Multiple sequence alignment - TraesCS5B01G038800

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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 TraesCS5B01G038800 chr5B 100.000 3906 0 0 1 3906 43907551 43903646 0.000000e+00 7214.0
1 TraesCS5B01G038800 chr5A 90.632 1868 90 25 1384 3201 698332972 698331140 0.000000e+00 2401.0
2 TraesCS5B01G038800 chr5A 92.479 718 39 8 3197 3905 698331096 698330385 0.000000e+00 1013.0
3 TraesCS5B01G038800 chr5A 93.829 551 30 1 796 1342 698333628 698333078 0.000000e+00 826.0
4 TraesCS5B01G038800 chr5A 93.172 454 25 2 2622 3073 698326421 698325972 0.000000e+00 662.0
5 TraesCS5B01G038800 chr5A 89.749 478 31 5 57 528 698334315 698333850 2.600000e-166 595.0
6 TraesCS5B01G038800 chr5A 77.380 1061 165 45 2005 3033 698342325 698341308 9.480000e-156 560.0
7 TraesCS5B01G038800 chr5A 84.672 548 54 14 795 1326 698343633 698343100 1.610000e-143 520.0
8 TraesCS5B01G038800 chr5A 81.785 549 47 22 794 1326 698349232 698348721 1.010000e-110 411.0
9 TraesCS5B01G038800 chr5A 78.299 576 109 12 1401 1967 698342974 698342406 1.330000e-94 357.0
10 TraesCS5B01G038800 chr5A 96.992 133 4 0 3069 3201 698322991 698322859 1.410000e-54 224.0
11 TraesCS5B01G038800 chr5A 93.651 63 4 0 1 63 698334400 698334338 1.160000e-15 95.3
12 TraesCS5B01G038800 chr6B 90.584 1848 103 30 1378 3201 117126208 117128008 0.000000e+00 2383.0
13 TraesCS5B01G038800 chr6B 93.784 547 33 1 796 1342 117125557 117126102 0.000000e+00 821.0
14 TraesCS5B01G038800 chr6B 92.870 547 32 2 796 1342 116823263 116822724 0.000000e+00 787.0
15 TraesCS5B01G038800 chr6B 83.628 678 84 19 3197 3859 117128052 117128717 2.580000e-171 612.0
16 TraesCS5B01G038800 chr6B 88.913 460 27 8 70 528 116823904 116823468 2.650000e-151 545.0
17 TraesCS5B01G038800 chr6B 91.667 360 15 10 70 415 117124905 117125263 5.870000e-133 484.0
18 TraesCS5B01G038800 chr6B 91.111 90 7 1 440 528 117125263 117125352 1.910000e-23 121.0
19 TraesCS5B01G038800 chr6B 100.000 37 0 0 1343 1379 117126120 117126156 7.000000e-08 69.4
20 TraesCS5B01G038800 chr6B 97.297 37 1 0 1343 1379 116822706 116822670 3.260000e-06 63.9
21 TraesCS5B01G038800 chr4B 91.655 1474 62 15 1378 2816 657289208 657290655 0.000000e+00 1984.0
22 TraesCS5B01G038800 chr4B 92.391 552 26 5 796 1344 657288565 657289103 0.000000e+00 773.0
23 TraesCS5B01G038800 chr4B 93.146 321 22 0 57 377 657287506 657287826 4.570000e-129 472.0
24 TraesCS5B01G038800 chr4B 93.651 63 4 0 1 63 657287421 657287483 1.160000e-15 95.3
25 TraesCS5B01G038800 chr4B 82.796 93 13 2 3707 3796 657295057 657295149 3.240000e-11 80.5
26 TraesCS5B01G038800 chr4B 97.368 38 1 0 1342 1379 657289119 657289156 9.060000e-07 65.8
27 TraesCS5B01G038800 chr6D 89.916 1428 79 29 1797 3201 54078772 54077387 0.000000e+00 1779.0
28 TraesCS5B01G038800 chr6D 94.150 547 32 0 796 1342 54079963 54079417 0.000000e+00 833.0
29 TraesCS5B01G038800 chr6D 92.888 464 28 3 70 528 54080651 54080188 0.000000e+00 669.0
