Multiple sequence alignment - TraesCS5A01G269800

Loading Multiple Alignment...

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 TraesCS5A01G269800 chr5A 100.000 4418 0 0 1 4418 480333855 480338272 0.000000e+00 8159.0
1 TraesCS5A01G269800 chr5A 98.120 851 16 0 3568 4418 36385142 36385992 0.000000e+00 1483.0
2 TraesCS5A01G269800 chr5A 90.323 62 5 1 1 61 495929883 495929944 3.660000e-11 80.5
3 TraesCS5A01G269800 chr5D 93.610 2598 116 17 971 3551 379837915 379840479 0.000000e+00 3832.0
4 TraesCS5A01G269800 chr5D 93.413 835 44 7 1 832 379811729 379812555 0.000000e+00 1227.0
5 TraesCS5A01G269800 chr5D 76.720 189 30 11 162 347 507766647 507766470 4.710000e-15 93.5
6 TraesCS5A01G269800 chr5B 88.467 2714 204 57 917 3554 455746516 455749196 0.000000e+00 3177.0
7 TraesCS5A01G269800 chr5B 79.532 171 26 9 295 464 536375027 536375189 3.610000e-21 113.0
8 TraesCS5A01G269800 chr7A 97.767 851 19 0 3568 4418 556331487 556330637 0.000000e+00 1467.0
9 TraesCS5A01G269800 chr1D 97.300 852 21 2 3568 4418 121402783 121401933 0.000000e+00 1445.0
10 TraesCS5A01G269800 chr1D 84.058 69 5 5 15 78 214831551 214831484 1.330000e-05 62.1
11 TraesCS5A01G269800 chr3D 96.596 852 28 1 3568 4418 464077235 464078086 0.000000e+00 1411.0
12 TraesCS5A01G269800 chr2B 94.393 856 42 5 3568 4418 15621865 15621011 0.000000e+00 1310.0
13 TraesCS5A01G269800 chr1B 94.042 856 45 5 3568 4418 582140088 582139234 0.000000e+00 1293.0
14 TraesCS5A01G269800 chr1B 93.772 851 50 3 3570 4418 46976430 46975581 0.000000e+00 1275.0
15 TraesCS5A01G269800 chr1B 100.000 28 0 0 2851 2878 599136244 599136271 8.000000e-03 52.8
16 TraesCS5A01G269800 chr2D 93.904 853 51 1 3567 4418 232813024 232812172 0.000000e+00 1286.0
17 TraesCS5A01G269800 chr2D 88.710 62 6 1 1 62 601397692 601397752 1.700000e-09 75.0
18 TraesCS5A01G269800 chr2D 100.000 28 0 0 2851 2878 638698785 638698758 8.000000e-03 52.8
19 TraesCS5A01G269800 chr3A 92.638 815 58 2 3602 4416 136431880 136432692 0.000000e+00 1171.0
20 TraesCS5A01G269800 chr7D 77.507 369 57 17 1 352 442036643 442037002 9.690000e-47 198.0
21 TraesCS5A01G269800 chr7D 80.105 191 27 9 162 347 223754909 223755093 9.970000e-27 132.0
22 TraesCS5A01G269800 chr1A 77.160 162 27 7 200 352 357187969 357188129 7.870000e-13 86.1
23 TraesCS5A01G269800 chrUn 100.000 31 0 0 162 192 42094139 42094169 1.720000e-04 58.4
24 TraesCS5A01G269800 chrUn 100.000 28 0 0 2851 2878 2061771 2061798 8.000000e-03 52.8
25 TraesCS5A01G269800 chr3B 100.000 28 0 0 2851 2878 753843852 753843879 8.000000e-03 52.8


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 TraesCS5A01G269800 chr5A 480333855 480338272 4417 False 8159 8159 100.000 1 4418 1 chr5A.!!$F2 4417
1 TraesCS5A01G269800 chr5A 36385142 36385992 850 False 1483 1483 98.120 3568 4418 1 chr5A.!!$F1 850
2 TraesCS5A01G269800 chr5D 379837915 379840479 2564 False 3832 3832 93.610 971 3551 1 chr5D.!!$F2 2580
3 TraesCS5A01G269800 chr5D 379811729 379812555 826 False 1227 1227 93.413 1 832 1 chr5D.!!$F1 831
4 TraesCS5A01G269800 chr5B 455746516 455749196 2680 False 3177 3177 88.467 917 3554 1 chr5B.!!$F1 2637
