Multiple sequence alignment - TraesCS5D01G071100

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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 TraesCS5D01G071100 chr5D 100.000 6522 0 0 1 6522 69101590 69108111 0.000000e+00 12044.0
1 TraesCS5D01G071100 chr5D 82.075 106 14 5 3941 4042 519655434 519655538 1.170000e-12 86.1
2 TraesCS5D01G071100 chr5A 94.230 6343 235 61 1 6254 59706081 59712381 0.000000e+00 9564.0
3 TraesCS5D01G071100 chr5A 83.333 450 42 9 5296 5736 59712830 59713255 1.030000e-102 385.0
4 TraesCS5D01G071100 chr5A 90.526 190 10 4 6323 6511 59712521 59712703 1.820000e-60 244.0
5 TraesCS5D01G071100 chr5B 94.767 5370 184 44 1 5311 74994203 74999534 0.000000e+00 8270.0
6 TraesCS5D01G071100 chr5B 90.811 838 64 10 5298 6126 74999549 75000382 0.000000e+00 1109.0
7 TraesCS5D01G071100 chr5B 88.836 627 57 8 5527 6146 75065833 75066453 0.000000e+00 758.0
8 TraesCS5D01G071100 chr5B 85.075 134 6 11 6124 6254 75000463 75000585 2.470000e-24 124.0
9 TraesCS5D01G071100 chr6D 88.079 151 15 2 1775 1925 41929222 41929075 6.720000e-40 176.0
10 TraesCS5D01G071100 chr6A 89.362 141 14 1 1785 1925 52399583 52399444 6.720000e-40 176.0
11 TraesCS5D01G071100 chr1A 87.582 153 18 1 1787 1939 35542274 35542123 6.720000e-40 176.0
12 TraesCS5D01G071100 chr7D 89.209 139 14 1 1784 1922 414518675 414518812 8.690000e-39 172.0
13 TraesCS5D01G071100 chrUn 86.331 139 18 1 1784 1922 67785104 67784967 4.070000e-32 150.0
14 TraesCS5D01G071100 chr2A 86.331 139 18 1 1784 1922 601333345 601333208 4.070000e-32 150.0
15 TraesCS5D01G071100 chr3B 84.615 143 19 3 1784 1925 434983353 434983493 8.820000e-29 139.0


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 TraesCS5D01G071100 chr5D 69101590 69108111 6521 False 12044.000000 12044 100.000000 1 6522 1 chr5D.!!$F1 6521
1 TraesCS5D01G071100 chr5A 59706081 59713255 7174 False 3397.666667 9564 89.363000 1 6511 3 chr5A.!!$F1 6510
2 TraesCS5D01G071100 chr5B 74994203 75000585 6382 False 3167.666667 8270 90.217667 1 6254 3 chr5B.!!$F2 6253
3 TraesCS5D01G071100 chr5B 75065833 75066453 620 False 758.000000 758 88.836000 5527 6146 1 chr5B.!!$F1 619

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
537 564 0.468226 GAGCGAGAGGGAGAGAGAGA 59.532 60.0 0.00 0.00 0.00 3.10 F
1847 1913 0.312102 GCTTTTCTGACCAAAGCGCT 59.688 50.0 2.64 2.64 44.94 5.92 F
2629 2706 0.961019 GGCAATCAGTGTGCTCCAAA 59.039 50.0 5.78 0.00 41.88 3.28 F
3428 3524 5.292101 GGTTCGAAACATCTCTTACTCATGG 59.708 44.0 8.70 0.00 0.00 3.66 F
4623 4734 1.192146 AGGAGCCTGTAACTTCCGCA 61.192 55.0 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2357 0.249699 TCGGCAACTCGAGCAAGAAA 60.250 50.000 13.61 0.0 34.82 2.52 R
2925 3007 0.110295 TGCAGGCCAAGCAAGTAAGA 59.890 50.000 19.15 0.0 39.39 2.10 R
3506 3602 2.123295 GCATGACCCCCATTCCCC 60.123 66.667 0.00 0.0 31.94 4.81 R
