Multiple sequence alignment - TraesCS4A01G424700

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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 TraesCS4A01G424700 chr4A 100.000 5220 0 0 1 5220 695973602 695978821 0.000000e+00 9640.0
1 TraesCS4A01G424700 chr4A 94.848 4387 169 19 797 5147 625833805 625829440 0.000000e+00 6796.0
2 TraesCS4A01G424700 chr4A 90.833 120 9 2 38 157 625834218 625834101 5.410000e-35 159.0
3 TraesCS4A01G424700 chr5D 94.288 4447 184 31 832 5220 543404682 543409116 0.000000e+00 6741.0
4 TraesCS4A01G424700 chr5D 89.474 399 41 1 40 438 543404197 543404594 2.170000e-138 503.0
5 TraesCS4A01G424700 chr5D 84.211 228 22 10 2550 2772 542111712 542111494 5.300000e-50 209.0
6 TraesCS4A01G424700 chr5B 95.776 4190 140 14 994 5154 557247616 557251797 0.000000e+00 6722.0
7 TraesCS4A01G424700 chr5B 87.125 901 64 18 38 887 557246718 557247617 0.000000e+00 974.0
8 TraesCS4A01G424700 chr5B 86.207 203 22 5 309 510 613176576 613176379 1.140000e-51 215.0
9 TraesCS4A01G424700 chr7D 80.000 585 80 27 191 744 5437325 5436747 1.050000e-106 398.0
10 TraesCS4A01G424700 chr2A 87.000 300 37 2 211 510 764782620 764782323 2.330000e-88 337.0
11 TraesCS4A01G424700 chr2A 89.583 48 4 1 188 234 42810603 42810650 5.650000e-05 60.2
12 TraesCS4A01G424700 chr7B 78.392 398 46 29 382 745 646215435 646215826 6.800000e-54 222.0
13 TraesCS4A01G424700 chr7B 100.000 38 0 0 1 38 668400492 668400455 2.610000e-08 71.3
14 TraesCS4A01G424700 chr7B 91.304 46 2 2 189 234 637611400 637611443 1.570000e-05 62.1
15 TraesCS4A01G424700 chr3B 88.506 174 18 2 333 506 618684971 618685142 5.300000e-50 209.0
16 TraesCS4A01G424700 chr3B 81.592 201 30 6 191 388 733070638 733070442 5.410000e-35 159.0
17 TraesCS4A01G424700 chr3B 97.561 41 0 1 1 41 792962832 792962871 9.380000e-08 69.4
18 TraesCS4A01G424700 chr3D 81.818 99 10 1 655 745 117629320 117629418 5.610000e-10 76.8
19 TraesCS4A01G424700 chr3A 100.000 39 0 0 1 39 449511750 449511788 7.250000e-09 73.1
20 TraesCS4A01G424700 chr3A 93.478 46 1 2 189 234 638896443 638896400 3.370000e-07 67.6
21 TraesCS4A01G424700 chr4B 100.000 38 0 0 2 39 314791152 314791115 2.610000e-08 71.3
22 TraesCS4A01G424700 chr4B 97.436 39 1 0 1 39 663073801 663073839 3.370000e-07 67.6
23 TraesCS4A01G424700 chr1D 100.000 38 0 0 1 38 462875174 462875211 2.610000e-08 71.3
24 TraesCS4A01G424700 chr6D 97.561 41 0 1 2 41 460310875 460310835 9.380000e-08 69.4
25 TraesCS4A01G424700 chr5A 97.561 41 0 1 1 41 456623975 456623936 9.380000e-08 69.4
26 TraesCS4A01G424700 chr1B 90.196 51 3 2 1 50 667886291 667886340 1.210000e-06 65.8
27 TraesCS4A01G424700 chrUn 91.304 46 2 2 189 234 87127808 87127851 1.570000e-05 62.1
28 TraesCS4A01G424700 chr2B 100.000 28 0 0 189 216 8351021 8350994 9.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G424700 chr4A 695973602 695978821 5219 False 9640.0 9640 100.0000 1 5220 1 chr4A.!!$F1 5219
1 TraesCS4A01G424700 chr4A 625829440 625834218 4778 True 3477.5 6796 92.8405 38 5147 2 chr4A.!!$R1 5109
2 TraesCS4A01G424700 chr5D 543404197 543409116 4919 False 3622.0 6741 91.8810 40 5220 2 chr5D.!!$F1 5180
3 TraesCS4A01G424700 chr5B 557246718 557251797 5079 False 3848.0 6722 91.4505 38 5154 2 chr5B.!!$F1 5116
