Multiple sequence alignment - TraesCS4A01G107400

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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 TraesCS4A01G107400 chr4A 100.000 5487 0 0 1 5487 124204364 124209850 0.000000e+00 10133.0
1 TraesCS4A01G107400 chr4A 100.000 30 0 0 4884 4913 533197361 533197390 7.680000e-04 56.5
2 TraesCS4A01G107400 chr4D 91.697 4962 179 62 1 4881 342091937 342087128 0.000000e+00 6665.0
3 TraesCS4A01G107400 chr4D 95.908 611 23 2 4877 5485 342081843 342081233 0.000000e+00 989.0
4 TraesCS4A01G107400 chr4D 92.405 79 6 0 670 748 342093045 342092967 4.490000e-21 113.0
5 TraesCS4A01G107400 chr4D 100.000 30 0 0 4884 4913 63087128 63087099 7.680000e-04 56.5
6 TraesCS4A01G107400 chr4B 91.121 4494 156 67 589 4955 424290255 424285878 0.000000e+00 5864.0
7 TraesCS4A01G107400 chr4B 95.881 437 17 1 4935 5371 424285222 424284787 0.000000e+00 706.0
8 TraesCS4A01G107400 chr4B 86.702 564 40 16 1 548 424290805 424290261 1.320000e-165 593.0
9 TraesCS4A01G107400 chr4B 95.690 116 5 0 5372 5487 424284689 424284574 2.610000e-43 187.0
10 TraesCS4A01G107400 chr5D 77.820 523 82 23 1 512 448945144 448944645 5.380000e-75 292.0
11 TraesCS4A01G107400 chr5B 81.935 310 46 9 1 306 548450922 548450619 2.540000e-63 254.0
12 TraesCS4A01G107400 chr5B 90.385 52 2 3 4864 4913 610507430 610507380 1.280000e-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 TraesCS4A01G107400 chr4A 124204364 124209850 5486 False 10133.0 10133 100.0000 1 5487 1 chr4A.!!$F1 5486
1 TraesCS4A01G107400 chr4D 342087128 342093045 5917 True 3389.0 6665 92.0510 1 4881 2 chr4D.!!$R3 4880
2 TraesCS4A01G107400 chr4D 342081233 342081843 610 True 989.0 989 95.9080 4877 5485 1 chr4D.!!$R2 608
3 TraesCS4A01G107400 chr4B 424284574 424290805 6231 True 1837.5 5864 92.3485 1 5487 4 chr4B.!!$R1 5486

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
614 1738 0.179150 CAGCTAGACTGCACTCGTCC 60.179 60.0 0.0 0.0 40.19 4.79 F
631 1755 0.320374 TCCGATATCCATCCAACGGC 59.680 55.0 0.0 0.0 40.12 5.68 F
1690 2824 0.323725 TTCCTCAGCCCTTGCATTCC 60.324 55.0 0.0 0.0 41.13 3.01 F
3028 4237 0.039256 TCAAGCTTTTCGGCACATGC 60.039 50.0 0.0 0.0 41.14 4.06 F
3710 4919 0.266152 AAGGGGAGGGACGATGAGAT 59.734 55.0 0.0 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 2836 0.189574 TGCTGCTAGGCTAGGAGGAT 59.810 55.0 34.70 0.0 43.57 3.24 R
2198 3367 0.250770 ACAACGCCCCTTCCTTTCTC 60.251 55.0 0.00 0.0 0.00 2.87 R
3590 4799 0.029433 GAAAATTGCCTCCGCCGATC 59.971 55.0 0.00 0.0 0.00 3.69 R
4007 5242 0.759346 AATCCTACTCATCCCCACGC 59.241 55.0 0.00 0.0 0.00 5.34 R
4896 6190 1.581934 CCGGTGTGCATCGTAATGAT 58.418 50.0 4.11 0.0 38.01 2.45 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
75 1184 3.119009 TGGGCCATTGGATGAAAATCT 57.881 42.857 0.00 0.00 0.00 2.40
90 1199 4.766891 TGAAAATCTGAGGGATGTGGTTTC 59.233 41.667 0.00 0.00 34.45 2.78
91 1200 4.387026 AAATCTGAGGGATGTGGTTTCA 57.613 40.909 0.00 0.00 34.45 2.69
