Multiple sequence alignment - TraesCS5D01G002300

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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 TraesCS5D01G002300 chr5D 100.000 2795 0 0 1 2795 2512993 2510199 0.000000e+00 5162
1 TraesCS5D01G002300 chr5A 89.561 1322 61 34 707 1976 1347789 1346493 0.000000e+00 1605
2 TraesCS5D01G002300 chr5A 92.146 713 47 7 1 708 1348531 1347823 0.000000e+00 998
3 TraesCS5D01G002300 chr5A 78.189 784 103 44 2040 2795 1346392 1345649 3.310000e-119 438
4 TraesCS5D01G002300 chr5B 88.796 1321 68 31 707 1976 3474552 3475843 0.000000e+00 1546
5 TraesCS5D01G002300 chr5B 91.922 718 45 10 1 708 3473804 3474518 0.000000e+00 992
6 TraesCS5D01G002300 chr5B 77.905 783 105 42 2040 2795 3475960 3476701 2.570000e-115 425
7 TraesCS5D01G002300 chr4D 87.574 169 21 0 1208 1376 18464576 18464744 2.200000e-46 196
8 TraesCS5D01G002300 chr4A 86.982 169 22 0 1208 1376 582840668 582840500 1.020000e-44 191
9 TraesCS5D01G002300 chr4B 86.391 169 23 0 1208 1376 30362604 30362772 4.750000e-43 185


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 TraesCS5D01G002300 chr5D 2510199 2512993 2794 True 5162.000000 5162 100.000000 1 2795 1 chr5D.!!$R1 2794
1 TraesCS5D01G002300 chr5A 1345649 1348531 2882 True 1013.666667 1605 86.632000 1 2795 3 chr5A.!!$R1 2794
2 TraesCS5D01G002300 chr5B 3473804 3476701 2897 False 987.666667 1546 86.207667 1 2795 3 chr5B.!!$F1 2794

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
753 799 1.202114 TCGAACAATTGCCATGCCTTC 59.798 47.619 5.05 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2345 0.320073 TTAAGGCGGGTGAAGTGACG 60.32 55.0 0.0 0.0 0.0 4.35 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
305 310 3.955524 TTGGTAACTTGTTGAGGGGAA 57.044 42.857 0.00 0.00 37.61 3.97
371 376 1.415672 TTTGGACTCCGTGCCTTCCT 61.416 55.000 0.00 0.00 0.00 3.36
390 395 7.290061 CCTTCCTAGGAATGATGTGGATTTTA 58.710 38.462 24.48 0.00 45.05 1.52
391 396 7.779798 CCTTCCTAGGAATGATGTGGATTTTAA 59.220 37.037 24.48 0.00 45.05 1.52
392 397 9.189156 CTTCCTAGGAATGATGTGGATTTTAAA 57.811 33.333 24.48 0.00 33.28 1.52
459 466 2.094649 ACTTGCTCCGTACTTGCTCTAC 60.095 50.000 0.00 0.00 0.00 2.59
482 489 1.566211 ACAGAGGATGGAGGACACAG 58.434 55.000 0.00 0.00 0.00 3.66
502 509 7.716612 ACACAGATCTTATTATGACGACATCA 58.283 34.615 3.03 0.00 43.13 3.07
620 631 2.158841 GTCGGACATTAACACATTGCGT 59.841 45.455 2.62 0.00 0.00 5.24
636 647 7.003072 CACATTGCGTTTGTATCAACATTTTC 58.997 34.615 0.00 0.00 34.97 2.29
641 652 7.418408 TGCGTTTGTATCAACATTTTCTAACA 58.582 30.769 0.00 0.00 34.97 2.41
735 781 7.763985 AGGCCATTAATTTGTTTCCTTTTATCG 59.236 33.333 5.01 0.00 0.00 2.92
753 799 1.202114 TCGAACAATTGCCATGCCTTC 59.798 47.619 5.05 0.00 0.00 3.46
814 864 5.708697 TCCTACCGGTATGTATGATGTGTAG 59.291 44.000 16.25 0.00 0.00 2.74
952 1008 7.656542 CAGGTATATATGACCATGAGATGATGC 59.343 40.741 10.37 0.00 39.65 3.91
1025 1090 3.782413 AATGGAAATGGGGATGGACTT 57.218 42.857 0.00 0.00 0.00 3.01
1036 1101 2.095461 GGATGGACTTTCTTTGGCCTC 58.905 52.381 3.32 0.00 0.00 4.70
1037 1102 2.555227 GGATGGACTTTCTTTGGCCTCA 60.555 50.000 3.32 0.00 0.00 3.86
1038 1103 1.981256 TGGACTTTCTTTGGCCTCAC 58.019 50.000 3.32 0.00 0.00 3.51
1078 1143 2.107366 CTCCTCTTCCTCCTTCCTCAC 58.893 57.143 0.00 0.00 0.00 3.51
1106 1171 3.964031 CCAGATGCCTTCTCCTACTACTT 59.036 47.826 0.00 0.00 29.93 2.24
1205 1276 2.683933 AAGATCGAGGGCGGTGGT 60.684 61.111 0.00 0.00 38.28 4.16
