Multiple sequence alignment - TraesCS2D01G222600

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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 TraesCS2D01G222600 chr2D 100.000 2812 0 0 1 2812 189602505 189599694 0.000000e+00 5193.0
1 TraesCS2D01G222600 chr2A 90.917 1112 74 9 1609 2702 203392633 203391531 0.000000e+00 1469.0
2 TraesCS2D01G222600 chr2A 89.404 755 45 10 760 1489 203393434 203392690 0.000000e+00 918.0
3 TraesCS2D01G222600 chr2A 89.147 516 36 6 9 520 203394201 203393702 2.380000e-175 625.0
4 TraesCS2D01G222600 chr2A 96.825 63 2 0 684 746 203393539 203393477 3.830000e-19 106.0
5 TraesCS2D01G222600 chr2B 89.259 1080 83 11 533 1598 245889813 245888753 0.000000e+00 1321.0
6 TraesCS2D01G222600 chr2B 89.588 413 39 4 1606 2017 245888418 245888009 3.210000e-144 521.0
7 TraesCS2D01G222600 chr2B 94.898 294 13 2 229 520 245890088 245889795 2.550000e-125 459.0
8 TraesCS2D01G222600 chr2B 92.015 263 18 1 1321 1583 245888844 245888585 1.590000e-97 366.0
9 TraesCS2D01G222600 chr2B 90.141 213 17 3 5 214 245892369 245892158 9.920000e-70 274.0
10 TraesCS2D01G222600 chr2B 82.877 146 10 5 1473 1617 245888625 245888494 1.770000e-22 117.0
11 TraesCS2D01G222600 chr2B 98.039 51 0 1 202 251 245890216 245890166 1.390000e-13 87.9


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 TraesCS2D01G222600 chr2D 189599694 189602505 2811 True 5193.000000 5193 100.000000 1 2812 1 chr2D.!!$R1 2811
1 TraesCS2D01G222600 chr2A 203391531 203394201 2670 True 779.500000 1469 91.573250 9 2702 4 chr2A.!!$R1 2693
2 TraesCS2D01G222600 chr2B 245888009 245892369 4360 True 449.414286 1321 90.973857 5 2017 7 chr2B.!!$R1 2012

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
994 3118 0.032615 TCCCATACAAACCCCCATGC 60.033 55.0 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2737 5238 0.107703 CGTACTGGGGCATGACATGT 60.108 55.0 16.62 0.0 0.0 3.21 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
120 123 3.953775 CGGGTGGCTGGACTTGGT 61.954 66.667 0.00 0.00 0.00 3.67
278 2338 3.569548 CGAGTGAAGATACATGCGCTAT 58.430 45.455 9.73 0.00 0.00 2.97
292 2352 2.224281 TGCGCTATTCGATGGATTTCCT 60.224 45.455 9.73 0.00 41.67 3.36
395 2456 7.227049 TGGCGAGTGTATCAGAAATATCATA 57.773 36.000 0.00 0.00 0.00 2.15
462 2523 3.372730 GGCGGCCAATTGTGCTGA 61.373 61.111 23.73 0.00 37.27 4.26
497 2558 1.270571 GGATGGAGCTAGCTAACTGCC 60.271 57.143 19.38 14.80 44.23 4.85
501 2562 2.032620 GGAGCTAGCTAACTGCCACTA 58.967 52.381 19.38 0.00 44.23 2.74
502 2563 2.035321 GGAGCTAGCTAACTGCCACTAG 59.965 54.545 19.38 0.00 44.23 2.57
516 2577 3.936661 GCCACTAGCAGTAAAATAACGC 58.063 45.455 0.00 0.00 42.97 4.84
517 2578 3.372822 GCCACTAGCAGTAAAATAACGCA 59.627 43.478 0.00 0.00 42.97 5.24
518 2579 4.035208 GCCACTAGCAGTAAAATAACGCAT 59.965 41.667 0.00 0.00 42.97 4.73
519 2580 5.448632 GCCACTAGCAGTAAAATAACGCATT 60.449 40.000 0.00 0.00 42.97 3.56
520 2581 6.551736 CCACTAGCAGTAAAATAACGCATTT 58.448 36.000 0.00 0.00 38.54 2.32
521 2582 6.687105 CCACTAGCAGTAAAATAACGCATTTC 59.313 38.462 0.00 0.00 35.74 2.17
522 2583 6.687105 CACTAGCAGTAAAATAACGCATTTCC 59.313 38.462 0.00 0.00 35.74 3.13
523 2584 4.993905 AGCAGTAAAATAACGCATTTCCC 58.006 39.130 0.00 0.00 35.74 3.97
524 2585 4.705023 AGCAGTAAAATAACGCATTTCCCT 59.295 37.500 0.00 0.00 35.74 4.20
525 2586 5.883673 AGCAGTAAAATAACGCATTTCCCTA 59.116 36.000 0.00 0.00 35.74 3.53
526 2587 6.376018 AGCAGTAAAATAACGCATTTCCCTAA 59.624 34.615 0.00 0.00 35.74 2.69
