Multiple sequence alignment - TraesCS6A01G287200

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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 TraesCS6A01G287200 chr6A 100.000 4996 0 0 1 4996 519222905 519227900 0.000000e+00 9226.0
1 TraesCS6A01G287200 chr6A 98.150 811 15 0 1878 2688 604629738 604630548 0.000000e+00 1415.0
2 TraesCS6A01G287200 chr6A 100.000 28 0 0 3724 3751 519226514 519226541 9.000000e-03 52.8
3 TraesCS6A01G287200 chr6A 100.000 28 0 0 3610 3637 519226628 519226655 9.000000e-03 52.8
4 TraesCS6A01G287200 chr6B 89.792 2263 118 35 2686 4881 564219019 564221235 0.000000e+00 2795.0
5 TraesCS6A01G287200 chr6B 92.089 1656 75 26 3 1620 564216963 564218600 0.000000e+00 2281.0
6 TraesCS6A01G287200 chr6B 94.909 275 10 2 1618 1892 564218761 564219031 1.290000e-115 427.0
7 TraesCS6A01G287200 chr6B 100.000 28 0 0 3610 3637 564220110 564220137 9.000000e-03 52.8
8 TraesCS6A01G287200 chr6D 91.759 1711 91 18 3 1690 377829763 377831446 0.000000e+00 2333.0
9 TraesCS6A01G287200 chr6D 90.877 1436 90 18 3587 4991 377832731 377834156 0.000000e+00 1888.0
10 TraesCS6A01G287200 chr6D 93.584 826 37 8 1878 2702 60541087 60541897 0.000000e+00 1218.0
11 TraesCS6A01G287200 chr6D 92.809 598 31 8 2688 3275 377831704 377832299 0.000000e+00 856.0
12 TraesCS6A01G287200 chr6D 91.981 212 17 0 3328 3539 377832517 377832728 1.050000e-76 298.0
13 TraesCS6A01G287200 chr6D 81.579 228 16 11 1689 1892 377831490 377831715 1.110000e-36 165.0
14 TraesCS6A01G287200 chr6D 100.000 28 0 0 3610 3637 377832871 377832898 9.000000e-03 52.8
15 TraesCS6A01G287200 chr1A 95.668 831 33 2 1860 2688 21990524 21991353 0.000000e+00 1332.0
16 TraesCS6A01G287200 chr1A 92.308 52 2 2 3535 3585 235687479 235687529 6.940000e-09 73.1
17 TraesCS6A01G287200 chr5D 94.183 808 31 8 1880 2686 475188243 475187451 0.000000e+00 1218.0
18 TraesCS6A01G287200 chr2D 93.521 818 38 9 1876 2692 607026248 607025445 0.000000e+00 1203.0
19 TraesCS6A01G287200 chr5B 93.481 813 36 9 1880 2690 349357329 349356532 0.000000e+00 1192.0
20 TraesCS6A01G287200 chr3D 93.564 808 36 8 1880 2686 403108474 403109266 0.000000e+00 1190.0
21 TraesCS6A01G287200 chr3D 93.325 809 37 9 1880 2686 8887588 8886795 0.000000e+00 1179.0
22 TraesCS6A01G287200 chr7A 93.235 813 39 8 1878 2689 436172391 436173188 0.000000e+00 1182.0
23 TraesCS6A01G287200 chr1B 88.710 62 5 2 3531 3590 225811691 225811752 1.930000e-09 75.0
24 TraesCS6A01G287200 chr7D 94.000 50 0 3 3530 3578 299188931 299188978 6.940000e-09 73.1
25 TraesCS6A01G287200 chr2B 93.878 49 1 2 3532 3578 136176054 136176102 6.940000e-09 73.1
26 TraesCS6A01G287200 chr2A 93.878 49 1 2 3532 3578 84959108 84959156 6.940000e-09 73.1
27 TraesCS6A01G287200 chr2A 93.878 49 1 2 3532 3578 84974329 84974377 6.940000e-09 73.1
28 TraesCS6A01G287200 chr1D 90.909 55 3 2 3535 3588 164421705 164421652 6.940000e-09 73.1