5061 5173 1.168407 TGCAGAGCAAAGACAGGTGC 61.168 55.000 0.00 0.0 41.22 5.01 R
5843 5993 0.319211 TTAGCGTGTTCCCGTGACAG 60.319 55.000 0.00 0.0 0.00 3.51 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
216 217 2.555199 CTAGCCACAGCATCACCTAAC 58.445 52.381 0.00 0.00 43.56 2.34
235 236 4.711949 CTTGCACGGGCCAGAGCT 62.712 66.667 23.84 0.00 40.13 4.09
294 296 3.118956 GCTCTACACCTCACTAAGCACAT 60.119 47.826 0.00 0.00 0.00 3.21
308 310 2.842462 ACATAGGCCGCGGATCCA 60.842 61.111 33.48 10.84 0.00 3.41
310 312 2.842462 ATAGGCCGCGGATCCACA 60.842 61.111 33.48 13.79 0.00 4.17
515 542 2.590114 GGGTTACGGGTGGCAGAGT 61.590 63.158 0.00 0.00 0.00 3.24
533 560 2.515057 GCGAGCGAGAGGGAGAGA 60.515 66.667 0.00 0.00 0.00 3.10
534 561 2.542907 GCGAGCGAGAGGGAGAGAG 61.543 68.421 0.00 0.00 0.00 3.20
535 562 1.145156 CGAGCGAGAGGGAGAGAGA 59.855 63.158 0.00 0.00 0.00 3.10
536 563 0.880278 CGAGCGAGAGGGAGAGAGAG 60.880 65.000 0.00 0.00 0.00 3.20
537 564 0.468226 GAGCGAGAGGGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
802 843 2.126850 GCCTTGGCTTTTCGCGTC 60.127 61.111 5.77 0.00 40.44 5.19
809 850 1.406970 GGCTTTTCGCGTCTCTCTCG 61.407 60.000 5.77 0.00 40.44 4.04
868 914 2.631545 AGTAGTGCCCGAGTTGTTTAGT 59.368 45.455 0.00 0.00 0.00 2.24
956 1009 2.418910 CGCGTCATCTCCCACCTCT 61.419 63.158 0.00 0.00 0.00 3.69
1026 1079 0.341609 CCTTCCTCCTCTCCCTCCTT 59.658 60.000 0.00 0.00 0.00 3.36
1033 1086 0.633921 CCTCTCCCTCCTTCTCCTCA 59.366 60.000 0.00 0.00 0.00 3.86
1164 1217 1.154093 CTTGCGCGTAGACTCCGAA 60.154 57.895 8.43 0.00 0.00 4.30
1167 1220 1.154073 GCGCGTAGACTCCGAAAGT 60.154 57.895 8.43 0.00 42.42 2.66
1207 1260 3.036429 GCCGTTCCATGCTCCTCCT 62.036 63.158 0.00 0.00 0.00 3.69
1208 1261 1.144936 CCGTTCCATGCTCCTCCTC 59.855 63.158 0.00 0.00 0.00 3.71
1209 1262 1.144936 CGTTCCATGCTCCTCCTCC 59.855 63.158 0.00 0.00 0.00 4.30
1210 1263 1.333636 CGTTCCATGCTCCTCCTCCT 61.334 60.000 0.00 0.00 0.00 3.69
1211 1264 0.467804 GTTCCATGCTCCTCCTCCTC 59.532 60.000 0.00 0.00 0.00 3.71
1212 1265 0.692419 TTCCATGCTCCTCCTCCTCC 60.692 60.000 0.00 0.00 0.00 4.30
1218 1274 1.655114 GCTCCTCCTCCTCCTCCTCT 61.655 65.000 0.00 0.00 0.00 3.69
1331 1391 2.433436 GCGTCCACCTTCTAATTGGTT 58.567 47.619 0.00 0.00 33.75 3.67
1333 1393 3.007635 CGTCCACCTTCTAATTGGTTCC 58.992 50.000 0.00 0.00 33.75 3.62
1336 1396 2.365582 CACCTTCTAATTGGTTCCCGG 58.634 52.381 0.00 0.00 33.75 5.73
1362 1422 2.515071 TTGGGGTTGGCAATGTGGC 61.515 57.895 1.92 0.00 44.03 5.01
1380 1441 0.721718 GCGGTGATGGTTTCTCTTCG 59.278 55.000 0.00 0.00 0.00 3.79
1381 1442 1.939838 GCGGTGATGGTTTCTCTTCGT 60.940 52.381 0.00 0.00 0.00 3.85
1463 1524 1.483316 CGTGTTCTGTACAGCGACAA 58.517 50.000 24.31 10.91 37.45 3.18
1493 1554 1.112113 GCTCGAAGGTGAGGATACCA 58.888 55.000 0.00 0.00 43.37 3.25
1497 1558 1.471676 CGAAGGTGAGGATACCACAGC 60.472 57.143 8.80 8.80 43.37 4.40
