Multiple sequence alignment - TraesCS5D01G328100

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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 TraesCS5D01G328100 chr5D 100.000 6571 0 0 1 6571 420716875 420710305 0.000000e+00 12135.0
1 TraesCS5D01G328100 chr5A 92.776 5094 240 81 980 6025 534121710 534116697 0.000000e+00 7251.0
2 TraesCS5D01G328100 chr5A 86.913 596 21 28 63 653 534130073 534129530 3.370000e-172 616.0
3 TraesCS5D01G328100 chr5B 95.613 3579 113 17 2223 5781 506792753 506789199 0.000000e+00 5699.0
4 TraesCS5D01G328100 chr5B 92.177 1240 65 19 980 2211 506793953 506792738 0.000000e+00 1724.0
5 TraesCS5D01G328100 chr5B 86.447 1033 66 32 1 997 506794965 506793971 0.000000e+00 1064.0
6 TraesCS5D01G328100 chr5B 94.881 293 8 2 5981 6267 506788698 506788407 1.000000e-122 451.0
7 TraesCS5D01G328100 chr5B 89.720 321 19 4 6250 6570 506788388 506788082 1.330000e-106 398.0
8 TraesCS5D01G328100 chr5B 90.948 232 14 3 5756 5985 506789030 506788804 8.280000e-79 305.0
9 TraesCS5D01G328100 chr1B 83.478 690 62 18 1165 1843 4548262 4548910 4.390000e-166 595.0
10 TraesCS5D01G328100 chr2A 79.109 651 110 17 3906 4553 501845703 501846330 6.090000e-115 425.0
11 TraesCS5D01G328100 chr2A 79.167 480 80 15 3176 3641 501844936 501845409 1.380000e-81 315.0
12 TraesCS5D01G328100 chr2D 79.123 479 82 15 3176 3641 371155669 371156142 1.380000e-81 315.0
13 TraesCS5D01G328100 chr2D 84.058 69 7 4 2956 3022 83925338 83925272 5.500000e-06 63.9
14 TraesCS5D01G328100 chr2B 78.750 480 83 16 3176 3641 440212231 440212705 2.980000e-78 303.0
15 TraesCS5D01G328100 chr1A 88.679 106 12 0 1201 1306 589867341 589867236 5.350000e-26 130.0
16 TraesCS5D01G328100 chr6A 84.000 75 12 0 2964 3038 220768858 220768784 9.140000e-09 73.1
17 TraesCS5D01G328100 chr6D 80.952 84 10 6 2958 3037 461966426 461966507 1.980000e-05 62.1


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 TraesCS5D01G328100 chr5D 420710305 420716875 6570 True 12135.000000 12135 100.000 1 6571 1 chr5D.!!$R1 6570
1 TraesCS5D01G328100 chr5A 534116697 534121710 5013 True 7251.000000 7251 92.776 980 6025 1 chr5A.!!$R1 5045
2 TraesCS5D01G328100 chr5A 534129530 534130073 543 True 616.000000 616 86.913 63 653 1 chr5A.!!$R2 590
3 TraesCS5D01G328100 chr5B 506788082 506794965 6883 True 1606.833333 5699 91.631 1 6570 6 chr5B.!!$R1 6569
4 TraesCS5D01G328100 chr1B 4548262 4548910 648 False 595.000000 595 83.478 1165 1843 1 chr1B.!!$F1 678
5 TraesCS5D01G328100 chr2A 501844936 501846330 1394 False 370.000000 425 79.138 3176 4553 2 chr2A.!!$F1 1377

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
600 625 0.036671 GGTACAACCGAACTGGAGGG 60.037 60.000 0.00 0.0 42.00 4.30 F
807 852 0.099968 CAGCAGCACCCATTCATTCG 59.900 55.000 0.00 0.0 0.00 3.34 F
809 854 0.527565 GCAGCACCCATTCATTCGTT 59.472 50.000 0.00 0.0 0.00 3.85 F
