Multiple sequence alignment - TraesCS1D01G268700

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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 TraesCS1D01G268700 chr1D 100.000 3316 0 0 1 3316 364231803 364228488 0.000000e+00 6124
1 TraesCS1D01G268700 chr1B 88.596 2394 138 45 1 2367 487674021 487671736 0.000000e+00 2784
2 TraesCS1D01G268700 chr1A 93.086 1157 39 17 1296 2442 463357979 463356854 0.000000e+00 1655
3 TraesCS1D01G268700 chr1A 88.086 512 40 8 753 1246 463358641 463358133 3.690000e-164 588
4 TraesCS1D01G268700 chr6A 90.723 636 44 5 2463 3096 466422954 466423576 0.000000e+00 833
5 TraesCS1D01G268700 chr6A 90.409 636 44 6 2463 3096 466166082 466166702 0.000000e+00 821
6 TraesCS1D01G268700 chr6A 94.444 90 2 2 3227 3316 466166816 466166902 5.770000e-28 135
7 TraesCS1D01G268700 chr6A 92.222 90 4 2 3227 3316 466423690 466423776 1.250000e-24 124
8 TraesCS1D01G268700 chr3D 88.183 567 50 5 2536 3096 361805865 361806420 0.000000e+00 660
9 TraesCS1D01G268700 chr3D 97.403 77 2 0 3240 3316 361806546 361806622 7.460000e-27 132
10 TraesCS1D01G268700 chr5B 86.667 225 27 2 2484 2706 659813189 659812966 2.550000e-61 246
11 TraesCS1D01G268700 chr5B 92.405 79 3 1 3241 3316 659812349 659812271 3.500000e-20 110
12 TraesCS1D01G268700 chr7B 83.553 152 21 4 2909 3058 63174234 63174383 4.460000e-29 139


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 TraesCS1D01G268700 chr1D 364228488 364231803 3315 True 6124.0 6124 100.0000 1 3316 1 chr1D.!!$R1 3315
1 TraesCS1D01G268700 chr1B 487671736 487674021 2285 True 2784.0 2784 88.5960 1 2367 1 chr1B.!!$R1 2366
2 TraesCS1D01G268700 chr1A 463356854 463358641 1787 True 1121.5 1655 90.5860 753 2442 2 chr1A.!!$R1 1689
3 TraesCS1D01G268700 chr6A 466422954 466423776 822 False 478.5 833 91.4725 2463 3316 2 chr6A.!!$F2 853
4 TraesCS1D01G268700 chr6A 466166082 466166902 820 False 478.0 821 92.4265 2463 3316 2 chr6A.!!$F1 853
5 TraesCS1D01G268700 chr3D 361805865 361806622 757 False 396.0 660 92.7930 2536 3316 2 chr3D.!!$F1 780

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
711 715 0.178953 AGAAGTTGCCAGGCCACAAT 60.179 50.0 17.76 6.08 0.00 2.71 F
1162 1220 0.041576 GTGTTCGTTTCCGTTCCTGC 60.042 55.0 0.00 0.00 35.01 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 1894 0.317020 GGTGACAAACGCAGAGCAAC 60.317 55.0 0.00 0.0 0.0 4.17 R
2453 2637 0.390209 TAGCCGCTCCCGTTAACAAC 60.390 55.0 6.39 0.0 0.0 3.32 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
169 170 6.399639 AATTACCAATTTCCAGACACGTTT 57.600 33.333 0.00 0.00 0.00 3.60
179 180 4.927422 TCCAGACACGTTTTGAATTTTCC 58.073 39.130 0.00 0.00 0.00 3.13
180 181 4.399618 TCCAGACACGTTTTGAATTTTCCA 59.600 37.500 0.00 0.00 0.00 3.53
386 390 9.574516 ACTGTATCAAAACAAGAATAGTTCCTT 57.425 29.630 0.00 0.00 0.00 3.36
397 401 9.232473 ACAAGAATAGTTCCTTAAATTCCAGAC 57.768 33.333 0.00 0.00 0.00 3.51
415 419 5.754406 TCCAGACAATTTTGAAAGCACAATG 59.246 36.000 0.00 0.00 0.00 2.82
420 424 8.513774 AGACAATTTTGAAAGCACAATGTTTTT 58.486 25.926 0.00 0.00 30.93 1.94
543 547 7.956420 AAAAAGAAACAGAAGAAAAACGGTT 57.044 28.000 0.00 0.00 0.00 4.44
564 568 8.517056 ACGGTTAAATATACAACAGGAAAAAGG 58.483 33.333 0.00 0.00 0.00 3.11
565 569 7.971722 CGGTTAAATATACAACAGGAAAAAGGG 59.028 37.037 2.76 0.00 0.00 3.95
566 570 9.027202 GGTTAAATATACAACAGGAAAAAGGGA 57.973 33.333 2.76 0.00 0.00 4.20
597 601 0.321653 ACGAACATGAACCTCCCAGC 60.322 55.000 0.00 0.00 0.00 4.85
