Multiple sequence alignment - TraesCS7B01G094700

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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 TraesCS7B01G094700 chr7B 100.000 3041 0 0 1 3041 108559667 108556627 0.000000e+00 5616
1 TraesCS7B01G094700 chr7B 95.397 956 36 5 2092 3041 743400631 743399678 0.000000e+00 1515
2 TraesCS7B01G094700 chr7D 96.009 927 32 3 1160 2081 146235901 146234975 0.000000e+00 1502
3 TraesCS7B01G094700 chr7D 87.957 739 35 20 34 740 146236726 146236010 0.000000e+00 822
4 TraesCS7B01G094700 chr2B 94.864 954 43 4 2092 3041 172680093 172681044 0.000000e+00 1485
5 TraesCS7B01G094700 chr2B 94.136 955 47 5 2090 3041 759681136 759680188 0.000000e+00 1445
6 TraesCS7B01G094700 chr2B 95.437 263 12 0 739 1001 450718232 450718494 1.300000e-113 420
7 TraesCS7B01G094700 chr6B 94.688 960 34 9 2092 3041 113844271 113845223 0.000000e+00 1474
8 TraesCS7B01G094700 chr6B 94.462 957 43 5 2089 3038 68722950 68723903 0.000000e+00 1465
9 TraesCS7B01G094700 chr6B 94.382 267 15 0 737 1003 712458224 712457958 7.850000e-111 411
10 TraesCS7B01G094700 chr5B 94.491 962 43 4 2088 3041 412655157 412654198 0.000000e+00 1474
11 TraesCS7B01G094700 chr5B 93.704 953 45 7 2092 3041 591528881 591527941 0.000000e+00 1413
12 TraesCS7B01G094700 chrUn 94.346 955 45 5 2090 3041 23144851 23145799 0.000000e+00 1456
13 TraesCS7B01G094700 chr3B 93.222 959 53 8 2092 3041 154703162 154702207 0.000000e+00 1400
14 TraesCS7B01G094700 chr7A 93.391 923 43 11 1178 2092 147052528 147051616 0.000000e+00 1351
15 TraesCS7B01G094700 chr7A 90.196 765 44 15 1 741 147053436 147052679 0.000000e+00 968
16 TraesCS7B01G094700 chr7A 95.472 265 12 0 739 1003 717840037 717839773 1.010000e-114 424
17 TraesCS7B01G094700 chr4B 96.958 263 8 0 739 1001 398126468 398126206 2.780000e-120 442
18 TraesCS7B01G094700 chr4B 96.958 263 8 0 739 1001 398161377 398161115 2.780000e-120 442
19 TraesCS7B01G094700 chr4B 96.958 263 8 0 739 1001 398196139 398195877 2.780000e-120 442
20 TraesCS7B01G094700 chr5A 94.717 265 14 0 739 1003 490049347 490049083 2.180000e-111 412
21 TraesCS7B01G094700 chr5A 94.361 266 15 0 736 1001 451457877 451458142 2.820000e-110 409
22 TraesCS7B01G094700 chr3A 94.717 265 14 0 738 1002 529744714 529744978 2.180000e-111 412


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 TraesCS7B01G094700 chr7B 108556627 108559667 3040 True 5616.0 5616 100.0000 1 3041 1 chr7B.!!$R1 3040
1 TraesCS7B01G094700 chr7B 743399678 743400631 953 True 1515.0 1515 95.3970 2092 3041 1 chr7B.!!$R2 949
2 TraesCS7B01G094700 chr7D 146234975 146236726 1751 True 1162.0 1502 91.9830 34 2081 2 chr7D.!!$R1 2047
