Multiple sequence alignment - TraesCS5B01G544800

Loading Multiple Alignment...

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 TraesCS5B01G544800 chr5B 100.000 5459 0 0 1 5459 697348287 697342829 0.000000e+00 10081.0
1 TraesCS5B01G544800 chr5B 90.738 745 48 8 3704 4433 697184403 697183665 0.000000e+00 974.0
2 TraesCS5B01G544800 chr5B 88.039 510 40 12 4084 4575 697178951 697178445 7.880000e-163 584.0
3 TraesCS5B01G544800 chr5B 91.220 410 33 3 4083 4490 697239622 697239214 6.180000e-154 555.0
4 TraesCS5B01G544800 chr4A 93.189 4434 226 28 170 4563 615108342 615103945 0.000000e+00 6445.0
5 TraesCS5B01G544800 chr4A 88.762 614 35 14 3973 4567 614911338 614910740 0.000000e+00 721.0
6 TraesCS5B01G544800 chr4A 93.299 388 14 3 4570 4947 614910688 614910303 3.690000e-156 562.0
7 TraesCS5B01G544800 chr4A 84.043 282 19 13 5175 5438 614910024 614909751 1.170000e-61 248.0
8 TraesCS5B01G544800 chr5D 95.008 3105 146 4 916 4016 553469606 553472705 0.000000e+00 4867.0
9 TraesCS5B01G544800 chr5D 89.721 3619 316 16 892 4490 553461515 553457933 0.000000e+00 4571.0
10 TraesCS5B01G544800 chr5D 92.847 1454 71 13 3124 4560 553063784 553065221 0.000000e+00 2078.0
11 TraesCS5B01G544800 chr5D 91.746 739 56 4 3704 4440 553509105 553509840 0.000000e+00 1022.0
12 TraesCS5B01G544800 chr5D 88.029 543 34 11 4050 4575 553472703 553473231 1.000000e-171 614.0
13 TraesCS5B01G544800 chr5D 86.749 483 51 4 4021 4490 553060445 553059963 4.840000e-145 525.0
14 TraesCS5B01G544800 chr5D 91.925 322 11 5 374 689 553465135 553465447 2.330000e-118 436.0
15 TraesCS5B01G544800 chr5D 82.838 437 52 9 5040 5458 553065711 553066142 2.400000e-98 370.0
16 TraesCS5B01G544800 chr5D 80.139 433 42 15 413 845 553461921 553461533 3.220000e-72 283.0
17 TraesCS5B01G544800 chr5D 88.584 219 17 3 4575 4792 553473281 553473492 5.420000e-65 259.0
18 TraesCS5B01G544800 chr5D 87.317 205 19 4 146 344 553462120 553461917 1.530000e-55 228.0
19 TraesCS5B01G544800 chr5D 85.806 155 11 5 697 840 553469451 553469605 2.630000e-33 154.0
20 TraesCS5B01G544800 chr7D 88.657 767 43 9 4570 5326 346569085 346569817 0.000000e+00 894.0
21 TraesCS5B01G544800 chr7D 71.712 403 91 13 3472 3855 436953867 436954265 2.090000e-14 91.6
22 TraesCS5B01G544800 chr7B 78.358 134 29 0 3722 3855 453449515 453449648 2.710000e-13 87.9
23 TraesCS5B01G544800 chr7A 71.464 403 92 13 3472 3855 485605828 485605430 9.740000e-13 86.1


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 TraesCS5B01G544800 chr5B 697342829 697348287 5458 True 10081.000000 10081 100.000000 1 5459 1 chr5B.!!$R4 5458
1 TraesCS5B01G544800 chr5B 697183665 697184403 738 True 974.000000 974 90.738000 3704 4433 1 chr5B.!!$R2 729
2 TraesCS5B01G544800 chr5B 697178445 697178951 506 True 584.000000 584 88.039000 4084 4575 1 chr5B.!!$R1 491
3 TraesCS5B01G544800 chr4A 615103945 615108342 4397 True 6445.000000 6445 93.189000 170 4563 1 chr4A.!!$R1 4393
4 TraesCS5B01G544800 chr4A 614909751 614911338 1587 True 510.333333 721 88.701333 3973 5438 3 chr4A.!!$R2 1465
5 TraesCS5B01G544800 chr5D 553457933 553462120 4187 True 1694.000000 4571 85.725667 146 4490 3 chr5D.!!$R2 4344
6 TraesCS5B01G544800 chr5D 553469451 553473492 4041 False 1473.500000 4867 89.356750 697 4792 4 chr5D.!!$F4 4095
7 TraesCS5B01G544800 chr5D 553063784 553066142 2358 False 1224.000000 2078 87.842500 3124 5458 2 chr5D.!!$F3 2334
8 TraesCS5B01G544800 chr5D 553509105 553509840 735 False 1022.000000 1022 91.746000 3704 4440 1 chr5D.!!$F2 736
9 TraesCS5B01G544800 chr7D 346569085 346569817 732 False 894.000000 894 88.657000 4570 5326 1 chr7D.!!$F1 756

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
938 987 0.035458 CAGCTCACCCGTTCTCCTTT 59.965 55.000 0.00 0.00 0.00 3.11 F
1132 1188 0.108424 CTTGAAGCTCCACCTCTCCG 60.108 60.000 0.00 0.00 0.00 4.63 F
1181 1237 0.108585 GTGCAGAACAACTCCCTCCA 59.891 55.000 0.00 0.00 0.00 3.86 F
