Multiple sequence alignment - TraesCS1D01G340700

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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 TraesCS1D01G340700 chr1D 100.000 3029 0 0 1 3029 430465495 430468523 0.000000e+00 5594.0
1 TraesCS1D01G340700 chr1B 91.888 2071 104 30 932 2975 581412091 581414124 0.000000e+00 2835.0
2 TraesCS1D01G340700 chr1B 89.643 560 49 7 1 556 581411186 581411740 0.000000e+00 704.0
3 TraesCS1D01G340700 chr1B 83.990 381 28 10 570 945 581411723 581412075 4.840000e-88 335.0
4 TraesCS1D01G340700 chr1A 96.150 1065 29 6 946 2010 528063644 528064696 0.000000e+00 1729.0
5 TraesCS1D01G340700 chr1A 90.437 962 53 18 2044 2975 528064698 528065650 0.000000e+00 1230.0
6 TraesCS1D01G340700 chrUn 88.125 320 37 1 2340 2658 110699814 110700133 2.200000e-101 379.0
7 TraesCS1D01G340700 chrUn 86.628 344 43 3 2313 2654 110690541 110690883 7.930000e-101 377.0
8 TraesCS1D01G340700 chrUn 85.933 327 39 4 2335 2654 110687551 110687877 2.890000e-90 342.0
9 TraesCS1D01G340700 chrUn 100.000 29 0 0 2654 2682 110700245 110700273 2.000000e-03 54.7
10 TraesCS1D01G340700 chr4B 87.888 322 37 2 2335 2654 660683372 660683693 7.930000e-101 377.0
11 TraesCS1D01G340700 chr4B 87.812 320 34 4 2338 2654 660519861 660519544 1.330000e-98 370.0
12 TraesCS1D01G340700 chr5A 87.461 319 38 2 2338 2654 700694851 700695169 1.720000e-97 366.0
13 TraesCS1D01G340700 chr5A 89.789 284 26 1 2371 2654 700785207 700785487 7.980000e-96 361.0
14 TraesCS1D01G340700 chr7B 84.942 259 31 6 1025 1282 80514387 80514136 3.880000e-64 255.0


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 TraesCS1D01G340700 chr1D 430465495 430468523 3028 False 5594.000000 5594 100.0000 1 3029 1 chr1D.!!$F1 3028
1 TraesCS1D01G340700 chr1B 581411186 581414124 2938 False 1291.333333 2835 88.5070 1 2975 3 chr1B.!!$F1 2974
2 TraesCS1D01G340700 chr1A 528063644 528065650 2006 False 1479.500000 1729 93.2935 946 2975 2 chr1A.!!$F1 2029
3 TraesCS1D01G340700 chrUn 110687551 110690883 3332 False 359.500000 377 86.2805 2313 2654 2 chrUn.!!$F1 341

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
367 372 0.301987 GCTCGATCTAACAAAGCGGC 59.698 55.0 0.00 0.0 0.00 6.53 F
1554 1596 0.318441 GAGTGCAGTGCCAGACTACA 59.682 55.0 13.72 0.0 31.73 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1977 0.476338 TCAAAGCAACAGGGGTGCTA 59.524 50.0 9.46 0.0 38.01 3.49 R
2497 5555 1.785041 GCTGCAGGAACTTTGCACGA 61.785 55.0 17.12 0.0 45.89 4.35 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
25 26 4.098914 AGAACTGTTTCACATGGCCTTA 57.901 40.909 3.32 0.00 33.72 2.69
62 64 9.840427 CTTATTTCCCTAGTTGTGTATTTTGTG 57.160 33.333 0.00 0.00 0.00 3.33
71 73 5.934625 AGTTGTGTATTTTGTGTTTTTGCCA 59.065 32.000 0.00 0.00 0.00 4.92
200 205 7.199766 TGTTATTCTCGCAATTTTTGAGTTGT 58.800 30.769 0.00 0.00 0.00 3.32
206 211 6.417635 TCTCGCAATTTTTGAGTTGTTCATTC 59.582 34.615 0.00 0.00 35.27 2.67
332 337 8.143835 GCCAGAATACCAATGTTGCTAATTTAT 58.856 33.333 0.00 0.00 0.00 1.40
360 365 9.541143 TTTAAATACATGATGCTCGATCTAACA 57.459 29.630 0.00 0.00 31.55 2.41
361 366 9.541143 TTAAATACATGATGCTCGATCTAACAA 57.459 29.630 0.00 0.00 31.55 2.83
367 372 0.301987 GCTCGATCTAACAAAGCGGC 59.698 55.000 0.00 0.00 0.00 6.53
