Multiple sequence alignment - TraesCS3B01G302400

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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 TraesCS3B01G302400 chr3B 100.000 4446 0 0 1 4446 486384106 486379661 0.000000e+00 8211.0
1 TraesCS3B01G302400 chr3D 94.995 2158 75 12 580 2716 372319950 372317805 0.000000e+00 3356.0
2 TraesCS3B01G302400 chr3D 92.844 1076 38 8 2741 3793 372317812 372316753 0.000000e+00 1524.0
3 TraesCS3B01G302400 chr3D 92.882 576 40 1 1 575 447611168 447610593 0.000000e+00 835.0
4 TraesCS3B01G302400 chr3D 87.121 396 38 12 3796 4185 372316710 372316322 1.900000e-118 436.0
5 TraesCS3B01G302400 chr3D 88.211 246 13 8 4205 4444 372316333 372316098 3.390000e-71 279.0
6 TraesCS3B01G302400 chr3A 91.937 1141 47 16 578 1701 493717082 493715970 0.000000e+00 1555.0
7 TraesCS3B01G302400 chr3A 93.509 647 28 4 2893 3538 493715573 493714940 0.000000e+00 950.0
8 TraesCS3B01G302400 chr3A 87.547 265 23 6 3537 3795 493714848 493714588 9.350000e-77 298.0
9 TraesCS3B01G302400 chr3A 90.043 231 16 2 2486 2716 493715931 493715708 4.350000e-75 292.0
10 TraesCS3B01G302400 chr3A 97.674 43 1 0 2824 2866 493715612 493715570 1.720000e-09 75.0
11 TraesCS3B01G302400 chr3A 91.111 45 1 2 4015 4059 493713931 493713890 1.730000e-04 58.4
12 TraesCS3B01G302400 chr7D 94.454 577 31 1 1 576 411019760 411020336 0.000000e+00 887.0
13 TraesCS3B01G302400 chr5D 94.356 567 31 1 9 574 321856459 321855893 0.000000e+00 869.0
14 TraesCS3B01G302400 chr5D 84.762 105 11 5 1779 1883 5804049 5804148 2.830000e-17 100.0
15 TraesCS3B01G302400 chr5D 84.848 99 12 3 1785 1881 354502065 354501968 3.660000e-16 97.1
16 TraesCS3B01G302400 chr6D 92.870 575 40 1 1 574 389531597 389532171 0.000000e+00 833.0
17 TraesCS3B01G302400 chr6D 85.589 569 70 11 1 564 249457227 249457788 1.780000e-163 586.0
18 TraesCS3B01G302400 chr2A 92.509 574 39 2 1 573 535707769 535708339 0.000000e+00 819.0
19 TraesCS3B01G302400 chr2A 87.215 571 66 6 5 572 715208105 715208671 1.040000e-180 643.0
20 TraesCS3B01G302400 chr7B 85.540 574 71 10 5 573 413111580 413112146 1.380000e-164 590.0
21 TraesCS3B01G302400 chr7B 85.147 579 74 12 1 574 616639783 616639212 2.300000e-162 582.0
22 TraesCS3B01G302400 chr7B 87.778 90 11 0 1793 1882 454616746 454616835 6.080000e-19 106.0
23 TraesCS3B01G302400 chr6B 92.623 122 8 1 3796 3916 6050521 6050642 1.640000e-39 174.0
24 TraesCS3B01G302400 chr2D 94.253 87 5 0 1797 1883 595166405 595166491 2.790000e-27 134.0
25 TraesCS3B01G302400 chr4B 89.873 79 7 1 1793 1871 670403337 670403260 2.830000e-17 100.0
26 TraesCS3B01G302400 chr4A 87.356 87 11 0 1795 1881 187263715 187263801 2.830000e-17 100.0
27 TraesCS3B01G302400 chr4A 91.429 70 5 1 1797 1865 4626027 4626096 1.320000e-15 95.3
28 TraesCS3B01G302400 chr1B 87.356 87 10 1 1796 1882 380693386 380693301 1.020000e-16 99.0


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 TraesCS3B01G302400 chr3B 486379661 486384106 4445 True 8211.000000 8211 100.000000 1 4446 1 chr3B.!!$R1 4445
1 TraesCS3B01G302400 chr3D 372316098 372319950 3852 True 1398.750000 3356 90.792750 580 4444 4 chr3D.!!$R2 3864
2 TraesCS3B01G302400 chr3D 447610593 447611168 575 True 835.000000 835 92.882000 1 575 1 chr3D.!!$R1 574
