Multiple sequence alignment - TraesCS4B01G359900

Loading Multiple Alignment...

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 TraesCS4B01G359900 chr4B 100.000 3608 0 0 1 3608 650268749 650272356 0.000000e+00 6663
1 TraesCS4B01G359900 chr4B 92.125 800 49 10 4 794 619422573 619421779 0.000000e+00 1116
2 TraesCS4B01G359900 chr4B 77.248 734 119 28 2880 3601 667563069 667563766 1.570000e-103 387
3 TraesCS4B01G359900 chr4D 93.622 1709 87 10 817 2516 503964474 503966169 0.000000e+00 2532
4 TraesCS4B01G359900 chr4D 96.606 442 15 0 3159 3600 503968827 503969268 0.000000e+00 734
5 TraesCS4B01G359900 chr4D 94.225 329 18 1 2817 3144 503968515 503968843 5.380000e-138 501
6 TraesCS4B01G359900 chr4D 94.118 85 5 0 1773 1857 504065617 504065701 2.920000e-26 130
7 TraesCS4B01G359900 chr4D 90.123 81 3 3 807 882 503964393 503964473 2.290000e-17 100
8 TraesCS4B01G359900 chr5A 92.130 1817 106 17 793 2587 688662544 688664345 0.000000e+00 2529
9 TraesCS4B01G359900 chr5A 88.673 565 61 3 2059 2620 706566137 706565573 0.000000e+00 686
10 TraesCS4B01G359900 chr5A 85.271 645 71 14 2976 3601 706565313 706564674 0.000000e+00 643
11 TraesCS4B01G359900 chr5A 81.039 770 122 18 2840 3602 688664785 688665537 3.100000e-165 592
12 TraesCS4B01G359900 chr1A 93.443 793 44 6 4 792 520781809 520781021 0.000000e+00 1170
13 TraesCS4B01G359900 chr3D 92.704 795 52 4 1 792 83913622 83914413 0.000000e+00 1142
14 TraesCS4B01G359900 chr3D 80.265 603 89 19 3022 3607 597399333 597398744 9.260000e-116 427
15 TraesCS4B01G359900 chr1D 92.812 793 49 6 4 792 11503759 11502971 0.000000e+00 1142
16 TraesCS4B01G359900 chr2B 92.308 793 51 8 6 793 634973044 634973831 0.000000e+00 1118
17 TraesCS4B01G359900 chr2B 90.251 718 62 7 45 757 602054425 602053711 0.000000e+00 931
18 TraesCS4B01G359900 chr7B 91.615 799 53 11 1 792 357976947 357977738 0.000000e+00 1092
19 TraesCS4B01G359900 chr7A 91.228 798 62 6 1 794 330521410 330522203 0.000000e+00 1079
20 TraesCS4B01G359900 chr2D 87.613 775 82 14 1 767 605853961 605853193 0.000000e+00 887
21 TraesCS4B01G359900 chrUn 85.304 592 75 7 3020 3601 30048776 30048187 5.150000e-168 601
22 TraesCS4B01G359900 chrUn 87.860 486 48 7 2059 2535 30083177 30082694 8.750000e-156 560
23 TraesCS4B01G359900 chrUn 87.647 170 19 2 2455 2623 30054137 30053969 2.840000e-46 196
24 TraesCS4B01G359900 chr5D 85.020 247 20 8 999 1234 28166446 28166686 6.020000e-58 235


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 TraesCS4B01G359900 chr4B 650268749 650272356 3607 False 6663.00 6663 100.0000 1 3608 1 chr4B.!!$F1 3607
1 TraesCS4B01G359900 chr4B 619421779 619422573 794 True 1116.00 1116 92.1250 4 794 1 chr4B.!!$R1 790
2 TraesCS4B01G359900 chr4B 667563069 667563766 697 False 387.00 387 77.2480 2880 3601 1 chr4B.!!$F2 721
3 TraesCS4B01G359900 chr4D 503964393 503969268 4875 False 966.75 2532 93.6440 807 3600 4 chr4D.!!$F2 2793
4 TraesCS4B01G359900 chr5A 688662544 688665537 2993 False 1560.50 2529 86.5845 793 3602 2 chr5A.!!$F1 2809
5 TraesCS4B01G359900 chr5A 706564674 706566137 1463 True 664.50 686 86.9720 2059 3601 2 chr5A.!!$R1 1542
6 TraesCS4B01G359900 chr1A 520781021 520781809 788 True 1170.00 1170 93.4430 4 792 1 chr1A.!!$R1 788
