Multiple sequence alignment - TraesCS1A01G198600

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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 TraesCS1A01G198600 chr1A 100.000 4061 0 0 1 4061 357061470 357065530 0.000000e+00 7500.0
1 TraesCS1A01G198600 chr1D 93.068 3650 140 50 1 3616 285440885 285444455 0.000000e+00 5234.0
2 TraesCS1A01G198600 chr1D 93.704 270 12 3 3795 4061 285444566 285444833 2.270000e-107 399.0
3 TraesCS1A01G198600 chr1D 90.244 82 3 2 3737 3813 285444464 285444545 7.180000e-18 102.0
4 TraesCS1A01G198600 chr1B 93.224 3424 141 47 217 3591 388007833 388011214 0.000000e+00 4953.0
5 TraesCS1A01G198600 chr1B 94.052 269 12 2 3797 4061 388011301 388011569 4.890000e-109 405.0
6 TraesCS1A01G198600 chr1B 89.796 147 8 2 38 181 388007476 388007618 8.970000e-42 182.0
7 TraesCS1A01G198600 chr1B 90.265 113 8 1 3672 3781 388011213 388011325 1.180000e-30 145.0
8 TraesCS1A01G198600 chr5B 93.007 429 19 4 2310 2737 545197224 545197642 2.070000e-172 616.0
9 TraesCS1A01G198600 chr5B 85.000 100 13 2 1772 1870 213250688 213250786 2.580000e-17 100.0
10 TraesCS1A01G198600 chr3B 92.130 432 23 6 2310 2740 61688216 61687795 2.090000e-167 599.0
11 TraesCS1A01G198600 chr6D 78.607 201 31 7 1724 1918 335375768 335375574 5.510000e-24 122.0
12 TraesCS1A01G198600 chr6A 78.607 201 31 8 1724 1918 475000336 475000142 5.510000e-24 122.0
13 TraesCS1A01G198600 chr5A 76.339 224 49 4 1697 1918 227923938 227924159 2.560000e-22 117.0
14 TraesCS1A01G198600 chr5D 75.336 223 53 2 1697 1918 197152220 197151999 5.550000e-19 106.0
15 TraesCS1A01G198600 chr4D 95.238 63 3 0 1772 1834 70119533 70119595 2.580000e-17 100.0
16 TraesCS1A01G198600 chr4B 95.238 63 3 0 1772 1834 103773393 103773455 2.580000e-17 100.0
17 TraesCS1A01G198600 chr2D 77.564 156 30 4 1562 1716 509941945 509942096 5.590000e-14 89.8
18 TraesCS1A01G198600 chr2A 77.564 156 30 4 1562 1716 653678188 653678339 5.590000e-14 89.8


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 TraesCS1A01G198600 chr1A 357061470 357065530 4060 False 7500.000000 7500 100.000000 1 4061 1 chr1A.!!$F1 4060
1 TraesCS1A01G198600 chr1D 285440885 285444833 3948 False 1911.666667 5234 92.338667 1 4061 3 chr1D.!!$F1 4060
2 TraesCS1A01G198600 chr1B 388007476 388011569 4093 False 1421.250000 4953 91.834250 38 4061 4 chr1B.!!$F1 4023

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
129 133 0.032952 ACGCTAACAGCCGAGACAAA 59.967 50.0 0.00 0.0 38.18 2.83 F
593 786 0.324830 AGGCCACTCCTAGAGACACC 60.325 60.0 5.01 0.0 45.41 4.16 F
1249 1486 0.034574 CATCCCCATCGTTTCCACCA 60.035 55.0 0.00 0.0 0.00 4.17 F
1767 2004 0.741221 GCAACATCCTCACCGTCTCC 60.741 60.0 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1479 0.107831 CCTCCTGTTTCGTGGTGGAA 59.892 55.000 0.0 0.00 38.80 3.53 R
2065 2302 0.461693 GCGAGCATCTTCTTGAGCCT 60.462 55.000 0.0 0.00 0.00 4.58 R
2831 3079 1.078285 TCGCATCTGCAATGCCAGA 60.078 52.632 20.7 6.31 45.16 3.86 R
3626 3879 0.547075 AGAGCCTCGGTAGCACTAGA 59.453 55.000 0.0 0.00 28.84 2.43 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
87 88 4.445453 AGCTGACTGATTAAATGCGATCA 58.555 39.130 0.00 0.00 0.00 2.92
129 133 0.032952 ACGCTAACAGCCGAGACAAA 59.967 50.000 0.00 0.00 38.18 2.83
130 134 0.716108 CGCTAACAGCCGAGACAAAG 59.284 55.000 0.00 0.00 38.18 2.77
131 135 0.444260 GCTAACAGCCGAGACAAAGC 59.556 55.000 0.00 0.00 34.48 3.51
132 136 1.941668 GCTAACAGCCGAGACAAAGCT 60.942 52.381 0.00 0.00 34.48 3.74
141 145 1.728971 CGAGACAAAGCTAGCCAACAG 59.271 52.381 12.13 0.00 0.00 3.16
