Multiple sequence alignment - TraesCS6D01G204900

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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 TraesCS6D01G204900 chr6D 100.000 2128 0 0 1 2128 290820956 290823083 0.000000e+00 3930.0
1 TraesCS6D01G204900 chr6D 99.103 2006 18 0 1 2006 377841380 377843385 0.000000e+00 3605.0
2 TraesCS6D01G204900 chr6D 100.000 310 0 0 2494 2803 290823449 290823758 8.710000e-160 573.0
3 TraesCS6D01G204900 chr6D 96.053 228 9 0 2533 2760 377840632 377840405 3.410000e-99 372.0
4 TraesCS6D01G204900 chr6D 96.018 226 7 2 2534 2759 114247930 114248153 1.590000e-97 366.0
5 TraesCS6D01G204900 chr6D 88.321 274 16 2 2494 2751 39716419 39716692 5.830000e-82 315.0
6 TraesCS6D01G204900 chr6D 91.743 218 18 0 2533 2750 443765678 443765895 1.260000e-78 303.0
7 TraesCS6D01G204900 chr6D 85.921 277 16 10 2494 2750 162228465 162228738 9.890000e-70 274.0
8 TraesCS6D01G204900 chr6D 99.200 125 1 0 2004 2128 439652195 439652319 2.810000e-55 226.0
9 TraesCS6D01G204900 chr6D 100.000 38 0 0 2494 2531 146436126 146436163 1.390000e-08 71.3
10 TraesCS6D01G204900 chr7D 99.352 2006 13 0 1 2006 415420578 415418573 0.000000e+00 3633.0
11 TraesCS6D01G204900 chr7D 99.153 2006 17 0 1 2006 235491248 235489243 0.000000e+00 3611.0
12 TraesCS6D01G204900 chr7D 98.754 2006 25 0 1 2006 95118308 95120313 0.000000e+00 3567.0
13 TraesCS6D01G204900 chr7D 98.643 221 3 0 2533 2753 235491990 235492210 2.620000e-105 392.0
14 TraesCS6D01G204900 chr7D 99.200 125 1 0 2004 2128 136945954 136945830 2.810000e-55 226.0
15 TraesCS6D01G204900 chr5D 99.252 2006 15 0 1 2006 64244188 64246193 0.000000e+00 3622.0
16 TraesCS6D01G204900 chr5D 99.003 2006 20 0 1 2006 324258169 324256164 0.000000e+00 3594.0
17 TraesCS6D01G204900 chr5D 98.630 219 3 0 2533 2751 64243447 64243229 3.390000e-104 388.0
18 TraesCS6D01G204900 chr5D 99.200 125 1 0 2004 2128 11805909 11806033 2.810000e-55 226.0
19 TraesCS6D01G204900 chr5D 99.200 125 1 0 2004 2128 324254790 324254666 2.810000e-55 226.0
20 TraesCS6D01G204900 chr3D 99.102 2004 18 0 1 2004 49761679 49763682 0.000000e+00 3602.0
21 TraesCS6D01G204900 chr3D 98.804 2006 24 0 1 2006 10366988 10368993 0.000000e+00 3572.0
22 TraesCS6D01G204900 chr3D 98.174 219 4 0 2533 2751 471820726 471820944 1.580000e-102 383.0
23 TraesCS6D01G204900 chr3D 99.200 125 1 0 2004 2128 10375464 10375588 2.810000e-55 226.0
24 TraesCS6D01G204900 chr3D 99.200 125 1 0 2004 2128 50069318 50069442 2.810000e-55 226.0
25 TraesCS6D01G204900 chr2D 99.053 2006 19 0 1 2006 8624801 8626806 0.000000e+00 3600.0
26 TraesCS6D01G204900 chr2D 97.727 220 5 0 2533 2752 50057242 50057461 2.040000e-101 379.0
27 TraesCS6D01G204900 chr1D 95.455 242 10 1 2510 2750 138060357 138060116 4.380000e-103 385.0
28 TraesCS6D01G204900 chr1D 97.717 219 5 0 2533 2751 138067471 138067689 7.330000e-101 377.0
29 TraesCS6D01G204900 chr1D 97.717 219 5 0 2533 2751 201296657 201296439 7.330000e-101 377.0
30 TraesCS6D01G204900 chr1D 99.200 125 1 0 2004 2128 20988617 20988741 2.810000e-55 226.0
31 TraesCS6D01G204900 chr4D 88.278 273 16 2 2494 2750 30211858 30212130 2.100000e-81 313.0
