Multiple sequence alignment - TraesCS3D01G203600

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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 TraesCS3D01G203600 chr3D 100.000 2924 0 0 1 2924 253531001 253528078 0.000000e+00 5400.0
1 TraesCS3D01G203600 chr3D 98.647 739 10 0 1143 1881 520652708 520653446 0.000000e+00 1310.0
2 TraesCS3D01G203600 chr3D 99.689 644 2 0 2281 2924 520653537 520654180 0.000000e+00 1179.0
3 TraesCS3D01G203600 chr4B 97.308 743 20 0 1139 1881 532722200 532722942 0.000000e+00 1262.0
4 TraesCS3D01G203600 chr4B 98.300 706 7 1 1883 2583 532722847 532723552 0.000000e+00 1232.0
5 TraesCS3D01G203600 chr4B 85.137 693 64 23 480 1142 527784200 527783517 0.000000e+00 673.0
6 TraesCS3D01G203600 chr4B 93.052 403 25 3 75 477 527784646 527784247 1.170000e-163 586.0
7 TraesCS3D01G203600 chr3B 96.770 743 23 1 1140 1881 805049273 805050015 0.000000e+00 1238.0
8 TraesCS3D01G203600 chr3B 92.816 515 16 11 1882 2387 805049919 805050421 0.000000e+00 726.0
9 TraesCS3D01G203600 chr3B 90.667 75 7 0 1 75 545097446 545097372 1.850000e-17 100.0
10 TraesCS3D01G203600 chr1A 97.746 710 10 2 1882 2586 586730698 586729990 0.000000e+00 1218.0
11 TraesCS3D01G203600 chr1A 94.340 742 18 1 1140 1881 586731319 586730602 0.000000e+00 1116.0
12 TraesCS3D01G203600 chr1A 99.700 333 1 0 2592 2924 586728008 586727676 6.930000e-171 610.0
13 TraesCS3D01G203600 chr1A 92.121 330 26 0 2595 2924 290214338 290214009 1.590000e-127 466.0
14 TraesCS3D01G203600 chr4A 97.737 707 11 1 1885 2586 502364229 502363523 0.000000e+00 1212.0
15 TraesCS3D01G203600 chr4A 97.465 710 13 1 1882 2586 90051999 90052708 0.000000e+00 1206.0
16 TraesCS3D01G203600 chr4A 97.454 707 13 1 1882 2583 90066359 90067065 0.000000e+00 1201.0
17 TraesCS3D01G203600 chr4A 95.270 740 11 1 1142 1881 502364851 502364136 0.000000e+00 1151.0
18 TraesCS3D01G203600 chr4A 94.886 743 14 1 1139 1881 90065737 90066455 0.000000e+00 1140.0
19 TraesCS3D01G203600 chr4A 93.378 740 22 3 1142 1881 90051383 90052095 0.000000e+00 1070.0
20 TraesCS3D01G203600 chr4A 94.331 635 12 1 1139 1773 90070887 90071497 0.000000e+00 952.0
21 TraesCS3D01G203600 chr4A 99.107 336 3 0 2589 2924 90054687 90055022 3.220000e-169 604.0
22 TraesCS3D01G203600 chr4A 98.214 336 5 1 2589 2924 90069047 90069381 1.170000e-163 586.0
23 TraesCS3D01G203600 chr4A 98.198 333 6 0 2592 2924 502361544 502361212 1.510000e-162 582.0
24 TraesCS3D01G203600 chr7A 96.901 710 17 1 1882 2586 700287864 700288573 0.000000e+00 1184.0
25 TraesCS3D01G203600 chr7A 96.761 710 17 2 1883 2586 66690625 66689916 0.000000e+00 1179.0
26 TraesCS3D01G203600 chr7A 94.892 744 13 8 1139 1881 700287241 700287960 0.000000e+00 1140.0
27 TraesCS3D01G203600 chr7A 97.205 644 13 1 1882 2520 38954429 38953786 0.000000e+00 1085.0
28 TraesCS3D01G203600 chr7A 99.107 336 3 0 2589 2924 700290567 700290902 3.220000e-169 604.0
29 TraesCS3D01G203600 chr7A 99.099 333 3 0 2592 2924 66688908 66688576 1.500000e-167 599.0
30 TraesCS3D01G203600 chr4D 95.418 742 9 3 1140 1881 82856467 82855751 0.000000e+00 1158.0
31 TraesCS3D01G203600 chr4D 95.666 646 8 3 2281 2924 82854982 82854355 0.000000e+00 1020.0
32 TraesCS3D01G203600 chr7B 94.579 535 27 2 1142 1674 56999471 56998937 0.000000e+00 826.0
33 TraesCS3D01G203600 chr7B 93.947 413 24 1 65 477 690538382 690538793 8.900000e-175 623.0
