Multiple sequence alignment - TraesCS7B01G499500

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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 TraesCS7B01G499500 chr7B 100.000 3137 0 0 1 3137 749573561 749570425 0.000000e+00 5794.0
1 TraesCS7B01G499500 chr7B 95.231 692 23 5 2446 3137 603829352 603828671 0.000000e+00 1086.0
2 TraesCS7B01G499500 chr7B 89.855 621 55 4 1 620 96400688 96401301 0.000000e+00 791.0
3 TraesCS7B01G499500 chr7A 92.915 1115 57 10 1244 2338 733499401 733500513 0.000000e+00 1602.0
4 TraesCS7B01G499500 chr7A 91.304 276 23 1 974 1248 733498931 733499206 2.950000e-100 375.0
5 TraesCS7B01G499500 chr7A 80.717 223 15 17 769 984 733498546 733498747 7.010000e-32 148.0
6 TraesCS7B01G499500 chr7A 78.756 193 41 0 2945 3137 140991783 140991975 2.540000e-26 130.0
7 TraesCS7B01G499500 chr7D 91.536 1146 81 6 1247 2381 633567613 633566473 0.000000e+00 1565.0
8 TraesCS7B01G499500 chr7D 89.938 646 54 8 1 644 617769544 617770180 0.000000e+00 822.0
9 TraesCS7B01G499500 chr7D 88.940 651 57 11 1 649 574886741 574887378 0.000000e+00 789.0
10 TraesCS7B01G499500 chr7D 91.156 294 19 1 962 1248 633568108 633567815 2.930000e-105 392.0
11 TraesCS7B01G499500 chr7D 91.367 139 6 2 689 827 633568418 633568286 5.340000e-43 185.0
12 TraesCS7B01G499500 chr7D 95.918 49 2 0 812 860 633568264 633568216 2.590000e-11 80.5
13 TraesCS7B01G499500 chr7D 100.000 35 0 0 802 836 633568218 633568184 7.260000e-07 65.8
14 TraesCS7B01G499500 chr6B 97.807 684 8 2 2455 3137 17393062 17392385 0.000000e+00 1173.0
15 TraesCS7B01G499500 chr6B 96.340 683 15 4 2455 3137 703531902 703532574 0.000000e+00 1114.0
16 TraesCS7B01G499500 chr6B 90.728 604 47 8 1 602 243232692 243233288 0.000000e+00 797.0
17 TraesCS7B01G499500 chr6B 96.629 445 9 4 2693 3137 25567310 25566872 0.000000e+00 734.0
18 TraesCS7B01G499500 chr6B 95.946 222 7 2 2453 2673 25567762 25567542 2.970000e-95 359.0
19 TraesCS7B01G499500 chr1B 90.174 631 53 8 1 629 367560002 367559379 0.000000e+00 813.0
20 TraesCS7B01G499500 chr1D 90.438 617 49 7 1 616 452335714 452335107 0.000000e+00 804.0
21 TraesCS7B01G499500 chr1D 90.438 617 49 7 1 616 452352383 452352990 0.000000e+00 804.0
22 TraesCS7B01G499500 chr3B 89.839 620 50 11 1 616 170822988 170823598 0.000000e+00 784.0
23 TraesCS7B01G499500 chr3B 89.806 618 53 9 1 616 349672213 349671604 0.000000e+00 784.0


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 TraesCS7B01G499500 chr7B 749570425 749573561 3136 True 5794.000000 5794 100.0000 1 3137 1 chr7B.!!$R2 3136
1 TraesCS7B01G499500 chr7B 603828671 603829352 681 True 1086.000000 1086 95.2310 2446 3137 1 chr7B.!!$R1 691
2 TraesCS7B01G499500 chr7B 96400688 96401301 613 False 791.000000 791 89.8550 1 620 1 chr7B.!!$F1 619
3 TraesCS7B01G499500 chr7A 733498546 733500513 1967 False 708.333333 1602 88.3120 769 2338 3 chr7A.!!$F2 1569
4 TraesCS7B01G499500 chr7D 617769544 617770180 636 False 822.000000 822 89.9380 1 644 1 chr7D.!!$F2 643
5 TraesCS7B01G499500 chr7D 574886741 574887378 637 False 789.000000 789 88.9400 1 649 1 chr7D.!!$F1 648
6 TraesCS7B01G499500 chr7D 633566473 633568418 1945 True 457.660000 1565 93.9954 689 2381 5 chr7D.!!$R1 1692
7 TraesCS7B01G499500 chr6B 17392385 17393062 677 True 1173.000000 1173 97.8070 2455 3137 1 chr6B.!!$R1 682
