Multiple sequence alignment - TraesCS2B01G358200

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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 TraesCS2B01G358200 chr2B 100.000 6280 0 0 1 6280 511131595 511137874 0.000000e+00 11598
1 TraesCS2B01G358200 chr2A 94.739 5341 198 38 88 5383 554105353 554100051 0.000000e+00 8229
2 TraesCS2B01G358200 chr2A 88.983 826 75 12 5468 6280 705942528 705941706 0.000000e+00 1007
3 TraesCS2B01G358200 chr2A 74.369 515 115 16 4605 5112 744331424 744331928 2.970000e-48 204
4 TraesCS2B01G358200 chr2A 95.798 119 4 1 5376 5494 554099757 554099640 2.310000e-44 191
5 TraesCS2B01G358200 chr2A 97.368 76 1 1 6 80 14572925 14573000 1.840000e-25 128
6 TraesCS2B01G358200 chr2A 74.510 306 73 5 4901 5206 554102494 554102194 1.840000e-25 128
7 TraesCS2B01G358200 chr2A 95.062 81 3 1 6 85 15364258 15364178 6.610000e-25 126
8 TraesCS2B01G358200 chr2A 96.104 77 2 1 6 81 15369447 15369371 2.380000e-24 124
9 TraesCS2B01G358200 chr2A 92.222 90 3 4 6 94 15814930 15815016 2.380000e-24 124
10 TraesCS2B01G358200 chr2D 94.370 4902 154 52 633 5489 432851589 432856413 0.000000e+00 7411
11 TraesCS2B01G358200 chr2D 92.279 816 52 5 5471 6275 590329762 590328947 0.000000e+00 1147
12 TraesCS2B01G358200 chr2D 89.186 823 69 10 5471 6278 194196018 194195201 0.000000e+00 1009
13 TraesCS2B01G358200 chr2D 85.902 532 41 14 100 611 432846554 432847071 2.580000e-148 536
14 TraesCS2B01G358200 chr2D 79.082 196 35 5 2964 3156 611898309 611898501 5.110000e-26 130
15 TraesCS2B01G358200 chr7D 90.987 821 60 8 5471 6280 568652071 568652888 0.000000e+00 1094
16 TraesCS2B01G358200 chr7D 90.036 823 66 8 5471 6280 104359724 104360543 0.000000e+00 1051
17 TraesCS2B01G358200 chr7D 90.036 823 67 8 5472 6280 568692918 568693739 0.000000e+00 1051
18 TraesCS2B01G358200 chr7D 75.851 323 62 13 2944 3261 298512594 298512905 3.920000e-32 150
19 TraesCS2B01G358200 chr5B 89.467 826 74 6 5467 6280 509680393 509679569 0.000000e+00 1031
20 TraesCS2B01G358200 chr3D 89.346 826 71 9 5468 6280 446355363 446356184 0.000000e+00 1022
21 TraesCS2B01G358200 chr4D 88.661 829 79 9 5466 6280 32246197 32247024 0.000000e+00 996
22 TraesCS2B01G358200 chr5A 85.135 518 47 11 3897 4407 28656580 28656086 2.610000e-138 503
23 TraesCS2B01G358200 chr5A 94.444 90 2 3 1 87 659881017 659880928 1.100000e-27 135
24 TraesCS2B01G358200 chr1A 81.538 260 45 2 4891 5150 64599482 64599738 1.770000e-50 211
25 TraesCS2B01G358200 chr1D 80.385 260 48 2 4891 5150 66096326 66096582 1.790000e-45 195
26 TraesCS2B01G358200 chr1B 80.460 261 46 4 4891 5150 106684881 106685137 1.790000e-45 195
27 TraesCS2B01G358200 chr6A 95.402 87 0 4 1 84 326797651 326797736 1.100000e-27 135
28 TraesCS2B01G358200 chr6A 96.386 83 0 3 1 80 70570914 70570996 3.950000e-27 134
29 TraesCS2B01G358200 chr6A 77.723 202 45 0 2964 3165 489226214 489226013 2.380000e-24 124
30 TraesCS2B01G358200 chr6B 95.349 86 1 3 1 83 559355100 559355015 3.950000e-27 134
31 TraesCS2B01G358200 chr6B 95.294 85 1 3 1 82 713948381 713948297 1.420000e-26 132
32 TraesCS2B01G358200 chr6B 77.723 202 45 0 2964 3165 525111783 525111582 2.380000e-24 124


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 TraesCS2B01G358200 chr2B 511131595 511137874 6279 False 11598.000000 11598 100.000 1 6280 1 chr2B.!!$F1 6279