34 TraesCS3D01G203600 chr7B 93.705 413 25 1 65 477 690512074 690512485 4.140000e-173 617.0
35 TraesCS3D01G203600 chr7B 93.705 413 25 1 65 477 690515672 690516083 4.140000e-173 617.0
36 TraesCS3D01G203600 chr7B 88.499 513 44 11 481 989 690516131 690516632 8.960000e-170 606.0
37 TraesCS3D01G203600 chr7B 93.220 413 27 1 65 477 690534785 690535196 8.960000e-170 606.0
38 TraesCS3D01G203600 chr7B 88.499 513 44 10 481 989 690538841 690539342 8.960000e-170 606.0
39 TraesCS3D01G203600 chr7B 88.304 513 46 11 481 989 690597419 690597921 1.160000e-168 603.0
40 TraesCS3D01G203600 chr7B 87.938 514 46 9 481 989 690512533 690513035 2.510000e-165 592.0
41 TraesCS3D01G203600 chr7B 87.938 514 47 10 481 989 690566724 690567227 2.510000e-165 592.0
42 TraesCS3D01G203600 chr7B 87.160 514 50 9 481 989 690535244 690535746 1.180000e-158 569.0
43 TraesCS3D01G203600 chr7B 86.022 93 8 1 992 1079 329930043 329929951 8.630000e-16 95.3
44 TraesCS3D01G203600 chr5A 94.390 410 22 1 68 477 665721935 665721527 1.910000e-176 628.0
45 TraesCS3D01G203600 chr5A 85.897 156 17 1 993 1143 665720931 665720776 8.390000e-36 161.0
46 TraesCS3D01G203600 chr5A 92.000 75 6 0 1 75 665722044 665721970 3.990000e-19 106.0
47 TraesCS3D01G203600 chrUn 94.500 400 21 1 77 476 234995714 234995316 1.490000e-172 616.0
48 TraesCS3D01G203600 chrUn 87.549 514 48 9 481 989 234998865 234998363 5.430000e-162 580.0
49 TraesCS3D01G203600 chrUn 87.549 514 48 9 481 989 427902852 427902350 5.430000e-162 580.0
50 TraesCS3D01G203600 chrUn 92.252 413 23 3 65 477 340273866 340274269 7.030000e-161 577.0
51 TraesCS3D01G203600 chrUn 92.439 410 22 3 68 477 369113203 369112803 7.030000e-161 577.0
52 TraesCS3D01G203600 chr1B 90.141 71 7 0 1 71 681700233 681700163 3.100000e-15 93.5


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 TraesCS3D01G203600 chr3D 253528078 253531001 2923 True 5400.000000 5400 100.000000 1 2924 1 chr3D.!!$R1 2923
1 TraesCS3D01G203600 chr3D 520652708 520654180 1472 False 1244.500000 1310 99.168000 1143 2924 2 chr3D.!!$F1 1781
2 TraesCS3D01G203600 chr4B 532722200 532723552 1352 False 1247.000000 1262 97.804000 1139 2583 2 chr4B.!!$F1 1444
3 TraesCS3D01G203600 chr4B 527783517 527784646 1129 True 629.500000 673 89.094500 75 1142 2 chr4B.!!$R1 1067
4 TraesCS3D01G203600 chr3B 805049273 805050421 1148 False 982.000000 1238 94.793000 1140 2387 2 chr3B.!!$F1 1247
5 TraesCS3D01G203600 chr1A 586727676 586731319 3643 True 981.333333 1218 97.262000 1140 2924 3 chr1A.!!$R2 1784
6 TraesCS3D01G203600 chr4A 502361212 502364851 3639 True 981.666667 1212 97.068333 1142 2924 3 chr4A.!!$R1 1782
7 TraesCS3D01G203600 chr4A 90065737 90071497 5760 False 969.750000 1201 96.221250 1139 2924 4 chr4A.!!$F2 1785
8 TraesCS3D01G203600 chr4A 90051383 90055022 3639 False 960.000000 1206 96.650000 1142 2924 3 chr4A.!!$F1 1782
9 TraesCS3D01G203600 chr7A 38953786 38954429 643 True 1085.000000 1085 97.205000 1882 2520 1 chr7A.!!$R1 638
10 TraesCS3D01G203600 chr7A 700287241 700290902 3661 False 976.000000 1184 96.966667 1139 2924 3 chr7A.!!$F1 1785
11 TraesCS3D01G203600 chr7A 66688576 66690625 2049 True 889.000000 1179 97.930000 1883 2924 2 chr7A.!!$R2 1041
12 TraesCS3D01G203600 chr4D 82854355 82856467 2112 True 1089.000000 1158 95.542000 1140 2924 2 chr4D.!!$R1 1784
