Multiple sequence alignment - TraesCS3B01G419300

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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 TraesCS3B01G419300 chr3B 100.000 3730 0 0 1 3730 655857559 655853830 0.000000e+00 6889
1 TraesCS3B01G419300 chr3B 86.068 323 37 6 333 649 720265231 720264911 1.280000e-89 340
2 TraesCS3B01G419300 chr3B 85.761 309 36 7 351 653 708954891 708954585 1.670000e-83 320
3 TraesCS3B01G419300 chr3B 85.761 309 36 7 351 653 709075553 709075247 1.670000e-83 320
4 TraesCS3B01G419300 chr3D 94.421 1452 50 14 1911 3343 496741561 496740122 0.000000e+00 2204
5 TraesCS3B01G419300 chr3D 88.966 1432 88 22 239 1643 496743171 496741783 0.000000e+00 1705
6 TraesCS3B01G419300 chr3D 94.684 301 7 3 3432 3724 496739827 496739528 3.390000e-125 459
7 TraesCS3B01G419300 chr3D 85.583 326 40 6 333 653 544444277 544443954 5.970000e-88 335
8 TraesCS3B01G419300 chr3D 86.184 304 35 6 351 651 536668904 536668605 4.650000e-84 322
9 TraesCS3B01G419300 chr3D 86.230 305 33 8 351 651 536881041 536880742 4.650000e-84 322
10 TraesCS3B01G419300 chr3D 94.872 117 6 0 3321 3437 337959509 337959625 2.290000e-42 183
11 TraesCS3B01G419300 chr3D 88.696 115 11 2 1 113 496743419 496743305 5.020000e-29 139
12 TraesCS3B01G419300 chr3A 87.538 1661 118 35 1641 3256 638065727 638067343 0.000000e+00 1838
13 TraesCS3B01G419300 chr3A 87.638 1448 104 31 239 1643 638064284 638065699 0.000000e+00 1613
14 TraesCS3B01G419300 chr3A 83.261 687 76 17 1641 2318 506244328 506243672 2.480000e-166 595
15 TraesCS3B01G419300 chr3A 85.321 218 17 6 2442 2655 127276120 127275914 1.050000e-50 211
16 TraesCS3B01G419300 chr3A 93.684 95 5 1 1 94 638064046 638064140 1.400000e-29 141
17 TraesCS3B01G419300 chr3A 86.087 115 11 2 3417 3531 638067538 638067647 6.540000e-23 119
18 TraesCS3B01G419300 chr1B 83.552 687 74 19 1641 2318 12934671 12935327 1.150000e-169 606
19 TraesCS3B01G419300 chr6B 83.115 687 77 21 1641 2318 600611920 600611264 1.150000e-164 590
20 TraesCS3B01G419300 chr1A 83.163 683 76 17 1641 2314 571890204 571890856 4.150000e-164 588
21 TraesCS3B01G419300 chr1A 85.115 477 50 12 1847 2318 553476118 553475658 5.640000e-128 468
22 TraesCS3B01G419300 chr1A 84.080 201 26 4 1641 1837 571889169 571889367 4.920000e-44 189
23 TraesCS3B01G419300 chr1A 84.615 195 25 3 1641 1831 579993779 579993586 4.920000e-44 189
24 TraesCS3B01G419300 chr7B 82.969 687 78 20 1641 2318 364243675 364243019 5.370000e-163 584
25 TraesCS3B01G419300 chr5A 82.945 686 80 19 1641 2318 490866737 490866081 5.370000e-163 584
26 TraesCS3B01G419300 chr5D 84.567 473 55 10 1847 2318 321794027 321793572 1.580000e-123 453
27 TraesCS3B01G419300 chr5D 81.194 335 45 9 1822 2152 55895144 55895464 1.720000e-63 254
28 TraesCS3B01G419300 chr5D 86.636 217 21 3 2442 2655 433474469 433474680 2.240000e-57 233
29 TraesCS3B01G419300 chr5B 84.519 478 51 14 1847 2318 206106263 206105803 5.680000e-123 451
30 TraesCS3B01G419300 chr5B 87.558 217 22 4 2442 2655 87118644 87118430 2.880000e-61 246
31 TraesCS3B01G419300 chr5B 86.697 218 19 6 2442 2655 589406673 589406884 2.240000e-57 233
