Multiple sequence alignment - TraesCS5B01G426900

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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 TraesCS5B01G426900 chr5B 100.000 7077 0 0 1 7077 602830151 602837227 0.000000e+00 13069.0
1 TraesCS5B01G426900 chr5B 85.455 110 16 0 666 775 444768826 444768935 1.610000e-21 115.0
2 TraesCS5B01G426900 chr5A 93.301 6329 234 78 838 7077 610217787 610224014 0.000000e+00 9164.0
3 TraesCS5B01G426900 chr5A 82.994 541 49 23 144 648 607624886 607625419 3.890000e-122 449.0
4 TraesCS5B01G426900 chr5A 92.188 64 2 2 786 849 610209083 610209143 3.520000e-13 87.9
5 TraesCS5B01G426900 chr5D 94.348 3450 124 26 1181 4610 489178177 489181575 0.000000e+00 5225.0
6 TraesCS5B01G426900 chr5D 94.360 1773 53 22 5334 7077 489182318 489184072 0.000000e+00 2676.0
7 TraesCS5B01G426900 chr5D 94.502 673 33 3 4660 5329 489181577 489182248 0.000000e+00 1035.0
8 TraesCS5B01G426900 chr5D 94.139 273 10 4 778 1048 489177550 489177818 1.840000e-110 411.0
9 TraesCS5B01G426900 chr3B 92.491 799 34 6 1 775 533448481 533447685 0.000000e+00 1120.0
10 TraesCS5B01G426900 chr3B 91.479 798 42 7 1 775 225260425 225261219 0.000000e+00 1074.0
11 TraesCS5B01G426900 chr3B 75.712 667 127 30 1 652 708229486 708228840 1.150000e-77 302.0
12 TraesCS5B01G426900 chr3B 89.320 103 11 0 674 776 708228851 708228749 5.760000e-26 130.0
13 TraesCS5B01G426900 chr4A 83.847 811 67 16 1 775 718148094 718147312 0.000000e+00 713.0
14 TraesCS5B01G426900 chr4A 83.600 811 68 24 1 775 718042767 718041986 0.000000e+00 701.0
15 TraesCS5B01G426900 chr2B 84.010 788 70 33 1 777 496952255 496951513 0.000000e+00 706.0
16 TraesCS5B01G426900 chr6B 88.095 588 21 16 213 778 202506394 202505834 0.000000e+00 652.0
17 TraesCS5B01G426900 chr2A 82.845 478 49 13 136 585 607871848 607872320 1.430000e-106 398.0
18 TraesCS5B01G426900 chr2D 89.216 102 10 1 668 769 462783633 462783733 7.450000e-25 126.0


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 TraesCS5B01G426900 chr5B 602830151 602837227 7076 False 13069.00 13069 100.00000 1 7077 1 chr5B.!!$F2 7076
1 TraesCS5B01G426900 chr5A 610217787 610224014 6227 False 9164.00 9164 93.30100 838 7077 1 chr5A.!!$F3 6239
2 TraesCS5B01G426900 chr5A 607624886 607625419 533 False 449.00 449 82.99400 144 648 1 chr5A.!!$F1 504
3 TraesCS5B01G426900 chr5D 489177550 489184072 6522 False 2336.75 5225 94.33725 778 7077 4 chr5D.!!$F1 6299
4 TraesCS5B01G426900 chr3B 533447685 533448481 796 True 1120.00 1120 92.49100 1 775 1 chr3B.!!$R1 774
5 TraesCS5B01G426900 chr3B 225260425 225261219 794 False 1074.00 1074 91.47900 1 775 1 chr3B.!!$F1 774
6 TraesCS5B01G426900 chr3B 708228749 708229486 737 True 216.00 302 82.51600 1 776 2 chr3B.!!$R2 775
7 TraesCS5B01G426900 chr4A 718147312 718148094 782 True 713.00 713 83.84700 1 775 1 chr4A.!!$R2 774
8 TraesCS5B01G426900 chr4A 718041986 718042767 781 True 701.00 701 83.60000 1 775 1 chr4A.!!$R1 774
9 TraesCS5B01G426900 chr2B 496951513 496952255 742 True 706.00 706 84.01000 1 777 1 chr2B.!!$R1 776
10 TraesCS5B01G426900 chr6B 202505834 202506394 560 True 652.00 652 88.09500 213 778 1 chr6B.!!$R1 565

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
782 953 0.612453 CTAGGACCTCCCGGCTATCC 60.612 65.000 0.00 0.00 40.87 2.59 F
805 976 1.072331 CCCACACCAACTACTTCTGCT 59.928 52.381 0.00 0.00 0.00 4.24 F
2125 2550 1.588082 GCCAACTTGATGCCCACTG 59.412 57.895 0.00 0.00 0.00 3.66 F
2522 2947 1.066215 TGCTTGTCTATCATGTGGCGT 60.066 47.619 0.00 0.00 0.00 5.68 F
