Multiple sequence alignment - TraesCS1B01G384000

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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 TraesCS1B01G384000 chr1B 100.000 2235 0 0 1 2235 616565343 616567577 0.000000e+00 4128
1 TraesCS1B01G384000 chr1B 85.880 602 60 10 1345 1932 615732509 615733099 3.150000e-173 617
2 TraesCS1B01G384000 chr1B 82.812 640 80 12 1228 1845 615581985 615582616 1.510000e-151 545
3 TraesCS1B01G384000 chr1B 86.472 377 36 5 1 371 615732894 615732527 1.240000e-107 399
4 TraesCS1B01G384000 chr1B 84.912 285 26 8 941 1224 616136712 616136444 2.830000e-69 272
5 TraesCS1B01G384000 chr1B 88.496 226 16 4 998 1221 615581736 615581953 4.730000e-67 265
6 TraesCS1B01G384000 chr1B 87.892 223 17 4 1001 1221 615732164 615732378 1.020000e-63 254
7 TraesCS1B01G384000 chr1D 86.632 1556 117 31 704 2213 450045978 450047488 0.000000e+00 1637
8 TraesCS1B01G384000 chr1D 89.613 491 16 13 1 478 450044457 450044925 1.910000e-165 592
9 TraesCS1B01G384000 chr1D 84.577 603 66 13 1345 1932 449847234 449847824 6.920000e-160 573
10 TraesCS1B01G384000 chr1D 85.631 515 52 9 1345 1845 449660758 449661264 2.540000e-144 521
11 TraesCS1B01G384000 chr1D 84.288 541 62 11 1319 1845 449674986 449675517 7.120000e-140 507
12 TraesCS1B01G384000 chr1D 85.450 378 38 9 1 371 449661143 449660776 5.830000e-101 377
13 TraesCS1B01G384000 chr1D 84.881 377 42 5 1 371 449847619 449847252 1.260000e-97 366
14 TraesCS1B01G384000 chr1D 86.310 336 36 5 37 371 449675352 449675026 7.590000e-95 357
15 TraesCS1B01G384000 chr1D 84.350 377 35 15 1 371 449982639 449982997 4.570000e-92 348
16 TraesCS1B01G384000 chr1D 81.651 436 45 16 793 1224 449983620 449983216 1.650000e-86 329
17 TraesCS1B01G384000 chr1D 85.766 274 27 6 130 393 449753281 449753010 1.690000e-71 279
18 TraesCS1B01G384000 chr1D 85.992 257 23 6 967 1221 449846817 449847062 1.700000e-66 263
19 TraesCS1B01G384000 chr1D 85.547 256 24 5 968 1221 449752609 449752853 2.850000e-64 255
20 TraesCS1B01G384000 chr1D 85.214 257 25 8 967 1221 449660365 449660610 3.680000e-63 252
21 TraesCS1B01G384000 chr1D 86.726 226 20 7 998 1221 449674644 449674861 2.220000e-60 243
22 TraesCS1B01G384000 chr1A 83.980 980 105 22 1247 2212 545299575 545300516 0.000000e+00 893
23 TraesCS1B01G384000 chr1A 86.714 700 45 24 1 691 545298893 545299553 0.000000e+00 734
24 TraesCS1B01G384000 chr1A 83.184 779 90 23 1228 1975 545009245 545008477 0.000000e+00 675
25 TraesCS1B01G384000 chr1A 83.775 641 72 12 1228 1844 544748545 544749177 1.490000e-161 579
26 TraesCS1B01G384000 chr1A 85.465 516 51 10 1345 1845 544928174 544928680 1.180000e-142 516
27 TraesCS1B01G384000 chr1A 85.309 388 43 8 37 422 544749016 544748641 2.690000e-104 388
28 TraesCS1B01G384000 chr1A 85.450 378 38 9 1 371 544928559 544928192 5.830000e-101 377
29 TraesCS1B01G384000 chr1A 84.309 376 39 12 1 369 545000963 545000601 1.270000e-92 350
30 TraesCS1B01G384000 chr1A 81.694 366 42 9 860 1224 545025375 545025034 4.700000e-72 281
31 TraesCS1B01G384000 chr1A 86.853 251 20 5 973 1221 544748274 544748513 3.660000e-68 268


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 TraesCS1B01G384000 chr1B 616565343 616567577 2234 False 4128.0 4128 100.0000 1 2235 1 chr1B.!!$F1 2234
