Multiple sequence alignment - TraesCS5A01G472300

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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 TraesCS5A01G472300 chr5A 100.000 3778 0 0 1 3778 649364068 649367845 0.000000e+00 6977.0
1 TraesCS5A01G472300 chr5A 81.498 227 39 3 2925 3148 619110673 619110447 2.320000e-42 183.0
2 TraesCS5A01G472300 chr5A 100.000 44 0 0 856 899 649364787 649364830 8.700000e-12 82.4
3 TraesCS5A01G472300 chr5A 100.000 44 0 0 720 763 649364923 649364966 8.700000e-12 82.4
4 TraesCS5A01G472300 chr5D 94.187 1101 57 6 924 2024 520805109 520806202 0.000000e+00 1672.0
5 TraesCS5A01G472300 chr5D 90.605 1107 63 13 889 1985 520839233 520840308 0.000000e+00 1430.0
6 TraesCS5A01G472300 chr5D 89.509 896 54 22 2912 3778 520841322 520842206 0.000000e+00 1098.0
7 TraesCS5A01G472300 chr5D 90.234 768 67 4 2117 2882 520840566 520841327 0.000000e+00 996.0
8 TraesCS5A01G472300 chr5D 91.794 719 50 7 2074 2792 520806288 520806997 0.000000e+00 992.0
9 TraesCS5A01G472300 chr5D 88.509 818 74 16 1 807 520804186 520804994 0.000000e+00 972.0
10 TraesCS5A01G472300 chr5D 90.306 196 17 1 2800 2995 520807083 520807276 4.840000e-64 255.0
11 TraesCS5A01G472300 chr5D 81.498 227 32 6 2925 3148 495064410 495064191 1.080000e-40 178.0
12 TraesCS5A01G472300 chr5B 92.735 1115 63 8 874 1985 656468206 656469305 0.000000e+00 1594.0
13 TraesCS5A01G472300 chr5B 89.671 1065 79 6 924 1985 656726067 656727103 0.000000e+00 1328.0
14 TraesCS5A01G472300 chr5B 89.655 812 61 13 1 807 656467416 656468209 0.000000e+00 1013.0
15 TraesCS5A01G472300 chr5B 90.909 671 58 3 2120 2788 656469419 656470088 0.000000e+00 898.0
16 TraesCS5A01G472300 chr5B 88.195 737 45 14 3079 3778 656470429 656471160 0.000000e+00 841.0
17 TraesCS5A01G472300 chr5B 89.628 646 64 3 2117 2760 656727359 656728003 0.000000e+00 819.0
18 TraesCS5A01G472300 chr5B 85.669 635 49 25 3170 3778 656730049 656730667 6.890000e-177 630.0
19 TraesCS5A01G472300 chr5B 87.634 372 44 2 42 411 656723843 656724214 7.500000e-117 431.0
20 TraesCS5A01G472300 chr5B 89.634 164 14 3 2912 3075 656470221 656470381 4.950000e-49 206.0
21 TraesCS5A01G472300 chr7D 83.843 817 111 6 1032 1842 629498012 629497211 0.000000e+00 758.0
22 TraesCS5A01G472300 chr6D 83.000 700 109 8 1127 1821 85626540 85625846 3.200000e-175 625.0
23 TraesCS5A01G472300 chr6B 82.621 702 109 11 1127 1821 160899141 160899836 3.230000e-170 608.0
24 TraesCS5A01G472300 chr6A 79.698 862 147 21 1127 1982 101858415 101859254 6.980000e-167 597.0
25 TraesCS5A01G472300 chrUn 79.454 696 122 16 1145 1831 95188243 95188926 1.230000e-129 473.0
26 TraesCS5A01G472300 chr3D 78.378 148 14 5 2905 3040 172377881 172378022 3.130000e-11 80.5
27 TraesCS5A01G472300 chr3A 79.070 129 13 4 2905 3020 210255735 210255862 4.050000e-10 76.8


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 TraesCS5A01G472300 chr5A 649364068 649367845 3777 False 2380.600000 6977 100.0000 1 3778 3 chr5A.!!$F1 3777
1 TraesCS5A01G472300 chr5D 520839233 520842206 2973 False 1174.666667 1430 90.1160 889 3778 3 chr5D.!!$F2 2889
2 TraesCS5A01G472300 chr5D 520804186 520807276 3090 False 972.750000 1672 91.1990 1 2995 4 chr5D.!!$F1 2994
