Multiple sequence alignment - TraesCS2D01G529300

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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 TraesCS2D01G529300 chr2D 100.000 3139 0 0 1 3139 616597930 616601068 0.000000e+00 5797
1 TraesCS2D01G529300 chr2D 95.855 941 23 9 1 941 538328761 538329685 0.000000e+00 1507
2 TraesCS2D01G529300 chr2D 97.965 688 13 1 4 691 259995554 259994868 0.000000e+00 1192
3 TraesCS2D01G529300 chr2D 85.897 156 17 2 2989 3139 475779526 475779681 9.010000e-36 161
4 TraesCS2D01G529300 chr2B 88.186 2260 138 55 976 3139 751571190 751573416 0.000000e+00 2575
5 TraesCS2D01G529300 chr4D 97.332 937 23 2 4 940 396485415 396484481 0.000000e+00 1591
6 TraesCS2D01G529300 chr4D 97.517 725 16 2 1 725 349546222 349546944 0.000000e+00 1238
7 TraesCS2D01G529300 chr4D 80.078 256 45 3 2889 3139 433503286 433503032 5.350000e-43 185
8 TraesCS2D01G529300 chr3D 96.478 937 21 3 4 940 384682365 384681441 0.000000e+00 1537
9 TraesCS2D01G529300 chr3D 80.769 650 85 19 2520 3139 404393539 404394178 3.660000e-129 472
10 TraesCS2D01G529300 chr3D 84.116 277 34 7 2870 3139 291175863 291176136 3.110000e-65 259
11 TraesCS2D01G529300 chr3D 79.227 414 51 18 2448 2834 31067145 31067550 4.020000e-64 255
12 TraesCS2D01G529300 chr3D 78.182 220 39 5 2917 3129 82366693 82366476 7.060000e-27 132
13 TraesCS2D01G529300 chr7D 95.957 940 26 3 1 940 23858941 23859868 0.000000e+00 1515
14 TraesCS2D01G529300 chr7D 80.080 251 41 6 2891 3138 522812278 522812522 8.950000e-41 178
15 TraesCS2D01G529300 chr5D 94.189 912 40 10 4 906 77870331 77869424 0.000000e+00 1378
16 TraesCS2D01G529300 chr5D 90.589 967 50 22 1 933 459895295 459896254 0.000000e+00 1243
17 TraesCS2D01G529300 chr5D 83.951 162 21 4 2979 3135 106509724 106509563 1.950000e-32 150
18 TraesCS2D01G529300 chr3A 90.491 957 70 7 4 941 827690 826736 0.000000e+00 1243
19 TraesCS2D01G529300 chr3A 87.604 960 94 10 1 940 577063580 577064534 0.000000e+00 1090
20 TraesCS2D01G529300 chr3A 85.452 653 85 10 287 933 712590826 712590178 0.000000e+00 671
21 TraesCS2D01G529300 chr3A 81.024 664 92 18 2506 3139 526853513 526854172 6.050000e-137 497
22 TraesCS2D01G529300 chr3A 84.760 479 46 17 463 933 20656409 20656868 3.690000e-124 455
23 TraesCS2D01G529300 chr5A 88.229 943 101 10 4 940 602197874 602196936 0.000000e+00 1118
24 TraesCS2D01G529300 chr5A 79.870 154 25 5 2891 3039 109274639 109274487 1.190000e-19 108
25 TraesCS2D01G529300 chr7A 88.072 939 103 9 1 935 126923370 126924303 0.000000e+00 1105
26 TraesCS2D01G529300 chr7A 79.755 652 97 22 2520 3139 660144422 660145070 1.030000e-119 440
27 TraesCS2D01G529300 chr6A 86.456 982 82 15 1 933 13656161 13657140 0.000000e+00 1029
28 TraesCS2D01G529300 chr6A 78.898 635 106 13 2505 3115 593680711 593680081 3.770000e-109 405
29 TraesCS2D01G529300 chr6A 80.392 255 35 8 2891 3139 600249279 600249034 2.490000e-41 180
30 TraesCS2D01G529300 chr6A 80.000 255 36 8 2891 3139 600273116 600272871 1.160000e-39 174
31 TraesCS2D01G529300 chr2A 92.504 627 36 3 1662 2280 746793469 746794092 0.000000e+00 887
32 TraesCS2D01G529300 chr2A 92.990 485 29 3 1182 1666 746775471 746775950 0.000000e+00 702
33 TraesCS2D01G529300 chr1A 92.149 242 18 1 1167 1407 305328851 305328610 1.080000e-89 340
34 TraesCS2D01G529300 chr1A 83.117 231 35 4 1167 1395 305006150 305005922 1.140000e-49 207
35 TraesCS2D01G529300 chr1A 79.909 219 39 2 2889 3102 520919573 520919791 4.190000e-34 156
