Multiple sequence alignment - TraesCS3A01G477900

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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 TraesCS3A01G477900 chr3A 100.000 4765 0 0 1 4765 710077632 710082396 0.000000e+00 8800.0
1 TraesCS3A01G477900 chr3A 91.759 3628 219 36 1000 4602 55062381 55058809 0.000000e+00 4970.0
2 TraesCS3A01G477900 chr3A 94.382 89 1 3 1 87 700766754 700766668 2.990000e-27 134.0
3 TraesCS3A01G477900 chr3A 97.727 44 1 0 168 211 136002898 136002855 5.110000e-10 76.8
4 TraesCS3A01G477900 chr2A 96.344 4158 133 11 455 4603 736729175 736733322 0.000000e+00 6818.0
5 TraesCS3A01G477900 chr2A 92.004 3627 216 29 997 4598 569299923 569296346 0.000000e+00 5024.0
6 TraesCS3A01G477900 chr2A 96.000 325 13 0 75 399 736728316 736728640 3.270000e-146 529.0
7 TraesCS3A01G477900 chr7B 94.802 3982 166 12 647 4599 99490600 99494569 0.000000e+00 6168.0
8 TraesCS3A01G477900 chr7B 85.828 882 83 17 997 1857 586936111 586936971 0.000000e+00 898.0
9 TraesCS3A01G477900 chr7B 88.787 437 36 6 209 645 255560053 255559630 1.520000e-144 523.0
10 TraesCS3A01G477900 chr7B 89.796 98 10 0 75 172 713855778 713855681 5.010000e-25 126.0
11 TraesCS3A01G477900 chr1B 91.690 3646 217 30 997 4602 442214357 442210758 0.000000e+00 4975.0
12 TraesCS3A01G477900 chr1B 97.727 44 1 0 168 211 374012177 374012134 5.110000e-10 76.8
13 TraesCS3A01G477900 chr1A 91.628 3631 231 25 997 4602 302028050 302024468 0.000000e+00 4953.0
14 TraesCS3A01G477900 chr1A 91.144 3207 237 28 1407 4602 58251746 58248576 0.000000e+00 4305.0
15 TraesCS3A01G477900 chr1A 89.879 2223 155 28 997 3195 555682741 555680565 0.000000e+00 2795.0
16 TraesCS3A01G477900 chr2B 90.777 3101 241 17 1515 4603 140591816 140588749 0.000000e+00 4100.0
17 TraesCS3A01G477900 chr2B 84.688 529 56 12 997 1510 140630541 140630023 5.500000e-139 505.0
18 TraesCS3A01G477900 chr2B 87.879 99 10 1 76 172 565280046 565279948 1.080000e-21 115.0
19 TraesCS3A01G477900 chr5B 86.345 3105 378 33 1520 4603 703940687 703937608 0.000000e+00 3343.0
20 TraesCS3A01G477900 chr5B 89.000 100 9 1 75 172 537618723 537618822 6.480000e-24 122.0
21 TraesCS3A01G477900 chr4B 91.805 1269 84 3 647 1898 512704663 512703398 0.000000e+00 1749.0
22 TraesCS3A01G477900 chr7A 90.000 1310 106 8 209 1503 59610701 59609402 0.000000e+00 1670.0
23 TraesCS3A01G477900 chr7A 97.561 82 2 0 1 82 132808098 132808179 1.790000e-29 141.0
24 TraesCS3A01G477900 chr7A 97.561 82 2 0 1 82 132829145 132829226 1.790000e-29 141.0
25 TraesCS3A01G477900 chr7A 93.548 93 3 3 1 92 513305972 513305882 8.320000e-28 135.0
26 TraesCS3A01G477900 chr7A 93.478 92 5 1 1 91 556822142 556822233 8.320000e-28 135.0
27 TraesCS3A01G477900 chr5A 89.671 1307 105 15 209 1500 544167281 544168572 0.000000e+00 1639.0
28 TraesCS3A01G477900 chr5A 94.382 89 1 4 1 86 516451737 516451650 2.990000e-27 134.0
29 TraesCS3A01G477900 chr4D 84.902 914 69 32 627 1522 11494903 11494041 0.000000e+00 859.0
30 TraesCS3A01G477900 chr4D 92.442 172 12 1 209 380 11495072 11494902 1.320000e-60 244.0
31 TraesCS3A01G477900 chr1D 84.026 914 77 36 627 1522 250206773 250207635 0.000000e+00 815.0
