Multiple sequence alignment - TraesCS3D01G380700

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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 TraesCS3D01G380700 chr3D 100.000 4642 0 0 1 4642 496784296 496788937 0.000000e+00 8573
1 TraesCS3D01G380700 chr3A 89.913 2409 116 51 1328 3698 638027692 638030011 0.000000e+00 2985
2 TraesCS3D01G380700 chr3A 95.309 1279 48 6 1 1275 638026423 638027693 0.000000e+00 2019
3 TraesCS3D01G380700 chr3A 94.645 915 37 9 3730 4642 736312129 736311225 0.000000e+00 1408
4 TraesCS3D01G380700 chr3B 88.993 2444 144 57 1325 3698 656289668 656292056 0.000000e+00 2907
5 TraesCS3D01G380700 chr3B 95.155 1321 52 8 1 1316 656288372 656289685 0.000000e+00 2074
6 TraesCS3D01G380700 chr2D 97.137 943 18 4 3700 4642 118846754 118847687 0.000000e+00 1583
7 TraesCS3D01G380700 chr2D 97.590 913 16 4 3730 4642 97628462 97629368 0.000000e+00 1559
8 TraesCS3D01G380700 chr1D 96.507 916 26 5 3730 4642 426912791 426913703 0.000000e+00 1509
9 TraesCS3D01G380700 chr1D 95.877 946 16 8 3698 4642 462395365 462394442 0.000000e+00 1509
10 TraesCS3D01G380700 chr1D 87.352 253 26 2 2551 2803 363250875 363250629 7.600000e-73 285
11 TraesCS3D01G380700 chr1D 83.770 191 26 5 2229 2418 363251082 363250896 4.770000e-40 176
12 TraesCS3D01G380700 chrUn 95.295 914 34 6 3730 4642 1076917 1077822 0.000000e+00 1441
13 TraesCS3D01G380700 chrUn 95.295 914 34 6 3730 4642 314685049 314685954 0.000000e+00 1441
14 TraesCS3D01G380700 chrUn 90.715 937 57 15 3730 4642 289620397 289621327 0.000000e+00 1221
15 TraesCS3D01G380700 chr1A 93.742 751 37 7 3895 4642 30878110 30877367 0.000000e+00 1118
16 TraesCS3D01G380700 chr1A 87.008 254 27 2 2551 2804 462401070 462400823 9.830000e-72 281
17 TraesCS3D01G380700 chr1A 83.246 191 27 5 2229 2418 462401277 462401091 2.220000e-38 171
18 TraesCS3D01G380700 chr1B 87.402 254 26 2 2551 2804 486489653 486489406 2.110000e-73 287
19 TraesCS3D01G380700 chr1B 82.723 191 28 5 2229 2418 486489860 486489674 1.030000e-36 165


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 TraesCS3D01G380700 chr3D 496784296 496788937 4641 False 8573.0 8573 100.000 1 4642 1 chr3D.!!$F1 4641
1 TraesCS3D01G380700 chr3A 638026423 638030011 3588 False 2502.0 2985 92.611 1 3698 2 chr3A.!!$F1 3697
2 TraesCS3D01G380700 chr3A 736311225 736312129 904 True 1408.0 1408 94.645 3730 4642 1 chr3A.!!$R1 912
3 TraesCS3D01G380700 chr3B 656288372 656292056 3684 False 2490.5 2907 92.074 1 3698 2 chr3B.!!$F1 3697
4 TraesCS3D01G380700 chr2D 118846754 118847687 933 False 1583.0 1583 97.137 3700 4642 1 chr2D.!!$F2 942
5 TraesCS3D01G380700 chr2D 97628462 97629368 906 False 1559.0 1559 97.590 3730 4642 1 chr2D.!!$F1 912
6 TraesCS3D01G380700 chr1D 426912791 426913703 912 False 1509.0 1509 96.507 3730 4642 1 chr1D.!!$F1 912
7 TraesCS3D01G380700 chr1D 462394442 462395365 923 True 1509.0 1509 95.877 3698 4642 1 chr1D.!!$R1 944
8 TraesCS3D01G380700 chrUn 1076917 1077822 905 False 1441.0 1441 95.295 3730 4642 1 chrUn.!!$F1 912