30 TraesCS5B01G038800 chr6D 85.386 609 54 19 3197 3779 54077343 54076744 2.010000e-167 599.0
31 TraesCS5B01G038800 chr6D 90.160 437 14 4 1384 1795 54079305 54078873 3.430000e-150 542.0
32 TraesCS5B01G038800 chr6D 100.000 37 0 0 1343 1379 54079399 54079363 7.000000e-08 69.4
33 TraesCS5B01G038800 chr4D 91.195 1113 56 13 1969 3053 509452791 509451693 0.000000e+00 1474.0
34 TraesCS5B01G038800 chr4D 88.684 1246 82 9 102 1342 509454796 509453605 0.000000e+00 1465.0
35 TraesCS5B01G038800 chr4D 95.273 677 26 4 1384 2059 509453492 509452821 0.000000e+00 1068.0
36 TraesCS5B01G038800 chr4D 77.320 1067 174 40 2005 3033 509457613 509456577 5.660000e-158 568.0
37 TraesCS5B01G038800 chr4D 90.845 426 25 6 3448 3859 509451566 509451141 3.410000e-155 558.0
38 TraesCS5B01G038800 chr4D 87.042 409 41 8 56 462 509455551 509455153 5.950000e-123 451.0
39 TraesCS5B01G038800 chr4D 81.651 545 54 20 795 1326 509458902 509458391 1.010000e-110 411.0
40 TraesCS5B01G038800 chr4D 78.299 576 109 12 1401 1967 509458262 509457694 1.330000e-94 357.0
41 TraesCS5B01G038800 chr4D 97.368 38 1 0 1342 1379 509453587 509453550 9.060000e-07 65.8
42 TraesCS5B01G038800 chr4A 79.195 447 63 18 858 1284 716267870 716268306 2.300000e-72 283.0
43 TraesCS5B01G038800 chr4A 90.909 55 2 1 87 141 716266978 716267029 1.950000e-08 71.3


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 TraesCS5B01G038800 chr5B 43903646 43907551 3905 True 7214.000000 7214 100.000000 1 3906 1 chr5B.!!$R1 3905
1 TraesCS5B01G038800 chr5A 698322859 698334400 11541 True 830.900000 2401 92.929143 1 3905 7 chr5A.!!$R2 3904
2 TraesCS5B01G038800 chr5A 698341308 698343633 2325 True 479.000000 560 80.117000 795 3033 3 chr5A.!!$R3 2238
3 TraesCS5B01G038800 chr5A 698348721 698349232 511 True 411.000000 411 81.785000 794 1326 1 chr5A.!!$R1 532
4 TraesCS5B01G038800 chr6B 117124905 117128717 3812 False 748.400000 2383 91.795667 70 3859 6 chr6B.!!$F1 3789
5 TraesCS5B01G038800 chr6B 116822670 116823904 1234 True 465.300000 787 93.026667 70 1379 3 chr6B.!!$R1 1309
6 TraesCS5B01G038800 chr4B 657287421 657290655 3234 False 678.020000 1984 93.642200 1 2816 5 chr4B.!!$F2 2815
7 TraesCS5B01G038800 chr6D 54076744 54080651 3907 True 748.566667 1779 92.083333 70 3779 6 chr6D.!!$R1 3709
8 TraesCS5B01G038800 chr4D 509451141 509458902 7761 True 713.088889 1474 87.519667 56 3859 9 chr4D.!!$R1 3803

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
966 5498 0.040351 CAGAGGAGTGAGACCCCAGA 59.960 60.0 0.00 0.0 0.00 3.86 F
1141 5682 0.106819 CCCTTCATGGCCTTCTCAGG 60.107 60.0 3.32 2.8 44.28 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2871 13202 1.134401 GGATGACGGATTCAAGCTCCA 60.134 52.381 0.0 0.0 37.92 3.86 R
3082 16421 3.340064 TGGTAGGAGGACCATGCAT 57.660 52.632 0.0 0.0 44.79 3.96 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
44 45 9.685276 TGTCAGTTCATGTATCATATTTTTCCT 57.315 29.630 0.00 0.00 0.00 3.36
