Multiple sequence alignment - TraesCS1A01G402000

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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 TraesCS1A01G402000 chr1A 100.000 3656 0 0 1 3656 565516753 565520408 0.000000e+00 6752.0
1 TraesCS1A01G402000 chr1D 89.576 3463 170 76 7 3375 471403625 471406990 0.000000e+00 4218.0
2 TraesCS1A01G402000 chr1D 86.826 167 10 4 3488 3654 471407005 471407159 3.750000e-40 176.0
3 TraesCS1A01G402000 chr1B 92.943 1913 105 18 1583 3483 655248644 655250538 0.000000e+00 2758.0
4 TraesCS1A01G402000 chr1B 83.206 1697 107 81 1 1637 655247157 655248735 0.000000e+00 1391.0
5 TraesCS1A01G402000 chr1B 87.234 188 8 1 3483 3654 655250475 655250662 2.230000e-47 200.0
6 TraesCS1A01G402000 chr5D 89.744 78 7 1 2577 2653 536253353 536253276 8.360000e-17 99.0
7 TraesCS1A01G402000 chr5D 90.541 74 6 1 2581 2653 536278669 536278596 3.010000e-16 97.1
8 TraesCS1A01G402000 chr5D 85.542 83 11 1 2572 2653 536026698 536026780 6.500000e-13 86.1
9 TraesCS1A01G402000 chr5D 85.185 81 12 0 2571 2651 536048712 536048792 2.340000e-12 84.2
10 TraesCS1A01G402000 chr5B 89.744 78 7 1 2577 2653 676536482 676536405 8.360000e-17 99.0
11 TraesCS1A01G402000 chr4A 90.541 74 6 1 2581 2653 635743247 635743174 3.010000e-16 97.1
12 TraesCS1A01G402000 chr4A 87.838 74 8 1 2581 2653 635300018 635299945 6.500000e-13 86.1
13 TraesCS1A01G402000 chr7D 100.000 32 0 0 3378 3409 303039786 303039817 3.940000e-05 60.2
14 TraesCS1A01G402000 chr7A 100.000 32 0 0 3378 3409 367258890 367258859 3.940000e-05 60.2


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 TraesCS1A01G402000 chr1A 565516753 565520408 3655 False 6752.000000 6752 100.000000 1 3656 1 chr1A.!!$F1 3655
1 TraesCS1A01G402000 chr1D 471403625 471407159 3534 False 2197.000000 4218 88.201000 7 3654 2 chr1D.!!$F1 3647
2 TraesCS1A01G402000 chr1B 655247157 655250662 3505 False 1449.666667 2758 87.794333 1 3654 3 chr1B.!!$F1 3653

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
893 962 0.039074 CGACCCACTCACACTCTCAC 60.039 60.0 0.00 0.0 0.0 3.51 F
1500 1614 0.101939 CGTTAGCTACCGTTCCCTCC 59.898 60.0 2.02 0.0 0.0 4.30 F
1979 2131 0.234884 GACGAGGTCTTTGCCAAACG 59.765 55.0 0.00 0.0 0.0 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 2617 0.108138 ACACCTAGGCTCATCAACGC 60.108 55.000 9.3 0.0 0.0 4.84 R
2532 2687 0.593128 GTTCATCGTTGCAGCCAAGT 59.407 50.000 0.0 0.0 0.0 3.16 R
3071 3234 1.282157 GGCCCTAACCATGTCAGTCTT 59.718 52.381 0.0 0.0 0.0 3.01 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
23 24 1.135603 CCACACATGTGCTTTCCATCG 60.136 52.381 25.68 0.00 44.34 3.84
80 84 6.593382 GCTACTTTCTTAGGGCAGATATCATG 59.407 42.308 5.32 1.93 0.00 3.07
105 109 3.576648 GCACGTAGCTAGCCCTAATTAG 58.423 50.000 12.13 5.43 41.15 1.73
112 120 4.076394 AGCTAGCCCTAATTAGACTCTCG 58.924 47.826 12.13 5.25 0.00 4.04
185 199 4.109050 GGATCTTAGCAATCCGATCGATC 58.891 47.826 18.66 15.68 33.78 3.69
193 207 0.600557 ATCCGATCGATCAGCAGGTC 59.399 55.000 24.40 0.00 0.00 3.85
204 218 3.049708 TCAGCAGGTCACATTCAGAAG 57.950 47.619 0.00 0.00 0.00 2.85
216 230 5.702670 TCACATTCAGAAGTCAAGACATTCC 59.297 40.000 2.72 0.00 0.00 3.01
225 239 3.776969 AGTCAAGACATTCCCAGCTATCA 59.223 43.478 2.72 0.00 0.00 2.15
268 282 2.807895 GCATGCTTGCCAAGTGCG 60.808 61.111 11.37 0.00 45.60 5.34
269 283 2.807895 CATGCTTGCCAAGTGCGC 60.808 61.111 6.28 0.00 45.60 6.09
270 284 4.409218 ATGCTTGCCAAGTGCGCG 62.409 61.111 0.00 0.00 45.60 6.86
