Multiple sequence alignment - TraesCS4A01G085300

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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 TraesCS4A01G085300 chr4A 100.000 3083 0 0 1 3083 89929139 89932221 0.000000e+00 5694
1 TraesCS4A01G085300 chr4D 92.546 2227 86 32 588 2789 374600504 374598333 0.000000e+00 3120
2 TraesCS4A01G085300 chr4D 87.444 223 16 5 2865 3083 374598206 374597992 2.370000e-61 246
3 TraesCS4A01G085300 chr4B 89.969 2243 117 55 596 2789 460870575 460868392 0.000000e+00 2796
4 TraesCS4A01G085300 chr4B 87.726 497 51 8 100 588 460871484 460870990 3.450000e-159 571
5 TraesCS4A01G085300 chr6D 78.835 515 102 6 5 514 151494270 151494782 1.060000e-89 340
6 TraesCS4A01G085300 chr6B 78.794 514 101 7 5 514 275917656 275918165 3.810000e-89 339
7 TraesCS4A01G085300 chr5B 85.833 120 16 1 1044 1163 696632881 696632999 3.230000e-25 126


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 TraesCS4A01G085300 chr4A 89929139 89932221 3082 False 5694.0 5694 100.0000 1 3083 1 chr4A.!!$F1 3082
1 TraesCS4A01G085300 chr4D 374597992 374600504 2512 True 1683.0 3120 89.9950 588 3083 2 chr4D.!!$R1 2495
2 TraesCS4A01G085300 chr4B 460868392 460871484 3092 True 1683.5 2796 88.8475 100 2789 2 chr4B.!!$R1 2689
3 TraesCS4A01G085300 chr6D 151494270 151494782 512 False 340.0 340 78.8350 5 514 1 chr6D.!!$F1 509
4 TraesCS4A01G085300 chr6B 275917656 275918165 509 False 339.0 339 78.7940 5 514 1 chr6B.!!$F1 509

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
79 80 0.166814 CTTCGCCTTGCTACACTTGC 59.833 55.0 0.0 0.0 0.0 4.01 F
82 83 0.391130 CGCCTTGCTACACTTGCCTA 60.391 55.0 0.0 0.0 0.0 3.93 F
362 366 0.464036 AGTGCCACAACTCAAGACGA 59.536 50.0 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 2088 1.446366 GATCAGTACGGCCCCCTTC 59.554 63.158 0.00 0.0 0.0 3.46 R
2046 2478 4.096003 ACGAAGGCCCGGATGTGG 62.096 66.667 0.73 0.0 0.0 4.17 R
2226 2678 1.202348 CGGCATTGGACCCTTTTCTTC 59.798 52.381 0.00 0.0 0.0 2.87 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
21 22 3.352648 CCAACCAATACCGTCTTTGGAT 58.647 45.455 16.36 5.49 44.23 3.41
24 25 4.028993 ACCAATACCGTCTTTGGATGTT 57.971 40.909 16.36 0.00 44.23 2.71
29 30 6.350110 CCAATACCGTCTTTGGATGTTTGATT 60.350 38.462 7.18 0.00 44.23 2.57
31 32 3.888930 ACCGTCTTTGGATGTTTGATTGT 59.111 39.130 0.00 0.00 0.00 2.71
32 33 4.340950 ACCGTCTTTGGATGTTTGATTGTT 59.659 37.500 0.00 0.00 0.00 2.83
34 35 5.280945 CGTCTTTGGATGTTTGATTGTTGT 58.719 37.500 0.00 0.00 0.00 3.32
37 38 4.669206 TTGGATGTTTGATTGTTGTGCT 57.331 36.364 0.00 0.00 0.00 4.40
39 40 3.236816 GGATGTTTGATTGTTGTGCTCG 58.763 45.455 0.00 0.00 0.00 5.03
40 41 3.304659 GGATGTTTGATTGTTGTGCTCGT 60.305 43.478 0.00 0.00 0.00 4.18
51 52 1.921243 TGTGCTCGTCATGGATTACG 58.079 50.000 0.00 0.00 40.40 3.18
52 53 1.474879 TGTGCTCGTCATGGATTACGA 59.525 47.619 7.10 7.10 45.17 3.43
61 62 1.349026 CATGGATTACGAGATGCCCCT 59.651 52.381 0.00 0.00 0.00 4.79
62 63 1.507140 TGGATTACGAGATGCCCCTT 58.493 50.000 0.00 0.00 0.00 3.95
71 72 4.052518 ATGCCCCTTCGCCTTGCT 62.053 61.111 0.00 0.00 0.00 3.91
79 80 0.166814 CTTCGCCTTGCTACACTTGC 59.833 55.000 0.00 0.00 0.00 4.01
82 83 0.391130 CGCCTTGCTACACTTGCCTA 60.391 55.000 0.00 0.00 0.00 3.93
148 149 1.135859 GCAAGAGAAGTGTGGCATTCG 60.136 52.381 0.00 0.00 0.00 3.34
184 185 2.611292 GAGAATCAACATCCAAGCTCCG 59.389 50.000 0.00 0.00 33.17 4.63