136 4142 7.038302 TGGTTTCCAAGATGAGTCATTAGTACT 60.038 37.037 7.16 0.00 0.00 2.73
338 4358 3.070159 CAGCTACACTACATATGCCCACT 59.930 47.826 1.58 0.00 0.00 4.00
360 4380 7.869429 CCACTCAATTAAAGAATTTCTGCAGTT 59.131 33.333 14.67 0.00 40.09 3.16
442 4686 6.647895 AGCCAAGCAGAACAAAATAAATTGAG 59.352 34.615 0.00 0.00 34.38 3.02
476 4720 6.819284 TCCAAAGTCAAAATTGAGCTGAAAT 58.181 32.000 0.00 0.00 37.98 2.17
480 4724 9.777575 CAAAGTCAAAATTGAGCTGAAATTTTT 57.222 25.926 19.61 8.46 41.95 1.94
517 4923 7.886629 ATTTGCTAGTCATGTATCATTTGGT 57.113 32.000 0.00 0.00 0.00 3.67
600 5096 4.911610 GTGCACAGCATACAGTTTTGTAAG 59.088 41.667 13.17 0.00 42.72 2.34
650 5150 6.573712 ATCTTCTTTCCTGCCTTAATCTCT 57.426 37.500 0.00 0.00 0.00 3.10
654 5154 6.723298 TCTTTCCTGCCTTAATCTCTCTAG 57.277 41.667 0.00 0.00 0.00 2.43
659 5159 4.280677 CCTGCCTTAATCTCTCTAGGTCTG 59.719 50.000 0.00 0.00 0.00 3.51
680 5180 7.327761 GGTCTGATTCAGAACACATGAAATTTG 59.672 37.037 23.78 0.00 46.41 2.32
706 5206 7.272948 GCATCTAGTCAGCAGAAATTTCTTTTG 59.727 37.037 18.16 17.48 34.74 2.44
727 5227 2.746279 TCCTGGTGGAATTTGTGTGT 57.254 45.000 0.00 0.00 39.87 3.72
728 5228 2.305928 TCCTGGTGGAATTTGTGTGTG 58.694 47.619 0.00 0.00 39.87 3.82
729 5229 2.031120 CCTGGTGGAATTTGTGTGTGT 58.969 47.619 0.00 0.00 34.57 3.72
730 5230 2.223782 CCTGGTGGAATTTGTGTGTGTG 60.224 50.000 0.00 0.00 34.57 3.82
731 5231 2.426738 CTGGTGGAATTTGTGTGTGTGT 59.573 45.455 0.00 0.00 0.00 3.72
732 5232 2.165234 TGGTGGAATTTGTGTGTGTGTG 59.835 45.455 0.00 0.00 0.00 3.82
733 5233 2.165437 GGTGGAATTTGTGTGTGTGTGT 59.835 45.455 0.00 0.00 0.00 3.72
734 5234 3.178267 GTGGAATTTGTGTGTGTGTGTG 58.822 45.455 0.00 0.00 0.00 3.82
735 5235 2.192624 GGAATTTGTGTGTGTGTGTGC 58.807 47.619 0.00 0.00 0.00 4.57
736 5236 1.845568 GAATTTGTGTGTGTGTGTGCG 59.154 47.619 0.00 0.00 0.00 5.34
737 5237 0.100325 ATTTGTGTGTGTGTGTGCGG 59.900 50.000 0.00 0.00 0.00 5.69
738 5238 1.927608 TTTGTGTGTGTGTGTGCGGG 61.928 55.000 0.00 0.00 0.00 6.13
739 5239 3.582120 GTGTGTGTGTGTGCGGGG 61.582 66.667 0.00 0.00 0.00 5.73
740 5240 4.866224 TGTGTGTGTGTGCGGGGG 62.866 66.667 0.00 0.00 0.00 5.40
774 5274 5.596361 TCATTTGCTCCAAACAAGGACTTAA 59.404 36.000 0.00 0.00 36.13 1.85
778 5278 3.304726 GCTCCAAACAAGGACTTAACAGC 60.305 47.826 0.00 0.00 33.19 4.40
793 5293 1.270907 ACAGCCAGGGAACTCTAGTG 58.729 55.000 0.00 0.00 40.21 2.74
873 5389 8.470657 AATAAAAAGAAAGAAGCAGAGGAAGT 57.529 30.769 0.00 0.00 0.00 3.01
881 5397 3.055458 AGAAGCAGAGGAAGTTAAGCTCC 60.055 47.826 0.00 0.00 0.00 4.70
883 5399 1.204941 GCAGAGGAAGTTAAGCTCCGA 59.795 52.381 0.00 0.00 0.00 4.55
918 5434 4.724279 AAATACCTCACCACCTTGTTCT 57.276 40.909 0.00 0.00 0.00 3.01
946 5462 4.594970 TCCAAAGAAACACAGAGTTCCAA 58.405 39.130 0.00 0.00 40.26 3.53
963 5495 0.610687 CAACAGAGGAGTGAGACCCC 59.389 60.000 0.00 0.00 0.00 4.95
966 5498 0.040351 CAGAGGAGTGAGACCCCAGA 59.960 60.000 0.00 0.00 0.00 3.86
1141 5682 0.106819 CCCTTCATGGCCTTCTCAGG 60.107 60.000 3.32 2.80 44.28 3.86
