Multiple sequence alignment - TraesCS3A01G528000

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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 TraesCS3A01G528000 chr3A 100.000 3979 0 0 1 3979 742331237 742335215 0.000000e+00 7348.0
1 TraesCS3A01G528000 chr3A 87.230 1433 141 15 2106 3514 742314006 742315420 0.000000e+00 1594.0
2 TraesCS3A01G528000 chr3A 88.530 619 47 12 647 1261 742277403 742278001 0.000000e+00 728.0
3 TraesCS3A01G528000 chr3A 87.805 533 57 5 978 1509 742355389 742355914 5.650000e-173 617.0
4 TraesCS3A01G528000 chr3A 85.159 566 71 8 1530 2094 742356233 742356786 5.770000e-158 568.0
5 TraesCS3A01G528000 chr3A 87.339 387 45 4 3594 3979 742315433 742315816 1.310000e-119 440.0
6 TraesCS3A01G528000 chr3B 88.830 1513 131 15 2106 3596 819382729 819384225 0.000000e+00 1823.0
7 TraesCS3A01G528000 chr3B 87.766 1553 140 19 1 1512 819648993 819650536 0.000000e+00 1770.0
8 TraesCS3A01G528000 chr3B 87.564 1552 143 19 1 1512 819521343 819522884 0.000000e+00 1751.0
9 TraesCS3A01G528000 chr3B 86.329 1558 143 31 1 1512 819380309 819381842 0.000000e+00 1633.0
10 TraesCS3A01G528000 chr3B 88.584 1349 125 12 2106 3430 819523532 819524875 0.000000e+00 1611.0
11 TraesCS3A01G528000 chr3B 90.956 962 75 7 2106 3067 819651630 819652579 0.000000e+00 1284.0
12 TraesCS3A01G528000 chr3B 90.350 943 84 3 2106 3048 819300499 819301434 0.000000e+00 1230.0
13 TraesCS3A01G528000 chr3B 85.714 973 100 21 3036 3979 819302169 819303131 0.000000e+00 990.0
14 TraesCS3A01G528000 chr3B 86.547 892 93 11 3058 3926 819653107 819653994 0.000000e+00 957.0
15 TraesCS3A01G528000 chr3B 95.122 574 26 2 941 1513 819298075 819298647 0.000000e+00 904.0
16 TraesCS3A01G528000 chr3B 92.599 581 38 2 1516 2094 819651071 819651648 0.000000e+00 830.0
17 TraesCS3A01G528000 chr3B 92.487 559 42 0 1536 2094 819299959 819300517 0.000000e+00 800.0
18 TraesCS3A01G528000 chr3B 91.710 579 44 2 1516 2094 819382173 819382747 0.000000e+00 800.0
19 TraesCS3A01G528000 chr3B 92.212 565 43 1 1530 2094 819522987 819523550 0.000000e+00 798.0
20 TraesCS3A01G528000 chr3B 86.654 532 67 3 981 1509 819740033 819740563 1.590000e-163 586.0
21 TraesCS3A01G528000 chr3B 85.052 582 71 8 1515 2094 819740871 819741438 2.670000e-161 579.0
22 TraesCS3A01G528000 chr3B 87.879 264 30 2 3718 3979 819545973 819546236 3.860000e-80 309.0
23 TraesCS3A01G528000 chr3B 81.395 129 22 2 428 555 440675609 440675736 1.960000e-18 104.0
24 TraesCS3A01G528000 chr3D 86.744 1554 129 27 1 1513 608949868 608951385 0.000000e+00 1657.0
25 TraesCS3A01G528000 chr3D 86.569 1571 124 26 1 1529 608980250 608981775 0.000000e+00 1652.0
26 TraesCS3A01G528000 chr3D 92.832 851 53 4 2106 2954 608952443 608953287 0.000000e+00 1227.0
27 TraesCS3A01G528000 chr3D 94.148 581 31 1 1514 2094 608951884 608952461 0.000000e+00 881.0
28 TraesCS3A01G528000 chr3D 81.351 1051 162 18 2112 3146 609005964 609006996 0.000000e+00 824.0
29 TraesCS3A01G528000 chr3D 91.592 559 45 2 2564 3121 608991546 608992103 0.000000e+00 771.0
30 TraesCS3A01G528000 chr3D 84.433 758 113 2 2160 2916 609286193 609285440 0.000000e+00 741.0
31 TraesCS3A01G528000 chr3D 93.240 429 26 1 1514 1942 608982201 608982626 2.610000e-176 628.0
32 TraesCS3A01G528000 chr3D 87.805 533 60 4 981 1509 609004575 609005106 1.570000e-173 619.0
