Multiple sequence alignment - TraesCS2A01G387000

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 TraesCS2A01G387000 chr2A 100.000 6464 0 0 1 6464 632630722 632624259 0.000000e+00 11937.0
1 TraesCS2A01G387000 chr2A 100.000 30 0 0 2059 2088 668457141 668457170 1.000000e-03 56.5
2 TraesCS2A01G387000 chr2B 93.424 4425 205 37 2108 6464 572592339 572587933 0.000000e+00 6481.0
3 TraesCS2A01G387000 chr2B 95.029 684 21 7 728 1408 572593702 572593029 0.000000e+00 1062.0
4 TraesCS2A01G387000 chr2B 92.017 714 35 8 1424 2134 572593046 572592352 0.000000e+00 983.0
5 TraesCS2A01G387000 chr2B 97.917 48 0 1 2059 2106 764537613 764537659 1.490000e-11 82.4
6 TraesCS2A01G387000 chr2B 97.727 44 0 1 2061 2104 539370780 539370738 2.500000e-09 75.0
7 TraesCS2A01G387000 chr2D 98.163 2014 31 3 2108 4117 488235738 488233727 0.000000e+00 3509.0
8 TraesCS2A01G387000 chr2D 97.120 1840 35 8 4115 5942 488233634 488231801 0.000000e+00 3088.0
9 TraesCS2A01G387000 chr2D 89.917 1200 52 23 585 1729 488237371 488236186 0.000000e+00 1482.0
10 TraesCS2A01G387000 chr2D 95.035 423 20 1 1712 2134 488236172 488235751 0.000000e+00 664.0
11 TraesCS2A01G387000 chr2D 86.125 591 78 4 1 589 488239506 488238918 9.140000e-178 634.0
12 TraesCS2A01G387000 chr2D 92.453 159 11 1 5951 6109 488231760 488231603 6.520000e-55 226.0
13 TraesCS2A01G387000 chr2D 91.391 151 10 2 6154 6302 488231525 488231376 3.060000e-48 204.0
14 TraesCS2A01G387000 chr2D 83.983 231 9 4 6262 6464 488231378 488231148 5.110000e-46 196.0
15 TraesCS2A01G387000 chr3B 89.820 167 17 0 1725 1891 254193047 254192881 1.410000e-51 215.0
16 TraesCS2A01G387000 chr3B 89.820 167 17 0 1725 1891 755478623 755478789 1.410000e-51 215.0
17 TraesCS2A01G387000 chr3B 89.583 48 4 1 2059 2106 45514862 45514816 7.000000e-05 60.2
18 TraesCS2A01G387000 chr7D 89.222 167 18 0 1725 1891 555059373 555059207 6.570000e-50 209.0
19 TraesCS2A01G387000 chr6B 88.757 169 19 0 1725 1893 9429417 9429249 2.360000e-49 207.0
20 TraesCS2A01G387000 chr6B 87.719 171 21 0 1725 1895 628238785 628238615 3.950000e-47 200.0
21 TraesCS2A01G387000 chr3D 88.757 169 18 1 1725 1892 475549789 475549957 8.500000e-49 206.0
22 TraesCS2A01G387000 chr4A 88.623 167 19 0 1725 1891 541367086 541366920 3.060000e-48 204.0
23 TraesCS2A01G387000 chr1A 97.368 38 0 1 2055 2092 531017464 531017428 5.410000e-06 63.9
24 TraesCS2A01G387000 chr1D 100.000 30 0 0 2063 2092 432401946 432401917 1.000000e-03 56.5


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 TraesCS2A01G387000 chr2A 632624259 632630722 6463 True 11937.000 11937 100.000000 1 6464 1 chr2A.!!$R1 6463
1 TraesCS2A01G387000 chr2B 572587933 572593702 5769 True 2842.000 6481 93.490000 728 6464 3 chr2B.!!$R2 5736
2 TraesCS2A01G387000 chr2D 488231148 488239506 8358 True 1250.375 3509 91.773375 1 6464 8 chr2D.!!$R1 6463

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
371 373 0.036306 CCACCACCTCAACTACCCAC 59.964 60.000 0.00 0.0 0.00 4.61 F
633 2186 0.108804 ACCCGTAGTCATCAGTTGCG 60.109 55.000 0.00 0.0 0.00 4.85 F
666 2219 0.108804 CAGGACCGCTTCGTGTATGT 60.109 55.000 0.00 0.0 35.69 2.29 F
2464 4149 0.107945 CTCCTAGCCTCTGCACCAAC 60.108 60.000 0.00 0.0 41.13 3.77 F
2557 4244 1.002430 CACTTGCTTGCTAGTCCCTCA 59.998 52.381 6.73 0.0 0.00 3.86 F
2853 4540 1.071471 AACTGCCGTCTGGGACAAG 59.929 57.895 0.00 0.0 38.70 3.16 F
