Multiple sequence alignment - TraesCS7A01G208500

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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 TraesCS7A01G208500 chr7A 100.000 3965 0 0 1 3965 171284366 171280402 0.000000e+00 7323.0
1 TraesCS7A01G208500 chr7A 92.571 700 42 5 2 700 150423197 150422507 0.000000e+00 996.0
2 TraesCS7A01G208500 chr7B 92.492 2131 124 13 893 2999 134307229 134305111 0.000000e+00 3016.0
3 TraesCS7A01G208500 chr7B 87.379 309 23 8 881 1187 134495861 134495567 1.360000e-89 340.0
4 TraesCS7A01G208500 chr7B 95.181 166 8 0 3079 3244 134304933 134304768 3.040000e-66 263.0
5 TraesCS7A01G208500 chr7B 90.270 185 18 0 926 1110 134313610 134313426 3.960000e-60 243.0
6 TraesCS7A01G208500 chr7B 95.714 70 3 0 2999 3068 134305082 134305013 3.240000e-21 113.0
7 TraesCS7A01G208500 chr7D 89.765 1407 95 11 839 2234 168813227 168811859 0.000000e+00 1755.0
8 TraesCS7A01G208500 chr7D 89.571 700 73 0 2300 2999 169041813 169041114 0.000000e+00 889.0
9 TraesCS7A01G208500 chr7D 91.007 278 13 6 891 1168 169027663 169027398 8.100000e-97 364.0
10 TraesCS7A01G208500 chr7D 93.976 83 5 0 3084 3166 169040932 169040850 4.160000e-25 126.0
11 TraesCS7A01G208500 chr7D 87.654 81 9 1 2998 3077 169041087 169041007 4.220000e-15 93.5
12 TraesCS7A01G208500 chr6A 97.991 697 11 3 3270 3965 85759482 85760176 0.000000e+00 1206.0
13 TraesCS7A01G208500 chr6A 94.364 692 35 3 3274 3965 559034998 559035685 0.000000e+00 1059.0
14 TraesCS7A01G208500 chr6A 93.883 703 36 6 2 703 600823166 600823862 0.000000e+00 1053.0
15 TraesCS7A01G208500 chr6A 94.092 694 37 3 3272 3965 559082306 559082995 0.000000e+00 1051.0
16 TraesCS7A01G208500 chr6A 93.305 702 45 2 2 703 97602978 97602279 0.000000e+00 1035.0
17 TraesCS7A01G208500 chr2A 97.131 697 19 1 3270 3965 613335514 613336210 0.000000e+00 1175.0
18 TraesCS7A01G208500 chr2A 93.020 702 45 2 2 703 726094042 726094739 0.000000e+00 1022.0
19 TraesCS7A01G208500 chr2A 87.255 102 11 2 702 802 755749892 755749792 9.000000e-22 115.0
20 TraesCS7A01G208500 chr6D 96.259 695 25 1 3271 3965 458349962 458350655 0.000000e+00 1138.0
21 TraesCS7A01G208500 chr5B 95.671 693 28 1 3273 3965 654769558 654768868 0.000000e+00 1112.0
22 TraesCS7A01G208500 chr5B 83.000 100 15 2 705 803 559155834 559155736 5.460000e-14 89.8
23 TraesCS7A01G208500 chr2B 94.864 701 30 5 3267 3965 207720307 207721003 0.000000e+00 1090.0
24 TraesCS7A01G208500 chr2B 95.266 676 29 3 3270 3944 684812064 684811391 0.000000e+00 1068.0
25 TraesCS7A01G208500 chr2B 82.828 99 15 2 705 802 78416137 78416040 1.960000e-13 87.9
26 TraesCS7A01G208500 chr2B 82.000 100 16 2 705 803 634959831 634959733 2.540000e-12 84.2
27 TraesCS7A01G208500 chr3A 93.723 701 44 0 3 703 663280555 663279855 0.000000e+00 1051.0
28 TraesCS7A01G208500 chr3A 92.877 702 47 3 2 703 583235936 583236634 0.000000e+00 1016.0
29 TraesCS7A01G208500 chr3A 92.571 700 48 3 2 701 718077010 718076315 0.000000e+00 1002.0
30 TraesCS7A01G208500 chr3A 88.660 97 11 0 704 800 718076220 718076124 6.960000e-23 119.0
31 TraesCS7A01G208500 chr1A 92.725 701 48 3 3 703 338838504 338837807 0.000000e+00 1009.0