29 TraesCS6A01G287200 chr1D 93.878 49 1 2 3532 3578 279100794 279100746 6.940000e-09 73.1


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 TraesCS6A01G287200 chr6A 519222905 519227900 4995 False 3110.533333 9226 100.000000 1 4996 3 chr6A.!!$F2 4995
1 TraesCS6A01G287200 chr6A 604629738 604630548 810 False 1415.000000 1415 98.150000 1878 2688 1 chr6A.!!$F1 810
2 TraesCS6A01G287200 chr6B 564216963 564221235 4272 False 1388.950000 2795 94.197500 3 4881 4 chr6B.!!$F1 4878
3 TraesCS6A01G287200 chr6D 60541087 60541897 810 False 1218.000000 1218 93.584000 1878 2702 1 chr6D.!!$F1 824
4 TraesCS6A01G287200 chr6D 377829763 377834156 4393 False 932.133333 2333 91.500833 3 4991 6 chr6D.!!$F2 4988
5 TraesCS6A01G287200 chr1A 21990524 21991353 829 False 1332.000000 1332 95.668000 1860 2688 1 chr1A.!!$F1 828
6 TraesCS6A01G287200 chr5D 475187451 475188243 792 True 1218.000000 1218 94.183000 1880 2686 1 chr5D.!!$R1 806
7 TraesCS6A01G287200 chr2D 607025445 607026248 803 True 1203.000000 1203 93.521000 1876 2692 1 chr2D.!!$R1 816
8 TraesCS6A01G287200 chr5B 349356532 349357329 797 True 1192.000000 1192 93.481000 1880 2690 1 chr5B.!!$R1 810
9 TraesCS6A01G287200 chr3D 403108474 403109266 792 False 1190.000000 1190 93.564000 1880 2686 1 chr3D.!!$F1 806
10 TraesCS6A01G287200 chr3D 8886795 8887588 793 True 1179.000000 1179 93.325000 1880 2686 1 chr3D.!!$R1 806
11 TraesCS6A01G287200 chr7A 436172391 436173188 797 False 1182.000000 1182 93.235000 1878 2689 1 chr7A.!!$F1 811

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
242 243 0.025001 CCGCGTACTTGAAATCTGCG 59.975 55.0 4.92 0.00 43.34 5.18 F
945 975 0.250513 ACCAGATTCTGCGGAGAACC 59.749 55.0 22.32 12.95 41.12 3.62 F
1195 1238 0.034960 CGAGTGGGAGGAGTCTCTGA 60.035 60.0 0.00 0.00 39.86 3.27 F
1395 1438 0.247736 ACGAGATTCACAGCCTCACC 59.752 55.0 0.00 0.00 0.00 4.02 F
3155 3444 0.463295 ATCAGGGCATTCAGTCTGCG 60.463 55.0 0.00 0.00 40.59 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1108 0.094387 GCTTCTTCTTCGCGCTCTTG 59.906 55.000 5.56 0.00 0.00 3.02 R
2103 2388 4.455877 ACCCAATTGCGTTTTTGTTTTGAA 59.544 33.333 0.00 0.00 0.00 2.69 R
2792 3080 6.147821 CAGTTCGGATGTTTACTCAGACAAAT 59.852 38.462 0.00 0.00 0.00 2.32 R
3276 3721 7.982761 AACACAATAACAAATTTGATGCCAT 57.017 28.000 24.64 6.98 0.00 4.40 R
4791 5312 0.549950 CATTGGGATGACAGCCTCCT 59.450 55.000 10.08 0.00 35.16 3.69 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
132 133 1.280206 CGTCCGGTCGAACTTGAACC 61.280 60.000 16.36 0.00 0.00 3.62
242 243 0.025001 CCGCGTACTTGAAATCTGCG 59.975 55.000 4.92 0.00 43.34 5.18
282 283 4.335315 TGAATCAAGAACGCAAAGTGAGTT 59.665 37.500 0.00 0.00 42.92 3.01
283 284 5.525745 TGAATCAAGAACGCAAAGTGAGTTA 59.474 36.000 0.00 0.00 40.39 2.24
