Multiple sequence alignment - TraesCS6A01G117100

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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 TraesCS6A01G117100 chr6A 100.000 6554 0 0 1 6554 87646743 87653296 0.000000e+00 12104.0
1 TraesCS6A01G117100 chr6A 88.462 208 22 2 1 208 593957576 593957371 3.920000e-62 250.0
2 TraesCS6A01G117100 chr6A 82.439 205 34 2 4 208 10912673 10912875 1.880000e-40 178.0
3 TraesCS6A01G117100 chr6D 94.331 3934 126 36 1759 5628 69927319 69931219 0.000000e+00 5939.0
4 TraesCS6A01G117100 chr6D 94.416 985 39 6 787 1766 69925048 69926021 0.000000e+00 1500.0
5 TraesCS6A01G117100 chr6D 94.007 801 29 9 1 793 69917769 69918558 0.000000e+00 1195.0
6 TraesCS6A01G117100 chr6D 86.704 707 66 6 1 706 69847689 69848368 0.000000e+00 760.0
7 TraesCS6A01G117100 chr6D 82.385 545 55 20 6026 6554 69931830 69932349 2.810000e-118 436.0
8 TraesCS6A01G117100 chr6B 96.354 2194 68 5 1693 3876 144889181 144891372 0.000000e+00 3598.0
9 TraesCS6A01G117100 chr6B 95.716 887 29 4 810 1695 144887619 144888497 0.000000e+00 1419.0
10 TraesCS6A01G117100 chr6B 91.756 837 46 13 4737 5567 144892490 144893309 0.000000e+00 1142.0
11 TraesCS6A01G117100 chr6B 91.834 747 33 6 12 757 144850584 144851303 0.000000e+00 1016.0
12 TraesCS6A01G117100 chr6B 91.496 682 22 11 3867 4522 144891684 144892355 0.000000e+00 905.0
13 TraesCS6A01G117100 chr6B 94.157 599 19 4 1008 1605 144795259 144795842 0.000000e+00 898.0
14 TraesCS6A01G117100 chr6B 86.243 567 51 9 441 993 144792903 144793456 2.040000e-164 590.0
15 TraesCS6A01G117100 chr6B 86.506 541 43 18 6024 6554 144919765 144920285 9.540000e-158 568.0
16 TraesCS6A01G117100 chr6B 90.036 281 21 5 5342 5620 144918837 144919112 2.250000e-94 357.0
17 TraesCS6A01G117100 chr6B 92.381 210 11 5 5702 5909 144919117 144919323 1.790000e-75 294.0
18 TraesCS6A01G117100 chr6B 97.436 78 2 0 4609 4686 144892404 144892481 4.120000e-27 134.0
19 TraesCS6A01G117100 chr6B 87.302 63 3 1 6026 6088 144896140 144896197 4.240000e-07 67.6
20 TraesCS6A01G117100 chr2B 87.859 313 19 9 5425 5736 756670685 756670979 3.760000e-92 350.0
21 TraesCS6A01G117100 chr2B 85.034 147 19 2 6026 6169 756673627 756673773 5.300000e-31 147.0
22 TraesCS6A01G117100 chr2B 78.571 210 35 8 1 204 613235505 613235300 5.330000e-26 130.0
23 TraesCS6A01G117100 chr2B 77.143 210 37 7 1 209 21740827 21741026 1.930000e-20 111.0
24 TraesCS6A01G117100 chr2B 92.000 75 6 0 5946 6020 756673504 756673578 8.990000e-19 106.0
25 TraesCS6A01G117100 chr3B 87.736 212 23 3 3 213 783147878 783148087 1.830000e-60 244.0
26 TraesCS6A01G117100 chr4A 82.160 213 30 6 1 208 7178932 7179141 6.750000e-40 176.0
27 TraesCS6A01G117100 chr7B 80.488 205 32 6 1 199 695092807 695093009 4.090000e-32 150.0


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 TraesCS6A01G117100 chr6A 87646743 87653296 6553 False 12104.000000 12104 100.000000 1 6554 1 chr6A.!!$F2 6553
1 TraesCS6A01G117100 chr6D 69925048 69932349 7301 False 2625.000000 5939 90.377333 787 6554 3 chr6D.!!$F3 5767
2 TraesCS6A01G117100 chr6D 69917769 69918558 789 False 1195.000000 1195 94.007000 1 793 1 chr6D.!!$F2 792
3 TraesCS6A01G117100 chr6D 69847689 69848368 679 False 760.000000 760 86.704000 1 706 1 chr6D.!!$F1 705
4 TraesCS6A01G117100 chr6B 144887619 144896197 8578 False 1210.933333 3598 93.343333 810 6088 6 chr6B.!!$F3 5278
