Multiple sequence alignment - TraesCS3A01G354900

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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 TraesCS3A01G354900 chr3A 100.000 3481 0 0 1 3481 602850524 602854004 0 6429
1 TraesCS3A01G354900 chr3D 89.651 3005 192 51 1 2928 460437002 460439964 0 3716
2 TraesCS3A01G354900 chr3D 94.964 556 18 5 2922 3473 460441142 460441691 0 863
3 TraesCS3A01G354900 chr3B 92.041 2073 107 20 800 2855 610531949 610533980 0 2861
4 TraesCS3A01G354900 chr3B 87.874 635 51 14 2849 3468 610534007 610534630 0 723


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 TraesCS3A01G354900 chr3A 602850524 602854004 3480 False 6429.0 6429 100.0000 1 3481 1 chr3A.!!$F1 3480
1 TraesCS3A01G354900 chr3D 460437002 460441691 4689 False 2289.5 3716 92.3075 1 3473 2 chr3D.!!$F1 3472
2 TraesCS3A01G354900 chr3B 610531949 610534630 2681 False 1792.0 2861 89.9575 800 3468 2 chr3B.!!$F1 2668

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
201 205 0.545309 ACTGCCTGGCAAGTCCTAGA 60.545 55.0 23.51 0.0 38.41 2.43 F
456 460 1.179174 TCGTGTGTCAGTGGAGAGGG 61.179 60.0 0.00 0.0 0.00 4.30 F
1514 1571 0.822944 TGTCGTCCCACAAGACCGTA 60.823 55.0 0.00 0.0 34.24 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1556 0.109412 CGTCTACGGTCTTGTGGGAC 60.109 60.0 0.00 0.00 35.37 4.46 R
1960 2017 0.746204 TGAGCAGTTTGGCGTGAACA 60.746 50.0 0.00 0.00 39.27 3.18 R
2693 2791 0.320247 CAGTGGGACAGTCAGCTCAC 60.320 60.0 2.17 5.35 41.96 3.51 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
34 35 6.760298 GCAGTCTCATGAATGTCAGATTTCTA 59.240 38.462 0.00 0.00 40.08 2.10
48 49 1.448985 TTTCTACTTGGCGGTGATGC 58.551 50.000 0.00 0.00 0.00 3.91
77 78 2.005451 CCAGTGATGTGACAGCTTAGC 58.995 52.381 1.47 0.00 0.00 3.09
84 85 1.974875 TGACAGCTTAGCCGTCCGA 60.975 57.895 16.73 0.00 0.00 4.55
89 90 1.108776 AGCTTAGCCGTCCGAATGTA 58.891 50.000 0.00 0.00 0.00 2.29
91 92 2.093869 AGCTTAGCCGTCCGAATGTAAA 60.094 45.455 0.00 0.00 0.00 2.01
125 126 3.646162 TGGATCTTGTGGTGTAGTGACTT 59.354 43.478 0.00 0.00 0.00 3.01
141 142 3.004629 GTGACTTGTGTGGCAATGATGAA 59.995 43.478 0.00 0.00 36.36 2.57
149 150 3.010027 TGTGGCAATGATGAAGGGTAGAA 59.990 43.478 0.00 0.00 0.00 2.10
153 154 4.578105 GGCAATGATGAAGGGTAGAAAGAG 59.422 45.833 0.00 0.00 0.00 2.85
157 158 3.452627 TGATGAAGGGTAGAAAGAGGAGC 59.547 47.826 0.00 0.00 0.00 4.70
159 160 4.332683 TGAAGGGTAGAAAGAGGAGCTA 57.667 45.455 0.00 0.00 0.00 3.32
187 191 2.229792 TGTCATTCCTTGTTGACTGCC 58.770 47.619 4.86 0.00 42.17 4.85
191 195 0.823356 TTCCTTGTTGACTGCCTGGC 60.823 55.000 12.87 12.87 0.00 4.85
193 197 1.108727 CCTTGTTGACTGCCTGGCAA 61.109 55.000 23.51 4.95 42.29 4.52
201 205 0.545309 ACTGCCTGGCAAGTCCTAGA 60.545 55.000 23.51 0.00 38.41 2.43
221 225 6.655003 CCTAGATTTGTCCTTGCAACTTCTTA 59.345 38.462 0.00 0.00 0.00 2.10
233 237 4.752604 TGCAACTTCTTATTTGTGTAGCGA 59.247 37.500 0.00 0.00 0.00 4.93
290 294 4.233789 GCAACAATGATACCTTGCGAAAA 58.766 39.130 0.00 0.00 30.45 2.29
298 302 6.474140 TGATACCTTGCGAAAAGTAGGATA 57.526 37.500 0.00 0.00 0.00 2.59
317 321 4.104102 GGATATACACCCAACAATCTCCCA 59.896 45.833 0.00 0.00 0.00 4.37
320 324 5.725551 ATACACCCAACAATCTCCCATAA 57.274 39.130 0.00 0.00 0.00 1.90
329 333 2.040009 ATCTCCCATAACACGCGGGG 62.040 60.000 15.46 11.90 40.68 5.73
330 334 4.476752 TCCCATAACACGCGGGGC 62.477 66.667 15.46 0.00 40.68 5.80
366 370 3.640231 GCATCTCTCATGCGAGGC 58.360 61.111 12.62 5.62 39.95 4.70
