Multiple sequence alignment - TraesCS6A01G290300

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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 TraesCS6A01G290300 chr6A 100.000 2795 0 0 1 2795 522038019 522040813 0.000000e+00 5162.0
1 TraesCS6A01G290300 chr6A 96.016 251 10 0 351 601 486271780 486271530 2.590000e-110 409.0
2 TraesCS6A01G290300 chrUn 94.748 1961 99 3 837 2795 102570504 102572462 0.000000e+00 3048.0
3 TraesCS6A01G290300 chrUn 76.344 186 33 10 100 276 269093936 269094119 3.830000e-14 89.8
4 TraesCS6A01G290300 chr2A 96.972 1222 36 1 1575 2795 779898553 779899774 0.000000e+00 2050.0
5 TraesCS6A01G290300 chr2A 86.554 1242 164 3 1449 2687 186445968 186447209 0.000000e+00 1365.0
6 TraesCS6A01G290300 chr2A 97.179 709 20 0 836 1544 779897847 779898555 0.000000e+00 1199.0
7 TraesCS6A01G290300 chr2A 95.635 252 11 0 350 601 529417643 529417894 3.350000e-109 405.0
8 TraesCS6A01G290300 chr2A 74.230 714 179 5 1069 1779 768540389 768539678 7.570000e-76 294.0
9 TraesCS6A01G290300 chr2A 81.319 91 11 6 194 278 605123389 605123479 5.000000e-08 69.4
10 TraesCS6A01G290300 chr7B 85.234 1964 269 14 837 2795 211120677 211122624 0.000000e+00 2001.0
11 TraesCS6A01G290300 chr7B 95.635 252 11 0 350 601 717149245 717149496 3.350000e-109 405.0
12 TraesCS6A01G290300 chr7B 95.635 252 11 0 350 601 717224717 717224968 3.350000e-109 405.0
13 TraesCS6A01G290300 chr5A 88.021 1678 200 1 1119 2795 482670539 482672216 0.000000e+00 1984.0
14 TraesCS6A01G290300 chr4B 84.028 1966 304 9 837 2795 568583402 568581440 0.000000e+00 1882.0
15 TraesCS6A01G290300 chr4B 95.618 251 11 0 351 601 416649241 416649491 1.210000e-108 403.0
16 TraesCS6A01G290300 chr3D 83.749 1963 308 9 837 2795 555740895 555738940 0.000000e+00 1847.0
17 TraesCS6A01G290300 chr7A 81.611 1974 341 14 833 2794 736275847 736277810 0.000000e+00 1615.0
18 TraesCS6A01G290300 chr7A 95.635 252 11 0 350 601 706650672 706650923 3.350000e-109 405.0
19 TraesCS6A01G290300 chr7A 79.699 133 23 4 100 230 6796451 6796321 2.960000e-15 93.5
20 TraesCS6A01G290300 chr1B 81.292 1796 317 15 1006 2788 593234741 593236530 0.000000e+00 1437.0
21 TraesCS6A01G290300 chr3A 83.488 969 149 9 838 1798 227926420 227927385 0.000000e+00 893.0
22 TraesCS6A01G290300 chr3A 82.418 91 10 6 194 278 727474559 727474469 1.070000e-09 75.0
23 TraesCS6A01G290300 chr6B 89.577 355 25 6 1 352 567843494 567843839 9.190000e-120 440.0
24 TraesCS6A01G290300 chr6B 98.361 61 1 0 615 675 567843837 567843897 1.060000e-19 108.0
25 TraesCS6A01G290300 chr2B 95.635 252 11 0 350 601 150597011 150596760 3.350000e-109 405.0
26 TraesCS6A01G290300 chr2B 95.635 252 11 0 350 601 161151215 161151466 3.350000e-109 405.0
27 TraesCS6A01G290300 chr2D 95.635 252 9 2 351 601 179426531 179426781 1.210000e-108 403.0
28 TraesCS6A01G290300 chr6D 84.874 357 30 15 1 352 380564880 380565217 3.450000e-89 339.0
29 TraesCS6A01G290300 chr6D 82.569 218 11 8 615 806 380565215 380565431 1.720000e-37 167.0
30 TraesCS6A01G290300 chr3B 78.261 184 23 9 156 324 800181510 800181329 4.930000e-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 TraesCS6A01G290300 chr6A 522038019 522040813 2794 False 5162.0 5162 100.0000 1 2795 1 chr6A.!!$F1 2794
