Multiple sequence alignment - TraesCS6B01G091300

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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 TraesCS6B01G091300 chr6B 100.000 5284 0 0 1 5284 66946565 66941282 0.000000e+00 9758.0
1 TraesCS6B01G091300 chr6B 96.190 4672 111 33 634 5284 66863451 66858826 0.000000e+00 7579.0
2 TraesCS6B01G091300 chr6B 95.407 4071 103 33 634 4667 66921332 66917309 0.000000e+00 6405.0
3 TraesCS6B01G091300 chr6B 87.038 2191 218 43 1464 3632 66755831 66753685 0.000000e+00 2412.0
4 TraesCS6B01G091300 chr6B 92.075 795 56 6 3603 4392 66784240 66783448 0.000000e+00 1112.0
5 TraesCS6B01G091300 chr6B 81.658 736 72 24 634 1348 66787314 66786621 2.150000e-153 553.0
6 TraesCS6B01G091300 chr6B 90.000 310 22 5 101 406 66922467 66922163 4.960000e-105 392.0
7 TraesCS6B01G091300 chr6B 83.455 411 29 24 99 474 66792484 66792078 3.920000e-91 346.0
8 TraesCS6B01G091300 chr6B 90.417 240 15 6 396 634 66863763 66863531 5.140000e-80 309.0
9 TraesCS6B01G091300 chr6B 90.417 240 15 6 396 634 66921644 66921412 5.140000e-80 309.0
10 TraesCS6B01G091300 chr6B 90.000 150 15 0 4393 4542 60087426 60087277 1.500000e-45 195.0
11 TraesCS6B01G091300 chr6B 81.743 241 12 17 400 640 66761544 66761336 7.040000e-39 172.0
12 TraesCS6B01G091300 chr6B 93.694 111 7 0 634 744 66756694 66756584 3.270000e-37 167.0
13 TraesCS6B01G091300 chr6B 90.741 108 4 3 532 634 66787500 66787394 7.140000e-29 139.0
14 TraesCS6B01G091300 chr6B 93.827 81 5 0 4 84 66946438 66946358 7.190000e-24 122.0
15 TraesCS6B01G091300 chr6B 90.244 82 8 0 3 84 66759363 66759282 2.010000e-19 108.0
16 TraesCS6B01G091300 chr6B 97.674 43 1 0 634 676 66866430 66866388 2.040000e-09 75.0
17 TraesCS6B01G091300 chr6B 97.674 43 1 0 634 676 66904669 66904627 2.040000e-09 75.0
18 TraesCS6B01G091300 chr6B 97.674 43 1 0 634 676 66927257 66927215 2.040000e-09 75.0
19 TraesCS6B01G091300 chr6B 100.000 28 0 0 649 676 66761261 66761234 1.000000e-02 52.8
20 TraesCS6B01G091300 chr6A 92.793 3982 191 39 635 4587 36056752 36052838 0.000000e+00 5675.0
21 TraesCS6B01G091300 chr6A 92.794 3983 188 42 635 4587 35991359 35987446 0.000000e+00 5674.0
22 TraesCS6B01G091300 chr6A 92.652 313 16 5 99 405 36057543 36057232 1.350000e-120 444.0
23 TraesCS6B01G091300 chr6A 82.798 436 39 10 105 509 35991988 35991558 1.810000e-94 357.0
24 TraesCS6B01G091300 chr6A 90.000 150 15 0 4393 4542 33185093 33184944 1.500000e-45 195.0
25 TraesCS6B01G091300 chr6A 92.857 84 6 0 1 84 36057517 36057434 7.190000e-24 122.0
26 TraesCS6B01G091300 chr6A 87.129 101 3 4 532 632 36056908 36056818 7.240000e-19 106.0
27 TraesCS6B01G091300 chr6A 88.136 59 1 2 532 584 35991553 35991495 1.230000e-06 65.8
28 TraesCS6B01G091300 chrUn 93.641 3428 171 18 998 4393 100489786 100493198 0.000000e+00 5079.0
29 TraesCS6B01G091300 chrUn 93.929 2553 112 18 2075 4587 100620877 100623426 0.000000e+00 3816.0
30 TraesCS6B01G091300 chrUn 93.146 2174 105 19 1089 3229 100637283 100639445 0.000000e+00 3149.0
31 TraesCS6B01G091300 chrUn 94.598 1814 74 8 998 2797 323636176 323637979 0.000000e+00 2785.0
32 TraesCS6B01G091300 chrUn 94.598 1814 73 9 998 2797 323668033 323669835 0.000000e+00 2784.0
33 TraesCS6B01G091300 chrUn 95.144 1565 62 5 2799 4349 344891260 344892824 0.000000e+00 2457.0
34 TraesCS6B01G091300 chrUn 94.885 1349 66 3 3240 4587 100660344 100661690 0.000000e+00 2106.0