393 397 2.526432 TCTAAGTCGAGCTCCCAGTTT 58.474 47.619 8.47 0.00 0.00 2.66
398 402 1.531578 GTCGAGCTCCCAGTTTTTGAC 59.468 52.381 8.47 2.48 0.00 3.18
399 403 1.416401 TCGAGCTCCCAGTTTTTGACT 59.584 47.619 8.47 0.00 39.89 3.41
414 418 6.310224 AGTTTTTGACTTGTTTGATCGGTTTG 59.690 34.615 0.00 0.00 33.92 2.93
430 434 3.317150 GGTTTGTTTAGCATGAACTGGC 58.683 45.455 0.00 0.00 0.00 4.85
432 436 2.284754 TGTTTAGCATGAACTGGCCA 57.715 45.000 4.71 4.71 0.00 5.36
433 437 2.806434 TGTTTAGCATGAACTGGCCAT 58.194 42.857 5.51 0.00 0.00 4.40
437 441 4.712051 TTAGCATGAACTGGCCATATCT 57.288 40.909 5.51 0.00 0.00 1.98
438 442 3.137446 AGCATGAACTGGCCATATCTC 57.863 47.619 5.51 0.78 0.00 2.75
450 454 2.814269 CCATATCTCGTGTGTCAGTGG 58.186 52.381 0.00 0.00 0.00 4.00
451 455 2.427095 CCATATCTCGTGTGTCAGTGGA 59.573 50.000 0.00 0.00 0.00 4.02
452 456 3.489908 CCATATCTCGTGTGTCAGTGGAG 60.490 52.174 0.00 0.00 0.00 3.86
453 457 1.911057 ATCTCGTGTGTCAGTGGAGA 58.089 50.000 0.00 0.00 38.06 3.71
454 458 1.239347 TCTCGTGTGTCAGTGGAGAG 58.761 55.000 0.00 0.00 30.75 3.20
456 460 1.179174 TCGTGTGTCAGTGGAGAGGG 61.179 60.000 0.00 0.00 0.00 4.30
457 461 1.179174 CGTGTGTCAGTGGAGAGGGA 61.179 60.000 0.00 0.00 0.00 4.20
458 462 1.270907 GTGTGTCAGTGGAGAGGGAT 58.729 55.000 0.00 0.00 0.00 3.85
459 463 1.625818 GTGTGTCAGTGGAGAGGGATT 59.374 52.381 0.00 0.00 0.00 3.01
463 475 4.536090 TGTGTCAGTGGAGAGGGATTATTT 59.464 41.667 0.00 0.00 0.00 1.40
467 479 5.946377 GTCAGTGGAGAGGGATTATTTGTTT 59.054 40.000 0.00 0.00 0.00 2.83
490 502 5.482006 TGTCATCAATGATTGAGTCGAAGT 58.518 37.500 13.79 0.00 43.98 3.01
491 503 5.578336 TGTCATCAATGATTGAGTCGAAGTC 59.422 40.000 13.79 0.61 43.98 3.01
525 537 6.461092 GGGAAGACGTGATGACAATGATAGTA 60.461 42.308 0.00 0.00 0.00 1.82
557 569 5.437191 ACCTCGACAATATTCCTTTCCTT 57.563 39.130 0.00 0.00 0.00 3.36
558 570 5.816682 ACCTCGACAATATTCCTTTCCTTT 58.183 37.500 0.00 0.00 0.00 3.11
566 578 6.667414 ACAATATTCCTTTCCTTTGTGGCATA 59.333 34.615 0.00 0.00 35.26 3.14
574 586 3.119319 TCCTTTGTGGCATATGGGTCTA 58.881 45.455 4.56 0.00 35.26 2.59
586 598 5.065218 GCATATGGGTCTATTTGGATAAGCG 59.935 44.000 4.56 0.00 0.00 4.68
595 607 3.857038 GGATAAGCGGGTCGGGCA 61.857 66.667 0.00 0.00 0.00 5.36
631 643 7.809546 TTTATGGGCGTGATGTATCATTTTA 57.190 32.000 0.00 0.00 39.30 1.52
632 644 5.947228 ATGGGCGTGATGTATCATTTTAG 57.053 39.130 0.00 0.00 39.30 1.85
633 645 5.029807 TGGGCGTGATGTATCATTTTAGA 57.970 39.130 0.00 0.00 39.30 2.10
634 646 5.432645 TGGGCGTGATGTATCATTTTAGAA 58.567 37.500 0.00 0.00 39.30 2.10
635 647 5.883115 TGGGCGTGATGTATCATTTTAGAAA 59.117 36.000 0.00 0.00 39.30 2.52
636 648 6.375736 TGGGCGTGATGTATCATTTTAGAAAA 59.624 34.615 0.00 0.00 39.30 2.29
637 649 6.691388 GGGCGTGATGTATCATTTTAGAAAAC 59.309 38.462 0.00 0.00 39.30 2.43
638 650 7.415206 GGGCGTGATGTATCATTTTAGAAAACT 60.415 37.037 0.00 0.00 39.30 2.66
639 651 7.429340 GGCGTGATGTATCATTTTAGAAAACTG 59.571 37.037 0.00 0.00 39.30 3.16
640 652 7.962918 GCGTGATGTATCATTTTAGAAAACTGT 59.037 33.333 0.00 0.00 39.30 3.55
662 700 7.610305 ACTGTTTTTAATCTATGGACCGAACAT 59.390 33.333 0.00 0.00 0.00 2.71
663 701 8.343168 TGTTTTTAATCTATGGACCGAACATT 57.657 30.769 0.00 0.00 0.00 2.71
670 708 4.897076 TCTATGGACCGAACATTAAGGCTA 59.103 41.667 0.00 0.00 0.00 3.93
714 761 3.909732 TCTTTCTGAGGCAAGGGAAAAA 58.090 40.909 0.00 0.00 0.00 1.94
717 764 4.871933 TTCTGAGGCAAGGGAAAAATTC 57.128 40.909 0.00 0.00 0.00 2.17
774 824 7.656542 GGTATTCCAAGTATTTACAGAGGTAGC 59.343 40.741 0.00 0.00 0.00 3.58