3410 3842 0.031857 CAGCGAGGTCATGAGCTAGG 59.968 60.000 28.64 22.75 39.57 3.02 F
3668 4100 0.676736 GAGGAATAGACCCAGCTCCG 59.323 60.000 0.00 0.00 0.00 4.63 F
4618 5057 0.244178 TATGCTGCGGACGTGTTACA 59.756 50.000 0.00 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 2874 0.810648 GGCCTCGCATTTGTCAATGA 59.189 50.0 0.00 0.00 42.35 2.57 R
2463 2888 1.372087 CGCCACATGAAAGAGGCCTC 61.372 60.0 26.22 26.22 41.50 4.70 R
2984 3413 0.034670 AGGCAGAGACAAGGGCAATC 60.035 55.0 0.00 0.00 0.00 2.67 R
3623 4055 0.391661 CAAGTGCACTACAGGCGGAT 60.392 55.0 22.01 0.00 0.00 4.18 R
4426 4865 0.467844 AGCATGTTCCAGCACCACAA 60.468 50.0 0.00 0.00 0.00 3.33 R
5662 6179 0.902531 GAGAGATTTGTCCCCGGTCA 59.097 55.0 0.00 0.00 0.00 4.02 R
6612 7158 0.322546 GAGAACAATTGTCCCGGCCT 60.323 55.0 12.39 2.78 0.00 5.19 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
513 682 9.750125 GTCAAAGAGATGTTTTTCCTATTTGTT 57.250 29.630 0.00 0.00 39.07 2.83
533 702 4.759183 TGTTGTCAACGGAATGATCATGAA 59.241 37.500 9.46 0.00 0.00 2.57
550 719 1.633432 TGAACAGGTGGTTATGAGGGG 59.367 52.381 0.00 0.00 40.63 4.79
595 764 2.358737 CGAACCCCAGCACTCACC 60.359 66.667 0.00 0.00 0.00 4.02
782 953 0.612453 CTAGGACCTCCCGGCTATCC 60.612 65.000 0.00 0.00 40.87 2.59
805 976 1.072331 CCCACACCAACTACTTCTGCT 59.928 52.381 0.00 0.00 0.00 4.24
835 1006 2.333014 GCACGACAAGAGAAGAGGAAG 58.667 52.381 0.00 0.00 0.00 3.46
886 1059 4.846779 TGCTTCGTCTTTGCCTAAAAAT 57.153 36.364 0.00 0.00 0.00 1.82
974 1147 3.175710 AAACCACACCGCCCTCCT 61.176 61.111 0.00 0.00 0.00 3.69
987 1160 4.410400 CTCCTCACCCCCAACCGC 62.410 72.222 0.00 0.00 0.00 5.68
1723 2122 2.492088 TGGTCGTCTGGAGATGTAACAG 59.508 50.000 0.00 0.00 33.00 3.16
1777 2176 4.833469 GTTTGTTCCAAAACCAAGTTCG 57.167 40.909 0.00 0.00 34.58 3.95
1794 2195 2.921754 GTTCGCTCGCATTTAGTACAGT 59.078 45.455 0.00 0.00 0.00 3.55
1842 2259 3.426159 CGATGTGCTTACCATTGTTCACC 60.426 47.826 0.00 0.00 0.00 4.02
1843 2260 2.937519 TGTGCTTACCATTGTTCACCA 58.062 42.857 0.00 0.00 0.00 4.17
2058 2483 9.167311 TGCTTCTTATAGAATTTGGAGAAGTTC 57.833 33.333 11.24 0.00 41.16 3.01
2070 2495 2.781646 GGAGAAGTTCGTTTTGCAAACG 59.218 45.455 12.39 17.77 44.29 3.60
2123 2548 1.907807 TGGCCAACTTGATGCCCAC 60.908 57.895 0.61 0.00 44.72 4.61
2124 2549 1.607467 GGCCAACTTGATGCCCACT 60.607 57.895 0.00 0.00 39.30 4.00
2125 2550 1.588082 GCCAACTTGATGCCCACTG 59.412 57.895 0.00 0.00 0.00 3.66
2154 2579 7.510549 TTGGTTTAGAAGAACATCCTTTCTG 57.489 36.000 0.00 0.00 35.92 3.02
2265 2690 5.278660 CCTTCAGCAGCAGTCAATTAACTTT 60.279 40.000 0.00 0.00 0.00 2.66
2267 2692 6.875948 TCAGCAGCAGTCAATTAACTTTTA 57.124 33.333 0.00 0.00 0.00 1.52
2276 2701 6.032775 CAGTCAATTAACTTTTATGTGCTGCG 59.967 38.462 0.00 0.00 0.00 5.18
2295 2720 2.476185 GCGTGATTAGTGTTGTCATGGC 60.476 50.000 0.00 0.00 31.25 4.40
2296 2721 2.095853 CGTGATTAGTGTTGTCATGGCC 59.904 50.000 0.00 0.00 0.00 5.36
2340 2765 7.789831 AGATGTGTTCCTATTCTTAGGTGGATA 59.210 37.037 0.00 0.00 44.75 2.59
2398 2823 2.591923 TGCACCTTGTCAATTGCCTAA 58.408 42.857 13.91 0.00 33.86 2.69
2399 2824 2.295909 TGCACCTTGTCAATTGCCTAAC 59.704 45.455 13.91 0.00 33.86 2.34
2409 2834 5.221224 TGTCAATTGCCTAACCTTTGACTTG 60.221 40.000 13.35 0.00 44.00 3.16
2449 2874 9.535878 TTCGCTTTTAAGTTCAAAACCAAATAT 57.464 25.926 0.00 0.00 0.00 1.28
2463 2888 6.890663 AACCAAATATCATTGACAAATGCG 57.109 33.333 0.00 0.00 42.55 4.73
2513 2938 8.883731 TCTGTAGCTTTTAAATGCTTGTCTATC 58.116 33.333 27.48 13.28 39.69 2.08
2519 2944 7.221452 GCTTTTAAATGCTTGTCTATCATGTGG 59.779 37.037 16.55 0.00 0.00 4.17