8 TraesCS7B01G499500 chr6B 703531902 703532574 672 False 1114.000000 1114 96.3400 2455 3137 1 chr6B.!!$F2 682
9 TraesCS7B01G499500 chr6B 243232692 243233288 596 False 797.000000 797 90.7280 1 602 1 chr6B.!!$F1 601
10 TraesCS7B01G499500 chr6B 25566872 25567762 890 True 546.500000 734 96.2875 2453 3137 2 chr6B.!!$R2 684
11 TraesCS7B01G499500 chr1B 367559379 367560002 623 True 813.000000 813 90.1740 1 629 1 chr1B.!!$R1 628
12 TraesCS7B01G499500 chr1D 452335107 452335714 607 True 804.000000 804 90.4380 1 616 1 chr1D.!!$R1 615
13 TraesCS7B01G499500 chr1D 452352383 452352990 607 False 804.000000 804 90.4380 1 616 1 chr1D.!!$F1 615
14 TraesCS7B01G499500 chr3B 170822988 170823598 610 False 784.000000 784 89.8390 1 616 1 chr3B.!!$F1 615
15 TraesCS7B01G499500 chr3B 349671604 349672213 609 True 784.000000 784 89.8060 1 616 1 chr3B.!!$R1 615

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
920 998 0.667993 CAACCTTTGACATGCCGTGT 59.332 50.0 0.00 0.0 45.83 4.49 F
1230 1503 0.106708 AGAACTTCACGGAGCTGCAA 59.893 50.0 5.91 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2404 0.249398 ACACCAGCTTATCCACGGTC 59.751 55.0 0.00 0.0 0.0 4.79 R
2946 3692 0.098728 CCCCAAATTCGTCGACATGC 59.901 55.0 17.16 0.0 0.0 4.06 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
110 112 5.633830 TTTCATGCATGTCCTCTCTTTTC 57.366 39.130 25.43 0.00 0.00 2.29
257 259 5.065859 TGCATGTCCTTATTTATTGGTGTCG 59.934 40.000 0.00 0.00 0.00 4.35
310 312 4.365514 TCCTGATTTTGCTGAGGTGTTA 57.634 40.909 0.00 0.00 0.00 2.41
322 324 5.045213 TGCTGAGGTGTTAATCCCAAATCTA 60.045 40.000 0.00 0.00 0.00 1.98
327 329 7.282224 TGAGGTGTTAATCCCAAATCTAAATCG 59.718 37.037 0.00 0.00 0.00 3.34
333 335 5.640158 ATCCCAAATCTAAATCGGTACCA 57.360 39.130 13.54 0.00 0.00 3.25
388 393 6.707608 TGATTAACATTGCAGCCTAGATAGTG 59.292 38.462 0.00 0.00 0.00 2.74
393 399 5.355350 ACATTGCAGCCTAGATAGTGTTTTC 59.645 40.000 0.00 0.00 0.00 2.29
394 400 4.826274 TGCAGCCTAGATAGTGTTTTCT 57.174 40.909 0.00 0.00 0.00 2.52
395 401 5.165961 TGCAGCCTAGATAGTGTTTTCTT 57.834 39.130 0.00 0.00 0.00 2.52
505 512 6.549912 AGTTACGGTTTAAAAGATGTGACC 57.450 37.500 0.00 0.00 0.00 4.02
594 604 2.434336 AGCATGACGGGCTAAGAATACA 59.566 45.455 0.00 0.00 40.47 2.29
671 681 8.896722 AGAAATAGGTAGTAGTCTTTCCTTCA 57.103 34.615 0.00 0.00 32.42 3.02
672 682 8.973182 AGAAATAGGTAGTAGTCTTTCCTTCAG 58.027 37.037 0.00 0.00 32.42 3.02
673 683 6.718522 ATAGGTAGTAGTCTTTCCTTCAGC 57.281 41.667 0.00 0.00 32.42 4.26
674 684 3.770388 AGGTAGTAGTCTTTCCTTCAGCC 59.230 47.826 0.00 0.00 0.00 4.85
675 685 3.770388 GGTAGTAGTCTTTCCTTCAGCCT 59.230 47.826 0.00 0.00 0.00 4.58
676 686 4.223255 GGTAGTAGTCTTTCCTTCAGCCTT 59.777 45.833 0.00 0.00 0.00 4.35
677 687 5.421374 GGTAGTAGTCTTTCCTTCAGCCTTA 59.579 44.000 0.00 0.00 0.00 2.69
678 688 5.669164 AGTAGTCTTTCCTTCAGCCTTAG 57.331 43.478 0.00 0.00 0.00 2.18
679 689 5.334421 AGTAGTCTTTCCTTCAGCCTTAGA 58.666 41.667 0.00 0.00 0.00 2.10
680 690 5.780793 AGTAGTCTTTCCTTCAGCCTTAGAA 59.219 40.000 0.00 0.00 0.00 2.10
681 691 5.159273 AGTCTTTCCTTCAGCCTTAGAAG 57.841 43.478 0.00 0.00 41.61 2.85
682 692 4.841246 AGTCTTTCCTTCAGCCTTAGAAGA 59.159 41.667 4.61 0.00 44.00 2.87
683 693 5.308237 AGTCTTTCCTTCAGCCTTAGAAGAA 59.692 40.000 4.61 0.00 44.00 2.52
