Multiple sequence alignment - TraesCS2D01G408700

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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 TraesCS2D01G408700 chr2D 100.000 3678 0 0 1 3678 523624419 523628096 0.000000e+00 6793.0
1 TraesCS2D01G408700 chr2B 92.877 3229 159 36 1 3209 617931288 617934465 0.000000e+00 4623.0
2 TraesCS2D01G408700 chr2B 79.070 172 11 15 3342 3511 617935634 617935782 1.090000e-15 95.3
3 TraesCS2D01G408700 chr2A 91.137 3238 166 53 1 3191 669429267 669432430 0.000000e+00 4277.0
4 TraesCS2D01G408700 chr2A 77.303 445 54 29 3248 3675 669434060 669434474 6.180000e-53 219.0


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 TraesCS2D01G408700 chr2D 523624419 523628096 3677 False 6793.00 6793 100.0000 1 3678 1 chr2D.!!$F1 3677
1 TraesCS2D01G408700 chr2B 617931288 617935782 4494 False 2359.15 4623 85.9735 1 3511 2 chr2B.!!$F1 3510
2 TraesCS2D01G408700 chr2A 669429267 669434474 5207 False 2248.00 4277 84.2200 1 3675 2 chr2A.!!$F1 3674

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
209 212 0.183731 CCCTTCCCTTGGGCTCATAC 59.816 60.0 0.00 0.00 37.99 2.39 F
1665 1690 0.391661 TTTCTGGCTCACTGATCGCC 60.392 55.0 2.88 2.88 44.02 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1783 0.102481 CTATCACCTCGGGGTCAACG 59.898 60.0 2.28 0.0 45.41 4.10 R
3373 5995 0.034896 ACATCGGCCACGTCTCTTTT 59.965 50.0 2.24 0.0 41.85 2.27 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
69 70 2.626840 CAACTTTAGCCTCTCTGCTCC 58.373 52.381 0.00 0.00 41.68 4.70
130 133 0.884704 TTGCTTCTGTTGTCGGGCTC 60.885 55.000 0.00 0.00 0.00 4.70
187 190 6.126215 TGCTTCTTCCCCTTTATATTCATCCA 60.126 38.462 0.00 0.00 0.00 3.41
209 212 0.183731 CCCTTCCCTTGGGCTCATAC 59.816 60.000 0.00 0.00 37.99 2.39
272 280 1.552337 GCTCAACTGGAGGTGAGATGA 59.448 52.381 23.22 0.00 44.22 2.92
273 281 2.418471 GCTCAACTGGAGGTGAGATGAG 60.418 54.545 23.22 6.95 44.22 2.90
274 282 3.095332 CTCAACTGGAGGTGAGATGAGA 58.905 50.000 15.49 0.00 40.86 3.27
312 320 6.396829 AAGGATGTTTTCTGTTCTCCTTTG 57.603 37.500 0.00 0.00 39.48 2.77
316 324 6.434340 GGATGTTTTCTGTTCTCCTTTGGTAT 59.566 38.462 0.00 0.00 0.00 2.73
352 363 4.627611 ATCAATCCAAGTTCAATCGCAG 57.372 40.909 0.00 0.00 0.00 5.18
373 384 6.568462 CGCAGTTCTTGATTTTGGTAGTGATT 60.568 38.462 0.00 0.00 0.00 2.57
394 405 5.924769 TTATTAGATCTTTCCCCCTTCCC 57.075 43.478 0.00 0.00 0.00 3.97
421 432 6.308766 CGACCAAATCTTCCAATCAATTTCAC 59.691 38.462 0.00 0.00 0.00 3.18
538 549 3.282920 GGCGCTTGGCTATCCTGC 61.283 66.667 7.64 0.00 42.94 4.85
559 570 6.151648 CCTGCTAGGTTGATTCTGATGAAAAA 59.848 38.462 0.00 0.00 35.63 1.94
579 590 8.911965 TGAAAAATGCTCATTTGTAGGCATATA 58.088 29.630 8.43 0.00 43.39 0.86
581 592 9.701098 AAAAATGCTCATTTGTAGGCATATATG 57.299 29.630 8.45 8.45 43.39 1.78
594 605 3.340928 GCATATATGTGCTGATGCCAGA 58.659 45.455 16.44 0.00 43.02 3.86
638 650 4.023279 AGTGATTTAACAATGTTGCGCTCA 60.023 37.500 9.73 8.76 0.00 4.26
639 651 4.088496 GTGATTTAACAATGTTGCGCTCAC 59.912 41.667 9.73 11.72 0.00 3.51
653 665 1.739067 GCTCACAACATCCCACCTAC 58.261 55.000 0.00 0.00 0.00 3.18
655 667 2.356125 GCTCACAACATCCCACCTACAT 60.356 50.000 0.00 0.00 0.00 2.29
663 675 4.703897 ACATCCCACCTACATAATTCGTG 58.296 43.478 0.00 0.00 0.00 4.35
676 688 6.591935 ACATAATTCGTGACATCCAACCTAT 58.408 36.000 0.00 0.00 0.00 2.57
