Multiple sequence alignment - TraesCS7D01G268500

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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 TraesCS7D01G268500 chr7D 100.000 5986 0 0 1 5986 252268022 252262037 0.000000e+00 11055.0
1 TraesCS7D01G268500 chr7D 96.429 504 10 5 5482 5980 71563755 71564255 0.000000e+00 824.0
2 TraesCS7D01G268500 chr7D 95.876 97 4 0 2737 2833 1299135 1299231 2.230000e-34 158.0
3 TraesCS7D01G268500 chr7D 91.228 57 3 2 5444 5498 136010694 136010750 6.430000e-10 76.8
4 TraesCS7D01G268500 chr7B 98.351 2608 34 7 2828 5432 229095698 229093097 0.000000e+00 4569.0
5 TraesCS7D01G268500 chr7B 97.248 2616 58 8 140 2746 229098307 229095697 0.000000e+00 4420.0
6 TraesCS7D01G268500 chr7B 93.893 131 3 3 3 128 229098423 229098293 6.120000e-45 193.0
7 TraesCS7D01G268500 chr7B 89.333 75 4 4 5428 5498 719074103 719074029 2.300000e-14 91.6
8 TraesCS7D01G268500 chr7A 92.534 2759 143 31 3 2728 268851072 268853800 0.000000e+00 3895.0
9 TraesCS7D01G268500 chr7A 91.501 1965 69 42 3280 5211 268856493 268858392 0.000000e+00 2614.0
10 TraesCS7D01G268500 chr7A 92.787 305 17 5 2963 3263 268853797 268854100 2.560000e-118 436.0
11 TraesCS7D01G268500 chr5D 97.967 492 5 4 5498 5986 253821155 253820666 0.000000e+00 848.0
12 TraesCS7D01G268500 chr5D 97.561 492 5 4 5498 5986 253814111 253813624 0.000000e+00 835.0
13 TraesCS7D01G268500 chr5D 75.571 1007 217 18 979 1964 406606180 406605182 2.530000e-128 470.0
14 TraesCS7D01G268500 chr5D 76.360 901 154 45 4087 4951 406602744 406601867 4.290000e-116 429.0
15 TraesCS7D01G268500 chr5D 88.312 154 9 6 2829 2979 233044460 233044607 6.170000e-40 176.0
16 TraesCS7D01G268500 chr5D 94.898 98 5 0 2739 2836 60072171 60072268 2.890000e-33 154.0
17 TraesCS7D01G268500 chr4D 97.211 502 7 4 5488 5986 59633976 59634473 0.000000e+00 843.0
18 TraesCS7D01G268500 chr4D 96.414 502 7 5 5488 5986 62642985 62643478 0.000000e+00 817.0
19 TraesCS7D01G268500 chr3D 97.352 491 9 2 5498 5986 349655191 349654703 0.000000e+00 832.0
20 TraesCS7D01G268500 chr3D 96.970 495 9 3 5498 5986 329660764 329661258 0.000000e+00 826.0
21 TraesCS7D01G268500 chr3D 96.875 32 1 0 5433 5464 33092921 33092890 3.000000e-03 54.7
22 TraesCS7D01G268500 chr3D 94.444 36 1 1 5429 5464 33147174 33147140 3.000000e-03 54.7
23 TraesCS7D01G268500 chr2D 97.363 493 5 4 5498 5986 63755314 63754826 0.000000e+00 832.0
24 TraesCS7D01G268500 chr1D 96.964 494 10 3 5498 5986 217918043 217917550 0.000000e+00 824.0
25 TraesCS7D01G268500 chr1D 82.573 241 28 6 2725 2965 95869230 95869004 3.660000e-47 200.0
26 TraesCS7D01G268500 chr5B 75.619 1009 213 22 979 1964 487711859 487710861 2.530000e-128 470.0
27 TraesCS7D01G268500 chr5B 76.598 923 147 54 4075 4951 487708523 487707624 1.530000e-120 444.0
28 TraesCS7D01G268500 chr5B 81.281 203 28 9 2725 2925 449753538 449753732 8.030000e-34 156.0
29 TraesCS7D01G268500 chr5B 90.141 71 4 3 5428 5495 588793894 588793964 8.260000e-14 89.8
30 TraesCS7D01G268500 chr5A 75.441 908 159 51 4087 4951 512254063 512253177 3.380000e-102 383.0
