Multiple sequence alignment - TraesCS6B01G083800

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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 TraesCS6B01G083800 chr6B 100.000 3946 0 0 1 3946 60656120 60660065 0.000000e+00 7287.0
1 TraesCS6B01G083800 chr6B 96.108 1593 23 6 1265 2837 60623134 60624707 0.000000e+00 2562.0
2 TraesCS6B01G083800 chr6B 95.505 1090 39 4 2860 3946 60624766 60625848 0.000000e+00 1733.0
3 TraesCS6B01G083800 chr6B 95.648 1080 20 9 988 2050 60631603 60632672 0.000000e+00 1709.0
4 TraesCS6B01G083800 chr6B 93.578 1090 58 6 2860 3946 60633887 60634967 0.000000e+00 1615.0
5 TraesCS6B01G083800 chr6B 92.676 1065 27 17 797 1841 60614737 60615770 0.000000e+00 1487.0
6 TraesCS6B01G083800 chr6B 87.140 591 56 14 55 634 60630606 60631187 0.000000e+00 652.0
7 TraesCS6B01G083800 chr6B 93.540 387 21 3 2453 2837 60633449 60633833 1.230000e-159 573.0
8 TraesCS6B01G083800 chr6B 86.765 476 41 7 1015 1484 59829620 59829161 9.780000e-141 510.0
9 TraesCS6B01G083800 chr6B 97.581 248 6 0 2039 2286 60632805 60633052 3.640000e-115 425.0
10 TraesCS6B01G083800 chr6B 83.412 422 43 8 1520 1918 59828867 59828450 2.240000e-97 366.0
11 TraesCS6B01G083800 chr6B 87.117 326 34 7 1954 2274 59828449 59828127 2.900000e-96 363.0
12 TraesCS6B01G083800 chr6B 84.021 388 42 11 3574 3946 59826289 59825907 4.850000e-94 355.0
13 TraesCS6B01G083800 chr6B 85.345 348 34 8 2499 2836 59827173 59826833 1.050000e-90 344.0
14 TraesCS6B01G083800 chr6B 84.615 169 11 8 904 1072 59731253 59731100 1.900000e-33 154.0
15 TraesCS6B01G083800 chr6B 93.000 100 5 1 2357 2454 60633311 60633410 1.140000e-30 145.0
16 TraesCS6B01G083800 chr6D 94.576 1936 56 17 876 2780 29094784 29092867 0.000000e+00 2948.0
17 TraesCS6B01G083800 chr6D 88.720 328 25 5 3251 3577 29098142 29097826 1.330000e-104 390.0
18 TraesCS6B01G083800 chr6D 87.956 274 30 3 2986 3258 29099115 29098844 1.770000e-83 320.0
19 TraesCS6B01G083800 chr6D 80.272 441 74 11 1066 1500 29194759 29195192 1.770000e-83 320.0
20 TraesCS6B01G083800 chr6A 94.154 1950 75 12 876 2803 33529724 33531656 0.000000e+00 2933.0
21 TraesCS6B01G083800 chr6A 95.624 1097 30 6 2860 3946 33531803 33532891 0.000000e+00 1744.0
22 TraesCS6B01G083800 chr6A 87.004 1285 134 14 1024 2285 33404208 33405482 0.000000e+00 1417.0
23 TraesCS6B01G083800 chr6A 85.934 910 99 10 1398 2282 33305579 33306484 0.000000e+00 944.0
24 TraesCS6B01G083800 chr6A 87.780 581 67 4 1707 2284 33016652 33016073 0.000000e+00 676.0
25 TraesCS6B01G083800 chr6A 83.580 609 78 14 3347 3946 45413840 45413245 5.760000e-153 551.0
26 TraesCS6B01G083800 chr6A 92.010 388 28 2 2453 2837 33307536 33307923 3.470000e-150 542.0
27 TraesCS6B01G083800 chr6A 85.118 551 51 14 874 1406 33304132 33304669 5.800000e-148 534.0
28 TraesCS6B01G083800 chr6A 88.858 359 37 2 2446 2802 33410149 33410506 4.680000e-119 438.0
29 TraesCS6B01G083800 chr6A 82.766 441 67 8 1046 1483 33255151 33255585 6.190000e-103 385.0
30 TraesCS6B01G083800 chr6A 81.857 463 69 9 177 633 33303554 33304007 3.720000e-100 375.0
31 TraesCS6B01G083800 chr6A 84.814 349 38 8 2499 2836 33014870 33014526 1.760000e-88 337.0