4 TraesCS4A01G424700 chr7D 5436747 5437325 578 True 398.0 398 80.0000 191 744 1 chr7D.!!$R1 553

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
463 536 0.036010 CAATCTCTTGTGGCTCCGGT 60.036 55.000 0.00 0.0 0.00 5.28 F
896 1067 0.102481 AGCGTGACACAGAACTTCGT 59.898 50.000 6.37 0.0 0.00 3.85 F
984 1155 0.174162 AATAAACCTCGTCCGTCCGG 59.826 55.000 0.00 0.0 0.00 5.14 F
1974 2269 0.652592 CGAATCAGAATGCGGTGGTC 59.347 55.000 0.00 0.0 34.76 4.02 F
3532 3838 2.540769 GCACAAAGCTTGCGTAGTTGAA 60.541 45.455 0.00 0.0 41.15 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1858 1.068741 GAGTTGGTCAGGAACACGTCT 59.931 52.381 0.00 0.0 0.00 4.18 R
2706 3002 1.602668 GCAAGCAATGAGAACGGCAAA 60.603 47.619 0.00 0.0 0.00 3.68 R
3003 3304 5.120674 GCAAATTGATTTTTGGAGCTACACC 59.879 40.000 0.00 0.0 37.13 4.16 R
3550 3856 1.065636 TCTTCAGCCTCAGCCATCTTG 60.066 52.381 0.00 0.0 41.25 3.02 R
5180 5549 0.107831 ACAACCCTGTTCTAGCGCAA 59.892 50.000 11.47 0.0 28.57 4.85 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
17 18 4.109693 GAAATTTCGGCCGGCGCA 62.110 61.111 27.83 6.00 36.38 6.09
18 19 4.413800 AAATTTCGGCCGGCGCAC 62.414 61.111 27.83 5.60 36.38 5.34
32 33 4.530857 GCACCGGCGCCTATCACT 62.531 66.667 26.68 0.00 0.00 3.41
33 34 2.279517 CACCGGCGCCTATCACTC 60.280 66.667 26.68 0.00 0.00 3.51
34 35 3.900892 ACCGGCGCCTATCACTCG 61.901 66.667 26.68 8.26 0.00 4.18
120 121 6.545666 TGGAAGAGTAGTGCTTTGAAATTGAA 59.454 34.615 0.00 0.00 0.00 2.69
236 237 5.977171 AAAACGCCAAACCTGTAAAATTC 57.023 34.783 0.00 0.00 0.00 2.17
237 238 4.929819 AACGCCAAACCTGTAAAATTCT 57.070 36.364 0.00 0.00 0.00 2.40
295 296 5.765182 CAGAACAGACCCTGTAAAAGTTCAT 59.235 40.000 0.00 0.00 44.62 2.57
307 308 8.388103 CCTGTAAAAGTTCATCGAATCGTAAAT 58.612 33.333 1.52 0.00 0.00 1.40
318 319 8.984764 TCATCGAATCGTAAATATTTTACAGGG 58.015 33.333 5.91 0.00 0.00 4.45
439 489 2.427245 CCGTACCAGAGGGCTCCAG 61.427 68.421 0.00 0.00 37.90 3.86
463 536 0.036010 CAATCTCTTGTGGCTCCGGT 60.036 55.000 0.00 0.00 0.00 5.28
510 583 1.198094 TCGCCTCAATCCCAACCAGA 61.198 55.000 0.00 0.00 0.00 3.86
512 585 1.396653 GCCTCAATCCCAACCAGATG 58.603 55.000 0.00 0.00 0.00 2.90
615 760 3.184683 GCGGAGAGCTGCGTCTTG 61.185 66.667 12.76 0.00 46.28 3.02
616 761 3.184683 CGGAGAGCTGCGTCTTGC 61.185 66.667 3.11 0.00 46.70 4.01
626 771 4.717629 CGTCTTGCGTGGCGAGGA 62.718 66.667 5.09 0.00 40.25 3.71
627 772 3.112709 GTCTTGCGTGGCGAGGAC 61.113 66.667 5.09 0.00 40.25 3.85
628 773 4.373116 TCTTGCGTGGCGAGGACC 62.373 66.667 5.09 0.00 40.25 4.46
732 885 1.746470 CGGTTTTCTCGGCCCTTATT 58.254 50.000 0.00 0.00 0.00 1.40
745 898 2.357465 GCCCTTATTCGGGGTTTAAGGT 60.357 50.000 7.08 0.00 44.83 3.50
812 983 4.927978 TGTTTTAACCCTGGTGTGATTG 57.072 40.909 0.00 0.00 0.00 2.67
892 1063 3.274393 GTCAGCGTGACACAGAACT 57.726 52.632 6.37 0.00 46.22 3.01
893 1064 1.571919 GTCAGCGTGACACAGAACTT 58.428 50.000 6.37 0.00 46.22 2.66
894 1065 1.523095 GTCAGCGTGACACAGAACTTC 59.477 52.381 6.37 0.00 46.22 3.01
895 1066 0.504384 CAGCGTGACACAGAACTTCG 59.496 55.000 6.37 0.00 0.00 3.79
896 1067 0.102481 AGCGTGACACAGAACTTCGT 59.898 50.000 6.37 0.00 0.00 3.85
897 1068 0.928229 GCGTGACACAGAACTTCGTT 59.072 50.000 6.37 0.00 0.00 3.85
898 1069 1.071436 GCGTGACACAGAACTTCGTTC 60.071 52.381 6.37 0.00 42.25 3.95