613 617 3.490890 GCATCCAGCGTCCAACTC 58.509 61.111 0.00 0.00 0.00 3.01
626 630 1.202710 TCCAACTCTGCTGGCGTTAAA 60.203 47.619 0.00 0.00 33.63 1.52
699 703 6.132056 GCATTATGCGTCAAGATAGAAGTTG 58.868 40.000 0.00 0.00 31.71 3.16
706 710 2.019984 CAAGATAGAAGTTGCCAGGCC 58.980 52.381 9.64 0.00 0.00 5.19
707 711 1.289160 AGATAGAAGTTGCCAGGCCA 58.711 50.000 9.64 0.00 0.00 5.36
708 712 1.065126 AGATAGAAGTTGCCAGGCCAC 60.065 52.381 9.64 8.55 0.00 5.01
709 713 0.698238 ATAGAAGTTGCCAGGCCACA 59.302 50.000 17.76 0.00 0.00 4.17
710 714 0.476338 TAGAAGTTGCCAGGCCACAA 59.524 50.000 17.76 3.21 0.00 3.33
711 715 0.178953 AGAAGTTGCCAGGCCACAAT 60.179 50.000 17.76 6.08 0.00 2.71
727 731 2.480610 AATGCCAGTATTGCGCGGG 61.481 57.895 8.83 0.00 0.00 6.13
733 737 1.610624 CCAGTATTGCGCGGGGATAAT 60.611 52.381 8.83 0.00 0.00 1.28
734 738 2.151202 CAGTATTGCGCGGGGATAATT 58.849 47.619 8.83 0.00 0.00 1.40
735 739 2.552315 CAGTATTGCGCGGGGATAATTT 59.448 45.455 8.83 0.00 0.00 1.82
736 740 3.004315 CAGTATTGCGCGGGGATAATTTT 59.996 43.478 8.83 0.00 0.00 1.82
764 769 3.146618 CGGTAATATAGCGCGGAGATT 57.853 47.619 8.83 6.09 42.95 2.40
836 845 1.976474 GGACCTGCATCGCCCAAAA 60.976 57.895 0.00 0.00 0.00 2.44
844 853 1.003262 CATCGCCCAAAACGCAACTG 61.003 55.000 0.00 0.00 0.00 3.16
846 855 2.661537 GCCCAAAACGCAACTGCC 60.662 61.111 0.00 0.00 37.91 4.85
871 900 4.115516 CCATTCGTCTGGACTTCATACAG 58.884 47.826 0.41 0.00 38.69 2.74
963 1008 3.606662 GGCTATCTCCCGCGCTCA 61.607 66.667 5.56 0.00 0.00 4.26
1162 1220 0.041576 GTGTTCGTTTCCGTTCCTGC 60.042 55.000 0.00 0.00 35.01 4.85
1179 1237 1.394917 CTGCGTTATCCACTTGCACTC 59.605 52.381 0.00 0.00 0.00 3.51
1180 1238 1.001974 TGCGTTATCCACTTGCACTCT 59.998 47.619 0.00 0.00 0.00 3.24
1181 1239 2.076863 GCGTTATCCACTTGCACTCTT 58.923 47.619 0.00 0.00 0.00 2.85
1188 1246 2.886523 TCCACTTGCACTCTTTTGATGG 59.113 45.455 0.00 0.00 0.00 3.51
1198 1256 0.897863 CTTTTGATGGCCCGAACCCA 60.898 55.000 0.00 0.00 36.66 4.51
1204 1262 0.252012 ATGGCCCGAACCCAATTTCA 60.252 50.000 0.00 0.00 35.67 2.69
1246 1304 5.010012 GGTCTGATCACACAAAAATTGGAGT 59.990 40.000 3.41 0.00 34.12 3.85
1247 1305 6.206634 GGTCTGATCACACAAAAATTGGAGTA 59.793 38.462 3.41 0.00 34.12 2.59
1248 1306 7.301054 GTCTGATCACACAAAAATTGGAGTAG 58.699 38.462 0.00 0.00 34.12 2.57
1249 1307 6.998074 TCTGATCACACAAAAATTGGAGTAGT 59.002 34.615 0.00 0.00 34.12 2.73
1250 1308 8.154203 TCTGATCACACAAAAATTGGAGTAGTA 58.846 33.333 0.00 0.00 34.12 1.82
1251 1309 8.684386 TGATCACACAAAAATTGGAGTAGTAA 57.316 30.769 0.00 0.00 34.12 2.24
1252 1310 9.295825 TGATCACACAAAAATTGGAGTAGTAAT 57.704 29.630 0.00 0.00 34.12 1.89
1292 1384 1.812571 GGACACCGTGATTGAGCAAAT 59.187 47.619 5.28 0.00 0.00 2.32
1323 1482 7.651808 CAACTATTGCAGTTTCTATATTGGGG 58.348 38.462 0.00 0.00 45.54 4.96
1338 1497 7.951806 TCTATATTGGGGAAATTTCAGATGCAT 59.048 33.333 19.49 0.00 0.00 3.96
1339 1498 9.246670 CTATATTGGGGAAATTTCAGATGCATA 57.753 33.333 19.49 8.10 0.00 3.14
1354 1513 0.514691 GCATATACTCAAGCCAGCGC 59.485 55.000 0.00 0.00 0.00 5.92
1703 1862 3.286329 ACAAGTAAACCAACCGACCTT 57.714 42.857 0.00 0.00 0.00 3.50
1708 1867 2.361865 AAACCAACCGACCTTCCCCC 62.362 60.000 0.00 0.00 0.00 5.40
1730 1889 3.412386 CTTCTCCGGTCCAATCACTTTT 58.588 45.455 0.00 0.00 0.00 2.27
1731 1890 3.502123 TCTCCGGTCCAATCACTTTTT 57.498 42.857 0.00 0.00 0.00 1.94
1786 1949 0.596577 ATCGATGGATGCTTGCATGC 59.403 50.000 17.19 17.19 33.54 4.06