32 TraesCS7A01G208500 chr1A 82.653 98 16 1 705 802 586127394 586127298 7.060000e-13 86.1
33 TraesCS7A01G208500 chr6B 92.165 702 51 4 2 703 129267676 129266979 0.000000e+00 989.0
34 TraesCS7A01G208500 chr5A 91.441 701 53 5 3270 3965 28360678 28361376 0.000000e+00 955.0
35 TraesCS7A01G208500 chr1D 87.260 730 75 10 972 1701 2454044 2454755 0.000000e+00 817.0
36 TraesCS7A01G208500 chr4D 88.298 94 9 2 713 805 325069507 325069415 1.160000e-20 111.0
37 TraesCS7A01G208500 chr4A 81.188 101 16 3 705 803 537959948 537960047 1.180000e-10 78.7
38 TraesCS7A01G208500 chr5D 80.612 98 19 0 705 802 37203883 37203786 4.250000e-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 TraesCS7A01G208500 chr7A 171280402 171284366 3964 True 7323.000000 7323 100.000000 1 3965 1 chr7A.!!$R2 3964
1 TraesCS7A01G208500 chr7A 150422507 150423197 690 True 996.000000 996 92.571000 2 700 1 chr7A.!!$R1 698
2 TraesCS7A01G208500 chr7B 134304768 134307229 2461 True 1130.666667 3016 94.462333 893 3244 3 chr7B.!!$R3 2351
3 TraesCS7A01G208500 chr7D 168811859 168813227 1368 True 1755.000000 1755 89.765000 839 2234 1 chr7D.!!$R1 1395
4 TraesCS7A01G208500 chr7D 169040850 169041813 963 True 369.500000 889 90.400333 2300 3166 3 chr7D.!!$R3 866
5 TraesCS7A01G208500 chr6A 85759482 85760176 694 False 1206.000000 1206 97.991000 3270 3965 1 chr6A.!!$F1 695
6 TraesCS7A01G208500 chr6A 559034998 559035685 687 False 1059.000000 1059 94.364000 3274 3965 1 chr6A.!!$F2 691
7 TraesCS7A01G208500 chr6A 600823166 600823862 696 False 1053.000000 1053 93.883000 2 703 1 chr6A.!!$F4 701
8 TraesCS7A01G208500 chr6A 559082306 559082995 689 False 1051.000000 1051 94.092000 3272 3965 1 chr6A.!!$F3 693
9 TraesCS7A01G208500 chr6A 97602279 97602978 699 True 1035.000000 1035 93.305000 2 703 1 chr6A.!!$R1 701
10 TraesCS7A01G208500 chr2A 613335514 613336210 696 False 1175.000000 1175 97.131000 3270 3965 1 chr2A.!!$F1 695
11 TraesCS7A01G208500 chr2A 726094042 726094739 697 False 1022.000000 1022 93.020000 2 703 1 chr2A.!!$F2 701
12 TraesCS7A01G208500 chr6D 458349962 458350655 693 False 1138.000000 1138 96.259000 3271 3965 1 chr6D.!!$F1 694
13 TraesCS7A01G208500 chr5B 654768868 654769558 690 True 1112.000000 1112 95.671000 3273 3965 1 chr5B.!!$R2 692
14 TraesCS7A01G208500 chr2B 207720307 207721003 696 False 1090.000000 1090 94.864000 3267 3965 1 chr2B.!!$F1 698
15 TraesCS7A01G208500 chr2B 684811391 684812064 673 True 1068.000000 1068 95.266000 3270 3944 1 chr2B.!!$R3 674
16 TraesCS7A01G208500 chr3A 663279855 663280555 700 True 1051.000000 1051 93.723000 3 703 1 chr3A.!!$R1 700
17 TraesCS7A01G208500 chr3A 583235936 583236634 698 False 1016.000000 1016 92.877000 2 703 1 chr3A.!!$F1 701
18 TraesCS7A01G208500 chr3A 718076124 718077010 886 True 560.500000 1002 90.615500 2 800 2 chr3A.!!$R2 798
19 TraesCS7A01G208500 chr1A 338837807 338838504 697 True 1009.000000 1009 92.725000 3 703 1 chr1A.!!$R1 700
20 TraesCS7A01G208500 chr6B 129266979 129267676 697 True 989.000000 989 92.165000 2 703 1 chr6B.!!$R1 701
21 TraesCS7A01G208500 chr5A 28360678 28361376 698 False 955.000000 955 91.441000 3270 3965 1 chr5A.!!$F1 695
22 TraesCS7A01G208500 chr1D 2454044 2454755 711 False 817.000000 817 87.260000 972 1701 1 chr1D.!!$F1 729

