Multiple sequence alignment - TraesCS7A01G250600

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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 TraesCS7A01G250600 chr7A 100.000 3629 0 0 1 3629 232747847 232751475 0.000000e+00 6702.0
1 TraesCS7A01G250600 chr7D 88.694 1371 72 39 445 1753 220513122 220514471 0.000000e+00 1596.0
2 TraesCS7A01G250600 chr7D 93.112 842 49 7 2051 2883 220514786 220515627 0.000000e+00 1225.0
3 TraesCS7A01G250600 chr7D 95.095 734 26 3 2896 3629 220515786 220516509 0.000000e+00 1147.0
4 TraesCS7A01G250600 chr7D 85.205 365 20 13 106 463 220512775 220513112 9.650000e-91 344.0
5 TraesCS7A01G250600 chr7D 90.717 237 12 6 1784 2011 220514553 220514788 1.270000e-79 307.0
6 TraesCS7A01G250600 chr7D 98.851 87 1 0 1 87 220512700 220512786 4.850000e-34 156.0
7 TraesCS7A01G250600 chr7B 89.850 1133 50 27 922 2010 178407566 178406455 0.000000e+00 1395.0
8 TraesCS7A01G250600 chr7B 94.414 734 28 4 2896 3629 178405413 178404693 0.000000e+00 1116.0
9 TraesCS7A01G250600 chr7B 87.386 880 52 14 2009 2883 178406384 178405559 0.000000e+00 955.0
10 TraesCS7A01G250600 chr7B 95.480 177 8 0 746 922 178407796 178407620 2.130000e-72 283.0
11 TraesCS7A01G250600 chr6A 79.024 205 38 3 450 651 115321771 115321973 6.320000e-28 135.0
12 TraesCS7A01G250600 chr3B 77.295 207 39 7 484 687 719827305 719827104 8.230000e-22 115.0
13 TraesCS7A01G250600 chr5B 78.889 180 28 8 513 688 617257464 617257637 2.960000e-21 113.0
14 TraesCS7A01G250600 chr5A 75.918 245 45 8 436 680 660884791 660884561 2.960000e-21 113.0
15 TraesCS7A01G250600 chr6D 75.248 202 37 7 483 672 333593571 333593771 2.320000e-12 84.2


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 TraesCS7A01G250600 chr7A 232747847 232751475 3628 False 6702.000000 6702 100.000000 1 3629 1 chr7A.!!$F1 3628
1 TraesCS7A01G250600 chr7D 220512700 220516509 3809 False 795.833333 1596 91.945667 1 3629 6 chr7D.!!$F1 3628
2 TraesCS7A01G250600 chr7B 178404693 178407796 3103 True 937.250000 1395 91.782500 746 3629 4 chr7B.!!$R1 2883

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
942 1041 0.252421 TGAGCCCTCTGTCACTCCAT 60.252 55.0 0.0 0.0 0.0 3.41 F
1063 1165 0.250727 CAGACACCAACCATTCCCGT 60.251 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2162 0.833834 ACCTCCAGTGTGACCTCCAG 60.834 60.000 0.0 0.0 0.00 3.86 R
2631 2909 1.004440 AGACTTTGGGCAGTCGCTC 60.004 57.895 0.0 0.0 46.85 5.03 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
140 141 1.916181 CAATAAGGAGGTGTCACCCCT 59.084 52.381 18.80 19.86 39.75 4.79
141 142 1.584724 ATAAGGAGGTGTCACCCCTG 58.415 55.000 24.66 0.00 39.75 4.45
172 174 4.577693 GCCTCTGAATCTATTGATGCACAA 59.422 41.667 0.00 0.00 42.95 3.33
174 176 6.726230 CCTCTGAATCTATTGATGCACAAAG 58.274 40.000 5.94 5.75 42.03 2.77
198 200 6.016276 AGCAAGTGTAAGATTCGTGGAAATTT 60.016 34.615 0.00 0.00 0.00 1.82
200 202 7.358352 GCAAGTGTAAGATTCGTGGAAATTTTG 60.358 37.037 0.00 0.00 0.00 2.44
202 204 7.360361 AGTGTAAGATTCGTGGAAATTTTGTC 58.640 34.615 0.00 0.00 0.00 3.18
217 219 4.365514 TTTTGTCTGCTCATTCCCTGTA 57.634 40.909 0.00 0.00 0.00 2.74
219 221 5.692115 TTTGTCTGCTCATTCCCTGTATA 57.308 39.130 0.00 0.00 0.00 1.47
220 222 5.894298 TTGTCTGCTCATTCCCTGTATAT 57.106 39.130 0.00 0.00 0.00 0.86
221 223 5.894298 TGTCTGCTCATTCCCTGTATATT 57.106 39.130 0.00 0.00 0.00 1.28
222 224 5.614308 TGTCTGCTCATTCCCTGTATATTG 58.386 41.667 0.00 0.00 0.00 1.90