7 TraesCS4B01G359900 chr3D 83913622 83914413 791 False 1142.00 1142 92.7040 1 792 1 chr3D.!!$F1 791
8 TraesCS4B01G359900 chr3D 597398744 597399333 589 True 427.00 427 80.2650 3022 3607 1 chr3D.!!$R1 585
9 TraesCS4B01G359900 chr1D 11502971 11503759 788 True 1142.00 1142 92.8120 4 792 1 chr1D.!!$R1 788
10 TraesCS4B01G359900 chr2B 634973044 634973831 787 False 1118.00 1118 92.3080 6 793 1 chr2B.!!$F1 787
11 TraesCS4B01G359900 chr2B 602053711 602054425 714 True 931.00 931 90.2510 45 757 1 chr2B.!!$R1 712
12 TraesCS4B01G359900 chr7B 357976947 357977738 791 False 1092.00 1092 91.6150 1 792 1 chr7B.!!$F1 791
13 TraesCS4B01G359900 chr7A 330521410 330522203 793 False 1079.00 1079 91.2280 1 794 1 chr7A.!!$F1 793
14 TraesCS4B01G359900 chr2D 605853193 605853961 768 True 887.00 887 87.6130 1 767 1 chr2D.!!$R1 766
15 TraesCS4B01G359900 chrUn 30048187 30048776 589 True 601.00 601 85.3040 3020 3601 1 chrUn.!!$R1 581

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
977 1064 0.594110 CCTTATCTCCTCCGTCTCGC 59.406 60.0 0.00 0.0 0.0 5.03 F
1632 1723 0.102481 CGGTCGATCGGATGAAAGGT 59.898 55.0 16.41 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 2664 0.107456 ACCGGTCATGGATGATCAGC 59.893 55.0 0.00 1.26 37.79 4.26 R
3484 5713 0.465278 TGGCACTGCAGCACTTGTTA 60.465 50.0 15.27 0.00 35.83 2.41 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
221 222 0.816018 TGGCGCGAGAGGTTTCAAAA 60.816 50.000 12.10 0.00 0.00 2.44
226 227 2.664568 CGCGAGAGGTTTCAAAACGATA 59.335 45.455 0.00 0.00 39.77 2.92
258 259 1.535860 GCACTTCATCGGAGAGAGAGC 60.536 57.143 0.00 0.00 43.63 4.09
284 285 3.449018 GGAGGTAGCTGAGAACAATCTGA 59.551 47.826 0.00 0.00 35.54 3.27
296 297 4.651503 AGAACAATCTGATCCTGACGGTAT 59.348 41.667 0.00 0.00 33.59 2.73
398 400 4.261781 CGTAGCCCGTACCTCCGC 62.262 72.222 0.00 0.00 0.00 5.54
564 566 1.743252 CAGCGGAGGAGGAAGCAAC 60.743 63.158 0.00 0.00 0.00 4.17
621 623 2.092429 TGGCCTGATACCATCTGAAACC 60.092 50.000 3.32 0.00 30.29 3.27
668 673 2.827129 CCATAGGGCAGCCAGGAGG 61.827 68.421 15.19 5.77 38.23 4.30
670 675 4.823732 TAGGGCAGCCAGGAGGGG 62.824 72.222 15.19 0.00 37.04 4.79
779 790 8.275040 ACAGCCTCCTAATCTATAACAACATTT 58.725 33.333 0.00 0.00 0.00 2.32
780 791 9.125026 CAGCCTCCTAATCTATAACAACATTTT 57.875 33.333 0.00 0.00 0.00 1.82
781 792 9.700831 AGCCTCCTAATCTATAACAACATTTTT 57.299 29.630 0.00 0.00 0.00 1.94
849 935 5.054477 TCAGGGAAAAGTTGAGTTTCTACG 58.946 41.667 0.00 0.00 35.68 3.51
864 950 6.171213 AGTTTCTACGTAAAAATCTGGGGAG 58.829 40.000 0.00 0.00 0.00 4.30
975 1062 1.338655 GCACCTTATCTCCTCCGTCTC 59.661 57.143 0.00 0.00 0.00 3.36
976 1063 1.604755 CACCTTATCTCCTCCGTCTCG 59.395 57.143 0.00 0.00 0.00 4.04
977 1064 0.594110 CCTTATCTCCTCCGTCTCGC 59.406 60.000 0.00 0.00 0.00 5.03
978 1065 1.600023 CTTATCTCCTCCGTCTCGCT 58.400 55.000 0.00 0.00 0.00 4.93
979 1066 1.533731 CTTATCTCCTCCGTCTCGCTC 59.466 57.143 0.00 0.00 0.00 5.03
980 1067 0.759959 TATCTCCTCCGTCTCGCTCT 59.240 55.000 0.00 0.00 0.00 4.09
1251 1341 2.444895 GTCCTCCAGGCCCTCGAT 60.445 66.667 0.00 0.00 34.44 3.59
1301 1391 4.824515 CCTCGAGGTCCGCTCCCT 62.825 72.222 24.04 0.00 38.37 4.20
1313 1404 2.371259 GCTCCCTCCTCAACCCCTC 61.371 68.421 0.00 0.00 0.00 4.30