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
803 902 0.179468 GCGGTGGAGTTGGCCTAATA 59.821 55.0 3.32 0.0 0.0 0.98 F
1392 1556 0.671796 TCGACAAGCTCTCCGTTTCA 59.328 50.0 0.00 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1811 0.033366 TGTGCAGCAGCTCTTTCGTA 59.967 50.0 1.76 0.0 42.74 3.43 R
3246 3528 0.176219 TACGGGATAAACAGGTGCGG 59.824 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
185 188 0.980231 GAGACCATGGCCCTCTCTGT 60.980 60.000 21.30 0.00 0.00 3.41
254 257 0.541764 GAGGCGATGGAGGAGGATCT 60.542 60.000 0.00 0.00 33.73 2.75
310 314 2.282040 GCTGGTCCTGCACTGCTT 60.282 61.111 15.42 0.00 0.00 3.91
488 492 1.423056 CCTACGTCGACCTCGTCAC 59.577 63.158 10.58 0.00 41.72 3.67
617 622 9.884636 GTTAATTATGAAACTGGGCCTTTTAAT 57.115 29.630 4.53 5.72 0.00 1.40
672 677 8.943002 CCGACCCCTATATATGTTTTATGTTTC 58.057 37.037 0.00 0.00 0.00 2.78
719 818 1.931172 AGTTTGACAAAGTCGGACACG 59.069 47.619 11.27 0.51 42.74 4.49
721 820 0.460722 TTGACAAAGTCGGACACGGA 59.539 50.000 11.27 0.00 41.39 4.69
727 826 1.450531 AAGTCGGACACGGACGAACT 61.451 55.000 11.27 0.00 41.17 3.01
743 842 2.749839 CTCATCGGCGCCCCAAAA 60.750 61.111 23.46 1.16 0.00 2.44
744 843 2.282532 TCATCGGCGCCCCAAAAA 60.283 55.556 23.46 0.00 0.00 1.94
755 854 3.118775 GCGCCCCAAAAAGATAAAATCCT 60.119 43.478 0.00 0.00 0.00 3.24
757 856 4.680440 CGCCCCAAAAAGATAAAATCCTGG 60.680 45.833 0.00 0.00 0.00 4.45
762 861 6.885918 CCCAAAAAGATAAAATCCTGGCAATT 59.114 34.615 0.00 0.00 0.00 2.32
764 863 7.607223 CCAAAAAGATAAAATCCTGGCAATTCA 59.393 33.333 0.00 0.00 0.00 2.57
771 870 0.976641 TCCTGGCAATTCAGACGTCT 59.023 50.000 13.58 13.58 36.93 4.18
800 899 4.077184 CGCGGTGGAGTTGGCCTA 62.077 66.667 3.32 0.00 0.00 3.93
801 900 2.349755 GCGGTGGAGTTGGCCTAA 59.650 61.111 3.32 0.00 0.00 2.69
802 901 1.077716 GCGGTGGAGTTGGCCTAAT 60.078 57.895 3.32 0.00 0.00 1.73
803 902 0.179468 GCGGTGGAGTTGGCCTAATA 59.821 55.000 3.32 0.00 0.00 0.98
804 903 1.407712 GCGGTGGAGTTGGCCTAATAA 60.408 52.381 3.32 0.00 0.00 1.40
805 904 2.285977 CGGTGGAGTTGGCCTAATAAC 58.714 52.381 3.32 0.00 0.00 1.89
806 905 2.355310 CGGTGGAGTTGGCCTAATAACA 60.355 50.000 3.32 0.00 0.00 2.41
807 906 3.014623 GGTGGAGTTGGCCTAATAACAC 58.985 50.000 3.32 8.76 0.00 3.32
808 907 3.560453 GGTGGAGTTGGCCTAATAACACA 60.560 47.826 18.25 9.46 0.00 3.72
809 908 3.689649 GTGGAGTTGGCCTAATAACACAG 59.310 47.826 3.32 0.00 0.00 3.66
810 909 3.585289 TGGAGTTGGCCTAATAACACAGA 59.415 43.478 3.32 0.00 0.00 3.41
811 910 4.227300 TGGAGTTGGCCTAATAACACAGAT 59.773 41.667 3.32 0.00 0.00 2.90
812 911 4.576463 GGAGTTGGCCTAATAACACAGATG 59.424 45.833 3.32 0.00 0.00 2.90
813 912 3.947834 AGTTGGCCTAATAACACAGATGC 59.052 43.478 3.32 0.00 0.00 3.91
814 913 3.643199 TGGCCTAATAACACAGATGCA 57.357 42.857 3.32 0.00 0.00 3.96
815 914 3.278574 TGGCCTAATAACACAGATGCAC 58.721 45.455 3.32 0.00 0.00 4.57
816 915 3.054434 TGGCCTAATAACACAGATGCACT 60.054 43.478 3.32 0.00 0.00 4.40
817 916 3.947834 GGCCTAATAACACAGATGCACTT 59.052 43.478 0.00 0.00 0.00 3.16
818 917 4.399303 GGCCTAATAACACAGATGCACTTT 59.601 41.667 0.00 0.00 0.00 2.66
819 918 5.105756 GGCCTAATAACACAGATGCACTTTT 60.106 40.000 0.00 0.00 0.00 2.27