32 TraesCS6B01G083800 chr6A 83.673 343 25 12 321 633 33391654 33391995 1.070000e-75 294.0
33 TraesCS6B01G083800 chr6A 80.769 364 36 16 3088 3429 33308164 33308515 1.820000e-63 254.0
34 TraesCS6B01G083800 chr6A 92.727 165 10 2 2882 3044 33307999 33308163 1.830000e-58 237.0
35 TraesCS6B01G083800 chr6A 92.157 153 9 2 2300 2450 33406403 33406554 3.090000e-51 213.0
36 TraesCS6B01G083800 chr6A 76.415 424 70 23 3416 3826 31162010 31162416 6.690000e-48 202.0
37 TraesCS6B01G083800 chr6A 87.195 164 16 4 633 791 5939077 5939240 8.710000e-42 182.0
38 TraesCS6B01G083800 chr6A 97.368 38 1 0 2800 2837 33454051 33454088 9.150000e-07 65.8
39 TraesCS6B01G083800 chrUn 84.270 534 63 13 3347 3873 112531424 112531943 5.890000e-138 501.0
40 TraesCS6B01G083800 chrUn 80.076 527 82 19 1047 1563 112648923 112649436 1.730000e-98 370.0
41 TraesCS6B01G083800 chrUn 84.393 346 33 11 2499 2834 112531083 112531417 1.770000e-83 320.0
42 TraesCS6B01G083800 chrUn 78.889 450 82 13 1101 1542 76751765 76751321 3.860000e-75 292.0
43 TraesCS6B01G083800 chrUn 86.667 165 15 6 633 791 96027809 96027972 4.050000e-40 176.0
44 TraesCS6B01G083800 chr5D 83.611 360 46 9 3348 3697 553761333 553761689 3.800000e-85 326.0
45 TraesCS6B01G083800 chr2A 86.667 165 17 4 632 791 38920870 38921034 1.130000e-40 178.0
46 TraesCS6B01G083800 chr2A 86.667 165 17 3 632 791 170932119 170932283 1.130000e-40 178.0
47 TraesCS6B01G083800 chr2B 86.228 167 18 3 630 791 148244181 148244347 4.050000e-40 176.0
48 TraesCS6B01G083800 chr5A 86.061 165 18 4 633 792 567110803 567110967 5.240000e-39 172.0
49 TraesCS6B01G083800 chr3D 85.799 169 16 5 630 792 498263637 498263803 5.240000e-39 172.0
50 TraesCS6B01G083800 chr7A 86.842 152 12 6 642 787 150409210 150409061 3.160000e-36 163.0
51 TraesCS6B01G083800 chr4D 85.030 167 18 6 631 791 498049951 498050116 3.160000e-36 163.0
52 TraesCS6B01G083800 chr3A 87.500 104 13 0 2300 2403 507293161 507293058 1.930000e-23 121.0
53 TraesCS6B01G083800 chr7D 86.885 61 8 0 2300 2360 608860629 608860689 7.080000e-08 69.4


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 TraesCS6B01G083800 chr6B 60656120 60660065 3945 False 7287.000000 7287 100.000000 1 3946 1 chr6B.!!$F2 3945
1 TraesCS6B01G083800 chr6B 60623134 60625848 2714 False 2147.500000 2562 95.806500 1265 3946 2 chr6B.!!$F3 2681
2 TraesCS6B01G083800 chr6B 60614737 60615770 1033 False 1487.000000 1487 92.676000 797 1841 1 chr6B.!!$F1 1044
3 TraesCS6B01G083800 chr6B 60630606 60634967 4361 False 853.166667 1709 93.414500 55 3946 6 chr6B.!!$F4 3891
4 TraesCS6B01G083800 chr6B 59825907 59829620 3713 True 387.600000 510 85.332000 1015 3946 5 chr6B.!!$R2 2931
5 TraesCS6B01G083800 chr6D 29092867 29099115 6248 True 1219.333333 2948 90.417333 876 3577 3 chr6D.!!$R1 2701
6 TraesCS6B01G083800 chr6A 33529724 33532891 3167 False 2338.500000 2933 94.889000 876 3946 2 chr6A.!!$F8 3070
7 TraesCS6B01G083800 chr6A 33404208 33410506 6298 False 689.333333 1417 89.339667 1024 2802 3 chr6A.!!$F7 1778
8 TraesCS6B01G083800 chr6A 45413245 45413840 595 True 551.000000 551 83.580000 3347 3946 1 chr6A.!!$R1 599
9 TraesCS6B01G083800 chr6A 33014526 33016652 2126 True 506.500000 676 86.297000 1707 2836 2 chr6A.!!$R2 1129