1234 1290 0.108662 ATCTCGTGTCATTGCGCTGA 60.109 50.000 9.73 1.04 0.00 4.26 F
1513 1569 0.247736 AAAGCTCCGCAATCTCTCGT 59.752 50.000 0.00 0.00 0.00 4.18 F
2304 2361 0.807667 CATTCCTCTCCTCGTTGGCG 60.808 60.000 0.00 0.00 39.92 5.69 F
2661 2718 1.080498 AGTGGACCCATTCCTAGGACA 59.920 52.381 12.22 0.82 46.10 4.02 F
3195 3253 1.403116 CCGCTTTGCTTTGCATCATCA 60.403 47.619 0.00 0.00 38.76 3.07 F
4274 4359 1.191535 ATCATCACCCCGAGTTTCGA 58.808 50.000 0.00 0.00 43.74 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 2487 0.106335 CTAGCTCTGGTGGGATGCTG 59.894 60.000 0.00 0.0 35.47 4.41 R
2991 3049 0.655733 CACCGCTCAAGTTGTTTCGT 59.344 50.000 2.11 0.0 0.00 3.85 R
3033 3091 6.941436 AGTTGAGAAGCTTCAGAGAATTGAAT 59.059 34.615 27.57 2.6 36.55 2.57 R
3195 3253 0.746659 GCCAAGTGTGCCAGTTTCTT 59.253 50.000 0.00 0.0 0.00 2.52 R
3199 3257 3.595758 GCGCCAAGTGTGCCAGTT 61.596 61.111 0.00 0.0 44.91 3.16 R
4104 4177 0.605589 AGCTATAGACATCGCCTGCC 59.394 55.000 3.21 0.0 0.00 4.85 R
4274 4359 0.620556 ATGGTCCACGCCTTCATCTT 59.379 50.000 0.00 0.0 0.00 2.40 R
4305 4402 0.695462 AGCTCAGCATCCCCACCATA 60.695 55.000 0.00 0.0 0.00 2.74 R
5214 5502 4.041198 TCTGGGTCCTGAAAAATCTACGTT 59.959 41.667 0.00 0.0 0.00 3.99 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
24 25 7.739498 TTCAGTTCAGGTATAAAACTTGTCC 57.261 36.000 0.00 0.00 36.59 4.02
25 26 6.833041 TCAGTTCAGGTATAAAACTTGTCCA 58.167 36.000 0.00 0.00 36.59 4.02
26 27 7.284074 TCAGTTCAGGTATAAAACTTGTCCAA 58.716 34.615 0.00 0.00 36.59 3.53
27 28 7.444183 TCAGTTCAGGTATAAAACTTGTCCAAG 59.556 37.037 5.51 5.51 43.79 3.61
35 36 3.343972 CTTGTCCAAGTGGCCACG 58.656 61.111 29.68 16.68 36.20 4.94
36 37 1.525995 CTTGTCCAAGTGGCCACGT 60.526 57.895 29.68 24.78 36.20 4.49
37 38 1.785041 CTTGTCCAAGTGGCCACGTG 61.785 60.000 36.17 36.17 39.87 4.49
38 39 3.660111 GTCCAAGTGGCCACGTGC 61.660 66.667 37.28 24.83 39.05 5.34
41 42 4.312231 CAAGTGGCCACGTGCGTG 62.312 66.667 33.79 21.36 45.02 5.34
50 51 2.945984 ACGTGCGTGAATTGGCTG 59.054 55.556 0.00 0.00 0.00 4.85
51 52 1.891919 ACGTGCGTGAATTGGCTGT 60.892 52.632 0.00 0.00 0.00 4.40
52 53 0.601576 ACGTGCGTGAATTGGCTGTA 60.602 50.000 0.00 0.00 0.00 2.74
53 54 0.179225 CGTGCGTGAATTGGCTGTAC 60.179 55.000 0.00 0.00 0.00 2.90
54 55 0.871722 GTGCGTGAATTGGCTGTACA 59.128 50.000 0.00 0.00 0.00 2.90
55 56 1.468520 GTGCGTGAATTGGCTGTACAT 59.531 47.619 0.00 0.00 0.00 2.29
56 57 1.468127 TGCGTGAATTGGCTGTACATG 59.532 47.619 0.00 0.00 0.00 3.21
57 58 1.468520 GCGTGAATTGGCTGTACATGT 59.531 47.619 2.69 2.69 0.00 3.21
58 59 2.095263 GCGTGAATTGGCTGTACATGTT 60.095 45.455 2.30 0.00 0.00 2.71
59 60 3.491356 CGTGAATTGGCTGTACATGTTG 58.509 45.455 2.30 0.00 0.00 3.33
60 61 3.188254 CGTGAATTGGCTGTACATGTTGA 59.812 43.478 2.30 0.00 0.00 3.18
61 62 4.320129 CGTGAATTGGCTGTACATGTTGAA 60.320 41.667 2.30 0.00 0.00 2.69
62 63 5.619757 CGTGAATTGGCTGTACATGTTGAAT 60.620 40.000 2.30 0.00 0.00 2.57
63 64 5.801947 GTGAATTGGCTGTACATGTTGAATC 59.198 40.000 2.30 0.00 0.00 2.52
64 65 5.476254 TGAATTGGCTGTACATGTTGAATCA 59.524 36.000 2.30 0.00 0.00 2.57
65 66 5.981088 ATTGGCTGTACATGTTGAATCAA 57.019 34.783 2.30 4.95 0.00 2.57
66 67 5.375417 TTGGCTGTACATGTTGAATCAAG 57.625 39.130 2.30 0.00 0.00 3.02
67 68 4.397420 TGGCTGTACATGTTGAATCAAGT 58.603 39.130 2.30 0.00 0.00 3.16
68 69 4.826733 TGGCTGTACATGTTGAATCAAGTT 59.173 37.500 2.30 0.00 0.00 2.66
69 70 6.000840 TGGCTGTACATGTTGAATCAAGTTA 58.999 36.000 2.30 0.00 0.00 2.24
70 71 6.658816 TGGCTGTACATGTTGAATCAAGTTAT 59.341 34.615 2.30 0.00 0.00 1.89
71 72 6.968904 GGCTGTACATGTTGAATCAAGTTATG 59.031 38.462 2.30 4.78 0.00 1.90
72 73 7.148255 GGCTGTACATGTTGAATCAAGTTATGA 60.148 37.037 2.30 0.00 43.67 2.15
88 89 9.023962 TCAAGTTATGATTGGGGATTAATATGC 57.976 33.333 0.00 0.00 31.50 3.14
89 90 9.028284 CAAGTTATGATTGGGGATTAATATGCT 57.972 33.333 0.00 0.00 0.00 3.79
90 91 9.605951 AAGTTATGATTGGGGATTAATATGCTT 57.394 29.630 0.00 0.00 0.00 3.91