527 2588 7.030768 GCAGTAAAATAACGCATTTCCCTAAA 58.969 34.615 0.00 0.00 35.74 1.85
528 2589 7.542824 GCAGTAAAATAACGCATTTCCCTAAAA 59.457 33.333 0.00 0.00 35.74 1.52
529 2590 9.413048 CAGTAAAATAACGCATTTCCCTAAAAA 57.587 29.630 0.00 0.00 35.74 1.94
610 2673 2.081462 GCCGTGTAACTTTATGCCTGT 58.919 47.619 0.00 0.00 31.75 4.00
628 2691 4.000557 CCGCGCACATACATCCGC 62.001 66.667 8.75 0.00 42.71 5.54
629 2692 4.000557 CGCGCACATACATCCGCC 62.001 66.667 8.75 0.00 43.16 6.13
630 2693 4.000557 GCGCACATACATCCGCCG 62.001 66.667 0.30 0.00 40.51 6.46
651 2714 1.268386 CGTACATACGTGTCCAGCGAT 60.268 52.381 0.00 0.00 44.13 4.58
661 2724 2.679837 GTGTCCAGCGATCATCATTTGT 59.320 45.455 0.00 0.00 0.00 2.83
673 2736 6.037940 CGATCATCATTTGTCATCTCCTTTGT 59.962 38.462 0.00 0.00 0.00 2.83
674 2737 6.748333 TCATCATTTGTCATCTCCTTTGTC 57.252 37.500 0.00 0.00 0.00 3.18
675 2738 5.649395 TCATCATTTGTCATCTCCTTTGTCC 59.351 40.000 0.00 0.00 0.00 4.02
677 2740 5.005740 TCATTTGTCATCTCCTTTGTCCAG 58.994 41.667 0.00 0.00 0.00 3.86
678 2741 2.479566 TGTCATCTCCTTTGTCCAGC 57.520 50.000 0.00 0.00 0.00 4.85
679 2742 1.338105 TGTCATCTCCTTTGTCCAGCG 60.338 52.381 0.00 0.00 0.00 5.18
680 2743 1.066858 GTCATCTCCTTTGTCCAGCGA 60.067 52.381 0.00 0.00 0.00 4.93
681 2744 1.833630 TCATCTCCTTTGTCCAGCGAT 59.166 47.619 0.00 0.00 0.00 4.58
682 2745 2.159043 TCATCTCCTTTGTCCAGCGATC 60.159 50.000 0.00 0.00 0.00 3.69
749 2869 8.722480 TGTCAAGAGGTAAAAGATGATATGTG 57.278 34.615 0.00 0.00 0.00 3.21
793 2917 2.396590 TGCCAAAGTTAGGTCCGATC 57.603 50.000 0.00 0.00 0.00 3.69
794 2918 1.287425 GCCAAAGTTAGGTCCGATCG 58.713 55.000 8.51 8.51 0.00 3.69
853 2977 5.410924 AGAGTTGAAAAGGAAAACAACAGC 58.589 37.500 0.00 0.00 43.06 4.40
915 3039 1.205460 GGTGTACCCATGACCCAGGT 61.205 60.000 0.00 0.00 37.69 4.00
916 3040 0.035439 GTGTACCCATGACCCAGGTG 60.035 60.000 0.00 0.00 35.02 4.00
918 3042 0.541863 GTACCCATGACCCAGGTGAG 59.458 60.000 0.00 0.00 35.02 3.51
963 3087 2.521708 GGTGTTGCTTGGCTGGGT 60.522 61.111 0.00 0.00 0.00 4.51
977 3101 2.553247 GGCTGGGTGCTCCTATAAATCC 60.553 54.545 4.53 0.00 42.39 3.01
979 3103 2.711009 CTGGGTGCTCCTATAAATCCCA 59.289 50.000 4.53 0.00 40.70 4.37
987 3111 6.206829 GTGCTCCTATAAATCCCATACAAACC 59.793 42.308 0.00 0.00 0.00 3.27
994 3118 0.032615 TCCCATACAAACCCCCATGC 60.033 55.000 0.00 0.00 0.00 4.06
995 3119 1.048160 CCCATACAAACCCCCATGCC 61.048 60.000 0.00 0.00 0.00 4.40
996 3120 0.325110 CCATACAAACCCCCATGCCA 60.325 55.000 0.00 0.00 0.00 4.92
997 3121 1.692121 CCATACAAACCCCCATGCCAT 60.692 52.381 0.00 0.00 0.00 4.40
998 3122 2.117865 CATACAAACCCCCATGCCATT 58.882 47.619 0.00 0.00 0.00 3.16
999 3123 2.334006 TACAAACCCCCATGCCATTT 57.666 45.000 0.00 0.00 0.00 2.32
1000 3124 0.691904 ACAAACCCCCATGCCATTTG 59.308 50.000 7.84 7.84 36.54 2.32
1001 3125 0.677414 CAAACCCCCATGCCATTTGC 60.677 55.000 0.00 0.00 41.77 3.68
1053 3177 2.499289 AGAGTGACCCAGCAAGTGATAG 59.501 50.000 0.00 0.00 0.00 2.08
1057 3181 4.716784 AGTGACCCAGCAAGTGATAGATAA 59.283 41.667 0.00 0.00 0.00 1.75
1059 3183 6.058183 GTGACCCAGCAAGTGATAGATAAAT 58.942 40.000 0.00 0.00 0.00 1.40
1060 3184 6.543831 GTGACCCAGCAAGTGATAGATAAATT 59.456 38.462 0.00 0.00 0.00 1.82
1082 3206 2.035442 GCACCAAGAAGACCTCGCC 61.035 63.158 0.00 0.00 0.00 5.54
1101 3225 1.077357 ACGATGAGGTCTCTCGGCT 60.077 57.895 17.28 3.01 42.79 5.52
1128 3252 1.228367 CTGTGCTTTCACCTGGCCT 60.228 57.895 3.32 0.00 42.46 5.19