820 919 6.094881 GGCCTAATAACACAGATGCACTTTTA 59.905 38.462 0.00 0.00 0.00 1.52
821 920 7.362574 GGCCTAATAACACAGATGCACTTTTAA 60.363 37.037 0.00 0.00 0.00 1.52
822 921 7.484959 GCCTAATAACACAGATGCACTTTTAAC 59.515 37.037 0.00 0.00 0.00 2.01
823 922 7.968405 CCTAATAACACAGATGCACTTTTAACC 59.032 37.037 0.00 0.00 0.00 2.85
824 923 6.892658 ATAACACAGATGCACTTTTAACCA 57.107 33.333 0.00 0.00 0.00 3.67
825 924 5.789643 AACACAGATGCACTTTTAACCAT 57.210 34.783 0.00 0.00 0.00 3.55
826 925 5.789643 ACACAGATGCACTTTTAACCATT 57.210 34.783 0.00 0.00 0.00 3.16
827 926 6.160576 ACACAGATGCACTTTTAACCATTT 57.839 33.333 0.00 0.00 0.00 2.32
828 927 5.984926 ACACAGATGCACTTTTAACCATTTG 59.015 36.000 0.00 0.00 0.00 2.32
829 928 5.406175 CACAGATGCACTTTTAACCATTTGG 59.594 40.000 0.00 0.00 42.17 3.28
830 929 4.931002 CAGATGCACTTTTAACCATTTGGG 59.069 41.667 0.96 0.00 44.81 4.12
831 930 4.837860 AGATGCACTTTTAACCATTTGGGA 59.162 37.500 0.96 0.00 41.15 4.37
832 931 5.484998 AGATGCACTTTTAACCATTTGGGAT 59.515 36.000 0.96 0.00 41.15 3.85
833 932 6.667414 AGATGCACTTTTAACCATTTGGGATA 59.333 34.615 0.96 0.00 41.15 2.59
834 933 6.672266 TGCACTTTTAACCATTTGGGATAA 57.328 33.333 0.96 0.00 41.15 1.75
835 934 7.251321 TGCACTTTTAACCATTTGGGATAAT 57.749 32.000 0.96 0.00 41.15 1.28
836 935 7.102346 TGCACTTTTAACCATTTGGGATAATG 58.898 34.615 0.96 0.00 41.15 1.90
837 936 7.038729 TGCACTTTTAACCATTTGGGATAATGA 60.039 33.333 0.96 0.00 41.15 2.57
857 956 2.121963 AGCCCCAACTCCCACAGA 60.122 61.111 0.00 0.00 0.00 3.41
858 957 1.774217 AGCCCCAACTCCCACAGAA 60.774 57.895 0.00 0.00 0.00 3.02
866 965 1.924731 ACTCCCACAGAACAGATCGA 58.075 50.000 0.00 0.00 0.00 3.59
886 985 1.846124 GGTCCACCTCAGTTCCCCA 60.846 63.158 0.00 0.00 0.00 4.96
902 1001 1.418334 CCCATTCGGTCTCTGGATCT 58.582 55.000 0.00 0.00 31.38 2.75
921 1020 4.612264 TCTACCTACAAGTCAACAACCC 57.388 45.455 0.00 0.00 0.00 4.11
990 1092 4.810661 GCTTCTGCTCGCCGCTCT 62.811 66.667 0.00 0.00 40.11 4.09
1074 1176 3.296709 AACAACGCGAGCGGAGGAT 62.297 57.895 21.69 2.68 44.69 3.24
1248 1381 4.424711 GCGTTCCCCATGGCCTCA 62.425 66.667 6.09 0.00 0.00 3.86
1249 1382 2.438434 CGTTCCCCATGGCCTCAC 60.438 66.667 6.09 0.00 0.00 3.51
1250 1383 2.043953 GTTCCCCATGGCCTCACC 60.044 66.667 6.09 0.00 39.84 4.02
1251 1384 3.346734 TTCCCCATGGCCTCACCC 61.347 66.667 6.09 0.00 37.83 4.61
1392 1556 0.671796 TCGACAAGCTCTCCGTTTCA 59.328 50.000 0.00 0.00 0.00 2.69
1473 1637 1.227527 CACGGTGAGAACCAGCACA 60.228 57.895 0.74 0.00 43.15 4.57
1489 1653 2.125350 CAGGCGAGTTGAGCTCCC 60.125 66.667 12.15 3.59 41.10 4.30
1502 1666 4.129737 CTCCCGCACCGTCGATGT 62.130 66.667 3.52 0.00 0.00 3.06
1503 1667 2.751036 TCCCGCACCGTCGATGTA 60.751 61.111 3.52 0.00 0.00 2.29
1506 1670 1.153901 CCGCACCGTCGATGTACTT 60.154 57.895 3.52 0.00 0.00 2.24
1559 1723 1.095600 CCTGATGTCTTCTCGGACGA 58.904 55.000 0.00 0.00 38.91 4.20
1569 1733 0.964358 TCTCGGACGAGGAGTTTCCC 60.964 60.000 20.17 0.00 42.20 3.97
1614 1778 1.079750 GAGCTTGTCCGTCCTCCAC 60.080 63.158 0.00 0.00 0.00 4.02
1653 1817 1.227031 CCGTGCCGGCTATACGAAA 60.227 57.895 32.09 7.06 41.17 3.46
1659 1823 1.772182 CCGGCTATACGAAAGAGCTG 58.228 55.000 9.90 9.90 41.41 4.24