677 689 7.732025 ACATAATTCGTGACATCCAACCTATA 58.268 34.615 0.00 0.00 0.00 1.31
678 690 8.208224 ACATAATTCGTGACATCCAACCTATAA 58.792 33.333 0.00 0.00 0.00 0.98
680 692 7.730364 AATTCGTGACATCCAACCTATAATC 57.270 36.000 0.00 0.00 0.00 1.75
683 695 7.533289 TCGTGACATCCAACCTATAATCATA 57.467 36.000 0.00 0.00 0.00 2.15
684 696 8.134202 TCGTGACATCCAACCTATAATCATAT 57.866 34.615 0.00 0.00 0.00 1.78
686 698 7.492669 CGTGACATCCAACCTATAATCATATCC 59.507 40.741 0.00 0.00 0.00 2.59
687 699 8.543774 GTGACATCCAACCTATAATCATATCCT 58.456 37.037 0.00 0.00 0.00 3.24
688 700 9.782900 TGACATCCAACCTATAATCATATCCTA 57.217 33.333 0.00 0.00 0.00 2.94
690 702 9.218525 ACATCCAACCTATAATCATATCCTAGG 57.781 37.037 0.82 0.82 0.00 3.02
691 703 9.439461 CATCCAACCTATAATCATATCCTAGGA 57.561 37.037 15.46 15.46 0.00 2.94
692 704 9.667607 ATCCAACCTATAATCATATCCTAGGAG 57.332 37.037 18.34 3.73 0.00 3.69
694 706 7.846823 CCAACCTATAATCATATCCTAGGAGGT 59.153 40.741 18.34 11.57 36.53 3.85
698 719 6.805016 ATAATCATATCCTAGGAGGTGCAG 57.195 41.667 18.34 4.06 36.53 4.41
702 723 5.655394 TCATATCCTAGGAGGTGCAGTATT 58.345 41.667 18.34 0.00 36.53 1.89
731 752 9.233232 GTGCTATTTATTTTATTTCAGGAACCG 57.767 33.333 0.00 0.00 0.00 4.44
732 753 9.179909 TGCTATTTATTTTATTTCAGGAACCGA 57.820 29.630 0.00 0.00 0.00 4.69
740 761 1.553706 TTCAGGAACCGACTAGTCCC 58.446 55.000 17.23 12.00 0.00 4.46
962 983 2.202892 GCCTTCTTCCCGGCTACG 60.203 66.667 0.00 0.00 42.98 3.51
968 989 1.255882 TCTTCCCGGCTACGTTAACA 58.744 50.000 6.39 0.00 38.78 2.41
969 990 1.203052 TCTTCCCGGCTACGTTAACAG 59.797 52.381 6.39 1.29 38.78 3.16
975 1000 3.429272 CCCGGCTACGTTAACAGATTGTA 60.429 47.826 6.39 0.00 38.78 2.41
1011 1036 2.600439 CTCACTCATGGGCTCCTCA 58.400 57.895 0.00 0.00 0.00 3.86
1019 1044 1.280133 CATGGGCTCCTCAACTGAGAA 59.720 52.381 8.33 0.00 44.74 2.87
1047 1072 4.000453 GCAGAATGGGTAGCATAAAGCCT 61.000 47.826 0.00 0.00 40.09 4.58
1104 1129 2.557924 CCCTCTCTCCTTCAGATCATCG 59.442 54.545 0.00 0.00 0.00 3.84
1251 1276 5.243981 CCCAGCCATATGTATCTTCAAGAG 58.756 45.833 1.24 0.00 0.00 2.85
1282 1307 3.000080 GCGAACAACACGGCTCTCG 62.000 63.158 0.00 0.00 45.88 4.04
1341 1366 2.642129 CTGCTCGGCGAGATCGAT 59.358 61.111 38.56 0.00 43.02 3.59
1342 1367 1.441849 CTGCTCGGCGAGATCGATC 60.442 63.158 38.56 20.49 43.02 3.69
1344 1369 1.284408 GCTCGGCGAGATCGATCTT 59.716 57.895 38.56 12.68 43.02 2.40
1365 1390 1.959508 GCATTCCTTGGGGTGTATGCA 60.960 52.381 0.00 0.00 39.83 3.96
1383 1408 2.419667 GCAATTGGCATGTTCTTTGCT 58.580 42.857 7.72 0.00 43.97 3.91
1390 1415 1.738030 GCATGTTCTTTGCTGGCCATC 60.738 52.381 5.51 1.26 37.14 3.51
1635 1660 1.374758 CTGGAACGCTCACACCTCC 60.375 63.158 0.00 0.00 0.00 4.30
1641 1666 4.394712 GCTCACACCTCCGTGGGG 62.395 72.222 0.00 0.00 44.14 4.96
1656 1681 0.776810 TGGGGAACATTTCTGGCTCA 59.223 50.000 0.00 0.00 0.00 4.26
1665 1690 0.391661 TTTCTGGCTCACTGATCGCC 60.392 55.000 2.88 2.88 44.02 5.54
1707 1732 1.569479 GGAGCTGGTCGTTTGCAGTC 61.569 60.000 0.00 0.00 0.00 3.51
1710 1735 1.071471 CTGGTCGTTTGCAGTCCCT 59.929 57.895 0.00 0.00 0.00 4.20
1758 1783 0.310854 CCGTGTTTCTGTTCTTGCCC 59.689 55.000 0.00 0.00 0.00 5.36
1764 1789 1.305201 TTCTGTTCTTGCCCGTTGAC 58.695 50.000 0.00 0.00 0.00 3.18
1767 1792 2.114411 TTCTTGCCCGTTGACCCC 59.886 61.111 0.00 0.00 0.00 4.95
1842 1867 1.300963 GGATGTGCCTCTGCTGGAA 59.699 57.895 0.00 0.00 38.71 3.53
