Multiple sequence alignment - TraesCS6A01G048400

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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 TraesCS6A01G048400 chr6A 100.000 3071 0 0 1 3071 24704518 24707588 0.000000e+00 5672.0
1 TraesCS6A01G048400 chr6A 79.460 1037 146 31 1312 2315 24571349 24572351 0.000000e+00 673.0
2 TraesCS6A01G048400 chr6A 80.510 785 122 16 964 1734 24573863 24574630 9.550000e-160 573.0
3 TraesCS6A01G048400 chr6A 100.000 33 0 0 2318 2350 24706802 24706834 9.190000e-06 62.1
4 TraesCS6A01G048400 chr6A 100.000 33 0 0 2285 2317 24706835 24706867 9.190000e-06 62.1
5 TraesCS6A01G048400 chr6A 97.143 35 1 0 2934 2968 24707359 24707393 3.310000e-05 60.2
6 TraesCS6A01G048400 chr6A 97.143 35 1 0 2842 2876 24707451 24707485 3.310000e-05 60.2
7 TraesCS6A01G048400 chr6B 91.678 1454 78 20 879 2317 43144723 43146148 0.000000e+00 1975.0
8 TraesCS6A01G048400 chr6B 82.140 1439 175 37 912 2306 42855439 42856839 0.000000e+00 1158.0
9 TraesCS6A01G048400 chr6B 82.602 1230 158 26 1000 2203 43090143 43088944 0.000000e+00 1035.0
10 TraesCS6A01G048400 chr6B 80.645 1395 192 40 964 2305 42860606 42861975 0.000000e+00 1009.0
11 TraesCS6A01G048400 chr6B 92.841 433 22 9 2318 2743 43146116 43146546 1.210000e-173 619.0
12 TraesCS6A01G048400 chr6B 83.962 318 45 5 2451 2764 42857106 42857421 1.790000e-77 300.0
13 TraesCS6A01G048400 chr6B 94.118 136 5 2 2934 3066 43146708 43146843 1.440000e-48 204.0
14 TraesCS6A01G048400 chr6B 87.931 174 15 5 1 169 43142380 43142552 1.870000e-47 200.0
15 TraesCS6A01G048400 chr6B 79.181 293 50 7 348 639 696881882 696881600 3.120000e-45 193.0
16 TraesCS6A01G048400 chr6B 84.375 160 18 5 2600 2753 43071753 43071595 1.910000e-32 150.0
17 TraesCS6A01G048400 chr6B 78.229 271 23 18 2799 3064 43071515 43071276 1.150000e-29 141.0
18 TraesCS6A01G048400 chr6B 84.553 123 9 7 2760 2876 43146624 43146742 2.500000e-21 113.0
19 TraesCS6A01G048400 chr6B 85.263 95 6 5 2799 2890 42857495 42857584 1.170000e-14 91.6
20 TraesCS6A01G048400 chr6B 100.000 33 0 0 2936 2968 42857538 42857570 9.190000e-06 62.1
21 TraesCS6A01G048400 chr6B 100.000 33 0 0 2936 2968 43071472 43071440 9.190000e-06 62.1
22 TraesCS6A01G048400 chrUn 91.866 922 50 12 1 920 93938405 93939303 0.000000e+00 1264.0
23 TraesCS6A01G048400 chrUn 93.627 816 41 1 1513 2317 93939363 93940178 0.000000e+00 1208.0
24 TraesCS6A01G048400 chrUn 81.799 1401 178 37 944 2306 93869405 93870766 0.000000e+00 1103.0
25 TraesCS6A01G048400 chrUn 81.469 1198 171 19 1148 2314 93879961 93881138 0.000000e+00 935.0
26 TraesCS6A01G048400 chrUn 78.403 1403 207 48 948 2315 93876845 93878186 0.000000e+00 824.0
27 TraesCS6A01G048400 chrUn 94.050 437 22 1 2318 2750 93940146 93940582 0.000000e+00 660.0
28 TraesCS6A01G048400 chrUn 81.278 454 51 16 2318 2764 93870745 93871171 1.360000e-88 337.0
29 TraesCS6A01G048400 chrUn 88.406 138 4 2 2934 3071 93940720 93940845 4.100000e-34 156.0
30 TraesCS6A01G048400 chrUn 90.625 96 8 1 2969 3064 93872712 93872806 3.210000e-25 126.0
31 TraesCS6A01G048400 chrUn 84.211 95 7 5 2799 2890 93871245 93871334 5.460000e-13 86.1
32 TraesCS6A01G048400 chrUn 100.000 33 0 0 2936 2968 93871288 93871320 9.190000e-06 62.1
33 TraesCS6A01G048400 chr7B 75.902 1386 241 65 859 2192 6375105 6373761 9.350000e-175 623.0
34 TraesCS6A01G048400 chr7B 75.895 726 133 22 1616 2311 6034032 6033319 1.760000e-87 333.0
