Multiple sequence alignment - TraesCS6D01G108800

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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 TraesCS6D01G108800 chr6D 100.000 4464 0 0 1 4464 73515180 73519643 0.000000e+00 8244.0
1 TraesCS6D01G108800 chr6B 92.012 3355 182 59 772 4075 147878471 147881790 0.000000e+00 4632.0
2 TraesCS6D01G108800 chr6B 89.388 801 53 21 1 782 147865128 147865915 0.000000e+00 979.0
3 TraesCS6D01G108800 chr6B 78.679 333 56 10 388 717 64865985 64866305 1.630000e-49 207.0
4 TraesCS6D01G108800 chr6B 95.604 91 2 1 4374 4464 147882166 147882254 1.290000e-30 145.0
5 TraesCS6D01G108800 chr6A 91.708 1628 61 27 711 2312 89964728 89966307 0.000000e+00 2191.0
6 TraesCS6D01G108800 chr6A 91.587 1355 80 20 2347 3688 89966553 89967886 0.000000e+00 1840.0
7 TraesCS6D01G108800 chr6A 94.947 376 10 7 4095 4464 89968173 89968545 8.320000e-162 580.0
8 TraesCS6D01G108800 chr6A 88.693 398 31 9 1 395 89964157 89964543 1.450000e-129 473.0
9 TraesCS6D01G108800 chr6A 85.619 299 28 6 3755 4047 89967888 89968177 2.610000e-77 300.0
10 TraesCS6D01G108800 chrUn 76.937 555 97 22 2327 2876 28698607 28698079 2.030000e-73 287.0
11 TraesCS6D01G108800 chrUn 80.000 340 53 12 388 722 101395522 101395193 2.080000e-58 237.0
12 TraesCS6D01G108800 chr1B 79.221 385 70 10 2495 2876 670293811 670293434 4.430000e-65 259.0
13 TraesCS6D01G108800 chr4B 77.545 334 51 13 385 713 168983147 168982833 3.550000e-41 180.0
14 TraesCS6D01G108800 chr5A 80.435 92 15 3 63 152 547724740 547724830 2.880000e-07 67.6


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 TraesCS6D01G108800 chr6D 73515180 73519643 4463 False 8244.0 8244 100.0000 1 4464 1 chr6D.!!$F1 4463
1 TraesCS6D01G108800 chr6B 147878471 147882254 3783 False 2388.5 4632 93.8080 772 4464 2 chr6B.!!$F3 3692
2 TraesCS6D01G108800 chr6B 147865128 147865915 787 False 979.0 979 89.3880 1 782 1 chr6B.!!$F2 781
3 TraesCS6D01G108800 chr6A 89964157 89968545 4388 False 1076.8 2191 90.5108 1 4464 5 chr6A.!!$F1 4463
4 TraesCS6D01G108800 chrUn 28698079 28698607 528 True 287.0 287 76.9370 2327 2876 1 chrUn.!!$R1 549

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
540 552 0.467474 ATGACATCGTAGGGGCTCGA 60.467 55.0 0.0 0.0 40.28 4.04 F
1448 1475 0.179018 ATTGGTTATGCCGAGGAGCC 60.179 55.0 0.0 0.0 41.21 4.70 F
1678 1705 0.108585 ACTCAAGTGTTGCCACCGAT 59.891 50.0 0.0 0.0 42.88 4.18 F
3060 3339 0.250553 TGTAAACACCCCCTTGCTCG 60.251 55.0 0.0 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 1634 0.250513 CTTCTGCCCCCACAGACTAC 59.749 60.0 0.00 0.0 46.13 2.73 R
3244 3526 0.176910 TGGCACAACAGACTGAACGA 59.823 50.0 10.08 0.0 31.92 3.85 R
3252 3534 0.254462 TGGTCAACTGGCACAACAGA 59.746 50.0 0.00 0.0 40.97 3.41 R
4347 4683 0.036306 GGCGTGGGGAAGAAGAAGAA 59.964 55.0 0.00 0.0 0.00 2.52 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
39 40 0.918258 TTCACCCTGGATGCATGCTA 59.082 50.000 20.33 5.73 0.00 3.49
57 58 0.988832 TACTGTAGGCTTTGGGGGTG 59.011 55.000 0.00 0.00 0.00 4.61