284 285 4.789095 TCAAGAACGCAAAGTGAGTTAC 57.211 40.909 0.00 0.00 40.39 2.50
285 286 4.439057 TCAAGAACGCAAAGTGAGTTACT 58.561 39.130 0.00 0.00 40.39 2.24
286 287 5.593968 TCAAGAACGCAAAGTGAGTTACTA 58.406 37.500 0.00 0.00 40.39 1.82
287 288 6.220930 TCAAGAACGCAAAGTGAGTTACTAT 58.779 36.000 0.00 0.00 40.39 2.12
288 289 6.704493 TCAAGAACGCAAAGTGAGTTACTATT 59.296 34.615 0.00 0.00 40.39 1.73
289 290 7.868922 TCAAGAACGCAAAGTGAGTTACTATTA 59.131 33.333 0.00 0.00 40.39 0.98
290 291 8.656849 CAAGAACGCAAAGTGAGTTACTATTAT 58.343 33.333 0.00 0.00 40.39 1.28
291 292 8.186178 AGAACGCAAAGTGAGTTACTATTATG 57.814 34.615 0.00 0.00 40.39 1.90
292 293 7.817962 AGAACGCAAAGTGAGTTACTATTATGT 59.182 33.333 0.00 0.00 40.39 2.29
293 294 8.991243 AACGCAAAGTGAGTTACTATTATGTA 57.009 30.769 0.00 0.00 38.58 2.29
294 295 8.630278 ACGCAAAGTGAGTTACTATTATGTAG 57.370 34.615 0.00 0.00 39.18 2.74
295 296 7.705325 ACGCAAAGTGAGTTACTATTATGTAGG 59.295 37.037 0.00 0.00 39.18 3.18
296 297 7.919091 CGCAAAGTGAGTTACTATTATGTAGGA 59.081 37.037 0.00 0.00 39.18 2.94
297 298 9.032420 GCAAAGTGAGTTACTATTATGTAGGAC 57.968 37.037 0.00 0.00 39.18 3.85
301 302 8.280084 AGTGAGTTACTATTATGTAGGACAGGA 58.720 37.037 0.00 0.00 38.04 3.86
311 312 8.792830 ATTATGTAGGACAGGAGTACCAAATA 57.207 34.615 0.00 0.00 38.94 1.40
318 319 7.112779 AGGACAGGAGTACCAAATAAATCAAG 58.887 38.462 0.00 0.00 38.94 3.02
322 323 7.397192 ACAGGAGTACCAAATAAATCAAGCAAT 59.603 33.333 0.00 0.00 38.94 3.56
325 326 9.736023 GGAGTACCAAATAAATCAAGCAATAAG 57.264 33.333 0.00 0.00 35.97 1.73
385 402 1.421410 GGATGCGACGGTAACTGCTG 61.421 60.000 0.00 0.00 0.00 4.41
386 403 2.025359 GATGCGACGGTAACTGCTGC 62.025 60.000 0.00 0.00 0.00 5.25
387 404 2.432628 GCGACGGTAACTGCTGCT 60.433 61.111 0.00 0.00 0.00 4.24
501 518 4.710695 CGCCGACGCTGTACACCA 62.711 66.667 0.00 0.00 0.00 4.17
604 631 1.492176 GGCCATTGGAGAAGGATCAGA 59.508 52.381 6.95 0.00 0.00 3.27
648 675 3.259374 AGTGGTGTTGGTGTGAGATCTAG 59.741 47.826 0.00 0.00 0.00 2.43
847 876 4.236935 GAGTCGTGGGTTGAATACGTAAA 58.763 43.478 0.00 0.00 38.80 2.01
855 884 3.441222 GGTTGAATACGTAAACCCCCTTG 59.559 47.826 14.28 0.00 37.90 3.61
856 885 4.325972 GTTGAATACGTAAACCCCCTTGA 58.674 43.478 0.00 0.00 0.00 3.02
868 897 1.475213 CCCCCTTGAGAGGCGTATTTC 60.475 57.143 0.00 0.00 42.09 2.17
884 913 4.853196 CGTATTTCCTCGAAGTACGTCAAA 59.147 41.667 16.61 2.58 45.90 2.69
888 917 2.486982 TCCTCGAAGTACGTCAAAGAGG 59.513 50.000 18.55 18.55 43.63 3.69
892 921 2.593257 GAAGTACGTCAAAGAGGGTCG 58.407 52.381 3.75 0.00 0.00 4.79
904 933 2.247358 AGAGGGTCGGTTTACGGTAAA 58.753 47.619 9.18 9.18 44.45 2.01
911 941 5.178067 GGGTCGGTTTACGGTAAATATCATG 59.822 44.000 15.70 4.21 44.45 3.07
913 943 6.258507 GGTCGGTTTACGGTAAATATCATGTT 59.741 38.462 15.70 0.00 44.45 2.71
917 947 6.412653 GGTTTACGGTAAATATCATGTTTGCG 59.587 38.462 15.70 0.00 0.00 4.85
