Multiple sequence alignment - TraesCS7B01G315700

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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 TraesCS7B01G315700 chr7B 100.000 5360 0 0 1 5360 564179808 564185167 0.000000e+00 9899.0
1 TraesCS7B01G315700 chr7B 89.076 119 11 2 5077 5194 564184841 564184958 4.330000e-31 147.0
2 TraesCS7B01G315700 chr7B 89.076 119 11 2 5034 5151 564184884 564185001 4.330000e-31 147.0
3 TraesCS7B01G315700 chr7D 95.014 5174 183 29 35 5195 527725153 527730264 0.000000e+00 8056.0
4 TraesCS7B01G315700 chr7D 94.718 284 14 1 5034 5317 527730276 527730558 1.770000e-119 440.0
5 TraesCS7B01G315700 chr7D 93.827 162 9 1 5034 5195 527730147 527730307 5.360000e-60 243.0
6 TraesCS7B01G315700 chr7D 93.827 162 9 1 5034 5195 527730233 527730393 5.360000e-60 243.0
7 TraesCS7B01G315700 chr7D 92.593 162 11 1 5034 5195 527730190 527730350 1.160000e-56 231.0
8 TraesCS7B01G315700 chr7D 93.277 119 7 1 5077 5195 527730104 527730221 1.980000e-39 174.0
9 TraesCS7B01G315700 chr7D 94.667 75 4 0 5121 5195 527730104 527730178 3.390000e-22 117.0
10 TraesCS7B01G315700 chr7A 96.980 4172 94 17 812 4962 607552530 607556690 0.000000e+00 6977.0
11 TraesCS7B01G315700 chr7A 97.015 201 6 0 5121 5321 607557305 607557505 6.650000e-89 339.0
12 TraesCS7B01G315700 chr7A 95.804 143 6 0 4961 5103 607557232 607557374 1.160000e-56 231.0
13 TraesCS7B01G315700 chr1A 81.507 146 19 7 149 293 274105222 274105360 4.390000e-21 113.0
14 TraesCS7B01G315700 chr1D 80.519 154 22 7 141 293 215061874 215062020 1.580000e-20 111.0
15 TraesCS7B01G315700 chr1D 85.185 81 12 0 2041 2121 18762685 18762765 3.440000e-12 84.2
16 TraesCS7B01G315700 chr6D 86.735 98 13 0 631 728 389871471 389871374 5.680000e-20 110.0
17 TraesCS7B01G315700 chr6B 87.000 100 9 3 629 728 73341539 73341444 5.680000e-20 110.0
18 TraesCS7B01G315700 chr2B 86.735 98 13 0 631 728 476377404 476377307 5.680000e-20 110.0
19 TraesCS7B01G315700 chr2B 84.694 98 12 3 631 728 597886768 597886862 1.590000e-15 95.3
20 TraesCS7B01G315700 chrUn 88.636 88 10 0 631 718 23391740 23391653 2.040000e-19 108.0
21 TraesCS7B01G315700 chrUn 88.636 88 10 0 631 718 267105747 267105660 2.040000e-19 108.0
22 TraesCS7B01G315700 chrUn 88.636 88 10 0 631 718 267123340 267123253 2.040000e-19 108.0
23 TraesCS7B01G315700 chrUn 85.185 81 12 0 2041 2121 162951 163031 3.440000e-12 84.2
24 TraesCS7B01G315700 chr5D 85.714 98 13 1 631 728 73469202 73469298 9.500000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G315700 chr7B 564179808 564185167 5359 False 3397.666667 9899 92.717333 1 5360 3 chr7B.!!$F1 5359
1 TraesCS7B01G315700 chr7D 527725153 527730558 5405 False 1357.714286 8056 93.989000 35 5317 7 chr7D.!!$F1 5282
2 TraesCS7B01G315700 chr7A 607552530 607557505 4975 False 2515.666667 6977 96.599667 812 5321 3 chr7A.!!$F1 4509

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
643 645 0.038526 CGGCCTTTGTAGTCGTCACT 60.039 55.000 0.00 0.00 36.55 3.41 F
1215 1225 0.109723 TGTAGTGGTCTGTTTGGGCC 59.890 55.000 0.00 0.00 0.00 5.80 F
1262 1272 0.474854 TCCAACTCTGGCCCAAGGTA 60.475 55.000 0.00 0.00 43.17 3.08 F
2094 2113 0.672401 TCGTCGATGGGTTTTCAGCC 60.672 55.000 4.48 0.00 41.49 4.85 F
2593 2613 2.376518 TCCTCTTGCCTGTTTCTCCAAT 59.623 45.455 0.00 0.00 0.00 3.16 F
