Multiple sequence alignment - TraesCS3B01G150900

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 TraesCS3B01G150900 chr3B 100.000 2746 0 0 2617 5362 141979414 141976669 0.000000e+00 5072.0
1 TraesCS3B01G150900 chr3B 100.000 2426 0 0 1 2426 141982030 141979605 0.000000e+00 4481.0
2 TraesCS3B01G150900 chr3B 85.333 150 18 4 2638 2783 475807480 475807331 9.300000e-33 152.0
3 TraesCS3B01G150900 chr3A 91.939 2568 149 15 2617 5174 545967466 545964947 0.000000e+00 3542.0
4 TraesCS3B01G150900 chr3A 90.222 1800 146 17 645 2425 545969317 545967529 0.000000e+00 2322.0
5 TraesCS3B01G150900 chr3D 93.333 2265 142 6 2620 4876 92384238 92381975 0.000000e+00 3338.0
6 TraesCS3B01G150900 chr3D 89.474 1805 148 19 645 2425 92386350 92384564 0.000000e+00 2242.0
7 TraesCS3B01G150900 chr3D 93.443 488 32 0 4875 5362 92379864 92379377 0.000000e+00 725.0
8 TraesCS3B01G150900 chr3D 75.443 790 148 30 923 1708 475550494 475551241 5.140000e-90 342.0
9 TraesCS3B01G150900 chr3D 84.795 171 24 2 2642 2811 20943666 20943835 2.570000e-38 171.0
10 TraesCS3B01G150900 chr4B 90.461 629 55 5 17 641 471194086 471193459 0.000000e+00 824.0
11 TraesCS3B01G150900 chr4B 85.714 189 20 5 2626 2809 25961783 25961597 5.480000e-45 193.0
12 TraesCS3B01G150900 chr6B 90.000 630 57 6 16 641 113464840 113465467 0.000000e+00 809.0
13 TraesCS3B01G150900 chr6B 90.671 611 50 6 35 641 467634208 467633601 0.000000e+00 806.0
14 TraesCS3B01G150900 chr1A 78.522 1313 225 39 663 1953 498206395 498207672 0.000000e+00 809.0
15 TraesCS3B01G150900 chr1A 77.035 1241 224 33 737 1953 498197539 498198742 0.000000e+00 656.0
16 TraesCS3B01G150900 chr1A 78.068 1035 193 20 737 1760 498322826 498323837 1.640000e-174 623.0
17 TraesCS3B01G150900 chrUn 89.968 628 57 6 17 641 37561435 37560811 0.000000e+00 806.0
18 TraesCS3B01G150900 chrUn 89.650 628 58 7 17 641 38274156 38273533 0.000000e+00 793.0
19 TraesCS3B01G150900 chr2B 89.952 627 59 4 17 641 685732041 685731417 0.000000e+00 806.0
20 TraesCS3B01G150900 chr2B 89.715 632 57 8 16 641 553678028 553678657 0.000000e+00 800.0
21 TraesCS3B01G150900 chr2B 81.818 187 25 7 2626 2809 137703201 137703021 1.200000e-31 148.0
22 TraesCS3B01G150900 chr2B 81.481 189 25 8 2626 2811 137131913 137131732 4.330000e-31 147.0
23 TraesCS3B01G150900 chr5B 89.666 629 57 7 17 639 382405853 382405227 0.000000e+00 795.0
24 TraesCS3B01G150900 chr7B 88.958 643 60 10 1 639 638810644 638811279 0.000000e+00 784.0
25 TraesCS3B01G150900 chr7B 84.940 166 25 0 2639 2804 57422390 57422225 9.240000e-38 169.0
26 TraesCS3B01G150900 chr1D 77.482 1128 208 28 644 1760 403152008 403153100 7.580000e-178 634.0
27 TraesCS3B01G150900 chr1D 78.896 815 141 20 1151 1953 403091588 403092383 1.710000e-144 523.0
28 TraesCS3B01G150900 chr1B 82.441 598 81 14 1389 1978 541410387 541410968 8.020000e-138 501.0
29 TraesCS3B01G150900 chr1B 82.817 355 48 7 1597 1944 541313153 541313501 6.750000e-79 305.0
30 TraesCS3B01G150900 chr1B 82.065 184 30 2 2625 2805 262529670 262529853 2.590000e-33 154.0
31 TraesCS3B01G150900 chr6A 100.000 29 0 0 2226 2254 83811104 83811132 3.000000e-03 54.7


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 TraesCS3B01G150900 chr3B 141976669 141982030 5361 True 4776.500000 5072 100.000000 1 5362 2 chr3B.!!$R2 5361
1 TraesCS3B01G150900 chr3A 545964947 545969317 4370 True 2932.000000 3542 91.080500 645 5174 2 chr3A.!!$R1 4529