35 TraesCS6A01G048400 chr7B 80.000 295 47 9 377 670 61744569 61744852 1.120000e-49 207.0
36 TraesCS6A01G048400 chr7B 79.675 246 32 10 1001 1246 7541517 7541744 8.810000e-36 161.0
37 TraesCS6A01G048400 chr7B 74.820 417 76 13 1594 1993 7542173 7542577 8.810000e-36 161.0
38 TraesCS6A01G048400 chr7A 75.446 1344 239 58 911 2192 68901976 68900662 1.240000e-158 569.0
39 TraesCS6A01G048400 chr7A 81.618 272 40 6 371 642 276106001 276105740 1.850000e-52 217.0
40 TraesCS6A01G048400 chr7D 75.649 1232 219 52 1014 2192 64736588 64735385 3.480000e-149 538.0
41 TraesCS6A01G048400 chr7D 79.474 380 52 17 891 1264 64468258 64467899 2.370000e-61 246.0
42 TraesCS6A01G048400 chr2B 81.562 320 43 15 323 639 87830540 87830846 1.830000e-62 250.0
43 TraesCS6A01G048400 chr2B 80.351 285 44 9 323 605 441895928 441895654 4.010000e-49 206.0
44 TraesCS6A01G048400 chr3A 78.963 328 58 8 347 670 730111353 730111673 2.400000e-51 213.0
45 TraesCS6A01G048400 chr6D 79.211 279 49 6 361 639 458464052 458463783 5.230000e-43 185.0
46 TraesCS6A01G048400 chr5D 77.673 318 57 10 323 639 521874377 521874681 6.760000e-42 182.0


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 TraesCS6A01G048400 chr6A 24704518 24707588 3070 False 1183.32 5672 98.85720 1 3071 5 chr6A.!!$F2 3070
1 TraesCS6A01G048400 chr6A 24571349 24574630 3281 False 623.00 673 79.98500 964 2315 2 chr6A.!!$F1 1351
2 TraesCS6A01G048400 chr6B 43088944 43090143 1199 True 1035.00 1035 82.60200 1000 2203 1 chr6B.!!$R1 1203
3 TraesCS6A01G048400 chr6B 43142380 43146843 4463 False 622.20 1975 90.22420 1 3066 5 chr6B.!!$F2 3065
4 TraesCS6A01G048400 chr6B 42855439 42861975 6536 False 524.14 1158 86.40200 912 2968 5 chr6B.!!$F1 2056
5 TraesCS6A01G048400 chrUn 93876845 93881138 4293 False 879.50 935 79.93600 948 2315 2 chrUn.!!$F2 1367
6 TraesCS6A01G048400 chrUn 93938405 93940845 2440 False 822.00 1264 91.98725 1 3071 4 chrUn.!!$F3 3070
7 TraesCS6A01G048400 chrUn 93869405 93872806 3401 False 342.84 1103 87.58260 944 3064 5 chrUn.!!$F1 2120
8 TraesCS6A01G048400 chr7B 6373761 6375105 1344 True 623.00 623 75.90200 859 2192 1 chr7B.!!$R2 1333
9 TraesCS6A01G048400 chr7B 6033319 6034032 713 True 333.00 333 75.89500 1616 2311 1 chr7B.!!$R1 695
10 TraesCS6A01G048400 chr7A 68900662 68901976 1314 True 569.00 569 75.44600 911 2192 1 chr7A.!!$R1 1281
11 TraesCS6A01G048400 chr7D 64735385 64736588 1203 True 538.00 538 75.64900 1014 2192 1 chr7D.!!$R2 1178

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
365 765 0.228490 AAAAATTGAAACGCGCGCAC 59.772 45.0 32.58 21.21 0.0 5.34 F
1138 2804 0.030908 GAAGATCCTCGGATTCGCGT 59.969 55.0 5.77 0.00 34.6 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 3581 0.179029 CCGGACCAACAAACAGGACT 60.179 55.0 0.0 0.0 0.0 3.85 R
2933 8453 0.029300 TTCAAAGAGCACTGCAACGC 59.971 50.0 3.3 0.0 0.0 4.84 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
100 107 7.367285 CCGAATCAAACTTGTCTTTTTCCATA 58.633 34.615 0.00 0.00 0.00 2.74
101 108 8.028938 CCGAATCAAACTTGTCTTTTTCCATAT 58.971 33.333 0.00 0.00 0.00 1.78
142 149 9.109393 TCTGTTTTATTATTGCCAGTATGTCTC 57.891 33.333 0.00 0.00 0.00 3.36
169 176 9.586435 CTTTGATTGTTTCCAAACTAAAAGAGT 57.414 29.630 3.92 0.00 41.56 3.24
275 675 5.820926 TTTGCATAAATGACTGCGAAAAC 57.179 34.783 0.00 0.00 41.32 2.43
283 683 2.869897 TGACTGCGAAAACCAAACAAC 58.130 42.857 0.00 0.00 0.00 3.32