35 TraesCS6B01G091300 chrUn 93.132 1092 54 6 998 2077 100619682 100620764 0.000000e+00 1581.0
36 TraesCS6B01G091300 chrUn 84.588 558 30 21 99 632 323635269 323635794 2.200000e-138 503.0
37 TraesCS6B01G091300 chrUn 84.588 558 30 21 99 632 323667126 323667651 2.200000e-138 503.0
38 TraesCS6B01G091300 chrUn 84.588 558 30 21 99 632 329023337 329023862 2.200000e-138 503.0
39 TraesCS6B01G091300 chrUn 84.588 558 30 21 99 632 329102700 329103225 2.200000e-138 503.0
40 TraesCS6B01G091300 chrUn 84.588 558 30 21 99 632 361925351 361925876 2.200000e-138 503.0
41 TraesCS6B01G091300 chrUn 84.452 566 27 22 96 632 100618767 100619300 7.900000e-138 501.0
42 TraesCS6B01G091300 chrUn 86.806 432 25 9 765 1196 478140904 478140505 2.240000e-123 453.0
43 TraesCS6B01G091300 chrUn 84.061 527 23 23 135 632 100488910 100489404 8.070000e-123 451.0
44 TraesCS6B01G091300 chrUn 82.292 576 37 30 96 640 100468314 100468855 6.280000e-119 438.0
45 TraesCS6B01G091300 chrUn 82.292 576 37 31 96 640 100627371 100627912 6.280000e-119 438.0
46 TraesCS6B01G091300 chrUn 86.458 384 23 13 96 453 100487969 100488349 1.380000e-105 394.0
47 TraesCS6B01G091300 chrUn 85.911 291 17 11 634 924 323635868 323636134 6.700000e-74 289.0
48 TraesCS6B01G091300 chrUn 85.911 291 17 11 634 924 323667725 323667991 6.700000e-74 289.0
49 TraesCS6B01G091300 chrUn 85.911 291 17 11 634 924 329023936 329024202 6.700000e-74 289.0
50 TraesCS6B01G091300 chrUn 85.911 291 17 11 634 924 329103299 329103565 6.700000e-74 289.0
51 TraesCS6B01G091300 chrUn 85.911 291 17 11 634 924 361925950 361926216 6.700000e-74 289.0
52 TraesCS6B01G091300 chrUn 91.667 84 7 0 1 84 323635295 323635378 3.340000e-22 117.0
53 TraesCS6B01G091300 chrUn 91.667 84 7 0 1 84 323667152 323667235 3.340000e-22 117.0
54 TraesCS6B01G091300 chrUn 91.667 84 7 0 1 84 329023363 329023446 3.340000e-22 117.0
55 TraesCS6B01G091300 chrUn 91.667 84 7 0 1 84 329102726 329102809 3.340000e-22 117.0
56 TraesCS6B01G091300 chrUn 91.667 84 7 0 1 84 361925377 361925460 3.340000e-22 117.0
57 TraesCS6B01G091300 chrUn 79.275 193 12 8 440 632 100488606 100488770 5.590000e-20 110.0
58 TraesCS6B01G091300 chrUn 90.789 76 7 0 9 84 100468350 100468425 9.360000e-18 102.0
59 TraesCS6B01G091300 chrUn 97.368 38 1 0 532 569 100596703 100596740 1.230000e-06 65.8
60 TraesCS6B01G091300 chr7A 94.937 1580 73 3 1555 3127 255897065 255895486 0.000000e+00 2468.0
61 TraesCS6B01G091300 chr2D 95.922 613 25 0 4672 5284 610724841 610725453 0.000000e+00 994.0
62 TraesCS6B01G091300 chr2D 95.277 614 28 1 4672 5284 11523568 11524181 0.000000e+00 972.0
63 TraesCS6B01G091300 chr2D 95.269 613 24 2 4672 5284 39792145 39791538 0.000000e+00 966.0
64 TraesCS6B01G091300 chr7B 95.595 613 27 0 4672 5284 262056355 262056967 0.000000e+00 983.0
65 TraesCS6B01G091300 chr7B 96.923 65 2 0 4583 4647 615810744 615810808 5.590000e-20 110.0
66 TraesCS6B01G091300 chr7B 86.458 96 8 5 4556 4647 410072141 410072047 3.370000e-17 100.0
67 TraesCS6B01G091300 chr6D 95.462 617 27 1 4669 5284 374598758 374599374 0.000000e+00 983.0
68 TraesCS6B01G091300 chr6D 91.333 150 13 0 4393 4542 29228853 29229002 6.940000e-49 206.0
69 TraesCS6B01G091300 chr4D 95.595 613 26 1 4672 5284 330420204 330420815 0.000000e+00 981.0
