Multiple sequence alignment - TraesCS2A01G332600

Loading Multiple Alignment...

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 TraesCS2A01G332600 chr2A 100.000 2481 0 0 1 2481 565312418 565314898 0.000000e+00 4582.0
1 TraesCS2A01G332600 chr2A 93.678 522 26 6 1085 1606 565262474 565262988 0.000000e+00 774.0
2 TraesCS2A01G332600 chr2A 93.319 479 21 3 1128 1606 565275033 565275500 0.000000e+00 697.0
3 TraesCS2A01G332600 chr2A 89.371 461 32 9 951 1410 565324094 565324538 4.630000e-157 564.0
4 TraesCS2A01G332600 chr2A 82.209 697 78 32 1036 1723 565282957 565283616 2.160000e-155 558.0
5 TraesCS2A01G332600 chr2A 86.192 478 43 8 1000 1467 565288308 565288772 1.710000e-136 496.0
6 TraesCS2A01G332600 chr2A 98.193 166 3 0 628 793 565323728 565323893 8.680000e-75 291.0
7 TraesCS2A01G332600 chr2A 88.496 226 21 2 2067 2291 565259144 565259365 4.070000e-68 268.0
8 TraesCS2A01G332600 chr2A 83.854 192 25 4 2290 2481 565259433 565259618 7.050000e-41 178.0
9 TraesCS2A01G332600 chr2A 84.049 163 19 2 2068 2223 565271005 565271167 1.540000e-32 150.0
10 TraesCS2A01G332600 chr2A 87.313 134 10 4 2168 2300 565271261 565271388 1.990000e-31 147.0
11 TraesCS2A01G332600 chr2A 89.286 56 4 2 2168 2223 565271163 565271216 4.430000e-08 69.4
12 TraesCS2A01G332600 chr2A 94.286 35 1 1 1814 1847 565283667 565283701 4.000000e-03 52.8
13 TraesCS2A01G332600 chr2A 100.000 28 0 0 245 272 589011102 589011075 4.000000e-03 52.8
14 TraesCS2A01G332600 chr2B 84.495 1148 87 29 628 1738 496079153 496078060 0.000000e+00 1050.0
15 TraesCS2A01G332600 chr2B 87.868 577 57 9 922 1492 496177262 496176693 0.000000e+00 665.0
16 TraesCS2A01G332600 chr2B 86.629 531 49 7 947 1470 496087947 496087432 3.580000e-158 568.0
17 TraesCS2A01G332600 chr2B 94.654 318 16 1 2164 2481 496077703 496077387 2.220000e-135 492.0
18 TraesCS2A01G332600 chr2B 86.751 317 11 10 628 921 496191674 496191366 8.560000e-85 324.0
19 TraesCS2A01G332600 chr2B 85.780 218 25 4 2084 2299 496117150 496116937 2.480000e-55 226.0
20 TraesCS2A01G332600 chr2B 88.824 170 13 3 629 793 495953234 495953066 1.160000e-48 204.0
21 TraesCS2A01G332600 chr2B 88.439 173 10 3 1919 2091 496077875 496077713 1.500000e-47 200.0
22 TraesCS2A01G332600 chr2B 80.488 205 15 13 426 611 496192995 496192797 1.550000e-27 134.0
23 TraesCS2A01G332600 chr2D 92.553 470 29 4 922 1385 423280456 423279987 0.000000e+00 669.0
24 TraesCS2A01G332600 chr2D 84.275 655 48 21 1036 1683 423347758 423347152 2.750000e-164 588.0
25 TraesCS2A01G332600 chr2D 89.117 487 32 9 1036 1522 423304565 423304100 9.890000e-164 586.0
26 TraesCS2A01G332600 chr2D 82.485 668 57 25 1000 1649 423292516 423291891 4.700000e-147 531.0
27 TraesCS2A01G332600 chr2D 83.813 278 44 1 7 284 423282944 423282668 1.890000e-66 263.0
28 TraesCS2A01G332600 chr2D 86.325 234 27 2 2067 2299 423308827 423308598 1.470000e-62 250.0
29 TraesCS2A01G332600 chr2D 80.317 315 41 10 1985 2294 423291546 423291248 4.150000e-53 219.0
30 TraesCS2A01G332600 chr2D 87.179 195 17 5 2293 2481 423291190 423290998 5.370000e-52 215.0
31 TraesCS2A01G332600 chr2D 78.616 159 21 6 2123 2278 423286513 423286365 2.630000e-15 93.5
32 TraesCS2A01G332600 chr2D 90.566 53 4 1 2008 2060 423277074 423277023 4.430000e-08 69.4
33 TraesCS2A01G332600 chrUn 86.692 526 45 14 951 1470 325760061 325760567 5.990000e-156 560.0