359 759 7.769766 TCGAGAACAAATAAAAATTGAAACGC 58.230 30.769 0.00 0.00 0.00 4.84
360 760 6.721426 CGAGAACAAATAAAAATTGAAACGCG 59.279 34.615 3.53 3.53 0.00 6.01
362 762 4.682997 ACAAATAAAAATTGAAACGCGCG 58.317 34.783 30.96 30.96 0.00 6.86
363 763 3.347306 AATAAAAATTGAAACGCGCGC 57.653 38.095 32.58 23.91 0.00 6.86
364 764 1.755161 TAAAAATTGAAACGCGCGCA 58.245 40.000 32.58 17.88 0.00 6.09
365 765 0.228490 AAAAATTGAAACGCGCGCAC 59.772 45.000 32.58 21.21 0.00 5.34
366 766 0.593773 AAAATTGAAACGCGCGCACT 60.594 45.000 32.58 14.96 0.00 4.40
367 767 0.996727 AAATTGAAACGCGCGCACTC 60.997 50.000 32.58 23.23 0.00 3.51
368 768 3.629491 ATTGAAACGCGCGCACTCG 62.629 57.895 32.58 17.34 39.07 4.18
420 820 6.256053 AGTTGATGTTTTGGTAAGATCCCAT 58.744 36.000 0.00 0.00 0.00 4.00
451 851 4.956700 TGGGTATGAGTAGAGGAAGACAAG 59.043 45.833 0.00 0.00 0.00 3.16
530 930 8.474025 TGTATGATGTTTCTTTTGGAAAAGTGT 58.526 29.630 10.83 0.00 44.34 3.55
533 933 7.035004 TGATGTTTCTTTTGGAAAAGTGTCAG 58.965 34.615 10.83 0.00 44.34 3.51
535 935 6.754193 TGTTTCTTTTGGAAAAGTGTCAGTT 58.246 32.000 10.83 0.00 44.34 3.16
568 968 4.587306 AGTTATAATGCACGCGTCAAATG 58.413 39.130 9.86 0.00 0.00 2.32
606 1007 2.153645 TGCGCTTGAGTGAAACATCAT 58.846 42.857 9.73 0.00 41.43 2.45
607 1008 2.160219 TGCGCTTGAGTGAAACATCATC 59.840 45.455 9.73 0.00 41.43 2.92
619 1020 2.575694 ACATCATCTGTCAGACGCTC 57.424 50.000 4.21 0.00 29.94 5.03
673 1074 2.125673 CGCTACCAACTCCCGTGG 60.126 66.667 0.00 0.00 0.00 4.94
713 1114 2.569404 ACCTACTGCTCCTCTTTCAAGG 59.431 50.000 0.00 0.00 37.81 3.61
718 1119 4.281657 ACTGCTCCTCTTTCAAGGTTTTT 58.718 39.130 0.00 0.00 37.69 1.94
725 1126 6.250711 TCCTCTTTCAAGGTTTTTATACCCC 58.749 40.000 0.00 0.00 39.08 4.95
780 1181 4.796038 ATCAACTTCCTTTCCTTGCATG 57.204 40.909 0.00 0.00 0.00 4.06
783 1184 3.795688 ACTTCCTTTCCTTGCATGAGA 57.204 42.857 0.00 0.00 0.00 3.27
789 1190 3.691118 CCTTTCCTTGCATGAGATTTCGA 59.309 43.478 0.00 0.00 0.00 3.71
790 1191 4.156556 CCTTTCCTTGCATGAGATTTCGAA 59.843 41.667 0.00 0.00 0.00 3.71
1030 2696 4.596585 AACCCACGGCCACCCAAG 62.597 66.667 2.24 0.00 0.00 3.61
1131 2797 2.961741 CCTCATTGAGAAGATCCTCGGA 59.038 50.000 15.36 0.00 35.99 4.55
1132 2798 3.577848 CCTCATTGAGAAGATCCTCGGAT 59.422 47.826 15.36 0.00 35.99 4.18
1133 2799 4.040217 CCTCATTGAGAAGATCCTCGGATT 59.960 45.833 15.36 0.00 35.99 3.01
1134 2800 5.207110 TCATTGAGAAGATCCTCGGATTC 57.793 43.478 0.00 0.00 35.99 2.52
1135 2801 3.717400 TTGAGAAGATCCTCGGATTCG 57.283 47.619 0.00 0.00 35.99 3.34
1136 2802 1.338337 TGAGAAGATCCTCGGATTCGC 59.662 52.381 0.00 0.00 35.99 4.70
1137 2803 0.312416 AGAAGATCCTCGGATTCGCG 59.688 55.000 0.00 0.00 34.60 5.87
1138 2804 0.030908 GAAGATCCTCGGATTCGCGT 59.969 55.000 5.77 0.00 34.60 6.01
1139 2805 0.030908 AAGATCCTCGGATTCGCGTC 59.969 55.000 5.77 0.00 34.60 5.19
1141 2807 2.071844 GATCCTCGGATTCGCGTCCA 62.072 60.000 15.23 2.93 38.21 4.02
1230 2896 3.155167 CTAGCGAGACCCACCCCC 61.155 72.222 0.00 0.00 0.00 5.40
1259 2925 3.044305 GCTCAAGCTCGCCAACGT 61.044 61.111 0.00 0.00 41.18 3.99
1278 2947 3.065306 CACAGCCAGTCCCCGTTA 58.935 61.111 0.00 0.00 0.00 3.18
1285 2954 1.667151 CAGTCCCCGTTACGGTTCA 59.333 57.895 22.78 2.67 46.80 3.18
1341 3010 1.443407 CATCTACTCCCTGCCGGTG 59.557 63.158 1.90 0.00 0.00 4.94
1342 3011 1.043116 CATCTACTCCCTGCCGGTGA 61.043 60.000 1.90 0.00 0.00 4.02
1423 3098 3.996363 CCCAAAAGGCATGAACTTTAAGC 59.004 43.478 13.90 0.00 37.18 3.09
