Multiple sequence alignment - TraesCS3B01G580800

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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 TraesCS3B01G580800 chr3B 100.000 4604 0 0 1 4604 809614422 809609819 0.000000e+00 8503.0
1 TraesCS3B01G580800 chr3B 85.434 1579 148 43 2211 3734 809833872 809835423 0.000000e+00 1567.0
2 TraesCS3B01G580800 chr3B 95.429 700 29 2 2908 3605 809650518 809649820 0.000000e+00 1112.0
3 TraesCS3B01G580800 chr3B 77.297 1524 265 61 2245 3735 28700645 28702120 0.000000e+00 822.0
4 TraesCS3B01G580800 chr3B 77.014 1527 279 54 2250 3739 823810694 823812185 0.000000e+00 809.0
5 TraesCS3B01G580800 chr3B 92.322 521 28 4 2226 2735 809651486 809650967 0.000000e+00 730.0
6 TraesCS3B01G580800 chr3B 81.196 920 115 26 538 1427 809832020 809832911 0.000000e+00 688.0
7 TraesCS3B01G580800 chr3B 83.540 565 54 22 605 1159 810250601 810251136 4.140000e-135 492.0
8 TraesCS3B01G580800 chr3B 81.988 483 55 15 1760 2211 809833227 809833708 9.350000e-102 381.0
9 TraesCS3B01G580800 chr3B 84.659 352 34 6 4133 4468 809649501 809649154 2.650000e-87 333.0
10 TraesCS3B01G580800 chr3B 97.315 149 4 0 2723 2871 809650670 809650522 2.130000e-63 254.0
11 TraesCS3B01G580800 chr3B 83.401 247 26 11 1995 2232 809652126 809651886 1.000000e-51 215.0
12 TraesCS3B01G580800 chr3B 94.186 86 5 0 2607 2692 809650751 809650666 1.040000e-26 132.0
13 TraesCS3B01G580800 chr3B 92.308 91 3 1 1499 1589 809833126 809833212 4.840000e-25 126.0
14 TraesCS3B01G580800 chr3B 100.000 42 0 0 1459 1500 809833003 809833044 1.370000e-10 78.7
15 TraesCS3B01G580800 chr3D 93.462 3166 125 26 505 3605 602458156 602455008 0.000000e+00 4625.0
16 TraesCS3B01G580800 chr3D 93.987 765 38 5 2844 3605 602376971 602376212 0.000000e+00 1151.0
17 TraesCS3B01G580800 chr3D 86.333 1039 89 28 2236 3237 602356577 602355555 0.000000e+00 1083.0
18 TraesCS3B01G580800 chr3D 90.000 810 64 12 95 900 602461050 602460254 0.000000e+00 1031.0
19 TraesCS3B01G580800 chr3D 90.272 771 63 9 187 954 602379251 602378490 0.000000e+00 998.0
20 TraesCS3B01G580800 chr3D 92.985 670 36 6 2125 2791 602377632 602376971 0.000000e+00 966.0
21 TraesCS3B01G580800 chr3D 82.075 1060 118 37 2403 3434 602443737 602442722 0.000000e+00 839.0
22 TraesCS3B01G580800 chr3D 88.567 691 47 12 505 1194 602477994 602477335 0.000000e+00 809.0
23 TraesCS3B01G580800 chr3D 89.903 515 45 4 3227 3740 602345924 602345416 0.000000e+00 656.0
24 TraesCS3B01G580800 chr3D 91.630 454 22 5 990 1427 602378491 602378038 8.470000e-172 614.0
25 TraesCS3B01G580800 chr3D 84.318 491 42 16 3944 4416 602434571 602434098 9.090000e-122 448.0
26 TraesCS3B01G580800 chr3D 85.579 423 45 13 4185 4604 602333794 602333385 3.290000e-116 429.0
27 TraesCS3B01G580800 chr3D 91.071 280 17 5 134 408 602498515 602498239 5.630000e-99 372.0
28 TraesCS3B01G580800 chr3D 81.720 465 50 16 1760 2200 602357228 602356775 5.670000e-94 355.0
29 TraesCS3B01G580800 chr3D 83.239 352 38 9 4133 4468 602454731 602454385 2.080000e-78 303.0
30 TraesCS3B01G580800 chr3D 85.121 289 37 5 4181 4468 602362776 602362493 1.620000e-74 291.0
