Multiple sequence alignment - TraesCS5D01G146300

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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 TraesCS5D01G146300 chr5D 100.000 3638 0 0 1 3638 233022787 233019150 0.000000e+00 6719.0
1 TraesCS5D01G146300 chr5D 79.245 159 26 5 3048 3205 320384063 320384215 1.790000e-18 104.0
2 TraesCS5D01G146300 chr5A 92.816 2784 128 33 902 3638 321928483 321931241 0.000000e+00 3967.0
3 TraesCS5D01G146300 chr5B 93.820 1246 52 14 1972 3211 271955436 271956662 0.000000e+00 1851.0
4 TraesCS5D01G146300 chr5B 93.761 1106 35 16 902 1976 271953592 271954694 0.000000e+00 1629.0
5 TraesCS5D01G146300 chr5B 88.088 319 8 3 3208 3508 271956726 271957032 5.780000e-93 351.0
6 TraesCS5D01G146300 chr5B 94.776 134 7 0 3505 3638 271957056 271957189 3.680000e-50 209.0
7 TraesCS5D01G146300 chr2D 93.467 796 34 7 1 791 161360266 161359484 0.000000e+00 1166.0
8 TraesCS5D01G146300 chr2D 81.132 159 23 5 3048 3205 427530337 427530489 1.770000e-23 121.0
9 TraesCS5D01G146300 chr2D 80.357 168 26 5 3048 3214 427540213 427540052 1.770000e-23 121.0
10 TraesCS5D01G146300 chr1B 92.982 798 47 9 4 793 234798286 234799082 0.000000e+00 1155.0
11 TraesCS5D01G146300 chr1B 90.909 187 14 3 1 185 566182922 566182737 7.800000e-62 248.0
12 TraesCS5D01G146300 chr1B 89.894 188 16 3 1 186 58913757 58913571 4.690000e-59 239.0
13 TraesCS5D01G146300 chr6D 91.635 801 46 14 1 791 414116821 414116032 0.000000e+00 1088.0
14 TraesCS5D01G146300 chr6D 84.615 273 24 7 525 791 100198001 100197741 4.660000e-64 255.0
15 TraesCS5D01G146300 chr6B 91.623 764 52 10 34 791 309683700 309684457 0.000000e+00 1046.0
16 TraesCS5D01G146300 chr3B 94.045 487 26 3 49 533 635270178 635270663 0.000000e+00 736.0
17 TraesCS5D01G146300 chr3B 88.889 585 60 4 211 791 586156795 586157378 0.000000e+00 715.0
18 TraesCS5D01G146300 chr2A 86.677 623 62 8 177 791 23980423 23981032 0.000000e+00 671.0
19 TraesCS5D01G146300 chr3D 86.656 622 59 11 177 791 342804610 342804006 0.000000e+00 667.0
20 TraesCS5D01G146300 chr3D 89.894 188 16 3 1 186 342805086 342804900 4.690000e-59 239.0
21 TraesCS5D01G146300 chr7D 84.887 622 61 9 177 791 495709301 495708706 6.720000e-167 597.0
22 TraesCS5D01G146300 chr7D 80.503 159 24 5 3048 3205 598434458 598434610 8.250000e-22 115.0
23 TraesCS5D01G146300 chr4D 84.876 443 43 11 360 793 493929017 493928590 3.360000e-115 425.0
24 TraesCS5D01G146300 chr4D 84.982 273 23 7 525 791 105941875 105941615 1.000000e-65 261.0
25 TraesCS5D01G146300 chr4A 84.687 431 46 8 368 791 660221068 660221485 2.610000e-111 412.0
26 TraesCS5D01G146300 chr7B 89.947 189 15 4 1 186 285338820 285338633 1.310000e-59 241.0
27 TraesCS5D01G146300 chr3A 95.652 46 1 1 2211 2255 296449301 296449256 5.040000e-09 73.1
28 TraesCS5D01G146300 chr2B 89.130 46 5 0 2206 2251 775028677 775028722 1.410000e-04 58.4


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 TraesCS5D01G146300 chr5D 233019150 233022787 3637 True 6719 6719 100.00000 1 3638 1 chr5D.!!$R1 3637
1 TraesCS5D01G146300 chr5A 321928483 321931241 2758 False 3967 3967 92.81600 902 3638 1 chr5A.!!$F1 2736
2 TraesCS5D01G146300 chr5B 271953592 271957189 3597 False 1010 1851 92.61125 902 3638 4 chr5B.!!$F1 2736
3 TraesCS5D01G146300 chr2D 161359484 161360266 782 True 1166 1166 93.46700 1 791 1 chr2D.!!$R1 790
4 TraesCS5D01G146300 chr1B 234798286 234799082 796 False 1155 1155 92.98200 4 793 1 chr1B.!!$F1 789
5 TraesCS5D01G146300 chr6D 414116032 414116821 789 True 1088 1088 91.63500 1 791 1 chr6D.!!$R2 790