31 TraesCS7D01G268500 chr5A 88.158 76 7 2 5425 5498 169169205 169169280 8.260000e-14 89.8
32 TraesCS7D01G268500 chr1B 84.232 241 34 2 2725 2965 156850339 156850575 1.300000e-56 231.0
33 TraesCS7D01G268500 chr1B 79.412 136 16 5 5309 5432 397860297 397860162 1.070000e-12 86.1
34 TraesCS7D01G268500 chr4B 81.224 245 38 7 2722 2965 100325028 100325265 2.200000e-44 191.0
35 TraesCS7D01G268500 chr2A 92.029 138 8 2 2828 2965 176673284 176673418 2.200000e-44 191.0
36 TraesCS7D01G268500 chr3A 90.345 145 9 2 2828 2972 498229954 498230093 1.020000e-42 185.0
37 TraesCS7D01G268500 chr3A 90.647 139 7 4 2828 2965 582283234 582283367 4.770000e-41 180.0
38 TraesCS7D01G268500 chr3A 90.625 64 4 2 5437 5498 475392842 475392779 3.840000e-12 84.2
39 TraesCS7D01G268500 chr6A 89.041 146 10 3 2822 2965 99403041 99403182 6.170000e-40 176.0
40 TraesCS7D01G268500 chr6A 98.876 89 1 0 2741 2829 607960035 607959947 6.210000e-35 159.0
41 TraesCS7D01G268500 chr3B 94.495 109 6 0 2725 2833 467226368 467226476 1.030000e-37 169.0
42 TraesCS7D01G268500 chrUn 98.901 91 1 0 2745 2835 62690554 62690464 4.800000e-36 163.0
43 TraesCS7D01G268500 chr2B 100.000 87 0 0 2744 2830 478114375 478114461 1.730000e-35 161.0
44 TraesCS7D01G268500 chr6B 82.659 173 16 6 2800 2965 578099811 578099976 2.250000e-29 141.0
45 TraesCS7D01G268500 chr6B 94.118 51 3 0 5382 5432 544636564 544636514 1.790000e-10 78.7
46 TraesCS7D01G268500 chr6D 89.855 69 6 1 5431 5498 93448203 93448135 2.970000e-13 87.9
47 TraesCS7D01G268500 chr6D 100.000 32 0 0 5433 5464 370775870 370775901 6.480000e-05 60.2


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 TraesCS7D01G268500 chr7D 252262037 252268022 5985 True 11055.000000 11055 100.000000 1 5986 1 chr7D.!!$R1 5985
1 TraesCS7D01G268500 chr7D 71563755 71564255 500 False 824.000000 824 96.429000 5482 5980 1 chr7D.!!$F2 498
2 TraesCS7D01G268500 chr7B 229093097 229098423 5326 True 3060.666667 4569 96.497333 3 5432 3 chr7B.!!$R2 5429
3 TraesCS7D01G268500 chr7A 268851072 268858392 7320 False 2315.000000 3895 92.274000 3 5211 3 chr7A.!!$F1 5208
4 TraesCS7D01G268500 chr5D 406601867 406606180 4313 True 449.500000 470 75.965500 979 4951 2 chr5D.!!$R3 3972
5 TraesCS7D01G268500 chr5B 487707624 487711859 4235 True 457.000000 470 76.108500 979 4951 2 chr5B.!!$R1 3972
6 TraesCS7D01G268500 chr5A 512253177 512254063 886 True 383.000000 383 75.441000 4087 4951 1 chr5A.!!$R1 864

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
118 124 0.031449 GCCTAGCAAGCCGTAGAGAG 59.969 60.000 0.0 0.0 0.0 3.20 F
292 298 0.392193 AGATTCGCTGCTTCACCCTG 60.392 55.000 0.0 0.0 0.0 4.45 F
475 489 0.690411 ACTCTCCATCCAGCCCTCAG 60.690 60.000 0.0 0.0 0.0 3.35 F
561 575 1.283905 AGTAATGTTGGGTGGGTAGGC 59.716 52.381 0.0 0.0 0.0 3.93 F
1502 1544 2.940410 TGAAGAACAACGGGACAGAAAC 59.060 45.455 0.0 0.0 0.0 2.78 F
1586 1628 4.252971 TCGACAAGAAGGAAGTGGTTAG 57.747 45.455 0.0 0.0 0.0 2.34 F
2758 2831 1.134491 CACAAATACTCCCTCCGTCCC 60.134 57.143 0.0 0.0 0.0 4.46 F
2759 2832 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 1544 1.576421 GTCAGCTGCGGTTTCTTGG 59.424 57.895 9.47 0.0 0.00 3.61 R