31 TraesCS3B01G580800 chr3D 87.266 267 18 5 2161 2411 602444174 602443908 1.620000e-74 291.0
32 TraesCS3B01G580800 chr3D 93.567 171 11 0 505 675 602752724 602752554 5.910000e-64 255.0
33 TraesCS3B01G580800 chr3D 93.567 171 11 0 505 675 603866112 603866282 5.910000e-64 255.0
34 TraesCS3B01G580800 chr3D 92.157 102 3 3 95 195 602381794 602381697 6.210000e-29 139.0
35 TraesCS3B01G580800 chr3D 92.222 90 7 0 3449 3538 602442734 602442645 1.340000e-25 128.0
36 TraesCS3B01G580800 chr3D 95.522 67 3 0 1459 1525 602357360 602357294 1.750000e-19 108.0
37 TraesCS3B01G580800 chr3D 77.604 192 30 2 1237 1427 602357653 602357474 2.270000e-18 104.0
38 TraesCS3B01G580800 chr3D 86.813 91 9 3 3980 4068 602344848 602344759 1.050000e-16 99.0
39 TraesCS3B01G580800 chr3D 98.077 52 1 0 1 52 602382378 602382327 1.760000e-14 91.6
40 TraesCS3B01G580800 chr3D 98.000 50 1 0 1 50 602461612 602461563 2.280000e-13 87.9
41 TraesCS3B01G580800 chr3D 100.000 28 0 0 95 122 602498542 602498515 8.000000e-03 52.8
42 TraesCS3B01G580800 chr3A 90.579 2420 160 35 2231 4604 732067495 732065098 0.000000e+00 3144.0
43 TraesCS3B01G580800 chr3A 92.112 1965 108 15 1777 3706 732300905 732302857 0.000000e+00 2726.0
44 TraesCS3B01G580800 chr3A 90.430 1139 45 24 505 1579 732299770 732300908 0.000000e+00 1441.0
45 TraesCS3B01G580800 chr3A 81.793 736 83 28 483 1201 732069267 732068566 1.860000e-158 569.0
46 TraesCS3B01G580800 chr3A 80.899 267 26 9 1760 2003 732067912 732067648 2.190000e-43 187.0
47 TraesCS3B01G580800 chr3A 94.030 67 4 0 1459 1525 732068050 732067984 8.150000e-18 102.0
48 TraesCS3B01G580800 chr7B 89.133 727 59 11 484 1201 356984522 356983807 0.000000e+00 887.0
49 TraesCS3B01G580800 chr7B 82.787 122 14 6 95 215 490891490 490891605 8.150000e-18 102.0
50 TraesCS3B01G580800 chr7B 80.800 125 17 3 95 218 301606998 301607116 1.760000e-14 91.6
51 TraesCS3B01G580800 chrUn 93.567 171 11 0 505 675 276044634 276044464 5.910000e-64 255.0
52 TraesCS3B01G580800 chrUn 83.886 211 31 2 3732 3940 136518075 136517866 1.010000e-46 198.0
53 TraesCS3B01G580800 chr6D 85.377 212 31 0 3737 3948 454270585 454270796 2.160000e-53 220.0
54 TraesCS3B01G580800 chr7A 86.432 199 27 0 3743 3941 82509021 82509219 7.760000e-53 219.0
55 TraesCS3B01G580800 chr7A 87.143 140 17 1 219 357 35007571 35007710 1.710000e-34 158.0
56 TraesCS3B01G580800 chr1B 85.024 207 30 1 3737 3942 527769841 527770047 4.670000e-50 209.0
57 TraesCS3B01G580800 chr2D 84.951 206 27 4 3739 3942 317234524 317234727 6.040000e-49 206.0
58 TraesCS3B01G580800 chr2D 80.992 121 16 5 97 216 77602626 77602740 6.340000e-14 89.8
59 TraesCS3B01G580800 chr2D 79.487 117 15 4 248 364 324605293 324605186 1.780000e-09 75.0
60 TraesCS3B01G580800 chr4B 83.732 209 32 2 3735 3942 30975016 30974809 3.630000e-46 196.0
61 TraesCS3B01G580800 chr6B 83.575 207 33 1 3737 3942 475659245 475659451 4.700000e-45 193.0
62 TraesCS3B01G580800 chr6B 85.484 124 11 3 95 217 93985284 93985401 6.260000e-24 122.0
63 TraesCS3B01G580800 chr1A 83.173 208 35 0 3734 3941 274330968 274330761 1.690000e-44 191.0