6 TraesCS5D01G146300 chr6B 309683700 309684457 757 False 1046 1046 91.62300 34 791 1 chr6B.!!$F1 757
7 TraesCS5D01G146300 chr3B 586156795 586157378 583 False 715 715 88.88900 211 791 1 chr3B.!!$F1 580
8 TraesCS5D01G146300 chr2A 23980423 23981032 609 False 671 671 86.67700 177 791 1 chr2A.!!$F1 614
9 TraesCS5D01G146300 chr3D 342804006 342805086 1080 True 453 667 88.27500 1 791 2 chr3D.!!$R1 790
10 TraesCS5D01G146300 chr7D 495708706 495709301 595 True 597 597 84.88700 177 791 1 chr7D.!!$R1 614

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
839 1191 0.034477 ACATAAAAGGGTCAGCCGGG 60.034 55.0 2.18 0.0 34.97 5.73 F
840 1192 0.034477 CATAAAAGGGTCAGCCGGGT 60.034 55.0 0.00 0.0 34.97 5.28 F
898 1250 0.233590 TCGTCCGCATGTCGTTTTTG 59.766 50.0 8.37 0.0 36.19 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 3148 1.602377 AGCTTTGCTACCGACAAACAC 59.398 47.619 0.00 0.0 36.99 3.32 R
2449 3599 2.289444 CCACGCTTCCTCCTTTACAGAA 60.289 50.000 0.00 0.0 0.00 3.02 R
2769 3921 2.760374 GATGCCGGATCCAGTTAAGAG 58.240 52.381 13.41 0.0 0.00 2.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 9.729023 CAGACTTTTGTGTCAAATACAACATTA 57.271 29.630 0.00 0.00 40.63 1.90
140 142 6.491745 TGGTAGCTTACAACCATCATTTCAAA 59.508 34.615 1.76 0.00 40.84 2.69
205 508 8.629158 TGAGTTAGCATTGATTTTAGTTGTTGT 58.371 29.630 0.00 0.00 0.00 3.32
273 578 7.523709 GCAAGACTGGATTGAGGAACAAAATAA 60.524 37.037 0.00 0.00 42.03 1.40
308 613 7.554476 TGGATGAATCATTGAACGGTATGTTAA 59.446 33.333 0.00 0.00 42.09 2.01
528 834 7.352079 TCTGCTATTGAAGATGTAGTCATGA 57.648 36.000 0.00 0.00 34.06 3.07
536 842 2.884012 AGATGTAGTCATGAGAGGCTCG 59.116 50.000 9.22 0.00 34.06 5.03
566 872 6.935167 ACCAATCCTTTGATTTGGTATCAAC 58.065 36.000 4.82 0.00 39.20 3.18
567 873 6.070824 ACCAATCCTTTGATTTGGTATCAACC 60.071 38.462 4.82 0.00 41.65 3.77
568 874 6.155049 CCAATCCTTTGATTTGGTATCAACCT 59.845 38.462 0.00 0.00 41.75 3.50
569 875 7.310609 CCAATCCTTTGATTTGGTATCAACCTT 60.311 37.037 0.00 0.00 41.75 3.50
570 876 7.797121 ATCCTTTGATTTGGTATCAACCTTT 57.203 32.000 0.00 0.00 46.91 3.11
571 877 6.991938 TCCTTTGATTTGGTATCAACCTTTG 58.008 36.000 0.00 0.00 46.91 2.77
572 878 6.553100 TCCTTTGATTTGGTATCAACCTTTGT 59.447 34.615 0.00 0.00 46.91 2.83
573 879 7.726291 TCCTTTGATTTGGTATCAACCTTTGTA 59.274 33.333 0.00 0.00 46.91 2.41
574 880 8.531146 CCTTTGATTTGGTATCAACCTTTGTAT 58.469 33.333 0.00 0.00 46.91 2.29
575 881 9.573133 CTTTGATTTGGTATCAACCTTTGTATC 57.427 33.333 0.00 0.00 46.91 2.24
576 882 8.642935 TTGATTTGGTATCAACCTTTGTATCA 57.357 30.769 0.00 0.00 46.91 2.15
577 883 8.642935 TGATTTGGTATCAACCTTTGTATCAA 57.357 30.769 0.00 0.00 46.91 2.57
721 1065 7.283807 TGCAACATAGATTGACTTTCATATGCT 59.716 33.333 0.00 0.00 0.00 3.79
728 1072 8.798859 AGATTGACTTTCATATGCTTAACTGT 57.201 30.769 0.00 0.00 0.00 3.55
729 1073 9.890629 AGATTGACTTTCATATGCTTAACTGTA 57.109 29.630 0.00 0.00 0.00 2.74
763 1115 8.803397 ATAGTTTTTAGCCCTTAATTTCTCGT 57.197 30.769 0.00 0.00 0.00 4.18
776 1128 3.374402 CTCGTCTGGGGCGTCAGT 61.374 66.667 6.41 0.00 36.25 3.41
781 1133 1.674817 CGTCTGGGGCGTCAGTTAATT 60.675 52.381 6.41 0.00 36.25 1.40
793 1145 1.927174 CAGTTAATTCTGGCTCCGTCG 59.073 52.381 0.00 0.00 0.00 5.12
794 1146 1.549170 AGTTAATTCTGGCTCCGTCGT 59.451 47.619 0.00 0.00 0.00 4.34
795 1147 2.028385 AGTTAATTCTGGCTCCGTCGTT 60.028 45.455 0.00 0.00 0.00 3.85
796 1148 2.004583 TAATTCTGGCTCCGTCGTTG 57.995 50.000 0.00 0.00 0.00 4.10
797 1149 0.320374 AATTCTGGCTCCGTCGTTGA 59.680 50.000 0.00 0.00 0.00 3.18
798 1150 0.537188 ATTCTGGCTCCGTCGTTGAT 59.463 50.000 0.00 0.00 0.00 2.57