1 TraesCS6A01G290300 chrUn 102570504 102572462 1958 False 3048.0 3048 94.7480 837 2795 1 chrUn.!!$F1 1958
2 TraesCS6A01G290300 chr2A 779897847 779899774 1927 False 1624.5 2050 97.0755 836 2795 2 chr2A.!!$F4 1959
3 TraesCS6A01G290300 chr2A 186445968 186447209 1241 False 1365.0 1365 86.5540 1449 2687 1 chr2A.!!$F1 1238
4 TraesCS6A01G290300 chr2A 768539678 768540389 711 True 294.0 294 74.2300 1069 1779 1 chr2A.!!$R1 710
5 TraesCS6A01G290300 chr7B 211120677 211122624 1947 False 2001.0 2001 85.2340 837 2795 1 chr7B.!!$F1 1958
6 TraesCS6A01G290300 chr5A 482670539 482672216 1677 False 1984.0 1984 88.0210 1119 2795 1 chr5A.!!$F1 1676
7 TraesCS6A01G290300 chr4B 568581440 568583402 1962 True 1882.0 1882 84.0280 837 2795 1 chr4B.!!$R1 1958
8 TraesCS6A01G290300 chr3D 555738940 555740895 1955 True 1847.0 1847 83.7490 837 2795 1 chr3D.!!$R1 1958
9 TraesCS6A01G290300 chr7A 736275847 736277810 1963 False 1615.0 1615 81.6110 833 2794 1 chr7A.!!$F2 1961
10 TraesCS6A01G290300 chr1B 593234741 593236530 1789 False 1437.0 1437 81.2920 1006 2788 1 chr1B.!!$F1 1782
11 TraesCS6A01G290300 chr3A 227926420 227927385 965 False 893.0 893 83.4880 838 1798 1 chr3A.!!$F1 960
12 TraesCS6A01G290300 chr6D 380564880 380565431 551 False 253.0 339 83.7215 1 806 2 chr6D.!!$F1 805

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
366 372 0.251077 ACGTACTCCCTCCGTTCTGT 60.251 55.0 0.00 0.0 0.00 3.41 F
811 843 0.536006 ACTTCCACTCCAGTGCTTGC 60.536 55.0 0.76 0.0 44.34 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1585 0.324943 CAATCTTCACCCTCACCCGT 59.675 55.000 0.00 0.00 0.00 5.28 R
2549 2639 1.339610 GCTGGTGTTTGCAATACCACA 59.660 47.619 24.36 13.38 46.12 4.17 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
40 41 7.490402 CCAAGCAAAGAAATCATAAAAGGCTAG 59.510 37.037 0.00 0.00 0.00 3.42
41 42 7.105241 AGCAAAGAAATCATAAAAGGCTAGG 57.895 36.000 0.00 0.00 0.00 3.02
44 45 7.915923 GCAAAGAAATCATAAAAGGCTAGGTAC 59.084 37.037 0.00 0.00 0.00 3.34
77 78 7.148239 GGGATTTGTAAAATTCTCTGACGTCAT 60.148 37.037 20.40 3.80 0.00 3.06
79 80 7.490962 TTTGTAAAATTCTCTGACGTCATGT 57.509 32.000 20.40 0.00 0.00 3.21
88 89 8.864069 ATTCTCTGACGTCATGTTAAAGATAG 57.136 34.615 20.40 2.54 0.00 2.08
89 90 7.392494 TCTCTGACGTCATGTTAAAGATAGT 57.608 36.000 20.40 0.00 0.00 2.12
91 92 8.613482 TCTCTGACGTCATGTTAAAGATAGTAG 58.387 37.037 20.40 1.14 0.00 2.57
93 94 9.387257 TCTGACGTCATGTTAAAGATAGTAGTA 57.613 33.333 20.40 0.00 0.00 1.82
115 116 8.964476 AGTATCATTTACTACATTTGTCCAGG 57.036 34.615 0.00 0.00 0.00 4.45
116 117 8.548877 AGTATCATTTACTACATTTGTCCAGGT 58.451 33.333 0.00 0.00 0.00 4.00
117 118 9.174166 GTATCATTTACTACATTTGTCCAGGTT 57.826 33.333 0.00 0.00 0.00 3.50
118 119 8.650143 ATCATTTACTACATTTGTCCAGGTTT 57.350 30.769 0.00 0.00 0.00 3.27
119 120 9.747898 ATCATTTACTACATTTGTCCAGGTTTA 57.252 29.630 0.00 0.00 0.00 2.01
120 121 9.747898 TCATTTACTACATTTGTCCAGGTTTAT 57.252 29.630 0.00 0.00 0.00 1.40
132 133 1.831106 CAGGTTTATTTGCCCCCTTCC 59.169 52.381 0.00 0.00 0.00 3.46
137 138 4.564821 GGTTTATTTGCCCCCTTCCTTTTC 60.565 45.833 0.00 0.00 0.00 2.29
140 141 0.491371 TTGCCCCCTTCCTTTTCCAT 59.509 50.000 0.00 0.00 0.00 3.41
316 322 2.287788 GGTGCCAATAAATCAGGATGCG 60.288 50.000 0.00 0.00 34.76 4.73
328 334 3.840991 TCAGGATGCGGGTAGTATTAGT 58.159 45.455 0.00 0.00 34.76 2.24