781 831 9.250624 CAAGTATTTACAGAGGTAGCAGTATTC 57.749 37.037 0.00 0.00 0.00 1.75
789 839 6.819146 ACAGAGGTAGCAGTATTCTTTTTAGC 59.181 38.462 0.00 0.00 0.00 3.09
790 840 6.258947 CAGAGGTAGCAGTATTCTTTTTAGCC 59.741 42.308 0.00 0.00 0.00 3.93
793 843 6.044682 GGTAGCAGTATTCTTTTTAGCCGTA 58.955 40.000 0.00 0.00 0.00 4.02
795 845 7.064966 GGTAGCAGTATTCTTTTTAGCCGTAAA 59.935 37.037 0.00 0.00 0.00 2.01
797 847 7.303261 AGCAGTATTCTTTTTAGCCGTAAAAC 58.697 34.615 0.00 0.00 37.76 2.43
798 848 7.174426 AGCAGTATTCTTTTTAGCCGTAAAACT 59.826 33.333 0.00 0.00 37.76 2.66
824 874 6.757897 ATTTATGAGCATTTCTCCGTTTCA 57.242 33.333 0.00 0.00 41.18 2.69
847 897 3.713826 ATTTACTTCTCTTTGGGCCGA 57.286 42.857 0.00 0.00 0.00 5.54
911 961 3.125316 CCAGACAATTAAAGTCCGACAGC 59.875 47.826 0.40 0.00 36.68 4.40
935 985 2.677979 GCTGCCGTTCTTTCCCGAC 61.678 63.158 0.00 0.00 0.00 4.79
938 988 2.341176 CCGTTCTTTCCCGACCGT 59.659 61.111 0.00 0.00 0.00 4.83
960 1010 2.161609 GCCTCAACAAATACCGAACCAG 59.838 50.000 0.00 0.00 0.00 4.00
965 1015 1.472480 ACAAATACCGAACCAGCATGC 59.528 47.619 10.51 10.51 31.97 4.06
974 1024 2.157738 GAACCAGCATGCTCTCTGTTT 58.842 47.619 19.68 1.60 31.97 2.83
1308 1365 2.981302 CACGGCACCATCTCTCCA 59.019 61.111 0.00 0.00 0.00 3.86
1309 1366 1.448540 CACGGCACCATCTCTCCAC 60.449 63.158 0.00 0.00 0.00 4.02
1310 1367 2.187946 CGGCACCATCTCTCCACC 59.812 66.667 0.00 0.00 0.00 4.61
1311 1368 2.592308 GGCACCATCTCTCCACCC 59.408 66.667 0.00 0.00 0.00 4.61
1321 1378 4.372656 CATCTCTCCACCCGTTAATTCTC 58.627 47.826 0.00 0.00 0.00 2.87
1322 1379 3.709587 TCTCTCCACCCGTTAATTCTCT 58.290 45.455 0.00 0.00 0.00 3.10
1323 1380 3.447586 TCTCTCCACCCGTTAATTCTCTG 59.552 47.826 0.00 0.00 0.00 3.35
1327 1384 2.615493 CCACCCGTTAATTCTCTGCTGT 60.615 50.000 0.00 0.00 0.00 4.40
1332 1389 4.508124 CCCGTTAATTCTCTGCTGTATCAC 59.492 45.833 0.00 0.00 0.00 3.06
1362 1419 3.887110 TGTCATTCTGCCATGGATTCATC 59.113 43.478 18.40 0.00 0.00 2.92
1365 1422 3.836365 TTCTGCCATGGATTCATCGTA 57.164 42.857 18.40 0.00 0.00 3.43
1383 1440 3.437741 TCGTACTGAAGCTGAACGATGTA 59.562 43.478 0.00 0.00 37.63 2.29
1389 1446 9.459640 GTACTGAAGCTGAACGATGTATTATTA 57.540 33.333 0.00 0.00 0.00 0.98
1514 1571 0.822944 TGTCGTCCCACAAGACCGTA 60.823 55.000 0.00 0.00 34.24 4.02
1652 1709 2.190578 CAGATCAAGCCCGGGTCC 59.809 66.667 24.63 6.10 0.00 4.46
1911 1968 3.660865 CACCTCTACAACAACTACACCC 58.339 50.000 0.00 0.00 0.00 4.61
1960 2017 4.363990 CGTGGAGTCGCAGGTGCT 62.364 66.667 0.00 0.00 39.32 4.40
1969 2026 4.030452 GCAGGTGCTGTTCACGCC 62.030 66.667 0.00 0.00 46.56 5.68
1982 2039 2.401583 TCACGCCAAACTGCTCATAT 57.598 45.000 0.00 0.00 0.00 1.78
1983 2040 2.279741 TCACGCCAAACTGCTCATATC 58.720 47.619 0.00 0.00 0.00 1.63
2020 2082 4.103357 CGTGTAGTGTGTAGTGCTAATCC 58.897 47.826 0.00 0.00 0.00 3.01
2032 2094 1.702491 GCTAATCCGCACGGTTGGTC 61.702 60.000 9.23 0.00 36.47 4.02
2038 2100 2.345991 GCACGGTTGGTCTGGCTA 59.654 61.111 0.00 0.00 0.00 3.93
2087 2149 2.040412 GAGGCAGGGGAGAAGAAGAAAA 59.960 50.000 0.00 0.00 0.00 2.29
2107 2169 2.425578 TGTTCACGTACATGAGCGAA 57.574 45.000 17.35 4.42 32.85 4.70
2152 2218 2.225467 GGGCCTTACAGATCTGCATTC 58.775 52.381 22.83 8.15 0.00 2.67
2216 2282 2.813042 GCGGACAGAGACTGCAGC 60.813 66.667 15.27 6.85 39.19 5.25
2397 2463 1.979155 CTCCTCGAGTCCTGCACCA 60.979 63.158 12.31 0.00 0.00 4.17
2459 2528 3.292936 GCACCTGCTGCTGCTGTT 61.293 61.111 17.00 1.63 43.33 3.16
2460 2529 2.643272 CACCTGCTGCTGCTGTTG 59.357 61.111 17.00 11.05 40.48 3.33