920 950 6.281848 ACGGTAAATATCATGTTTGCGTAG 57.718 37.500 0.00 0.00 0.00 3.51
921 951 6.044046 ACGGTAAATATCATGTTTGCGTAGA 58.956 36.000 0.00 0.00 0.00 2.59
935 965 1.751924 GCGTAGACTCCACCAGATTCT 59.248 52.381 0.00 0.00 38.09 2.40
936 966 2.480416 GCGTAGACTCCACCAGATTCTG 60.480 54.545 6.70 6.70 35.43 3.02
944 974 1.363744 CACCAGATTCTGCGGAGAAC 58.636 55.000 22.32 15.01 41.12 3.01
945 975 0.250513 ACCAGATTCTGCGGAGAACC 59.749 55.000 22.32 12.95 41.12 3.62
1012 1055 2.125552 TTGAGATGGCTGACGGCG 60.126 61.111 4.80 4.80 42.94 6.46
1065 1108 3.378399 GAACCCTCCGCAGCTCTCC 62.378 68.421 0.00 0.00 0.00 3.71
1195 1238 0.034960 CGAGTGGGAGGAGTCTCTGA 60.035 60.000 0.00 0.00 39.86 3.27
1395 1438 0.247736 ACGAGATTCACAGCCTCACC 59.752 55.000 0.00 0.00 0.00 4.02
1429 1475 1.413118 CCCTTGTCCTTGTTGCCTTT 58.587 50.000 0.00 0.00 0.00 3.11
1476 1528 9.761504 CACTAAGTAACATTGATGATCAGAGAT 57.238 33.333 0.09 0.00 0.00 2.75
1524 1576 7.965107 GGGATTATGCGATTCTTGATGATTTAC 59.035 37.037 0.00 0.00 0.00 2.01
1749 2009 9.887629 ATAATTTGTGACATGGCATATTTTTCA 57.112 25.926 3.50 0.00 0.00 2.69
1781 2064 5.584649 TCTCAAGAACTTACCAGTTTGTGTG 59.415 40.000 0.00 0.00 43.79 3.82
1851 2134 9.442047 AATTCTTTCTCGTCTATCTGAAACATT 57.558 29.630 0.00 0.00 0.00 2.71
2733 3021 5.907207 TGAGAGTACCATTTCTGATACTGC 58.093 41.667 0.00 0.00 0.00 4.40
2792 3080 9.613428 CCAAGATACTTTACACCTTCATGAATA 57.387 33.333 8.96 0.00 0.00 1.75
3155 3444 0.463295 ATCAGGGCATTCAGTCTGCG 60.463 55.000 0.00 0.00 40.59 5.18
3303 3748 6.578172 GGCATCAAATTTGTTATTGTGTTTGC 59.422 34.615 17.47 11.06 0.00 3.68
3320 3765 9.553064 TTGTGTTTGCATTTCAAAATATACCTT 57.447 25.926 0.00 0.00 45.35 3.50
3324 3769 7.487822 TTGCATTTCAAAATATACCTTGGGA 57.512 32.000 0.00 0.00 0.00 4.37
3325 3770 7.673641 TGCATTTCAAAATATACCTTGGGAT 57.326 32.000 0.00 0.00 0.00 3.85
3326 3771 7.725251 TGCATTTCAAAATATACCTTGGGATC 58.275 34.615 0.00 0.00 0.00 3.36
3424 3892 7.810260 AGGAACCTAGAGAGCATTTTATGAAT 58.190 34.615 0.00 0.00 0.00 2.57
3502 3970 0.036732 AATGCAGAAACCGGAGAGCA 59.963 50.000 9.46 11.44 36.34 4.26
3542 4010 7.551617 TGCTGCTTATTTTAAACTACTACTCCC 59.448 37.037 0.00 0.00 0.00 4.30
3545 4013 9.043548 TGCTTATTTTAAACTACTACTCCCTCT 57.956 33.333 0.00 0.00 0.00 3.69
3570 4039 7.747155 TTCCATAATTCTTGTCGTGGTTTTA 57.253 32.000 0.00 0.00 0.00 1.52
3603 4094 5.596845 ACAAAACAAGTTGTCAACTGTTGT 58.403 33.333 18.84 19.98 41.91 3.32
3604 4095 6.045955 ACAAAACAAGTTGTCAACTGTTGTT 58.954 32.000 21.99 21.99 41.91 2.83
3605 4096 6.019156 ACAAAACAAGTTGTCAACTGTTGTTG 60.019 34.615 25.71 25.45 41.91 3.33
3632 4129 5.163794 CGTTCTTACAGTCAACCAAGTGTTT 60.164 40.000 0.00 0.00 34.00 2.83
3655 4152 7.849804 TTGAGAATGTATTAGTCTTGGCTTC 57.150 36.000 0.00 0.00 33.08 3.86
3719 4216 7.307131 TGACTCTCCTTGCATATTGATCATA 57.693 36.000 0.00 0.00 0.00 2.15
3914 4411 6.477053 TTAGAAGAGGAGGTTGATGATGAG 57.523 41.667 0.00 0.00 0.00 2.90