1503 1564 1.555075 TGAGGATACCACAGCCAGTTC 59.445 52.381 0.00 0.00 33.97 3.01
1505 1566 1.556911 AGGATACCACAGCCAGTTCAG 59.443 52.381 0.00 0.00 33.97 3.02
1515 1576 1.906574 AGCCAGTTCAGATTTCCCGTA 59.093 47.619 0.00 0.00 0.00 4.02
1739 1805 4.966965 TTTACGTTGCTTCTGGTTTCAA 57.033 36.364 0.00 0.00 0.00 2.69
1780 1846 5.843673 TGAATGGTTCTGTGCAAAGTTTA 57.156 34.783 3.21 0.00 0.00 2.01
1781 1847 6.214191 TGAATGGTTCTGTGCAAAGTTTAA 57.786 33.333 3.21 0.00 0.00 1.52
1817 1883 5.857268 AGGCATTAATTGTGAGTTTTTGCT 58.143 33.333 0.00 0.00 0.00 3.91
1847 1913 0.312102 GCTTTTCTGACCAAAGCGCT 59.688 50.000 2.64 2.64 44.94 5.92
1848 1914 1.269257 GCTTTTCTGACCAAAGCGCTT 60.269 47.619 18.98 18.98 44.94 4.68
1962 2031 6.071278 TGGTTGTGTGTACAGTATACATGCTA 60.071 38.462 12.80 3.10 38.23 3.49
1972 2041 3.835978 AGTATACATGCTATTGGCCCGTA 59.164 43.478 0.00 0.00 40.92 4.02
2163 2232 6.511416 TGGGATTCTGTTGTTTGTTTATGTG 58.489 36.000 0.00 0.00 0.00 3.21
2269 2346 7.617723 TGGTTGGAATAATAACTTTACCATGCT 59.382 33.333 0.00 0.00 0.00 3.79
2309 2386 3.186909 TCGAGTTGCCGAACTGATAATG 58.813 45.455 0.00 0.00 42.80 1.90
2351 2428 2.287188 CCGCATCTGATAATGTGCCAAC 60.287 50.000 0.00 0.00 36.13 3.77
2625 2702 1.467734 CTTGAGGCAATCAGTGTGCTC 59.532 52.381 5.78 3.05 41.88 4.26
2629 2706 0.961019 GGCAATCAGTGTGCTCCAAA 59.039 50.000 5.78 0.00 41.88 3.28
2837 2918 7.953005 TTCATATTGAAGAAAACCTGGCATA 57.047 32.000 0.00 0.00 31.83 3.14
3428 3524 5.292101 GGTTCGAAACATCTCTTACTCATGG 59.708 44.000 8.70 0.00 0.00 3.66
3506 3602 7.156876 TGCAAGTATTAAGGTGGAATTTGAG 57.843 36.000 0.00 0.00 0.00 3.02
3677 3773 3.129988 GCTGGCATTAGCAGTTGAGAAAT 59.870 43.478 0.00 0.00 44.61 2.17
3919 4015 5.046014 CCCTCTATGGATTGTAGGATTCCAG 60.046 48.000 5.29 0.00 42.53 3.86
4029 4125 6.493166 TCCATAAGAATTTGAACATCCACCT 58.507 36.000 0.00 0.00 0.00 4.00
4038 4134 2.224523 TGAACATCCACCTGAACCTCAC 60.225 50.000 0.00 0.00 0.00 3.51
4071 4167 7.770801 TTAATCACGTAGGATCAAGTCAATG 57.229 36.000 0.00 0.00 0.00 2.82
4103 4199 6.096001 GGTTTCATCCAAATGACTATTCTGCT 59.904 38.462 0.00 0.00 41.62 4.24
4124 4220 4.093261 GCTGTTTTTCTGTGTTGTGCAATT 59.907 37.500 0.00 0.00 0.00 2.32
4219 4317 5.787380 ACCTTCCTTTGATCATTTCTTTGC 58.213 37.500 0.00 0.00 0.00 3.68
4384 4494 5.186198 AGGAATAGTGAGCATGGTTTGTAC 58.814 41.667 0.00 0.00 0.00 2.90
4414 4524 5.048224 TGTTGTAGACTAGGTGCTCAGTTAC 60.048 44.000 0.00 0.00 0.00 2.50
4425 4535 7.050970 AGGTGCTCAGTTACATATTCGAATA 57.949 36.000 19.63 19.63 0.00 1.75
4483 4594 5.690865 TGGTCAACCAACATCTTAAGAAGT 58.309 37.500 9.71 8.53 44.35 3.01
4523 4634 9.868277 CTTGCCCACATTATATTTTTCTAACAA 57.132 29.630 0.00 0.00 0.00 2.83
4623 4734 1.192146 AGGAGCCTGTAACTTCCGCA 61.192 55.000 0.00 0.00 0.00 5.69
5004 5116 3.550030 GCAACGTGGTGCTTTACTTCATT 60.550 43.478 1.88 0.00 41.51 2.57
