Multiple sequence alignment - TraesCS3D01G012000

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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 TraesCS3D01G012000 chr3D 100.000 4803 0 0 1 4803 4183940 4179138 0.000000e+00 8870.0
1 TraesCS3D01G012000 chr3A 93.205 4150 191 36 25 4140 9847443 9843351 0.000000e+00 6017.0
2 TraesCS3D01G012000 chr3A 79.806 1337 212 39 2295 3604 9812896 9811591 0.000000e+00 920.0
3 TraesCS3D01G012000 chr3A 80.331 605 95 12 1394 1983 11027597 11027002 2.050000e-118 436.0
4 TraesCS3D01G012000 chr3A 80.000 570 88 16 1430 1983 11065425 11064866 9.690000e-107 398.0
5 TraesCS3D01G012000 chr3A 79.965 569 90 14 1430 1983 11071634 11071075 9.690000e-107 398.0
6 TraesCS3D01G012000 chr3A 83.007 306 44 5 978 1276 9814630 9814326 2.200000e-68 270.0
7 TraesCS3D01G012000 chr3A 85.271 258 35 1 1021 1275 11028152 11027895 3.690000e-66 263.0
8 TraesCS3D01G012000 chr3A 91.228 114 8 2 4691 4803 9843340 9843228 2.310000e-33 154.0
9 TraesCS3D01G012000 chr3B 90.500 2000 117 23 210 2160 6673718 6671743 0.000000e+00 2573.0
10 TraesCS3D01G012000 chr3B 92.913 1524 87 13 2624 4140 6671559 6670050 0.000000e+00 2196.0
11 TraesCS3D01G012000 chr3B 79.829 937 151 27 3550 4459 6451375 6450450 0.000000e+00 649.0
12 TraesCS3D01G012000 chr3B 76.656 634 119 20 1367 1984 3601925 3602545 1.670000e-84 324.0
13 TraesCS3D01G012000 chr3B 94.712 208 9 2 1 208 6674008 6673803 6.000000e-84 322.0
14 TraesCS3D01G012000 chr3B 75.621 644 117 22 1367 1984 5234286 5233657 2.830000e-72 283.0
15 TraesCS3D01G012000 chr3B 81.728 301 51 3 975 1271 3601441 3601741 1.030000e-61 248.0
16 TraesCS3D01G012000 chr3B 81.879 298 50 3 978 1271 5234767 5234470 1.030000e-61 248.0
17 TraesCS3D01G012000 chr3B 75.432 521 105 16 1467 1983 545205911 545205410 1.040000e-56 231.0
18 TraesCS3D01G012000 chr3B 92.969 128 4 4 2328 2451 6671685 6671559 1.060000e-41 182.0
19 TraesCS3D01G012000 chr3B 90.351 114 10 1 4691 4803 6670039 6669926 1.080000e-31 148.0
20 TraesCS3D01G012000 chr3B 77.824 239 50 3 3304 3541 3603268 3603504 1.390000e-30 145.0
21 TraesCS3D01G012000 chr3B 77.824 239 50 3 3304 3541 5232934 5232698 1.390000e-30 145.0
22 TraesCS3D01G012000 chr3B 76.804 194 27 12 4573 4748 6668455 6668262 5.120000e-15 93.5
23 TraesCS3D01G012000 chrUn 82.288 1530 198 47 2657 4171 35628603 35630074 0.000000e+00 1256.0
24 TraesCS3D01G012000 chrUn 80.840 976 129 32 1365 2307 327485193 327484243 0.000000e+00 713.0
25 TraesCS3D01G012000 chrUn 79.829 937 151 27 3550 4459 268398833 268397908 0.000000e+00 649.0
26 TraesCS3D01G012000 chrUn 79.829 937 151 27 3550 4459 272388646 272387721 0.000000e+00 649.0
27 TraesCS3D01G012000 chr7A 100.000 42 0 0 1275 1316 643081899 643081858 1.430000e-10 78.7
28 TraesCS3D01G012000 chr6B 100.000 42 0 0 1275 1316 15233256 15233297 1.430000e-10 78.7
29 TraesCS3D01G012000 chr4A 91.071 56 3 1 1261 1314 137185794 137185739 1.850000e-09 75.0
30 TraesCS3D01G012000 chr6D 97.619 42 1 0 1275 1316 358227689 358227648 6.670000e-09 73.1
31 TraesCS3D01G012000 chr6A 97.619 42 1 0 1275 1316 189573557 189573516 6.670000e-09 73.1
32 TraesCS3D01G012000 chr6A 97.222 36 1 0 4706 4741 587776276 587776241 1.440000e-05 62.1
33 TraesCS3D01G012000 chr5A 86.885 61 6 2 1258 1316 681286279 681286339 3.100000e-07 67.6
34 TraesCS3D01G012000 chr2D 86.885 61 6 2 1256 1316 586695532 586695590 3.100000e-07 67.6


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 TraesCS3D01G012000 chr3D 4179138 4183940 4802 True 8870.000000 8870 100.000000 1 4803 1 chr3D.!!$R1 4802
1 TraesCS3D01G012000 chr3A 9843228 9847443 4215 True 3085.500000 6017 92.216500 25 4803 2 chr3A.!!$R4 4778
2 TraesCS3D01G012000 chr3A 9811591 9814630 3039 True 595.000000 920 81.406500 978 3604 2 chr3A.!!$R3 2626
3 TraesCS3D01G012000 chr3A 11064866 11065425 559 True 398.000000 398 80.000000 1430 1983 1 chr3A.!!$R1 553
4 TraesCS3D01G012000 chr3A 11071075 11071634 559 True 398.000000 398 79.965000 1430 1983 1 chr3A.!!$R2 553
5 TraesCS3D01G012000 chr3A 11027002 11028152 1150 True 349.500000 436 82.801000 1021 1983 2 chr3A.!!$R5 962
6 TraesCS3D01G012000 chr3B 6668262 6674008 5746 True 919.083333 2573 89.708167 1 4803 6 chr3B.!!$R4 4802