36 TraesCS2D01G529300 chr1D 93.043 230 16 0 1167 1396 240599280 240599051 1.390000e-88 337
37 TraesCS2D01G529300 chr1D 89.506 162 17 0 1167 1328 240595807 240595646 4.100000e-49 206
38 TraesCS2D01G529300 chr1B 93.043 230 16 0 1167 1396 333601685 333601914 1.390000e-88 337
39 TraesCS2D01G529300 chr1B 83.550 231 34 4 1167 1395 333625820 333626048 2.450000e-51 213
40 TraesCS2D01G529300 chr1B 80.105 191 34 4 2949 3135 518243402 518243592 4.220000e-29 139
41 TraesCS2D01G529300 chr6D 79.953 429 55 10 2507 2908 60122551 60122127 1.420000e-73 287
42 TraesCS2D01G529300 chr7B 74.887 661 94 33 2520 3139 100355440 100356069 5.230000e-58 235
43 TraesCS2D01G529300 chr5B 76.957 447 72 13 2421 2839 559563164 559563607 3.150000e-55 226
44 TraesCS2D01G529300 chr4B 78.676 272 51 4 2870 3135 40214341 40214071 1.160000e-39 174


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 TraesCS2D01G529300 chr2D 616597930 616601068 3138 False 5797.0 5797 100.0000 1 3139 1 chr2D.!!$F3 3138
1 TraesCS2D01G529300 chr2D 538328761 538329685 924 False 1507.0 1507 95.8550 1 941 1 chr2D.!!$F2 940
2 TraesCS2D01G529300 chr2D 259994868 259995554 686 True 1192.0 1192 97.9650 4 691 1 chr2D.!!$R1 687
3 TraesCS2D01G529300 chr2B 751571190 751573416 2226 False 2575.0 2575 88.1860 976 3139 1 chr2B.!!$F1 2163
4 TraesCS2D01G529300 chr4D 396484481 396485415 934 True 1591.0 1591 97.3320 4 940 1 chr4D.!!$R1 936
5 TraesCS2D01G529300 chr4D 349546222 349546944 722 False 1238.0 1238 97.5170 1 725 1 chr4D.!!$F1 724
6 TraesCS2D01G529300 chr3D 384681441 384682365 924 True 1537.0 1537 96.4780 4 940 1 chr3D.!!$R2 936
7 TraesCS2D01G529300 chr3D 404393539 404394178 639 False 472.0 472 80.7690 2520 3139 1 chr3D.!!$F3 619
8 TraesCS2D01G529300 chr7D 23858941 23859868 927 False 1515.0 1515 95.9570 1 940 1 chr7D.!!$F1 939
9 TraesCS2D01G529300 chr5D 77869424 77870331 907 True 1378.0 1378 94.1890 4 906 1 chr5D.!!$R1 902
10 TraesCS2D01G529300 chr5D 459895295 459896254 959 False 1243.0 1243 90.5890 1 933 1 chr5D.!!$F1 932
11 TraesCS2D01G529300 chr3A 826736 827690 954 True 1243.0 1243 90.4910 4 941 1 chr3A.!!$R1 937
12 TraesCS2D01G529300 chr3A 577063580 577064534 954 False 1090.0 1090 87.6040 1 940 1 chr3A.!!$F3 939
13 TraesCS2D01G529300 chr3A 712590178 712590826 648 True 671.0 671 85.4520 287 933 1 chr3A.!!$R2 646
14 TraesCS2D01G529300 chr3A 526853513 526854172 659 False 497.0 497 81.0240 2506 3139 1 chr3A.!!$F2 633
15 TraesCS2D01G529300 chr5A 602196936 602197874 938 True 1118.0 1118 88.2290 4 940 1 chr5A.!!$R2 936
16 TraesCS2D01G529300 chr7A 126923370 126924303 933 False 1105.0 1105 88.0720 1 935 1 chr7A.!!$F1 934
17 TraesCS2D01G529300 chr7A 660144422 660145070 648 False 440.0 440 79.7550 2520 3139 1 chr7A.!!$F2 619
18 TraesCS2D01G529300 chr6A 13656161 13657140 979 False 1029.0 1029 86.4560 1 933 1 chr6A.!!$F1 932
19 TraesCS2D01G529300 chr6A 593680081 593680711 630 True 405.0 405 78.8980 2505 3115 1 chr6A.!!$R1 610
20 TraesCS2D01G529300 chr2A 746793469 746794092 623 False 887.0 887 92.5040 1662 2280 1 chr2A.!!$F2 618
21 TraesCS2D01G529300 chr1D 240595646 240599280 3634 True 271.5 337 91.2745 1167 1396 2 chr1D.!!$R1 229
22 TraesCS2D01G529300 chr7B 100355440 100356069 629 False 235.0 235 74.8870 2520 3139 1 chr7B.!!$F1 619

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
998 1212 1.220477 GGAGGTCTGAAGGAGCAGC 59.78 63.158 0.0 0.0 44.16 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2814 3570 0.036388 GATGCGGAGGACACCAAGAA 60.036 55.0 0.0 0.0 0.0 2.52 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