5005 5117 4.606961 CAACGTGGTGCTTTACTTCATTT 58.393 39.130 0.00 0.00 0.00 2.32
5006 5118 4.483476 ACGTGGTGCTTTACTTCATTTC 57.517 40.909 0.00 0.00 0.00 2.17
5007 5119 4.134563 ACGTGGTGCTTTACTTCATTTCT 58.865 39.130 0.00 0.00 0.00 2.52
5008 5120 5.302360 ACGTGGTGCTTTACTTCATTTCTA 58.698 37.500 0.00 0.00 0.00 2.10
5009 5121 5.408604 ACGTGGTGCTTTACTTCATTTCTAG 59.591 40.000 0.00 0.00 0.00 2.43
5010 5122 5.408604 CGTGGTGCTTTACTTCATTTCTAGT 59.591 40.000 0.00 0.00 0.00 2.57
5044 5156 7.085746 TCATTTTAGTGCATTCATTGTGAGTG 58.914 34.615 0.00 0.00 37.20 3.51
5061 5173 3.175152 GAGTGCTCTCGAGTAACACATG 58.825 50.000 25.60 0.00 33.69 3.21
5149 5261 2.016393 CTCCGCTCCTCCATAACGCA 62.016 60.000 0.00 0.00 0.00 5.24
5578 5722 9.857656 AGAATGGTCTAATTTGTGATGTGATAT 57.142 29.630 0.00 0.00 29.93 1.63
5597 5741 2.371910 TCGTGTGGCGTTGATTATGA 57.628 45.000 0.00 0.00 42.13 2.15
5611 5755 5.856126 TGATTATGAACGTGAAACCACTC 57.144 39.130 0.00 0.00 32.53 3.51
5623 5767 5.281727 GTGAAACCACTCAAGGTCAAAATC 58.718 41.667 0.00 0.00 42.25 2.17
5624 5768 4.340950 TGAAACCACTCAAGGTCAAAATCC 59.659 41.667 0.00 0.00 42.25 3.01
5629 5773 4.136796 CACTCAAGGTCAAAATCCTGTCA 58.863 43.478 0.00 0.00 35.27 3.58
5643 5787 5.954153 ATCCTGTCAGTCTCATTCTGAAT 57.046 39.130 0.00 0.00 42.42 2.57
5656 5800 6.481313 TCTCATTCTGAATCCATTTTCTAGCG 59.519 38.462 0.00 0.00 0.00 4.26
5666 5816 2.762535 TTTTCTAGCGGTTCTCTGGG 57.237 50.000 0.00 0.00 0.00 4.45
5686 5836 8.624019 TCTGGGGATTTTATCTAGAAGAAAGA 57.376 34.615 0.00 0.00 0.00 2.52
5692 5842 7.659799 GGATTTTATCTAGAAGAAAGAGCCTCC 59.340 40.741 0.00 1.53 0.00 4.30
5699 5849 3.199727 AGAAGAAAGAGCCTCCCTGATTC 59.800 47.826 0.00 0.00 0.00 2.52
5700 5850 1.843206 AGAAAGAGCCTCCCTGATTCC 59.157 52.381 0.00 0.00 0.00 3.01
5702 5852 1.341156 AAGAGCCTCCCTGATTCCCG 61.341 60.000 0.00 0.00 0.00 5.14
5710 5860 1.320344 CCCTGATTCCCGTGACTCGA 61.320 60.000 0.00 0.00 42.86 4.04
5750 5900 6.507568 AGAAAACATAATAATTCCACCCCCA 58.492 36.000 0.00 0.00 0.00 4.96
5763 5913 3.466723 TCCACCCCCATGTTGAATCATAT 59.533 43.478 0.00 0.00 0.00 1.78
5771 5921 6.904463 CCATGTTGAATCATATGGGAATGA 57.096 37.500 15.26 0.00 40.07 2.57
5772 5922 6.920817 CCATGTTGAATCATATGGGAATGAG 58.079 40.000 15.26 0.00 39.18 2.90
5777 5927 9.865152 TGTTGAATCATATGGGAATGAGAAATA 57.135 29.630 2.13 0.00 39.18 1.40
5810 5960 3.902881 ATAGAAGGTCTCTGGTTGCAG 57.097 47.619 0.00 0.00 35.41 4.41
5817 5967 0.983467 TCTCTGGTTGCAGCATGGTA 59.017 50.000 2.05 0.00 35.86 3.25
5843 5993 7.826690 TGAACTTTACTGAAGGATTAATTGCC 58.173 34.615 0.00 0.00 39.79 4.52
5871 6021 1.379527 GAACACGCTAAATCCAGGGG 58.620 55.000 0.00 0.00 32.99 4.79
5878 6028 0.186143 CTAAATCCAGGGGCCCCTTC 59.814 60.000 42.71 15.64 45.70 3.46
5915 6065 8.704849 TTTTCATAGGAAATTTGAAGGACTGA 57.295 30.769 3.00 0.00 42.31 3.41
5972 6125 7.016153 TGGTTTGTAGGATTGACTTCTACAT 57.984 36.000 0.00 0.00 41.69 2.29
