Multiple sequence alignment - TraesCS7A01G092700

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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 TraesCS7A01G092700 chr7A 100.000 2824 0 0 1 2824 56243995 56246818 0.000000e+00 5216.0
1 TraesCS7A01G092700 chr7A 88.266 946 92 12 1887 2824 56739736 56740670 0.000000e+00 1114.0
2 TraesCS7A01G092700 chr7A 95.058 688 28 4 1 688 80985219 80984538 0.000000e+00 1077.0
3 TraesCS7A01G092700 chr7A 94.143 683 36 2 1 683 290934966 290935644 0.000000e+00 1037.0
4 TraesCS7A01G092700 chr7A 95.016 622 22 7 1926 2540 56324953 56325572 0.000000e+00 968.0
5 TraesCS7A01G092700 chr7A 94.212 622 27 7 1926 2540 56449953 56450572 0.000000e+00 941.0
6 TraesCS7A01G092700 chr7A 93.760 609 31 6 1235 1837 56324294 56324901 0.000000e+00 907.0
7 TraesCS7A01G092700 chr7A 93.729 606 32 3 1235 1837 56449299 56449901 0.000000e+00 904.0
8 TraesCS7A01G092700 chr7A 80.544 699 83 39 1136 1797 55922802 55923484 3.270000e-134 488.0
9 TraesCS7A01G092700 chr7A 82.616 581 69 23 1126 1689 55918377 55918942 4.230000e-133 484.0
10 TraesCS7A01G092700 chr7A 81.833 600 84 19 1105 1689 56974838 56975427 5.470000e-132 481.0
11 TraesCS7A01G092700 chr7A 79.431 598 79 32 1092 1661 55930377 55930958 1.590000e-102 383.0
12 TraesCS7A01G092700 chr7A 83.102 432 59 14 1239 1661 56235623 56236049 5.710000e-102 381.0
13 TraesCS7A01G092700 chr7A 90.291 103 8 1 1126 1228 56324155 56324255 1.760000e-27 134.0
14 TraesCS7A01G092700 chr7A 88.288 111 11 1 1126 1236 56235479 56235587 6.350000e-27 132.0
15 TraesCS7A01G092700 chr7A 100.000 30 0 0 852 881 55918199 55918228 3.930000e-04 56.5
16 TraesCS7A01G092700 chr3A 95.882 680 26 1 4 683 710167061 710167738 0.000000e+00 1099.0
17 TraesCS7A01G092700 chr3A 94.729 683 32 2 1 683 146199247 146198569 0.000000e+00 1059.0
18 TraesCS7A01G092700 chr6A 95.468 684 28 3 1 683 181561903 181561222 0.000000e+00 1088.0
19 TraesCS7A01G092700 chr5A 95.315 683 28 2 1 683 522608093 522607415 0.000000e+00 1081.0
20 TraesCS7A01G092700 chr1A 93.869 685 36 3 1 683 555087944 555087264 0.000000e+00 1027.0
21 TraesCS7A01G092700 chr2D 93.824 680 35 5 1 680 21108853 21108181 0.000000e+00 1016.0
22 TraesCS7A01G092700 chr2D 88.387 155 18 0 2149 2303 593512495 593512649 1.340000e-43 187.0
23 TraesCS7A01G092700 chr6D 93.558 683 36 6 1 683 3827192 3827866 0.000000e+00 1011.0
24 TraesCS7A01G092700 chr7D 82.753 603 58 27 1126 1689 53529811 53530406 1.950000e-136 496.0
25 TraesCS7A01G092700 chr7D 81.544 596 92 14 1131 1720 53606176 53606759 2.550000e-130 475.0
26 TraesCS7A01G092700 chr7D 81.754 570 65 29 1112 1660 53699844 53700395 9.290000e-120 440.0
27 TraesCS7A01G092700 chr7D 83.726 467 52 20 1235 1689 53565011 53565465 1.210000e-113 420.0
28 TraesCS7A01G092700 chr7D 80.200 601 80 26 1123 1688 53524562 53525158 5.630000e-112 414.0
29 TraesCS7A01G092700 chr7D 82.828 396 45 19 1311 1687 53539429 53539820 1.620000e-87 333.0
30 TraesCS7A01G092700 chr7D 79.830 352 38 10 725 1050 53557977 53558321 2.830000e-55 226.0
31 TraesCS7A01G092700 chr7D 88.387 155 18 0 2149 2303 629832202 629832356 1.340000e-43 187.0
32 TraesCS7A01G092700 chr7D 87.500 160 20 0 2147 2306 199348850 199349009 4.800000e-43 185.0
33 TraesCS7A01G092700 chr7D 95.536 112 5 0 1686 1797 53565509 53565620 2.240000e-41 180.0
34 TraesCS7A01G092700 chr7D 89.524 105 10 1 779 882 53562390 53562494 6.350000e-27 132.0
35 TraesCS7A01G092700 chr7D 85.841 113 12 3 1982 2090 53565820 53565932 1.780000e-22 117.0
36 TraesCS7A01G092700 chr7D 90.625 64 5 1 680 743 53529370 53529432 1.800000e-12 84.2
37 TraesCS7A01G092700 chr7D 84.524 84 11 2 1280 1362 53705052 53705134 6.480000e-12 82.4