162 166 2.086869 CCACCTGTCATGCAACCTAAG 58.913 52.381 0.00 0.00 0.00 2.18
163 167 2.290260 CCACCTGTCATGCAACCTAAGA 60.290 50.000 0.00 0.00 0.00 2.10
164 168 3.411446 CACCTGTCATGCAACCTAAGAA 58.589 45.455 0.00 0.00 0.00 2.52
213 218 1.918293 CAGGCCACCCAGACCTACA 60.918 63.158 5.01 0.00 30.84 2.74
330 335 2.109774 CAGAAGAGTCCTGCTCATCCT 58.890 52.381 0.00 0.00 46.47 3.24
414 419 1.609501 CACCTCCGTCTGAAGGGGA 60.610 63.158 11.34 2.37 0.00 4.81
788 1001 1.675310 CAGCCCAATCGTCCAGCAA 60.675 57.895 0.00 0.00 0.00 3.91
955 1169 8.902040 AAATTTTAGCTAAAAGAGAAGCATCG 57.098 30.769 29.69 0.00 41.32 3.84
956 1170 7.849804 ATTTTAGCTAAAAGAGAAGCATCGA 57.150 32.000 29.69 8.86 41.32 3.59
957 1171 7.849804 TTTTAGCTAAAAGAGAAGCATCGAT 57.150 32.000 24.42 0.00 41.32 3.59
958 1172 7.470289 TTTAGCTAAAAGAGAAGCATCGATC 57.530 36.000 16.53 0.00 41.32 3.69
959 1173 5.016051 AGCTAAAAGAGAAGCATCGATCA 57.984 39.130 0.00 0.00 41.32 2.92
960 1174 4.808364 AGCTAAAAGAGAAGCATCGATCAC 59.192 41.667 0.00 0.00 41.32 3.06
961 1175 4.568359 GCTAAAAGAGAAGCATCGATCACA 59.432 41.667 0.00 0.00 38.63 3.58
962 1176 4.935885 AAAAGAGAAGCATCGATCACAC 57.064 40.909 0.00 0.00 0.00 3.82
963 1177 2.593346 AGAGAAGCATCGATCACACC 57.407 50.000 0.00 0.00 0.00 4.16
964 1178 1.827344 AGAGAAGCATCGATCACACCA 59.173 47.619 0.00 0.00 0.00 4.17
965 1179 2.433604 AGAGAAGCATCGATCACACCAT 59.566 45.455 0.00 0.00 0.00 3.55
966 1180 2.799412 GAGAAGCATCGATCACACCATC 59.201 50.000 0.00 0.00 0.00 3.51
967 1181 2.433604 AGAAGCATCGATCACACCATCT 59.566 45.455 0.00 0.00 0.00 2.90
968 1182 3.638627 AGAAGCATCGATCACACCATCTA 59.361 43.478 0.00 0.00 0.00 1.98
969 1183 3.377346 AGCATCGATCACACCATCTAC 57.623 47.619 0.00 0.00 0.00 2.59
970 1184 2.961741 AGCATCGATCACACCATCTACT 59.038 45.455 0.00 0.00 0.00 2.57
971 1185 3.386078 AGCATCGATCACACCATCTACTT 59.614 43.478 0.00 0.00 0.00 2.24
972 1186 3.492383 GCATCGATCACACCATCTACTTG 59.508 47.826 0.00 0.00 0.00 3.16
973 1187 3.801114 TCGATCACACCATCTACTTGG 57.199 47.619 0.00 0.00 42.82 3.61
974 1188 3.361786 TCGATCACACCATCTACTTGGA 58.638 45.455 0.00 0.00 39.25 3.53
998 1212 1.220477 GGAGGTCTGAAGGAGCAGC 59.780 63.158 0.00 0.00 44.16 5.25
1038 1252 2.597805 ACACAGCTCTCCGTCCGT 60.598 61.111 0.00 0.00 0.00 4.69
1071 1285 3.537580 ACACGTTGCTCAAGTAGGAAAA 58.462 40.909 0.00 0.00 37.28 2.29
1075 1289 3.186613 CGTTGCTCAAGTAGGAAAAGGTC 59.813 47.826 0.00 0.00 37.28 3.85
1078 1292 3.391296 TGCTCAAGTAGGAAAAGGTCAGT 59.609 43.478 0.00 0.00 0.00 3.41
1088 1302 6.248569 AGGAAAAGGTCAGTGACTTTTCTA 57.751 37.500 32.03 1.77 40.12 2.10
1089 1303 6.292150 AGGAAAAGGTCAGTGACTTTTCTAG 58.708 40.000 32.03 0.00 40.12 2.43
1099 1315 4.516698 AGTGACTTTTCTAGTGTTGGCATG 59.483 41.667 0.00 0.00 37.17 4.06
1100 1316 4.515191 GTGACTTTTCTAGTGTTGGCATGA 59.485 41.667 0.00 0.00 37.17 3.07
1125 1349 2.106683 CCGTCGAGCCCACCAAATC 61.107 63.158 0.00 0.00 0.00 2.17
1127 1351 1.299976 GTCGAGCCCACCAAATCCT 59.700 57.895 0.00 0.00 0.00 3.24
1141 1365 4.721776 ACCAAATCCTATGGAGTAAGCAGA 59.278 41.667 0.00 0.00 40.56 4.26
1146 1378 3.133003 TCCTATGGAGTAAGCAGAGCAAC 59.867 47.826 0.00 0.00 0.00 4.17
1169 1424 2.103771 GAGGAGCTAATGGATCTGTGCA 59.896 50.000 0.00 0.00 0.00 4.57
1401 1656 0.753111 CCATCCCCAAGGTAAGCAGC 60.753 60.000 0.00 0.00 0.00 5.25
1402 1657 0.034186 CATCCCCAAGGTAAGCAGCA 60.034 55.000 0.00 0.00 0.00 4.41
1403 1658 0.034089 ATCCCCAAGGTAAGCAGCAC 60.034 55.000 0.00 0.00 0.00 4.40
