Multiple sequence alignment - TraesCS5B01G517600

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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 TraesCS5B01G517600 chr5B 100.000 4331 0 0 1 4331 680992391 680996721 0.000000e+00 7998.0
1 TraesCS5B01G517600 chr5B 90.807 446 32 1 3895 4331 685447842 685448287 4.820000e-164 588.0
2 TraesCS5B01G517600 chr5D 89.233 3195 225 44 158 3319 539452821 539455929 0.000000e+00 3884.0
3 TraesCS5B01G517600 chr5D 82.514 692 96 14 1 669 384882694 384882005 6.240000e-163 584.0
4 TraesCS5B01G517600 chr5D 81.936 692 99 11 1 668 433006755 433007444 2.920000e-156 562.0
5 TraesCS5B01G517600 chr5D 74.684 474 83 24 1 442 474302554 474303022 4.450000e-40 176.0
6 TraesCS5B01G517600 chr5D 73.367 398 70 23 1 367 130559718 130559326 9.840000e-22 115.0
7 TraesCS5B01G517600 chr4A 85.436 2156 281 22 1171 3308 681920616 681918476 0.000000e+00 2211.0
8 TraesCS5B01G517600 chr4A 87.836 1825 177 30 165 1954 629295241 629293427 0.000000e+00 2098.0
9 TraesCS5B01G517600 chr4A 84.335 932 104 22 2638 3546 629293438 629292526 0.000000e+00 874.0
10 TraesCS5B01G517600 chr4D 84.920 2175 290 26 1153 3308 475179100 475176945 0.000000e+00 2165.0
11 TraesCS5B01G517600 chr4B 84.833 2156 294 21 1171 3308 599887144 599885004 0.000000e+00 2139.0
12 TraesCS5B01G517600 chr3B 92.741 799 46 3 3542 4331 693651233 693650438 0.000000e+00 1144.0
13 TraesCS5B01G517600 chr3B 80.958 793 113 20 1 759 773033188 773033976 1.040000e-165 593.0
14 TraesCS5B01G517600 chr3B 76.840 557 83 27 1 545 684454041 684454563 5.520000e-69 272.0
15 TraesCS5B01G517600 chr3B 91.489 94 7 1 1 93 646011901 646011994 1.260000e-25 128.0
16 TraesCS5B01G517600 chr2B 91.272 802 59 3 3541 4331 611426832 611427633 0.000000e+00 1083.0
17 TraesCS5B01G517600 chr2B 91.757 643 37 6 3699 4331 52692383 52691747 0.000000e+00 880.0
18 TraesCS5B01G517600 chr2B 91.463 574 35 4 3771 4331 216857621 216857049 0.000000e+00 776.0
19 TraesCS5B01G517600 chr2B 91.413 361 28 2 3544 3901 52692613 52692253 3.890000e-135 492.0
20 TraesCS5B01G517600 chr2B 88.496 339 36 2 3544 3879 584844908 584844570 1.450000e-109 407.0
21 TraesCS5B01G517600 chr2B 90.123 81 7 1 1 81 658588901 658588980 2.130000e-18 104.0
22 TraesCS5B01G517600 chr2B 100.000 31 0 0 1872 1902 73615513 73615483 1.680000e-04 58.4
23 TraesCS5B01G517600 chr1B 91.375 800 56 5 3544 4331 344365850 344366648 0.000000e+00 1083.0
24 TraesCS5B01G517600 chr1B 88.850 574 32 9 3771 4330 266932635 266932080 0.000000e+00 676.0
25 TraesCS5B01G517600 chr1B 78.039 510 77 13 1 477 9419451 9418944 5.480000e-74 289.0
26 TraesCS5B01G517600 chr7B 91.136 801 58 3 3544 4331 585912251 585911451 0.000000e+00 1074.0
27 TraesCS5B01G517600 chr7B 90.280 679 45 7 3664 4331 529148187 529148855 0.000000e+00 869.0
28 TraesCS5B01G517600 chr7B 87.729 709 56 6 3552 4250 614360259 614359572 0.000000e+00 798.0
29 TraesCS5B01G517600 chr7B 89.565 575 28 8 3771 4331 604110542 604109986 0.000000e+00 701.0
30 TraesCS5B01G517600 chr7B 79.412 748 121 15 1 718 238600573 238599829 8.360000e-137 497.0
31 TraesCS5B01G517600 chr7B 93.289 298 16 3 3541 3834 586333281 586332984 1.850000e-118 436.0
32 TraesCS5B01G517600 chr7B 73.684 475 86 26 1 442 448867838 448868306 9.700000e-32 148.0