7 TraesCS3D01G012000 chr3B 6450450 6451375 925 True 649.000000 649 79.829000 3550 4459 1 chr3B.!!$R1 909
8 TraesCS3D01G012000 chr3B 3601441 3603504 2063 False 239.000000 324 78.736000 975 3541 3 chr3B.!!$F1 2566
9 TraesCS3D01G012000 chr3B 545205410 545205911 501 True 231.000000 231 75.432000 1467 1983 1 chr3B.!!$R2 516
10 TraesCS3D01G012000 chr3B 5232698 5234767 2069 True 225.333333 283 78.441333 978 3541 3 chr3B.!!$R3 2563
11 TraesCS3D01G012000 chrUn 35628603 35630074 1471 False 1256.000000 1256 82.288000 2657 4171 1 chrUn.!!$F1 1514
12 TraesCS3D01G012000 chrUn 327484243 327485193 950 True 713.000000 713 80.840000 1365 2307 1 chrUn.!!$R3 942
13 TraesCS3D01G012000 chrUn 268397908 268398833 925 True 649.000000 649 79.829000 3550 4459 1 chrUn.!!$R1 909
14 TraesCS3D01G012000 chrUn 272387721 272388646 925 True 649.000000 649 79.829000 3550 4459 1 chrUn.!!$R2 909

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
761 872 0.242825 GTTGGTAAAAAGGGAGCGGC 59.757 55.000 0.00 0.00 0.00 6.53 F
767 878 0.463833 AAAAAGGGAGCGGCGATAGG 60.464 55.000 12.98 0.00 0.00 2.57 F
965 1077 1.200760 ATAGCACACCTGTGGAGCCA 61.201 55.000 7.53 1.65 45.72 4.75 F
2694 3468 1.738099 GTGCTAGCCGGTGTGACTG 60.738 63.158 13.29 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2179 2.633488 GGTAATCACCTGAAGACAGCC 58.367 52.381 0.00 0.00 42.11 4.85 R
2694 3468 4.367386 AATATTGTGAAAGAGCTGCTGC 57.633 40.909 7.01 7.62 40.05 5.25 R
3019 3810 6.202954 GGTAACATATGTCTGTTCATAGTGGC 59.797 42.308 9.23 0.00 39.88 5.01 R
4626 6606 0.046397 ATAAGCCTTGGAGGGGAGGT 59.954 55.000 0.00 0.00 35.37 3.85 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
35 36 0.459899 CGATGGCTACTACACCTGCA 59.540 55.000 0.00 0.00 0.00 4.41
123 124 3.680786 CGGTGGCACGACCTCTCA 61.681 66.667 12.17 0.00 40.22 3.27
128 129 1.739562 GGCACGACCTCTCAGCAAG 60.740 63.158 0.00 0.00 34.51 4.01
175 176 3.688694 ATTAAGGTCGGCACAGTTACA 57.311 42.857 0.00 0.00 0.00 2.41
192 193 2.595124 ACATGATTGCACCGTCGATA 57.405 45.000 0.00 0.00 0.00 2.92
202 203 1.133598 CACCGTCGATAACCTAGCACA 59.866 52.381 0.00 0.00 0.00 4.57
249 334 2.943033 AGAACGTCTGGTTGGTCAAAAG 59.057 45.455 0.00 0.00 39.50 2.27
251 336 1.210967 ACGTCTGGTTGGTCAAAAGGA 59.789 47.619 0.00 0.00 0.00 3.36
298 383 8.034215 TGAATTATTCAAACCCACATAAAGCAG 58.966 33.333 5.03 0.00 36.59 4.24
379 464 4.638865 ACACTGGACCTACAACTCAAAAAC 59.361 41.667 0.00 0.00 0.00 2.43
492 578 4.267928 GTCGAATCACCTAGCACACATAAC 59.732 45.833 0.00 0.00 0.00 1.89
498 584 5.670485 TCACCTAGCACACATAACTTATGG 58.330 41.667 12.48 5.17 40.47 2.74
542 628 1.272490 GTTGGTAAAAAGGGGAGCAGC 59.728 52.381 0.00 0.00 0.00 5.25
610 719 3.323979 GTCCACCAACTTCTGACCTCTAA 59.676 47.826 0.00 0.00 0.00 2.10
648 757 6.295575 CCTCACAGGGAATTGGATACTAGATC 60.296 46.154 0.00 0.00 37.61 2.75
649 758 5.243954 TCACAGGGAATTGGATACTAGATCG 59.756 44.000 0.00 0.00 37.61 3.69
734 845 8.917088 ACCTTTTAAGATTGATACATCCATTGG 58.083 33.333 0.00 0.00 0.00 3.16
761 872 0.242825 GTTGGTAAAAAGGGAGCGGC 59.757 55.000 0.00 0.00 0.00 6.53
762 873 1.238625 TTGGTAAAAAGGGAGCGGCG 61.239 55.000 0.51 0.51 0.00 6.46
767 878 0.463833 AAAAAGGGAGCGGCGATAGG 60.464 55.000 12.98 0.00 0.00 2.57
789 900 5.484998 AGGAAATTGATAGCCAACCAATTGT 59.515 36.000 4.43 0.00 39.56 2.71
811 922 2.481289 TATCCAATTCCACACACGCA 57.519 45.000 0.00 0.00 0.00 5.24
828 939 4.943705 ACACGCAATCTAATGACAAGGAAT 59.056 37.500 0.00 0.00 0.00 3.01
949 1061 7.518188 ACCTTCCTTCCCAACACAATATATAG 58.482 38.462 0.00 0.00 0.00 1.31
965 1077 1.200760 ATAGCACACCTGTGGAGCCA 61.201 55.000 7.53 1.65 45.72 4.75
1089 1203 2.948979 GGAATGTGCCGACAATTCCATA 59.051 45.455 15.51 0.00 38.43 2.74
1697 2129 2.693864 AGGGTGCCAGCTATGCCT 60.694 61.111 5.07 0.00 0.00 4.75
1747 2179 2.202756 GCGAGAACCACGGCCTAG 60.203 66.667 0.00 0.00 0.00 3.02
1799 2234 2.067766 GCGTGGTTTTGGTCGTATGTA 58.932 47.619 0.00 0.00 0.00 2.29
2008 2455 6.019801 CGTACGTAAAGCTGCTCAATCTTATT 60.020 38.462 7.22 0.00 0.00 1.40
2378 3144 8.989653 ATAACCTTTTGACGAAAACTGAAAAA 57.010 26.923 0.00 0.00 0.00 1.94
2694 3468 1.738099 GTGCTAGCCGGTGTGACTG 60.738 63.158 13.29 0.00 0.00 3.51