1406 1661 1.244019 CCCAAGGTAAGCAGCACCAC 61.244 60.000 4.77 0.00 38.62 4.16
1410 1665 1.228429 GGTAAGCAGCACCACCCAA 60.228 57.895 0.00 0.00 36.01 4.12
1411 1666 1.244019 GGTAAGCAGCACCACCCAAG 61.244 60.000 0.00 0.00 36.01 3.61
1422 1677 1.062505 ACCACCCAAGAAAACCATGGT 60.063 47.619 13.00 13.00 31.88 3.55
1429 1684 2.965147 CAAGAAAACCATGGTCCCAAGT 59.035 45.455 20.07 0.00 0.00 3.16
1430 1685 2.876581 AGAAAACCATGGTCCCAAGTC 58.123 47.619 20.07 9.29 0.00 3.01
1431 1686 2.447047 AGAAAACCATGGTCCCAAGTCT 59.553 45.455 20.07 11.37 0.00 3.24
1432 1687 2.586648 AAACCATGGTCCCAAGTCTC 57.413 50.000 20.07 0.00 0.00 3.36
1434 1689 1.444933 ACCATGGTCCCAAGTCTCAA 58.555 50.000 13.00 0.00 0.00 3.02
1435 1690 1.073923 ACCATGGTCCCAAGTCTCAAC 59.926 52.381 13.00 0.00 0.00 3.18
1436 1691 1.352352 CCATGGTCCCAAGTCTCAACT 59.648 52.381 2.57 0.00 37.32 3.16
1446 1701 1.629043 AGTCTCAACTCCCAAGCGTA 58.371 50.000 0.00 0.00 0.00 4.42
1449 1704 1.000506 TCTCAACTCCCAAGCGTACAC 59.999 52.381 0.00 0.00 0.00 2.90
1456 1711 0.108804 CCCAAGCGTACACGAGTGAT 60.109 55.000 10.50 0.00 43.02 3.06
1466 1721 4.248985 CGAGTGATCGTCGTCGTC 57.751 61.111 8.71 0.38 38.33 4.20
1473 1728 1.001048 TGATCGTCGTCGTCCTTGTTT 60.001 47.619 1.33 0.00 38.33 2.83
1476 1731 1.066002 TCGTCGTCGTCCTTGTTTTCT 59.934 47.619 1.33 0.00 38.33 2.52
1483 1738 4.552184 CGTCGTCCTTGTTTTCTTTCCTTC 60.552 45.833 0.00 0.00 0.00 3.46
1614 1873 3.797353 GCATCCCCTTCAGCCCGA 61.797 66.667 0.00 0.00 0.00 5.14
1616 1875 1.072159 CATCCCCTTCAGCCCGATC 59.928 63.158 0.00 0.00 0.00 3.69
1856 2115 2.572647 GACCTCGACGTGTACGCG 60.573 66.667 26.18 26.18 44.43 6.01
2020 2389 4.814294 GTTCGAGGCCGCCGTGAT 62.814 66.667 17.73 0.00 35.37 3.06
2281 2824 4.381932 CCAAATCCAAGTGCCCTTGTATTC 60.382 45.833 8.17 0.00 45.49 1.75
2322 2871 2.069273 GACGTGACAACTCTGGAATGG 58.931 52.381 0.00 0.00 0.00 3.16
2332 2881 5.301805 ACAACTCTGGAATGGTAAAACTTGG 59.698 40.000 0.00 0.00 0.00 3.61
2348 2897 4.601406 ACTTGGATGGTTAGGGCATTTA 57.399 40.909 0.00 0.00 0.00 1.40
2352 2901 3.139077 GGATGGTTAGGGCATTTACTCG 58.861 50.000 0.00 0.00 0.00 4.18
2353 2902 2.702592 TGGTTAGGGCATTTACTCGG 57.297 50.000 0.00 0.00 0.00 4.63
2356 2905 0.913205 TTAGGGCATTTACTCGGGCA 59.087 50.000 0.00 0.00 0.00 5.36
2359 2908 1.172812 GGGCATTTACTCGGGCATCC 61.173 60.000 0.00 0.00 0.00 3.51
2376 2925 3.474806 CGTCAGCGGACATGGAAC 58.525 61.111 17.26 0.00 44.54 3.62
2377 2926 2.100631 CGTCAGCGGACATGGAACC 61.101 63.158 17.26 0.00 44.54 3.62
2378 2927 1.003839 GTCAGCGGACATGGAACCA 60.004 57.895 12.41 0.00 43.73 3.67
2379 2928 1.021390 GTCAGCGGACATGGAACCAG 61.021 60.000 12.41 0.00 43.73 4.00
2380 2929 1.191489 TCAGCGGACATGGAACCAGA 61.191 55.000 0.00 0.00 0.00 3.86
2381 2930 1.021390 CAGCGGACATGGAACCAGAC 61.021 60.000 0.00 0.00 0.00 3.51
2382 2931 1.194781 AGCGGACATGGAACCAGACT 61.195 55.000 0.00 0.00 0.00 3.24
2383 2932 1.021390 GCGGACATGGAACCAGACTG 61.021 60.000 0.00 0.00 0.00 3.51
2387 2936 2.026822 GGACATGGAACCAGACTGACAT 60.027 50.000 3.32 0.37 0.00 3.06
2389 2938 2.639347 ACATGGAACCAGACTGACATGA 59.361 45.455 23.63 2.54 39.08 3.07
2399 2948 2.298446 AGACTGACATGAGACCACACTG 59.702 50.000 0.00 0.00 0.00 3.66
2406 2955 1.448540 GAGACCACACTGATGCCGG 60.449 63.158 0.00 0.00 0.00 6.13
2409 2958 2.821366 CCACACTGATGCCGGAGC 60.821 66.667 5.05 0.00 40.48 4.70
2417 2966 3.757248 GATGCCGGAGCCGACCATT 62.757 63.158 5.05 0.00 42.83 3.16
2422 2971 1.079127 CGGAGCCGACCATTCAACT 60.079 57.895 2.00 0.00 42.83 3.16