33 TraesCS3A01G528000 chr3D 85.052 582 66 13 1515 2094 609005414 609005976 1.240000e-159 573.0
34 TraesCS3A01G528000 chr2D 84.637 703 95 7 2110 2810 623439031 623439722 0.000000e+00 688.0
35 TraesCS3A01G528000 chr2B 87.773 458 56 0 1637 2094 765455181 765455638 1.630000e-148 536.0
36 TraesCS3A01G528000 chr2B 82.848 309 34 8 2110 2415 765455624 765455916 3.940000e-65 259.0
37 TraesCS3A01G528000 chr5B 74.731 558 126 13 36 587 707437607 707438155 6.650000e-58 235.0
38 TraesCS3A01G528000 chr5B 77.931 145 29 1 443 587 548425164 548425023 1.970000e-13 87.9
39 TraesCS3A01G528000 chr7D 75.048 525 120 7 45 564 634043525 634043007 2.390000e-57 233.0
40 TraesCS3A01G528000 chr6A 74.600 500 112 11 45 537 11128037 11128528 5.210000e-49 206.0
41 TraesCS3A01G528000 chr6A 74.400 500 113 11 45 537 10350514 10350023 2.430000e-47 200.0
42 TraesCS3A01G528000 chr6A 74.400 500 113 11 45 537 10354961 10354470 2.430000e-47 200.0
43 TraesCS3A01G528000 chrUn 74.400 500 113 11 45 537 315895567 315895076 2.430000e-47 200.0
44 TraesCS3A01G528000 chrUn 74.400 500 113 11 45 537 315906394 315905903 2.430000e-47 200.0
45 TraesCS3A01G528000 chrUn 74.400 500 113 11 45 537 323249157 323249648 2.430000e-47 200.0
46 TraesCS3A01G528000 chr6B 72.962 503 110 15 60 554 659672349 659671865 6.890000e-33 152.0
47 TraesCS3A01G528000 chr7B 80.597 134 21 4 262 393 561049545 561049675 9.100000e-17 99.0


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 TraesCS3A01G528000 chr3A 742331237 742335215 3978 False 7348.000000 7348 100.000000 1 3979 1 chr3A.!!$F2 3978
1 TraesCS3A01G528000 chr3A 742314006 742315816 1810 False 1017.000000 1594 87.284500 2106 3979 2 chr3A.!!$F3 1873
2 TraesCS3A01G528000 chr3A 742277403 742278001 598 False 728.000000 728 88.530000 647 1261 1 chr3A.!!$F1 614
3 TraesCS3A01G528000 chr3A 742355389 742356786 1397 False 592.500000 617 86.482000 978 2094 2 chr3A.!!$F4 1116
4 TraesCS3A01G528000 chr3B 819380309 819384225 3916 False 1418.666667 1823 88.956333 1 3596 3 chr3B.!!$F4 3595
5 TraesCS3A01G528000 chr3B 819521343 819524875 3532 False 1386.666667 1751 89.453333 1 3430 3 chr3B.!!$F5 3429
6 TraesCS3A01G528000 chr3B 819648993 819653994 5001 False 1210.250000 1770 89.467000 1 3926 4 chr3B.!!$F6 3925
7 TraesCS3A01G528000 chr3B 819298075 819303131 5056 False 981.000000 1230 90.918250 941 3979 4 chr3B.!!$F3 3038
8 TraesCS3A01G528000 chr3B 819740033 819741438 1405 False 582.500000 586 85.853000 981 2094 2 chr3B.!!$F7 1113
9 TraesCS3A01G528000 chr3D 608949868 608953287 3419 False 1255.000000 1657 91.241333 1 2954 3 chr3D.!!$F2 2953
10 TraesCS3A01G528000 chr3D 608980250 608982626 2376 False 1140.000000 1652 89.904500 1 1942 2 chr3D.!!$F3 1941
11 TraesCS3A01G528000 chr3D 608991546 608992103 557 False 771.000000 771 91.592000 2564 3121 1 chr3D.!!$F1 557
12 TraesCS3A01G528000 chr3D 609285440 609286193 753 True 741.000000 741 84.433000 2160 2916 1 chr3D.!!$R1 756
13 TraesCS3A01G528000 chr3D 609004575 609006996 2421 False 672.000000 824 84.736000 981 3146 3 chr3D.!!$F4 2165
14 TraesCS3A01G528000 chr2D 623439031 623439722 691 False 688.000000 688 84.637000 2110 2810 1 chr2D.!!$F1 700
15 TraesCS3A01G528000 chr2B 765455181 765455916 735 False 397.500000 536 85.310500 1637 2415 2 chr2B.!!$F1 778
16 TraesCS3A01G528000 chr5B 707437607 707438155 548 False 235.000000 235 74.731000 36 587 1 chr5B.!!$F1 551