899 1070 2.190161 CGTGACACAGAACTTCGTTCA 58.810 47.619 6.37 0.58 44.11 3.18
900 1071 2.034842 CGTGACACAGAACTTCGTTCAC 60.035 50.000 6.37 9.11 44.11 3.18
901 1072 2.927477 GTGACACAGAACTTCGTTCACA 59.073 45.455 9.16 0.06 44.11 3.58
902 1073 3.555956 GTGACACAGAACTTCGTTCACAT 59.444 43.478 9.16 0.00 44.11 3.21
903 1074 3.802139 TGACACAGAACTTCGTTCACATC 59.198 43.478 9.16 2.66 44.11 3.06
904 1075 3.131396 ACACAGAACTTCGTTCACATCC 58.869 45.455 9.16 0.00 44.11 3.51
905 1076 2.480419 CACAGAACTTCGTTCACATCCC 59.520 50.000 9.16 0.00 44.11 3.85
906 1077 2.076863 CAGAACTTCGTTCACATCCCC 58.923 52.381 9.16 0.00 44.11 4.81
907 1078 1.697432 AGAACTTCGTTCACATCCCCA 59.303 47.619 9.16 0.00 44.11 4.96
908 1079 2.305927 AGAACTTCGTTCACATCCCCAT 59.694 45.455 9.16 0.00 44.11 4.00
909 1080 2.403252 ACTTCGTTCACATCCCCATC 57.597 50.000 0.00 0.00 0.00 3.51
910 1081 1.909302 ACTTCGTTCACATCCCCATCT 59.091 47.619 0.00 0.00 0.00 2.90
911 1082 2.305927 ACTTCGTTCACATCCCCATCTT 59.694 45.455 0.00 0.00 0.00 2.40
912 1083 3.244911 ACTTCGTTCACATCCCCATCTTT 60.245 43.478 0.00 0.00 0.00 2.52
913 1084 2.985896 TCGTTCACATCCCCATCTTTC 58.014 47.619 0.00 0.00 0.00 2.62
914 1085 2.017049 CGTTCACATCCCCATCTTTCC 58.983 52.381 0.00 0.00 0.00 3.13
915 1086 2.356125 CGTTCACATCCCCATCTTTCCT 60.356 50.000 0.00 0.00 0.00 3.36
916 1087 3.118408 CGTTCACATCCCCATCTTTCCTA 60.118 47.826 0.00 0.00 0.00 2.94
917 1088 4.200092 GTTCACATCCCCATCTTTCCTAC 58.800 47.826 0.00 0.00 0.00 3.18
918 1089 3.736094 TCACATCCCCATCTTTCCTACT 58.264 45.455 0.00 0.00 0.00 2.57
919 1090 3.711704 TCACATCCCCATCTTTCCTACTC 59.288 47.826 0.00 0.00 0.00 2.59
920 1091 3.049344 ACATCCCCATCTTTCCTACTCC 58.951 50.000 0.00 0.00 0.00 3.85
921 1092 2.961536 TCCCCATCTTTCCTACTCCA 57.038 50.000 0.00 0.00 0.00 3.86
922 1093 3.214694 TCCCCATCTTTCCTACTCCAA 57.785 47.619 0.00 0.00 0.00 3.53
923 1094 3.115390 TCCCCATCTTTCCTACTCCAAG 58.885 50.000 0.00 0.00 0.00 3.61
924 1095 2.846827 CCCCATCTTTCCTACTCCAAGT 59.153 50.000 0.00 0.00 0.00 3.16
925 1096 3.370953 CCCCATCTTTCCTACTCCAAGTG 60.371 52.174 0.00 0.00 0.00 3.16
926 1097 3.264450 CCCATCTTTCCTACTCCAAGTGT 59.736 47.826 0.00 0.00 0.00 3.55
927 1098 4.256920 CCATCTTTCCTACTCCAAGTGTG 58.743 47.826 0.00 0.00 0.00 3.82
928 1099 4.020218 CCATCTTTCCTACTCCAAGTGTGA 60.020 45.833 0.00 0.00 0.00 3.58
929 1100 5.338708 CCATCTTTCCTACTCCAAGTGTGAT 60.339 44.000 0.00 0.00 0.00 3.06
930 1101 5.407407 TCTTTCCTACTCCAAGTGTGATC 57.593 43.478 0.00 0.00 0.00 2.92
931 1102 5.087323 TCTTTCCTACTCCAAGTGTGATCT 58.913 41.667 0.00 0.00 0.00 2.75
932 1103 5.186021 TCTTTCCTACTCCAAGTGTGATCTC 59.814 44.000 0.00 0.00 0.00 2.75
933 1104 3.366396 TCCTACTCCAAGTGTGATCTCC 58.634 50.000 0.00 0.00 0.00 3.71
934 1105 3.099905 CCTACTCCAAGTGTGATCTCCA 58.900 50.000 0.00 0.00 0.00 3.86
935 1106 3.515502 CCTACTCCAAGTGTGATCTCCAA 59.484 47.826 0.00 0.00 0.00 3.53
936 1107 3.692257 ACTCCAAGTGTGATCTCCAAG 57.308 47.619 0.00 0.00 0.00 3.61
937 1108 2.304180 ACTCCAAGTGTGATCTCCAAGG 59.696 50.000 0.00 0.00 0.00 3.61
938 1109 1.630369 TCCAAGTGTGATCTCCAAGGG 59.370 52.381 0.00 0.00 0.00 3.95
939 1110 1.630369 CCAAGTGTGATCTCCAAGGGA 59.370 52.381 0.00 0.00 0.00 4.20
949 1120 2.795231 CTCCAAGGGAGCAATGAAGA 57.205 50.000 0.00 0.00 43.29 2.87
950 1121 3.077484 CTCCAAGGGAGCAATGAAGAA 57.923 47.619 0.00 0.00 43.29 2.52