3 TraesCS5A01G472300 chr5B 656467416 656471160 3744 False 910.400000 1594 90.2256 1 3778 5 chr5B.!!$F1 3777
4 TraesCS5A01G472300 chr5B 656723843 656730667 6824 False 802.000000 1328 88.1505 42 3778 4 chr5B.!!$F2 3736
5 TraesCS5A01G472300 chr7D 629497211 629498012 801 True 758.000000 758 83.8430 1032 1842 1 chr7D.!!$R1 810
6 TraesCS5A01G472300 chr6D 85625846 85626540 694 True 625.000000 625 83.0000 1127 1821 1 chr6D.!!$R1 694
7 TraesCS5A01G472300 chr6B 160899141 160899836 695 False 608.000000 608 82.6210 1127 1821 1 chr6B.!!$F1 694
8 TraesCS5A01G472300 chr6A 101858415 101859254 839 False 597.000000 597 79.6980 1127 1982 1 chr6A.!!$F1 855
9 TraesCS5A01G472300 chrUn 95188243 95188926 683 False 473.000000 473 79.4540 1145 1831 1 chrUn.!!$F1 686

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
734 747 0.038618 ACGAGCTCATACGTGCACAA 60.039 50.0 18.64 4.27 41.17 3.33 F
968 2463 0.180406 ACGCACCCAACAAGAGAGTT 59.820 50.0 0.00 0.00 0.00 3.01 F
2510 4234 0.032515 TCTGGCCGGAGAGGTTCATA 60.033 55.0 11.27 0.00 43.70 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 4197 0.179070 GAACTCCTCCGCCTTCATCC 60.179 60.0 0.00 0.00 0.0 3.51 R
2623 4347 0.393820 AACAAGGTTGGCAAGCATGG 59.606 50.0 30.34 21.06 32.4 3.66 R
3632 7127 0.179189 GCATTTCGGGAGCTTTCACG 60.179 55.0 0.00 0.00 0.0 4.35 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
27 29 3.510388 TCGGACTAAGTTGAGCTCATG 57.490 47.619 19.04 8.26 0.00 3.07
110 112 3.064545 GCTTCCATCGATCTTGGTCAAAG 59.935 47.826 0.00 8.46 35.64 2.77
177 179 4.706842 TTTAGGCTCACTTGAGGTTCTT 57.293 40.909 8.32 0.00 42.29 2.52
205 208 5.276773 GCTCGATCTTATCAACAAGCTCAAG 60.277 44.000 0.00 0.00 0.00 3.02
215 218 6.691754 TCAACAAGCTCAAGTGTCAATTTA 57.308 33.333 0.00 0.00 0.00 1.40
246 249 4.768968 CCAAAGCTTATAGCCAGGCATAAT 59.231 41.667 15.80 6.70 43.77 1.28
271 275 6.734104 ATTAATTGCAGTTCAGTCTCACTC 57.266 37.500 0.00 0.00 0.00 3.51
285 289 4.039366 AGTCTCACTCAAGGTTCTACCAAC 59.961 45.833 0.00 0.00 41.95 3.77
296 300 4.652822 GGTTCTACCAACCTCAATGAAGT 58.347 43.478 0.00 0.00 38.42 3.01
374 378 1.276421 AGCGTGATCCTAGCAACAAGT 59.724 47.619 6.87 0.00 0.00 3.16
421 425 1.135915 AGGTCTGCTCATGCTTCTACG 59.864 52.381 0.00 0.00 40.48 3.51
429 433 3.114809 CTCATGCTTCTACGAAGCTCAG 58.885 50.000 23.95 15.54 43.38 3.35
497 502 6.860080 TGGAGTAGAAAACTTATGGACGTAG 58.140 40.000 0.00 0.00 39.07 3.51
625 632 7.713764 TGCACATGTCACATATAGTAATGTC 57.286 36.000 0.00 0.00 38.01 3.06
660 667 2.297701 GTAATGACGCATTCCCACCAT 58.702 47.619 8.09 0.00 35.54 3.55
732 745 0.640768 GAACGAGCTCATACGTGCAC 59.359 55.000 15.40 6.82 42.43 4.57
734 747 0.038618 ACGAGCTCATACGTGCACAA 60.039 50.000 18.64 4.27 41.17 3.33
735 748 1.280982 CGAGCTCATACGTGCACAAT 58.719 50.000 18.64 6.76 34.00 2.71
737 750 2.535534 CGAGCTCATACGTGCACAATTG 60.536 50.000 18.64 10.39 34.00 2.32
739 752 2.813754 AGCTCATACGTGCACAATTGTT 59.186 40.909 18.64 0.00 34.00 2.83
740 753 2.910482 GCTCATACGTGCACAATTGTTG 59.090 45.455 18.64 2.99 0.00 3.33
742 755 2.291741 TCATACGTGCACAATTGTTGCA 59.708 40.909 23.13 23.13 36.09 4.08
748 761 2.811855 TGCACAATTGTTGCACTCTTG 58.188 42.857 23.13 6.97 33.24 3.02
749 762 2.166050 TGCACAATTGTTGCACTCTTGT 59.834 40.909 23.13 0.00 33.24 3.16