1 TraesCS1B01G384000 chr1B 615732164 615733099 935 False 435.5 617 86.8860 1001 1932 2 chr1B.!!$F3 931
2 TraesCS1B01G384000 chr1B 615581736 615582616 880 False 405.0 545 85.6540 998 1845 2 chr1B.!!$F2 847
3 TraesCS1B01G384000 chr1D 450044457 450047488 3031 False 1114.5 1637 88.1225 1 2213 2 chr1D.!!$F6 2212
4 TraesCS1B01G384000 chr1D 449846817 449847824 1007 False 418.0 573 85.2845 967 1932 2 chr1D.!!$F5 965
5 TraesCS1B01G384000 chr1D 449660365 449661264 899 False 386.5 521 85.4225 967 1845 2 chr1D.!!$F3 878
6 TraesCS1B01G384000 chr1D 449674644 449675517 873 False 375.0 507 85.5070 998 1845 2 chr1D.!!$F4 847
7 TraesCS1B01G384000 chr1A 545298893 545300516 1623 False 813.5 893 85.3470 1 2212 2 chr1A.!!$F3 2211
8 TraesCS1B01G384000 chr1A 545008477 545009245 768 True 675.0 675 83.1840 1228 1975 1 chr1A.!!$R4 747
9 TraesCS1B01G384000 chr1A 544928174 544928680 506 False 516.0 516 85.4650 1345 1845 1 chr1A.!!$F1 500
10 TraesCS1B01G384000 chr1A 544748274 544749177 903 False 423.5 579 85.3140 973 1844 2 chr1A.!!$F2 871

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
942 1908 0.1791 TTGGCTAGCTGCTTAGCTCG 60.179 55.0 15.72 0.71 45.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 2829 0.325296 TAGCCCAGGTTCTCCGACAT 60.325 55.0 0.0 0.0 39.05 3.06 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
97 103 4.717629 CGACGAACCTGCTGCCGA 62.718 66.667 0.00 0.00 0.00 5.54
102 108 2.357517 AACCTGCTGCCGAAGTCG 60.358 61.111 0.00 0.00 39.44 4.18
129 135 3.001406 ACGGGGAAGGGGTCGAAG 61.001 66.667 0.00 0.00 0.00 3.79
130 136 3.001406 CGGGGAAGGGGTCGAAGT 61.001 66.667 0.00 0.00 0.00 3.01
131 137 2.987962 GGGGAAGGGGTCGAAGTC 59.012 66.667 0.00 0.00 0.00 3.01
132 138 2.577593 GGGAAGGGGTCGAAGTCG 59.422 66.667 0.00 0.00 41.45 4.18
424 438 5.361857 AGCATGTTATCCCAAATCTTTCAGG 59.638 40.000 0.00 0.00 0.00 3.86
425 439 5.594926 CATGTTATCCCAAATCTTTCAGGC 58.405 41.667 0.00 0.00 0.00 4.85
426 440 4.934356 TGTTATCCCAAATCTTTCAGGCT 58.066 39.130 0.00 0.00 0.00 4.58
427 441 5.332743 TGTTATCCCAAATCTTTCAGGCTT 58.667 37.500 0.00 0.00 0.00 4.35
428 442 5.779771 TGTTATCCCAAATCTTTCAGGCTTT 59.220 36.000 0.00 0.00 0.00 3.51
429 443 6.071391 TGTTATCCCAAATCTTTCAGGCTTTC 60.071 38.462 0.00 0.00 0.00 2.62
430 444 3.843422 TCCCAAATCTTTCAGGCTTTCA 58.157 40.909 0.00 0.00 0.00 2.69
431 445 3.828451 TCCCAAATCTTTCAGGCTTTCAG 59.172 43.478 0.00 0.00 0.00 3.02
454 468 0.941463 ACTCACTCTGCTTGAACGCG 60.941 55.000 3.53 3.53 0.00 6.01
455 469 0.664466 CTCACTCTGCTTGAACGCGA 60.664 55.000 15.93 0.00 0.00 5.87
478 493 6.402550 CGAGAGCACTGCAAAATTAATGTACT 60.403 38.462 3.30 0.00 0.00 2.73
483 498 5.794945 CACTGCAAAATTAATGTACTCGTGG 59.205 40.000 0.00 0.00 0.00 4.94
493 508 3.277211 TACTCGTGGTCGCAGGCAC 62.277 63.158 0.00 0.00 36.96 5.01
494 509 4.662961 CTCGTGGTCGCAGGCACA 62.663 66.667 0.00 0.00 36.96 4.57
495 510 3.939837 CTCGTGGTCGCAGGCACAT 62.940 63.158 0.00 0.00 36.96 3.21
496 511 3.490759 CGTGGTCGCAGGCACATC 61.491 66.667 0.00 0.00 0.00 3.06
535 550 6.709397 AGTACGTACTAGGATGAATGAATCGA 59.291 38.462 26.36 0.00 34.13 3.59
541 556 3.464907 AGGATGAATGAATCGACAGCAG 58.535 45.455 0.00 0.00 0.00 4.24