1679 1721 3.979495 CACTTTTGTTCTCTGCTTCATGC 59.021 43.478 0.00 0.0 43.25 4.06 R
2688 2761 5.217393 CAGTTCCATATTTGCATCATTCCG 58.783 41.667 0.00 0.0 0.00 4.30 R
2745 2818 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.0 0.00 3.85 R
2746 2819 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.0 0.00 4.30 R
2813 2886 1.854939 TCTTATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.0 0.00 4.37 R
4969 8128 2.284405 GTCACCCCTTCCTCCCGA 60.284 66.667 0.00 0.0 0.00 5.14 R
5039 8200 9.589111 AACGAAAAATAACTTAGCTTCCAAAAA 57.411 25.926 0.00 0.0 0.00 1.94 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
115 121 2.282827 TTGCCTAGCAAGCCGTAGA 58.717 52.632 0.00 0.00 43.99 2.59
116 122 0.175760 TTGCCTAGCAAGCCGTAGAG 59.824 55.000 0.00 0.00 43.99 2.43
117 123 0.683179 TGCCTAGCAAGCCGTAGAGA 60.683 55.000 0.00 0.00 34.76 3.10
118 124 0.031449 GCCTAGCAAGCCGTAGAGAG 59.969 60.000 0.00 0.00 0.00 3.20
119 125 1.681538 CCTAGCAAGCCGTAGAGAGA 58.318 55.000 0.00 0.00 0.00 3.10
120 126 1.606668 CCTAGCAAGCCGTAGAGAGAG 59.393 57.143 0.00 0.00 0.00 3.20
121 127 2.566913 CTAGCAAGCCGTAGAGAGAGA 58.433 52.381 0.00 0.00 0.00 3.10
122 128 1.388547 AGCAAGCCGTAGAGAGAGAG 58.611 55.000 0.00 0.00 0.00 3.20
123 129 1.065053 AGCAAGCCGTAGAGAGAGAGA 60.065 52.381 0.00 0.00 0.00 3.10
124 130 1.333619 GCAAGCCGTAGAGAGAGAGAG 59.666 57.143 0.00 0.00 0.00 3.20
125 131 2.912771 CAAGCCGTAGAGAGAGAGAGA 58.087 52.381 0.00 0.00 0.00 3.10
126 132 2.872245 CAAGCCGTAGAGAGAGAGAGAG 59.128 54.545 0.00 0.00 0.00 3.20
251 257 0.954449 CACTGGCTGCCAAGTCTCAG 60.954 60.000 23.51 11.43 30.80 3.35
292 298 0.392193 AGATTCGCTGCTTCACCCTG 60.392 55.000 0.00 0.00 0.00 4.45
304 310 2.963599 TCACCCTGTCCTTTTTACCC 57.036 50.000 0.00 0.00 0.00 3.69
318 324 8.640651 GTCCTTTTTACCCCTGTTTGTTTATAA 58.359 33.333 0.00 0.00 0.00 0.98
319 325 9.382307 TCCTTTTTACCCCTGTTTGTTTATAAT 57.618 29.630 0.00 0.00 0.00 1.28
324 330 8.824756 TTACCCCTGTTTGTTTATAATATGCA 57.175 30.769 0.00 0.00 0.00 3.96
325 331 7.346751 ACCCCTGTTTGTTTATAATATGCAG 57.653 36.000 0.00 0.00 0.00 4.41
327 333 7.398904 ACCCCTGTTTGTTTATAATATGCAGTT 59.601 33.333 0.00 0.00 0.00 3.16
328 334 7.920682 CCCCTGTTTGTTTATAATATGCAGTTC 59.079 37.037 0.00 0.00 0.00 3.01
329 335 8.686334 CCCTGTTTGTTTATAATATGCAGTTCT 58.314 33.333 0.00 0.00 0.00 3.01
402 416 4.101114 TGCTCCTGTTTATCTTCCCACTA 58.899 43.478 0.00 0.00 0.00 2.74
463 477 1.000019 CCACCGTCCCTACTCTCCA 60.000 63.158 0.00 0.00 0.00 3.86
475 489 0.690411 ACTCTCCATCCAGCCCTCAG 60.690 60.000 0.00 0.00 0.00 3.35
488 502 1.681327 CCTCAGCCCTTGCAGCAAT 60.681 57.895 8.67 0.00 41.13 3.56
561 575 1.283905 AGTAATGTTGGGTGGGTAGGC 59.716 52.381 0.00 0.00 0.00 3.93
585 599 6.690460 GCATAGGTACACCAATCTTCCCATTA 60.690 42.308 0.38 0.00 38.89 1.90
733 749 3.876914 TGTGAGCCTATAAAGGATTTGCG 59.123 43.478 0.00 0.00 43.21 4.85
1502 1544 2.940410 TGAAGAACAACGGGACAGAAAC 59.060 45.455 0.00 0.00 0.00 2.78
1586 1628 4.252971 TCGACAAGAAGGAAGTGGTTAG 57.747 45.455 0.00 0.00 0.00 2.34
2744 2817 6.350445 GCAATGTACTCCCTTCATTCACAAAT 60.350 38.462 0.00 0.00 30.74 2.32
