Multiple sequence alignment - TraesCS4D01G004200

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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 TraesCS4D01G004200 chr4D 100.000 6523 0 0 1 6523 1871486 1878008 0.000000e+00 12046
1 TraesCS4D01G004200 chr4D 88.308 2985 281 42 3216 6147 1823276 1826245 0.000000e+00 3517
2 TraesCS4D01G004200 chr4D 87.666 2035 199 20 39 2057 1821010 1823008 0.000000e+00 2320
3 TraesCS4D01G004200 chr4D 86.316 285 25 4 219 493 1695292 1695572 1.380000e-76 298
4 TraesCS4D01G004200 chrUn 88.780 4590 400 41 1222 5755 47658279 47662809 0.000000e+00 5517
5 TraesCS4D01G004200 chrUn 87.928 2568 273 24 3212 5749 47452162 47454722 0.000000e+00 2990
6 TraesCS4D01G004200 chrUn 88.637 2209 235 11 3212 5409 47631561 47633764 0.000000e+00 2675
7 TraesCS4D01G004200 chrUn 84.910 1279 176 16 786 2057 47630021 47631289 0.000000e+00 1277
8 TraesCS4D01G004200 chrUn 83.848 1263 192 11 786 2042 48044670 48045926 0.000000e+00 1192
9 TraesCS4D01G004200 chrUn 83.769 1263 193 11 786 2042 48074941 48076197 0.000000e+00 1186
10 TraesCS4D01G004200 chrUn 83.568 1278 181 17 786 2057 47450636 47451890 0.000000e+00 1170
11 TraesCS4D01G004200 chrUn 93.766 770 30 2 5755 6523 47454771 47455523 0.000000e+00 1140
12 TraesCS4D01G004200 chrUn 84.824 369 28 9 91 453 48043224 48043570 4.840000e-91 346
13 TraesCS4D01G004200 chrUn 84.824 369 28 9 91 453 403973443 403973097 4.840000e-91 346
14 TraesCS4D01G004200 chrUn 84.553 369 29 9 91 453 48073495 48073841 2.250000e-89 340
15 TraesCS4D01G004200 chrUn 80.808 198 14 3 613 790 47629801 47629994 4.100000e-27 134
16 TraesCS4D01G004200 chr4A 92.179 2864 178 22 2536 5393 602872306 602875129 0.000000e+00 4006
17 TraesCS4D01G004200 chr4A 88.807 3136 302 27 2402 5530 602609001 602612094 0.000000e+00 3801
18 TraesCS4D01G004200 chr4A 93.579 1246 79 1 821 2066 602870631 602871875 0.000000e+00 1857
19 TraesCS4D01G004200 chr4A 90.385 936 80 5 3669 4602 602726157 602727084 0.000000e+00 1221
20 TraesCS4D01G004200 chr4A 87.554 932 107 7 4422 5347 602722320 602723248 0.000000e+00 1070
21 TraesCS4D01G004200 chr4A 94.258 418 22 1 2057 2474 602871894 602872309 7.130000e-179 638
22 TraesCS4D01G004200 chr4A 87.257 463 44 8 4945 5406 602725315 602725763 1.250000e-141 514
23 TraesCS4D01G004200 chr4A 83.738 412 56 9 5747 6147 602875720 602876131 4.770000e-101 379
24 TraesCS4D01G004200 chr4A 84.701 268 16 11 5443 5688 602875330 602875594 1.820000e-60 244
25 TraesCS4D01G004200 chr4A 91.860 86 7 0 2319 2404 602608822 602608907 3.190000e-23 121
26 TraesCS4D01G004200 chr4B 92.444 2488 164 15 2421 4905 3340965 3338499 0.000000e+00 3531
27 TraesCS4D01G004200 chr4B 90.358 2344 154 13 71 2380 3343268 3340963 0.000000e+00 3011
28 TraesCS4D01G004200 chr4B 87.935 2213 246 14 3212 5409 3733776 3735982 0.000000e+00 2588
29 TraesCS4D01G004200 chr4B 84.907 1239 178 9 821 2054 3732267 3733501 0.000000e+00 1243
30 TraesCS4D01G004200 chr4B 83.690 1263 194 11 786 2042 3514410 3513154 0.000000e+00 1181
31 TraesCS4D01G004200 chr4B 83.690 1263 193 12 786 2042 3484436 3483181 0.000000e+00 1179
32 TraesCS4D01G004200 chr4B 84.184 1176 176 9 786 1956 3454322 3453152 0.000000e+00 1133
33 TraesCS4D01G004200 chr4B 84.910 888 123 10 786 1668 3427846 3426965 0.000000e+00 887