3 TraesCS3B01G302400 chr3A 493713890 493717082 3192 True 538.066667 1555 91.970167 578 4059 6 chr3A.!!$R1 3481
4 TraesCS3B01G302400 chr7D 411019760 411020336 576 False 887.000000 887 94.454000 1 576 1 chr7D.!!$F1 575
5 TraesCS3B01G302400 chr5D 321855893 321856459 566 True 869.000000 869 94.356000 9 574 1 chr5D.!!$R1 565
6 TraesCS3B01G302400 chr6D 389531597 389532171 574 False 833.000000 833 92.870000 1 574 1 chr6D.!!$F2 573
7 TraesCS3B01G302400 chr6D 249457227 249457788 561 False 586.000000 586 85.589000 1 564 1 chr6D.!!$F1 563
8 TraesCS3B01G302400 chr2A 535707769 535708339 570 False 819.000000 819 92.509000 1 573 1 chr2A.!!$F1 572
9 TraesCS3B01G302400 chr2A 715208105 715208671 566 False 643.000000 643 87.215000 5 572 1 chr2A.!!$F2 567
10 TraesCS3B01G302400 chr7B 413111580 413112146 566 False 590.000000 590 85.540000 5 573 1 chr7B.!!$F1 568
11 TraesCS3B01G302400 chr7B 616639212 616639783 571 True 582.000000 582 85.147000 1 574 1 chr7B.!!$R1 573

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
399 415 1.035385 TGACGCGGCTAGAGGATTGA 61.035 55.000 15.8 0.0 0.00 2.57 F
798 821 1.081641 GCGTGACCGTCTTTCTCGA 60.082 57.895 0.0 0.0 32.96 4.04 F
2210 2254 1.068588 GCAACTGGTGGTCCCTTTTTC 59.931 52.381 0.0 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1756 0.667993 CTTTGACCCTTCTTTGCGCA 59.332 50.0 5.66 5.66 0.00 6.09 R
2569 2616 0.586802 GTTCGCTTTGGAGTGTCACC 59.413 55.0 0.00 0.00 34.94 4.02 R
4152 4761 0.262876 ATCCCATGCTTCTTTCCCCC 59.737 55.0 0.00 0.00 0.00 5.40 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
60 68 1.186200 CCCTCTCGATCAGGTTGTGA 58.814 55.000 9.21 0.00 40.38 3.58
61 69 1.134965 CCCTCTCGATCAGGTTGTGAC 60.135 57.143 9.21 0.00 38.28 3.67
146 154 1.532604 TTGAGAGCATCGTGGACGGT 61.533 55.000 0.00 0.00 42.67 4.83
167 175 1.955663 CTTGGCTTGGCGGTTTTGC 60.956 57.895 0.00 0.00 0.00 3.68
357 371 1.898574 CCGGCTGGAGTTGTTGCTT 60.899 57.895 5.28 0.00 37.49 3.91
399 415 1.035385 TGACGCGGCTAGAGGATTGA 61.035 55.000 15.80 0.00 0.00 2.57
448 465 4.839668 TGTAATTGTTGTGGTGGCTAAC 57.160 40.909 0.00 0.00 0.00 2.34
650 669 4.144703 GTCGGTTCCTCTCCGGCC 62.145 72.222 0.00 0.00 45.74 6.13
690 709 4.508124 GCAGATAATTACCGAGTTCACCTG 59.492 45.833 0.00 0.00 0.00 4.00
727 746 3.236816 CATGCTTGACGAATTGTGGAAC 58.763 45.455 0.00 0.00 37.35 3.62
759 782 4.748892 TCGTGCTTGTTTCAAATTTTCCA 58.251 34.783 0.00 0.00 0.00 3.53
798 821 1.081641 GCGTGACCGTCTTTCTCGA 60.082 57.895 0.00 0.00 32.96 4.04
803 826 3.314553 GTGACCGTCTTTCTCGAATGAA 58.685 45.455 0.00 0.00 0.00 2.57
1057 1080 3.256960 ACCCATTGGTGGCTCCGT 61.257 61.111 1.20 0.00 45.58 4.69
1181 1204 4.487412 GGTACACCGCCGTCTCCG 62.487 72.222 0.00 0.00 0.00 4.63
1191 1214 4.944372 CGTCTCCGGGCCGTATGC 62.944 72.222 26.32 11.21 40.16 3.14
1256 1279 2.245582 AGAGCTTTTCATGCCTTTGCT 58.754 42.857 0.00 0.00 38.71 3.91
1461 1484 3.508762 CCATTGAGTTCTTGCAAGCATC 58.491 45.455 21.99 17.63 0.00 3.91
1531 1555 2.224018 GCAAATGGCAACTCTGTTTGGA 60.224 45.455 10.09 0.00 43.97 3.53
1540 1564 4.439289 GCAACTCTGTTTGGATATTGCCTC 60.439 45.833 0.00 0.00 34.20 4.70
1650 1690 7.099764 TGAAGATTCTGAACTGGATACTGAAC 58.900 38.462 0.00 0.00 39.15 3.18
1710 1751 6.369065 GGTTAATTATCCTTATCTCACCTGCG 59.631 42.308 5.46 0.00 0.00 5.18
1729 1770 1.518903 GAAGCTGCGCAAAGAAGGGT 61.519 55.000 13.05 0.22 0.00 4.34