3128 3919 1.475682 GATCCCCTTGAGTACGTTCGT 59.524 52.381 0.00 2.91 0.00 3.85
3289 4080 6.582295 CAGTATAACATTGCACAAACTTGGAC 59.418 38.462 0.00 0.00 0.00 4.02
3305 4096 8.522830 CAAACTTGGACCAAACATTATGTCTAT 58.477 33.333 8.59 0.00 0.00 1.98
3345 4137 3.866883 ATTGCAACGACCCTTTAATGG 57.133 42.857 0.00 0.26 0.00 3.16
3542 4335 2.083774 TGCATTCTTAGGTTGCTTCGG 58.916 47.619 8.31 0.00 37.28 4.30
3647 4452 1.340017 GGTCTATGCAGGCTTTGACCA 60.340 52.381 24.81 0.00 41.70 4.02
3664 4469 6.935741 TTGACCATGCACTACCATAATTAC 57.064 37.500 0.00 0.00 0.00 1.89
3750 4555 2.212900 GATGGTTTTGCCGAGGCCAC 62.213 60.000 12.05 0.00 41.21 5.01
3813 4618 6.832384 ACAACATCAATCTAGAATGGCAAGAT 59.168 34.615 7.95 0.00 0.00 2.40
3902 4715 3.684305 TGTGTCATGCTAGTATGTTGTGC 59.316 43.478 18.78 8.15 0.00 4.57
4066 4882 6.704512 TGTTTTTGTGAAGAAAAGCTTGAC 57.295 33.333 0.00 0.00 40.60 3.18
4105 5819 1.606668 GCAAATCCACCTTTCGTGTGA 59.393 47.619 0.00 0.00 41.26 3.58
4108 5822 4.475944 CAAATCCACCTTTCGTGTGATTC 58.524 43.478 0.00 0.00 39.46 2.52
4110 5824 2.766313 TCCACCTTTCGTGTGATTCTG 58.234 47.619 0.00 0.00 41.26 3.02
4165 5881 5.945191 TGATGAAAGAATATGTGTTGCTCCA 59.055 36.000 0.00 0.00 0.00 3.86
4174 5890 1.213182 TGTGTTGCTCCAAACTGGGTA 59.787 47.619 0.00 0.00 38.32 3.69
4177 5893 1.202348 GTTGCTCCAAACTGGGTATGC 59.798 52.381 0.00 0.00 38.32 3.14
4192 5908 4.223320 GGTATGCGATAACCCACAAATG 57.777 45.455 0.00 0.00 0.00 2.32
4196 5912 2.258755 GCGATAACCCACAAATGTTGC 58.741 47.619 0.00 0.00 0.00 4.17
4198 5914 2.160615 CGATAACCCACAAATGTTGCGA 59.839 45.455 0.00 0.00 0.00 5.10
4234 5953 9.287373 TCTTTTTAATAAATAAGTGTGTCGGGT 57.713 29.630 0.00 0.00 0.00 5.28
4235 5954 9.902196 CTTTTTAATAAATAAGTGTGTCGGGTT 57.098 29.630 0.00 0.00 0.00 4.11
4236 5955 9.896263 TTTTTAATAAATAAGTGTGTCGGGTTC 57.104 29.630 0.00 0.00 0.00 3.62
4237 5956 8.618702 TTTAATAAATAAGTGTGTCGGGTTCA 57.381 30.769 0.00 0.00 0.00 3.18
4238 5957 8.618702 TTAATAAATAAGTGTGTCGGGTTCAA 57.381 30.769 0.00 0.00 0.00 2.69
4239 5958 4.823790 AAATAAGTGTGTCGGGTTCAAC 57.176 40.909 0.00 0.00 0.00 3.18
4241 5960 0.176219 AAGTGTGTCGGGTTCAACGA 59.824 50.000 0.00 0.00 38.13 3.85
4242 5961 0.176219 AGTGTGTCGGGTTCAACGAA 59.824 50.000 0.00 0.00 42.55 3.85
4245 5964 0.857287 GTGTCGGGTTCAACGAAGAC 59.143 55.000 0.00 2.76 42.55 3.01
4249 5968 1.566018 CGGGTTCAACGAAGACCAGC 61.566 60.000 0.00 0.00 0.00 4.85
4251 5970 0.868406 GGTTCAACGAAGACCAGCAG 59.132 55.000 0.00 0.00 0.00 4.24
4265 5984 3.040965 AGCAGGAATTGGTGTGTGG 57.959 52.632 0.00 0.00 35.85 4.17
4268 5987 1.686052 GCAGGAATTGGTGTGTGGAAA 59.314 47.619 0.00 0.00 0.00 3.13
4272 5991 3.324556 AGGAATTGGTGTGTGGAAATTGG 59.675 43.478 0.00 0.00 0.00 3.16
4273 5992 3.070878 GGAATTGGTGTGTGGAAATTGGT 59.929 43.478 0.00 0.00 0.00 3.67
4282 6001 3.826157 GTGTGGAAATTGGTCAGGAATCA 59.174 43.478 0.00 0.00 0.00 2.57
4285 6004 4.156739 GTGGAAATTGGTCAGGAATCACTC 59.843 45.833 0.00 0.00 0.00 3.51
4301 6021 6.434340 GGAATCACTCCAGTTACCAAAAGAAT 59.566 38.462 0.00 0.00 44.67 2.40
4302 6022 7.039714 GGAATCACTCCAGTTACCAAAAGAATT 60.040 37.037 0.00 0.00 44.67 2.17
4304 6024 5.534654 TCACTCCAGTTACCAAAAGAATTGG 59.465 40.000 5.69 5.69 44.91 3.16
4330 6050 8.711457 GTGGTTGTTTATTTCATTCATTGGAAG 58.289 33.333 0.00 0.00 36.25 3.46
4331 6051 7.877097 TGGTTGTTTATTTCATTCATTGGAAGG 59.123 33.333 0.00 0.00 36.25 3.46
4332 6052 7.148423 GGTTGTTTATTTCATTCATTGGAAGGC 60.148 37.037 0.00 0.00 36.25 4.35
4333 6053 7.243604 TGTTTATTTCATTCATTGGAAGGCT 57.756 32.000 0.00 0.00 36.25 4.58
4334 6054 7.098477 TGTTTATTTCATTCATTGGAAGGCTG 58.902 34.615 0.00 0.00 36.25 4.85
4340 6065 4.460382 TCATTCATTGGAAGGCTGAAGAAC 59.540 41.667 0.00 0.00 36.25 3.01
4376 6103 7.575414 TTTAAAAAGAGTACATCAAGTGGCA 57.425 32.000 0.00 0.00 0.00 4.92
4377 6104 7.575414 TTAAAAAGAGTACATCAAGTGGCAA 57.425 32.000 0.00 0.00 0.00 4.52
4386 6113 5.534207 ACATCAAGTGGCAAAATTCTCAA 57.466 34.783 0.00 0.00 0.00 3.02
4389 6116 7.669427 ACATCAAGTGGCAAAATTCTCAATTA 58.331 30.769 0.00 0.00 0.00 1.40
4391 6118 9.806203 CATCAAGTGGCAAAATTCTCAATTATA 57.194 29.630 0.00 0.00 0.00 0.98
4393 6120 9.023962 TCAAGTGGCAAAATTCTCAATTATAGT 57.976 29.630 0.00 0.00 0.00 2.12