3608 3639 1.376942 CCAAGCACAGGAGCTCTGG 60.377 63.158 14.64 7.62 45.89 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2350 1.486726 GCCATAGCCTCTGGTGTTACT 59.513 52.381 0.00 0.0 36.10 2.24 R
2965 2987 1.134907 ACGAACGAACTGACACTTGGT 60.135 47.619 0.14 0.0 0.00 3.67 R
3256 3279 2.037772 GTGCTCCATCCCATCGATAAGT 59.962 50.000 0.00 0.0 0.00 2.24 R
3262 3285 0.949397 CAATGTGCTCCATCCCATCG 59.051 55.000 0.00 0.0 31.75 3.84 R
3785 3816 1.228862 GCCCCCACAATCACACCTT 60.229 57.895 0.00 0.0 0.00 3.50 R
5328 6074 0.033920 TGAGCGTTCACACTCAGCAT 59.966 50.000 0.00 0.0 37.99 3.79 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
27 28 5.666969 CAAAGTGTTGGTCAATCTAACGA 57.333 39.130 0.00 0.00 39.81 3.85
28 29 5.440685 CAAAGTGTTGGTCAATCTAACGAC 58.559 41.667 0.00 0.00 39.81 4.34
29 30 3.314553 AGTGTTGGTCAATCTAACGACG 58.685 45.455 0.00 0.00 39.81 5.12
30 31 3.054878 GTGTTGGTCAATCTAACGACGT 58.945 45.455 0.00 0.00 39.81 4.34
31 32 3.492011 GTGTTGGTCAATCTAACGACGTT 59.508 43.478 18.47 18.47 39.81 3.99
32 33 3.491639 TGTTGGTCAATCTAACGACGTTG 59.508 43.478 23.00 12.69 39.81 4.10
33 34 3.646611 TGGTCAATCTAACGACGTTGA 57.353 42.857 23.00 17.16 32.74 3.18
96 98 4.806342 TGAATGCTCATCATCAACATCG 57.194 40.909 0.00 0.00 33.40 3.84
98 100 4.271776 TGAATGCTCATCATCAACATCGTC 59.728 41.667 0.00 0.00 33.40 4.20
102 104 3.490155 GCTCATCATCAACATCGTCTCAG 59.510 47.826 0.00 0.00 0.00 3.35
117 119 3.059884 GTCTCAGCATCTTCGTTGTTCA 58.940 45.455 0.00 0.00 0.00 3.18
137 139 8.545229 TGTTCAAAACTGACAAATCAACAAAT 57.455 26.923 0.00 0.00 33.30 2.32
139 141 9.824534 GTTCAAAACTGACAAATCAACAAATTT 57.175 25.926 0.00 0.00 33.30 1.82
172 174 2.550830 TCACCAAGCTCCTTGTTCTC 57.449 50.000 4.48 0.00 39.58 2.87
189 191 6.456584 CTTGTTCTCAAAGTCATCATCCGATG 60.457 42.308 1.55 1.55 40.54 3.84
238 240 7.285401 TGAGCAAAAGAATCTAGAAAAACCACT 59.715 33.333 0.00 0.00 0.00 4.00
239 241 7.652727 AGCAAAAGAATCTAGAAAAACCACTC 58.347 34.615 0.00 0.00 0.00 3.51
280 282 2.029307 GAGGGCGAGGTGTATGTCCC 62.029 65.000 0.00 0.00 0.00 4.46
284 286 1.664321 GCGAGGTGTATGTCCCGAGT 61.664 60.000 0.00 0.00 0.00 4.18
285 287 1.671979 CGAGGTGTATGTCCCGAGTA 58.328 55.000 0.00 0.00 0.00 2.59
294 296 3.878237 ATGTCCCGAGTAGTAGGATGA 57.122 47.619 0.00 0.00 30.92 2.92
296 298 4.180377 TGTCCCGAGTAGTAGGATGAAT 57.820 45.455 0.00 0.00 30.92 2.57
299 301 2.488545 CCCGAGTAGTAGGATGAATCGG 59.511 54.545 3.65 3.65 45.88 4.18
308 310 1.572085 GGATGAATCGGAGCGGCATG 61.572 60.000 1.45 0.00 0.00 4.06
360 362 2.933834 AGTCGGGAGGGGTTTGGG 60.934 66.667 0.00 0.00 0.00 4.12
362 364 4.603097 TCGGGAGGGGTTTGGGGT 62.603 66.667 0.00 0.00 0.00 4.95
365 367 4.735358 GGAGGGGTTTGGGGTCGC 62.735 72.222 0.00 0.00 0.00 5.19
366 368 4.735358 GAGGGGTTTGGGGTCGCC 62.735 72.222 0.00 0.00 37.01 5.54
370 372 4.629523 GGTTTGGGGTCGCCGACA 62.630 66.667 20.08 0.00 33.68 4.35
371 373 2.359478 GTTTGGGGTCGCCGACAT 60.359 61.111 20.08 0.00 33.68 3.06
373 375 2.884980 TTTGGGGTCGCCGACATCA 61.885 57.895 20.08 13.12 33.68 3.07
395 397 2.201732 CGATGTGGGTTATGGAAGACG 58.798 52.381 0.00 0.00 0.00 4.18
421 423 1.152567 CAGGAAAAGGGGTGGCACA 60.153 57.895 20.82 0.00 0.00 4.57
426 428 2.304901 AAAAGGGGTGGCACAAACGC 62.305 55.000 20.82 10.47 44.16 4.84
433 435 1.599518 TGGCACAAACGCGGAAGAT 60.600 52.632 12.47 0.00 31.92 2.40
442 444 2.209838 ACGCGGAAGATATGTGACAG 57.790 50.000 12.47 0.00 0.00 3.51