2 TraesCS3B01G150900 chr3D 92379377 92386350 6973 True 2101.666667 3338 92.083333 645 5362 3 chr3D.!!$R1 4717
3 TraesCS3B01G150900 chr3D 475550494 475551241 747 False 342.000000 342 75.443000 923 1708 1 chr3D.!!$F2 785
4 TraesCS3B01G150900 chr4B 471193459 471194086 627 True 824.000000 824 90.461000 17 641 1 chr4B.!!$R2 624
5 TraesCS3B01G150900 chr6B 113464840 113465467 627 False 809.000000 809 90.000000 16 641 1 chr6B.!!$F1 625
6 TraesCS3B01G150900 chr6B 467633601 467634208 607 True 806.000000 806 90.671000 35 641 1 chr6B.!!$R1 606
7 TraesCS3B01G150900 chr1A 498206395 498207672 1277 False 809.000000 809 78.522000 663 1953 1 chr1A.!!$F2 1290
8 TraesCS3B01G150900 chr1A 498197539 498198742 1203 False 656.000000 656 77.035000 737 1953 1 chr1A.!!$F1 1216
9 TraesCS3B01G150900 chr1A 498322826 498323837 1011 False 623.000000 623 78.068000 737 1760 1 chr1A.!!$F3 1023
10 TraesCS3B01G150900 chrUn 37560811 37561435 624 True 806.000000 806 89.968000 17 641 1 chrUn.!!$R1 624
11 TraesCS3B01G150900 chrUn 38273533 38274156 623 True 793.000000 793 89.650000 17 641 1 chrUn.!!$R2 624
12 TraesCS3B01G150900 chr2B 685731417 685732041 624 True 806.000000 806 89.952000 17 641 1 chr2B.!!$R3 624
13 TraesCS3B01G150900 chr2B 553678028 553678657 629 False 800.000000 800 89.715000 16 641 1 chr2B.!!$F1 625
14 TraesCS3B01G150900 chr5B 382405227 382405853 626 True 795.000000 795 89.666000 17 639 1 chr5B.!!$R1 622
15 TraesCS3B01G150900 chr7B 638810644 638811279 635 False 784.000000 784 88.958000 1 639 1 chr7B.!!$F1 638
16 TraesCS3B01G150900 chr1D 403152008 403153100 1092 False 634.000000 634 77.482000 644 1760 1 chr1D.!!$F2 1116
17 TraesCS3B01G150900 chr1D 403091588 403092383 795 False 523.000000 523 78.896000 1151 1953 1 chr1D.!!$F1 802
18 TraesCS3B01G150900 chr1B 541410387 541410968 581 False 501.000000 501 82.441000 1389 1978 1 chr1B.!!$F3 589

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
86 89 0.254638 TCCTTCTCCCTCTCCCCCTA 60.255 60.000 0.0 0.0 0.00 3.53 F
1332 1361 0.250295 CTTCCAAAGGAGCGTGGACA 60.250 55.000 0.0 0.0 43.67 4.02 F
1571 1606 0.606401 CTGGACAAATCACCTGCGGT 60.606 55.000 0.0 0.0 35.62 5.68 F
2338 2396 2.069273 CGGTCCAGCTTTAAGTCACAG 58.931 52.381 0.0 0.0 0.00 3.66 F
4167 4370 0.034863 GTCCTTCCCGCCCAACAATA 60.035 55.000 0.0 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2015 0.105964 CTCAGCCACCCCTAGCTCTA 60.106 60.000 0.00 0.00 37.18 2.43 R
2315 2373 0.389426 GACTTAAAGCTGGACCGCGA 60.389 55.000 8.23 0.00 34.40 5.87 R
2831 3025 1.476291 GGTTTTACCCCCAGCTATCCG 60.476 57.143 0.00 0.00 30.04 4.18 R
4320 4523 0.036952 GGATCATCGATGCCACCGAT 60.037 55.000 20.81 7.62 46.32 4.18 R
5037 7352 0.332632 ACATAGGCCACATTGCACCT 59.667 50.000 5.01 0.00 36.27 4.00 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
86 89 0.254638 TCCTTCTCCCTCTCCCCCTA 60.255 60.000 0.00 0.00 0.00 3.53
97 100 2.859404 CTCTCCCCCTATTTCCCCTTTT 59.141 50.000 0.00 0.00 0.00 2.27
103 107 2.317900 CCCTATTTCCCCTTTTCCCCTT 59.682 50.000 0.00 0.00 0.00 3.95
169 174 1.128188 GGACTCCCCTCACTTGGTGT 61.128 60.000 0.00 0.00 34.79 4.16
300 308 0.387929 TCCTCCGGTCATATTGTCGC 59.612 55.000 0.00 0.00 0.00 5.19
301 309 0.939577 CCTCCGGTCATATTGTCGCG 60.940 60.000 0.00 0.00 0.00 5.87
344 352 1.086696 GATCACATCACCAACACCGG 58.913 55.000 0.00 0.00 0.00 5.28
441 449 2.059541 GAGCTGAACGTGTGTAGAACC 58.940 52.381 0.00 0.00 0.00 3.62
