Multiple sequence alignment - TraesCS7B01G287100

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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 TraesCS7B01G287100 chr7B 100.000 9890 0 0 1 9890 522718981 522728870 0.000000e+00 18264
1 TraesCS7B01G287100 chr7B 88.502 287 20 4 1070 1350 750221719 750221998 1.590000e-87 335
2 TraesCS7B01G287100 chr7B 90.541 222 13 3 1134 1349 411384866 411385085 4.520000e-73 287
3 TraesCS7B01G287100 chr7D 95.919 7474 194 40 1797 9211 494749251 494756672 0.000000e+00 12009
4 TraesCS7B01G287100 chr7D 92.391 1840 82 30 9 1796 494747372 494749205 0.000000e+00 2569
5 TraesCS7B01G287100 chr7D 89.390 688 44 13 9210 9890 494756747 494757412 0.000000e+00 839
6 TraesCS7B01G287100 chr7D 91.450 269 22 1 9623 9890 494858710 494858978 1.570000e-97 368
7 TraesCS7B01G287100 chr7D 83.614 415 32 11 9216 9628 494767357 494767737 3.400000e-94 357
8 TraesCS7B01G287100 chr7D 92.268 194 13 2 1157 1350 105206134 105206325 3.520000e-69 274
9 TraesCS7B01G287100 chr7D 92.683 123 8 1 9081 9203 494767168 494767289 1.020000e-39 176
10 TraesCS7B01G287100 chr7A 96.015 5295 147 26 933 6180 560304557 560309834 0.000000e+00 8551
11 TraesCS7B01G287100 chr7A 95.732 3069 65 20 6179 9211 560309938 560312976 0.000000e+00 4881
12 TraesCS7B01G287100 chr7A 91.644 742 28 15 157 868 560303582 560304319 0.000000e+00 996
13 TraesCS7B01G287100 chr7A 89.522 544 37 9 9207 9748 560313303 560313828 0.000000e+00 671
14 TraesCS7B01G287100 chr7A 94.534 311 12 5 9578 9884 560867900 560868209 8.990000e-130 475
15 TraesCS7B01G287100 chr7A 90.333 300 22 3 9403 9700 560585500 560585794 4.330000e-103 387
16 TraesCS7B01G287100 chr7A 89.895 287 16 4 1070 1350 706304580 706304301 3.400000e-94 357
17 TraesCS7B01G287100 chr7A 95.604 91 4 0 7800 7890 560585406 560585496 8.000000e-31 147
18 TraesCS7B01G287100 chr4A 81.945 1501 196 36 6217 7678 723606428 723607892 0.000000e+00 1201
19 TraesCS7B01G287100 chr4A 82.790 1226 127 33 3873 5028 723603103 723604314 0.000000e+00 1018
20 TraesCS7B01G287100 chr4A 80.796 427 57 15 7630 8046 723607952 723608363 2.680000e-80 311
21 TraesCS7B01G287100 chr4A 79.866 298 44 14 5652 5937 723605884 723606177 4.680000e-48 204
22 TraesCS7B01G287100 chr3A 95.882 170 7 0 2330 2499 34532446 34532615 9.780000e-70 276
23 TraesCS7B01G287100 chr3B 95.294 170 8 0 2330 2499 42630815 42630984 4.550000e-68 270
24 TraesCS7B01G287100 chr2A 88.646 229 13 4 1070 1292 4811514 4811735 5.890000e-67 267
25 TraesCS7B01G287100 chr3D 95.181 166 8 0 2334 2499 71517679 71517844 7.620000e-66 263
26 TraesCS7B01G287100 chr3D 94.675 169 9 0 2332 2500 426451858 426452026 7.620000e-66 263
27 TraesCS7B01G287100 chr3D 94.220 173 7 2 2330 2499 25132932 25133104 2.740000e-65 261
28 TraesCS7B01G287100 chr1D 94.675 169 9 0 2331 2499 175819834 175820002 7.620000e-66 263
29 TraesCS7B01G287100 chr1A 94.578 166 9 0 2331 2496 218526839 218527004 3.540000e-64 257


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 TraesCS7B01G287100 chr7B 522718981 522728870 9889 False 18264.00 18264 100.000000 1 9890 1 chr7B.!!$F2 9889
