Multiple sequence alignment - TraesCS6B01G313500

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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 TraesCS6B01G313500 chr6B 100.000 7565 0 0 1 7565 561294170 561286606 0.000000e+00 13971.0
1 TraesCS6B01G313500 chr6B 98.901 91 1 0 4392 4482 561289928 561289838 6.070000e-36 163.0
2 TraesCS6B01G313500 chr6B 98.551 69 1 0 4329 4397 561289574 561289642 1.030000e-23 122.0
3 TraesCS6B01G313500 chr6B 100.000 66 0 0 4529 4594 561289774 561289839 1.030000e-23 122.0
4 TraesCS6B01G313500 chr6D 96.784 4477 101 20 2559 7007 374127054 374122593 0.000000e+00 7430.0
5 TraesCS6B01G313500 chr6D 96.049 2556 67 14 2 2535 374130016 374127473 0.000000e+00 4130.0
6 TraesCS6B01G313500 chr6D 86.811 417 28 12 7132 7533 374122117 374121713 2.510000e-119 440.0
7 TraesCS6B01G313500 chr6D 87.019 208 18 2 1326 1524 460156497 460156704 7.640000e-55 226.0
8 TraesCS6B01G313500 chr6D 98.901 91 1 0 4243 4333 374125214 374125124 6.070000e-36 163.0
9 TraesCS6B01G313500 chr6D 98.901 91 1 0 4392 4482 374125363 374125273 6.070000e-36 163.0
10 TraesCS6B01G313500 chr6D 100.000 66 0 0 4529 4594 374125209 374125274 1.030000e-23 122.0
11 TraesCS6B01G313500 chr6D 100.000 65 0 0 4333 4397 374125013 374125077 3.710000e-23 121.0
12 TraesCS6B01G313500 chr6D 85.981 107 15 0 6099 6205 189171762 189171656 1.720000e-21 115.0
13 TraesCS6B01G313500 chr6D 85.981 107 15 0 6099 6205 257504918 257505024 1.720000e-21 115.0
14 TraesCS6B01G313500 chr6D 90.769 65 6 0 7049 7113 374122164 374122100 3.760000e-13 87.9
15 TraesCS6B01G313500 chr6D 94.737 38 2 0 2539 2576 374127448 374127411 8.200000e-05 60.2
16 TraesCS6B01G313500 chr6A 94.710 2174 90 9 164 2319 516261806 516259640 0.000000e+00 3354.0
17 TraesCS6B01G313500 chr6A 95.250 1600 63 7 2743 4333 516258864 516257269 0.000000e+00 2521.0
18 TraesCS6B01G313500 chr6A 93.533 1237 56 13 4392 5618 516257359 516256137 0.000000e+00 1820.0
19 TraesCS6B01G313500 chr6A 91.411 1269 64 16 5884 7112 516256137 516254874 0.000000e+00 1698.0
20 TraesCS6B01G313500 chr6A 95.150 433 17 3 7133 7565 516254889 516254461 0.000000e+00 680.0
21 TraesCS6B01G313500 chr6A 85.542 415 39 14 2317 2713 516259612 516259201 1.520000e-111 414.0
22 TraesCS6B01G313500 chr5A 88.163 566 57 6 3702 4259 613927142 613927705 0.000000e+00 665.0
23 TraesCS6B01G313500 chr5A 83.591 518 54 11 3756 4257 504009690 504010192 2.490000e-124 457.0
24 TraesCS6B01G313500 chr5A 85.768 267 31 1 5620 5886 535518504 535518763 7.480000e-70 276.0
25 TraesCS6B01G313500 chr5A 87.383 214 24 3 4121 4333 504010193 504010404 7.580000e-60 243.0
26 TraesCS6B01G313500 chr7A 87.207 555 60 6 3711 4256 628830753 628830201 8.340000e-174 621.0
27 TraesCS6B01G313500 chr7A 85.249 522 53 13 3712 4229 732068063 732068564 4.050000e-142 516.0
28 TraesCS6B01G313500 chr7A 86.142 267 30 2 5620 5886 694496625 694496884 1.610000e-71 281.0
29 TraesCS6B01G313500 chr7A 89.202 213 20 3 4122 4333 628830198 628829988 5.820000e-66 263.0
30 TraesCS6B01G313500 chr7A 89.947 189 19 0 3294 3482 732067826 732068014 2.110000e-60 244.0