32 TraesCS6D01G204900 chr4D 99.200 125 1 0 2004 2128 30211688 30211812 2.810000e-55 226.0
33 TraesCS6D01G204900 chr4D 100.000 38 0 0 2494 2531 189690473 189690510 1.390000e-08 71.3
34 TraesCS6D01G204900 chr4D 100.000 38 0 0 2494 2531 310380052 310380015 1.390000e-08 71.3
35 TraesCS6D01G204900 chr4D 93.478 46 3 0 2494 2539 401519381 401519336 5.010000e-08 69.4
36 TraesCS6D01G204900 chrUn 99.200 125 1 0 2004 2128 255032180 255032056 2.810000e-55 226.0
37 TraesCS6D01G204900 chr6B 98.039 51 0 1 2748 2797 451480883 451480933 1.380000e-13 87.9
38 TraesCS6D01G204900 chr6A 96.078 51 1 1 2748 2797 432877010 432876960 6.440000e-12 82.4


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 TraesCS6D01G204900 chr6D 290820956 290823758 2802 False 2251.5 3930 100.0000 1 2803 2 chr6D.!!$F8 2802
1 TraesCS6D01G204900 chr6D 377841380 377843385 2005 False 3605.0 3605 99.1030 1 2006 1 chr6D.!!$F5 2005
2 TraesCS6D01G204900 chr7D 415418573 415420578 2005 True 3633.0 3633 99.3520 1 2006 1 chr7D.!!$R3 2005
3 TraesCS6D01G204900 chr7D 235489243 235491248 2005 True 3611.0 3611 99.1530 1 2006 1 chr7D.!!$R2 2005
4 TraesCS6D01G204900 chr7D 95118308 95120313 2005 False 3567.0 3567 98.7540 1 2006 1 chr7D.!!$F1 2005
5 TraesCS6D01G204900 chr5D 64244188 64246193 2005 False 3622.0 3622 99.2520 1 2006 1 chr5D.!!$F2 2005
6 TraesCS6D01G204900 chr5D 324254666 324258169 3503 True 1910.0 3594 99.1015 1 2128 2 chr5D.!!$R2 2127
7 TraesCS6D01G204900 chr3D 49761679 49763682 2003 False 3602.0 3602 99.1020 1 2004 1 chr3D.!!$F3 2003
8 TraesCS6D01G204900 chr3D 10366988 10368993 2005 False 3572.0 3572 98.8040 1 2006 1 chr3D.!!$F1 2005
9 TraesCS6D01G204900 chr2D 8624801 8626806 2005 False 3600.0 3600 99.0530 1 2006 1 chr2D.!!$F1 2005

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
1086 1087 8.508875 TGCATAAGTGATTATCATGCTTGTATG 58.491 33.333 16.27 10.18 41.94 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 1983 0.039617 GGCGCTGCAACATGTACAAA 60.04 50.0 7.64 0.0 0.0 2.83 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
1086 1087 8.508875 TGCATAAGTGATTATCATGCTTGTATG 58.491 33.333 16.27 10.18 41.94 2.39
1155 1156 1.209747 GGAGCCGTATGGAAAAGGAGT 59.790 52.381 4.73 0.00 37.49 3.85
1345 1346 2.413837 GACACGGACAAGTTGCTACAT 58.586 47.619 1.81 0.00 0.00 2.29
1542 1543 0.467290 TGGAAAACGAGCCCAGCTTT 60.467 50.000 0.00 0.00 39.88 3.51
1982 1983 4.081142 TGGTACGTTCCATGTCTCATTCAT 60.081 41.667 10.19 0.00 31.96 2.57
2052 3429 2.803956 GGTTTGACTTCGAAATCCACGA 59.196 45.455 3.88 0.00 37.99 4.35
2514 3891 2.768253 TGGCTGGATAAGTCACAGTG 57.232 50.000 0.00 0.00 34.88 3.66
2515 3892 1.339055 TGGCTGGATAAGTCACAGTGC 60.339 52.381 0.00 0.00 34.88 4.40
2516 3893 1.339055 GGCTGGATAAGTCACAGTGCA 60.339 52.381 0.00 0.00 34.79 4.57
2517 3894 2.005451 GCTGGATAAGTCACAGTGCAG 58.995 52.381 0.00 0.00 34.79 4.41
2518 3895 2.005451 CTGGATAAGTCACAGTGCAGC 58.995 52.381 0.00 0.00 0.00 5.25
2519 3896 1.002366 GGATAAGTCACAGTGCAGCG 58.998 55.000 0.00 0.00 0.00 5.18
2520 3897 0.371645 GATAAGTCACAGTGCAGCGC 59.628 55.000 0.00 0.00 0.00 5.92
2521 3898 1.021390 ATAAGTCACAGTGCAGCGCC 61.021 55.000 2.29 0.00 0.00 6.53