811 856 1.086696 AGCACCCATTCATTCGTTCG 58.913 50.000 0.00 0.0 0.00 3.95 F
1861 1976 1.447314 GTGGTCCGCGGGAAGTAAG 60.447 63.158 27.83 0.0 31.38 2.34 F
2903 3028 0.815615 GCAATCTACTGAAGCCCCCG 60.816 60.000 0.00 0.0 0.00 5.73 F
2929 3054 2.224523 CCAGAGGTGAACTGCAGGTAAA 60.225 50.000 19.93 0.0 34.47 2.01 F
4245 4426 4.945543 TGTCCTGATCATCCTGTTTTCATG 59.054 41.667 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2070 0.320771 CGCTCCCAAGCTACAACAGT 60.321 55.000 0.00 0.00 46.91 3.55 R
1946 2071 1.021390 CCGCTCCCAAGCTACAACAG 61.021 60.000 0.00 0.00 46.91 3.16 R
2452 2577 1.614996 TTGCAATCCGAAGAGCCAAA 58.385 45.000 0.00 0.00 0.00 3.28 R
2755 2880 9.669353 CAATCATTAGTATTTATGACCAAGTGC 57.331 33.333 0.00 0.00 33.90 4.40 R
3787 3949 0.475906 AGCCTTATCCTGATGTGGCC 59.524 55.000 16.35 0.00 39.57 5.36 R
4529 4710 0.459237 GTGAGTCTGCCAGATGACCG 60.459 60.000 0.00 0.00 34.02 4.79 R
4645 4831 3.476552 TCTGCAGGGACAAGTTTTACTG 58.523 45.455 15.13 0.00 0.00 2.74 R
6175 6717 0.228238 GATCGATTCGAGCGTGCTTG 59.772 55.000 14.81 2.53 39.91 4.01 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
83 85 2.045926 AGCCACCGGAAGCATGTC 60.046 61.111 9.46 0.00 0.00 3.06
165 168 2.279069 CGGATCTGGATCTCCCCCG 61.279 68.421 9.96 2.66 37.92 5.73
169 172 0.472734 ATCTGGATCTCCCCCGGAAG 60.473 60.000 0.73 0.00 41.94 3.46
170 173 1.383248 CTGGATCTCCCCCGGAAGT 60.383 63.158 0.73 0.00 34.29 3.01
172 175 2.499827 GGATCTCCCCCGGAAGTCG 61.500 68.421 0.73 0.00 38.88 4.18
183 186 2.350134 GAAGTCGGAACCCACCCC 59.650 66.667 0.00 0.00 0.00 4.95
205 208 3.186047 GTCGACGTTGATGGCCGG 61.186 66.667 9.14 0.00 0.00 6.13
208 211 2.358247 GACGTTGATGGCCGGTGT 60.358 61.111 1.90 0.00 0.00 4.16
220 223 0.534203 GCCGGTGTGTTGAAGAGGAA 60.534 55.000 1.90 0.00 0.00 3.36
263 266 0.241481 GAAGACAAGAGGACGAGCGT 59.759 55.000 0.00 0.00 0.00 5.07
385 398 1.006102 CTTTCCGTCCACGTGAGCT 60.006 57.895 19.30 0.00 37.74 4.09
386 399 1.284982 CTTTCCGTCCACGTGAGCTG 61.285 60.000 19.30 5.79 37.74 4.24
387 400 1.740332 TTTCCGTCCACGTGAGCTGA 61.740 55.000 19.30 8.15 37.74 4.26
388 401 1.740332 TTCCGTCCACGTGAGCTGAA 61.740 55.000 19.30 13.56 37.74 3.02
389 402 1.734477 CCGTCCACGTGAGCTGAAG 60.734 63.158 19.30 7.78 37.74 3.02
390 403 1.734477 CGTCCACGTGAGCTGAAGG 60.734 63.158 19.30 0.00 34.11 3.46
391 404 2.029844 GTCCACGTGAGCTGAAGGC 61.030 63.158 19.30 0.00 42.19 4.35
392 405 2.743928 CCACGTGAGCTGAAGGCC 60.744 66.667 19.30 0.00 43.05 5.19
393 406 2.345244 CACGTGAGCTGAAGGCCT 59.655 61.111 10.90 0.00 43.05 5.19
475 493 3.978193 AGCGGCCAAACCATCCCA 61.978 61.111 2.24 0.00 39.03 4.37
516 534 3.179265 GGCGATCCACACGACACG 61.179 66.667 0.00 0.00 38.75 4.49
517 535 2.126618 GCGATCCACACGACACGA 60.127 61.111 0.00 0.00 0.00 4.35
518 536 2.434134 GCGATCCACACGACACGAC 61.434 63.158 0.00 0.00 0.00 4.34
519 537 1.081708 CGATCCACACGACACGACA 60.082 57.895 0.00 0.00 0.00 4.35