1 TraesCS2B01G358200 chr2A 554099640 554105353 5713 True 2849.333333 8229 88.349 88 5494 3 chr2A.!!$R4 5406
2 TraesCS2B01G358200 chr2A 705941706 705942528 822 True 1007.000000 1007 88.983 5468 6280 1 chr2A.!!$R3 812
3 TraesCS2B01G358200 chr2A 744331424 744331928 504 False 204.000000 204 74.369 4605 5112 1 chr2A.!!$F3 507
4 TraesCS2B01G358200 chr2D 432851589 432856413 4824 False 7411.000000 7411 94.370 633 5489 1 chr2D.!!$F2 4856
5 TraesCS2B01G358200 chr2D 590328947 590329762 815 True 1147.000000 1147 92.279 5471 6275 1 chr2D.!!$R2 804
6 TraesCS2B01G358200 chr2D 194195201 194196018 817 True 1009.000000 1009 89.186 5471 6278 1 chr2D.!!$R1 807
7 TraesCS2B01G358200 chr2D 432846554 432847071 517 False 536.000000 536 85.902 100 611 1 chr2D.!!$F1 511
8 TraesCS2B01G358200 chr7D 568652071 568652888 817 False 1094.000000 1094 90.987 5471 6280 1 chr7D.!!$F3 809
9 TraesCS2B01G358200 chr7D 104359724 104360543 819 False 1051.000000 1051 90.036 5471 6280 1 chr7D.!!$F1 809
10 TraesCS2B01G358200 chr7D 568692918 568693739 821 False 1051.000000 1051 90.036 5472 6280 1 chr7D.!!$F4 808
11 TraesCS2B01G358200 chr5B 509679569 509680393 824 True 1031.000000 1031 89.467 5467 6280 1 chr5B.!!$R1 813
12 TraesCS2B01G358200 chr3D 446355363 446356184 821 False 1022.000000 1022 89.346 5468 6280 1 chr3D.!!$F1 812
13 TraesCS2B01G358200 chr4D 32246197 32247024 827 False 996.000000 996 88.661 5466 6280 1 chr4D.!!$F1 814

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
61 62 0.110328 TTCGCGAAGTCTCAGTCGAC 60.110 55.000 19.38 7.70 39.64 4.20 F
1480 1534 0.108138 GTTCTCCTGACCCATGTCGG 60.108 60.000 0.00 0.00 44.86 4.79 F
1874 1944 0.321671 CCTTCCTCTTCTTCGTGCCA 59.678 55.000 0.00 0.00 0.00 4.92 F
2223 2293 0.451783 CTTGGCGGGAATGTAAGCAC 59.548 55.000 0.00 0.00 0.00 4.40 F
3671 3745 1.170290 TCTTCCTCGCGATCGCCATA 61.170 55.000 32.63 17.97 37.98 2.74 F
4175 4249 1.522569 CCCGAGGAAGGACACCATC 59.477 63.158 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1819 0.040204 ACCATGGGAAGCTGAAAGGG 59.960 55.000 18.09 0.0 0.00 3.95 R
2380 2450 0.038709 GGAGCTTCTCGATCATCCCG 60.039 60.000 0.00 0.0 0.00 5.14 R
3647 3721 0.588737 CGATCGCGAGGAAGATGAGA 59.411 55.000 16.66 0.0 40.82 3.27 R
3704 3778 1.448893 GCCCATGACGGCGAAGTTA 60.449 57.895 16.62 0.0 39.64 2.24 R
4485 4559 0.554792 CCCTTGATCCCCTTCTGCAT 59.445 55.000 0.00 0.0 0.00 3.96 R
5789 6183 0.322816 ACGGGTAGCGGTGACTAGAA 60.323 55.000 4.14 0.0 0.00 2.10 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
33 34 7.872163 TTTTTCTTGCATACTACATTGCTTG 57.128 32.000 0.00 0.00 39.60 4.01
34 35 6.816134 TTTCTTGCATACTACATTGCTTGA 57.184 33.333 0.00 0.00 39.60 3.02
35 36 5.801350 TCTTGCATACTACATTGCTTGAC 57.199 39.130 0.00 0.00 39.60 3.18
36 37 5.491070 TCTTGCATACTACATTGCTTGACT 58.509 37.500 0.00 0.00 39.60 3.41
37 38 5.352293 TCTTGCATACTACATTGCTTGACTG 59.648 40.000 0.00 0.00 39.60 3.51
38 39 4.831107 TGCATACTACATTGCTTGACTGA 58.169 39.130 0.00 0.00 39.60 3.41
39 40 4.872124 TGCATACTACATTGCTTGACTGAG 59.128 41.667 0.00 0.00 39.60 3.35
40 41 5.111989 GCATACTACATTGCTTGACTGAGA 58.888 41.667 0.00 0.00 35.95 3.27
41 42 5.006165 GCATACTACATTGCTTGACTGAGAC 59.994 44.000 0.00 0.00 35.95 3.36
42 43 4.881019 ACTACATTGCTTGACTGAGACT 57.119 40.909 0.00 0.00 0.00 3.24
