Multiple sequence alignment - TraesCS1A01G213500

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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 TraesCS1A01G213500 chr1A 100.000 4206 0 0 1 4206 376758918 376754713 0.000000e+00 7768
1 TraesCS1A01G213500 chr1A 95.041 121 3 3 2564 2684 343396813 343396696 2.000000e-43 187
2 TraesCS1A01G213500 chr1B 93.736 1804 77 8 759 2556 407600907 407599134 0.000000e+00 2673
3 TraesCS1A01G213500 chr1B 91.728 1487 73 29 2683 4136 407599102 407597633 0.000000e+00 2019
4 TraesCS1A01G213500 chr1D 94.556 1543 57 12 2683 4206 302075684 302074150 0.000000e+00 2359
5 TraesCS1A01G213500 chr1D 95.230 1216 49 2 777 1992 302077845 302076639 0.000000e+00 1916
6 TraesCS1A01G213500 chr1D 89.673 765 65 11 1 756 202314718 202315477 0.000000e+00 963
7 TraesCS1A01G213500 chr1D 96.078 561 22 0 1996 2556 302076276 302075716 0.000000e+00 915
8 TraesCS1A01G213500 chr6D 90.132 760 64 10 5 757 422220527 422221282 0.000000e+00 977
9 TraesCS1A01G213500 chr6D 94.355 124 5 2 2578 2700 468640999 468640877 5.550000e-44 189
10 TraesCS1A01G213500 chr2A 89.921 764 66 9 1 757 768684816 768684057 0.000000e+00 974
11 TraesCS1A01G213500 chr2A 98.198 111 2 0 2577 2687 116161079 116161189 1.190000e-45 195
12 TraesCS1A01G213500 chr2A 96.491 114 4 0 2578 2691 391874312 391874425 5.550000e-44 189
13 TraesCS1A01G213500 chr7D 89.882 761 69 6 1 757 610766742 610765986 0.000000e+00 972
14 TraesCS1A01G213500 chr6A 89.908 763 64 10 1 753 577070568 577071327 0.000000e+00 970
15 TraesCS1A01G213500 chr3A 89.605 760 71 7 1 757 585061933 585062687 0.000000e+00 959
16 TraesCS1A01G213500 chr5A 89.398 764 72 6 1 757 296306288 296307049 0.000000e+00 953
17 TraesCS1A01G213500 chr2D 89.351 770 67 11 1 760 119370744 119369980 0.000000e+00 953
18 TraesCS1A01G213500 chr3D 89.309 767 63 14 1 757 90351391 90352148 0.000000e+00 944
19 TraesCS1A01G213500 chr5B 98.230 113 1 1 2574 2686 679807036 679806925 3.320000e-46 196
20 TraesCS1A01G213500 chr5D 95.798 119 5 0 2569 2687 29168319 29168201 4.290000e-45 193
21 TraesCS1A01G213500 chr4A 96.522 115 4 0 2572 2686 278329148 278329262 1.540000e-44 191
22 TraesCS1A01G213500 chr4A 96.522 115 4 0 2578 2692 416231501 416231387 1.540000e-44 191
23 TraesCS1A01G213500 chr7A 91.176 136 10 2 2577 2710 724130041 724129906 2.580000e-42 183


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 TraesCS1A01G213500 chr1A 376754713 376758918 4205 True 7768 7768 100.000 1 4206 1 chr1A.!!$R2 4205
1 TraesCS1A01G213500 chr1B 407597633 407600907 3274 True 2346 2673 92.732 759 4136 2 chr1B.!!$R1 3377
2 TraesCS1A01G213500 chr1D 302074150 302077845 3695 True 1730 2359 95.288 777 4206 3 chr1D.!!$R1 3429
3 TraesCS1A01G213500 chr1D 202314718 202315477 759 False 963 963 89.673 1 756 1 chr1D.!!$F1 755
4 TraesCS1A01G213500 chr6D 422220527 422221282 755 False 977 977 90.132 5 757 1 chr6D.!!$F1 752
5 TraesCS1A01G213500 chr2A 768684057 768684816 759 True 974 974 89.921 1 757 1 chr2A.!!$R1 756
6 TraesCS1A01G213500 chr7D 610765986 610766742 756 True 972 972 89.882 1 757 1 chr7D.!!$R1 756
7 TraesCS1A01G213500 chr6A 577070568 577071327 759 False 970 970 89.908 1 753 1 chr6A.!!$F1 752
8 TraesCS1A01G213500 chr3A 585061933 585062687 754 False 959 959 89.605 1 757 1 chr3A.!!$F1 756
9 TraesCS1A01G213500 chr5A 296306288 296307049 761 False 953 953 89.398 1 757 1 chr5A.!!$F1 756