34 TraesCS4D01G004200 chr4B 85.175 715 73 15 4902 5614 3337652 3336969 0.000000e+00 702
35 TraesCS4D01G004200 chr4B 79.443 574 59 27 91 631 3433391 3432844 1.040000e-92 351
36 TraesCS4D01G004200 chr4B 79.443 574 59 27 91 631 3485874 3485327 1.040000e-92 351
37 TraesCS4D01G004200 chr4B 84.824 369 28 9 91 453 3455760 3455414 4.840000e-91 346
38 TraesCS4D01G004200 chr4B 78.736 348 43 18 311 631 3429079 3428736 3.080000e-48 204
39 TraesCS4D01G004200 chr3B 85.714 406 45 3 3706 4111 60502711 60503103 3.640000e-112 416


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 TraesCS4D01G004200 chr4D 1871486 1878008 6522 False 12046.000000 12046 100.000000 1 6523 1 chr4D.!!$F2 6522
1 TraesCS4D01G004200 chr4D 1821010 1826245 5235 False 2918.500000 3517 87.987000 39 6147 2 chr4D.!!$F3 6108
2 TraesCS4D01G004200 chrUn 47658279 47662809 4530 False 5517.000000 5517 88.780000 1222 5755 1 chrUn.!!$F1 4533
3 TraesCS4D01G004200 chrUn 47450636 47455523 4887 False 1766.666667 2990 88.420667 786 6523 3 chrUn.!!$F2 5737
4 TraesCS4D01G004200 chrUn 47629801 47633764 3963 False 1362.000000 2675 84.785000 613 5409 3 chrUn.!!$F3 4796
5 TraesCS4D01G004200 chrUn 48043224 48045926 2702 False 769.000000 1192 84.336000 91 2042 2 chrUn.!!$F4 1951
6 TraesCS4D01G004200 chrUn 48073495 48076197 2702 False 763.000000 1186 84.161000 91 2042 2 chrUn.!!$F5 1951
7 TraesCS4D01G004200 chr4A 602608822 602612094 3272 False 1961.000000 3801 90.333500 2319 5530 2 chr4A.!!$F1 3211
8 TraesCS4D01G004200 chr4A 602870631 602876131 5500 False 1424.800000 4006 89.691000 821 6147 5 chr4A.!!$F3 5326
9 TraesCS4D01G004200 chr4A 602722320 602727084 4764 False 935.000000 1221 88.398667 3669 5406 3 chr4A.!!$F2 1737
10 TraesCS4D01G004200 chr4B 3336969 3343268 6299 True 2414.666667 3531 89.325667 71 5614 3 chr4B.!!$R2 5543
11 TraesCS4D01G004200 chr4B 3732267 3735982 3715 False 1915.500000 2588 86.421000 821 5409 2 chr4B.!!$F1 4588
12 TraesCS4D01G004200 chr4B 3513154 3514410 1256 True 1181.000000 1181 83.690000 786 2042 1 chr4B.!!$R1 1256
13 TraesCS4D01G004200 chr4B 3483181 3485874 2693 True 765.000000 1179 81.566500 91 2042 2 chr4B.!!$R5 1951
14 TraesCS4D01G004200 chr4B 3453152 3455760 2608 True 739.500000 1133 84.504000 91 1956 2 chr4B.!!$R4 1865
15 TraesCS4D01G004200 chr4B 3426965 3433391 6426 True 480.666667 887 81.029667 91 1668 3 chr4B.!!$R3 1577

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
840 1668 0.597568 TTTGCAAGCCACATTCTCCG 59.402 50.000 0.00 0.0 0.00 4.63 F
1320 3010 1.396301 CTCCTCTTCTGCATGCGAAAC 59.604 52.381 20.08 0.0 0.00 2.78 F
1579 3269 1.598130 GGCAGCGACAAGACTGGTT 60.598 57.895 0.00 0.0 34.38 3.67 F
2316 4068 0.516877 CACCGTTGTACACCATGCAG 59.483 55.000 0.00 0.0 0.00 4.41 F
3898 6077 1.200020 CTCAAAATTCAGCGTGGGGAC 59.800 52.381 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2296 4048 0.179043 TGCATGGTGTACAACGGTGT 60.179 50.0 12.53 12.53 42.09 4.16 R
2316 4068 0.391597 TACGGCAAGGGCAGTATAGC 59.608 55.0 0.00 0.00 46.79 2.97 R
3326 5498 1.862049 TTGCTGCATAGAAGCCCCCA 61.862 55.0 1.84 0.00 40.06 4.96 R
4212 6391 2.504175 TCAGTATAGGCTGGAAACCCAC 59.496 50.0 0.00 0.00 37.12 4.61 R
5856 9650 0.179140 GAGAACAGAGCAGAGCCGAG 60.179 60.0 0.00 0.00 0.00 4.63 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
30 31 8.603242 ACTTAAAACAAGTACTGTATGTGAGG 57.397 34.615 0.00 0.00 37.23 3.86