95 96 8.579850 TGATTGGGGATTAATATGCTTACATC 57.420 34.615 0.00 0.00 37.74 3.06
96 97 8.169393 TGATTGGGGATTAATATGCTTACATCA 58.831 33.333 0.00 0.00 37.74 3.07
97 98 8.585471 ATTGGGGATTAATATGCTTACATCAG 57.415 34.615 0.00 0.00 37.74 2.90
98 99 5.945784 TGGGGATTAATATGCTTACATCAGC 59.054 40.000 0.00 0.00 40.55 4.26
99 100 6.183347 GGGGATTAATATGCTTACATCAGCT 58.817 40.000 0.00 0.00 40.79 4.24
100 101 6.660949 GGGGATTAATATGCTTACATCAGCTT 59.339 38.462 0.00 0.00 40.79 3.74
101 102 7.148171 GGGGATTAATATGCTTACATCAGCTTC 60.148 40.741 0.00 0.00 40.79 3.86
102 103 7.391554 GGGATTAATATGCTTACATCAGCTTCA 59.608 37.037 0.00 0.00 40.79 3.02
103 104 8.449397 GGATTAATATGCTTACATCAGCTTCAG 58.551 37.037 0.00 0.00 40.79 3.02
104 105 8.915057 ATTAATATGCTTACATCAGCTTCAGT 57.085 30.769 0.00 0.00 40.79 3.41
105 106 8.737168 TTAATATGCTTACATCAGCTTCAGTT 57.263 30.769 0.00 0.00 40.79 3.16
106 107 6.857777 ATATGCTTACATCAGCTTCAGTTC 57.142 37.500 0.00 0.00 40.79 3.01
107 108 3.338249 TGCTTACATCAGCTTCAGTTCC 58.662 45.455 0.00 0.00 40.79 3.62
108 109 2.680339 GCTTACATCAGCTTCAGTTCCC 59.320 50.000 0.00 0.00 36.79 3.97
109 110 3.869912 GCTTACATCAGCTTCAGTTCCCA 60.870 47.826 0.00 0.00 36.79 4.37
110 111 2.191128 ACATCAGCTTCAGTTCCCAC 57.809 50.000 0.00 0.00 0.00 4.61
111 112 1.271597 ACATCAGCTTCAGTTCCCACC 60.272 52.381 0.00 0.00 0.00 4.61
112 113 1.067295 ATCAGCTTCAGTTCCCACCA 58.933 50.000 0.00 0.00 0.00 4.17
113 114 1.067295 TCAGCTTCAGTTCCCACCAT 58.933 50.000 0.00 0.00 0.00 3.55
114 115 1.171308 CAGCTTCAGTTCCCACCATG 58.829 55.000 0.00 0.00 0.00 3.66
115 116 0.038744 AGCTTCAGTTCCCACCATGG 59.961 55.000 11.19 11.19 37.25 3.66
116 117 0.038166 GCTTCAGTTCCCACCATGGA 59.962 55.000 21.47 0.00 40.96 3.41
117 118 1.547675 GCTTCAGTTCCCACCATGGAA 60.548 52.381 21.47 0.00 40.96 3.53
118 119 2.875296 CTTCAGTTCCCACCATGGAAA 58.125 47.619 21.47 4.11 45.67 3.13
119 120 2.584835 TCAGTTCCCACCATGGAAAG 57.415 50.000 21.47 7.71 45.67 2.62
120 121 0.890683 CAGTTCCCACCATGGAAAGC 59.109 55.000 21.47 3.25 45.67 3.51
121 122 0.609131 AGTTCCCACCATGGAAAGCG 60.609 55.000 21.47 0.15 45.67 4.68
122 123 1.304052 TTCCCACCATGGAAAGCGG 60.304 57.895 21.47 10.10 41.40 5.52
123 124 2.035626 CCCACCATGGAAAGCGGT 59.964 61.111 21.47 0.00 40.96 5.68
125 126 4.079446 CACCATGGAAAGCGGTGT 57.921 55.556 21.47 0.00 44.27 4.16
126 127 1.580942 CACCATGGAAAGCGGTGTG 59.419 57.895 21.47 0.00 44.27 3.82
127 128 0.888736 CACCATGGAAAGCGGTGTGA 60.889 55.000 21.47 0.00 44.27 3.58
128 129 0.606401 ACCATGGAAAGCGGTGTGAG 60.606 55.000 21.47 0.00 0.00 3.51
129 130 1.503542 CATGGAAAGCGGTGTGAGC 59.496 57.895 0.00 0.00 0.00 4.26
130 131 1.675641 ATGGAAAGCGGTGTGAGCC 60.676 57.895 0.00 0.00 34.64 4.70
131 132 3.056328 GGAAAGCGGTGTGAGCCC 61.056 66.667 0.00 0.00 34.64 5.19
137 138 4.308458 CGGTGTGAGCCCGGTTGA 62.308 66.667 0.00 0.00 41.78 3.18
138 139 2.112297 GGTGTGAGCCCGGTTGAA 59.888 61.111 0.00 0.00 0.00 2.69
139 140 1.527380 GGTGTGAGCCCGGTTGAAA 60.527 57.895 0.00 0.00 0.00 2.69
140 141 1.104577 GGTGTGAGCCCGGTTGAAAA 61.105 55.000 0.00 0.00 0.00 2.29
141 142 0.741915 GTGTGAGCCCGGTTGAAAAA 59.258 50.000 0.00 0.00 0.00 1.94
165 166 0.623723 GTAGCCACCATGGAAAGGGA 59.376 55.000 21.47 0.00 40.96 4.20
171 172 3.444029 CCACCATGGAAAGGGAAGAAAT 58.556 45.455 21.47 0.00 40.96 2.17
176 177 4.501071 CATGGAAAGGGAAGAAATTGCAG 58.499 43.478 0.00 0.00 0.00 4.41
177 178 3.575805 TGGAAAGGGAAGAAATTGCAGT 58.424 40.909 0.00 0.00 0.00 4.40
178 179 3.573967 TGGAAAGGGAAGAAATTGCAGTC 59.426 43.478 0.00 0.00 0.00 3.51
214 215 0.969149 TGACTGACGACTCCTTGCAT 59.031 50.000 0.00 0.00 0.00 3.96
239 240 8.890124 TGAGTATCATGTAGTGTAGAGAGTAC 57.110 38.462 0.00 0.00 42.56 2.73
279 280 9.685828 TTTTCTAATTTGTTGGTAATTTCGGAG 57.314 29.630 0.00 0.00 0.00 4.63
375 380 4.970860 ATACCATGTAGATTGCAGAGCT 57.029 40.909 0.00 0.00 0.00 4.09
376 381 6.425210 AATACCATGTAGATTGCAGAGCTA 57.575 37.500 0.00 0.00 0.00 3.32