17 TraesCS3A01G528000 chr7D 634043007 634043525 518 True 233.000000 233 75.048000 45 564 1 chr7D.!!$R1 519

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
455 462 0.164217 GACGCGATAGGAGCTAGACG 59.836 60.0 15.93 0.0 0.00 4.18 F
1513 1616 0.537188 AGCATCAGGTACGGACAAGG 59.463 55.0 0.00 0.0 33.98 3.61 F
1699 3530 0.677098 AGAGACGGTAGCGCTCAAGA 60.677 55.0 27.78 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 3587 0.307760 GGGAACTTGTCGCTGTTGTG 59.692 55.0 0.0 0.0 36.28 3.33 R
2737 4584 0.179000 CCTTCCTCCTGCACGCTAAT 59.821 55.0 0.0 0.0 0.00 1.73 R
3367 6539 0.248866 CAAAAGTGTCCGTGTTGCCC 60.249 55.0 0.0 0.0 0.00 5.36 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
38 39 7.534282 ACCTTTGTTTTATTTTGTGGCAAAAG 58.466 30.769 11.77 0.00 0.00 2.27
40 41 7.484324 CCTTTGTTTTATTTTGTGGCAAAAGTG 59.516 33.333 11.77 0.00 0.00 3.16
72 73 4.847198 TCATCAAACATCATGGCAGTACT 58.153 39.130 0.00 0.00 0.00 2.73
73 74 4.637091 TCATCAAACATCATGGCAGTACTG 59.363 41.667 18.93 18.93 0.00 2.74
83 84 3.552132 TGGCAGTACTGAGAACACAAA 57.448 42.857 27.08 0.00 0.00 2.83
122 123 8.328055 TGCATCAATATCCATAGATCACCTAT 57.672 34.615 0.00 0.00 38.59 2.57
135 136 6.525578 AGATCACCTATCGACAACTACAAA 57.474 37.500 0.00 0.00 39.79 2.83
187 192 3.717294 GCCCCTTCCTCGAGCCAA 61.717 66.667 6.99 0.59 0.00 4.52
252 257 1.200020 GCACCAAAAGATTAGCGCACT 59.800 47.619 11.47 0.00 0.00 4.40
260 265 6.073548 CCAAAAGATTAGCGCACTAGAATAGG 60.074 42.308 11.47 0.00 44.97 2.57
271 276 0.748450 TAGAATAGGAACCACCGCCG 59.252 55.000 0.00 0.00 44.74 6.46
324 329 6.649141 TCCAACTTGTAGACACATGAACATAC 59.351 38.462 0.00 0.00 33.76 2.39
325 330 6.128282 CCAACTTGTAGACACATGAACATACC 60.128 42.308 0.00 0.00 33.76 2.73
329 334 5.487433 TGTAGACACATGAACATACCCAAG 58.513 41.667 0.00 0.00 0.00 3.61
382 388 1.269448 CAAACACCAACCGAATCCAGG 59.731 52.381 0.00 0.00 0.00 4.45
397 403 1.445095 CAGGGAGATTCGCCAGAGG 59.555 63.158 8.78 0.00 0.00 3.69
408 414 3.621225 CCAGAGGCACATCTCCGA 58.379 61.111 0.00 0.00 34.46 4.55
437 443 4.248058 TCTAACGACACGAGATGTACTGA 58.752 43.478 0.00 0.00 43.56 3.41
455 462 0.164217 GACGCGATAGGAGCTAGACG 59.836 60.000 15.93 0.00 0.00 4.18
458 465 0.605860 GCGATAGGAGCTAGACGGGA 60.606 60.000 0.00 0.00 0.00 5.14
503 510 2.227089 CTGTCGCCGCCTTACCTTCT 62.227 60.000 0.00 0.00 0.00 2.85
564 572 5.188359 ACCTAAAAACGAAGTATGAGCCCTA 59.812 40.000 0.00 0.00 45.00 3.53
589 597 3.554342 CCAGGGCCAGGATCCTCG 61.554 72.222 12.69 6.66 0.00 4.63
653 710 9.387123 GAAATGTCCGATGCTCTAATTTATTTC 57.613 33.333 0.00 0.00 0.00 2.17
656 723 8.087982 TGTCCGATGCTCTAATTTATTTCATC 57.912 34.615 0.00 0.00 0.00 2.92
691 758 7.264373 GGATGACCCACTTTCATTATAACTG 57.736 40.000 0.00 0.00 33.70 3.16
694 761 9.561069 GATGACCCACTTTCATTATAACTGTAT 57.439 33.333 0.00 0.00 33.70 2.29
747 815 2.202810 CGGGAAAGGAGAGCGAGC 60.203 66.667 0.00 0.00 0.00 5.03
799 867 3.991051 CGCCCACGAGACACCTGT 61.991 66.667 0.00 0.00 43.93 4.00
801 869 1.668151 GCCCACGAGACACCTGTTC 60.668 63.158 0.00 0.00 0.00 3.18
859 932 6.518493 ACGTCTCAGAAAACAGTACCATAAA 58.482 36.000 0.00 0.00 0.00 1.40
950 1027 5.532557 CAAAAGGAGTTTAAAAGGCCTCTG 58.467 41.667 5.23 3.85 0.00 3.35
1008 1085 2.728846 GCAGCATATCACCAAACACACG 60.729 50.000 0.00 0.00 0.00 4.49
1035 1114 3.703052 AGAAAATCAATGGCCATCTCACC 59.297 43.478 21.08 5.59 0.00 4.02