1742 1783 2.800250 AGAAGGGTCAAAGGAGCATTG 58.200 47.619 0.00 0.00 44.54 2.82
1805 1846 6.096987 GTGTTGATCTCTTATGTACTCCCTCA 59.903 42.308 0.00 0.00 0.00 3.86
1834 1875 9.386010 ACCATAATATAAGACGTTTTTGCAGTA 57.614 29.630 0.00 0.00 0.00 2.74
1869 1910 7.173562 ACTGCAAAAACGTCTTACATTATGGTA 59.826 33.333 0.00 0.00 0.00 3.25
1871 1912 6.744082 GCAAAAACGTCTTACATTATGGTACC 59.256 38.462 4.43 4.43 0.00 3.34
1872 1913 7.573469 GCAAAAACGTCTTACATTATGGTACCA 60.573 37.037 18.99 18.99 0.00 3.25
1882 1923 5.535029 ACATTATGGTACCAAGGGAGTAGA 58.465 41.667 20.76 0.00 0.00 2.59
1914 1955 8.854614 AGGAATGTGATATACAAATAGGAAGC 57.145 34.615 0.00 0.00 43.77 3.86
2086 2128 9.797556 ACATTTTAAAGGTGAAAGTGTAGTTTC 57.202 29.630 8.99 5.45 35.66 2.78
2092 2134 3.246936 GGTGAAAGTGTAGTTTCGTCACC 59.753 47.826 4.33 4.33 38.99 4.02
2093 2135 3.866910 GTGAAAGTGTAGTTTCGTCACCA 59.133 43.478 7.47 0.00 38.99 4.17
2094 2136 4.510340 GTGAAAGTGTAGTTTCGTCACCAT 59.490 41.667 7.47 0.00 38.99 3.55
2095 2137 4.509970 TGAAAGTGTAGTTTCGTCACCATG 59.490 41.667 7.47 0.00 38.99 3.66
2097 2139 4.330944 AGTGTAGTTTCGTCACCATGAA 57.669 40.909 0.00 0.00 33.21 2.57
2100 2142 5.179368 AGTGTAGTTTCGTCACCATGAAATG 59.821 40.000 0.00 0.00 46.21 2.32
2102 2144 4.749245 AGTTTCGTCACCATGAAATGTC 57.251 40.909 0.00 0.00 44.81 3.06
2103 2145 4.389374 AGTTTCGTCACCATGAAATGTCT 58.611 39.130 0.00 0.00 44.81 3.41
2104 2146 4.214119 AGTTTCGTCACCATGAAATGTCTG 59.786 41.667 0.00 0.00 44.81 3.51
2105 2147 2.076100 TCGTCACCATGAAATGTCTGC 58.924 47.619 0.00 0.00 44.81 4.26
2120 2164 8.845227 TGAAATGTCTGCTTGAAGTTAAATGTA 58.155 29.630 0.00 0.00 0.00 2.29
2210 2254 1.068588 GCAACTGGTGGTCCCTTTTTC 59.931 52.381 0.00 0.00 0.00 2.29
2273 2317 1.194121 TAGCACTGGAGGCTTGCTGA 61.194 55.000 19.07 3.60 46.10 4.26
2282 2326 4.539726 TGGAGGCTTGCTGATAAATGATT 58.460 39.130 0.00 0.00 0.00 2.57
2283 2327 4.957954 TGGAGGCTTGCTGATAAATGATTT 59.042 37.500 0.00 0.00 0.00 2.17
2292 2337 8.455903 TTGCTGATAAATGATTTTAGAGAGGG 57.544 34.615 0.00 0.00 31.07 4.30
2350 2395 3.802675 GCTTATAGGGCCAAAGGTACTCG 60.803 52.174 6.18 0.00 38.49 4.18
2374 2419 2.036475 AGGCCATAGCTCATAACTCACG 59.964 50.000 5.01 0.00 39.73 4.35
2376 2421 2.054363 CCATAGCTCATAACTCACGCG 58.946 52.381 3.53 3.53 0.00 6.01
2569 2616 9.490663 GGTTCATATGATAGTGAAAAGAAAACG 57.509 33.333 6.17 0.00 36.23 3.60
2665 2712 9.521841 TCTCTTGTTATCATCTATTCCGACTAT 57.478 33.333 0.00 0.00 0.00 2.12
2706 2753 6.947733 ACATGATGTTCTGAGGGTCAATTTTA 59.052 34.615 0.00 0.00 0.00 1.52
2707 2754 6.817765 TGATGTTCTGAGGGTCAATTTTAC 57.182 37.500 0.00 0.00 0.00 2.01
2708 2755 6.542821 TGATGTTCTGAGGGTCAATTTTACT 58.457 36.000 0.00 0.00 0.00 2.24
2709 2756 7.004086 TGATGTTCTGAGGGTCAATTTTACTT 58.996 34.615 0.00 0.00 0.00 2.24
2710 2757 7.505585 TGATGTTCTGAGGGTCAATTTTACTTT 59.494 33.333 0.00 0.00 0.00 2.66
2711 2758 7.038154 TGTTCTGAGGGTCAATTTTACTTTG 57.962 36.000 0.00 0.00 0.00 2.77
2712 2759 6.831353 TGTTCTGAGGGTCAATTTTACTTTGA 59.169 34.615 0.00 0.00 0.00 2.69
2722 2769 7.736447 GTCAATTTTACTTTGACTACTACCCG 58.264 38.462 8.82 0.00 46.03 5.28
2723 2770 6.369615 TCAATTTTACTTTGACTACTACCCGC 59.630 38.462 0.00 0.00 0.00 6.13
2724 2771 4.870123 TTTACTTTGACTACTACCCGCA 57.130 40.909 0.00 0.00 0.00 5.69
