Multiple sequence alignment - TraesCS2B01G425400

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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 TraesCS2B01G425400 chr2B 100.000 3605 0 0 1 3605 611191217 611194821 0.000000e+00 6658.0
1 TraesCS2B01G425400 chr2B 96.364 55 1 1 3551 3605 677013231 677013178 4.960000e-14 89.8
2 TraesCS2B01G425400 chr2B 100.000 34 0 0 3517 3550 677013310 677013343 3.000000e-06 63.9
3 TraesCS2B01G425400 chr2D 90.443 3411 129 70 1 3312 518968247 518971559 0.000000e+00 4311.0
4 TraesCS2B01G425400 chr2D 96.364 55 1 1 3551 3605 565145462 565145409 4.960000e-14 89.8
5 TraesCS2B01G425400 chr2D 100.000 34 0 0 3517 3550 565145511 565145544 3.000000e-06 63.9
6 TraesCS2B01G425400 chr2A 93.793 2497 67 26 404 2873 663147344 663144909 0.000000e+00 3672.0
7 TraesCS2B01G425400 chr2A 89.466 655 25 8 2874 3521 663144778 663144161 0.000000e+00 787.0
8 TraesCS2B01G425400 chr2A 84.722 360 42 10 1226 1579 10979572 10979924 7.410000e-92 348.0
9 TraesCS2B01G425400 chr2A 84.928 345 22 10 1 317 663147777 663147435 4.490000e-84 322.0
10 TraesCS2B01G425400 chr2A 100.000 34 0 0 3517 3550 705586509 705586542 3.000000e-06 63.9
11 TraesCS2B01G425400 chr6A 88.132 1601 172 12 997 2588 456011562 456013153 0.000000e+00 1888.0
12 TraesCS2B01G425400 chr6B 87.679 1607 176 16 1001 2596 505683192 505681597 0.000000e+00 1851.0
13 TraesCS2B01G425400 chr6D 87.625 1600 180 12 997 2587 318453703 318455293 0.000000e+00 1842.0
14 TraesCS2B01G425400 chr4B 85.078 449 45 6 1558 2001 86080378 86079947 4.270000e-119 438.0
15 TraesCS2B01G425400 chr3B 78.240 625 120 14 1901 2517 631049171 631049787 1.570000e-103 387.0
16 TraesCS2B01G425400 chr3B 77.031 714 132 26 1024 1718 631048309 631049009 7.300000e-102 381.0
17 TraesCS2B01G425400 chr3B 98.182 55 1 0 3551 3605 45266409 45266355 2.960000e-16 97.1
18 TraesCS2B01G425400 chr3B 98.182 55 1 0 3551 3605 45273806 45273752 2.960000e-16 97.1
19 TraesCS2B01G425400 chr3A 78.240 625 120 14 1901 2517 617074295 617074911 1.570000e-103 387.0
20 TraesCS2B01G425400 chr3A 76.858 713 135 24 1024 1718 617073433 617074133 3.400000e-100 375.0
21 TraesCS2B01G425400 chr3D 78.080 625 121 14 1901 2517 474655592 474656208 7.300000e-102 381.0
22 TraesCS2B01G425400 chr3D 76.611 714 123 30 1024 1718 474654742 474655430 1.590000e-93 353.0
23 TraesCS2B01G425400 chr3D 98.182 55 1 0 3551 3605 26617562 26617508 2.960000e-16 97.1
24 TraesCS2B01G425400 chrUn 98.182 55 1 0 3551 3605 380277878 380277932 2.960000e-16 97.1
25 TraesCS2B01G425400 chrUn 100.000 51 0 0 3555 3605 38777233 38777283 1.070000e-15 95.3
26 TraesCS2B01G425400 chr4A 96.364 55 2 0 3551 3605 358867089 358867143 1.380000e-14 91.6
27 TraesCS2B01G425400 chr4D 94.545 55 3 0 3551 3605 298967665 298967611 6.410000e-13 86.1


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 TraesCS2B01G425400 chr2B 611191217 611194821 3604 False 6658.000000 6658 100.000000 1 3605 1 chr2B.!!$F1 3604
1 TraesCS2B01G425400 chr2D 518968247 518971559 3312 False 4311.000000 4311 90.443000 1 3312 1 chr2D.!!$F1 3311
2 TraesCS2B01G425400 chr2A 663144161 663147777 3616 True 1593.666667 3672 89.395667 1 3521 3 chr2A.!!$R1 3520
3 TraesCS2B01G425400 chr6A 456011562 456013153 1591 False 1888.000000 1888 88.132000 997 2588 1 chr6A.!!$F1 1591