1928 2091 1.588082 GTGCAGGAAATGGCTGGTG 59.412 57.895 0.00 0.00 0.00 4.17
2294 2460 1.329906 GCGATGATGAAGAGCTGGTTG 59.670 52.381 0.00 0.00 0.00 3.77
2316 2482 1.165907 CGACCACCTGCTTGCTTGAA 61.166 55.000 0.00 0.00 0.00 2.69
2323 2499 2.224719 ACCTGCTTGCTTGAACTGATCT 60.225 45.455 0.00 0.00 0.00 2.75
2324 2500 2.161808 CCTGCTTGCTTGAACTGATCTG 59.838 50.000 0.00 0.00 0.00 2.90
2325 2501 3.072211 CTGCTTGCTTGAACTGATCTGA 58.928 45.455 6.60 0.00 0.00 3.27
2326 2502 3.682696 TGCTTGCTTGAACTGATCTGAT 58.317 40.909 6.60 0.00 0.00 2.90
2327 2503 3.688185 TGCTTGCTTGAACTGATCTGATC 59.312 43.478 10.72 10.72 0.00 2.92
2377 2559 1.732941 TGCTGTGTTCGTTGTTCTGT 58.267 45.000 0.00 0.00 0.00 3.41
2388 2570 4.350346 TCGTTGTTCTGTTTGATTGCAAG 58.650 39.130 4.94 0.00 35.04 4.01
2390 2572 4.562394 CGTTGTTCTGTTTGATTGCAAGTT 59.438 37.500 4.94 0.00 35.04 2.66
2391 2573 5.275881 CGTTGTTCTGTTTGATTGCAAGTTC 60.276 40.000 4.94 0.00 35.04 3.01
2392 2574 4.350346 TGTTCTGTTTGATTGCAAGTTCG 58.650 39.130 4.94 0.00 35.04 3.95
2393 2575 2.998772 TCTGTTTGATTGCAAGTTCGC 58.001 42.857 4.94 0.00 35.04 4.70
2400 2582 2.487918 TTGCAAGTTCGCAACTGGT 58.512 47.368 0.00 0.00 46.61 4.00
2401 2583 0.100325 TTGCAAGTTCGCAACTGGTG 59.900 50.000 0.00 0.00 46.61 4.17
2402 2584 0.746204 TGCAAGTTCGCAACTGGTGA 60.746 50.000 0.00 0.00 41.91 4.02
2403 2585 0.380378 GCAAGTTCGCAACTGGTGAA 59.620 50.000 0.00 0.00 41.91 3.18
2404 2586 1.001378 GCAAGTTCGCAACTGGTGAAT 60.001 47.619 0.00 0.00 46.81 2.57
2410 2592 4.219944 AGTTCGCAACTGGTGAATAGACTA 59.780 41.667 0.00 0.00 46.81 2.59
2418 2600 6.287589 ACTGGTGAATAGACTAAAGAGGTG 57.712 41.667 0.00 0.00 0.00 4.00
2442 2626 5.835113 AGTGCATTGTTAACACTCAACTT 57.165 34.783 8.07 0.00 40.56 2.66
2443 2627 6.207691 AGTGCATTGTTAACACTCAACTTT 57.792 33.333 8.07 0.00 40.56 2.66
2444 2628 6.630071 AGTGCATTGTTAACACTCAACTTTT 58.370 32.000 8.07 0.00 40.56 2.27
2445 2629 7.096551 AGTGCATTGTTAACACTCAACTTTTT 58.903 30.769 8.07 0.00 40.56 1.94
2490 2674 1.478510 CTACCTGCCAATCGACTGACT 59.521 52.381 0.00 0.00 0.00 3.41
2529 2713 5.849081 GTCGAATGACAAAAACAGCGAATAA 59.151 36.000 0.00 0.00 44.82 1.40
2534 2718 8.816640 AATGACAAAAACAGCGAATAAAGAAT 57.183 26.923 0.00 0.00 0.00 2.40
2565 2749 7.004086 AGAATGATTTGACTGACCCAAACTTA 58.996 34.615 0.00 0.00 36.48 2.24
2589 2773 1.537202 CCAGTCGAAAAGCCCAGAAAG 59.463 52.381 0.00 0.00 0.00 2.62
2590 2774 2.494059 CAGTCGAAAAGCCCAGAAAGA 58.506 47.619 0.00 0.00 0.00 2.52
2591 2775 2.481952 CAGTCGAAAAGCCCAGAAAGAG 59.518 50.000 0.00 0.00 0.00 2.85
2592 2776 2.104963 AGTCGAAAAGCCCAGAAAGAGT 59.895 45.455 0.00 0.00 0.00 3.24
2593 2777 3.323979 AGTCGAAAAGCCCAGAAAGAGTA 59.676 43.478 0.00 0.00 0.00 2.59
2594 2778 3.680458 GTCGAAAAGCCCAGAAAGAGTAG 59.320 47.826 0.00 0.00 0.00 2.57
2595 2779 2.416893 CGAAAAGCCCAGAAAGAGTAGC 59.583 50.000 0.00 0.00 0.00 3.58
2596 2780 2.498644 AAAGCCCAGAAAGAGTAGCC 57.501 50.000 0.00 0.00 0.00 3.93
2597 2781 1.662686 AAGCCCAGAAAGAGTAGCCT 58.337 50.000 0.00 0.00 0.00 4.58
2598 2782 1.199615 AGCCCAGAAAGAGTAGCCTC 58.800 55.000 0.00 0.00 38.04 4.70
2636 2820 1.131638 TTCTGTCTTCTGGCCACAGT 58.868 50.000 17.24 0.00 45.14 3.55
2645 2829 0.675837 CTGGCCACAGTCCACATCTG 60.676 60.000 0.00 0.00 39.92 2.90
2668 2852 2.824489 GGCCTGAACCCGCTAAGC 60.824 66.667 0.00 0.00 0.00 3.09
2746 2935 2.488347 CCCTTTCTTCCCGAAACCAGAA 60.488 50.000 0.00 0.00 36.72 3.02
2747 2936 2.552743 CCTTTCTTCCCGAAACCAGAAC 59.447 50.000 0.00 0.00 36.72 3.01