750 763 3.189285 GCACAATTGTTGCACTCTTGTT 58.811 40.909 20.83 0.00 0.00 2.83
751 764 3.000523 GCACAATTGTTGCACTCTTGTTG 59.999 43.478 20.83 4.42 0.00 3.33
752 765 4.422840 CACAATTGTTGCACTCTTGTTGA 58.577 39.130 8.77 0.00 0.00 3.18
754 767 3.996150 ATTGTTGCACTCTTGTTGAGG 57.004 42.857 0.00 0.00 46.72 3.86
755 768 2.708216 TGTTGCACTCTTGTTGAGGA 57.292 45.000 0.00 0.00 46.72 3.71
756 769 2.288666 TGTTGCACTCTTGTTGAGGAC 58.711 47.619 0.00 0.00 46.72 3.85
757 770 2.288666 GTTGCACTCTTGTTGAGGACA 58.711 47.619 0.00 0.00 46.72 4.02
758 771 2.880890 GTTGCACTCTTGTTGAGGACAT 59.119 45.455 0.00 0.00 46.72 3.06
765 778 5.297776 CACTCTTGTTGAGGACATGTTTTCT 59.702 40.000 0.00 0.00 46.72 2.52
779 792 5.177696 ACATGTTTTCTAGAGAGAACGCAAC 59.822 40.000 8.05 0.14 41.52 4.17
803 816 4.563337 TGTGGACCGAAAGAGATATACG 57.437 45.455 0.00 0.00 0.00 3.06
807 820 4.400251 TGGACCGAAAGAGATATACGTTGT 59.600 41.667 0.00 0.00 0.00 3.32
808 821 5.105635 TGGACCGAAAGAGATATACGTTGTT 60.106 40.000 0.00 0.00 0.00 2.83
809 822 5.458126 GGACCGAAAGAGATATACGTTGTTC 59.542 44.000 0.00 0.00 0.00 3.18
810 823 5.346522 ACCGAAAGAGATATACGTTGTTCC 58.653 41.667 0.00 0.00 0.00 3.62
811 824 4.743644 CCGAAAGAGATATACGTTGTTCCC 59.256 45.833 0.00 0.00 0.00 3.97
812 825 4.743644 CGAAAGAGATATACGTTGTTCCCC 59.256 45.833 0.00 0.00 0.00 4.81
813 826 4.317671 AAGAGATATACGTTGTTCCCCG 57.682 45.455 0.00 0.00 0.00 5.73
814 827 2.035576 AGAGATATACGTTGTTCCCCGC 59.964 50.000 0.00 0.00 0.00 6.13
816 829 2.168936 AGATATACGTTGTTCCCCGCAA 59.831 45.455 0.00 0.00 0.00 4.85
817 830 2.695127 TATACGTTGTTCCCCGCAAT 57.305 45.000 0.00 0.00 0.00 3.56
818 831 2.695127 ATACGTTGTTCCCCGCAATA 57.305 45.000 0.00 0.00 0.00 1.90
819 832 2.469274 TACGTTGTTCCCCGCAATAA 57.531 45.000 0.00 0.00 0.00 1.40
820 833 1.606903 ACGTTGTTCCCCGCAATAAA 58.393 45.000 0.00 0.00 0.00 1.40
821 834 1.955080 ACGTTGTTCCCCGCAATAAAA 59.045 42.857 0.00 0.00 0.00 1.52
841 854 4.380841 AAAAGAGATATACGTGCACGGA 57.619 40.909 39.21 34.78 44.95 4.69
842 855 4.585955 AAAGAGATATACGTGCACGGAT 57.414 40.909 36.89 36.89 46.11 4.18
843 856 3.833545 AGAGATATACGTGCACGGATC 57.166 47.619 38.66 32.75 42.81 3.36
844 857 2.488545 AGAGATATACGTGCACGGATCC 59.511 50.000 38.66 29.16 42.81 3.36
845 858 2.228103 GAGATATACGTGCACGGATCCA 59.772 50.000 38.66 24.05 42.81 3.41
847 860 0.386476 TATACGTGCACGGATCCACC 59.614 55.000 38.66 0.00 42.81 4.61
848 861 2.306255 ATACGTGCACGGATCCACCC 62.306 60.000 39.21 0.00 38.88 4.61
849 862 4.082523 CGTGCACGGATCCACCCT 62.083 66.667 31.15 0.00 35.37 4.34
850 863 2.125106 GTGCACGGATCCACCCTC 60.125 66.667 13.41 0.00 34.64 4.30
851 864 2.606213 TGCACGGATCCACCCTCA 60.606 61.111 13.41 0.00 34.64 3.86
852 865 2.187946 GCACGGATCCACCCTCAG 59.812 66.667 13.41 0.00 34.64 3.35
853 866 2.187946 CACGGATCCACCCTCAGC 59.812 66.667 13.41 0.00 34.64 4.26
854 867 3.461773 ACGGATCCACCCTCAGCG 61.462 66.667 13.41 0.00 34.64 5.18
855 868 4.227134 CGGATCCACCCTCAGCGG 62.227 72.222 13.41 0.00 34.64 5.52
860 873 3.790437 CCACCCTCAGCGGCTCAT 61.790 66.667 0.00 0.00 0.00 2.90
861 874 2.434843 CCACCCTCAGCGGCTCATA 61.435 63.158 0.00 0.00 0.00 2.15
863 876 2.028190 CCCTCAGCGGCTCATACG 59.972 66.667 0.00 0.00 0.00 3.06