5 TraesCS5A01G269800 chr7A 556330637 556331487 850 True 1467 1467 97.767 3568 4418 1 chr7A.!!$R1 850
6 TraesCS5A01G269800 chr1D 121401933 121402783 850 True 1445 1445 97.300 3568 4418 1 chr1D.!!$R1 850
7 TraesCS5A01G269800 chr3D 464077235 464078086 851 False 1411 1411 96.596 3568 4418 1 chr3D.!!$F1 850
8 TraesCS5A01G269800 chr2B 15621011 15621865 854 True 1310 1310 94.393 3568 4418 1 chr2B.!!$R1 850
9 TraesCS5A01G269800 chr1B 582139234 582140088 854 True 1293 1293 94.042 3568 4418 1 chr1B.!!$R2 850
10 TraesCS5A01G269800 chr1B 46975581 46976430 849 True 1275 1275 93.772 3570 4418 1 chr1B.!!$R1 848
11 TraesCS5A01G269800 chr2D 232812172 232813024 852 True 1286 1286 93.904 3567 4418 1 chr2D.!!$R1 851
12 TraesCS5A01G269800 chr3A 136431880 136432692 812 False 1171 1171 92.638 3602 4416 1 chr3A.!!$F1 814

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
867 871 0.108377 CCAAAAATTAGCCCGGCCAC 60.108 55.0 5.55 0.0 0.0 5.01 F
1382 1415 0.107456 CACCATGGCGCTCCTCTTAT 59.893 55.0 13.04 0.0 0.0 1.73 F
2010 2051 0.322187 GCCGCCCTCCTCAAGTAAAA 60.322 55.0 0.00 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2051 0.949105 GGTGTTGATCTGTCGGCGTT 60.949 55.0 6.85 0.0 0.00 4.84 R
3073 3187 0.533755 GGAGAATCACCGGCATCCTG 60.534 60.0 0.00 0.0 36.25 3.86 R
3559 3682 0.394192 TAGGCTCCTTCATCATGGCG 59.606 55.0 0.00 0.0 0.00 5.69 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
51 52 7.339207 CAATTTTCTGTGTAAATTGTGTGCAG 58.661 34.615 11.10 0.00 43.20 4.41
67 68 6.567959 TGTGTGCAGATTTTGTCATGTTTAA 58.432 32.000 0.00 0.00 0.00 1.52
173 175 4.341806 GCCATGGATCAAATACCAATGTCA 59.658 41.667 18.40 0.00 39.69 3.58
364 366 9.231297 CCACTAATTCATTCCTTGTTAGAGAAA 57.769 33.333 0.00 0.00 0.00 2.52
593 596 2.951229 ATTTGTATAAGGGGGAGCCG 57.049 50.000 0.00 0.00 0.00 5.52
620 623 4.873259 GGCTAGAGAAGGTAGAAGCTTTTG 59.127 45.833 0.00 0.00 35.86 2.44
628 631 2.742589 GGTAGAAGCTTTTGAGTTCCCG 59.257 50.000 0.00 0.00 0.00 5.14
630 633 2.222027 AGAAGCTTTTGAGTTCCCGTG 58.778 47.619 0.00 0.00 0.00 4.94
639 642 1.507141 GAGTTCCCGTGTGCACAAGG 61.507 60.000 36.17 36.17 43.72 3.61
672 675 8.339113 GTGAACCGATTCATCGTCATGTACAC 62.339 46.154 0.00 5.28 46.43 2.90
677 680 3.131240 TCATCGTCATGTACACGTCTG 57.869 47.619 0.00 0.00 38.45 3.51
754 757 3.321497 CTGAGTTAGCTCTGTTGGACAC 58.679 50.000 8.15 0.00 42.13 3.67
758 761 2.486636 TAGCTCTGTTGGACACGCCG 62.487 60.000 0.00 0.00 40.66 6.46
768 771 3.479505 TGGACACGCCGAAATAAAATG 57.520 42.857 0.00 0.00 40.66 2.32
782 785 8.247562 CCGAAATAAAATGAAATAACTGACCCA 58.752 33.333 0.00 0.00 0.00 4.51
794 798 9.803315 GAAATAACTGACCCAAATTAGGAATTC 57.197 33.333 0.00 0.00 0.00 2.17
802 806 4.335594 CCCAAATTAGGAATTCAGTCGTCC 59.664 45.833 7.93 0.00 0.00 4.79
832 836 2.034685 GCCACTCCCAAAAGAGTCAAAC 59.965 50.000 0.00 0.00 45.38 2.93
833 837 3.555966 CCACTCCCAAAAGAGTCAAACT 58.444 45.455 0.00 0.00 45.38 2.66
834 838 3.316308 CCACTCCCAAAAGAGTCAAACTG 59.684 47.826 0.00 0.00 45.38 3.16
835 839 4.199310 CACTCCCAAAAGAGTCAAACTGA 58.801 43.478 0.00 0.00 45.38 3.41