951 1122 3.424703 CTCCAAGGGAGCAATGAAGAAA 58.575 45.455 0.00 0.00 43.29 2.52
952 1123 3.828451 CTCCAAGGGAGCAATGAAGAAAA 59.172 43.478 0.00 0.00 43.29 2.29
953 1124 4.222336 TCCAAGGGAGCAATGAAGAAAAA 58.778 39.130 0.00 0.00 0.00 1.94
976 1147 7.727578 AAATGGGGAAATTAATAAACCTCGT 57.272 32.000 0.00 0.00 0.00 4.18
977 1148 6.954487 ATGGGGAAATTAATAAACCTCGTC 57.046 37.500 0.00 0.00 0.00 4.20
978 1149 5.195185 TGGGGAAATTAATAAACCTCGTCC 58.805 41.667 0.00 0.00 0.00 4.79
979 1150 4.274214 GGGGAAATTAATAAACCTCGTCCG 59.726 45.833 0.00 0.00 0.00 4.79
980 1151 4.877823 GGGAAATTAATAAACCTCGTCCGT 59.122 41.667 0.00 0.00 0.00 4.69
981 1152 5.007039 GGGAAATTAATAAACCTCGTCCGTC 59.993 44.000 0.00 0.00 0.00 4.79
982 1153 5.007039 GGAAATTAATAAACCTCGTCCGTCC 59.993 44.000 0.00 0.00 0.00 4.79
983 1154 2.849880 TAATAAACCTCGTCCGTCCG 57.150 50.000 0.00 0.00 0.00 4.79
984 1155 0.174162 AATAAACCTCGTCCGTCCGG 59.826 55.000 0.00 0.00 0.00 5.14
985 1156 0.967380 ATAAACCTCGTCCGTCCGGT 60.967 55.000 0.00 0.00 36.47 5.28
986 1157 1.586154 TAAACCTCGTCCGTCCGGTC 61.586 60.000 0.00 0.00 36.47 4.79
989 1160 3.730761 CTCGTCCGTCCGGTCGTT 61.731 66.667 19.43 0.00 44.67 3.85
990 1161 3.657835 CTCGTCCGTCCGGTCGTTC 62.658 68.421 19.43 10.74 44.67 3.95
991 1162 4.766088 CGTCCGTCCGGTCGTTCC 62.766 72.222 19.43 6.15 40.78 3.62
1563 1858 3.286751 GTGAGTGGGCTTGCGCAA 61.287 61.111 23.48 23.48 38.10 4.85
1617 1912 0.745845 ACGCCAAGTGCAGGATGATC 60.746 55.000 0.00 0.00 39.69 2.92
1654 1949 3.881019 TTCGACCGGGCTGAGGAGT 62.881 63.158 5.33 0.00 0.00 3.85
1881 2176 4.457949 GGTTTGGACTTGGATATGTTCGTT 59.542 41.667 0.00 0.00 0.00 3.85
1974 2269 0.652592 CGAATCAGAATGCGGTGGTC 59.347 55.000 0.00 0.00 34.76 4.02
2152 2447 3.941188 CGGTGCACTGTGGGAGGT 61.941 66.667 17.96 0.00 0.00 3.85
2190 2485 8.863086 CATGTTATATTCAATGGGTTTCAGGAT 58.137 33.333 0.00 0.00 0.00 3.24
2230 2525 2.930887 GCGCTGATCAACTTGTACTCCA 60.931 50.000 0.00 0.00 0.00 3.86
2337 2632 3.323729 TTCGCGCATGATGAGAATTTC 57.676 42.857 8.75 0.00 0.00 2.17
2706 3002 7.910162 GTGTCGTGATAAATGATAATGCTTTGT 59.090 33.333 0.00 0.00 0.00 2.83
3003 3304 4.100529 GTTGTGCAATGCAACATAGCTAG 58.899 43.478 10.44 0.00 43.91 3.42
3160 3464 3.985008 TGTAGCTTGCGTTCAGTTTCTA 58.015 40.909 0.00 0.00 0.00 2.10
3401 3705 3.181456 GCAGTCTCCTCTATTTCTGGCAT 60.181 47.826 0.00 0.00 0.00 4.40
3404 3708 6.586344 CAGTCTCCTCTATTTCTGGCATTTA 58.414 40.000 0.00 0.00 0.00 1.40
3444 3750 9.630098 AACAATGTTCACAATTCATCAAGTATC 57.370 29.630 0.00 0.00 0.00 2.24
3445 3751 9.017509 ACAATGTTCACAATTCATCAAGTATCT 57.982 29.630 0.00 0.00 0.00 1.98
3448 3754 7.809665 TGTTCACAATTCATCAAGTATCTGTG 58.190 34.615 0.00 0.00 35.40 3.66
3463 3769 7.744087 AGTATCTGTGTTTTTGTAATGCAGA 57.256 32.000 0.00 0.00 36.21 4.26
3466 3772 6.389830 TCTGTGTTTTTGTAATGCAGACAT 57.610 33.333 5.15 0.00 38.49 3.06
3532 3838 2.540769 GCACAAAGCTTGCGTAGTTGAA 60.541 45.455 0.00 0.00 41.15 2.69
3876 4182 2.874701 CTGATGGAAATAACTCCTGCCG 59.125 50.000 0.00 0.00 36.35 5.69
3911 4217 5.668471 CAGTTCATGCCAGATTAGAAGAGA 58.332 41.667 0.00 0.00 0.00 3.10
4004 4310 0.250513 GGATGGCGAGACCTCACTTT 59.749 55.000 0.00 0.00 40.22 2.66
4154 4460 5.423931 GCAAGGGAAAACAGGGGAATAATTA 59.576 40.000 0.00 0.00 0.00 1.40