2461 2530 3.292936 ACCTGCTGCTGCTGTTGC 61.293 61.111 17.00 4.76 40.48 4.17
2462 2531 2.984155 CCTGCTGCTGCTGTTGCT 60.984 61.111 17.00 0.00 40.48 3.91
2463 2532 2.255554 CTGCTGCTGCTGTTGCTG 59.744 61.111 17.00 4.65 40.48 4.41
2469 2538 4.266983 CTGCTGTTGCTGCTACGA 57.733 55.556 9.51 0.00 40.48 3.43
2470 2539 1.784062 CTGCTGTTGCTGCTACGAC 59.216 57.895 9.51 4.82 40.48 4.34
2471 2540 0.945743 CTGCTGTTGCTGCTACGACA 60.946 55.000 9.51 8.80 40.48 4.35
2472 2541 0.320683 TGCTGTTGCTGCTACGACAT 60.321 50.000 9.51 0.00 40.48 3.06
2473 2542 0.371645 GCTGTTGCTGCTACGACATC 59.628 55.000 9.51 0.00 33.48 3.06
2474 2543 2.001812 CTGTTGCTGCTACGACATCT 57.998 50.000 9.51 0.00 33.48 2.90
2475 2544 1.657594 CTGTTGCTGCTACGACATCTG 59.342 52.381 9.51 0.00 33.48 2.90
2476 2545 1.000843 TGTTGCTGCTACGACATCTGT 59.999 47.619 9.51 0.00 0.00 3.41
2513 2604 7.028962 TGAAATTTTAGAGCACGATCCAAATG 58.971 34.615 0.00 0.00 0.00 2.32
2547 2638 4.737054 ACAATAACGAACCACCGTACTAG 58.263 43.478 0.00 0.00 42.54 2.57
2548 2639 2.919666 TAACGAACCACCGTACTAGC 57.080 50.000 0.00 0.00 42.54 3.42
2571 2668 8.913487 AGCATTATGTTTGACAGATATGATCA 57.087 30.769 0.00 0.00 0.00 2.92
2572 2669 9.346005 AGCATTATGTTTGACAGATATGATCAA 57.654 29.630 0.00 0.00 0.00 2.57
2603 2700 3.243234 ACGAACGATATCTGAAGCTCTGG 60.243 47.826 0.34 0.00 0.00 3.86
2616 2713 2.950781 AGCTCTGGATTCCATAGTCGA 58.049 47.619 16.85 5.85 31.46 4.20
2685 2783 3.243177 GGAATAAGATTGCGACGTGACTC 59.757 47.826 0.00 0.00 0.00 3.36
2693 2791 1.132453 TGCGACGTGACTCAGAATAGG 59.868 52.381 0.00 0.00 0.00 2.57
2697 2795 3.486043 CGACGTGACTCAGAATAGGTGAG 60.486 52.174 0.00 0.00 45.94 3.51
2706 2804 3.445450 TCAGAATAGGTGAGCTGACTGTC 59.555 47.826 2.58 0.00 32.85 3.51
2720 2818 3.176411 TGACTGTCCCACTGATTCTGAT 58.824 45.455 5.17 0.00 0.00 2.90
2734 2832 0.867329 TCTGATCGAATGCACTCGCG 60.867 55.000 13.61 0.00 42.97 5.87
2735 2833 2.243810 GATCGAATGCACTCGCGC 59.756 61.111 13.61 3.10 42.97 6.86
2771 2869 1.169661 TTGTTTTCCATGCTCGCCGT 61.170 50.000 0.00 0.00 0.00 5.68
2772 2870 1.134694 GTTTTCCATGCTCGCCGTC 59.865 57.895 0.00 0.00 0.00 4.79
2773 2871 2.387445 TTTTCCATGCTCGCCGTCG 61.387 57.895 0.00 0.00 0.00 5.12
2783 2881 2.126228 CGCCGTCGCTGGAGTTTA 60.126 61.111 0.00 0.00 0.00 2.01
2813 2912 6.487103 GCAAGTTGTAGATTTAAATCTCCCG 58.513 40.000 29.45 15.19 44.30 5.14
2847 2946 0.250424 TGTCACCATCTGCACACAGG 60.250 55.000 0.00 0.00 44.59 4.00
2863 2995 2.023882 GGCTCGTACTACGCCGTC 59.976 66.667 0.00 0.00 42.21 4.79
2876 3008 2.349755 CCGTCCCATTCCGTTGGT 59.650 61.111 0.00 0.00 34.77 3.67
3051 4372 2.618709 GCCATGGTATGTTAAGGAGCAC 59.381 50.000 14.67 0.00 0.00 4.40
3160 4481 6.323996 TCAAGTATGAAGAGGTCGGTTCATAT 59.676 38.462 7.77 0.00 43.88 1.78
3181 4502 2.357517 CCGCAGCACTCCGAAGTT 60.358 61.111 0.00 0.00 31.71 2.66
3192 4513 3.060070 CACTCCGAAGTTTAAACACGGTC 60.060 47.826 33.79 20.37 44.77 4.79
3239 4563 5.127693 TGCTAACTCTGAAGTCTGAACTC 57.872 43.478 0.00 0.00 33.48 3.01
3298 4622 1.915614 CTGTTCACCTGCGCATGGAC 61.916 60.000 26.07 20.68 0.00 4.02
3353 4678 1.002257 TGCCATGGTACCAGTGCAG 60.002 57.895 28.16 13.79 33.49 4.41
3355 4680 1.308069 GCCATGGTACCAGTGCAGTG 61.308 60.000 25.69 14.95 0.00 3.66
3356 4681 1.308069 CCATGGTACCAGTGCAGTGC 61.308 60.000 21.41 8.58 0.00 4.40
3357 4682 0.606130 CATGGTACCAGTGCAGTGCA 60.606 55.000 21.41 15.37 35.60 4.57
3425 4756 3.279434 ACAAGTGTTCTTCTTGGTGTCC 58.721 45.455 9.82 0.00 44.29 4.02
3475 4806 5.925397 CAGTGTATCAATGAGAGATACTGCC 59.075 44.000 12.78 3.73 46.00 4.85