141 1251 8.419076 TTGCAAAATTGTCCTTCTACTTTTTC 57.581 30.769 0.00 0.00 0.00 2.29
142 1252 6.695278 TGCAAAATTGTCCTTCTACTTTTTCG 59.305 34.615 0.00 0.00 0.00 3.46
144 1254 7.434013 GCAAAATTGTCCTTCTACTTTTTCGAA 59.566 33.333 0.00 0.00 0.00 3.71
151 1261 6.427242 GTCCTTCTACTTTTTCGAATGAACCT 59.573 38.462 0.00 0.00 32.71 3.50
172 1282 2.164422 TGCACTCCACATCTTACTCTCG 59.836 50.000 0.00 0.00 0.00 4.04
174 1284 1.751924 ACTCCACATCTTACTCTCGCC 59.248 52.381 0.00 0.00 0.00 5.54
175 1285 1.751351 CTCCACATCTTACTCTCGCCA 59.249 52.381 0.00 0.00 0.00 5.69
176 1286 2.363680 CTCCACATCTTACTCTCGCCAT 59.636 50.000 0.00 0.00 0.00 4.40
177 1287 2.362397 TCCACATCTTACTCTCGCCATC 59.638 50.000 0.00 0.00 0.00 3.51
179 1289 3.430790 CCACATCTTACTCTCGCCATCAA 60.431 47.826 0.00 0.00 0.00 2.57
279 1391 9.077885 TCTGTTTTGGCTATAATCTTTGTTTCT 57.922 29.630 0.00 0.00 0.00 2.52
354 1467 1.593196 TATAGATGTTGCGGCCAAGC 58.407 50.000 2.24 0.00 37.71 4.01
358 1471 2.855728 GATGTTGCGGCCAAGCTTCG 62.856 60.000 2.24 0.00 38.13 3.79
366 1479 0.519077 GGCCAAGCTTCGAAACAGAG 59.481 55.000 0.00 0.00 0.00 3.35
376 1489 7.730364 AGCTTCGAAACAGAGAAATAGAAAA 57.270 32.000 0.00 0.00 0.00 2.29
524 1648 7.786030 TCTACATTTAATGTTGAGAGAGGGAG 58.214 38.462 16.08 3.69 41.63 4.30
549 1673 2.225491 GTGTAGTGCGGCTTGATTTTGA 59.775 45.455 0.00 0.00 0.00 2.69
552 1676 3.764885 AGTGCGGCTTGATTTTGATAC 57.235 42.857 0.00 0.00 0.00 2.24
608 1732 2.871022 CCATTCATCAGCTAGACTGCAC 59.129 50.000 8.72 0.00 46.76 4.57
614 1738 0.179150 CAGCTAGACTGCACTCGTCC 60.179 60.000 0.00 0.00 40.19 4.79
631 1755 0.320374 TCCGATATCCATCCAACGGC 59.680 55.000 0.00 0.00 40.12 5.68
643 1767 0.377203 CCAACGGCCGAAAATAGCTC 59.623 55.000 35.90 0.00 0.00 4.09
793 1918 4.475135 GTGCCGCTTCCTCCCTCC 62.475 72.222 0.00 0.00 0.00 4.30
862 1987 2.677003 AAATTCGCGTCCGCCACTG 61.677 57.895 5.77 0.00 37.98 3.66
896 2021 2.260822 ACCAGGCTACAATCAGACAGT 58.739 47.619 0.00 0.00 0.00 3.55
978 2112 4.537433 GCTGCGGCTAGGGAGGTG 62.537 72.222 11.21 0.00 35.22 4.00
979 2113 3.077556 CTGCGGCTAGGGAGGTGT 61.078 66.667 0.00 0.00 0.00 4.16
1246 2380 4.864334 CCATGGACCGGAGCCTGC 62.864 72.222 9.46 0.00 0.00 4.85
1470 2604 4.873129 CGCGACACGGGGATCCTG 62.873 72.222 12.58 7.36 38.44 3.86
1485 2619 2.264794 CTGTACCGCCACCTGACC 59.735 66.667 0.00 0.00 0.00 4.02
1690 2824 0.323725 TTCCTCAGCCCTTGCATTCC 60.324 55.000 0.00 0.00 41.13 3.01
1698 2832 2.280079 CTTGCATTCCCCCTCCCC 59.720 66.667 0.00 0.00 0.00 4.81
1709 2843 4.888325 CCTCCCCCGCATCCTCCT 62.888 72.222 0.00 0.00 0.00 3.69
1710 2844 2.201490 CTCCCCCGCATCCTCCTA 59.799 66.667 0.00 0.00 0.00 2.94
1711 2845 1.910772 CTCCCCCGCATCCTCCTAG 60.911 68.421 0.00 0.00 0.00 3.02
1712 2846 3.631046 CCCCCGCATCCTCCTAGC 61.631 72.222 0.00 0.00 0.00 3.42
1713 2847 3.631046 CCCCGCATCCTCCTAGCC 61.631 72.222 0.00 0.00 0.00 3.93
1714 2848 2.525381 CCCGCATCCTCCTAGCCT 60.525 66.667 0.00 0.00 0.00 4.58
1761 2895 5.734855 TCACTCGAGGAAAACAAGAAAAG 57.265 39.130 18.41 0.00 0.00 2.27