1242 1313 2.111043 AAGATATGCACGGCGGGG 59.889 61.111 12.74 3.41 0.00 5.73
1277 1348 4.101448 GATGCGGCTGTCCCTGGT 62.101 66.667 0.00 0.00 0.00 4.00
1417 1500 3.518552 TTGTCGGAGGAGGACGGGT 62.519 63.158 0.00 0.00 37.22 5.28
1418 1501 3.139469 GTCGGAGGAGGACGGGTC 61.139 72.222 0.00 0.00 0.00 4.46
1419 1502 4.790962 TCGGAGGAGGACGGGTCG 62.791 72.222 0.00 0.00 0.00 4.79
1498 1587 0.179009 AAACAAGCAGCAGGAGCAGA 60.179 50.000 0.00 0.00 45.49 4.26
1499 1588 0.037877 AACAAGCAGCAGGAGCAGAT 59.962 50.000 0.00 0.00 45.49 2.90
1502 1591 3.210528 GCAGCAGGAGCAGATGCC 61.211 66.667 0.14 0.00 43.60 4.40
1503 1592 2.895865 CAGCAGGAGCAGATGCCG 60.896 66.667 0.14 0.00 43.60 5.69
1578 1682 3.412408 GCCCCTGTTCTCCTCCCC 61.412 72.222 0.00 0.00 0.00 4.81
1582 1686 1.609501 CCTGTTCTCCTCCCCGACA 60.610 63.158 0.00 0.00 0.00 4.35
1583 1687 1.192146 CCTGTTCTCCTCCCCGACAA 61.192 60.000 0.00 0.00 0.00 3.18
1584 1688 0.685097 CTGTTCTCCTCCCCGACAAA 59.315 55.000 0.00 0.00 0.00 2.83
1599 1703 2.983592 AAAAAGGCGTCCAGGGCG 60.984 61.111 9.85 9.85 37.59 6.13
1626 1730 2.757508 CAGCGGGCCAGAGAGAGA 60.758 66.667 7.23 0.00 0.00 3.10
1731 1844 3.676324 GCAGCAACAACTACTACGAGGAT 60.676 47.826 0.00 0.00 0.00 3.24
1752 1865 1.304282 GGAGCAAGAGCCATGGGAA 59.696 57.895 15.13 0.00 43.56 3.97
1807 1920 3.571828 CCAGTACTGATCATCCAGTCGAT 59.428 47.826 24.68 0.00 45.37 3.59
1912 2027 4.447389 GCTTTTCTATCTCGATCTTGCCTC 59.553 45.833 0.00 0.00 0.00 4.70
1917 2032 6.227298 TCTATCTCGATCTTGCCTCTTTTT 57.773 37.500 0.00 0.00 0.00 1.94
1963 2078 5.313712 TCATCCATCCATCAGTGATGAATG 58.686 41.667 30.63 26.16 42.09 2.67
1976 2091 7.752638 TCAGTGATGAATGGATGGATTAATCT 58.247 34.615 14.95 0.00 27.95 2.40
1977 2092 8.883302 TCAGTGATGAATGGATGGATTAATCTA 58.117 33.333 14.95 9.72 27.95 1.98
1993 2130 9.455847 GGATTAATCTATTTGCTTGCTTTGTAG 57.544 33.333 14.95 0.00 0.00 2.74
1997 2134 7.921786 ATCTATTTGCTTGCTTTGTAGTACA 57.078 32.000 0.00 0.00 0.00 2.90
2005 2142 2.415168 TGCTTTGTAGTACATCTTGCGC 59.585 45.455 3.28 0.00 0.00 6.09
2013 2150 4.864916 AGTACATCTTGCGCTGTTTATG 57.135 40.909 9.73 8.01 0.00 1.90
2014 2151 3.623060 AGTACATCTTGCGCTGTTTATGG 59.377 43.478 9.73 0.00 0.00 2.74
2015 2152 2.710377 ACATCTTGCGCTGTTTATGGA 58.290 42.857 9.73 0.00 0.00 3.41
2017 2154 3.696051 ACATCTTGCGCTGTTTATGGATT 59.304 39.130 9.73 0.00 0.00 3.01
2061 2230 6.086765 CGAGTGCTTTAATTTGTTGATGTGAC 59.913 38.462 0.00 0.00 0.00 3.67
2080 2249 7.956420 TGTGACTTACTAGTTTGTAACCATG 57.044 36.000 0.00 0.00 33.84 3.66
2082 2251 7.654520 TGTGACTTACTAGTTTGTAACCATGAC 59.345 37.037 0.00 0.00 33.84 3.06
2085 2254 8.603242 ACTTACTAGTTTGTAACCATGACAAG 57.397 34.615 0.00 0.00 38.03 3.16
2086 2255 8.426489 ACTTACTAGTTTGTAACCATGACAAGA 58.574 33.333 0.00 0.00 38.03 3.02
2087 2256 9.268268 CTTACTAGTTTGTAACCATGACAAGAA 57.732 33.333 0.00 0.00 38.03 2.52
2088 2257 9.787435 TTACTAGTTTGTAACCATGACAAGAAT 57.213 29.630 0.00 0.00 38.03 2.40
2113 2282 9.950496 ATATAACTTGCAACCCTTCTCTATATG 57.050 33.333 0.00 0.00 0.00 1.78
2118 2289 6.161855 TGCAACCCTTCTCTATATGTGTAG 57.838 41.667 0.00 0.00 0.00 2.74
2119 2290 5.897250 TGCAACCCTTCTCTATATGTGTAGA 59.103 40.000 0.00 0.00 0.00 2.59
2152 2323 8.049117 AGAGATGAAATATTGTTTGAGCTACCA 58.951 33.333 0.00 0.00 0.00 3.25
2154 2325 8.627403 AGATGAAATATTGTTTGAGCTACCATG 58.373 33.333 0.00 0.00 0.00 3.66
2159 2330 4.551702 TTGTTTGAGCTACCATGCTAGA 57.448 40.909 0.00 0.00 44.17 2.43
2165 2336 5.932619 TGAGCTACCATGCTAGAGTTTAA 57.067 39.130 0.00 0.00 44.17 1.52