1146 3270 0.037303 CTTGCTTCTCCTCCTTGCCA 59.963 55.000 0.00 0.00 0.00 4.92
1193 3317 1.670590 CGATGGAGGGAGGCTCATC 59.329 63.158 17.69 13.19 34.37 2.92
1288 3418 0.401250 AACCCAAACCCAAAGCCCAT 60.401 50.000 0.00 0.00 0.00 4.00
1294 3424 0.609131 AACCCAAAGCCCATGACTCG 60.609 55.000 0.00 0.00 0.00 4.18
1370 3525 2.534396 AATGCCTCAACCGGACCCA 61.534 57.895 9.46 0.00 0.00 4.51
1394 3549 2.037641 GCCAACTCCTGAAAAGCCAAAT 59.962 45.455 0.00 0.00 0.00 2.32
1532 3870 1.477558 CCAGAAGTCAAGCCACAACCT 60.478 52.381 0.00 0.00 0.00 3.50
1541 3879 0.396974 AGCCACAACCTCAGCCAAAA 60.397 50.000 0.00 0.00 0.00 2.44
1575 3970 0.752658 AAAACCCACTCCTGCAAAGC 59.247 50.000 0.00 0.00 0.00 3.51
1584 3979 2.268920 CTGCAAAGCCGGAGCCTA 59.731 61.111 5.05 0.00 41.25 3.93
1655 4137 2.180159 GACCGTCCAAGCCTAAGCCA 62.180 60.000 0.00 0.00 41.25 4.75
1707 4189 1.142748 CCCCTCAACTGAGCTAGCG 59.857 63.158 9.55 0.00 40.75 4.26
1708 4190 1.142748 CCCTCAACTGAGCTAGCGG 59.857 63.158 9.55 6.47 40.75 5.52
1768 4250 1.133790 GTCACGTATACCGACAGGCTT 59.866 52.381 12.88 0.00 42.76 4.35
1769 4251 2.355756 GTCACGTATACCGACAGGCTTA 59.644 50.000 12.88 0.00 42.76 3.09
1773 4255 4.913924 CACGTATACCGACAGGCTTATAAC 59.086 45.833 0.00 0.00 42.76 1.89
1809 4291 1.073763 TGGAATAAGCAGCAGTGTGGT 59.926 47.619 0.00 0.00 0.00 4.16
2039 4537 5.652518 ACCTAATTTCTGACTTACGAGAGC 58.347 41.667 0.00 0.00 0.00 4.09
2112 4610 4.378356 CCCGATCATGCAAAATATACCACG 60.378 45.833 0.00 0.00 0.00 4.94
2129 4627 9.872757 ATATACCACGCAAACTTTTATTATTCG 57.127 29.630 0.00 0.00 0.00 3.34
2221 4719 9.552114 CAACAATACATTTTTGAAAAGTTGCAA 57.448 25.926 0.00 0.00 31.02 4.08
2291 4790 9.303537 GCTAATTCTCATCTAAGAAAGTACGTT 57.696 33.333 0.00 0.00 38.69 3.99
2310 4809 8.718734 AGTACGTTGAACTTCTAATCCATTTTC 58.281 33.333 0.00 0.00 0.00 2.29
2313 4812 6.151144 CGTTGAACTTCTAATCCATTTTCCCT 59.849 38.462 0.00 0.00 0.00 4.20
2354 4855 9.896645 ATCTATTTGTTATATGCGGAGATTCAT 57.103 29.630 0.00 0.00 0.00 2.57
2457 4958 2.933878 AAACTTGCACGTCCGCCTGA 62.934 55.000 0.00 0.00 0.00 3.86
2458 4959 2.434884 CTTGCACGTCCGCCTGAT 60.435 61.111 0.00 0.00 0.00 2.90
2461 4962 2.742372 GCACGTCCGCCTGATTGT 60.742 61.111 0.00 0.00 0.00 2.71
2464 4965 1.070786 ACGTCCGCCTGATTGTTGT 59.929 52.632 0.00 0.00 0.00 3.32
2479 4980 7.485913 CCTGATTGTTGTCAATTATAGTTGCAC 59.514 37.037 3.19 4.06 43.33 4.57
2498 4999 3.061139 GCACGTCTTCGACTATGCAATAC 60.061 47.826 12.39 0.00 40.01 1.89
2500 5001 4.438145 CACGTCTTCGACTATGCAATACTC 59.562 45.833 0.00 0.00 40.62 2.59
2509 5010 6.015434 TCGACTATGCAATACTCCATGTACAT 60.015 38.462 1.41 1.41 33.45 2.29
2512 5013 7.508687 ACTATGCAATACTCCATGTACATTGA 58.491 34.615 5.37 7.58 33.45 2.57
2514 5015 6.866010 TGCAATACTCCATGTACATTGATC 57.134 37.500 5.37 0.00 33.45 2.92
2520 5021 4.342378 ACTCCATGTACATTGATCGTAGCT 59.658 41.667 5.37 0.00 0.00 3.32
2521 5022 5.163405 ACTCCATGTACATTGATCGTAGCTT 60.163 40.000 5.37 0.00 0.00 3.74
2523 5024 5.069119 TCCATGTACATTGATCGTAGCTTCT 59.931 40.000 5.37 0.00 0.00 2.85
2529 5030 5.237815 ACATTGATCGTAGCTTCTGTTTCA 58.762 37.500 0.00 0.00 0.00 2.69
2550 5051 1.734465 CAGATTTGGTCTTCGGCTCAC 59.266 52.381 0.00 0.00 34.00 3.51
2558 5059 0.902984 TCTTCGGCTCACAAGGCCTA 60.903 55.000 5.16 0.00 46.73 3.93
2601 5102 2.584835 TATTGGTTTGCTGGTGCTCT 57.415 45.000 0.00 0.00 40.48 4.09
2602 5103 0.963962 ATTGGTTTGCTGGTGCTCTG 59.036 50.000 0.00 0.00 40.48 3.35
2603 5104 1.737355 TTGGTTTGCTGGTGCTCTGC 61.737 55.000 3.40 3.40 40.48 4.26