2520 2945 4.644103 AAATGCTTGTCTATCATGTGGC 57.356 40.909 0.00 0.00 0.00 5.01
2521 2946 1.655484 TGCTTGTCTATCATGTGGCG 58.345 50.000 0.00 0.00 0.00 5.69
2522 2947 1.066215 TGCTTGTCTATCATGTGGCGT 60.066 47.619 0.00 0.00 0.00 5.68
2525 2950 3.430218 GCTTGTCTATCATGTGGCGTATC 59.570 47.826 0.00 0.00 0.00 2.24
2528 2953 4.145052 TGTCTATCATGTGGCGTATCTCT 58.855 43.478 0.00 0.00 0.00 3.10
2529 2954 4.022849 TGTCTATCATGTGGCGTATCTCTG 60.023 45.833 0.00 0.00 0.00 3.35
2530 2955 4.022762 GTCTATCATGTGGCGTATCTCTGT 60.023 45.833 0.00 0.00 0.00 3.41
2531 2956 5.181433 GTCTATCATGTGGCGTATCTCTGTA 59.819 44.000 0.00 0.00 0.00 2.74
2532 2957 3.990318 TCATGTGGCGTATCTCTGTAG 57.010 47.619 0.00 0.00 0.00 2.74
2533 2958 3.288092 TCATGTGGCGTATCTCTGTAGT 58.712 45.455 0.00 0.00 0.00 2.73
2534 2959 3.699538 TCATGTGGCGTATCTCTGTAGTT 59.300 43.478 0.00 0.00 0.00 2.24
2535 2960 3.777465 TGTGGCGTATCTCTGTAGTTC 57.223 47.619 0.00 0.00 0.00 3.01
2536 2961 3.086282 TGTGGCGTATCTCTGTAGTTCA 58.914 45.455 0.00 0.00 0.00 3.18
2537 2962 3.508402 TGTGGCGTATCTCTGTAGTTCAA 59.492 43.478 0.00 0.00 0.00 2.69
2538 2963 4.021807 TGTGGCGTATCTCTGTAGTTCAAA 60.022 41.667 0.00 0.00 0.00 2.69
2539 2964 4.927425 GTGGCGTATCTCTGTAGTTCAAAA 59.073 41.667 0.00 0.00 0.00 2.44
2540 2965 4.927425 TGGCGTATCTCTGTAGTTCAAAAC 59.073 41.667 0.00 0.00 0.00 2.43
2541 2966 4.329256 GGCGTATCTCTGTAGTTCAAAACC 59.671 45.833 0.00 0.00 0.00 3.27
2542 2967 4.927425 GCGTATCTCTGTAGTTCAAAACCA 59.073 41.667 0.00 0.00 0.00 3.67
2543 2968 5.407387 GCGTATCTCTGTAGTTCAAAACCAA 59.593 40.000 0.00 0.00 0.00 3.67
2544 2969 6.073440 GCGTATCTCTGTAGTTCAAAACCAAA 60.073 38.462 0.00 0.00 0.00 3.28
2545 2970 7.360946 GCGTATCTCTGTAGTTCAAAACCAAAT 60.361 37.037 0.00 0.00 0.00 2.32
2546 2971 9.146984 CGTATCTCTGTAGTTCAAAACCAAATA 57.853 33.333 0.00 0.00 0.00 1.40
2564 2989 9.889128 AACCAAATATTTGAGTATTTCATTGGG 57.111 29.630 26.32 9.28 41.84 4.12
2585 3010 2.872858 GCTGTCCAAATAATCCGTCTCC 59.127 50.000 0.00 0.00 0.00 3.71
2773 3198 7.390996 ACATGTACGGTGGTTTATCAATGTTAA 59.609 33.333 0.00 0.00 0.00 2.01
2880 3308 8.800370 TTTGATCTATATTTGTTACTGGTGCA 57.200 30.769 0.00 0.00 0.00 4.57
2881 3309 8.978874 TTGATCTATATTTGTTACTGGTGCAT 57.021 30.769 0.00 0.00 0.00 3.96
2926 3354 4.892934 TGCACTATCTTTCCCAAACACTTT 59.107 37.500 0.00 0.00 0.00 2.66
2983 3412 5.541868 AGTGATATCTGAATGATTCCGGTCT 59.458 40.000 0.00 0.00 36.65 3.85
2984 3413 5.636965 GTGATATCTGAATGATTCCGGTCTG 59.363 44.000 0.00 0.00 36.65 3.51
2985 3414 5.539955 TGATATCTGAATGATTCCGGTCTGA 59.460 40.000 0.00 0.00 36.65 3.27
3101 3532 5.333299 TCGCTAAGGCATTTTACAGAGTA 57.667 39.130 0.00 0.00 38.60 2.59
3192 3623 0.539438 TGCAAGGTTTAGGCCACCAG 60.539 55.000 12.97 6.24 36.67 4.00
3193 3624 1.877576 GCAAGGTTTAGGCCACCAGC 61.878 60.000 12.97 11.83 36.67 4.85
3201 3632 1.617018 TAGGCCACCAGCAGTGCTAG 61.617 60.000 19.26 13.93 45.83 3.42
3286 3718 6.530019 GGAACACCAATTCCATTATCAGTT 57.470 37.500 0.00 0.00 46.49 3.16
3287 3719 6.935167 GGAACACCAATTCCATTATCAGTTT 58.065 36.000 0.00 0.00 46.49 2.66
3288 3720 8.062065 GGAACACCAATTCCATTATCAGTTTA 57.938 34.615 0.00 0.00 46.49 2.01
3289 3721 8.695456 GGAACACCAATTCCATTATCAGTTTAT 58.305 33.333 0.00 0.00 46.49 1.40
3290 3722 9.736023 GAACACCAATTCCATTATCAGTTTATC 57.264 33.333 0.00 0.00 0.00 1.75
3291 3723 8.821686 ACACCAATTCCATTATCAGTTTATCA 57.178 30.769 0.00 0.00 0.00 2.15
3410 3842 0.031857 CAGCGAGGTCATGAGCTAGG 59.968 60.000 28.64 22.75 39.57 3.02
3623 4055 1.625759 CTTCAGTACACGCATGCGCA 61.626 55.000 38.15 21.69 44.19 6.09
