Multiple sequence alignment - TraesCS3B01G169600

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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 TraesCS3B01G169600 chr3B 100.000 2711 0 0 1 2711 169670725 169668015 0.000000e+00 5007.0
1 TraesCS3B01G169600 chr3B 95.212 898 41 2 896 1791 169830742 169829845 0.000000e+00 1419.0
2 TraesCS3B01G169600 chr3B 94.994 839 26 4 1836 2658 171120078 171120916 0.000000e+00 1303.0
3 TraesCS3B01G169600 chr3B 90.146 893 45 10 1 868 169831616 169830742 0.000000e+00 1122.0
4 TraesCS3B01G169600 chr3B 94.643 56 3 0 2656 2711 5705984 5705929 1.340000e-13 87.9
5 TraesCS3B01G169600 chr3D 92.141 1018 53 10 798 1791 116154466 116153452 0.000000e+00 1411.0
6 TraesCS3B01G169600 chr3D 82.333 583 77 18 1 566 116156860 116156287 1.460000e-132 483.0
7 TraesCS3B01G169600 chr3D 83.137 255 30 9 1 249 116157478 116157231 1.260000e-53 220.0
8 TraesCS3B01G169600 chr3D 96.491 57 2 0 2655 2711 362196001 362195945 7.990000e-16 95.3
9 TraesCS3B01G169600 chr4B 94.743 837 29 5 1833 2655 28682349 28681514 0.000000e+00 1288.0
10 TraesCS3B01G169600 chr4B 94.624 837 30 4 1836 2658 665293819 665292984 0.000000e+00 1282.0
11 TraesCS3B01G169600 chr4B 93.240 858 39 5 1821 2664 662088265 662087413 0.000000e+00 1245.0
12 TraesCS3B01G169600 chr7B 94.320 845 33 4 1832 2663 664047622 664046780 0.000000e+00 1280.0
13 TraesCS3B01G169600 chr7B 74.617 457 81 27 6 437 707612180 707612626 4.640000e-38 169.0
14 TraesCS3B01G169600 chr7B 94.643 56 2 1 2656 2711 581382286 581382340 4.810000e-13 86.1
15 TraesCS3B01G169600 chr7B 96.000 50 2 0 1787 1836 676287413 676287462 6.220000e-12 82.4
16 TraesCS3B01G169600 chr7B 94.000 50 3 0 1787 1836 604367266 604367315 2.890000e-10 76.8
17 TraesCS3B01G169600 chr5B 93.757 865 34 9 1824 2673 686831913 686832772 0.000000e+00 1280.0
18 TraesCS3B01G169600 chr5B 94.504 837 33 5 1833 2656 63252432 63251596 0.000000e+00 1279.0
19 TraesCS3B01G169600 chr5B 94.118 850 34 5 1826 2661 203678583 203679430 0.000000e+00 1279.0
20 TraesCS3B01G169600 chr5B 93.882 850 35 6 1828 2661 155711936 155711088 0.000000e+00 1266.0
21 TraesCS3B01G169600 chr5B 93.750 848 38 4 1830 2662 646263183 646264030 0.000000e+00 1258.0
22 TraesCS3B01G169600 chr5B 74.341 569 103 29 6 545 639157510 639158064 4.580000e-48 202.0
23 TraesCS3B01G169600 chr5A 94.705 831 30 3 1840 2656 664389696 664388866 0.000000e+00 1279.0
24 TraesCS3B01G169600 chr5A 74.675 462 88 23 129 568 577796862 577797316 7.710000e-41 178.0
25 TraesCS3B01G169600 chr6B 93.677 854 40 3 1830 2670 646916035 646915183 0.000000e+00 1266.0
26 TraesCS3B01G169600 chr6B 94.258 836 29 7 1836 2658 713754052 713754881 0.000000e+00 1260.0
27 TraesCS3B01G169600 chr6B 94.437 737 24 6 1823 2545 705993445 705992712 0.000000e+00 1118.0