2725 2772 4.870123 TTACTTTGACTACTACCCGCAA 57.130 40.909 0.00 0.00 0.00 4.85
2726 2773 3.756933 ACTTTGACTACTACCCGCAAA 57.243 42.857 0.00 0.00 0.00 3.68
2727 2774 4.075963 ACTTTGACTACTACCCGCAAAA 57.924 40.909 0.00 0.00 0.00 2.44
2728 2775 4.453751 ACTTTGACTACTACCCGCAAAAA 58.546 39.130 0.00 0.00 0.00 1.94
2787 2836 1.473258 TGCATTCAACCTACCATGGC 58.527 50.000 13.04 0.00 0.00 4.40
2789 2838 1.024271 CATTCAACCTACCATGGCCG 58.976 55.000 13.04 2.31 0.00 6.13
2865 2934 4.424061 TTGTTTTCTGCGAATCAGGATG 57.576 40.909 0.00 0.00 43.06 3.51
2867 2936 2.042686 TTTCTGCGAATCAGGATGGG 57.957 50.000 0.00 0.00 43.06 4.00
2876 2945 2.627515 ATCAGGATGGGATGACGTTG 57.372 50.000 0.00 0.00 36.16 4.10
2882 2951 0.392998 ATGGGATGACGTTGCTCACC 60.393 55.000 0.00 0.00 0.00 4.02
2901 2970 1.404717 CCTGTCCAGGTGATGAACTCG 60.405 57.143 5.11 0.00 43.61 4.18
2924 2993 6.959871 TCGCGATATACTAAGCTTTTATCTCG 59.040 38.462 20.14 20.14 32.00 4.04
3027 3096 1.376942 CTCTGGAAGCAGTGCCCTG 60.377 63.158 12.58 10.98 41.91 4.45
3118 3188 2.023695 TGAACCGAAGTAGGAGGGGTAT 60.024 50.000 0.00 0.00 34.73 2.73
3178 3248 6.245115 TGTCATAGATTTGCAACACTCAAG 57.755 37.500 0.00 0.00 0.00 3.02
3182 3252 6.369890 TCATAGATTTGCAACACTCAAGTCTC 59.630 38.462 0.00 0.00 39.87 3.36
3228 3298 4.466828 CATGTTGGAGTTGCTAAACTTCG 58.533 43.478 0.00 0.00 46.84 3.79
3277 3347 0.109272 CGCTTACGGAGTCTTGCAGA 60.109 55.000 0.00 0.00 43.93 4.26
3492 3562 5.598769 GGTAACATACCGTATCTGAAGCTT 58.401 41.667 0.00 0.00 39.39 3.74
3610 3776 7.349598 AGATTATTCAGGGCTTACAACATTCT 58.650 34.615 0.00 0.00 0.00 2.40
3702 3871 9.701098 ATAACATCTGCAAAATAGCATTAATGG 57.299 29.630 17.02 0.00 44.68 3.16
3733 3902 0.607489 AAGTCTCTGCATGCACCCAC 60.607 55.000 18.46 12.81 0.00 4.61
3743 3912 2.765122 CATGCACCCACGGAAAATTTT 58.235 42.857 2.28 2.28 0.00 1.82
3806 4018 9.748708 CAATGTTTCAAAAGGTCTGAAAAGATA 57.251 29.630 0.00 0.00 42.73 1.98
3821 4034 0.487772 AGATATACCACCTCCCGGCT 59.512 55.000 0.00 0.00 0.00 5.52
3830 4043 2.669133 CCTCCCGGCTGTTGGATGA 61.669 63.158 0.00 0.00 0.00 2.92
3835 4048 0.962356 CCGGCTGTTGGATGAAAGCT 60.962 55.000 0.00 0.00 35.93 3.74
3840 4053 3.127721 GGCTGTTGGATGAAAGCTAGAAC 59.872 47.826 0.00 0.00 35.93 3.01
3849 4062 4.002906 TGAAAGCTAGAACGACCATTGT 57.997 40.909 0.00 0.00 0.00 2.71
3886 4099 2.030274 CCCCGTTGAAACCAGTGATTTC 60.030 50.000 2.70 2.70 36.73 2.17
3893 4106 5.004922 TGAAACCAGTGATTTCCAACAAC 57.995 39.130 7.53 0.00 35.57 3.32
3926 4139 1.277273 CTCAGTCTCTGCAACATGGGA 59.723 52.381 0.00 0.00 0.00 4.37
3943 4156 5.990996 ACATGGGACTTATTGCAACAAAAAG 59.009 36.000 0.00 6.22 0.00 2.27
3991 4217 4.401022 TGAAACACAATCTCCTCATTGCT 58.599 39.130 0.00 0.00 37.28 3.91
4054 4663 4.887748 TGTTGGAGAAACATCTCTGACTC 58.112 43.478 5.87 0.00 43.96 3.36
4055 4664 4.590647 TGTTGGAGAAACATCTCTGACTCT 59.409 41.667 5.87 0.00 43.96 3.24
4056 4665 4.797800 TGGAGAAACATCTCTGACTCTG 57.202 45.455 5.87 0.00 36.97 3.35
4152 4761 2.621763 GCATTAGCCGACCATGGAG 58.378 57.895 21.47 11.91 33.58 3.86
4153 4762 0.886490 GCATTAGCCGACCATGGAGG 60.886 60.000 21.47 21.43 38.00 4.30
4158 4767 2.690881 CCGACCATGGAGGGGGAA 60.691 66.667 21.47 0.00 43.89 3.97
4160 4769 1.224592 CGACCATGGAGGGGGAAAG 59.775 63.158 21.47 0.00 43.89 2.62
4162 4771 0.999712 GACCATGGAGGGGGAAAGAA 59.000 55.000 21.47 0.00 43.89 2.52