454 456 0.325933 TGTGACAGGAAGATGGCAGG 59.674 55.000 0.00 0.00 39.42 4.85
466 468 2.849646 GGCAGGTAGGGCTAGGGG 60.850 72.222 0.00 0.00 0.00 4.79
487 489 3.678548 GGTGTGGACGATTTAGAGACAAC 59.321 47.826 0.00 0.00 0.00 3.32
500 502 3.348119 AGAGACAACTGAGATGCGTCTA 58.652 45.455 8.83 0.00 37.08 2.59
502 504 3.085533 AGACAACTGAGATGCGTCTAGT 58.914 45.455 8.83 9.89 35.24 2.57
513 515 3.404224 TGCGTCTAGTCTATCGGATCT 57.596 47.619 0.00 0.00 0.00 2.75
519 521 5.163903 CGTCTAGTCTATCGGATCTGACATG 60.164 48.000 6.33 13.56 32.41 3.21
539 541 6.471146 ACATGGAGTCCTCATAATTATCTGC 58.529 40.000 11.33 0.00 0.00 4.26
558 560 2.685897 TGCCGTACATAATTTGAAGGGC 59.314 45.455 0.00 0.00 37.56 5.19
585 587 4.214971 AGACATGAACATTTGTGCTGACTC 59.785 41.667 0.00 0.00 0.00 3.36
595 597 4.672587 TTGTGCTGACTCTAAAGTGTCT 57.327 40.909 12.05 0.00 38.82 3.41
596 598 3.982475 TGTGCTGACTCTAAAGTGTCTG 58.018 45.455 12.05 12.11 38.82 3.51
600 602 5.119898 GTGCTGACTCTAAAGTGTCTGATTG 59.880 44.000 17.77 5.13 38.74 2.67
605 607 6.875726 TGACTCTAAAGTGTCTGATTGAATGG 59.124 38.462 12.05 0.00 38.82 3.16
617 619 9.513906 TGTCTGATTGAATGGTGTTTTATTAGA 57.486 29.630 0.00 0.00 0.00 2.10
628 630 6.316890 TGGTGTTTTATTAGATCTAAACGGCC 59.683 38.462 18.79 17.62 34.16 6.13
642 644 0.319297 ACGGCCTTTGTAGTCGTCAC 60.319 55.000 0.00 0.00 0.00 3.67
643 645 0.038526 CGGCCTTTGTAGTCGTCACT 60.039 55.000 0.00 0.00 36.55 3.41
644 646 1.200716 CGGCCTTTGTAGTCGTCACTA 59.799 52.381 0.00 0.00 33.62 2.74
645 647 2.731341 CGGCCTTTGTAGTCGTCACTAG 60.731 54.545 0.00 0.00 35.67 2.57
646 648 2.490903 GGCCTTTGTAGTCGTCACTAGA 59.509 50.000 0.00 0.00 35.67 2.43
665 667 4.862902 AGATGGTCTACGAATCTGGATG 57.137 45.455 0.00 0.00 29.52 3.51
668 670 6.013379 AGATGGTCTACGAATCTGGATGTAT 58.987 40.000 0.00 0.00 29.52 2.29
698 700 3.305398 TTTCCGTTGTTTGTTGCACTT 57.695 38.095 0.00 0.00 0.00 3.16
700 702 2.869897 TCCGTTGTTTGTTGCACTTTC 58.130 42.857 0.00 0.00 0.00 2.62
711 713 5.771153 TGTTGCACTTTCATGATTGAAGA 57.229 34.783 11.68 0.00 42.60 2.87
713 715 7.451501 TGTTGCACTTTCATGATTGAAGATA 57.548 32.000 11.68 0.00 42.60 1.98
777 780 1.595929 GTTGGCCGGACGTTTGAGA 60.596 57.895 5.05 0.00 0.00 3.27
782 785 1.606224 GGCCGGACGTTTGAGAAAGTA 60.606 52.381 5.05 0.00 0.00 2.24
783 786 1.458445 GCCGGACGTTTGAGAAAGTAC 59.542 52.381 5.05 0.00 0.00 2.73
785 788 1.717645 CGGACGTTTGAGAAAGTACGG 59.282 52.381 0.00 0.00 44.47 4.02
796 799 2.827921 AGAAAGTACGGTCCGGTTGTAT 59.172 45.455 17.28 0.00 0.00 2.29
798 801 4.096984 AGAAAGTACGGTCCGGTTGTATAG 59.903 45.833 17.28 0.00 0.00 1.31
799 802 3.281727 AGTACGGTCCGGTTGTATAGA 57.718 47.619 17.28 0.00 0.00 1.98
800 803 3.825328 AGTACGGTCCGGTTGTATAGAT 58.175 45.455 17.28 0.00 0.00 1.98
801 804 3.567164 AGTACGGTCCGGTTGTATAGATG 59.433 47.826 17.28 0.00 0.00 2.90
804 807 2.555325 CGGTCCGGTTGTATAGATGCTA 59.445 50.000 2.34 0.00 0.00 3.49
805 808 3.192844 CGGTCCGGTTGTATAGATGCTAT 59.807 47.826 2.34 0.00 0.00 2.97
806 809 4.495422 GGTCCGGTTGTATAGATGCTATG 58.505 47.826 0.00 0.00 0.00 2.23
807 810 4.219944 GGTCCGGTTGTATAGATGCTATGA 59.780 45.833 0.00 0.00 0.00 2.15
808 811 5.403246 GTCCGGTTGTATAGATGCTATGAG 58.597 45.833 0.00 0.00 0.00 2.90
817 820 1.693062 AGATGCTATGAGAGGCCACAG 59.307 52.381 5.01 0.00 0.00 3.66
885 888 2.898612 GCTATCCTACCTACCACCTTCC 59.101 54.545 0.00 0.00 0.00 3.46