223 225 4.453819 GTCTGCTCATTCCCTGTATATTGC 59.546 45.833 0.00 0.00 0.00 3.56
224 226 4.349048 TCTGCTCATTCCCTGTATATTGCT 59.651 41.667 0.00 0.00 0.00 3.91
225 227 5.052693 TGCTCATTCCCTGTATATTGCTT 57.947 39.130 0.00 0.00 0.00 3.91
226 228 5.448654 TGCTCATTCCCTGTATATTGCTTT 58.551 37.500 0.00 0.00 0.00 3.51
227 229 5.300034 TGCTCATTCCCTGTATATTGCTTTG 59.700 40.000 0.00 0.00 0.00 2.77
228 230 5.278660 GCTCATTCCCTGTATATTGCTTTGG 60.279 44.000 0.00 0.00 0.00 3.28
229 231 4.584325 TCATTCCCTGTATATTGCTTTGGC 59.416 41.667 0.00 0.00 39.26 4.52
230 232 3.951563 TCCCTGTATATTGCTTTGGCT 57.048 42.857 0.00 0.00 39.59 4.75
231 233 3.820557 TCCCTGTATATTGCTTTGGCTC 58.179 45.455 0.00 0.00 39.59 4.70
256 258 6.503524 GTTTGGAGCTCAGAAAATTTGTACA 58.496 36.000 17.19 0.00 0.00 2.90
262 264 8.084684 GGAGCTCAGAAAATTTGTACAGAAAAT 58.915 33.333 17.19 0.00 0.00 1.82
281 283 8.621286 CAGAAAATAAACTACAGTTTGTCTGGT 58.379 33.333 15.87 0.00 46.56 4.00
307 309 0.747283 ACGGATCGACCTAGCGTTCT 60.747 55.000 0.00 0.00 36.31 3.01
327 329 4.695014 TGCTGGGGCAGAAAACAA 57.305 50.000 0.00 0.00 44.28 2.83
328 330 2.907703 TGCTGGGGCAGAAAACAAA 58.092 47.368 0.00 0.00 44.28 2.83
329 331 0.463620 TGCTGGGGCAGAAAACAAAC 59.536 50.000 0.00 0.00 44.28 2.93
330 332 0.752658 GCTGGGGCAGAAAACAAACT 59.247 50.000 0.00 0.00 38.54 2.66
331 333 1.960689 GCTGGGGCAGAAAACAAACTA 59.039 47.619 0.00 0.00 38.54 2.24
332 334 2.288213 GCTGGGGCAGAAAACAAACTAC 60.288 50.000 0.00 0.00 38.54 2.73
333 335 2.955660 CTGGGGCAGAAAACAAACTACA 59.044 45.455 0.00 0.00 32.44 2.74
334 336 2.955660 TGGGGCAGAAAACAAACTACAG 59.044 45.455 0.00 0.00 0.00 2.74
335 337 2.956333 GGGGCAGAAAACAAACTACAGT 59.044 45.455 0.00 0.00 0.00 3.55
336 338 3.383505 GGGGCAGAAAACAAACTACAGTT 59.616 43.478 0.00 0.00 40.50 3.16
337 339 8.298349 CTGGGGCAGAAAACAAACTACAGTTT 62.298 42.308 1.47 1.47 40.14 2.66
396 398 3.576078 TTCCAGACTGAACAATGTGGT 57.424 42.857 3.32 0.00 0.00 4.16
397 399 4.698201 TTCCAGACTGAACAATGTGGTA 57.302 40.909 3.32 0.00 0.00 3.25
399 401 4.641396 TCCAGACTGAACAATGTGGTAAG 58.359 43.478 3.32 0.00 0.00 2.34
418 426 1.112950 GGGGTACGAGAGGAAGGAAG 58.887 60.000 0.00 0.00 0.00 3.46
432 440 3.304458 GGAAGGAAGTGGTTAAAGTTGCG 60.304 47.826 0.00 0.00 0.00 4.85
446 482 7.642586 GGTTAAAGTTGCGGTAATGCTATTAAG 59.357 37.037 0.00 0.00 35.36 1.85
456 492 7.448228 CGGTAATGCTATTAAGATGATGTTCG 58.552 38.462 0.00 0.00 0.00 3.95
482 518 3.006752 GGCAGGGATGACAAATCAAACAA 59.993 43.478 0.00 0.00 38.69 2.83
508 544 7.979115 TTTTTATGGCAGTTTATATTGTCGC 57.021 32.000 0.00 0.00 0.00 5.19
510 546 1.937223 TGGCAGTTTATATTGTCGCGG 59.063 47.619 6.13 0.00 0.00 6.46
520 556 0.322997 ATTGTCGCGGGGATGGAAAA 60.323 50.000 6.13 0.00 0.00 2.29
523 559 0.815095 GTCGCGGGGATGGAAAATTT 59.185 50.000 6.13 0.00 0.00 1.82
524 560 2.018515 GTCGCGGGGATGGAAAATTTA 58.981 47.619 6.13 0.00 0.00 1.40
525 561 2.032924 GTCGCGGGGATGGAAAATTTAG 59.967 50.000 6.13 0.00 0.00 1.85
527 563 2.425668 CGCGGGGATGGAAAATTTAGTT 59.574 45.455 0.00 0.00 0.00 2.24
528 564 3.119280 CGCGGGGATGGAAAATTTAGTTT 60.119 43.478 0.00 0.00 0.00 2.66
567 603 8.868522 ATCCTGACAAATAACTGAATTGAAGA 57.131 30.769 0.00 0.00 0.00 2.87
568 604 8.690203 TCCTGACAAATAACTGAATTGAAGAA 57.310 30.769 0.00 0.00 0.00 2.52
589 625 4.978083 AGATTTGCCATGCTTGTCTAAG 57.022 40.909 0.00 0.00 36.97 2.18
603 639 6.406093 CTTGTCTAAGCTTGTCATTCTCAG 57.594 41.667 9.86 0.00 0.00 3.35
605 641 3.620821 GTCTAAGCTTGTCATTCTCAGCC 59.379 47.826 9.86 0.00 0.00 4.85