2171 2342 8.145122 AGCTACCATGCTAGAGTTTAAAGATAC 58.855 37.037 0.00 0.00 42.10 2.24
2173 2344 9.817809 CTACCATGCTAGAGTTTAAAGATACAA 57.182 33.333 0.00 0.00 0.00 2.41
2174 2345 8.494016 ACCATGCTAGAGTTTAAAGATACAAC 57.506 34.615 0.00 0.00 0.00 3.32
2175 2346 7.277981 ACCATGCTAGAGTTTAAAGATACAACG 59.722 37.037 0.00 0.00 0.00 4.10
2176 2347 7.277981 CCATGCTAGAGTTTAAAGATACAACGT 59.722 37.037 0.00 0.00 0.00 3.99
2177 2348 7.807687 TGCTAGAGTTTAAAGATACAACGTC 57.192 36.000 0.00 0.00 0.00 4.34
2178 2349 7.372714 TGCTAGAGTTTAAAGATACAACGTCA 58.627 34.615 0.00 0.00 0.00 4.35
2179 2350 7.327761 TGCTAGAGTTTAAAGATACAACGTCAC 59.672 37.037 0.00 0.00 0.00 3.67
2180 2351 7.541437 GCTAGAGTTTAAAGATACAACGTCACT 59.459 37.037 0.00 0.00 0.00 3.41
2182 2353 8.295569 AGAGTTTAAAGATACAACGTCACTTC 57.704 34.615 0.00 0.00 0.00 3.01
2183 2354 7.924412 AGAGTTTAAAGATACAACGTCACTTCA 59.076 33.333 0.00 0.00 0.00 3.02
2184 2355 7.848491 AGTTTAAAGATACAACGTCACTTCAC 58.152 34.615 0.00 0.00 0.00 3.18
2185 2356 6.774354 TTAAAGATACAACGTCACTTCACC 57.226 37.500 0.00 0.00 0.00 4.02
2186 2357 3.314541 AGATACAACGTCACTTCACCC 57.685 47.619 0.00 0.00 0.00 4.61
2187 2358 1.990563 GATACAACGTCACTTCACCCG 59.009 52.381 0.00 0.00 0.00 5.28
2188 2359 0.598158 TACAACGTCACTTCACCCGC 60.598 55.000 0.00 0.00 0.00 6.13
2189 2360 2.280592 AACGTCACTTCACCCGCC 60.281 61.111 0.00 0.00 0.00 6.13
2190 2361 2.803817 AACGTCACTTCACCCGCCT 61.804 57.895 0.00 0.00 0.00 5.52
2191 2362 2.030562 CGTCACTTCACCCGCCTT 59.969 61.111 0.00 0.00 0.00 4.35
2192 2363 1.290955 CGTCACTTCACCCGCCTTA 59.709 57.895 0.00 0.00 0.00 2.69
2193 2364 0.320073 CGTCACTTCACCCGCCTTAA 60.320 55.000 0.00 0.00 0.00 1.85
2194 2365 1.674817 CGTCACTTCACCCGCCTTAAT 60.675 52.381 0.00 0.00 0.00 1.40
2195 2366 2.433436 GTCACTTCACCCGCCTTAATT 58.567 47.619 0.00 0.00 0.00 1.40
2202 2373 5.589050 ACTTCACCCGCCTTAATTCTTAATC 59.411 40.000 0.00 0.00 0.00 1.75
2207 2378 5.359860 ACCCGCCTTAATTCTTAATCTTTGG 59.640 40.000 0.00 0.00 0.00 3.28
2208 2379 5.359860 CCCGCCTTAATTCTTAATCTTTGGT 59.640 40.000 0.00 0.00 0.00 3.67
2209 2380 6.265577 CCGCCTTAATTCTTAATCTTTGGTG 58.734 40.000 0.00 0.00 0.00 4.17
2211 2382 6.094881 CGCCTTAATTCTTAATCTTTGGTGGA 59.905 38.462 0.00 0.00 0.00 4.02
2212 2383 7.362574 CGCCTTAATTCTTAATCTTTGGTGGAA 60.363 37.037 0.00 0.00 0.00 3.53
2213 2384 8.311109 GCCTTAATTCTTAATCTTTGGTGGAAA 58.689 33.333 0.00 0.00 0.00 3.13
2220 2391 7.722363 TCTTAATCTTTGGTGGAAAAGGAAAC 58.278 34.615 0.00 0.00 37.67 2.78
2242 2413 8.833976 AAACTTTGTGTTTTTGAAACAAGTTG 57.166 26.923 16.52 0.00 45.69 3.16
2258 2429 9.696917 GAAACAAGTTGAAAATGGAAGATGTAT 57.303 29.630 10.54 0.00 0.00 2.29
2271 2442 9.574577 AATGGAAGATGTATATATTACCCTCCA 57.425 33.333 0.00 0.00 0.00 3.86
2272 2443 8.609617 TGGAAGATGTATATATTACCCTCCAG 57.390 38.462 0.00 0.00 0.00 3.86
2274 2445 7.125811 GGAAGATGTATATATTACCCTCCAGCA 59.874 40.741 0.00 0.00 0.00 4.41
2275 2446 8.629821 AAGATGTATATATTACCCTCCAGCAT 57.370 34.615 0.00 0.00 0.00 3.79
2277 2448 8.070604 AGATGTATATATTACCCTCCAGCATCT 58.929 37.037 0.00 0.00 35.01 2.90
2278 2449 7.423844 TGTATATATTACCCTCCAGCATCTG 57.576 40.000 0.00 0.00 0.00 2.90
2280 2451 8.119891 TGTATATATTACCCTCCAGCATCTGTA 58.880 37.037 0.00 0.00 0.00 2.74
2281 2452 9.148879 GTATATATTACCCTCCAGCATCTGTAT 57.851 37.037 0.00 0.00 0.00 2.29
2283 2454 1.043816 ACCCTCCAGCATCTGTATCG 58.956 55.000 0.00 0.00 0.00 2.92
2284 2455 1.043816 CCCTCCAGCATCTGTATCGT 58.956 55.000 0.00 0.00 0.00 3.73