73 74 2.561569 GGGTGTATATATGGCCGATGC 58.438 52.381 0.00 0.00 0.00 3.91
80 81 2.645838 ATATGGCCGATGCTGTTTCT 57.354 45.000 0.00 0.00 37.74 2.52
120 124 7.625498 TTTTCTTAAATGAAAATGGGGTCCT 57.375 32.000 0.00 0.00 39.92 3.85
174 182 5.865552 CACATGAAAACCTCTTTAATGGCAG 59.134 40.000 0.00 0.00 0.00 4.85
177 185 4.522789 TGAAAACCTCTTTAATGGCAGGAC 59.477 41.667 0.00 0.00 0.00 3.85
182 190 6.079712 ACCTCTTTAATGGCAGGACTAAAT 57.920 37.500 0.00 0.00 0.00 1.40
189 197 9.353999 CTTTAATGGCAGGACTAAATAAACAAC 57.646 33.333 0.00 0.00 0.00 3.32
192 201 6.509418 TGGCAGGACTAAATAAACAACATC 57.491 37.500 0.00 0.00 0.00 3.06
216 225 5.825151 CAGAATAAAGGAGGATTCCAAGGTC 59.175 44.000 5.29 0.00 46.64 3.85
238 247 8.699283 GGTCATTACCCACTCGAATATTATAC 57.301 38.462 0.00 0.00 40.21 1.47
239 248 8.529476 GGTCATTACCCACTCGAATATTATACT 58.471 37.037 0.00 0.00 40.21 2.12
246 255 9.256228 ACCCACTCGAATATTATACTGTATGAT 57.744 33.333 10.51 10.03 0.00 2.45
247 256 9.521503 CCCACTCGAATATTATACTGTATGATG 57.478 37.037 13.54 1.11 0.00 3.07
339 349 8.762426 ACAAAGAGTTTCTCGAATAAGTTACAC 58.238 33.333 0.00 0.00 35.36 2.90
345 355 5.386958 TCTCGAATAAGTTACACTGCACT 57.613 39.130 0.00 0.00 0.00 4.40
394 404 0.736053 TGAGGACAACGTTTTGGTGC 59.264 50.000 0.00 0.00 37.00 5.01
399 409 0.681564 ACAACGTTTTGGTGCTGGGA 60.682 50.000 0.00 0.00 37.00 4.37
482 493 8.733857 ATTTCGATTTCTTTGACATGAAAGAC 57.266 30.769 8.65 0.00 40.80 3.01
509 521 8.021396 GCACAAGTTTTCTAGGGTATGTAAAAG 58.979 37.037 0.00 0.00 0.00 2.27
516 528 9.629878 TTTTCTAGGGTATGTAAAAGTTTGTGA 57.370 29.630 0.00 0.00 0.00 3.58
519 531 4.758165 AGGGTATGTAAAAGTTTGTGACGG 59.242 41.667 0.00 0.00 0.00 4.79
539 551 1.068472 GTATGACATCGTAGGGGCTCG 60.068 57.143 0.00 0.00 0.00 5.03
540 552 0.467474 ATGACATCGTAGGGGCTCGA 60.467 55.000 0.00 0.00 40.28 4.04
545 557 0.820074 ATCGTAGGGGCTCGAGACAG 60.820 60.000 22.31 5.61 39.38 3.51
738 752 4.837093 AATTTACTGTTCATCCGGGAGA 57.163 40.909 0.00 0.00 0.00 3.71
761 782 4.870426 ACTCGTGTCCAGCTATGTATTTTG 59.130 41.667 0.00 0.00 0.00 2.44
790 811 1.221466 TGCGCTAATGTATGAGCCGC 61.221 55.000 9.73 9.59 38.12 6.53
795 816 2.469826 CTAATGTATGAGCCGCGACAA 58.530 47.619 8.23 0.00 0.00 3.18
870 894 8.560124 AATCCATTTGGGCCTGTTTATAATTA 57.440 30.769 4.53 0.00 36.21 1.40
871 895 7.595819 TCCATTTGGGCCTGTTTATAATTAG 57.404 36.000 4.53 0.00 36.21 1.73
872 896 7.358263 TCCATTTGGGCCTGTTTATAATTAGA 58.642 34.615 4.53 0.00 36.21 2.10
874 898 8.482128 CCATTTGGGCCTGTTTATAATTAGAAA 58.518 33.333 4.53 1.14 0.00 2.52
875 899 9.883142 CATTTGGGCCTGTTTATAATTAGAAAA 57.117 29.630 4.53 0.00 0.00 2.29
895 919 5.750352 AAAAATCGTCAGAGGGGTTAGTA 57.250 39.130 0.00 0.00 0.00 1.82
904 928 5.837438 GTCAGAGGGGTTAGTATAAGGCTTA 59.163 44.000 9.79 9.79 0.00 3.09
994 1021 4.394712 CCCAGGACAGGTGACGCC 62.395 72.222 0.00 0.00 37.58 5.68
997 1024 4.988716 AGGACAGGTGACGCCCGA 62.989 66.667 0.08 0.00 38.26 5.14
1252 1279 3.782443 CCGAACCTTCCGGGGGAG 61.782 72.222 18.76 7.30 43.05 4.30
1298 1325 5.232414 GTGTTAGATGAAATGCCTACGAGAC 59.768 44.000 0.00 0.00 0.00 3.36