470 478 3.119424 TGTCGTGCATTCGGTACTTGATA 60.119 43.478 0.00 0.00 0.00 2.15
595 605 9.135189 GATATGCATCTCCTAGATAGATCTTGT 57.865 37.037 0.19 0.00 38.32 3.16
596 606 6.832520 TGCATCTCCTAGATAGATCTTGTC 57.167 41.667 0.00 0.00 38.32 3.18
641 654 3.098377 TGCATGCTACATTTCCCAACAT 58.902 40.909 20.33 0.00 0.00 2.71
642 655 3.119065 TGCATGCTACATTTCCCAACATG 60.119 43.478 20.33 0.00 37.17 3.21
660 673 2.594303 CGCAACAGTTGGCCTCCA 60.594 61.111 15.28 0.00 0.00 3.86
670 685 2.031870 GTTGGCCTCCAAAGACAACTT 58.968 47.619 3.32 0.00 45.73 2.66
697 712 1.001520 CCTCATGTACACGGACCACAA 59.998 52.381 0.00 0.00 0.00 3.33
728 743 0.824109 GACAGTGATGGGATCCGACA 59.176 55.000 5.45 0.00 0.00 4.35
729 744 0.537188 ACAGTGATGGGATCCGACAC 59.463 55.000 19.79 19.79 34.36 3.67
802 817 9.887629 TGGAACGTTATATATTGGACAGTTTTA 57.112 29.630 0.00 0.00 0.00 1.52
816 831 5.533903 GGACAGTTTTATGCCATCTGATGAT 59.466 40.000 18.92 7.99 0.00 2.45
827 842 1.302033 CTGATGATAGTGGGGCCGC 60.302 63.158 14.01 14.01 0.00 6.53
840 858 1.037030 GGGCCGCAGATGAATGGAAA 61.037 55.000 0.00 0.00 0.00 3.13
867 888 4.707448 CACCTCCTCCTCTATATTATGCGT 59.293 45.833 0.00 0.00 0.00 5.24
870 891 5.393569 CCTCCTCCTCTATATTATGCGTGTG 60.394 48.000 0.00 0.00 0.00 3.82
903 924 5.362430 TGACATCAACTTGCCTTTTTACCTT 59.638 36.000 0.00 0.00 0.00 3.50
912 933 5.715434 TGCCTTTTTACCTTTGTCATACC 57.285 39.130 0.00 0.00 0.00 2.73
913 934 4.525100 TGCCTTTTTACCTTTGTCATACCC 59.475 41.667 0.00 0.00 0.00 3.69
914 935 4.081862 GCCTTTTTACCTTTGTCATACCCC 60.082 45.833 0.00 0.00 0.00 4.95
915 936 5.081032 CCTTTTTACCTTTGTCATACCCCA 58.919 41.667 0.00 0.00 0.00 4.96
916 937 5.047590 CCTTTTTACCTTTGTCATACCCCAC 60.048 44.000 0.00 0.00 0.00 4.61
917 938 3.724732 TTACCTTTGTCATACCCCACC 57.275 47.619 0.00 0.00 0.00 4.61
953 974 1.684869 GCCCGATCCCTCCAAAATTCA 60.685 52.381 0.00 0.00 0.00 2.57
989 1010 1.043022 CTGGCTTGCTTCCAACCTTT 58.957 50.000 0.00 0.00 32.41 3.11
1068 1097 1.254975 TGACGAATGAGGCGGAAGGA 61.255 55.000 0.00 0.00 0.00 3.36
1177 1206 2.550699 ATCGCCCATTTCCGGCTTCA 62.551 55.000 0.00 0.00 44.73 3.02
1306 1335 2.760650 TCCTTGAAGAATAGCAGAGCGA 59.239 45.455 0.00 0.00 0.00 4.93
1332 1361 0.250295 CTTCCAAAGGAGCGTGGACA 60.250 55.000 0.00 0.00 43.67 4.02
1345 1374 1.048601 GTGGACACAGGAAGAGGACA 58.951 55.000 0.00 0.00 0.00 4.02
1353 1382 3.504906 CACAGGAAGAGGACAAGTACGTA 59.495 47.826 0.00 0.00 0.00 3.57
1405 1435 2.102394 CTTGATCTCGCGGCATGCAG 62.102 60.000 21.36 17.62 46.97 4.41
1406 1436 2.279717 GATCTCGCGGCATGCAGA 60.280 61.111 22.57 14.72 46.97 4.26
1407 1437 1.667191 GATCTCGCGGCATGCAGAT 60.667 57.895 22.57 18.84 46.97 2.90
1408 1438 1.226686 GATCTCGCGGCATGCAGATT 61.227 55.000 22.57 7.10 46.97 2.40
1418 1448 4.484236 CGGCATGCAGATTTGTTTTTCTA 58.516 39.130 21.36 0.00 0.00 2.10
1479 1513 3.459232 TCTCAAGATATTGGTGGCTCG 57.541 47.619 0.00 0.00 0.00 5.03
1481 1515 2.868583 CTCAAGATATTGGTGGCTCGTG 59.131 50.000 0.00 0.00 0.00 4.35
1543 1578 1.523758 GACGAATTGGGAAGCAGTGT 58.476 50.000 0.00 0.00 0.00 3.55
1571 1606 0.606401 CTGGACAAATCACCTGCGGT 60.606 55.000 0.00 0.00 35.62 5.68
1612 1647 6.839124 TTGGTCATTCTTTTCATGCATAGT 57.161 33.333 0.00 0.00 0.00 2.12
1953 2006 3.277142 AACACGGTTTCTGGAGTCTTT 57.723 42.857 0.00 0.00 0.00 2.52
1954 2007 4.411256 AACACGGTTTCTGGAGTCTTTA 57.589 40.909 0.00 0.00 0.00 1.85
1962 2015 5.011840 GGTTTCTGGAGTCTTTAGTAGTGGT 59.988 44.000 0.00 0.00 0.00 4.16