10 TraesCS1A01G213500 chr2D 119369980 119370744 764 True 953 953 89.351 1 760 1 chr2D.!!$R1 759
11 TraesCS1A01G213500 chr3D 90351391 90352148 757 False 944 944 89.309 1 757 1 chr3D.!!$F1 756

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
676 700 0.532862 CTCAGGTTGCGACAAGTGGT 60.533 55.0 6.39 0.0 0.00 4.16 F
2197 2586 0.107263 TCAGCTGTCTGGTTTGTGCA 60.107 50.0 14.67 0.0 40.69 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 3065 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.0 0.0 0.0 0.0 4.30 R
3534 3945 0.179000 GGCTGAACCCATCGTGATCT 59.821 55.0 0.0 0.0 0.0 2.75 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 52 2.430244 TTTCGCGAGAGTCACGGC 60.430 61.111 9.59 3.61 43.69 5.68
54 58 2.720758 CGAGAGTCACGGCTTTGCG 61.721 63.158 1.62 0.00 0.00 4.85
56 60 1.222115 GAGAGTCACGGCTTTGCGTT 61.222 55.000 0.00 0.00 0.00 4.84
196 203 3.325072 CACGGTTGTGCTTACGCA 58.675 55.556 0.00 0.00 45.60 5.24
206 213 1.573026 TGCTTACGCAAAAGTCACGA 58.427 45.000 0.00 0.00 44.62 4.35
218 225 1.300697 GTCACGACCGTGCCTCTTT 60.301 57.895 16.76 0.00 45.04 2.52
293 307 2.144833 TTTCGCGAGAGGCACGGTTA 62.145 55.000 9.59 0.00 43.84 2.85
306 320 1.393539 CACGGTTATGCTTTCACGAGG 59.606 52.381 0.00 0.00 0.00 4.63
311 325 3.071479 GTTATGCTTTCACGAGGGTCAA 58.929 45.455 0.00 0.00 0.00 3.18
419 441 1.880027 GGTTGTGATTTTGCGAGAGGT 59.120 47.619 0.00 0.00 0.00 3.85
544 567 7.638444 TCAAAACCTATCAACATGGGATCTAA 58.362 34.615 5.52 0.00 34.16 2.10
555 578 9.258629 TCAACATGGGATCTAATTTTGAAGATT 57.741 29.630 0.00 0.00 32.60 2.40
604 627 1.144969 GTTCGAGATTTGGACGCACA 58.855 50.000 0.00 0.00 0.00 4.57
676 700 0.532862 CTCAGGTTGCGACAAGTGGT 60.533 55.000 6.39 0.00 0.00 4.16
757 781 9.286946 CGAGTACTTCTTAATTAGTGATTTCGT 57.713 33.333 0.00 0.00 0.00 3.85
799 824 9.908152 AAGAAAAAGAAACGAAAGAGAAAAGAA 57.092 25.926 0.00 0.00 0.00 2.52
846 871 4.367023 AAGACGCGCGTTGGGCTA 62.367 61.111 38.03 0.00 39.38 3.93
875 904 2.222640 CGTCGACAGTTTGTTTTGACGT 60.223 45.455 17.16 0.00 41.42 4.34
878 907 5.495502 GTCGACAGTTTGTTTTGACGTAAT 58.504 37.500 11.55 0.00 34.86 1.89
891 920 2.280186 GTAATGGGCGGCCTCGAG 60.280 66.667 29.87 5.13 39.00 4.04
892 921 4.235762 TAATGGGCGGCCTCGAGC 62.236 66.667 29.87 1.69 42.60 5.03
948 977 4.779733 ACCGAGCGACCCCATCCT 62.780 66.667 0.00 0.00 0.00 3.24
963 992 3.494924 CCCATCCTCACAATAATCTCGCA 60.495 47.826 0.00 0.00 0.00 5.10
981 1010 3.785189 AACCACGCGACGCACTCTT 62.785 57.895 21.35 2.30 0.00 2.85
1406 1435 0.688087 AGCTGGCCTAGGGTACAGAC 60.688 60.000 11.72 0.00 33.79 3.51
1415 1444 0.681564 AGGGTACAGACGCTCTCCAG 60.682 60.000 0.00 0.00 45.20 3.86
1525 1555 3.214250 CTGGCGACTCCTATCGGGC 62.214 68.421 0.00 0.00 42.49 6.13
1604 1634 4.976116 TCATTCACATACTTGCGTAGATCG 59.024 41.667 0.00 0.00 43.12 3.69
1685 1715 8.172352 ACCTATTGAGCTATACTAGTCTGTTG 57.828 38.462 0.00 0.00 0.00 3.33
1732 1762 2.438021 AGTGGGTGAGTTGTTAGCTGAA 59.562 45.455 0.00 0.00 0.00 3.02
1783 1813 4.873817 TGCAGTCAAGGTCAATTGATTTG 58.126 39.130 20.88 20.88 41.05 2.32
1834 1864 2.493278 TGTGGTTACTTAGGTAGACCGC 59.507 50.000 16.14 16.14 42.08 5.68
1866 1896 2.633481 AGACAGGTTCCCAGTAGTTGAC 59.367 50.000 0.00 0.00 0.00 3.18
1868 1898 2.633481 ACAGGTTCCCAGTAGTTGACTC 59.367 50.000 0.00 0.00 35.64 3.36
1875 1905 3.506455 TCCCAGTAGTTGACTCTTTCTCG 59.494 47.826 0.00 0.00 35.64 4.04
