Multiple sequence alignment - TraesCS2B01G132100

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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 TraesCS2B01G132100 chr2B 100.000 3580 0 0 1 3580 98432363 98435942 0.000000e+00 6612.0
1 TraesCS2B01G132100 chr2B 92.018 2205 110 35 721 2892 99247040 99249211 0.000000e+00 3037.0
2 TraesCS2B01G132100 chr2B 92.683 2132 108 26 721 2826 98816913 98819022 0.000000e+00 3029.0
3 TraesCS2B01G132100 chr2B 94.343 1538 67 9 1134 2661 98914591 98916118 0.000000e+00 2340.0
4 TraesCS2B01G132100 chr2B 86.907 1749 190 28 811 2546 98812504 98810782 0.000000e+00 1925.0
5 TraesCS2B01G132100 chr2A 90.671 2294 162 34 539 2804 65176632 65178901 0.000000e+00 3003.0
6 TraesCS2B01G132100 chr2A 87.216 1760 184 35 810 2546 65091133 65089392 0.000000e+00 1965.0
7 TraesCS2B01G132100 chr2D 90.104 2304 167 34 539 2804 63561873 63564153 0.000000e+00 2935.0
8 TraesCS2B01G132100 chr2D 87.150 1751 196 25 810 2546 63548915 63547180 0.000000e+00 1960.0
9 TraesCS2B01G132100 chr2D 84.746 1770 212 39 807 2545 63530594 63532336 0.000000e+00 1720.0
10 TraesCS2B01G132100 chr2D 86.402 706 64 19 1 703 63550909 63551585 0.000000e+00 743.0
11 TraesCS2B01G132100 chr2D 85.714 637 65 17 2952 3580 630082845 630082227 0.000000e+00 649.0
12 TraesCS2B01G132100 chr2D 87.549 257 25 5 530 782 63553454 63553707 1.260000e-74 291.0
13 TraesCS2B01G132100 chr2D 84.167 240 26 11 425 660 63553836 63554067 4.650000e-54 222.0
14 TraesCS2B01G132100 chr7D 87.421 636 55 15 2950 3580 560829559 560828944 0.000000e+00 708.0
15 TraesCS2B01G132100 chr1D 87.284 637 55 17 2952 3580 383360908 383360290 0.000000e+00 704.0
16 TraesCS2B01G132100 chr6D 85.086 637 70 16 2952 3580 257990858 257991477 8.440000e-176 627.0
17 TraesCS2B01G132100 chr5A 86.851 578 51 14 2952 3522 671451673 671452232 1.090000e-174 623.0
18 TraesCS2B01G132100 chr5A 81.846 325 25 20 3273 3580 565287804 565287497 3.570000e-60 243.0
19 TraesCS2B01G132100 chr7A 89.370 508 30 13 3075 3578 635201342 635200855 5.080000e-173 617.0
20 TraesCS2B01G132100 chr7A 80.710 648 71 35 2959 3580 204190312 204190931 4.210000e-124 455.0
21 TraesCS2B01G132100 chr3A 86.214 515 53 10 2952 3459 669777109 669776606 3.140000e-150 542.0
22 TraesCS2B01G132100 chr6A 80.521 652 70 37 2952 3580 602798928 602798311 7.050000e-122 448.0
23 TraesCS2B01G132100 chr3B 80.277 649 73 33 2953 3580 657788722 657789336 4.240000e-119 438.0
24 TraesCS2B01G132100 chr3D 88.793 232 6 12 3352 3580 305618576 305618362 2.120000e-67 267.0
25 TraesCS2B01G132100 chr4B 79.832 238 24 15 3345 3580 603291987 603291772 6.190000e-33 152.0
26 TraesCS2B01G132100 chr5B 81.921 177 28 3 7 183 450852393 450852221 2.880000e-31 147.0
27 TraesCS2B01G132100 chr5B 92.982 57 4 0 572 628 603980010 603980066 2.290000e-12 84.2
28 TraesCS2B01G132100 chr5D 83.893 149 18 4 484 629 489805697 489805842 1.730000e-28 137.0
29 TraesCS2B01G132100 chr5D 80.791 177 31 3 7 183 377544715 377544542 6.230000e-28 135.0
30 TraesCS2B01G132100 chrUn 81.197 117 17 5 516 629 255308916 255308802 4.920000e-14 89.8
31 TraesCS2B01G132100 chrUn 81.197 117 17 5 516 629 255319631 255319517 4.920000e-14 89.8
32 TraesCS2B01G132100 chrUn 80.833 120 18 5 513 629 307904454 307904571 4.920000e-14 89.8
33 TraesCS2B01G132100 chr4A 78.472 144 21 8 492 629 470676789 470676928 6.370000e-13 86.1


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 TraesCS2B01G132100 chr2B 98432363 98435942 3579 False 6612.000000 6612 100.000000 1 3580 1 chr2B.!!$F1 3579