520 538 1.334992 CGATCCACACGACACGACAC 61.335 60.000 0.00 0.00 0.00 3.67
521 539 1.006571 ATCCACACGACACGACACC 60.007 57.895 0.00 0.00 0.00 4.16
522 540 2.430382 ATCCACACGACACGACACCC 62.430 60.000 0.00 0.00 0.00 4.61
523 541 2.105328 CACACGACACGACACCCA 59.895 61.111 0.00 0.00 0.00 4.51
524 542 2.105528 ACACGACACGACACCCAC 59.894 61.111 0.00 0.00 0.00 4.61
525 543 2.660552 CACGACACGACACCCACC 60.661 66.667 0.00 0.00 0.00 4.61
526 544 3.148963 ACGACACGACACCCACCA 61.149 61.111 0.00 0.00 0.00 4.17
527 545 2.355837 CGACACGACACCCACCAG 60.356 66.667 0.00 0.00 0.00 4.00
599 624 3.527434 GGTACAACCGAACTGGAGG 57.473 57.895 0.00 0.00 42.00 4.30
600 625 0.036671 GGTACAACCGAACTGGAGGG 60.037 60.000 0.00 0.00 42.00 4.30
601 626 0.672711 GTACAACCGAACTGGAGGGC 60.673 60.000 0.00 0.00 42.00 5.19
602 627 0.834687 TACAACCGAACTGGAGGGCT 60.835 55.000 0.00 0.00 42.00 5.19
659 684 2.743126 AAACCGCCGTCCCTTTCCTC 62.743 60.000 0.00 0.00 0.00 3.71
660 685 4.814294 CCGCCGTCCCTTTCCTCG 62.814 72.222 0.00 0.00 0.00 4.63
699 724 2.417719 GCACAGTTCCTGATCGTTCTT 58.582 47.619 0.00 0.00 35.18 2.52
700 725 2.413453 GCACAGTTCCTGATCGTTCTTC 59.587 50.000 0.00 0.00 35.18 2.87
703 728 3.574396 ACAGTTCCTGATCGTTCTTCTCA 59.426 43.478 0.00 0.00 35.18 3.27
712 737 0.388649 CGTTCTTCTCACCTCCACCG 60.389 60.000 0.00 0.00 0.00 4.94
713 738 0.966920 GTTCTTCTCACCTCCACCGA 59.033 55.000 0.00 0.00 0.00 4.69
714 739 1.067495 GTTCTTCTCACCTCCACCGAG 60.067 57.143 0.00 0.00 35.72 4.63
747 792 1.961277 CCTTGCGTGCTTCCTTCGT 60.961 57.895 0.00 0.00 0.00 3.85
749 794 0.946221 CTTGCGTGCTTCCTTCGTCT 60.946 55.000 0.00 0.00 0.00 4.18
807 852 0.099968 CAGCAGCACCCATTCATTCG 59.900 55.000 0.00 0.00 0.00 3.34
809 854 0.527565 GCAGCACCCATTCATTCGTT 59.472 50.000 0.00 0.00 0.00 3.85
811 856 1.086696 AGCACCCATTCATTCGTTCG 58.913 50.000 0.00 0.00 0.00 3.95
842 894 1.490574 AAAGCTCTCGCCCAGTAGAT 58.509 50.000 0.00 0.00 36.60 1.98
869 921 7.490725 ACACACACGTAGATACTACTACTACTG 59.509 40.741 0.00 0.00 40.11 2.74
874 926 9.905171 CACGTAGATACTACTACTACTGATACA 57.095 37.037 0.00 0.00 40.11 2.29
914 966 5.653507 AGTGGTTCGATTACGTTAGCATAA 58.346 37.500 0.00 0.00 40.69 1.90
951 1004 2.936919 TCATTTCATCTCATCCGGGG 57.063 50.000 0.00 0.00 0.00 5.73
963 1016 1.762957 CATCCGGGGTCTGTCAGTTAT 59.237 52.381 0.00 0.00 0.00 1.89
972 1025 3.508762 GTCTGTCAGTTATACCACGGTG 58.491 50.000 0.00 0.00 0.00 4.94
1121 1212 3.237741 GGGAGGAGGGATCCGCAG 61.238 72.222 5.45 0.00 37.75 5.18
1596 1699 3.053544 TCCTCAGAAGGTAGGTACTCCAG 60.054 52.174 0.00 0.00 43.82 3.86
1603 1706 6.154706 CAGAAGGTAGGTACTCCAGTTATGTT 59.845 42.308 0.00 0.00 41.75 2.71
1608 1711 6.604795 GGTAGGTACTCCAGTTATGTTCAGTA 59.395 42.308 0.00 0.00 41.75 2.74
1673 1786 6.036300 CACCACCAATTATTCATTCATTGTGC 59.964 38.462 0.00 0.00 0.00 4.57
1681 1794 1.752498 TCATTCATTGTGCTGCCATCC 59.248 47.619 0.00 0.00 0.00 3.51
1763 1876 2.031516 CCCTTGTGAGCTGAGCACG 61.032 63.158 7.39 0.00 39.07 5.34
