Multiple sequence alignment - TraesCS5D01G336500

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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 TraesCS5D01G336500 chr5D 100.000 2270 0 0 1 2270 425987371 425985102 0.000000e+00 4193.0
1 TraesCS5D01G336500 chr5D 75.814 215 28 12 1443 1642 34439518 34439313 1.120000e-13 87.9
2 TraesCS5D01G336500 chr5D 93.333 45 3 0 1383 1427 214366273 214366229 1.460000e-07 67.6
3 TraesCS5D01G336500 chr7D 98.675 1358 18 0 1 1358 412651188 412649831 0.000000e+00 2409.0
4 TraesCS5D01G336500 chr7D 98.173 1368 23 2 1 1368 21281177 21279812 0.000000e+00 2386.0
5 TraesCS5D01G336500 chr1D 98.601 1358 19 0 1 1358 45481229 45482586 0.000000e+00 2403.0
6 TraesCS5D01G336500 chr3A 98.234 1359 23 1 1 1358 483249712 483248354 0.000000e+00 2375.0
7 TraesCS5D01G336500 chr3B 97.877 1366 29 0 1 1366 478100307 478101672 0.000000e+00 2362.0
8 TraesCS5D01G336500 chr2A 97.645 1359 25 2 1 1358 388673142 388674494 0.000000e+00 2326.0
9 TraesCS5D01G336500 chr2B 97.496 1358 33 1 1 1357 681405652 681407009 0.000000e+00 2318.0
10 TraesCS5D01G336500 chr2B 97.493 1356 34 0 3 1358 507822521 507821166 0.000000e+00 2316.0
11 TraesCS5D01G336500 chr4B 97.057 1359 39 1 1 1358 495288431 495289789 0.000000e+00 2287.0
12 TraesCS5D01G336500 chr5A 91.737 472 35 4 1443 1910 540273550 540273079 0.000000e+00 652.0
13 TraesCS5D01G336500 chr5A 90.393 229 20 2 1910 2138 540272334 540272108 1.320000e-77 300.0
14 TraesCS5D01G336500 chr5A 96.850 127 4 0 2144 2270 540263457 540263331 1.770000e-51 213.0
15 TraesCS5D01G336500 chr5A 89.091 55 5 1 1442 1496 22975341 22975288 1.460000e-07 67.6
16 TraesCS5D01G336500 chr5B 90.659 364 28 5 1910 2270 515382936 515382576 1.580000e-131 479.0
17 TraesCS5D01G336500 chr5B 91.667 228 19 0 1443 1670 515396103 515395876 1.310000e-82 316.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G336500 chr5D 425985102 425987371 2269 True 4193 4193 100.000 1 2270 1 chr5D.!!$R3 2269
1 TraesCS5D01G336500 chr7D 412649831 412651188 1357 True 2409 2409 98.675 1 1358 1 chr7D.!!$R2 1357
2 TraesCS5D01G336500 chr7D 21279812 21281177 1365 True 2386 2386 98.173 1 1368 1 chr7D.!!$R1 1367
3 TraesCS5D01G336500 chr1D 45481229 45482586 1357 False 2403 2403 98.601 1 1358 1 chr1D.!!$F1 1357
4 TraesCS5D01G336500 chr3A 483248354 483249712 1358 True 2375 2375 98.234 1 1358 1 chr3A.!!$R1 1357
5 TraesCS5D01G336500 chr3B 478100307 478101672 1365 False 2362 2362 97.877 1 1366 1 chr3B.!!$F1 1365
6 TraesCS5D01G336500 chr2A 388673142 388674494 1352 False 2326 2326 97.645 1 1358 1 chr2A.!!$F1 1357
7 TraesCS5D01G336500 chr2B 681405652 681407009 1357 False 2318 2318 97.496 1 1357 1 chr2B.!!$F1 1356
8 TraesCS5D01G336500 chr2B 507821166 507822521 1355 True 2316 2316 97.493 3 1358 1 chr2B.!!$R1 1355
9 TraesCS5D01G336500 chr4B 495288431 495289789 1358 False 2287 2287 97.057 1 1358 1 chr4B.!!$F1 1357
10 TraesCS5D01G336500 chr5A 540272108 540273550 1442 True 476 652 91.065 1443 2138 2 chr5A.!!$R3 695

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
128 129 1.376609 GCTGTCCTAACCGCCATTGG 61.377 60.0 0.0 0.0 30.1 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1416 0.113776 TCCGGGAGTAGGTGTCAGTT 59.886 55.0 0.0 0.0 0.0 3.16 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
128 129 1.376609 GCTGTCCTAACCGCCATTGG 61.377 60.000 0.00 0.00 30.10 3.16
261 262 2.568623 AGGTTAACTGGGAGCTTGTG 57.431 50.000 5.42 0.00 0.00 3.33