10 TraesCS6B01G083800 chr6A 33303554 33308515 4961 False 481.000000 944 86.402500 177 3429 6 chr6A.!!$F6 3252
11 TraesCS6B01G083800 chrUn 112531083 112531943 860 False 410.500000 501 84.331500 2499 3873 2 chrUn.!!$F3 1374
12 TraesCS6B01G083800 chrUn 112648923 112649436 513 False 370.000000 370 80.076000 1047 1563 1 chrUn.!!$F2 516

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
293 296 0.105039 GTGCCATCTACCTCCCTTCG 59.895 60.0 0.0 0.0 0.00 3.79 F
983 4501 0.312102 TACTGCATCCAGATCGAGCG 59.688 55.0 0.0 0.0 41.77 5.03 F
2792 12877 0.603569 ACTGCCACTCCTCAAGTACG 59.396 55.0 0.0 0.0 36.07 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 12487 0.762418 TGGAGACAACACCACGGAAT 59.238 50.000 0.0 0.0 37.44 3.01 R
2842 12929 3.304911 TGTGGACAAAAACCATCTCCA 57.695 42.857 0.0 0.0 39.69 3.86 R
3617 14099 1.761784 AGTCATCAGCCATCAGAGGAC 59.238 52.381 0.0 0.0 43.64 3.85 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
22 23 5.957842 TTGTACATTCGCAAATTCCTTCT 57.042 34.783 0.00 0.00 0.00 2.85
23 24 5.295431 TGTACATTCGCAAATTCCTTCTG 57.705 39.130 0.00 0.00 0.00 3.02
24 25 4.759693 TGTACATTCGCAAATTCCTTCTGT 59.240 37.500 0.00 0.00 0.00 3.41
25 26 5.935206 TGTACATTCGCAAATTCCTTCTGTA 59.065 36.000 0.00 0.00 0.00 2.74
26 27 5.551760 ACATTCGCAAATTCCTTCTGTAG 57.448 39.130 0.00 0.00 0.00 2.74
27 28 5.245531 ACATTCGCAAATTCCTTCTGTAGA 58.754 37.500 0.00 0.00 0.00 2.59
29 30 6.375455 ACATTCGCAAATTCCTTCTGTAGATT 59.625 34.615 0.00 0.00 0.00 2.40
30 31 6.817765 TTCGCAAATTCCTTCTGTAGATTT 57.182 33.333 0.00 0.00 0.00 2.17
31 32 6.817765 TCGCAAATTCCTTCTGTAGATTTT 57.182 33.333 0.00 0.00 0.00 1.82
32 33 7.214467 TCGCAAATTCCTTCTGTAGATTTTT 57.786 32.000 0.00 0.00 0.00 1.94
78 79 5.657745 AGCATCATGATTTGGTTAACCATCA 59.342 36.000 27.57 26.54 46.97 3.07
80 81 6.406177 GCATCATGATTTGGTTAACCATCAGT 60.406 38.462 27.57 15.30 46.97 3.41
81 82 7.201812 GCATCATGATTTGGTTAACCATCAGTA 60.202 37.037 27.57 19.03 46.97 2.74
83 84 7.171653 TCATGATTTGGTTAACCATCAGTACA 58.828 34.615 27.57 19.65 46.97 2.90
133 134 6.387041 TGATATCCGGAGTAACAGTTACAG 57.613 41.667 22.81 14.02 38.60 2.74
182 184 5.172687 TCATCTATGTGTTTTGCCCTACA 57.827 39.130 0.00 0.00 0.00 2.74
183 185 4.941263 TCATCTATGTGTTTTGCCCTACAC 59.059 41.667 0.00 0.00 43.76 2.90
195 197 1.813786 GCCCTACACGCAACCAAATTA 59.186 47.619 0.00 0.00 0.00 1.40
223 225 2.557924 TCAACCAATCTCACCAATGCAC 59.442 45.455 0.00 0.00 0.00 4.57
262 265 2.833631 ACTTTCCCCTACACTCAACG 57.166 50.000 0.00 0.00 0.00 4.10
287 290 4.899352 AATCTATGGTGCCATCTACCTC 57.101 45.455 7.03 0.00 39.01 3.85
293 296 0.105039 GTGCCATCTACCTCCCTTCG 59.895 60.000 0.00 0.00 0.00 3.79
334 341 1.668751 ACGCGTGTGTGTCAGAAATTT 59.331 42.857 12.93 0.00 31.97 1.82
341 348 7.112287 CGCGTGTGTGTCAGAAATTTAAAATAA 59.888 33.333 0.00 0.00 0.00 1.40
366 373 1.226073 GACTCGACGAAGCTCGACC 60.226 63.158 11.64 3.65 43.74 4.79
527 536 5.507315 GCGGATAATTGGACCTACAATTTGG 60.507 44.000 9.14 0.00 45.94 3.28
690 700 9.221933 AGAGATTTCACTATAGACTACATACCG 57.778 37.037 6.78 0.00 0.00 4.02
691 701 9.217278 GAGATTTCACTATAGACTACATACCGA 57.783 37.037 6.78 0.00 0.00 4.69
695 705 8.510243 TTCACTATAGACTACATACCGAACAA 57.490 34.615 6.78 0.00 0.00 2.83