684 694 5.998363 GTCTTTCCTTCAGCCTTAGAAGAAA 59.002 40.000 4.61 3.54 44.00 2.52
685 695 6.486993 GTCTTTCCTTCAGCCTTAGAAGAAAA 59.513 38.462 4.61 0.00 44.00 2.29
686 696 6.712547 TCTTTCCTTCAGCCTTAGAAGAAAAG 59.287 38.462 7.92 7.92 44.11 2.27
687 697 5.825593 TCCTTCAGCCTTAGAAGAAAAGA 57.174 39.130 4.61 0.00 44.00 2.52
703 713 7.964011 AGAAGAAAAGATACGTACTTTCTCTCG 59.036 37.037 20.73 0.00 36.71 4.04
724 734 5.670485 TCGTATCCTTTGCTTACATGTGAT 58.330 37.500 9.11 2.44 0.00 3.06
725 735 5.523552 TCGTATCCTTTGCTTACATGTGATG 59.476 40.000 9.11 0.00 0.00 3.07
726 736 5.294306 CGTATCCTTTGCTTACATGTGATGT 59.706 40.000 9.11 0.00 46.92 3.06
727 737 5.571784 ATCCTTTGCTTACATGTGATGTG 57.428 39.130 9.11 0.00 44.60 3.21
728 738 4.650734 TCCTTTGCTTACATGTGATGTGA 58.349 39.130 9.11 0.00 44.60 3.58
729 739 5.255687 TCCTTTGCTTACATGTGATGTGAT 58.744 37.500 9.11 0.00 44.60 3.06
737 747 6.346919 GCTTACATGTGATGTGATTCCGTATC 60.347 42.308 9.11 0.00 44.60 2.24
760 770 8.970691 ATCTCAATTTTATTGTCAGTTTTCGG 57.029 30.769 0.00 0.00 0.00 4.30
866 916 1.862806 GTGTTGGCTTCACGAGAGC 59.137 57.895 0.00 0.00 0.00 4.09
909 987 2.223479 CCACCGTTCTTGTCAACCTTTG 60.223 50.000 0.00 0.00 0.00 2.77
910 988 2.680841 CACCGTTCTTGTCAACCTTTGA 59.319 45.455 0.00 0.00 37.33 2.69
918 996 3.412722 TCAACCTTTGACATGCCGT 57.587 47.368 0.00 0.00 34.08 5.68
919 997 0.950836 TCAACCTTTGACATGCCGTG 59.049 50.000 0.00 0.00 34.08 4.94
920 998 0.667993 CAACCTTTGACATGCCGTGT 59.332 50.000 0.00 0.00 45.83 4.49
921 999 0.667993 AACCTTTGACATGCCGTGTG 59.332 50.000 0.00 0.00 42.36 3.82
922 1000 1.081242 CCTTTGACATGCCGTGTGC 60.081 57.895 0.00 0.00 42.36 4.57
923 1001 1.440850 CTTTGACATGCCGTGTGCG 60.441 57.895 0.00 0.00 45.60 5.34
924 1002 2.116736 CTTTGACATGCCGTGTGCGT 62.117 55.000 0.00 0.00 45.60 5.24
942 1020 1.522676 CGTGCATCAATACGGCTGTAG 59.477 52.381 11.78 0.00 36.71 2.74
943 1021 2.550978 GTGCATCAATACGGCTGTAGT 58.449 47.619 11.78 5.57 33.17 2.73
944 1022 3.713288 GTGCATCAATACGGCTGTAGTA 58.287 45.455 11.78 0.00 33.17 1.82
947 1025 5.236478 GTGCATCAATACGGCTGTAGTATTT 59.764 40.000 11.78 0.00 41.31 1.40
950 1028 6.564125 GCATCAATACGGCTGTAGTATTTGAC 60.564 42.308 17.53 6.61 41.31 3.18
958 1036 3.242413 GCTGTAGTATTTGACATGCCGTG 60.242 47.826 0.00 0.00 0.00 4.94
959 1037 3.932710 CTGTAGTATTTGACATGCCGTGT 59.067 43.478 0.00 0.00 45.83 4.49
960 1038 3.682377 TGTAGTATTTGACATGCCGTGTG 59.318 43.478 0.00 0.00 42.36 3.82
985 1258 3.118261 TGCACACAAGAGAAGGAAACTCT 60.118 43.478 0.00 0.00 45.13 3.24
992 1265 3.158676 AGAGAAGGAAACTCTAGCGTGT 58.841 45.455 0.00 0.00 42.68 4.49
1038 1311 3.090765 CCCCTTGTAGCCCTGCTT 58.909 61.111 0.00 0.00 40.44 3.91
1047 1320 1.068264 GTAGCCCTGCTTTGCTTGTTC 60.068 52.381 0.00 0.00 40.44 3.18
1158 1431 0.968901 ATGAGTACGAACCTCCGCCA 60.969 55.000 0.00 0.00 0.00 5.69
1223 1496 0.679505 CTGTGGGAGAACTTCACGGA 59.320 55.000 10.31 0.00 39.42 4.69
1230 1503 0.106708 AGAACTTCACGGAGCTGCAA 59.893 50.000 5.91 0.00 0.00 4.08
1240 1513 2.530151 AGCTGCAAGAGGACCCCA 60.530 61.111 1.02 0.00 34.07 4.96
1401 1912 3.382803 CTCCGGCTTCAGCTCCAGG 62.383 68.421 0.00 0.00 41.70 4.45
1470 1981 2.335369 GTCCTCGTGACGCACAGT 59.665 61.111 0.00 0.00 33.40 3.55
1503 2014 2.264794 GCCACGGTGTTCCTCGAT 59.735 61.111 7.45 0.00 0.00 3.59