32 TraesCS3A01G477900 chr1D 91.279 172 14 1 209 380 250206604 250206774 2.870000e-57 233.0
33 TraesCS3A01G477900 chr3D 94.253 174 8 1 4591 4762 574744469 574744642 1.020000e-66 265.0
34 TraesCS3A01G477900 chr3B 90.909 165 14 1 209 373 748432008 748432171 2.230000e-53 220.0
35 TraesCS3A01G477900 chr4A 98.734 79 1 0 1 79 459563023 459562945 1.790000e-29 141.0
36 TraesCS3A01G477900 chr4A 91.753 97 2 4 1 97 108932445 108932355 3.870000e-26 130.0
37 TraesCS3A01G477900 chr6D 91.837 98 8 0 75 172 69409324 69409227 2.310000e-28 137.0
38 TraesCS3A01G477900 chr6A 94.382 89 5 0 1 89 551446407 551446319 2.310000e-28 137.0
39 TraesCS3A01G477900 chr6B 97.872 47 1 0 4685 4731 17054556 17054602 1.100000e-11 82.4


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 TraesCS3A01G477900 chr3A 710077632 710082396 4764 False 8800.0 8800 100.0000 1 4765 1 chr3A.!!$F1 4764
1 TraesCS3A01G477900 chr3A 55058809 55062381 3572 True 4970.0 4970 91.7590 1000 4602 1 chr3A.!!$R1 3602
2 TraesCS3A01G477900 chr2A 569296346 569299923 3577 True 5024.0 5024 92.0040 997 4598 1 chr2A.!!$R1 3601
3 TraesCS3A01G477900 chr2A 736728316 736733322 5006 False 3673.5 6818 96.1720 75 4603 2 chr2A.!!$F1 4528
4 TraesCS3A01G477900 chr7B 99490600 99494569 3969 False 6168.0 6168 94.8020 647 4599 1 chr7B.!!$F1 3952
5 TraesCS3A01G477900 chr7B 586936111 586936971 860 False 898.0 898 85.8280 997 1857 1 chr7B.!!$F2 860
6 TraesCS3A01G477900 chr1B 442210758 442214357 3599 True 4975.0 4975 91.6900 997 4602 1 chr1B.!!$R2 3605
7 TraesCS3A01G477900 chr1A 302024468 302028050 3582 True 4953.0 4953 91.6280 997 4602 1 chr1A.!!$R2 3605
8 TraesCS3A01G477900 chr1A 58248576 58251746 3170 True 4305.0 4305 91.1440 1407 4602 1 chr1A.!!$R1 3195
9 TraesCS3A01G477900 chr1A 555680565 555682741 2176 True 2795.0 2795 89.8790 997 3195 1 chr1A.!!$R3 2198
10 TraesCS3A01G477900 chr2B 140588749 140591816 3067 True 4100.0 4100 90.7770 1515 4603 1 chr2B.!!$R1 3088
11 TraesCS3A01G477900 chr2B 140630023 140630541 518 True 505.0 505 84.6880 997 1510 1 chr2B.!!$R2 513
12 TraesCS3A01G477900 chr5B 703937608 703940687 3079 True 3343.0 3343 86.3450 1520 4603 1 chr5B.!!$R1 3083
13 TraesCS3A01G477900 chr4B 512703398 512704663 1265 True 1749.0 1749 91.8050 647 1898 1 chr4B.!!$R1 1251
14 TraesCS3A01G477900 chr7A 59609402 59610701 1299 True 1670.0 1670 90.0000 209 1503 1 chr7A.!!$R1 1294
15 TraesCS3A01G477900 chr5A 544167281 544168572 1291 False 1639.0 1639 89.6710 209 1500 1 chr5A.!!$F1 1291
16 TraesCS3A01G477900 chr4D 11494041 11495072 1031 True 551.5 859 88.6720 209 1522 2 chr4D.!!$R1 1313
17 TraesCS3A01G477900 chr1D 250206604 250207635 1031 False 524.0 815 87.6525 209 1522 2 chr1D.!!$F1 1313

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
449 450 0.258774 CCCACCCCTTGGTAATGGAG 59.741 60.0 0.00 0.00 45.57 3.86 F
1236 1746 0.392060 TGATCATGTCGCTGCTTGCT 60.392 50.0 0.00 0.00 40.11 3.91 F
1676 2222 2.099633 ATTGTGTTGTTTGCGACGTC 57.900 45.0 5.18 5.18 0.00 4.34 F
3503 4067 0.597637 GTCACATAGGCGGTCATCGG 60.598 60.0 0.00 0.00 39.69 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 2004 1.668294 CAGGACCAGCAGAACGACT 59.332 57.895 0.00 0.0 0.00 4.18 R
2300 2851 1.693606 CAAACCAAAAGGAGGCACCAT 59.306 47.619 3.18 0.0 42.04 3.55 R