2423 2972 0.174845 CGGAGCCGACCATTCAACTA 59.825 55.000 2.00 0.00 42.83 2.24
2428 2979 4.202223 GGAGCCGACCATTCAACTATCTTA 60.202 45.833 0.00 0.00 0.00 2.10
2432 2983 8.362464 AGCCGACCATTCAACTATCTTATATA 57.638 34.615 0.00 0.00 0.00 0.86
2444 2995 9.561270 CAACTATCTTATATATGTCCGTCAGTG 57.439 37.037 0.00 0.00 0.00 3.66
2447 2998 9.995957 CTATCTTATATATGTCCGTCAGTGAAG 57.004 37.037 0.00 0.00 0.00 3.02
2449 3000 2.604046 ATATGTCCGTCAGTGAAGGC 57.396 50.000 19.24 14.51 31.44 4.35
2450 3001 1.557099 TATGTCCGTCAGTGAAGGCT 58.443 50.000 19.24 9.44 31.44 4.58
2462 3013 7.812669 CCGTCAGTGAAGGCTAATTTAAAATTT 59.187 33.333 12.37 0.00 0.00 1.82
2483 3035 8.773033 AATTTAATGAGTCCAATCCATAAGCT 57.227 30.769 0.00 0.00 0.00 3.74
2484 3036 7.807977 TTTAATGAGTCCAATCCATAAGCTC 57.192 36.000 0.00 0.00 0.00 4.09
2496 3048 0.603569 ATAAGCTCGCCGGGTCATAG 59.396 55.000 2.18 0.00 0.00 2.23
2499 3051 3.043419 CTCGCCGGGTCATAGGAG 58.957 66.667 2.18 0.00 0.00 3.69
2501 3053 4.647615 CGCCGGGTCATAGGAGCG 62.648 72.222 2.18 0.00 42.46 5.03
2503 3055 3.090219 GCCGGGTCATAGGAGCGTT 62.090 63.158 2.18 0.00 42.46 4.84
2512 3064 2.499693 TCATAGGAGCGTTGGATCACAA 59.500 45.455 0.00 0.00 36.54 3.33
2539 3091 1.200103 GATCACATGCGCGATCACG 59.800 57.895 12.10 0.00 38.33 4.35
2589 3178 4.386867 TTTTACATGCCGACCACAAAAA 57.613 36.364 0.00 0.00 0.00 1.94
2594 3183 3.509575 ACATGCCGACCACAAAAACATAT 59.490 39.130 0.00 0.00 0.00 1.78
2595 3184 3.840890 TGCCGACCACAAAAACATATC 57.159 42.857 0.00 0.00 0.00 1.63
2596 3185 3.149981 TGCCGACCACAAAAACATATCA 58.850 40.909 0.00 0.00 0.00 2.15
2597 3186 3.190327 TGCCGACCACAAAAACATATCAG 59.810 43.478 0.00 0.00 0.00 2.90
2598 3187 3.190535 GCCGACCACAAAAACATATCAGT 59.809 43.478 0.00 0.00 0.00 3.41
2599 3188 4.671766 GCCGACCACAAAAACATATCAGTC 60.672 45.833 0.00 0.00 0.00 3.51
2600 3189 4.695455 CCGACCACAAAAACATATCAGTCT 59.305 41.667 0.00 0.00 0.00 3.24
2601 3190 5.390885 CCGACCACAAAAACATATCAGTCTG 60.391 44.000 0.00 0.00 0.00 3.51
2612 3217 0.891373 ATCAGTCTGTCAGTCCGTGG 59.109 55.000 0.00 0.00 0.00 4.94
2613 3218 1.179174 TCAGTCTGTCAGTCCGTGGG 61.179 60.000 0.00 0.00 0.00 4.61
2672 3378 3.130516 CGAGCTTCCATACTCAAGGTGTA 59.869 47.826 0.00 0.00 30.50 2.90
2688 3411 2.364317 TAGCCAGCCTCCGCTTCT 60.364 61.111 0.00 0.00 45.55 2.85
2722 3445 2.691241 GCCTCCATCTCCTCCTTGTCTA 60.691 54.545 0.00 0.00 0.00 2.59
2730 3453 1.359474 TCCTCCTTGTCTACTGCCTCT 59.641 52.381 0.00 0.00 0.00 3.69
2756 3480 1.277842 TCTTTCTGCCGCTCCAACATA 59.722 47.619 0.00 0.00 0.00 2.29
2814 3570 4.216257 CGACATCCAAATTCAAGGTCAACT 59.784 41.667 0.00 0.00 0.00 3.16
2878 3634 0.033504 TCGAGCAACGCCTTCTTCTT 59.966 50.000 0.00 0.00 42.26 2.52
2943 3720 0.917939 GAGCGCTAGTTTCTTCTCGC 59.082 55.000 11.50 0.00 42.46 5.03
2945 3722 1.351153 GCGCTAGTTTCTTCTCGCTT 58.649 50.000 0.00 0.00 39.51 4.68
2947 3724 2.329379 CGCTAGTTTCTTCTCGCTTGT 58.671 47.619 0.00 0.00 0.00 3.16
3006 3784 1.361668 CTTGATGTCGGACCGCTTGG 61.362 60.000 9.66 0.00 39.35 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.019278 GCATCGTCGAAGGGCAAGAA 61.019 55.000 0.00 0.00 0.00 2.52
162 166 5.382618 TGAGGAGGTACGTAAAGAACTTC 57.617 43.478 0.00 0.00 0.00 3.01
163 167 5.997384 ATGAGGAGGTACGTAAAGAACTT 57.003 39.130 0.00 0.00 0.00 2.66
164 168 5.593502 CCTATGAGGAGGTACGTAAAGAACT 59.406 44.000 0.00 0.00 37.67 3.01
330 335 5.389859 TTTCGATCGTAGTTTTCACCCTA 57.610 39.130 15.94 0.00 0.00 3.53
711 908 2.363795 CAGGGTCCAGTCGGCCTA 60.364 66.667 0.00 0.00 0.00 3.93
781 994 1.679944 GCCTATCTGCTTGTTGCTGGA 60.680 52.381 0.00 0.00 43.37 3.86