1928 1958 6.042552 ACACTAAGTTAGCCATAGCATGATCT 59.957 38.462 9.92 0.00 43.56 2.75
1966 1996 2.957402 AGGAGTGCAAAGGTGATTCA 57.043 45.000 0.00 0.00 0.00 2.57
2035 2424 6.765989 TGTATGTAGGAACAAACATAGGATGC 59.234 38.462 0.00 0.00 39.14 3.91
2043 2432 3.758554 ACAAACATAGGATGCAGGAACAC 59.241 43.478 0.00 0.00 0.00 3.32
2190 2579 2.706190 ACCTTTACTTCAGCTGTCTGGT 59.294 45.455 14.67 10.40 40.69 4.00
2197 2586 0.107263 TCAGCTGTCTGGTTTGTGCA 60.107 50.000 14.67 0.00 40.69 4.57
2239 2628 9.482627 GGATCCAAGTTGTATGAATAGTTCTAG 57.517 37.037 6.95 0.00 0.00 2.43
2264 2653 2.027192 TGAGCACCTTCTCATACCCAAC 60.027 50.000 0.00 0.00 38.11 3.77
2265 2654 2.237392 GAGCACCTTCTCATACCCAACT 59.763 50.000 0.00 0.00 33.41 3.16
2419 2808 0.547712 CCCCTCTTCTCCTTGGGACA 60.548 60.000 0.00 0.00 42.11 4.02
2460 2849 6.183360 GCTATTGAGGTAAATGGCCATCTTTT 60.183 38.462 21.08 13.50 37.89 2.27
2461 2850 5.404466 TTGAGGTAAATGGCCATCTTTTG 57.596 39.130 21.08 0.00 0.00 2.44
2505 2894 9.346725 CTCCACTTATTTAAATCACTTCAAAGC 57.653 33.333 3.39 0.00 0.00 3.51
2587 2986 7.760131 TTCGTATTAATTGTTACTCCTTCCG 57.240 36.000 0.00 0.00 0.00 4.30
2588 2987 6.866480 TCGTATTAATTGTTACTCCTTCCGT 58.134 36.000 0.00 0.00 0.00 4.69
2589 2988 7.322664 TCGTATTAATTGTTACTCCTTCCGTT 58.677 34.615 0.00 0.00 0.00 4.44
2590 2989 7.489113 TCGTATTAATTGTTACTCCTTCCGTTC 59.511 37.037 0.00 0.00 0.00 3.95
2591 2990 6.997239 ATTAATTGTTACTCCTTCCGTTCC 57.003 37.500 0.00 0.00 0.00 3.62
2592 2991 4.360951 AATTGTTACTCCTTCCGTTCCA 57.639 40.909 0.00 0.00 0.00 3.53
2593 2992 3.842007 TTGTTACTCCTTCCGTTCCAA 57.158 42.857 0.00 0.00 0.00 3.53
2594 2993 3.842007 TGTTACTCCTTCCGTTCCAAA 57.158 42.857 0.00 0.00 0.00 3.28
2595 2994 4.360951 TGTTACTCCTTCCGTTCCAAAT 57.639 40.909 0.00 0.00 0.00 2.32
2596 2995 4.721132 TGTTACTCCTTCCGTTCCAAATT 58.279 39.130 0.00 0.00 0.00 1.82
2597 2996 5.867330 TGTTACTCCTTCCGTTCCAAATTA 58.133 37.500 0.00 0.00 0.00 1.40
2598 2997 5.702209 TGTTACTCCTTCCGTTCCAAATTAC 59.298 40.000 0.00 0.00 0.00 1.89
2599 2998 4.635699 ACTCCTTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2600 2999 4.576879 ACTCCTTCCGTTCCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2601 3000 3.592059 TCCTTCCGTTCCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
2602 3001 3.007182 TCCTTCCGTTCCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
2603 3002 3.370061 CCTTCCGTTCCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
2604 3003 2.598589 TCCGTTCCAAATTACTCGTCG 58.401 47.619 0.00 0.00 0.00 5.12
2605 3004 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
2606 3005 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2607 3006 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2608 3007 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2609 3008 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2610 3009 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2611 3010 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2612 3011 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
2613 3012 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
2614 3013 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
2615 3014 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
2616 3015 4.642445 TTACTCGTCGCAGAAATGGATA 57.358 40.909 0.00 0.00 39.69 2.59
2617 3016 3.735237 ACTCGTCGCAGAAATGGATAT 57.265 42.857 0.00 0.00 39.69 1.63