3584 4148 0.620556 TCTCAGGCCACTTGGGATTC 59.379 55.000 5.01 0.0 40.01 2.52 R
4721 5296 0.109458 GACCAGTCGTGTCGCATACA 60.109 55.000 0.00 0.0 35.06 2.29 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
33 34 9.725019 TCCAAAACAGTAGATAATATAGCATGG 57.275 33.333 0.00 0.00 0.00 3.66
34 35 9.725019 CCAAAACAGTAGATAATATAGCATGGA 57.275 33.333 0.00 0.00 0.00 3.41
36 37 9.442047 AAAACAGTAGATAATATAGCATGGAGC 57.558 33.333 0.00 0.00 46.19 4.70
57 58 9.337396 TGGAGCAATCAAAAATTATAGATACGT 57.663 29.630 0.00 0.00 0.00 3.57
60 61 9.950680 AGCAATCAAAAATTATAGATACGTTGG 57.049 29.630 0.00 0.00 0.00 3.77
61 62 9.944663 GCAATCAAAAATTATAGATACGTTGGA 57.055 29.630 0.00 0.00 0.00 3.53
76 77 2.612672 CGTTGGAGACGTATCAGCTCTA 59.387 50.000 12.92 0.00 46.49 2.43
109 110 1.766496 ACGTCCAGTTTCTTTCCCAGA 59.234 47.619 0.00 0.00 0.00 3.86
113 114 4.006319 GTCCAGTTTCTTTCCCAGATCTG 58.994 47.826 16.24 16.24 35.39 2.90
302 303 8.443953 AAATCTTGAACATAAGCCATCTACTC 57.556 34.615 0.00 0.00 0.00 2.59
316 317 5.163405 GCCATCTACTCTTGATGTCCTGTTA 60.163 44.000 0.00 0.00 39.54 2.41
399 400 4.156455 TGGACAAGGCAAATATCTCCTC 57.844 45.455 0.00 0.00 0.00 3.71
449 450 0.258774 CCCACCCCTTGGTAATGGAG 59.741 60.000 0.00 0.00 45.57 3.86
450 451 1.295020 CCACCCCTTGGTAATGGAGA 58.705 55.000 0.00 0.00 45.57 3.71
491 971 6.385649 TGAACCTTTAACCTGACATCAAAC 57.614 37.500 0.00 0.00 0.00 2.93
492 972 5.888724 TGAACCTTTAACCTGACATCAAACA 59.111 36.000 0.00 0.00 0.00 2.83
551 1031 5.413309 TGGGTCTTTTTCTTTCTTTTGCA 57.587 34.783 0.00 0.00 0.00 4.08
557 1037 3.724508 TTTCTTTCTTTTGCATGCGGA 57.275 38.095 14.09 5.82 0.00 5.54
569 1049 1.265635 GCATGCGGAAAACTACACACA 59.734 47.619 0.00 0.00 0.00 3.72
836 1331 5.827797 ACTGGATCTTTCTGTTAACAAGCAA 59.172 36.000 10.03 0.22 0.00 3.91
876 1371 2.866156 TGTCCAATCGCTCGATCATTTC 59.134 45.455 5.17 0.00 33.08 2.17
1027 1522 5.813717 TCTGATGTATACTTACGTGGTTCG 58.186 41.667 0.00 0.00 46.00 3.95
1201 1711 3.577415 GGCCGTGGAGGTTCTAATATAGT 59.423 47.826 0.00 0.00 43.70 2.12
1236 1746 0.392060 TGATCATGTCGCTGCTTGCT 60.392 50.000 0.00 0.00 40.11 3.91
1289 1799 2.338015 GCGTAGGGGTGTGAGTCGA 61.338 63.158 0.00 0.00 0.00 4.20
1467 2004 2.632996 GCTATACATGTGTCTGCCCCTA 59.367 50.000 9.11 0.00 0.00 3.53
1493 2030 3.391382 GCTGGTCCTGGGTACGCT 61.391 66.667 11.59 0.00 0.00 5.07
1522 2059 2.110213 GCGTGTGTTGGTCCCTGA 59.890 61.111 0.00 0.00 0.00 3.86
1676 2222 2.099633 ATTGTGTTGTTTGCGACGTC 57.900 45.000 5.18 5.18 0.00 4.34
1805 2353 6.034577 GTGAAAGTTCTTAGTTTGTTGTTGGC 59.965 38.462 0.00 0.00 0.00 4.52
2300 2851 4.080807 TCCGGATTTCTTGTGCCAATACTA 60.081 41.667 0.00 0.00 0.00 1.82
2707 3259 7.753630 AGACATAGGATGAATGCCTTAAATCT 58.246 34.615 0.00 0.00 36.96 2.40
2967 3524 4.499183 CTTCACGTTAGAGGCATCTTCTT 58.501 43.478 6.05 0.00 36.96 2.52
3018 3575 3.624861 CGGTTTGCAGCAGATATCTTCTT 59.375 43.478 1.33 0.00 29.93 2.52
3030 3587 6.183360 GCAGATATCTTCTTTGAACACTGCAT 60.183 38.462 1.33 0.00 43.87 3.96
3087 3646 0.787084 AGAGAGAGGGTTCCAGGTGA 59.213 55.000 0.00 0.00 0.00 4.02
3196 3760 1.794714 TCCTCTCCATACCCTTCTGC 58.205 55.000 0.00 0.00 0.00 4.26
3213 3777 2.819595 CGGGTGGTGATGCTTCCG 60.820 66.667 0.00 0.00 0.00 4.30