43 44 5.220710 ACTACATTGCTTGACTGAGACTT 57.779 39.130 0.00 0.00 0.00 3.01
44 45 5.233988 ACTACATTGCTTGACTGAGACTTC 58.766 41.667 0.00 0.00 0.00 3.01
45 46 3.062763 ACATTGCTTGACTGAGACTTCG 58.937 45.455 0.00 0.00 0.00 3.79
46 47 1.502231 TTGCTTGACTGAGACTTCGC 58.498 50.000 0.00 0.00 0.00 4.70
47 48 0.664466 TGCTTGACTGAGACTTCGCG 60.664 55.000 0.00 0.00 0.00 5.87
48 49 0.387367 GCTTGACTGAGACTTCGCGA 60.387 55.000 3.71 3.71 0.00 5.87
49 50 1.930817 GCTTGACTGAGACTTCGCGAA 60.931 52.381 22.01 22.01 0.00 4.70
50 51 1.982223 CTTGACTGAGACTTCGCGAAG 59.018 52.381 39.55 39.55 43.79 3.79
59 60 2.631303 CTTCGCGAAGTCTCAGTCG 58.369 57.895 34.97 12.16 40.24 4.18
60 61 0.166161 CTTCGCGAAGTCTCAGTCGA 59.834 55.000 34.97 4.60 39.64 4.20
61 62 0.110328 TTCGCGAAGTCTCAGTCGAC 60.110 55.000 19.38 7.70 39.64 4.20
62 63 0.949588 TCGCGAAGTCTCAGTCGACT 60.950 55.000 13.58 13.58 45.73 4.18
63 64 0.791238 CGCGAAGTCTCAGTCGACTG 60.791 60.000 34.76 34.76 43.14 3.51
74 75 2.701107 CAGTCGACTGAGACCTAGACA 58.299 52.381 36.73 0.00 46.59 3.41
75 76 3.075148 CAGTCGACTGAGACCTAGACAA 58.925 50.000 36.73 0.00 46.59 3.18
76 77 3.502595 CAGTCGACTGAGACCTAGACAAA 59.497 47.826 36.73 0.00 46.59 2.83
77 78 3.502979 AGTCGACTGAGACCTAGACAAAC 59.497 47.826 19.30 0.00 41.83 2.93
78 79 2.818432 TCGACTGAGACCTAGACAAACC 59.182 50.000 0.00 0.00 0.00 3.27
79 80 2.094649 CGACTGAGACCTAGACAAACCC 60.095 54.545 0.00 0.00 0.00 4.11
80 81 2.897969 GACTGAGACCTAGACAAACCCA 59.102 50.000 0.00 0.00 0.00 4.51
81 82 3.515901 GACTGAGACCTAGACAAACCCAT 59.484 47.826 0.00 0.00 0.00 4.00
82 83 3.910627 ACTGAGACCTAGACAAACCCATT 59.089 43.478 0.00 0.00 0.00 3.16
83 84 5.091552 ACTGAGACCTAGACAAACCCATTA 58.908 41.667 0.00 0.00 0.00 1.90
84 85 5.546499 ACTGAGACCTAGACAAACCCATTAA 59.454 40.000 0.00 0.00 0.00 1.40
85 86 6.215636 ACTGAGACCTAGACAAACCCATTAAT 59.784 38.462 0.00 0.00 0.00 1.40
86 87 7.027874 TGAGACCTAGACAAACCCATTAATT 57.972 36.000 0.00 0.00 0.00 1.40
87 88 8.153221 TGAGACCTAGACAAACCCATTAATTA 57.847 34.615 0.00 0.00 0.00 1.40
88 89 8.607713 TGAGACCTAGACAAACCCATTAATTAA 58.392 33.333 0.00 0.00 0.00 1.40
89 90 9.628500 GAGACCTAGACAAACCCATTAATTAAT 57.372 33.333 4.81 4.81 0.00 1.40
90 91 9.990868 AGACCTAGACAAACCCATTAATTAATT 57.009 29.630 8.01 5.89 0.00 1.40
143 145 2.968574 TGTCTTTCTCTGAGCTGACCTT 59.031 45.455 16.03 0.00 0.00 3.50
197 199 0.240945 CGGAACCAATCACTTGTGCC 59.759 55.000 0.00 0.00 0.00 5.01
262 264 4.209288 CCAAGTCCGTAATCAAAGATAGCG 59.791 45.833 0.00 0.00 0.00 4.26
280 282 3.305964 AGCGTCACGGAATATGATAACG 58.694 45.455 0.00 0.00 0.00 3.18
286 288 3.303495 CACGGAATATGATAACGGCGATC 59.697 47.826 16.62 7.90 0.00 3.69
289 291 3.617263 GGAATATGATAACGGCGATCCAC 59.383 47.826 16.62 1.20 0.00 4.02
391 405 1.608590 ACATGCGGGACACAAAGAAAG 59.391 47.619 0.00 0.00 0.00 2.62
400 414 3.627577 GGACACAAAGAAAGAGACAAGCA 59.372 43.478 0.00 0.00 0.00 3.91
431 448 5.206299 GCAGAGTACACGTACATGATAGAC 58.794 45.833 9.85 0.00 38.48 2.59
526 549 3.306364 GGCTGTCTTTCTCTAAGCTGACA 60.306 47.826 0.00 0.00 34.29 3.58
539 562 3.331478 AGCTGACATCCACTTGAGAAG 57.669 47.619 0.00 0.00 0.00 2.85
540 563 2.636893 AGCTGACATCCACTTGAGAAGT 59.363 45.455 0.00 0.00 44.06 3.01
541 564 3.834813 AGCTGACATCCACTTGAGAAGTA 59.165 43.478 0.00 0.00 40.46 2.24
