Multiple sequence alignment - TraesCS7A01G222200

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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 TraesCS7A01G222200 chr7A 100.000 3094 0 0 1 3094 191666180 191663087 0.000000e+00 5714.0
1 TraesCS7A01G222200 chr7A 85.567 776 109 2 1322 2094 152507432 152508207 0.000000e+00 809.0
2 TraesCS7A01G222200 chr7A 88.051 703 53 11 1126 1824 191693785 191694460 0.000000e+00 804.0
3 TraesCS7A01G222200 chr7A 85.116 215 29 2 1001 1212 152084470 152084684 1.870000e-52 217.0
4 TraesCS7A01G222200 chr7A 84.091 220 32 1 994 1210 152507142 152507361 3.130000e-50 209.0
5 TraesCS7A01G222200 chr7A 94.340 53 2 1 2147 2198 191694971 191695023 2.560000e-11 80.5
6 TraesCS7A01G222200 chr7B 87.397 2174 166 57 977 3094 154161983 154159862 0.000000e+00 2398.0
7 TraesCS7A01G222200 chr7B 85.213 798 103 9 1313 2096 113539542 113538746 0.000000e+00 806.0
8 TraesCS7A01G222200 chr7B 89.633 463 18 6 360 806 154162469 154162021 2.080000e-156 562.0
9 TraesCS7A01G222200 chr7B 92.737 358 23 1 5 359 154163013 154162656 5.920000e-142 514.0
10 TraesCS7A01G222200 chr7B 86.705 346 45 1 1793 2138 154178804 154179148 1.740000e-102 383.0
11 TraesCS7A01G222200 chr7B 97.959 147 3 0 826 972 687415326 687415180 3.960000e-64 255.0
12 TraesCS7A01G222200 chr7B 85.253 217 26 4 1000 1210 113802830 113802614 5.190000e-53 219.0
13 TraesCS7A01G222200 chr7B 84.018 219 33 2 994 1210 113922550 113922768 3.130000e-50 209.0
14 TraesCS7A01G222200 chr7B 91.837 49 4 0 2147 2195 154353335 154353383 5.540000e-08 69.4
15 TraesCS7A01G222200 chr7D 94.228 1230 62 7 977 2203 184574652 184573429 0.000000e+00 1869.0
16 TraesCS7A01G222200 chr7D 91.207 671 23 13 158 806 184575346 184574690 0.000000e+00 880.0
17 TraesCS7A01G222200 chr7D 85.057 783 105 3 1324 2094 151769869 151769087 0.000000e+00 787.0
18 TraesCS7A01G222200 chr7D 84.752 787 108 4 1322 2096 151779173 151778387 0.000000e+00 778.0
19 TraesCS7A01G222200 chr7D 92.802 514 32 3 2585 3094 184572636 184572124 0.000000e+00 739.0
20 TraesCS7A01G222200 chr7D 96.078 306 8 3 2238 2540 184572939 184572635 2.140000e-136 496.0
21 TraesCS7A01G222200 chr7D 88.150 346 40 1 1793 2138 184582214 184582558 7.990000e-111 411.0
22 TraesCS7A01G222200 chr7D 92.135 178 10 3 1 174 184575543 184575366 6.630000e-62 248.0
23 TraesCS7A01G222200 chr7D 83.556 225 31 4 994 1212 151824832 151825056 4.040000e-49 206.0
24 TraesCS7A01G222200 chr7D 83.556 225 31 4 994 1212 151931013 151931237 4.040000e-49 206.0
25 TraesCS7A01G222200 chr1A 82.502 1103 165 21 999 2090 539323188 539324273 0.000000e+00 942.0
26 TraesCS7A01G222200 chr1A 96.774 155 5 0 830 984 487698417 487698263 3.060000e-65 259.0
27 TraesCS7A01G222200 chr1A 98.630 146 2 0 830 975 542181655 542181510 3.060000e-65 259.0
28 TraesCS7A01G222200 chrUn 81.412 1119 165 25 994 2094 85701074 85702167 0.000000e+00 874.0
29 TraesCS7A01G222200 chr1D 85.935 775 100 6 1323 2094 439414977 439414209 0.000000e+00 819.0
30 TraesCS7A01G222200 chr2B 98.639 147 2 0 828 974 466189148 466189002 8.510000e-66 261.0
31 TraesCS7A01G222200 chr3A 98.630 146 2 0 832 977 368668562 368668417 3.060000e-65 259.0
32 TraesCS7A01G222200 chr3A 99.270 137 1 0 834 970 671285291 671285155 6.630000e-62 248.0
33 TraesCS7A01G222200 chr4B 97.368 152 3 1 830 980 27250511 27250360 1.100000e-64 257.0
34 TraesCS7A01G222200 chr6A 97.945 146 2 1 835 980 151458920 151458776 5.120000e-63 252.0
35 TraesCS7A01G222200 chr1B 84.977 213 29 2 1001 1210 596248584 596248372 2.420000e-51 213.0
36 TraesCS7A01G222200 chr5D 92.806 139 9 1 834 972 391727103 391726966 1.880000e-47 200.0