4 TraesCS2B01G425400 chr6B 505681597 505683192 1595 True 1851.000000 1851 87.679000 1001 2596 1 chr6B.!!$R1 1595
5 TraesCS2B01G425400 chr6D 318453703 318455293 1590 False 1842.000000 1842 87.625000 997 2587 1 chr6D.!!$F1 1590
6 TraesCS2B01G425400 chr3B 631048309 631049787 1478 False 384.000000 387 77.635500 1024 2517 2 chr3B.!!$F1 1493
7 TraesCS2B01G425400 chr3A 617073433 617074911 1478 False 381.000000 387 77.549000 1024 2517 2 chr3A.!!$F1 1493
8 TraesCS2B01G425400 chr3D 474654742 474656208 1466 False 367.000000 381 77.345500 1024 2517 2 chr3D.!!$F1 1493

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
265 315 0.095245 CGCATGCTACACTGTTTCCG 59.905 55.0 17.13 0.0 0.0 4.30 F
742 847 0.173481 GCCTCCATATATCTCGCGCA 59.827 55.0 8.75 0.0 0.0 6.09 F
884 995 0.813184 ATTGCCAACCATCTTGCTCG 59.187 50.0 0.00 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2237 0.251922 AGGTACACTAGGCGGTCCAA 60.252 55.000 0.00 0.00 33.74 3.53 R
2328 2479 2.559840 CTGTACGAGTCGTGCGGT 59.440 61.111 28.11 6.16 44.75 5.68 R
2812 2981 1.531602 GCTGCCCCTGTGTTTTCCT 60.532 57.895 0.00 0.00 0.00 3.36 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
118 142 2.260844 TGCATCTACCTGCATTAGCC 57.739 50.000 0.00 0.00 46.76 3.93
160 192 1.600023 CGTTTTGGCACCAACCTCTA 58.400 50.000 0.45 0.00 35.46 2.43
177 214 1.350019 TCTACTCTCTCACACGTCCCA 59.650 52.381 0.00 0.00 0.00 4.37
239 289 0.391661 CGTACTCCCTGTTGCATGCT 60.392 55.000 20.33 0.00 0.00 3.79
265 315 0.095245 CGCATGCTACACTGTTTCCG 59.905 55.000 17.13 0.00 0.00 4.30
276 326 2.174349 GTTTCCGCAAGCGAGCTG 59.826 61.111 16.97 0.00 42.83 4.24
310 360 0.741927 CTGCATGCACACTCCGATCA 60.742 55.000 18.46 0.00 0.00 2.92
317 367 2.028567 TGCACACTCCGATCATGTGTAA 60.029 45.455 12.83 4.92 44.52 2.41
329 410 5.220912 CGATCATGTGTAAATCAAGCATGGT 60.221 40.000 0.00 0.00 37.92 3.55
336 417 3.947910 AAATCAAGCATGGTTCACCTG 57.052 42.857 7.29 0.00 36.82 4.00
339 426 0.896940 CAAGCATGGTTCACCTGGCT 60.897 55.000 7.29 8.59 44.06 4.75
341 428 0.698238 AGCATGGTTCACCTGGCTAA 59.302 50.000 11.73 0.00 41.75 3.09
342 429 1.098050 GCATGGTTCACCTGGCTAAG 58.902 55.000 0.00 0.00 36.82 2.18
355 442 1.079127 GCTAAGGTGAGCAAGCCGA 60.079 57.895 0.00 0.00 42.36 5.54
367 454 2.334946 AAGCCGAGCGTACCGTGTA 61.335 57.895 0.00 0.00 0.00 2.90
369 456 2.753966 GCCGAGCGTACCGTGTAGA 61.754 63.158 0.00 0.00 0.00 2.59
370 457 1.351012 CCGAGCGTACCGTGTAGAG 59.649 63.158 0.00 0.00 0.00 2.43
371 458 1.364626 CCGAGCGTACCGTGTAGAGT 61.365 60.000 0.00 0.00 0.00 3.24
375 462 3.448686 GAGCGTACCGTGTAGAGTAGTA 58.551 50.000 0.00 0.00 0.00 1.82
376 463 3.190874 AGCGTACCGTGTAGAGTAGTAC 58.809 50.000 0.00 0.00 0.00 2.73
377 464 3.825498 CGTACCGTGTAGAGTAGTACG 57.175 52.381 6.62 6.62 46.78 3.67
378 465 3.179830 CGTACCGTGTAGAGTAGTACGT 58.820 50.000 11.65 0.00 46.75 3.57
379 466 3.000674 CGTACCGTGTAGAGTAGTACGTG 60.001 52.174 11.65 0.00 46.75 4.49
380 467 1.734465 ACCGTGTAGAGTAGTACGTGC 59.266 52.381 0.00 0.00 34.96 5.34
381 468 2.005451 CCGTGTAGAGTAGTACGTGCT 58.995 52.381 11.87 11.87 34.96 4.40
382 469 3.190079 CCGTGTAGAGTAGTACGTGCTA 58.810 50.000 9.49 9.49 34.96 3.49
383 470 3.618594 CCGTGTAGAGTAGTACGTGCTAA 59.381 47.826 15.26 0.00 34.96 3.09