356 362 0.865769 CAACACTGCAACGTACTCCC 59.134 55.000 0.00 0.00 0.00 4.30
357 363 0.756903 AACACTGCAACGTACTCCCT 59.243 50.000 0.00 0.00 0.00 4.20
358 364 0.317479 ACACTGCAACGTACTCCCTC 59.683 55.000 0.00 0.00 0.00 4.30
359 365 0.389948 CACTGCAACGTACTCCCTCC 60.390 60.000 0.00 0.00 0.00 4.30
360 366 1.153823 CTGCAACGTACTCCCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
361 367 1.874345 CTGCAACGTACTCCCTCCGT 61.874 60.000 0.00 0.00 36.17 4.69
362 368 1.291272 GCAACGTACTCCCTCCGTT 59.709 57.895 0.00 0.00 44.81 4.44
363 369 0.735287 GCAACGTACTCCCTCCGTTC 60.735 60.000 0.00 0.00 42.34 3.95
364 370 0.886563 CAACGTACTCCCTCCGTTCT 59.113 55.000 0.00 0.00 42.34 3.01
365 371 0.886563 AACGTACTCCCTCCGTTCTG 59.113 55.000 0.00 0.00 40.46 3.02
366 372 0.251077 ACGTACTCCCTCCGTTCTGT 60.251 55.000 0.00 0.00 0.00 3.41
367 373 1.003580 ACGTACTCCCTCCGTTCTGTA 59.996 52.381 0.00 0.00 0.00 2.74
368 374 2.086869 CGTACTCCCTCCGTTCTGTAA 58.913 52.381 0.00 0.00 0.00 2.41
369 375 2.686915 CGTACTCCCTCCGTTCTGTAAT 59.313 50.000 0.00 0.00 0.00 1.89
370 376 3.488721 CGTACTCCCTCCGTTCTGTAATG 60.489 52.174 0.00 0.00 0.00 1.90
371 377 2.537143 ACTCCCTCCGTTCTGTAATGT 58.463 47.619 0.00 0.00 0.00 2.71
372 378 3.705051 ACTCCCTCCGTTCTGTAATGTA 58.295 45.455 0.00 0.00 0.00 2.29
373 379 3.700038 ACTCCCTCCGTTCTGTAATGTAG 59.300 47.826 0.00 0.00 0.00 2.74
374 380 2.429610 TCCCTCCGTTCTGTAATGTAGC 59.570 50.000 0.00 0.00 0.00 3.58
375 381 2.460918 CCTCCGTTCTGTAATGTAGCG 58.539 52.381 0.00 0.00 0.00 4.26
376 382 1.852895 CTCCGTTCTGTAATGTAGCGC 59.147 52.381 0.00 0.00 0.00 5.92
377 383 1.202817 TCCGTTCTGTAATGTAGCGCA 59.797 47.619 11.47 0.00 0.00 6.09
378 384 2.159156 TCCGTTCTGTAATGTAGCGCAT 60.159 45.455 11.47 0.00 40.03 4.73
379 385 3.067040 TCCGTTCTGTAATGTAGCGCATA 59.933 43.478 11.47 0.00 36.67 3.14
380 386 3.987868 CCGTTCTGTAATGTAGCGCATAT 59.012 43.478 11.47 0.00 36.67 1.78
381 387 5.048573 TCCGTTCTGTAATGTAGCGCATATA 60.049 40.000 11.47 0.00 36.67 0.86
382 388 5.286320 CCGTTCTGTAATGTAGCGCATATAG 59.714 44.000 11.47 2.61 36.67 1.31
383 389 6.084277 CGTTCTGTAATGTAGCGCATATAGA 58.916 40.000 11.47 4.98 36.67 1.98
384 390 6.747739 CGTTCTGTAATGTAGCGCATATAGAT 59.252 38.462 11.47 0.00 36.67 1.98
385 391 7.273598 CGTTCTGTAATGTAGCGCATATAGATT 59.726 37.037 11.47 6.47 36.67 2.40
386 392 8.926710 GTTCTGTAATGTAGCGCATATAGATTT 58.073 33.333 11.47 0.00 36.67 2.17
387 393 9.489084 TTCTGTAATGTAGCGCATATAGATTTT 57.511 29.630 11.47 0.00 36.67 1.82
388 394 9.140286 TCTGTAATGTAGCGCATATAGATTTTC 57.860 33.333 11.47 2.33 36.67 2.29
389 395 9.144747 CTGTAATGTAGCGCATATAGATTTTCT 57.855 33.333 11.47 0.00 36.67 2.52
393 399 9.489084 AATGTAGCGCATATAGATTTTCTACAA 57.511 29.630 11.47 0.00 38.67 2.41
394 400 8.880878 TGTAGCGCATATAGATTTTCTACAAA 57.119 30.769 11.47 0.00 34.20 2.83
395 401 8.978539 TGTAGCGCATATAGATTTTCTACAAAG 58.021 33.333 11.47 0.00 34.20 2.77
396 402 8.979574 GTAGCGCATATAGATTTTCTACAAAGT 58.020 33.333 11.47 0.00 30.79 2.66
397 403 8.077836 AGCGCATATAGATTTTCTACAAAGTC 57.922 34.615 11.47 0.00 30.79 3.01
398 404 7.710907 AGCGCATATAGATTTTCTACAAAGTCA 59.289 33.333 11.47 0.00 32.03 3.41
399 405 8.335356 GCGCATATAGATTTTCTACAAAGTCAA 58.665 33.333 0.30 0.00 32.03 3.18
496 502 8.879342 AAGTATGTCTTGTGATGTATCTAAGC 57.121 34.615 0.00 0.00 34.77 3.09