3 TraesCS7B01G094700 chr2B 172680093 172681044 951 False 1485.0 1485 94.8640 2092 3041 1 chr2B.!!$F1 949
4 TraesCS7B01G094700 chr2B 759680188 759681136 948 True 1445.0 1445 94.1360 2090 3041 1 chr2B.!!$R1 951
5 TraesCS7B01G094700 chr6B 113844271 113845223 952 False 1474.0 1474 94.6880 2092 3041 1 chr6B.!!$F2 949
6 TraesCS7B01G094700 chr6B 68722950 68723903 953 False 1465.0 1465 94.4620 2089 3038 1 chr6B.!!$F1 949
7 TraesCS7B01G094700 chr5B 412654198 412655157 959 True 1474.0 1474 94.4910 2088 3041 1 chr5B.!!$R1 953
8 TraesCS7B01G094700 chr5B 591527941 591528881 940 True 1413.0 1413 93.7040 2092 3041 1 chr5B.!!$R2 949
9 TraesCS7B01G094700 chrUn 23144851 23145799 948 False 1456.0 1456 94.3460 2090 3041 1 chrUn.!!$F1 951
10 TraesCS7B01G094700 chr3B 154702207 154703162 955 True 1400.0 1400 93.2220 2092 3041 1 chr3B.!!$R1 949
11 TraesCS7B01G094700 chr7A 147051616 147053436 1820 True 1159.5 1351 91.7935 1 2092 2 chr7A.!!$R2 2091

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
741 792 0.243907 AACAGAGCGCACGACATACT 59.756 50.0 11.47 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2571 2679 0.106708 GCCAGGACTCCATTGCGATA 59.893 55.0 0.0 0.0 0.0 2.92 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.748450 ATGTATGTGCAATGGCTGGC 59.252 50.000 0.00 0.00 41.91 4.85
162 166 2.112380 TGATCGTGATGGTGCATGTT 57.888 45.000 0.00 0.00 0.00 2.71
192 197 5.814188 TCTTGCATGTAATAGAAGCAGACAG 59.186 40.000 0.00 0.00 36.47 3.51
233 239 3.181512 GCATCTTTTTCTCTCCTTCGCTG 60.182 47.826 0.00 0.00 0.00 5.18
262 277 4.024893 CGCTAGGGCAAAGTTATATGTGTG 60.025 45.833 0.00 0.00 38.60 3.82
305 322 7.225931 TGACTCGTTAAGTTTCTTGCAGTAATT 59.774 33.333 0.00 0.00 38.74 1.40
320 337 5.066893 TGCAGTAATTCTCTGATTGAATGGC 59.933 40.000 12.74 0.00 34.74 4.40
321 338 5.066893 GCAGTAATTCTCTGATTGAATGGCA 59.933 40.000 12.74 0.00 34.74 4.92
322 339 6.493116 CAGTAATTCTCTGATTGAATGGCAC 58.507 40.000 0.00 0.00 34.74 5.01
323 340 6.318144 CAGTAATTCTCTGATTGAATGGCACT 59.682 38.462 0.00 0.00 34.74 4.40
324 341 5.831702 AATTCTCTGATTGAATGGCACTC 57.168 39.130 0.00 0.00 34.74 3.51
352 373 5.821097 AGCTAGGATTGAGTTAGCCTTTTT 58.179 37.500 0.00 0.00 40.44 1.94
382 404 9.903682 ACTGAATCTGATAGTGTTTGATTTTTG 57.096 29.630 0.00 0.00 0.00 2.44
457 486 9.152595 CAGTTAGTATGATTGATCATGGAGATG 57.847 37.037 15.03 5.17 46.34 2.90
470 499 3.832615 TGGAGATGATGATCACACCAG 57.167 47.619 0.00 0.00 30.50 4.00
637 688 2.110967 CGTGATGAAGCAGGGCAGG 61.111 63.158 0.00 0.00 0.00 4.85
741 792 0.243907 AACAGAGCGCACGACATACT 59.756 50.000 11.47 0.00 0.00 2.12