1320 1411 1.287739 CTCCTCAACCCCTCTCTCTCT 59.712 57.143 0.00 0.00 0.00 3.10
1321 1412 1.286553 TCCTCAACCCCTCTCTCTCTC 59.713 57.143 0.00 0.00 0.00 3.20
1322 1413 1.287739 CCTCAACCCCTCTCTCTCTCT 59.712 57.143 0.00 0.00 0.00 3.10
1323 1414 2.654863 CTCAACCCCTCTCTCTCTCTC 58.345 57.143 0.00 0.00 0.00 3.20
1324 1415 2.242196 CTCAACCCCTCTCTCTCTCTCT 59.758 54.545 0.00 0.00 0.00 3.10
1325 1416 2.241176 TCAACCCCTCTCTCTCTCTCTC 59.759 54.545 0.00 0.00 0.00 3.20
1326 1417 2.242196 CAACCCCTCTCTCTCTCTCTCT 59.758 54.545 0.00 0.00 0.00 3.10
1327 1418 2.127708 ACCCCTCTCTCTCTCTCTCTC 58.872 57.143 0.00 0.00 0.00 3.20
1328 1419 1.070758 CCCCTCTCTCTCTCTCTCTCG 59.929 61.905 0.00 0.00 0.00 4.04
1329 1420 1.762957 CCCTCTCTCTCTCTCTCTCGT 59.237 57.143 0.00 0.00 0.00 4.18
1337 1428 2.772515 TCTCTCTCTCTCGTATGGTCCA 59.227 50.000 0.00 0.00 0.00 4.02
1342 1433 2.076622 CTCTCGTATGGTCCAGCCGG 62.077 65.000 11.75 0.00 41.21 6.13
1346 1437 4.155733 TATGGTCCAGCCGGTGCG 62.156 66.667 1.90 0.00 44.33 5.34
1371 1462 1.337260 ACCTGTTCGACTGATGCTCAC 60.337 52.381 0.00 0.00 0.00 3.51
1445 1536 3.893763 CGAGCCGAGGACGCAGAT 61.894 66.667 0.00 0.00 38.29 2.90
1470 1561 1.448119 CCAGGCTGCTGATGATGCTG 61.448 60.000 9.56 0.00 0.00 4.41
1622 1713 2.658593 GATGGCCACGGTCGATCG 60.659 66.667 18.18 18.18 0.00 3.69
1632 1723 0.102481 CGGTCGATCGGATGAAAGGT 59.898 55.000 16.41 0.00 0.00 3.50
1671 1762 1.451067 CGGACGAGTACACCTTCTCT 58.549 55.000 0.00 0.00 0.00 3.10
1683 1774 3.843027 ACACCTTCTCTGTCCTCATCAAT 59.157 43.478 0.00 0.00 0.00 2.57
1851 1942 2.490903 GCTGTCCAACATGCTTCAAGAT 59.509 45.455 0.00 0.00 0.00 2.40
1941 2032 2.975489 GGATGACATGGAGAGGTGGTAT 59.025 50.000 0.00 0.00 0.00 2.73
1983 2074 1.320344 TTGAGCCAGATACGCGGACT 61.320 55.000 12.47 3.29 0.00 3.85
2052 2143 5.643379 AAATGTTGTCGGTGCTGAAATAT 57.357 34.783 0.00 0.00 0.00 1.28
2055 2146 8.445275 AAATGTTGTCGGTGCTGAAATATATA 57.555 30.769 0.00 0.00 0.00 0.86
2064 2155 3.120338 TGCTGAAATATATAAAGCGGCGC 60.120 43.478 26.86 26.86 36.66 6.53
2082 2173 0.392327 GCTTCTTCTCACCCTCTGCC 60.392 60.000 0.00 0.00 0.00 4.85
2106 2197 6.088217 CCGCTACGTTCAACATAATCATAGAG 59.912 42.308 0.00 0.00 0.00 2.43
2193 2284 0.538516 TCAAACCCAACCCCATCACG 60.539 55.000 0.00 0.00 0.00 4.35
2240 2331 2.883386 GCAAATCTGGGCTCCTTGATAG 59.117 50.000 0.00 0.00 0.00 2.08
2259 2350 2.654863 AGGGTTCCTGCAATTATTCGG 58.345 47.619 0.00 0.00 29.57 4.30
2274 2365 1.461091 TTCGGCAGACGGAGAACACT 61.461 55.000 0.00 0.00 44.45 3.55
2408 2501 6.770785 TGTAAGCCTGGCAAGGTAATTTATAG 59.229 38.462 22.65 0.00 46.43 1.31
2460 2553 4.142004 GGAATGGAGGAAGACGCTAAGTTA 60.142 45.833 0.00 0.00 0.00 2.24
2488 2581 5.485662 AAAAGAACTGGAAAGAGTTGACG 57.514 39.130 0.00 0.00 36.27 4.35
2493 2586 3.983741 ACTGGAAAGAGTTGACGAGAAG 58.016 45.455 0.00 0.00 0.00 2.85
2520 2614 7.028962 TGCTGTAAGTGCTTTGCTATATTTTG 58.971 34.615 0.00 0.00 35.30 2.44
2556 2664 6.812656 TGTTGATTTATGCCTGCATTAAACTG 59.187 34.615 10.27 0.00 37.82 3.16
2562 2670 2.424601 TGCCTGCATTAAACTGCTGATC 59.575 45.455 8.92 0.00 41.92 2.92
2572 2686 2.634815 ACTGCTGATCATCCATGACC 57.365 50.000 0.00 0.00 40.03 4.02
2587 2701 4.457603 TCCATGACCGGTTATCTTTGTTTG 59.542 41.667 9.42 0.00 0.00 2.93