31 TraesCS6B01G313500 chr4D 84.238 387 43 9 3713 4094 461484154 461483781 2.010000e-95 361.0
32 TraesCS6B01G313500 chr4D 84.871 271 27 9 5620 5886 280179612 280179352 2.090000e-65 261.0
33 TraesCS6B01G313500 chr1D 89.412 255 26 1 4003 4257 468134817 468134564 3.410000e-83 320.0
34 TraesCS6B01G313500 chr1D 88.263 213 23 2 4121 4333 468134563 468134353 3.500000e-63 254.0
35 TraesCS6B01G313500 chr1D 85.366 246 27 5 3758 3994 468135104 468134859 5.860000e-61 246.0
36 TraesCS6B01G313500 chr1D 87.037 108 14 0 6099 6206 253201650 253201757 1.030000e-23 122.0
37 TraesCS6B01G313500 chr1D 86.916 107 14 0 6099 6205 76971212 76971106 3.710000e-23 121.0
38 TraesCS6B01G313500 chr4A 85.874 269 26 7 5620 5886 467684110 467683852 7.480000e-70 276.0
39 TraesCS6B01G313500 chr3D 85.185 270 28 5 5615 5882 546338183 546337924 4.500000e-67 267.0
40 TraesCS6B01G313500 chr3A 84.615 273 34 3 5613 5885 419388428 419388692 1.620000e-66 265.0
41 TraesCS6B01G313500 chr7D 84.328 268 33 4 5620 5887 125521151 125520893 3.500000e-63 254.0
42 TraesCS6B01G313500 chr7D 85.946 185 18 3 3713 3890 8998768 8998951 2.790000e-44 191.0
43 TraesCS6B01G313500 chr5B 83.395 271 37 6 5616 5885 663989055 663988792 2.110000e-60 244.0
44 TraesCS6B01G313500 chr4B 89.157 166 18 0 1326 1491 37561119 37561284 2.770000e-49 207.0
45 TraesCS6B01G313500 chr2D 76.619 278 63 2 1745 2021 600296412 600296688 1.310000e-32 152.0
46 TraesCS6B01G313500 chr2D 85.470 117 16 1 6090 6205 519342504 519342388 3.710000e-23 121.0
47 TraesCS6B01G313500 chr1B 86.275 102 14 0 6099 6200 634014464 634014565 2.230000e-20 111.0
48 TraesCS6B01G313500 chr1A 85.294 102 15 0 6099 6200 491425364 491425465 1.040000e-18 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G313500 chr6B 561286606 561294170 7564 True 13971.000000 13971 100.000000 1 7565 1 chr6B.!!$R1 7564
1 TraesCS6B01G313500 chr6D 374121713 374130016 8303 True 1782.014286 7430 94.707429 2 7533 7 chr6D.!!$R2 7531
2 TraesCS6B01G313500 chr6A 516254461 516261806 7345 True 1747.833333 3354 92.599333 164 7565 6 chr6A.!!$R1 7401
3 TraesCS6B01G313500 chr5A 613927142 613927705 563 False 665.000000 665 88.163000 3702 4259 1 chr5A.!!$F2 557
4 TraesCS6B01G313500 chr5A 504009690 504010404 714 False 350.000000 457 85.487000 3756 4333 2 chr5A.!!$F3 577
5 TraesCS6B01G313500 chr7A 628829988 628830753 765 True 442.000000 621 88.204500 3711 4333 2 chr7A.!!$R1 622
6 TraesCS6B01G313500 chr7A 732067826 732068564 738 False 380.000000 516 87.598000 3294 4229 2 chr7A.!!$F2 935
7 TraesCS6B01G313500 chr1D 468134353 468135104 751 True 273.333333 320 87.680333 3758 4333 3 chr1D.!!$R2 575

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
908 922 0.531974 TGGTTTGTGGCAGAGTCGAC 60.532 55.000 7.70 7.70 0.00 4.20 F
2741 3529 0.318120 CTGGGTGTGCCATGGAAAAC 59.682 55.000 18.40 11.02 36.17 2.43 F
2823 3611 0.963962 CAGACCAGCATTGCACCTTT 59.036 50.000 11.91 0.00 0.00 3.11 F
4231 5224 2.039831 GGATCCCCTGTAGCCCCA 60.040 66.667 0.00 0.00 0.00 4.96 F
4489 5483 1.896220 TCATGTTCTCACTTGCCACC 58.104 50.000 0.00 0.00 0.00 4.61 F