13 TraesCS3D01G203600 chr7B 56998937 56999471 534 True 826.000000 826 94.579000 1142 1674 1 chr7B.!!$R1 532
14 TraesCS3D01G203600 chr7B 690512074 690516632 4558 False 608.000000 617 90.961750 65 989 4 chr7B.!!$F3 924
15 TraesCS3D01G203600 chr7B 690597419 690597921 502 False 603.000000 603 88.304000 481 989 1 chr7B.!!$F2 508
16 TraesCS3D01G203600 chr7B 690534785 690539342 4557 False 601.000000 623 90.706500 65 989 4 chr7B.!!$F4 924
17 TraesCS3D01G203600 chr7B 690566724 690567227 503 False 592.000000 592 87.938000 481 989 1 chr7B.!!$F1 508
18 TraesCS3D01G203600 chr5A 665720776 665722044 1268 True 298.333333 628 90.762333 1 1143 3 chr5A.!!$R1 1142
19 TraesCS3D01G203600 chrUn 234995316 234998865 3549 True 598.000000 616 91.024500 77 989 2 chrUn.!!$R3 912
20 TraesCS3D01G203600 chrUn 427902350 427902852 502 True 580.000000 580 87.549000 481 989 1 chrUn.!!$R2 508

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
739 826 0.250640 GCAGGAGATAGGGTGCATGG 60.251 60.0 0.0 0.0 35.91 3.66 F
1122 1218 0.035343 AGACGGTGAGATCGAGGTCA 60.035 55.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 3482 0.035458 AAGGACCTTGAGCCGACTTG 59.965 55.0 5.76 0.0 0.00 3.16 R
2803 9552 1.444933 TGAGGGGCTTCTCCTTTCAA 58.555 50.0 6.08 0.0 34.21 2.69 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
33 34 6.349944 GGCTCAAACATTCCATATGGATCATC 60.350 42.308 25.07 7.68 44.98 2.92
51 52 1.961277 CTGTCTGGTCGTTGCCCAC 60.961 63.158 0.00 0.00 0.00 4.61
165 208 7.581213 TCATTATCCGGCATATTTTCAAGTT 57.419 32.000 0.00 0.00 0.00 2.66
170 213 6.279513 TCCGGCATATTTTCAAGTTGATTT 57.720 33.333 6.36 0.00 0.00 2.17
185 228 3.426787 TGATTTGAGCCGGTAAAAGGA 57.573 42.857 1.90 0.00 0.00 3.36
294 337 2.592102 ACCTGCATCTTCAATGGTGT 57.408 45.000 0.00 0.00 0.00 4.16
359 402 1.482182 GAAATTTGGATGTGAGGGCCC 59.518 52.381 16.46 16.46 0.00 5.80
395 438 9.855021 GTAAATTTTATCCACAAGTTAGCACAT 57.145 29.630 0.00 0.00 0.00 3.21
477 520 3.658757 TGGTTGTTGCTTAAATCCTGC 57.341 42.857 0.00 0.00 0.00 4.85
478 521 3.230134 TGGTTGTTGCTTAAATCCTGCT 58.770 40.909 0.00 0.00 0.00 4.24
553 640 9.124807 GTGCATATAATCATGAACATCAACATG 57.875 33.333 0.00 0.00 43.31 3.21
560 647 4.996758 TCATGAACATCAACATGAGACGTT 59.003 37.500 0.00 1.59 44.86 3.99
563 650 4.574421 TGAACATCAACATGAGACGTTTGT 59.426 37.500 0.00 0.00 33.72 2.83
567 654 5.743398 ACATCAACATGAGACGTTTGTTTTG 59.257 36.000 0.00 2.02 31.48 2.44
634 721 9.132923 TGTAAACATACCACATTGTCCTTTTTA 57.867 29.630 0.00 0.00 0.00 1.52
666 753 5.047847 GTGTTTCAGCAGAGTTGTACACTA 58.952 41.667 0.00 0.00 35.01 2.74
707 794 8.419076 TGTAAATTCTGAAAGCCAACTTTTTC 57.581 30.769 0.00 0.00 46.20 2.29
708 795 6.925610 AAATTCTGAAAGCCAACTTTTTCC 57.074 33.333 0.00 0.00 46.20 3.13
712 799 2.962421 TGAAAGCCAACTTTTTCCCGAT 59.038 40.909 0.00 0.00 46.20 4.18
739 826 0.250640 GCAGGAGATAGGGTGCATGG 60.251 60.000 0.00 0.00 35.91 3.66
740 827 1.135094 CAGGAGATAGGGTGCATGGT 58.865 55.000 0.00 0.00 0.00 3.55
743 830 4.096681 CAGGAGATAGGGTGCATGGTATA 58.903 47.826 0.00 0.00 0.00 1.47
770 858 7.649057 AGTTAGAAAAACAGATAAGGTGCAAC 58.351 34.615 0.00 0.00 0.00 4.17
828 920 5.970317 ATCATGAGAAATGTTGCAACAGA 57.030 34.783 33.44 23.18 43.04 3.41
830 922 5.705902 TCATGAGAAATGTTGCAACAGATG 58.294 37.500 33.44 24.58 43.04 2.90
858 950 1.527311 GTCGAACCTGAAGAAGTGCAC 59.473 52.381 9.40 9.40 0.00 4.57