542 565 3.929610 GCTGACATCCACTTGAGAAGTAC 59.070 47.826 0.00 0.00 40.46 2.73
543 566 4.561530 GCTGACATCCACTTGAGAAGTACA 60.562 45.833 0.00 0.00 40.46 2.90
552 577 5.452776 CCACTTGAGAAGTACAGTAACCACA 60.453 44.000 0.00 0.00 40.46 4.17
595 620 4.431416 ACCACCTGTACTCAAATTCACA 57.569 40.909 0.00 0.00 0.00 3.58
627 652 3.391049 AGTAAACAAGGCACGTTCTCTC 58.609 45.455 0.00 0.00 0.00 3.20
701 726 2.973945 TCGATCTCTCTCGACTGAACA 58.026 47.619 0.00 0.00 42.38 3.18
717 742 4.044336 TGAACAAGTACGAAAGTCGGAA 57.956 40.909 2.38 0.00 45.59 4.30
721 746 2.061740 AGTACGAAAGTCGGAAGCAC 57.938 50.000 2.38 0.00 45.59 4.40
768 793 0.389391 CCGGTCAGCATATTCCTCGT 59.611 55.000 0.00 0.00 0.00 4.18
771 796 2.481276 CGGTCAGCATATTCCTCGTTCA 60.481 50.000 0.00 0.00 0.00 3.18
878 903 4.296690 ACGATTTACCGATAAGTAGCTGC 58.703 43.478 0.00 0.00 0.00 5.25
898 923 4.626081 CCCGCCCCATGATCGGAC 62.626 72.222 17.72 0.00 45.53 4.79
903 928 1.068083 CCCCATGATCGGACGACAG 59.932 63.158 0.00 0.00 0.00 3.51
904 929 1.391933 CCCCATGATCGGACGACAGA 61.392 60.000 0.00 0.00 0.00 3.41
905 930 0.459899 CCCATGATCGGACGACAGAA 59.540 55.000 0.00 0.00 0.00 3.02
907 932 1.135112 CCATGATCGGACGACAGAACA 60.135 52.381 0.00 0.88 0.00 3.18
908 933 1.920574 CATGATCGGACGACAGAACAC 59.079 52.381 0.00 0.00 0.00 3.32
909 934 0.955905 TGATCGGACGACAGAACACA 59.044 50.000 0.00 0.00 0.00 3.72
910 935 1.068541 TGATCGGACGACAGAACACAG 60.069 52.381 0.00 0.00 0.00 3.66
911 936 1.199327 GATCGGACGACAGAACACAGA 59.801 52.381 0.00 0.00 0.00 3.41
912 937 1.026584 TCGGACGACAGAACACAGAA 58.973 50.000 0.00 0.00 0.00 3.02
913 938 1.001706 TCGGACGACAGAACACAGAAG 60.002 52.381 0.00 0.00 0.00 2.85
914 939 1.269102 CGGACGACAGAACACAGAAGT 60.269 52.381 0.00 0.00 0.00 3.01
939 964 8.005466 GTCTGAGTAAAACGACTATCGATCTAG 58.995 40.741 0.00 0.00 43.74 2.43
948 973 5.179742 ACGACTATCGATCTAGCTGGTTAAG 59.820 44.000 0.00 0.00 43.74 1.85
1245 1290 4.678509 TGGCGCTAAAAACATACTTCTG 57.321 40.909 7.64 0.00 0.00 3.02
1253 1298 6.072452 GCTAAAAACATACTTCTGCTCCACTT 60.072 38.462 0.00 0.00 0.00 3.16
1277 1322 7.918536 TGCTACCAGCTACAGTAGTATATAC 57.081 40.000 9.42 4.60 42.97 1.47
1278 1323 6.592994 TGCTACCAGCTACAGTAGTATATACG 59.407 42.308 9.42 0.00 42.97 3.06
1470 1524 1.550524 CGGACTGAATGGTTCTCCTGA 59.449 52.381 0.00 0.00 34.23 3.86
1480 1534 0.108138 GTTCTCCTGACCCATGTCGG 60.108 60.000 0.00 0.00 44.86 4.79
1680 1734 1.181786 CTTCCTCAGCGAGAAGGTCT 58.818 55.000 7.07 0.00 0.00 3.85
1708 1762 0.475632 ATCCCCACTCCCTTGACACA 60.476 55.000 0.00 0.00 0.00 3.72
1709 1763 1.127567 TCCCCACTCCCTTGACACAG 61.128 60.000 0.00 0.00 0.00 3.66
1746 1816 0.671781 GGCACGCTCTCTTGACATGT 60.672 55.000 0.00 0.00 0.00 3.21
1749 1819 2.412065 GCACGCTCTCTTGACATGTTTC 60.412 50.000 0.00 0.00 0.00 2.78
1817 1887 1.626654 CCATGTCCGTGTGCTTCGTC 61.627 60.000 0.00 0.00 0.00 4.20
1874 1944 0.321671 CCTTCCTCTTCTTCGTGCCA 59.678 55.000 0.00 0.00 0.00 4.92
1901 1971 3.869272 CTCGGCAAGCGCATGGTC 61.869 66.667 15.22 0.76 41.24 4.02
2026 2096 2.586792 GCTGGAGCGGTTCAGGAT 59.413 61.111 23.79 0.00 0.00 3.24
2084 2154 3.197790 CTCATCAAGGGCGCCGTG 61.198 66.667 24.39 21.80 34.41 4.94
2223 2293 0.451783 CTTGGCGGGAATGTAAGCAC 59.548 55.000 0.00 0.00 0.00 4.40
2231 2301 3.691498 GGGAATGTAAGCACGCAAATAC 58.309 45.455 0.00 0.00 0.00 1.89