1448 1475 0.179018 ATTGGTTATGCCGAGGAGCC 60.179 55.000 0.00 0.00 41.21 4.70
1494 1521 0.318120 CTGCTGTGCGGGGAAATTTT 59.682 50.000 0.00 0.00 0.00 1.82
1550 1577 3.126171 TCGAACCCACTGCAAATTATTCG 59.874 43.478 13.11 13.11 39.14 3.34
1578 1605 8.226448 CGATTGAGATGCTATTTCAATTCCTAC 58.774 37.037 12.70 3.92 40.56 3.18
1607 1634 7.308348 CCCCAGTAAACCAAAATATATGTAGCG 60.308 40.741 0.00 0.00 0.00 4.26
1619 1646 1.112113 ATGTAGCGTAGTCTGTGGGG 58.888 55.000 0.00 0.00 0.00 4.96
1624 1651 1.982395 CGTAGTCTGTGGGGGCAGA 60.982 63.158 0.00 0.00 42.56 4.26
1678 1705 0.108585 ACTCAAGTGTTGCCACCGAT 59.891 50.000 0.00 0.00 42.88 4.18
1686 1713 3.440173 AGTGTTGCCACCGATTTCTAATG 59.560 43.478 0.00 0.00 42.88 1.90
1857 1884 2.079925 AGTTCTGAATCCAAGAAGCGC 58.920 47.619 0.00 0.00 0.00 5.92
1926 1954 4.778534 AATTCAGCATTCTTCCACAGTG 57.221 40.909 0.00 0.00 0.00 3.66
1939 1977 1.543208 CCACAGTGCAGTCCAGCTTTA 60.543 52.381 0.00 0.00 34.99 1.85
1944 1982 5.048782 CACAGTGCAGTCCAGCTTTATTTTA 60.049 40.000 0.00 0.00 34.99 1.52
1945 1983 5.711976 ACAGTGCAGTCCAGCTTTATTTTAT 59.288 36.000 0.00 0.00 34.99 1.40
1946 1984 6.209391 ACAGTGCAGTCCAGCTTTATTTTATT 59.791 34.615 0.00 0.00 34.99 1.40
1947 1985 7.092716 CAGTGCAGTCCAGCTTTATTTTATTT 58.907 34.615 0.00 0.00 34.99 1.40
1948 1986 7.599998 CAGTGCAGTCCAGCTTTATTTTATTTT 59.400 33.333 0.00 0.00 34.99 1.82
1949 1987 8.802267 AGTGCAGTCCAGCTTTATTTTATTTTA 58.198 29.630 0.00 0.00 34.99 1.52
1950 1988 9.586435 GTGCAGTCCAGCTTTATTTTATTTTAT 57.414 29.630 0.00 0.00 34.99 1.40
2027 2068 2.560105 GCTGAGGTTGGAAGAAGCATTT 59.440 45.455 0.00 0.00 0.00 2.32
2028 2069 3.006217 GCTGAGGTTGGAAGAAGCATTTT 59.994 43.478 0.00 0.00 0.00 1.82
2029 2070 4.218417 GCTGAGGTTGGAAGAAGCATTTTA 59.782 41.667 0.00 0.00 0.00 1.52
2030 2071 5.278957 GCTGAGGTTGGAAGAAGCATTTTAA 60.279 40.000 0.00 0.00 0.00 1.52
2031 2072 6.331369 TGAGGTTGGAAGAAGCATTTTAAG 57.669 37.500 0.00 0.00 0.00 1.85
2033 2074 6.323739 TGAGGTTGGAAGAAGCATTTTAAGTT 59.676 34.615 0.00 0.00 0.00 2.66
2034 2075 7.124573 AGGTTGGAAGAAGCATTTTAAGTTT 57.875 32.000 0.00 0.00 0.00 2.66
2180 2237 9.720769 GCTAGGCTGGTGAATTTATAATACTAA 57.279 33.333 0.00 0.00 0.00 2.24
2226 2285 2.937591 TCATTGTCGGTCGTCAACTAC 58.062 47.619 5.33 0.00 0.00 2.73
2227 2286 2.555325 TCATTGTCGGTCGTCAACTACT 59.445 45.455 5.33 0.00 0.00 2.57
2305 2364 5.758296 TGTCCTTTACACTTGTGAGATTGAC 59.242 40.000 7.83 8.56 31.43 3.18
2383 2656 5.686841 TGATCTGATTGTTTTTCTGTTTGCG 59.313 36.000 0.00 0.00 0.00 4.85
2447 2720 4.887655 AGGTGCTAGGGTTTAATATGCAAC 59.112 41.667 0.00 0.00 36.97 4.17
2466 2739 4.508861 GCAACATAATCATGCCCATCAAAC 59.491 41.667 0.00 0.00 35.39 2.93
2493 2766 7.974482 TGGACTATTTCTGATATGCTTGATG 57.026 36.000 0.00 0.00 0.00 3.07
2583 2857 5.608437 AGATTGCTATCCATGGAAGAGGTAA 59.392 40.000 20.67 14.16 0.00 2.85
2592 2866 5.191722 TCCATGGAAGAGGTAATTAACTGCT 59.808 40.000 13.46 2.36 0.00 4.24
2619 2893 6.547141 TCCAAGCATCCAGTTAATCCATAAAG 59.453 38.462 0.00 0.00 0.00 1.85
2731 3006 4.249661 GGAGAGCAAACTCAGGTAAAGAG 58.750 47.826 0.00 0.00 46.09 2.85