2590 2705 2.490509 GACCGGTTATCTTTGTTTGGGG 59.509 50.000 9.42 0.00 0.00 4.96
2600 2716 3.138283 TCTTTGTTTGGGGTCAGTGATCT 59.862 43.478 2.82 0.00 0.00 2.75
2620 2736 4.259356 TCTGTTCTGAGATTGAATGCCAG 58.741 43.478 0.00 0.00 0.00 4.85
2623 2739 4.828939 TGTTCTGAGATTGAATGCCAGTTT 59.171 37.500 0.00 0.00 0.00 2.66
2624 2740 5.302568 TGTTCTGAGATTGAATGCCAGTTTT 59.697 36.000 0.00 0.00 0.00 2.43
2625 2741 6.183360 TGTTCTGAGATTGAATGCCAGTTTTT 60.183 34.615 0.00 0.00 0.00 1.94
2626 2742 5.775686 TCTGAGATTGAATGCCAGTTTTTG 58.224 37.500 0.00 0.00 0.00 2.44
2638 2908 2.159114 CCAGTTTTTGGTGACCCAGTTG 60.159 50.000 0.00 0.00 43.15 3.16
2652 2922 1.894466 CCAGTTGGATGCCAATGACAA 59.106 47.619 1.79 0.00 45.80 3.18
2656 2926 2.299867 GTTGGATGCCAATGACAAGGTT 59.700 45.455 1.79 0.00 45.80 3.50
2669 2940 7.095187 CCAATGACAAGGTTACTAGAAGTTCAC 60.095 40.741 5.50 0.00 0.00 3.18
2670 2941 6.474140 TGACAAGGTTACTAGAAGTTCACA 57.526 37.500 5.50 0.00 0.00 3.58
2671 2942 6.880484 TGACAAGGTTACTAGAAGTTCACAA 58.120 36.000 5.50 0.00 0.00 3.33
2672 2943 6.759827 TGACAAGGTTACTAGAAGTTCACAAC 59.240 38.462 5.50 3.45 0.00 3.32
2726 2998 7.148188 CCAAATTAAGCTGAGCTGAAATAGACA 60.148 37.037 8.16 0.00 39.62 3.41
2733 3008 6.378564 AGCTGAGCTGAAATAGACACTAACTA 59.621 38.462 5.97 0.00 37.57 2.24
2745 3020 8.928270 ATAGACACTAACTATTGTTCTTTCCG 57.072 34.615 0.00 0.00 37.59 4.30
2753 3028 6.248569 ACTATTGTTCTTTCCGTATCCCAT 57.751 37.500 0.00 0.00 0.00 4.00
2758 3033 4.881273 TGTTCTTTCCGTATCCCATCAATG 59.119 41.667 0.00 0.00 0.00 2.82
2760 3035 4.960938 TCTTTCCGTATCCCATCAATGAG 58.039 43.478 0.00 0.00 0.00 2.90
2765 3040 3.403038 CGTATCCCATCAATGAGGAACC 58.597 50.000 0.00 0.00 33.12 3.62
2767 3042 2.806945 TCCCATCAATGAGGAACCAC 57.193 50.000 0.00 0.00 0.00 4.16
2768 3043 2.278245 TCCCATCAATGAGGAACCACT 58.722 47.619 0.00 0.00 0.00 4.00
2775 3050 5.512942 TCAATGAGGAACCACTTGGAATA 57.487 39.130 1.14 0.00 38.94 1.75
2778 3053 5.983333 ATGAGGAACCACTTGGAATAGAT 57.017 39.130 1.14 0.00 38.94 1.98
2781 3056 7.265599 TGAGGAACCACTTGGAATAGATAAA 57.734 36.000 1.14 0.00 38.94 1.40
2782 3057 7.872138 TGAGGAACCACTTGGAATAGATAAAT 58.128 34.615 1.14 0.00 38.94 1.40
2783 3058 8.336235 TGAGGAACCACTTGGAATAGATAAATT 58.664 33.333 1.14 0.00 38.94 1.82
2784 3059 9.847224 GAGGAACCACTTGGAATAGATAAATTA 57.153 33.333 1.14 0.00 38.94 1.40
2785 3060 9.853177 AGGAACCACTTGGAATAGATAAATTAG 57.147 33.333 1.14 0.00 38.94 1.73
2793 3068 6.822442 TGGAATAGATAAATTAGTCGTGGCA 58.178 36.000 0.00 0.00 0.00 4.92
2811 3086 2.945447 CATGTTGTGCCATCGGAAAT 57.055 45.000 0.00 0.00 0.00 2.17
2812 3087 2.532235 CATGTTGTGCCATCGGAAATG 58.468 47.619 0.00 0.00 0.00 2.32
2819 3094 1.272425 TGCCATCGGAAATGGGAGTTT 60.272 47.619 6.22 0.00 39.53 2.66
2823 3098 1.803334 TCGGAAATGGGAGTTTCACG 58.197 50.000 2.32 3.76 39.33 4.35
2825 3100 1.243902 GGAAATGGGAGTTTCACGCA 58.756 50.000 2.32 0.00 39.33 5.24
2831 3106 0.741221 GGGAGTTTCACGCAGCCTAG 60.741 60.000 0.00 0.00 0.00 3.02
2836 3144 3.024547 AGTTTCACGCAGCCTAGATCTA 58.975 45.455 1.69 1.69 0.00 1.98
2838 3146 4.100189 AGTTTCACGCAGCCTAGATCTAAT 59.900 41.667 3.57 0.00 0.00 1.73
2854 3162 7.986085 AGATCTAATTGCACAAGTACAAACT 57.014 32.000 0.00 0.00 37.65 2.66