865 878 1.589993 CCTCAGCGGCTCATACGTG 60.590 63.158 0.00 0.00 0.00 4.49
869 1677 2.813474 GCGGCTCATACGTGCACA 60.813 61.111 18.64 0.00 33.19 4.57
872 1680 0.726827 CGGCTCATACGTGCACAATT 59.273 50.000 18.64 2.52 33.19 2.32
925 2417 3.278367 CATGAATTGCATCCACGGATC 57.722 47.619 0.00 0.00 34.15 3.36
926 2418 1.679139 TGAATTGCATCCACGGATCC 58.321 50.000 0.00 0.00 31.62 3.36
927 2419 1.064832 TGAATTGCATCCACGGATCCA 60.065 47.619 13.41 0.00 31.62 3.41
928 2420 1.605710 GAATTGCATCCACGGATCCAG 59.394 52.381 13.41 7.30 31.62 3.86
967 2462 0.532862 CACGCACCCAACAAGAGAGT 60.533 55.000 0.00 0.00 0.00 3.24
968 2463 0.180406 ACGCACCCAACAAGAGAGTT 59.820 50.000 0.00 0.00 0.00 3.01
971 2466 1.876156 GCACCCAACAAGAGAGTTCTG 59.124 52.381 0.00 0.00 32.79 3.02
973 2468 1.490490 ACCCAACAAGAGAGTTCTGCA 59.510 47.619 0.00 0.00 32.79 4.41
974 2469 2.107204 ACCCAACAAGAGAGTTCTGCAT 59.893 45.455 0.00 0.00 32.79 3.96
975 2470 2.746362 CCCAACAAGAGAGTTCTGCATC 59.254 50.000 0.00 0.00 32.79 3.91
978 2473 3.051081 ACAAGAGAGTTCTGCATCCAC 57.949 47.619 0.00 0.00 32.79 4.02
980 2475 3.260740 CAAGAGAGTTCTGCATCCACTC 58.739 50.000 10.65 10.65 37.76 3.51
992 2487 2.806019 GCATCCACTCTCAGCCATAGTG 60.806 54.545 0.00 0.00 40.24 2.74
994 2489 2.540383 TCCACTCTCAGCCATAGTGTT 58.460 47.619 0.00 0.00 39.17 3.32
1107 2611 3.181485 GCTACTACTTGGCAAGACGATCT 60.181 47.826 32.50 12.31 0.00 2.75
1824 3341 0.308068 AGATCATAGACGACCACGCG 59.692 55.000 3.53 3.53 43.96 6.01
1911 3431 5.540337 ACAAGATGAAGACAGAGACTTGGTA 59.460 40.000 0.00 0.00 37.93 3.25
1995 3515 3.687698 TGTTGGTAATTCGCTTAGCTTCC 59.312 43.478 1.76 0.00 38.40 3.46
2009 3529 1.157585 GCTTCCTGAACGTTTCCCTC 58.842 55.000 0.46 0.00 0.00 4.30
2013 3533 2.043992 TCCTGAACGTTTCCCTCTGAA 58.956 47.619 0.46 0.00 0.00 3.02
2024 3550 5.404667 CGTTTCCCTCTGAACTAAACACTAC 59.595 44.000 0.00 0.00 31.05 2.73
2026 3552 5.979288 TCCCTCTGAACTAAACACTACTC 57.021 43.478 0.00 0.00 0.00 2.59
2030 3556 5.105675 CCTCTGAACTAAACACTACTCCCTC 60.106 48.000 0.00 0.00 0.00 4.30
2035 3561 8.253867 TGAACTAAACACTACTCCCTCTTAAA 57.746 34.615 0.00 0.00 0.00 1.52
2036 3562 8.707449 TGAACTAAACACTACTCCCTCTTAAAA 58.293 33.333 0.00 0.00 0.00 1.52
2037 3563 9.551734 GAACTAAACACTACTCCCTCTTAAAAA 57.448 33.333 0.00 0.00 0.00 1.94
2063 3589 8.943909 AATATAAGAACGTTTAGAACAGAGGG 57.056 34.615 0.46 0.00 0.00 4.30
2064 3590 4.950205 AAGAACGTTTAGAACAGAGGGA 57.050 40.909 0.46 0.00 0.00 4.20
2065 3591 4.522722 AGAACGTTTAGAACAGAGGGAG 57.477 45.455 0.46 0.00 0.00 4.30
2067 3593 5.075493 AGAACGTTTAGAACAGAGGGAGTA 58.925 41.667 0.46 0.00 0.00 2.59
2068 3594 5.537674 AGAACGTTTAGAACAGAGGGAGTAA 59.462 40.000 0.46 0.00 0.00 2.24
2069 3595 5.997384 ACGTTTAGAACAGAGGGAGTAAT 57.003 39.130 0.00 0.00 0.00 1.89
2070 3596 6.356186 ACGTTTAGAACAGAGGGAGTAATT 57.644 37.500 0.00 0.00 0.00 1.40
2071 3597 6.766429 ACGTTTAGAACAGAGGGAGTAATTT 58.234 36.000 0.00 0.00 0.00 1.82
2073 3599 7.718314 ACGTTTAGAACAGAGGGAGTAATTTTT 59.282 33.333 0.00 0.00 0.00 1.94
2074 3600 9.211485 CGTTTAGAACAGAGGGAGTAATTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
2315 4035 1.958288 ACATGTCCTACCTCAAGGCT 58.042 50.000 0.00 0.00 39.32 4.58
2318 4038 0.976641 TGTCCTACCTCAAGGCTGTG 59.023 55.000 0.00 0.00 39.32 3.66