836 840 4.274459 CACTCCCAAAAGAGTCAAACTGAG 59.726 45.833 0.00 0.00 45.38 3.35
837 841 3.817647 CTCCCAAAAGAGTCAAACTGAGG 59.182 47.826 0.00 0.00 0.00 3.86
838 842 3.458118 TCCCAAAAGAGTCAAACTGAGGA 59.542 43.478 0.00 0.00 0.00 3.71
839 843 3.565902 CCCAAAAGAGTCAAACTGAGGAC 59.434 47.826 0.00 0.00 0.00 3.85
840 844 4.199310 CCAAAAGAGTCAAACTGAGGACA 58.801 43.478 0.00 0.00 36.50 4.02
841 845 4.640201 CCAAAAGAGTCAAACTGAGGACAA 59.360 41.667 0.00 0.00 36.50 3.18
842 846 5.125417 CCAAAAGAGTCAAACTGAGGACAAA 59.875 40.000 0.00 0.00 36.50 2.83
843 847 6.350110 CCAAAAGAGTCAAACTGAGGACAAAA 60.350 38.462 0.00 0.00 36.50 2.44
844 848 7.260603 CAAAAGAGTCAAACTGAGGACAAAAT 58.739 34.615 0.00 0.00 36.50 1.82
845 849 6.625873 AAGAGTCAAACTGAGGACAAAATC 57.374 37.500 0.00 0.00 36.50 2.17
846 850 5.684704 AGAGTCAAACTGAGGACAAAATCA 58.315 37.500 0.00 0.00 36.50 2.57
847 851 6.302269 AGAGTCAAACTGAGGACAAAATCAT 58.698 36.000 0.00 0.00 36.50 2.45
848 852 6.429385 AGAGTCAAACTGAGGACAAAATCATC 59.571 38.462 0.00 0.00 38.67 2.92
849 853 5.474876 AGTCAAACTGAGGACAAAATCATCC 59.525 40.000 0.00 0.00 37.32 3.51
850 854 5.241506 GTCAAACTGAGGACAAAATCATCCA 59.758 40.000 0.00 0.00 37.32 3.41
851 855 5.832595 TCAAACTGAGGACAAAATCATCCAA 59.167 36.000 0.00 0.00 37.32 3.53
852 856 6.323482 TCAAACTGAGGACAAAATCATCCAAA 59.677 34.615 0.00 0.00 37.32 3.28
853 857 6.729690 AACTGAGGACAAAATCATCCAAAA 57.270 33.333 0.00 0.00 37.32 2.44
854 858 6.729690 ACTGAGGACAAAATCATCCAAAAA 57.270 33.333 0.00 0.00 37.32 1.94
855 859 7.307131 ACTGAGGACAAAATCATCCAAAAAT 57.693 32.000 0.00 0.00 37.32 1.82
856 860 7.738847 ACTGAGGACAAAATCATCCAAAAATT 58.261 30.769 0.00 0.00 37.32 1.82
857 861 8.869109 ACTGAGGACAAAATCATCCAAAAATTA 58.131 29.630 0.00 0.00 37.32 1.40
858 862 9.362539 CTGAGGACAAAATCATCCAAAAATTAG 57.637 33.333 0.00 0.00 37.32 1.73
859 863 7.818930 TGAGGACAAAATCATCCAAAAATTAGC 59.181 33.333 0.00 0.00 37.32 3.09
860 864 7.105588 AGGACAAAATCATCCAAAAATTAGCC 58.894 34.615 0.00 0.00 37.47 3.93
861 865 6.316140 GGACAAAATCATCCAAAAATTAGCCC 59.684 38.462 0.00 0.00 34.87 5.19
862 866 5.874261 ACAAAATCATCCAAAAATTAGCCCG 59.126 36.000 0.00 0.00 0.00 6.13
863 867 4.670896 AATCATCCAAAAATTAGCCCGG 57.329 40.909 0.00 0.00 0.00 5.73
864 868 1.754226 TCATCCAAAAATTAGCCCGGC 59.246 47.619 0.00 0.00 0.00 6.13
865 869 1.119684 ATCCAAAAATTAGCCCGGCC 58.880 50.000 5.55 0.00 0.00 6.13
866 870 0.251832 TCCAAAAATTAGCCCGGCCA 60.252 50.000 5.55 0.00 0.00 5.36
867 871 0.108377 CCAAAAATTAGCCCGGCCAC 60.108 55.000 5.55 0.00 0.00 5.01
868 872 0.457681 CAAAAATTAGCCCGGCCACG 60.458 55.000 5.55 0.00 40.55 4.94
869 873 0.609681 AAAAATTAGCCCGGCCACGA 60.610 50.000 5.55 0.00 44.60 4.35
870 874 1.029947 AAAATTAGCCCGGCCACGAG 61.030 55.000 5.55 0.00 44.60 4.18
871 875 4.547367 ATTAGCCCGGCCACGAGC 62.547 66.667 5.55 0.00 44.86 5.03
892 896 3.803082 CGCCACGCACAGGGAATG 61.803 66.667 0.00 0.00 0.00 2.67
893 897 3.443045 GCCACGCACAGGGAATGG 61.443 66.667 0.00 0.00 0.00 3.16
894 898 2.034066 CCACGCACAGGGAATGGT 59.966 61.111 0.00 0.00 0.00 3.55
895 899 2.334946 CCACGCACAGGGAATGGTG 61.335 63.158 0.00 0.00 38.05 4.17