788 1001 0.254178 CTGGTGGCCTATCTGCTTGT 59.746 55.000 3.32 0.00 0.00 3.16
941 1155 3.686726 GGTGTGATCGATGCTTCTCTTTT 59.313 43.478 0.54 0.00 0.00 2.27
942 1156 3.265791 GGTGTGATCGATGCTTCTCTTT 58.734 45.455 0.54 0.00 0.00 2.52
943 1157 2.234661 TGGTGTGATCGATGCTTCTCTT 59.765 45.455 0.54 0.00 0.00 2.85
944 1158 1.827344 TGGTGTGATCGATGCTTCTCT 59.173 47.619 0.54 0.00 0.00 3.10
945 1159 2.299993 TGGTGTGATCGATGCTTCTC 57.700 50.000 0.54 0.00 0.00 2.87
946 1160 2.433604 AGATGGTGTGATCGATGCTTCT 59.566 45.455 0.54 0.00 0.00 2.85
947 1161 2.831333 AGATGGTGTGATCGATGCTTC 58.169 47.619 0.54 0.00 0.00 3.86
948 1162 2.996249 AGATGGTGTGATCGATGCTT 57.004 45.000 0.54 0.00 0.00 3.91
949 1163 2.961741 AGTAGATGGTGTGATCGATGCT 59.038 45.455 0.54 0.00 0.00 3.79
950 1164 3.377346 AGTAGATGGTGTGATCGATGC 57.623 47.619 0.54 0.00 0.00 3.91
951 1165 4.053983 CCAAGTAGATGGTGTGATCGATG 58.946 47.826 0.54 0.00 35.65 3.84
952 1166 3.960755 TCCAAGTAGATGGTGTGATCGAT 59.039 43.478 0.00 0.00 41.46 3.59
953 1167 3.361786 TCCAAGTAGATGGTGTGATCGA 58.638 45.455 0.00 0.00 41.46 3.59
954 1168 3.711086 CTCCAAGTAGATGGTGTGATCG 58.289 50.000 0.00 0.00 41.46 3.69
955 1169 3.462021 GCTCCAAGTAGATGGTGTGATC 58.538 50.000 0.00 0.00 41.46 2.92
956 1170 2.171448 GGCTCCAAGTAGATGGTGTGAT 59.829 50.000 0.00 0.00 41.46 3.06
957 1171 1.555075 GGCTCCAAGTAGATGGTGTGA 59.445 52.381 0.00 0.00 41.46 3.58
958 1172 1.556911 AGGCTCCAAGTAGATGGTGTG 59.443 52.381 0.00 0.00 41.46 3.82
959 1173 1.958288 AGGCTCCAAGTAGATGGTGT 58.042 50.000 0.00 0.00 41.46 4.16
960 1174 2.636830 CAAGGCTCCAAGTAGATGGTG 58.363 52.381 0.00 0.00 41.46 4.17
961 1175 1.561542 CCAAGGCTCCAAGTAGATGGT 59.438 52.381 0.00 0.00 41.46 3.55
962 1176 1.839994 TCCAAGGCTCCAAGTAGATGG 59.160 52.381 0.00 0.00 42.12 3.51
963 1177 2.158842 CCTCCAAGGCTCCAAGTAGATG 60.159 54.545 0.00 0.00 0.00 2.90
964 1178 2.122768 CCTCCAAGGCTCCAAGTAGAT 58.877 52.381 0.00 0.00 0.00 1.98
965 1179 1.203313 ACCTCCAAGGCTCCAAGTAGA 60.203 52.381 0.00 0.00 39.63 2.59
966 1180 1.208293 GACCTCCAAGGCTCCAAGTAG 59.792 57.143 0.00 0.00 39.63 2.57
967 1181 1.203313 AGACCTCCAAGGCTCCAAGTA 60.203 52.381 0.00 0.00 39.63 2.24
968 1182 0.474660 AGACCTCCAAGGCTCCAAGT 60.475 55.000 0.00 0.00 39.63 3.16
969 1183 0.035630 CAGACCTCCAAGGCTCCAAG 60.036 60.000 0.00 0.00 39.63 3.61
970 1184 0.473694 TCAGACCTCCAAGGCTCCAA 60.474 55.000 0.00 0.00 39.63 3.53
971 1185 0.473694 TTCAGACCTCCAAGGCTCCA 60.474 55.000 0.00 0.00 39.63 3.86
972 1186 0.251634 CTTCAGACCTCCAAGGCTCC 59.748 60.000 0.00 0.00 39.63 4.70
973 1187 0.251634 CCTTCAGACCTCCAAGGCTC 59.748 60.000 0.00 0.00 39.63 4.70
974 1188 0.178891 TCCTTCAGACCTCCAAGGCT 60.179 55.000 0.00 0.00 39.63 4.58
998 1212 1.530293 GCTCTATCTCTTGCGCCATTG 59.470 52.381 4.18 0.00 0.00 2.82
1008 1222 2.455557 AGCTGTGTGTGCTCTATCTCT 58.544 47.619 0.00 0.00 35.67 3.10
1042 1256 0.608130 TGAGCAACGTGTAGGCTGAT 59.392 50.000 8.71 0.00 38.15 2.90
1050 1264 2.902705 TTCCTACTTGAGCAACGTGT 57.097 45.000 0.00 0.00 0.00 4.49
1071 1285 5.360591 CAACACTAGAAAAGTCACTGACCT 58.639 41.667 5.51 0.00 35.76 3.85
1075 1289 3.876914 TGCCAACACTAGAAAAGTCACTG 59.123 43.478 0.00 0.00 35.76 3.66
1078 1292 4.515191 GTCATGCCAACACTAGAAAAGTCA 59.485 41.667 0.00 0.00 35.76 3.41
1110 1334 1.140852 CATAGGATTTGGTGGGCTCGA 59.859 52.381 0.00 0.00 0.00 4.04
1125 1349 3.133721 AGTTGCTCTGCTTACTCCATAGG 59.866 47.826 0.00 0.00 0.00 2.57
1127 1351 3.769300 TCAGTTGCTCTGCTTACTCCATA 59.231 43.478 4.94 0.00 43.32 2.74