2734 3009 5.930135 AGAGCAAACTCAGGTAAAGAGAAA 58.070 37.500 0.00 0.00 46.09 2.52
2735 3010 5.994668 AGAGCAAACTCAGGTAAAGAGAAAG 59.005 40.000 0.00 0.00 46.09 2.62
2742 3017 5.061721 TCAGGTAAAGAGAAAGGCCTTTT 57.938 39.130 30.89 20.11 34.74 2.27
2749 3024 3.969553 AGAGAAAGGCCTTTTATGGGAC 58.030 45.455 30.89 16.40 32.11 4.46
3010 3289 5.012239 TCTAAACTTGCTTCCATGCTGATT 58.988 37.500 0.00 0.00 0.00 2.57
3023 3302 3.937778 TGCTGATTCCTTGGATCATCA 57.062 42.857 0.00 4.54 33.39 3.07
3056 3335 5.505780 TCTGATAATGTAAACACCCCCTTG 58.494 41.667 0.00 0.00 0.00 3.61
3057 3336 4.020543 TGATAATGTAAACACCCCCTTGC 58.979 43.478 0.00 0.00 0.00 4.01
3058 3337 2.694616 AATGTAAACACCCCCTTGCT 57.305 45.000 0.00 0.00 0.00 3.91
3059 3338 2.215942 ATGTAAACACCCCCTTGCTC 57.784 50.000 0.00 0.00 0.00 4.26
3060 3339 0.250553 TGTAAACACCCCCTTGCTCG 60.251 55.000 0.00 0.00 0.00 5.03
3164 3444 6.396829 AGCTTAAAACTGCAGAAAATGAGT 57.603 33.333 23.35 0.00 0.00 3.41
3171 3451 6.699575 AACTGCAGAAAATGAGTGTAAGTT 57.300 33.333 23.35 0.00 0.00 2.66
3182 3462 7.923414 AATGAGTGTAAGTTTAATCTGGACC 57.077 36.000 0.00 0.00 0.00 4.46
3204 3484 2.412870 GTGGGCCAAATAAACAAGTGC 58.587 47.619 8.40 0.00 0.00 4.40
3223 3504 3.764885 GCTTTTGCGAACCATGTAGAT 57.235 42.857 0.00 0.00 34.86 1.98
3226 3507 4.558860 GCTTTTGCGAACCATGTAGATTTC 59.441 41.667 0.00 0.00 34.86 2.17
3244 3526 6.472016 AGATTTCAAACAGTTTTGGGTTGTT 58.528 32.000 0.00 0.00 42.23 2.83
3251 3533 3.119637 ACAGTTTTGGGTTGTTCGTTCAG 60.120 43.478 0.00 0.00 0.00 3.02
3252 3534 3.086282 AGTTTTGGGTTGTTCGTTCAGT 58.914 40.909 0.00 0.00 0.00 3.41
3255 3537 1.948104 TGGGTTGTTCGTTCAGTCTG 58.052 50.000 0.00 0.00 0.00 3.51
3267 3556 1.667236 TCAGTCTGTTGTGCCAGTTG 58.333 50.000 0.00 0.00 34.02 3.16
3275 3564 1.102154 TTGTGCCAGTTGACCACTTG 58.898 50.000 0.00 0.00 30.92 3.16
3283 3572 2.355756 CAGTTGACCACTTGTTGACAGG 59.644 50.000 0.00 0.00 30.92 4.00
3284 3573 1.676006 GTTGACCACTTGTTGACAGGG 59.324 52.381 0.00 0.00 0.00 4.45
3289 3578 3.222603 ACCACTTGTTGACAGGGATTTC 58.777 45.455 0.00 0.00 0.00 2.17
3296 3590 4.335416 TGTTGACAGGGATTTCATCTTCC 58.665 43.478 0.00 0.00 0.00 3.46
3475 3769 3.746949 CTCATGAGAGCCGGCACCC 62.747 68.421 31.54 15.00 34.61 4.61
3508 3802 0.883370 GTTCCAAACCCTTCGTCGCT 60.883 55.000 0.00 0.00 0.00 4.93
3512 3806 0.921347 CAAACCCTTCGTCGCTATCG 59.079 55.000 0.00 0.00 0.00 2.92
3543 3845 1.151246 TTTCCCTCCCCAATCCCCA 60.151 57.895 0.00 0.00 0.00 4.96
3544 3846 1.514864 TTTCCCTCCCCAATCCCCAC 61.515 60.000 0.00 0.00 0.00 4.61
3545 3847 3.429580 CCCTCCCCAATCCCCACC 61.430 72.222 0.00 0.00 0.00 4.61
3546 3848 2.287194 CCTCCCCAATCCCCACCT 60.287 66.667 0.00 0.00 0.00 4.00
3547 3849 2.386935 CCTCCCCAATCCCCACCTC 61.387 68.421 0.00 0.00 0.00 3.85
3548 3850 2.286885 TCCCCAATCCCCACCTCC 60.287 66.667 0.00 0.00 0.00 4.30
3549 3851 2.616893 CCCCAATCCCCACCTCCA 60.617 66.667 0.00 0.00 0.00 3.86
3557 3859 1.979809 TCCCCACCTCCAATGTACAT 58.020 50.000 1.41 1.41 0.00 2.29
3563 3865 3.440173 CCACCTCCAATGTACATTCACAC 59.560 47.826 18.25 0.00 0.00 3.82