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 TraesCS7A01G222200 chr7A 191663087 191666180 3093 True 5714.00 5714 100.000000 1 3094 1 chr7A.!!$R1 3093
1 TraesCS7A01G222200 chr7A 152507142 152508207 1065 False 509.00 809 84.829000 994 2094 2 chr7A.!!$F2 1100
2 TraesCS7A01G222200 chr7A 191693785 191695023 1238 False 442.25 804 91.195500 1126 2198 2 chr7A.!!$F3 1072
3 TraesCS7A01G222200 chr7B 154159862 154163013 3151 True 1158.00 2398 89.922333 5 3094 3 chr7B.!!$R4 3089
4 TraesCS7A01G222200 chr7B 113538746 113539542 796 True 806.00 806 85.213000 1313 2096 1 chr7B.!!$R1 783
5 TraesCS7A01G222200 chr7D 184572124 184575543 3419 True 846.40 1869 93.290000 1 3094 5 chr7D.!!$R3 3093
6 TraesCS7A01G222200 chr7D 151769087 151769869 782 True 787.00 787 85.057000 1324 2094 1 chr7D.!!$R1 770
7 TraesCS7A01G222200 chr7D 151778387 151779173 786 True 778.00 778 84.752000 1322 2096 1 chr7D.!!$R2 774
8 TraesCS7A01G222200 chr1A 539323188 539324273 1085 False 942.00 942 82.502000 999 2090 1 chr1A.!!$F1 1091
9 TraesCS7A01G222200 chrUn 85701074 85702167 1093 False 874.00 874 81.412000 994 2094 1 chrUn.!!$F1 1100
10 TraesCS7A01G222200 chr1D 439414209 439414977 768 True 819.00 819 85.935000 1323 2094 1 chr1D.!!$R1 771

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
927 1180 0.108520 TTAAACTGTAGCTCCGGCCG 60.109 55.0 21.04 21.04 39.73 6.13 F
952 1205 0.253610 GGAGAGAGTCGAGGAGTGGA 59.746 60.0 0.00 0.00 0.00 4.02 F
956 1209 0.393808 AGAGTCGAGGAGTGGAGAGC 60.394 60.0 0.00 0.00 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2137 0.441533 GACAGCATGCTCTTGTCGTG 59.558 55.000 19.68 7.55 42.53 4.35 R
2047 2534 0.753848 TATGTCTCCATCACGGCCGA 60.754 55.000 35.90 11.57 32.29 5.54 R
2840 3878 1.670811 CTTGTTTTCCTCTGCACGTGT 59.329 47.619 18.38 0.00 0.00 4.49 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 32 1.064979 GTCCTTCCTCTCGTCTCCTCT 60.065 57.143 0.00 0.00 0.00 3.69
47 52 4.981812 TCTAGACACTTATCCTGCCGATA 58.018 43.478 0.00 0.00 31.92 2.92
147 152 6.017440 TGTTTATCAGGCAGCGAATTATAACC 60.017 38.462 0.00 0.00 0.00 2.85
174 179 6.426633 TGTCTGTCAAATAACCAGTGTACATG 59.573 38.462 0.00 0.00 0.00 3.21
175 180 5.411361 TCTGTCAAATAACCAGTGTACATGC 59.589 40.000 0.00 0.00 0.00 4.06
201 242 1.963515 GGTCTGCAGGTTGTTCCAAAT 59.036 47.619 15.13 0.00 39.02 2.32
342 386 1.555075 TCACCCAAGAATTCCTCCTCG 59.445 52.381 0.65 0.00 0.00 4.63
379 609 0.458889 TATTCCCTTGGCGACGAACG 60.459 55.000 0.00 0.00 45.66 3.95
408 638 4.051167 TGGCCAGCCACATGGAGG 62.051 66.667 7.43 3.78 43.57 4.30
437 667 5.999044 TCCCTTCGTCTATTACTGTACTCT 58.001 41.667 0.00 0.00 0.00 3.24
482 716 3.682292 ATTGCCTTCCCGTCCGCTC 62.682 63.158 0.00 0.00 0.00 5.03
518 753 3.244215 CGGGCAAGATGACATAGGTACAT 60.244 47.826 0.00 0.00 0.00 2.29
752 998 1.315690 CGTAATCAGCGGTCCTCCTA 58.684 55.000 0.00 0.00 0.00 2.94
769 1015 9.091220 GGTCCTCCTAACACATCTATAAATACT 57.909 37.037 0.00 0.00 0.00 2.12
795 1041 3.470709 ACTGCAAGGACATATCAATCCG 58.529 45.455 0.00 0.00 40.20 4.18
796 1042 3.118261 ACTGCAAGGACATATCAATCCGT 60.118 43.478 0.00 0.00 40.20 4.69
801 1047 3.469008 GGACATATCAATCCGTCCACA 57.531 47.619 0.00 0.00 45.96 4.17
806 1052 4.511454 ACATATCAATCCGTCCACATTTCG 59.489 41.667 0.00 0.00 0.00 3.46
807 1053 2.753055 TCAATCCGTCCACATTTCGA 57.247 45.000 0.00 0.00 0.00 3.71
808 1054 2.616960 TCAATCCGTCCACATTTCGAG 58.383 47.619 0.00 0.00 0.00 4.04
809 1055 1.062587 CAATCCGTCCACATTTCGAGC 59.937 52.381 0.00 0.00 0.00 5.03
810 1056 0.537188 ATCCGTCCACATTTCGAGCT 59.463 50.000 0.00 0.00 0.00 4.09
822 1075 6.019479 CCACATTTCGAGCTTAGATCACTTAC 60.019 42.308 0.00 0.00 0.00 2.34