70 TraesCS6B01G091300 chr3D 95.595 613 24 1 4672 5284 28006312 28006921 0.000000e+00 979.0
71 TraesCS6B01G091300 chr3D 94.822 618 30 1 4667 5284 28005975 28005360 0.000000e+00 963.0
72 TraesCS6B01G091300 chr3D 94.118 68 3 1 4582 4648 28505613 28505546 9.360000e-18 102.0
73 TraesCS6B01G091300 chr5D 92.208 77 4 2 4573 4648 368983617 368983542 2.010000e-19 108.0
74 TraesCS6B01G091300 chr3B 96.875 64 2 0 4584 4647 802923678 802923615 2.010000e-19 108.0
75 TraesCS6B01G091300 chr4B 92.208 77 3 2 4573 4647 548610804 548610729 7.240000e-19 106.0
76 TraesCS6B01G091300 chr2A 91.026 78 6 1 4571 4647 31150021 31149944 2.600000e-18 104.0


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 TraesCS6B01G091300 chr6B 66941282 66946565 5283 True 4940.000000 9758 96.913500 1 5284 2 chr6B.!!$R9 5283
1 TraesCS6B01G091300 chr6B 66858826 66866430 7604 True 2654.333333 7579 94.760333 396 5284 3 chr6B.!!$R7 4888
2 TraesCS6B01G091300 chr6B 66917309 66922467 5158 True 2368.666667 6405 91.941333 101 4667 3 chr6B.!!$R8 4566
3 TraesCS6B01G091300 chr6B 66783448 66787500 4052 True 601.333333 1112 88.158000 532 4392 3 chr6B.!!$R6 3860
4 TraesCS6B01G091300 chr6B 66753685 66761544 7859 True 582.360000 2412 90.543800 3 3632 5 chr6B.!!$R5 3629
5 TraesCS6B01G091300 chr6A 35987446 35991988 4542 True 2032.266667 5674 87.909333 105 4587 3 chr6A.!!$R2 4482
6 TraesCS6B01G091300 chr6A 36052838 36057543 4705 True 1586.750000 5675 91.357750 1 4587 4 chr6A.!!$R3 4586
7 TraesCS6B01G091300 chrUn 100637283 100639445 2162 False 3149.000000 3149 93.146000 1089 3229 1 chrUn.!!$F2 2140
8 TraesCS6B01G091300 chrUn 344891260 344892824 1564 False 2457.000000 2457 95.144000 2799 4349 1 chrUn.!!$F4 1550
9 TraesCS6B01G091300 chrUn 100660344 100661690 1346 False 2106.000000 2106 94.885000 3240 4587 1 chrUn.!!$F3 1347
10 TraesCS6B01G091300 chrUn 100618767 100627912 9145 False 1584.000000 3816 88.451250 96 4587 4 chrUn.!!$F7 4491
11 TraesCS6B01G091300 chrUn 100487969 100493198 5229 False 1508.500000 5079 85.858750 96 4393 4 chrUn.!!$F6 4297
12 TraesCS6B01G091300 chrUn 323635269 323637979 2710 False 923.500000 2785 89.191000 1 2797 4 chrUn.!!$F8 2796
13 TraesCS6B01G091300 chrUn 323667126 323669835 2709 False 923.250000 2784 89.191000 1 2797 4 chrUn.!!$F9 2796
14 TraesCS6B01G091300 chrUn 329023337 329024202 865 False 303.000000 503 87.388667 1 924 3 chrUn.!!$F10 923
15 TraesCS6B01G091300 chrUn 329102700 329103565 865 False 303.000000 503 87.388667 1 924 3 chrUn.!!$F11 923
16 TraesCS6B01G091300 chrUn 361925351 361926216 865 False 303.000000 503 87.388667 1 924 3 chrUn.!!$F12 923
17 TraesCS6B01G091300 chrUn 100468314 100468855 541 False 270.000000 438 86.540500 9 640 2 chrUn.!!$F5 631
18 TraesCS6B01G091300 chr7A 255895486 255897065 1579 True 2468.000000 2468 94.937000 1555 3127 1 chr7A.!!$R1 1572
19 TraesCS6B01G091300 chr2D 610724841 610725453 612 False 994.000000 994 95.922000 4672 5284 1 chr2D.!!$F2 612
20 TraesCS6B01G091300 chr2D 11523568 11524181 613 False 972.000000 972 95.277000 4672 5284 1 chr2D.!!$F1 612
21 TraesCS6B01G091300 chr2D 39791538 39792145 607 True 966.000000 966 95.269000 4672 5284 1 chr2D.!!$R1 612
22 TraesCS6B01G091300 chr7B 262056355 262056967 612 False 983.000000 983 95.595000 4672 5284 1 chr7B.!!$F1 612
23 TraesCS6B01G091300 chr6D 374598758 374599374 616 False 983.000000 983 95.462000 4669 5284 1 chr6D.!!$F2 615