33 TraesCS5B01G517600 chr7B 88.043 92 10 1 1 91 679718549 679718458 1.650000e-19 108.0
34 TraesCS5B01G517600 chr6B 91.343 797 52 8 3544 4331 517461100 517460312 0.000000e+00 1074.0
35 TraesCS5B01G517600 chr6B 93.274 446 21 1 3895 4331 701622178 701622623 0.000000e+00 649.0
36 TraesCS5B01G517600 chr7D 80.922 781 112 28 1 755 478369011 478368242 2.240000e-162 582.0
37 TraesCS5B01G517600 chr7D 97.059 34 1 0 2841 2874 101138992 101138959 1.680000e-04 58.4
38 TraesCS5B01G517600 chr5A 81.556 694 95 11 1 661 485923400 485922707 3.810000e-150 542.0
39 TraesCS5B01G517600 chr5A 81.439 695 94 14 1 661 485865131 485864438 1.770000e-148 536.0
40 TraesCS5B01G517600 chr5A 78.553 788 121 20 1 754 22612323 22613096 3.920000e-130 475.0
41 TraesCS5B01G517600 chr2A 82.531 561 91 7 113 668 496388996 496388438 1.810000e-133 486.0
42 TraesCS5B01G517600 chr2A 74.414 469 84 26 5 442 257065181 257064718 7.450000e-38 169.0
43 TraesCS5B01G517600 chr2A 81.026 195 28 7 569 756 144918106 144918298 3.490000e-31 147.0
44 TraesCS5B01G517600 chr3D 82.168 572 78 16 110 668 545025097 545025657 1.820000e-128 470.0
45 TraesCS5B01G517600 chr7A 97.059 34 1 0 2841 2874 103400206 103400173 1.680000e-04 58.4


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 TraesCS5B01G517600 chr5B 680992391 680996721 4330 False 7998 7998 100.0000 1 4331 1 chr5B.!!$F1 4330
1 TraesCS5B01G517600 chr5D 539452821 539455929 3108 False 3884 3884 89.2330 158 3319 1 chr5D.!!$F3 3161
2 TraesCS5B01G517600 chr5D 384882005 384882694 689 True 584 584 82.5140 1 669 1 chr5D.!!$R2 668
3 TraesCS5B01G517600 chr5D 433006755 433007444 689 False 562 562 81.9360 1 668 1 chr5D.!!$F1 667
4 TraesCS5B01G517600 chr4A 681918476 681920616 2140 True 2211 2211 85.4360 1171 3308 1 chr4A.!!$R1 2137
5 TraesCS5B01G517600 chr4A 629292526 629295241 2715 True 1486 2098 86.0855 165 3546 2 chr4A.!!$R2 3381
6 TraesCS5B01G517600 chr4D 475176945 475179100 2155 True 2165 2165 84.9200 1153 3308 1 chr4D.!!$R1 2155
7 TraesCS5B01G517600 chr4B 599885004 599887144 2140 True 2139 2139 84.8330 1171 3308 1 chr4B.!!$R1 2137
8 TraesCS5B01G517600 chr3B 693650438 693651233 795 True 1144 1144 92.7410 3542 4331 1 chr3B.!!$R1 789
9 TraesCS5B01G517600 chr3B 773033188 773033976 788 False 593 593 80.9580 1 759 1 chr3B.!!$F3 758
10 TraesCS5B01G517600 chr3B 684454041 684454563 522 False 272 272 76.8400 1 545 1 chr3B.!!$F2 544
11 TraesCS5B01G517600 chr2B 611426832 611427633 801 False 1083 1083 91.2720 3541 4331 1 chr2B.!!$F1 790
12 TraesCS5B01G517600 chr2B 216857049 216857621 572 True 776 776 91.4630 3771 4331 1 chr2B.!!$R2 560
13 TraesCS5B01G517600 chr2B 52691747 52692613 866 True 686 880 91.5850 3544 4331 2 chr2B.!!$R4 787
14 TraesCS5B01G517600 chr1B 344365850 344366648 798 False 1083 1083 91.3750 3544 4331 1 chr1B.!!$F1 787
15 TraesCS5B01G517600 chr1B 266932080 266932635 555 True 676 676 88.8500 3771 4330 1 chr1B.!!$R2 559
16 TraesCS5B01G517600 chr1B 9418944 9419451 507 True 289 289 78.0390 1 477 1 chr1B.!!$R1 476
17 TraesCS5B01G517600 chr7B 585911451 585912251 800 True 1074 1074 91.1360 3544 4331 1 chr7B.!!$R2 787
18 TraesCS5B01G517600 chr7B 529148187 529148855 668 False 869 869 90.2800 3664 4331 1 chr7B.!!$F2 667
19 TraesCS5B01G517600 chr7B 614359572 614360259 687 True 798 798 87.7290 3552 4250 1 chr7B.!!$R5 698