828 1081 5.594725 TCGAGCTTAGATCACTTACCAATCT 59.405 40.000 0.00 0.00 34.29 2.40
830 1083 6.858993 CGAGCTTAGATCACTTACCAATCTAC 59.141 42.308 0.00 0.00 33.02 2.59
832 1085 8.312669 AGCTTAGATCACTTACCAATCTACTT 57.687 34.615 0.00 0.00 33.02 2.24
833 1086 9.422681 AGCTTAGATCACTTACCAATCTACTTA 57.577 33.333 0.00 0.00 33.02 2.24
834 1087 9.685828 GCTTAGATCACTTACCAATCTACTTAG 57.314 37.037 0.00 0.00 33.02 2.18
836 1089 7.056844 AGATCACTTACCAATCTACTTAGGC 57.943 40.000 0.00 0.00 0.00 3.93
837 1090 5.609533 TCACTTACCAATCTACTTAGGCC 57.390 43.478 0.00 0.00 0.00 5.19
838 1091 4.407945 TCACTTACCAATCTACTTAGGCCC 59.592 45.833 0.00 0.00 0.00 5.80
839 1092 4.409247 CACTTACCAATCTACTTAGGCCCT 59.591 45.833 0.00 0.00 0.00 5.19
840 1093 4.409247 ACTTACCAATCTACTTAGGCCCTG 59.591 45.833 0.00 0.00 0.00 4.45
841 1094 2.846950 ACCAATCTACTTAGGCCCTGT 58.153 47.619 0.00 0.00 0.00 4.00
842 1095 3.190439 ACCAATCTACTTAGGCCCTGTT 58.810 45.455 0.00 0.00 0.00 3.16
843 1096 3.200165 ACCAATCTACTTAGGCCCTGTTC 59.800 47.826 0.00 0.00 0.00 3.18
844 1097 3.458189 CAATCTACTTAGGCCCTGTTCG 58.542 50.000 0.00 0.00 0.00 3.95
845 1098 1.481871 TCTACTTAGGCCCTGTTCGG 58.518 55.000 0.00 0.00 0.00 4.30
867 1120 4.496336 GGCCCAGCTCCGCAGAAT 62.496 66.667 0.00 0.00 0.00 2.40
868 1121 2.505982 GCCCAGCTCCGCAGAATA 59.494 61.111 0.00 0.00 0.00 1.75
869 1122 1.889573 GCCCAGCTCCGCAGAATAC 60.890 63.158 0.00 0.00 0.00 1.89
870 1123 1.592669 CCCAGCTCCGCAGAATACG 60.593 63.158 0.00 0.00 0.00 3.06
871 1124 1.437573 CCAGCTCCGCAGAATACGA 59.562 57.895 0.00 0.00 0.00 3.43
872 1125 0.596083 CCAGCTCCGCAGAATACGAG 60.596 60.000 0.00 0.00 0.00 4.18
873 1126 0.596083 CAGCTCCGCAGAATACGAGG 60.596 60.000 0.00 0.00 0.00 4.63
874 1127 0.752009 AGCTCCGCAGAATACGAGGA 60.752 55.000 0.00 0.00 0.00 3.71
875 1128 0.315568 GCTCCGCAGAATACGAGGAT 59.684 55.000 0.00 0.00 0.00 3.24
876 1129 1.667467 GCTCCGCAGAATACGAGGATC 60.667 57.143 0.00 0.00 0.00 3.36
877 1130 1.883275 CTCCGCAGAATACGAGGATCT 59.117 52.381 0.00 0.00 0.00 2.75
878 1131 1.609072 TCCGCAGAATACGAGGATCTG 59.391 52.381 0.00 0.00 42.70 2.90
881 1134 2.057503 CAGAATACGAGGATCTGCGG 57.942 55.000 11.33 0.00 34.72 5.69
882 1135 1.609072 CAGAATACGAGGATCTGCGGA 59.391 52.381 0.00 0.00 34.72 5.54
883 1136 1.883275 AGAATACGAGGATCTGCGGAG 59.117 52.381 0.00 0.00 0.00 4.63
884 1137 1.609555 GAATACGAGGATCTGCGGAGT 59.390 52.381 3.10 3.21 0.00 3.85
885 1138 2.563261 ATACGAGGATCTGCGGAGTA 57.437 50.000 3.10 0.00 0.00 2.59
886 1139 1.590932 TACGAGGATCTGCGGAGTAC 58.409 55.000 3.10 0.00 0.00 2.73
887 1140 1.102222 ACGAGGATCTGCGGAGTACC 61.102 60.000 3.10 8.81 0.00 3.34
888 1141 0.820074 CGAGGATCTGCGGAGTACCT 60.820 60.000 19.53 19.53 0.00 3.08
889 1142 0.955905 GAGGATCTGCGGAGTACCTC 59.044 60.000 25.08 25.08 36.38 3.85
890 1143 0.553819 AGGATCTGCGGAGTACCTCT 59.446 55.000 15.60 1.83 0.00 3.69
891 1144 1.063567 AGGATCTGCGGAGTACCTCTT 60.064 52.381 15.60 0.00 0.00 2.85
892 1145 1.338655 GGATCTGCGGAGTACCTCTTC 59.661 57.143 3.10 0.00 0.00 2.87
893 1146 1.002251 GATCTGCGGAGTACCTCTTCG 60.002 57.143 3.10 0.00 47.00 3.79
894 1147 1.030488 TCTGCGGAGTACCTCTTCGG 61.030 60.000 3.10 0.00 44.65 4.30
895 1148 2.104530 GCGGAGTACCTCTTCGGC 59.895 66.667 0.00 0.00 44.65 5.54
896 1149 2.806237 CGGAGTACCTCTTCGGCC 59.194 66.667 0.00 0.00 41.13 6.13
897 1150 2.050350 CGGAGTACCTCTTCGGCCA 61.050 63.158 2.24 0.00 41.13 5.36
898 1151 1.516423 GGAGTACCTCTTCGGCCAC 59.484 63.158 2.24 0.00 35.61 5.01
899 1152 0.971447 GGAGTACCTCTTCGGCCACT 60.971 60.000 2.24 0.00 34.87 4.00
900 1153 0.456628 GAGTACCTCTTCGGCCACTC 59.543 60.000 2.24 1.10 39.54 3.51