272 286 4.107051 GCTTGCCAAGTGCGCGAT 62.107 61.111 12.10 0.00 45.60 4.58
273 287 2.202388 CTTGCCAAGTGCGCGATG 60.202 61.111 12.10 2.00 45.60 3.84
274 288 4.403137 TTGCCAAGTGCGCGATGC 62.403 61.111 12.10 2.33 45.60 3.91
320 334 1.298413 CGTCCGTATGTCGCTGGAG 60.298 63.158 0.00 0.00 38.35 3.86
321 335 1.589196 GTCCGTATGTCGCTGGAGC 60.589 63.158 0.00 0.00 38.35 4.70
364 390 2.336809 CGGCCACGAGATAGCTCC 59.663 66.667 2.24 0.00 44.60 4.70
383 409 1.687054 CCCCGGCGACCCTATATATGA 60.687 57.143 9.30 0.00 0.00 2.15
391 420 4.338682 GCGACCCTATATATGACTAGGTGG 59.661 50.000 0.00 0.00 33.93 4.61
392 421 4.338682 CGACCCTATATATGACTAGGTGGC 59.661 50.000 0.00 0.00 33.93 5.01
393 422 5.520751 GACCCTATATATGACTAGGTGGCT 58.479 45.833 0.00 0.00 33.93 4.75
394 423 6.634268 CGACCCTATATATGACTAGGTGGCTA 60.634 46.154 0.00 0.00 33.93 3.93
395 424 6.674573 ACCCTATATATGACTAGGTGGCTAG 58.325 44.000 0.00 0.00 33.93 3.42
396 425 6.071984 CCCTATATATGACTAGGTGGCTAGG 58.928 48.000 0.00 0.00 33.93 3.02
397 426 6.126156 CCCTATATATGACTAGGTGGCTAGGA 60.126 46.154 0.00 0.00 33.93 2.94
398 427 6.773685 CCTATATATGACTAGGTGGCTAGGAC 59.226 46.154 0.00 0.00 31.60 3.85
408 437 2.489437 GGTGGCTAGGACTAGGAGGTAG 60.489 59.091 8.33 0.00 33.87 3.18
409 438 1.145325 TGGCTAGGACTAGGAGGTAGC 59.855 57.143 8.33 1.11 36.23 3.58
521 558 4.537433 GCTTGGCGGGAGAGCGAT 62.537 66.667 0.00 0.00 38.18 4.58
527 564 4.674904 CGGGAGAGCGATCGAGCG 62.675 72.222 20.40 20.40 43.00 5.03
531 568 2.892334 GAGAGCGATCGAGCGAGCT 61.892 63.158 29.29 21.78 43.33 4.09
532 569 1.561717 GAGAGCGATCGAGCGAGCTA 61.562 60.000 29.29 0.00 40.39 3.32
533 570 1.154488 GAGCGATCGAGCGAGCTAG 60.154 63.158 29.29 0.00 40.39 3.42
534 571 2.799088 GCGATCGAGCGAGCTAGC 60.799 66.667 29.29 11.29 37.41 3.42
535 572 2.498676 CGATCGAGCGAGCTAGCG 60.499 66.667 20.02 1.31 43.00 4.26
661 713 3.855853 GGGCCGGAAGAGAGCTCC 61.856 72.222 10.93 1.70 0.00 4.70
747 803 2.839632 AGGATGGAGATCGCGGCA 60.840 61.111 6.13 0.00 0.00 5.69
749 805 2.356793 GATGGAGATCGCGGCAGG 60.357 66.667 6.13 0.00 0.00 4.85
811 877 2.761465 GGCAGGGATGGAGGAAGGG 61.761 68.421 0.00 0.00 0.00 3.95
814 880 1.059006 CAGGGATGGAGGAAGGGAGG 61.059 65.000 0.00 0.00 0.00 4.30
815 881 1.772156 GGGATGGAGGAAGGGAGGG 60.772 68.421 0.00 0.00 0.00 4.30
816 882 1.318380 GGATGGAGGAAGGGAGGGA 59.682 63.158 0.00 0.00 0.00 4.20
817 883 0.766288 GGATGGAGGAAGGGAGGGAG 60.766 65.000 0.00 0.00 0.00 4.30
818 884 0.266152 GATGGAGGAAGGGAGGGAGA 59.734 60.000 0.00 0.00 0.00 3.71
819 885 0.725133 ATGGAGGAAGGGAGGGAGAA 59.275 55.000 0.00 0.00 0.00 2.87
820 886 0.043334 TGGAGGAAGGGAGGGAGAAG 59.957 60.000 0.00 0.00 0.00 2.85
849 915 0.394352 CTAGGTCGGCCCAAGCAAAT 60.394 55.000 0.08 0.00 42.56 2.32
850 916 0.913205 TAGGTCGGCCCAAGCAAATA 59.087 50.000 0.08 0.00 42.56 1.40
851 917 0.394352 AGGTCGGCCCAAGCAAATAG 60.394 55.000 0.08 0.00 42.56 1.73
863 929 6.094881 GCCCAAGCAAATAGTATAAACAGACA 59.905 38.462 0.00 0.00 39.53 3.41
864 930 7.472543 CCCAAGCAAATAGTATAAACAGACAC 58.527 38.462 0.00 0.00 0.00 3.67
871 937 4.451629 AGTATAAACAGACACCACCTCG 57.548 45.455 0.00 0.00 0.00 4.63
874 940 2.676163 AAACAGACACCACCTCGCCC 62.676 60.000 0.00 0.00 0.00 6.13
875 941 4.742201 CAGACACCACCTCGCCCG 62.742 72.222 0.00 0.00 0.00 6.13
893 962 0.039074 CGACCCACTCACACTCTCAC 60.039 60.000 0.00 0.00 0.00 3.51
912 981 1.271488 ACCTTCGTCTCGACCTCTTCT 60.271 52.381 0.00 0.00 34.89 2.85