1345 1427 3.695606 GAGGACTGCTGCACCCGA 61.696 66.667 0.00 0.00 0.00 5.14
1513 1616 0.537188 AGCATCAGGTACGGACAAGG 59.463 55.000 0.00 0.00 33.98 3.61
1523 1626 3.319972 GGTACGGACAAGGATACATGCTA 59.680 47.826 0.00 0.00 39.40 3.49
1524 1627 4.021368 GGTACGGACAAGGATACATGCTAT 60.021 45.833 0.00 0.00 39.40 2.97
1525 1628 4.689612 ACGGACAAGGATACATGCTATT 57.310 40.909 0.00 0.00 39.40 1.73
1526 1629 4.632153 ACGGACAAGGATACATGCTATTC 58.368 43.478 0.00 0.00 39.40 1.75
1527 1630 4.100963 ACGGACAAGGATACATGCTATTCA 59.899 41.667 0.00 0.00 39.40 2.57
1534 3360 7.658982 ACAAGGATACATGCTATTCAGTACATG 59.341 37.037 0.00 0.00 44.29 3.21
1619 3450 8.979574 GTGCATAGTATAAAACCTCATGTACTC 58.020 37.037 0.00 0.00 31.26 2.59
1658 3489 6.592607 GTCGATTAGGTGGACAAACTAATGAA 59.407 38.462 4.78 0.00 37.49 2.57
1699 3530 0.677098 AGAGACGGTAGCGCTCAAGA 60.677 55.000 27.78 0.00 0.00 3.02
1756 3587 0.803380 GCTTGGATTTGGCGACATGC 60.803 55.000 0.00 0.00 42.32 4.06
1825 3656 1.079127 GAGGCCATACACGTGCAGT 60.079 57.895 17.22 0.00 0.00 4.40
1839 3670 2.863153 CAGTCCAGCTTTTCCGCG 59.137 61.111 0.00 0.00 34.40 6.46
1896 3729 1.675310 CCAAATCACTGGCCTCGCA 60.675 57.895 3.32 0.00 0.00 5.10
1912 3745 2.278206 CATCTCGTCGTGAGCGGG 60.278 66.667 3.18 0.00 44.86 6.13
1922 3755 1.004440 GTGAGCGGGTCTTCAAGCT 60.004 57.895 8.82 0.00 43.33 3.74
1971 3804 0.694771 AGCAGCATCTTGACCCTCAA 59.305 50.000 0.00 0.00 34.79 3.02
1983 3816 1.227823 CCCTCAACGTGTCAAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
2030 3863 4.520874 TCTCATCGATCTATGGAAGGACAC 59.479 45.833 7.33 0.00 0.00 3.67
2039 3872 1.150536 GGAAGGACACCAGTGGCAA 59.849 57.895 9.78 0.00 41.42 4.52
2159 3994 2.967599 TGTCATGTCTCGATTGAGGG 57.032 50.000 10.19 0.00 42.79 4.30
2186 4025 8.682936 AAAAAGATCAACTAACTGACATCACT 57.317 30.769 0.00 0.00 0.00 3.41
2187 4026 7.897575 AAAGATCAACTAACTGACATCACTC 57.102 36.000 0.00 0.00 0.00 3.51
2188 4027 5.645624 AGATCAACTAACTGACATCACTCG 58.354 41.667 0.00 0.00 0.00 4.18
2340 4187 2.040544 CGTGGTGGGAGGCAATGAC 61.041 63.158 0.00 0.00 0.00 3.06
2362 4209 1.213013 GTGCGACCAGACGATCTGT 59.787 57.895 12.10 0.00 42.80 3.41
2488 4335 1.873591 GCTATGACGTATTGGCCAAGG 59.126 52.381 24.94 17.25 0.00 3.61
2685 4532 2.426023 GCCACCGTGGAGTTCACT 59.574 61.111 22.37 0.00 40.96 3.41
2705 4552 0.839946 CTGGCCAACCTGCTATACCT 59.160 55.000 7.01 0.00 36.63 3.08
2743 4590 0.387367 CGAGGGGATCGTGATTAGCG 60.387 60.000 0.00 0.00 46.62 4.26
2776 4623 1.258676 CGAGCTTATCCCCCTCCTAC 58.741 60.000 0.00 0.00 0.00 3.18
2822 4669 1.487976 CCCATACCAGCACATCTGAGT 59.512 52.381 0.00 0.00 45.72 3.41
2837 4684 0.973632 TGAGTACAACGAGGCATGGT 59.026 50.000 0.00 0.00 0.00 3.55
2838 4685 1.346395 TGAGTACAACGAGGCATGGTT 59.654 47.619 0.00 0.00 0.00 3.67
2846 4693 0.238289 CGAGGCATGGTTTGACACAC 59.762 55.000 0.00 0.00 34.87 3.82
2876 4725 7.611855 AGAGAGATCCGGTCAAAATTAATTTGT 59.388 33.333 14.04 2.59 46.89 2.83
2884 4733 6.402011 CGGTCAAAATTAATTTGTTCCCATGC 60.402 38.462 14.04 4.11 46.89 4.06
2927 4781 8.254508 AGTAATCTTGTCACTCTTATCCACTTC 58.745 37.037 0.00 0.00 0.00 3.01
3084 6229 7.127339 ACATATAGAGGTACAAACTTGGTGGAT 59.873 37.037 0.00 0.00 0.00 3.41
3110 6255 4.325084 AGCCTAGAGACTAGGAGTGTTT 57.675 45.455 23.71 3.84 36.85 2.83
3187 6334 4.571919 TCGTATTCGAACATTCCCTTTGT 58.428 39.130 0.00 0.00 43.34 2.83