1172 5713 2.381589 TCTCTGTATATTTGACGCGCG 58.618 47.619 30.96 30.96 0.00 6.86
1379 5956 3.384146 ACTTTGTGTTTGATGCCACATGA 59.616 39.130 0.00 0.00 40.94 3.07
1382 5966 4.397481 TGTGTTTGATGCCACATGAAAA 57.603 36.364 0.00 0.00 36.70 2.29
1383 5967 4.763073 TGTGTTTGATGCCACATGAAAAA 58.237 34.783 0.00 0.00 36.70 1.94
1384 5968 5.366460 TGTGTTTGATGCCACATGAAAAAT 58.634 33.333 0.00 0.00 36.70 1.82
1385 5969 5.236695 TGTGTTTGATGCCACATGAAAAATG 59.763 36.000 0.00 0.00 36.70 2.32
1386 5970 5.236911 GTGTTTGATGCCACATGAAAAATGT 59.763 36.000 0.00 0.00 0.00 2.71
1389 5973 6.542574 TTGATGCCACATGAAAAATGTTTC 57.457 33.333 0.00 1.01 43.04 2.78
1620 6274 5.901552 TGTCATTGGGAAAGACAAGAAAAC 58.098 37.500 0.00 0.00 39.15 2.43
1683 6337 2.071778 ACATGTTCAGTGCCCAACTT 57.928 45.000 0.00 0.00 36.83 2.66
2023 6826 7.936496 TTTGGATCTAACATGCATAAGTCAA 57.064 32.000 0.00 2.84 0.00 3.18
2073 7012 6.422333 ACTTTCCATTTGGTTCCAAACATTT 58.578 32.000 17.59 1.34 38.52 2.32
2074 7013 7.569240 ACTTTCCATTTGGTTCCAAACATTTA 58.431 30.769 17.59 5.09 38.52 1.40
2075 7014 8.217111 ACTTTCCATTTGGTTCCAAACATTTAT 58.783 29.630 17.59 0.34 38.52 1.40
2076 7015 8.986929 TTTCCATTTGGTTCCAAACATTTATT 57.013 26.923 17.59 0.00 38.52 1.40
2085 7024 8.625651 TGGTTCCAAACATTTATTATACCATCG 58.374 33.333 0.00 0.00 0.00 3.84
2086 7025 8.626526 GGTTCCAAACATTTATTATACCATCGT 58.373 33.333 0.00 0.00 0.00 3.73
2092 7042 9.724839 AAACATTTATTATACCATCGTTTTCCG 57.275 29.630 0.00 0.00 38.13 4.30
2298 7275 9.709495 TTCTGATGCCCATAATAAATAAAATGC 57.291 29.630 0.00 0.00 0.00 3.56
2332 7309 5.888982 TTTGAGTCTTTCAGGTTAGAGGT 57.111 39.130 0.00 0.00 37.07 3.85
2468 7445 2.743126 TCACTAAAAATTACCCACGCCG 59.257 45.455 0.00 0.00 0.00 6.46
2661 7669 2.103373 TCGGATCCTGTTCTGAAGGAG 58.897 52.381 10.75 0.00 46.85 3.69
2713 7721 2.873472 GGAGCTCAGATTCAGATGCAAG 59.127 50.000 17.19 0.00 0.00 4.01
2746 7761 5.238650 GCTCTTGAAACTAGTAAACCTTGCA 59.761 40.000 0.00 0.00 0.00 4.08
2753 7768 8.904834 TGAAACTAGTAAACCTTGCATGTTTTA 58.095 29.630 16.96 8.75 37.18 1.52
2763 7778 9.786105 AAACCTTGCATGTTTTAAAAAGATTTG 57.214 25.926 1.31 0.00 32.17 2.32
2850 13181 1.557269 AAGCAGCTCGGATGGGTTCT 61.557 55.000 0.00 0.00 0.00 3.01
2913 13247 4.271049 CCATTCGCGTCTCTGAATAATGTT 59.729 41.667 5.77 0.00 33.23 2.71
2914 13248 5.427082 CATTCGCGTCTCTGAATAATGTTC 58.573 41.667 5.77 0.00 33.23 3.18
2915 13249 3.105937 TCGCGTCTCTGAATAATGTTCG 58.894 45.455 5.77 0.00 0.00 3.95
2916 13250 3.105937 CGCGTCTCTGAATAATGTTCGA 58.894 45.455 0.00 0.00 0.00 3.71
2961 13299 4.378459 CCTTAACGAGAACAAATCAGTGCC 60.378 45.833 0.00 0.00 0.00 5.01
3003 13345 3.071602 ACTGTATGATGCTCCCGCTTATT 59.928 43.478 0.00 0.00 36.97 1.40
3205 16592 1.134310 CCCTGAGCATGCATGTCACTA 60.134 52.381 26.79 9.31 0.00 2.74
3212 16599 5.416639 TGAGCATGCATGTCACTAAGAATTT 59.583 36.000 26.79 1.02 0.00 1.82
3214 16601 4.802039 GCATGCATGTCACTAAGAATTTGG 59.198 41.667 26.79 0.00 0.00 3.28