9 TraesCS3D01G380700 chrUn 314685049 314685954 905 False 1441.0 1441 95.295 3730 4642 1 chrUn.!!$F3 912
10 TraesCS3D01G380700 chrUn 289620397 289621327 930 False 1221.0 1221 90.715 3730 4642 1 chrUn.!!$F2 912
11 TraesCS3D01G380700 chr1A 30877367 30878110 743 True 1118.0 1118 93.742 3895 4642 1 chr1A.!!$R1 747

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
930 935 0.108186 TGCTCACGCAACCTATCAGG 60.108 55.0 0.0 0.0 44.62 3.86 F
1738 1756 0.036010 AGCCACTCGTTTCCATCCTG 60.036 55.0 0.0 0.0 0.00 3.86 F
2258 2315 0.318762 ACAAGGCGGTGTCTTCTCTC 59.681 55.0 0.0 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2239 0.179234 TGTGTTTTCGTCAGAGGGCA 59.821 50.0 0.0 0.0 0.00 5.36 R
3458 3552 0.031585 CTGTTGTTCCGGTCAGACGA 59.968 55.0 0.0 0.0 35.47 4.20 R
3890 3990 0.655915 CGTGACGTGCAATGCGAAAA 60.656 50.0 0.0 0.0 0.00 2.29 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
285 286 8.220559 AGCAGGTATTCAACTTATCCATTACAT 58.779 33.333 0.00 0.00 0.00 2.29
544 546 8.974060 TCCTGCAAGTATAATTAAGTTAAGGG 57.026 34.615 1.21 0.00 0.00 3.95
560 562 5.932883 AGTTAAGGGAAGTCTCGAATTGTTC 59.067 40.000 0.00 0.00 0.00 3.18
820 823 8.496751 GCTTTATCCGTAGATGGAAAAGAATAC 58.503 37.037 19.13 7.01 42.46 1.89
865 869 7.171678 AGCTTACGTATTATCTTTGCATTCTCC 59.828 37.037 0.00 0.00 0.00 3.71
875 879 1.216064 TGCATTCTCCCAGCATACCT 58.784 50.000 0.00 0.00 32.55 3.08
878 882 2.569059 CATTCTCCCAGCATACCTGTG 58.431 52.381 0.00 0.00 40.06 3.66
890 895 3.307782 GCATACCTGTGAAATTGCAATGC 59.692 43.478 13.82 9.08 0.00 3.56
930 935 0.108186 TGCTCACGCAACCTATCAGG 60.108 55.000 0.00 0.00 44.62 3.86
969 976 3.555956 GGGATTACTTGCAGTCGTATGTG 59.444 47.826 0.00 0.00 0.00 3.21
1051 1058 5.627135 TGACGGTATGGTACTATCAGATGA 58.373 41.667 0.00 0.00 0.00 2.92
1134 1141 8.905702 GTTTTGTGAACTAGCAACTTGATAATG 58.094 33.333 0.00 0.00 0.00 1.90
1180 1189 1.999735 CATCAAATCGTACCGTGCAGT 59.000 47.619 0.00 0.00 0.00 4.40
1230 1239 4.991056 GCAGTCAGTTACTTCAGTGAATCA 59.009 41.667 5.91 0.00 35.76 2.57
1303 1312 4.254709 TGCGTGTTGGAGCAGCCT 62.255 61.111 0.00 0.00 38.59 4.58
1304 1313 3.426568 GCGTGTTGGAGCAGCCTC 61.427 66.667 0.00 0.00 37.63 4.70
1305 1314 2.345244 CGTGTTGGAGCAGCCTCT 59.655 61.111 0.00 0.00 38.21 3.69
1306 1315 2.031516 CGTGTTGGAGCAGCCTCTG 61.032 63.158 0.00 0.00 38.21 3.35
1307 1316 1.072159 GTGTTGGAGCAGCCTCTGT 59.928 57.895 0.00 0.00 38.21 3.41
1308 1317 0.321671 GTGTTGGAGCAGCCTCTGTA 59.678 55.000 0.00 0.00 38.21 2.74
1309 1318 1.055849 TGTTGGAGCAGCCTCTGTAA 58.944 50.000 0.00 0.00 38.21 2.41
1310 1319 1.270839 TGTTGGAGCAGCCTCTGTAAC 60.271 52.381 0.00 0.00 38.21 2.50
1311 1320 1.002544 GTTGGAGCAGCCTCTGTAACT 59.997 52.381 0.00 0.00 38.21 2.24
1312 1321 0.898320 TGGAGCAGCCTCTGTAACTC 59.102 55.000 0.00 0.00 38.21 3.01
1313 1322 1.190643 GGAGCAGCCTCTGTAACTCT 58.809 55.000 0.00 0.00 38.21 3.24
1314 1323 1.552792 GGAGCAGCCTCTGTAACTCTT 59.447 52.381 0.00 0.00 38.21 2.85
