Multiple sequence alignment - TraesCS1D01G296700

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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 TraesCS1D01G296700 chr1D 100.000 2792 0 0 1 2792 394703625 394706416 0.000000e+00 5156
1 TraesCS1D01G296700 chr1B 93.755 1217 50 17 856 2059 526569635 526568432 0.000000e+00 1803
2 TraesCS1D01G296700 chr1B 95.362 733 26 4 2067 2792 324349587 324348856 0.000000e+00 1158
3 TraesCS1D01G296700 chr1B 84.141 681 55 19 31 681 526570323 526569666 6.610000e-171 610
4 TraesCS1D01G296700 chr1A 91.034 1093 55 25 842 1907 490316105 490315029 0.000000e+00 1435
5 TraesCS1D01G296700 chr1A 89.035 684 38 18 12 679 490316783 490316121 0.000000e+00 813
6 TraesCS1D01G296700 chr7D 96.448 732 16 4 2067 2792 604369908 604369181 0.000000e+00 1199
7 TraesCS1D01G296700 chr7D 96.306 731 22 1 2067 2792 604364440 604363710 0.000000e+00 1195
8 TraesCS1D01G296700 chr7D 95.788 736 21 4 2067 2792 252055520 252056255 0.000000e+00 1179
9 TraesCS1D01G296700 chr7D 95.355 732 26 3 2067 2792 113797893 113798622 0.000000e+00 1157
10 TraesCS1D01G296700 chr7D 94.479 163 9 0 682 844 573953276 573953114 4.620000e-63 252
11 TraesCS1D01G296700 chr2D 96.196 736 18 3 2067 2792 432018030 432017295 0.000000e+00 1195
12 TraesCS1D01G296700 chr5D 95.616 730 27 3 2067 2792 424889667 424890395 0.000000e+00 1166
13 TraesCS1D01G296700 chr5D 95.225 733 25 7 2067 2792 554761600 554760871 0.000000e+00 1151
14 TraesCS1D01G296700 chr3A 95.592 726 31 1 2067 2792 748204231 748203507 0.000000e+00 1162
15 TraesCS1D01G296700 chr6D 92.737 179 11 2 667 845 90890269 90890445 9.920000e-65 257
16 TraesCS1D01G296700 chr2B 93.143 175 10 2 682 855 664125038 664125211 3.570000e-64 255
17 TraesCS1D01G296700 chrUn 93.976 166 10 0 679 844 232153311 232153476 4.620000e-63 252
18 TraesCS1D01G296700 chrUn 93.976 166 10 0 679 844 237972350 237972515 4.620000e-63 252
19 TraesCS1D01G296700 chr7B 94.479 163 9 0 682 844 497576786 497576624 4.620000e-63 252
20 TraesCS1D01G296700 chr3B 93.976 166 10 0 679 844 764446104 764446269 4.620000e-63 252
21 TraesCS1D01G296700 chr4B 92.486 173 13 0 679 851 427361561 427361733 5.970000e-62 248
22 TraesCS1D01G296700 chr6B 90.323 186 16 2 679 863 35822509 35822693 2.780000e-60 243


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 TraesCS1D01G296700 chr1D 394703625 394706416 2791 False 5156.0 5156 100.0000 1 2792 1 chr1D.!!$F1 2791
1 TraesCS1D01G296700 chr1B 526568432 526570323 1891 True 1206.5 1803 88.9480 31 2059 2 chr1B.!!$R2 2028
2 TraesCS1D01G296700 chr1B 324348856 324349587 731 True 1158.0 1158 95.3620 2067 2792 1 chr1B.!!$R1 725
3 TraesCS1D01G296700 chr1A 490315029 490316783 1754 True 1124.0 1435 90.0345 12 1907 2 chr1A.!!$R1 1895
4 TraesCS1D01G296700 chr7D 604369181 604369908 727 True 1199.0 1199 96.4480 2067 2792 1 chr7D.!!$R3 725
5 TraesCS1D01G296700 chr7D 604363710 604364440 730 True 1195.0 1195 96.3060 2067 2792 1 chr7D.!!$R2 725
6 TraesCS1D01G296700 chr7D 252055520 252056255 735 False 1179.0 1179 95.7880 2067 2792 1 chr7D.!!$F2 725
7 TraesCS1D01G296700 chr7D 113797893 113798622 729 False 1157.0 1157 95.3550 2067 2792 1 chr7D.!!$F1 725
8 TraesCS1D01G296700 chr2D 432017295 432018030 735 True 1195.0 1195 96.1960 2067 2792 1 chr2D.!!$R1 725