3252 16639 4.582701 TCACACAAAAATAAGCACAGGG 57.417 40.909 0.00 0.00 0.00 4.45
3256 16643 5.634859 CACACAAAAATAAGCACAGGGAATC 59.365 40.000 0.00 0.00 0.00 2.52
3258 16645 5.865552 CACAAAAATAAGCACAGGGAATCAG 59.134 40.000 0.00 0.00 0.00 2.90
3267 16655 4.414846 AGCACAGGGAATCAGAGGAATAAT 59.585 41.667 0.00 0.00 0.00 1.28
3299 16687 8.166726 AGTGAGAAAAGGTTTATTGATCCTCTT 58.833 33.333 0.00 0.00 0.00 2.85
3300 16688 8.239998 GTGAGAAAAGGTTTATTGATCCTCTTG 58.760 37.037 0.00 0.00 0.00 3.02
3301 16689 7.944554 TGAGAAAAGGTTTATTGATCCTCTTGT 59.055 33.333 0.00 0.00 0.00 3.16
3312 16701 6.834168 TTGATCCTCTTGTGGGAAATTAAC 57.166 37.500 0.00 0.00 36.37 2.01
3315 16704 7.638444 TGATCCTCTTGTGGGAAATTAACATA 58.362 34.615 0.00 0.00 36.37 2.29
3317 16706 9.136323 GATCCTCTTGTGGGAAATTAACATAAT 57.864 33.333 0.00 0.00 36.37 1.28
3360 16749 9.010029 AGGGTTGTAGAAATACATTTTGTACAG 57.990 33.333 0.00 0.00 35.42 2.74
3407 16796 5.569059 CGGTTTTGCTTGTGATTATTGACTC 59.431 40.000 0.00 0.00 0.00 3.36
3430 16819 1.040339 TTTTTGCCACTGGTCGCCTT 61.040 50.000 0.00 0.00 0.00 4.35
3462 16867 6.115446 TCTTTCTGAGTGTGTGATTTCTGTT 58.885 36.000 0.00 0.00 0.00 3.16
3485 16890 7.716560 TGTTGATTCCATCTCAGTTATGTATGG 59.283 37.037 0.00 0.00 39.95 2.74
3509 16914 5.005779 GTGTTATAGCTTGGATCAGTTCACG 59.994 44.000 0.00 0.00 0.00 4.35
3518 16923 3.265791 GGATCAGTTCACGCTTCAGAAT 58.734 45.455 0.00 0.00 0.00 2.40
3559 16964 5.057149 GGACCTTTTGATCATGTATACGCT 58.943 41.667 0.00 0.00 0.00 5.07
3602 17008 5.884792 GCTATATTCAGGCTGCAAGGATTAT 59.115 40.000 10.34 1.71 0.00 1.28
3607 17013 4.343231 TCAGGCTGCAAGGATTATTTTCA 58.657 39.130 10.34 0.00 0.00 2.69
3637 17043 8.245195 TGGTAATCTTTTGGCCCTTATATTTC 57.755 34.615 0.00 0.00 0.00 2.17
3685 17091 4.932146 ACACCAGTTGCACATTTTCTAAC 58.068 39.130 0.00 0.00 0.00 2.34
3713 17124 7.927092 TGTGTAACTACTTGTAATGTGCAACTA 59.073 33.333 0.00 0.00 35.72 2.24
3718 17129 9.496873 AACTACTTGTAATGTGCAACTATGTTA 57.503 29.630 0.00 0.00 38.04 2.41
3762 17176 3.288092 GGTCTCCAAACTCTGTTTGGTT 58.712 45.455 29.63 2.14 46.75 3.67
3772 17186 4.196971 ACTCTGTTTGGTTTGTGGTACTC 58.803 43.478 0.00 0.00 0.00 2.59
3781 17199 6.436738 TGGTTTGTGGTACTCCTAATACAA 57.563 37.500 0.00 0.00 34.23 2.41
3820 17238 1.635487 AGATGTGCCACCCATGTACTT 59.365 47.619 0.00 0.00 0.00 2.24
3821 17239 2.843730 AGATGTGCCACCCATGTACTTA 59.156 45.455 0.00 0.00 0.00 2.24
3859 17283 7.033791 GGTTCATTTGATTCTCTACTCGTACA 58.966 38.462 0.00 0.00 0.00 2.90
3860 17284 7.707035 GGTTCATTTGATTCTCTACTCGTACAT 59.293 37.037 0.00 0.00 0.00 2.29
3861 17285 9.088512 GTTCATTTGATTCTCTACTCGTACATT 57.911 33.333 0.00 0.00 0.00 2.71
3862 17286 9.653287 TTCATTTGATTCTCTACTCGTACATTT 57.347 29.630 0.00 0.00 0.00 2.32
3863 17287 9.653287 TCATTTGATTCTCTACTCGTACATTTT 57.347 29.630 0.00 0.00 0.00 1.82
3864 17288 9.694520 CATTTGATTCTCTACTCGTACATTTTG 57.305 33.333 0.00 0.00 0.00 2.44
3865 17289 9.653287 ATTTGATTCTCTACTCGTACATTTTGA 57.347 29.630 0.00 0.00 0.00 2.69