1662 1826 2.131183 GGCTATACGAAAGAGCTGCTG 58.869 52.381 7.01 0.00 36.43 4.41
1709 1873 5.006941 GCGAAGTTTTAGACAGGTACAAACA 59.993 40.000 0.00 0.00 31.06 2.83
1721 1885 7.016268 AGACAGGTACAAACAGAATCCTCTTTA 59.984 37.037 0.00 0.00 0.00 1.85
1837 2021 3.433615 CAGGTTCTTGTCGATTCTCCAAC 59.566 47.826 0.00 0.00 0.00 3.77
1968 2152 2.593956 GGTGGAGAAGGCCCTCGTT 61.594 63.158 0.00 0.00 34.08 3.85
1969 2153 1.262640 GGTGGAGAAGGCCCTCGTTA 61.263 60.000 0.00 0.00 34.08 3.18
2025 2209 1.531578 GCCTTCGACAGGTTCAAGAAC 59.468 52.381 13.06 4.39 46.07 3.01
2032 2216 3.549423 CGACAGGTTCAAGAACGACTACA 60.549 47.826 6.84 0.00 42.02 2.74
2509 2693 2.333069 CCAAGCTGGAGGAGATATCCA 58.667 52.381 9.50 0.00 44.63 3.41
2517 2701 1.976112 GGAGATATCCACCCTCCGC 59.024 63.158 0.18 0.00 37.35 5.54
2649 2833 3.168604 CGAGTCGAGCAGCACGTG 61.169 66.667 12.28 12.28 0.00 4.49
2946 3130 0.319555 TGTTTGAAGGAGAGGACGCG 60.320 55.000 3.53 3.53 0.00 6.01
2947 3131 0.319641 GTTTGAAGGAGAGGACGCGT 60.320 55.000 13.85 13.85 0.00 6.01
2955 3139 4.814294 GAGGACGCGTCGGGCAAT 62.814 66.667 30.99 13.42 43.84 3.56
2956 3140 4.814294 AGGACGCGTCGGGCAATC 62.814 66.667 30.99 16.32 43.84 2.67
2958 3142 2.890474 GACGCGTCGGGCAATCAT 60.890 61.111 25.19 0.00 43.84 2.45
3012 3225 3.492313 GGATTCTGTGTTCGATTGCAAC 58.508 45.455 0.00 0.00 0.00 4.17
3014 3227 1.234821 TCTGTGTTCGATTGCAACCC 58.765 50.000 0.00 0.00 0.00 4.11
3068 3281 4.159135 GGTCATGAATTTGCAGATCAGGTT 59.841 41.667 0.00 0.00 0.00 3.50
3073 3286 5.559770 TGAATTTGCAGATCAGGTTACAGA 58.440 37.500 0.00 0.00 0.00 3.41
3074 3287 5.412594 TGAATTTGCAGATCAGGTTACAGAC 59.587 40.000 0.00 0.00 0.00 3.51
3082 3295 3.384348 GGTTACAGACCTGGGCGA 58.616 61.111 0.00 0.00 45.55 5.54
3083 3296 1.079336 GGTTACAGACCTGGGCGAC 60.079 63.158 0.00 0.00 45.55 5.19
3084 3297 1.669440 GTTACAGACCTGGGCGACA 59.331 57.895 0.00 0.00 34.19 4.35
3134 3416 2.040544 AAAAGATCGCGGCCTGTGG 61.041 57.895 6.13 0.00 0.00 4.17
3181 3463 1.473278 GTTCTAGACGACTGGACCAGG 59.527 57.143 25.34 11.09 35.51 4.45
3206 3488 0.460109 CACCATCCGCAAGATCGACA 60.460 55.000 0.00 0.00 43.02 4.35
3224 3506 3.740128 ATCGACGCCATGGACAGCC 62.740 63.158 18.40 0.00 0.00 4.85
3244 3526 3.077556 CCCGACCTGGACCTGGAG 61.078 72.222 23.36 15.43 42.00 3.86
3245 3527 3.775654 CCGACCTGGACCTGGAGC 61.776 72.222 23.36 13.25 42.00 4.70
3246 3528 3.775654 CGACCTGGACCTGGAGCC 61.776 72.222 23.36 10.78 0.00 4.70
3247 3529 3.403558 GACCTGGACCTGGAGCCC 61.404 72.222 23.36 6.32 0.00 5.19
3256 3538 4.335647 CTGGAGCCCGCACCTGTT 62.336 66.667 4.76 0.00 0.00 3.16
3257 3539 3.850098 CTGGAGCCCGCACCTGTTT 62.850 63.158 4.76 0.00 0.00 2.83
3258 3540 2.349755 GGAGCCCGCACCTGTTTA 59.650 61.111 0.00 0.00 0.00 2.01
3259 3541 1.077716 GGAGCCCGCACCTGTTTAT 60.078 57.895 0.00 0.00 0.00 1.40
3260 3542 1.095807 GGAGCCCGCACCTGTTTATC 61.096 60.000 0.00 0.00 0.00 1.75
3261 3543 1.077716 AGCCCGCACCTGTTTATCC 60.078 57.895 0.00 0.00 0.00 2.59
3262 3544 2.119029 GCCCGCACCTGTTTATCCC 61.119 63.158 0.00 0.00 0.00 3.85
3263 3545 1.817941 CCCGCACCTGTTTATCCCG 60.818 63.158 0.00 0.00 0.00 5.14
3264 3546 1.078708 CCGCACCTGTTTATCCCGT 60.079 57.895 0.00 0.00 0.00 5.28
3265 3547 0.176219 CCGCACCTGTTTATCCCGTA 59.824 55.000 0.00 0.00 0.00 4.02