1861 1976 1.447314 GTGGTCCGCGGGAAGTAAG 60.447 63.158 27.83 0.00 31.38 2.34
1876 1991 6.308282 CGGGAAGTAAGCGATTATACTCATTC 59.692 42.308 0.00 0.00 31.31 2.67
1898 2013 6.889301 TCGTAAGATCACGTAGGGATTATT 57.111 37.500 5.60 0.00 45.01 1.40
1925 2045 2.543012 GCCATCATCGATCAGACTTGTG 59.457 50.000 0.00 0.00 0.00 3.33
2136 2261 6.659824 TCCTTGAGTAAAAAGAAAGGTCAGT 58.340 36.000 0.00 0.00 38.81 3.41
2142 2267 8.262227 TGAGTAAAAAGAAAGGTCAGTAGTCAA 58.738 33.333 0.00 0.00 0.00 3.18
2149 2274 6.622549 AGAAAGGTCAGTAGTCAACTATTCG 58.377 40.000 0.00 0.00 35.76 3.34
2155 2280 6.380190 GTCAGTAGTCAACTATTCGAGTGTT 58.620 40.000 0.00 0.00 38.87 3.32
2158 2283 8.570488 TCAGTAGTCAACTATTCGAGTGTTAAA 58.430 33.333 0.00 0.00 38.87 1.52
2159 2284 8.636843 CAGTAGTCAACTATTCGAGTGTTAAAC 58.363 37.037 0.00 0.00 38.87 2.01
2279 2404 3.997021 CTCTGTTTCAGATAAAGGTGCGT 59.003 43.478 0.00 0.00 39.92 5.24
2281 2406 4.213270 TCTGTTTCAGATAAAGGTGCGTTG 59.787 41.667 0.00 0.00 35.39 4.10
2437 2562 1.611977 GAGGCTGGTGTTGGTAAAACC 59.388 52.381 0.00 0.00 39.22 3.27
2560 2685 7.604549 TCTGCATTTATGAAATTCTCTTGCAA 58.395 30.769 0.00 0.00 0.00 4.08
2903 3028 0.815615 GCAATCTACTGAAGCCCCCG 60.816 60.000 0.00 0.00 0.00 5.73
2929 3054 2.224523 CCAGAGGTGAACTGCAGGTAAA 60.225 50.000 19.93 0.00 34.47 2.01
3125 3260 9.802039 ATACTCCACCTTAAATGTTAAACAGAA 57.198 29.630 0.00 0.00 0.00 3.02
3299 3450 6.381133 AGCCAGGTAAAGATATTTTCCTTTGG 59.619 38.462 8.14 9.55 34.74 3.28
3381 3534 7.377766 TGCTGTGAAAATATTACTTGGTCTC 57.622 36.000 0.00 0.00 0.00 3.36
4242 4423 5.188434 TCATGTCCTGATCATCCTGTTTTC 58.812 41.667 0.00 0.00 0.00 2.29
4244 4425 5.183530 TGTCCTGATCATCCTGTTTTCAT 57.816 39.130 0.00 0.00 0.00 2.57
4245 4426 4.945543 TGTCCTGATCATCCTGTTTTCATG 59.054 41.667 0.00 0.00 0.00 3.07
4606 4788 5.274718 CAACCGCTGTTGTTTTATGTACAA 58.725 37.500 12.39 0.00 45.51 2.41
4680 4889 6.127647 TGTCCCTGCAGATTTTATGCTAAAAG 60.128 38.462 17.39 0.00 44.17 2.27
4726 4935 5.964958 TCCTTTTCTAGCCATTCAAACTG 57.035 39.130 0.00 0.00 0.00 3.16
4730 4939 5.705609 TTTCTAGCCATTCAAACTGTTCC 57.294 39.130 0.00 0.00 0.00 3.62
4856 5066 3.131223 TCCAGATGCAGTAGTAGACTTGC 59.869 47.826 0.00 0.30 35.64 4.01
4988 5198 4.443621 TGACATCAAACGTTGGTTCTACA 58.556 39.130 0.00 0.00 34.62 2.74
4997 5207 6.627395 AACGTTGGTTCTACATCAATTTCA 57.373 33.333 0.00 0.00 0.00 2.69
5030 5240 3.350833 GAGCATGGGTTTCTCAACAGAT 58.649 45.455 0.00 0.00 34.15 2.90
5046 5256 1.667724 CAGATGACACCGAATCAAGCC 59.332 52.381 0.00 0.00 0.00 4.35
5135 5345 2.600420 CAGAATCGATGAGACGGTTGTG 59.400 50.000 0.00 0.00 40.14 3.33
5178 5388 3.074687 TCAGGTCTGTCTCTCACTTACCT 59.925 47.826 0.00 0.00 39.89 3.08
5198 5408 5.607477 ACCTCTTTGTTCTGAATTCGTACA 58.393 37.500 0.04 2.25 0.00 2.90
5226 5436 2.554032 GGTGAACTTCAACCACATCAGG 59.446 50.000 0.00 0.00 32.79 3.86
5297 5507 3.108847 CTCCTAGAGGAACTGAAGGGT 57.891 52.381 0.00 0.00 44.91 4.34