1781 2915 0.932399 CTTTTGCCTTGTGTTGCTGC 59.068 50.000 0.00 0.00 0.00 5.25
1782 2916 0.805322 TTTTGCCTTGTGTTGCTGCG 60.805 50.000 0.00 0.00 0.00 5.18
1783 2917 1.661498 TTTGCCTTGTGTTGCTGCGA 61.661 50.000 0.00 0.00 0.00 5.10
1784 2918 2.062361 TTGCCTTGTGTTGCTGCGAG 62.062 55.000 0.00 0.00 0.00 5.03
1785 2919 2.253452 CCTTGTGTTGCTGCGAGC 59.747 61.111 0.00 1.70 42.82 5.03
1992 3135 0.543277 GCCATGTGATGTGAGGAGGA 59.457 55.000 0.00 0.00 0.00 3.71
1993 3136 1.474677 GCCATGTGATGTGAGGAGGAG 60.475 57.143 0.00 0.00 0.00 3.69
1995 3138 2.113807 CATGTGATGTGAGGAGGAGGA 58.886 52.381 0.00 0.00 0.00 3.71
1996 3139 1.857965 TGTGATGTGAGGAGGAGGAG 58.142 55.000 0.00 0.00 0.00 3.69
2078 3221 3.402681 AGGCCTGCGCTGTACCAT 61.403 61.111 20.64 7.62 34.44 3.55
2079 3222 2.063979 AGGCCTGCGCTGTACCATA 61.064 57.895 20.64 0.00 34.44 2.74
2080 3223 1.887707 GGCCTGCGCTGTACCATAC 60.888 63.158 9.73 0.00 34.44 2.39
2201 3370 4.670199 CCAATGGCAGGCATGAGA 57.330 55.556 10.84 0.00 0.00 3.27
2206 3375 0.627451 ATGGCAGGCATGAGAAAGGA 59.373 50.000 9.06 0.00 0.00 3.36
2207 3376 0.405198 TGGCAGGCATGAGAAAGGAA 59.595 50.000 0.62 0.00 0.00 3.36
2208 3377 1.101331 GGCAGGCATGAGAAAGGAAG 58.899 55.000 0.62 0.00 0.00 3.46
2210 3379 1.760192 CAGGCATGAGAAAGGAAGGG 58.240 55.000 0.00 0.00 0.00 3.95
2211 3380 0.627986 AGGCATGAGAAAGGAAGGGG 59.372 55.000 0.00 0.00 0.00 4.79
2212 3381 1.039785 GGCATGAGAAAGGAAGGGGC 61.040 60.000 0.00 0.00 0.00 5.80
2275 3444 0.609662 GCACCCCTCAACTAACGGTA 59.390 55.000 0.00 0.00 0.00 4.02
2469 3667 2.681848 CTGTTATTTCCAGGCTGCTGAG 59.318 50.000 9.56 0.00 0.00 3.35
2511 3709 0.378962 TGGTTTTGTTCAGTTCGCCG 59.621 50.000 0.00 0.00 0.00 6.46
2528 3727 1.200252 GCCGAAAAGGAAAGGAAGAGC 59.800 52.381 0.00 0.00 45.00 4.09
2561 3763 8.963130 CGTCAGATCAATTCTACTATTGTCTTC 58.037 37.037 0.00 0.00 36.95 2.87
2565 3767 9.323985 AGATCAATTCTACTATTGTCTTCTTGC 57.676 33.333 0.00 0.00 36.95 4.01
2583 3785 3.063510 TGCTTCTGATTCTTGACCCTG 57.936 47.619 0.00 0.00 0.00 4.45
2590 3792 2.079925 GATTCTTGACCCTGTGCAGTC 58.920 52.381 0.00 0.00 0.00 3.51
2593 3795 0.668706 CTTGACCCTGTGCAGTCTCG 60.669 60.000 5.54 0.00 34.02 4.04
2626 3828 4.259356 ACTCGGTTTACTCCTATTTTGGC 58.741 43.478 0.00 0.00 0.00 4.52
2652 3854 1.947456 TCGTAGTATCTGCAGCATCGT 59.053 47.619 9.47 0.00 0.00 3.73
2671 3873 1.997606 GTTCCCGTCGTGTTAGATTGG 59.002 52.381 0.00 0.00 0.00 3.16
2736 3938 5.049680 CGGCAGTACTACTCAATTTGTTTGT 60.050 40.000 0.00 0.00 36.65 2.83
2758 3960 7.379098 TGTGCAGTTCTCCGAGTATATATAG 57.621 40.000 0.00 0.00 0.00 1.31
2759 3961 6.374613 TGTGCAGTTCTCCGAGTATATATAGG 59.625 42.308 0.00 0.00 0.00 2.57
2761 3963 5.591067 GCAGTTCTCCGAGTATATATAGGCT 59.409 44.000 0.00 0.00 0.00 4.58
2846 4055 4.036971 ACGTCTAGCATAGTTAGGCAGAAG 59.963 45.833 0.00 4.74 40.38 2.85
2937 4146 4.396166 ACATGCTTAATCACCAGTACAAGC 59.604 41.667 0.00 0.00 39.02 4.01
2962 4171 7.141363 CACCATATTTAGCAAGCCACTAATTC 58.859 38.462 0.00 0.00 30.07 2.17