4168 4474 6.342111 GGGAATAATTATCAGAGATCCGACC 58.658 44.000 0.00 0.00 0.00 4.79
4281 4616 1.898574 CCAGCGGAACAGTTTGGCT 60.899 57.895 6.28 6.28 0.00 4.75
4361 4696 6.021030 AGGATTACAGTAAAGGGTACAGTGA 58.979 40.000 0.00 0.00 0.00 3.41
4378 4713 4.000331 AGTGACATTCCACTGAACAGAG 58.000 45.455 8.87 0.58 44.93 3.35
4444 4779 3.242641 CGATTGTGCTTGATGATGTCCAG 60.243 47.826 0.00 0.00 0.00 3.86
4484 4820 1.749609 GCGATTAAGCGTCCACGTCC 61.750 60.000 15.30 0.00 42.22 4.79
4508 4845 3.940221 GAGCTGTTCATCTCTGCTGAAAT 59.060 43.478 0.00 0.00 39.47 2.17
4512 4849 5.072040 TGTTCATCTCTGCTGAAATCGTA 57.928 39.130 0.00 0.00 34.59 3.43
4538 4875 1.339438 GCTGGAGATGTGAAGGCAGAA 60.339 52.381 0.00 0.00 0.00 3.02
4576 4913 5.046304 TCTCAGCTAGAACTGTGGCTTAATT 60.046 40.000 0.00 0.00 38.84 1.40
4642 4979 2.730094 CCGGCAGCTGCTGTTTTT 59.270 55.556 38.29 0.00 45.66 1.94
4697 5034 5.064325 CAGCACGTACACTATAGTCACACTA 59.936 44.000 1.26 0.00 34.82 2.74
4930 5289 6.038161 TGAAATTATACCCTTGTGCTCAATCG 59.962 38.462 0.99 0.00 32.82 3.34
5011 5372 7.973388 CAGGAGTTTTTACTGATTCAAAACACA 59.027 33.333 12.03 0.00 41.09 3.72
5012 5373 8.695456 AGGAGTTTTTACTGATTCAAAACACAT 58.305 29.630 12.03 3.62 41.09 3.21
5180 5549 6.308015 TGCCTGTATACTAGTTTGGTGATT 57.692 37.500 0.00 0.00 0.00 2.57
5183 5552 6.458342 GCCTGTATACTAGTTTGGTGATTTGC 60.458 42.308 0.00 0.00 0.00 3.68
5185 5554 2.989422 ACTAGTTTGGTGATTTGCGC 57.011 45.000 0.00 0.00 0.00 6.09
5196 5565 1.003118 TGATTTGCGCTAGAACAGGGT 59.997 47.619 9.73 0.00 39.38 4.34
5211 5580 1.031571 AGGGTTGTGCTGTGTGTGTG 61.032 55.000 0.00 0.00 0.00 3.82
5212 5581 1.312371 GGGTTGTGCTGTGTGTGTGT 61.312 55.000 0.00 0.00 0.00 3.72
5213 5582 1.374560 GGTTGTGCTGTGTGTGTGTA 58.625 50.000 0.00 0.00 0.00 2.90
5214 5583 1.330521 GGTTGTGCTGTGTGTGTGTAG 59.669 52.381 0.00 0.00 0.00 2.74
5215 5584 2.006888 GTTGTGCTGTGTGTGTGTAGT 58.993 47.619 0.00 0.00 0.00 2.73
5216 5585 2.394930 TGTGCTGTGTGTGTGTAGTT 57.605 45.000 0.00 0.00 0.00 2.24
5217 5586 3.528597 TGTGCTGTGTGTGTGTAGTTA 57.471 42.857 0.00 0.00 0.00 2.24
5218 5587 3.191669 TGTGCTGTGTGTGTGTAGTTAC 58.808 45.455 0.00 0.00 0.00 2.50
5219 5588 2.542595 GTGCTGTGTGTGTGTAGTTACC 59.457 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.109693 TGCGCCGGCCGAAATTTC 62.110 61.111 30.73 8.20 40.02 2.17
1 2 4.413800 GTGCGCCGGCCGAAATTT 62.414 61.111 30.73 0.00 40.02 1.82
15 16 4.530857 AGTGATAGGCGCCGGTGC 62.531 66.667 31.86 31.86 0.00 5.01
16 17 2.279517 GAGTGATAGGCGCCGGTG 60.280 66.667 23.20 11.67 0.00 4.94
17 18 3.900892 CGAGTGATAGGCGCCGGT 61.901 66.667 23.20 14.30 0.00 5.28
22 23 1.269723 TCAATAGGCGAGTGATAGGCG 59.730 52.381 0.00 0.00 38.03 5.52
23 24 3.386768 TTCAATAGGCGAGTGATAGGC 57.613 47.619 0.00 0.00 30.90 3.93
24 25 5.991606 TGATTTTCAATAGGCGAGTGATAGG 59.008 40.000 0.00 0.00 30.90 2.57
25 26 7.664082 ATGATTTTCAATAGGCGAGTGATAG 57.336 36.000 0.00 0.00 30.90 2.08
26 27 8.585018 TCTATGATTTTCAATAGGCGAGTGATA 58.415 33.333 0.00 0.00 30.90 2.15
27 28 7.445121 TCTATGATTTTCAATAGGCGAGTGAT 58.555 34.615 0.00 0.00 30.90 3.06
28 29 6.816136 TCTATGATTTTCAATAGGCGAGTGA 58.184 36.000 0.00 0.00 0.00 3.41
29 30 6.925718 TCTCTATGATTTTCAATAGGCGAGTG 59.074 38.462 0.00 0.00 0.00 3.51
30 31 7.055667 TCTCTATGATTTTCAATAGGCGAGT 57.944 36.000 0.00 0.00 0.00 4.18