497 503 8.011844 AGTATGTCTTGTGATGTATCTAAGCA 57.988 34.615 0.00 0.00 0.00 3.91
498 504 7.923344 AGTATGTCTTGTGATGTATCTAAGCAC 59.077 37.037 0.00 0.00 0.00 4.40
499 505 6.036577 TGTCTTGTGATGTATCTAAGCACA 57.963 37.500 0.00 0.00 37.66 4.57
500 506 6.643388 TGTCTTGTGATGTATCTAAGCACAT 58.357 36.000 0.00 0.00 39.00 3.21
501 507 6.536224 TGTCTTGTGATGTATCTAAGCACATG 59.464 38.462 0.00 0.00 39.00 3.21
502 508 6.536582 GTCTTGTGATGTATCTAAGCACATGT 59.463 38.462 0.00 0.00 39.00 3.21
503 509 7.706607 GTCTTGTGATGTATCTAAGCACATGTA 59.293 37.037 0.00 0.00 39.00 2.29
504 510 8.424133 TCTTGTGATGTATCTAAGCACATGTAT 58.576 33.333 0.00 0.00 39.00 2.29
505 511 8.962884 TTGTGATGTATCTAAGCACATGTATT 57.037 30.769 0.00 0.00 39.00 1.89
506 512 8.962884 TGTGATGTATCTAAGCACATGTATTT 57.037 30.769 0.00 0.00 35.55 1.40
587 593 9.716507 TTGACTTTTAGAAAAATCTATATGCGC 57.283 29.630 0.00 0.00 0.00 6.09
588 594 9.109393 TGACTTTTAGAAAAATCTATATGCGCT 57.891 29.630 9.73 0.00 0.00 5.92
595 601 8.383318 AGAAAAATCTATATGCGCTACATTGT 57.617 30.769 9.73 0.00 40.38 2.71
596 602 8.285394 AGAAAAATCTATATGCGCTACATTGTG 58.715 33.333 9.73 0.00 40.38 3.33
597 603 6.486253 AAATCTATATGCGCTACATTGTGG 57.514 37.500 9.73 0.00 40.38 4.17
598 604 4.864704 TCTATATGCGCTACATTGTGGA 57.135 40.909 9.73 0.00 40.38 4.02
599 605 5.208463 TCTATATGCGCTACATTGTGGAA 57.792 39.130 9.73 0.00 40.38 3.53
600 606 4.988540 TCTATATGCGCTACATTGTGGAAC 59.011 41.667 9.73 0.00 40.38 3.62
601 607 2.113860 ATGCGCTACATTGTGGAACT 57.886 45.000 9.73 0.00 34.40 3.01
602 608 1.890876 TGCGCTACATTGTGGAACTT 58.109 45.000 9.73 0.00 38.04 2.66
603 609 1.804151 TGCGCTACATTGTGGAACTTC 59.196 47.619 9.73 0.00 38.04 3.01
604 610 1.130561 GCGCTACATTGTGGAACTTCC 59.869 52.381 0.00 0.20 38.04 3.46
605 611 2.422597 CGCTACATTGTGGAACTTCCA 58.577 47.619 6.39 6.39 45.98 3.53
612 618 2.738480 TGGAACTTCCACGGACGG 59.262 61.111 6.39 0.00 42.67 4.79
613 619 1.833492 TGGAACTTCCACGGACGGA 60.833 57.895 6.39 0.00 42.67 4.69
614 620 1.080025 GGAACTTCCACGGACGGAG 60.080 63.158 2.62 0.00 36.28 4.63
615 621 1.813728 GGAACTTCCACGGACGGAGT 61.814 60.000 2.62 0.00 39.63 3.85
693 724 4.272018 CCACGAGGCTCTTGATCAAATAAG 59.728 45.833 21.32 8.44 0.00 1.73
712 744 8.526147 CAAATAAGTGAAAGAACATCCATTCCT 58.474 33.333 0.00 0.00 0.00 3.36
713 745 9.753674 AAATAAGTGAAAGAACATCCATTCCTA 57.246 29.630 0.00 0.00 0.00 2.94
721 753 2.050144 ACATCCATTCCTACTGCCGAT 58.950 47.619 0.00 0.00 0.00 4.18
748 780 2.901051 ATAGGACGCCGCTTCCAACG 62.901 60.000 17.56 0.00 35.33 4.10
764 796 0.889186 AACGTTTAGCTGGCCCAGTG 60.889 55.000 13.35 0.00 33.43 3.66
775 807 1.005450 TGGCCCAGTGAAAACCCTATC 59.995 52.381 0.00 0.00 0.00 2.08
806 838 3.307059 CCCTTTCTACTTCCACTCCAGTG 60.307 52.174 0.00 0.00 45.23 3.66
807 839 3.330267 CTTTCTACTTCCACTCCAGTGC 58.670 50.000 0.76 0.00 44.34 4.40
808 840 2.310779 TCTACTTCCACTCCAGTGCT 57.689 50.000 0.76 0.00 44.34 4.40
809 841 2.609747 TCTACTTCCACTCCAGTGCTT 58.390 47.619 0.76 0.00 44.34 3.91
810 842 2.300152 TCTACTTCCACTCCAGTGCTTG 59.700 50.000 0.76 0.00 44.34 4.01
811 843 0.536006 ACTTCCACTCCAGTGCTTGC 60.536 55.000 0.76 0.00 44.34 4.01
812 844 1.228245 TTCCACTCCAGTGCTTGCC 60.228 57.895 0.76 0.00 44.34 4.52
813 845 1.708993 TTCCACTCCAGTGCTTGCCT 61.709 55.000 0.76 0.00 44.34 4.75