5973 6126 6.878923 TGGTTTGTAGGATTGACTTCTACATG 59.121 38.462 0.00 0.00 41.69 3.21
6068 6231 5.185828 ACCTTTTGTTTTCTCCTATGATGCC 59.814 40.000 0.00 0.00 0.00 4.40
6084 6247 0.681887 TGCCATCATTGCTGTCCCTG 60.682 55.000 0.00 0.00 0.00 4.45
6154 6400 4.864334 GATGTGGCTCCTGCGGGG 62.864 72.222 12.87 3.48 40.82 5.73
6159 6405 3.062466 GGCTCCTGCGGGGTTTTC 61.062 66.667 12.87 0.00 40.82 2.29
6254 6501 6.271391 TCCTTCAAAACTTCCTATGGTACTCA 59.729 38.462 0.00 0.00 0.00 3.41
6255 6502 6.940298 CCTTCAAAACTTCCTATGGTACTCAA 59.060 38.462 0.00 0.00 0.00 3.02
6258 6505 7.918076 TCAAAACTTCCTATGGTACTCAATCT 58.082 34.615 0.00 0.00 0.00 2.40
6259 6506 8.383175 TCAAAACTTCCTATGGTACTCAATCTT 58.617 33.333 0.00 0.00 0.00 2.40
6260 6507 9.014297 CAAAACTTCCTATGGTACTCAATCTTT 57.986 33.333 0.00 0.00 0.00 2.52
6261 6508 9.588096 AAAACTTCCTATGGTACTCAATCTTTT 57.412 29.630 0.00 0.00 0.00 2.27
6263 6510 9.668497 AACTTCCTATGGTACTCAATCTTTTAC 57.332 33.333 0.00 0.00 0.00 2.01
6264 6511 9.047947 ACTTCCTATGGTACTCAATCTTTTACT 57.952 33.333 0.00 0.00 0.00 2.24
6265 6512 9.319143 CTTCCTATGGTACTCAATCTTTTACTG 57.681 37.037 0.00 0.00 0.00 2.74
6311 6598 7.835822 TCTATGGAATATTCTCAAGAGCTAGC 58.164 38.462 14.95 6.62 0.00 3.42
6312 6599 6.684897 ATGGAATATTCTCAAGAGCTAGCT 57.315 37.500 19.45 19.45 0.00 3.32
6313 6600 7.789202 ATGGAATATTCTCAAGAGCTAGCTA 57.211 36.000 19.38 0.03 0.00 3.32
6314 6601 7.225784 TGGAATATTCTCAAGAGCTAGCTAG 57.774 40.000 19.38 16.84 0.00 3.42
6315 6602 6.210385 TGGAATATTCTCAAGAGCTAGCTAGG 59.790 42.308 19.38 10.29 0.00 3.02
6316 6603 6.435904 GGAATATTCTCAAGAGCTAGCTAGGA 59.564 42.308 19.38 14.11 0.00 2.94
6317 6604 7.124147 GGAATATTCTCAAGAGCTAGCTAGGAT 59.876 40.741 19.38 13.90 0.00 3.24
6318 6605 5.982890 ATTCTCAAGAGCTAGCTAGGATC 57.017 43.478 19.38 4.85 0.00 3.36
6319 6606 3.761897 TCTCAAGAGCTAGCTAGGATCC 58.238 50.000 19.38 2.48 0.00 3.36
6320 6607 3.397618 TCTCAAGAGCTAGCTAGGATCCT 59.602 47.826 19.38 20.48 0.00 3.24
6321 6608 3.758554 CTCAAGAGCTAGCTAGGATCCTC 59.241 52.174 20.22 17.94 0.00 3.71
6337 6655 1.883926 TCCTCTTTTTAACCGGCAAGC 59.116 47.619 0.00 0.00 0.00 4.01
6358 6676 2.731976 CAGACGAAGGAGTTAAGTGCAC 59.268 50.000 9.40 9.40 0.00 4.57
6368 6686 1.804151 GTTAAGTGCACCATCGCTTGA 59.196 47.619 14.63 0.00 37.37 3.02
6385 6703 1.735920 GACAGCTGCCGTGACAGAG 60.736 63.158 15.27 0.00 40.25 3.35
6398 6716 1.069159 TGACAGAGACTCGCGTTCTTC 60.069 52.381 5.77 5.02 0.00 2.87
6445 6764 5.222048 TGCCAAGTAAAATAACAGGACTCCT 60.222 40.000 0.00 0.00 0.00 3.69
6456 6775 1.122019 AGGACTCCTCCCACACACAC 61.122 60.000 0.00 0.00 37.25 3.82
6501 6820 2.608261 GGACTGCAGGAGTATACGATGC 60.608 54.545 19.93 17.72 33.83 3.91
6511 6830 1.466025 TATACGATGCCGACCCCCAC 61.466 60.000 0.00 0.00 39.50 4.61
6514 6833 3.861797 GATGCCGACCCCCACGAT 61.862 66.667 0.00 0.00 0.00 3.73
6518 6837 4.096003 CCGACCCCCACGATGCTT 62.096 66.667 0.00 0.00 0.00 3.91