859 951 1.412710 TCGAACCTGAAGAAGTGCACT 59.587 47.619 15.25 15.25 0.00 4.40
868 960 3.742882 TGAAGAAGTGCACTGAAGAATCG 59.257 43.478 22.49 0.00 0.00 3.34
983 1079 0.470833 GGCTCTATCTCTCCTGGGCA 60.471 60.000 0.00 0.00 0.00 5.36
984 1080 0.678950 GCTCTATCTCTCCTGGGCAC 59.321 60.000 0.00 0.00 0.00 5.01
989 1085 2.836672 ATCTCTCCTGGGCACTGGCT 62.837 60.000 7.08 0.00 40.87 4.75
991 1087 1.965754 CTCTCCTGGGCACTGGCTAC 61.966 65.000 7.08 0.00 40.87 3.58
992 1088 2.203922 TCCTGGGCACTGGCTACA 60.204 61.111 7.08 0.00 40.87 2.74
993 1089 1.841302 CTCCTGGGCACTGGCTACAA 61.841 60.000 7.08 0.00 40.87 2.41
994 1090 1.207488 TCCTGGGCACTGGCTACAAT 61.207 55.000 7.08 0.00 40.87 2.71
995 1091 0.749454 CCTGGGCACTGGCTACAATC 60.749 60.000 0.00 0.00 40.87 2.67
996 1092 1.078497 TGGGCACTGGCTACAATCG 60.078 57.895 2.14 0.00 40.87 3.34
997 1093 1.819632 GGGCACTGGCTACAATCGG 60.820 63.158 2.14 0.00 40.87 4.18
998 1094 2.472909 GGCACTGGCTACAATCGGC 61.473 63.158 0.00 0.00 40.87 5.54
999 1095 1.745115 GCACTGGCTACAATCGGCA 60.745 57.895 0.00 0.00 36.96 5.69
1000 1096 1.305219 GCACTGGCTACAATCGGCAA 61.305 55.000 0.00 0.00 36.46 4.52
1001 1097 1.382522 CACTGGCTACAATCGGCAAT 58.617 50.000 0.00 0.00 36.46 3.56
1002 1098 1.064505 CACTGGCTACAATCGGCAATG 59.935 52.381 0.00 0.00 36.46 2.82
1003 1099 0.664761 CTGGCTACAATCGGCAATGG 59.335 55.000 0.00 0.00 36.46 3.16
1004 1100 1.360192 GGCTACAATCGGCAATGGC 59.640 57.895 0.00 0.00 40.13 4.40
1013 1109 3.121934 GGCAATGGCGATCATGCA 58.878 55.556 7.54 0.00 42.47 3.96
1014 1110 1.299620 GGCAATGGCGATCATGCAC 60.300 57.895 7.54 0.00 42.47 4.57
1015 1111 1.656263 GCAATGGCGATCATGCACG 60.656 57.895 0.00 6.93 35.99 5.34
1016 1112 1.009335 CAATGGCGATCATGCACGG 60.009 57.895 11.81 0.00 35.99 4.94
1017 1113 1.153188 AATGGCGATCATGCACGGA 60.153 52.632 11.81 0.00 35.99 4.69
1018 1114 1.162181 AATGGCGATCATGCACGGAG 61.162 55.000 11.81 0.00 35.99 4.63
1019 1115 2.969238 GGCGATCATGCACGGAGG 60.969 66.667 11.81 0.00 36.28 4.30
1020 1116 3.643978 GCGATCATGCACGGAGGC 61.644 66.667 11.81 0.00 34.15 4.70
1021 1117 3.333189 CGATCATGCACGGAGGCG 61.333 66.667 0.00 0.00 36.28 5.52
1022 1118 2.106938 GATCATGCACGGAGGCGA 59.893 61.111 0.00 0.00 36.28 5.54
1023 1119 2.202932 ATCATGCACGGAGGCGAC 60.203 61.111 0.00 0.00 36.28 5.19
1024 1120 4.794439 TCATGCACGGAGGCGACG 62.794 66.667 0.00 2.44 36.28 5.12
1060 1156 3.426568 GCCGTGCAAGCAGGAGAC 61.427 66.667 15.55 2.20 34.13 3.36
1061 1157 3.114616 CCGTGCAAGCAGGAGACG 61.115 66.667 15.55 5.76 34.13 4.18
1062 1158 3.782244 CGTGCAAGCAGGAGACGC 61.782 66.667 8.95 0.00 34.13 5.19
1063 1159 2.358003 GTGCAAGCAGGAGACGCT 60.358 61.111 0.00 0.00 40.90 5.07
1064 1160 2.357881 TGCAAGCAGGAGACGCTG 60.358 61.111 0.00 0.00 39.50 5.18
1065 1161 2.358003 GCAAGCAGGAGACGCTGT 60.358 61.111 0.00 0.00 39.50 4.40
1066 1162 1.963338 GCAAGCAGGAGACGCTGTT 60.963 57.895 0.00 0.00 39.50 3.16
1067 1163 1.864862 CAAGCAGGAGACGCTGTTG 59.135 57.895 0.00 0.00 39.50 3.33
1068 1164 1.302033 AAGCAGGAGACGCTGTTGG 60.302 57.895 0.00 0.00 39.50 3.77
1069 1165 2.031163 GCAGGAGACGCTGTTGGT 59.969 61.111 0.00 0.00 0.00 3.67
1070 1166 2.320587 GCAGGAGACGCTGTTGGTG 61.321 63.158 0.00 0.00 0.00 4.17
1071 1167 1.669115 CAGGAGACGCTGTTGGTGG 60.669 63.158 0.00 0.00 0.00 4.61
1072 1168 2.358737 GGAGACGCTGTTGGTGGG 60.359 66.667 0.00 0.00 0.00 4.61