5536 5746 1.219522 CGTCTGAACCAACCACCGAC 61.220 60.000 0.00 0.00 0.00 4.79
5584 5794 3.006323 ACATTCTGAAGTGAAGCTCTCGT 59.994 43.478 0.00 0.00 0.00 4.18
5781 6200 8.990163 ATATTGTCCTCCGGTTTATAACAAAT 57.010 30.769 0.00 0.00 0.00 2.32
5783 6202 7.614124 TTGTCCTCCGGTTTATAACAAATAC 57.386 36.000 0.00 0.00 0.00 1.89
5784 6203 6.709281 TGTCCTCCGGTTTATAACAAATACA 58.291 36.000 0.00 0.00 0.00 2.29
5785 6204 6.819649 TGTCCTCCGGTTTATAACAAATACAG 59.180 38.462 0.00 0.00 0.00 2.74
5869 6289 1.028905 TTTTCCTTTCACCGGCACAG 58.971 50.000 0.00 0.00 0.00 3.66
5900 6320 5.851047 ATTTGCAGCTGCTTTTTAATGAC 57.149 34.783 36.61 6.43 42.66 3.06
5963 6383 3.055591 CAATAGCAGACGAGCCATGTAG 58.944 50.000 0.00 0.00 34.23 2.74
6052 6594 5.047660 GTCATTTATGGCCTGTTTGGTTACA 60.048 40.000 3.32 0.00 38.35 2.41
6102 6644 1.039856 TGACTTTTGGAGGCTTTGGC 58.960 50.000 0.00 0.00 33.09 4.52
6175 6717 1.476007 ATCTCCGGGTCCAGCTATGC 61.476 60.000 0.00 0.00 0.00 3.14
6227 6769 2.790791 AAGCCCGAGCGATGAGAGG 61.791 63.158 0.00 0.00 46.67 3.69
6252 6794 4.767255 CGTGGGTGGAGGCAGCTC 62.767 72.222 0.00 0.00 0.00 4.09
6253 6795 4.416738 GTGGGTGGAGGCAGCTCC 62.417 72.222 2.23 2.23 43.60 4.70
6298 6875 1.448013 GAAGCGGCGCCTTAACTCT 60.448 57.895 30.40 3.74 0.00 3.24
6300 6877 3.255379 GCGGCGCCTTAACTCTCG 61.255 66.667 26.68 8.83 0.00 4.04
6308 6885 1.135053 GCCTTAACTCTCGTCACCCTC 60.135 57.143 0.00 0.00 0.00 4.30
6356 6933 1.302383 ACTCTCTCTCACTGGCGACG 61.302 60.000 0.00 0.00 0.00 5.12
6374 6951 0.930310 CGACCACAATATCTGCACGG 59.070 55.000 0.00 0.00 0.00 4.94
6401 6978 2.357517 GCGGGCATACATCGGAGG 60.358 66.667 0.00 0.00 0.00 4.30
6403 6980 2.828868 GGGCATACATCGGAGGCA 59.171 61.111 0.00 0.00 0.00 4.75
6404 6981 1.148273 GGGCATACATCGGAGGCAA 59.852 57.895 0.00 0.00 0.00 4.52
6405 6982 0.886490 GGGCATACATCGGAGGCAAG 60.886 60.000 0.00 0.00 0.00 4.01
6406 6983 1.510480 GGCATACATCGGAGGCAAGC 61.510 60.000 0.00 0.00 0.00 4.01
6407 6984 0.533755 GCATACATCGGAGGCAAGCT 60.534 55.000 0.00 0.00 0.00 3.74
6408 6985 1.506493 CATACATCGGAGGCAAGCTC 58.494 55.000 0.00 0.00 0.00 4.09
6409 6986 1.069823 CATACATCGGAGGCAAGCTCT 59.930 52.381 0.00 0.00 0.00 4.09
6419 6996 2.029844 GCAAGCTCTGGACGGTGAC 61.030 63.158 0.00 0.00 0.00 3.67
6432 7009 4.065110 GTGACCACCAGCTTCACC 57.935 61.111 4.43 0.00 34.72 4.02
6433 7010 1.961277 GTGACCACCAGCTTCACCG 60.961 63.158 4.43 0.00 34.72 4.94
6434 7011 3.050275 GACCACCAGCTTCACCGC 61.050 66.667 0.00 0.00 0.00 5.68
6435 7012 4.643387 ACCACCAGCTTCACCGCC 62.643 66.667 0.00 0.00 0.00 6.13
6478 7055 1.384643 GGTATGCCCTCTGTCCCCT 60.385 63.158 0.00 0.00 0.00 4.79
6479 7056 1.411651 GGTATGCCCTCTGTCCCCTC 61.412 65.000 0.00 0.00 0.00 4.30
6490 7067 3.845259 TCCCCTCGATTTCCCGCG 61.845 66.667 0.00 0.00 0.00 6.46
6526 7103 9.877137 GATTTATCGTTGATTATACATTGCACA 57.123 29.630 0.00 0.00 0.00 4.57