3348 5035 1.078426 AAAGGAACCGGATGAGGCG 60.078 57.895 9.46 0.0 33.69 5.52 F
4727 6522 0.607489 GAGCAGTGCTGGTTGATGGT 60.607 55.000 25.35 0.0 39.88 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 3943 0.313987 GGCCCGTCAAAAGAGTTTGG 59.686 55.000 0.0 0.0 43.70 3.28 R
2449 4134 0.037326 CTTCGTTGGTGCAGAGGCTA 60.037 55.000 0.0 0.0 41.91 3.93 R
2548 4235 1.082194 AGGGGAAATGGTGAGGGACTA 59.918 52.381 0.0 0.0 41.55 2.59 R
3339 5026 0.532573 TCTTCACAGTCGCCTCATCC 59.467 55.000 0.0 0.0 0.00 3.51 R
3543 5230 6.276832 CCAGAAAATGGTTCATCATCACTT 57.723 37.500 0.0 0.0 44.91 3.16 R
4727 6522 4.545208 TGAATCAACATCGTGGTAGGAA 57.455 40.909 0.0 0.0 0.00 3.36 R
5263 7071 3.985925 CAGCAAAGCAAGTTCAATTCTCC 59.014 43.478 0.0 0.0 0.00 3.71 R
6357 8315 1.068541 GGACAACGGATGCAAAGGAAC 60.069 52.381 0.0 0.0 0.00 3.62 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
21 22 0.460284 CTTGTCATAACGAGCCGGCT 60.460 55.000 33.48 33.48 30.15 5.52
39 40 1.586154 CTGCAACAACCACCGGATCC 61.586 60.000 9.46 0.00 0.00 3.36
71 72 0.835941 ATCCTCCCACTCACATGCTC 59.164 55.000 0.00 0.00 0.00 4.26
80 81 3.129502 CACATGCTCCAGCCACCG 61.130 66.667 0.00 0.00 41.18 4.94
98 99 2.282816 CAACCATTGCCACCGGGA 60.283 61.111 6.32 0.00 35.59 5.14
99 100 1.905843 CAACCATTGCCACCGGGAA 60.906 57.895 6.32 0.00 37.45 3.97
111 112 3.361977 CGGGAAAACCACCGCTGG 61.362 66.667 0.00 0.00 43.96 4.85
112 113 3.680786 GGGAAAACCACCGCTGGC 61.681 66.667 0.00 0.00 42.08 4.85
136 137 2.053638 CATCATCGAAGCGCGCAC 60.054 61.111 35.10 24.51 40.61 5.34
144 145 1.425031 GAAGCGCGCACATCATTGA 59.575 52.632 35.10 0.00 0.00 2.57
154 155 4.731961 GCGCACATCATTGATTACAGAAAG 59.268 41.667 0.30 0.00 0.00 2.62
165 166 4.701171 TGATTACAGAAAGCATGCACATCA 59.299 37.500 21.98 11.35 0.00 3.07
179 180 2.089201 CACATCAGCCATGTCACACAT 58.911 47.619 0.00 0.00 44.60 3.21
230 231 2.482142 GCCAGATCAAGAGGTAGAACGG 60.482 54.545 0.00 0.00 0.00 4.44
258 259 0.956633 TAGAGTTGGTTGAGTCGCGT 59.043 50.000 5.77 0.00 0.00 6.01
261 262 2.355363 TTGGTTGAGTCGCGTCCG 60.355 61.111 5.77 0.00 0.00 4.79
275 276 2.106131 TCCGCCATCGATGAACGG 59.894 61.111 35.08 35.08 43.83 4.44
280 281 2.180204 CCATCGATGAACGGCCACC 61.180 63.158 26.86 0.00 42.82 4.61
333 335 1.298859 GCCACACCGAGGACAATGAC 61.299 60.000 0.00 0.00 0.00 3.06
339 341 2.668632 GAGGACAATGACGCCCCA 59.331 61.111 0.00 0.00 0.00 4.96
355 357 3.434319 CACGCTGGCATCACCCAC 61.434 66.667 0.00 0.00 37.83 4.61
357 359 4.720902 CGCTGGCATCACCCACCA 62.721 66.667 0.00 0.00 37.83 4.17
365 367 0.401738 CATCACCCACCACCTCAACT 59.598 55.000 0.00 0.00 0.00 3.16
370 372 1.131303 CCCACCACCTCAACTACCCA 61.131 60.000 0.00 0.00 0.00 4.51
371 373 0.036306 CCACCACCTCAACTACCCAC 59.964 60.000 0.00 0.00 0.00 4.61
372 374 0.036306 CACCACCTCAACTACCCACC 59.964 60.000 0.00 0.00 0.00 4.61
378 380 2.162338 CTCAACTACCCACCGCCGAA 62.162 60.000 0.00 0.00 0.00 4.30
398 400 0.684535 TCTCACGGATCTTTGTGCCA 59.315 50.000 7.97 0.00 36.06 4.92
407 409 3.456280 GATCTTTGTGCCAAGCAACAAA 58.544 40.909 13.02 13.02 41.47 2.83
412 414 0.594796 GTGCCAAGCAACAAAGTCGG 60.595 55.000 0.00 0.00 41.47 4.79
419 421 0.663153 GCAACAAAGTCGGCTCACTT 59.337 50.000 0.00 0.00 38.30 3.16
432 434 2.359478 CACTTACGCACCACCCCC 60.359 66.667 0.00 0.00 0.00 5.40
434 436 2.046314 CTTACGCACCACCCCCAG 60.046 66.667 0.00 0.00 0.00 4.45