1993 2046 4.891037 GCTGAGGGGGAGCCATGC 62.891 72.222 0.00 0.00 0.00 4.06
2060 2116 8.870075 ATATATGGGGATTTAGCTCTGTTTTC 57.130 34.615 0.00 0.00 0.00 2.29
2069 2125 6.854496 TTTAGCTCTGTTTTCGTTGTACAT 57.146 33.333 0.00 0.00 0.00 2.29
2104 2160 7.102993 TCATATATACCATGTGAATTGTCGGG 58.897 38.462 0.00 0.00 0.00 5.14
2183 2239 4.579869 CCACAATTGCCTACTAGTCAAGT 58.420 43.478 5.05 0.00 42.62 3.16
2193 2249 9.835389 TTGCCTACTAGTCAAGTTTTTAGTTAA 57.165 29.630 0.00 0.00 39.80 2.01
2260 2316 3.252974 ACTATTGAAGGGAGAAGTGCG 57.747 47.619 0.00 0.00 0.00 5.34
2272 2328 3.865929 AAGTGCGTCTGCCCGTCTG 62.866 63.158 0.00 0.00 41.78 3.51
2295 2353 5.063880 GTCACATGATTTACAGATACCCCC 58.936 45.833 0.00 0.00 0.00 5.40
2315 2373 3.617284 CCCGCCTTTCCAGTAATAAACT 58.383 45.455 0.00 0.00 39.81 2.66
2325 2383 2.858344 CAGTAATAAACTCGCGGTCCAG 59.142 50.000 6.13 0.00 35.76 3.86
2338 2396 2.069273 CGGTCCAGCTTTAAGTCACAG 58.931 52.381 0.00 0.00 0.00 3.66
2410 2472 8.477984 TGCTAATTAAATTGCAATCCAACTTC 57.522 30.769 13.38 0.26 35.99 3.01
2799 2993 6.862711 ATCAGTAGCACATGATTCATCTTG 57.137 37.500 0.00 0.00 37.79 3.02
2815 3009 5.961272 TCATCTTGCTTTCATACTGACGTA 58.039 37.500 0.00 0.00 0.00 3.57
2817 3011 7.041721 TCATCTTGCTTTCATACTGACGTAAT 58.958 34.615 0.00 0.00 0.00 1.89
2818 3012 7.549134 TCATCTTGCTTTCATACTGACGTAATT 59.451 33.333 0.00 0.00 0.00 1.40
2858 3052 2.963599 TGGGGGTAAAACCAGACTTC 57.036 50.000 0.00 0.00 41.02 3.01
2882 3076 2.043551 TGCGGGGCATGGCAAATA 60.044 55.556 22.06 1.40 35.98 1.40
2996 3190 5.799213 ACCTATAGTTGCATAGAATGGCTC 58.201 41.667 0.00 0.00 31.24 4.70
3016 3210 4.156556 GCTCTTTCAAACATGTCCATGCTA 59.843 41.667 0.00 0.00 42.39 3.49
3049 3243 6.544928 TCTAGATGTTCATGGCAAGTTCTA 57.455 37.500 0.00 0.00 0.00 2.10
3141 3335 5.888412 AGCATGCTTGTTTTTAGAAAACG 57.112 34.783 16.30 1.01 33.05 3.60
3147 3341 9.198065 CATGCTTGTTTTTAGAAAACGAAAAAG 57.802 29.630 10.59 9.44 35.72 2.27
3500 3700 7.814264 AATTGCATCCATTGTTTTTGGTTTA 57.186 28.000 0.00 0.00 35.64 2.01
3567 3770 2.435372 AGCCTGTCCAACAGTTCAAA 57.565 45.000 6.37 0.00 44.50 2.69
3576 3779 6.292150 TGTCCAACAGTTCAAAAACCTTTTT 58.708 32.000 0.00 0.00 40.75 1.94
3684 3887 8.789762 TGCTTCACATAATCATATTCCAGAATG 58.210 33.333 3.10 0.00 32.50 2.67
3766 3969 2.549754 ACAGTTGGTCAAAGATCGCAAG 59.450 45.455 0.00 0.00 0.00 4.01
3814 4017 3.876914 TCCATCAAGAATCATTGGTACGC 59.123 43.478 0.00 0.00 0.00 4.42
3842 4045 1.330655 GGGGCCTGACATCGAAGAGA 61.331 60.000 0.84 0.00 43.63 3.10
3898 4101 1.942657 GTACATCCGCAGCACAATCAT 59.057 47.619 0.00 0.00 0.00 2.45
3905 4108 1.108776 GCAGCACAATCATGGGTGAT 58.891 50.000 14.52 7.43 46.91 3.06
3912 4115 4.201657 CACAATCATGGGTGATAAGAGCA 58.798 43.478 7.12 0.00 44.20 4.26
3925 4128 0.322816 AAGAGCACGGCATCACCATT 60.323 50.000 0.00 0.00 39.03 3.16
3986 4189 0.550914 AGGTTGTTCCAAGTGCCTCA 59.449 50.000 0.00 0.00 39.02 3.86
3987 4190 1.064017 AGGTTGTTCCAAGTGCCTCAA 60.064 47.619 0.00 0.00 39.02 3.02
3999 4202 1.980772 GCCTCAACAATGCTGGCCT 60.981 57.895 3.32 0.00 38.85 5.19
4046 4249 2.036098 CTCCACCCAGGCAATGCA 59.964 61.111 7.79 0.00 37.29 3.96
4058 4261 1.395635 GCAATGCACCTGGATCATCA 58.604 50.000 0.00 0.00 0.00 3.07
4113 4316 5.172934 TGCTACCAAAACTCAATACCTACG 58.827 41.667 0.00 0.00 0.00 3.51
4127 4330 1.068083 CTACGGCGGTGAGATGCAT 59.932 57.895 13.24 0.00 0.00 3.96
4137 4340 1.718178 GTGAGATGCATCAGCGATACG 59.282 52.381 27.81 0.00 46.23 3.06