2417 4137 3.792736 GGCTACATGGTCCCGGCA 61.793 66.667 0.00 0.00 0.00 5.69
2474 4198 3.391382 GACACCGAGTCCTGGGGG 61.391 72.222 0.00 0.00 41.56 5.40
2475 4199 3.899545 GACACCGAGTCCTGGGGGA 62.900 68.421 4.46 0.00 41.56 4.81
2476 4200 2.365635 CACCGAGTCCTGGGGGAT 60.366 66.667 0.29 0.00 44.33 3.85
2510 4234 0.032515 TCTGGCCGGAGAGGTTCATA 60.033 55.000 11.27 0.00 43.70 2.15
2555 4279 3.142028 ACTTCAAAGGGAGGGATTTCCAA 59.858 43.478 0.00 0.00 39.09 3.53
2609 4333 2.442830 GGGATGGGCTTTGGGCTC 60.443 66.667 0.00 0.00 42.93 4.70
2630 4354 3.706373 ACGGTCGAGGCCATGCTT 61.706 61.111 5.01 0.00 0.00 3.91
2642 4366 0.393820 CCATGCTTGCCAACCTTGTT 59.606 50.000 0.00 0.00 0.00 2.83
2687 4411 3.551407 GGGATGCGGGAGGAGGAC 61.551 72.222 0.00 0.00 0.00 3.85
2738 4462 1.079750 GCGTCGGAAGGAGAAGCTT 60.080 57.895 0.00 0.00 39.42 3.74
2795 4523 2.675772 TGCATGCGCACCATTCCA 60.676 55.556 14.90 0.22 45.36 3.53
2821 4632 7.698506 ACTATCAGTTAGTATAGCCGCAATA 57.301 36.000 0.00 0.00 39.44 1.90
2852 4663 9.739276 TTTAGACCAACTCAAATATGAACATCT 57.261 29.630 0.00 0.00 34.49 2.90
2913 5073 4.532834 AGGAACTGTACTTTTTGCAGGAA 58.467 39.130 0.00 0.00 42.06 3.36
3008 6304 4.219288 AGCAAATGTTGAGAATCCTCCAAC 59.781 41.667 0.00 0.00 38.66 3.77
3153 6493 6.650120 TGTTCTAAACTGGGCCTAAATCTAG 58.350 40.000 4.53 0.00 0.00 2.43
3165 6505 3.459969 CCTAAATCTAGGCCTCCTTTGGT 59.540 47.826 9.68 0.00 38.50 3.67
3167 6507 1.512735 ATCTAGGCCTCCTTTGGTCC 58.487 55.000 9.68 0.00 34.61 4.46
3168 6508 0.417841 TCTAGGCCTCCTTTGGTCCT 59.582 55.000 9.68 0.00 37.39 3.85
3216 6678 2.289819 TGGAGGCTTAAGTGGGTTTACG 60.290 50.000 4.02 0.00 0.00 3.18
3218 6680 2.998670 GAGGCTTAAGTGGGTTTACGAC 59.001 50.000 4.02 0.00 0.00 4.34
3229 6691 4.696402 GTGGGTTTACGACATAATGTGGAA 59.304 41.667 0.00 0.00 30.32 3.53
3239 6701 4.469657 ACATAATGTGGAATAACGGCCAT 58.530 39.130 2.24 0.00 36.41 4.40
3275 6738 4.220382 CCCAAACAGCCATGAATTAGTTGA 59.780 41.667 0.00 0.00 0.00 3.18
3286 6756 7.012704 GCCATGAATTAGTTGAGCTCAAGATTA 59.987 37.037 29.13 17.98 36.39 1.75
3356 6828 5.247862 TCCCCGTATAGAACCAAAGAAAAC 58.752 41.667 0.00 0.00 0.00 2.43
3359 6831 6.376177 CCCGTATAGAACCAAAGAAAACAAC 58.624 40.000 0.00 0.00 0.00 3.32
3375 6847 2.758009 ACAACTGTGCATTTTCCATGC 58.242 42.857 0.00 0.00 44.76 4.06
3383 6855 1.937899 GCATTTTCCATGCATGAAGGC 59.062 47.619 28.31 21.80 44.00 4.35
3407 6880 5.009410 CCTGAGGATGTCAAAATGATTAGGC 59.991 44.000 0.00 0.00 33.60 3.93
3452 6947 1.236628 CTAGCCAGCATGCCTTGATC 58.763 55.000 15.66 2.83 31.97 2.92
3632 7127 0.745486 GCCCTTGCCATGGAATTTGC 60.745 55.000 18.40 8.13 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.569943 TCAACATGAGCTCAACTTAGTCC 58.430 43.478 22.50 0.00 0.00 3.85
11 12 5.474578 TCTCAACATGAGCTCAACTTAGT 57.525 39.130 22.50 11.45 43.95 2.24
12 13 6.981762 AATCTCAACATGAGCTCAACTTAG 57.018 37.500 22.50 14.26 43.95 2.18
13 14 7.750229 AAAATCTCAACATGAGCTCAACTTA 57.250 32.000 22.50 4.78 43.95 2.24
14 15 6.645790 AAAATCTCAACATGAGCTCAACTT 57.354 33.333 22.50 11.85 43.95 2.66
27 29 3.000575 GCTCGAGCTCGTAAAATCTCAAC 60.001 47.826 33.33 4.72 40.80 3.18
83 85 5.041191 ACCAAGATCGATGGAAGCTTAAT 57.959 39.130 22.64 0.00 40.56 1.40