1315 1324 2.027653 GGAGCAGCCTCTGTAACTCTTT 60.028 50.000 0.00 0.00 38.21 2.52
1316 1325 3.558109 GGAGCAGCCTCTGTAACTCTTTT 60.558 47.826 0.00 0.00 38.21 2.27
1317 1326 4.068599 GAGCAGCCTCTGTAACTCTTTTT 58.931 43.478 0.00 0.00 35.16 1.94
1414 1424 2.597305 CCTCACGTGAAACATACTACGC 59.403 50.000 20.49 0.00 39.94 4.42
1529 1539 1.209128 CATAGGCGTGGCGTTCTTAG 58.791 55.000 0.00 0.00 0.00 2.18
1542 1552 0.669318 TTCTTAGCGCGAACTGGGTG 60.669 55.000 12.10 0.00 0.00 4.61
1543 1553 1.080093 CTTAGCGCGAACTGGGTGA 60.080 57.895 12.10 0.00 0.00 4.02
1544 1554 0.669318 CTTAGCGCGAACTGGGTGAA 60.669 55.000 12.10 0.00 0.00 3.18
1545 1555 0.669318 TTAGCGCGAACTGGGTGAAG 60.669 55.000 12.10 0.00 0.00 3.02
1546 1556 2.501223 TAGCGCGAACTGGGTGAAGG 62.501 60.000 12.10 0.00 0.00 3.46
1547 1557 2.742372 CGCGAACTGGGTGAAGGG 60.742 66.667 0.00 0.00 0.00 3.95
1548 1558 2.359975 GCGAACTGGGTGAAGGGG 60.360 66.667 0.00 0.00 0.00 4.79
1549 1559 2.359975 CGAACTGGGTGAAGGGGC 60.360 66.667 0.00 0.00 0.00 5.80
1610 1620 1.890041 TCACGCAAACTGAACCCCG 60.890 57.895 0.00 0.00 0.00 5.73
1662 1672 2.660258 GATGGGCAGATAACCGGCGT 62.660 60.000 6.01 0.00 36.81 5.68
1679 1691 1.520368 CGTTTTTCATAACGCGGCTC 58.480 50.000 12.47 0.00 43.51 4.70
1680 1692 1.520368 GTTTTTCATAACGCGGCTCG 58.480 50.000 12.47 0.00 45.38 5.03
1737 1755 0.693049 AAGCCACTCGTTTCCATCCT 59.307 50.000 0.00 0.00 0.00 3.24
1738 1756 0.036010 AGCCACTCGTTTCCATCCTG 60.036 55.000 0.00 0.00 0.00 3.86
1739 1757 1.026718 GCCACTCGTTTCCATCCTGG 61.027 60.000 0.00 0.00 39.43 4.45
1809 1843 3.125487 CGTGCGATCGATTCTATCCTAGT 59.875 47.826 21.57 0.00 0.00 2.57
1811 1845 4.854291 GTGCGATCGATTCTATCCTAGTTG 59.146 45.833 21.57 0.00 0.00 3.16
1812 1846 3.854809 GCGATCGATTCTATCCTAGTTGC 59.145 47.826 21.57 0.00 0.00 4.17
1814 1848 5.092105 CGATCGATTCTATCCTAGTTGCTG 58.908 45.833 10.26 0.00 0.00 4.41
1815 1849 5.106515 CGATCGATTCTATCCTAGTTGCTGA 60.107 44.000 10.26 0.00 0.00 4.26
1816 1850 6.568653 CGATCGATTCTATCCTAGTTGCTGAA 60.569 42.308 10.26 0.00 0.00 3.02
1818 1852 7.055667 TCGATTCTATCCTAGTTGCTGAATT 57.944 36.000 0.00 0.00 0.00 2.17
1823 1857 9.771534 ATTCTATCCTAGTTGCTGAATTAACTC 57.228 33.333 0.00 0.00 38.11 3.01
1829 1863 6.763135 CCTAGTTGCTGAATTAACTCATGCTA 59.237 38.462 8.89 1.18 38.11 3.49
1861 1895 1.468520 CGAAACTGATCATTTGCGGGT 59.531 47.619 16.41 0.00 0.00 5.28
1875 1909 3.023946 TGCGGGTGTGAAATTTTGATG 57.976 42.857 0.00 0.00 0.00 3.07
1876 1910 2.625314 TGCGGGTGTGAAATTTTGATGA 59.375 40.909 0.00 0.00 0.00 2.92
1877 1911 3.257873 TGCGGGTGTGAAATTTTGATGAT 59.742 39.130 0.00 0.00 0.00 2.45
1918 1952 4.082523 TGGAGAAGAAGGCGCCCG 62.083 66.667 26.15 0.00 0.00 6.13
2049 2083 2.058675 CTCCCGGGTGAACAAGACT 58.941 57.895 22.86 0.00 0.00 3.24
2166 2203 3.578716 ACCACGCTATCCAGTAAGCATAT 59.421 43.478 0.00 0.00 38.70 1.78
2167 2204 4.040461 ACCACGCTATCCAGTAAGCATATT 59.960 41.667 0.00 0.00 38.70 1.28
2168 2205 4.997395 CCACGCTATCCAGTAAGCATATTT 59.003 41.667 0.00 0.00 38.70 1.40