20 TraesCS5B01G517600 chr7B 604109986 604110542 556 True 701 701 89.5650 3771 4331 1 chr7B.!!$R4 560
21 TraesCS5B01G517600 chr7B 238599829 238600573 744 True 497 497 79.4120 1 718 1 chr7B.!!$R1 717
22 TraesCS5B01G517600 chr6B 517460312 517461100 788 True 1074 1074 91.3430 3544 4331 1 chr6B.!!$R1 787
23 TraesCS5B01G517600 chr7D 478368242 478369011 769 True 582 582 80.9220 1 755 1 chr7D.!!$R2 754
24 TraesCS5B01G517600 chr5A 485922707 485923400 693 True 542 542 81.5560 1 661 1 chr5A.!!$R2 660
25 TraesCS5B01G517600 chr5A 485864438 485865131 693 True 536 536 81.4390 1 661 1 chr5A.!!$R1 660
26 TraesCS5B01G517600 chr5A 22612323 22613096 773 False 475 475 78.5530 1 754 1 chr5A.!!$F1 753
27 TraesCS5B01G517600 chr2A 496388438 496388996 558 True 486 486 82.5310 113 668 1 chr2A.!!$R2 555
28 TraesCS5B01G517600 chr3D 545025097 545025657 560 False 470 470 82.1680 110 668 1 chr3D.!!$F1 558

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
717 816 0.109342 ATGGCTTCCATGATCCGGAC 59.891 55.0 6.12 0.9 43.39 4.79 F
2055 2190 0.393132 TCGTCATGCTCGACCTCTCT 60.393 55.0 8.33 0.0 31.91 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2257 0.608856 TTGAGCCGGTTGCACATGAT 60.609 50.0 1.90 0.00 44.83 2.45 R
3990 4315 0.180642 TAGGAGATGCGTCGTCCTCT 59.819 55.0 22.54 10.73 41.21 3.69 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
48 49 1.594194 GCCGATGGTCATGGTGCAAA 61.594 55.000 0.00 0.00 0.00 3.68
72 73 4.021925 GCAAGGGTGGAGCGGAGT 62.022 66.667 0.00 0.00 0.00 3.85
177 217 1.692762 GGTGGCCATCTCCTTCTCCTA 60.693 57.143 9.72 0.00 0.00 2.94
216 258 1.451028 GAGAGCTTTGGCGGCAGAT 60.451 57.895 12.87 0.00 44.37 2.90
221 263 1.669999 GCTTTGGCGGCAGATGGATT 61.670 55.000 12.87 0.00 0.00 3.01
236 288 1.526887 GATTCATGGCGGGGAGTGA 59.473 57.895 0.00 0.00 0.00 3.41
247 299 0.980231 GGGGAGTGATGCAGAGAGGT 60.980 60.000 0.00 0.00 0.00 3.85
316 405 2.910737 TAGAGGGACGGACGGGTGT 61.911 63.158 0.00 0.00 0.00 4.16
560 652 3.744719 CGAGAACACGCGGGAGGA 61.745 66.667 19.19 0.00 0.00 3.71
565 657 3.881019 AACACGCGGGAGGAGGAGA 62.881 63.158 19.19 0.00 0.00 3.71
630 724 2.593956 GGACTCCCGCAAACCTCCT 61.594 63.158 0.00 0.00 0.00 3.69
672 771 2.177654 GAAAAATCACGTCCGGCGCA 62.178 55.000 10.83 5.75 46.11 6.09
714 813 2.938354 GGATGGCTTCCATGATCCG 58.062 57.895 14.15 0.00 45.26 4.18
717 816 0.109342 ATGGCTTCCATGATCCGGAC 59.891 55.000 6.12 0.90 43.39 4.79
719 818 1.595382 GCTTCCATGATCCGGACCG 60.595 63.158 6.12 6.99 30.29 4.79
741 840 2.669240 CGGGAGGTTTGAGGGTCC 59.331 66.667 0.00 0.00 0.00 4.46
748 847 1.595929 GTTTGAGGGTCCGCGTTGA 60.596 57.895 4.92 0.00 0.00 3.18
767 868 6.975772 GCGTTGAATGCCCTAACAATATTTTA 59.024 34.615 0.00 0.00 0.00 1.52
768 869 7.167468 GCGTTGAATGCCCTAACAATATTTTAG 59.833 37.037 0.00 8.97 0.00 1.85
868 970 5.065235 TGAAGATGTGATTGCTGACTGAAA 58.935 37.500 0.00 0.00 0.00 2.69
908 1011 0.810031 ACTCGCAACGCAGTCAACTT 60.810 50.000 0.00 0.00 45.00 2.66
912 1015 1.746760 GCAACGCAGTCAACTTGAAG 58.253 50.000 0.00 0.00 45.00 3.02
928 1031 6.452244 ACTTGAAGCGCAACAATAATTTTC 57.548 33.333 11.47 0.37 31.96 2.29
929 1032 5.116983 ACTTGAAGCGCAACAATAATTTTCG 59.883 36.000 11.47 3.72 31.96 3.46
950 1053 6.636562 TCGAAGCAATTTTACAGGGTTTTA 57.363 33.333 0.00 0.00 0.00 1.52
1074 1178 6.042552 TCCATTTCCCTATTGCTTCAAACAAA 59.957 34.615 0.00 0.00 0.00 2.83