4166 4369 1.304134 GTCCTTCCCGCCCAACAAT 60.304 57.895 0.00 0.00 0.00 2.71
4167 4370 0.034863 GTCCTTCCCGCCCAACAATA 60.035 55.000 0.00 0.00 0.00 1.90
4190 4393 2.986290 CACTATGGACCACCGCCA 59.014 61.111 0.00 0.00 40.24 5.69
4191 4394 1.298340 CACTATGGACCACCGCCAA 59.702 57.895 0.00 0.00 39.21 4.52
4215 4418 4.935352 TTTCAGCAAATGTTTAGCCAGT 57.065 36.364 0.00 0.00 0.00 4.00
4255 4458 2.254546 TGCTCGAACATGAACCTGTT 57.745 45.000 0.00 0.00 41.92 3.16
4276 4479 2.082231 CCCGTTACTCAAGAGTCTCGA 58.918 52.381 20.27 0.00 42.54 4.04
4288 4491 0.976641 AGTCTCGATCTTGGTGGCAA 59.023 50.000 0.00 0.00 0.00 4.52
4301 4504 1.002087 GGTGGCAACTACTACTGCAGT 59.998 52.381 25.12 25.12 40.46 4.40
4352 4555 2.608016 CGATGATCCGGACGACATCAAT 60.608 50.000 29.89 13.83 38.99 2.57
4368 4571 1.412710 TCAATGTCGTCTAGATGGCCC 59.587 52.381 13.92 2.72 0.00 5.80
4389 4592 1.895020 CGGGGATTTCCTGACGTCCA 61.895 60.000 14.12 0.01 44.90 4.02
4415 4618 5.337009 GGACGAACCTAACTGGATTCAACTA 60.337 44.000 0.00 0.00 39.71 2.24
4423 4626 5.733620 AACTGGATTCAACTAAGACGGTA 57.266 39.130 0.00 0.00 0.00 4.02
4431 4634 4.597004 TCAACTAAGACGGTACATCCTCT 58.403 43.478 0.00 0.00 0.00 3.69
4462 4665 7.335627 CAGTACCCTATCCATTACTTTGTCAA 58.664 38.462 0.00 0.00 0.00 3.18
4534 4737 2.811431 CACTATTGCCCGAAGAACACAA 59.189 45.455 0.00 0.00 0.00 3.33
4535 4738 3.074412 ACTATTGCCCGAAGAACACAAG 58.926 45.455 0.00 0.00 0.00 3.16
4569 4772 2.017049 GGCGTGGCATGTATCTTTTCT 58.983 47.619 8.75 0.00 0.00 2.52
4577 4780 6.096001 GTGGCATGTATCTTTTCTGGATTTCT 59.904 38.462 0.00 0.00 0.00 2.52
4696 4899 1.890876 TCCAGCGCTATTGTGTGTTT 58.109 45.000 10.99 0.00 0.00 2.83
4713 4916 5.403766 GTGTGTTTAGCTAGGATGATGATCG 59.596 44.000 0.00 0.00 0.00 3.69
4717 4920 6.014242 TGTTTAGCTAGGATGATGATCGGAAT 60.014 38.462 0.00 0.00 0.00 3.01
4718 4921 6.611613 TTAGCTAGGATGATGATCGGAATT 57.388 37.500 0.00 0.00 0.00 2.17
4734 4937 4.521639 TCGGAATTATGCACGGAGTACTAT 59.478 41.667 0.00 0.00 41.61 2.12
4753 4956 8.046708 AGTACTATAGGAAACATGACATTTGCA 58.953 33.333 0.00 0.00 30.42 4.08
4806 5009 4.553330 TCAATAGACCAAAGGAGTCACC 57.447 45.455 0.00 0.00 36.68 4.02
4834 5037 4.985409 GTCACACTCGACAAAGATTTCTCT 59.015 41.667 0.00 0.00 35.88 3.10
4993 7308 1.525995 CTGTGCCACCTCGGTTTGT 60.526 57.895 0.00 0.00 36.97 2.83
4994 7309 1.077357 TGTGCCACCTCGGTTTGTT 60.077 52.632 0.00 0.00 36.97 2.83
4997 7312 1.098712 TGCCACCTCGGTTTGTTGAC 61.099 55.000 0.00 0.00 36.97 3.18
5001 7316 2.014128 CACCTCGGTTTGTTGACTGTT 58.986 47.619 0.00 0.00 0.00 3.16
5015 7330 4.877378 TGACTGTTACTTACGGGTGATT 57.123 40.909 0.00 0.00 37.45 2.57
5037 7352 0.449786 CAAACACCAGTGCACGACAA 59.550 50.000 12.01 0.00 0.00 3.18
5062 7377 2.445427 CAATGTGGCCTATGTGTTGGA 58.555 47.619 3.32 0.00 0.00 3.53
5072 7387 3.244561 CCTATGTGTTGGAGAGTGTTGGT 60.245 47.826 0.00 0.00 0.00 3.67
5076 7391 0.307760 GTTGGAGAGTGTTGGTTGCG 59.692 55.000 0.00 0.00 0.00 4.85
5117 7432 4.135153 CCGAGCACCCTCCAGTCG 62.135 72.222 0.00 0.00 34.49 4.18
5199 7514 2.683968 GTGTACGGATCAAGAGCAACA 58.316 47.619 0.00 0.00 0.00 3.33
5203 7518 0.994995 CGGATCAAGAGCAACAGTCG 59.005 55.000 0.00 0.00 0.00 4.18
5216 7531 1.350193 ACAGTCGCGAAGTGCAATAG 58.650 50.000 12.06 0.00 46.97 1.73
5222 7537 5.050490 AGTCGCGAAGTGCAATAGAATAAT 58.950 37.500 12.06 0.00 46.97 1.28
5248 7563 5.240183 AATGTCTCCATTCACACAAGAAGTG 59.760 40.000 0.00 0.00 44.69 3.16