24 TraesCS6B01G091300 chr4D 330420204 330420815 611 False 981.000000 981 95.595000 4672 5284 1 chr4D.!!$F1 612
25 TraesCS6B01G091300 chr3D 28006312 28006921 609 False 979.000000 979 95.595000 4672 5284 1 chr3D.!!$F1 612
26 TraesCS6B01G091300 chr3D 28005360 28005975 615 True 963.000000 963 94.822000 4667 5284 1 chr3D.!!$R1 617

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
759 6174 0.036952 CCCCTAGGTCGCATGCATAG 60.037 60.000 19.57 12.9 0.00 2.23 F
1041 6478 0.039764 TCTCCTTCTCCTCCTTCGCA 59.960 55.000 0.00 0.0 0.00 5.10 F
2242 7953 0.110295 TGTCACACCTCAACATGGGG 59.890 55.000 0.00 0.0 45.84 4.96 F
2705 8446 2.003830 TGGTGGGTGGATTTGGGATTA 58.996 47.619 0.00 0.0 0.00 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 7953 2.289694 TGCCTTGTAGAGTGAAGCTTCC 60.290 50.000 23.42 14.41 0.00 3.46 R
2705 8446 3.693807 TGCAGCTGGAATTTCTTGAGAT 58.306 40.909 17.12 0.00 0.00 2.75 R
3140 8905 1.833630 AGCAGCCTTGAGTATGCACTA 59.166 47.619 0.00 0.00 41.14 2.74 R
4587 10415 1.497161 AGTATTTCCAGACGGAGGGG 58.503 55.000 0.00 0.00 44.10 4.79 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
20 21 3.022607 ACTTTTTCCGTCTGTCTACCG 57.977 47.619 0.00 0.00 0.00 4.02
21 22 2.363359 ACTTTTTCCGTCTGTCTACCGT 59.637 45.455 0.00 0.00 0.00 4.83
22 23 3.181472 ACTTTTTCCGTCTGTCTACCGTT 60.181 43.478 0.00 0.00 0.00 4.44
25 26 1.608055 TCCGTCTGTCTACCGTTCAA 58.392 50.000 0.00 0.00 0.00 2.69
26 27 1.267806 TCCGTCTGTCTACCGTTCAAC 59.732 52.381 0.00 0.00 0.00 3.18
29 30 2.915463 CGTCTGTCTACCGTTCAACATC 59.085 50.000 0.00 0.00 0.00 3.06
30 31 3.610821 CGTCTGTCTACCGTTCAACATCA 60.611 47.826 0.00 0.00 0.00 3.07
33 34 5.408604 GTCTGTCTACCGTTCAACATCAAAT 59.591 40.000 0.00 0.00 0.00 2.32
34 35 5.995282 TCTGTCTACCGTTCAACATCAAATT 59.005 36.000 0.00 0.00 0.00 1.82
39 40 5.427036 ACCGTTCAACATCAAATTTACGT 57.573 34.783 0.00 0.00 0.00 3.57
40 41 5.209240 ACCGTTCAACATCAAATTTACGTG 58.791 37.500 0.00 1.50 0.00 4.49
41 42 4.615121 CCGTTCAACATCAAATTTACGTGG 59.385 41.667 0.00 0.00 0.00 4.94
43 44 6.083630 CGTTCAACATCAAATTTACGTGGAT 58.916 36.000 0.00 0.00 0.00 3.41
44 45 6.032355 CGTTCAACATCAAATTTACGTGGATG 59.968 38.462 11.79 11.79 40.78 3.51
47 48 7.081349 TCAACATCAAATTTACGTGGATGAAC 58.919 34.615 17.61 0.00 38.87 3.18
48 49 6.567687 ACATCAAATTTACGTGGATGAACA 57.432 33.333 17.61 0.00 38.87 3.18
49 50 6.611381 ACATCAAATTTACGTGGATGAACAG 58.389 36.000 17.61 0.00 38.87 3.16
50 51 6.206634 ACATCAAATTTACGTGGATGAACAGT 59.793 34.615 17.61 0.00 38.87 3.55
51 52 5.996219 TCAAATTTACGTGGATGAACAGTG 58.004 37.500 0.00 0.00 0.00 3.66
53 54 2.831685 TTACGTGGATGAACAGTGCT 57.168 45.000 0.00 0.00 0.00 4.40
54 55 2.363788 TACGTGGATGAACAGTGCTC 57.636 50.000 0.00 0.00 0.00 4.26
55 56 0.681733 ACGTGGATGAACAGTGCTCT 59.318 50.000 0.00 0.00 0.00 4.09
56 57 1.070758 ACGTGGATGAACAGTGCTCTT 59.929 47.619 0.00 0.00 0.00 2.85
57 58 2.146342 CGTGGATGAACAGTGCTCTTT 58.854 47.619 0.00 0.00 0.00 2.52
62 63 4.696877 TGGATGAACAGTGCTCTTTGTATG 59.303 41.667 0.00 0.00 0.00 2.39
63 64 4.095483 GGATGAACAGTGCTCTTTGTATGG 59.905 45.833 0.00 0.00 0.00 2.74
65 66 4.713553 TGAACAGTGCTCTTTGTATGGAA 58.286 39.130 0.00 0.00 0.00 3.53
66 67 4.515191 TGAACAGTGCTCTTTGTATGGAAC 59.485 41.667 0.00 0.00 0.00 3.62
67 68 3.067106 ACAGTGCTCTTTGTATGGAACG 58.933 45.455 0.00 0.00 0.00 3.95