4163 4772 1.002857 ACCATGGAGGGGGAAAGAAG 58.997 55.000 21.47 0.00 43.89 2.85
4164 4773 0.396278 CCATGGAGGGGGAAAGAAGC 60.396 60.000 5.56 0.00 0.00 3.86
4165 4774 0.332632 CATGGAGGGGGAAAGAAGCA 59.667 55.000 0.00 0.00 0.00 3.91
4168 4777 0.396278 GGAGGGGGAAAGAAGCATGG 60.396 60.000 0.00 0.00 0.00 3.66
4175 4784 3.369787 GGGGAAAGAAGCATGGGATTTTG 60.370 47.826 0.00 0.00 0.00 2.44
4176 4785 3.264947 GGAAAGAAGCATGGGATTTTGC 58.735 45.455 0.00 0.00 39.17 3.68
4177 4786 3.264947 GAAAGAAGCATGGGATTTTGCC 58.735 45.455 0.00 0.00 39.72 4.52
4178 4787 1.941377 AGAAGCATGGGATTTTGCCA 58.059 45.000 0.00 0.00 43.78 4.92
4179 4788 1.551883 AGAAGCATGGGATTTTGCCAC 59.448 47.619 0.00 0.00 41.95 5.01
4180 4789 0.614812 AAGCATGGGATTTTGCCACC 59.385 50.000 0.00 0.00 41.95 4.61
4181 4790 1.153588 GCATGGGATTTTGCCACCG 60.154 57.895 0.00 0.00 41.95 4.94
4182 4791 1.153588 CATGGGATTTTGCCACCGC 60.154 57.895 0.00 0.00 41.95 5.68
4183 4792 2.358372 ATGGGATTTTGCCACCGCC 61.358 57.895 0.00 0.00 41.95 6.13
4184 4793 4.128388 GGGATTTTGCCACCGCCG 62.128 66.667 0.00 0.00 0.00 6.46
4185 4794 3.370231 GGATTTTGCCACCGCCGT 61.370 61.111 0.00 0.00 0.00 5.68
4186 4795 2.648454 GATTTTGCCACCGCCGTT 59.352 55.556 0.00 0.00 0.00 4.44
4187 4796 1.006688 GATTTTGCCACCGCCGTTT 60.007 52.632 0.00 0.00 0.00 3.60
4188 4797 1.281566 GATTTTGCCACCGCCGTTTG 61.282 55.000 0.00 0.00 0.00 2.93
4189 4798 4.577246 TTTGCCACCGCCGTTTGC 62.577 61.111 0.00 0.00 0.00 3.68
4193 4802 3.893763 CCACCGCCGTTTGCAACA 61.894 61.111 0.00 0.00 41.33 3.33
4194 4803 2.653766 CACCGCCGTTTGCAACAC 60.654 61.111 0.00 0.00 41.33 3.32
4195 4804 3.894947 ACCGCCGTTTGCAACACC 61.895 61.111 0.00 0.00 41.33 4.16
4196 4805 3.591835 CCGCCGTTTGCAACACCT 61.592 61.111 0.00 0.00 41.33 4.00
4197 4806 2.411290 CGCCGTTTGCAACACCTT 59.589 55.556 0.00 0.00 41.33 3.50
4198 4807 1.226831 CGCCGTTTGCAACACCTTT 60.227 52.632 0.00 0.00 41.33 3.11
4199 4808 1.478622 CGCCGTTTGCAACACCTTTG 61.479 55.000 0.00 0.00 41.33 2.77
4200 4809 1.761244 GCCGTTTGCAACACCTTTGC 61.761 55.000 0.00 1.95 45.11 3.68
4331 4942 2.159517 CGGCTAAACCTCTCAACAATGC 60.160 50.000 0.00 0.00 35.61 3.56
4350 4961 0.323633 CACATGGATGGGTGGCTTGA 60.324 55.000 0.00 0.00 0.00 3.02
4351 4962 0.323725 ACATGGATGGGTGGCTTGAC 60.324 55.000 0.00 0.00 0.00 3.18
4352 4963 0.033796 CATGGATGGGTGGCTTGACT 60.034 55.000 0.00 0.00 0.00 3.41
4353 4964 0.706433 ATGGATGGGTGGCTTGACTT 59.294 50.000 0.00 0.00 0.00 3.01
4356 4967 0.038166 GATGGGTGGCTTGACTTGGA 59.962 55.000 0.00 0.00 0.00 3.53
4357 4968 0.038744 ATGGGTGGCTTGACTTGGAG 59.961 55.000 0.00 0.00 0.00 3.86
4358 4969 1.973812 GGGTGGCTTGACTTGGAGC 60.974 63.158 0.00 0.00 38.17 4.70
4359 4970 2.328099 GGTGGCTTGACTTGGAGCG 61.328 63.158 0.00 0.00 39.78 5.03
4360 4971 2.032528 TGGCTTGACTTGGAGCGG 59.967 61.111 0.00 0.00 39.78 5.52
4388 4999 2.435938 TCGCGGCAAATCCTGGAC 60.436 61.111 6.13 0.00 0.00 4.02
4411 5022 0.096628 GCTGCAAGTGAGAAGATGCG 59.903 55.000 0.00 0.00 41.61 4.73
4433 5046 5.339990 CGAGAAAGATTGAGAGGAAGAGAC 58.660 45.833 0.00 0.00 0.00 3.36
4437 5050 7.512992 AGAAAGATTGAGAGGAAGAGACAAAA 58.487 34.615 0.00 0.00 0.00 2.44
4444 5057 1.002087 AGGAAGAGACAAAACGGCGAT 59.998 47.619 16.62 0.00 0.00 4.58