143 147 3.614150 CGAGACAAAGCTAGCCAACAGTA 60.614 47.826 12.13 0.00 0.00 2.74
181 185 6.308041 GGCCACATCGAATTAAAGAAAGAAAC 59.692 38.462 0.00 0.00 0.00 2.78
204 226 2.864931 GCGCGTAGATGTGCAGCTC 61.865 63.158 8.43 0.00 44.59 4.09
219 247 2.420687 GCAGCTCCACTTTAGCCATACT 60.421 50.000 0.00 0.00 41.02 2.12
220 248 3.201290 CAGCTCCACTTTAGCCATACTG 58.799 50.000 0.00 0.00 41.02 2.74
221 249 1.943340 GCTCCACTTTAGCCATACTGC 59.057 52.381 0.00 0.00 33.73 4.40
222 250 2.205074 CTCCACTTTAGCCATACTGCG 58.795 52.381 0.00 0.00 36.02 5.18
282 472 3.581024 TGAACATGCAAGGAAATCAGC 57.419 42.857 0.00 0.00 0.00 4.26
298 488 3.861276 TCAGCCAATCTTTGCAATCAG 57.139 42.857 0.00 0.00 0.00 2.90
450 640 5.947228 AACCCATGATAATAATGCACTCG 57.053 39.130 0.00 0.00 0.00 4.18
464 654 2.037902 TGCACTCGGTTGTTATTGAGGA 59.962 45.455 0.00 0.00 32.76 3.71
467 657 3.056107 CACTCGGTTGTTATTGAGGAGGA 60.056 47.826 0.00 0.00 32.76 3.71
468 658 3.581332 ACTCGGTTGTTATTGAGGAGGAA 59.419 43.478 0.00 0.00 32.76 3.36
469 659 4.184629 CTCGGTTGTTATTGAGGAGGAAG 58.815 47.826 0.00 0.00 0.00 3.46
470 660 3.835978 TCGGTTGTTATTGAGGAGGAAGA 59.164 43.478 0.00 0.00 0.00 2.87
471 661 4.285003 TCGGTTGTTATTGAGGAGGAAGAA 59.715 41.667 0.00 0.00 0.00 2.52
477 670 6.940739 TGTTATTGAGGAGGAAGAAGAAGAG 58.059 40.000 0.00 0.00 0.00 2.85
525 718 1.078988 TAACCGTCGTCAATGGGGC 60.079 57.895 0.00 0.00 38.50 5.80
590 783 1.681486 GCCAGGCCACTCCTAGAGAC 61.681 65.000 5.01 0.00 45.52 3.36
593 786 0.324830 AGGCCACTCCTAGAGACACC 60.325 60.000 5.01 0.00 45.41 4.16
635 828 2.552315 TCAACCTGCCAATTCTCGTTTC 59.448 45.455 0.00 0.00 0.00 2.78
659 854 7.218614 TCTTAATCTGGTCGTTTTGTTTAGGA 58.781 34.615 0.00 0.00 0.00 2.94
662 857 5.534207 TCTGGTCGTTTTGTTTAGGAGTA 57.466 39.130 0.00 0.00 0.00 2.59
672 867 9.769093 CGTTTTGTTTAGGAGTAATAATCCTTG 57.231 33.333 14.83 0.00 45.13 3.61
706 901 7.982761 ATTCATTCAGCTTCAGATCTAATCC 57.017 36.000 0.00 0.00 0.00 3.01
763 961 2.279120 GAGCCGATCAGCCGACAG 60.279 66.667 0.00 0.00 0.00 3.51
785 983 4.803908 CTGCCTTCCTTCCCCGCC 62.804 72.222 0.00 0.00 0.00 6.13
787 985 4.803908 GCCTTCCTTCCCCGCCAG 62.804 72.222 0.00 0.00 0.00 4.85
788 986 4.803908 CCTTCCTTCCCCGCCAGC 62.804 72.222 0.00 0.00 0.00 4.85
853 1054 1.298014 CAACCTCTGCTCCCCTGTC 59.702 63.158 0.00 0.00 0.00 3.51
862 1067 3.920093 CTCCCCTGTCCCGTTTGGC 62.920 68.421 0.00 0.00 0.00 4.52
879 1084 1.885887 TGGCTCCAAACTTCCAATTCG 59.114 47.619 0.00 0.00 0.00 3.34
919 1125 2.679355 TGCGTTCCAAAAGTTCATCG 57.321 45.000 0.00 0.00 0.00 3.84
920 1126 1.944024 TGCGTTCCAAAAGTTCATCGT 59.056 42.857 0.00 0.00 0.00 3.73
921 1127 2.032377 TGCGTTCCAAAAGTTCATCGTC 60.032 45.455 0.00 0.00 0.00 4.20
922 1128 2.822827 CGTTCCAAAAGTTCATCGTCG 58.177 47.619 0.00 0.00 0.00 5.12
923 1129 2.220133 CGTTCCAAAAGTTCATCGTCGT 59.780 45.455 0.00 0.00 0.00 4.34
924 1130 3.660904 CGTTCCAAAAGTTCATCGTCGTC 60.661 47.826 0.00 0.00 0.00 4.20
927 1133 3.005472 TCCAAAAGTTCATCGTCGTCTCT 59.995 43.478 0.00 0.00 0.00 3.10
928 1134 3.121944 CCAAAAGTTCATCGTCGTCTCTG 59.878 47.826 0.00 0.00 0.00 3.35
929 1135 2.638556 AAGTTCATCGTCGTCTCTGG 57.361 50.000 0.00 0.00 0.00 3.86
938 1158 4.041740 TCGTCGTCTCTGGGATAATTTG 57.958 45.455 0.00 0.00 0.00 2.32
949 1169 4.527944 TGGGATAATTTGGTTGCGTATCA 58.472 39.130 0.00 0.00 0.00 2.15
1004 1224 3.485216 GGTTTGTTACCGATTCTGATGCG 60.485 47.826 0.00 0.00 37.12 4.73
1011 1231 2.890109 GATTCTGATGCGCTGCCCG 61.890 63.158 9.73 0.00 40.75 6.13
1242 1479 0.179009 CCAGCATCATCCCCATCGTT 60.179 55.000 0.00 0.00 0.00 3.85