634 670 3.802722 TTGCAATGCAAATTTTACCGC 57.197 38.095 19.21 0.00 45.96 5.68
661 697 3.257933 GCTTCCCAGCTGACGTTG 58.742 61.111 17.39 0.00 43.51 4.10
663 699 1.371183 CTTCCCAGCTGACGTTGGA 59.629 57.895 17.39 10.14 43.57 3.53
729 765 1.994779 CGGAATTGCAGTGCCAAAATC 59.005 47.619 13.72 3.68 0.00 2.17
918 963 4.711949 AGTGGCTGGCTCCGCTTG 62.712 66.667 2.00 0.00 44.01 4.01
942 1041 0.252421 TGAGCCCTCTGTCACTCCAT 60.252 55.000 0.00 0.00 0.00 3.41
958 1057 2.436911 CTCCATGAGTCCATGTCCATGA 59.563 50.000 8.82 0.00 46.68 3.07
1063 1165 0.250727 CAGACACCAACCATTCCCGT 60.251 55.000 0.00 0.00 0.00 5.28
1064 1166 0.476771 AGACACCAACCATTCCCGTT 59.523 50.000 0.00 0.00 0.00 4.44
1065 1167 0.879090 GACACCAACCATTCCCGTTC 59.121 55.000 0.00 0.00 0.00 3.95
1066 1168 0.538746 ACACCAACCATTCCCGTTCC 60.539 55.000 0.00 0.00 0.00 3.62
1067 1169 1.076014 ACCAACCATTCCCGTTCCC 59.924 57.895 0.00 0.00 0.00 3.97
1068 1170 2.043980 CCAACCATTCCCGTTCCCG 61.044 63.158 0.00 0.00 0.00 5.14
1093 1207 3.299977 CAAGGGCAGCAGCAGCAA 61.300 61.111 12.41 0.00 45.49 3.91
1129 1243 3.181967 CCAAGAAGTCGAGGCGCG 61.182 66.667 3.60 3.60 42.69 6.86
1513 1645 0.392336 GATGCTCTCCTGCAGGGTAG 59.608 60.000 32.23 27.17 46.71 3.18
1514 1646 1.053264 ATGCTCTCCTGCAGGGTAGG 61.053 60.000 32.23 19.54 46.71 3.18
1515 1647 1.381872 GCTCTCCTGCAGGGTAGGA 60.382 63.158 32.23 21.61 41.91 2.94
1522 1654 1.482593 CCTGCAGGGTAGGAGTACTTG 59.517 57.143 26.14 0.00 37.52 3.16
1524 1656 1.196012 GCAGGGTAGGAGTACTTGCT 58.804 55.000 0.00 0.00 37.05 3.91
1555 1687 2.213499 CGCTTGATTCCATGGACCTAC 58.787 52.381 15.91 6.82 0.00 3.18
1556 1688 2.576615 GCTTGATTCCATGGACCTACC 58.423 52.381 15.91 2.56 39.54 3.18
1557 1689 2.173569 GCTTGATTCCATGGACCTACCT 59.826 50.000 15.91 0.00 39.86 3.08
1558 1690 3.391296 GCTTGATTCCATGGACCTACCTA 59.609 47.826 15.91 0.00 39.86 3.08
1573 1705 5.395611 ACCTACCTATTCTCCCTGTGATAC 58.604 45.833 0.00 0.00 0.00 2.24
1580 1712 4.672587 TTCTCCCTGTGATACATACAGC 57.327 45.455 0.00 0.00 43.19 4.40
1677 1811 1.065199 TCAGGTCACCAATCCATGCTC 60.065 52.381 0.00 0.00 0.00 4.26
1680 1814 1.340405 GGTCACCAATCCATGCTCAGT 60.340 52.381 0.00 0.00 0.00 3.41
1681 1815 2.012673 GTCACCAATCCATGCTCAGTC 58.987 52.381 0.00 0.00 0.00 3.51
1703 1838 7.648908 CAGTCACATTCTTCACAAGCATTTTTA 59.351 33.333 0.00 0.00 0.00 1.52
1705 1840 8.981647 GTCACATTCTTCACAAGCATTTTTATT 58.018 29.630 0.00 0.00 0.00 1.40
1753 1888 9.502091 AGTTGCATCAGTTATTCAGTTAGTTTA 57.498 29.630 0.00 0.00 0.00 2.01
1976 2173 2.094026 CGATGTCAATCTGGAGGTCACA 60.094 50.000 0.00 0.00 0.00 3.58
1991 2189 4.362677 AGGTCACACTGGAGGTAATATGT 58.637 43.478 0.00 0.00 0.00 2.29
2001 2199 8.204160 CACTGGAGGTAATATGTCATTCAGTTA 58.796 37.037 4.07 0.00 30.56 2.24
2002 2200 8.424918 ACTGGAGGTAATATGTCATTCAGTTAG 58.575 37.037 0.00 0.00 0.00 2.34
2003 2201 8.319057 TGGAGGTAATATGTCATTCAGTTAGT 57.681 34.615 0.00 0.00 0.00 2.24
2004 2202 8.204160 TGGAGGTAATATGTCATTCAGTTAGTG 58.796 37.037 0.00 0.00 0.00 2.74
2005 2203 8.421784 GGAGGTAATATGTCATTCAGTTAGTGA 58.578 37.037 0.00 0.00 0.00 3.41
2006 2204 9.988815 GAGGTAATATGTCATTCAGTTAGTGAT 57.011 33.333 0.00 0.00 34.17 3.06
2007 2205 9.770097 AGGTAATATGTCATTCAGTTAGTGATG 57.230 33.333 0.00 0.00 34.17 3.07
2008 2206 9.547753 GGTAATATGTCATTCAGTTAGTGATGT 57.452 33.333 0.00 0.00 34.17 3.06
2016 2214 9.400638 GTCATTCAGTTAGTGATGTAGTATAGC 57.599 37.037 0.00 0.00 34.17 2.97