380 385 2.510238 GCGGCAGCACCACTCTAG 60.510 66.667 3.18 0.00 44.35 2.43
382 387 1.293498 CGGCAGCACCACTCTAGTT 59.707 57.895 0.00 0.00 39.03 2.24
383 388 0.530744 CGGCAGCACCACTCTAGTTA 59.469 55.000 0.00 0.00 39.03 2.24
385 390 2.418746 CGGCAGCACCACTCTAGTTAAT 60.419 50.000 0.00 0.00 39.03 1.40
391 396 6.127897 GCAGCACCACTCTAGTTAATGAAATT 60.128 38.462 0.00 0.00 41.28 1.82
421 426 7.729124 AAATTAGTACAACTGAGGCTAGGTA 57.271 36.000 0.00 0.00 0.00 3.08
424 429 5.855740 AGTACAACTGAGGCTAGGTAATC 57.144 43.478 0.00 0.00 0.00 1.75
436 441 4.566907 GGCTAGGTAATCAGAAAACCACCA 60.567 45.833 7.19 0.00 35.64 4.17
437 442 5.193679 GCTAGGTAATCAGAAAACCACCAT 58.806 41.667 7.19 0.00 35.64 3.55
439 444 5.255397 AGGTAATCAGAAAACCACCATCA 57.745 39.130 7.19 0.00 35.64 3.07
454 459 2.031508 ACCATCAAACGCTAAAACCACG 60.032 45.455 0.00 0.00 0.00 4.94
456 461 3.186817 CCATCAAACGCTAAAACCACGTA 59.813 43.478 0.00 0.00 39.49 3.57
466 471 3.507103 AAAACCACGTAAAACCACCAC 57.493 42.857 0.00 0.00 0.00 4.16
469 474 1.744522 ACCACGTAAAACCACCACAAC 59.255 47.619 0.00 0.00 0.00 3.32
507 512 1.071041 ACGTAACACTTTCGCGCTTTC 60.071 47.619 5.56 0.00 0.00 2.62
519 524 2.680913 CGCTTTCGCCTCCTGGTTG 61.681 63.158 0.00 0.00 35.27 3.77
535 540 2.070783 GGTTGCGTAATCGAAAGGTCA 58.929 47.619 0.00 0.00 35.06 4.02
538 543 3.239587 TGCGTAATCGAAAGGTCATCA 57.760 42.857 0.00 0.00 39.71 3.07
539 544 3.792401 TGCGTAATCGAAAGGTCATCAT 58.208 40.909 0.00 0.00 39.71 2.45
540 545 3.802139 TGCGTAATCGAAAGGTCATCATC 59.198 43.478 0.00 0.00 39.71 2.92
541 546 3.184581 GCGTAATCGAAAGGTCATCATCC 59.815 47.826 0.00 0.00 39.71 3.51
542 547 4.621991 CGTAATCGAAAGGTCATCATCCT 58.378 43.478 0.00 0.00 39.71 3.24
543 548 4.681942 CGTAATCGAAAGGTCATCATCCTC 59.318 45.833 0.00 0.00 39.71 3.71
544 549 4.760530 AATCGAAAGGTCATCATCCTCA 57.239 40.909 0.00 0.00 33.76 3.86
545 550 4.760530 ATCGAAAGGTCATCATCCTCAA 57.239 40.909 0.00 0.00 33.76 3.02
546 551 4.128925 TCGAAAGGTCATCATCCTCAAG 57.871 45.455 0.00 0.00 33.76 3.02
547 552 3.515502 TCGAAAGGTCATCATCCTCAAGT 59.484 43.478 0.00 0.00 33.76 3.16
548 553 3.868077 CGAAAGGTCATCATCCTCAAGTC 59.132 47.826 0.00 0.00 33.76 3.01
549 554 4.382470 CGAAAGGTCATCATCCTCAAGTCT 60.382 45.833 0.00 0.00 33.76 3.24
550 555 5.495640 GAAAGGTCATCATCCTCAAGTCTT 58.504 41.667 0.00 0.00 33.76 3.01
551 556 5.511386 AAGGTCATCATCCTCAAGTCTTT 57.489 39.130 0.00 0.00 33.76 2.52
552 557 5.511386 AGGTCATCATCCTCAAGTCTTTT 57.489 39.130 0.00 0.00 0.00 2.27
553 558 5.251764 AGGTCATCATCCTCAAGTCTTTTG 58.748 41.667 0.00 0.00 0.00 2.44
554 559 4.142513 GGTCATCATCCTCAAGTCTTTTGC 60.143 45.833 0.00 0.00 0.00 3.68
555 560 4.699257 GTCATCATCCTCAAGTCTTTTGCT 59.301 41.667 0.00 0.00 0.00 3.91
556 561 5.182760 GTCATCATCCTCAAGTCTTTTGCTT 59.817 40.000 0.00 0.00 0.00 3.91
557 562 5.771666 TCATCATCCTCAAGTCTTTTGCTTT 59.228 36.000 0.00 0.00 0.00 3.51
558 563 6.266103 TCATCATCCTCAAGTCTTTTGCTTTT 59.734 34.615 0.00 0.00 0.00 2.27
559 564 6.469782 TCATCCTCAAGTCTTTTGCTTTTT 57.530 33.333 0.00 0.00 0.00 1.94
637 642 2.797074 GGGCTCCGAGATACTGTAAC 57.203 55.000 0.00 0.00 0.00 2.50
638 643 2.308690 GGGCTCCGAGATACTGTAACT 58.691 52.381 0.00 0.00 0.00 2.24
639 644 3.484407 GGGCTCCGAGATACTGTAACTA 58.516 50.000 0.00 0.00 0.00 2.24