814 846 1.673665 CCACTCCAGTGCTTGCCTC 60.674 63.158 0.76 0.00 44.34 4.70
815 847 2.031516 CACTCCAGTGCTTGCCTCG 61.032 63.158 0.00 0.00 39.39 4.63
816 848 3.123620 CTCCAGTGCTTGCCTCGC 61.124 66.667 0.00 0.00 0.00 5.03
817 849 3.602513 CTCCAGTGCTTGCCTCGCT 62.603 63.158 0.00 0.00 0.00 4.93
818 850 3.123620 CCAGTGCTTGCCTCGCTC 61.124 66.667 0.00 0.00 0.00 5.03
819 851 2.357881 CAGTGCTTGCCTCGCTCA 60.358 61.111 0.00 0.00 0.00 4.26
820 852 2.358003 AGTGCTTGCCTCGCTCAC 60.358 61.111 0.00 0.00 0.00 3.51
821 853 2.358003 GTGCTTGCCTCGCTCACT 60.358 61.111 0.00 0.00 0.00 3.41
822 854 2.047844 TGCTTGCCTCGCTCACTC 60.048 61.111 0.00 0.00 0.00 3.51
823 855 3.184683 GCTTGCCTCGCTCACTCG 61.185 66.667 0.00 0.00 0.00 4.18
824 856 2.568612 CTTGCCTCGCTCACTCGA 59.431 61.111 0.00 0.00 36.94 4.04
825 857 1.803519 CTTGCCTCGCTCACTCGAC 60.804 63.158 0.00 0.00 34.46 4.20
826 858 2.477972 CTTGCCTCGCTCACTCGACA 62.478 60.000 0.00 0.00 34.46 4.35
827 859 2.082629 TTGCCTCGCTCACTCGACAA 62.083 55.000 0.00 0.00 34.46 3.18
828 860 1.153745 GCCTCGCTCACTCGACAAT 60.154 57.895 0.00 0.00 34.46 2.71
829 861 0.737715 GCCTCGCTCACTCGACAATT 60.738 55.000 0.00 0.00 34.46 2.32
830 862 0.994995 CCTCGCTCACTCGACAATTG 59.005 55.000 3.24 3.24 34.46 2.32
831 863 1.670087 CCTCGCTCACTCGACAATTGT 60.670 52.381 11.78 11.78 34.46 2.71
832 864 2.061773 CTCGCTCACTCGACAATTGTT 58.938 47.619 13.36 0.00 34.46 2.83
833 865 2.476619 CTCGCTCACTCGACAATTGTTT 59.523 45.455 13.36 0.00 34.46 2.83
834 866 2.475111 TCGCTCACTCGACAATTGTTTC 59.525 45.455 13.36 0.00 33.02 2.78
835 867 2.476619 CGCTCACTCGACAATTGTTTCT 59.523 45.455 13.36 0.00 0.00 2.52
842 874 3.821033 CTCGACAATTGTTTCTTCCCCTT 59.179 43.478 13.36 0.00 0.00 3.95
887 922 2.962569 CGGCGACTTGTCTCCTCA 59.037 61.111 0.00 0.00 0.00 3.86
1042 1079 2.158900 ACTAAGGAAGATGGTGCATCCG 60.159 50.000 0.00 0.00 41.36 4.18
1140 1183 1.909302 GTGGAGGAGGATGAACTTCCA 59.091 52.381 8.94 0.00 45.67 3.53
1534 1577 1.359130 AGTCCCAAGATTTTGAGGGGG 59.641 52.381 0.00 0.00 41.77 5.40
1542 1585 2.158325 AGATTTTGAGGGGGACTTTGCA 60.158 45.455 0.00 0.00 0.00 4.08
1697 1773 1.490490 TGGTTATCTGGGGCATCTGTC 59.510 52.381 0.00 0.00 0.00 3.51
1765 1841 2.756907 AGGATCTGAAAGCTAGCTGGA 58.243 47.619 20.16 14.30 0.00 3.86
1941 2029 5.556006 TCACAATGGATGATGCTGATCTA 57.444 39.130 0.00 0.00 0.00 1.98
2360 2449 9.346725 CATTAGGTTTTGATAAGAGTTTTGCTC 57.653 33.333 0.00 0.00 44.45 4.26
2431 2520 5.934043 AGCAATAAAGTTGGAAATTCTTGGC 59.066 36.000 0.00 0.00 0.00 4.52
2525 2615 2.030805 GGAGAAGCACAAACGCAAGAAT 60.031 45.455 0.00 0.00 43.62 2.40
2582 2672 1.077212 ACCAGCAGTCATCCATGGC 60.077 57.895 6.96 0.00 34.24 4.40
2592 2684 0.881600 CATCCATGGCTTGCGATCGA 60.882 55.000 21.57 0.59 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 8.732746 ACCTGGACAAATGTAGTAAATGATAC 57.267 34.615 0.00 0.00 0.00 2.24
93 94 8.650143 AAACCTGGACAAATGTAGTAAATGAT 57.350 30.769 0.00 0.00 0.00 2.45
94 95 9.747898 ATAAACCTGGACAAATGTAGTAAATGA 57.252 29.630 0.00 0.00 0.00 2.57
98 99 8.301002 GCAAATAAACCTGGACAAATGTAGTAA 58.699 33.333 0.00 0.00 0.00 2.24
99 100 7.094118 GGCAAATAAACCTGGACAAATGTAGTA 60.094 37.037 0.00 0.00 0.00 1.82
100 101 6.295067 GGCAAATAAACCTGGACAAATGTAGT 60.295 38.462 0.00 0.00 0.00 2.73