3571 3873 2.073056 TGTACATTCACACGCACCATC 58.927 47.619 0.00 0.00 0.00 3.51
3574 3876 1.270785 ACATTCACACGCACCATCTCA 60.271 47.619 0.00 0.00 0.00 3.27
3575 3877 1.805943 CATTCACACGCACCATCTCAA 59.194 47.619 0.00 0.00 0.00 3.02
3576 3878 1.225855 TTCACACGCACCATCTCAAC 58.774 50.000 0.00 0.00 0.00 3.18
3578 3880 0.884259 CACACGCACCATCTCAACCA 60.884 55.000 0.00 0.00 0.00 3.67
3579 3881 0.036732 ACACGCACCATCTCAACCAT 59.963 50.000 0.00 0.00 0.00 3.55
3580 3882 0.729116 CACGCACCATCTCAACCATC 59.271 55.000 0.00 0.00 0.00 3.51
3581 3883 0.324614 ACGCACCATCTCAACCATCA 59.675 50.000 0.00 0.00 0.00 3.07
3593 3895 4.761739 TCTCAACCATCACAGTGATTTTCC 59.238 41.667 13.79 0.00 34.28 3.13
3604 3906 3.753272 CAGTGATTTTCCCGTGTTGAGAT 59.247 43.478 0.00 0.00 0.00 2.75
3640 3947 3.864789 ATGGTCATACAATCAGGGGTC 57.135 47.619 0.00 0.00 0.00 4.46
3718 4025 1.222113 TGGCACGTTCAGTTCCACA 59.778 52.632 0.00 0.00 41.20 4.17
3735 4042 7.012327 CAGTTCCACACTTTGATGTTCTTCTTA 59.988 37.037 0.00 0.00 30.92 2.10
3758 4066 0.530211 CGAAGCATGCAGAGGAGAGG 60.530 60.000 21.98 0.00 0.00 3.69
3759 4067 0.829333 GAAGCATGCAGAGGAGAGGA 59.171 55.000 21.98 0.00 0.00 3.71
3760 4068 0.831966 AAGCATGCAGAGGAGAGGAG 59.168 55.000 21.98 0.00 0.00 3.69
3761 4069 0.032316 AGCATGCAGAGGAGAGGAGA 60.032 55.000 21.98 0.00 0.00 3.71
3762 4070 0.390124 GCATGCAGAGGAGAGGAGAG 59.610 60.000 14.21 0.00 0.00 3.20
3856 4167 6.665680 ACATGTTATGAGAACTGGTAGAGACT 59.334 38.462 0.00 0.00 0.00 3.24
3910 4221 6.350103 TGGAAGTGACAAATACAGTACACAA 58.650 36.000 0.00 0.00 0.00 3.33
4054 4368 2.202395 AGCGTTTGGTGGCTTGCAT 61.202 52.632 0.00 0.00 35.61 3.96
4060 4374 0.037139 TTGGTGGCTTGCATTGCATC 60.037 50.000 12.95 7.47 38.76 3.91
4102 4438 1.475280 CATTGCATTCCCTGGTGTCTG 59.525 52.381 0.00 0.00 0.00 3.51
4172 4508 1.438814 CAGGCCCATTGCGATTTCC 59.561 57.895 0.00 0.00 42.61 3.13
4341 4677 2.277072 CTCCCCCGCTCTCTCTCA 59.723 66.667 0.00 0.00 0.00 3.27
4343 4679 3.151022 CCCCCGCTCTCTCTCACC 61.151 72.222 0.00 0.00 0.00 4.02
4345 4681 2.363018 CCCGCTCTCTCTCACCCA 60.363 66.667 0.00 0.00 0.00 4.51
4347 4683 1.680651 CCGCTCTCTCTCACCCACT 60.681 63.158 0.00 0.00 0.00 4.00
4348 4684 1.254284 CCGCTCTCTCTCACCCACTT 61.254 60.000 0.00 0.00 0.00 3.16
4369 4705 1.838073 TTCTTCTTCCCCACGCCTCC 61.838 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.908453 TCCAGGGTGAAAAACTAAAAGAAAAA 58.092 30.769 0.00 0.00 0.00 1.94
39 40 1.065997 ACACCCCCAAAGCCTACAGT 61.066 55.000 0.00 0.00 0.00 3.55
57 58 5.178797 AGAAACAGCATCGGCCATATATAC 58.821 41.667 2.24 0.00 42.56 1.47
120 124 3.524095 TTTCAATCAAAGGAGCCTCCA 57.476 42.857 14.46 0.00 39.61 3.86
182 190 9.753674 AATCCTCCTTTATTCTGATGTTGTTTA 57.246 29.630 0.00 0.00 0.00 2.01
189 197 6.489361 CCTTGGAATCCTCCTTTATTCTGATG 59.511 42.308 0.00 0.00 42.94 3.07
192 201 5.760131 ACCTTGGAATCCTCCTTTATTCTG 58.240 41.667 0.00 0.00 42.94 3.02
339 349 6.541278 TCTTCTGATGATTTTATCCAGTGCAG 59.459 38.462 0.00 0.00 0.00 4.41
345 355 6.885918 TGTGCTTCTTCTGATGATTTTATCCA 59.114 34.615 0.00 0.00 0.00 3.41