34 TraesCS2A01G332600 chr5D 79.104 268 40 8 5 272 425701773 425702024 1.180000e-38 171.0
35 TraesCS2A01G332600 chr5D 78.022 182 32 6 5 184 507431671 507431496 9.380000e-20 108.0
36 TraesCS2A01G332600 chr6B 77.358 265 51 9 5 266 216347974 216348232 5.530000e-32 148.0
37 TraesCS2A01G332600 chr5A 76.190 273 51 9 3 275 229472712 229472970 5.570000e-27 132.0
38 TraesCS2A01G332600 chr3A 77.368 190 36 6 64 252 512577849 512578032 3.370000e-19 106.0
39 TraesCS2A01G332600 chr3B 87.654 81 10 0 104 184 605295909 605295989 7.300000e-16 95.3
40 TraesCS2A01G332600 chr3B 79.070 129 25 1 22 150 416858957 416858831 1.220000e-13 87.9
41 TraesCS2A01G332600 chr7D 82.353 85 15 0 3 87 573773725 573773641 9.520000e-10 75.0
42 TraesCS2A01G332600 chr6A 100.000 37 0 0 723 759 109957466 109957502 4.430000e-08 69.4


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 TraesCS2A01G332600 chr2A 565312418 565314898 2480 False 4582.000000 4582 100.00000 1 2481 1 chr2A.!!$F2 2480
1 TraesCS2A01G332600 chr2A 565323728 565324538 810 False 427.500000 564 93.78200 628 1410 2 chr2A.!!$F6 782
2 TraesCS2A01G332600 chr2A 565259144 565262988 3844 False 406.666667 774 88.67600 1085 2481 3 chr2A.!!$F3 1396
3 TraesCS2A01G332600 chr2A 565282957 565283701 744 False 305.400000 558 88.24750 1036 1847 2 chr2A.!!$F5 811
4 TraesCS2A01G332600 chr2A 565271005 565275500 4495 False 265.850000 697 88.49175 1128 2300 4 chr2A.!!$F4 1172
5 TraesCS2A01G332600 chr2B 496176693 496177262 569 True 665.000000 665 87.86800 922 1492 1 chr2B.!!$R4 570
6 TraesCS2A01G332600 chr2B 496077387 496079153 1766 True 580.666667 1050 89.19600 628 2481 3 chr2B.!!$R5 1853
7 TraesCS2A01G332600 chr2B 496087432 496087947 515 True 568.000000 568 86.62900 947 1470 1 chr2B.!!$R2 523
8 TraesCS2A01G332600 chr2B 496191366 496192995 1629 True 229.000000 324 83.61950 426 921 2 chr2B.!!$R6 495
9 TraesCS2A01G332600 chr2D 423347152 423347758 606 True 588.000000 588 84.27500 1036 1683 1 chr2D.!!$R3 647
10 TraesCS2A01G332600 chr2D 423290998 423292516 1518 True 321.666667 531 83.32700 1000 2481 3 chr2D.!!$R5 1481
11 TraesCS2A01G332600 chr2D 423277023 423286513 9490 True 273.725000 669 86.38700 7 2278 4 chr2D.!!$R4 2271
12 TraesCS2A01G332600 chrUn 325760061 325760567 506 False 560.000000 560 86.69200 951 1470 1 chrUn.!!$F1 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
524 5526 0.036732 CACACTACACCCAGCACCAT 59.963 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 10782 0.249489 GTCACGAGCTTGTGGTCAGT 60.249 55.0 29.69 0.0 40.44 3.41 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
41 3605 1.499949 GCTTCAATGCGGCGTAACA 59.500 52.632 9.37 0.00 0.00 2.41
44 3608 0.238817 TTCAATGCGGCGTAACAACC 59.761 50.000 9.37 0.00 0.00 3.77
67 3631 3.269178 GAGTTGATTCCTCAGGAAGCTG 58.731 50.000 22.25 0.00 46.83 4.24
70 3634 1.435408 GATTCCTCAGGAAGCTGCGC 61.435 60.000 14.88 0.00 45.48 6.09
102 3666 3.586430 GCGGTTGCCAAAAAGTGAT 57.414 47.368 0.00 0.00 33.98 3.06
103 3667 1.139163 GCGGTTGCCAAAAAGTGATG 58.861 50.000 0.00 0.00 33.98 3.07
114 3678 1.291877 AAAGTGATGTCGGTCAGCGC 61.292 55.000 0.00 0.00 42.40 5.92
115 3679 3.188786 GTGATGTCGGTCAGCGCC 61.189 66.667 2.29 0.00 37.03 6.53
152 3716 3.863543 CGCGCGGCATCAATGTCA 61.864 61.111 24.84 0.00 31.41 3.58
157 3721 3.909662 GGCATCAATGTCAGCCGT 58.090 55.556 0.00 0.00 37.41 5.68