101 102 6.099341 GGCAAATAAACCTGGACAAATGTAG 58.901 40.000 0.00 0.00 0.00 2.74
104 105 4.252878 GGGCAAATAAACCTGGACAAATG 58.747 43.478 0.00 0.00 0.00 2.32
105 106 3.263170 GGGGCAAATAAACCTGGACAAAT 59.737 43.478 0.00 0.00 0.00 2.32
106 107 2.635427 GGGGCAAATAAACCTGGACAAA 59.365 45.455 0.00 0.00 0.00 2.83
107 108 2.252714 GGGGCAAATAAACCTGGACAA 58.747 47.619 0.00 0.00 0.00 3.18
108 109 1.551329 GGGGGCAAATAAACCTGGACA 60.551 52.381 0.00 0.00 0.00 4.02
109 110 1.191535 GGGGGCAAATAAACCTGGAC 58.808 55.000 0.00 0.00 0.00 4.02
110 111 1.089123 AGGGGGCAAATAAACCTGGA 58.911 50.000 0.00 0.00 0.00 3.86
111 112 1.831106 GAAGGGGGCAAATAAACCTGG 59.169 52.381 0.00 0.00 0.00 4.45
112 113 1.831106 GGAAGGGGGCAAATAAACCTG 59.169 52.381 0.00 0.00 0.00 4.00
113 114 1.722271 AGGAAGGGGGCAAATAAACCT 59.278 47.619 0.00 0.00 0.00 3.50
114 115 2.247699 AGGAAGGGGGCAAATAAACC 57.752 50.000 0.00 0.00 0.00 3.27
115 116 4.564821 GGAAAAGGAAGGGGGCAAATAAAC 60.565 45.833 0.00 0.00 0.00 2.01
116 117 3.585289 GGAAAAGGAAGGGGGCAAATAAA 59.415 43.478 0.00 0.00 0.00 1.40
117 118 3.178046 GGAAAAGGAAGGGGGCAAATAA 58.822 45.455 0.00 0.00 0.00 1.40
118 119 2.112691 TGGAAAAGGAAGGGGGCAAATA 59.887 45.455 0.00 0.00 0.00 1.40
119 120 1.132560 TGGAAAAGGAAGGGGGCAAAT 60.133 47.619 0.00 0.00 0.00 2.32
120 121 0.266152 TGGAAAAGGAAGGGGGCAAA 59.734 50.000 0.00 0.00 0.00 3.68
270 276 8.848474 CCTCGTATTTAGGGTCATCATAATTT 57.152 34.615 0.00 0.00 0.00 1.82
316 322 3.121544 GCACGAGCAACTAATACTACCC 58.878 50.000 0.00 0.00 41.58 3.69
351 357 2.537143 ACATTACAGAACGGAGGGAGT 58.463 47.619 0.00 0.00 0.00 3.85
352 358 3.491104 GCTACATTACAGAACGGAGGGAG 60.491 52.174 0.00 0.00 0.00 4.30
353 359 2.429610 GCTACATTACAGAACGGAGGGA 59.570 50.000 0.00 0.00 0.00 4.20
354 360 2.798499 CGCTACATTACAGAACGGAGGG 60.798 54.545 0.00 0.00 0.00 4.30
355 361 2.460918 CGCTACATTACAGAACGGAGG 58.539 52.381 0.00 0.00 0.00 4.30
356 362 1.852895 GCGCTACATTACAGAACGGAG 59.147 52.381 0.00 0.00 0.00 4.63
357 363 1.202817 TGCGCTACATTACAGAACGGA 59.797 47.619 9.73 0.00 0.00 4.69
358 364 1.635844 TGCGCTACATTACAGAACGG 58.364 50.000 9.73 0.00 0.00 4.44
359 365 6.084277 TCTATATGCGCTACATTACAGAACG 58.916 40.000 9.73 0.00 40.38 3.95
360 366 8.467402 AATCTATATGCGCTACATTACAGAAC 57.533 34.615 9.73 0.00 40.38 3.01
361 367 9.489084 AAAATCTATATGCGCTACATTACAGAA 57.511 29.630 9.73 0.00 40.38 3.02
362 368 9.140286 GAAAATCTATATGCGCTACATTACAGA 57.860 33.333 9.73 0.82 40.38 3.41
363 369 9.144747 AGAAAATCTATATGCGCTACATTACAG 57.855 33.333 9.73 0.00 40.38 2.74
367 373 9.489084 TTGTAGAAAATCTATATGCGCTACATT 57.511 29.630 9.73 0.00 40.38 2.71
368 374 9.489084 TTTGTAGAAAATCTATATGCGCTACAT 57.511 29.630 9.73 1.21 43.18 2.29
369 375 8.880878 TTTGTAGAAAATCTATATGCGCTACA 57.119 30.769 9.73 0.63 36.25 2.74
370 376 8.979574 ACTTTGTAGAAAATCTATATGCGCTAC 58.020 33.333 9.73 0.00 30.76 3.58
371 377 9.193133 GACTTTGTAGAAAATCTATATGCGCTA 57.807 33.333 9.73 0.00 30.76 4.26
372 378 7.710907 TGACTTTGTAGAAAATCTATATGCGCT 59.289 33.333 9.73 0.00 30.76 5.92
373 379 7.851508 TGACTTTGTAGAAAATCTATATGCGC 58.148 34.615 0.00 0.00 30.76 6.09
470 476 9.319143 GCTTAGATACATCACAAGACATACTTT 57.681 33.333 7.43 0.00 36.61 2.66
471 477 8.478066 TGCTTAGATACATCACAAGACATACTT 58.522 33.333 7.43 0.00 39.70 2.24