38 TraesCS7A01G092700 chr7D 91.071 56 5 0 680 735 53564483 53564538 3.020000e-10 76.8
39 TraesCS7A01G092700 chr7D 100.000 39 0 0 901 939 53529594 53529632 3.900000e-09 73.1
40 TraesCS7A01G092700 chr7D 95.556 45 1 1 701 745 53557903 53557946 1.400000e-08 71.3
41 TraesCS7A01G092700 chr7D 79.646 113 12 7 829 939 53605913 53606016 1.400000e-08 71.3
42 TraesCS7A01G092700 chr7D 86.207 58 6 2 826 881 53524293 53524350 8.450000e-06 62.1
43 TraesCS7A01G092700 chr4A 81.387 591 64 38 1126 1697 668306119 668306682 9.290000e-120 440.0
44 TraesCS7A01G092700 chr4A 83.613 476 57 19 1235 1697 668285243 668285710 7.230000e-116 427.0
45 TraesCS7A01G092700 chr4A 80.517 580 70 31 1126 1689 668323586 668324138 3.390000e-109 405.0
46 TraesCS7A01G092700 chr4A 79.522 586 70 34 1093 1661 668287990 668288542 3.440000e-99 372.0
47 TraesCS7A01G092700 chr4A 93.720 207 11 1 1887 2093 668306963 668307167 2.730000e-80 309.0
48 TraesCS7A01G092700 chr4A 85.398 226 25 4 2248 2472 668307188 668307406 7.870000e-56 228.0
49 TraesCS7A01G092700 chr4A 86.387 191 20 5 1101 1291 668358795 668358979 1.330000e-48 204.0
50 TraesCS7A01G092700 chr4A 93.701 127 8 0 2698 2824 668311292 668311418 1.030000e-44 191.0
51 TraesCS7A01G092700 chr4A 91.964 112 8 1 1126 1236 668285100 668285211 3.770000e-34 156.0
52 TraesCS7A01G092700 chr4A 78.148 270 30 17 680 939 668284687 668284937 8.150000e-31 145.0
53 TraesCS7A01G092700 chr4A 100.000 45 0 0 697 741 668287590 668287634 1.800000e-12 84.2
54 TraesCS7A01G092700 chr4A 90.625 64 5 1 680 743 668305741 668305803 1.800000e-12 84.2
55 TraesCS7A01G092700 chr4A 84.746 59 6 2 826 881 668277847 668277905 3.930000e-04 56.5
56 TraesCS7A01G092700 chr5D 88.415 164 18 1 2149 2311 461072756 461072593 2.220000e-46 196.0
57 TraesCS7A01G092700 chr3D 88.024 167 19 1 2149 2314 588123555 588123721 2.220000e-46 196.0
58 TraesCS7A01G092700 chr3D 87.730 163 18 2 2152 2314 149764774 149764614 3.710000e-44 189.0
59 TraesCS7A01G092700 chr3D 97.143 35 1 0 769 803 5050885 5050919 3.040000e-05 60.2


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 TraesCS7A01G092700 chr7A 56243995 56246818 2823 False 5216.000000 5216 100.000000 1 2824 1 chr7A.!!$F2 2823
1 TraesCS7A01G092700 chr7A 56739736 56740670 934 False 1114.000000 1114 88.266000 1887 2824 1 chr7A.!!$F3 937
2 TraesCS7A01G092700 chr7A 80984538 80985219 681 True 1077.000000 1077 95.058000 1 688 1 chr7A.!!$R1 687
3 TraesCS7A01G092700 chr7A 290934966 290935644 678 False 1037.000000 1037 94.143000 1 683 1 chr7A.!!$F5 682
4 TraesCS7A01G092700 chr7A 56449299 56450572 1273 False 922.500000 941 93.970500 1235 2540 2 chr7A.!!$F9 1305
5 TraesCS7A01G092700 chr7A 56324155 56325572 1417 False 669.666667 968 93.022333 1126 2540 3 chr7A.!!$F8 1414
6 TraesCS7A01G092700 chr7A 56974838 56975427 589 False 481.000000 481 81.833000 1105 1689 1 chr7A.!!$F4 584
7 TraesCS7A01G092700 chr7A 55930377 55930958 581 False 383.000000 383 79.431000 1092 1661 1 chr7A.!!$F1 569
8 TraesCS7A01G092700 chr7A 55918199 55923484 5285 False 342.833333 488 87.720000 852 1797 3 chr7A.!!$F6 945
9 TraesCS7A01G092700 chr7A 56235479 56236049 570 False 256.500000 381 85.695000 1126 1661 2 chr7A.!!$F7 535
10 TraesCS7A01G092700 chr3A 710167061 710167738 677 False 1099.000000 1099 95.882000 4 683 1 chr3A.!!$F1 679
11 TraesCS7A01G092700 chr3A 146198569 146199247 678 True 1059.000000 1059 94.729000 1 683 1 chr3A.!!$R1 682
12 TraesCS7A01G092700 chr6A 181561222 181561903 681 True 1088.000000 1088 95.468000 1 683 1 chr6A.!!$R1 682
13 TraesCS7A01G092700 chr5A 522607415 522608093 678 True 1081.000000 1081 95.315000 1 683 1 chr5A.!!$R1 682