454 456 3.050275 GCCACCACAGCCGTTCTC 61.050 66.667 0.00 0.00 0.00 2.87
455 457 2.743718 CCACCACAGCCGTTCTCT 59.256 61.111 0.00 0.00 0.00 3.10
456 458 1.374758 CCACCACAGCCGTTCTCTC 60.375 63.158 0.00 0.00 0.00 3.20
499 501 2.014093 GAAGAGCAACGCGTCATCCG 62.014 60.000 14.44 0.00 40.40 4.18
510 512 2.084610 CGTCATCCGCCATCATACAT 57.915 50.000 0.00 0.00 0.00 2.29
512 514 2.771089 GTCATCCGCCATCATACATGT 58.229 47.619 2.69 2.69 0.00 3.21
560 562 2.110627 GCCGCTGCCATGAGATCT 59.889 61.111 0.00 0.00 0.00 2.75
562 564 1.145598 CCGCTGCCATGAGATCTGT 59.854 57.895 0.00 0.00 0.00 3.41
568 570 1.069668 TGCCATGAGATCTGTCATCCG 59.930 52.381 0.00 0.00 34.81 4.18
569 571 1.607509 GCCATGAGATCTGTCATCCGG 60.608 57.143 0.00 0.00 34.81 5.14
570 572 1.690893 CCATGAGATCTGTCATCCGGT 59.309 52.381 0.00 0.00 34.81 5.28
572 574 3.305676 CCATGAGATCTGTCATCCGGTAC 60.306 52.174 0.00 0.00 34.81 3.34
574 576 3.747708 ATGAGATCTGTCATCCGGTACGA 60.748 47.826 0.00 1.91 44.51 3.43
633 2186 0.108804 ACCCGTAGTCATCAGTTGCG 60.109 55.000 0.00 0.00 0.00 4.85
661 2214 2.432628 GGTCAGGACCGCTTCGTG 60.433 66.667 2.15 0.00 42.29 4.35
662 2215 2.338984 GTCAGGACCGCTTCGTGT 59.661 61.111 5.20 0.00 40.43 4.49
663 2216 1.582968 GTCAGGACCGCTTCGTGTA 59.417 57.895 5.20 0.00 40.43 2.90
664 2217 0.172803 GTCAGGACCGCTTCGTGTAT 59.827 55.000 5.20 0.00 40.43 2.29
665 2218 0.172578 TCAGGACCGCTTCGTGTATG 59.827 55.000 5.20 0.00 40.43 2.39
666 2219 0.108804 CAGGACCGCTTCGTGTATGT 60.109 55.000 0.00 0.00 35.69 2.29
667 2220 0.172803 AGGACCGCTTCGTGTATGTC 59.827 55.000 0.00 0.00 0.00 3.06
670 2223 2.334838 GACCGCTTCGTGTATGTCTTT 58.665 47.619 0.00 0.00 0.00 2.52
672 2225 2.735134 ACCGCTTCGTGTATGTCTTTTC 59.265 45.455 0.00 0.00 0.00 2.29
676 2230 3.751698 GCTTCGTGTATGTCTTTTCCCTT 59.248 43.478 0.00 0.00 0.00 3.95
706 2260 7.044052 GCACGACCTAAATGAAATTGCTAATTC 60.044 37.037 0.00 0.00 36.10 2.17
721 2275 9.472361 AATTGCTAATTCTGATCATGTTAATGC 57.528 29.630 0.00 0.00 33.47 3.56
722 2276 7.812690 TGCTAATTCTGATCATGTTAATGCT 57.187 32.000 0.00 0.00 33.47 3.79
723 2277 8.229253 TGCTAATTCTGATCATGTTAATGCTT 57.771 30.769 0.00 0.00 33.47 3.91
793 2375 6.882656 AGAAATCTCATAAGCAAGTAGAGCA 58.117 36.000 0.00 0.00 0.00 4.26
802 2384 9.448438 TCATAAGCAAGTAGAGCAGAAATAAAA 57.552 29.630 0.00 0.00 0.00 1.52
899 2482 2.588314 CAGCATCAGAGCGGCTCC 60.588 66.667 25.49 10.48 40.15 4.70
1264 2849 1.079127 CATTCCTGCCGAGTCCGTT 60.079 57.895 0.00 0.00 0.00 4.44
1310 2895 3.958748 GCTATTGCGCTAGGGAGC 58.041 61.111 11.61 8.18 46.00 4.70
1336 2921 2.125512 CTAGGCGTGGGTGCAGAC 60.126 66.667 0.00 0.00 36.28 3.51
1413 2998 4.974368 AATGACCAAGAGAGTAGAGACG 57.026 45.455 0.00 0.00 0.00 4.18
1414 2999 2.712709 TGACCAAGAGAGTAGAGACGG 58.287 52.381 0.00 0.00 0.00 4.79
1472 3079 3.054875 TCCATGAGAGTTGGAGTGGATTG 60.055 47.826 0.00 0.00 38.35 2.67
1481 3088 1.509923 GAGTGGATTGCAAGCCAGC 59.490 57.895 35.50 27.18 46.55 4.85
1482 3089 1.228644 AGTGGATTGCAAGCCAGCA 60.229 52.632 35.50 12.72 46.55 4.41
1597 3207 0.244450 TACGGTTGTTAGTGGGCTCG 59.756 55.000 0.00 0.00 0.00 5.03
1668 3278 6.308766 GCTCAATACTTGGTGTAAAAGCAATG 59.691 38.462 0.00 0.00 44.90 2.82
1729 3370 6.634035 GGTCTGTAAAATGTAACGTTGGTTTC 59.366 38.462 11.99 0.00 37.58 2.78
1756 3397 5.221925 TGGATGCTAGAAATCCTATGGGAAC 60.222 44.000 19.93 0.00 45.78 3.62