1 TraesCS2B01G132100 chr2B 99247040 99249211 2171 False 3037.000000 3037 92.018000 721 2892 1 chr2B.!!$F4 2171
2 TraesCS2B01G132100 chr2B 98816913 98819022 2109 False 3029.000000 3029 92.683000 721 2826 1 chr2B.!!$F2 2105
3 TraesCS2B01G132100 chr2B 98914591 98916118 1527 False 2340.000000 2340 94.343000 1134 2661 1 chr2B.!!$F3 1527
4 TraesCS2B01G132100 chr2B 98810782 98812504 1722 True 1925.000000 1925 86.907000 811 2546 1 chr2B.!!$R1 1735
5 TraesCS2B01G132100 chr2A 65176632 65178901 2269 False 3003.000000 3003 90.671000 539 2804 1 chr2A.!!$F1 2265
6 TraesCS2B01G132100 chr2A 65089392 65091133 1741 True 1965.000000 1965 87.216000 810 2546 1 chr2A.!!$R1 1736
7 TraesCS2B01G132100 chr2D 63561873 63564153 2280 False 2935.000000 2935 90.104000 539 2804 1 chr2D.!!$F2 2265
8 TraesCS2B01G132100 chr2D 63547180 63548915 1735 True 1960.000000 1960 87.150000 810 2546 1 chr2D.!!$R1 1736
9 TraesCS2B01G132100 chr2D 63530594 63532336 1742 False 1720.000000 1720 84.746000 807 2545 1 chr2D.!!$F1 1738
10 TraesCS2B01G132100 chr2D 630082227 630082845 618 True 649.000000 649 85.714000 2952 3580 1 chr2D.!!$R2 628
11 TraesCS2B01G132100 chr2D 63550909 63554067 3158 False 418.666667 743 86.039333 1 782 3 chr2D.!!$F3 781
12 TraesCS2B01G132100 chr7D 560828944 560829559 615 True 708.000000 708 87.421000 2950 3580 1 chr7D.!!$R1 630
13 TraesCS2B01G132100 chr1D 383360290 383360908 618 True 704.000000 704 87.284000 2952 3580 1 chr1D.!!$R1 628
14 TraesCS2B01G132100 chr6D 257990858 257991477 619 False 627.000000 627 85.086000 2952 3580 1 chr6D.!!$F1 628
15 TraesCS2B01G132100 chr5A 671451673 671452232 559 False 623.000000 623 86.851000 2952 3522 1 chr5A.!!$F1 570
16 TraesCS2B01G132100 chr7A 204190312 204190931 619 False 455.000000 455 80.710000 2959 3580 1 chr7A.!!$F1 621
17 TraesCS2B01G132100 chr3A 669776606 669777109 503 True 542.000000 542 86.214000 2952 3459 1 chr3A.!!$R1 507
18 TraesCS2B01G132100 chr6A 602798311 602798928 617 True 448.000000 448 80.521000 2952 3580 1 chr6A.!!$R1 628
19 TraesCS2B01G132100 chr3B 657788722 657789336 614 False 438.000000 438 80.277000 2953 3580 1 chr3B.!!$F1 627

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
328 330 0.992695 AGGACTTAAACCCTGGCTCC 59.007 55.0 0.00 0.0 0.00 4.70 F
1105 3235 0.487772 GTAGATCCTCCTAGGCCCCA 59.512 60.0 2.96 0.0 34.61 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 4112 0.107993 CATCTGCCGGTCTGACATGT 60.108 55.0 10.38 0.0 0.0 3.21 R
2893 5120 0.168128 CCTCCGTCCAAAATTGCGTC 59.832 55.0 0.00 0.0 0.0 5.19 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
43 45 3.963129 ACTCCCAACTTTGTGTTCTTCA 58.037 40.909 0.00 0.00 36.63 3.02
69 71 1.909700 AACATGGTTTCTGCACGGAT 58.090 45.000 0.00 0.00 0.00 4.18
76 78 3.243367 TGGTTTCTGCACGGATTGAAAAG 60.243 43.478 0.00 0.00 31.47 2.27
82 84 2.428890 TGCACGGATTGAAAAGGTTGTT 59.571 40.909 0.00 0.00 0.00 2.83
86 88 2.035832 CGGATTGAAAAGGTTGTTGGCT 59.964 45.455 0.00 0.00 0.00 4.75
114 116 3.067180 CCACATTGCACTTGAGTTCAACT 59.933 43.478 0.00 0.00 34.31 3.16
115 117 4.039703 CACATTGCACTTGAGTTCAACTG 58.960 43.478 0.00 2.71 34.31 3.16
116 118 3.947196 ACATTGCACTTGAGTTCAACTGA 59.053 39.130 0.00 0.00 34.31 3.41
124 126 6.324819 CACTTGAGTTCAACTGACAACAAAT 58.675 36.000 0.00 0.00 0.00 2.32
130 132 5.650266 AGTTCAACTGACAACAAATGTGGTA 59.350 36.000 0.00 0.00 44.12 3.25
145 147 1.960689 GTGGTAAAGGCACAACCATGT 59.039 47.619 7.91 0.00 44.69 3.21
208 210 4.445452 GGTTCTGTACCACACTCGATAA 57.555 45.455 0.00 0.00 46.92 1.75
219 221 4.211389 CACACTCGATAAAGCAACACAAC 58.789 43.478 0.00 0.00 0.00 3.32
227 229 1.109323 AAGCAACACAACAGGAGCCC 61.109 55.000 0.00 0.00 0.00 5.19