2017 2215 9.131791 TCATTCAGTTAGTGATGTAGTATAGCA 57.868 33.333 0.00 0.00 34.17 3.49
2019 2217 7.273320 TCAGTTAGTGATGTAGTATAGCACC 57.727 40.000 11.17 0.00 0.00 5.01
2021 2219 7.013369 TCAGTTAGTGATGTAGTATAGCACCTG 59.987 40.741 11.17 11.22 0.00 4.00
2040 2308 3.581770 CCTGCTAGATGAGAATGGGATCA 59.418 47.826 0.00 0.00 0.00 2.92
2077 2345 4.609947 TGCATCACAAAATTCACACTGAC 58.390 39.130 0.00 0.00 0.00 3.51
2083 2351 2.981805 CAAAATTCACACTGACGCATGG 59.018 45.455 0.00 0.00 0.00 3.66
2084 2352 1.896220 AATTCACACTGACGCATGGT 58.104 45.000 0.00 0.00 0.00 3.55
2089 2357 2.163613 TCACACTGACGCATGGTACTAG 59.836 50.000 0.00 0.00 0.00 2.57
2129 2400 5.549228 TGAATATTACCATCATCCCAGCTCT 59.451 40.000 0.00 0.00 0.00 4.09
2146 2417 4.220382 CAGCTCTTAGGGATGAGTAGATGG 59.780 50.000 0.00 0.00 33.22 3.51
2168 2439 3.735591 CAAGGGTTTCCTACAAGACGAA 58.264 45.455 0.00 0.00 44.07 3.85
2189 2460 4.762289 ACCCTCAAGTTCCTCATATGTC 57.238 45.455 1.90 0.00 0.00 3.06
2191 2462 3.384789 CCCTCAAGTTCCTCATATGTCGA 59.615 47.826 1.90 0.00 0.00 4.20
2192 2463 4.039730 CCCTCAAGTTCCTCATATGTCGAT 59.960 45.833 1.90 0.00 0.00 3.59
2290 2561 3.127721 GCATTCCTTAGAAGTTCCTGCAC 59.872 47.826 0.00 0.00 34.55 4.57
2299 2570 3.281727 AAGTTCCTGCACTTCAGAACA 57.718 42.857 4.73 0.00 45.72 3.18
2301 2572 3.825328 AGTTCCTGCACTTCAGAACAAT 58.175 40.909 4.73 0.00 45.72 2.71
2302 2573 4.973168 AGTTCCTGCACTTCAGAACAATA 58.027 39.130 4.73 0.00 45.72 1.90
2303 2574 5.376625 AGTTCCTGCACTTCAGAACAATAA 58.623 37.500 4.73 0.00 45.72 1.40
2304 2575 5.239525 AGTTCCTGCACTTCAGAACAATAAC 59.760 40.000 4.73 0.00 45.72 1.89
2320 2593 7.665559 AGAACAATAACTTCCTGATGCTTACAA 59.334 33.333 0.00 0.00 0.00 2.41
2329 2606 3.366679 CCTGATGCTTACAAAGTGGCAAG 60.367 47.826 0.00 0.00 38.21 4.01
2372 2649 2.890109 GCGCCCATCGAGATGCTTG 61.890 63.158 7.53 1.00 41.67 4.01
2374 2651 1.493950 CGCCCATCGAGATGCTTGAC 61.494 60.000 7.53 0.00 41.67 3.18
2407 2684 2.668250 GCCTCAATTTACGCCGTTTTT 58.332 42.857 0.00 0.00 0.00 1.94
2417 2694 1.405821 ACGCCGTTTTTCCAATTGTCA 59.594 42.857 4.43 0.00 0.00 3.58
2427 2704 7.009999 CGTTTTTCCAATTGTCATGAAACTGAA 59.990 33.333 4.43 0.00 0.00 3.02
2465 2742 9.573133 TCAAAGAAGAAGAAAACTGAATTTGAC 57.427 29.630 0.00 0.00 30.43 3.18
2589 2867 1.219393 GCTGCTGAGGGACTACCAC 59.781 63.158 0.00 0.00 41.55 4.16
2619 2897 2.435586 CAGCAGGCCCAGTCTTCG 60.436 66.667 0.00 0.00 0.00 3.79
2631 2909 0.453793 AGTCTTCGTCCTCATGAGCG 59.546 55.000 17.76 15.86 0.00 5.03
2634 2912 0.869454 CTTCGTCCTCATGAGCGAGC 60.869 60.000 17.76 9.49 34.78 5.03
2654 2932 1.946768 CGACTGCCCAAAGTCTGAAAA 59.053 47.619 3.13 0.00 43.71 2.29
2655 2933 2.357637 CGACTGCCCAAAGTCTGAAAAA 59.642 45.455 3.13 0.00 43.71 1.94
2697 2975 3.797507 CTGGGATTCATGGCCGGGG 62.798 68.421 2.18 0.00 0.00 5.73
2716 2994 1.469767 GGCGGCTTTCATCAAATCCAC 60.470 52.381 0.00 0.00 29.40 4.02
2797 3078 7.578852 TGCTTGCATGATATAAGAAAGAATCG 58.421 34.615 3.33 0.00 0.00 3.34
2883 3164 4.332828 AGCTAACTTTTGACCCATGTACC 58.667 43.478 0.00 0.00 0.00 3.34
2884 3165 4.076394 GCTAACTTTTGACCCATGTACCA 58.924 43.478 0.00 0.00 0.00 3.25
2885 3166 4.082949 GCTAACTTTTGACCCATGTACCAC 60.083 45.833 0.00 0.00 0.00 4.16
2886 3167 3.586470 ACTTTTGACCCATGTACCACA 57.414 42.857 0.00 0.00 0.00 4.17
2888 3169 3.218453 CTTTTGACCCATGTACCACACA 58.782 45.455 0.00 0.00 42.69 3.72
2890 3171 2.779755 TGACCCATGTACCACACATC 57.220 50.000 0.00 0.00 44.99 3.06