1823 3464 5.125900 TCCTATGAATCAAACAGCCAACATG 59.874 40.000 0.00 0.00 0.00 3.21
1870 3511 8.670521 AATCCTCCAAATTTCCTATGAAAACT 57.329 30.769 0.00 0.00 43.37 2.66
1872 3513 6.374333 TCCTCCAAATTTCCTATGAAAACTCG 59.626 38.462 0.00 0.00 43.37 4.18
1886 3527 6.443934 TGAAAACTCGTTGAATCAAAGGAA 57.556 33.333 8.90 0.00 0.00 3.36
1939 3580 4.518970 CCAAAGTACTTGCAGCTCCTTTAA 59.481 41.667 9.34 0.00 33.27 1.52
2066 3707 9.838339 CATGTATTAAAGTTTATCACTCCCTCT 57.162 33.333 0.00 0.00 32.94 3.69
2088 3729 5.362717 TCTGATCCATAATAAGTGTCGTGGT 59.637 40.000 0.00 0.00 0.00 4.16
2200 3880 0.676782 ACGAAGGAAAATGGAGCCCG 60.677 55.000 0.00 0.00 0.00 6.13
2245 3925 1.715519 GCATGCTTTTACTGTGCAACG 59.284 47.619 11.37 0.00 42.39 4.10
2260 3943 6.036517 ACTGTGCAACGAAATCATAGATTCTC 59.963 38.462 0.00 0.00 42.39 2.87
2449 4134 9.533831 TTTTAAGATTATGGAAGCTTTTCTCCT 57.466 29.630 0.00 0.00 38.09 3.69
2464 4149 0.107945 CTCCTAGCCTCTGCACCAAC 60.108 60.000 0.00 0.00 41.13 3.77
2557 4244 1.002430 CACTTGCTTGCTAGTCCCTCA 59.998 52.381 6.73 0.00 0.00 3.86
2575 4262 3.006859 CCTCACCATTTCCCCTTGAAAAC 59.993 47.826 0.00 0.00 45.67 2.43
2596 4283 6.594788 AACCAATCATTGTGTTCAGCTTAT 57.405 33.333 0.00 0.00 0.00 1.73
2597 4284 7.701539 AACCAATCATTGTGTTCAGCTTATA 57.298 32.000 0.00 0.00 0.00 0.98
2853 4540 1.071471 AACTGCCGTCTGGGACAAG 59.929 57.895 0.00 0.00 38.70 3.16
2937 4624 1.978617 CAGGGTGTTGGATGGTGCC 60.979 63.158 0.00 0.00 0.00 5.01
3339 5026 4.501743 GGCTATCTAGAAGGAAAGGAACCG 60.502 50.000 0.00 0.00 0.00 4.44
3348 5035 1.078426 AAAGGAACCGGATGAGGCG 60.078 57.895 9.46 0.00 33.69 5.52
3543 5230 5.181245 GGAATTGATTCTTGAAAGACGTCCA 59.819 40.000 13.01 0.00 37.00 4.02
4201 5984 4.323485 CCTTTCTATGCTTACACTGTCCCA 60.323 45.833 0.00 0.00 0.00 4.37
4382 6177 3.550030 CCGCCTTAACCTGAAAACAGTTG 60.550 47.826 0.00 0.00 0.00 3.16
4383 6178 3.066203 CGCCTTAACCTGAAAACAGTTGT 59.934 43.478 0.00 0.00 0.00 3.32
4727 6522 0.607489 GAGCAGTGCTGGTTGATGGT 60.607 55.000 25.35 0.00 39.88 3.55
4781 6576 1.914764 CCAAATTGCAGCCAGGGGT 60.915 57.895 0.00 0.00 0.00 4.95
5145 6952 3.191581 GTCAGCTATAGCCGAGCATCTAA 59.808 47.826 21.17 0.00 42.69 2.10
5146 6953 3.191581 TCAGCTATAGCCGAGCATCTAAC 59.808 47.826 21.17 0.00 42.69 2.34
5152 6959 3.266510 AGCCGAGCATCTAACATTCAA 57.733 42.857 0.00 0.00 0.00 2.69
5154 6961 4.960938 AGCCGAGCATCTAACATTCAATA 58.039 39.130 0.00 0.00 0.00 1.90
5158 6966 5.049405 CCGAGCATCTAACATTCAATAACCC 60.049 44.000 0.00 0.00 0.00 4.11
5263 7071 6.766944 AGGATCTGCTGTCTGAAATATTTCTG 59.233 38.462 24.77 23.56 38.02 3.02
5557 7365 1.798813 CTTTGTAGTGTCGAACCCAGC 59.201 52.381 0.00 0.00 0.00 4.85
5655 7463 3.242739 CCTTGTCAAGTTCTCACAAACGG 60.243 47.826 11.61 0.00 34.27 4.44
5986 7826 4.497473 TTTGGTGTAGCTGTTATTGCAC 57.503 40.909 0.00 0.00 0.00 4.57
5988 7828 2.811431 TGGTGTAGCTGTTATTGCACAC 59.189 45.455 0.00 0.00 39.40 3.82
5989 7829 2.161609 GGTGTAGCTGTTATTGCACACC 59.838 50.000 13.79 13.79 45.36 4.16
6075 7923 2.435805 CTGTATCTTGCCAGGCCTCTAA 59.564 50.000 9.64 0.00 0.00 2.10
6098 7946 4.405358 ACTTCATCCCTTTGTGCTTTTTGA 59.595 37.500 0.00 0.00 0.00 2.69
6108 7956 7.333174 CCCTTTGTGCTTTTTGACTTCTTTTTA 59.667 33.333 0.00 0.00 0.00 1.52
6119 7967 3.497332 ACTTCTTTTTAGGCCCTGAACC 58.503 45.455 0.00 0.00 0.00 3.62
6120 7968 3.117284 ACTTCTTTTTAGGCCCTGAACCA 60.117 43.478 0.00 0.00 0.00 3.67