3917 4414 3.307506 AGAGGAGGTTGATGATGAGGAG 58.692 50.000 0.00 0.00 0.00 3.69
4024 4521 0.033601 TTTGGTGCAGTGGTGGAAGT 60.034 50.000 0.00 0.00 0.00 3.01
4039 4536 1.414550 GGAAGTGACTCCTGGATAGGC 59.585 57.143 0.00 0.00 44.22 3.93
4098 4596 1.654105 CTGTGCCGACGACTGAAATAC 59.346 52.381 0.00 0.00 0.00 1.89
4131 4629 9.961265 TCTCCAAGTGTATCATTACTATTAACG 57.039 33.333 0.00 0.00 0.00 3.18
4162 4660 7.722285 TGAACTGCTTTGTTTACCTAGGTTTAT 59.278 33.333 22.11 0.00 0.00 1.40
4252 4752 4.736896 GGCGCGAGGAAGGAACGT 62.737 66.667 12.10 0.00 0.00 3.99
4316 4819 6.432162 TCATCTTTGATGGTTTTCTCTTGGAG 59.568 38.462 7.58 0.00 0.00 3.86
4319 4822 6.607198 TCTTTGATGGTTTTCTCTTGGAGTTT 59.393 34.615 0.00 0.00 0.00 2.66
4356 4859 8.673711 TGTATTTTTATAGACAACACAGGCATC 58.326 33.333 0.00 0.00 0.00 3.91
4392 4895 4.908601 ACACAGATATCACCCAAACTCA 57.091 40.909 5.32 0.00 0.00 3.41
4409 4912 0.319555 TCAAGCGTGCCTACAGACAC 60.320 55.000 0.00 0.00 0.00 3.67
4430 4933 2.251371 GCTGCGTTCGTTTGGGTC 59.749 61.111 0.00 0.00 0.00 4.46
4437 4940 0.596082 GTTCGTTTGGGTCCACATGG 59.404 55.000 0.00 0.00 0.00 3.66
4480 4992 1.529948 ACGGACAGGAGACGGACAA 60.530 57.895 0.00 0.00 0.00 3.18
4499 5011 2.280321 CCGTTTGTCCGTTCGGGT 60.280 61.111 11.37 0.00 39.41 5.28
4506 5018 2.838693 TCCGTTCGGGTCCACACA 60.839 61.111 11.37 0.00 37.00 3.72
4524 5036 3.329542 ATCAGCCACCCAACGCGAT 62.330 57.895 15.93 0.00 0.00 4.58
4555 5067 2.831685 TCTAAATGCCACGAGTGTGT 57.168 45.000 2.36 0.00 44.92 3.72
4557 5069 2.143122 CTAAATGCCACGAGTGTGTGT 58.857 47.619 2.36 0.00 44.92 3.72
4558 5070 1.388547 AAATGCCACGAGTGTGTGTT 58.611 45.000 2.36 0.00 44.92 3.32
4561 5073 2.542907 GCCACGAGTGTGTGTTGGG 61.543 63.158 2.36 0.00 44.92 4.12
4563 5075 1.153249 CACGAGTGTGTGTTGGGGT 60.153 57.895 0.00 0.00 41.34 4.95
4566 5078 1.529796 GAGTGTGTGTTGGGGTGGA 59.470 57.895 0.00 0.00 0.00 4.02
4568 5080 1.528309 GTGTGTGTTGGGGTGGAGG 60.528 63.158 0.00 0.00 0.00 4.30
4648 5169 2.586425 CAATGTTGTGGAAGTGGACCT 58.414 47.619 0.00 0.00 0.00 3.85
4652 5173 1.764571 TTGTGGAAGTGGACCTCGGG 61.765 60.000 0.00 0.00 0.00 5.14
4682 5203 3.213402 GAGGCCGACTCCTCCTCG 61.213 72.222 0.00 0.00 45.40 4.63
4717 5238 1.227438 CACCCTTCACCGTGACGTT 60.227 57.895 3.64 0.00 31.36 3.99
4774 5295 1.011968 GCATGTACGTTCCAGTCGCA 61.012 55.000 0.00 0.00 0.00 5.10
4791 5312 1.198408 CGCAACGTGTCAGAGGTACTA 59.802 52.381 0.00 0.00 41.55 1.82
4798 5319 1.923850 TGTCAGAGGTACTAGGAGGCT 59.076 52.381 0.00 0.00 41.55 4.58
4808 5329 1.273838 ACTAGGAGGCTGTCATCCCAA 60.274 52.381 0.00 0.00 36.14 4.12
4815 5336 0.183492 GCTGTCATCCCAATGCCCTA 59.817 55.000 0.00 0.00 32.58 3.53
4946 5467 0.242286 CTACTGCCCGATGATCTCCG 59.758 60.000 0.00 0.00 0.00 4.63
4958 5479 2.381665 GATCTCCGCCACGACTCGAG 62.382 65.000 11.84 11.84 0.00 4.04
4959 5480 4.838486 CTCCGCCACGACTCGAGC 62.838 72.222 13.61 4.47 0.00 5.03