2996 4205 0.465705 ATGACATGGACGCCCTACTG 59.534 55.000 0.00 0.00 0.00 2.74
3027 4236 2.420628 TTCAAGCTTTTCGGCACATG 57.579 45.000 0.00 0.00 34.17 3.21
3028 4237 0.039256 TCAAGCTTTTCGGCACATGC 60.039 50.000 0.00 0.00 41.14 4.06
3029 4238 0.318869 CAAGCTTTTCGGCACATGCA 60.319 50.000 6.15 0.00 44.36 3.96
3030 4239 0.318955 AAGCTTTTCGGCACATGCAC 60.319 50.000 6.15 0.00 44.36 4.57
3062 4271 7.497909 CCGTTTCCACCATCTAAATATTGTAGT 59.502 37.037 0.00 0.00 0.00 2.73
3063 4272 9.537192 CGTTTCCACCATCTAAATATTGTAGTA 57.463 33.333 0.00 0.00 0.00 1.82
3065 4274 9.555727 TTTCCACCATCTAAATATTGTAGTAGC 57.444 33.333 0.00 0.00 0.00 3.58
3389 4598 0.321996 GACAAGTCCCAGGTCAGTCC 59.678 60.000 0.00 0.00 0.00 3.85
3423 4632 1.061131 CATTGCGCAGTACAGTACAGC 59.939 52.381 16.26 16.26 37.77 4.40
3544 4753 4.418392 GGAACTAACAGCAAGCATTCATG 58.582 43.478 0.00 0.00 0.00 3.07
3546 4755 5.458041 AACTAACAGCAAGCATTCATGTT 57.542 34.783 0.00 0.00 37.49 2.71
3548 4757 4.520111 ACTAACAGCAAGCATTCATGTTGA 59.480 37.500 6.82 0.00 35.36 3.18
3592 4801 2.513897 GCGGCTGCGGGTTTAGAT 60.514 61.111 0.00 0.00 0.00 1.98
3593 4802 2.534903 GCGGCTGCGGGTTTAGATC 61.535 63.158 0.00 0.00 0.00 2.75
3594 4803 2.237751 CGGCTGCGGGTTTAGATCG 61.238 63.158 0.00 0.00 0.00 3.69
3595 4804 1.887707 GGCTGCGGGTTTAGATCGG 60.888 63.158 0.00 0.00 0.00 4.18
3596 4805 2.534903 GCTGCGGGTTTAGATCGGC 61.535 63.158 0.00 0.00 0.00 5.54
3629 4838 2.690778 GCCATGAAAGCGGCGTCTT 61.691 57.895 9.37 9.80 38.82 3.01
3640 4849 3.426568 GCGTCTTGCCCTGTCTGC 61.427 66.667 0.00 0.00 37.76 4.26
3641 4850 2.345244 CGTCTTGCCCTGTCTGCT 59.655 61.111 0.00 0.00 0.00 4.24
3642 4851 1.591703 CGTCTTGCCCTGTCTGCTA 59.408 57.895 0.00 0.00 0.00 3.49
3643 4852 0.459237 CGTCTTGCCCTGTCTGCTAG 60.459 60.000 0.00 0.00 33.68 3.42
3696 4905 2.863988 AGGTGGGGTTGGAAGGGG 60.864 66.667 0.00 0.00 0.00 4.79
3697 4906 2.861974 GGTGGGGTTGGAAGGGGA 60.862 66.667 0.00 0.00 0.00 4.81
3699 4908 2.534272 TGGGGTTGGAAGGGGAGG 60.534 66.667 0.00 0.00 0.00 4.30
3700 4909 3.347590 GGGGTTGGAAGGGGAGGG 61.348 72.222 0.00 0.00 0.00 4.30
3701 4910 2.204244 GGGTTGGAAGGGGAGGGA 60.204 66.667 0.00 0.00 0.00 4.20
3702 4911 2.613482 GGGTTGGAAGGGGAGGGAC 61.613 68.421 0.00 0.00 0.00 4.46
3710 4919 0.266152 AAGGGGAGGGACGATGAGAT 59.734 55.000 0.00 0.00 0.00 2.75
3712 4921 0.470080 GGGGAGGGACGATGAGATGA 60.470 60.000 0.00 0.00 0.00 2.92
3713 4922 0.965439 GGGAGGGACGATGAGATGAG 59.035 60.000 0.00 0.00 0.00 2.90
3714 4923 1.479573 GGGAGGGACGATGAGATGAGA 60.480 57.143 0.00 0.00 0.00 3.27
3715 4924 2.311463 GGAGGGACGATGAGATGAGAA 58.689 52.381 0.00 0.00 0.00 2.87
3716 4925 2.295909 GGAGGGACGATGAGATGAGAAG 59.704 54.545 0.00 0.00 0.00 2.85
3749 4961 0.536460 TCTGTCCCAACTTTTCCGGC 60.536 55.000 0.00 0.00 0.00 6.13
3792 5004 5.227805 CGTCCTTCAATTTCGCATAAACATG 59.772 40.000 0.00 0.00 0.00 3.21
3822 5039 1.407437 CCCTCCTTCGTTTCATCAGGG 60.407 57.143 0.00 0.00 33.36 4.45
3828 5045 5.076873 TCCTTCGTTTCATCAGGGAAATTT 58.923 37.500 0.00 0.00 38.86 1.82