2285 2456 1.414181 CCCTCCAGCATCTGTATCGTT 59.586 52.381 0.00 0.00 0.00 3.85
2287 2458 2.101415 CCTCCAGCATCTGTATCGTTGA 59.899 50.000 0.00 0.00 0.00 3.18
2288 2459 3.244009 CCTCCAGCATCTGTATCGTTGAT 60.244 47.826 0.00 0.00 0.00 2.57
2289 2460 3.721035 TCCAGCATCTGTATCGTTGATG 58.279 45.455 0.00 0.00 40.16 3.07
2294 2465 3.806958 CATCTGTATCGTTGATGCATGC 58.193 45.455 11.82 11.82 34.48 4.06
2295 2466 1.860326 TCTGTATCGTTGATGCATGCG 59.140 47.619 14.09 6.23 34.48 4.73
2296 2467 1.594397 CTGTATCGTTGATGCATGCGT 59.406 47.619 13.43 13.43 34.48 5.24
2301 2472 4.588805 ATCGTTGATGCATGCGTATATG 57.411 40.909 13.55 9.27 0.00 1.78
2302 2473 3.389221 TCGTTGATGCATGCGTATATGT 58.611 40.909 13.55 0.00 0.00 2.29
2308 2479 6.833342 TGATGCATGCGTATATGTCATATC 57.167 37.500 13.55 5.86 30.49 1.63
2328 2499 8.506921 TCATATCTTTATTATGGACCAAACCCA 58.493 33.333 0.00 0.00 38.19 4.51
2331 2502 7.857404 TCTTTATTATGGACCAAACCCAAAA 57.143 32.000 0.00 0.00 37.22 2.44
2332 2503 8.442660 TCTTTATTATGGACCAAACCCAAAAT 57.557 30.769 0.00 0.00 37.22 1.82
2333 2504 9.548631 TCTTTATTATGGACCAAACCCAAAATA 57.451 29.630 0.00 0.00 37.22 1.40
2335 2506 5.669164 TTATGGACCAAACCCAAAATAGC 57.331 39.130 0.00 0.00 37.22 2.97
2336 2507 3.252554 TGGACCAAACCCAAAATAGCT 57.747 42.857 0.00 0.00 0.00 3.32
2337 2508 4.390129 TGGACCAAACCCAAAATAGCTA 57.610 40.909 0.00 0.00 0.00 3.32
2338 2509 4.083565 TGGACCAAACCCAAAATAGCTAC 58.916 43.478 0.00 0.00 0.00 3.58
2339 2510 4.202631 TGGACCAAACCCAAAATAGCTACT 60.203 41.667 0.00 0.00 0.00 2.57
2340 2511 4.398358 GGACCAAACCCAAAATAGCTACTC 59.602 45.833 0.00 0.00 0.00 2.59
2341 2512 4.007659 ACCAAACCCAAAATAGCTACTCG 58.992 43.478 0.00 0.00 0.00 4.18
2343 2514 2.327200 ACCCAAAATAGCTACTCGGC 57.673 50.000 0.00 0.00 0.00 5.54
2348 2520 4.192317 CCAAAATAGCTACTCGGCTTTCT 58.808 43.478 0.00 0.00 42.97 2.52
2359 2531 5.926214 ACTCGGCTTTCTTAGTTTCTTTC 57.074 39.130 0.00 0.00 0.00 2.62
2422 2594 9.435570 ACCTTAGTTCCTTAGATATATGTGTGT 57.564 33.333 0.00 0.00 0.00 3.72
2423 2595 9.915629 CCTTAGTTCCTTAGATATATGTGTGTC 57.084 37.037 0.00 0.00 0.00 3.67
2438 2610 3.274095 TGTGTCCACACTTGTTCATCA 57.726 42.857 11.07 0.00 46.55 3.07
2442 2614 2.549754 GTCCACACTTGTTCATCACCAG 59.450 50.000 0.00 0.00 0.00 4.00
2451 2623 5.048504 ACTTGTTCATCACCAGCAACTAATG 60.049 40.000 0.00 0.00 0.00 1.90
2454 2626 6.000840 TGTTCATCACCAGCAACTAATGTTA 58.999 36.000 0.00 0.00 34.60 2.41
2463 2635 8.274939 CACCAGCAACTAATGTTACAAATTTTG 58.725 33.333 7.59 7.59 34.60 2.44
2468 2640 7.571059 GCAACTAATGTTACAAATTTTGCCTGG 60.571 37.037 9.04 0.00 34.60 4.45
2474 2646 6.640518 TGTTACAAATTTTGCCTGGTTGTTA 58.359 32.000 9.04 0.00 34.43 2.41
2486 2658 6.894682 TGCCTGGTTGTTATATCAGTTGATA 58.105 36.000 4.44 4.44 40.85 2.15
2489 2661 7.171678 GCCTGGTTGTTATATCAGTTGATACTC 59.828 40.741 4.07 0.27 39.57 2.59
2490 2662 8.424918 CCTGGTTGTTATATCAGTTGATACTCT 58.575 37.037 4.07 0.00 39.57 3.24
2491 2663 9.823647 CTGGTTGTTATATCAGTTGATACTCTT 57.176 33.333 4.07 0.00 39.57 2.85
2501 2673 7.496346 TCAGTTGATACTCTTTAGTCCCAAT 57.504 36.000 0.00 0.00 37.15 3.16
2549 2725 9.661563 ATGTTCAATCAAGAAACATGCAAATAT 57.338 25.926 0.00 0.00 0.00 1.28
2576 2752 8.467402 AGATAACGAAGCAGCATGTATATAAC 57.533 34.615 0.00 0.00 39.31 1.89
2577 2753 8.088365 AGATAACGAAGCAGCATGTATATAACA 58.912 33.333 0.00 0.00 43.86 2.41
2604 2789 6.822667 ATATCGCATGAAAAATATCCAGCA 57.177 33.333 0.00 0.00 0.00 4.41
2607 2792 3.067180 CGCATGAAAAATATCCAGCACCT 59.933 43.478 0.00 0.00 0.00 4.00