234 236 3.771160 AACAGGAGCCCTACCGCG 61.771 66.667 0.00 0.00 29.64 6.46
274 276 1.404391 CCTCAAGCATGTTGGATCTGC 59.596 52.381 0.00 0.00 36.15 4.26
289 291 1.730501 TCTGCTTCAAAGATGGCTCG 58.269 50.000 0.00 0.00 0.00 5.03
292 294 1.066215 TGCTTCAAAGATGGCTCGCTA 60.066 47.619 0.00 0.00 0.00 4.26
293 295 2.216898 GCTTCAAAGATGGCTCGCTAT 58.783 47.619 0.00 0.00 0.00 2.97
294 296 3.181466 TGCTTCAAAGATGGCTCGCTATA 60.181 43.478 0.00 0.00 0.00 1.31
316 318 3.136809 AGAGGTATCGCTGAGAGGACTTA 59.863 47.826 0.00 0.00 0.00 2.24
323 325 2.675317 CGCTGAGAGGACTTAAACCCTG 60.675 54.545 0.43 0.00 31.84 4.45
328 330 0.992695 AGGACTTAAACCCTGGCTCC 59.007 55.000 0.00 0.00 0.00 4.70
372 374 5.850614 TCGTATAGGAGTGGATTTTTAGCC 58.149 41.667 0.00 0.00 0.00 3.93
397 407 3.502164 CTCCATGGAGCCCGAAAAT 57.498 52.632 28.45 0.00 35.31 1.82
406 416 4.967036 TGGAGCCCGAAAATTTCAAAAAT 58.033 34.783 6.53 0.00 0.00 1.82
410 420 8.314751 TGGAGCCCGAAAATTTCAAAAATAATA 58.685 29.630 6.53 0.00 0.00 0.98
524 534 8.244802 ACAAGTATTCATAGATGTATACTCGGC 58.755 37.037 17.19 0.00 44.96 5.54
570 2617 2.543777 ACGTATTGGTGTGAGCTGTT 57.456 45.000 0.00 0.00 0.00 3.16
577 2624 6.523201 CGTATTGGTGTGAGCTGTTAAAAATC 59.477 38.462 0.00 0.00 0.00 2.17
629 2676 8.791675 TGTGCTAGAAATATGTGATTTTGTCAA 58.208 29.630 0.00 0.00 38.90 3.18
631 2678 8.791675 TGCTAGAAATATGTGATTTTGTCAACA 58.208 29.630 0.00 0.00 38.90 3.33
632 2679 9.624697 GCTAGAAATATGTGATTTTGTCAACAA 57.375 29.630 0.00 0.00 38.90 2.83
666 2713 4.216472 TGCACAAAACAGTATTTCGCCATA 59.784 37.500 0.00 0.00 0.00 2.74
670 2717 7.647715 GCACAAAACAGTATTTCGCCATAATAT 59.352 33.333 0.00 0.00 0.00 1.28
687 2735 9.919348 GCCATAATATTTTGCAAACAAATAGTG 57.081 29.630 12.39 6.04 44.96 2.74
785 2836 3.567478 ATCGAGTTGTGCGCCGTCA 62.567 57.895 4.18 0.00 0.00 4.35
826 2877 2.942710 TCTCGAACGTGATGGAAGAAC 58.057 47.619 0.00 0.00 0.00 3.01
917 2977 4.864334 CGCAGCCCATGACCTCCC 62.864 72.222 0.00 0.00 0.00 4.30
957 3022 3.767806 CTCGCTGAGCTCCCTGCA 61.768 66.667 12.15 3.89 45.94 4.41
958 3023 4.074526 TCGCTGAGCTCCCTGCAC 62.075 66.667 12.15 0.00 45.94 4.57
960 3025 4.385405 GCTGAGCTCCCTGCACGT 62.385 66.667 12.15 0.00 45.94 4.49
961 3026 3.006756 GCTGAGCTCCCTGCACGTA 62.007 63.158 12.15 0.00 45.94 3.57
962 3027 1.153745 CTGAGCTCCCTGCACGTAC 60.154 63.158 12.15 0.00 45.94 3.67
963 3028 2.202623 GAGCTCCCTGCACGTACG 60.203 66.667 15.01 15.01 45.94 3.67
964 3029 2.989824 AGCTCCCTGCACGTACGT 60.990 61.111 16.72 16.72 45.94 3.57
999 3097 0.616395 TGGTCAGCCCATTACTCCGA 60.616 55.000 0.00 0.00 38.72 4.55
1000 3098 0.759346 GGTCAGCCCATTACTCCGAT 59.241 55.000 0.00 0.00 0.00 4.18
1039 3137 2.748605 GAAGGCCGTAGATCACATCAG 58.251 52.381 0.00 0.00 0.00 2.90
1046 3151 4.737649 GCCGTAGATCACATCAGACATCAA 60.738 45.833 0.00 0.00 0.00 2.57
1065 3170 5.499139 TCAAACAGCACGAAGAAGAATTT 57.501 34.783 0.00 0.00 0.00 1.82
1105 3235 0.487772 GTAGATCCTCCTAGGCCCCA 59.512 60.000 2.96 0.00 34.61 4.96
1110 3240 2.066999 CCTCCTAGGCCCCACTCAC 61.067 68.421 2.96 0.00 0.00 3.51
1119 3249 2.657237 CCCACTCACTCACCGACC 59.343 66.667 0.00 0.00 0.00 4.79
1124 3254 2.920912 TCACTCACCGACCCACCC 60.921 66.667 0.00 0.00 0.00 4.61
1979 4112 0.393402 TCCTTCGGCAGCGAGTACTA 60.393 55.000 0.00 0.00 0.00 1.82
2232 4365 2.352422 GTGCTGGAGTCCATGGCA 59.648 61.111 19.38 19.38 33.32 4.92
2280 4413 2.887568 CACATCGACCAGCCGCTC 60.888 66.667 0.00 0.00 0.00 5.03
2404 4537 0.824595 TGTCAACGGGAGAGAACGGA 60.825 55.000 0.00 0.00 0.00 4.69
2540 4673 0.963355 GCCGTGCCAAATTAGTGGGA 60.963 55.000 0.00 0.00 39.26 4.37
2599 4749 3.493503 CGAATAAATAAGACAGTCGGGCC 59.506 47.826 0.00 0.00 0.00 5.80