3829 5046 5.048083 TCCTTCGTTTCATCAGGGAAATTTG 60.048 40.000 0.00 0.00 38.86 2.32
3830 5047 4.173036 TCGTTTCATCAGGGAAATTTGC 57.827 40.909 0.22 0.22 38.86 3.68
3833 5050 4.749099 CGTTTCATCAGGGAAATTTGCAAA 59.251 37.500 15.44 15.44 38.86 3.68
3836 5071 6.616774 TTCATCAGGGAAATTTGCAAAAAC 57.383 33.333 17.19 10.12 0.00 2.43
4082 5330 2.029288 CCACAGCACCAGCAGTACG 61.029 63.158 0.00 0.00 45.49 3.67
4090 5338 2.582498 CAGCAGTACGGCCGTAGC 60.582 66.667 37.18 33.92 38.76 3.58
4258 5516 3.072211 CTCTGTAATGCGATGATGCCAT 58.928 45.455 0.00 0.00 35.29 4.40
4274 5532 2.634453 TGCCATGACGACCTATGATGAT 59.366 45.455 0.00 0.00 0.00 2.45
4312 5570 6.603095 CCAGAGCTAACATGTTTTCTTGTAC 58.397 40.000 17.78 2.86 37.23 2.90
4313 5571 6.204688 CCAGAGCTAACATGTTTTCTTGTACA 59.795 38.462 17.78 0.00 37.23 2.90
4387 5645 2.834638 ATAGCAAGGTGAAGGGCATT 57.165 45.000 0.00 0.00 0.00 3.56
4488 5747 3.502488 CCGGGGAATAAGAGGAGGTAGAT 60.502 52.174 0.00 0.00 0.00 1.98
4510 5769 3.948473 TGGGAGAGTTGTAGAAGAGATCG 59.052 47.826 0.00 0.00 0.00 3.69
4824 6111 5.640189 AGAATGAAATGAACAGAAGGCAG 57.360 39.130 0.00 0.00 0.00 4.85
4825 6112 5.319453 AGAATGAAATGAACAGAAGGCAGA 58.681 37.500 0.00 0.00 0.00 4.26
4826 6113 5.182760 AGAATGAAATGAACAGAAGGCAGAC 59.817 40.000 0.00 0.00 0.00 3.51
4827 6114 3.819368 TGAAATGAACAGAAGGCAGACA 58.181 40.909 0.00 0.00 0.00 3.41
4828 6115 4.401022 TGAAATGAACAGAAGGCAGACAT 58.599 39.130 0.00 0.00 0.00 3.06
4833 6125 3.244526 TGAACAGAAGGCAGACATAAGCA 60.245 43.478 0.00 0.00 0.00 3.91
4845 6137 6.475076 GGCAGACATAAGCAGAAGATATATCG 59.525 42.308 7.08 0.00 0.00 2.92
4896 6190 1.695239 ATCATCCCTGGCCTCTGCA 60.695 57.895 3.32 0.00 40.13 4.41
4964 6935 7.500892 TGCTTGAACTGAAGTTACCAAAGAATA 59.499 33.333 0.00 0.00 38.56 1.75
4967 6938 9.793259 TTGAACTGAAGTTACCAAAGAATATCT 57.207 29.630 0.00 0.00 38.56 1.98
5041 7012 0.324923 ACGTACCCTGCCCTATGTGA 60.325 55.000 0.00 0.00 0.00 3.58
5188 7160 1.215647 GTGGCCAGTGGAGTAGACG 59.784 63.158 15.20 0.00 0.00 4.18
5320 7292 3.197983 AGCTAGTCATGTGGTAGGGTTTC 59.802 47.826 0.00 0.00 0.00 2.78
5321 7293 3.197983 GCTAGTCATGTGGTAGGGTTTCT 59.802 47.826 0.00 0.00 0.00 2.52
5398 7467 2.063266 GCATGCTGTTGGTGATTTGTG 58.937 47.619 11.37 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 1122 1.398390 GCACAGATTAGCCCGTTTCAG 59.602 52.381 0.00 0.00 0.00 3.02
47 1156 2.021262 TCCAATGGCCCAAAATCACA 57.979 45.000 0.00 0.00 0.00 3.58
75 1184 3.516586 TCTAGTGAAACCACATCCCTCA 58.483 45.455 0.00 0.00 37.80 3.86
90 1199 5.221028 TGTGCCAACAATTCACTTTCTAGTG 60.221 40.000 0.00 0.00 42.36 2.74
91 1200 4.887071 TGTGCCAACAATTCACTTTCTAGT 59.113 37.500 0.00 0.00 31.82 2.57
134 1243 3.632145 AGTGCAGGTTCATTCGAAAAAGT 59.368 39.130 0.00 0.00 31.43 2.66
141 1251 0.798776 GTGGAGTGCAGGTTCATTCG 59.201 55.000 0.00 0.00 0.00 3.34
142 1252 1.896220 TGTGGAGTGCAGGTTCATTC 58.104 50.000 0.00 0.00 0.00 2.67
144 1254 1.632409 AGATGTGGAGTGCAGGTTCAT 59.368 47.619 0.00 0.00 0.00 2.57
151 1261 2.164422 CGAGAGTAAGATGTGGAGTGCA 59.836 50.000 0.00 0.00 0.00 4.57