14 TraesCS7A01G092700 chr1A 555087264 555087944 680 True 1027.000000 1027 93.869000 1 683 1 chr1A.!!$R1 682
15 TraesCS7A01G092700 chr2D 21108181 21108853 672 True 1016.000000 1016 93.824000 1 680 1 chr2D.!!$R1 679
16 TraesCS7A01G092700 chr6D 3827192 3827866 674 False 1011.000000 1011 93.558000 1 683 1 chr6D.!!$F1 682
17 TraesCS7A01G092700 chr7D 53699844 53700395 551 False 440.000000 440 81.754000 1112 1660 1 chr7D.!!$F2 548
18 TraesCS7A01G092700 chr7D 53605913 53606759 846 False 273.150000 475 80.595000 829 1720 2 chr7D.!!$F10 891
19 TraesCS7A01G092700 chr7D 53524293 53525158 865 False 238.050000 414 83.203500 826 1688 2 chr7D.!!$F6 862
20 TraesCS7A01G092700 chr7D 53529370 53530406 1036 False 217.766667 496 91.126000 680 1689 3 chr7D.!!$F7 1009
21 TraesCS7A01G092700 chr4A 668323586 668324138 552 False 405.000000 405 80.517000 1126 1689 1 chr4A.!!$F2 563
22 TraesCS7A01G092700 chr4A 668305741 668311418 5677 False 250.440000 440 88.966200 680 2824 5 chr4A.!!$F5 2144
23 TraesCS7A01G092700 chr4A 668284687 668288542 3855 False 236.840000 427 86.649400 680 1697 5 chr4A.!!$F4 1017

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
820 862 0.179073 AATGAATCAGAGACCGCGGG 60.179 55.0 31.76 11.5 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 9573 0.401356 TGTCAAAGGATGCTCTGCCA 59.599 50.0 0.0 0.0 0.0 4.92 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
49 50 4.778143 GCGCAGTCCGGGGATTGT 62.778 66.667 0.30 0.00 34.84 2.71
78 79 2.047179 GAGAGTCGGGTTGTGGGC 60.047 66.667 0.00 0.00 0.00 5.36
116 117 2.103042 GCTTGGCTCGACGCTTCAT 61.103 57.895 6.78 0.00 39.13 2.57
578 582 1.812571 CTTGTATCAGCCGCTTGGTTT 59.187 47.619 0.00 0.00 34.16 3.27
608 612 6.031751 TGCTTTTCTTGTTAGTTGGTGTTT 57.968 33.333 0.00 0.00 0.00 2.83
620 624 7.339721 TGTTAGTTGGTGTTTTTGTAATCCTGA 59.660 33.333 0.00 0.00 0.00 3.86
627 631 5.239087 GTGTTTTTGTAATCCTGACCGGTTA 59.761 40.000 9.42 2.68 0.00 2.85
643 647 6.104146 ACCGGTTAATGGCTTTGTTAATTT 57.896 33.333 0.00 0.00 0.00 1.82
648 652 9.413048 CGGTTAATGGCTTTGTTAATTTAAAGA 57.587 29.630 11.62 0.00 36.29 2.52
654 658 9.643693 ATGGCTTTGTTAATTTAAAGAGTCATG 57.356 29.630 11.10 0.00 36.29 3.07
655 659 8.637986 TGGCTTTGTTAATTTAAAGAGTCATGT 58.362 29.630 11.62 0.00 36.29 3.21
656 660 9.476202 GGCTTTGTTAATTTAAAGAGTCATGTT 57.524 29.630 11.62 0.00 36.29 2.71
748 790 2.277591 GCACATGCTCCCTGCCAAA 61.278 57.895 0.00 0.00 42.00 3.28
756 798 2.440247 CCCTGCCAAACCCGATCC 60.440 66.667 0.00 0.00 0.00 3.36
757 799 2.354729 CCTGCCAAACCCGATCCA 59.645 61.111 0.00 0.00 0.00 3.41
775 817 6.654793 GATCCATCGATGCCTTATCTTTAC 57.345 41.667 20.25 0.00 33.44 2.01
784 826 3.245087 TGCCTTATCTTTACCCAGTTGCA 60.245 43.478 0.00 0.00 0.00 4.08
788 830 3.508845 ATCTTTACCCAGTTGCAGTGT 57.491 42.857 0.00 0.00 0.00 3.55
797 839 1.867233 CAGTTGCAGTGTAGTGGTCAC 59.133 52.381 0.00 0.00 36.22 3.67
803 845 2.884639 GCAGTGTAGTGGTCACCAAAAT 59.115 45.455 0.00 0.00 34.18 1.82
805 847 4.133820 CAGTGTAGTGGTCACCAAAATGA 58.866 43.478 0.00 0.00 34.18 2.57
813 855 4.761739 GTGGTCACCAAAATGAATCAGAGA 59.238 41.667 0.00 0.00 34.18 3.10
815 857 4.156739 GGTCACCAAAATGAATCAGAGACC 59.843 45.833 0.00 0.00 35.57 3.85
816 858 4.002982 TCACCAAAATGAATCAGAGACCG 58.997 43.478 0.00 0.00 0.00 4.79
817 859 2.749621 ACCAAAATGAATCAGAGACCGC 59.250 45.455 0.00 0.00 0.00 5.68
818 860 2.223112 CCAAAATGAATCAGAGACCGCG 60.223 50.000 0.00 0.00 0.00 6.46
819 861 1.656652 AAATGAATCAGAGACCGCGG 58.343 50.000 26.86 26.86 0.00 6.46
820 862 0.179073 AATGAATCAGAGACCGCGGG 60.179 55.000 31.76 11.50 0.00 6.13
821 863 2.032860 ATGAATCAGAGACCGCGGGG 62.033 60.000 31.76 18.33 40.11 5.73