2522 3899 2.099652 TAAGTCACAGTGCAGCGCCT 62.100 55.000 2.29 0.00 0.00 5.52
2523 3900 2.048222 GTCACAGTGCAGCGCCTA 60.048 61.111 2.29 0.00 0.00 3.93
2524 3901 2.097038 GTCACAGTGCAGCGCCTAG 61.097 63.158 2.29 0.00 0.00 3.02
2537 3914 4.350620 CCTAGCGGCTATGTGCAG 57.649 61.111 10.62 0.00 45.15 4.41
2543 3920 2.108976 GGCTATGTGCAGCGCCTA 59.891 61.111 2.29 0.00 45.15 3.93
2544 3921 1.523711 GGCTATGTGCAGCGCCTAA 60.524 57.895 2.29 0.00 45.15 2.69
2545 3922 1.643832 GCTATGTGCAGCGCCTAAC 59.356 57.895 2.29 0.00 42.31 2.34
2546 3923 0.811616 GCTATGTGCAGCGCCTAACT 60.812 55.000 2.29 0.00 42.31 2.24
2547 3924 1.212616 CTATGTGCAGCGCCTAACTC 58.787 55.000 2.29 0.00 0.00 3.01
2548 3925 0.527600 TATGTGCAGCGCCTAACTCG 60.528 55.000 2.29 0.00 0.00 4.18
2549 3926 3.188786 GTGCAGCGCCTAACTCGG 61.189 66.667 2.29 0.00 0.00 4.63
2550 3927 3.378602 TGCAGCGCCTAACTCGGA 61.379 61.111 2.29 0.00 0.00 4.55
2551 3928 2.583593 GCAGCGCCTAACTCGGAG 60.584 66.667 2.29 2.83 0.00 4.63
2552 3929 2.105128 CAGCGCCTAACTCGGAGG 59.895 66.667 2.29 0.00 37.12 4.30
2557 3934 4.496670 CCTAACTCGGAGGCGTTG 57.503 61.111 10.23 0.00 0.00 4.10
2558 3935 1.810030 CCTAACTCGGAGGCGTTGC 60.810 63.158 10.23 0.00 0.00 4.17
2559 3936 1.080093 CTAACTCGGAGGCGTTGCA 60.080 57.895 10.23 0.00 0.00 4.08
2560 3937 1.352156 CTAACTCGGAGGCGTTGCAC 61.352 60.000 10.23 0.00 0.00 4.57
2561 3938 1.812686 TAACTCGGAGGCGTTGCACT 61.813 55.000 10.23 0.00 0.00 4.40
2562 3939 3.114616 CTCGGAGGCGTTGCACTG 61.115 66.667 0.00 0.00 0.00 3.66
2565 3942 3.730761 GGAGGCGTTGCACTGCTG 61.731 66.667 9.04 0.00 0.00 4.41
2566 3943 3.730761 GAGGCGTTGCACTGCTGG 61.731 66.667 9.04 0.00 0.00 4.85
2569 3946 4.332637 GCGTTGCACTGCTGGGTG 62.333 66.667 1.98 0.00 39.91 4.61
2598 3975 4.626081 GCTGCCACGGTGGACACT 62.626 66.667 30.65 0.00 40.96 3.55
2599 3976 2.666190 CTGCCACGGTGGACACTG 60.666 66.667 30.65 12.73 40.96 3.66
2600 3977 4.248842 TGCCACGGTGGACACTGG 62.249 66.667 30.65 10.57 40.96 4.00
2601 3978 4.250305 GCCACGGTGGACACTGGT 62.250 66.667 30.65 5.27 40.96 4.00
2602 3979 2.280797 CCACGGTGGACACTGGTG 60.281 66.667 22.77 15.24 40.96 4.17
2603 3980 2.972505 CACGGTGGACACTGGTGC 60.973 66.667 15.11 0.00 41.89 5.01
2604 3981 3.475494 ACGGTGGACACTGGTGCA 61.475 61.111 15.11 0.00 43.61 4.57
2608 3985 2.899838 TGGACACTGGTGCAACGC 60.900 61.111 0.00 0.00 42.81 4.84
2609 3986 3.660111 GGACACTGGTGCAACGCC 61.660 66.667 0.00 0.00 38.12 5.68
2610 3987 3.660111 GACACTGGTGCAACGCCC 61.660 66.667 0.00 0.00 38.12 6.13
2620 3997 4.530857 CAACGCCCCGGAGCTAGG 62.531 72.222 6.33 0.00 0.00 3.02
2632 4009 4.508128 GCTAGGCGCTGCACCGTA 62.508 66.667 7.64 0.00 35.14 4.02
2633 4010 2.278857 CTAGGCGCTGCACCGTAG 60.279 66.667 7.64 2.34 0.00 3.51
2666 4043 4.627801 TGGCGGGCGCTACACAAA 62.628 61.111 7.64 0.00 41.60 2.83
2667 4044 3.358707 GGCGGGCGCTACACAAAA 61.359 61.111 7.64 0.00 41.60 2.44
2668 4045 2.175811 GCGGGCGCTACACAAAAG 59.824 61.111 7.64 0.00 38.26 2.27
2669 4046 2.867472 CGGGCGCTACACAAAAGG 59.133 61.111 7.64 0.00 0.00 3.11
2670 4047 2.686816 CGGGCGCTACACAAAAGGG 61.687 63.158 7.64 0.00 0.00 3.95
2671 4048 1.602605 GGGCGCTACACAAAAGGGT 60.603 57.895 7.64 0.00 0.00 4.34