1563 2074 2.581354 GTCATGCTCTGCCTCGGT 59.419 61.111 0.00 0.00 0.00 4.69
1565 2076 3.200593 CATGCTCTGCCTCGGTGC 61.201 66.667 0.00 0.00 0.00 5.01
1738 2249 4.077184 TGGTGATCACGCGGGACC 62.077 66.667 16.24 12.86 0.00 4.46
1827 2338 1.080025 GTACAGAACGAGGGCGCTT 60.080 57.895 7.64 0.00 42.48 4.68
1903 2414 4.501714 GCGTGCCGACCGTGGATA 62.502 66.667 0.00 0.00 0.00 2.59
1937 2448 1.067071 GGACGGTAACTTCAGTGGGAG 60.067 57.143 0.00 0.00 36.36 4.30
1953 2464 0.329596 GGAGGCCTCAGTTGGTGAAT 59.670 55.000 33.29 0.00 33.60 2.57
2010 2521 1.591327 GGCGTTGCAAAGGTTGGTG 60.591 57.895 14.31 0.00 33.49 4.17
2041 2552 1.275291 CGGACCAGCCTTACTTCAAGA 59.725 52.381 0.00 0.00 36.22 3.02
2085 2596 2.037772 GCACAAGGGTATGATCTCGGAT 59.962 50.000 0.00 0.00 0.00 4.18
2165 2694 4.021719 GGCATTTATCATGGCAGCATACTT 60.022 41.667 3.65 0.00 43.15 2.24
2181 2710 6.003950 AGCATACTTTGTTGGTTATGTGACT 58.996 36.000 0.00 0.00 0.00 3.41
2184 2713 8.458843 GCATACTTTGTTGGTTATGTGACTTAT 58.541 33.333 0.00 0.00 0.00 1.73
2186 2715 6.677913 ACTTTGTTGGTTATGTGACTTATGC 58.322 36.000 0.00 0.00 0.00 3.14
2250 2781 5.691754 ACTTCCTCAAATTCGTCATTTTTGC 59.308 36.000 0.00 0.00 32.24 3.68
2289 2821 2.783135 TGACTTCAGATTTGGCAGGAC 58.217 47.619 0.00 0.00 0.00 3.85
2320 2852 7.865385 TGACAAAGTGAGCAAAATAATTGGTAC 59.135 33.333 0.00 0.00 0.00 3.34
2324 2856 6.389906 AGTGAGCAAAATAATTGGTACTTGC 58.610 36.000 4.53 4.53 39.50 4.01
2342 2874 9.169592 GGTACTTGCTTTAATTACTATGTCCAA 57.830 33.333 0.00 0.00 0.00 3.53
2393 2925 8.810990 AGCTACCATTATACACTACTCTATCC 57.189 38.462 0.00 0.00 0.00 2.59
2394 2926 7.553402 AGCTACCATTATACACTACTCTATCCG 59.447 40.741 0.00 0.00 0.00 4.18
2395 2927 7.336427 GCTACCATTATACACTACTCTATCCGT 59.664 40.741 0.00 0.00 0.00 4.69
2396 2928 7.684937 ACCATTATACACTACTCTATCCGTC 57.315 40.000 0.00 0.00 0.00 4.79
2397 2929 6.658391 ACCATTATACACTACTCTATCCGTCC 59.342 42.308 0.00 0.00 0.00 4.79
2398 2930 6.095160 CCATTATACACTACTCTATCCGTCCC 59.905 46.154 0.00 0.00 0.00 4.46
2399 2931 4.719026 ATACACTACTCTATCCGTCCCA 57.281 45.455 0.00 0.00 0.00 4.37
2400 2932 3.377253 ACACTACTCTATCCGTCCCAA 57.623 47.619 0.00 0.00 0.00 4.12
2401 2933 3.912248 ACACTACTCTATCCGTCCCAAT 58.088 45.455 0.00 0.00 0.00 3.16
2402 2934 5.057843 ACACTACTCTATCCGTCCCAATA 57.942 43.478 0.00 0.00 0.00 1.90
2403 2935 5.452255 ACACTACTCTATCCGTCCCAATAA 58.548 41.667 0.00 0.00 0.00 1.40
2404 2936 6.075984 ACACTACTCTATCCGTCCCAATAAT 58.924 40.000 0.00 0.00 0.00 1.28
2405 2937 7.236529 ACACTACTCTATCCGTCCCAATAATA 58.763 38.462 0.00 0.00 0.00 0.98
2406 2938 7.727186 ACACTACTCTATCCGTCCCAATAATAA 59.273 37.037 0.00 0.00 0.00 1.40
2407 2939 8.582437 CACTACTCTATCCGTCCCAATAATAAA 58.418 37.037 0.00 0.00 0.00 1.40
2408 2940 9.322769 ACTACTCTATCCGTCCCAATAATAAAT 57.677 33.333 0.00 0.00 0.00 1.40
2409 2941 9.587772 CTACTCTATCCGTCCCAATAATAAATG 57.412 37.037 0.00 0.00 0.00 2.32
2410 2942 8.202461 ACTCTATCCGTCCCAATAATAAATGA 57.798 34.615 0.00 0.00 0.00 2.57
2411 2943 8.095169 ACTCTATCCGTCCCAATAATAAATGAC 58.905 37.037 0.00 0.00 0.00 3.06
2412 2944 8.202461 TCTATCCGTCCCAATAATAAATGACT 57.798 34.615 0.00 0.00 0.00 3.41
2413 2945 8.311836 TCTATCCGTCCCAATAATAAATGACTC 58.688 37.037 0.00 0.00 0.00 3.36
2414 2946 5.294356 TCCGTCCCAATAATAAATGACTCG 58.706 41.667 0.00 0.00 0.00 4.18