3866 17290 9.653287 TTTGATTCTCTACTCGTACATTTTGAT 57.347 29.630 0.00 0.00 0.00 2.57
3867 17291 9.653287 TTGATTCTCTACTCGTACATTTTGATT 57.347 29.630 0.00 0.00 0.00 2.57
3868 17292 9.653287 TGATTCTCTACTCGTACATTTTGATTT 57.347 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 9.461312 ACTCCATGAAGCAACATAGTATAAAAA 57.539 29.630 0.00 0.00 0.00 1.94
45 46 8.892723 CACTCCATGAAGCAACATAGTATAAAA 58.107 33.333 0.00 0.00 0.00 1.52
46 47 7.498900 CCACTCCATGAAGCAACATAGTATAAA 59.501 37.037 0.00 0.00 0.00 1.40
47 48 6.992123 CCACTCCATGAAGCAACATAGTATAA 59.008 38.462 0.00 0.00 0.00 0.98
48 49 6.326323 TCCACTCCATGAAGCAACATAGTATA 59.674 38.462 0.00 0.00 0.00 1.47
49 50 5.130975 TCCACTCCATGAAGCAACATAGTAT 59.869 40.000 0.00 0.00 0.00 2.12
50 51 4.469586 TCCACTCCATGAAGCAACATAGTA 59.530 41.667 0.00 0.00 0.00 1.82
51 52 3.264193 TCCACTCCATGAAGCAACATAGT 59.736 43.478 0.00 0.00 0.00 2.12
52 53 3.875727 CTCCACTCCATGAAGCAACATAG 59.124 47.826 0.00 0.00 0.00 2.23
55 56 1.699083 TCTCCACTCCATGAAGCAACA 59.301 47.619 0.00 0.00 0.00 3.33
57 58 3.009363 TCAATCTCCACTCCATGAAGCAA 59.991 43.478 0.00 0.00 0.00 3.91
58 59 2.573009 TCAATCTCCACTCCATGAAGCA 59.427 45.455 0.00 0.00 0.00 3.91
59 60 3.272574 TCAATCTCCACTCCATGAAGC 57.727 47.619 0.00 0.00 0.00 3.86
63 3360 2.679837 CGGTTTCAATCTCCACTCCATG 59.320 50.000 0.00 0.00 0.00 3.66
136 4142 6.208599 GGGTATGCTTATTGCTAGCCAAATAA 59.791 38.462 13.29 14.77 43.37 1.40
153 4159 4.227300 TGTTCACTATGAAAGGGGTATGCT 59.773 41.667 0.00 0.00 38.22 3.79
159 4165 3.506067 GGTTGTGTTCACTATGAAAGGGG 59.494 47.826 4.59 0.00 38.22 4.79
200 4206 6.603201 GGTTCCCATTTCTGTCTTGATCATAA 59.397 38.462 0.00 0.00 0.00 1.90
393 4413 8.385858 GCTGTACATGATACACATATATGCAAG 58.614 37.037 12.79 5.83 37.46 4.01
442 4686 8.599774 TCAATTTTGACTTTGGAAATTCGAAAC 58.400 29.630 0.00 0.00 35.27 2.78
480 4724 6.121590 TGACTAGCAAATAATGAGGCATCAA 58.878 36.000 4.62 0.00 39.39 2.57
572 4978 1.147473 CTGTATGCTGTGCACGACAA 58.853 50.000 13.13 0.00 43.04 3.18
619 5115 6.072199 AGGCAGGAAAGAAGATTTAGACAT 57.928 37.500 0.00 0.00 0.00 3.06
637 5137 5.136828 TCAGACCTAGAGAGATTAAGGCAG 58.863 45.833 0.00 0.00 31.98 4.85
650 5150 5.716703 TCATGTGTTCTGAATCAGACCTAGA 59.283 40.000 13.17 4.11 40.46 2.43
654 5154 5.947228 TTTCATGTGTTCTGAATCAGACC 57.053 39.130 13.17 6.66 40.46 3.85
659 5159 7.544566 AGATGCAAATTTCATGTGTTCTGAATC 59.455 33.333 0.00 0.00 32.94 2.52
680 5180 6.434018 AAGAAATTTCTGCTGACTAGATGC 57.566 37.500 21.15 0.00 37.65 3.91
722 5222 3.582120 CCCCGCACACACACACAC 61.582 66.667 0.00 0.00 0.00 3.82
723 5223 4.866224 CCCCCGCACACACACACA 62.866 66.667 0.00 0.00 0.00 3.72
745 5245 0.608130 GTTTGGAGCAAATGACCCCC 59.392 55.000 0.00 0.00 35.74 5.40
746 5246 1.337118 TGTTTGGAGCAAATGACCCC 58.663 50.000 0.00 0.00 35.74 4.95
747 5247 2.289010 CCTTGTTTGGAGCAAATGACCC 60.289 50.000 0.00 0.00 35.74 4.46
748 5248 2.627699 TCCTTGTTTGGAGCAAATGACC 59.372 45.455 0.00 0.00 35.74 4.02
749 5249 3.319122 AGTCCTTGTTTGGAGCAAATGAC 59.681 43.478 0.00 0.00 35.74 3.06