5120 6122 2.026915 TGTTCATCCACATACTGCAGCT 60.027 45.455 15.27 3.67 0.00 4.24 F
5646 6651 2.678336 CCCGTCCTTTTTAGTCTGCATC 59.322 50.000 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2879 3667 0.627986 CAAGAGGAAGGGGCCAGATT 59.372 55.000 4.39 0.0 0.00 2.40 R
3799 4606 0.110486 GGCCTTTGTTGGACCTCAGA 59.890 55.000 0.00 0.0 0.00 3.27 R
4430 5424 2.238521 TGGCAGAATTGAGGGAACAAC 58.761 47.619 0.00 0.0 32.50 3.32 R
5563 6566 2.367567 TCTAACCGAACTCCTTGCAGTT 59.632 45.455 0.00 0.0 39.43 3.16 R
6352 7368 3.625764 ACTGAACAAATTGTACACAGCGT 59.374 39.130 19.49 7.1 33.13 5.07 R
6521 7537 2.027745 TGCACCAAACCAAAAAGAAGCA 60.028 40.909 0.00 0.0 0.00 3.91 R
7480 8938 0.110295 TCTGGCAGCTGGCTGTTTTA 59.890 50.000 36.39 19.6 45.24 1.52 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
296 298 2.698075 GGGGACGAGGGAGGGAGTA 61.698 68.421 0.00 0.00 0.00 2.59
297 299 1.152715 GGGACGAGGGAGGGAGTAG 60.153 68.421 0.00 0.00 0.00 2.57
625 639 2.827383 GATCGGATCTAGCTGCGGGC 62.827 65.000 10.73 0.00 42.19 6.13
819 833 1.798813 ACGAGTTCGATGTTTTCCAGC 59.201 47.619 8.72 0.00 43.02 4.85
854 868 7.816640 TGAATTCAGTTCTAACCTGTATTTGC 58.183 34.615 3.38 0.00 37.72 3.68
864 878 3.944087 ACCTGTATTTGCTTGTCTCTCC 58.056 45.455 0.00 0.00 0.00 3.71
905 919 1.065551 GTGTTGGTTTGTGGCAGAGTC 59.934 52.381 0.00 0.00 0.00 3.36
908 922 0.531974 TGGTTTGTGGCAGAGTCGAC 60.532 55.000 7.70 7.70 0.00 4.20
918 932 2.179517 GAGTCGACGCTCCAGTGG 59.820 66.667 12.41 1.40 0.00 4.00
919 933 3.343788 GAGTCGACGCTCCAGTGGG 62.344 68.421 12.41 0.89 0.00 4.61
920 934 3.681835 GTCGACGCTCCAGTGGGT 61.682 66.667 9.92 0.00 35.79 4.51
1014 1030 2.039418 CGGAGAATGTCAGGTATGGGA 58.961 52.381 0.00 0.00 0.00 4.37
1038 1054 4.877251 TGTTGTTGGTTGTTCTGTAGGTAC 59.123 41.667 0.00 0.00 0.00 3.34
1047 1063 4.901868 TGTTCTGTAGGTACATGGGTTTC 58.098 43.478 0.00 0.00 35.36 2.78
1073 1089 7.117667 CACGGATACAATGCAGCTAATGTTATA 59.882 37.037 0.00 0.00 0.00 0.98
1155 1175 2.124693 CGAGAGGAGGGACAGAGCC 61.125 68.421 0.00 0.00 0.00 4.70
1200 1220 1.377725 AAAGCACAGGAGGATGCGG 60.378 57.895 0.00 0.00 46.74 5.69
1275 1295 1.959710 AGAGGGGGAAGAGGAAAGTC 58.040 55.000 0.00 0.00 0.00 3.01
1320 1340 1.332195 TAGAGGATGTCAGGGATGCG 58.668 55.000 0.00 0.00 0.00 4.73
1341 1361 2.210013 TGAAGAGCAGGCGGTCAGT 61.210 57.895 10.23 0.00 42.32 3.41
1516 1545 7.981225 TGCAGATTTTTGAAAGCTAGAAAGTTT 59.019 29.630 0.00 0.00 0.00 2.66
1522 1551 8.856490 TTTTGAAAGCTAGAAAGTTTGATGTC 57.144 30.769 0.00 0.00 0.00 3.06
1616 1645 7.451877 TGGAAGTAAGAACACTGTCTATTCTCT 59.548 37.037 0.46 0.00 31.44 3.10
1619 1648 5.413309 AAGAACACTGTCTATTCTCTGGG 57.587 43.478 0.46 0.00 31.44 4.45
1628 1657 3.563390 GTCTATTCTCTGGGCTGATTTGC 59.437 47.826 0.00 0.00 0.00 3.68
1653 1682 9.655769 GCAAATATATGAAACACTGTACAGATG 57.344 33.333 29.30 22.70 0.00 2.90
1706 1735 7.004086 ACTGCCTGCTATATAATTTGCCTTAA 58.996 34.615 0.00 0.00 0.00 1.85
1734 1763 5.520288 GTCGTGCATACTGATGACAACTAAT 59.480 40.000 0.00 0.00 34.73 1.73
1962 1991 2.601905 AGTTTCCTGCCTGCTCAATTT 58.398 42.857 0.00 0.00 0.00 1.82
2033 2062 3.181510 GCGTGGTATGTTCATTGTCCTTC 60.182 47.826 0.00 0.00 0.00 3.46