1 TraesCS7B01G287100 chr7D 494747372 494757412 10040 False 5139.00 12009 92.566667 9 9890 3 chr7D.!!$F3 9881
2 TraesCS7B01G287100 chr7D 494767168 494767737 569 False 266.50 357 88.148500 9081 9628 2 chr7D.!!$F4 547
3 TraesCS7B01G287100 chr7A 560303582 560313828 10246 False 3774.75 8551 93.228250 157 9748 4 chr7A.!!$F2 9591
4 TraesCS7B01G287100 chr4A 723603103 723608363 5260 False 683.50 1201 81.349250 3873 8046 4 chr4A.!!$F1 4173

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
331 363 1.066573 CAGCTCGAATCAACCACTCCT 60.067 52.381 0.00 0.0 0.00 3.69 F
1350 1583 0.896940 CCAAGCACATCAAGGCCACT 60.897 55.000 5.01 0.0 0.00 4.00 F
3158 3459 0.035820 GGTAAACATGGCCCGACTGA 60.036 55.000 0.00 0.0 0.00 3.41 F
3535 3836 1.246056 TGCTCCATGCTTTGTCTGGC 61.246 55.000 0.00 0.0 43.37 4.85 F
4228 4542 2.222213 CGGCATCTTTTGTAACGTGTGA 59.778 45.455 0.00 0.0 0.00 3.58 F
5617 6994 1.087501 GTTCACATCCTTTCCGCCTC 58.912 55.000 0.00 0.0 0.00 4.70 F
5756 7161 2.030628 TGTCTGTGTATTTCGACTCGCA 60.031 45.455 0.00 0.0 0.00 5.10 F
6023 7440 3.249799 CGACTTGTGCATGGTTTTGAGTA 59.750 43.478 0.00 0.0 0.00 2.59 F
7440 9006 3.498397 ACTCGCTGTGTTTATTTGTCAGG 59.502 43.478 0.00 0.0 0.00 3.86 F
8690 10417 0.251634 GCCTGGGAGCATAGGATAGC 59.748 60.000 0.00 0.0 36.11 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2106 0.542333 TTCCCATATTCCCGTTCGCA 59.458 50.000 0.00 0.0 0.00 5.10 R
3312 3613 0.987294 CAGGAGCTTGGGAGAAGGAA 59.013 55.000 0.00 0.0 0.00 3.36 R
4701 5045 0.664761 ATGGGCGCATTTTCATCTCG 59.335 50.000 11.00 0.0 0.00 4.04 R
5086 5888 3.476552 TCACTGTCAAGTTCCAATGGAC 58.523 45.455 0.00 0.0 32.98 4.02 R
5756 7161 1.412079 TGGCAATGCAAACCAGTTCT 58.588 45.000 7.79 0.0 0.00 3.01 R
6736 8274 2.165998 GGGTGAGCTGCAGAAAAAGAT 58.834 47.619 20.43 0.0 0.00 2.40 R
7470 9038 6.474819 TTGTTACAGTGATGGTAAACGATG 57.525 37.500 0.00 0.0 32.94 3.84 R
7884 9569 1.336795 GCAGCGCCAAAGTAACCAAAT 60.337 47.619 2.29 0.0 0.00 2.32 R
8693 10420 0.318441 CACGAGAACCTGAAGGCTGA 59.682 55.000 0.00 0.0 39.32 4.26 R
9793 11861 0.606130 TACCGGCGGTTTTCCCTTTC 60.606 55.000 38.73 0.0 37.09 2.62 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
23 24 4.234574 GGAAATCCGCAACCTTTGTTAAG 58.765 43.478 0.00 0.00 32.09 1.85
25 26 5.336451 GGAAATCCGCAACCTTTGTTAAGAT 60.336 40.000 0.00 0.00 32.92 2.40
49 53 1.224075 CAGCTCGATGAAATCCGCAT 58.776 50.000 0.00 0.00 41.39 4.73
102 106 5.173774 ACAAATACCAGCATATTCAAGCG 57.826 39.130 0.00 0.00 35.48 4.68
105 109 2.334307 CCAGCATATTCAAGCGGGG 58.666 57.895 0.00 0.00 41.54 5.73
134 142 4.096382 CCCTACCTTGAACATTGGAAATCG 59.904 45.833 0.00 0.00 0.00 3.34
186 198 2.175811 GCAATGTTCGGCCGACAC 59.824 61.111 31.19 26.91 0.00 3.67
201 213 3.608474 GCCGACACGAATGTTAGCTTTTT 60.608 43.478 0.00 0.00 39.95 1.94
213 225 6.524101 TGTTAGCTTTTTGTTTTCCTGACT 57.476 33.333 0.00 0.00 0.00 3.41
223 235 9.447157 TTTTTGTTTTCCTGACTTTCAATCAAT 57.553 25.926 0.00 0.00 0.00 2.57
316 345 1.459450 TCCATTAAAACGGCCAGCTC 58.541 50.000 2.24 0.00 0.00 4.09
331 363 1.066573 CAGCTCGAATCAACCACTCCT 60.067 52.381 0.00 0.00 0.00 3.69
332 364 1.066573 AGCTCGAATCAACCACTCCTG 60.067 52.381 0.00 0.00 0.00 3.86