542 557 2.547211 GGATGAATGAATCGACAGCAGG 59.453 50.000 0.00 0.00 0.00 4.85
543 558 2.768253 TGAATGAATCGACAGCAGGT 57.232 45.000 0.00 0.00 0.00 4.00
544 559 2.349590 TGAATGAATCGACAGCAGGTG 58.650 47.619 0.00 0.00 0.00 4.00
545 560 2.028203 TGAATGAATCGACAGCAGGTGA 60.028 45.455 6.61 0.00 0.00 4.02
546 561 2.306341 ATGAATCGACAGCAGGTGAG 57.694 50.000 6.61 0.00 0.00 3.51
547 562 0.247460 TGAATCGACAGCAGGTGAGG 59.753 55.000 6.61 0.00 0.00 3.86
548 563 0.247736 GAATCGACAGCAGGTGAGGT 59.752 55.000 6.61 0.00 0.00 3.85
549 564 0.687354 AATCGACAGCAGGTGAGGTT 59.313 50.000 6.61 0.00 0.00 3.50
550 565 0.247736 ATCGACAGCAGGTGAGGTTC 59.752 55.000 6.61 0.00 0.00 3.62
551 566 1.112916 TCGACAGCAGGTGAGGTTCA 61.113 55.000 6.61 0.00 0.00 3.18
552 567 0.249868 CGACAGCAGGTGAGGTTCAA 60.250 55.000 6.61 0.00 0.00 2.69
553 568 1.810031 CGACAGCAGGTGAGGTTCAAA 60.810 52.381 6.61 0.00 0.00 2.69
554 569 2.297701 GACAGCAGGTGAGGTTCAAAA 58.702 47.619 6.61 0.00 0.00 2.44
555 570 2.687935 GACAGCAGGTGAGGTTCAAAAA 59.312 45.455 6.61 0.00 0.00 1.94
579 594 1.993956 TACAAATTGGCAGCAGGTGT 58.006 45.000 0.66 0.00 0.00 4.16
587 602 1.656441 GCAGCAGGTGTGGTTCAAG 59.344 57.895 0.66 0.00 29.64 3.02
599 614 5.220796 GGTGTGGTTCAAGAAAGAAGTACAC 60.221 44.000 0.00 11.69 40.79 2.90
600 615 5.585047 GTGTGGTTCAAGAAAGAAGTACACT 59.415 40.000 0.00 0.00 39.69 3.55
601 616 6.759827 GTGTGGTTCAAGAAAGAAGTACACTA 59.240 38.462 0.00 0.00 39.69 2.74
602 617 6.984474 TGTGGTTCAAGAAAGAAGTACACTAG 59.016 38.462 0.00 0.00 33.05 2.57
603 618 6.985059 GTGGTTCAAGAAAGAAGTACACTAGT 59.015 38.462 0.00 0.00 31.04 2.57
604 619 8.139989 GTGGTTCAAGAAAGAAGTACACTAGTA 58.860 37.037 0.00 0.00 31.04 1.82
645 683 1.416243 ACTGGGGAACACGAGTACAA 58.584 50.000 0.00 0.00 0.00 2.41
692 1623 7.756395 ATCTACGCCTAGCAATAAGTTACTA 57.244 36.000 0.00 0.00 0.00 1.82
693 1624 6.963796 TCTACGCCTAGCAATAAGTTACTAC 58.036 40.000 0.00 0.00 0.00 2.73
694 1625 5.848833 ACGCCTAGCAATAAGTTACTACT 57.151 39.130 0.00 0.00 35.68 2.57
699 1630 8.133627 CGCCTAGCAATAAGTTACTACTCTAAA 58.866 37.037 0.00 0.00 31.99 1.85
701 1632 9.465985 CCTAGCAATAAGTTACTACTCTAAAGC 57.534 37.037 0.00 0.00 31.99 3.51
709 1640 5.950549 AGTTACTACTCTAAAGCTACCTGCA 59.049 40.000 0.00 0.00 45.94 4.41
737 1668 4.379174 CAGGTTTGTCGGACCCTG 57.621 61.111 14.73 14.73 37.93 4.45
791 1742 2.202570 CGTCGTCGGGCTTACTGG 60.203 66.667 0.00 0.00 0.00 4.00
813 1766 2.082629 TTGCGGCTTCTCACTCACGA 62.083 55.000 0.00 0.00 0.00 4.35
833 1786 3.954904 CGATTCTCCCAGATATACCCGAT 59.045 47.826 0.00 0.00 0.00 4.18
837 1790 5.727243 TCTCCCAGATATACCCGATCATA 57.273 43.478 0.00 0.00 0.00 2.15
839 1792 6.071320 TCTCCCAGATATACCCGATCATATG 58.929 44.000 0.00 0.00 0.00 1.78
842 1795 7.004691 TCCCAGATATACCCGATCATATGTAG 58.995 42.308 1.90 0.00 0.00 2.74
843 1796 6.778069 CCCAGATATACCCGATCATATGTAGT 59.222 42.308 1.90 0.00 0.00 2.73
844 1797 7.942894 CCCAGATATACCCGATCATATGTAGTA 59.057 40.741 1.90 0.00 0.00 1.82
845 1798 9.004717 CCAGATATACCCGATCATATGTAGTAG 57.995 40.741 1.90 0.00 0.00 2.57
846 1799 8.508062 CAGATATACCCGATCATATGTAGTAGC 58.492 40.741 1.90 0.00 0.00 3.58
847 1800 8.218488 AGATATACCCGATCATATGTAGTAGCA 58.782 37.037 1.90 0.00 0.00 3.49
848 1801 6.701145 ATACCCGATCATATGTAGTAGCAG 57.299 41.667 1.90 0.00 0.00 4.24