2862 3170 3.248602 GCACAAGTACAAACTCAGACAGG 59.751 47.826 0.00 0.00 33.75 4.00
2863 3171 4.442706 CACAAGTACAAACTCAGACAGGT 58.557 43.478 0.00 0.00 33.75 4.00
2864 3172 5.597806 CACAAGTACAAACTCAGACAGGTA 58.402 41.667 0.00 0.00 33.75 3.08
2865 3173 5.692204 CACAAGTACAAACTCAGACAGGTAG 59.308 44.000 0.00 0.00 33.75 3.18
2885 3196 3.549794 AGCTTGGAATATCTGGAAGTGC 58.450 45.455 0.00 0.00 33.76 4.40
2914 3231 1.270678 ACGGTACAGCAAAGAAGGTCC 60.271 52.381 0.00 0.00 0.00 4.46
2916 3233 1.001633 GGTACAGCAAAGAAGGTCCGA 59.998 52.381 0.00 0.00 0.00 4.55
2930 3247 0.820871 GTCCGATTCAGAGCTCCAGT 59.179 55.000 10.93 0.00 0.00 4.00
2932 3249 1.110442 CCGATTCAGAGCTCCAGTCT 58.890 55.000 10.93 0.00 0.00 3.24
2942 3259 9.989296 ATTCAGAGCTCCAGTCTAGTATATATT 57.011 33.333 10.93 0.00 0.00 1.28
2946 3263 9.407380 AGAGCTCCAGTCTAGTATATATTCATG 57.593 37.037 10.93 0.00 0.00 3.07
2972 3291 9.315525 GTCAGAATATGTAAACCTAGTTTCCTC 57.684 37.037 0.00 0.00 37.01 3.71
2980 3322 4.415224 AACCTAGTTTCCTCTGGGTCTA 57.585 45.455 2.51 0.00 46.09 2.59
2981 3323 4.628661 ACCTAGTTTCCTCTGGGTCTAT 57.371 45.455 0.00 0.00 44.07 1.98
2982 3324 4.548669 ACCTAGTTTCCTCTGGGTCTATC 58.451 47.826 0.00 0.00 44.07 2.08
2999 3341 3.938963 TCTATCGGAAAATTCACTGCCAC 59.061 43.478 0.00 0.00 0.00 5.01
3003 3345 3.131223 TCGGAAAATTCACTGCCACAAAA 59.869 39.130 0.00 0.00 0.00 2.44
3004 3346 3.245048 CGGAAAATTCACTGCCACAAAAC 59.755 43.478 0.00 0.00 0.00 2.43
3005 3347 4.441792 GGAAAATTCACTGCCACAAAACT 58.558 39.130 0.00 0.00 0.00 2.66
3017 3365 4.098807 TGCCACAAAACTAAAGGGAGAAAC 59.901 41.667 0.00 0.00 0.00 2.78
3018 3366 4.791734 GCCACAAAACTAAAGGGAGAAACG 60.792 45.833 0.00 0.00 0.00 3.60
3032 3380 4.102649 GGAGAAACGGAACAACACAAAAG 58.897 43.478 0.00 0.00 0.00 2.27
3097 5289 4.756642 CACCAATAAGTTCAGAGCACAGAA 59.243 41.667 0.00 0.00 0.00 3.02
3130 5322 4.022762 TCGAAGAGAAGTTCAGTCTTCCAG 60.023 45.833 20.76 12.67 42.13 3.86
3149 5349 3.081048 TGGACACACCAGGCAGATA 57.919 52.632 0.00 0.00 44.64 1.98
3153 5353 3.134623 TGGACACACCAGGCAGATAATAG 59.865 47.826 0.00 0.00 44.64 1.73
3191 5410 6.036470 CGACTAGAACTGCATACTTCAATCA 58.964 40.000 0.00 0.00 0.00 2.57
3205 5426 6.889301 ACTTCAATCAAAATTCTGAGCTGA 57.111 33.333 0.00 0.00 0.00 4.26
3457 5686 5.570320 TCTTCACAAATAGCCTTTAGCCTT 58.430 37.500 0.00 0.00 45.47 4.35
3484 5713 0.031314 CATACCGATCTGCAGCGACT 59.969 55.000 9.47 0.00 0.00 4.18
3498 5727 0.164647 GCGACTAACAAGTGCTGCAG 59.835 55.000 10.11 10.11 0.00 4.41
3602 5831 4.629092 CTCCATGTCATCGATCTTGATGT 58.371 43.478 0.00 0.00 44.82 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.289834 CGCCAACCAGCTTGCTGT 61.290 61.111 19.49 6.83 0.00 4.40
221 222 1.448540 GCTGCAGCAGGTGTATCGT 60.449 57.895 33.36 0.00 41.59 3.73
258 259 0.741915 GTTCTCAGCTACCTCCTCGG 59.258 60.000 0.00 0.00 39.35 4.63
296 297 0.625316 ACCCTGCATATGCCAACTGA 59.375 50.000 24.54 4.10 41.18 3.41
398 400 0.312416 CTTCCTCCTCTACGCATCGG 59.688 60.000 0.00 0.00 0.00 4.18
406 408 4.345854 GAGTTCAGGTTCTTCCTCCTCTA 58.654 47.826 0.00 0.00 46.24 2.43
425 427 1.482593 CAACTTCCTCCTATGGCGAGT 59.517 52.381 0.00 0.00 0.00 4.18
614 616 3.686726 CCAATCTCCTTCTTCGGTTTCAG 59.313 47.826 0.00 0.00 0.00 3.02