799 1151 0.389817 TTCTGGCTCCGTCGTTGATG 60.390 55.000 0.00 0.00 0.00 3.07
800 1152 1.079819 CTGGCTCCGTCGTTGATGT 60.080 57.895 0.00 0.00 0.00 3.06
801 1153 1.078759 CTGGCTCCGTCGTTGATGTC 61.079 60.000 0.00 0.00 0.00 3.06
802 1154 2.158959 GGCTCCGTCGTTGATGTCG 61.159 63.158 0.00 0.00 0.00 4.35
803 1155 1.443872 GCTCCGTCGTTGATGTCGT 60.444 57.895 0.00 0.00 0.00 4.34
804 1156 1.403972 GCTCCGTCGTTGATGTCGTC 61.404 60.000 0.00 0.00 0.00 4.20
805 1157 0.168348 CTCCGTCGTTGATGTCGTCT 59.832 55.000 0.00 0.00 0.00 4.18
806 1158 1.395954 CTCCGTCGTTGATGTCGTCTA 59.604 52.381 0.00 0.00 0.00 2.59
807 1159 1.805943 TCCGTCGTTGATGTCGTCTAA 59.194 47.619 0.00 0.00 0.00 2.10
808 1160 1.909532 CCGTCGTTGATGTCGTCTAAC 59.090 52.381 0.00 0.00 0.00 2.34
809 1161 2.413765 CCGTCGTTGATGTCGTCTAACT 60.414 50.000 0.00 0.00 0.00 2.24
810 1162 2.588539 CGTCGTTGATGTCGTCTAACTG 59.411 50.000 0.00 0.00 0.00 3.16
811 1163 3.562505 GTCGTTGATGTCGTCTAACTGT 58.437 45.455 0.00 0.00 0.00 3.55
812 1164 3.602915 GTCGTTGATGTCGTCTAACTGTC 59.397 47.826 0.00 0.00 0.00 3.51
813 1165 2.588539 CGTTGATGTCGTCTAACTGTCG 59.411 50.000 0.00 0.00 0.00 4.35
814 1166 2.913777 TGATGTCGTCTAACTGTCGG 57.086 50.000 0.00 0.00 0.00 4.79
815 1167 1.471287 TGATGTCGTCTAACTGTCGGG 59.529 52.381 0.00 0.00 0.00 5.14
816 1168 0.172803 ATGTCGTCTAACTGTCGGGC 59.827 55.000 0.00 0.00 0.00 6.13
817 1169 1.513586 GTCGTCTAACTGTCGGGCG 60.514 63.158 1.55 1.55 0.00 6.13
818 1170 1.968017 TCGTCTAACTGTCGGGCGT 60.968 57.895 6.80 0.00 0.00 5.68
819 1171 1.513586 CGTCTAACTGTCGGGCGTC 60.514 63.158 0.10 0.00 0.00 5.19
820 1172 1.582968 GTCTAACTGTCGGGCGTCA 59.417 57.895 0.00 0.00 0.00 4.35
821 1173 0.731855 GTCTAACTGTCGGGCGTCAC 60.732 60.000 0.00 0.00 0.00 3.67
822 1174 1.174078 TCTAACTGTCGGGCGTCACA 61.174 55.000 0.00 0.00 0.00 3.58
823 1175 0.108804 CTAACTGTCGGGCGTCACAT 60.109 55.000 0.00 0.00 0.00 3.21
824 1176 1.133598 CTAACTGTCGGGCGTCACATA 59.866 52.381 0.00 0.00 0.00 2.29
825 1177 0.319083 AACTGTCGGGCGTCACATAA 59.681 50.000 0.00 0.00 0.00 1.90
826 1178 0.319083 ACTGTCGGGCGTCACATAAA 59.681 50.000 0.00 0.00 0.00 1.40
827 1179 1.270412 ACTGTCGGGCGTCACATAAAA 60.270 47.619 0.00 0.00 0.00 1.52
828 1180 1.393539 CTGTCGGGCGTCACATAAAAG 59.606 52.381 0.00 0.00 0.00 2.27
829 1181 0.725117 GTCGGGCGTCACATAAAAGG 59.275 55.000 0.00 0.00 0.00 3.11
830 1182 0.391927 TCGGGCGTCACATAAAAGGG 60.392 55.000 0.00 0.00 0.00 3.95
831 1183 0.675522 CGGGCGTCACATAAAAGGGT 60.676 55.000 0.00 0.00 0.00 4.34
832 1184 1.092348 GGGCGTCACATAAAAGGGTC 58.908 55.000 0.00 0.00 0.00 4.46
833 1185 1.612199 GGGCGTCACATAAAAGGGTCA 60.612 52.381 0.00 0.00 0.00 4.02
834 1186 1.737793 GGCGTCACATAAAAGGGTCAG 59.262 52.381 0.00 0.00 0.00 3.51
835 1187 1.130561 GCGTCACATAAAAGGGTCAGC 59.869 52.381 0.00 0.00 0.00 4.26
836 1188 1.737793 CGTCACATAAAAGGGTCAGCC 59.262 52.381 0.00 0.00 0.00 4.85
837 1189 1.737793 GTCACATAAAAGGGTCAGCCG 59.262 52.381 0.00 0.00 34.97 5.52
838 1190 1.094785 CACATAAAAGGGTCAGCCGG 58.905 55.000 0.00 0.00 34.97 6.13
839 1191 0.034477 ACATAAAAGGGTCAGCCGGG 60.034 55.000 2.18 0.00 34.97 5.73
840 1192 0.034477 CATAAAAGGGTCAGCCGGGT 60.034 55.000 0.00 0.00 34.97 5.28
841 1193 0.034477 ATAAAAGGGTCAGCCGGGTG 60.034 55.000 27.73 27.73 34.97 4.61
842 1194 1.128809 TAAAAGGGTCAGCCGGGTGA 61.129 55.000 31.67 31.67 34.97 4.02
843 1195 2.002018 AAAAGGGTCAGCCGGGTGAA 62.002 55.000 36.14 18.65 34.97 3.18
844 1196 2.002018 AAAGGGTCAGCCGGGTGAAA 62.002 55.000 36.14 14.77 34.97 2.69
845 1197 2.002018 AAGGGTCAGCCGGGTGAAAA 62.002 55.000 36.14 13.96 34.97 2.29