3668 4100 0.676736 GAGGAATAGACCCAGCTCCG 59.323 60.000 0.00 0.00 0.00 4.63
3794 4232 1.675310 CTGCCATTGCTCCGGTTGA 60.675 57.895 0.00 0.00 38.71 3.18
3843 4281 4.934356 TGGTTTTTCTTCTGCATATCCCT 58.066 39.130 0.00 0.00 0.00 4.20
4045 4483 4.227300 TGTCTGTTGCCCTTAGTCCATAAT 59.773 41.667 0.00 0.00 0.00 1.28
4063 4501 5.361857 CCATAATCAACCTCCAGCATTTCTT 59.638 40.000 0.00 0.00 0.00 2.52
4073 4511 5.065731 CCTCCAGCATTTCTTGAGTATGTTC 59.934 44.000 0.00 0.00 33.86 3.18
4135 4573 8.902806 TGCAAATGTCTAATTTAATCTCGGAAT 58.097 29.630 0.00 0.00 0.00 3.01
4177 4616 6.216569 CCGTTCTGTTAGCTGATGTATATGT 58.783 40.000 0.00 0.00 0.00 2.29
4179 4618 6.697455 CGTTCTGTTAGCTGATGTATATGTGT 59.303 38.462 0.00 0.00 0.00 3.72
4426 4865 6.839124 TCAATTGTGAATATGCCTTGTTCT 57.161 33.333 5.13 0.00 0.00 3.01
4595 5034 7.282224 TGTGTGCTTGATATTTTACTGTATCCC 59.718 37.037 0.00 0.00 0.00 3.85
4611 5050 0.317160 TCCCTATTATGCTGCGGACG 59.683 55.000 0.00 0.00 0.00 4.79
4618 5057 0.244178 TATGCTGCGGACGTGTTACA 59.756 50.000 0.00 0.00 0.00 2.41
4631 5078 5.064707 GGACGTGTTACATTAATGTCATGCT 59.935 40.000 24.00 12.29 41.97 3.79
4654 5101 9.225436 TGCTTTTTATCTAATGTGACATGTACA 57.775 29.630 0.00 0.00 0.00 2.90
4655 5102 9.708222 GCTTTTTATCTAATGTGACATGTACAG 57.292 33.333 0.00 0.00 0.00 2.74
4695 5142 2.942376 TGTACTGAACACTTGGTGCTTG 59.058 45.455 0.00 0.00 36.98 4.01
4803 5250 3.916761 TGTGTTGACGTGGATAGTTACC 58.083 45.455 0.00 0.00 0.00 2.85
4831 5278 7.862873 GGGCATTTATAACTCTTTATCTTGTGC 59.137 37.037 0.00 0.00 0.00 4.57
4834 5281 7.548196 TTTATAACTCTTTATCTTGTGCCCG 57.452 36.000 0.00 0.00 0.00 6.13
4944 5391 9.502091 TGCAGTTATGAGTTAAGATTTAGTTGT 57.498 29.630 0.00 0.00 0.00 3.32
4961 5408 8.450578 TTTAGTTGTCAACAGAACAGATTCAT 57.549 30.769 17.78 0.00 37.29 2.57
5034 5481 4.718961 ACTGAGCAACTAAGTCATTTGGT 58.281 39.130 0.00 0.00 33.77 3.67
5053 5500 9.695526 CATTTGGTTTCAACTCAATTATTCTCA 57.304 29.630 0.00 0.00 31.78 3.27
5059 5506 9.897744 GTTTCAACTCAATTATTCTCAATCACA 57.102 29.630 0.00 0.00 0.00 3.58
5121 5569 2.949177 TTAACCGGATATGCATGGCT 57.051 45.000 9.46 0.00 0.00 4.75
5181 5631 8.551682 TTCCAAATCTTAAATTGGCCTGATAT 57.448 30.769 3.32 0.00 44.63 1.63
5182 5632 8.551682 TCCAAATCTTAAATTGGCCTGATATT 57.448 30.769 3.32 0.00 44.63 1.28
5183 5633 8.423349 TCCAAATCTTAAATTGGCCTGATATTG 58.577 33.333 3.32 0.00 44.63 1.90
5198 5648 6.016276 GCCTGATATTGTTTAACTGGGTATGG 60.016 42.308 0.00 0.00 0.00 2.74
5207 5657 1.595311 ACTGGGTATGGATGGCTGAA 58.405 50.000 0.00 0.00 0.00 3.02
5233 5683 7.505585 AGTGTTTTTCTTTCATGGTATCTGGAA 59.494 33.333 0.00 0.00 0.00 3.53
5412 5927 4.272504 TCGAAATTACCCGAAATGATCTGC 59.727 41.667 0.00 0.00 0.00 4.26
5544 6061 3.220110 CAACTGATGCTAGGATGCCATT 58.780 45.455 0.00 0.00 0.00 3.16
5662 6179 6.773976 TTTCATGTCTTTCTCTTGGTGTTT 57.226 33.333 0.00 0.00 0.00 2.83
5905 6422 1.002087 CCTTACTCTGACAAAGGCGGT 59.998 52.381 1.48 0.00 33.84 5.68
5909 6426 0.895530 CTCTGACAAAGGCGGTAGGA 59.104 55.000 0.00 0.00 0.00 2.94
6099 6616 2.358737 GGTGCCCCTGTGAACTCG 60.359 66.667 0.00 0.00 0.00 4.18
6139 6656 2.869801 TGCTGTACGAAACTTGGACAAG 59.130 45.455 10.34 10.34 43.79 3.16
6217 6734 3.609853 TGCCACTATTTAGTTCCAGCAG 58.390 45.455 0.00 0.00 33.46 4.24
6227 6744 0.804989 GTTCCAGCAGACGGGATTTG 59.195 55.000 0.00 0.00 40.09 2.32
6242 6759 5.418840 ACGGGATTTGCTTTTGATATCTTGT 59.581 36.000 3.98 0.00 0.00 3.16
6330 6847 4.158394 TGAACAAGAGAAAGCCATTATGCC 59.842 41.667 0.00 0.00 0.00 4.40
