Multiple sequence alignment - TraesCS3D01G245500

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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 TraesCS3D01G245500 chr3D 100.000 6902 0 0 1 6902 341682594 341675693 0.000000e+00 12746.0
1 TraesCS3D01G245500 chr3D 94.737 38 1 1 6528 6565 341675936 341675900 2.690000e-04 58.4
2 TraesCS3D01G245500 chr3D 97.143 35 0 1 6520 6554 341676018 341675985 2.690000e-04 58.4
3 TraesCS3D01G245500 chr3D 94.737 38 1 1 6659 6695 341676067 341676030 2.690000e-04 58.4
4 TraesCS3D01G245500 chr3D 97.143 35 0 1 6577 6610 341676075 341676041 2.690000e-04 58.4
5 TraesCS3D01G245500 chr3B 92.209 3363 170 40 2878 6195 440518587 440515272 0.000000e+00 4674.0
6 TraesCS3D01G245500 chr3B 94.432 2748 74 24 4 2738 440521615 440518934 0.000000e+00 4154.0
7 TraesCS3D01G245500 chr3B 87.336 229 9 10 6183 6393 440514968 440514742 1.920000e-60 244.0
8 TraesCS3D01G245500 chr3B 82.105 95 17 0 5374 5468 266452605 266452511 1.600000e-11 82.4
9 TraesCS3D01G245500 chr3A 94.702 1793 48 15 4 1775 461387963 461389729 0.000000e+00 2741.0
10 TraesCS3D01G245500 chr3A 90.634 2018 121 32 2836 4808 461391240 461393234 0.000000e+00 2617.0
11 TraesCS3D01G245500 chr3A 96.795 1404 38 5 4995 6393 461393548 461394949 0.000000e+00 2337.0
12 TraesCS3D01G245500 chr3A 92.827 962 37 14 1861 2804 461389877 461390824 0.000000e+00 1365.0
13 TraesCS3D01G245500 chr3A 97.297 333 7 2 6399 6731 461395026 461395356 1.300000e-156 564.0
14 TraesCS3D01G245500 chr3A 97.126 174 4 1 6730 6902 461395519 461395692 6.770000e-75 292.0
15 TraesCS3D01G245500 chr3A 89.855 138 5 4 1803 1932 461389722 461389858 1.190000e-37 169.0
16 TraesCS3D01G245500 chr3A 93.671 79 5 0 4847 4925 461393462 461393540 1.220000e-22 119.0
17 TraesCS3D01G245500 chr3A 81.944 144 21 5 4916 5056 737659655 737659796 4.370000e-22 117.0
18 TraesCS3D01G245500 chr3A 78.981 157 29 2 4481 4633 128129038 128129194 3.410000e-18 104.0
19 TraesCS3D01G245500 chr3A 88.889 54 4 1 4916 4967 180027559 180027506 1.610000e-06 65.8
20 TraesCS3D01G245500 chr3A 97.143 35 0 1 6577 6610 461395146 461395180 2.690000e-04 58.4
21 TraesCS3D01G245500 chr3A 94.737 38 1 1 6659 6695 461395154 461395191 2.690000e-04 58.4
22 TraesCS3D01G245500 chr3A 97.143 35 0 1 6520 6554 461395203 461395236 2.690000e-04 58.4
23 TraesCS3D01G245500 chr5A 82.353 170 24 5 4908 5074 81499100 81499266 7.220000e-30 143.0
24 TraesCS3D01G245500 chr5A 78.082 219 31 12 4446 4655 321914658 321914868 9.400000e-24 122.0
25 TraesCS3D01G245500 chr5A 84.167 120 13 5 4481 4599 708832988 708833102 2.030000e-20 111.0
26 TraesCS3D01G245500 chr6D 76.817 289 29 20 4346 4599 152249362 152249077 2.020000e-25 128.0
27 TraesCS3D01G245500 chr7B 86.441 118 11 4 4481 4597 720969535 720969648 2.610000e-24 124.0
28 TraesCS3D01G245500 chr5D 82.517 143 21 4 4916 5055 278311371 278311230 9.400000e-24 122.0
29 TraesCS3D01G245500 chr5D 81.053 95 18 0 5374 5468 396349276 396349370 7.420000e-10 76.8
30 TraesCS3D01G245500 chr1D 78.531 177 35 3 4916 5091 111093503 111093677 5.660000e-21 113.0
31 TraesCS3D01G245500 chr1D 86.420 81 10 1 4912 4991 396741850 396741770 3.430000e-13 87.9
32 TraesCS3D01G245500 chr1D 82.292 96 15 2 5374 5468 151663948 151663854 1.600000e-11 82.4
33 TraesCS3D01G245500 chr1B 80.255 157 23 6 4481 4633 641488622 641488774 2.030000e-20 111.0
34 TraesCS3D01G245500 chr6B 75.620 242 32 19 4437 4661 36769256 36769487 2.050000e-15 95.3