2745 2818 7.148086 GCAATGTACTCCCTTCATTCACAAATA 60.148 37.037 0.00 0.00 30.74 1.40
2746 2819 7.865706 ATGTACTCCCTTCATTCACAAATAC 57.134 36.000 0.00 0.00 0.00 1.89
2747 2820 7.016153 TGTACTCCCTTCATTCACAAATACT 57.984 36.000 0.00 0.00 0.00 2.12
2748 2821 7.103641 TGTACTCCCTTCATTCACAAATACTC 58.896 38.462 0.00 0.00 0.00 2.59
2749 2822 5.501156 ACTCCCTTCATTCACAAATACTCC 58.499 41.667 0.00 0.00 0.00 3.85
2750 2823 4.855340 TCCCTTCATTCACAAATACTCCC 58.145 43.478 0.00 0.00 0.00 4.30
2751 2824 4.540099 TCCCTTCATTCACAAATACTCCCT 59.460 41.667 0.00 0.00 0.00 4.20
2752 2825 4.884164 CCCTTCATTCACAAATACTCCCTC 59.116 45.833 0.00 0.00 0.00 4.30
2753 2826 4.884164 CCTTCATTCACAAATACTCCCTCC 59.116 45.833 0.00 0.00 0.00 4.30
2754 2827 4.137116 TCATTCACAAATACTCCCTCCG 57.863 45.455 0.00 0.00 0.00 4.63
2755 2828 3.517901 TCATTCACAAATACTCCCTCCGT 59.482 43.478 0.00 0.00 0.00 4.69
2756 2829 3.604875 TTCACAAATACTCCCTCCGTC 57.395 47.619 0.00 0.00 0.00 4.79
2757 2830 1.829222 TCACAAATACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
2758 2831 1.134491 CACAAATACTCCCTCCGTCCC 60.134 57.143 0.00 0.00 0.00 4.46
2759 2832 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
2760 2833 1.768870 CAAATACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
2761 2834 2.969950 CAAATACTCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
2762 2835 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2763 2836 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2764 2837 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2765 2838 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2766 2839 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2767 2840 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2768 2841 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2769 2842 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2770 2843 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2772 2845 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2773 2846 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2774 2847 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2775 2848 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2776 2849 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2824 2897 3.990369 TCCTATATTATGGGACGGAGGG 58.010 50.000 4.74 0.00 34.71 4.30
2825 2898 3.599240 TCCTATATTATGGGACGGAGGGA 59.401 47.826 4.74 0.00 34.71 4.20
2826 2899 3.961408 CCTATATTATGGGACGGAGGGAG 59.039 52.174 0.00 0.00 31.57 4.30
2843 2916 9.151177 ACGGAGGGAGTATAAGATATTTTAACA 57.849 33.333 0.00 0.00 0.00 2.41
3571 6025 6.256104 TGAGAATGCAACATGAAACAGTTTTG 59.744 34.615 0.00 0.00 0.00 2.44
3989 6850 2.639839 TCTTTTACCTCCAGCTCTGCTT 59.360 45.455 0.00 0.00 36.40 3.91
4781 7925 1.590259 GCTCAGCGAGATCGGGAAC 60.590 63.158 4.18 0.00 40.23 3.62
5051 8212 1.248101 GCCGGGCTTTTTGGAAGCTA 61.248 55.000 12.87 0.00 42.62 3.32
5118 8279 7.688343 TCAAAGAAAAATATCTGGCCCATTTT 58.312 30.769 0.00 4.51 34.24 1.82
5164 8325 9.880064 TTTGCCTTTTTGTTTTTAAAAGTACAC 57.120 25.926 5.20 0.23 39.71 2.90