1881 1906 1.002134 CGAGGCAGTGGGGTTCATT 60.002 57.895 0.00 0.00 0.00 2.57
1962 1987 1.089920 TCGCCTACACGTTCCTCTAC 58.910 55.000 0.00 0.00 0.00 2.59
1968 1993 1.339097 ACACGTTCCTCTACTGGCTT 58.661 50.000 0.00 0.00 0.00 4.35
1977 2002 3.207777 TCCTCTACTGGCTTCCCTTCTAT 59.792 47.826 0.00 0.00 0.00 1.98
1998 2023 1.227527 CAGCCACACAGGTTCGTCA 60.228 57.895 0.00 0.00 40.61 4.35
2002 2027 1.539496 GCCACACAGGTTCGTCAAGTA 60.539 52.381 0.00 0.00 40.61 2.24
2005 2030 3.454375 CACACAGGTTCGTCAAGTAGTT 58.546 45.455 0.00 0.00 0.00 2.24
2006 2031 3.489785 CACACAGGTTCGTCAAGTAGTTC 59.510 47.826 0.00 0.00 0.00 3.01
2007 2032 3.383825 ACACAGGTTCGTCAAGTAGTTCT 59.616 43.478 0.00 0.00 0.00 3.01
2008 2033 4.581824 ACACAGGTTCGTCAAGTAGTTCTA 59.418 41.667 0.00 0.00 0.00 2.10
2009 2034 5.243283 ACACAGGTTCGTCAAGTAGTTCTAT 59.757 40.000 0.00 0.00 0.00 1.98
2010 2035 6.432162 ACACAGGTTCGTCAAGTAGTTCTATA 59.568 38.462 0.00 0.00 0.00 1.31
2011 2036 7.122353 ACACAGGTTCGTCAAGTAGTTCTATAT 59.878 37.037 0.00 0.00 0.00 0.86
2012 2037 8.618677 CACAGGTTCGTCAAGTAGTTCTATATA 58.381 37.037 0.00 0.00 0.00 0.86
2013 2038 8.838365 ACAGGTTCGTCAAGTAGTTCTATATAG 58.162 37.037 3.10 3.10 0.00 1.31
2014 2039 8.838365 CAGGTTCGTCAAGTAGTTCTATATAGT 58.162 37.037 9.58 0.00 0.00 2.12
2015 2040 9.406113 AGGTTCGTCAAGTAGTTCTATATAGTT 57.594 33.333 9.58 0.52 0.00 2.24
2016 2041 9.662545 GGTTCGTCAAGTAGTTCTATATAGTTC 57.337 37.037 9.58 4.62 0.00 3.01
2030 2055 9.595823 TTCTATATAGTTCTTTTCTTGGGTTCG 57.404 33.333 9.58 0.00 0.00 3.95
2034 2059 1.314730 TCTTTTCTTGGGTTCGTGCC 58.685 50.000 0.00 0.00 0.00 5.01
2035 2060 1.028905 CTTTTCTTGGGTTCGTGCCA 58.971 50.000 1.03 0.00 0.00 4.92
2036 2061 1.613437 CTTTTCTTGGGTTCGTGCCAT 59.387 47.619 0.00 0.00 0.00 4.40
2037 2062 1.698506 TTTCTTGGGTTCGTGCCATT 58.301 45.000 0.00 0.00 0.00 3.16
2055 2080 6.207691 GCCATTAGCAGTTGGAGATAAAAA 57.792 37.500 3.27 0.00 42.97 1.94
2263 2288 0.528684 CCTTCACCTTCTCCGCGATC 60.529 60.000 8.23 0.00 0.00 3.69
2637 2662 2.125106 GCAGAGGCCCGTCGAATT 60.125 61.111 0.00 0.00 0.00 2.17
2647 2672 2.695646 GTCGAATTGGCGAGCGAC 59.304 61.111 14.52 14.52 44.83 5.19
2722 2747 1.101049 ACATTGAATTAGGGCGGCGG 61.101 55.000 9.78 0.00 0.00 6.13
2782 2822 0.106469 GGGCTCCCCTCTGATTTTCC 60.106 60.000 0.00 0.00 41.34 3.13
2812 2852 1.355916 CGTGTAGTAGGGCGCTCTC 59.644 63.158 16.37 5.72 0.00 3.20
3060 3107 4.219143 ACATTGATTGTAGCGCATGATG 57.781 40.909 11.47 4.68 36.57 3.07
3141 3188 1.135228 GTGTTTGTCAAGTGGCGGTTT 60.135 47.619 0.00 0.00 0.00 3.27
3214 4778 1.960689 AGGCTGGCGTAAAACAATGTT 59.039 42.857 0.00 0.00 0.00 2.71
3258 4878 7.987458 CAGGAGGTTGTTACATAATACTGATGT 59.013 37.037 0.00 0.00 40.59 3.06
3303 4923 3.818787 CGGCAGCATGTTGAGGGC 61.819 66.667 14.38 0.00 39.31 5.19
3319 4939 0.451783 GGGCATGTCATGTCCGTTTC 59.548 55.000 20.40 0.00 46.34 2.78
3339 5960 1.593006 CGTGAAGAGCTTGAAACACGT 59.407 47.619 17.68 0.00 43.47 4.49
3366 5988 2.898746 TCATTTGTTTTCGAACGCTCG 58.101 42.857 0.82 0.82 46.87 5.03
3395 6020 2.047274 AGACGTGGCCGATGTTGG 60.047 61.111 0.00 0.00 37.88 3.77
3404 6029 0.955428 GCCGATGTTGGTCAGCTCAA 60.955 55.000 0.00 0.00 0.00 3.02
3413 6038 5.626142 TGTTGGTCAGCTCAAAGGTATTAA 58.374 37.500 0.00 0.00 0.00 1.40
3414 6039 5.472137 TGTTGGTCAGCTCAAAGGTATTAAC 59.528 40.000 0.00 0.00 0.00 2.01
3415 6040 4.250464 TGGTCAGCTCAAAGGTATTAACG 58.750 43.478 0.00 0.00 0.00 3.18
