0.00 37.60 3.35
74 75 1.975680 GGGATACGAATAAGGGGCAGA 59.024 52.381 0.00 0.00 37.60 4.26
75 76 1.003233 GGGGATACGAATAAGGGGCAG 59.997 57.143 0.00 0.00 37.60 4.85
76 77 1.061546 GGGGATACGAATAAGGGGCA 58.938 55.000 0.00 0.00 37.60 5.36
77 78 1.359168 AGGGGATACGAATAAGGGGC 58.641 55.000 0.00 0.00 37.60 5.80
78 79 3.787742 ACTAGGGGATACGAATAAGGGG 58.212 50.000 0.00 0.00 37.60 4.79
79 80 5.184671 GTGTACTAGGGGATACGAATAAGGG 59.815 48.000 0.00 0.00 37.60 3.95
80 81 5.771666 TGTGTACTAGGGGATACGAATAAGG 59.228 44.000 0.00 0.00 37.60 2.69
81 82 6.889301 TGTGTACTAGGGGATACGAATAAG 57.111 41.667 0.00 0.00 37.60 1.73
82 83 7.288389 ACAATGTGTACTAGGGGATACGAATAA 59.712 37.037 0.00 0.00 37.60 1.40
83 84 6.779049 ACAATGTGTACTAGGGGATACGAATA 59.221 38.462 0.00 0.00 37.60 1.75
84 85 5.601313 ACAATGTGTACTAGGGGATACGAAT 59.399 40.000 0.00 0.00 37.60 3.34
85 86 4.957954 ACAATGTGTACTAGGGGATACGAA 59.042 41.667 0.00 0.00 37.60 3.85
86 87 4.539726 ACAATGTGTACTAGGGGATACGA 58.460 43.478 0.00 0.00 37.60 3.43
87 88 4.340097 TGACAATGTGTACTAGGGGATACG 59.660 45.833 0.00 0.00 37.60 3.06
88 89 5.363005 ACTGACAATGTGTACTAGGGGATAC 59.637 44.000 0.00 0.00 0.00 2.24
89 90 5.525484 ACTGACAATGTGTACTAGGGGATA 58.475 41.667 0.00 0.00 0.00 2.59
90 91 4.362677 ACTGACAATGTGTACTAGGGGAT 58.637 43.478 0.00 0.00 0.00 3.85
91 92 3.786553 ACTGACAATGTGTACTAGGGGA 58.213 45.455 0.00 0.00 0.00 4.81
92 93 5.362717 TGATACTGACAATGTGTACTAGGGG 59.637 44.000 0.00 0.00 0.00 4.79
93 94 6.465439 TGATACTGACAATGTGTACTAGGG 57.535 41.667 0.00 0.00 0.00 3.53
94 95 9.464714 GTTATGATACTGACAATGTGTACTAGG 57.535 37.037 0.00 0.00 0.00 3.02
95 96 9.464714 GGTTATGATACTGACAATGTGTACTAG 57.535 37.037 0.00 0.00 0.00 2.57
96 97 8.418662 GGGTTATGATACTGACAATGTGTACTA 58.581 37.037 0.00 0.00 0.00 1.82
97 98 7.272978 GGGTTATGATACTGACAATGTGTACT 58.727 38.462 0.00 0.00 0.00 2.73
98 99 6.482308 GGGGTTATGATACTGACAATGTGTAC 59.518 42.308 0.00 0.00 0.00 2.90
99 100 6.588204 GGGGTTATGATACTGACAATGTGTA 58.412 40.000 0.00 0.00 0.00 2.90
100 101 5.437060 GGGGTTATGATACTGACAATGTGT 58.563 41.667 0.00 0.00 0.00 3.72
101 102 4.511454 CGGGGTTATGATACTGACAATGTG 59.489 45.833 0.00 0.00 0.00 3.21
102 103 4.407621 TCGGGGTTATGATACTGACAATGT 59.592 41.667 0.00 0.00 0.00 2.71
103 104 4.750098 GTCGGGGTTATGATACTGACAATG 59.250 45.833 0.00 0.00 0.00 2.82
104 105 4.407621 TGTCGGGGTTATGATACTGACAAT 59.592 41.667 0.00 0.00 32.68 2.71
105 106 3.770388 TGTCGGGGTTATGATACTGACAA 59.230 43.478 0.00 0.00 32.68 3.18
106 107 3.367321 TGTCGGGGTTATGATACTGACA 58.633 45.455 0.00 0.00 33.14 3.58