3476 4807 5.837979 AGTGTATCAATGAGAGATACTGCCT 59.162 40.000 12.78 5.43 45.06 4.75
3477 4808 6.015519 AGTGTATCAATGAGAGATACTGCCTC 60.016 42.308 12.78 0.00 45.06 4.70
3478 4809 4.888326 ATCAATGAGAGATACTGCCTCC 57.112 45.455 0.00 0.00 0.00 4.30
3479 4810 2.968574 TCAATGAGAGATACTGCCTCCC 59.031 50.000 0.00 0.00 0.00 4.30
3480 4811 1.626686 ATGAGAGATACTGCCTCCCG 58.373 55.000 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.980662 AGTAGAAATCTGACATTCATGAGACTG 59.019 37.037 0.00 0.00 0.00 3.51
20 21 3.941483 CCGCCAAGTAGAAATCTGACATT 59.059 43.478 0.00 0.00 0.00 2.71
48 49 0.391661 CACATCACTGGTCCCTTCGG 60.392 60.000 0.00 0.00 0.00 4.30
50 51 1.347707 TGTCACATCACTGGTCCCTTC 59.652 52.381 0.00 0.00 0.00 3.46
61 62 0.608130 ACGGCTAAGCTGTCACATCA 59.392 50.000 0.00 0.00 45.94 3.07
62 63 3.442996 ACGGCTAAGCTGTCACATC 57.557 52.632 0.00 0.00 45.94 3.06
77 78 2.088950 ACACCTTTACATTCGGACGG 57.911 50.000 0.00 0.00 0.00 4.79
125 126 1.203038 ACCCTTCATCATTGCCACACA 60.203 47.619 0.00 0.00 0.00 3.72
141 142 3.269906 TGTCTAGCTCCTCTTTCTACCCT 59.730 47.826 0.00 0.00 0.00 4.34
149 150 4.464069 GACATGTTGTCTAGCTCCTCTT 57.536 45.455 0.00 0.00 43.73 2.85
171 175 1.915141 CCAGGCAGTCAACAAGGAAT 58.085 50.000 0.00 0.00 0.00 3.01
175 179 0.313043 CTTGCCAGGCAGTCAACAAG 59.687 55.000 15.50 3.15 40.61 3.16
187 191 3.054802 AGGACAAATCTAGGACTTGCCAG 60.055 47.826 0.00 0.00 40.02 4.85
191 195 4.326826 TGCAAGGACAAATCTAGGACTTG 58.673 43.478 0.00 0.00 37.48 3.16
193 197 4.042187 AGTTGCAAGGACAAATCTAGGACT 59.958 41.667 0.00 0.00 0.00 3.85
201 205 7.439056 CACAAATAAGAAGTTGCAAGGACAAAT 59.561 33.333 0.00 0.00 34.03 2.32
233 237 5.767168 GGTAACACTATACCTCCGACTACAT 59.233 44.000 0.00 0.00 41.80 2.29
245 249 4.285292 CATGTCGTCCGGTAACACTATAC 58.715 47.826 0.00 0.00 0.00 1.47
249 253 0.245539 CCATGTCGTCCGGTAACACT 59.754 55.000 0.00 0.00 0.00 3.55
279 283 6.047231 GTGTATATCCTACTTTTCGCAAGGT 58.953 40.000 0.00 0.00 38.47 3.50
290 294 6.270231 GGAGATTGTTGGGTGTATATCCTACT 59.730 42.308 5.09 0.00 34.41 2.57
298 302 5.044476 TGTTATGGGAGATTGTTGGGTGTAT 60.044 40.000 0.00 0.00 0.00 2.29
317 321 2.186903 CAGAGCCCCGCGTGTTAT 59.813 61.111 4.92 0.00 0.00 1.89
366 370 2.158841 GGAGCTCGACTTAGATAGCGAG 59.841 54.545 7.83 0.00 45.24 5.03
375 379 3.070446 TCAAAAACTGGGAGCTCGACTTA 59.930 43.478 7.83 0.00 0.00 2.24
384 388 5.323371 TCAAACAAGTCAAAAACTGGGAG 57.677 39.130 0.00 0.00 38.58 4.30
393 397 5.317733 ACAAACCGATCAAACAAGTCAAA 57.682 34.783 0.00 0.00 0.00 2.69
398 402 5.277825 TGCTAAACAAACCGATCAAACAAG 58.722 37.500 0.00 0.00 0.00 3.16
399 403 5.250235 TGCTAAACAAACCGATCAAACAA 57.750 34.783 0.00 0.00 0.00 2.83
414 418 4.823989 AGATATGGCCAGTTCATGCTAAAC 59.176 41.667 13.05 0.00 0.00 2.01
430 434 2.427095 TCCACTGACACACGAGATATGG 59.573 50.000 0.00 0.00 0.00 2.74
432 436 3.621558 TCTCCACTGACACACGAGATAT 58.378 45.455 0.00 0.00 0.00 1.63
433 437 3.010420 CTCTCCACTGACACACGAGATA 58.990 50.000 0.00 0.00 0.00 1.98
437 441 1.179174 CCCTCTCCACTGACACACGA 61.179 60.000 0.00 0.00 0.00 4.35
438 442 1.179174 TCCCTCTCCACTGACACACG 61.179 60.000 0.00 0.00 0.00 4.49
450 454 7.630242 TGATGACAAACAAATAATCCCTCTC 57.370 36.000 0.00 0.00 0.00 3.20
451 455 8.472413 CATTGATGACAAACAAATAATCCCTCT 58.528 33.333 3.28 0.00 39.54 3.69
452 456 8.469200 TCATTGATGACAAACAAATAATCCCTC 58.531 33.333 3.28 0.00 39.54 4.30
453 457 8.365060 TCATTGATGACAAACAAATAATCCCT 57.635 30.769 3.28 0.00 39.54 4.20
