Multiple sequence alignment - TraesCS5D01G502800

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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 TraesCS5D01G502800 chr5D 100.000 3589 0 0 958 4546 530051247 530054835 0.000000e+00 6628
1 TraesCS5D01G502800 chr5D 100.000 643 0 0 1 643 530050290 530050932 0.000000e+00 1188
2 TraesCS5D01G502800 chr5D 91.818 110 9 0 1707 1816 526911676 526911567 2.190000e-33 154
3 TraesCS5D01G502800 chr5A 91.399 3639 160 70 958 4546 657775277 657778812 0.000000e+00 4844
4 TraesCS5D01G502800 chr5A 87.956 548 42 14 69 603 657774716 657775252 3.860000e-175 625
5 TraesCS5D01G502800 chr5B 90.587 1583 61 26 3018 4546 669231325 669232873 0.000000e+00 2017
6 TraesCS5D01G502800 chr5B 85.902 1369 117 30 958 2284 669229226 669230560 0.000000e+00 1389
7 TraesCS5D01G502800 chr5B 88.716 514 32 11 39 542 669228493 669228990 5.030000e-169 604
8 TraesCS5D01G502800 chr5B 92.580 283 20 1 2345 2626 669230739 669231021 5.480000e-109 405


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 TraesCS5D01G502800 chr5D 530050290 530054835 4545 False 3908.00 6628 100.00000 1 4546 2 chr5D.!!$F1 4545
1 TraesCS5D01G502800 chr5A 657774716 657778812 4096 False 2734.50 4844 89.67750 69 4546 2 chr5A.!!$F1 4477
2 TraesCS5D01G502800 chr5B 669228493 669232873 4380 False 1103.75 2017 89.44625 39 4546 4 chr5B.!!$F1 4507

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
299 316 0.037232 CCAACACTCGTCTTCCTCCC 60.037 60.0 0.00 0.00 0.00 4.30 F
1236 1412 0.027324 GATTGCTTCTGCGCTAGTGC 59.973 55.0 21.44 21.44 43.34 4.40 F
1319 1497 0.108615 CCGACTGACCGATTGCTTCT 60.109 55.0 0.00 0.00 0.00 2.85 F
2194 2420 0.179084 TATCAGCTGTAAGTGGCGGC 60.179 55.0 14.67 0.00 38.44 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 1502 0.238289 CGACAGCCTGCGAAACAAAT 59.762 50.000 2.97 0.00 0.00 2.32 R
2881 3257 0.037232 GACACAGTACTGGAGCACCC 60.037 60.000 26.12 5.11 34.81 4.61 R
2928 3305 1.373497 AAAGTCAGAGCTGCGGACG 60.373 57.895 13.57 0.00 44.96 4.79 R
3643 4051 0.029035 CGAAATCCCGATCGACTCGT 59.971 55.000 18.66 0.00 46.18 4.18 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
20 21 3.904136 ACAAGCGTCCTCTGAAAATTG 57.096 42.857 0.00 0.00 0.00 2.32
21 22 2.554032 ACAAGCGTCCTCTGAAAATTGG 59.446 45.455 0.00 0.00 0.00 3.16
22 23 2.554032 CAAGCGTCCTCTGAAAATTGGT 59.446 45.455 0.00 0.00 0.00 3.67
23 24 2.427506 AGCGTCCTCTGAAAATTGGTC 58.572 47.619 0.00 0.00 0.00 4.02
24 25 1.468914 GCGTCCTCTGAAAATTGGTCC 59.531 52.381 0.00 0.00 0.00 4.46
25 26 2.876079 GCGTCCTCTGAAAATTGGTCCT 60.876 50.000 0.00 0.00 0.00 3.85
26 27 3.003480 CGTCCTCTGAAAATTGGTCCTC 58.997 50.000 0.00 0.00 0.00 3.71
27 28 3.557054 CGTCCTCTGAAAATTGGTCCTCA 60.557 47.826 0.00 0.00 0.00 3.86
28 29 4.398319 GTCCTCTGAAAATTGGTCCTCAA 58.602 43.478 0.00 0.00 40.01 3.02
29 30 4.827284 GTCCTCTGAAAATTGGTCCTCAAA 59.173 41.667 0.00 0.00 39.05 2.69
30 31 4.827284 TCCTCTGAAAATTGGTCCTCAAAC 59.173 41.667 0.00 0.00 39.05 2.93
31 32 4.021981 CCTCTGAAAATTGGTCCTCAAACC 60.022 45.833 0.00 0.00 39.05 3.27
32 33 3.568007 TCTGAAAATTGGTCCTCAAACCG 59.432 43.478 0.00 0.00 42.62 4.44
33 34 2.035321 TGAAAATTGGTCCTCAAACCGC 59.965 45.455 0.00 0.00 42.62 5.68
34 35 0.966179 AAATTGGTCCTCAAACCGCC 59.034 50.000 0.00 0.00 42.62 6.13
35 36 1.241315 AATTGGTCCTCAAACCGCCG 61.241 55.000 0.00 0.00 42.62 6.46
36 37 2.119484 ATTGGTCCTCAAACCGCCGA 62.119 55.000 0.00 0.00 42.62 5.54