171 3735 2.032528 CCGTTGCTTGCTCTGGGA 59.967 61.111 0.00 0.00 0.00 4.37
209 3773 1.742831 GGTAAGCGGCATGTTCATCAA 59.257 47.619 1.45 0.00 0.00 2.57
213 3777 2.161855 AGCGGCATGTTCATCAAAAGA 58.838 42.857 1.45 0.00 0.00 2.52
222 3786 4.992688 TGTTCATCAAAAGAAAAGCGTGT 58.007 34.783 0.00 0.00 0.00 4.49
229 3793 1.230324 AAGAAAAGCGTGTGAGAGGC 58.770 50.000 0.00 0.00 35.57 4.70
279 3843 2.048127 AGACGCGGGCTTGAGAAC 60.048 61.111 12.47 0.00 0.00 3.01
284 3848 2.434359 CGGGCTTGAGAACGGTCC 60.434 66.667 0.00 0.00 0.00 4.46
285 3849 2.747686 GGGCTTGAGAACGGTCCA 59.252 61.111 0.00 0.00 0.00 4.02
290 3854 1.593196 CTTGAGAACGGTCCAAAGCA 58.407 50.000 0.00 0.00 0.00 3.91
294 3858 0.182775 AGAACGGTCCAAAGCACCTT 59.817 50.000 0.00 0.00 0.00 3.50
295 3859 1.418637 AGAACGGTCCAAAGCACCTTA 59.581 47.619 0.00 0.00 0.00 2.69
296 3860 1.534163 GAACGGTCCAAAGCACCTTAC 59.466 52.381 0.00 0.00 0.00 2.34
297 3861 0.470766 ACGGTCCAAAGCACCTTACA 59.529 50.000 0.00 0.00 0.00 2.41
300 3864 2.152016 GGTCCAAAGCACCTTACAGAC 58.848 52.381 0.00 0.00 0.00 3.51
303 3867 2.301870 TCCAAAGCACCTTACAGACGAT 59.698 45.455 0.00 0.00 0.00 3.73
304 3868 3.512329 TCCAAAGCACCTTACAGACGATA 59.488 43.478 0.00 0.00 0.00 2.92
305 3869 3.617263 CCAAAGCACCTTACAGACGATAC 59.383 47.826 0.00 0.00 0.00 2.24
307 3871 4.737855 AAGCACCTTACAGACGATACAT 57.262 40.909 0.00 0.00 0.00 2.29
310 3874 6.015027 AGCACCTTACAGACGATACATATC 57.985 41.667 0.00 0.00 0.00 1.63
311 3875 5.047943 AGCACCTTACAGACGATACATATCC 60.048 44.000 0.00 0.00 0.00 2.59
312 3876 5.278808 GCACCTTACAGACGATACATATCCA 60.279 44.000 0.00 0.00 0.00 3.41
313 3877 6.572509 GCACCTTACAGACGATACATATCCAT 60.573 42.308 0.00 0.00 0.00 3.41
314 3878 6.808704 CACCTTACAGACGATACATATCCATG 59.191 42.308 0.00 0.00 38.21 3.66
316 3880 7.015292 ACCTTACAGACGATACATATCCATGTT 59.985 37.037 0.00 0.00 42.98 2.71
317 3881 7.329471 CCTTACAGACGATACATATCCATGTTG 59.671 40.741 0.00 0.00 42.98 3.33
318 3882 5.541845 ACAGACGATACATATCCATGTTGG 58.458 41.667 0.00 0.00 42.98 3.77
338 3902 3.118186 TGGATGATTTTTACGGTCCGGAT 60.118 43.478 17.28 0.00 0.00 4.18
339 3903 4.101274 TGGATGATTTTTACGGTCCGGATA 59.899 41.667 17.28 0.00 0.00 2.59
344 3908 4.741321 TTTTTACGGTCCGGATAGATGT 57.259 40.909 17.28 4.80 0.00 3.06
348 3912 1.113517 CGGTCCGGATAGATGTGGGT 61.114 60.000 7.81 0.00 0.00 4.51
363 3927 2.203294 GGTGGTTTGCCGGTCAGT 60.203 61.111 1.90 0.00 37.67 3.41
368 3932 0.534203 GGTTTGCCGGTCAGTCTTGA 60.534 55.000 1.90 0.00 0.00 3.02
374 3938 1.066858 GCCGGTCAGTCTTGAAGATGA 60.067 52.381 1.90 0.94 34.49 2.92
375 3939 2.612972 GCCGGTCAGTCTTGAAGATGAA 60.613 50.000 1.90 0.00 34.49 2.57
376 3940 3.257393 CCGGTCAGTCTTGAAGATGAAG 58.743 50.000 0.00 2.37 34.49 3.02
378 3942 3.677121 CGGTCAGTCTTGAAGATGAAGTG 59.323 47.826 0.00 0.00 34.49 3.16
381 3945 4.928615 GTCAGTCTTGAAGATGAAGTGAGG 59.071 45.833 0.00 0.00 34.49 3.86
382 3946 3.683822 CAGTCTTGAAGATGAAGTGAGGC 59.316 47.826 0.00 0.00 0.00 4.70
424 5416 3.039134 CAACCCCTTCGTTGCACC 58.961 61.111 0.00 0.00 36.96 5.01
489 5491 4.084223 AGTGCCATTCGTACGTAAAAGTTG 60.084 41.667 16.05 0.25 31.32 3.16
510 5512 4.358851 TGTACGTACTTTTTACGCACACT 58.641 39.130 25.12 0.00 40.80 3.55
515 5517 4.375305 CGTACTTTTTACGCACACTACACC 60.375 45.833 0.00 0.00 34.07 4.16
521 5523 2.317609 CGCACACTACACCCAGCAC 61.318 63.158 0.00 0.00 0.00 4.40
522 5524 1.966451 GCACACTACACCCAGCACC 60.966 63.158 0.00 0.00 0.00 5.01