2672 4049 1.583495 GGGCGCTACACAAAAGGGTC 61.583 60.000 7.64 0.00 0.00 4.46
2673 4050 0.887387 GGCGCTACACAAAAGGGTCA 60.887 55.000 7.64 0.00 32.25 4.02
2674 4051 0.517316 GCGCTACACAAAAGGGTCAG 59.483 55.000 0.00 0.00 0.00 3.51
2675 4052 1.156736 CGCTACACAAAAGGGTCAGG 58.843 55.000 0.00 0.00 0.00 3.86
2676 4053 1.534729 GCTACACAAAAGGGTCAGGG 58.465 55.000 0.00 0.00 0.00 4.45
2677 4054 1.886655 GCTACACAAAAGGGTCAGGGG 60.887 57.143 0.00 0.00 0.00 4.79
2678 4055 1.423921 CTACACAAAAGGGTCAGGGGT 59.576 52.381 0.00 0.00 0.00 4.95
2679 4056 0.106217 ACACAAAAGGGTCAGGGGTG 60.106 55.000 0.00 0.00 0.00 4.61
2680 4057 0.106217 CACAAAAGGGTCAGGGGTGT 60.106 55.000 0.00 0.00 0.00 4.16
2681 4058 0.106217 ACAAAAGGGTCAGGGGTGTG 60.106 55.000 0.00 0.00 0.00 3.82
2682 4059 0.184933 CAAAAGGGTCAGGGGTGTGA 59.815 55.000 0.00 0.00 0.00 3.58
2683 4060 0.930726 AAAAGGGTCAGGGGTGTGAA 59.069 50.000 0.00 0.00 0.00 3.18
2684 4061 0.930726 AAAGGGTCAGGGGTGTGAAA 59.069 50.000 0.00 0.00 0.00 2.69
2685 4062 1.158007 AAGGGTCAGGGGTGTGAAAT 58.842 50.000 0.00 0.00 0.00 2.17
2686 4063 2.053747 AGGGTCAGGGGTGTGAAATA 57.946 50.000 0.00 0.00 0.00 1.40
2687 4064 1.916181 AGGGTCAGGGGTGTGAAATAG 59.084 52.381 0.00 0.00 0.00 1.73
2688 4065 1.633945 GGGTCAGGGGTGTGAAATAGT 59.366 52.381 0.00 0.00 0.00 2.12
2689 4066 2.041216 GGGTCAGGGGTGTGAAATAGTT 59.959 50.000 0.00 0.00 0.00 2.24
2690 4067 3.264964 GGGTCAGGGGTGTGAAATAGTTA 59.735 47.826 0.00 0.00 0.00 2.24
2691 4068 4.259356 GGTCAGGGGTGTGAAATAGTTAC 58.741 47.826 0.00 0.00 0.00 2.50
2692 4069 3.930848 GTCAGGGGTGTGAAATAGTTACG 59.069 47.826 0.00 0.00 0.00 3.18
2693 4070 3.055675 TCAGGGGTGTGAAATAGTTACGG 60.056 47.826 0.00 0.00 0.00 4.02
2694 4071 3.055675 CAGGGGTGTGAAATAGTTACGGA 60.056 47.826 0.00 0.00 0.00 4.69
2695 4072 3.583966 AGGGGTGTGAAATAGTTACGGAA 59.416 43.478 0.00 0.00 0.00 4.30
2696 4073 3.686241 GGGGTGTGAAATAGTTACGGAAC 59.314 47.826 0.95 0.95 35.64 3.62
2697 4074 3.686241 GGGTGTGAAATAGTTACGGAACC 59.314 47.826 6.97 0.00 36.08 3.62
2698 4075 4.317488 GGTGTGAAATAGTTACGGAACCA 58.683 43.478 6.97 0.00 36.08 3.67
2699 4076 4.390909 GGTGTGAAATAGTTACGGAACCAG 59.609 45.833 6.97 0.00 36.08 4.00
2700 4077 4.992951 GTGTGAAATAGTTACGGAACCAGT 59.007 41.667 6.97 0.00 36.08 4.00
2701 4078 5.467735 GTGTGAAATAGTTACGGAACCAGTT 59.532 40.000 6.97 0.00 36.08 3.16
2702 4079 5.697633 TGTGAAATAGTTACGGAACCAGTTC 59.302 40.000 11.46 11.46 33.62 3.01
2703 4080 5.697633 GTGAAATAGTTACGGAACCAGTTCA 59.302 40.000 16.10 16.10 38.39 3.18
2704 4081 6.370718 GTGAAATAGTTACGGAACCAGTTCAT 59.629 38.462 21.39 0.00 41.15 2.57
2705 4082 6.938030 TGAAATAGTTACGGAACCAGTTCATT 59.062 34.615 16.10 1.13 36.70 2.57
2706 4083 6.980051 AATAGTTACGGAACCAGTTCATTC 57.020 37.500 6.97 0.00 41.20 2.67
2707 4084 4.618920 AGTTACGGAACCAGTTCATTCT 57.381 40.909 6.97 1.31 41.20 2.40
2708 4085 4.315803 AGTTACGGAACCAGTTCATTCTG 58.684 43.478 6.97 0.00 41.20 3.02
2709 4086 2.930826 ACGGAACCAGTTCATTCTGT 57.069 45.000 12.32 0.00 41.20 3.41
2710 4087 2.494059 ACGGAACCAGTTCATTCTGTG 58.506 47.619 12.32 0.00 41.76 3.66
2711 4088 2.104111 ACGGAACCAGTTCATTCTGTGA 59.896 45.455 12.32 0.00 41.76 3.58