621 623 3.126831 CGAATCCCAATCTCCTTCTTCG 58.873 50.000 0.00 0.00 0.00 3.79
659 662 2.158460 GCATATTTAACCCCTCCTGGCT 60.158 50.000 0.00 0.00 0.00 4.75
663 666 2.158460 GGCTGCATATTTAACCCCTCCT 60.158 50.000 0.50 0.00 0.00 3.69
668 673 4.327680 CCTAGAGGCTGCATATTTAACCC 58.672 47.826 0.50 0.00 0.00 4.11
779 790 9.883142 AAATCTCCAATTTGTGTTAAACAGAAA 57.117 25.926 0.00 0.00 43.89 2.52
797 808 7.953005 TCCAGCAAAATTACATAAATCTCCA 57.047 32.000 0.00 0.00 0.00 3.86
849 935 5.102313 CGATTTTGCTCCCCAGATTTTTAC 58.898 41.667 0.00 0.00 0.00 2.01
864 950 3.092334 ACTGTTTGGAACCGATTTTGC 57.908 42.857 0.00 0.00 0.00 3.68
907 994 0.322546 GAAACTGCTCCCGTCCCATT 60.323 55.000 0.00 0.00 0.00 3.16
953 1040 1.049289 ACGGAGGAGATAAGGTGCCC 61.049 60.000 0.00 0.00 0.00 5.36
1240 1330 4.918201 GGCGGAATCGAGGGCCTG 62.918 72.222 12.95 3.26 42.29 4.85
1301 1391 1.286553 GAGAGAGAGAGGGGTTGAGGA 59.713 57.143 0.00 0.00 0.00 3.71
1313 1404 4.307432 GACCATACGAGAGAGAGAGAGAG 58.693 52.174 0.00 0.00 0.00 3.20
1320 1411 1.681538 GCTGGACCATACGAGAGAGA 58.318 55.000 0.00 0.00 0.00 3.10
1321 1412 0.671251 GGCTGGACCATACGAGAGAG 59.329 60.000 0.00 0.00 38.86 3.20
1322 1413 1.101635 CGGCTGGACCATACGAGAGA 61.102 60.000 11.36 0.00 39.03 3.10
1323 1414 1.360551 CGGCTGGACCATACGAGAG 59.639 63.158 11.36 0.00 39.03 3.20
1324 1415 2.125326 CCGGCTGGACCATACGAGA 61.125 63.158 5.28 0.00 39.03 4.04
1325 1416 2.417516 CCGGCTGGACCATACGAG 59.582 66.667 5.28 5.99 39.03 4.18
1326 1417 2.363276 ACCGGCTGGACCATACGA 60.363 61.111 21.41 0.00 39.03 3.43
1327 1418 2.202878 CACCGGCTGGACCATACG 60.203 66.667 21.41 10.15 39.03 3.06
1328 1419 2.513897 GCACCGGCTGGACCATAC 60.514 66.667 21.41 0.00 39.03 2.39
1329 1420 4.155733 CGCACCGGCTGGACCATA 62.156 66.667 21.41 0.00 39.03 2.74
1342 1433 3.838795 CGAACAGGTAGCGCGCAC 61.839 66.667 35.10 26.65 0.00 5.34
1346 1437 0.179134 ATCAGTCGAACAGGTAGCGC 60.179 55.000 0.00 0.00 0.00 5.92
1371 1462 3.074412 AGAAACAGCAATCCTTACGTGG 58.926 45.455 0.00 0.00 0.00 4.94
1445 1536 2.060383 ATCAGCAGCCTGGCGTAGA 61.060 57.895 13.96 10.56 39.61 2.59
1622 1713 1.796796 GCGTCAGCACCTTTCATCC 59.203 57.895 0.00 0.00 44.35 3.51
1671 1762 2.089201 CAGCAGCAATTGATGAGGACA 58.911 47.619 27.03 0.00 46.04 4.02
1683 1774 2.667318 GCGCGACTTACAGCAGCAA 61.667 57.895 12.10 0.00 34.72 3.91
1851 1942 3.253061 TCCGGCACATTGTCCCCA 61.253 61.111 0.00 0.00 0.00 4.96
1941 2032 2.862541 CCCATCAACTGAAACTCACCA 58.137 47.619 0.00 0.00 0.00 4.17
1983 2074 9.045223 CCGTAAGACTTCATCATGATATTGAAA 57.955 33.333 8.15 0.00 43.02 2.69
2041 2132 4.394795 CGCCGCTTTATATATTTCAGCAC 58.605 43.478 9.78 2.81 0.00 4.40
2043 2134 3.125316 AGCGCCGCTTTATATATTTCAGC 59.875 43.478 5.39 0.00 33.89 4.26
2064 2155 0.108424 CGGCAGAGGGTGAGAAGAAG 60.108 60.000 0.00 0.00 0.00 2.85
2082 2173 6.637254 ACTCTATGATTATGTTGAACGTAGCG 59.363 38.462 0.00 0.00 0.00 4.26
2106 2197 1.367471 GCCAGCCCTTCCAAAACAC 59.633 57.895 0.00 0.00 0.00 3.32
2193 2284 1.933853 CCATTAACCAGCGAGCAGTAC 59.066 52.381 0.00 0.00 0.00 2.73
2240 2331 1.067060 GCCGAATAATTGCAGGAACCC 59.933 52.381 0.00 0.00 0.00 4.11
2259 2350 1.337260 ACATCAGTGTTCTCCGTCTGC 60.337 52.381 0.00 0.00 34.01 4.26
2274 2365 5.894298 ATGGAGTATCTAAGGCAACATCA 57.106 39.130 0.00 0.00 34.38 3.07