2630 5131 1.781429 CTACGATTTGCATCTCGACGG 59.219 52.381 21.07 9.33 38.24 4.79
2659 5160 2.993220 GGTCAATGGCGGTTTCAAATTC 59.007 45.455 0.00 0.00 0.00 2.17
2669 5170 4.208253 GCGGTTTCAAATTCGATTGTTTGT 59.792 37.500 14.26 0.00 36.83 2.83
2672 5173 5.431309 GTTTCAAATTCGATTGTTTGTGGC 58.569 37.500 14.26 6.08 36.83 5.01
2681 5182 3.047877 GTTTGTGGCGACCCCGAG 61.048 66.667 0.00 0.00 38.22 4.63
2731 5232 8.902540 ATGGGGATTCTTTTTGTAAAGTTTTC 57.097 30.769 0.00 0.00 41.25 2.29
2732 5233 8.084985 TGGGGATTCTTTTTGTAAAGTTTTCT 57.915 30.769 0.00 0.00 41.25 2.52
2733 5234 7.984617 TGGGGATTCTTTTTGTAAAGTTTTCTG 59.015 33.333 0.00 0.00 41.25 3.02
2734 5235 8.201464 GGGGATTCTTTTTGTAAAGTTTTCTGA 58.799 33.333 0.00 0.00 41.25 3.27
2735 5236 9.594478 GGGATTCTTTTTGTAAAGTTTTCTGAA 57.406 29.630 0.00 0.00 41.25 3.02
2742 5243 9.921637 TTTTTGTAAAGTTTTCTGAAGACATGT 57.078 25.926 12.82 0.00 0.00 3.21
2743 5244 9.567848 TTTTGTAAAGTTTTCTGAAGACATGTC 57.432 29.630 18.47 18.47 0.00 3.06
2744 5245 7.857734 TGTAAAGTTTTCTGAAGACATGTCA 57.142 32.000 27.02 7.08 0.00 3.58
2745 5246 8.450578 TGTAAAGTTTTCTGAAGACATGTCAT 57.549 30.769 27.02 16.37 0.00 3.06
2746 5247 8.344831 TGTAAAGTTTTCTGAAGACATGTCATG 58.655 33.333 27.02 11.41 0.00 3.07
2747 5248 5.368256 AGTTTTCTGAAGACATGTCATGC 57.632 39.130 27.02 15.55 0.00 4.06
2748 5249 4.217118 AGTTTTCTGAAGACATGTCATGCC 59.783 41.667 27.02 12.97 0.00 4.40
2749 5250 2.408271 TCTGAAGACATGTCATGCCC 57.592 50.000 27.02 11.34 0.00 5.36
2750 5251 1.065199 TCTGAAGACATGTCATGCCCC 60.065 52.381 27.02 9.74 0.00 5.80
2751 5252 0.697658 TGAAGACATGTCATGCCCCA 59.302 50.000 27.02 11.98 0.00 4.96
2752 5253 1.340308 TGAAGACATGTCATGCCCCAG 60.340 52.381 27.02 0.00 0.00 4.45
2753 5254 0.700564 AAGACATGTCATGCCCCAGT 59.299 50.000 27.02 0.42 0.00 4.00
2754 5255 1.583556 AGACATGTCATGCCCCAGTA 58.416 50.000 27.02 0.00 0.00 2.74
2755 5256 1.210478 AGACATGTCATGCCCCAGTAC 59.790 52.381 27.02 0.00 0.00 2.73
2756 5257 0.107703 ACATGTCATGCCCCAGTACG 60.108 55.000 12.91 0.00 0.00 3.67
2757 5258 0.177836 CATGTCATGCCCCAGTACGA 59.822 55.000 0.00 0.00 0.00 3.43
2758 5259 0.178068 ATGTCATGCCCCAGTACGAC 59.822 55.000 0.00 0.00 0.00 4.34
2759 5260 0.902984 TGTCATGCCCCAGTACGACT 60.903 55.000 0.00 0.00 0.00 4.18
2760 5261 0.460284 GTCATGCCCCAGTACGACTG 60.460 60.000 7.72 7.72 45.53 3.51
2761 5262 1.815421 CATGCCCCAGTACGACTGC 60.815 63.158 8.85 0.94 44.63 4.40
2762 5263 1.990060 ATGCCCCAGTACGACTGCT 60.990 57.895 8.85 0.00 44.63 4.24
2763 5264 0.686441 ATGCCCCAGTACGACTGCTA 60.686 55.000 8.85 0.00 44.63 3.49
2764 5265 1.320344 TGCCCCAGTACGACTGCTAG 61.320 60.000 8.85 0.00 44.63 3.42
2765 5266 1.321074 GCCCCAGTACGACTGCTAGT 61.321 60.000 8.85 0.00 44.63 2.57
2766 5267 1.183549 CCCCAGTACGACTGCTAGTT 58.816 55.000 8.85 0.00 44.63 2.24
2767 5268 1.549170 CCCCAGTACGACTGCTAGTTT 59.451 52.381 8.85 0.00 44.63 2.66
2768 5269 2.416972 CCCCAGTACGACTGCTAGTTTC 60.417 54.545 8.85 0.00 44.63 2.78
2769 5270 2.416972 CCCAGTACGACTGCTAGTTTCC 60.417 54.545 8.85 0.00 44.63 3.13
2770 5271 2.516923 CAGTACGACTGCTAGTTTCCG 58.483 52.381 0.00 0.00 39.62 4.30
2771 5272 1.135460 AGTACGACTGCTAGTTTCCGC 60.135 52.381 0.00 0.00 0.00 5.54
2772 5273 0.883153 TACGACTGCTAGTTTCCGCA 59.117 50.000 0.00 0.00 34.54 5.69
2773 5274 0.246635 ACGACTGCTAGTTTCCGCAT 59.753 50.000 0.00 0.00 35.32 4.73
2774 5275 0.647410 CGACTGCTAGTTTCCGCATG 59.353 55.000 0.00 0.00 35.32 4.06