384 471 4.272018 CCGTGTAGAGTAGTACGTGCTAAT 59.728 45.833 15.26 14.34 34.96 1.73
385 472 5.463392 CCGTGTAGAGTAGTACGTGCTAATA 59.537 44.000 15.26 6.24 34.96 0.98
386 473 6.018751 CCGTGTAGAGTAGTACGTGCTAATAA 60.019 42.308 15.26 3.45 34.96 1.40
387 474 7.307632 CCGTGTAGAGTAGTACGTGCTAATAAT 60.308 40.741 15.26 8.91 34.96 1.28
388 475 7.739477 CGTGTAGAGTAGTACGTGCTAATAATC 59.261 40.741 15.26 10.71 0.00 1.75
389 476 7.739477 GTGTAGAGTAGTACGTGCTAATAATCG 59.261 40.741 15.26 0.00 27.90 3.34
390 477 6.238610 AGAGTAGTACGTGCTAATAATCGG 57.761 41.667 15.26 0.00 27.90 4.18
391 478 5.762218 AGAGTAGTACGTGCTAATAATCGGT 59.238 40.000 15.26 0.00 27.90 4.69
392 479 5.755813 AGTAGTACGTGCTAATAATCGGTG 58.244 41.667 15.26 0.00 0.00 4.94
393 480 4.644103 AGTACGTGCTAATAATCGGTGT 57.356 40.909 3.62 0.00 0.00 4.16
394 481 4.357142 AGTACGTGCTAATAATCGGTGTG 58.643 43.478 3.62 0.00 0.00 3.82
395 482 3.241067 ACGTGCTAATAATCGGTGTGT 57.759 42.857 0.00 0.00 0.00 3.72
396 483 2.927477 ACGTGCTAATAATCGGTGTGTG 59.073 45.455 0.00 0.00 0.00 3.82
397 484 2.285602 CGTGCTAATAATCGGTGTGTGC 60.286 50.000 0.00 0.00 0.00 4.57
398 485 2.031683 GTGCTAATAATCGGTGTGTGCC 59.968 50.000 0.00 0.00 0.00 5.01
496 584 0.748005 CCCCATTGTTAGGTGCGAGG 60.748 60.000 0.00 0.00 0.00 4.63
680 785 4.082523 CCACGGACGAGTGCCCAT 62.083 66.667 0.00 0.00 40.59 4.00
681 786 2.509336 CACGGACGAGTGCCCATC 60.509 66.667 0.00 0.00 35.17 3.51
682 787 4.129737 ACGGACGAGTGCCCATCG 62.130 66.667 0.00 1.29 45.54 3.84
683 788 4.873129 CGGACGAGTGCCCATCGG 62.873 72.222 7.15 0.00 44.36 4.18
684 789 3.771160 GGACGAGTGCCCATCGGT 61.771 66.667 7.15 0.00 44.36 4.69
685 790 2.202756 GACGAGTGCCCATCGGTC 60.203 66.667 7.15 0.25 44.36 4.79
736 841 0.252696 TGCCCCGCCTCCATATATCT 60.253 55.000 0.00 0.00 0.00 1.98
742 847 0.173481 GCCTCCATATATCTCGCGCA 59.827 55.000 8.75 0.00 0.00 6.09
829 940 3.399181 CTGGCCGCCTTCCCAGTA 61.399 66.667 11.61 0.00 42.87 2.74
872 983 1.810959 GCAAGCCAATTCATTGCCAA 58.189 45.000 7.30 0.00 42.70 4.52
878 989 2.093341 GCCAATTCATTGCCAACCATCT 60.093 45.455 0.00 0.00 36.48 2.90
879 990 3.620472 GCCAATTCATTGCCAACCATCTT 60.620 43.478 0.00 0.00 36.48 2.40
880 991 3.936453 CCAATTCATTGCCAACCATCTTG 59.064 43.478 0.00 0.00 36.48 3.02
883 994 1.820519 TCATTGCCAACCATCTTGCTC 59.179 47.619 0.00 0.00 0.00 4.26
884 995 0.813184 ATTGCCAACCATCTTGCTCG 59.187 50.000 0.00 0.00 0.00 5.03
885 996 1.865788 TTGCCAACCATCTTGCTCGC 61.866 55.000 0.00 0.00 0.00 5.03
886 997 3.056313 GCCAACCATCTTGCTCGCC 62.056 63.158 0.00 0.00 0.00 5.54
887 998 2.409870 CCAACCATCTTGCTCGCCC 61.410 63.158 0.00 0.00 0.00 6.13
889 1000 3.976701 AACCATCTTGCTCGCCCCG 62.977 63.158 0.00 0.00 0.00 5.73
911 1027 0.818296 CGGCCGCTTCTATATAGCCT 59.182 55.000 14.67 0.00 38.27 4.58
958 1074 2.055042 CCACCTCTCCCGTCCTCAG 61.055 68.421 0.00 0.00 0.00 3.35
962 1078 1.077068 CTCTCCCGTCCTCAGCTCT 60.077 63.158 0.00 0.00 0.00 4.09
964 1080 1.379176 CTCCCGTCCTCAGCTCTCA 60.379 63.158 0.00 0.00 0.00 3.27
965 1081 1.662438 CTCCCGTCCTCAGCTCTCAC 61.662 65.000 0.00 0.00 0.00 3.51
966 1082 1.680651 CCCGTCCTCAGCTCTCACT 60.681 63.158 0.00 0.00 0.00 3.41
970 1091 2.183811 CCTCAGCTCTCACTGCGG 59.816 66.667 0.00 0.00 36.28 5.69
1008 1129 2.037620 CTAGCTTGGCGATGGAGGCT 62.038 60.000 0.00 0.00 37.59 4.58