110 112 2.530177 TGAGATCATTTCGACTGACGC 58.470 47.619 0.00 0.00 42.26 5.19
177 179 4.568359 GCTTGTTGATAAGATCGAGCTTGA 59.432 41.667 25.40 6.01 0.00 3.02
205 208 3.658757 TGGCAAGCCTTAAATTGACAC 57.341 42.857 12.96 0.00 39.49 3.67
246 249 7.877612 TGAGTGAGACTGAACTGCAATTAATTA 59.122 33.333 0.00 0.00 0.00 1.40
285 289 2.964740 TCAAGAGCGACTTCATTGAGG 58.035 47.619 0.00 0.00 36.61 3.86
296 300 1.478105 TGCTGCTAGAATCAAGAGCGA 59.522 47.619 0.00 0.00 39.14 4.93
374 378 4.804108 CAAGTAACGATTGGGCATTCAAA 58.196 39.130 0.00 0.00 0.00 2.69
421 425 5.183140 GGTAGGATCTGATAGACTGAGCTTC 59.817 48.000 0.00 0.00 34.23 3.86
429 433 3.687698 GCTCGAGGTAGGATCTGATAGAC 59.312 52.174 15.58 0.00 0.00 2.59
640 647 1.745232 TGGTGGGAATGCGTCATTAC 58.255 50.000 6.32 6.32 33.90 1.89
643 650 1.851304 AAATGGTGGGAATGCGTCAT 58.149 45.000 0.00 0.00 0.00 3.06
708 721 3.180584 GCACGTATGAGCTCGTTCTTATG 59.819 47.826 14.93 8.53 38.23 1.90
732 745 4.046462 CCTCAACAAGAGTGCAACAATTG 58.954 43.478 3.24 3.24 43.12 2.32
734 747 3.316308 GTCCTCAACAAGAGTGCAACAAT 59.684 43.478 0.00 0.00 43.12 2.71
735 748 2.682856 GTCCTCAACAAGAGTGCAACAA 59.317 45.455 0.00 0.00 43.12 2.83
737 750 2.288666 TGTCCTCAACAAGAGTGCAAC 58.711 47.619 0.00 0.00 43.12 4.17
739 752 2.158769 ACATGTCCTCAACAAGAGTGCA 60.159 45.455 0.00 0.00 42.37 4.57
740 753 2.498167 ACATGTCCTCAACAAGAGTGC 58.502 47.619 0.00 0.00 42.37 4.40
742 755 5.440610 AGAAAACATGTCCTCAACAAGAGT 58.559 37.500 0.00 0.00 42.37 3.24
743 756 6.931281 TCTAGAAAACATGTCCTCAACAAGAG 59.069 38.462 0.00 0.00 42.37 2.85
744 757 6.826668 TCTAGAAAACATGTCCTCAACAAGA 58.173 36.000 0.00 0.00 42.37 3.02
745 758 6.931281 TCTCTAGAAAACATGTCCTCAACAAG 59.069 38.462 0.00 0.00 42.37 3.16
746 759 6.826668 TCTCTAGAAAACATGTCCTCAACAA 58.173 36.000 0.00 0.00 42.37 2.83
748 761 6.692486 TCTCTCTAGAAAACATGTCCTCAAC 58.308 40.000 0.00 0.00 0.00 3.18
749 762 6.918067 TCTCTCTAGAAAACATGTCCTCAA 57.082 37.500 0.00 0.00 0.00 3.02
750 763 6.570571 CGTTCTCTCTAGAAAACATGTCCTCA 60.571 42.308 0.00 0.00 43.30 3.86
751 764 5.802956 CGTTCTCTCTAGAAAACATGTCCTC 59.197 44.000 0.00 0.00 43.30 3.71
752 765 5.715070 CGTTCTCTCTAGAAAACATGTCCT 58.285 41.667 0.00 0.00 43.30 3.85
753 766 4.327627 GCGTTCTCTCTAGAAAACATGTCC 59.672 45.833 0.00 0.00 43.30 4.02
754 767 4.923871 TGCGTTCTCTCTAGAAAACATGTC 59.076 41.667 0.00 0.00 43.30 3.06
755 768 4.883083 TGCGTTCTCTCTAGAAAACATGT 58.117 39.130 0.00 0.00 43.30 3.21
756 769 5.406780 AGTTGCGTTCTCTCTAGAAAACATG 59.593 40.000 10.98 0.00 43.30 3.21
757 770 5.542779 AGTTGCGTTCTCTCTAGAAAACAT 58.457 37.500 10.98 0.00 43.30 2.71
758 771 4.945246 AGTTGCGTTCTCTCTAGAAAACA 58.055 39.130 10.98 0.00 43.30 2.83
765 778 4.014406 TCCACATAGTTGCGTTCTCTCTA 58.986 43.478 0.00 0.00 0.00 2.43
779 792 6.072618 ACGTATATCTCTTTCGGTCCACATAG 60.073 42.308 0.00 0.00 0.00 2.23
819 832 4.751060 TCCGTGCACGTATATCTCTTTTT 58.249 39.130 34.81 0.00 37.74 1.94
820 833 4.380841 TCCGTGCACGTATATCTCTTTT 57.619 40.909 34.81 0.00 37.74 2.27
821 834 4.547532 GATCCGTGCACGTATATCTCTTT 58.452 43.478 34.81 4.10 37.74 2.52
823 836 2.488545 GGATCCGTGCACGTATATCTCT 59.511 50.000 34.81 5.72 37.74 3.10
824 837 2.228103 TGGATCCGTGCACGTATATCTC 59.772 50.000 34.81 24.04 37.74 2.75