743 794 0.867753 CAGAGCGCACGACATACTCC 60.868 60.000 11.47 0.00 0.00 3.85
744 795 1.589196 GAGCGCACGACATACTCCC 60.589 63.158 11.47 0.00 0.00 4.30
745 796 2.005960 GAGCGCACGACATACTCCCT 62.006 60.000 11.47 0.00 0.00 4.20
746 797 1.589196 GCGCACGACATACTCCCTC 60.589 63.158 0.30 0.00 0.00 4.30
747 798 1.065928 CGCACGACATACTCCCTCC 59.934 63.158 0.00 0.00 0.00 4.30
748 799 1.065928 GCACGACATACTCCCTCCG 59.934 63.158 0.00 0.00 0.00 4.63
749 800 1.664321 GCACGACATACTCCCTCCGT 61.664 60.000 0.00 0.00 0.00 4.69
750 801 0.381089 CACGACATACTCCCTCCGTC 59.619 60.000 0.00 0.00 0.00 4.79
751 802 0.750911 ACGACATACTCCCTCCGTCC 60.751 60.000 0.00 0.00 0.00 4.79
752 803 0.750546 CGACATACTCCCTCCGTCCA 60.751 60.000 0.00 0.00 0.00 4.02
753 804 1.705873 GACATACTCCCTCCGTCCAT 58.294 55.000 0.00 0.00 0.00 3.41
754 805 2.812983 CGACATACTCCCTCCGTCCATA 60.813 54.545 0.00 0.00 0.00 2.74
755 806 3.228453 GACATACTCCCTCCGTCCATAA 58.772 50.000 0.00 0.00 0.00 1.90
756 807 3.640029 GACATACTCCCTCCGTCCATAAA 59.360 47.826 0.00 0.00 0.00 1.40
757 808 4.232091 ACATACTCCCTCCGTCCATAAAT 58.768 43.478 0.00 0.00 0.00 1.40
758 809 5.399991 ACATACTCCCTCCGTCCATAAATA 58.600 41.667 0.00 0.00 0.00 1.40
759 810 5.842328 ACATACTCCCTCCGTCCATAAATAA 59.158 40.000 0.00 0.00 0.00 1.40
760 811 4.957684 ACTCCCTCCGTCCATAAATAAG 57.042 45.455 0.00 0.00 0.00 1.73
761 812 4.296056 ACTCCCTCCGTCCATAAATAAGT 58.704 43.478 0.00 0.00 0.00 2.24
762 813 4.101119 ACTCCCTCCGTCCATAAATAAGTG 59.899 45.833 0.00 0.00 0.00 3.16
763 814 4.035112 TCCCTCCGTCCATAAATAAGTGT 58.965 43.478 0.00 0.00 0.00 3.55
764 815 5.210430 TCCCTCCGTCCATAAATAAGTGTA 58.790 41.667 0.00 0.00 0.00 2.90
765 816 5.069516 TCCCTCCGTCCATAAATAAGTGTAC 59.930 44.000 0.00 0.00 0.00 2.90
766 817 5.163385 CCCTCCGTCCATAAATAAGTGTACA 60.163 44.000 0.00 0.00 0.00 2.90
767 818 6.463897 CCCTCCGTCCATAAATAAGTGTACAT 60.464 42.308 0.00 0.00 0.00 2.29
768 819 6.645415 CCTCCGTCCATAAATAAGTGTACATC 59.355 42.308 0.00 0.00 0.00 3.06
769 820 7.356089 TCCGTCCATAAATAAGTGTACATCT 57.644 36.000 0.00 0.00 0.00 2.90
770 821 8.467963 TCCGTCCATAAATAAGTGTACATCTA 57.532 34.615 0.00 0.00 0.00 1.98
771 822 8.573885 TCCGTCCATAAATAAGTGTACATCTAG 58.426 37.037 0.00 0.00 0.00 2.43
772 823 7.328737 CCGTCCATAAATAAGTGTACATCTAGC 59.671 40.741 0.00 0.00 0.00 3.42
773 824 8.082852 CGTCCATAAATAAGTGTACATCTAGCT 58.917 37.037 0.00 0.00 0.00 3.32
774 825 9.765795 GTCCATAAATAAGTGTACATCTAGCTT 57.234 33.333 0.00 0.00 0.00 3.74
781 832 9.726438 AATAAGTGTACATCTAGCTTTTGTTCT 57.274 29.630 0.00 0.00 0.00 3.01
784 835 8.764524 AGTGTACATCTAGCTTTTGTTCTAAG 57.235 34.615 0.00 0.00 0.00 2.18