9 TraesCS1D01G296700 chr5D 424889667 424890395 728 False 1166.0 1166 95.6160 2067 2792 1 chr5D.!!$F1 725
10 TraesCS1D01G296700 chr5D 554760871 554761600 729 True 1151.0 1151 95.2250 2067 2792 1 chr5D.!!$R1 725
11 TraesCS1D01G296700 chr3A 748203507 748204231 724 True 1162.0 1162 95.5920 2067 2792 1 chr3A.!!$R1 725

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
351 363 0.034198 TCGTGCGAGGTTCATTCCAA 59.966 50.0 0.0 0.0 0.0 3.53 F
1093 1162 0.183971 TCGGCACCAAGGAAAAGGAA 59.816 50.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 1261 1.219393 GAAGGAGAGCAGGAACCGG 59.781 63.158 0.0 0.0 0.0 5.28 R
2440 2559 0.033920 GTAAACCCCACGTCCGAGTT 59.966 55.000 0.0 0.0 0.0 3.01 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
35 36 4.422073 AATAGTATGGCTGCAGCTAACA 57.578 40.909 35.82 26.02 41.70 2.41
52 53 2.969443 ACAGCGTCTTATTTGTGCAC 57.031 45.000 10.75 10.75 0.00 4.57
84 85 0.455633 CCGGTTTACACGAGACGAGG 60.456 60.000 0.00 0.00 0.00 4.63
223 229 1.040893 TCCCGCCGAAGCATCTTCTA 61.041 55.000 5.22 0.00 39.83 2.10
226 232 1.000283 CCGCCGAAGCATCTTCTATCT 60.000 52.381 5.22 0.00 39.83 1.98
291 303 1.620822 GGCAATGTTTGACCTGACCT 58.379 50.000 0.00 0.00 30.38 3.85
299 311 0.119155 TTGACCTGACCTGATCCCCT 59.881 55.000 0.00 0.00 0.00 4.79
328 340 4.702081 GCACGCCTCGTCTGTCGT 62.702 66.667 0.00 0.00 38.32 4.34
343 355 4.695231 CGTCCGTCGTGCGAGGTT 62.695 66.667 12.25 0.00 44.77 3.50
351 363 0.034198 TCGTGCGAGGTTCATTCCAA 59.966 50.000 0.00 0.00 0.00 3.53
352 364 0.443869 CGTGCGAGGTTCATTCCAAG 59.556 55.000 0.00 0.00 0.00 3.61
355 367 2.293399 GTGCGAGGTTCATTCCAAGTTT 59.707 45.455 0.00 0.00 0.00 2.66
357 369 2.095212 GCGAGGTTCATTCCAAGTTTCC 60.095 50.000 0.00 0.00 0.00 3.13
358 370 3.146066 CGAGGTTCATTCCAAGTTTCCA 58.854 45.455 0.00 0.00 0.00 3.53
359 371 3.568007 CGAGGTTCATTCCAAGTTTCCAA 59.432 43.478 0.00 0.00 0.00 3.53
360 372 4.556699 CGAGGTTCATTCCAAGTTTCCAAC 60.557 45.833 0.00 0.00 0.00 3.77
415 455 2.970324 GGCCGACACGACAGCAAA 60.970 61.111 0.00 0.00 0.00 3.68
502 542 6.146510 CAGAATACCAGTAGTGCACGTAAAAA 59.853 38.462 12.01 0.00 0.00 1.94
656 713 0.320247 GGAGAGCATGCATCTACCGG 60.320 60.000 21.98 0.00 0.00 5.28
681 744 4.655762 ACGTGTATGCATGTAGAGATGT 57.344 40.909 10.16 0.00 42.54 3.06
682 745 5.767816 ACGTGTATGCATGTAGAGATGTA 57.232 39.130 10.16 0.00 42.54 2.29
683 746 5.520632 ACGTGTATGCATGTAGAGATGTAC 58.479 41.667 10.16 0.00 42.54 2.90
685 748 5.853810 CGTGTATGCATGTAGAGATGTACTC 59.146 44.000 10.16 0.00 45.22 2.59
687 750 4.881019 ATGCATGTAGAGATGTACTCCC 57.119 45.455 0.00 0.00 45.96 4.30
688 751 3.916035 TGCATGTAGAGATGTACTCCCT 58.084 45.455 0.00 0.00 45.96 4.20
689 752 3.891977 TGCATGTAGAGATGTACTCCCTC 59.108 47.826 0.00 0.00 45.96 4.30
690 753 3.257127 GCATGTAGAGATGTACTCCCTCC 59.743 52.174 0.00 0.00 45.96 4.30
691 754 3.210232 TGTAGAGATGTACTCCCTCCG 57.790 52.381 0.00 0.00 45.96 4.63
692 755 2.508716 TGTAGAGATGTACTCCCTCCGT 59.491 50.000 0.00 0.00 45.96 4.69
694 757 2.657143 AGAGATGTACTCCCTCCGTTC 58.343 52.381 0.00 0.00 45.96 3.95
696 759 3.025262 GAGATGTACTCCCTCCGTTCTT 58.975 50.000 0.00 0.00 39.53 2.52
697 760 4.079901 AGAGATGTACTCCCTCCGTTCTTA 60.080 45.833 0.00 0.00 45.96 2.10