28 TraesCS3B01G169600 chr6B 92.453 106 4 4 552 654 153532448 153532344 6.050000e-32 148.0
29 TraesCS3B01G169600 chr6B 95.833 48 2 0 1789 1836 641292574 641292621 8.050000e-11 78.7
30 TraesCS3B01G169600 chr2B 93.669 853 40 3 1823 2662 675208177 675209028 0.000000e+00 1264.0
31 TraesCS3B01G169600 chr2B 71.965 453 102 21 6 436 768566260 768565811 2.850000e-20 110.0
32 TraesCS3B01G169600 chr2B 95.918 49 2 0 1787 1835 695437639 695437591 2.240000e-11 80.5
33 TraesCS3B01G169600 chr2B 89.831 59 4 2 1779 1835 449361186 449361128 1.040000e-09 75.0
34 TraesCS3B01G169600 chr1B 92.723 852 40 8 1829 2666 614584630 614583787 0.000000e+00 1210.0
35 TraesCS3B01G169600 chr1B 92.226 849 48 6 1827 2659 288390511 288391357 0.000000e+00 1186.0
36 TraesCS3B01G169600 chr1B 93.443 61 4 0 2651 2711 492861057 492860997 1.030000e-14 91.6
37 TraesCS3B01G169600 chr1B 95.833 48 2 0 1788 1835 471023340 471023387 8.050000e-11 78.7
38 TraesCS3B01G169600 chr3A 93.137 816 50 4 978 1791 125063805 125062994 0.000000e+00 1192.0
39 TraesCS3B01G169600 chr3A 82.253 586 71 25 1 566 125089322 125088750 2.440000e-130 475.0
40 TraesCS3B01G169600 chr3A 82.288 542 73 18 39 566 125066295 125065763 5.320000e-122 448.0
41 TraesCS3B01G169600 chr7D 74.684 553 85 34 50 568 117542982 117542451 7.660000e-46 195.0
42 TraesCS3B01G169600 chr7D 91.667 108 6 3 562 666 561960134 561960241 2.180000e-31 147.0
43 TraesCS3B01G169600 chr7D 92.982 57 4 0 2655 2711 398878017 398877961 1.730000e-12 84.2
44 TraesCS3B01G169600 chr5D 75.227 440 84 20 128 545 537685391 537684955 4.610000e-43 185.0
45 TraesCS3B01G169600 chr5D 94.737 95 5 0 560 654 347656212 347656118 6.050000e-32 148.0
46 TraesCS3B01G169600 chr5D 93.814 97 4 1 570 664 301581319 301581415 7.820000e-31 145.0
47 TraesCS3B01G169600 chrUn 94.737 95 5 0 560 654 67634469 67634375 6.050000e-32 148.0
48 TraesCS3B01G169600 chrUn 96.471 85 3 0 570 654 37006447 37006363 1.010000e-29 141.0
49 TraesCS3B01G169600 chrUn 96.471 85 3 0 570 654 38258668 38258584 1.010000e-29 141.0
50 TraesCS3B01G169600 chrUn 96.471 85 3 0 570 654 108327593 108327677 1.010000e-29 141.0
51 TraesCS3B01G169600 chrUn 96.471 85 3 0 570 654 196709562 196709646 1.010000e-29 141.0
52 TraesCS3B01G169600 chrUn 74.074 378 79 13 34 395 26526710 26526336 1.310000e-28 137.0
53 TraesCS3B01G169600 chrUn 95.294 85 4 0 570 654 36921071 36920987 4.710000e-28 135.0
54 TraesCS3B01G169600 chrUn 95.294 85 4 0 570 654 242182866 242182950 4.710000e-28 135.0
55 TraesCS3B01G169600 chrUn 94.118 85 5 0 570 654 162568743 162568827 2.190000e-26 130.0
56 TraesCS3B01G169600 chrUn 93.182 88 6 0 570 657 364537864 364537777 2.190000e-26 130.0
57 TraesCS3B01G169600 chrUn 90.625 96 8 1 567 662 58070906 58071000 2.830000e-25 126.0
58 TraesCS3B01G169600 chrUn 92.857 56 4 0 2656 2711 37949032 37948977 6.220000e-12 82.4