3231 6378 7.500227 ACATACCATTAGGACTGAACATGATTG 59.500 37.037 0.00 0.00 38.69 2.67
3261 6433 3.126858 TGAATAAGATGCCTTTCGTGTGC 59.873 43.478 0.00 0.00 33.94 4.57
3263 6435 0.593128 AAGATGCCTTTCGTGTGCAC 59.407 50.000 10.75 10.75 37.92 4.57
3305 6477 2.034066 CACCTGTCCATTGCCGGT 59.966 61.111 1.90 0.00 0.00 5.28
3327 6499 1.931841 CATGAGCTGTCTTGATGACCG 59.068 52.381 0.00 0.00 44.75 4.79
3367 6539 3.834489 AGGAGCATCATGAACAGTAGG 57.166 47.619 0.00 0.00 36.25 3.18
3390 6562 1.944024 CAACACGGACACTTTTGGCTA 59.056 47.619 0.00 0.00 0.00 3.93
3406 6578 2.766970 GCTAGAGTAGAAGCCGTCAG 57.233 55.000 0.00 0.00 32.40 3.51
3408 6580 2.683867 GCTAGAGTAGAAGCCGTCAGAA 59.316 50.000 0.00 0.00 32.40 3.02
3409 6581 3.487879 GCTAGAGTAGAAGCCGTCAGAAC 60.488 52.174 0.00 0.00 32.40 3.01
3440 6612 3.440173 CGAGGTGATAACCATTGTTGCTT 59.560 43.478 0.85 0.00 35.87 3.91
3442 6614 5.296780 CGAGGTGATAACCATTGTTGCTTAT 59.703 40.000 0.85 0.00 35.87 1.73
3454 6626 5.528043 TTGTTGCTTATGTCATTGTGGTT 57.472 34.783 0.00 0.00 0.00 3.67
3462 6634 6.540189 GCTTATGTCATTGTGGTTGAGAGTAT 59.460 38.462 0.00 0.00 0.00 2.12
3466 6638 2.489938 TTGTGGTTGAGAGTATGGGC 57.510 50.000 0.00 0.00 0.00 5.36
3482 6654 4.367023 GCGTGGTAGCCGTGGTCA 62.367 66.667 5.04 0.00 0.00 4.02
3493 6665 1.406341 GCCGTGGTCAGTTAAGCCATA 60.406 52.381 0.00 0.00 34.52 2.74
3523 6695 1.374758 CGAGGGAGGAGCAACACAC 60.375 63.158 0.00 0.00 0.00 3.82
3535 6707 3.141398 AGCAACACACAATGTAGGAGTG 58.859 45.455 0.80 0.80 42.31 3.51
3586 6758 0.905357 CGGTCACTGAGGGAGGAATT 59.095 55.000 0.00 0.00 0.00 2.17
3589 6761 2.507471 GGTCACTGAGGGAGGAATTGAT 59.493 50.000 0.00 0.00 0.00 2.57
3596 6768 3.074390 TGAGGGAGGAATTGATGTTGTGT 59.926 43.478 0.00 0.00 0.00 3.72
3599 6771 3.420893 GGAGGAATTGATGTTGTGTGGA 58.579 45.455 0.00 0.00 0.00 4.02
3656 6828 2.819608 GGCTTGTAGCAAAGATGAACCA 59.180 45.455 0.67 0.00 44.75 3.67
3662 6834 3.806949 AGCAAAGATGAACCAAGGGTA 57.193 42.857 0.00 0.00 33.12 3.69
3668 6840 2.644798 AGATGAACCAAGGGTAAGCACT 59.355 45.455 0.00 0.00 33.12 4.40
3683 6855 4.320456 ACTCTGGTGCGGGTGCTG 62.320 66.667 0.00 0.00 43.34 4.41
3705 6877 3.855950 GCTTCCGATTTTCAGCATCAAAG 59.144 43.478 0.00 0.00 32.17 2.77
3710 6883 5.095490 CCGATTTTCAGCATCAAAGGTTAC 58.905 41.667 0.00 0.00 0.00 2.50
3711 6884 5.106157 CCGATTTTCAGCATCAAAGGTTACT 60.106 40.000 0.00 0.00 0.00 2.24
3712 6885 6.093495 CCGATTTTCAGCATCAAAGGTTACTA 59.907 38.462 0.00 0.00 0.00 1.82
3766 6939 4.431416 TTGGTAGTGGTCTGAATGTGTT 57.569 40.909 0.00 0.00 0.00 3.32
3774 6947 5.470098 AGTGGTCTGAATGTGTTTGTATGTC 59.530 40.000 0.00 0.00 0.00 3.06
3778 6951 7.014134 TGGTCTGAATGTGTTTGTATGTCAAAT 59.986 33.333 0.00 0.00 45.88 2.32
3786 6959 6.915300 TGTGTTTGTATGTCAAATAAGTGTGC 59.085 34.615 0.00 0.00 45.88 4.57
3791 6964 6.941857 TGTATGTCAAATAAGTGTGCTAGGA 58.058 36.000 0.00 0.00 0.00 2.94
3820 6993 8.773645 CATATTTTGTTAGTGCTATCGATGGAA 58.226 33.333 13.60 0.00 0.00 3.53
3865 7040 6.956202 TTTATTGACCTTTACGGGTTTGAA 57.044 33.333 0.00 0.00 40.06 2.69
3891 7066 1.278413 GGACAGTACTTGACCCCCTTC 59.722 57.143 0.00 0.00 35.86 3.46
3950 7125 5.297799 ACCCCCTAAGAGGTAAGATGAAAT 58.702 41.667 0.00 0.00 33.52 2.17
3961 7136 9.336171 AGAGGTAAGATGAAATTTTGATCTAGC 57.664 33.333 10.87 9.17 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.045955 TGCCACAAAATAAAACAAAGGTCTC 58.954 36.000 0.00 0.00 0.00 3.36
