Multiple sequence alignment - TraesCS5D01G313400

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 TraesCS5D01G313400 chr5D 100.000 3830 0 0 1 3830 408651713 408647884 0.000000e+00 7073.0
1 TraesCS5D01G313400 chr5D 85.659 781 103 4 2009 2786 408770093 408769319 0.000000e+00 813.0
2 TraesCS5D01G313400 chr5D 89.008 373 40 1 2016 2388 408666643 408666272 9.690000e-126 460.0
3 TraesCS5D01G313400 chr5D 76.959 868 117 36 2012 2830 408659772 408658939 5.920000e-113 418.0
4 TraesCS5D01G313400 chr5D 76.613 868 126 38 2012 2833 408742464 408741628 1.280000e-109 407.0
5 TraesCS5D01G313400 chr5D 84.713 157 20 4 1318 1470 88467173 88467329 1.840000e-33 154.0
6 TraesCS5D01G313400 chr5B 91.159 1640 101 16 735 2344 490236348 490234723 0.000000e+00 2185.0
7 TraesCS5D01G313400 chr5B 97.674 516 9 2 2339 2854 490232666 490232154 0.000000e+00 883.0
8 TraesCS5D01G313400 chr5B 88.015 776 34 20 1 737 490238466 490237711 0.000000e+00 863.0
9 TraesCS5D01G313400 chr5B 83.227 781 116 5 2009 2786 490612043 490611275 0.000000e+00 702.0
10 TraesCS5D01G313400 chr5B 80.409 587 87 14 2258 2833 490359198 490358629 4.570000e-114 422.0
11 TraesCS5D01G313400 chr5B 82.972 323 48 7 1317 1636 512498926 512498608 6.260000e-73 285.0
12 TraesCS5D01G313400 chr5B 85.973 221 22 3 2052 2272 490304610 490304399 1.070000e-55 228.0
13 TraesCS5D01G313400 chr1D 98.465 977 15 0 2854 3830 301746523 301745547 0.000000e+00 1722.0
14 TraesCS5D01G313400 chr1D 86.475 244 31 2 1395 1638 424909780 424909539 2.270000e-67 267.0
15 TraesCS5D01G313400 chr4D 98.626 946 13 0 2855 3800 402951671 402952616 0.000000e+00 1676.0
16 TraesCS5D01G313400 chr4D 88.095 840 95 3 2861 3699 47473805 47474640 0.000000e+00 992.0
17 TraesCS5D01G313400 chr4D 87.771 785 91 3 2940 3723 245070504 245069724 0.000000e+00 913.0
18 TraesCS5D01G313400 chr7D 88.581 867 94 3 2861 3726 612274829 612273967 0.000000e+00 1048.0
19 TraesCS5D01G313400 chr7D 85.340 191 22 4 1637 1822 201977213 201977024 3.900000e-45 193.0
20 TraesCS5D01G313400 chr7D 100.000 28 0 0 944 971 91658490 91658517 7.000000e-03 52.8
21 TraesCS5D01G313400 chr3D 87.630 865 100 5 2861 3723 921421 920562 0.000000e+00 998.0
22 TraesCS5D01G313400 chr3D 79.661 472 62 16 1173 1636 36573079 36572634 3.720000e-80 309.0
23 TraesCS5D01G313400 chr6D 88.095 840 95 3 2861 3699 42117261 42118096 0.000000e+00 992.0
24 TraesCS5D01G313400 chr3B 84.504 968 137 9 2863 3828 798133038 798133994 0.000000e+00 944.0
25 TraesCS5D01G313400 chr1A 83.282 969 151 9 2864 3828 465353992 465353031 0.000000e+00 881.0
26 TraesCS5D01G313400 chr1A 93.750 272 16 1 602 872 566497044 566496773 1.280000e-109 407.0
27 TraesCS5D01G313400 chr1A 87.692 130 16 0 1016 1145 58839856 58839727 6.630000e-33 152.0
28 TraesCS5D01G313400 chr4A 82.990 970 153 8 2862 3828 618138714 618137754 0.000000e+00 867.0
29 TraesCS5D01G313400 chr5A 85.019 781 108 4 2009 2786 519693939 519693165 0.000000e+00 785.0
30 TraesCS5D01G313400 chr5A 83.236 859 122 9 2009 2854 518411847 518412696 0.000000e+00 769.0
31 TraesCS5D01G313400 chr5A 79.352 586 95 12 2258 2833 515495810 515495241 4.640000e-104 388.0
32 TraesCS5D01G313400 chr5A 91.005 189 14 2 2016 2203 515952140 515952326 6.350000e-63 252.0
33 TraesCS5D01G313400 chr4B 88.743 382 27 2 602 982 548186330 548185964 1.620000e-123 453.0
34 TraesCS5D01G313400 chr4B 100.000 38 0 0 565 602 548186352 548186315 1.910000e-08 71.3