6564 7141 1.327764 GGCTTCGATTTGTGACCGATC 59.672 52.381 0.00 0.00 32.07 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.045926 GACATGCTTCCGGTGGCT 60.046 61.111 18.56 3.02 0.00 4.75
72 73 2.892425 GGCCGAGACATGCTTCCG 60.892 66.667 0.00 0.00 0.00 4.30
106 108 2.262915 CTGCCACCGACCTCTGTC 59.737 66.667 0.00 0.00 38.18 3.51
110 112 2.266055 CTTCCTGCCACCGACCTC 59.734 66.667 0.00 0.00 0.00 3.85
149 152 0.471971 TTCCGGGGGAGATCCAGATC 60.472 60.000 0.00 0.00 37.91 2.75
165 168 2.350134 GGGTGGGTTCCGACTTCC 59.650 66.667 4.20 0.00 0.00 3.46
169 172 3.246880 ACTGGGGTGGGTTCCGAC 61.247 66.667 0.00 0.00 0.00 4.79
170 173 2.926242 GACTGGGGTGGGTTCCGA 60.926 66.667 0.00 0.00 0.00 4.55
172 175 3.246880 ACGACTGGGGTGGGTTCC 61.247 66.667 0.00 0.00 0.00 3.62
173 176 2.346365 GACGACTGGGGTGGGTTC 59.654 66.667 0.00 0.00 0.00 3.62
174 177 3.622826 CGACGACTGGGGTGGGTT 61.623 66.667 0.00 0.00 0.00 4.11
179 182 2.908940 AACGTCGACGACTGGGGT 60.909 61.111 41.52 17.01 43.02 4.95
183 186 1.674611 GCCATCAACGTCGACGACTG 61.675 60.000 41.52 33.25 43.02 3.51
205 208 5.008118 CCTTTCTTCTTCCTCTTCAACACAC 59.992 44.000 0.00 0.00 0.00 3.82
208 211 4.137543 GCCTTTCTTCTTCCTCTTCAACA 58.862 43.478 0.00 0.00 0.00 3.33
220 223 1.973812 GCCTTGCCGCCTTTCTTCT 60.974 57.895 0.00 0.00 0.00 2.85
602 627 2.750637 GTGGAGGACTCGAGGCGA 60.751 66.667 18.41 0.00 0.00 5.54
683 708 3.056465 GGTGAGAAGAACGATCAGGAACT 60.056 47.826 0.00 0.00 43.88 3.01
718 743 2.358737 CGCAAGGAAACGAGGCCT 60.359 61.111 3.86 3.86 35.61 5.19
747 792 4.440525 CGTATAAAAGTACCGCTGGGAAGA 60.441 45.833 0.00 0.00 36.97 2.87
749 794 3.784338 CGTATAAAAGTACCGCTGGGAA 58.216 45.455 0.00 0.00 36.97 3.97
794 839 1.062587 GAGCGAACGAATGAATGGGTG 59.937 52.381 0.00 0.00 0.00 4.61
828 873 2.022195 GTGTGTATCTACTGGGCGAGA 58.978 52.381 2.65 0.00 0.00 4.04
829 874 1.749063 TGTGTGTATCTACTGGGCGAG 59.251 52.381 0.00 0.00 0.00 5.03
842 894 8.687242 AGTAGTAGTAGTATCTACGTGTGTGTA 58.313 37.037 0.00 0.00 43.31 2.90
891 943 3.581024 TGCTAACGTAATCGAACCACT 57.419 42.857 0.00 0.00 40.62 4.00
895 947 6.564854 AGTGTTATGCTAACGTAATCGAAC 57.435 37.500 0.00 0.00 40.62 3.95
897 949 5.911280 GCTAGTGTTATGCTAACGTAATCGA 59.089 40.000 0.00 0.00 40.62 3.59
951 1004 3.508762 CACCGTGGTATAACTGACAGAC 58.491 50.000 10.08 0.00 0.00 3.51
963 1016 1.203052 GCAACTACTAGCACCGTGGTA 59.797 52.381 9.96 9.96 0.00 3.25
972 1025 0.108804 TCACCGCAGCAACTACTAGC 60.109 55.000 0.00 0.00 0.00 3.42
1596 1699 6.486993 GGGAATTCCTGGATACTGAACATAAC 59.513 42.308 23.63 0.00 37.83 1.89
1603 1706 3.438131 AGGGGAATTCCTGGATACTGA 57.562 47.619 23.63 0.00 35.47 3.41
1608 1711 1.923148 ACGAAAGGGGAATTCCTGGAT 59.077 47.619 23.63 8.58 37.20 3.41
1673 1786 0.904649 TCAGTACTGGTGGATGGCAG 59.095 55.000 22.48 0.00 0.00 4.85
1681 1794 8.442632 ACATGATTATTTGATCAGTACTGGTG 57.557 34.615 22.48 1.79 39.26 4.17
1837 1952 4.020378 CCCGCGGACCACGTTTTG 62.020 66.667 30.73 0.44 46.52 2.44