901 1154 0.971447 AGTACCTCTTCGGCCACTCC 60.971 60.000 2.24 0.00 35.61 3.85
902 1155 1.077805 TACCTCTTCGGCCACTCCA 59.922 57.895 2.24 0.00 35.61 3.86
903 1156 0.325296 TACCTCTTCGGCCACTCCAT 60.325 55.000 2.24 0.00 35.61 3.41
904 1157 0.325296 ACCTCTTCGGCCACTCCATA 60.325 55.000 2.24 0.00 35.61 2.74
905 1158 0.830648 CCTCTTCGGCCACTCCATAA 59.169 55.000 2.24 0.00 34.01 1.90
906 1159 1.417890 CCTCTTCGGCCACTCCATAAT 59.582 52.381 2.24 0.00 34.01 1.28
907 1160 2.158755 CCTCTTCGGCCACTCCATAATT 60.159 50.000 2.24 0.00 34.01 1.40
908 1161 3.545703 CTCTTCGGCCACTCCATAATTT 58.454 45.455 2.24 0.00 34.01 1.82
909 1162 3.947834 CTCTTCGGCCACTCCATAATTTT 59.052 43.478 2.24 0.00 34.01 1.82
910 1163 5.105567 TCTTCGGCCACTCCATAATTTTA 57.894 39.130 2.24 0.00 34.01 1.52
911 1164 5.502079 TCTTCGGCCACTCCATAATTTTAA 58.498 37.500 2.24 0.00 34.01 1.52
912 1165 5.946972 TCTTCGGCCACTCCATAATTTTAAA 59.053 36.000 2.24 0.00 34.01 1.52
913 1166 5.570234 TCGGCCACTCCATAATTTTAAAC 57.430 39.130 2.24 0.00 34.01 2.01
914 1167 5.258051 TCGGCCACTCCATAATTTTAAACT 58.742 37.500 2.24 0.00 34.01 2.66
915 1168 5.124776 TCGGCCACTCCATAATTTTAAACTG 59.875 40.000 2.24 0.00 34.01 3.16
916 1169 5.105917 CGGCCACTCCATAATTTTAAACTGT 60.106 40.000 2.24 0.00 34.01 3.55
917 1170 6.094325 CGGCCACTCCATAATTTTAAACTGTA 59.906 38.462 2.24 0.00 34.01 2.74
918 1171 7.480810 GGCCACTCCATAATTTTAAACTGTAG 58.519 38.462 0.00 0.00 34.01 2.74
919 1172 6.972901 GCCACTCCATAATTTTAAACTGTAGC 59.027 38.462 0.00 0.00 0.00 3.58
920 1173 7.148069 GCCACTCCATAATTTTAAACTGTAGCT 60.148 37.037 0.00 0.00 0.00 3.32
921 1174 8.398665 CCACTCCATAATTTTAAACTGTAGCTC 58.601 37.037 0.00 0.00 0.00 4.09
922 1175 8.398665 CACTCCATAATTTTAAACTGTAGCTCC 58.601 37.037 0.00 0.00 0.00 4.70
923 1176 7.280205 ACTCCATAATTTTAAACTGTAGCTCCG 59.720 37.037 0.00 0.00 0.00 4.63
924 1177 6.540914 TCCATAATTTTAAACTGTAGCTCCGG 59.459 38.462 0.00 0.00 0.00 5.14
925 1178 4.696899 AATTTTAAACTGTAGCTCCGGC 57.303 40.909 0.00 0.00 39.06 6.13
926 1179 2.103537 TTTAAACTGTAGCTCCGGCC 57.896 50.000 0.00 0.00 39.73 6.13
927 1180 0.108520 TTAAACTGTAGCTCCGGCCG 60.109 55.000 21.04 21.04 39.73 6.13
928 1181 2.567564 TAAACTGTAGCTCCGGCCGC 62.568 60.000 22.85 6.25 39.73 6.53
930 1183 4.577246 CTGTAGCTCCGGCCGCTC 62.577 72.222 22.85 10.71 38.86 5.03
942 1195 3.213402 CCGCTCCGGGAGAGAGTC 61.213 72.222 27.95 8.32 46.50 3.36
943 1196 3.578272 CGCTCCGGGAGAGAGTCG 61.578 72.222 27.95 16.41 46.50 4.18
944 1197 2.124653 GCTCCGGGAGAGAGTCGA 60.125 66.667 27.95 0.00 46.50 4.20
945 1198 2.184167 GCTCCGGGAGAGAGTCGAG 61.184 68.421 27.95 0.00 46.50 4.04
946 1199 1.525077 CTCCGGGAGAGAGTCGAGG 60.525 68.421 19.57 0.00 46.50 4.63
947 1200 1.973816 CTCCGGGAGAGAGTCGAGGA 61.974 65.000 19.57 0.00 46.50 3.71
948 1201 1.525077 CCGGGAGAGAGTCGAGGAG 60.525 68.421 0.00 0.00 0.00 3.69
949 1202 1.222387 CGGGAGAGAGTCGAGGAGT 59.778 63.158 0.00 0.00 0.00 3.85
950 1203 1.092921 CGGGAGAGAGTCGAGGAGTG 61.093 65.000 0.00 0.00 0.00 3.51
951 1204 0.750182 GGGAGAGAGTCGAGGAGTGG 60.750 65.000 0.00 0.00 0.00 4.00
952 1205 0.253610 GGAGAGAGTCGAGGAGTGGA 59.746 60.000 0.00 0.00 0.00 4.02
953 1206 1.663695 GAGAGAGTCGAGGAGTGGAG 58.336 60.000 0.00 0.00 0.00 3.86
954 1207 1.208535 GAGAGAGTCGAGGAGTGGAGA 59.791 57.143 0.00 0.00 0.00 3.71
955 1208 1.209504 AGAGAGTCGAGGAGTGGAGAG 59.790 57.143 0.00 0.00 0.00 3.20
956 1209 0.393808 AGAGTCGAGGAGTGGAGAGC 60.394 60.000 0.00 0.00 0.00 4.09
957 1210 1.379309 AGTCGAGGAGTGGAGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
958 1211 1.379309 GTCGAGGAGTGGAGAGCCT 60.379 63.158 0.00 0.00 34.31 4.58
959 1212 1.077357 TCGAGGAGTGGAGAGCCTC 60.077 63.158 0.00 0.00 43.73 4.70