385 390 6.605995 TGTAGATTGCAGAGCTAAGGTTAGTA 59.394 38.462 0.00 0.00 33.32 1.82
510 515 7.661968 CCACCTCGAAGATCTTATCAATTAGA 58.338 38.462 8.25 0.00 33.89 2.10
643 670 5.381174 TCTTTTTGGTCTTCATGCATCTG 57.619 39.130 0.00 0.00 0.00 2.90
745 776 5.481122 GGAAAGGTAGTCTGAAACTAGGACT 59.519 44.000 0.00 0.00 41.17 3.85
767 809 4.560128 TGAGAAGAGTTGAATTCCTCACG 58.440 43.478 12.49 0.00 32.21 4.35
790 832 5.631992 GTGGCAGAAATAGCAAGAAAGTAC 58.368 41.667 0.00 0.00 0.00 2.73
821 863 5.649395 TGCAGATGTGGAAGAAGAATTTAGG 59.351 40.000 0.00 0.00 0.00 2.69
831 873 5.975988 AGAAGAATTTAGGGGCTCACATA 57.024 39.130 0.00 0.00 0.00 2.29
858 900 3.060615 GCAAGCAGAGCACCCAGG 61.061 66.667 0.00 0.00 0.00 4.45
869 911 2.847234 ACCCAGGCCACTTGTCGA 60.847 61.111 5.01 0.00 0.00 4.20
876 918 4.389374 CCAGGCCACTTGTCGATAATTAT 58.611 43.478 5.01 0.00 0.00 1.28
938 987 0.035458 CAGCTCACCCGTTCTCCTTT 59.965 55.000 0.00 0.00 0.00 3.11
1053 1103 6.073003 CCATTGTTGTTGTAACCTCTCTTCTC 60.073 42.308 0.00 0.00 0.00 2.87
1132 1188 0.108424 CTTGAAGCTCCACCTCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
1181 1237 0.108585 GTGCAGAACAACTCCCTCCA 59.891 55.000 0.00 0.00 0.00 3.86
1234 1290 0.108662 ATCTCGTGTCATTGCGCTGA 60.109 50.000 9.73 1.04 0.00 4.26
1317 1373 0.618458 CAAGAATCCACTTCCCGGGA 59.382 55.000 22.63 22.63 37.64 5.14
1362 1418 2.659016 CAACTCGGGCAGCTGAGA 59.341 61.111 20.43 12.15 36.11 3.27
1455 1511 2.240667 CCTCCAGGTGATTGATCTTGGT 59.759 50.000 0.00 0.00 0.00 3.67
1482 1538 2.366916 CAAGTTCAGCGGAGATATCCCT 59.633 50.000 0.00 0.00 0.00 4.20
1494 1550 3.242867 AGATATCCCTGAAAGCATCGGA 58.757 45.455 0.00 0.00 36.44 4.55
1496 1552 2.806945 ATCCCTGAAAGCATCGGAAA 57.193 45.000 0.23 0.00 36.44 3.13
1513 1569 0.247736 AAAGCTCCGCAATCTCTCGT 59.752 50.000 0.00 0.00 0.00 4.18
1537 1593 4.410743 GCCTTGCTCGCAACAGCC 62.411 66.667 0.00 0.00 38.80 4.85
1836 1892 7.539366 GCTCTTATATTGTCGGTGAATACTCTC 59.461 40.741 0.00 0.00 0.00 3.20
1963 2019 4.761739 TCCCAAACTTGCAAGAACTAGATG 59.238 41.667 32.50 17.26 0.00 2.90
1990 2046 5.778241 TCTTACAACATTCTGTCAGGGACTA 59.222 40.000 0.00 0.00 36.02 2.59
2040 2096 5.331069 TCACTCACCTACCTTAGTTTAGCT 58.669 41.667 0.00 0.00 0.00 3.32
2304 2361 0.807667 CATTCCTCTCCTCGTTGGCG 60.808 60.000 0.00 0.00 39.92 5.69
2430 2487 2.792542 GCACGCAAATAAGATGTCTGGC 60.793 50.000 0.00 0.00 0.00 4.85
2436 2493 4.792057 GCAAATAAGATGTCTGGCAGCATC 60.792 45.833 28.85 28.85 41.13 3.91
2661 2718 1.080498 AGTGGACCCATTCCTAGGACA 59.920 52.381 12.22 0.82 46.10 4.02
2838 2895 5.550011 TGGCTTGATTAATATAGGGCCACTA 59.450 40.000 6.18 3.99 42.57 2.74
2841 2898 7.615757 GGCTTGATTAATATAGGGCCACTAAAT 59.384 37.037 6.18 0.65 38.35 1.40
2922 2980 1.483004 GAGTCCCTTCACTTAGAGGGC 59.517 57.143 3.52 0.03 41.99 5.19
2953 3011 3.118482 TGATGGCAGAATTCCTCAGTCTC 60.118 47.826 0.65 0.00 0.00 3.36
3033 3091 5.423610 TGAAATCCCAAACTTTTTCCAGTCA 59.576 36.000 0.00 0.00 0.00 3.41
3195 3253 1.403116 CCGCTTTGCTTTGCATCATCA 60.403 47.619 0.00 0.00 38.76 3.07
3199 3257 3.991773 GCTTTGCTTTGCATCATCAAGAA 59.008 39.130 0.00 0.00 38.76 2.52
3202 3260 4.859304 TGCTTTGCATCATCAAGAAACT 57.141 36.364 0.00 0.00 31.71 2.66
3269 3327 3.429410 GCTCTTGCTTTGGTCTGTTTGTT 60.429 43.478 0.00 0.00 36.03 2.83
3303 3361 5.606348 TTATTCTCTTGAAGAGGAGGAGC 57.394 43.478 21.04 0.00 42.54 4.70
3450 3508 6.921486 TCAGTATACAAGGGTGTACTTGAA 57.079 37.500 12.36 0.00 46.06 2.69
3719 3777 3.462021 GCTCCAGAGTAACAATAGCAGG 58.538 50.000 0.00 0.00 0.00 4.85
3753 3811 7.816031 GCTGCTGCATTGGATTATTTACATAAT 59.184 33.333 11.11 0.00 37.43 1.28
3944 4004 3.380320 GGATACATTGCACCAGGTAAACC 59.620 47.826 0.00 0.00 0.00 3.27
4104 4177 2.363788 TCGGGAACAAGATCTCAACG 57.636 50.000 0.00 0.00 0.00 4.10
4274 4359 1.191535 ATCATCACCCCGAGTTTCGA 58.808 50.000 0.00 0.00 43.74 3.71
4278 4363 1.263356 TCACCCCGAGTTTCGAAGAT 58.737 50.000 0.00 0.00 43.74 2.40
4359 4456 2.369860 TGTTCAGCTTGGTCTCTCATGT 59.630 45.455 0.00 0.00 0.00 3.21