2775 5276 1.726853 GACTGCTAGTTTCCGCATGT 58.273 50.000 0.00 0.00 35.32 3.21
2776 5277 2.734175 CGACTGCTAGTTTCCGCATGTA 60.734 50.000 0.00 0.00 35.32 2.29
2777 5278 3.458189 GACTGCTAGTTTCCGCATGTAT 58.542 45.455 0.00 0.00 35.32 2.29
2778 5279 3.198068 ACTGCTAGTTTCCGCATGTATG 58.802 45.455 0.00 0.00 35.32 2.39
2779 5280 3.198068 CTGCTAGTTTCCGCATGTATGT 58.802 45.455 0.00 0.00 35.32 2.29
2780 5281 4.142026 ACTGCTAGTTTCCGCATGTATGTA 60.142 41.667 0.00 0.00 35.32 2.29
2781 5282 4.956085 TGCTAGTTTCCGCATGTATGTAT 58.044 39.130 0.00 0.00 0.00 2.29
2782 5283 4.749598 TGCTAGTTTCCGCATGTATGTATG 59.250 41.667 0.00 0.00 0.00 2.39
2783 5284 4.750098 GCTAGTTTCCGCATGTATGTATGT 59.250 41.667 0.00 0.00 0.00 2.29
2784 5285 5.924254 GCTAGTTTCCGCATGTATGTATGTA 59.076 40.000 0.00 0.00 0.00 2.29
2785 5286 6.590292 GCTAGTTTCCGCATGTATGTATGTAT 59.410 38.462 0.00 0.00 0.00 2.29
2786 5287 6.785488 AGTTTCCGCATGTATGTATGTATG 57.215 37.500 0.00 0.00 0.00 2.39
2787 5288 6.288294 AGTTTCCGCATGTATGTATGTATGT 58.712 36.000 0.00 0.00 0.00 2.29
2788 5289 7.438564 AGTTTCCGCATGTATGTATGTATGTA 58.561 34.615 0.00 0.00 0.00 2.29
2789 5290 8.094548 AGTTTCCGCATGTATGTATGTATGTAT 58.905 33.333 0.00 0.00 0.00 2.29
2790 5291 7.826260 TTCCGCATGTATGTATGTATGTATG 57.174 36.000 0.00 0.00 0.00 2.39
2791 5292 6.930731 TCCGCATGTATGTATGTATGTATGT 58.069 36.000 0.00 0.00 0.00 2.29
2792 5293 8.057536 TCCGCATGTATGTATGTATGTATGTA 57.942 34.615 0.00 0.00 0.00 2.29
2793 5294 8.691797 TCCGCATGTATGTATGTATGTATGTAT 58.308 33.333 0.00 0.00 0.00 2.29
2794 5295 8.755018 CCGCATGTATGTATGTATGTATGTATG 58.245 37.037 0.00 0.00 0.00 2.39
2795 5296 9.301153 CGCATGTATGTATGTATGTATGTATGT 57.699 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 33 8.537016 GCATAGTAAAAGGAAAAACCCCTAAAT 58.463 33.333 0.00 0.00 40.05 1.40
43 46 2.536365 CACGAGCGCATAGTAAAAGGA 58.464 47.619 11.47 0.00 0.00 3.36
45 48 2.353257 GCACGAGCGCATAGTAAAAG 57.647 50.000 11.47 0.00 0.00 2.27
65 68 1.909376 TCGCGCAGTAGTTCAATCTC 58.091 50.000 8.75 0.00 0.00 2.75
111 114 0.685097 GCACTCACCTACCAAGTCCA 59.315 55.000 0.00 0.00 0.00 4.02
120 123 3.390521 CGCAGGGGCACTCACCTA 61.391 66.667 0.00 0.00 41.24 3.08
251 2209 3.797184 GCATGTATCTTCACTCGGTCTCC 60.797 52.174 0.00 0.00 0.00 3.71
278 2338 8.580720 TCACAAATAAAAAGGAAATCCATCGAA 58.419 29.630 1.67 0.00 38.89 3.71
497 2558 6.687105 GGAAATGCGTTATTTTACTGCTAGTG 59.313 38.462 0.00 0.00 39.06 2.74
501 2562 4.705023 AGGGAAATGCGTTATTTTACTGCT 59.295 37.500 0.00 0.00 39.06 4.24
502 2563 4.993905 AGGGAAATGCGTTATTTTACTGC 58.006 39.130 0.00 0.00 39.06 4.40
503 2564 8.973835 TTTTAGGGAAATGCGTTATTTTACTG 57.026 30.769 0.00 0.00 39.06 2.74
528 2589 6.270064 ACAGTGCGTTATTTTACTGCTTTTT 58.730 32.000 0.00 0.00 43.18 1.94
529 2590 5.827666 ACAGTGCGTTATTTTACTGCTTTT 58.172 33.333 0.00 0.00 43.18 2.27
530 2591 5.432885 ACAGTGCGTTATTTTACTGCTTT 57.567 34.783 0.00 0.00 43.18 3.51
531 2592 5.212194 CAACAGTGCGTTATTTTACTGCTT 58.788 37.500 0.00 0.00 43.18 3.91
585 2648 2.285977 CATAAAGTTACACGGCCCCTC 58.714 52.381 0.00 0.00 0.00 4.30
610 2673 2.279186 CGGATGTATGTGCGCGGA 60.279 61.111 8.83 0.00 0.00 5.54
651 2714 5.649395 GGACAAAGGAGATGACAAATGATGA 59.351 40.000 0.00 0.00 0.00 2.92
661 2724 1.266178 TCGCTGGACAAAGGAGATGA 58.734 50.000 0.00 0.00 0.00 2.92
673 2736 0.804364 GTTGCAACATGATCGCTGGA 59.196 50.000 24.52 0.00 0.00 3.86
674 2737 0.521867 CGTTGCAACATGATCGCTGG 60.522 55.000 28.01 4.98 0.00 4.85