2065 2094 2.096013 GGTTTCTCTACGCCAGCAATTC 59.904 50.000 0.00 0.00 0.00 2.17
2079 2108 4.869297 CCAGCAATTCTTGTCTAGACTCTG 59.131 45.833 23.01 12.87 30.90 3.35
2116 2145 5.751243 TTAGCAAAAGGAAGTGTTGTCTC 57.249 39.130 0.00 0.00 0.00 3.36
2164 2193 5.535030 ACCTTCTGTTGATAAAACCTTCCAC 59.465 40.000 0.00 0.00 0.00 4.02
2310 2339 7.331687 ACAACTGAAAATTTTCACAGAAGTTGG 59.668 33.333 35.76 26.88 44.20 3.77
2312 2341 7.260603 ACTGAAAATTTTCACAGAAGTTGGAG 58.739 34.615 26.01 15.40 41.88 3.86
2360 2420 5.183904 GGATTTGTGAAGATGTACAAGCCTT 59.816 40.000 0.00 3.91 37.98 4.35
2438 2498 0.819582 ATGCTTGGTGGCACAATAGC 59.180 50.000 20.82 22.05 45.36 2.97
2537 2623 9.467258 AGATAAAATACAATGGATTTGATTGCG 57.533 29.630 3.91 0.00 38.76 4.85
2614 3074 2.110578 AGCCTGGCAGAAAACAAAACT 58.889 42.857 22.65 0.00 0.00 2.66
2741 3529 0.318120 CTGGGTGTGCCATGGAAAAC 59.682 55.000 18.40 11.02 36.17 2.43
2755 3543 3.547746 TGGAAAACGTCTTAGTGCCTTT 58.452 40.909 0.00 0.00 0.00 3.11
2756 3544 3.949113 TGGAAAACGTCTTAGTGCCTTTT 59.051 39.130 0.00 0.00 0.00 2.27
2823 3611 0.963962 CAGACCAGCATTGCACCTTT 59.036 50.000 11.91 0.00 0.00 3.11
2879 3667 3.402110 CACATGGTTAGACTGTTGAGCA 58.598 45.455 0.00 0.00 0.00 4.26
3070 3859 9.630098 CAAAACTGTTGATATTGCTAGAATTGT 57.370 29.630 0.00 0.00 0.00 2.71
3247 4036 6.636447 TCTGCAAAATAGTTGAAAATGACGTG 59.364 34.615 0.00 0.00 0.00 4.49
3262 4051 5.592104 ATGACGTGTGTATCTGTTCCATA 57.408 39.130 0.00 0.00 0.00 2.74
3355 4144 4.280174 GTGACTATTATCCCGAGGCAAGTA 59.720 45.833 0.00 0.00 27.53 2.24
3799 4606 2.551270 TGCTCTAACCAAGGAGGATGT 58.449 47.619 0.00 0.00 41.22 3.06
3943 4761 6.980978 TCTGCTACAGCTGATTATGAACTTAC 59.019 38.462 23.35 0.00 42.71 2.34
4117 4971 8.224389 TGTTCAATGAGTCAATCTCTTTTCAA 57.776 30.769 0.00 0.00 43.13 2.69
4231 5224 2.039831 GGATCCCCTGTAGCCCCA 60.040 66.667 0.00 0.00 0.00 4.96
4458 5452 8.224025 TGTTCCCTCAATTCTGCCATTATATTA 58.776 33.333 0.00 0.00 0.00 0.98
4489 5483 1.896220 TCATGTTCTCACTTGCCACC 58.104 50.000 0.00 0.00 0.00 4.61
4608 5602 4.440839 AAAATGTTAGGCTGTTGCTAGC 57.559 40.909 8.10 8.10 42.94 3.42
4735 5737 4.633565 CCTCTTTCAGTGGATAAAGCTGTC 59.366 45.833 0.00 0.00 33.61 3.51
4752 5754 5.112686 AGCTGTCGAGTCCAATAAAAGATC 58.887 41.667 0.00 0.00 0.00 2.75
4757 5759 6.750501 TGTCGAGTCCAATAAAAGATCTAACG 59.249 38.462 0.00 0.00 0.00 3.18
4792 5794 2.157834 TAAGGCAGTACAACACACGG 57.842 50.000 0.00 0.00 0.00 4.94
4885 5887 6.362248 ACATCTATAAAAACTTATGGGGCGT 58.638 36.000 0.00 0.00 0.00 5.68
5120 6122 2.026915 TGTTCATCCACATACTGCAGCT 60.027 45.455 15.27 3.67 0.00 4.24
5421 6423 4.381566 GCTTTTTACCACATAAGTGTTGCG 59.618 41.667 0.00 0.00 44.39 4.85
5592 6595 3.581332 AGGAGTTCGGTTAGAATCCAACA 59.419 43.478 0.00 0.00 41.49 3.33
5627 6632 4.038042 GCAAGTTAAATAATGCTCCCTCCC 59.962 45.833 0.00 0.00 35.93 4.30
5646 6651 2.678336 CCCGTCCTTTTTAGTCTGCATC 59.322 50.000 0.00 0.00 0.00 3.91
5656 6661 8.352942 CCTTTTTAGTCTGCATCTAAGTTTTGT 58.647 33.333 10.09 0.00 0.00 2.83
5657 6662 9.387123 CTTTTTAGTCTGCATCTAAGTTTTGTC 57.613 33.333 10.09 0.00 0.00 3.18