5 TraesCS6A01G117100 chr6B 144850584 144851303 719 False 1016.000000 1016 91.834000 12 757 1 chr6B.!!$F1 745
6 TraesCS6A01G117100 chr6B 144792903 144795842 2939 False 744.000000 898 90.200000 441 1605 2 chr6B.!!$F2 1164
7 TraesCS6A01G117100 chr6B 144918837 144920285 1448 False 406.333333 568 89.641000 5342 6554 3 chr6B.!!$F4 1212
8 TraesCS6A01G117100 chr2B 756670685 756673773 3088 False 201.000000 350 88.297667 5425 6169 3 chr2B.!!$F2 744

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
518 525 0.323633 CAGCACCAACCCCATCATCA 60.324 55.000 0.00 0.0 0.00 3.07 F
1345 3169 0.179045 CAAATCTCGGGTGGGCCTAG 60.179 60.000 4.53 0.0 34.45 3.02 F
1500 3324 1.303282 GCCTCAAATCCTCCCCGTT 59.697 57.895 0.00 0.0 0.00 4.44 F
1660 3489 1.351707 GATGTATGTGCCCGTTGCG 59.648 57.895 0.00 0.0 45.60 4.85 F
3388 7222 1.765314 AGCGGAGATATTGGAGCTGTT 59.235 47.619 0.00 0.0 33.31 3.16 F
4782 9015 1.675714 GCATTCACCATGACCGACTGA 60.676 52.381 0.00 0.0 34.31 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 4228 0.316442 CGTCTGCAACACAGCACAAG 60.316 55.000 0.00 0.0 46.76 3.16 R
2574 6399 0.524862 CCACAAGCTTGTCCTGCATC 59.475 55.000 28.97 0.0 39.91 3.91 R
3069 6903 4.090761 AGAGAAACATCAAAGTCTGGCA 57.909 40.909 0.00 0.0 0.00 4.92 R
3555 7389 3.507162 TGGAACATTGCAAGGAGAAGA 57.493 42.857 19.41 0.0 0.00 2.87 R
4890 9124 1.118838 GGTCTGGCAGAGCTACTCAT 58.881 55.000 33.17 0.0 39.50 2.90 R
6023 14852 0.039256 CCGCCATCTGTGTTGTTTGG 60.039 55.000 0.00 0.0 0.00 3.28 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
180 184 2.151502 ACCCAACAACACCAATGACA 57.848 45.000 0.00 0.00 0.00 3.58
189 193 2.378038 ACACCAATGACACAGCAAAGT 58.622 42.857 0.00 0.00 0.00 2.66
286 290 4.699257 GTCCAGTCTCCTCTAAACGAGTTA 59.301 45.833 0.00 0.00 38.11 2.24
424 431 9.755122 AAATAAGAAATTGCTACCTAGACCTTT 57.245 29.630 0.00 0.00 0.00 3.11
425 432 8.738645 ATAAGAAATTGCTACCTAGACCTTTG 57.261 34.615 0.00 0.00 0.00 2.77
515 522 1.379916 CTCAGCACCAACCCCATCA 59.620 57.895 0.00 0.00 0.00 3.07
518 525 0.323633 CAGCACCAACCCCATCATCA 60.324 55.000 0.00 0.00 0.00 3.07
544 551 2.609737 GGACGATGTTGACTTTCTCCGT 60.610 50.000 0.00 0.00 0.00 4.69
612 619 3.049708 CAGAAGTGGAAGATGCAGACA 57.950 47.619 0.00 0.00 0.00 3.41
904 924 0.981183 ACACAGCCCGAACTGGAATA 59.019 50.000 9.11 0.00 42.21 1.75
1176 2989 0.765135 TTCTCCCCAACCTTCCACGA 60.765 55.000 0.00 0.00 0.00 4.35
1177 2990 1.003718 CTCCCCAACCTTCCACGAC 60.004 63.158 0.00 0.00 0.00 4.34
1178 2991 2.358247 CCCCAACCTTCCACGACG 60.358 66.667 0.00 0.00 0.00 5.12
1335 3159 2.683362 GCCTAAACCTTCCAAATCTCGG 59.317 50.000 0.00 0.00 0.00 4.63
1336 3160 3.279434 CCTAAACCTTCCAAATCTCGGG 58.721 50.000 0.00 0.00 0.00 5.14
1337 3161 2.971901 AAACCTTCCAAATCTCGGGT 57.028 45.000 0.00 0.00 0.00 5.28
1338 3162 2.200373 AACCTTCCAAATCTCGGGTG 57.800 50.000 0.00 0.00 0.00 4.61
1339 3163 0.328258 ACCTTCCAAATCTCGGGTGG 59.672 55.000 0.00 0.00 0.00 4.61
1340 3164 0.394352 CCTTCCAAATCTCGGGTGGG 60.394 60.000 0.00 0.00 32.95 4.61
1341 3165 1.001393 TTCCAAATCTCGGGTGGGC 60.001 57.895 0.00 0.00 32.95 5.36
1342 3166 2.440247 CCAAATCTCGGGTGGGCC 60.440 66.667 0.00 0.00 0.00 5.80
1343 3167 2.677228 CAAATCTCGGGTGGGCCT 59.323 61.111 4.53 0.00 34.45 5.19
1344 3168 1.632018 CCAAATCTCGGGTGGGCCTA 61.632 60.000 4.53 0.00 34.45 3.93
1345 3169 0.179045 CAAATCTCGGGTGGGCCTAG 60.179 60.000 4.53 0.00 34.45 3.02
1371 3195 2.023414 TTCGGAGTGTCACTTGCCGT 62.023 55.000 24.59 0.00 37.05 5.68