1836 3557 1.587613 GCGCTTCCTCTGCTACTCG 60.588 63.158 0.00 0.00 0.00 4.18
1860 3581 3.003173 CTGGAGTCGGAAGGGGCA 61.003 66.667 0.00 0.00 0.00 5.36
1948 3670 0.613260 GGTGTACAGGCTGGATGTCA 59.387 55.000 20.34 1.34 32.02 3.58
2077 3810 3.650942 TCTACTTTGTGGGTGAGGTTGAT 59.349 43.478 0.00 0.00 0.00 2.57
2232 6925 3.572337 TGCACGTGCGCATTGTAT 58.428 50.000 33.22 0.00 45.83 2.29
2254 6947 3.211865 ACTCGGGAGAAAGGACAAAAAC 58.788 45.455 2.08 0.00 39.18 2.43
2331 7025 8.060090 GCAGTTAAATGCATATTTTGAGAATGC 58.940 33.333 22.11 0.91 45.77 3.56
2594 7547 3.530535 GCTGTTTGATTTGGTTGGTGTT 58.469 40.909 0.00 0.00 0.00 3.32
2702 7659 1.384989 GGAACGGCGGATCTCTCTCA 61.385 60.000 13.24 0.00 0.00 3.27
2711 7668 3.927854 CGGATCTCTCTCAGTCCGTATA 58.072 50.000 4.60 0.00 46.29 1.47
2726 8075 3.116300 CCGTATATGATATGGCGAGCAC 58.884 50.000 11.06 0.00 0.00 4.40
2787 8209 4.818534 ACTTTGTGATGCAGTGTACTTG 57.181 40.909 0.00 0.00 0.00 3.16
2807 8324 7.209471 ACTTGTAGAGTTGTTTTGTTGACAA 57.791 32.000 0.00 0.00 33.92 3.18
2809 8326 7.807907 ACTTGTAGAGTTGTTTTGTTGACAAAG 59.192 33.333 9.04 0.00 40.17 2.77
2810 8327 6.616947 TGTAGAGTTGTTTTGTTGACAAAGG 58.383 36.000 9.04 0.00 45.34 3.11
2811 8328 5.722021 AGAGTTGTTTTGTTGACAAAGGT 57.278 34.783 9.04 0.00 45.34 3.50
2815 8332 6.930731 AGTTGTTTTGTTGACAAAGGTGTAT 58.069 32.000 9.04 0.00 45.34 2.29
2816 8333 6.811170 AGTTGTTTTGTTGACAAAGGTGTATG 59.189 34.615 9.04 0.00 45.34 2.39
2817 8334 5.655488 TGTTTTGTTGACAAAGGTGTATGG 58.345 37.500 9.04 0.00 45.34 2.74
2845 8365 1.039856 AAATTCTGTGCCAAGGCGTT 58.960 45.000 6.60 0.00 45.51 4.84
2846 8366 0.314935 AATTCTGTGCCAAGGCGTTG 59.685 50.000 12.17 12.17 45.51 4.10
2854 8374 3.257933 CAAGGCGTTGGAGTGCTC 58.742 61.111 11.31 0.00 0.00 4.26
2855 8375 1.302033 CAAGGCGTTGGAGTGCTCT 60.302 57.895 11.31 0.00 0.00 4.09
2856 8376 0.886490 CAAGGCGTTGGAGTGCTCTT 60.886 55.000 11.31 0.00 0.00 2.85
2857 8377 0.179018 AAGGCGTTGGAGTGCTCTTT 60.179 50.000 0.00 0.00 0.00 2.52
2858 8378 0.886490 AGGCGTTGGAGTGCTCTTTG 60.886 55.000 0.00 0.00 0.00 2.77
2859 8379 0.884704 GGCGTTGGAGTGCTCTTTGA 60.885 55.000 0.00 0.00 0.00 2.69
2860 8380 0.944386 GCGTTGGAGTGCTCTTTGAA 59.056 50.000 0.00 0.00 0.00 2.69
2861 8381 1.537202 GCGTTGGAGTGCTCTTTGAAT 59.463 47.619 0.00 0.00 0.00 2.57
2862 8382 2.413371 GCGTTGGAGTGCTCTTTGAATC 60.413 50.000 0.00 0.00 0.00 2.52
2863 8383 2.160417 CGTTGGAGTGCTCTTTGAATCC 59.840 50.000 0.00 0.00 0.00 3.01
2864 8384 3.416156 GTTGGAGTGCTCTTTGAATCCT 58.584 45.455 0.00 0.00 0.00 3.24
2865 8385 3.795688 TGGAGTGCTCTTTGAATCCTT 57.204 42.857 0.00 0.00 0.00 3.36
2866 8386 4.104383 TGGAGTGCTCTTTGAATCCTTT 57.896 40.909 0.00 0.00 0.00 3.11
2867 8387 3.822735 TGGAGTGCTCTTTGAATCCTTTG 59.177 43.478 0.00 0.00 0.00 2.77
2868 8388 3.192212 GGAGTGCTCTTTGAATCCTTTGG 59.808 47.826 0.00 0.00 0.00 3.28
2869 8389 2.560105 AGTGCTCTTTGAATCCTTTGGC 59.440 45.455 0.00 0.00 0.00 4.52
2870 8390 2.560105 GTGCTCTTTGAATCCTTTGGCT 59.440 45.455 0.00 0.00 0.00 4.75
2871 8391 2.821969 TGCTCTTTGAATCCTTTGGCTC 59.178 45.455 0.00 0.00 0.00 4.70
2872 8392 3.087781 GCTCTTTGAATCCTTTGGCTCT 58.912 45.455 0.00 0.00 0.00 4.09
2873 8393 3.119566 GCTCTTTGAATCCTTTGGCTCTG 60.120 47.826 0.00 0.00 0.00 3.35
2874 8394 4.330250 CTCTTTGAATCCTTTGGCTCTGA 58.670 43.478 0.00 0.00 0.00 3.27
2875 8395 4.927049 TCTTTGAATCCTTTGGCTCTGAT 58.073 39.130 0.00 0.00 0.00 2.90