675 2738 1.129879 GCGTTGCAACATGATCGCTG 61.130 55.000 28.01 10.28 40.39 5.18
677 2740 2.210375 CGCGTTGCAACATGATCGC 61.210 57.895 28.01 22.15 40.19 4.58
678 2741 1.580893 CCGCGTTGCAACATGATCG 60.581 57.895 28.01 19.97 0.00 3.69
679 2742 1.226379 CCCGCGTTGCAACATGATC 60.226 57.895 28.01 10.72 0.00 2.92
680 2743 0.675208 TACCCGCGTTGCAACATGAT 60.675 50.000 28.01 12.10 0.00 2.45
681 2744 1.295357 CTACCCGCGTTGCAACATGA 61.295 55.000 28.01 6.87 0.00 3.07
682 2745 1.134487 CTACCCGCGTTGCAACATG 59.866 57.895 28.01 18.79 0.00 3.21
773 2897 2.741878 CGATCGGACCTAACTTTGGCAT 60.742 50.000 7.38 0.00 0.00 4.40
868 2992 1.067416 CATGATGTGCCATGCAGCC 59.933 57.895 0.00 0.00 40.08 4.85
913 3037 2.226912 CCTCCGTATCGATCTTCTCACC 59.773 54.545 0.00 0.00 0.00 4.02
915 3039 2.105993 TCCCTCCGTATCGATCTTCTCA 59.894 50.000 0.00 0.00 0.00 3.27
916 3040 2.485038 GTCCCTCCGTATCGATCTTCTC 59.515 54.545 0.00 0.00 0.00 2.87
918 3042 2.030981 GTGTCCCTCCGTATCGATCTTC 60.031 54.545 0.00 0.00 0.00 2.87
963 3087 6.303839 GGTTTGTATGGGATTTATAGGAGCA 58.696 40.000 0.00 0.00 0.00 4.26
977 3101 0.325110 TGGCATGGGGGTTTGTATGG 60.325 55.000 0.00 0.00 0.00 2.74
979 3103 2.504996 CAAATGGCATGGGGGTTTGTAT 59.495 45.455 0.00 0.00 0.00 2.29
1001 3125 2.792674 CTGTTTCTGCTGTGCAATTGTG 59.207 45.455 7.40 0.00 38.41 3.33
1002 3126 2.689471 TCTGTTTCTGCTGTGCAATTGT 59.311 40.909 7.40 0.00 38.41 2.71
1005 3129 1.610522 GGTCTGTTTCTGCTGTGCAAT 59.389 47.619 0.00 0.00 38.41 3.56
1016 3140 3.566523 CACTCTACGTGAGGTCTGTTTC 58.433 50.000 16.04 0.00 46.81 2.78
1053 3177 6.151817 AGGTCTTCTTGGTGCTCAAATTTATC 59.848 38.462 0.00 0.00 34.56 1.75
1057 3181 3.823304 GAGGTCTTCTTGGTGCTCAAATT 59.177 43.478 0.00 0.00 34.56 1.82
1059 3183 2.806745 CGAGGTCTTCTTGGTGCTCAAA 60.807 50.000 0.00 0.00 34.56 2.69
1060 3184 1.270305 CGAGGTCTTCTTGGTGCTCAA 60.270 52.381 0.00 0.00 0.00 3.02
1082 3206 1.064946 GCCGAGAGACCTCATCGTG 59.935 63.158 13.54 8.86 39.39 4.35
1128 3252 0.700564 ATGGCAAGGAGGAGAAGCAA 59.299 50.000 0.00 0.00 0.00 3.91
1146 3270 1.069765 GATCATCCGCCGTGACCAT 59.930 57.895 0.00 0.00 0.00 3.55
1193 3317 4.426313 GGGGAAGGCTTGGGGTCG 62.426 72.222 3.46 0.00 0.00 4.79
1268 3392 1.051556 TGGGCTTTGGGTTTGGGTTC 61.052 55.000 0.00 0.00 0.00 3.62
1288 3418 2.652382 TTCCGGCTTTGCACGAGTCA 62.652 55.000 0.00 0.00 0.00 3.41
1294 3424 2.494530 TTGGGTTCCGGCTTTGCAC 61.495 57.895 0.00 0.00 0.00 4.57
1370 3525 1.688735 GGCTTTTCAGGAGTTGGCTTT 59.311 47.619 0.00 0.00 0.00 3.51
1394 3549 0.178873 ACCCTGGCTGAGGTTTAGGA 60.179 55.000 0.00 0.00 40.87 2.94
1481 3636 1.886655 GCTGGGTTTGTCCTAGGGTTG 60.887 57.143 9.46 0.00 43.80 3.77
1532 3870 2.203625 GGCTGGGGTTTTGGCTGA 60.204 61.111 0.00 0.00 0.00 4.26
1541 3879 1.003573 TTTTGGGTTTGGCTGGGGT 59.996 52.632 0.00 0.00 0.00 4.95
1575 3970 2.125269 CCGTGGTTTAGGCTCCGG 60.125 66.667 0.00 0.00 0.00 5.14
1584 3979 2.764637 GATGGTCCTGGCCGTGGTTT 62.765 60.000 13.43 0.00 0.00 3.27
1634 4116 1.900545 GCTTAGGCTTGGACGGTCCT 61.901 60.000 26.41 9.70 34.77 3.85
1655 4137 4.688419 CGACGTGCGTACACCGGT 62.688 66.667 0.00 0.00 44.40 5.28
1684 4166 2.338785 GCTCAGTTGAGGGGCTTGC 61.339 63.158 10.88 0.00 42.29 4.01
1707 4189 3.628646 ATGTTCCACGAGCCAGCCC 62.629 63.158 0.00 0.00 0.00 5.19
1708 4190 2.045926 ATGTTCCACGAGCCAGCC 60.046 61.111 0.00 0.00 0.00 4.85
1809 4291 5.526111 GCTTTACAACTCACAGGACTAACAA 59.474 40.000 0.00 0.00 0.00 2.83
1927 4424 3.386768 AAGCTAGTCGAACACACATGT 57.613 42.857 0.00 0.00 42.46 3.21