37 38 2.031465 GGTCCTCAAACCGCCGAA 59.969 61.111 0.00 0.00 0.00 4.30
46 47 4.201783 CCTCAAACCGCCGAAGTTATTTAG 60.202 45.833 0.00 0.00 0.00 1.85
49 50 2.897436 ACCGCCGAAGTTATTTAGGAC 58.103 47.619 0.00 0.00 33.73 3.85
53 54 3.709987 GCCGAAGTTATTTAGGACGCTA 58.290 45.455 0.00 0.00 33.73 4.26
54 55 3.734735 GCCGAAGTTATTTAGGACGCTAG 59.265 47.826 0.00 0.00 33.73 3.42
64 65 1.300233 GGACGCTAGCAAGGGATCG 60.300 63.158 16.45 0.00 38.96 3.69
67 68 1.300233 CGCTAGCAAGGGATCGGAC 60.300 63.158 16.45 0.00 37.88 4.79
79 80 2.701951 GGGATCGGACTATTTGTGGGTA 59.298 50.000 0.00 0.00 0.00 3.69
80 81 3.244112 GGGATCGGACTATTTGTGGGTAG 60.244 52.174 0.00 0.00 0.00 3.18
87 88 6.211184 TCGGACTATTTGTGGGTAGAAAGTTA 59.789 38.462 0.00 0.00 0.00 2.24
88 89 7.046033 CGGACTATTTGTGGGTAGAAAGTTAT 58.954 38.462 0.00 0.00 0.00 1.89
89 90 8.199449 CGGACTATTTGTGGGTAGAAAGTTATA 58.801 37.037 0.00 0.00 0.00 0.98
125 127 2.477104 AATTTTGGAGGGGGCCATAG 57.523 50.000 4.39 0.00 37.86 2.23
126 128 0.562674 ATTTTGGAGGGGGCCATAGG 59.437 55.000 4.39 0.00 37.86 2.57
134 136 0.555769 GGGGGCCATAGGAACATTCA 59.444 55.000 4.39 0.00 0.00 2.57
137 144 2.430694 GGGGCCATAGGAACATTCAAAC 59.569 50.000 4.39 0.00 0.00 2.93
159 169 4.274950 ACTTTGAACCACAACGTAGAATGG 59.725 41.667 0.00 0.00 38.80 3.16
219 229 0.104304 AACATAGCGTAGGAAGGCCG 59.896 55.000 0.00 0.00 39.96 6.13
220 230 1.041447 ACATAGCGTAGGAAGGCCGT 61.041 55.000 0.00 0.00 39.96 5.68
299 316 0.037232 CCAACACTCGTCTTCCTCCC 60.037 60.000 0.00 0.00 0.00 4.30
300 317 0.969894 CAACACTCGTCTTCCTCCCT 59.030 55.000 0.00 0.00 0.00 4.20
301 318 1.067495 CAACACTCGTCTTCCTCCCTC 60.067 57.143 0.00 0.00 0.00 4.30
302 319 0.612453 ACACTCGTCTTCCTCCCTCC 60.612 60.000 0.00 0.00 0.00 4.30
303 320 0.612174 CACTCGTCTTCCTCCCTCCA 60.612 60.000 0.00 0.00 0.00 3.86
304 321 0.612453 ACTCGTCTTCCTCCCTCCAC 60.612 60.000 0.00 0.00 0.00 4.02
305 322 0.323908 CTCGTCTTCCTCCCTCCACT 60.324 60.000 0.00 0.00 0.00 4.00
306 323 0.323542 TCGTCTTCCTCCCTCCACTC 60.324 60.000 0.00 0.00 0.00 3.51
307 324 1.324005 CGTCTTCCTCCCTCCACTCC 61.324 65.000 0.00 0.00 0.00 3.85
313 330 3.965026 CTCCCTCCACTCCGCTCCA 62.965 68.421 0.00 0.00 0.00 3.86
451 479 4.003788 CCCGCGTTGACCCACTCT 62.004 66.667 4.92 0.00 0.00 3.24
453 481 2.432628 CGCGTTGACCCACTCTCC 60.433 66.667 0.00 0.00 0.00 3.71
549 577 2.174319 GCGTCGAAAGGCATCTCCC 61.174 63.158 0.00 0.00 36.30 4.30
558 586 4.843331 GCATCTCCCCCTCCCCCA 62.843 72.222 0.00 0.00 0.00 4.96
574 602 2.310538 CCCCATTTTAGCATCTCCCAC 58.689 52.381 0.00 0.00 0.00 4.61
612 640 4.806339 CGCCTCCTCCTCCCCCTT 62.806 72.222 0.00 0.00 0.00 3.95
613 641 3.093172 GCCTCCTCCTCCCCCTTG 61.093 72.222 0.00 0.00 0.00 3.61
620 648 2.203549 CTCCTCCCCCTTGGAAGCAC 62.204 65.000 0.00 0.00 44.57 4.40
622 650 2.121506 TCCCCCTTGGAAGCACCT 60.122 61.111 1.91 0.00 41.40 4.00
635 807 2.361610 CACCTCCGCCCTGCATTT 60.362 61.111 0.00 0.00 0.00 2.32
636 808 2.044946 ACCTCCGCCCTGCATTTC 60.045 61.111 0.00 0.00 0.00 2.17
637 809 2.273449 CCTCCGCCCTGCATTTCT 59.727 61.111 0.00 0.00 0.00 2.52
638 810 1.379044 CCTCCGCCCTGCATTTCTT 60.379 57.895 0.00 0.00 0.00 2.52
639 811 0.967380 CCTCCGCCCTGCATTTCTTT 60.967 55.000 0.00 0.00 0.00 2.52
640 812 0.453390 CTCCGCCCTGCATTTCTTTC 59.547 55.000 0.00 0.00 0.00 2.62
641 813 0.965363 TCCGCCCTGCATTTCTTTCC 60.965 55.000 0.00 0.00 0.00 3.13
642 814 1.512694 CGCCCTGCATTTCTTTCCC 59.487 57.895 0.00 0.00 0.00 3.97