35 TraesCS5D01G313400 chr4B 100.000 28 0 0 1173 1200 477644202 477644175 7.000000e-03 52.8
36 TraesCS5D01G313400 chr7A 93.416 243 15 1 602 843 223686902 223686660 3.640000e-95 359.0
37 TraesCS5D01G313400 chr7A 93.750 208 12 1 602 808 223693128 223692921 1.030000e-80 311.0
38 TraesCS5D01G313400 chr7B 83.081 396 49 7 1166 1547 653985880 653985489 1.020000e-90 344.0
39 TraesCS5D01G313400 chr7B 89.542 153 16 0 817 969 53256865 53257017 1.090000e-45 195.0
40 TraesCS5D01G313400 chr7B 87.324 71 9 0 912 982 560508148 560508078 8.820000e-12 82.4
41 TraesCS5D01G313400 chr2A 83.152 368 51 11 1278 1639 667012161 667011799 3.690000e-85 326.0
42 TraesCS5D01G313400 chr2A 92.694 219 15 1 763 981 145379143 145379360 7.990000e-82 315.0
43 TraesCS5D01G313400 chr2A 87.500 56 6 1 926 980 744367336 744367391 3.190000e-06 63.9
44 TraesCS5D01G313400 chr2D 79.624 319 47 10 1166 1470 526097499 526097813 3.000000e-51 213.0
45 TraesCS5D01G313400 chr2D 87.791 172 18 3 1465 1636 634281223 634281055 8.390000e-47 198.0
46 TraesCS5D01G313400 chr2B 87.640 178 20 2 1459 1636 777302739 777302564 5.020000e-49 206.0
47 TraesCS5D01G313400 chr2B 86.792 159 19 2 1479 1637 74061328 74061484 3.930000e-40 176.0
48 TraesCS5D01G313400 chrUn 87.059 170 20 2 1464 1632 12884524 12884356 1.400000e-44 191.0
49 TraesCS5D01G313400 chr6B 87.975 158 13 5 1321 1473 695940543 695940387 8.450000e-42 182.0
50 TraesCS5D01G313400 chr3A 77.622 143 24 6 1320 1459 696279816 696279679 3.170000e-11 80.5


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 TraesCS5D01G313400 chr5D 408647884 408651713 3829 True 7073.000000 7073 100.000000 1 3830 1 chr5D.!!$R1 3829
1 TraesCS5D01G313400 chr5D 408769319 408770093 774 True 813.000000 813 85.659000 2009 2786 1 chr5D.!!$R5 777
2 TraesCS5D01G313400 chr5D 408658939 408659772 833 True 418.000000 418 76.959000 2012 2830 1 chr5D.!!$R2 818
3 TraesCS5D01G313400 chr5D 408741628 408742464 836 True 407.000000 407 76.613000 2012 2833 1 chr5D.!!$R4 821
4 TraesCS5D01G313400 chr5B 490232154 490238466 6312 True 1310.333333 2185 92.282667 1 2854 3 chr5B.!!$R5 2853
5 TraesCS5D01G313400 chr5B 490611275 490612043 768 True 702.000000 702 83.227000 2009 2786 1 chr5B.!!$R3 777
6 TraesCS5D01G313400 chr5B 490358629 490359198 569 True 422.000000 422 80.409000 2258 2833 1 chr5B.!!$R2 575
7 TraesCS5D01G313400 chr1D 301745547 301746523 976 True 1722.000000 1722 98.465000 2854 3830 1 chr1D.!!$R1 976
8 TraesCS5D01G313400 chr4D 402951671 402952616 945 False 1676.000000 1676 98.626000 2855 3800 1 chr4D.!!$F2 945
9 TraesCS5D01G313400 chr4D 47473805 47474640 835 False 992.000000 992 88.095000 2861 3699 1 chr4D.!!$F1 838
10 TraesCS5D01G313400 chr4D 245069724 245070504 780 True 913.000000 913 87.771000 2940 3723 1 chr4D.!!$R1 783
11 TraesCS5D01G313400 chr7D 612273967 612274829 862 True 1048.000000 1048 88.581000 2861 3726 1 chr7D.!!$R2 865
12 TraesCS5D01G313400 chr3D 920562 921421 859 True 998.000000 998 87.630000 2861 3723 1 chr3D.!!$R1 862
13 TraesCS5D01G313400 chr6D 42117261 42118096 835 False 992.000000 992 88.095000 2861 3699 1 chr6D.!!$F1 838
14 TraesCS5D01G313400 chr3B 798133038 798133994 956 False 944.000000 944 84.504000 2863 3828 1 chr3B.!!$F1 965
15 TraesCS5D01G313400 chr1A 465353031 465353992 961 True 881.000000 881 83.282000 2864 3828 1 chr1A.!!$R2 964