59 TraesCS3B01G169600 chrUn 95.745 47 2 0 1789 1835 37406957 37406911 2.890000e-10 76.8
60 TraesCS3B01G169600 chr6D 94.737 95 5 0 560 654 356639973 356639879 6.050000e-32 148.0
61 TraesCS3B01G169600 chr6D 95.604 91 3 1 570 659 149721665 149721755 7.820000e-31 145.0
62 TraesCS3B01G169600 chr6D 82.301 113 11 5 462 568 366546162 366546271 3.720000e-14 89.8
63 TraesCS3B01G169600 chr6D 88.525 61 5 2 1778 1836 76197705 76197765 3.740000e-09 73.1
64 TraesCS3B01G169600 chr2D 94.737 95 5 0 560 654 513253219 513253125 6.050000e-32 148.0
65 TraesCS3B01G169600 chr2D 92.079 101 7 1 561 660 645267905 645267805 1.010000e-29 141.0
66 TraesCS3B01G169600 chr2D 92.982 57 4 0 2655 2711 591303891 591303947 1.730000e-12 84.2
67 TraesCS3B01G169600 chr2D 95.833 48 2 0 1789 1836 572920024 572920071 8.050000e-11 78.7
68 TraesCS3B01G169600 chr1D 94.737 95 5 0 560 654 135048025 135048119 6.050000e-32 148.0
69 TraesCS3B01G169600 chr1D 96.552 87 3 0 568 654 91235218 91235132 7.820000e-31 145.0
70 TraesCS3B01G169600 chr1D 96.512 86 3 0 569 654 268929921 268929836 2.810000e-30 143.0
71 TraesCS3B01G169600 chr1D 93.684 95 6 0 560 654 483185680 483185774 2.810000e-30 143.0
72 TraesCS3B01G169600 chr1D 96.471 85 3 0 570 654 446425090 446425006 1.010000e-29 141.0
73 TraesCS3B01G169600 chr1D 93.548 93 5 1 563 654 199114305 199114213 1.310000e-28 137.0
74 TraesCS3B01G169600 chr1D 93.548 93 5 1 563 654 473933023 473932931 1.310000e-28 137.0
75 TraesCS3B01G169600 chr1D 92.553 94 7 0 561 654 437574213 437574306 4.710000e-28 135.0
76 TraesCS3B01G169600 chr1D 84.921 126 13 6 539 658 243753263 243753388 3.670000e-24 122.0
77 TraesCS3B01G169600 chr1A 94.681 94 4 1 562 654 486046170 486046077 7.820000e-31 145.0
78 TraesCS3B01G169600 chr1A 75.075 333 57 17 256 568 60503244 60503570 6.090000e-27 132.0
79 TraesCS3B01G169600 chr4D 93.684 95 6 0 560 654 29238222 29238316 2.810000e-30 143.0
80 TraesCS3B01G169600 chr4D 94.624 93 4 1 563 654 41339607 41339515 2.810000e-30 143.0
81 TraesCS3B01G169600 chr4D 93.684 95 6 0 560 654 262040771 262040865 2.810000e-30 143.0
82 TraesCS3B01G169600 chr4D 93.684 95 6 0 560 654 337701190 337701284 2.810000e-30 143.0
83 TraesCS3B01G169600 chr4D 89.720 107 9 2 570 675 329883022 329882917 4.710000e-28 135.0
84 TraesCS3B01G169600 chr6A 94.737 57 3 0 2655 2711 6606395 6606451 3.720000e-14 89.8
85 TraesCS3B01G169600 chr4A 92.982 57 4 0 2655 2711 709423293 709423349 1.730000e-12 84.2
86 TraesCS3B01G169600 chr2A 100.000 28 0 0 517 544 193762151 193762178 5.000000e-03 52.8


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 TraesCS3B01G169600 chr3B 169668015 169670725 2710 True 5007.000000 5007 100.000000 1 2711 1 chr3B.!!$R2 2710
1 TraesCS3B01G169600 chr3B 171120078 171120916 838 False 1303.000000 1303 94.994000 1836 2658 1 chr3B.!!$F1 822