256 257 1.561643 ACAGGAAGATGCGAAGAGGA 58.438 50.000 0.00 0.00 0.00 3.71
264 265 2.428890 AGATGCGAAGAGGATTCGACTT 59.571 45.455 13.68 4.01 43.97 3.01
294 295 5.337813 CCATAGAAATTGCTTGGGCTCTTTT 60.338 40.000 0.00 0.00 39.59 2.27
299 300 3.457610 TTGCTTGGGCTCTTTTGAAAG 57.542 42.857 0.00 0.00 39.59 2.62
308 309 5.596361 TGGGCTCTTTTGAAAGAATGTAACA 59.404 36.000 7.51 0.30 43.84 2.41
337 338 4.051237 TGTTCAACAACATCTCGAGACAG 58.949 43.478 19.30 15.87 37.61 3.51
343 344 4.693283 ACAACATCTCGAGACAGAAAACA 58.307 39.130 19.30 0.00 0.00 2.83
345 346 4.592485 ACATCTCGAGACAGAAAACAGT 57.408 40.909 19.30 2.72 0.00 3.55
362 366 0.464036 AGTGCCACAACTCAAGACGA 59.536 50.000 0.00 0.00 0.00 4.20
385 389 7.330946 ACGAAAATACTTGACGAGATTGATGAA 59.669 33.333 0.00 0.00 0.00 2.57
397 401 2.442236 TTGATGAATGGAGGAAGGCC 57.558 50.000 0.00 0.00 0.00 5.19
404 408 2.683933 GGAGGAAGGCCGGTCTGA 60.684 66.667 10.71 0.00 39.96 3.27
417 421 3.923864 TCTGAGCGGCGTTGGTGT 61.924 61.111 9.37 0.00 0.00 4.16
428 432 2.418976 GGCGTTGGTGTTTTAGATCCTC 59.581 50.000 0.00 0.00 0.00 3.71
462 466 4.946478 AGTCTTCATGTATCTAGGGTGC 57.054 45.455 0.00 0.00 0.00 5.01
464 468 4.716784 AGTCTTCATGTATCTAGGGTGCAA 59.283 41.667 0.00 0.00 0.00 4.08
514 519 0.829990 TCGCATCATGTTAGGGCTCA 59.170 50.000 0.00 0.00 0.00 4.26
526 531 7.289084 TCATGTTAGGGCTCATGTACATAACTA 59.711 37.037 8.32 4.37 41.22 2.24
530 535 6.352016 AGGGCTCATGTACATAACTATCTG 57.648 41.667 8.32 0.00 0.00 2.90
532 537 5.279708 GGGCTCATGTACATAACTATCTGCT 60.280 44.000 8.32 0.00 0.00 4.24
537 542 8.877808 TCATGTACATAACTATCTGCTTTCTG 57.122 34.615 8.32 0.00 0.00 3.02
553 558 9.378551 TCTGCTTTCTGTAAAAATATGATACGT 57.621 29.630 0.00 0.00 0.00 3.57
609 1032 1.068055 TCTTTAGGAACACGACGAGCC 60.068 52.381 0.00 0.00 0.00 4.70
737 1165 2.045340 CGAATCACCCACCCCCAC 60.045 66.667 0.00 0.00 0.00 4.61
746 1174 3.517497 CACCCCCACCCCCACTTT 61.517 66.667 0.00 0.00 0.00 2.66
801 1229 3.612681 CGACACCTGTCCCACCGT 61.613 66.667 0.00 0.00 41.86 4.83
921 1352 1.678970 CAACCCAAGGCCTAGCACC 60.679 63.158 5.16 0.00 0.00 5.01
922 1353 2.160171 AACCCAAGGCCTAGCACCA 61.160 57.895 5.16 0.00 0.00 4.17
923 1354 2.044946 CCCAAGGCCTAGCACCAC 60.045 66.667 5.16 0.00 0.00 4.16
935 1366 1.617322 AGCACCACTCTCGTTGTCTA 58.383 50.000 0.00 0.00 0.00 2.59
938 1369 0.522180 ACCACTCTCGTTGTCTAGCG 59.478 55.000 0.00 0.00 0.00 4.26
945 1376 3.188786 GTTGTCTAGCGCCTGCCG 61.189 66.667 2.29 0.00 44.31 5.69
1302 1734 3.246880 AAGGTCCCCGTGGTGGTC 61.247 66.667 0.00 0.00 35.15 4.02
1502 1934 3.294493 GCAGGCGGGCAGAAACAA 61.294 61.111 3.78 0.00 0.00 2.83
1506 1938 4.700365 GCGGGCAGAAACAACGCC 62.700 66.667 0.00 0.00 44.01 5.68
1566 1998 2.355363 TTCGACCGCGTGTTCCTG 60.355 61.111 4.92 0.00 38.98 3.86
1731 2163 4.728110 AAGAGCATGCCGCAGCCA 62.728 61.111 15.66 0.00 46.13 4.75
2086 2518 2.667418 CCAGGTCCAGCTGACAGG 59.333 66.667 17.39 12.69 46.38 4.00
2089 2521 2.046507 GGTCCAGCTGACAGGCAG 60.047 66.667 17.39 0.00 46.38 4.85
2127 2559 2.034879 CCATGTCAGTGTCACCCGC 61.035 63.158 0.00 0.00 0.00 6.13
2182 2634 3.637229 AGTAGATGCCGTGTAAGCAGTAT 59.363 43.478 0.00 0.00 44.90 2.12
2184 2636 4.665833 AGATGCCGTGTAAGCAGTATTA 57.334 40.909 0.00 0.00 44.90 0.98
2185 2637 4.621991 AGATGCCGTGTAAGCAGTATTAG 58.378 43.478 0.00 0.00 44.90 1.73
2186 2638 2.546778 TGCCGTGTAAGCAGTATTAGC 58.453 47.619 0.00 0.00 34.69 3.09