965 1034 4.858680 GAACCCTAGCCAGCGCCC 62.859 72.222 2.29 0.00 34.57 6.13
1330 1417 0.380378 CTAGCTCACTCTGCTCCGTC 59.620 60.000 0.00 0.00 41.46 4.79
1413 1517 0.943835 CGTCTGGTTCGTGCATGTCA 60.944 55.000 5.68 2.88 0.00 3.58
1500 1614 0.101939 CGTTAGCTACCGTTCCCTCC 59.898 60.000 2.02 0.00 0.00 4.30
1579 1693 3.782443 GGTTGGGGTCGCGGAGAT 61.782 66.667 6.13 0.00 0.00 2.75
1580 1694 2.267961 GTTGGGGTCGCGGAGATT 59.732 61.111 6.13 0.00 0.00 2.40
1581 1695 2.106683 GTTGGGGTCGCGGAGATTG 61.107 63.158 6.13 0.00 0.00 2.67
1591 1705 2.031163 GGAGATTGCCGCCGCTAT 59.969 61.111 0.00 0.00 35.36 2.97
1598 1712 4.849310 GCCGCCGCTATGGGTTGA 62.849 66.667 0.00 0.00 38.63 3.18
1634 1782 2.435410 CGCTACGGGTTGGGGTTC 60.435 66.667 0.00 0.00 0.00 3.62
1638 1786 0.671472 CTACGGGTTGGGGTTCGAAC 60.671 60.000 20.14 20.14 0.00 3.95
1798 1950 5.650543 CACTTTTGACTAACCTGCACTTTT 58.349 37.500 0.00 0.00 0.00 2.27
1922 2074 1.213926 CATCAAGGGGGAGGAAGAAGG 59.786 57.143 0.00 0.00 0.00 3.46
1947 2099 2.204291 AAGGGGGAGGACATGGCA 60.204 61.111 0.00 0.00 0.00 4.92
1979 2131 0.234884 GACGAGGTCTTTGCCAAACG 59.765 55.000 0.00 0.00 0.00 3.60
2004 2156 2.030451 GCAGAAGGTTGCCAAGAAGAAG 60.030 50.000 0.00 0.00 38.13 2.85
2064 2216 0.919710 GGGGGCATAAGAAGACCACT 59.080 55.000 0.00 0.00 0.00 4.00
2133 2285 3.299503 ACTTTGGGTGTGCAAGAAGAAT 58.700 40.909 0.00 0.00 0.00 2.40
2188 2340 1.259609 CCAGCCTGATTCCTTTTGCA 58.740 50.000 0.00 0.00 0.00 4.08
2204 2356 7.971201 TCCTTTTGCATATATCACTCAGATCT 58.029 34.615 0.00 0.00 38.19 2.75
2313 2465 3.254411 GTGAGGGGTACTTATACTACGCC 59.746 52.174 12.10 12.10 44.07 5.68
2378 2530 5.880332 GCAATGTACTGGAATCTTTACCTGA 59.120 40.000 0.00 0.00 0.00 3.86
2462 2617 2.466982 ATCAAGCGGCATCAGCACG 61.467 57.895 1.45 0.00 44.61 5.34
2488 2643 2.238084 TGAGCCTAGGTGTGATGAGT 57.762 50.000 11.31 0.00 0.00 3.41
2659 2814 5.062528 TCAAGTCATTGATGTGTTAGCACA 58.937 37.500 15.12 15.12 45.14 4.57
2755 2913 4.002906 ACACTACCATGGTGTTAGTGTG 57.997 45.455 35.29 27.43 46.40 3.82
2830 2990 3.326297 AGGTAGAGCTTGGCAGGATATTC 59.674 47.826 0.00 0.00 0.00 1.75
2901 3063 4.634184 ACAAGGTACTGCAGTATACTCG 57.366 45.455 28.37 20.31 40.86 4.18
2916 3078 8.133627 GCAGTATACTCGAGTAATTTGTTAGGA 58.866 37.037 27.90 3.99 33.76 2.94
2917 3079 9.448294 CAGTATACTCGAGTAATTTGTTAGGAC 57.552 37.037 27.90 12.70 33.76 3.85
2918 3080 9.406113 AGTATACTCGAGTAATTTGTTAGGACT 57.594 33.333 27.90 14.34 33.76 3.85
2922 3084 7.545489 ACTCGAGTAATTTGTTAGGACTTAGG 58.455 38.462 18.46 0.00 0.00 2.69
2923 3085 7.178097 ACTCGAGTAATTTGTTAGGACTTAGGT 59.822 37.037 18.46 0.00 0.00 3.08
2924 3086 7.318141 TCGAGTAATTTGTTAGGACTTAGGTG 58.682 38.462 0.00 0.00 0.00 4.00
2925 3087 7.039504 TCGAGTAATTTGTTAGGACTTAGGTGT 60.040 37.037 0.00 0.00 0.00 4.16
2926 3088 7.063074 CGAGTAATTTGTTAGGACTTAGGTGTG 59.937 40.741 0.00 0.00 0.00 3.82
2927 3089 7.166167 AGTAATTTGTTAGGACTTAGGTGTGG 58.834 38.462 0.00 0.00 0.00 4.17
2945 3107 7.836842 AGGTGTGGTATTGGTTTATTTTGATC 58.163 34.615 0.00 0.00 0.00 2.92
2950 3112 9.520204 GTGGTATTGGTTTATTTTGATCTGATG 57.480 33.333 0.00 0.00 0.00 3.07
3071 3234 3.239449 TCTCTGCAGTTCTTTAGGACCA 58.761 45.455 14.67 0.00 0.00 4.02
3096 3259 1.557832 TGACATGGTTAGGGCCTGTAC 59.442 52.381 18.53 14.05 0.00 2.90
3217 3388 8.961294 AGCTATTTGATCAGATAATAGGCATC 57.039 34.615 19.94 8.98 34.14 3.91
3409 3582 6.151691 ACATAAGCTAACACATGCAGTTTTG 58.848 36.000 9.12 5.18 0.00 2.44
3451 3625 9.717892 AGTTCTCTGTTTTTATTCGTTTTCTTC 57.282 29.630 0.00 0.00 0.00 2.87