698 761 4.607239 AGATGTACTCCCTCCGTTCTTAA 58.393 43.478 0.00 0.00 0.00 1.85
700 763 5.661759 AGATGTACTCCCTCCGTTCTTAAAT 59.338 40.000 0.00 0.00 0.00 1.40
701 764 6.837568 AGATGTACTCCCTCCGTTCTTAAATA 59.162 38.462 0.00 0.00 0.00 1.40
702 765 7.509659 AGATGTACTCCCTCCGTTCTTAAATAT 59.490 37.037 0.00 0.00 0.00 1.28
703 766 8.716674 ATGTACTCCCTCCGTTCTTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
704 767 8.537728 TGTACTCCCTCCGTTCTTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
705 768 8.980596 TGTACTCCCTCCGTTCTTAAATATAAA 58.019 33.333 0.00 0.00 0.00 1.40
706 769 9.993454 GTACTCCCTCCGTTCTTAAATATAAAT 57.007 33.333 0.00 0.00 0.00 1.40
708 771 8.935741 ACTCCCTCCGTTCTTAAATATAAATCT 58.064 33.333 0.00 0.00 0.00 2.40
709 772 9.780186 CTCCCTCCGTTCTTAAATATAAATCTT 57.220 33.333 0.00 0.00 0.00 2.40
729 792 9.829507 AAATCTTTGTAGAGATTCCACTAGATG 57.170 33.333 0.00 0.00 43.66 2.90
730 793 7.961351 ATCTTTGTAGAGATTCCACTAGATGG 58.039 38.462 0.00 0.43 41.18 3.51
731 794 7.786943 ATCTTTGTAGAGATTCCACTAGATGGA 59.213 37.037 9.25 9.25 44.43 3.41
745 808 6.573434 CACTAGATGGACTACATACAAAGCA 58.427 40.000 0.00 0.00 40.72 3.91
746 809 7.041721 CACTAGATGGACTACATACAAAGCAA 58.958 38.462 0.00 0.00 40.72 3.91
747 810 7.549134 CACTAGATGGACTACATACAAAGCAAA 59.451 37.037 0.00 0.00 40.72 3.68
748 811 8.100791 ACTAGATGGACTACATACAAAGCAAAA 58.899 33.333 0.00 0.00 40.72 2.44
749 812 7.944729 AGATGGACTACATACAAAGCAAAAT 57.055 32.000 0.00 0.00 40.72 1.82
751 814 9.461312 AGATGGACTACATACAAAGCAAAATAA 57.539 29.630 0.00 0.00 40.72 1.40
788 851 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
792 855 7.953158 AATGCATCTATATACATCCGTATGC 57.047 36.000 0.00 0.00 38.79 3.14
793 856 6.463995 TGCATCTATATACATCCGTATGCA 57.536 37.500 0.00 0.00 38.79 3.96
794 857 6.507023 TGCATCTATATACATCCGTATGCAG 58.493 40.000 0.00 0.00 38.79 4.41
795 858 6.096846 TGCATCTATATACATCCGTATGCAGT 59.903 38.462 0.00 0.00 38.79 4.40
796 859 6.980978 GCATCTATATACATCCGTATGCAGTT 59.019 38.462 0.00 0.00 38.79 3.16
797 860 7.492669 GCATCTATATACATCCGTATGCAGTTT 59.507 37.037 0.00 0.00 38.79 2.66
803 866 9.803315 ATATACATCCGTATGCAGTTTATAGTG 57.197 33.333 0.00 0.00 38.79 2.74
804 867 5.297547 ACATCCGTATGCAGTTTATAGTGG 58.702 41.667 0.00 0.00 36.50 4.00
805 868 5.069914 ACATCCGTATGCAGTTTATAGTGGA 59.930 40.000 0.00 0.00 36.50 4.02
806 869 5.601583 TCCGTATGCAGTTTATAGTGGAA 57.398 39.130 0.00 0.00 0.00 3.53
807 870 6.169557 TCCGTATGCAGTTTATAGTGGAAT 57.830 37.500 0.00 0.00 0.00 3.01
808 871 6.220930 TCCGTATGCAGTTTATAGTGGAATC 58.779 40.000 0.00 0.00 0.00 2.52
809 872 6.041637 TCCGTATGCAGTTTATAGTGGAATCT 59.958 38.462 0.00 0.00 0.00 2.40
810 873 6.366332 CCGTATGCAGTTTATAGTGGAATCTC 59.634 42.308 0.00 0.00 0.00 2.75
811 874 7.148641 CGTATGCAGTTTATAGTGGAATCTCT 58.851 38.462 0.00 0.00 0.00 3.10
812 875 8.297426 CGTATGCAGTTTATAGTGGAATCTCTA 58.703 37.037 0.00 0.00 0.00 2.43
813 876 9.413048 GTATGCAGTTTATAGTGGAATCTCTAC 57.587 37.037 0.00 0.00 0.00 2.59
814 877 7.418337 TGCAGTTTATAGTGGAATCTCTACA 57.582 36.000 0.00 0.00 29.47 2.74
815 878 7.847096 TGCAGTTTATAGTGGAATCTCTACAA 58.153 34.615 0.00 0.00 29.47 2.41
816 879 8.318412 TGCAGTTTATAGTGGAATCTCTACAAA 58.682 33.333 0.00 0.00 29.47 2.83