3416 6041 4.251268 GGTCAGCTCAAAGGTATTAACGT 58.749 43.478 0.00 0.00 0.00 3.99
3417 6042 5.047164 TGGTCAGCTCAAAGGTATTAACGTA 60.047 40.000 0.00 0.00 0.00 3.57
3418 6043 6.047231 GGTCAGCTCAAAGGTATTAACGTAT 58.953 40.000 0.00 0.00 0.00 3.06
3419 6044 6.537660 GGTCAGCTCAAAGGTATTAACGTATT 59.462 38.462 0.00 0.00 0.00 1.89
3420 6045 7.707893 GGTCAGCTCAAAGGTATTAACGTATTA 59.292 37.037 0.00 0.00 0.00 0.98
3445 6073 2.420628 TTGGCTCAATCGTTGCTTTG 57.579 45.000 0.00 0.00 0.00 2.77
3448 6076 1.266718 GGCTCAATCGTTGCTTTGTGA 59.733 47.619 0.00 0.00 0.00 3.58
3449 6077 2.095059 GGCTCAATCGTTGCTTTGTGAT 60.095 45.455 0.00 0.00 0.00 3.06
3450 6078 3.568538 GCTCAATCGTTGCTTTGTGATT 58.431 40.909 0.00 0.00 0.00 2.57
3452 6080 5.335127 GCTCAATCGTTGCTTTGTGATTAT 58.665 37.500 0.00 0.00 30.33 1.28
3453 6081 6.458206 GGCTCAATCGTTGCTTTGTGATTATA 60.458 38.462 0.00 0.00 30.33 0.98
3454 6082 6.630443 GCTCAATCGTTGCTTTGTGATTATAG 59.370 38.462 0.00 0.00 30.33 1.31
3455 6083 7.609760 TCAATCGTTGCTTTGTGATTATAGT 57.390 32.000 0.00 0.00 30.33 2.12
3457 6085 8.817100 TCAATCGTTGCTTTGTGATTATAGTAG 58.183 33.333 0.00 0.00 30.33 2.57
3458 6086 6.583912 TCGTTGCTTTGTGATTATAGTAGC 57.416 37.500 0.00 0.00 0.00 3.58
3459 6087 6.103330 TCGTTGCTTTGTGATTATAGTAGCA 58.897 36.000 0.00 0.00 35.56 3.49
3460 6088 6.592220 TCGTTGCTTTGTGATTATAGTAGCAA 59.408 34.615 0.00 0.00 42.74 3.91
3461 6089 6.901887 CGTTGCTTTGTGATTATAGTAGCAAG 59.098 38.462 0.00 0.00 44.74 4.01
3462 6090 7.413000 CGTTGCTTTGTGATTATAGTAGCAAGT 60.413 37.037 0.00 0.00 44.74 3.16
3463 6091 8.879759 GTTGCTTTGTGATTATAGTAGCAAGTA 58.120 33.333 0.00 0.00 44.74 2.24
3464 6092 9.443323 TTGCTTTGTGATTATAGTAGCAAGTAA 57.557 29.630 0.00 0.00 40.86 2.24
3465 6093 9.613428 TGCTTTGTGATTATAGTAGCAAGTAAT 57.387 29.630 0.00 0.00 34.55 1.89
3511 6139 2.157863 GCAACGAGACCTCTGTTTTAGC 59.842 50.000 0.00 0.00 0.00 3.09
3512 6140 3.390135 CAACGAGACCTCTGTTTTAGCA 58.610 45.455 0.00 0.00 0.00 3.49
3513 6141 3.305398 ACGAGACCTCTGTTTTAGCAG 57.695 47.619 0.00 0.00 37.81 4.24
3514 6142 2.891580 ACGAGACCTCTGTTTTAGCAGA 59.108 45.455 0.00 0.00 42.56 4.26
3523 6151 4.134563 TCTGTTTTAGCAGAGTTTGGTCC 58.865 43.478 0.00 0.00 40.23 4.46
3524 6152 3.882888 CTGTTTTAGCAGAGTTTGGTCCA 59.117 43.478 0.00 0.00 38.70 4.02
3525 6153 3.882888 TGTTTTAGCAGAGTTTGGTCCAG 59.117 43.478 0.00 0.00 38.70 3.86
3526 6154 2.859165 TTAGCAGAGTTTGGTCCAGG 57.141 50.000 0.00 0.00 38.70 4.45
3527 6155 2.024176 TAGCAGAGTTTGGTCCAGGA 57.976 50.000 0.00 0.00 38.70 3.86
3528 6156 0.398318 AGCAGAGTTTGGTCCAGGAC 59.602 55.000 11.70 11.70 29.81 3.85
3562 6190 0.394216 ATTGCAATAGCGTGCTCCCA 60.394 50.000 11.02 0.00 45.17 4.37
3564 6192 1.026182 TGCAATAGCGTGCTCCCAAG 61.026 55.000 0.00 0.00 45.17 3.61
3565 6193 1.026718 GCAATAGCGTGCTCCCAAGT 61.027 55.000 0.00 0.00 41.51 3.16
3566 6194 1.009829 CAATAGCGTGCTCCCAAGTC 58.990 55.000 0.00 0.00 0.00 3.01
3568 6196 0.108138 ATAGCGTGCTCCCAAGTCAC 60.108 55.000 0.00 0.00 0.00 3.67
3569 6197 1.468506 TAGCGTGCTCCCAAGTCACA 61.469 55.000 0.00 0.00 32.46 3.58
3570 6198 1.891919 GCGTGCTCCCAAGTCACAA 60.892 57.895 0.00 0.00 32.46 3.33
3571 6199 1.941812 CGTGCTCCCAAGTCACAAC 59.058 57.895 0.00 0.00 32.46 3.32
3572 6200 1.831389 CGTGCTCCCAAGTCACAACG 61.831 60.000 0.00 0.00 32.46 4.10
3573 6201 1.227823 TGCTCCCAAGTCACAACGG 60.228 57.895 0.00 0.00 0.00 4.44