846 1198 1.529713 GGGTCAGCCGGGTGAAAAA 60.530 57.895 36.14 13.55 34.97 1.94
869 1221 7.784633 AAATTTCATCAACGGTTCATTTTGT 57.215 28.000 0.00 0.00 0.00 2.83
870 1222 7.784633 AATTTCATCAACGGTTCATTTTGTT 57.215 28.000 0.00 0.00 0.00 2.83
871 1223 8.879342 AATTTCATCAACGGTTCATTTTGTTA 57.121 26.923 0.00 0.00 0.00 2.41
872 1224 9.487790 AATTTCATCAACGGTTCATTTTGTTAT 57.512 25.926 0.00 0.00 0.00 1.89
875 1227 9.781834 TTCATCAACGGTTCATTTTGTTATATC 57.218 29.630 0.00 0.00 0.00 1.63
876 1228 8.119845 TCATCAACGGTTCATTTTGTTATATCG 58.880 33.333 0.00 0.00 0.00 2.92
877 1229 7.367159 TCAACGGTTCATTTTGTTATATCGT 57.633 32.000 0.00 0.00 0.00 3.73
878 1230 7.808672 TCAACGGTTCATTTTGTTATATCGTT 58.191 30.769 0.00 0.00 37.55 3.85
879 1231 8.291032 TCAACGGTTCATTTTGTTATATCGTTT 58.709 29.630 0.00 0.00 35.41 3.60
880 1232 8.572151 CAACGGTTCATTTTGTTATATCGTTTC 58.428 33.333 0.00 0.00 35.41 2.78
881 1233 6.957077 ACGGTTCATTTTGTTATATCGTTTCG 59.043 34.615 0.00 0.00 0.00 3.46
882 1234 6.957077 CGGTTCATTTTGTTATATCGTTTCGT 59.043 34.615 0.00 0.00 0.00 3.85
883 1235 7.161418 CGGTTCATTTTGTTATATCGTTTCGTC 59.839 37.037 0.00 0.00 0.00 4.20
884 1236 7.427318 GGTTCATTTTGTTATATCGTTTCGTCC 59.573 37.037 0.00 0.00 0.00 4.79
885 1237 6.698107 TCATTTTGTTATATCGTTTCGTCCG 58.302 36.000 0.00 0.00 0.00 4.79
886 1238 4.503767 TTTGTTATATCGTTTCGTCCGC 57.496 40.909 0.00 0.00 0.00 5.54
887 1239 3.148026 TGTTATATCGTTTCGTCCGCA 57.852 42.857 0.00 0.00 0.00 5.69
888 1240 3.708890 TGTTATATCGTTTCGTCCGCAT 58.291 40.909 0.00 0.00 0.00 4.73
889 1241 3.487942 TGTTATATCGTTTCGTCCGCATG 59.512 43.478 0.00 0.00 0.00 4.06
890 1242 2.218953 ATATCGTTTCGTCCGCATGT 57.781 45.000 0.00 0.00 0.00 3.21
891 1243 1.552226 TATCGTTTCGTCCGCATGTC 58.448 50.000 0.00 0.00 0.00 3.06
892 1244 1.410737 ATCGTTTCGTCCGCATGTCG 61.411 55.000 0.00 0.00 38.08 4.35
893 1245 2.369629 CGTTTCGTCCGCATGTCGT 61.370 57.895 8.37 0.00 36.19 4.34
894 1246 1.857364 GTTTCGTCCGCATGTCGTT 59.143 52.632 8.37 0.00 36.19 3.85
895 1247 0.233848 GTTTCGTCCGCATGTCGTTT 59.766 50.000 8.37 0.00 36.19 3.60
896 1248 0.938713 TTTCGTCCGCATGTCGTTTT 59.061 45.000 8.37 0.00 36.19 2.43
897 1249 0.938713 TTCGTCCGCATGTCGTTTTT 59.061 45.000 8.37 0.00 36.19 1.94
898 1250 0.233590 TCGTCCGCATGTCGTTTTTG 59.766 50.000 8.37 0.00 36.19 2.44
899 1251 1.327292 CGTCCGCATGTCGTTTTTGC 61.327 55.000 8.37 0.00 36.19 3.68
900 1252 1.001745 GTCCGCATGTCGTTTTTGCC 61.002 55.000 8.37 0.00 36.19 4.52
966 1318 2.507992 CGCAGAGCTCCACTTCCG 60.508 66.667 10.93 0.54 0.00 4.30
1065 1417 2.100603 GTCTTCTCCTCGCCGACG 59.899 66.667 0.00 0.00 42.01 5.12
1086 1438 3.272847 AACCCCTTCGGCCCCAAT 61.273 61.111 0.00 0.00 33.26 3.16
1266 1618 2.125512 GACATCCGCAAGCTCCGT 60.126 61.111 6.08 0.00 0.00 4.69
1347 1699 2.827642 GACGACGGAGGGGACGAT 60.828 66.667 0.00 0.00 34.93 3.73
1371 1723 1.453379 CTTCATGGGCCTGGAGCTG 60.453 63.158 4.53 0.00 43.05 4.24
1484 1836 3.695060 GTCGTGGTGATCTTCTCCTCTTA 59.305 47.826 0.00 0.00 31.62 2.10
1787 2178 4.984295 TGATGTTCCTTTCATGGACTCAA 58.016 39.130 0.00 0.00 35.58 3.02
1788 2179 5.573219 TGATGTTCCTTTCATGGACTCAAT 58.427 37.500 0.00 0.00 35.58 2.57
1789 2180 5.416639 TGATGTTCCTTTCATGGACTCAATG 59.583 40.000 0.00 0.00 35.58 2.82
2002 3148 3.118555 TGGACAGATAACATTACCACGGG 60.119 47.826 0.00 0.00 0.00 5.28
2436 3584 5.657474 GGACTTCATGAATGTCCTTACGTA 58.343 41.667 30.16 0.00 44.84 3.57
2442 3592 8.420374 TTCATGAATGTCCTTACGTAATCTTC 57.580 34.615 8.76 8.12 0.00 2.87
2444 3594 6.288941 TGAATGTCCTTACGTAATCTTCCA 57.711 37.500 8.76 2.55 0.00 3.53