2232 2302 3.127895 GGGAATGTAAGCACGCAAATACA 59.872 43.478 5.28 5.28 33.24 2.29
2233 2303 4.342772 GGAATGTAAGCACGCAAATACAG 58.657 43.478 7.89 0.00 32.31 2.74
2299 2369 4.912214 TCGATCATGTCATTGTGCATTTC 58.088 39.130 0.00 0.00 0.00 2.17
2525 2595 2.108157 TGCTCAACGGCGTCAACT 59.892 55.556 15.17 0.00 34.52 3.16
2880 2951 4.393680 CCACCGTAACAATTTTGCTAGCTA 59.606 41.667 17.23 5.31 0.00 3.32
2881 2952 5.065988 CCACCGTAACAATTTTGCTAGCTAT 59.934 40.000 17.23 4.05 0.00 2.97
2898 2969 8.370940 TGCTAGCTATAGTTCATTGCTAAGATT 58.629 33.333 17.23 0.00 44.07 2.40
3170 3241 3.118454 CGCAAGGCCGACACGATT 61.118 61.111 0.00 0.00 0.00 3.34
3626 3700 2.697761 CGACCACGACCTCATCCGT 61.698 63.158 0.00 0.00 42.66 4.69
3647 3721 1.280457 CAAAGACCAGGGCCTACTCT 58.720 55.000 5.28 5.97 0.00 3.24
3671 3745 1.170290 TCTTCCTCGCGATCGCCATA 61.170 55.000 32.63 17.97 37.98 2.74
3704 3778 1.743772 GCCAACATCGTGGAGCACTAT 60.744 52.381 0.00 0.00 41.65 2.12
3943 4017 2.126580 GGCGCTCTACGTGTCGTT 60.127 61.111 7.64 0.00 46.11 3.85
4175 4249 1.522569 CCCGAGGAAGGACACCATC 59.477 63.158 0.00 0.00 0.00 3.51
4446 4520 2.112198 GCGATCAAATCCGGCACCA 61.112 57.895 0.00 0.00 0.00 4.17
4452 4526 3.545124 AAATCCGGCACCAGCGACA 62.545 57.895 0.00 0.00 43.41 4.35
4485 4559 0.516001 CGACGACGACAAGGAGAAGA 59.484 55.000 0.00 0.00 42.66 2.87
4991 5065 0.456221 TGAAGAACGCGAGGATCCTC 59.544 55.000 29.15 29.15 39.55 3.71
4992 5066 0.741915 GAAGAACGCGAGGATCCTCT 59.258 55.000 33.70 19.07 40.69 3.69
5463 5839 3.755812 GCACTCCTACTAGGGATAGGCTT 60.756 52.174 2.04 0.00 39.36 4.35
5520 5896 1.061421 CGCCGCGCTGAAAAATTAGTA 59.939 47.619 5.56 0.00 0.00 1.82
5598 5978 3.706698 GCGACATATCTAGTTCAGCACA 58.293 45.455 0.00 0.00 0.00 4.57
5693 6080 4.256180 CTACCCCATCCAGCCGCC 62.256 72.222 0.00 0.00 0.00 6.13
5740 6132 2.091102 TTTCTTCCGGCGACCGTTCT 62.091 55.000 9.30 0.00 46.80 3.01
5789 6183 1.524482 GCGGCTTTCTCCATCTCCT 59.476 57.895 0.00 0.00 0.00 3.69
5803 6197 3.215151 CATCTCCTTCTAGTCACCGCTA 58.785 50.000 0.00 0.00 0.00 4.26
5887 6281 1.063469 CAAGGTGTTCGACAAAACGCT 59.937 47.619 0.00 0.00 39.16 5.07
5920 6315 9.065871 GTATGTATTGCTTCAACTTCACATTTC 57.934 33.333 0.00 0.00 0.00 2.17
6065 6465 3.582714 TGATCCTAGCTATGCACATCG 57.417 47.619 0.00 0.00 0.00 3.84
6171 6571 5.184892 AGGCACTATTTTGTGGAGAATCT 57.815 39.130 0.00 0.00 36.02 2.40
6210 6611 2.164219 ACTTTCGTCGCGGTTTAGGATA 59.836 45.455 6.13 0.00 0.00 2.59
6230 6631 1.598130 GCACCGAGTTGTTCAGGCT 60.598 57.895 0.00 0.00 0.00 4.58
6257 6658 1.137872 AGAGAAACTAGCGAGCCATGG 59.862 52.381 7.63 7.63 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.594758 GTCAAGCAATGTAGTATGCAAGAAAAA 59.405 33.333 0.00 0.00 44.95 1.94
10 11 7.040478 AGTCAAGCAATGTAGTATGCAAGAAAA 60.040 33.333 0.00 0.00 44.95 2.29
11 12 6.430925 AGTCAAGCAATGTAGTATGCAAGAAA 59.569 34.615 0.00 0.00 44.95 2.52
12 13 5.939883 AGTCAAGCAATGTAGTATGCAAGAA 59.060 36.000 0.00 0.00 44.95 2.52
13 14 5.352293 CAGTCAAGCAATGTAGTATGCAAGA 59.648 40.000 0.00 0.00 44.95 3.02
14 15 5.352293 TCAGTCAAGCAATGTAGTATGCAAG 59.648 40.000 0.00 0.00 44.95 4.01
16 17 4.831107 TCAGTCAAGCAATGTAGTATGCA 58.169 39.130 0.00 0.00 44.95 3.96
17 18 5.006165 GTCTCAGTCAAGCAATGTAGTATGC 59.994 44.000 0.00 0.00 42.87 3.14
18 19 6.336566 AGTCTCAGTCAAGCAATGTAGTATG 58.663 40.000 0.00 0.00 0.00 2.39