5658 6663 8.677148 TTTTAGTCTGCATCTAAGTTTTGTCT 57.323 30.769 10.09 0.00 0.00 3.41
5659 6664 7.658179 TTAGTCTGCATCTAAGTTTTGTCTG 57.342 36.000 7.21 0.00 0.00 3.51
5660 6665 5.858381 AGTCTGCATCTAAGTTTTGTCTGA 58.142 37.500 0.00 0.00 0.00 3.27
5661 6666 6.291377 AGTCTGCATCTAAGTTTTGTCTGAA 58.709 36.000 0.00 0.00 0.00 3.02
5662 6667 6.203723 AGTCTGCATCTAAGTTTTGTCTGAAC 59.796 38.462 0.00 0.00 0.00 3.18
5847 6852 4.485163 GTTGCAAAGTTTGACTTGACACT 58.515 39.130 19.82 0.00 38.66 3.55
5875 6880 8.153221 TCTTATACATGGAGTAAAAAGGACCA 57.847 34.615 0.00 0.00 36.05 4.02
5968 6974 6.824305 ATTTGAAGGACCACTAGTGAAATG 57.176 37.500 24.68 9.76 0.00 2.32
6001 7007 7.562135 TGTAGTTTTTACTGTCTTCCACTTCT 58.438 34.615 0.00 0.00 0.00 2.85
6341 7357 6.816640 GTCATAGAGTAAGCAACACCACATTA 59.183 38.462 0.00 0.00 0.00 1.90
6481 7497 4.859629 ATGCGTTTCGGATTTACTCTTC 57.140 40.909 0.00 0.00 33.43 2.87
6492 7508 7.439381 TCGGATTTACTCTTCGGCTTATATTT 58.561 34.615 0.00 0.00 0.00 1.40
6512 7528 5.759506 TTTGAGGTTAATTTTGCGAGACA 57.240 34.783 0.00 0.00 0.00 3.41
6513 7529 4.742438 TGAGGTTAATTTTGCGAGACAC 57.258 40.909 0.00 0.00 0.00 3.67
6514 7530 4.385825 TGAGGTTAATTTTGCGAGACACT 58.614 39.130 0.00 0.00 0.00 3.55
6515 7531 5.543714 TGAGGTTAATTTTGCGAGACACTA 58.456 37.500 0.00 0.00 0.00 2.74
6516 7532 5.992829 TGAGGTTAATTTTGCGAGACACTAA 59.007 36.000 0.00 0.00 0.00 2.24
6518 7534 6.842163 AGGTTAATTTTGCGAGACACTAATG 58.158 36.000 0.00 0.00 0.00 1.90
6520 7536 7.040686 AGGTTAATTTTGCGAGACACTAATGTT 60.041 33.333 0.00 0.00 39.95 2.71
6521 7537 7.593644 GGTTAATTTTGCGAGACACTAATGTTT 59.406 33.333 0.00 0.00 39.95 2.83
6522 7538 6.991485 AATTTTGCGAGACACTAATGTTTG 57.009 33.333 0.00 0.00 39.95 2.93
6796 7820 6.493802 TCCTGGAAGATAACTGAATATAGCGT 59.506 38.462 0.00 0.00 34.07 5.07
7043 8486 5.749109 CCTACTTTCAGAGTAAGCAATACCG 59.251 44.000 0.00 0.00 40.25 4.02
7098 8541 2.804421 GTTGCTGCAACAAACCAAAC 57.196 45.000 33.76 9.82 43.09 2.93
7099 8542 2.072298 GTTGCTGCAACAAACCAAACA 58.928 42.857 33.76 0.00 43.09 2.83
7100 8543 2.462456 TGCTGCAACAAACCAAACAA 57.538 40.000 0.00 0.00 0.00 2.83
7101 8544 2.344950 TGCTGCAACAAACCAAACAAG 58.655 42.857 0.00 0.00 0.00 3.16
7102 8545 1.062440 GCTGCAACAAACCAAACAAGC 59.938 47.619 0.00 0.00 0.00 4.01
7103 8546 2.344950 CTGCAACAAACCAAACAAGCA 58.655 42.857 0.00 0.00 0.00 3.91
7104 8547 2.344950 TGCAACAAACCAAACAAGCAG 58.655 42.857 0.00 0.00 0.00 4.24
7105 8548 1.665169 GCAACAAACCAAACAAGCAGG 59.335 47.619 0.00 0.00 0.00 4.85
7106 8549 2.676463 GCAACAAACCAAACAAGCAGGA 60.676 45.455 0.00 0.00 0.00 3.86
7107 8550 2.929398 CAACAAACCAAACAAGCAGGAC 59.071 45.455 0.00 0.00 0.00 3.85
7108 8551 2.175202 ACAAACCAAACAAGCAGGACA 58.825 42.857 0.00 0.00 0.00 4.02
7109 8552 2.765699 ACAAACCAAACAAGCAGGACAT 59.234 40.909 0.00 0.00 0.00 3.06
7110 8553 3.125316 CAAACCAAACAAGCAGGACATG 58.875 45.455 0.00 0.00 0.00 3.21
7111 8554 1.331214 ACCAAACAAGCAGGACATGG 58.669 50.000 0.00 0.00 0.00 3.66
7112 8555 1.331214 CCAAACAAGCAGGACATGGT 58.669 50.000 0.00 0.00 42.89 3.55
7215 8659 0.109723 TGTACAGCCCTGGGTTGTTC 59.890 55.000 35.33 30.06 44.47 3.18