640 645 3.502979 GGGCTCCGAGATACTGTAACTAG 59.497 52.174 0.00 0.00 0.00 2.57
641 646 3.058085 GGCTCCGAGATACTGTAACTAGC 60.058 52.174 0.00 8.86 0.00 3.42
652 657 3.515502 ACTGTAACTAGCAAGCATCCAGA 59.484 43.478 0.00 0.00 0.00 3.86
669 674 3.008375 TCCAGAGTAGCTGCATTGACTTT 59.992 43.478 4.12 0.00 43.50 2.66
674 679 4.508662 AGTAGCTGCATTGACTTTACTCC 58.491 43.478 4.12 0.00 0.00 3.85
675 680 3.423539 AGCTGCATTGACTTTACTCCA 57.576 42.857 1.02 0.00 0.00 3.86
681 686 6.094048 GCTGCATTGACTTTACTCCAATTCTA 59.906 38.462 0.00 0.00 0.00 2.10
687 692 7.252612 TGACTTTACTCCAATTCTATCCACA 57.747 36.000 0.00 0.00 0.00 4.17
713 718 3.532892 CTACACAAGCTTGCAGAGTTG 57.467 47.619 26.27 17.32 0.00 3.16
751 760 2.759973 CAGGTGGCTCTCCGGCTA 60.760 66.667 0.00 0.00 39.32 3.93
764 773 2.491693 CTCCGGCTAGATTCAGATCTCC 59.508 54.545 0.00 0.00 41.68 3.71
771 780 6.375736 CGGCTAGATTCAGATCTCCACTATTA 59.624 42.308 0.00 0.00 41.68 0.98
782 791 8.807118 CAGATCTCCACTATTATAAGCACCTAA 58.193 37.037 0.00 0.00 0.00 2.69
783 792 9.554053 AGATCTCCACTATTATAAGCACCTAAT 57.446 33.333 0.00 0.00 0.00 1.73
791 800 9.367444 ACTATTATAAGCACCTAATAATCACGC 57.633 33.333 0.00 0.00 30.50 5.34
818 827 2.419673 TCGTTCTAATCCGAGTGCGTTA 59.580 45.455 0.00 0.00 35.23 3.18
851 860 2.203422 TGGTGGCCCCGAAAACTG 60.203 61.111 0.00 0.00 35.15 3.16
852 861 3.680786 GGTGGCCCCGAAAACTGC 61.681 66.667 0.00 0.00 0.00 4.40
945 954 2.810274 CGGCTCCATTAATCCAGTGATG 59.190 50.000 0.00 0.00 0.00 3.07
946 955 3.494924 CGGCTCCATTAATCCAGTGATGA 60.495 47.826 0.00 0.00 0.00 2.92
960 999 2.200067 GTGATGATCACCTCTTCAGCG 58.800 52.381 14.48 0.00 41.37 5.18
962 1001 2.100418 TGATGATCACCTCTTCAGCGAG 59.900 50.000 0.00 0.00 34.17 5.03
1359 1401 2.418669 CCCCTAGCTTTAATCCCTCCA 58.581 52.381 0.00 0.00 0.00 3.86
1379 1421 2.034221 GTTCCTTCCCCAAGCGCT 59.966 61.111 2.64 2.64 0.00 5.92
1392 1434 1.103803 AAGCGCTAATCGAGAGGTCA 58.896 50.000 12.05 0.00 41.67 4.02
1544 1586 0.603707 ATCAACCCGTGAGTGCAGTG 60.604 55.000 0.00 0.00 40.43 3.66
1554 1596 0.318441 GAGTGCAGTGCCAGACTACA 59.682 55.000 13.72 0.00 31.73 2.74
1559 1601 2.271800 GCAGTGCCAGACTACATGTAC 58.728 52.381 2.85 0.00 31.73 2.90
1645 1688 5.494724 CATATATGCCACATGTAAGCCTCT 58.505 41.667 15.36 3.83 0.00 3.69
1731 1774 4.276926 AGTGAAATTTCTGGACTGCAGTTC 59.723 41.667 22.65 20.74 0.00 3.01
1761 1804 1.588861 GAGCTCGCACTTTATCGAACC 59.411 52.381 0.00 0.00 34.07 3.62
1764 1807 1.582502 CTCGCACTTTATCGAACCGAC 59.417 52.381 0.00 0.00 39.18 4.79
1767 1810 1.392510 GCACTTTATCGAACCGACACC 59.607 52.381 0.00 0.00 39.18 4.16
1902 1945 8.410912 GGGGTCTTGTAATATTATGTTTTCACC 58.589 37.037 0.00 0.17 0.00 4.02
1934 1977 8.239314 GTGTTTGATGTAATGATGTGAATGTCT 58.761 33.333 0.00 0.00 0.00 3.41
1990 2033 0.395724 CATTGGACCTACCTTGGGGC 60.396 60.000 0.00 0.00 39.86 5.80
2010 2053 0.553819 TTACCTTGCCACTTGTGGGT 59.446 50.000 19.89 11.97 0.00 4.51
2061 2104 7.660208 GCCTTTCGTCTAAAATATATCTTGGGA 59.340 37.037 0.00 0.00 0.00 4.37
2323 2369 7.905604 TTTAGGTGACACAAGACATTCTATG 57.094 36.000 8.08 0.00 0.00 2.23
2359 2405 2.271800 GTGATGCAGCACTACAGTACC 58.728 52.381 27.11 0.00 35.91 3.34
2373 2425 2.235155 ACAGTACCGCATACAATGGTCA 59.765 45.455 0.00 0.00 37.20 4.02
2374 2426 2.866156 CAGTACCGCATACAATGGTCAG 59.134 50.000 0.00 0.00 37.20 3.51