5283 7598 2.303175 GCAAACACCTGACTAAACCCA 58.697 47.619 0.00 0.00 0.00 4.51
5285 7600 2.621526 CAAACACCTGACTAAACCCACC 59.378 50.000 0.00 0.00 0.00 4.61
5305 7620 1.683011 CCATCTTCCAGACGGGCAAAT 60.683 52.381 0.00 0.00 36.21 2.32
5326 7641 2.418368 AAGCATCGCCTCCACATTTA 57.582 45.000 0.00 0.00 0.00 1.40
5341 7656 6.363882 TCCACATTTATATCCACTGCATCAA 58.636 36.000 0.00 0.00 0.00 2.57
5344 7659 7.201848 CCACATTTATATCCACTGCATCAACTT 60.202 37.037 0.00 0.00 0.00 2.66
5353 7668 1.816835 CTGCATCAACTTGTCATGGCT 59.183 47.619 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.447801 CAATTCGAACTCCCTTGCGG 59.552 55.000 0.00 0.00 0.00 5.69
20 21 0.447801 CCAATTCGAACTCCCTTGCG 59.552 55.000 0.00 0.00 0.00 4.85
21 22 1.468914 GTCCAATTCGAACTCCCTTGC 59.531 52.381 0.00 0.00 0.00 4.01
31 32 0.037590 CCACCCCTTGTCCAATTCGA 59.962 55.000 0.00 0.00 0.00 3.71
86 89 3.116356 ACAGAAAGGGGAAAAGGGGAAAT 60.116 43.478 0.00 0.00 0.00 2.17
97 100 1.827792 TCCTTCCAACAGAAAGGGGA 58.172 50.000 1.58 0.00 32.88 4.81
103 107 0.777446 CCCCCTTCCTTCCAACAGAA 59.223 55.000 0.00 0.00 0.00 3.02
376 384 3.181329 TCCAATAGAGGCACAAAGGAGA 58.819 45.455 0.00 0.00 0.00 3.71
441 449 2.047274 AATGCACGACACCTCCGG 60.047 61.111 0.00 0.00 0.00 5.14
454 462 7.360438 GGAATCAATCTATCAAGTACCGAATGC 60.360 40.741 0.00 0.00 0.00 3.56
470 478 5.409826 GTCAAACGTCTTCTGGAATCAATCT 59.590 40.000 0.00 0.00 0.00 2.40
614 627 5.558818 TGGGAAATGTAGCATGCAATTTTT 58.441 33.333 21.98 13.71 31.62 1.94
641 654 3.286751 GAGGCCAACTGTTGCGCA 61.287 61.111 24.85 5.66 0.00 6.09
642 655 4.043200 GGAGGCCAACTGTTGCGC 62.043 66.667 14.94 17.51 0.00 6.09
660 673 1.065551 GAGGCGCAACAAGTTGTCTTT 59.934 47.619 10.83 0.00 42.31 2.52
670 685 1.288419 CGTGTACATGAGGCGCAACA 61.288 55.000 10.83 9.20 0.00 3.33
697 712 3.244353 CCATCACTGTCCAACTCTGTCTT 60.244 47.826 0.00 0.00 0.00 3.01
728 743 0.543174 AAGAGAGGTGAAGCTCGGGT 60.543 55.000 4.00 0.00 36.29 5.28
729 744 0.108424 CAAGAGAGGTGAAGCTCGGG 60.108 60.000 4.00 0.00 36.29 5.14
802 817 2.307980 CCCCACTATCATCAGATGGCAT 59.692 50.000 10.67 0.00 36.29 4.40
816 831 1.344953 ATTCATCTGCGGCCCCACTA 61.345 55.000 0.00 0.00 0.00 2.74
827 842 1.133025 GGTGCCGTTTCCATTCATCTG 59.867 52.381 0.00 0.00 0.00 2.90
840 858 0.851469 TATAGAGGAGGAGGTGCCGT 59.149 55.000 0.00 0.00 43.43 5.68
867 888 5.411831 AGTTGATGTCAAGATCTAGCACA 57.588 39.130 0.00 0.00 36.39 4.57
870 891 4.034975 GGCAAGTTGATGTCAAGATCTAGC 59.965 45.833 7.16 0.00 36.39 3.42
903 924 3.844063 GGGGGTGGGGTATGACAA 58.156 61.111 0.00 0.00 0.00 3.18
953 974 2.154074 AGGAACTGCGAAGGGGGTT 61.154 57.895 0.00 0.00 37.18 4.11
1052 1081 0.811616 CCTTCCTTCCGCCTCATTCG 60.812 60.000 0.00 0.00 0.00 3.34
1055 1084 1.208165 AACCCTTCCTTCCGCCTCAT 61.208 55.000 0.00 0.00 0.00 2.90
1108 1137 1.283793 CAACTTGCTGGAAGTGCCG 59.716 57.895 15.44 3.93 44.68 5.69
1109 1138 1.662044 CCAACTTGCTGGAAGTGCC 59.338 57.895 15.44 0.00 44.68 5.01
1289 1318 2.804572 GCCATCGCTCTGCTATTCTTCA 60.805 50.000 0.00 0.00 0.00 3.02
1332 1361 2.595238 ACGTACTTGTCCTCTTCCTGT 58.405 47.619 0.00 0.00 0.00 4.00
1479 1513 1.271054 CCCATCTCCGATTCCCATCAC 60.271 57.143 0.00 0.00 0.00 3.06
1481 1515 1.277557 CTCCCATCTCCGATTCCCATC 59.722 57.143 0.00 0.00 0.00 3.51
1528 1563 1.202758 TCACGACACTGCTTCCCAATT 60.203 47.619 0.00 0.00 0.00 2.32
1543 1578 1.005037 ATTTGTCCAGCGCTCACGA 60.005 52.632 7.13 4.08 43.93 4.35
1726 1768 9.174166 GTGCCACTAGAATTTCTAATCCTTTAA 57.826 33.333 7.51 0.00 0.00 1.52