1248 1485 0.254747 TCATCCCCATCGTTTCCACC 59.745 55.000 0.00 0.00 0.00 4.61
1249 1486 0.034574 CATCCCCATCGTTTCCACCA 60.035 55.000 0.00 0.00 0.00 4.17
1557 1794 1.338105 TGGATCAACAGCCAGAAGTCG 60.338 52.381 0.00 0.00 31.09 4.18
1663 1900 3.391665 GACCTCATGGCCGACCTGG 62.392 68.421 0.00 0.00 42.50 4.45
1758 1995 2.825836 CTGGCCCGCAACATCCTC 60.826 66.667 0.00 0.00 0.00 3.71
1764 2001 2.100631 CCGCAACATCCTCACCGTC 61.101 63.158 0.00 0.00 0.00 4.79
1767 2004 0.741221 GCAACATCCTCACCGTCTCC 60.741 60.000 0.00 0.00 0.00 3.71
2629 2866 2.758089 CCAACTGCATCCTGCTCGC 61.758 63.158 0.34 0.00 45.31 5.03
2631 2868 4.827087 ACTGCATCCTGCTCGCCG 62.827 66.667 0.34 0.00 45.31 6.46
2632 2869 4.827087 CTGCATCCTGCTCGCCGT 62.827 66.667 0.34 0.00 45.31 5.68
2633 2870 4.819761 TGCATCCTGCTCGCCGTC 62.820 66.667 0.34 0.00 45.31 4.79
2634 2871 4.819761 GCATCCTGCTCGCCGTCA 62.820 66.667 0.00 0.00 40.96 4.35
2635 2872 2.584418 CATCCTGCTCGCCGTCAG 60.584 66.667 2.97 2.97 0.00 3.51
2636 2873 2.755876 ATCCTGCTCGCCGTCAGA 60.756 61.111 9.86 0.00 32.26 3.27
2638 2875 1.680522 ATCCTGCTCGCCGTCAGATT 61.681 55.000 9.86 0.00 32.26 2.40
2639 2876 1.448540 CCTGCTCGCCGTCAGATTT 60.449 57.895 9.86 0.00 32.26 2.17
2640 2877 1.021390 CCTGCTCGCCGTCAGATTTT 61.021 55.000 9.86 0.00 32.26 1.82
2641 2878 1.640428 CTGCTCGCCGTCAGATTTTA 58.360 50.000 3.72 0.00 32.26 1.52
2642 2879 1.590238 CTGCTCGCCGTCAGATTTTAG 59.410 52.381 3.72 0.00 32.26 1.85
2643 2880 1.203758 TGCTCGCCGTCAGATTTTAGA 59.796 47.619 0.00 0.00 0.00 2.10
2644 2881 2.268298 GCTCGCCGTCAGATTTTAGAA 58.732 47.619 0.00 0.00 0.00 2.10
2645 2882 2.029365 GCTCGCCGTCAGATTTTAGAAC 59.971 50.000 0.00 0.00 0.00 3.01
2646 2883 3.250744 CTCGCCGTCAGATTTTAGAACA 58.749 45.455 0.00 0.00 0.00 3.18
2650 2887 3.312697 GCCGTCAGATTTTAGAACATCCC 59.687 47.826 0.00 0.00 0.00 3.85
2652 2889 3.555956 CGTCAGATTTTAGAACATCCCCG 59.444 47.826 0.00 0.00 0.00 5.73
2657 2894 2.871096 TTTAGAACATCCCCGTTGCT 57.129 45.000 0.00 0.00 0.00 3.91
2663 2900 3.054361 AGAACATCCCCGTTGCTAGAATT 60.054 43.478 0.00 0.00 0.00 2.17
2770 3007 1.337823 ACCGCAGAATCACACAGGTAC 60.338 52.381 0.00 0.00 0.00 3.34
2811 3059 6.053650 CACATATTCAGCAAGGAAGATCTCA 58.946 40.000 0.00 0.00 0.00 3.27
2820 3068 4.615452 GCAAGGAAGATCTCAAAGTTGCTG 60.615 45.833 15.56 1.25 36.86 4.41
2825 3073 2.037772 AGATCTCAAAGTTGCTGACCGT 59.962 45.455 0.00 0.00 0.00 4.83
2830 3078 3.271729 TCAAAGTTGCTGACCGTTTGTA 58.728 40.909 0.00 0.00 29.95 2.41
2831 3079 3.880490 TCAAAGTTGCTGACCGTTTGTAT 59.120 39.130 0.00 0.00 29.95 2.29
2865 3113 1.800586 TGCGAGATGAAGTTTGTGCTC 59.199 47.619 0.00 0.00 0.00 4.26
3072 3320 4.208632 GCATAGCTGCGAACCAGT 57.791 55.556 0.00 0.00 43.71 4.00
3077 3325 3.188786 GCTGCGAACCAGTAGCCG 61.189 66.667 0.00 0.00 42.74 5.52
3086 3334 1.005037 CCAGTAGCCGCAGTGACAA 60.005 57.895 0.00 0.00 0.00 3.18
3155 3403 3.655777 ACACTTTGATAGAACAAGGGGGA 59.344 43.478 0.00 0.00 35.15 4.81
3156 3404 4.292306 ACACTTTGATAGAACAAGGGGGAT 59.708 41.667 0.00 0.00 35.15 3.85
3346 3594 3.067106 CCGAATACTGTATGCATGTCCC 58.933 50.000 10.16 0.00 0.00 4.46
3497 3745 2.607635 AGTTAGTTGTGTGTTGCTGTCG 59.392 45.455 0.00 0.00 0.00 4.35
3565 3818 7.544566 TCTCTTTGTTTTCTAGTTATACAGCCG 59.455 37.037 0.00 0.00 0.00 5.52
3598 3851 1.945394 ACTGACACTGCAGCTTTGAAG 59.055 47.619 15.27 10.45 39.51 3.02
3605 3858 4.058124 CACTGCAGCTTTGAAGTAGTACA 58.942 43.478 15.27 0.00 0.00 2.90
3606 3859 4.692625 CACTGCAGCTTTGAAGTAGTACAT 59.307 41.667 15.27 0.00 0.00 2.29
3607 3860 4.692625 ACTGCAGCTTTGAAGTAGTACATG 59.307 41.667 15.27 0.00 0.00 3.21