2415 2947 5.069383 TCCGTCCCAATAATAAATGACTCGA 59.931 40.000 0.00 0.00 0.00 4.04
2416 2948 5.176958 CCGTCCCAATAATAAATGACTCGAC 59.823 44.000 0.00 0.00 0.00 4.20
2417 2949 5.983720 CGTCCCAATAATAAATGACTCGACT 59.016 40.000 0.00 0.00 0.00 4.18
2418 2950 6.479001 CGTCCCAATAATAAATGACTCGACTT 59.521 38.462 0.00 0.00 0.00 3.01
2419 2951 7.011109 CGTCCCAATAATAAATGACTCGACTTT 59.989 37.037 0.00 0.00 0.00 2.66
2420 2952 9.321562 GTCCCAATAATAAATGACTCGACTTTA 57.678 33.333 0.00 0.00 0.00 1.85
2433 2965 8.842358 TGACTCGACTTTATCTTAAATTTGGT 57.158 30.769 0.00 0.00 0.00 3.67
2434 2966 8.717821 TGACTCGACTTTATCTTAAATTTGGTG 58.282 33.333 0.00 0.00 0.00 4.17
2435 2967 8.617290 ACTCGACTTTATCTTAAATTTGGTGT 57.383 30.769 0.00 0.00 0.00 4.16
2436 2968 9.715121 ACTCGACTTTATCTTAAATTTGGTGTA 57.285 29.630 0.00 0.00 0.00 2.90
2438 2970 9.715121 TCGACTTTATCTTAAATTTGGTGTAGT 57.285 29.630 0.00 0.00 0.00 2.73
2586 3119 8.832521 CGTAATTGCTTACTTAAATGGGATACA 58.167 33.333 0.00 0.00 35.98 2.29
2867 3612 4.036262 TCTGTTGATTCCTCCGTGTTTTTG 59.964 41.667 0.00 0.00 0.00 2.44
2944 3690 0.107456 CCACCGCTCTCCATAGCATT 59.893 55.000 0.00 0.00 42.91 3.56
2945 3691 1.344438 CCACCGCTCTCCATAGCATTA 59.656 52.381 0.00 0.00 42.91 1.90
2946 3692 2.611473 CCACCGCTCTCCATAGCATTAG 60.611 54.545 0.00 0.00 42.91 1.73
2947 3693 1.001406 ACCGCTCTCCATAGCATTAGC 59.999 52.381 0.00 0.00 42.91 3.09
2948 3694 1.001293 CCGCTCTCCATAGCATTAGCA 59.999 52.381 0.00 0.00 45.49 3.49
2949 3695 2.354503 CCGCTCTCCATAGCATTAGCAT 60.355 50.000 0.00 0.00 45.49 3.79
3029 3775 3.494398 GGCTGTTTATCCCGATTCTGCTA 60.494 47.826 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
310 312 6.008696 TGGTACCGATTTAGATTTGGGATT 57.991 37.500 7.57 0.00 0.00 3.01
480 487 7.714377 TGGTCACATCTTTTAAACCGTAACTTA 59.286 33.333 0.00 0.00 0.00 2.24
527 536 1.468520 CTGACATTAAACCCGCAGTGG 59.531 52.381 0.00 0.00 37.55 4.00
528 537 2.422597 TCTGACATTAAACCCGCAGTG 58.577 47.619 0.00 0.00 0.00 3.66
564 574 3.616219 AGCCCGTCATGCTATTTTGTAA 58.384 40.909 0.00 0.00 37.28 2.41
649 659 6.098552 GGCTGAAGGAAAGACTACTACCTATT 59.901 42.308 0.00 0.00 34.50 1.73
650 660 5.599242 GGCTGAAGGAAAGACTACTACCTAT 59.401 44.000 0.00 0.00 34.50 2.57
651 661 4.954826 GGCTGAAGGAAAGACTACTACCTA 59.045 45.833 0.00 0.00 34.50 3.08
652 662 3.770388 GGCTGAAGGAAAGACTACTACCT 59.230 47.826 0.00 0.00 35.67 3.08
653 663 3.770388 AGGCTGAAGGAAAGACTACTACC 59.230 47.826 0.00 0.00 28.47 3.18
654 664 5.408880 AAGGCTGAAGGAAAGACTACTAC 57.591 43.478 0.00 0.00 29.14 2.73
655 665 6.491383 TCTAAGGCTGAAGGAAAGACTACTA 58.509 40.000 0.00 0.00 29.14 1.82
656 666 5.334421 TCTAAGGCTGAAGGAAAGACTACT 58.666 41.667 0.00 0.00 29.14 2.57
657 667 5.662674 TCTAAGGCTGAAGGAAAGACTAC 57.337 43.478 0.00 0.00 29.14 2.73
658 668 6.017192 TCTTCTAAGGCTGAAGGAAAGACTA 58.983 40.000 12.96 0.00 40.73 2.59
659 669 4.841246 TCTTCTAAGGCTGAAGGAAAGACT 59.159 41.667 12.96 0.00 40.73 3.24
660 670 5.153950 TCTTCTAAGGCTGAAGGAAAGAC 57.846 43.478 12.96 0.00 40.73 3.01
661 671 5.825593 TTCTTCTAAGGCTGAAGGAAAGA 57.174 39.130 12.96 6.13 40.73 2.52
662 672 6.884280 TTTTCTTCTAAGGCTGAAGGAAAG 57.116 37.500 14.07 5.15 41.44 2.62
663 673 6.601332 TCTTTTCTTCTAAGGCTGAAGGAAA 58.399 36.000 16.14 16.14 43.04 3.13