2891 3172 2.265367 TGACCCATGTACCACACATCT 58.735 47.619 0.00 0.00 44.99 2.90
2892 3173 3.445987 TGACCCATGTACCACACATCTA 58.554 45.455 0.00 0.00 44.99 1.98
2893 3174 3.196901 TGACCCATGTACCACACATCTAC 59.803 47.826 0.00 0.00 44.99 2.59
2904 3331 5.710984 ACCACACATCTACTAGAAAACTCG 58.289 41.667 0.00 0.00 0.00 4.18
2943 3370 4.097741 TGATGTTGAAGGTTCTGGTTGTTG 59.902 41.667 0.00 0.00 0.00 3.33
2953 3380 5.070313 AGGTTCTGGTTGTTGTTATTGCATT 59.930 36.000 0.00 0.00 0.00 3.56
3009 3436 2.029649 ACATGTTCAAACAGCATGAGGC 60.030 45.455 10.22 0.00 43.04 4.70
3031 3458 4.553323 CTTTCCCTCAAGAAATTGCAGTG 58.447 43.478 0.00 0.00 35.30 3.66
3049 3476 5.069914 TGCAGTGGTTGAAACTTCTCTAGTA 59.930 40.000 0.00 0.00 35.54 1.82
3233 3660 8.628630 TTTTCAGATGACATGTACAACCATAA 57.371 30.769 0.00 0.00 0.00 1.90
3234 3661 8.806429 TTTCAGATGACATGTACAACCATAAT 57.194 30.769 0.00 0.00 0.00 1.28
3269 3696 8.991783 AATCTGTGGTAAAGATCATCATCATT 57.008 30.769 0.00 0.00 33.17 2.57
3275 3702 7.221452 GTGGTAAAGATCATCATCATTGTTTGC 59.779 37.037 0.00 0.00 0.00 3.68
3302 3729 9.226606 CCTGTACATTCCTTCACAAAAACTATA 57.773 33.333 0.00 0.00 0.00 1.31
3374 3801 0.974010 TCGGTAGGCGAGTTCCCAAT 60.974 55.000 0.00 0.00 0.00 3.16
3473 3900 1.376037 GGTCAAGGGAAGGCGAGTG 60.376 63.158 0.00 0.00 0.00 3.51
3474 3901 1.371558 GTCAAGGGAAGGCGAGTGT 59.628 57.895 0.00 0.00 0.00 3.55
3485 3912 2.110967 GCGAGTGTGGCAGCATCAT 61.111 57.895 0.00 0.00 0.00 2.45
3489 3916 0.393944 AGTGTGGCAGCATCATGGAG 60.394 55.000 0.00 0.00 0.00 3.86
3584 4011 0.895530 ATCTCCGTCATTGTCCGTGT 59.104 50.000 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 174 4.002906 TCCACGAATCTTACACTTGCTT 57.997 40.909 0.00 0.00 0.00 3.91
174 176 4.742438 TTTCCACGAATCTTACACTTGC 57.258 40.909 0.00 0.00 0.00 4.01
198 200 5.894298 ATATACAGGGAATGAGCAGACAA 57.106 39.130 0.00 0.00 0.00 3.18
200 202 4.453819 GCAATATACAGGGAATGAGCAGAC 59.546 45.833 0.00 0.00 0.00 3.51
202 204 4.649692 AGCAATATACAGGGAATGAGCAG 58.350 43.478 0.00 0.00 0.00 4.24
217 219 3.088532 TCCAAACGAGCCAAAGCAATAT 58.911 40.909 0.00 0.00 43.56 1.28
219 221 1.270550 CTCCAAACGAGCCAAAGCAAT 59.729 47.619 0.00 0.00 43.56 3.56
220 222 0.667993 CTCCAAACGAGCCAAAGCAA 59.332 50.000 0.00 0.00 43.56 3.91
221 223 2.330254 CTCCAAACGAGCCAAAGCA 58.670 52.632 0.00 0.00 43.56 3.91
229 231 4.756084 AATTTTCTGAGCTCCAAACGAG 57.244 40.909 12.15 0.13 42.04 4.18
230 232 4.338118 ACAAATTTTCTGAGCTCCAAACGA 59.662 37.500 12.15 0.00 0.00 3.85
231 233 4.610945 ACAAATTTTCTGAGCTCCAAACG 58.389 39.130 12.15 3.54 0.00 3.60
256 258 8.747538 ACCAGACAAACTGTAGTTTATTTTCT 57.252 30.769 9.47 6.89 45.54 2.52
262 264 6.017440 GCATGAACCAGACAAACTGTAGTTTA 60.017 38.462 9.47 0.00 45.54 2.01
270 272 1.603802 CGTGCATGAACCAGACAAACT 59.396 47.619 0.00 0.00 0.00 2.66
281 283 1.067060 CTAGGTCGATCCGTGCATGAA 59.933 52.381 7.72 0.00 41.99 2.57
327 329 3.613030 ACGGACCAAACAAACTGTAGTT 58.387 40.909 0.00 0.00 40.50 2.24
328 330 3.271055 ACGGACCAAACAAACTGTAGT 57.729 42.857 0.00 0.00 0.00 2.73
329 331 4.625972 AAACGGACCAAACAAACTGTAG 57.374 40.909 0.00 0.00 0.00 2.74
330 332 4.217983 ACAAAACGGACCAAACAAACTGTA 59.782 37.500 0.00 0.00 0.00 2.74
331 333 3.006003 ACAAAACGGACCAAACAAACTGT 59.994 39.130 0.00 0.00 0.00 3.55
332 334 3.580731 ACAAAACGGACCAAACAAACTG 58.419 40.909 0.00 0.00 0.00 3.16
333 335 3.945981 ACAAAACGGACCAAACAAACT 57.054 38.095 0.00 0.00 0.00 2.66
334 336 3.988517 TCAACAAAACGGACCAAACAAAC 59.011 39.130 0.00 0.00 0.00 2.93