35 TraesCS3D01G245500 chr7D 82.105 95 17 0 5374 5468 379382996 379383090 1.600000e-11 82.4
36 TraesCS3D01G245500 chr4A 82.292 96 15 2 5374 5468 565194133 565194039 1.600000e-11 82.4
37 TraesCS3D01G245500 chr4B 81.915 94 17 0 5374 5467 267272324 267272417 5.740000e-11 80.5
38 TraesCS3D01G245500 chr7A 83.333 84 12 2 4940 5022 207089119 207089201 7.420000e-10 76.8
39 TraesCS3D01G245500 chr1A 81.053 95 18 0 5374 5468 35369267 35369173 7.420000e-10 76.8
40 TraesCS3D01G245500 chr2A 90.196 51 4 1 4430 4479 735398869 735398919 1.610000e-06 65.8


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 TraesCS3D01G245500 chr3D 341675693 341682594 6901 True 12746.000000 12746 100.000000 1 6902 1 chr3D.!!$R1 6901
1 TraesCS3D01G245500 chr3B 440514742 440521615 6873 True 3024.000000 4674 91.325667 4 6393 3 chr3B.!!$R2 6389
2 TraesCS3D01G245500 chr3A 461387963 461395692 7729 False 943.563636 2741 94.720909 4 6902 11 chr3A.!!$F3 6898

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
812 831 0.963355 CCCCGATCTCCCTCGATCTC 60.963 65.000 0.00 0.0 41.12 2.75 F
1210 1230 0.097674 CTGCACGCCAACTTGCTATC 59.902 55.000 0.00 0.0 41.44 2.08 F
1635 1660 0.393077 ATTAGTTGCGCGGGCTCTAT 59.607 50.000 25.62 11.1 40.82 1.98 F
2832 2969 0.177141 TATAGTGTTGCGGGCTGTCC 59.823 55.000 0.00 0.0 0.00 4.02 F
3833 4376 0.463654 GGTTGCATACCGATCTGGCA 60.464 55.000 3.85 0.0 43.94 4.92 F
4621 5202 1.055849 TGCTATGGTATCCGGTGCAT 58.944 50.000 0.00 0.0 0.00 3.96 F
5461 6234 2.667724 CGTCGTCTCCAAGGTGTTCTAC 60.668 54.545 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1751 1.454847 AATCGCTCTCTCTCGCCCT 60.455 57.895 0.00 0.00 0.00 5.19 R
2813 2950 0.177141 GGACAGCCCGCAACACTATA 59.823 55.000 0.00 0.00 0.00 1.31 R
2858 3379 0.334676 TGGGTTGGGGCCTGAAATAG 59.665 55.000 0.84 0.00 0.00 1.73 R
4264 4813 0.609957 TCTCCCTGCATGCACAAAGG 60.610 55.000 18.46 16.47 0.00 3.11 R
5395 6168 0.393077 CGGAGCCTAGGTGGTATTGG 59.607 60.000 11.31 0.00 38.35 3.16 R
5608 6381 0.452184 CTGCAGCTTCCTTCAGCATG 59.548 55.000 0.00 0.00 42.84 4.06 R
6417 7600 1.559682 TCATTTAGTCTCCTGGGTGCC 59.440 52.381 0.00 0.00 0.00 5.01 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
74 75 1.463056 ACACACACACGTCAACAACTG 59.537 47.619 0.00 0.00 0.00 3.16
199 200 4.537433 GCAGAGAATCCGGCGGCT 62.537 66.667 23.83 13.36 33.66 5.52
200 201 2.279784 CAGAGAATCCGGCGGCTC 60.280 66.667 23.83 21.63 33.66 4.70
220 221 2.359975 CCTGGTTTCCGGCTCACC 60.360 66.667 0.00 2.66 0.00 4.02
353 362 5.248248 TCTCTCTCTCTCTCTCTCTCAACAA 59.752 44.000 0.00 0.00 0.00 2.83
385 394 2.377193 ACAAACCCATAAGCTGGTGGTA 59.623 45.455 14.58 0.00 44.30 3.25
496 508 7.775053 TTATTAATTTCTCCTTTGTGCCTGT 57.225 32.000 0.00 0.00 0.00 4.00
638 650 5.028549 TGGTGAGAATTCTATTCCTCTGC 57.971 43.478 8.25 0.00 0.00 4.26
809 828 2.601966 GCCCCGATCTCCCTCGAT 60.602 66.667 0.00 0.00 41.12 3.59
810 829 2.641277 GCCCCGATCTCCCTCGATC 61.641 68.421 0.00 0.00 41.12 3.69
811 830 1.075836 CCCCGATCTCCCTCGATCT 59.924 63.158 0.00 0.00 41.12 2.75
812 831 0.963355 CCCCGATCTCCCTCGATCTC 60.963 65.000 0.00 0.00 41.12 2.75
813 832 0.963355 CCCGATCTCCCTCGATCTCC 60.963 65.000 0.00 0.00 41.12 3.71
841 860 3.326880 TCTCCTCTTTTTACCCTGTCACC 59.673 47.826 0.00 0.00 0.00 4.02
855 874 1.619363 TCACCCATTCCCTCCCAGG 60.619 63.158 0.00 0.00 34.30 4.45
1186 1206 3.736126 GCAGTATGAACAGGTACGTACCC 60.736 52.174 35.52 22.81 43.36 3.69
1205 1225 2.949106 CTCCTGCACGCCAACTTG 59.051 61.111 0.00 0.00 0.00 3.16