456 467 9.185192 GTCTTTCATGTCAAAGAAATCGAAATT 57.815 29.630 10.29 0.00 42.68 1.82
457 468 7.535258 CGTCTTTCATGTCAAAGAAATCGAAAT 59.465 33.333 10.29 0.00 42.68 2.17
461 472 4.551126 GCGTCTTTCATGTCAAAGAAATCG 59.449 41.667 10.29 10.77 42.68 3.34
462 473 5.340667 GTGCGTCTTTCATGTCAAAGAAATC 59.659 40.000 10.29 4.97 42.68 2.17
463 474 5.215160 GTGCGTCTTTCATGTCAAAGAAAT 58.785 37.500 10.29 0.00 42.68 2.17
482 493 4.000988 ACATACCCTAGAAAACTTGTGCG 58.999 43.478 0.00 0.00 0.00 5.34
509 521 2.991190 ACGATGTCATACCGTCACAAAC 59.009 45.455 0.00 0.00 29.82 2.93
516 528 1.325355 CCCCTACGATGTCATACCGT 58.675 55.000 5.10 5.10 39.94 4.83
519 531 1.068472 CGAGCCCCTACGATGTCATAC 60.068 57.143 0.00 0.00 0.00 2.39
611 624 0.261991 ACATAGGAGGAGCTCGGGAA 59.738 55.000 7.83 0.00 0.00 3.97
738 752 4.737855 AAATACATAGCTGGACACGAGT 57.262 40.909 0.00 0.00 0.00 4.18
790 811 5.281376 GTGTCAAATTGATTGTCGATTGTCG 59.719 40.000 0.00 0.00 40.11 4.35
795 816 4.518590 TGTGGTGTCAAATTGATTGTCGAT 59.481 37.500 0.00 0.00 40.11 3.59
874 898 5.952347 ATACTAACCCCTCTGACGATTTT 57.048 39.130 0.00 0.00 0.00 1.82
875 899 6.041751 CCTTATACTAACCCCTCTGACGATTT 59.958 42.308 0.00 0.00 0.00 2.17
876 900 5.539193 CCTTATACTAACCCCTCTGACGATT 59.461 44.000 0.00 0.00 0.00 3.34
877 901 5.078256 CCTTATACTAACCCCTCTGACGAT 58.922 45.833 0.00 0.00 0.00 3.73
904 928 5.478407 CGAAAATGAAAATTAACCAGGCCT 58.522 37.500 0.00 0.00 0.00 5.19
908 932 4.201580 GCGGCGAAAATGAAAATTAACCAG 60.202 41.667 12.98 0.00 0.00 4.00
1174 1201 2.554893 TGGCGTTGATCCAAACCTAAAC 59.445 45.455 0.00 0.00 0.00 2.01
1252 1279 2.025359 GAGCGTATCTGTGTTGGCGC 62.025 60.000 0.00 0.00 44.36 6.53
1263 1290 4.569761 TCATCTAACACCTGAGCGTATC 57.430 45.455 0.00 0.00 0.00 2.24
1494 1521 2.288213 CGCTGGAGTTGAACTACTGTGA 60.288 50.000 19.45 0.00 39.85 3.58
1550 1577 7.041508 AGGAATTGAAATAGCATCTCAATCGAC 60.042 37.037 0.00 0.53 38.52 4.20
1578 1605 6.544564 ACATATATTTTGGTTTACTGGGGACG 59.455 38.462 0.00 0.00 0.00 4.79
1607 1634 0.250513 CTTCTGCCCCCACAGACTAC 59.749 60.000 0.00 0.00 46.13 2.73
1619 1646 6.749923 ATTACAAAATCACTCTCTTCTGCC 57.250 37.500 0.00 0.00 0.00 4.85
1624 1651 8.295288 CAGCAGAAATTACAAAATCACTCTCTT 58.705 33.333 0.00 0.00 0.00 2.85
1678 1705 8.637986 AGGCAATGAAAACTGTTACATTAGAAA 58.362 29.630 18.38 0.00 32.75 2.52
1686 1713 8.865590 TTTTCTTAGGCAATGAAAACTGTTAC 57.134 30.769 0.00 0.00 35.57 2.50
1734 1761 5.892160 AGATCAACACATCACAGGAAATG 57.108 39.130 0.00 0.00 0.00 2.32
1857 1884 2.194800 TATGCGACTCAAGAGCTTCG 57.805 50.000 5.92 5.92 32.29 3.79
1954 1992 9.590451 CATGATTTACATTAACAGGAAAGCAAT 57.410 29.630 8.82 0.00 37.07 3.56
2113 2154 7.621991 CACATAGCATTACAGTAAGTAGCAAC 58.378 38.462 14.23 0.00 33.43 4.17
2149 2190 1.776662 ATTCACCAGCCTAGCGTAGA 58.223 50.000 0.00 0.00 0.00 2.59
2210 2269 1.002142 CACAGTAGTTGACGACCGACA 60.002 52.381 0.00 0.00 0.00 4.35
2226 2285 8.722480 TTAACTGATTTCATCTACATCCACAG 57.278 34.615 0.00 0.00 0.00 3.66
2227 2286 8.321353 ACTTAACTGATTTCATCTACATCCACA 58.679 33.333 0.00 0.00 0.00 4.17