335 337 3.988517 GTCAACAAAACGGACCAAACAAA 59.011 39.130 0.00 0.00 0.00 2.83
336 338 3.005472 TGTCAACAAAACGGACCAAACAA 59.995 39.130 0.00 0.00 0.00 2.83
337 339 2.557056 TGTCAACAAAACGGACCAAACA 59.443 40.909 0.00 0.00 0.00 2.83
338 340 3.219052 TGTCAACAAAACGGACCAAAC 57.781 42.857 0.00 0.00 0.00 2.93
339 341 3.444034 TCATGTCAACAAAACGGACCAAA 59.556 39.130 0.00 0.00 0.00 3.28
396 398 1.925255 TCCTTCCTCTCGTACCCCTTA 59.075 52.381 0.00 0.00 0.00 2.69
397 399 0.708802 TCCTTCCTCTCGTACCCCTT 59.291 55.000 0.00 0.00 0.00 3.95
399 401 1.112950 CTTCCTTCCTCTCGTACCCC 58.887 60.000 0.00 0.00 0.00 4.95
418 426 3.057806 AGCATTACCGCAACTTTAACCAC 60.058 43.478 0.00 0.00 0.00 4.16
432 440 8.311650 ACGAACATCATCTTAATAGCATTACC 57.688 34.615 0.00 0.00 0.00 2.85
446 482 1.133025 CCCTGCCAAACGAACATCATC 59.867 52.381 0.00 0.00 0.00 2.92
456 492 2.562298 TGATTTGTCATCCCTGCCAAAC 59.438 45.455 0.00 0.00 0.00 2.93
459 495 2.562298 GTTTGATTTGTCATCCCTGCCA 59.438 45.455 0.00 0.00 0.00 4.92
495 531 2.482721 CCATCCCCGCGACAATATAAAC 59.517 50.000 8.23 0.00 0.00 2.01
508 544 4.180817 GCAAACTAAATTTTCCATCCCCG 58.819 43.478 0.00 0.00 0.00 5.73
510 546 5.122239 GCTTGCAAACTAAATTTTCCATCCC 59.878 40.000 0.00 0.00 0.00 3.85
520 556 1.339610 TGCCGTGCTTGCAAACTAAAT 59.660 42.857 0.00 0.00 35.40 1.40
523 559 2.409399 TTGCCGTGCTTGCAAACTA 58.591 47.368 0.00 0.00 45.11 2.24
524 560 3.205395 TTGCCGTGCTTGCAAACT 58.795 50.000 0.00 0.00 45.11 2.66
527 563 1.006337 GGATTTGCCGTGCTTGCAA 60.006 52.632 0.00 0.00 46.30 4.08
528 564 1.902918 AGGATTTGCCGTGCTTGCA 60.903 52.632 0.00 0.00 43.43 4.08
567 603 5.320549 CTTAGACAAGCATGGCAAATCTT 57.679 39.130 0.00 0.00 36.86 2.40
568 604 4.978083 CTTAGACAAGCATGGCAAATCT 57.022 40.909 0.00 0.00 36.86 2.40
589 625 1.881973 TGTTGGCTGAGAATGACAAGC 59.118 47.619 0.00 0.00 0.00 4.01
603 639 4.681835 TTGCATTGCAATTTATGTTGGC 57.318 36.364 19.77 8.15 43.99 4.52
625 661 2.093553 AGCATGGCAATTGCGGTAAAAT 60.094 40.909 23.48 7.74 44.82 1.82
627 663 0.894141 AGCATGGCAATTGCGGTAAA 59.106 45.000 23.48 7.50 44.82 2.01
630 666 1.216178 GAAGCATGGCAATTGCGGT 59.784 52.632 23.48 12.96 44.82 5.68
631 667 1.519898 GGAAGCATGGCAATTGCGG 60.520 57.895 23.48 16.14 44.82 5.69
632 668 1.519898 GGGAAGCATGGCAATTGCG 60.520 57.895 23.48 11.57 44.82 4.85
633 669 0.461339 CTGGGAAGCATGGCAATTGC 60.461 55.000 22.47 22.47 40.45 3.56
634 670 0.461339 GCTGGGAAGCATGGCAATTG 60.461 55.000 0.00 0.00 34.41 2.32
661 697 1.125633 TAGGACCGGCTTAACCATCC 58.874 55.000 0.00 0.00 41.81 3.51
663 699 2.574824 ACTTTAGGACCGGCTTAACCAT 59.425 45.455 0.00 0.00 39.03 3.55
708 744 0.749649 TTTTGGCACTGCAATTCCGT 59.250 45.000 2.82 0.00 0.00 4.69
729 765 4.981806 TTTCCAGATAAATTTGAGCGGG 57.018 40.909 0.00 0.74 0.00 6.13
790 830 1.077123 CTCACATGCTCTGCTGTCAC 58.923 55.000 0.00 0.00 0.00 3.67
942 1041 2.026915 CCTGTTCATGGACATGGACTCA 60.027 50.000 20.94 4.88 45.46 3.41
958 1057 2.325082 CGCAGCGGCTTTACCTGTT 61.325 57.895 7.00 0.00 38.10 3.16
1029 1131 1.380515 TCTGGCGAGGAGGAAGGAG 60.381 63.158 0.00 0.00 0.00 3.69
1063 1165 0.106719 GCCCTTGATGATTCCGGGAA 60.107 55.000 12.67 12.67 34.89 3.97
1064 1166 1.278302 TGCCCTTGATGATTCCGGGA 61.278 55.000 0.00 0.00 34.89 5.14
1065 1167 0.820891 CTGCCCTTGATGATTCCGGG 60.821 60.000 0.00 0.00 35.63 5.73
1066 1168 1.450531 GCTGCCCTTGATGATTCCGG 61.451 60.000 0.00 0.00 0.00 5.14
1067 1169 0.749091 TGCTGCCCTTGATGATTCCG 60.749 55.000 0.00 0.00 0.00 4.30