2701 4923 1.228459 ACTGGTTTCGGCCTTTCCC 60.228 57.895 0.00 0.00 0.00 3.97
2718 4940 5.353123 CCTTTCCCGAATGAACTAATTTCGA 59.647 40.000 5.91 0.00 43.61 3.71
2722 4944 4.270325 CCCGAATGAACTAATTTCGACCTC 59.730 45.833 5.91 0.00 43.61 3.85
2826 5053 3.671716 ACTCCCGTGAACCAAGATAAAC 58.328 45.455 0.00 0.00 0.00 2.01
2833 5060 4.433805 CGTGAACCAAGATAAACTACACGC 60.434 45.833 0.00 0.00 40.93 5.34
2835 5062 5.865552 GTGAACCAAGATAAACTACACGCTA 59.134 40.000 0.00 0.00 0.00 4.26
2842 5069 6.830114 AGATAAACTACACGCTAAGAATGC 57.170 37.500 0.00 0.00 0.00 3.56
2847 5074 2.472695 ACACGCTAAGAATGCCAGAA 57.527 45.000 0.00 0.00 0.00 3.02
2864 5091 3.942829 CAGAAGTGGAGTGATAAAGGCA 58.057 45.455 0.00 0.00 0.00 4.75
2868 5095 3.445008 AGTGGAGTGATAAAGGCAGAGA 58.555 45.455 0.00 0.00 0.00 3.10
2871 5098 5.069781 AGTGGAGTGATAAAGGCAGAGATAC 59.930 44.000 0.00 0.00 0.00 2.24
2894 5121 1.502231 GCTCTTGCAAGACACTTCGA 58.498 50.000 25.16 2.76 39.41 3.71
2895 5122 1.193426 GCTCTTGCAAGACACTTCGAC 59.807 52.381 25.16 7.29 39.41 4.20
2896 5123 1.453524 CTCTTGCAAGACACTTCGACG 59.546 52.381 25.16 8.51 0.00 5.12
2897 5124 0.111089 CTTGCAAGACACTTCGACGC 60.111 55.000 22.31 0.00 0.00 5.19
2898 5125 0.808060 TTGCAAGACACTTCGACGCA 60.808 50.000 0.00 0.00 0.00 5.24
2899 5126 0.808060 TGCAAGACACTTCGACGCAA 60.808 50.000 0.00 0.00 0.00 4.85
2900 5127 0.512952 GCAAGACACTTCGACGCAAT 59.487 50.000 0.00 0.00 0.00 3.56
2901 5128 1.069906 GCAAGACACTTCGACGCAATT 60.070 47.619 0.00 0.00 0.00 2.32
2902 5129 2.602217 GCAAGACACTTCGACGCAATTT 60.602 45.455 0.00 0.00 0.00 1.82
2903 5130 3.617669 CAAGACACTTCGACGCAATTTT 58.382 40.909 0.00 0.00 0.00 1.82
2904 5131 3.253371 AGACACTTCGACGCAATTTTG 57.747 42.857 0.00 0.00 0.00 2.44
2905 5132 2.032030 AGACACTTCGACGCAATTTTGG 60.032 45.455 0.00 0.00 0.00 3.28
2906 5133 1.944024 ACACTTCGACGCAATTTTGGA 59.056 42.857 0.00 0.00 0.00 3.53
2907 5134 2.286772 ACACTTCGACGCAATTTTGGAC 60.287 45.455 0.00 0.00 0.00 4.02
2908 5135 1.070175 ACTTCGACGCAATTTTGGACG 60.070 47.619 0.00 0.00 0.00 4.79
2909 5136 0.236187 TTCGACGCAATTTTGGACGG 59.764 50.000 0.00 0.00 0.00 4.79
2910 5137 0.600518 TCGACGCAATTTTGGACGGA 60.601 50.000 0.00 0.00 0.00 4.69
2911 5138 0.179225 CGACGCAATTTTGGACGGAG 60.179 55.000 0.00 0.00 0.00 4.63
2912 5139 0.168128 GACGCAATTTTGGACGGAGG 59.832 55.000 0.00 0.00 0.00 4.30
2913 5140 1.241315 ACGCAATTTTGGACGGAGGG 61.241 55.000 0.00 0.00 0.00 4.30
2914 5141 0.958382 CGCAATTTTGGACGGAGGGA 60.958 55.000 0.00 0.00 0.00 4.20
2915 5142 0.811281 GCAATTTTGGACGGAGGGAG 59.189 55.000 0.00 0.00 0.00 4.30
2916 5143 1.886655 GCAATTTTGGACGGAGGGAGT 60.887 52.381 0.00 0.00 0.00 3.85
2917 5144 2.617021 GCAATTTTGGACGGAGGGAGTA 60.617 50.000 0.00 0.00 0.00 2.59
2918 5145 3.007635 CAATTTTGGACGGAGGGAGTAC 58.992 50.000 0.00 0.00 0.00 2.73
2919 5146 1.719529 TTTTGGACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
2920 5147 1.719529 TTTGGACGGAGGGAGTACAA 58.280 50.000 0.00 0.00 40.35 2.41
2921 5148 1.263356 TTGGACGGAGGGAGTACAAG 58.737 55.000 0.00 0.00 37.50 3.16
2922 5149 0.613853 TGGACGGAGGGAGTACAAGG 60.614 60.000 0.00 0.00 27.89 3.61
2923 5150 0.614134 GGACGGAGGGAGTACAAGGT 60.614 60.000 0.00 0.00 0.00 3.50
2924 5151 1.341383 GGACGGAGGGAGTACAAGGTA 60.341 57.143 0.00 0.00 0.00 3.08
2925 5152 2.450476 GACGGAGGGAGTACAAGGTAA 58.550 52.381 0.00 0.00 0.00 2.85
2926 5153 2.165234 GACGGAGGGAGTACAAGGTAAC 59.835 54.545 0.00 0.00 0.00 2.50
2945 5172 7.781548 GGTAACTTCATATTTATGGACGTGT 57.218 36.000 0.00 0.00 34.50 4.49
2946 5173 7.848491 GGTAACTTCATATTTATGGACGTGTC 58.152 38.462 0.00 0.00 34.50 3.67