490 537 2.750350 CCCCCACCTGTCACTCAC 59.250 66.667 0.00 0.00 0.00 3.51
491 538 2.750350 CCCCACCTGTCACTCACC 59.250 66.667 0.00 0.00 0.00 4.02
492 539 2.750350 CCCACCTGTCACTCACCC 59.250 66.667 0.00 0.00 0.00 4.61
549 596 1.202031 CGCCTCCTTTCGAATTTTCCG 60.202 52.381 0.00 0.00 0.00 4.30
635 682 3.385079 CGTTACGCTTGAATTTCCTCC 57.615 47.619 0.00 0.00 0.00 4.30
636 683 3.000727 CGTTACGCTTGAATTTCCTCCT 58.999 45.455 0.00 0.00 0.00 3.69
640 687 1.769026 GCTTGAATTTCCTCCTCCCC 58.231 55.000 0.00 0.00 0.00 4.81
641 688 2.019156 GCTTGAATTTCCTCCTCCCCG 61.019 57.143 0.00 0.00 0.00 5.73
642 689 1.282157 CTTGAATTTCCTCCTCCCCGT 59.718 52.381 0.00 0.00 0.00 5.28
643 690 2.257391 TGAATTTCCTCCTCCCCGTA 57.743 50.000 0.00 0.00 0.00 4.02
829 889 4.772231 TCCCCCTCTTCGTCCCCG 62.772 72.222 0.00 0.00 0.00 5.73
939 1172 2.641277 GCTAGCTAGCTAGGCCCCG 61.641 68.421 39.60 22.86 45.62 5.73
1350 1583 0.896940 CCAAGCACATCAAGGCCACT 60.897 55.000 5.01 0.00 0.00 4.00
1611 1844 1.445582 GACCGTCGCCGTCAAGATT 60.446 57.895 0.00 0.00 0.00 2.40
1730 1964 1.999071 TAACCGCCATGCATTTCGCC 61.999 55.000 10.84 0.00 41.33 5.54
1802 2081 2.295253 ATCGAGGTTGAACGATCACC 57.705 50.000 0.00 0.66 44.14 4.02
1827 2106 6.656693 CCTTAGATTTGTCACTGAATCTTGGT 59.343 38.462 10.87 0.00 41.49 3.67
1896 2175 6.757947 TGGTTATAGGCTCACGTACAATTTAC 59.242 38.462 0.00 0.00 0.00 2.01
1897 2176 6.757947 GGTTATAGGCTCACGTACAATTTACA 59.242 38.462 0.00 0.00 0.00 2.41
1898 2177 7.042925 GGTTATAGGCTCACGTACAATTTACAG 60.043 40.741 0.00 0.00 0.00 2.74
1899 2178 4.530710 AGGCTCACGTACAATTTACAGA 57.469 40.909 0.00 0.00 0.00 3.41
2635 2932 1.574702 GCTGCCGTTACAACCCTGTC 61.575 60.000 0.00 0.00 36.96 3.51
2874 3173 1.150081 GAGCAGGCATGGCATACCT 59.850 57.895 22.64 13.72 36.63 3.08
3158 3459 0.035820 GGTAAACATGGCCCGACTGA 60.036 55.000 0.00 0.00 0.00 3.41
3360 3661 2.358898 CCATATCAGTTTCCAAAGGCGG 59.641 50.000 0.00 0.00 0.00 6.13
3518 3819 4.458989 TGGTGTTCCATCTCTAACATTTGC 59.541 41.667 0.00 0.00 39.03 3.68
3532 3833 2.895404 ACATTTGCTCCATGCTTTGTCT 59.105 40.909 0.00 0.00 43.37 3.41
3535 3836 1.246056 TGCTCCATGCTTTGTCTGGC 61.246 55.000 0.00 0.00 43.37 4.85
3747 4048 3.907894 TCGAAAATGCCACCTGTAAAC 57.092 42.857 0.00 0.00 0.00 2.01
3750 4051 3.005367 CGAAAATGCCACCTGTAAACCTT 59.995 43.478 0.00 0.00 0.00 3.50
3857 4159 3.117888 GGGTCAGCTCCTCATTTGGATAA 60.118 47.826 0.00 0.00 35.30 1.75
4228 4542 2.222213 CGGCATCTTTTGTAACGTGTGA 59.778 45.455 0.00 0.00 0.00 3.58
4323 4640 3.942130 AGCCAGGTACTTTTTGCAATC 57.058 42.857 0.00 0.00 34.60 2.67
4329 4646 5.385617 CAGGTACTTTTTGCAATCTCTTCG 58.614 41.667 0.00 0.00 34.60 3.79
4336 4653 3.953712 TTGCAATCTCTTCGTCCACTA 57.046 42.857 0.00 0.00 0.00 2.74
4351 4668 7.337480 TCGTCCACTACAAACTAGCAATATA 57.663 36.000 0.00 0.00 0.00 0.86
4586 4928 7.397221 CCATCTTATCCCATTGCACTCTATTA 58.603 38.462 0.00 0.00 0.00 0.98
4613 4955 8.575649 TCTTTCTTCCAAGGGACATTTATTAC 57.424 34.615 0.00 0.00 0.00 1.89
4701 5045 5.310720 ACAGAACTTCCTTTTCACAACAC 57.689 39.130 0.00 0.00 0.00 3.32
5086 5888 3.193267 TCTGATGAAGCCAAAAATTCCCG 59.807 43.478 0.00 0.00 0.00 5.14