1208 1228 1.965930 CCTGCACGCCAACTTGCTA 60.966 57.895 0.00 0.00 41.44 3.49
1210 1230 0.097674 CTGCACGCCAACTTGCTATC 59.902 55.000 0.00 0.00 41.44 2.08
1212 1232 1.305219 GCACGCCAACTTGCTATCCA 61.305 55.000 0.00 0.00 38.02 3.41
1213 1233 1.382522 CACGCCAACTTGCTATCCAT 58.617 50.000 0.00 0.00 0.00 3.41
1214 1234 1.331756 CACGCCAACTTGCTATCCATC 59.668 52.381 0.00 0.00 0.00 3.51
1216 1236 1.869767 CGCCAACTTGCTATCCATCTC 59.130 52.381 0.00 0.00 0.00 2.75
1217 1237 2.484417 CGCCAACTTGCTATCCATCTCT 60.484 50.000 0.00 0.00 0.00 3.10
1218 1238 3.137533 GCCAACTTGCTATCCATCTCTC 58.862 50.000 0.00 0.00 0.00 3.20
1219 1239 3.181456 GCCAACTTGCTATCCATCTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
1220 1240 4.378774 CCAACTTGCTATCCATCTCTCTG 58.621 47.826 0.00 0.00 0.00 3.35
1238 1259 1.064946 GGGTCTGAGTGAGATCGCG 59.935 63.158 0.00 0.00 31.69 5.87
1257 1278 3.244579 CGCGGCATGACTATATGATGATG 59.755 47.826 0.00 0.00 0.00 3.07
1296 1321 3.512516 GATCAGTTGCAGGCGGCC 61.513 66.667 12.11 12.11 43.89 6.13
1502 1527 4.392138 GCTTCCAGGTATTGTTACACTCAC 59.608 45.833 0.00 0.00 0.00 3.51
1628 1653 3.307512 TGTACATGTTATTAGTTGCGCGG 59.692 43.478 8.83 0.00 0.00 6.46
1635 1660 0.393077 ATTAGTTGCGCGGGCTCTAT 59.607 50.000 25.62 11.10 40.82 1.98
1641 1666 3.303135 CGCGGGCTCTATGGGCTA 61.303 66.667 0.00 0.00 0.00 3.93
1642 1667 2.650116 CGCGGGCTCTATGGGCTAT 61.650 63.158 0.00 0.00 0.00 2.97
1690 1720 1.243902 AAGCGCCGGATTTCAAAAGA 58.756 45.000 5.05 0.00 0.00 2.52
1696 1726 4.295051 CGCCGGATTTCAAAAGAAAAAGA 58.705 39.130 5.05 0.00 0.00 2.52
1697 1727 4.923281 CGCCGGATTTCAAAAGAAAAAGAT 59.077 37.500 5.05 0.00 0.00 2.40
1698 1728 6.090129 CGCCGGATTTCAAAAGAAAAAGATA 58.910 36.000 5.05 0.00 0.00 1.98
1699 1729 6.751888 CGCCGGATTTCAAAAGAAAAAGATAT 59.248 34.615 5.05 0.00 0.00 1.63
1718 1748 9.726438 AAAGATATATTTCGGATTAGGACAAGG 57.274 33.333 0.00 0.00 0.00 3.61
1721 1751 1.187974 TTCGGATTAGGACAAGGCGA 58.812 50.000 0.00 0.00 0.00 5.54
1735 1767 4.264638 GCGAGGGCGAGAGAGAGC 62.265 72.222 0.00 0.00 40.82 4.09
1808 1840 5.220681 GGATTGATTCTGCGTCTAAAACTCC 60.221 44.000 0.00 0.00 0.00 3.85
1913 1949 7.783209 ACAAAAAGAAAATTGCATAAGCGTAC 58.217 30.769 0.00 0.00 46.23 3.67
2094 2227 5.106197 CCACATTGGAAAAATGAGATCGACA 60.106 40.000 5.13 0.00 40.96 4.35
2095 2228 5.796935 CACATTGGAAAAATGAGATCGACAC 59.203 40.000 5.13 0.00 0.00 3.67
2096 2229 5.473162 ACATTGGAAAAATGAGATCGACACA 59.527 36.000 5.13 0.00 0.00 3.72
2097 2230 6.016360 ACATTGGAAAAATGAGATCGACACAA 60.016 34.615 5.13 0.00 0.00 3.33
2384 2519 9.884636 GCATTATCTTTACCCCAAAATTTAAGT 57.115 29.630 0.00 0.00 0.00 2.24
2406 2541 7.961326 AGTTCTTATTTTGATTATGCCAGGT 57.039 32.000 0.00 0.00 0.00 4.00
2407 2542 9.474313 AAGTTCTTATTTTGATTATGCCAGGTA 57.526 29.630 0.00 0.00 0.00 3.08
2408 2543 8.903820 AGTTCTTATTTTGATTATGCCAGGTAC 58.096 33.333 0.00 0.00 0.00 3.34
2467 2602 7.928706 CACGTCAATCCTCTCCTATTATTTTCT 59.071 37.037 0.00 0.00 0.00 2.52
2494 2629 3.372206 GTGACGGAAAGAGTGATGAATGG 59.628 47.826 0.00 0.00 0.00 3.16
2804 2941 9.634163 CCAATTAATACACTTCTTTTTGGGTAC 57.366 33.333 0.00 0.00 0.00 3.34
2810 2947 8.843885 ATACACTTCTTTTTGGGTACTAGAAC 57.156 34.615 0.00 0.00 0.00 3.01
2811 2948 6.896883 ACACTTCTTTTTGGGTACTAGAACT 58.103 36.000 0.00 0.00 0.00 3.01
2812 2949 8.026396 ACACTTCTTTTTGGGTACTAGAACTA 57.974 34.615 0.00 0.00 0.00 2.24
2813 2950 8.657712 ACACTTCTTTTTGGGTACTAGAACTAT 58.342 33.333 0.00 0.00 0.00 2.12