2618 3017 4.848562 ACTCGTCGCAGAAATGGATATA 57.151 40.909 0.00 0.00 39.69 0.86
2619 3018 5.392767 ACTCGTCGCAGAAATGGATATAT 57.607 39.130 0.00 0.00 39.69 0.86
2620 3019 5.403246 ACTCGTCGCAGAAATGGATATATC 58.597 41.667 3.96 3.96 39.69 1.63
2621 3020 5.184096 ACTCGTCGCAGAAATGGATATATCT 59.816 40.000 12.42 0.00 39.69 1.98
2622 3021 6.374613 ACTCGTCGCAGAAATGGATATATCTA 59.625 38.462 12.42 6.97 39.69 1.98
2623 3022 6.786207 TCGTCGCAGAAATGGATATATCTAG 58.214 40.000 12.42 0.00 39.69 2.43
2624 3023 6.598064 TCGTCGCAGAAATGGATATATCTAGA 59.402 38.462 12.42 0.00 39.69 2.43
2625 3024 7.120726 TCGTCGCAGAAATGGATATATCTAGAA 59.879 37.037 12.42 0.00 39.69 2.10
2626 3025 7.219154 CGTCGCAGAAATGGATATATCTAGAAC 59.781 40.741 12.42 2.68 39.69 3.01
2627 3026 8.247562 GTCGCAGAAATGGATATATCTAGAACT 58.752 37.037 12.42 4.71 39.69 3.01
2628 3027 9.462606 TCGCAGAAATGGATATATCTAGAACTA 57.537 33.333 12.42 0.00 0.00 2.24
2656 3055 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
2657 3056 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
2658 3057 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
2659 3058 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
2660 3059 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
2661 3060 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
2662 3061 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
2663 3062 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
2664 3063 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
2665 3064 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
2666 3065 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
2667 3066 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
2668 3067 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
2669 3068 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
2670 3069 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
2671 3070 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
2672 3071 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
2673 3072 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
2731 3130 2.894902 TGAGCGTTTGTCTGTACAACA 58.105 42.857 0.00 1.96 45.18 3.33
2752 3151 7.864379 ACAACAAAGCATTTCATCAGTTTAGAG 59.136 33.333 0.00 0.00 35.03 2.43
2815 3214 2.749621 GTCACCCTTGCATTGTAGAAGG 59.250 50.000 0.00 0.00 36.73 3.46
2840 3239 8.154856 GGGTAGTTCAACCTAGATGCAAATATA 58.845 37.037 0.00 0.00 39.65 0.86
2936 3336 8.352137 TCATGTGTTATTTCTGGATGTTGAAT 57.648 30.769 0.00 0.00 0.00 2.57
2991 3391 4.181578 GTTCTTCTGCAGTAATCGGCTAA 58.818 43.478 14.67 0.00 35.86 3.09
2992 3392 4.672587 TCTTCTGCAGTAATCGGCTAAT 57.327 40.909 14.67 0.00 35.86 1.73
2994 3394 5.529791 TCTTCTGCAGTAATCGGCTAATAC 58.470 41.667 14.67 0.00 35.86 1.89
2995 3395 4.252971 TCTGCAGTAATCGGCTAATACC 57.747 45.455 14.67 0.00 35.86 2.73
2996 3396 3.639561 TCTGCAGTAATCGGCTAATACCA 59.360 43.478 14.67 0.00 35.86 3.25
2997 3397 3.990092 TGCAGTAATCGGCTAATACCAG 58.010 45.455 0.00 0.00 35.86 4.00
2998 3398 2.737252 GCAGTAATCGGCTAATACCAGC 59.263 50.000 0.00 0.00 41.02 4.85
2999 3399 3.802329 GCAGTAATCGGCTAATACCAGCA 60.802 47.826 0.00 0.00 43.67 4.41
3000 3400 3.990469 CAGTAATCGGCTAATACCAGCAG 59.010 47.826 0.00 0.00 43.67 4.24
3001 3401 3.641906 AGTAATCGGCTAATACCAGCAGT 59.358 43.478 0.00 0.00 43.67 4.40
3011 3418 1.257743 TACCAGCAGTCACTGACCTC 58.742 55.000 9.70 0.00 40.25 3.85