5166 8327 9.052759 TGCCTTTTTGTTTTTAAAAGTACACAA 57.947 25.926 10.45 10.45 39.71 3.33
5167 8328 9.536558 GCCTTTTTGTTTTTAAAAGTACACAAG 57.463 29.630 13.00 12.59 39.71 3.16
5337 8499 7.946655 TTTCTAGAACACAATACAGACACAG 57.053 36.000 4.18 0.00 0.00 3.66
5350 8512 2.991866 CAGACACAGGCGCTCATATATG 59.008 50.000 7.64 6.36 0.00 1.78
5365 8527 5.278604 TCATATATGCACACGTACACTCAC 58.721 41.667 7.92 0.00 0.00 3.51
5372 8534 0.169672 CACGTACACTCACCCCTACG 59.830 60.000 0.00 0.00 38.33 3.51
5432 8594 9.656040 AATGAGCTGACATATAATCTTGAGATC 57.344 33.333 0.00 0.00 32.75 2.75
5433 8595 7.609960 TGAGCTGACATATAATCTTGAGATCC 58.390 38.462 0.00 0.00 32.75 3.36
5434 8596 7.454066 TGAGCTGACATATAATCTTGAGATCCT 59.546 37.037 0.00 0.00 32.75 3.24
5435 8597 8.891985 AGCTGACATATAATCTTGAGATCCTA 57.108 34.615 0.00 0.00 32.75 2.94
5436 8598 9.319060 AGCTGACATATAATCTTGAGATCCTAA 57.681 33.333 0.00 0.00 32.75 2.69
5437 8599 9.935241 GCTGACATATAATCTTGAGATCCTAAA 57.065 33.333 0.00 0.00 32.75 1.85
5459 8621 9.891535 CTAAAATAAATCAAGAAAAATGCGAGC 57.108 29.630 0.00 0.00 0.00 5.03
5460 8622 7.887996 AAATAAATCAAGAAAAATGCGAGCA 57.112 28.000 0.00 0.00 0.00 4.26
5461 8623 6.875926 ATAAATCAAGAAAAATGCGAGCAC 57.124 33.333 0.00 0.00 0.00 4.40
5462 8624 2.704725 TCAAGAAAAATGCGAGCACC 57.295 45.000 0.00 0.00 0.00 5.01
5463 8625 1.952990 TCAAGAAAAATGCGAGCACCA 59.047 42.857 0.00 0.00 0.00 4.17
5464 8626 2.030893 TCAAGAAAAATGCGAGCACCAG 60.031 45.455 0.00 0.00 0.00 4.00
5465 8627 0.883833 AGAAAAATGCGAGCACCAGG 59.116 50.000 0.00 0.00 0.00 4.45
5466 8628 0.881118 GAAAAATGCGAGCACCAGGA 59.119 50.000 0.00 0.00 0.00 3.86
5467 8629 1.269448 GAAAAATGCGAGCACCAGGAA 59.731 47.619 0.00 0.00 0.00 3.36
5468 8630 1.549203 AAAATGCGAGCACCAGGAAT 58.451 45.000 0.00 0.00 0.00 3.01
5469 8631 1.549203 AAATGCGAGCACCAGGAATT 58.451 45.000 0.00 0.00 0.00 2.17
5470 8632 0.813184 AATGCGAGCACCAGGAATTG 59.187 50.000 0.00 0.00 0.00 2.32
5471 8633 0.035152 ATGCGAGCACCAGGAATTGA 60.035 50.000 0.00 0.00 0.00 2.57
5472 8634 0.250684 TGCGAGCACCAGGAATTGAA 60.251 50.000 0.00 0.00 0.00 2.69
5473 8635 0.169009 GCGAGCACCAGGAATTGAAC 59.831 55.000 0.00 0.00 0.00 3.18
5474 8636 0.804989 CGAGCACCAGGAATTGAACC 59.195 55.000 0.00 0.00 0.00 3.62
5475 8637 1.177401 GAGCACCAGGAATTGAACCC 58.823 55.000 0.00 0.00 0.00 4.11
5476 8638 0.779997 AGCACCAGGAATTGAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
5480 8642 2.183409 CAGGAATTGAACCCTGGCG 58.817 57.895 7.37 0.00 44.68 5.69
5718 8880 1.481019 CCGCGTTCAACACACGTACA 61.481 55.000 4.92 0.00 39.92 2.90
5733 8895 1.066114 GTACAGTGCAGCGACGTCTC 61.066 60.000 14.70 5.55 0.00 3.36
5757 8919 0.332632 TTCTTGATCCAGCAAGGGGG 59.667 55.000 4.79 0.00 44.14 5.40
5760 8922 1.009997 TTGATCCAGCAAGGGGGAAT 58.990 50.000 0.00 0.00 36.62 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 71 3.078891 AGCAAATCTTGAGGGAGGAAC 57.921 47.619 0.00 0.00 0.00 3.62
110 116 4.822350 TCTCTCTCTCTCTCTCTCTCTACG 59.178 50.000 0.00 0.00 0.00 3.51
115 121 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
116 122 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