968 971 1.118838 CCTCTCCTCGCTTTCCATCT 58.881 55.000 0.00 0.00 0.00 2.90
976 979 0.177141 CGCTTTCCATCTTACCCCGA 59.823 55.000 0.00 0.00 0.00 5.14
1119 1126 4.610605 TTACAGTCGAAATCACTTGGGA 57.389 40.909 0.00 0.00 0.00 4.37
1151 1158 4.861389 TCGACAAGTAGAAGAGATCGAC 57.139 45.455 0.00 0.00 32.61 4.20
1197 1204 2.290896 TGAGCACCAAACCCTAGGATTG 60.291 50.000 11.48 14.60 35.63 2.67
1215 1225 0.109723 TGTAGTGGTCTGTTTGGGCC 59.890 55.000 0.00 0.00 0.00 5.80
1236 1246 0.626916 AGCTTCGGACTAGAGGAGGT 59.373 55.000 0.00 0.00 0.00 3.85
1248 1258 2.108970 AGAGGAGGTTCGGTATCCAAC 58.891 52.381 0.00 0.00 35.45 3.77
1250 1260 2.101082 GAGGAGGTTCGGTATCCAACTC 59.899 54.545 0.00 0.00 35.45 3.01
1262 1272 0.474854 TCCAACTCTGGCCCAAGGTA 60.475 55.000 0.00 0.00 43.17 3.08
1272 1282 4.479056 TCTGGCCCAAGGTATATTTGGTTA 59.521 41.667 0.00 3.99 42.85 2.85
1276 1286 5.070685 GCCCAAGGTATATTTGGTTAGAGG 58.929 45.833 14.40 3.69 42.85 3.69
1462 1477 5.643379 TTCATATGGAAGAAACAGTTGCC 57.357 39.130 2.13 0.00 0.00 4.52
1490 1505 6.757897 TTATGAGGGATAACTGCACAAAAG 57.242 37.500 0.00 0.00 0.00 2.27
1520 1535 0.837691 AGGGCATGGAGTCACTCACA 60.838 55.000 7.24 2.69 31.08 3.58
1690 1709 5.123227 GCTACAACCTACAAGGCATTATGA 58.877 41.667 0.00 0.00 39.63 2.15
1937 1956 6.375736 TCGGTTCACTTGGCAAATAATAATCA 59.624 34.615 0.00 0.00 0.00 2.57
2094 2113 0.672401 TCGTCGATGGGTTTTCAGCC 60.672 55.000 4.48 0.00 41.49 4.85
2330 2350 4.436113 TCTTATAATGGCAGCATCCACA 57.564 40.909 0.00 0.00 39.25 4.17
2593 2613 2.376518 TCCTCTTGCCTGTTTCTCCAAT 59.623 45.455 0.00 0.00 0.00 3.16
3083 3105 8.492673 TCGAATATGAAAGCTACAGTTTGATT 57.507 30.769 0.00 0.00 0.00 2.57
3184 3207 7.004086 ACAGATATAGGAGAAAGAGAGACAGG 58.996 42.308 0.00 0.00 0.00 4.00
3256 3279 5.545063 TTGAATCCTATTGCTACCGATCA 57.455 39.130 0.00 0.00 0.00 2.92
3262 3285 6.268825 TCCTATTGCTACCGATCACTTATC 57.731 41.667 0.00 0.00 0.00 1.75
3303 3326 3.633525 GCAATGATCAAGGTAAGCATCCA 59.366 43.478 0.00 0.00 0.00 3.41
3478 3505 3.926058 AACCTCAACCAGTTGTACAGT 57.074 42.857 10.17 2.06 41.16 3.55
3523 3550 2.756760 AGCAGCAATGTATTGTGGGAAG 59.243 45.455 6.48 0.00 39.88 3.46
3608 3639 1.376942 CCAAGCACAGGAGCTCTGG 60.377 63.158 14.64 7.62 45.89 3.86
3785 3816 4.532126 ACTGGAGATATATTTGGATCGGCA 59.468 41.667 0.00 0.00 0.00 5.69
4448 4479 7.953005 TTCTCCAATTTTGATTATACCTGCA 57.047 32.000 0.00 0.00 0.00 4.41
4633 4664 0.884704 TGTCCTGCGCCTCTTTGAAC 60.885 55.000 4.18 0.00 0.00 3.18
4642 4673 3.733684 GCGCCTCTTTGAACTGTTTTTGA 60.734 43.478 0.00 0.00 0.00 2.69
4679 4710 6.006449 ACTTAAATGAGTTTGTGAGCCAGAT 58.994 36.000 0.00 0.00 0.00 2.90
4686 4717 3.953612 AGTTTGTGAGCCAGATTGTTGAA 59.046 39.130 0.00 0.00 0.00 2.69
4773 4804 3.672808 ACTTGAGCTCAGTTTCATCTGG 58.327 45.455 17.43 1.57 36.25 3.86
4820 4851 0.808755 CGGCACCACCTGTTAAATCC 59.191 55.000 0.00 0.00 35.61 3.01
4826 4857 1.408266 CCACCTGTTAAATCCCGAGGG 60.408 57.143 0.65 0.65 0.00 4.30
4931 4963 7.148440 GCAATAGAGATGAGCAATCCACTATTC 60.148 40.741 16.89 12.28 40.02 1.75
4997 5572 4.460263 ACTGACACTGCTGGTTTTTATCA 58.540 39.130 0.00 0.00 0.00 2.15
5044 5619 2.445682 TTTGGCAGTGTAAAGTGGGT 57.554 45.000 0.00 0.00 0.00 4.51
5151 5854 4.178540 GGAATTCCACAGTTCATGCAATG 58.821 43.478 20.04 0.00 40.16 2.82
5317 6063 6.338146 TCTTCGGAGTATCAACCATAAACTG 58.662 40.000 0.00 0.00 36.25 3.16