1023 1199 4.704833 CTGGACCACAGCCCCACG 62.705 72.222 0.00 0.00 40.97 4.94
1218 1394 2.436417 GCCTCCAACAAGTAATGCAGA 58.564 47.619 0.00 0.00 0.00 4.26
1219 1395 3.019564 GCCTCCAACAAGTAATGCAGAT 58.980 45.455 0.00 0.00 0.00 2.90
1220 1396 3.445096 GCCTCCAACAAGTAATGCAGATT 59.555 43.478 0.00 0.00 0.00 2.40
1222 1398 4.418392 CTCCAACAAGTAATGCAGATTGC 58.582 43.478 0.00 0.00 45.29 3.56
1223 1399 4.081406 TCCAACAAGTAATGCAGATTGCT 58.919 39.130 2.48 0.00 45.31 3.91
1226 1402 5.336213 CCAACAAGTAATGCAGATTGCTTCT 60.336 40.000 0.96 0.00 45.31 2.85
1234 1410 1.649664 CAGATTGCTTCTGCGCTAGT 58.350 50.000 9.73 0.00 45.16 2.57
1235 1411 1.326852 CAGATTGCTTCTGCGCTAGTG 59.673 52.381 9.73 0.00 45.16 2.74
1236 1412 0.027324 GATTGCTTCTGCGCTAGTGC 59.973 55.000 21.44 21.44 43.34 4.40
1257 1435 3.817647 GCCTGTCACTCTGTCAAATTTCT 59.182 43.478 0.00 0.00 0.00 2.52
1266 1444 7.027760 CACTCTGTCAAATTTCTTCATGGATG 58.972 38.462 0.00 0.00 0.00 3.51
1267 1445 5.957798 TCTGTCAAATTTCTTCATGGATGC 58.042 37.500 0.00 0.00 0.00 3.91
1269 1447 4.107622 GTCAAATTTCTTCATGGATGCCG 58.892 43.478 0.00 0.00 0.00 5.69
1277 1455 2.191513 CATGGATGCCGGCTTCAGG 61.192 63.158 35.03 23.85 0.00 3.86
1278 1456 3.426309 ATGGATGCCGGCTTCAGGG 62.426 63.158 35.03 0.00 0.00 4.45
1279 1457 3.797353 GGATGCCGGCTTCAGGGA 61.797 66.667 35.03 13.49 0.00 4.20
1280 1458 2.512896 GATGCCGGCTTCAGGGAT 59.487 61.111 31.35 14.72 42.69 3.85
1281 1459 1.895707 GATGCCGGCTTCAGGGATG 60.896 63.158 31.35 0.00 40.00 3.51
1287 1465 1.152368 GGCTTCAGGGATGGATGGG 59.848 63.158 0.00 0.00 0.00 4.00
1296 1474 0.761802 GGATGGATGGGTGGAGAGAC 59.238 60.000 0.00 0.00 0.00 3.36
1301 1479 1.677637 GATGGGTGGAGAGACCGACC 61.678 65.000 0.00 0.00 42.61 4.79
1315 1493 2.158959 CGACCGACTGACCGATTGC 61.159 63.158 0.00 0.00 0.00 3.56
1318 1496 0.389948 ACCGACTGACCGATTGCTTC 60.390 55.000 0.00 0.00 0.00 3.86
1319 1497 0.108615 CCGACTGACCGATTGCTTCT 60.109 55.000 0.00 0.00 0.00 2.85
1324 1502 2.358615 ACCGATTGCTTCTGCGCA 60.359 55.556 10.98 10.98 43.34 6.09
1325 1503 1.709147 GACCGATTGCTTCTGCGCAT 61.709 55.000 12.24 0.00 43.34 4.73
1326 1504 1.308069 ACCGATTGCTTCTGCGCATT 61.308 50.000 12.24 0.00 43.34 3.56
1505 1683 3.076621 CAGCTACAACTTCAATGCTGGA 58.923 45.455 0.00 0.00 42.64 3.86
1536 1714 5.730550 TCATGTTGTACCAGGTAATCAGTC 58.269 41.667 0.00 0.00 0.00 3.51
1543 1721 6.931838 TGTACCAGGTAATCAGTCTGTTTAG 58.068 40.000 0.00 0.00 0.00 1.85
1548 1726 7.036220 CCAGGTAATCAGTCTGTTTAGTACTG 58.964 42.308 5.39 15.20 41.58 2.74
1597 1775 9.191479 AGTAGTAACTTCATAGCTCAATACTGT 57.809 33.333 0.00 0.00 29.00 3.55
1801 1992 8.177119 TCATTTTTGTTGGAATGCTAGTAACT 57.823 30.769 0.00 0.00 34.15 2.24
1815 2006 5.953548 TGCTAGTAACTGGAATGTACAGGTA 59.046 40.000 0.33 0.00 40.23 3.08
1816 2007 6.610020 TGCTAGTAACTGGAATGTACAGGTAT 59.390 38.462 0.33 0.00 40.00 2.73
1828 2026 8.301002 GGAATGTACAGGTATTTAAAAGTGCAA 58.699 33.333 0.33 0.00 0.00 4.08
1836 2034 7.649306 CAGGTATTTAAAAGTGCAATCCATAGC 59.351 37.037 0.00 0.00 0.00 2.97
1839 2037 5.835113 TTAAAAGTGCAATCCATAGCCTC 57.165 39.130 0.00 0.00 0.00 4.70
1842 2040 2.928334 AGTGCAATCCATAGCCTCAAG 58.072 47.619 0.00 0.00 0.00 3.02
1845 2043 1.952296 GCAATCCATAGCCTCAAGTGG 59.048 52.381 0.00 0.00 0.00 4.00
1852 2050 4.721776 TCCATAGCCTCAAGTGGTTTCTAT 59.278 41.667 0.00 0.00 33.47 1.98
1856 2054 5.184892 AGCCTCAAGTGGTTTCTATGATT 57.815 39.130 0.00 0.00 0.00 2.57