696 706 8.510243 TCACTATAGACTACATACCGAACAAA 57.490 34.615 6.78 0.00 0.00 2.83
698 708 9.745880 CACTATAGACTACATACCGAACAAAAT 57.254 33.333 6.78 0.00 0.00 1.82
704 714 8.308931 AGACTACATACCGAACAAAATTAGTGA 58.691 33.333 0.00 0.00 0.00 3.41
705 715 8.836268 ACTACATACCGAACAAAATTAGTGAA 57.164 30.769 0.00 0.00 0.00 3.18
706 716 8.715088 ACTACATACCGAACAAAATTAGTGAAC 58.285 33.333 0.00 0.00 0.00 3.18
707 717 7.739498 ACATACCGAACAAAATTAGTGAACT 57.261 32.000 0.00 0.00 0.00 3.01
708 718 8.161699 ACATACCGAACAAAATTAGTGAACTT 57.838 30.769 0.00 0.00 0.00 2.66
709 719 8.073768 ACATACCGAACAAAATTAGTGAACTTG 58.926 33.333 0.00 0.00 0.00 3.16
710 720 6.445357 ACCGAACAAAATTAGTGAACTTGT 57.555 33.333 0.00 0.00 0.00 3.16
711 721 7.556733 ACCGAACAAAATTAGTGAACTTGTA 57.443 32.000 0.00 0.00 30.30 2.41
712 722 7.412063 ACCGAACAAAATTAGTGAACTTGTAC 58.588 34.615 0.00 0.00 30.30 2.90
714 724 7.797123 CCGAACAAAATTAGTGAACTTGTACTC 59.203 37.037 0.00 0.00 30.30 2.59
715 725 8.332464 CGAACAAAATTAGTGAACTTGTACTCA 58.668 33.333 0.00 0.00 30.30 3.41
716 726 9.997482 GAACAAAATTAGTGAACTTGTACTCAA 57.003 29.630 0.00 0.00 30.30 3.02
752 762 8.221251 ACATCTGAATGTAGTCTCTATAGTGGA 58.779 37.037 0.00 0.00 44.38 4.02
755 765 9.647918 TCTGAATGTAGTCTCTATAGTGGAATT 57.352 33.333 0.00 0.00 0.00 2.17
786 796 8.904099 AATGACTAATATTTAGGAACGGAAGG 57.096 34.615 0.00 0.00 0.00 3.46
787 797 7.664552 TGACTAATATTTAGGAACGGAAGGA 57.335 36.000 0.00 0.00 0.00 3.36
789 799 7.343833 TGACTAATATTTAGGAACGGAAGGAGT 59.656 37.037 0.00 0.00 0.00 3.85
791 801 8.637099 ACTAATATTTAGGAACGGAAGGAGTAC 58.363 37.037 0.00 0.00 0.00 2.73
792 802 3.855689 TTTAGGAACGGAAGGAGTACG 57.144 47.619 0.00 0.00 0.00 3.67
793 803 2.496899 TAGGAACGGAAGGAGTACGT 57.503 50.000 0.00 0.00 43.43 3.57
794 804 0.886563 AGGAACGGAAGGAGTACGTG 59.113 55.000 0.00 0.00 41.12 4.49
795 805 0.600057 GGAACGGAAGGAGTACGTGT 59.400 55.000 0.00 0.00 41.12 4.49
796 806 1.668047 GGAACGGAAGGAGTACGTGTG 60.668 57.143 0.00 0.00 41.12 3.82
797 807 1.000938 GAACGGAAGGAGTACGTGTGT 60.001 52.381 0.00 0.00 41.12 3.72
801 811 1.137513 GAAGGAGTACGTGTGTGTGC 58.862 55.000 0.00 0.00 0.00 4.57
828 842 5.633747 CGCGTGCGTTAAATATTCATTTTC 58.366 37.500 6.00 0.00 34.02 2.29
831 845 7.512887 CGCGTGCGTTAAATATTCATTTTCAAT 60.513 33.333 6.00 0.00 34.02 2.57
866 1154 6.894339 AAACAGACGTCCTCCATTTTATTT 57.106 33.333 13.01 0.00 0.00 1.40
867 1155 7.989416 AAACAGACGTCCTCCATTTTATTTA 57.011 32.000 13.01 0.00 0.00 1.40
868 1156 7.611213 AACAGACGTCCTCCATTTTATTTAG 57.389 36.000 13.01 0.00 0.00 1.85
869 1157 6.942976 ACAGACGTCCTCCATTTTATTTAGA 58.057 36.000 13.01 0.00 0.00 2.10
870 1158 7.042335 ACAGACGTCCTCCATTTTATTTAGAG 58.958 38.462 13.01 0.00 0.00 2.43
871 1159 7.042335 CAGACGTCCTCCATTTTATTTAGAGT 58.958 38.462 13.01 0.00 0.00 3.24
872 1160 8.195436 CAGACGTCCTCCATTTTATTTAGAGTA 58.805 37.037 13.01 0.00 0.00 2.59
873 1161 8.755977 AGACGTCCTCCATTTTATTTAGAGTAA 58.244 33.333 13.01 0.00 0.00 2.24
940 4451 2.031012 CACTCTCACGGCCTGCAA 59.969 61.111 0.00 0.00 0.00 4.08
952 4463 3.860681 CTGCAAGGCACTGGGTTT 58.139 55.556 0.00 0.00 40.86 3.27
954 4465 1.381056 TGCAAGGCACTGGGTTTGT 60.381 52.632 0.00 0.00 40.86 2.83