4466 4564 3.310774 CGCATCAAGGAATAGGACACTTG 59.689 47.826 0.00 0.00 41.14 3.16
4477 4575 6.183360 GGAATAGGACACTTGTGTTTTGTTCA 60.183 38.462 18.93 3.15 0.00 3.18
4494 4592 7.767745 TTTGTTCACGTGTATGTTACAAGTA 57.232 32.000 16.51 2.19 46.88 2.24
4505 4620 8.504005 GTGTATGTTACAAGTAAGTTTGCTCAT 58.496 33.333 0.00 0.00 40.93 2.90
4535 4651 2.901291 AGATATCTTCCTGAGAGGCCC 58.099 52.381 0.00 0.00 37.93 5.80
4564 4680 5.776173 TGGGCTTCTTCGAATTTTTGTTA 57.224 34.783 0.00 0.00 0.00 2.41
4568 4684 6.750501 GGGCTTCTTCGAATTTTTGTTATACC 59.249 38.462 0.00 0.00 0.00 2.73
4597 4765 5.068636 AGAAAACATGTTCTCAGTCTGCAT 58.931 37.500 14.17 0.00 32.16 3.96
4636 4805 7.424803 TGTCTGGTTTATTCTGAATGTGTTTG 58.575 34.615 13.01 0.63 0.00 2.93
4708 4877 6.926630 TCCTAAAGTTAAAATGGTGGCATT 57.073 33.333 0.00 0.00 0.00 3.56
4709 4878 7.309770 TCCTAAAGTTAAAATGGTGGCATTT 57.690 32.000 0.00 0.00 36.44 2.32
4751 4920 9.594038 GATGATTGCATTCATAATTTTCATTGC 57.406 29.630 20.90 4.08 36.48 3.56
4761 4930 4.686191 AATTTTCATTGCCAGTTGTCCA 57.314 36.364 0.00 0.00 0.00 4.02
4826 5013 9.420118 TGTTTTGTCTGGCATAGGATTATATTT 57.580 29.630 0.00 0.00 0.00 1.40
4925 5126 1.425066 ACTGGAGGCAAGATTCACCAA 59.575 47.619 0.00 0.00 0.00 3.67
4978 5235 0.392193 AGTGTGTCATAGCTGCAGCC 60.392 55.000 34.39 19.29 43.38 4.85
4986 5243 4.202451 TGTCATAGCTGCAGCCCATAAATA 60.202 41.667 34.39 18.70 43.38 1.40
5041 5298 3.615937 CACTCTGTGTCTGTGTATGCATC 59.384 47.826 0.19 0.00 0.00 3.91
5042 5299 3.259123 ACTCTGTGTCTGTGTATGCATCA 59.741 43.478 0.19 0.00 0.00 3.07
5073 5330 3.432186 CCCAATTCAGCGAGATACCTTGA 60.432 47.826 0.00 0.00 0.00 3.02
5134 5397 1.116308 TGTGCCATAGCTACGCCTTA 58.884 50.000 11.17 0.00 40.80 2.69
5247 5536 3.955471 TCAGGACCCAGAGCTAAAATTG 58.045 45.455 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.284074 TGGACAAGTTTTATACCTGAACTGAA 58.716 34.615 0.00 0.00 34.13 3.02
2 3 7.504924 TTGGACAAGTTTTATACCTGAACTG 57.495 36.000 0.00 0.00 34.13 3.16
3 4 7.745620 CTTGGACAAGTTTTATACCTGAACT 57.254 36.000 3.93 0.00 35.27 3.01
21 22 3.660111 GCACGTGGCCACTTGGAC 61.660 66.667 35.35 20.77 45.93 4.02
24 25 4.312231 CACGCACGTGGCCACTTG 62.312 66.667 32.27 32.27 42.00 3.16
25 26 4.539083 TCACGCACGTGGCCACTT 62.539 61.111 32.28 22.25 45.43 3.16
26 27 3.825160 ATTCACGCACGTGGCCACT 62.825 57.895 32.28 17.29 45.43 4.00
27 28 2.903547 AATTCACGCACGTGGCCAC 61.904 57.895 26.78 26.78 45.43 5.01
28 29 2.593148 AATTCACGCACGTGGCCA 60.593 55.556 21.73 0.00 45.43 5.36
29 30 2.126888 CAATTCACGCACGTGGCC 60.127 61.111 21.73 0.00 45.43 5.36
30 31 2.126888 CCAATTCACGCACGTGGC 60.127 61.111 21.73 8.78 45.43 5.01
31 32 2.126888 GCCAATTCACGCACGTGG 60.127 61.111 21.73 10.05 45.43 4.94
32 33 1.440850 CAGCCAATTCACGCACGTG 60.441 57.895 16.73 16.73 46.64 4.49
33 34 0.601576 TACAGCCAATTCACGCACGT 60.602 50.000 0.00 0.00 0.00 4.49
34 35 0.179225 GTACAGCCAATTCACGCACG 60.179 55.000 0.00 0.00 0.00 5.34
35 36 0.871722 TGTACAGCCAATTCACGCAC 59.128 50.000 0.00 0.00 0.00 5.34
36 37 1.468127 CATGTACAGCCAATTCACGCA 59.532 47.619 0.33 0.00 0.00 5.24
37 38 1.468520 ACATGTACAGCCAATTCACGC 59.531 47.619 0.00 0.00 0.00 5.34
38 39 3.188254 TCAACATGTACAGCCAATTCACG 59.812 43.478 0.00 0.00 0.00 4.35
39 40 4.764679 TCAACATGTACAGCCAATTCAC 57.235 40.909 0.00 0.00 0.00 3.18
40 41 5.476254 TGATTCAACATGTACAGCCAATTCA 59.524 36.000 0.00 0.00 0.00 2.57
41 42 5.953183 TGATTCAACATGTACAGCCAATTC 58.047 37.500 0.00 0.00 0.00 2.17
42 43 5.981088 TGATTCAACATGTACAGCCAATT 57.019 34.783 0.00 0.00 0.00 2.32
43 44 5.477984 ACTTGATTCAACATGTACAGCCAAT 59.522 36.000 0.00 0.00 0.00 3.16
44 45 4.826733 ACTTGATTCAACATGTACAGCCAA 59.173 37.500 0.00 0.94 0.00 4.52
45 46 4.397420 ACTTGATTCAACATGTACAGCCA 58.603 39.130 0.00 0.00 0.00 4.75
46 47 5.376854 AACTTGATTCAACATGTACAGCC 57.623 39.130 0.00 0.00 0.00 4.85
47 48 7.751732 TCATAACTTGATTCAACATGTACAGC 58.248 34.615 0.00 0.00 0.00 4.40
62 63 9.023962 GCATATTAATCCCCAATCATAACTTGA 57.976 33.333 0.00 0.00 39.12 3.02