774 5274 1.270907 CACTAGAGTTCCCTGGCTGT 58.729 55.000 0.00 0.00 0.00 4.40
778 5278 4.469945 TGTAATTCCACTAGAGTTCCCTGG 59.530 45.833 0.00 0.00 0.00 4.45
793 5293 7.672983 TTCTTCTCAAGTGATGTGTAATTCC 57.327 36.000 0.00 0.00 0.00 3.01
918 5434 4.136796 CTCTGTGTTTCTTTGGATGGTGA 58.863 43.478 0.00 0.00 0.00 4.02
946 5462 0.252012 CTGGGGTCTCACTCCTCTGT 60.252 60.000 0.00 0.00 40.26 3.41
963 5495 0.590195 GAGCTGTGGTTTGCACTCTG 59.410 55.000 0.00 0.00 0.00 3.35
966 5498 1.450531 GCTGAGCTGTGGTTTGCACT 61.451 55.000 0.00 0.00 0.00 4.40
983 5515 1.544917 ATGGTGGGGGAAGAAGGCT 60.545 57.895 0.00 0.00 0.00 4.58
1036 5570 1.144936 CGATTGGGAGCAGGAGGAC 59.855 63.158 0.00 0.00 0.00 3.85
1118 5655 0.035056 AGAAGGCCATGAAGGGTTCG 60.035 55.000 5.01 0.00 38.09 3.95
1141 5682 8.178313 GTCAAATATACAGAGAAAACCTCAAGC 58.822 37.037 0.00 0.00 44.40 4.01
1172 5713 1.807142 GGCTGCAGAGGTACAGAAAAC 59.193 52.381 20.43 0.00 35.90 2.43
1379 5956 7.276878 CCTCTGTGGTAAAAACGAAACATTTTT 59.723 33.333 0.00 0.00 41.11 1.94
1382 5966 5.735070 GCCTCTGTGGTAAAAACGAAACATT 60.735 40.000 0.00 0.00 38.35 2.71
1383 5967 4.261447 GCCTCTGTGGTAAAAACGAAACAT 60.261 41.667 0.00 0.00 38.35 2.71
1384 5968 3.065648 GCCTCTGTGGTAAAAACGAAACA 59.934 43.478 0.00 0.00 38.35 2.83
1385 5969 3.549423 GGCCTCTGTGGTAAAAACGAAAC 60.549 47.826 0.00 0.00 38.35 2.78
1386 5970 2.619646 GGCCTCTGTGGTAAAAACGAAA 59.380 45.455 0.00 0.00 38.35 3.46
1389 5973 1.265905 GTGGCCTCTGTGGTAAAAACG 59.734 52.381 3.32 0.00 38.35 3.60
1620 6274 1.140161 TCGTACCCGAAAGCGATGG 59.860 57.895 0.00 0.00 40.86 3.51
1662 6316 3.222173 AGTTGGGCACTGAACATGTAA 57.778 42.857 0.00 0.00 32.83 2.41
1663 6317 2.949177 AGTTGGGCACTGAACATGTA 57.051 45.000 0.00 0.00 32.83 2.29
1664 6318 2.071778 AAGTTGGGCACTGAACATGT 57.928 45.000 0.00 0.00 35.12 3.21
1683 6337 5.450274 CCGTGCATCATCAACATCCAAATAA 60.450 40.000 0.00 0.00 0.00 1.40
2018 6821 9.678260 AAGCAATAATGATACTCTTCTTTGACT 57.322 29.630 0.00 0.00 0.00 3.41
2085 7024 3.396560 AGTAGTACAACCTGCGGAAAAC 58.603 45.455 2.52 0.00 0.00 2.43
2086 7025 3.069872 TGAGTAGTACAACCTGCGGAAAA 59.930 43.478 2.52 0.00 0.00 2.29
2092 7042 2.353803 CCAGGTGAGTAGTACAACCTGC 60.354 54.545 31.32 9.69 42.30 4.85
2099 7049 1.682323 GCTAGGCCAGGTGAGTAGTAC 59.318 57.143 5.01 0.00 0.00 2.73
2661 7669 4.509600 CCTCCGATCAAGATAAAGTTCAGC 59.490 45.833 0.00 0.00 0.00 4.26
2713 7721 2.576615 AGTTTCAAGAGCCTGGACAAC 58.423 47.619 0.00 0.00 0.00 3.32
2761 7776 5.592282 TGCAGAACAGAGGTTGAAATTACAA 59.408 36.000 0.00 0.00 37.36 2.41
2763 7778 5.689383 TGCAGAACAGAGGTTGAAATTAC 57.311 39.130 0.00 0.00 37.36 1.89
2871 13202 1.134401 GGATGACGGATTCAAGCTCCA 60.134 52.381 0.00 0.00 37.92 3.86
2915 13249 6.758886 AGGTTTTTGTCTATGTCGATCTGATC 59.241 38.462 7.60 7.60 0.00 2.92
2916 13250 6.644347 AGGTTTTTGTCTATGTCGATCTGAT 58.356 36.000 0.00 0.00 0.00 2.90
3003 13345 7.011950 CCTCAGTATGCCAACATTTTATTCGTA 59.988 37.037 0.00 0.00 37.74 3.43