32 TraesCS3B01G419300 chr7D 86.230 305 36 6 358 658 549283718 549284020 3.590000e-85 326
33 TraesCS3B01G419300 chr7D 86.636 217 21 3 2442 2655 406870511 406870722 2.240000e-57 233
34 TraesCS3B01G419300 chr7D 86.636 217 21 4 2442 2655 553809433 553809644 2.240000e-57 233
35 TraesCS3B01G419300 chr7A 81.167 377 44 14 1641 2003 195758911 195759274 1.020000e-70 278
36 TraesCS3B01G419300 chr2A 82.298 322 33 16 1651 1957 418926159 418926471 1.330000e-64 257
37 TraesCS3B01G419300 chr2A 93.388 121 8 0 3318 3438 401660878 401660998 2.960000e-41 180
38 TraesCS3B01G419300 chr2A 93.388 121 8 0 3318 3438 403652670 403652790 2.960000e-41 180
39 TraesCS3B01G419300 chr4B 86.175 217 17 4 2442 2655 445023254 445023460 4.850000e-54 222
40 TraesCS3B01G419300 chr4B 92.562 121 9 0 3321 3441 613958687 613958807 1.380000e-39 174
41 TraesCS3B01G419300 chr2B 85.128 195 24 3 1641 1831 762200585 762200392 1.060000e-45 195
42 TraesCS3B01G419300 chr2B 91.200 125 11 0 3314 3438 723434226 723434350 1.780000e-38 171
43 TraesCS3B01G419300 chrUn 84.615 195 25 3 1641 1831 459710682 459710875 4.920000e-44 189
44 TraesCS3B01G419300 chr2D 94.215 121 7 0 3320 3440 585680863 585680983 6.360000e-43 185
45 TraesCS3B01G419300 chr2D 94.118 119 7 0 3319 3437 441576791 441576673 8.230000e-42 182
46 TraesCS3B01G419300 chr6D 93.548 124 7 1 3318 3441 348647335 348647457 2.290000e-42 183
47 TraesCS3B01G419300 chr4A 93.443 122 8 0 3318 3439 624989646 624989525 8.230000e-42 182


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 TraesCS3B01G419300 chr3B 655853830 655857559 3729 True 6889.00 6889 100.00000 1 3730 1 chr3B.!!$R1 3729
1 TraesCS3B01G419300 chr3D 496739528 496743419 3891 True 1126.75 2204 91.69175 1 3724 4 chr3D.!!$R4 3723
2 TraesCS3B01G419300 chr3A 638064046 638067647 3601 False 927.75 1838 88.73675 1 3531 4 chr3A.!!$F1 3530
3 TraesCS3B01G419300 chr3A 506243672 506244328 656 True 595.00 595 83.26100 1641 2318 1 chr3A.!!$R2 677
4 TraesCS3B01G419300 chr1B 12934671 12935327 656 False 606.00 606 83.55200 1641 2318 1 chr1B.!!$F1 677
5 TraesCS3B01G419300 chr6B 600611264 600611920 656 True 590.00 590 83.11500 1641 2318 1 chr6B.!!$R1 677
6 TraesCS3B01G419300 chr1A 571889169 571890856 1687 False 388.50 588 83.62150 1641 2314 2 chr1A.!!$F1 673
7 TraesCS3B01G419300 chr7B 364243019 364243675 656 True 584.00 584 82.96900 1641 2318 1 chr7B.!!$R1 677
8 TraesCS3B01G419300 chr5A 490866081 490866737 656 True 584.00 584 82.94500 1641 2318 1 chr5A.!!$R1 677

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
972 1050 0.103876 ACCAAACCCCTCTTCCTCCT 60.104 55.000 0.0 0.0 0.0 3.69 F
979 1057 1.076339 CCTCTTCCTCCTCGCCTCT 60.076 63.158 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 3572 0.242555 GAGTGATAGCTAGGCCGCTC 59.757 60.000 8.56 14.32 41.3 5.03 R
3013 4211 3.924918 ACCTGCTAGCACGTATATGAG 57.075 47.619 14.93 0.04 0.0 2.90 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
88 90 7.461182 TTTTTAACGGACAGGAAATCATCAT 57.539 32.000 0.00 0.00 0.00 2.45