1012 1131 0.675083 CTCTGCCGCATCTCATCTCT 59.325 55.000 0.00 0.00 0.00 3.10
1017 1147 1.850377 CCGCATCTCATCTCTCACAC 58.150 55.000 0.00 0.00 0.00 3.82
1018 1148 1.135721 CCGCATCTCATCTCTCACACA 59.864 52.381 0.00 0.00 0.00 3.72
1019 1149 2.191802 CGCATCTCATCTCTCACACAC 58.808 52.381 0.00 0.00 0.00 3.82
1040 1170 0.249657 CCGCTACTCATCTTGCCTCC 60.250 60.000 0.00 0.00 0.00 4.30
1041 1171 0.461548 CGCTACTCATCTTGCCTCCA 59.538 55.000 0.00 0.00 0.00 3.86
1045 1175 3.620966 GCTACTCATCTTGCCTCCAACTT 60.621 47.826 0.00 0.00 0.00 2.66
1047 1177 2.290577 ACTCATCTTGCCTCCAACTTCC 60.291 50.000 0.00 0.00 0.00 3.46
1048 1178 1.004745 TCATCTTGCCTCCAACTTCCC 59.995 52.381 0.00 0.00 0.00 3.97
1049 1179 1.005215 CATCTTGCCTCCAACTTCCCT 59.995 52.381 0.00 0.00 0.00 4.20
1051 1181 1.628846 TCTTGCCTCCAACTTCCCTAC 59.371 52.381 0.00 0.00 0.00 3.18
1052 1182 1.630878 CTTGCCTCCAACTTCCCTACT 59.369 52.381 0.00 0.00 0.00 2.57
1053 1183 2.634639 TGCCTCCAACTTCCCTACTA 57.365 50.000 0.00 0.00 0.00 1.82
1054 1184 2.185387 TGCCTCCAACTTCCCTACTAC 58.815 52.381 0.00 0.00 0.00 2.73
1055 1185 2.225547 TGCCTCCAACTTCCCTACTACT 60.226 50.000 0.00 0.00 0.00 2.57
1056 1186 2.431419 GCCTCCAACTTCCCTACTACTC 59.569 54.545 0.00 0.00 0.00 2.59
1057 1187 3.882515 GCCTCCAACTTCCCTACTACTCT 60.883 52.174 0.00 0.00 0.00 3.24
1058 1188 4.354662 CCTCCAACTTCCCTACTACTCTT 58.645 47.826 0.00 0.00 0.00 2.85
1059 1189 4.403113 CCTCCAACTTCCCTACTACTCTTC 59.597 50.000 0.00 0.00 0.00 2.87
1060 1190 4.351127 TCCAACTTCCCTACTACTCTTCC 58.649 47.826 0.00 0.00 0.00 3.46
1061 1191 4.045590 TCCAACTTCCCTACTACTCTTCCT 59.954 45.833 0.00 0.00 0.00 3.36
1062 1192 4.403113 CCAACTTCCCTACTACTCTTCCTC 59.597 50.000 0.00 0.00 0.00 3.71
1063 1193 4.254039 ACTTCCCTACTACTCTTCCTCC 57.746 50.000 0.00 0.00 0.00 4.30
1064 1194 3.859859 ACTTCCCTACTACTCTTCCTCCT 59.140 47.826 0.00 0.00 0.00 3.69
1065 1195 3.955524 TCCCTACTACTCTTCCTCCTG 57.044 52.381 0.00 0.00 0.00 3.86
1066 1196 2.091775 TCCCTACTACTCTTCCTCCTGC 60.092 54.545 0.00 0.00 0.00 4.85
1067 1197 2.091555 CCCTACTACTCTTCCTCCTGCT 60.092 54.545 0.00 0.00 0.00 4.24
1068 1198 2.955660 CCTACTACTCTTCCTCCTGCTG 59.044 54.545 0.00 0.00 0.00 4.41
1069 1199 1.190643 ACTACTCTTCCTCCTGCTGC 58.809 55.000 0.00 0.00 0.00 5.25
1070 1200 0.463620 CTACTCTTCCTCCTGCTGCC 59.536 60.000 0.00 0.00 0.00 4.85
1071 1201 1.323271 TACTCTTCCTCCTGCTGCCG 61.323 60.000 0.00 0.00 0.00 5.69
1072 1202 4.087892 TCTTCCTCCTGCTGCCGC 62.088 66.667 0.00 0.00 0.00 6.53
1073 1203 4.093291 CTTCCTCCTGCTGCCGCT 62.093 66.667 0.70 0.00 36.97 5.52
1074 1204 3.618780 CTTCCTCCTGCTGCCGCTT 62.619 63.158 0.70 0.00 36.97 4.68
1075 1205 3.907260 TTCCTCCTGCTGCCGCTTG 62.907 63.158 0.70 0.00 36.97 4.01
1078 1208 3.670637 CTCCTGCTGCCGCTTGCTA 62.671 63.158 0.70 0.00 42.00 3.49
1079 1209 3.503363 CCTGCTGCCGCTTGCTAC 61.503 66.667 0.70 0.00 42.00 3.58
1080 1210 2.435586 CTGCTGCCGCTTGCTACT 60.436 61.111 0.70 0.00 42.00 2.57
1081 1211 1.153568 CTGCTGCCGCTTGCTACTA 60.154 57.895 0.70 0.00 42.00 1.82
1082 1212 1.150567 CTGCTGCCGCTTGCTACTAG 61.151 60.000 0.70 0.00 42.00 2.57
1083 1213 1.153549 GCTGCCGCTTGCTACTAGT 60.154 57.895 0.00 0.00 42.00 2.57
1084 1214 0.741221 GCTGCCGCTTGCTACTAGTT 60.741 55.000 0.00 0.00 42.00 2.24
1085 1215 1.281899 CTGCCGCTTGCTACTAGTTC 58.718 55.000 0.00 0.00 42.00 3.01
1086 1216 0.606096 TGCCGCTTGCTACTAGTTCA 59.394 50.000 0.00 0.00 42.00 3.18
1087 1217 1.000145 GCCGCTTGCTACTAGTTCAC 59.000 55.000 0.00 0.00 36.87 3.18
1088 1218 1.404315 GCCGCTTGCTACTAGTTCACT 60.404 52.381 0.00 0.00 36.87 3.41
1089 1219 2.931320 GCCGCTTGCTACTAGTTCACTT 60.931 50.000 0.00 0.00 36.87 3.16