228 1340 8.986929 ATCTGAATTTAGACATTCCCCTAAAG 57.013 34.615 1.44 0.00 38.00 1.85
233 1345 6.360618 ACAGATCTGAATTTAGACATTCCCC 58.639 40.000 29.27 0.00 32.86 4.81
234 1346 7.872113 AACAGATCTGAATTTAGACATTCCC 57.128 36.000 29.27 0.00 32.86 3.97
240 1352 7.150783 AGCCAAAACAGATCTGAATTTAGAC 57.849 36.000 29.27 17.97 0.00 2.59
250 1362 8.814038 ACAAAGATTATAGCCAAAACAGATCT 57.186 30.769 0.00 0.00 0.00 2.75
281 1393 9.745018 AATATTGTTCTTCTTCCAAAGATCTCA 57.255 29.630 0.00 0.00 37.38 3.27
321 1433 6.261826 GCAACATCTATAAGCTCCAAGTCATT 59.738 38.462 0.00 0.00 0.00 2.57
463 1576 0.179020 TCAAGCATAGGAATGGCCGG 60.179 55.000 0.00 0.00 43.43 6.13
524 1648 0.391130 TCAAGCCGCACTACACCATC 60.391 55.000 0.00 0.00 0.00 3.51
549 1673 2.674852 CAACAATGCTCTCACGCAGTAT 59.325 45.455 0.00 0.00 41.61 2.12
552 1676 3.670500 CAACAATGCTCTCACGCAG 57.330 52.632 0.00 0.00 44.10 5.18
608 1732 2.668556 CGTTGGATGGATATCGGACGAG 60.669 54.545 0.00 0.00 41.10 4.18
614 1738 1.014044 CGGCCGTTGGATGGATATCG 61.014 60.000 19.50 0.00 33.98 2.92
650 1774 2.254459 CATCGACTCTATATGCACGGC 58.746 52.381 0.00 0.00 0.00 5.68
664 1788 2.033448 TGCCCCAACCACATCGAC 59.967 61.111 0.00 0.00 0.00 4.20
862 1987 4.752879 TGGTTAGGCAGCGGCGAC 62.753 66.667 12.98 1.23 42.47 5.19
896 2021 1.373748 GCCGTGTCGTAGCCAGAAA 60.374 57.895 0.00 0.00 0.00 2.52
977 2111 2.520020 AGACCACCACCGACGACA 60.520 61.111 0.00 0.00 0.00 4.35
978 2112 2.049433 CAGACCACCACCGACGAC 60.049 66.667 0.00 0.00 0.00 4.34
979 2113 3.986006 GCAGACCACCACCGACGA 61.986 66.667 0.00 0.00 0.00 4.20
1192 2326 2.954753 CTTGCGGCGTCTTCACCAC 61.955 63.158 9.37 0.00 0.00 4.16
1311 2445 2.402787 GTAGGCGTCGACTCGGTC 59.597 66.667 14.70 0.00 0.00 4.79
1470 2604 1.252904 TGTAGGTCAGGTGGCGGTAC 61.253 60.000 0.00 0.00 0.00 3.34
1485 2619 2.338500 GCCGTGAAGTTCTCCTTGTAG 58.662 52.381 4.17 0.00 32.03 2.74
1698 2832 1.882989 GCTAGGCTAGGAGGATGCGG 61.883 65.000 22.40 0.00 0.00 5.69
1702 2836 0.189574 TGCTGCTAGGCTAGGAGGAT 59.810 55.000 34.70 0.00 43.57 3.24
1709 2843 3.417069 TTTCACTTTGCTGCTAGGCTA 57.583 42.857 0.00 0.00 0.00 3.93
1710 2844 2.276732 TTTCACTTTGCTGCTAGGCT 57.723 45.000 0.00 0.00 0.00 4.58
1711 2845 3.369546 TTTTTCACTTTGCTGCTAGGC 57.630 42.857 0.00 0.00 0.00 3.93
1761 2895 0.932399 CAGCAACACAAGGCAAAAGC 59.068 50.000 0.00 0.00 0.00 3.51
1854 2997 0.895559 GTTGCTTGCAACTAGCCCCT 60.896 55.000 25.56 0.00 44.83 4.79
1855 2998 0.895559 AGTTGCTTGCAACTAGCCCC 60.896 55.000 31.61 9.82 42.92 5.80
1992 3135 2.284995 GAGGGTGAGTGGCCTCCT 60.285 66.667 3.32 0.00 36.86 3.69
1993 3136 3.403558 GGAGGGTGAGTGGCCTCC 61.404 72.222 3.32 0.00 41.38 4.30
2041 3184 0.977627 GGCAGGGGAAAAGAATGGGG 60.978 60.000 0.00 0.00 0.00 4.96
2078 3221 4.223953 GAGATCCATCCCAAGTGGTAGTA 58.776 47.826 0.00 0.00 37.96 1.82
2079 3222 3.041946 GAGATCCATCCCAAGTGGTAGT 58.958 50.000 0.00 0.00 37.96 2.73
2080 3223 2.370189 GGAGATCCATCCCAAGTGGTAG 59.630 54.545 0.00 0.00 37.96 3.18