5106 5908 2.224079 CGTCCATTGGAACTTGACAGTG 59.776 50.000 7.05 0.00 31.38 3.66
5112 5914 5.163519 CCATTGGAACTTGACAGTGAACTTT 60.164 40.000 0.00 0.00 31.60 2.66
5301 6112 1.279496 TCTGCCTCCAGCTAATGTGT 58.721 50.000 0.00 0.00 44.23 3.72
5444 6265 2.754552 GTGATTTCTATGTGGCAGCCAA 59.245 45.455 18.28 7.27 34.18 4.52
5463 6284 5.104374 GCCAAACATCACAAGACAATATGG 58.896 41.667 0.00 0.00 0.00 2.74
5469 6290 9.912634 AAACATCACAAGACAATATGGTAAAAG 57.087 29.630 0.00 0.00 0.00 2.27
5617 6994 1.087501 GTTCACATCCTTTCCGCCTC 58.912 55.000 0.00 0.00 0.00 4.70
5703 7108 4.413087 ACTGCGATAGAAACGAACAGTAG 58.587 43.478 0.00 0.00 34.39 2.57
5708 7113 5.213675 CGATAGAAACGAACAGTAGGATCC 58.786 45.833 2.48 2.48 39.76 3.36
5756 7161 2.030628 TGTCTGTGTATTTCGACTCGCA 60.031 45.455 0.00 0.00 0.00 5.10
5895 7305 8.753175 GCAGTAATAAAGATAGTAACTCAACGG 58.247 37.037 0.00 0.00 0.00 4.44
6023 7440 3.249799 CGACTTGTGCATGGTTTTGAGTA 59.750 43.478 0.00 0.00 0.00 2.59
6736 8274 7.557724 TGAGACCGTAATACAAACATATTCCA 58.442 34.615 0.00 0.00 0.00 3.53
7070 8627 5.016173 AGCCTTTTGCCAATACAATGAGTA 58.984 37.500 0.00 0.00 42.71 2.59
7267 8825 4.637534 TGCTCTTATTGACAATCAGAAGGC 59.362 41.667 12.07 12.61 0.00 4.35
7440 9006 3.498397 ACTCGCTGTGTTTATTTGTCAGG 59.502 43.478 0.00 0.00 0.00 3.86
7515 9083 8.908786 ACAATATGGTTTAGTGATACATGAGG 57.091 34.615 0.00 0.00 0.00 3.86
7523 9091 3.657610 AGTGATACATGAGGGATGGTGA 58.342 45.455 0.00 0.00 36.23 4.02
8153 9865 4.982241 TTTGATCATCCTATCTGGGGTC 57.018 45.455 0.00 0.00 36.20 4.46
8273 9985 2.897271 TATGCAACCACCCAGTCAAT 57.103 45.000 0.00 0.00 0.00 2.57
8372 10090 4.336713 AGTTGTTTCTGGTTGAGCTTCTTC 59.663 41.667 0.00 0.00 0.00 2.87
8373 10091 3.214328 TGTTTCTGGTTGAGCTTCTTCC 58.786 45.455 0.00 0.00 0.00 3.46
8512 10236 4.179579 GAATTCTGTGCCGCGGCC 62.180 66.667 44.42 34.24 41.09 6.13
8560 10284 0.842635 ACAGATGGGAGGAGATTGCC 59.157 55.000 0.00 0.00 0.00 4.52
8673 10400 1.648467 GCATTTGTCTCAGTCGGGCC 61.648 60.000 0.00 0.00 0.00 5.80
8690 10417 0.251634 GCCTGGGAGCATAGGATAGC 59.748 60.000 0.00 0.00 36.11 2.97
8691 10418 0.908198 CCTGGGAGCATAGGATAGCC 59.092 60.000 0.00 0.00 36.11 3.93
8693 10420 2.264455 CTGGGAGCATAGGATAGCCTT 58.736 52.381 4.04 0.00 43.90 4.35
8694 10421 2.235898 CTGGGAGCATAGGATAGCCTTC 59.764 54.545 4.04 0.00 43.90 3.46
8695 10422 2.260822 GGGAGCATAGGATAGCCTTCA 58.739 52.381 4.04 0.00 43.90 3.02
8696 10423 2.235898 GGGAGCATAGGATAGCCTTCAG 59.764 54.545 4.04 0.00 43.90 3.02
8701 10428 3.867984 GCATAGGATAGCCTTCAGCCTTC 60.868 52.174 4.04 0.00 43.90 3.46
8723 10450 2.147958 GGTTCTCGTGCCACACAATAA 58.852 47.619 0.00 0.00 33.40 1.40
9183 10919 4.048504 CGTCTGGTATCAATGCATCGTTA 58.951 43.478 0.00 0.00 0.00 3.18
9194 10930 1.999051 CATCGTTACAGCTGGTCGC 59.001 57.895 19.93 4.27 39.57 5.19
9197 10933 0.249531 TCGTTACAGCTGGTCGCAAA 60.250 50.000 19.93 1.41 42.61 3.68
9234 11298 7.466746 AACATTTTAAGTACATGCCATGTCT 57.533 32.000 14.74 8.62 43.67 3.41
9242 11306 6.455360 AGTACATGCCATGTCTAAAAATGG 57.545 37.500 14.74 0.00 43.67 3.16
9244 11308 6.835488 AGTACATGCCATGTCTAAAAATGGAT 59.165 34.615 14.74 0.00 45.29 3.41