785 836 8.368668 AGTGTACATCTAGCTTTTGTTCTAAGT 58.631 33.333 0.00 0.00 0.00 2.24
786 837 8.648968 GTGTACATCTAGCTTTTGTTCTAAGTC 58.351 37.037 0.00 0.00 0.00 3.01
787 838 8.364894 TGTACATCTAGCTTTTGTTCTAAGTCA 58.635 33.333 0.00 0.00 0.00 3.41
788 839 9.204570 GTACATCTAGCTTTTGTTCTAAGTCAA 57.795 33.333 0.00 0.00 0.00 3.18
789 840 8.677148 ACATCTAGCTTTTGTTCTAAGTCAAA 57.323 30.769 0.00 0.00 32.75 2.69
790 841 8.778358 ACATCTAGCTTTTGTTCTAAGTCAAAG 58.222 33.333 0.00 0.00 35.47 2.77
791 842 8.778358 CATCTAGCTTTTGTTCTAAGTCAAAGT 58.222 33.333 0.00 0.00 35.47 2.66
792 843 8.732746 TCTAGCTTTTGTTCTAAGTCAAAGTT 57.267 30.769 0.00 0.00 35.47 2.66
793 844 9.174166 TCTAGCTTTTGTTCTAAGTCAAAGTTT 57.826 29.630 0.00 0.00 35.47 2.66
794 845 9.788960 CTAGCTTTTGTTCTAAGTCAAAGTTTT 57.211 29.630 0.00 0.00 35.47 2.43
900 951 9.832445 ACGAATCTAATGATACTAATTTGGTGT 57.168 29.630 0.00 0.00 31.70 4.16
910 961 9.407380 TGATACTAATTTGGTGTCATAAATGCT 57.593 29.630 8.00 0.00 31.69 3.79
917 968 8.986477 ATTTGGTGTCATAAATGCTTTTACTC 57.014 30.769 6.92 0.00 30.33 2.59
918 969 7.759489 TTGGTGTCATAAATGCTTTTACTCT 57.241 32.000 6.92 0.00 30.33 3.24
919 970 7.759489 TGGTGTCATAAATGCTTTTACTCTT 57.241 32.000 6.92 0.00 30.33 2.85
920 971 8.177119 TGGTGTCATAAATGCTTTTACTCTTT 57.823 30.769 6.92 0.00 30.33 2.52
921 972 8.296713 TGGTGTCATAAATGCTTTTACTCTTTC 58.703 33.333 6.92 0.00 30.33 2.62
922 973 7.755373 GGTGTCATAAATGCTTTTACTCTTTCC 59.245 37.037 6.92 3.64 30.33 3.13
923 974 8.515414 GTGTCATAAATGCTTTTACTCTTTCCT 58.485 33.333 6.92 0.00 30.33 3.36
924 975 9.733556 TGTCATAAATGCTTTTACTCTTTCCTA 57.266 29.630 6.92 0.00 30.33 2.94
933 984 8.576442 TGCTTTTACTCTTTCCTAGAAATTTGG 58.424 33.333 0.00 0.00 30.91 3.28
934 985 8.577296 GCTTTTACTCTTTCCTAGAAATTTGGT 58.423 33.333 0.00 0.00 30.91 3.67
936 987 9.635404 TTTTACTCTTTCCTAGAAATTTGGTCA 57.365 29.630 0.00 0.00 30.91 4.02
937 988 9.635404 TTTACTCTTTCCTAGAAATTTGGTCAA 57.365 29.630 0.00 0.00 30.91 3.18
938 989 9.635404 TTACTCTTTCCTAGAAATTTGGTCAAA 57.365 29.630 0.00 0.00 30.91 2.69
939 990 8.171164 ACTCTTTCCTAGAAATTTGGTCAAAG 57.829 34.615 0.00 0.00 30.70 2.77
940 991 7.780271 ACTCTTTCCTAGAAATTTGGTCAAAGT 59.220 33.333 0.00 0.00 30.70 2.66
941 992 9.284968 CTCTTTCCTAGAAATTTGGTCAAAGTA 57.715 33.333 0.00 0.00 30.70 2.24
942 993 9.807921 TCTTTCCTAGAAATTTGGTCAAAGTAT 57.192 29.630 0.00 0.00 33.32 2.12
973 1024 9.736023 ACTTTGACTTAAAACAAAAGCTAGATG 57.264 29.630 0.00 0.00 35.95 2.90
974 1025 9.736023 CTTTGACTTAAAACAAAAGCTAGATGT 57.264 29.630 0.00 0.00 35.95 3.06
977 1028 9.332502 TGACTTAAAACAAAAGCTAGATGTACA 57.667 29.630 0.00 0.00 0.00 2.90