117 123 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
118 124 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
119 125 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
120 126 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
121 127 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
122 128 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
123 129 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
124 130 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
125 131 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
126 132 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
167 173 2.179427 TGTGATGTCCCAGAATCGAGT 58.821 47.619 0.00 0.00 0.00 4.18
292 298 5.347620 AAACAAACAGGGGTAAAAAGGAC 57.652 39.130 0.00 0.00 0.00 3.85
318 324 4.756564 TCTCCCATCCTAGAACTGCATAT 58.243 43.478 0.00 0.00 0.00 1.78
319 325 4.199002 TCTCCCATCCTAGAACTGCATA 57.801 45.455 0.00 0.00 0.00 3.14
320 326 3.051940 TCTCCCATCCTAGAACTGCAT 57.948 47.619 0.00 0.00 0.00 3.96
321 327 2.550277 TCTCCCATCCTAGAACTGCA 57.450 50.000 0.00 0.00 0.00 4.41
323 329 4.093011 CCCTATCTCCCATCCTAGAACTG 58.907 52.174 0.00 0.00 0.00 3.16
324 330 3.503227 GCCCTATCTCCCATCCTAGAACT 60.503 52.174 0.00 0.00 0.00 3.01
325 331 2.835156 GCCCTATCTCCCATCCTAGAAC 59.165 54.545 0.00 0.00 0.00 3.01
327 333 1.362932 GGCCCTATCTCCCATCCTAGA 59.637 57.143 0.00 0.00 0.00 2.43
328 334 1.872773 GGCCCTATCTCCCATCCTAG 58.127 60.000 0.00 0.00 0.00 3.02
329 335 0.041238 CGGCCCTATCTCCCATCCTA 59.959 60.000 0.00 0.00 0.00 2.94
330 336 1.229336 CGGCCCTATCTCCCATCCT 60.229 63.158 0.00 0.00 0.00 3.24
402 416 5.882000 TGATTGATTGATTCGATTCAGTGGT 59.118 36.000 9.67 0.00 0.00 4.16
463 477 2.286732 AAGGGCTGAGGGCTGGAT 60.287 61.111 0.00 0.00 41.46 3.41
488 502 3.003394 ACACATAAATGGCAGCAGCTA 57.997 42.857 0.00 0.00 41.70 3.32
543 557 1.373536 TGCCTACCCACCCAACATTA 58.626 50.000 0.00 0.00 0.00 1.90
561 575 4.771114 TGGGAAGATTGGTGTACCTATG 57.229 45.455 2.74 0.00 36.82 2.23
585 599 5.048224 CACAGAGCAATTCAAGTTGAGGAAT 60.048 40.000 5.56 0.00 35.34 3.01
643 657 9.303116 CAGGAAGGATAGTGAAGTACAGTATAT 57.697 37.037 0.00 0.00 42.91 0.86
705 719 8.636213 CAAATCCTTTATAGGCTCACAATGAAT 58.364 33.333 0.00 0.00 41.69 2.57
733 749 8.329203 ACTACTAGTACTAACAAGTGTGTACC 57.671 38.462 3.76 0.00 36.80 3.34
770 786 7.067008 GCAATAAAGGTTCCAGCTTTGTAGATA 59.933 37.037 10.48 0.00 44.58 1.98
867 888 3.755905 TGAAAAGCGAGCAAATGGTGATA 59.244 39.130 0.00 0.00 0.00 2.15
925 948 5.134202 ACGGCGATCATTGTATTGAGATA 57.866 39.130 16.62 0.00 0.00 1.98
926 949 3.995199 ACGGCGATCATTGTATTGAGAT 58.005 40.909 16.62 0.00 0.00 2.75
927 950 3.452755 ACGGCGATCATTGTATTGAGA 57.547 42.857 16.62 0.00 0.00 3.27
1502 1544 1.576421 GTCAGCTGCGGTTTCTTGG 59.424 57.895 9.47 0.00 0.00 3.61
1560 1602 4.127171 CCACTTCCTTCTTGTCGAAAAGA 58.873 43.478 14.22 14.22 34.36 2.52
1586 1628 4.370364 TTGTTTGACTTCACCTTTGAGC 57.630 40.909 0.00 0.00 31.71 4.26
1679 1721 3.979495 CACTTTTGTTCTCTGCTTCATGC 59.021 43.478 0.00 0.00 43.25 4.06
2688 2761 5.217393 CAGTTCCATATTTGCATCATTCCG 58.783 41.667 0.00 0.00 0.00 4.30