3592 6244 1.618837 GGAGCTGGACTGTGTGACTTA 59.381 52.381 0.00 0.00 0.00 2.24
3596 6248 2.922758 GCTGGACTGTGTGACTTACTCG 60.923 54.545 0.00 0.00 0.00 4.18
3598 6250 1.269998 GGACTGTGTGACTTACTCGCT 59.730 52.381 0.00 0.00 0.00 4.93
3601 6253 2.054363 CTGTGTGACTTACTCGCTGTG 58.946 52.381 0.00 0.00 0.00 3.66
3621 6273 4.426112 TGCTGGCTCGCAGACTCG 62.426 66.667 0.00 0.00 34.44 4.18
3623 6275 4.426112 CTGGCTCGCAGACTCGCA 62.426 66.667 0.00 0.00 0.00 5.10
3643 6295 0.688087 GTCCACCCCTCCTACTCTGG 60.688 65.000 0.00 0.00 0.00 3.86
3650 6302 2.524306 CCCTCCTACTCTGGCTAGATG 58.476 57.143 0.00 0.00 31.21 2.90
3651 6303 2.158385 CCCTCCTACTCTGGCTAGATGT 60.158 54.545 0.00 3.95 31.21 3.06
3661 6313 4.517285 TCTGGCTAGATGTTGGCTAAAAG 58.483 43.478 0.00 0.00 33.09 2.27
3662 6314 4.019321 TCTGGCTAGATGTTGGCTAAAAGT 60.019 41.667 0.00 0.00 33.09 2.66
3663 6315 4.009675 TGGCTAGATGTTGGCTAAAAGTG 58.990 43.478 0.00 0.00 33.09 3.16
3675 6328 2.400269 TAAAAGTGGGGCGGCGAGTT 62.400 55.000 12.98 0.00 0.00 3.01
3676 6329 2.400269 AAAAGTGGGGCGGCGAGTTA 62.400 55.000 12.98 0.00 0.00 2.24
3677 6330 2.193087 AAAGTGGGGCGGCGAGTTAT 62.193 55.000 12.98 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.317040 AGACAACCGTTGAGGAGAAGA 58.683 47.619 18.19 0.00 45.00 2.87
14 15 1.670811 ACTTGCAAGACAACCGTTGAG 59.329 47.619 32.50 2.24 33.68 3.02
69 70 4.892433 TCTTCAGAAAGAGAAAGCAGAGG 58.108 43.478 0.00 0.00 36.59 3.69
130 133 3.140506 TTGCAAGCAAGGCAAGGG 58.859 55.556 2.89 0.00 45.57 3.95
272 280 0.322277 CTTCCACCACAGCAGCATCT 60.322 55.000 0.00 0.00 0.00 2.90
273 281 1.310933 CCTTCCACCACAGCAGCATC 61.311 60.000 0.00 0.00 0.00 3.91
274 282 1.303888 CCTTCCACCACAGCAGCAT 60.304 57.895 0.00 0.00 0.00 3.79
373 384 5.163390 GAGGGAAGGGGGAAAGATCTAATA 58.837 45.833 0.00 0.00 0.00 0.98
384 395 2.699607 TTTGGTCGAGGGAAGGGGGA 62.700 60.000 0.00 0.00 0.00 4.81
394 405 5.824904 ATTGATTGGAAGATTTGGTCGAG 57.175 39.130 0.00 0.00 0.00 4.04
447 458 5.082059 CGGATTGAACAGAGAAAACAATCG 58.918 41.667 0.00 0.00 44.05 3.34
538 549 7.769220 AGCATTTTTCATCAGAATCAACCTAG 58.231 34.615 0.00 0.00 32.89 3.02
579 590 1.453379 GGCTCTGGCATCAGCACAT 60.453 57.895 17.56 0.00 44.61 3.21
581 592 3.200593 CGGCTCTGGCATCAGCAC 61.201 66.667 17.56 8.30 44.61 4.40
594 605 2.622942 TGAATCTTTTGTTTGAGCGGCT 59.377 40.909 0.00 0.00 0.00 5.52
638 650 5.123227 CGAATTATGTAGGTGGGATGTTGT 58.877 41.667 0.00 0.00 0.00 3.32
639 651 5.007626 CACGAATTATGTAGGTGGGATGTTG 59.992 44.000 0.00 0.00 0.00 3.33
653 665 8.601845 TTATAGGTTGGATGTCACGAATTATG 57.398 34.615 0.00 0.00 0.00 1.90
655 667 8.425703 TGATTATAGGTTGGATGTCACGAATTA 58.574 33.333 0.00 0.00 0.00 1.40
676 688 5.655394 ACTGCACCTCCTAGGATATGATTA 58.345 41.667 21.29 9.23 37.67 1.75
677 689 4.497516 ACTGCACCTCCTAGGATATGATT 58.502 43.478 21.29 6.03 37.67 2.57
678 690 4.139162 ACTGCACCTCCTAGGATATGAT 57.861 45.455 21.29 7.27 37.67 2.45
680 692 5.728471 CAATACTGCACCTCCTAGGATATG 58.272 45.833 13.12 14.42 37.67 1.78
702 723 7.990917 TCCTGAAATAAAATAAATAGCACGCA 58.009 30.769 0.00 0.00 0.00 5.24
731 752 0.988678 ATTGGGGCCAGGGACTAGTC 60.989 60.000 14.87 14.87 36.02 2.59
732 753 0.345502 TATTGGGGCCAGGGACTAGT 59.654 55.000 4.39 0.00 36.02 2.57
740 761 2.961510 TGGATGAATTATTGGGGCCAG 58.038 47.619 4.39 0.00 0.00 4.85
962 983 7.435068 TTTGGCTTCTCTACAATCTGTTAAC 57.565 36.000 0.00 0.00 0.00 2.01