64 TraesCS3B01G580800 chr2A 79.487 117 15 4 248 364 394010630 394010737 1.780000e-09 75.0


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 TraesCS3B01G580800 chr3B 809609819 809614422 4603 True 8503.000000 8503 100.000000 1 4604 1 chr3B.!!$R1 4603
1 TraesCS3B01G580800 chr3B 28700645 28702120 1475 False 822.000000 822 77.297000 2245 3735 1 chr3B.!!$F1 1490
2 TraesCS3B01G580800 chr3B 823810694 823812185 1491 False 809.000000 809 77.014000 2250 3739 1 chr3B.!!$F3 1489
3 TraesCS3B01G580800 chr3B 809832020 809835423 3403 False 568.140000 1567 88.185200 538 3734 5 chr3B.!!$F4 3196
4 TraesCS3B01G580800 chr3B 810250601 810251136 535 False 492.000000 492 83.540000 605 1159 1 chr3B.!!$F2 554
5 TraesCS3B01G580800 chr3B 809649154 809652126 2972 True 462.666667 1112 91.218667 1995 4468 6 chr3B.!!$R2 2473
6 TraesCS3B01G580800 chr3D 602454385 602461612 7227 True 1511.725000 4625 91.175250 1 4468 4 chr3D.!!$R10 4467
7 TraesCS3B01G580800 chr3D 602477335 602477994 659 True 809.000000 809 88.567000 505 1194 1 chr3D.!!$R4 689
8 TraesCS3B01G580800 chr3D 602376212 602382378 6166 True 659.933333 1151 93.184667 1 3605 6 chr3D.!!$R8 3604
9 TraesCS3B01G580800 chr3D 602442645 602444174 1529 True 419.333333 839 87.187667 2161 3538 3 chr3D.!!$R9 1377
10 TraesCS3B01G580800 chr3D 602355555 602357653 2098 True 412.500000 1083 85.294750 1237 3237 4 chr3D.!!$R7 2000
11 TraesCS3B01G580800 chr3D 602344759 602345924 1165 True 377.500000 656 88.358000 3227 4068 2 chr3D.!!$R6 841
12 TraesCS3B01G580800 chr3A 732299770 732302857 3087 False 2083.500000 2726 91.271000 505 3706 2 chr3A.!!$F1 3201
13 TraesCS3B01G580800 chr3A 732065098 732069267 4169 True 1000.500000 3144 86.825250 483 4604 4 chr3A.!!$R1 4121
14 TraesCS3B01G580800 chr7B 356983807 356984522 715 True 887.000000 887 89.133000 484 1201 1 chr7B.!!$R1 717

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
670 6118 0.179084 TTGTCGAATCGGATGGGAGC 60.179 55.0 1.76 0.0 0.00 4.70 F
1202 6677 0.471191 CCTCCTGCATGCCTGTCATA 59.529 55.0 16.68 0.0 33.19 2.15 F
1601 7560 0.689745 ATGCGAGCTAGTAACCCCCA 60.690 55.0 0.00 0.0 0.00 4.96 F
2652 9688 0.317160 TAGTGGTCTGAGTTGCGTGG 59.683 55.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 7713 0.475828 AACCTCAGGCCCCTAACAGT 60.476 55.0 0.0 0.0 0.0 3.55 R
2639 9675 0.944386 GCTTTTCCACGCAACTCAGA 59.056 50.0 0.0 0.0 0.0 3.27 R
3280 10670 0.321210 TATGCAAGACCACACCACGG 60.321 55.0 0.0 0.0 0.0 4.94 R
3886 11345 0.112412 GGCTCCTCCCCAACTTTTCA 59.888 55.0 0.0 0.0 0.0 2.69 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 44 1.810151 TGGCCGCTAAAGCTAAAACTG 59.190 47.619 0.00 0.00 39.32 3.16
52 53 6.567701 CGCTAAAGCTAAAACTGATGTGGAAA 60.568 38.462 0.00 0.00 39.32 3.13
54 55 7.814587 GCTAAAGCTAAAACTGATGTGGAAATT 59.185 33.333 0.00 0.00 38.21 1.82
57 58 8.635765 AAGCTAAAACTGATGTGGAAATTAGA 57.364 30.769 0.00 0.00 0.00 2.10
59 60 6.969473 GCTAAAACTGATGTGGAAATTAGAGC 59.031 38.462 0.00 0.00 0.00 4.09
60 61 7.148171 GCTAAAACTGATGTGGAAATTAGAGCT 60.148 37.037 0.00 0.00 0.00 4.09