9285 11349 2.225467 GTCTCAGCAGTTTTTCAGGCT 58.775 47.619 0.00 0.00 36.99 4.58
9286 11350 2.225255 GTCTCAGCAGTTTTTCAGGCTC 59.775 50.000 0.00 0.00 33.60 4.70
9287 11351 2.105477 TCTCAGCAGTTTTTCAGGCTCT 59.895 45.455 0.00 0.00 33.60 4.09
9288 11352 2.224606 TCAGCAGTTTTTCAGGCTCTG 58.775 47.619 0.00 0.00 33.60 3.35
9289 11353 1.952296 CAGCAGTTTTTCAGGCTCTGT 59.048 47.619 1.30 0.00 33.60 3.41
9290 11354 2.360165 CAGCAGTTTTTCAGGCTCTGTT 59.640 45.455 1.30 0.00 33.60 3.16
9325 11390 0.740868 TCATCTTCCTTTCCGCTGCG 60.741 55.000 16.34 16.34 0.00 5.18
9371 11436 2.833631 TTTCCCTCTGAAGTTCCGTC 57.166 50.000 0.00 0.00 33.63 4.79
9372 11437 2.011122 TTCCCTCTGAAGTTCCGTCT 57.989 50.000 0.00 0.00 0.00 4.18
9380 11445 2.663602 CTGAAGTTCCGTCTTGTCGATG 59.336 50.000 0.00 0.00 0.00 3.84
9381 11446 2.295070 TGAAGTTCCGTCTTGTCGATGA 59.705 45.455 0.00 0.00 0.00 2.92
9405 11471 1.749334 GAGGAGGTCAGCCCCGTATG 61.749 65.000 0.00 0.00 34.57 2.39
9454 11520 0.877071 CACCACTCGAAGCTGCAAAT 59.123 50.000 1.02 0.00 0.00 2.32
9480 11546 2.403378 GCTGTCTCTCGCCGTCTCT 61.403 63.158 0.00 0.00 0.00 3.10
9482 11548 1.711060 CTGTCTCTCGCCGTCTCTCC 61.711 65.000 0.00 0.00 0.00 3.71
9491 11557 2.182030 CGTCTCTCCGCAGTTCCC 59.818 66.667 0.00 0.00 0.00 3.97
9492 11558 2.579738 GTCTCTCCGCAGTTCCCC 59.420 66.667 0.00 0.00 0.00 4.81
9493 11559 2.683933 TCTCTCCGCAGTTCCCCC 60.684 66.667 0.00 0.00 0.00 5.40
9494 11560 2.685380 CTCTCCGCAGTTCCCCCT 60.685 66.667 0.00 0.00 0.00 4.79
9495 11561 3.003173 TCTCCGCAGTTCCCCCTG 61.003 66.667 0.00 0.00 35.49 4.45
9496 11562 3.003173 CTCCGCAGTTCCCCCTGA 61.003 66.667 0.00 0.00 34.23 3.86
9504 11570 2.124996 TTCCCCCTGACCCTGAGG 59.875 66.667 0.00 0.00 40.04 3.86
9596 11662 4.319549 GCTGAAACCGATCGGAATTAATCC 60.320 45.833 39.55 19.90 45.57 3.01
9667 11735 3.885297 AGGCGAGGGAATTATTTGTGATG 59.115 43.478 0.00 0.00 0.00 3.07
9694 11762 7.040617 CCAGTTACAGACTTGTACTTGTCTCTA 60.041 40.741 15.12 8.32 41.06 2.43
9695 11763 7.804129 CAGTTACAGACTTGTACTTGTCTCTAC 59.196 40.741 15.12 13.13 41.06 2.59
9700 11768 6.587990 CAGACTTGTACTTGTCTCTACAATGG 59.412 42.308 15.12 2.87 44.43 3.16
9748 11816 2.619849 CCATGACAAGGAGATGGCACTT 60.620 50.000 0.00 0.00 42.20 3.16
9751 11819 2.237143 TGACAAGGAGATGGCACTTAGG 59.763 50.000 0.00 0.00 32.00 2.69
9793 11861 6.514063 TGCTAGAAAGAGAGATGTGATGATG 58.486 40.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.812358 AACAAAGGTTGCGGATTTCC 57.188 45.000 0.00 0.00 35.46 3.13
2 3 5.116069 TCTTAACAAAGGTTGCGGATTTC 57.884 39.130 0.00 0.00 37.88 2.17
3 4 5.010617 ACATCTTAACAAAGGTTGCGGATTT 59.989 36.000 0.00 0.00 37.88 2.17
4 5 4.522789 ACATCTTAACAAAGGTTGCGGATT 59.477 37.500 0.00 0.00 37.88 3.01
5 6 4.079253 ACATCTTAACAAAGGTTGCGGAT 58.921 39.130 0.00 0.00 37.88 4.18
6 7 3.482436 ACATCTTAACAAAGGTTGCGGA 58.518 40.909 0.00 0.00 37.88 5.54
7 8 3.915437 ACATCTTAACAAAGGTTGCGG 57.085 42.857 0.00 0.00 37.88 5.69
11 12 4.342092 AGCTGCAACATCTTAACAAAGGTT 59.658 37.500 1.02 0.00 41.06 3.50
23 24 3.547613 GGATTTCATCGAGCTGCAACATC 60.548 47.826 1.02 0.00 0.00 3.06
25 26 1.739466 GGATTTCATCGAGCTGCAACA 59.261 47.619 1.02 0.00 0.00 3.33