337 338 2.491022 GCTCTACGGCTCCGATGGT 61.491 63.158 15.95 0.00 42.83 3.55
513 514 2.282110 CCCCGTGACATTGCACCA 60.282 61.111 0.00 0.00 35.37 4.17
661 663 2.588027 TTGGGAAAAGGTTTCAACGC 57.412 45.000 3.35 0.00 0.00 4.84
862 864 6.953520 TCTTCAAAATAGGGTTTGGACATCAT 59.046 34.615 0.00 0.00 38.72 2.45
981 983 2.545526 CTCTTTGCGCATATGGAACGAT 59.454 45.455 12.75 0.00 0.00 3.73
1080 1082 5.326200 ACGATAACCTTCAGATTCGTCTT 57.674 39.130 0.00 0.00 35.09 3.01
1227 1230 0.109723 AGGTGTCGCTTTGGGCTTTA 59.890 50.000 0.00 0.00 39.13 1.85
1391 1394 4.360951 AAAAACCACTTCTACGGGATGA 57.639 40.909 0.00 0.00 0.00 2.92
1392 1395 3.329929 AAACCACTTCTACGGGATGAC 57.670 47.619 0.00 0.00 0.00 3.06
1393 1396 1.192428 ACCACTTCTACGGGATGACC 58.808 55.000 0.00 0.00 0.00 4.02
1407 1410 5.509716 GGGATGACCGTAAAATTTAAGGG 57.490 43.478 19.05 11.28 36.97 3.95
1408 1411 5.195185 GGGATGACCGTAAAATTTAAGGGA 58.805 41.667 19.05 8.01 36.97 4.20
1409 1412 5.653330 GGGATGACCGTAAAATTTAAGGGAA 59.347 40.000 19.05 9.11 36.97 3.97
1410 1413 6.183360 GGGATGACCGTAAAATTTAAGGGAAG 60.183 42.308 19.05 0.00 36.97 3.46
1411 1414 6.376299 GGATGACCGTAAAATTTAAGGGAAGT 59.624 38.462 19.05 5.20 0.00 3.01
1412 1415 7.094075 GGATGACCGTAAAATTTAAGGGAAGTT 60.094 37.037 19.05 1.01 0.00 2.66
1413 1416 8.866970 ATGACCGTAAAATTTAAGGGAAGTTA 57.133 30.769 19.05 0.00 0.00 2.24
1414 1417 8.688747 TGACCGTAAAATTTAAGGGAAGTTAA 57.311 30.769 19.05 0.00 0.00 2.01
1415 1418 8.567104 TGACCGTAAAATTTAAGGGAAGTTAAC 58.433 33.333 19.05 0.00 0.00 2.01
1416 1419 8.696043 ACCGTAAAATTTAAGGGAAGTTAACT 57.304 30.769 19.05 1.12 0.00 2.24
1417 1420 8.570488 ACCGTAAAATTTAAGGGAAGTTAACTG 58.430 33.333 19.05 0.00 0.00 3.16
1418 1421 8.785946 CCGTAAAATTTAAGGGAAGTTAACTGA 58.214 33.333 9.34 0.00 0.00 3.41
1419 1422 9.603298 CGTAAAATTTAAGGGAAGTTAACTGAC 57.397 33.333 9.34 6.70 0.00 3.51
1422 1425 7.520451 AATTTAAGGGAAGTTAACTGACACC 57.480 36.000 9.34 9.17 0.00 4.16
1423 1426 5.899631 TTAAGGGAAGTTAACTGACACCT 57.100 39.130 9.34 11.25 0.00 4.00
1424 1427 6.999705 TTAAGGGAAGTTAACTGACACCTA 57.000 37.500 9.34 0.00 0.00 3.08
1425 1428 4.886496 AGGGAAGTTAACTGACACCTAC 57.114 45.455 9.34 0.00 0.00 3.18
1426 1429 4.490706 AGGGAAGTTAACTGACACCTACT 58.509 43.478 9.34 2.52 0.00 2.57
1427 1430 4.527427 AGGGAAGTTAACTGACACCTACTC 59.473 45.833 9.34 0.00 0.00 2.59
1428 1431 4.322574 GGGAAGTTAACTGACACCTACTCC 60.323 50.000 9.34 8.63 0.00 3.85
1429 1432 4.322574 GGAAGTTAACTGACACCTACTCCC 60.323 50.000 9.34 0.00 0.00 4.30
1430 1433 2.824341 AGTTAACTGACACCTACTCCCG 59.176 50.000 7.48 0.00 0.00 5.14
1431 1434 1.843368 TAACTGACACCTACTCCCGG 58.157 55.000 0.00 0.00 0.00 5.73
1432 1435 0.113776 AACTGACACCTACTCCCGGA 59.886 55.000 0.73 0.00 0.00 5.14
1433 1436 0.113776 ACTGACACCTACTCCCGGAA 59.886 55.000 0.73 0.00 0.00 4.30
1434 1437 1.273098 ACTGACACCTACTCCCGGAAT 60.273 52.381 0.73 0.00 0.00 3.01
1435 1438 2.024655 ACTGACACCTACTCCCGGAATA 60.025 50.000 0.73 0.00 0.00 1.75
1436 1439 3.028850 CTGACACCTACTCCCGGAATAA 58.971 50.000 0.73 0.00 0.00 1.40
1437 1440 3.028850 TGACACCTACTCCCGGAATAAG 58.971 50.000 0.73 0.00 0.00 1.73
1438 1441 3.029570 GACACCTACTCCCGGAATAAGT 58.970 50.000 0.73 3.32 0.00 2.24
1439 1442 2.764572 ACACCTACTCCCGGAATAAGTG 59.235 50.000 0.73 5.96 0.00 3.16
1440 1443 2.764572 CACCTACTCCCGGAATAAGTGT 59.235 50.000 0.73 0.00 0.00 3.55
1441 1444 3.197116 CACCTACTCCCGGAATAAGTGTT 59.803 47.826 0.73 0.00 0.00 3.32