3499 4063 0.613572 TCCAGTCACATAGGCGGTCA 60.614 55.000 0.00 0.00 0.00 4.02
3503 4067 0.597637 GTCACATAGGCGGTCATCGG 60.598 60.000 0.00 0.00 39.69 4.18
3555 4119 2.589442 TTTGTCGGGTGCACGGTC 60.589 61.111 11.45 3.88 0.00 4.79
3556 4120 3.096633 TTTGTCGGGTGCACGGTCT 62.097 57.895 11.45 0.00 0.00 3.85
3584 4148 5.138125 ACATATTTGCCACTTTCACTTGG 57.862 39.130 0.00 0.00 35.81 3.61
3648 4212 2.769209 AGACACCTTCTGATAGGGCAT 58.231 47.619 9.61 0.00 39.76 4.40
3673 4237 9.998106 ATATATTGTTGTTAGGGTCTATCACAC 57.002 33.333 0.00 0.00 0.00 3.82
3713 4277 2.957006 GGACGAGATTAAGTCAGGCCTA 59.043 50.000 3.98 0.00 39.01 3.93
3714 4278 3.574826 GGACGAGATTAAGTCAGGCCTAT 59.425 47.826 3.98 0.00 39.01 2.57
3742 4306 0.951558 CCCATTACGGCTGGTATTGC 59.048 55.000 0.00 0.00 33.27 3.56
3763 4330 2.671070 CGACTGCTGTGCTATGTGTGTA 60.671 50.000 0.00 0.00 0.00 2.90
3768 4335 2.415491 GCTGTGCTATGTGTGTAGTCGA 60.415 50.000 0.00 0.00 0.00 4.20
3772 4340 4.396790 TGTGCTATGTGTGTAGTCGATGTA 59.603 41.667 0.00 0.00 0.00 2.29
3777 4345 8.357402 TGCTATGTGTGTAGTCGATGTATTTAT 58.643 33.333 0.00 0.00 0.00 1.40
3801 4372 7.639113 TTGATGTTTTACTTCTTCTGTTGGT 57.361 32.000 0.00 0.00 0.00 3.67
3840 4413 6.545666 TGAGCTTTTATGTCCTTTTTCAGTGA 59.454 34.615 0.00 0.00 0.00 3.41
3859 4432 5.516696 CAGTGATGTATACTGTTGAGTTCCG 59.483 44.000 4.17 0.00 40.43 4.30
3917 4490 0.690077 GGAGAGGGGGTAACGGTGAT 60.690 60.000 0.00 0.00 37.60 3.06
4066 4639 1.340889 TGTCTGCATGAAAAAGGGTGC 59.659 47.619 0.00 0.00 0.00 5.01
4141 4714 3.916359 TGGGTTTGCCTTATATCGACA 57.084 42.857 0.00 0.00 34.45 4.35
4240 4813 3.831323 TGCTCAAGAAATTTCAGGGACA 58.169 40.909 19.99 9.53 0.00 4.02
4241 4814 4.410099 TGCTCAAGAAATTTCAGGGACAT 58.590 39.130 19.99 0.00 0.00 3.06
4242 4815 5.569355 TGCTCAAGAAATTTCAGGGACATA 58.431 37.500 19.99 0.00 0.00 2.29
4243 4816 6.189859 TGCTCAAGAAATTTCAGGGACATAT 58.810 36.000 19.99 0.00 0.00 1.78
4344 4917 6.668283 ACTCTAAGGTCATGTTAGAAAGGCTA 59.332 38.462 5.94 0.00 36.34 3.93
4380 4955 1.806542 TCTGGTTGTCGTACGGTAGAC 59.193 52.381 16.52 6.65 37.85 2.59
4438 5013 0.318107 GTATGATGCATTGTGGCGCC 60.318 55.000 22.73 22.73 36.28 6.53
4487 5062 0.816421 CCGTCGGTTCAAAGGTTGGT 60.816 55.000 2.08 0.00 0.00 3.67
4602 5177 2.231215 CCGAATGGTTTGTTGCCAAA 57.769 45.000 0.00 0.00 39.72 3.28
4618 5193 9.509855 TTGTTGCCAAACATATCGATATAAAAC 57.490 29.630 17.35 13.10 45.54 2.43
4619 5194 8.898761 TGTTGCCAAACATATCGATATAAAACT 58.101 29.630 17.35 0.00 41.41 2.66
4620 5195 9.730420 GTTGCCAAACATATCGATATAAAACTT 57.270 29.630 17.35 4.63 36.24 2.66
4623 5198 9.821662 GCCAAACATATCGATATAAAACTTACC 57.178 33.333 17.35 0.00 0.00 2.85
4633 5208 9.081204 TCGATATAAAACTTACCTATGCCTACA 57.919 33.333 0.00 0.00 0.00 2.74
4634 5209 9.136952 CGATATAAAACTTACCTATGCCTACAC 57.863 37.037 0.00 0.00 0.00 2.90
4635 5210 9.433153 GATATAAAACTTACCTATGCCTACACC 57.567 37.037 0.00 0.00 0.00 4.16
4636 5211 5.508280 AAAACTTACCTATGCCTACACCA 57.492 39.130 0.00 0.00 0.00 4.17
4637 5212 5.508280 AAACTTACCTATGCCTACACCAA 57.492 39.130 0.00 0.00 0.00 3.67
4638 5213 5.508280 AACTTACCTATGCCTACACCAAA 57.492 39.130 0.00 0.00 0.00 3.28
4639 5214 5.508280 ACTTACCTATGCCTACACCAAAA 57.492 39.130 0.00 0.00 0.00 2.44