962 4478 4.025401 CTGGGTTTGTGGTCGCGC 62.025 66.667 0.00 0.00 0.00 6.86
975 4493 2.963854 CGCGCCTACTGCATCCAG 60.964 66.667 0.00 0.00 44.80 3.86
982 4500 1.336702 CCTACTGCATCCAGATCGAGC 60.337 57.143 0.00 0.00 41.77 5.03
983 4501 0.312102 TACTGCATCCAGATCGAGCG 59.688 55.000 0.00 0.00 41.77 5.03
984 4502 2.279717 TGCATCCAGATCGAGCGC 60.280 61.111 0.00 0.00 0.00 5.92
1003 4524 1.559065 CCCTAACCCACGTCCCACAT 61.559 60.000 0.00 0.00 0.00 3.21
1020 4541 3.309138 CCACATCGCATTCTTCTTCTGAG 59.691 47.826 0.00 0.00 0.00 3.35
1065 4597 4.925861 GGCGAGATGAGCAGCCCC 62.926 72.222 0.00 0.00 43.54 5.80
1066 4598 4.925861 GCGAGATGAGCAGCCCCC 62.926 72.222 0.00 0.00 34.19 5.40
1067 4599 4.598894 CGAGATGAGCAGCCCCCG 62.599 72.222 0.00 0.00 0.00 5.73
2471 12487 9.219603 GATAATCAGATCCGGTTTCATTTATCA 57.780 33.333 0.00 0.00 0.00 2.15
2476 12492 5.470098 AGATCCGGTTTCATTTATCATTCCG 59.530 40.000 0.00 0.00 37.04 4.30
2496 12512 2.616376 CGTGGTGTTGTCTCCAAATTGA 59.384 45.455 0.00 0.00 38.66 2.57
2528 12551 5.932303 TCAAACTACAGCTGTGAGTTTATCC 59.068 40.000 31.44 0.00 40.54 2.59
2683 12713 8.144478 TCTTGTCCAGTTAGATATGCTATTGTC 58.856 37.037 0.00 0.00 0.00 3.18
2792 12877 0.603569 ACTGCCACTCCTCAAGTACG 59.396 55.000 0.00 0.00 36.07 3.67
2837 12924 3.221771 ACACTTTGCTTAGATGTTGCCA 58.778 40.909 0.00 0.00 0.00 4.92
2838 12925 3.254166 ACACTTTGCTTAGATGTTGCCAG 59.746 43.478 0.00 0.00 0.00 4.85
2839 12926 3.254166 CACTTTGCTTAGATGTTGCCAGT 59.746 43.478 0.00 0.00 0.00 4.00
2842 12929 3.423539 TGCTTAGATGTTGCCAGTCTT 57.576 42.857 0.00 0.00 0.00 3.01
2858 12945 5.113502 CAGTCTTGGAGATGGTTTTTGTC 57.886 43.478 0.00 0.00 0.00 3.18
2908 13035 3.710326 TCTGGAGAAATCGACCATACG 57.290 47.619 0.00 0.00 33.08 3.06
2912 13039 4.823157 TGGAGAAATCGACCATACGAAAA 58.177 39.130 0.00 0.00 45.16 2.29
3091 13220 8.883731 TCTAGTCTCTTAATTGCAGCAAAATAC 58.116 33.333 12.97 4.23 0.00 1.89
3111 13240 7.466746 AATACAATGTTTGCACTAGTGGAAT 57.533 32.000 27.57 15.52 40.52 3.01
3172 13301 0.109153 ACAATGGCTGTGACTGAGCA 59.891 50.000 0.00 0.00 38.27 4.26
3208 13345 8.025243 TCACTTGTTAGGAATATGAACGAAAC 57.975 34.615 0.00 0.00 0.00 2.78
3285 13451 3.671716 ACTTATTTTGAGTGGACCGGTC 58.328 45.455 27.04 27.04 0.00 4.79
3286 13452 3.071892 ACTTATTTTGAGTGGACCGGTCA 59.928 43.478 34.40 18.59 0.00 4.02
3287 13453 1.892209 ATTTTGAGTGGACCGGTCAC 58.108 50.000 34.40 27.41 35.51 3.67
3288 13454 0.179040 TTTTGAGTGGACCGGTCACC 60.179 55.000 34.40 23.38 35.87 4.02
3399 13565 6.712095 ACTGCATATTTGACAGTCTTTTCTCA 59.288 34.615 1.31 0.00 36.26 3.27
3614 14096 1.439543 AGTGCAGGTTCTTCTCCCTT 58.560 50.000 0.00 0.00 0.00 3.95
3617 14099 3.008485 AGTGCAGGTTCTTCTCCCTTTAG 59.992 47.826 0.00 0.00 0.00 1.85
3644 14126 3.106827 TGATGGCTGATGACTTAGGACA 58.893 45.455 0.00 0.00 0.00 4.02
3924 14425 7.576666 GCACATTTTACACTGGTGATATTTGGA 60.577 37.037 7.78 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.817765 AAAATCTACAGAAGGAATTTGCGA 57.182 33.333 0.00 0.00 0.00 5.10
47 48 2.351447 CCAAATCATGATGCTCATCCGC 60.351 50.000 9.46 0.00 34.28 5.54
48 49 2.882761 ACCAAATCATGATGCTCATCCG 59.117 45.455 9.46 0.00 34.28 4.18
49 50 4.931661 AACCAAATCATGATGCTCATCC 57.068 40.909 9.46 0.00 34.28 3.51