967 1220 3.839432 GGAGAGCCTCCGAACGGG 61.839 72.222 13.29 4.35 41.08 5.28
972 1225 4.717313 GCCTCCGAACGGGCCTTT 62.717 66.667 13.29 0.00 42.30 3.11
973 1226 2.983791 CCTCCGAACGGGCCTTTA 59.016 61.111 13.29 0.00 34.94 1.85
974 1227 1.153429 CCTCCGAACGGGCCTTTAG 60.153 63.158 13.29 0.00 34.94 1.85
975 1228 1.595357 CTCCGAACGGGCCTTTAGT 59.405 57.895 13.29 0.00 34.94 2.24
996 1249 4.774726 AGTAGACATCCTTGCTTCTGAAGA 59.225 41.667 21.06 3.76 0.00 2.87
1077 1336 2.124403 GTGGCCCAGCTGGAGATG 60.124 66.667 34.91 18.17 37.39 2.90
1228 1487 3.307059 GGTAAGCACATCTCTCCACACTT 60.307 47.826 0.00 0.00 0.00 3.16
1481 1767 4.409218 GTGTCCTGCGCCGACGTA 62.409 66.667 16.98 1.46 42.83 3.57
1570 1856 4.664677 AGACGGCAGCGTGTCCAC 62.665 66.667 11.67 0.00 35.71 4.02
1745 2055 1.669440 GCTCTACAACACCACCGGA 59.331 57.895 9.46 0.00 0.00 5.14
1815 2137 1.905922 GCTCAAGTGCAAGAGCGTCC 61.906 60.000 17.74 0.00 46.53 4.79
1877 2364 0.824759 GGACCTTCGACACCAGCTAT 59.175 55.000 0.00 0.00 0.00 2.97
1883 2370 1.466856 TCGACACCAGCTATTACCGT 58.533 50.000 0.00 0.00 0.00 4.83
2047 2534 1.714899 GGCAACATCGGCGTGCTTAT 61.715 55.000 17.77 0.00 0.00 1.73
2057 2544 1.591594 CGTGCTTATCGGCCGTGAT 60.592 57.895 27.15 15.20 0.00 3.06
2138 2625 2.675844 CGTGGAACAAGTGTCTGTTGAA 59.324 45.455 0.00 0.00 44.16 2.69
2145 2633 5.009854 ACAAGTGTCTGTTGAAAATTGGG 57.990 39.130 2.30 0.00 39.16 4.12
2559 3565 2.148916 CCGACTATGCGGCAAATAGA 57.851 50.000 15.52 0.00 45.38 1.98
2567 3573 7.042797 ACTATGCGGCAAATAGAATTTTCAT 57.957 32.000 15.52 0.00 32.85 2.57
2569 3575 8.076178 ACTATGCGGCAAATAGAATTTTCATAC 58.924 33.333 15.52 0.00 32.85 2.39
2572 3578 7.093354 TGCGGCAAATAGAATTTTCATACAAA 58.907 30.769 0.00 0.00 0.00 2.83
2573 3579 7.600375 TGCGGCAAATAGAATTTTCATACAAAA 59.400 29.630 0.00 0.00 0.00 2.44
2574 3580 8.110002 GCGGCAAATAGAATTTTCATACAAAAG 58.890 33.333 0.00 0.00 0.00 2.27
2575 3581 9.352784 CGGCAAATAGAATTTTCATACAAAAGA 57.647 29.630 0.00 0.00 0.00 2.52
2588 3594 6.500041 TCATACAAAAGAAAAAGAACCCGTG 58.500 36.000 0.00 0.00 0.00 4.94
2629 3639 1.802960 CCATGCGATCTGGACTATTGC 59.197 52.381 0.00 0.00 35.70 3.56
2790 3804 6.919721 ACACTTAGCTGTGAACAAAGAAAAA 58.080 32.000 10.91 0.00 40.12 1.94
2812 3826 3.106827 TGTGGACTGGAATCAGCTATGA 58.893 45.455 0.00 0.00 44.59 2.15
2896 3950 8.487970 GTGTTGTATCATCATGAGGTATTTACG 58.512 37.037 7.33 0.00 0.00 3.18
3042 4096 2.121689 ACAGGTTGGGCCCACCTA 60.122 61.111 32.88 16.89 41.11 3.08
3045 4099 1.230149 AGGTTGGGCCCACCTATCA 60.230 57.895 32.65 14.98 41.11 2.15
3051 4105 1.763770 GGCCCACCTATCAGGATGG 59.236 63.158 0.00 3.44 37.67 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 32 4.981812 TCTATCGGCAGGATAAGTGTCTA 58.018 43.478 0.00 0.00 37.18 2.59
47 52 7.177878 ACCACAAATTTCAGTTGAGGATATCT 58.822 34.615 7.29 0.00 38.56 1.98
135 140 4.439057 TGACAGACAGGGTTATAATTCGC 58.561 43.478 0.00 0.00 0.00 4.70
136 141 6.978343 TTTGACAGACAGGGTTATAATTCG 57.022 37.500 0.00 0.00 0.00 3.34
147 152 4.389374 ACACTGGTTATTTGACAGACAGG 58.611 43.478 0.00 0.00 36.17 4.00
174 179 0.940126 CAACCTGCAGACCGATATGC 59.060 55.000 17.39 0.00 43.66 3.14
175 180 2.315925 ACAACCTGCAGACCGATATG 57.684 50.000 17.39 5.61 0.00 1.78
342 386 6.943718 AGGGAATAGTAGTATAGCTCTGTGAC 59.056 42.308 0.00 0.00 0.00 3.67
398 628 3.669939 AGGGAATAAACCTCCATGTGG 57.330 47.619 0.00 0.00 34.34 4.17
408 638 9.242477 GTACAGTAATAGACGAAGGGAATAAAC 57.758 37.037 0.00 0.00 0.00 2.01
459 689 1.202651 CGGACGGGAAGGCAATTATCT 60.203 52.381 0.00 0.00 0.00 1.98
518 753 1.065926 GTCCATCACAGCAGGATGACA 60.066 52.381 12.22 0.00 43.80 3.58
525 760 3.190849 CCGCGTCCATCACAGCAG 61.191 66.667 4.92 0.00 0.00 4.24