4445 5058 1.393883 GGAAGAGACAAAACGGCGATC 59.606 52.381 16.62 2.71 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 119 2.225019 TCTCAACAGAGTAACGACGTCC 59.775 50.000 10.58 0.00 0.00 4.79
146 154 1.040339 AAAACCGCCAAGCCAAGTCA 61.040 50.000 0.00 0.00 0.00 3.41
167 175 2.100631 GCACCGGAGAACCACATCG 61.101 63.158 9.46 0.00 35.59 3.84
357 371 0.103208 AAATGCCGAACACCGCAAAA 59.897 45.000 0.00 0.00 36.84 2.44
419 435 2.792116 CCACAACAATTACAAACACGGC 59.208 45.455 0.00 0.00 0.00 5.68
421 437 3.794028 CCACCACAACAATTACAAACACG 59.206 43.478 0.00 0.00 0.00 4.49
448 465 1.066143 ACACCCGAGCTAATCAACAGG 60.066 52.381 0.00 0.00 0.00 4.00
576 595 4.222886 GGTCATCGACGAGATTCACATAG 58.777 47.826 3.01 0.00 37.52 2.23
577 596 3.303791 CGGTCATCGACGAGATTCACATA 60.304 47.826 3.01 0.00 42.43 2.29
578 597 2.541794 CGGTCATCGACGAGATTCACAT 60.542 50.000 3.01 0.00 42.43 3.21
650 669 1.165907 TGCACGCTTCACTCCCTTTG 61.166 55.000 0.00 0.00 0.00 2.77
690 709 3.323243 AGCATGTCAAATCTTTGCAAGC 58.677 40.909 0.00 13.96 38.21 4.01
700 719 4.919168 CACAATTCGTCAAGCATGTCAAAT 59.081 37.500 0.00 0.00 0.00 2.32
702 721 3.304592 CCACAATTCGTCAAGCATGTCAA 60.305 43.478 0.00 0.00 0.00 3.18
710 729 5.149273 CAAGATGTTCCACAATTCGTCAAG 58.851 41.667 0.00 0.00 0.00 3.02
727 746 0.806868 ACAAGCACGATGGCAAGATG 59.193 50.000 0.00 0.00 35.83 2.90
759 782 5.417580 ACGCCCACAATAATCATGTTAACTT 59.582 36.000 7.22 0.00 0.00 2.66
798 821 4.959080 ACCCACCCAAAATCCTATTCATT 58.041 39.130 0.00 0.00 0.00 2.57
803 826 2.358195 GCTGACCCACCCAAAATCCTAT 60.358 50.000 0.00 0.00 0.00 2.57
1057 1080 0.749818 TTGCCCAGCAGAAACGACAA 60.750 50.000 0.00 0.00 40.61 3.18
1197 1220 0.040067 GCAAAGTTTCTGCCACGGAG 60.040 55.000 0.00 0.00 33.51 4.63
1256 1279 4.980805 GCACCCACGCCGAGTCAA 62.981 66.667 0.00 0.00 0.00 3.18
1461 1484 4.676546 TCAATCTAGCATCAGACAGAACG 58.323 43.478 0.00 0.00 0.00 3.95
1531 1555 8.041323 CCTATAACGAATACCAAGAGGCAATAT 58.959 37.037 0.00 0.00 39.06 1.28
1540 1564 4.625742 CGATGGCCTATAACGAATACCAAG 59.374 45.833 3.32 0.00 0.00 3.61
1602 1634 8.315391 TCAGATATGAACAATATAACTGCAGC 57.685 34.615 15.27 0.00 33.47 5.25
1715 1756 0.667993 CTTTGACCCTTCTTTGCGCA 59.332 50.000 5.66 5.66 0.00 6.09
1729 1770 4.381185 GCAATGACATCAATGCTCCTTTGA 60.381 41.667 13.51 0.00 46.30 2.69
1761 1802 7.220740 TCAACACAACTCCACATAAATCAGTA 58.779 34.615 0.00 0.00 0.00 2.74
1805 1846 9.386010 TGCAAAAACGTCTTATATTATGGTACT 57.614 29.630 0.00 0.00 0.00 2.73
1834 1875 6.720012 AGACGTTTTTGCAGTTCAAATTTT 57.280 29.167 0.00 0.00 43.53 1.82
1860 1901 6.494666 TTCTACTCCCTTGGTACCATAATG 57.505 41.667 17.17 8.04 0.00 1.90
1869 1910 5.600749 TCCTTTCTATTCTACTCCCTTGGT 58.399 41.667 0.00 0.00 0.00 3.67
1871 1912 7.497249 CACATTCCTTTCTATTCTACTCCCTTG 59.503 40.741 0.00 0.00 0.00 3.61
1872 1913 7.403231 TCACATTCCTTTCTATTCTACTCCCTT 59.597 37.037 0.00 0.00 0.00 3.95
1914 1955 1.290203 ATATTGCAGGCGTCAACTCG 58.710 50.000 0.00 0.00 0.00 4.18
1955 1996 8.823220 ACTATAGGTTTGTGCCATTTATTCTT 57.177 30.769 4.43 0.00 0.00 2.52
2071 2113 3.866910 TGGTGACGAAACTACACTTTCAC 59.133 43.478 0.00 0.00 35.28 3.18
2086 2128 2.079158 AGCAGACATTTCATGGTGACG 58.921 47.619 0.00 0.00 33.60 4.35
2092 2134 8.644619 CATTTAACTTCAAGCAGACATTTCATG 58.355 33.333 0.00 0.00 0.00 3.07
2093 2135 8.362639 ACATTTAACTTCAAGCAGACATTTCAT 58.637 29.630 0.00 0.00 0.00 2.57