6126 7974 3.926058 TTAGGCCCTGAACCATAGAAC 57.074 47.619 0.00 0.00 0.00 3.01
6128 7976 1.992557 AGGCCCTGAACCATAGAACAA 59.007 47.619 0.00 0.00 0.00 2.83
6129 7977 2.582636 AGGCCCTGAACCATAGAACAAT 59.417 45.455 0.00 0.00 0.00 2.71
6130 7978 3.785887 AGGCCCTGAACCATAGAACAATA 59.214 43.478 0.00 0.00 0.00 1.90
6131 7979 4.137543 GGCCCTGAACCATAGAACAATAG 58.862 47.826 0.00 0.00 0.00 1.73
6132 7980 4.385310 GGCCCTGAACCATAGAACAATAGT 60.385 45.833 0.00 0.00 0.00 2.12
6133 7981 5.193679 GCCCTGAACCATAGAACAATAGTT 58.806 41.667 0.00 0.00 41.64 2.24
6134 7982 5.652452 GCCCTGAACCATAGAACAATAGTTT 59.348 40.000 0.00 0.00 38.30 2.66
6203 8120 5.127194 GTGGAGGAACAAAAGGAAGAAAACT 59.873 40.000 0.00 0.00 0.00 2.66
6357 8315 3.187227 CGGCATTTCTGAATATCCTTCCG 59.813 47.826 0.00 0.00 0.00 4.30
6371 8329 0.447801 CTTCCGTTCCTTTGCATCCG 59.552 55.000 0.00 0.00 0.00 4.18
6372 8330 0.250553 TTCCGTTCCTTTGCATCCGT 60.251 50.000 0.00 0.00 0.00 4.69
6398 8381 3.181434 CCATTGCTATAGGGGCTGGTAAA 60.181 47.826 1.04 0.00 0.00 2.01
6412 8395 3.183574 GCTGGTAAATTTTCCAACGCAAC 59.816 43.478 16.28 0.00 33.06 4.17
6415 8398 5.175859 TGGTAAATTTTCCAACGCAACAAA 58.824 33.333 13.60 0.00 0.00 2.83
6435 8421 8.971321 CAACAAAGTCCTCATAAAAAGACATTG 58.029 33.333 5.67 5.67 41.35 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.153647 CAGCCGGCTCGTTATGACA 60.154 57.895 30.29 0.00 0.00 3.58
21 22 1.602323 GGATCCGGTGGTTGTTGCA 60.602 57.895 0.00 0.00 0.00 4.08
39 40 4.924187 AGGATCCTCCGCCTCCCG 62.924 72.222 9.02 0.00 42.75 5.14
71 72 2.990967 AATGGTTGCGGTGGCTGG 60.991 61.111 0.00 0.00 40.82 4.85
95 96 3.680786 GCCAGCGGTGGTTTTCCC 61.681 66.667 32.48 12.89 46.96 3.97
96 97 2.597510 AGCCAGCGGTGGTTTTCC 60.598 61.111 32.48 16.85 46.96 3.13
98 99 3.605664 GCAGCCAGCGGTGGTTTT 61.606 61.111 32.48 17.11 46.96 2.43
109 110 2.515290 CGATGATGCTGGCAGCCA 60.515 61.111 34.58 26.18 41.51 4.75
111 112 1.647629 CTTCGATGATGCTGGCAGC 59.352 57.895 31.91 31.91 42.82 5.25
112 113 1.647629 GCTTCGATGATGCTGGCAG 59.352 57.895 10.94 10.94 31.35 4.85
118 119 3.928769 TGCGCGCTTCGATGATGC 61.929 61.111 33.29 4.39 41.67 3.91
121 122 2.509111 ATGTGCGCGCTTCGATGA 60.509 55.556 33.29 6.82 41.67 2.92
123 124 1.431488 AATGATGTGCGCGCTTCGAT 61.431 50.000 33.29 17.70 41.67 3.59
124 125 2.100031 AATGATGTGCGCGCTTCGA 61.100 52.632 33.29 9.09 41.67 3.71
136 137 6.198403 GTGCATGCTTTCTGTAATCAATGATG 59.802 38.462 20.33 0.00 0.00 3.07
144 145 4.439700 GCTGATGTGCATGCTTTCTGTAAT 60.440 41.667 20.33 0.80 0.00 1.89
154 155 0.248907 GACATGGCTGATGTGCATGC 60.249 55.000 11.82 11.82 45.90 4.06
165 166 1.746615 GCGGATGTGTGACATGGCT 60.747 57.895 0.00 0.00 39.27 4.75
218 219 2.177734 GGGAACTTCCGTTCTACCTCT 58.822 52.381 1.53 0.00 46.84 3.69
230 231 4.040584 ACTCAACCAACTCTAGGGAACTTC 59.959 45.833 0.00 0.00 43.67 3.01
234 235 2.561419 CGACTCAACCAACTCTAGGGAA 59.439 50.000 0.00 0.00 0.00 3.97
237 238 1.732732 CGCGACTCAACCAACTCTAGG 60.733 57.143 0.00 0.00 0.00 3.02
258 259 2.106131 CCGTTCATCGATGGCGGA 59.894 61.111 36.27 16.00 43.76 5.54
261 262 2.513666 TGGCCGTTCATCGATGGC 60.514 61.111 24.61 19.27 46.82 4.40
339 341 4.722700 GGTGGGTGATGCCAGCGT 62.723 66.667 0.00 0.00 41.47 5.07
341 343 3.064324 GTGGTGGGTGATGCCAGC 61.064 66.667 0.00 0.00 39.65 4.85
355 357 1.295423 CGGTGGGTAGTTGAGGTGG 59.705 63.158 0.00 0.00 0.00 4.61