527 762 3.188786 GACCGCGTCCATCACAGC 61.189 66.667 4.92 0.00 0.00 4.40
558 793 2.931713 AATTAGACGCCGCCGAGACG 62.932 60.000 0.00 0.00 38.29 4.18
559 794 0.804933 AAATTAGACGCCGCCGAGAC 60.805 55.000 0.00 0.00 38.29 3.36
560 795 0.804544 CAAATTAGACGCCGCCGAGA 60.805 55.000 0.00 0.00 38.29 4.04
561 796 1.082117 ACAAATTAGACGCCGCCGAG 61.082 55.000 0.00 0.00 38.29 4.63
562 797 0.671163 AACAAATTAGACGCCGCCGA 60.671 50.000 0.00 0.00 38.29 5.54
563 798 0.167251 AAACAAATTAGACGCCGCCG 59.833 50.000 0.00 0.00 41.14 6.46
564 799 1.789054 CGAAACAAATTAGACGCCGCC 60.789 52.381 0.00 0.00 0.00 6.13
565 800 1.520368 CGAAACAAATTAGACGCCGC 58.480 50.000 0.00 0.00 0.00 6.53
566 801 1.520368 GCGAAACAAATTAGACGCCG 58.480 50.000 0.00 0.00 40.14 6.46
567 802 1.136169 ACGCGAAACAAATTAGACGCC 60.136 47.619 15.93 0.00 42.42 5.68
568 803 2.155802 GACGCGAAACAAATTAGACGC 58.844 47.619 15.93 0.00 42.07 5.19
569 804 3.427516 TGACGCGAAACAAATTAGACG 57.572 42.857 15.93 0.00 0.00 4.18
752 998 7.499232 GCAGTTCCCAGTATTTATAGATGTGTT 59.501 37.037 0.00 0.00 0.00 3.32
769 1015 2.575735 TGATATGTCCTTGCAGTTCCCA 59.424 45.455 0.00 0.00 0.00 4.37
795 1041 4.268884 GTGATCTAAGCTCGAAATGTGGAC 59.731 45.833 0.00 0.00 0.00 4.02
796 1042 4.160439 AGTGATCTAAGCTCGAAATGTGGA 59.840 41.667 0.00 0.00 0.00 4.02
801 1047 6.222038 TGGTAAGTGATCTAAGCTCGAAAT 57.778 37.500 0.00 0.00 0.00 2.17
806 1052 7.947282 AGTAGATTGGTAAGTGATCTAAGCTC 58.053 38.462 0.00 0.00 35.00 4.09
807 1053 7.906199 AGTAGATTGGTAAGTGATCTAAGCT 57.094 36.000 0.00 0.00 35.00 3.74
808 1054 9.685828 CTAAGTAGATTGGTAAGTGATCTAAGC 57.314 37.037 0.00 0.00 35.00 3.09
810 1056 8.639761 GCCTAAGTAGATTGGTAAGTGATCTAA 58.360 37.037 0.00 0.00 35.00 2.10
822 1075 3.741388 CGAACAGGGCCTAAGTAGATTGG 60.741 52.174 5.28 0.00 0.00 3.16
857 1110 1.883275 AGATCCTCGTATTCTGCGGAG 59.117 52.381 0.00 0.00 0.00 4.63
858 1111 1.609072 CAGATCCTCGTATTCTGCGGA 59.391 52.381 0.00 0.00 31.35 5.54
859 1112 2.057503 CAGATCCTCGTATTCTGCGG 57.942 55.000 0.00 0.00 31.35 5.69
862 1115 1.609072 TCCGCAGATCCTCGTATTCTG 59.391 52.381 3.95 0.00 39.87 3.02
863 1116 1.883275 CTCCGCAGATCCTCGTATTCT 59.117 52.381 3.95 0.00 0.00 2.40
864 1117 1.609555 ACTCCGCAGATCCTCGTATTC 59.390 52.381 3.95 0.00 0.00 1.75
865 1118 1.693627 ACTCCGCAGATCCTCGTATT 58.306 50.000 3.95 0.00 0.00 1.89
866 1119 2.152830 GTACTCCGCAGATCCTCGTAT 58.847 52.381 3.95 0.00 0.00 3.06
867 1120 1.590932 GTACTCCGCAGATCCTCGTA 58.409 55.000 3.95 0.00 0.00 3.43
868 1121 1.102222 GGTACTCCGCAGATCCTCGT 61.102 60.000 0.00 0.00 0.00 4.18
869 1122 0.820074 AGGTACTCCGCAGATCCTCG 60.820 60.000 0.00 0.00 39.05 4.63
870 1123 3.119225 AGGTACTCCGCAGATCCTC 57.881 57.895 0.00 0.00 39.05 3.71
882 1135 3.637803 TGGAGTGGCCGAAGAGGTACT 62.638 57.143 0.00 0.00 43.70 2.73
883 1136 1.255667 TGGAGTGGCCGAAGAGGTAC 61.256 60.000 0.00 0.00 43.70 3.34
884 1137 0.325296 ATGGAGTGGCCGAAGAGGTA 60.325 55.000 0.00 0.00 43.70 3.08
885 1138 0.325296 TATGGAGTGGCCGAAGAGGT 60.325 55.000 0.00 0.00 43.70 3.85
886 1139 0.830648 TTATGGAGTGGCCGAAGAGG 59.169 55.000 0.00 0.00 44.97 3.69
887 1140 2.918712 ATTATGGAGTGGCCGAAGAG 57.081 50.000 0.00 0.00 40.66 2.85
888 1141 3.644966 AAATTATGGAGTGGCCGAAGA 57.355 42.857 0.00 0.00 40.66 2.87
889 1142 5.828299 TTAAAATTATGGAGTGGCCGAAG 57.172 39.130 0.00 0.00 40.66 3.79
890 1143 5.712917 AGTTTAAAATTATGGAGTGGCCGAA 59.287 36.000 0.00 0.00 40.66 4.30
891 1144 5.124776 CAGTTTAAAATTATGGAGTGGCCGA 59.875 40.000 0.00 0.00 40.66 5.54
892 1145 5.105917 ACAGTTTAAAATTATGGAGTGGCCG 60.106 40.000 0.00 0.00 40.66 6.13
893 1146 6.280855 ACAGTTTAAAATTATGGAGTGGCC 57.719 37.500 0.00 0.00 37.10 5.36