1103 1228 4.455533 TGATGTAAACACAAAGCTAGCTGG 59.544 41.667 20.16 16.24 0.00 4.85
1104 1229 3.815809 TGTAAACACAAAGCTAGCTGGT 58.184 40.909 20.16 16.94 0.00 4.00
1105 1230 3.813166 TGTAAACACAAAGCTAGCTGGTC 59.187 43.478 20.16 8.05 0.00 4.02
1106 1231 2.638480 AACACAAAGCTAGCTGGTCA 57.362 45.000 20.16 0.00 0.00 4.02
1107 1232 2.638480 ACACAAAGCTAGCTGGTCAA 57.362 45.000 20.16 0.00 0.00 3.18
1108 1233 2.498167 ACACAAAGCTAGCTGGTCAAG 58.502 47.619 20.16 10.47 0.00 3.02
1109 1234 1.808945 CACAAAGCTAGCTGGTCAAGG 59.191 52.381 20.16 4.40 0.00 3.61
1110 1235 1.699634 ACAAAGCTAGCTGGTCAAGGA 59.300 47.619 20.16 0.00 0.00 3.36
1111 1236 2.079925 CAAAGCTAGCTGGTCAAGGAC 58.920 52.381 20.16 0.00 0.00 3.85
1112 1237 1.650528 AAGCTAGCTGGTCAAGGACT 58.349 50.000 20.16 0.00 32.47 3.85
1113 1238 2.534042 AGCTAGCTGGTCAAGGACTA 57.466 50.000 18.57 0.00 32.47 2.59
1114 1239 2.383855 AGCTAGCTGGTCAAGGACTAG 58.616 52.381 18.57 5.49 42.71 2.57
1115 1240 1.410882 GCTAGCTGGTCAAGGACTAGG 59.589 57.143 7.70 0.00 40.67 3.02
1116 1241 2.950874 GCTAGCTGGTCAAGGACTAGGA 60.951 54.545 7.70 0.00 40.67 2.94
1117 1242 1.859302 AGCTGGTCAAGGACTAGGAG 58.141 55.000 11.01 0.00 40.67 3.69
1118 1243 1.077993 AGCTGGTCAAGGACTAGGAGT 59.922 52.381 11.01 0.00 40.67 3.85
1119 1244 1.205893 GCTGGTCAAGGACTAGGAGTG 59.794 57.143 11.01 0.00 40.67 3.51
1134 1259 3.702792 AGGAGTGAAGAATCGAAGGAGA 58.297 45.455 0.00 0.00 0.00 3.71
1136 1261 3.697045 GGAGTGAAGAATCGAAGGAGAGA 59.303 47.826 0.00 0.00 0.00 3.10
1137 1262 4.439563 GGAGTGAAGAATCGAAGGAGAGAC 60.440 50.000 0.00 0.00 0.00 3.36
1139 1264 3.127203 GTGAAGAATCGAAGGAGAGACGA 59.873 47.826 0.00 0.00 40.18 4.20
1140 1265 3.375610 TGAAGAATCGAAGGAGAGACGAG 59.624 47.826 0.00 0.00 39.31 4.18
1141 1266 1.673920 AGAATCGAAGGAGAGACGAGC 59.326 52.381 0.00 0.00 39.31 5.03
1142 1267 1.673920 GAATCGAAGGAGAGACGAGCT 59.326 52.381 0.00 0.00 39.31 4.09
1143 1268 1.305201 ATCGAAGGAGAGACGAGCTC 58.695 55.000 2.73 2.73 44.29 4.09
1204 1338 2.342948 GCACGCTTCTTCTTCTTAGTCG 59.657 50.000 0.00 0.00 0.00 4.18
1228 1362 1.959899 CTCATTGTCGCTCGTGTGCC 61.960 60.000 0.00 0.00 0.00 5.01
1304 1438 3.207669 CATCAGGGCCTTGCTCGC 61.208 66.667 10.65 0.00 32.17 5.03
1326 1460 2.608988 CCACTGGGGGAGCTCAGT 60.609 66.667 17.19 8.08 44.12 3.41
1338 1473 4.106925 CTCAGTGGCTGGGGCTCC 62.107 72.222 0.00 0.00 38.73 4.70
1554 1689 2.405594 GAGCTCGACGTCAGCGAT 59.594 61.111 24.38 14.32 42.14 4.58
1620 1755 1.153958 GCTGGCGCATTTCAACTCC 60.154 57.895 10.83 0.00 35.78 3.85
1683 1818 4.500116 GCCACCGAGCTCGAGACC 62.500 72.222 36.59 17.82 43.02 3.85
1875 2010 4.996434 CCGATCCCAGCGGCCATC 62.996 72.222 2.24 0.00 42.55 3.51
2029 2164 3.259633 AAGGAGCTCGGCAACCTGG 62.260 63.158 7.83 0.00 37.57 4.45
2055 2190 0.393132 TCGTCATGCTCGACCTCTCT 60.393 55.000 8.33 0.00 31.91 3.10
2061 2196 3.196469 TCATGCTCGACCTCTCTGAAAAT 59.804 43.478 0.00 0.00 0.00 1.82
2122 2257 1.152902 AACCTGCAGCTGCTCAACA 60.153 52.632 36.61 17.40 42.66 3.33
2697 2832 2.510238 GCACTCTCCGCGCTTGAT 60.510 61.111 5.56 0.00 0.00 2.57
2982 3117 1.226603 GACGATCAACCCCGACGAG 60.227 63.158 0.00 0.00 0.00 4.18
2985 3120 1.519455 GATCAACCCCGACGAGCTG 60.519 63.158 0.00 0.00 0.00 4.24
3042 3177 4.577677 TGCCTGGCCAACGCTTCA 62.578 61.111 21.66 5.34 34.44 3.02