1494 1497 7.244166 TCAAAACCACAACTTATGCAATTTG 57.756 32.000 0.00 0.00 32.22 2.32
1531 1534 6.153212 ACGTTCATAGTCAAATTCGAACAG 57.847 37.500 0.00 0.00 33.93 3.16
1577 1580 9.820725 TTGAAAGTTCAAACATGAAGATCAAAT 57.179 25.926 0.00 0.00 43.62 2.32
1609 1612 4.380843 TGGTTCTTGAGATAAAGGGCAA 57.619 40.909 0.00 0.00 0.00 4.52
1621 1624 8.522830 TGAGATAAAGGGCAAGAACAAATAAAG 58.477 33.333 0.00 0.00 0.00 1.85
1625 1628 6.603940 AAGGGCAAGAACAAATAAAGCATA 57.396 33.333 0.00 0.00 0.00 3.14
1626 1629 6.212888 AGGGCAAGAACAAATAAAGCATAG 57.787 37.500 0.00 0.00 0.00 2.23
1646 1649 3.851098 AGATAGTTGAAAGACGACTGGC 58.149 45.455 0.00 0.00 42.57 4.85
1647 1650 2.450609 TAGTTGAAAGACGACTGGCC 57.549 50.000 0.00 0.00 42.57 5.36
1666 1669 0.401738 CAGGACTTGGTCATGGTGGT 59.598 55.000 4.68 0.00 40.11 4.16
1732 1738 2.047179 GGCAGGTCCTCCGTTGTC 60.047 66.667 0.00 0.00 39.05 3.18
1772 1778 2.416747 CTTTTGCAGATGTGACTCCGA 58.583 47.619 0.00 0.00 0.00 4.55
1779 1785 1.229209 ATGTGACTCCGACCCCAGT 60.229 57.895 0.00 0.00 0.00 4.00
1785 1792 3.302347 CTCCGACCCCAGTGTGCTC 62.302 68.421 0.00 0.00 0.00 4.26
1869 1876 1.333636 CCGAGTCTGCAATCCCCTCT 61.334 60.000 0.00 0.00 0.00 3.69
1882 1889 0.897863 CCCCTCTAGATCCTGGCTCG 60.898 65.000 0.00 0.00 0.00 5.03
1884 1891 1.074084 CCCTCTAGATCCTGGCTCGTA 59.926 57.143 0.00 0.00 0.00 3.43
1895 1902 2.514013 GGCTCGTATGCGTTGTCGG 61.514 63.158 2.37 0.00 39.49 4.79
1931 2683 4.899239 CGGGCCGAGCATCTCACC 62.899 72.222 24.41 0.00 0.00 4.02
1966 2718 2.159393 GCATCATGCTCACGCCTTTTTA 60.159 45.455 1.02 0.00 40.96 1.52
1968 2720 1.463056 TCATGCTCACGCCTTTTTACG 59.537 47.619 0.00 0.00 34.43 3.18
1973 2725 1.788308 CTCACGCCTTTTTACGTTCGA 59.212 47.619 0.00 0.00 41.32 3.71
1981 2733 3.058501 CCTTTTTACGTTCGAGCCATGTT 60.059 43.478 0.00 0.00 0.00 2.71
1989 2741 4.873827 ACGTTCGAGCCATGTTATTGTATT 59.126 37.500 0.00 0.00 0.00 1.89
1992 2744 6.238103 CGTTCGAGCCATGTTATTGTATTCTT 60.238 38.462 0.00 0.00 0.00 2.52
1993 2745 6.844696 TCGAGCCATGTTATTGTATTCTTC 57.155 37.500 0.00 0.00 0.00 2.87
1995 2747 5.760253 CGAGCCATGTTATTGTATTCTTCCT 59.240 40.000 0.00 0.00 0.00 3.36
2044 2796 8.613060 TCAATGAGAGGATATGTAAGAATTGC 57.387 34.615 0.00 0.00 0.00 3.56
2051 2803 7.542477 AGAGGATATGTAAGAATTGCGTATTCG 59.458 37.037 5.91 0.00 41.88 3.34
2072 2824 4.384846 TCGCAGAAAGAACGAAGAATACAC 59.615 41.667 0.00 0.00 31.97 2.90
2076 2828 6.312918 GCAGAAAGAACGAAGAATACACCATA 59.687 38.462 0.00 0.00 0.00 2.74
2091 2843 9.557338 GAATACACCATACGAGTAAGTCATATC 57.443 37.037 0.00 0.00 0.00 1.63
2132 2884 9.574516 AAATAGAATTACCTTGGGCTTACTATG 57.425 33.333 0.00 0.00 0.00 2.23
2139 2891 8.967779 TTACCTTGGGCTTACTATGTATATCT 57.032 34.615 0.00 0.00 0.00 1.98
2140 2892 7.873699 ACCTTGGGCTTACTATGTATATCTT 57.126 36.000 0.00 0.00 0.00 2.40
2141 2893 8.276453 ACCTTGGGCTTACTATGTATATCTTT 57.724 34.615 0.00 0.00 0.00 2.52
2142 2894 8.724310 ACCTTGGGCTTACTATGTATATCTTTT 58.276 33.333 0.00 0.00 0.00 2.27
2143 2895 9.574516 CCTTGGGCTTACTATGTATATCTTTTT 57.425 33.333 0.00 0.00 0.00 1.94
2185 2937 1.981256 TCTTGTTTGAACAGGGGAGC 58.019 50.000 6.21 0.00 40.50 4.70
2186 2938 1.494721 TCTTGTTTGAACAGGGGAGCT 59.505 47.619 6.21 0.00 40.50 4.09
2187 2939 2.091885 TCTTGTTTGAACAGGGGAGCTT 60.092 45.455 6.21 0.00 40.50 3.74
2188 2940 2.452600 TGTTTGAACAGGGGAGCTTT 57.547 45.000 0.00 0.00 34.30 3.51
2189 2941 3.586470 TGTTTGAACAGGGGAGCTTTA 57.414 42.857 0.00 0.00 34.30 1.85