50 51 6.183360 TGGTTAACCAAATCATGATGCTCATC 60.183 38.462 25.19 3.03 44.35 2.92
51 52 5.657745 TGGTTAACCAAATCATGATGCTCAT 59.342 36.000 25.19 0.00 44.35 2.90
52 53 5.015515 TGGTTAACCAAATCATGATGCTCA 58.984 37.500 25.19 0.00 44.35 4.26
53 54 5.581126 TGGTTAACCAAATCATGATGCTC 57.419 39.130 25.19 0.00 44.35 4.26
67 68 9.826574 TCTATTGTATTGTACTGATGGTTAACC 57.173 33.333 18.27 18.27 0.00 2.85
168 170 0.382515 TTGCGTGTAGGGCAAAACAC 59.617 50.000 0.00 6.26 46.49 3.32
174 176 0.538516 ATTTGGTTGCGTGTAGGGCA 60.539 50.000 0.00 0.00 38.93 5.36
182 184 2.162809 GACCGGAATAATTTGGTTGCGT 59.837 45.455 9.46 0.00 37.45 5.24
183 185 2.162608 TGACCGGAATAATTTGGTTGCG 59.837 45.455 9.46 5.33 38.62 4.85
195 197 2.618045 GGTGAGATTGGTTGACCGGAAT 60.618 50.000 9.46 0.00 39.43 3.01
230 232 9.281371 GTGTAGGGGAAAGTATTATTTGTATCC 57.719 37.037 0.00 0.00 0.00 2.59
234 236 7.924541 TGAGTGTAGGGGAAAGTATTATTTGT 58.075 34.615 0.00 0.00 0.00 2.83
235 237 8.674607 GTTGAGTGTAGGGGAAAGTATTATTTG 58.325 37.037 0.00 0.00 0.00 2.32
242 244 3.499338 TCGTTGAGTGTAGGGGAAAGTA 58.501 45.455 0.00 0.00 0.00 2.24
244 246 3.396260 TTCGTTGAGTGTAGGGGAAAG 57.604 47.619 0.00 0.00 0.00 2.62
257 260 4.075682 TGGCACCATAGATTTTTCGTTGA 58.924 39.130 0.00 0.00 0.00 3.18
262 265 6.064717 AGGTAGATGGCACCATAGATTTTTC 58.935 40.000 1.19 0.00 38.62 2.29
287 290 1.792949 GCGCATACACTATTCGAAGGG 59.207 52.381 0.30 1.14 0.00 3.95
293 296 0.927537 TGCACGCGCATACACTATTC 59.072 50.000 5.73 0.00 45.36 1.75
334 341 4.634004 TCGTCGAGTCGGGTAGTTATTTTA 59.366 41.667 13.54 0.00 0.00 1.52
341 348 1.642952 GCTTCGTCGAGTCGGGTAGT 61.643 60.000 13.54 0.00 0.00 2.73
480 489 6.148948 GCATATTTGTTTTCTGTGTAGCACA 58.851 36.000 1.88 1.88 42.45 4.57
482 491 5.389778 CGCATATTTGTTTTCTGTGTAGCA 58.610 37.500 0.00 0.00 0.00 3.49
527 536 3.092334 ACAAAAAGCGGATCCACAAAC 57.908 42.857 13.41 0.00 0.00 2.93
666 676 9.570468 TTCGGTATGTAGTCTATAGTGAAATCT 57.430 33.333 0.00 0.00 0.00 2.40
667 677 9.609950 GTTCGGTATGTAGTCTATAGTGAAATC 57.390 37.037 0.00 0.00 0.00 2.17
668 678 9.128404 TGTTCGGTATGTAGTCTATAGTGAAAT 57.872 33.333 0.00 0.00 0.00 2.17
669 679 8.510243 TGTTCGGTATGTAGTCTATAGTGAAA 57.490 34.615 0.00 0.00 0.00 2.69
670 680 8.510243 TTGTTCGGTATGTAGTCTATAGTGAA 57.490 34.615 0.00 0.00 0.00 3.18
671 681 8.510243 TTTGTTCGGTATGTAGTCTATAGTGA 57.490 34.615 0.00 0.00 0.00 3.41
672 682 9.745880 ATTTTGTTCGGTATGTAGTCTATAGTG 57.254 33.333 0.00 0.00 0.00 2.74
677 687 9.577110 CACTAATTTTGTTCGGTATGTAGTCTA 57.423 33.333 0.00 0.00 0.00 2.59
678 688 8.308931 TCACTAATTTTGTTCGGTATGTAGTCT 58.691 33.333 0.00 0.00 0.00 3.24
680 690 8.715088 GTTCACTAATTTTGTTCGGTATGTAGT 58.285 33.333 0.00 0.00 0.00 2.73
681 691 8.932791 AGTTCACTAATTTTGTTCGGTATGTAG 58.067 33.333 0.00 0.00 0.00 2.74
682 692 8.836268 AGTTCACTAATTTTGTTCGGTATGTA 57.164 30.769 0.00 0.00 0.00 2.29
683 693 7.739498 AGTTCACTAATTTTGTTCGGTATGT 57.261 32.000 0.00 0.00 0.00 2.29
685 695 8.161699 ACAAGTTCACTAATTTTGTTCGGTAT 57.838 30.769 0.00 0.00 0.00 2.73
686 696 7.556733 ACAAGTTCACTAATTTTGTTCGGTA 57.443 32.000 0.00 0.00 0.00 4.02
688 698 7.636326 AGTACAAGTTCACTAATTTTGTTCGG 58.364 34.615 0.00 0.00 0.00 4.30
690 700 9.997482 TTGAGTACAAGTTCACTAATTTTGTTC 57.003 29.630 0.00 0.00 0.00 3.18