523 5525 1.449782 CACACTACACCCAGCACCA 59.550 57.895 0.00 0.00 0.00 4.17
524 5526 0.036732 CACACTACACCCAGCACCAT 59.963 55.000 0.00 0.00 0.00 3.55
525 5527 0.324943 ACACTACACCCAGCACCATC 59.675 55.000 0.00 0.00 0.00 3.51
530 5532 3.640407 ACCCAGCACCATCAGCGT 61.640 61.111 0.00 0.00 37.01 5.07
552 5554 1.349688 TGGTTAGCAAAGATCACGGGT 59.650 47.619 0.00 0.00 0.00 5.28
608 5621 6.596888 AGGAATAGCATTACCGATCATTGATG 59.403 38.462 3.32 0.00 0.00 3.07
611 6696 4.321718 AGCATTACCGATCATTGATGGAG 58.678 43.478 16.95 8.18 0.00 3.86
696 6830 0.861450 GGACGCGTTTACATGCATGC 60.861 55.000 26.53 11.82 34.13 4.06
697 6831 0.179202 GACGCGTTTACATGCATGCA 60.179 50.000 26.53 25.04 34.13 3.96
698 6832 0.451383 ACGCGTTTACATGCATGCAT 59.549 45.000 27.46 27.46 34.13 3.96
720 6854 1.270839 GCTACTTGCTCAGTTGGTGGA 60.271 52.381 0.00 0.00 36.88 4.02
845 7015 1.635817 TAAGGACAGGGGCTGCATCC 61.636 60.000 0.50 0.00 34.37 3.51
877 7050 4.682860 CACAAAATCATCACAAGCCACTTC 59.317 41.667 0.00 0.00 0.00 3.01
878 7051 4.240096 CAAAATCATCACAAGCCACTTCC 58.760 43.478 0.00 0.00 0.00 3.46
879 7052 3.446442 AATCATCACAAGCCACTTCCT 57.554 42.857 0.00 0.00 0.00 3.36
935 7144 3.423154 GTGGCCTCGCTTGAACGG 61.423 66.667 3.32 0.00 0.00 4.44
1108 7330 3.258971 ACTCTGAAGCTGAAGCATACC 57.741 47.619 4.90 0.00 45.16 2.73
1116 7338 1.863454 GCTGAAGCATACCACTGATCG 59.137 52.381 0.00 0.00 41.59 3.69
1119 7341 4.375272 CTGAAGCATACCACTGATCGATT 58.625 43.478 0.00 0.00 0.00 3.34
1169 7403 3.996921 AGATTGTCATCCAGTTGAGCT 57.003 42.857 0.00 0.00 0.00 4.09
1273 7507 2.208349 AGGGACCAGCTGGAGGTT 59.792 61.111 39.19 17.35 40.09 3.50
1601 7884 6.571887 CGCGCGTGTATATTAATTCATTGAAA 59.428 34.615 24.19 0.00 0.00 2.69
1626 7912 8.472683 AGAAATGAAAAAGACGAGAGATACTG 57.527 34.615 0.00 0.00 0.00 2.74
1698 9243 6.205464 CGAAGCAAACTCCATGGTTATATGAT 59.795 38.462 12.58 2.05 38.51 2.45
1744 9292 6.808008 TCTTGGTGAAGATGAAGTTCATTC 57.192 37.500 19.19 14.57 37.20 2.67
1757 9305 7.523293 TGAAGTTCATTCATAAACCACATGT 57.477 32.000 0.08 0.00 43.09 3.21
1758 9306 7.369607 TGAAGTTCATTCATAAACCACATGTG 58.630 34.615 19.31 19.31 43.09 3.21
1797 9345 1.439353 GCCATGTGCCCGATGTGTAG 61.439 60.000 0.00 0.00 0.00 2.74
1812 9360 0.485543 TGTAGGGTGACTGGTGAGGA 59.514 55.000 0.00 0.00 0.00 3.71
1844 9407 7.795887 CCAAACAGGACAGCACGATAGTACA 62.796 48.000 0.00 0.00 46.18 2.90
1846 9409 9.706059 CCAAACAGGACAGCACGATAGTACATA 62.706 44.444 0.00 0.00 46.18 2.29
1857 9420 4.470462 CGATAGTACATACAGGTAACCGC 58.530 47.826 0.00 0.00 37.17 5.68
1858 9421 2.857592 AGTACATACAGGTAACCGCG 57.142 50.000 0.00 0.00 37.17 6.46
1859 9422 1.406539 AGTACATACAGGTAACCGCGG 59.593 52.381 26.86 26.86 37.17 6.46
1860 9423 1.134946 GTACATACAGGTAACCGCGGT 59.865 52.381 28.70 28.70 37.17 5.68
1861 9424 0.174162 ACATACAGGTAACCGCGGTC 59.826 55.000 34.29 20.55 37.17 4.79
1862 9425 0.529119 CATACAGGTAACCGCGGTCC 60.529 60.000 34.29 28.86 37.17 4.46
1867 9430 2.571231 GTAACCGCGGTCCCGTAA 59.429 61.111 34.29 10.27 42.09 3.18
1868 9431 1.805539 GTAACCGCGGTCCCGTAAC 60.806 63.158 34.29 18.17 42.09 2.50
1869 9432 3.000693 TAACCGCGGTCCCGTAACC 62.001 63.158 34.29 0.00 42.09 2.85
1879 9637 2.888534 CCGTAACCGCGGTCCATG 60.889 66.667 34.29 25.59 46.11 3.66
1891 9649 1.812507 GTCCATGTAACCGCGGTCC 60.813 63.158 34.29 24.98 0.00 4.46
1892 9650 2.512974 CCATGTAACCGCGGTCCC 60.513 66.667 34.29 24.59 0.00 4.46