3452 3626 9.498307 GTTCTCTGTTTTTATTCGTTTTCTTCA 57.502 29.630 0.00 0.00 0.00 3.02
3454 3628 9.716507 TCTCTGTTTTTATTCGTTTTCTTCAAG 57.283 29.630 0.00 0.00 0.00 3.02
3455 3629 8.335256 TCTGTTTTTATTCGTTTTCTTCAAGC 57.665 30.769 0.00 0.00 0.00 4.01
3456 3630 8.188139 TCTGTTTTTATTCGTTTTCTTCAAGCT 58.812 29.630 0.00 0.00 0.00 3.74
3457 3631 9.445786 CTGTTTTTATTCGTTTTCTTCAAGCTA 57.554 29.630 0.00 0.00 0.00 3.32
3458 3632 9.228636 TGTTTTTATTCGTTTTCTTCAAGCTAC 57.771 29.630 0.00 0.00 0.00 3.58
3459 3633 9.228636 GTTTTTATTCGTTTTCTTCAAGCTACA 57.771 29.630 0.00 0.00 0.00 2.74
3460 3634 9.959749 TTTTTATTCGTTTTCTTCAAGCTACAT 57.040 25.926 0.00 0.00 0.00 2.29
3461 3635 9.959749 TTTTATTCGTTTTCTTCAAGCTACATT 57.040 25.926 0.00 0.00 0.00 2.71
3462 3636 9.959749 TTTATTCGTTTTCTTCAAGCTACATTT 57.040 25.926 0.00 0.00 0.00 2.32
3465 3639 9.774742 ATTCGTTTTCTTCAAGCTACATTTATC 57.225 29.630 0.00 0.00 0.00 1.75
3466 3640 8.547967 TCGTTTTCTTCAAGCTACATTTATCT 57.452 30.769 0.00 0.00 0.00 1.98
3467 3641 8.443160 TCGTTTTCTTCAAGCTACATTTATCTG 58.557 33.333 0.00 0.00 0.00 2.90
3468 3642 8.230486 CGTTTTCTTCAAGCTACATTTATCTGT 58.770 33.333 0.00 0.00 0.00 3.41
3472 3646 8.370493 TCTTCAAGCTACATTTATCTGTATGC 57.630 34.615 0.00 0.00 31.49 3.14
3473 3647 8.206867 TCTTCAAGCTACATTTATCTGTATGCT 58.793 33.333 0.00 0.00 37.53 3.79
3474 3648 9.481340 CTTCAAGCTACATTTATCTGTATGCTA 57.519 33.333 0.00 0.00 36.23 3.49
3475 3649 9.481340 TTCAAGCTACATTTATCTGTATGCTAG 57.519 33.333 0.00 0.00 36.23 3.42
3476 3650 7.600375 TCAAGCTACATTTATCTGTATGCTAGC 59.400 37.037 8.10 8.10 36.23 3.42
3477 3651 7.238486 AGCTACATTTATCTGTATGCTAGCT 57.762 36.000 17.23 4.07 37.16 3.32
3478 3652 7.319646 AGCTACATTTATCTGTATGCTAGCTC 58.680 38.462 17.23 7.19 37.26 4.09
3479 3653 7.039434 AGCTACATTTATCTGTATGCTAGCTCA 60.039 37.037 17.23 11.33 37.26 4.26
3480 3654 7.062839 GCTACATTTATCTGTATGCTAGCTCAC 59.937 40.741 17.23 13.65 33.52 3.51
3481 3655 6.820335 ACATTTATCTGTATGCTAGCTCACA 58.180 36.000 17.23 17.33 0.00 3.58
3482 3656 6.703607 ACATTTATCTGTATGCTAGCTCACAC 59.296 38.462 17.23 8.72 0.00 3.82
3483 3657 6.471233 TTTATCTGTATGCTAGCTCACACT 57.529 37.500 17.23 9.72 0.00 3.55
3484 3658 3.790152 TCTGTATGCTAGCTCACACTG 57.210 47.619 17.23 11.53 0.00 3.66
3485 3659 3.092301 TCTGTATGCTAGCTCACACTGT 58.908 45.455 17.23 0.00 0.00 3.55
3486 3660 3.129462 TCTGTATGCTAGCTCACACTGTC 59.871 47.826 17.23 0.00 0.00 3.51
3487 3661 2.825532 TGTATGCTAGCTCACACTGTCA 59.174 45.455 17.23 0.00 0.00 3.58
3488 3662 3.258123 TGTATGCTAGCTCACACTGTCAA 59.742 43.478 17.23 0.00 0.00 3.18
3489 3663 2.445565 TGCTAGCTCACACTGTCAAG 57.554 50.000 17.23 0.00 0.00 3.02
3490 3664 1.688735 TGCTAGCTCACACTGTCAAGT 59.311 47.619 17.23 0.00 36.98 3.16
3491 3665 2.103094 TGCTAGCTCACACTGTCAAGTT 59.897 45.455 17.23 0.00 32.98 2.66
3492 3666 2.734079 GCTAGCTCACACTGTCAAGTTC 59.266 50.000 7.70 0.00 32.98 3.01
3493 3667 3.553922 GCTAGCTCACACTGTCAAGTTCT 60.554 47.826 7.70 0.00 32.98 3.01
3494 3668 3.104843 AGCTCACACTGTCAAGTTCTC 57.895 47.619 0.00 0.00 32.98 2.87
3495 3669 2.697751 AGCTCACACTGTCAAGTTCTCT 59.302 45.455 0.00 0.00 32.98 3.10
3496 3670 2.799412 GCTCACACTGTCAAGTTCTCTG 59.201 50.000 0.00 0.00 32.98 3.35
3497 3671 3.739519 GCTCACACTGTCAAGTTCTCTGT 60.740 47.826 0.00 0.00 32.98 3.41
3498 3672 4.437239 CTCACACTGTCAAGTTCTCTGTT 58.563 43.478 0.00 0.00 32.98 3.16
3499 3673 4.832248 TCACACTGTCAAGTTCTCTGTTT 58.168 39.130 0.00 0.00 32.98 2.83