968 989 5.884792 CCTGAATTTGGCTTCTCTACAATCT 59.115 40.000 0.00 0.00 0.00 2.40
969 990 5.449725 GCCTGAATTTGGCTTCTCTACAATC 60.450 44.000 13.95 0.00 46.38 2.67
1011 1036 4.070716 CCATTCTGCTTCTGTTCTCAGTT 58.929 43.478 0.00 0.00 41.91 3.16
1019 1044 1.630369 TGCTACCCATTCTGCTTCTGT 59.370 47.619 0.00 0.00 0.00 3.41
1047 1072 2.564504 CTCGATGAGCTGAATCCCCATA 59.435 50.000 0.00 0.00 0.00 2.74
1104 1129 1.656441 CACCAACACAAGAGCCTGC 59.344 57.895 0.00 0.00 0.00 4.85
1282 1307 4.154347 CGGAGCCCAGCCACTCTC 62.154 72.222 0.00 0.00 33.29 3.20
1321 1346 2.657944 GATCTCGCCGAGCAGCTG 60.658 66.667 9.77 10.11 0.00 4.24
1341 1366 0.482446 ACACCCCAAGGAATGCAAGA 59.518 50.000 0.00 0.00 36.73 3.02
1342 1367 2.214376 TACACCCCAAGGAATGCAAG 57.786 50.000 0.00 0.00 36.73 4.01
1344 1369 1.959508 GCATACACCCCAAGGAATGCA 60.960 52.381 0.00 0.00 42.12 3.96
1347 1372 2.917713 TTGCATACACCCCAAGGAAT 57.082 45.000 0.00 0.00 36.73 3.01
1365 1390 2.872842 GCCAGCAAAGAACATGCCAATT 60.873 45.455 0.00 0.00 44.91 2.32
1383 1408 3.716195 CGGTCACCCAGATGGCCA 61.716 66.667 8.56 8.56 45.29 5.36
1390 1415 3.009115 ATCCACCCGGTCACCCAG 61.009 66.667 0.00 0.00 0.00 4.45
1437 1462 3.047877 GTGAACAGCCCGGTTCCG 61.048 66.667 0.00 4.08 45.12 4.30
1554 1579 3.547249 GACGACTGCGACCACGGAA 62.547 63.158 0.00 0.00 39.65 4.30
1566 1591 1.289109 CGAACCAATTGCCGACGACT 61.289 55.000 0.00 0.00 0.00 4.18
1635 1660 0.609131 AGCCAGAAATGTTCCCCACG 60.609 55.000 0.00 0.00 0.00 4.94
1641 1666 3.063180 CGATCAGTGAGCCAGAAATGTTC 59.937 47.826 2.13 0.00 0.00 3.18
1656 1681 4.166888 ATGGCAGCGGCGATCAGT 62.167 61.111 12.98 0.00 42.47 3.41
1665 1690 1.136147 GAACTTCAGCATGGCAGCG 59.864 57.895 0.00 0.00 40.15 5.18
1707 1732 2.903855 GCGATCATGGCACCAGGG 60.904 66.667 0.89 0.00 0.00 4.45
1710 1735 4.471908 AGCGCGATCATGGCACCA 62.472 61.111 12.10 0.00 0.00 4.17
1758 1783 0.102481 CTATCACCTCGGGGTCAACG 59.898 60.000 2.28 0.00 45.41 4.10
1764 1789 2.838225 ACGCCTATCACCTCGGGG 60.838 66.667 0.00 0.00 36.87 5.73
1767 1792 1.280142 CTCGACGCCTATCACCTCG 59.720 63.158 0.00 0.00 0.00 4.63
1842 1867 3.100671 GTCTCTACCACTGGAATGTCCT 58.899 50.000 0.71 0.00 37.46 3.85
1851 1876 0.453793 CTGCCTCGTCTCTACCACTG 59.546 60.000 0.00 0.00 0.00 3.66
1857 1882 1.379977 CCCCACTGCCTCGTCTCTA 60.380 63.158 0.00 0.00 0.00 2.43
1858 1883 2.681778 CCCCACTGCCTCGTCTCT 60.682 66.667 0.00 0.00 0.00 3.10
1881 1906 2.234586 GGGGATTCTCCATGCCTGA 58.765 57.895 0.00 0.00 43.18 3.86
1962 1987 2.224257 GCTGAGATAGAAGGGAAGCCAG 60.224 54.545 0.00 0.00 0.00 4.85
1968 1993 2.111384 GTGTGGCTGAGATAGAAGGGA 58.889 52.381 0.00 0.00 0.00 4.20
1977 2002 1.367471 CGAACCTGTGTGGCTGAGA 59.633 57.895 0.00 0.00 40.22 3.27
2005 2030 8.755977 ACGAACCCAAGAAAAGAACTATATAGA 58.244 33.333 16.79 0.00 0.00 1.98
2006 2031 8.818057 CACGAACCCAAGAAAAGAACTATATAG 58.182 37.037 8.27 8.27 0.00 1.31
2007 2032 7.279313 GCACGAACCCAAGAAAAGAACTATATA 59.721 37.037 0.00 0.00 0.00 0.86
2008 2033 6.093633 GCACGAACCCAAGAAAAGAACTATAT 59.906 38.462 0.00 0.00 0.00 0.86
2009 2034 5.410439 GCACGAACCCAAGAAAAGAACTATA 59.590 40.000 0.00 0.00 0.00 1.31
2010 2035 4.215613 GCACGAACCCAAGAAAAGAACTAT 59.784 41.667 0.00 0.00 0.00 2.12
2011 2036 3.562557 GCACGAACCCAAGAAAAGAACTA 59.437 43.478 0.00 0.00 0.00 2.24
2012 2037 2.357952 GCACGAACCCAAGAAAAGAACT 59.642 45.455 0.00 0.00 0.00 3.01
2013 2038 2.543031 GGCACGAACCCAAGAAAAGAAC 60.543 50.000 0.00 0.00 0.00 3.01