3243 3650 2.351726 GCACTTTACACGGGCTAATCAG 59.648 50.000 0.00 0.00 0.00 2.90
3268 3675 2.046292 GGAGGAGAGGGAATGAGAAGG 58.954 57.143 0.00 0.00 0.00 3.46
3324 3734 2.303163 ATATGCGGCTGTGTTCGTTA 57.697 45.000 0.00 0.00 0.00 3.18
3325 3735 2.303163 TATGCGGCTGTGTTCGTTAT 57.697 45.000 0.00 0.00 0.00 1.89
3326 3736 1.448985 ATGCGGCTGTGTTCGTTATT 58.551 45.000 0.00 0.00 0.00 1.40
3487 3898 6.071952 GCCACTTCAGTAATGAATCTTGGAAA 60.072 38.462 22.69 0.00 30.13 3.13
3489 3900 7.025963 CACTTCAGTAATGAATCTTGGAAAGC 58.974 38.462 6.00 0.00 45.70 3.51
3490 3901 6.716628 ACTTCAGTAATGAATCTTGGAAAGCA 59.283 34.615 6.00 0.00 45.70 3.91
3553 3964 0.179000 AGATCACGATGGGTTCAGCC 59.821 55.000 0.00 0.00 0.00 4.85
3712 4133 2.349886 GCGTGTTCATCTGAGAATGGAC 59.650 50.000 0.00 0.00 35.94 4.02
3715 4136 3.686726 GTGTTCATCTGAGAATGGACCAC 59.313 47.826 0.00 0.00 34.70 4.16
3716 4137 3.584406 TGTTCATCTGAGAATGGACCACT 59.416 43.478 0.00 0.00 34.70 4.00
3718 4139 3.176411 TCATCTGAGAATGGACCACTGT 58.824 45.455 0.00 0.00 0.00 3.55
3720 4141 4.777366 TCATCTGAGAATGGACCACTGTAA 59.223 41.667 0.00 0.00 0.00 2.41
3721 4142 5.426509 TCATCTGAGAATGGACCACTGTAAT 59.573 40.000 0.00 0.00 0.00 1.89
3723 4144 4.777366 TCTGAGAATGGACCACTGTAATGA 59.223 41.667 0.00 0.00 0.00 2.57
3773 4203 1.425066 GGAATGCATCCTGTCCCCATA 59.575 52.381 0.00 0.00 45.56 2.74
3778 4208 3.992999 TGCATCCTGTCCCCATATTTTT 58.007 40.909 0.00 0.00 0.00 1.94
3790 4220 6.039829 GTCCCCATATTTTTGACAGGAAGATC 59.960 42.308 0.00 0.00 0.00 2.75
3796 4226 6.917217 ATTTTTGACAGGAAGATCTCGATC 57.083 37.500 0.00 0.00 38.09 3.69
3851 4281 0.827368 GAGCGAGGAGGAAGTTGGAT 59.173 55.000 0.00 0.00 0.00 3.41
3944 4398 3.735029 GGACAGCAGCAGCAGCAC 61.735 66.667 12.92 3.10 45.49 4.40
3945 4399 2.976350 GACAGCAGCAGCAGCACA 60.976 61.111 12.92 0.00 45.49 4.57
3955 4409 0.033920 CAGCAGCACAGGTGACAGTA 59.966 55.000 3.10 0.00 39.26 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 15 5.060446 CGCGAAAGAAAACAAACAGAAAACT 59.940 36.000 0.00 0.00 0.00 2.66
25 28 3.156723 GTGACTCTCGCGAAAGAAAAC 57.843 47.619 17.91 7.27 0.00 2.43
48 52 2.772189 CCTCTCGCGAACGCAAAG 59.228 61.111 11.33 14.33 42.06 2.77
206 213 0.472471 TCCTTTCAAAGAGGCACGGT 59.528 50.000 0.00 0.00 34.17 4.83
293 307 1.611673 CCTTGACCCTCGTGAAAGCAT 60.612 52.381 0.00 0.00 0.00 3.79
363 385 5.067805 GGAAGAAAAACCATGACTCTTGTGT 59.932 40.000 0.00 0.00 0.00 3.72
367 389 4.275936 CGTGGAAGAAAAACCATGACTCTT 59.724 41.667 0.00 0.00 43.47 2.85
419 441 2.263540 GAAAGAGGCACGCCCGTA 59.736 61.111 3.95 0.00 39.21 4.02
544 567 1.466950 TCGCGCCGAAATCTTCAAAAT 59.533 42.857 0.00 0.00 31.06 1.82
555 578 2.587322 ATTGGATTCCTCGCGCCGAA 62.587 55.000 0.00 5.60 34.74 4.30
648 672 1.416401 TCGCAACCTGAGAGTTTTCCT 59.584 47.619 0.00 0.00 0.00 3.36
705 729 4.381505 GCAAAGAACACTTCACTTTCCCAA 60.382 41.667 0.00 0.00 32.59 4.12
775 799 9.556030 TCTTCTTTTCTCTTTCGTTTCTTTTTC 57.444 29.630 0.00 0.00 0.00 2.29
799 824 3.947834 CCCAACTCGGCTTATCATTTTCT 59.052 43.478 0.00 0.00 0.00 2.52
875 904 4.235762 GCTCGAGGCCGCCCATTA 62.236 66.667 15.58 0.00 35.37 1.90
948 977 2.670905 CGTGGTTGCGAGATTATTGTGA 59.329 45.455 0.00 0.00 0.00 3.58
963 992 3.785189 AAGAGTGCGTCGCGTGGTT 62.785 57.895 13.38 0.72 0.00 3.67
1320 1349 3.113386 CTCGGCGTCGATCTCAGCA 62.113 63.158 14.65 0.00 45.04 4.41
1415 1444 2.349886 GCGCTAATAGGTCATAGCATGC 59.650 50.000 10.51 10.51 43.71 4.06