6519 6838 2.511600 CGACCCCCACGATGCTTC 60.512 66.667 0.00 0.00 0.00 3.86
6521 6840 3.699134 GACCCCCACGATGCTTCCC 62.699 68.421 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 5.551233 TGTGCAGAGAGTTTATGCTACTTT 58.449 37.500 1.72 0.00 40.62 2.66
278 280 2.555199 GCCTATGTGCTTAGTGAGGTG 58.445 52.381 0.00 0.00 0.00 4.00
294 296 3.845259 GTGTGGATCCGCGGCCTA 61.845 66.667 23.51 10.03 0.00 3.93
308 310 3.650369 CGCTTAGGGTTTGCGTGT 58.350 55.556 0.00 0.00 44.00 4.49
515 542 2.826287 CTCTCCCTCTCGCTCGCA 60.826 66.667 0.00 0.00 0.00 5.10
533 560 1.755179 GCTCTGCACTCTCTCTCTCT 58.245 55.000 0.00 0.00 0.00 3.10
534 561 0.378257 CGCTCTGCACTCTCTCTCTC 59.622 60.000 0.00 0.00 0.00 3.20
535 562 0.322456 ACGCTCTGCACTCTCTCTCT 60.322 55.000 0.00 0.00 0.00 3.10
536 563 0.179166 CACGCTCTGCACTCTCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
537 564 0.607762 TCACGCTCTGCACTCTCTCT 60.608 55.000 0.00 0.00 0.00 3.10
733 769 1.065701 CCGCCGCAGCTAGTATATAGG 59.934 57.143 0.00 0.00 36.60 2.57
868 914 1.731160 ACCACGAAACAAACGAACGAA 59.269 42.857 0.14 0.00 34.70 3.85
1164 1217 1.609501 TACCTGGCGCTGGAGACTT 60.610 57.895 22.75 6.23 0.00 3.01
1167 1220 2.283604 TGTACCTGGCGCTGGAGA 60.284 61.111 22.75 10.05 0.00 3.71
1207 1260 1.706575 CAAGGGGAGAGGAGGAGGA 59.293 63.158 0.00 0.00 0.00 3.71
1208 1261 2.069430 GCAAGGGGAGAGGAGGAGG 61.069 68.421 0.00 0.00 0.00 4.30
1209 1262 2.430610 CGCAAGGGGAGAGGAGGAG 61.431 68.421 0.00 0.00 0.00 3.69
1210 1263 2.364317 CGCAAGGGGAGAGGAGGA 60.364 66.667 0.00 0.00 0.00 3.71
1211 1264 4.168291 GCGCAAGGGGAGAGGAGG 62.168 72.222 0.30 0.00 38.28 4.30
1212 1265 3.080121 AGCGCAAGGGGAGAGGAG 61.080 66.667 11.47 0.00 38.28 3.69
1218 1274 2.672996 GAAAGCAGCGCAAGGGGA 60.673 61.111 11.47 0.00 38.28 4.81
1331 1391 0.622154 ACCCCAACATATCACCGGGA 60.622 55.000 6.32 0.00 39.44 5.14
1333 1393 1.388547 CAACCCCAACATATCACCGG 58.611 55.000 0.00 0.00 0.00 5.28
1336 1396 1.846007 TGCCAACCCCAACATATCAC 58.154 50.000 0.00 0.00 0.00 3.06
1362 1422 1.993370 GACGAAGAGAAACCATCACCG 59.007 52.381 0.00 0.00 0.00 4.94
1380 1441 1.266718 TCAATCTGCGCAACCAAAGAC 59.733 47.619 13.05 0.00 0.00 3.01
1381 1442 1.603456 TCAATCTGCGCAACCAAAGA 58.397 45.000 13.05 4.02 0.00 2.52
1463 1524 0.392193 CCTTCGAGCTTGCACATCCT 60.392 55.000 0.00 0.00 0.00 3.24
1493 1554 1.611673 CGGGAAATCTGAACTGGCTGT 60.612 52.381 0.00 0.00 0.00 4.40
1497 1558 2.629051 GGTACGGGAAATCTGAACTGG 58.371 52.381 0.00 0.00 0.00 4.00
1503 1564 1.134491 GTCAGGGGTACGGGAAATCTG 60.134 57.143 0.00 0.00 0.00 2.90
1505 1566 1.138464 GAGTCAGGGGTACGGGAAATC 59.862 57.143 0.00 0.00 0.00 2.17
1515 1576 2.283966 CCCTCACGAGTCAGGGGT 60.284 66.667 4.08 0.00 45.39 4.95
1962 2031 2.038269 CACGCTGTTACGGGCCAAT 61.038 57.895 4.39 0.00 37.37 3.16
1972 2041 1.174712 AGGCAGAAATGCACGCTGTT 61.175 50.000 12.23 1.65 36.33 3.16