16 TraesCS5D01G313400 chr4A 618137754 618138714 960 True 867.000000 867 82.990000 2862 3828 1 chr4A.!!$R1 966
17 TraesCS5D01G313400 chr5A 519693165 519693939 774 True 785.000000 785 85.019000 2009 2786 1 chr5A.!!$R2 777
18 TraesCS5D01G313400 chr5A 518411847 518412696 849 False 769.000000 769 83.236000 2009 2854 1 chr5A.!!$F2 845
19 TraesCS5D01G313400 chr5A 515495241 515495810 569 True 388.000000 388 79.352000 2258 2833 1 chr5A.!!$R1 575

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
598 637 0.179073 GCATGTAGCCGATGTGGTCT 60.179 55.0 0.00 0.0 41.21 3.85 F
600 639 0.385751 ATGTAGCCGATGTGGTCTCG 59.614 55.0 0.00 0.0 41.21 4.04 F
1744 3175 0.451383 CGCCGGATTGCTTGATGAAA 59.549 50.0 5.05 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 2919 0.494551 TCTTAGGGTTCAGGGTGGGA 59.505 55.000 0.00 0.0 0.00 4.37 R
1884 3320 0.811616 CAAGCTATCGTCTGGCCCAC 60.812 60.000 0.00 0.0 30.08 4.61 R
3139 6685 1.078988 GATGTACAACCCGCCGGAA 60.079 57.895 5.05 0.0 0.00 4.30 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
28 30 7.696992 AAGACAACAGGAAAGAAACAAGTTA 57.303 32.000 0.00 0.00 0.00 2.24
63 65 4.656041 GAAAGCTAGCTACAAGCAACATG 58.344 43.478 19.70 0.00 45.56 3.21
90 92 2.846193 TGCATTATAAAGAGGACCGGC 58.154 47.619 0.00 0.00 0.00 6.13
110 112 3.328237 CTTAACCAGCAAACGTTCGTT 57.672 42.857 0.00 4.72 0.00 3.85
129 131 4.465512 GCGGCATGACAACTGCGG 62.466 66.667 0.00 4.66 40.59 5.69
131 133 2.108514 CGGCATGACAACTGCGGAT 61.109 57.895 0.00 0.00 41.05 4.18
139 153 3.669536 TGACAACTGCGGATGATTTGTA 58.330 40.909 10.13 0.00 30.60 2.41
141 155 4.094739 TGACAACTGCGGATGATTTGTATG 59.905 41.667 10.13 0.00 30.60 2.39
144 158 3.206150 ACTGCGGATGATTTGTATGGTC 58.794 45.455 0.00 0.00 0.00 4.02
145 159 2.549754 CTGCGGATGATTTGTATGGTCC 59.450 50.000 0.00 0.00 0.00 4.46
153 167 0.537653 TTTGTATGGTCCGCGGATGA 59.462 50.000 33.58 21.26 0.00 2.92
161 175 1.202143 GGTCCGCGGATGACAATTTTC 60.202 52.381 33.58 13.99 34.36 2.29
236 250 5.726980 TGCTTCCTCAAACAATTTGCTAT 57.273 34.783 0.00 0.00 40.43 2.97
247 261 7.283127 TCAAACAATTTGCTATCCCTATGACTC 59.717 37.037 0.00 0.00 40.43 3.36
279 293 4.280929 ACCTTAAGAACCTTTCATTGTGCC 59.719 41.667 3.36 0.00 0.00 5.01
351 366 5.513141 CGGTGTATCATAAGCATGATACTCG 59.487 44.000 25.68 23.89 44.91 4.18
395 434 4.534500 ACACCAATAATCCTACACCACTGA 59.466 41.667 0.00 0.00 0.00 3.41
396 435 5.013704 ACACCAATAATCCTACACCACTGAA 59.986 40.000 0.00 0.00 0.00 3.02
406 445 5.472137 TCCTACACCACTGAATTTTTACAGC 59.528 40.000 0.00 0.00 37.61 4.40
463 502 6.103838 TCCCCTTCTAAAATTCATTGGGAT 57.896 37.500 0.00 0.00 34.67 3.85
510 549 9.947433 TTCAATTCTAAACCTCCGTAAAATCTA 57.053 29.630 0.00 0.00 0.00 1.98
596 635 4.540153 GCATGTAGCCGATGTGGT 57.460 55.556 0.00 0.00 41.21 4.16
597 636 2.311294 GCATGTAGCCGATGTGGTC 58.689 57.895 0.00 0.00 41.21 4.02
598 637 0.179073 GCATGTAGCCGATGTGGTCT 60.179 55.000 0.00 0.00 41.21 3.85
599 638 1.858091 CATGTAGCCGATGTGGTCTC 58.142 55.000 0.00 0.00 41.21 3.36
600 639 0.385751 ATGTAGCCGATGTGGTCTCG 59.614 55.000 0.00 0.00 41.21 4.04
605 644 3.822192 CGATGTGGTCTCGGCCGA 61.822 66.667 29.03 29.03 32.58 5.54
606 645 2.815308 GATGTGGTCTCGGCCGAT 59.185 61.111 31.19 12.41 0.00 4.18
607 646 1.592669 GATGTGGTCTCGGCCGATG 60.593 63.158 31.19 22.08 0.00 3.84
640 679 1.225855 ATCAGAAGCGTTGCGTCAAA 58.774 45.000 7.43 0.00 39.36 2.69
651 690 1.086696 TGCGTCAAAGGCTAATGCTC 58.913 50.000 9.26 0.18 39.59 4.26