29 30 9.056005 TGATGAATAGATATACACTTTTGCCAC 57.944 33.333 0.00 0.00 0.00 5.01
98 99 7.598118 CGATAGGTGATCTATGGATATTGATGC 59.402 40.741 0.00 0.00 38.71 3.91
103 104 8.470805 GTTGTCGATAGGTGATCTATGGATATT 58.529 37.037 0.75 0.00 42.43 1.28
106 107 6.013379 AGTTGTCGATAGGTGATCTATGGAT 58.987 40.000 0.75 0.00 42.43 3.41
110 111 7.818997 TTGTAGTTGTCGATAGGTGATCTAT 57.181 36.000 0.00 0.00 41.14 1.98
122 123 3.131577 ACTCCAGTGTTTGTAGTTGTCGA 59.868 43.478 0.00 0.00 0.00 4.20
135 136 0.249911 GCTTCGGTTCACTCCAGTGT 60.250 55.000 6.61 0.00 45.76 3.55
187 192 3.245300 TGTCTACTACAGGAAGGTCTGCT 60.245 47.826 0.00 0.00 38.26 4.24
234 239 4.202245 TCTAGTGCGCTAATCTTTTGGT 57.798 40.909 9.73 0.00 0.00 3.67
244 249 3.067742 GTGGTTCCTATTCTAGTGCGCTA 59.932 47.826 9.73 6.84 0.00 4.26
252 257 0.748450 CGGCGGTGGTTCCTATTCTA 59.252 55.000 0.00 0.00 0.00 2.10
260 265 2.046700 TTCATCCGGCGGTGGTTC 60.047 61.111 27.32 0.00 0.00 3.62
271 276 5.366460 TCTGATCAATGCTTCTCTTCATCC 58.634 41.667 0.00 0.00 0.00 3.51
324 329 3.074412 GTGTATGTGGTCTTCACTTGGG 58.926 50.000 0.00 0.00 46.20 4.12
325 330 3.498397 GTGTGTATGTGGTCTTCACTTGG 59.502 47.826 0.00 0.00 46.20 3.61
329 334 3.990092 TCTGTGTGTATGTGGTCTTCAC 58.010 45.455 0.00 0.00 46.23 3.18
397 403 1.153086 AGGGCATTCGGAGATGTGC 60.153 57.895 0.00 0.00 44.29 4.57
407 413 1.135199 TCGTGTCGTTAGAGGGCATTC 60.135 52.381 0.00 0.00 0.00 2.67
408 414 0.892755 TCGTGTCGTTAGAGGGCATT 59.107 50.000 0.00 0.00 0.00 3.56
432 438 2.036862 TCTAGCTCCTATCGCGTCAGTA 59.963 50.000 5.77 0.00 0.00 2.74
437 443 1.229315 CCGTCTAGCTCCTATCGCGT 61.229 60.000 5.77 0.00 0.00 6.01
455 462 7.703058 TTCAAGATGGAATAAAGTTCTTCCC 57.297 36.000 12.36 1.92 40.22 3.97
458 465 8.518702 GCTCTTTCAAGATGGAATAAAGTTCTT 58.481 33.333 0.00 0.00 33.93 2.52
479 486 2.646175 TAAGGCGGCGACAGCTCTT 61.646 57.895 18.30 1.56 44.37 2.85
503 510 9.629878 TCTTTTTAGGGTTTGTGTTATACTCAA 57.370 29.630 0.00 0.00 30.75 3.02
554 562 1.410850 GGCTGGCTGTAGGGCTCATA 61.411 60.000 0.00 0.00 41.48 2.15
632 689 8.316640 AGATGAAATAAATTAGAGCATCGGAC 57.683 34.615 0.00 0.00 42.67 4.79
653 710 4.324267 GGGTCATCCCGGTATAAAAGATG 58.676 47.826 0.00 4.41 44.74 2.90
689 756 9.965824 GGATGGTTTTGTATTTCCATTATACAG 57.034 33.333 0.00 0.00 40.24 2.74
690 757 9.480861 TGGATGGTTTTGTATTTCCATTATACA 57.519 29.630 0.00 0.00 40.24 2.29
694 761 8.875168 ACTTTGGATGGTTTTGTATTTCCATTA 58.125 29.630 0.00 0.00 40.24 1.90
695 762 7.744733 ACTTTGGATGGTTTTGTATTTCCATT 58.255 30.769 0.00 0.00 40.24 3.16
696 763 7.315066 ACTTTGGATGGTTTTGTATTTCCAT 57.685 32.000 0.00 0.00 42.44 3.41
697 764 6.739331 ACTTTGGATGGTTTTGTATTTCCA 57.261 33.333 0.00 0.00 0.00 3.53
717 784 5.541484 TCTCCTTTCCCGTCTACTTAAACTT 59.459 40.000 0.00 0.00 0.00 2.66
726 793 0.034767 TCGCTCTCCTTTCCCGTCTA 60.035 55.000 0.00 0.00 0.00 2.59
799 867 2.281900 CGGGTTTTCGCCCCAGAA 60.282 61.111 0.00 0.00 45.91 3.02
801 869 3.053896 GTCGGGTTTTCGCCCCAG 61.054 66.667 0.00 0.00 45.91 4.45
859 932 2.213499 CTCGCTTGTGAACCTGTTCTT 58.787 47.619 11.03 0.00 40.14 2.52
950 1027 5.828747 TCTTATACATGTGTTACGAGCCTC 58.171 41.667 9.11 0.00 0.00 4.70
993 1070 5.456548 TCTTAGTCGTGTGTTTGGTGATA 57.543 39.130 0.00 0.00 0.00 2.15
1008 1085 6.319658 TGAGATGGCCATTGATTTTCTTAGTC 59.680 38.462 21.84 1.95 0.00 2.59
1071 1150 3.087666 GCCAGAAGGAGGAGGAGCG 62.088 68.421 0.00 0.00 36.89 5.03