978 1029 9.595357 GACTTAAAACAAAAGCTAGATGTACAC 57.405 33.333 0.00 0.00 0.00 2.90
979 1030 9.338622 ACTTAAAACAAAAGCTAGATGTACACT 57.661 29.630 0.00 0.13 0.00 3.55
985 1036 9.502091 AACAAAAGCTAGATGTACACTTATTCA 57.498 29.630 0.00 0.00 0.00 2.57
986 1037 8.936864 ACAAAAGCTAGATGTACACTTATTCAC 58.063 33.333 0.00 0.00 0.00 3.18
987 1038 7.757097 AAAGCTAGATGTACACTTATTCACG 57.243 36.000 0.00 0.00 0.00 4.35
988 1039 5.833082 AGCTAGATGTACACTTATTCACGG 58.167 41.667 0.00 0.00 0.00 4.94
989 1040 5.593095 AGCTAGATGTACACTTATTCACGGA 59.407 40.000 0.00 0.00 0.00 4.69
990 1041 5.686397 GCTAGATGTACACTTATTCACGGAC 59.314 44.000 0.00 0.00 0.00 4.79
991 1042 4.669318 AGATGTACACTTATTCACGGACG 58.331 43.478 0.00 0.00 0.00 4.79
992 1043 3.220507 TGTACACTTATTCACGGACGG 57.779 47.619 0.00 0.00 0.00 4.79
993 1044 2.819019 TGTACACTTATTCACGGACGGA 59.181 45.455 0.00 0.00 0.00 4.69
994 1045 3.255395 TGTACACTTATTCACGGACGGAA 59.745 43.478 0.00 0.00 0.00 4.30
995 1046 2.955614 ACACTTATTCACGGACGGAAG 58.044 47.619 0.00 0.00 0.00 3.46
996 1047 2.268298 CACTTATTCACGGACGGAAGG 58.732 52.381 0.00 0.00 0.00 3.46
997 1048 2.094390 CACTTATTCACGGACGGAAGGA 60.094 50.000 0.00 0.00 0.00 3.36
998 1049 2.165845 ACTTATTCACGGACGGAAGGAG 59.834 50.000 0.00 2.86 0.00 3.69
999 1050 1.843368 TATTCACGGACGGAAGGAGT 58.157 50.000 0.00 0.00 0.00 3.85
1000 1051 1.843368 ATTCACGGACGGAAGGAGTA 58.157 50.000 0.00 0.00 0.00 2.59
1001 1052 1.843368 TTCACGGACGGAAGGAGTAT 58.157 50.000 0.00 0.00 0.00 2.12
1002 1053 1.100510 TCACGGACGGAAGGAGTATG 58.899 55.000 0.00 0.00 0.00 2.39
1003 1054 0.527817 CACGGACGGAAGGAGTATGC 60.528 60.000 0.00 0.00 0.00 3.14
1004 1055 0.968901 ACGGACGGAAGGAGTATGCA 60.969 55.000 0.00 0.00 0.00 3.96
1005 1056 0.389391 CGGACGGAAGGAGTATGCAT 59.611 55.000 3.79 3.79 0.00 3.96
1006 1057 1.869754 CGGACGGAAGGAGTATGCATG 60.870 57.143 10.16 0.00 0.00 4.06
1007 1058 1.139058 GGACGGAAGGAGTATGCATGT 59.861 52.381 10.16 0.00 0.00 3.21
1008 1059 2.205074 GACGGAAGGAGTATGCATGTG 58.795 52.381 10.16 0.00 0.00 3.21
1009 1060 1.555075 ACGGAAGGAGTATGCATGTGT 59.445 47.619 10.16 0.00 0.00 3.72
1010 1061 1.935873 CGGAAGGAGTATGCATGTGTG 59.064 52.381 10.16 0.00 0.00 3.82
1048 1099 1.371022 CGCTCCACATCGGATCTCG 60.371 63.158 0.00 0.00 45.19 4.04
1073 1124 1.855360 GCAATGTACAGCTAGCTCGAC 59.145 52.381 16.15 15.87 0.00 4.20
1074 1125 2.480416 GCAATGTACAGCTAGCTCGACT 60.480 50.000 16.15 0.00 0.00 4.18
1079 1130 2.649531 ACAGCTAGCTCGACTCCTAT 57.350 50.000 16.15 0.00 0.00 2.57
1084 1135 5.048364 ACAGCTAGCTCGACTCCTATTTATG 60.048 44.000 16.15 0.77 0.00 1.90
1139 1213 4.341502 CAACACAAAGCGGCCGGG 62.342 66.667 29.38 0.00 0.00 5.73