4991 5519 1.203199 CCCTCCCTCCCACTAGGATAC 60.203 61.905 0.00 0.00 46.33 2.24
4992 5520 1.548128 CCTCCCTCCCACTAGGATACG 60.548 61.905 0.00 0.00 46.33 3.06
4993 5521 1.145325 CTCCCTCCCACTAGGATACGT 59.855 57.143 0.00 0.00 46.33 3.57
4994 5522 1.572415 TCCCTCCCACTAGGATACGTT 59.428 52.381 0.00 0.00 46.33 3.99
4995 5523 2.023695 TCCCTCCCACTAGGATACGTTT 60.024 50.000 0.00 0.00 46.33 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
282 283 8.049165 TGGTACTCCTGTCCTACATAATAGTA 57.951 38.462 0.00 0.00 34.23 1.82
283 284 6.919158 TGGTACTCCTGTCCTACATAATAGT 58.081 40.000 0.00 0.00 34.23 2.12
284 285 7.834881 TTGGTACTCCTGTCCTACATAATAG 57.165 40.000 0.00 0.00 34.23 1.73
285 286 8.792830 ATTTGGTACTCCTGTCCTACATAATA 57.207 34.615 0.00 0.00 34.23 0.98
286 287 7.691993 ATTTGGTACTCCTGTCCTACATAAT 57.308 36.000 0.00 0.00 34.23 1.28
287 288 8.612486 TTATTTGGTACTCCTGTCCTACATAA 57.388 34.615 0.00 0.00 34.23 1.90
288 289 8.612486 TTTATTTGGTACTCCTGTCCTACATA 57.388 34.615 0.00 0.00 34.23 2.29
289 290 7.504926 TTTATTTGGTACTCCTGTCCTACAT 57.495 36.000 0.00 0.00 34.23 2.29
290 291 6.938698 TTTATTTGGTACTCCTGTCCTACA 57.061 37.500 0.00 0.00 34.23 2.74
291 292 7.562135 TGATTTATTTGGTACTCCTGTCCTAC 58.438 38.462 0.00 0.00 34.23 3.18
292 293 7.743116 TGATTTATTTGGTACTCCTGTCCTA 57.257 36.000 0.00 0.00 34.23 2.94
293 294 6.636454 TGATTTATTTGGTACTCCTGTCCT 57.364 37.500 0.00 0.00 34.23 3.85
294 295 6.183360 GCTTGATTTATTTGGTACTCCTGTCC 60.183 42.308 0.00 0.00 34.23 4.02
295 296 6.374333 TGCTTGATTTATTTGGTACTCCTGTC 59.626 38.462 0.00 0.00 34.23 3.51
296 297 6.245408 TGCTTGATTTATTTGGTACTCCTGT 58.755 36.000 0.00 0.00 34.23 4.00
297 298 6.757897 TGCTTGATTTATTTGGTACTCCTG 57.242 37.500 0.00 0.00 34.23 3.86
298 299 7.961326 ATTGCTTGATTTATTTGGTACTCCT 57.039 32.000 0.00 0.00 34.23 3.69
299 300 9.736023 CTTATTGCTTGATTTATTTGGTACTCC 57.264 33.333 0.00 0.00 0.00 3.85
301 302 8.197439 GCCTTATTGCTTGATTTATTTGGTACT 58.803 33.333 0.00 0.00 0.00 2.73
322 323 3.945346 TCTTGATTACCGCAAAGCCTTA 58.055 40.909 0.00 0.00 0.00 2.69
325 326 2.747446 TCTTCTTGATTACCGCAAAGCC 59.253 45.455 0.00 0.00 0.00 4.35
334 339 3.743396 CCCATAGCGCTCTTCTTGATTAC 59.257 47.826 16.34 0.00 0.00 1.89
385 402 2.508663 GCGACGTCCTGGGTAAGC 60.509 66.667 10.58 0.58 0.00 3.09
386 403 2.183555 GGCGACGTCCTGGGTAAG 59.816 66.667 10.58 0.00 0.00 2.34
536 553 4.631773 TGCTGCTGCATTCTCCTC 57.368 55.556 14.93 0.00 45.31 3.71
556 573 4.754667 TCCTCGCTGCTGCTGCTG 62.755 66.667 25.43 16.73 40.48 4.41
577 594 2.046023 CTCCAATGGCCAGCGTCA 60.046 61.111 13.05 0.00 0.00 4.35
850 879 1.486726 AGGAAATACGCCTCTCAAGGG 59.513 52.381 0.00 0.00 43.58 3.95
868 897 2.415625 CCCTCTTTGACGTACTTCGAGG 60.416 54.545 12.21 12.21 42.86 4.63
871 900 2.593257 GACCCTCTTTGACGTACTTCG 58.407 52.381 0.00 0.00 46.00 3.79