63 64 9.028284 AGCATATTAATCCCCAATCATAACTTG 57.972 33.333 0.00 0.00 0.00 3.16
64 65 9.605951 AAGCATATTAATCCCCAATCATAACTT 57.394 29.630 0.00 0.00 0.00 2.66
69 70 9.193806 GATGTAAGCATATTAATCCCCAATCAT 57.806 33.333 0.00 0.00 35.07 2.45
70 71 8.169393 TGATGTAAGCATATTAATCCCCAATCA 58.831 33.333 0.00 0.00 35.07 2.57
71 72 8.579850 TGATGTAAGCATATTAATCCCCAATC 57.420 34.615 0.00 0.00 35.07 2.67
72 73 7.123247 GCTGATGTAAGCATATTAATCCCCAAT 59.877 37.037 0.00 0.00 43.01 3.16
73 74 6.434028 GCTGATGTAAGCATATTAATCCCCAA 59.566 38.462 0.00 0.00 43.01 4.12
74 75 5.945784 GCTGATGTAAGCATATTAATCCCCA 59.054 40.000 0.00 0.00 43.01 4.96
75 76 6.183347 AGCTGATGTAAGCATATTAATCCCC 58.817 40.000 0.00 0.00 46.08 4.81
76 77 7.391554 TGAAGCTGATGTAAGCATATTAATCCC 59.608 37.037 0.00 0.00 46.08 3.85
77 78 8.327941 TGAAGCTGATGTAAGCATATTAATCC 57.672 34.615 0.00 0.00 46.08 3.01
78 79 8.997323 ACTGAAGCTGATGTAAGCATATTAATC 58.003 33.333 0.00 0.00 46.08 1.75
79 80 8.915057 ACTGAAGCTGATGTAAGCATATTAAT 57.085 30.769 0.00 0.00 46.08 1.40
80 81 8.737168 AACTGAAGCTGATGTAAGCATATTAA 57.263 30.769 0.00 0.00 46.08 1.40
81 82 7.442364 GGAACTGAAGCTGATGTAAGCATATTA 59.558 37.037 0.00 0.00 46.08 0.98
82 83 6.261826 GGAACTGAAGCTGATGTAAGCATATT 59.738 38.462 0.00 0.00 46.08 1.28
83 84 5.762218 GGAACTGAAGCTGATGTAAGCATAT 59.238 40.000 0.00 0.00 46.08 1.78
84 85 5.118990 GGAACTGAAGCTGATGTAAGCATA 58.881 41.667 0.00 0.00 46.08 3.14
85 86 3.944015 GGAACTGAAGCTGATGTAAGCAT 59.056 43.478 0.00 0.00 46.08 3.79
86 87 3.338249 GGAACTGAAGCTGATGTAAGCA 58.662 45.455 0.00 0.00 46.08 3.91
87 88 2.680339 GGGAACTGAAGCTGATGTAAGC 59.320 50.000 0.00 0.00 43.88 3.09
88 89 3.686726 GTGGGAACTGAAGCTGATGTAAG 59.313 47.826 0.00 0.00 0.00 2.34
89 90 3.559171 GGTGGGAACTGAAGCTGATGTAA 60.559 47.826 0.00 0.00 0.00 2.41
90 91 2.027192 GGTGGGAACTGAAGCTGATGTA 60.027 50.000 0.00 0.00 0.00 2.29
91 92 1.271597 GGTGGGAACTGAAGCTGATGT 60.272 52.381 0.00 0.00 0.00 3.06
92 93 1.271543 TGGTGGGAACTGAAGCTGATG 60.272 52.381 0.00 0.00 0.00 3.07
93 94 1.067295 TGGTGGGAACTGAAGCTGAT 58.933 50.000 0.00 0.00 0.00 2.90
94 95 1.067295 ATGGTGGGAACTGAAGCTGA 58.933 50.000 0.00 0.00 0.00 4.26
95 96 1.171308 CATGGTGGGAACTGAAGCTG 58.829 55.000 0.00 0.00 0.00 4.24
96 97 0.038744 CCATGGTGGGAACTGAAGCT 59.961 55.000 2.57 0.00 32.67 3.74
97 98 0.038166 TCCATGGTGGGAACTGAAGC 59.962 55.000 12.58 0.00 38.32 3.86
98 99 2.584835 TTCCATGGTGGGAACTGAAG 57.415 50.000 12.58 0.00 41.92 3.02
99 100 2.875296 CTTTCCATGGTGGGAACTGAA 58.125 47.619 12.58 0.00 46.28 3.02
100 101 1.547675 GCTTTCCATGGTGGGAACTGA 60.548 52.381 12.58 0.00 46.28 3.41
101 102 0.890683 GCTTTCCATGGTGGGAACTG 59.109 55.000 12.58 0.00 46.28 3.16
102 103 0.609131 CGCTTTCCATGGTGGGAACT 60.609 55.000 12.58 0.00 46.28 3.01
103 104 1.595093 CCGCTTTCCATGGTGGGAAC 61.595 60.000 12.58 0.00 46.28 3.62
104 105 1.304052 CCGCTTTCCATGGTGGGAA 60.304 57.895 12.58 0.00 45.00 3.97
105 106 2.354729 CCGCTTTCCATGGTGGGA 59.645 61.111 12.58 0.00 38.32 4.37
106 107 2.035626 ACCGCTTTCCATGGTGGG 59.964 61.111 12.58 11.24 38.32 4.61
109 110 0.606401 CTCACACCGCTTTCCATGGT 60.606 55.000 12.58 0.00 36.10 3.55
110 111 1.926511 GCTCACACCGCTTTCCATGG 61.927 60.000 4.97 4.97 0.00 3.66
111 112 1.503542 GCTCACACCGCTTTCCATG 59.496 57.895 0.00 0.00 0.00 3.66
112 113 1.675641 GGCTCACACCGCTTTCCAT 60.676 57.895 0.00 0.00 0.00 3.41
113 114 2.281484 GGCTCACACCGCTTTCCA 60.281 61.111 0.00 0.00 0.00 3.53
114 115 3.056328 GGGCTCACACCGCTTTCC 61.056 66.667 0.00 0.00 0.00 3.13
115 116 3.423154 CGGGCTCACACCGCTTTC 61.423 66.667 0.00 0.00 45.34 2.62
121 122 1.104577 TTTTCAACCGGGCTCACACC 61.105 55.000 6.32 0.00 0.00 4.16
122 123 0.741915 TTTTTCAACCGGGCTCACAC 59.258 50.000 6.32 0.00 0.00 3.82
123 124 3.192799 TTTTTCAACCGGGCTCACA 57.807 47.368 6.32 0.00 0.00 3.58
141 142 3.578282 CCTTTCCATGGTGGCTACTTTTT 59.422 43.478 12.58 0.00 37.47 1.94