3608 3861 4.893608 TGCAGCTTTGAAGTAGTACATGA 58.106 39.130 0.00 0.00 0.00 3.07
3609 3862 5.491070 TGCAGCTTTGAAGTAGTACATGAT 58.509 37.500 0.00 0.00 0.00 2.45
3610 3863 6.639563 TGCAGCTTTGAAGTAGTACATGATA 58.360 36.000 0.00 0.00 0.00 2.15
3611 3864 6.535150 TGCAGCTTTGAAGTAGTACATGATAC 59.465 38.462 0.00 0.00 0.00 2.24
3612 3865 6.535150 GCAGCTTTGAAGTAGTACATGATACA 59.465 38.462 0.00 0.00 0.00 2.29
3613 3866 7.064609 GCAGCTTTGAAGTAGTACATGATACAA 59.935 37.037 0.00 0.00 0.00 2.41
3614 3867 8.598924 CAGCTTTGAAGTAGTACATGATACAAG 58.401 37.037 0.00 1.33 0.00 3.16
3615 3868 8.531982 AGCTTTGAAGTAGTACATGATACAAGA 58.468 33.333 0.00 0.00 0.00 3.02
3616 3869 9.319143 GCTTTGAAGTAGTACATGATACAAGAT 57.681 33.333 0.00 0.00 0.00 2.40
3618 3871 9.599866 TTTGAAGTAGTACATGATACAAGATGG 57.400 33.333 0.00 0.00 0.00 3.51
3619 3872 7.726216 TGAAGTAGTACATGATACAAGATGGG 58.274 38.462 0.00 0.00 0.00 4.00
3620 3873 6.672266 AGTAGTACATGATACAAGATGGGG 57.328 41.667 0.00 0.00 0.00 4.96
3621 3874 6.382087 AGTAGTACATGATACAAGATGGGGA 58.618 40.000 0.00 0.00 0.00 4.81
3622 3875 6.844388 AGTAGTACATGATACAAGATGGGGAA 59.156 38.462 0.00 0.00 0.00 3.97
3623 3876 6.575244 AGTACATGATACAAGATGGGGAAA 57.425 37.500 0.00 0.00 0.00 3.13
3624 3877 7.154191 AGTACATGATACAAGATGGGGAAAT 57.846 36.000 0.00 0.00 0.00 2.17
3625 3878 8.275187 AGTACATGATACAAGATGGGGAAATA 57.725 34.615 0.00 0.00 0.00 1.40
3626 3879 8.894592 AGTACATGATACAAGATGGGGAAATAT 58.105 33.333 0.00 0.00 0.00 1.28
3627 3880 9.167311 GTACATGATACAAGATGGGGAAATATC 57.833 37.037 0.00 0.00 0.00 1.63
3628 3881 7.993416 ACATGATACAAGATGGGGAAATATCT 58.007 34.615 0.00 0.00 35.25 1.98
3629 3882 9.116080 ACATGATACAAGATGGGGAAATATCTA 57.884 33.333 0.00 0.00 33.49 1.98
3630 3883 9.610705 CATGATACAAGATGGGGAAATATCTAG 57.389 37.037 0.00 0.00 33.49 2.43
3631 3884 8.742125 TGATACAAGATGGGGAAATATCTAGT 57.258 34.615 0.00 0.00 33.49 2.57
3632 3885 8.597167 TGATACAAGATGGGGAAATATCTAGTG 58.403 37.037 0.00 0.00 33.49 2.74
3633 3886 5.625150 ACAAGATGGGGAAATATCTAGTGC 58.375 41.667 0.00 0.00 33.49 4.40
3634 3887 5.370880 ACAAGATGGGGAAATATCTAGTGCT 59.629 40.000 0.00 0.00 33.49 4.40
3635 3888 6.558775 ACAAGATGGGGAAATATCTAGTGCTA 59.441 38.462 0.00 0.00 33.49 3.49
3636 3889 6.613153 AGATGGGGAAATATCTAGTGCTAC 57.387 41.667 0.00 0.00 32.13 3.58
3637 3890 5.485708 AGATGGGGAAATATCTAGTGCTACC 59.514 44.000 0.00 0.00 32.13 3.18
3638 3891 3.576982 TGGGGAAATATCTAGTGCTACCG 59.423 47.826 0.00 0.00 0.00 4.02
3639 3892 3.830755 GGGGAAATATCTAGTGCTACCGA 59.169 47.826 0.00 0.00 0.00 4.69
3640 3893 4.082136 GGGGAAATATCTAGTGCTACCGAG 60.082 50.000 0.00 0.00 0.00 4.63
3641 3894 4.082136 GGGAAATATCTAGTGCTACCGAGG 60.082 50.000 0.00 0.00 0.00 4.63
3642 3895 4.487019 GAAATATCTAGTGCTACCGAGGC 58.513 47.826 0.00 0.00 0.00 4.70
3643 3896 2.953284 TATCTAGTGCTACCGAGGCT 57.047 50.000 0.00 0.00 0.00 4.58
3644 3897 1.611519 ATCTAGTGCTACCGAGGCTC 58.388 55.000 3.87 3.87 0.00 4.70
3645 3898 0.547075 TCTAGTGCTACCGAGGCTCT 59.453 55.000 13.50 0.00 37.33 4.09
3646 3899 0.665835 CTAGTGCTACCGAGGCTCTG 59.334 60.000 13.50 8.83 35.56 3.35
3647 3900 0.752009 TAGTGCTACCGAGGCTCTGG 60.752 60.000 19.32 19.32 35.56 3.86
3648 3901 2.037367 TGCTACCGAGGCTCTGGT 59.963 61.111 26.15 26.15 42.34 4.00
3649 3902 2.351244 TGCTACCGAGGCTCTGGTG 61.351 63.158 29.01 21.90 39.30 4.17
3650 3903 2.496817 CTACCGAGGCTCTGGTGC 59.503 66.667 29.01 0.50 39.30 5.01
3651 3904 2.037367 TACCGAGGCTCTGGTGCT 59.963 61.111 29.01 13.60 39.30 4.40
3652 3905 0.752009 CTACCGAGGCTCTGGTGCTA 60.752 60.000 29.01 15.80 39.30 3.49