3043 3178 3.064324 GCCTGGCCAACGCTTCAT 61.064 61.111 7.01 0.00 34.44 2.57
3044 3179 3.056313 GCCTGGCCAACGCTTCATC 62.056 63.158 7.01 0.00 34.44 2.92
3045 3180 2.409870 CCTGGCCAACGCTTCATCC 61.410 63.158 7.01 0.00 34.44 3.51
3046 3181 1.377725 CTGGCCAACGCTTCATCCT 60.378 57.895 7.01 0.00 34.44 3.24
3048 3183 2.464459 GGCCAACGCTTCATCCTCG 61.464 63.158 0.00 0.00 34.44 4.63
3049 3184 2.464459 GCCAACGCTTCATCCTCGG 61.464 63.158 0.00 0.00 0.00 4.63
3050 3185 1.218047 CCAACGCTTCATCCTCGGA 59.782 57.895 0.00 0.00 0.00 4.55
3051 3186 0.391130 CCAACGCTTCATCCTCGGAA 60.391 55.000 0.00 0.00 0.00 4.30
3052 3187 1.002366 CAACGCTTCATCCTCGGAAG 58.998 55.000 0.00 0.00 43.59 3.46
3062 3197 2.492090 CTCGGAAGCGTCCTCCAG 59.508 66.667 16.94 6.00 42.44 3.86
3117 3264 3.928779 TGGGCGATCGGCATCTCC 61.929 66.667 37.72 22.84 46.16 3.71
3163 3316 0.741221 CTTCCTCGGTAAGGTGCTGC 60.741 60.000 0.00 0.00 46.32 5.25
3321 3487 2.362120 GGCAGCAAGTCCAGCCAT 60.362 61.111 0.00 0.00 46.26 4.40
3338 3504 2.885554 GCCATCCCTCATGAAGTGGTTT 60.886 50.000 13.59 0.27 33.80 3.27
3364 3530 5.981315 CAGCTGAAGAAGAAAAATGAAGCAA 59.019 36.000 8.42 0.00 0.00 3.91
3365 3531 6.645415 CAGCTGAAGAAGAAAAATGAAGCAAT 59.355 34.615 8.42 0.00 0.00 3.56
3366 3532 7.811236 CAGCTGAAGAAGAAAAATGAAGCAATA 59.189 33.333 8.42 0.00 0.00 1.90
3367 3533 8.529476 AGCTGAAGAAGAAAAATGAAGCAATAT 58.471 29.630 0.00 0.00 0.00 1.28
3402 3568 1.939597 CGATAGCGTAGGAGCACGA 59.060 57.895 0.00 0.00 44.69 4.35
3403 3569 0.384477 CGATAGCGTAGGAGCACGAC 60.384 60.000 0.00 0.00 44.69 4.34
3406 3572 0.750546 TAGCGTAGGAGCACGACCAT 60.751 55.000 0.00 0.00 44.69 3.55
3407 3573 0.750546 AGCGTAGGAGCACGACCATA 60.751 55.000 0.00 0.00 44.69 2.74
3409 3575 1.864435 GCGTAGGAGCACGACCATAAG 60.864 57.143 0.00 0.00 44.69 1.73
3410 3576 1.404391 CGTAGGAGCACGACCATAAGT 59.596 52.381 0.00 0.00 44.69 2.24
3412 3578 3.303857 CGTAGGAGCACGACCATAAGTAG 60.304 52.174 0.00 0.00 44.69 2.57
3415 3581 3.381908 AGGAGCACGACCATAAGTAGAAG 59.618 47.826 0.00 0.00 0.00 2.85
3416 3582 3.491104 GGAGCACGACCATAAGTAGAAGG 60.491 52.174 0.00 0.00 0.00 3.46
3418 3584 3.767673 AGCACGACCATAAGTAGAAGGAA 59.232 43.478 0.00 0.00 0.00 3.36
3419 3585 3.864003 GCACGACCATAAGTAGAAGGAAC 59.136 47.826 0.00 0.00 0.00 3.62
3420 3586 4.103357 CACGACCATAAGTAGAAGGAACG 58.897 47.826 0.00 0.00 0.00 3.95
3422 3588 3.428452 CGACCATAAGTAGAAGGAACGCA 60.428 47.826 0.00 0.00 0.00 5.24
3423 3589 4.694339 GACCATAAGTAGAAGGAACGCAT 58.306 43.478 0.00 0.00 0.00 4.73
3424 3590 4.694339 ACCATAAGTAGAAGGAACGCATC 58.306 43.478 0.00 0.00 0.00 3.91
3425 3591 4.406003 ACCATAAGTAGAAGGAACGCATCT 59.594 41.667 0.00 0.00 0.00 2.90
3427 3593 5.921408 CCATAAGTAGAAGGAACGCATCTAC 59.079 44.000 4.43 4.43 43.69 2.59
3428 3594 6.461092 CCATAAGTAGAAGGAACGCATCTACA 60.461 42.308 12.98 0.00 45.05 2.74
3429 3595 5.599999 AAGTAGAAGGAACGCATCTACAT 57.400 39.130 12.98 0.60 45.05 2.29
3430 3596 6.710597 AAGTAGAAGGAACGCATCTACATA 57.289 37.500 12.98 0.00 45.05 2.29
3431 3597 6.710597 AGTAGAAGGAACGCATCTACATAA 57.289 37.500 12.98 0.00 45.05 1.90
3432 3598 7.108841 AGTAGAAGGAACGCATCTACATAAA 57.891 36.000 12.98 0.00 45.05 1.40
3433 3599 7.553334 AGTAGAAGGAACGCATCTACATAAAA 58.447 34.615 12.98 0.00 45.05 1.52
3435 3601 7.865706 AGAAGGAACGCATCTACATAAAAAT 57.134 32.000 0.00 0.00 0.00 1.82