1073 1169 3.050275 GAGACGCTGTTGGTGGGC 61.050 66.667 0.00 0.00 0.00 5.36
1090 1186 3.991051 CGGCGTCTGACACCAGGT 61.991 66.667 14.66 0.00 40.76 4.00
1098 1194 2.509336 GACACCAGGTCGCCATCG 60.509 66.667 0.00 0.00 36.65 3.84
1099 1195 3.296709 GACACCAGGTCGCCATCGT 62.297 63.158 0.00 0.00 36.65 3.73
1100 1196 2.815211 CACCAGGTCGCCATCGTG 60.815 66.667 0.00 0.00 36.96 4.35
1101 1197 4.760047 ACCAGGTCGCCATCGTGC 62.760 66.667 0.00 0.00 36.96 5.34
1103 1199 4.758251 CAGGTCGCCATCGTGCCA 62.758 66.667 0.00 0.00 35.51 4.92
1104 1200 4.457496 AGGTCGCCATCGTGCCAG 62.457 66.667 0.00 0.00 35.51 4.85
1105 1201 4.451150 GGTCGCCATCGTGCCAGA 62.451 66.667 0.00 0.00 36.96 3.86
1106 1202 3.188786 GTCGCCATCGTGCCAGAC 61.189 66.667 0.00 0.00 36.96 3.51
1114 1210 2.573869 CGTGCCAGACGGTGAGAT 59.426 61.111 0.00 0.00 44.85 2.75
1115 1211 1.517257 CGTGCCAGACGGTGAGATC 60.517 63.158 0.00 0.00 44.85 2.75
1116 1212 1.517257 GTGCCAGACGGTGAGATCG 60.517 63.158 0.00 0.00 33.28 3.69
1117 1213 1.677633 TGCCAGACGGTGAGATCGA 60.678 57.895 0.00 0.00 33.28 3.59
1118 1214 1.064946 GCCAGACGGTGAGATCGAG 59.935 63.158 0.00 0.00 33.28 4.04
1119 1215 1.730487 CCAGACGGTGAGATCGAGG 59.270 63.158 0.00 0.00 0.00 4.63
1120 1216 1.032657 CCAGACGGTGAGATCGAGGT 61.033 60.000 0.00 0.00 0.00 3.85
1121 1217 0.378962 CAGACGGTGAGATCGAGGTC 59.621 60.000 0.00 0.00 0.00 3.85
1122 1218 0.035343 AGACGGTGAGATCGAGGTCA 60.035 55.000 0.00 0.00 0.00 4.02
1123 1219 0.809385 GACGGTGAGATCGAGGTCAA 59.191 55.000 1.24 0.00 0.00 3.18
1124 1220 0.811915 ACGGTGAGATCGAGGTCAAG 59.188 55.000 1.24 2.54 0.00 3.02
1125 1221 0.101399 CGGTGAGATCGAGGTCAAGG 59.899 60.000 1.24 0.00 0.00 3.61
1126 1222 0.461961 GGTGAGATCGAGGTCAAGGG 59.538 60.000 1.24 0.00 0.00 3.95
1127 1223 0.179097 GTGAGATCGAGGTCAAGGGC 60.179 60.000 1.24 0.00 0.00 5.19
1128 1224 1.066587 GAGATCGAGGTCAAGGGCG 59.933 63.158 0.00 0.00 0.00 6.13
1129 1225 1.668101 GAGATCGAGGTCAAGGGCGT 61.668 60.000 0.00 0.00 0.00 5.68
1130 1226 1.519455 GATCGAGGTCAAGGGCGTG 60.519 63.158 0.00 0.00 0.00 5.34
1131 1227 2.907897 GATCGAGGTCAAGGGCGTGG 62.908 65.000 0.00 0.00 0.00 4.94
1132 1228 3.691342 CGAGGTCAAGGGCGTGGA 61.691 66.667 0.00 0.00 0.00 4.02
1133 1229 2.266055 GAGGTCAAGGGCGTGGAG 59.734 66.667 0.00 0.00 0.00 3.86
1134 1230 2.526873 AGGTCAAGGGCGTGGAGT 60.527 61.111 0.00 0.00 0.00 3.85
1135 1231 2.113243 GAGGTCAAGGGCGTGGAGTT 62.113 60.000 0.00 0.00 0.00 3.01
1136 1232 1.966451 GGTCAAGGGCGTGGAGTTG 60.966 63.158 0.00 0.00 0.00 3.16
1137 1233 2.281484 TCAAGGGCGTGGAGTTGC 60.281 61.111 0.00 0.00 0.00 4.17
1455 1632 3.369366 CCTTCCAAATTTCCCCAAATCGG 60.369 47.826 0.00 0.00 30.37 4.18
1626 2283 4.100084 CATCTGCTGGTCCCGCCA 62.100 66.667 2.46 0.00 46.95 5.69
1726 2522 0.482446 AACAAGCACTTGGATCCCCA 59.518 50.000 9.90 0.00 44.45 4.96
1866 3472 2.638480 TGGCTGGCAATATGGACTAC 57.362 50.000 0.00 0.00 0.00 2.73
1867 3473 2.126882 TGGCTGGCAATATGGACTACT 58.873 47.619 0.00 0.00 0.00 2.57
1868 3474 2.104792 TGGCTGGCAATATGGACTACTC 59.895 50.000 0.00 0.00 0.00 2.59
1869 3475 2.370189 GGCTGGCAATATGGACTACTCT 59.630 50.000 0.00 0.00 0.00 3.24
1874 3480 4.284490 TGGCAATATGGACTACTCTGATCC 59.716 45.833 0.00 0.00 0.00 3.36
1875 3481 4.284490 GGCAATATGGACTACTCTGATCCA 59.716 45.833 0.52 0.52 46.36 3.41
1876 3482 5.233988 GCAATATGGACTACTCTGATCCAC 58.766 45.833 0.02 0.00 45.15 4.02
1877 3483 5.221521 GCAATATGGACTACTCTGATCCACA 60.222 44.000 0.02 0.00 45.15 4.17