3500 3674 5.245531 TCACACTGTCAAGTTCTCTGTTTT 58.754 37.500 0.00 0.00 32.98 2.43
3501 3675 5.705441 TCACACTGTCAAGTTCTCTGTTTTT 59.295 36.000 0.00 0.00 32.98 1.94
3502 3676 6.876789 TCACACTGTCAAGTTCTCTGTTTTTA 59.123 34.615 0.00 0.00 32.98 1.52
3503 3677 7.552687 TCACACTGTCAAGTTCTCTGTTTTTAT 59.447 33.333 0.00 0.00 32.98 1.40
3504 3678 8.184192 CACACTGTCAAGTTCTCTGTTTTTATT 58.816 33.333 0.00 0.00 32.98 1.40
3505 3679 8.739972 ACACTGTCAAGTTCTCTGTTTTTATTT 58.260 29.630 0.00 0.00 32.98 1.40
3506 3680 9.013490 CACTGTCAAGTTCTCTGTTTTTATTTG 57.987 33.333 0.00 0.00 32.98 2.32
3507 3681 8.739972 ACTGTCAAGTTCTCTGTTTTTATTTGT 58.260 29.630 0.00 0.00 30.14 2.83
3508 3682 9.573133 CTGTCAAGTTCTCTGTTTTTATTTGTT 57.427 29.630 0.00 0.00 0.00 2.83
3509 3683 9.921637 TGTCAAGTTCTCTGTTTTTATTTGTTT 57.078 25.926 0.00 0.00 0.00 2.83
3552 3726 5.673514 TGAATGCTAGCTAACACATGATGA 58.326 37.500 17.23 0.00 0.00 2.92
3579 3753 0.610232 ATCCTTGCAGCCCTTGTGAC 60.610 55.000 0.00 0.00 0.00 3.67
3581 3755 2.594303 TTGCAGCCCTTGTGACGG 60.594 61.111 0.00 0.00 0.00 4.79
3583 3757 2.281484 GCAGCCCTTGTGACGGAA 60.281 61.111 0.00 0.00 0.00 4.30
3584 3758 2.617274 GCAGCCCTTGTGACGGAAC 61.617 63.158 0.00 0.00 0.00 3.62
3585 3759 1.071471 CAGCCCTTGTGACGGAACT 59.929 57.895 0.00 0.00 0.00 3.01
3588 3762 1.228657 GCCCTTGTGACGGAACTGAC 61.229 60.000 0.00 0.00 0.00 3.51
3590 3764 1.502231 CCTTGTGACGGAACTGACAG 58.498 55.000 0.00 0.00 0.00 3.51
3591 3765 1.068588 CCTTGTGACGGAACTGACAGA 59.931 52.381 10.08 0.00 0.00 3.41
3592 3766 2.398498 CTTGTGACGGAACTGACAGAG 58.602 52.381 10.08 0.19 0.00 3.35
3593 3767 1.687563 TGTGACGGAACTGACAGAGA 58.312 50.000 10.08 0.00 0.00 3.10
3594 3768 2.028876 TGTGACGGAACTGACAGAGAA 58.971 47.619 10.08 0.00 0.00 2.87
3595 3769 2.429250 TGTGACGGAACTGACAGAGAAA 59.571 45.455 10.08 0.00 0.00 2.52
3596 3770 2.795470 GTGACGGAACTGACAGAGAAAC 59.205 50.000 10.08 0.00 0.00 2.78
3597 3771 2.693591 TGACGGAACTGACAGAGAAACT 59.306 45.455 10.08 0.00 0.00 2.66
3654 3856 5.788533 TCCTTTTCCATTACCTAGTTCCTCA 59.211 40.000 0.00 0.00 0.00 3.86
3655 3857 5.880887 CCTTTTCCATTACCTAGTTCCTCAC 59.119 44.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.956426 TCCATAATCTGGTCAAAATTACTGAAC 58.044 33.333 0.00 0.00 46.08 3.18
51 52 3.003480 CTGCCCTAAGAAAGTAGCACAC 58.997 50.000 0.00 0.00 31.36 3.82
105 109 0.723981 GTGCTGCCATTTCGAGAGTC 59.276 55.000 0.00 0.00 0.00 3.36
112 120 1.210155 GTGTCCGTGCTGCCATTTC 59.790 57.895 0.00 0.00 0.00 2.17
148 156 6.174760 GCTAAGATCCACTACTAGCTAGCTA 58.825 44.000 22.85 22.85 34.16 3.32
185 199 2.740981 GACTTCTGAATGTGACCTGCTG 59.259 50.000 0.00 0.00 0.00 4.41
193 207 5.106396 GGGAATGTCTTGACTTCTGAATGTG 60.106 44.000 2.35 0.00 0.00 3.21
204 218 3.873952 GTGATAGCTGGGAATGTCTTGAC 59.126 47.826 0.00 0.00 0.00 3.18
278 292 4.796231 CTGGTTCGACCCGGCTCG 62.796 72.222 13.09 13.09 37.50 5.03
279 293 4.452733 CCTGGTTCGACCCGGCTC 62.453 72.222 1.45 0.00 35.82 4.70
364 390 1.407979 GTCATATATAGGGTCGCCGGG 59.592 57.143 2.18 0.00 0.00 5.73
377 403 5.862422 AGTCCTAGCCACCTAGTCATATA 57.138 43.478 0.00 0.00 39.56 0.86
383 409 2.444010 CTCCTAGTCCTAGCCACCTAGT 59.556 54.545 0.00 0.00 39.56 2.57
391 420 2.660670 TGCTACCTCCTAGTCCTAGC 57.339 55.000 0.00 0.00 31.95 3.42
392 421 4.076394 GACATGCTACCTCCTAGTCCTAG 58.924 52.174 0.00 0.00 0.00 3.02
393 422 3.496337 CGACATGCTACCTCCTAGTCCTA 60.496 52.174 0.00 0.00 0.00 2.94
394 423 2.750135 CGACATGCTACCTCCTAGTCCT 60.750 54.545 0.00 0.00 0.00 3.85