4640 5215 5.250982 ACTTACCTATGCCTACACCAAAAC 58.749 41.667 0.00 0.00 0.00 2.43
4641 5216 3.799432 ACCTATGCCTACACCAAAACA 57.201 42.857 0.00 0.00 0.00 2.83
4642 5217 4.107127 ACCTATGCCTACACCAAAACAA 57.893 40.909 0.00 0.00 0.00 2.83
4643 5218 4.672899 ACCTATGCCTACACCAAAACAAT 58.327 39.130 0.00 0.00 0.00 2.71
4644 5219 4.462483 ACCTATGCCTACACCAAAACAATG 59.538 41.667 0.00 0.00 0.00 2.82
4645 5220 4.704540 CCTATGCCTACACCAAAACAATGA 59.295 41.667 0.00 0.00 0.00 2.57
4646 5221 4.789012 ATGCCTACACCAAAACAATGAG 57.211 40.909 0.00 0.00 0.00 2.90
4647 5222 3.826524 TGCCTACACCAAAACAATGAGA 58.173 40.909 0.00 0.00 0.00 3.27
4648 5223 4.211125 TGCCTACACCAAAACAATGAGAA 58.789 39.130 0.00 0.00 0.00 2.87
4649 5224 4.037446 TGCCTACACCAAAACAATGAGAAC 59.963 41.667 0.00 0.00 0.00 3.01
4650 5225 4.278419 GCCTACACCAAAACAATGAGAACT 59.722 41.667 0.00 0.00 0.00 3.01
4651 5226 5.472137 GCCTACACCAAAACAATGAGAACTA 59.528 40.000 0.00 0.00 0.00 2.24
4652 5227 6.151144 GCCTACACCAAAACAATGAGAACTAT 59.849 38.462 0.00 0.00 0.00 2.12
4653 5228 7.309194 GCCTACACCAAAACAATGAGAACTATT 60.309 37.037 0.00 0.00 0.00 1.73
4654 5229 9.226606 CCTACACCAAAACAATGAGAACTATTA 57.773 33.333 0.00 0.00 0.00 0.98
4690 5265 9.689976 ATGAACAAAAATAACAAATCGACATGA 57.310 25.926 0.00 0.00 0.00 3.07
4691 5266 9.689976 TGAACAAAAATAACAAATCGACATGAT 57.310 25.926 0.00 0.00 39.67 2.45
4699 5274 9.800433 AATAACAAATCGACATGATAAAATGCA 57.200 25.926 0.00 0.00 35.84 3.96
4700 5275 9.800433 ATAACAAATCGACATGATAAAATGCAA 57.200 25.926 0.00 0.00 35.84 4.08
4701 5276 7.745022 ACAAATCGACATGATAAAATGCAAG 57.255 32.000 0.00 0.00 35.84 4.01
4702 5277 7.537715 ACAAATCGACATGATAAAATGCAAGA 58.462 30.769 0.00 0.00 35.84 3.02
4703 5278 8.028354 ACAAATCGACATGATAAAATGCAAGAA 58.972 29.630 0.00 0.00 35.84 2.52
4704 5279 8.862074 CAAATCGACATGATAAAATGCAAGAAA 58.138 29.630 0.00 0.00 35.84 2.52
4705 5280 8.984891 AATCGACATGATAAAATGCAAGAAAA 57.015 26.923 0.00 0.00 35.84 2.29
4706 5281 8.984891 ATCGACATGATAAAATGCAAGAAAAA 57.015 26.923 0.00 0.00 34.83 1.94
4707 5282 8.984891 TCGACATGATAAAATGCAAGAAAAAT 57.015 26.923 0.00 0.00 0.00 1.82
4734 5309 8.751302 ACATAAATATAATGTATGCGACACGA 57.249 30.769 0.00 0.00 42.17 4.35
4735 5310 8.644619 ACATAAATATAATGTATGCGACACGAC 58.355 33.333 0.00 0.00 42.17 4.34
4736 5311 8.860128 CATAAATATAATGTATGCGACACGACT 58.140 33.333 0.00 0.00 42.17 4.18
4737 5312 6.690704 AATATAATGTATGCGACACGACTG 57.309 37.500 0.00 0.00 42.17 3.51
4738 5313 1.640428 AATGTATGCGACACGACTGG 58.360 50.000 0.00 0.00 42.17 4.00
4739 5314 0.530744 ATGTATGCGACACGACTGGT 59.469 50.000 0.00 0.00 42.17 4.00
4740 5315 0.109458 TGTATGCGACACGACTGGTC 60.109 55.000 0.00 0.00 31.20 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.725019 CCATGCTATATTATCTACTGTTTTGGA 57.275 33.333 0.00 0.00 0.00 3.53
8 9 9.725019 TCCATGCTATATTATCTACTGTTTTGG 57.275 33.333 0.00 0.00 0.00 3.28
10 11 9.442047 GCTCCATGCTATATTATCTACTGTTTT 57.558 33.333 0.00 0.00 38.95 2.43
11 12 8.597167 TGCTCCATGCTATATTATCTACTGTTT 58.403 33.333 0.00 0.00 43.37 2.83
12 13 8.138928 TGCTCCATGCTATATTATCTACTGTT 57.861 34.615 0.00 0.00 43.37 3.16
13 14 7.724490 TGCTCCATGCTATATTATCTACTGT 57.276 36.000 0.00 0.00 43.37 3.55