3653 3906 1.035932 TACCGAGGCTCTGGTGCTAC 61.036 60.000 29.01 0.00 39.30 3.58
3654 3907 2.496817 CGAGGCTCTGGTGCTACC 59.503 66.667 13.50 0.00 39.22 3.18
3678 3931 4.512484 TGAATCCATGATACAAGACGCAA 58.488 39.130 0.00 0.00 0.00 4.85
3770 4026 3.193267 TGCATAATTGACCAAAGGACTGC 59.807 43.478 0.00 0.00 0.00 4.40
3889 4195 2.502538 CCATTTACCTTCCCGTCTACCA 59.497 50.000 0.00 0.00 0.00 3.25
4032 4341 1.616628 AATCCCTGCTTCCCTCCGT 60.617 57.895 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.813042 GTGAGCCAGTGAGCGAGC 60.813 66.667 0.00 0.00 38.01 5.03
31 32 1.188219 GGGAGTGAGTGAGCCAGTGA 61.188 60.000 0.00 0.00 0.00 3.41
32 33 1.190833 AGGGAGTGAGTGAGCCAGTG 61.191 60.000 0.00 0.00 0.00 3.66
36 37 0.902516 AGTGAGGGAGTGAGTGAGCC 60.903 60.000 0.00 0.00 0.00 4.70
87 88 2.497273 GCATTACAAGATGGGTTTGGCT 59.503 45.455 0.00 0.00 0.00 4.75
129 133 4.499865 CGTACATCATACTGTTGGCTAGCT 60.500 45.833 15.72 0.00 0.00 3.32
130 134 3.736252 CGTACATCATACTGTTGGCTAGC 59.264 47.826 6.04 6.04 0.00 3.42
131 135 4.976731 GTCGTACATCATACTGTTGGCTAG 59.023 45.833 0.00 0.00 0.00 3.42
132 136 4.202080 GGTCGTACATCATACTGTTGGCTA 60.202 45.833 0.00 0.00 0.00 3.93
141 145 0.386476 TGGCCGGTCGTACATCATAC 59.614 55.000 0.00 0.00 0.00 2.39
143 147 1.143183 GTGGCCGGTCGTACATCAT 59.857 57.895 0.00 0.00 0.00 2.45
181 185 2.849966 GCACATCTACGCGCGTGAG 61.850 63.158 42.78 31.91 0.00 3.51
204 226 0.657840 GCGCAGTATGGCTAAAGTGG 59.342 55.000 0.30 0.00 35.86 4.00
282 472 2.749076 TCGTCCTGATTGCAAAGATTGG 59.251 45.455 1.71 2.10 0.00 3.16
319 509 4.869861 GGTGAAAACAAGTCACATGCTTTT 59.130 37.500 6.86 0.00 45.94 2.27
320 510 4.432712 GGTGAAAACAAGTCACATGCTTT 58.567 39.130 6.86 0.00 45.94 3.51
374 564 9.039870 CCAAAGCAAACATCAATAGTTTTACAA 57.960 29.630 0.00 0.00 37.10 2.41
375 565 7.655328 CCCAAAGCAAACATCAATAGTTTTACA 59.345 33.333 0.00 0.00 37.10 2.41
376 566 7.655732 ACCCAAAGCAAACATCAATAGTTTTAC 59.344 33.333 0.00 0.00 37.10 2.01
379 569 6.173427 ACCCAAAGCAAACATCAATAGTTT 57.827 33.333 0.00 0.00 39.61 2.66
380 570 5.806654 ACCCAAAGCAAACATCAATAGTT 57.193 34.783 0.00 0.00 0.00 2.24
381 571 5.511202 CCAACCCAAAGCAAACATCAATAGT 60.511 40.000 0.00 0.00 0.00 2.12
382 572 4.931002 CCAACCCAAAGCAAACATCAATAG 59.069 41.667 0.00 0.00 0.00 1.73
384 574 3.742385 CCAACCCAAAGCAAACATCAAT 58.258 40.909 0.00 0.00 0.00 2.57
386 576 1.202627 GCCAACCCAAAGCAAACATCA 60.203 47.619 0.00 0.00 0.00 3.07
387 577 1.511850 GCCAACCCAAAGCAAACATC 58.488 50.000 0.00 0.00 0.00 3.06
388 578 0.108396 GGCCAACCCAAAGCAAACAT 59.892 50.000 0.00 0.00 0.00 2.71
450 640 5.805728 TCTTCTTCCTCCTCAATAACAACC 58.194 41.667 0.00 0.00 0.00 3.77
464 654 2.763448 CCATCGTCCTCTTCTTCTTCCT 59.237 50.000 0.00 0.00 0.00 3.36
467 657 3.165875 TCACCATCGTCCTCTTCTTCTT 58.834 45.455 0.00 0.00 0.00 2.52
468 658 2.808919 TCACCATCGTCCTCTTCTTCT 58.191 47.619 0.00 0.00 0.00 2.85
469 659 3.452474 CATCACCATCGTCCTCTTCTTC 58.548 50.000 0.00 0.00 0.00 2.87
470 660 2.169352 CCATCACCATCGTCCTCTTCTT 59.831 50.000 0.00 0.00 0.00 2.52
471 661 1.759445 CCATCACCATCGTCCTCTTCT 59.241 52.381 0.00 0.00 0.00 2.85
477 670 0.179073 CACTCCCATCACCATCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
525 718 3.072211 GACACTCGGGGAGTTTTAAAGG 58.928 50.000 0.00 0.00 41.37 3.11
551 744 2.277084 CCGCCCTCTGTTTGTGTATAC 58.723 52.381 0.00 0.00 0.00 1.47
552 745 1.406341 GCCGCCCTCTGTTTGTGTATA 60.406 52.381 0.00 0.00 0.00 1.47
553 746 0.676782 GCCGCCCTCTGTTTGTGTAT 60.677 55.000 0.00 0.00 0.00 2.29
581 774 4.834406 ATTATGGGAGGTGTCTCTAGGA 57.166 45.455 0.00 0.00 39.86 2.94