2169 2206 5.120830 CCACGCTATCCAGTAAGCATATTTC 59.879 44.000 0.00 0.00 38.70 2.17
2170 2207 5.928839 CACGCTATCCAGTAAGCATATTTCT 59.071 40.000 0.00 0.00 38.70 2.52
2171 2208 6.425114 CACGCTATCCAGTAAGCATATTTCTT 59.575 38.462 0.00 0.00 38.70 2.52
2172 2209 6.992715 ACGCTATCCAGTAAGCATATTTCTTT 59.007 34.615 0.00 0.00 38.70 2.52
2173 2210 7.171678 ACGCTATCCAGTAAGCATATTTCTTTC 59.828 37.037 0.00 0.00 38.70 2.62
2174 2211 7.386299 CGCTATCCAGTAAGCATATTTCTTTCT 59.614 37.037 0.00 0.00 38.70 2.52
2175 2212 8.716909 GCTATCCAGTAAGCATATTTCTTTCTC 58.283 37.037 0.00 0.00 38.63 2.87
2176 2213 9.770097 CTATCCAGTAAGCATATTTCTTTCTCA 57.230 33.333 0.00 0.00 0.00 3.27
2177 2214 7.849804 TCCAGTAAGCATATTTCTTTCTCAC 57.150 36.000 0.00 0.00 0.00 3.51
2178 2215 7.394016 TCCAGTAAGCATATTTCTTTCTCACA 58.606 34.615 0.00 0.00 0.00 3.58
2179 2216 7.882791 TCCAGTAAGCATATTTCTTTCTCACAA 59.117 33.333 0.00 0.00 0.00 3.33
2180 2217 8.514594 CCAGTAAGCATATTTCTTTCTCACAAA 58.485 33.333 0.00 0.00 0.00 2.83
2195 2232 2.556189 TCACAAACCACCATGCATGTAC 59.444 45.455 24.58 0.00 0.00 2.90
2196 2233 2.557924 CACAAACCACCATGCATGTACT 59.442 45.455 24.58 4.51 0.00 2.73
2197 2234 3.755905 CACAAACCACCATGCATGTACTA 59.244 43.478 24.58 0.00 0.00 1.82
2198 2235 3.756434 ACAAACCACCATGCATGTACTAC 59.244 43.478 24.58 0.00 0.00 2.73
2199 2236 2.309528 ACCACCATGCATGTACTACG 57.690 50.000 24.58 10.99 0.00 3.51
2201 2238 2.159099 ACCACCATGCATGTACTACGAG 60.159 50.000 24.58 9.57 0.00 4.18
2202 2239 2.159099 CCACCATGCATGTACTACGAGT 60.159 50.000 24.58 10.21 0.00 4.18
2205 2242 1.860950 CATGCATGTACTACGAGTGCC 59.139 52.381 18.91 0.00 35.03 5.01
2216 2273 1.289066 CGAGTGCCCTCTGACGAAA 59.711 57.895 0.00 0.00 35.43 3.46
2217 2274 0.319555 CGAGTGCCCTCTGACGAAAA 60.320 55.000 0.00 0.00 35.43 2.29
2226 2283 3.458189 CCTCTGACGAAAACACACTTCT 58.542 45.455 0.00 0.00 0.00 2.85
2258 2315 0.318762 ACAAGGCGGTGTCTTCTCTC 59.681 55.000 0.00 0.00 0.00 3.20
2270 2327 3.118223 TGTCTTCTCTCGAGATGGAGCTA 60.118 47.826 17.03 4.32 37.29 3.32
2282 2339 3.518998 GAGCTAGCCGTGGAGCGA 61.519 66.667 12.13 0.00 43.72 4.93
2285 2342 3.522731 CTAGCCGTGGAGCGAGCT 61.523 66.667 0.00 0.00 44.73 4.09
2432 2489 2.172717 GGTGCCCTCAGGTAACATACAT 59.827 50.000 0.00 0.00 35.09 2.29
2433 2490 3.467803 GTGCCCTCAGGTAACATACATC 58.532 50.000 0.00 0.00 41.41 3.06
2434 2491 3.111484 TGCCCTCAGGTAACATACATCA 58.889 45.455 0.00 0.00 41.41 3.07
2435 2492 3.716353 TGCCCTCAGGTAACATACATCAT 59.284 43.478 0.00 0.00 41.41 2.45
2487 2554 1.575922 TGCAATGCAGCAACGAGTC 59.424 52.632 2.72 0.00 42.46 3.36
2492 2559 3.248363 GCAATGCAGCAACGAGTCATATA 59.752 43.478 0.00 0.00 0.00 0.86
2493 2560 4.766007 CAATGCAGCAACGAGTCATATAC 58.234 43.478 0.00 0.00 0.00 1.47
2494 2561 2.821546 TGCAGCAACGAGTCATATACC 58.178 47.619 0.00 0.00 0.00 2.73
2495 2562 2.167487 TGCAGCAACGAGTCATATACCA 59.833 45.455 0.00 0.00 0.00 3.25
2497 2564 3.185188 GCAGCAACGAGTCATATACCATG 59.815 47.826 0.00 0.00 0.00 3.66