1878 3484 6.686378 GCAATATGGACTACTCTGATCCACAA 60.686 42.308 0.02 0.00 45.15 3.33
1879 3485 6.662865 ATATGGACTACTCTGATCCACAAG 57.337 41.667 0.02 0.00 45.15 3.16
1880 3486 3.779444 TGGACTACTCTGATCCACAAGT 58.221 45.455 0.00 0.00 37.60 3.16
2018 3958 2.346803 TGCTTAACTCTGAATCGTGGC 58.653 47.619 0.00 0.00 0.00 5.01
2194 4495 5.809001 TCTTTCTTTGATGTACAGGAGCAT 58.191 37.500 0.33 0.00 0.00 3.79
2586 5350 3.740115 AGTTACTTTCAGAACACGGCAT 58.260 40.909 0.00 0.00 0.00 4.40
2587 5351 4.134563 AGTTACTTTCAGAACACGGCATT 58.865 39.130 0.00 0.00 0.00 3.56
2588 5352 4.024048 AGTTACTTTCAGAACACGGCATTG 60.024 41.667 0.00 0.00 0.00 2.82
2589 5353 2.571212 ACTTTCAGAACACGGCATTGA 58.429 42.857 0.00 0.00 0.00 2.57
2590 5354 3.149196 ACTTTCAGAACACGGCATTGAT 58.851 40.909 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.961277 GTGGGCAACGACCAGACAG 60.961 63.158 0.00 0.00 43.97 3.51
148 191 6.098679 TCAAATCAACTTGAAAATATGCCGG 58.901 36.000 0.00 0.00 32.39 6.13
165 208 3.426787 TCCTTTTACCGGCTCAAATCA 57.573 42.857 0.00 0.00 0.00 2.57
170 213 1.281419 TGGATCCTTTTACCGGCTCA 58.719 50.000 14.23 0.00 0.00 4.26
185 228 6.012508 TCTCTTTCCTTTGTTCAGGTATGGAT 60.013 38.462 0.00 0.00 35.15 3.41
294 337 3.704566 AGCAGAATACGTGACCCAGATTA 59.295 43.478 0.00 0.00 0.00 1.75
359 402 9.729023 TTGTGGATAAAATTTACTATGAATGCG 57.271 29.630 0.00 0.00 0.00 4.73
395 438 4.676723 GCCTACTGTTTTTGTTGTTGCTCA 60.677 41.667 0.00 0.00 0.00 4.26
477 520 7.797038 TGACATGAATATTCACATGAAGGAG 57.203 36.000 20.19 5.11 44.28 3.69
478 521 8.756486 AATGACATGAATATTCACATGAAGGA 57.244 30.769 20.19 4.12 44.28 3.36
553 640 8.492748 TGTCAGTAATATCAAAACAAACGTCTC 58.507 33.333 0.00 0.00 0.00 3.36
560 647 6.939730 TCTGCCTGTCAGTAATATCAAAACAA 59.060 34.615 0.00 0.00 43.32 2.83
563 650 9.330063 CTTATCTGCCTGTCAGTAATATCAAAA 57.670 33.333 0.00 0.00 43.32 2.44
567 654 6.459066 TGCTTATCTGCCTGTCAGTAATATC 58.541 40.000 0.00 0.00 43.32 1.63
634 721 7.040201 ACAACTCTGCTGAAACACAATATCAAT 60.040 33.333 0.00 0.00 0.00 2.57
666 753 5.772825 ATTTACAACAGTGACTTGTGCAT 57.227 34.783 8.89 0.00 33.79 3.96
707 794 1.457643 TCCTGCTCCTGGTATCGGG 60.458 63.158 0.00 0.00 40.84 5.14
708 795 0.468214 TCTCCTGCTCCTGGTATCGG 60.468 60.000 0.00 0.00 0.00 4.18
712 799 1.148027 CCCTATCTCCTGCTCCTGGTA 59.852 57.143 0.00 0.00 0.00 3.25
743 830 9.515226 TTGCACCTTATCTGTTTTTCTAACTAT 57.485 29.630 0.00 0.00 0.00 2.12
814 905 3.896888 TCTTCCCATCTGTTGCAACATTT 59.103 39.130 31.17 18.90 38.41 2.32
828 920 2.257207 TCAGGTTCGACTTCTTCCCAT 58.743 47.619 0.00 0.00 0.00 4.00
830 922 2.299297 TCTTCAGGTTCGACTTCTTCCC 59.701 50.000 0.00 0.00 0.00 3.97
886 978 4.323477 CCGCGTCCCCTGAACCAA 62.323 66.667 4.92 0.00 0.00 3.67
954 1047 0.112801 AGATAGAGCCTACCCCGACC 59.887 60.000 0.00 0.00 0.00 4.79
956 1049 1.351683 GAGAGATAGAGCCTACCCCGA 59.648 57.143 0.00 0.00 0.00 5.14
957 1050 1.614850 GGAGAGATAGAGCCTACCCCG 60.615 61.905 0.00 0.00 0.00 5.73
962 1055 1.076350 GCCCAGGAGAGATAGAGCCTA 59.924 57.143 0.00 0.00 0.00 3.93
983 1079 1.382522 CATTGCCGATTGTAGCCAGT 58.617 50.000 0.00 0.00 0.00 4.00
984 1080 0.664761 CCATTGCCGATTGTAGCCAG 59.335 55.000 0.00 0.00 0.00 4.85
989 1085 1.225855 GATCGCCATTGCCGATTGTA 58.774 50.000 3.86 0.00 44.60 2.41
991 1087 0.594602 ATGATCGCCATTGCCGATTG 59.405 50.000 3.86 0.00 44.60 2.67