1525 1555 1.269778 TGAACTCACAGACAAGGCTCG 60.270 52.381 0.00 0.00 0.00 5.03
1604 1634 2.793278 AGCAAAATCCAAACGGTGAC 57.207 45.000 0.00 0.00 0.00 3.67
1685 1715 6.963083 TCCTAAACTAGATCAGGACTTAGC 57.037 41.667 0.00 0.00 32.20 3.09
1732 1762 8.553696 CAACAAATTCTTTCTGCAAAATTAGCT 58.446 29.630 0.00 0.00 0.00 3.32
1783 1813 0.536006 AGACACCACTTCAAGCCTGC 60.536 55.000 0.00 0.00 0.00 4.85
1866 1896 1.480137 AGCATCAGACCCGAGAAAGAG 59.520 52.381 0.00 0.00 0.00 2.85
1868 1898 2.005451 CAAGCATCAGACCCGAGAAAG 58.995 52.381 0.00 0.00 0.00 2.62
1875 1905 1.093159 CAAGCTCAAGCATCAGACCC 58.907 55.000 4.59 0.00 45.16 4.46
1914 1944 8.201554 TCGATATTTTAAGATCATGCTATGGC 57.798 34.615 0.00 0.00 39.26 4.40
1928 1958 6.015350 CACTCCTAGCCTCCTCGATATTTTAA 60.015 42.308 0.00 0.00 0.00 1.52
1966 1996 5.295292 CGATCTTCAAGTGGCTATTTCACAT 59.705 40.000 0.00 0.00 37.58 3.21
2035 2424 6.480524 TCTTTTCATATGTTCGTGTTCCTG 57.519 37.500 1.90 0.00 0.00 3.86
2043 2432 7.588143 AGTCTCACTTCTTTTCATATGTTCG 57.412 36.000 1.90 0.00 0.00 3.95
2239 2628 2.680339 GGTATGAGAAGGTGCTCAAAGC 59.320 50.000 0.00 0.00 46.94 3.51
2419 2808 5.016173 TCAATAGCAACCCTGTTAGCAAAT 58.984 37.500 0.00 0.00 0.00 2.32
2460 2849 7.391620 AGTGGAGGACGAAATACTAAATTTCA 58.608 34.615 10.20 0.00 37.76 2.69
2461 2850 7.845066 AGTGGAGGACGAAATACTAAATTTC 57.155 36.000 0.00 1.26 35.34 2.17
2505 2894 0.610174 TAGGGACTGCTGCAGACTTG 59.390 55.000 34.28 10.48 41.52 3.16
2579 2978 3.617263 CGAGTAATTTGGAACGGAAGGAG 59.383 47.826 0.00 0.00 0.00 3.69
2580 2979 3.007182 ACGAGTAATTTGGAACGGAAGGA 59.993 43.478 0.00 0.00 0.00 3.36
2581 2980 3.332034 ACGAGTAATTTGGAACGGAAGG 58.668 45.455 0.00 0.00 0.00 3.46
2582 2981 3.060363 CGACGAGTAATTTGGAACGGAAG 59.940 47.826 0.00 0.00 0.00 3.46
2583 2982 2.988493 CGACGAGTAATTTGGAACGGAA 59.012 45.455 0.00 0.00 0.00 4.30
2584 2983 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
2585 2984 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
2586 2985 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2587 2986 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
2588 2987 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
2589 2988 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
2590 2989 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
2591 2990 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
2592 2991 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
2593 2992 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
2594 2993 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
2595 2994 3.520290 ATCCATTTCTGCGACGAGTAA 57.480 42.857 0.00 0.00 0.00 2.24
2596 2995 4.848562 ATATCCATTTCTGCGACGAGTA 57.151 40.909 0.00 0.00 0.00 2.59
2597 2996 3.735237 ATATCCATTTCTGCGACGAGT 57.265 42.857 0.00 0.00 0.00 4.18
2598 2997 5.645624 AGATATATCCATTTCTGCGACGAG 58.354 41.667 9.18 0.00 0.00 4.18
2599 2998 5.644977 AGATATATCCATTTCTGCGACGA 57.355 39.130 9.18 0.00 0.00 4.20
2600 2999 6.786207 TCTAGATATATCCATTTCTGCGACG 58.214 40.000 9.18 0.00 0.00 5.12
2601 3000 8.247562 AGTTCTAGATATATCCATTTCTGCGAC 58.752 37.037 9.18 0.00 0.00 5.19
2602 3001 8.354711 AGTTCTAGATATATCCATTTCTGCGA 57.645 34.615 9.18 0.00 0.00 5.10
2630 3029 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
2631 3030 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
2632 3031 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