6338 6855 4.652421 AGAAAGCCATTATGCCATGTTCAT 59.348 37.500 0.00 0.00 0.00 2.57
6447 6964 6.655078 ATGTTGCTGTTTCCTTTGAATACT 57.345 33.333 0.00 0.00 0.00 2.12
6448 6965 6.463995 TGTTGCTGTTTCCTTTGAATACTT 57.536 33.333 0.00 0.00 0.00 2.24
6480 6997 3.056821 GGGTGTTCCTTTGAATACTTGCC 60.057 47.826 2.91 0.00 41.05 4.52
6482 6999 4.546570 GTGTTCCTTTGAATACTTGCCAC 58.453 43.478 0.00 0.00 38.96 5.01
6483 7000 3.252215 TGTTCCTTTGAATACTTGCCACG 59.748 43.478 0.00 0.00 31.98 4.94
6521 7041 7.961351 AGTTTGAGATGGAGTTAGATAGGATG 58.039 38.462 0.00 0.00 0.00 3.51
6555 7075 1.287146 GACCCTGGACCCTGTACTCTA 59.713 57.143 0.00 0.00 0.00 2.43
6556 7076 1.006878 ACCCTGGACCCTGTACTCTAC 59.993 57.143 0.00 0.00 0.00 2.59
6557 7077 1.288335 CCCTGGACCCTGTACTCTACT 59.712 57.143 0.00 0.00 0.00 2.57
6569 7089 9.183368 ACCCTGTACTCTACTACAACTAAATAC 57.817 37.037 0.00 0.00 0.00 1.89
6570 7090 9.182214 CCCTGTACTCTACTACAACTAAATACA 57.818 37.037 0.00 0.00 0.00 2.29
6575 7121 6.666546 ACTCTACTACAACTAAATACAGCCCA 59.333 38.462 0.00 0.00 0.00 5.36
6614 7160 1.829849 TCATCAAGTGAGGCAGAGAGG 59.170 52.381 0.00 0.00 31.80 3.69
6615 7161 0.540923 ATCAAGTGAGGCAGAGAGGC 59.459 55.000 0.00 0.00 44.61 4.70
6640 7194 3.935828 GGACAATTGTTCTCTGTAGAGGC 59.064 47.826 13.36 3.85 42.30 4.70
6693 7247 5.724854 ACACTTAGGACCCAGCTATTAAAGA 59.275 40.000 0.00 0.00 0.00 2.52
6695 7249 6.539103 CACTTAGGACCCAGCTATTAAAGAAC 59.461 42.308 0.00 0.00 0.00 3.01
6765 7338 1.270550 GGAAGTTGCACATGGTTCCTG 59.729 52.381 0.00 0.00 34.89 3.86
6769 7342 3.766545 AGTTGCACATGGTTCCTGTATT 58.233 40.909 0.00 0.00 0.00 1.89
6771 7344 3.719268 TGCACATGGTTCCTGTATTCT 57.281 42.857 0.00 0.00 0.00 2.40
6774 7347 3.346315 CACATGGTTCCTGTATTCTGCA 58.654 45.455 0.00 0.00 0.00 4.41
6775 7348 3.376234 CACATGGTTCCTGTATTCTGCAG 59.624 47.826 7.63 7.63 0.00 4.41
6776 7349 3.009473 ACATGGTTCCTGTATTCTGCAGT 59.991 43.478 14.67 0.00 32.41 4.40
6790 7363 3.196463 TCTGCAGTAGTAGTACGAGCTC 58.804 50.000 14.67 2.73 36.55 4.09
6861 7434 4.379243 CGCGGCTGTCCTGTCCTT 62.379 66.667 0.00 0.00 0.00 3.36
6927 7500 1.068055 CAGTTCAACTGCAGGAATGGC 60.068 52.381 19.93 10.30 39.62 4.40
7040 7613 4.576374 GCGGTCCCCTATCCCCCT 62.576 72.222 0.00 0.00 0.00 4.79
7045 7618 0.841158 GTCCCCTATCCCCCTTAGCC 60.841 65.000 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 124 9.657121 GTTCAACAATTTTGAAAACAAAACTCA 57.343 25.926 13.68 0.00 39.76 3.41
164 232 8.833231 AAAGTTCATCATCTCGAGAAAAAGTA 57.167 30.769 20.91 1.31 0.00 2.24
497 665 6.037098 CCGTTGACAACAAATAGGAAAAACA 58.963 36.000 18.09 0.00 37.77 2.83
513 682 4.322567 TGTTCATGATCATTCCGTTGACA 58.677 39.130 5.16 1.08 0.00 3.58
533 702 0.550147 AGCCCCTCATAACCACCTGT 60.550 55.000 0.00 0.00 0.00 4.00
550 719 1.638467 CGCGAGGTTTGATAGCAGC 59.362 57.895 0.00 0.00 0.00 5.25
595 764 2.229675 TCATACTCCTGCAGCGATTG 57.770 50.000 8.66 1.93 0.00 2.67
652 821 7.576236 TGCTCTTAAAAACTGATTCTCGAAAG 58.424 34.615 0.00 0.00 0.00 2.62
671 842 2.692557 ACATCGCTCACTATCTGCTCTT 59.307 45.455 0.00 0.00 0.00 2.85
724 895 2.436115 GGACAAGTGGCGCCTACC 60.436 66.667 29.70 15.51 0.00 3.18
782 953 1.072331 AGAAGTAGTTGGTGTGGGCTG 59.928 52.381 0.00 0.00 0.00 4.85
835 1006 2.586357 GAACGCGGGGATGCTCTC 60.586 66.667 12.47 0.00 0.00 3.20
886 1059 4.657075 GGAAGACGAAGCGAAATGTTTA 57.343 40.909 0.00 0.00 0.00 2.01
987 1160 4.530857 GACATGGTCGAGGCGGGG 62.531 72.222 0.00 0.00 0.00 5.73
1410 1809 2.203195 GCATCCACATAGCCGCCA 60.203 61.111 0.00 0.00 0.00 5.69
1777 2176 7.695869 ACTATAAACTGTACTAAATGCGAGC 57.304 36.000 0.00 0.00 0.00 5.03