2608 2793 4.275689 CGCATGAAAAATATCCAGCACCTA 59.724 41.667 0.00 0.00 0.00 3.08
2609 2794 5.221028 CGCATGAAAAATATCCAGCACCTAA 60.221 40.000 0.00 0.00 0.00 2.69
2612 2797 7.631377 GCATGAAAAATATCCAGCACCTAACTT 60.631 37.037 0.00 0.00 0.00 2.66
2614 2799 8.871629 TGAAAAATATCCAGCACCTAACTTAA 57.128 30.769 0.00 0.00 0.00 1.85
2625 2810 7.553044 CCAGCACCTAACTTAATTAAGCTTAGT 59.447 37.037 25.67 17.79 36.79 2.24
2687 2872 8.584157 AGCACCAGAATTTTACATCACAAAATA 58.416 29.630 0.00 0.00 35.15 1.40
2688 2873 9.202273 GCACCAGAATTTTACATCACAAAATAA 57.798 29.630 0.00 0.00 35.15 1.40
2766 2954 6.491403 AGGAATTTAGTGTCATGCAAGTTTCT 59.509 34.615 0.00 0.00 0.00 2.52
2777 2965 8.668353 TGTCATGCAAGTTTCTCTTATTACATC 58.332 33.333 0.00 0.00 34.66 3.06
2783 2971 8.272176 GCAAGTTTCTCTTATTACATCATCGAG 58.728 37.037 0.00 0.00 34.66 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.957631 TCCATATTTTGTCACTGTCCATAGT 58.042 36.000 0.00 0.00 0.00 2.12
50 51 6.088085 CACGTGCAAAGGTATTTTTGAGATTC 59.912 38.462 0.82 0.00 39.79 2.52
253 258 3.995199 CACACTACATGGTGCTATAGGG 58.005 50.000 1.04 0.00 40.52 3.53
305 310 9.425248 AGGATATGTGTGGAATTTATTTGTCAT 57.575 29.630 0.00 0.00 0.00 3.06
361 366 2.158900 ACATCATTCCTAGGAAGGCACG 60.159 50.000 27.62 20.05 43.31 5.34
365 370 4.989875 ATCCACATCATTCCTAGGAAGG 57.010 45.455 26.76 26.76 45.21 3.46
459 466 1.062886 TGTCCTCCATCCTCTGTAGGG 60.063 57.143 0.00 0.00 43.84 3.53
509 516 2.972713 AGTACCTGGTCATATCCGCAAT 59.027 45.455 0.63 0.00 0.00 3.56
564 572 4.346734 GATGCACACATCCAACAACTAG 57.653 45.455 0.00 0.00 45.94 2.57
677 688 3.364964 GCATGGACCAACTAAGTTGAACG 60.365 47.826 0.00 0.00 45.28 3.95
735 781 4.454728 TTAGAAGGCATGGCAATTGTTC 57.545 40.909 22.64 15.16 0.00 3.18
797 847 7.241042 ACATACCCTACACATCATACATACC 57.759 40.000 0.00 0.00 0.00 2.73
814 864 6.542370 AGTGTATGCTTGTTCAATACATACCC 59.458 38.462 21.86 16.34 41.40 3.69
922 978 5.089970 TCATGGTCATATATACCTGCAGC 57.910 43.478 8.66 0.00 37.91 5.25
952 1008 5.276584 CCTTCTGAGCTCGAAATAATTCACG 60.277 44.000 17.50 6.83 35.15 4.35
983 1039 5.537300 TTCCATCACTATCTCCTGTTAGC 57.463 43.478 0.00 0.00 0.00 3.09
987 1052 4.971282 TCCATTTCCATCACTATCTCCTGT 59.029 41.667 0.00 0.00 0.00 4.00
1036 1101 0.609131 GGAGGGTGTTGATGGTGGTG 60.609 60.000 0.00 0.00 0.00 4.17
1037 1102 0.772124 AGGAGGGTGTTGATGGTGGT 60.772 55.000 0.00 0.00 0.00 4.16
1038 1103 0.035056 GAGGAGGGTGTTGATGGTGG 60.035 60.000 0.00 0.00 0.00 4.61
1078 1143 2.503356 AGGAGAAGGCATCTGGTACTTG 59.497 50.000 0.00 0.00 38.96 3.16
1106 1171 1.035139 GGCGAACGGAGGGTAATAGA 58.965 55.000 0.00 0.00 0.00 1.98
1140 1205 2.591311 CGTTGGGTTGTCCGTCGTG 61.591 63.158 0.00 0.00 38.76 4.35
1205 1276 1.908619 TGCTATGCCTGTCTTTCCTCA 59.091 47.619 0.00 0.00 0.00 3.86
1365 1436 4.740822 AGGTGGTTGATGCCGGCC 62.741 66.667 26.77 10.34 0.00 6.13
1417 1500 2.997315 CTGGTCCAGGAGCACCGA 60.997 66.667 17.89 0.00 41.83 4.69
1433 1522 1.885850 GCGTGGTCGTTGTTGTCCT 60.886 57.895 0.00 0.00 39.49 3.85
1502 1591 1.407258 CTGGACTTCTCCTAGCCTTCG 59.593 57.143 0.00 0.00 37.48 3.79
1503 1592 1.138069 GCTGGACTTCTCCTAGCCTTC 59.862 57.143 0.00 0.00 37.48 3.46
1512 1610 4.930592 GCAGGAGCTGGACTTCTC 57.069 61.111 0.00 0.00 28.33 2.87
1532 1630 5.467705 CATTTTTGCTCTTCTTCCTTGGAG 58.532 41.667 0.00 0.00 0.00 3.86
1578 1682 1.574428 CCTGGACGCCTTTTTGTCG 59.426 57.895 0.00 0.00 35.95 4.35
1582 1686 2.983592 CGCCCTGGACGCCTTTTT 60.984 61.111 0.00 0.00 0.00 1.94
1583 1687 3.901797 CTCGCCCTGGACGCCTTTT 62.902 63.158 0.00 0.00 0.00 2.27