14 15 9.258826 GATTGCTCCATGCTATATTATCTACTG 57.741 37.037 0.00 0.00 43.37 2.74
15 16 8.985922 TGATTGCTCCATGCTATATTATCTACT 58.014 33.333 0.00 0.00 43.37 2.57
16 17 9.605275 TTGATTGCTCCATGCTATATTATCTAC 57.395 33.333 0.00 0.00 43.37 2.59
18 19 9.524496 TTTTGATTGCTCCATGCTATATTATCT 57.476 29.630 0.00 0.00 43.37 1.98
26 27 9.353431 TCTATAATTTTTGATTGCTCCATGCTA 57.647 29.630 0.00 0.00 43.37 3.49
27 28 8.241497 TCTATAATTTTTGATTGCTCCATGCT 57.759 30.769 0.00 0.00 43.37 3.79
31 32 9.337396 ACGTATCTATAATTTTTGATTGCTCCA 57.663 29.630 0.00 0.00 0.00 3.86
34 35 9.950680 CCAACGTATCTATAATTTTTGATTGCT 57.049 29.630 0.00 0.00 0.00 3.91
35 36 9.944663 TCCAACGTATCTATAATTTTTGATTGC 57.055 29.630 0.00 0.00 0.00 3.56
39 40 9.027129 CGTCTCCAACGTATCTATAATTTTTGA 57.973 33.333 0.00 0.00 46.42 2.69
56 57 4.634184 TTAGAGCTGATACGTCTCCAAC 57.366 45.455 0.00 0.00 0.00 3.77
57 58 4.461431 TGTTTAGAGCTGATACGTCTCCAA 59.539 41.667 0.00 0.00 0.00 3.53
58 59 4.014406 TGTTTAGAGCTGATACGTCTCCA 58.986 43.478 0.00 0.00 0.00 3.86
59 60 4.634184 TGTTTAGAGCTGATACGTCTCC 57.366 45.455 0.00 0.00 0.00 3.71
60 61 5.051374 GCATTGTTTAGAGCTGATACGTCTC 60.051 44.000 0.00 0.00 0.00 3.36
61 62 4.806247 GCATTGTTTAGAGCTGATACGTCT 59.194 41.667 0.00 0.00 0.00 4.18
62 63 4.566759 TGCATTGTTTAGAGCTGATACGTC 59.433 41.667 0.00 0.00 0.00 4.34
63 64 4.503910 TGCATTGTTTAGAGCTGATACGT 58.496 39.130 0.00 0.00 0.00 3.57
64 65 5.663795 ATGCATTGTTTAGAGCTGATACG 57.336 39.130 0.00 0.00 0.00 3.06
65 66 6.909357 GTCAATGCATTGTTTAGAGCTGATAC 59.091 38.462 32.67 18.04 38.84 2.24
66 67 6.238184 CGTCAATGCATTGTTTAGAGCTGATA 60.238 38.462 32.67 11.19 38.84 2.15
67 68 5.448225 CGTCAATGCATTGTTTAGAGCTGAT 60.448 40.000 32.67 0.00 38.84 2.90
68 69 4.142838 CGTCAATGCATTGTTTAGAGCTGA 60.143 41.667 32.67 12.10 38.84 4.26
69 70 4.093514 CGTCAATGCATTGTTTAGAGCTG 58.906 43.478 32.67 9.98 38.84 4.24
70 71 3.753272 ACGTCAATGCATTGTTTAGAGCT 59.247 39.130 32.67 10.19 38.84 4.09
71 72 4.083581 ACGTCAATGCATTGTTTAGAGC 57.916 40.909 32.67 16.61 38.84 4.09
72 73 4.154015 TGGACGTCAATGCATTGTTTAGAG 59.846 41.667 32.67 21.31 38.84 2.43
73 74 4.068599 TGGACGTCAATGCATTGTTTAGA 58.931 39.130 32.67 15.26 38.84 2.10
76 77 2.622942 ACTGGACGTCAATGCATTGTTT 59.377 40.909 32.67 20.57 38.84 2.83
109 110 0.817654 TCAGCGACGAATGGACAGAT 59.182 50.000 0.00 0.00 0.00 2.90
113 114 1.121240 CGTATCAGCGACGAATGGAC 58.879 55.000 0.00 0.00 42.98 4.02
270 271 6.826741 TGGCTTATGTTCAAGATTTACCTACC 59.173 38.462 0.00 0.00 0.00 3.18
302 303 3.686726 GCCTTGTCTAACAGGACATCAAG 59.313 47.826 0.00 0.00 44.30 3.02
316 317 5.883685 TCTGATTAGATCATGCCTTGTCT 57.116 39.130 0.00 0.00 38.85 3.41
449 450 0.737715 AGCGGTTGAGCGAACTGATC 60.738 55.000 13.04 0.00 42.88 2.92
450 451 1.016130 CAGCGGTTGAGCGAACTGAT 61.016 55.000 13.04 5.26 42.88 2.90
491 971 3.328939 CGAAGCGAAGACGTTTGTG 57.671 52.632 0.00 0.00 42.37 3.33
551 1031 5.001232 ACTAATGTGTGTAGTTTTCCGCAT 58.999 37.500 0.00 0.00 0.00 4.73
569 1049 7.806180 AGGTCTTGTGCAAGGAATATACTAAT 58.194 34.615 11.47 0.00 38.88 1.73
836 1331 4.961099 GGACATTAGTACCTTGGGTCTAGT 59.039 45.833 0.00 0.00 37.09 2.57
1027 1522 4.082571 ACATGCTGGACAAATAAGAAGCAC 60.083 41.667 0.00 0.00 42.88 4.40
1201 1711 0.478072 ATCAGAAACAGGGGCACACA 59.522 50.000 0.00 0.00 0.00 3.72