992 1088 0.594602 CATGATCGCCATTGCCGATT 59.405 50.000 3.86 0.00 44.60 3.34
993 1089 1.859427 GCATGATCGCCATTGCCGAT 61.859 55.000 1.68 1.68 46.95 4.18
994 1090 2.545596 GCATGATCGCCATTGCCGA 61.546 57.895 0.00 0.00 39.24 5.54
995 1091 2.050714 GCATGATCGCCATTGCCG 60.051 61.111 0.00 0.00 31.94 5.69
996 1092 1.299620 GTGCATGATCGCCATTGCC 60.300 57.895 0.00 0.00 31.94 4.52
997 1093 1.656263 CGTGCATGATCGCCATTGC 60.656 57.895 0.00 0.00 31.94 3.56
998 1094 1.009335 CCGTGCATGATCGCCATTG 60.009 57.895 7.72 0.00 31.94 2.82
999 1095 1.153188 TCCGTGCATGATCGCCATT 60.153 52.632 7.72 0.00 31.94 3.16
1000 1096 1.596203 CTCCGTGCATGATCGCCAT 60.596 57.895 7.72 0.00 35.44 4.40
1001 1097 2.202919 CTCCGTGCATGATCGCCA 60.203 61.111 7.72 0.00 0.00 5.69
1002 1098 2.969238 CCTCCGTGCATGATCGCC 60.969 66.667 7.72 0.00 0.00 5.54
1003 1099 3.643978 GCCTCCGTGCATGATCGC 61.644 66.667 7.72 1.27 0.00 4.58
1004 1100 3.333189 CGCCTCCGTGCATGATCG 61.333 66.667 7.72 0.00 0.00 3.69
1005 1101 2.106938 TCGCCTCCGTGCATGATC 59.893 61.111 7.72 0.00 35.54 2.92
1006 1102 2.202932 GTCGCCTCCGTGCATGAT 60.203 61.111 7.72 0.00 35.54 2.45
1007 1103 4.794439 CGTCGCCTCCGTGCATGA 62.794 66.667 7.72 0.00 35.54 3.07
1043 1139 3.426568 GTCTCCTGCTTGCACGGC 61.427 66.667 4.11 4.11 0.00 5.68
1044 1140 3.114616 CGTCTCCTGCTTGCACGG 61.115 66.667 0.00 0.00 0.00 4.94
1045 1141 3.782244 GCGTCTCCTGCTTGCACG 61.782 66.667 0.00 0.00 0.00 5.34
1046 1142 2.358003 AGCGTCTCCTGCTTGCAC 60.358 61.111 0.00 0.00 40.48 4.57
1047 1143 2.357881 CAGCGTCTCCTGCTTGCA 60.358 61.111 0.00 0.00 41.72 4.08
1048 1144 1.963338 AACAGCGTCTCCTGCTTGC 60.963 57.895 0.00 0.00 41.72 4.01
1049 1145 1.572085 CCAACAGCGTCTCCTGCTTG 61.572 60.000 0.00 0.00 41.72 4.01
1050 1146 1.302033 CCAACAGCGTCTCCTGCTT 60.302 57.895 0.00 0.00 41.72 3.91
1051 1147 2.345244 CCAACAGCGTCTCCTGCT 59.655 61.111 0.00 0.00 45.31 4.24
1052 1148 2.031163 ACCAACAGCGTCTCCTGC 59.969 61.111 0.00 0.00 36.29 4.85
1053 1149 1.669115 CCACCAACAGCGTCTCCTG 60.669 63.158 0.00 0.00 38.78 3.86
1054 1150 2.743718 CCACCAACAGCGTCTCCT 59.256 61.111 0.00 0.00 0.00 3.69
1055 1151 2.358737 CCCACCAACAGCGTCTCC 60.359 66.667 0.00 0.00 0.00 3.71
1056 1152 3.050275 GCCCACCAACAGCGTCTC 61.050 66.667 0.00 0.00 0.00 3.36
1057 1153 4.988598 CGCCCACCAACAGCGTCT 62.989 66.667 0.00 0.00 44.65 4.18
1075 1171 2.430921 CGACCTGGTGTCAGACGC 60.431 66.667 2.82 5.46 44.71 5.19
1076 1172 2.430921 GCGACCTGGTGTCAGACG 60.431 66.667 2.82 0.81 44.71 4.18
1077 1173 2.048127 GGCGACCTGGTGTCAGAC 60.048 66.667 2.82 0.00 44.71 3.51
1078 1174 1.888436 GATGGCGACCTGGTGTCAGA 61.888 60.000 2.82 0.00 44.71 3.27
1079 1175 1.448540 GATGGCGACCTGGTGTCAG 60.449 63.158 2.82 0.00 44.71 3.51
1080 1176 2.662596 GATGGCGACCTGGTGTCA 59.337 61.111 2.82 4.96 44.71 3.58
1081 1177 2.509336 CGATGGCGACCTGGTGTC 60.509 66.667 2.82 0.00 40.82 3.67
1082 1178 3.311110 ACGATGGCGACCTGGTGT 61.311 61.111 2.82 0.00 41.64 4.16
1083 1179 2.815211 CACGATGGCGACCTGGTG 60.815 66.667 2.82 0.00 41.64 4.17
1084 1180 4.760047 GCACGATGGCGACCTGGT 62.760 66.667 0.00 0.00 41.64 4.00
1098 1194 1.517257 CGATCTCACCGTCTGGCAC 60.517 63.158 0.00 0.00 39.70 5.01
1099 1195 1.657751 CTCGATCTCACCGTCTGGCA 61.658 60.000 0.00 0.00 39.70 4.92
1100 1196 1.064946 CTCGATCTCACCGTCTGGC 59.935 63.158 0.00 0.00 39.70 4.85
1101 1197 1.032657 ACCTCGATCTCACCGTCTGG 61.033 60.000 0.00 0.00 42.84 3.86