849 1802 3.764434 ACCCGATCATATGTAGTAGCAGG 59.236 47.826 1.90 0.00 0.00 4.85
850 1803 3.429547 CCCGATCATATGTAGTAGCAGGC 60.430 52.174 1.90 0.00 0.00 4.85
851 1804 3.193479 CCGATCATATGTAGTAGCAGGCA 59.807 47.826 1.90 0.00 0.00 4.75
852 1805 4.321974 CCGATCATATGTAGTAGCAGGCAA 60.322 45.833 1.90 0.00 0.00 4.52
853 1806 4.861462 CGATCATATGTAGTAGCAGGCAAG 59.139 45.833 1.90 0.00 0.00 4.01
854 1807 5.335976 CGATCATATGTAGTAGCAGGCAAGA 60.336 44.000 1.90 0.00 0.00 3.02
855 1808 6.617782 ATCATATGTAGTAGCAGGCAAGAT 57.382 37.500 1.90 0.00 0.00 2.40
856 1809 5.787380 TCATATGTAGTAGCAGGCAAGATG 58.213 41.667 1.90 0.00 0.00 2.90
857 1810 2.315925 TGTAGTAGCAGGCAAGATGC 57.684 50.000 0.00 0.00 44.08 3.91
873 1836 0.532862 ATGCAACCATCGATCGGGAC 60.533 55.000 16.41 5.73 0.00 4.46
888 1851 1.235281 GGGACGAAGCAAGGGTTGAC 61.235 60.000 0.00 0.00 0.00 3.18
892 1855 0.673644 CGAAGCAAGGGTTGACCGAT 60.674 55.000 0.00 0.00 46.96 4.18
894 1857 0.322546 AAGCAAGGGTTGACCGATCC 60.323 55.000 0.00 0.00 46.96 3.36
898 1861 0.919289 AAGGGTTGACCGATCCCCAT 60.919 55.000 5.40 0.00 46.96 4.00
900 1863 0.841289 GGGTTGACCGATCCCCATTA 59.159 55.000 0.00 0.00 37.09 1.90
922 1888 5.142061 ACATTAGTGTACAACCATCGACA 57.858 39.130 0.00 0.00 36.63 4.35
929 1895 2.779755 ACAACCATCGACATTGGCTA 57.220 45.000 3.39 0.00 37.81 3.93
937 1903 1.480545 TCGACATTGGCTAGCTGCTTA 59.519 47.619 15.72 0.00 42.39 3.09
938 1904 1.863454 CGACATTGGCTAGCTGCTTAG 59.137 52.381 15.72 4.66 42.39 2.18
939 1905 1.601430 GACATTGGCTAGCTGCTTAGC 59.399 52.381 15.72 14.17 44.20 3.09
941 1907 1.872313 CATTGGCTAGCTGCTTAGCTC 59.128 52.381 15.72 15.52 45.00 4.09
942 1908 0.179100 TTGGCTAGCTGCTTAGCTCG 60.179 55.000 15.72 0.71 45.00 5.03
943 1909 1.037579 TGGCTAGCTGCTTAGCTCGA 61.038 55.000 15.72 10.22 45.00 4.04
963 1933 3.181499 CGATCGTGGAAGTAGCTACAAGT 60.181 47.826 25.28 10.32 0.00 3.16
994 1964 1.258982 GCTACCGCAGACGAATCAATG 59.741 52.381 0.00 0.00 43.93 2.82
995 1965 1.860950 CTACCGCAGACGAATCAATGG 59.139 52.381 0.00 0.00 43.93 3.16
996 1966 0.744414 ACCGCAGACGAATCAATGGG 60.744 55.000 0.00 0.00 43.93 4.00
999 1969 1.740380 CGCAGACGAATCAATGGGAGT 60.740 52.381 0.00 0.00 43.93 3.85
1099 2077 1.484653 TCTACAACCACATCATCCGGG 59.515 52.381 0.00 0.00 0.00 5.73
1100 2078 1.484653 CTACAACCACATCATCCGGGA 59.515 52.381 0.00 0.00 0.00 5.14
1101 2079 0.918983 ACAACCACATCATCCGGGAT 59.081 50.000 2.97 2.97 0.00 3.85
1102 2080 1.134098 ACAACCACATCATCCGGGATC 60.134 52.381 6.55 0.00 0.00 3.36
1103 2081 0.474184 AACCACATCATCCGGGATCC 59.526 55.000 6.55 1.92 0.00 3.36
1236 2240 2.943690 CTGCTTGTCAATCTCCATGAGG 59.056 50.000 0.00 0.00 0.00 3.86
1602 2651 1.608542 CCGAACAACCGGTGGTATTCA 60.609 52.381 16.93 0.00 44.23 2.57
1633 2704 2.183300 GTGCACCGACTATGGCGA 59.817 61.111 5.22 0.00 0.00 5.54
1673 2755 2.438434 GGCAGCATTGTACGGCCT 60.438 61.111 0.00 0.00 43.98 5.19
1677 2759 1.676006 GCAGCATTGTACGGCCTATTT 59.324 47.619 0.00 0.00 0.00 1.40
1704 2786 2.683933 AAGGAGGGCGTGGACGAT 60.684 61.111 2.73 0.00 43.02 3.73
1710 2792 3.630148 GGCGTGGACGATGATGCG 61.630 66.667 2.73 0.00 43.02 4.73
1711 2793 2.582226 GCGTGGACGATGATGCGA 60.582 61.111 2.73 0.00 43.02 5.10
1764 2851 0.325296 ATGTCGGAGAACCTGGGCTA 60.325 55.000 0.00 0.00 39.69 3.93