1090 1220 3.326747 CCGCTTGCTACTAGTTCACTTT 58.673 45.455 0.00 0.00 0.00 2.66
1108 1241 5.710567 TCACTTTCTTCACTAGCTAGCTACA 59.289 40.000 20.67 3.45 0.00 2.74
1124 1257 3.069729 AGCTACAAGTTCACTTCCTTCGT 59.930 43.478 0.00 0.00 33.11 3.85
1252 1441 2.159085 GCCTGCCGTTCTGTTCTAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
1294 1496 2.288666 GTCTGTGCTGAAACTTGGTGA 58.711 47.619 0.00 0.00 0.00 4.02
1406 6042 3.867493 GCCCACCGTAAGTACTTCATTAC 59.133 47.826 12.39 3.70 0.00 1.89
1604 6346 0.326904 AGACCATCCTCTCCATGGCA 60.327 55.000 6.96 0.00 44.32 4.92
1663 9272 6.231211 TCAAGAACACCTCCTTCAACTAATC 58.769 40.000 0.00 0.00 0.00 1.75
1741 9402 3.123620 GCGAGGCTTGCAGACAGG 61.124 66.667 21.86 0.00 0.00 4.00
1830 9510 9.672673 AATAATGACTAGCATTTGTACAACTCT 57.327 29.630 8.07 8.08 44.68 3.24
1837 9517 4.580167 AGCATTTGTACAACTCTGCTTCAA 59.420 37.500 23.73 3.43 36.62 2.69
1838 9518 5.067674 AGCATTTGTACAACTCTGCTTCAAA 59.932 36.000 23.73 2.99 36.62 2.69
1841 9521 6.449635 TTTGTACAACTCTGCTTCAAATGT 57.550 33.333 8.07 0.00 0.00 2.71
1842 9522 5.422666 TGTACAACTCTGCTTCAAATGTG 57.577 39.130 0.00 0.00 0.00 3.21
1843 9523 3.996150 ACAACTCTGCTTCAAATGTGG 57.004 42.857 0.00 0.00 0.00 4.17
1845 9525 3.067180 ACAACTCTGCTTCAAATGTGGTG 59.933 43.478 0.00 0.00 0.00 4.17
1847 9527 3.554934 ACTCTGCTTCAAATGTGGTGAA 58.445 40.909 0.00 0.00 33.97 3.18
1858 9552 1.468985 TGTGGTGAACTTGTTGGTGG 58.531 50.000 0.00 0.00 0.00 4.61
1863 9557 3.634448 TGGTGAACTTGTTGGTGGTTATG 59.366 43.478 0.00 0.00 0.00 1.90
1864 9558 3.886505 GGTGAACTTGTTGGTGGTTATGA 59.113 43.478 0.00 0.00 0.00 2.15
1871 9565 7.301868 ACTTGTTGGTGGTTATGATTTGAAT 57.698 32.000 0.00 0.00 0.00 2.57
1875 9569 7.504403 TGTTGGTGGTTATGATTTGAATTGTT 58.496 30.769 0.00 0.00 0.00 2.83
1876 9570 7.655328 TGTTGGTGGTTATGATTTGAATTGTTC 59.345 33.333 0.00 0.00 0.00 3.18
1877 9571 7.295322 TGGTGGTTATGATTTGAATTGTTCA 57.705 32.000 0.00 0.00 38.04 3.18
1878 9572 7.151308 TGGTGGTTATGATTTGAATTGTTCAC 58.849 34.615 0.00 0.00 39.87 3.18
1879 9573 7.015098 TGGTGGTTATGATTTGAATTGTTCACT 59.985 33.333 0.00 0.00 39.87 3.41
1880 9574 7.329226 GGTGGTTATGATTTGAATTGTTCACTG 59.671 37.037 0.00 0.00 39.87 3.66
1882 9576 6.311200 GGTTATGATTTGAATTGTTCACTGGC 59.689 38.462 0.00 0.00 39.87 4.85
1883 9577 4.933505 TGATTTGAATTGTTCACTGGCA 57.066 36.364 0.00 0.00 39.87 4.92
1884 9578 4.873817 TGATTTGAATTGTTCACTGGCAG 58.126 39.130 14.16 14.16 39.87 4.85
1885 9579 4.583907 TGATTTGAATTGTTCACTGGCAGA 59.416 37.500 23.66 0.00 39.87 4.26
1896 9616 0.694771 ACTGGCAGAGCATCCTTTGA 59.305 50.000 23.66 0.00 33.66 2.69
1897 9617 1.093159 CTGGCAGAGCATCCTTTGAC 58.907 55.000 9.42 0.00 33.66 3.18
1968 9692 5.104735 ACCCCACTTTGTTAAATCTTTTGCA 60.105 36.000 0.00 0.00 0.00 4.08
1979 9703 1.600636 CTTTTGCAGACCGGGCTGA 60.601 57.895 41.85 22.83 38.14 4.26
2147 9871 8.361139 TCTTTGACCTTTTAGTTGAAAAACACA 58.639 29.630 0.00 0.00 36.59 3.72
2370 10101 7.282224 TGTCCTAATATTGGTACATGAACTTGC 59.718 37.037 0.00 0.00 39.30 4.01
2386 10117 3.705051 ACTTGCCATGGAAATCTCACAT 58.295 40.909 18.40 0.00 0.00 3.21
2405 10136 6.973843 TCACATGATTTCTCAAAAAGTGGAG 58.026 36.000 0.00 0.00 34.37 3.86
2491 12894 2.956132 TCAAACCTTGGGCAGATTTCA 58.044 42.857 0.00 0.00 0.00 2.69
2574 12977 5.915504 AGCACAAGCATTCAACCATTTGAAA 60.916 36.000 4.04 0.00 45.40 2.69
2585 12988 7.865875 TCAACCATTTGAAATACATTGTTCG 57.134 32.000 0.00 0.00 38.87 3.95
2597 13000 1.784283 CATTGTTCGCCAAACGGAAAC 59.216 47.619 0.00 0.00 43.89 2.78
2650 13279 4.141251 GGATCCCCATACATTACCACAACT 60.141 45.833 0.00 0.00 0.00 3.16
2695 13324 4.338379 ACTCCTTGTACTTGTGTTCTCC 57.662 45.455 0.00 0.00 0.00 3.71