2 TraesCS3B01G169600 chr3B 169829845 169831616 1771 True 1270.500000 1419 92.679000 1 1791 2 chr3B.!!$R3 1790
3 TraesCS3B01G169600 chr3D 116153452 116157478 4026 True 704.666667 1411 85.870333 1 1791 3 chr3D.!!$R2 1790
4 TraesCS3B01G169600 chr4B 28681514 28682349 835 True 1288.000000 1288 94.743000 1833 2655 1 chr4B.!!$R1 822
5 TraesCS3B01G169600 chr4B 665292984 665293819 835 True 1282.000000 1282 94.624000 1836 2658 1 chr4B.!!$R3 822
6 TraesCS3B01G169600 chr4B 662087413 662088265 852 True 1245.000000 1245 93.240000 1821 2664 1 chr4B.!!$R2 843
7 TraesCS3B01G169600 chr7B 664046780 664047622 842 True 1280.000000 1280 94.320000 1832 2663 1 chr7B.!!$R1 831
8 TraesCS3B01G169600 chr5B 686831913 686832772 859 False 1280.000000 1280 93.757000 1824 2673 1 chr5B.!!$F4 849
9 TraesCS3B01G169600 chr5B 63251596 63252432 836 True 1279.000000 1279 94.504000 1833 2656 1 chr5B.!!$R1 823
10 TraesCS3B01G169600 chr5B 203678583 203679430 847 False 1279.000000 1279 94.118000 1826 2661 1 chr5B.!!$F1 835
11 TraesCS3B01G169600 chr5B 155711088 155711936 848 True 1266.000000 1266 93.882000 1828 2661 1 chr5B.!!$R2 833
12 TraesCS3B01G169600 chr5B 646263183 646264030 847 False 1258.000000 1258 93.750000 1830 2662 1 chr5B.!!$F3 832
13 TraesCS3B01G169600 chr5B 639157510 639158064 554 False 202.000000 202 74.341000 6 545 1 chr5B.!!$F2 539
14 TraesCS3B01G169600 chr5A 664388866 664389696 830 True 1279.000000 1279 94.705000 1840 2656 1 chr5A.!!$R1 816
15 TraesCS3B01G169600 chr6B 646915183 646916035 852 True 1266.000000 1266 93.677000 1830 2670 1 chr6B.!!$R2 840
16 TraesCS3B01G169600 chr6B 713754052 713754881 829 False 1260.000000 1260 94.258000 1836 2658 1 chr6B.!!$F2 822
17 TraesCS3B01G169600 chr6B 705992712 705993445 733 True 1118.000000 1118 94.437000 1823 2545 1 chr6B.!!$R3 722
18 TraesCS3B01G169600 chr2B 675208177 675209028 851 False 1264.000000 1264 93.669000 1823 2662 1 chr2B.!!$F1 839
19 TraesCS3B01G169600 chr1B 614583787 614584630 843 True 1210.000000 1210 92.723000 1829 2666 1 chr1B.!!$R2 837
20 TraesCS3B01G169600 chr1B 288390511 288391357 846 False 1186.000000 1186 92.226000 1827 2659 1 chr1B.!!$F1 832
21 TraesCS3B01G169600 chr3A 125062994 125066295 3301 True 820.000000 1192 87.712500 39 1791 2 chr3A.!!$R2 1752
22 TraesCS3B01G169600 chr3A 125088750 125089322 572 True 475.000000 475 82.253000 1 566 1 chr3A.!!$R1 565

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
353 993 0.253610 ATCTCCCTCACTCGTCGACT 59.746 55.0 14.70 0.00 0.0 4.18 F
742 1614 0.315251 GGCTCAACTGGCTTTGAACC 59.685 55.0 6.23 6.23 35.2 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 3805 0.669318 TTCGGTGTCAAGGTCGATGC 60.669 55.0 0.00 0.0 0.00 3.91 R
2370 4995 0.806868 CACTGCAGTTGCCATAGTGG 59.193 55.0 18.94 0.0 38.29 4.00 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