2394 2446 6.930722 GGTCAGTACTCTGTACTATCTAGTCC 59.069 46.154 9.65 2.64 41.91 3.85
2497 5555 1.321474 CAATGTTGAGGTGGTGCTGT 58.679 50.000 0.00 0.00 0.00 4.40
2628 5686 5.636123 TGGTTCTGGCCTTTCATAAACTAA 58.364 37.500 3.32 0.00 0.00 2.24
2693 5763 7.942341 AGAGTAATTCAACTTGGTGGAAACATA 59.058 33.333 0.00 0.00 46.14 2.29
2694 5764 7.882179 AGTAATTCAACTTGGTGGAAACATAC 58.118 34.615 0.00 0.00 46.14 2.39
2695 5765 5.722021 ATTCAACTTGGTGGAAACATACC 57.278 39.130 0.00 0.00 46.14 2.73
2696 5766 4.171878 TCAACTTGGTGGAAACATACCA 57.828 40.909 0.00 0.00 46.14 3.25
2733 5803 5.353938 TCTGCAACGTAGTCTACTTTGTTT 58.646 37.500 23.01 2.82 45.00 2.83
2734 5804 5.233476 TCTGCAACGTAGTCTACTTTGTTTG 59.767 40.000 23.01 15.77 45.00 2.93
2735 5805 4.871557 TGCAACGTAGTCTACTTTGTTTGT 59.128 37.500 23.01 5.25 45.00 2.83
2737 5807 5.900242 GCAACGTAGTCTACTTTGTTTGTTC 59.100 40.000 23.01 8.15 45.00 3.18
2738 5808 6.238022 GCAACGTAGTCTACTTTGTTTGTTCT 60.238 38.462 23.01 0.00 45.00 3.01
2739 5809 7.043192 GCAACGTAGTCTACTTTGTTTGTTCTA 60.043 37.037 23.01 0.00 45.00 2.10
2740 5810 8.477709 CAACGTAGTCTACTTTGTTTGTTCTAG 58.522 37.037 17.13 0.00 45.00 2.43
2742 5812 7.144000 CGTAGTCTACTTTGTTTGTTCTAGGT 58.856 38.462 8.37 0.00 0.00 3.08
2743 5813 8.292448 CGTAGTCTACTTTGTTTGTTCTAGGTA 58.708 37.037 8.37 0.00 0.00 3.08
2802 5883 6.662414 TGTTCTGCTGTATATGTTAGTTGC 57.338 37.500 0.00 0.00 0.00 4.17
2806 5887 6.216569 TCTGCTGTATATGTTAGTTGCTAGC 58.783 40.000 8.10 8.10 0.00 3.42
2890 5971 5.595885 TGGATTTTGTGTTTGTACATGTGG 58.404 37.500 9.11 0.00 36.50 4.17
2894 5975 7.440856 GGATTTTGTGTTTGTACATGTGGAAAT 59.559 33.333 9.11 0.28 36.50 2.17
2895 5976 9.469807 GATTTTGTGTTTGTACATGTGGAAATA 57.530 29.630 9.11 2.86 36.50 1.40
2975 6063 4.569943 TCTTGCTTCTTTAGGCTGTACAG 58.430 43.478 18.93 18.93 0.00 2.74
2976 6064 4.040461 TCTTGCTTCTTTAGGCTGTACAGT 59.960 41.667 23.44 7.94 0.00 3.55
2977 6065 3.664107 TGCTTCTTTAGGCTGTACAGTG 58.336 45.455 23.44 0.92 0.00 3.66
2978 6066 3.003480 GCTTCTTTAGGCTGTACAGTGG 58.997 50.000 23.44 8.25 0.00 4.00
2979 6067 2.762535 TCTTTAGGCTGTACAGTGGC 57.237 50.000 23.44 12.29 0.00 5.01
2980 6068 1.278127 TCTTTAGGCTGTACAGTGGCC 59.722 52.381 23.44 19.10 45.57 5.36
2983 6071 3.987404 GGCTGTACAGTGGCCTTG 58.013 61.111 23.44 5.16 42.31 3.61
2984 6072 1.073199 GGCTGTACAGTGGCCTTGT 59.927 57.895 23.44 16.06 42.31 3.16
2985 6073 0.955919 GGCTGTACAGTGGCCTTGTC 60.956 60.000 23.44 3.95 42.31 3.18
2986 6074 0.035458 GCTGTACAGTGGCCTTGTCT 59.965 55.000 23.44 1.16 0.00 3.41
2987 6075 1.543429 GCTGTACAGTGGCCTTGTCTT 60.543 52.381 23.44 0.00 0.00 3.01
2988 6076 2.289444 GCTGTACAGTGGCCTTGTCTTA 60.289 50.000 23.44 4.74 0.00 2.10
2989 6077 3.805807 GCTGTACAGTGGCCTTGTCTTAA 60.806 47.826 23.44 0.00 0.00 1.85
2990 6078 4.579869 CTGTACAGTGGCCTTGTCTTAAT 58.420 43.478 15.06 0.00 0.00 1.40
2991 6079 4.323417 TGTACAGTGGCCTTGTCTTAATG 58.677 43.478 15.39 0.00 0.00 1.90
2992 6080 3.508845 ACAGTGGCCTTGTCTTAATGT 57.491 42.857 3.32 0.00 0.00 2.71
2993 6081 3.832527 ACAGTGGCCTTGTCTTAATGTT 58.167 40.909 3.32 0.00 0.00 2.71
2994 6082 4.215109 ACAGTGGCCTTGTCTTAATGTTT 58.785 39.130 3.32 0.00 0.00 2.83
2995 6083 4.649218 ACAGTGGCCTTGTCTTAATGTTTT 59.351 37.500 3.32 0.00 0.00 2.43