2744 2817 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2745 2818 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2746 2819 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2747 2820 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2748 2821 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2749 2822 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2750 2823 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2751 2824 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2802 2875 3.705072 CCCTCCGTCCCATAATATAGGAC 59.295 52.174 7.65 7.65 45.49 3.85
2803 2876 3.599240 TCCCTCCGTCCCATAATATAGGA 59.401 47.826 0.00 0.00 0.00 2.94
2804 2877 3.961408 CTCCCTCCGTCCCATAATATAGG 59.039 52.174 0.00 0.00 0.00 2.57
2805 2878 4.611367 ACTCCCTCCGTCCCATAATATAG 58.389 47.826 0.00 0.00 0.00 1.31
2806 2879 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2807 2880 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2808 2881 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
2809 2882 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2810 2883 4.106825 TCTTATACTCCCTCCGTCCCATAA 59.893 45.833 0.00 0.00 0.00 1.90
2811 2884 3.659195 TCTTATACTCCCTCCGTCCCATA 59.341 47.826 0.00 0.00 0.00 2.74
2812 2885 2.449730 TCTTATACTCCCTCCGTCCCAT 59.550 50.000 0.00 0.00 0.00 4.00
2813 2886 1.854939 TCTTATACTCCCTCCGTCCCA 59.145 52.381 0.00 0.00 0.00 4.37
2814 2887 2.671896 TCTTATACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
2815 2888 6.854091 AAATATCTTATACTCCCTCCGTCC 57.146 41.667 0.00 0.00 0.00 4.79
2816 2889 9.636879 GTTAAAATATCTTATACTCCCTCCGTC 57.363 37.037 0.00 0.00 0.00 4.79
2817 2890 9.151177 TGTTAAAATATCTTATACTCCCTCCGT 57.849 33.333 0.00 0.00 0.00 4.69
2861 2934 9.820229 CAAACACACTAAAACGTGTCAATATAT 57.180 29.630 0.00 0.00 45.74 0.86
3571 6025 7.365741 CCATGTGAAATTTGGATGCTATCTAC 58.634 38.462 0.00 0.00 31.94 2.59
3989 6850 7.711846 TGGTGTTACTGTAAAACTCTTACGTA 58.288 34.615 17.84 0.00 0.00 3.57
4969 8128 2.284405 GTCACCCCTTCCTCCCGA 60.284 66.667 0.00 0.00 0.00 5.14
5039 8200 9.589111 AACGAAAAATAACTTAGCTTCCAAAAA 57.411 25.926 0.00 0.00 0.00 1.94
5051 8212 4.342665 TCTTGCCCCAACGAAAAATAACTT 59.657 37.500 0.00 0.00 0.00 2.66
5093 8254 6.872585 AATGGGCCAGATATTTTTCTTTGA 57.127 33.333 13.78 0.00 0.00 2.69
5215 8376 2.222886 CGTTCATCTGCCTTCACGAATG 60.223 50.000 0.00 0.00 0.00 2.67
5304 8466 9.944663 TGTATTGTGTTCTAGAAAACATGTTTC 57.055 29.630 25.63 16.16 40.96 2.78
5329 8491 2.800881 TATATGAGCGCCTGTGTCTG 57.199 50.000 2.29 0.00 0.00 3.51
5337 8499 0.439985 CGTGTGCATATATGAGCGCC 59.560 55.000 17.10 0.00 40.37 6.53
5350 8512 1.666872 GGGGTGAGTGTACGTGTGC 60.667 63.158 0.00 0.00 0.00 4.57
5365 8527 1.067354 GGTAGTGTGTGTTCGTAGGGG 60.067 57.143 0.00 0.00 0.00 4.79
5372 8534 5.805994 GTGCTTATAGAGGTAGTGTGTGTTC 59.194 44.000 0.00 0.00 0.00 3.18
5433 8595 9.891535 GCTCGCATTTTTCTTGATTTATTTTAG 57.108 29.630 0.00 0.00 0.00 1.85
5434 8596 9.416794 TGCTCGCATTTTTCTTGATTTATTTTA 57.583 25.926 0.00 0.00 0.00 1.52
5435 8597 8.223100 GTGCTCGCATTTTTCTTGATTTATTTT 58.777 29.630 0.00 0.00 0.00 1.82