826 839 2.325761 GTGGATCCGTGCACGTATATC 58.674 52.381 34.81 29.61 36.94 1.63
827 840 1.000506 GGTGGATCCGTGCACGTATAT 59.999 52.381 34.81 24.79 46.49 0.86
828 841 0.386476 GGTGGATCCGTGCACGTATA 59.614 55.000 34.81 21.42 46.49 1.47
830 843 2.574929 GGTGGATCCGTGCACGTA 59.425 61.111 34.81 23.28 46.49 3.57
831 844 4.388499 GGGTGGATCCGTGCACGT 62.388 66.667 34.81 20.11 46.49 4.49
832 845 4.082523 AGGGTGGATCCGTGCACG 62.083 66.667 31.77 31.77 46.49 5.34
834 847 2.606213 TGAGGGTGGATCCGTGCA 60.606 61.111 7.39 0.00 37.00 4.57
836 849 2.187946 GCTGAGGGTGGATCCGTG 59.812 66.667 7.39 0.00 37.00 4.94
847 860 1.589993 CACGTATGAGCCGCTGAGG 60.590 63.158 0.00 0.00 44.97 3.86
848 861 2.233654 GCACGTATGAGCCGCTGAG 61.234 63.158 0.00 0.00 0.00 3.35
849 862 2.202743 GCACGTATGAGCCGCTGA 60.203 61.111 0.00 0.00 0.00 4.26
850 863 2.509111 TGCACGTATGAGCCGCTG 60.509 61.111 0.00 0.00 0.00 5.18
851 864 2.509336 GTGCACGTATGAGCCGCT 60.509 61.111 0.00 0.00 0.00 5.52
852 865 1.705337 ATTGTGCACGTATGAGCCGC 61.705 55.000 13.13 0.00 0.00 6.53
853 866 0.726827 AATTGTGCACGTATGAGCCG 59.273 50.000 13.13 0.00 0.00 5.52
854 867 1.468520 ACAATTGTGCACGTATGAGCC 59.531 47.619 11.07 0.00 0.00 4.70
855 868 2.900122 ACAATTGTGCACGTATGAGC 57.100 45.000 11.07 0.00 0.00 4.26
865 878 2.813061 ACAAGAGTGCAACAATTGTGC 58.187 42.857 12.82 17.19 43.26 4.57
869 1677 3.953612 TCCTCAACAAGAGTGCAACAATT 59.046 39.130 0.00 0.00 43.12 2.32
872 1680 2.288666 GTCCTCAACAAGAGTGCAACA 58.711 47.619 0.00 0.00 43.12 3.33
967 2462 0.251354 GGCTGAGAGTGGATGCAGAA 59.749 55.000 0.00 0.00 0.00 3.02
968 2463 0.906282 TGGCTGAGAGTGGATGCAGA 60.906 55.000 0.00 0.00 0.00 4.26
971 2466 1.415659 ACTATGGCTGAGAGTGGATGC 59.584 52.381 0.00 0.00 0.00 3.91
973 2468 2.756907 ACACTATGGCTGAGAGTGGAT 58.243 47.619 13.31 0.00 46.50 3.41
974 2469 2.238084 ACACTATGGCTGAGAGTGGA 57.762 50.000 13.31 0.00 46.50 4.02
975 2470 3.701542 TCTAACACTATGGCTGAGAGTGG 59.298 47.826 13.31 0.14 46.50 4.00
978 2473 4.211125 TCCTCTAACACTATGGCTGAGAG 58.789 47.826 0.00 0.00 0.00 3.20
980 2475 4.798924 GCATCCTCTAACACTATGGCTGAG 60.799 50.000 0.00 0.00 0.00 3.35
981 2476 3.070159 GCATCCTCTAACACTATGGCTGA 59.930 47.826 0.00 0.00 0.00 4.26
992 2487 0.315568 ATCGCCTCGCATCCTCTAAC 59.684 55.000 0.00 0.00 0.00 2.34
994 2489 1.745653 CATATCGCCTCGCATCCTCTA 59.254 52.381 0.00 0.00 0.00 2.43
1107 2611 1.878734 TGATCACTGCAATTGTTCGCA 59.121 42.857 7.40 0.00 36.52 5.10
1554 3071 3.336715 CTCGGTCATGTCGACGGCA 62.337 63.158 3.85 3.85 46.42 5.69
1734 3251 2.035940 ACTCGCCGGAGAAGACCT 59.964 61.111 9.83 0.00 43.27 3.85
1760 3277 0.739112 CTTCAGCCTCCTCGTCTTGC 60.739 60.000 0.00 0.00 0.00 4.01
1824 3341 3.004752 ACTAGCCATGGTGATTTGGTC 57.995 47.619 14.67 0.00 35.34 4.02
1911 3431 5.047377 GTGTTGAAGAGAGAGGAGAACATCT 60.047 44.000 0.00 0.00 39.95 2.90
1995 3515 3.113260 AGTTCAGAGGGAAACGTTCAG 57.887 47.619 0.00 0.00 37.23 3.02
2009 3529 5.986501 AGAGGGAGTAGTGTTTAGTTCAG 57.013 43.478 0.00 0.00 0.00 3.02
2037 3563 9.379791 CCCTCTGTTCTAAACGTTCTTATATTT 57.620 33.333 0.00 0.00 0.00 1.40
2040 3566 7.395489 ACTCCCTCTGTTCTAAACGTTCTTATA 59.605 37.037 0.00 0.00 0.00 0.98
2045 3571 4.254402 ACTCCCTCTGTTCTAAACGTTC 57.746 45.455 0.00 0.00 0.00 3.95