664 674 6.187727 TCTTTTCTTCTAAGGCTGAAGGAA 57.812 37.500 12.96 8.93 40.73 3.36
665 675 5.825593 TCTTTTCTTCTAAGGCTGAAGGA 57.174 39.130 12.96 3.54 40.73 3.36
666 676 6.256757 CGTATCTTTTCTTCTAAGGCTGAAGG 59.743 42.308 12.96 0.27 40.73 3.46
667 677 6.814146 ACGTATCTTTTCTTCTAAGGCTGAAG 59.186 38.462 7.99 7.99 41.46 3.02
668 678 6.698380 ACGTATCTTTTCTTCTAAGGCTGAA 58.302 36.000 0.00 0.00 0.00 3.02
669 679 6.282199 ACGTATCTTTTCTTCTAAGGCTGA 57.718 37.500 0.00 0.00 0.00 4.26
670 680 7.259161 AGTACGTATCTTTTCTTCTAAGGCTG 58.741 38.462 0.00 0.00 0.00 4.85
671 681 7.407393 AGTACGTATCTTTTCTTCTAAGGCT 57.593 36.000 0.00 0.00 0.00 4.58
672 682 8.476657 AAAGTACGTATCTTTTCTTCTAAGGC 57.523 34.615 13.78 0.00 32.14 4.35
673 683 9.857957 AGAAAGTACGTATCTTTTCTTCTAAGG 57.142 33.333 18.83 0.00 35.62 2.69
677 687 7.964011 CGAGAGAAAGTACGTATCTTTTCTTCT 59.036 37.037 22.43 20.42 35.62 2.85
678 688 7.750014 ACGAGAGAAAGTACGTATCTTTTCTTC 59.250 37.037 22.43 19.74 37.22 2.87
679 689 7.592051 ACGAGAGAAAGTACGTATCTTTTCTT 58.408 34.615 22.43 16.17 37.22 2.52
680 690 7.143514 ACGAGAGAAAGTACGTATCTTTTCT 57.856 36.000 22.04 22.04 37.22 2.52
702 712 5.294306 ACATCACATGTAAGCAAAGGATACG 59.706 40.000 0.00 0.00 42.78 3.06
703 713 6.316140 TCACATCACATGTAAGCAAAGGATAC 59.684 38.462 0.00 0.00 42.70 2.24
708 718 6.032094 GGAATCACATCACATGTAAGCAAAG 58.968 40.000 0.00 0.00 42.70 2.77
724 734 9.173021 ACAATAAAATTGAGATACGGAATCACA 57.827 29.630 6.64 0.43 37.03 3.58
725 735 9.651718 GACAATAAAATTGAGATACGGAATCAC 57.348 33.333 6.64 0.00 37.03 3.06
726 736 9.389755 TGACAATAAAATTGAGATACGGAATCA 57.610 29.630 6.64 0.00 37.03 2.57
727 737 9.869844 CTGACAATAAAATTGAGATACGGAATC 57.130 33.333 6.64 0.00 34.52 2.52
728 738 9.396022 ACTGACAATAAAATTGAGATACGGAAT 57.604 29.630 6.64 0.00 0.00 3.01
729 739 8.786826 ACTGACAATAAAATTGAGATACGGAA 57.213 30.769 6.64 0.00 0.00 4.30
737 747 6.089417 GGCCGAAAACTGACAATAAAATTGAG 59.911 38.462 6.64 0.00 0.00 3.02
760 770 1.227674 CGCCAAGACTGGATAGGGC 60.228 63.158 0.00 0.00 46.92 5.19
853 903 1.739562 CCACTGCTCTCGTGAAGCC 60.740 63.158 4.48 0.00 34.35 4.35
866 916 1.798813 GGAGCGACTTGTTTACCACTG 59.201 52.381 0.00 0.00 0.00 3.66
909 987 4.741781 GCACGCACACGGCATGTC 62.742 66.667 0.00 0.00 46.04 3.06
911 989 4.105733 ATGCACGCACACGGCATG 62.106 61.111 11.66 0.00 46.94 4.06
915 993 0.247655 GTATTGATGCACGCACACGG 60.248 55.000 0.00 0.00 46.04 4.94
917 995 0.247655 CCGTATTGATGCACGCACAC 60.248 55.000 0.00 0.00 36.85 3.82
918 996 1.976478 GCCGTATTGATGCACGCACA 61.976 55.000 0.00 0.00 36.85 4.57
919 997 1.297598 GCCGTATTGATGCACGCAC 60.298 57.895 0.00 0.00 36.85 5.34
920 998 1.449423 AGCCGTATTGATGCACGCA 60.449 52.632 0.00 0.00 36.85 5.24
921 999 1.010797 CAGCCGTATTGATGCACGC 60.011 57.895 0.00 0.00 36.85 5.34
922 1000 1.522676 CTACAGCCGTATTGATGCACG 59.477 52.381 0.00 0.00 37.89 5.34
923 1001 2.550978 ACTACAGCCGTATTGATGCAC 58.449 47.619 0.00 0.00 0.00 4.57
924 1002 2.979814 ACTACAGCCGTATTGATGCA 57.020 45.000 0.00 0.00 0.00 3.96
925 1003 5.465390 TCAAATACTACAGCCGTATTGATGC 59.535 40.000 0.00 0.00 37.56 3.91
926 1004 6.478673 TGTCAAATACTACAGCCGTATTGATG 59.521 38.462 0.00 0.00 37.56 3.07
942 1020 1.790123 CGCACACGGCATGTCAAATAC 60.790 52.381 0.00 0.00 45.17 1.89
943 1021 0.445829 CGCACACGGCATGTCAAATA 59.554 50.000 0.00 0.00 45.17 1.40