32 33 6.861065 AAAACAAGTACTGTATGTGAGGTG 57.139 37.500 0.00 0.00 37.23 4.00
33 34 3.926616 ACAAGTACTGTATGTGAGGTGC 58.073 45.455 0.00 0.00 36.10 5.01
35 36 4.020218 ACAAGTACTGTATGTGAGGTGCAT 60.020 41.667 0.00 0.00 36.10 3.96
36 37 5.186992 ACAAGTACTGTATGTGAGGTGCATA 59.813 40.000 0.00 0.00 36.10 3.14
37 38 6.127054 ACAAGTACTGTATGTGAGGTGCATAT 60.127 38.462 0.00 0.00 36.10 1.78
40 41 5.474578 ACTGTATGTGAGGTGCATATAGG 57.525 43.478 11.66 0.00 40.23 2.57
46 47 3.321968 TGTGAGGTGCATATAGGTAGCTG 59.678 47.826 11.86 0.00 31.30 4.24
63 64 1.691196 CTGGCTTTCTTGTTGGACCA 58.309 50.000 0.00 0.00 0.00 4.02
180 181 1.315257 GGTGTTGATTGCCGCATCCT 61.315 55.000 0.00 0.00 0.00 3.24
230 245 5.306394 TGGATCTGGATAGTAGTACGACTG 58.694 45.833 17.80 1.91 0.00 3.51
232 247 5.764192 GGATCTGGATAGTAGTACGACTGTT 59.236 44.000 17.80 6.07 0.00 3.16
235 250 5.583854 TCTGGATAGTAGTACGACTGTTGAC 59.416 44.000 17.80 7.35 0.00 3.18
273 301 1.876799 CTCGCTGGATCTACATCGACT 59.123 52.381 0.00 0.00 34.53 4.18
275 303 1.777101 GCTGGATCTACATCGACTGC 58.223 55.000 0.00 0.00 0.00 4.40
276 304 1.067669 GCTGGATCTACATCGACTGCA 59.932 52.381 0.00 0.00 0.00 4.41
392 430 3.131709 AGAGATGGTCTTGGTTGTGTG 57.868 47.619 0.00 0.00 27.07 3.82
512 570 2.890808 TGAGTGAATCTGGTATCCGC 57.109 50.000 0.00 0.00 0.00 5.54
530 588 4.641645 CTTCAGGTGGCCGGTGCA 62.642 66.667 1.90 0.00 40.13 4.57
549 627 4.634443 GTGCACCCTAACTTGTAATACAGG 59.366 45.833 5.22 0.72 0.00 4.00
671 1447 3.806949 TTTGCTCTGGAATAAGGGTGT 57.193 42.857 0.00 0.00 0.00 4.16
672 1448 3.350219 TTGCTCTGGAATAAGGGTGTC 57.650 47.619 0.00 0.00 0.00 3.67
786 1583 6.442952 CATTTCCGTTTGAATTCTTGGTGTA 58.557 36.000 7.05 0.00 31.67 2.90
840 1668 0.597568 TTTGCAAGCCACATTCTCCG 59.402 50.000 0.00 0.00 0.00 4.63
1038 1875 1.676014 GCTTTGGCATCCTACGTGACT 60.676 52.381 0.00 0.00 38.54 3.41
1157 2847 4.592942 AGTTTCCTTGCTGATGCTGATAA 58.407 39.130 0.00 0.00 40.48 1.75
1188 2878 2.636412 CGAAGAGAGTGTGCGGGGA 61.636 63.158 0.00 0.00 0.00 4.81
1287 2977 3.433835 TCCATCCAAGGACATGGGA 57.566 52.632 8.50 3.46 41.05 4.37
1320 3010 1.396301 CTCCTCTTCTGCATGCGAAAC 59.604 52.381 20.08 0.00 0.00 2.78
1372 3062 3.507162 TCAAGGCATTGAACAAGGAGA 57.493 42.857 12.07 0.00 42.47 3.71
1398 3088 2.753043 ATCTGCAAGCGGGGCAAG 60.753 61.111 0.37 0.00 41.39 4.01
1416 3106 6.148948 GGGCAAGAAATTTAAATTTGCCAAC 58.851 36.000 34.54 23.74 45.24 3.77
1579 3269 1.598130 GGCAGCGACAAGACTGGTT 60.598 57.895 0.00 0.00 34.38 3.67
1586 3276 2.673833 CGACAAGACTGGTTACCTCAC 58.326 52.381 2.07 0.00 0.00 3.51
1677 3367 3.494045 GCTATCAAAGGCAAGTTCACC 57.506 47.619 0.00 0.00 0.00 4.02
2127 3879 7.915293 TTGTTGGATCAATACGTAGTGATTT 57.085 32.000 31.95 17.49 45.73 2.17
2128 3880 7.915293 TGTTGGATCAATACGTAGTGATTTT 57.085 32.000 31.95 16.82 45.73 1.82
2132 3884 8.014070 TGGATCAATACGTAGTGATTTTAGGA 57.986 34.615 31.95 14.47 45.73 2.94
2155 3907 9.553064 AGGATAACATATGTGAGATGAACTTTC 57.447 33.333 9.63 0.00 0.00 2.62
2160 3912 6.533012 ACATATGTGAGATGAACTTTCGACTG 59.467 38.462 7.78 0.00 0.00 3.51
2210 3962 5.725551 ATTTATTGTGTCCCTCCATACCA 57.274 39.130 0.00 0.00 0.00 3.25
2296 4048 4.942944 TCCTCAGAAGAATAGTGTGGGTA 58.057 43.478 0.00 0.00 0.00 3.69
2297 4049 4.710375 TCCTCAGAAGAATAGTGTGGGTAC 59.290 45.833 0.00 0.00 0.00 3.34
2316 4068 0.516877 CACCGTTGTACACCATGCAG 59.483 55.000 0.00 0.00 0.00 4.41