7248 8694 1.806542 CAACGTTCCATGGGTTCTCAG 59.193 52.381 13.02 0.00 0.00 3.35
7265 8718 3.696051 TCTCAGCCCAAATTGTAGATTGC 59.304 43.478 0.00 0.00 0.00 3.56
7379 8833 3.516586 TGTTGAGGGAGTGGTATTCTGA 58.483 45.455 0.00 0.00 0.00 3.27
7403 8857 1.963338 GGTGAGCTGTGTGGCACTC 60.963 63.158 19.83 16.03 35.11 3.51
7516 8974 2.158986 CCAGATTGAAGACGGCATCTCT 60.159 50.000 0.00 0.00 36.27 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
283 285 0.109723 CTCCTCTACTCCCTCCCTCG 59.890 65.000 0.00 0.00 0.00 4.63
296 298 1.555533 CCTTTTTCCGCCTACTCCTCT 59.444 52.381 0.00 0.00 0.00 3.69
297 299 1.553704 TCCTTTTTCCGCCTACTCCTC 59.446 52.381 0.00 0.00 0.00 3.71
702 716 1.269621 GCGATCGCCTAACCTACACAT 60.270 52.381 29.48 0.00 34.56 3.21
819 833 7.095439 GGTTAGAACTGAATTCAGAGAGTTGTG 60.095 40.741 36.15 12.44 46.59 3.33
854 868 5.472137 TCCGTTTATTTTTGGGAGAGACAAG 59.528 40.000 0.00 0.00 0.00 3.16
864 878 8.859156 CAACACAGATTATCCGTTTATTTTTGG 58.141 33.333 0.00 0.00 0.00 3.28
918 932 7.210174 TGATCTGAAACTATATGTACAGCACC 58.790 38.462 0.33 0.00 35.10 5.01
919 933 7.923344 ACTGATCTGAAACTATATGTACAGCAC 59.077 37.037 6.60 0.00 35.10 4.40
920 934 7.922811 CACTGATCTGAAACTATATGTACAGCA 59.077 37.037 6.60 0.00 35.10 4.41
1014 1030 4.532834 ACCTACAGAACAACCAACAACAT 58.467 39.130 0.00 0.00 0.00 2.71
1038 1054 3.489059 GCATTGTATCCGTGAAACCCATG 60.489 47.826 0.00 0.00 0.00 3.66
1047 1063 3.561310 ACATTAGCTGCATTGTATCCGTG 59.439 43.478 1.02 0.00 0.00 4.94
1073 1089 5.706833 TCTGAAACAGCACATCATAACACAT 59.293 36.000 0.00 0.00 0.00 3.21
1155 1175 0.248825 CCTCTGAGTTCTCGGCATCG 60.249 60.000 3.66 0.00 37.82 3.84
1200 1220 4.193653 GCCTTCTTCCTCAGCGAC 57.806 61.111 0.00 0.00 0.00 5.19
1320 1340 3.959991 GACCGCCTGCTCTTCACCC 62.960 68.421 0.00 0.00 0.00 4.61
1420 1440 2.568623 ACGAGGCAAAGTTTCATCCT 57.431 45.000 0.00 1.38 0.00 3.24
1516 1545 0.874390 GTGCTGCCTTTTCGACATCA 59.126 50.000 0.00 0.00 0.00 3.07
1522 1551 1.788308 CACATTTGTGCTGCCTTTTCG 59.212 47.619 0.00 0.00 39.39 3.46
1616 1645 6.728089 TTCATATATTTGCAAATCAGCCCA 57.272 33.333 27.28 10.11 0.00 5.36
1619 1648 8.537223 CAGTGTTTCATATATTTGCAAATCAGC 58.463 33.333 27.28 11.18 0.00 4.26
1653 1682 8.692110 TTCAAATTCACATCAAATGCATCTAC 57.308 30.769 0.00 0.00 0.00 2.59
1706 1735 3.254060 GTCATCAGTATGCACGACACTT 58.746 45.455 0.00 0.00 34.76 3.16
2033 2062 5.927115 GGCGTAGAGAAACCATATTTAGGAG 59.073 44.000 0.00 0.00 0.00 3.69
2065 2094 6.369340 TCTTACGTCTTCAGAGTCTAGACAAG 59.631 42.308 24.44 17.70 38.52 3.16
2079 2108 8.287503 TCCTTTTGCTAATTTTCTTACGTCTTC 58.712 33.333 0.00 0.00 0.00 2.87
2116 2145 5.519722 AGTTTCGGAAAAATGTTACTGCAG 58.480 37.500 13.48 13.48 0.00 4.41
2291 2320 6.097412 AGAGCTCCAACTTCTGTGAAAATTTT 59.903 34.615 10.93 2.28 0.00 1.82
2438 2498 5.228945 TGTTTCTCTCTAACTTCCAAGGG 57.771 43.478 0.00 0.00 0.00 3.95
2573 2659 1.628447 TACGTTTTGCGCCGCTTAGG 61.628 55.000 11.67 3.80 46.11 2.69
2623 3083 2.514205 TTTTGCAGCTTTGCTTCCTC 57.486 45.000 0.00 0.00 36.40 3.71
2755 3543 1.144708 TGTGGATGTTGGAAGGAGCAA 59.855 47.619 0.00 0.00 0.00 3.91
2756 3544 0.770499 TGTGGATGTTGGAAGGAGCA 59.230 50.000 0.00 0.00 0.00 4.26