1894 9652 3.384532 ATGTAACCGCGGTCCCGT 61.385 61.111 34.29 22.64 42.09 5.28
1895 9653 2.051518 ATGTAACCGCGGTCCCGTA 61.052 57.895 34.29 17.95 42.09 4.02
1897 9655 1.080161 GTAACCGCGGTCCCGTAAA 60.080 57.895 34.29 8.36 42.09 2.01
1898 9656 0.669012 GTAACCGCGGTCCCGTAAAA 60.669 55.000 34.29 6.84 42.09 1.52
1926 10444 5.886960 ATAAGATCTGCACTGTCAAAACC 57.113 39.130 0.00 0.00 0.00 3.27
1955 10523 2.168313 TCAGGTCTGCAGCGATTTCATA 59.832 45.455 9.47 0.00 0.00 2.15
1956 10524 2.543012 CAGGTCTGCAGCGATTTCATAG 59.457 50.000 9.47 0.00 0.00 2.23
1957 10525 2.432146 AGGTCTGCAGCGATTTCATAGA 59.568 45.455 9.47 0.00 0.00 1.98
1958 10526 2.799412 GGTCTGCAGCGATTTCATAGAG 59.201 50.000 9.47 0.00 0.00 2.43
1959 10527 3.452474 GTCTGCAGCGATTTCATAGAGT 58.548 45.455 9.47 0.00 0.00 3.24
1960 10528 3.868077 GTCTGCAGCGATTTCATAGAGTT 59.132 43.478 9.47 0.00 0.00 3.01
1990 10577 7.935520 AGGAAAAGAGACTCAAAATTCTTCAC 58.064 34.615 5.02 0.00 0.00 3.18
2006 10601 1.795768 TCACCGATTTCACAGCAGTC 58.204 50.000 0.00 0.00 0.00 3.51
2019 10614 2.052690 GCAGTCGAGTGGCCCTCTA 61.053 63.158 21.39 5.72 38.11 2.43
2063 10710 2.636412 GCCTGGTTTTCTTCGGCCC 61.636 63.158 0.00 0.00 34.75 5.80
2091 10738 2.741759 TCGTCTTGCTGCATCAGTTA 57.258 45.000 1.84 0.00 33.43 2.24
2096 10743 1.741706 CTTGCTGCATCAGTTAGTGGG 59.258 52.381 1.84 0.00 33.43 4.61
2099 10746 1.742761 CTGCATCAGTTAGTGGGGTG 58.257 55.000 0.00 0.00 0.00 4.61
2100 10747 0.327924 TGCATCAGTTAGTGGGGTGG 59.672 55.000 0.00 0.00 0.00 4.61
2102 10749 0.394352 CATCAGTTAGTGGGGTGGGC 60.394 60.000 0.00 0.00 0.00 5.36
2103 10750 1.571773 ATCAGTTAGTGGGGTGGGCC 61.572 60.000 0.00 0.00 0.00 5.80
2104 10751 3.327404 AGTTAGTGGGGTGGGCCG 61.327 66.667 0.00 0.00 34.97 6.13
2105 10752 4.419921 GTTAGTGGGGTGGGCCGG 62.420 72.222 0.00 0.00 34.97 6.13
2147 10794 4.584327 AACCAAATTACTGACCACAAGC 57.416 40.909 0.00 0.00 0.00 4.01
2149 10796 3.821033 ACCAAATTACTGACCACAAGCTC 59.179 43.478 0.00 0.00 0.00 4.09
2155 10802 1.278172 CTGACCACAAGCTCGTGACG 61.278 60.000 6.31 0.00 39.34 4.35
2156 10803 2.022129 GACCACAAGCTCGTGACGG 61.022 63.158 6.31 1.95 39.34 4.79
2248 10895 1.310933 GGCCACCAACTGCAGAGATG 61.311 60.000 23.35 15.49 0.00 2.90
2305 11008 4.035675 CGGGATTTAGGAATGTTTGCTCTC 59.964 45.833 0.00 0.00 31.99 3.20
2341 11044 5.178996 TCGAGCTCCTAATACTAGCTTTACG 59.821 44.000 8.47 0.00 46.29 3.18
2358 11061 5.220989 GCTTTACGGAATAGTTGGAAATCCC 60.221 44.000 0.00 0.00 34.29 3.85
2389 11092 3.006110 CAGAGCAACCAATTCCACAACAT 59.994 43.478 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.303549 CTGACTGCCCCTTCGCCTAG 62.304 65.000 0.00 0.00 0.00 3.02
2 3 3.710722 CTGACTGCCCCTTCGCCT 61.711 66.667 0.00 0.00 0.00 5.52
14 3578 2.042831 GCATTGAAGCGGGCTGACT 61.043 57.895 0.00 0.00 0.00 3.41
41 3605 1.279271 CCTGAGGAATCAACTCCGGTT 59.721 52.381 0.00 0.00 40.75 4.44
44 3608 2.898705 CTTCCTGAGGAATCAACTCCG 58.101 52.381 15.35 0.00 41.23 4.63
52 3616 4.950479 CGCAGCTTCCTGAGGAAT 57.050 55.556 15.35 0.00 41.23 3.01
88 3652 2.028130 ACCGACATCACTTTTTGGCAA 58.972 42.857 0.00 0.00 0.00 4.52
95 3659 1.291877 GCGCTGACCGACATCACTTT 61.292 55.000 0.00 0.00 40.02 2.66
157 3721 2.032528 CCGTCCCAGAGCAAGCAA 59.967 61.111 0.00 0.00 0.00 3.91
184 3748 4.856801 CATGCCGCTTACCGCCCT 62.857 66.667 0.00 0.00 35.03 5.19
186 3750 3.108357 GAACATGCCGCTTACCGCC 62.108 63.158 0.00 0.00 35.03 6.13