2947 5174 7.709613 GGTAACTTCATATTTATGGACGTGTCT 59.290 37.037 0.00 0.00 34.50 3.41
2948 5175 7.539712 AACTTCATATTTATGGACGTGTCTG 57.460 36.000 0.00 0.00 34.50 3.51
3021 5249 0.249489 CCGTCCAGGATAGGAAAGCG 60.249 60.000 7.95 0.00 45.00 4.68
3053 5284 3.192922 GATTCCCGCGTCCAACCG 61.193 66.667 4.92 0.00 0.00 4.44
3054 5285 3.652539 GATTCCCGCGTCCAACCGA 62.653 63.158 4.92 0.00 0.00 4.69
3163 5404 2.504996 CCATCTTCTTCTCTCCCAAGCT 59.495 50.000 0.00 0.00 0.00 3.74
3174 5415 4.289672 TCTCTCCCAAGCTAAAAAGGACAT 59.710 41.667 0.00 0.00 0.00 3.06
3195 5437 3.090532 GCCCCTTCCCCTCGTCAT 61.091 66.667 0.00 0.00 0.00 3.06
3216 5459 4.935352 TTTCCAGATCCACAAAACCTTG 57.065 40.909 0.00 0.00 38.61 3.61
3249 5492 1.353022 TGACGGCTCCATTAGGGTTTT 59.647 47.619 0.00 0.00 38.11 2.43
3285 5528 2.160721 AGGGAGCTCGTTCCAGATTA 57.839 50.000 7.83 0.00 39.09 1.75
3402 5650 9.635632 CAGTTATGCAACAAAATTGTGTAAAAG 57.364 29.630 0.55 0.00 41.31 2.27
3403 5651 9.593134 AGTTATGCAACAAAATTGTGTAAAAGA 57.407 25.926 0.55 0.00 41.31 2.52
3408 5784 7.125113 GCAACAAAATTGTGTAAAAGATGTGG 58.875 34.615 0.55 0.00 41.31 4.17
3455 5833 7.041372 TGTTTAGTCTGATGTTTAGGCAAGTTC 60.041 37.037 0.00 0.00 0.00 3.01
3456 5834 4.973168 AGTCTGATGTTTAGGCAAGTTCA 58.027 39.130 0.00 0.00 0.00 3.18
3458 5836 3.753272 TCTGATGTTTAGGCAAGTTCAGC 59.247 43.478 0.00 0.00 31.46 4.26
3465 5843 1.676967 GGCAAGTTCAGCCCTCCTG 60.677 63.158 0.00 0.00 46.50 3.86
3466 5844 1.073897 GCAAGTTCAGCCCTCCTGT 59.926 57.895 0.00 0.00 42.38 4.00
3469 5847 2.814097 GCAAGTTCAGCCCTCCTGTTTA 60.814 50.000 0.00 0.00 42.38 2.01
3478 5856 1.824852 CCCTCCTGTTTATGGGCAAAC 59.175 52.381 0.00 0.00 38.60 2.93
3496 5885 4.368315 CAAACTCAGTAGTACTGTGCACA 58.632 43.478 25.83 20.37 46.03 4.57
3498 5887 2.296471 ACTCAGTAGTACTGTGCACACC 59.704 50.000 25.83 6.88 46.03 4.16
3499 5888 2.558795 CTCAGTAGTACTGTGCACACCT 59.441 50.000 25.83 14.14 46.03 4.00
3500 5889 3.756963 CTCAGTAGTACTGTGCACACCTA 59.243 47.826 25.83 13.11 46.03 3.08
3501 5890 4.146564 TCAGTAGTACTGTGCACACCTAA 58.853 43.478 25.83 3.90 46.03 2.69
3527 5916 6.681777 AGTGATAGTTCTTGCCAATTTTCAC 58.318 36.000 0.00 0.00 29.66 3.18
3542 5931 8.238631 GCCAATTTTCACATTCTATTTGCAAAT 58.761 29.630 26.72 26.72 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.745227 TGGGAGTTCATGAGGAAATAAGTC 58.255 41.667 0.00 0.00 37.23 3.01
14 15 3.254166 CACAAAGTTGGGAGTTCATGAGG 59.746 47.826 0.00 0.00 31.80 3.86
43 45 4.082787 CGTGCAGAAACCATGTTTTAGGAT 60.083 41.667 0.00 0.00 0.00 3.24
69 71 4.817318 AGAAAGCCAACAACCTTTTCAA 57.183 36.364 0.00 0.00 31.85 2.69
76 78 1.754226 TGTGGAAGAAAGCCAACAACC 59.246 47.619 0.00 0.00 37.12 3.77
82 84 1.340889 GTGCAATGTGGAAGAAAGCCA 59.659 47.619 0.00 0.00 0.00 4.75
86 88 3.953612 ACTCAAGTGCAATGTGGAAGAAA 59.046 39.130 0.00 0.00 0.00 2.52
114 116 3.701542 TGCCTTTACCACATTTGTTGTCA 59.298 39.130 0.00 0.00 36.00 3.58
115 117 4.048504 GTGCCTTTACCACATTTGTTGTC 58.951 43.478 0.00 0.00 36.00 3.18
116 118 3.449018 TGTGCCTTTACCACATTTGTTGT 59.551 39.130 0.00 0.00 38.21 3.32
124 126 1.959985 CATGGTTGTGCCTTTACCACA 59.040 47.619 0.00 0.00 44.16 4.17
130 132 3.902881 TGAAAACATGGTTGTGCCTTT 57.097 38.095 0.00 0.00 35.83 3.11
204 206 3.366374 GGCTCCTGTTGTGTTGCTTTATC 60.366 47.826 0.00 0.00 0.00 1.75
208 210 1.109323 GGGCTCCTGTTGTGTTGCTT 61.109 55.000 0.00 0.00 0.00 3.91
227 229 4.329697 CGAGGCCTAGCGCGGTAG 62.330 72.222 32.72 32.72 38.94 3.18
234 236 1.478916 GGAAGATATCCGAGGCCTAGC 59.521 57.143 4.42 0.00 38.79 3.42
246 248 4.166725 TCCAACATGCTTGAGGGAAGATAT 59.833 41.667 6.60 0.00 32.82 1.63