1523 1626 8.862325 TTAATCCACTGAAACATGTACTGAAT 57.138 30.769 0.00 0.00 0.00 2.57
1524 1627 8.729756 CATTAATCCACTGAAACATGTACTGAA 58.270 33.333 0.00 0.00 0.00 3.02
1525 1628 7.882791 ACATTAATCCACTGAAACATGTACTGA 59.117 33.333 0.00 0.00 0.00 3.41
1526 1629 7.964559 CACATTAATCCACTGAAACATGTACTG 59.035 37.037 0.00 3.66 0.00 2.74
1527 1630 7.121168 CCACATTAATCCACTGAAACATGTACT 59.879 37.037 0.00 0.00 0.00 2.73
1534 3360 4.485163 GTGCCACATTAATCCACTGAAAC 58.515 43.478 0.00 0.00 0.00 2.78
1619 3450 4.997395 CCTAATCGACCATGGGTTCAATAG 59.003 45.833 18.09 10.61 35.25 1.73
1625 3456 1.211949 CCACCTAATCGACCATGGGTT 59.788 52.381 18.09 7.85 35.25 4.11
1658 3489 2.281761 CCAAGCCGCTCAAGGTGT 60.282 61.111 0.00 0.00 0.00 4.16
1684 3515 1.446272 GCTTCTTGAGCGCTACCGT 60.446 57.895 11.50 0.00 42.46 4.83
1699 3530 1.467920 GCCAGGCTTAAGATGTGCTT 58.532 50.000 6.67 0.00 40.68 3.91
1756 3587 0.307760 GGGAACTTGTCGCTGTTGTG 59.692 55.000 0.00 0.00 36.28 3.33
1825 3656 2.047274 CTCCGCGGAAAAGCTGGA 60.047 61.111 30.53 2.79 37.44 3.86
1896 3729 2.750637 ACCCGCTCACGACGAGAT 60.751 61.111 0.00 0.00 45.45 2.75
1922 3755 4.081697 TGACCTCGAAGAATGTATCAAGCA 60.082 41.667 0.00 0.00 34.09 3.91
1983 3816 1.518774 AACGAGGTCACCGTTGTGT 59.481 52.632 0.00 0.00 46.77 3.72
2030 3863 0.883833 GATGTTGAGGTTGCCACTGG 59.116 55.000 0.00 0.00 0.00 4.00
2039 3872 2.705658 TGGTCTCTTGTGATGTTGAGGT 59.294 45.455 0.00 0.00 0.00 3.85
2126 3959 6.072230 CGAGACATGACATGATGTATAGAGGT 60.072 42.308 22.19 0.00 36.67 3.85
2131 3964 7.885297 TCAATCGAGACATGACATGATGTATA 58.115 34.615 22.19 3.42 36.67 1.47
2132 3965 6.752168 TCAATCGAGACATGACATGATGTAT 58.248 36.000 22.19 0.00 36.67 2.29
2185 4024 1.450848 ATGCATGGTGGTGAGCGAG 60.451 57.895 0.00 0.00 0.00 5.03
2186 4025 1.746239 CATGCATGGTGGTGAGCGA 60.746 57.895 19.40 0.00 0.00 4.93
2187 4026 2.795973 CATGCATGGTGGTGAGCG 59.204 61.111 19.40 0.00 0.00 5.03
2188 4027 1.672854 ATGCATGCATGGTGGTGAGC 61.673 55.000 31.74 11.35 35.03 4.26
2337 4184 2.523168 TCTGGTCGCACCCTGTCA 60.523 61.111 3.33 0.00 37.50 3.58
2340 4187 2.890847 GATCGTCTGGTCGCACCCTG 62.891 65.000 3.33 0.00 37.50 4.45
2362 4209 1.902508 CTTGAGGTAGACCAGCTTGGA 59.097 52.381 8.91 0.00 40.96 3.53
2488 4335 0.921347 ACGTTCACATAGATTCGCGC 59.079 50.000 0.00 0.00 0.00 6.86
2565 4412 0.456995 CGCTCGTCTCAAACCTCTCC 60.457 60.000 0.00 0.00 0.00 3.71
2685 4532 0.837272 GGTATAGCAGGTTGGCCAGA 59.163 55.000 5.11 0.00 37.19 3.86
2705 4552 2.186903 GGAGCGCCCAATCGAAGA 59.813 61.111 2.29 0.00 36.13 2.87
2737 4584 0.179000 CCTTCCTCCTGCACGCTAAT 59.821 55.000 0.00 0.00 0.00 1.73
2743 4590 2.125350 CTCGCCTTCCTCCTGCAC 60.125 66.667 0.00 0.00 0.00 4.57
2758 4605 2.158295 TCTGTAGGAGGGGGATAAGCTC 60.158 54.545 0.00 0.00 0.00 4.09
2822 4669 2.147958 GTCAAACCATGCCTCGTTGTA 58.852 47.619 0.00 0.00 0.00 2.41
2837 4684 1.801242 TCTCTCTGGGGTGTGTCAAA 58.199 50.000 0.00 0.00 0.00 2.69
2838 4685 1.902508 GATCTCTCTGGGGTGTGTCAA 59.097 52.381 0.00 0.00 0.00 3.18
2884 4733 7.325660 AGATTACTTGCATGTTTACTCCATG 57.674 36.000 10.85 0.00 42.06 3.66
2901 4750 7.726033 AGTGGATAAGAGTGACAAGATTACT 57.274 36.000 0.00 0.00 0.00 2.24
2927 4781 7.976135 AGGTAATAGACTGGTAGTACATACG 57.024 40.000 2.06 0.00 34.99 3.06
2981 4842 0.667993 ACAACAACATGAAGGTGCCG 59.332 50.000 0.00 0.00 39.04 5.69