61 62 9.383519 CTAAAACTGATGTGGAAATTAGAGCTA 57.616 33.333 0.00 0.00 0.00 3.32
62 63 7.856145 AAACTGATGTGGAAATTAGAGCTAG 57.144 36.000 0.00 0.00 0.00 3.42
64 65 5.163258 ACTGATGTGGAAATTAGAGCTAGGG 60.163 44.000 0.00 0.00 0.00 3.53
66 67 5.428457 TGATGTGGAAATTAGAGCTAGGGAA 59.572 40.000 0.00 0.00 0.00 3.97
69 70 5.066593 GTGGAAATTAGAGCTAGGGAATGG 58.933 45.833 0.00 0.00 0.00 3.16
70 71 4.975147 TGGAAATTAGAGCTAGGGAATGGA 59.025 41.667 0.00 0.00 0.00 3.41
71 72 5.431731 TGGAAATTAGAGCTAGGGAATGGAA 59.568 40.000 0.00 0.00 0.00 3.53
73 74 7.007116 GGAAATTAGAGCTAGGGAATGGAAAT 58.993 38.462 0.00 0.00 0.00 2.17
74 75 7.507277 GGAAATTAGAGCTAGGGAATGGAAATT 59.493 37.037 0.00 0.00 0.00 1.82
75 76 9.574516 GAAATTAGAGCTAGGGAATGGAAATTA 57.425 33.333 0.00 0.00 0.00 1.40
76 77 9.579932 AAATTAGAGCTAGGGAATGGAAATTAG 57.420 33.333 0.00 0.00 0.00 1.73
77 78 7.931015 TTAGAGCTAGGGAATGGAAATTAGA 57.069 36.000 0.00 0.00 0.00 2.10
79 80 4.979335 AGCTAGGGAATGGAAATTAGAGC 58.021 43.478 0.00 0.00 0.00 4.09
80 81 4.662650 AGCTAGGGAATGGAAATTAGAGCT 59.337 41.667 0.00 0.00 0.00 4.09
83 84 6.998673 GCTAGGGAATGGAAATTAGAGCTAAA 59.001 38.462 0.00 0.00 0.00 1.85
169 662 5.795079 TCTATTGTTTGGTCTATAGGGGGA 58.205 41.667 0.00 0.00 0.00 4.81
170 663 4.790718 ATTGTTTGGTCTATAGGGGGAC 57.209 45.455 0.00 0.00 0.00 4.46
178 671 4.090819 GGTCTATAGGGGGACTGAGAATC 58.909 52.174 0.00 0.00 33.46 2.52
184 677 3.959920 AGGGGGACTGAGAATCCATAAT 58.040 45.455 0.00 0.00 38.06 1.28
185 678 5.106631 AGGGGGACTGAGAATCCATAATA 57.893 43.478 0.00 0.00 38.06 0.98
186 679 5.486332 AGGGGGACTGAGAATCCATAATAA 58.514 41.667 0.00 0.00 38.06 1.40
220 3167 4.079970 TGTACTTGAGACTCCAACTCGAT 58.920 43.478 0.00 0.00 37.22 3.59
245 3192 7.510675 TTGGAAGGGATCTATTTTAGTGAGT 57.489 36.000 0.00 0.00 0.00 3.41
320 3268 2.359531 TCAATTCCCACGAACCAACAAC 59.640 45.455 0.00 0.00 0.00 3.32
326 3274 2.548904 CCCACGAACCAACAACGAAATA 59.451 45.455 0.00 0.00 0.00 1.40
330 3278 4.210537 CACGAACCAACAACGAAATAGAGT 59.789 41.667 0.00 0.00 0.00 3.24
408 3357 2.022934 GGAGTAGGCTTAGTACGCTGT 58.977 52.381 0.00 0.00 0.00 4.40
456 3406 5.125578 CCAAAAGGGACTGCCTTCTTATAAC 59.874 44.000 1.71 0.00 40.86 1.89
459 3409 5.514500 AGGGACTGCCTTCTTATAACAAA 57.486 39.130 0.00 0.00 37.18 2.83
461 3411 6.311735 AGGGACTGCCTTCTTATAACAAAAA 58.688 36.000 0.00 0.00 37.18 1.94
498 3448 2.258013 CGAACGGGCCTGCTTTCAA 61.258 57.895 12.89 0.00 0.00 2.69
668 6116 0.464036 CCTTGTCGAATCGGATGGGA 59.536 55.000 1.76 0.00 0.00 4.37
669 6117 1.539065 CCTTGTCGAATCGGATGGGAG 60.539 57.143 1.76 0.00 0.00 4.30
670 6118 0.179084 TTGTCGAATCGGATGGGAGC 60.179 55.000 1.76 0.00 0.00 4.70
767 6230 0.649475 CGAGTACGAGTCCAGGTACG 59.351 60.000 0.00 0.00 42.86 3.67
969 6432 2.826337 TCCATGGACGAGATGGAGG 58.174 57.895 11.44 0.00 43.71 4.30
1080 6547 6.096987 ACATAGTAGATGAAGTTGACACCGAT 59.903 38.462 0.00 0.00 0.00 4.18
1111 6580 0.541998 TGAAGAGGAGGCGAACAGGA 60.542 55.000 0.00 0.00 0.00 3.86
1201 6676 1.226542 CCTCCTGCATGCCTGTCAT 59.773 57.895 16.68 0.00 35.31 3.06
1202 6677 0.471191 CCTCCTGCATGCCTGTCATA 59.529 55.000 16.68 0.00 33.19 2.15