2224 2676 2.306847 GCCCAAGTGAAGGAAAAGACA 58.693 47.619 0.00 0.00 0.00 3.41
2225 2677 2.693074 GCCCAAGTGAAGGAAAAGACAA 59.307 45.455 0.00 0.00 0.00 3.18
2226 2678 3.243535 GCCCAAGTGAAGGAAAAGACAAG 60.244 47.826 0.00 0.00 0.00 3.16
2260 2722 0.744414 ATGCCGAACTTGGATCGTGG 60.744 55.000 0.00 0.00 38.60 4.94
2280 2742 2.450160 GTGTCGGAAAGCAAAAGTGTG 58.550 47.619 0.00 0.00 0.00 3.82
2284 2746 1.215014 GGAAAGCAAAAGTGTGGCGC 61.215 55.000 0.00 0.00 0.00 6.53
2293 2755 4.513581 CAAAAGTGTGGCGCAAAAATAAC 58.486 39.130 10.83 0.00 0.00 1.89
2297 2759 3.120041 GTGTGGCGCAAAAATAACACTT 58.880 40.909 10.83 0.00 36.01 3.16
2298 2760 3.553917 GTGTGGCGCAAAAATAACACTTT 59.446 39.130 10.83 0.00 36.01 2.66
2315 2790 7.615582 AACACTTTCTCCATGTATGTATGTG 57.384 36.000 0.00 0.00 0.00 3.21
2335 2810 6.218025 TGTGTATCGTGTTGTTCATTGTAC 57.782 37.500 0.00 0.00 0.00 2.90
2336 2811 5.986741 TGTGTATCGTGTTGTTCATTGTACT 59.013 36.000 0.00 0.00 0.00 2.73
2337 2812 6.144886 TGTGTATCGTGTTGTTCATTGTACTC 59.855 38.462 0.00 0.00 0.00 2.59
2338 2813 5.636121 TGTATCGTGTTGTTCATTGTACTCC 59.364 40.000 0.00 0.00 0.00 3.85
2339 2814 4.330944 TCGTGTTGTTCATTGTACTCCT 57.669 40.909 0.00 0.00 0.00 3.69
2340 2815 5.456548 TCGTGTTGTTCATTGTACTCCTA 57.543 39.130 0.00 0.00 0.00 2.94
2344 2819 6.864685 CGTGTTGTTCATTGTACTCCTACTTA 59.135 38.462 0.00 0.00 0.00 2.24
2425 2908 4.508861 TGTTTAAGTAACAACTCGGCTGAC 59.491 41.667 0.00 0.00 43.58 3.51
2439 2923 0.179181 GCTGACGGTGTTGCATGATG 60.179 55.000 0.00 0.00 0.00 3.07
2448 2932 1.272037 TGTTGCATGATGAGGGAAGCA 60.272 47.619 0.00 0.00 0.00 3.91
2467 2951 0.476771 AAGAAAAGGCTCCGGGAACA 59.523 50.000 0.00 0.00 0.00 3.18
2468 2952 0.476771 AGAAAAGGCTCCGGGAACAA 59.523 50.000 0.00 0.00 0.00 2.83
2469 2953 1.133606 AGAAAAGGCTCCGGGAACAAA 60.134 47.619 0.00 0.00 0.00 2.83
2492 2979 1.527034 TCATTGTCTGCTTGTCTGGC 58.473 50.000 0.00 0.00 0.00 4.85
2515 3002 3.815396 GCGCTTTGCACTAGCCCC 61.815 66.667 12.95 2.97 45.45 5.80
2517 3004 1.675641 CGCTTTGCACTAGCCCCTT 60.676 57.895 12.95 0.00 41.13 3.95
2518 3005 1.648467 CGCTTTGCACTAGCCCCTTC 61.648 60.000 12.95 0.00 41.13 3.46
2519 3006 0.322906 GCTTTGCACTAGCCCCTTCT 60.323 55.000 8.49 0.00 41.13 2.85
2520 3007 1.888391 GCTTTGCACTAGCCCCTTCTT 60.888 52.381 8.49 0.00 41.13 2.52
2521 3008 2.519013 CTTTGCACTAGCCCCTTCTTT 58.481 47.619 0.00 0.00 41.13 2.52
2563 3050 2.001076 CTTTGGGAAGGTTCAGGCTT 57.999 50.000 0.00 0.00 0.00 4.35
2564 3051 2.319844 CTTTGGGAAGGTTCAGGCTTT 58.680 47.619 0.00 0.00 0.00 3.51
2565 3052 1.703411 TTGGGAAGGTTCAGGCTTTG 58.297 50.000 0.00 0.00 0.00 2.77
2566 3053 0.827507 TGGGAAGGTTCAGGCTTTGC 60.828 55.000 0.00 0.00 0.00 3.68
2605 3092 1.980052 CCCGGGACTTGTCTAAGCA 59.020 57.895 18.48 0.00 37.43 3.91
2606 3093 0.108138 CCCGGGACTTGTCTAAGCAG 60.108 60.000 18.48 0.00 37.43 4.24
2607 3094 0.741221 CCGGGACTTGTCTAAGCAGC 60.741 60.000 0.00 0.00 37.43 5.25
2619 3106 0.659427 TAAGCAGCGCAATCATCAGC 59.341 50.000 11.47 0.00 0.00 4.26
2629 3119 2.775890 CAATCATCAGCCGGCTAGATT 58.224 47.619 32.30 30.91 0.00 2.40
2637 3127 1.230324 GCCGGCTAGATTTTAGGCTG 58.770 55.000 22.15 1.45 41.21 4.85
2638 3128 1.884235 CCGGCTAGATTTTAGGCTGG 58.116 55.000 0.00 0.00 43.46 4.85
2639 3129 1.230324 CGGCTAGATTTTAGGCTGGC 58.770 55.000 0.00 0.00 37.89 4.85
2640 3130 1.475034 CGGCTAGATTTTAGGCTGGCA 60.475 52.381 3.38 0.00 39.97 4.92
2641 3131 1.950216 GGCTAGATTTTAGGCTGGCAC 59.050 52.381 3.38 0.00 39.97 5.01