896 900 2.034066 ACGCACAGGGAATGGTGG 59.966 61.111 0.00 0.00 35.58 4.61
897 901 2.350895 CGCACAGGGAATGGTGGA 59.649 61.111 0.00 0.00 35.58 4.02
898 902 1.746615 CGCACAGGGAATGGTGGAG 60.747 63.158 0.00 0.00 35.58 3.86
899 903 2.048603 GCACAGGGAATGGTGGAGC 61.049 63.158 0.00 0.00 35.58 4.70
900 904 1.379916 CACAGGGAATGGTGGAGCA 59.620 57.895 0.00 0.00 0.00 4.26
901 905 0.962356 CACAGGGAATGGTGGAGCAC 60.962 60.000 0.00 0.00 0.00 4.40
902 906 1.746615 CAGGGAATGGTGGAGCACG 60.747 63.158 0.00 0.00 34.83 5.34
903 907 3.134127 GGGAATGGTGGAGCACGC 61.134 66.667 0.00 0.00 34.83 5.34
904 908 3.499737 GGAATGGTGGAGCACGCG 61.500 66.667 3.53 3.53 34.83 6.01
905 909 4.166011 GAATGGTGGAGCACGCGC 62.166 66.667 5.73 0.00 34.83 6.86
1009 1013 3.809013 GACCGGCCATGTCCCCAT 61.809 66.667 0.00 0.00 0.00 4.00
1091 1095 2.364579 ACGTTATCCCAGCCCGGA 60.365 61.111 0.73 0.00 36.56 5.14
1093 1097 2.111251 GTTATCCCAGCCCGGAGC 59.889 66.667 0.73 4.57 44.25 4.70
1195 1200 1.141881 CAGGGGAATCCGAGTGACG 59.858 63.158 0.00 0.00 41.52 4.35
1199 1204 1.226603 GGAATCCGAGTGACGTCCG 60.227 63.158 14.12 9.44 40.78 4.79
1217 1222 1.988406 GGGGAGTAACTGGAGCGGT 60.988 63.158 0.00 0.00 0.00 5.68
1228 1233 2.052690 GGAGCGGTGGAGAGCTACA 61.053 63.158 0.00 0.00 43.56 2.74
1229 1234 1.435515 GAGCGGTGGAGAGCTACAG 59.564 63.158 0.00 0.00 44.69 2.74
1374 1407 2.510906 GGGTATCACCATGGCGCT 59.489 61.111 13.04 0.00 41.02 5.92
1377 1410 1.447643 GTATCACCATGGCGCTCCT 59.552 57.895 13.04 0.00 0.00 3.69
1380 1413 1.630126 ATCACCATGGCGCTCCTCTT 61.630 55.000 13.04 0.00 0.00 2.85
1382 1415 0.107456 CACCATGGCGCTCCTCTTAT 59.893 55.000 13.04 0.00 0.00 1.73
1386 1419 2.534298 CATGGCGCTCCTCTTATATCG 58.466 52.381 7.64 0.00 0.00 2.92
1491 1524 1.179814 AGCAGGACCTCGTCTTCGTT 61.180 55.000 0.00 0.00 38.33 3.85
1535 1568 2.416972 GCTCCCGAACTGTAAGGTACTG 60.417 54.545 0.00 0.00 40.86 2.74
1627 1668 1.936436 AAATGATGCCATGCGCGTGT 61.936 50.000 26.86 9.95 42.08 4.49
1684 1725 2.896443 GTCCGGAGCAAGGAGAGG 59.104 66.667 3.06 0.00 38.65 3.69
2010 2051 0.322187 GCCGCCCTCCTCAAGTAAAA 60.322 55.000 0.00 0.00 0.00 1.52
2019 2060 1.868498 CCTCAAGTAAAAACGCCGACA 59.132 47.619 0.00 0.00 0.00 4.35
2027 2068 1.588674 AAAACGCCGACAGATCAACA 58.411 45.000 0.00 0.00 0.00 3.33
2029 2070 0.949105 AACGCCGACAGATCAACACC 60.949 55.000 0.00 0.00 0.00 4.16
2033 2074 1.878102 GCCGACAGATCAACACCACTT 60.878 52.381 0.00 0.00 0.00 3.16
2035 2076 2.289072 CCGACAGATCAACACCACTTCT 60.289 50.000 0.00 0.00 0.00 2.85
2036 2077 3.393800 CGACAGATCAACACCACTTCTT 58.606 45.455 0.00 0.00 0.00 2.52
2052 2097 4.570772 CACTTCTTTCTTTCGAACCAGACA 59.429 41.667 0.00 0.00 0.00 3.41
2054 2099 5.467063 ACTTCTTTCTTTCGAACCAGACATC 59.533 40.000 0.00 0.00 0.00 3.06
2082 2127 4.222588 TGGCCAAGGATTAATGGAGTTTTG 59.777 41.667 0.61 0.00 39.12 2.44
2318 2363 4.025401 CGTGCGTGGCCAAGAACC 62.025 66.667 22.57 6.05 0.00 3.62
2350 2395 1.127567 ACTGCAAGGTGGTGGAGCTA 61.128 55.000 0.00 0.00 40.39 3.32
2543 2627 2.623915 GCAGTTGCAGCACCTCCAG 61.624 63.158 2.55 0.00 41.59 3.86
2602 2698 4.680237 CCGGCACCGACAGCTGAA 62.680 66.667 23.35 0.00 40.83 3.02