2094 2136 7.715657 ACATTTAACTTCAAGCAGACATTTCA 58.284 30.769 0.00 0.00 0.00 2.69
2095 2137 9.846248 ATACATTTAACTTCAAGCAGACATTTC 57.154 29.630 0.00 0.00 0.00 2.17
2210 2254 6.443792 ACAGTTGTTTAGCGAAAATAAAGGG 58.556 36.000 0.00 0.00 31.00 3.95
2239 2283 6.065374 TCCAGTGCTAGTTTTTGGTATTTGA 58.935 36.000 0.00 0.00 0.00 2.69
2273 2317 7.449704 GGATGTGCCCTCTCTAAAATCATTTAT 59.550 37.037 0.00 0.00 30.88 1.40
2282 2326 3.073798 TGTTTGGATGTGCCCTCTCTAAA 59.926 43.478 0.00 0.00 34.97 1.85
2283 2327 2.642311 TGTTTGGATGTGCCCTCTCTAA 59.358 45.455 0.00 0.00 34.97 2.10
2292 2337 3.119495 GGACCACTATTGTTTGGATGTGC 60.119 47.826 0.00 0.00 36.28 4.57
2324 2369 2.042433 ACCTTTGGCCCTATAAGCAACA 59.958 45.455 0.00 0.00 0.00 3.33
2350 2395 2.810852 GAGTTATGAGCTATGGCCTTGC 59.189 50.000 3.32 5.63 39.73 4.01
2374 2419 2.949644 ACCTAATTCTTACAATGCCCGC 59.050 45.455 0.00 0.00 0.00 6.13
2376 2421 6.524101 TGAAACCTAATTCTTACAATGCCC 57.476 37.500 0.00 0.00 0.00 5.36
2569 2616 0.586802 GTTCGCTTTGGAGTGTCACC 59.413 55.000 0.00 0.00 34.94 4.02
2658 2705 7.375834 TGTGCCATAGTAATAAAGATAGTCGG 58.624 38.462 0.00 0.00 0.00 4.79
2665 2712 8.978874 AACATCATGTGCCATAGTAATAAAGA 57.021 30.769 0.00 0.00 0.00 2.52
2679 2726 2.012673 GACCCTCAGAACATCATGTGC 58.987 52.381 0.00 0.00 0.00 4.57
2706 2753 3.756933 TTTGCGGGTAGTAGTCAAAGT 57.243 42.857 0.00 0.00 0.00 2.66
2737 2784 9.853555 CAAAAATATTGCCACATAGTCAAAGTA 57.146 29.630 0.00 0.00 0.00 2.24
2738 2785 8.367156 ACAAAAATATTGCCACATAGTCAAAGT 58.633 29.630 0.00 0.00 0.00 2.66
2739 2786 8.761575 ACAAAAATATTGCCACATAGTCAAAG 57.238 30.769 0.00 0.00 0.00 2.77
2752 2799 8.478494 GGTTGAATGCAAAAACAAAAATATTGC 58.522 29.630 10.52 2.07 44.93 3.56
2757 2804 7.337942 TGGTAGGTTGAATGCAAAAACAAAAAT 59.662 29.630 10.52 0.56 35.42 1.82
2787 2836 9.490663 GATTACACTCTTTTGACAAATATTCGG 57.509 33.333 0.50 0.00 0.00 4.30
2865 2934 1.021390 CAGGTGAGCAACGTCATCCC 61.021 60.000 0.00 0.00 0.00 3.85
2867 2936 1.071605 GACAGGTGAGCAACGTCATC 58.928 55.000 0.00 0.00 0.00 2.92
2882 2951 2.001812 CGAGTTCATCACCTGGACAG 57.998 55.000 0.00 0.00 35.59 3.51
2901 2970 7.964011 AGACGAGATAAAAGCTTAGTATATCGC 59.036 37.037 28.91 23.91 40.71 4.58
2991 3060 5.470098 TCCAGAGTTCAGAAACTTTACATGC 59.530 40.000 0.00 0.00 45.80 4.06
3027 3096 1.818642 AGACAACTGCAGATGGAAGC 58.181 50.000 25.57 12.94 0.00 3.86
3118 3188 0.674581 CCGCCAGCAAGATGAGTCAA 60.675 55.000 0.00 0.00 0.00 3.18
3163 3233 3.248602 GTCGAGACTTGAGTGTTGCAAAT 59.751 43.478 0.00 0.00 0.00 2.32
3166 3236 1.538204 GGTCGAGACTTGAGTGTTGCA 60.538 52.381 3.09 0.00 0.00 4.08
3178 3248 4.433615 ACAATGTACATGATGGTCGAGAC 58.566 43.478 9.63 0.00 0.00 3.36
3182 3252 5.220662 GGAAAGACAATGTACATGATGGTCG 60.221 44.000 9.63 0.00 0.00 4.79
3492 3562 8.706322 AGCTTTAAGTTTCCCAAAGAATCTAA 57.294 30.769 0.91 0.00 34.13 2.10
3702 3871 4.005650 TGCAGAGACTTCATGTTCCATTC 58.994 43.478 0.00 0.00 0.00 2.67
3718 3887 3.129502 CCGTGGGTGCATGCAGAG 61.130 66.667 23.41 10.49 0.00 3.35
3768 3937 8.900762 CCTTTTGAAACATTGTTGTTGTTTTTC 58.099 29.630 2.13 0.00 45.30 2.29
3793 3962 5.454897 GGGAGGTGGTATATCTTTTCAGACC 60.455 48.000 0.00 0.00 0.00 3.85
3821 4034 3.994392 GTCGTTCTAGCTTTCATCCAACA 59.006 43.478 0.00 0.00 0.00 3.33
3830 4043 5.978814 AGATACAATGGTCGTTCTAGCTTT 58.021 37.500 0.00 0.00 0.00 3.51