2246 2305 7.122353 TCTCGAGCTAAGACCATTAACTTAACT 59.878 37.037 7.81 0.00 30.85 2.24
2255 2314 3.093057 ACAGTCTCGAGCTAAGACCATT 58.907 45.455 19.94 6.76 43.41 3.16
2305 2364 4.083110 GGACCAGAATGTCAACACATGAAG 60.083 45.833 0.00 0.00 42.89 3.02
2447 2720 6.434965 TCCATAGTTTGATGGGCATGATTATG 59.565 38.462 0.00 0.00 45.67 1.90
2466 2739 9.887629 ATCAAGCATATCAGAAATAGTCCATAG 57.112 33.333 0.00 0.00 0.00 2.23
2592 2866 4.671831 TGGATTAACTGGATGCTTGGAAA 58.328 39.130 0.00 0.00 0.00 3.13
2731 3006 2.163613 CACGTCCCATAAAAGGCCTTTC 59.836 50.000 30.49 15.10 31.45 2.62
2734 3009 0.988832 TCACGTCCCATAAAAGGCCT 59.011 50.000 0.00 0.00 0.00 5.19
2735 3010 1.092348 GTCACGTCCCATAAAAGGCC 58.908 55.000 0.00 0.00 0.00 5.19
2742 3017 6.208007 CCTACAGTAATATGTCACGTCCCATA 59.792 42.308 6.24 6.24 34.56 2.74
2749 3024 6.387041 TTCTCCCTACAGTAATATGTCACG 57.613 41.667 0.00 0.00 34.56 4.35
2811 3086 5.409826 CGGAAGTTAGCTCTTCAGTTTTCAT 59.590 40.000 15.01 0.00 43.72 2.57
3010 3289 5.471424 AGATAAGAGGTGATGATCCAAGGA 58.529 41.667 0.00 0.00 0.00 3.36
3056 3335 5.505165 TCGTTTTTATCTGTAACACGAGC 57.495 39.130 0.00 0.00 33.81 5.03
3057 3336 8.477709 GGATATCGTTTTTATCTGTAACACGAG 58.522 37.037 0.00 0.00 38.31 4.18
3058 3337 7.975058 TGGATATCGTTTTTATCTGTAACACGA 59.025 33.333 0.00 0.00 38.81 4.35
3059 3338 8.122306 TGGATATCGTTTTTATCTGTAACACG 57.878 34.615 0.00 0.00 32.11 4.49
3060 3339 8.548721 CCTGGATATCGTTTTTATCTGTAACAC 58.451 37.037 0.00 0.00 0.00 3.32
3164 3444 4.563993 CCACCGGTCCAGATTAAACTTACA 60.564 45.833 2.59 0.00 0.00 2.41
3171 3451 1.605453 GCCCACCGGTCCAGATTAA 59.395 57.895 2.59 0.00 0.00 1.40
3182 3462 1.616374 ACTTGTTTATTTGGCCCACCG 59.384 47.619 0.00 0.00 39.70 4.94
3204 3484 5.698832 TGAAATCTACATGGTTCGCAAAAG 58.301 37.500 0.00 0.00 0.00 2.27
3210 3490 6.241207 ACTGTTTGAAATCTACATGGTTCG 57.759 37.500 0.00 0.00 0.00 3.95
3211 3491 8.755018 CAAAACTGTTTGAAATCTACATGGTTC 58.245 33.333 6.53 0.00 45.99 3.62
3216 3497 7.360113 ACCCAAAACTGTTTGAAATCTACAT 57.640 32.000 6.53 0.00 45.99 2.29
3219 3500 7.176589 ACAACCCAAAACTGTTTGAAATCTA 57.823 32.000 6.53 0.00 45.99 1.98
3223 3504 4.686554 CGAACAACCCAAAACTGTTTGAAA 59.313 37.500 6.53 0.00 45.99 2.69
3226 3507 3.580731 ACGAACAACCCAAAACTGTTTG 58.419 40.909 6.53 1.63 43.26 2.93
3244 3526 0.176910 TGGCACAACAGACTGAACGA 59.823 50.000 10.08 0.00 31.92 3.85
3251 3533 0.663153 GGTCAACTGGCACAACAGAC 59.337 55.000 0.00 0.00 40.97 3.51
3252 3534 0.254462 TGGTCAACTGGCACAACAGA 59.746 50.000 0.00 0.00 40.97 3.41
3255 3537 1.102978 AAGTGGTCAACTGGCACAAC 58.897 50.000 0.00 0.00 39.81 3.32
3267 3556 2.568623 ATCCCTGTCAACAAGTGGTC 57.431 50.000 0.00 0.00 0.00 4.02
3370 3664 1.005748 CTGCTTCAGCGACTCCACA 60.006 57.895 0.00 0.00 45.83 4.17
3494 3788 0.813184 TCGATAGCGACGAAGGGTTT 59.187 50.000 0.00 0.00 42.51 3.27
3512 3806 2.419713 GGAGGGAAACTACGATGGGTTC 60.420 54.545 0.00 0.00 0.00 3.62
3516 3810 0.468648 GGGGAGGGAAACTACGATGG 59.531 60.000 0.00 0.00 0.00 3.51
3519 3813 1.835531 GATTGGGGAGGGAAACTACGA 59.164 52.381 0.00 0.00 0.00 3.43