90 92 7.461182 TTTAACGGACAGGAAATCATCATTT 57.539 32.000 0.00 0.00 34.70 2.32
91 93 5.982890 AACGGACAGGAAATCATCATTTT 57.017 34.783 0.00 0.00 31.94 1.82
92 94 5.982890 ACGGACAGGAAATCATCATTTTT 57.017 34.783 0.00 0.00 31.94 1.94
113 115 7.491254 TTTTTCTCAAATACGCAAATCATCG 57.509 32.000 0.00 0.00 0.00 3.84
114 116 5.794687 TTCTCAAATACGCAAATCATCGT 57.205 34.783 0.00 0.00 42.09 3.73
115 117 5.389642 TCTCAAATACGCAAATCATCGTC 57.610 39.130 0.00 0.00 39.79 4.20
116 118 4.867608 TCTCAAATACGCAAATCATCGTCA 59.132 37.500 0.00 0.00 39.79 4.35
117 119 4.892655 TCAAATACGCAAATCATCGTCAC 58.107 39.130 0.00 0.00 39.79 3.67
153 155 6.684686 ACACAGGAAATCATCACTTGAATTG 58.315 36.000 0.00 0.00 38.03 2.32
154 156 6.266103 ACACAGGAAATCATCACTTGAATTGT 59.734 34.615 0.00 0.00 38.03 2.71
185 187 5.443261 GCAAACTTTGAATTGCTAAAAGCC 58.557 37.500 5.65 0.00 46.42 4.35
186 188 5.237127 GCAAACTTTGAATTGCTAAAAGCCT 59.763 36.000 5.65 0.00 46.42 4.58
204 211 4.104831 AGCCTAAGTTACTCCAACCTGAT 58.895 43.478 0.00 0.00 37.93 2.90
234 241 2.035449 GGGCCCACAACTACTGTTTTTC 59.965 50.000 19.95 0.00 35.47 2.29
245 288 7.224167 ACAACTACTGTTTTTCCTTTCTAGACG 59.776 37.037 0.00 0.00 32.99 4.18
260 303 3.358076 GACGAGAAGAGGTGCCCGG 62.358 68.421 0.00 0.00 0.00 5.73
298 353 2.967887 GGCCCAATTCAGCAGGATATTT 59.032 45.455 0.00 0.00 0.00 1.40
302 357 3.243975 CCAATTCAGCAGGATATTTGCCC 60.244 47.826 8.92 0.00 42.48 5.36
371 445 2.597305 GCGACTCGTTTAGTACCACATG 59.403 50.000 0.00 0.00 39.07 3.21
525 599 4.440145 GGGTCATGTGCCCACAAT 57.560 55.556 18.74 0.00 45.41 2.71
529 603 1.135527 GGTCATGTGCCCACAATGATG 59.864 52.381 5.08 0.00 45.41 3.07
566 640 4.494515 GGAAGGGTCCACCACAAC 57.505 61.111 0.00 0.00 44.26 3.32
576 650 2.203480 ACCACAACGGCTTGCCAT 60.203 55.556 12.45 0.00 39.03 4.40
582 656 1.305213 AACGGCTTGCCATTGGGAT 60.305 52.632 12.45 0.00 35.59 3.85
614 688 0.108585 CCCAGGTGTTGCACTACAGT 59.891 55.000 0.00 0.00 34.40 3.55
645 719 2.549778 CGCACCCCAACCAAATCAATTT 60.550 45.455 0.00 0.00 0.00 1.82
653 727 9.868160 ACCCCAACCAAATCAATTTAAATTTTA 57.132 25.926 10.77 3.25 0.00 1.52
726 800 9.234827 CAGCATTATTAAGATGTCATGGGATTA 57.765 33.333 0.00 0.00 0.00 1.75
731 805 3.784511 AGATGTCATGGGATTAGCTGG 57.215 47.619 0.00 0.00 0.00 4.85
753 827 2.122564 GAAGAGCAGCACAAACTTTGC 58.877 47.619 1.14 0.00 40.52 3.68
754 828 1.105457 AGAGCAGCACAAACTTTGCA 58.895 45.000 1.14 0.00 42.83 4.08
873 948 3.499338 ACACCAAAATCAGATTCTGGCA 58.501 40.909 14.65 0.00 31.51 4.92
877 952 3.258872 CCAAAATCAGATTCTGGCACCAA 59.741 43.478 13.59 0.00 31.51 3.67
881 956 2.783135 TCAGATTCTGGCACCAAAGTC 58.217 47.619 13.59 0.00 31.51 3.01
929 1007 3.170717 GTTCCGATATATCTGGGACCCA 58.829 50.000 14.08 14.08 0.00 4.51
969 1047 0.482887 CCAACCAAACCCCTCTTCCT 59.517 55.000 0.00 0.00 0.00 3.36
971 1049 0.778083 AACCAAACCCCTCTTCCTCC 59.222 55.000 0.00 0.00 0.00 4.30
972 1050 0.103876 ACCAAACCCCTCTTCCTCCT 60.104 55.000 0.00 0.00 0.00 3.69
978 1056 2.131067 CCCTCTTCCTCCTCGCCTC 61.131 68.421 0.00 0.00 0.00 4.70
979 1057 1.076339 CCTCTTCCTCCTCGCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