395 424 1.609555 CGACATGCTACCTCCTAGTCC 59.390 57.143 0.00 0.00 0.00 3.85
396 425 1.001158 GCGACATGCTACCTCCTAGTC 60.001 57.143 0.00 0.00 41.73 2.59
397 426 1.033574 GCGACATGCTACCTCCTAGT 58.966 55.000 0.00 0.00 41.73 2.57
398 427 1.000827 CTGCGACATGCTACCTCCTAG 60.001 57.143 0.00 0.00 46.63 3.02
408 437 2.249557 CTTCACCTGCTGCGACATGC 62.250 60.000 0.00 0.00 46.70 4.06
409 438 0.671472 TCTTCACCTGCTGCGACATG 60.671 55.000 0.00 0.00 0.00 3.21
479 513 1.728672 CCTCTAACCCTCGAGCGTC 59.271 63.158 6.99 0.00 0.00 5.19
521 558 4.538283 GCACGCTAGCTCGCTCGA 62.538 66.667 13.93 0.00 0.00 4.04
630 682 3.827898 GCCCCGTCCGTCTCTCTG 61.828 72.222 0.00 0.00 0.00 3.35
801 863 0.043334 CTTCTCCCTCCCTTCCTCCA 59.957 60.000 0.00 0.00 0.00 3.86
807 873 0.326713 GCTACCCTTCTCCCTCCCTT 60.327 60.000 0.00 0.00 0.00 3.95
811 877 1.133294 AGCTAGCTACCCTTCTCCCTC 60.133 57.143 17.69 0.00 0.00 4.30
814 880 2.158430 ACCTAGCTAGCTACCCTTCTCC 60.158 54.545 20.67 0.00 0.00 3.71
815 881 3.151554 GACCTAGCTAGCTACCCTTCTC 58.848 54.545 20.67 5.33 0.00 2.87
816 882 2.487625 CGACCTAGCTAGCTACCCTTCT 60.488 54.545 20.67 0.00 0.00 2.85
817 883 1.881324 CGACCTAGCTAGCTACCCTTC 59.119 57.143 20.67 12.37 0.00 3.46
818 884 1.479021 CCGACCTAGCTAGCTACCCTT 60.479 57.143 20.67 4.97 0.00 3.95
819 885 0.110869 CCGACCTAGCTAGCTACCCT 59.889 60.000 20.67 5.62 0.00 4.34
820 886 1.525718 GCCGACCTAGCTAGCTACCC 61.526 65.000 20.67 11.00 0.00 3.69
849 915 4.142315 GCGAGGTGGTGTCTGTTTATACTA 60.142 45.833 0.00 0.00 0.00 1.82
850 916 3.368116 GCGAGGTGGTGTCTGTTTATACT 60.368 47.826 0.00 0.00 0.00 2.12
851 917 2.928116 GCGAGGTGGTGTCTGTTTATAC 59.072 50.000 0.00 0.00 0.00 1.47
871 937 3.591254 GAGTGTGAGTGGGTCGGGC 62.591 68.421 0.00 0.00 0.00 6.13
874 940 0.039074 GTGAGAGTGTGAGTGGGTCG 60.039 60.000 0.00 0.00 0.00 4.79
875 941 0.318762 GGTGAGAGTGTGAGTGGGTC 59.681 60.000 0.00 0.00 0.00 4.46
880 946 1.609555 GACGAAGGTGAGAGTGTGAGT 59.390 52.381 0.00 0.00 0.00 3.41
881 947 1.883275 AGACGAAGGTGAGAGTGTGAG 59.117 52.381 0.00 0.00 0.00 3.51
882 948 1.880675 GAGACGAAGGTGAGAGTGTGA 59.119 52.381 0.00 0.00 0.00 3.58
893 962 1.131504 CAGAAGAGGTCGAGACGAAGG 59.868 57.143 0.00 0.00 37.72 3.46
933 1002 2.052104 GTTCGGGATTTGGGCTGGG 61.052 63.158 0.00 0.00 0.00 4.45
970 1039 4.851252 AGGGATCTGGGCTGGGGG 62.851 72.222 0.00 0.00 0.00 5.40
1318 1405 3.753434 CGCCAGACGGAGCAGAGT 61.753 66.667 0.00 0.00 38.44 3.24
1413 1517 2.359967 GCCGCAGAGGAACCCTAGT 61.360 63.158 0.00 0.00 45.00 2.57
1465 1569 1.140407 AACGCGCGCTAGAGATCAAC 61.140 55.000 32.58 0.00 0.00 3.18
1466 1570 0.379316 TAACGCGCGCTAGAGATCAA 59.621 50.000 32.58 0.00 0.00 2.57
1500 1614 0.455972 CGCCGGCCACAAATTACAAG 60.456 55.000 23.46 0.00 0.00 3.16
1562 1676 3.325201 AATCTCCGCGACCCCAACC 62.325 63.158 8.23 0.00 0.00 3.77
1563 1677 2.106683 CAATCTCCGCGACCCCAAC 61.107 63.158 8.23 0.00 0.00 3.77
1564 1678 2.267642 CAATCTCCGCGACCCCAA 59.732 61.111 8.23 0.00 0.00 4.12
1565 1679 4.467084 GCAATCTCCGCGACCCCA 62.467 66.667 8.23 0.00 0.00 4.96
1574 1688 2.031163 ATAGCGGCGGCAATCTCC 59.969 61.111 19.21 0.00 43.41 3.71
1575 1689 2.320587 CCATAGCGGCGGCAATCTC 61.321 63.158 19.21 0.00 43.41 2.75
1576 1690 2.281070 CCATAGCGGCGGCAATCT 60.281 61.111 19.21 5.17 43.41 2.40
1577 1691 3.357079 CCCATAGCGGCGGCAATC 61.357 66.667 19.21 0.00 43.41 2.67
1578 1692 3.714487 AACCCATAGCGGCGGCAAT 62.714 57.895 19.21 0.80 43.41 3.56
1579 1693 4.418328 AACCCATAGCGGCGGCAA 62.418 61.111 19.21 0.00 43.41 4.52