2198 3367 0.250770 ACAACGCCCCTTCCTTTCTC 60.251 55.000 0.00 0.00 0.00 2.87
2201 3370 1.744320 GCAACAACGCCCCTTCCTTT 61.744 55.000 0.00 0.00 0.00 3.11
2206 3375 1.964373 CTACGCAACAACGCCCCTT 60.964 57.895 0.00 0.00 36.19 3.95
2207 3376 2.358247 CTACGCAACAACGCCCCT 60.358 61.111 0.00 0.00 36.19 4.79
2208 3377 3.428282 CCTACGCAACAACGCCCC 61.428 66.667 0.00 0.00 36.19 5.80
2210 3379 1.373748 TCTCCTACGCAACAACGCC 60.374 57.895 0.00 0.00 36.19 5.68
2211 3380 1.779683 GTCTCCTACGCAACAACGC 59.220 57.895 0.00 0.00 36.19 4.84
2212 3381 2.059575 CGTCTCCTACGCAACAACG 58.940 57.895 0.00 0.00 46.10 4.10
2511 3709 4.257731 AGATCGCTCTTCCTTTCCTTTTC 58.742 43.478 0.00 0.00 0.00 2.29
2545 3744 8.535335 TCAGAAGCAAGAAGACAATAGTAGAAT 58.465 33.333 0.00 0.00 0.00 2.40
2561 3763 3.439476 CAGGGTCAAGAATCAGAAGCAAG 59.561 47.826 0.00 0.00 0.00 4.01
2565 3767 2.746362 GCACAGGGTCAAGAATCAGAAG 59.254 50.000 0.00 0.00 0.00 2.85
2590 3792 2.101770 GAGTAACCGACGGGCGAG 59.898 66.667 20.00 0.00 44.57 5.03
2626 3828 6.237411 CGATGCTGCAGATACTACGAATATTG 60.237 42.308 20.43 0.00 0.00 1.90
2652 3854 1.619827 ACCAATCTAACACGACGGGAA 59.380 47.619 2.90 0.00 0.00 3.97
2671 3873 4.274459 CCACTAATGCAGGAGATTGCTAAC 59.726 45.833 4.72 0.00 44.38 2.34
2736 3938 5.357314 GCCTATATATACTCGGAGAACTGCA 59.643 44.000 12.86 0.00 34.09 4.41
2758 3960 7.713734 TGGACATACTATATAAGTACCAGCC 57.286 40.000 0.00 0.00 43.47 4.85
2759 3961 9.804758 GATTGGACATACTATATAAGTACCAGC 57.195 37.037 0.00 0.00 43.47 4.85
2866 4075 4.103357 GCATGCAGTTTCTGAAGCATTAG 58.897 43.478 14.21 5.05 44.63 1.73
2937 4146 6.639632 ATTAGTGGCTTGCTAAATATGGTG 57.360 37.500 0.00 0.00 32.92 4.17
2996 4205 3.930634 AAGCTTGAAAAGATGCTGGTC 57.069 42.857 0.00 0.00 45.10 4.02
3062 4271 6.513180 CGTTAGAGGTTTGGATTAGATGCTA 58.487 40.000 0.00 0.00 0.00 3.49
3063 4272 5.360591 CGTTAGAGGTTTGGATTAGATGCT 58.639 41.667 0.00 0.00 0.00 3.79
3064 4273 4.024809 GCGTTAGAGGTTTGGATTAGATGC 60.025 45.833 0.00 0.00 0.00 3.91
3065 4274 4.209288 CGCGTTAGAGGTTTGGATTAGATG 59.791 45.833 0.00 0.00 0.00 2.90
3078 4287 2.853731 ACAGATTCTCGCGTTAGAGG 57.146 50.000 5.77 0.00 38.71 3.69
3201 4410 2.581354 CAGCCGAGGACCTTGGAG 59.419 66.667 29.72 17.35 37.20 3.86
3279 4488 0.526524 GGACGTCAATCTCAGGCGAG 60.527 60.000 18.91 0.77 40.98 5.03
3285 4494 1.080093 GCCGTGGACGTCAATCTCA 60.080 57.895 18.91 2.27 37.74 3.27
3389 4598 1.135315 CGCAATGAAGGGTTGATGGTG 60.135 52.381 0.00 0.00 0.00 4.17
3423 4632 2.188524 CTACTGCTACTGCGATGTGTG 58.811 52.381 0.00 0.00 43.34 3.82
3512 4721 0.693622 TGTTAGTTCCGGGGAATGCA 59.306 50.000 0.00 0.00 36.45 3.96
3514 4723 1.339631 TGCTGTTAGTTCCGGGGAATG 60.340 52.381 0.00 0.00 36.45 2.67
3515 4724 0.988832 TGCTGTTAGTTCCGGGGAAT 59.011 50.000 0.00 0.00 36.45 3.01
3516 4725 0.766131 TTGCTGTTAGTTCCGGGGAA 59.234 50.000 0.00 0.00 0.00 3.97
3517 4726 0.323629 CTTGCTGTTAGTTCCGGGGA 59.676 55.000 0.00 0.00 0.00 4.81
3518 4727 1.305930 GCTTGCTGTTAGTTCCGGGG 61.306 60.000 0.00 0.00 0.00 5.73