2708 14101 3.325425 TGTGTTCTCCGGGAATGTAGAAA 59.675 43.478 0.00 0.00 36.24 2.52
2719 14112 8.895737 TCCGGGAATGTAGAAAAATAATACAAC 58.104 33.333 0.00 0.00 33.44 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.435970 TCTCTCGCCGCCCCTACA 62.436 66.667 0.00 0.00 0.00 2.74
49 50 4.124943 ACTCTCTCGCCGCCCCTA 62.125 66.667 0.00 0.00 0.00 3.53
78 79 2.268920 CCACCCTCCACCATCACG 59.731 66.667 0.00 0.00 0.00 4.35
116 117 2.037871 GCCACCGAAGAAAAGGCAA 58.962 52.632 0.00 0.00 44.59 4.52
578 582 7.875554 ACCAACTAACAAGAAAAGCAAAAAGAA 59.124 29.630 0.00 0.00 0.00 2.52
608 612 4.944930 CCATTAACCGGTCAGGATTACAAA 59.055 41.667 8.04 0.00 45.00 2.83
620 624 5.731957 AATTAACAAAGCCATTAACCGGT 57.268 34.783 0.00 0.00 0.00 5.28
643 647 5.010617 GGCCCAAGAAAAACATGACTCTTTA 59.989 40.000 0.00 0.00 0.00 1.85
648 652 2.962859 AGGCCCAAGAAAAACATGACT 58.037 42.857 0.00 0.00 0.00 3.41
649 653 3.653344 GAAGGCCCAAGAAAAACATGAC 58.347 45.455 0.00 0.00 0.00 3.06
650 654 2.295909 CGAAGGCCCAAGAAAAACATGA 59.704 45.455 0.00 0.00 0.00 3.07
651 655 2.035832 ACGAAGGCCCAAGAAAAACATG 59.964 45.455 0.00 0.00 0.00 3.21
652 656 2.316108 ACGAAGGCCCAAGAAAAACAT 58.684 42.857 0.00 0.00 0.00 2.71
653 657 1.770294 ACGAAGGCCCAAGAAAAACA 58.230 45.000 0.00 0.00 0.00 2.83
654 658 2.361119 AGAACGAAGGCCCAAGAAAAAC 59.639 45.455 0.00 0.00 0.00 2.43
655 659 2.661718 AGAACGAAGGCCCAAGAAAAA 58.338 42.857 0.00 0.00 0.00 1.94
656 660 2.358322 AGAACGAAGGCCCAAGAAAA 57.642 45.000 0.00 0.00 0.00 2.29
657 661 3.495434 TTAGAACGAAGGCCCAAGAAA 57.505 42.857 0.00 0.00 0.00 2.52
694 698 1.068541 GTTTTGTTGGCGATCTGTCCC 60.069 52.381 0.00 0.00 0.00 4.46
695 699 1.399727 CGTTTTGTTGGCGATCTGTCC 60.400 52.381 0.00 0.00 0.00 4.02
696 700 1.399727 CCGTTTTGTTGGCGATCTGTC 60.400 52.381 0.00 0.00 0.00 3.51
704 708 2.338620 GCCCTCCGTTTTGTTGGC 59.661 61.111 0.00 0.00 0.00 4.52
756 798 4.641396 TGGGTAAAGATAAGGCATCGATG 58.359 43.478 21.27 21.27 38.81 3.84
757 799 4.348168 ACTGGGTAAAGATAAGGCATCGAT 59.652 41.667 0.00 0.00 38.81 3.59
760 802 4.036852 GCAACTGGGTAAAGATAAGGCATC 59.963 45.833 0.00 0.00 0.00 3.91
767 809 4.634012 ACACTGCAACTGGGTAAAGATA 57.366 40.909 0.00 0.00 0.00 1.98
775 817 0.108585 ACCACTACACTGCAACTGGG 59.891 55.000 0.00 0.00 0.00 4.45
784 826 4.431416 TCATTTTGGTGACCACTACACT 57.569 40.909 2.46 0.00 38.20 3.55
788 830 5.875224 TCTGATTCATTTTGGTGACCACTA 58.125 37.500 2.46 0.00 30.78 2.74
797 839 2.223112 CGCGGTCTCTGATTCATTTTGG 60.223 50.000 0.00 0.00 0.00 3.28
803 845 2.721167 CCCCGCGGTCTCTGATTCA 61.721 63.158 26.12 0.00 0.00 2.57
805 847 1.380785 TACCCCGCGGTCTCTGATT 60.381 57.895 26.12 1.15 43.29 2.57
815 857 0.678684 AAAAACCATCCTACCCCGCG 60.679 55.000 0.00 0.00 0.00 6.46
816 858 2.423446 TAAAAACCATCCTACCCCGC 57.577 50.000 0.00 0.00 0.00 6.13
817 859 4.457949 GCATATAAAAACCATCCTACCCCG 59.542 45.833 0.00 0.00 0.00 5.73
818 860 4.457949 CGCATATAAAAACCATCCTACCCC 59.542 45.833 0.00 0.00 0.00 4.95
819 861 4.457949 CCGCATATAAAAACCATCCTACCC 59.542 45.833 0.00 0.00 0.00 3.69
820 862 5.180680 GTCCGCATATAAAAACCATCCTACC 59.819 44.000 0.00 0.00 0.00 3.18
821 863 5.180680 GGTCCGCATATAAAAACCATCCTAC 59.819 44.000 0.00 0.00 0.00 3.18
823 865 4.142038 GGTCCGCATATAAAAACCATCCT 58.858 43.478 0.00 0.00 0.00 3.24
885 933 2.646175 GGATAGATGGCCGGCGCTA 61.646 63.158 22.54 21.01 34.44 4.26
886 934 4.008933 GGATAGATGGCCGGCGCT 62.009 66.667 22.54 19.48 34.44 5.92
888 936 4.742201 CGGGATAGATGGCCGGCG 62.742 72.222 22.54 0.00 0.00 6.46
890 938 4.394712 GGCGGGATAGATGGCCGG 62.395 72.222 0.00 0.00 35.59 6.13
956 1071 4.023707 CCCGATTTATAGGCTGCAAGAAAG 60.024 45.833 0.50 0.00 34.07 2.62
1000 1119 2.928757 GTGTGTGTGAGAGATGAGATGC 59.071 50.000 0.00 0.00 0.00 3.91