197 3761 4.445385 ACGCTTTTCTTTTGATGAACATGC 59.555 37.500 0.00 0.00 0.00 4.06
199 3763 5.459762 CACACGCTTTTCTTTTGATGAACAT 59.540 36.000 0.00 0.00 0.00 2.71
200 3764 4.797868 CACACGCTTTTCTTTTGATGAACA 59.202 37.500 0.00 0.00 0.00 3.18
209 3773 1.604278 GCCTCTCACACGCTTTTCTTT 59.396 47.619 0.00 0.00 0.00 2.52
213 3777 1.961277 CCGCCTCTCACACGCTTTT 60.961 57.895 0.00 0.00 0.00 2.27
242 3806 4.256180 CCGCCCTAGCCCATCCAC 62.256 72.222 0.00 0.00 34.57 4.02
246 3810 3.164269 CTGACCGCCCTAGCCCAT 61.164 66.667 0.00 0.00 34.57 4.00
279 3843 1.156736 CTGTAAGGTGCTTTGGACCG 58.843 55.000 2.74 0.00 38.64 4.79
284 3848 4.242475 TGTATCGTCTGTAAGGTGCTTTG 58.758 43.478 0.00 0.00 0.00 2.77
285 3849 4.530710 TGTATCGTCTGTAAGGTGCTTT 57.469 40.909 0.00 0.00 0.00 3.51
290 3854 6.493802 ACATGGATATGTATCGTCTGTAAGGT 59.506 38.462 0.00 0.00 45.45 3.50
294 3858 6.492087 TCCAACATGGATATGTATCGTCTGTA 59.508 38.462 0.00 0.00 46.54 2.74
295 3859 5.304357 TCCAACATGGATATGTATCGTCTGT 59.696 40.000 0.00 0.00 46.54 3.41
296 3860 5.783111 TCCAACATGGATATGTATCGTCTG 58.217 41.667 0.00 0.00 46.54 3.51
310 3874 5.323371 ACCGTAAAAATCATCCAACATGG 57.677 39.130 0.00 0.00 39.43 3.66
311 3875 5.339990 GGACCGTAAAAATCATCCAACATG 58.660 41.667 0.00 0.00 0.00 3.21
312 3876 4.095782 CGGACCGTAAAAATCATCCAACAT 59.904 41.667 5.48 0.00 0.00 2.71
313 3877 3.437395 CGGACCGTAAAAATCATCCAACA 59.563 43.478 5.48 0.00 0.00 3.33
314 3878 3.181504 CCGGACCGTAAAAATCATCCAAC 60.182 47.826 13.94 0.00 0.00 3.77
315 3879 3.011119 CCGGACCGTAAAAATCATCCAA 58.989 45.455 13.94 0.00 0.00 3.53
316 3880 2.236644 TCCGGACCGTAAAAATCATCCA 59.763 45.455 13.94 0.00 0.00 3.41
317 3881 2.908916 TCCGGACCGTAAAAATCATCC 58.091 47.619 13.94 0.00 0.00 3.51
318 3882 5.535333 TCTATCCGGACCGTAAAAATCATC 58.465 41.667 6.12 0.00 0.00 2.92
320 3884 5.163385 ACATCTATCCGGACCGTAAAAATCA 60.163 40.000 6.12 0.00 0.00 2.57
322 3886 5.054477 CACATCTATCCGGACCGTAAAAAT 58.946 41.667 6.12 0.00 0.00 1.82
324 3888 3.181473 CCACATCTATCCGGACCGTAAAA 60.181 47.826 6.12 0.00 0.00 1.52
325 3889 2.363038 CCACATCTATCCGGACCGTAAA 59.637 50.000 6.12 0.00 0.00 2.01
326 3890 1.958579 CCACATCTATCCGGACCGTAA 59.041 52.381 6.12 0.26 0.00 3.18
327 3891 1.612676 CCACATCTATCCGGACCGTA 58.387 55.000 6.12 0.00 0.00 4.02
328 3892 1.113517 CCCACATCTATCCGGACCGT 61.114 60.000 6.12 0.00 0.00 4.83
330 3894 0.393077 CACCCACATCTATCCGGACC 59.607 60.000 6.12 0.00 0.00 4.46
338 3902 0.322098 CGGCAAACCACCCACATCTA 60.322 55.000 0.00 0.00 34.57 1.98
339 3903 1.603455 CGGCAAACCACCCACATCT 60.603 57.895 0.00 0.00 34.57 2.90
344 3908 3.783362 CTGACCGGCAAACCACCCA 62.783 63.158 0.00 0.00 34.57 4.51
348 3912 0.817634 CAAGACTGACCGGCAAACCA 60.818 55.000 0.00 0.00 34.57 3.67
363 3927 2.639347 TGGCCTCACTTCATCTTCAAGA 59.361 45.455 3.32 0.00 0.00 3.02
368 3932 2.842496 TCATCTGGCCTCACTTCATCTT 59.158 45.455 3.32 0.00 0.00 2.40
374 3938 3.726557 TGATTTCATCTGGCCTCACTT 57.273 42.857 3.32 0.00 0.00 3.16
375 3939 3.265221 TCTTGATTTCATCTGGCCTCACT 59.735 43.478 3.32 0.00 0.00 3.41
376 3940 3.614092 TCTTGATTTCATCTGGCCTCAC 58.386 45.455 3.32 0.00 0.00 3.51
378 3942 4.277921 GGAATCTTGATTTCATCTGGCCTC 59.722 45.833 3.32 0.00 0.00 4.70
381 3945 4.213513 AGGGAATCTTGATTTCATCTGGC 58.786 43.478 4.28 0.00 0.00 4.85
382 3946 5.008415 CGAAGGGAATCTTGATTTCATCTGG 59.992 44.000 4.28 0.00 35.50 3.86