1102 1198 0.378962 GACCTCGATCTCACCGTCTG 59.621 60.000 0.00 0.00 0.00 3.51
1103 1199 0.035343 TGACCTCGATCTCACCGTCT 60.035 55.000 0.00 0.00 0.00 4.18
1104 1200 0.809385 TTGACCTCGATCTCACCGTC 59.191 55.000 0.00 0.00 0.00 4.79
1105 1201 0.811915 CTTGACCTCGATCTCACCGT 59.188 55.000 0.00 0.00 0.00 4.83
1106 1202 0.101399 CCTTGACCTCGATCTCACCG 59.899 60.000 0.00 0.00 0.00 4.94
1107 1203 0.461961 CCCTTGACCTCGATCTCACC 59.538 60.000 0.00 0.00 0.00 4.02
1108 1204 0.179097 GCCCTTGACCTCGATCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
1109 1205 1.667154 CGCCCTTGACCTCGATCTCA 61.667 60.000 0.00 0.00 0.00 3.27
1110 1206 1.066587 CGCCCTTGACCTCGATCTC 59.933 63.158 0.00 0.00 0.00 2.75
1111 1207 1.682684 ACGCCCTTGACCTCGATCT 60.683 57.895 0.00 0.00 0.00 2.75
1112 1208 1.519455 CACGCCCTTGACCTCGATC 60.519 63.158 0.00 0.00 0.00 3.69
1113 1209 2.579201 CACGCCCTTGACCTCGAT 59.421 61.111 0.00 0.00 0.00 3.59
1114 1210 3.691342 CCACGCCCTTGACCTCGA 61.691 66.667 0.00 0.00 0.00 4.04
1115 1211 3.649277 CTCCACGCCCTTGACCTCG 62.649 68.421 0.00 0.00 0.00 4.63
1116 1212 2.113243 AACTCCACGCCCTTGACCTC 62.113 60.000 0.00 0.00 0.00 3.85
1117 1213 2.147387 AACTCCACGCCCTTGACCT 61.147 57.895 0.00 0.00 0.00 3.85
1118 1214 1.966451 CAACTCCACGCCCTTGACC 60.966 63.158 0.00 0.00 0.00 4.02
1119 1215 2.617274 GCAACTCCACGCCCTTGAC 61.617 63.158 0.00 0.00 0.00 3.18
1120 1216 2.281484 GCAACTCCACGCCCTTGA 60.281 61.111 0.00 0.00 0.00 3.02
1121 1217 3.365265 GGCAACTCCACGCCCTTG 61.365 66.667 0.00 0.00 42.82 3.61
1133 1229 8.089115 CCTTATTATACTTGCTCTAAGGCAAC 57.911 38.462 0.00 0.00 45.64 4.17
1137 1233 7.600752 GTCAGCCTTATTATACTTGCTCTAAGG 59.399 40.741 0.00 0.00 40.84 2.69
1455 1632 1.677637 CTAGGGTTCGGGAGAGGTGC 61.678 65.000 0.00 0.00 41.75 5.01
1726 2522 2.366916 CCAGAGACTCTTGTGGTCTTGT 59.633 50.000 0.98 0.00 43.13 3.16
1866 3472 0.534412 AGCCGACTTGTGGATCAGAG 59.466 55.000 0.00 0.00 0.00 3.35
1867 3473 0.532573 GAGCCGACTTGTGGATCAGA 59.467 55.000 0.00 0.00 41.53 3.27
1868 3474 0.247460 TGAGCCGACTTGTGGATCAG 59.753 55.000 0.00 0.00 46.28 2.90
1874 3480 0.951040 GGACCTTGAGCCGACTTGTG 60.951 60.000 0.00 0.00 0.00 3.33
1875 3481 1.122019 AGGACCTTGAGCCGACTTGT 61.122 55.000 0.00 0.00 0.00 3.16
1876 3482 0.035458 AAGGACCTTGAGCCGACTTG 59.965 55.000 5.76 0.00 0.00 3.16
1877 3483 0.035458 CAAGGACCTTGAGCCGACTT 59.965 55.000 27.43 0.00 43.42 3.01
1878 3484 1.674057 CAAGGACCTTGAGCCGACT 59.326 57.895 27.43 0.00 43.42 4.18
1879 3485 2.035442 GCAAGGACCTTGAGCCGAC 61.035 63.158 33.92 13.95 43.42 4.79
1880 3486 2.217038 AGCAAGGACCTTGAGCCGA 61.217 57.895 33.92 0.00 43.42 5.54
2018 3958 3.305629 GTCAGCAGCTCTAAGAAATGACG 59.694 47.826 0.00 0.00 0.00 4.35
2194 4495 2.595124 TCAGCAAACGAGAAGTCACA 57.405 45.000 0.00 0.00 0.00 3.58
2586 5350 6.602803 TGCAATCAATACTTCCTAGCAATCAA 59.397 34.615 0.00 0.00 0.00 2.57
2587 5351 6.121590 TGCAATCAATACTTCCTAGCAATCA 58.878 36.000 0.00 0.00 0.00 2.57
2588 5352 6.624352 TGCAATCAATACTTCCTAGCAATC 57.376 37.500 0.00 0.00 0.00 2.67
2589 5353 6.516194 GCATGCAATCAATACTTCCTAGCAAT 60.516 38.462 14.21 0.00 32.83 3.56
2590 5354 5.221106 GCATGCAATCAATACTTCCTAGCAA 60.221 40.000 14.21 0.00 32.83 3.91
2803 9552 1.444933 TGAGGGGCTTCTCCTTTCAA 58.555 50.000 6.08 0.00 34.21 2.69


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

AutoCloner maintained by Alex Coulton.