454 458 9.603921 AATCATTGATGACAAACAAATAATCCC 57.396 29.630 0.00 0.00 40.03 3.85
459 463 9.844790 GACTCAATCATTGATGACAAACAAATA 57.155 29.630 0.00 0.00 40.03 1.40
463 475 5.700373 TCGACTCAATCATTGATGACAAACA 59.300 36.000 0.00 0.00 40.03 2.83
467 479 5.482006 ACTTCGACTCAATCATTGATGACA 58.518 37.500 0.00 0.00 40.03 3.58
481 493 1.656095 CCGAGCAAATGACTTCGACTC 59.344 52.381 0.00 0.00 0.00 3.36
484 496 0.606096 TCCCGAGCAAATGACTTCGA 59.394 50.000 0.00 0.00 0.00 3.71
490 502 0.320374 ACGTCTTCCCGAGCAAATGA 59.680 50.000 0.00 0.00 0.00 2.57
491 503 0.443869 CACGTCTTCCCGAGCAAATG 59.556 55.000 0.00 0.00 0.00 2.32
539 551 5.640732 CCACAAAGGAAAGGAATATTGTCG 58.359 41.667 0.00 0.00 41.22 4.35
557 569 4.079500 TCCAAATAGACCCATATGCCACAA 60.080 41.667 0.00 0.00 0.00 3.33
558 570 3.461458 TCCAAATAGACCCATATGCCACA 59.539 43.478 0.00 0.00 0.00 4.17
566 578 3.244911 CCCGCTTATCCAAATAGACCCAT 60.245 47.826 0.00 0.00 0.00 4.00
574 586 0.179029 CCCGACCCGCTTATCCAAAT 60.179 55.000 0.00 0.00 0.00 2.32
605 617 6.707440 AATGATACATCACGCCCATAAAAA 57.293 33.333 0.00 0.00 40.03 1.94
606 618 6.707440 AAATGATACATCACGCCCATAAAA 57.293 33.333 0.00 0.00 40.03 1.52
610 622 5.620206 TCTAAAATGATACATCACGCCCAT 58.380 37.500 0.00 0.00 40.03 4.00
631 643 8.512138 CGGTCCATAGATTAAAAACAGTTTTCT 58.488 33.333 11.77 7.37 38.01 2.52
632 644 8.508875 TCGGTCCATAGATTAAAAACAGTTTTC 58.491 33.333 11.77 0.00 38.01 2.29
633 645 8.398878 TCGGTCCATAGATTAAAAACAGTTTT 57.601 30.769 5.37 5.37 40.15 2.43
634 646 7.989416 TCGGTCCATAGATTAAAAACAGTTT 57.011 32.000 0.00 0.00 0.00 2.66
635 647 7.446013 TGTTCGGTCCATAGATTAAAAACAGTT 59.554 33.333 0.00 0.00 0.00 3.16
636 648 6.938030 TGTTCGGTCCATAGATTAAAAACAGT 59.062 34.615 0.00 0.00 0.00 3.55
637 649 7.372451 TGTTCGGTCCATAGATTAAAAACAG 57.628 36.000 0.00 0.00 0.00 3.16
638 650 7.931578 ATGTTCGGTCCATAGATTAAAAACA 57.068 32.000 0.00 0.00 0.00 2.83
655 693 1.931172 CACCGTAGCCTTAATGTTCGG 59.069 52.381 0.00 0.00 41.77 4.30
656 694 2.347452 CACACCGTAGCCTTAATGTTCG 59.653 50.000 0.00 0.00 0.00 3.95
662 700 3.488778 TTTTCCACACCGTAGCCTTAA 57.511 42.857 0.00 0.00 0.00 1.85
663 701 3.488778 TTTTTCCACACCGTAGCCTTA 57.511 42.857 0.00 0.00 0.00 2.69
687 725 4.006319 CCCTTGCCTCAGAAAGAACTTAG 58.994 47.826 0.00 0.00 0.00 2.18
688 726 3.650942 TCCCTTGCCTCAGAAAGAACTTA 59.349 43.478 0.00 0.00 0.00 2.24
689 727 2.443255 TCCCTTGCCTCAGAAAGAACTT 59.557 45.455 0.00 0.00 0.00 2.66
691 729 2.568623 TCCCTTGCCTCAGAAAGAAC 57.431 50.000 0.00 0.00 0.00 3.01
693 731 3.593442 TTTTCCCTTGCCTCAGAAAGA 57.407 42.857 0.00 0.00 30.49 2.52
694 732 4.879197 ATTTTTCCCTTGCCTCAGAAAG 57.121 40.909 0.00 0.00 30.49 2.62
774 824 8.287503 ACAGTTTTACGGCTAAAAAGAATACTG 58.712 33.333 0.00 0.00 34.33 2.74
789 839 9.221775 GAAATGCTCATAAATACAGTTTTACGG 57.778 33.333 0.00 0.00 0.00 4.02
790 840 9.988350 AGAAATGCTCATAAATACAGTTTTACG 57.012 29.630 0.00 0.00 0.00 3.18
793 843 8.184192 CGGAGAAATGCTCATAAATACAGTTTT 58.816 33.333 0.00 0.00 45.81 2.43
795 845 6.823689 ACGGAGAAATGCTCATAAATACAGTT 59.176 34.615 0.00 0.00 45.81 3.16
797 847 6.851222 ACGGAGAAATGCTCATAAATACAG 57.149 37.500 0.00 0.00 45.81 2.74
798 848 7.335673 TGAAACGGAGAAATGCTCATAAATACA 59.664 33.333 0.00 0.00 45.81 2.29
824 874 4.830600 TCGGCCCAAAGAGAAGTAAATTTT 59.169 37.500 0.00 0.00 0.00 1.82
857 907 4.980805 TGAGTTGTGTCGCGGGGC 62.981 66.667 6.13 0.00 0.00 5.80
911 961 1.600413 GGAAAGAACGGCAGCTGTTTG 60.600 52.381 20.85 7.98 32.62 2.93
919 969 2.031465 GGTCGGGAAAGAACGGCA 59.969 61.111 0.00 0.00 36.23 5.69