2996 6084 5.221244 ACAGTGGCCTTGTCTTAATGTTTTC 60.221 40.000 3.32 0.00 0.00 2.29
2997 6085 4.280929 AGTGGCCTTGTCTTAATGTTTTCC 59.719 41.667 3.32 0.00 0.00 3.13
2998 6086 4.038642 GTGGCCTTGTCTTAATGTTTTCCA 59.961 41.667 3.32 0.00 0.00 3.53
2999 6087 4.837860 TGGCCTTGTCTTAATGTTTTCCAT 59.162 37.500 3.32 0.00 34.36 3.41
3000 6088 5.306678 TGGCCTTGTCTTAATGTTTTCCATT 59.693 36.000 3.32 0.00 45.68 3.16
3001 6089 6.183361 TGGCCTTGTCTTAATGTTTTCCATTT 60.183 34.615 3.32 0.00 41.01 2.32
3002 6090 6.368791 GGCCTTGTCTTAATGTTTTCCATTTC 59.631 38.462 0.00 0.00 41.01 2.17
3003 6091 6.928492 GCCTTGTCTTAATGTTTTCCATTTCA 59.072 34.615 0.00 0.00 41.01 2.69
3004 6092 7.603784 GCCTTGTCTTAATGTTTTCCATTTCAT 59.396 33.333 0.00 0.00 41.01 2.57
3005 6093 9.492973 CCTTGTCTTAATGTTTTCCATTTCATT 57.507 29.630 0.00 0.00 41.01 2.57
3008 6096 8.772705 TGTCTTAATGTTTTCCATTTCATTTGC 58.227 29.630 0.00 0.00 41.01 3.68
3009 6097 8.772705 GTCTTAATGTTTTCCATTTCATTTGCA 58.227 29.630 0.00 0.00 41.01 4.08
3010 6098 9.334947 TCTTAATGTTTTCCATTTCATTTGCAA 57.665 25.926 0.00 0.00 41.01 4.08
3011 6099 9.947669 CTTAATGTTTTCCATTTCATTTGCAAA 57.052 25.926 15.44 15.44 41.01 3.68
3013 6101 8.631676 AATGTTTTCCATTTCATTTGCAAAAC 57.368 26.923 17.19 5.66 41.01 2.43
3014 6102 7.149569 TGTTTTCCATTTCATTTGCAAAACA 57.850 28.000 17.19 8.31 38.99 2.83
3015 6103 7.769220 TGTTTTCCATTTCATTTGCAAAACAT 58.231 26.923 17.19 3.11 37.34 2.71
3016 6104 8.896744 TGTTTTCCATTTCATTTGCAAAACATA 58.103 25.926 17.19 2.99 37.34 2.29
3017 6105 9.168353 GTTTTCCATTTCATTTGCAAAACATAC 57.832 29.630 17.19 0.00 34.08 2.39
3018 6106 8.674263 TTTCCATTTCATTTGCAAAACATACT 57.326 26.923 17.19 0.00 0.00 2.12
3019 6107 9.770097 TTTCCATTTCATTTGCAAAACATACTA 57.230 25.926 17.19 0.00 0.00 1.82
3020 6108 9.770097 TTCCATTTCATTTGCAAAACATACTAA 57.230 25.926 17.19 4.59 0.00 2.24
3021 6109 9.941325 TCCATTTCATTTGCAAAACATACTAAT 57.059 25.926 17.19 6.59 0.00 1.73
3022 6110 9.976255 CCATTTCATTTGCAAAACATACTAATG 57.024 29.630 17.19 16.19 39.17 1.90
3025 6113 9.755804 TTTCATTTGCAAAACATACTAATGTCA 57.244 25.926 17.19 0.00 45.79 3.58
3026 6114 9.926158 TTCATTTGCAAAACATACTAATGTCAT 57.074 25.926 17.19 0.00 45.79 3.06
3027 6115 9.926158 TCATTTGCAAAACATACTAATGTCATT 57.074 25.926 17.19 3.06 45.79 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.254286 GGCAAAAACACAAAATACACAACTAGG 60.254 37.037 0.00 0.00 0.00 3.02
185 189 6.421405 GGTGAATGAACAACTCAAAAATTGC 58.579 36.000 0.00 0.00 37.67 3.56
189 194 4.399618 TCCGGTGAATGAACAACTCAAAAA 59.600 37.500 0.00 0.00 37.67 1.94
200 205 6.588719 ATGAAAGAAATTCCGGTGAATGAA 57.411 33.333 0.00 0.00 40.34 2.57
247 252 5.247507 TGCAAATTGAAACTATGGATCGG 57.752 39.130 0.00 0.00 0.00 4.18
340 345 5.463392 GCTTTGTTAGATCGAGCATCATGTA 59.537 40.000 2.38 0.00 33.29 2.29
349 354 1.590238 CTGCCGCTTTGTTAGATCGAG 59.410 52.381 0.00 0.00 0.00 4.04
367 372 6.992063 ATTTCATTAACTAGAGTGGTGCTG 57.008 37.500 0.00 0.00 0.00 4.41
391 396 7.221450 AGCCTCAGTTGTACTAATTTTGTGTA 58.779 34.615 0.00 0.00 0.00 2.90
401 406 6.429151 TGATTACCTAGCCTCAGTTGTACTA 58.571 40.000 0.00 0.00 0.00 1.82
421 426 4.795962 GCGTTTGATGGTGGTTTTCTGATT 60.796 41.667 0.00 0.00 0.00 2.57
424 429 2.034558 AGCGTTTGATGGTGGTTTTCTG 59.965 45.455 0.00 0.00 0.00 3.02