2446 3596 8.014070 TGAATGTCCTTACGTAATCTTCCATA 57.986 34.615 8.76 0.00 0.00 2.74
2449 3599 9.847224 AATGTCCTTACGTAATCTTCCATATTT 57.153 29.630 8.76 0.00 0.00 1.40
2468 3618 3.764237 TTTCTGTAAAGGAGGAAGCGT 57.236 42.857 0.00 0.00 0.00 5.07
2469 3619 2.743636 TCTGTAAAGGAGGAAGCGTG 57.256 50.000 0.00 0.00 0.00 5.34
2482 3633 2.754002 GGAAGCGTGGTCTACTTCTACT 59.246 50.000 0.00 0.00 39.77 2.57
2495 3646 7.285858 GGTCTACTTCTACTTCCACATATCACT 59.714 40.741 0.00 0.00 0.00 3.41
2506 3657 6.925610 TCCACATATCACTTGCAATAGAAC 57.074 37.500 0.00 0.00 0.00 3.01
2583 3735 0.810648 TTGAAGCATGTGGATTCGGC 59.189 50.000 0.00 0.00 44.83 5.54
2726 3878 1.001764 CTGCCACCTGAGAATGCCA 60.002 57.895 0.00 0.00 0.00 4.92
2746 3898 4.636249 CCAACTGTAAAGAGAGTTCTGCT 58.364 43.478 0.00 0.00 37.07 4.24
2769 3921 1.824852 CCAGCAAGTGATTTTACCCCC 59.175 52.381 0.00 0.00 0.00 5.40
2770 3922 2.557452 CCAGCAAGTGATTTTACCCCCT 60.557 50.000 0.00 0.00 0.00 4.79
2771 3923 2.755103 CAGCAAGTGATTTTACCCCCTC 59.245 50.000 0.00 0.00 0.00 4.30
2772 3924 2.649816 AGCAAGTGATTTTACCCCCTCT 59.350 45.455 0.00 0.00 0.00 3.69
2786 3938 0.106894 CCCTCTTAACTGGATCCGGC 59.893 60.000 21.17 0.00 0.00 6.13
2829 3981 2.317040 TCTGTCTTCGAGGAAACCACT 58.683 47.619 0.00 0.00 0.00 4.00
2867 4019 2.295349 ACTTGTGGACACGGTAGTACAG 59.705 50.000 2.06 0.10 31.75 2.74
2929 4083 1.084370 GTTCAGAATCCGGACCAGCG 61.084 60.000 6.12 0.00 0.00 5.18
2944 4098 4.149910 ACCAGCGTTTGTAAATTTACCG 57.850 40.909 22.47 19.14 32.72 4.02
2945 4099 3.565063 ACCAGCGTTTGTAAATTTACCGT 59.435 39.130 22.47 9.24 32.72 4.83
2962 4118 2.030274 ACCGTTGATGGTAAAAGCTTGC 60.030 45.455 0.00 0.00 41.55 4.01
2967 4123 2.030007 TGATGGTAAAAGCTTGCTGTGC 60.030 45.455 0.00 0.00 0.00 4.57
2986 4142 7.606073 TGCTGTGCTTACAGAGATAAATGTTTA 59.394 33.333 11.32 0.00 39.53 2.01
3044 4201 7.800380 CACTTGACAAAGAGTGAATCACATAAC 59.200 37.037 16.38 4.25 44.65 1.89
3046 4203 5.408299 TGACAAAGAGTGAATCACATAACGG 59.592 40.000 16.38 3.13 36.74 4.44
3062 4224 7.709182 TCACATAACGGGAACTTTGATATACAG 59.291 37.037 0.00 0.00 0.00 2.74
3108 4270 5.923204 TGGTGCTGTCAAAATTTTATTGGT 58.077 33.333 2.44 0.00 0.00 3.67
3151 4313 0.179137 TTGCAGGATAGACGACAGCG 60.179 55.000 0.00 0.00 44.79 5.18
3179 4341 0.614697 TCAAGGGAGATGTCCGCAGA 60.615 55.000 2.25 0.00 45.05 4.26
3272 4501 4.083110 TGCTCTACGTCTACCACTTTACAC 60.083 45.833 0.00 0.00 0.00 2.90
3302 4531 6.655425 AGAAGTTTTAGTTACAGGAAGATGGC 59.345 38.462 0.00 0.00 0.00 4.40
3310 4539 3.287867 ACAGGAAGATGGCGATTTCAT 57.712 42.857 0.00 0.00 0.00 2.57
3437 4672 9.509956 TGTATATAAACACCCATGGCTATTAAC 57.490 33.333 6.09 0.00 0.00 2.01
3591 4879 4.478206 TCCAAATGCTCTCTGTAGGAAG 57.522 45.455 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 8.439971 TCTTGTATCTTCCATATTTGGCACTAT 58.560 33.333 0.00 0.00 43.29 2.12
81 83 1.628846 AGTCCTTGAACGCCCATTAGT 59.371 47.619 0.00 0.00 0.00 2.24
219 522 3.233507 TCATTGCTGAGAAGGCCTTTTT 58.766 40.909 21.54 11.53 0.00 1.94
247 552 2.783135 TGTTCCTCAATCCAGTCTTGC 58.217 47.619 0.00 0.00 0.00 4.01
308 613 7.458409 ACTCACAAATACATCTTGCTCAATT 57.542 32.000 0.00 0.00 0.00 2.32
489 795 6.942576 TCAATAGCAGAAGAAGCTAAACCTTT 59.057 34.615 0.00 0.00 46.55 3.11
528 834 1.139853 GATTGGTTGATCCGAGCCTCT 59.860 52.381 0.00 0.00 39.52 3.69
536 842 5.046376 ACCAAATCAAAGGATTGGTTGATCC 60.046 40.000 3.67 0.00 42.87 3.36
640 983 6.146601 TGACAGCATTTGTTTCTTGATGAA 57.853 33.333 0.00 0.00 41.05 2.57
736 1088 8.889717 CGAGAAATTAAGGGCTAAAAACTATCA 58.110 33.333 0.00 0.00 0.00 2.15
738 1090 8.803397 ACGAGAAATTAAGGGCTAAAAACTAT 57.197 30.769 0.00 0.00 0.00 2.12