944 1022 1.209898 CGCACACGGCATGTCAAAT 59.790 52.632 0.00 0.00 45.17 2.32
947 1025 3.345011 CACGCACACGGCATGTCA 61.345 61.111 0.00 0.00 46.04 3.58
958 1036 0.041839 CTTCTCTTGTGTGCACGCAC 60.042 55.000 31.59 16.27 46.33 5.34
959 1037 1.159713 CCTTCTCTTGTGTGCACGCA 61.160 55.000 28.44 28.44 34.11 5.24
960 1038 0.880278 TCCTTCTCTTGTGTGCACGC 60.880 55.000 23.40 23.40 0.00 5.34
985 1258 0.458889 GCCATTACCGTGACACGCTA 60.459 55.000 22.46 10.72 40.91 4.26
992 1265 0.390603 CTGGAACGCCATTACCGTGA 60.391 55.000 0.00 0.00 44.91 4.35
1038 1311 1.227409 TGGAGCGACGAACAAGCAA 60.227 52.632 0.00 0.00 0.00 3.91
1047 1320 2.579787 GACGATGGTGGAGCGACG 60.580 66.667 0.00 0.00 36.78 5.12
1140 1413 1.592400 CTGGCGGAGGTTCGTACTCA 61.592 60.000 0.00 0.00 36.70 3.41
1194 1467 3.612247 CTCCCACAGCCGGAACCAG 62.612 68.421 5.05 0.00 0.00 4.00
1223 1496 2.530151 TGGGGTCCTCTTGCAGCT 60.530 61.111 0.00 0.00 0.00 4.24
1240 1513 2.915604 ACACATTCCTGATCAAGAGGGT 59.084 45.455 0.00 0.00 0.00 4.34
1401 1912 3.005539 TCCACCAGGAGCCTGAGC 61.006 66.667 17.88 0.00 46.30 4.26
1571 2082 2.029288 CACATGTTGAGCGGCGAGT 61.029 57.895 12.98 0.00 0.00 4.18
1753 2264 2.100631 GGAACTCCGGCATGTCGTG 61.101 63.158 19.75 13.29 0.00 4.35
1785 2296 1.658686 CCACCTCGTCCTCGGAGAAG 61.659 65.000 6.58 0.00 34.09 2.85
1827 2338 3.846405 AAGGCTGAGGGTCACCGGA 62.846 63.158 9.46 0.00 43.47 5.14
1893 2404 0.249398 ACACCAGCTTATCCACGGTC 59.751 55.000 0.00 0.00 0.00 4.79
1903 2414 1.071471 CGTCCCAGAACACCAGCTT 59.929 57.895 0.00 0.00 0.00 3.74
1937 2448 1.598701 GCCATTCACCAACTGAGGCC 61.599 60.000 0.00 0.00 35.17 5.19
2041 2552 3.005367 GTCGTGTTGGGGATCAAAATTGT 59.995 43.478 0.00 0.00 37.08 2.71
2143 2663 4.778534 AGTATGCTGCCATGATAAATGC 57.221 40.909 0.00 0.00 32.85 3.56
2165 2694 6.832520 ATGCATAAGTCACATAACCAACAA 57.167 33.333 0.00 0.00 0.00 2.83
2203 2734 7.060421 AGTAAAATGGACTTCTTCCTTTGACA 58.940 34.615 0.00 0.00 46.10 3.58
2204 2735 7.511959 AGTAAAATGGACTTCTTCCTTTGAC 57.488 36.000 0.00 0.00 46.10 3.18
2277 2809 1.398390 GTCACATCGTCCTGCCAAATC 59.602 52.381 0.00 0.00 0.00 2.17
2289 2821 3.607422 TTTGCTCACTTTGTCACATCG 57.393 42.857 0.00 0.00 0.00 3.84
2369 2901 7.336427 ACGGATAGAGTAGTGTATAATGGTAGC 59.664 40.741 0.00 0.00 0.00 3.58
2381 2913 6.591750 ATTATTGGGACGGATAGAGTAGTG 57.408 41.667 0.00 0.00 0.00 2.74
2382 2914 8.716674 TTTATTATTGGGACGGATAGAGTAGT 57.283 34.615 0.00 0.00 0.00 2.73
2383 2915 9.587772 CATTTATTATTGGGACGGATAGAGTAG 57.412 37.037 0.00 0.00 0.00 2.57
2384 2916 9.316594 TCATTTATTATTGGGACGGATAGAGTA 57.683 33.333 0.00 0.00 0.00 2.59
2385 2917 8.095169 GTCATTTATTATTGGGACGGATAGAGT 58.905 37.037 0.00 0.00 0.00 3.24
2386 2918 8.314751 AGTCATTTATTATTGGGACGGATAGAG 58.685 37.037 0.00 0.00 0.00 2.43
2387 2919 8.202461 AGTCATTTATTATTGGGACGGATAGA 57.798 34.615 0.00 0.00 0.00 1.98
2388 2920 7.275779 CGAGTCATTTATTATTGGGACGGATAG 59.724 40.741 0.00 0.00 0.00 2.08
2389 2921 7.039574 TCGAGTCATTTATTATTGGGACGGATA 60.040 37.037 0.00 0.00 0.00 2.59
2390 2922 5.932303 CGAGTCATTTATTATTGGGACGGAT 59.068 40.000 0.00 0.00 0.00 4.18
2391 2923 5.069383 TCGAGTCATTTATTATTGGGACGGA 59.931 40.000 0.00 0.00 0.00 4.69
2392 2924 5.176958 GTCGAGTCATTTATTATTGGGACGG 59.823 44.000 0.00 0.00 0.00 4.79
2393 2925 5.983720 AGTCGAGTCATTTATTATTGGGACG 59.016 40.000 0.00 0.00 0.00 4.79