2712 4089 3.244561 ACGGAACCAGTTCATTCTGTGAT 60.245 43.478 12.32 0.00 41.76 3.06
2713 4090 3.753272 CGGAACCAGTTCATTCTGTGATT 59.247 43.478 12.32 0.00 41.20 2.57
2714 4091 4.216257 CGGAACCAGTTCATTCTGTGATTT 59.784 41.667 12.32 0.00 41.20 2.17
2715 4092 5.464168 GGAACCAGTTCATTCTGTGATTTG 58.536 41.667 12.32 0.00 41.20 2.32
2716 4093 5.241506 GGAACCAGTTCATTCTGTGATTTGA 59.758 40.000 12.32 0.00 41.20 2.69
2717 4094 6.071728 GGAACCAGTTCATTCTGTGATTTGAT 60.072 38.462 12.32 0.00 41.20 2.57
2718 4095 6.906157 ACCAGTTCATTCTGTGATTTGATT 57.094 33.333 0.00 0.00 36.54 2.57
2719 4096 7.294017 ACCAGTTCATTCTGTGATTTGATTT 57.706 32.000 0.00 0.00 36.54 2.17
2720 4097 7.373493 ACCAGTTCATTCTGTGATTTGATTTC 58.627 34.615 0.00 0.00 36.54 2.17
2721 4098 6.525628 CCAGTTCATTCTGTGATTTGATTTCG 59.474 38.462 0.00 0.00 36.54 3.46
2722 4099 7.300320 CAGTTCATTCTGTGATTTGATTTCGA 58.700 34.615 0.00 0.00 36.54 3.71
2723 4100 7.966753 CAGTTCATTCTGTGATTTGATTTCGAT 59.033 33.333 0.00 0.00 36.54 3.59
2724 4101 8.517878 AGTTCATTCTGTGATTTGATTTCGATT 58.482 29.630 0.00 0.00 36.54 3.34
2725 4102 9.773328 GTTCATTCTGTGATTTGATTTCGATTA 57.227 29.630 0.00 0.00 36.54 1.75
2730 4107 9.613428 TTCTGTGATTTGATTTCGATTATAGGT 57.387 29.630 0.00 0.00 0.00 3.08
2731 4108 9.261180 TCTGTGATTTGATTTCGATTATAGGTC 57.739 33.333 0.00 0.00 0.00 3.85
2732 4109 8.956533 TGTGATTTGATTTCGATTATAGGTCA 57.043 30.769 0.00 0.00 0.00 4.02
2733 4110 9.389755 TGTGATTTGATTTCGATTATAGGTCAA 57.610 29.630 0.00 0.00 0.00 3.18
2754 4131 5.655893 AAATTTGTCAAATTTGCCGTCAG 57.344 34.783 27.61 0.00 46.30 3.51
2755 4132 4.582701 ATTTGTCAAATTTGCCGTCAGA 57.417 36.364 13.54 5.92 0.00 3.27
2756 4133 3.624326 TTGTCAAATTTGCCGTCAGAG 57.376 42.857 13.54 0.00 0.00 3.35
2757 4134 1.879380 TGTCAAATTTGCCGTCAGAGG 59.121 47.619 13.54 0.00 0.00 3.69
2776 4153 0.382515 GCTACAGCCTACAGGAGTCG 59.617 60.000 0.00 0.00 37.39 4.18
2777 4154 1.752683 CTACAGCCTACAGGAGTCGT 58.247 55.000 0.00 0.00 37.39 4.34
2778 4155 2.093106 CTACAGCCTACAGGAGTCGTT 58.907 52.381 0.00 0.00 37.39 3.85
2779 4156 0.889306 ACAGCCTACAGGAGTCGTTC 59.111 55.000 0.00 0.00 37.39 3.95
2780 4157 1.178276 CAGCCTACAGGAGTCGTTCT 58.822 55.000 0.00 0.00 37.39 3.01
2781 4158 1.133407 CAGCCTACAGGAGTCGTTCTC 59.867 57.143 0.00 2.71 42.07 2.87
2790 4167 3.198582 GTCGTTCTCCGGCTAGCT 58.801 61.111 15.72 0.00 38.41 3.32
2791 4168 2.401967 GTCGTTCTCCGGCTAGCTA 58.598 57.895 15.72 0.00 38.41 3.32
2792 4169 0.308376 GTCGTTCTCCGGCTAGCTAG 59.692 60.000 16.84 16.84 38.41 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
658 659 2.311542 ACCCCAACTCCATTTGCTATCA 59.688 45.455 0.00 0.00 0.00 2.15
1086 1087 7.697710 TCAATGCAAAATTGATATCGAGTGAAC 59.302 33.333 0.00 0.00 33.55 3.18
1155 1156 7.236019 TGAACTCTATAGGGTTACCAAAACTCA 59.764 37.037 18.07 5.98 40.13 3.41
1345 1346 7.929245 TGCTCAAGGTTAATTATATCTTACGCA 59.071 33.333 0.00 0.63 0.00 5.24
1542 1543 3.321648 ATCCGGGCAGTGCTCACA 61.322 61.111 16.85 0.00 0.00 3.58
1982 1983 0.039617 GGCGCTGCAACATGTACAAA 60.040 50.000 7.64 0.00 0.00 2.83
2493 3870 2.027745 CACTGTGACTTATCCAGCCACT 60.028 50.000 0.32 0.00 30.41 4.00
2494 3871 2.350522 CACTGTGACTTATCCAGCCAC 58.649 52.381 0.32 0.00 30.41 5.01