1862 2060 8.025445 CCTCAAGTGGTTTCTATGATTTTCTTG 58.975 37.037 0.00 0.00 0.00 3.02
1863 2061 7.885297 TCAAGTGGTTTCTATGATTTTCTTGG 58.115 34.615 0.00 0.00 32.39 3.61
1915 2114 4.320870 TCCCCTTTTGTTTCTATCACGTC 58.679 43.478 0.00 0.00 0.00 4.34
1950 2149 3.831333 ACATAAATGTTGCCATGGTGACA 59.169 39.130 19.96 19.96 41.47 3.58
1984 2183 6.320494 ACATGACAAACATTTTAACGGCTA 57.680 33.333 0.00 0.00 37.07 3.93
2043 2242 0.409484 AGGTTTGGGCTGCCTTATGT 59.591 50.000 19.68 0.00 0.00 2.29
2059 2258 5.184479 GCCTTATGTATGATGGTACGTCCTA 59.816 44.000 0.00 0.00 37.07 2.94
2092 2315 4.837567 GCATTAGCTAATGAACTTCACCG 58.162 43.478 38.63 16.74 44.40 4.94
2097 2320 2.159517 GCTAATGAACTTCACCGCCAAG 60.160 50.000 0.00 0.00 0.00 3.61
2107 2330 1.335496 TCACCGCCAAGCTGTTTTAAC 59.665 47.619 0.00 0.00 0.00 2.01
2157 2383 1.346068 ACCTCAGTGCACTTTCTCTCC 59.654 52.381 18.94 0.00 0.00 3.71
2194 2420 0.179084 TATCAGCTGTAAGTGGCGGC 60.179 55.000 14.67 0.00 38.44 6.53
2219 2445 7.041916 GCATGACAGATCTTTCTTTCCATCTAG 60.042 40.741 10.15 0.00 29.19 2.43
2290 2516 3.432252 CGGTTAGTTCATGTTGTCCTCAC 59.568 47.826 0.00 0.00 0.00 3.51
2295 2521 3.118261 AGTTCATGTTGTCCTCACAGTGT 60.118 43.478 0.00 0.00 32.71 3.55
2296 2522 3.558931 TCATGTTGTCCTCACAGTGTT 57.441 42.857 0.00 0.00 32.71 3.32
2297 2523 4.681074 TCATGTTGTCCTCACAGTGTTA 57.319 40.909 0.00 0.00 32.71 2.41
2298 2524 5.227569 TCATGTTGTCCTCACAGTGTTAT 57.772 39.130 0.00 0.00 32.71 1.89
2299 2525 4.996758 TCATGTTGTCCTCACAGTGTTATG 59.003 41.667 0.00 0.00 32.71 1.90
2300 2526 3.138304 TGTTGTCCTCACAGTGTTATGC 58.862 45.455 0.00 0.00 32.71 3.14
2301 2527 3.138304 GTTGTCCTCACAGTGTTATGCA 58.862 45.455 0.00 0.00 32.71 3.96
2312 2538 3.783327 TTATGCACACGCGCACGG 61.783 61.111 5.73 0.00 46.56 4.94
2357 2732 3.745975 TGTTTAACCTTGACTGATCGCTG 59.254 43.478 0.00 0.00 0.00 5.18
2454 2829 5.877012 TCTCTCAATGAAGTTTCTATGGTGC 59.123 40.000 0.00 0.00 0.00 5.01
2626 3002 6.825721 AGCAACTCTTATTTATTCAGGACTGG 59.174 38.462 0.00 0.00 0.00 4.00
2647 3023 7.953752 ACTGGGTATTTATTTTGTTTCCGAAA 58.046 30.769 0.00 0.00 0.00 3.46
2734 3110 6.183360 GCACTAACTTTTCCATTTATGCAAGC 60.183 38.462 0.00 0.00 0.00 4.01
2786 3162 4.836125 TGCTCTGTTCCACTTTGAAATC 57.164 40.909 0.00 0.00 0.00 2.17
2986 3364 7.530426 AGTGCTTTCAAAGGTAGAATTCATT 57.470 32.000 8.44 0.00 0.00 2.57
2995 3373 4.072131 AGGTAGAATTCATTGTTGTGCGT 58.928 39.130 8.44 0.00 0.00 5.24
3166 3544 4.452455 CCAACAACTTACAGGTGAGATGAC 59.548 45.833 8.16 0.00 33.95 3.06
3283 3687 8.812513 TCACATGTTGATAATCATTTTCTCCT 57.187 30.769 0.00 0.00 0.00 3.69
3284 3688 9.246670 TCACATGTTGATAATCATTTTCTCCTT 57.753 29.630 0.00 0.00 0.00 3.36
3292 3696 8.680903 TGATAATCATTTTCTCCTTTTCTCAGC 58.319 33.333 0.00 0.00 0.00 4.26
3424 3828 8.450578 TTCTTTCATCAAGTGTTGAGTTATGT 57.549 30.769 0.00 0.00 43.98 2.29
3425 3829 8.450578 TCTTTCATCAAGTGTTGAGTTATGTT 57.549 30.769 0.00 0.00 43.98 2.71
3497 3901 2.799412 CTCGATCTTAACATCTGCAGGC 59.201 50.000 15.13 0.00 0.00 4.85
3558 3962 4.884164 CCAAGTCCTAATGTTCATTCTCCC 59.116 45.833 1.11 0.00 0.00 4.30
3643 4051 3.812156 TCAGAGTCCGTTTGAACTTGA 57.188 42.857 0.00 0.00 0.00 3.02
3699 4107 7.865385 TGTTTATTCTTTCCCAGATTTGTTTCG 59.135 33.333 0.00 0.00 0.00 3.46
3715 4123 3.685272 TGTTTCGTAACTGTGTCAAGCAA 59.315 39.130 6.48 0.00 35.24 3.91
3811 4219 6.071391 AGCAGGACAACCATACAAAATAAAGG 60.071 38.462 0.00 0.00 38.94 3.11
3812 4220 6.071616 GCAGGACAACCATACAAAATAAAGGA 60.072 38.462 0.00 0.00 38.94 3.36