2499 2566 4.811024 CAGCAACGAGTCATATACCATGTT 59.189 41.667 0.00 0.00 0.00 2.71
2500 2567 5.294306 CAGCAACGAGTCATATACCATGTTT 59.706 40.000 0.00 0.00 0.00 2.83
2502 2569 7.011016 CAGCAACGAGTCATATACCATGTTTAA 59.989 37.037 0.00 0.00 0.00 1.52
2504 2571 8.342634 GCAACGAGTCATATACCATGTTTAATT 58.657 33.333 0.00 0.00 0.00 1.40
2505 2572 9.650371 CAACGAGTCATATACCATGTTTAATTG 57.350 33.333 0.00 0.00 0.00 2.32
2506 2573 9.607988 AACGAGTCATATACCATGTTTAATTGA 57.392 29.630 0.00 0.00 0.00 2.57
2507 2574 9.778741 ACGAGTCATATACCATGTTTAATTGAT 57.221 29.630 0.00 0.00 0.00 2.57
2586 2653 1.515736 GATCGTGGTCCGGTTCGTC 60.516 63.158 0.00 0.43 37.11 4.20
2983 3063 2.290323 GCCTGTCCTGTCACAAAGGTAT 60.290 50.000 0.00 0.00 36.14 2.73
2990 3070 9.396022 CTGTCCTGTCACAAAGGTATAATAATT 57.604 33.333 0.00 0.00 36.14 1.40
3060 3142 4.277921 GCTGAATTTCCTTCCATCCATCTC 59.722 45.833 0.00 0.00 32.49 2.75
3069 3151 3.981071 TCCATCCATCTCGTTCTTGTT 57.019 42.857 0.00 0.00 0.00 2.83
3074 3156 2.632996 TCCATCTCGTTCTTGTTGGTCT 59.367 45.455 0.00 0.00 0.00 3.85
3081 3163 2.035961 CGTTCTTGTTGGTCTCAGAGGA 59.964 50.000 0.00 0.00 0.00 3.71
3132 3214 2.426887 GGGGACGTCGGGAACAAA 59.573 61.111 9.92 0.00 0.00 2.83
3240 3322 7.609760 TTTTCTTTTCTTTTCTTTGGAAGCC 57.390 32.000 0.00 0.00 32.61 4.35
3241 3323 5.930837 TCTTTTCTTTTCTTTGGAAGCCA 57.069 34.783 0.00 0.00 32.61 4.75
3242 3324 6.293004 TCTTTTCTTTTCTTTGGAAGCCAA 57.707 33.333 0.00 0.00 42.29 4.52
3243 3325 6.888105 TCTTTTCTTTTCTTTGGAAGCCAAT 58.112 32.000 0.00 0.00 43.55 3.16
3244 3326 6.986231 TCTTTTCTTTTCTTTGGAAGCCAATC 59.014 34.615 0.00 0.00 43.55 2.67
3245 3327 6.484364 TTTCTTTTCTTTGGAAGCCAATCT 57.516 33.333 0.00 0.00 43.55 2.40
3287 3375 0.659427 ATGTTTGCATCTGCGATCGG 59.341 50.000 18.30 0.48 45.83 4.18
3376 3464 2.711922 GGAGGTGGAGCACGTCGAT 61.712 63.158 0.00 0.00 46.21 3.59
3430 3518 4.764336 TACGCCGAGCCACGAACG 62.764 66.667 0.00 8.20 45.77 3.95
3434 3528 2.514013 GCCGAGCCACGAACGTATG 61.514 63.158 0.00 0.00 45.77 2.39
3436 3530 1.138036 CGAGCCACGAACGTATGGA 59.862 57.895 15.62 0.00 45.77 3.41
3510 3609 1.270826 CAGACTGCGAGTGGAAGAAGA 59.729 52.381 0.00 0.00 0.00 2.87
3646 3745 2.573869 CGTCGCCACCTGATCTGT 59.426 61.111 0.00 0.00 0.00 3.41
3647 3746 1.807165 CGTCGCCACCTGATCTGTG 60.807 63.158 8.47 8.47 0.00 3.66
3702 3801 1.668628 GCGTGCTGTTTAATGTTGGGG 60.669 52.381 0.00 0.00 0.00 4.96
3890 3990 2.094026 GCAGATCGGCCCATTTTTCTTT 60.094 45.455 6.57 0.00 0.00 2.52
3933 4033 3.677424 GCTCGTGCTATGTTCCTTCTCTT 60.677 47.826 1.41 0.00 36.03 2.85
3934 4034 4.109050 CTCGTGCTATGTTCCTTCTCTTC 58.891 47.826 0.00 0.00 0.00 2.87
4294 4407 3.215151 AGACTTCGTGAAGACTCAGTCA 58.785 45.455 16.10 0.00 38.66 3.41
4335 4469 5.303165 ACATATATGACATCAGCACAGGTG 58.697 41.667 19.63 0.00 0.00 4.00
4408 4543 3.079578 GGGTTGGCTTTGTACTTCTACC 58.920 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.701750 GCTGCTCATCATTCATCACTATCTT 59.298 40.000 0.00 0.00 0.00 2.40
285 286 3.283751 TCCAGAAAAGGAAACGCTTCAA 58.716 40.909 0.35 0.00 33.93 2.69