2876 8396 6.065976 TCTTTGAATCCTTTGGCTCTGATA 57.934 37.500 0.00 0.00 0.00 2.15
2877 8397 6.484288 TCTTTGAATCCTTTGGCTCTGATAA 58.516 36.000 0.00 0.00 0.00 1.75
2878 8398 7.121382 TCTTTGAATCCTTTGGCTCTGATAAT 58.879 34.615 0.00 0.00 0.00 1.28
2879 8399 6.704289 TTGAATCCTTTGGCTCTGATAATG 57.296 37.500 0.00 0.00 0.00 1.90
2880 8400 5.135383 TGAATCCTTTGGCTCTGATAATGG 58.865 41.667 0.00 0.00 0.00 3.16
2881 8401 3.582998 TCCTTTGGCTCTGATAATGGG 57.417 47.619 0.00 0.00 0.00 4.00
2882 8402 2.852449 TCCTTTGGCTCTGATAATGGGT 59.148 45.455 0.00 0.00 0.00 4.51
2883 8403 2.954318 CCTTTGGCTCTGATAATGGGTG 59.046 50.000 0.00 0.00 0.00 4.61
2884 8404 2.734755 TTGGCTCTGATAATGGGTGG 57.265 50.000 0.00 0.00 0.00 4.61
2885 8405 1.595311 TGGCTCTGATAATGGGTGGT 58.405 50.000 0.00 0.00 0.00 4.16
2886 8406 1.922447 TGGCTCTGATAATGGGTGGTT 59.078 47.619 0.00 0.00 0.00 3.67
2887 8407 2.311542 TGGCTCTGATAATGGGTGGTTT 59.688 45.455 0.00 0.00 0.00 3.27
2888 8408 2.952310 GGCTCTGATAATGGGTGGTTTC 59.048 50.000 0.00 0.00 0.00 2.78
2889 8409 3.372025 GGCTCTGATAATGGGTGGTTTCT 60.372 47.826 0.00 0.00 0.00 2.52
2890 8410 3.629398 GCTCTGATAATGGGTGGTTTCTG 59.371 47.826 0.00 0.00 0.00 3.02
2891 8411 4.202441 CTCTGATAATGGGTGGTTTCTGG 58.798 47.826 0.00 0.00 0.00 3.86
2892 8412 3.591527 TCTGATAATGGGTGGTTTCTGGT 59.408 43.478 0.00 0.00 0.00 4.00
2893 8413 4.785914 TCTGATAATGGGTGGTTTCTGGTA 59.214 41.667 0.00 0.00 0.00 3.25
2894 8414 5.104527 TCTGATAATGGGTGGTTTCTGGTAG 60.105 44.000 0.00 0.00 0.00 3.18
2895 8415 2.215942 AATGGGTGGTTTCTGGTAGC 57.784 50.000 0.00 0.00 0.00 3.58
2896 8416 1.072266 ATGGGTGGTTTCTGGTAGCA 58.928 50.000 0.00 0.00 0.00 3.49
2897 8417 0.847373 TGGGTGGTTTCTGGTAGCAA 59.153 50.000 0.00 0.00 0.00 3.91
2898 8418 1.427368 TGGGTGGTTTCTGGTAGCAAT 59.573 47.619 0.00 0.00 0.00 3.56
2899 8419 2.158385 TGGGTGGTTTCTGGTAGCAATT 60.158 45.455 0.00 0.00 0.00 2.32
2900 8420 2.897326 GGGTGGTTTCTGGTAGCAATTT 59.103 45.455 0.00 0.00 0.00 1.82
2901 8421 3.323691 GGGTGGTTTCTGGTAGCAATTTT 59.676 43.478 0.00 0.00 0.00 1.82
2902 8422 4.202315 GGGTGGTTTCTGGTAGCAATTTTT 60.202 41.667 0.00 0.00 0.00 1.94
2918 8438 2.835580 TTTTTGTGATGGGCATGGTG 57.164 45.000 0.00 0.00 0.00 4.17
2919 8439 2.006805 TTTTGTGATGGGCATGGTGA 57.993 45.000 0.00 0.00 0.00 4.02
2920 8440 1.548081 TTTGTGATGGGCATGGTGAG 58.452 50.000 0.00 0.00 0.00 3.51
2921 8441 0.323633 TTGTGATGGGCATGGTGAGG 60.324 55.000 0.00 0.00 0.00 3.86
2922 8442 1.304282 GTGATGGGCATGGTGAGGT 59.696 57.895 0.00 0.00 0.00 3.85
2923 8443 1.033746 GTGATGGGCATGGTGAGGTG 61.034 60.000 0.00 0.00 0.00 4.00
2924 8444 1.304282 GATGGGCATGGTGAGGTGT 59.696 57.895 0.00 0.00 0.00 4.16
2925 8445 1.000521 ATGGGCATGGTGAGGTGTG 60.001 57.895 0.00 0.00 0.00 3.82
2926 8446 3.064324 GGGCATGGTGAGGTGTGC 61.064 66.667 0.00 0.00 36.88 4.57
2927 8447 2.282391 GGCATGGTGAGGTGTGCA 60.282 61.111 0.00 0.00 39.27 4.57
2928 8448 1.679977 GGCATGGTGAGGTGTGCAT 60.680 57.895 0.00 0.00 39.27 3.96
2929 8449 0.394216 GGCATGGTGAGGTGTGCATA 60.394 55.000 0.00 0.00 39.27 3.14
2930 8450 1.683943 GCATGGTGAGGTGTGCATAT 58.316 50.000 0.00 0.00 37.52 1.78
2931 8451 1.335810 GCATGGTGAGGTGTGCATATG 59.664 52.381 0.00 0.00 37.52 1.78
2932 8452 2.646930 CATGGTGAGGTGTGCATATGT 58.353 47.619 4.29 0.00 0.00 2.29
2933 8453 2.112380 TGGTGAGGTGTGCATATGTG 57.888 50.000 4.29 0.00 0.00 3.21