657 696 4.142622 CGTCAAAGGCTAATGCTCATTCAA 60.143 41.667 0.00 0.00 39.59 2.69
666 705 4.796038 AATGCTCATTCAAAGTCTTGGG 57.204 40.909 0.00 0.00 33.01 4.12
686 725 2.415357 GGTGTGCCAACATAATTGTCCG 60.415 50.000 0.00 0.00 38.92 4.79
691 730 2.097466 GCCAACATAATTGTCCGGACTG 59.903 50.000 33.39 24.61 34.06 3.51
703 742 1.407618 TCCGGACTGATAATGTGACCG 59.592 52.381 0.00 0.00 38.37 4.79
741 2146 6.708502 TGAATTTGAACGAGGTTACTCAATGA 59.291 34.615 0.00 0.00 44.17 2.57
752 2157 1.913778 ACTCAATGATTGCAGCACCA 58.086 45.000 0.00 0.00 0.00 4.17
782 2187 6.633668 AATGAATGTCGAAGTCTACTTTCG 57.366 37.500 0.00 1.28 36.11 3.46
816 2221 6.123651 AGGGTACTTGTTGAACATTGTAACA 58.876 36.000 20.42 1.82 31.37 2.41
827 2232 5.298276 TGAACATTGTAACAGGGAGTCAAAC 59.702 40.000 0.00 0.00 0.00 2.93
828 2233 4.787551 ACATTGTAACAGGGAGTCAAACA 58.212 39.130 0.00 0.00 0.00 2.83
871 2276 4.961585 AGGTTTAGGAGGAGTAATCCACT 58.038 43.478 12.54 11.42 41.47 4.00
884 2289 4.841246 AGTAATCCACTGACTTTCTGGTCT 59.159 41.667 0.00 0.00 35.62 3.85
896 2301 2.919772 TCTGGTCTGATACACCTCCA 57.080 50.000 0.00 0.00 34.66 3.86
910 2315 7.719633 TGATACACCTCCAAGCTTTATTATTCC 59.280 37.037 0.00 0.00 0.00 3.01
921 2326 9.638239 CAAGCTTTATTATTCCTTTGTTAGCAA 57.362 29.630 0.00 0.00 0.00 3.91
958 2363 8.574251 TTGATTTGAGTTAATAAAGCTAGCCA 57.426 30.769 12.13 0.00 0.00 4.75
963 2368 8.574251 TTGAGTTAATAAAGCTAGCCATGAAA 57.426 30.769 12.13 0.00 0.00 2.69
969 2374 2.521547 AGCTAGCCATGAAAGCCTTT 57.478 45.000 12.13 0.00 36.92 3.11
971 2376 1.406898 GCTAGCCATGAAAGCCTTTCC 59.593 52.381 14.35 0.00 38.90 3.13
1003 2408 4.724697 CAACGCGCAAGAGCCGTG 62.725 66.667 5.73 0.00 43.46 4.94
1008 2413 2.668212 CGCAAGAGCCGTGGGAAA 60.668 61.111 0.00 0.00 43.02 3.13
1009 2414 2.258013 CGCAAGAGCCGTGGGAAAA 61.258 57.895 0.00 0.00 43.02 2.29
1010 2415 1.586154 CGCAAGAGCCGTGGGAAAAT 61.586 55.000 0.00 0.00 43.02 1.82
1011 2416 1.459450 GCAAGAGCCGTGGGAAAATA 58.541 50.000 0.00 0.00 33.58 1.40
1054 2459 2.028930 ACCTGGTCTCACGTTTCATCTC 60.029 50.000 0.00 0.00 0.00 2.75
1063 2468 4.720090 TCACGTTTCATCTCGTAAGACTC 58.280 43.478 0.00 0.00 45.01 3.36
1064 2469 4.454847 TCACGTTTCATCTCGTAAGACTCT 59.545 41.667 0.00 0.00 45.01 3.24
1065 2470 4.789119 CACGTTTCATCTCGTAAGACTCTC 59.211 45.833 0.00 0.00 45.01 3.20
1092 2497 1.519408 AATGCCACGTGTACTTCACC 58.481 50.000 15.65 0.00 43.51 4.02
1104 2509 4.455533 GTGTACTTCACCAATCTTGATGCA 59.544 41.667 0.00 0.00 40.84 3.96
1114 2519 4.096081 CCAATCTTGATGCACCTCTTCTTC 59.904 45.833 0.00 0.00 0.00 2.87
1121 2526 1.004745 TGCACCTCTTCTTCCCCAATC 59.995 52.381 0.00 0.00 0.00 2.67
1130 2535 1.082879 TCTTCCCCAATCCTCCTTCCT 59.917 52.381 0.00 0.00 0.00 3.36
1134 2539 1.064389 CCCCAATCCTCCTTCCTGAAC 60.064 57.143 0.00 0.00 0.00 3.18
1151 2556 2.069165 AACTTGACACCTCCAGCCCC 62.069 60.000 0.00 0.00 0.00 5.80
1171 2576 4.447180 CCCCATGAATCCTAAACGGGTTAT 60.447 45.833 0.00 0.00 35.81 1.89
1172 2577 4.518970 CCCATGAATCCTAAACGGGTTATG 59.481 45.833 0.00 0.00 35.81 1.90
1178 2583 5.562298 ATCCTAAACGGGTTATGCTACAT 57.438 39.130 0.00 0.00 0.00 2.29
1179 2584 4.699637 TCCTAAACGGGTTATGCTACATG 58.300 43.478 0.00 0.00 0.00 3.21
1187 2592 3.123804 GGTTATGCTACATGTCAGTCGG 58.876 50.000 0.00 0.00 0.00 4.79
1214 2619 4.342862 TTTTTGAAATTGGGCCAATCGA 57.657 36.364 30.79 17.88 32.43 3.59
1252 2657 1.357137 TCCATATCCAATGGCGCCTA 58.643 50.000 29.70 14.84 39.01 3.93
1266 2671 1.137282 GCGCCTAGCCTTTCTTCTACT 59.863 52.381 0.00 0.00 40.81 2.57