3813 4221 7.538575 CAGGACAACCATACAAAATAAAGGAG 58.461 38.462 0.00 0.00 38.94 3.69
3814 4222 7.176690 CAGGACAACCATACAAAATAAAGGAGT 59.823 37.037 0.00 0.00 38.94 3.85
3893 4301 5.359576 GCTTCCTCTGTTTCTCTCTCTGATA 59.640 44.000 0.00 0.00 0.00 2.15
4064 4473 3.947834 AGCAAGCTTAACATGGGTACATC 59.052 43.478 0.00 0.00 34.35 3.06
4068 4486 4.917385 AGCTTAACATGGGTACATCACAA 58.083 39.130 0.00 0.00 34.35 3.33
4069 4487 4.700213 AGCTTAACATGGGTACATCACAAC 59.300 41.667 0.00 0.00 34.35 3.32
4070 4488 4.457603 GCTTAACATGGGTACATCACAACA 59.542 41.667 0.00 0.00 34.35 3.33
4157 4583 2.036604 TCATTTGAGTAGTCACACCGCA 59.963 45.455 0.00 0.00 30.10 5.69
4159 4585 3.945981 TTTGAGTAGTCACACCGCATA 57.054 42.857 0.00 0.00 30.10 3.14
4224 4654 6.368243 ACAGCAATAAATCGAGCTATGAGATG 59.632 38.462 0.00 0.00 35.19 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.554032 CCAATTTTCAGAGGACGCTTGT 59.446 45.455 0.00 0.00 0.00 3.16
1 2 2.554032 ACCAATTTTCAGAGGACGCTTG 59.446 45.455 0.00 0.00 0.00 4.01
2 3 2.814336 GACCAATTTTCAGAGGACGCTT 59.186 45.455 0.00 0.00 0.00 4.68
3 4 2.427506 GACCAATTTTCAGAGGACGCT 58.572 47.619 0.00 0.00 0.00 5.07
4 5 1.468914 GGACCAATTTTCAGAGGACGC 59.531 52.381 0.00 0.00 0.00 5.19
5 6 3.003480 GAGGACCAATTTTCAGAGGACG 58.997 50.000 0.00 0.00 0.00 4.79
6 7 4.021102 TGAGGACCAATTTTCAGAGGAC 57.979 45.455 0.00 0.00 0.00 3.85
7 8 4.722526 TTGAGGACCAATTTTCAGAGGA 57.277 40.909 0.00 0.00 0.00 3.71
8 9 4.021981 GGTTTGAGGACCAATTTTCAGAGG 60.022 45.833 0.00 0.00 39.57 3.69
9 10 4.320494 CGGTTTGAGGACCAATTTTCAGAG 60.320 45.833 0.00 0.00 39.78 3.35
10 11 3.568007 CGGTTTGAGGACCAATTTTCAGA 59.432 43.478 0.00 0.00 39.78 3.27
11 12 3.857010 GCGGTTTGAGGACCAATTTTCAG 60.857 47.826 0.00 0.00 39.78 3.02
12 13 2.035321 GCGGTTTGAGGACCAATTTTCA 59.965 45.455 0.00 0.00 39.78 2.69
13 14 2.609491 GGCGGTTTGAGGACCAATTTTC 60.609 50.000 0.00 0.00 39.78 2.29
14 15 1.343142 GGCGGTTTGAGGACCAATTTT 59.657 47.619 0.00 0.00 39.78 1.82
15 16 0.966179 GGCGGTTTGAGGACCAATTT 59.034 50.000 0.00 0.00 39.78 1.82
16 17 1.241315 CGGCGGTTTGAGGACCAATT 61.241 55.000 0.00 0.00 39.78 2.32
17 18 1.674322 CGGCGGTTTGAGGACCAAT 60.674 57.895 0.00 0.00 39.78 3.16
18 19 2.281208 CGGCGGTTTGAGGACCAA 60.281 61.111 0.00 0.00 39.78 3.67
19 20 2.725203 CTTCGGCGGTTTGAGGACCA 62.725 60.000 7.21 0.00 39.78 4.02
20 21 2.031465 TTCGGCGGTTTGAGGACC 59.969 61.111 7.21 0.00 36.31 4.46
21 22 0.883370 AACTTCGGCGGTTTGAGGAC 60.883 55.000 7.21 0.00 0.00 3.85
22 23 0.680618 TAACTTCGGCGGTTTGAGGA 59.319 50.000 7.21 0.00 0.00 3.71
23 24 1.734163 ATAACTTCGGCGGTTTGAGG 58.266 50.000 7.21 0.00 0.00 3.86
24 25 3.824414 AAATAACTTCGGCGGTTTGAG 57.176 42.857 7.21 0.30 0.00 3.02
25 26 3.685756 CCTAAATAACTTCGGCGGTTTGA 59.314 43.478 7.21 0.00 0.00 2.69
26 27 3.685756 TCCTAAATAACTTCGGCGGTTTG 59.314 43.478 7.21 0.00 0.00 2.93
27 28 3.686241 GTCCTAAATAACTTCGGCGGTTT 59.314 43.478 7.21 0.00 0.00 3.27
28 29 3.264947 GTCCTAAATAACTTCGGCGGTT 58.735 45.455 7.21 6.93 0.00 4.44
29 30 2.736400 CGTCCTAAATAACTTCGGCGGT 60.736 50.000 7.21 0.00 0.00 5.68
30 31 1.856597 CGTCCTAAATAACTTCGGCGG 59.143 52.381 7.21 0.00 0.00 6.13
31 32 1.257155 GCGTCCTAAATAACTTCGGCG 59.743 52.381 0.00 0.00 0.00 6.46
32 33 2.547826 AGCGTCCTAAATAACTTCGGC 58.452 47.619 0.00 0.00 0.00 5.54
33 34 3.734735 GCTAGCGTCCTAAATAACTTCGG 59.265 47.826 0.00 0.00 0.00 4.30