274 276 4.876125 TCTATAGCGAGCCATCTTTGAAG 58.124 43.478 0.00 0.00 0.00 3.02
289 291 3.625764 CCTCTCAGCGATACCTCTATAGC 59.374 52.174 0.00 0.00 32.58 2.97
292 294 3.329520 AGTCCTCTCAGCGATACCTCTAT 59.670 47.826 0.00 0.00 0.00 1.98
293 295 2.706723 AGTCCTCTCAGCGATACCTCTA 59.293 50.000 0.00 0.00 0.00 2.43
294 296 1.493022 AGTCCTCTCAGCGATACCTCT 59.507 52.381 0.00 0.00 0.00 3.69
316 318 1.304713 CATGCTGGAGCCAGGGTTT 60.305 57.895 17.64 0.00 43.77 3.27
323 325 0.668401 GTTTGCAACATGCTGGAGCC 60.668 55.000 0.00 0.00 45.31 4.70
345 347 5.952347 AAAATCCACTCCTATACGAAGGT 57.048 39.130 0.00 0.00 37.91 3.50
355 357 2.092914 CGAGGGCTAAAAATCCACTCCT 60.093 50.000 0.00 0.00 0.00 3.69
385 387 7.609760 ATTATTTTTGAAATTTTCGGGCTCC 57.390 32.000 4.76 0.00 0.00 4.70
521 531 2.330231 ATGAAATTTCACACACGCCG 57.670 45.000 22.71 0.00 40.49 6.46
577 2624 7.468441 TGTACTGTTCACACAAAAAGTACATG 58.532 34.615 13.27 0.00 36.58 3.21
596 2643 8.599055 ATCACATATTTCTAGCACATGTACTG 57.401 34.615 8.95 0.00 0.00 2.74
633 2680 8.661352 AATACTGTTTTGTGCAAGCTATTTTT 57.339 26.923 0.00 0.00 0.00 1.94
634 2681 8.661352 AAATACTGTTTTGTGCAAGCTATTTT 57.339 26.923 0.00 0.00 0.00 1.82
635 2682 7.114811 CGAAATACTGTTTTGTGCAAGCTATTT 59.885 33.333 0.00 0.00 0.00 1.40
636 2683 6.582295 CGAAATACTGTTTTGTGCAAGCTATT 59.418 34.615 0.00 0.00 0.00 1.73
637 2684 6.086222 CGAAATACTGTTTTGTGCAAGCTAT 58.914 36.000 0.00 0.00 0.00 2.97
652 2699 8.572828 TTGCAAAATATTATGGCGAAATACTG 57.427 30.769 0.00 0.00 0.00 2.74
670 2717 8.932945 TGAATGTACACTATTTGTTTGCAAAA 57.067 26.923 14.67 0.00 46.23 2.44
717 2768 8.310122 ACCATAGGTCCGTAATAAAACTAGAA 57.690 34.615 0.00 0.00 0.00 2.10
757 2808 4.523813 CGCACAACTCGATTTTTGTTACT 58.476 39.130 3.96 0.00 33.59 2.24
785 2836 2.379005 TGCCTGTGTGACTCGATCTAT 58.621 47.619 0.00 0.00 0.00 1.98
864 2924 1.591863 GCGCGGAGTCACTATTCCC 60.592 63.158 8.83 0.00 0.00 3.97
943 3008 3.006756 TACGTGCAGGGAGCTCAGC 62.007 63.158 17.19 16.23 45.94 4.26
999 3097 1.530323 GGGGCGCGTGGATTTATAAT 58.470 50.000 8.43 0.00 0.00 1.28
1000 3098 0.881159 CGGGGCGCGTGGATTTATAA 60.881 55.000 16.48 0.00 0.00 0.98
1039 3137 3.494626 TCTTCTTCGTGCTGTTTGATGTC 59.505 43.478 0.00 0.00 0.00 3.06
1046 3151 4.555511 GCTGAAATTCTTCTTCGTGCTGTT 60.556 41.667 0.00 0.00 32.33 3.16
1065 3170 0.321671 GGTTCAGTACAGCTGGCTGA 59.678 55.000 28.08 28.08 46.30 4.26
1105 3235 2.207924 GGTGGGTCGGTGAGTGAGT 61.208 63.158 0.00 0.00 0.00 3.41
1110 3240 4.016706 GGTGGGTGGGTCGGTGAG 62.017 72.222 0.00 0.00 0.00 3.51
1119 3249 4.175337 ATGGCGATCGGTGGGTGG 62.175 66.667 18.30 0.00 0.00 4.61
1720 3853 4.632458 GTCGCGCTCGGGGATCTC 62.632 72.222 5.56 0.00 40.03 2.75
1942 4075 2.028484 GACGAGCACCACGGAACA 59.972 61.111 0.00 0.00 34.93 3.18
1944 4077 2.649034 GAGACGAGCACCACGGAA 59.351 61.111 0.00 0.00 34.93 4.30
1979 4112 0.107993 CATCTGCCGGTCTGACATGT 60.108 55.000 10.38 0.00 0.00 3.21
2337 4470 1.741770 CGCCTTGAACTCCCCGAAG 60.742 63.158 0.00 0.00 0.00 3.79
2440 4573 4.025401 GTTGTTCCGCGCCACCAG 62.025 66.667 0.00 0.00 0.00 4.00
2548 4681 8.696410 AAAACAACAGTTGAAAATACGTTCAT 57.304 26.923 20.56 0.00 37.36 2.57
2609 4759 0.766674 AAGGTACAGGTGGGCTGTGA 60.767 55.000 0.00 0.00 36.37 3.58
2635 4786 3.199727 ACAGATGGGTTGTTTGCCTTTTT 59.800 39.130 0.00 0.00 0.00 1.94
2636 4787 2.771372 ACAGATGGGTTGTTTGCCTTTT 59.229 40.909 0.00 0.00 0.00 2.27
2648 4807 1.153168 GCGGCATGTACAGATGGGT 60.153 57.895 0.33 0.00 0.00 4.51
2681 4903 1.574702 GGAAAGGCCGAAACCAGTCG 61.575 60.000 0.00 0.00 40.77 4.18
2686 4908 1.601477 TTCGGGAAAGGCCGAAACC 60.601 57.895 0.00 0.00 43.82 3.27