1203 6678 1.073444 CCTCCTGCATGCCTGTCATAT 59.927 52.381 16.68 0.00 33.19 1.78
1204 6679 2.303890 CCTCCTGCATGCCTGTCATATA 59.696 50.000 16.68 0.00 33.19 0.86
1205 6680 3.597255 CTCCTGCATGCCTGTCATATAG 58.403 50.000 16.68 1.79 33.19 1.31
1421 7112 4.192317 GGCTAGTCCCTTGTAATGAAGTG 58.808 47.826 0.00 0.00 0.00 3.16
1601 7560 0.689745 ATGCGAGCTAGTAACCCCCA 60.690 55.000 0.00 0.00 0.00 4.96
1686 7645 2.648059 CCTCAAATCATCAGGACCACC 58.352 52.381 0.00 0.00 0.00 4.61
1687 7646 2.648059 CTCAAATCATCAGGACCACCC 58.352 52.381 0.00 0.00 36.73 4.61
1738 7697 4.619973 CATCTTGGCTAGTCTGATCACTC 58.380 47.826 0.00 0.00 0.00 3.51
1754 7713 9.868160 TCTGATCACTCTTTAGGATATCACTTA 57.132 33.333 4.83 0.00 0.00 2.24
1927 7926 1.507141 CCCGAGAGTTGTTGGTGCAC 61.507 60.000 8.80 8.80 0.00 4.57
1992 8003 1.775869 GCAAGGAGCAAGCTTGTTTC 58.224 50.000 26.55 20.24 44.79 2.78
2154 8185 0.965363 AATTTCCTCGGGTGCGCAAT 60.965 50.000 14.00 0.00 0.00 3.56
2156 8187 1.175983 TTTCCTCGGGTGCGCAATTT 61.176 50.000 14.00 0.00 0.00 1.82
2201 8233 7.278868 GTGCAACTACTTGAATCAGTAATAGCT 59.721 37.037 0.00 0.00 0.00 3.32
2261 9050 4.650734 TGTCCACTGCATGTTATTCTCAA 58.349 39.130 0.00 0.00 0.00 3.02
2465 9455 9.736023 AAGTTTAAAACTCTGCTCAGTATTTTG 57.264 29.630 16.53 0.00 41.91 2.44
2466 9456 7.862873 AGTTTAAAACTCTGCTCAGTATTTTGC 59.137 33.333 16.53 10.59 37.02 3.68
2467 9457 7.510549 TTAAAACTCTGCTCAGTATTTTGCT 57.489 32.000 16.53 2.77 32.79 3.91
2470 9460 5.368256 ACTCTGCTCAGTATTTTGCTTTG 57.632 39.130 0.00 0.00 0.00 2.77
2485 9487 5.669164 TTGCTTTGTTTTTGGGACTAACT 57.331 34.783 0.00 0.00 0.00 2.24
2515 9519 3.999663 GGTCTTGACAGTGGATTGAAGAG 59.000 47.826 3.08 0.00 0.00 2.85
2639 9675 6.724905 ACTTGTCTGTCCTACTATTTAGTGGT 59.275 38.462 0.45 0.00 37.10 4.16
2644 9680 6.829298 TCTGTCCTACTATTTAGTGGTCTGAG 59.171 42.308 0.45 0.00 37.10 3.35
2652 9688 0.317160 TAGTGGTCTGAGTTGCGTGG 59.683 55.000 0.00 0.00 0.00 4.94
2717 9753 1.484240 ACATTCCTCTGAGCCTAGCAC 59.516 52.381 0.00 0.00 0.00 4.40
2901 10252 2.409870 GGAAGCTGGTCAATGGGCG 61.410 63.158 0.00 0.00 0.00 6.13
3127 10509 1.278127 TCGTTGGGATTGGAGGAAGAC 59.722 52.381 0.00 0.00 0.00 3.01
3178 10563 8.506437 CACAGACTTTCTATTTGCTGTTTCATA 58.494 33.333 0.00 0.00 34.66 2.15
3280 10670 4.267349 TCAGCAAGGAAGTAAGTACACC 57.733 45.455 0.00 0.00 0.00 4.16
3281 10671 3.007614 TCAGCAAGGAAGTAAGTACACCC 59.992 47.826 0.00 0.00 0.00 4.61
3542 10951 0.108329 AGGTATGTGCAGTACGCCAC 60.108 55.000 10.75 10.75 41.33 5.01
3620 11062 0.107459 TAGTGTGTGTGTTGCTGGCA 60.107 50.000 0.00 0.00 0.00 4.92
3631 11073 1.298157 TTGCTGGCATGCGTAGTGTC 61.298 55.000 12.44 0.00 35.36 3.67
3708 11160 3.252400 CACGTATGGTTAAACGCCTACA 58.748 45.455 0.00 0.00 42.74 2.74
3748 11206 4.248174 TGTGATTTGATTATGGGCCAGA 57.752 40.909 13.78 3.79 0.00 3.86
3786 11245 4.668138 AAAAATAAGCTACCTGTCCCCA 57.332 40.909 0.00 0.00 0.00 4.96
3787 11246 4.668138 AAAATAAGCTACCTGTCCCCAA 57.332 40.909 0.00 0.00 0.00 4.12
3795 11254 4.083565 GCTACCTGTCCCCAACATAAAAA 58.916 43.478 0.00 0.00 37.23 1.94
3817 11276 1.047801 AAGCCGCTCCCAAATTTTGT 58.952 45.000 8.26 0.00 0.00 2.83