539 541 5.740290 AGAACAATTCGAGACTTCCCTTA 57.260 39.130 0.00 0.00 34.02 2.69
544 546 7.041984 ACCAAACTAAGAACAATTCGAGACTTC 60.042 37.037 0.00 0.00 34.02 3.01
800 802 4.102054 GGGGTATTCTTTTCCATCTACGGA 59.898 45.833 0.00 0.00 0.00 4.69
820 823 1.615392 CTTTGAGTTTCTGCAAGGGGG 59.385 52.381 0.00 0.00 0.00 5.40
865 869 2.492881 TGCAATTTCACAGGTATGCTGG 59.507 45.455 0.00 0.00 34.97 4.85
875 879 2.484651 GCCAATGCATTGCAATTTCACA 59.515 40.909 30.15 6.44 43.62 3.58
878 882 1.062880 CCGCCAATGCATTGCAATTTC 59.937 47.619 30.15 14.29 43.62 2.17
890 895 2.552315 ACACTTCTGTTAACCGCCAATG 59.448 45.455 2.48 0.00 0.00 2.82
930 935 1.357761 TCCCTCCCCCAAAAAGATGAC 59.642 52.381 0.00 0.00 0.00 3.06
969 976 8.042515 TGGAATTTGAATTTGATGAATCCTTCC 58.957 33.333 0.00 0.00 0.00 3.46
979 986 9.542462 CTTCATATGCTGGAATTTGAATTTGAT 57.458 29.630 0.00 0.00 30.43 2.57
980 987 8.751242 TCTTCATATGCTGGAATTTGAATTTGA 58.249 29.630 0.00 0.00 30.43 2.69
981 988 8.936070 TCTTCATATGCTGGAATTTGAATTTG 57.064 30.769 0.00 0.00 30.43 2.32
982 989 9.595823 CTTCTTCATATGCTGGAATTTGAATTT 57.404 29.630 0.00 0.00 30.43 1.82
983 990 8.755977 ACTTCTTCATATGCTGGAATTTGAATT 58.244 29.630 0.00 0.00 30.43 2.17
1051 1058 9.553064 TTACATTGTTCAAACTAAAATGGCATT 57.447 25.926 6.96 6.96 33.50 3.56
1230 1239 7.155328 CGGATAAAACTAGCTCAATGGATAGT 58.845 38.462 0.00 0.00 39.66 2.12
1317 1326 6.524101 AAGAGTTACAAAGGCTGTCAAAAA 57.476 33.333 0.00 0.00 39.64 1.94
1318 1327 6.329496 CAAAGAGTTACAAAGGCTGTCAAAA 58.671 36.000 0.00 0.00 39.64 2.44
1319 1328 5.678616 GCAAAGAGTTACAAAGGCTGTCAAA 60.679 40.000 0.00 0.00 39.64 2.69
1320 1329 4.202010 GCAAAGAGTTACAAAGGCTGTCAA 60.202 41.667 0.00 0.00 39.64 3.18
1321 1330 3.315191 GCAAAGAGTTACAAAGGCTGTCA 59.685 43.478 0.00 0.00 39.64 3.58
1322 1331 3.565902 AGCAAAGAGTTACAAAGGCTGTC 59.434 43.478 0.00 0.00 39.64 3.51
1323 1332 3.555966 AGCAAAGAGTTACAAAGGCTGT 58.444 40.909 0.00 0.00 42.47 4.40
1324 1333 3.817647 AGAGCAAAGAGTTACAAAGGCTG 59.182 43.478 0.00 0.00 0.00 4.85
1325 1334 4.092116 AGAGCAAAGAGTTACAAAGGCT 57.908 40.909 0.00 0.00 0.00 4.58
1326 1335 6.149474 TCAATAGAGCAAAGAGTTACAAAGGC 59.851 38.462 0.00 0.00 0.00 4.35
1383 1393 1.775385 TCACGTGAGGATAGCCATGA 58.225 50.000 15.76 0.00 36.29 3.07
1389 1399 5.907945 CGTAGTATGTTTCACGTGAGGATAG 59.092 44.000 19.11 0.79 0.00 2.08
1414 1424 0.250640 GGTGATAGGCATGGCTGAGG 60.251 60.000 30.53 0.00 0.00 3.86
1529 1539 3.423154 CCTTCACCCAGTTCGCGC 61.423 66.667 0.00 0.00 0.00 6.86
1662 1672 1.127213 GTCGAGCCGCGTTATGAAAAA 59.873 47.619 4.92 0.00 41.80 1.94
1686 1698 4.906065 TGAAGAGGTGATTTATGCATGC 57.094 40.909 11.82 11.82 0.00 4.06
1689 1701 3.689161 CCGTTGAAGAGGTGATTTATGCA 59.311 43.478 0.00 0.00 0.00 3.96
1690 1702 3.065371 CCCGTTGAAGAGGTGATTTATGC 59.935 47.826 0.00 0.00 0.00 3.14
1691 1703 4.261801 ACCCGTTGAAGAGGTGATTTATG 58.738 43.478 0.00 0.00 30.97 1.90
1737 1755 1.540363 GCACTCGAAACTCCAGAACCA 60.540 52.381 0.00 0.00 0.00 3.67