3436 3602 7.920738 AGAAGGAACGCATCTACATAAAAATC 58.079 34.615 0.00 0.00 0.00 2.17
3437 3603 6.619801 AGGAACGCATCTACATAAAAATCC 57.380 37.500 0.00 0.00 0.00 3.01
3438 3604 5.531287 AGGAACGCATCTACATAAAAATCCC 59.469 40.000 0.00 0.00 0.00 3.85
3439 3605 5.418310 AACGCATCTACATAAAAATCCCG 57.582 39.130 0.00 0.00 0.00 5.14
3440 3606 4.448210 ACGCATCTACATAAAAATCCCGT 58.552 39.130 0.00 0.00 0.00 5.28
3441 3607 4.272504 ACGCATCTACATAAAAATCCCGTG 59.727 41.667 0.00 0.00 0.00 4.94
3461 3627 3.062639 GTGTTCATTGAGCACGGATGTAG 59.937 47.826 16.34 0.00 34.48 2.74
3464 3635 4.041740 TCATTGAGCACGGATGTAGTAC 57.958 45.455 0.00 0.00 0.00 2.73
3473 3644 4.496010 GCACGGATGTAGTACAGTACTCAG 60.496 50.000 16.91 6.42 40.14 3.35
3590 3774 1.270971 CCGCGCGCTAAAAACTACTA 58.729 50.000 30.48 0.00 0.00 1.82
3643 3827 2.253758 GCAGCGCTGACTCCAACAA 61.254 57.895 40.21 0.00 0.00 2.83
3648 3832 1.891919 GCTGACTCCAACAACCGCA 60.892 57.895 0.00 0.00 0.00 5.69
3801 4058 6.027749 CCTGCTTCCACGATACAAAATAAAC 58.972 40.000 0.00 0.00 0.00 2.01
3859 4117 4.480541 CACATAGCCTGCTTCTACGATAG 58.519 47.826 0.00 0.00 46.19 2.08
3882 4207 7.544804 AGAAAATAAAACTGGCTTCTCCAAT 57.455 32.000 0.00 0.00 46.01 3.16
3925 4250 1.395608 CGTTCTCCGACTCAGACTCTC 59.604 57.143 0.00 0.00 39.56 3.20
3962 4287 0.107361 TCCGACGTCTGAGCATAGGA 60.107 55.000 14.70 7.22 0.00 2.94
3979 4304 2.048127 AGTCAAGGAACCGCTCGC 60.048 61.111 0.00 0.00 0.00 5.03
4020 4345 1.270305 GCATCTCCTAGCGCCATGTTA 60.270 52.381 2.29 0.00 0.00 2.41
4031 4358 4.253685 AGCGCCATGTTATATTTAGCGAT 58.746 39.130 2.29 2.18 44.51 4.58
4098 4425 1.576368 TTCTCTCCTCCCTCTCCGCT 61.576 60.000 0.00 0.00 0.00 5.52
4246 4582 1.747745 GTGGTAAGCCGCGGGAAAT 60.748 57.895 29.38 0.20 37.67 2.17
4304 4640 2.582052 GGTGAAGTTCATGTCCCAACA 58.418 47.619 9.18 0.00 40.38 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.686110 CCTACTCCGCTCCACCCTT 60.686 63.158 0.00 0.00 0.00 3.95
143 183 0.463654 GCCACCATTGATGCCGACTA 60.464 55.000 0.00 0.00 0.00 2.59
152 192 1.002069 AAGGAGATGGCCACCATTGA 58.998 50.000 8.16 0.00 45.26 2.57
177 217 2.597805 ACAGGCTGACGTCGGAGT 60.598 61.111 28.38 18.35 0.00 3.85
216 258 2.000701 ACTCCCCGCCATGAATCCA 61.001 57.895 0.00 0.00 0.00 3.41
221 263 2.910360 CATCACTCCCCGCCATGA 59.090 61.111 0.00 0.00 0.00 3.07
236 288 4.535294 AGCCATAATCATACCTCTCTGCAT 59.465 41.667 0.00 0.00 0.00 3.96
272 353 2.231478 CCACCAGTGCTATATAGACCGG 59.769 54.545 14.16 0.00 0.00 5.28
277 358 2.891580 ACCGTCCACCAGTGCTATATAG 59.108 50.000 5.30 5.30 0.00 1.31
316 405 2.688666 AGGCATCTCCTCCGGCAA 60.689 61.111 0.00 0.00 43.20 4.52
456 545 3.055719 CGCCGGCATTGAAGTGGT 61.056 61.111 28.98 0.00 0.00 4.16
495 584 3.831883 CATTCATGCCCGGTCAGG 58.168 61.111 0.00 0.00 40.63 3.86
560 652 1.460699 GCCCACCAAAACCTCTCCT 59.539 57.895 0.00 0.00 0.00 3.69
630 724 2.286713 CGCAAACGAAGACAAACATGGA 60.287 45.455 0.00 0.00 43.93 3.41
672 771 0.249322 CAATTCGGTATCGGTCCGCT 60.249 55.000 6.34 0.00 46.49 5.52
719 818 2.747855 CTCAAACCTCCCGCAGCC 60.748 66.667 0.00 0.00 0.00 4.85
721 820 2.045926 CCCTCAAACCTCCCGCAG 60.046 66.667 0.00 0.00 0.00 5.18
741 840 0.519519 TTGTTAGGGCATTCAACGCG 59.480 50.000 3.53 3.53 0.00 6.01
767 868 3.009143 AGGACGAAGCCTGTAAATTTCCT 59.991 43.478 0.00 0.00 36.76 3.36
768 869 3.344515 AGGACGAAGCCTGTAAATTTCC 58.655 45.455 0.00 0.00 36.76 3.13