1012 1131 0.966179 ATGAGTAGCGGTGTGTGTGA 59.034 50.000 0.00 0.00 0.00 3.58
1017 1147 1.002366 GCAAGATGAGTAGCGGTGTG 58.998 55.000 0.00 0.00 0.00 3.82
1018 1148 0.108138 GGCAAGATGAGTAGCGGTGT 60.108 55.000 0.00 0.00 0.00 4.16
1019 1149 0.176680 AGGCAAGATGAGTAGCGGTG 59.823 55.000 0.00 0.00 0.00 4.94
1040 1170 4.403113 GGAGGAAGAGTAGTAGGGAAGTTG 59.597 50.000 0.00 0.00 0.00 3.16
1041 1171 4.295506 AGGAGGAAGAGTAGTAGGGAAGTT 59.704 45.833 0.00 0.00 0.00 2.66
1045 1175 2.091775 GCAGGAGGAAGAGTAGTAGGGA 60.092 54.545 0.00 0.00 0.00 4.20
1047 1177 2.955660 CAGCAGGAGGAAGAGTAGTAGG 59.044 54.545 0.00 0.00 0.00 3.18
1048 1178 2.360801 GCAGCAGGAGGAAGAGTAGTAG 59.639 54.545 0.00 0.00 0.00 2.57
1049 1179 2.379972 GCAGCAGGAGGAAGAGTAGTA 58.620 52.381 0.00 0.00 0.00 1.82
1051 1181 0.463620 GGCAGCAGGAGGAAGAGTAG 59.536 60.000 0.00 0.00 0.00 2.57
1052 1182 1.323271 CGGCAGCAGGAGGAAGAGTA 61.323 60.000 0.00 0.00 0.00 2.59
1053 1183 2.654079 CGGCAGCAGGAGGAAGAGT 61.654 63.158 0.00 0.00 0.00 3.24
1054 1184 2.186384 CGGCAGCAGGAGGAAGAG 59.814 66.667 0.00 0.00 0.00 2.85
1055 1185 4.087892 GCGGCAGCAGGAGGAAGA 62.088 66.667 3.18 0.00 44.35 2.87
1068 1198 1.000145 GTGAACTAGTAGCAAGCGGC 59.000 55.000 0.00 0.00 45.30 6.53
1069 1199 2.656560 AGTGAACTAGTAGCAAGCGG 57.343 50.000 0.00 0.00 0.00 5.52
1070 1200 4.238514 AGAAAGTGAACTAGTAGCAAGCG 58.761 43.478 0.00 0.00 0.00 4.68
1071 1201 5.696724 TGAAGAAAGTGAACTAGTAGCAAGC 59.303 40.000 0.00 0.00 0.00 4.01
1072 1202 6.926272 AGTGAAGAAAGTGAACTAGTAGCAAG 59.074 38.462 0.00 0.00 0.00 4.01
1073 1203 6.817184 AGTGAAGAAAGTGAACTAGTAGCAA 58.183 36.000 0.00 0.00 0.00 3.91
1074 1204 6.406692 AGTGAAGAAAGTGAACTAGTAGCA 57.593 37.500 0.00 0.00 0.00 3.49
1075 1205 6.528774 GCTAGTGAAGAAAGTGAACTAGTAGC 59.471 42.308 0.00 0.00 41.46 3.58
1076 1206 7.822658 AGCTAGTGAAGAAAGTGAACTAGTAG 58.177 38.462 0.00 0.00 41.46 2.57
1077 1207 7.762588 AGCTAGTGAAGAAAGTGAACTAGTA 57.237 36.000 0.00 0.00 41.46 1.82
1078 1208 6.658188 AGCTAGTGAAGAAAGTGAACTAGT 57.342 37.500 9.25 0.00 41.46 2.57
1079 1209 6.750039 GCTAGCTAGTGAAGAAAGTGAACTAG 59.250 42.308 21.62 0.00 42.03 2.57
1080 1210 6.434652 AGCTAGCTAGTGAAGAAAGTGAACTA 59.565 38.462 17.69 0.00 0.00 2.24
1081 1211 5.245075 AGCTAGCTAGTGAAGAAAGTGAACT 59.755 40.000 17.69 2.60 0.00 3.01
1082 1212 5.474825 AGCTAGCTAGTGAAGAAAGTGAAC 58.525 41.667 17.69 0.26 0.00 3.18
1083 1213 5.730296 AGCTAGCTAGTGAAGAAAGTGAA 57.270 39.130 17.69 0.00 0.00 3.18
1084 1214 5.710567 TGTAGCTAGCTAGTGAAGAAAGTGA 59.289 40.000 24.78 0.00 0.00 3.41
1085 1215 5.955488 TGTAGCTAGCTAGTGAAGAAAGTG 58.045 41.667 24.78 0.00 0.00 3.16
1086 1216 6.209788 ACTTGTAGCTAGCTAGTGAAGAAAGT 59.790 38.462 28.58 22.12 0.00 2.66
1087 1217 6.626302 ACTTGTAGCTAGCTAGTGAAGAAAG 58.374 40.000 28.58 21.70 0.00 2.62
1088 1218 6.591750 ACTTGTAGCTAGCTAGTGAAGAAA 57.408 37.500 28.58 15.08 0.00 2.52
1089 1219 6.208797 TGAACTTGTAGCTAGCTAGTGAAGAA 59.791 38.462 28.58 15.54 0.00 2.52
1090 1220 5.710567 TGAACTTGTAGCTAGCTAGTGAAGA 59.289 40.000 28.58 14.42 0.00 2.87
1108 1241 2.169769 TGGTGACGAAGGAAGTGAACTT 59.830 45.455 0.00 0.00 39.23 2.66
1124 1257 2.650116 GCCGGAGAGAGCTTGGTGA 61.650 63.158 5.05 0.00 0.00 4.02
1252 1441 7.598869 CAGACAGTACAGAAAGCTACAATGTAA 59.401 37.037 0.00 0.00 0.00 2.41
1294 1496 6.774656 GGAATGAACAGAGGGATGTTAATGAT 59.225 38.462 0.00 0.00 43.32 2.45
1406 6042 1.610038 TGCAGAGTGAATGGTTGCTTG 59.390 47.619 0.00 0.00 35.85 4.01
1583 6325 2.050144 GCCATGGAGAGGATGGTCTTA 58.950 52.381 18.40 0.00 42.25 2.10
1679 9291 9.192642 TGCCTGAACATTACAGTACTACTAATA 57.807 33.333 0.00 0.00 34.04 0.98
1830 9510 3.446873 ACAAGTTCACCACATTTGAAGCA 59.553 39.130 0.00 0.00 33.63 3.91