1765 2852 1.255667 TGTCGGAGAACCTGGGCTAC 61.256 60.000 0.00 0.00 39.69 3.58
1766 2853 2.050350 TCGGAGAACCTGGGCTACG 61.050 63.158 14.92 14.92 39.77 3.51
1767 2854 2.901042 GGAGAACCTGGGCTACGG 59.099 66.667 0.00 0.00 0.00 4.02
1768 2855 2.187163 GAGAACCTGGGCTACGGC 59.813 66.667 0.00 0.00 37.82 5.68
1792 2879 1.293498 GGGAGAGCTCGAGCAACAA 59.707 57.895 36.87 0.00 45.16 2.83
1802 2889 0.657312 CGAGCAACAACAGCAACTGA 59.343 50.000 0.78 0.00 35.18 3.41
1902 2998 3.730761 CACCGCTGGAGCACAAGC 61.731 66.667 0.00 0.00 42.21 4.01
1951 3054 5.851703 GCCTCATTTCGACTTCAACTTAAAC 59.148 40.000 0.00 0.00 0.00 2.01
1952 3055 6.512741 GCCTCATTTCGACTTCAACTTAAACA 60.513 38.462 0.00 0.00 0.00 2.83
1987 3091 7.037297 TGACTTTTCTTTCTCCCTCCATTAGAT 60.037 37.037 0.00 0.00 0.00 1.98
2028 3132 2.096013 GGGAGTTCGAGCAGTAATTTGC 59.904 50.000 1.01 0.00 44.41 3.68
2071 3175 3.874392 ATAGGCACATTGGTTTGCTTC 57.126 42.857 0.00 0.00 38.85 3.86
2087 3191 1.406614 GCTTCCTGTAGCATGCTGAGT 60.407 52.381 30.42 6.42 40.89 3.41
2091 3195 1.539929 CCTGTAGCATGCTGAGTAGGC 60.540 57.143 30.42 0.00 0.00 3.93
2110 3214 8.868635 AGTAGGCAACGAGTATTTTATTAGAC 57.131 34.615 0.00 0.00 46.39 2.59
2112 3216 5.751990 AGGCAACGAGTATTTTATTAGACCG 59.248 40.000 0.00 0.00 46.39 4.79
2119 3223 8.125448 ACGAGTATTTTATTAGACCGTCTACAC 58.875 37.037 7.81 0.00 0.00 2.90
2134 3238 4.379603 CGTCTACACTCGGACTCTTCAAAT 60.380 45.833 0.00 0.00 0.00 2.32
2155 3259 6.540438 AATCGGCTCTATATTTCCGGATTA 57.460 37.500 4.15 0.16 41.98 1.75
2178 3282 1.606480 CGGCATCGCTCATATCCAACT 60.606 52.381 0.00 0.00 0.00 3.16
2179 3283 1.802960 GGCATCGCTCATATCCAACTG 59.197 52.381 0.00 0.00 0.00 3.16
2213 3317 1.207329 GTATGAGAAGGCCCGAACACT 59.793 52.381 0.00 0.00 0.00 3.55
2214 3318 1.568504 ATGAGAAGGCCCGAACACTA 58.431 50.000 0.00 0.00 0.00 2.74
2215 3319 0.606604 TGAGAAGGCCCGAACACTAC 59.393 55.000 0.00 0.00 0.00 2.73
2216 3320 0.108281 GAGAAGGCCCGAACACTACC 60.108 60.000 0.00 0.00 0.00 3.18
2217 3321 1.447314 GAAGGCCCGAACACTACCG 60.447 63.158 0.00 0.00 0.00 4.02
2218 3322 2.847435 GAAGGCCCGAACACTACCGG 62.847 65.000 0.00 0.00 44.94 5.28
2221 3325 3.697747 CCCGAACACTACCGGCCA 61.698 66.667 0.00 0.00 44.07 5.36
2222 3326 2.582436 CCGAACACTACCGGCCAT 59.418 61.111 0.00 0.00 39.22 4.40
2223 3327 1.813753 CCGAACACTACCGGCCATG 60.814 63.158 0.00 0.00 39.22 3.66
2224 3328 1.079405 CGAACACTACCGGCCATGT 60.079 57.895 0.00 0.95 0.00 3.21
2225 3329 1.082117 CGAACACTACCGGCCATGTC 61.082 60.000 0.00 0.00 0.00 3.06
2226 3330 1.079405 AACACTACCGGCCATGTCG 60.079 57.895 0.00 0.00 0.00 4.35
2233 3337 4.189580 CGGCCATGTCGGGGGAAT 62.190 66.667 2.24 0.00 34.06 3.01
2234 3338 2.519302 GGCCATGTCGGGGGAATG 60.519 66.667 0.00 0.00 34.06 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 165 3.749064 GCGGAGGCTGACGACAGA 61.749 66.667 19.07 0.00 46.03 3.41
399 413 6.211587 TGAAAGATTTGGGATAACATGCTG 57.788 37.500 0.00 0.00 0.00 4.41
400 414 5.361857 CCTGAAAGATTTGGGATAACATGCT 59.638 40.000 0.00 0.00 34.07 3.79
425 439 1.805869 CAGAGTGAGTGGGCTGAAAG 58.194 55.000 0.00 0.00 0.00 2.62
426 440 0.250467 GCAGAGTGAGTGGGCTGAAA 60.250 55.000 0.00 0.00 0.00 2.69
427 441 1.123861 AGCAGAGTGAGTGGGCTGAA 61.124 55.000 0.00 0.00 32.76 3.02