4396 6123 9.461312 AGTGGCAAAATTCTCAATTATAGTACA 57.539 29.630 0.00 0.00 0.00 2.90
4403 6130 9.871238 AAATTCTCAATTATAGTACAGACACGT 57.129 29.630 0.00 0.00 0.00 4.49
4412 6139 6.701432 ATAGTACAGACACGTTAGTTTTGC 57.299 37.500 0.00 0.00 0.00 3.68
4413 6140 3.805971 AGTACAGACACGTTAGTTTTGCC 59.194 43.478 0.00 0.00 0.00 4.52
4426 6153 6.761714 CGTTAGTTTTGCCTCTTATATGGACT 59.238 38.462 0.00 0.00 0.00 3.85
4431 6158 9.343539 AGTTTTGCCTCTTATATGGACTAAATC 57.656 33.333 0.00 0.00 0.00 2.17
4432 6159 7.962964 TTTGCCTCTTATATGGACTAAATCG 57.037 36.000 0.00 0.00 0.00 3.34
4443 6170 5.614324 TGGACTAAATCGTTCTCATGGAT 57.386 39.130 0.00 0.00 0.00 3.41
4446 6173 4.130118 ACTAAATCGTTCTCATGGATGGC 58.870 43.478 0.00 0.00 0.00 4.40
4459 6186 1.425066 TGGATGGCTGGAATATCACCC 59.575 52.381 0.00 0.00 0.00 4.61
4461 6188 2.042162 GGATGGCTGGAATATCACCCAT 59.958 50.000 0.00 0.00 35.88 4.00
4463 6190 2.134354 TGGCTGGAATATCACCCATCA 58.866 47.619 0.00 0.00 0.00 3.07
4464 6191 2.718062 TGGCTGGAATATCACCCATCAT 59.282 45.455 0.00 0.00 0.00 2.45
4465 6192 3.915711 TGGCTGGAATATCACCCATCATA 59.084 43.478 0.00 0.00 0.00 2.15
4466 6193 4.353489 TGGCTGGAATATCACCCATCATAA 59.647 41.667 0.00 0.00 0.00 1.90
4467 6194 5.015497 TGGCTGGAATATCACCCATCATAAT 59.985 40.000 0.00 0.00 0.00 1.28
4468 6195 5.359009 GGCTGGAATATCACCCATCATAATG 59.641 44.000 0.00 0.00 0.00 1.90
4491 6417 7.187244 TGGTTTGCATTGATTTTGTTGTATG 57.813 32.000 0.00 0.00 0.00 2.39
4492 6418 6.204301 TGGTTTGCATTGATTTTGTTGTATGG 59.796 34.615 0.00 0.00 0.00 2.74
4493 6419 6.348376 GGTTTGCATTGATTTTGTTGTATGGG 60.348 38.462 0.00 0.00 0.00 4.00
4505 6431 4.616553 TGTTGTATGGGTAGAGCCTAAGA 58.383 43.478 0.00 0.00 37.43 2.10
4512 6438 6.613153 ATGGGTAGAGCCTAAGATTATGTC 57.387 41.667 0.00 0.00 37.43 3.06
4521 6447 7.066766 AGAGCCTAAGATTATGTCTTGCAAAAG 59.933 37.037 0.00 0.00 46.50 2.27
4526 6452 9.979270 CTAAGATTATGTCTTGCAAAAGTACTG 57.021 33.333 0.00 0.00 46.50 2.74
4528 6454 8.034058 AGATTATGTCTTGCAAAAGTACTGAC 57.966 34.615 0.00 3.13 31.47 3.51
4538 6464 5.465390 TGCAAAAGTACTGACTCACACATAC 59.535 40.000 0.00 0.00 33.58 2.39
4539 6465 5.696724 GCAAAAGTACTGACTCACACATACT 59.303 40.000 0.00 0.00 33.58 2.12
4540 6466 6.202954 GCAAAAGTACTGACTCACACATACTT 59.797 38.462 0.00 0.00 37.12 2.24
4553 6479 8.704668 ACTCACACATACTTATGATTACATCCA 58.295 33.333 3.19 0.00 37.87 3.41
4564 6490 9.513727 CTTATGATTACATCCATAGAGACATCG 57.486 37.037 0.00 0.00 37.87 3.84
4565 6491 6.901081 TGATTACATCCATAGAGACATCGT 57.099 37.500 0.00 0.00 0.00 3.73
4566 6492 7.996098 TGATTACATCCATAGAGACATCGTA 57.004 36.000 0.00 0.00 0.00 3.43
4567 6493 8.045176 TGATTACATCCATAGAGACATCGTAG 57.955 38.462 0.00 0.00 0.00 3.51
4568 6494 4.775058 ACATCCATAGAGACATCGTAGC 57.225 45.455 0.00 0.00 0.00 3.58
4569 6495 4.402829 ACATCCATAGAGACATCGTAGCT 58.597 43.478 0.00 0.00 0.00 3.32
4570 6496 5.561679 ACATCCATAGAGACATCGTAGCTA 58.438 41.667 0.00 0.00 0.00 3.32
4571 6497 5.413213 ACATCCATAGAGACATCGTAGCTAC 59.587 44.000 14.19 14.19 0.00 3.58
4577 6557 5.238006 AGAGACATCGTAGCTACTTCAAC 57.762 43.478 21.20 10.00 0.00 3.18
4578 6558 4.096682 AGAGACATCGTAGCTACTTCAACC 59.903 45.833 21.20 6.62 0.00 3.77
4585 6565 3.119101 CGTAGCTACTTCAACCCTCATGT 60.119 47.826 21.20 0.00 0.00 3.21
4588 6568 5.091261 AGCTACTTCAACCCTCATGTTAG 57.909 43.478 0.00 0.00 0.00 2.34
4604 6584 7.066284 CCTCATGTTAGAACTCATAAACTTGGG 59.934 40.741 0.00 0.00 31.51 4.12
4607 6587 6.607019 TGTTAGAACTCATAAACTTGGGGTT 58.393 36.000 0.00 0.00 40.28 4.11
4608 6588 6.713450 TGTTAGAACTCATAAACTTGGGGTTC 59.287 38.462 0.00 0.00 37.12 3.62
4610 6590 3.067684 ACTCATAAACTTGGGGTTCGG 57.932 47.619 0.00 0.00 37.12 4.30
4613 6593 4.226620 ACTCATAAACTTGGGGTTCGGTAT 59.773 41.667 0.00 0.00 37.12 2.73
4625 6605 1.990563 GTTCGGTATTGTGTCACTCCG 59.009 52.381 16.87 16.87 39.40 4.63
4626 6606 1.536940 TCGGTATTGTGTCACTCCGA 58.463 50.000 19.60 19.60 43.52 4.55
4631 6611 0.608640 ATTGTGTCACTCCGACCTCC 59.391 55.000 4.27 0.00 44.71 4.30
4637 6617 3.273654 ACTCCGACCTCCCCTCCA 61.274 66.667 0.00 0.00 0.00 3.86
4640 6620 3.083997 CCGACCTCCCCTCCAAGG 61.084 72.222 0.00 0.00 38.70 3.61
4645 6625 0.046397 ACCTCCCCTCCAAGGCTTAT 59.954 55.000 0.00 0.00 36.01 1.73