1288 2693 4.278975 TCCAGCTTTTCTCCTTCTTCTC 57.721 45.455 0.00 0.00 0.00 2.87
1293 2698 3.500299 GCTTTTCTCCTTCTTCTCCACAC 59.500 47.826 0.00 0.00 0.00 3.82
1294 2699 3.771577 TTTCTCCTTCTTCTCCACACC 57.228 47.619 0.00 0.00 0.00 4.16
1393 2824 4.162690 CCCCACCGCCTGTCTAGC 62.163 72.222 0.00 0.00 0.00 3.42
1419 2850 2.210711 CCCGGCCATCCCTCTAGAC 61.211 68.421 2.24 0.00 0.00 2.59
1420 2851 2.210711 CCGGCCATCCCTCTAGACC 61.211 68.421 2.24 0.00 0.00 3.85
1423 2854 2.873525 GCCATCCCTCTAGACCCGC 61.874 68.421 0.00 0.00 0.00 6.13
1426 2857 2.711899 ATCCCTCTAGACCCGCCCA 61.712 63.158 0.00 0.00 0.00 5.36
1527 2958 7.181125 CCTAAGATAGATAATGGGGTAGCACTT 59.819 40.741 0.00 0.00 0.00 3.16
1555 2986 1.562008 CCCCTTCCTTCTCCTTCCTTC 59.438 57.143 0.00 0.00 0.00 3.46
1571 3002 3.539593 TTCCCTCCGGCTCACTCCA 62.540 63.158 0.00 0.00 0.00 3.86
1591 3022 3.441572 CCAGCCAACTCTTGAAAATCGAT 59.558 43.478 0.00 0.00 0.00 3.59
1594 3025 4.761739 AGCCAACTCTTGAAAATCGATTGA 59.238 37.500 12.25 3.17 0.00 2.57
1595 3026 4.853743 GCCAACTCTTGAAAATCGATTGAC 59.146 41.667 12.25 9.40 0.00 3.18
1600 3031 5.045869 ACTCTTGAAAATCGATTGACCCCTA 60.046 40.000 12.25 0.00 0.00 3.53
1649 3080 5.735766 AGCTAAACTGATCCTAAACAGTCC 58.264 41.667 0.00 0.00 44.94 3.85
1705 3136 2.416431 GGCACAATGGAAAAGCTAGCTG 60.416 50.000 20.16 6.39 0.00 4.24
1739 3170 3.430862 GCACGCCGGATTGCTTGA 61.431 61.111 17.97 0.00 35.74 3.02
1740 3171 2.764314 GCACGCCGGATTGCTTGAT 61.764 57.895 17.97 0.00 35.74 2.57
1741 3172 1.063006 CACGCCGGATTGCTTGATG 59.937 57.895 5.05 0.00 32.66 3.07
1743 3174 0.676466 ACGCCGGATTGCTTGATGAA 60.676 50.000 5.05 0.00 0.00 2.57
1744 3175 0.451383 CGCCGGATTGCTTGATGAAA 59.549 50.000 5.05 0.00 0.00 2.69
1789 3225 3.737047 GCGGAGACAAAATACAGATCGGA 60.737 47.826 0.00 0.00 0.00 4.55
1802 3238 8.988064 AATACAGATCGGACATATACACATTC 57.012 34.615 0.00 0.00 0.00 2.67
1847 3283 1.002366 CGCCAATCTCTTTGTCTCCG 58.998 55.000 0.00 0.00 33.15 4.63
1858 3294 1.978455 TTGTCTCCGTTGCACCAGGT 61.978 55.000 0.00 0.00 0.00 4.00
1860 3296 2.137528 TCTCCGTTGCACCAGGTCA 61.138 57.895 0.00 0.00 0.00 4.02
1877 3313 5.221185 CCAGGTCAATAGATCTTTTGCATGG 60.221 44.000 24.14 24.14 31.17 3.66
1878 3314 5.591472 CAGGTCAATAGATCTTTTGCATGGA 59.409 40.000 18.06 0.00 31.17 3.41
1879 3315 5.826737 AGGTCAATAGATCTTTTGCATGGAG 59.173 40.000 18.06 0.00 28.25 3.86
1880 3316 5.824624 GGTCAATAGATCTTTTGCATGGAGA 59.175 40.000 18.06 0.31 0.00 3.71
1881 3317 6.238593 GGTCAATAGATCTTTTGCATGGAGAC 60.239 42.308 18.06 10.59 0.00 3.36
1919 3355 1.550976 GCTTGGCACACTAGTAGACCT 59.449 52.381 3.59 0.00 39.29 3.85
1952 3388 1.135527 CAGGTAATACCGACGCTTCCA 59.864 52.381 3.47 0.00 44.90 3.53
2185 3621 1.394618 CGAGGAGGGAGACTACTTGG 58.605 60.000 0.00 0.00 41.79 3.61
2388 5916 4.065281 GCCGTGCCTACCGTGTCT 62.065 66.667 0.00 0.00 0.00 3.41
2401 5929 1.591703 GTGTCTCGCATGGACAGGA 59.408 57.895 3.81 0.00 43.17 3.86
2613 6147 1.614711 GATGGTGGGGAAGGATGCA 59.385 57.895 0.00 0.00 0.00 3.96
2841 6387 5.370679 GACAACTCCTAGCTAGCTACTAGT 58.629 45.833 20.67 20.86 36.53 2.57
2842 6388 6.497624 ACAACTCCTAGCTAGCTACTAGTA 57.502 41.667 24.47 8.20 36.53 1.82
2843 6389 6.527423 ACAACTCCTAGCTAGCTACTAGTAG 58.473 44.000 24.47 23.25 36.53 2.57
2844 6390 6.327104 ACAACTCCTAGCTAGCTACTAGTAGA 59.673 42.308 30.09 11.90 36.53 2.59
2845 6391 7.016858 ACAACTCCTAGCTAGCTACTAGTAGAT 59.983 40.741 30.09 26.65 36.53 1.98