1373 3197 1.557443 CGGAGTGTCACTTGCCGTTC 61.557 60.000 19.94 2.08 32.76 3.95
1484 3308 3.339141 CTTCCCTACTCAAACTTCTGCC 58.661 50.000 0.00 0.00 0.00 4.85
1500 3324 1.303282 GCCTCAAATCCTCCCCGTT 59.697 57.895 0.00 0.00 0.00 4.44
1587 3416 5.022021 GCACGTAGATTTGTTGCAGAATAC 58.978 41.667 0.00 0.00 0.00 1.89
1609 3438 1.554583 TTATGGGCTGGGTGCGTACA 61.555 55.000 5.86 0.00 44.05 2.90
1660 3489 1.351707 GATGTATGTGCCCGTTGCG 59.648 57.895 0.00 0.00 45.60 4.85
1713 4228 4.333926 CCTACAGCAAATCCTTAGAACAGC 59.666 45.833 0.00 0.00 0.00 4.40
1756 4271 5.711976 GGCCACCATTTCTAGCATATGTTAT 59.288 40.000 0.00 0.00 0.00 1.89
1795 5615 3.675225 CCTGTCGCCGATTCATATAACTG 59.325 47.826 0.00 0.00 0.00 3.16
1796 5616 4.546570 CTGTCGCCGATTCATATAACTGA 58.453 43.478 0.00 0.00 0.00 3.41
1822 5642 2.783135 TCTTTCATCTTGGTGGCAGTC 58.217 47.619 0.00 0.00 0.00 3.51
1831 5651 3.365265 GTGGCAGTCGGCTTTGGG 61.365 66.667 0.00 0.00 44.01 4.12
1873 5693 4.015872 TGATCTACTTTGGCTTTCCGTT 57.984 40.909 0.00 0.00 34.14 4.44
1890 5710 2.482235 CGTTATTGTGTCGCGTTCTTG 58.518 47.619 5.77 0.00 0.00 3.02
1900 5720 1.781025 CGCGTTCTTGCCAAGACCAA 61.781 55.000 6.65 0.00 37.23 3.67
1907 5727 4.365514 TCTTGCCAAGACCAATGTTCTA 57.634 40.909 2.24 0.00 31.20 2.10
1922 5742 8.035394 ACCAATGTTCTATATAAGTGGATAGCG 58.965 37.037 5.80 0.00 0.00 4.26
1930 5750 6.787085 ATATAAGTGGATAGCGCTTGTTTC 57.213 37.500 18.68 8.04 0.00 2.78
1931 5751 2.472695 AGTGGATAGCGCTTGTTTCA 57.527 45.000 18.68 2.97 0.00 2.69
2036 5860 5.065731 GTGATGCTTTCTTCTGATTCCGATT 59.934 40.000 0.00 0.00 0.00 3.34
2434 6259 4.273724 AGAAAAGTTCCTGCGAAAAGAGAC 59.726 41.667 0.00 0.00 0.00 3.36
2476 6301 5.112686 GCTCCCATTCTAGTTAGTGACTTG 58.887 45.833 0.00 0.00 39.86 3.16
2565 6390 3.335579 ACAACCCGAAGATGAAGCTAAC 58.664 45.455 0.00 0.00 0.00 2.34
2574 6399 5.220303 CGAAGATGAAGCTAACGAGGAAAAG 60.220 44.000 0.00 0.00 0.00 2.27
2869 6702 6.763715 AGGTATGATAAGTTCTAATGGCCA 57.236 37.500 8.56 8.56 0.00 5.36
3089 6923 4.836125 TTGCCAGACTTTGATGTTTCTC 57.164 40.909 0.00 0.00 0.00 2.87
3259 7093 5.692115 TGCCTGGAAGAGATTATTACACA 57.308 39.130 0.00 0.00 34.07 3.72
3388 7222 1.765314 AGCGGAGATATTGGAGCTGTT 59.235 47.619 0.00 0.00 33.31 3.16
3790 7624 5.640357 GGTTTGTCGACCATAACATGAGTTA 59.360 40.000 14.12 0.00 43.83 2.24
3892 8048 9.793252 GATGTATTAGTTGCATTCTGTTTCAAT 57.207 29.630 0.00 0.00 29.94 2.57
3905 8061 2.288948 TGTTTCAATGGATGCAACTGCC 60.289 45.455 0.00 0.00 36.32 4.85
3911 8067 2.113860 TGGATGCAACTGCCTACTTC 57.886 50.000 0.00 0.00 41.18 3.01
4054 8210 5.233902 GCTATCTGCTGTCAGTTGTAATCAG 59.766 44.000 0.93 0.00 41.10 2.90
4243 8452 6.978674 TTTCTCACAATCGGTATCCTCTAT 57.021 37.500 0.00 0.00 0.00 1.98
4289 8498 3.287867 TTTGATTCAGATGGAGAGGGC 57.712 47.619 0.00 0.00 0.00 5.19
4323 8532 6.650807 TCATGAACTTAACGCTTCTCAGAATT 59.349 34.615 0.00 0.00 0.00 2.17
4339 8548 8.728337 TCTCAGAATTATCCAAACAATGAGAG 57.272 34.615 0.00 0.00 36.61 3.20
4484 8693 6.432581 TCAGATACTTACATGTCCCTAGTGT 58.567 40.000 0.00 0.45 0.00 3.55
4569 8801 3.498481 CCAACTTCTCAGACCCCATTTGA 60.498 47.826 0.00 0.00 0.00 2.69
4717 8949 8.934023 ACTTTTGATGGACATTTAAGGACTTA 57.066 30.769 0.00 0.00 0.00 2.24
4719 8951 6.978343 TTGATGGACATTTAAGGACTTACG 57.022 37.500 0.00 0.00 0.00 3.18
4724 8956 6.961576 TGGACATTTAAGGACTTACGTTTTG 58.038 36.000 0.00 0.00 0.00 2.44
4769 9002 4.114794 GTCATGCCCTTTATTGCATTCAC 58.885 43.478 0.00 0.00 45.52 3.18