4647 6627 1.133668 CCTCCCCTCCAAGGCTTATTG 60.134 57.143 0.00 0.00 32.73 1.90
4654 6634 3.694566 CCTCCAAGGCTTATTGTAACACC 59.305 47.826 0.00 0.00 0.00 4.16
4666 6646 3.334583 TGTAACACCATGCTCTCCTTC 57.665 47.619 0.00 0.00 0.00 3.46
4672 6652 1.153005 CATGCTCTCCTTCAGGCCC 60.153 63.158 0.00 0.00 34.44 5.80
4674 6654 0.992431 ATGCTCTCCTTCAGGCCCAT 60.992 55.000 0.00 0.00 34.44 4.00
4681 6661 0.107017 CCTTCAGGCCCATGTAGGTG 60.107 60.000 0.00 0.00 34.11 4.00
4684 6664 1.367346 TCAGGCCCATGTAGGTGAAA 58.633 50.000 0.00 0.00 34.66 2.69
4690 6670 2.423538 GCCCATGTAGGTGAAATGACAC 59.576 50.000 0.00 0.00 39.70 3.67
4691 6671 3.684908 CCCATGTAGGTGAAATGACACA 58.315 45.455 0.00 0.00 41.88 3.72
4692 6672 3.440173 CCCATGTAGGTGAAATGACACAC 59.560 47.826 0.00 0.00 41.88 3.82
4693 6673 4.071423 CCATGTAGGTGAAATGACACACA 58.929 43.478 0.00 0.00 41.88 3.72
4696 6676 4.967036 TGTAGGTGAAATGACACACATCA 58.033 39.130 0.00 0.00 41.88 3.07
4697 6677 4.754618 TGTAGGTGAAATGACACACATCAC 59.245 41.667 0.00 0.00 41.88 3.06
4698 6678 4.090761 AGGTGAAATGACACACATCACT 57.909 40.909 13.99 0.00 41.88 3.41
4701 6681 4.977963 GGTGAAATGACACACATCACTTTG 59.022 41.667 13.99 0.00 41.88 2.77
4702 6682 5.450412 GGTGAAATGACACACATCACTTTGT 60.450 40.000 13.99 0.00 41.88 2.83
4703 6683 6.035843 GTGAAATGACACACATCACTTTGTT 58.964 36.000 0.00 0.00 38.38 2.83
4704 6684 6.020440 GTGAAATGACACACATCACTTTGTTG 60.020 38.462 0.00 0.00 38.38 3.33
4775 6773 9.702253 TCTATATGACTATTGACTAGGGGATTC 57.298 37.037 0.00 0.00 0.00 2.52
4776 6774 9.707957 CTATATGACTATTGACTAGGGGATTCT 57.292 37.037 0.00 0.00 0.00 2.40
4777 6775 6.926630 ATGACTATTGACTAGGGGATTCTC 57.073 41.667 0.00 0.00 0.00 2.87
4778 6776 5.148502 TGACTATTGACTAGGGGATTCTCC 58.851 45.833 0.00 0.00 35.23 3.71
4790 6788 3.205784 GGATTCTCCCATGTCCTCAAG 57.794 52.381 0.00 0.00 0.00 3.02
4791 6789 2.774234 GGATTCTCCCATGTCCTCAAGA 59.226 50.000 0.00 0.00 0.00 3.02
4792 6790 3.200825 GGATTCTCCCATGTCCTCAAGAA 59.799 47.826 0.00 0.00 0.00 2.52
4793 6791 3.703001 TTCTCCCATGTCCTCAAGAAC 57.297 47.619 0.00 0.00 0.00 3.01
4794 6792 1.550524 TCTCCCATGTCCTCAAGAACG 59.449 52.381 0.00 0.00 0.00 3.95
4795 6793 1.276421 CTCCCATGTCCTCAAGAACGT 59.724 52.381 0.00 0.00 0.00 3.99
4796 6794 1.001974 TCCCATGTCCTCAAGAACGTG 59.998 52.381 0.00 0.00 0.00 4.49
4797 6795 1.001974 CCCATGTCCTCAAGAACGTGA 59.998 52.381 0.00 0.00 0.00 4.35
4798 6796 2.355108 CCCATGTCCTCAAGAACGTGAT 60.355 50.000 0.00 0.00 0.00 3.06
4799 6797 2.674852 CCATGTCCTCAAGAACGTGATG 59.325 50.000 0.00 0.00 0.00 3.07
4800 6798 2.455674 TGTCCTCAAGAACGTGATGG 57.544 50.000 0.00 0.00 0.00 3.51
4801 6799 1.967779 TGTCCTCAAGAACGTGATGGA 59.032 47.619 0.00 0.00 0.00 3.41
4802 6800 2.367241 TGTCCTCAAGAACGTGATGGAA 59.633 45.455 0.00 2.05 31.15 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.555199 CTCATTGCAGGTGTAGTAGCC 58.445 52.381 0.00 0.00 0.00 3.93
35 36 2.421952 CCATGGATCCGTTGTCCTCATT 60.422 50.000 5.56 0.00 36.68 2.57
123 124 2.688958 GTCACCTAGTATCCGACTTGCT 59.311 50.000 0.00 0.00 39.81 3.91
175 176 2.158957 AGGTTATCGACGGTGCAATCAT 60.159 45.455 0.00 0.00 0.00 2.45
337 422 4.083110 AGTGTGCTGTTTTATCATGTGCTC 60.083 41.667 0.00 0.00 0.00 4.26
348 433 2.092646 TGTAGGTCCAGTGTGCTGTTTT 60.093 45.455 0.00 0.00 41.02 2.43
362 447 8.828688 ACAGTATAGTTTTTGAGTTGTAGGTC 57.171 34.615 0.00 0.00 0.00 3.85
448 534 6.649141 TCGACAGTGCAATAAATTGTCTAGTT 59.351 34.615 4.71 0.00 39.88 2.24
450 536 6.647212 TCGACAGTGCAATAAATTGTCTAG 57.353 37.500 4.71 0.00 39.88 2.43
468 554 1.616374 TGTGTGCTAGGTGATTCGACA 59.384 47.619 0.00 0.00 0.00 4.35
492 578 9.070179 TCATTTCATGGATGTATCAACCATAAG 57.930 33.333 10.34 2.00 43.52 1.73
498 584 6.319658 ACCACTCATTTCATGGATGTATCAAC 59.680 38.462 9.01 0.00 36.94 3.18
542 628 9.927668 AATTGGTTTGGTATGAAATTTCTACTG 57.072 29.630 18.64 0.00 0.00 2.74
610 719 2.842462 TGAGGTCACGCCACCAGT 60.842 61.111 6.17 0.00 39.16 4.00
648 757 1.303309 CCTTAATTGCTCTCAGGGCG 58.697 55.000 0.00 0.00 0.00 6.13
649 758 2.293170 GACCTTAATTGCTCTCAGGGC 58.707 52.381 0.00 0.00 0.00 5.19
734 845 5.354513 GCTCCCTTTTTACCAACTAGTCATC 59.645 44.000 0.00 0.00 0.00 2.92
761 872 5.063204 TGGTTGGCTATCAATTTCCTATCG 58.937 41.667 0.00 0.00 37.73 2.92