2633 3032 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
2634 3033 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
2635 3034 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
2636 3035 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
2637 3036 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
2638 3037 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
2639 3038 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
2640 3039 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
2641 3040 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
2642 3041 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
2643 3042 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
2644 3043 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
2645 3044 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
2646 3045 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
2647 3046 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
2648 3047 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
2649 3048 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
2650 3049 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
2651 3050 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
2652 3051 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
2653 3052 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
2654 3053 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2655 3054 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2656 3055 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
2657 3056 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2658 3057 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2659 3058 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2660 3059 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2661 3060 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2662 3061 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2663 3062 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2664 3063 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
2665 3064 1.064166 TCTACTCCCTCCGTTCCGAAT 60.064 52.381 0.00 0.00 0.00 3.34
2666 3065 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
2667 3066 0.329261 TTCTACTCCCTCCGTTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
2668 3067 0.455005 GTTCTACTCCCTCCGTTCCG 59.545 60.000 0.00 0.00 0.00 4.30
2669 3068 0.822811 GGTTCTACTCCCTCCGTTCC 59.177 60.000 0.00 0.00 0.00 3.62
2670 3069 1.849977 AGGTTCTACTCCCTCCGTTC 58.150 55.000 0.00 0.00 0.00 3.95
2671 3070 3.363627 CTTAGGTTCTACTCCCTCCGTT 58.636 50.000 0.00 0.00 32.08 4.44
2672 3071 2.949508 GCTTAGGTTCTACTCCCTCCGT 60.950 54.545 0.00 0.00 32.08 4.69
2673 3072 1.682323 GCTTAGGTTCTACTCCCTCCG 59.318 57.143 0.00 0.00 32.08 4.63
2674 3073 2.748388 TGCTTAGGTTCTACTCCCTCC 58.252 52.381 0.00 0.00 32.08 4.30
2675 3074 5.360649 AAATGCTTAGGTTCTACTCCCTC 57.639 43.478 0.00 0.00 32.08 4.30
2676 3075 5.014228 ACAAAATGCTTAGGTTCTACTCCCT 59.986 40.000 0.00 0.00 34.74 4.20
2677 3076 5.254115 ACAAAATGCTTAGGTTCTACTCCC 58.746 41.667 0.00 0.00 0.00 4.30
2678 3077 6.430000 TGAACAAAATGCTTAGGTTCTACTCC 59.570 38.462 0.00 0.00 38.82 3.85
2679 3078 7.435068 TGAACAAAATGCTTAGGTTCTACTC 57.565 36.000 0.00 0.00 38.82 2.59
2680 3079 7.817418 TTGAACAAAATGCTTAGGTTCTACT 57.183 32.000 0.00 0.00 38.82 2.57