1584 1688 4.394712 CTCGCCCTGGACGCCTTT 62.395 66.667 0.00 0.00 0.00 3.11
1609 1713 2.354401 TTCTCTCTCTGGCCCGCTG 61.354 63.158 0.00 0.00 0.00 5.18
1612 1716 2.896443 GGTTCTCTCTCTGGCCCG 59.104 66.667 0.00 0.00 0.00 6.13
1626 1730 2.603776 AGGCGGTTCCTCTCGGTT 60.604 61.111 0.00 0.00 43.20 4.44
1731 1844 2.679092 CATGGCTCTTGCTCCCCA 59.321 61.111 0.00 0.00 39.59 4.96
1752 1865 1.202818 GCAAAGACAACTCCTCCCAGT 60.203 52.381 0.00 0.00 0.00 4.00
1807 1920 3.094484 ACCGATTTGGATGGCCTTTAA 57.906 42.857 3.32 0.00 42.00 1.52
1918 2033 6.686630 TGAAGTTGTTGCAGAGAAAGAAAAA 58.313 32.000 0.00 0.00 0.00 1.94
1919 2034 6.266168 TGAAGTTGTTGCAGAGAAAGAAAA 57.734 33.333 0.00 0.00 0.00 2.29
1920 2035 5.895636 TGAAGTTGTTGCAGAGAAAGAAA 57.104 34.783 0.00 0.00 0.00 2.52
1921 2036 5.009010 GGATGAAGTTGTTGCAGAGAAAGAA 59.991 40.000 0.00 0.00 0.00 2.52
1922 2037 4.516698 GGATGAAGTTGTTGCAGAGAAAGA 59.483 41.667 0.00 0.00 0.00 2.52
1923 2038 4.276678 TGGATGAAGTTGTTGCAGAGAAAG 59.723 41.667 0.00 0.00 0.00 2.62
1924 2039 4.206375 TGGATGAAGTTGTTGCAGAGAAA 58.794 39.130 0.00 0.00 0.00 2.52
1929 2044 2.821378 TGGATGGATGAAGTTGTTGCAG 59.179 45.455 0.00 0.00 0.00 4.41
1931 2046 3.444742 TGATGGATGGATGAAGTTGTTGC 59.555 43.478 0.00 0.00 0.00 4.17
1963 2078 7.224522 AGCAAGCAAATAGATTAATCCATCC 57.775 36.000 11.92 0.00 0.00 3.51
1964 2079 8.975439 CAAAGCAAGCAAATAGATTAATCCATC 58.025 33.333 11.92 0.00 0.00 3.51
1976 2091 7.921786 AGATGTACTACAAAGCAAGCAAATA 57.078 32.000 0.00 0.00 0.00 1.40
1977 2092 6.824305 AGATGTACTACAAAGCAAGCAAAT 57.176 33.333 0.00 0.00 0.00 2.32
1997 2134 7.928307 ATATAATCCATAAACAGCGCAAGAT 57.072 32.000 11.47 0.00 43.02 2.40
2017 2154 8.309656 AGCACTCGATGATCATTCAGAAATATA 58.690 33.333 10.14 0.00 34.73 0.86
2029 2190 6.741992 ACAAATTAAAGCACTCGATGATCA 57.258 33.333 0.00 0.00 0.00 2.92
2033 2194 6.803320 ACATCAACAAATTAAAGCACTCGATG 59.197 34.615 0.00 0.00 33.36 3.84
2061 2230 8.827177 TCTTGTCATGGTTACAAACTAGTAAG 57.173 34.615 0.00 0.00 36.46 2.34
2080 2249 6.759497 AGGGTTGCAAGTTATATTCTTGTC 57.241 37.500 0.00 11.51 42.67 3.18
2082 2251 7.337942 AGAGAAGGGTTGCAAGTTATATTCTTG 59.662 37.037 0.00 12.86 43.31 3.02
2085 2254 8.910351 ATAGAGAAGGGTTGCAAGTTATATTC 57.090 34.615 0.00 0.00 0.00 1.75
2087 2256 9.950496 CATATAGAGAAGGGTTGCAAGTTATAT 57.050 33.333 0.00 0.00 0.00 0.86
2088 2257 8.934697 ACATATAGAGAAGGGTTGCAAGTTATA 58.065 33.333 0.00 0.00 0.00 0.98
2089 2258 7.716998 CACATATAGAGAAGGGTTGCAAGTTAT 59.283 37.037 0.00 0.00 0.00 1.89
2127 2298 8.213518 TGGTAGCTCAAACAATATTTCATCTC 57.786 34.615 0.00 0.00 0.00 2.75
2128 2299 8.627403 CATGGTAGCTCAAACAATATTTCATCT 58.373 33.333 0.00 0.00 0.00 2.90
2133 2304 6.780457 AGCATGGTAGCTCAAACAATATTT 57.220 33.333 0.00 0.00 42.18 1.40
2141 2312 4.826274 AACTCTAGCATGGTAGCTCAAA 57.174 40.909 24.11 8.31 45.26 2.69
2152 2323 8.033038 TGACGTTGTATCTTTAAACTCTAGCAT 58.967 33.333 0.00 0.00 0.00 3.79
2154 2325 7.541437 AGTGACGTTGTATCTTTAAACTCTAGC 59.459 37.037 0.00 0.00 0.00 3.42
2159 2330 7.042254 GGTGAAGTGACGTTGTATCTTTAAACT 60.042 37.037 0.00 0.00 0.00 2.66
2165 2336 3.660865 GGGTGAAGTGACGTTGTATCTT 58.339 45.455 0.00 0.00 0.00 2.40
2171 2342 2.604174 GGCGGGTGAAGTGACGTTG 61.604 63.158 0.00 0.00 0.00 4.10
2173 2344 1.466025 TAAGGCGGGTGAAGTGACGT 61.466 55.000 0.00 0.00 0.00 4.34
2174 2345 0.320073 TTAAGGCGGGTGAAGTGACG 60.320 55.000 0.00 0.00 0.00 4.35
2175 2346 2.109425 ATTAAGGCGGGTGAAGTGAC 57.891 50.000 0.00 0.00 0.00 3.67
2176 2347 2.304761 AGAATTAAGGCGGGTGAAGTGA 59.695 45.455 0.00 0.00 0.00 3.41