762 873 6.959639 TTGGTTGGCTATCAATTTCCTATC 57.040 37.500 0.00 0.00 37.73 2.08
767 878 8.947055 AATACAATTGGTTGGCTATCAATTTC 57.053 30.769 15.86 0.00 38.55 2.17
789 900 4.518249 TGCGTGTGTGGAATTGGATAATA 58.482 39.130 0.00 0.00 0.00 0.98
811 922 7.928706 CGGACTCTAATTCCTTGTCATTAGATT 59.071 37.037 2.82 0.00 39.93 2.40
828 939 0.389426 GCAAAGCCGTCGGACTCTAA 60.389 55.000 17.49 0.00 0.00 2.10
949 1061 2.203337 TTGGCTCCACAGGTGTGC 60.203 61.111 4.48 3.49 44.34 4.57
965 1077 7.441458 GGTCGATTGTTAATTACTATGGCTCTT 59.559 37.037 0.00 0.00 0.00 2.85
1089 1203 0.563173 TAGGGCTCATGGGCTCTACT 59.437 55.000 23.78 15.14 41.80 2.57
1697 2129 4.947147 GTGCGCTTGGGTGGTGGA 62.947 66.667 9.73 0.00 0.00 4.02
1747 2179 2.633488 GGTAATCACCTGAAGACAGCC 58.367 52.381 0.00 0.00 42.11 4.85
2022 2469 9.542462 GTGCAGGTGATTTCAATTAGTACTATA 57.458 33.333 2.79 0.00 0.00 1.31
2023 2470 8.046708 TGTGCAGGTGATTTCAATTAGTACTAT 58.953 33.333 2.79 0.00 0.00 2.12
2024 2471 7.390823 TGTGCAGGTGATTTCAATTAGTACTA 58.609 34.615 0.00 0.00 0.00 1.82
2025 2472 6.237901 TGTGCAGGTGATTTCAATTAGTACT 58.762 36.000 0.00 0.00 0.00 2.73
2026 2473 6.494893 TGTGCAGGTGATTTCAATTAGTAC 57.505 37.500 0.00 0.00 0.00 2.73
2170 2673 7.892241 TCCTATACTTTACCTACACACTTCTGT 59.108 37.037 0.00 0.00 0.00 3.41
2183 2686 7.399245 TGGTTTGCAAATCCTATACTTTACC 57.601 36.000 19.51 10.19 36.63 2.85
2694 3468 4.367386 AATATTGTGAAAGAGCTGCTGC 57.633 40.909 7.01 7.62 40.05 5.25
3019 3810 6.202954 GGTAACATATGTCTGTTCATAGTGGC 59.797 42.308 9.23 0.00 39.88 5.01
3128 3919 6.606796 TCCTATGCATAAATCTTTTTGCCTCA 59.393 34.615 8.00 0.00 42.12 3.86
3315 4106 4.396166 AGGGTCGTTGCAATAATCAGAAAG 59.604 41.667 0.59 0.00 0.00 2.62
3345 4137 4.522114 AGATAAAAGCTCCTGCCTTCTTC 58.478 43.478 0.00 0.00 40.80 2.87
3542 4335 6.319658 ACACATGATGATGGATGTTTTAGTCC 59.680 38.462 0.00 0.00 33.39 3.85
3625 4423 2.648059 GTCAAAGCCTGCATAGACCAT 58.352 47.619 0.00 0.00 0.00 3.55
3664 4469 6.439599 CAGAACTACCTTGATATCACTACCG 58.560 44.000 4.48 0.00 0.00 4.02
3750 4555 6.372185 GCTGCTGCATTCTTAATGATTCTAG 58.628 40.000 11.11 0.00 41.46 2.43
3813 4618 6.566942 GCACCAATACAATTGTCGTTACTCAA 60.567 38.462 15.85 0.00 0.00 3.02
3885 4698 5.657470 AATACGCACAACATACTAGCATG 57.343 39.130 1.10 1.10 0.00 4.06
3946 4759 7.587037 AGCATACAGTTATTGGCATAAACAT 57.413 32.000 13.06 5.36 0.00 2.71
3955 4768 4.704540 TGACCCAAAGCATACAGTTATTGG 59.295 41.667 0.00 0.00 37.61 3.16
3962 4775 4.853924 AAGTTTGACCCAAAGCATACAG 57.146 40.909 0.00 0.00 33.82 2.74
4037 4853 5.812127 GCTTTTCTTCACAAAAACATGGAGT 59.188 36.000 0.00 0.00 0.00 3.85
4052 4868 5.238214 ACTCATCACAGTCAAGCTTTTCTTC 59.762 40.000 0.00 0.00 31.27 2.87
4066 4882 6.831727 TTTGCAAAAATTGACTCATCACAG 57.168 33.333 10.02 0.00 33.38 3.66
4083 4899 2.791383 CACGAAAGGTGGATTTGCAA 57.209 45.000 0.00 0.00 43.16 4.08
4158 5874 1.544724 GCATACCCAGTTTGGAGCAA 58.455 50.000 0.00 0.00 40.96 3.91
4174 5890 3.675775 GCAACATTTGTGGGTTATCGCAT 60.676 43.478 0.00 0.00 38.69 4.73
4177 5893 2.160615 TCGCAACATTTGTGGGTTATCG 59.839 45.455 0.00 0.00 41.37 2.92
4187 5903 8.624701 AAAGATCTATTGATTCGCAACATTTG 57.375 30.769 0.00 0.00 39.78 2.32
4233 5952 0.868406 CCTGCTGGTCTTCGTTGAAC 59.132 55.000 0.51 0.00 0.00 3.18
4234 5953 0.756294 TCCTGCTGGTCTTCGTTGAA 59.244 50.000 9.73 0.00 34.23 2.69
4235 5954 0.756294 TTCCTGCTGGTCTTCGTTGA 59.244 50.000 9.73 0.00 34.23 3.18
4236 5955 1.813513 ATTCCTGCTGGTCTTCGTTG 58.186 50.000 9.73 0.00 34.23 4.10
4237 5956 2.154462 CAATTCCTGCTGGTCTTCGTT 58.846 47.619 9.73 0.00 34.23 3.85
4238 5957 1.611673 CCAATTCCTGCTGGTCTTCGT 60.612 52.381 9.73 0.00 34.23 3.85
4239 5958 1.089920 CCAATTCCTGCTGGTCTTCG 58.910 55.000 9.73 0.00 34.23 3.79
4241 5960 1.145738 ACACCAATTCCTGCTGGTCTT 59.854 47.619 9.73 1.90 44.30 3.01
4242 5961 0.773644 ACACCAATTCCTGCTGGTCT 59.226 50.000 9.73 0.00 44.30 3.85
4245 5964 0.599558 CACACACCAATTCCTGCTGG 59.400 55.000 2.58 2.58 38.77 4.85
4249 5968 4.309099 CAATTTCCACACACCAATTCCTG 58.691 43.478 0.00 0.00 0.00 3.86
4251 5970 3.070878 ACCAATTTCCACACACCAATTCC 59.929 43.478 0.00 0.00 0.00 3.01
4265 5984 4.335416 TGGAGTGATTCCTGACCAATTTC 58.665 43.478 0.00 0.00 46.92 2.17