3835 4048 3.640029 GGGGAGATACAATGGTCGTTCTA 59.360 47.826 0.00 0.00 0.00 2.10
3840 4053 2.104792 ACATGGGGAGATACAATGGTCG 59.895 50.000 0.00 0.00 0.00 4.79
3849 4062 1.518367 GGGGTTCACATGGGGAGATA 58.482 55.000 0.00 0.00 0.00 1.98
3893 4106 5.119898 GCAGAGACTGAGTGTAACAATTGAG 59.880 44.000 13.59 0.00 32.93 3.02
3903 4116 2.549563 CCATGTTGCAGAGACTGAGTGT 60.550 50.000 0.00 0.00 32.44 3.55
3926 4139 6.560711 AGAACGTCTTTTTGTTGCAATAAGT 58.439 32.000 8.69 0.08 0.00 2.24
3963 4178 9.941664 CAATGAGGAGATTGTGTTTCATAATAC 57.058 33.333 0.00 0.00 0.00 1.89
3965 4180 7.341256 AGCAATGAGGAGATTGTGTTTCATAAT 59.659 33.333 0.00 0.00 35.98 1.28
3968 4183 5.014858 AGCAATGAGGAGATTGTGTTTCAT 58.985 37.500 0.00 0.00 35.98 2.57
3991 4217 5.000012 AGGTTTGCAACAACGATTTTGTA 58.000 34.783 0.00 0.00 31.50 2.41
4144 4753 1.002857 CTTCTTTCCCCCTCCATGGT 58.997 55.000 12.58 0.00 0.00 3.55
4150 4759 0.396278 CCCATGCTTCTTTCCCCCTC 60.396 60.000 0.00 0.00 0.00 4.30
4152 4761 0.262876 ATCCCATGCTTCTTTCCCCC 59.737 55.000 0.00 0.00 0.00 5.40
4153 4762 2.165357 AATCCCATGCTTCTTTCCCC 57.835 50.000 0.00 0.00 0.00 4.81
4157 4766 2.638855 TGGCAAAATCCCATGCTTCTTT 59.361 40.909 0.00 0.00 42.20 2.52
4158 4767 2.027837 GTGGCAAAATCCCATGCTTCTT 60.028 45.455 0.00 0.00 42.20 2.52
4160 4769 1.405933 GGTGGCAAAATCCCATGCTTC 60.406 52.381 0.00 0.00 42.20 3.86
4162 4771 1.606885 CGGTGGCAAAATCCCATGCT 61.607 55.000 0.00 0.00 42.20 3.79
4163 4772 1.153588 CGGTGGCAAAATCCCATGC 60.154 57.895 0.00 0.00 41.82 4.06
4164 4773 1.153588 GCGGTGGCAAAATCCCATG 60.154 57.895 0.00 0.00 39.62 3.66
4165 4774 2.358372 GGCGGTGGCAAAATCCCAT 61.358 57.895 0.00 0.00 42.47 4.00
4168 4777 2.428960 AAACGGCGGTGGCAAAATCC 62.429 55.000 13.24 0.00 42.47 3.01
4188 4797 1.269257 GGAGTTCTGCAAAGGTGTTGC 60.269 52.381 4.12 4.12 45.11 4.17
4189 4798 2.023673 TGGAGTTCTGCAAAGGTGTTG 58.976 47.619 0.00 0.00 0.00 3.33
4190 4799 2.024414 GTGGAGTTCTGCAAAGGTGTT 58.976 47.619 0.00 0.00 0.00 3.32
4191 4800 1.680338 GTGGAGTTCTGCAAAGGTGT 58.320 50.000 0.00 0.00 0.00 4.16
4192 4801 0.954452 GGTGGAGTTCTGCAAAGGTG 59.046 55.000 0.00 0.00 0.00 4.00
4193 4802 0.535102 CGGTGGAGTTCTGCAAAGGT 60.535 55.000 0.00 0.00 0.00 3.50
4194 4803 1.856265 GCGGTGGAGTTCTGCAAAGG 61.856 60.000 0.00 0.00 37.18 3.11
4195 4804 1.576421 GCGGTGGAGTTCTGCAAAG 59.424 57.895 0.00 0.00 37.18 2.77
4196 4805 1.896660 GGCGGTGGAGTTCTGCAAA 60.897 57.895 0.00 0.00 38.75 3.68
4197 4806 2.281484 GGCGGTGGAGTTCTGCAA 60.281 61.111 0.00 0.00 38.75 4.08
4198 4807 4.680237 CGGCGGTGGAGTTCTGCA 62.680 66.667 0.00 0.00 38.75 4.41
4292 4903 4.927782 TCGGGTTGCTGCGTGCTT 62.928 61.111 0.00 0.00 43.37 3.91
4331 4942 0.323633 TCAAGCCACCCATCCATGTG 60.324 55.000 0.00 0.00 0.00 3.21
4350 4961 2.980233 GCAAGTGCCGCTCCAAGT 60.980 61.111 0.00 0.00 34.31 3.16
4351 4962 4.093952 CGCAAGTGCCGCTCCAAG 62.094 66.667 0.00 0.00 37.91 3.61
4373 4984 4.179579 GCGTCCAGGATTTGCCGC 62.180 66.667 5.70 5.70 43.43 6.53
4374 4985 3.508840 GGCGTCCAGGATTTGCCG 61.509 66.667 13.00 3.64 43.43 5.69
4388 4999 3.020026 CTTCTCACTTGCAGCGGCG 62.020 63.158 0.51 0.51 45.35 6.46
4409 5020 4.111916 CTCTTCCTCTCAATCTTTCTCGC 58.888 47.826 0.00 0.00 0.00 5.03
4411 5022 6.279513 TGTCTCTTCCTCTCAATCTTTCTC 57.720 41.667 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.