2642 3132 2.643551 GCTAGATTTTAGGCTGGCACA 58.356 47.619 3.38 0.00 38.34 4.57
2643 3133 3.217626 GCTAGATTTTAGGCTGGCACAT 58.782 45.455 3.38 0.00 38.34 3.21
2671 3161 7.708752 CACCTGGTAAGAACAGAATAGAATCTC 59.291 40.741 0.00 0.00 38.20 2.75
2674 3164 6.605995 TGGTAAGAACAGAATAGAATCTCGGA 59.394 38.462 0.00 0.00 0.00 4.55
2709 3199 2.903855 GGCCGGCCATCACATGAG 60.904 66.667 40.73 0.00 35.81 2.90
2719 3209 3.443045 CACATGAGCCCCAACCGC 61.443 66.667 0.00 0.00 0.00 5.68
2720 3210 3.965258 ACATGAGCCCCAACCGCA 61.965 61.111 0.00 0.00 0.00 5.69
2745 3236 2.964925 GACACAAGTGCGGTGCGA 60.965 61.111 0.00 0.00 39.87 5.10
2773 3266 2.801483 TAGTGCCGCTGCTGCAATGA 62.801 55.000 25.20 9.84 41.06 2.57
2774 3267 2.752640 TGCCGCTGCTGCAATGAT 60.753 55.556 16.44 0.00 39.64 2.45
2775 3268 2.278596 GCCGCTGCTGCAATGATG 60.279 61.111 16.29 0.00 39.64 3.07
2789 3283 2.688446 CAATGATGCATCAGACAAGCCT 59.312 45.455 31.36 12.02 40.64 4.58
2801 3295 0.681733 ACAAGCCTGTCGATCACTGT 59.318 50.000 0.00 0.00 0.00 3.55
2803 3297 2.299013 ACAAGCCTGTCGATCACTGTAA 59.701 45.455 0.00 0.00 0.00 2.41
2807 3301 2.094182 GCCTGTCGATCACTGTAAGGAA 60.094 50.000 0.00 0.00 39.30 3.36
2810 3304 2.094182 TGTCGATCACTGTAAGGAAGCC 60.094 50.000 0.00 0.00 39.30 4.35
2813 3307 2.796383 CGATCACTGTAAGGAAGCCTCG 60.796 54.545 0.00 0.00 39.30 4.63
2814 3308 1.919240 TCACTGTAAGGAAGCCTCGA 58.081 50.000 0.00 0.00 39.30 4.04
2815 3309 1.819288 TCACTGTAAGGAAGCCTCGAG 59.181 52.381 5.13 5.13 39.30 4.04
2816 3310 1.546476 CACTGTAAGGAAGCCTCGAGT 59.454 52.381 12.31 0.00 39.30 4.18
2817 3311 1.546476 ACTGTAAGGAAGCCTCGAGTG 59.454 52.381 12.31 4.07 39.30 3.51
2819 3313 2.753452 CTGTAAGGAAGCCTCGAGTGTA 59.247 50.000 12.31 0.00 30.89 2.90
2820 3314 3.362706 TGTAAGGAAGCCTCGAGTGTAT 58.637 45.455 12.31 0.00 30.89 2.29
2821 3315 4.529897 TGTAAGGAAGCCTCGAGTGTATA 58.470 43.478 12.31 0.00 30.89 1.47
2822 3316 5.138276 TGTAAGGAAGCCTCGAGTGTATAT 58.862 41.667 12.31 0.00 30.89 0.86
2823 3317 4.592485 AAGGAAGCCTCGAGTGTATATG 57.408 45.455 12.31 0.00 30.89 1.78
2824 3318 3.567397 AGGAAGCCTCGAGTGTATATGT 58.433 45.455 12.31 0.00 0.00 2.29
2825 3319 3.961408 AGGAAGCCTCGAGTGTATATGTT 59.039 43.478 12.31 0.00 0.00 2.71
2828 3342 5.234543 GGAAGCCTCGAGTGTATATGTTTTC 59.765 44.000 12.31 3.32 0.00 2.29
2832 3346 4.207224 CCTCGAGTGTATATGTTTTCTGCG 59.793 45.833 12.31 0.00 0.00 5.18
2842 3356 3.073144 TGTTTTCTGCGGCTTGTAAAC 57.927 42.857 15.58 15.58 0.00 2.01
2857 3371 1.234615 TAAACTGGAAGGCACGCAGC 61.235 55.000 0.00 0.00 39.30 5.25
2877 3418 2.624766 CGCTCTTGTTGTTGTTGTACG 58.375 47.619 0.00 0.00 0.00 3.67
2879 3420 3.350912 GCTCTTGTTGTTGTTGTACGTG 58.649 45.455 0.00 0.00 0.00 4.49
2905 3446 0.106769 TTGCTTGGTTGCCTGTCTCA 60.107 50.000 0.00 0.00 0.00 3.27
2912 3453 0.465460 GTTGCCTGTCTCACCAACCA 60.465 55.000 0.00 0.00 33.33 3.67
2936 3477 4.794439 GGCGGCCGGCAAACAATC 62.794 66.667 42.94 15.90 46.16 2.67
2974 3519 3.391049 ACATCATGCGTGATCATCTGAG 58.609 45.455 18.67 8.35 43.14 3.35
2980 3525 3.019564 TGCGTGATCATCTGAGAAGAGA 58.980 45.455 0.00 0.00 0.00 3.10
2986 3531 4.815846 TGATCATCTGAGAAGAGACTCGAG 59.184 45.833 11.84 11.84 39.49 4.04
2991 3536 1.649390 GAGAAGAGACTCGAGCGGCA 61.649 60.000 13.61 0.00 0.00 5.69
3005 3550 1.377725 CGGCAGCATTGGGAAGTCT 60.378 57.895 0.00 0.00 0.00 3.24
3025 3570 4.212847 GTCTAGCCACAATGCACATGATAG 59.787 45.833 0.00 4.60 0.00 2.08