894 1147 6.972901 GCTACAGTTTAAAATTATGGAGTGGC 59.027 38.462 0.00 0.00 0.00 5.01
895 1148 8.281212 AGCTACAGTTTAAAATTATGGAGTGG 57.719 34.615 0.00 0.00 0.00 4.00
896 1149 8.398665 GGAGCTACAGTTTAAAATTATGGAGTG 58.601 37.037 0.00 0.00 0.00 3.51
897 1150 7.280205 CGGAGCTACAGTTTAAAATTATGGAGT 59.720 37.037 0.00 0.00 0.00 3.85
898 1151 7.254795 CCGGAGCTACAGTTTAAAATTATGGAG 60.255 40.741 0.00 0.00 0.00 3.86
899 1152 6.540914 CCGGAGCTACAGTTTAAAATTATGGA 59.459 38.462 0.00 0.00 0.00 3.41
900 1153 6.725246 CCGGAGCTACAGTTTAAAATTATGG 58.275 40.000 0.00 0.00 0.00 2.74
901 1154 6.199393 GCCGGAGCTACAGTTTAAAATTATG 58.801 40.000 5.05 0.00 35.50 1.90
902 1155 5.298527 GGCCGGAGCTACAGTTTAAAATTAT 59.701 40.000 5.05 0.00 39.73 1.28
903 1156 4.637091 GGCCGGAGCTACAGTTTAAAATTA 59.363 41.667 5.05 0.00 39.73 1.40
904 1157 3.442625 GGCCGGAGCTACAGTTTAAAATT 59.557 43.478 5.05 0.00 39.73 1.82
905 1158 3.014623 GGCCGGAGCTACAGTTTAAAAT 58.985 45.455 5.05 0.00 39.73 1.82
906 1159 2.429478 GGCCGGAGCTACAGTTTAAAA 58.571 47.619 5.05 0.00 39.73 1.52
907 1160 1.673626 CGGCCGGAGCTACAGTTTAAA 60.674 52.381 20.10 0.00 39.73 1.52
908 1161 0.108520 CGGCCGGAGCTACAGTTTAA 60.109 55.000 20.10 0.00 39.73 1.52
909 1162 1.514087 CGGCCGGAGCTACAGTTTA 59.486 57.895 20.10 0.00 39.73 2.01
910 1163 2.264794 CGGCCGGAGCTACAGTTT 59.735 61.111 20.10 0.00 39.73 2.66
911 1164 4.452733 GCGGCCGGAGCTACAGTT 62.453 66.667 29.38 0.00 39.73 3.16
913 1166 4.577246 GAGCGGCCGGAGCTACAG 62.577 72.222 29.38 0.00 46.13 2.74
926 1179 3.578272 CGACTCTCTCCCGGAGCG 61.578 72.222 9.87 3.52 41.60 5.03
927 1180 2.124653 TCGACTCTCTCCCGGAGC 60.125 66.667 9.87 0.00 41.60 4.70
928 1181 1.525077 CCTCGACTCTCTCCCGGAG 60.525 68.421 8.30 8.30 43.12 4.63
929 1182 1.973816 CTCCTCGACTCTCTCCCGGA 61.974 65.000 0.73 0.00 0.00 5.14
930 1183 1.525077 CTCCTCGACTCTCTCCCGG 60.525 68.421 0.00 0.00 0.00 5.73
931 1184 1.092921 CACTCCTCGACTCTCTCCCG 61.093 65.000 0.00 0.00 0.00 5.14
932 1185 0.750182 CCACTCCTCGACTCTCTCCC 60.750 65.000 0.00 0.00 0.00 4.30
933 1186 0.253610 TCCACTCCTCGACTCTCTCC 59.746 60.000 0.00 0.00 0.00 3.71
934 1187 1.208535 TCTCCACTCCTCGACTCTCTC 59.791 57.143 0.00 0.00 0.00 3.20
935 1188 1.209504 CTCTCCACTCCTCGACTCTCT 59.790 57.143 0.00 0.00 0.00 3.10
936 1189 1.663695 CTCTCCACTCCTCGACTCTC 58.336 60.000 0.00 0.00 0.00 3.20
937 1190 0.393808 GCTCTCCACTCCTCGACTCT 60.394 60.000 0.00 0.00 0.00 3.24
938 1191 1.381165 GGCTCTCCACTCCTCGACTC 61.381 65.000 0.00 0.00 0.00 3.36
939 1192 1.379309 GGCTCTCCACTCCTCGACT 60.379 63.158 0.00 0.00 0.00 4.18
940 1193 1.379309 AGGCTCTCCACTCCTCGAC 60.379 63.158 0.00 0.00 33.74 4.20
941 1194 1.077357 GAGGCTCTCCACTCCTCGA 60.077 63.158 7.40 0.00 37.28 4.04
942 1195 3.520402 GAGGCTCTCCACTCCTCG 58.480 66.667 7.40 0.00 37.28 4.63
950 1203 3.839432 CCCGTTCGGAGGCTCTCC 61.839 72.222 15.23 10.35 46.44 3.71
951 1204 4.516195 GCCCGTTCGGAGGCTCTC 62.516 72.222 15.23 3.67 46.14 3.20
956 1209 1.153429 CTAAAGGCCCGTTCGGAGG 60.153 63.158 13.08 0.00 0.00 4.30
957 1210 0.819582 TACTAAAGGCCCGTTCGGAG 59.180 55.000 13.08 3.55 0.00 4.63
958 1211 0.819582 CTACTAAAGGCCCGTTCGGA 59.180 55.000 13.08 0.00 0.00 4.55
959 1212 0.819582 TCTACTAAAGGCCCGTTCGG 59.180 55.000 0.00 4.08 0.00 4.30
960 1213 1.203052 TGTCTACTAAAGGCCCGTTCG 59.797 52.381 0.00 0.00 0.00 3.95
961 1214 3.455327 GATGTCTACTAAAGGCCCGTTC 58.545 50.000 0.00 0.00 0.00 3.95
962 1215 2.169978 GGATGTCTACTAAAGGCCCGTT 59.830 50.000 0.00 0.00 0.00 4.44
963 1216 1.761198 GGATGTCTACTAAAGGCCCGT 59.239 52.381 0.00 0.00 0.00 5.28
964 1217 2.040178 AGGATGTCTACTAAAGGCCCG 58.960 52.381 0.00 0.00 0.00 6.13