2582 4700 5.818136 ACTAACATGCGCATAACTTCATT 57.182 34.783 24.84 10.88 0.00 2.57
2619 4737 4.760530 TCAGGACCATGTCAAATCCTAG 57.239 45.455 0.00 0.00 39.66 3.02
2694 4820 6.658816 TGCTTAAGCCTCTGTTTTTCATGATA 59.341 34.615 24.30 0.00 41.18 2.15
2695 4821 7.176515 TGCTTAAGCCTCTGTTTTTCATGATAA 59.823 33.333 24.30 0.00 41.18 1.75
2696 4822 8.193438 GCTTAAGCCTCTGTTTTTCATGATAAT 58.807 33.333 17.00 0.00 34.31 1.28
2700 4826 9.860898 AAGCCTCTGTTTTTCATGATAATAAAC 57.139 29.630 0.00 6.31 0.00 2.01
2701 4827 9.023962 AGCCTCTGTTTTTCATGATAATAAACA 57.976 29.630 17.49 17.49 36.63 2.83
2702 4828 9.638239 GCCTCTGTTTTTCATGATAATAAACAA 57.362 29.630 18.36 12.38 37.99 2.83
2828 4996 4.142643 GCCATTTAATTTTGGTGGTGCATG 60.143 41.667 0.00 0.00 35.34 4.06
2843 5011 6.322491 GTGGTGCATGACTTTTATTCCTTAC 58.678 40.000 0.00 0.00 0.00 2.34
2893 5061 8.087750 GGGTCAGTCAAATATTTCAAAACATCA 58.912 33.333 0.00 0.00 0.00 3.07
2922 5090 7.568199 AACTGTAGATATTTTACCCACATGC 57.432 36.000 0.00 0.00 0.00 4.06
2923 5091 6.658849 ACTGTAGATATTTTACCCACATGCA 58.341 36.000 0.00 0.00 0.00 3.96
2966 5134 6.707608 ACACTACTACATCCATGTGCAATATG 59.292 38.462 2.26 5.45 41.89 1.78
3064 5232 7.469343 TCACCATGAAAACTATGCCCATATAT 58.531 34.615 0.00 0.00 0.00 0.86
3070 5238 9.821240 ATGAAAACTATGCCCATATATAAACCA 57.179 29.630 0.00 0.00 0.00 3.67
3071 5239 9.295825 TGAAAACTATGCCCATATATAAACCAG 57.704 33.333 0.00 0.00 0.00 4.00
3228 5400 9.052759 ACATTTAAACTGTTTGTAGGTACTCAG 57.947 33.333 15.69 0.00 41.75 3.35
3246 5418 4.264172 ACTCAGTACAGAGGAGAATGGACT 60.264 45.833 18.35 0.00 41.40 3.85
3326 5498 8.876790 GTTTACCACTCGCTATAAAAGTAATGT 58.123 33.333 0.00 0.00 0.00 2.71
3521 5696 5.691754 CCCAAAAAGTCTGTGCTAAATGTTC 59.308 40.000 0.00 0.00 0.00 3.18
3810 5989 3.328535 AGAAACCAAAGGTGTGGGAAT 57.671 42.857 0.00 0.00 43.56 3.01
3891 6070 3.004734 ACTGGAAACCTCAAAATTCAGCG 59.995 43.478 0.00 0.00 0.00 5.18
3898 6077 1.200020 CTCAAAATTCAGCGTGGGGAC 59.800 52.381 0.00 0.00 0.00 4.46
3915 6094 3.307199 GGGGACTCGTTGATTAACTTCCA 60.307 47.826 11.95 0.00 33.15 3.53
4157 6336 9.043548 TGAGATATCTTGATATGGATGACACAT 57.956 33.333 6.70 0.00 0.00 3.21
4212 6391 7.770897 AGCTCTTACAAATTTGAGGGTACTATG 59.229 37.037 24.64 7.12 0.00 2.23
4400 6579 1.276622 ATGTGGTGGTAGAGTGGGAC 58.723 55.000 0.00 0.00 0.00 4.46
4510 6689 6.682423 TGCATAGAACAAATCAACATCGAT 57.318 33.333 0.00 0.00 0.00 3.59
4664 6843 5.878116 CCGTATTTGGAGTGGATAAAAGTGA 59.122 40.000 0.00 0.00 0.00 3.41
4665 6844 6.542370 CCGTATTTGGAGTGGATAAAAGTGAT 59.458 38.462 0.00 0.00 0.00 3.06
4666 6845 7.409697 CGTATTTGGAGTGGATAAAAGTGATG 58.590 38.462 0.00 0.00 0.00 3.07
4669 6848 8.599624 ATTTGGAGTGGATAAAAGTGATGAAT 57.400 30.769 0.00 0.00 0.00 2.57
4792 6977 5.687166 AGTTGCATTTTGATGGAATGGAT 57.313 34.783 0.00 0.00 35.28 3.41
4795 6980 5.270893 TGCATTTTGATGGAATGGATGAG 57.729 39.130 0.00 0.00 35.54 2.90
4871 7056 3.192001 ACTTCGCATCAGTGATTGCAAAT 59.808 39.130 20.28 0.00 33.60 2.32
4928 7963 4.318121 CGATGGCGTTGAAGAAGCTAATAC 60.318 45.833 0.00 0.00 0.00 1.89
4934 7969 5.177696 GCGTTGAAGAAGCTAATACTATGGG 59.822 44.000 0.00 0.00 0.00 4.00
4994 8029 0.753262 AGTTGAGCTCGACCTGTGTT 59.247 50.000 27.31 7.88 0.00 3.32
5001 8036 2.159421 AGCTCGACCTGTGTTACATACG 60.159 50.000 0.00 0.00 0.00 3.06
5024 8077 3.494924 CGAACTGGCCATGATCTCCAATA 60.495 47.826 5.51 0.00 0.00 1.90