2823 2960 8.174733 TGGGTACTAGAACTATATAGTGTTGC 57.825 38.462 16.11 6.67 34.57 4.17
2824 2961 7.040892 TGGGTACTAGAACTATATAGTGTTGCG 60.041 40.741 16.11 6.96 34.57 4.85
2825 2962 7.303998 GGTACTAGAACTATATAGTGTTGCGG 58.696 42.308 16.11 7.49 34.57 5.69
2826 2963 6.328641 ACTAGAACTATATAGTGTTGCGGG 57.671 41.667 16.11 6.15 36.50 6.13
2827 2964 3.991367 AGAACTATATAGTGTTGCGGGC 58.009 45.455 16.11 0.10 36.50 6.13
2828 2965 3.641906 AGAACTATATAGTGTTGCGGGCT 59.358 43.478 16.11 0.00 36.50 5.19
2829 2966 3.386768 ACTATATAGTGTTGCGGGCTG 57.613 47.619 14.71 0.00 34.72 4.85
2830 2967 2.698797 ACTATATAGTGTTGCGGGCTGT 59.301 45.455 14.71 0.00 34.72 4.40
2831 2968 2.240493 ATATAGTGTTGCGGGCTGTC 57.760 50.000 0.00 0.00 0.00 3.51
2832 2969 0.177141 TATAGTGTTGCGGGCTGTCC 59.823 55.000 0.00 0.00 0.00 4.02
2833 2970 1.836999 ATAGTGTTGCGGGCTGTCCA 61.837 55.000 0.00 0.00 34.36 4.02
2834 2971 2.046009 TAGTGTTGCGGGCTGTCCAA 62.046 55.000 0.00 0.00 34.36 3.53
2858 3379 4.454161 GGTTTAAATTTTGGGGCACATGAC 59.546 41.667 0.00 0.00 0.00 3.06
3016 3541 4.501071 GAGGTGCCGATGAAACTAGTTAA 58.499 43.478 8.92 0.64 0.00 2.01
3120 3645 5.083821 ACACCACATAGGGCAAATTTTAGT 58.916 37.500 0.00 0.00 43.89 2.24
3132 3657 7.713507 AGGGCAAATTTTAGTAGGTTTGAAAAC 59.286 33.333 0.00 0.00 34.38 2.43
3162 3687 1.599542 AGAAAAGAAGCTCGTGTGTGC 59.400 47.619 0.00 0.00 34.85 4.57
3247 3772 3.621214 GCTCCCCTCTTTCCTTCTTCTTC 60.621 52.174 0.00 0.00 0.00 2.87
3275 3800 9.844790 CTTTCATTCATGTTCATGCTTACTAAA 57.155 29.630 7.80 3.93 0.00 1.85
3346 3871 6.047870 TGCACTTCTAAACACAAAATTGCAT 58.952 32.000 0.00 0.00 33.92 3.96
3347 3872 6.018913 TGCACTTCTAAACACAAAATTGCATG 60.019 34.615 0.00 0.00 33.92 4.06
3385 3910 1.600023 TAGGTTCCACGCAAAACCAG 58.400 50.000 13.83 0.00 46.05 4.00
3449 3974 3.864583 GCAAAAGATGTTCACTTGCACAA 59.135 39.130 5.80 0.00 41.55 3.33
3454 3979 6.592798 AAGATGTTCACTTGCACAAAAATG 57.407 33.333 0.00 0.00 0.00 2.32
3457 3982 5.070770 TGTTCACTTGCACAAAAATGAGT 57.929 34.783 0.00 0.00 0.00 3.41
3486 4011 8.647226 GCAATTGCACAACTTTAAAAGGTATAG 58.353 33.333 25.36 0.00 41.59 1.31
3576 4118 8.174757 ACCCCCTTACAAATACAAAAGACTATT 58.825 33.333 0.00 0.00 0.00 1.73
3661 4203 0.606604 GTGGGTTCTAACTCTGGCGA 59.393 55.000 0.00 0.00 0.00 5.54
3676 4218 0.726827 GGCGAACGCATGATTTCTCA 59.273 50.000 20.16 0.00 44.11 3.27
3696 4238 7.822161 TCTCATTCCTGATTCTCAAAACAAA 57.178 32.000 0.00 0.00 0.00 2.83
3833 4376 0.463654 GGTTGCATACCGATCTGGCA 60.464 55.000 3.85 0.00 43.94 4.92
3894 4437 6.655425 GCTTCTACCTTTCCAAACATTAGAGT 59.345 38.462 0.00 0.00 0.00 3.24
4011 4554 6.919115 GGAGAAATTAGTCGAATAGAGTGGAC 59.081 42.308 0.00 0.00 33.80 4.02
4155 4702 4.319177 GACTAAGGTTGCACACTTCAGAT 58.681 43.478 5.41 0.00 0.00 2.90
4158 4705 4.574599 AAGGTTGCACACTTCAGATTTC 57.425 40.909 0.00 0.00 0.00 2.17
4187 4734 3.005050 ACGGAAACACGTGATAGAACTGA 59.995 43.478 25.01 0.00 46.64 3.41
4287 4836 2.042686 TGTGCATGCAGGGAGAATAC 57.957 50.000 23.41 6.40 0.00 1.89
4479 5043 9.914834 ACATAAGTTAGACTTTATATTTGGCCA 57.085 29.630 0.00 0.00 39.51 5.36
4506 5087 4.840401 TGTCATTTTTGTATCTCGAGCG 57.160 40.909 7.81 0.00 0.00 5.03
4566 5147 4.801891 ACATTGATGTTGTGTCAATCTGC 58.198 39.130 0.00 0.00 42.68 4.26
4567 5148 4.521639 ACATTGATGTTGTGTCAATCTGCT 59.478 37.500 0.00 0.00 42.68 4.24
4568 5149 5.706833 ACATTGATGTTGTGTCAATCTGCTA 59.293 36.000 0.00 0.00 42.68 3.49
4621 5202 1.055849 TGCTATGGTATCCGGTGCAT 58.944 50.000 0.00 0.00 0.00 3.96
4695 5276 7.367285 GGCACATAAACTACAAAGTCATTTCA 58.633 34.615 0.00 0.00 33.75 2.69