582 775 4.503991 GCAATTATGGGAGGTGTCTCTAGG 60.504 50.000 0.00 0.00 39.86 3.02
590 783 1.035139 GCAGGCAATTATGGGAGGTG 58.965 55.000 0.00 0.00 0.00 4.00
593 786 0.106066 TGGGCAGGCAATTATGGGAG 60.106 55.000 0.00 0.00 0.00 4.30
635 828 7.172703 ACTCCTAAACAAAACGACCAGATTAAG 59.827 37.037 0.00 0.00 0.00 1.85
672 867 8.677300 TCTGAAGCTGAATGAATATAAAACCAC 58.323 33.333 0.00 0.00 0.00 4.16
706 901 9.448294 GAGATTTACGTTACTACTCCATTACTG 57.552 37.037 0.00 0.00 0.00 2.74
785 983 3.487711 GGTCGGTCGATATATAGCTGCTG 60.488 52.174 13.43 0.00 0.00 4.41
786 984 2.683867 GGTCGGTCGATATATAGCTGCT 59.316 50.000 7.57 7.57 0.00 4.24
787 985 2.539142 CGGTCGGTCGATATATAGCTGC 60.539 54.545 0.00 0.00 0.00 5.25
788 986 2.934553 TCGGTCGGTCGATATATAGCTG 59.065 50.000 0.00 0.00 33.92 4.24
817 1018 1.153549 GCGAGGCCTTGAAGACGAT 60.154 57.895 25.25 0.00 0.00 3.73
818 1019 2.094757 TTGCGAGGCCTTGAAGACGA 62.095 55.000 25.25 2.51 0.00 4.20
819 1020 1.667830 TTGCGAGGCCTTGAAGACG 60.668 57.895 25.25 14.62 0.00 4.18
820 1021 1.578206 GGTTGCGAGGCCTTGAAGAC 61.578 60.000 25.25 16.62 0.00 3.01
849 1050 0.821711 TTTGGAGCCAAACGGGACAG 60.822 55.000 10.49 0.00 40.51 3.51
850 1051 1.227664 TTTGGAGCCAAACGGGACA 59.772 52.632 10.49 0.00 40.51 4.02
862 1067 2.488153 GGGTCGAATTGGAAGTTTGGAG 59.512 50.000 0.00 0.00 0.00 3.86
899 1105 2.356382 ACGATGAACTTTTGGAACGCAA 59.644 40.909 0.00 0.00 0.00 4.85
901 1107 2.571206 GACGATGAACTTTTGGAACGC 58.429 47.619 0.00 0.00 0.00 4.84
902 1108 2.220133 ACGACGATGAACTTTTGGAACG 59.780 45.455 0.00 0.00 0.00 3.95
903 1109 3.493503 AGACGACGATGAACTTTTGGAAC 59.506 43.478 0.00 0.00 0.00 3.62
904 1110 3.724374 AGACGACGATGAACTTTTGGAA 58.276 40.909 0.00 0.00 0.00 3.53
905 1111 3.005472 AGAGACGACGATGAACTTTTGGA 59.995 43.478 0.00 0.00 0.00 3.53
906 1112 3.121944 CAGAGACGACGATGAACTTTTGG 59.878 47.826 0.00 0.00 0.00 3.28
907 1113 3.121944 CCAGAGACGACGATGAACTTTTG 59.878 47.826 0.00 0.00 0.00 2.44
908 1114 3.318017 CCAGAGACGACGATGAACTTTT 58.682 45.455 0.00 0.00 0.00 2.27
911 1117 0.811915 CCCAGAGACGACGATGAACT 59.188 55.000 0.00 0.00 0.00 3.01
912 1118 0.809385 TCCCAGAGACGACGATGAAC 59.191 55.000 0.00 0.00 0.00 3.18
913 1119 1.763968 ATCCCAGAGACGACGATGAA 58.236 50.000 0.00 0.00 0.00 2.57
914 1120 2.632987 TATCCCAGAGACGACGATGA 57.367 50.000 0.00 0.00 0.00 2.92
915 1121 3.924918 ATTATCCCAGAGACGACGATG 57.075 47.619 0.00 0.00 0.00 3.84
918 1124 3.123804 CCAAATTATCCCAGAGACGACG 58.876 50.000 0.00 0.00 0.00 5.12
919 1125 4.138487 ACCAAATTATCCCAGAGACGAC 57.862 45.455 0.00 0.00 0.00 4.34
920 1126 4.513442 CAACCAAATTATCCCAGAGACGA 58.487 43.478 0.00 0.00 0.00 4.20
921 1127 3.065371 GCAACCAAATTATCCCAGAGACG 59.935 47.826 0.00 0.00 0.00 4.18
922 1128 3.065371 CGCAACCAAATTATCCCAGAGAC 59.935 47.826 0.00 0.00 0.00 3.36
923 1129 3.278574 CGCAACCAAATTATCCCAGAGA 58.721 45.455 0.00 0.00 0.00 3.10
924 1130 3.016736 ACGCAACCAAATTATCCCAGAG 58.983 45.455 0.00 0.00 0.00 3.35
927 1133 4.527944 TGATACGCAACCAAATTATCCCA 58.472 39.130 0.00 0.00 0.00 4.37
928 1134 4.023193 CCTGATACGCAACCAAATTATCCC 60.023 45.833 0.00 0.00 0.00 3.85
929 1135 4.578928 ACCTGATACGCAACCAAATTATCC 59.421 41.667 0.00 0.00 0.00 2.59
938 1158 1.520787 CCGGACCTGATACGCAACC 60.521 63.158 0.00 0.00 30.85 3.77
949 1169 2.125673 CACGCGATTTCCGGACCT 60.126 61.111 15.93 0.00 39.04 3.85
1242 1479 0.107831 CCTCCTGTTTCGTGGTGGAA 59.892 55.000 0.00 0.00 38.80 3.53
1248 1485 1.376037 GGAGCCCTCCTGTTTCGTG 60.376 63.158 7.08 0.00 46.16 4.35
1249 1486 3.069778 GGAGCCCTCCTGTTTCGT 58.930 61.111 7.08 0.00 46.16 3.85