428 442 1.123861 AAGCAGAGTGAGTGGGCTGA 61.124 55.000 0.00 0.00 34.56 4.26
429 443 0.954449 CAAGCAGAGTGAGTGGGCTG 60.954 60.000 0.00 0.00 34.56 4.85
430 444 1.123861 TCAAGCAGAGTGAGTGGGCT 61.124 55.000 0.00 0.00 36.13 5.19
431 445 0.250467 TTCAAGCAGAGTGAGTGGGC 60.250 55.000 0.00 0.00 0.00 5.36
454 468 6.846350 AGTACATTAATTTTGCAGTGCTCTC 58.154 36.000 17.60 0.00 0.00 3.20
455 469 6.402550 CGAGTACATTAATTTTGCAGTGCTCT 60.403 38.462 17.60 0.00 36.84 4.09
478 493 3.932580 GATGTGCCTGCGACCACGA 62.933 63.158 0.00 0.00 42.66 4.35
483 498 3.104766 CATGGATGTGCCTGCGAC 58.895 61.111 0.00 0.00 37.63 5.19
493 508 2.425143 ACTTGGGTAGTGCATGGATG 57.575 50.000 0.00 0.00 35.19 3.51
494 509 2.158957 CGTACTTGGGTAGTGCATGGAT 60.159 50.000 0.00 0.00 39.21 3.41
495 510 1.206132 CGTACTTGGGTAGTGCATGGA 59.794 52.381 0.00 0.00 39.21 3.41
496 511 1.066430 ACGTACTTGGGTAGTGCATGG 60.066 52.381 0.00 0.00 39.21 3.66
504 519 5.372343 TCATCCTAGTACGTACTTGGGTA 57.628 43.478 38.31 27.79 45.36 3.69
506 521 5.301045 TCATTCATCCTAGTACGTACTTGGG 59.699 44.000 38.31 32.71 45.36 4.12
535 550 2.435372 TTTTGAACCTCACCTGCTGT 57.565 45.000 0.00 0.00 0.00 4.40
552 567 5.702209 CCTGCTGCCAATTTGTATTCTTTTT 59.298 36.000 0.00 0.00 0.00 1.94
553 568 5.221702 ACCTGCTGCCAATTTGTATTCTTTT 60.222 36.000 0.00 0.00 0.00 2.27
554 569 4.284234 ACCTGCTGCCAATTTGTATTCTTT 59.716 37.500 0.00 0.00 0.00 2.52
555 570 3.834231 ACCTGCTGCCAATTTGTATTCTT 59.166 39.130 0.00 0.00 0.00 2.52
556 571 3.194116 CACCTGCTGCCAATTTGTATTCT 59.806 43.478 0.00 0.00 0.00 2.40
557 572 3.056607 ACACCTGCTGCCAATTTGTATTC 60.057 43.478 0.00 0.00 0.00 1.75
558 573 2.899256 ACACCTGCTGCCAATTTGTATT 59.101 40.909 0.00 0.00 0.00 1.89
559 574 2.231964 CACACCTGCTGCCAATTTGTAT 59.768 45.455 0.00 0.00 0.00 2.29
560 575 1.612950 CACACCTGCTGCCAATTTGTA 59.387 47.619 0.00 0.00 0.00 2.41
561 576 0.390124 CACACCTGCTGCCAATTTGT 59.610 50.000 0.00 0.00 0.00 2.83
562 577 0.320073 CCACACCTGCTGCCAATTTG 60.320 55.000 0.00 0.00 0.00 2.32
563 578 0.760189 ACCACACCTGCTGCCAATTT 60.760 50.000 0.00 0.00 0.00 1.82
564 579 0.760189 AACCACACCTGCTGCCAATT 60.760 50.000 0.00 0.00 0.00 2.32
565 580 1.152483 AACCACACCTGCTGCCAAT 60.152 52.632 0.00 0.00 0.00 3.16
566 581 1.827789 GAACCACACCTGCTGCCAA 60.828 57.895 0.00 0.00 0.00 4.52
567 582 2.203337 GAACCACACCTGCTGCCA 60.203 61.111 0.00 0.00 0.00 4.92
568 583 1.799258 CTTGAACCACACCTGCTGCC 61.799 60.000 0.00 0.00 0.00 4.85
569 584 0.819259 TCTTGAACCACACCTGCTGC 60.819 55.000 0.00 0.00 0.00 5.25
570 585 1.679139 TTCTTGAACCACACCTGCTG 58.321 50.000 0.00 0.00 0.00 4.41
571 586 2.092429 TCTTTCTTGAACCACACCTGCT 60.092 45.455 0.00 0.00 0.00 4.24
572 587 2.297701 TCTTTCTTGAACCACACCTGC 58.702 47.619 0.00 0.00 0.00 4.85
573 588 3.947834 ACTTCTTTCTTGAACCACACCTG 59.052 43.478 0.00 0.00 0.00 4.00
574 589 4.236527 ACTTCTTTCTTGAACCACACCT 57.763 40.909 0.00 0.00 0.00 4.00
579 594 7.120923 ACTAGTGTACTTCTTTCTTGAACCA 57.879 36.000 0.00 0.00 0.00 3.67
604 619 9.924650 CCAGTTAAGTTTACAATCTAGTACTGT 57.075 33.333 5.39 0.00 0.00 3.55
607 622 8.534496 TCCCCAGTTAAGTTTACAATCTAGTAC 58.466 37.037 0.00 0.00 0.00 2.73
608 623 8.669055 TCCCCAGTTAAGTTTACAATCTAGTA 57.331 34.615 0.00 0.00 0.00 1.82
609 624 7.563724 TCCCCAGTTAAGTTTACAATCTAGT 57.436 36.000 0.00 0.00 0.00 2.57