5327 6073 0.168788 CCATAAACTGGTGCTGCACG 59.831 55.000 24.86 15.32 40.49 5.34
5328 6074 1.155889 CATAAACTGGTGCTGCACGA 58.844 50.000 24.86 20.75 34.83 4.35
5329 6075 1.739466 CATAAACTGGTGCTGCACGAT 59.261 47.619 24.86 11.03 34.83 3.73
5330 6076 1.155889 TAAACTGGTGCTGCACGATG 58.844 50.000 24.86 18.64 34.83 3.84
5331 6077 2.133742 AAACTGGTGCTGCACGATGC 62.134 55.000 24.86 12.57 45.29 3.91
5332 6078 2.745100 CTGGTGCTGCACGATGCT 60.745 61.111 24.86 0.00 45.31 3.79
5333 6079 3.035576 CTGGTGCTGCACGATGCTG 62.036 63.158 24.86 11.94 45.31 4.41
5334 6080 2.743538 GGTGCTGCACGATGCTGA 60.744 61.111 24.86 0.00 45.31 4.26
5335 6081 2.747822 GGTGCTGCACGATGCTGAG 61.748 63.158 24.86 6.89 45.31 3.35
5336 6082 2.031516 GTGCTGCACGATGCTGAGT 61.032 57.895 17.93 0.00 45.31 3.41
5337 6083 2.030958 TGCTGCACGATGCTGAGTG 61.031 57.895 16.67 2.46 45.31 3.51
5338 6084 2.031516 GCTGCACGATGCTGAGTGT 61.032 57.895 16.67 0.00 45.31 3.55
5339 6085 1.785951 CTGCACGATGCTGAGTGTG 59.214 57.895 10.54 0.00 45.31 3.82
5340 6086 0.668401 CTGCACGATGCTGAGTGTGA 60.668 55.000 10.54 0.00 45.31 3.58
5341 6087 0.249826 TGCACGATGCTGAGTGTGAA 60.250 50.000 10.54 0.00 45.31 3.18
5342 6088 0.164647 GCACGATGCTGAGTGTGAAC 59.835 55.000 0.00 0.00 40.96 3.18
5343 6089 0.436150 CACGATGCTGAGTGTGAACG 59.564 55.000 0.00 0.00 34.29 3.95
5344 6090 1.284982 ACGATGCTGAGTGTGAACGC 61.285 55.000 0.00 0.00 0.00 4.84
5345 6091 1.010935 CGATGCTGAGTGTGAACGCT 61.011 55.000 0.00 0.00 39.79 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.440685 GTCGTTAGATTGACCAACACTTTG 58.559 41.667 0.00 0.00 0.00 2.77
6 7 4.210537 CGTCGTTAGATTGACCAACACTTT 59.789 41.667 0.00 0.00 0.00 2.66
7 8 3.739300 CGTCGTTAGATTGACCAACACTT 59.261 43.478 0.00 0.00 0.00 3.16
8 9 3.243636 ACGTCGTTAGATTGACCAACACT 60.244 43.478 0.00 0.00 0.00 3.55
9 10 3.054878 ACGTCGTTAGATTGACCAACAC 58.945 45.455 0.00 0.00 0.00 3.32
10 11 3.374220 ACGTCGTTAGATTGACCAACA 57.626 42.857 0.00 0.00 0.00 3.33
11 12 3.737266 TCAACGTCGTTAGATTGACCAAC 59.263 43.478 10.86 0.00 0.00 3.77
12 13 3.737266 GTCAACGTCGTTAGATTGACCAA 59.263 43.478 10.86 0.00 43.28 3.67
13 14 3.311106 GTCAACGTCGTTAGATTGACCA 58.689 45.455 10.86 0.00 43.28 4.02
14 15 3.967080 GTCAACGTCGTTAGATTGACC 57.033 47.619 10.86 0.00 43.28 4.02
16 17 6.207928 TGTTTAGTCAACGTCGTTAGATTGA 58.792 36.000 10.86 1.07 38.36 2.57
17 18 6.442487 TGTTTAGTCAACGTCGTTAGATTG 57.558 37.500 10.86 0.00 38.36 2.67
18 19 6.400727 GCATGTTTAGTCAACGTCGTTAGATT 60.401 38.462 10.86 9.86 38.36 2.40
19 20 5.061808 GCATGTTTAGTCAACGTCGTTAGAT 59.938 40.000 10.86 2.02 38.36 1.98
20 21 4.383649 GCATGTTTAGTCAACGTCGTTAGA 59.616 41.667 10.86 8.09 38.36 2.10
21 22 4.384846 AGCATGTTTAGTCAACGTCGTTAG 59.615 41.667 10.86 5.82 38.36 2.34
22 23 4.300803 AGCATGTTTAGTCAACGTCGTTA 58.699 39.130 10.86 0.00 38.36 3.18
23 24 3.128349 AGCATGTTTAGTCAACGTCGTT 58.872 40.909 4.40 4.40 38.36 3.85
24 25 2.729882 GAGCATGTTTAGTCAACGTCGT 59.270 45.455 0.00 0.00 38.36 4.34
25 26 2.092211 GGAGCATGTTTAGTCAACGTCG 59.908 50.000 0.00 0.00 38.36 5.12
26 27 3.064207 TGGAGCATGTTTAGTCAACGTC 58.936 45.455 0.00 0.00 38.36 4.34
27 28 2.806244 GTGGAGCATGTTTAGTCAACGT 59.194 45.455 0.00 0.00 38.36 3.99
28 29 2.159627 GGTGGAGCATGTTTAGTCAACG 59.840 50.000 0.00 0.00 38.36 4.10
29 30 3.412386 AGGTGGAGCATGTTTAGTCAAC 58.588 45.455 0.00 0.00 35.71 3.18