2781 2970 2.299582 CCATGGATGCTGAAACAAACCA 59.700 45.455 5.56 0.00 35.58 3.67
2809 2998 6.259346 TGATCTGATCTCTTCTGACCTCTA 57.741 41.667 17.82 0.00 35.42 2.43
2814 3003 8.218423 TCTGATCTCTTCTGACCTCTATCTAT 57.782 38.462 0.00 0.00 0.00 1.98
2820 3009 9.958180 TCTCTTCTGACCTCTATCTATATCTTG 57.042 37.037 0.00 0.00 0.00 3.02
2826 3015 9.407380 CTGACCTCTATCTATATCTTGTGCTAT 57.593 37.037 0.00 0.00 0.00 2.97
2857 3046 0.322546 CCCAAAACCCTTCTCCTCCG 60.323 60.000 0.00 0.00 0.00 4.63
2866 3055 4.689549 TCTCCTCCGGTCGCCCAA 62.690 66.667 0.00 0.00 0.00 4.12
2969 3158 4.950205 AAACCGAGAAGAGACAAACCTA 57.050 40.909 0.00 0.00 0.00 3.08
2995 3184 5.687730 AGATGAATCTGCTACACGTATTTCG 59.312 40.000 0.00 0.00 39.62 3.46
2998 3187 6.040247 TGAATCTGCTACACGTATTTCGAAT 58.960 36.000 0.00 0.00 42.86 3.34
3029 3218 3.267551 GGTAATCCCCCACCACTTCTTTA 59.732 47.826 0.00 0.00 34.77 1.85
3047 3236 6.737720 TCTTTACTCAGGCATCATATCAGT 57.262 37.500 0.00 0.00 0.00 3.41
3096 3286 6.963117 TCCCCTTTTACTAGATCAGGAAAA 57.037 37.500 12.08 12.08 43.51 2.29
3098 3288 7.402862 TCCCCTTTTACTAGATCAGGAAAAAG 58.597 38.462 13.08 15.28 44.73 2.27
3099 3289 7.018249 TCCCCTTTTACTAGATCAGGAAAAAGT 59.982 37.037 19.26 0.00 44.73 2.66
3100 3290 8.326529 CCCCTTTTACTAGATCAGGAAAAAGTA 58.673 37.037 19.26 0.00 44.73 2.24
3101 3291 9.163899 CCCTTTTACTAGATCAGGAAAAAGTAC 57.836 37.037 19.26 0.00 44.73 2.73
3102 3292 9.720769 CCTTTTACTAGATCAGGAAAAAGTACA 57.279 33.333 19.26 3.93 44.73 2.90
3106 3296 9.706691 TTACTAGATCAGGAAAAAGTACACTTG 57.293 33.333 0.00 0.00 36.12 3.16
3107 3297 5.948992 AGATCAGGAAAAAGTACACTTGC 57.051 39.130 0.00 0.00 36.12 4.01
3108 3298 5.625150 AGATCAGGAAAAAGTACACTTGCT 58.375 37.500 0.00 0.00 36.12 3.91
3109 3299 5.703130 AGATCAGGAAAAAGTACACTTGCTC 59.297 40.000 0.00 0.00 36.12 4.26
3110 3300 5.036117 TCAGGAAAAAGTACACTTGCTCT 57.964 39.130 0.00 0.00 36.12 4.09
3111 3301 5.437060 TCAGGAAAAAGTACACTTGCTCTT 58.563 37.500 0.00 0.00 36.12 2.85
3112 3302 5.885912 TCAGGAAAAAGTACACTTGCTCTTT 59.114 36.000 0.00 0.00 36.12 2.52
3113 3303 6.377146 TCAGGAAAAAGTACACTTGCTCTTTT 59.623 34.615 0.00 0.00 40.35 2.27
3114 3304 7.035612 CAGGAAAAAGTACACTTGCTCTTTTT 58.964 34.615 17.09 17.09 46.00 1.94
3118 3308 7.391148 AAAAGTACACTTGCTCTTTTTCAGA 57.609 32.000 0.00 0.00 36.96 3.27
3119 3309 7.391148 AAAGTACACTTGCTCTTTTTCAGAA 57.609 32.000 0.00 0.00 36.12 3.02
3120 3310 6.610741 AGTACACTTGCTCTTTTTCAGAAG 57.389 37.500 0.00 0.00 0.00 2.85
3121 3311 6.349300 AGTACACTTGCTCTTTTTCAGAAGA 58.651 36.000 0.00 0.00 34.63 2.87
3122 3312 6.995091 AGTACACTTGCTCTTTTTCAGAAGAT 59.005 34.615 0.00 0.00 35.27 2.40
3123 3313 8.150945 AGTACACTTGCTCTTTTTCAGAAGATA 58.849 33.333 0.00 0.00 35.27 1.98
3124 3314 7.195839 ACACTTGCTCTTTTTCAGAAGATAC 57.804 36.000 0.00 0.00 35.27 2.24
3125 3315 6.767902 ACACTTGCTCTTTTTCAGAAGATACA 59.232 34.615 0.00 0.00 35.27 2.29
3126 3316 7.074502 CACTTGCTCTTTTTCAGAAGATACAC 58.925 38.462 0.00 0.00 35.27 2.90
3127 3317 6.205658 ACTTGCTCTTTTTCAGAAGATACACC 59.794 38.462 0.00 0.00 35.27 4.16
3128 3318 5.869579 TGCTCTTTTTCAGAAGATACACCT 58.130 37.500 0.00 0.00 35.27 4.00
3129 3319 5.702670 TGCTCTTTTTCAGAAGATACACCTG 59.297 40.000 0.00 0.00 35.27 4.00
3130 3320 5.934625 GCTCTTTTTCAGAAGATACACCTGA 59.065 40.000 0.00 0.00 35.27 3.86
3131 3321 6.128418 GCTCTTTTTCAGAAGATACACCTGAC 60.128 42.308 0.00 0.00 36.75 3.51
3132 3322 6.826668 TCTTTTTCAGAAGATACACCTGACA 58.173 36.000 0.00 0.00 36.75 3.58