2846 6392 8.533657 CAACTCCTAGCTAGCTACTAGTAGATA 58.466 40.741 30.09 26.35 36.53 1.98
2847 6393 8.071177 ACTCCTAGCTAGCTACTAGTAGATAC 57.929 42.308 30.09 21.09 36.53 2.24
2848 6394 7.124750 ACTCCTAGCTAGCTACTAGTAGATACC 59.875 44.444 30.09 20.12 36.53 2.73
2849 6395 7.191210 TCCTAGCTAGCTACTAGTAGATACCT 58.809 42.308 30.09 25.00 36.53 3.08
2850 6396 8.343028 TCCTAGCTAGCTACTAGTAGATACCTA 58.657 40.741 30.09 24.81 36.53 3.08
2851 6397 8.636213 CCTAGCTAGCTACTAGTAGATACCTAG 58.364 44.444 30.16 30.16 38.64 3.02
2852 6398 9.412460 CTAGCTAGCTACTAGTAGATACCTAGA 57.588 40.741 31.76 18.49 39.90 2.43
3049 6595 1.659098 CTTTTGACACCGGCTACGATC 59.341 52.381 0.00 0.00 44.60 3.69
3077 6623 1.918293 TGGCGGAGATTGTGGAGGT 60.918 57.895 0.00 0.00 0.00 3.85
3089 6635 2.122954 GGAGGTGGTGGTCCCTCT 59.877 66.667 5.73 0.00 45.46 3.69
3139 6685 0.600255 CGGCGAGAACTTGGAGTTGT 60.600 55.000 0.00 0.00 38.80 3.32
3501 7047 2.427506 GGCTCTTTGGACGAGAACATT 58.572 47.619 0.00 0.00 0.00 2.71
3805 7355 4.028490 CTGGGGCTAACCGTGGCA 62.028 66.667 0.00 0.00 41.60 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 30 4.878397 AGCTAGCTTTCGCTTTGATTACAT 59.122 37.500 12.68 0.00 46.47 2.29
63 65 6.073222 CGGTCCTCTTTATAATGCATTGGTAC 60.073 42.308 22.27 11.39 0.00 3.34
90 92 3.033185 CAACGAACGTTTGCTGGTTAAG 58.967 45.455 15.63 0.00 36.00 1.85
100 102 2.548295 ATGCCGCCAACGAACGTTT 61.548 52.632 9.87 0.00 43.93 3.60
110 112 3.364441 GCAGTTGTCATGCCGCCA 61.364 61.111 0.00 0.00 37.73 5.69
129 131 1.531149 CCGCGGACCATACAAATCATC 59.469 52.381 24.07 0.00 0.00 2.92
131 133 0.537653 TCCGCGGACCATACAAATCA 59.462 50.000 27.28 0.00 0.00 2.57
139 153 0.107214 AATTGTCATCCGCGGACCAT 60.107 50.000 33.75 13.03 34.36 3.55
141 155 0.808755 AAAATTGTCATCCGCGGACC 59.191 50.000 33.75 21.54 34.36 4.46
144 158 2.919666 AAGAAAATTGTCATCCGCGG 57.080 45.000 22.12 22.12 0.00 6.46
145 159 4.557301 GGTTAAAGAAAATTGTCATCCGCG 59.443 41.667 0.00 0.00 0.00 6.46
153 167 5.306678 TGCCATCCTGGTTAAAGAAAATTGT 59.693 36.000 0.00 0.00 40.46 2.71
161 175 3.181487 CGGATTTGCCATCCTGGTTAAAG 60.181 47.826 9.72 0.00 40.46 1.85
263 277 1.337167 GGCTGGCACAATGAAAGGTTC 60.337 52.381 0.00 0.00 38.70 3.62
297 312 9.524106 CTTTATACGGTGATGTTATTGTGTAGA 57.476 33.333 0.00 0.00 0.00 2.59
339 354 3.068732 ACATGTACAGCGAGTATCATGCT 59.931 43.478 20.63 12.87 41.14 3.79
351 366 0.179111 TGCCGCTCTACATGTACAGC 60.179 55.000 19.80 19.80 0.00 4.40
395 434 4.688021 TCTGCAAAACGGCTGTAAAAATT 58.312 34.783 0.00 0.00 34.71 1.82
396 435 4.314740 TCTGCAAAACGGCTGTAAAAAT 57.685 36.364 0.00 0.00 34.71 1.82
406 445 4.455877 AGTTAGGAAAGATCTGCAAAACGG 59.544 41.667 0.00 0.00 0.00 4.44
434 473 8.542926 CCAATGAATTTTAGAAGGGGAAGAAAT 58.457 33.333 0.00 0.00 0.00 2.17
477 516 6.149633 CGGAGGTTTAGAATTGAAAACAAGG 58.850 40.000 12.08 0.00 37.33 3.61
529 568 2.202743 GCCGTGCGATGCTAGACA 60.203 61.111 0.00 0.00 0.00 3.41
560 599 3.515330 GCTCCATGCAAGCAGTTTATT 57.485 42.857 12.07 0.00 42.31 1.40
589 628 1.592669 CATCGGCCGAGACCACATC 60.593 63.158 33.87 0.00 0.00 3.06
593 632 3.770040 CCACATCGGCCGAGACCA 61.770 66.667 33.87 10.46 0.00 4.02
594 633 3.718210 GACCACATCGGCCGAGACC 62.718 68.421 33.87 14.60 39.03 3.85
595 634 2.202756 GACCACATCGGCCGAGAC 60.203 66.667 33.87 15.95 39.03 3.36
596 635 2.362503 AGACCACATCGGCCGAGA 60.363 61.111 33.87 12.25 39.03 4.04
597 636 2.105128 GAGACCACATCGGCCGAG 59.895 66.667 33.87 25.42 39.03 4.63