872 901 2.593257 CGACCCTCTTTGACGTACTTC 58.407 52.381 0.00 0.00 0.00 3.01
884 913 1.923356 TTACCGTAAACCGACCCTCT 58.077 50.000 0.00 0.00 39.56 3.69
888 917 5.754890 ACATGATATTTACCGTAAACCGACC 59.245 40.000 5.86 0.00 39.56 4.79
892 921 6.412653 CGCAAACATGATATTTACCGTAAACC 59.587 38.462 5.86 0.56 0.00 3.27
904 933 5.050490 GTGGAGTCTACGCAAACATGATAT 58.950 41.667 0.00 0.00 0.00 1.63
911 941 1.000506 TCTGGTGGAGTCTACGCAAAC 59.999 52.381 0.01 0.00 0.00 2.93
913 943 1.557099 ATCTGGTGGAGTCTACGCAA 58.443 50.000 0.01 0.00 0.00 4.85
917 947 2.480416 CGCAGAATCTGGTGGAGTCTAC 60.480 54.545 12.66 0.00 46.01 2.59
920 950 0.460987 CCGCAGAATCTGGTGGAGTC 60.461 60.000 12.66 0.00 39.10 3.36
921 951 0.904865 TCCGCAGAATCTGGTGGAGT 60.905 55.000 12.66 0.00 38.70 3.85
936 966 2.675423 GGGTTTGGGGTTCTCCGC 60.675 66.667 0.00 0.00 45.39 5.54
944 974 2.228480 TTCGGAGAGGGGTTTGGGG 61.228 63.158 0.00 0.00 38.43 4.96
945 975 1.002502 GTTCGGAGAGGGGTTTGGG 60.003 63.158 0.00 0.00 38.43 4.12
1062 1105 0.109086 TCTTCTTCGCGCTCTTGGAG 60.109 55.000 5.56 0.00 0.00 3.86
1065 1108 0.094387 GCTTCTTCTTCGCGCTCTTG 59.906 55.000 5.56 0.00 0.00 3.02
1395 1438 4.344237 GGGGAATTCACCTGCTGG 57.656 61.111 20.11 8.29 36.20 4.85
1429 1475 2.736721 GTGAGCACAAAACATAGCGAGA 59.263 45.455 0.00 0.00 0.00 4.04
1553 1605 1.402720 CCAATTACAGCAACAAGGCCG 60.403 52.381 0.00 0.00 0.00 6.13
1620 1672 8.443953 AGGAGCTTATCTGAATATTGAACAAC 57.556 34.615 0.00 0.00 0.00 3.32
1740 2000 9.415544 GTTCTTGAGATGCAAACTGAAAAATAT 57.584 29.630 0.00 0.00 35.74 1.28
1746 2006 6.017109 GGTAAGTTCTTGAGATGCAAACTGAA 60.017 38.462 0.00 0.00 35.74 3.02
1749 2009 5.376625 TGGTAAGTTCTTGAGATGCAAACT 58.623 37.500 0.00 0.00 35.74 2.66
1781 2064 9.884465 GATTAACAATTGATAGATAGCAACACC 57.116 33.333 13.59 0.00 34.11 4.16
2103 2388 4.455877 ACCCAATTGCGTTTTTGTTTTGAA 59.544 33.333 0.00 0.00 0.00 2.69
2792 3080 6.147821 CAGTTCGGATGTTTACTCAGACAAAT 59.852 38.462 0.00 0.00 0.00 2.32
3276 3721 7.982761 AACACAATAACAAATTTGATGCCAT 57.017 28.000 24.64 6.98 0.00 4.40
3400 3868 7.040823 CCATTCATAAAATGCTCTCTAGGTTCC 60.041 40.741 0.00 0.00 0.00 3.62
3407 3875 7.909485 ATTTCCCATTCATAAAATGCTCTCT 57.091 32.000 0.00 0.00 0.00 3.10
3424 3892 7.382110 CAAAAACATGTGTGGTATATTTCCCA 58.618 34.615 0.00 0.00 0.00 4.37
3542 4010 5.643777 ACCACGACAAGAATTATGGAAAGAG 59.356 40.000 0.00 0.00 0.00 2.85
3545 4013 6.642707 AAACCACGACAAGAATTATGGAAA 57.357 33.333 0.00 0.00 0.00 3.13
3570 4039 7.653647 TGACAACTTGTTTTGTACTTTGAACT 58.346 30.769 0.00 0.00 39.88 3.01
3603 4094 4.951254 TGGTTGACTGTAAGAACGATCAA 58.049 39.130 0.00 0.00 37.43 2.57
3604 4095 4.594123 TGGTTGACTGTAAGAACGATCA 57.406 40.909 0.00 0.00 37.43 2.92
3605 4096 4.989168 ACTTGGTTGACTGTAAGAACGATC 59.011 41.667 0.00 0.00 37.43 3.69
3632 4129 6.042777 CGAAGCCAAGACTAATACATTCTCA 58.957 40.000 0.00 0.00 0.00 3.27