2190 2942 3.486383 TGTTTGAACAGGGGAGCTTTAG 58.514 45.455 0.00 0.00 34.30 1.85
2191 2943 2.200373 TTGAACAGGGGAGCTTTAGC 57.800 50.000 0.00 0.00 42.49 3.09
2192 2944 6.520805 TGTTTGAACAGGGGAGCTTTAGCT 62.521 45.833 3.45 3.45 43.49 3.32
2209 2961 7.024171 GCTTTAGCTCTATGAAGAAAAACACC 58.976 38.462 0.00 0.00 38.21 4.16
2210 2962 7.308589 GCTTTAGCTCTATGAAGAAAAACACCA 60.309 37.037 0.00 0.00 38.21 4.17
2211 2963 7.672983 TTAGCTCTATGAAGAAAAACACCAG 57.327 36.000 0.00 0.00 0.00 4.00
2212 2964 4.457257 AGCTCTATGAAGAAAAACACCAGC 59.543 41.667 0.00 0.00 0.00 4.85
2213 2965 4.216257 GCTCTATGAAGAAAAACACCAGCA 59.784 41.667 0.00 0.00 0.00 4.41
2214 2966 5.689383 TCTATGAAGAAAAACACCAGCAC 57.311 39.130 0.00 0.00 0.00 4.40
2215 2967 5.129634 TCTATGAAGAAAAACACCAGCACA 58.870 37.500 0.00 0.00 0.00 4.57
2216 2968 3.502191 TGAAGAAAAACACCAGCACAC 57.498 42.857 0.00 0.00 0.00 3.82
2217 2969 2.822561 TGAAGAAAAACACCAGCACACA 59.177 40.909 0.00 0.00 0.00 3.72
2218 2970 2.939460 AGAAAAACACCAGCACACAC 57.061 45.000 0.00 0.00 0.00 3.82
2219 2971 1.476488 AGAAAAACACCAGCACACACC 59.524 47.619 0.00 0.00 0.00 4.16
2220 2972 1.476488 GAAAAACACCAGCACACACCT 59.524 47.619 0.00 0.00 0.00 4.00
2221 2973 2.428544 AAAACACCAGCACACACCTA 57.571 45.000 0.00 0.00 0.00 3.08
2222 2974 2.428544 AAACACCAGCACACACCTAA 57.571 45.000 0.00 0.00 0.00 2.69
2223 2975 2.428544 AACACCAGCACACACCTAAA 57.571 45.000 0.00 0.00 0.00 1.85
2224 2976 1.675552 ACACCAGCACACACCTAAAC 58.324 50.000 0.00 0.00 0.00 2.01
2225 2977 1.211949 ACACCAGCACACACCTAAACT 59.788 47.619 0.00 0.00 0.00 2.66
2226 2978 2.436542 ACACCAGCACACACCTAAACTA 59.563 45.455 0.00 0.00 0.00 2.24
2227 2979 2.806244 CACCAGCACACACCTAAACTAC 59.194 50.000 0.00 0.00 0.00 2.73
2228 2980 2.224450 ACCAGCACACACCTAAACTACC 60.224 50.000 0.00 0.00 0.00 3.18
2229 2981 2.224426 CCAGCACACACCTAAACTACCA 60.224 50.000 0.00 0.00 0.00 3.25
2230 2982 2.806244 CAGCACACACCTAAACTACCAC 59.194 50.000 0.00 0.00 0.00 4.16
2231 2983 2.704065 AGCACACACCTAAACTACCACT 59.296 45.455 0.00 0.00 0.00 4.00
2232 2984 3.899360 AGCACACACCTAAACTACCACTA 59.101 43.478 0.00 0.00 0.00 2.74
2233 2985 4.345837 AGCACACACCTAAACTACCACTAA 59.654 41.667 0.00 0.00 0.00 2.24
2234 2986 4.450080 GCACACACCTAAACTACCACTAAC 59.550 45.833 0.00 0.00 0.00 2.34
2235 2987 5.603596 CACACACCTAAACTACCACTAACA 58.396 41.667 0.00 0.00 0.00 2.41
2236 2988 6.050432 CACACACCTAAACTACCACTAACAA 58.950 40.000 0.00 0.00 0.00 2.83
2237 2989 6.018507 CACACACCTAAACTACCACTAACAAC 60.019 42.308 0.00 0.00 0.00 3.32
2238 2990 5.467735 CACACCTAAACTACCACTAACAACC 59.532 44.000 0.00 0.00 0.00 3.77
2239 2991 5.130809 ACACCTAAACTACCACTAACAACCA 59.869 40.000 0.00 0.00 0.00 3.67
2240 2992 6.056884 CACCTAAACTACCACTAACAACCAA 58.943 40.000 0.00 0.00 0.00 3.67
2241 2993 6.543100 CACCTAAACTACCACTAACAACCAAA 59.457 38.462 0.00 0.00 0.00 3.28
2242 2994 7.067251 CACCTAAACTACCACTAACAACCAAAA 59.933 37.037 0.00 0.00 0.00 2.44
2243 2995 7.614974 ACCTAAACTACCACTAACAACCAAAAA 59.385 33.333 0.00 0.00 0.00 1.94
2244 2996 8.635328 CCTAAACTACCACTAACAACCAAAAAT 58.365 33.333 0.00 0.00 0.00 1.82
2245 2997 9.673454 CTAAACTACCACTAACAACCAAAAATC 57.327 33.333 0.00 0.00 0.00 2.17
2246 2998 6.644248 ACTACCACTAACAACCAAAAATCC 57.356 37.500 0.00 0.00 0.00 3.01
2247 2999 6.370453 ACTACCACTAACAACCAAAAATCCT 58.630 36.000 0.00 0.00 0.00 3.24
2248 3000 6.837048 ACTACCACTAACAACCAAAAATCCTT 59.163 34.615 0.00 0.00 0.00 3.36