3026 3571 3.286329 AGCCACAATGCACATGATAGA 57.714 42.857 0.00 0.00 0.00 1.98
3028 3573 4.976864 AGCCACAATGCACATGATAGATA 58.023 39.130 0.00 0.00 0.00 1.98
3029 3574 5.379187 AGCCACAATGCACATGATAGATAA 58.621 37.500 0.00 0.00 0.00 1.75
3030 3575 6.008331 AGCCACAATGCACATGATAGATAAT 58.992 36.000 0.00 0.00 0.00 1.28
3031 3576 7.170277 AGCCACAATGCACATGATAGATAATA 58.830 34.615 0.00 0.00 0.00 0.98
3032 3577 7.666804 AGCCACAATGCACATGATAGATAATAA 59.333 33.333 0.00 0.00 0.00 1.40
3033 3578 7.966753 GCCACAATGCACATGATAGATAATAAG 59.033 37.037 0.00 0.00 0.00 1.73
3034 3579 9.006839 CCACAATGCACATGATAGATAATAAGT 57.993 33.333 0.00 0.00 0.00 2.24
3036 3581 9.783081 ACAATGCACATGATAGATAATAAGTCA 57.217 29.630 0.00 0.00 0.00 3.41
3051 3596 2.281484 TCAGTTGCTTGGTCGCCC 60.281 61.111 0.00 0.00 0.00 6.13
3063 3608 2.022129 GTCGCCCGCGGAATGATAG 61.022 63.158 30.73 9.14 40.25 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.785562 TCCAAAGACGGTATTGGTTGG 58.214 47.619 19.07 10.48 45.12 3.77
2 3 4.028993 ACATCCAAAGACGGTATTGGTT 57.971 40.909 19.07 11.76 45.12 3.67
3 4 3.713826 ACATCCAAAGACGGTATTGGT 57.286 42.857 19.07 8.70 45.12 3.67
13 14 5.049167 GCACAACAATCAAACATCCAAAGA 58.951 37.500 0.00 0.00 0.00 2.52
14 15 5.051816 AGCACAACAATCAAACATCCAAAG 58.948 37.500 0.00 0.00 0.00 2.77
16 17 4.619973 GAGCACAACAATCAAACATCCAA 58.380 39.130 0.00 0.00 0.00 3.53
21 22 2.680339 TGACGAGCACAACAATCAAACA 59.320 40.909 0.00 0.00 0.00 2.83
24 25 2.226200 CCATGACGAGCACAACAATCAA 59.774 45.455 0.00 0.00 0.00 2.57
29 30 2.183478 AATCCATGACGAGCACAACA 57.817 45.000 0.00 0.00 0.00 3.33
31 32 2.094442 TCGTAATCCATGACGAGCACAA 60.094 45.455 3.47 0.00 42.80 3.33
32 33 1.474879 TCGTAATCCATGACGAGCACA 59.525 47.619 3.47 0.00 42.80 4.57
37 38 2.288213 GGCATCTCGTAATCCATGACGA 60.288 50.000 7.10 7.10 45.28 4.20
39 40 2.417719 GGGCATCTCGTAATCCATGAC 58.582 52.381 0.00 0.00 0.00 3.06
40 41 1.347707 GGGGCATCTCGTAATCCATGA 59.652 52.381 0.00 0.00 0.00 3.07
51 52 1.821332 CAAGGCGAAGGGGCATCTC 60.821 63.158 0.00 0.00 45.36 2.75
52 53 2.273449 CAAGGCGAAGGGGCATCT 59.727 61.111 0.00 0.00 45.36 2.90
61 62 1.234615 GGCAAGTGTAGCAAGGCGAA 61.235 55.000 0.00 0.00 0.00 4.70
62 63 1.671054 GGCAAGTGTAGCAAGGCGA 60.671 57.895 0.00 0.00 0.00 5.54
79 80 6.314896 GGTCAACATTCTCTTCATCTTGTAGG 59.685 42.308 0.00 0.00 0.00 3.18
82 83 5.624159 TGGTCAACATTCTCTTCATCTTGT 58.376 37.500 0.00 0.00 0.00 3.16
148 149 0.518636 TTCTCAGCGCATGAAAGCAC 59.481 50.000 11.47 0.00 37.52 4.40
184 185 5.657474 TCTATGAATGTTACTTCCGTGGAC 58.343 41.667 0.00 0.00 0.00 4.02
256 257 8.345565 GCAATTTCTATGGTTATGAAGTCGAAT 58.654 33.333 0.00 0.00 0.00 3.34
264 265 5.068987 GCCCAAGCAATTTCTATGGTTATGA 59.931 40.000 0.00 0.00 36.44 2.15
308 309 4.271049 CGAGATGTTGTTGAACACTCTTGT 59.729 41.667 0.00 0.00 44.90 3.16
337 338 3.128589 TCTTGAGTTGTGGCACTGTTTTC 59.871 43.478 19.83 9.69 0.00 2.29
343 344 0.464036 TCGTCTTGAGTTGTGGCACT 59.536 50.000 19.83 0.00 0.00 4.40
345 346 2.031258 TTTCGTCTTGAGTTGTGGCA 57.969 45.000 0.00 0.00 0.00 4.92
362 366 8.400947 CCATTCATCAATCTCGTCAAGTATTTT 58.599 33.333 0.00 0.00 0.00 1.82
385 389 2.041265 AGACCGGCCTTCCTCCAT 59.959 61.111 0.00 0.00 0.00 3.41
404 408 0.533308 TCTAAAACACCAACGCCGCT 60.533 50.000 0.00 0.00 0.00 5.52
428 432 4.634004 ACATGAAGACTACTCTCTCACGAG 59.366 45.833 0.00 0.00 38.67 4.18
462 466 2.270986 GCCAACAGACCCAGGCTTG 61.271 63.158 0.00 0.00 43.70 4.01