965 1218 3.809905 CAAGGATGTCTACTAAAGGCCC 58.190 50.000 0.00 0.00 0.00 5.80
966 1219 3.118223 AGCAAGGATGTCTACTAAAGGCC 60.118 47.826 0.00 0.00 0.00 5.19
967 1220 4.143986 AGCAAGGATGTCTACTAAAGGC 57.856 45.455 0.00 0.00 0.00 4.35
968 1221 5.814705 CAGAAGCAAGGATGTCTACTAAAGG 59.185 44.000 0.00 0.00 0.00 3.11
969 1222 6.634805 TCAGAAGCAAGGATGTCTACTAAAG 58.365 40.000 0.00 0.00 0.00 1.85
970 1223 6.605471 TCAGAAGCAAGGATGTCTACTAAA 57.395 37.500 0.00 0.00 0.00 1.85
971 1224 6.437477 TCTTCAGAAGCAAGGATGTCTACTAA 59.563 38.462 5.15 0.00 0.00 2.24
972 1225 5.952347 TCTTCAGAAGCAAGGATGTCTACTA 59.048 40.000 5.15 0.00 0.00 1.82
973 1226 4.774726 TCTTCAGAAGCAAGGATGTCTACT 59.225 41.667 5.15 0.00 0.00 2.57
974 1227 5.078411 TCTTCAGAAGCAAGGATGTCTAC 57.922 43.478 5.15 0.00 0.00 2.59
975 1228 5.946942 ATCTTCAGAAGCAAGGATGTCTA 57.053 39.130 5.15 0.00 0.00 2.59
996 1249 0.552848 AAGACCCCATCGCCATGAAT 59.447 50.000 0.00 0.00 30.57 2.57
1027 1280 0.394565 GCGAGAACCAGCAGGGATAT 59.605 55.000 0.00 0.00 41.15 1.63
1077 1336 2.755650 CATGACTTGCGGTAGTATCCC 58.244 52.381 0.00 0.00 0.00 3.85
1228 1487 3.067040 CCATCATGATCAATGGAACGCAA 59.933 43.478 18.15 0.00 44.37 4.85
1317 1603 2.683859 CGTCACAGCCCTGCATGTG 61.684 63.158 11.18 11.18 46.52 3.21
1319 1605 3.807538 GCGTCACAGCCCTGCATG 61.808 66.667 0.00 0.00 0.00 4.06
1481 1767 4.457496 CGGGCCATGAGCGTGAGT 62.457 66.667 4.39 0.00 45.17 3.41
1815 2137 0.441533 GACAGCATGCTCTTGTCGTG 59.558 55.000 19.68 7.55 42.53 4.35
1877 2364 1.372004 CTTGGCGACGTGACGGTAA 60.372 57.895 10.66 0.00 0.00 2.85
1925 2412 2.740055 GTGGCGTCAGTGAGCAGG 60.740 66.667 14.02 0.00 34.54 4.85
2047 2534 0.753848 TATGTCTCCATCACGGCCGA 60.754 55.000 35.90 11.57 32.29 5.54
2052 2539 4.655762 TCTTCCTTATGTCTCCATCACG 57.344 45.455 0.00 0.00 32.29 4.35
2057 2544 5.441718 AGCATTTCTTCCTTATGTCTCCA 57.558 39.130 0.00 0.00 0.00 3.86
2567 3573 6.512342 TTCACGGGTTCTTTTTCTTTTGTA 57.488 33.333 0.00 0.00 0.00 2.41
2569 3575 6.367695 ACTTTTCACGGGTTCTTTTTCTTTTG 59.632 34.615 0.00 0.00 0.00 2.44
2572 3578 5.184287 TCACTTTTCACGGGTTCTTTTTCTT 59.816 36.000 0.00 0.00 0.00 2.52
2573 3579 4.703093 TCACTTTTCACGGGTTCTTTTTCT 59.297 37.500 0.00 0.00 0.00 2.52
2574 3580 4.989044 TCACTTTTCACGGGTTCTTTTTC 58.011 39.130 0.00 0.00 0.00 2.29
2575 3581 5.047590 AGTTCACTTTTCACGGGTTCTTTTT 60.048 36.000 0.00 0.00 0.00 1.94
2576 3582 4.461431 AGTTCACTTTTCACGGGTTCTTTT 59.539 37.500 0.00 0.00 0.00 2.27
2580 3586 3.060070 CGTAGTTCACTTTTCACGGGTTC 60.060 47.826 0.00 0.00 0.00 3.62
2583 3589 1.796459 CCGTAGTTCACTTTTCACGGG 59.204 52.381 10.10 0.00 43.90 5.28
2584 3590 1.796459 CCCGTAGTTCACTTTTCACGG 59.204 52.381 10.77 10.77 46.43 4.94
2588 3594 3.249320 GGTTGTCCCGTAGTTCACTTTTC 59.751 47.826 0.00 0.00 0.00 2.29
2629 3639 2.279582 AGACGTTGGATCGTGCTTAG 57.720 50.000 0.00 0.00 44.21 2.18
2664 3674 5.591877 GGGAGTTATCTACGACCTCTTACAA 59.408 44.000 0.00 0.00 0.00 2.41
2790 3804 3.713248 TCATAGCTGATTCCAGTCCACAT 59.287 43.478 0.00 0.00 42.35 3.21
2840 3878 1.670811 CTTGTTTTCCTCTGCACGTGT 59.329 47.619 18.38 0.00 0.00 4.49
2896 3950 8.732746 TCTAGCCCTAAATGTGATAGTTTTTC 57.267 34.615 0.00 0.00 0.00 2.29
2934 3988 3.321497 GTGCTCTGACCAGAAAGTAGTG 58.679 50.000 1.08 0.00 36.94 2.74
2979 4033 6.351711 CAAATCTGACCATCAATACTCTCCA 58.648 40.000 0.00 0.00 0.00 3.86
3042 4096 0.260816 ACAAGCCATGCCATCCTGAT 59.739 50.000 0.00 0.00 0.00 2.90
3045 4099 2.102578 GTAAACAAGCCATGCCATCCT 58.897 47.619 0.00 0.00 0.00 3.24
3051 4105 4.433186 TGTACATGTAAACAAGCCATGC 57.567 40.909 7.25 0.00 39.62 4.06


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

AutoCloner maintained by Alex Coulton.