3544 4753 4.007940 TGCCGCGCGAAAGTCAAC 62.008 61.111 34.63 10.03 0.00 3.18
3585 4794 0.461339 TTGCCTCCGCCGATCTAAAC 60.461 55.000 0.00 0.00 0.00 2.01
3586 4795 0.468226 ATTGCCTCCGCCGATCTAAA 59.532 50.000 0.00 0.00 0.00 1.85
3587 4796 0.468226 AATTGCCTCCGCCGATCTAA 59.532 50.000 0.00 0.00 0.00 2.10
3588 4797 0.468226 AAATTGCCTCCGCCGATCTA 59.532 50.000 0.00 0.00 0.00 1.98
3589 4798 0.394352 AAAATTGCCTCCGCCGATCT 60.394 50.000 0.00 0.00 0.00 2.75
3590 4799 0.029433 GAAAATTGCCTCCGCCGATC 59.971 55.000 0.00 0.00 0.00 3.69
3591 4800 1.384222 GGAAAATTGCCTCCGCCGAT 61.384 55.000 0.00 0.00 0.00 4.18
3592 4801 2.043980 GGAAAATTGCCTCCGCCGA 61.044 57.895 0.00 0.00 0.00 5.54
3593 4802 2.489751 GGAAAATTGCCTCCGCCG 59.510 61.111 0.00 0.00 0.00 6.46
3629 4838 0.614697 TAGCACTAGCAGACAGGGCA 60.615 55.000 0.00 0.00 45.23 5.36
3696 4905 2.295909 CCTTCTCATCTCATCGTCCCTC 59.704 54.545 0.00 0.00 0.00 4.30
3697 4906 2.315176 CCTTCTCATCTCATCGTCCCT 58.685 52.381 0.00 0.00 0.00 4.20
3699 4908 1.270041 GGCCTTCTCATCTCATCGTCC 60.270 57.143 0.00 0.00 0.00 4.79
3700 4909 1.686052 AGGCCTTCTCATCTCATCGTC 59.314 52.381 0.00 0.00 0.00 4.20
3701 4910 1.686052 GAGGCCTTCTCATCTCATCGT 59.314 52.381 6.77 0.00 42.02 3.73
3702 4911 1.335780 CGAGGCCTTCTCATCTCATCG 60.336 57.143 6.77 0.00 42.55 3.84
3749 4961 2.043411 CGCGTGACAAGTTGAATTTGG 58.957 47.619 10.54 0.00 0.00 3.28
4007 5242 0.759346 AATCCTACTCATCCCCACGC 59.241 55.000 0.00 0.00 0.00 5.34
4047 5282 3.601685 GCCAACCACCAACACCGG 61.602 66.667 0.00 0.00 0.00 5.28
4090 5338 3.679389 CATTAGCTATTAGCCAGGGGTG 58.321 50.000 12.05 0.45 43.77 4.61
4312 5570 2.222886 CGAGTCCTGCGAAACAATGATG 60.223 50.000 0.00 0.00 0.00 3.07
4313 5571 2.002586 CGAGTCCTGCGAAACAATGAT 58.997 47.619 0.00 0.00 0.00 2.45
4488 5747 3.948473 CGATCTCTTCTACAACTCTCCCA 59.052 47.826 0.00 0.00 0.00 4.37
4510 5769 3.207354 TCGGCTCTTGGATCCGAC 58.793 61.111 7.39 0.00 43.82 4.79
4752 6039 7.284074 TGTAATCACCTAAACCTCTTGAAACA 58.716 34.615 0.00 0.00 0.00 2.83
4824 6111 8.165428 GCAAACGATATATCTTCTGCTTATGTC 58.835 37.037 9.62 0.00 0.00 3.06
4825 6112 7.875041 AGCAAACGATATATCTTCTGCTTATGT 59.125 33.333 12.89 0.00 35.44 2.29
4826 6113 8.249327 AGCAAACGATATATCTTCTGCTTATG 57.751 34.615 12.89 2.06 35.44 1.90
4827 6114 8.310382 AGAGCAAACGATATATCTTCTGCTTAT 58.690 33.333 18.10 9.76 38.92 1.73
4828 6115 7.661968 AGAGCAAACGATATATCTTCTGCTTA 58.338 34.615 18.10 0.00 38.92 3.09
4833 6125 8.630054 AGTAGAGAGCAAACGATATATCTTCT 57.370 34.615 10.93 4.40 0.00 2.85
4896 6190 1.581934 CCGGTGTGCATCGTAATGAT 58.418 50.000 4.11 0.00 38.01 2.45
4964 6935 7.295672 TGTTCAATCCCCCTATGAGAATTAGAT 59.704 37.037 0.00 0.00 0.00 1.98
4967 6938 6.840090 TGTTCAATCCCCCTATGAGAATTA 57.160 37.500 0.00 0.00 0.00 1.40
5054 7025 3.763897 ACCCTTGTGTCTTAATGAATGGC 59.236 43.478 0.00 0.00 0.00 4.40
5080 7051 2.475666 GCAAGGAAGCTGCTCGATT 58.524 52.632 1.00 0.00 36.84 3.34
5398 7467 2.088950 TAACCTACCAACAAGCTCGC 57.911 50.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.