142 143 3.165071 CCTTTCCATGGTGGCTACTTTT 58.835 45.455 12.58 0.00 37.47 2.27
143 144 2.557452 CCCTTTCCATGGTGGCTACTTT 60.557 50.000 12.58 0.00 37.47 2.66
144 145 1.005924 CCCTTTCCATGGTGGCTACTT 59.994 52.381 12.58 0.00 37.47 2.24
145 146 0.625849 CCCTTTCCATGGTGGCTACT 59.374 55.000 12.58 0.00 37.47 2.57
146 147 0.623723 TCCCTTTCCATGGTGGCTAC 59.376 55.000 12.58 0.00 37.47 3.58
147 148 1.284785 CTTCCCTTTCCATGGTGGCTA 59.715 52.381 12.58 1.70 37.47 3.93
148 149 0.040204 CTTCCCTTTCCATGGTGGCT 59.960 55.000 12.58 0.00 37.47 4.75
149 150 0.039618 TCTTCCCTTTCCATGGTGGC 59.960 55.000 12.58 0.00 37.47 5.01
150 151 2.603075 TTCTTCCCTTTCCATGGTGG 57.397 50.000 12.58 12.34 39.43 4.61
151 152 4.824289 CAATTTCTTCCCTTTCCATGGTG 58.176 43.478 12.58 3.46 0.00 4.17
152 153 3.261643 GCAATTTCTTCCCTTTCCATGGT 59.738 43.478 12.58 0.00 0.00 3.55
153 154 3.261390 TGCAATTTCTTCCCTTTCCATGG 59.739 43.478 4.97 4.97 0.00 3.66
158 159 4.853924 TGACTGCAATTTCTTCCCTTTC 57.146 40.909 0.00 0.00 0.00 2.62
165 166 3.255149 CCAGCTCTTGACTGCAATTTCTT 59.745 43.478 0.00 0.00 33.65 2.52
171 172 0.181114 ACACCAGCTCTTGACTGCAA 59.819 50.000 0.00 0.00 33.65 4.08
176 177 3.433615 GTCAATGTACACCAGCTCTTGAC 59.566 47.826 16.29 16.29 35.69 3.18
177 178 3.324846 AGTCAATGTACACCAGCTCTTGA 59.675 43.478 0.00 0.00 0.00 3.02
178 179 3.434641 CAGTCAATGTACACCAGCTCTTG 59.565 47.826 0.00 0.00 0.00 3.02
214 215 8.706521 AGTACTCTCTACACTACATGATACTCA 58.293 37.037 0.00 0.00 0.00 3.41
226 227 5.386924 ACTGGACAAAGTACTCTCTACACT 58.613 41.667 0.00 0.00 0.00 3.55
228 229 5.382616 TGACTGGACAAAGTACTCTCTACA 58.617 41.667 0.00 0.00 0.00 2.74
232 233 4.857509 ACTGACTGGACAAAGTACTCTC 57.142 45.455 0.00 0.00 0.00 3.20
239 240 8.190784 ACAAATTAGAAAACTGACTGGACAAAG 58.809 33.333 0.00 0.00 0.00 2.77
376 381 8.934023 TTGTGAAATCCAAGAATACTAACCTT 57.066 30.769 0.00 0.00 0.00 3.50
468 473 2.162408 GGTGGCACTTTGACTAGCAATC 59.838 50.000 18.45 0.00 36.15 2.67
558 581 2.499685 CCAACTCGATCGTCCCCC 59.500 66.667 15.94 0.00 0.00 5.40
559 582 1.896122 AACCCAACTCGATCGTCCCC 61.896 60.000 15.94 0.00 0.00 4.81
560 583 0.459759 GAACCCAACTCGATCGTCCC 60.460 60.000 15.94 0.00 0.00 4.46
561 584 0.459759 GGAACCCAACTCGATCGTCC 60.460 60.000 15.94 8.18 0.00 4.79
562 585 0.531200 AGGAACCCAACTCGATCGTC 59.469 55.000 15.94 2.13 0.00 4.20
563 586 1.843368 TAGGAACCCAACTCGATCGT 58.157 50.000 15.94 0.00 0.00 3.73
564 587 4.202080 TGTTATAGGAACCCAACTCGATCG 60.202 45.833 9.36 9.36 0.00 3.69
630 657 3.372897 ACCTCTCTCAGATGCATGAAGA 58.627 45.455 2.46 2.90 0.00 2.87
643 670 7.100409 ACTAAGTTGATTTTGCTACCTCTCTC 58.900 38.462 0.00 0.00 0.00 3.20
745 776 4.039245 ACGTGAGGAATTCAACTCTTCTCA 59.961 41.667 7.93 6.05 37.61 3.27
767 809 4.773323 ACTTTCTTGCTATTTCTGCCAC 57.227 40.909 0.00 0.00 0.00 5.01
790 832 2.002586 CTTCCACATCTGCACCTAACG 58.997 52.381 0.00 0.00 0.00 3.18
821 863 2.099756 GCCATTTCTGTTATGTGAGCCC 59.900 50.000 0.00 0.00 0.00 5.19
831 873 1.271656 GCTCTGCTTGCCATTTCTGTT 59.728 47.619 0.00 0.00 0.00 3.16
938 987 7.864108 ACTGATATGCTGCACTTATACAAAA 57.136 32.000 3.57 0.00 0.00 2.44
1064 1114 1.276138 TGGATGAAGAAGAAGCAGCGA 59.724 47.619 0.00 0.00 0.00 4.93
1132 1188 4.432741 GAGGGAGTTGGGGCTGCC 62.433 72.222 11.05 11.05 45.84 4.85
1181 1237 2.753043 CGGGCCAGCTGCAGAAAT 60.753 61.111 20.43 0.00 43.89 2.17
1225 1281 0.037326 TTCTCGAGGTTCAGCGCAAT 60.037 50.000 13.56 0.00 0.00 3.56
1234 1290 2.647158 GGCCGGAGTTCTCGAGGTT 61.647 63.158 13.56 0.00 0.00 3.50
1266 1322 1.668793 GTTGGCAATGCAAGGTGGC 60.669 57.895 7.79 13.11 40.55 5.01
1269 1325 0.469705 TGAGGTTGGCAATGCAAGGT 60.470 50.000 7.79 0.00 0.00 3.50
1272 1328 1.470996 GGGTGAGGTTGGCAATGCAA 61.471 55.000 7.79 0.00 0.00 4.08
1278 1334 2.121963 AGGAGGGTGAGGTTGGCA 60.122 61.111 0.00 0.00 0.00 4.92
1455 1511 3.462483 TCTCCGCTGAACTTGTTGTTA 57.538 42.857 0.00 0.00 39.30 2.41
1465 1521 2.381752 TCAGGGATATCTCCGCTGAA 57.618 50.000 12.79 2.18 41.74 3.02