30 31 3.559171 GGAGGTGGAGCATGTTTAGTCAA 60.559 47.826 0.00 0.00 0.00 3.18
31 32 2.027192 GGAGGTGGAGCATGTTTAGTCA 60.027 50.000 0.00 0.00 0.00 3.41
32 33 2.237392 AGGAGGTGGAGCATGTTTAGTC 59.763 50.000 0.00 0.00 0.00 2.59
33 34 2.269940 AGGAGGTGGAGCATGTTTAGT 58.730 47.619 0.00 0.00 0.00 2.24
96 98 3.059884 TGAACAACGAAGATGCTGAGAC 58.940 45.455 0.00 0.00 31.73 3.36
98 100 4.472691 TTTGAACAACGAAGATGCTGAG 57.527 40.909 0.00 0.00 31.73 3.35
102 104 4.437820 GTCAGTTTTGAACAACGAAGATGC 59.562 41.667 0.00 0.00 34.49 3.91
139 141 7.615365 AGGAGCTTGGTGAATTCATATACAAAA 59.385 33.333 12.12 0.00 0.00 2.44
189 191 9.884465 CTCATTTATAGGAAAAACGATGGATTC 57.116 33.333 0.00 0.00 0.00 2.52
197 199 8.964420 TCTTTTGCTCATTTATAGGAAAAACG 57.036 30.769 0.00 0.00 41.67 3.60
253 255 0.179100 CACCTCGCCCTCTATGTGTG 60.179 60.000 0.00 0.00 0.00 3.82
258 260 2.240279 GACATACACCTCGCCCTCTAT 58.760 52.381 0.00 0.00 0.00 1.98
280 282 3.120130 GCTCCGATTCATCCTACTACTCG 60.120 52.174 0.00 0.00 0.00 4.18
284 286 2.160205 CCGCTCCGATTCATCCTACTA 58.840 52.381 0.00 0.00 0.00 1.82
285 287 0.962489 CCGCTCCGATTCATCCTACT 59.038 55.000 0.00 0.00 0.00 2.57
294 296 3.814615 ATCGCATGCCGCTCCGATT 62.815 57.895 13.15 0.00 37.13 3.34
329 331 2.361737 GACTGCCCTTCTTGCCCC 60.362 66.667 0.00 0.00 0.00 5.80
334 336 2.294078 CCTCCCGACTGCCCTTCTT 61.294 63.158 0.00 0.00 0.00 2.52
343 345 2.933834 CCCAAACCCCTCCCGACT 60.934 66.667 0.00 0.00 0.00 4.18
370 372 1.768275 TCCATAACCCACATCGCTGAT 59.232 47.619 0.00 0.00 0.00 2.90
371 373 1.199615 TCCATAACCCACATCGCTGA 58.800 50.000 0.00 0.00 0.00 4.26
373 375 1.837439 TCTTCCATAACCCACATCGCT 59.163 47.619 0.00 0.00 0.00 4.93
395 397 1.377333 CCCTTTTCCTGGCTCCGTC 60.377 63.158 0.00 0.00 0.00 4.79
418 420 2.670905 TCACATATCTTCCGCGTTTGTG 59.329 45.455 4.92 8.07 35.49 3.33
421 423 2.930040 CTGTCACATATCTTCCGCGTTT 59.070 45.455 4.92 0.00 0.00 3.60
426 428 4.655762 TCTTCCTGTCACATATCTTCCG 57.344 45.455 0.00 0.00 0.00 4.30
433 435 2.171237 CCTGCCATCTTCCTGTCACATA 59.829 50.000 0.00 0.00 0.00 2.29
442 444 1.149401 GCCCTACCTGCCATCTTCC 59.851 63.158 0.00 0.00 0.00 3.46
454 456 1.002533 TCCACACCCCTAGCCCTAC 59.997 63.158 0.00 0.00 0.00 3.18
466 468 4.386049 CAGTTGTCTCTAAATCGTCCACAC 59.614 45.833 0.00 0.00 0.00 3.82
487 489 3.124466 CCGATAGACTAGACGCATCTCAG 59.876 52.174 0.00 0.00 35.33 3.35
500 502 4.078537 CTCCATGTCAGATCCGATAGACT 58.921 47.826 12.29 0.00 39.76 3.24
502 504 4.075682 GACTCCATGTCAGATCCGATAGA 58.924 47.826 0.00 0.00 44.73 1.98
519 521 4.021016 ACGGCAGATAATTATGAGGACTCC 60.021 45.833 1.78 0.00 0.00 3.85
539 541 2.940410 ACGCCCTTCAAATTATGTACGG 59.060 45.455 0.00 0.00 0.00 4.02
558 560 3.058708 AGCACAAATGTTCATGTCTGACG 60.059 43.478 2.98 0.00 0.00 4.35
585 587 6.808008 ACACCATTCAATCAGACACTTTAG 57.192 37.500 0.00 0.00 0.00 1.85
600 602 9.931210 CCGTTTAGATCTAATAAAACACCATTC 57.069 33.333 15.82 0.00 32.61 2.67
605 607 7.549615 AGGCCGTTTAGATCTAATAAAACAC 57.450 36.000 15.82 8.96 32.61 3.32
617 619 3.056322 ACGACTACAAAGGCCGTTTAGAT 60.056 43.478 19.44 9.54 34.07 1.98
628 630 5.124138 AGACCATCTAGTGACGACTACAAAG 59.876 44.000 0.00 0.00 33.21 2.77
642 644 5.475220 ACATCCAGATTCGTAGACCATCTAG 59.525 44.000 0.00 0.00 32.36 2.43
643 645 5.386060 ACATCCAGATTCGTAGACCATCTA 58.614 41.667 0.00 0.00 32.36 1.98