817 880 8.821894 GCAGTTTATAGTGGAATCTCTACAAAG 58.178 37.037 0.00 0.00 29.47 2.77
824 887 7.540474 AGTGGAATCTCTACAAAGACTTACA 57.460 36.000 0.00 0.00 29.47 2.41
825 888 8.140112 AGTGGAATCTCTACAAAGACTTACAT 57.860 34.615 0.00 0.00 29.47 2.29
826 889 8.598041 AGTGGAATCTCTACAAAGACTTACATT 58.402 33.333 0.00 0.00 29.47 2.71
827 890 9.220767 GTGGAATCTCTACAAAGACTTACATTT 57.779 33.333 0.00 0.00 0.00 2.32
833 896 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
834 897 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95
835 898 8.579006 TCTACAAAGACTTACATTTAGGAACGA 58.421 33.333 0.00 0.00 0.00 3.85
836 899 9.199982 CTACAAAGACTTACATTTAGGAACGAA 57.800 33.333 0.00 0.00 0.00 3.85
837 900 8.084590 ACAAAGACTTACATTTAGGAACGAAG 57.915 34.615 0.00 0.00 0.00 3.79
838 901 7.172703 ACAAAGACTTACATTTAGGAACGAAGG 59.827 37.037 0.00 0.00 0.00 3.46
839 902 5.731591 AGACTTACATTTAGGAACGAAGGG 58.268 41.667 0.00 0.00 0.00 3.95
840 903 5.482878 AGACTTACATTTAGGAACGAAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
854 917 4.616181 CGAAGGGAGTATTTCGCAAAAT 57.384 40.909 0.00 0.00 39.55 1.82
855 918 5.728351 CGAAGGGAGTATTTCGCAAAATA 57.272 39.130 0.00 0.00 39.55 1.40
856 919 6.114221 CGAAGGGAGTATTTCGCAAAATAA 57.886 37.500 0.00 0.00 38.68 1.40
857 920 6.548171 CGAAGGGAGTATTTCGCAAAATAAA 58.452 36.000 0.00 0.00 38.68 1.40
858 921 6.687105 CGAAGGGAGTATTTCGCAAAATAAAG 59.313 38.462 0.00 0.00 38.68 1.85
859 922 7.413657 CGAAGGGAGTATTTCGCAAAATAAAGA 60.414 37.037 0.00 0.00 38.68 2.52
860 923 7.696992 AGGGAGTATTTCGCAAAATAAAGAA 57.303 32.000 0.00 0.00 38.68 2.52
893 960 4.433615 CTCTGTATGTGCGTACATTCCTT 58.566 43.478 24.19 3.04 45.01 3.36
936 1004 4.012895 GCCGCACTGACCAACGTG 62.013 66.667 0.00 0.00 0.00 4.49
1008 1077 4.508662 CTCTCGCCCTCTCACTTTTAATT 58.491 43.478 0.00 0.00 0.00 1.40
1011 1080 2.683362 CGCCCTCTCACTTTTAATTCCC 59.317 50.000 0.00 0.00 0.00 3.97
1031 1100 8.733092 ATTCCCTCTCATTATTATCTGTCTCA 57.267 34.615 0.00 0.00 0.00 3.27
1033 1102 7.069344 TCCCTCTCATTATTATCTGTCTCACA 58.931 38.462 0.00 0.00 0.00 3.58
1046 1115 3.743521 TGTCTCACATTGTTTGCTAGCT 58.256 40.909 17.23 0.00 0.00 3.32
1047 1116 4.893608 TGTCTCACATTGTTTGCTAGCTA 58.106 39.130 17.23 5.31 0.00 3.32
1048 1117 4.690748 TGTCTCACATTGTTTGCTAGCTAC 59.309 41.667 17.23 14.15 0.00 3.58
1049 1118 4.932200 GTCTCACATTGTTTGCTAGCTACT 59.068 41.667 17.23 0.00 0.00 2.57
1050 1119 5.062809 GTCTCACATTGTTTGCTAGCTACTC 59.937 44.000 17.23 5.05 0.00 2.59
1051 1120 4.253685 TCACATTGTTTGCTAGCTACTCC 58.746 43.478 17.23 0.00 0.00 3.85
1052 1121 4.020218 TCACATTGTTTGCTAGCTACTCCT 60.020 41.667 17.23 1.23 0.00 3.69
1090 1159 0.537371 ACCTCGGCACCAAGGAAAAG 60.537 55.000 0.00 0.00 36.46 2.27
1093 1162 0.183971 TCGGCACCAAGGAAAAGGAA 59.816 50.000 0.00 0.00 0.00 3.36
1186 1261 1.737008 GACGGCGGTGAAGAAGGTC 60.737 63.158 13.24 0.00 0.00 3.85
1426 1504 4.549516 GCGGCGTCGGAGTACTCC 62.550 72.222 29.18 29.18 46.18 3.85
1561 1639 4.101448 ATGGAGCGGCAGGTGTCC 62.101 66.667 1.45 0.00 0.00 4.02
1672 1752 5.511377 GCATTGCGATTCTTGTTAATTTCGA 59.489 36.000 0.00 0.00 0.00 3.71
1797 1890 7.275779 CACAGAGTGCGAGTAGTACAAATAAAT 59.724 37.037 2.52 0.00 37.96 1.40
1823 1916 1.705186 TCTTTGAGAACTTGGGGGAGG 59.295 52.381 0.00 0.00 0.00 4.30