436 441 5.421212 TTTACGTGGTTTTAGCGTTTGAT 57.579 34.783 0.00 0.00 39.64 2.57
437 442 4.871993 TTTACGTGGTTTTAGCGTTTGA 57.128 36.364 0.00 0.00 39.64 2.69
439 444 4.142513 TGGTTTTACGTGGTTTTAGCGTTT 60.143 37.500 0.00 0.00 39.64 3.60
454 459 1.684450 CCCCAGTTGTGGTGGTTTTAC 59.316 52.381 0.00 0.00 43.23 2.01
456 461 1.334384 GCCCCAGTTGTGGTGGTTTT 61.334 55.000 0.00 0.00 43.23 2.43
466 471 2.114670 CGCATACCTGCCCCAGTTG 61.115 63.158 0.00 0.00 46.07 3.16
469 474 2.203070 GTCGCATACCTGCCCCAG 60.203 66.667 0.00 0.00 46.07 4.45
513 518 2.073816 ACCTTTCGATTACGCAACCAG 58.926 47.619 0.00 0.00 39.58 4.00
519 524 3.184581 GGATGATGACCTTTCGATTACGC 59.815 47.826 0.00 0.00 39.58 4.42
535 540 6.661304 AAAAGCAAAAGACTTGAGGATGAT 57.339 33.333 0.00 0.00 0.00 2.45
557 562 4.062991 GACTTAAGGACCGCTCAGAAAAA 58.937 43.478 7.53 0.00 0.00 1.94
558 563 3.323979 AGACTTAAGGACCGCTCAGAAAA 59.676 43.478 7.53 0.00 0.00 2.29
559 564 2.897969 AGACTTAAGGACCGCTCAGAAA 59.102 45.455 7.53 0.00 0.00 2.52
560 565 2.526432 AGACTTAAGGACCGCTCAGAA 58.474 47.619 7.53 0.00 0.00 3.02
561 566 2.217510 AGACTTAAGGACCGCTCAGA 57.782 50.000 7.53 0.00 0.00 3.27
562 567 3.320673 AAAGACTTAAGGACCGCTCAG 57.679 47.619 7.53 0.00 0.00 3.35
563 568 3.399330 CAAAAGACTTAAGGACCGCTCA 58.601 45.455 7.53 0.00 0.00 4.26
564 569 2.159824 GCAAAAGACTTAAGGACCGCTC 59.840 50.000 7.53 0.00 0.00 5.03
565 570 2.152016 GCAAAAGACTTAAGGACCGCT 58.848 47.619 7.53 0.00 0.00 5.52
566 571 2.152016 AGCAAAAGACTTAAGGACCGC 58.848 47.619 7.53 1.91 0.00 5.68
567 572 5.614013 CGTTTAGCAAAAGACTTAAGGACCG 60.614 44.000 7.53 0.00 0.00 4.79
568 573 5.467735 TCGTTTAGCAAAAGACTTAAGGACC 59.532 40.000 7.53 0.00 0.00 4.46
618 623 2.308690 AGTTACAGTATCTCGGAGCCC 58.691 52.381 0.00 0.00 0.00 5.19
620 625 3.564644 TGCTAGTTACAGTATCTCGGAGC 59.435 47.826 0.00 5.46 0.00 4.70
621 626 5.752892 TTGCTAGTTACAGTATCTCGGAG 57.247 43.478 0.00 0.00 0.00 4.63
622 627 4.036498 GCTTGCTAGTTACAGTATCTCGGA 59.964 45.833 0.00 0.00 0.00 4.55
623 628 4.202020 TGCTTGCTAGTTACAGTATCTCGG 60.202 45.833 0.00 0.00 0.00 4.63
624 629 4.921547 TGCTTGCTAGTTACAGTATCTCG 58.078 43.478 0.00 0.00 0.00 4.04
627 632 5.601662 TGGATGCTTGCTAGTTACAGTATC 58.398 41.667 0.00 0.00 0.00 2.24
628 633 5.363868 TCTGGATGCTTGCTAGTTACAGTAT 59.636 40.000 10.53 0.00 0.00 2.12
629 634 4.709886 TCTGGATGCTTGCTAGTTACAGTA 59.290 41.667 10.53 0.00 0.00 2.74
631 636 4.118410 CTCTGGATGCTTGCTAGTTACAG 58.882 47.826 6.26 6.26 0.00 2.74
632 637 3.515502 ACTCTGGATGCTTGCTAGTTACA 59.484 43.478 0.00 0.00 0.00 2.41
633 638 4.130286 ACTCTGGATGCTTGCTAGTTAC 57.870 45.455 0.00 0.00 0.00 2.50
634 639 4.202161 GCTACTCTGGATGCTTGCTAGTTA 60.202 45.833 0.00 0.00 0.00 2.24
635 640 3.431486 GCTACTCTGGATGCTTGCTAGTT 60.431 47.826 0.00 0.00 0.00 2.24
636 641 2.102252 GCTACTCTGGATGCTTGCTAGT 59.898 50.000 0.00 5.41 0.00 2.57
637 642 2.364970 AGCTACTCTGGATGCTTGCTAG 59.635 50.000 0.00 0.00 30.96 3.42
638 643 2.102084 CAGCTACTCTGGATGCTTGCTA 59.898 50.000 0.00 0.00 39.15 3.49
639 644 1.134461 CAGCTACTCTGGATGCTTGCT 60.134 52.381 0.00 0.00 39.15 3.91
640 645 1.297664 CAGCTACTCTGGATGCTTGC 58.702 55.000 0.00 0.00 39.15 4.01
641 646 1.297664 GCAGCTACTCTGGATGCTTG 58.702 55.000 0.00 0.00 43.06 4.01