1140 1214 4.887190 AACACAAAGCGGCCGGGT 62.887 61.111 29.38 10.63 0.00 5.28
1143 1217 4.572571 ACAAAGCGGCCGGGTCAA 62.573 61.111 29.38 0.00 0.00 3.18
1144 1218 3.291383 CAAAGCGGCCGGGTCAAA 61.291 61.111 29.38 0.00 0.00 2.69
1145 1219 2.519780 AAAGCGGCCGGGTCAAAA 60.520 55.556 29.38 0.00 0.00 2.44
1146 1220 2.852180 AAAGCGGCCGGGTCAAAAC 61.852 57.895 29.38 7.21 0.00 2.43
1159 1233 2.226674 GGTCAAAACCAACTAGCTCAGC 59.773 50.000 0.00 0.00 45.68 4.26
1160 1234 2.226674 GTCAAAACCAACTAGCTCAGCC 59.773 50.000 0.00 0.00 0.00 4.85
1161 1235 2.106511 TCAAAACCAACTAGCTCAGCCT 59.893 45.455 0.00 0.00 0.00 4.58
1162 1236 2.481289 AAACCAACTAGCTCAGCCTC 57.519 50.000 0.00 0.00 0.00 4.70
1163 1237 0.615850 AACCAACTAGCTCAGCCTCC 59.384 55.000 0.00 0.00 0.00 4.30
1164 1238 0.545309 ACCAACTAGCTCAGCCTCCA 60.545 55.000 0.00 0.00 0.00 3.86
1165 1239 0.615331 CCAACTAGCTCAGCCTCCAA 59.385 55.000 0.00 0.00 0.00 3.53
1166 1240 1.677217 CCAACTAGCTCAGCCTCCAAC 60.677 57.143 0.00 0.00 0.00 3.77
1167 1241 1.002430 CAACTAGCTCAGCCTCCAACA 59.998 52.381 0.00 0.00 0.00 3.33
1168 1242 1.352083 ACTAGCTCAGCCTCCAACAA 58.648 50.000 0.00 0.00 0.00 2.83
1169 1243 1.277557 ACTAGCTCAGCCTCCAACAAG 59.722 52.381 0.00 0.00 0.00 3.16
1170 1244 0.615331 TAGCTCAGCCTCCAACAAGG 59.385 55.000 0.00 0.00 39.62 3.61
1176 1250 2.747855 CCTCCAACAAGGCGCTCC 60.748 66.667 7.64 0.00 37.29 4.70
1177 1251 2.032528 CTCCAACAAGGCGCTCCA 59.967 61.111 7.64 0.00 37.29 3.86
1178 1252 2.281484 TCCAACAAGGCGCTCCAC 60.281 61.111 7.64 0.00 37.29 4.02
1308 1382 4.069232 TCGGACAAGGCGGCTCTG 62.069 66.667 13.70 15.14 0.00 3.35
1405 1479 4.819761 GCATCTCCTGCGACGCCA 62.820 66.667 18.69 4.55 41.97 5.69
1524 1598 0.689745 TGGCCTACAACCGCCTCTAT 60.690 55.000 3.32 0.00 45.90 1.98
1584 1658 2.581354 CTCACCTTCCTCCGCCTG 59.419 66.667 0.00 0.00 0.00 4.85
1783 1857 4.309950 GGGTGAACTCGGTGCGGT 62.310 66.667 0.00 0.00 0.00 5.68
1806 1880 4.302172 CGCAACCGGTTCGCGTTT 62.302 61.111 35.23 10.76 43.86 3.60
2056 2135 2.001361 CTAGGTACGGTGGCCACTCG 62.001 65.000 33.91 32.84 0.00 4.18
2098 2179 6.367983 ACTGATGATGTATTGTTAGGGCATT 58.632 36.000 0.00 0.00 0.00 3.56
2556 2664 1.594310 GCGCTCCTTCACCTTCTCT 59.406 57.895 0.00 0.00 0.00 3.10
2561 2669 0.541998 TCCTTCACCTTCTCTCGGCA 60.542 55.000 0.00 0.00 0.00 5.69
2832 2942 2.968737 CGATGAGGATCGGGAGGAT 58.031 57.895 0.00 0.00 46.51 3.24
2853 2963 1.156322 AAGAGGAGGAGGAGGACCCA 61.156 60.000 0.00 0.00 37.41 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.245539 TGTAACGTCACTAGCCAGCC 59.754 55.000 0.00 0.00 0.00 4.85
20 21 5.570344 CACTCCTACATGTAACGTCACTAG 58.430 45.833 7.06 0.00 0.00 2.57