610 625 7.881232 TGTTCCCCAGTTAAGTTTACAATCTAG 59.119 37.037 0.00 0.00 0.00 2.43
668 708 6.651975 AGTAACTTATTGCTAGGCGTAGAT 57.348 37.500 17.40 5.37 0.00 1.98
683 1614 7.613022 TGCAGGTAGCTTTAGAGTAGTAACTTA 59.387 37.037 0.00 0.00 45.94 2.24
692 1623 2.637872 TGGTTGCAGGTAGCTTTAGAGT 59.362 45.455 0.00 0.00 45.94 3.24
693 1624 3.334583 TGGTTGCAGGTAGCTTTAGAG 57.665 47.619 0.00 0.00 45.94 2.43
694 1625 3.072476 ACTTGGTTGCAGGTAGCTTTAGA 59.928 43.478 0.00 0.00 45.94 2.10
699 1630 1.059913 AGACTTGGTTGCAGGTAGCT 58.940 50.000 0.00 0.00 45.94 3.32
701 1632 3.589988 CTGTAGACTTGGTTGCAGGTAG 58.410 50.000 0.00 0.00 0.00 3.18
702 1633 2.301870 CCTGTAGACTTGGTTGCAGGTA 59.698 50.000 0.00 0.00 38.80 3.08
709 1640 3.463944 CGACAAACCTGTAGACTTGGTT 58.536 45.455 0.00 0.00 44.92 3.67
791 1742 2.359230 AGTGAGAAGCCGCAAGCC 60.359 61.111 0.00 0.00 45.47 4.35
813 1766 4.947883 TGATCGGGTATATCTGGGAGAAT 58.052 43.478 0.00 0.00 0.00 2.40
833 1786 5.787380 CATCTTGCCTGCTACTACATATGA 58.213 41.667 10.38 0.00 0.00 2.15
837 1790 2.171237 TGCATCTTGCCTGCTACTACAT 59.829 45.455 0.00 0.00 44.23 2.29
839 1792 2.315925 TGCATCTTGCCTGCTACTAC 57.684 50.000 0.00 0.00 44.23 2.73
842 1795 0.453390 GGTTGCATCTTGCCTGCTAC 59.547 55.000 0.00 2.04 44.23 3.58
843 1796 0.038021 TGGTTGCATCTTGCCTGCTA 59.962 50.000 0.00 0.00 44.23 3.49
844 1797 0.613853 ATGGTTGCATCTTGCCTGCT 60.614 50.000 0.00 0.00 44.23 4.24
845 1798 0.179119 GATGGTTGCATCTTGCCTGC 60.179 55.000 0.00 0.00 44.23 4.85
846 1799 0.099968 CGATGGTTGCATCTTGCCTG 59.900 55.000 0.00 0.00 44.23 4.85
847 1800 0.035152 TCGATGGTTGCATCTTGCCT 60.035 50.000 0.00 0.00 44.23 4.75
848 1801 1.002033 GATCGATGGTTGCATCTTGCC 60.002 52.381 0.54 0.00 44.23 4.52
849 1802 1.333524 CGATCGATGGTTGCATCTTGC 60.334 52.381 10.26 0.00 45.29 4.01
850 1803 1.262417 CCGATCGATGGTTGCATCTTG 59.738 52.381 18.66 0.00 0.00 3.02
851 1804 1.586422 CCGATCGATGGTTGCATCTT 58.414 50.000 18.66 0.00 0.00 2.40
852 1805 0.250038 CCCGATCGATGGTTGCATCT 60.250 55.000 18.66 0.00 0.00 2.90
853 1806 0.249868 TCCCGATCGATGGTTGCATC 60.250 55.000 18.66 0.00 0.00 3.91
854 1807 0.532862 GTCCCGATCGATGGTTGCAT 60.533 55.000 18.66 0.00 0.00 3.96
855 1808 1.153449 GTCCCGATCGATGGTTGCA 60.153 57.895 18.66 0.00 0.00 4.08
856 1809 2.237751 CGTCCCGATCGATGGTTGC 61.238 63.158 18.66 4.80 0.00 4.17
857 1810 0.179121 TTCGTCCCGATCGATGGTTG 60.179 55.000 18.66 7.40 37.18 3.77
858 1811 0.102481 CTTCGTCCCGATCGATGGTT 59.898 55.000 18.66 0.00 37.18 3.67
859 1812 1.734137 CTTCGTCCCGATCGATGGT 59.266 57.895 18.66 0.00 37.18 3.55
860 1813 1.661821 GCTTCGTCCCGATCGATGG 60.662 63.158 18.66 10.61 37.18 3.51
861 1814 0.527600 TTGCTTCGTCCCGATCGATG 60.528 55.000 18.66 7.52 37.18 3.84
873 1836 0.673644 ATCGGTCAACCCTTGCTTCG 60.674 55.000 0.00 0.00 0.00 3.79
881 1844 0.841289 TAATGGGGATCGGTCAACCC 59.159 55.000 3.16 3.16 43.64 4.11
888 1851 4.351874 ACACTAATGTAATGGGGATCGG 57.648 45.455 0.00 0.00 37.26 4.18
892 1855 5.251005 TGGTTGTACACTAATGTAATGGGGA 59.749 40.000 0.00 0.00 42.99 4.81
894 1857 6.018262 CGATGGTTGTACACTAATGTAATGGG 60.018 42.308 0.00 0.00 42.99 4.00
898 1861 6.689554 TGTCGATGGTTGTACACTAATGTAA 58.310 36.000 0.00 0.00 42.99 2.41
900 1863 5.142061 TGTCGATGGTTGTACACTAATGT 57.858 39.130 0.00 0.00 43.30 2.71