1425 1552 2.668550 GAGTTCACCACCCGCACC 60.669 66.667 0.00 0.00 0.00 5.01
1808 1944 4.880537 CGAGCTCGCCGGCAAGAT 62.881 66.667 28.98 18.56 34.17 2.40
1817 1953 2.582498 CGGCAAGATCGACGGGTC 60.582 66.667 0.00 0.00 32.24 4.46
1884 2020 4.575180 GGGACCTACTCCGACGAT 57.425 61.111 0.00 0.00 40.56 3.73
2097 2248 0.974010 ACGAGGAATTGGACCGCCTA 60.974 55.000 0.00 0.00 34.31 3.93
2328 2479 1.952133 CGACGGCACCAAGTTCGAA 60.952 57.895 0.00 0.00 0.00 3.71
2448 2602 3.827898 CTCCTCCGTCACCGCCTC 61.828 72.222 0.00 0.00 0.00 4.70
2611 2771 1.226974 GCCTGCGCGTAGAAGATCA 60.227 57.895 26.43 1.84 0.00 2.92
2612 2772 1.211818 GCCTGCGCGTAGAAGATCAG 61.212 60.000 26.43 12.21 0.00 2.90
2614 2774 1.333931 CCTGCGCGTAGAAGATCAGTA 59.666 52.381 26.43 0.00 0.00 2.74
2616 2776 2.285977 TGCGCGTAGAAGATCAGTAGA 58.714 47.619 8.43 0.00 0.00 2.59
2617 2777 2.031807 TGCGCGTAGAAGATCAGTAGAC 59.968 50.000 8.43 0.00 0.00 2.59
2705 2873 5.118286 CAAAGTTGGAAGTGGCAAGAAAAT 58.882 37.500 0.00 0.00 0.00 1.82
2777 2946 8.746530 GGTGAGTATATCTACATCGGGATAAAA 58.253 37.037 0.00 0.00 0.00 1.52
2829 2999 1.413118 AAAGGAAAACACAGGGGCAG 58.587 50.000 0.00 0.00 0.00 4.85
2858 3028 1.118838 ATGCTCCTCTCCTGTACTGC 58.881 55.000 0.00 0.00 0.00 4.40
2868 3043 3.832490 TCTCCTGTACTGCAATGTACTGT 59.168 43.478 15.04 0.00 42.22 3.55
2872 3047 4.864806 CCTGTACTGCAATGTACTGTACTG 59.135 45.833 17.98 10.47 42.22 2.74
2882 3182 2.099427 TGTACTGTACTGCGTGTGACAA 59.901 45.455 17.98 0.00 0.00 3.18
2894 3194 4.211389 GCGTGTGACAAATTAGAAGTGTG 58.789 43.478 0.00 0.00 0.00 3.82
2898 3200 5.007626 GTGTGACAAATTAGAAGTGTGAGCA 59.992 40.000 0.00 0.00 0.00 4.26
2989 3307 4.216472 TGCAAACGCAAGGTGAAACATATA 59.784 37.500 0.00 0.00 46.39 0.86
2990 3308 4.557301 GCAAACGCAAGGTGAAACATATAC 59.443 41.667 0.00 0.00 46.39 1.47
2991 3309 5.694816 CAAACGCAAGGTGAAACATATACA 58.305 37.500 0.00 0.00 46.39 2.29
2992 3310 5.950758 AACGCAAGGTGAAACATATACAA 57.049 34.783 0.00 0.00 46.39 2.41
2993 3311 5.291293 ACGCAAGGTGAAACATATACAAC 57.709 39.130 0.00 0.00 46.39 3.32
2994 3312 5.001232 ACGCAAGGTGAAACATATACAACT 58.999 37.500 0.00 0.00 46.39 3.16
2995 3313 5.121768 ACGCAAGGTGAAACATATACAACTC 59.878 40.000 0.00 0.00 46.39 3.01
2996 3314 5.560148 GCAAGGTGAAACATATACAACTCG 58.440 41.667 0.00 0.00 39.98 4.18
2997 3315 5.350365 GCAAGGTGAAACATATACAACTCGA 59.650 40.000 0.00 0.00 39.98 4.04
2998 3316 6.037172 GCAAGGTGAAACATATACAACTCGAT 59.963 38.462 0.00 0.00 39.98 3.59
2999 3317 7.621991 CAAGGTGAAACATATACAACTCGATC 58.378 38.462 0.00 0.00 39.98 3.69
3000 3318 5.977725 AGGTGAAACATATACAACTCGATCG 59.022 40.000 9.36 9.36 39.98 3.69
3001 3319 5.975344 GGTGAAACATATACAACTCGATCGA 59.025 40.000 18.32 18.32 39.98 3.59
3002 3320 6.142480 GGTGAAACATATACAACTCGATCGAG 59.858 42.308 36.95 36.95 43.27 4.04
3173 3503 1.302591 TGCACGAGACCGAGAGAGT 60.303 57.895 0.00 0.00 39.50 3.24
3180 3510 2.156098 GAGACCGAGAGAGTGACACTT 58.844 52.381 10.01 0.00 0.00 3.16
3181 3511 2.554893 GAGACCGAGAGAGTGACACTTT 59.445 50.000 10.01 3.48 0.00 2.66
3182 3512 2.959707 AGACCGAGAGAGTGACACTTTT 59.040 45.455 10.01 1.19 0.00 2.27
3183 3513 3.385111 AGACCGAGAGAGTGACACTTTTT 59.615 43.478 10.01 0.00 0.00 1.94
3201 3531 1.988293 TTTTCCCGCTTTGATGGTGA 58.012 45.000 0.00 0.00 0.00 4.02
3229 3564 2.492019 TTGTCGAGGCGATACATCAG 57.508 50.000 0.00 0.00 38.42 2.90