1068 1170 1.030457 CTGCTGCCCTTGATGATTCC 58.970 55.000 0.00 0.00 0.00 3.01
1069 1171 0.384669 GCTGCTGCCCTTGATGATTC 59.615 55.000 3.85 0.00 0.00 2.52
1070 1172 0.323999 TGCTGCTGCCCTTGATGATT 60.324 50.000 13.47 0.00 38.71 2.57
1093 1207 2.514592 CGGCTTGCATGGATCGGT 60.515 61.111 1.34 0.00 0.00 4.69
1513 1645 4.561606 CGTGTGTATGTTAGCAAGTACTCC 59.438 45.833 0.00 0.00 0.00 3.85
1514 1646 4.031426 GCGTGTGTATGTTAGCAAGTACTC 59.969 45.833 0.00 0.00 0.00 2.59
1515 1647 3.924686 GCGTGTGTATGTTAGCAAGTACT 59.075 43.478 0.00 0.00 0.00 2.73
1516 1648 3.924686 AGCGTGTGTATGTTAGCAAGTAC 59.075 43.478 0.00 0.00 0.00 2.73
1522 1654 4.494199 GGAATCAAGCGTGTGTATGTTAGC 60.494 45.833 0.00 0.00 0.00 3.09
1524 1656 4.570930 TGGAATCAAGCGTGTGTATGTTA 58.429 39.130 0.00 0.00 0.00 2.41
1555 1687 6.573289 GCTGTATGTATCACAGGGAGAATAGG 60.573 46.154 4.79 0.00 42.99 2.57
1556 1688 6.210385 AGCTGTATGTATCACAGGGAGAATAG 59.790 42.308 4.79 0.00 42.99 1.73
1557 1689 6.015095 CAGCTGTATGTATCACAGGGAGAATA 60.015 42.308 5.25 0.00 42.99 1.75
1558 1690 4.904251 AGCTGTATGTATCACAGGGAGAAT 59.096 41.667 4.79 0.00 42.99 2.40
1573 1705 9.582431 AATTGAAAAGATCATTTCAGCTGTATG 57.418 29.630 21.42 17.48 46.63 2.39
1580 1712 7.900782 AGGCAAATTGAAAAGATCATTTCAG 57.099 32.000 21.42 13.54 46.63 3.02
1665 1799 2.118313 TGTGACTGAGCATGGATTGG 57.882 50.000 0.00 0.00 0.00 3.16
1677 1811 4.761235 ATGCTTGTGAAGAATGTGACTG 57.239 40.909 0.00 0.00 0.00 3.51
1680 1814 9.545105 AAATAAAAATGCTTGTGAAGAATGTGA 57.455 25.926 0.00 0.00 0.00 3.58
1703 1838 8.497745 ACTATTCCACCATTGACAGAGATAAAT 58.502 33.333 0.00 0.00 0.00 1.40
1705 1840 7.437713 ACTATTCCACCATTGACAGAGATAA 57.562 36.000 0.00 0.00 0.00 1.75
1774 1934 6.965500 CAGAGATATCAAATGTTGCAAGTGTC 59.035 38.462 0.00 0.00 0.00 3.67
1965 2162 0.833834 ACCTCCAGTGTGACCTCCAG 60.834 60.000 0.00 0.00 0.00 3.86
1976 2173 6.814954 ACTGAATGACATATTACCTCCAGT 57.185 37.500 0.00 0.00 0.00 4.00
1991 2189 9.131791 TGCTATACTACATCACTAACTGAATGA 57.868 33.333 0.00 0.00 30.60 2.57
2001 2199 4.592485 GCAGGTGCTATACTACATCACT 57.408 45.455 0.00 0.00 38.21 3.41
2015 2213 2.492012 CCATTCTCATCTAGCAGGTGC 58.508 52.381 0.00 0.00 42.49 5.01
2016 2214 2.702478 TCCCATTCTCATCTAGCAGGTG 59.298 50.000 0.00 0.00 0.00 4.00
2017 2215 3.051940 TCCCATTCTCATCTAGCAGGT 57.948 47.619 0.00 0.00 0.00 4.00
2019 2217 4.040095 TGTGATCCCATTCTCATCTAGCAG 59.960 45.833 0.00 0.00 0.00 4.24
2021 2219 4.613925 TGTGATCCCATTCTCATCTAGC 57.386 45.455 0.00 0.00 0.00 3.42
2031 2299 4.411540 AGCTAGTGAGATTGTGATCCCATT 59.588 41.667 0.00 0.00 32.44 3.16
2033 2301 3.378512 AGCTAGTGAGATTGTGATCCCA 58.621 45.455 0.00 0.00 32.44 4.37
2077 2345 5.330455 ACATATCATCCTAGTACCATGCG 57.670 43.478 0.00 0.00 0.00 4.73
2129 2400 3.648067 CCTTGCCATCTACTCATCCCTAA 59.352 47.826 0.00 0.00 0.00 2.69
2146 2417 1.804748 CGTCTTGTAGGAAACCCTTGC 59.195 52.381 0.00 0.00 35.26 4.01
2168 2439 3.133003 CGACATATGAGGAACTTGAGGGT 59.867 47.826 10.38 0.00 41.55 4.34
2189 2460 3.423123 GCTTCGTGTACACCTGAAAATCG 60.423 47.826 20.11 5.45 0.00 3.34
2191 2462 2.812011 GGCTTCGTGTACACCTGAAAAT 59.188 45.455 20.11 0.00 0.00 1.82
2192 2463 2.215196 GGCTTCGTGTACACCTGAAAA 58.785 47.619 20.11 6.38 0.00 2.29
2290 2561 6.373774 AGCATCAGGAAGTTATTGTTCTGAAG 59.626 38.462 0.00 0.00 0.00 3.02
2293 2564 6.506500 AAGCATCAGGAAGTTATTGTTCTG 57.493 37.500 0.00 0.00 0.00 3.02
2298 2569 7.752239 CACTTTGTAAGCATCAGGAAGTTATTG 59.248 37.037 0.00 0.00 0.00 1.90