107 108 3.383825 ACTGTCGGGGTTATGATACTGAC 59.616 47.826 0.00 0.00 0.00 3.51
108 109 3.638860 ACTGTCGGGGTTATGATACTGA 58.361 45.455 0.00 0.00 0.00 3.41
109 110 4.022242 CCTACTGTCGGGGTTATGATACTG 60.022 50.000 0.00 0.00 0.00 2.74
110 111 4.150359 CCTACTGTCGGGGTTATGATACT 58.850 47.826 0.00 0.00 0.00 2.12
111 112 3.257624 CCCTACTGTCGGGGTTATGATAC 59.742 52.174 9.49 0.00 38.08 2.24
112 113 3.140707 TCCCTACTGTCGGGGTTATGATA 59.859 47.826 16.59 0.00 43.00 2.15
113 114 2.090943 TCCCTACTGTCGGGGTTATGAT 60.091 50.000 16.59 0.00 43.00 2.45
114 115 1.288633 TCCCTACTGTCGGGGTTATGA 59.711 52.381 16.59 0.00 43.00 2.15
115 116 1.411612 GTCCCTACTGTCGGGGTTATG 59.588 57.143 16.59 0.00 43.00 1.90
116 117 1.690527 GGTCCCTACTGTCGGGGTTAT 60.691 57.143 16.59 0.00 43.00 1.89
117 118 0.324645 GGTCCCTACTGTCGGGGTTA 60.325 60.000 16.59 0.00 43.00 2.85
118 119 1.611556 GGTCCCTACTGTCGGGGTT 60.612 63.158 16.59 0.00 43.00 4.11
119 120 2.038490 GGTCCCTACTGTCGGGGT 59.962 66.667 16.59 0.00 43.00 4.95
120 121 1.305887 AAGGTCCCTACTGTCGGGG 60.306 63.158 16.59 13.71 42.23 5.73
121 122 1.328430 GGAAGGTCCCTACTGTCGGG 61.328 65.000 11.05 11.05 43.38 5.14
122 123 2.200052 GGAAGGTCCCTACTGTCGG 58.800 63.158 0.00 0.00 0.00 4.79
174 175 6.923199 AAATGTGAGAAACCTCATTTGGAT 57.077 33.333 0.00 0.00 42.11 3.41
205 206 4.081917 ACAAAAGTTTCCATTGACGTGGTT 60.082 37.500 0.00 0.00 40.27 3.67
210 211 6.826893 AATGAACAAAAGTTTCCATTGACG 57.173 33.333 0.00 0.00 0.00 4.35
246 247 5.308014 TGAATTATCAATAGCGGACTGCAT 58.692 37.500 9.39 0.00 38.32 3.96
284 285 0.176219 AAACATTGGCCATGATGCGG 59.824 50.000 15.96 0.13 36.24 5.69
419 420 3.840890 AACAAACAAACGAGAAGCACA 57.159 38.095 0.00 0.00 0.00 4.57
421 422 4.799678 TGAAAACAAACAAACGAGAAGCA 58.200 34.783 0.00 0.00 0.00 3.91
424 425 5.054390 AGCTGAAAACAAACAAACGAGAA 57.946 34.783 0.00 0.00 0.00 2.87
432 433 6.094325 CGGGGTAATATAGCTGAAAACAAACA 59.906 38.462 0.00 0.00 0.00 2.83
433 434 6.492254 CGGGGTAATATAGCTGAAAACAAAC 58.508 40.000 0.00 0.00 0.00 2.93
444 445 3.508793 TGTAGTCAGCGGGGTAATATAGC 59.491 47.826 0.00 0.00 0.00 2.97
445 446 5.916661 ATGTAGTCAGCGGGGTAATATAG 57.083 43.478 0.00 0.00 0.00 1.31
467 468 9.603298 CGTTTGAATATACGAAGCTACATAGTA 57.397 33.333 0.00 0.00 40.03 1.82
536 537 7.569677 TTTTGTGTTTTTACGAGGAAACAAG 57.430 32.000 13.44 0.00 44.53 3.16
569 573 8.353423 AGTGTAACATCTTGATGGCTAAAAAT 57.647 30.769 14.18 0.00 41.43 1.82
599 603 1.745489 GGACATTCCCGTGACCTGC 60.745 63.158 0.00 0.00 32.31 4.85
600 604 0.253044 ATGGACATTCCCGTGACCTG 59.747 55.000 0.00 0.00 35.03 4.00
639 643 3.376234 CCCGATTGGCTATATGCAATCAG 59.624 47.826 0.00 0.00 45.15 2.90