980 1058 1.106944 CCTCTTCCTCCTCGCCTCTC 61.107 65.000 0.00 0.00 0.00 3.20
981 1059 1.076632 TCTTCCTCCTCGCCTCTCC 60.077 63.158 0.00 0.00 0.00 3.71
982 1060 2.042843 TTCCTCCTCGCCTCTCCC 60.043 66.667 0.00 0.00 0.00 4.30
983 1061 3.680920 TTCCTCCTCGCCTCTCCCC 62.681 68.421 0.00 0.00 0.00 4.81
985 1063 4.150454 CTCCTCGCCTCTCCCCCT 62.150 72.222 0.00 0.00 0.00 4.79
986 1064 4.144727 TCCTCGCCTCTCCCCCTC 62.145 72.222 0.00 0.00 0.00 4.30
1307 1391 2.716017 GGTGAGCCTCCTCCGTCAG 61.716 68.421 0.00 0.00 37.29 3.51
1308 1392 1.979693 GTGAGCCTCCTCCGTCAGT 60.980 63.158 0.00 0.00 37.29 3.41
1316 1400 2.644676 CTCCTCCGTCAGTAGTGATCA 58.355 52.381 2.99 0.00 34.36 2.92
1342 1426 1.135083 GGAACGCTAGCTTCTAGTGCA 60.135 52.381 13.93 0.00 0.00 4.57
1508 1595 8.000709 AGATATGGAATTGCATCTAAGGTCAAA 58.999 33.333 16.40 0.00 0.00 2.69
1519 1606 6.566753 GCATCTAAGGTCAAACTCAAAGTGTC 60.567 42.308 0.00 0.00 0.00 3.67
1672 1793 3.684788 ACTGGCTATTGTTGTCATTCGAC 59.315 43.478 0.00 0.00 42.93 4.20
1698 2858 3.834610 CTTGCAGCAGAAAATCAAGAGG 58.165 45.455 0.00 0.00 37.03 3.69
1712 2874 7.798596 AAATCAAGAGGACTGTTATGCATAG 57.201 36.000 6.50 0.00 0.00 2.23
1716 2878 3.452264 AGAGGACTGTTATGCATAGCACA 59.548 43.478 18.14 13.85 43.04 4.57
1717 2879 4.080919 AGAGGACTGTTATGCATAGCACAA 60.081 41.667 18.14 0.00 43.04 3.33
1736 2898 5.735922 GCACAATGCCTTTCAGTTTGTAGAA 60.736 40.000 0.00 0.00 37.42 2.10
1737 2899 5.687285 CACAATGCCTTTCAGTTTGTAGAAC 59.313 40.000 0.00 0.00 29.48 3.01
1794 2959 8.589335 TCCTATCAGATAAATAAACTGAACGC 57.411 34.615 0.00 0.00 42.55 4.84
1801 2966 1.732941 ATAAACTGAACGCCGCATCA 58.267 45.000 0.00 0.00 0.00 3.07
1818 2983 4.033817 CGCATCATTTTGGTGTTTGTTTGT 59.966 37.500 0.00 0.00 29.39 2.83
1872 3040 9.729281 AGACTAATTTAACCCGTCATTTTTCTA 57.271 29.630 0.00 0.00 0.00 2.10
1882 3050 9.990360 AACCCGTCATTTTTCTATTTATTGTTT 57.010 25.926 0.00 0.00 0.00 2.83
1883 3051 9.418045 ACCCGTCATTTTTCTATTTATTGTTTG 57.582 29.630 0.00 0.00 0.00 2.93
1884 3052 9.632807 CCCGTCATTTTTCTATTTATTGTTTGA 57.367 29.630 0.00 0.00 0.00 2.69
1960 3134 9.781834 TTTTTAATCTTGTGTACTTGTGAGTTG 57.218 29.630 0.00 0.00 37.33 3.16
1961 3135 8.500753 TTTAATCTTGTGTACTTGTGAGTTGT 57.499 30.769 0.00 0.00 37.33 3.32
1962 3136 5.991328 ATCTTGTGTACTTGTGAGTTGTG 57.009 39.130 0.00 0.00 37.33 3.33
1963 3137 5.079689 TCTTGTGTACTTGTGAGTTGTGA 57.920 39.130 0.00 0.00 37.33 3.58
1982 3156 4.278170 TGTGACCTCACTTTTTATGCCTTG 59.722 41.667 6.97 0.00 46.55 3.61
2036 3210 3.502211 CACACGCTCCAGGTAAATTTCTT 59.498 43.478 0.00 0.00 0.00 2.52
2097 3275 8.410141 CGTAAAATGCATTCCCTATTTTCCTTA 58.590 33.333 13.38 0.18 36.02 2.69
2115 3293 8.584063 TTTCCTTATACCATTTTGTAACCCTC 57.416 34.615 0.00 0.00 0.00 4.30
2185 3363 6.640518 TGGGAAATCTGTATCTGTTGTCTAC 58.359 40.000 0.00 0.00 0.00 2.59
2254 3432 6.663523 CCTGGGAGTTATAATTGGTTCAGTTT 59.336 38.462 0.00 0.00 0.00 2.66
2255 3433 7.362920 CCTGGGAGTTATAATTGGTTCAGTTTG 60.363 40.741 0.00 0.00 0.00 2.93
2256 3434 7.007723 TGGGAGTTATAATTGGTTCAGTTTGT 58.992 34.615 0.00 0.00 0.00 2.83
2257 3435 7.507616 TGGGAGTTATAATTGGTTCAGTTTGTT 59.492 33.333 0.00 0.00 0.00 2.83