19 20 6.537453 AGTCTCAGTCAAGCAATGTAGTAT 57.463 37.500 0.00 0.00 0.00 2.12
20 21 5.984695 AGTCTCAGTCAAGCAATGTAGTA 57.015 39.130 0.00 0.00 0.00 1.82
21 22 4.881019 AGTCTCAGTCAAGCAATGTAGT 57.119 40.909 0.00 0.00 0.00 2.73
22 23 4.325741 CGAAGTCTCAGTCAAGCAATGTAG 59.674 45.833 0.00 0.00 0.00 2.74
23 24 4.237724 CGAAGTCTCAGTCAAGCAATGTA 58.762 43.478 0.00 0.00 0.00 2.29
24 25 3.062763 CGAAGTCTCAGTCAAGCAATGT 58.937 45.455 0.00 0.00 0.00 2.71
25 26 2.159734 GCGAAGTCTCAGTCAAGCAATG 60.160 50.000 0.00 0.00 0.00 2.82
26 27 2.072298 GCGAAGTCTCAGTCAAGCAAT 58.928 47.619 0.00 0.00 0.00 3.56
27 28 1.502231 GCGAAGTCTCAGTCAAGCAA 58.498 50.000 0.00 0.00 0.00 3.91
28 29 0.664466 CGCGAAGTCTCAGTCAAGCA 60.664 55.000 0.00 0.00 0.00 3.91
29 30 0.387367 TCGCGAAGTCTCAGTCAAGC 60.387 55.000 6.20 0.00 0.00 4.01
30 31 1.982223 CTTCGCGAAGTCTCAGTCAAG 59.018 52.381 34.97 10.93 33.87 3.02
31 32 2.051879 CTTCGCGAAGTCTCAGTCAA 57.948 50.000 34.97 4.60 33.87 3.18
32 33 3.775065 CTTCGCGAAGTCTCAGTCA 57.225 52.632 34.97 5.14 33.87 3.41
41 42 0.166161 TCGACTGAGACTTCGCGAAG 59.834 55.000 39.55 39.55 43.79 3.79
42 43 0.110328 GTCGACTGAGACTTCGCGAA 60.110 55.000 22.01 22.01 38.09 4.70
43 44 1.496393 GTCGACTGAGACTTCGCGA 59.504 57.895 3.71 3.71 38.09 5.87
44 45 4.044024 GTCGACTGAGACTTCGCG 57.956 61.111 8.70 0.00 38.09 5.87
54 55 2.701107 TGTCTAGGTCTCAGTCGACTG 58.299 52.381 34.76 34.76 45.08 3.51
55 56 3.420300 TTGTCTAGGTCTCAGTCGACT 57.580 47.619 13.58 13.58 34.38 4.18
56 57 3.366171 GGTTTGTCTAGGTCTCAGTCGAC 60.366 52.174 7.70 7.70 0.00 4.20
57 58 2.818432 GGTTTGTCTAGGTCTCAGTCGA 59.182 50.000 0.00 0.00 0.00 4.20
58 59 2.094649 GGGTTTGTCTAGGTCTCAGTCG 60.095 54.545 0.00 0.00 0.00 4.18
59 60 2.897969 TGGGTTTGTCTAGGTCTCAGTC 59.102 50.000 0.00 0.00 0.00 3.51
60 61 2.972348 TGGGTTTGTCTAGGTCTCAGT 58.028 47.619 0.00 0.00 0.00 3.41
61 62 4.559862 AATGGGTTTGTCTAGGTCTCAG 57.440 45.455 0.00 0.00 0.00 3.35
62 63 6.636454 ATTAATGGGTTTGTCTAGGTCTCA 57.364 37.500 0.00 0.00 0.00 3.27
63 64 9.628500 ATTAATTAATGGGTTTGTCTAGGTCTC 57.372 33.333 9.93 0.00 0.00 3.36
64 65 9.990868 AATTAATTAATGGGTTTGTCTAGGTCT 57.009 29.630 11.42 0.00 0.00 3.85
94 95 9.210426 CGTTTGCATGATTGAGTTATTAAGTAC 57.790 33.333 0.00 0.00 0.00 2.73
95 96 7.908082 GCGTTTGCATGATTGAGTTATTAAGTA 59.092 33.333 0.00 0.00 42.15 2.24
96 97 6.747280 GCGTTTGCATGATTGAGTTATTAAGT 59.253 34.615 0.00 0.00 42.15 2.24
97 98 6.968904 AGCGTTTGCATGATTGAGTTATTAAG 59.031 34.615 0.00 0.00 46.23 1.85
98 99 6.746822 CAGCGTTTGCATGATTGAGTTATTAA 59.253 34.615 0.00 0.00 46.23 1.40
101 102 4.156556 ACAGCGTTTGCATGATTGAGTTAT 59.843 37.500 0.00 0.00 46.23 1.89
116 117 2.139118 GCTCAGAGAAAGACAGCGTTT 58.861 47.619 0.00 0.00 0.00 3.60
143 145 6.016192 TGTTTGGTGTTTAACTTGTCAAGTGA 60.016 34.615 18.84 8.93 41.91 3.41
208 210 1.594862 GATCTCGCCATTTTCTGTCCG 59.405 52.381 0.00 0.00 0.00 4.79
262 264 2.407361 CGCCGTTATCATATTCCGTGAC 59.593 50.000 0.00 0.00 0.00 3.67
280 282 1.436983 GAACCGGATTGTGGATCGCC 61.437 60.000 9.46 0.00 35.49 5.54
286 288 3.658757 ACAATTTGAACCGGATTGTGG 57.341 42.857 9.46 0.00 41.14 4.17
289 291 2.730928 GCACACAATTTGAACCGGATTG 59.269 45.455 9.46 10.09 36.95 2.67
391 405 2.982744 GCCGGCCTTTGCTTGTCTC 61.983 63.158 18.11 0.00 37.74 3.36
400 414 1.003718 GTGTACTCTGCCGGCCTTT 60.004 57.895 26.77 8.17 0.00 3.11