2989 4850 6.852858 TCATCTCGTTTTACAACAACATGA 57.147 33.333 0.00 0.00 32.54 3.07
3084 6229 5.666718 ACACTCCTAGTCTCTAGGCTACTTA 59.333 44.000 15.60 0.30 34.74 2.24
3166 6313 4.153475 ACACAAAGGGAATGTTCGAATACG 59.847 41.667 0.00 0.00 41.26 3.06
3173 6320 5.106157 CCACTATGACACAAAGGGAATGTTC 60.106 44.000 0.00 0.00 0.00 3.18
3183 6330 2.621055 GTTGCCACCACTATGACACAAA 59.379 45.455 0.00 0.00 0.00 2.83
3187 6334 1.141858 TGTGTTGCCACCACTATGACA 59.858 47.619 0.00 0.00 41.09 3.58
3208 6355 6.157820 TCCAATCATGTTCAGTCCTAATGGTA 59.842 38.462 0.00 0.00 34.23 3.25
3216 6363 5.964958 TCTTTTCCAATCATGTTCAGTCC 57.035 39.130 0.00 0.00 0.00 3.85
3231 6378 6.914757 CGAAAGGCATCTTATTCATCTTTTCC 59.085 38.462 0.00 0.00 32.01 3.13
3327 6499 0.859232 ACGACTTCGAACACACATGC 59.141 50.000 5.47 0.00 43.02 4.06
3367 6539 0.248866 CAAAAGTGTCCGTGTTGCCC 60.249 55.000 0.00 0.00 0.00 5.36
3390 6562 2.490115 CAGTTCTGACGGCTTCTACTCT 59.510 50.000 0.00 0.00 0.00 3.24
3406 6578 0.319900 TCACCTCGCTTGAGCAGTTC 60.320 55.000 3.65 0.00 42.21 3.01
3408 6580 1.186200 TATCACCTCGCTTGAGCAGT 58.814 50.000 3.65 0.00 42.21 4.40
3409 6581 1.929836 GTTATCACCTCGCTTGAGCAG 59.070 52.381 3.65 0.42 42.21 4.24
3440 6612 6.348498 CCATACTCTCAACCACAATGACATA 58.652 40.000 0.00 0.00 0.00 2.29
3442 6614 4.565444 CCCATACTCTCAACCACAATGACA 60.565 45.833 0.00 0.00 0.00 3.58
3454 6626 1.399714 CTACCACGCCCATACTCTCA 58.600 55.000 0.00 0.00 0.00 3.27
3466 6638 2.126071 CTGACCACGGCTACCACG 60.126 66.667 0.00 0.00 37.36 4.94
3476 6648 3.055385 TCACCTATGGCTTAACTGACCAC 60.055 47.826 0.00 0.00 35.99 4.16
3482 6654 3.741388 GCGTCATCACCTATGGCTTAACT 60.741 47.826 0.00 0.00 38.10 2.24
3493 6665 3.461773 CCCTCGGCGTCATCACCT 61.462 66.667 6.85 0.00 0.00 4.00
3523 6695 4.769688 TGTCTAATGCCACTCCTACATTG 58.230 43.478 0.00 0.00 35.68 2.82
3535 6707 6.506147 TCAACATATTTGCATGTCTAATGCC 58.494 36.000 7.78 0.00 43.94 4.40
3574 6746 3.074390 ACACAACATCAATTCCTCCCTCA 59.926 43.478 0.00 0.00 0.00 3.86
3586 6758 4.141937 GCTAGGATAGTCCACACAACATCA 60.142 45.833 0.00 0.00 41.93 3.07
3589 6761 3.169908 TGCTAGGATAGTCCACACAACA 58.830 45.455 0.00 0.00 41.93 3.33
3596 6768 5.066913 TCTCTCAATGCTAGGATAGTCCA 57.933 43.478 0.00 0.00 41.93 4.02
3599 6771 5.211973 TGGTTCTCTCAATGCTAGGATAGT 58.788 41.667 0.00 0.00 41.93 2.12
3675 6847 1.586154 AAAATCGGAAGCAGCACCCG 61.586 55.000 16.70 16.70 44.22 5.28
3683 6855 3.492421 TTGATGCTGAAAATCGGAAGC 57.508 42.857 0.00 0.00 36.18 3.86
3705 6877 6.382282 ACTCAAACCCCTACACTATAGTAACC 59.618 42.308 4.74 0.00 0.00 2.85
3710 6883 7.931948 CCATAAACTCAAACCCCTACACTATAG 59.068 40.741 0.00 0.00 0.00 1.31
3711 6884 7.624478 TCCATAAACTCAAACCCCTACACTATA 59.376 37.037 0.00 0.00 0.00 1.31
3712 6885 6.445786 TCCATAAACTCAAACCCCTACACTAT 59.554 38.462 0.00 0.00 0.00 2.12
3766 6939 7.390823 TCCTAGCACACTTATTTGACATACAA 58.609 34.615 0.00 0.00 36.65 2.41
3786 6959 7.502120 AGCACTAACAAAATATGCATCCTAG 57.498 36.000 0.19 0.00 38.79 3.02
3791 6964 7.728847 TCGATAGCACTAACAAAATATGCAT 57.271 32.000 3.79 3.79 38.79 3.96
3847 7022 4.462133 TGATTTCAAACCCGTAAAGGTCA 58.538 39.130 0.00 0.00 40.05 4.02
3853 7028 4.399219 TGTCCATGATTTCAAACCCGTAA 58.601 39.130 0.00 0.00 0.00 3.18
3865 7040 3.054361 GGGGTCAAGTACTGTCCATGATT 60.054 47.826 0.00 0.00 35.13 2.57


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

AutoCloner maintained by Alex Coulton.