3860 11319 3.206964 GGCATAACTAGTTCAGAAGCCC 58.793 50.000 12.39 0.95 33.68 5.19
3879 11338 0.820891 CCAATGAATGAGGGAGGCGG 60.821 60.000 0.00 0.00 0.00 6.13
3886 11345 4.021925 GAGGGAGGCGGCTTGTGT 62.022 66.667 14.76 0.00 0.00 3.72
3887 11346 4.335647 AGGGAGGCGGCTTGTGTG 62.336 66.667 14.76 0.00 0.00 3.82
3893 11352 0.751643 AGGCGGCTTGTGTGAAAAGT 60.752 50.000 5.25 0.00 0.00 2.66
3898 11357 1.202521 GGCTTGTGTGAAAAGTTGGGG 60.203 52.381 0.00 0.00 0.00 4.96
3911 11370 1.229820 TTGGGGAGGAGCCAGCTTA 60.230 57.895 0.00 0.00 38.95 3.09
3912 11371 0.624500 TTGGGGAGGAGCCAGCTTAT 60.625 55.000 0.00 0.00 38.95 1.73
3959 11418 3.195661 CCTACGTATCCTTGGAGCAAAC 58.804 50.000 0.00 0.00 0.00 2.93
3967 11426 4.842531 TCCTTGGAGCAAACTGATCATA 57.157 40.909 0.00 0.00 33.81 2.15
3968 11427 5.378230 TCCTTGGAGCAAACTGATCATAT 57.622 39.130 0.00 0.00 33.81 1.78
3969 11428 5.759059 TCCTTGGAGCAAACTGATCATATT 58.241 37.500 0.00 0.00 33.81 1.28
3970 11429 6.899089 TCCTTGGAGCAAACTGATCATATTA 58.101 36.000 0.00 0.00 33.81 0.98
4004 11997 3.899980 ACTTAAACCGTGTCCCTACTTCT 59.100 43.478 0.00 0.00 0.00 2.85
4041 12034 9.705290 ATACATTTGATTTGGTTTGTAAGGAAC 57.295 29.630 0.00 0.00 0.00 3.62
4130 12149 9.495754 CTTTCAGCAGCTAGAACATTTATAAAC 57.504 33.333 0.00 0.00 0.00 2.01
4271 12306 3.584406 AGTAGCTCAACACAGTAGCAG 57.416 47.619 0.00 0.00 38.75 4.24
4513 12548 5.350914 TGTGTTTGAACTTTGGAAATGCAAG 59.649 36.000 0.00 0.00 0.00 4.01
4599 12634 4.703897 TCCCAACTGTAGAGTGAACTTTG 58.296 43.478 0.00 0.00 30.61 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.552870 TCCCTAGCTCTAATTTCCACATC 57.447 43.478 0.00 0.00 0.00 3.06
52 53 8.511748 TCTAATTTCCATTCCCTAGCTCTAAT 57.488 34.615 0.00 0.00 0.00 1.73
54 55 6.014156 GCTCTAATTTCCATTCCCTAGCTCTA 60.014 42.308 0.00 0.00 0.00 2.43
56 57 5.000591 GCTCTAATTTCCATTCCCTAGCTC 58.999 45.833 0.00 0.00 0.00 4.09
57 58 4.662650 AGCTCTAATTTCCATTCCCTAGCT 59.337 41.667 0.00 0.00 0.00 3.32
59 60 7.174080 GCTTTAGCTCTAATTTCCATTCCCTAG 59.826 40.741 0.00 0.00 38.21 3.02
60 61 6.998673 GCTTTAGCTCTAATTTCCATTCCCTA 59.001 38.462 0.00 0.00 38.21 3.53
61 62 5.830457 GCTTTAGCTCTAATTTCCATTCCCT 59.170 40.000 0.00 0.00 38.21 4.20
62 63 6.078202 GCTTTAGCTCTAATTTCCATTCCC 57.922 41.667 0.00 0.00 38.21 3.97
79 80 6.844097 TTACCCCCATTGTTTTAGCTTTAG 57.156 37.500 0.00 0.00 0.00 1.85
80 81 7.800300 AATTACCCCCATTGTTTTAGCTTTA 57.200 32.000 0.00 0.00 0.00 1.85
83 84 6.737608 TCTAATTACCCCCATTGTTTTAGCT 58.262 36.000 0.00 0.00 0.00 3.32
86 87 6.737608 AGCTCTAATTACCCCCATTGTTTTA 58.262 36.000 0.00 0.00 0.00 1.52
89 90 4.881157 AGCTCTAATTACCCCCATTGTT 57.119 40.909 0.00 0.00 0.00 2.83
91 92 4.263506 CCCTAGCTCTAATTACCCCCATTG 60.264 50.000 0.00 0.00 0.00 2.82
92 93 3.916989 CCCTAGCTCTAATTACCCCCATT 59.083 47.826 0.00 0.00 0.00 3.16
93 94 3.146055 TCCCTAGCTCTAATTACCCCCAT 59.854 47.826 0.00 0.00 0.00 4.00
161 654 3.663298 ATGGATTCTCAGTCCCCCTAT 57.337 47.619 0.00 0.00 34.76 2.57
186 679 8.697292 GGAGTCTCAAGTACATTACTATTTCCT 58.303 37.037 1.47 0.00 38.26 3.36
200 3147 5.470368 CAAATCGAGTTGGAGTCTCAAGTA 58.530 41.667 17.48 0.00 31.14 2.24