2289 3470 3.678056 TGGGTGTACACTGATCTTGTC 57.322 47.619 24.55 5.35 0.00 3.18
2295 3476 5.325494 GTGTACACTGATCTTGTCTACTCG 58.675 45.833 18.92 0.00 0.00 4.18
2303 3484 2.762745 TCTTGTCTACTCGGTTTTGGC 58.237 47.619 0.00 0.00 0.00 4.52
2343 3524 2.265589 TCATGGACTATGCATGCTGG 57.734 50.000 20.33 11.04 44.48 4.85
2347 3528 3.084536 TGGACTATGCATGCTGGAAAA 57.915 42.857 20.33 0.00 0.00 2.29
2388 3571 6.946340 TGATTTGTATGTGGAGTGATGTAGT 58.054 36.000 0.00 0.00 0.00 2.73
2389 3572 6.818142 TGATTTGTATGTGGAGTGATGTAGTG 59.182 38.462 0.00 0.00 0.00 2.74
2416 3599 3.738282 GCCTAGCTATCACTCAATGTTCG 59.262 47.826 0.00 0.00 0.00 3.95
2420 3603 7.371159 CCTAGCTATCACTCAATGTTCGATTA 58.629 38.462 0.00 0.00 0.00 1.75
2917 4115 5.872963 TGCTCTGAATGGTATGCTTATGAT 58.127 37.500 0.00 0.00 0.00 2.45
3124 4330 4.012374 CCACATTGTCCTATGGCCATATC 58.988 47.826 25.62 17.97 0.00 1.63
3204 4424 6.648725 TGGTGACTTGTTTCCTTTTTCAAAAG 59.351 34.615 5.21 5.21 43.82 2.27
3328 4598 4.162509 AGGTTGCTAAGAATGTACTCCCTC 59.837 45.833 0.00 0.00 0.00 4.30
3329 4599 4.162509 GGTTGCTAAGAATGTACTCCCTCT 59.837 45.833 0.00 0.00 0.00 3.69
3332 4602 4.402793 TGCTAAGAATGTACTCCCTCTGTC 59.597 45.833 0.00 0.00 0.00 3.51
3334 4604 2.379972 AGAATGTACTCCCTCTGTCCG 58.620 52.381 0.00 0.00 0.00 4.79
3335 4605 1.409427 GAATGTACTCCCTCTGTCCGG 59.591 57.143 0.00 0.00 0.00 5.14
3343 4613 2.766828 CTCCCTCTGTCCGGAAATACTT 59.233 50.000 5.23 0.00 0.00 2.24
3344 4614 2.500098 TCCCTCTGTCCGGAAATACTTG 59.500 50.000 5.23 0.00 0.00 3.16
3345 4615 2.236395 CCCTCTGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
3346 4616 3.522553 CCTCTGTCCGGAAATACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
3368 4680 7.735917 TGTCCGAGGAATGAATGTATTTAGAT 58.264 34.615 0.00 0.00 0.00 1.98
3369 4681 7.657354 TGTCCGAGGAATGAATGTATTTAGATG 59.343 37.037 0.00 0.00 0.00 2.90
3412 4862 9.436957 ACATCCATTTATATCCATTTCTACGAC 57.563 33.333 0.00 0.00 0.00 4.34
3413 4863 9.435688 CATCCATTTATATCCATTTCTACGACA 57.564 33.333 0.00 0.00 0.00 4.35
3415 4865 9.489084 TCCATTTATATCCATTTCTACGACAAG 57.511 33.333 0.00 0.00 0.00 3.16
3422 4898 7.787725 ATCCATTTCTACGACAAGTATTTCC 57.212 36.000 0.00 0.00 34.34 3.13
3424 4900 5.006358 CCATTTCTACGACAAGTATTTCCGG 59.994 44.000 0.00 0.00 34.34 5.14
3450 4926 6.781507 ACGGAGGGAGTAGTTATTATAAGCTT 59.218 38.462 3.48 3.48 0.00 3.74
3671 5155 1.485480 TCTTGTGGGAACGTTGGTACA 59.515 47.619 5.00 4.69 0.00 2.90
3691 5175 6.492087 GGTACAATCTCTATAGCTGAGAAGGT 59.508 42.308 6.36 9.49 42.84 3.50
3724 5208 4.742438 TTTTCTTCGAAAGGAACCGATG 57.258 40.909 0.00 0.00 34.58 3.84
3725 5209 3.671008 TTCTTCGAAAGGAACCGATGA 57.329 42.857 0.00 0.00 37.25 2.92
3726 5210 2.955614 TCTTCGAAAGGAACCGATGAC 58.044 47.619 0.00 0.00 35.18 3.06
3727 5211 2.000447 CTTCGAAAGGAACCGATGACC 59.000 52.381 0.00 0.00 34.58 4.02
3728 5212 0.970640 TCGAAAGGAACCGATGACCA 59.029 50.000 0.00 0.00 0.00 4.02
3729 5213 1.345089 TCGAAAGGAACCGATGACCAA 59.655 47.619 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 71 5.982890 AAAATGATGATTTCCTGTCCGTT 57.017 34.783 0.00 0.00 30.02 4.44