1470 1526 3.594134 GATGCTTTCAGGGATATCTCCG 58.406 50.000 0.00 0.00 43.11 4.63
1482 1538 1.453155 GGAGCTTTCCGATGCTTTCA 58.547 50.000 0.00 0.00 39.91 2.69
1513 1569 0.663688 TTGCGAGCAAGGCGTAAAAA 59.336 45.000 6.39 0.00 30.75 1.94
1551 1607 2.964978 CTTCCAAGCCAAAGCGGG 59.035 61.111 0.00 0.00 46.67 6.13
1836 1892 2.890474 GACGGTATGGTGCCTGCG 60.890 66.667 0.00 0.00 0.00 5.18
1990 2046 4.771114 TGTTGAATATGGAGAACGGGAT 57.229 40.909 0.00 0.00 0.00 3.85
1995 2051 7.335422 AGTGAAGACATGTTGAATATGGAGAAC 59.665 37.037 0.00 0.00 0.00 3.01
2212 2269 6.101296 AGGTTAGAAAGAGACCCAAAAGAAGA 59.899 38.462 0.00 0.00 33.89 2.87
2430 2487 0.106335 CTAGCTCTGGTGGGATGCTG 59.894 60.000 0.00 0.00 35.47 4.41
2436 2493 1.627297 GGTTCCCTAGCTCTGGTGGG 61.627 65.000 0.00 0.00 40.95 4.61
2661 2718 1.276622 ACCTTCGGCAATCACCTAGT 58.723 50.000 0.00 0.00 0.00 2.57
2804 2861 7.756395 ATATTAATCAAGCCACCAATCTCAG 57.244 36.000 0.00 0.00 0.00 3.35
2805 2862 7.884877 CCTATATTAATCAAGCCACCAATCTCA 59.115 37.037 0.00 0.00 0.00 3.27
2838 2895 5.583061 GGAAAGACGGTTGTTGGAAAAATTT 59.417 36.000 0.00 0.00 0.00 1.82
2841 2898 3.427773 CGGAAAGACGGTTGTTGGAAAAA 60.428 43.478 0.00 0.00 0.00 1.94
2867 2925 2.355108 GCACCTAGAGCAGTTGGAATGA 60.355 50.000 0.00 0.00 0.00 2.57
2922 2980 4.096984 GGAATTCTGCCATCAAGTAGGTTG 59.903 45.833 5.23 0.00 37.52 3.77
2991 3049 0.655733 CACCGCTCAAGTTGTTTCGT 59.344 50.000 2.11 0.00 0.00 3.85
3033 3091 6.941436 AGTTGAGAAGCTTCAGAGAATTGAAT 59.059 34.615 27.57 2.60 36.55 2.57
3195 3253 0.746659 GCCAAGTGTGCCAGTTTCTT 59.253 50.000 0.00 0.00 0.00 2.52
3199 3257 3.595758 GCGCCAAGTGTGCCAGTT 61.596 61.111 0.00 0.00 44.91 3.16
3303 3361 7.277539 GGTTGATCTGACTGTTTAGATCTCTTG 59.722 40.741 24.03 0.00 45.99 3.02
3450 3508 6.816640 CAGCAATCATTCCATTTGTTTCAGAT 59.183 34.615 0.00 0.00 0.00 2.90
3537 3595 7.984050 AGATTATGATGACGAGTGTTTCTGAAT 59.016 33.333 0.00 0.00 0.00 2.57
3719 3777 0.666913 CAATGCAGCAGCTATGTCCC 59.333 55.000 0.00 0.00 42.74 4.46
3753 3811 1.062428 ACTATAGGGGGCACACAGCTA 60.062 52.381 4.43 0.00 44.79 3.32
3827 3886 3.584848 AGCTAACCCAAAGTCACTGAGAT 59.415 43.478 0.00 0.00 0.00 2.75
4104 4177 0.605589 AGCTATAGACATCGCCTGCC 59.394 55.000 3.21 0.00 0.00 4.85
4262 4347 2.271800 CTTCATCTTCGAAACTCGGGG 58.728 52.381 0.00 0.00 40.88 5.73
4274 4359 0.620556 ATGGTCCACGCCTTCATCTT 59.379 50.000 0.00 0.00 0.00 2.40
4278 4363 1.773856 TTCCATGGTCCACGCCTTCA 61.774 55.000 12.58 0.00 0.00 3.02
4305 4402 0.695462 AGCTCAGCATCCCCACCATA 60.695 55.000 0.00 0.00 0.00 2.74
4359 4456 1.487142 TCTTTTGGTGTCTCCGTGGAA 59.513 47.619 0.00 0.00 39.52 3.53
4466 4564 6.249359 TGTAACATACACGTGAACAAAACAC 58.751 36.000 25.01 10.26 32.89 3.32
4477 4575 6.480981 AGCAAACTTACTTGTAACATACACGT 59.519 34.615 5.23 5.23 42.72 4.49
4494 4592 3.213206 TCCAGTCACATGAGCAAACTT 57.787 42.857 0.00 0.00 0.00 2.66
4535 4651 5.567138 AATTCGAAGAAGCCCAACATAAG 57.433 39.130 3.35 0.00 45.90 1.73
4564 4680 5.794894 AGAACATGTTTTCTCAGTCGGTAT 58.205 37.500 13.36 0.00 29.24 2.73
4597 4765 5.762179 AACCAGACAACTCATCCTTATGA 57.238 39.130 0.00 0.00 39.87 2.15
4708 4877 8.358895 TGCAATCATCAGATTTAACAACAGAAA 58.641 29.630 0.00 0.00 42.46 2.52
4709 4878 7.884257 TGCAATCATCAGATTTAACAACAGAA 58.116 30.769 0.00 0.00 42.46 3.02
4761 4930 6.550108 ACTGTAATATCACGAGGGTAATCAGT 59.450 38.462 0.00 0.00 0.00 3.41
4770 4939 5.891451 TCTTCACACTGTAATATCACGAGG 58.109 41.667 0.00 0.00 0.00 4.63
4826 5013 4.502105 TTCAGAACATGCCAGGCTAATA 57.498 40.909 14.15 0.00 0.00 0.98
4978 5235 9.499479 AGTGCTAAGATCTGAACATATTTATGG 57.501 33.333 0.00 0.00 38.00 2.74
4986 5243 7.663081 TCTTTTTCAGTGCTAAGATCTGAACAT 59.337 33.333 0.00 0.00 44.34 2.71
5041 5298 4.493547 TCGCTGAATTGGGCTTAAAATTG 58.506 39.130 0.00 0.00 0.00 2.32
5042 5299 4.462483 TCTCGCTGAATTGGGCTTAAAATT 59.538 37.500 0.00 0.00 0.00 1.82
5214 5502 4.041198 TCTGGGTCCTGAAAAATCTACGTT 59.959 41.667 0.00 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.