661 665 4.825085 TCTAACCATGGTTTGAGGTGAAAC 59.175 41.667 34.04 0.00 39.31 2.78
726 731 5.507817 CCGCGTGTGATTATACTAGGGTAAA 60.508 44.000 4.92 0.00 0.00 2.01
737 742 0.249489 GGAGAGCCGCGTGTGATTAT 60.249 55.000 4.92 0.00 0.00 1.28
746 751 2.357517 ACACAAAGGAGAGCCGCG 60.358 61.111 0.00 0.00 39.96 6.46
782 791 7.010460 GCTTTGCTTATTGTTGTTTCAGAGTTT 59.990 33.333 0.00 0.00 0.00 2.66
890 902 2.347114 CACACGCCCATCTCACCA 59.653 61.111 0.00 0.00 0.00 4.17
998 1014 1.707239 GCTGCTCAGAGCTGACATGC 61.707 60.000 28.45 16.07 41.94 4.06
1050 1066 2.456443 GGGGAATGGAGAGGGAGCC 61.456 68.421 0.00 0.00 0.00 4.70
1093 1109 3.525537 CCATCCTGTGTATGACTGACAC 58.474 50.000 0.00 0.00 46.07 3.67
1098 1114 1.137086 GACGCCATCCTGTGTATGACT 59.863 52.381 0.00 0.00 0.00 3.41
1103 1119 2.889617 CGGACGCCATCCTGTGTA 59.110 61.111 0.44 0.00 46.69 2.90
1398 1414 2.559840 GCGTCGAACTCGTCCTGA 59.440 61.111 0.00 0.00 40.80 3.86
1680 1699 3.445805 TGGTTTTCTGAAAAGGAAACGCT 59.554 39.130 15.39 0.00 33.22 5.07
1784 1807 5.982516 TCGAATTGTTTTGTTTTGATGGGAG 59.017 36.000 0.00 0.00 0.00 4.30
1818 1851 3.157087 CATTTGGCTTCTGGTTAGTGGT 58.843 45.455 0.00 0.00 0.00 4.16
1882 1915 5.048083 TGCGAAATTGAGTTGAAGCCTAAAT 60.048 36.000 0.00 0.00 0.00 1.40
1887 1920 2.704725 TGCGAAATTGAGTTGAAGCC 57.295 45.000 0.00 0.00 0.00 4.35
1918 1951 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
1919 1952 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
1920 1953 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
1921 1954 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
1923 1956 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1932 2095 1.133544 GTACTACTCCCTCCGTCCCAT 60.134 57.143 0.00 0.00 0.00 4.00
1933 2096 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
1936 2099 2.416680 ACAGTACTACTCCCTCCGTC 57.583 55.000 0.00 0.00 0.00 4.79
1949 2112 9.186323 CATATATGCTGAGAACAACTACAGTAC 57.814 37.037 0.00 0.00 33.57 2.73
1952 2115 9.486497 AATCATATATGCTGAGAACAACTACAG 57.514 33.333 7.92 0.00 0.00 2.74
1953 2116 9.836864 AAATCATATATGCTGAGAACAACTACA 57.163 29.630 7.92 0.00 0.00 2.74
1955 2118 9.836864 ACAAATCATATATGCTGAGAACAACTA 57.163 29.630 7.92 0.00 0.00 2.24
1956 2119 8.618677 CACAAATCATATATGCTGAGAACAACT 58.381 33.333 7.92 0.00 0.00 3.16
1957 2120 8.400947 ACACAAATCATATATGCTGAGAACAAC 58.599 33.333 7.92 0.00 0.00 3.32
1958 2121 8.510243 ACACAAATCATATATGCTGAGAACAA 57.490 30.769 7.92 0.00 0.00 2.83
1959 2122 8.510243 AACACAAATCATATATGCTGAGAACA 57.490 30.769 7.92 0.00 0.00 3.18