2014 2039 1.679153 GGCACGAACCCAAGAAAAGAA 59.321 47.619 0.00 0.00 0.00 2.52
2015 2040 1.314730 GGCACGAACCCAAGAAAAGA 58.685 50.000 0.00 0.00 0.00 2.52
2016 2041 1.028905 TGGCACGAACCCAAGAAAAG 58.971 50.000 0.00 0.00 0.00 2.27
2017 2042 1.698506 ATGGCACGAACCCAAGAAAA 58.301 45.000 0.00 0.00 35.67 2.29
2018 2043 1.698506 AATGGCACGAACCCAAGAAA 58.301 45.000 0.00 0.00 35.67 2.52
2019 2044 2.432444 CTAATGGCACGAACCCAAGAA 58.568 47.619 0.00 0.00 35.67 2.52
2020 2045 1.948611 GCTAATGGCACGAACCCAAGA 60.949 52.381 0.00 0.00 41.35 3.02
2021 2046 0.451783 GCTAATGGCACGAACCCAAG 59.548 55.000 0.00 0.00 41.35 3.61
2022 2047 2.562125 GCTAATGGCACGAACCCAA 58.438 52.632 0.00 0.00 41.35 4.12
2023 2048 4.312052 GCTAATGGCACGAACCCA 57.688 55.556 0.00 0.00 41.35 4.51
2055 2080 7.069826 TGGTCAGGTCAGAAAAAGATTCATTTT 59.930 33.333 0.00 0.00 33.86 1.82
2056 2081 6.550854 TGGTCAGGTCAGAAAAAGATTCATTT 59.449 34.615 0.00 0.00 0.00 2.32
2070 2095 0.944386 CAAAACGGTGGTCAGGTCAG 59.056 55.000 0.00 0.00 0.00 3.51
2242 2267 1.738099 CGCGGAGAAGGTGAAGGTG 60.738 63.158 0.00 0.00 0.00 4.00
2263 2288 1.227002 GTAGAAGAAGAGCGCCGGG 60.227 63.158 2.29 0.00 0.00 5.73
2782 2822 1.736645 CTACACGCCACCTCGGTTG 60.737 63.158 0.00 0.00 36.97 3.77
2812 2852 2.002586 GACACAATCACATGAGACCCG 58.997 52.381 0.00 0.00 0.00 5.28
3060 3107 6.765036 TGAAAGGATATCTCAGATTTCACAGC 59.235 38.462 7.35 0.00 33.16 4.40
3141 3188 4.223923 ACAAAATTGTGTGTTTTGGGGAGA 59.776 37.500 0.00 0.00 45.92 3.71
3173 3220 9.912634 CAGCCTTAGTTCAATTTTTCTTTGATA 57.087 29.630 0.00 0.00 33.37 2.15
3198 3250 2.224549 CCTCGAACATTGTTTTACGCCA 59.775 45.455 3.08 0.00 0.00 5.69
3214 4778 3.094572 CCTGTAACTCCCTTAACCTCGA 58.905 50.000 0.00 0.00 0.00 4.04
3303 4923 2.065512 TCACGAAACGGACATGACATG 58.934 47.619 14.02 14.02 0.00 3.21
3314 4934 3.242284 TGTTTCAAGCTCTTCACGAAACG 60.242 43.478 14.08 0.00 45.27 3.60
3319 4939 2.285319 CGTGTTTCAAGCTCTTCACG 57.715 50.000 12.57 12.57 41.40 4.35
3339 5960 7.577979 AGCGTTCGAAAACAAATGAATAAGTA 58.422 30.769 0.00 0.00 34.93 2.24
3366 5988 3.062234 CGGCCACGTCTCTTTTTCTAATC 59.938 47.826 2.24 0.00 34.81 1.75
3370 5992 0.391597 TCGGCCACGTCTCTTTTTCT 59.608 50.000 2.24 0.00 41.85 2.52
3373 5995 0.034896 ACATCGGCCACGTCTCTTTT 59.965 50.000 2.24 0.00 41.85 2.27
3395 6020 7.535489 AATACGTTAATACCTTTGAGCTGAC 57.465 36.000 0.00 0.00 0.00 3.51
3404 6029 6.647895 CCAATCCGCTAATACGTTAATACCTT 59.352 38.462 0.00 0.00 0.00 3.50
3413 6038 1.411246 TGAGCCAATCCGCTAATACGT 59.589 47.619 0.00 0.00 39.87 3.57
3414 6039 2.148916 TGAGCCAATCCGCTAATACG 57.851 50.000 0.00 0.00 39.87 3.06
3415 6040 3.123621 CGATTGAGCCAATCCGCTAATAC 59.876 47.826 17.13 0.00 45.03 1.89
3416 6041 3.244078 ACGATTGAGCCAATCCGCTAATA 60.244 43.478 17.13 0.00 45.03 0.98
3417 6042 2.146342 CGATTGAGCCAATCCGCTAAT 58.854 47.619 17.13 0.00 45.03 1.73
3418 6043 1.134521 ACGATTGAGCCAATCCGCTAA 60.135 47.619 17.13 0.00 45.03 3.09
3419 6044 0.464036 ACGATTGAGCCAATCCGCTA 59.536 50.000 17.13 0.00 45.03 4.26
3420 6045 0.392998 AACGATTGAGCCAATCCGCT 60.393 50.000 17.13 0.00 45.03 5.52
3465 6093 9.162764 GCAGTCTGTAACTTGATTCCTTTTATA 57.837 33.333 0.93 0.00 35.45 0.98
3466 6094 7.665559 TGCAGTCTGTAACTTGATTCCTTTTAT 59.334 33.333 0.93 0.00 35.45 1.40
3467 6095 6.995686 TGCAGTCTGTAACTTGATTCCTTTTA 59.004 34.615 0.93 0.00 35.45 1.52