1141 1365 2.191400 TCCATTAGCTCCTCAGTTGCT 58.809 47.619 0.00 0.00 40.43 3.91
1146 1378 3.803021 GCACAGATCCATTAGCTCCTCAG 60.803 52.174 0.00 0.00 0.00 3.35
1151 1383 2.225963 GCATGCACAGATCCATTAGCTC 59.774 50.000 14.21 0.00 0.00 4.09
1169 1424 0.463295 CGTCCCAAGCTCATCTGCAT 60.463 55.000 0.00 0.00 34.99 3.96
1401 1656 1.344114 CCATGGTTTTCTTGGGTGGTG 59.656 52.381 2.57 0.00 37.12 4.17
1402 1657 1.062505 ACCATGGTTTTCTTGGGTGGT 60.063 47.619 13.00 0.00 42.97 4.16
1403 1658 1.618343 GACCATGGTTTTCTTGGGTGG 59.382 52.381 20.85 0.00 42.97 4.61
1406 1661 1.266178 GGGACCATGGTTTTCTTGGG 58.734 55.000 20.85 0.00 42.97 4.12
1410 1665 2.447047 AGACTTGGGACCATGGTTTTCT 59.553 45.455 20.85 11.28 0.00 2.52
1411 1666 2.820197 GAGACTTGGGACCATGGTTTTC 59.180 50.000 20.85 12.06 0.00 2.29
1422 1677 1.699634 CTTGGGAGTTGAGACTTGGGA 59.300 52.381 0.00 0.00 35.88 4.37
1429 1684 1.000506 GTGTACGCTTGGGAGTTGAGA 59.999 52.381 0.00 0.00 0.00 3.27
1430 1685 1.429463 GTGTACGCTTGGGAGTTGAG 58.571 55.000 0.00 0.00 0.00 3.02
1431 1686 0.319211 CGTGTACGCTTGGGAGTTGA 60.319 55.000 4.67 0.00 0.00 3.18
1432 1687 0.319211 TCGTGTACGCTTGGGAGTTG 60.319 55.000 4.67 0.00 39.60 3.16
1434 1689 1.177256 ACTCGTGTACGCTTGGGAGT 61.177 55.000 4.67 6.84 39.60 3.85
1435 1690 0.732880 CACTCGTGTACGCTTGGGAG 60.733 60.000 4.67 6.22 39.60 4.30
1436 1691 1.174078 TCACTCGTGTACGCTTGGGA 61.174 55.000 4.67 0.76 39.60 4.37
1456 1711 1.066002 AGAAAACAAGGACGACGACGA 59.934 47.619 15.32 0.00 42.66 4.20
1464 1719 4.598062 CACGAAGGAAAGAAAACAAGGAC 58.402 43.478 0.00 0.00 0.00 3.85
1466 1721 3.372060 GCACGAAGGAAAGAAAACAAGG 58.628 45.455 0.00 0.00 0.00 3.61
1473 1728 1.827315 CGCACGCACGAAGGAAAGAA 61.827 55.000 0.00 0.00 34.06 2.52
1476 1731 2.586635 ACGCACGCACGAAGGAAA 60.587 55.556 4.54 0.00 36.70 3.13
1614 1873 2.901042 GGCGAAGTCGAAGGGGAT 59.099 61.111 4.59 0.00 43.02 3.85
1772 2031 1.687612 CATGGTCTCCTGGCCTTGT 59.312 57.895 3.32 0.00 0.00 3.16
1814 2073 4.265056 GTGAACCACCCCGGCAGT 62.265 66.667 0.00 0.00 39.03 4.40
2159 2529 2.046314 GTGTCATCCCCACCACGG 60.046 66.667 0.00 0.00 0.00 4.94
2281 2824 1.139989 CACAGAGTACAAGGCACACG 58.860 55.000 0.00 0.00 0.00 4.49
2322 2871 4.083565 TGCCCTAACCATCCAAGTTTTAC 58.916 43.478 0.00 0.00 0.00 2.01
2332 2881 3.139077 CCGAGTAAATGCCCTAACCATC 58.861 50.000 0.00 0.00 0.00 3.51
2359 2908 2.100631 GGTTCCATGTCCGCTGACG 61.101 63.158 3.71 0.00 44.86 4.35
2363 2912 1.194781 AGTCTGGTTCCATGTCCGCT 61.195 55.000 0.00 0.00 0.00 5.52
2367 2916 2.839486 TGTCAGTCTGGTTCCATGTC 57.161 50.000 0.00 0.00 0.00 3.06
2368 2917 2.639347 TCATGTCAGTCTGGTTCCATGT 59.361 45.455 15.74 0.00 33.27 3.21
2369 2918 3.055602 TCTCATGTCAGTCTGGTTCCATG 60.056 47.826 0.00 7.90 0.00 3.66
2370 2919 3.055530 GTCTCATGTCAGTCTGGTTCCAT 60.056 47.826 0.00 0.00 0.00 3.41
2371 2920 2.300152 GTCTCATGTCAGTCTGGTTCCA 59.700 50.000 0.00 0.00 0.00 3.53
2372 2921 2.354203 GGTCTCATGTCAGTCTGGTTCC 60.354 54.545 0.00 0.00 0.00 3.62
2373 2922 2.300152 TGGTCTCATGTCAGTCTGGTTC 59.700 50.000 0.00 0.00 0.00 3.62
2374 2923 2.037772 GTGGTCTCATGTCAGTCTGGTT 59.962 50.000 0.00 0.00 0.00 3.67
2375 2924 1.620819 GTGGTCTCATGTCAGTCTGGT 59.379 52.381 0.00 0.00 0.00 4.00
2376 2925 1.620323 TGTGGTCTCATGTCAGTCTGG 59.380 52.381 0.00 0.00 0.00 3.86
2377 2926 2.298446 AGTGTGGTCTCATGTCAGTCTG 59.702 50.000 0.00 0.00 0.00 3.51
2378 2927 2.298446 CAGTGTGGTCTCATGTCAGTCT 59.702 50.000 0.00 0.00 0.00 3.24
2379 2928 2.297315 TCAGTGTGGTCTCATGTCAGTC 59.703 50.000 0.00 0.00 0.00 3.51