3033 9944 4.874970 AGATGCCAAATTCTGTTTGTGTC 58.125 39.130 0.55 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.635030 AGGAACGTAGAATTTCTTGCTTTT 57.365 33.333 3.86 0.00 0.00 2.27
134 141 6.817765 TGGAAACAATCAAAGGAGACATAC 57.182 37.500 0.00 0.00 37.44 2.39
212 219 1.246056 CCTGCCTGCTTGCTGCTTTA 61.246 55.000 0.00 0.00 43.37 1.85
283 683 5.095490 ACCTACTTTTTCCGTACGTAATCG 58.905 41.667 15.21 0.00 43.34 3.34
336 736 6.511642 GCGCGTTTCAATTTTTATTTGTTCTC 59.488 34.615 8.43 0.00 0.00 2.87
341 741 3.528779 GCGCGCGTTTCAATTTTTATTTG 59.471 39.130 32.35 0.00 0.00 2.32
342 742 3.182572 TGCGCGCGTTTCAATTTTTATTT 59.817 34.783 32.35 0.00 0.00 1.40
345 745 1.448677 GTGCGCGCGTTTCAATTTTTA 59.551 42.857 32.35 0.00 0.00 1.52
420 820 7.265599 TCCTCTACTCATACCCAAATCAAAA 57.734 36.000 0.00 0.00 0.00 2.44
551 951 0.449786 CCCATTTGACGCGTGCATTA 59.550 50.000 20.70 6.49 0.00 1.90
552 952 1.212490 CCCATTTGACGCGTGCATT 59.788 52.632 20.70 2.79 0.00 3.56
554 954 4.036804 GCCCATTTGACGCGTGCA 62.037 61.111 20.70 12.29 0.00 4.57
555 955 3.737172 AGCCCATTTGACGCGTGC 61.737 61.111 20.70 12.64 0.00 5.34
606 1007 1.077123 GACTACGAGCGTCTGACAGA 58.923 55.000 8.73 0.00 0.00 3.41
607 1008 0.247340 CGACTACGAGCGTCTGACAG 60.247 60.000 8.73 0.00 42.66 3.51
619 1020 6.718388 TCACCAACACTATATTACGACTACG 58.282 40.000 0.00 0.00 45.75 3.51
673 1074 1.330655 TTCGTGCATCTCTCCTCCCC 61.331 60.000 0.00 0.00 0.00 4.81
680 1081 1.134965 GCAGTAGGTTCGTGCATCTCT 60.135 52.381 0.00 0.00 37.16 3.10
780 1181 3.718815 AGACGGGCTATTTCGAAATCTC 58.281 45.455 25.89 17.67 0.00 2.75
783 1184 2.169769 TGGAGACGGGCTATTTCGAAAT 59.830 45.455 25.48 25.48 0.00 2.17
789 1190 1.682087 GGCTTTGGAGACGGGCTATTT 60.682 52.381 0.00 0.00 0.00 1.40
790 1191 0.107165 GGCTTTGGAGACGGGCTATT 60.107 55.000 0.00 0.00 0.00 1.73
1012 2678 4.904590 TTGGGTGGCCGTGGGTTG 62.905 66.667 0.00 0.00 0.00 3.77
1030 2696 3.621394 GACGCGGATCTTGCTCGC 61.621 66.667 12.47 3.55 45.15 5.03
1230 2896 2.664851 TTGAGCGCGAACAGGTGG 60.665 61.111 12.10 0.00 0.00 4.61
1755 3472 1.377725 CTTCTTCAGGCGCCATGGT 60.378 57.895 31.54 4.11 0.00 3.55
1836 3557 3.240134 TTCCGACTCCAGCAGGTGC 62.240 63.158 0.00 0.00 42.49 5.01
1860 3581 0.179029 CCGGACCAACAAACAGGACT 60.179 55.000 0.00 0.00 0.00 3.85
2077 3810 2.617276 CCAGGTGACGTAGGAGTAGTCA 60.617 54.545 0.00 0.00 41.90 3.41
2232 6925 4.383173 GTTTTTGTCCTTTCTCCCGAGTA 58.617 43.478 0.00 0.00 0.00 2.59
2254 6947 6.153680 AGTCAGATGTACCTGAAGAACTTAGG 59.846 42.308 3.71 0.00 43.94 2.69
2317 7011 8.915057 ACTGCTATACTGCATTCTCAAAATAT 57.085 30.769 0.00 0.00 42.48 1.28
2318 7012 8.737168 AACTGCTATACTGCATTCTCAAAATA 57.263 30.769 0.00 0.00 42.48 1.40
2319 7013 7.636150 AACTGCTATACTGCATTCTCAAAAT 57.364 32.000 0.00 0.00 42.48 1.82
2320 7014 8.560355 TTAACTGCTATACTGCATTCTCAAAA 57.440 30.769 0.00 0.00 42.48 2.44
2321 7015 8.560355 TTTAACTGCTATACTGCATTCTCAAA 57.440 30.769 0.00 0.00 42.48 2.69
2322 7016 8.615211 CATTTAACTGCTATACTGCATTCTCAA 58.385 33.333 0.00 0.00 42.48 3.02
2323 7017 7.254898 GCATTTAACTGCTATACTGCATTCTCA 60.255 37.037 10.33 0.00 42.48 3.27
2324 7018 7.074502 GCATTTAACTGCTATACTGCATTCTC 58.925 38.462 10.33 0.00 42.48 2.87
2325 7019 6.963796 GCATTTAACTGCTATACTGCATTCT 58.036 36.000 10.33 0.00 42.48 2.40
2338 7032 5.335127 CCATCTGTGTTAGCATTTAACTGC 58.665 41.667 9.64 9.64 42.62 4.40
2339 7033 5.124457 AGCCATCTGTGTTAGCATTTAACTG 59.876 40.000 0.00 0.00 0.00 3.16
2340 7034 5.256474 AGCCATCTGTGTTAGCATTTAACT 58.744 37.500 0.00 0.00 0.00 2.24