3520 3814 1.134189 GGATTGGGGAGGGAAACTACG 60.134 57.143 0.00 0.00 0.00 3.51
3543 3845 3.334691 CGTGTGAATGTACATTGGAGGT 58.665 45.455 25.42 0.00 32.43 3.85
3544 3846 2.095853 GCGTGTGAATGTACATTGGAGG 59.904 50.000 25.42 14.04 32.43 4.30
3545 3847 2.741517 TGCGTGTGAATGTACATTGGAG 59.258 45.455 25.42 12.40 32.43 3.86
3546 3848 2.482336 GTGCGTGTGAATGTACATTGGA 59.518 45.455 25.42 9.21 32.43 3.53
3547 3849 2.414029 GGTGCGTGTGAATGTACATTGG 60.414 50.000 25.42 10.06 32.43 3.16
3548 3850 2.225255 TGGTGCGTGTGAATGTACATTG 59.775 45.455 25.42 11.63 32.43 2.82
3549 3851 2.499197 TGGTGCGTGTGAATGTACATT 58.501 42.857 20.93 20.93 32.43 2.71
3557 3859 1.225855 GTTGAGATGGTGCGTGTGAA 58.774 50.000 0.00 0.00 0.00 3.18
3563 3865 0.729116 GTGATGGTTGAGATGGTGCG 59.271 55.000 0.00 0.00 0.00 5.34
3571 3873 4.082571 GGGAAAATCACTGTGATGGTTGAG 60.083 45.833 22.91 0.00 37.15 3.02
3574 3876 2.819608 CGGGAAAATCACTGTGATGGTT 59.180 45.455 22.91 18.88 37.15 3.67
3575 3877 2.224769 ACGGGAAAATCACTGTGATGGT 60.225 45.455 22.91 14.02 37.15 3.55
3576 3878 2.162208 CACGGGAAAATCACTGTGATGG 59.838 50.000 22.91 11.04 44.70 3.51
3578 3880 3.140325 ACACGGGAAAATCACTGTGAT 57.860 42.857 17.24 17.24 44.70 3.06
3579 3881 2.616376 CAACACGGGAAAATCACTGTGA 59.384 45.455 13.60 13.60 44.70 3.58
3580 3882 2.616376 TCAACACGGGAAAATCACTGTG 59.384 45.455 0.17 0.17 46.69 3.66
3581 3883 2.878406 CTCAACACGGGAAAATCACTGT 59.122 45.455 0.00 0.00 0.00 3.55
3593 3895 3.393800 ACTGTTTCTCATCTCAACACGG 58.606 45.455 0.00 0.00 0.00 4.94
3640 3947 4.929808 GGTAATCAGTGGTCTTACTGTGTG 59.070 45.833 5.89 0.00 46.32 3.82
3653 3960 6.566564 GCATACATTTCATCCGGTAATCAGTG 60.567 42.308 0.00 0.00 0.00 3.66
3718 4025 6.049955 TCGGGATAAGAAGAACATCAAAGT 57.950 37.500 0.00 0.00 0.00 2.66
3735 4042 1.147824 CCTCTGCATGCTTCGGGAT 59.852 57.895 20.33 0.00 0.00 3.85
3835 4144 5.163499 CCCAGTCTCTACCAGTTCTCATAAC 60.163 48.000 0.00 0.00 0.00 1.89
3856 4167 1.694150 CTCTGAACAGAACACTCCCCA 59.306 52.381 6.01 0.00 36.94 4.96
3910 4221 3.276857 CTCCAGCATGCATACTCACTTT 58.723 45.455 21.98 0.00 31.97 2.66
4081 4417 0.819582 GACACCAGGGAATGCAATGG 59.180 55.000 0.00 0.00 38.83 3.16
4092 4428 3.978272 GCTGAAGCAGACACCAGG 58.022 61.111 0.00 0.00 41.59 4.45
4102 4438 1.470098 ACGAACCAATCATGCTGAAGC 59.530 47.619 0.00 0.00 42.50 3.86
4113 4449 1.068434 CACAGGGCAAAACGAACCAAT 59.932 47.619 0.00 0.00 0.00 3.16
4114 4450 0.457851 CACAGGGCAAAACGAACCAA 59.542 50.000 0.00 0.00 0.00 3.67
4151 4487 1.669999 AAATCGCAATGGGCCTGCTC 61.670 55.000 14.92 0.00 40.31 4.26
4341 4677 1.705745 GGGGAAGAAGAAGAAGTGGGT 59.294 52.381 0.00 0.00 0.00 4.51
4343 4679 2.784347 GTGGGGAAGAAGAAGAAGTGG 58.216 52.381 0.00 0.00 0.00 4.00
4345 4681 1.270893 GCGTGGGGAAGAAGAAGAAGT 60.271 52.381 0.00 0.00 0.00 3.01
4347 4683 0.036306 GGCGTGGGGAAGAAGAAGAA 59.964 55.000 0.00 0.00 0.00 2.52
4348 4684 0.836400 AGGCGTGGGGAAGAAGAAGA 60.836 55.000 0.00 0.00 0.00 2.87
4369 4705 2.124695 GGTTTAGCAGGCGGAGGG 60.125 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.