2603 2699 3.414700 CGGCACCGACAGCTGAAC 61.415 66.667 23.35 12.87 40.83 3.18
2604 2700 3.050275 GGCACCGACAGCTGAACC 61.050 66.667 23.35 8.06 0.00 3.62
2605 2701 2.280797 GCACCGACAGCTGAACCA 60.281 61.111 23.35 0.00 0.00 3.67
2606 2702 2.320587 GCACCGACAGCTGAACCAG 61.321 63.158 23.35 8.25 34.12 4.00
2638 2734 3.673484 GCAAAAGCAGAGCGGCCA 61.673 61.111 2.24 0.00 0.00 5.36
2682 2779 1.068741 GAACCGCGGAACTGATATCCT 59.931 52.381 35.90 0.00 34.66 3.24
2683 2780 0.389391 ACCGCGGAACTGATATCCTG 59.611 55.000 35.90 0.00 34.66 3.86
2684 2781 0.673985 CCGCGGAACTGATATCCTGA 59.326 55.000 24.07 0.00 34.66 3.86
2692 2792 4.321601 GGAACTGATATCCTGATGGACTCG 60.322 50.000 0.00 0.00 46.51 4.18
2712 2812 4.116961 TCGTGGTAATGGACGATCATTTC 58.883 43.478 11.69 7.91 39.59 2.17
2715 2815 4.511826 GTGGTAATGGACGATCATTTCCTC 59.488 45.833 21.08 16.95 41.87 3.71
2718 2818 6.042666 TGGTAATGGACGATCATTTCCTCATA 59.957 38.462 21.08 7.89 41.87 2.15
2960 3073 4.202441 ACTGATGTTACATCCTTGGCATC 58.798 43.478 20.91 0.00 34.30 3.91
2961 3074 3.554934 TGATGTTACATCCTTGGCATCC 58.445 45.455 20.91 0.00 33.53 3.51
3004 3118 7.000472 TCTGATGGATCCATTAATTTCCTGAC 59.000 38.462 27.93 11.17 36.70 3.51
3073 3187 0.240411 CAGGAGCAGCAGCAAGAAAC 59.760 55.000 3.17 0.00 45.49 2.78
3132 3246 2.755876 TCTCCGGATGCAGCGACT 60.756 61.111 3.57 0.00 0.00 4.18
3275 3392 5.189934 CCAGGTACTAATTTCTCCCTGTCTT 59.810 44.000 0.00 0.00 38.20 3.01
3307 3424 0.462375 GCTCATGGCAATGGCATTCA 59.538 50.000 20.02 6.92 46.61 2.57
3328 3448 4.211164 TCAAATTCACGCGTATGATCCATC 59.789 41.667 13.44 0.00 0.00 3.51
3466 3588 2.932261 ACCTTTTCTTTTCCTGCTCGT 58.068 42.857 0.00 0.00 0.00 4.18
3467 3589 2.879026 ACCTTTTCTTTTCCTGCTCGTC 59.121 45.455 0.00 0.00 0.00 4.20
3468 3590 2.096218 CCTTTTCTTTTCCTGCTCGTCG 60.096 50.000 0.00 0.00 0.00 5.12
3469 3591 2.519377 TTTCTTTTCCTGCTCGTCGA 57.481 45.000 0.00 0.00 0.00 4.20
3551 3674 7.164662 CGAGAAATACAAATGTACACGACGATA 59.835 37.037 0.00 0.00 32.72 2.92
3552 3675 8.112099 AGAAATACAAATGTACACGACGATAC 57.888 34.615 0.00 4.47 32.72 2.24
3553 3676 7.756272 AGAAATACAAATGTACACGACGATACA 59.244 33.333 15.54 15.54 35.82 2.29
3554 3677 7.445900 AATACAAATGTACACGACGATACAG 57.554 36.000 17.31 9.80 34.88 2.74
3555 3678 3.611113 ACAAATGTACACGACGATACAGC 59.389 43.478 17.31 0.00 34.88 4.40
3556 3679 2.486951 ATGTACACGACGATACAGCC 57.513 50.000 17.31 0.00 34.88 4.85
3557 3680 0.097499 TGTACACGACGATACAGCCG 59.903 55.000 0.00 0.00 0.00 5.52
3558 3681 0.374758 GTACACGACGATACAGCCGA 59.625 55.000 0.00 0.00 0.00 5.54
3559 3682 0.374758 TACACGACGATACAGCCGAC 59.625 55.000 0.00 0.00 0.00 4.79
3560 3683 1.933041 CACGACGATACAGCCGACG 60.933 63.158 0.00 0.00 46.63 5.12
3561 3684 3.017314 CGACGATACAGCCGACGC 61.017 66.667 0.00 0.00 38.15 5.19
3562 3685 2.654404 GACGATACAGCCGACGCC 60.654 66.667 0.00 0.00 34.57 5.68
3563 3686 3.405592 GACGATACAGCCGACGCCA 62.406 63.158 0.00 0.00 34.57 5.69
3564 3687 2.027605 CGATACAGCCGACGCCAT 59.972 61.111 0.00 0.00 34.57 4.40
3565 3688 2.302952 CGATACAGCCGACGCCATG 61.303 63.158 0.00 0.00 34.57 3.66
3585 3709 4.755266 TGATGAAGGAGCCTAAACTACC 57.245 45.455 0.00 0.00 0.00 3.18