3266 3548 1.405797 CCGCACCTGTTTATCCCGTAA 60.406 52.381 0.00 0.00 0.00 3.18
3267 3549 2.348660 CGCACCTGTTTATCCCGTAAA 58.651 47.619 0.00 0.00 0.00 2.01
3321 3603 6.439487 TGCCTCATTCATTAATTAAAGGGGA 58.561 36.000 7.54 0.08 0.00 4.81
3436 3719 0.252927 ACCCAGAGCCTAGCTTCCTT 60.253 55.000 0.00 0.00 39.88 3.36
3632 3917 3.761218 TGGTGTTGATATCGCCAATTTGT 59.239 39.130 0.00 0.00 41.60 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.155167 GGAGACGGGGAAGGCGAT 61.155 66.667 0.00 0.00 0.00 4.58
233 236 3.610669 CCTCCTCCATCGCCTCCG 61.611 72.222 0.00 0.00 0.00 4.63
424 428 2.203728 TGCGTGGTAGACAGGGGT 60.204 61.111 0.00 0.00 35.55 4.95
429 433 4.367023 GGCGGTGCGTGGTAGACA 62.367 66.667 0.00 0.00 0.00 3.41
488 492 1.626654 GCTGGTGTCGTTGTCATCGG 61.627 60.000 3.59 0.00 0.00 4.18
496 500 4.988598 CTGGCCGCTGGTGTCGTT 62.989 66.667 0.00 0.00 0.00 3.85
585 589 9.520515 AGGCCCAGTTTCATAATTAACATATAG 57.479 33.333 0.00 0.00 0.00 1.31
617 622 1.302993 GCCCAGTTTCTACGGCCAA 60.303 57.895 2.24 0.00 0.00 4.52
625 630 1.756538 CCACAAAACAGCCCAGTTTCT 59.243 47.619 0.75 0.00 40.60 2.52
711 810 1.239296 ATGAGTTCGTCCGTGTCCGA 61.239 55.000 0.00 0.00 35.63 4.55
719 818 3.255379 GCGCCGATGAGTTCGTCC 61.255 66.667 0.00 0.00 46.65 4.79
721 820 4.814294 GGGCGCCGATGAGTTCGT 62.814 66.667 22.54 0.00 46.65 3.85
727 826 2.282532 TTTTTGGGGCGCCGATGA 60.283 55.556 22.54 3.38 0.00 2.92
743 842 6.183360 CGTCTGAATTGCCAGGATTTTATCTT 60.183 38.462 0.00 0.00 34.99 2.40
744 843 5.297776 CGTCTGAATTGCCAGGATTTTATCT 59.702 40.000 0.00 0.00 34.99 1.98
755 854 2.254546 AACAGACGTCTGAATTGCCA 57.745 45.000 43.55 0.00 46.59 4.92
757 856 2.350772 CCCAAACAGACGTCTGAATTGC 60.351 50.000 43.55 5.47 46.59 3.56
762 861 1.067846 CGATCCCAAACAGACGTCTGA 60.068 52.381 43.55 25.34 46.59 3.27
764 863 0.389948 GCGATCCCAAACAGACGTCT 60.390 55.000 13.58 13.58 0.00 4.18
771 870 4.690719 ACCGCGCGATCCCAAACA 62.691 61.111 34.63 0.00 0.00 2.83
800 899 7.283625 TGGTTAAAAGTGCATCTGTGTTATT 57.716 32.000 0.00 0.00 0.00 1.40
801 900 6.892658 TGGTTAAAAGTGCATCTGTGTTAT 57.107 33.333 0.00 0.00 0.00 1.89
802 901 6.892658 ATGGTTAAAAGTGCATCTGTGTTA 57.107 33.333 0.00 0.00 0.00 2.41
803 902 5.789643 ATGGTTAAAAGTGCATCTGTGTT 57.210 34.783 0.00 0.00 0.00 3.32
804 903 5.789643 AATGGTTAAAAGTGCATCTGTGT 57.210 34.783 0.00 0.00 0.00 3.72
805 904 5.406175 CCAAATGGTTAAAAGTGCATCTGTG 59.594 40.000 0.00 0.00 0.00 3.66
806 905 5.511202 CCCAAATGGTTAAAAGTGCATCTGT 60.511 40.000 0.00 0.00 0.00 3.41
807 906 4.931002 CCCAAATGGTTAAAAGTGCATCTG 59.069 41.667 0.00 0.00 0.00 2.90
808 907 4.837860 TCCCAAATGGTTAAAAGTGCATCT 59.162 37.500 0.00 0.00 34.77 2.90
809 908 5.146010 TCCCAAATGGTTAAAAGTGCATC 57.854 39.130 0.00 0.00 34.77 3.91
810 909 5.760484 ATCCCAAATGGTTAAAAGTGCAT 57.240 34.783 0.00 0.00 34.77 3.96
811 910 6.672266 TTATCCCAAATGGTTAAAAGTGCA 57.328 33.333 0.00 0.00 34.77 4.57
812 911 7.327214 TCATTATCCCAAATGGTTAAAAGTGC 58.673 34.615 0.00 0.00 37.44 4.40
813 912 9.533253 GATCATTATCCCAAATGGTTAAAAGTG 57.467 33.333 0.00 0.00 37.44 3.16
814 913 9.265862 TGATCATTATCCCAAATGGTTAAAAGT 57.734 29.630 0.00 0.00 37.44 2.66