220 3167 7.928873 ACTCACTAAAATAGATCCCTTCCAAA 58.071 34.615 0.00 0.00 0.00 3.28
231 3178 9.886132 GGGTTAAGATTGACTCACTAAAATAGA 57.114 33.333 0.00 0.00 0.00 1.98
232 3179 9.892130 AGGGTTAAGATTGACTCACTAAAATAG 57.108 33.333 0.00 0.00 0.00 1.73
320 3268 9.548208 GAGAATTTGAGGAAAAACTCTATTTCG 57.452 33.333 0.00 0.00 37.51 3.46
326 3274 7.830099 ATGTGAGAATTTGAGGAAAAACTCT 57.170 32.000 0.00 0.00 38.32 3.24
369 3317 9.790344 CCTACTCCTTCTGATTCAATCATAATT 57.210 33.333 0.00 0.00 38.85 1.40
381 3330 4.822896 CGTACTAAGCCTACTCCTTCTGAT 59.177 45.833 0.00 0.00 0.00 2.90
426 3375 2.110011 AGGCAGTCCCTTTTGGTTATGT 59.890 45.455 0.00 0.00 43.06 2.29
462 3412 3.412237 TCGGTCCCGAGATTTCTTTTT 57.588 42.857 3.90 0.00 44.01 1.94
477 3427 4.699522 AAGCAGGCCCGTTCGGTC 62.700 66.667 0.00 0.00 35.94 4.79
479 3429 3.431725 GAAAGCAGGCCCGTTCGG 61.432 66.667 0.00 4.08 0.00 4.30
481 3431 0.109132 CATTGAAAGCAGGCCCGTTC 60.109 55.000 0.00 0.00 0.00 3.95
767 6230 2.021039 GCGAGGCGAGCATCTCATC 61.021 63.158 8.11 0.00 34.19 2.92
1080 6547 4.285517 GCCTCCTCTTCATCCAATCTATCA 59.714 45.833 0.00 0.00 0.00 2.15
1111 6580 1.268625 TCGTGCGTACTTGTGACTGAT 59.731 47.619 1.24 0.00 0.00 2.90
1204 6679 9.523168 GAAGGACAGATGAGTAAGGTATATACT 57.477 37.037 12.54 0.00 36.34 2.12
1205 6680 9.523168 AGAAGGACAGATGAGTAAGGTATATAC 57.477 37.037 4.14 4.14 0.00 1.47
1370 7061 2.579201 CTCAAGGTCGCGGGTGAT 59.421 61.111 6.13 0.00 0.00 3.06
1421 7112 6.578023 ACTGAGCTGAAAGTAATGGATACTC 58.422 40.000 0.00 0.00 44.22 2.59
1625 7584 3.857038 GACTATTGGCGCCCCGGA 61.857 66.667 26.77 7.76 0.00 5.14
1686 7645 3.826157 TGGTAGGCAGTTTCAGAAAATGG 59.174 43.478 21.66 6.87 36.99 3.16
1687 7646 4.520492 AGTGGTAGGCAGTTTCAGAAAATG 59.480 41.667 17.28 17.28 39.31 2.32
1738 7697 8.368668 CCCCTAACAGTAAGTGATATCCTAAAG 58.631 40.741 0.00 0.00 0.00 1.85
1754 7713 0.475828 AACCTCAGGCCCCTAACAGT 60.476 55.000 0.00 0.00 0.00 3.55
1858 7821 4.564372 CACACATTCTGAGATCTTACACGG 59.436 45.833 0.00 0.00 0.00 4.94
1927 7926 7.956943 GGAATGTTTTTAATTGATGAAAAGCCG 59.043 33.333 0.00 0.00 0.00 5.52
2141 8172 1.298157 TGAGAAATTGCGCACCCGAG 61.298 55.000 11.12 0.00 36.29 4.63
2145 8176 4.448732 AGAAATTTTGAGAAATTGCGCACC 59.551 37.500 11.12 0.00 43.01 5.01
2172 8204 3.815401 ACTGATTCAAGTAGTTGCACACC 59.185 43.478 5.35 0.00 33.23 4.16
2201 8233 2.224499 TGCTCTTAGGATTGTGTGTGCA 60.224 45.455 0.00 0.00 0.00 4.57
2261 9050 3.287867 AGCAACATATTACTGCTGCCT 57.712 42.857 0.00 0.00 44.56 4.75
2465 9455 5.068067 TGGTAGTTAGTCCCAAAAACAAAGC 59.932 40.000 0.00 0.00 0.00 3.51
2466 9456 6.702716 TGGTAGTTAGTCCCAAAAACAAAG 57.297 37.500 0.00 0.00 0.00 2.77
2467 9457 7.663043 AATGGTAGTTAGTCCCAAAAACAAA 57.337 32.000 0.00 0.00 0.00 2.83
2470 9460 6.452242 CCAAATGGTAGTTAGTCCCAAAAAC 58.548 40.000 0.00 0.00 0.00 2.43
2515 9519 3.426695 CCATATAGCCTTTAAGCGCATGC 60.427 47.826 11.47 7.91 43.24 4.06
2587 9591 5.719173 TGTGATGCTACTATGCGCATATAA 58.281 37.500 29.09 18.70 46.06 0.98
2639 9675 0.944386 GCTTTTCCACGCAACTCAGA 59.056 50.000 0.00 0.00 0.00 3.27
2644 9680 1.215014 GCCAAGCTTTTCCACGCAAC 61.215 55.000 0.00 0.00 0.00 4.17