231 862 2.905075 TGCATCCACCGATGTAGAAAG 58.095 47.619 2.35 0.00 46.56 2.62
348 988 1.063642 TCCATCATCTCCCTCACTCGT 60.064 52.381 0.00 0.00 0.00 4.18
353 993 0.253610 ATCTCCCTCACTCGTCGACT 59.746 55.000 14.70 0.00 0.00 4.18
582 1256 3.766051 TCTAAAAAGTACTCCCTCCGTCC 59.234 47.826 0.00 0.00 0.00 4.79
589 1263 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
592 1266 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
595 1269 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
596 1270 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
597 1271 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
632 1306 9.322773 ACTAGTGTAGTGTTAAAAACTTTCCTC 57.677 33.333 0.00 0.00 37.69 3.71
633 1307 9.543783 CTAGTGTAGTGTTAAAAACTTTCCTCT 57.456 33.333 0.00 0.00 0.00 3.69
644 1318 7.669089 AAAAACTTTCCTCTATTTTGGGACA 57.331 32.000 0.00 0.00 0.00 4.02
652 1326 3.777522 CTCTATTTTGGGACAGAGGGAGT 59.222 47.826 0.00 0.00 42.39 3.85
653 1327 4.955335 TCTATTTTGGGACAGAGGGAGTA 58.045 43.478 0.00 0.00 42.39 2.59
654 1328 5.347124 TCTATTTTGGGACAGAGGGAGTAA 58.653 41.667 0.00 0.00 42.39 2.24
655 1329 5.788533 TCTATTTTGGGACAGAGGGAGTAAA 59.211 40.000 0.00 0.00 42.39 2.01
656 1330 4.799715 TTTTGGGACAGAGGGAGTAAAA 57.200 40.909 0.00 0.00 42.39 1.52
658 1332 5.333566 TTTGGGACAGAGGGAGTAAAAAT 57.666 39.130 0.00 0.00 42.39 1.82
742 1614 0.315251 GGCTCAACTGGCTTTGAACC 59.685 55.000 6.23 6.23 35.20 3.62
832 3213 1.298859 GCCTTCCGAATTGTGAGCGT 61.299 55.000 0.00 0.00 0.00 5.07
888 3269 3.547746 GGGCCCACGTTAATTTCATCTA 58.452 45.455 19.95 0.00 0.00 1.98
895 3276 6.425114 CCCACGTTAATTTCATCTAGATCCTG 59.575 42.308 1.03 0.00 0.00 3.86
920 3301 2.113807 GGAACCCTACCTCGTATTGGT 58.886 52.381 0.00 0.00 41.28 3.67
1295 3898 1.883084 CGCCGGACATAGCCAAGTC 60.883 63.158 5.05 0.00 0.00 3.01
1370 3973 1.301479 GTTCCAAGTCCTTCCGCGT 60.301 57.895 4.92 0.00 0.00 6.01
1458 4061 1.979155 CTGGAGGACCTGCGTCAGA 60.979 63.158 8.65 0.00 41.13 3.27
1611 4214 4.256180 GGCGCCCATCGGATTCCT 62.256 66.667 18.11 0.00 38.94 3.36
1646 4249 0.610174 TTCTGCTCCGAGACTTGCAT 59.390 50.000 0.00 0.00 34.79 3.96
1650 4253 1.513158 CTCCGAGACTTGCATCCGT 59.487 57.895 0.00 0.00 0.00 4.69
1671 4274 0.168788 AACACATTCGCCGCATTGAG 59.831 50.000 0.00 0.00 0.00 3.02
1679 4282 2.745884 CCGCATTGAGGAACGCCA 60.746 61.111 0.00 0.00 36.29 5.69
1744 4347 5.362430 CAGGTCAGAGGAGTAGCTTTAATCT 59.638 44.000 0.00 0.00 0.00 2.40
1745 4348 6.547880 CAGGTCAGAGGAGTAGCTTTAATCTA 59.452 42.308 0.00 0.00 0.00 1.98
1803 4411 6.629182 GAGTTTTTATACTCACTCCGTCAC 57.371 41.667 0.00 0.00 43.23 3.67
1804 4412 6.092955 AGTTTTTATACTCACTCCGTCACA 57.907 37.500 0.00 0.00 0.00 3.58
1805 4413 6.518493 AGTTTTTATACTCACTCCGTCACAA 58.482 36.000 0.00 0.00 0.00 3.33