2177 2348 2.711542 AGAATTAAGGCGGGTGAAGTG 58.288 47.619 0.00 0.00 0.00 3.16
2178 2349 3.434940 AAGAATTAAGGCGGGTGAAGT 57.565 42.857 0.00 0.00 0.00 3.01
2179 2350 5.823045 AGATTAAGAATTAAGGCGGGTGAAG 59.177 40.000 0.00 0.00 44.82 3.02
2180 2351 5.751586 AGATTAAGAATTAAGGCGGGTGAA 58.248 37.500 0.00 0.00 44.82 3.18
2182 2353 6.265577 CAAAGATTAAGAATTAAGGCGGGTG 58.734 40.000 0.00 0.00 44.82 4.61
2183 2354 5.359860 CCAAAGATTAAGAATTAAGGCGGGT 59.640 40.000 0.00 0.00 44.82 5.28
2184 2355 5.359860 ACCAAAGATTAAGAATTAAGGCGGG 59.640 40.000 0.00 0.00 44.82 6.13
2185 2356 6.265577 CACCAAAGATTAAGAATTAAGGCGG 58.734 40.000 0.00 0.00 44.82 6.13
2186 2357 6.094881 TCCACCAAAGATTAAGAATTAAGGCG 59.905 38.462 0.00 0.00 44.82 5.52
2187 2358 7.404671 TCCACCAAAGATTAAGAATTAAGGC 57.595 36.000 0.00 0.00 44.82 4.35
2191 2362 9.594936 TCCTTTTCCACCAAAGATTAAGAATTA 57.405 29.630 0.00 0.00 36.03 1.40
2192 2363 8.491045 TCCTTTTCCACCAAAGATTAAGAATT 57.509 30.769 0.00 0.00 36.03 2.17
2193 2364 8.491045 TTCCTTTTCCACCAAAGATTAAGAAT 57.509 30.769 0.00 0.00 36.03 2.40
2194 2365 7.906199 TTCCTTTTCCACCAAAGATTAAGAA 57.094 32.000 0.00 0.00 36.03 2.52
2195 2366 7.563556 AGTTTCCTTTTCCACCAAAGATTAAGA 59.436 33.333 0.00 0.00 36.03 2.10
2202 2373 5.351189 CACAAAGTTTCCTTTTCCACCAAAG 59.649 40.000 0.00 0.00 38.87 2.77
2220 2391 9.495754 TTTTCAACTTGTTTCAAAAACACAAAG 57.504 25.926 4.82 3.60 30.15 2.77
2224 2395 8.286097 TCCATTTTCAACTTGTTTCAAAAACAC 58.714 29.630 4.82 0.00 0.00 3.32
2225 2396 8.383318 TCCATTTTCAACTTGTTTCAAAAACA 57.617 26.923 1.27 1.27 0.00 2.83
2226 2397 9.328721 CTTCCATTTTCAACTTGTTTCAAAAAC 57.671 29.630 0.00 0.00 0.00 2.43
2232 2403 9.696917 ATACATCTTCCATTTTCAACTTGTTTC 57.303 29.630 0.00 0.00 0.00 2.78
2258 2429 6.321435 CGATACAGATGCTGGAGGGTAATATA 59.679 42.308 0.00 0.00 35.51 0.86
2259 2430 5.127845 CGATACAGATGCTGGAGGGTAATAT 59.872 44.000 0.00 0.00 35.51 1.28
2260 2431 4.462834 CGATACAGATGCTGGAGGGTAATA 59.537 45.833 0.00 0.00 35.51 0.98
2261 2432 3.259374 CGATACAGATGCTGGAGGGTAAT 59.741 47.826 0.00 0.00 35.51 1.89
2263 2434 2.239400 CGATACAGATGCTGGAGGGTA 58.761 52.381 0.00 0.00 35.51 3.69
2264 2435 1.043816 CGATACAGATGCTGGAGGGT 58.956 55.000 0.00 0.00 35.51 4.34
2265 2436 1.043816 ACGATACAGATGCTGGAGGG 58.956 55.000 0.00 0.00 35.51 4.30
2266 2437 2.101415 TCAACGATACAGATGCTGGAGG 59.899 50.000 0.00 0.00 35.51 4.30
2268 2439 3.721035 CATCAACGATACAGATGCTGGA 58.279 45.455 0.00 0.00 35.51 3.86
2274 2445 2.477754 CGCATGCATCAACGATACAGAT 59.522 45.455 19.57 0.00 0.00 2.90
2275 2446 1.860326 CGCATGCATCAACGATACAGA 59.140 47.619 19.57 0.00 0.00 3.41
2277 2448 1.650825 ACGCATGCATCAACGATACA 58.349 45.000 19.57 0.00 0.00 2.29
2278 2449 5.062183 ACATATACGCATGCATCAACGATAC 59.938 40.000 19.57 0.00 0.00 2.24
2280 2451 3.996363 ACATATACGCATGCATCAACGAT 59.004 39.130 19.57 10.19 0.00 3.73
2281 2452 3.389221 ACATATACGCATGCATCAACGA 58.611 40.909 19.57 0.00 0.00 3.85
2283 2454 4.730600 TGACATATACGCATGCATCAAC 57.269 40.909 19.57 1.63 0.00 3.18
2284 2455 7.043565 AGATATGACATATACGCATGCATCAA 58.956 34.615 19.57 0.00 30.55 2.57
2285 2456 6.576185 AGATATGACATATACGCATGCATCA 58.424 36.000 19.57 9.13 30.55 3.07
2287 2458 7.854557 AAAGATATGACATATACGCATGCAT 57.145 32.000 19.57 4.54 31.83 3.96
2288 2459 8.947055 ATAAAGATATGACATATACGCATGCA 57.053 30.769 19.57 0.00 0.00 3.96
2301 2472 8.793592 GGGTTTGGTCCATAATAAAGATATGAC 58.206 37.037 0.00 0.00 33.49 3.06