2249 3001 6.553953 ACCACTAACAACCAAAAATCCTTT 57.446 33.333 0.00 0.00 0.00 3.11
2250 3002 6.953101 ACCACTAACAACCAAAAATCCTTTT 58.047 32.000 0.00 0.00 35.02 2.27
2251 3003 7.398829 ACCACTAACAACCAAAAATCCTTTTT 58.601 30.769 0.00 0.00 43.20 1.94
2252 3004 8.541234 ACCACTAACAACCAAAAATCCTTTTTA 58.459 29.630 0.00 0.00 40.65 1.52
2253 3005 8.822855 CCACTAACAACCAAAAATCCTTTTTAC 58.177 33.333 0.00 0.00 40.65 2.01
2254 3006 8.822855 CACTAACAACCAAAAATCCTTTTTACC 58.177 33.333 0.00 0.00 40.65 2.85
2255 3007 7.988599 ACTAACAACCAAAAATCCTTTTTACCC 59.011 33.333 0.00 0.00 40.65 3.69
2256 3008 6.314899 ACAACCAAAAATCCTTTTTACCCA 57.685 33.333 0.00 0.00 40.65 4.51
2257 3009 6.722328 ACAACCAAAAATCCTTTTTACCCAA 58.278 32.000 0.00 0.00 40.65 4.12
2258 3010 7.175797 ACAACCAAAAATCCTTTTTACCCAAA 58.824 30.769 0.00 0.00 40.65 3.28
2259 3011 7.121463 ACAACCAAAAATCCTTTTTACCCAAAC 59.879 33.333 0.00 0.00 40.65 2.93
2260 3012 6.722328 ACCAAAAATCCTTTTTACCCAAACA 58.278 32.000 0.00 0.00 40.65 2.83
2261 3013 7.175797 ACCAAAAATCCTTTTTACCCAAACAA 58.824 30.769 0.00 0.00 40.65 2.83
2262 3014 7.836685 ACCAAAAATCCTTTTTACCCAAACAAT 59.163 29.630 0.00 0.00 40.65 2.71
2263 3015 8.690884 CCAAAAATCCTTTTTACCCAAACAATT 58.309 29.630 0.00 0.00 40.65 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 0.601311 GGGCGTGAGGTGATAGATGC 60.601 60.000 0.00 0.00 0.00 3.91
261 262 2.963101 ACCCTTTTCCTTAGGTTTGCAC 59.037 45.455 0.00 0.00 0.00 4.57
337 338 4.941263 CCTATCAGTCCATTCGAACCAAAA 59.059 41.667 0.00 0.00 0.00 2.44
513 514 2.167487 GCGAGAAAGATGGAAGAGGTCT 59.833 50.000 0.00 0.00 0.00 3.85
661 663 1.333636 ACTTCATCCTCGAGGGCCAG 61.334 60.000 30.80 21.74 35.41 4.85
727 729 0.744771 GCCTTGTAAGCCGAGGAAGG 60.745 60.000 0.00 0.00 46.66 3.46
862 864 1.138036 CACGACGGATCAAGCGGTA 59.862 57.895 0.00 0.00 0.00 4.02
972 974 2.037251 CCACGGGAGAATATCGTTCCAT 59.963 50.000 0.00 0.00 34.73 3.41
1370 1373 4.070009 GTCATCCCGTAGAAGTGGTTTTT 58.930 43.478 0.00 0.00 0.00 1.94
1371 1374 3.558533 GGTCATCCCGTAGAAGTGGTTTT 60.559 47.826 0.00 0.00 0.00 2.43
1372 1375 2.027469 GGTCATCCCGTAGAAGTGGTTT 60.027 50.000 0.00 0.00 0.00 3.27
1373 1376 1.553704 GGTCATCCCGTAGAAGTGGTT 59.446 52.381 0.00 0.00 0.00 3.67
1374 1377 1.192428 GGTCATCCCGTAGAAGTGGT 58.808 55.000 0.00 0.00 0.00 4.16
1385 1388 5.195185 TCCCTTAAATTTTACGGTCATCCC 58.805 41.667 9.96 0.00 0.00 3.85
1386 1389 6.376299 ACTTCCCTTAAATTTTACGGTCATCC 59.624 38.462 9.96 0.00 0.00 3.51
1387 1390 7.387119 ACTTCCCTTAAATTTTACGGTCATC 57.613 36.000 9.96 0.00 0.00 2.92
1388 1391 7.770366 AACTTCCCTTAAATTTTACGGTCAT 57.230 32.000 9.96 0.00 0.00 3.06
1389 1392 8.567104 GTTAACTTCCCTTAAATTTTACGGTCA 58.433 33.333 9.96 0.00 0.00 4.02
1390 1393 8.786898 AGTTAACTTCCCTTAAATTTTACGGTC 58.213 33.333 1.12 0.00 0.00 4.79
1391 1394 8.570488 CAGTTAACTTCCCTTAAATTTTACGGT 58.430 33.333 5.07 0.00 0.00 4.83
1392 1395 8.785946 TCAGTTAACTTCCCTTAAATTTTACGG 58.214 33.333 5.07 5.00 0.00 4.02
1393 1396 9.603298 GTCAGTTAACTTCCCTTAAATTTTACG 57.397 33.333 5.07 0.00 0.00 3.18
1396 1399 8.418662 GGTGTCAGTTAACTTCCCTTAAATTTT 58.581 33.333 5.07 0.00 0.00 1.82
1397 1400 7.783119 AGGTGTCAGTTAACTTCCCTTAAATTT 59.217 33.333 5.07 0.00 0.00 1.82
1398 1401 7.295340 AGGTGTCAGTTAACTTCCCTTAAATT 58.705 34.615 5.07 0.00 0.00 1.82
1399 1402 6.849151 AGGTGTCAGTTAACTTCCCTTAAAT 58.151 36.000 5.07 0.00 0.00 1.40
1400 1403 6.256643 AGGTGTCAGTTAACTTCCCTTAAA 57.743 37.500 5.07 0.00 0.00 1.52