1806 4414 6.987992 AGTTTTTATACTCACTCCGTCACAAA 59.012 34.615 0.00 0.00 0.00 2.83
1807 4415 7.496591 AGTTTTTATACTCACTCCGTCACAAAA 59.503 33.333 0.00 0.00 0.00 2.44
1808 4416 7.972832 TTTTATACTCACTCCGTCACAAAAT 57.027 32.000 0.00 0.00 0.00 1.82
1809 4417 9.491675 TTTTTATACTCACTCCGTCACAAAATA 57.508 29.630 0.00 0.00 0.00 1.40
1810 4418 9.491675 TTTTATACTCACTCCGTCACAAAATAA 57.508 29.630 0.00 0.00 0.00 1.40
1811 4419 8.697846 TTATACTCACTCCGTCACAAAATAAG 57.302 34.615 0.00 0.00 0.00 1.73
1812 4420 4.957296 ACTCACTCCGTCACAAAATAAGT 58.043 39.130 0.00 0.00 0.00 2.24
1813 4421 4.750098 ACTCACTCCGTCACAAAATAAGTG 59.250 41.667 0.00 0.00 38.32 3.16
1814 4422 4.699637 TCACTCCGTCACAAAATAAGTGT 58.300 39.130 0.00 0.00 38.16 3.55
1815 4423 4.748102 TCACTCCGTCACAAAATAAGTGTC 59.252 41.667 0.00 0.00 38.16 3.67
1816 4424 4.750098 CACTCCGTCACAAAATAAGTGTCT 59.250 41.667 0.00 0.00 38.16 3.41
1817 4425 5.236478 CACTCCGTCACAAAATAAGTGTCTT 59.764 40.000 0.00 0.00 38.16 3.01
1818 4426 5.236478 ACTCCGTCACAAAATAAGTGTCTTG 59.764 40.000 0.00 0.00 38.16 3.02
1819 4427 5.361427 TCCGTCACAAAATAAGTGTCTTGA 58.639 37.500 0.00 0.00 38.16 3.02
1820 4428 5.465390 TCCGTCACAAAATAAGTGTCTTGAG 59.535 40.000 0.00 0.00 38.16 3.02
1821 4429 5.140177 CGTCACAAAATAAGTGTCTTGAGC 58.860 41.667 0.00 0.00 38.16 4.26
1822 4430 5.050091 CGTCACAAAATAAGTGTCTTGAGCT 60.050 40.000 0.00 0.00 38.16 4.09
1823 4431 6.511767 CGTCACAAAATAAGTGTCTTGAGCTT 60.512 38.462 0.00 0.00 38.16 3.74
1824 4432 7.307160 CGTCACAAAATAAGTGTCTTGAGCTTA 60.307 37.037 0.00 0.00 38.16 3.09
1825 4433 8.012241 GTCACAAAATAAGTGTCTTGAGCTTAG 58.988 37.037 0.00 0.00 38.16 2.18
1826 4434 7.715249 TCACAAAATAAGTGTCTTGAGCTTAGT 59.285 33.333 0.00 0.00 38.16 2.24
1827 4435 8.988934 CACAAAATAAGTGTCTTGAGCTTAGTA 58.011 33.333 0.00 0.00 32.44 1.82
1880 4488 2.948720 GCAGGAAGGGAGACGCACT 61.949 63.158 0.00 0.00 0.00 4.40
2008 4628 4.142249 CCGTTTTCACCATTAAATCCCTCC 60.142 45.833 0.00 0.00 0.00 4.30
2039 4659 5.011090 TCTTCGAAACTAGATCCCATGTG 57.989 43.478 0.00 0.00 0.00 3.21
2137 4761 6.015180 ACACTGAAGTTGCCATGATATGTTTT 60.015 34.615 0.00 0.00 0.00 2.43
2140 4764 7.394359 ACTGAAGTTGCCATGATATGTTTTAGT 59.606 33.333 0.00 0.00 0.00 2.24
2246 4870 3.738830 AATTGCCATGATACATGCACC 57.261 42.857 0.00 0.00 32.63 5.01
2272 4896 7.437793 AAAATTGCCATGGTTCATACAAAAG 57.562 32.000 14.67 0.00 0.00 2.27
2326 4951 6.751888 GCCATCGTCAAAATACTAAAATTGCT 59.248 34.615 0.00 0.00 0.00 3.91
2372 4997 5.221342 CCACATGGCAACTTTAGTTTAACCA 60.221 40.000 0.00 9.82 37.34 3.67
2688 5326 8.461249 ACTAGAACTAGTACAAAGTTGAGACA 57.539 34.615 15.86 0.15 43.98 3.41
2689 5327 9.080097 ACTAGAACTAGTACAAAGTTGAGACAT 57.920 33.333 15.86 0.00 43.98 3.06
2690 5328 9.915629 CTAGAACTAGTACAAAGTTGAGACATT 57.084 33.333 15.86 0.00 37.31 2.71
2698 5336 9.965824 AGTACAAAGTTGAGACATTTATTTTGG 57.034 29.630 0.00 0.00 0.00 3.28