90 92 6.607689 ACGATGATTTGCGTATTTGAGAAAA 58.392 32.000 0.00 0.00 39.21 2.29
91 93 6.128418 TGACGATGATTTGCGTATTTGAGAAA 60.128 34.615 0.00 0.00 41.34 2.52
92 94 5.350091 TGACGATGATTTGCGTATTTGAGAA 59.650 36.000 0.00 0.00 41.34 2.87
93 95 4.867608 TGACGATGATTTGCGTATTTGAGA 59.132 37.500 0.00 0.00 41.34 3.27
94 96 4.957967 GTGACGATGATTTGCGTATTTGAG 59.042 41.667 0.00 0.00 41.34 3.02
95 97 4.629634 AGTGACGATGATTTGCGTATTTGA 59.370 37.500 0.00 0.00 41.34 2.69
96 98 4.897224 AGTGACGATGATTTGCGTATTTG 58.103 39.130 0.00 0.00 41.34 2.32
97 99 5.545658 AAGTGACGATGATTTGCGTATTT 57.454 34.783 0.00 0.00 41.34 1.40
98 100 5.545658 AAAGTGACGATGATTTGCGTATT 57.454 34.783 0.00 0.00 41.34 1.89
99 101 5.545658 AAAAGTGACGATGATTTGCGTAT 57.454 34.783 0.00 0.00 41.34 3.06
100 102 5.351233 AAAAAGTGACGATGATTTGCGTA 57.649 34.783 0.00 0.00 41.34 4.42
101 103 3.896648 AAAAGTGACGATGATTTGCGT 57.103 38.095 0.00 0.00 44.33 5.24
125 127 4.213564 AGTGATGATTTCCTGTGTCTCC 57.786 45.455 0.00 0.00 0.00 3.71
169 171 8.404107 AGTAACTTAGGCTTTTAGCAATTCAA 57.596 30.769 0.00 0.00 44.75 2.69
177 179 6.371825 CAGGTTGGAGTAACTTAGGCTTTTAG 59.628 42.308 0.00 0.00 39.31 1.85
180 182 4.349930 TCAGGTTGGAGTAACTTAGGCTTT 59.650 41.667 0.00 0.00 39.31 3.51
183 185 3.975168 TCAGGTTGGAGTAACTTAGGC 57.025 47.619 0.00 0.00 39.31 3.93
184 186 4.636206 GCAATCAGGTTGGAGTAACTTAGG 59.364 45.833 0.00 0.00 39.31 2.69
185 187 4.636206 GGCAATCAGGTTGGAGTAACTTAG 59.364 45.833 0.00 0.00 39.31 2.18
186 188 4.042311 TGGCAATCAGGTTGGAGTAACTTA 59.958 41.667 0.00 0.00 39.31 2.24
219 226 7.224167 CGTCTAGAAAGGAAAAACAGTAGTTGT 59.776 37.037 0.00 0.00 43.45 3.32
234 241 3.428316 GCACCTCTTCTCGTCTAGAAAGG 60.428 52.174 0.00 10.89 43.66 3.11
302 357 4.047125 ACATGGGCCTCCGGGTTG 62.047 66.667 4.53 0.00 35.24 3.77
322 377 1.080705 GAACTGGCTACGCGTGACT 60.081 57.895 24.59 0.00 0.00 3.41
331 386 1.592400 CGAGGACGGTGAACTGGCTA 61.592 60.000 0.00 0.00 35.72 3.93
344 399 0.167689 ACTAAACGAGTCGCGAGGAC 59.832 55.000 10.24 0.00 46.45 3.85
371 445 3.133946 CTTCCTCCTCGCTAGGCC 58.866 66.667 0.00 0.00 43.31 5.19
397 471 1.342819 CCAGCTCTTTATAGCCTCGCT 59.657 52.381 0.00 0.00 43.86 4.93
428 502 4.142227 GCCGAGAAAGGTATGAGTTGTAGA 60.142 45.833 0.00 0.00 0.00 2.59
429 503 4.113354 GCCGAGAAAGGTATGAGTTGTAG 58.887 47.826 0.00 0.00 0.00 2.74
431 505 2.354805 GGCCGAGAAAGGTATGAGTTGT 60.355 50.000 0.00 0.00 0.00 3.32
511 585 2.219080 ACATCATTGTGGGCACATGA 57.781 45.000 0.00 0.00 41.52 3.07
556 630 2.904866 GCAAGCCGTTGTGGTGGA 60.905 61.111 0.00 0.00 41.21 4.02
565 639 1.754234 GATCCCAATGGCAAGCCGT 60.754 57.895 6.60 2.79 39.42 5.68
566 640 2.492773 GGATCCCAATGGCAAGCCG 61.493 63.158 0.00 0.00 39.42 5.52
576 650 2.355986 CGACACCCGAGGATCCCAA 61.356 63.158 8.55 0.00 41.76 4.12
601 675 0.250295 GCCCAGACTGTAGTGCAACA 60.250 55.000 0.93 0.00 41.43 3.33
698 772 5.336213 CCCATGACATCTTAATAATGCTGCC 60.336 44.000 0.00 0.00 0.00 4.85
715 789 3.118261 TCTTCACCAGCTAATCCCATGAC 60.118 47.826 0.00 0.00 0.00 3.06
731 805 3.111098 CAAAGTTTGTGCTGCTCTTCAC 58.889 45.455 7.48 0.00 0.00 3.18
742 816 8.389603 ACTGAAACATTAATTGCAAAGTTTGTG 58.610 29.630 16.70 7.83 30.23 3.33