2334 2425 8.517878 AGCATTTCCTCCATTATTTTGATATCG 58.482 33.333 0.00 0.00 0.00 2.92
2408 2501 5.647589 CAATATATGCCTGAATCATGGTGC 58.352 41.667 0.00 0.00 0.00 5.01
2439 2532 3.983044 AACTTAGCGTCTTCCTCCATT 57.017 42.857 0.00 0.00 0.00 3.16
2445 2538 9.148104 TCTTTTTCTAATAACTTAGCGTCTTCC 57.852 33.333 0.00 0.00 35.32 3.46
2450 2543 8.718734 CCAGTTCTTTTTCTAATAACTTAGCGT 58.281 33.333 0.00 0.00 35.32 5.07
2460 2553 9.408648 TCAACTCTTTCCAGTTCTTTTTCTAAT 57.591 29.630 0.00 0.00 34.17 1.73
2473 2566 3.983741 ACTTCTCGTCAACTCTTTCCAG 58.016 45.455 0.00 0.00 0.00 3.86
2488 2581 4.531332 CAAAGCACTTACAGCAACTTCTC 58.469 43.478 0.00 0.00 0.00 2.87
2493 2586 2.781945 AGCAAAGCACTTACAGCAAC 57.218 45.000 0.00 0.00 0.00 4.17
2520 2614 5.098211 GCATAAATCAACAAGAAGCTCACC 58.902 41.667 0.00 0.00 0.00 4.02
2556 2664 0.107456 ACCGGTCATGGATGATCAGC 59.893 55.000 0.00 1.26 37.79 4.26
2562 2670 4.199310 ACAAAGATAACCGGTCATGGATG 58.801 43.478 8.04 6.68 0.00 3.51
2572 2686 3.150767 TGACCCCAAACAAAGATAACCG 58.849 45.455 0.00 0.00 0.00 4.44
2587 2701 1.902508 TCAGAACAGATCACTGACCCC 59.097 52.381 0.00 0.00 46.03 4.95
2590 2705 5.718146 TCAATCTCAGAACAGATCACTGAC 58.282 41.667 0.00 0.00 46.03 3.51
2600 2716 4.025040 ACTGGCATTCAATCTCAGAACA 57.975 40.909 4.07 0.00 0.00 3.18
2625 2741 1.074775 GCATCCAACTGGGTCACCA 59.925 57.895 0.00 0.00 46.94 4.17
2626 2742 1.678970 GGCATCCAACTGGGTCACC 60.679 63.158 0.00 0.00 38.11 4.02
2627 2743 0.539438 TTGGCATCCAACTGGGTCAC 60.539 55.000 0.00 0.00 38.75 3.67
2629 2745 0.819582 CATTGGCATCCAACTGGGTC 59.180 55.000 0.00 0.00 46.95 4.46
2638 2908 3.356290 AGTAACCTTGTCATTGGCATCC 58.644 45.455 0.00 0.00 0.00 3.51
2669 2940 9.305925 GCCAAAGATAAATTCCATAGAAAGTTG 57.694 33.333 0.00 0.00 35.09 3.16
2670 2941 9.259832 AGCCAAAGATAAATTCCATAGAAAGTT 57.740 29.630 0.00 0.00 35.09 2.66
2671 2942 8.689972 CAGCCAAAGATAAATTCCATAGAAAGT 58.310 33.333 0.00 0.00 35.09 2.66
2672 2943 8.689972 ACAGCCAAAGATAAATTCCATAGAAAG 58.310 33.333 0.00 0.00 35.09 2.62
2703 2975 7.108847 AGTGTCTATTTCAGCTCAGCTTAATT 58.891 34.615 0.00 0.00 36.40 1.40
2707 2979 4.550076 AGTGTCTATTTCAGCTCAGCTT 57.450 40.909 0.00 0.00 36.40 3.74
2726 2998 7.093201 TGGGATACGGAAAGAACAATAGTTAGT 60.093 37.037 0.00 0.00 35.89 2.24
2733 3008 5.110814 TGATGGGATACGGAAAGAACAAT 57.889 39.130 0.00 0.00 37.60 2.71
2745 3020 4.137543 GTGGTTCCTCATTGATGGGATAC 58.862 47.826 0.00 0.00 30.70 2.24
2753 3028 3.874383 TTCCAAGTGGTTCCTCATTGA 57.126 42.857 0.00 0.00 36.34 2.57
2758 3033 8.753497 AATTTATCTATTCCAAGTGGTTCCTC 57.247 34.615 0.00 0.00 36.34 3.71
2760 3035 9.628500 ACTAATTTATCTATTCCAAGTGGTTCC 57.372 33.333 0.00 0.00 36.34 3.62
2765 3040 8.765219 CCACGACTAATTTATCTATTCCAAGTG 58.235 37.037 0.00 0.00 0.00 3.16
2767 3042 7.441157 TGCCACGACTAATTTATCTATTCCAAG 59.559 37.037 0.00 0.00 0.00 3.61
2768 3043 7.276658 TGCCACGACTAATTTATCTATTCCAA 58.723 34.615 0.00 0.00 0.00 3.53
2775 3050 5.880332 ACAACATGCCACGACTAATTTATCT 59.120 36.000 0.00 0.00 0.00 1.98
2778 3053 5.289917 CACAACATGCCACGACTAATTTA 57.710 39.130 0.00 0.00 0.00 1.40
2811 3086 1.476845 TAGGCTGCGTGAAACTCCCA 61.477 55.000 4.91 0.00 31.75 4.37
2812 3087 0.741221 CTAGGCTGCGTGAAACTCCC 60.741 60.000 4.91 0.00 31.75 4.30