2341 7035 5.567138 AGCCATCTGTGTTAGCATTTAAC 57.433 39.130 0.00 0.00 0.00 2.01
2342 7036 5.945784 AGAAGCCATCTGTGTTAGCATTTAA 59.054 36.000 0.00 0.00 36.88 1.52
2343 7037 5.500234 AGAAGCCATCTGTGTTAGCATTTA 58.500 37.500 0.00 0.00 36.88 1.40
2344 7038 4.338879 AGAAGCCATCTGTGTTAGCATTT 58.661 39.130 0.00 0.00 36.88 2.32
2345 7039 3.960571 AGAAGCCATCTGTGTTAGCATT 58.039 40.909 0.00 0.00 36.88 3.56
2346 7040 3.641434 AGAAGCCATCTGTGTTAGCAT 57.359 42.857 0.00 0.00 36.88 3.79
2347 7041 3.423539 AAGAAGCCATCTGTGTTAGCA 57.576 42.857 0.00 0.00 38.79 3.49
2348 7042 4.773323 AAAAGAAGCCATCTGTGTTAGC 57.227 40.909 0.00 0.00 38.79 3.09
2349 7043 6.094603 AGCATAAAAGAAGCCATCTGTGTTAG 59.905 38.462 0.00 0.00 38.79 2.34
2594 7547 4.400884 ACAAGGTCTACAACAACATGCAAA 59.599 37.500 0.00 0.00 0.00 3.68
2702 7659 3.066900 GCTCGCCATATCATATACGGACT 59.933 47.826 0.71 0.00 0.00 3.85
2711 7668 1.669115 GCCGTGCTCGCCATATCAT 60.669 57.895 1.89 0.00 35.54 2.45
2726 8075 2.949714 GGTGATGAACATAATCGCCG 57.050 50.000 0.60 0.00 42.97 6.46
2773 8195 5.230942 ACAACTCTACAAGTACACTGCATC 58.769 41.667 0.00 0.00 37.17 3.91
2787 8209 6.526674 CACCTTTGTCAACAAAACAACTCTAC 59.473 38.462 9.40 0.00 44.24 2.59
2807 8324 1.502690 TGGCCGATACCATACACCTT 58.497 50.000 0.00 0.00 33.75 3.50
2809 8326 2.335316 TTTGGCCGATACCATACACC 57.665 50.000 0.00 0.00 40.13 4.16
2810 8327 4.024048 CAGAATTTGGCCGATACCATACAC 60.024 45.833 0.00 0.00 40.13 2.90
2811 8328 4.133820 CAGAATTTGGCCGATACCATACA 58.866 43.478 0.00 0.00 40.13 2.29
2815 8332 2.364632 CACAGAATTTGGCCGATACCA 58.635 47.619 0.00 0.00 38.16 3.25
2816 8333 1.065551 GCACAGAATTTGGCCGATACC 59.934 52.381 0.00 0.00 0.00 2.73
2817 8334 1.065551 GGCACAGAATTTGGCCGATAC 59.934 52.381 0.00 0.00 34.75 2.24
2845 8365 3.795688 AAGGATTCAAAGAGCACTCCA 57.204 42.857 0.00 0.00 0.00 3.86
2846 8366 3.192212 CCAAAGGATTCAAAGAGCACTCC 59.808 47.826 0.00 0.00 0.00 3.85
2847 8367 3.366781 GCCAAAGGATTCAAAGAGCACTC 60.367 47.826 0.00 0.00 0.00 3.51
2848 8368 2.560105 GCCAAAGGATTCAAAGAGCACT 59.440 45.455 0.00 0.00 0.00 4.40
2849 8369 2.560105 AGCCAAAGGATTCAAAGAGCAC 59.440 45.455 0.00 0.00 0.00 4.40
2850 8370 2.821969 GAGCCAAAGGATTCAAAGAGCA 59.178 45.455 0.00 0.00 0.00 4.26
2851 8371 3.087781 AGAGCCAAAGGATTCAAAGAGC 58.912 45.455 0.00 0.00 0.00 4.09
2852 8372 4.330250 TCAGAGCCAAAGGATTCAAAGAG 58.670 43.478 0.00 0.00 0.00 2.85
2853 8373 4.371624 TCAGAGCCAAAGGATTCAAAGA 57.628 40.909 0.00 0.00 0.00 2.52
2854 8374 6.764308 TTATCAGAGCCAAAGGATTCAAAG 57.236 37.500 0.00 0.00 0.00 2.77
2855 8375 6.097270 CCATTATCAGAGCCAAAGGATTCAAA 59.903 38.462 0.00 0.00 0.00 2.69
2856 8376 5.595542 CCATTATCAGAGCCAAAGGATTCAA 59.404 40.000 0.00 0.00 0.00 2.69
2857 8377 5.135383 CCATTATCAGAGCCAAAGGATTCA 58.865 41.667 0.00 0.00 0.00 2.57
2858 8378 4.522022 CCCATTATCAGAGCCAAAGGATTC 59.478 45.833 0.00 0.00 0.00 2.52
2859 8379 4.078980 ACCCATTATCAGAGCCAAAGGATT 60.079 41.667 0.00 0.00 0.00 3.01
2860 8380 3.464833 ACCCATTATCAGAGCCAAAGGAT 59.535 43.478 0.00 0.00 0.00 3.24
2861 8381 2.852449 ACCCATTATCAGAGCCAAAGGA 59.148 45.455 0.00 0.00 0.00 3.36
2862 8382 2.954318 CACCCATTATCAGAGCCAAAGG 59.046 50.000 0.00 0.00 0.00 3.11
2863 8383 2.954318 CCACCCATTATCAGAGCCAAAG 59.046 50.000 0.00 0.00 0.00 2.77
2864 8384 2.311542 ACCACCCATTATCAGAGCCAAA 59.688 45.455 0.00 0.00 0.00 3.28
2865 8385 1.922447 ACCACCCATTATCAGAGCCAA 59.078 47.619 0.00 0.00 0.00 4.52