644 646 4.219115 ACATCCAGATTCGTAGACCATCT 58.781 43.478 0.00 0.00 34.75 2.90
645 647 4.592485 ACATCCAGATTCGTAGACCATC 57.408 45.455 0.00 0.00 34.32 3.51
646 648 6.672266 AATACATCCAGATTCGTAGACCAT 57.328 37.500 0.00 0.00 34.32 3.55
682 684 3.856521 TCATGAAAGTGCAACAAACAACG 59.143 39.130 0.00 0.00 41.43 4.10
683 685 5.971895 ATCATGAAAGTGCAACAAACAAC 57.028 34.783 0.00 0.00 41.43 3.32
689 691 5.771153 TCTTCAATCATGAAAGTGCAACA 57.229 34.783 0.00 0.00 44.64 3.33
732 734 6.614160 CCCGAACACCGTTTAGATTATTTTT 58.386 36.000 0.00 0.00 36.31 1.94
733 735 5.392272 GCCCGAACACCGTTTAGATTATTTT 60.392 40.000 0.00 0.00 36.31 1.82
737 739 2.234414 AGCCCGAACACCGTTTAGATTA 59.766 45.455 0.00 0.00 36.31 1.75
740 742 0.320073 CAGCCCGAACACCGTTTAGA 60.320 55.000 0.00 0.00 36.31 2.10
741 743 0.601841 ACAGCCCGAACACCGTTTAG 60.602 55.000 0.00 0.00 36.31 1.85
742 744 0.179051 AACAGCCCGAACACCGTTTA 60.179 50.000 0.00 0.00 36.31 2.01
743 745 1.452470 AACAGCCCGAACACCGTTT 60.452 52.632 0.00 0.00 36.31 3.60
744 746 2.184167 CAACAGCCCGAACACCGTT 61.184 57.895 0.00 0.00 36.31 4.44
745 747 2.590575 CAACAGCCCGAACACCGT 60.591 61.111 0.00 0.00 36.31 4.83
746 748 3.353836 CCAACAGCCCGAACACCG 61.354 66.667 0.00 0.00 38.18 4.94
747 749 3.670377 GCCAACAGCCCGAACACC 61.670 66.667 0.00 0.00 34.35 4.16
777 780 4.016444 TCTATACAACCGGACCGTACTTT 58.984 43.478 9.46 0.00 0.00 2.66
782 785 1.068127 GCATCTATACAACCGGACCGT 59.932 52.381 9.46 4.17 0.00 4.83
783 786 1.340248 AGCATCTATACAACCGGACCG 59.660 52.381 9.46 6.99 0.00 4.79
785 788 5.183331 TCTCATAGCATCTATACAACCGGAC 59.817 44.000 9.46 0.00 0.00 4.79
796 799 2.896044 CTGTGGCCTCTCATAGCATCTA 59.104 50.000 3.32 0.00 0.00 1.98
798 801 1.877258 GCTGTGGCCTCTCATAGCATC 60.877 57.143 3.32 0.00 46.56 3.91
799 802 0.108207 GCTGTGGCCTCTCATAGCAT 59.892 55.000 3.32 0.00 46.56 3.79
800 803 1.524002 GCTGTGGCCTCTCATAGCA 59.476 57.895 3.32 0.00 46.56 3.49
801 804 4.453093 GCTGTGGCCTCTCATAGC 57.547 61.111 3.32 1.16 42.77 2.97
804 807 1.615384 GGAAAAGCTGTGGCCTCTCAT 60.615 52.381 3.32 0.00 39.73 2.90
805 808 0.250901 GGAAAAGCTGTGGCCTCTCA 60.251 55.000 3.32 0.00 39.73 3.27
806 809 0.962855 GGGAAAAGCTGTGGCCTCTC 60.963 60.000 3.32 0.00 39.73 3.20
807 810 1.075659 GGGAAAAGCTGTGGCCTCT 59.924 57.895 3.32 0.00 39.73 3.69
808 811 1.979155 GGGGAAAAGCTGTGGCCTC 60.979 63.158 3.32 0.00 39.73 4.70
1119 1126 7.981142 TCTTCTACTTGTCGAACAACATTTTT 58.019 30.769 0.00 0.00 33.96 1.94
1197 1204 0.109723 TGGCCCAAACAGACCACTAC 59.890 55.000 0.00 0.00 0.00 2.73
1215 1225 1.407258 CCTCCTCTAGTCCGAAGCTTG 59.593 57.143 2.10 0.00 0.00 4.01
1248 1258 3.117512 ACCAAATATACCTTGGGCCAGAG 60.118 47.826 6.23 7.52 46.48 3.35
1250 1260 3.312736 ACCAAATATACCTTGGGCCAG 57.687 47.619 6.23 0.00 46.48 4.85
1262 1272 9.911788 CATGGCTATATTCCTCTAACCAAATAT 57.088 33.333 0.00 0.00 0.00 1.28
1272 1282 7.805083 AACTACATCATGGCTATATTCCTCT 57.195 36.000 0.00 0.00 0.00 3.69
1462 1477 3.139077 GCAGTTATCCCTCATAAACCGG 58.861 50.000 0.00 0.00 0.00 5.28
1490 1505 2.360165 CTCCATGCCCTTTGTATCTTGC 59.640 50.000 0.00 0.00 0.00 4.01
1520 1535 5.643777 ACGCACAAAGCTAATAATGAGTTCT 59.356 36.000 0.00 0.00 42.61 3.01
1690 1709 5.938125 GGTAATCTTGTGTCCTGTTGTGTAT 59.062 40.000 0.00 0.00 0.00 2.29
1890 1909 4.009370 ACTGGTTCTCCTTAAGCTGTTC 57.991 45.455 0.00 0.00 36.13 3.18