3655 4152 1.475403 TAGCTCTCCAAAGTCCTCCG 58.525 55.000 0.00 0.00 0.00 4.63
3719 4216 6.183361 ACACTTGGTTGACTGTAAGAACCTAT 60.183 38.462 13.81 1.76 40.47 2.57
3914 4411 0.403271 CCCCATCACCATCATCCTCC 59.597 60.000 0.00 0.00 0.00 4.30
3917 4414 1.706866 TCATCCCCATCACCATCATCC 59.293 52.381 0.00 0.00 0.00 3.51
4024 4521 6.159172 AGATAATAGCCTATCCAGGAGTCA 57.841 41.667 0.00 0.00 45.91 3.41
4039 4536 4.082845 TCTGCTCTTCCCGGAGATAATAG 58.917 47.826 0.73 0.00 35.52 1.73
4098 4596 4.639135 TGATACACTTGGAGATGACTCG 57.361 45.455 0.00 0.00 43.44 4.18
4131 4629 3.796717 GGTAAACAAAGCAGTTCAGCAAC 59.203 43.478 0.00 0.00 36.85 4.17
4162 4660 4.163458 ACACCTCAGAGTACTCCAAACAAA 59.837 41.667 19.38 0.00 0.00 2.83
4356 4859 9.755804 TGATATCTGTGTTTCTAAAGCAGATAG 57.244 33.333 21.34 5.49 41.69 2.08
4392 4895 4.675404 GTGTCTGTAGGCACGCTT 57.325 55.556 0.35 0.00 0.00 4.68
4410 4913 2.427410 CCAAACGAACGCAGCAGC 60.427 61.111 0.00 0.00 37.42 5.25
4411 4914 2.252260 CCCAAACGAACGCAGCAG 59.748 61.111 0.00 0.00 0.00 4.24
4437 4940 2.223711 ACGCAAAACCATGGTTTCTGTC 60.224 45.455 36.64 26.50 46.22 3.51
4480 4992 2.663852 CCGAACGGACAAACGGCT 60.664 61.111 7.53 0.00 38.98 5.52
4487 4999 2.838693 TGTGGACCCGAACGGACA 60.839 61.111 15.07 7.99 37.50 4.02
4493 5005 1.003839 GCTGATGTGTGGACCCGAA 60.004 57.895 0.00 0.00 0.00 4.30
4499 5011 1.714011 TTGGGTGGCTGATGTGTGGA 61.714 55.000 0.00 0.00 0.00 4.02
4506 5018 1.966901 TATCGCGTTGGGTGGCTGAT 61.967 55.000 5.77 0.00 0.00 2.90
4524 5036 2.370849 GGCATTTAGAAGGACCCGGATA 59.629 50.000 0.73 0.00 0.00 2.59
4555 5067 2.763215 GATGCCTCCACCCCAACA 59.237 61.111 0.00 0.00 0.00 3.33
4557 5069 3.727258 CGGATGCCTCCACCCCAA 61.727 66.667 8.86 0.00 42.19 4.12
4561 5073 2.125106 GTCACGGATGCCTCCACC 60.125 66.667 8.86 0.00 42.19 4.61
4563 5075 2.606213 TGGTCACGGATGCCTCCA 60.606 61.111 8.86 0.00 42.19 3.86
4566 5078 1.610673 AGAGTGGTCACGGATGCCT 60.611 57.895 0.00 0.00 36.20 4.75
4568 5080 2.103042 GCAGAGTGGTCACGGATGC 61.103 63.158 10.59 10.59 36.20 3.91
4576 5090 2.997897 ACGGGGAGCAGAGTGGTC 60.998 66.667 0.00 0.00 43.63 4.02
4622 5143 3.550339 TTCCACAACATTGCGCCGC 62.550 57.895 4.18 0.00 0.00 6.53
4652 5173 4.077188 GCCTCGTCGTTGTGCTGC 62.077 66.667 0.00 0.00 0.00 5.25
4774 5295 3.345414 CTCCTAGTACCTCTGACACGTT 58.655 50.000 0.00 0.00 0.00 3.99
4791 5312 0.549950 CATTGGGATGACAGCCTCCT 59.450 55.000 10.08 0.00 35.16 3.69
4798 5319 0.846015 CCTAGGGCATTGGGATGACA 59.154 55.000 0.00 0.00 43.53 3.58
4815 5336 2.360350 CAGTTGCACATCCGGCCT 60.360 61.111 0.00 0.00 0.00 5.19
4857 5378 2.156098 GACCGGCACTGAAACCATTTA 58.844 47.619 0.00 0.00 0.00 1.40
4896 5417 3.399181 TGGATCTCCACCGCACCC 61.399 66.667 0.00 0.00 42.01 4.61
4915 5436 0.941463 GGCAGTAGATCGTGATGGCG 60.941 60.000 0.00 0.00 0.00 5.69
4969 5490 2.287251 CTAGTGGGAGGGAGGGGG 59.713 72.222 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.