763 1115 1.906574 AGAATTAACTGACGCCCCAGA 59.093 47.619 6.96 0.00 37.59 3.86
776 1128 2.028839 TCAACGACGGAGCCAGAATTAA 60.029 45.455 0.00 0.00 0.00 1.40
781 1133 1.215382 CATCAACGACGGAGCCAGA 59.785 57.895 0.00 0.00 0.00 3.86
793 1145 2.915463 CCGACAGTTAGACGACATCAAC 59.085 50.000 0.00 0.00 37.60 3.18
794 1146 2.094906 CCCGACAGTTAGACGACATCAA 60.095 50.000 0.00 0.00 37.60 2.57
795 1147 1.471287 CCCGACAGTTAGACGACATCA 59.529 52.381 0.00 0.00 37.60 3.07
796 1148 1.798079 GCCCGACAGTTAGACGACATC 60.798 57.143 0.00 0.00 37.60 3.06
797 1149 0.172803 GCCCGACAGTTAGACGACAT 59.827 55.000 0.00 0.00 37.60 3.06
798 1150 1.582968 GCCCGACAGTTAGACGACA 59.417 57.895 0.00 0.00 37.60 4.35
799 1151 1.513586 CGCCCGACAGTTAGACGAC 60.514 63.158 0.00 0.00 37.60 4.34
800 1152 1.915614 GACGCCCGACAGTTAGACGA 61.916 60.000 0.00 0.00 37.60 4.20
801 1153 1.513586 GACGCCCGACAGTTAGACG 60.514 63.158 0.00 0.00 35.18 4.18
802 1154 0.731855 GTGACGCCCGACAGTTAGAC 60.732 60.000 0.00 0.00 0.00 2.59
803 1155 1.174078 TGTGACGCCCGACAGTTAGA 61.174 55.000 0.00 0.00 0.00 2.10
804 1156 0.108804 ATGTGACGCCCGACAGTTAG 60.109 55.000 0.00 0.00 0.00 2.34
805 1157 1.175654 TATGTGACGCCCGACAGTTA 58.824 50.000 0.00 0.00 0.00 2.24
806 1158 0.319083 TTATGTGACGCCCGACAGTT 59.681 50.000 0.00 0.00 0.00 3.16
807 1159 0.319083 TTTATGTGACGCCCGACAGT 59.681 50.000 0.00 0.00 0.00 3.55
808 1160 1.393539 CTTTTATGTGACGCCCGACAG 59.606 52.381 0.00 0.00 0.00 3.51
809 1161 1.434555 CTTTTATGTGACGCCCGACA 58.565 50.000 0.00 0.00 0.00 4.35
810 1162 0.725117 CCTTTTATGTGACGCCCGAC 59.275 55.000 0.00 0.00 0.00 4.79
811 1163 0.391927 CCCTTTTATGTGACGCCCGA 60.392 55.000 0.00 0.00 0.00 5.14
812 1164 0.675522 ACCCTTTTATGTGACGCCCG 60.676 55.000 0.00 0.00 0.00 6.13
813 1165 1.092348 GACCCTTTTATGTGACGCCC 58.908 55.000 0.00 0.00 0.00 6.13
814 1166 1.737793 CTGACCCTTTTATGTGACGCC 59.262 52.381 0.00 0.00 0.00 5.68
815 1167 1.130561 GCTGACCCTTTTATGTGACGC 59.869 52.381 0.00 0.00 0.00 5.19
816 1168 1.737793 GGCTGACCCTTTTATGTGACG 59.262 52.381 0.00 0.00 0.00 4.35
817 1169 1.737793 CGGCTGACCCTTTTATGTGAC 59.262 52.381 0.00 0.00 0.00 3.67
818 1170 1.339631 CCGGCTGACCCTTTTATGTGA 60.340 52.381 0.00 0.00 0.00 3.58
819 1171 1.094785 CCGGCTGACCCTTTTATGTG 58.905 55.000 0.00 0.00 0.00 3.21
820 1172 0.034477 CCCGGCTGACCCTTTTATGT 60.034 55.000 0.00 0.00 0.00 2.29
821 1173 0.034477 ACCCGGCTGACCCTTTTATG 60.034 55.000 0.00 0.00 0.00 1.90
822 1174 0.034477 CACCCGGCTGACCCTTTTAT 60.034 55.000 0.00 0.00 0.00 1.40
823 1175 1.128809 TCACCCGGCTGACCCTTTTA 61.129 55.000 0.00 0.00 0.00 1.52
824 1176 2.002018 TTCACCCGGCTGACCCTTTT 62.002 55.000 0.00 0.00 0.00 2.27
825 1177 2.002018 TTTCACCCGGCTGACCCTTT 62.002 55.000 0.00 0.00 0.00 3.11
826 1178 2.002018 TTTTCACCCGGCTGACCCTT 62.002 55.000 0.00 0.00 0.00 3.95
827 1179 2.002018 TTTTTCACCCGGCTGACCCT 62.002 55.000 0.00 0.00 0.00 4.34
828 1180 1.529713 TTTTTCACCCGGCTGACCC 60.530 57.895 0.00 0.00 0.00 4.46
829 1181 4.167597 TTTTTCACCCGGCTGACC 57.832 55.556 0.00 0.00 0.00 4.02
843 1195 8.672815 ACAAAATGAACCGTTGATGAAATTTTT 58.327 25.926 0.00 0.00 0.00 1.94
844 1196 8.207521 ACAAAATGAACCGTTGATGAAATTTT 57.792 26.923 0.00 0.00 0.00 1.82
845 1197 7.784633 ACAAAATGAACCGTTGATGAAATTT 57.215 28.000 0.00 0.00 0.00 1.82
846 1198 7.784633 AACAAAATGAACCGTTGATGAAATT 57.215 28.000 0.00 0.00 0.00 1.82
849 1201 9.781834 GATATAACAAAATGAACCGTTGATGAA 57.218 29.630 0.00 0.00 0.00 2.57
850 1202 8.119845 CGATATAACAAAATGAACCGTTGATGA 58.880 33.333 0.00 0.00 0.00 2.92
851 1203 7.908082 ACGATATAACAAAATGAACCGTTGATG 59.092 33.333 0.00 0.00 0.00 3.07