746 820 6.420604 CCGACTGAAACATTAATTGCAAAGTT 59.579 34.615 1.71 0.00 0.00 2.66
797 871 3.922171 TTTGAACAAATTTGGCCCTGT 57.078 38.095 21.74 0.00 0.00 4.00
799 873 3.625313 CGTTTTTGAACAAATTTGGCCCT 59.375 39.130 21.74 3.83 0.00 5.19
855 929 2.827322 TGGTGCCAGAATCTGATTTTGG 59.173 45.455 27.11 27.11 44.84 3.28
873 948 3.086282 ACCAAGTTTTGTCGACTTTGGT 58.914 40.909 23.38 23.38 35.26 3.67
877 952 2.021457 CCCACCAAGTTTTGTCGACTT 58.979 47.619 17.92 0.00 37.82 3.01
881 956 1.394618 TTCCCCACCAAGTTTTGTCG 58.605 50.000 0.00 0.00 0.00 4.35
929 1007 3.181329 GGTTTTGGGAATGGGGAAAGAT 58.819 45.455 0.00 0.00 0.00 2.40
969 1047 4.144727 GAGGGGGAGAGGCGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
1110 1188 3.965026 CTCCTCCGACAGGGGCTCA 62.965 68.421 0.94 0.00 43.67 4.26
1316 1400 1.204941 AGAAGCTAGCGTTCCGTGAAT 59.795 47.619 9.55 0.00 0.00 2.57
1322 1406 1.135083 TGCACTAGAAGCTAGCGTTCC 60.135 52.381 9.55 0.00 0.00 3.62
1324 1408 1.732732 CGTGCACTAGAAGCTAGCGTT 60.733 52.381 16.19 4.03 0.00 4.84
1327 1411 0.173708 ACCGTGCACTAGAAGCTAGC 59.826 55.000 16.19 6.62 0.00 3.42
1335 1419 1.588404 CTAAATCGCACCGTGCACTAG 59.412 52.381 22.89 12.48 45.36 2.57
1342 1426 0.108329 CCAGACCTAAATCGCACCGT 60.108 55.000 0.00 0.00 0.00 4.83
1508 1595 3.990469 CAGATGTAAGCGACACTTTGAGT 59.010 43.478 0.00 0.00 42.17 3.41
1519 1606 6.537301 TGGGAAAATAACTACAGATGTAAGCG 59.463 38.462 0.00 0.00 0.00 4.68
1611 1702 4.222114 CAAGTTTTTCTGATGAACCTCGC 58.778 43.478 1.51 0.00 31.02 5.03
1615 1706 6.738114 TGATCACAAGTTTTTCTGATGAACC 58.262 36.000 0.00 0.00 31.02 3.62
1690 2850 5.163269 TGCTATGCATAACAGTCCTCTTGAT 60.163 40.000 8.00 0.00 31.71 2.57
1712 2874 2.825205 ACAAACTGAAAGGCATTGTGC 58.175 42.857 0.00 0.00 44.08 4.57
1716 2878 4.819630 TCGTTCTACAAACTGAAAGGCATT 59.180 37.500 0.00 0.00 39.30 3.56
1717 2879 4.385825 TCGTTCTACAAACTGAAAGGCAT 58.614 39.130 0.00 0.00 39.30 4.40
1794 2959 2.753296 ACAAACACCAAAATGATGCGG 58.247 42.857 0.00 0.00 0.00 5.69
1801 2966 4.469586 AGGAGGACAAACAAACACCAAAAT 59.530 37.500 0.00 0.00 0.00 1.82
1818 2983 3.442076 GGTTCTAAGGTTCTCAGGAGGA 58.558 50.000 0.00 0.00 0.00 3.71
1882 3050 7.379750 TCATGTGAATTGAAGCAATTTCATCA 58.620 30.769 6.82 0.00 44.90 3.07
1883 3051 7.821595 TCATGTGAATTGAAGCAATTTCATC 57.178 32.000 6.82 0.00 44.90 2.92
1884 3052 8.038351 TGATCATGTGAATTGAAGCAATTTCAT 58.962 29.630 6.82 10.85 44.90 2.57
1885 3053 7.379750 TGATCATGTGAATTGAAGCAATTTCA 58.620 30.769 6.82 9.40 43.05 2.69
1898 3066 7.230712 AGCATGTATGTTCATGATCATGTGAAT 59.769 33.333 30.01 22.84 45.41 2.57
1960 3134 4.278419 ACAAGGCATAAAAAGTGAGGTCAC 59.722 41.667 1.60 1.60 46.77 3.67
1961 3135 4.278170 CACAAGGCATAAAAAGTGAGGTCA 59.722 41.667 0.00 0.00 0.00 4.02
1962 3136 4.798574 CACAAGGCATAAAAAGTGAGGTC 58.201 43.478 0.00 0.00 0.00 3.85
1963 3137 3.005791 GCACAAGGCATAAAAAGTGAGGT 59.994 43.478 0.00 0.00 43.97 3.85
1982 3156 1.172180 TGTTAGCAAGGTGCCTGCAC 61.172 55.000 13.75 13.75 46.52 4.57
2097 3275 4.929479 TGCAGAGGGTTACAAAATGGTAT 58.071 39.130 0.00 0.00 0.00 2.73
2185 3363 2.755655 AGTTCCATAGAGAGTCACACGG 59.244 50.000 0.00 0.00 0.00 4.94