2701 4923 6.310467 TGAAGAGGTCGAAATTAGTTCATTCG 59.690 38.462 1.03 1.03 45.32 3.34
2718 4940 5.373812 TTCTTGAAGGAAACTGAAGAGGT 57.626 39.130 0.00 0.00 42.68 3.85
2777 5003 3.635591 CCTGATGGGCTTTTGGTAGAAT 58.364 45.455 0.00 0.00 0.00 2.40
2778 5004 3.085952 CCTGATGGGCTTTTGGTAGAA 57.914 47.619 0.00 0.00 0.00 2.10
2826 5053 3.165058 TCTGGCATTCTTAGCGTGTAG 57.835 47.619 0.00 0.00 0.00 2.74
2833 5060 3.937706 CACTCCACTTCTGGCATTCTTAG 59.062 47.826 0.00 0.00 37.49 2.18
2835 5062 2.373169 TCACTCCACTTCTGGCATTCTT 59.627 45.455 0.00 0.00 37.49 2.52
2842 5069 3.274288 GCCTTTATCACTCCACTTCTGG 58.726 50.000 0.00 0.00 39.23 3.86
2847 5074 3.445008 TCTCTGCCTTTATCACTCCACT 58.555 45.455 0.00 0.00 0.00 4.00
2892 5119 0.179225 CTCCGTCCAAAATTGCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
2893 5120 0.168128 CCTCCGTCCAAAATTGCGTC 59.832 55.000 0.00 0.00 0.00 5.19
2894 5121 1.241315 CCCTCCGTCCAAAATTGCGT 61.241 55.000 0.00 0.00 0.00 5.24
2895 5122 0.958382 TCCCTCCGTCCAAAATTGCG 60.958 55.000 0.00 0.00 0.00 4.85
2896 5123 0.811281 CTCCCTCCGTCCAAAATTGC 59.189 55.000 0.00 0.00 0.00 3.56
2897 5124 2.200373 ACTCCCTCCGTCCAAAATTG 57.800 50.000 0.00 0.00 0.00 2.32
2898 5125 2.640826 TGTACTCCCTCCGTCCAAAATT 59.359 45.455 0.00 0.00 0.00 1.82
2899 5126 2.262637 TGTACTCCCTCCGTCCAAAAT 58.737 47.619 0.00 0.00 0.00 1.82
2900 5127 1.719529 TGTACTCCCTCCGTCCAAAA 58.280 50.000 0.00 0.00 0.00 2.44
2901 5128 1.621814 CTTGTACTCCCTCCGTCCAAA 59.378 52.381 0.00 0.00 0.00 3.28
2902 5129 1.263356 CTTGTACTCCCTCCGTCCAA 58.737 55.000 0.00 0.00 0.00 3.53
2903 5130 0.613853 CCTTGTACTCCCTCCGTCCA 60.614 60.000 0.00 0.00 0.00 4.02
2904 5131 0.614134 ACCTTGTACTCCCTCCGTCC 60.614 60.000 0.00 0.00 0.00 4.79
2905 5132 2.134789 TACCTTGTACTCCCTCCGTC 57.865 55.000 0.00 0.00 0.00 4.79
2906 5133 2.174360 GTTACCTTGTACTCCCTCCGT 58.826 52.381 0.00 0.00 0.00 4.69
2907 5134 2.454538 AGTTACCTTGTACTCCCTCCG 58.545 52.381 0.00 0.00 0.00 4.63
2908 5135 3.836562 TGAAGTTACCTTGTACTCCCTCC 59.163 47.826 0.00 0.00 0.00 4.30
2909 5136 5.678955 ATGAAGTTACCTTGTACTCCCTC 57.321 43.478 0.00 0.00 0.00 4.30
2910 5137 7.750947 AATATGAAGTTACCTTGTACTCCCT 57.249 36.000 0.00 0.00 0.00 4.20
2916 5143 9.537192 CGTCCATAAATATGAAGTTACCTTGTA 57.463 33.333 1.98 0.00 35.75 2.41
2917 5144 8.044908 ACGTCCATAAATATGAAGTTACCTTGT 58.955 33.333 1.98 0.00 35.75 3.16
2918 5145 8.335356 CACGTCCATAAATATGAAGTTACCTTG 58.665 37.037 1.98 0.00 35.75 3.61
2919 5146 8.044908 ACACGTCCATAAATATGAAGTTACCTT 58.955 33.333 1.98 0.00 35.75 3.50
2920 5147 7.562135 ACACGTCCATAAATATGAAGTTACCT 58.438 34.615 1.98 0.00 35.75 3.08
2921 5148 7.709613 AGACACGTCCATAAATATGAAGTTACC 59.290 37.037 1.98 0.00 35.75 2.85
2922 5149 8.540492 CAGACACGTCCATAAATATGAAGTTAC 58.460 37.037 1.98 0.00 35.75 2.50
2923 5150 7.709182 CCAGACACGTCCATAAATATGAAGTTA 59.291 37.037 1.98 0.00 35.75 2.24
2924 5151 6.538742 CCAGACACGTCCATAAATATGAAGTT 59.461 38.462 1.98 0.00 35.75 2.66
2925 5152 6.049149 CCAGACACGTCCATAAATATGAAGT 58.951 40.000 1.98 0.00 35.75 3.01
2926 5153 5.050091 GCCAGACACGTCCATAAATATGAAG 60.050 44.000 1.98 0.00 35.75 3.02
2927 5154 4.814234 GCCAGACACGTCCATAAATATGAA 59.186 41.667 1.98 0.00 35.75 2.57
2928 5155 4.100963 AGCCAGACACGTCCATAAATATGA 59.899 41.667 1.98 0.00 35.75 2.15
2929 5156 4.212004 CAGCCAGACACGTCCATAAATATG 59.788 45.833 0.00 0.00 0.00 1.78
2930 5157 4.380531 CAGCCAGACACGTCCATAAATAT 58.619 43.478 0.00 0.00 0.00 1.28
2931 5158 3.792401 CAGCCAGACACGTCCATAAATA 58.208 45.455 0.00 0.00 0.00 1.40
2932 5159 2.632377 CAGCCAGACACGTCCATAAAT 58.368 47.619 0.00 0.00 0.00 1.40
2933 5160 1.943968 GCAGCCAGACACGTCCATAAA 60.944 52.381 0.00 0.00 0.00 1.40