1401 1404 5.899631 AGGTGTCAGTTAACTTCCCTTAA 57.100 39.130 5.07 0.00 0.00 1.85
1402 1405 6.080009 AGTAGGTGTCAGTTAACTTCCCTTA 58.920 40.000 5.07 0.00 0.00 2.69
1403 1406 4.906060 AGTAGGTGTCAGTTAACTTCCCTT 59.094 41.667 5.07 0.00 0.00 3.95
1404 1407 4.490706 AGTAGGTGTCAGTTAACTTCCCT 58.509 43.478 5.07 10.71 0.00 4.20
1405 1408 4.322574 GGAGTAGGTGTCAGTTAACTTCCC 60.323 50.000 5.07 3.62 0.00 3.97
1406 1409 4.322574 GGGAGTAGGTGTCAGTTAACTTCC 60.323 50.000 5.07 7.00 0.00 3.46
1407 1410 4.617762 CGGGAGTAGGTGTCAGTTAACTTC 60.618 50.000 5.07 3.08 0.00 3.01
1408 1411 3.257624 CGGGAGTAGGTGTCAGTTAACTT 59.742 47.826 5.07 0.00 0.00 2.66
1409 1412 2.824341 CGGGAGTAGGTGTCAGTTAACT 59.176 50.000 1.12 1.12 0.00 2.24
1410 1413 2.094338 CCGGGAGTAGGTGTCAGTTAAC 60.094 54.545 0.00 0.00 0.00 2.01
1411 1414 2.173519 CCGGGAGTAGGTGTCAGTTAA 58.826 52.381 0.00 0.00 0.00 2.01
1412 1415 1.355381 TCCGGGAGTAGGTGTCAGTTA 59.645 52.381 0.00 0.00 0.00 2.24
1413 1416 0.113776 TCCGGGAGTAGGTGTCAGTT 59.886 55.000 0.00 0.00 0.00 3.16
1414 1417 0.113776 TTCCGGGAGTAGGTGTCAGT 59.886 55.000 0.00 0.00 0.00 3.41
1415 1418 1.486211 ATTCCGGGAGTAGGTGTCAG 58.514 55.000 0.00 0.00 0.00 3.51
1416 1419 2.832643 TATTCCGGGAGTAGGTGTCA 57.167 50.000 0.00 0.00 0.00 3.58
1417 1420 3.029570 ACTTATTCCGGGAGTAGGTGTC 58.970 50.000 12.55 0.00 0.00 3.67
1418 1421 2.764572 CACTTATTCCGGGAGTAGGTGT 59.235 50.000 24.61 12.30 31.09 4.16
1419 1422 2.764572 ACACTTATTCCGGGAGTAGGTG 59.235 50.000 28.52 28.52 37.66 4.00
1420 1423 3.111741 ACACTTATTCCGGGAGTAGGT 57.888 47.619 8.28 8.28 0.00 3.08
1421 1424 4.482952 AAACACTTATTCCGGGAGTAGG 57.517 45.455 0.00 7.07 0.00 3.18
1422 1425 5.353400 GGAAAAACACTTATTCCGGGAGTAG 59.647 44.000 0.00 0.00 33.86 2.57
1423 1426 5.247862 GGAAAAACACTTATTCCGGGAGTA 58.752 41.667 0.00 0.00 33.86 2.59
1424 1427 4.077108 GGAAAAACACTTATTCCGGGAGT 58.923 43.478 0.00 0.00 33.86 3.85
1425 1428 4.696899 GGAAAAACACTTATTCCGGGAG 57.303 45.455 0.00 0.00 33.86 4.30
1430 1433 7.605410 TGTCTATCGGAAAAACACTTATTCC 57.395 36.000 0.00 0.00 39.38 3.01
1432 1435 9.886132 AGTATGTCTATCGGAAAAACACTTATT 57.114 29.630 0.00 0.00 0.00 1.40
1433 1436 9.886132 AAGTATGTCTATCGGAAAAACACTTAT 57.114 29.630 0.00 0.00 0.00 1.73
1434 1437 9.146984 CAAGTATGTCTATCGGAAAAACACTTA 57.853 33.333 0.00 0.00 0.00 2.24
1435 1438 7.876068 TCAAGTATGTCTATCGGAAAAACACTT 59.124 33.333 0.00 0.00 0.00 3.16
1436 1439 7.383687 TCAAGTATGTCTATCGGAAAAACACT 58.616 34.615 0.00 0.00 0.00 3.55
1437 1440 7.591006 TCAAGTATGTCTATCGGAAAAACAC 57.409 36.000 0.00 0.00 0.00 3.32
1438 1441 9.309516 GTATCAAGTATGTCTATCGGAAAAACA 57.690 33.333 0.00 0.00 0.00 2.83
1439 1442 9.530633 AGTATCAAGTATGTCTATCGGAAAAAC 57.469 33.333 0.00 0.00 0.00 2.43
1494 1497 6.888430 ACTATGAACGTTGAGTCAAAATGTC 58.112 36.000 5.00 3.91 0.00 3.06
1531 1534 9.994432 CTTTCAATCAGTTACCAGATATTGTTC 57.006 33.333 0.00 0.00 0.00 3.18
1542 1545 8.134895 TCATGTTTGAACTTTCAATCAGTTACC 58.865 33.333 16.57 0.00 44.98 2.85
1547 1550 9.125906 GATCTTCATGTTTGAACTTTCAATCAG 57.874 33.333 16.57 10.96 44.98 2.90
1550 1553 9.820725 TTTGATCTTCATGTTTGAACTTTCAAT 57.179 25.926 5.26 0.00 45.65 2.57
1621 1624 5.460419 CCAGTCGTCTTTCAACTATCTATGC 59.540 44.000 0.00 0.00 0.00 3.14
1625 1628 3.368531 GGCCAGTCGTCTTTCAACTATCT 60.369 47.826 0.00 0.00 0.00 1.98
1626 1629 2.930682 GGCCAGTCGTCTTTCAACTATC 59.069 50.000 0.00 0.00 0.00 2.08
1647 1650 0.401738 ACCACCATGACCAAGTCCTG 59.598 55.000 0.00 0.00 0.00 3.86