3618 3744 0.322546 ATCTCGGTTTGGGGCAACTC 60.323 55.000 0.00 0.00 37.88 3.01
3721 3849 6.127479 GGCCGAGATCTGTTAGAGATATCAAT 60.127 42.308 13.13 0.00 46.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 139 4.100653 TGATCCATGGCTTCTCTACTTCTG 59.899 45.833 6.96 0.00 0.00 3.02
149 151 4.549668 ACATTGGTATTTGATCCATGGCT 58.450 39.130 6.96 0.00 33.50 4.75
332 334 7.716799 ACAAGGAATGAATTAGTGGCATTAA 57.283 32.000 4.86 4.86 32.80 1.40
591 594 1.957877 CTACCTTCTCTAGCCTTCCGG 59.042 57.143 0.00 0.00 0.00 5.14
593 596 3.069016 GCTTCTACCTTCTCTAGCCTTCC 59.931 52.174 0.00 0.00 0.00 3.46
620 623 1.507141 CCTTGTGCACACGGGAACTC 61.507 60.000 29.83 0.00 32.20 3.01
628 631 0.881118 CATACCCACCTTGTGCACAC 59.119 55.000 21.56 0.00 31.34 3.82
630 633 0.881118 CACATACCCACCTTGTGCAC 59.119 55.000 10.75 10.75 34.89 4.57
639 642 2.980568 TGAATCGGTTCACATACCCAC 58.019 47.619 7.11 0.00 39.36 4.61
672 675 1.875813 GGTGCAGCTCGATCAGACG 60.876 63.158 9.07 0.00 0.00 4.18
694 697 6.248433 ACCAAGGAAGAAATGACACATATGT 58.752 36.000 1.41 1.41 43.71 2.29
702 705 5.763088 GTGAGAAACCAAGGAAGAAATGAC 58.237 41.667 0.00 0.00 0.00 3.06
754 757 7.044314 GGTCAGTTATTTCATTTTATTTCGGCG 60.044 37.037 0.00 0.00 0.00 6.46
768 771 9.803315 GAATTCCTAATTTGGGTCAGTTATTTC 57.197 33.333 6.08 0.00 0.00 2.17
782 785 5.080969 TCGGACGACTGAATTCCTAATTT 57.919 39.130 2.27 0.00 0.00 1.82
794 798 1.009900 GCTACGGATCGGACGACTG 60.010 63.158 7.35 0.00 34.93 3.51
802 806 1.672854 TTGGGAGTGGCTACGGATCG 61.673 60.000 0.00 0.00 0.00 3.69
832 836 9.362539 CTAATTTTTGGATGATTTTGTCCTCAG 57.637 33.333 0.00 0.00 35.49 3.35
833 837 7.818930 GCTAATTTTTGGATGATTTTGTCCTCA 59.181 33.333 0.00 0.00 35.49 3.86
834 838 7.278646 GGCTAATTTTTGGATGATTTTGTCCTC 59.721 37.037 0.00 0.00 35.49 3.71
835 839 7.105588 GGCTAATTTTTGGATGATTTTGTCCT 58.894 34.615 0.00 0.00 35.49 3.85
836 840 6.316140 GGGCTAATTTTTGGATGATTTTGTCC 59.684 38.462 0.00 0.00 35.02 4.02
837 841 6.035975 CGGGCTAATTTTTGGATGATTTTGTC 59.964 38.462 0.00 0.00 0.00 3.18
838 842 5.874261 CGGGCTAATTTTTGGATGATTTTGT 59.126 36.000 0.00 0.00 0.00 2.83
839 843 5.294060 CCGGGCTAATTTTTGGATGATTTTG 59.706 40.000 0.00 0.00 0.00 2.44
840 844 5.427378 CCGGGCTAATTTTTGGATGATTTT 58.573 37.500 0.00 0.00 0.00 1.82
841 845 4.683129 GCCGGGCTAATTTTTGGATGATTT 60.683 41.667 12.87 0.00 0.00 2.17
842 846 3.181466 GCCGGGCTAATTTTTGGATGATT 60.181 43.478 12.87 0.00 0.00 2.57
843 847 2.365293 GCCGGGCTAATTTTTGGATGAT 59.635 45.455 12.87 0.00 0.00 2.45
844 848 1.754226 GCCGGGCTAATTTTTGGATGA 59.246 47.619 12.87 0.00 0.00 2.92
845 849 1.202521 GGCCGGGCTAATTTTTGGATG 60.203 52.381 22.87 0.00 0.00 3.51
846 850 1.119684 GGCCGGGCTAATTTTTGGAT 58.880 50.000 22.87 0.00 0.00 3.41
847 851 0.251832 TGGCCGGGCTAATTTTTGGA 60.252 50.000 29.87 0.62 0.00 3.53
848 852 0.108377 GTGGCCGGGCTAATTTTTGG 60.108 55.000 29.87 0.00 0.00 3.28
849 853 0.457681 CGTGGCCGGGCTAATTTTTG 60.458 55.000 29.87 5.83 0.00 2.44
850 854 0.609681 TCGTGGCCGGGCTAATTTTT 60.610 50.000 29.87 0.00 33.95 1.94
851 855 1.001887 TCGTGGCCGGGCTAATTTT 60.002 52.632 29.87 0.00 33.95 1.82