2061 4559 4.247380 CGATGGCTGGGAGAGGGC 62.247 72.222 0.00 0.00 0.00 5.19
2094 4592 4.972514 TTGCGTGGTATATTTTGCATGA 57.027 36.364 0.00 0.00 31.70 3.07
2195 4693 9.552114 TTGCAACTTTTCAAAAATGTATTGTTG 57.448 25.926 0.00 1.83 36.54 3.33
2221 4719 9.920946 ACTGTAATTTGGTTGTATCCTTGATAT 57.079 29.630 0.00 0.00 0.00 1.63
2288 4787 6.151144 AGGGAAAATGGATTAGAAGTTCAACG 59.849 38.462 5.50 0.00 0.00 4.10
2291 4790 9.594936 TTTTAGGGAAAATGGATTAGAAGTTCA 57.405 29.630 5.50 0.00 29.38 3.18
2339 4840 6.949352 AGAAAAACATGAATCTCCGCATAT 57.051 33.333 0.00 0.00 0.00 1.78
2342 4843 5.452078 AAAGAAAAACATGAATCTCCGCA 57.548 34.783 0.00 0.00 0.00 5.69
2395 4896 9.964303 AAAAAGACAAAAGCAGAACAAATTTTT 57.036 22.222 0.00 0.00 0.00 1.94
2447 4948 0.948623 TGACAACAATCAGGCGGACG 60.949 55.000 0.00 0.00 0.00 4.79
2457 4958 6.908825 ACGTGCAACTATAATTGACAACAAT 58.091 32.000 0.00 0.00 40.88 2.71
2458 4959 6.203915 AGACGTGCAACTATAATTGACAACAA 59.796 34.615 0.00 0.00 35.88 2.83
2461 4962 6.400621 CGAAGACGTGCAACTATAATTGACAA 60.401 38.462 0.00 0.00 34.56 3.18
2464 4965 5.404096 TCGAAGACGTGCAACTATAATTGA 58.596 37.500 0.00 0.00 40.69 2.57
2498 4999 4.876125 AGCTACGATCAATGTACATGGAG 58.124 43.478 17.79 8.31 0.00 3.86
2500 5001 5.176406 CAGAAGCTACGATCAATGTACATGG 59.824 44.000 9.63 6.50 0.00 3.66
2509 5010 4.627058 TGTGAAACAGAAGCTACGATCAA 58.373 39.130 0.00 0.00 45.67 2.57
2529 5030 1.347707 TGAGCCGAAGACCAAATCTGT 59.652 47.619 0.00 0.00 37.88 3.41
2533 5034 2.154462 CTTGTGAGCCGAAGACCAAAT 58.846 47.619 0.00 0.00 0.00 2.32
2534 5035 1.593196 CTTGTGAGCCGAAGACCAAA 58.407 50.000 0.00 0.00 0.00 3.28
2537 5038 2.035442 GCCTTGTGAGCCGAAGACC 61.035 63.158 0.00 0.00 0.00 3.85
2572 5073 4.037208 CCAGCAAACCAATATTCAGGCTAG 59.963 45.833 0.00 0.00 0.00 3.42
2574 5075 2.762327 CCAGCAAACCAATATTCAGGCT 59.238 45.455 0.00 0.00 0.00 4.58
2577 5078 3.194116 AGCACCAGCAAACCAATATTCAG 59.806 43.478 0.00 0.00 45.49 3.02
2601 5102 1.277842 TGCAAATCGTAGGAAGAGGCA 59.722 47.619 0.00 0.00 0.00 4.75
2602 5103 2.024176 TGCAAATCGTAGGAAGAGGC 57.976 50.000 0.00 0.00 0.00 4.70
2603 5104 4.054671 GAGATGCAAATCGTAGGAAGAGG 58.945 47.826 0.00 0.00 0.00 3.69
2630 5131 3.512516 GCCATTGACCGCCAGCTC 61.513 66.667 0.00 0.00 0.00 4.09
2642 5143 3.866883 ATCGAATTTGAAACCGCCATT 57.133 38.095 0.00 0.00 0.00 3.16
2659 5160 1.209127 GGGTCGCCACAAACAATCG 59.791 57.895 0.00 0.00 0.00 3.34
2669 5170 2.488771 TAAGTCTCTCGGGGTCGCCA 62.489 60.000 6.75 0.00 36.13 5.69
2672 5173 2.165845 ACAAATAAGTCTCTCGGGGTCG 59.834 50.000 0.00 0.00 37.82 4.79
2705 5206 9.990360 GAAAACTTTACAAAAAGAATCCCCATA 57.010 29.630 4.95 0.00 44.14 2.74
2706 5207 8.713971 AGAAAACTTTACAAAAAGAATCCCCAT 58.286 29.630 4.95 0.00 44.14 4.00
2707 5208 7.984617 CAGAAAACTTTACAAAAAGAATCCCCA 59.015 33.333 4.95 0.00 44.14 4.96
2708 5209 8.201464 TCAGAAAACTTTACAAAAAGAATCCCC 58.799 33.333 4.95 0.00 44.14 4.81
2709 5210 9.594478 TTCAGAAAACTTTACAAAAAGAATCCC 57.406 29.630 4.95 0.00 44.14 3.85
2716 5217 9.921637 ACATGTCTTCAGAAAACTTTACAAAAA 57.078 25.926 0.00 0.00 0.00 1.94
2717 5218 9.567848 GACATGTCTTCAGAAAACTTTACAAAA 57.432 29.630 18.83 0.00 0.00 2.44
2718 5219 8.735315 TGACATGTCTTCAGAAAACTTTACAAA 58.265 29.630 25.55 0.00 0.00 2.83
2719 5220 8.275015 TGACATGTCTTCAGAAAACTTTACAA 57.725 30.769 25.55 0.00 0.00 2.41
2720 5221 7.857734 TGACATGTCTTCAGAAAACTTTACA 57.142 32.000 25.55 0.00 0.00 2.41
2721 5222 7.324616 GCATGACATGTCTTCAGAAAACTTTAC 59.675 37.037 25.55 0.00 0.00 2.01