1738 1756 1.149148 GCACTCGAAACTCCAGAACC 58.851 55.000 0.00 0.00 0.00 3.62
1739 1757 2.156343 AGCACTCGAAACTCCAGAAC 57.844 50.000 0.00 0.00 0.00 3.01
1799 1833 8.306313 TGAGTTAATTCAGCAACTAGGATAGA 57.694 34.615 0.00 0.00 42.77 1.98
1809 1843 6.094048 GGAACTAGCATGAGTTAATTCAGCAA 59.906 38.462 17.84 2.04 39.79 3.91
1811 1845 5.277058 CGGAACTAGCATGAGTTAATTCAGC 60.277 44.000 6.81 9.70 39.79 4.26
1812 1846 5.812642 ACGGAACTAGCATGAGTTAATTCAG 59.187 40.000 6.81 0.99 39.79 3.02
1814 1848 5.581085 ACACGGAACTAGCATGAGTTAATTC 59.419 40.000 0.00 0.00 39.79 2.17
1815 1849 5.351465 CACACGGAACTAGCATGAGTTAATT 59.649 40.000 0.00 0.00 39.79 1.40
1816 1850 4.870426 CACACGGAACTAGCATGAGTTAAT 59.130 41.667 0.00 0.00 39.79 1.40
1818 1852 3.368013 CCACACGGAACTAGCATGAGTTA 60.368 47.826 0.00 0.00 39.79 2.24
1823 1857 1.695893 CGCCACACGGAACTAGCATG 61.696 60.000 0.00 0.00 38.44 4.06
1861 1895 7.324178 TGCATCATCATCATCAAAATTTCACA 58.676 30.769 0.00 0.00 0.00 3.58
2032 2066 0.395312 GAAGTCTTGTTCACCCGGGA 59.605 55.000 32.02 1.07 0.00 5.14
2034 2068 1.512926 CAGAAGTCTTGTTCACCCGG 58.487 55.000 0.00 0.00 0.00 5.73
2035 2069 0.868406 GCAGAAGTCTTGTTCACCCG 59.132 55.000 0.00 0.00 0.00 5.28
2036 2070 2.147150 GAGCAGAAGTCTTGTTCACCC 58.853 52.381 0.00 0.00 0.00 4.61
2124 2161 2.932234 CGTCCTGGACACCTCGCTT 61.932 63.158 25.42 0.00 32.09 4.68
2151 2188 9.547753 GTGAGAAAGAAATATGCTTACTGGATA 57.452 33.333 0.00 0.00 33.54 2.59
2166 2203 4.441356 GCATGGTGGTTTGTGAGAAAGAAA 60.441 41.667 0.00 0.00 0.00 2.52
2167 2204 3.068024 GCATGGTGGTTTGTGAGAAAGAA 59.932 43.478 0.00 0.00 0.00 2.52
2168 2205 2.622942 GCATGGTGGTTTGTGAGAAAGA 59.377 45.455 0.00 0.00 0.00 2.52
2169 2206 2.361757 TGCATGGTGGTTTGTGAGAAAG 59.638 45.455 0.00 0.00 0.00 2.62
2170 2207 2.382882 TGCATGGTGGTTTGTGAGAAA 58.617 42.857 0.00 0.00 0.00 2.52
2171 2208 2.064434 TGCATGGTGGTTTGTGAGAA 57.936 45.000 0.00 0.00 0.00 2.87
2172 2209 1.887854 CATGCATGGTGGTTTGTGAGA 59.112 47.619 19.40 0.00 0.00 3.27
2173 2210 1.614903 ACATGCATGGTGGTTTGTGAG 59.385 47.619 29.41 0.88 0.00 3.51
2174 2211 1.702182 ACATGCATGGTGGTTTGTGA 58.298 45.000 29.41 0.00 0.00 3.58
2175 2212 2.557924 AGTACATGCATGGTGGTTTGTG 59.442 45.455 29.41 3.23 0.00 3.33
2176 2213 2.875296 AGTACATGCATGGTGGTTTGT 58.125 42.857 29.41 10.93 0.00 2.83
2177 2214 3.181511 CGTAGTACATGCATGGTGGTTTG 60.182 47.826 29.41 10.55 0.00 2.93
2178 2215 3.006940 CGTAGTACATGCATGGTGGTTT 58.993 45.455 29.41 10.82 0.00 3.27
2179 2216 2.235155 TCGTAGTACATGCATGGTGGTT 59.765 45.455 29.41 11.55 0.00 3.67
2180 2217 1.828595 TCGTAGTACATGCATGGTGGT 59.171 47.619 29.41 11.93 0.00 4.16
2199 2236 1.149148 GTTTTCGTCAGAGGGCACTC 58.851 55.000 8.30 8.30 44.31 3.51
2201 2238 0.586802 GTGTTTTCGTCAGAGGGCAC 59.413 55.000 0.00 0.00 0.00 5.01
2202 2239 0.179234 TGTGTTTTCGTCAGAGGGCA 59.821 50.000 0.00 0.00 0.00 5.36
2205 2242 3.458189 AGAAGTGTGTTTTCGTCAGAGG 58.542 45.455 0.00 0.00 0.00 3.69
2216 2273 0.249911 GCGACCTGGAGAAGTGTGTT 60.250 55.000 0.00 0.00 0.00 3.32