5068 8121 1.896220 TCAAGTACTGCCCAAAGCTG 58.104 50.000 0.00 0.00 44.23 4.24
5123 8176 1.070821 CGAGCTGAGCATTTTCGACA 58.929 50.000 7.39 0.00 33.38 4.35
5263 8316 4.569943 AGTTCAGTCATATCAAGCACGTT 58.430 39.130 0.00 0.00 0.00 3.99
5372 8431 5.934402 TCAGGTAATACTTTGGTCTCTCC 57.066 43.478 0.00 0.00 0.00 3.71
5614 9268 9.408069 ACAACTTCTACTAGTTTTGAGTATTCG 57.592 33.333 0.00 0.00 36.24 3.34
5636 9290 6.163476 TCGTACTAATAATGCCATGACCATC 58.837 40.000 0.00 0.00 0.00 3.51
5688 9342 0.619255 TGCAGGGATACGGGGAAAGA 60.619 55.000 0.00 0.00 37.60 2.52
5856 9650 6.284459 ACTAATGGAGTTTATGCTACTCTGC 58.716 40.000 0.00 0.00 41.37 4.26
5857 9651 5.365021 AATGGAGTTTATGCTACTCTGCT 57.635 39.130 0.00 0.00 41.37 4.24
5858 9652 4.392921 TGGAGTTTATGCTACTCTGCTC 57.607 45.455 0.00 0.00 41.37 4.26
5859 9653 3.181486 TGGAGTTTATGCTACTCTGCTCG 60.181 47.826 0.00 0.00 41.37 5.03
5860 9654 3.376540 GAGTTTATGCTACTCTGCTCGG 58.623 50.000 0.00 0.00 39.12 4.63
6183 10147 4.474226 AGCAATCTGTTGTTTCTTCGAC 57.526 40.909 0.00 0.00 37.65 4.20
6195 10159 2.542020 TCTTCGACCAGTGCAATCAA 57.458 45.000 0.00 0.00 0.00 2.57
6250 10214 7.332926 GTCTATATATGTTGTGGATGGAAGCAG 59.667 40.741 0.00 0.00 0.00 4.24
6263 10227 3.287222 TGGAAGCAGCTAACTTGTGTTT 58.713 40.909 5.93 0.00 37.59 2.83
6270 10234 6.340522 AGCAGCTAACTTGTGTTTCAAATTT 58.659 32.000 0.00 0.00 37.59 1.82
6277 10241 7.595311 AACTTGTGTTTCAAATTTTGACTCC 57.405 32.000 11.30 3.68 39.87 3.85
6363 10327 8.339714 GCAATGTACTAGTGTTGTACTTTTGAA 58.660 33.333 5.39 0.00 40.89 2.69
6374 10338 8.469125 GTGTTGTACTTTTGAAACGATGAATTC 58.531 33.333 0.00 0.00 0.00 2.17
6382 10346 5.862924 TGAAACGATGAATTCTTCAGTCC 57.137 39.130 18.39 12.81 43.98 3.85
6404 10368 3.575687 CCCCCATTCTTATGAGCAATTCC 59.424 47.826 0.00 0.00 33.37 3.01
6405 10369 3.575687 CCCCATTCTTATGAGCAATTCCC 59.424 47.826 0.00 0.00 33.37 3.97
6407 10371 4.280174 CCCATTCTTATGAGCAATTCCCAG 59.720 45.833 0.00 0.00 33.37 4.45
6408 10372 4.891756 CCATTCTTATGAGCAATTCCCAGT 59.108 41.667 0.00 0.00 33.37 4.00
6409 10373 5.009410 CCATTCTTATGAGCAATTCCCAGTC 59.991 44.000 0.00 0.00 33.37 3.51
6410 10374 5.441718 TTCTTATGAGCAATTCCCAGTCT 57.558 39.130 0.00 0.00 0.00 3.24
6446 10410 2.348411 ATGTTCCCGGCTATTCAAGG 57.652 50.000 0.00 0.00 0.00 3.61
6494 10458 6.761099 TGGCAAGTAAACTAAAGAACACAA 57.239 33.333 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.701098 CCTCACATACAGTACTTGTTTTAAGTA 57.299 33.333 0.00 0.00 41.29 2.24
5 6 8.208903 ACCTCACATACAGTACTTGTTTTAAGT 58.791 33.333 0.00 0.00 41.29 2.24
6 7 8.495949 CACCTCACATACAGTACTTGTTTTAAG 58.504 37.037 0.00 0.00 41.29 1.85
7 8 7.041644 GCACCTCACATACAGTACTTGTTTTAA 60.042 37.037 0.00 0.00 41.29 1.52
8 9 6.425721 GCACCTCACATACAGTACTTGTTTTA 59.574 38.462 0.00 0.00 41.29 1.52
9 10 5.238650 GCACCTCACATACAGTACTTGTTTT 59.761 40.000 0.00 0.00 41.29 2.43
10 11 4.755123 GCACCTCACATACAGTACTTGTTT 59.245 41.667 0.00 0.00 41.29 2.83
11 12 4.202315 TGCACCTCACATACAGTACTTGTT 60.202 41.667 0.00 0.00 41.29 2.83
13 14 3.925379 TGCACCTCACATACAGTACTTG 58.075 45.455 0.00 0.00 0.00 3.16
14 15 4.826274 ATGCACCTCACATACAGTACTT 57.174 40.909 0.00 0.00 0.00 2.24
15 16 6.209589 CCTATATGCACCTCACATACAGTACT 59.790 42.308 0.00 0.00 33.03 2.73
16 17 6.015350 ACCTATATGCACCTCACATACAGTAC 60.015 42.308 0.00 0.00 33.03 2.73
17 18 6.075315 ACCTATATGCACCTCACATACAGTA 58.925 40.000 0.00 0.00 33.03 2.74