357 359 2.590114 GGCGGTGGGTAGTTGAGGT 61.590 63.158 0.00 0.00 0.00 3.85
365 367 1.683025 TGAGATTCGGCGGTGGGTA 60.683 57.895 7.21 0.00 0.00 3.69
370 372 2.351336 GATCCGTGAGATTCGGCGGT 62.351 60.000 7.21 0.00 46.49 5.68
371 373 1.661821 GATCCGTGAGATTCGGCGG 60.662 63.158 7.21 9.30 46.49 6.13
372 374 0.249073 AAGATCCGTGAGATTCGGCG 60.249 55.000 0.00 0.00 46.49 6.46
378 380 1.278985 TGGCACAAAGATCCGTGAGAT 59.721 47.619 10.77 0.00 33.57 2.75
392 394 0.100325 CGACTTTGTTGCTTGGCACA 59.900 50.000 0.00 0.00 38.71 4.57
398 400 0.663153 GTGAGCCGACTTTGTTGCTT 59.337 50.000 0.00 0.00 33.41 3.91
407 409 1.080705 GTGCGTAAGTGAGCCGACT 60.081 57.895 0.00 0.00 41.68 4.18
412 414 2.033194 GGGTGGTGCGTAAGTGAGC 61.033 63.158 0.00 0.00 41.68 4.26
445 447 1.513158 CGATGGTGAGAGAACGGCT 59.487 57.895 0.00 0.00 0.00 5.52
446 448 1.519455 CCGATGGTGAGAGAACGGC 60.519 63.158 0.00 0.00 34.36 5.68
451 453 2.359169 GGTGCCCGATGGTGAGAGA 61.359 63.158 0.00 0.00 0.00 3.10
454 456 1.077501 ATTGGTGCCCGATGGTGAG 60.078 57.895 0.00 0.00 0.00 3.51
455 457 1.378382 CATTGGTGCCCGATGGTGA 60.378 57.895 11.71 0.00 40.71 4.02
456 458 0.752743 ATCATTGGTGCCCGATGGTG 60.753 55.000 16.92 0.00 43.67 4.17
481 483 2.094659 CGGATGACGCGTTGCTCTT 61.095 57.895 15.53 0.00 34.82 2.85
495 497 2.084610 CGACATGTATGATGGCGGAT 57.915 50.000 0.00 0.00 46.03 4.18
499 501 0.233074 CGCACGACATGTATGATGGC 59.767 55.000 12.66 8.09 0.00 4.40
503 505 1.469079 CCTCACGCACGACATGTATGA 60.469 52.381 12.66 3.75 0.00 2.15
505 507 0.815095 TCCTCACGCACGACATGTAT 59.185 50.000 0.00 0.00 0.00 2.29
510 512 1.299850 CTTGTCCTCACGCACGACA 60.300 57.895 0.00 0.00 34.80 4.35
512 514 1.007734 GACTTGTCCTCACGCACGA 60.008 57.895 0.00 0.00 0.00 4.35
546 548 2.144730 GATGACAGATCTCATGGCAGC 58.855 52.381 2.37 0.00 39.56 5.25
553 555 1.947456 CGTACCGGATGACAGATCTCA 59.053 52.381 9.46 0.00 0.00 3.27
560 562 0.533491 CCCTTTCGTACCGGATGACA 59.467 55.000 9.46 0.00 0.00 3.58
562 564 1.332144 CCCCCTTTCGTACCGGATGA 61.332 60.000 9.46 0.00 0.00 2.92
568 570 3.381333 CTCGGCCCCCTTTCGTACC 62.381 68.421 0.00 0.00 0.00 3.34
569 571 2.186125 CTCGGCCCCCTTTCGTAC 59.814 66.667 0.00 0.00 0.00 3.67
570 572 3.777910 GCTCGGCCCCCTTTCGTA 61.778 66.667 0.00 0.00 0.00 3.43
614 2167 0.108804 CGCAACTGATGACTACGGGT 60.109 55.000 0.00 0.00 0.00 5.28
618 2171 1.135489 TCGACCGCAACTGATGACTAC 60.135 52.381 0.00 0.00 0.00 2.73
647 2200 0.108804 ACATACACGAAGCGGTCCTG 60.109 55.000 0.00 0.00 0.00 3.86
654 2207 3.335579 AGGGAAAAGACATACACGAAGC 58.664 45.455 0.00 0.00 0.00 3.86
655 2208 4.091509 CGAAGGGAAAAGACATACACGAAG 59.908 45.833 0.00 0.00 0.00 3.79
656 2209 3.991773 CGAAGGGAAAAGACATACACGAA 59.008 43.478 0.00 0.00 0.00 3.85
658 2211 3.122948 CACGAAGGGAAAAGACATACACG 59.877 47.826 0.00 0.00 0.00 4.49
659 2212 3.120304 GCACGAAGGGAAAAGACATACAC 60.120 47.826 0.00 0.00 0.00 2.90
660 2213 3.071479 GCACGAAGGGAAAAGACATACA 58.929 45.455 0.00 0.00 0.00 2.29
661 2214 3.071479 TGCACGAAGGGAAAAGACATAC 58.929 45.455 0.00 0.00 0.00 2.39
662 2215 3.071479 GTGCACGAAGGGAAAAGACATA 58.929 45.455 0.00 0.00 0.00 2.29
663 2216 1.880027 GTGCACGAAGGGAAAAGACAT 59.120 47.619 0.00 0.00 0.00 3.06
664 2217 1.305201 GTGCACGAAGGGAAAAGACA 58.695 50.000 0.00 0.00 0.00 3.41
665 2218 0.234884 CGTGCACGAAGGGAAAAGAC 59.765 55.000 34.93 0.00 43.02 3.01
666 2219 0.105224 TCGTGCACGAAGGGAAAAGA 59.895 50.000 37.68 12.73 46.30 2.52