815 914 9.754382 CTGATCATTATCCCAAATGGTTAAAAG 57.246 33.333 0.00 0.00 37.44 2.27
816 915 8.203485 GCTGATCATTATCCCAAATGGTTAAAA 58.797 33.333 0.00 0.00 37.44 1.52
817 916 7.201992 GGCTGATCATTATCCCAAATGGTTAAA 60.202 37.037 0.00 0.00 37.44 1.52
818 917 6.267471 GGCTGATCATTATCCCAAATGGTTAA 59.733 38.462 0.00 0.00 37.44 2.01
819 918 5.774690 GGCTGATCATTATCCCAAATGGTTA 59.225 40.000 0.00 0.00 37.44 2.85
820 919 4.590222 GGCTGATCATTATCCCAAATGGTT 59.410 41.667 0.00 0.00 37.44 3.67
821 920 4.154942 GGCTGATCATTATCCCAAATGGT 58.845 43.478 0.00 0.00 37.44 3.55
822 921 3.512724 GGGCTGATCATTATCCCAAATGG 59.487 47.826 14.17 0.00 37.44 3.16
823 922 3.512724 GGGGCTGATCATTATCCCAAATG 59.487 47.826 18.38 0.00 38.72 2.32
824 923 3.142597 TGGGGCTGATCATTATCCCAAAT 59.857 43.478 17.66 0.00 41.01 2.32
825 924 2.517553 TGGGGCTGATCATTATCCCAAA 59.482 45.455 17.66 7.56 41.01 3.28
826 925 2.142756 TGGGGCTGATCATTATCCCAA 58.857 47.619 17.66 8.56 41.01 4.12
827 926 1.831835 TGGGGCTGATCATTATCCCA 58.168 50.000 16.63 16.63 41.63 4.37
828 927 2.108952 AGTTGGGGCTGATCATTATCCC 59.891 50.000 12.97 12.97 36.25 3.85
829 928 3.416156 GAGTTGGGGCTGATCATTATCC 58.584 50.000 0.00 0.00 0.00 2.59
830 929 3.416156 GGAGTTGGGGCTGATCATTATC 58.584 50.000 0.00 0.00 0.00 1.75
831 930 2.108952 GGGAGTTGGGGCTGATCATTAT 59.891 50.000 0.00 0.00 0.00 1.28
832 931 1.494721 GGGAGTTGGGGCTGATCATTA 59.505 52.381 0.00 0.00 0.00 1.90
833 932 0.259938 GGGAGTTGGGGCTGATCATT 59.740 55.000 0.00 0.00 0.00 2.57
834 933 0.920763 TGGGAGTTGGGGCTGATCAT 60.921 55.000 0.00 0.00 0.00 2.45
835 934 1.541118 TGGGAGTTGGGGCTGATCA 60.541 57.895 0.00 0.00 0.00 2.92
836 935 1.077429 GTGGGAGTTGGGGCTGATC 60.077 63.158 0.00 0.00 0.00 2.92
837 936 1.852157 TGTGGGAGTTGGGGCTGAT 60.852 57.895 0.00 0.00 0.00 2.90
857 956 1.645710 AGGTGGACCTTCGATCTGTT 58.354 50.000 0.00 0.00 46.09 3.16
858 957 3.383162 AGGTGGACCTTCGATCTGT 57.617 52.632 0.00 0.00 46.09 3.41
886 985 3.603965 AGGTAGATCCAGAGACCGAAT 57.396 47.619 0.00 0.00 37.04 3.34
902 1001 3.712733 ACTGGGTTGTTGACTTGTAGGTA 59.287 43.478 0.00 0.00 0.00 3.08
921 1020 0.037232 GGACCTTGACCCGAAGACTG 60.037 60.000 0.00 0.00 0.00 3.51
990 1092 4.783621 GCGCCCATGCAGAGGTCA 62.784 66.667 0.00 0.00 37.32 4.02
1206 1308 4.718774 TGCATCTCCTTGAGGAAGACTATT 59.281 41.667 0.76 0.00 44.91 1.73
1372 1536 1.272490 TGAAACGGAGAGCTTGTCGAT 59.728 47.619 9.81 0.00 0.00 3.59
1489 1653 1.580704 GTAAAGTACATCGACGGTGCG 59.419 52.381 8.31 0.00 0.00 5.34
1502 1666 1.137404 GAGCCGGACGCGTAAAGTA 59.863 57.895 13.97 0.00 44.76 2.24
1503 1667 2.126189 GAGCCGGACGCGTAAAGT 60.126 61.111 13.97 0.00 44.76 2.66
1559 1723 0.827368 GAGCTCATCGGGAAACTCCT 59.173 55.000 9.40 0.00 36.57 3.69
1647 1811 0.033366 TGTGCAGCAGCTCTTTCGTA 59.967 50.000 1.76 0.00 42.74 3.43
1653 1817 1.958205 GAACGTGTGCAGCAGCTCT 60.958 57.895 1.76 0.00 42.74 4.09
1721 1885 9.525826 AGATCTGTACCTTTCAATCAAGAATTT 57.474 29.630 0.00 0.00 0.00 1.82
1741 1905 3.869246 GCCAAATGCCAAATTCAGATCTG 59.131 43.478 17.07 17.07 0.00 2.90
1767 1951 5.528690 CCAGTTCATCAACTCTGACAGAAAA 59.471 40.000 6.61 0.00 41.24 2.29
1871 2055 3.361794 TCTCATAGCTGATTGACTCGC 57.638 47.619 0.00 0.00 0.00 5.03
1878 2062 1.409064 TCGGCGTTCTCATAGCTGATT 59.591 47.619 6.85 0.00 40.86 2.57