68 72 6.054295 TGCTGGTATTTGTTGCAAAATTTCT 58.946 32.000 0.00 0.00 32.16 2.52
74 78 6.695429 TGAATATGCTGGTATTTGTTGCAAA 58.305 32.000 0.00 0.00 37.20 3.68
85 89 1.202758 CCCCGCTTGAATATGCTGGTA 60.203 52.381 0.00 0.00 31.92 3.25
86 90 0.466189 CCCCGCTTGAATATGCTGGT 60.466 55.000 0.00 0.00 31.92 4.00
105 109 5.303333 TCCAATGTTCAAGGTAGGGTTTTTC 59.697 40.000 0.00 0.00 0.00 2.29
146 154 6.263516 CTCCCACATAAATGGAGCATATTG 57.736 41.667 0.00 0.00 43.02 1.90
186 198 6.695278 TCAGGAAAACAAAAAGCTAACATTCG 59.305 34.615 0.00 0.00 0.00 3.34
201 213 7.345422 TGATTGATTGAAAGTCAGGAAAACA 57.655 32.000 0.00 0.00 0.00 2.83
246 275 3.626028 TCTTTTCTTTCTTTCCGCTGC 57.374 42.857 0.00 0.00 0.00 5.25
316 345 0.798776 GTGCAGGAGTGGTTGATTCG 59.201 55.000 0.00 0.00 0.00 3.34
520 567 1.921869 GAAAGGAGGCGGATGGGGAA 61.922 60.000 0.00 0.00 0.00 3.97
557 604 2.486504 GTCATGGACGTACCGCGA 59.513 61.111 8.23 0.00 44.77 5.87
621 668 1.769026 GGGGAGGAGGAAATTCAAGC 58.231 55.000 0.00 0.00 0.00 4.01
631 678 3.217743 GCTCGTACGGGGAGGAGG 61.218 72.222 18.45 0.00 32.99 4.30
635 682 4.253257 GCTCGCTCGTACGGGGAG 62.253 72.222 29.37 29.37 43.58 4.30
640 687 4.592936 CCCTCGCTCGCTCGTACG 62.593 72.222 9.53 9.53 0.00 3.67
641 688 4.253257 CCCCTCGCTCGCTCGTAC 62.253 72.222 0.00 0.00 0.00 3.67
642 689 4.478371 TCCCCTCGCTCGCTCGTA 62.478 66.667 0.00 0.00 0.00 3.43
829 889 1.226128 GTCGCGAAGGCAGAAATGC 60.226 57.895 12.06 0.00 39.92 3.56
923 994 0.826672 GTTCGGGGCCTAGCTAGCTA 60.827 60.000 22.85 22.85 0.00 3.32
927 998 1.658053 TAGGGTTCGGGGCCTAGCTA 61.658 60.000 0.84 0.00 0.00 3.32
939 1172 0.688749 TCGGGCTAGGGTTAGGGTTC 60.689 60.000 0.00 0.00 0.00 3.62
1467 1700 1.792006 ATCCGAACGTCTTGTCCAAC 58.208 50.000 0.00 0.00 0.00 3.77
1611 1844 3.711704 CCCTCACCTTAGCTTTGGAGATA 59.288 47.826 11.06 0.00 0.00 1.98
1730 1964 3.327757 TCCCTTACTAGCTATGCAATGGG 59.672 47.826 0.00 2.32 0.00 4.00
1760 1994 4.093850 TCATTCAGATCATCAACAAGCACG 59.906 41.667 0.00 0.00 0.00 5.34
1789 2023 5.411669 ACAAATCTAAGGGTGATCGTTCAAC 59.588 40.000 2.77 2.77 38.96 3.18
1802 2081 6.656693 ACCAAGATTCAGTGACAAATCTAAGG 59.343 38.462 19.16 19.16 40.47 2.69
1827 2106 0.542333 TTCCCATATTCCCGTTCGCA 59.458 50.000 0.00 0.00 0.00 5.10
1896 2175 8.535592 CGTGAAGCATTAGTTTTAGTCTATCTG 58.464 37.037 0.00 0.00 0.00 2.90
1897 2176 8.251721 ACGTGAAGCATTAGTTTTAGTCTATCT 58.748 33.333 0.00 0.00 0.00 1.98
1898 2177 8.408743 ACGTGAAGCATTAGTTTTAGTCTATC 57.591 34.615 0.00 0.00 0.00 2.08
1899 2178 8.773404 AACGTGAAGCATTAGTTTTAGTCTAT 57.227 30.769 0.00 0.00 0.00 1.98
2015 2301 5.153950 ACATGGGAAGAACACTCTAGAAC 57.846 43.478 0.00 0.00 0.00 3.01
2635 2932 7.596749 ACTCTGATCAAAACTAACAATACCG 57.403 36.000 0.00 0.00 0.00 4.02
2874 3173 5.455755 GGATCAATCCAGGATTCAGATCACA 60.456 44.000 28.08 3.73 46.38 3.58
3158 3459 1.288127 GGAGTACAACGCGGTCTGT 59.712 57.895 12.47 13.41 0.00 3.41
3312 3613 0.987294 CAGGAGCTTGGGAGAAGGAA 59.013 55.000 0.00 0.00 0.00 3.36
3360 3661 6.506500 AATGATGTCCTGTGATGTCTTTTC 57.493 37.500 0.00 0.00 0.00 2.29
3518 3819 1.471684 GAAGCCAGACAAAGCATGGAG 59.528 52.381 0.00 0.00 36.09 3.86