3133 3323 6.931281 TCTTTTTCAGAAGATACACCTGACAG 59.069 38.462 0.00 0.00 36.75 3.51
3134 3324 6.419484 TTTTCAGAAGATACACCTGACAGA 57.581 37.500 3.32 0.00 36.75 3.41
3135 3325 6.611613 TTTCAGAAGATACACCTGACAGAT 57.388 37.500 3.32 0.00 36.75 2.90
3136 3326 7.718334 TTTCAGAAGATACACCTGACAGATA 57.282 36.000 3.32 0.00 36.75 1.98
3137 3327 7.718334 TTCAGAAGATACACCTGACAGATAA 57.282 36.000 3.32 0.00 36.75 1.75
3138 3328 7.718334 TCAGAAGATACACCTGACAGATAAA 57.282 36.000 3.32 0.00 32.57 1.40
3139 3329 8.134202 TCAGAAGATACACCTGACAGATAAAA 57.866 34.615 3.32 0.00 32.57 1.52
3140 3330 8.593679 TCAGAAGATACACCTGACAGATAAAAA 58.406 33.333 3.32 0.00 32.57 1.94
3172 3363 8.774586 GTTATGTGTTCAGAAACTAGTGAATGT 58.225 33.333 0.00 0.00 35.22 2.71
3203 3394 8.079203 GTGTGTTGTGGTGATTTCAAACATATA 58.921 33.333 0.00 0.00 0.00 0.86
3238 3430 6.054941 TGCACATTCAGAGAACTAAAGTTGA 58.945 36.000 0.00 0.00 38.56 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 6.039941 TCAAAACGTGTCTGGAAATTGGTAAT 59.960 34.615 0.00 0.00 0.00 1.89
155 156 5.808030 GGAAAATTCAAAACGTGTCTGGAAA 59.192 36.000 0.00 0.00 0.00 3.13
380 384 9.541143 TTCAAAATTGTCTGGAATTTAAGGAAC 57.459 29.630 0.00 0.00 35.01 3.62
384 388 9.044150 TGCTTTCAAAATTGTCTGGAATTTAAG 57.956 29.630 0.00 0.00 35.01 1.85
386 390 7.984050 TGTGCTTTCAAAATTGTCTGGAATTTA 59.016 29.630 0.00 0.00 35.01 1.40
576 580 2.504367 CTGGGAGGTTCATGTTCGTTT 58.496 47.619 0.00 0.00 0.00 3.60
593 597 2.046023 TTGGACGCTGGATGCTGG 60.046 61.111 0.00 0.00 40.11 4.85
597 601 1.364626 GCAGAGTTGGACGCTGGATG 61.365 60.000 12.53 0.00 44.58 3.51
613 617 1.139520 GCCCATTTAACGCCAGCAG 59.860 57.895 0.00 0.00 0.00 4.24
647 651 0.924090 GTCGGCTTGTCGCATAGAAG 59.076 55.000 0.00 0.00 41.67 2.85
659 663 0.246635 ATGCGTCAAGTAGTCGGCTT 59.753 50.000 0.00 0.00 0.00 4.35
706 710 0.862701 CGCGCAATACTGGCATTGTG 60.863 55.000 8.75 8.18 45.18 3.33
707 711 1.429021 CGCGCAATACTGGCATTGT 59.571 52.632 8.75 0.00 38.04 2.71
708 712 1.298563 CCGCGCAATACTGGCATTG 60.299 57.895 8.75 0.00 38.65 2.82
709 713 2.480610 CCCGCGCAATACTGGCATT 61.481 57.895 8.75 0.00 0.00 3.56
710 714 2.901840 CCCGCGCAATACTGGCAT 60.902 61.111 8.75 0.00 0.00 4.40
745 750 7.168804 GGTTTATAATCTCCGCGCTATATTACC 59.831 40.741 5.56 6.93 0.00 2.85
764 769 6.115446 GCTGCAGCTATGGATATGGTTTATA 58.885 40.000 31.33 0.00 38.21 0.98
805 814 3.773370 GGTCCTGAGTCGTGACCA 58.227 61.111 20.41 0.00 46.29 4.02
818 827 1.976474 TTTTGGGCGATGCAGGTCC 60.976 57.895 4.30 4.30 0.00 4.46
836 845 2.281484 AATGGACGGCAGTTGCGT 60.281 55.556 0.00 0.00 43.26 5.24
844 853 2.577059 TCCAGACGAATGGACGGC 59.423 61.111 8.92 0.00 44.56 5.68
891 920 2.949644 CTCGGGTGTGGATATTTTTCCC 59.050 50.000 0.00 0.00 34.67 3.97
1162 1220 4.213270 TCAAAAGAGTGCAAGTGGATAACG 59.787 41.667 0.00 0.00 0.00 3.18
1179 1237 0.897863 TGGGTTCGGGCCATCAAAAG 60.898 55.000 4.39 0.00 0.00 2.27
1180 1238 0.470080 TTGGGTTCGGGCCATCAAAA 60.470 50.000 4.39 0.00 0.00 2.44
1181 1239 0.252012 ATTGGGTTCGGGCCATCAAA 60.252 50.000 4.39 0.00 0.00 2.69
1188 1246 1.215382 GCTGAAATTGGGTTCGGGC 59.785 57.895 0.00 0.00 34.90 6.13
1198 1256 5.916318 TCACAACCAATTCAAGCTGAAATT 58.084 33.333 0.00 0.00 40.12 1.82
1204 1262 2.887152 GACCTCACAACCAATTCAAGCT 59.113 45.455 0.00 0.00 0.00 3.74
1239 1297 8.982723 ACACACAGAATAGATTACTACTCCAAT 58.017 33.333 0.00 0.00 0.00 3.16
1250 1308 9.295825 TGTCCAATTAAACACACAGAATAGATT 57.704 29.630 0.00 0.00 0.00 2.40
1251 1309 8.730680 GTGTCCAATTAAACACACAGAATAGAT 58.269 33.333 14.48 0.00 44.10 1.98