68 69 3.244078 ACAGTGCTCTTTGTATGGAACGA 60.244 43.478 0.00 0.00 0.00 3.85
69 70 3.745975 CAGTGCTCTTTGTATGGAACGAA 59.254 43.478 0.00 0.00 0.00 3.85
81 401 7.513371 TGTATGGAACGAACCAAAAGTAAAT 57.487 32.000 9.02 0.00 43.47 1.40
82 402 8.618702 TGTATGGAACGAACCAAAAGTAAATA 57.381 30.769 9.02 0.00 43.47 1.40
87 407 8.414778 TGGAACGAACCAAAAGTAAATAAACAT 58.585 29.630 0.00 0.00 36.96 2.71
88 408 9.896263 GGAACGAACCAAAAGTAAATAAACATA 57.104 29.630 0.00 0.00 0.00 2.29
126 2182 3.074094 ACCCTTTCTGTCCCTTTTCTACC 59.926 47.826 0.00 0.00 0.00 3.18
238 3220 3.157087 GACCCAAGAATTCCAGAAAGCA 58.843 45.455 0.65 0.00 0.00 3.91
248 3230 3.788227 TCCAGAAAGCACCACTTACAT 57.212 42.857 0.00 0.00 37.75 2.29
379 3377 2.574018 GCTGGGGGTCAAAGTTGGC 61.574 63.158 0.00 0.00 0.00 4.52
384 3382 0.755327 GGGGTCAAAGTTGGCACTGT 60.755 55.000 0.00 0.00 36.20 3.55
466 5740 2.417719 GTCAATCTGCAGACCTTTCGT 58.582 47.619 20.97 0.00 0.00 3.85
512 5791 4.310769 CTTTTGTCCAGGTGTCAGAGTAG 58.689 47.826 0.00 0.00 0.00 2.57
513 5792 2.677542 TGTCCAGGTGTCAGAGTAGT 57.322 50.000 0.00 0.00 0.00 2.73
587 5907 0.877071 AGAGTACGTACGTGTGTGGG 59.123 55.000 30.25 0.00 0.00 4.61
588 5908 0.730494 GAGTACGTACGTGTGTGGGC 60.730 60.000 30.25 11.11 0.00 5.36
589 5909 1.174712 AGTACGTACGTGTGTGGGCT 61.175 55.000 30.25 12.98 0.00 5.19
590 5910 0.730494 GTACGTACGTGTGTGGGCTC 60.730 60.000 30.25 6.02 0.00 4.70
647 6059 0.179181 GCACGATGCATGGTTCACTG 60.179 55.000 12.10 1.82 44.26 3.66
723 6135 1.801618 CGCATGCATGACGTTTAGTG 58.198 50.000 30.64 3.10 0.00 2.74
730 6145 6.128849 GCATGCATGACGTTTAGTGAATTTTT 60.129 34.615 30.64 0.00 0.00 1.94
733 6148 6.975197 TGCATGACGTTTAGTGAATTTTTCAA 59.025 30.769 0.00 0.00 42.15 2.69
741 6156 7.359181 CGTTTAGTGAATTTTTCAAATGGCTCC 60.359 37.037 0.00 0.00 42.15 4.70
744 6159 3.909364 TGAATTTTTCAAATGGCTCCCCT 59.091 39.130 0.00 0.00 36.59 4.79
745 6160 5.046663 GTGAATTTTTCAAATGGCTCCCCTA 60.047 40.000 0.00 0.00 42.15 3.53
746 6161 5.187576 TGAATTTTTCAAATGGCTCCCCTAG 59.812 40.000 0.00 0.00 36.59 3.02
747 6162 2.826674 TTTCAAATGGCTCCCCTAGG 57.173 50.000 0.06 0.06 0.00 3.02
748 6163 1.681229 TTCAAATGGCTCCCCTAGGT 58.319 50.000 8.29 0.00 0.00 3.08
749 6164 1.213296 TCAAATGGCTCCCCTAGGTC 58.787 55.000 8.29 0.00 0.00 3.85
750 6165 0.179045 CAAATGGCTCCCCTAGGTCG 60.179 60.000 8.29 0.00 0.00 4.79
751 6166 1.984288 AAATGGCTCCCCTAGGTCGC 61.984 60.000 8.29 6.82 0.00 5.19
752 6167 3.696518 ATGGCTCCCCTAGGTCGCA 62.697 63.158 8.29 0.00 33.94 5.10
753 6168 2.844839 GGCTCCCCTAGGTCGCAT 60.845 66.667 8.29 0.00 33.94 4.73
754 6169 2.423446 GCTCCCCTAGGTCGCATG 59.577 66.667 8.29 0.00 32.97 4.06
755 6170 2.423446 CTCCCCTAGGTCGCATGC 59.577 66.667 7.91 7.91 0.00 4.06
756 6171 2.364973 TCCCCTAGGTCGCATGCA 60.365 61.111 19.57 1.73 0.00 3.96
757 6172 1.762522 CTCCCCTAGGTCGCATGCAT 61.763 60.000 19.57 0.00 0.00 3.96
758 6173 0.471022 TCCCCTAGGTCGCATGCATA 60.471 55.000 19.57 1.39 0.00 3.14
759 6174 0.036952 CCCCTAGGTCGCATGCATAG 60.037 60.000 19.57 12.90 0.00 2.23
760 6175 0.681733 CCCTAGGTCGCATGCATAGT 59.318 55.000 19.57 1.44 0.00 2.12
761 6176 1.337260 CCCTAGGTCGCATGCATAGTC 60.337 57.143 19.57 1.99 0.00 2.59
762 6177 1.615883 CCTAGGTCGCATGCATAGTCT 59.384 52.381 19.57 9.55 0.00 3.24
763 6178 2.036475 CCTAGGTCGCATGCATAGTCTT 59.964 50.000 19.57 1.84 0.00 3.01
764 6179 2.231215 AGGTCGCATGCATAGTCTTC 57.769 50.000 19.57 0.00 0.00 2.87