598 637 3.822192 CGAGACCACATCGGCCGA 61.822 66.667 33.12 33.12 39.03 5.54
603 642 2.629050 ATTCGGCCGAGACCACATCG 62.629 60.000 29.20 0.00 39.86 3.84
604 643 0.876342 GATTCGGCCGAGACCACATC 60.876 60.000 29.20 22.24 0.00 3.06
605 644 1.144057 GATTCGGCCGAGACCACAT 59.856 57.895 29.20 17.99 0.00 3.21
606 645 2.225791 CTGATTCGGCCGAGACCACA 62.226 60.000 29.20 21.14 0.00 4.17
607 646 1.519455 CTGATTCGGCCGAGACCAC 60.519 63.158 29.20 17.96 0.00 4.16
640 679 4.853007 AGACTTTGAATGAGCATTAGCCT 58.147 39.130 0.00 0.00 43.56 4.58
651 690 2.288395 GGCACACCCAAGACTTTGAATG 60.288 50.000 0.00 0.00 36.36 2.67
666 705 2.415357 CCGGACAATTATGTTGGCACAC 60.415 50.000 0.00 0.00 40.74 3.82
686 725 2.093658 ACCACGGTCACATTATCAGTCC 60.094 50.000 0.00 0.00 0.00 3.85
691 730 3.799232 GCCTCTACCACGGTCACATTATC 60.799 52.174 0.00 0.00 0.00 1.75
703 742 3.071479 TCAAATTCAACGCCTCTACCAC 58.929 45.455 0.00 0.00 0.00 4.16
731 770 3.419943 TGGTGCTGCAATCATTGAGTAA 58.580 40.909 2.77 0.00 0.00 2.24
733 772 1.913778 TGGTGCTGCAATCATTGAGT 58.086 45.000 2.77 0.00 0.00 3.41
741 2146 6.528537 TTCATTAAGTATTGGTGCTGCAAT 57.471 33.333 2.77 0.00 0.00 3.56
777 2182 2.109425 ACCCTCCCGAAATTCGAAAG 57.891 50.000 17.75 12.61 43.74 2.62
782 2187 3.345508 ACAAGTACCCTCCCGAAATTC 57.654 47.619 0.00 0.00 0.00 2.17
816 2221 1.145738 AGCAACCATGTTTGACTCCCT 59.854 47.619 7.23 0.00 0.00 4.20
871 2276 4.160329 AGGTGTATCAGACCAGAAAGTCA 58.840 43.478 0.00 0.00 39.34 3.41
884 2289 7.719633 GGAATAATAAAGCTTGGAGGTGTATCA 59.280 37.037 0.00 0.00 26.71 2.15
921 2326 9.715121 ATTAACTCAAATCAAACTTGCATCATT 57.285 25.926 0.00 0.00 0.00 2.57
934 2339 8.623903 CATGGCTAGCTTTATTAACTCAAATCA 58.376 33.333 15.72 0.00 0.00 2.57
980 2385 4.947147 TCTTGCGCGTTGGCCCTT 62.947 61.111 8.43 0.00 35.02 3.95
993 2398 3.181487 CCATTATTTTCCCACGGCTCTTG 60.181 47.826 0.00 0.00 0.00 3.02
1011 2416 9.720769 CAGGTCGTATAGTATTATTTTCCCATT 57.279 33.333 0.00 0.00 0.00 3.16
1054 2459 6.590292 TGGCATTTTCTAAAGAGAGTCTTACG 59.410 38.462 0.00 0.00 35.27 3.18
1063 2468 4.749245 ACACGTGGCATTTTCTAAAGAG 57.251 40.909 21.57 0.00 0.00 2.85
1064 2469 5.302360 AGTACACGTGGCATTTTCTAAAGA 58.698 37.500 21.57 0.00 0.00 2.52
1065 2470 5.607119 AGTACACGTGGCATTTTCTAAAG 57.393 39.130 21.57 0.00 0.00 1.85
1092 2497 4.096081 GGAAGAAGAGGTGCATCAAGATTG 59.904 45.833 0.00 0.00 0.00 2.67
1104 2509 2.200955 GAGGATTGGGGAAGAAGAGGT 58.799 52.381 0.00 0.00 0.00 3.85
1114 2519 1.064389 GTTCAGGAAGGAGGATTGGGG 60.064 57.143 0.00 0.00 0.00 4.96
1121 2526 2.551071 GGTGTCAAGTTCAGGAAGGAGG 60.551 54.545 0.00 0.00 0.00 4.30
1130 2535 0.108585 GGCTGGAGGTGTCAAGTTCA 59.891 55.000 0.00 0.00 0.00 3.18
1134 2539 1.856539 ATGGGGCTGGAGGTGTCAAG 61.857 60.000 0.00 0.00 0.00 3.02
1151 2556 4.821805 AGCATAACCCGTTTAGGATTCATG 59.178 41.667 0.00 0.00 45.00 3.07
1171 2576 2.276869 AGCCGACTGACATGTAGCA 58.723 52.632 0.00 0.00 0.00 3.49
1187 2592 3.819902 TGGCCCAATTTCAAAAATTCAGC 59.180 39.130 0.00 7.11 0.00 4.26
1192 2597 4.904241 TCGATTGGCCCAATTTCAAAAAT 58.096 34.783 10.97 0.00 33.90 1.82
1214 2619 4.956085 TGGATCGGACGTTCAATATTGAT 58.044 39.130 18.61 4.36 37.00 2.57
1252 2657 2.909662 AGCTGGAAGTAGAAGAAAGGCT 59.090 45.455 0.00 0.00 35.30 4.58
1266 2671 4.505742 GGAGAAGAAGGAGAAAAGCTGGAA 60.506 45.833 0.00 0.00 0.00 3.53
1402 2833 2.210711 GGTCTAGAGGGATGGCCGG 61.211 68.421 0.00 0.00 33.83 6.13
1419 2850 0.669619 AAAAACTAAACGTGGGCGGG 59.330 50.000 0.00 0.00 43.45 6.13