937 1903 0.382515 GCTACTTCCACGATCGAGCT 59.617 55.000 24.34 0.00 0.00 4.09
938 1904 0.382515 AGCTACTTCCACGATCGAGC 59.617 55.000 24.34 17.80 0.00 5.03
939 1905 2.612672 TGTAGCTACTTCCACGATCGAG 59.387 50.000 24.34 14.64 0.00 4.04
940 1906 2.635714 TGTAGCTACTTCCACGATCGA 58.364 47.619 24.34 0.00 0.00 3.59
941 1907 3.181499 ACTTGTAGCTACTTCCACGATCG 60.181 47.826 23.84 14.88 0.00 3.69
942 1908 4.352887 GACTTGTAGCTACTTCCACGATC 58.647 47.826 23.84 7.37 0.00 3.69
943 1909 3.130693 GGACTTGTAGCTACTTCCACGAT 59.869 47.826 23.84 2.12 0.00 3.73
994 1964 1.732417 GACGGACGTCCCATACTCCC 61.732 65.000 28.52 1.12 39.08 4.30
995 1965 1.732308 GACGGACGTCCCATACTCC 59.268 63.158 28.52 1.93 39.08 3.85
996 1966 1.354506 CGACGGACGTCCCATACTC 59.645 63.158 28.52 13.58 41.76 2.59
1105 2083 4.374702 CAGCAACAGACGCCGTGC 62.375 66.667 0.00 0.00 0.00 5.34
1115 2093 2.343758 GACGGAGCTCCAGCAACA 59.656 61.111 31.67 0.00 45.16 3.33
1117 2095 3.706373 GGGACGGAGCTCCAGCAA 61.706 66.667 31.67 0.00 45.16 3.91
1236 2240 0.614134 ACGGACCTGTTCCCTAGGAC 60.614 60.000 11.48 1.30 42.27 3.85
1651 2722 4.536687 GTACAATGCTGCCGCGCC 62.537 66.667 0.00 0.00 39.65 6.53
1652 2723 4.868900 CGTACAATGCTGCCGCGC 62.869 66.667 0.00 0.00 39.65 6.86
1673 2755 3.137459 CCTTGCCGCCGCCAAATA 61.137 61.111 0.00 0.00 0.00 1.40
1745 2829 0.325296 TAGCCCAGGTTCTCCGACAT 60.325 55.000 0.00 0.00 39.05 3.06
1769 2856 3.522731 CTCGAGCTCTCCCCGTGG 61.523 72.222 12.85 0.00 0.00 4.94
1770 2857 4.200283 GCTCGAGCTCTCCCCGTG 62.200 72.222 29.88 0.68 38.21 4.94
1792 2879 1.226746 GCCGTAGTTTCAGTTGCTGT 58.773 50.000 0.00 0.00 32.61 4.40
1802 2889 3.688159 ACCTCGCCGCCGTAGTTT 61.688 61.111 0.00 0.00 35.54 2.66
1902 2998 3.368190 CTGGGCAGGACAGCGAGAG 62.368 68.421 0.00 0.00 34.64 3.20
1911 3007 2.596851 GGCTCTGTTCTGGGCAGGA 61.597 63.158 4.16 0.00 34.89 3.86
1951 3054 8.293157 GGGAGAAAGAAAAGTCAGAACTATTTG 58.707 37.037 0.00 0.00 33.48 2.32
1952 3055 8.221251 AGGGAGAAAGAAAAGTCAGAACTATTT 58.779 33.333 0.00 0.00 33.48 1.40
2028 3132 2.105006 AATGGTACTGCTCTGTGCTG 57.895 50.000 6.99 6.99 44.70 4.41
2071 3175 1.539929 GCCTACTCAGCATGCTACAGG 60.540 57.143 22.19 22.39 34.76 4.00
2087 3191 6.919662 CGGTCTAATAAAATACTCGTTGCCTA 59.080 38.462 0.00 0.00 0.00 3.93
2091 3195 7.982371 AGACGGTCTAATAAAATACTCGTTG 57.018 36.000 9.33 0.00 0.00 4.10
2112 3216 4.500603 TTTGAAGAGTCCGAGTGTAGAC 57.499 45.455 0.00 0.00 0.00 2.59
2119 3223 1.134965 AGCCGATTTGAAGAGTCCGAG 60.135 52.381 0.00 0.00 0.00 4.63
2124 3228 6.931840 GGAAATATAGAGCCGATTTGAAGAGT 59.068 38.462 0.00 0.00 0.00 3.24
2134 3238 5.337009 GGTTAATCCGGAAATATAGAGCCGA 60.337 44.000 9.01 0.00 46.29 5.54
2163 3267 5.282055 AGATTTCAGTTGGATATGAGCGA 57.718 39.130 0.00 0.00 0.00 4.93
2165 3269 6.648725 GTCCTAGATTTCAGTTGGATATGAGC 59.351 42.308 0.00 0.00 0.00 4.26
2178 3282 4.800023 TCTCATACCCGTCCTAGATTTCA 58.200 43.478 0.00 0.00 0.00 2.69
2179 3283 5.279056 CCTTCTCATACCCGTCCTAGATTTC 60.279 48.000 0.00 0.00 0.00 2.17
2216 3320 4.189580 ATTCCCCCGACATGGCCG 62.190 66.667 0.00 0.00 35.87 6.13
2217 3321 2.519302 CATTCCCCCGACATGGCC 60.519 66.667 0.00 0.00 35.87 5.36


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

AutoCloner maintained by Alex Coulton.