3468 6096 5.827797 TGCAGTCTGTAACTTGATTCCTTTT 59.172 36.000 0.93 0.00 35.45 2.27
3469 6097 5.376625 TGCAGTCTGTAACTTGATTCCTTT 58.623 37.500 0.93 0.00 35.45 3.11
3470 6098 4.973168 TGCAGTCTGTAACTTGATTCCTT 58.027 39.130 0.93 0.00 35.45 3.36
3511 6139 0.951040 GCGTCCTGGACCAAACTCTG 60.951 60.000 20.68 5.57 0.00 3.35
3512 6140 1.371558 GCGTCCTGGACCAAACTCT 59.628 57.895 20.68 0.00 0.00 3.24
3513 6141 2.027625 CGCGTCCTGGACCAAACTC 61.028 63.158 20.68 3.13 0.00 3.01
3514 6142 2.030562 CGCGTCCTGGACCAAACT 59.969 61.111 20.68 0.00 0.00 2.66
3515 6143 2.798148 ATCCGCGTCCTGGACCAAAC 62.798 60.000 20.68 7.40 38.60 2.93
3516 6144 2.589157 ATCCGCGTCCTGGACCAAA 61.589 57.895 20.68 4.93 38.60 3.28
3517 6145 3.000819 ATCCGCGTCCTGGACCAA 61.001 61.111 20.68 4.58 38.60 3.67
3518 6146 3.770040 CATCCGCGTCCTGGACCA 61.770 66.667 20.68 3.27 38.60 4.02
3519 6147 4.530857 CCATCCGCGTCCTGGACC 62.531 72.222 20.68 12.38 38.60 4.46
3520 6148 3.432051 CTCCATCCGCGTCCTGGAC 62.432 68.421 16.99 16.99 38.60 4.02
3521 6149 3.147595 CTCCATCCGCGTCCTGGA 61.148 66.667 17.30 17.30 40.46 3.86
3522 6150 2.635229 CTTCTCCATCCGCGTCCTGG 62.635 65.000 4.92 8.97 0.00 4.45
3523 6151 1.227089 CTTCTCCATCCGCGTCCTG 60.227 63.158 4.92 0.00 0.00 3.86
3524 6152 3.082579 GCTTCTCCATCCGCGTCCT 62.083 63.158 4.92 0.00 0.00 3.85
3525 6153 2.586357 GCTTCTCCATCCGCGTCC 60.586 66.667 4.92 0.00 0.00 4.79
3526 6154 0.811616 AATGCTTCTCCATCCGCGTC 60.812 55.000 4.92 0.00 0.00 5.19
3527 6155 1.091771 CAATGCTTCTCCATCCGCGT 61.092 55.000 4.92 0.00 0.00 6.01
3528 6156 1.645455 CAATGCTTCTCCATCCGCG 59.355 57.895 0.00 0.00 0.00 6.46
3562 6190 0.249911 GTCCAGCTCCGTTGTGACTT 60.250 55.000 0.00 0.00 0.00 3.01
3564 6192 0.946221 CAGTCCAGCTCCGTTGTGAC 60.946 60.000 0.00 0.00 0.00 3.67
3565 6193 1.367471 CAGTCCAGCTCCGTTGTGA 59.633 57.895 0.00 0.00 0.00 3.58
3566 6194 1.069765 ACAGTCCAGCTCCGTTGTG 59.930 57.895 0.00 0.00 0.00 3.33
3568 6196 1.069765 ACACAGTCCAGCTCCGTTG 59.930 57.895 0.00 0.00 0.00 4.10
3569 6197 1.069765 CACACAGTCCAGCTCCGTT 59.930 57.895 0.00 0.00 0.00 4.44
3570 6198 1.832608 TCACACAGTCCAGCTCCGT 60.833 57.895 0.00 0.00 0.00 4.69
3571 6199 1.373497 GTCACACAGTCCAGCTCCG 60.373 63.158 0.00 0.00 0.00 4.63
3572 6200 0.394565 AAGTCACACAGTCCAGCTCC 59.605 55.000 0.00 0.00 0.00 4.70
3573 6201 2.297597 AGTAAGTCACACAGTCCAGCTC 59.702 50.000 0.00 0.00 0.00 4.09
3592 6244 4.694233 CCAGCAGCCACAGCGAGT 62.694 66.667 0.00 0.00 46.67 4.18
3615 6267 2.997897 GGGGTGGACTGCGAGTCT 60.998 66.667 13.59 0.00 44.46 3.24
3616 6268 2.997897 AGGGGTGGACTGCGAGTC 60.998 66.667 7.52 7.52 44.32 3.36
3617 6269 2.997897 GAGGGGTGGACTGCGAGT 60.998 66.667 0.00 0.00 0.00 4.18
3618 6270 2.856039 TAGGAGGGGTGGACTGCGAG 62.856 65.000 0.00 0.00 0.00 5.03
3619 6271 2.926326 TAGGAGGGGTGGACTGCGA 61.926 63.158 0.00 0.00 0.00 5.10
3620 6272 2.363795 TAGGAGGGGTGGACTGCG 60.364 66.667 0.00 0.00 0.00 5.18
3621 6273 1.306226 AGTAGGAGGGGTGGACTGC 60.306 63.158 0.00 0.00 0.00 4.40
3622 6274 0.336737 AGAGTAGGAGGGGTGGACTG 59.663 60.000 0.00 0.00 0.00 3.51
3623 6275 0.336737 CAGAGTAGGAGGGGTGGACT 59.663 60.000 0.00 0.00 0.00 3.85
3643 6295 3.378427 CCCACTTTTAGCCAACATCTAGC 59.622 47.826 0.00 0.00 0.00 3.42
3650 6302 1.584495 CGCCCCACTTTTAGCCAAC 59.416 57.895 0.00 0.00 0.00 3.77
3651 6303 1.605165 CCGCCCCACTTTTAGCCAA 60.605 57.895 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.