1843 1958 1.447314 CTTACTTCCCGCGGACCAC 60.447 63.158 30.73 0.00 0.00 4.16
1844 1959 2.975536 CTTACTTCCCGCGGACCA 59.024 61.111 30.73 7.08 0.00 4.02
1850 1965 3.910648 AGTATAATCGCTTACTTCCCGC 58.089 45.455 0.00 0.00 0.00 6.13
1852 1967 6.308282 CGAATGAGTATAATCGCTTACTTCCC 59.692 42.308 0.00 0.00 0.00 3.97
1861 1976 7.253027 CGTGATCTTACGAATGAGTATAATCGC 60.253 40.741 0.00 0.00 46.46 4.58
1898 2013 3.309682 GTCTGATCGATGATGGCGAAAAA 59.690 43.478 0.54 0.00 41.52 1.94
1945 2070 0.320771 CGCTCCCAAGCTACAACAGT 60.321 55.000 0.00 0.00 46.91 3.55
1946 2071 1.021390 CCGCTCCCAAGCTACAACAG 61.021 60.000 0.00 0.00 46.91 3.16
2136 2261 9.531942 TTTGTTTAACACTCGAATAGTTGACTA 57.468 29.630 0.00 0.00 35.76 2.59
2231 2356 9.905713 GATCCCATGGCTTGTATTAGAATAATA 57.094 33.333 6.09 0.00 0.00 0.98
2232 2357 8.618385 AGATCCCATGGCTTGTATTAGAATAAT 58.382 33.333 6.09 0.00 0.00 1.28
2233 2358 7.988937 AGATCCCATGGCTTGTATTAGAATAA 58.011 34.615 6.09 0.00 0.00 1.40
2234 2359 7.459125 AGAGATCCCATGGCTTGTATTAGAATA 59.541 37.037 6.09 0.00 0.00 1.75
2235 2360 6.274200 AGAGATCCCATGGCTTGTATTAGAAT 59.726 38.462 6.09 0.00 0.00 2.40
2279 2404 7.174946 GGTCAAATCTAGACAAAACTGATCCAA 59.825 37.037 0.00 0.00 37.74 3.53
2281 2406 6.655003 TGGTCAAATCTAGACAAAACTGATCC 59.345 38.462 0.00 0.00 37.74 3.36
2335 2460 2.632996 CTCCTCCTCACGGCCAATAATA 59.367 50.000 2.24 0.00 0.00 0.98
2359 2484 5.827797 GCATATTATCTGAACCACCCTTTCA 59.172 40.000 0.00 0.00 0.00 2.69
2437 2562 3.186047 AAACCTTCGGCGATCGCG 61.186 61.111 31.76 25.66 43.06 5.87
2452 2577 1.614996 TTGCAATCCGAAGAGCCAAA 58.385 45.000 0.00 0.00 0.00 3.28
2755 2880 9.669353 CAATCATTAGTATTTATGACCAAGTGC 57.331 33.333 0.00 0.00 33.90 4.40
2903 3028 1.860484 GCAGTTCACCTCTGGCAAGC 61.860 60.000 0.00 0.00 33.98 4.01
2929 3054 4.042187 ACCACTAAGAAGCAGGATGAACTT 59.958 41.667 0.00 0.00 39.69 2.66
3555 3708 1.258676 AGAGAACGGAAGACTGTCCC 58.741 55.000 3.76 0.00 34.15 4.46
3787 3949 0.475906 AGCCTTATCCTGATGTGGCC 59.524 55.000 16.35 0.00 39.57 5.36
4242 4423 4.083377 TCAAAACATCGGTGACATGACATG 60.083 41.667 14.02 14.02 0.00 3.21
4244 4425 3.471680 TCAAAACATCGGTGACATGACA 58.528 40.909 0.65 0.00 0.00 3.58
4245 4426 4.685169 ATCAAAACATCGGTGACATGAC 57.315 40.909 0.65 0.00 0.00 3.06
4303 4484 7.596494 CATAGCAGATTCCTGTTCAAAAAGAA 58.404 34.615 0.00 0.00 42.35 2.52
4529 4710 0.459237 GTGAGTCTGCCAGATGACCG 60.459 60.000 0.00 0.00 34.02 4.79
4614 4796 9.533831 ACCTCTAAAAGAATACATTGTTTCCAT 57.466 29.630 0.00 0.00 32.87 3.41
4645 4831 3.476552 TCTGCAGGGACAAGTTTTACTG 58.523 45.455 15.13 0.00 0.00 2.74
4726 4935 8.379457 AGTCACTAAACTTGAAGTTATGGAAC 57.621 34.615 11.43 7.67 37.47 3.62
4988 5198 2.158841 CCGTCGTCCGTTTGAAATTGAT 59.841 45.455 0.00 0.00 33.66 2.57
4997 5207 1.736645 CATGCTCCGTCGTCCGTTT 60.737 57.895 0.00 0.00 33.66 3.60
5030 5240 0.249120 ATCGGCTTGATTCGGTGTCA 59.751 50.000 0.00 0.00 31.57 3.58