1871 1965 8.743085 AGAAATATCTTTGTATGTGCATCACT 57.257 30.769 0.00 0.00 31.16 3.41
1938 2035 8.763984 AGCCAGAATCAATTAATCAAGAATCT 57.236 30.769 0.00 0.00 0.00 2.40
1968 2065 7.217028 TGGTACTATCTCCTTGTAGGTCTAA 57.783 40.000 0.00 0.00 36.53 2.10
1979 2076 9.765795 CTCCTTGTAGGTCTAAAATATTCGATT 57.234 33.333 0.00 0.00 36.53 3.34
2044 2141 5.841957 AGGTCTGGCATATTCAATTTCAC 57.158 39.130 0.00 0.00 0.00 3.18
2050 2147 4.060205 GGCATATTCAATTTCACATGGGC 58.940 43.478 0.00 0.00 0.00 5.36
2051 2148 4.443175 GGCATATTCAATTTCACATGGGCA 60.443 41.667 0.00 0.00 0.00 5.36
2052 2149 5.117584 GCATATTCAATTTCACATGGGCAA 58.882 37.500 0.00 0.00 0.00 4.52
2053 2150 5.006941 GCATATTCAATTTCACATGGGCAAC 59.993 40.000 0.00 0.00 0.00 4.17
2054 2151 4.620589 ATTCAATTTCACATGGGCAACA 57.379 36.364 0.00 0.00 39.74 3.33
2059 2156 4.989279 ATTTCACATGGGCAACATCTAC 57.011 40.909 0.00 0.00 37.84 2.59
2060 2157 3.719268 TTCACATGGGCAACATCTACT 57.281 42.857 0.00 0.00 37.84 2.57
2061 2158 3.266510 TCACATGGGCAACATCTACTC 57.733 47.619 0.00 0.00 37.84 2.59
2062 2159 2.840038 TCACATGGGCAACATCTACTCT 59.160 45.455 0.00 0.00 37.84 3.24
2063 2160 4.030216 TCACATGGGCAACATCTACTCTA 58.970 43.478 0.00 0.00 37.84 2.43
2064 2161 4.655649 TCACATGGGCAACATCTACTCTAT 59.344 41.667 0.00 0.00 37.84 1.98
2065 2162 5.838521 TCACATGGGCAACATCTACTCTATA 59.161 40.000 0.00 0.00 37.84 1.31
2091 2188 4.705023 GGAATTTTGCTAGTAGGCCTTTGA 59.295 41.667 12.58 0.00 0.00 2.69
2122 2219 7.381323 AGCCCAACTAAAATTCTGAAATTCTG 58.619 34.615 0.00 0.00 33.93 3.02
2138 2235 1.140161 CTGTTGGCCCATTCATGCG 59.860 57.895 0.00 0.00 0.00 4.73
2261 2358 3.640967 GAGCATGACAAGAGGAGACCTAT 59.359 47.826 0.00 0.00 31.76 2.57
2312 2429 2.046314 CGGGTTGCGGGATTGAGT 60.046 61.111 0.00 0.00 0.00 3.41
2440 2559 3.000041 CCGATTCTTTTGGATCGTGACA 59.000 45.455 6.06 0.00 35.03 3.58
2651 2779 1.103803 GCCTCTCGTGATCCTGTACA 58.896 55.000 0.00 0.00 0.00 2.90
2732 2860 0.386985 GCGAACGACGACTTCTTCCT 60.387 55.000 0.00 0.00 45.77 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.177696 GCCATACTATTTTACGAGGCAAGAG 59.822 44.000 0.00 0.00 40.50 2.85
2 3 5.050091 CAGCCATACTATTTTACGAGGCAAG 60.050 44.000 0.00 0.00 43.13 4.01
3 4 4.814234 CAGCCATACTATTTTACGAGGCAA 59.186 41.667 0.00 0.00 43.13 4.52
4 5 4.377021 CAGCCATACTATTTTACGAGGCA 58.623 43.478 0.00 0.00 43.13 4.75
5 6 3.186613 GCAGCCATACTATTTTACGAGGC 59.813 47.826 0.00 0.00 41.08 4.70
6 7 4.377021 TGCAGCCATACTATTTTACGAGG 58.623 43.478 0.00 0.00 0.00 4.63
7 8 4.084328 GCTGCAGCCATACTATTTTACGAG 60.084 45.833 28.76 0.00 34.31 4.18
8 9 3.807622 GCTGCAGCCATACTATTTTACGA 59.192 43.478 28.76 0.00 34.31 3.43
9 10 3.809832 AGCTGCAGCCATACTATTTTACG 59.190 43.478 34.39 0.00 43.38 3.18
10 11 6.260050 TGTTAGCTGCAGCCATACTATTTTAC 59.740 38.462 34.39 16.53 43.38 2.01
35 36 2.616376 TGTTGTGCACAAATAAGACGCT 59.384 40.909 32.61 0.00 37.63 5.07
52 53 3.530910 AACCGGCTCCGACCTGTTG 62.531 63.158 10.28 0.00 42.83 3.33
84 85 3.662186 CGTTTGGTTGATTTGTCGCTTAC 59.338 43.478 0.00 0.00 0.00 2.34
205 211 0.034059 ATAGAAGATGCTTCGGCGGG 59.966 55.000 7.21 1.20 45.37 6.13
223 229 1.380785 TCCGGCCCGTTGTCTAGAT 60.381 57.895 0.85 0.00 0.00 1.98
226 232 2.162338 CTTGTCCGGCCCGTTGTCTA 62.162 60.000 0.85 0.00 0.00 2.59
261 267 2.821366 CATTGCCGCTCCGCTTCT 60.821 61.111 0.00 0.00 0.00 2.85