1467 2004 1.668294 CAGGACCAGCAGAACGACT 59.332 57.895 0.00 0.00 0.00 4.18
1522 2059 2.527100 GCACGTAACGTCTAGCAATCT 58.473 47.619 0.00 0.00 38.32 2.40
1676 2222 1.737793 GAAACCAGCCATCACCTAACG 59.262 52.381 0.00 0.00 0.00 3.18
1805 2353 3.296322 ACACACAACCAACAACAACAG 57.704 42.857 0.00 0.00 0.00 3.16
2300 2851 1.693606 CAAACCAAAAGGAGGCACCAT 59.306 47.619 3.18 0.00 42.04 3.55
2353 2904 6.939551 GCGATTATAAACCATCTTACGCTA 57.060 37.500 0.00 0.00 39.38 4.26
2355 2906 5.840940 AGCGATTATAAACCATCTTACGC 57.159 39.130 0.00 0.00 42.03 4.42
2507 3059 2.009774 CCCATCGAAGTGAAAGCGAAT 58.990 47.619 0.00 0.00 37.60 3.34
2707 3259 4.044317 CACCCCTAGTAGGCTTATCCTCTA 59.956 50.000 11.08 0.00 43.20 2.43
2724 3276 2.774234 CAATACTCTCATCCACACCCCT 59.226 50.000 0.00 0.00 0.00 4.79
2967 3524 3.190327 CGACTGCAAACAACAATATCCCA 59.810 43.478 0.00 0.00 0.00 4.37
3087 3646 5.242393 CAGGAACAATCAAGTGAGGAACATT 59.758 40.000 0.00 0.00 0.00 2.71
3196 3760 2.819595 CGGAAGCATCACCACCCG 60.820 66.667 0.00 0.00 0.00 5.28
3213 3777 4.691216 GGTCATCCTATTCCGACTATTTGC 59.309 45.833 0.00 0.00 0.00 3.68
3499 4063 5.949354 TGGAAATTTTCATGGAAGTACCGAT 59.051 36.000 11.09 0.00 42.61 4.18
3503 4067 7.707893 CCATCATGGAAATTTTCATGGAAGTAC 59.292 37.037 30.55 0.00 40.96 2.73
3555 4119 3.287867 AGTGGCAAATATGTCAGGGAG 57.712 47.619 0.00 0.00 43.00 4.30
3556 4120 3.737559 AAGTGGCAAATATGTCAGGGA 57.262 42.857 0.00 0.00 43.00 4.20
3570 4134 1.546029 GGGATTCCAAGTGAAAGTGGC 59.454 52.381 4.80 0.00 36.33 5.01
3584 4148 0.620556 TCTCAGGCCACTTGGGATTC 59.379 55.000 5.01 0.00 40.01 2.52
3648 4212 8.139350 CGTGTGATAGACCCTAACAACAATATA 58.861 37.037 0.00 0.00 0.00 0.86
3673 4237 1.618861 CAAGTACTCGGTGAGCTTCG 58.381 55.000 0.00 0.00 32.04 3.79
3713 4277 1.775385 CCGTAATGGGGCCAAAAGAT 58.225 50.000 4.39 0.00 0.00 2.40
3714 4278 0.968393 GCCGTAATGGGGCCAAAAGA 60.968 55.000 4.39 0.00 44.97 2.52
3742 4306 0.717784 CACACATAGCACAGCAGTCG 59.282 55.000 0.00 0.00 0.00 4.18
3777 4345 7.639113 ACCAACAGAAGAAGTAAAACATCAA 57.361 32.000 0.00 0.00 0.00 2.57
3801 4372 3.439857 AAGCTCAATTAGACAGCCCAA 57.560 42.857 0.00 0.00 33.28 4.12
3840 4413 5.661458 CTTCCGGAACTCAACAGTATACAT 58.339 41.667 14.35 0.00 30.14 2.29
3859 4432 4.475135 GAGGCAGTCCCCGCTTCC 62.475 72.222 0.00 0.00 29.74 3.46
4380 4955 5.475220 ACATATCAGATACTCCTGAACCTCG 59.525 44.000 0.00 0.00 45.22 4.63
4607 5182 9.081204 TGTAGGCATAGGTAAGTTTTATATCGA 57.919 33.333 0.00 0.00 0.00 3.59
4608 5183 9.136952 GTGTAGGCATAGGTAAGTTTTATATCG 57.863 37.037 0.00 0.00 0.00 2.92
4609 5184 9.433153 GGTGTAGGCATAGGTAAGTTTTATATC 57.567 37.037 0.00 0.00 0.00 1.63
4610 5185 8.940982 TGGTGTAGGCATAGGTAAGTTTTATAT 58.059 33.333 0.00 0.00 0.00 0.86
4611 5186 8.321621 TGGTGTAGGCATAGGTAAGTTTTATA 57.678 34.615 0.00 0.00 0.00 0.98
4612 5187 7.202972 TGGTGTAGGCATAGGTAAGTTTTAT 57.797 36.000 0.00 0.00 0.00 1.40
4613 5188 6.623979 TGGTGTAGGCATAGGTAAGTTTTA 57.376 37.500 0.00 0.00 0.00 1.52
4614 5189 5.508280 TGGTGTAGGCATAGGTAAGTTTT 57.492 39.130 0.00 0.00 0.00 2.43
4615 5190 5.508280 TTGGTGTAGGCATAGGTAAGTTT 57.492 39.130 0.00 0.00 0.00 2.66
4616 5191 5.508280 TTTGGTGTAGGCATAGGTAAGTT 57.492 39.130 0.00 0.00 0.00 2.66