1335 1572 1.101331 GGGTGTAGTCCTGGTAGTCG 58.899 60.000 0.00 0.00 0.00 4.18
1663 1900 2.124695 GTCCTTCATGCCGGGGAC 60.125 66.667 2.18 6.57 40.86 4.46
2046 2283 1.289380 GTCGAAGTCGGCCTTCTGT 59.711 57.895 0.00 0.00 46.23 3.41
2065 2302 0.461693 GCGAGCATCTTCTTGAGCCT 60.462 55.000 0.00 0.00 0.00 4.58
2629 2866 3.877508 GGGGATGTTCTAAAATCTGACGG 59.122 47.826 0.00 0.00 0.00 4.79
2631 2868 4.514401 ACGGGGATGTTCTAAAATCTGAC 58.486 43.478 0.00 0.00 0.00 3.51
2632 2869 4.837093 ACGGGGATGTTCTAAAATCTGA 57.163 40.909 0.00 0.00 0.00 3.27
2633 2870 4.438744 GCAACGGGGATGTTCTAAAATCTG 60.439 45.833 0.00 0.00 0.00 2.90
2634 2871 3.694566 GCAACGGGGATGTTCTAAAATCT 59.305 43.478 0.00 0.00 0.00 2.40
2635 2872 3.694566 AGCAACGGGGATGTTCTAAAATC 59.305 43.478 0.00 0.00 0.00 2.17
2636 2873 3.697166 AGCAACGGGGATGTTCTAAAAT 58.303 40.909 0.00 0.00 0.00 1.82
2638 2875 2.871096 AGCAACGGGGATGTTCTAAA 57.129 45.000 0.00 0.00 0.00 1.85
2639 2876 3.101437 TCTAGCAACGGGGATGTTCTAA 58.899 45.455 0.00 0.00 0.00 2.10
2640 2877 2.742348 TCTAGCAACGGGGATGTTCTA 58.258 47.619 0.00 0.00 0.00 2.10
2641 2878 1.568504 TCTAGCAACGGGGATGTTCT 58.431 50.000 0.00 0.00 0.00 3.01
2642 2879 2.396590 TTCTAGCAACGGGGATGTTC 57.603 50.000 0.00 0.00 0.00 3.18
2643 2880 3.016736 CAATTCTAGCAACGGGGATGTT 58.983 45.455 0.00 0.00 0.00 2.71
2644 2881 2.238646 TCAATTCTAGCAACGGGGATGT 59.761 45.455 0.00 0.00 0.00 3.06
2645 2882 2.917933 TCAATTCTAGCAACGGGGATG 58.082 47.619 0.00 0.00 0.00 3.51
2646 2883 3.644966 TTCAATTCTAGCAACGGGGAT 57.355 42.857 0.00 0.00 0.00 3.85
2650 2887 6.258160 CAGGTTAATTCAATTCTAGCAACGG 58.742 40.000 0.00 0.00 0.00 4.44
2652 2889 6.749118 CAGCAGGTTAATTCAATTCTAGCAAC 59.251 38.462 0.00 0.00 0.00 4.17
2657 2894 9.466497 AAGAATCAGCAGGTTAATTCAATTCTA 57.534 29.630 7.07 0.00 32.32 2.10
2663 2900 9.342308 CCTAATAAGAATCAGCAGGTTAATTCA 57.658 33.333 7.07 0.00 31.90 2.57
2770 3007 2.793946 GGGCAGCAGCACATTACG 59.206 61.111 2.65 0.00 45.91 3.18
2811 3059 4.024048 CAGATACAAACGGTCAGCAACTTT 60.024 41.667 0.00 0.00 0.00 2.66
2820 3068 2.477863 GCAATGCCAGATACAAACGGTC 60.478 50.000 0.00 0.00 0.00 4.79
2831 3079 1.078285 TCGCATCTGCAATGCCAGA 60.078 52.632 20.70 6.31 45.16 3.86
2865 3113 2.301505 GATGCGGTCCATCTCAACG 58.698 57.895 0.00 0.00 45.58 4.10
3072 3320 2.076100 CAATTCTTGTCACTGCGGCTA 58.924 47.619 0.00 0.00 0.00 3.93
3077 3325 3.503363 TCATGGTCAATTCTTGTCACTGC 59.497 43.478 0.00 0.00 0.00 4.40
3086 3334 3.372349 CCACTGGGATCATGGTCAATTCT 60.372 47.826 8.54 0.00 35.59 2.40
3346 3594 5.215903 CAATCACAGTACCGACTAGCTATG 58.784 45.833 0.00 0.00 33.32 2.23
3427 3675 4.005650 CACTGCATCACTATCACTTGGTT 58.994 43.478 0.00 0.00 0.00 3.67
3430 3678 4.248058 TGACACTGCATCACTATCACTTG 58.752 43.478 0.00 0.00 0.00 3.16
3598 3851 6.665992 TCCCCATCTTGTATCATGTACTAC 57.334 41.667 0.00 0.00 0.00 2.73
3605 3858 9.343994 ACTAGATATTTCCCCATCTTGTATCAT 57.656 33.333 0.00 0.00 36.11 2.45
3606 3859 8.597167 CACTAGATATTTCCCCATCTTGTATCA 58.403 37.037 0.00 0.00 35.83 2.15
3607 3860 7.550906 GCACTAGATATTTCCCCATCTTGTATC 59.449 40.741 0.00 0.00 35.83 2.24
3608 3861 7.238514 AGCACTAGATATTTCCCCATCTTGTAT 59.761 37.037 0.00 0.00 35.83 2.29
3609 3862 6.558775 AGCACTAGATATTTCCCCATCTTGTA 59.441 38.462 0.00 0.00 35.83 2.41
3610 3863 5.370880 AGCACTAGATATTTCCCCATCTTGT 59.629 40.000 0.00 0.00 37.61 3.16
3611 3864 5.874093 AGCACTAGATATTTCCCCATCTTG 58.126 41.667 0.00 0.00 33.58 3.02
3612 3865 6.013293 GGTAGCACTAGATATTTCCCCATCTT 60.013 42.308 0.00 0.00 33.58 2.40