18 19 4.901849 ACCTATATGCACCTCACATACAGT 59.098 41.667 0.00 0.00 33.03 3.55
19 20 5.474578 ACCTATATGCACCTCACATACAG 57.525 43.478 0.00 0.00 33.03 2.74
20 21 5.047306 GCTACCTATATGCACCTCACATACA 60.047 44.000 0.00 0.00 33.03 2.29
22 23 5.185828 CAGCTACCTATATGCACCTCACATA 59.814 44.000 0.00 0.00 34.64 2.29
23 24 4.020751 CAGCTACCTATATGCACCTCACAT 60.021 45.833 0.00 0.00 0.00 3.21
24 25 3.321968 CAGCTACCTATATGCACCTCACA 59.678 47.826 0.00 0.00 0.00 3.58
25 26 3.306364 CCAGCTACCTATATGCACCTCAC 60.306 52.174 0.00 0.00 0.00 3.51
26 27 2.899900 CCAGCTACCTATATGCACCTCA 59.100 50.000 0.00 0.00 0.00 3.86
27 28 2.354203 GCCAGCTACCTATATGCACCTC 60.354 54.545 0.00 0.00 0.00 3.85
28 29 1.625818 GCCAGCTACCTATATGCACCT 59.374 52.381 0.00 0.00 0.00 4.00
30 31 3.409026 AAGCCAGCTACCTATATGCAC 57.591 47.619 0.00 0.00 0.00 4.57
32 33 4.278975 AGAAAGCCAGCTACCTATATGC 57.721 45.455 0.00 0.00 0.00 3.14
33 34 5.615289 ACAAGAAAGCCAGCTACCTATATG 58.385 41.667 0.00 0.00 0.00 1.78
35 36 5.428253 CAACAAGAAAGCCAGCTACCTATA 58.572 41.667 0.00 0.00 0.00 1.31
36 37 4.265073 CAACAAGAAAGCCAGCTACCTAT 58.735 43.478 0.00 0.00 0.00 2.57
37 38 3.559171 CCAACAAGAAAGCCAGCTACCTA 60.559 47.826 0.00 0.00 0.00 3.08
40 41 2.226674 GTCCAACAAGAAAGCCAGCTAC 59.773 50.000 0.00 0.00 0.00 3.58
46 47 3.751479 AATTGGTCCAACAAGAAAGCC 57.249 42.857 6.41 0.00 33.23 4.35
180 181 2.614481 GGGAGTTACAAGCGATCCAACA 60.614 50.000 0.00 0.00 0.00 3.33
230 245 2.996621 GAGATATATGGCAGCCGTCAAC 59.003 50.000 10.31 0.00 0.00 3.18
232 247 1.550524 GGAGATATATGGCAGCCGTCA 59.449 52.381 10.31 0.00 0.00 4.35
235 250 1.137872 GAGGGAGATATATGGCAGCCG 59.862 57.143 7.03 0.00 0.00 5.52
273 301 0.906775 TGATGAGGAGTGAGCATGCA 59.093 50.000 21.98 0.00 0.00 3.96
275 303 1.568606 CGTGATGAGGAGTGAGCATG 58.431 55.000 0.00 0.00 0.00 4.06
276 304 0.179089 GCGTGATGAGGAGTGAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
392 430 4.805219 ACGCCAACAATTCTAATGGAAAC 58.195 39.130 0.00 0.00 37.49 2.78
478 516 7.911651 AGATTCACTCATCTGAAGGAAAACTA 58.088 34.615 0.00 0.00 33.65 2.24
530 588 4.472470 GTCCCCTGTATTACAAGTTAGGGT 59.528 45.833 13.98 0.00 42.64 4.34
549 627 5.391312 AACATGCAGTTAAAATGAGTCCC 57.609 39.130 0.00 0.00 39.09 4.46
671 1447 0.335019 TCAGAGACGGATCTTGGGGA 59.665 55.000 0.00 0.00 34.34 4.81
672 1448 1.342819 GATCAGAGACGGATCTTGGGG 59.657 57.143 0.00 0.00 38.47 4.96
786 1583 3.560896 GCACACAAATTTGGCTTGAACAT 59.439 39.130 21.74 0.00 0.00 2.71
840 1668 7.062839 CACTAGAGACTAGCAAGAAATCACAAC 59.937 40.741 0.00 0.00 0.00 3.32
1157 2847 2.757868 CTCTCTTCGGTGATGTTCCTCT 59.242 50.000 0.00 0.00 0.00 3.69
1188 2878 0.329596 GCTTCAGTTCTCCCACCCAT 59.670 55.000 0.00 0.00 0.00 4.00
1197 2887 0.250467 ACATGGCACGCTTCAGTTCT 60.250 50.000 0.00 0.00 0.00 3.01
1287 2977 1.972588 AGAGGAGTGGGTTAAGGCAT 58.027 50.000 0.00 0.00 0.00 4.40
1320 3010 2.042762 TCATGGGAGTGGAGGGGG 59.957 66.667 0.00 0.00 0.00 5.40
1372 3062 1.520494 CGCTTGCAGATGCTATCCAT 58.480 50.000 6.35 0.00 42.66 3.41
1398 3088 8.443160 GCTTCTAGGTTGGCAAATTTAAATTTC 58.557 33.333 20.71 15.39 36.52 2.17
1416 3106 3.769844 TCAAGTCTTGGTAGGCTTCTAGG 59.230 47.826 12.66 0.00 42.60 3.02
1579 3269 3.376078 GGCGACCACGGTGAGGTA 61.376 66.667 10.28 0.00 40.09 3.08
1586 3276 2.560861 CAACAATGGCGACCACGG 59.439 61.111 0.50 0.00 35.80 4.94