2495 3872 1.339055 GCACTGTGACTTATCCAGCCA 60.339 52.381 12.86 0.00 30.41 4.75
2496 3873 1.339055 TGCACTGTGACTTATCCAGCC 60.339 52.381 12.86 0.00 30.41 4.85
2497 3874 2.005451 CTGCACTGTGACTTATCCAGC 58.995 52.381 12.86 0.00 30.41 4.85
2498 3875 2.005451 GCTGCACTGTGACTTATCCAG 58.995 52.381 12.86 8.32 32.42 3.86
2499 3876 1.672737 CGCTGCACTGTGACTTATCCA 60.673 52.381 12.86 0.00 0.00 3.41
2500 3877 1.002366 CGCTGCACTGTGACTTATCC 58.998 55.000 12.86 0.00 0.00 2.59
2501 3878 0.371645 GCGCTGCACTGTGACTTATC 59.628 55.000 12.86 0.00 0.00 1.75
2502 3879 1.021390 GGCGCTGCACTGTGACTTAT 61.021 55.000 12.86 0.00 0.00 1.73
2503 3880 1.667830 GGCGCTGCACTGTGACTTA 60.668 57.895 12.86 0.00 0.00 2.24
2504 3881 2.099652 TAGGCGCTGCACTGTGACTT 62.100 55.000 12.86 0.00 37.04 3.01
2505 3882 2.498291 CTAGGCGCTGCACTGTGACT 62.498 60.000 12.86 0.10 39.42 3.41
2506 3883 2.048222 TAGGCGCTGCACTGTGAC 60.048 61.111 12.86 3.63 0.00 3.67
2507 3884 2.262603 CTAGGCGCTGCACTGTGA 59.737 61.111 12.86 0.00 0.00 3.58
2508 3885 3.494336 GCTAGGCGCTGCACTGTG 61.494 66.667 7.64 2.76 35.14 3.66
2520 3897 4.350620 CTGCACATAGCCGCTAGG 57.649 61.111 10.47 10.47 44.83 3.02
2527 3904 0.811616 AGTTAGGCGCTGCACATAGC 60.812 55.000 7.64 0.00 45.96 2.97
2528 3905 1.212616 GAGTTAGGCGCTGCACATAG 58.787 55.000 7.64 0.00 0.00 2.23
2529 3906 0.527600 CGAGTTAGGCGCTGCACATA 60.528 55.000 7.64 0.00 0.00 2.29
2530 3907 1.811266 CGAGTTAGGCGCTGCACAT 60.811 57.895 7.64 0.00 0.00 3.21
2531 3908 2.432456 CGAGTTAGGCGCTGCACA 60.432 61.111 7.64 0.00 0.00 4.57
2532 3909 3.188786 CCGAGTTAGGCGCTGCAC 61.189 66.667 7.64 0.76 0.00 4.57
2533 3910 3.356639 CTCCGAGTTAGGCGCTGCA 62.357 63.158 7.64 0.00 0.00 4.41
2534 3911 2.583593 CTCCGAGTTAGGCGCTGC 60.584 66.667 7.64 0.00 0.00 5.25
2535 3912 2.105128 CCTCCGAGTTAGGCGCTG 59.895 66.667 7.64 0.00 0.00 5.18
2540 3917 1.810030 GCAACGCCTCCGAGTTAGG 60.810 63.158 0.00 0.00 38.29 2.69
2541 3918 1.080093 TGCAACGCCTCCGAGTTAG 60.080 57.895 0.00 0.00 38.29 2.34
2542 3919 1.373748 GTGCAACGCCTCCGAGTTA 60.374 57.895 0.00 0.00 38.29 2.24
2543 3920 2.665185 GTGCAACGCCTCCGAGTT 60.665 61.111 0.00 0.00 38.29 3.01
2544 3921 3.616721 AGTGCAACGCCTCCGAGT 61.617 61.111 0.00 0.00 45.86 4.18
2545 3922 3.114616 CAGTGCAACGCCTCCGAG 61.115 66.667 0.00 0.00 45.86 4.63
2548 3925 3.730761 CAGCAGTGCAACGCCTCC 61.731 66.667 19.20 0.00 45.86 4.30
2549 3926 3.730761 CCAGCAGTGCAACGCCTC 61.731 66.667 19.20 0.00 45.86 4.70
2552 3929 4.332637 CACCCAGCAGTGCAACGC 62.333 66.667 19.20 0.31 45.86 4.84
2581 3958 4.626081 AGTGTCCACCGTGGCAGC 62.626 66.667 13.19 6.22 37.47 5.25
2582 3959 2.666190 CAGTGTCCACCGTGGCAG 60.666 66.667 13.19 0.60 37.47 4.85
2583 3960 4.248842 CCAGTGTCCACCGTGGCA 62.249 66.667 13.19 11.19 37.47 4.92
2584 3961 4.250305 ACCAGTGTCCACCGTGGC 62.250 66.667 13.19 8.69 37.47 5.01
2585 3962 2.280797 CACCAGTGTCCACCGTGG 60.281 66.667 11.73 11.73 39.43 4.94
2586 3963 2.972505 GCACCAGTGTCCACCGTG 60.973 66.667 9.67 9.67 36.03 4.94
2587 3964 3.037686 TTGCACCAGTGTCCACCGT 62.038 57.895 0.00 0.00 0.00 4.83
2588 3965 2.203139 TTGCACCAGTGTCCACCG 60.203 61.111 0.00 0.00 0.00 4.94