784 886 1.028905 TTCACCCAGCAAAAAGGACG 58.971 50.000 0.00 0.00 0.00 4.79
908 1011 4.788690 TCGAAAATTATTGTTGCGCTTCA 58.211 34.783 9.73 4.82 0.00 3.02
912 1015 3.363426 TGCTTCGAAAATTATTGTTGCGC 59.637 39.130 0.00 0.00 0.00 6.09
928 1031 6.921307 ACTTAAAACCCTGTAAAATTGCTTCG 59.079 34.615 0.00 0.00 0.00 3.79
929 1032 8.657074 AACTTAAAACCCTGTAAAATTGCTTC 57.343 30.769 0.00 0.00 0.00 3.86
960 1063 8.586744 GTTATAGTAAACCAAAAATTCACCCCA 58.413 33.333 0.00 0.00 0.00 4.96
1034 1138 2.808906 ATGGAGGGAAACTAACAGCC 57.191 50.000 0.00 0.00 0.00 4.85
1074 1178 6.207691 AGCTTTGTGTTTACATCAACAAGT 57.792 33.333 0.00 0.00 38.40 3.16
1103 1228 5.656480 GATTCTTCACTCCTAGTCCTTGAC 58.344 45.833 0.00 0.00 0.00 3.18
1104 1229 4.399618 CGATTCTTCACTCCTAGTCCTTGA 59.600 45.833 0.00 0.00 0.00 3.02
1105 1230 4.399618 TCGATTCTTCACTCCTAGTCCTTG 59.600 45.833 0.00 0.00 0.00 3.61
1106 1231 4.601084 TCGATTCTTCACTCCTAGTCCTT 58.399 43.478 0.00 0.00 0.00 3.36
1107 1232 4.237976 TCGATTCTTCACTCCTAGTCCT 57.762 45.455 0.00 0.00 0.00 3.85
1108 1233 4.202070 CCTTCGATTCTTCACTCCTAGTCC 60.202 50.000 0.00 0.00 0.00 3.85
1109 1234 4.641094 TCCTTCGATTCTTCACTCCTAGTC 59.359 45.833 0.00 0.00 0.00 2.59
1110 1235 4.601084 TCCTTCGATTCTTCACTCCTAGT 58.399 43.478 0.00 0.00 0.00 2.57
1111 1236 4.884744 TCTCCTTCGATTCTTCACTCCTAG 59.115 45.833 0.00 0.00 0.00 3.02
1112 1237 4.856509 TCTCCTTCGATTCTTCACTCCTA 58.143 43.478 0.00 0.00 0.00 2.94
1113 1238 3.699038 CTCTCCTTCGATTCTTCACTCCT 59.301 47.826 0.00 0.00 0.00 3.69
1114 1239 3.697045 TCTCTCCTTCGATTCTTCACTCC 59.303 47.826 0.00 0.00 0.00 3.85
1115 1240 4.668289 GTCTCTCCTTCGATTCTTCACTC 58.332 47.826 0.00 0.00 0.00 3.51
1116 1241 3.127895 CGTCTCTCCTTCGATTCTTCACT 59.872 47.826 0.00 0.00 0.00 3.41
1117 1242 3.127203 TCGTCTCTCCTTCGATTCTTCAC 59.873 47.826 0.00 0.00 0.00 3.18
1118 1243 3.344515 TCGTCTCTCCTTCGATTCTTCA 58.655 45.455 0.00 0.00 0.00 3.02
1119 1244 3.790789 GCTCGTCTCTCCTTCGATTCTTC 60.791 52.174 0.00 0.00 33.26 2.87
1141 1266 1.640069 CATTCGCCATGCTCGTGAG 59.360 57.895 5.68 0.00 0.00 3.51
1142 1267 3.798380 CATTCGCCATGCTCGTGA 58.202 55.556 5.68 0.00 0.00 4.35
1204 1338 1.651138 CACGAGCGACAATGAGAAGAC 59.349 52.381 0.00 0.00 0.00 3.01
1750 1885 2.815647 CGCGAGCCCCAAGAACTC 60.816 66.667 0.00 0.00 0.00 3.01
1821 1956 1.340088 AGCCGATGATGATCTGCTCT 58.660 50.000 5.28 0.00 43.51 4.09
1875 2010 1.301677 GGAGGTTCTTGAGCTTGCCG 61.302 60.000 0.00 0.00 35.91 5.69
2029 2164 2.107953 GAGCATGACGAGGGAGGC 59.892 66.667 0.00 0.00 0.00 4.70
2055 2190 1.851021 CGCCGGTGAGTGCATTTTCA 61.851 55.000 10.20 0.00 0.00 2.69
2122 2257 0.608856 TTGAGCCGGTTGCACATGAT 60.609 50.000 1.90 0.00 44.83 2.45
2457 2592 2.256591 GCGATCCAGGCGATGCAAT 61.257 57.895 0.00 0.00 0.00 3.56
2838 2973 1.132689 AGGAGGTTGTTGGAGAGGTCT 60.133 52.381 0.00 0.00 0.00 3.85
2959 3094 0.686441 TCGGGGTTGATCGTCCTCAT 60.686 55.000 6.66 0.00 0.00 2.90
3028 3163 1.372087 GAGGATGAAGCGTTGGCCAG 61.372 60.000 5.11 0.00 41.24 4.85
3029 3164 1.377202 GAGGATGAAGCGTTGGCCA 60.377 57.895 0.00 0.00 41.24 5.36
3040 3175 3.207354 GGACGCTTCCGAGGATGA 58.793 61.111 8.95 0.00 38.29 2.92
3086 3230 3.770040 CCCACCCGACAGCGATGA 61.770 66.667 8.12 0.00 40.82 2.92
3172 3325 2.435938 AGCACCATTGGCGTACCG 60.436 61.111 1.54 0.00 39.70 4.02