4707 5288 6.015940 ACAAAGTCATTTCATTCTTGACCCTC 60.016 38.462 0.00 0.00 40.46 4.30
4848 5618 7.003939 ACGGTAGTGTTTTGTTTTGTACTAC 57.996 36.000 0.00 0.00 39.60 2.73
5434 6207 2.688477 GATGAGGAGGAGAAGGATGGT 58.312 52.381 0.00 0.00 0.00 3.55
5461 6234 2.667724 CGTCGTCTCCAAGGTGTTCTAC 60.668 54.545 0.00 0.00 0.00 2.59
5608 6381 1.000274 GAGGATGGCCACAACAACAAC 60.000 52.381 8.16 0.00 36.29 3.32
5675 6448 1.206745 CGCAGCACTAATCGGGTACG 61.207 60.000 0.00 0.00 42.74 3.67
6228 7324 7.553760 AGAATATAAACATCATGAGTGCACACA 59.446 33.333 19.36 19.36 0.00 3.72
6267 7375 4.093703 CGGTCAACACTAAAACAGACACAA 59.906 41.667 0.00 0.00 0.00 3.33
6367 7479 1.514003 TGCATTTCAAACGACGCCTA 58.486 45.000 0.00 0.00 0.00 3.93
6393 7505 5.247862 AGAAGTGAATGATGTGCATGTGTA 58.752 37.500 0.00 0.00 37.28 2.90
6394 7506 5.353400 AGAAGTGAATGATGTGCATGTGTAG 59.647 40.000 0.00 0.00 37.28 2.74
6395 7507 4.835678 AGTGAATGATGTGCATGTGTAGA 58.164 39.130 0.00 0.00 37.28 2.59
6396 7508 4.874396 AGTGAATGATGTGCATGTGTAGAG 59.126 41.667 0.00 0.00 37.28 2.43
6397 7509 4.872124 GTGAATGATGTGCATGTGTAGAGA 59.128 41.667 0.00 0.00 37.28 3.10
6410 7593 6.584954 CATGTGTAGAGAACAAAAAGAGACG 58.415 40.000 0.00 0.00 40.63 4.18
6417 7600 3.871594 AGAACAAAAAGAGACGTGACCTG 59.128 43.478 0.00 0.00 0.00 4.00
6465 7648 1.001706 CATGAGGCAATGCAATCTCGG 60.002 52.381 7.79 0.00 0.00 4.63
6475 7658 1.671054 CAATCTCGGTGTGGGCGTT 60.671 57.895 0.00 0.00 0.00 4.84
6685 7868 8.133627 GCACATTTTCTGCACAATATTATCTCT 58.866 33.333 0.00 0.00 34.56 3.10
6836 8183 0.613777 ATCACCTTCGGGAAGTGACC 59.386 55.000 7.58 0.00 36.72 4.02
6846 8193 2.233922 CGGGAAGTGACCTGTTACATCT 59.766 50.000 0.00 0.00 0.00 2.90
6891 8238 6.614694 TTACCTACCTAATCAGCAAGACAA 57.385 37.500 0.00 0.00 0.00 3.18
6895 8242 5.352569 CCTACCTAATCAGCAAGACAACAAG 59.647 44.000 0.00 0.00 0.00 3.16
6896 8243 4.973168 ACCTAATCAGCAAGACAACAAGA 58.027 39.130 0.00 0.00 0.00 3.02
6897 8244 4.999950 ACCTAATCAGCAAGACAACAAGAG 59.000 41.667 0.00 0.00 0.00 2.85
6898 8245 4.999950 CCTAATCAGCAAGACAACAAGAGT 59.000 41.667 0.00 0.00 0.00 3.24
6900 8247 6.650807 CCTAATCAGCAAGACAACAAGAGTTA 59.349 38.462 0.00 0.00 35.85 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.662153 CCGCACACACAGCATGCA 61.662 61.111 21.98 0.00 42.53 3.96
2 3 1.974249 CTAGCCGCACACACAGCATG 61.974 60.000 0.00 0.00 46.00 4.06
74 75 0.741221 GTCAAGTCCACCCATCGAGC 60.741 60.000 0.00 0.00 0.00 5.03
353 362 5.335348 GCTTATGGGTTTGTACGTGTCAATT 60.335 40.000 0.00 0.00 0.00 2.32
496 508 1.074084 ACGAGAGACCAGGTTGAGAGA 59.926 52.381 0.00 0.00 0.00 3.10
638 650 4.026744 TGGGTTTCTCTCTCTATCTGGTG 58.973 47.826 0.00 0.00 0.00 4.17
809 828 4.412060 AAAAAGAGGAGAGGAGAGGAGA 57.588 45.455 0.00 0.00 0.00 3.71
810 829 4.404394 GGTAAAAAGAGGAGAGGAGAGGAG 59.596 50.000 0.00 0.00 0.00 3.69
811 830 4.354662 GGTAAAAAGAGGAGAGGAGAGGA 58.645 47.826 0.00 0.00 0.00 3.71
812 831 3.452990 GGGTAAAAAGAGGAGAGGAGAGG 59.547 52.174 0.00 0.00 0.00 3.69
813 832 4.161377 CAGGGTAAAAAGAGGAGAGGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
841 860 4.195334 CCGCCTGGGAGGGAATGG 62.195 72.222 1.28 0.00 38.47 3.16
881 900 1.296715 CTAGCCCGTCCCCATATGC 59.703 63.158 0.00 0.00 0.00 3.14
942 962 5.991606 CCACGTACTTAATGATGATGGATGT 59.008 40.000 0.00 0.00 0.00 3.06
1080 1100 2.987547 TGCTGCTGCTTCTTGGCC 60.988 61.111 17.00 0.00 40.48 5.36
1161 1181 1.734377 CGTACCTGTTCATACTGCGCA 60.734 52.381 10.98 10.98 0.00 6.09