4771 9004 2.533916 TGCCCTTTATTGCATTCACCA 58.466 42.857 0.00 0.00 31.31 4.17
4775 9008 4.685924 CCCTTTATTGCATTCACCATGAC 58.314 43.478 0.00 0.00 34.31 3.06
4782 9015 1.675714 GCATTCACCATGACCGACTGA 60.676 52.381 0.00 0.00 34.31 3.41
4838 9072 7.997773 ATATCGAGTAGTTAAGACCATAGCA 57.002 36.000 0.00 0.00 0.00 3.49
4904 9140 0.249826 GGCTGATGAGTAGCTCTGCC 60.250 60.000 0.00 0.00 45.33 4.85
4908 9144 1.753649 TGATGAGTAGCTCTGCCAGAC 59.246 52.381 0.00 0.00 0.00 3.51
4972 9210 7.393841 AAGACTACTACTCTGTTACCACATC 57.606 40.000 0.00 0.00 30.39 3.06
4978 9216 3.002791 ACTCTGTTACCACATCGCAATG 58.997 45.455 0.00 0.00 38.93 2.82
5085 9323 4.563786 GGAACAAGGAAAACCCAAACAACA 60.564 41.667 0.00 0.00 37.41 3.33
5168 9406 6.206634 TGAACTAGTTTGTGAAATAGCAAGGG 59.793 38.462 10.02 0.00 37.03 3.95
5245 9483 7.547370 CAGGTTTGGATATAGAGTAGCTATTGC 59.453 40.741 0.00 0.00 40.30 3.56
5261 9499 2.512692 TTGCTGAGCCCACATGTTAT 57.487 45.000 0.23 0.00 0.00 1.89
5262 9500 1.753930 TGCTGAGCCCACATGTTATG 58.246 50.000 0.23 0.00 0.00 1.90
5274 9512 4.240881 ACATGTTATGTGATCTGGGCTT 57.759 40.909 0.00 0.00 43.01 4.35
5283 9540 2.684881 GTGATCTGGGCTTATTGGTGTG 59.315 50.000 0.00 0.00 0.00 3.82
5339 9597 8.458843 GGAAACACAGTGTTGTAATGCTAATAT 58.541 33.333 19.84 0.00 40.14 1.28
5374 9632 4.579869 ACTGGTAGTTAGCCAATTCAGTG 58.420 43.478 0.00 0.00 35.32 3.66
5377 9635 4.286032 TGGTAGTTAGCCAATTCAGTGTCT 59.714 41.667 0.00 0.00 32.29 3.41
5394 9652 6.037500 TCAGTGTCTGAGAAATCAAACACTTG 59.962 38.462 13.25 9.88 43.40 3.16
5497 9756 0.800631 AACATGCAGCTGTGTGATCG 59.199 50.000 21.94 5.87 0.00 3.69
5536 9796 5.484173 TTCTGAATGTTTATAGCTTGCGG 57.516 39.130 0.00 0.00 0.00 5.69
5582 9842 9.787532 TTCATATATGCTTTTGTGCTTTAAGAC 57.212 29.630 7.92 0.00 0.00 3.01
5604 9864 2.979813 GCAATTGAATTGTCCACACGTC 59.020 45.455 18.12 0.00 42.20 4.34
5628 9888 3.788797 GCTGACTGAAACTGGAACAAACG 60.789 47.826 0.00 0.00 38.70 3.60
5629 9889 3.340034 TGACTGAAACTGGAACAAACGT 58.660 40.909 0.00 0.00 38.70 3.99
5630 9890 4.505808 TGACTGAAACTGGAACAAACGTA 58.494 39.130 0.00 0.00 38.70 3.57
5631 9891 4.569162 TGACTGAAACTGGAACAAACGTAG 59.431 41.667 0.00 0.00 38.70 3.51
5663 9923 4.319766 CCCGTGAAACTGTGATGAAGAAAG 60.320 45.833 0.00 0.00 31.75 2.62
5700 9960 2.888594 CGTGACCATCATCGGTTTAGT 58.111 47.619 0.00 0.00 40.22 2.24
5736 9997 2.479049 CGATTTTGGAAGGCATGCTCTG 60.479 50.000 18.92 0.00 0.00 3.35
5742 10003 0.747283 GAAGGCATGCTCTGTCCAGG 60.747 60.000 18.92 0.00 0.00 4.45
5763 10025 6.234177 CAGGAACCAGAAGTAACTTCAGAAT 58.766 40.000 0.00 0.00 42.37 2.40
5793 10055 1.134965 GCAGCCGTGTCAGATTAGAGT 60.135 52.381 0.00 0.00 0.00 3.24
5795 10057 2.425312 CAGCCGTGTCAGATTAGAGTCT 59.575 50.000 0.00 0.00 0.00 3.24
5909 12582 3.694072 ACGTGCACAATATACCAAAGCAT 59.306 39.130 18.64 0.00 32.75 3.79
5912 12585 5.449041 CGTGCACAATATACCAAAGCATCTT 60.449 40.000 18.64 0.00 32.75 2.40
5913 12586 5.973565 GTGCACAATATACCAAAGCATCTTC 59.026 40.000 13.17 0.00 32.75 2.87
5914 12587 5.067674 TGCACAATATACCAAAGCATCTTCC 59.932 40.000 0.00 0.00 0.00 3.46
5915 12588 5.751680 CACAATATACCAAAGCATCTTCCG 58.248 41.667 0.00 0.00 0.00 4.30
5922 14338 3.253432 ACCAAAGCATCTTCCGTTCTTTC 59.747 43.478 0.00 0.00 0.00 2.62
5925 14341 4.954092 AAGCATCTTCCGTTCTTTCATC 57.046 40.909 0.00 0.00 0.00 2.92
6023 14852 3.059461 CACGACGTAGGATCTAGAAGCTC 60.059 52.174 0.00 0.00 0.00 4.09