1997 2182 1.328680 CCTACACAGCACGAATCATGC 59.671 52.381 0.00 0.00 43.74 4.06
2355 2540 5.067674 CCCATCGAAGAAAATGCAGGATTAA 59.932 40.000 0.00 0.00 43.58 1.40
2392 2578 1.618837 ACGCAGCTGTTAGAAAGAGGA 59.381 47.619 16.64 0.00 0.00 3.71
2655 2842 4.510571 AGGGGTGATGTTTATTGTACGAC 58.489 43.478 0.00 0.00 0.00 4.34
2706 2893 9.562583 GTGTCAAAAACGCTTTTATATTATGGA 57.437 29.630 0.00 0.00 32.85 3.41
2750 2937 4.141801 CCTCCGTCCCATAATACAAGAACA 60.142 45.833 0.00 0.00 0.00 3.18
2751 2938 4.377897 CCTCCGTCCCATAATACAAGAAC 58.622 47.826 0.00 0.00 0.00 3.01
2825 3012 7.060383 ACAGTATCATCAATAGAGGTCTTGG 57.940 40.000 0.00 0.00 0.00 3.61
3166 3353 5.211174 TGAGGAGCATGATTATGTCTGAG 57.789 43.478 0.00 0.00 36.65 3.35
3229 3423 2.961741 GAGCACAGGAGGATGTAGATCA 59.038 50.000 1.87 0.00 0.00 2.92
3475 3710 7.588123 CGTGCATGCATTTACGGTAATAAAATA 59.412 33.333 25.64 0.00 33.27 1.40
3576 3832 5.698545 GCCTAGCCATATGTAGTTTCTTGAG 59.301 44.000 1.24 0.00 0.00 3.02
3644 3900 5.123186 CGTGGCATAAAAAGAGGTCACATTA 59.877 40.000 0.00 0.00 0.00 1.90
3724 3980 1.629043 GTGACAGTGAGACACCCCTA 58.371 55.000 0.00 0.00 37.00 3.53
3737 3993 1.673033 CGGCTTCTGGTAAGGTGACAG 60.673 57.143 0.00 0.00 0.00 3.51
3739 3995 0.391263 CCGGCTTCTGGTAAGGTGAC 60.391 60.000 0.00 0.00 0.00 3.67
3815 4089 2.044946 AAGCCTTGCGGGACCATC 60.045 61.111 0.00 0.00 37.23 3.51
3835 4109 1.588674 CGGTTGCCTTGTCTTGTACA 58.411 50.000 0.00 0.00 35.88 2.90
3941 4266 5.648092 AGCTCTATGGTTTTGTGTTGTATCC 59.352 40.000 0.00 0.00 0.00 2.59
3968 4294 5.064834 GGTTACAAAGATCGAGGGATTGAAC 59.935 44.000 9.21 8.65 31.51 3.18
3969 4295 5.183228 GGTTACAAAGATCGAGGGATTGAA 58.817 41.667 9.21 0.00 31.51 2.69
4012 4338 5.221803 CGAGGTAATACCCTACTCCTACTCA 60.222 48.000 5.71 0.00 39.75 3.41
4039 4365 1.679977 CATGTTCAGGCCCCTGGTG 60.680 63.158 14.02 5.32 43.75 4.17
4043 4369 0.849094 TTACCCATGTTCAGGCCCCT 60.849 55.000 0.00 0.00 0.00 4.79
4044 4370 0.040499 TTTACCCATGTTCAGGCCCC 59.960 55.000 0.00 0.00 0.00 5.80
4046 4372 2.492088 GAGTTTTACCCATGTTCAGGCC 59.508 50.000 0.00 0.00 0.00 5.19
4049 4375 4.074970 AGCAGAGTTTTACCCATGTTCAG 58.925 43.478 0.00 0.00 0.00 3.02
4092 4418 7.926674 TCCGATATTGTATACGACCATAAGA 57.073 36.000 0.00 0.00 0.00 2.10
4094 4420 6.976349 GCATCCGATATTGTATACGACCATAA 59.024 38.462 0.00 0.00 0.00 1.90
4099 4425 4.740268 TGGCATCCGATATTGTATACGAC 58.260 43.478 0.00 0.00 0.00 4.34
4100 4426 5.394224 TTGGCATCCGATATTGTATACGA 57.606 39.130 0.00 0.00 0.00 3.43
4102 4428 9.769093 GTATTTTTGGCATCCGATATTGTATAC 57.231 33.333 0.00 0.00 0.00 1.47


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.