2681 3080 7.755373 GGATTGAACAAAATGCTTAGGTTCTAC 59.245 37.037 0.00 0.00 38.82 2.59
2682 3081 7.093945 GGGATTGAACAAAATGCTTAGGTTCTA 60.094 37.037 0.00 0.00 38.82 2.10
2683 3082 6.295292 GGGATTGAACAAAATGCTTAGGTTCT 60.295 38.462 0.00 0.00 38.82 3.01
2731 3130 7.231317 TCCAACTCTAAACTGATGAAATGCTTT 59.769 33.333 0.00 0.00 0.00 3.51
2752 3151 9.220767 GATGTGGGATAAAACTATAGATCCAAC 57.779 37.037 14.76 14.76 41.21 3.77
2772 3171 3.185330 CTCATTCGAGTCACTGATGTGG 58.815 50.000 0.00 0.00 43.94 4.17
2815 3214 9.209175 CTATATTTGCATCTAGGTTGAACTACC 57.791 37.037 0.00 0.00 38.53 3.18
2840 3239 2.746362 GCTGCATACAAGAAGAGCAACT 59.254 45.455 0.00 0.00 34.45 3.16
2850 3249 4.970662 AAAGTGGTATGCTGCATACAAG 57.029 40.909 38.60 0.00 45.86 3.16
2853 3252 3.876914 TGCTAAAGTGGTATGCTGCATAC 59.123 43.478 33.94 33.94 44.03 2.39
2936 3336 0.812811 GCGATGCTGCAGAGGATTCA 60.813 55.000 20.43 4.70 28.67 2.57
2991 3391 1.827969 GAGGTCAGTGACTGCTGGTAT 59.172 52.381 22.18 0.00 37.12 2.73
2992 3392 1.257743 GAGGTCAGTGACTGCTGGTA 58.742 55.000 22.18 0.00 37.12 3.25
2994 3394 1.080230 CGAGGTCAGTGACTGCTGG 60.080 63.158 22.18 9.74 37.12 4.85
2995 3395 0.881796 TACGAGGTCAGTGACTGCTG 59.118 55.000 22.18 12.28 37.81 4.41
2996 3396 1.542030 CTTACGAGGTCAGTGACTGCT 59.458 52.381 22.18 12.11 32.47 4.24
2997 3397 1.269998 ACTTACGAGGTCAGTGACTGC 59.730 52.381 22.18 13.29 32.47 4.40
2998 3398 3.644884 AACTTACGAGGTCAGTGACTG 57.355 47.619 22.18 6.18 32.47 3.51
2999 3399 4.667519 AAAACTTACGAGGTCAGTGACT 57.332 40.909 22.18 8.90 32.47 3.41
3000 3400 5.527033 AGTAAAACTTACGAGGTCAGTGAC 58.473 41.667 15.24 15.24 0.00 3.67
3001 3401 5.779529 AGTAAAACTTACGAGGTCAGTGA 57.220 39.130 0.00 0.00 0.00 3.41
3011 3418 4.565564 CGATCCCTGGAAGTAAAACTTACG 59.434 45.833 0.00 0.00 41.99 3.18
3243 3650 2.066999 ATTCCCTCTCCTCCACGCC 61.067 63.158 0.00 0.00 0.00 5.68
3325 3735 9.727859 ACATATAATGTACAACAACACACCTAA 57.272 29.630 0.00 0.00 42.78 2.69
3326 3736 9.157104 CACATATAATGTACAACAACACACCTA 57.843 33.333 0.00 0.00 42.70 3.08
3533 3944 1.576356 GCTGAACCCATCGTGATCTC 58.424 55.000 0.00 0.00 0.00 2.75
3534 3945 0.179000 GGCTGAACCCATCGTGATCT 59.821 55.000 0.00 0.00 0.00 2.75
3535 3946 1.154205 CGGCTGAACCCATCGTGATC 61.154 60.000 0.00 0.00 33.26 2.92
3553 3964 0.749649 CCAAGAGGAGGATGGACTCG 59.250 60.000 0.00 0.00 38.39 4.18
3712 4133 5.551233 TCTTCAGAAACCTCATTACAGTGG 58.449 41.667 0.00 0.00 0.00 4.00
3715 4136 6.875726 TCACATCTTCAGAAACCTCATTACAG 59.124 38.462 0.00 0.00 0.00 2.74
3716 4137 6.768483 TCACATCTTCAGAAACCTCATTACA 58.232 36.000 0.00 0.00 0.00 2.41
3718 4139 8.733458 CATTTCACATCTTCAGAAACCTCATTA 58.267 33.333 0.00 0.00 34.47 1.90
3720 4141 6.944290 TCATTTCACATCTTCAGAAACCTCAT 59.056 34.615 0.00 0.00 34.47 2.90
3721 4142 6.205464 GTCATTTCACATCTTCAGAAACCTCA 59.795 38.462 0.00 0.00 34.47 3.86
3723 4144 5.474876 GGTCATTTCACATCTTCAGAAACCT 59.525 40.000 0.00 0.00 34.47 3.50
3773 4203 5.819901 GGATCGAGATCTTCCTGTCAAAAAT 59.180 40.000 12.22 0.00 37.92 1.82
3778 4208 3.218453 GAGGATCGAGATCTTCCTGTCA 58.782 50.000 17.50 0.00 39.98 3.58
3851 4281 2.646719 GTGGTCCTGTACGTCGCA 59.353 61.111 0.00 0.00 0.00 5.10
3944 4398 2.628178 TCCTGTCACTTACTGTCACCTG 59.372 50.000 0.00 0.00 0.00 4.00
3945 4399 2.628657 GTCCTGTCACTTACTGTCACCT 59.371 50.000 0.00 0.00 0.00 4.00
3955 4409 3.862642 GCGAGAAATGAGTCCTGTCACTT 60.863 47.826 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.