472 478 7.923344 GTGCTTAGATACATCACAAGACATACT 59.077 37.037 7.43 0.00 0.00 2.12
473 479 7.706607 TGTGCTTAGATACATCACAAGACATAC 59.293 37.037 7.43 0.00 35.08 2.39
474 480 7.781056 TGTGCTTAGATACATCACAAGACATA 58.219 34.615 7.43 2.88 35.08 2.29
475 481 6.643388 TGTGCTTAGATACATCACAAGACAT 58.357 36.000 7.43 0.00 35.08 3.06
476 482 6.036577 TGTGCTTAGATACATCACAAGACA 57.963 37.500 7.43 6.40 35.08 3.41
477 483 6.536582 ACATGTGCTTAGATACATCACAAGAC 59.463 38.462 0.00 4.73 40.46 3.01
478 484 6.643388 ACATGTGCTTAGATACATCACAAGA 58.357 36.000 0.00 0.00 40.46 3.02
479 485 6.915544 ACATGTGCTTAGATACATCACAAG 57.084 37.500 0.00 0.00 40.46 3.16
480 486 8.962884 AATACATGTGCTTAGATACATCACAA 57.037 30.769 9.11 0.00 40.46 3.33
481 487 8.962884 AAATACATGTGCTTAGATACATCACA 57.037 30.769 9.11 0.00 41.18 3.58
561 567 9.716507 GCGCATATAGATTTTTCTAAAAGTCAA 57.283 29.630 0.30 0.46 37.17 3.18
562 568 9.109393 AGCGCATATAGATTTTTCTAAAAGTCA 57.891 29.630 11.47 1.42 37.17 3.41
569 575 9.489084 ACAATGTAGCGCATATAGATTTTTCTA 57.511 29.630 11.47 0.00 36.67 2.10
570 576 8.285394 CACAATGTAGCGCATATAGATTTTTCT 58.715 33.333 11.47 0.00 36.67 2.52
571 577 7.535258 CCACAATGTAGCGCATATAGATTTTTC 59.465 37.037 11.47 0.00 36.67 2.29
572 578 7.228507 TCCACAATGTAGCGCATATAGATTTTT 59.771 33.333 11.47 0.00 36.67 1.94
573 579 6.710295 TCCACAATGTAGCGCATATAGATTTT 59.290 34.615 11.47 0.00 36.67 1.82
574 580 6.230472 TCCACAATGTAGCGCATATAGATTT 58.770 36.000 11.47 0.00 36.67 2.17
575 581 5.793817 TCCACAATGTAGCGCATATAGATT 58.206 37.500 11.47 0.41 36.67 2.40
576 582 5.405935 TCCACAATGTAGCGCATATAGAT 57.594 39.130 11.47 0.00 36.67 1.98
577 583 4.864704 TCCACAATGTAGCGCATATAGA 57.135 40.909 11.47 0.00 36.67 1.98
578 584 4.991056 AGTTCCACAATGTAGCGCATATAG 59.009 41.667 11.47 0.00 36.67 1.31
579 585 4.956085 AGTTCCACAATGTAGCGCATATA 58.044 39.130 11.47 0.00 36.67 0.86
580 586 3.808728 AGTTCCACAATGTAGCGCATAT 58.191 40.909 11.47 0.00 36.67 1.78
581 587 3.260475 AGTTCCACAATGTAGCGCATA 57.740 42.857 11.47 0.00 36.67 3.14
582 588 2.113860 AGTTCCACAATGTAGCGCAT 57.886 45.000 11.47 0.00 40.03 4.73
583 589 1.804151 GAAGTTCCACAATGTAGCGCA 59.196 47.619 11.47 0.00 0.00 6.09
584 590 1.130561 GGAAGTTCCACAATGTAGCGC 59.869 52.381 17.44 0.00 36.28 5.92
585 591 2.422597 TGGAAGTTCCACAATGTAGCG 58.577 47.619 21.05 0.00 42.67 4.26
595 601 1.812686 CTCCGTCCGTGGAAGTTCCA 61.813 60.000 21.05 21.05 45.98 3.53
596 602 1.080025 CTCCGTCCGTGGAAGTTCC 60.080 63.158 15.50 15.50 37.64 3.62
597 603 0.883833 TACTCCGTCCGTGGAAGTTC 59.116 55.000 0.00 0.00 37.64 3.01
598 604 1.000171 GTTACTCCGTCCGTGGAAGTT 60.000 52.381 1.24 0.00 37.64 2.66
599 605 0.600057 GTTACTCCGTCCGTGGAAGT 59.400 55.000 1.24 0.00 37.64 3.01
600 606 0.599558 TGTTACTCCGTCCGTGGAAG 59.400 55.000 0.00 0.00 37.64 3.46
601 607 1.259609 ATGTTACTCCGTCCGTGGAA 58.740 50.000 0.00 0.00 37.64 3.53
602 608 1.259609 AATGTTACTCCGTCCGTGGA 58.740 50.000 0.00 0.00 36.37 4.02
603 609 2.088950 AAATGTTACTCCGTCCGTGG 57.911 50.000 0.00 0.00 0.00 4.94
673 679 5.111989 TCACTTATTTGATCAAGAGCCTCG 58.888 41.667 8.41 0.00 0.00 4.63
675 681 7.170965 TCTTTCACTTATTTGATCAAGAGCCT 58.829 34.615 8.41 0.00 0.00 4.58
693 724 5.163713 GCAGTAGGAATGGATGTTCTTTCAC 60.164 44.000 0.00 0.00 0.00 3.18
721 753 3.804329 GGCGTCCTATGGGCCCAA 61.804 66.667 32.58 17.36 41.01 4.12