6024 14853 2.481185 CGACGTAGGATCTAGAAGCTCC 59.519 54.545 0.00 0.00 30.80 4.70
6067 14965 1.531578 GCGAGGACAAGGTTTTCAGTC 59.468 52.381 0.00 0.00 0.00 3.51
6122 15020 1.445410 GGGAAATTTCGCCGCCAAC 60.445 57.895 21.33 1.69 34.41 3.77
6148 15046 5.619202 CGAAATTTCGTCCAAAATTTTTGGC 59.381 36.000 28.57 22.70 44.66 4.52
6149 15047 6.510960 CGAAATTTCGTCCAAAATTTTTGGCT 60.511 34.615 28.57 11.82 44.66 4.75
6153 15051 2.871633 CGTCCAAAATTTTTGGCTGCTT 59.128 40.909 28.57 0.00 39.38 3.91
6154 15052 4.054671 CGTCCAAAATTTTTGGCTGCTTA 58.945 39.130 28.57 13.06 39.38 3.09
6160 15062 6.912051 CCAAAATTTTTGGCTGCTTAAAACTC 59.088 34.615 24.03 0.00 32.18 3.01
6260 15175 3.866883 ATATTTCAAACACCCGCCAAG 57.133 42.857 0.00 0.00 0.00 3.61
6263 15178 0.821711 TTCAAACACCCGCCAAGGAG 60.822 55.000 0.00 0.00 45.00 3.69
6266 15181 2.692273 AAACACCCGCCAAGGAGGTC 62.692 60.000 8.11 0.00 45.00 3.85
6271 15186 1.521681 CCGCCAAGGAGGTCGATTC 60.522 63.158 0.10 0.00 45.00 2.52
6295 15210 0.242825 CTACCTTCGCAACTGACCGA 59.757 55.000 0.00 0.00 0.00 4.69
6309 15224 3.411517 CCGACCAAGCCCCTGGAT 61.412 66.667 0.00 0.00 38.96 3.41
6310 15225 2.190578 CGACCAAGCCCCTGGATC 59.809 66.667 0.00 0.00 38.96 3.36
6357 15272 1.086696 CAAACCCACGCCTACAGATG 58.913 55.000 0.00 0.00 0.00 2.90
6382 15297 6.626623 GCAAATCTGAGCATAGGAACAACAAT 60.627 38.462 0.00 0.00 0.00 2.71
6396 15315 2.093973 ACAACAATGGGCAAACGAACAA 60.094 40.909 0.00 0.00 0.00 2.83
6399 15318 2.933260 ACAATGGGCAAACGAACAAAAC 59.067 40.909 0.00 0.00 0.00 2.43
6521 15440 3.635373 CCCAGCTACTCCGACATAACTAA 59.365 47.826 0.00 0.00 0.00 2.24
6529 15448 4.081087 ACTCCGACATAACTAAGCAATGGT 60.081 41.667 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 158 3.772025 TCATTGGTGTTGTTGGGTTTTCT 59.228 39.130 0.00 0.00 0.00 2.52
157 159 3.868661 GTCATTGGTGTTGTTGGGTTTTC 59.131 43.478 0.00 0.00 0.00 2.29
158 160 3.261897 TGTCATTGGTGTTGTTGGGTTTT 59.738 39.130 0.00 0.00 0.00 2.43
180 184 0.748005 AGTTGGACGCACTTTGCTGT 60.748 50.000 0.00 0.00 42.25 4.40
189 193 6.206243 GGTATATACTAGAAGAGTTGGACGCA 59.794 42.308 12.54 0.00 39.81 5.24
464 471 2.239400 GTAGGATTAGGGCCCAATTGC 58.761 52.381 27.56 13.06 0.00 3.56
515 522 5.344743 AAGTCAACATCGTCCTATGTGAT 57.655 39.130 0.00 0.00 39.98 3.06
518 525 5.407407 AGAAAGTCAACATCGTCCTATGT 57.593 39.130 0.00 0.00 41.87 2.29
544 551 2.668144 AACCGTTTCAATTCCCAGGA 57.332 45.000 0.00 0.00 0.00 3.86
612 619 2.167662 GTGATTGGGTTTCGGTTGGAT 58.832 47.619 0.00 0.00 0.00 3.41
766 784 3.802866 CTCTATGGAGTTCCTGGAAAGC 58.197 50.000 11.40 5.99 36.82 3.51
904 924 1.667510 CTTTGCGCGGCCCAAATTT 60.668 52.632 12.69 0.00 32.34 1.82
957 977 1.197812 GCCGGGTTAGGAACTTAGGA 58.802 55.000 2.18 0.00 41.75 2.94
958 978 0.179702 GGCCGGGTTAGGAACTTAGG 59.820 60.000 2.18 0.00 41.75 2.69
959 979 0.179092 CGGCCGGGTTAGGAACTTAG 60.179 60.000 20.10 0.00 41.75 2.18
960 980 1.899617 CGGCCGGGTTAGGAACTTA 59.100 57.895 20.10 0.00 41.75 2.24
961 981 2.666812 CGGCCGGGTTAGGAACTT 59.333 61.111 20.10 0.00 41.75 2.66
962 982 4.091939 GCGGCCGGGTTAGGAACT 62.092 66.667 29.38 0.00 46.37 3.01
963 983 4.397832 TGCGGCCGGGTTAGGAAC 62.398 66.667 29.38 7.00 0.00 3.62
964 984 4.090588 CTGCGGCCGGGTTAGGAA 62.091 66.667 29.38 0.00 0.00 3.36
1335 3159 1.822506 GAACAAACTCTAGGCCCACC 58.177 55.000 0.00 0.00 0.00 4.61
1336 3160 1.439679 CGAACAAACTCTAGGCCCAC 58.560 55.000 0.00 0.00 0.00 4.61
1337 3161 0.323629 CCGAACAAACTCTAGGCCCA 59.676 55.000 0.00 0.00 0.00 5.36