31 32 7.412781 GCATCTCTATGATTTTCAATAGGCGAG 60.413 40.741 0.00 0.00 34.84 5.03
32 33 6.369890 GCATCTCTATGATTTTCAATAGGCGA 59.630 38.462 0.00 0.00 34.84 5.54
33 34 6.148315 TGCATCTCTATGATTTTCAATAGGCG 59.852 38.462 0.00 0.00 34.84 5.52
34 35 7.444629 TGCATCTCTATGATTTTCAATAGGC 57.555 36.000 0.00 0.00 34.84 3.93
98 99 6.038271 ACGTTCAATTTCAAAGCACTACTCTT 59.962 34.615 0.00 0.00 0.00 2.85
102 103 7.349711 TCTTACGTTCAATTTCAAAGCACTAC 58.650 34.615 0.00 0.00 0.00 2.73
120 121 8.597227 GGCAACTTTTGTTTATTTTTCTTACGT 58.403 29.630 0.00 0.00 41.35 3.57
209 210 5.831702 TTACAGGTTTGGCGTTTTTAAGA 57.168 34.783 0.00 0.00 0.00 2.10
295 296 6.762187 TGCCCTGTAAAATATTTACGATTCGA 59.238 34.615 13.95 0.00 0.00 3.71
362 402 1.148498 GTGGCCTGTATACTGCCCC 59.852 63.158 24.90 15.54 44.72 5.80
415 465 3.066190 CCTCTGGTACGGACGGCA 61.066 66.667 0.00 0.00 39.80 5.69
510 583 1.463674 GCCGTGAGAAATTGGACCAT 58.536 50.000 0.00 0.00 0.00 3.55
512 585 1.644786 CCGCCGTGAGAAATTGGACC 61.645 60.000 0.00 0.00 0.00 4.46
559 646 2.467826 GCTCAGATTGCTCACCCGC 61.468 63.158 0.00 0.00 0.00 6.13
560 647 2.169789 CGCTCAGATTGCTCACCCG 61.170 63.158 0.00 0.00 0.00 5.28
610 755 3.112709 GTCCTCGCCACGCAAGAC 61.113 66.667 0.00 0.00 43.62 3.01
611 756 4.373116 GGTCCTCGCCACGCAAGA 62.373 66.667 0.00 0.00 43.62 3.02
676 829 3.353836 GGCTGCGGCGAAACAGAA 61.354 61.111 12.98 0.00 39.81 3.02
702 855 2.313234 GAGAAAACCGCGGTTTAAAGC 58.687 47.619 45.99 34.42 46.22 3.51
732 885 2.028203 CCTCGTAAACCTTAAACCCCGA 60.028 50.000 0.00 0.00 0.00 5.14
745 898 2.408271 TCTCTAGCGGACCTCGTAAA 57.592 50.000 0.00 0.00 41.72 2.01
783 953 6.866248 CACACCAGGGTTAAAACATTTACATC 59.134 38.462 0.00 0.00 0.00 3.06
812 983 1.160137 CAGCCTCCAAACTACTGTGC 58.840 55.000 0.00 0.00 0.00 4.57
891 1062 2.698855 AGATGGGGATGTGAACGAAG 57.301 50.000 0.00 0.00 0.00 3.79
892 1063 3.343617 GAAAGATGGGGATGTGAACGAA 58.656 45.455 0.00 0.00 0.00 3.85
893 1064 2.355716 GGAAAGATGGGGATGTGAACGA 60.356 50.000 0.00 0.00 0.00 3.85
894 1065 2.017049 GGAAAGATGGGGATGTGAACG 58.983 52.381 0.00 0.00 0.00 3.95
895 1066 3.372440 AGGAAAGATGGGGATGTGAAC 57.628 47.619 0.00 0.00 0.00 3.18
896 1067 4.111577 AGTAGGAAAGATGGGGATGTGAA 58.888 43.478 0.00 0.00 0.00 3.18
897 1068 3.711704 GAGTAGGAAAGATGGGGATGTGA 59.288 47.826 0.00 0.00 0.00 3.58
898 1069 3.181450 GGAGTAGGAAAGATGGGGATGTG 60.181 52.174 0.00 0.00 0.00 3.21
899 1070 3.049344 GGAGTAGGAAAGATGGGGATGT 58.951 50.000 0.00 0.00 0.00 3.06
900 1071 3.048600 TGGAGTAGGAAAGATGGGGATG 58.951 50.000 0.00 0.00 0.00 3.51
901 1072 3.438131 TGGAGTAGGAAAGATGGGGAT 57.562 47.619 0.00 0.00 0.00 3.85
902 1073 2.961536 TGGAGTAGGAAAGATGGGGA 57.038 50.000 0.00 0.00 0.00 4.81
903 1074 2.846827 ACTTGGAGTAGGAAAGATGGGG 59.153 50.000 0.00 0.00 0.00 4.96
904 1075 3.264450 ACACTTGGAGTAGGAAAGATGGG 59.736 47.826 0.00 0.00 0.00 4.00
905 1076 4.020218 TCACACTTGGAGTAGGAAAGATGG 60.020 45.833 0.00 0.00 0.00 3.51
906 1077 5.152623 TCACACTTGGAGTAGGAAAGATG 57.847 43.478 0.00 0.00 0.00 2.90
907 1078 5.723887 AGATCACACTTGGAGTAGGAAAGAT 59.276 40.000 0.00 0.00 0.00 2.40
908 1079 5.087323 AGATCACACTTGGAGTAGGAAAGA 58.913 41.667 0.00 0.00 0.00 2.52
909 1080 5.413309 AGATCACACTTGGAGTAGGAAAG 57.587 43.478 0.00 0.00 0.00 2.62
910 1081 4.223032 GGAGATCACACTTGGAGTAGGAAA 59.777 45.833 0.00 0.00 0.00 3.13