2823 3611 4.058124 GCTGTGTGATGACTGAGTGTTTA 58.942 43.478 0.00 0.00 0.00 2.01
2879 3667 0.627986 CAAGAGGAAGGGGCCAGATT 59.372 55.000 4.39 0.00 0.00 2.40
3051 3840 7.538575 ACCAACACAATTCTAGCAATATCAAC 58.461 34.615 0.00 0.00 0.00 3.18
3070 3859 1.305219 GCAATAGCAGCCGACCAACA 61.305 55.000 0.00 0.00 41.58 3.33
3168 3957 4.503910 TCAGACCACAAAATCATCCTACG 58.496 43.478 0.00 0.00 0.00 3.51
3262 4051 3.118531 AGTTCTTCCAGCCCTACATCAT 58.881 45.455 0.00 0.00 0.00 2.45
3355 4144 9.578576 AACACATGCCTATATTTCATCAGTAAT 57.421 29.630 0.00 0.00 0.00 1.89
3728 4524 8.551440 TGGTAATTGGCTGCAGATATATTCTAT 58.449 33.333 20.43 0.00 31.77 1.98
3799 4606 0.110486 GGCCTTTGTTGGACCTCAGA 59.890 55.000 0.00 0.00 0.00 3.27
3943 4761 7.630026 TGCTATGTACGATCTGCAATAAAAAG 58.370 34.615 0.00 0.00 0.00 2.27
4117 4971 6.977213 AGGACAGTGCATAAAACGTTAAAAT 58.023 32.000 0.00 0.00 0.00 1.82
4231 5224 8.844244 GCCAAACTATGATATTCAACATCTTCT 58.156 33.333 0.00 0.00 0.00 2.85
4430 5424 2.238521 TGGCAGAATTGAGGGAACAAC 58.761 47.619 0.00 0.00 32.50 3.32
4458 5452 8.517878 CAAGTGAGAACATGAATGGAACTTATT 58.482 33.333 0.00 0.00 0.00 1.40
4489 5483 5.781210 TCATCTGAATACAGGAGCTACTG 57.219 43.478 25.03 25.03 43.60 2.74
4527 5521 4.393680 TGTCGGGACCAAAAAGAAATATCG 59.606 41.667 0.00 0.00 0.00 2.92
4608 5602 3.565764 TGCCATGTTGAGGATAAGGAG 57.434 47.619 0.00 0.00 0.00 3.69
4735 5737 7.391786 CAACGTTAGATCTTTTATTGGACTCG 58.608 38.462 0.00 0.00 0.00 4.18
4752 5754 7.186804 CCTTAATACATTTCCAGCAACGTTAG 58.813 38.462 0.00 0.00 0.00 2.34
4757 5759 5.105756 ACTGCCTTAATACATTTCCAGCAAC 60.106 40.000 0.00 0.00 0.00 4.17
5086 6088 5.221224 TGTGGATGAACATTTTCCAACTGTC 60.221 40.000 0.00 0.00 41.05 3.51
5120 6122 6.134535 AGATTTGGTTGATTACTGGGTACA 57.865 37.500 0.00 0.00 0.00 2.90
5421 6423 9.678941 GCAGACCATAAGTTTATTTATAAAGGC 57.321 33.333 3.94 0.00 33.31 4.35
5563 6566 2.367567 TCTAACCGAACTCCTTGCAGTT 59.632 45.455 0.00 0.00 39.43 3.16
5592 6595 9.260002 CATTATTTAACTTGCAAAAGTTGGACT 57.740 29.630 13.00 1.05 42.47 3.85
5627 6632 5.869888 ACTTAGATGCAGACTAAAAAGGACG 59.130 40.000 14.20 6.43 30.95 4.79
5646 6651 7.492669 TGACTTCAGAGTTCAGACAAAACTTAG 59.507 37.037 0.00 0.00 37.10 2.18
5656 6661 5.127845 AGACACTTTGACTTCAGAGTTCAGA 59.872 40.000 0.00 0.00 38.99 3.27
5657 6662 5.355596 AGACACTTTGACTTCAGAGTTCAG 58.644 41.667 0.00 0.00 38.99 3.02
5658 6663 5.127845 AGAGACACTTTGACTTCAGAGTTCA 59.872 40.000 0.00 0.00 38.99 3.18
5659 6664 5.596845 AGAGACACTTTGACTTCAGAGTTC 58.403 41.667 0.00 3.00 38.99 3.01
5660 6665 5.606348 AGAGACACTTTGACTTCAGAGTT 57.394 39.130 0.00 0.00 38.99 3.01
5661 6666 6.716934 TTAGAGACACTTTGACTTCAGAGT 57.283 37.500 0.00 0.00 41.31 3.24
5662 6667 8.494347 CAAATTAGAGACACTTTGACTTCAGAG 58.506 37.037 0.00 0.00 34.59 3.35
5875 6880 7.200434 TCTTTTTATGCTTCATACTCCCTCT 57.800 36.000 0.00 0.00 0.00 3.69
5945 6951 5.711976 CCATTTCACTAGTGGTCCTTCAAAT 59.288 40.000 22.48 14.99 0.00 2.32
5949 6955 4.287766 ACCATTTCACTAGTGGTCCTTC 57.712 45.455 22.48 0.00 42.35 3.46
5968 6974 7.492352 AGACAGTAAAAACTACATTGTGACC 57.508 36.000 0.00 0.00 0.00 4.02