667 2220 2.612200 TCGTGCACGAAGGGAAAAG 58.388 52.632 37.68 7.11 46.30 2.27
719 2273 7.229707 TGAAGCCTTGTGTACTTTATTTAAGCA 59.770 33.333 0.00 0.00 37.37 3.91
720 2274 7.590279 TGAAGCCTTGTGTACTTTATTTAAGC 58.410 34.615 0.00 0.00 37.37 3.09
773 2355 6.477053 TTCTGCTCTACTTGCTTATGAGAT 57.523 37.500 0.00 0.00 0.00 2.75
781 2363 5.163814 CGCTTTTATTTCTGCTCTACTTGCT 60.164 40.000 0.00 0.00 0.00 3.91
786 2368 3.374058 TGCCGCTTTTATTTCTGCTCTAC 59.626 43.478 0.00 0.00 0.00 2.59
793 2375 4.799564 TTGGATTGCCGCTTTTATTTCT 57.200 36.364 0.00 0.00 36.79 2.52
802 2384 1.169661 TCACGTTTTGGATTGCCGCT 61.170 50.000 0.00 0.00 36.79 5.52
899 2482 1.226101 CCGCGCTTATGTGTGCTTG 60.226 57.895 5.56 0.00 40.87 4.01
1254 2839 2.490903 TCTAAAGAAGGAACGGACTCGG 59.509 50.000 0.00 0.00 41.39 4.63
1306 2891 2.117779 GCCTAGGCTTGCTTGCTCC 61.118 63.158 27.17 0.00 38.26 4.70
1308 2893 2.437359 CGCCTAGGCTTGCTTGCT 60.437 61.111 30.55 0.00 39.32 3.91
1309 2894 2.747855 ACGCCTAGGCTTGCTTGC 60.748 61.111 30.55 2.63 39.32 4.01
1310 2895 2.401766 CCACGCCTAGGCTTGCTTG 61.402 63.158 30.00 17.11 38.77 4.01
1311 2896 2.045926 CCACGCCTAGGCTTGCTT 60.046 61.111 30.00 8.56 38.77 3.91
1312 2897 4.101448 CCCACGCCTAGGCTTGCT 62.101 66.667 30.00 9.22 38.77 3.91
1334 2919 1.281899 GGCTCTGCATAGAACACGTC 58.718 55.000 2.78 0.00 31.21 4.34
1336 2921 1.148157 CGGGCTCTGCATAGAACACG 61.148 60.000 2.78 0.00 39.27 4.49
1407 2992 5.585047 GGTCATTTTATAAAGCACCGTCTCT 59.415 40.000 0.00 0.00 0.00 3.10
1408 2993 5.353123 TGGTCATTTTATAAAGCACCGTCTC 59.647 40.000 13.51 0.00 0.00 3.36
1409 2994 5.250200 TGGTCATTTTATAAAGCACCGTCT 58.750 37.500 13.51 0.00 0.00 4.18
1411 2996 5.708230 TCTTGGTCATTTTATAAAGCACCGT 59.292 36.000 13.51 0.00 0.00 4.83
1413 2998 7.121315 ACTCTCTTGGTCATTTTATAAAGCACC 59.879 37.037 12.30 12.30 0.00 5.01
1414 2999 8.045176 ACTCTCTTGGTCATTTTATAAAGCAC 57.955 34.615 0.00 0.00 0.00 4.40
1452 3059 2.681848 GCAATCCACTCCAACTCTCATG 59.318 50.000 0.00 0.00 0.00 3.07
1456 3063 2.787994 CTTGCAATCCACTCCAACTCT 58.212 47.619 0.00 0.00 0.00 3.24
1472 3079 4.264253 TCACCATATATATGCTGGCTTGC 58.736 43.478 16.08 0.00 33.12 4.01
1495 3102 7.776030 TGACTATCCAAAAGAACACACCTAAAA 59.224 33.333 0.00 0.00 0.00 1.52
1573 3183 2.706890 CCCACTAACAACCGTAAGCAT 58.293 47.619 0.00 0.00 0.00 3.79
1597 3207 8.568794 GTTACTTCCTCAATTATTTATCTGGCC 58.431 37.037 0.00 0.00 0.00 5.36
1691 3301 9.787435 ACATTTTACAGACCAACTCTAATAACA 57.213 29.630 0.00 0.00 0.00 2.41
1719 3329 0.951558 GCATCCAGTGAAACCAACGT 59.048 50.000 0.00 0.00 37.80 3.99
1720 3330 1.238439 AGCATCCAGTGAAACCAACG 58.762 50.000 0.00 0.00 37.80 4.10
1729 3370 5.243981 CCATAGGATTTCTAGCATCCAGTG 58.756 45.833 18.29 15.45 42.63 3.66
1795 3436 4.098349 TGGCTGTTTGATTCATAGGATTGC 59.902 41.667 0.00 0.00 0.00 3.56
1869 3510 3.412386 AGGGTTCCTTTGATTCAACGAG 58.588 45.455 4.57 0.00 0.00 4.18
1870 3511 3.502123 AGGGTTCCTTTGATTCAACGA 57.498 42.857 4.57 0.00 0.00 3.85
1872 3513 5.048013 CCACTAAGGGTTCCTTTGATTCAAC 60.048 44.000 13.40 0.00 41.69 3.18
2047 3688 6.672218 TGGATCAGAGGGAGTGATAAACTTTA 59.328 38.462 0.00 0.00 40.07 1.85
2057 3698 6.042552 ACACTTATTATGGATCAGAGGGAGTG 59.957 42.308 0.00 3.22 36.58 3.51
2066 3707 5.607939 ACCACGACACTTATTATGGATCA 57.392 39.130 0.00 0.00 0.00 2.92
2200 3880 2.081462 ACACACCGCAGTAAATAAGGC 58.919 47.619 0.00 0.00 0.00 4.35