4268 5987 2.915604 ACTGGAGTGATTCCTGACCAAT 59.084 45.455 7.83 0.00 46.92 3.16
4272 5991 3.260884 TGGTAACTGGAGTGATTCCTGAC 59.739 47.826 7.83 0.00 46.92 3.51
4273 5992 3.516586 TGGTAACTGGAGTGATTCCTGA 58.483 45.455 7.83 0.00 46.92 3.86
4301 6021 7.443575 CCAATGAATGAAATAAACAACCACCAA 59.556 33.333 0.00 0.00 0.00 3.67
4302 6022 6.933521 CCAATGAATGAAATAAACAACCACCA 59.066 34.615 0.00 0.00 0.00 4.17
4304 6024 8.600449 TTCCAATGAATGAAATAAACAACCAC 57.400 30.769 0.00 0.00 0.00 4.16
4306 6026 7.148423 GCCTTCCAATGAATGAAATAAACAACC 60.148 37.037 0.00 0.00 0.00 3.77
4314 6034 5.718130 TCTTCAGCCTTCCAATGAATGAAAT 59.282 36.000 0.00 0.00 30.60 2.17
4330 6050 3.402628 TGTACTTCCAGTTCTTCAGCC 57.597 47.619 0.00 0.00 0.00 4.85
4331 6051 5.948992 AATTGTACTTCCAGTTCTTCAGC 57.051 39.130 0.00 0.00 0.00 4.26
4352 6077 7.575414 TGCCACTTGATGTACTCTTTTTAAA 57.425 32.000 0.00 0.00 0.00 1.52
4353 6078 7.575414 TTGCCACTTGATGTACTCTTTTTAA 57.425 32.000 0.00 0.00 0.00 1.52
4355 6082 6.463995 TTTGCCACTTGATGTACTCTTTTT 57.536 33.333 0.00 0.00 0.00 1.94
4373 6100 9.937175 GTCTGTACTATAATTGAGAATTTTGCC 57.063 33.333 0.00 0.00 32.38 4.52
4377 6104 9.871238 ACGTGTCTGTACTATAATTGAGAATTT 57.129 29.630 0.00 0.00 32.38 1.82
4386 6113 8.866956 GCAAAACTAACGTGTCTGTACTATAAT 58.133 33.333 0.00 0.00 0.00 1.28
4389 6116 5.636543 GGCAAAACTAACGTGTCTGTACTAT 59.363 40.000 0.00 0.00 0.00 2.12
4391 6118 3.805971 GGCAAAACTAACGTGTCTGTACT 59.194 43.478 0.00 0.00 0.00 2.73
4392 6119 3.805971 AGGCAAAACTAACGTGTCTGTAC 59.194 43.478 0.00 0.00 0.00 2.90
4393 6120 4.053295 GAGGCAAAACTAACGTGTCTGTA 58.947 43.478 0.00 0.00 0.00 2.74
4394 6121 2.870411 GAGGCAAAACTAACGTGTCTGT 59.130 45.455 0.00 0.00 0.00 3.41
4395 6122 3.131396 AGAGGCAAAACTAACGTGTCTG 58.869 45.455 0.00 0.00 0.00 3.51
4396 6123 3.470645 AGAGGCAAAACTAACGTGTCT 57.529 42.857 0.00 0.00 0.00 3.41
4401 6128 6.761714 AGTCCATATAAGAGGCAAAACTAACG 59.238 38.462 0.00 0.00 0.00 3.18
4409 6136 7.062749 ACGATTTAGTCCATATAAGAGGCAA 57.937 36.000 0.00 0.00 0.00 4.52
4412 6139 8.577296 TGAGAACGATTTAGTCCATATAAGAGG 58.423 37.037 0.00 0.00 0.00 3.69
4426 6153 4.129380 CAGCCATCCATGAGAACGATTTA 58.871 43.478 0.00 0.00 0.00 1.40
4431 6158 0.178767 TCCAGCCATCCATGAGAACG 59.821 55.000 0.00 0.00 0.00 3.95
4432 6159 2.425143 TTCCAGCCATCCATGAGAAC 57.575 50.000 0.00 0.00 0.00 3.01
4459 6186 8.670135 ACAAAATCAATGCAAACCATTATGATG 58.330 29.630 0.00 0.00 42.15 3.07
4461 6188 8.504815 CAACAAAATCAATGCAAACCATTATGA 58.495 29.630 0.00 0.00 42.15 2.15
4463 6190 8.393671 ACAACAAAATCAATGCAAACCATTAT 57.606 26.923 0.00 0.00 42.15 1.28
4464 6191 7.798596 ACAACAAAATCAATGCAAACCATTA 57.201 28.000 0.00 0.00 42.15 1.90
4465 6192 6.696441 ACAACAAAATCAATGCAAACCATT 57.304 29.167 0.00 0.00 44.86 3.16
4466 6193 7.094720 CCATACAACAAAATCAATGCAAACCAT 60.095 33.333 0.00 0.00 35.06 3.55
4467 6194 6.204301 CCATACAACAAAATCAATGCAAACCA 59.796 34.615 0.00 0.00 0.00 3.67
4468 6195 6.348376 CCCATACAACAAAATCAATGCAAACC 60.348 38.462 0.00 0.00 0.00 3.27
4472 6199 5.480642 ACCCATACAACAAAATCAATGCA 57.519 34.783 0.00 0.00 0.00 3.96
4473 6200 6.862209 TCTACCCATACAACAAAATCAATGC 58.138 36.000 0.00 0.00 0.00 3.56
4474 6201 6.974622 GCTCTACCCATACAACAAAATCAATG 59.025 38.462 0.00 0.00 0.00 2.82
4476 6203 5.417580 GGCTCTACCCATACAACAAAATCAA 59.582 40.000 0.00 0.00 0.00 2.57
4478 6205 5.193679 AGGCTCTACCCATACAACAAAATC 58.806 41.667 0.00 0.00 40.58 2.17
4479 6206 5.193099 AGGCTCTACCCATACAACAAAAT 57.807 39.130 0.00 0.00 40.58 1.82
4480 6207 4.650972 AGGCTCTACCCATACAACAAAA 57.349 40.909 0.00 0.00 40.58 2.44
4491 6417 6.459923 CAAGACATAATCTTAGGCTCTACCC 58.540 44.000 0.00 0.00 46.52 3.69
4492 6418 5.929415 GCAAGACATAATCTTAGGCTCTACC 59.071 44.000 0.00 0.00 46.52 3.18
4493 6419 6.516718 TGCAAGACATAATCTTAGGCTCTAC 58.483 40.000 0.00 0.00 46.52 2.59
4505 6431 7.661437 TGAGTCAGTACTTTTGCAAGACATAAT 59.339 33.333 13.27 0.00 35.56 1.28
4512 6438 4.332543 TGTGTGAGTCAGTACTTTTGCAAG 59.667 41.667 0.00 0.00 35.56 4.01
4548 6474 5.645929 AGTAGCTACGATGTCTCTATGGATG 59.354 44.000 17.99 0.00 0.00 3.51
4553 6479 6.016943 GGTTGAAGTAGCTACGATGTCTCTAT 60.017 42.308 17.99 0.00 0.00 1.98
4557 6483 3.130693 GGGTTGAAGTAGCTACGATGTCT 59.869 47.826 17.99 0.00 0.00 3.41