1581 1695 4.849310 TCAACCCATAGCGGCGGC 62.849 66.667 9.78 8.43 40.37 6.53
1591 1705 3.691342 CTCCGCGACCTCAACCCA 61.691 66.667 8.23 0.00 0.00 4.51
1798 1950 5.477984 CCACCTCCTGAAGAATGAAAAATCA 59.522 40.000 0.00 0.00 0.00 2.57
1896 2048 3.089874 TCCCCCTTGATGGAGGCG 61.090 66.667 0.00 0.00 38.35 5.52
1922 2074 4.845307 CCTCCCCCTTCCCCTCCC 62.845 77.778 0.00 0.00 0.00 4.30
1947 2099 1.133325 ACCTCGTCAGCCATATCTCCT 60.133 52.381 0.00 0.00 0.00 3.69
1986 2138 2.816672 CCTCTTCTTCTTGGCAACCTTC 59.183 50.000 0.00 0.00 0.00 3.46
2004 2156 3.999663 CTCTGTTTTCCATGACTGTCCTC 59.000 47.826 5.17 0.00 0.00 3.71
2064 2216 2.229062 GTCGTCATCACTCTGAACCTCA 59.771 50.000 0.00 0.00 0.00 3.86
2133 2285 0.472471 AAAACCTCCTCTTGCCGTCA 59.528 50.000 0.00 0.00 0.00 4.35
2175 2327 8.212995 TCTGAGTGATATATGCAAAAGGAATCA 58.787 33.333 0.00 0.00 0.00 2.57
2188 2340 8.458052 CGCAGACTTAAGATCTGAGTGATATAT 58.542 37.037 26.05 0.00 45.46 0.86
2204 2356 3.118454 GCGGCAGCGCAGACTTAA 61.118 61.111 11.47 0.00 34.62 1.85
2224 2376 1.841302 TTGGAGGCCGCTGATGAAGT 61.841 55.000 6.40 0.00 0.00 3.01
2235 2387 2.356667 CTGGAGGGTTTGGAGGCC 59.643 66.667 0.00 0.00 0.00 5.19
2378 2530 0.252479 CAGTGCCTCCTCTTGCTCAT 59.748 55.000 0.00 0.00 0.00 2.90
2462 2617 0.108138 ACACCTAGGCTCATCAACGC 60.108 55.000 9.30 0.00 0.00 4.84
2532 2687 0.593128 GTTCATCGTTGCAGCCAAGT 59.407 50.000 0.00 0.00 0.00 3.16
2659 2814 4.389374 GGCATGCATGTACAGGTATAAGT 58.611 43.478 26.79 0.00 0.00 2.24
2781 2941 8.969260 AATCTGTCATGTATGCTTCTGAATTA 57.031 30.769 0.00 0.00 0.00 1.40
2830 2990 5.990386 CAGAGTTGGTATCTTCCATGATCTG 59.010 44.000 0.00 0.00 37.33 2.90
2872 3032 4.398319 ACTGCAGTACCTTGTAAAGCATT 58.602 39.130 20.16 0.00 44.44 3.56
2880 3040 4.267536 TCGAGTATACTGCAGTACCTTGT 58.732 43.478 28.28 14.80 32.72 3.16
2901 3063 7.333672 CCACACCTAAGTCCTAACAAATTACTC 59.666 40.741 0.00 0.00 0.00 2.59
2916 3078 8.581578 CAAAATAAACCAATACCACACCTAAGT 58.418 33.333 0.00 0.00 0.00 2.24
2917 3079 8.798402 TCAAAATAAACCAATACCACACCTAAG 58.202 33.333 0.00 0.00 0.00 2.18
2918 3080 8.707796 TCAAAATAAACCAATACCACACCTAA 57.292 30.769 0.00 0.00 0.00 2.69
2919 3081 8.887264 ATCAAAATAAACCAATACCACACCTA 57.113 30.769 0.00 0.00 0.00 3.08
2921 3083 7.759433 CAGATCAAAATAAACCAATACCACACC 59.241 37.037 0.00 0.00 0.00 4.16
2922 3084 8.519526 TCAGATCAAAATAAACCAATACCACAC 58.480 33.333 0.00 0.00 0.00 3.82
2923 3085 8.642935 TCAGATCAAAATAAACCAATACCACA 57.357 30.769 0.00 0.00 0.00 4.17
2924 3086 9.520204 CATCAGATCAAAATAAACCAATACCAC 57.480 33.333 0.00 0.00 0.00 4.16
2925 3087 8.196771 GCATCAGATCAAAATAAACCAATACCA 58.803 33.333 0.00 0.00 0.00 3.25
2926 3088 8.416329 AGCATCAGATCAAAATAAACCAATACC 58.584 33.333 0.00 0.00 0.00 2.73
2950 3112 6.031751 AGCAGTCTTAATACTATGCCTAGC 57.968 41.667 0.00 0.00 0.00 3.42
2965 3128 1.903183 GACTTGTCCCCTAGCAGTCTT 59.097 52.381 0.00 0.00 0.00 3.01
3071 3234 1.282157 GGCCCTAACCATGTCAGTCTT 59.718 52.381 0.00 0.00 0.00 3.01
3096 3259 4.402474 GTCCAAAAATCCCAACCTCTATGG 59.598 45.833 0.00 0.00 42.93 2.74
3409 3582 6.130058 CAGAGAACTTAACAGAAAACTTCGC 58.870 40.000 0.00 0.00 34.02 4.70
3410 3583 7.235430 ACAGAGAACTTAACAGAAAACTTCG 57.765 36.000 0.00 0.00 34.02 3.79
3451 3625 7.601886 AGCTAGCATACAGATAAATGTAGCTTG 59.398 37.037 18.83 11.95 38.47 4.01
3452 3626 7.675062 AGCTAGCATACAGATAAATGTAGCTT 58.325 34.615 18.83 0.00 38.47 3.74
3453 3627 7.039434 TGAGCTAGCATACAGATAAATGTAGCT 60.039 37.037 18.83 13.92 41.00 3.32