3233 3568 1.604278 TCGAGGCGATACATCAGACTG 59.396 52.381 0.00 0.00 0.00 3.51
3286 3621 6.571150 GCAATGCAAACTGATAAAGAGTTCCT 60.571 38.462 0.00 0.00 32.33 3.36
3413 3749 5.575606 TCACTTTATTTCTGAATCGTCCGAC 59.424 40.000 0.00 0.00 0.00 4.79
3425 3761 0.179119 CGTCCGACCAGTATCCAACC 60.179 60.000 0.00 0.00 0.00 3.77
3464 3800 5.713861 CAGAAGGAAAGAGGGAAAATGTGAT 59.286 40.000 0.00 0.00 0.00 3.06
3521 3857 1.644509 TGTGCTCAGGTACACTCCAT 58.355 50.000 0.00 0.00 37.68 3.41
3522 3858 1.276138 TGTGCTCAGGTACACTCCATG 59.724 52.381 0.00 0.00 37.68 3.66
3523 3859 0.904649 TGCTCAGGTACACTCCATGG 59.095 55.000 4.97 4.97 0.00 3.66
3524 3860 1.195115 GCTCAGGTACACTCCATGGA 58.805 55.000 15.27 15.27 0.00 3.41
3525 3861 1.137872 GCTCAGGTACACTCCATGGAG 59.862 57.143 35.55 35.55 46.91 3.86
3526 3862 1.137872 CTCAGGTACACTCCATGGAGC 59.862 57.143 36.78 22.27 45.54 4.70
3527 3863 3.719939 AGGTACACTCCATGGAGCT 57.280 52.632 36.78 25.44 45.73 4.09
3529 3865 0.103208 GGTACACTCCATGGAGCTCG 59.897 60.000 36.78 27.49 45.54 5.03
3530 3866 0.818296 GTACACTCCATGGAGCTCGT 59.182 55.000 36.78 30.83 45.54 4.18
3531 3867 1.103803 TACACTCCATGGAGCTCGTC 58.896 55.000 36.78 0.00 45.54 4.20
3532 3868 1.142748 CACTCCATGGAGCTCGTCC 59.857 63.158 36.78 0.00 45.54 4.79
3539 3875 4.379174 GGAGCTCGTCCTTTGCAA 57.621 55.556 7.83 0.00 42.99 4.08
3540 3876 1.869690 GGAGCTCGTCCTTTGCAAC 59.130 57.895 7.83 0.00 42.99 4.17
3541 3877 1.493311 GAGCTCGTCCTTTGCAACG 59.507 57.895 0.00 0.00 40.17 4.10
3542 3878 2.127232 GCTCGTCCTTTGCAACGC 60.127 61.111 0.00 0.00 38.72 4.84
3543 3879 2.556287 CTCGTCCTTTGCAACGCC 59.444 61.111 0.00 0.00 38.72 5.68
3544 3880 2.203084 TCGTCCTTTGCAACGCCA 60.203 55.556 0.00 0.00 38.72 5.69
3545 3881 2.051345 CGTCCTTTGCAACGCCAC 60.051 61.111 0.00 0.00 31.48 5.01
3546 3882 2.829206 CGTCCTTTGCAACGCCACA 61.829 57.895 0.00 0.00 31.48 4.17
3547 3883 1.299089 GTCCTTTGCAACGCCACAC 60.299 57.895 0.00 0.00 0.00 3.82
3548 3884 1.453015 TCCTTTGCAACGCCACACT 60.453 52.632 0.00 0.00 0.00 3.55
3549 3885 1.008538 CCTTTGCAACGCCACACTC 60.009 57.895 0.00 0.00 0.00 3.51
3550 3886 1.723608 CCTTTGCAACGCCACACTCA 61.724 55.000 0.00 0.00 0.00 3.41
3551 3887 0.311790 CTTTGCAACGCCACACTCAT 59.688 50.000 0.00 0.00 0.00 2.90
3552 3888 0.030504 TTTGCAACGCCACACTCATG 59.969 50.000 0.00 0.00 0.00 3.07
3553 3889 1.794151 TTGCAACGCCACACTCATGG 61.794 55.000 0.00 0.00 43.26 3.66
3554 3890 1.965930 GCAACGCCACACTCATGGA 60.966 57.895 0.00 0.00 43.02 3.41
3555 3891 1.308069 GCAACGCCACACTCATGGAT 61.308 55.000 0.00 0.00 43.02 3.41
3556 3892 2.011548 GCAACGCCACACTCATGGATA 61.012 52.381 0.00 0.00 43.02 2.59
3557 3893 2.564771 CAACGCCACACTCATGGATAT 58.435 47.619 0.00 0.00 43.02 1.63
3558 3894 2.945008 CAACGCCACACTCATGGATATT 59.055 45.455 0.00 0.00 43.02 1.28
3559 3895 2.838736 ACGCCACACTCATGGATATTC 58.161 47.619 0.00 0.00 43.02 1.75
3560 3896 2.435805 ACGCCACACTCATGGATATTCT 59.564 45.455 0.00 0.00 43.02 2.40
3561 3897 3.118261 ACGCCACACTCATGGATATTCTT 60.118 43.478 0.00 0.00 43.02 2.52
3562 3898 3.496130 CGCCACACTCATGGATATTCTTC 59.504 47.826 0.00 0.00 43.02 2.87
3563 3899 4.454678 GCCACACTCATGGATATTCTTCA 58.545 43.478 0.00 0.00 43.02 3.02
3564 3900 4.883585 GCCACACTCATGGATATTCTTCAA 59.116 41.667 0.00 0.00 43.02 2.69