4558 6484 3.130693 AGGGTTGAAGTAGCTACGATGTC 59.869 47.826 17.99 13.83 0.00 3.06
4563 6489 3.119101 ACATGAGGGTTGAAGTAGCTACG 60.119 47.826 17.99 1.96 0.00 3.51
4564 6490 4.473477 ACATGAGGGTTGAAGTAGCTAC 57.527 45.455 16.43 16.43 0.00 3.58
4565 6491 5.955959 TCTAACATGAGGGTTGAAGTAGCTA 59.044 40.000 0.00 0.00 32.29 3.32
4566 6492 4.777896 TCTAACATGAGGGTTGAAGTAGCT 59.222 41.667 0.00 0.00 32.29 3.32
4567 6493 5.086104 TCTAACATGAGGGTTGAAGTAGC 57.914 43.478 0.00 0.00 32.29 3.58
4568 6494 6.702329 AGTTCTAACATGAGGGTTGAAGTAG 58.298 40.000 0.00 0.00 32.29 2.57
4569 6495 6.269077 TGAGTTCTAACATGAGGGTTGAAGTA 59.731 38.462 0.00 0.00 32.29 2.24
4570 6496 5.071788 TGAGTTCTAACATGAGGGTTGAAGT 59.928 40.000 0.00 0.00 32.29 3.01
4571 6497 5.551233 TGAGTTCTAACATGAGGGTTGAAG 58.449 41.667 0.00 0.00 32.29 3.02
4577 6557 7.066284 CCAAGTTTATGAGTTCTAACATGAGGG 59.934 40.741 0.00 0.00 0.00 4.30
4578 6558 7.066284 CCCAAGTTTATGAGTTCTAACATGAGG 59.934 40.741 0.00 0.00 0.00 3.86
4585 6565 5.935789 CGAACCCCAAGTTTATGAGTTCTAA 59.064 40.000 0.00 0.00 39.40 2.10
4588 6568 3.439129 CCGAACCCCAAGTTTATGAGTTC 59.561 47.826 0.00 0.00 39.40 3.01
4604 6584 2.344025 GGAGTGACACAATACCGAACC 58.656 52.381 8.59 0.00 0.00 3.62
4607 6587 1.536940 TCGGAGTGACACAATACCGA 58.463 50.000 22.33 22.33 45.36 4.69
4625 6605 0.620700 TAAGCCTTGGAGGGGAGGTC 60.621 60.000 0.00 0.00 35.37 3.85
4626 6606 0.046397 ATAAGCCTTGGAGGGGAGGT 59.954 55.000 0.00 0.00 35.37 3.85
4631 6611 3.694566 GTGTTACAATAAGCCTTGGAGGG 59.305 47.826 0.00 0.00 35.37 4.30
4637 6617 4.344104 AGCATGGTGTTACAATAAGCCTT 58.656 39.130 0.00 0.00 0.00 4.35
4640 6620 4.035675 GGAGAGCATGGTGTTACAATAAGC 59.964 45.833 0.00 0.00 0.00 3.09
4645 6625 3.072330 TGAAGGAGAGCATGGTGTTACAA 59.928 43.478 0.00 0.00 0.00 2.41
4647 6627 3.265791 CTGAAGGAGAGCATGGTGTTAC 58.734 50.000 0.00 0.00 0.00 2.50
4654 6634 1.153005 GGGCCTGAAGGAGAGCATG 60.153 63.158 0.84 0.00 37.39 4.06
4666 6646 2.026641 CATTTCACCTACATGGGCCTG 58.973 52.381 4.53 3.00 41.11 4.85
4672 6652 5.412286 TGATGTGTGTCATTTCACCTACATG 59.588 40.000 7.26 0.00 36.11 3.21
4674 6654 4.754618 GTGATGTGTGTCATTTCACCTACA 59.245 41.667 0.00 0.00 36.83 2.74
4681 6661 6.264832 TCAACAAAGTGATGTGTGTCATTTC 58.735 36.000 0.00 0.00 36.83 2.17
4684 6664 6.395426 AATCAACAAAGTGATGTGTGTCAT 57.605 33.333 0.00 0.00 38.28 3.06
4690 6670 5.914635 GTGGTGTAATCAACAAAGTGATGTG 59.085 40.000 0.00 0.00 43.29 3.21
4691 6671 5.592282 TGTGGTGTAATCAACAAAGTGATGT 59.408 36.000 0.00 0.00 43.29 3.06
4692 6672 6.070897 TGTGGTGTAATCAACAAAGTGATG 57.929 37.500 0.00 0.00 43.29 3.07
4693 6673 6.096141 TGTTGTGGTGTAATCAACAAAGTGAT 59.904 34.615 7.36 0.00 45.05 3.06
4696 6676 5.906113 TGTTGTGGTGTAATCAACAAAGT 57.094 34.783 7.36 0.00 45.05 2.66
4749 6747 9.702253 GAATCCCCTAGTCAATAGTCATATAGA 57.298 37.037 0.00 0.00 0.00 1.98
4750 6748 9.707957 AGAATCCCCTAGTCAATAGTCATATAG 57.292 37.037 0.00 0.00 0.00 1.31
4751 6749 9.702253 GAGAATCCCCTAGTCAATAGTCATATA 57.298 37.037 0.00 0.00 0.00 0.86
4752 6750 8.602472 GAGAATCCCCTAGTCAATAGTCATAT 57.398 38.462 0.00 0.00 0.00 1.78
4754 6752 6.926630 GAGAATCCCCTAGTCAATAGTCAT 57.073 41.667 0.00 0.00 0.00 3.06
4771 6769 4.195416 GTTCTTGAGGACATGGGAGAATC 58.805 47.826 0.00 0.00 0.00 2.52
4772 6770 3.369892 CGTTCTTGAGGACATGGGAGAAT 60.370 47.826 0.00 0.00 0.00 2.40
4773 6771 2.028112 CGTTCTTGAGGACATGGGAGAA 60.028 50.000 0.00 0.00 0.00 2.87
4774 6772 1.550524 CGTTCTTGAGGACATGGGAGA 59.449 52.381 0.00 0.00 0.00 3.71
4775 6773 1.276421 ACGTTCTTGAGGACATGGGAG 59.724 52.381 0.00 0.00 0.00 4.30
4776 6774 1.001974 CACGTTCTTGAGGACATGGGA 59.998 52.381 0.00 0.00 0.00 4.37
4777 6775 1.001974 TCACGTTCTTGAGGACATGGG 59.998 52.381 0.00 0.00 0.00 4.00
4778 6776 2.455674 TCACGTTCTTGAGGACATGG 57.544 50.000 0.00 0.00 0.00 3.66
4779 6777 2.674852 CCATCACGTTCTTGAGGACATG 59.325 50.000 0.00 0.00 28.33 3.21
4780 6778 2.567169 TCCATCACGTTCTTGAGGACAT 59.433 45.455 0.00 0.00 28.33 3.06
4781 6779 1.967779 TCCATCACGTTCTTGAGGACA 59.032 47.619 0.00 0.00 28.33 4.02
4782 6780 2.743636 TCCATCACGTTCTTGAGGAC 57.256 50.000 0.00 0.00 28.33 3.85


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

AutoCloner maintained by Alex Coulton.