3747 4048 6.073222 CCAAAAGTGCTAGTAACTGTACAAGG 60.073 42.308 0.00 0.00 32.12 3.61
3750 4051 6.164417 TCCAAAAGTGCTAGTAACTGTACA 57.836 37.500 0.00 0.00 32.12 2.90
4191 4505 9.463443 AAAAGATGCCGTAAATAATGCTTATTC 57.537 29.630 2.85 0.00 34.88 1.75
4228 4542 6.006449 ACAAGATGAGAAAAATACTGCCTGT 58.994 36.000 0.00 0.00 0.00 4.00
4323 4640 4.167268 GCTAGTTTGTAGTGGACGAAGAG 58.833 47.826 0.00 0.00 31.69 2.85
4329 4646 9.765795 AAGATATATTGCTAGTTTGTAGTGGAC 57.234 33.333 0.00 0.00 0.00 4.02
4586 4928 8.670521 AATAAATGTCCCTTGGAAGAAAGAAT 57.329 30.769 0.00 0.00 31.38 2.40
4613 4955 3.322254 ACAGGATTTGGAGGCTATAGACG 59.678 47.826 3.21 0.00 0.00 4.18
4701 5045 0.664761 ATGGGCGCATTTTCATCTCG 59.335 50.000 11.00 0.00 0.00 4.04
4889 5259 9.988815 TTTACAATAAGCAATTAAGCAGGAAAA 57.011 25.926 0.00 0.00 36.85 2.29
5086 5888 3.476552 TCACTGTCAAGTTCCAATGGAC 58.523 45.455 0.00 0.00 32.98 4.02
5214 6025 8.034804 AGCATTTTACAAGGAAGCGATTTAAAT 58.965 29.630 0.00 0.00 0.00 1.40
5444 6265 9.077885 ACTTTTACCATATTGTCTTGTGATGTT 57.922 29.630 0.00 0.00 0.00 2.71
5463 6284 9.899226 AGACTTCTGCAATTATTTCACTTTTAC 57.101 29.630 0.00 0.00 0.00 2.01
5469 6290 8.801715 TCAAAAGACTTCTGCAATTATTTCAC 57.198 30.769 0.00 0.00 0.00 3.18
5542 6366 5.422012 TGTGAGATGGTAGAAAGCTGACATA 59.578 40.000 0.00 0.00 0.00 2.29
5653 7030 9.916397 GATACGTTAACTAAAACATTCCATCAG 57.084 33.333 3.71 0.00 0.00 2.90
5703 7108 3.452627 AGGACATTATATCTGCGGGATCC 59.547 47.826 1.92 1.92 35.98 3.36
5708 7113 6.710744 AGGTAAAAAGGACATTATATCTGCGG 59.289 38.462 0.00 0.00 0.00 5.69
5756 7161 1.412079 TGGCAATGCAAACCAGTTCT 58.588 45.000 7.79 0.00 0.00 3.01
5895 7305 5.607119 ATGTACCATTTTCTTGACACGAC 57.393 39.130 0.00 0.00 0.00 4.34
6023 7440 9.965902 TGGCCAATAACCAAATGTTTTTATATT 57.034 25.926 0.61 0.00 38.42 1.28
6629 8165 9.698309 TTCACAAAGAAAACACAAAATGAGTAA 57.302 25.926 0.00 0.00 32.05 2.24
6736 8274 2.165998 GGGTGAGCTGCAGAAAAAGAT 58.834 47.619 20.43 0.00 0.00 2.40
7267 8825 7.159322 TGAGGTAAAGAGCTAACTGTTAGAG 57.841 40.000 27.14 8.65 35.20 2.43
7440 9006 8.408154 CGTTTGAATTTCAAATGTGTAAATGC 57.592 30.769 25.76 11.51 46.55 3.56
7470 9038 6.474819 TTGTTACAGTGATGGTAAACGATG 57.525 37.500 0.00 0.00 32.94 3.84
7515 9083 7.663081 TCAGATAAAAATCTAGCATCACCATCC 59.337 37.037 0.00 0.00 0.00 3.51
7884 9569 1.336795 GCAGCGCCAAAGTAACCAAAT 60.337 47.619 2.29 0.00 0.00 2.32
8153 9865 6.824305 ACATGTGTAAGATTTCAAAGGGAG 57.176 37.500 0.00 0.00 0.00 4.30
8328 10040 5.592054 ACTACATCAGGTATCAACACATCG 58.408 41.667 0.00 0.00 0.00 3.84
8331 10043 6.109156 ACAACTACATCAGGTATCAACACA 57.891 37.500 0.00 0.00 0.00 3.72
8332 10044 7.387948 AGAAACAACTACATCAGGTATCAACAC 59.612 37.037 0.00 0.00 0.00 3.32
8333 10045 7.387673 CAGAAACAACTACATCAGGTATCAACA 59.612 37.037 0.00 0.00 0.00 3.33
8512 10236 3.209410 CTCAAGCTGGTAAGGGCTTATG 58.791 50.000 0.00 0.00 45.48 1.90
8560 10284 0.947244 AGTGCTGAAAAGCTGTTCCG 59.053 50.000 14.20 8.90 35.49 4.30
8673 10400 1.949799 AGGCTATCCTATGCTCCCAG 58.050 55.000 0.00 0.00 42.06 4.45
8690 10417 1.674221 CGAGAACCTGAAGGCTGAAGG 60.674 57.143 12.91 12.91 39.32 3.46
8691 10418 1.001406 ACGAGAACCTGAAGGCTGAAG 59.999 52.381 0.00 0.00 39.32 3.02