2394 2926 7.787725 AAGTCGAGTCATTTATTATTGGGAC 57.212 36.000 0.00 0.00 0.00 4.46
2407 2939 9.449719 ACCAAATTTAAGATAAAGTCGAGTCAT 57.550 29.630 0.00 0.00 0.00 3.06
2408 2940 8.717821 CACCAAATTTAAGATAAAGTCGAGTCA 58.282 33.333 0.00 0.00 0.00 3.41
2409 2941 8.718734 ACACCAAATTTAAGATAAAGTCGAGTC 58.281 33.333 0.00 0.00 0.00 3.36
2410 2942 8.617290 ACACCAAATTTAAGATAAAGTCGAGT 57.383 30.769 0.00 0.00 0.00 4.18
2412 2944 9.715121 ACTACACCAAATTTAAGATAAAGTCGA 57.285 29.630 0.00 0.00 0.00 4.20
2428 2960 9.768662 CCTTAACTTTCTACTAACTACACCAAA 57.231 33.333 0.00 0.00 0.00 3.28
2429 2961 8.370182 CCCTTAACTTTCTACTAACTACACCAA 58.630 37.037 0.00 0.00 0.00 3.67
2430 2962 7.729881 TCCCTTAACTTTCTACTAACTACACCA 59.270 37.037 0.00 0.00 0.00 4.17
2431 2963 8.127150 TCCCTTAACTTTCTACTAACTACACC 57.873 38.462 0.00 0.00 0.00 4.16
2432 2964 9.583765 CATCCCTTAACTTTCTACTAACTACAC 57.416 37.037 0.00 0.00 0.00 2.90
2433 2965 8.255905 GCATCCCTTAACTTTCTACTAACTACA 58.744 37.037 0.00 0.00 0.00 2.74
2434 2966 7.434602 CGCATCCCTTAACTTTCTACTAACTAC 59.565 40.741 0.00 0.00 0.00 2.73
2435 2967 7.340232 TCGCATCCCTTAACTTTCTACTAACTA 59.660 37.037 0.00 0.00 0.00 2.24
2436 2968 6.154021 TCGCATCCCTTAACTTTCTACTAACT 59.846 38.462 0.00 0.00 0.00 2.24
2437 2969 6.335777 TCGCATCCCTTAACTTTCTACTAAC 58.664 40.000 0.00 0.00 0.00 2.34
2438 2970 6.534475 TCGCATCCCTTAACTTTCTACTAA 57.466 37.500 0.00 0.00 0.00 2.24
2439 2971 6.534475 TTCGCATCCCTTAACTTTCTACTA 57.466 37.500 0.00 0.00 0.00 1.82
2440 2972 5.416271 TTCGCATCCCTTAACTTTCTACT 57.584 39.130 0.00 0.00 0.00 2.57
2441 2973 6.679327 AATTCGCATCCCTTAACTTTCTAC 57.321 37.500 0.00 0.00 0.00 2.59
2442 2974 7.392113 TGAAAATTCGCATCCCTTAACTTTCTA 59.608 33.333 0.00 0.00 0.00 2.10
2443 2975 6.208599 TGAAAATTCGCATCCCTTAACTTTCT 59.791 34.615 0.00 0.00 0.00 2.52
2444 2976 6.386654 TGAAAATTCGCATCCCTTAACTTTC 58.613 36.000 0.00 0.00 0.00 2.62
2445 2977 6.339587 TGAAAATTCGCATCCCTTAACTTT 57.660 33.333 0.00 0.00 0.00 2.66
2446 2978 5.105756 CCTGAAAATTCGCATCCCTTAACTT 60.106 40.000 0.00 0.00 0.00 2.66
2447 2979 4.399303 CCTGAAAATTCGCATCCCTTAACT 59.601 41.667 0.00 0.00 0.00 2.24
2448 2980 4.398044 TCCTGAAAATTCGCATCCCTTAAC 59.602 41.667 0.00 0.00 0.00 2.01
2449 2981 4.398044 GTCCTGAAAATTCGCATCCCTTAA 59.602 41.667 0.00 0.00 0.00 1.85
2450 2982 3.945285 GTCCTGAAAATTCGCATCCCTTA 59.055 43.478 0.00 0.00 0.00 2.69
2451 2983 2.755103 GTCCTGAAAATTCGCATCCCTT 59.245 45.455 0.00 0.00 0.00 3.95
2485 3017 2.585869 CGCTCGCGATTACGGCATT 61.586 57.895 10.36 0.00 42.83 3.56
2586 3119 0.913924 CACAAAGGGGTATACGGGGT 59.086 55.000 0.00 0.00 0.00 4.95
2867 3612 4.389374 TGATGCGATAATCCTCCTTTTCC 58.611 43.478 0.00 0.00 0.00 3.13
2944 3690 2.276201 CCCAAATTCGTCGACATGCTA 58.724 47.619 17.16 0.00 0.00 3.49
2945 3691 1.086696 CCCAAATTCGTCGACATGCT 58.913 50.000 17.16 0.00 0.00 3.79
2946 3692 0.098728 CCCCAAATTCGTCGACATGC 59.901 55.000 17.16 0.00 0.00 4.06
2947 3693 1.396996 GACCCCAAATTCGTCGACATG 59.603 52.381 17.16 5.91 0.00 3.21
2948 3694 1.002659 TGACCCCAAATTCGTCGACAT 59.997 47.619 17.16 0.00 0.00 3.06
2949 3695 0.393448 TGACCCCAAATTCGTCGACA 59.607 50.000 17.16 0.00 0.00 4.35
3029 3775 2.038033 TCCCCGACTCGTTCTCAAAAAT 59.962 45.455 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.