1252 1310 7.174253 GGTGTCCAATTAAACACACAGAATAGA 59.826 37.037 18.81 0.00 45.99 1.98
1309 1468 9.971922 CATCTGAAATTTCCCCAATATAGAAAC 57.028 33.333 15.48 0.00 32.67 2.78
1323 1482 7.806960 GGCTTGAGTATATGCATCTGAAATTTC 59.193 37.037 11.41 11.41 0.00 2.17
1354 1513 1.135731 GTCGTCAGAGCACGGAGAG 59.864 63.158 0.00 0.00 40.35 3.20
1361 1520 2.717580 ATTGTTACGTCGTCAGAGCA 57.282 45.000 0.00 0.00 0.00 4.26
1672 1831 1.196127 GTTTACTTGTAGCCGTGGCAC 59.804 52.381 14.29 7.79 44.88 5.01
1708 1867 0.905357 AGTGATTGGACCGGAGAAGG 59.095 55.000 9.46 0.00 37.30 3.46
1734 1893 0.657840 GTGACAAACGCAGAGCAACT 59.342 50.000 0.00 0.00 0.00 3.16
1735 1894 0.317020 GGTGACAAACGCAGAGCAAC 60.317 55.000 0.00 0.00 0.00 4.17
1736 1895 0.463654 AGGTGACAAACGCAGAGCAA 60.464 50.000 0.00 0.00 0.00 3.91
1737 1896 0.880278 GAGGTGACAAACGCAGAGCA 60.880 55.000 0.00 0.00 0.00 4.26
1738 1897 0.601311 AGAGGTGACAAACGCAGAGC 60.601 55.000 0.00 0.00 0.00 4.09
1739 1898 1.795286 GAAGAGGTGACAAACGCAGAG 59.205 52.381 0.00 0.00 0.00 3.35
1740 1899 1.138069 TGAAGAGGTGACAAACGCAGA 59.862 47.619 0.00 0.00 0.00 4.26
1741 1900 1.581934 TGAAGAGGTGACAAACGCAG 58.418 50.000 0.00 0.00 0.00 5.18
1742 1901 1.872952 CATGAAGAGGTGACAAACGCA 59.127 47.619 0.00 0.00 0.00 5.24
1745 1904 3.565482 TCAAGCATGAAGAGGTGACAAAC 59.435 43.478 0.00 0.00 30.99 2.93
1786 1949 2.177531 GCACCAGAACGCTGCATG 59.822 61.111 0.00 0.00 40.91 4.06
2042 2208 4.492160 TAGAAGCAGACGCCCGCG 62.492 66.667 7.69 7.69 46.03 6.46
2267 2433 1.145759 TCTTCATCATCGCGAACGCC 61.146 55.000 15.24 0.00 39.84 5.68
2323 2499 1.341209 ACGACACAAGACAGCTGATCA 59.659 47.619 23.35 0.00 0.00 2.92
2324 2500 1.723542 CACGACACAAGACAGCTGATC 59.276 52.381 23.35 14.11 0.00 2.92
2325 2501 1.069204 ACACGACACAAGACAGCTGAT 59.931 47.619 23.35 5.42 0.00 2.90
2326 2502 0.459899 ACACGACACAAGACAGCTGA 59.540 50.000 23.35 0.00 0.00 4.26
2327 2503 0.578683 CACACGACACAAGACAGCTG 59.421 55.000 13.48 13.48 0.00 4.24
2388 2570 3.326747 AGTCTATTCACCAGTTGCGAAC 58.673 45.455 0.00 0.00 0.00 3.95
2390 2572 4.794278 TTAGTCTATTCACCAGTTGCGA 57.206 40.909 0.00 0.00 0.00 5.10
2391 2573 5.168569 TCTTTAGTCTATTCACCAGTTGCG 58.831 41.667 0.00 0.00 0.00 4.85
2392 2574 5.582665 CCTCTTTAGTCTATTCACCAGTTGC 59.417 44.000 0.00 0.00 0.00 4.17
2393 2575 6.591834 CACCTCTTTAGTCTATTCACCAGTTG 59.408 42.308 0.00 0.00 0.00 3.16
2395 2577 6.017192 TCACCTCTTTAGTCTATTCACCAGT 58.983 40.000 0.00 0.00 0.00 4.00
2396 2578 6.531503 TCACCTCTTTAGTCTATTCACCAG 57.468 41.667 0.00 0.00 0.00 4.00
2397 2579 6.497259 ACTTCACCTCTTTAGTCTATTCACCA 59.503 38.462 0.00 0.00 0.00 4.17
2398 2580 6.814146 CACTTCACCTCTTTAGTCTATTCACC 59.186 42.308 0.00 0.00 0.00 4.02
2399 2581 6.311690 GCACTTCACCTCTTTAGTCTATTCAC 59.688 42.308 0.00 0.00 0.00 3.18
2400 2582 6.014584 TGCACTTCACCTCTTTAGTCTATTCA 60.015 38.462 0.00 0.00 0.00 2.57
2401 2583 6.398918 TGCACTTCACCTCTTTAGTCTATTC 58.601 40.000 0.00 0.00 0.00 1.75
2402 2584 6.360370 TGCACTTCACCTCTTTAGTCTATT 57.640 37.500 0.00 0.00 0.00 1.73
2403 2585 6.552445 ATGCACTTCACCTCTTTAGTCTAT 57.448 37.500 0.00 0.00 0.00 1.98
2404 2586 6.166279 CAATGCACTTCACCTCTTTAGTCTA 58.834 40.000 0.00 0.00 0.00 2.59
2410 2592 5.359576 TGTTAACAATGCACTTCACCTCTTT 59.640 36.000 5.64 0.00 0.00 2.52
2418 2600 5.821204 AGTTGAGTGTTAACAATGCACTTC 58.179 37.500 14.13 0.00 42.71 3.01
2444 2628 4.261280 GCTCCCGTTAACAACTGCTAAAAA 60.261 41.667 6.39 0.00 0.00 1.94
2445 2629 3.251487 GCTCCCGTTAACAACTGCTAAAA 59.749 43.478 6.39 0.00 0.00 1.52