2260 3943 0.313987 GGCCCGTCAAAAGAGTTTGG 59.686 55.000 0.00 0.00 43.70 3.28
2449 4134 0.037326 CTTCGTTGGTGCAGAGGCTA 60.037 55.000 0.00 0.00 41.91 3.93
2464 4149 1.236616 TTGGCTGTGTGCATCCTTCG 61.237 55.000 0.00 0.00 45.15 3.79
2485 4170 5.699458 ACTTCAGAACGTTAATTGGTCGATT 59.301 36.000 0.00 0.00 0.00 3.34
2548 4235 1.082194 AGGGGAAATGGTGAGGGACTA 59.918 52.381 0.00 0.00 41.55 2.59
2557 4244 3.053359 TGGTTTTCAAGGGGAAATGGT 57.947 42.857 0.00 0.00 44.59 3.55
2597 4284 9.762933 TCAAAAGAAGCAAGCATTTAAGTTATT 57.237 25.926 0.00 0.00 0.00 1.40
2724 4411 8.611654 TTTTGTAGTTCCTTCCAGTGTAATAC 57.388 34.615 0.00 0.00 0.00 1.89
2853 4540 9.884465 GGAGTGTCAATAATGTTAATTCTATGC 57.116 33.333 0.00 0.00 0.00 3.14
2958 4645 2.257409 ATTGTGGCTCTACCCCAGCG 62.257 60.000 0.00 0.00 37.81 5.18
3339 5026 0.532573 TCTTCACAGTCGCCTCATCC 59.467 55.000 0.00 0.00 0.00 3.51
3348 5035 8.663911 CCTTTTCTGATTAATCTCTTCACAGTC 58.336 37.037 16.24 0.00 0.00 3.51
3543 5230 6.276832 CCAGAAAATGGTTCATCATCACTT 57.723 37.500 0.00 0.00 44.91 3.16
4293 6076 7.337689 CAGTAAGATTTTGAGTGGGAATGATGA 59.662 37.037 0.00 0.00 0.00 2.92
4382 6177 6.734104 AAGTTAACATGAGAGAGAATGCAC 57.266 37.500 8.61 0.00 0.00 4.57
4383 6178 7.331934 GTGTAAGTTAACATGAGAGAGAATGCA 59.668 37.037 8.61 0.00 0.00 3.96
4727 6522 4.545208 TGAATCAACATCGTGGTAGGAA 57.455 40.909 0.00 0.00 0.00 3.36
5059 6862 9.295825 AGACTCAGAATTAGTACATCAGATAGG 57.704 37.037 0.00 0.00 0.00 2.57
5066 6869 7.646130 GTGCACTAGACTCAGAATTAGTACATC 59.354 40.741 10.32 0.00 0.00 3.06
5078 6882 4.199432 AGATTTGGTGCACTAGACTCAG 57.801 45.455 17.98 0.00 0.00 3.35
5263 7071 3.985925 CAGCAAAGCAAGTTCAATTCTCC 59.014 43.478 0.00 0.00 0.00 3.71
5557 7365 5.452078 ACAATGGCAAATAATATCACCCG 57.548 39.130 0.00 0.00 0.00 5.28
5655 7463 8.974408 AGCAAAATTTATAACGAACTGTTTTCC 58.026 29.630 0.00 0.00 42.09 3.13
5989 7829 3.803082 CACCACCGATGCCTTGCG 61.803 66.667 0.00 0.00 0.00 4.85
6045 7893 2.754552 TGGCAAGATACAGGCATCAAAC 59.245 45.455 0.00 0.00 35.21 2.93
6069 7917 3.691609 GCACAAAGGGATGAAGTTAGAGG 59.308 47.826 0.00 0.00 0.00 3.69
6075 7923 4.405358 TCAAAAAGCACAAAGGGATGAAGT 59.595 37.500 0.00 0.00 0.00 3.01
6098 7946 3.117284 TGGTTCAGGGCCTAAAAAGAAGT 60.117 43.478 5.28 0.00 0.00 3.01
6108 7956 1.668826 TGTTCTATGGTTCAGGGCCT 58.331 50.000 0.00 0.00 0.00 5.19
6162 8010 9.583765 GTTCCTCCACTTGTAACTTATTACTAG 57.416 37.037 6.98 6.98 44.74 2.57
6179 8096 5.127194 AGTTTTCTTCCTTTTGTTCCTCCAC 59.873 40.000 0.00 0.00 0.00 4.02
6180 8097 5.269189 AGTTTTCTTCCTTTTGTTCCTCCA 58.731 37.500 0.00 0.00 0.00 3.86
6268 8226 4.025040 ACTTGCTCAATCACAGAATCCA 57.975 40.909 0.00 0.00 0.00 3.41
6270 8228 6.150140 ACCTAAACTTGCTCAATCACAGAATC 59.850 38.462 0.00 0.00 0.00 2.52
6357 8315 1.068541 GGACAACGGATGCAAAGGAAC 60.069 52.381 0.00 0.00 0.00 3.62
6371 8329 2.158608 AGCCCCTATAGCAATGGACAAC 60.159 50.000 0.00 0.00 0.00 3.32
6372 8330 2.135189 AGCCCCTATAGCAATGGACAA 58.865 47.619 0.00 0.00 0.00 3.18
6398 8381 3.132111 AGGACTTTGTTGCGTTGGAAAAT 59.868 39.130 0.00 0.00 0.00 1.82
6412 8395 7.373493 AGCAATGTCTTTTTATGAGGACTTTG 58.627 34.615 12.80 12.80 41.96 2.77
6415 8398 6.479884 AGAGCAATGTCTTTTTATGAGGACT 58.520 36.000 0.00 0.00 0.00 3.85
6435 8421 5.364157 TCTTAATCCCAGGTAGAAGAAGAGC 59.636 44.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.