34 35 4.357142 TGCTAGCGTCCTAAATAACTTCG 58.643 43.478 10.77 0.00 0.00 3.79
35 36 5.234543 CCTTGCTAGCGTCCTAAATAACTTC 59.765 44.000 10.77 0.00 0.00 3.01
36 37 5.116882 CCTTGCTAGCGTCCTAAATAACTT 58.883 41.667 10.77 0.00 0.00 2.66
37 38 4.443034 CCCTTGCTAGCGTCCTAAATAACT 60.443 45.833 10.77 0.00 0.00 2.24
46 47 1.300233 CGATCCCTTGCTAGCGTCC 60.300 63.158 10.77 0.00 0.00 4.79
49 50 1.300233 GTCCGATCCCTTGCTAGCG 60.300 63.158 10.77 0.00 0.00 4.26
53 54 2.505819 ACAAATAGTCCGATCCCTTGCT 59.494 45.455 0.00 0.00 0.00 3.91
54 55 2.614057 CACAAATAGTCCGATCCCTTGC 59.386 50.000 0.00 0.00 0.00 4.01
64 65 9.895138 TTATAACTTTCTACCCACAAATAGTCC 57.105 33.333 0.00 0.00 0.00 3.85
79 80 9.768215 TCCCTGATTTGGATTTTATAACTTTCT 57.232 29.630 0.00 0.00 0.00 2.52
103 104 0.546507 TGGCCCCCTCCAAAATTTCC 60.547 55.000 0.00 0.00 32.18 3.13
115 117 0.555769 TGAATGTTCCTATGGCCCCC 59.444 55.000 0.00 0.00 0.00 5.40
116 118 2.430694 GTTTGAATGTTCCTATGGCCCC 59.569 50.000 0.00 0.00 0.00 5.80
134 136 5.883503 TTCTACGTTGTGGTTCAAAGTTT 57.116 34.783 0.00 0.00 43.84 2.66
137 144 4.513692 TCCATTCTACGTTGTGGTTCAAAG 59.486 41.667 0.00 0.00 40.39 2.77
144 151 4.123497 TCAGATCCATTCTACGTTGTGG 57.877 45.455 0.00 0.00 31.77 4.17
159 169 0.607489 CCCGCCCATGGATTCAGATC 60.607 60.000 15.22 0.00 0.00 2.75
219 229 1.335780 TGTTGGCGCACAATGATGAAC 60.336 47.619 10.83 0.00 41.95 3.18
220 230 0.957362 TGTTGGCGCACAATGATGAA 59.043 45.000 10.83 0.00 41.95 2.57
299 316 4.803426 GCGTGGAGCGGAGTGGAG 62.803 72.222 0.00 0.00 41.69 3.86
447 475 0.469331 TTCGGTGGTGAGTGGAGAGT 60.469 55.000 0.00 0.00 0.00 3.24
449 477 1.185618 CCTTCGGTGGTGAGTGGAGA 61.186 60.000 0.00 0.00 0.00 3.71
451 479 2.879233 GCCTTCGGTGGTGAGTGGA 61.879 63.158 0.00 0.00 0.00 4.02
453 481 2.738521 CGCCTTCGGTGGTGAGTG 60.739 66.667 2.69 0.00 39.82 3.51
549 577 1.500736 AGATGCTAAAATGGGGGAGGG 59.499 52.381 0.00 0.00 0.00 4.30
558 586 1.217942 GGGGGTGGGAGATGCTAAAAT 59.782 52.381 0.00 0.00 0.00 1.82
596 624 3.093172 CAAGGGGGAGGAGGAGGC 61.093 72.222 0.00 0.00 0.00 4.70
605 633 2.121506 AGGTGCTTCCAAGGGGGA 60.122 61.111 1.79 0.00 46.61 4.81
606 634 2.356667 GAGGTGCTTCCAAGGGGG 59.643 66.667 1.79 0.00 39.02 5.40
607 635 2.356667 GGAGGTGCTTCCAAGGGG 59.643 66.667 0.00 0.00 39.02 4.79
608 636 2.045926 CGGAGGTGCTTCCAAGGG 60.046 66.667 1.37 0.00 37.05 3.95
609 637 2.747855 GCGGAGGTGCTTCCAAGG 60.748 66.667 1.37 0.00 37.05 3.61
610 638 2.747855 GGCGGAGGTGCTTCCAAG 60.748 66.667 1.37 0.00 37.05 3.61
611 639 4.344865 GGGCGGAGGTGCTTCCAA 62.345 66.667 1.37 0.00 37.05 3.53
613 641 4.785453 CAGGGCGGAGGTGCTTCC 62.785 72.222 0.00 0.00 34.52 3.46
620 648 0.967380 AAAGAAATGCAGGGCGGAGG 60.967 55.000 0.00 0.00 0.00 4.30
622 650 0.965363 GGAAAGAAATGCAGGGCGGA 60.965 55.000 0.00 0.00 0.00 5.54
1023 1199 2.753043 TACACGACGAGGGAGCCC 60.753 66.667 0.00 0.00 0.00 5.19
1218 1394 1.372087 GGCACTAGCGCAGAAGCAAT 61.372 55.000 11.47 0.00 43.41 3.56
1219 1395 2.034879 GGCACTAGCGCAGAAGCAA 61.035 57.895 11.47 0.00 43.41 3.91
1220 1396 2.434884 GGCACTAGCGCAGAAGCA 60.435 61.111 11.47 0.00 43.41 3.91
1222 1398 1.079543 ACAGGCACTAGCGCAGAAG 60.080 57.895 11.47 6.52 43.41 2.85
1223 1399 1.079819 GACAGGCACTAGCGCAGAA 60.080 57.895 11.47 0.00 43.41 3.02
1226 1402 2.048222 GTGACAGGCACTAGCGCA 60.048 61.111 11.47 0.00 44.27 6.09
1234 1410 2.936919 ATTTGACAGAGTGACAGGCA 57.063 45.000 0.00 0.00 0.00 4.75
1235 1411 3.817647 AGAAATTTGACAGAGTGACAGGC 59.182 43.478 0.00 0.00 0.00 4.85