2589 3966 2.542907 CGTTGCACCAGTGTCCACC 61.543 63.158 0.00 0.00 0.00 4.61
2590 3967 3.022287 CGTTGCACCAGTGTCCAC 58.978 61.111 0.00 0.00 0.00 4.02
2591 3968 2.899838 GCGTTGCACCAGTGTCCA 60.900 61.111 0.00 0.00 0.00 4.02
2592 3969 3.660111 GGCGTTGCACCAGTGTCC 61.660 66.667 0.00 0.00 0.00 4.02
2593 3970 3.660111 GGGCGTTGCACCAGTGTC 61.660 66.667 0.00 0.00 0.00 3.67
2603 3980 4.530857 CCTAGCTCCGGGGCGTTG 62.531 72.222 23.34 14.92 37.29 4.10
2616 3993 2.278857 CTACGGTGCAGCGCCTAG 60.279 66.667 35.78 25.87 0.00 3.02
2617 3994 3.833645 CCTACGGTGCAGCGCCTA 61.834 66.667 35.78 21.25 0.00 3.93
2649 4026 4.627801 TTTGTGTAGCGCCCGCCA 62.628 61.111 2.29 0.00 43.17 5.69
2650 4027 3.322706 CTTTTGTGTAGCGCCCGCC 62.323 63.158 2.29 0.00 43.17 6.13
2651 4028 2.175811 CTTTTGTGTAGCGCCCGC 59.824 61.111 2.29 4.20 42.33 6.13
2652 4029 2.686816 CCCTTTTGTGTAGCGCCCG 61.687 63.158 2.29 0.00 0.00 6.13
2653 4030 1.583495 GACCCTTTTGTGTAGCGCCC 61.583 60.000 2.29 0.00 0.00 6.13
2654 4031 0.887387 TGACCCTTTTGTGTAGCGCC 60.887 55.000 2.29 0.00 0.00 6.53
2655 4032 0.517316 CTGACCCTTTTGTGTAGCGC 59.483 55.000 0.00 0.00 0.00 5.92
2656 4033 1.156736 CCTGACCCTTTTGTGTAGCG 58.843 55.000 0.00 0.00 0.00 4.26
2657 4034 1.534729 CCCTGACCCTTTTGTGTAGC 58.465 55.000 0.00 0.00 0.00 3.58
2658 4035 1.423921 ACCCCTGACCCTTTTGTGTAG 59.576 52.381 0.00 0.00 0.00 2.74
2659 4036 1.144093 CACCCCTGACCCTTTTGTGTA 59.856 52.381 0.00 0.00 0.00 2.90
2660 4037 0.106217 CACCCCTGACCCTTTTGTGT 60.106 55.000 0.00 0.00 0.00 3.72
2661 4038 0.106217 ACACCCCTGACCCTTTTGTG 60.106 55.000 0.00 0.00 0.00 3.33
2662 4039 0.106217 CACACCCCTGACCCTTTTGT 60.106 55.000 0.00 0.00 0.00 2.83
2663 4040 0.184933 TCACACCCCTGACCCTTTTG 59.815 55.000 0.00 0.00 0.00 2.44
2664 4041 0.930726 TTCACACCCCTGACCCTTTT 59.069 50.000 0.00 0.00 0.00 2.27
2665 4042 0.930726 TTTCACACCCCTGACCCTTT 59.069 50.000 0.00 0.00 0.00 3.11
2666 4043 1.158007 ATTTCACACCCCTGACCCTT 58.842 50.000 0.00 0.00 0.00 3.95
2667 4044 1.916181 CTATTTCACACCCCTGACCCT 59.084 52.381 0.00 0.00 0.00 4.34
2668 4045 1.633945 ACTATTTCACACCCCTGACCC 59.366 52.381 0.00 0.00 0.00 4.46
2669 4046 3.434940 AACTATTTCACACCCCTGACC 57.565 47.619 0.00 0.00 0.00 4.02
2670 4047 3.930848 CGTAACTATTTCACACCCCTGAC 59.069 47.826 0.00 0.00 0.00 3.51
2671 4048 3.055675 CCGTAACTATTTCACACCCCTGA 60.056 47.826 0.00 0.00 0.00 3.86
2672 4049 3.055675 TCCGTAACTATTTCACACCCCTG 60.056 47.826 0.00 0.00 0.00 4.45
2673 4050 3.175594 TCCGTAACTATTTCACACCCCT 58.824 45.455 0.00 0.00 0.00 4.79
2674 4051 3.615224 TCCGTAACTATTTCACACCCC 57.385 47.619 0.00 0.00 0.00 4.95
2675 4052 3.686241 GGTTCCGTAACTATTTCACACCC 59.314 47.826 0.00 0.00 35.81 4.61
2676 4053 4.317488 TGGTTCCGTAACTATTTCACACC 58.683 43.478 0.00 0.00 35.81 4.16
2677 4054 4.992951 ACTGGTTCCGTAACTATTTCACAC 59.007 41.667 0.00 0.00 35.81 3.82
2678 4055 5.217978 ACTGGTTCCGTAACTATTTCACA 57.782 39.130 0.00 0.00 35.81 3.58
2679 4056 5.697633 TGAACTGGTTCCGTAACTATTTCAC 59.302 40.000 6.05 0.00 39.31 3.18
2680 4057 5.856156 TGAACTGGTTCCGTAACTATTTCA 58.144 37.500 6.05 6.05 40.77 2.69
2681 4058 6.980051 ATGAACTGGTTCCGTAACTATTTC 57.020 37.500 10.44 1.49 36.73 2.17