2163 2232 7.985634 TTGCTAACAACTTTCAAATTCAGAC 57.014 32.000 0.00 0.00 0.00 3.51
2280 2357 0.249699 TCGGCAACTCGAGCAAGAAA 60.250 50.000 13.61 0.00 34.82 2.52
2283 2360 0.946221 AGTTCGGCAACTCGAGCAAG 60.946 55.000 13.61 3.49 38.62 4.01
2284 2361 1.069090 AGTTCGGCAACTCGAGCAA 59.931 52.632 13.61 0.00 38.62 3.91
2309 2386 4.393062 CGGTCATTCCTATCATGCCAATAC 59.607 45.833 0.00 0.00 0.00 1.89
2625 2702 9.838339 ATTAGTAGACAGAATTCATACCTTTGG 57.162 33.333 8.44 0.00 0.00 3.28
2692 2770 7.729116 ACAATGGCCTAATATCAATCCAAAAG 58.271 34.615 3.32 0.00 0.00 2.27
2844 2925 0.858583 CGAGCGTGTGACAACATTGA 59.141 50.000 0.00 0.00 38.92 2.57
2925 3007 0.110295 TGCAGGCCAAGCAAGTAAGA 59.890 50.000 19.15 0.00 39.39 2.10
3199 3295 6.861065 TGTCAACTGTCCTTTTTAGTGATC 57.139 37.500 0.00 0.00 0.00 2.92
3506 3602 2.123295 GCATGACCCCCATTCCCC 60.123 66.667 0.00 0.00 31.94 4.81
3677 3773 7.962441 TCTATCGATCCTGATTCCAAAACATA 58.038 34.615 0.00 0.00 0.00 2.29
4029 4125 8.717821 CGTGATTAAATCTTAAAGTGAGGTTCA 58.282 33.333 0.00 0.00 0.00 3.18
4071 4167 5.047092 AGTCATTTGGATGAAACCCATGAAC 60.047 40.000 0.00 0.00 43.58 3.18
4103 4199 5.477510 AGAATTGCACAACACAGAAAAACA 58.522 33.333 0.00 0.00 0.00 2.83
4145 4241 5.930837 AGGAAAACCACAGAAATTTGACA 57.069 34.783 0.00 0.00 0.00 3.58
4219 4317 9.630098 AGATGTGCATTTATTTTAACAGTTGAG 57.370 29.630 0.00 0.00 0.00 3.02
4272 4381 6.341316 TGTTAAGTCTCATGGCTTAGCTAAG 58.659 40.000 26.20 26.20 36.40 2.18
4384 4494 6.095580 TGAGCACCTAGTCTACAACAGATAAG 59.904 42.308 0.00 0.00 35.17 1.73
4523 4634 9.862371 CTGCAGAATACCTATACGAGAATAATT 57.138 33.333 8.42 0.00 0.00 1.40
4533 4644 6.334202 GGATGTAGCTGCAGAATACCTATAC 58.666 44.000 20.43 7.05 0.00 1.47
4727 4839 7.884877 AGATTTGTGAACCTTCTCAATGACATA 59.115 33.333 3.95 0.00 39.50 2.29
5044 5156 1.656095 GTGCATGTGTTACTCGAGAGC 59.344 52.381 21.68 8.96 0.00 4.09
5061 5173 1.168407 TGCAGAGCAAAGACAGGTGC 61.168 55.000 0.00 0.00 41.22 5.01
5503 5647 2.501723 TGCTCACTCCAGGGATAGTTTC 59.498 50.000 0.00 0.00 0.00 2.78
5611 5755 4.392940 AGACTGACAGGATTTTGACCTTG 58.607 43.478 7.51 0.00 35.35 3.61
5643 5787 3.369471 CCAGAGAACCGCTAGAAAATGGA 60.369 47.826 0.00 0.00 0.00 3.41
5656 5800 6.749036 TCTAGATAAAATCCCCAGAGAACC 57.251 41.667 0.00 0.00 0.00 3.62
5666 5816 7.659799 GGAGGCTCTTTCTTCTAGATAAAATCC 59.340 40.741 15.23 0.00 0.00 3.01
5686 5836 2.041265 ACGGGAATCAGGGAGGCT 59.959 61.111 0.00 0.00 0.00 4.58
5692 5842 0.530744 TTCGAGTCACGGGAATCAGG 59.469 55.000 16.26 0.00 38.00 3.86
5750 5900 8.771521 TTTCTCATTCCCATATGATTCAACAT 57.228 30.769 3.65 0.00 34.24 2.71
5763 5913 4.019681 ACCTTCACGTATTTCTCATTCCCA 60.020 41.667 0.00 0.00 0.00 4.37
5771 5921 5.730550 TCTATTGCACCTTCACGTATTTCT 58.269 37.500 0.00 0.00 0.00 2.52
5772 5922 6.417191 TTCTATTGCACCTTCACGTATTTC 57.583 37.500 0.00 0.00 0.00 2.17