1201 1221 2.971330 CCCAGAGAGATGGATAGCAAGT 59.029 50.000 0.00 0.00 43.57 3.16
1205 1225 2.562298 CAGACCCAGAGAGATGGATAGC 59.438 54.545 0.00 0.00 43.57 2.97
1208 1228 2.247111 ACTCAGACCCAGAGAGATGGAT 59.753 50.000 0.00 0.00 43.57 3.41
1210 1230 1.755959 CACTCAGACCCAGAGAGATGG 59.244 57.143 0.00 0.00 40.29 3.51
1212 1232 2.580322 TCTCACTCAGACCCAGAGAGAT 59.420 50.000 0.00 0.00 34.01 2.75
1213 1233 1.988846 TCTCACTCAGACCCAGAGAGA 59.011 52.381 0.00 0.00 35.85 3.10
1214 1234 2.505650 TCTCACTCAGACCCAGAGAG 57.494 55.000 0.00 0.00 36.91 3.20
1216 1236 1.675483 CGATCTCACTCAGACCCAGAG 59.325 57.143 0.00 0.00 39.04 3.35
1217 1237 1.756430 CGATCTCACTCAGACCCAGA 58.244 55.000 0.00 0.00 32.26 3.86
1218 1238 0.102120 GCGATCTCACTCAGACCCAG 59.898 60.000 0.00 0.00 32.26 4.45
1219 1239 1.657751 CGCGATCTCACTCAGACCCA 61.658 60.000 0.00 0.00 32.26 4.51
1220 1240 1.064946 CGCGATCTCACTCAGACCC 59.935 63.158 0.00 0.00 32.26 4.46
1238 1259 8.502105 TTGATTCATCATCATATAGTCATGCC 57.498 34.615 0.00 0.00 41.82 4.40
1296 1321 0.999228 GCAGATCCTGTATCGTCGCG 60.999 60.000 0.00 0.00 39.79 5.87
1628 1653 1.674221 CGCAAGATAGCCCATAGAGCC 60.674 57.143 0.00 0.00 43.02 4.70
1635 1660 2.169561 TGATGTAACGCAAGATAGCCCA 59.830 45.455 0.00 0.00 43.62 5.36
1639 1664 5.732647 CCGTTTTTGATGTAACGCAAGATAG 59.267 40.000 0.00 0.00 44.14 2.08
1640 1665 5.391097 CCCGTTTTTGATGTAACGCAAGATA 60.391 40.000 0.00 0.00 44.14 1.98
1641 1666 4.472286 CCGTTTTTGATGTAACGCAAGAT 58.528 39.130 0.00 0.00 44.14 2.40
1642 1667 3.304123 CCCGTTTTTGATGTAACGCAAGA 60.304 43.478 0.00 0.00 44.14 3.02
1696 1726 6.070995 TCGCCTTGTCCTAATCCGAAATATAT 60.071 38.462 0.00 0.00 0.00 0.86
1697 1727 5.244402 TCGCCTTGTCCTAATCCGAAATATA 59.756 40.000 0.00 0.00 0.00 0.86
1698 1728 4.039973 TCGCCTTGTCCTAATCCGAAATAT 59.960 41.667 0.00 0.00 0.00 1.28
1699 1729 3.385433 TCGCCTTGTCCTAATCCGAAATA 59.615 43.478 0.00 0.00 0.00 1.40
1718 1748 4.264638 GCTCTCTCTCGCCCTCGC 62.265 72.222 0.00 0.00 35.26 5.03
1721 1751 1.454847 AATCGCTCTCTCTCGCCCT 60.455 57.895 0.00 0.00 0.00 5.19
1735 1767 1.599071 CCCATGACGGATCAACAATCG 59.401 52.381 0.00 0.00 38.69 3.34
1763 1795 9.166173 CAATCCATATCTAACAAGAGTTTGTGA 57.834 33.333 0.00 0.00 46.54 3.58
1839 1871 4.450976 GGCAAGGAAACCAAACTGAAAAT 58.549 39.130 0.00 0.00 0.00 1.82
2078 2211 5.853282 CCTTGTTGTGTCGATCTCATTTTTC 59.147 40.000 0.00 0.00 0.00 2.29
2094 2227 2.699846 ACATTTGATGGCACCTTGTTGT 59.300 40.909 0.00 0.00 33.60 3.32
2095 2228 3.006110 AGACATTTGATGGCACCTTGTTG 59.994 43.478 0.00 0.00 42.15 3.33
2096 2229 3.233507 AGACATTTGATGGCACCTTGTT 58.766 40.909 0.00 0.00 42.15 2.83
2097 2230 2.880443 AGACATTTGATGGCACCTTGT 58.120 42.857 0.00 0.00 42.15 3.16
2236 2370 8.015658 AGCACGTAACTTTGAGATAAAACAATC 58.984 33.333 0.00 0.00 0.00 2.67
2397 2532 5.748670 TCTTGTTTGTAGTACCTGGCATA 57.251 39.130 0.00 0.00 0.00 3.14
2467 2602 4.878971 TCATCACTCTTTCCGTCACAAAAA 59.121 37.500 0.00 0.00 0.00 1.94
2542 2678 5.875359 CCTACAGAAAAACTAAGTAGGGCAG 59.125 44.000 8.66 0.00 45.04 4.85
2655 2792 6.270064 ACAAGTGCACAACAAGGTATTAAAC 58.730 36.000 21.04 0.00 0.00 2.01
2697 2834 9.010366 GTAAAGACTCTTGTGAATGTTTTTCAC 57.990 33.333 10.71 10.71 46.57 3.18
2786 2923 8.026396 AGTTCTAGTACCCAAAAAGAAGTGTA 57.974 34.615 0.00 0.00 30.59 2.90
2804 2941 5.047943 AGCCCGCAACACTATATAGTTCTAG 60.048 44.000 12.87 4.68 33.46 2.43
2806 2943 3.641906 AGCCCGCAACACTATATAGTTCT 59.358 43.478 12.87 0.38 33.46 3.01
2807 2944 3.741344 CAGCCCGCAACACTATATAGTTC 59.259 47.826 12.87 2.59 33.46 3.01