852 856 1.451387 CTCGTGGCCGGGCTAATTT 60.451 57.895 29.87 0.00 33.95 1.82
853 857 2.189521 CTCGTGGCCGGGCTAATT 59.810 61.111 29.87 0.00 33.95 1.40
875 879 3.803082 CATTCCCTGTGCGTGGCG 61.803 66.667 0.00 0.00 0.00 5.69
876 880 3.443045 CCATTCCCTGTGCGTGGC 61.443 66.667 0.00 0.00 0.00 5.01
877 881 2.034066 ACCATTCCCTGTGCGTGG 59.966 61.111 0.00 0.00 36.06 4.94
878 882 2.334946 CCACCATTCCCTGTGCGTG 61.335 63.158 0.00 0.00 0.00 5.34
879 883 2.034066 CCACCATTCCCTGTGCGT 59.966 61.111 0.00 0.00 0.00 5.24
880 884 1.746615 CTCCACCATTCCCTGTGCG 60.747 63.158 0.00 0.00 0.00 5.34
881 885 2.048603 GCTCCACCATTCCCTGTGC 61.049 63.158 0.00 0.00 0.00 4.57
882 886 0.962356 GTGCTCCACCATTCCCTGTG 60.962 60.000 0.00 0.00 0.00 3.66
883 887 1.380302 GTGCTCCACCATTCCCTGT 59.620 57.895 0.00 0.00 0.00 4.00
884 888 1.746615 CGTGCTCCACCATTCCCTG 60.747 63.158 0.00 0.00 0.00 4.45
885 889 2.671070 CGTGCTCCACCATTCCCT 59.329 61.111 0.00 0.00 0.00 4.20
886 890 3.134127 GCGTGCTCCACCATTCCC 61.134 66.667 0.00 0.00 0.00 3.97
887 891 3.499737 CGCGTGCTCCACCATTCC 61.500 66.667 0.00 0.00 0.00 3.01
888 892 4.166011 GCGCGTGCTCCACCATTC 62.166 66.667 15.02 0.00 38.39 2.67
906 910 4.961511 TGCGTGGTGACTGCGTCC 62.962 66.667 6.30 0.00 33.33 4.79
907 911 3.702555 GTGCGTGGTGACTGCGTC 61.703 66.667 2.32 2.32 33.33 5.19
1008 1012 1.794714 AGAGAACCGAGGTGGCATAT 58.205 50.000 0.00 0.00 43.94 1.78
1009 1013 1.480954 GAAGAGAACCGAGGTGGCATA 59.519 52.381 0.00 0.00 43.94 3.14
1195 1200 1.957765 GCTCCAGTTACTCCCCGGAC 61.958 65.000 0.73 0.00 0.00 4.79
1199 1204 1.988406 ACCGCTCCAGTTACTCCCC 60.988 63.158 0.00 0.00 0.00 4.81
1217 1222 2.363018 AGCCGCTGTAGCTCTCCA 60.363 61.111 0.00 0.00 34.91 3.86
1228 1233 2.026734 CATGTCGATCGAGCCGCT 59.973 61.111 20.09 0.00 0.00 5.52
1229 1234 3.032609 CCATGTCGATCGAGCCGC 61.033 66.667 20.09 7.32 0.00 6.53
1233 1266 1.006805 GGCCTCCATGTCGATCGAG 60.007 63.158 20.09 6.93 0.00 4.04
1374 1407 1.732809 CGAGCGAGCGATATAAGAGGA 59.267 52.381 0.00 0.00 0.00 3.71
1377 1410 0.168348 GGCGAGCGAGCGATATAAGA 59.832 55.000 1.41 0.00 38.18 2.10
1380 1413 2.697761 GGGGCGAGCGAGCGATATA 61.698 63.158 1.41 0.00 38.18 0.86
1521 1554 3.825014 TCGAAGAGCAGTACCTTACAGTT 59.175 43.478 0.00 0.00 0.00 3.16
1524 1557 3.418995 AGTCGAAGAGCAGTACCTTACA 58.581 45.455 0.00 0.00 36.95 2.41
1535 1568 1.797441 TCGAGCAGAGTCGAAGAGC 59.203 57.895 0.00 0.00 45.74 4.09
1593 1626 5.117584 GCATCATTTCCCAAATGCATTACA 58.882 37.500 13.39 0.00 46.09 2.41
1876 1917 1.007618 GTAGTCGATGCGGTAGGGC 60.008 63.158 0.00 0.00 0.00 5.19
2010 2051 0.949105 GGTGTTGATCTGTCGGCGTT 60.949 55.000 6.85 0.00 0.00 4.84
2019 2060 5.237344 CGAAAGAAAGAAGTGGTGTTGATCT 59.763 40.000 0.00 0.00 0.00 2.75
2052 2097 4.141959 CCATTAATCCTTGGCCAAAACGAT 60.142 41.667 20.91 16.72 0.00 3.73
2054 2099 3.194542 TCCATTAATCCTTGGCCAAAACG 59.805 43.478 20.91 8.00 32.80 3.60
2082 2127 1.059173 GCTGCTCGATCGATCATGTC 58.941 55.000 24.40 10.29 0.00 3.06
2296 2341 4.743975 TTGGCCACGCACGCGATA 62.744 61.111 19.66 0.00 42.83 2.92
2329 2374 0.955919 GCTCCACCACCTTGCAGTAC 60.956 60.000 0.00 0.00 0.00 2.73