911 1082 3.769844 GGAGATCACACTTGGAGTAGGAA 59.230 47.826 0.00 0.00 0.00 3.36
912 1083 3.245622 TGGAGATCACACTTGGAGTAGGA 60.246 47.826 0.00 0.00 0.00 2.94
913 1084 3.099905 TGGAGATCACACTTGGAGTAGG 58.900 50.000 0.00 0.00 0.00 3.18
914 1085 4.382470 CCTTGGAGATCACACTTGGAGTAG 60.382 50.000 0.00 0.00 0.00 2.57
915 1086 3.515502 CCTTGGAGATCACACTTGGAGTA 59.484 47.826 0.00 0.00 0.00 2.59
916 1087 2.304180 CCTTGGAGATCACACTTGGAGT 59.696 50.000 0.00 0.00 0.00 3.85
917 1088 2.355513 CCCTTGGAGATCACACTTGGAG 60.356 54.545 0.00 0.00 0.00 3.86
918 1089 1.630369 CCCTTGGAGATCACACTTGGA 59.370 52.381 0.00 0.00 0.00 3.53
919 1090 1.630369 TCCCTTGGAGATCACACTTGG 59.370 52.381 0.00 0.00 0.00 3.61
931 1102 3.524095 TTTCTTCATTGCTCCCTTGGA 57.476 42.857 0.00 0.00 0.00 3.53
932 1103 4.605640 TTTTTCTTCATTGCTCCCTTGG 57.394 40.909 0.00 0.00 0.00 3.61
950 1121 8.598916 ACGAGGTTTATTAATTTCCCCATTTTT 58.401 29.630 0.00 0.00 0.00 1.94
951 1122 8.141298 ACGAGGTTTATTAATTTCCCCATTTT 57.859 30.769 0.00 0.00 0.00 1.82
952 1123 7.147794 GGACGAGGTTTATTAATTTCCCCATTT 60.148 37.037 0.00 0.00 0.00 2.32
953 1124 6.322969 GGACGAGGTTTATTAATTTCCCCATT 59.677 38.462 0.00 0.00 0.00 3.16
954 1125 5.831525 GGACGAGGTTTATTAATTTCCCCAT 59.168 40.000 0.00 0.00 0.00 4.00
955 1126 5.195185 GGACGAGGTTTATTAATTTCCCCA 58.805 41.667 0.00 0.00 0.00 4.96
956 1127 4.274214 CGGACGAGGTTTATTAATTTCCCC 59.726 45.833 0.00 0.00 0.00 4.81
957 1128 4.877823 ACGGACGAGGTTTATTAATTTCCC 59.122 41.667 0.00 0.00 0.00 3.97
958 1129 5.007039 GGACGGACGAGGTTTATTAATTTCC 59.993 44.000 0.00 0.00 0.00 3.13
959 1130 5.276536 CGGACGGACGAGGTTTATTAATTTC 60.277 44.000 0.00 0.00 35.47 2.17
960 1131 4.567959 CGGACGGACGAGGTTTATTAATTT 59.432 41.667 0.00 0.00 35.47 1.82
961 1132 4.114794 CGGACGGACGAGGTTTATTAATT 58.885 43.478 0.00 0.00 35.47 1.40
962 1133 3.491447 CCGGACGGACGAGGTTTATTAAT 60.491 47.826 4.40 0.00 37.50 1.40
963 1134 2.159254 CCGGACGGACGAGGTTTATTAA 60.159 50.000 4.40 0.00 37.50 1.40
964 1135 1.405105 CCGGACGGACGAGGTTTATTA 59.595 52.381 4.40 0.00 37.50 0.98
965 1136 0.174162 CCGGACGGACGAGGTTTATT 59.826 55.000 4.40 0.00 37.50 1.40
966 1137 0.967380 ACCGGACGGACGAGGTTTAT 60.967 55.000 18.80 0.00 38.96 1.40
967 1138 1.586154 GACCGGACGGACGAGGTTTA 61.586 60.000 18.80 0.00 37.07 2.01
968 1139 2.914097 ACCGGACGGACGAGGTTT 60.914 61.111 18.80 0.00 38.96 3.27
969 1140 3.368571 GACCGGACGGACGAGGTT 61.369 66.667 18.80 0.00 37.07 3.50
987 1158 2.158959 CAGCATCGGTCGTCGGAAC 61.159 63.158 0.00 0.00 39.77 3.62
988 1159 2.180769 CAGCATCGGTCGTCGGAA 59.819 61.111 0.00 0.00 39.77 4.30
989 1160 4.492160 GCAGCATCGGTCGTCGGA 62.492 66.667 0.00 0.00 39.77 4.55
990 1161 4.498520 AGCAGCATCGGTCGTCGG 62.499 66.667 0.00 0.00 39.77 4.79
991 1162 2.951745 GAGCAGCATCGGTCGTCG 60.952 66.667 0.00 0.00 40.90 5.12
992 1163 2.583593 GGAGCAGCATCGGTCGTC 60.584 66.667 0.00 0.00 34.16 4.20
1563 1858 1.068741 GAGTTGGTCAGGAACACGTCT 59.931 52.381 0.00 0.00 0.00 4.18
1609 1904 1.313772 CTCACCTCGTCGATCATCCT 58.686 55.000 0.00 0.00 0.00 3.24
1617 1912 3.374402 ACCAGCCTCACCTCGTCG 61.374 66.667 0.00 0.00 0.00 5.12
1689 1984 2.513666 CACCCCATGCGCACGTAT 60.514 61.111 14.90 0.00 0.00 3.06
1974 2269 2.302952 CGCGATCATGGCACCGTAG 61.303 63.158 0.00 0.00 0.00 3.51