3613 3866 5.485708 GGTAGCACTAGATATTTCCCCATCT 59.514 44.000 0.00 0.00 35.67 2.90
3614 3867 5.624738 CGGTAGCACTAGATATTTCCCCATC 60.625 48.000 0.00 0.00 0.00 3.51
3615 3868 4.223032 CGGTAGCACTAGATATTTCCCCAT 59.777 45.833 0.00 0.00 0.00 4.00
3616 3869 3.576982 CGGTAGCACTAGATATTTCCCCA 59.423 47.826 0.00 0.00 0.00 4.96
3617 3870 3.830755 TCGGTAGCACTAGATATTTCCCC 59.169 47.826 0.00 0.00 0.00 4.81
3618 3871 4.082136 CCTCGGTAGCACTAGATATTTCCC 60.082 50.000 0.00 0.00 0.00 3.97
3619 3872 4.618693 GCCTCGGTAGCACTAGATATTTCC 60.619 50.000 0.00 0.00 0.00 3.13
3620 3873 4.218852 AGCCTCGGTAGCACTAGATATTTC 59.781 45.833 0.00 0.00 0.00 2.17
3621 3874 4.153411 AGCCTCGGTAGCACTAGATATTT 58.847 43.478 0.00 0.00 0.00 1.40
3622 3875 3.759618 GAGCCTCGGTAGCACTAGATATT 59.240 47.826 0.00 0.00 0.00 1.28
3623 3876 3.009695 AGAGCCTCGGTAGCACTAGATAT 59.990 47.826 0.00 0.00 28.84 1.63
3624 3877 2.372504 AGAGCCTCGGTAGCACTAGATA 59.627 50.000 0.00 0.00 28.84 1.98
3625 3878 1.144093 AGAGCCTCGGTAGCACTAGAT 59.856 52.381 0.00 0.00 28.84 1.98
3626 3879 0.547075 AGAGCCTCGGTAGCACTAGA 59.453 55.000 0.00 0.00 28.84 2.43
3627 3880 0.665835 CAGAGCCTCGGTAGCACTAG 59.334 60.000 0.00 0.00 29.59 2.57
3628 3881 0.752009 CCAGAGCCTCGGTAGCACTA 60.752 60.000 0.00 0.00 29.59 2.74
3629 3882 2.055042 CCAGAGCCTCGGTAGCACT 61.055 63.158 0.00 0.00 0.00 4.40
3630 3883 2.352032 ACCAGAGCCTCGGTAGCAC 61.352 63.158 6.47 0.00 32.31 4.40
3631 3884 2.037367 ACCAGAGCCTCGGTAGCA 59.963 61.111 6.47 0.00 32.31 3.49
3632 3885 2.496817 CACCAGAGCCTCGGTAGC 59.503 66.667 7.71 0.00 32.98 3.58
3633 3886 0.752009 TAGCACCAGAGCCTCGGTAG 60.752 60.000 7.71 5.01 32.98 3.18
3634 3887 1.035932 GTAGCACCAGAGCCTCGGTA 61.036 60.000 7.71 0.00 32.98 4.02
3635 3888 2.037367 TAGCACCAGAGCCTCGGT 59.963 61.111 2.93 2.93 35.27 4.69
3636 3889 2.496817 GTAGCACCAGAGCCTCGG 59.503 66.667 1.76 1.76 34.23 4.63
3637 3890 2.351244 TGGTAGCACCAGAGCCTCG 61.351 63.158 4.16 0.00 44.79 4.63
3638 3891 3.713650 TGGTAGCACCAGAGCCTC 58.286 61.111 4.16 0.00 44.79 4.70
3646 3899 4.697352 GTATCATGGATTCATGGTAGCACC 59.303 45.833 14.21 0.00 44.80 5.01
3647 3900 5.308014 TGTATCATGGATTCATGGTAGCAC 58.692 41.667 14.21 3.03 44.80 4.40
3648 3901 5.565455 TGTATCATGGATTCATGGTAGCA 57.435 39.130 14.21 9.25 44.80 3.49
3649 3902 6.148480 GTCTTGTATCATGGATTCATGGTAGC 59.852 42.308 14.21 6.95 44.80 3.58
3650 3903 6.367149 CGTCTTGTATCATGGATTCATGGTAG 59.633 42.308 14.21 1.73 44.80 3.18
3655 3908 4.707105 TGCGTCTTGTATCATGGATTCAT 58.293 39.130 0.00 0.00 0.00 2.57
3656 3909 4.135747 TGCGTCTTGTATCATGGATTCA 57.864 40.909 0.00 0.00 0.00 2.57
3657 3910 5.484173 TTTGCGTCTTGTATCATGGATTC 57.516 39.130 0.00 0.00 0.00 2.52
3658 3911 5.895636 TTTTGCGTCTTGTATCATGGATT 57.104 34.783 0.00 0.00 0.00 3.01
3659 3912 6.455360 AATTTTGCGTCTTGTATCATGGAT 57.545 33.333 0.00 0.00 0.00 3.41
3660 3913 5.895636 AATTTTGCGTCTTGTATCATGGA 57.104 34.783 0.00 0.00 0.00 3.41
3661 3914 6.321873 CAAATTTTGCGTCTTGTATCATGG 57.678 37.500 0.00 0.00 0.00 3.66
3696 3949 2.348666 ACTGTAATCAAATCGAGCGTGC 59.651 45.455 0.00 0.00 0.00 5.34
3770 4026 6.314400 GTGGTCACTACTCTAACTCTACTCAG 59.686 46.154 0.00 0.00 0.00 3.35
3834 4134 1.999634 AAGGCAAGCCACTCCACACT 62.000 55.000 14.40 0.00 38.92 3.55
3835 4135 1.518903 GAAGGCAAGCCACTCCACAC 61.519 60.000 14.40 0.00 38.92 3.82
3836 4136 1.228245 GAAGGCAAGCCACTCCACA 60.228 57.895 14.40 0.00 38.92 4.17
3889 4195 1.896660 GGAGCGGAGAGAGCGAGAT 60.897 63.158 0.00 0.00 40.04 2.75
4032 4341 0.541063 TGGTGGCTACGAGGAGAACA 60.541 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.