2217 2274 1.115930 AGCGACCTGGAGAAGTGTGT 61.116 55.000 0.00 0.00 0.00 3.72
2258 2315 1.007964 CACGGCTAGCTCCATCTCG 60.008 63.158 15.72 10.14 0.00 4.04
2492 2559 6.709846 CCACCAACAAATCAATTAAACATGGT 59.290 34.615 0.00 0.00 37.92 3.55
2493 2560 6.709846 ACCACCAACAAATCAATTAAACATGG 59.290 34.615 0.00 0.00 0.00 3.66
2494 2561 7.359097 CGACCACCAACAAATCAATTAAACATG 60.359 37.037 0.00 0.00 0.00 3.21
2495 2562 6.644592 CGACCACCAACAAATCAATTAAACAT 59.355 34.615 0.00 0.00 0.00 2.71
2497 2564 5.107645 GCGACCACCAACAAATCAATTAAAC 60.108 40.000 0.00 0.00 0.00 2.01
2499 2566 4.551388 GCGACCACCAACAAATCAATTAA 58.449 39.130 0.00 0.00 0.00 1.40
2500 2567 3.365465 CGCGACCACCAACAAATCAATTA 60.365 43.478 0.00 0.00 0.00 1.40
2502 2569 1.068610 CGCGACCACCAACAAATCAAT 60.069 47.619 0.00 0.00 0.00 2.57
2504 2571 1.945522 CGCGACCACCAACAAATCA 59.054 52.632 0.00 0.00 0.00 2.57
2505 2572 1.442017 GCGCGACCACCAACAAATC 60.442 57.895 12.10 0.00 0.00 2.17
2506 2573 2.642700 GCGCGACCACCAACAAAT 59.357 55.556 12.10 0.00 0.00 2.32
2507 2574 3.943034 CGCGCGACCACCAACAAA 61.943 61.111 28.94 0.00 0.00 2.83
2529 2596 2.186384 CTCAGCTTCTCCCCTGCG 59.814 66.667 0.00 0.00 0.00 5.18
2530 2597 1.970352 CTCCTCAGCTTCTCCCCTGC 61.970 65.000 0.00 0.00 0.00 4.85
2983 3063 5.555631 GCACGTGATTTCGCTCGAATTATTA 60.556 40.000 22.23 0.00 33.79 0.98
2990 3070 2.092291 GGCACGTGATTTCGCTCGA 61.092 57.895 22.23 0.00 0.00 4.04
3060 3142 2.035961 TCCTCTGAGACCAACAAGAACG 59.964 50.000 6.17 0.00 0.00 3.95
3069 3151 2.685106 ACTTCACTCCTCTGAGACCA 57.315 50.000 6.17 0.00 41.42 4.02
3074 3156 2.160205 CGTGGTACTTCACTCCTCTGA 58.840 52.381 0.00 0.00 35.63 3.27
3081 3163 1.585006 CGGCTCGTGGTACTTCACT 59.415 57.895 0.00 0.00 35.63 3.41
3132 3214 2.125269 GTGGCGTGCCGGAAGTAT 60.125 61.111 5.05 0.00 39.42 2.12
3244 3326 4.562000 CGTCAGAATGTCTCACAGATTGAG 59.438 45.833 0.00 0.00 44.30 3.02
3245 3327 4.218417 TCGTCAGAATGTCTCACAGATTGA 59.782 41.667 0.00 0.00 37.40 2.57
3403 3491 4.720902 TCGGCGTACGGACCTGGA 62.721 66.667 18.39 1.65 44.45 3.86
3430 3518 1.964223 TGGGCGAAGAGAGATCCATAC 59.036 52.381 0.00 0.00 0.00 2.39
3434 3528 0.602372 GCATGGGCGAAGAGAGATCC 60.602 60.000 0.00 0.00 0.00 3.36
3456 3550 0.857287 GTTGTTCCGGTCAGACGAAC 59.143 55.000 12.20 12.20 35.47 3.95
3457 3551 0.460722 TGTTGTTCCGGTCAGACGAA 59.539 50.000 0.00 0.00 35.47 3.85
3458 3552 0.031585 CTGTTGTTCCGGTCAGACGA 59.968 55.000 0.00 0.00 35.47 4.20
3459 3553 1.557443 GCTGTTGTTCCGGTCAGACG 61.557 60.000 0.00 0.00 0.00 4.18
3646 3745 1.618888 GCTACTCCCACCACTACTCCA 60.619 57.143 0.00 0.00 0.00 3.86
3647 3746 1.112950 GCTACTCCCACCACTACTCC 58.887 60.000 0.00 0.00 0.00 3.85
3702 3801 0.747255 TCGACTGATTCCTAGCCAGC 59.253 55.000 0.00 0.00 0.00 4.85
3890 3990 0.655915 CGTGACGTGCAATGCGAAAA 60.656 50.000 0.00 0.00 0.00 2.29
4225 4336 6.719370 ACCCTACATGCAACTGAGATTTTTAA 59.281 34.615 0.00 0.00 0.00 1.52
4408 4543 4.884164 AGAAAAAGATGAGATAAAGGCCCG 59.116 41.667 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.