467 471 1.207329 GTAGGTAGCCAACAGACCCAG 59.793 57.143 0.00 0.00 33.40 4.45
473 477 2.427453 ACATCTCGTAGGTAGCCAACAG 59.573 50.000 0.00 0.00 0.00 3.16
576 581 5.307196 TGTTCCTAAAGAGCCTCTACACTTT 59.693 40.000 0.00 0.00 35.18 2.66
577 582 4.838986 TGTTCCTAAAGAGCCTCTACACTT 59.161 41.667 0.00 0.00 0.00 3.16
590 1013 1.347320 GGCTCGTCGTGTTCCTAAAG 58.653 55.000 0.00 0.00 0.00 1.85
591 1014 0.387622 CGGCTCGTCGTGTTCCTAAA 60.388 55.000 0.00 0.00 0.00 1.85
592 1015 1.210931 CGGCTCGTCGTGTTCCTAA 59.789 57.895 0.00 0.00 0.00 2.69
593 1016 1.028330 ATCGGCTCGTCGTGTTCCTA 61.028 55.000 0.00 0.00 0.00 2.94
594 1017 1.028330 TATCGGCTCGTCGTGTTCCT 61.028 55.000 0.00 0.00 0.00 3.36
609 1032 0.023732 CGTTTGCACGCTGTCTATCG 59.976 55.000 0.00 0.00 40.18 2.92
684 1107 4.393062 AGTGTGTGAAATGATCCATTCGTC 59.607 41.667 0.00 0.00 32.43 4.20
685 1108 4.326826 AGTGTGTGAAATGATCCATTCGT 58.673 39.130 0.00 0.00 32.43 3.85
686 1109 4.952262 AGTGTGTGAAATGATCCATTCG 57.048 40.909 0.00 0.00 32.43 3.34
687 1110 5.327091 CGAAGTGTGTGAAATGATCCATTC 58.673 41.667 0.00 0.00 32.43 2.67
688 1111 4.379813 GCGAAGTGTGTGAAATGATCCATT 60.380 41.667 0.00 0.00 35.39 3.16
737 1165 2.359975 GGACTCGCAAAGTGGGGG 60.360 66.667 0.00 0.00 38.74 5.40
889 1317 2.633657 GTTGTCTGTGCGCTGTGG 59.366 61.111 9.73 0.00 0.00 4.17
923 1354 0.524392 CAGGCGCTAGACAACGAGAG 60.524 60.000 7.64 0.00 0.00 3.20
996 1428 3.307550 CCATCCTCCTCCTTATCATGCAG 60.308 52.174 0.00 0.00 0.00 4.41
1338 1770 4.082523 TGGTAGCAGCTCCACGCC 62.083 66.667 0.00 0.00 40.39 5.68
1446 1878 2.504244 GTGAGCCCGTCGTCGAAG 60.504 66.667 2.98 0.00 39.71 3.79
1492 1924 4.700365 GGCGGCGTTGTTTCTGCC 62.700 66.667 9.37 0.00 46.19 4.85
1656 2088 1.446366 GATCAGTACGGCCCCCTTC 59.554 63.158 0.00 0.00 0.00 3.46
2046 2478 4.096003 ACGAAGGCCCGGATGTGG 62.096 66.667 0.73 0.00 0.00 4.17
2086 2518 2.262915 CGGAGGAGTGGTGTCTGC 59.737 66.667 0.00 0.00 0.00 4.26
2089 2521 4.436998 CGGCGGAGGAGTGGTGTC 62.437 72.222 0.00 0.00 0.00 3.67
2091 2523 4.742201 CACGGCGGAGGAGTGGTG 62.742 72.222 13.24 0.00 32.68 4.17
2109 2541 2.034879 GCGGGTGACACTGACATGG 61.035 63.158 5.39 0.00 0.00 3.66
2127 2559 9.204570 CTGGTAGTGGATTAAGTAATTAATCGG 57.795 37.037 22.54 6.27 42.13 4.18
2185 2637 1.630148 CGAGTACCACAAGCTACTGC 58.370 55.000 0.00 0.00 40.05 4.40
2186 2638 1.630148 GCGAGTACCACAAGCTACTG 58.370 55.000 0.00 0.00 0.00 2.74
2224 2676 2.899900 GGCATTGGACCCTTTTCTTCTT 59.100 45.455 0.00 0.00 0.00 2.52
2225 2677 2.529632 GGCATTGGACCCTTTTCTTCT 58.470 47.619 0.00 0.00 0.00 2.85
2226 2678 1.202348 CGGCATTGGACCCTTTTCTTC 59.798 52.381 0.00 0.00 0.00 2.87
2260 2722 2.450160 CACACTTTTGCTTTCCGACAC 58.550 47.619 0.00 0.00 0.00 3.67
2280 2742 3.673338 GGAGAAAGTGTTATTTTTGCGCC 59.327 43.478 4.18 0.00 0.00 6.53
2284 2746 9.912634 ACATACATGGAGAAAGTGTTATTTTTG 57.087 29.630 0.00 0.00 0.00 2.44
2293 2755 8.893219 ATACACATACATACATGGAGAAAGTG 57.107 34.615 0.00 0.00 0.00 3.16
2297 2759 7.145323 CACGATACACATACATACATGGAGAA 58.855 38.462 0.00 0.00 0.00 2.87
2298 2760 6.264518 ACACGATACACATACATACATGGAGA 59.735 38.462 0.00 0.00 0.00 3.71
2315 2790 5.867716 AGGAGTACAATGAACAACACGATAC 59.132 40.000 0.00 0.00 0.00 2.24
2335 2810 2.673368 CGCCTTTGCAAGTAAGTAGGAG 59.327 50.000 15.31 8.99 37.32 3.69
2336 2811 2.614481 CCGCCTTTGCAAGTAAGTAGGA 60.614 50.000 15.31 0.00 37.32 2.94