652 657 4.020218 TGGAGTAAAGTCAATGCAGCTACT 60.020 41.667 0.00 0.00 0.00 2.57
669 674 5.629133 GCCACTTGTGGATAGAATTGGAGTA 60.629 44.000 22.52 0.00 33.35 2.59
674 679 5.065218 GTGTAGCCACTTGTGGATAGAATTG 59.935 44.000 22.52 0.00 38.61 2.32
675 680 5.186198 GTGTAGCCACTTGTGGATAGAATT 58.814 41.667 22.52 2.42 38.61 2.17
681 686 2.783135 CTTGTGTAGCCACTTGTGGAT 58.217 47.619 22.52 18.81 42.34 3.41
693 698 3.532892 CAACTCTGCAAGCTTGTGTAG 57.467 47.619 26.55 21.13 32.97 2.74
708 713 4.219033 CAGTGATTAACAAACGGCAACTC 58.781 43.478 0.00 0.00 0.00 3.01
709 714 3.550030 GCAGTGATTAACAAACGGCAACT 60.550 43.478 0.00 0.00 35.46 3.16
710 715 2.724174 GCAGTGATTAACAAACGGCAAC 59.276 45.455 0.00 0.00 35.46 4.17
711 716 2.359214 TGCAGTGATTAACAAACGGCAA 59.641 40.909 8.63 0.00 41.05 4.52
712 717 1.950216 TGCAGTGATTAACAAACGGCA 59.050 42.857 0.00 7.44 41.60 5.69
713 718 2.584791 CTGCAGTGATTAACAAACGGC 58.415 47.619 5.25 3.28 35.86 5.68
714 719 2.031245 TGCTGCAGTGATTAACAAACGG 60.031 45.455 16.64 0.00 0.00 4.44
715 720 3.228749 CTGCTGCAGTGATTAACAAACG 58.771 45.455 21.21 0.00 0.00 3.60
751 760 9.319060 TGCTTATAATAGTGGAGATCTGAATCT 57.681 33.333 0.00 0.00 45.16 2.40
771 780 8.792830 ATAATGCGTGATTATTAGGTGCTTAT 57.207 30.769 0.00 0.00 34.07 1.73
782 791 8.656849 GGATTAGAACGAATAATGCGTGATTAT 58.343 33.333 0.00 0.00 41.75 1.28
783 792 7.148869 CGGATTAGAACGAATAATGCGTGATTA 60.149 37.037 17.46 0.00 44.45 1.75
784 793 6.346598 CGGATTAGAACGAATAATGCGTGATT 60.347 38.462 17.46 0.00 44.45 2.57
785 794 5.118664 CGGATTAGAACGAATAATGCGTGAT 59.881 40.000 17.46 0.00 44.45 3.06
786 795 4.443063 CGGATTAGAACGAATAATGCGTGA 59.557 41.667 17.46 0.00 44.45 4.35
787 796 4.688063 CGGATTAGAACGAATAATGCGTG 58.312 43.478 17.46 0.97 44.45 5.34
788 797 4.966850 CGGATTAGAACGAATAATGCGT 57.033 40.909 17.46 0.00 44.45 5.24
790 799 5.612709 GCACTCGGATTAGAACGAATAATGC 60.613 44.000 0.00 0.00 38.79 3.56
791 800 5.387444 CGCACTCGGATTAGAACGAATAATG 60.387 44.000 0.00 0.00 38.79 1.90
851 860 0.037697 GGGTCCCGGTTTTCAAATGC 60.038 55.000 0.00 0.00 0.00 3.56
852 861 0.606096 GGGGTCCCGGTTTTCAAATG 59.394 55.000 0.48 0.00 0.00 2.32
895 904 0.250381 TTTGTTCCATACGGGTGCGT 60.250 50.000 0.00 0.00 38.11 5.24
902 911 0.315869 GCCGCGATTTGTTCCATACG 60.316 55.000 8.23 0.00 0.00 3.06
903 912 0.730265 TGCCGCGATTTGTTCCATAC 59.270 50.000 8.23 0.00 0.00 2.39
904 913 0.730265 GTGCCGCGATTTGTTCCATA 59.270 50.000 8.23 0.00 0.00 2.74
905 914 1.506262 GTGCCGCGATTTGTTCCAT 59.494 52.632 8.23 0.00 0.00 3.41
906 915 2.622011 GGTGCCGCGATTTGTTCCA 61.622 57.895 8.23 0.00 0.00 3.53
907 916 2.178273 GGTGCCGCGATTTGTTCC 59.822 61.111 8.23 0.00 0.00 3.62
908 917 2.202298 CGGTGCCGCGATTTGTTC 60.202 61.111 8.23 0.00 0.00 3.18
919 928 1.172812 GGATTAATGGAGCCGGTGCC 61.173 60.000 1.90 5.43 38.69 5.01
932 941 6.156775 TGAAGAGGTGATCATCACTGGATTAA 59.843 38.462 17.46 0.00 46.19 1.40
960 999 0.108585 TGGGAAGCCGAATATGCCTC 59.891 55.000 0.00 0.00 0.00 4.70
962 1001 1.172812 GGTGGGAAGCCGAATATGCC 61.173 60.000 0.00 0.00 0.00 4.40
1359 1401 1.073199 CGCTTGGGGAAGGAACAGT 59.927 57.895 0.00 0.00 0.00 3.55
1379 1421 3.130516 AGAACGCATTGACCTCTCGATTA 59.869 43.478 0.00 0.00 0.00 1.75
1392 1434 1.609061 CCACACCTCTCAGAACGCATT 60.609 52.381 0.00 0.00 0.00 3.56