291 303 1.628727 CTGGAGGAGGAGGGGATCA 59.371 63.158 0.00 0.00 0.00 2.92
328 340 2.149803 AATGAACCTCGCACGACGGA 62.150 55.000 13.16 0.00 43.89 4.69
351 363 4.658280 GCGCAAGGTTGTGTTGGAAACT 62.658 50.000 0.30 0.00 43.44 2.66
352 364 2.389031 GCGCAAGGTTGTGTTGGAAAC 61.389 52.381 0.30 0.00 43.37 2.78
355 367 3.115556 GCGCAAGGTTGTGTTGGA 58.884 55.556 0.30 0.00 40.65 3.53
502 542 2.668550 GAAGGAACGGCGGCAGTT 60.669 61.111 18.17 18.17 34.07 3.16
578 621 5.065988 ACCGAGCAACATGTACATATTTTCC 59.934 40.000 8.32 0.00 0.00 3.13
579 622 6.119144 ACCGAGCAACATGTACATATTTTC 57.881 37.500 8.32 3.32 0.00 2.29
580 623 5.645929 TGACCGAGCAACATGTACATATTTT 59.354 36.000 8.32 0.00 0.00 1.82
641 698 1.341531 GTAGACCGGTAGATGCATGCT 59.658 52.381 20.33 4.11 0.00 3.79
656 713 5.419760 TCTCTACATGCATACACGTAGAC 57.580 43.478 16.58 0.00 44.34 2.59
682 745 8.935741 AGATTTATATTTAAGAACGGAGGGAGT 58.064 33.333 0.00 0.00 0.00 3.85
683 746 9.780186 AAGATTTATATTTAAGAACGGAGGGAG 57.220 33.333 0.00 0.00 0.00 4.30
703 766 9.829507 CATCTAGTGGAATCTCTACAAAGATTT 57.170 33.333 1.05 0.00 44.16 2.17
721 784 6.573434 TGCTTTGTATGTAGTCCATCTAGTG 58.427 40.000 0.00 0.00 34.86 2.74
722 785 6.791867 TGCTTTGTATGTAGTCCATCTAGT 57.208 37.500 0.00 0.00 34.86 2.57
723 786 8.492673 TTTTGCTTTGTATGTAGTCCATCTAG 57.507 34.615 0.00 0.00 34.86 2.43
725 788 7.944729 ATTTTGCTTTGTATGTAGTCCATCT 57.055 32.000 0.00 0.00 34.86 2.90
762 825 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
766 829 8.830580 GCATACGGATGTATATAGATGCATTTT 58.169 33.333 9.90 0.00 38.38 1.82
767 830 7.986889 TGCATACGGATGTATATAGATGCATTT 59.013 33.333 9.90 0.00 38.38 2.32
768 831 7.500141 TGCATACGGATGTATATAGATGCATT 58.500 34.615 9.90 1.23 38.38 3.56
769 832 7.054491 TGCATACGGATGTATATAGATGCAT 57.946 36.000 9.90 0.00 40.68 3.96
770 833 6.096846 ACTGCATACGGATGTATATAGATGCA 59.903 38.462 9.90 7.54 39.28 3.96
771 834 6.507900 ACTGCATACGGATGTATATAGATGC 58.492 40.000 9.90 0.00 39.28 3.91
772 835 8.932945 AAACTGCATACGGATGTATATAGATG 57.067 34.615 9.90 0.00 39.28 2.90
777 840 9.803315 CACTATAAACTGCATACGGATGTATAT 57.197 33.333 9.90 2.70 39.28 0.86
778 841 8.248253 CCACTATAAACTGCATACGGATGTATA 58.752 37.037 9.90 2.44 39.28 1.47
779 842 7.039293 TCCACTATAAACTGCATACGGATGTAT 60.039 37.037 9.90 1.29 42.03 2.29
780 843 6.265876 TCCACTATAAACTGCATACGGATGTA 59.734 38.462 9.90 3.37 35.30 2.29
781 844 5.069914 TCCACTATAAACTGCATACGGATGT 59.930 40.000 9.90 0.00 35.30 3.06
782 845 5.538118 TCCACTATAAACTGCATACGGATG 58.462 41.667 2.22 2.22 36.02 3.51
783 846 5.801531 TCCACTATAAACTGCATACGGAT 57.198 39.130 0.00 0.00 0.00 4.18
784 847 5.601583 TTCCACTATAAACTGCATACGGA 57.398 39.130 0.00 0.00 0.00 4.69
785 848 6.223852 AGATTCCACTATAAACTGCATACGG 58.776 40.000 0.00 0.00 0.00 4.02
786 849 7.148641 AGAGATTCCACTATAAACTGCATACG 58.851 38.462 0.00 0.00 0.00 3.06
787 850 9.413048 GTAGAGATTCCACTATAAACTGCATAC 57.587 37.037 0.00 0.00 0.00 2.39
788 851 9.143155 TGTAGAGATTCCACTATAAACTGCATA 57.857 33.333 0.00 0.00 0.00 3.14
789 852 8.023021 TGTAGAGATTCCACTATAAACTGCAT 57.977 34.615 0.00 0.00 0.00 3.96
790 853 7.418337 TGTAGAGATTCCACTATAAACTGCA 57.582 36.000 0.00 0.00 0.00 4.41
791 854 8.718102 TTTGTAGAGATTCCACTATAAACTGC 57.282 34.615 0.00 0.00 29.58 4.40