1677 3367 5.761726 TGTGATGCTAAGCCATATCTTCTTG 59.238 40.000 0.00 0.00 0.00 3.02
2132 3884 9.035607 GTCGAAAGTTCATCTCACATATGTTAT 57.964 33.333 5.37 0.00 0.00 1.89
2155 3907 2.741517 TGATTGTAACACCATGCAGTCG 59.258 45.455 0.00 0.00 0.00 4.18
2160 3912 8.755696 TCTTTAAATTGATTGTAACACCATGC 57.244 30.769 0.00 0.00 0.00 4.06
2210 3962 2.385013 TGCACAATGACGCACTAGAT 57.615 45.000 0.00 0.00 31.95 1.98
2268 4020 7.331026 CCACACTATTCTTCTGAGGAACAATA 58.669 38.462 4.21 0.00 0.00 1.90
2275 4027 4.466370 TGTACCCACACTATTCTTCTGAGG 59.534 45.833 0.00 0.00 0.00 3.86
2276 4028 5.661056 TGTACCCACACTATTCTTCTGAG 57.339 43.478 0.00 0.00 0.00 3.35
2296 4048 0.179043 TGCATGGTGTACAACGGTGT 60.179 50.000 12.53 12.53 42.09 4.16
2297 4049 0.516877 CTGCATGGTGTACAACGGTG 59.483 55.000 6.39 8.96 0.00 4.94
2316 4068 0.391597 TACGGCAAGGGCAGTATAGC 59.608 55.000 0.00 0.00 46.79 2.97
2433 4281 9.374838 TCTCGTAAAAATCTAATAAGGACCAAC 57.625 33.333 0.00 0.00 0.00 3.77
2582 4700 7.135591 TGGTCCTGATGTTGATACATTGATA 57.864 36.000 0.00 0.00 44.90 2.15
2843 5011 8.251721 CCCAAGTCCTAAGATAACCTATATTCG 58.748 40.741 0.00 0.00 0.00 3.34
2908 5076 7.180322 TGTTATCAATGCATGTGGGTAAAAT 57.820 32.000 0.00 0.00 0.00 1.82
2911 5079 5.890419 TCATGTTATCAATGCATGTGGGTAA 59.110 36.000 0.00 0.00 40.40 2.85
2919 5087 8.255206 AGTGTCAATTTCATGTTATCAATGCAT 58.745 29.630 0.00 0.00 0.00 3.96
2920 5088 7.604549 AGTGTCAATTTCATGTTATCAATGCA 58.395 30.769 0.00 0.00 0.00 3.96
2921 5089 9.013490 GTAGTGTCAATTTCATGTTATCAATGC 57.987 33.333 0.00 0.00 0.00 3.56
3027 5195 4.320608 TTCATGGTGAAACAAGCTTTCC 57.679 40.909 0.00 0.00 39.98 3.13
3069 5237 8.986847 CCTTCTGACTATAAATGTATTCTGCTG 58.013 37.037 0.00 0.00 0.00 4.41
3070 5238 8.928448 TCCTTCTGACTATAAATGTATTCTGCT 58.072 33.333 0.00 0.00 0.00 4.24
3071 5239 9.202273 CTCCTTCTGACTATAAATGTATTCTGC 57.798 37.037 0.00 0.00 0.00 4.26
3086 5254 6.936968 ACCAAACTAATACTCCTTCTGACT 57.063 37.500 0.00 0.00 0.00 3.41
3163 5331 6.015434 GGGGAACATAACATCTGAAAGTGTTT 60.015 38.462 0.96 0.00 38.49 2.83
3165 5333 5.010282 GGGGAACATAACATCTGAAAGTGT 58.990 41.667 0.00 0.00 33.76 3.55
3228 5400 4.142049 CCTCAAGTCCATTCTCCTCTGTAC 60.142 50.000 0.00 0.00 0.00 2.90
3246 5418 4.365514 TCCTTTAGCACATCAACCTCAA 57.634 40.909 0.00 0.00 0.00 3.02
3326 5498 1.862049 TTGCTGCATAGAAGCCCCCA 61.862 55.000 1.84 0.00 40.06 4.96
3521 5696 4.757799 TCCACATGGACACAATTTTACG 57.242 40.909 0.00 0.00 39.78 3.18
3891 6070 3.329929 AGTTAATCAACGAGTCCCCAC 57.670 47.619 0.00 0.00 39.78 4.61
3898 6077 6.787085 AGACTTTGGAAGTTAATCAACGAG 57.213 37.500 0.00 0.00 43.03 4.18
3915 6094 7.569639 TCTATATGCAGAAGACGTAGACTTT 57.430 36.000 0.00 0.00 43.34 2.66
4157 6336 6.096164 ACCCCTAGGAATACTACTTACACA 57.904 41.667 11.48 0.00 36.73 3.72
4212 6391 2.504175 TCAGTATAGGCTGGAAACCCAC 59.496 50.000 0.00 0.00 37.12 4.61
4367 6546 5.838529 ACCACCACATTTTAAAGCAAGTAC 58.161 37.500 0.00 0.00 0.00 2.73
4400 6579 0.698238 TCTCCTTGGACCAACCCATG 59.302 55.000 1.69 0.00 35.87 3.66
4510 6689 1.414919 AGCCGGCGACCAAAATATCTA 59.585 47.619 23.20 0.00 0.00 1.98
4554 6733 0.747255 GCTCTCGAGAGGCACCATAA 59.253 55.000 36.65 3.84 42.29 1.90
4664 6843 5.503927 ACACTTGATTACTGGAGCATTCAT 58.496 37.500 0.00 0.00 0.00 2.57
4665 6844 4.910195 ACACTTGATTACTGGAGCATTCA 58.090 39.130 0.00 0.00 0.00 2.57
4666 6845 7.412853 CAATACACTTGATTACTGGAGCATTC 58.587 38.462 0.00 0.00 0.00 2.67