3565 3901 5.008415 GCCACACTCATGGATATTCTTCAAG 59.992 44.000 0.00 0.00 43.02 3.02
3566 3902 6.118170 CCACACTCATGGATATTCTTCAAGT 58.882 40.000 0.00 0.00 43.02 3.16
3567 3903 7.275183 CCACACTCATGGATATTCTTCAAGTA 58.725 38.462 0.00 0.00 43.02 2.24
3568 3904 7.935755 CCACACTCATGGATATTCTTCAAGTAT 59.064 37.037 0.00 0.00 43.02 2.12
3569 3905 8.771766 CACACTCATGGATATTCTTCAAGTATG 58.228 37.037 0.00 0.00 0.00 2.39
3570 3906 8.489489 ACACTCATGGATATTCTTCAAGTATGT 58.511 33.333 0.00 0.00 0.00 2.29
3571 3907 9.987272 CACTCATGGATATTCTTCAAGTATGTA 57.013 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
118 142 3.144506 CATTACTATCAGGCCAGGCAAG 58.855 50.000 15.19 4.71 0.00 4.01
160 192 0.178987 AGTGGGACGTGTGAGAGAGT 60.179 55.000 0.00 0.00 0.00 3.24
190 227 1.549203 CTTGATTTGGTGGGGAGGTG 58.451 55.000 0.00 0.00 0.00 4.00
225 262 2.747460 GCGAGCATGCAACAGGGA 60.747 61.111 21.98 0.00 34.15 4.20
226 263 3.057548 TGCGAGCATGCAACAGGG 61.058 61.111 21.98 2.95 43.02 4.45
310 360 5.336690 GGTGAACCATGCTTGATTTACACAT 60.337 40.000 4.31 0.00 35.64 3.21
317 367 2.173519 CCAGGTGAACCATGCTTGATT 58.826 47.619 1.62 0.00 38.89 2.57
336 417 3.911137 GGCTTGCTCACCTTAGCC 58.089 61.111 0.00 0.00 45.57 3.93
339 426 1.079127 GCTCGGCTTGCTCACCTTA 60.079 57.895 0.00 0.00 0.00 2.69
341 428 4.749310 CGCTCGGCTTGCTCACCT 62.749 66.667 0.00 0.00 0.00 4.00
342 429 3.642778 TACGCTCGGCTTGCTCACC 62.643 63.158 0.00 0.00 0.00 4.02
343 430 2.126071 TACGCTCGGCTTGCTCAC 60.126 61.111 0.00 0.00 0.00 3.51
344 431 2.126071 GTACGCTCGGCTTGCTCA 60.126 61.111 0.00 0.00 0.00 4.26
345 432 2.886124 GGTACGCTCGGCTTGCTC 60.886 66.667 0.00 0.00 0.00 4.26
367 454 5.762218 ACCGATTATTAGCACGTACTACTCT 59.238 40.000 0.00 0.00 0.00 3.24
369 456 5.297776 ACACCGATTATTAGCACGTACTACT 59.702 40.000 0.00 0.00 0.00 2.57
370 457 5.397534 CACACCGATTATTAGCACGTACTAC 59.602 44.000 0.00 0.00 0.00 2.73
371 458 5.066375 ACACACCGATTATTAGCACGTACTA 59.934 40.000 0.00 0.00 0.00 1.82
375 462 2.927477 CACACACCGATTATTAGCACGT 59.073 45.455 0.00 0.00 0.00 4.49
376 463 2.285602 GCACACACCGATTATTAGCACG 60.286 50.000 0.00 0.00 0.00 5.34
377 464 2.031683 GGCACACACCGATTATTAGCAC 59.968 50.000 0.00 0.00 0.00 4.40
378 465 2.285083 GGCACACACCGATTATTAGCA 58.715 47.619 0.00 0.00 0.00 3.49
453 540 2.417257 GGGAGCCATTCAATGCGCA 61.417 57.895 14.96 14.96 0.00 6.09
666 771 4.873129 CCGATGGGCACTCGTCCG 62.873 72.222 6.98 0.00 41.18 4.79
667 772 3.718210 GACCGATGGGCACTCGTCC 62.718 68.421 6.98 0.00 37.45 4.79
668 773 2.202756 GACCGATGGGCACTCGTC 60.203 66.667 6.98 2.39 36.48 4.20
669 774 3.771160 GGACCGATGGGCACTCGT 61.771 66.667 6.98 0.00 36.48 4.18
670 775 4.873129 CGGACCGATGGGCACTCG 62.873 72.222 8.64 1.41 36.48 4.18
671 776 4.530857 CCGGACCGATGGGCACTC 62.531 72.222 17.49 0.00 36.48 3.51
676 781 4.467084 CACCACCGGACCGATGGG 62.467 72.222 31.08 21.82 37.86 4.00
677 782 3.387091 TCACCACCGGACCGATGG 61.387 66.667 26.69 26.69 39.57 3.51
678 783 2.125673 GTCACCACCGGACCGATG 60.126 66.667 17.49 8.87 0.00 3.84
679 784 3.387947 GGTCACCACCGGACCGAT 61.388 66.667 17.49 0.00 44.80 4.18
777 882 2.820037 GTAGGCCAAGGCAGTCGC 60.820 66.667 13.87 0.00 44.11 5.19
778 883 1.153549 GAGTAGGCCAAGGCAGTCG 60.154 63.158 13.87 0.00 44.11 4.18
779 884 1.222113 GGAGTAGGCCAAGGCAGTC 59.778 63.158 13.87 5.63 44.11 3.51