2699 5337 9.191995 GTACAAAGTTGAGACATTTATTTTGGG 57.808 33.333 0.00 0.00 0.00 4.12
2700 5338 8.017418 ACAAAGTTGAGACATTTATTTTGGGA 57.983 30.769 0.00 0.00 0.00 4.37
2701 5339 7.926018 ACAAAGTTGAGACATTTATTTTGGGAC 59.074 33.333 0.00 0.00 0.00 4.46
2702 5340 7.595819 AAGTTGAGACATTTATTTTGGGACA 57.404 32.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 27 4.602340 AAAAGCTCCAAGACTAACGAGA 57.398 40.909 0.00 0.00 0.00 4.04
231 862 4.809426 CGAACCCATACTTATGTGAGGAAC 59.191 45.833 3.72 0.00 31.82 3.62
436 1082 9.757227 TTTTTCTTATCGTCCATGTTGATTTTT 57.243 25.926 0.00 0.00 0.00 1.94
589 1263 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
592 1266 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
617 1291 9.472361 GTCCCAAAATAGAGGAAAGTTTTTAAC 57.528 33.333 0.00 0.00 0.00 2.01
619 1293 8.770010 TGTCCCAAAATAGAGGAAAGTTTTTA 57.230 30.769 0.00 0.00 0.00 1.52
630 1304 3.777522 ACTCCCTCTGTCCCAAAATAGAG 59.222 47.826 0.00 0.00 37.11 2.43
632 1306 5.693769 TTACTCCCTCTGTCCCAAAATAG 57.306 43.478 0.00 0.00 0.00 1.73
633 1307 6.457159 TTTTACTCCCTCTGTCCCAAAATA 57.543 37.500 0.00 0.00 0.00 1.40
637 1311 5.333566 AATTTTTACTCCCTCTGTCCCAA 57.666 39.130 0.00 0.00 0.00 4.12
780 1656 0.905337 AGACTAGAAGGGTTGGCGCT 60.905 55.000 7.64 0.00 39.77 5.92
888 3269 0.336737 AGGGTTCCGAGTCAGGATCT 59.663 55.000 4.84 2.11 40.48 2.75
895 3276 0.679321 ACGAGGTAGGGTTCCGAGTC 60.679 60.000 0.00 0.00 0.00 3.36
1200 3803 1.374252 GGTGTCAAGGTCGATGCGT 60.374 57.895 0.00 0.00 0.00 5.24
1202 3805 0.669318 TTCGGTGTCAAGGTCGATGC 60.669 55.000 0.00 0.00 0.00 3.91
1295 3898 2.434843 TAGTCCTGCGCCCTCATGG 61.435 63.158 4.18 0.00 37.09 3.66
1646 4249 1.628447 GCGGCGAATGTGTTTACGGA 61.628 55.000 12.98 0.00 0.00 4.69
1650 4253 1.807142 TCAATGCGGCGAATGTGTTTA 59.193 42.857 12.98 0.00 0.00 2.01
1795 4403 5.465390 TCAAGACACTTATTTTGTGACGGAG 59.535 40.000 0.00 0.00 38.65 4.63
1796 4404 5.361427 TCAAGACACTTATTTTGTGACGGA 58.639 37.500 0.00 0.00 38.65 4.69
1797 4405 5.666969 TCAAGACACTTATTTTGTGACGG 57.333 39.130 0.00 0.00 38.65 4.79
1798 4406 5.050091 AGCTCAAGACACTTATTTTGTGACG 60.050 40.000 0.00 0.00 38.65 4.35
1799 4407 6.305693 AGCTCAAGACACTTATTTTGTGAC 57.694 37.500 0.00 0.00 38.65 3.67
1800 4408 6.942532 AAGCTCAAGACACTTATTTTGTGA 57.057 33.333 0.00 0.00 38.65 3.58
1801 4409 7.865707 ACTAAGCTCAAGACACTTATTTTGTG 58.134 34.615 3.19 0.00 40.87 3.33
1802 4410 9.726438 ATACTAAGCTCAAGACACTTATTTTGT 57.274 29.630 3.19 0.00 0.00 2.83
1816 4424 8.823818 GCGAACCTAAATTTATACTAAGCTCAA 58.176 33.333 0.00 0.00 0.00 3.02
1817 4425 7.168637 CGCGAACCTAAATTTATACTAAGCTCA 59.831 37.037 0.00 0.00 0.00 4.26
1818 4426 7.499868 CGCGAACCTAAATTTATACTAAGCTC 58.500 38.462 0.00 0.00 0.00 4.09
1819 4427 6.073927 GCGCGAACCTAAATTTATACTAAGCT 60.074 38.462 12.10 0.00 0.00 3.74