1338 3162 0.611714 TCCGAACAAACTCTAGGCCC 59.388 55.000 0.00 0.00 0.00 5.80
1339 3163 1.275573 ACTCCGAACAAACTCTAGGCC 59.724 52.381 0.00 0.00 0.00 5.19
1340 3164 2.288886 ACACTCCGAACAAACTCTAGGC 60.289 50.000 0.00 0.00 0.00 3.93
1341 3165 3.005472 TGACACTCCGAACAAACTCTAGG 59.995 47.826 0.00 0.00 0.00 3.02
1342 3166 3.982058 GTGACACTCCGAACAAACTCTAG 59.018 47.826 0.00 0.00 0.00 2.43
1343 3167 3.635373 AGTGACACTCCGAACAAACTCTA 59.365 43.478 1.07 0.00 0.00 2.43
1344 3168 2.431057 AGTGACACTCCGAACAAACTCT 59.569 45.455 1.07 0.00 0.00 3.24
1345 3169 2.822764 AGTGACACTCCGAACAAACTC 58.177 47.619 1.07 0.00 0.00 3.01
1371 3195 1.054406 CCTCCGGCTGATTAGGGGAA 61.054 60.000 0.00 0.00 0.00 3.97
1373 3197 3.151906 CCTCCGGCTGATTAGGGG 58.848 66.667 0.00 0.00 0.00 4.79
1484 3308 3.906720 TCTTAACGGGGAGGATTTGAG 57.093 47.619 0.00 0.00 0.00 3.02
1500 3324 0.738975 CAGTCGGAGTCGCCATCTTA 59.261 55.000 0.00 0.00 35.94 2.10
1545 3370 1.950954 GCAGGCTGTTCCCCTAAAGAC 60.951 57.143 17.16 0.00 34.51 3.01
1551 3376 4.335647 CGTGCAGGCTGTTCCCCT 62.336 66.667 17.16 0.00 34.51 4.79
1587 3416 1.037030 ACGCACCCAGCCCATAAATG 61.037 55.000 0.00 0.00 41.38 2.32
1622 3451 2.033299 TCAACACAGTAAGCAGCAAAGC 59.967 45.455 0.00 0.00 0.00 3.51
1660 3489 1.398390 CTAACTCAAATCTGCACCGGC 59.602 52.381 0.00 0.00 41.68 6.13
1661 3490 2.009774 CCTAACTCAAATCTGCACCGG 58.990 52.381 0.00 0.00 0.00 5.28
1713 4228 0.316442 CGTCTGCAACACAGCACAAG 60.316 55.000 0.00 0.00 46.76 3.16
1756 4271 2.293184 ACAGGGCAGGATAAGAGGAGAA 60.293 50.000 0.00 0.00 0.00 2.87
1795 5615 4.023365 GCCACCAAGATGAAAGATAGCATC 60.023 45.833 0.00 0.00 40.85 3.91
1796 5616 3.887716 GCCACCAAGATGAAAGATAGCAT 59.112 43.478 0.00 0.00 0.00 3.79
1831 5651 4.518970 TCAAGAACAACATACTGGCTTTCC 59.481 41.667 0.00 0.00 0.00 3.13
1873 5693 0.793861 GGCAAGAACGCGACACAATA 59.206 50.000 15.93 0.00 0.00 1.90
1890 5710 7.041098 CCACTTATATAGAACATTGGTCTTGGC 60.041 40.741 9.98 0.00 0.00 4.52
1900 5720 7.411486 AGCGCTATCCACTTATATAGAACAT 57.589 36.000 8.99 0.00 0.00 2.71
1907 5727 6.202954 GTGAAACAAGCGCTATCCACTTATAT 59.797 38.462 12.05 0.00 36.32 0.86
1951 5775 3.248363 CCATTCATATGTGTGTAGCCGTG 59.752 47.826 1.90 0.00 0.00 4.94
2036 5860 1.906574 AGGGCTATTTCCACGAGAACA 59.093 47.619 0.00 0.00 32.95 3.18
2287 6112 2.431454 CTGTTTCCAGGAGAAGCTTCC 58.569 52.381 22.81 9.76 36.69 3.46
2405 6230 4.330944 TCGCAGGAACTTTTCTTACAGA 57.669 40.909 0.00 0.00 34.60 3.41
2434 6259 4.500035 GGAGCCTTCTCATTAGTCTTACCG 60.500 50.000 0.00 0.00 41.13 4.02
2565 6390 2.099141 TGTCCTGCATCTTTTCCTCG 57.901 50.000 0.00 0.00 0.00 4.63
2574 6399 0.524862 CCACAAGCTTGTCCTGCATC 59.475 55.000 28.97 0.00 39.91 3.91
2668 6501 7.575720 GCTGGAGCTTGACAAGTACAATTTAAT 60.576 37.037 16.39 0.00 38.21 1.40
2869 6702 6.934645 TCTTTGCAATTAAGCAGTACTAGTGT 59.065 34.615 5.39 0.00 46.54 3.55
3069 6903 4.090761 AGAGAAACATCAAAGTCTGGCA 57.909 40.909 0.00 0.00 0.00 4.92
3089 6923 5.755375 CAGGGAACAAGTACATGTAGCATAG 59.245 44.000 5.62 0.00 32.02 2.23
3208 7042 7.014518 CCATATATTCCAAAAGGCAAGATGTCA 59.985 37.037 0.00 0.00 0.00 3.58
3259 7093 4.658063 AGGTATGCGCTACTCTAGAGATT 58.342 43.478 26.57 7.44 0.00 2.40
3388 7222 6.194235 ACCATTTGAAATTACTATCCTGCCA 58.806 36.000 0.00 0.00 0.00 4.92
3555 7389 3.507162 TGGAACATTGCAAGGAGAAGA 57.493 42.857 19.41 0.00 0.00 2.87
3790 7624 9.706691 CCACGGAGAAGTTAAATACACATATAT 57.293 33.333 0.00 0.00 0.00 0.86