775 6190 2.735762 GCATAGTCTTCACTCGGTGGAC 60.736 54.545 4.52 5.23 33.62 4.02
875 6290 2.763039 TCCATCCCAAGACATAGCAGA 58.237 47.619 0.00 0.00 0.00 4.26
876 6291 3.114606 TCCATCCCAAGACATAGCAGAA 58.885 45.455 0.00 0.00 0.00 3.02
877 6292 3.135348 TCCATCCCAAGACATAGCAGAAG 59.865 47.826 0.00 0.00 0.00 2.85
976 6405 2.947852 AGTCGATCAGCTGTAACACAC 58.052 47.619 14.67 4.56 0.00 3.82
1041 6478 0.039764 TCTCCTTCTCCTCCTTCGCA 59.960 55.000 0.00 0.00 0.00 5.10
1082 6519 2.836154 GGTGGCCAGAAGTGGTGA 59.164 61.111 5.11 0.00 46.96 4.02
1382 6959 6.804770 CAATTCATGGATTGCCTTTTCAAA 57.195 33.333 13.80 0.00 31.00 2.69
1494 7076 9.458727 AAGAGCAAAATTTCAATCTCTATCTCA 57.541 29.630 10.07 0.00 31.42 3.27
1495 7077 9.629878 AGAGCAAAATTTCAATCTCTATCTCAT 57.370 29.630 8.68 0.00 0.00 2.90
1496 7078 9.881529 GAGCAAAATTTCAATCTCTATCTCATC 57.118 33.333 0.00 0.00 0.00 2.92
1801 7388 8.597167 AGGATGAAATCGATAACATAATGGAGA 58.403 33.333 14.34 0.00 46.86 3.71
1954 7547 3.859386 CAGTTTGGAAACTTGAGTGCAAC 59.141 43.478 1.90 0.00 46.52 4.17
2064 7660 4.141937 CCTTGTGTAGCATAGAAGCACCTA 60.142 45.833 0.00 0.00 36.85 3.08
2079 7790 4.876125 AGCACCTATCATGAGACGTATTG 58.124 43.478 0.09 0.00 0.00 1.90
2242 7953 0.110295 TGTCACACCTCAACATGGGG 59.890 55.000 0.00 0.00 45.84 4.96
2705 8446 2.003830 TGGTGGGTGGATTTGGGATTA 58.996 47.619 0.00 0.00 0.00 1.75
3433 9202 4.476628 TCATCTCAAGCAAGCAGTATGA 57.523 40.909 0.00 0.00 39.69 2.15
3523 9293 4.755411 ACCACCTCACGTATTTCTATGTG 58.245 43.478 0.00 0.00 43.42 3.21
3786 9609 1.754803 TGACAGAGGACAACAACGACT 59.245 47.619 0.00 0.00 0.00 4.18
3892 9717 5.408356 AGAAGTTTATCGCACGACTATGTT 58.592 37.500 0.00 0.00 0.00 2.71
3959 9785 1.000274 GGTGGGTGTGCATTCAAGTTC 60.000 52.381 0.00 0.00 0.00 3.01
4122 9948 0.603975 GATAGCGGGTGAATGGGAGC 60.604 60.000 0.00 0.00 0.00 4.70
4297 10123 7.046292 TGCTCTTTTGAATAATGCATGCTAT 57.954 32.000 20.33 10.10 0.00 2.97
4547 10375 0.663688 CATAGCACGACTCTAGCGGT 59.336 55.000 0.00 0.00 0.00 5.68
4558 10386 2.492484 ACTCTAGCGGTTGTGTTCCTAG 59.508 50.000 0.00 0.00 0.00 3.02
4695 11334 2.552367 ACTAGGGAAAAGCCTAGCAGT 58.448 47.619 0.00 0.00 39.48 4.40
4748 11387 0.033090 GGCGGCGCTACTAATAAGGT 59.967 55.000 32.30 0.00 0.00 3.50
4892 11808 1.264557 CTACTGCTACTATCGCGCTGT 59.735 52.381 5.56 2.11 38.90 4.40
4897 11813 1.560923 CTACTATCGCGCTGTTGCTT 58.439 50.000 5.56 0.00 36.97 3.91
5029 12847 9.346005 ATGTCATCATGATACACATACAAATGT 57.654 29.630 22.44 5.58 38.66 2.71
5108 13248 5.415389 TCATCATCCAACACAAAGTGGTATG 59.585 40.000 1.93 0.00 37.94 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.022607 ACGGTAGACAGACGGAAAAAG 57.977 47.619 0.00 0.00 0.00 2.27
2 3 3.181477 TGAACGGTAGACAGACGGAAAAA 60.181 43.478 0.00 0.00 0.00 1.94
9 10 3.909430 TGATGTTGAACGGTAGACAGAC 58.091 45.455 0.00 0.00 0.00 3.51
10 11 4.594123 TTGATGTTGAACGGTAGACAGA 57.406 40.909 0.00 0.00 0.00 3.41
11 12 5.862924 ATTTGATGTTGAACGGTAGACAG 57.137 39.130 0.00 0.00 0.00 3.51
12 13 6.627395 AAATTTGATGTTGAACGGTAGACA 57.373 33.333 0.00 0.00 0.00 3.41
15 16 6.518395 CACGTAAATTTGATGTTGAACGGTAG 59.482 38.462 0.00 0.00 33.65 3.18
16 17 6.364261 CACGTAAATTTGATGTTGAACGGTA 58.636 36.000 0.00 0.00 33.65 4.02
17 18 5.209240 CACGTAAATTTGATGTTGAACGGT 58.791 37.500 0.00 0.00 33.65 4.83
19 20 5.444983 TCCACGTAAATTTGATGTTGAACG 58.555 37.500 0.00 2.67 35.38 3.95