1820 4428 6.069563 GCGCGAACCTAAATTTATACTAAGC 58.930 40.000 12.10 0.92 0.00 3.09
1821 4429 7.404139 AGCGCGAACCTAAATTTATACTAAG 57.596 36.000 12.10 0.00 0.00 2.18
1822 4430 8.755018 GTTAGCGCGAACCTAAATTTATACTAA 58.245 33.333 21.09 0.00 0.00 2.24
1823 4431 8.137437 AGTTAGCGCGAACCTAAATTTATACTA 58.863 33.333 26.65 0.00 0.00 1.82
1824 4432 6.982724 AGTTAGCGCGAACCTAAATTTATACT 59.017 34.615 26.65 3.47 0.00 2.12
1825 4433 7.061634 CAGTTAGCGCGAACCTAAATTTATAC 58.938 38.462 26.65 1.08 0.00 1.47
1826 4434 6.292488 GCAGTTAGCGCGAACCTAAATTTATA 60.292 38.462 26.65 0.00 0.00 0.98
1827 4435 5.503520 GCAGTTAGCGCGAACCTAAATTTAT 60.504 40.000 26.65 5.10 0.00 1.40
1880 4488 9.478768 TCAATCTGTTTACATTAAAGACGTGTA 57.521 29.630 0.00 0.00 0.00 2.90
2008 4628 5.425577 TCTAGTTTCGAAGATCTCATCGG 57.574 43.478 15.04 0.89 37.62 4.18
2063 4685 5.649782 AGACATGGCAACTTTTAATCCAG 57.350 39.130 0.00 0.00 37.61 3.86
2246 4870 8.545229 TTTTGTATGAACCATGGCAATTTTAG 57.455 30.769 13.04 0.00 0.00 1.85
2326 4951 9.237187 TGTGGCAATTTTAGTTTGTAGATCATA 57.763 29.630 0.00 0.00 0.00 2.15
2370 4995 0.806868 CACTGCAGTTGCCATAGTGG 59.193 55.000 18.94 0.00 38.29 4.00
2372 4997 3.417069 TTACACTGCAGTTGCCATAGT 57.583 42.857 18.94 12.72 41.18 2.12
2419 5044 7.484641 CCATGTTGATATGTTTCGACGATTTTT 59.515 33.333 0.00 0.00 33.42 1.94
2420 5045 6.966632 CCATGTTGATATGTTTCGACGATTTT 59.033 34.615 0.00 0.00 33.42 1.82
2421 5046 6.458206 CCCATGTTGATATGTTTCGACGATTT 60.458 38.462 0.00 0.00 33.42 2.17
2672 5310 9.965824 CCAAAATAAATGTCTCAACTTTGTACT 57.034 29.630 0.00 0.00 0.00 2.73
2673 5311 9.191995 CCCAAAATAAATGTCTCAACTTTGTAC 57.808 33.333 0.00 0.00 0.00 2.90
2674 5312 9.137459 TCCCAAAATAAATGTCTCAACTTTGTA 57.863 29.630 0.00 0.00 0.00 2.41
2675 5313 7.926018 GTCCCAAAATAAATGTCTCAACTTTGT 59.074 33.333 0.00 0.00 0.00 2.83
2676 5314 7.925483 TGTCCCAAAATAAATGTCTCAACTTTG 59.075 33.333 0.00 0.00 0.00 2.77
2677 5315 8.017418 TGTCCCAAAATAAATGTCTCAACTTT 57.983 30.769 0.00 0.00 0.00 2.66
2678 5316 7.595819 TGTCCCAAAATAAATGTCTCAACTT 57.404 32.000 0.00 0.00 0.00 2.66
2679 5317 7.595819 TTGTCCCAAAATAAATGTCTCAACT 57.404 32.000 0.00 0.00 0.00 3.16
2680 5318 7.384932 CCTTTGTCCCAAAATAAATGTCTCAAC 59.615 37.037 0.00 0.00 0.00 3.18
2681 5319 7.441017 CCTTTGTCCCAAAATAAATGTCTCAA 58.559 34.615 0.00 0.00 0.00 3.02
2682 5320 6.014669 CCCTTTGTCCCAAAATAAATGTCTCA 60.015 38.462 0.00 0.00 0.00 3.27
2683 5321 6.210584 TCCCTTTGTCCCAAAATAAATGTCTC 59.789 38.462 0.00 0.00 0.00 3.36
2684 5322 6.081356 TCCCTTTGTCCCAAAATAAATGTCT 58.919 36.000 0.00 0.00 0.00 3.41
2685 5323 6.014584 ACTCCCTTTGTCCCAAAATAAATGTC 60.015 38.462 0.00 0.00 0.00 3.06
2686 5324 5.843969 ACTCCCTTTGTCCCAAAATAAATGT 59.156 36.000 0.00 0.00 0.00 2.71
2687 5325 6.358974 ACTCCCTTTGTCCCAAAATAAATG 57.641 37.500 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.