1842 2259 8.610896 CAATAGCAGGAGAAGTAAAGATTTCTG 58.389 37.037 0.00 0.00 32.16 3.02
1843 2260 8.543774 TCAATAGCAGGAGAAGTAAAGATTTCT 58.456 33.333 0.00 0.00 34.54 2.52
2100 2525 3.055719 ATCAAGTTGGCCACCGCG 61.056 61.111 3.88 0.00 35.02 6.46
2110 2535 3.508845 AACTACAGTGGGCATCAAGTT 57.491 42.857 0.00 0.00 0.00 2.66
2115 2540 2.200373 ACCAAACTACAGTGGGCATC 57.800 50.000 0.00 0.00 39.39 3.91
2123 2548 7.661847 AGGATGTTCTTCTAAACCAAACTACAG 59.338 37.037 0.00 0.00 0.00 2.74
2124 2549 7.514721 AGGATGTTCTTCTAAACCAAACTACA 58.485 34.615 0.00 0.00 0.00 2.74
2125 2550 7.981102 AGGATGTTCTTCTAAACCAAACTAC 57.019 36.000 0.00 0.00 0.00 2.73
2265 2690 3.595173 ACACTAATCACGCAGCACATAA 58.405 40.909 0.00 0.00 0.00 1.90
2267 2692 2.099141 ACACTAATCACGCAGCACAT 57.901 45.000 0.00 0.00 0.00 3.21
2276 2701 2.095853 CGGCCATGACAACACTAATCAC 59.904 50.000 2.24 0.00 0.00 3.06
2295 2720 4.471904 TCTTATATAGCCCATCAAGCGG 57.528 45.455 0.00 0.00 34.64 5.52
2296 2721 5.292834 CACATCTTATATAGCCCATCAAGCG 59.707 44.000 0.00 0.00 34.64 4.68
2340 2765 9.971922 GAAGCTGAAAACAAATTATGCCTATAT 57.028 29.630 0.00 0.00 0.00 0.86
2346 2771 9.667989 AAAAATGAAGCTGAAAACAAATTATGC 57.332 25.926 0.00 0.00 0.00 3.14
2360 2785 4.494526 GGTGCAACAACAAAAATGAAGCTG 60.495 41.667 0.00 0.00 39.98 4.24
2398 2823 7.539034 AACCTAAAATATGCAAGTCAAAGGT 57.461 32.000 0.00 0.00 35.18 3.50
2399 2824 8.831715 AAAACCTAAAATATGCAAGTCAAAGG 57.168 30.769 0.00 0.00 0.00 3.11
2409 2834 9.135843 ACTTAAAAGCGAAAACCTAAAATATGC 57.864 29.630 0.00 0.00 0.00 3.14
2449 2874 0.810648 GGCCTCGCATTTGTCAATGA 59.189 50.000 0.00 0.00 42.35 2.57
2463 2888 1.372087 CGCCACATGAAAGAGGCCTC 61.372 60.000 26.22 26.22 41.50 4.70
2513 2938 3.717400 ACTACAGAGATACGCCACATG 57.283 47.619 0.00 0.00 0.00 3.21
2519 2944 4.927425 TGGTTTTGAACTACAGAGATACGC 59.073 41.667 0.00 0.00 0.00 4.42
2520 2945 7.416154 TTTGGTTTTGAACTACAGAGATACG 57.584 36.000 0.00 0.00 0.00 3.06
2538 2963 9.889128 CCCAATGAAATACTCAAATATTTGGTT 57.111 29.630 24.40 15.32 37.44 3.67
2539 2964 7.986889 GCCCAATGAAATACTCAAATATTTGGT 59.013 33.333 24.40 21.60 37.44 3.67
2540 2965 8.206189 AGCCCAATGAAATACTCAAATATTTGG 58.794 33.333 24.40 17.88 38.28 3.28
2541 2966 9.037737 CAGCCCAATGAAATACTCAAATATTTG 57.962 33.333 20.13 20.13 37.67 2.32
2542 2967 8.761689 ACAGCCCAATGAAATACTCAAATATTT 58.238 29.630 0.00 0.00 37.67 1.40
2543 2968 8.310122 ACAGCCCAATGAAATACTCAAATATT 57.690 30.769 0.00 0.00 37.67 1.28
2544 2969 7.014615 GGACAGCCCAATGAAATACTCAAATAT 59.985 37.037 0.00 0.00 34.25 1.28
2545 2970 6.321181 GGACAGCCCAATGAAATACTCAAATA 59.679 38.462 0.00 0.00 34.25 1.40
2546 2971 5.127682 GGACAGCCCAATGAAATACTCAAAT 59.872 40.000 0.00 0.00 34.25 2.32
2547 2972 4.462483 GGACAGCCCAATGAAATACTCAAA 59.538 41.667 0.00 0.00 34.25 2.69
2548 2973 4.016444 GGACAGCCCAATGAAATACTCAA 58.984 43.478 0.00 0.00 34.25 3.02
2549 2974 3.010027 TGGACAGCCCAATGAAATACTCA 59.990 43.478 0.00 0.00 43.29 3.41
2550 2975 3.620488 TGGACAGCCCAATGAAATACTC 58.380 45.455 0.00 0.00 43.29 2.59
2564 2989 2.872858 GGAGACGGATTATTTGGACAGC 59.127 50.000 0.00 0.00 0.00 4.40
2880 3308 7.394359 TGCAAGAAAAGAATACCTAAGCTGAAT 59.606 33.333 0.00 0.00 0.00 2.57
2881 3309 6.714810 TGCAAGAAAAGAATACCTAAGCTGAA 59.285 34.615 0.00 0.00 0.00 3.02
2926 3354 3.011257 CCTATTCCAAGGTCTTTTGGGGA 59.989 47.826 5.06 0.00 46.16 4.81
2972 3401 0.107214 GGGCAATCAGACCGGAATCA 60.107 55.000 9.46 0.00 34.00 2.57
2983 3412 0.322816 GGCAGAGACAAGGGCAATCA 60.323 55.000 0.00 0.00 0.00 2.57
2984 3413 0.034670 AGGCAGAGACAAGGGCAATC 60.035 55.000 0.00 0.00 0.00 2.67