1760 1802 7.938563 AATATAACAAAAACAAAGAGCGCAA 57.061 28.000 11.47 0.00 0.00 4.85
1805 1852 3.636764 AGATTCGCAACCTTGGTCTTTTT 59.363 39.130 0.00 0.00 0.00 1.94
1806 1853 3.222603 AGATTCGCAACCTTGGTCTTTT 58.777 40.909 0.00 0.00 0.00 2.27
1810 1857 1.087501 GGAGATTCGCAACCTTGGTC 58.912 55.000 0.00 0.00 0.00 4.02
1868 1920 1.202675 GGGGACATTAATCGGCCGTAA 60.203 52.381 27.15 17.84 0.00 3.18
1953 2006 3.137913 CACCCCTAGCTCTACCACTACTA 59.862 52.174 0.00 0.00 0.00 1.82
1954 2007 2.091775 CACCCCTAGCTCTACCACTACT 60.092 54.545 0.00 0.00 0.00 2.57
1962 2015 0.105964 CTCAGCCACCCCTAGCTCTA 60.106 60.000 0.00 0.00 37.18 2.43
2193 2249 8.404107 TCAAACTTAGCTAAACTAAAATGGCT 57.596 30.769 7.74 0.00 40.36 4.75
2244 2300 1.048601 AGACGCACTTCTCCCTTCAA 58.951 50.000 0.00 0.00 0.00 2.69
2260 2316 1.016130 CATGTGACAGACGGGCAGAC 61.016 60.000 0.00 0.00 0.00 3.51
2272 2328 5.063880 GGGGGTATCTGTAAATCATGTGAC 58.936 45.833 0.00 0.00 0.00 3.67
2295 2353 3.308866 CGAGTTTATTACTGGAAAGGCGG 59.691 47.826 0.00 0.00 37.17 6.13
2296 2354 3.242316 GCGAGTTTATTACTGGAAAGGCG 60.242 47.826 0.00 0.00 37.17 5.52
2297 2355 3.242316 CGCGAGTTTATTACTGGAAAGGC 60.242 47.826 0.00 0.00 37.17 4.35
2299 2357 3.930848 ACCGCGAGTTTATTACTGGAAAG 59.069 43.478 8.23 0.00 37.17 2.62
2315 2373 0.389426 GACTTAAAGCTGGACCGCGA 60.389 55.000 8.23 0.00 34.40 5.87
2325 2383 4.916870 ACGTTTTTCCTGTGACTTAAAGC 58.083 39.130 0.00 0.00 0.00 3.51
2366 2425 2.041216 GCAGAAAGGAGGGGGTTTTCTA 59.959 50.000 0.00 0.00 38.68 2.10
2374 2436 6.683861 GCAATTTAATTAGCAGAAAGGAGGGG 60.684 42.308 7.05 0.00 0.00 4.79
2778 2972 4.575236 AGCAAGATGAATCATGTGCTACTG 59.425 41.667 22.32 6.86 38.92 2.74
2831 3025 1.476291 GGTTTTACCCCCAGCTATCCG 60.476 57.143 0.00 0.00 30.04 4.18
2882 3076 9.565090 AATCATGTGACATGCTATATACAAAGT 57.435 29.630 20.23 0.00 0.00 2.66
2996 3190 6.925165 ACTTTTAGCATGGACATGTTTGAAAG 59.075 34.615 21.54 21.54 40.80 2.62
3016 3210 8.486210 TGCCATGAACATCTAGATAGTACTTTT 58.514 33.333 4.54 0.00 0.00 2.27
3283 3478 8.893219 AATACCATGTCAACACATATAGTCAG 57.107 34.615 0.00 0.00 41.69 3.51
3525 3727 6.542370 GCTAGCCCAAAATTGACATCTAACTA 59.458 38.462 2.29 0.00 0.00 2.24
3535 3737 2.446435 GACAGGCTAGCCCAAAATTGA 58.554 47.619 30.42 0.00 36.58 2.57
3684 3887 4.452733 CTCGGTCCACGGGGCTTC 62.453 72.222 0.00 0.00 44.45 3.86
3766 3969 1.298488 GATCGACCGAAGAGGCGTC 60.298 63.158 0.00 0.00 46.52 5.19
3814 4017 4.697756 TCAGGCCCCGCTTTGTCG 62.698 66.667 0.00 0.00 0.00 4.35
3830 4033 2.520979 CTGAACCGTCTCTTCGATGTC 58.479 52.381 0.00 0.00 0.00 3.06
3857 4060 2.044252 TCGAGGAGGGAGAACCGG 60.044 66.667 0.00 0.00 46.96 5.28
3898 4101 1.220749 GCCGTGCTCTTATCACCCA 59.779 57.895 0.00 0.00 0.00 4.51
3905 4108 0.541392 ATGGTGATGCCGTGCTCTTA 59.459 50.000 0.00 0.00 41.21 2.10
3912 4115 1.303561 ACTGCAATGGTGATGCCGT 60.304 52.632 0.00 0.00 43.16 5.68
3971 4174 2.136298 TTGTTGAGGCACTTGGAACA 57.864 45.000 0.00 0.00 41.55 3.18
3986 4189 0.112995 TGGAGAAGGCCAGCATTGTT 59.887 50.000 5.01 0.00 33.10 2.83
3987 4190 1.769665 TGGAGAAGGCCAGCATTGT 59.230 52.632 5.01 0.00 33.10 2.71
3999 4202 2.252012 ATCCCGGGTAGGCTGGAGAA 62.252 60.000 22.86 0.00 39.21 2.87
4058 4261 2.040464 ATGGTCGCTCCCTGGGAT 60.040 61.111 17.51 0.00 39.82 3.85
4113 4316 2.541120 GCTGATGCATCTCACCGCC 61.541 63.158 26.32 0.00 39.41 6.13
4127 4330 0.818445 GGGAGGAGTCGTATCGCTGA 60.818 60.000 0.00 0.00 0.00 4.26