2866 8386 1.595311 ACCACCCATTATCAGAGCCA 58.405 50.000 0.00 0.00 0.00 4.75
2867 8387 2.736670 AACCACCCATTATCAGAGCC 57.263 50.000 0.00 0.00 0.00 4.70
2868 8388 3.629398 CAGAAACCACCCATTATCAGAGC 59.371 47.826 0.00 0.00 0.00 4.09
2869 8389 4.202441 CCAGAAACCACCCATTATCAGAG 58.798 47.826 0.00 0.00 0.00 3.35
2870 8390 3.591527 ACCAGAAACCACCCATTATCAGA 59.408 43.478 0.00 0.00 0.00 3.27
2871 8391 3.968265 ACCAGAAACCACCCATTATCAG 58.032 45.455 0.00 0.00 0.00 2.90
2872 8392 4.627741 GCTACCAGAAACCACCCATTATCA 60.628 45.833 0.00 0.00 0.00 2.15
2873 8393 3.883489 GCTACCAGAAACCACCCATTATC 59.117 47.826 0.00 0.00 0.00 1.75
2874 8394 3.268334 TGCTACCAGAAACCACCCATTAT 59.732 43.478 0.00 0.00 0.00 1.28
2875 8395 2.645297 TGCTACCAGAAACCACCCATTA 59.355 45.455 0.00 0.00 0.00 1.90
2876 8396 1.427368 TGCTACCAGAAACCACCCATT 59.573 47.619 0.00 0.00 0.00 3.16
2877 8397 1.072266 TGCTACCAGAAACCACCCAT 58.928 50.000 0.00 0.00 0.00 4.00
2878 8398 0.847373 TTGCTACCAGAAACCACCCA 59.153 50.000 0.00 0.00 0.00 4.51
2879 8399 2.215942 ATTGCTACCAGAAACCACCC 57.784 50.000 0.00 0.00 0.00 4.61
2880 8400 4.600692 AAAATTGCTACCAGAAACCACC 57.399 40.909 0.00 0.00 0.00 4.61
2899 8419 2.299582 CTCACCATGCCCATCACAAAAA 59.700 45.455 0.00 0.00 0.00 1.94
2900 8420 1.894466 CTCACCATGCCCATCACAAAA 59.106 47.619 0.00 0.00 0.00 2.44
2901 8421 1.548081 CTCACCATGCCCATCACAAA 58.452 50.000 0.00 0.00 0.00 2.83
2902 8422 0.323633 CCTCACCATGCCCATCACAA 60.324 55.000 0.00 0.00 0.00 3.33
2903 8423 1.303948 CCTCACCATGCCCATCACA 59.696 57.895 0.00 0.00 0.00 3.58
2904 8424 1.033746 CACCTCACCATGCCCATCAC 61.034 60.000 0.00 0.00 0.00 3.06
2905 8425 1.303948 CACCTCACCATGCCCATCA 59.696 57.895 0.00 0.00 0.00 3.07
2906 8426 1.033746 CACACCTCACCATGCCCATC 61.034 60.000 0.00 0.00 0.00 3.51
2907 8427 1.000521 CACACCTCACCATGCCCAT 60.001 57.895 0.00 0.00 0.00 4.00
2908 8428 2.435663 CACACCTCACCATGCCCA 59.564 61.111 0.00 0.00 0.00 5.36
2909 8429 3.064324 GCACACCTCACCATGCCC 61.064 66.667 0.00 0.00 31.71 5.36
2910 8430 0.394216 TATGCACACCTCACCATGCC 60.394 55.000 0.00 0.00 37.26 4.40
2911 8431 1.335810 CATATGCACACCTCACCATGC 59.664 52.381 0.00 0.00 38.59 4.06
2912 8432 2.356695 CACATATGCACACCTCACCATG 59.643 50.000 1.58 0.00 0.00 3.66
2913 8433 2.646930 CACATATGCACACCTCACCAT 58.353 47.619 1.58 0.00 0.00 3.55
2914 8434 2.112380 CACATATGCACACCTCACCA 57.888 50.000 1.58 0.00 0.00 4.17
2926 8446 0.448990 AGCACTGCAACGCACATATG 59.551 50.000 9.48 0.00 33.79 1.78
2927 8447 0.729116 GAGCACTGCAACGCACATAT 59.271 50.000 9.48 0.00 33.79 1.78
2928 8448 0.320683 AGAGCACTGCAACGCACATA 60.321 50.000 9.48 0.00 33.79 2.29
2929 8449 1.168407 AAGAGCACTGCAACGCACAT 61.168 50.000 9.48 0.00 33.79 3.21
2930 8450 1.375853 AAAGAGCACTGCAACGCACA 61.376 50.000 9.48 0.00 33.79 4.57
2931 8451 0.931662 CAAAGAGCACTGCAACGCAC 60.932 55.000 9.48 3.38 33.79 5.34
2932 8452 1.094650 TCAAAGAGCACTGCAACGCA 61.095 50.000 9.48 0.00 36.92 5.24
2933 8453 0.029300 TTCAAAGAGCACTGCAACGC 59.971 50.000 3.30 0.00 0.00 4.84
2934 8454 2.578495 GATTCAAAGAGCACTGCAACG 58.422 47.619 3.30 0.00 0.00 4.10
2935 8455 2.555757 AGGATTCAAAGAGCACTGCAAC 59.444 45.455 3.30 0.00 0.00 4.17
2936 8456 2.867624 AGGATTCAAAGAGCACTGCAA 58.132 42.857 3.30 0.00 0.00 4.08
3033 9944 4.933400 CCTCCAATTTCAGGCTTCAAATTG 59.067 41.667 23.13 23.13 44.43 2.32


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

AutoCloner maintained by Alex Coulton.