729 761 1.153429 GTTGGAAGCGGCGTCCTAT 60.153 57.895 30.13 0.00 36.03 2.57
748 780 1.616159 TTTCACTGGGCCAGCTAAAC 58.384 50.000 33.04 0.00 34.37 2.01
764 796 4.477581 AGGGGAAAGTAGGATAGGGTTTTC 59.522 45.833 0.00 0.00 0.00 2.29
775 807 4.534897 TGGAAGTAGAAAGGGGAAAGTAGG 59.465 45.833 0.00 0.00 0.00 3.18
806 838 3.184683 CGAGTGAGCGAGGCAAGC 61.185 66.667 0.00 0.00 0.00 4.01
807 839 1.803519 GTCGAGTGAGCGAGGCAAG 60.804 63.158 0.00 0.00 41.49 4.01
808 840 2.082629 TTGTCGAGTGAGCGAGGCAA 62.083 55.000 0.00 0.00 41.49 4.52
809 841 1.877576 ATTGTCGAGTGAGCGAGGCA 61.878 55.000 0.00 0.00 41.49 4.75
810 842 0.737715 AATTGTCGAGTGAGCGAGGC 60.738 55.000 0.00 0.00 41.49 4.70
811 843 0.994995 CAATTGTCGAGTGAGCGAGG 59.005 55.000 0.00 0.00 41.49 4.63
812 844 1.702886 ACAATTGTCGAGTGAGCGAG 58.297 50.000 4.92 0.00 41.49 5.03
813 845 2.148916 AACAATTGTCGAGTGAGCGA 57.851 45.000 12.39 0.00 38.07 4.93
814 846 2.476619 AGAAACAATTGTCGAGTGAGCG 59.523 45.455 12.39 0.00 0.00 5.03
815 847 4.458708 GAAGAAACAATTGTCGAGTGAGC 58.541 43.478 12.39 0.00 0.00 4.26
816 848 4.083802 GGGAAGAAACAATTGTCGAGTGAG 60.084 45.833 12.39 0.00 0.00 3.51
817 849 3.813166 GGGAAGAAACAATTGTCGAGTGA 59.187 43.478 12.39 0.00 0.00 3.41
818 850 3.058224 GGGGAAGAAACAATTGTCGAGTG 60.058 47.826 12.39 0.00 0.00 3.51
819 851 3.146847 GGGGAAGAAACAATTGTCGAGT 58.853 45.455 12.39 0.00 0.00 4.18
820 852 3.412386 AGGGGAAGAAACAATTGTCGAG 58.588 45.455 12.39 0.00 0.00 4.04
821 853 3.502123 AGGGGAAGAAACAATTGTCGA 57.498 42.857 12.39 0.00 0.00 4.20
822 854 4.584327 AAAGGGGAAGAAACAATTGTCG 57.416 40.909 12.39 0.00 0.00 4.35
823 855 5.670485 ACAAAAGGGGAAGAAACAATTGTC 58.330 37.500 12.39 0.00 0.00 3.18
824 856 5.692115 ACAAAAGGGGAAGAAACAATTGT 57.308 34.783 4.92 4.92 0.00 2.71
825 857 6.705825 CCTAACAAAAGGGGAAGAAACAATTG 59.294 38.462 3.24 3.24 32.55 2.32
826 858 6.826668 CCTAACAAAAGGGGAAGAAACAATT 58.173 36.000 0.00 0.00 32.55 2.32
827 859 6.419484 CCTAACAAAAGGGGAAGAAACAAT 57.581 37.500 0.00 0.00 32.55 2.71
828 860 5.862678 CCTAACAAAAGGGGAAGAAACAA 57.137 39.130 0.00 0.00 32.55 2.83
842 874 5.137551 CCAGAGGAAGAAAACCCTAACAAA 58.862 41.667 0.00 0.00 31.84 2.83
887 922 2.625790 GGTAGATCAAGATCTCTGCGGT 59.374 50.000 15.37 0.00 44.37 5.68
989 1026 0.687354 AGAAACCATGTCCACGAGCT 59.313 50.000 0.00 0.00 0.00 4.09
1065 1108 2.062971 ATTCTTCCATCATTGCCGCT 57.937 45.000 0.00 0.00 0.00 5.52
1534 1577 1.966451 CCCTCACCCGTGCAAAGTC 60.966 63.158 0.00 0.00 0.00 3.01
1542 1585 0.324943 CAATCTTCACCCTCACCCGT 59.675 55.000 0.00 0.00 0.00 5.28
1697 1773 2.289444 ACACCGTCACCACATTCCTTAG 60.289 50.000 0.00 0.00 0.00 2.18
1765 1841 3.878667 GCTGCCCGGGCCTCTAAT 61.879 66.667 41.75 0.00 41.09 1.73
1792 1868 4.591498 TCTGTTACTGTTGCCTCTTCCTTA 59.409 41.667 0.00 0.00 0.00 2.69
1941 2029 2.059756 TCATCCCCCTCTTCCTGTTT 57.940 50.000 0.00 0.00 0.00 2.83
2360 2449 4.951094 ACCACTTCTACCTCTACTGCTTAG 59.049 45.833 0.00 0.00 0.00 2.18
2525 2615 9.639563 ACACAACATATCCCATGTTTTATATCA 57.360 29.630 0.00 0.00 39.94 2.15
2549 2639 1.339610 GCTGGTGTTTGCAATACCACA 59.660 47.619 24.36 13.38 46.12 4.17
2582 2672 3.553105 TCATTGAAGTCATCGATCGCAAG 59.447 43.478 11.09 2.44 28.98 4.01


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

AutoCloner maintained by Alex Coulton.