510 5512 1.299648 GCTGATGGTGCTGGGTGTA 59.700 57.895 0.00 0.00 0.00 2.90
515 5517 1.162181 CCATACGCTGATGGTGCTGG 61.162 60.000 5.73 0.00 41.42 4.85
522 5524 3.871006 TCTTTGCTAACCATACGCTGATG 59.129 43.478 0.00 0.00 0.00 3.07
523 5525 4.137116 TCTTTGCTAACCATACGCTGAT 57.863 40.909 0.00 0.00 0.00 2.90
524 5526 3.603158 TCTTTGCTAACCATACGCTGA 57.397 42.857 0.00 0.00 0.00 4.26
525 5527 3.871006 TGATCTTTGCTAACCATACGCTG 59.129 43.478 0.00 0.00 0.00 5.18
530 5532 3.199071 ACCCGTGATCTTTGCTAACCATA 59.801 43.478 0.00 0.00 0.00 2.74
552 5554 2.851263 ACGGAGTAGATTGCAACCAA 57.149 45.000 0.00 0.00 41.94 3.67
720 6854 3.799232 GCTCCGAGTGAGTAAACAAGTGT 60.799 47.826 0.00 0.00 43.48 3.55
845 7015 4.463539 TGTGATGATTTTGTGAAGGGGATG 59.536 41.667 0.00 0.00 0.00 3.51
877 7050 1.901085 GTGGGTGTCTAGAGGCAGG 59.099 63.158 0.00 0.00 0.00 4.85
878 7051 1.513158 CGTGGGTGTCTAGAGGCAG 59.487 63.158 0.00 0.00 0.00 4.85
879 7052 2.646175 GCGTGGGTGTCTAGAGGCA 61.646 63.158 0.00 0.00 0.00 4.75
935 7144 7.084486 AGAAATAGAAACTCGGAAAATGTTGC 58.916 34.615 0.00 0.00 0.00 4.17
936 7145 8.289618 TGAGAAATAGAAACTCGGAAAATGTTG 58.710 33.333 0.00 0.00 33.93 3.33
993 7202 1.923356 TCCTCACCTTCATTTTGGGC 58.077 50.000 0.00 0.00 0.00 5.36
995 7204 6.840780 ATAAGTTCCTCACCTTCATTTTGG 57.159 37.500 0.00 0.00 0.00 3.28
1015 7224 5.819991 AGAATGGGAGCAGAAACTGAATAA 58.180 37.500 2.81 0.00 32.44 1.40
1108 7330 5.869753 AGGAGAAAAACAATCGATCAGTG 57.130 39.130 0.00 0.00 0.00 3.66
1116 7338 7.043125 GCAACAAGAAGAAGGAGAAAAACAATC 60.043 37.037 0.00 0.00 0.00 2.67
1119 7341 5.184864 TGCAACAAGAAGAAGGAGAAAAACA 59.815 36.000 0.00 0.00 0.00 2.83
1186 7420 0.107410 TTGTCAGTGCTTTGGACCGT 60.107 50.000 0.00 0.00 0.00 4.83
1601 7884 8.091449 ACAGTATCTCTCGTCTTTTTCATTTCT 58.909 33.333 0.00 0.00 0.00 2.52
1698 9243 0.681733 AAGCGCCTGAGAACTGAGAA 59.318 50.000 2.29 0.00 0.00 2.87
1737 9285 6.676950 TGTCACATGTGGTTTATGAATGAAC 58.323 36.000 25.16 11.55 0.00 3.18
1738 9286 6.890979 TGTCACATGTGGTTTATGAATGAA 57.109 33.333 25.16 0.00 0.00 2.57
1739 9287 6.433716 ACATGTCACATGTGGTTTATGAATGA 59.566 34.615 22.97 0.00 0.00 2.57
1741 9289 6.623486 CACATGTCACATGTGGTTTATGAAT 58.377 36.000 34.63 3.35 44.04 2.57
1742 9290 6.011476 CACATGTCACATGTGGTTTATGAA 57.989 37.500 34.63 0.44 44.04 2.57
1743 9291 5.625921 CACATGTCACATGTGGTTTATGA 57.374 39.130 34.63 1.24 44.04 2.15
1751 9299 2.288334 CCCAAACCACATGTCACATGTG 60.288 50.000 35.07 35.07 46.49 3.21
1752 9300 1.962807 CCCAAACCACATGTCACATGT 59.037 47.619 18.20 18.20 0.00 3.21
1753 9301 1.273048 CCCCAAACCACATGTCACATG 59.727 52.381 16.68 16.68 0.00 3.21
1754 9302 1.631405 CCCCAAACCACATGTCACAT 58.369 50.000 0.00 0.00 0.00 3.21
1755 9303 1.112315 GCCCCAAACCACATGTCACA 61.112 55.000 0.00 0.00 0.00 3.58
1756 9304 0.827507 AGCCCCAAACCACATGTCAC 60.828 55.000 0.00 0.00 0.00 3.67
1757 9305 0.827089 CAGCCCCAAACCACATGTCA 60.827 55.000 0.00 0.00 0.00 3.58
1758 9306 1.535204 CCAGCCCCAAACCACATGTC 61.535 60.000 0.00 0.00 0.00 3.06
1797 9345 1.878656 CTCGTCCTCACCAGTCACCC 61.879 65.000 0.00 0.00 0.00 4.61
1812 9360 1.371558 GTCCTGTTTGGCTCCTCGT 59.628 57.895 0.00 0.00 35.26 4.18
1844 9407 1.679559 GGGACCGCGGTTACCTGTAT 61.680 60.000 33.18 11.80 0.00 2.29
1846 9409 3.698820 GGGACCGCGGTTACCTGT 61.699 66.667 33.18 13.23 0.00 4.00
1847 9410 4.807039 CGGGACCGCGGTTACCTG 62.807 72.222 35.09 30.82 0.00 4.00