1236 1412 5.528690 TGAAGAAATTTGACAGAGTGACAGG 59.471 40.000 0.00 0.00 0.00 4.00
1257 1435 0.749091 CTGAAGCCGGCATCCATGAA 60.749 55.000 31.54 8.96 0.00 2.57
1266 1444 3.125376 ATCCATCCCTGAAGCCGGC 62.125 63.158 21.89 21.89 0.00 6.13
1267 1445 1.228063 CATCCATCCCTGAAGCCGG 60.228 63.158 0.00 0.00 0.00 6.13
1269 1447 1.152368 CCCATCCATCCCTGAAGCC 59.848 63.158 0.00 0.00 0.00 4.35
1277 1455 0.761802 GTCTCTCCACCCATCCATCC 59.238 60.000 0.00 0.00 0.00 3.51
1278 1456 0.761802 GGTCTCTCCACCCATCCATC 59.238 60.000 0.00 0.00 35.97 3.51
1279 1457 1.050988 CGGTCTCTCCACCCATCCAT 61.051 60.000 0.00 0.00 35.57 3.41
1280 1458 1.685765 CGGTCTCTCCACCCATCCA 60.686 63.158 0.00 0.00 35.57 3.41
1281 1459 1.381327 TCGGTCTCTCCACCCATCC 60.381 63.158 0.00 0.00 35.57 3.51
1287 1465 1.674980 AGTCGGTCGGTCTCTCCAC 60.675 63.158 0.00 0.00 35.57 4.02
1296 1474 1.516386 CAATCGGTCAGTCGGTCGG 60.516 63.158 0.00 0.00 0.00 4.79
1301 1479 0.994995 CAGAAGCAATCGGTCAGTCG 59.005 55.000 0.00 0.00 0.00 4.18
1324 1502 0.238289 CGACAGCCTGCGAAACAAAT 59.762 50.000 2.97 0.00 0.00 2.32
1325 1503 0.812014 TCGACAGCCTGCGAAACAAA 60.812 50.000 8.43 0.00 33.04 2.83
1326 1504 1.221466 CTCGACAGCCTGCGAAACAA 61.221 55.000 11.29 0.00 35.95 2.83
1505 1683 4.287067 ACCTGGTACAACATGAGTGAGATT 59.713 41.667 0.00 0.00 38.70 2.40
1536 1714 9.182933 GTTCAACTAAGAGACAGTACTAAACAG 57.817 37.037 0.00 0.00 0.00 3.16
1543 1721 7.329717 CAGAATGGTTCAACTAAGAGACAGTAC 59.670 40.741 0.00 0.00 0.00 2.73
1548 1726 6.931840 ACTTCAGAATGGTTCAACTAAGAGAC 59.068 38.462 0.00 0.00 36.16 3.36
1597 1775 4.420522 TGCAAGCACCACATCTCATATA 57.579 40.909 0.00 0.00 0.00 0.86
1635 1826 5.007430 GTCATGATCAGCTCAACGATGAATT 59.993 40.000 0.00 0.00 42.04 2.17
1643 1834 5.064452 CCAAAGTAGTCATGATCAGCTCAAC 59.936 44.000 0.00 0.00 37.44 3.18
1801 1992 7.448777 TGCACTTTTAAATACCTGTACATTCCA 59.551 33.333 0.00 0.00 0.00 3.53
1815 2006 6.380846 TGAGGCTATGGATTGCACTTTTAAAT 59.619 34.615 0.00 0.00 0.00 1.40
1816 2007 5.714333 TGAGGCTATGGATTGCACTTTTAAA 59.286 36.000 0.00 0.00 0.00 1.52
1822 2020 2.240667 ACTTGAGGCTATGGATTGCACT 59.759 45.455 0.00 0.00 0.00 4.40
1828 2026 3.525199 AGAAACCACTTGAGGCTATGGAT 59.475 43.478 12.14 0.00 36.04 3.41
1836 2034 7.693969 AGAAAATCATAGAAACCACTTGAGG 57.306 36.000 0.00 0.00 0.00 3.86
1839 2037 7.885297 TCCAAGAAAATCATAGAAACCACTTG 58.115 34.615 0.00 0.00 0.00 3.16
1856 2054 9.919416 TTAGGTCATCATCAATATTCCAAGAAA 57.081 29.630 0.00 0.00 0.00 2.52
1862 2060 8.160106 AGAAGGTTAGGTCATCATCAATATTCC 58.840 37.037 0.00 0.00 0.00 3.01
1863 2061 9.566432 AAGAAGGTTAGGTCATCATCAATATTC 57.434 33.333 0.00 0.00 0.00 1.75
1908 2106 5.196341 TGTACTTCAAACTGAGACGTGAT 57.804 39.130 0.00 0.00 0.00 3.06
1915 2114 7.538678 GGCAACATTTATGTACTTCAAACTGAG 59.461 37.037 0.00 0.00 40.80 3.35
1984 2183 8.757307 TTCCTGAAAACATATATCTCCCCTAT 57.243 34.615 0.00 0.00 0.00 2.57
2043 2242 7.828508 ACAAATACTAGGACGTACCATCATA 57.171 36.000 0.00 0.00 42.04 2.15
2084 2306 0.751643 AAACAGCTTGGCGGTGAAGT 60.752 50.000 0.00 0.00 43.75 3.01
2085 2307 0.385390 AAAACAGCTTGGCGGTGAAG 59.615 50.000 0.00 0.00 43.75 3.02
2087 2309 1.335496 GTTAAAACAGCTTGGCGGTGA 59.665 47.619 0.00 0.00 43.75 4.02
2088 2310 1.066303 TGTTAAAACAGCTTGGCGGTG 59.934 47.619 0.00 0.00 46.37 4.94
2089 2311 1.394618 TGTTAAAACAGCTTGGCGGT 58.605 45.000 0.00 0.00 38.82 5.68
2107 2330 4.574421 TCATGTTGGTCTGTTGTTACACTG 59.426 41.667 0.00 0.00 0.00 3.66