1908 2092 2.029666 CGGATCATGTCCTCCGCC 59.970 66.667 16.86 0.00 46.87 6.13
1955 2139 1.413077 GCATAGTAACGAGGGCCTTCT 59.587 52.381 7.89 4.53 0.00 2.85
2025 2209 1.516161 CCATGGCCATGATGTAGTCG 58.484 55.000 41.32 21.30 41.20 4.18
2032 2216 2.198287 GCTTCGCCATGGCCATGAT 61.198 57.895 41.32 9.82 41.20 2.45
2058 2242 2.223900 TGCGAATCTGAGCAGGATGTAG 60.224 50.000 0.00 0.00 38.59 2.74
2061 2245 3.374506 TGCGAATCTGAGCAGGATG 57.625 52.632 0.00 0.00 38.59 3.51
2265 2449 2.280524 CGGACCTTTGTGACGGCA 60.281 61.111 0.00 0.00 0.00 5.69
2291 2475 4.154347 CCTGCGTCCCAGAGCTCC 62.154 72.222 10.93 0.00 44.64 4.70
2292 2476 4.154347 CCCTGCGTCCCAGAGCTC 62.154 72.222 5.27 5.27 44.64 4.09
2748 2932 1.738830 GTGGCCGCTGTACGCTTTA 60.739 57.895 9.68 0.00 41.76 1.85
2754 2938 2.877582 CGTACGTGGCCGCTGTAC 60.878 66.667 27.18 27.18 37.70 2.90
2829 3013 2.514013 GCCATAAGCACCGACGACG 61.514 63.158 0.00 0.00 42.97 5.12
2890 3074 2.202878 CAGGGTATCGGGCGTGTG 60.203 66.667 0.00 0.00 0.00 3.82
2946 3130 1.230324 GCTAGGAATGATTGCCCGAC 58.770 55.000 0.00 0.00 0.00 4.79
2947 3131 0.836606 TGCTAGGAATGATTGCCCGA 59.163 50.000 0.00 0.00 0.00 5.14
2951 3135 2.290093 GAGCAGTGCTAGGAATGATTGC 59.710 50.000 19.77 6.82 39.88 3.56
2954 3138 2.522836 CGAGCAGTGCTAGGAATGAT 57.477 50.000 19.77 9.36 39.88 2.45
2987 3171 1.927895 ATCGAACACAGAATCCGAGC 58.072 50.000 0.00 0.00 32.60 5.03
3014 3227 0.517316 CCAAGAAAGAAACCGCCTCG 59.483 55.000 0.00 0.00 0.00 4.63
3068 3281 0.965866 CTCTGTCGCCCAGGTCTGTA 60.966 60.000 2.66 0.00 41.83 2.74
3079 3292 4.373116 TTCACCGGCCTCTGTCGC 62.373 66.667 0.00 0.00 38.57 5.19
3080 3293 2.432628 GTTCACCGGCCTCTGTCG 60.433 66.667 0.00 0.00 39.93 4.35
3081 3294 2.047179 GGTTCACCGGCCTCTGTC 60.047 66.667 0.00 0.00 0.00 3.51
3082 3295 2.847234 TGGTTCACCGGCCTCTGT 60.847 61.111 0.00 0.00 39.43 3.41
3083 3296 2.358737 GTGGTTCACCGGCCTCTG 60.359 66.667 0.00 0.00 39.43 3.35
3084 3297 4.003788 CGTGGTTCACCGGCCTCT 62.004 66.667 0.00 0.00 39.43 3.69
3134 3416 0.888285 AGGTGCTTCTGCTGCTTGTC 60.888 55.000 0.00 0.00 40.48 3.18
3181 3463 2.361104 TTGCGGATGGTGAAGCCC 60.361 61.111 0.00 0.00 36.04 5.19
3206 3488 2.202932 GCTGTCCATGGCGTCGAT 60.203 61.111 6.96 0.00 0.00 3.59
3244 3526 2.119029 GGGATAAACAGGTGCGGGC 61.119 63.158 0.00 0.00 0.00 6.13
3245 3527 1.817941 CGGGATAAACAGGTGCGGG 60.818 63.158 0.00 0.00 0.00 6.13
3246 3528 0.176219 TACGGGATAAACAGGTGCGG 59.824 55.000 0.00 0.00 0.00 5.69
3247 3529 2.012937 TTACGGGATAAACAGGTGCG 57.987 50.000 0.00 0.00 0.00 5.34
3316 3598 3.244457 CGACTTAAACCTTGTCTTCCCCT 60.244 47.826 0.00 0.00 0.00 4.79
3321 3603 3.400255 GCTCCGACTTAAACCTTGTCTT 58.600 45.455 0.00 0.00 0.00 3.01
3410 3693 1.001631 TAGGCTCTGGGTGCTAGCA 59.998 57.895 14.93 14.93 38.01 3.49
3436 3719 6.861065 AAGTTATCTTGCGAAACTTGAAGA 57.139 33.333 0.00 0.00 40.85 2.87
3493 3776 9.618890 CCTGGACTATTTGAAATGAGAGAAATA 57.381 33.333 0.00 0.00 0.00 1.40
3632 3917 4.968719 TGGAGGCTGATTAGAGATTGGTTA 59.031 41.667 0.00 0.00 0.00 2.85
3768 4053 1.271707 CCAAAATAGGGTGTGGACGGT 60.272 52.381 0.00 0.00 32.54 4.83


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

AutoCloner maintained by Alex Coulton.