852 1204 7.981142 ACGATATAACAAAATGAACCGTTGAT 58.019 30.769 0.00 0.00 0.00 2.57
853 1205 7.367159 ACGATATAACAAAATGAACCGTTGA 57.633 32.000 0.00 0.00 0.00 3.18
854 1206 8.442605 AAACGATATAACAAAATGAACCGTTG 57.557 30.769 0.00 0.00 36.76 4.10
855 1207 7.479291 CGAAACGATATAACAAAATGAACCGTT 59.521 33.333 0.00 0.00 37.99 4.44
856 1208 6.957077 CGAAACGATATAACAAAATGAACCGT 59.043 34.615 0.00 0.00 0.00 4.83
857 1209 6.957077 ACGAAACGATATAACAAAATGAACCG 59.043 34.615 0.00 0.00 0.00 4.44
858 1210 7.427318 GGACGAAACGATATAACAAAATGAACC 59.573 37.037 0.00 0.00 0.00 3.62
859 1211 7.161418 CGGACGAAACGATATAACAAAATGAAC 59.839 37.037 0.00 0.00 0.00 3.18
860 1212 7.174746 CGGACGAAACGATATAACAAAATGAA 58.825 34.615 0.00 0.00 0.00 2.57
861 1213 6.698107 CGGACGAAACGATATAACAAAATGA 58.302 36.000 0.00 0.00 0.00 2.57
862 1214 5.391433 GCGGACGAAACGATATAACAAAATG 59.609 40.000 0.00 0.00 0.00 2.32
863 1215 5.063691 TGCGGACGAAACGATATAACAAAAT 59.936 36.000 0.00 0.00 0.00 1.82
864 1216 4.388165 TGCGGACGAAACGATATAACAAAA 59.612 37.500 0.00 0.00 0.00 2.44
865 1217 3.925299 TGCGGACGAAACGATATAACAAA 59.075 39.130 0.00 0.00 0.00 2.83
866 1218 3.509740 TGCGGACGAAACGATATAACAA 58.490 40.909 0.00 0.00 0.00 2.83
867 1219 3.148026 TGCGGACGAAACGATATAACA 57.852 42.857 0.00 0.00 0.00 2.41
868 1220 3.488310 ACATGCGGACGAAACGATATAAC 59.512 43.478 0.00 0.00 0.00 1.89
869 1221 3.708890 ACATGCGGACGAAACGATATAA 58.291 40.909 0.00 0.00 0.00 0.98
870 1222 3.302555 GACATGCGGACGAAACGATATA 58.697 45.455 0.00 0.00 0.00 0.86
871 1223 2.124903 GACATGCGGACGAAACGATAT 58.875 47.619 0.00 0.00 0.00 1.63
872 1224 1.552226 GACATGCGGACGAAACGATA 58.448 50.000 0.00 0.00 0.00 2.92
873 1225 1.410737 CGACATGCGGACGAAACGAT 61.411 55.000 0.00 0.00 36.03 3.73
874 1226 2.084101 CGACATGCGGACGAAACGA 61.084 57.895 0.00 0.00 36.03 3.85
875 1227 1.882682 AACGACATGCGGACGAAACG 61.883 55.000 12.85 0.00 46.49 3.60
876 1228 0.233848 AAACGACATGCGGACGAAAC 59.766 50.000 12.85 0.00 46.49 2.78
877 1229 0.938713 AAAACGACATGCGGACGAAA 59.061 45.000 12.85 0.00 46.49 3.46
878 1230 0.938713 AAAAACGACATGCGGACGAA 59.061 45.000 12.85 0.00 46.49 3.85
879 1231 0.233590 CAAAAACGACATGCGGACGA 59.766 50.000 12.85 0.00 46.49 4.20
880 1232 1.327292 GCAAAAACGACATGCGGACG 61.327 55.000 12.85 7.38 46.49 4.79
881 1233 1.001745 GGCAAAAACGACATGCGGAC 61.002 55.000 12.85 0.00 46.49 4.79
882 1234 1.284408 GGCAAAAACGACATGCGGA 59.716 52.632 12.85 0.00 46.49 5.54
883 1235 1.732683 GGGCAAAAACGACATGCGG 60.733 57.895 12.85 0.00 46.49 5.69
885 1237 1.792367 GAAAGGGCAAAAACGACATGC 59.208 47.619 0.00 0.00 39.33 4.06
886 1238 2.403259 GGAAAGGGCAAAAACGACATG 58.597 47.619 0.00 0.00 0.00 3.21
887 1239 1.343142 GGGAAAGGGCAAAAACGACAT 59.657 47.619 0.00 0.00 0.00 3.06
888 1240 0.747852 GGGAAAGGGCAAAAACGACA 59.252 50.000 0.00 0.00 0.00 4.35
889 1241 0.318360 CGGGAAAGGGCAAAAACGAC 60.318 55.000 0.00 0.00 0.00 4.34
890 1242 0.752376 ACGGGAAAGGGCAAAAACGA 60.752 50.000 0.00 0.00 0.00 3.85
891 1243 0.103390 AACGGGAAAGGGCAAAAACG 59.897 50.000 0.00 0.00 0.00 3.60
892 1244 1.860676 GAACGGGAAAGGGCAAAAAC 58.139 50.000 0.00 0.00 0.00 2.43
893 1245 0.386113 CGAACGGGAAAGGGCAAAAA 59.614 50.000 0.00 0.00 0.00 1.94
894 1246 0.465824 TCGAACGGGAAAGGGCAAAA 60.466 50.000 0.00 0.00 0.00 2.44
895 1247 0.250989 ATCGAACGGGAAAGGGCAAA 60.251 50.000 0.00 0.00 0.00 3.68
896 1248 0.250989 AATCGAACGGGAAAGGGCAA 60.251 50.000 0.00 0.00 0.00 4.52
897 1249 0.675522 GAATCGAACGGGAAAGGGCA 60.676 55.000 0.00 0.00 0.00 5.36
898 1250 1.702491 CGAATCGAACGGGAAAGGGC 61.702 60.000 0.00 0.00 0.00 5.19