431 448 2.159184 ACATGCATGTACTCTCGTCAGG 60.159 50.000 30.50 0.00 39.68 3.86
455 475 2.690786 TCCGTCCAAAATGAACGTAGG 58.309 47.619 0.00 0.00 34.71 3.18
487 507 1.741706 AGCCTTTGCATGATTGAGTCG 59.258 47.619 0.00 0.00 41.13 4.18
526 549 5.542635 TGGTTACTGTACTTCTCAAGTGGAT 59.457 40.000 0.00 0.00 42.84 3.41
539 562 6.704493 TGATCTTCTGTTTGTGGTTACTGTAC 59.296 38.462 0.00 0.00 0.00 2.90
540 563 6.822442 TGATCTTCTGTTTGTGGTTACTGTA 58.178 36.000 0.00 0.00 0.00 2.74
541 564 5.680619 TGATCTTCTGTTTGTGGTTACTGT 58.319 37.500 0.00 0.00 0.00 3.55
542 565 5.334414 GCTGATCTTCTGTTTGTGGTTACTG 60.334 44.000 0.00 0.00 0.00 2.74
543 566 4.757149 GCTGATCTTCTGTTTGTGGTTACT 59.243 41.667 0.00 0.00 0.00 2.24
552 577 4.613925 TGAGTCTGCTGATCTTCTGTTT 57.386 40.909 0.00 0.00 0.00 2.83
595 620 3.368531 GCCTTGTTTACTCGGAGATGTCT 60.369 47.826 12.86 0.00 33.89 3.41
627 652 3.718036 CGAGTGCGTTACTTGTTCAATCG 60.718 47.826 0.00 0.00 40.53 3.34
695 720 3.635331 TCCGACTTTCGTACTTGTTCAG 58.365 45.455 0.00 0.00 38.40 3.02
701 726 2.401351 GTGCTTCCGACTTTCGTACTT 58.599 47.619 0.00 0.00 38.40 2.24
717 742 1.039856 GTTGGACATTTGGTGGTGCT 58.960 50.000 0.00 0.00 0.00 4.40
721 746 0.881118 CGGAGTTGGACATTTGGTGG 59.119 55.000 0.00 0.00 0.00 4.61
768 793 1.613255 GCCGGATGGAGGTTTTCTGAA 60.613 52.381 5.05 0.00 37.49 3.02
771 796 1.078426 CGCCGGATGGAGGTTTTCT 60.078 57.895 5.05 0.00 37.49 2.52
878 903 2.359107 CGATCATGGGGCGGGATG 60.359 66.667 0.00 0.00 0.00 3.51
898 923 3.243234 ACTCAGACTTCTGTGTTCTGTCG 60.243 47.826 7.91 0.00 45.16 4.35
903 928 5.747197 TCGTTTTACTCAGACTTCTGTGTTC 59.253 40.000 16.75 7.15 45.16 3.18
904 929 5.519206 GTCGTTTTACTCAGACTTCTGTGTT 59.481 40.000 16.75 4.63 45.16 3.32
907 932 5.517322 AGTCGTTTTACTCAGACTTCTGT 57.483 39.130 6.15 0.00 44.12 3.41
908 933 6.466413 CGATAGTCGTTTTACTCAGACTTCTG 59.534 42.308 2.22 0.00 42.99 3.02
909 934 6.370994 TCGATAGTCGTTTTACTCAGACTTCT 59.629 38.462 2.22 0.00 42.99 2.85
910 935 6.541086 TCGATAGTCGTTTTACTCAGACTTC 58.459 40.000 2.22 0.97 42.99 3.01
911 936 6.492007 TCGATAGTCGTTTTACTCAGACTT 57.508 37.500 2.22 0.00 42.99 3.01
912 937 6.539464 AGATCGATAGTCGTTTTACTCAGACT 59.461 38.462 0.00 2.50 44.90 3.24
913 938 6.717413 AGATCGATAGTCGTTTTACTCAGAC 58.283 40.000 0.00 0.00 41.35 3.51
914 939 6.922247 AGATCGATAGTCGTTTTACTCAGA 57.078 37.500 0.00 0.00 41.35 3.27
948 973 4.168291 CGCTGGGGAAGAGGGAGC 62.168 72.222 0.00 0.00 0.00 4.70
949 974 1.553690 TTTCGCTGGGGAAGAGGGAG 61.554 60.000 0.78 0.00 34.26 4.30
950 975 1.131303 TTTTCGCTGGGGAAGAGGGA 61.131 55.000 0.78 0.00 0.00 4.20
951 976 0.960861 GTTTTCGCTGGGGAAGAGGG 60.961 60.000 0.78 0.00 0.00 4.30
952 977 0.036875 AGTTTTCGCTGGGGAAGAGG 59.963 55.000 0.78 0.00 0.00 3.69
956 981 1.604604 CTCAAGTTTTCGCTGGGGAA 58.395 50.000 0.00 0.00 0.00 3.97
1245 1290 0.537188 TAGCTGGTAGCAAGTGGAGC 59.463 55.000 0.00 0.00 45.56 4.70
1253 1298 6.592994 CGTATATACTACTGTAGCTGGTAGCA 59.407 42.308 14.55 9.61 45.56 3.49
1277 1322 3.120130 GGAGACAGACTGACAGAACTACG 60.120 52.174 10.08 0.73 0.00 3.51
1278 1323 4.076394 AGGAGACAGACTGACAGAACTAC 58.924 47.826 10.08 1.92 0.00 2.73
1480 1534 3.325753 ACACCCCCTCTGCTCAGC 61.326 66.667 0.00 0.00 0.00 4.26
1529 1583 1.227380 GTACAGCCTCCGCATCCTG 60.227 63.158 0.00 0.00 37.52 3.86