5972 6978 7.773690 AGTGGAAGACAGTAAAAACTACATTGT 59.226 33.333 0.00 0.00 0.00 2.71
6001 7007 6.102615 AGTTTCATAATAATGGCTCCCCACTA 59.897 38.462 0.00 0.00 45.77 2.74
6009 7019 8.236585 TGTTATGCAGTTTCATAATAATGGCT 57.763 30.769 0.00 0.00 40.00 4.75
6206 7218 7.217200 ACGGAACACTACATAAATAGATGCAT 58.783 34.615 0.00 0.00 0.00 3.96
6341 7357 3.818210 TGTACACAGCGTTTGAAATCCAT 59.182 39.130 0.00 0.00 0.00 3.41
6352 7368 3.625764 ACTGAACAAATTGTACACAGCGT 59.374 39.130 19.49 7.10 33.13 5.07
6481 7497 7.096640 CGCAAAATTAACCTCAAATATAAGCCG 60.097 37.037 0.00 0.00 0.00 5.52
6492 7508 4.385825 AGTGTCTCGCAAAATTAACCTCA 58.614 39.130 0.00 0.00 0.00 3.86
6512 7528 7.065683 CCAAACCAAAAAGAAGCAAACATTAGT 59.934 33.333 0.00 0.00 0.00 2.24
6513 7529 7.065683 ACCAAACCAAAAAGAAGCAAACATTAG 59.934 33.333 0.00 0.00 0.00 1.73
6514 7530 6.881602 ACCAAACCAAAAAGAAGCAAACATTA 59.118 30.769 0.00 0.00 0.00 1.90
6515 7531 5.709631 ACCAAACCAAAAAGAAGCAAACATT 59.290 32.000 0.00 0.00 0.00 2.71
6516 7532 5.123661 CACCAAACCAAAAAGAAGCAAACAT 59.876 36.000 0.00 0.00 0.00 2.71
6518 7534 4.671508 GCACCAAACCAAAAAGAAGCAAAC 60.672 41.667 0.00 0.00 0.00 2.93
6520 7536 3.006247 GCACCAAACCAAAAAGAAGCAA 58.994 40.909 0.00 0.00 0.00 3.91
6521 7537 2.027745 TGCACCAAACCAAAAAGAAGCA 60.028 40.909 0.00 0.00 0.00 3.91
6522 7538 2.609002 CTGCACCAAACCAAAAAGAAGC 59.391 45.455 0.00 0.00 0.00 3.86
6611 7632 3.251004 GTCGGAAAGCAGTCATCAAAGTT 59.749 43.478 0.00 0.00 0.00 2.66
6796 7820 7.938140 ACTTTCTTTTGCTGTATATAAGCCA 57.062 32.000 11.79 2.30 40.06 4.75
6990 8033 3.165875 ACTAGTATATGCATGGACGCCT 58.834 45.455 10.16 0.00 0.00 5.52
7043 8486 3.153735 GCGTCACGAAAAGAAAGTATGC 58.846 45.455 0.00 0.00 0.00 3.14
7120 8563 7.581213 TGTCCTGCTTATTCTTTCTCAAAAA 57.419 32.000 0.00 0.00 0.00 1.94
7121 8564 7.309377 CCATGTCCTGCTTATTCTTTCTCAAAA 60.309 37.037 0.00 0.00 0.00 2.44
7122 8565 6.151648 CCATGTCCTGCTTATTCTTTCTCAAA 59.848 38.462 0.00 0.00 0.00 2.69
7123 8566 5.649395 CCATGTCCTGCTTATTCTTTCTCAA 59.351 40.000 0.00 0.00 0.00 3.02
7124 8567 5.188434 CCATGTCCTGCTTATTCTTTCTCA 58.812 41.667 0.00 0.00 0.00 3.27
7125 8568 5.065731 CACCATGTCCTGCTTATTCTTTCTC 59.934 44.000 0.00 0.00 0.00 2.87
7126 8569 4.946157 CACCATGTCCTGCTTATTCTTTCT 59.054 41.667 0.00 0.00 0.00 2.52
7127 8570 4.702131 ACACCATGTCCTGCTTATTCTTTC 59.298 41.667 0.00 0.00 0.00 2.62
7128 8571 4.666512 ACACCATGTCCTGCTTATTCTTT 58.333 39.130 0.00 0.00 0.00 2.52
7129 8572 4.307032 ACACCATGTCCTGCTTATTCTT 57.693 40.909 0.00 0.00 0.00 2.52
7130 8573 4.012374 CAACACCATGTCCTGCTTATTCT 58.988 43.478 0.00 0.00 0.00 2.40
7223 8667 1.354101 ACCCATGGAACGTTGGTAGA 58.646 50.000 15.22 0.00 33.08 2.59
7230 8676 0.321653 GCTGAGAACCCATGGAACGT 60.322 55.000 15.22 0.00 0.00 3.99
7379 8833 4.221422 ACACAGCTCACCGCACGT 62.221 61.111 0.00 0.00 42.61 4.49
7403 8857 6.682746 AGCTTGATGTGGTAGTATATCTTCG 58.317 40.000 0.00 0.00 0.00 3.79
7480 8938 0.110295 TCTGGCAGCTGGCTGTTTTA 59.890 50.000 36.39 19.60 45.24 1.52
7516 8974 2.037251 CCTTCGTCTTCTGTTGGAGGAA 59.963 50.000 0.00 0.00 35.81 3.36


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

AutoCloner maintained by Alex Coulton.