2985 3414 0.407139 AAGGCAGAGACAAGGGCAAT 59.593 50.000 0.00 0.00 0.00 3.56
3056 3487 3.052490 ACTGGATGCTAGAGTTAGGGACT 60.052 47.826 0.00 0.00 46.37 3.85
3192 3623 8.928270 TTATAAGACTTAGTTTCTAGCACTGC 57.072 34.615 0.73 0.00 0.00 4.40
3284 3716 4.829064 TTGTTGTGCCTGAGTGATAAAC 57.171 40.909 0.00 0.00 0.00 2.01
3285 3717 4.260990 CGTTTGTTGTGCCTGAGTGATAAA 60.261 41.667 0.00 0.00 0.00 1.40
3286 3718 3.249799 CGTTTGTTGTGCCTGAGTGATAA 59.750 43.478 0.00 0.00 0.00 1.75
3287 3719 2.805671 CGTTTGTTGTGCCTGAGTGATA 59.194 45.455 0.00 0.00 0.00 2.15
3288 3720 1.603802 CGTTTGTTGTGCCTGAGTGAT 59.396 47.619 0.00 0.00 0.00 3.06
3289 3721 1.013596 CGTTTGTTGTGCCTGAGTGA 58.986 50.000 0.00 0.00 0.00 3.41
3290 3722 0.732571 ACGTTTGTTGTGCCTGAGTG 59.267 50.000 0.00 0.00 0.00 3.51
3291 3723 0.732571 CACGTTTGTTGTGCCTGAGT 59.267 50.000 0.00 0.00 0.00 3.41
3315 3747 3.448686 CTGATGTAAGCTACGTTGAGGG 58.551 50.000 0.00 0.00 0.00 4.30
3384 3816 2.343426 ATGACCTCGCTGCTGTCGA 61.343 57.895 0.00 9.06 34.52 4.20
3410 3842 5.484715 TGTGTGCCTAGAGGTTGTATTAAC 58.515 41.667 0.00 0.00 37.57 2.01
3504 3936 4.037208 GCAATCCACCGATTTTGATCTGAT 59.963 41.667 0.00 0.00 36.54 2.90
3517 3949 2.514592 AGGCGATGCAATCCACCG 60.515 61.111 0.00 0.00 41.39 4.94
3623 4055 0.391661 CAAGTGCACTACAGGCGGAT 60.392 55.000 22.01 0.00 0.00 4.18
3703 4135 0.984961 CAGAGGAGGCTGGGGATTCA 60.985 60.000 0.00 0.00 32.26 2.57
3794 4232 2.334006 ACTCTGGATCAGGGACAGTT 57.666 50.000 1.38 0.00 35.18 3.16
4045 4483 3.415212 CTCAAGAAATGCTGGAGGTTGA 58.585 45.455 0.00 0.00 40.46 3.18
4063 4501 3.496884 GTGAAGGCAAACGAACATACTCA 59.503 43.478 0.00 0.00 0.00 3.41
4073 4511 1.532868 CTCTGAAGGTGAAGGCAAACG 59.467 52.381 0.00 0.00 0.00 3.60
4130 4568 4.362279 CCCTTATTGATTTGCACATTCCG 58.638 43.478 0.00 0.00 0.00 4.30
4135 4573 1.476085 CGGCCCTTATTGATTTGCACA 59.524 47.619 0.00 0.00 0.00 4.57
4177 4616 3.192541 AGCCGAATGTACATGCATACA 57.807 42.857 14.37 0.90 39.35 2.29
4179 4618 4.062293 GGTTAGCCGAATGTACATGCATA 58.938 43.478 14.37 0.97 0.00 3.14
4274 4713 1.055849 ACATCAGCACCACAGGTACA 58.944 50.000 0.00 0.00 32.11 2.90
4426 4865 0.467844 AGCATGTTCCAGCACCACAA 60.468 50.000 0.00 0.00 0.00 3.33
4595 5034 1.852942 ACACGTCCGCAGCATAATAG 58.147 50.000 0.00 0.00 0.00 1.73
4675 5122 2.943033 ACAAGCACCAAGTGTTCAGTAC 59.057 45.455 0.00 0.00 35.75 2.73
4769 5216 2.423538 GTCAACACAGCAACTTCCAACT 59.576 45.455 0.00 0.00 0.00 3.16
4803 5250 9.125026 ACAAGATAAAGAGTTATAAATGCCCAG 57.875 33.333 0.00 0.00 29.69 4.45
4831 5278 6.633856 TGATATGATAGTCATGAATCACGGG 58.366 40.000 11.41 0.00 37.70 5.28
4834 5281 7.042858 GCGGATGATATGATAGTCATGAATCAC 60.043 40.741 11.41 3.00 35.73 3.06
4944 5391 9.681692 CATTAAAACATGAATCTGTTCTGTTGA 57.318 29.630 0.00 0.00 38.38 3.18
4961 5408 7.384439 TGAAGATATGAACCGCATTAAAACA 57.616 32.000 0.00 0.00 38.44 2.83
5024 5471 9.696917 GAATAATTGAGTTGAAACCAAATGACT 57.303 29.630 0.00 0.00 0.00 3.41
5053 5500 4.536765 ACAGAAACCACTTCCTTGTGATT 58.463 39.130 0.00 0.00 40.12 2.57
5121 5569 6.037062 CAGATACCACGAAATAAAGCATGTCA 59.963 38.462 0.00 0.00 0.00 3.58
5132 5580 4.056050 GCGTATTCCAGATACCACGAAAT 58.944 43.478 0.00 0.00 0.00 2.17
5181 5631 4.020543 GCCATCCATACCCAGTTAAACAA 58.979 43.478 0.00 0.00 0.00 2.83
5182 5632 3.268334 AGCCATCCATACCCAGTTAAACA 59.732 43.478 0.00 0.00 0.00 2.83
5183 5633 3.632145 CAGCCATCCATACCCAGTTAAAC 59.368 47.826 0.00 0.00 0.00 2.01
5198 5648 5.591099 TGAAAGAAAAACACTTCAGCCATC 58.409 37.500 0.00 0.00 0.00 3.51