5777 5927 2.038557 ACCTTCTATTGCACCTTCACGT 59.961 45.455 0.00 0.00 0.00 4.49
5810 5960 5.880332 TCCTTCAGTAAAGTTCATACCATGC 59.120 40.000 0.00 0.00 32.69 4.06
5817 5967 8.470002 GGCAATTAATCCTTCAGTAAAGTTCAT 58.530 33.333 0.00 0.00 32.69 2.57
5843 5993 0.319211 TTAGCGTGTTCCCGTGACAG 60.319 55.000 0.00 0.00 0.00 3.51
5878 6028 9.533253 AATTTCCTATGAAAATTATTTGAGCCG 57.467 29.630 0.00 0.00 43.37 5.52
5888 6038 9.933723 CAGTCCTTCAAATTTCCTATGAAAATT 57.066 29.630 0.00 0.00 43.37 1.82
5942 6095 6.391227 AGTCAATCCTACAAACCAAACAAG 57.609 37.500 0.00 0.00 0.00 3.16
6068 6231 2.118313 TCACAGGGACAGCAATGATG 57.882 50.000 0.00 0.00 0.00 3.07
6154 6400 2.159037 CGCTAGGACGGGAAAAGAAAAC 59.841 50.000 0.00 0.00 0.00 2.43
6159 6405 1.804601 AAACGCTAGGACGGGAAAAG 58.195 50.000 0.00 0.00 37.37 2.27
6193 6440 6.155221 TGCAGTTTCAGAGAACTCCATAGTAT 59.845 38.462 0.00 0.00 37.76 2.12
6194 6441 5.480422 TGCAGTTTCAGAGAACTCCATAGTA 59.520 40.000 0.00 0.00 37.76 1.82
6196 6443 4.825422 TGCAGTTTCAGAGAACTCCATAG 58.175 43.478 0.00 0.00 37.76 2.23
6198 6445 3.777106 TGCAGTTTCAGAGAACTCCAT 57.223 42.857 0.00 0.00 37.76 3.41
6199 6446 3.777106 ATGCAGTTTCAGAGAACTCCA 57.223 42.857 0.00 0.00 37.76 3.86
6200 6447 5.423015 TCATATGCAGTTTCAGAGAACTCC 58.577 41.667 0.00 0.00 37.76 3.85
6201 6448 6.593382 ACTTCATATGCAGTTTCAGAGAACTC 59.407 38.462 1.81 0.00 37.76 3.01
6202 6449 6.471146 ACTTCATATGCAGTTTCAGAGAACT 58.529 36.000 1.81 0.00 40.37 3.01
6203 6450 6.734104 ACTTCATATGCAGTTTCAGAGAAC 57.266 37.500 1.81 0.00 0.00 3.01
6204 6451 7.615403 ACTACTTCATATGCAGTTTCAGAGAA 58.385 34.615 13.31 0.00 0.00 2.87
6311 6598 4.127907 GCCGGTTAAAAAGAGGATCCTAG 58.872 47.826 16.16 0.00 33.66 3.02
6312 6599 3.520317 TGCCGGTTAAAAAGAGGATCCTA 59.480 43.478 16.16 0.00 33.66 2.94
6313 6600 2.307686 TGCCGGTTAAAAAGAGGATCCT 59.692 45.455 16.13 16.13 33.66 3.24
6314 6601 2.718563 TGCCGGTTAAAAAGAGGATCC 58.281 47.619 2.48 2.48 33.66 3.36
6315 6602 3.427638 GCTTGCCGGTTAAAAAGAGGATC 60.428 47.826 1.90 0.00 0.00 3.36
6316 6603 2.492088 GCTTGCCGGTTAAAAAGAGGAT 59.508 45.455 1.90 0.00 0.00 3.24
6317 6604 1.883926 GCTTGCCGGTTAAAAAGAGGA 59.116 47.619 1.90 0.00 0.00 3.71
6318 6605 1.611491 TGCTTGCCGGTTAAAAAGAGG 59.389 47.619 1.90 0.00 0.00 3.69
6319 6606 2.552315 TCTGCTTGCCGGTTAAAAAGAG 59.448 45.455 1.90 1.02 0.00 2.85
6320 6607 2.292292 GTCTGCTTGCCGGTTAAAAAGA 59.708 45.455 1.90 2.46 0.00 2.52
6321 6608 2.661594 GTCTGCTTGCCGGTTAAAAAG 58.338 47.619 1.90 0.99 0.00 2.27
6337 6655 2.731976 GTGCACTTAACTCCTTCGTCTG 59.268 50.000 10.32 0.00 0.00 3.51
6345 6663 0.727398 GCGATGGTGCACTTAACTCC 59.273 55.000 17.98 0.00 34.15 3.85
6346 6664 1.726853 AGCGATGGTGCACTTAACTC 58.273 50.000 17.98 5.79 37.31 3.01
6368 6686 2.203082 TCTCTGTCACGGCAGCTGT 61.203 57.895 16.64 0.00 36.49 4.40
6501 6820 4.096003 AAGCATCGTGGGGGTCGG 62.096 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.