2157 2383 6.702972 CTGATATAATCTGCAGGAGAAACG 57.297 41.667 15.13 0.00 33.12 3.60
2194 2420 7.986320 ACTAGATGGAAAGAAAGATCTGTCATG 59.014 37.037 15.45 0.00 41.11 3.07
2219 2445 0.389426 ATCTGCCACGTGTAACCGAC 60.389 55.000 15.65 0.00 0.00 4.79
2308 2534 1.343821 GCGTCTTTATGCGTCCGTG 59.656 57.895 0.00 0.00 0.00 4.94
2312 2538 0.743345 AAGGGGCGTCTTTATGCGTC 60.743 55.000 0.00 0.00 38.61 5.19
2357 2732 5.615289 AGCTGGTATGAGAAACCATATGTC 58.385 41.667 1.24 0.00 45.74 3.06
2454 2829 3.435566 TCGAGAGCGCATTGTTAAGTAG 58.564 45.455 11.47 0.00 37.46 2.57
2538 2913 7.870445 GCTGAGATAGGGAGTAAGATTAAGTTG 59.130 40.741 0.00 0.00 0.00 3.16
2786 3162 3.982576 AAACGTCCAAGGCAAGTTAAG 57.017 42.857 0.00 0.00 0.00 1.85
2875 3251 2.026822 CAGTACTGGAGCACCCTTTCAT 60.027 50.000 15.49 0.00 35.38 2.57
2876 3252 1.347707 CAGTACTGGAGCACCCTTTCA 59.652 52.381 15.49 0.00 35.38 2.69
2877 3253 1.348036 ACAGTACTGGAGCACCCTTTC 59.652 52.381 26.12 0.00 35.38 2.62
2880 3256 0.471971 ACACAGTACTGGAGCACCCT 60.472 55.000 26.12 0.00 35.38 4.34
2881 3257 0.037232 GACACAGTACTGGAGCACCC 60.037 60.000 26.12 5.11 34.81 4.61
2883 3259 0.037232 GGGACACAGTACTGGAGCAC 60.037 60.000 26.12 12.04 34.19 4.40
2928 3305 1.373497 AAAGTCAGAGCTGCGGACG 60.373 57.895 13.57 0.00 44.96 4.79
3279 3683 2.555757 CCAACAAGGCTGAGAAAAGGAG 59.444 50.000 0.00 0.00 0.00 3.69
3280 3684 2.586425 CCAACAAGGCTGAGAAAAGGA 58.414 47.619 0.00 0.00 0.00 3.36
3424 3828 1.406341 GGGTAGCGAGGTAACATGCAA 60.406 52.381 0.00 0.00 40.97 4.08
3425 3829 0.177141 GGGTAGCGAGGTAACATGCA 59.823 55.000 0.00 0.00 40.97 3.96
3467 3871 7.436673 GCAGATGTTAAGATCGAGTAGAAACAT 59.563 37.037 12.79 12.79 38.54 2.71
3468 3872 6.752351 GCAGATGTTAAGATCGAGTAGAAACA 59.248 38.462 6.93 0.00 32.44 2.83
3469 3873 6.752351 TGCAGATGTTAAGATCGAGTAGAAAC 59.248 38.462 6.93 0.00 0.00 2.78
3497 3901 4.734695 GCGAAGAATATCCCAGCAAAAAGG 60.735 45.833 0.00 0.00 0.00 3.11
3643 4051 0.029035 CGAAATCCCGATCGACTCGT 59.971 55.000 18.66 0.00 46.18 4.18
3699 4107 3.558505 CATGCTTGCTTGACACAGTTAC 58.441 45.455 2.83 0.00 0.00 2.50
3749 4157 6.541641 GCAGAGATCAACAATTGGATAGAGTT 59.458 38.462 10.83 0.00 0.00 3.01
3811 4219 2.496899 TGGCCAGATCTTTTCCACTC 57.503 50.000 0.00 0.00 0.00 3.51
3812 4220 3.463048 AATGGCCAGATCTTTTCCACT 57.537 42.857 13.05 0.00 0.00 4.00
3813 4221 3.511146 TGAAATGGCCAGATCTTTTCCAC 59.489 43.478 20.72 3.53 31.42 4.02
3814 4222 3.777087 TGAAATGGCCAGATCTTTTCCA 58.223 40.909 20.72 10.74 31.42 3.53
3824 4232 1.586028 CCGGTGTTGAAATGGCCAG 59.414 57.895 13.05 0.00 0.00 4.85
3980 4388 6.719370 TGGGACTGCTGATTTTAAACATAAGT 59.281 34.615 0.00 0.00 0.00 2.24
3981 4389 7.121168 TCTGGGACTGCTGATTTTAAACATAAG 59.879 37.037 0.00 0.00 0.00 1.73
4064 4473 6.875726 TCTGGAGTAATTTCTCTCATGTTGTG 59.124 38.462 11.35 0.00 35.11 3.33
4068 4486 7.251321 ACTTCTGGAGTAATTTCTCTCATGT 57.749 36.000 11.35 3.33 36.65 3.21
4069 4487 7.605691 ACAACTTCTGGAGTAATTTCTCTCATG 59.394 37.037 11.35 6.05 37.72 3.07
4070 4488 7.605691 CACAACTTCTGGAGTAATTTCTCTCAT 59.394 37.037 11.35 0.00 37.72 2.90
4157 4583 9.993454 ATCGCAGAGATTTGCATATATGTATAT 57.007 29.630 14.14 10.08 43.63 0.86
4159 4585 7.767659 ACATCGCAGAGATTTGCATATATGTAT 59.232 33.333 14.14 5.84 43.63 2.29
4172 4602 4.701651 TCCATGAAAAACATCGCAGAGATT 59.298 37.500 0.00 0.00 43.63 2.40
4224 4654 4.043200 GCTTGGGTGCGTGCTTCC 62.043 66.667 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.