3454 3628 7.062839 GTGAGCTAGCATACAGATAAATGTAGC 59.937 40.741 18.83 0.00 38.96 3.58
3455 3629 8.084684 TGTGAGCTAGCATACAGATAAATGTAG 58.915 37.037 18.83 0.00 38.96 2.74
3456 3630 7.867909 GTGTGAGCTAGCATACAGATAAATGTA 59.132 37.037 18.83 0.00 39.85 2.29
3457 3631 6.703607 GTGTGAGCTAGCATACAGATAAATGT 59.296 38.462 18.83 0.00 37.19 2.71
3458 3632 6.927936 AGTGTGAGCTAGCATACAGATAAATG 59.072 38.462 18.83 0.00 32.99 2.32
3459 3633 6.927936 CAGTGTGAGCTAGCATACAGATAAAT 59.072 38.462 18.83 0.00 32.99 1.40
3460 3634 6.127338 ACAGTGTGAGCTAGCATACAGATAAA 60.127 38.462 18.83 0.00 32.99 1.40
3461 3635 5.360999 ACAGTGTGAGCTAGCATACAGATAA 59.639 40.000 18.83 0.00 32.99 1.75
3462 3636 4.889995 ACAGTGTGAGCTAGCATACAGATA 59.110 41.667 18.83 0.00 32.99 1.98
3463 3637 3.703556 ACAGTGTGAGCTAGCATACAGAT 59.296 43.478 18.83 9.80 32.99 2.90
3464 3638 3.092301 ACAGTGTGAGCTAGCATACAGA 58.908 45.455 18.83 9.67 32.99 3.41
3465 3639 3.119352 TGACAGTGTGAGCTAGCATACAG 60.119 47.826 18.83 12.16 32.99 2.74
3466 3640 2.825532 TGACAGTGTGAGCTAGCATACA 59.174 45.455 18.83 17.75 32.99 2.29
3467 3641 3.510388 TGACAGTGTGAGCTAGCATAC 57.490 47.619 18.83 15.29 0.00 2.39
3468 3642 3.511540 ACTTGACAGTGTGAGCTAGCATA 59.488 43.478 18.83 1.62 0.00 3.14
3469 3643 2.301296 ACTTGACAGTGTGAGCTAGCAT 59.699 45.455 18.83 1.44 0.00 3.79
3470 3644 1.688735 ACTTGACAGTGTGAGCTAGCA 59.311 47.619 18.83 0.00 0.00 3.49
3471 3645 2.447244 ACTTGACAGTGTGAGCTAGC 57.553 50.000 6.62 6.62 0.00 3.42
3472 3646 4.022416 AGAGAACTTGACAGTGTGAGCTAG 60.022 45.833 0.00 0.00 31.60 3.42
3473 3647 3.891977 AGAGAACTTGACAGTGTGAGCTA 59.108 43.478 0.00 0.00 31.60 3.32
3474 3648 2.697751 AGAGAACTTGACAGTGTGAGCT 59.302 45.455 0.00 0.00 31.60 4.09
3475 3649 2.799412 CAGAGAACTTGACAGTGTGAGC 59.201 50.000 0.00 0.00 31.60 4.26
3476 3650 4.052159 ACAGAGAACTTGACAGTGTGAG 57.948 45.455 0.00 0.59 31.60 3.51
3477 3651 4.471904 AACAGAGAACTTGACAGTGTGA 57.528 40.909 0.00 0.00 31.60 3.58
3478 3652 5.551760 AAAACAGAGAACTTGACAGTGTG 57.448 39.130 0.00 0.00 31.60 3.82
3479 3653 7.865706 ATAAAAACAGAGAACTTGACAGTGT 57.134 32.000 0.00 0.00 31.60 3.55
3480 3654 9.013490 CAAATAAAAACAGAGAACTTGACAGTG 57.987 33.333 0.00 0.00 31.60 3.66
3481 3655 8.739972 ACAAATAAAAACAGAGAACTTGACAGT 58.260 29.630 0.00 0.00 33.11 3.55
3482 3656 9.573133 AACAAATAAAAACAGAGAACTTGACAG 57.427 29.630 0.00 0.00 0.00 3.51
3483 3657 9.921637 AAACAAATAAAAACAGAGAACTTGACA 57.078 25.926 0.00 0.00 0.00 3.58
3510 3684 9.672673 AGCATTCAGATAAAAGTAGCTTAAAGA 57.327 29.630 0.00 0.00 0.00 2.52
3513 3687 9.046296 GCTAGCATTCAGATAAAAGTAGCTTAA 57.954 33.333 10.63 0.00 0.00 1.85
3522 3696 8.615211 CATGTGTTAGCTAGCATTCAGATAAAA 58.385 33.333 18.83 0.00 0.00 1.52
3552 3726 2.102578 GGGCTGCAAGGATACAAATGT 58.897 47.619 0.50 0.00 41.41 2.71
3579 3753 2.224066 ACCAGTTTCTCTGTCAGTTCCG 60.224 50.000 0.00 0.00 42.19 4.30
3581 3755 3.002759 GCAACCAGTTTCTCTGTCAGTTC 59.997 47.826 0.00 0.00 42.19 3.01
3583 3757 2.171448 AGCAACCAGTTTCTCTGTCAGT 59.829 45.455 0.00 0.00 42.19 3.41
3584 3758 2.547211 CAGCAACCAGTTTCTCTGTCAG 59.453 50.000 0.00 0.00 42.19 3.51
3585 3759 2.170397 TCAGCAACCAGTTTCTCTGTCA 59.830 45.455 0.00 0.00 42.19 3.58
3588 3762 3.549625 GCTTTCAGCAACCAGTTTCTCTG 60.550 47.826 0.00 0.00 41.89 3.35
3590 3764 3.005341 GCTTTCAGCAACCAGTTTCTC 57.995 47.619 0.00 0.00 41.89 2.87


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

AutoCloner maintained by Alex Coulton.