2819 3094 3.800261 GCAATTAGATCTAGGCTGCGTGA 60.800 47.826 13.69 1.37 0.00 4.35
2823 3098 3.470709 TGTGCAATTAGATCTAGGCTGC 58.529 45.455 18.72 18.72 0.00 5.25
2825 3100 5.365021 ACTTGTGCAATTAGATCTAGGCT 57.635 39.130 18.18 0.00 0.00 4.58
2831 3106 7.806690 TGAGTTTGTACTTGTGCAATTAGATC 58.193 34.615 5.22 0.00 33.84 2.75
2836 3144 5.356751 TGTCTGAGTTTGTACTTGTGCAATT 59.643 36.000 5.22 0.00 33.84 2.32
2838 3146 4.257731 TGTCTGAGTTTGTACTTGTGCAA 58.742 39.130 0.34 0.34 33.84 4.08
2854 3162 5.069648 CAGATATTCCAAGCTACCTGTCTGA 59.930 44.000 0.00 0.00 33.13 3.27
2862 3170 4.513318 GCACTTCCAGATATTCCAAGCTAC 59.487 45.833 0.00 0.00 0.00 3.58
2863 3171 4.164030 TGCACTTCCAGATATTCCAAGCTA 59.836 41.667 0.00 0.00 0.00 3.32
2864 3172 3.054139 TGCACTTCCAGATATTCCAAGCT 60.054 43.478 0.00 0.00 0.00 3.74
2865 3173 3.282021 TGCACTTCCAGATATTCCAAGC 58.718 45.455 0.00 0.00 0.00 4.01
2885 3196 0.892755 TGCTGTACCGTACTCCCTTG 59.107 55.000 10.03 0.00 0.00 3.61
2914 3231 2.948979 ACTAGACTGGAGCTCTGAATCG 59.051 50.000 14.64 0.05 0.00 3.34
2916 3233 9.989296 AATATATACTAGACTGGAGCTCTGAAT 57.011 33.333 14.64 0.00 0.00 2.57
2946 3263 9.315525 GAGGAAACTAGGTTTACATATTCTGAC 57.684 37.037 0.00 0.00 44.43 3.51
2951 3268 7.184022 ACCCAGAGGAAACTAGGTTTACATATT 59.816 37.037 0.00 0.00 44.43 1.28
2952 3269 6.677076 ACCCAGAGGAAACTAGGTTTACATAT 59.323 38.462 0.00 0.00 44.43 1.78
2968 3287 2.840640 TTTCCGATAGACCCAGAGGA 57.159 50.000 0.00 0.00 36.73 3.71
2972 3291 4.572389 CAGTGAATTTTCCGATAGACCCAG 59.428 45.833 0.00 0.00 39.76 4.45
2980 3322 2.513753 TGTGGCAGTGAATTTTCCGAT 58.486 42.857 0.00 0.00 0.00 4.18
2981 3323 1.974265 TGTGGCAGTGAATTTTCCGA 58.026 45.000 0.00 0.00 0.00 4.55
2982 3324 2.791383 TTGTGGCAGTGAATTTTCCG 57.209 45.000 0.00 0.00 0.00 4.30
2999 3341 5.066764 TGTTCCGTTTCTCCCTTTAGTTTTG 59.933 40.000 0.00 0.00 0.00 2.44
3003 3345 4.132336 GTTGTTCCGTTTCTCCCTTTAGT 58.868 43.478 0.00 0.00 0.00 2.24
3004 3346 4.024302 GTGTTGTTCCGTTTCTCCCTTTAG 60.024 45.833 0.00 0.00 0.00 1.85
3005 3347 3.878699 GTGTTGTTCCGTTTCTCCCTTTA 59.121 43.478 0.00 0.00 0.00 1.85
3017 3365 5.631512 TGTTTCTTTCTTTTGTGTTGTTCCG 59.368 36.000 0.00 0.00 0.00 4.30
3018 3366 7.414814 TTGTTTCTTTCTTTTGTGTTGTTCC 57.585 32.000 0.00 0.00 0.00 3.62
3032 3380 8.424274 AATTCACATGGTTCTTTGTTTCTTTC 57.576 30.769 0.00 0.00 0.00 2.62
3097 5289 4.592485 ACTTCTCTTCGAGAATGTGTGT 57.408 40.909 6.75 0.00 45.84 3.72
3130 5322 0.613260 TATCTGCCTGGTGTGTCCAC 59.387 55.000 0.00 0.00 41.93 4.02
3143 5343 7.915923 TCGTATCCATCGATTTCTATTATCTGC 59.084 37.037 0.00 0.00 32.30 4.26
3149 5349 8.563123 TCTAGTCGTATCCATCGATTTCTATT 57.437 34.615 0.00 0.00 39.45 1.73
3153 5353 6.579292 CAGTTCTAGTCGTATCCATCGATTTC 59.421 42.308 0.00 0.00 39.45 2.17
3191 5410 8.317679 AGTATGAGTAGTTCAGCTCAGAATTTT 58.682 33.333 0.00 0.00 43.81 1.82
3205 5426 5.394224 CCCATCGTCACAAGTATGAGTAGTT 60.394 44.000 0.00 0.00 0.00 2.24
3457 5686 1.412710 GCAGATCGGTATGGACTGGAA 59.587 52.381 0.00 0.00 32.25 3.53
3484 5713 0.465278 TGGCACTGCAGCACTTGTTA 60.465 50.000 15.27 0.00 35.83 2.41
3498 5727 3.609373 CGATGTTGATCAAAATGTGGCAC 59.391 43.478 16.05 11.55 0.00 5.01


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

AutoCloner maintained by Alex Coulton.