1848 9411 3.936772 TACGGGACCGCGGTTACCT 62.937 63.158 35.09 27.19 44.19 3.08
1850 9413 1.805539 GTTACGGGACCGCGGTTAC 60.806 63.158 34.65 27.01 44.19 2.50
1851 9414 2.571231 GTTACGGGACCGCGGTTA 59.429 61.111 34.65 18.32 44.19 2.85
1852 9415 4.377708 GGTTACGGGACCGCGGTT 62.378 66.667 34.65 19.55 44.19 4.44
1867 9430 2.266689 GGTTACATGGACCGCGGT 59.733 61.111 34.89 34.89 0.00 5.68
1872 9435 1.812507 GACCGCGGTTACATGGACC 60.813 63.158 34.65 12.57 0.00 4.46
1873 9436 1.812507 GGACCGCGGTTACATGGAC 60.813 63.158 34.65 16.78 0.00 4.02
1879 9637 0.669012 TTTTACGGGACCGCGGTTAC 60.669 55.000 34.65 27.01 44.19 2.50
1885 9643 1.228533 TTCAGTTTTTACGGGACCGC 58.771 50.000 11.21 0.00 44.19 5.68
1891 9649 6.961554 GTGCAGATCTTATTCAGTTTTTACGG 59.038 38.462 0.00 0.00 0.00 4.02
1892 9650 7.689812 CAGTGCAGATCTTATTCAGTTTTTACG 59.310 37.037 0.00 0.00 0.00 3.18
1894 9652 8.621532 ACAGTGCAGATCTTATTCAGTTTTTA 57.378 30.769 0.00 0.00 0.00 1.52
1895 9653 7.229306 TGACAGTGCAGATCTTATTCAGTTTTT 59.771 33.333 0.00 0.00 0.00 1.94
1897 9655 6.233434 TGACAGTGCAGATCTTATTCAGTTT 58.767 36.000 0.00 0.00 0.00 2.66
1898 9656 5.798132 TGACAGTGCAGATCTTATTCAGTT 58.202 37.500 0.00 0.00 0.00 3.16
1926 10444 2.012673 GCTGCAGACCTGAAACTATGG 58.987 52.381 20.43 0.00 0.00 2.74
1955 10523 7.546250 TGAGTCTCTTTTCCTATGAAACTCT 57.454 36.000 0.65 0.00 40.12 3.24
1956 10524 8.608844 TTTGAGTCTCTTTTCCTATGAAACTC 57.391 34.615 0.65 0.00 40.12 3.01
1957 10525 8.980481 TTTTGAGTCTCTTTTCCTATGAAACT 57.020 30.769 0.65 0.00 40.12 2.66
1960 10528 9.799106 AGAATTTTGAGTCTCTTTTCCTATGAA 57.201 29.630 0.65 0.00 0.00 2.57
1990 10577 0.994995 CTCGACTGCTGTGAAATCGG 59.005 55.000 0.00 0.00 33.66 4.18
2019 10614 6.263168 CACTGTAAGAACATTGAAAGGAAGGT 59.737 38.462 0.00 0.00 38.26 3.50
2063 10710 1.660333 GCAGCAAGACGAAGAAAACCG 60.660 52.381 0.00 0.00 0.00 4.44
2102 10749 4.180946 CTCTCGTCGCTGACCCGG 62.181 72.222 0.00 0.00 0.00 5.73
2103 10750 2.037913 CTACTCTCGTCGCTGACCCG 62.038 65.000 3.65 0.00 0.00 5.28
2104 10751 0.743701 TCTACTCTCGTCGCTGACCC 60.744 60.000 3.65 0.00 0.00 4.46
2105 10752 0.653636 CTCTACTCTCGTCGCTGACC 59.346 60.000 3.65 0.00 0.00 4.02
2107 10754 2.928757 GTTACTCTACTCTCGTCGCTGA 59.071 50.000 0.00 0.00 0.00 4.26
2108 10755 2.030701 GGTTACTCTACTCTCGTCGCTG 59.969 54.545 0.00 0.00 0.00 5.18
2109 10756 2.278854 GGTTACTCTACTCTCGTCGCT 58.721 52.381 0.00 0.00 0.00 4.93
2110 10757 2.005451 TGGTTACTCTACTCTCGTCGC 58.995 52.381 0.00 0.00 0.00 5.19
2111 10758 4.675190 TTTGGTTACTCTACTCTCGTCG 57.325 45.455 0.00 0.00 0.00 5.12
2133 10780 1.684450 TCACGAGCTTGTGGTCAGTAA 59.316 47.619 29.69 9.49 40.44 2.24
2135 10782 0.249489 GTCACGAGCTTGTGGTCAGT 60.249 55.000 29.69 0.00 40.44 3.41
2143 10790 1.493772 TTGTTACCGTCACGAGCTTG 58.506 50.000 0.00 0.00 0.00 4.01
2147 10794 4.043750 TGTACTTTTGTTACCGTCACGAG 58.956 43.478 0.00 0.00 0.00 4.18
2149 10796 4.503734 TCTTGTACTTTTGTTACCGTCACG 59.496 41.667 0.00 0.00 0.00 4.35
2155 10802 6.492254 CCAACAGTCTTGTACTTTTGTTACC 58.508 40.000 0.00 0.00 42.09 2.85
2156 10803 5.969435 GCCAACAGTCTTGTACTTTTGTTAC 59.031 40.000 0.00 0.00 42.09 2.50
2305 11008 6.680874 TTAGGAGCTCGAAGTTTACTCTAG 57.319 41.667 7.83 0.00 0.00 2.43
2358 11061 4.789012 ATTGGTTGCTCTGGTTGTATTG 57.211 40.909 0.00 0.00 0.00 1.90
2389 11092 4.282703 GTCATTTCCGGGCTCCTATAGTTA 59.717 45.833 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.