829 940 4.421479 CGCGACGACTTGGGAGCT 62.421 66.667 0.00 0.00 0.00 4.09
872 983 4.473520 CGGGGCGAGCAAGATGGT 62.474 66.667 0.00 0.00 0.00 3.55
889 1000 0.179108 CTATATAGAAGCGGCCGGCC 60.179 60.000 36.69 36.69 45.17 6.13
890 1001 0.806492 GCTATATAGAAGCGGCCGGC 60.806 60.000 29.38 21.18 44.05 6.13
911 1027 2.835701 GAATGTGCTCGGCAGGACGA 62.836 60.000 0.00 0.00 43.86 4.20
923 1039 2.481795 GGTGGTGCAATATGGAATGTGC 60.482 50.000 0.00 0.00 38.65 4.57
958 1074 4.803426 CCGGACCGCAGTGAGAGC 62.803 72.222 8.86 0.00 0.00 4.09
970 1091 2.956964 CAAGCTCGATCGCCGGAC 60.957 66.667 11.09 0.00 39.14 4.79
2085 2236 0.828677 GGTACACTAGGCGGTCCAAT 59.171 55.000 0.00 0.00 33.74 3.16
2086 2237 0.251922 AGGTACACTAGGCGGTCCAA 60.252 55.000 0.00 0.00 33.74 3.53
2097 2248 2.663196 GCCGCCTTGAGGTACACT 59.337 61.111 0.00 0.00 37.57 3.55
2328 2479 2.559840 CTGTACGAGTCGTGCGGT 59.440 61.111 28.11 6.16 44.75 5.68
2804 2973 4.441792 CCCCTGTGTTTTCCTTTTCTTTG 58.558 43.478 0.00 0.00 0.00 2.77
2812 2981 1.531602 GCTGCCCCTGTGTTTTCCT 60.532 57.895 0.00 0.00 0.00 3.36
2829 2999 3.950395 AGGAGAGGAGCATTATTGTTTGC 59.050 43.478 0.00 0.00 39.17 3.68
2858 3028 3.121279 GTCACACGCAGTACAGTACATTG 59.879 47.826 13.37 4.69 41.61 2.82
2868 3043 5.176774 CACTTCTAATTTGTCACACGCAGTA 59.823 40.000 0.00 0.00 41.61 2.74
2872 3047 4.025229 TCACACTTCTAATTTGTCACACGC 60.025 41.667 0.00 0.00 0.00 5.34
2882 3182 6.568462 CGAATTTGGTGCTCACACTTCTAATT 60.568 38.462 2.21 0.64 46.57 1.40
2894 3194 0.804989 CCCAGACGAATTTGGTGCTC 59.195 55.000 0.00 0.00 32.40 4.26
2898 3200 1.674322 CCGCCCAGACGAATTTGGT 60.674 57.895 0.00 0.00 34.06 3.67
2972 3277 5.545658 AGTTGTATATGTTTCACCTTGCG 57.454 39.130 0.00 0.00 0.00 4.85
2975 3280 6.475727 CGATCGAGTTGTATATGTTTCACCTT 59.524 38.462 10.26 0.00 0.00 3.50
2993 3311 7.113684 GTCCATACAGAAAATAACTCGATCGAG 59.886 40.741 36.95 36.95 46.91 4.04
2994 3312 6.916387 GTCCATACAGAAAATAACTCGATCGA 59.084 38.462 18.32 18.32 0.00 3.59
2995 3313 6.144080 GGTCCATACAGAAAATAACTCGATCG 59.856 42.308 9.36 9.36 0.00 3.69
2996 3314 6.424207 GGGTCCATACAGAAAATAACTCGATC 59.576 42.308 0.00 0.00 0.00 3.69
2997 3315 6.289064 GGGTCCATACAGAAAATAACTCGAT 58.711 40.000 0.00 0.00 0.00 3.59
2998 3316 5.667466 GGGTCCATACAGAAAATAACTCGA 58.333 41.667 0.00 0.00 0.00 4.04
2999 3317 4.506654 CGGGTCCATACAGAAAATAACTCG 59.493 45.833 0.00 0.00 0.00 4.18
3000 3318 5.425630 ACGGGTCCATACAGAAAATAACTC 58.574 41.667 0.00 0.00 0.00 3.01
3001 3319 5.431179 ACGGGTCCATACAGAAAATAACT 57.569 39.130 0.00 0.00 0.00 2.24
3002 3320 5.163693 CCAACGGGTCCATACAGAAAATAAC 60.164 44.000 0.00 0.00 0.00 1.89
3074 3395 2.361119 CGTGCCATCAGTAGCTACCTAA 59.639 50.000 20.31 6.59 0.00 2.69
3181 3511 2.295909 CTCACCATCAAAGCGGGAAAAA 59.704 45.455 0.00 0.00 0.00 1.94
3182 3512 1.885887 CTCACCATCAAAGCGGGAAAA 59.114 47.619 0.00 0.00 0.00 2.29
3183 3513 1.073125 TCTCACCATCAAAGCGGGAAA 59.927 47.619 0.00 0.00 0.00 3.13
3184 3514 0.690192 TCTCACCATCAAAGCGGGAA 59.310 50.000 0.00 0.00 0.00 3.97
3185 3515 0.036388 GTCTCACCATCAAAGCGGGA 60.036 55.000 0.00 0.00 0.00 5.14
3186 3516 0.036010 AGTCTCACCATCAAAGCGGG 60.036 55.000 0.00 0.00 0.00 6.13
3187 3517 1.734465 GAAGTCTCACCATCAAAGCGG 59.266 52.381 0.00 0.00 0.00 5.52
3190 3520 4.823989 ACAAAGGAAGTCTCACCATCAAAG 59.176 41.667 0.00 0.00 0.00 2.77