4617 5192 5.221966 TGTTTTGGTGTAGGCATAGGTAAGT 60.222 40.000 0.00 0.00 0.00 2.24
4618 5193 5.250200 TGTTTTGGTGTAGGCATAGGTAAG 58.750 41.667 0.00 0.00 0.00 2.34
4619 5194 5.244189 TGTTTTGGTGTAGGCATAGGTAA 57.756 39.130 0.00 0.00 0.00 2.85
4620 5195 4.912317 TGTTTTGGTGTAGGCATAGGTA 57.088 40.909 0.00 0.00 0.00 3.08
4621 5196 3.799432 TGTTTTGGTGTAGGCATAGGT 57.201 42.857 0.00 0.00 0.00 3.08
4622 5197 4.704540 TCATTGTTTTGGTGTAGGCATAGG 59.295 41.667 0.00 0.00 0.00 2.57
4623 5198 5.647658 TCTCATTGTTTTGGTGTAGGCATAG 59.352 40.000 0.00 0.00 0.00 2.23
4624 5199 5.565509 TCTCATTGTTTTGGTGTAGGCATA 58.434 37.500 0.00 0.00 0.00 3.14
4625 5200 4.406456 TCTCATTGTTTTGGTGTAGGCAT 58.594 39.130 0.00 0.00 0.00 4.40
4626 5201 3.826524 TCTCATTGTTTTGGTGTAGGCA 58.173 40.909 0.00 0.00 0.00 4.75
4627 5202 4.278419 AGTTCTCATTGTTTTGGTGTAGGC 59.722 41.667 0.00 0.00 0.00 3.93
4628 5203 7.687941 ATAGTTCTCATTGTTTTGGTGTAGG 57.312 36.000 0.00 0.00 0.00 3.18
4664 5239 9.689976 TCATGTCGATTTGTTATTTTTGTTCAT 57.310 25.926 0.00 0.00 0.00 2.57
4665 5240 9.689976 ATCATGTCGATTTGTTATTTTTGTTCA 57.310 25.926 0.00 0.00 0.00 3.18
4673 5248 9.800433 TGCATTTTATCATGTCGATTTGTTATT 57.200 25.926 0.00 0.00 35.39 1.40
4674 5249 9.800433 TTGCATTTTATCATGTCGATTTGTTAT 57.200 25.926 0.00 0.00 35.39 1.89
4675 5250 9.288124 CTTGCATTTTATCATGTCGATTTGTTA 57.712 29.630 0.00 0.00 35.39 2.41
4676 5251 8.028354 TCTTGCATTTTATCATGTCGATTTGTT 58.972 29.630 0.00 0.00 35.39 2.83
4677 5252 7.537715 TCTTGCATTTTATCATGTCGATTTGT 58.462 30.769 0.00 0.00 35.39 2.83
4678 5253 7.974243 TCTTGCATTTTATCATGTCGATTTG 57.026 32.000 0.00 0.00 35.39 2.32
4679 5254 8.984891 TTTCTTGCATTTTATCATGTCGATTT 57.015 26.923 0.00 0.00 35.39 2.17
4680 5255 8.984891 TTTTCTTGCATTTTATCATGTCGATT 57.015 26.923 0.00 0.00 35.39 3.34
4681 5256 8.984891 TTTTTCTTGCATTTTATCATGTCGAT 57.015 26.923 0.00 0.00 38.21 3.59
4682 5257 8.984891 ATTTTTCTTGCATTTTATCATGTCGA 57.015 26.923 0.00 0.00 0.00 4.20
4708 5283 9.198837 TCGTGTCGCATACATTATATTTATGTT 57.801 29.630 8.04 0.00 41.10 2.71
4709 5284 8.644619 GTCGTGTCGCATACATTATATTTATGT 58.355 33.333 7.89 7.89 41.10 2.29
4710 5285 8.860128 AGTCGTGTCGCATACATTATATTTATG 58.140 33.333 0.00 0.00 41.10 1.90
4711 5286 8.860128 CAGTCGTGTCGCATACATTATATTTAT 58.140 33.333 0.00 0.00 41.10 1.40
4712 5287 7.327518 CCAGTCGTGTCGCATACATTATATTTA 59.672 37.037 0.00 0.00 41.10 1.40
4713 5288 6.145534 CCAGTCGTGTCGCATACATTATATTT 59.854 38.462 0.00 0.00 41.10 1.40
4714 5289 5.633601 CCAGTCGTGTCGCATACATTATATT 59.366 40.000 0.00 0.00 41.10 1.28
4715 5290 5.161358 CCAGTCGTGTCGCATACATTATAT 58.839 41.667 0.00 0.00 41.10 0.86
4716 5291 4.037089 ACCAGTCGTGTCGCATACATTATA 59.963 41.667 0.00 0.00 41.10 0.98
4717 5292 3.181479 ACCAGTCGTGTCGCATACATTAT 60.181 43.478 0.00 0.00 41.10 1.28
4718 5293 2.164827 ACCAGTCGTGTCGCATACATTA 59.835 45.455 0.00 0.00 41.10 1.90
4719 5294 1.067142 ACCAGTCGTGTCGCATACATT 60.067 47.619 0.00 0.00 41.10 2.71
4720 5295 0.530744 ACCAGTCGTGTCGCATACAT 59.469 50.000 0.00 0.00 41.10 2.29
4721 5296 0.109458 GACCAGTCGTGTCGCATACA 60.109 55.000 0.00 0.00 35.06 2.29
4722 5297 2.650163 GACCAGTCGTGTCGCATAC 58.350 57.895 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.