2380 2929 2.319844 TCAGTGTGGTCTCATGTCAGT 58.680 47.619 0.00 0.00 0.00 3.41
2381 2930 3.259902 CATCAGTGTGGTCTCATGTCAG 58.740 50.000 0.00 0.00 0.00 3.51
2382 2931 2.613725 GCATCAGTGTGGTCTCATGTCA 60.614 50.000 0.00 0.00 0.00 3.58
2383 2932 2.005451 GCATCAGTGTGGTCTCATGTC 58.995 52.381 0.00 0.00 0.00 3.06
2387 2936 1.293179 CGGCATCAGTGTGGTCTCA 59.707 57.895 0.00 0.00 0.00 3.27
2389 2938 1.892819 CTCCGGCATCAGTGTGGTCT 61.893 60.000 0.00 0.00 0.00 3.85
2399 2948 3.757248 AATGGTCGGCTCCGGCATC 62.757 63.158 15.18 0.00 46.91 3.91
2406 2955 3.460857 AGATAGTTGAATGGTCGGCTC 57.539 47.619 0.00 0.00 0.00 4.70
2417 2966 9.516546 ACTGACGGACATATATAAGATAGTTGA 57.483 33.333 0.00 0.00 0.00 3.18
2422 2971 8.957466 CCTTCACTGACGGACATATATAAGATA 58.043 37.037 0.00 0.00 0.00 1.98
2423 2972 7.577807 GCCTTCACTGACGGACATATATAAGAT 60.578 40.741 5.74 0.00 0.00 2.40
2428 2979 3.898123 AGCCTTCACTGACGGACATATAT 59.102 43.478 5.74 0.00 0.00 0.86
2432 2983 1.557099 TAGCCTTCACTGACGGACAT 58.443 50.000 5.74 0.00 0.00 3.06
2462 3013 5.541845 CGAGCTTATGGATTGGACTCATTA 58.458 41.667 0.00 0.00 0.00 1.90
2466 3018 2.139118 GCGAGCTTATGGATTGGACTC 58.861 52.381 0.00 0.00 0.00 3.36
2470 3022 1.230635 CCGGCGAGCTTATGGATTGG 61.231 60.000 9.30 0.00 0.00 3.16
2471 3023 1.230635 CCCGGCGAGCTTATGGATTG 61.231 60.000 9.30 0.00 0.00 2.67
2472 3024 1.071471 CCCGGCGAGCTTATGGATT 59.929 57.895 9.30 0.00 0.00 3.01
2480 3032 3.227276 CCTATGACCCGGCGAGCT 61.227 66.667 9.30 0.00 0.00 4.09
2483 3035 3.224324 GCTCCTATGACCCGGCGA 61.224 66.667 9.30 0.00 0.00 5.54
2484 3036 4.647615 CGCTCCTATGACCCGGCG 62.648 72.222 0.00 0.00 36.89 6.46
2503 3055 1.302431 CCGCCACTGTTGTGATCCA 60.302 57.895 0.00 0.00 46.55 3.41
2512 3064 1.746615 GCATGTGATCCGCCACTGT 60.747 57.895 0.00 0.00 37.89 3.55
2518 3070 3.341043 ATCGCGCATGTGATCCGC 61.341 61.111 11.26 7.54 41.41 5.54
2567 3124 4.592485 TTTTGTGGTCGGCATGTAAAAT 57.408 36.364 0.00 0.00 0.00 1.82
2589 3178 3.129462 CACGGACTGACAGACTGATATGT 59.871 47.826 18.73 2.36 31.29 2.29
2594 3183 1.179174 CCCACGGACTGACAGACTGA 61.179 60.000 18.73 0.00 0.00 3.41
2595 3184 1.179174 TCCCACGGACTGACAGACTG 61.179 60.000 10.08 10.93 0.00 3.51
2596 3185 0.469331 TTCCCACGGACTGACAGACT 60.469 55.000 10.08 0.00 0.00 3.24
2597 3186 0.391597 TTTCCCACGGACTGACAGAC 59.608 55.000 10.08 2.35 0.00 3.51
2598 3187 1.124780 TTTTCCCACGGACTGACAGA 58.875 50.000 10.08 0.00 0.00 3.41
2599 3188 1.961793 TTTTTCCCACGGACTGACAG 58.038 50.000 0.00 0.00 0.00 3.51
2600 3189 2.649531 ATTTTTCCCACGGACTGACA 57.350 45.000 0.00 0.00 0.00 3.58
2601 3190 4.320870 TCTAATTTTTCCCACGGACTGAC 58.679 43.478 0.00 0.00 0.00 3.51
2641 3246 0.610174 ATGGAAGCTCGAACTGCTGA 59.390 50.000 0.00 0.00 41.03 4.26
2688 3411 3.077556 GAGGCGGCAGAGGAGGAA 61.078 66.667 13.08 0.00 0.00 3.36
2722 3445 3.118811 GCAGAAAGATGACTAGAGGCAGT 60.119 47.826 0.00 0.00 0.00 4.40
2730 3453 1.137086 GGAGCGGCAGAAAGATGACTA 59.863 52.381 1.45 0.00 0.00 2.59
2814 3570 0.036388 GATGCGGAGGACACCAAGAA 60.036 55.000 0.00 0.00 0.00 2.52
2840 3596 2.414481 CGAAGACAAGAAGGTGCAGATG 59.586 50.000 0.00 0.00 0.00 2.90
2943 3720 5.506317 GGTTCAAACTGTTGATGGAGACAAG 60.506 44.000 0.00 0.00 43.29 3.16
2945 3722 3.882888 GGTTCAAACTGTTGATGGAGACA 59.117 43.478 0.00 0.00 43.29 3.41
2947 3724 4.103153 AGAGGTTCAAACTGTTGATGGAGA 59.897 41.667 0.00 0.00 43.29 3.71
3006 3784 1.258445 TGTCGAAGAAGGAGGAGGCC 61.258 60.000 0.00 0.00 39.69 5.19


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

AutoCloner maintained by Alex Coulton.