1659 1662 1.304381 GCCATGACCACACCACCAT 60.304 57.895 0.00 0.00 0.00 3.55
1707 1710 3.842925 GAGGACCTGCCGCCACAAA 62.843 63.158 0.00 0.00 43.43 2.83
1779 1785 1.555075 GGACATAACTCCCAGAGCACA 59.445 52.381 0.00 0.00 32.04 4.57
1847 1854 2.586792 GGATTGCAGACTCGGGCT 59.413 61.111 0.00 0.00 0.00 5.19
1853 1860 2.856760 TCTAGAGGGGATTGCAGACT 57.143 50.000 0.00 0.00 0.00 3.24
1854 1861 2.301583 GGATCTAGAGGGGATTGCAGAC 59.698 54.545 0.00 0.00 0.00 3.51
1859 1866 1.627834 GCCAGGATCTAGAGGGGATTG 59.372 57.143 0.00 0.00 0.00 2.67
1860 1867 1.511747 AGCCAGGATCTAGAGGGGATT 59.488 52.381 0.00 0.00 0.00 3.01
1861 1868 1.078656 GAGCCAGGATCTAGAGGGGAT 59.921 57.143 0.00 0.00 0.00 3.85
1869 1876 0.881796 CGCATACGAGCCAGGATCTA 59.118 55.000 2.51 0.00 43.93 1.98
1882 1889 2.795389 GACGGCCGACAACGCATAC 61.795 63.158 35.90 5.60 38.29 2.39
1895 1902 4.261888 ACAAGATGTGACGACGGC 57.738 55.556 0.00 0.00 0.00 5.68
1914 2666 4.899239 GGTGAGATGCTCGGCCCG 62.899 72.222 0.00 0.00 32.35 6.13
1966 2718 2.695359 ACAATAACATGGCTCGAACGT 58.305 42.857 0.00 0.00 0.00 3.99
1968 2720 6.604735 AGAATACAATAACATGGCTCGAAC 57.395 37.500 0.00 0.00 0.00 3.95
1973 2725 6.891908 ACAAGGAAGAATACAATAACATGGCT 59.108 34.615 0.00 0.00 0.00 4.75
1989 2741 8.896722 AGAAGTTAGAATAGGTACAAGGAAGA 57.103 34.615 0.00 0.00 0.00 2.87
1992 2744 8.896722 AGAAGAAGTTAGAATAGGTACAAGGA 57.103 34.615 0.00 0.00 0.00 3.36
2026 2778 7.667283 CGAATACGCAATTCTTACATATCCTC 58.333 38.462 8.84 0.00 41.68 3.71
2044 2796 3.606777 TCTTCGTTCTTTCTGCGAATACG 59.393 43.478 0.00 0.00 42.50 3.06
2051 2803 4.451096 TGGTGTATTCTTCGTTCTTTCTGC 59.549 41.667 0.00 0.00 0.00 4.26
2058 2810 5.338365 ACTCGTATGGTGTATTCTTCGTTC 58.662 41.667 0.00 0.00 0.00 3.95
2062 2814 7.478322 TGACTTACTCGTATGGTGTATTCTTC 58.522 38.462 0.00 0.00 0.00 2.87
2076 2828 9.587772 GCCAAATATATGATATGACTTACTCGT 57.412 33.333 0.00 0.00 0.00 4.18
2096 2848 7.337938 CAAGGTAATTCTATTTTGGGCCAAAT 58.662 34.615 30.82 21.74 33.19 2.32
2099 2851 4.714308 CCAAGGTAATTCTATTTTGGGCCA 59.286 41.667 0.00 0.00 33.22 5.36
2101 2853 5.276461 CCCAAGGTAATTCTATTTTGGGC 57.724 43.478 7.12 0.00 45.69 5.36
2159 2911 7.885399 GCTCCCCTGTTCAAACAAGATATATAT 59.115 37.037 0.00 0.00 38.66 0.86
2160 2912 7.072454 AGCTCCCCTGTTCAAACAAGATATATA 59.928 37.037 0.00 0.00 38.66 0.86
2161 2913 6.064717 GCTCCCCTGTTCAAACAAGATATAT 58.935 40.000 0.00 0.00 38.66 0.86
2162 2914 5.191722 AGCTCCCCTGTTCAAACAAGATATA 59.808 40.000 0.00 0.00 38.66 0.86
2163 2915 4.018050 AGCTCCCCTGTTCAAACAAGATAT 60.018 41.667 0.00 0.00 38.66 1.63
2164 2916 3.330701 AGCTCCCCTGTTCAAACAAGATA 59.669 43.478 0.00 0.00 38.66 1.98
2165 2917 2.108952 AGCTCCCCTGTTCAAACAAGAT 59.891 45.455 0.00 0.00 38.66 2.40
2166 2918 1.494721 AGCTCCCCTGTTCAAACAAGA 59.505 47.619 0.00 0.00 38.66 3.02
2167 2919 1.986882 AGCTCCCCTGTTCAAACAAG 58.013 50.000 0.00 0.00 38.66 3.16
2168 2920 2.452600 AAGCTCCCCTGTTCAAACAA 57.547 45.000 0.00 0.00 38.66 2.83
2169 2921 2.452600 AAAGCTCCCCTGTTCAAACA 57.547 45.000 0.00 0.00 37.37 2.83
2170 2922 2.229062 GCTAAAGCTCCCCTGTTCAAAC 59.771 50.000 0.00 0.00 38.21 2.93
2171 2923 2.514803 GCTAAAGCTCCCCTGTTCAAA 58.485 47.619 0.00 0.00 38.21 2.69
2172 2924 2.200373 GCTAAAGCTCCCCTGTTCAA 57.800 50.000 0.00 0.00 38.21 2.69
2173 2925 3.957288 GCTAAAGCTCCCCTGTTCA 57.043 52.632 0.00 0.00 38.21 3.18
2184 2936 7.024171 GGTGTTTTTCTTCATAGAGCTAAAGC 58.976 38.462 0.00 0.00 42.49 3.51