798 861 9.256228 TGTAAGTCTTTGTAGAGATTCCACTAT 57.744 33.333 0.00 0.00 0.00 2.12
799 862 8.645814 TGTAAGTCTTTGTAGAGATTCCACTA 57.354 34.615 0.00 0.00 0.00 2.74
800 863 7.540474 TGTAAGTCTTTGTAGAGATTCCACT 57.460 36.000 0.00 0.00 0.00 4.00
801 864 8.779354 AATGTAAGTCTTTGTAGAGATTCCAC 57.221 34.615 0.00 0.00 0.00 4.02
807 870 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
808 871 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
809 872 8.579006 TCGTTCCTAAATGTAAGTCTTTGTAGA 58.421 33.333 0.00 0.00 0.00 2.59
810 873 8.752766 TCGTTCCTAAATGTAAGTCTTTGTAG 57.247 34.615 0.00 0.00 0.00 2.74
811 874 9.199982 CTTCGTTCCTAAATGTAAGTCTTTGTA 57.800 33.333 0.00 0.00 0.00 2.41
812 875 7.172703 CCTTCGTTCCTAAATGTAAGTCTTTGT 59.827 37.037 0.00 0.00 0.00 2.83
813 876 7.360946 CCCTTCGTTCCTAAATGTAAGTCTTTG 60.361 40.741 0.00 0.00 0.00 2.77
814 877 6.653740 CCCTTCGTTCCTAAATGTAAGTCTTT 59.346 38.462 0.00 0.00 0.00 2.52
815 878 6.013984 TCCCTTCGTTCCTAAATGTAAGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
816 879 5.482878 TCCCTTCGTTCCTAAATGTAAGTCT 59.517 40.000 0.00 0.00 0.00 3.24
817 880 5.727434 TCCCTTCGTTCCTAAATGTAAGTC 58.273 41.667 0.00 0.00 0.00 3.01
818 881 5.247792 ACTCCCTTCGTTCCTAAATGTAAGT 59.752 40.000 0.00 0.00 0.00 2.24
819 882 5.731591 ACTCCCTTCGTTCCTAAATGTAAG 58.268 41.667 0.00 0.00 0.00 2.34
820 883 5.750352 ACTCCCTTCGTTCCTAAATGTAA 57.250 39.130 0.00 0.00 0.00 2.41
821 884 7.427989 AATACTCCCTTCGTTCCTAAATGTA 57.572 36.000 0.00 0.00 0.00 2.29
822 885 5.952347 ATACTCCCTTCGTTCCTAAATGT 57.048 39.130 0.00 0.00 0.00 2.71
823 886 6.018994 CGAAATACTCCCTTCGTTCCTAAATG 60.019 42.308 0.00 0.00 39.60 2.32
824 887 6.047231 CGAAATACTCCCTTCGTTCCTAAAT 58.953 40.000 0.00 0.00 39.60 1.40
825 888 5.413499 CGAAATACTCCCTTCGTTCCTAAA 58.587 41.667 0.00 0.00 39.60 1.85
826 889 4.678840 GCGAAATACTCCCTTCGTTCCTAA 60.679 45.833 6.14 0.00 44.82 2.69
827 890 3.181483 GCGAAATACTCCCTTCGTTCCTA 60.181 47.826 6.14 0.00 44.82 2.94
828 891 2.418334 GCGAAATACTCCCTTCGTTCCT 60.418 50.000 6.14 0.00 44.82 3.36
829 892 1.931841 GCGAAATACTCCCTTCGTTCC 59.068 52.381 6.14 0.00 44.82 3.62
830 893 2.613691 TGCGAAATACTCCCTTCGTTC 58.386 47.619 6.14 0.00 44.82 3.95
831 894 2.754946 TGCGAAATACTCCCTTCGTT 57.245 45.000 6.14 0.00 44.82 3.85
832 895 2.754946 TTGCGAAATACTCCCTTCGT 57.245 45.000 6.14 0.00 44.82 3.85
833 896 4.616181 ATTTTGCGAAATACTCCCTTCG 57.384 40.909 10.32 0.06 45.58 3.79
834 897 7.758495 TCTTTATTTTGCGAAATACTCCCTTC 58.242 34.615 17.14 0.00 37.43 3.46
835 898 7.696992 TCTTTATTTTGCGAAATACTCCCTT 57.303 32.000 17.14 0.00 37.43 3.95
836 899 7.696992 TTCTTTATTTTGCGAAATACTCCCT 57.303 32.000 17.14 0.00 37.43 4.20
837 900 8.751302 TTTTCTTTATTTTGCGAAATACTCCC 57.249 30.769 17.14 0.00 37.43 4.30
893 960 5.938125 AGCTACTCGGCTTTAAGAAATTTCA 59.062 36.000 19.99 0.00 39.86 2.69
936 1004 3.053291 TGGAAATGTCGCCCACGC 61.053 61.111 0.00 0.00 39.84 5.34
1008 1077 7.069344 TGTGAGACAGATAATAATGAGAGGGA 58.931 38.462 0.00 0.00 0.00 4.20
1011 1080 9.761504 ACAATGTGAGACAGATAATAATGAGAG 57.238 33.333 0.00 0.00 0.00 3.20
1021 1090 5.582269 GCTAGCAAACAATGTGAGACAGATA 59.418 40.000 10.63 0.00 0.00 1.98
1022 1091 4.394300 GCTAGCAAACAATGTGAGACAGAT 59.606 41.667 10.63 0.00 0.00 2.90