935 985 0.446222 CGGTATTTGTTGAGGCACGG 59.554 55.000 0.00 0.00 0.00 4.94
938 988 2.156098 GGTTCGGTATTTGTTGAGGCA 58.844 47.619 0.00 0.00 0.00 4.75
960 1010 2.551459 AGTGAACAAACAGAGAGCATGC 59.449 45.455 10.51 10.51 0.00 4.06
965 1015 4.384247 GTGATCGAGTGAACAAACAGAGAG 59.616 45.833 0.00 0.00 0.00 3.20
974 1024 2.239400 AGGACAGTGATCGAGTGAACA 58.761 47.619 0.00 0.00 0.00 3.18
1308 1365 4.161565 TGATACAGCAGAGAATTAACGGGT 59.838 41.667 0.00 0.00 0.00 5.28
1309 1366 4.508124 GTGATACAGCAGAGAATTAACGGG 59.492 45.833 0.00 0.00 0.00 5.28
1310 1367 4.508124 GGTGATACAGCAGAGAATTAACGG 59.492 45.833 0.00 0.00 0.00 4.44
1311 1368 5.109210 TGGTGATACAGCAGAGAATTAACG 58.891 41.667 0.00 0.00 36.93 3.18
1321 1378 2.210961 CAGCAGATGGTGATACAGCAG 58.789 52.381 6.15 0.00 45.01 4.24
1322 1379 1.556451 ACAGCAGATGGTGATACAGCA 59.444 47.619 18.18 6.12 45.66 4.41
1323 1380 2.208431 GACAGCAGATGGTGATACAGC 58.792 52.381 18.18 0.00 45.66 4.40
1327 1384 4.700700 CAGAATGACAGCAGATGGTGATA 58.299 43.478 18.18 7.14 45.57 2.15
1362 1419 2.596452 ACATCGTTCAGCTTCAGTACG 58.404 47.619 0.00 0.00 0.00 3.67
1365 1422 8.942338 TTAATAATACATCGTTCAGCTTCAGT 57.058 30.769 0.00 0.00 0.00 3.41
1383 1440 2.804212 CGGGCCCGTCGTCTTTAATAAT 60.804 50.000 36.64 0.00 34.35 1.28
1499 1556 0.109412 CGTCTACGGTCTTGTGGGAC 60.109 60.000 0.00 0.00 35.37 4.46
1535 1592 4.722700 CCCTTGCCGGACAGGGTG 62.723 72.222 24.49 13.01 44.06 4.61
1553 1610 2.448705 GCACTCGCGGAGAAGAAGC 61.449 63.158 6.13 2.70 33.32 3.86
1652 1709 4.248842 TCCACCCACACGTGCCTG 62.249 66.667 17.22 7.38 32.10 4.85
1911 1968 4.256180 GTAGATGCCCCAGCCCCG 62.256 72.222 0.00 0.00 38.69 5.73
1960 2017 0.746204 TGAGCAGTTTGGCGTGAACA 60.746 50.000 0.00 0.00 39.27 3.18
1969 2026 3.243301 GCATGTGGGATATGAGCAGTTTG 60.243 47.826 0.00 0.00 0.00 2.93
1982 2039 0.747644 CACGCTTATGGCATGTGGGA 60.748 55.000 10.98 0.00 41.91 4.37
1983 2040 1.031571 ACACGCTTATGGCATGTGGG 61.032 55.000 10.98 12.81 45.99 4.61
2003 2060 1.548719 TGCGGATTAGCACTACACACT 59.451 47.619 0.00 0.00 42.92 3.55
2004 2061 2.004583 TGCGGATTAGCACTACACAC 57.995 50.000 0.00 0.00 42.92 3.82
2020 2082 3.583276 TAGCCAGACCAACCGTGCG 62.583 63.158 0.00 0.00 0.00 5.34
2032 2094 1.833630 TGGGAGACAATCTGTAGCCAG 59.166 52.381 0.00 0.00 40.25 4.85
2038 2100 1.059098 TGCACTGGGAGACAATCTGT 58.941 50.000 0.00 0.00 0.00 3.41
2087 2149 2.647529 TCGCTCATGTACGTGAACAT 57.352 45.000 18.15 0.00 40.75 2.71
2107 2169 7.033791 CAGTGTAAATGTAATACGAGACCTGT 58.966 38.462 0.00 0.00 0.00 4.00
2216 2282 3.197790 CGGATGCGCCCACTTGAG 61.198 66.667 4.18 0.00 0.00 3.02
2384 2450 2.433838 CAGCTGGTGCAGGACTCG 60.434 66.667 5.57 0.00 42.74 4.18
2455 2524 1.657594 CAGATGTCGTAGCAGCAACAG 59.342 52.381 0.00 0.00 0.00 3.16
2456 2525 1.000843 ACAGATGTCGTAGCAGCAACA 59.999 47.619 0.00 0.00 0.00 3.33
2457 2526 1.656095 GACAGATGTCGTAGCAGCAAC 59.344 52.381 0.00 0.00 35.12 4.17
2458 2527 1.996292 GACAGATGTCGTAGCAGCAA 58.004 50.000 0.00 0.00 35.12 3.91
2459 2528 3.721625 GACAGATGTCGTAGCAGCA 57.278 52.632 0.00 0.00 35.12 4.41
2468 2537 3.256879 TCAGAGTGGTTCAGACAGATGTC 59.743 47.826 4.77 4.77 45.08 3.06
2469 2538 3.234353 TCAGAGTGGTTCAGACAGATGT 58.766 45.455 0.00 0.00 0.00 3.06
2470 2539 3.949842 TCAGAGTGGTTCAGACAGATG 57.050 47.619 0.00 0.00 0.00 2.90
2471 2540 4.963318 TTTCAGAGTGGTTCAGACAGAT 57.037 40.909 0.00 0.00 0.00 2.90
2472 2541 4.963318 ATTTCAGAGTGGTTCAGACAGA 57.037 40.909 0.00 0.00 0.00 3.41
2473 2542 6.382869 AAAATTTCAGAGTGGTTCAGACAG 57.617 37.500 0.00 0.00 0.00 3.51