2934 5161 0.391130 GCAGCCAGACACGTCCATAA 60.391 55.000 0.00 0.00 0.00 1.90
2935 5162 1.218047 GCAGCCAGACACGTCCATA 59.782 57.895 0.00 0.00 0.00 2.74
2936 5163 2.046892 GCAGCCAGACACGTCCAT 60.047 61.111 0.00 0.00 0.00 3.41
2937 5164 3.226429 GAGCAGCCAGACACGTCCA 62.226 63.158 0.00 0.00 0.00 4.02
2938 5165 2.433318 GAGCAGCCAGACACGTCC 60.433 66.667 0.00 0.00 0.00 4.79
2939 5166 2.433318 GGAGCAGCCAGACACGTC 60.433 66.667 0.00 0.00 36.34 4.34
2940 5167 4.008933 GGGAGCAGCCAGACACGT 62.009 66.667 0.00 0.00 38.95 4.49
2941 5168 2.290122 CTAGGGAGCAGCCAGACACG 62.290 65.000 0.00 0.00 38.95 4.49
2942 5169 1.519719 CTAGGGAGCAGCCAGACAC 59.480 63.158 0.00 0.00 38.95 3.67
2943 5170 4.040645 CTAGGGAGCAGCCAGACA 57.959 61.111 0.00 0.00 38.95 3.41
2966 5193 2.457813 ATATTTGGATGGCTGCCACA 57.542 45.000 25.99 16.00 35.80 4.17
3070 5301 3.412408 GGAAGGGGAGGACCAGGC 61.412 72.222 0.00 0.00 42.91 4.85
3163 5404 1.353022 AGGGGCGTGATGTCCTTTTTA 59.647 47.619 0.00 0.00 44.07 1.52
3192 5434 4.739793 AGGTTTTGTGGATCTGGAAATGA 58.260 39.130 0.00 0.00 0.00 2.57
3195 5437 4.340950 GTCAAGGTTTTGTGGATCTGGAAA 59.659 41.667 0.00 0.00 35.73 3.13
3216 5459 2.854522 CCGTCATTGGAGGGTTGTC 58.145 57.895 0.00 0.00 42.76 3.18
3249 5492 4.644685 GCTCCCTTGATTTGCCTACATAAA 59.355 41.667 0.00 0.00 0.00 1.40
3252 5495 2.243221 AGCTCCCTTGATTTGCCTACAT 59.757 45.455 0.00 0.00 0.00 2.29
3270 5513 2.362717 GCTAGGTAATCTGGAACGAGCT 59.637 50.000 0.00 0.00 0.00 4.09
3318 5562 7.496346 TCTGGAAGTGATGTAAATCTAACCT 57.504 36.000 0.00 0.00 33.76 3.50
3330 5574 2.368221 GAGGAGGGATCTGGAAGTGATG 59.632 54.545 0.00 0.00 33.76 3.07
3331 5575 2.249743 AGAGGAGGGATCTGGAAGTGAT 59.750 50.000 0.00 0.00 33.76 3.06
3387 5635 8.430801 TTTCCCACATCTTTTACACAATTTTG 57.569 30.769 0.00 0.00 0.00 2.44
3392 5640 6.549364 ACATCTTTCCCACATCTTTTACACAA 59.451 34.615 0.00 0.00 0.00 3.33
3393 5641 6.016360 CACATCTTTCCCACATCTTTTACACA 60.016 38.462 0.00 0.00 0.00 3.72
3394 5642 6.206634 TCACATCTTTCCCACATCTTTTACAC 59.793 38.462 0.00 0.00 0.00 2.90
3396 5644 6.817765 TCACATCTTTCCCACATCTTTTAC 57.182 37.500 0.00 0.00 0.00 2.01
3398 5646 5.776716 ACATCACATCTTTCCCACATCTTTT 59.223 36.000 0.00 0.00 0.00 2.27
3400 5648 4.927049 ACATCACATCTTTCCCACATCTT 58.073 39.130 0.00 0.00 0.00 2.40
3402 5650 6.678900 GCTTAACATCACATCTTTCCCACATC 60.679 42.308 0.00 0.00 0.00 3.06
3403 5651 5.126061 GCTTAACATCACATCTTTCCCACAT 59.874 40.000 0.00 0.00 0.00 3.21
3408 5784 6.199937 ACATGCTTAACATCACATCTTTCC 57.800 37.500 0.00 0.00 36.64 3.13
3455 5833 3.502164 CCCATAAACAGGAGGGCTG 57.498 57.895 0.00 0.00 33.91 4.85
3458 5836 1.824852 GTTTGCCCATAAACAGGAGGG 59.175 52.381 0.00 0.00 44.37 4.30
3459 5837 2.755103 GAGTTTGCCCATAAACAGGAGG 59.245 50.000 0.00 0.00 41.76 4.30
3461 5839 3.181434 ACTGAGTTTGCCCATAAACAGGA 60.181 43.478 0.00 0.00 41.76 3.86
3465 5843 6.171213 AGTACTACTGAGTTTGCCCATAAAC 58.829 40.000 0.00 0.00 40.08 2.01
3466 5844 6.368779 AGTACTACTGAGTTTGCCCATAAA 57.631 37.500 0.00 0.00 37.10 1.40
3496 5885 5.876357 TGGCAAGAACTATCACTTTTAGGT 58.124 37.500 0.00 0.00 0.00 3.08
3498 5887 9.696917 AAAATTGGCAAGAACTATCACTTTTAG 57.303 29.630 5.96 0.00 0.00 1.85
3499 5888 9.691362 GAAAATTGGCAAGAACTATCACTTTTA 57.309 29.630 5.96 0.00 0.00 1.52
3500 5889 8.203485 TGAAAATTGGCAAGAACTATCACTTTT 58.797 29.630 5.96 3.43 0.00 2.27
3501 5890 7.653311 GTGAAAATTGGCAAGAACTATCACTTT 59.347 33.333 5.96 0.00 32.78 2.66
3552 5941 5.796935 GCTTACAGCTTACAATGTGTTCATG 59.203 40.000 0.00 0.00 38.45 3.07


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

AutoCloner maintained by Alex Coulton.