2302 2473 8.506921 TGGGTTTGGTCCATAATAAAGATATGA 58.493 33.333 0.00 0.00 33.49 2.15
2308 2479 9.816354 CTATTTTGGGTTTGGTCCATAATAAAG 57.184 33.333 0.00 0.00 37.56 1.85
2316 2487 3.252554 AGCTATTTTGGGTTTGGTCCA 57.747 42.857 0.00 0.00 0.00 4.02
2328 2499 6.641474 ACTAAGAAAGCCGAGTAGCTATTTT 58.359 36.000 0.00 0.00 44.11 1.82
2331 2502 5.855740 AACTAAGAAAGCCGAGTAGCTAT 57.144 39.130 0.00 0.00 44.11 2.97
2332 2503 5.418209 AGAAACTAAGAAAGCCGAGTAGCTA 59.582 40.000 0.00 0.00 44.11 3.32
2335 2506 6.183359 CGAAAGAAACTAAGAAAGCCGAGTAG 60.183 42.308 0.00 0.00 0.00 2.57
2336 2507 5.632347 CGAAAGAAACTAAGAAAGCCGAGTA 59.368 40.000 0.00 0.00 0.00 2.59
2337 2508 4.448060 CGAAAGAAACTAAGAAAGCCGAGT 59.552 41.667 0.00 0.00 0.00 4.18
2338 2509 4.666908 GCGAAAGAAACTAAGAAAGCCGAG 60.667 45.833 0.00 0.00 0.00 4.63
2339 2510 3.185797 GCGAAAGAAACTAAGAAAGCCGA 59.814 43.478 0.00 0.00 0.00 5.54
2340 2511 3.059188 TGCGAAAGAAACTAAGAAAGCCG 60.059 43.478 0.00 0.00 0.00 5.52
2341 2512 4.483476 TGCGAAAGAAACTAAGAAAGCC 57.517 40.909 0.00 0.00 0.00 4.35
2387 2559 7.801893 TCTAAGGAACTAAGGTAAACCATGA 57.198 36.000 1.26 0.00 38.49 3.07
2421 2593 2.549754 CTGGTGATGAACAAGTGTGGAC 59.450 50.000 0.00 0.00 0.00 4.02
2422 2594 2.849942 CTGGTGATGAACAAGTGTGGA 58.150 47.619 0.00 0.00 0.00 4.02
2423 2595 1.267806 GCTGGTGATGAACAAGTGTGG 59.732 52.381 0.00 0.00 31.64 4.17
2427 2599 2.936202 AGTTGCTGGTGATGAACAAGT 58.064 42.857 0.00 0.00 31.64 3.16
2428 2600 5.048504 ACATTAGTTGCTGGTGATGAACAAG 60.049 40.000 0.00 0.00 32.25 3.16
2431 2603 5.376854 AACATTAGTTGCTGGTGATGAAC 57.623 39.130 0.00 0.00 36.39 3.18
2433 2605 5.555966 TGTAACATTAGTTGCTGGTGATGA 58.444 37.500 0.00 0.00 40.49 2.92
2437 2609 7.945033 AAATTTGTAACATTAGTTGCTGGTG 57.055 32.000 0.00 0.00 40.49 4.17
2438 2610 7.042119 GCAAAATTTGTAACATTAGTTGCTGGT 60.042 33.333 7.60 0.00 40.49 4.00
2442 2614 7.290118 CAGGCAAAATTTGTAACATTAGTTGC 58.710 34.615 7.60 0.00 40.29 4.17
2451 2623 7.722795 ATAACAACCAGGCAAAATTTGTAAC 57.277 32.000 7.60 0.00 30.28 2.50
2454 2626 7.675062 TGATATAACAACCAGGCAAAATTTGT 58.325 30.769 7.60 0.00 31.74 2.83
2463 2635 6.992715 AGTATCAACTGATATAACAACCAGGC 59.007 38.462 2.85 0.00 39.03 4.85
2474 2646 8.783660 TGGGACTAAAGAGTATCAACTGATAT 57.216 34.615 2.85 0.00 39.03 1.63
2486 2658 9.753674 TTTCAAATATCATTGGGACTAAAGAGT 57.246 29.630 0.00 0.00 39.20 3.24
2521 2693 8.883954 TTTGCATGTTTCTTGATTGAACATAA 57.116 26.923 0.00 0.00 0.00 1.90
2523 2695 7.972832 ATTTGCATGTTTCTTGATTGAACAT 57.027 28.000 0.00 0.00 0.00 2.71
2524 2696 9.491675 AATATTTGCATGTTTCTTGATTGAACA 57.508 25.926 0.00 0.00 0.00 3.18
2536 2708 9.450807 GCTTCGTTATCTAATATTTGCATGTTT 57.549 29.630 0.00 0.00 0.00 2.83
2540 2712 7.041167 TGCTGCTTCGTTATCTAATATTTGCAT 60.041 33.333 0.00 0.00 0.00 3.96
2553 2729 8.777865 ATGTTATATACATGCTGCTTCGTTAT 57.222 30.769 0.00 0.00 45.71 1.89
2577 2753 9.793252 GCTGGATATTTTTCATGCGATATAAAT 57.207 29.630 0.00 0.00 0.00 1.40
2580 2765 7.148255 GGTGCTGGATATTTTTCATGCGATATA 60.148 37.037 0.00 0.00 0.00 0.86
2586 2771 4.660789 AGGTGCTGGATATTTTTCATGC 57.339 40.909 0.00 0.00 0.00 4.06
2597 2782 6.663734 AGCTTAATTAAGTTAGGTGCTGGAT 58.336 36.000 22.94 0.00 35.75 3.41
2599 2784 6.759497 AAGCTTAATTAAGTTAGGTGCTGG 57.241 37.500 22.94 0.00 35.75 4.85
2661 2846 6.403866 TTTGTGATGTAAAATTCTGGTGCT 57.596 33.333 0.00 0.00 0.00 4.40
2717 2903 8.078596 CCTTAATTAATGGAATCTTGCTGTAGC 58.921 37.037 0.00 0.00 42.50 3.58


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

AutoCloner maintained by Alex Coulton.