2808 2945 3.134081 ACAGCCCGCAACACTATATAGTT 59.866 43.478 12.87 2.65 33.46 2.24
2809 2946 2.698797 ACAGCCCGCAACACTATATAGT 59.301 45.455 9.71 9.71 36.90 2.12
2810 2947 3.318017 GACAGCCCGCAACACTATATAG 58.682 50.000 8.27 8.27 0.00 1.31
2811 2948 2.036733 GGACAGCCCGCAACACTATATA 59.963 50.000 0.00 0.00 0.00 0.86
2812 2949 1.202651 GGACAGCCCGCAACACTATAT 60.203 52.381 0.00 0.00 0.00 0.86
2813 2950 0.177141 GGACAGCCCGCAACACTATA 59.823 55.000 0.00 0.00 0.00 1.31
2814 2951 1.078426 GGACAGCCCGCAACACTAT 60.078 57.895 0.00 0.00 0.00 2.12
2815 2952 2.046009 TTGGACAGCCCGCAACACTA 62.046 55.000 0.00 0.00 37.93 2.74
2816 2953 3.414136 TTGGACAGCCCGCAACACT 62.414 57.895 0.00 0.00 37.93 3.55
2817 2954 2.904866 TTGGACAGCCCGCAACAC 60.905 61.111 0.00 0.00 37.93 3.32
2818 2955 2.594303 CTTGGACAGCCCGCAACA 60.594 61.111 0.00 0.00 37.93 3.33
2819 2956 3.365265 CCTTGGACAGCCCGCAAC 61.365 66.667 0.00 0.00 37.93 4.17
2820 2957 2.920076 AAACCTTGGACAGCCCGCAA 62.920 55.000 0.00 0.00 37.93 4.85
2821 2958 2.058125 TAAACCTTGGACAGCCCGCA 62.058 55.000 0.00 0.00 37.93 5.69
2822 2959 0.891904 TTAAACCTTGGACAGCCCGC 60.892 55.000 0.00 0.00 37.93 6.13
2823 2960 1.611519 TTTAAACCTTGGACAGCCCG 58.388 50.000 0.00 0.00 37.93 6.13
2824 2961 4.617253 AAATTTAAACCTTGGACAGCCC 57.383 40.909 0.00 0.00 0.00 5.19
2825 2962 4.754618 CCAAAATTTAAACCTTGGACAGCC 59.245 41.667 19.00 0.00 40.72 4.85
2826 2963 4.754618 CCCAAAATTTAAACCTTGGACAGC 59.245 41.667 22.97 0.00 40.72 4.40
2827 2964 5.304778 CCCCAAAATTTAAACCTTGGACAG 58.695 41.667 22.97 11.85 40.72 3.51
2828 2965 4.445019 GCCCCAAAATTTAAACCTTGGACA 60.445 41.667 22.97 0.00 40.72 4.02
2829 2966 4.069304 GCCCCAAAATTTAAACCTTGGAC 58.931 43.478 22.97 14.67 40.72 4.02
2830 2967 3.716872 TGCCCCAAAATTTAAACCTTGGA 59.283 39.130 22.97 8.12 40.72 3.53
2831 2968 3.818210 GTGCCCCAAAATTTAAACCTTGG 59.182 43.478 17.63 17.63 38.45 3.61
2832 2969 4.455606 TGTGCCCCAAAATTTAAACCTTG 58.544 39.130 0.00 0.00 0.00 3.61
2833 2970 4.779993 TGTGCCCCAAAATTTAAACCTT 57.220 36.364 0.00 0.00 0.00 3.50
2834 2971 4.349342 TCATGTGCCCCAAAATTTAAACCT 59.651 37.500 0.00 0.00 0.00 3.50
2858 3379 0.334676 TGGGTTGGGGCCTGAAATAG 59.665 55.000 0.84 0.00 0.00 1.73
2909 3430 9.168451 TCATACTAAATACATTTTCTCGGCAAA 57.832 29.630 0.00 0.00 0.00 3.68
2911 3432 8.725405 TTCATACTAAATACATTTTCTCGGCA 57.275 30.769 0.00 0.00 0.00 5.69
2989 3510 2.158900 AGTTTCATCGGCACCTCCATAG 60.159 50.000 0.00 0.00 34.01 2.23
2991 3512 0.620556 AGTTTCATCGGCACCTCCAT 59.379 50.000 0.00 0.00 34.01 3.41
2992 3513 1.207089 CTAGTTTCATCGGCACCTCCA 59.793 52.381 0.00 0.00 34.01 3.86
3120 3645 8.314751 TTTCTTGTGAATTGGTTTTCAAACCTA 58.685 29.630 19.83 14.06 45.31 3.08
3132 3657 4.913924 CGAGCTTCTTTTCTTGTGAATTGG 59.086 41.667 0.00 0.00 31.56 3.16
3162 3687 7.378966 TGATATAGACAATCGCTAAAGGAAGG 58.621 38.462 0.00 0.00 0.00 3.46
3247 3772 7.759465 AGTAAGCATGAACATGAATGAAAGAG 58.241 34.615 17.40 0.00 41.20 2.85
3319 3844 7.095060 TGCAATTTTGTGTTTAGAAGTGCAAAA 60.095 29.630 7.47 0.00 45.99 2.44
3343 3868 6.983474 AAATTTAAACATACTTGCCCATGC 57.017 33.333 0.00 0.00 38.26 4.06
3346 3871 7.784470 ACCTAAATTTAAACATACTTGCCCA 57.216 32.000 0.00 0.00 0.00 5.36
3347 3872 7.762615 GGAACCTAAATTTAAACATACTTGCCC 59.237 37.037 0.00 0.00 0.00 5.36
3421 3946 4.325028 AGTGAACATCTTTTGCATGCAA 57.675 36.364 28.80 28.80 0.00 4.08
3551 4076 8.589701 AATAGTCTTTTGTATTTGTAAGGGGG 57.410 34.615 0.00 0.00 0.00 5.40