5178 5388 6.704050 TGTCATGTACGAATTCAGAACAAAGA 59.296 34.615 6.22 6.32 0.00 2.52
5198 5408 3.569701 GTGGTTGAAGTTCACCATGTCAT 59.430 43.478 22.05 0.00 32.87 3.06
5297 5507 2.577059 CCGACGGCCAAGAGCTTA 59.423 61.111 2.24 0.00 43.05 3.09
5536 5746 0.673985 TGAGTCAGACACTTGGACGG 59.326 55.000 2.66 0.00 34.41 4.79
5584 5794 5.498393 CTCTACTCTACCAAGTCTACCACA 58.502 45.833 0.00 0.00 0.00 4.17
5781 6200 5.065474 GCAGCCGTTCCAAAATTATACTGTA 59.935 40.000 0.00 0.00 0.00 2.74
5782 6201 4.142469 GCAGCCGTTCCAAAATTATACTGT 60.142 41.667 0.00 0.00 0.00 3.55
5783 6202 4.142491 TGCAGCCGTTCCAAAATTATACTG 60.142 41.667 0.00 0.00 0.00 2.74
5784 6203 4.013728 TGCAGCCGTTCCAAAATTATACT 58.986 39.130 0.00 0.00 0.00 2.12
5785 6204 4.364415 TGCAGCCGTTCCAAAATTATAC 57.636 40.909 0.00 0.00 0.00 1.47
5796 6215 2.401766 CCACTCCATGCAGCCGTTC 61.402 63.158 0.00 0.00 0.00 3.95
5869 6289 4.954092 AGCAGCTGCAAATACTAACTTC 57.046 40.909 38.24 5.78 45.16 3.01
5900 6320 6.696148 AGAGTGTAAACAGAAGTTACTGAACG 59.304 38.462 0.00 0.00 40.76 3.95
5942 6362 1.945387 ACATGGCTCGTCTGCTATTG 58.055 50.000 0.00 0.00 31.76 1.90
6052 6594 1.331214 CCTGGTTGAGGTTGTTGCAT 58.669 50.000 0.00 0.00 37.02 3.96
6080 6622 2.430332 CCAAAGCCTCCAAAAGTCACAA 59.570 45.455 0.00 0.00 0.00 3.33
6102 6644 2.376808 TTTGCACACAACCAAACAGG 57.623 45.000 0.00 0.00 45.67 4.00
6103 6645 2.030701 GCATTTGCACACAACCAAACAG 59.969 45.455 0.00 0.00 41.59 3.16
6175 6717 0.228238 GATCGATTCGAGCGTGCTTG 59.772 55.000 14.81 2.53 39.91 4.01
6280 6857 1.422179 GAGAGTTAAGGCGCCGCTTC 61.422 60.000 23.20 15.32 0.00 3.86
6298 6875 1.304217 GGTGAGAGGAGGGTGACGA 60.304 63.158 0.00 0.00 0.00 4.20
6300 6877 3.007973 GCGGTGAGAGGAGGGTGAC 62.008 68.421 0.00 0.00 0.00 3.67
6308 6885 1.662438 GGAGAGTGAGCGGTGAGAGG 61.662 65.000 0.00 0.00 0.00 3.69
6356 6933 0.657840 GCCGTGCAGATATTGTGGTC 59.342 55.000 0.00 0.00 0.00 4.02
6384 6961 2.357517 CCTCCGATGTATGCCCGC 60.358 66.667 0.00 0.00 0.00 6.13
6386 6963 0.886490 CTTGCCTCCGATGTATGCCC 60.886 60.000 0.00 0.00 0.00 5.36
6401 6978 2.029844 GTCACCGTCCAGAGCTTGC 61.030 63.158 0.00 0.00 0.00 4.01
6403 6980 1.837051 TGGTCACCGTCCAGAGCTT 60.837 57.895 0.00 0.00 33.63 3.74
6404 6981 2.203640 TGGTCACCGTCCAGAGCT 60.204 61.111 0.00 0.00 33.63 4.09
6405 6982 2.048127 GTGGTCACCGTCCAGAGC 60.048 66.667 0.00 0.00 35.49 4.09
6406 6983 2.657237 GGTGGTCACCGTCCAGAG 59.343 66.667 4.22 0.00 42.29 3.35
6470 7047 1.144057 CGGGAAATCGAGGGGACAG 59.856 63.158 0.00 0.00 0.00 3.51
6478 7055 3.751246 ACGGTCGCGGGAAATCGA 61.751 61.111 21.31 2.75 0.00 3.59
6479 7056 3.550992 CACGGTCGCGGGAAATCG 61.551 66.667 6.13 11.27 0.00 3.34
6510 7087 6.917217 TCGAATGTGTGCAATGTATAATCA 57.083 33.333 0.00 0.00 0.00 2.57
6515 7092 5.816449 TGAATCGAATGTGTGCAATGTAT 57.184 34.783 0.00 0.00 0.00 2.29
6526 7103 4.222124 AGCCTAACCTTGAATCGAATGT 57.778 40.909 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.