5207 5657 7.004086 TCCAGATACCATGAAAGAAAAACACT 58.996 34.615 0.00 0.00 0.00 3.55
5233 5683 2.238646 TGACAGGTTGTGGAAAGAGTGT 59.761 45.455 0.00 0.00 0.00 3.55
5247 5697 1.271379 CAGTTGCATTGCATGACAGGT 59.729 47.619 12.95 0.00 38.76 4.00
5412 5927 6.738114 TCTTTAAGCAGATTTTGTTCACCAG 58.262 36.000 0.00 0.00 0.00 4.00
5444 5959 2.938956 ACTGCATATAGGAACTGCCC 57.061 50.000 0.00 0.00 41.52 5.36
5662 6179 0.902531 GAGAGATTTGTCCCCGGTCA 59.097 55.000 0.00 0.00 0.00 4.02
5905 6422 5.012664 TGAGGTTGCTGAACTTAATGTCCTA 59.987 40.000 0.00 0.00 32.15 2.94
5909 6426 5.413833 CAGATGAGGTTGCTGAACTTAATGT 59.586 40.000 0.00 0.00 32.15 2.71
6099 6616 1.061131 CATGTCCGCGTCAGTTCAATC 59.939 52.381 4.92 0.00 0.00 2.67
6217 6734 5.757850 AGATATCAAAAGCAAATCCCGTC 57.242 39.130 5.32 0.00 0.00 4.79
6227 6744 7.041508 CCAGGATAGACACAAGATATCAAAAGC 60.042 40.741 5.32 0.00 0.00 3.51
6242 6759 1.977854 ACACAGCAACCAGGATAGACA 59.022 47.619 0.00 0.00 0.00 3.41
6316 6833 4.389890 TGAACATGGCATAATGGCTTTC 57.610 40.909 0.00 0.00 44.10 2.62
6330 6847 2.809446 CAAGGCATGCTGATGAACATG 58.191 47.619 18.92 0.00 45.19 3.21
6370 6887 8.641498 AAAAAGAGATAACATGAACATGGAGT 57.359 30.769 17.25 6.48 42.91 3.85
6406 6923 7.549134 CAGCAACATAAAGATCAAGTAGTACCA 59.451 37.037 0.00 0.00 0.00 3.25
6407 6924 7.549488 ACAGCAACATAAAGATCAAGTAGTACC 59.451 37.037 0.00 0.00 0.00 3.34
6408 6925 8.480643 ACAGCAACATAAAGATCAAGTAGTAC 57.519 34.615 0.00 0.00 0.00 2.73
6409 6926 9.502091 AAACAGCAACATAAAGATCAAGTAGTA 57.498 29.630 0.00 0.00 0.00 1.82
6410 6927 7.986085 AACAGCAACATAAAGATCAAGTAGT 57.014 32.000 0.00 0.00 0.00 2.73
6411 6928 7.965107 GGAAACAGCAACATAAAGATCAAGTAG 59.035 37.037 0.00 0.00 0.00 2.57
6412 6929 7.665559 AGGAAACAGCAACATAAAGATCAAGTA 59.334 33.333 0.00 0.00 0.00 2.24
6416 6933 6.899393 AAGGAAACAGCAACATAAAGATCA 57.101 33.333 0.00 0.00 0.00 2.92
6420 6937 7.951530 ATTCAAAGGAAACAGCAACATAAAG 57.048 32.000 0.00 0.00 36.43 1.85
6480 6997 6.333416 TCTCAAACTCCAGAAATATCTCGTG 58.667 40.000 0.00 0.00 32.03 4.35
6482 6999 6.423302 CCATCTCAAACTCCAGAAATATCTCG 59.577 42.308 0.00 0.00 32.03 4.04
6483 7000 7.504403 TCCATCTCAAACTCCAGAAATATCTC 58.496 38.462 0.00 0.00 32.03 2.75
6521 7041 5.821470 GGTCCAGGGTCTAACTTTAAATAGC 59.179 44.000 0.00 0.00 0.00 2.97
6555 7075 5.013808 AGGTTGGGCTGTATTTAGTTGTAGT 59.986 40.000 0.00 0.00 0.00 2.73
6556 7076 5.497474 AGGTTGGGCTGTATTTAGTTGTAG 58.503 41.667 0.00 0.00 0.00 2.74
6557 7077 5.508280 AGGTTGGGCTGTATTTAGTTGTA 57.492 39.130 0.00 0.00 0.00 2.41
6569 7089 3.483954 CCTGTCATAGGTTGGGCTG 57.516 57.895 0.00 0.00 42.00 4.85
6612 7158 0.322546 GAGAACAATTGTCCCGGCCT 60.323 55.000 12.39 2.78 0.00 5.19
6613 7159 0.322546 AGAGAACAATTGTCCCGGCC 60.323 55.000 12.39 0.00 0.00 6.13
6614 7160 0.804989 CAGAGAACAATTGTCCCGGC 59.195 55.000 12.39 5.39 0.00 6.13
6615 7161 2.185004 ACAGAGAACAATTGTCCCGG 57.815 50.000 12.39 7.37 0.00 5.73
6640 7194 5.305585 ACAGTGGGTGTGAGTAATAAGTTG 58.694 41.667 0.00 0.00 38.28 3.16
6693 7247 4.280929 GGTCAGCCTTAATTTGTTCCTGTT 59.719 41.667 0.00 0.00 0.00 3.16
6695 7249 3.193479 GGGTCAGCCTTAATTTGTTCCTG 59.807 47.826 0.00 0.00 34.45 3.86
6765 7338 5.236911 AGCTCGTACTACTACTGCAGAATAC 59.763 44.000 23.35 11.32 0.00 1.89
6769 7342 3.196463 GAGCTCGTACTACTACTGCAGA 58.804 50.000 23.35 2.95 0.00 4.26
6771 7344 1.931841 CGAGCTCGTACTACTACTGCA 59.068 52.381 27.79 0.00 34.11 4.41
6860 7433 2.409651 GACCACGCACGCCAAAAA 59.590 55.556 0.00 0.00 0.00 1.94
6861 7434 3.587933 GGACCACGCACGCCAAAA 61.588 61.111 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.