3892 8048 1.350684 TGAAGTAGGCAGTTGCATCCA 59.649 47.619 6.43 0.00 44.36 3.41
3905 8061 7.164803 ACAAAGGAAGAGGAGAATTGAAGTAG 58.835 38.462 0.00 0.00 0.00 2.57
3911 8067 7.826252 TCAATCTACAAAGGAAGAGGAGAATTG 59.174 37.037 0.00 0.00 0.00 2.32
4101 8264 6.995364 AGACTTCTCCCAACTAGTTAAGAAC 58.005 40.000 17.84 11.70 0.00 3.01
4102 8265 7.289317 TGAAGACTTCTCCCAACTAGTTAAGAA 59.711 37.037 17.84 18.31 0.00 2.52
4103 8266 6.781014 TGAAGACTTCTCCCAACTAGTTAAGA 59.219 38.462 17.84 13.58 0.00 2.10
4104 8267 6.994221 TGAAGACTTCTCCCAACTAGTTAAG 58.006 40.000 16.02 10.33 0.00 1.85
4105 8268 6.989155 TGAAGACTTCTCCCAACTAGTTAA 57.011 37.500 16.02 0.00 0.00 2.01
4106 8269 6.154706 GGATGAAGACTTCTCCCAACTAGTTA 59.845 42.308 16.02 0.00 0.00 2.24
4107 8270 5.046231 GGATGAAGACTTCTCCCAACTAGTT 60.046 44.000 16.02 1.12 0.00 2.24
4108 8271 4.468153 GGATGAAGACTTCTCCCAACTAGT 59.532 45.833 16.02 0.00 0.00 2.57
4112 8275 3.703001 TGGATGAAGACTTCTCCCAAC 57.297 47.619 19.79 6.40 32.07 3.77
4289 8498 4.318121 GCGTTAAGTTCATGAAGCCTATCG 60.318 45.833 8.80 11.57 0.00 2.92
4323 8532 7.623630 TGATCTTCACTCTCATTGTTTGGATA 58.376 34.615 0.00 0.00 0.00 2.59
4339 8548 4.569719 TTCCCCTTAGGTTGATCTTCAC 57.430 45.455 0.00 0.00 36.75 3.18
4484 8693 9.653067 CATTAACGTGTGTAATAAACAGTTCAA 57.347 29.630 0.00 0.00 39.29 2.69
4525 8750 5.527214 TGGAAATATGCTGAAGTAACCGATG 59.473 40.000 0.00 0.00 0.00 3.84
4681 8913 9.829507 AATGTCCATCAAAAGTTGAAATGTTTA 57.170 25.926 0.00 0.00 43.95 2.01
4686 8918 9.492973 CCTTAAATGTCCATCAAAAGTTGAAAT 57.507 29.630 0.00 0.00 43.95 2.17
4687 8919 8.700051 TCCTTAAATGTCCATCAAAAGTTGAAA 58.300 29.630 0.00 0.00 43.95 2.69
4689 8921 7.505585 AGTCCTTAAATGTCCATCAAAAGTTGA 59.494 33.333 0.00 0.00 45.01 3.18
4717 8949 6.534079 GGATATGAGCAAGTACTACAAAACGT 59.466 38.462 0.00 0.00 0.00 3.99
4719 8951 7.549488 ACAGGATATGAGCAAGTACTACAAAAC 59.451 37.037 0.00 0.00 0.00 2.43
4724 8956 6.574350 ACAACAGGATATGAGCAAGTACTAC 58.426 40.000 0.00 0.00 0.00 2.73
4769 9002 2.751166 AAGAAGTCAGTCGGTCATGG 57.249 50.000 0.00 0.00 0.00 3.66
4771 9004 4.608948 AAGAAAGAAGTCAGTCGGTCAT 57.391 40.909 0.00 0.00 0.00 3.06
4775 9008 3.134458 AGCAAAGAAAGAAGTCAGTCGG 58.866 45.455 0.00 0.00 0.00 4.79
4782 9015 4.677673 AATGCCAAGCAAAGAAAGAAGT 57.322 36.364 0.00 0.00 43.62 3.01
4838 9072 5.733373 GCTCGAGAAAACTTTTGGATGTGTT 60.733 40.000 18.75 0.00 0.00 3.32
4890 9124 1.118838 GGTCTGGCAGAGCTACTCAT 58.881 55.000 33.17 0.00 39.50 2.90
4895 9129 1.279496 AACATGGTCTGGCAGAGCTA 58.721 50.000 37.38 26.90 42.83 3.32
4972 9210 2.667969 TCAGAAACTCGATGACATTGCG 59.332 45.455 0.00 0.00 0.00 4.85
4978 9216 2.621338 TGCCATCAGAAACTCGATGAC 58.379 47.619 0.00 0.00 41.28 3.06
5085 9323 2.550830 TTGCCTTCTTCGCTCTCTTT 57.449 45.000 0.00 0.00 0.00 2.52
5241 9479 2.512692 TAACATGTGGGCTCAGCAAT 57.487 45.000 0.00 0.00 0.00 3.56
5261 9499 2.308570 ACACCAATAAGCCCAGATCACA 59.691 45.455 0.00 0.00 0.00 3.58
5262 9500 2.684881 CACACCAATAAGCCCAGATCAC 59.315 50.000 0.00 0.00 0.00 3.06
5339 9597 7.664731 GGCTAACTACCAGTACAGAGTATATGA 59.335 40.741 0.00 0.00 0.00 2.15
5348 9606 5.730550 TGAATTGGCTAACTACCAGTACAG 58.269 41.667 0.00 0.00 38.73 2.74
5444 9703 1.001633 ACGGGATCACAGTGTACAACC 59.998 52.381 0.00 0.00 0.00 3.77
5497 9756 7.067981 ACATTCAGAATTCTATTTTCCTGCTCC 59.932 37.037 7.86 0.00 0.00 4.70
5536 9796 2.755650 AGTGTCCACTGAAATGACGTC 58.244 47.619 9.11 9.11 40.75 4.34