725 735 9.508642 CCACTATAGAGACTACATTCAGATGTA 57.491 37.037 6.78 0.00 44.51 2.29
727 737 8.628630 TCCACTATAGAGACTACATTCAGATG 57.371 38.462 6.78 0.00 39.25 2.90
728 738 9.821240 ATTCCACTATAGAGACTACATTCAGAT 57.179 33.333 6.78 0.00 0.00 2.90
729 739 9.647918 AATTCCACTATAGAGACTACATTCAGA 57.352 33.333 6.78 0.00 0.00 3.27
762 772 8.258850 TCCTTCCGTTCCTAAATATTAGTCAT 57.741 34.615 0.00 0.00 0.00 3.06
763 773 7.343833 ACTCCTTCCGTTCCTAAATATTAGTCA 59.656 37.037 0.00 0.00 0.00 3.41
764 774 7.724287 ACTCCTTCCGTTCCTAAATATTAGTC 58.276 38.462 0.00 0.00 0.00 2.59
765 775 7.672122 ACTCCTTCCGTTCCTAAATATTAGT 57.328 36.000 0.00 0.00 0.00 2.24
768 778 6.097412 ACGTACTCCTTCCGTTCCTAAATATT 59.903 38.462 0.00 0.00 0.00 1.28
769 779 5.595952 ACGTACTCCTTCCGTTCCTAAATAT 59.404 40.000 0.00 0.00 0.00 1.28
770 780 4.949856 ACGTACTCCTTCCGTTCCTAAATA 59.050 41.667 0.00 0.00 0.00 1.40
771 781 3.766051 ACGTACTCCTTCCGTTCCTAAAT 59.234 43.478 0.00 0.00 0.00 1.40
773 783 2.489329 CACGTACTCCTTCCGTTCCTAA 59.511 50.000 0.00 0.00 31.46 2.69
774 784 2.086869 CACGTACTCCTTCCGTTCCTA 58.913 52.381 0.00 0.00 31.46 2.94
775 785 0.886563 CACGTACTCCTTCCGTTCCT 59.113 55.000 0.00 0.00 31.46 3.36
776 786 0.600057 ACACGTACTCCTTCCGTTCC 59.400 55.000 0.00 0.00 31.46 3.62
777 787 1.000938 ACACACGTACTCCTTCCGTTC 60.001 52.381 0.00 0.00 31.46 3.95
778 788 1.035139 ACACACGTACTCCTTCCGTT 58.965 50.000 0.00 0.00 31.46 4.44
779 789 0.313043 CACACACGTACTCCTTCCGT 59.687 55.000 0.00 0.00 34.71 4.69
781 791 1.779569 CACACACACGTACTCCTTCC 58.220 55.000 0.00 0.00 0.00 3.46
782 792 1.137513 GCACACACACGTACTCCTTC 58.862 55.000 0.00 0.00 0.00 3.46
783 793 0.596600 CGCACACACACGTACTCCTT 60.597 55.000 0.00 0.00 0.00 3.36
784 794 1.007734 CGCACACACACGTACTCCT 60.008 57.895 0.00 0.00 0.00 3.69
785 795 1.299620 ACGCACACACACGTACTCC 60.300 57.895 0.00 0.00 41.48 3.85
786 796 1.844003 CACGCACACACACGTACTC 59.156 57.895 0.00 0.00 41.32 2.59
787 797 2.235016 GCACGCACACACACGTACT 61.235 57.895 0.00 0.00 41.32 2.73
789 799 3.323903 CGCACGCACACACACGTA 61.324 61.111 0.00 0.00 41.32 3.57
848 1136 8.815189 GTTACTCTAAATAAAATGGAGGACGTC 58.185 37.037 7.13 7.13 0.00 4.34
858 1146 8.446599 CCACGATGGGTTACTCTAAATAAAAT 57.553 34.615 0.00 0.00 32.67 1.82
859 1147 7.852971 CCACGATGGGTTACTCTAAATAAAA 57.147 36.000 0.00 0.00 32.67 1.52
893 4404 1.153756 CCCAAAACTGGGCTGGACT 59.846 57.895 0.00 0.00 42.99 3.85
914 4425 1.602165 GCCGTGAGAGTGAGAACGAAA 60.602 52.381 0.00 0.00 38.27 3.46
940 4451 1.152756 GACCACAAACCCAGTGCCT 60.153 57.895 0.00 0.00 35.69 4.75
942 4453 3.030652 CGACCACAAACCCAGTGC 58.969 61.111 0.00 0.00 35.69 4.40
947 4458 3.887335 TAGGCGCGACCACAAACCC 62.887 63.158 9.25 0.00 43.14 4.11
948 4459 2.357760 TAGGCGCGACCACAAACC 60.358 61.111 9.25 0.00 43.14 3.27
949 4460 1.666872 AGTAGGCGCGACCACAAAC 60.667 57.895 14.30 9.20 43.14 2.93
951 4462 2.048597 CAGTAGGCGCGACCACAA 60.049 61.111 14.30 0.00 43.14 3.33
952 4463 4.735132 GCAGTAGGCGCGACCACA 62.735 66.667 14.30 1.71 43.14 4.17
962 4478 1.336702 GCTCGATCTGGATGCAGTAGG 60.337 57.143 14.43 4.66 0.00 3.18
975 4493 2.029221 GGGTTAGGGCGCTCGATC 59.971 66.667 6.54 0.00 0.00 3.69
982 4500 4.462280 GGGACGTGGGTTAGGGCG 62.462 72.222 0.00 0.00 0.00 6.13