8692 10419 1.048601 ACGAGAACCTGAAGGCTGAA 58.951 50.000 0.00 0.00 39.32 3.02
8693 10420 0.318441 CACGAGAACCTGAAGGCTGA 59.682 55.000 0.00 0.00 39.32 4.26
8694 10421 1.294659 GCACGAGAACCTGAAGGCTG 61.295 60.000 0.00 0.00 39.32 4.85
8695 10422 1.004440 GCACGAGAACCTGAAGGCT 60.004 57.895 0.00 0.00 39.32 4.58
8696 10423 2.035442 GGCACGAGAACCTGAAGGC 61.035 63.158 0.00 0.00 39.32 4.35
8701 10428 0.813610 TTGTGTGGCACGAGAACCTG 60.814 55.000 13.77 0.00 37.14 4.00
8723 10450 0.552615 AATGGGGAGGCCAGGTTAGT 60.553 55.000 5.01 0.00 0.00 2.24
9183 10919 1.963338 GAGCTTTGCGACCAGCTGT 60.963 57.895 13.81 0.11 46.72 4.40
9228 11292 4.818546 AGGAGCGATCCATTTTTAGACATG 59.181 41.667 23.83 0.00 0.00 3.21
9234 11298 3.812156 TCGAGGAGCGATCCATTTTTA 57.188 42.857 23.83 0.00 45.59 1.52
9285 11349 1.599667 GCACGTGAGAGAACGAACAGA 60.600 52.381 22.23 0.00 46.49 3.41
9286 11350 0.778815 GCACGTGAGAGAACGAACAG 59.221 55.000 22.23 0.00 46.49 3.16
9287 11351 0.384309 AGCACGTGAGAGAACGAACA 59.616 50.000 22.23 0.00 46.49 3.18
9288 11352 1.053811 GAGCACGTGAGAGAACGAAC 58.946 55.000 22.23 0.00 46.49 3.95
9289 11353 0.666374 TGAGCACGTGAGAGAACGAA 59.334 50.000 22.23 0.00 46.49 3.85
9290 11354 0.881796 ATGAGCACGTGAGAGAACGA 59.118 50.000 22.23 0.00 46.49 3.85
9371 11436 2.417924 CCTCCTCCACTTCATCGACAAG 60.418 54.545 4.70 4.70 0.00 3.16
9372 11437 1.550524 CCTCCTCCACTTCATCGACAA 59.449 52.381 0.00 0.00 0.00 3.18
9380 11445 1.599576 GGCTGACCTCCTCCACTTC 59.400 63.158 0.00 0.00 0.00 3.01
9381 11446 1.920835 GGGCTGACCTCCTCCACTT 60.921 63.158 0.00 0.00 35.85 3.16
9454 11520 1.502231 GCGAGAGACAGCACAGAAAA 58.498 50.000 0.00 0.00 0.00 2.29
9480 11546 3.319198 GTCAGGGGGAACTGCGGA 61.319 66.667 0.00 0.00 38.36 5.54
9482 11548 4.410400 GGGTCAGGGGGAACTGCG 62.410 72.222 0.00 0.00 38.36 5.18
9492 11558 1.362224 TTTCTTCCCTCAGGGTCAGG 58.638 55.000 10.50 0.00 44.74 3.86
9493 11559 3.728385 ATTTTCTTCCCTCAGGGTCAG 57.272 47.619 10.50 7.54 44.74 3.51
9494 11560 3.559171 CGAATTTTCTTCCCTCAGGGTCA 60.559 47.826 10.50 0.00 44.74 4.02
9495 11561 3.010420 CGAATTTTCTTCCCTCAGGGTC 58.990 50.000 10.50 0.00 44.74 4.46
9496 11562 2.880167 GCGAATTTTCTTCCCTCAGGGT 60.880 50.000 10.50 0.00 44.74 4.34
9504 11570 1.269448 TGGCACAGCGAATTTTCTTCC 59.731 47.619 0.00 0.00 0.00 3.46
9541 11607 1.741401 CGCGATTTGACAGAGGCCA 60.741 57.895 5.01 0.00 0.00 5.36
9596 11662 3.005050 TCAACATCCAGCTGCAGAAAAAG 59.995 43.478 20.43 4.38 0.00 2.27
9667 11735 4.377897 ACAAGTACAAGTCTGTAACTGGC 58.622 43.478 0.00 0.00 39.75 4.85
9694 11762 2.699846 ACCAATGAAACAGTGCCATTGT 59.300 40.909 21.61 12.95 43.19 2.71
9695 11763 3.389925 ACCAATGAAACAGTGCCATTG 57.610 42.857 18.81 18.81 43.89 2.82
9700 11768 5.049167 TGAAATCAACCAATGAAACAGTGC 58.951 37.500 0.00 0.00 42.54 4.40
9779 11847 5.705397 TTCCCTTTCATCATCACATCTCT 57.295 39.130 0.00 0.00 0.00 3.10
9783 11851 4.158394 CGGTTTTCCCTTTCATCATCACAT 59.842 41.667 0.00 0.00 36.42 3.21
9793 11861 0.606130 TACCGGCGGTTTTCCCTTTC 60.606 55.000 38.73 0.00 37.09 2.62


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

AutoCloner maintained by Alex Coulton.