2254 3432 2.315176 CACCCAAACCAAGATCCAACA 58.685 47.619 0.00 0.00 0.00 3.33
2255 3433 2.316108 ACACCCAAACCAAGATCCAAC 58.684 47.619 0.00 0.00 0.00 3.77
2256 3434 2.765689 ACACCCAAACCAAGATCCAA 57.234 45.000 0.00 0.00 0.00 3.53
2257 3435 2.443632 TGTACACCCAAACCAAGATCCA 59.556 45.455 0.00 0.00 0.00 3.41
2289 3470 2.068837 TACACGCCAAAACCGAGTAG 57.931 50.000 0.00 0.00 32.19 2.57
2295 3476 4.957759 ACTGATTATACACGCCAAAACC 57.042 40.909 0.00 0.00 0.00 3.27
2303 3484 8.278408 CCATGATCAAAGAACTGATTATACACG 58.722 37.037 0.00 0.00 36.15 4.49
2388 3571 0.468214 AGTGATAGCTAGGCCGCTCA 60.468 55.000 8.56 0.00 41.30 4.26
2389 3572 0.242555 GAGTGATAGCTAGGCCGCTC 59.757 60.000 8.56 14.32 41.30 5.03
3013 4211 3.924918 ACCTGCTAGCACGTATATGAG 57.075 47.619 14.93 0.04 0.00 2.90
3124 4330 6.016777 AGCTTTGACCTGACAACAAATAGAAG 60.017 38.462 0.00 0.00 33.97 2.85
3334 4604 4.766375 TCATTCCTCGGACAAGTATTTCC 58.234 43.478 0.00 0.00 0.00 3.13
3335 4605 6.316390 ACATTCATTCCTCGGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
3343 4613 7.119709 TCTAAATACATTCATTCCTCGGACA 57.880 36.000 0.00 0.00 0.00 4.02
3344 4614 7.657761 ACATCTAAATACATTCATTCCTCGGAC 59.342 37.037 0.00 0.00 0.00 4.79
3345 4615 7.735917 ACATCTAAATACATTCATTCCTCGGA 58.264 34.615 0.00 0.00 0.00 4.55
3346 4616 7.969536 ACATCTAAATACATTCATTCCTCGG 57.030 36.000 0.00 0.00 0.00 4.63
3387 4837 9.435688 TGTCGTAGAAATGGATATAAATGGATG 57.564 33.333 0.00 0.00 39.69 3.51
3390 4840 9.273016 ACTTGTCGTAGAAATGGATATAAATGG 57.727 33.333 0.00 0.00 39.69 3.16
3400 4850 5.006358 CCGGAAATACTTGTCGTAGAAATGG 59.994 44.000 0.00 0.00 39.69 3.16
3404 4854 4.672542 CGTCCGGAAATACTTGTCGTAGAA 60.673 45.833 5.23 0.00 39.69 2.10
3405 4855 3.181507 CGTCCGGAAATACTTGTCGTAGA 60.182 47.826 5.23 0.00 0.00 2.59
3406 4856 3.103738 CGTCCGGAAATACTTGTCGTAG 58.896 50.000 5.23 0.00 0.00 3.51
3409 4859 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
3411 4861 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3412 4862 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3413 4863 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3414 4864 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3415 4865 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3421 4897 0.107017 TAACTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
3422 4898 1.978454 ATAACTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
3424 4900 6.433716 AGCTTATAATAACTACTCCCTCCGTC 59.566 42.308 0.00 0.00 0.00 4.79
3450 4926 6.142139 CAGTTCTATGACAATGACGCAAAAA 58.858 36.000 0.00 0.00 0.00 1.94
3555 5036 3.137484 TGTCCATTGACAGCTACGC 57.863 52.632 0.00 0.00 46.40 4.42
3580 5064 9.619316 GAGTACTACGAGTCTACGATATTAAGA 57.381 37.037 0.00 0.00 37.03 2.10
3584 5068 7.656412 TCAGAGTACTACGAGTCTACGATATT 58.344 38.462 0.00 0.00 37.03 1.28
3671 5155 4.283212 GGCACCTTCTCAGCTATAGAGATT 59.717 45.833 3.21 0.00 41.42 2.40
3683 5167 1.361204 TCAATCCAGGCACCTTCTCA 58.639 50.000 0.00 0.00 0.00 3.27
3691 5175 3.684908 TCGAAGAAAATCAATCCAGGCA 58.315 40.909 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.