2682 4059 7.119262 CAGAATGAACTGGTTCCGTAACTATTT 59.881 37.037 10.44 0.00 39.69 1.40
2683 4060 6.594159 CAGAATGAACTGGTTCCGTAACTATT 59.406 38.462 10.44 2.78 39.69 1.73
2684 4061 6.106673 CAGAATGAACTGGTTCCGTAACTAT 58.893 40.000 10.44 0.00 39.69 2.12
2685 4062 5.011329 ACAGAATGAACTGGTTCCGTAACTA 59.989 40.000 10.44 0.00 39.69 2.24
2686 4063 4.202326 ACAGAATGAACTGGTTCCGTAACT 60.202 41.667 10.44 1.99 39.69 2.24
2687 4064 4.062991 ACAGAATGAACTGGTTCCGTAAC 58.937 43.478 10.44 0.00 39.69 2.50
2688 4065 4.062293 CACAGAATGAACTGGTTCCGTAA 58.938 43.478 10.44 0.00 39.69 3.18
2689 4066 3.322541 TCACAGAATGAACTGGTTCCGTA 59.677 43.478 10.44 0.00 39.69 4.02
2690 4067 2.104111 TCACAGAATGAACTGGTTCCGT 59.896 45.455 10.44 0.00 39.69 4.69
2691 4068 2.766313 TCACAGAATGAACTGGTTCCG 58.234 47.619 10.44 0.00 39.69 4.30
2692 4069 5.241506 TCAAATCACAGAATGAACTGGTTCC 59.758 40.000 10.44 0.00 41.93 3.62
2693 4070 6.317789 TCAAATCACAGAATGAACTGGTTC 57.682 37.500 6.53 6.53 41.93 3.62
2694 4071 6.906157 ATCAAATCACAGAATGAACTGGTT 57.094 33.333 0.00 0.00 41.93 3.67
2695 4072 6.906157 AATCAAATCACAGAATGAACTGGT 57.094 33.333 0.00 0.00 41.93 4.00
2696 4073 6.525628 CGAAATCAAATCACAGAATGAACTGG 59.474 38.462 0.00 0.00 41.93 4.00
2697 4074 7.300320 TCGAAATCAAATCACAGAATGAACTG 58.700 34.615 0.00 0.00 41.93 3.16
2698 4075 7.439157 TCGAAATCAAATCACAGAATGAACT 57.561 32.000 0.00 0.00 41.93 3.01
2699 4076 8.679288 AATCGAAATCAAATCACAGAATGAAC 57.321 30.769 0.00 0.00 41.93 3.18
2704 4081 9.613428 ACCTATAATCGAAATCAAATCACAGAA 57.387 29.630 0.00 0.00 0.00 3.02
2705 4082 9.261180 GACCTATAATCGAAATCAAATCACAGA 57.739 33.333 0.00 0.00 0.00 3.41
2706 4083 9.045223 TGACCTATAATCGAAATCAAATCACAG 57.955 33.333 0.00 0.00 0.00 3.66
2707 4084 8.956533 TGACCTATAATCGAAATCAAATCACA 57.043 30.769 0.00 0.00 0.00 3.58
2733 4110 4.942852 TCTGACGGCAAATTTGACAAATT 58.057 34.783 23.49 18.41 42.62 1.82
2734 4111 4.549458 CTCTGACGGCAAATTTGACAAAT 58.451 39.130 23.49 7.62 35.35 2.32
2735 4112 3.243367 CCTCTGACGGCAAATTTGACAAA 60.243 43.478 23.49 2.48 35.35 2.83
2736 4113 2.293122 CCTCTGACGGCAAATTTGACAA 59.707 45.455 23.49 7.75 35.35 3.18
2737 4114 1.879380 CCTCTGACGGCAAATTTGACA 59.121 47.619 23.49 13.99 35.35 3.58
2738 4115 2.619013 CCTCTGACGGCAAATTTGAC 57.381 50.000 22.31 18.50 0.00 3.18
2757 4134 0.382515 CGACTCCTGTAGGCTGTAGC 59.617 60.000 0.00 0.00 41.14 3.58
2758 4135 1.752683 ACGACTCCTGTAGGCTGTAG 58.247 55.000 0.00 0.00 34.44 2.74
2759 4136 2.089980 GAACGACTCCTGTAGGCTGTA 58.910 52.381 0.00 0.00 34.44 2.74
2760 4137 0.889306 GAACGACTCCTGTAGGCTGT 59.111 55.000 0.00 0.00 34.44 4.40
2761 4138 1.133407 GAGAACGACTCCTGTAGGCTG 59.867 57.143 0.00 0.00 39.53 4.85
2762 4139 1.465794 GAGAACGACTCCTGTAGGCT 58.534 55.000 0.00 0.00 39.53 4.58
2773 4150 3.584592 GCTAGCTAGCCGGAGAACGAC 62.585 61.905 31.67 2.80 43.39 4.34
2774 4151 1.445716 GCTAGCTAGCCGGAGAACGA 61.446 60.000 31.67 0.00 43.39 3.85
2775 4152 1.008309 GCTAGCTAGCCGGAGAACG 60.008 63.158 31.67 0.00 43.39 3.95
2785 4162 4.654412 CGCGCCCAGGCTAGCTAG 62.654 72.222 16.84 16.84 39.32 3.42


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

AutoCloner maintained by Alex Coulton.