983 4501 3.324108 TGGGACGTGGGTTAGGGC 61.324 66.667 0.00 0.00 0.00 5.19
984 4502 1.559065 ATGTGGGACGTGGGTTAGGG 61.559 60.000 0.00 0.00 0.00 3.53
2471 12487 0.762418 TGGAGACAACACCACGGAAT 59.238 50.000 0.00 0.00 37.44 3.01
2528 12551 4.412796 TGAGGAGGCATCAAGATACTTG 57.587 45.455 0.00 5.29 0.00 3.16
2683 12713 4.201783 GCTTACCTGCGTAACCAGTAAATG 60.202 45.833 0.00 0.00 31.13 2.32
2792 12877 5.805728 TGTAGAGAAAATTTGGGTCCTCTC 58.194 41.667 7.07 7.07 33.58 3.20
2803 12890 9.120538 TCTAAGCAAAGTGTTGTAGAGAAAATT 57.879 29.630 0.00 0.00 37.06 1.82
2837 12924 4.145052 GGACAAAAACCATCTCCAAGACT 58.855 43.478 0.00 0.00 0.00 3.24
2838 12925 3.888930 TGGACAAAAACCATCTCCAAGAC 59.111 43.478 0.00 0.00 32.03 3.01
2839 12926 3.888930 GTGGACAAAAACCATCTCCAAGA 59.111 43.478 0.00 0.00 39.69 3.02
2842 12929 3.304911 TGTGGACAAAAACCATCTCCA 57.695 42.857 0.00 0.00 39.69 3.86
2844 12931 7.331687 CCAAATATTGTGGACAAAAACCATCTC 59.668 37.037 9.73 0.00 39.55 2.75
2847 12934 7.016072 TCTCCAAATATTGTGGACAAAAACCAT 59.984 33.333 12.57 0.00 40.33 3.55
2848 12935 6.325028 TCTCCAAATATTGTGGACAAAAACCA 59.675 34.615 12.57 0.00 40.33 3.67
2850 12937 8.711457 CATTCTCCAAATATTGTGGACAAAAAC 58.289 33.333 12.57 0.00 40.33 2.43
2851 12938 7.877097 CCATTCTCCAAATATTGTGGACAAAAA 59.123 33.333 12.57 7.66 40.33 1.94
2852 12939 7.016072 ACCATTCTCCAAATATTGTGGACAAAA 59.984 33.333 12.57 9.27 40.33 2.44
2853 12940 6.496565 ACCATTCTCCAAATATTGTGGACAAA 59.503 34.615 12.57 10.89 40.33 2.83
2854 12941 6.015918 ACCATTCTCCAAATATTGTGGACAA 58.984 36.000 12.57 10.48 40.33 3.18
2855 12942 5.579047 ACCATTCTCCAAATATTGTGGACA 58.421 37.500 12.57 3.97 40.33 4.02
2856 12943 6.530019 AACCATTCTCCAAATATTGTGGAC 57.470 37.500 12.57 0.00 40.33 4.02
2858 12945 7.877097 TGAAAAACCATTCTCCAAATATTGTGG 59.123 33.333 9.25 9.25 37.51 4.17
2912 13039 9.898152 TGTTTTCTTCATTGAAGGGTAATTTTT 57.102 25.926 22.86 0.00 39.82 1.94
3091 13220 5.531634 ACAATTCCACTAGTGCAAACATTG 58.468 37.500 17.86 18.62 0.00 2.82
3208 13345 4.530875 AGAAAAAGGCAGTATGGGATCTG 58.469 43.478 0.00 0.00 35.86 2.90
3285 13451 3.783362 TTCACTTGCCCCACCGGTG 62.783 63.158 28.26 28.26 0.00 4.94
3286 13452 3.491598 CTTCACTTGCCCCACCGGT 62.492 63.158 0.00 0.00 0.00 5.28
3287 13453 2.672996 CTTCACTTGCCCCACCGG 60.673 66.667 0.00 0.00 0.00 5.28
3288 13454 3.365265 GCTTCACTTGCCCCACCG 61.365 66.667 0.00 0.00 0.00 4.94
3289 13455 2.116125 AGCTTCACTTGCCCCACC 59.884 61.111 0.00 0.00 0.00 4.61
3290 13456 0.823356 TTCAGCTTCACTTGCCCCAC 60.823 55.000 0.00 0.00 0.00 4.61
3291 13457 0.823356 GTTCAGCTTCACTTGCCCCA 60.823 55.000 0.00 0.00 0.00 4.96
3399 13565 0.329596 GGATGAGGAAGCAGGGTGTT 59.670 55.000 0.00 0.00 0.00 3.32
3614 14096 3.386078 GTCATCAGCCATCAGAGGACTAA 59.614 47.826 0.00 0.00 41.05 2.24
3617 14099 1.761784 AGTCATCAGCCATCAGAGGAC 59.238 52.381 0.00 0.00 43.64 3.85
3644 14126 3.778265 ACATATGCACAAAAGGGGAAGT 58.222 40.909 1.58 0.00 0.00 3.01
3780 14264 8.715191 TTAACCATACAAAATGATCAAATGCC 57.285 30.769 0.00 0.00 0.00 4.40
3873 14361 2.901192 TGGCATAGCTATAAGCCCGTAA 59.099 45.455 24.87 9.69 43.71 3.18


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

AutoCloner maintained by Alex Coulton.