1475 2906 3.716195 TGGGAGCGGTGGTGGATG 61.716 66.667 0.00 0.00 0.00 3.51
1476 2907 3.717294 GTGGGAGCGGTGGTGGAT 61.717 66.667 0.00 0.00 0.00 3.41
1488 2919 0.494551 TCTTAGGGTTCAGGGTGGGA 59.505 55.000 0.00 0.00 0.00 4.37
1489 2920 1.596496 ATCTTAGGGTTCAGGGTGGG 58.404 55.000 0.00 0.00 0.00 4.61
1496 2927 6.399013 ACCCCATTATCTATCTTAGGGTTCA 58.601 40.000 0.00 0.00 44.14 3.18
1497 2928 6.954352 ACCCCATTATCTATCTTAGGGTTC 57.046 41.667 0.00 0.00 44.14 3.62
1571 3002 4.761739 TCAATCGATTTTCAAGAGTTGGCT 59.238 37.500 8.21 0.00 0.00 4.75
1578 3009 4.301072 AGGGGTCAATCGATTTTCAAGA 57.699 40.909 8.21 0.00 0.00 3.02
1591 3022 7.169591 TCGACTGAATTTAAAATAGGGGTCAA 58.830 34.615 0.00 0.00 0.00 3.18
1594 3025 7.614192 ACAATCGACTGAATTTAAAATAGGGGT 59.386 33.333 0.00 0.00 0.00 4.95
1595 3026 7.996385 ACAATCGACTGAATTTAAAATAGGGG 58.004 34.615 0.00 0.00 0.00 4.79
1689 3120 5.181748 CACTAGACAGCTAGCTTTTCCATT 58.818 41.667 16.46 1.82 46.55 3.16
1691 3122 3.617531 GCACTAGACAGCTAGCTTTTCCA 60.618 47.826 16.46 2.72 46.55 3.53
1705 3136 2.181021 CCCGTCGGTGCACTAGAC 59.819 66.667 25.43 25.43 0.00 2.59
1740 3171 9.618890 TGTTTTGGGATTTGATGTTTAATTTCA 57.381 25.926 0.00 0.00 0.00 2.69
1743 3174 7.095271 CGCTGTTTTGGGATTTGATGTTTAATT 60.095 33.333 0.00 0.00 0.00 1.40
1744 3175 6.368516 CGCTGTTTTGGGATTTGATGTTTAAT 59.631 34.615 0.00 0.00 0.00 1.40
1802 3238 6.999956 ATCACTGTTGAATCGAATATCTCG 57.000 37.500 0.00 2.18 41.41 4.04
1814 3250 1.974265 TTGGCGGAATCACTGTTGAA 58.026 45.000 0.00 0.00 34.61 2.69
1847 3283 3.878778 AGATCTATTGACCTGGTGCAAC 58.121 45.455 2.82 0.00 0.00 4.17
1858 3294 6.317140 GTGTCTCCATGCAAAAGATCTATTGA 59.683 38.462 0.00 0.00 0.00 2.57
1860 3296 5.295292 CGTGTCTCCATGCAAAAGATCTATT 59.705 40.000 0.00 0.00 0.00 1.73
1877 3313 2.048127 GTCTGGCCCACGTGTCTC 60.048 66.667 15.65 3.62 0.00 3.36
1878 3314 3.991051 CGTCTGGCCCACGTGTCT 61.991 66.667 15.65 0.00 32.41 3.41
1879 3315 1.940883 TATCGTCTGGCCCACGTGTC 61.941 60.000 20.45 5.64 38.45 3.67
1880 3316 1.945354 CTATCGTCTGGCCCACGTGT 61.945 60.000 20.45 14.16 38.45 4.49
1881 3317 1.226974 CTATCGTCTGGCCCACGTG 60.227 63.158 20.45 9.08 38.45 4.49
1882 3318 3.077519 GCTATCGTCTGGCCCACGT 62.078 63.158 20.45 12.29 38.45 4.49
1883 3319 2.279517 GCTATCGTCTGGCCCACG 60.280 66.667 16.41 16.41 38.67 4.94
1884 3320 0.811616 CAAGCTATCGTCTGGCCCAC 60.812 60.000 0.00 0.00 30.08 4.61
1989 3425 2.772077 TATGTTTTGCTGCTCCCGTA 57.228 45.000 0.00 0.00 0.00 4.02
1991 3427 1.066002 CCATATGTTTTGCTGCTCCCG 59.934 52.381 0.00 0.00 0.00 5.14
2241 3686 3.223661 CTTCTTCGCTGAAGCCTGT 57.776 52.632 11.80 0.00 39.29 4.00
2337 5865 2.203294 AACCGGCGGTTCAGCTTT 60.203 55.556 36.82 15.33 43.05 3.51
2388 5916 2.359169 GGAGGTCCTGTCCATGCGA 61.359 63.158 0.00 0.00 33.84 5.10
2572 6106 2.261361 CTCCACCACATCGTCGCA 59.739 61.111 0.00 0.00 0.00 5.10
2848 6394 1.284408 GCATCGACGCCTCCTCTAG 59.716 63.158 0.00 0.00 0.00 2.43
2849 6395 3.433319 GCATCGACGCCTCCTCTA 58.567 61.111 0.00 0.00 0.00 2.43
3049 6595 4.135153 CTCCGCCACCTCGTCCTG 62.135 72.222 0.00 0.00 0.00 3.86
3089 6635 1.228184 GTCCTCGCCGGATCCTCTA 60.228 63.158 5.05 0.00 45.44 2.43
3139 6685 1.078988 GATGTACAACCCGCCGGAA 60.079 57.895 5.05 0.00 0.00 4.30
3501 7047 1.364536 TGCCTCTCGCACGTAAACA 59.635 52.632 0.00 0.00 44.64 2.83


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

AutoCloner maintained by Alex Coulton.