2315 4035 1.666011 GAGCGTCTCCTTCACCACA 59.334 57.895 0.00 0.00 0.00 4.17
2417 4137 1.141881 GATGATGACGCGTGTCCCT 59.858 57.895 25.28 13.34 44.86 4.20
2472 4196 1.627297 AACTCCTCCGCCTTCATCCC 61.627 60.000 0.00 0.00 0.00 3.85
2473 4197 0.179070 GAACTCCTCCGCCTTCATCC 60.179 60.000 0.00 0.00 0.00 3.51
2474 4198 0.827368 AGAACTCCTCCGCCTTCATC 59.173 55.000 0.00 0.00 0.00 2.92
2475 4199 0.539051 CAGAACTCCTCCGCCTTCAT 59.461 55.000 0.00 0.00 0.00 2.57
2476 4200 1.544825 CCAGAACTCCTCCGCCTTCA 61.545 60.000 0.00 0.00 0.00 3.02
2555 4279 1.678970 GGCTCCAAACGGCAGGAAT 60.679 57.895 0.00 0.00 32.57 3.01
2615 4339 3.512516 GCAAGCATGGCCTCGACC 61.513 66.667 3.32 0.00 0.00 4.79
2623 4347 0.393820 AACAAGGTTGGCAAGCATGG 59.606 50.000 30.34 21.06 32.40 3.66
2630 4354 3.551863 CGAAGCAATAAACAAGGTTGGCA 60.552 43.478 0.00 0.00 0.00 4.92
2642 4366 1.555075 AGCTCCCAGTCGAAGCAATAA 59.445 47.619 8.64 0.00 38.51 1.40
2687 4411 2.736995 ACGTCGGCCATGTCAACG 60.737 61.111 2.24 4.91 39.16 4.10
2814 4625 7.087639 TGAGTTGGTCTAAATTTTTATTGCGG 58.912 34.615 0.00 0.00 0.00 5.69
2815 4626 8.514136 TTGAGTTGGTCTAAATTTTTATTGCG 57.486 30.769 0.00 0.00 0.00 4.85
2852 4663 6.014771 TGTAGGAGAGAAGCATAACTAGGA 57.985 41.667 0.00 0.00 0.00 2.94
2898 5058 7.770801 AAGAAACAATTCCTGCAAAAAGTAC 57.229 32.000 0.00 0.00 36.12 2.73
2902 5062 7.560368 TCCTAAAGAAACAATTCCTGCAAAAA 58.440 30.769 0.00 0.00 36.12 1.94
2906 5066 5.630121 TCTCCTAAAGAAACAATTCCTGCA 58.370 37.500 0.00 0.00 36.12 4.41
3008 6304 3.508845 TCCTTCCTTTTCCTTCCAGTG 57.491 47.619 0.00 0.00 0.00 3.66
3106 6446 9.634163 AACAAAAGAACTTTACAAGAATTTCGT 57.366 25.926 0.14 0.00 31.63 3.85
3153 6493 1.000771 GGAAGGACCAAAGGAGGCC 60.001 63.158 0.00 0.00 38.79 5.19
3163 6503 4.878397 CACTAGATCATGTTTGGAAGGACC 59.122 45.833 0.00 0.00 39.54 4.46
3165 6505 4.536090 ACCACTAGATCATGTTTGGAAGGA 59.464 41.667 0.00 0.00 0.00 3.36
3167 6507 5.583854 CAGACCACTAGATCATGTTTGGAAG 59.416 44.000 0.00 0.00 0.00 3.46
3168 6508 5.491070 CAGACCACTAGATCATGTTTGGAA 58.509 41.667 0.00 0.00 0.00 3.53
3216 6678 3.880490 TGGCCGTTATTCCACATTATGTC 59.120 43.478 0.00 0.00 0.00 3.06
3218 6680 4.518590 TGATGGCCGTTATTCCACATTATG 59.481 41.667 0.00 0.00 34.81 1.90
3239 6701 4.947388 GGCTGTTTGGGTCATTAGTAATGA 59.053 41.667 19.51 19.51 45.19 2.57
3261 6724 6.939132 ATCTTGAGCTCAACTAATTCATGG 57.061 37.500 25.16 11.38 0.00 3.66
3314 6786 4.215613 GGGGATTGGCGTTCAATAGTATTC 59.784 45.833 6.20 0.00 45.36 1.75
3323 6795 1.069513 CTATACGGGGATTGGCGTTCA 59.930 52.381 0.00 0.00 0.00 3.18
3326 6798 1.069668 GTTCTATACGGGGATTGGCGT 59.930 52.381 0.00 0.00 0.00 5.68
3375 6847 1.211212 TGACATCCTCAGGCCTTCATG 59.789 52.381 0.00 5.43 0.00 3.07
3377 6849 1.361204 TTGACATCCTCAGGCCTTCA 58.639 50.000 0.00 0.00 0.00 3.02
3379 6851 2.978156 TTTTGACATCCTCAGGCCTT 57.022 45.000 0.00 0.00 0.00 4.35
3381 6853 2.726821 TCATTTTGACATCCTCAGGCC 58.273 47.619 0.00 0.00 0.00 5.19
3382 6854 4.996788 AATCATTTTGACATCCTCAGGC 57.003 40.909 0.00 0.00 0.00 4.85
3383 6855 5.009410 GCCTAATCATTTTGACATCCTCAGG 59.991 44.000 0.00 0.00 0.00 3.86
3452 6947 2.402305 TGTTTTAAGCGGCAATGCAAG 58.598 42.857 7.79 1.06 37.31 4.01
3632 7127 0.179189 GCATTTCGGGAGCTTTCACG 60.179 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.