2299 2570 7.094205 CCACTTTGTAAGCATCAGGAAGTTATT 60.094 37.037 0.00 0.00 0.00 1.40
2301 2572 5.705441 CCACTTTGTAAGCATCAGGAAGTTA 59.295 40.000 0.00 0.00 0.00 2.24
2302 2573 4.520492 CCACTTTGTAAGCATCAGGAAGTT 59.480 41.667 0.00 0.00 0.00 2.66
2303 2574 4.074970 CCACTTTGTAAGCATCAGGAAGT 58.925 43.478 0.00 0.00 0.00 3.01
2304 2575 3.119708 GCCACTTTGTAAGCATCAGGAAG 60.120 47.826 0.00 0.00 0.00 3.46
2320 2593 3.251004 CGAAAGCTAGTTTCTTGCCACTT 59.749 43.478 12.75 0.00 42.28 3.16
2356 2633 1.162800 GGTCAAGCATCTCGATGGGC 61.163 60.000 8.81 0.00 39.16 5.36
2407 2684 9.474920 GTAAAATTCAGTTTCATGACAATTGGA 57.525 29.630 10.83 0.00 0.00 3.53
2619 2897 1.587613 GTCGCTCGCTCATGAGGAC 60.588 63.158 23.89 17.08 36.47 3.85
2631 2909 1.004440 AGACTTTGGGCAGTCGCTC 60.004 57.895 0.00 0.00 46.85 5.03
2634 2912 1.593196 TTTCAGACTTTGGGCAGTCG 58.407 50.000 0.00 0.00 46.85 4.18
2654 2932 6.351966 GGAATCTGCTAGGTAGGTAGTGTTTT 60.352 42.308 0.00 0.00 0.00 2.43
2655 2933 5.128991 GGAATCTGCTAGGTAGGTAGTGTTT 59.871 44.000 0.00 0.00 0.00 2.83
2716 2994 3.371063 CTTGGTGCTGCTGCCAGG 61.371 66.667 13.47 12.18 39.54 4.45
2797 3078 6.053650 GGTTAGGATGGGATGTACAGTAAAC 58.946 44.000 0.33 0.00 0.00 2.01
2883 3164 5.061064 GCACGAGTTTTCTAGTAGATGTGTG 59.939 44.000 0.00 6.04 34.17 3.82
2884 3165 5.047943 AGCACGAGTTTTCTAGTAGATGTGT 60.048 40.000 0.00 0.00 34.17 3.72
2885 3166 5.287274 CAGCACGAGTTTTCTAGTAGATGTG 59.713 44.000 0.00 5.10 34.17 3.21
2886 3167 5.403246 CAGCACGAGTTTTCTAGTAGATGT 58.597 41.667 0.00 0.00 34.17 3.06
2888 3169 4.082190 TGCAGCACGAGTTTTCTAGTAGAT 60.082 41.667 0.00 0.00 34.17 1.98
2889 3170 3.254903 TGCAGCACGAGTTTTCTAGTAGA 59.745 43.478 0.00 0.00 34.17 2.59
2890 3171 3.365220 GTGCAGCACGAGTTTTCTAGTAG 59.635 47.826 10.47 0.00 34.17 2.57
2891 3172 3.243602 TGTGCAGCACGAGTTTTCTAGTA 60.244 43.478 20.67 0.00 37.14 1.82
2892 3173 2.135933 GTGCAGCACGAGTTTTCTAGT 58.864 47.619 10.47 0.00 36.24 2.57
2893 3174 2.135139 TGTGCAGCACGAGTTTTCTAG 58.865 47.619 20.67 0.00 37.14 2.43
2974 3401 8.845227 TGTTTGAACATGTGTAATGTAACATCT 58.155 29.630 0.00 0.00 34.81 2.90
2975 3402 9.117145 CTGTTTGAACATGTGTAATGTAACATC 57.883 33.333 0.00 0.00 38.41 3.06
2976 3403 7.594758 GCTGTTTGAACATGTGTAATGTAACAT 59.405 33.333 0.00 0.00 38.41 2.71
2977 3404 6.915300 GCTGTTTGAACATGTGTAATGTAACA 59.085 34.615 0.00 3.34 38.41 2.41
2978 3405 6.915300 TGCTGTTTGAACATGTGTAATGTAAC 59.085 34.615 0.00 0.00 38.41 2.50
3009 3436 4.553323 CACTGCAATTTCTTGAGGGAAAG 58.447 43.478 0.00 0.00 38.38 2.62
3031 3458 6.641723 GTCACTGTACTAGAGAAGTTTCAACC 59.358 42.308 0.00 0.00 39.80 3.77
3269 3696 2.969821 AGGAATGTACAGGGCAAACA 57.030 45.000 0.33 0.00 0.00 2.83
3275 3702 5.301805 AGTTTTTGTGAAGGAATGTACAGGG 59.698 40.000 0.33 0.00 0.00 4.45
3302 3729 1.302907 ACCTTGAAGCCCTGATGGAT 58.697 50.000 0.00 0.00 35.39 3.41
3374 3801 1.522092 CCTAACAGAGCGATGCCCA 59.478 57.895 0.00 0.00 0.00 5.36
3473 3900 2.487532 GGCTCCATGATGCTGCCAC 61.488 63.158 17.72 0.00 42.79 5.01
3474 3901 2.124024 GGCTCCATGATGCTGCCA 60.124 61.111 17.72 0.00 42.79 4.92
3485 3912 1.305633 CAGAGAGACTGGGGCTCCA 60.306 63.158 4.49 4.49 42.39 3.86
3489 3916 2.880629 TAGGGCAGAGAGACTGGGGC 62.881 65.000 0.00 0.00 45.82 5.80
3519 3946 0.241749 TGGTGCGACGAAGAATACGT 59.758 50.000 0.00 0.00 46.58 3.57
3584 4011 3.483421 CTCCTCTTATGCATGGCAATCA 58.517 45.455 10.16 0.00 43.62 2.57


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

AutoCloner maintained by Alex Coulton.