5436 8598 7.148590 GGTGCTCGCATTTTTCTTGATTTATTT 60.149 33.333 0.00 0.00 0.00 1.40
5437 8599 6.311200 GGTGCTCGCATTTTTCTTGATTTATT 59.689 34.615 0.00 0.00 0.00 1.40
5438 8600 5.807011 GGTGCTCGCATTTTTCTTGATTTAT 59.193 36.000 0.00 0.00 0.00 1.40
5439 8601 5.160641 GGTGCTCGCATTTTTCTTGATTTA 58.839 37.500 0.00 0.00 0.00 1.40
5440 8602 3.989817 GGTGCTCGCATTTTTCTTGATTT 59.010 39.130 0.00 0.00 0.00 2.17
5441 8603 3.005684 TGGTGCTCGCATTTTTCTTGATT 59.994 39.130 0.00 0.00 0.00 2.57
5442 8604 2.557924 TGGTGCTCGCATTTTTCTTGAT 59.442 40.909 0.00 0.00 0.00 2.57
5443 8605 1.952990 TGGTGCTCGCATTTTTCTTGA 59.047 42.857 0.00 0.00 0.00 3.02
5444 8606 2.322161 CTGGTGCTCGCATTTTTCTTG 58.678 47.619 0.00 0.00 0.00 3.02
5445 8607 1.270550 CCTGGTGCTCGCATTTTTCTT 59.729 47.619 0.00 0.00 0.00 2.52
5446 8608 0.883833 CCTGGTGCTCGCATTTTTCT 59.116 50.000 0.00 0.00 0.00 2.52
5447 8609 0.881118 TCCTGGTGCTCGCATTTTTC 59.119 50.000 0.00 0.00 0.00 2.29
5448 8610 1.327303 TTCCTGGTGCTCGCATTTTT 58.673 45.000 0.00 0.00 0.00 1.94
5449 8611 1.549203 ATTCCTGGTGCTCGCATTTT 58.451 45.000 0.00 0.00 0.00 1.82
5450 8612 1.203052 CAATTCCTGGTGCTCGCATTT 59.797 47.619 0.00 0.00 0.00 2.32
5451 8613 0.813184 CAATTCCTGGTGCTCGCATT 59.187 50.000 0.00 0.00 0.00 3.56
5452 8614 0.035152 TCAATTCCTGGTGCTCGCAT 60.035 50.000 0.00 0.00 0.00 4.73
5453 8615 0.250684 TTCAATTCCTGGTGCTCGCA 60.251 50.000 0.00 0.00 0.00 5.10
5454 8616 0.169009 GTTCAATTCCTGGTGCTCGC 59.831 55.000 0.00 0.00 0.00 5.03
5455 8617 0.804989 GGTTCAATTCCTGGTGCTCG 59.195 55.000 0.00 0.00 0.00 5.03
5456 8618 1.177401 GGGTTCAATTCCTGGTGCTC 58.823 55.000 0.00 0.00 0.00 4.26
5457 8619 0.779997 AGGGTTCAATTCCTGGTGCT 59.220 50.000 0.00 0.00 31.11 4.40
5458 8620 0.890683 CAGGGTTCAATTCCTGGTGC 59.109 55.000 3.47 0.00 44.99 5.01
5463 8625 1.000896 CCGCCAGGGTTCAATTCCT 60.001 57.895 0.00 0.00 0.00 3.36
5464 8626 3.603365 CCGCCAGGGTTCAATTCC 58.397 61.111 0.00 0.00 0.00 3.01
5474 8636 4.256180 GTATCCCAGCCCGCCAGG 62.256 72.222 0.00 0.00 39.47 4.45
5475 8637 4.256180 GGTATCCCAGCCCGCCAG 62.256 72.222 0.00 0.00 0.00 4.85
5477 8639 4.564110 GTGGTATCCCAGCCCGCC 62.564 72.222 0.00 0.00 42.94 6.13
5478 8640 3.480133 AGTGGTATCCCAGCCCGC 61.480 66.667 0.00 0.00 42.94 6.13
5479 8641 2.367202 ACAGTGGTATCCCAGCCCG 61.367 63.158 0.00 0.00 42.94 6.13
5480 8642 1.224592 CACAGTGGTATCCCAGCCC 59.775 63.158 0.00 0.00 42.94 5.19
5485 8647 3.695830 TTCTCAACACAGTGGTATCCC 57.304 47.619 5.31 0.00 0.00 3.85
5486 8648 3.865745 CGATTCTCAACACAGTGGTATCC 59.134 47.826 5.31 0.00 0.00 2.59
5495 8657 7.609760 AAATTATGCTACGATTCTCAACACA 57.390 32.000 0.00 0.00 0.00 3.72
5496 8658 9.982291 TTAAAATTATGCTACGATTCTCAACAC 57.018 29.630 0.00 0.00 0.00 3.32
5718 8880 2.983930 GAGGAGACGTCGCTGCACT 61.984 63.158 18.88 7.35 0.00 4.40
5733 8895 2.641305 CTTGCTGGATCAAGAAGGAGG 58.359 52.381 0.00 0.00 44.61 4.30
5757 8919 4.102210 TGGATCTCCATCAACCTCTCATTC 59.898 45.833 0.00 0.00 42.01 2.67
5760 8922 3.036819 CTGGATCTCCATCAACCTCTCA 58.963 50.000 0.00 0.00 46.46 3.27
5900 9064 4.416738 GGAGGGAGGGCAGCACAC 62.417 72.222 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.