2652 9688 4.250080 CTTGGCGCCAAGCTTTTC 57.750 55.556 46.06 11.90 45.38 2.29
2717 9753 5.943416 TGAACAGTACCTGGAAACCATAATG 59.057 40.000 0.00 0.00 35.51 1.90
2901 10252 5.817296 TGATGTACAATGCTGACCTTATCAC 59.183 40.000 0.00 0.00 32.37 3.06
3040 10422 1.192428 ACGGGTTCTCCTCATACACC 58.808 55.000 0.00 0.00 0.00 4.16
3145 10530 6.373774 AGCAAATAGAAAGTCTGTGAATGGAG 59.626 38.462 0.00 0.00 0.00 3.86
3214 10600 5.087323 ACTACAAGGAGAGGTGATCAAAGA 58.913 41.667 0.00 0.00 0.00 2.52
3280 10670 0.321210 TATGCAAGACCACACCACGG 60.321 55.000 0.00 0.00 0.00 4.94
3281 10671 0.796312 GTATGCAAGACCACACCACG 59.204 55.000 0.00 0.00 0.00 4.94
3542 10951 2.998670 TCTGCAATCTTGAGCTTCTTCG 59.001 45.455 0.00 0.00 0.00 3.79
3620 11062 2.066262 CCAAAAGACGACACTACGCAT 58.934 47.619 0.00 0.00 36.70 4.73
3663 11105 6.210784 TGGAGTAGCTAACCTTGCGATATTAT 59.789 38.462 16.01 0.00 35.28 1.28
3708 11160 4.761227 TCACATGCACATACATTCAAGTGT 59.239 37.500 0.00 0.00 34.59 3.55
3795 11254 3.260632 ACAAAATTTGGGAGCGGCTTATT 59.739 39.130 10.71 0.00 34.12 1.40
3801 11260 2.295909 TCTCAACAAAATTTGGGAGCGG 59.704 45.455 18.55 4.04 36.64 5.52
3834 11293 6.712547 GGCTTCTGAACTAGTTATGCCATTAT 59.287 38.462 20.77 0.00 37.91 1.28
3860 11319 0.820891 CCGCCTCCCTCATTCATTGG 60.821 60.000 0.00 0.00 0.00 3.16
3879 11338 1.754226 TCCCCAACTTTTCACACAAGC 59.246 47.619 0.00 0.00 0.00 4.01
3886 11345 0.112412 GGCTCCTCCCCAACTTTTCA 59.888 55.000 0.00 0.00 0.00 2.69
3887 11346 0.112412 TGGCTCCTCCCCAACTTTTC 59.888 55.000 0.00 0.00 0.00 2.29
3893 11352 0.624500 ATAAGCTGGCTCCTCCCCAA 60.625 55.000 0.00 0.00 30.66 4.12
3930 11389 4.472108 TCCAAGGATACGTAGGGTCAATTT 59.528 41.667 0.08 0.00 46.39 1.82
3942 11401 2.972625 TCAGTTTGCTCCAAGGATACG 58.027 47.619 0.00 0.00 46.39 3.06
3943 11402 4.517285 TGATCAGTTTGCTCCAAGGATAC 58.483 43.478 0.00 0.00 0.00 2.24
3967 11426 9.478768 CACGGTTTAAGTTGGGTAAAAATTAAT 57.521 29.630 0.00 0.00 31.80 1.40
3968 11427 8.473219 ACACGGTTTAAGTTGGGTAAAAATTAA 58.527 29.630 0.00 0.00 30.24 1.40
3969 11428 8.005192 ACACGGTTTAAGTTGGGTAAAAATTA 57.995 30.769 0.00 0.00 0.00 1.40
3970 11429 6.876155 ACACGGTTTAAGTTGGGTAAAAATT 58.124 32.000 0.00 0.00 0.00 1.82
4004 11997 6.462207 CCAAATCAAATGTATTTATCGGGCCA 60.462 38.462 4.39 0.00 0.00 5.36
4041 12034 0.515127 TAACAAACCGCATGCGACAG 59.485 50.000 39.90 25.57 42.83 3.51
4130 12149 6.473397 AACTGTCTTTTCTTCAGAATAGCG 57.527 37.500 2.94 0.00 34.50 4.26
4215 12250 7.882791 TGTCCTTTCTAGACTGCAAATAATCAA 59.117 33.333 0.00 0.00 35.21 2.57
4271 12306 3.587797 TCGGTGACTGGAATAGTGTTC 57.412 47.619 0.00 0.00 40.53 3.18
4336 12371 1.153449 CTGGTAATTGCCCTCGCGA 60.153 57.895 9.26 9.26 38.08 5.87
4442 12477 4.568152 AAGTTGGGTCGTGATTTTTCTG 57.432 40.909 0.00 0.00 0.00 3.02
4490 12525 5.727515 GCTTGCATTTCCAAAGTTCAAACAC 60.728 40.000 0.00 0.00 0.00 3.32
4513 12548 7.713764 ACCAAAACTTACAATTTCTGAATGC 57.286 32.000 0.00 0.00 0.00 3.56
4562 12597 6.573434 ACAGTTGGGAAAATTCTGAAAGTTC 58.427 36.000 0.00 1.31 33.76 3.01


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

AutoCloner maintained by Alex Coulton.