2337 2812 1.737793 CCGCCTTTGCAAGTAAGTAGG 59.262 52.381 8.04 8.04 37.32 3.18
2338 2813 2.695359 TCCGCCTTTGCAAGTAAGTAG 58.305 47.619 0.00 0.00 37.32 2.57
2339 2814 2.843401 TCCGCCTTTGCAAGTAAGTA 57.157 45.000 0.00 0.00 37.32 2.24
2340 2815 2.084546 GATCCGCCTTTGCAAGTAAGT 58.915 47.619 0.00 0.00 37.32 2.24
2344 2819 1.549203 ATTGATCCGCCTTTGCAAGT 58.451 45.000 0.00 0.00 37.32 3.16
2425 2908 0.392863 TCCCTCATCATGCAACACCG 60.393 55.000 0.00 0.00 0.00 4.94
2439 2923 1.815613 GAGCCTTTTCTTGCTTCCCTC 59.184 52.381 0.00 0.00 38.11 4.30
2448 2932 0.476771 TGTTCCCGGAGCCTTTTCTT 59.523 50.000 0.73 0.00 0.00 2.52
2468 2952 5.535333 CCAGACAAGCAGACAATGATTTTT 58.465 37.500 0.00 0.00 34.61 1.94
2469 2953 4.560108 GCCAGACAAGCAGACAATGATTTT 60.560 41.667 0.00 0.00 34.61 1.82
2500 2987 0.322906 AGAAGGGGCTAGTGCAAAGC 60.323 55.000 12.76 12.76 41.91 3.51
2521 3008 3.187637 CAGCGACGGGAAACATAGAAAAA 59.812 43.478 0.00 0.00 0.00 1.94
2563 3050 2.353307 CCATCATCAAGCAAGCAAGCAA 60.353 45.455 3.19 0.00 36.85 3.91
2564 3051 1.203758 CCATCATCAAGCAAGCAAGCA 59.796 47.619 3.19 0.00 36.85 3.91
2565 3052 1.475280 TCCATCATCAAGCAAGCAAGC 59.525 47.619 0.00 0.00 0.00 4.01
2566 3053 2.479730 GCTCCATCATCAAGCAAGCAAG 60.480 50.000 0.00 0.00 36.06 4.01
2605 3092 2.898840 CCGGCTGATGATTGCGCT 60.899 61.111 9.73 0.00 0.00 5.92
2606 3093 4.619140 GCCGGCTGATGATTGCGC 62.619 66.667 22.15 0.00 0.00 6.09
2607 3094 1.563435 CTAGCCGGCTGATGATTGCG 61.563 60.000 38.98 11.10 0.00 4.85
2619 3106 1.884235 CCAGCCTAAAATCTAGCCGG 58.116 55.000 0.00 0.00 0.00 6.13
2629 3119 1.250154 GGTGCATGTGCCAGCCTAAA 61.250 55.000 2.07 0.00 41.18 1.85
2637 3127 0.322456 TCTTACCAGGTGCATGTGCC 60.322 55.000 0.76 0.00 41.18 5.01
2638 3128 1.200020 GTTCTTACCAGGTGCATGTGC 59.800 52.381 0.76 0.00 42.50 4.57
2639 3129 2.485426 CTGTTCTTACCAGGTGCATGTG 59.515 50.000 0.76 0.00 0.00 3.21
2640 3130 2.371841 TCTGTTCTTACCAGGTGCATGT 59.628 45.455 0.76 0.00 0.00 3.21
2641 3131 3.057969 TCTGTTCTTACCAGGTGCATG 57.942 47.619 0.76 0.00 0.00 4.06
2642 3132 3.788227 TTCTGTTCTTACCAGGTGCAT 57.212 42.857 0.76 0.00 0.00 3.96
2643 3133 3.788227 ATTCTGTTCTTACCAGGTGCA 57.212 42.857 0.76 0.00 0.00 4.57
2671 3161 2.895039 CCATCGGGAAACGTATCCG 58.105 57.895 15.19 15.19 44.69 4.18
2697 3187 1.380246 TTGGGGCTCATGTGATGGC 60.380 57.895 0.00 0.00 0.00 4.40
2698 3188 1.039233 GGTTGGGGCTCATGTGATGG 61.039 60.000 0.00 0.00 0.00 3.51
2699 3189 1.378882 CGGTTGGGGCTCATGTGATG 61.379 60.000 0.00 0.00 0.00 3.07
2700 3190 1.077501 CGGTTGGGGCTCATGTGAT 60.078 57.895 0.00 0.00 0.00 3.06
2719 3209 1.368019 CACTTGTGTCGTTGCGCTG 60.368 57.895 9.73 0.00 0.00 5.18
2720 3210 3.014036 CACTTGTGTCGTTGCGCT 58.986 55.556 9.73 0.00 0.00 5.92
2728 3218 2.964925 TCGCACCGCACTTGTGTC 60.965 61.111 2.61 0.00 36.11 3.67
2773 3266 3.972368 ACAGGCTTGTCTGATGCAT 57.028 47.368 9.36 0.00 38.11 3.96
2782 3276 0.681733 ACAGTGATCGACAGGCTTGT 59.318 50.000 0.00 0.00 41.18 3.16
2784 3278 2.093973 CCTTACAGTGATCGACAGGCTT 60.094 50.000 0.00 0.00 0.00 4.35
2785 3279 1.478510 CCTTACAGTGATCGACAGGCT 59.521 52.381 0.00 0.00 0.00 4.58
2786 3280 1.476891 TCCTTACAGTGATCGACAGGC 59.523 52.381 0.00 0.00 0.00 4.85
2789 3283 2.094182 GGCTTCCTTACAGTGATCGACA 60.094 50.000 0.00 0.00 0.00 4.35
2797 3291 1.546476 CACTCGAGGCTTCCTTACAGT 59.454 52.381 18.41 0.00 31.76 3.55
2801 3295 5.138276 ACATATACACTCGAGGCTTCCTTA 58.862 41.667 18.41 0.00 31.76 2.69