2185 2937 8.099364 TGGTGTTTTTCTTCATAGAGCTAAAG 57.901 34.615 0.00 0.00 0.00 1.85
2186 2938 7.308589 GCTGGTGTTTTTCTTCATAGAGCTAAA 60.309 37.037 0.00 0.00 0.00 1.85
2187 2939 6.149474 GCTGGTGTTTTTCTTCATAGAGCTAA 59.851 38.462 0.00 0.00 0.00 3.09
2188 2940 5.643777 GCTGGTGTTTTTCTTCATAGAGCTA 59.356 40.000 0.00 0.00 0.00 3.32
2189 2941 4.457257 GCTGGTGTTTTTCTTCATAGAGCT 59.543 41.667 0.00 0.00 0.00 4.09
2190 2942 4.216257 TGCTGGTGTTTTTCTTCATAGAGC 59.784 41.667 0.00 0.00 0.00 4.09
2191 2943 5.239306 TGTGCTGGTGTTTTTCTTCATAGAG 59.761 40.000 0.00 0.00 0.00 2.43
2192 2944 5.008613 GTGTGCTGGTGTTTTTCTTCATAGA 59.991 40.000 0.00 0.00 0.00 1.98
2193 2945 5.215160 GTGTGCTGGTGTTTTTCTTCATAG 58.785 41.667 0.00 0.00 0.00 2.23
2194 2946 4.642437 TGTGTGCTGGTGTTTTTCTTCATA 59.358 37.500 0.00 0.00 0.00 2.15
2195 2947 3.446873 TGTGTGCTGGTGTTTTTCTTCAT 59.553 39.130 0.00 0.00 0.00 2.57
2196 2948 2.822561 TGTGTGCTGGTGTTTTTCTTCA 59.177 40.909 0.00 0.00 0.00 3.02
2197 2949 3.179048 GTGTGTGCTGGTGTTTTTCTTC 58.821 45.455 0.00 0.00 0.00 2.87
2198 2950 2.094234 GGTGTGTGCTGGTGTTTTTCTT 60.094 45.455 0.00 0.00 0.00 2.52
2199 2951 1.476488 GGTGTGTGCTGGTGTTTTTCT 59.524 47.619 0.00 0.00 0.00 2.52
2200 2952 1.476488 AGGTGTGTGCTGGTGTTTTTC 59.524 47.619 0.00 0.00 0.00 2.29
2201 2953 1.555967 AGGTGTGTGCTGGTGTTTTT 58.444 45.000 0.00 0.00 0.00 1.94
2202 2954 2.428544 TAGGTGTGTGCTGGTGTTTT 57.571 45.000 0.00 0.00 0.00 2.43
2203 2955 2.425668 GTTTAGGTGTGTGCTGGTGTTT 59.574 45.455 0.00 0.00 0.00 2.83
2204 2956 2.021457 GTTTAGGTGTGTGCTGGTGTT 58.979 47.619 0.00 0.00 0.00 3.32
2205 2957 1.211949 AGTTTAGGTGTGTGCTGGTGT 59.788 47.619 0.00 0.00 0.00 4.16
2206 2958 1.967319 AGTTTAGGTGTGTGCTGGTG 58.033 50.000 0.00 0.00 0.00 4.17
2207 2959 2.224450 GGTAGTTTAGGTGTGTGCTGGT 60.224 50.000 0.00 0.00 0.00 4.00
2208 2960 2.224426 TGGTAGTTTAGGTGTGTGCTGG 60.224 50.000 0.00 0.00 0.00 4.85
2209 2961 2.806244 GTGGTAGTTTAGGTGTGTGCTG 59.194 50.000 0.00 0.00 0.00 4.41
2210 2962 2.704065 AGTGGTAGTTTAGGTGTGTGCT 59.296 45.455 0.00 0.00 0.00 4.40
2211 2963 3.121738 AGTGGTAGTTTAGGTGTGTGC 57.878 47.619 0.00 0.00 0.00 4.57
2212 2964 5.603596 TGTTAGTGGTAGTTTAGGTGTGTG 58.396 41.667 0.00 0.00 0.00 3.82
2213 2965 5.874897 TGTTAGTGGTAGTTTAGGTGTGT 57.125 39.130 0.00 0.00 0.00 3.72
2214 2966 5.467735 GGTTGTTAGTGGTAGTTTAGGTGTG 59.532 44.000 0.00 0.00 0.00 3.82
2215 2967 5.130809 TGGTTGTTAGTGGTAGTTTAGGTGT 59.869 40.000 0.00 0.00 0.00 4.16
2216 2968 5.613329 TGGTTGTTAGTGGTAGTTTAGGTG 58.387 41.667 0.00 0.00 0.00 4.00
2217 2969 5.892524 TGGTTGTTAGTGGTAGTTTAGGT 57.107 39.130 0.00 0.00 0.00 3.08
2218 2970 7.571080 TTTTGGTTGTTAGTGGTAGTTTAGG 57.429 36.000 0.00 0.00 0.00 2.69
2219 2971 9.673454 GATTTTTGGTTGTTAGTGGTAGTTTAG 57.327 33.333 0.00 0.00 0.00 1.85
2220 2972 8.631797 GGATTTTTGGTTGTTAGTGGTAGTTTA 58.368 33.333 0.00 0.00 0.00 2.01
2221 2973 7.343574 AGGATTTTTGGTTGTTAGTGGTAGTTT 59.656 33.333 0.00 0.00 0.00 2.66
2222 2974 6.837048 AGGATTTTTGGTTGTTAGTGGTAGTT 59.163 34.615 0.00 0.00 0.00 2.24
2223 2975 6.370453 AGGATTTTTGGTTGTTAGTGGTAGT 58.630 36.000 0.00 0.00 0.00 2.73
2224 2976 6.894339 AGGATTTTTGGTTGTTAGTGGTAG 57.106 37.500 0.00 0.00 0.00 3.18
2225 2977 7.663043 AAAGGATTTTTGGTTGTTAGTGGTA 57.337 32.000 0.00 0.00 31.62 3.25
2226 2978 6.553953 AAAGGATTTTTGGTTGTTAGTGGT 57.446 33.333 0.00 0.00 31.62 4.16


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

AutoCloner maintained by Alex Coulton.