1023 1092 3.748048 GCTAGCAAACAATGTGAGACAGA 59.252 43.478 10.63 0.00 0.00 3.41
1031 1100 4.559862 AGGAGTAGCTAGCAAACAATGT 57.440 40.909 18.83 0.00 0.00 2.71
1033 1102 5.941555 AGTAGGAGTAGCTAGCAAACAAT 57.058 39.130 18.83 7.19 0.00 2.71
1046 1115 2.005451 GAGTCGTCGCAAGTAGGAGTA 58.995 52.381 0.00 0.00 39.48 2.59
1047 1116 0.803740 GAGTCGTCGCAAGTAGGAGT 59.196 55.000 0.00 0.00 39.48 3.85
1048 1117 0.099082 GGAGTCGTCGCAAGTAGGAG 59.901 60.000 0.00 0.00 39.48 3.69
1049 1118 0.607217 TGGAGTCGTCGCAAGTAGGA 60.607 55.000 0.00 0.00 39.48 2.94
1050 1119 0.242825 TTGGAGTCGTCGCAAGTAGG 59.757 55.000 0.00 0.00 39.48 3.18
1051 1120 2.060326 TTTGGAGTCGTCGCAAGTAG 57.940 50.000 0.00 0.00 39.48 2.57
1052 1121 2.129607 GTTTTGGAGTCGTCGCAAGTA 58.870 47.619 0.00 0.00 39.48 2.24
1090 1159 2.092882 CGAGGACGGCGACTTTTCC 61.093 63.158 16.62 10.04 35.72 3.13
1113 1188 0.382515 CTTCTCGGACTCCATCGGAC 59.617 60.000 0.00 0.00 33.40 4.79
1186 1261 1.219393 GAAGGAGAGCAGGAACCGG 59.781 63.158 0.00 0.00 0.00 5.28
1355 1433 3.063084 GAGGCTCACCGTCCTCGT 61.063 66.667 10.25 0.00 42.76 4.18
1357 1435 3.827898 CCGAGGCTCACCGTCCTC 61.828 72.222 15.95 0.00 44.14 3.71
1561 1639 2.816958 CAGTACCGCAGCTGCAGG 60.817 66.667 36.03 34.55 42.21 4.85
1672 1752 4.335315 CACATACACACACCTGTTTTCACT 59.665 41.667 0.00 0.00 0.00 3.41
1765 1858 1.539157 ACTCGCACTCTGTGATCTCA 58.461 50.000 1.52 0.00 36.18 3.27
1771 1864 3.554259 TTGTACTACTCGCACTCTGTG 57.446 47.619 0.00 0.00 36.51 3.66
1823 1916 5.423015 TCAATGTTGAGGAGAATACTCAGC 58.577 41.667 0.00 0.00 44.91 4.26
1871 1965 5.190528 AGCCTATTCTCCTCACTTTCAATGA 59.809 40.000 0.00 0.00 0.00 2.57
1938 2035 4.603131 ACAAGGAGATAGTACCAACCGTA 58.397 43.478 0.00 0.00 0.00 4.02
1968 2065 5.737063 GCTGCCCATGTGAAATCGAATATTT 60.737 40.000 0.00 0.00 0.00 1.40
1979 2076 3.203086 TTCCGGCTGCCCATGTGAA 62.203 57.895 14.12 5.70 0.00 3.18
2023 2120 5.581126 TGTGAAATTGAATATGCCAGACC 57.419 39.130 0.00 0.00 0.00 3.85
2027 2124 4.443175 GCCCATGTGAAATTGAATATGCCA 60.443 41.667 0.00 0.00 0.00 4.92
2044 2141 6.596888 CCAATATAGAGTAGATGTTGCCCATG 59.403 42.308 0.00 0.00 32.56 3.66
2059 2156 8.940952 GCCTACTAGCAAAATTCCAATATAGAG 58.059 37.037 0.00 0.00 0.00 2.43
2060 2157 7.883311 GGCCTACTAGCAAAATTCCAATATAGA 59.117 37.037 0.00 0.00 0.00 1.98
2061 2158 7.885399 AGGCCTACTAGCAAAATTCCAATATAG 59.115 37.037 1.29 0.00 0.00 1.31
2062 2159 7.755618 AGGCCTACTAGCAAAATTCCAATATA 58.244 34.615 1.29 0.00 0.00 0.86
2063 2160 6.614657 AGGCCTACTAGCAAAATTCCAATAT 58.385 36.000 1.29 0.00 0.00 1.28
2064 2161 6.013554 AGGCCTACTAGCAAAATTCCAATA 57.986 37.500 1.29 0.00 0.00 1.90
2065 2162 4.871822 AGGCCTACTAGCAAAATTCCAAT 58.128 39.130 1.29 0.00 0.00 3.16
2091 2188 4.040339 CAGAATTTTAGTTGGGCTTTGGGT 59.960 41.667 0.00 0.00 0.00 4.51
2138 2235 1.270518 ACTCACTCCACTCACATGTGC 60.271 52.381 21.38 0.00 36.68 4.57
2312 2429 2.253403 TAGCTCTGTCCTCGGCTCGA 62.253 60.000 0.00 0.00 36.40 4.04
2440 2559 0.033920 GTAAACCCCACGTCCGAGTT 59.966 55.000 0.00 0.00 0.00 3.01
2651 2779 2.123077 CCTGATCGCCCCTCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
2732 2860 1.945354 GATGAGGTTGCCGAGGTCGA 61.945 60.000 0.00 0.00 43.02 4.20


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

AutoCloner maintained by Alex Coulton.