5582 9842 1.978097 CGTGTGGACAATTCAATTGCG 59.022 47.619 10.21 0.87 43.98 4.85
5604 9864 2.564771 TGTTCCAGTTTCAGTCAGCAG 58.435 47.619 0.00 0.00 0.00 4.24
5648 9908 1.160137 GCGCCTTTCTTCATCACAGT 58.840 50.000 0.00 0.00 0.00 3.55
5675 9935 0.305617 CCGATGATGGTCACGCAATG 59.694 55.000 0.00 0.00 0.00 2.82
5676 9936 0.107703 ACCGATGATGGTCACGCAAT 60.108 50.000 0.00 0.00 37.91 3.56
5700 9960 5.010516 TCCAAAATCGATTCAGCCAAAAAGA 59.989 36.000 11.83 0.00 0.00 2.52
5736 9997 4.202326 TGAAGTTACTTCTGGTTCCTGGAC 60.202 45.833 23.27 0.00 40.73 4.02
5742 10003 7.730364 TCAATTCTGAAGTTACTTCTGGTTC 57.270 36.000 24.60 2.88 40.73 3.62
5763 10025 2.289382 TGACACGGCTGCTCTATTTCAA 60.289 45.455 0.00 0.00 0.00 2.69
5812 10074 9.142515 CAAATCATAACACATGCAATACAAGTT 57.857 29.630 0.00 0.00 0.00 2.66
5820 10082 6.513806 AGCTACAAATCATAACACATGCAA 57.486 33.333 0.00 0.00 0.00 4.08
5822 10084 5.230726 GCAAGCTACAAATCATAACACATGC 59.769 40.000 0.00 0.00 0.00 4.06
5835 10097 0.538057 AGCTGCAGGCAAGCTACAAA 60.538 50.000 17.12 0.00 44.79 2.83
5895 12206 6.357367 AGAACGGAAGATGCTTTGGTATATT 58.643 36.000 0.00 0.00 0.00 1.28
5933 14349 5.351465 GCAGATGAAAGAACGGAATTGTCTA 59.649 40.000 0.00 0.00 0.00 2.59
5935 14351 4.406943 GCAGATGAAAGAACGGAATTGTC 58.593 43.478 0.00 0.00 0.00 3.18
5938 14354 3.420893 TGGCAGATGAAAGAACGGAATT 58.579 40.909 0.00 0.00 0.00 2.17
5939 14355 3.071874 TGGCAGATGAAAGAACGGAAT 57.928 42.857 0.00 0.00 0.00 3.01
6023 14852 0.039256 CCGCCATCTGTGTTGTTTGG 60.039 55.000 0.00 0.00 0.00 3.28
6024 14853 0.039256 CCCGCCATCTGTGTTGTTTG 60.039 55.000 0.00 0.00 0.00 2.93
6056 14954 2.668550 GCGGGCGACTGAAAACCT 60.669 61.111 0.00 0.00 39.98 3.50
6057 14955 3.733960 GGCGGGCGACTGAAAACC 61.734 66.667 0.00 0.00 39.98 3.27
6148 15046 0.721718 CCCGCTCGAGTTTTAAGCAG 59.278 55.000 15.13 0.00 35.76 4.24
6149 15047 0.319083 TCCCGCTCGAGTTTTAAGCA 59.681 50.000 15.13 0.00 35.76 3.91
6153 15051 6.335471 TCATAATATCCCGCTCGAGTTTTA 57.665 37.500 15.13 0.17 0.00 1.52
6154 15052 5.209818 TCATAATATCCCGCTCGAGTTTT 57.790 39.130 15.13 0.00 0.00 2.43
6160 15062 5.569059 GCAAAATTTCATAATATCCCGCTCG 59.431 40.000 0.00 0.00 0.00 5.03
6231 15146 5.977129 CGGGTGTTTGAAATATTTGGCTATC 59.023 40.000 5.17 0.00 0.00 2.08
6263 15178 1.138464 GAAGGTAGGTGGGAATCGACC 59.862 57.143 0.00 0.00 41.41 4.79
6266 15181 0.529992 GCGAAGGTAGGTGGGAATCG 60.530 60.000 0.00 0.00 0.00 3.34
6271 15186 0.673644 CAGTTGCGAAGGTAGGTGGG 60.674 60.000 0.00 0.00 0.00 4.61
6295 15210 2.311854 CCAGATCCAGGGGCTTGGT 61.312 63.158 8.13 0.00 39.35 3.67
6309 15224 4.639078 TGTCCTGTGAATTTCATCCAGA 57.361 40.909 15.14 3.85 0.00 3.86
6310 15225 4.945543 TCATGTCCTGTGAATTTCATCCAG 59.054 41.667 1.78 6.25 0.00 3.86
6357 15272 4.156556 TGTTGTTCCTATGCTCAGATTTGC 59.843 41.667 0.00 0.00 0.00 3.68
6370 15285 2.294791 CGTTTGCCCATTGTTGTTCCTA 59.705 45.455 0.00 0.00 0.00 2.94
6373 15288 2.500509 TCGTTTGCCCATTGTTGTTC 57.499 45.000 0.00 0.00 0.00 3.18
6374 15289 2.093973 TGTTCGTTTGCCCATTGTTGTT 60.094 40.909 0.00 0.00 0.00 2.83
6382 15297 2.166459 TGATGTTTTGTTCGTTTGCCCA 59.834 40.909 0.00 0.00 0.00 5.36
6396 15315 5.754890 GGAACAATGAGTTGCTTTGATGTTT 59.245 36.000 0.00 0.00 44.29 2.83
6521 15440 1.078426 GGCGTAGGTGACCATTGCT 60.078 57.895 3.63 0.00 0.00 3.91
6529 15448 1.550130 CCCCAAGAAGGCGTAGGTGA 61.550 60.000 0.00 0.00 35.39 4.02


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

AutoCloner maintained by Alex Coulton.