899 1251 0.390735 ACGAATCGAACGGGAAAGGG 60.391 55.000 10.55 0.00 34.93 3.95
900 1252 0.997196 GACGAATCGAACGGGAAAGG 59.003 55.000 10.55 0.00 34.93 3.11
966 1318 2.126424 GAGTGGTCGTGGTCTCGC 60.126 66.667 0.00 0.00 0.00 5.03
1037 1389 1.664965 GAGAAGACCGCAAGCGTGT 60.665 57.895 13.80 10.62 37.81 4.49
1484 1836 8.594550 AGTTCACTACTGACCACTTGTATAATT 58.405 33.333 0.00 0.00 35.19 1.40
1505 1883 0.040514 CATTGGTTTCGCGCAGTTCA 60.041 50.000 8.75 0.00 0.00 3.18
1641 2022 4.523943 TCACCAGAAAAATCCAATGTCAGG 59.476 41.667 0.00 0.00 0.00 3.86
1787 2178 3.181471 CGGTGCAAGAGGTCTCTATTCAT 60.181 47.826 0.43 0.00 39.39 2.57
1788 2179 2.166459 CGGTGCAAGAGGTCTCTATTCA 59.834 50.000 0.43 0.00 39.39 2.57
1789 2180 2.427453 TCGGTGCAAGAGGTCTCTATTC 59.573 50.000 0.43 0.00 39.39 1.75
2002 3148 1.602377 AGCTTTGCTACCGACAAACAC 59.398 47.619 0.00 0.00 36.99 3.32
2436 3584 9.413734 CCTCCTTTACAGAAAATATGGAAGATT 57.586 33.333 0.00 0.00 0.00 2.40
2442 3592 6.238484 CGCTTCCTCCTTTACAGAAAATATGG 60.238 42.308 0.00 0.00 0.00 2.74
2444 3594 6.316390 CACGCTTCCTCCTTTACAGAAAATAT 59.684 38.462 0.00 0.00 0.00 1.28
2446 3596 4.455877 CACGCTTCCTCCTTTACAGAAAAT 59.544 41.667 0.00 0.00 0.00 1.82
2449 3599 2.289444 CCACGCTTCCTCCTTTACAGAA 60.289 50.000 0.00 0.00 0.00 3.02
2468 3618 7.068348 GTGATATGTGGAAGTAGAAGTAGACCA 59.932 40.741 0.00 0.00 0.00 4.02
2469 3619 7.285858 AGTGATATGTGGAAGTAGAAGTAGACC 59.714 40.741 0.00 0.00 0.00 3.85
2482 3633 6.318648 GGTTCTATTGCAAGTGATATGTGGAA 59.681 38.462 4.94 0.00 0.00 3.53
2726 3878 6.211584 TGGATAGCAGAACTCTCTTTACAGTT 59.788 38.462 0.00 0.00 35.48 3.16
2746 3898 4.532834 GGGGTAAAATCACTTGCTGGATA 58.467 43.478 0.00 0.00 0.00 2.59
2755 3907 5.281037 CCAGTTAAGAGGGGGTAAAATCACT 60.281 44.000 0.00 0.00 0.00 3.41
2769 3921 2.760374 GATGCCGGATCCAGTTAAGAG 58.240 52.381 13.41 0.00 0.00 2.85
2770 3922 2.910688 GATGCCGGATCCAGTTAAGA 57.089 50.000 13.41 0.00 0.00 2.10
2805 3957 4.334481 GTGGTTTCCTCGAAGACAGAAAAA 59.666 41.667 0.00 0.00 36.07 1.94
2829 3981 8.932791 GTCCACAAGTTTCTCTAATTTATTCGA 58.067 33.333 0.00 0.00 0.00 3.71
2867 4019 6.325919 TCCACACATGATAAAAAGGTGAAC 57.674 37.500 0.00 0.00 33.82 3.18
2944 4098 3.983344 CACAGCAAGCTTTTACCATCAAC 59.017 43.478 0.00 0.00 0.00 3.18
2945 4099 3.552684 GCACAGCAAGCTTTTACCATCAA 60.553 43.478 0.00 0.00 0.00 2.57
2986 4142 3.196463 TGACGACAAAAACACCGTGTAT 58.804 40.909 4.17 0.00 35.22 2.29
2992 4148 3.004315 ACATCCATGACGACAAAAACACC 59.996 43.478 0.00 0.00 0.00 4.16
2993 4149 4.219033 GACATCCATGACGACAAAAACAC 58.781 43.478 0.00 0.00 0.00 3.32
3000 4156 0.607620 TGCTGACATCCATGACGACA 59.392 50.000 0.00 0.00 0.00 4.35
3044 4201 6.594159 ACAGTTTCTGTATATCAAAGTTCCCG 59.406 38.462 0.27 0.00 43.46 5.14
3046 4203 9.871238 TCTACAGTTTCTGTATATCAAAGTTCC 57.129 33.333 9.55 0.00 44.49 3.62
3108 4270 9.672086 CAACATTACTTGACGAAGGAAAAATTA 57.328 29.630 0.00 0.00 35.54 1.40
3121 4283 5.005779 CGTCTATCCTGCAACATTACTTGAC 59.994 44.000 0.00 0.00 0.00 3.18
3151 4313 6.293462 GCGGACATCTCCCTTGATTTATTTAC 60.293 42.308 0.00 0.00 31.93 2.01
3205 4367 8.824159 AATGTCATAGATGTATCAACTACTGC 57.176 34.615 0.00 0.00 0.00 4.40
3302 4531 5.379827 CATCGAATCATCACCATGAAATCG 58.620 41.667 13.30 13.30 45.17 3.34
3310 4539 1.140852 GGTCCCATCGAATCATCACCA 59.859 52.381 0.00 0.00 0.00 4.17
3437 4672 6.018425 CAGTTTAACGATTGGAGATCCATCAG 60.018 42.308 1.61 0.00 46.97 2.90
3591 4879 0.662374 TCCTTTCAGTCGTCGAACGC 60.662 55.000 0.00 0.00 42.21 4.84


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

AutoCloner maintained by Alex Coulton.