3082 16421 3.340064 TGGTAGGAGGACCATGCAT 57.660 52.632 0.00 0.00 44.79 3.96
3152 16491 2.285977 CTGTGCATGCAATAGCTCTGA 58.714 47.619 24.58 0.00 42.74 3.27
3205 16592 9.631257 AACAATTCAAAGATTTCCCAAATTCTT 57.369 25.926 0.00 0.00 36.91 2.52
3212 16599 6.127225 TGTGTGAACAATTCAAAGATTTCCCA 60.127 34.615 0.00 0.00 42.15 4.37
3214 16601 7.769272 TTGTGTGAACAATTCAAAGATTTCC 57.231 32.000 0.00 0.00 42.15 3.13
3252 16639 7.950512 TCACTCTCTCATTATTCCTCTGATTC 58.049 38.462 0.00 0.00 0.00 2.52
3256 16643 6.957920 TCTCACTCTCTCATTATTCCTCTG 57.042 41.667 0.00 0.00 0.00 3.35
3258 16645 7.710475 CCTTTTCTCACTCTCTCATTATTCCTC 59.290 40.741 0.00 0.00 0.00 3.71
3267 16655 7.735917 TCAATAAACCTTTTCTCACTCTCTCA 58.264 34.615 0.00 0.00 0.00 3.27
3299 16687 8.415950 AGTGTTGATTATGTTAATTTCCCACA 57.584 30.769 0.00 0.00 0.00 4.17
3346 16735 8.686334 GGGTCATCAAATCTGTACAAAATGTAT 58.314 33.333 0.00 0.00 35.05 2.29
3348 16737 6.721208 AGGGTCATCAAATCTGTACAAAATGT 59.279 34.615 0.00 0.00 0.00 2.71
3360 16749 6.128172 CCGCATAAGATTAGGGTCATCAAATC 60.128 42.308 0.00 0.00 0.00 2.17
3430 16819 7.447374 TCACACACTCAGAAAGAAAGAAAAA 57.553 32.000 0.00 0.00 0.00 1.94
3435 16824 7.130917 CAGAAATCACACACTCAGAAAGAAAG 58.869 38.462 0.00 0.00 0.00 2.62
3437 16826 6.115446 ACAGAAATCACACACTCAGAAAGAA 58.885 36.000 0.00 0.00 0.00 2.52
3439 16828 5.998454 ACAGAAATCACACACTCAGAAAG 57.002 39.130 0.00 0.00 0.00 2.62
3441 16830 5.427378 TCAACAGAAATCACACACTCAGAA 58.573 37.500 0.00 0.00 0.00 3.02
3443 16832 5.936686 ATCAACAGAAATCACACACTCAG 57.063 39.130 0.00 0.00 0.00 3.35
3446 16835 5.132502 TGGAATCAACAGAAATCACACACT 58.867 37.500 0.00 0.00 0.00 3.55
3485 16890 5.005779 CGTGAACTGATCCAAGCTATAACAC 59.994 44.000 0.00 0.00 0.00 3.32
3509 16914 4.526970 TGGACCTCCAATAATTCTGAAGC 58.473 43.478 0.00 0.00 44.35 3.86
3518 16923 3.144068 TCCATCCTGGACCTCCAATAA 57.856 47.619 0.00 0.00 46.97 1.40
3590 16996 6.127253 ACCATTCCTGAAAATAATCCTTGCAG 60.127 38.462 0.00 0.00 0.00 4.41
3602 17008 6.463360 GCCAAAAGATTACCATTCCTGAAAA 58.537 36.000 0.00 0.00 0.00 2.29
3607 17013 3.012844 AGGGCCAAAAGATTACCATTCCT 59.987 43.478 6.18 0.00 0.00 3.36
3644 17050 4.455877 GGTGTAGATTAAAAGTGCAGCTGT 59.544 41.667 16.64 0.00 0.00 4.40
3685 17091 7.127917 TGCACATTACAAGTAGTTACACATG 57.872 36.000 0.00 0.00 0.00 3.21
3718 17129 9.561069 GACCCATAGTACAAATAACAGAATCAT 57.439 33.333 0.00 0.00 0.00 2.45
3762 17176 7.913789 ACTGATTTGTATTAGGAGTACCACAA 58.086 34.615 0.00 0.00 38.94 3.33
3772 17186 8.649841 CAAAATGTGCAACTGATTTGTATTAGG 58.350 33.333 0.00 0.00 37.54 2.69
3781 17199 6.422701 CACATCTTCAAAATGTGCAACTGATT 59.577 34.615 3.56 0.00 45.23 2.57
3807 17225 5.129634 TGCACATTATAAGTACATGGGTGG 58.870 41.667 0.00 0.00 0.00 4.61
3820 17238 7.459795 TCAAATGAACCAGTTGCACATTATA 57.540 32.000 2.68 0.00 38.97 0.98
3821 17239 6.343716 TCAAATGAACCAGTTGCACATTAT 57.656 33.333 2.68 0.00 38.97 1.28


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

AutoCloner maintained by Alex Coulton.