4669 6848 5.185454 CCAATACACTTGATTACTGGAGCA 58.815 41.667 0.00 0.00 0.00 4.26
4792 6977 0.401395 AAACCCACTCCTCCCACTCA 60.401 55.000 0.00 0.00 0.00 3.41
4795 6980 1.074951 CCAAACCCACTCCTCCCAC 59.925 63.158 0.00 0.00 0.00 4.61
4928 7963 1.409427 GAGACCTTGGACGTCCCATAG 59.591 57.143 31.19 23.09 46.10 2.23
4934 7969 0.244178 GAGTGGAGACCTTGGACGTC 59.756 60.000 7.13 7.13 0.00 4.34
4994 8029 0.462375 ATGGCCAGTTCGCGTATGTA 59.538 50.000 13.05 0.00 0.00 2.29
5001 8036 1.162800 GGAGATCATGGCCAGTTCGC 61.163 60.000 13.05 9.47 0.00 4.70
5068 8121 0.250381 CCATCTCCTGCAGCATCTCC 60.250 60.000 8.66 0.00 0.00 3.71
5120 8173 4.773323 CTGGAAGTTGATTTTCCCTGTC 57.227 45.455 1.88 0.00 42.79 3.51
5272 8325 1.685517 TCATCTTCTCCATCCTCTGCG 59.314 52.381 0.00 0.00 0.00 5.18
5614 9268 5.351465 CCGATGGTCATGGCATTATTAGTAC 59.649 44.000 0.00 0.00 0.00 2.73
5636 9290 7.601508 TGATCATCATCTAAACATGAGATTCCG 59.398 37.037 0.00 0.00 36.22 4.30
5688 9342 6.487828 AGTGTATATGGCATTATGGCTGATT 58.512 36.000 19.22 5.10 44.10 2.57
5856 9650 0.179140 GAGAACAGAGCAGAGCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
5857 9651 0.610509 AGAGAACAGAGCAGAGCCGA 60.611 55.000 0.00 0.00 0.00 5.54
5858 9652 0.458197 CAGAGAACAGAGCAGAGCCG 60.458 60.000 0.00 0.00 0.00 5.52
5859 9653 0.894141 TCAGAGAACAGAGCAGAGCC 59.106 55.000 0.00 0.00 0.00 4.70
5860 9654 2.739885 TTCAGAGAACAGAGCAGAGC 57.260 50.000 0.00 0.00 0.00 4.09
6183 10147 5.865552 CCTGAACTTAATTTGATTGCACTGG 59.134 40.000 0.00 0.00 0.00 4.00
6195 10159 5.304357 CCCCAGAACAAACCTGAACTTAATT 59.696 40.000 0.00 0.00 33.65 1.40
6250 10214 8.185003 AGTCAAAATTTGAAACACAAGTTAGC 57.815 30.769 10.27 0.00 42.15 3.09
6263 10227 4.204012 AGTGTTCCGGAGTCAAAATTTGA 58.796 39.130 3.34 4.03 37.33 2.69
6270 10234 5.889853 ACAGTATATAGTGTTCCGGAGTCAA 59.110 40.000 16.10 0.00 36.50 3.18
6321 10285 6.984474 AGTACATTGCTACATAGTACGCATTT 59.016 34.615 0.00 0.00 39.84 2.32
6323 10287 6.085555 AGTACATTGCTACATAGTACGCAT 57.914 37.500 0.00 0.00 39.84 4.73
6382 10346 3.575687 GGAATTGCTCATAAGAATGGGGG 59.424 47.826 0.00 0.00 33.81 5.40
6394 10358 1.538047 GCAAGACTGGGAATTGCTCA 58.462 50.000 0.00 0.00 44.57 4.26
6397 10361 1.067354 CCAAGCAAGACTGGGAATTGC 60.067 52.381 1.02 1.02 43.15 3.56
6398 10362 1.067354 GCCAAGCAAGACTGGGAATTG 60.067 52.381 0.00 0.00 43.15 2.32
6399 10363 1.260544 GCCAAGCAAGACTGGGAATT 58.739 50.000 0.00 0.00 43.15 2.17
6400 10364 0.613012 GGCCAAGCAAGACTGGGAAT 60.613 55.000 0.00 0.00 43.15 3.01
6401 10365 1.228552 GGCCAAGCAAGACTGGGAA 60.229 57.895 0.00 0.00 43.15 3.97
6402 10366 2.436109 GGCCAAGCAAGACTGGGA 59.564 61.111 0.00 0.00 43.15 4.37
6404 10368 0.829182 AAAGGGCCAAGCAAGACTGG 60.829 55.000 6.18 0.00 0.00 4.00
6405 10369 1.043022 AAAAGGGCCAAGCAAGACTG 58.957 50.000 6.18 0.00 0.00 3.51
6407 10371 0.752658 ACAAAAGGGCCAAGCAAGAC 59.247 50.000 6.18 0.00 0.00 3.01
6408 10372 2.373335 TACAAAAGGGCCAAGCAAGA 57.627 45.000 6.18 0.00 0.00 3.02
6409 10373 2.299867 ACATACAAAAGGGCCAAGCAAG 59.700 45.455 6.18 0.00 0.00 4.01
6410 10374 2.324541 ACATACAAAAGGGCCAAGCAA 58.675 42.857 6.18 0.00 0.00 3.91
6490 10454 5.570262 TCGTGATAGTTTTCGAACTTGTG 57.430 39.130 0.00 0.00 34.37 3.33
6494 10458 4.977963 TCGTTTCGTGATAGTTTTCGAACT 59.022 37.500 0.00 0.00 40.95 3.01


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

AutoCloner maintained by Alex Coulton.