20 21 7.081349 TCATCCACGTAAATTTGATGTTGAAC 58.919 34.615 12.57 0.00 35.47 3.18
21 22 7.208225 TCATCCACGTAAATTTGATGTTGAA 57.792 32.000 12.57 0.00 35.47 2.69
22 23 6.809630 TCATCCACGTAAATTTGATGTTGA 57.190 33.333 12.57 5.78 35.47 3.18
25 26 6.206634 ACTGTTCATCCACGTAAATTTGATGT 59.793 34.615 12.57 1.93 35.47 3.06
26 27 6.524239 CACTGTTCATCCACGTAAATTTGATG 59.476 38.462 0.00 5.14 35.32 3.07
29 30 4.616802 GCACTGTTCATCCACGTAAATTTG 59.383 41.667 0.00 0.00 0.00 2.32
30 31 4.518970 AGCACTGTTCATCCACGTAAATTT 59.481 37.500 0.00 0.00 0.00 1.82
33 34 3.064207 GAGCACTGTTCATCCACGTAAA 58.936 45.455 0.00 0.00 0.00 2.01
34 35 2.299013 AGAGCACTGTTCATCCACGTAA 59.701 45.455 0.00 0.00 0.00 3.18
39 40 3.213206 ACAAAGAGCACTGTTCATCCA 57.787 42.857 0.00 0.00 0.00 3.41
40 41 4.095483 CCATACAAAGAGCACTGTTCATCC 59.905 45.833 0.00 0.00 0.00 3.51
41 42 4.937620 TCCATACAAAGAGCACTGTTCATC 59.062 41.667 0.00 0.00 0.00 2.92
43 44 4.350368 TCCATACAAAGAGCACTGTTCA 57.650 40.909 0.00 0.00 0.00 3.18
44 45 4.377431 CGTTCCATACAAAGAGCACTGTTC 60.377 45.833 0.00 0.00 0.00 3.18
47 48 3.325870 TCGTTCCATACAAAGAGCACTG 58.674 45.455 0.00 0.00 0.00 3.66
48 49 3.678056 TCGTTCCATACAAAGAGCACT 57.322 42.857 0.00 0.00 0.00 4.40
49 50 3.120304 GGTTCGTTCCATACAAAGAGCAC 60.120 47.826 0.00 0.00 0.00 4.40
50 51 3.071479 GGTTCGTTCCATACAAAGAGCA 58.929 45.455 0.00 0.00 0.00 4.26
51 52 3.071479 TGGTTCGTTCCATACAAAGAGC 58.929 45.455 0.00 0.00 31.96 4.09
53 54 5.591067 ACTTTTGGTTCGTTCCATACAAAGA 59.409 36.000 19.93 0.06 36.81 2.52
54 55 5.827666 ACTTTTGGTTCGTTCCATACAAAG 58.172 37.500 15.47 15.47 38.11 2.77
55 56 5.838531 ACTTTTGGTTCGTTCCATACAAA 57.161 34.783 2.66 0.00 37.33 2.83
56 57 6.939132 TTACTTTTGGTTCGTTCCATACAA 57.061 33.333 2.66 0.00 37.33 2.41
57 58 6.939132 TTTACTTTTGGTTCGTTCCATACA 57.061 33.333 2.66 0.00 37.33 2.29
62 63 8.806177 ATGTTTATTTACTTTTGGTTCGTTCC 57.194 30.769 0.00 0.00 0.00 3.62
97 2152 0.325272 GGACAGAAAGGGTGGAGACC 59.675 60.000 0.00 0.00 42.27 3.85
126 2182 6.866770 TGTTGAACGGTAGATAGACAGAAAAG 59.133 38.462 0.00 0.00 0.00 2.27
238 3220 4.225042 TGGCATTGTCTCTATGTAAGTGGT 59.775 41.667 0.00 0.00 0.00 4.16
248 3230 3.580895 TGGTACAGTTGGCATTGTCTCTA 59.419 43.478 8.23 0.86 0.00 2.43
348 3346 0.974010 CCCCAGCTGAACCATGCATT 60.974 55.000 17.39 0.00 0.00 3.56
384 3382 1.037493 ACGTACTGAACCACTGCTGA 58.963 50.000 0.00 0.00 0.00 4.26
466 5740 3.203934 GTCTAGGTAGTAGAGGGGTCCAA 59.796 52.174 0.00 0.00 38.52 3.53
575 5895 1.566018 GCAAGAGCCCACACACGTAC 61.566 60.000 0.00 0.00 33.58 3.67
597 5918 3.663176 CTGCACCGCACCCACAAG 61.663 66.667 0.00 0.00 33.79 3.16
647 6059 4.559153 CACCATCCATTCTTTGTTTGGAC 58.441 43.478 0.00 0.00 42.09 4.02
723 6135 4.558226 AGGGGAGCCATTTGAAAAATTC 57.442 40.909 0.00 0.00 0.00 2.17
730 6145 1.213296 GACCTAGGGGAGCCATTTGA 58.787 55.000 14.81 0.00 36.25 2.69
733 6148 2.444256 GCGACCTAGGGGAGCCATT 61.444 63.158 14.81 0.00 35.23 3.16
741 6156 0.681733 ACTATGCATGCGACCTAGGG 59.318 55.000 14.81 0.00 0.00 3.53
744 6159 2.693074 TGAAGACTATGCATGCGACCTA 59.307 45.455 14.09 0.00 0.00 3.08
745 6160 1.482182 TGAAGACTATGCATGCGACCT 59.518 47.619 14.09 2.70 0.00 3.85
746 6161 1.594862 GTGAAGACTATGCATGCGACC 59.405 52.381 14.09 0.20 0.00 4.79
747 6162 2.537625 GAGTGAAGACTATGCATGCGAC 59.462 50.000 14.09 0.81 30.16 5.19
748 6163 2.796032 CGAGTGAAGACTATGCATGCGA 60.796 50.000 14.09 2.19 30.16 5.10