2474 2543 7.279615 TCTAAAATTTCAGAGTGGTTCAGACA 58.720 34.615 0.00 0.00 0.00 3.41
2475 2544 7.572168 GCTCTAAAATTTCAGAGTGGTTCAGAC 60.572 40.741 17.84 0.00 40.40 3.51
2476 2545 6.428159 GCTCTAAAATTTCAGAGTGGTTCAGA 59.572 38.462 17.84 0.00 40.40 3.27
2513 2604 7.058693 GTGGTTCGTTATTGTTCGTGTAAATTC 59.941 37.037 0.00 0.00 0.00 2.17
2570 2667 8.061125 TCAGATATCGTTCGTGTTATTGATTG 57.939 34.615 0.00 0.00 0.00 2.67
2571 2668 8.642908 TTCAGATATCGTTCGTGTTATTGATT 57.357 30.769 0.00 0.00 0.00 2.57
2572 2669 7.096023 GCTTCAGATATCGTTCGTGTTATTGAT 60.096 37.037 0.00 0.00 0.00 2.57
2573 2670 6.198403 GCTTCAGATATCGTTCGTGTTATTGA 59.802 38.462 0.00 0.00 0.00 2.57
2630 2728 4.774124 TCATCAGATCCACAGATTTGGTC 58.226 43.478 0.00 0.00 35.73 4.02
2685 2783 3.430098 GGACAGTCAGCTCACCTATTCTG 60.430 52.174 2.17 0.00 0.00 3.02
2693 2791 0.320247 CAGTGGGACAGTCAGCTCAC 60.320 60.000 2.17 5.35 41.96 3.51
2697 2795 1.277557 AGAATCAGTGGGACAGTCAGC 59.722 52.381 2.17 0.00 41.96 4.26
2706 2804 2.547211 GCATTCGATCAGAATCAGTGGG 59.453 50.000 9.03 1.46 45.95 4.61
2720 2818 2.889154 ATCTGCGCGAGTGCATTCGA 62.889 55.000 32.41 13.57 45.26 3.71
2734 2832 2.020559 CGCGCGTGAGAAATCTGC 59.979 61.111 24.19 0.00 0.00 4.26
2735 2833 0.517132 CAACGCGCGTGAGAAATCTG 60.517 55.000 38.44 23.86 0.00 2.90
2771 2869 1.270274 TGCGTAACTAAACTCCAGCGA 59.730 47.619 0.00 0.00 0.00 4.93
2772 2870 1.705256 TGCGTAACTAAACTCCAGCG 58.295 50.000 0.00 0.00 0.00 5.18
2773 2871 3.064931 ACTTGCGTAACTAAACTCCAGC 58.935 45.455 0.00 0.00 0.00 4.85
2774 2872 4.510340 ACAACTTGCGTAACTAAACTCCAG 59.490 41.667 0.00 0.00 0.00 3.86
2775 2873 4.444536 ACAACTTGCGTAACTAAACTCCA 58.555 39.130 0.00 0.00 0.00 3.86
2776 2874 5.922544 TCTACAACTTGCGTAACTAAACTCC 59.077 40.000 0.00 0.00 0.00 3.85
2783 2881 9.216117 AGATTTAAATCTACAACTTGCGTAACT 57.784 29.630 25.81 0.00 43.66 2.24
2813 2912 5.957716 TGGTGACACCGATTCCTTCGAAC 62.958 52.174 19.67 0.00 43.21 3.95
2847 2946 2.023882 GGACGGCGTAGTACGAGC 59.976 66.667 26.29 9.17 46.05 5.03
2863 2995 0.678950 AAGCAAACCAACGGAATGGG 59.321 50.000 8.71 0.00 45.18 4.00
2876 3008 1.407258 CCCACAAGAAACCGAAGCAAA 59.593 47.619 0.00 0.00 0.00 3.68
2998 4319 5.354234 TCAGAACTCCTTTTGAACAAGTGAC 59.646 40.000 0.00 0.00 0.00 3.67
3012 4333 1.280421 GGCCATGTCTTCAGAACTCCT 59.720 52.381 0.00 0.00 0.00 3.69
3051 4372 6.414732 TGGTATGAAATCACTGTTTCTAGGG 58.585 40.000 0.00 0.00 38.58 3.53
3056 4377 7.592938 TCACAATGGTATGAAATCACTGTTTC 58.407 34.615 0.00 0.00 38.32 2.78
3181 4502 7.863666 ACGATGAAAATTAAGACCGTGTTTAA 58.136 30.769 0.00 0.00 0.00 1.52
3192 4513 3.474961 CGCGAGCAACGATGAAAATTAAG 59.525 43.478 0.00 0.00 45.77 1.85
3239 4563 7.484975 AGTTCACGATAAACTCCTAGAGATTG 58.515 38.462 0.00 0.00 31.36 2.67
3298 4622 4.876081 GCTCTGAATTGCGCGGCG 62.876 66.667 19.62 19.62 0.00 6.46
3325 4649 3.202818 TGGTACCATGGCAGATGAAGATT 59.797 43.478 11.60 0.00 0.00 2.40
3353 4678 0.902516 AGAGAGAGTGGGGAGTGCAC 60.903 60.000 9.40 9.40 0.00 4.57
3355 4680 1.960689 GATAGAGAGAGTGGGGAGTGC 59.039 57.143 0.00 0.00 0.00 4.40
3356 4681 3.138283 AGAGATAGAGAGAGTGGGGAGTG 59.862 52.174 0.00 0.00 0.00 3.51
3357 4682 3.138283 CAGAGATAGAGAGAGTGGGGAGT 59.862 52.174 0.00 0.00 0.00 3.85
3358 4683 3.754965 CAGAGATAGAGAGAGTGGGGAG 58.245 54.545 0.00 0.00 0.00 4.30
3359 4684 2.158534 GCAGAGATAGAGAGAGTGGGGA 60.159 54.545 0.00 0.00 0.00 4.81
3360 4685 2.158475 AGCAGAGATAGAGAGAGTGGGG 60.158 54.545 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.