2446 2630 2.809696 GCTCCCGTTAACAACTGCTAAA 59.190 45.455 6.39 0.00 0.00 1.85
2447 2631 2.419667 GCTCCCGTTAACAACTGCTAA 58.580 47.619 6.39 0.00 0.00 3.09
2448 2632 1.670674 CGCTCCCGTTAACAACTGCTA 60.671 52.381 6.39 0.00 0.00 3.49
2449 2633 0.949105 CGCTCCCGTTAACAACTGCT 60.949 55.000 6.39 0.00 0.00 4.24
2450 2634 1.495951 CGCTCCCGTTAACAACTGC 59.504 57.895 6.39 3.78 0.00 4.40
2451 2635 1.908066 GCCGCTCCCGTTAACAACTG 61.908 60.000 6.39 0.00 0.00 3.16
2452 2636 1.670083 GCCGCTCCCGTTAACAACT 60.670 57.895 6.39 0.00 0.00 3.16
2453 2637 0.390209 TAGCCGCTCCCGTTAACAAC 60.390 55.000 6.39 0.00 0.00 3.32
2454 2638 0.390209 GTAGCCGCTCCCGTTAACAA 60.390 55.000 6.39 0.00 0.00 2.83
2455 2639 1.216178 GTAGCCGCTCCCGTTAACA 59.784 57.895 6.39 0.00 0.00 2.41
2456 2640 1.520120 GGTAGCCGCTCCCGTTAAC 60.520 63.158 0.00 0.00 0.00 2.01
2457 2641 1.683365 AGGTAGCCGCTCCCGTTAA 60.683 57.895 0.00 0.00 0.00 2.01
2458 2642 2.043652 AGGTAGCCGCTCCCGTTA 60.044 61.111 0.00 0.00 0.00 3.18
2459 2643 3.771160 CAGGTAGCCGCTCCCGTT 61.771 66.667 0.00 0.00 0.00 4.44
2477 2661 2.996621 GTTTCTGGAGTCAGTCGATTGG 59.003 50.000 8.17 0.00 41.59 3.16
2490 2674 0.824595 TCGACTGACCCGTTTCTGGA 60.825 55.000 0.00 0.00 0.00 3.86
2522 2706 9.727627 AATCATTCTTCTGAATTCTTTATTCGC 57.272 29.630 7.05 0.00 44.67 4.70
2529 2713 9.293404 TCAGTCAAATCATTCTTCTGAATTCTT 57.707 29.630 7.05 0.00 40.61 2.52
2534 2718 5.707298 GGGTCAGTCAAATCATTCTTCTGAA 59.293 40.000 0.00 0.00 33.36 3.02
2565 2749 2.034221 GGCTTTTCGACTGGCCCT 59.966 61.111 0.00 0.00 38.77 5.19
2569 2753 1.537202 CTTTCTGGGCTTTTCGACTGG 59.463 52.381 0.00 0.00 0.00 4.00
2589 2773 4.212214 CAGAAACAAACACAGAGGCTACTC 59.788 45.833 0.00 0.00 44.31 2.59
2590 2774 4.130118 CAGAAACAAACACAGAGGCTACT 58.870 43.478 0.00 0.00 0.00 2.57
2591 2775 3.877508 ACAGAAACAAACACAGAGGCTAC 59.122 43.478 0.00 0.00 0.00 3.58
2592 2776 4.150897 ACAGAAACAAACACAGAGGCTA 57.849 40.909 0.00 0.00 0.00 3.93
2593 2777 3.004752 ACAGAAACAAACACAGAGGCT 57.995 42.857 0.00 0.00 0.00 4.58
2594 2778 5.438761 AATACAGAAACAAACACAGAGGC 57.561 39.130 0.00 0.00 0.00 4.70
2595 2779 7.645340 CAGAAAATACAGAAACAAACACAGAGG 59.355 37.037 0.00 0.00 0.00 3.69
2596 2780 8.184192 ACAGAAAATACAGAAACAAACACAGAG 58.816 33.333 0.00 0.00 0.00 3.35
2597 2781 8.050778 ACAGAAAATACAGAAACAAACACAGA 57.949 30.769 0.00 0.00 0.00 3.41
2598 2782 8.184192 AGACAGAAAATACAGAAACAAACACAG 58.816 33.333 0.00 0.00 0.00 3.66
2599 2783 8.050778 AGACAGAAAATACAGAAACAAACACA 57.949 30.769 0.00 0.00 0.00 3.72
2636 2820 1.002624 GGCCCGTTTCAGATGTGGA 60.003 57.895 0.00 0.00 0.00 4.02
2668 2852 6.001460 TGGATCTTGTTAAGTGGGTTAGTTG 58.999 40.000 0.00 0.00 0.00 3.16
2814 3003 7.220030 GGAGGAAGAAATGATAGCACAAGATA 58.780 38.462 0.00 0.00 0.00 1.98
2820 3009 4.156455 TGGGAGGAAGAAATGATAGCAC 57.844 45.455 0.00 0.00 0.00 4.40
2826 3015 3.142028 AGGGTTTTGGGAGGAAGAAATGA 59.858 43.478 0.00 0.00 0.00 2.57
2866 3055 2.376518 TGGTTCTTCAGCTTGGGATCTT 59.623 45.455 0.00 0.00 0.00 2.40
2969 3158 6.398234 AATACGTGTAGCAGATTCATCTCT 57.602 37.500 0.00 0.00 34.22 3.10
2995 3184 6.436218 GGTGGGGGATTACCATTATTACATTC 59.564 42.308 0.00 0.00 42.91 2.67
2998 3187 4.732443 TGGTGGGGGATTACCATTATTACA 59.268 41.667 0.00 0.00 41.80 2.41
3008 3197 3.451402 AAAGAAGTGGTGGGGGATTAC 57.549 47.619 0.00 0.00 0.00 1.89
3029 3218 5.363562 TGAAACTGATATGATGCCTGAGT 57.636 39.130 0.00 0.00 0.00 3.41