3213 3366 4.361971 ACGCTCCCGTCCTCCTCA 62.362 66.667 0.00 0.00 46.39 3.86
3321 3487 3.559171 GCTGTAAACCACTTCATGAGGGA 60.559 47.826 9.90 0.00 0.00 4.20
3338 3504 6.262944 TGCTTCATTTTTCTTCTTCAGCTGTA 59.737 34.615 14.67 2.58 0.00 2.74
3402 3568 4.406003 AGATGCGTTCCTTCTACTTATGGT 59.594 41.667 0.00 0.00 0.00 3.55
3403 3569 4.950050 AGATGCGTTCCTTCTACTTATGG 58.050 43.478 0.00 0.00 0.00 2.74
3406 3572 6.710597 ATGTAGATGCGTTCCTTCTACTTA 57.289 37.500 13.82 1.00 44.98 2.24
3407 3573 5.599999 ATGTAGATGCGTTCCTTCTACTT 57.400 39.130 13.82 7.80 44.98 2.24
3409 3575 7.766219 TTTTATGTAGATGCGTTCCTTCTAC 57.234 36.000 8.56 8.56 44.97 2.59
3410 3576 8.958119 ATTTTTATGTAGATGCGTTCCTTCTA 57.042 30.769 0.00 0.00 31.17 2.10
3412 3578 7.132863 GGATTTTTATGTAGATGCGTTCCTTC 58.867 38.462 0.00 0.00 0.00 3.46
3415 3581 5.560183 CGGGATTTTTATGTAGATGCGTTCC 60.560 44.000 0.00 0.00 0.00 3.62
3416 3582 5.007332 ACGGGATTTTTATGTAGATGCGTTC 59.993 40.000 0.00 0.00 0.00 3.95
3418 3584 4.272504 CACGGGATTTTTATGTAGATGCGT 59.727 41.667 0.00 0.00 0.00 5.24
3419 3585 4.272504 ACACGGGATTTTTATGTAGATGCG 59.727 41.667 0.00 0.00 0.00 4.73
3420 3586 5.751243 ACACGGGATTTTTATGTAGATGC 57.249 39.130 0.00 0.00 0.00 3.91
3422 3588 8.405531 CAATGAACACGGGATTTTTATGTAGAT 58.594 33.333 0.00 0.00 0.00 1.98
3423 3589 7.608376 TCAATGAACACGGGATTTTTATGTAGA 59.392 33.333 0.00 0.00 0.00 2.59
3424 3590 7.757526 TCAATGAACACGGGATTTTTATGTAG 58.242 34.615 0.00 0.00 0.00 2.74
3425 3591 7.627513 GCTCAATGAACACGGGATTTTTATGTA 60.628 37.037 0.00 0.00 0.00 2.29
3427 3593 5.516339 GCTCAATGAACACGGGATTTTTATG 59.484 40.000 0.00 0.00 0.00 1.90
3428 3594 5.184864 TGCTCAATGAACACGGGATTTTTAT 59.815 36.000 0.00 0.00 0.00 1.40
3429 3595 4.520874 TGCTCAATGAACACGGGATTTTTA 59.479 37.500 0.00 0.00 0.00 1.52
3430 3596 3.320541 TGCTCAATGAACACGGGATTTTT 59.679 39.130 0.00 0.00 0.00 1.94
3431 3597 2.890311 TGCTCAATGAACACGGGATTTT 59.110 40.909 0.00 0.00 0.00 1.82
3432 3598 2.228822 GTGCTCAATGAACACGGGATTT 59.771 45.455 0.73 0.00 0.00 2.17
3433 3599 1.812571 GTGCTCAATGAACACGGGATT 59.187 47.619 0.73 0.00 0.00 3.01
3435 3601 2.927004 GTGCTCAATGAACACGGGA 58.073 52.632 0.73 0.00 0.00 5.14
3439 3605 1.806542 ACATCCGTGCTCAATGAACAC 59.193 47.619 6.71 6.71 0.00 3.32
3440 3606 2.183478 ACATCCGTGCTCAATGAACA 57.817 45.000 5.44 0.00 0.00 3.18
3441 3607 3.262420 ACTACATCCGTGCTCAATGAAC 58.738 45.455 5.44 0.00 0.00 3.18
3634 3818 2.335316 TTTAGTGCGGTTGTTGGAGT 57.665 45.000 0.00 0.00 0.00 3.85
3648 3832 2.098298 CGCGCGCTGCATTTTAGT 59.902 55.556 30.48 0.00 46.97 2.24
3801 4058 6.692486 ACTATATATCGTTGGAGAAGCAAGG 58.308 40.000 0.00 0.00 0.00 3.61
3925 4250 1.381872 AGGAGGACATCACCGAGGG 60.382 63.158 0.00 0.00 34.73 4.30
3962 4287 2.048127 GCGAGCGGTTCCTTGACT 60.048 61.111 0.00 0.00 0.00 3.41
3979 4304 2.888863 GTCCTCTGACTCCAGCGG 59.111 66.667 0.00 0.00 44.61 5.52
3983 4308 2.333417 GCGTCGTCCTCTGACTCCA 61.333 63.158 0.00 0.00 39.47 3.86
3990 4315 0.180642 TAGGAGATGCGTCGTCCTCT 59.819 55.000 22.54 10.73 41.21 3.69
3991 4316 0.589223 CTAGGAGATGCGTCGTCCTC 59.411 60.000 22.54 7.16 41.21 3.71
4020 4345 2.607187 CGGAAGGCGATCGCTAAATAT 58.393 47.619 36.25 17.66 41.60 1.28
4246 4582 3.364441 GGCACATGAGTTGGCGCA 61.364 61.111 10.83 0.00 31.41 6.09


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

AutoCloner maintained by Alex Coulton.