1544 1586 4.811557 GGATCAAAGTACATGTAGTCTGGC 59.188 45.833 13.58 6.49 0.00 4.85
1554 1596 7.448161 TGTCAATGTTTCAGGATCAAAGTACAT 59.552 33.333 0.00 0.00 0.00 2.29
1559 1601 6.742109 ACTTGTCAATGTTTCAGGATCAAAG 58.258 36.000 0.00 0.00 0.00 2.77
1645 1688 4.283337 TCGTCTGTTAGATCCCCATACAA 58.717 43.478 0.00 0.00 0.00 2.41
1761 1804 2.295253 AGCTTTTATCCTCGGTGTCG 57.705 50.000 0.00 0.00 37.82 4.35
1764 1807 2.939103 CTCCAAGCTTTTATCCTCGGTG 59.061 50.000 0.00 0.00 0.00 4.94
1767 1810 3.118592 AGGACTCCAAGCTTTTATCCTCG 60.119 47.826 11.01 0.00 28.75 4.63
1934 1977 0.476338 TCAAAGCAACAGGGGTGCTA 59.524 50.000 9.46 0.00 38.01 3.49
2171 2214 9.696917 AAAAGATAAACTCAGGCTTTTACAATG 57.303 29.630 0.00 0.00 37.11 2.82
2304 2350 6.183360 GCAGTACATAGAATGTCTTGTGTCAC 60.183 42.308 0.00 0.00 43.67 3.67
2308 2354 5.639082 TGTGCAGTACATAGAATGTCTTGTG 59.361 40.000 0.00 0.00 43.67 3.33
2347 2393 2.572191 TGTATGCGGTACTGTAGTGC 57.428 50.000 3.10 4.69 34.27 4.40
2359 2405 3.798878 CAGAGTACTGACCATTGTATGCG 59.201 47.826 0.00 0.00 46.03 4.73
2373 2425 8.012477 AGTAGGGACTAGATAGTACAGAGTACT 58.988 40.741 13.64 13.64 44.14 2.73
2374 2426 8.193953 AGTAGGGACTAGATAGTACAGAGTAC 57.806 42.308 4.66 0.00 44.14 2.73
2394 2446 3.841255 AGAAAGTTCTCAAGGGGAGTAGG 59.159 47.826 0.00 0.00 44.40 3.18
2497 5555 1.785041 GCTGCAGGAACTTTGCACGA 61.785 55.000 17.12 0.00 45.89 4.35
2614 5672 6.808704 GCCAAGAGCTTTTAGTTTATGAAAGG 59.191 38.462 0.00 0.00 35.55 3.11
2628 5686 4.605064 TTGCAGGCCAAGAGCTTT 57.395 50.000 5.01 0.00 43.05 3.51
2693 5763 6.258727 CGTTGCAGATAAATGACTAGATTGGT 59.741 38.462 0.00 0.00 0.00 3.67
2694 5764 6.258727 ACGTTGCAGATAAATGACTAGATTGG 59.741 38.462 0.00 0.00 0.00 3.16
2695 5765 7.239166 ACGTTGCAGATAAATGACTAGATTG 57.761 36.000 0.00 0.00 0.00 2.67
2696 5766 8.198109 ACTACGTTGCAGATAAATGACTAGATT 58.802 33.333 0.00 0.00 0.00 2.40
2697 5767 7.717568 ACTACGTTGCAGATAAATGACTAGAT 58.282 34.615 0.00 0.00 0.00 1.98
2698 5768 7.067129 AGACTACGTTGCAGATAAATGACTAGA 59.933 37.037 0.00 0.00 0.00 2.43
2869 5950 7.763172 TTTCCACATGTACAAACACAAAATC 57.237 32.000 0.00 0.00 38.78 2.17
2937 6025 5.757850 AGCAAGAACTCTTAAAACAGTGG 57.242 39.130 0.00 0.00 34.28 4.00
2943 6031 7.502561 AGCCTAAAGAAGCAAGAACTCTTAAAA 59.497 33.333 0.00 0.00 34.28 1.52
2975 6063 4.038642 TGGAAAACATTAAGACAAGGCCAC 59.961 41.667 5.01 0.00 0.00 5.01
2976 6064 4.219115 TGGAAAACATTAAGACAAGGCCA 58.781 39.130 5.01 0.00 0.00 5.36
2977 6065 4.864704 TGGAAAACATTAAGACAAGGCC 57.135 40.909 0.00 0.00 0.00 5.19
2992 6080 9.118300 AGTATGTTTTGCAAATGAAATGGAAAA 57.882 25.926 13.65 2.46 43.03 2.29
2993 6081 8.674263 AGTATGTTTTGCAAATGAAATGGAAA 57.326 26.923 13.65 0.00 36.50 3.13
2994 6082 9.770097 TTAGTATGTTTTGCAAATGAAATGGAA 57.230 25.926 13.65 0.00 0.00 3.53
2995 6083 9.941325 ATTAGTATGTTTTGCAAATGAAATGGA 57.059 25.926 13.65 0.00 0.00 3.41
2996 6084 9.976255 CATTAGTATGTTTTGCAAATGAAATGG 57.024 29.630 13.65 0.00 0.00 3.16
2999 6087 9.755804 TGACATTAGTATGTTTTGCAAATGAAA 57.244 25.926 13.65 0.00 44.90 2.69
3000 6088 9.926158 ATGACATTAGTATGTTTTGCAAATGAA 57.074 25.926 13.65 1.99 44.90 2.57
3001 6089 9.926158 AATGACATTAGTATGTTTTGCAAATGA 57.074 25.926 13.65 2.76 44.90 2.57


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

AutoCloner maintained by Alex Coulton.