2094 2113 5.836347 TCTAGGTCAAGTTCATCATCATCG 58.164 41.667 0.00 0.00 0.00 3.84
2330 2350 1.486726 GCCATAGCCTCTGGTGTTACT 59.513 52.381 0.00 0.00 36.10 2.24
2396 2416 5.087323 TGTAGTCTTTCCAGGTCATCTTCT 58.913 41.667 0.00 0.00 0.00 2.85
2550 2570 7.582719 AGGAGAAAGTAAAATATGCCCATACA 58.417 34.615 0.00 0.00 0.00 2.29
2551 2571 7.939588 AGAGGAGAAAGTAAAATATGCCCATAC 59.060 37.037 0.00 0.00 0.00 2.39
2668 2690 1.229428 TGCAAGTGCTAGAACTGTGC 58.771 50.000 21.76 21.76 42.66 4.57
2921 2943 5.645067 CCTAATCAAGTCTGCAATTGAGACA 59.355 40.000 26.06 14.60 42.07 3.41
2965 2987 1.134907 ACGAACGAACTGACACTTGGT 60.135 47.619 0.14 0.00 0.00 3.67
3184 3207 2.475487 GACACAAAGACGTTCTACCAGC 59.525 50.000 0.00 0.00 0.00 4.85
3256 3279 2.037772 GTGCTCCATCCCATCGATAAGT 59.962 50.000 0.00 0.00 0.00 2.24
3262 3285 0.949397 CAATGTGCTCCATCCCATCG 59.051 55.000 0.00 0.00 31.75 3.84
3303 3326 6.708054 GCAAGTGACTACCTATATTTGCTCAT 59.292 38.462 0.00 0.00 37.34 2.90
3478 3505 4.901250 TCACCATGATCTTGCAGTATAGGA 59.099 41.667 3.07 0.00 0.00 2.94
3523 3550 9.305925 CAGCATTCATTATTTAAGAAGGTTTCC 57.694 33.333 0.00 0.00 0.00 3.13
3608 3639 7.496263 GGGGAATTCTACTTCTACTGTGAAATC 59.504 40.741 5.23 0.00 0.00 2.17
3785 3816 1.228862 GCCCCCACAATCACACCTT 60.229 57.895 0.00 0.00 0.00 3.50
4022 4053 6.313905 CAGGAGTTGTAATACAAGCGAATTCT 59.686 38.462 6.03 0.00 39.00 2.40
4524 4555 1.525175 TACAAACCAAGGTGGAGGGT 58.475 50.000 0.18 0.00 40.96 4.34
4633 4664 6.795399 AGTGATACACTTTGGTCAAAAACAG 58.205 36.000 0.00 0.00 42.59 3.16
4679 4710 7.560368 ACCAATTCAAATTACCAGTTCAACAA 58.440 30.769 0.00 0.00 0.00 2.83
4686 4717 9.541143 CAACTTTAACCAATTCAAATTACCAGT 57.459 29.630 0.00 0.00 0.00 4.00
4773 4804 3.879892 GCCCTCATATCACTCACTTTTCC 59.120 47.826 0.00 0.00 0.00 3.13
4808 4839 1.838077 CTCCCTCGGGATTTAACAGGT 59.162 52.381 4.90 0.00 44.24 4.00
4820 4851 0.322456 TTTTGGCATGACTCCCTCGG 60.322 55.000 0.00 0.00 0.00 4.63
4826 4857 3.191371 CCCAACTAGTTTTGGCATGACTC 59.809 47.826 5.07 0.00 44.29 3.36
4931 4963 8.229253 TCTCCCATGAATGTGATATTTCTTTG 57.771 34.615 0.00 0.00 0.00 2.77
4997 5572 0.675633 GCCAGCAACTGTCAACCAAT 59.324 50.000 0.00 0.00 0.00 3.16
5044 5619 9.952030 TTTGACTATTGTATCAACTGTGGAATA 57.048 29.630 0.00 0.00 34.61 1.75
5053 5628 8.564574 TCCAAGTGTTTTGACTATTGTATCAAC 58.435 33.333 0.00 0.00 34.61 3.18
5059 5634 7.404671 ACTTTCCAAGTGTTTTGACTATTGT 57.595 32.000 0.00 0.00 41.01 2.71
5085 5660 4.933505 TTTGCATCAACTGTGGAATTCA 57.066 36.364 7.93 0.00 0.00 2.57
5143 5846 3.495377 CCAAGTGTTTTGACCATTGCATG 59.505 43.478 0.00 0.00 0.00 4.06
5323 6069 0.164647 GTTCACACTCAGCATCGTGC 59.835 55.000 2.28 2.28 45.46 5.34
5324 6070 0.436150 CGTTCACACTCAGCATCGTG 59.564 55.000 0.00 0.00 37.18 4.35
5325 6071 1.284982 GCGTTCACACTCAGCATCGT 61.285 55.000 0.00 0.00 0.00 3.73
5326 6072 1.010935 AGCGTTCACACTCAGCATCG 61.011 55.000 0.00 0.00 0.00 3.84
5327 6073 0.718343 GAGCGTTCACACTCAGCATC 59.282 55.000 0.00 0.00 32.98 3.91
5328 6074 0.033920 TGAGCGTTCACACTCAGCAT 59.966 50.000 0.00 0.00 37.99 3.79
5329 6075 1.441311 TGAGCGTTCACACTCAGCA 59.559 52.632 0.00 0.00 37.99 4.41
5330 6076 4.343581 TGAGCGTTCACACTCAGC 57.656 55.556 0.00 0.00 37.99 4.26
5332 6078 4.343581 GCTGAGCGTTCACACTCA 57.656 55.556 0.00 0.00 40.54 3.41


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

AutoCloner maintained by Alex Coulton.