749 6164 1.520174 CGAGTGAAGACTATGCATGCG 59.480 52.381 14.09 2.64 30.16 4.73
750 6165 1.863454 CCGAGTGAAGACTATGCATGC 59.137 52.381 11.82 11.82 30.16 4.06
751 6166 2.862536 CACCGAGTGAAGACTATGCATG 59.137 50.000 10.16 1.82 35.23 4.06
752 6167 2.159043 CCACCGAGTGAAGACTATGCAT 60.159 50.000 3.79 3.79 35.23 3.96
753 6168 1.204704 CCACCGAGTGAAGACTATGCA 59.795 52.381 5.71 0.00 35.23 3.96
754 6169 1.476891 TCCACCGAGTGAAGACTATGC 59.523 52.381 5.71 0.00 35.23 3.14
755 6170 2.478031 CGTCCACCGAGTGAAGACTATG 60.478 54.545 5.71 0.00 39.56 2.23
756 6171 1.743958 CGTCCACCGAGTGAAGACTAT 59.256 52.381 5.71 0.00 39.56 2.12
757 6172 1.162698 CGTCCACCGAGTGAAGACTA 58.837 55.000 5.71 0.00 39.56 2.59
758 6173 0.536687 TCGTCCACCGAGTGAAGACT 60.537 55.000 5.71 0.00 41.60 3.24
759 6174 1.954528 TCGTCCACCGAGTGAAGAC 59.045 57.895 5.71 5.01 41.60 3.01
760 6175 4.486887 TCGTCCACCGAGTGAAGA 57.513 55.556 5.71 0.57 41.60 2.87
798 6213 0.280392 TATAGGGGGAGGGGAGGAGA 59.720 60.000 0.00 0.00 0.00 3.71
976 6405 7.997107 TCACTAGCGTACTTAAATAATGTGG 57.003 36.000 0.00 0.00 0.00 4.17
1041 6478 0.323725 AAGCCGAATGGAGCAATGGT 60.324 50.000 0.00 0.00 37.49 3.55
1082 6519 1.071471 CTGTTTCGGCCACTCTGGT 59.929 57.895 2.24 0.00 40.46 4.00
1341 6805 8.892723 CATGAATTGCTAGACTGTGGTTATAAA 58.107 33.333 0.00 0.00 0.00 1.40
1448 7029 9.241919 TGCTCTTTCCAGAAACATCATTAATTA 57.758 29.630 0.00 0.00 0.00 1.40
1449 7030 8.125978 TGCTCTTTCCAGAAACATCATTAATT 57.874 30.769 0.00 0.00 0.00 1.40
1469 7050 9.629878 ATGAGATAGAGATTGAAATTTTGCTCT 57.370 29.630 13.71 13.71 36.72 4.09
1751 7338 4.265073 GAAATAGTGGTCAATGCAGAGGT 58.735 43.478 0.00 0.00 0.00 3.85
2038 7634 3.455910 TGCTTCTATGCTACACAAGGGAT 59.544 43.478 0.00 0.00 0.00 3.85
2079 7790 7.483307 AGGTGCATGTCATACATAATGAAAAC 58.517 34.615 0.00 0.00 46.17 2.43
2242 7953 2.289694 TGCCTTGTAGAGTGAAGCTTCC 60.290 50.000 23.42 14.41 0.00 3.46
2705 8446 3.693807 TGCAGCTGGAATTTCTTGAGAT 58.306 40.909 17.12 0.00 0.00 2.75
3140 8905 1.833630 AGCAGCCTTGAGTATGCACTA 59.166 47.619 0.00 0.00 41.14 2.74
3345 9114 8.777413 CGATATCATTTGTGATGGTGTAAAGAT 58.223 33.333 3.12 0.00 0.00 2.40
3767 9590 2.510768 AGTCGTTGTTGTCCTCTGTC 57.489 50.000 0.00 0.00 0.00 3.51
3786 9609 4.483950 CAGGAGATGACCCTAAGGATGTA 58.516 47.826 0.00 0.00 36.73 2.29
3959 9785 5.313520 TCATGCCTAATGTTGTCAATGTG 57.686 39.130 0.00 0.00 37.56 3.21
4250 10076 5.144159 ACATCCTAGTGTAATCCTCCAGA 57.856 43.478 0.00 0.00 0.00 3.86
4419 10247 2.620112 ATGTTGTGCACAGCTCGGC 61.620 57.895 30.06 13.81 39.40 5.54
4547 10375 3.389983 ACCACTAGCAACTAGGAACACAA 59.610 43.478 6.58 0.00 38.30 3.33
4587 10415 1.497161 AGTATTTCCAGACGGAGGGG 58.503 55.000 0.00 0.00 44.10 4.79
4695 11334 2.566833 TATACCTAGAACCCGCGCTA 57.433 50.000 5.56 0.00 0.00 4.26
4892 11808 2.806244 GCGAGTGGAGAAAAGTAAGCAA 59.194 45.455 0.00 0.00 0.00 3.91
4897 11813 3.367087 GCAGTAGCGAGTGGAGAAAAGTA 60.367 47.826 3.71 0.00 0.00 2.24
5029 12847 3.394674 TTACATTTGTGGTCTCGCAGA 57.605 42.857 0.00 0.00 34.60 4.26
5108 13248 5.232202 TCGCTATTTTCGAGATGATGACAAC 59.768 40.000 0.00 0.00 0.00 3.32
5190 14515 3.504134 TCATAGTGATAGCTCTTCTCGCC 59.496 47.826 0.00 0.00 0.00 5.54
5220 14547 4.037565 CGCCTCATGTACTGTATAGTTCCA 59.962 45.833 0.00 0.00 38.36 3.53
5229 14556 2.184322 CGCCGCCTCATGTACTGT 59.816 61.111 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.