2722 5223 7.362662 GCATGACATGTCTTCAGAAAACTTTA 58.637 34.615 25.55 1.39 0.00 1.85
2723 5224 6.211515 GCATGACATGTCTTCAGAAAACTTT 58.788 36.000 25.55 0.00 0.00 2.66
2724 5225 5.278660 GGCATGACATGTCTTCAGAAAACTT 60.279 40.000 25.55 0.00 30.66 2.66
2725 5226 4.217118 GGCATGACATGTCTTCAGAAAACT 59.783 41.667 25.55 0.00 30.66 2.66
2726 5227 4.479619 GGCATGACATGTCTTCAGAAAAC 58.520 43.478 25.55 5.93 30.66 2.43
2727 5228 3.507233 GGGCATGACATGTCTTCAGAAAA 59.493 43.478 25.55 4.07 34.67 2.29
2728 5229 3.084039 GGGCATGACATGTCTTCAGAAA 58.916 45.455 25.55 4.83 34.67 2.52
2729 5230 2.618816 GGGGCATGACATGTCTTCAGAA 60.619 50.000 25.55 5.58 34.67 3.02
2730 5231 1.065199 GGGGCATGACATGTCTTCAGA 60.065 52.381 25.55 6.34 34.67 3.27
2731 5232 1.340308 TGGGGCATGACATGTCTTCAG 60.340 52.381 25.55 13.65 34.67 3.02
2732 5233 0.697658 TGGGGCATGACATGTCTTCA 59.302 50.000 25.55 14.41 34.67 3.02
2733 5234 1.340405 ACTGGGGCATGACATGTCTTC 60.340 52.381 25.55 14.12 34.67 2.87
2734 5235 0.700564 ACTGGGGCATGACATGTCTT 59.299 50.000 25.55 17.25 34.67 3.01
2735 5236 1.210478 GTACTGGGGCATGACATGTCT 59.790 52.381 25.55 9.43 34.67 3.41
2736 5237 1.668419 GTACTGGGGCATGACATGTC 58.332 55.000 19.27 19.27 0.00 3.06
2737 5238 0.107703 CGTACTGGGGCATGACATGT 60.108 55.000 16.62 0.00 0.00 3.21
2738 5239 0.177836 TCGTACTGGGGCATGACATG 59.822 55.000 11.27 11.27 0.00 3.21
2739 5240 0.178068 GTCGTACTGGGGCATGACAT 59.822 55.000 0.00 0.00 0.00 3.06
2740 5241 0.902984 AGTCGTACTGGGGCATGACA 60.903 55.000 0.00 0.00 0.00 3.58
2741 5242 0.460284 CAGTCGTACTGGGGCATGAC 60.460 60.000 0.00 0.00 42.35 3.06
2742 5243 1.897423 CAGTCGTACTGGGGCATGA 59.103 57.895 0.00 0.00 42.35 3.07
2743 5244 1.815421 GCAGTCGTACTGGGGCATG 60.815 63.158 14.19 0.00 46.01 4.06
2744 5245 0.686441 TAGCAGTCGTACTGGGGCAT 60.686 55.000 14.19 0.00 46.01 4.40
2745 5246 1.304630 TAGCAGTCGTACTGGGGCA 60.305 57.895 14.19 0.00 46.01 5.36
2746 5247 1.321074 ACTAGCAGTCGTACTGGGGC 61.321 60.000 14.19 3.50 46.01 5.80
2747 5248 1.183549 AACTAGCAGTCGTACTGGGG 58.816 55.000 14.19 0.00 46.01 4.96
2748 5249 2.416972 GGAAACTAGCAGTCGTACTGGG 60.417 54.545 14.19 0.00 46.01 4.45
2749 5250 2.731341 CGGAAACTAGCAGTCGTACTGG 60.731 54.545 14.19 3.80 46.01 4.00
2751 5252 1.135460 GCGGAAACTAGCAGTCGTACT 60.135 52.381 0.00 0.00 0.00 2.73
2752 5253 1.266466 GCGGAAACTAGCAGTCGTAC 58.734 55.000 0.00 0.00 0.00 3.67
2753 5254 0.883153 TGCGGAAACTAGCAGTCGTA 59.117 50.000 0.00 0.00 38.59 3.43
2754 5255 1.663739 TGCGGAAACTAGCAGTCGT 59.336 52.632 0.00 0.00 38.59 4.34
2755 5256 4.571250 TGCGGAAACTAGCAGTCG 57.429 55.556 0.00 0.00 38.59 4.18
2760 5261 4.750098 ACATACATACATGCGGAAACTAGC 59.250 41.667 0.00 0.00 0.00 3.42
2761 5262 7.598869 ACATACATACATACATGCGGAAACTAG 59.401 37.037 0.00 0.00 0.00 2.57
2762 5263 7.438564 ACATACATACATACATGCGGAAACTA 58.561 34.615 0.00 0.00 0.00 2.24
2763 5264 6.288294 ACATACATACATACATGCGGAAACT 58.712 36.000 0.00 0.00 0.00 2.66
2764 5265 6.539649 ACATACATACATACATGCGGAAAC 57.460 37.500 0.00 0.00 0.00 2.78
2765 5266 7.875554 ACATACATACATACATACATGCGGAAA 59.124 33.333 0.00 0.00 0.00 3.13
2766 5267 7.382898 ACATACATACATACATACATGCGGAA 58.617 34.615 0.00 0.00 0.00 4.30
2767 5268 6.930731 ACATACATACATACATACATGCGGA 58.069 36.000 0.00 0.00 0.00 5.54
2768 5269 8.755018 CATACATACATACATACATACATGCGG 58.245 37.037 0.00 0.00 0.00 5.69
2769 5270 9.301153 ACATACATACATACATACATACATGCG 57.699 33.333 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.