2521 2605 2.908940 GGTGCTGCAACTGCTGGT 60.909 61.111 11.11 0.00 42.66 4.00
2529 2613 2.595463 GTGCTGGAGGTGCTGCAA 60.595 61.111 2.77 0.00 37.17 4.08
2647 2743 1.408474 GGTTCACTTACGCCGCGTAG 61.408 60.000 23.56 19.26 43.21 3.51
2682 2779 2.167693 GTCCATTACCACGAGTCCATCA 59.832 50.000 0.00 0.00 0.00 3.07
2683 2780 2.798499 CGTCCATTACCACGAGTCCATC 60.798 54.545 0.00 0.00 38.32 3.51
2684 2781 1.136305 CGTCCATTACCACGAGTCCAT 59.864 52.381 0.00 0.00 38.32 3.41
2692 2792 4.451900 AGGAAATGATCGTCCATTACCAC 58.548 43.478 11.32 0.00 35.86 4.16
2712 2812 4.930405 TGCAATGCAACAAAATGTATGAGG 59.070 37.500 5.01 0.00 34.76 3.86
2715 2815 4.691685 ACCTGCAATGCAACAAAATGTATG 59.308 37.500 9.92 0.00 38.41 2.39
2718 2818 3.196939 ACCTGCAATGCAACAAAATGT 57.803 38.095 9.92 0.00 38.41 2.71
2818 2921 4.778143 GCCGGTACAGGTGCAGGG 62.778 72.222 13.86 1.52 31.88 4.45
2827 2930 4.323477 GGTGCTGGTGCCGGTACA 62.323 66.667 24.62 9.70 39.23 2.90
2829 2932 4.015406 CTGGTGCTGGTGCCGGTA 62.015 66.667 1.90 0.00 38.71 4.02
2961 3074 1.134965 AGAGGCCGAATTCTTCACTCG 60.135 52.381 3.52 0.00 32.91 4.18
3073 3187 0.533755 GGAGAATCACCGGCATCCTG 60.534 60.000 0.00 0.00 36.25 3.86
3129 3243 3.736482 CTCGGCGGTCGTGCTAGTC 62.736 68.421 7.21 0.00 40.32 2.59
3165 3282 2.750888 GGAATCCAACAGCGGCGAC 61.751 63.158 12.98 1.23 0.00 5.19
3211 3328 3.716195 TGGATCACCAGTGGCGGG 61.716 66.667 9.78 0.00 41.77 6.13
3237 3354 0.676782 ACCTGGCGTATGGTGAAAGC 60.677 55.000 0.00 0.00 34.90 3.51
3307 3424 3.498397 GGATGGATCATACGCGTGAATTT 59.502 43.478 24.59 2.23 0.00 1.82
3328 3448 6.053650 TGCAATTAATCAGACAGAGAGATGG 58.946 40.000 0.00 0.00 0.00 3.51
3551 3674 2.512286 CATCATGGCGTCGGCTGT 60.512 61.111 20.29 5.91 39.81 4.40
3552 3675 1.769098 CTTCATCATGGCGTCGGCTG 61.769 60.000 20.29 14.72 39.81 4.85
3553 3676 1.522355 CTTCATCATGGCGTCGGCT 60.522 57.895 20.29 2.64 39.81 5.52
3554 3677 2.537560 CCTTCATCATGGCGTCGGC 61.538 63.158 12.58 12.58 38.90 5.54
3555 3678 0.877649 CTCCTTCATCATGGCGTCGG 60.878 60.000 0.00 0.00 0.00 4.79
3556 3679 1.493950 GCTCCTTCATCATGGCGTCG 61.494 60.000 0.00 0.00 0.00 5.12
3557 3680 1.162800 GGCTCCTTCATCATGGCGTC 61.163 60.000 0.00 0.00 0.00 5.19
3558 3681 1.153086 GGCTCCTTCATCATGGCGT 60.153 57.895 0.00 0.00 0.00 5.68
3559 3682 0.394192 TAGGCTCCTTCATCATGGCG 59.606 55.000 0.00 0.00 0.00 5.69
3560 3683 2.620585 GTTTAGGCTCCTTCATCATGGC 59.379 50.000 0.00 0.00 0.00 4.40
3561 3684 4.162040 AGTTTAGGCTCCTTCATCATGG 57.838 45.455 0.00 0.00 0.00 3.66
3562 3685 5.059833 GGTAGTTTAGGCTCCTTCATCATG 58.940 45.833 0.00 0.00 0.00 3.07
3563 3686 4.721776 TGGTAGTTTAGGCTCCTTCATCAT 59.278 41.667 0.00 0.00 0.00 2.45
3564 3687 4.101114 TGGTAGTTTAGGCTCCTTCATCA 58.899 43.478 0.00 0.00 0.00 3.07
3565 3688 4.755266 TGGTAGTTTAGGCTCCTTCATC 57.245 45.455 0.00 0.00 0.00 2.92
3585 3709 1.927174 CCGAGATTACTCTTGCCGTTG 59.073 52.381 0.00 0.00 40.65 4.10
3618 3744 9.976511 ATAGCAACTATTCCAATCAATGAAATG 57.023 29.630 0.00 0.00 0.00 2.32
3670 3798 6.207221 TGATCTTGCTATTCTTCTTGTGCAAA 59.793 34.615 0.00 0.00 39.42 3.68


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

AutoCloner maintained by Alex Coulton.