60 61 8.934507 TTTAACGAAATCAAACCTTGAATGTT 57.065 26.923 0.00 0.30 43.95 2.71
162 166 8.907222 TGCTTCTATTACATGCAAGATCATTA 57.093 30.769 0.00 0.00 0.00 1.90
185 190 0.105778 GGGTCAGCCTATCTGTCTGC 59.894 60.000 0.00 0.00 43.32 4.26
192 197 1.002544 GCATGTAGGGGTCAGCCTATC 59.997 57.143 0.00 0.00 34.45 2.08
233 239 1.523938 CTTTGCCCTAGCGCCTACC 60.524 63.158 2.29 0.00 44.31 3.18
277 292 5.177696 ACTGCAAGAAACTTAACGAGTCATC 59.822 40.000 0.00 0.00 35.52 2.92
281 296 7.441458 AGAATTACTGCAAGAAACTTAACGAGT 59.559 33.333 0.00 0.00 37.59 4.18
305 322 3.262660 ACAGAGTGCCATTCAATCAGAGA 59.737 43.478 0.00 0.00 41.89 3.10
320 337 5.590530 ACTCAATCCTAGCTTACAGAGTG 57.409 43.478 0.00 0.00 34.17 3.51
321 338 6.183360 GCTAACTCAATCCTAGCTTACAGAGT 60.183 42.308 0.00 0.00 36.06 3.24
322 339 6.212955 GCTAACTCAATCCTAGCTTACAGAG 58.787 44.000 0.00 0.00 36.06 3.35
323 340 5.069251 GGCTAACTCAATCCTAGCTTACAGA 59.931 44.000 0.00 0.00 38.47 3.41
324 341 5.069781 AGGCTAACTCAATCCTAGCTTACAG 59.930 44.000 0.00 0.00 38.47 2.74
352 373 7.239763 TCAAACACTATCAGATTCAGTACCA 57.760 36.000 0.00 0.00 0.00 3.25
382 404 3.426695 GCTACACATTGAGTTCACATGCC 60.427 47.826 0.00 0.00 0.00 4.40
457 486 2.277969 CACTCTGCTGGTGTGATCATC 58.722 52.381 0.00 0.00 40.61 2.92
470 499 0.326264 AGTTCCATGGTCCACTCTGC 59.674 55.000 12.58 0.00 0.00 4.26
637 688 2.890808 TCTGCCCTCGTCAATGATAC 57.109 50.000 0.00 0.00 0.00 2.24
684 735 0.317603 CGTTCGGCATCCCTACGTAG 60.318 60.000 15.92 15.92 34.27 3.51
685 736 1.031571 ACGTTCGGCATCCCTACGTA 61.032 55.000 1.44 0.00 43.53 3.57
686 737 2.345760 ACGTTCGGCATCCCTACGT 61.346 57.895 0.00 0.00 41.84 3.57
687 738 1.876714 CACGTTCGGCATCCCTACG 60.877 63.158 0.00 0.00 40.47 3.51
741 792 4.035112 ACACTTATTTATGGACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
743 794 5.909477 TGTACACTTATTTATGGACGGAGG 58.091 41.667 0.00 0.00 31.76 4.30
744 795 7.434492 AGATGTACACTTATTTATGGACGGAG 58.566 38.462 0.00 0.00 31.76 4.63
745 796 7.356089 AGATGTACACTTATTTATGGACGGA 57.644 36.000 0.00 0.00 31.76 4.69
746 797 7.328737 GCTAGATGTACACTTATTTATGGACGG 59.671 40.741 0.00 0.00 31.76 4.79
747 798 8.082852 AGCTAGATGTACACTTATTTATGGACG 58.917 37.037 0.00 0.00 31.76 4.79
748 799 9.765795 AAGCTAGATGTACACTTATTTATGGAC 57.234 33.333 0.00 0.00 0.00 4.02
755 806 9.726438 AGAACAAAAGCTAGATGTACACTTATT 57.274 29.630 0.00 0.00 0.00 1.40
758 809 9.209175 CTTAGAACAAAAGCTAGATGTACACTT 57.791 33.333 0.00 0.00 0.00 3.16
759 810 8.368668 ACTTAGAACAAAAGCTAGATGTACACT 58.631 33.333 0.00 0.13 0.00 3.55
760 811 8.535690 ACTTAGAACAAAAGCTAGATGTACAC 57.464 34.615 0.00 0.00 0.00 2.90