3197 3527 2.610727 CCTCGACAAAGGAAGTCTCACC 60.611 54.545 0.00 0.00 38.87 4.02
3201 3531 0.038159 CGCCTCGACAAAGGAAGTCT 60.038 55.000 0.00 0.00 38.87 3.24
3229 3564 0.038159 CCGTCCTGGAGAACACAGTC 60.038 60.000 0.00 0.00 42.00 3.51
3233 3568 1.668151 GCACCGTCCTGGAGAACAC 60.668 63.158 0.00 0.00 42.00 3.32
3286 3621 2.403378 GGGAATGCAAAGGCGCGTA 61.403 57.895 8.43 0.00 45.35 4.42
3314 3649 6.087159 GTGAACATAAATTTTCGACCGGAAAC 59.913 38.462 9.46 0.00 44.07 2.78
3386 3722 6.750501 CGGACGATTCAGAAATAAAGTGACTA 59.249 38.462 0.00 0.00 0.00 2.59
3413 3749 5.007034 TGTATGTTGTTGGTTGGATACTGG 58.993 41.667 0.00 0.00 37.61 4.00
3425 3761 5.749596 TCCTTCTGTGTTGTATGTTGTTG 57.250 39.130 0.00 0.00 0.00 3.33
3494 3830 1.475280 GTACCTGAGCACATGTACGGA 59.525 52.381 12.36 0.00 37.96 4.69
3495 3831 1.203758 TGTACCTGAGCACATGTACGG 59.796 52.381 19.16 5.32 44.83 4.02
3496 3832 2.094700 AGTGTACCTGAGCACATGTACG 60.095 50.000 19.16 0.00 44.83 3.67
3497 3833 3.512680 GAGTGTACCTGAGCACATGTAC 58.487 50.000 18.19 18.19 43.39 2.90
3498 3834 2.496070 GGAGTGTACCTGAGCACATGTA 59.504 50.000 0.00 0.00 38.02 2.29
3499 3835 1.276421 GGAGTGTACCTGAGCACATGT 59.724 52.381 0.00 0.00 38.02 3.21
3500 3836 1.276138 TGGAGTGTACCTGAGCACATG 59.724 52.381 0.00 0.00 38.02 3.21
3521 3857 0.884704 GTTGCAAAGGACGAGCTCCA 60.885 55.000 8.47 0.00 42.46 3.86
3522 3858 1.869690 GTTGCAAAGGACGAGCTCC 59.130 57.895 8.47 0.00 39.81 4.70
3523 3859 1.493311 CGTTGCAAAGGACGAGCTC 59.507 57.895 0.00 2.73 41.53 4.09
3524 3860 2.607892 GCGTTGCAAAGGACGAGCT 61.608 57.895 14.31 0.00 41.53 4.09
3525 3861 2.127232 GCGTTGCAAAGGACGAGC 60.127 61.111 14.31 2.20 41.53 5.03
3526 3862 2.250939 TGGCGTTGCAAAGGACGAG 61.251 57.895 14.31 0.00 44.25 4.18
3527 3863 2.203084 TGGCGTTGCAAAGGACGA 60.203 55.556 14.31 0.00 44.25 4.20
3528 3864 2.051345 GTGGCGTTGCAAAGGACG 60.051 61.111 14.31 9.35 44.25 4.79
3529 3865 1.299089 GTGTGGCGTTGCAAAGGAC 60.299 57.895 14.31 6.09 40.95 3.85
3530 3866 1.444119 GAGTGTGGCGTTGCAAAGGA 61.444 55.000 14.31 0.00 32.44 3.36
3531 3867 1.008538 GAGTGTGGCGTTGCAAAGG 60.009 57.895 14.31 4.49 34.21 3.11
3532 3868 0.311790 ATGAGTGTGGCGTTGCAAAG 59.688 50.000 8.11 8.11 0.00 2.77
3533 3869 0.030504 CATGAGTGTGGCGTTGCAAA 59.969 50.000 0.00 0.00 0.00 3.68
3534 3870 1.653667 CATGAGTGTGGCGTTGCAA 59.346 52.632 0.00 0.00 0.00 4.08
3535 3871 2.260154 CCATGAGTGTGGCGTTGCA 61.260 57.895 0.00 0.00 31.43 4.08
3536 3872 1.308069 ATCCATGAGTGTGGCGTTGC 61.308 55.000 0.00 0.00 39.19 4.17
3537 3873 2.022764 TATCCATGAGTGTGGCGTTG 57.977 50.000 0.00 0.00 39.19 4.10
3538 3874 3.118261 AGAATATCCATGAGTGTGGCGTT 60.118 43.478 0.00 0.00 39.19 4.84
3539 3875 2.435805 AGAATATCCATGAGTGTGGCGT 59.564 45.455 0.00 0.00 39.19 5.68
3540 3876 3.117491 AGAATATCCATGAGTGTGGCG 57.883 47.619 0.00 0.00 39.19 5.69
3541 3877 4.454678 TGAAGAATATCCATGAGTGTGGC 58.545 43.478 0.00 0.00 39.19 5.01
3542 3878 6.118170 ACTTGAAGAATATCCATGAGTGTGG 58.882 40.000 0.00 0.00 40.76 4.17
3543 3879 8.771766 CATACTTGAAGAATATCCATGAGTGTG 58.228 37.037 0.00 0.00 0.00 3.82
3544 3880 8.489489 ACATACTTGAAGAATATCCATGAGTGT 58.511 33.333 0.00 0.00 0.00 3.55
3545 3881 8.899427 ACATACTTGAAGAATATCCATGAGTG 57.101 34.615 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.