1837 9517 2.430332 CCACCAACAAGTTCACCACATT 59.570 45.455 0.00 0.00 0.00 2.71
1838 9518 2.031120 CCACCAACAAGTTCACCACAT 58.969 47.619 0.00 0.00 0.00 3.21
1841 9521 2.223803 AACCACCAACAAGTTCACCA 57.776 45.000 0.00 0.00 0.00 4.17
1842 9522 3.886505 TCATAACCACCAACAAGTTCACC 59.113 43.478 0.00 0.00 0.00 4.02
1843 9523 5.705609 ATCATAACCACCAACAAGTTCAC 57.294 39.130 0.00 0.00 0.00 3.18
1845 9525 6.744112 TCAAATCATAACCACCAACAAGTTC 58.256 36.000 0.00 0.00 0.00 3.01
1847 9527 6.723298 TTCAAATCATAACCACCAACAAGT 57.277 33.333 0.00 0.00 0.00 3.16
1858 9552 6.867816 TGCCAGTGAACAATTCAAATCATAAC 59.132 34.615 0.00 0.00 42.15 1.89
1863 9557 5.125100 TCTGCCAGTGAACAATTCAAATC 57.875 39.130 0.00 0.00 42.15 2.17
1864 9558 4.560108 GCTCTGCCAGTGAACAATTCAAAT 60.560 41.667 0.00 0.00 42.15 2.32
1871 9565 1.527034 GATGCTCTGCCAGTGAACAA 58.473 50.000 0.00 0.00 0.00 2.83
1875 9569 0.694771 AAAGGATGCTCTGCCAGTGA 59.305 50.000 0.00 0.00 0.00 3.41
1876 9570 0.809385 CAAAGGATGCTCTGCCAGTG 59.191 55.000 0.00 0.00 0.00 3.66
1877 9571 0.694771 TCAAAGGATGCTCTGCCAGT 59.305 50.000 0.00 0.00 0.00 4.00
1878 9572 1.093159 GTCAAAGGATGCTCTGCCAG 58.907 55.000 0.00 0.00 0.00 4.85
1879 9573 0.401356 TGTCAAAGGATGCTCTGCCA 59.599 50.000 0.00 0.00 0.00 4.92
1880 9574 1.674962 GATGTCAAAGGATGCTCTGCC 59.325 52.381 0.00 0.00 0.00 4.85
1882 9576 2.295885 GGGATGTCAAAGGATGCTCTG 58.704 52.381 0.00 0.00 0.00 3.35
1883 9577 1.213926 GGGGATGTCAAAGGATGCTCT 59.786 52.381 0.00 0.00 0.00 4.09
1884 9578 1.213926 AGGGGATGTCAAAGGATGCTC 59.786 52.381 0.00 0.00 0.00 4.26
1885 9579 1.064166 CAGGGGATGTCAAAGGATGCT 60.064 52.381 0.00 0.00 0.00 3.79
1896 9616 2.367512 GGGAGGAGCAGGGGATGT 60.368 66.667 0.00 0.00 0.00 3.06
1897 9617 3.174265 GGGGAGGAGCAGGGGATG 61.174 72.222 0.00 0.00 0.00 3.51
1968 9692 4.787280 CCTCCCTCAGCCCGGTCT 62.787 72.222 0.00 0.00 0.00 3.85
1979 9703 4.345286 AGAGCCACCTGCCTCCCT 62.345 66.667 0.00 0.00 42.71 4.20
2010 9734 8.465999 ACACAACATTTGAAGTGAAAGATTACA 58.534 29.630 11.85 0.00 35.97 2.41
2129 9853 7.749539 AACGGATGTGTTTTTCAACTAAAAG 57.250 32.000 0.00 0.00 38.29 2.27
2147 9871 8.762481 AAAAGGGCTTATATTTAGAAACGGAT 57.238 30.769 0.00 0.00 0.00 4.18
2186 9913 9.292195 TGTCTATATACATCCGAACATAGTTCA 57.708 33.333 10.15 0.00 0.00 3.18
2405 10136 6.098266 AGGGGCCATTTGTAGTAAATGATTTC 59.902 38.462 4.39 2.47 39.36 2.17
2414 10146 3.372241 GCCTAAAGGGGCCATTTGTAGTA 60.372 47.826 25.27 4.68 45.92 1.82
2491 12894 9.487442 TTTGGAGAAATTTTGGCCTATATTAGT 57.513 29.630 3.32 0.00 0.00 2.24
2540 12943 6.151663 TGAATGCTTGTGCTATGCAATTAT 57.848 33.333 0.00 0.00 41.47 1.28
2546 12949 2.094597 TGGTTGAATGCTTGTGCTATGC 60.095 45.455 0.00 0.00 40.48 3.14
2549 12952 4.280425 TCAAATGGTTGAATGCTTGTGCTA 59.720 37.500 0.00 0.00 40.87 3.49
2574 12977 2.428491 TCCGTTTGGCGAACAATGTAT 58.572 42.857 17.41 0.00 44.77 2.29
2581 12984 2.973419 TATGTTTCCGTTTGGCGAAC 57.027 45.000 7.59 7.59 44.77 3.95
2585 12988 3.357166 TGTGTTATGTTTCCGTTTGGC 57.643 42.857 0.00 0.00 34.14 4.52
2597 13000 3.002791 ACGCTGGAGTTGATGTGTTATG 58.997 45.455 0.00 0.00 0.00 1.90
2650 13279 4.850680 AGCGGAAAATGTAGGGATTTGTA 58.149 39.130 0.00 0.00 0.00 2.41
2695 13324 8.605746 TCGTTGTATTATTTTTCTACATTCCCG 58.394 33.333 0.00 0.00 0.00 5.14
2708 14101 7.375053 ACTGTGCCATTTTCGTTGTATTATTT 58.625 30.769 0.00 0.00 0.00 1.40
2719 14112 3.904136 AGAAAGACTGTGCCATTTTCG 57.096 42.857 0.00 0.00 34.01 3.46
2724 14117 4.322567 GAAGAGAAGAAAGACTGTGCCAT 58.677 43.478 0.00 0.00 0.00 4.40
2790 14183 2.811317 GACGCGGACCTGCTTCAG 60.811 66.667 12.47 0.00 33.67 3.02


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

AutoCloner maintained by Alex Coulton.