2803 3297 3.567397 ACATATACACTCGAGGCTTCCT 58.433 45.455 18.41 0.00 36.03 3.36
2807 3301 5.352284 CAGAAAACATATACACTCGAGGCT 58.648 41.667 18.41 3.20 0.00 4.58
2810 3304 4.207224 CCGCAGAAAACATATACACTCGAG 59.793 45.833 11.84 11.84 0.00 4.04
2813 3307 3.871594 AGCCGCAGAAAACATATACACTC 59.128 43.478 0.00 0.00 0.00 3.51
2814 3308 3.873910 AGCCGCAGAAAACATATACACT 58.126 40.909 0.00 0.00 0.00 3.55
2815 3309 4.142687 ACAAGCCGCAGAAAACATATACAC 60.143 41.667 0.00 0.00 0.00 2.90
2816 3310 4.006989 ACAAGCCGCAGAAAACATATACA 58.993 39.130 0.00 0.00 0.00 2.29
2817 3311 4.616181 ACAAGCCGCAGAAAACATATAC 57.384 40.909 0.00 0.00 0.00 1.47
2819 3313 5.183140 AGTTTACAAGCCGCAGAAAACATAT 59.817 36.000 11.01 0.00 31.02 1.78
2820 3314 4.517453 AGTTTACAAGCCGCAGAAAACATA 59.483 37.500 11.01 0.00 31.02 2.29
2821 3315 3.317993 AGTTTACAAGCCGCAGAAAACAT 59.682 39.130 11.01 0.00 31.02 2.71
2822 3316 2.685897 AGTTTACAAGCCGCAGAAAACA 59.314 40.909 11.01 0.00 31.02 2.83
2823 3317 3.042887 CAGTTTACAAGCCGCAGAAAAC 58.957 45.455 0.00 0.00 0.00 2.43
2824 3318 2.034053 CCAGTTTACAAGCCGCAGAAAA 59.966 45.455 0.00 0.00 0.00 2.29
2825 3319 1.606668 CCAGTTTACAAGCCGCAGAAA 59.393 47.619 0.00 0.00 0.00 2.52
2828 3342 1.197721 CTTCCAGTTTACAAGCCGCAG 59.802 52.381 0.00 0.00 0.00 5.18
2832 3346 1.269723 GTGCCTTCCAGTTTACAAGCC 59.730 52.381 0.00 0.00 0.00 4.35
2857 3371 2.029970 ACGTACAACAACAACAAGAGCG 59.970 45.455 0.00 0.00 0.00 5.03
2859 3373 3.372822 ACCACGTACAACAACAACAAGAG 59.627 43.478 0.00 0.00 0.00 2.85
2861 3375 3.750639 ACCACGTACAACAACAACAAG 57.249 42.857 0.00 0.00 0.00 3.16
2863 3377 4.439968 TGATACCACGTACAACAACAACA 58.560 39.130 0.00 0.00 0.00 3.33
2877 3418 2.417243 GGCAACCAAGCAATGATACCAC 60.417 50.000 0.00 0.00 35.83 4.16
2879 3420 2.102578 AGGCAACCAAGCAATGATACC 58.897 47.619 0.00 0.00 35.83 2.73
2925 3466 3.165318 GCACGCGATTGTTTGCCG 61.165 61.111 15.93 0.00 0.00 5.69
2930 3471 1.081906 CTGCTTGCACGCGATTGTT 60.082 52.632 15.93 0.00 0.00 2.83
2931 3472 2.557805 CTGCTTGCACGCGATTGT 59.442 55.556 15.93 0.00 0.00 2.71
2932 3473 2.202388 CCTGCTTGCACGCGATTG 60.202 61.111 15.93 1.64 0.00 2.67
2974 3519 1.226547 CTGCCGCTCGAGTCTCTTC 60.227 63.158 15.13 0.00 0.00 2.87
2980 3525 2.816958 CAATGCTGCCGCTCGAGT 60.817 61.111 15.13 0.00 36.97 4.18
2986 3531 3.056313 GACTTCCCAATGCTGCCGC 62.056 63.158 0.00 0.00 0.00 6.53
2991 3536 1.065126 GTGGCTAGACTTCCCAATGCT 60.065 52.381 0.00 0.00 0.00 3.79
3005 3550 4.420522 TCTATCATGTGCATTGTGGCTA 57.579 40.909 0.00 0.00 34.04 3.93
3025 3570 5.502544 GCGACCAAGCAACTGACTTATTATC 60.503 44.000 0.00 0.00 37.05 1.75
3026 3571 4.332819 GCGACCAAGCAACTGACTTATTAT 59.667 41.667 0.00 0.00 37.05 1.28
3028 3573 2.484264 GCGACCAAGCAACTGACTTATT 59.516 45.455 0.00 0.00 37.05 1.40
3029 3574 2.076863 GCGACCAAGCAACTGACTTAT 58.923 47.619 0.00 0.00 37.05 1.73
3030 3575 1.508632 GCGACCAAGCAACTGACTTA 58.491 50.000 0.00 0.00 37.05 2.24
3031 3576 1.166531 GGCGACCAAGCAACTGACTT 61.167 55.000 0.00 0.00 39.27 3.01
3032 3577 1.598130 GGCGACCAAGCAACTGACT 60.598 57.895 0.00 0.00 39.27 3.41
3033 3578 2.946762 GGCGACCAAGCAACTGAC 59.053 61.111 0.00 0.00 39.27 3.51
3051 3596 2.605823 GGTCTCAGTCTATCATTCCGCG 60.606 54.545 0.00 0.00 0.00 6.46
3053 3598 4.554292 CATGGTCTCAGTCTATCATTCCG 58.446 47.826 0.00 0.00 0.00 4.30
3055 3600 4.953667 TGCATGGTCTCAGTCTATCATTC 58.046 43.478 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.