1680 1734 2.863484 AGTGGGGATTGGTGGCCA 60.863 61.111 0.00 0.00 0.00 5.36
1746 1816 2.528564 CATGGGAAGCTGAAAGGGAAA 58.471 47.619 0.00 0.00 0.00 3.13
1749 1819 0.040204 ACCATGGGAAGCTGAAAGGG 59.960 55.000 18.09 0.00 0.00 3.95
1874 1944 3.883744 CTTGCCGAGGACCACGCTT 62.884 63.158 5.72 0.00 0.00 4.68
2223 2293 4.438200 GGGTTGGATTGTACTGTATTTGCG 60.438 45.833 0.00 0.00 0.00 4.85
2231 2301 2.308866 AGGAAGGGGTTGGATTGTACTG 59.691 50.000 0.00 0.00 0.00 2.74
2232 2302 2.644151 AGGAAGGGGTTGGATTGTACT 58.356 47.619 0.00 0.00 0.00 2.73
2233 2303 3.451402 AAGGAAGGGGTTGGATTGTAC 57.549 47.619 0.00 0.00 0.00 2.90
2299 2369 1.830279 TGATGGAGCTGAAAAGGCAG 58.170 50.000 0.00 0.00 38.91 4.85
2380 2450 0.038709 GGAGCTTCTCGATCATCCCG 60.039 60.000 0.00 0.00 0.00 5.14
2525 2595 2.668632 GCCCTCGGACATGGTCAA 59.331 61.111 0.00 0.00 33.68 3.18
2743 2813 2.476686 CGTCTCGTTGCCGAACAGTATA 60.477 50.000 0.00 0.00 43.69 1.47
2806 2876 1.003839 GGTGATGAACTCGTGGGCA 60.004 57.895 0.00 0.00 0.00 5.36
2857 2927 3.190535 AGCTAGCAAAATTGTTACGGTGG 59.809 43.478 18.83 0.00 0.00 4.61
3449 3523 4.400961 GACTTCTGGGGCTGCGCT 62.401 66.667 16.51 0.00 0.00 5.92
3455 3529 1.648467 GATGCAACGACTTCTGGGGC 61.648 60.000 0.00 0.00 0.00 5.80
3461 3535 2.091277 CAGACGAAGATGCAACGACTTC 59.909 50.000 11.53 12.23 37.32 3.01
3536 3610 1.781555 CACCGCGCCGAATATGATC 59.218 57.895 0.00 0.00 0.00 2.92
3626 3700 1.133809 AGTAGGCCCTGGTCTTTGCA 61.134 55.000 0.00 0.00 0.00 4.08
3647 3721 0.588737 CGATCGCGAGGAAGATGAGA 59.411 55.000 16.66 0.00 40.82 3.27
3671 3745 4.393155 TTGGCGGCGATGCAGACT 62.393 61.111 12.98 0.00 31.81 3.24
3704 3778 1.448893 GCCCATGACGGCGAAGTTA 60.449 57.895 16.62 0.00 39.64 2.24
4175 4249 1.734477 CGAGAACCAGGACTGCGTG 60.734 63.158 0.00 0.00 0.00 5.34
4247 4321 1.972198 CTTGCCTCCGTACCACAGA 59.028 57.895 0.00 0.00 0.00 3.41
4446 4520 4.731612 CTCGCTGGCACTGTCGCT 62.732 66.667 0.00 0.00 0.00 4.93
4452 4526 4.057428 GTCGGACTCGCTGGCACT 62.057 66.667 0.00 0.00 36.13 4.40
4485 4559 0.554792 CCCTTGATCCCCTTCTGCAT 59.445 55.000 0.00 0.00 0.00 3.96
4991 5065 2.811317 GTCGCCTCGTCCAGCAAG 60.811 66.667 0.00 0.00 0.00 4.01
4992 5066 4.717629 CGTCGCCTCGTCCAGCAA 62.718 66.667 0.00 0.00 0.00 3.91
5238 5312 4.530857 GCTATGGCAGGGCGACGT 62.531 66.667 0.00 0.00 38.54 4.34
5342 5416 9.597170 TGACAAATGAATGATTGTGAAGAAAAA 57.403 25.926 0.00 0.00 39.73 1.94
5425 5801 4.102838 AGGAGTGCTTGATTAGATGATGCT 59.897 41.667 0.00 0.00 0.00 3.79
5463 5839 2.305635 TGTTGGAGATGCTCTTAGCCAA 59.694 45.455 0.00 0.00 41.51 4.52
5670 6050 1.307866 CTGGATGGGGTAGGTGGGT 60.308 63.158 0.00 0.00 0.00 4.51
5671 6051 2.757124 GCTGGATGGGGTAGGTGGG 61.757 68.421 0.00 0.00 0.00 4.61
5712 6104 1.674322 CCGGAAGAAATGGCGTGGT 60.674 57.895 0.00 0.00 0.00 4.16
5717 6109 2.761195 GGTCGCCGGAAGAAATGGC 61.761 63.158 5.05 0.00 45.39 4.40
5778 6170 3.685835 CGGTGACTAGAAGGAGATGGAGA 60.686 52.174 0.00 0.00 0.00 3.71
5789 6183 0.322816 ACGGGTAGCGGTGACTAGAA 60.323 55.000 4.14 0.00 0.00 2.10
5920 6315 5.927689 ACAACATGCACCAAATTCATGTAAG 59.072 36.000 9.40 8.30 46.92 2.34
6171 6571 1.065199 AGTACGACTCGGGGTATGTGA 60.065 52.381 2.98 0.00 0.00 3.58
6210 6611 1.166531 GCCTGAACAACTCGGTGCTT 61.167 55.000 0.00 0.00 0.00 3.91
6230 6631 3.515630 CTCGCTAGTTTCTCTGCAATGA 58.484 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.