3047 3236 6.380560 TGTGATGCCCAATTATCTTCATGAAA 59.619 34.615 9.88 1.39 0.00 2.69
3096 3286 6.823689 TCTTCTGAAAAAGAGCAAGTGTACTT 59.176 34.615 0.00 0.00 35.91 2.24
3098 3288 6.604735 TCTTCTGAAAAAGAGCAAGTGTAC 57.395 37.500 0.00 0.00 35.91 2.90
3099 3289 7.931407 TGTATCTTCTGAAAAAGAGCAAGTGTA 59.069 33.333 0.00 0.00 38.60 2.90
3100 3290 6.767902 TGTATCTTCTGAAAAAGAGCAAGTGT 59.232 34.615 0.00 0.00 38.60 3.55
3101 3291 7.074502 GTGTATCTTCTGAAAAAGAGCAAGTG 58.925 38.462 0.00 0.00 38.60 3.16
3102 3292 6.205658 GGTGTATCTTCTGAAAAAGAGCAAGT 59.794 38.462 0.00 0.00 38.60 3.16
3103 3293 6.429385 AGGTGTATCTTCTGAAAAAGAGCAAG 59.571 38.462 0.00 0.00 38.60 4.01
3104 3294 6.205464 CAGGTGTATCTTCTGAAAAAGAGCAA 59.795 38.462 0.00 0.00 38.60 3.91
3105 3295 5.702670 CAGGTGTATCTTCTGAAAAAGAGCA 59.297 40.000 0.00 0.00 38.60 4.26
3106 3296 5.934625 TCAGGTGTATCTTCTGAAAAAGAGC 59.065 40.000 0.00 0.00 38.60 4.09
3107 3297 6.931281 TGTCAGGTGTATCTTCTGAAAAAGAG 59.069 38.462 0.00 0.00 38.60 2.85
3108 3298 6.826668 TGTCAGGTGTATCTTCTGAAAAAGA 58.173 36.000 0.00 0.00 38.97 2.52
3109 3299 6.931281 TCTGTCAGGTGTATCTTCTGAAAAAG 59.069 38.462 0.00 0.00 38.97 2.27
3110 3300 6.826668 TCTGTCAGGTGTATCTTCTGAAAAA 58.173 36.000 0.00 0.00 38.97 1.94
3111 3301 6.419484 TCTGTCAGGTGTATCTTCTGAAAA 57.581 37.500 0.00 0.00 38.97 2.29
3112 3302 6.611613 ATCTGTCAGGTGTATCTTCTGAAA 57.388 37.500 0.00 0.00 38.97 2.69
3113 3303 7.718334 TTATCTGTCAGGTGTATCTTCTGAA 57.282 36.000 0.00 0.00 38.97 3.02
3114 3304 7.718334 TTTATCTGTCAGGTGTATCTTCTGA 57.282 36.000 0.00 0.00 35.45 3.27
3115 3305 8.777865 TTTTTATCTGTCAGGTGTATCTTCTG 57.222 34.615 0.00 0.00 0.00 3.02
3139 3329 9.950680 CTAGTTTCTGAACACATAACACATTTT 57.049 29.630 0.00 0.00 38.26 1.82
3140 3330 9.120538 ACTAGTTTCTGAACACATAACACATTT 57.879 29.630 0.00 0.00 38.26 2.32
3141 3331 8.559536 CACTAGTTTCTGAACACATAACACATT 58.440 33.333 0.00 0.00 38.26 2.71
3142 3332 7.931407 TCACTAGTTTCTGAACACATAACACAT 59.069 33.333 0.00 0.00 38.26 3.21
3143 3333 7.269316 TCACTAGTTTCTGAACACATAACACA 58.731 34.615 0.00 0.00 38.26 3.72
3144 3334 7.709269 TCACTAGTTTCTGAACACATAACAC 57.291 36.000 0.00 0.00 38.26 3.32
3145 3335 8.773645 CATTCACTAGTTTCTGAACACATAACA 58.226 33.333 0.00 0.00 38.26 2.41
3146 3336 8.774586 ACATTCACTAGTTTCTGAACACATAAC 58.225 33.333 0.00 0.00 38.26 1.89
3147 3337 8.773645 CACATTCACTAGTTTCTGAACACATAA 58.226 33.333 0.00 0.00 38.26 1.90
3148 3338 7.095229 GCACATTCACTAGTTTCTGAACACATA 60.095 37.037 0.00 0.00 38.26 2.29
3149 3339 6.293626 GCACATTCACTAGTTTCTGAACACAT 60.294 38.462 0.00 0.00 38.26 3.21
3150 3340 5.007626 GCACATTCACTAGTTTCTGAACACA 59.992 40.000 0.00 0.00 38.26 3.72
3151 3341 5.237344 AGCACATTCACTAGTTTCTGAACAC 59.763 40.000 0.00 0.00 38.26 3.32
3152 3342 5.237127 CAGCACATTCACTAGTTTCTGAACA 59.763 40.000 0.00 0.00 38.26 3.18
3153 3343 5.334414 CCAGCACATTCACTAGTTTCTGAAC 60.334 44.000 0.00 0.00 35.97 3.18
3154 3344 4.756642 CCAGCACATTCACTAGTTTCTGAA 59.243 41.667 0.00 0.00 0.00 3.02
3155 3345 4.202357 ACCAGCACATTCACTAGTTTCTGA 60.202 41.667 0.00 0.00 0.00 3.27
3162 3353 2.771089 ACACACCAGCACATTCACTAG 58.229 47.619 0.00 0.00 0.00 2.57
3172 3363 0.106769 ATCACCACAACACACCAGCA 60.107 50.000 0.00 0.00 0.00 4.41
3203 3394 7.333528 TCTCTGAATGTGCAACTTTTTACTT 57.666 32.000 0.00 0.00 38.04 2.24
3208 3399 5.841957 AGTTCTCTGAATGTGCAACTTTT 57.158 34.783 0.00 0.00 38.04 2.27
3238 3430 7.029563 GCGAGAATTAGAAACAAATTGACCAT 58.970 34.615 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.