3576 4118 8.542497 ACTAGTTTGTTGCGATTAAATGTAGA 57.458 30.769 0.00 0.00 0.00 2.59
3661 4203 4.264253 TCAGGAATGAGAAATCATGCGTT 58.736 39.130 0.00 0.00 0.00 4.84
3696 4238 2.679059 CGGGAGATCTGTGCAGAATTGT 60.679 50.000 0.00 0.00 41.36 2.71
3777 4320 7.923888 AGTGAATTCGATGATTTTCCATACAG 58.076 34.615 0.04 0.00 0.00 2.74
3778 4321 7.864108 AGTGAATTCGATGATTTTCCATACA 57.136 32.000 0.04 0.00 0.00 2.29
3781 4324 8.960591 AGTAAAGTGAATTCGATGATTTTCCAT 58.039 29.630 0.04 0.00 0.00 3.41
3853 4396 5.995897 GGTAGAAGCCAGTTCAACTAAAGAA 59.004 40.000 0.00 0.00 37.67 2.52
4011 4554 7.857885 GTGTTCAAGTTCTCCAACAAATAAGAG 59.142 37.037 0.00 0.00 34.60 2.85
4066 4613 5.491635 TGCAAACAAGTTTTAAAATGGGC 57.508 34.783 3.52 6.15 0.00 5.36
4236 4785 2.431782 GCATGTGGCATTAATCCCAAGT 59.568 45.455 0.00 0.00 43.97 3.16
4264 4813 0.609957 TCTCCCTGCATGCACAAAGG 60.610 55.000 18.46 16.47 0.00 3.11
4305 4854 1.156736 CGGGAGTTTTAGTGCACCAG 58.843 55.000 14.63 0.00 0.00 4.00
4464 5028 9.737844 ATGACAAATTTTGGCCAAATATAAAGT 57.262 25.926 30.78 22.30 38.13 2.66
4470 5034 8.689972 ACAAAAATGACAAATTTTGGCCAAATA 58.310 25.926 30.78 20.85 45.99 1.40
4479 5043 8.915654 GCTCGAGATACAAAAATGACAAATTTT 58.084 29.630 18.75 0.00 33.12 1.82
4568 5149 9.797556 GTTTGTAAAAACTGAAAACCATCTAGT 57.202 29.630 0.94 0.00 0.00 2.57
4607 5188 2.549992 GCTATCAATGCACCGGATACCA 60.550 50.000 9.46 0.00 0.00 3.25
4621 5202 4.216042 CACTCACATTTGTGGTGCTATCAA 59.784 41.667 10.60 0.00 45.65 2.57
4805 5416 9.428097 ACTACCGTAACTTTATTTTGTAGGAAG 57.572 33.333 0.00 0.00 31.13 3.46
4848 5618 2.159142 AGATAACTCGCGGTACCCTTTG 60.159 50.000 6.13 0.00 0.00 2.77
4950 5720 5.194473 AGTGGTGTAGGAGTTAGATGAGA 57.806 43.478 0.00 0.00 0.00 3.27
4951 5721 5.923733 AAGTGGTGTAGGAGTTAGATGAG 57.076 43.478 0.00 0.00 0.00 2.90
4952 5722 7.973048 ATTAAGTGGTGTAGGAGTTAGATGA 57.027 36.000 0.00 0.00 0.00 2.92
5036 5809 7.682787 ACCAAGTCTCATCTAATTCCTACAT 57.317 36.000 0.00 0.00 0.00 2.29
5308 6081 4.142038 TCTTTTTGTACCCCTTGAGCTTC 58.858 43.478 0.00 0.00 0.00 3.86
5395 6168 0.393077 CGGAGCCTAGGTGGTATTGG 59.607 60.000 11.31 0.00 38.35 3.16
5434 6207 1.587043 CCTTGGAGACGACGAGCTCA 61.587 60.000 15.40 4.00 32.83 4.26
5608 6381 0.452184 CTGCAGCTTCCTTCAGCATG 59.548 55.000 0.00 0.00 42.84 4.06
5656 6429 1.206745 CGTACCCGATTAGTGCTGCG 61.207 60.000 0.00 0.00 35.63 5.18
5685 6458 0.984230 CCTGTTGTTAGGAGGAGCCA 59.016 55.000 0.00 0.00 40.42 4.75
6078 6857 8.786826 ATTCTTATTACGGAACAACAGATCAA 57.213 30.769 0.00 0.00 0.00 2.57
6228 7324 1.871039 GACCGTGTGCATTGTAACTGT 59.129 47.619 0.00 0.00 0.00 3.55
6367 7479 4.521639 ACATGCACATCATTCACTTCTTGT 59.478 37.500 0.00 0.00 31.79 3.16
6393 7505 4.120589 GGTCACGTCTCTTTTTGTTCTCT 58.879 43.478 0.00 0.00 0.00 3.10
6394 7506 4.025647 CAGGTCACGTCTCTTTTTGTTCTC 60.026 45.833 0.00 0.00 0.00 2.87
6395 7507 3.871594 CAGGTCACGTCTCTTTTTGTTCT 59.128 43.478 0.00 0.00 0.00 3.01
6396 7508 3.002348 CCAGGTCACGTCTCTTTTTGTTC 59.998 47.826 0.00 0.00 0.00 3.18
6397 7509 2.943033 CCAGGTCACGTCTCTTTTTGTT 59.057 45.455 0.00 0.00 0.00 2.83
6417 7600 1.559682 TCATTTAGTCTCCTGGGTGCC 59.440 52.381 0.00 0.00 0.00 5.01
6475 7658 2.339556 GCCACATTAGGGCGCACAA 61.340 57.895 14.57 4.42 42.39 3.33
6516 7699 4.984161 AGAAAATGTAGCACACAATGTTGC 59.016 37.500 10.90 10.90 41.55 4.17
6776 8123 6.822442 TGAGAGGTATGTACTTTTGTGAACA 58.178 36.000 0.00 0.00 0.00 3.18
6846 8193 9.104965 GGTAATCACAGTATAATGTAGCACAAA 57.895 33.333 5.36 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.