4137 4340 2.059190 GGAAGGACGGGGAGGAGTC 61.059 68.421 0.00 0.00 36.70 3.36
4166 4369 1.140852 GGTGGTCCATAGTGCAGCATA 59.859 52.381 0.00 0.00 0.00 3.14
4167 4370 0.107017 GGTGGTCCATAGTGCAGCAT 60.107 55.000 0.00 0.00 0.00 3.79
4255 4458 2.082231 CGAGACTCTTGAGTAACGGGA 58.918 52.381 15.66 0.00 0.00 5.14
4276 4479 3.619979 GCAGTAGTAGTTGCCACCAAGAT 60.620 47.826 0.00 0.00 34.28 2.40
4288 4491 2.085320 CCGTCTCACTGCAGTAGTAGT 58.915 52.381 21.20 0.00 41.69 2.73
4301 4504 4.680237 CTTGTGCGGCCCGTCTCA 62.680 66.667 4.45 1.44 0.00 3.27
4320 4523 0.036952 GGATCATCGATGCCACCGAT 60.037 55.000 20.81 7.62 46.32 4.18
4352 4555 1.760875 GGGGGCCATCTAGACGACA 60.761 63.158 4.39 0.00 0.00 4.35
4368 4571 2.189521 CGTCAGGAAATCCCCGGG 59.810 66.667 15.80 15.80 36.42 5.73
4389 4592 3.581332 TGAATCCAGTTAGGTTCGTCCTT 59.419 43.478 7.16 0.00 45.67 3.36
4396 4599 6.164176 CGTCTTAGTTGAATCCAGTTAGGTT 58.836 40.000 0.00 0.00 39.02 3.50
4401 4604 4.618920 ACCGTCTTAGTTGAATCCAGTT 57.381 40.909 0.00 0.00 0.00 3.16
4415 4618 2.526888 TCCAGAGGATGTACCGTCTT 57.473 50.000 0.00 0.00 44.74 3.01
4423 4626 2.683768 GGTACTGGATCCAGAGGATGT 58.316 52.381 41.91 24.64 43.27 3.06
4534 4737 0.392461 ACGCCACACAAACACAGACT 60.392 50.000 0.00 0.00 0.00 3.24
4535 4738 0.248054 CACGCCACACAAACACAGAC 60.248 55.000 0.00 0.00 0.00 3.51
4548 4751 1.742831 GAAAAGATACATGCCACGCCA 59.257 47.619 0.00 0.00 0.00 5.69
4696 4899 7.685398 GCATAATTCCGATCATCATCCTAGCTA 60.685 40.741 0.00 0.00 0.00 3.32
4713 4916 6.152323 TCCTATAGTACTCCGTGCATAATTCC 59.848 42.308 0.00 0.00 0.00 3.01
4717 4920 6.321945 TGTTTCCTATAGTACTCCGTGCATAA 59.678 38.462 0.00 0.00 0.00 1.90
4718 4921 5.829391 TGTTTCCTATAGTACTCCGTGCATA 59.171 40.000 0.00 0.00 0.00 3.14
4734 4937 8.839343 CATACTATGCAAATGTCATGTTTCCTA 58.161 33.333 0.00 0.00 0.00 2.94
4780 4983 6.655003 GTGACTCCTTTGGTCTATTGATTTCA 59.345 38.462 0.00 0.00 35.04 2.69
4788 4991 2.761208 CTCGGTGACTCCTTTGGTCTAT 59.239 50.000 0.00 0.00 35.04 1.98
4789 4992 2.168496 CTCGGTGACTCCTTTGGTCTA 58.832 52.381 0.00 0.00 35.04 2.59
4793 4996 0.393077 ACACTCGGTGACTCCTTTGG 59.607 55.000 10.46 0.00 36.96 3.28
4834 5037 2.422597 CTTGTCGAAAGGGTGCATGTA 58.577 47.619 0.00 0.00 0.00 2.29
4993 7308 4.877378 ATCACCCGTAAGTAACAGTCAA 57.123 40.909 0.00 0.00 0.00 3.18
4994 7309 4.561938 CCAATCACCCGTAAGTAACAGTCA 60.562 45.833 0.00 0.00 0.00 3.41
4997 7312 2.676342 GCCAATCACCCGTAAGTAACAG 59.324 50.000 0.00 0.00 0.00 3.16
5001 7316 3.075884 GTTTGCCAATCACCCGTAAGTA 58.924 45.455 0.00 0.00 0.00 2.24
5015 7330 2.769539 CGTGCACTGGTGTTTGCCA 61.770 57.895 16.19 0.00 38.00 4.92
5037 7352 0.332632 ACATAGGCCACATTGCACCT 59.667 50.000 5.01 0.00 36.27 4.00
5062 7377 2.372040 TACGCCGCAACCAACACTCT 62.372 55.000 0.00 0.00 0.00 3.24
5072 7387 4.666397 TTGCCGAGTACGCCGCAA 62.666 61.111 18.19 18.19 41.49 4.85
5076 7391 3.023591 GCTGTTTGCCGAGTACGCC 62.024 63.158 0.00 0.00 38.29 5.68
5117 7432 2.745821 GGGGTGGTATTTTTCGAGTGTC 59.254 50.000 0.00 0.00 0.00 3.67
5199 7514 2.363788 TTCTATTGCACTTCGCGACT 57.636 45.000 9.15 0.00 46.97 4.18
5203 7518 7.134815 ACATTGATTATTCTATTGCACTTCGC 58.865 34.615 0.00 0.00 42.89 4.70
5248 7563 0.968405 TTTGCATGACAAGGGAAGCC 59.032 50.000 0.00 0.00 40.06 4.35
5305 7620 2.418368 AATGTGGAGGCGATGCTTAA 57.582 45.000 0.00 0.00 0.00 1.85
5326 7641 4.847198 TGACAAGTTGATGCAGTGGATAT 58.153 39.130 10.54 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.