2152 2447 8.655651 TTGAATATAACATGAGCGTGTATCAA 57.344 30.769 0.00 0.00 0.00 2.57
2190 2485 2.348362 CGCATTTGCTATGAACTCGTCA 59.652 45.455 0.51 0.00 38.81 4.35
2230 2525 2.480845 GTCACTTACTGACCGTGCTTT 58.519 47.619 0.00 0.00 43.35 3.51
2706 3002 1.602668 GCAAGCAATGAGAACGGCAAA 60.603 47.619 0.00 0.00 0.00 3.68
3003 3304 5.120674 GCAAATTGATTTTTGGAGCTACACC 59.879 40.000 0.00 0.00 37.13 4.16
3021 3322 2.225066 AATGTGGGGCATTTGGCAAATT 60.225 40.909 22.26 5.95 44.82 1.82
3175 3479 7.037153 TGGACATTGGTAACTAGGAAAGGTATT 60.037 37.037 0.00 0.00 37.61 1.89
3188 3492 2.711542 CAGTCCCTGGACATTGGTAAC 58.288 52.381 18.12 0.00 46.76 2.50
3367 3671 5.281314 AGAGGAGACTGCCCTATTTCTAAA 58.719 41.667 0.00 0.00 44.43 1.85
3404 3708 7.448161 TGTGAACATTGTTGAGAAGTTGGATAT 59.552 33.333 6.80 0.00 0.00 1.63
3444 3750 8.641155 CATAATGTCTGCATTACAAAAACACAG 58.359 33.333 6.16 0.00 46.55 3.66
3445 3751 8.355913 TCATAATGTCTGCATTACAAAAACACA 58.644 29.630 6.16 0.00 46.55 3.72
3448 3754 9.282247 CTCTCATAATGTCTGCATTACAAAAAC 57.718 33.333 6.16 0.00 46.55 2.43
3463 3769 6.356186 TCTGATAGCATGCTCTCATAATGT 57.644 37.500 29.41 5.22 30.57 2.71
3466 3772 7.985752 CCATAATCTGATAGCATGCTCTCATAA 59.014 37.037 29.41 22.12 30.57 1.90
3532 3838 2.113139 CCAACACGGCCAAGGAGT 59.887 61.111 2.24 0.00 0.00 3.85
3550 3856 1.065636 TCTTCAGCCTCAGCCATCTTG 60.066 52.381 0.00 0.00 41.25 3.02
3557 3863 5.278364 CCATTATGAAATCTTCAGCCTCAGC 60.278 44.000 0.00 0.00 43.98 4.26
3911 4217 2.158769 TCTGTTTCACACTGACCAGCAT 60.159 45.455 0.00 0.00 30.10 3.79
3978 4284 2.431057 GAGGTCTCGCCATCCTTTCTAA 59.569 50.000 0.00 0.00 40.61 2.10
3979 4285 2.032620 GAGGTCTCGCCATCCTTTCTA 58.967 52.381 0.00 0.00 40.61 2.10
4004 4310 1.059098 AGCAGTTCACCATGTCTGGA 58.941 50.000 0.00 0.00 46.37 3.86
4154 4460 3.455910 TGAAAATGGGTCGGATCTCTGAT 59.544 43.478 0.00 0.00 33.23 2.90
4168 4474 6.158598 ACCTTGATCAAAACGATGAAAATGG 58.841 36.000 9.88 4.92 33.17 3.16
4263 4571 0.605319 TAGCCAAACTGTTCCGCTGG 60.605 55.000 19.02 12.71 0.00 4.85
4281 4616 3.701205 TCAACCTCAGCTGCAAGAATA 57.299 42.857 9.47 0.00 34.07 1.75
4361 4696 1.701847 AGCCTCTGTTCAGTGGAATGT 59.298 47.619 20.54 3.48 35.05 2.71
4378 4713 1.537202 GTTCAGTGGAATGACACAGCC 59.463 52.381 0.00 0.00 43.72 4.85
4444 4779 3.503363 GTGATGCGTGGCTGGAGC 61.503 66.667 0.00 0.00 41.14 4.70
4508 4845 2.101415 CACATCTCCAGCAATCCTACGA 59.899 50.000 0.00 0.00 0.00 3.43
4512 4849 2.092538 CCTTCACATCTCCAGCAATCCT 60.093 50.000 0.00 0.00 0.00 3.24
4576 4913 6.892456 TCACAAAAATGCCCCAAGTATATACA 59.108 34.615 15.18 0.00 0.00 2.29
4642 4979 1.078497 AGATTCGACCATGGCGCAA 60.078 52.632 13.04 12.39 0.00 4.85
4697 5034 2.598565 TCTGACCACAGCTTCTACAGT 58.401 47.619 0.00 0.00 43.17 3.55
4903 5254 5.815581 TGAGCACAAGGGTATAATTTCAGT 58.184 37.500 0.00 0.00 0.00 3.41
5057 5426 7.792364 TCTGACCTAAGGAGATTGTTTTCTA 57.208 36.000 0.00 0.00 0.00 2.10
5064 5433 9.757227 CTAAATAGTTCTGACCTAAGGAGATTG 57.243 37.037 0.00 0.00 0.00 2.67
5180 5549 0.107831 ACAACCCTGTTCTAGCGCAA 59.892 50.000 11.47 0.00 28.57 4.85
5183 5552 0.320771 AGCACAACCCTGTTCTAGCG 60.321 55.000 0.00 0.00 31.64 4.26
5185 5554 2.146342 CACAGCACAACCCTGTTCTAG 58.854 52.381 0.00 0.00 41.34 2.43
5196 5565 2.394930 ACTACACACACACAGCACAA 57.605 45.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.