761 812 8.364894 TGACTTAGAACAAAAGCTAGATGTACA 58.635 33.333 0.00 0.00 0.00 2.90
762 813 8.758633 TGACTTAGAACAAAAGCTAGATGTAC 57.241 34.615 0.00 0.00 0.00 2.90
763 814 9.772973 TTTGACTTAGAACAAAAGCTAGATGTA 57.227 29.630 0.00 0.00 33.90 2.29
764 815 8.677148 TTTGACTTAGAACAAAAGCTAGATGT 57.323 30.769 0.00 0.00 33.90 3.06
765 816 8.778358 ACTTTGACTTAGAACAAAAGCTAGATG 58.222 33.333 0.00 0.00 35.95 2.90
766 817 8.910351 ACTTTGACTTAGAACAAAAGCTAGAT 57.090 30.769 0.00 0.00 35.95 1.98
767 818 8.732746 AACTTTGACTTAGAACAAAAGCTAGA 57.267 30.769 0.00 0.00 35.95 2.43
768 819 9.788960 AAAACTTTGACTTAGAACAAAAGCTAG 57.211 29.630 0.00 0.00 35.95 3.42
874 925 9.832445 ACACCAAATTAGTATCATTAGATTCGT 57.168 29.630 0.00 0.00 35.67 3.85
884 935 9.407380 AGCATTTATGACACCAAATTAGTATCA 57.593 29.630 0.00 0.00 0.00 2.15
891 942 9.423061 GAGTAAAAGCATTTATGACACCAAATT 57.577 29.630 0.00 0.00 37.28 1.82
892 943 8.806146 AGAGTAAAAGCATTTATGACACCAAAT 58.194 29.630 0.00 0.00 37.28 2.32
893 944 8.177119 AGAGTAAAAGCATTTATGACACCAAA 57.823 30.769 0.00 0.00 37.28 3.28
894 945 7.759489 AGAGTAAAAGCATTTATGACACCAA 57.241 32.000 0.00 0.00 37.28 3.67
895 946 7.759489 AAGAGTAAAAGCATTTATGACACCA 57.241 32.000 0.00 0.00 37.28 4.17
896 947 7.755373 GGAAAGAGTAAAAGCATTTATGACACC 59.245 37.037 0.00 0.00 37.28 4.16
897 948 8.515414 AGGAAAGAGTAAAAGCATTTATGACAC 58.485 33.333 0.00 0.00 37.28 3.67
898 949 8.635765 AGGAAAGAGTAAAAGCATTTATGACA 57.364 30.769 0.00 0.00 37.28 3.58
907 958 8.576442 CCAAATTTCTAGGAAAGAGTAAAAGCA 58.424 33.333 0.00 0.00 35.05 3.91
908 959 8.577296 ACCAAATTTCTAGGAAAGAGTAAAAGC 58.423 33.333 0.28 0.00 35.05 3.51
910 961 9.635404 TGACCAAATTTCTAGGAAAGAGTAAAA 57.365 29.630 0.28 0.00 35.05 1.52
911 962 9.635404 TTGACCAAATTTCTAGGAAAGAGTAAA 57.365 29.630 0.28 0.00 35.05 2.01
912 963 9.635404 TTTGACCAAATTTCTAGGAAAGAGTAA 57.365 29.630 0.28 0.00 35.05 2.24
913 964 9.284968 CTTTGACCAAATTTCTAGGAAAGAGTA 57.715 33.333 0.28 0.00 35.05 2.59
914 965 7.780271 ACTTTGACCAAATTTCTAGGAAAGAGT 59.220 33.333 11.26 3.83 35.05 3.24
915 966 8.171164 ACTTTGACCAAATTTCTAGGAAAGAG 57.829 34.615 11.26 3.41 35.05 2.85
916 967 9.807921 ATACTTTGACCAAATTTCTAGGAAAGA 57.192 29.630 11.26 0.00 0.00 2.52
947 998 9.736023 CATCTAGCTTTTGTTTTAAGTCAAAGT 57.264 29.630 0.00 2.00 35.47 2.66
948 999 9.736023 ACATCTAGCTTTTGTTTTAAGTCAAAG 57.264 29.630 0.00 0.00 35.47 2.77
951 1002 9.332502 TGTACATCTAGCTTTTGTTTTAAGTCA 57.667 29.630 0.00 0.00 0.00 3.41
952 1003 9.595357 GTGTACATCTAGCTTTTGTTTTAAGTC 57.405 33.333 0.00 0.00 0.00 3.01
953 1004 9.338622 AGTGTACATCTAGCTTTTGTTTTAAGT 57.661 29.630 0.00 0.00 0.00 2.24
959 1010 9.502091 TGAATAAGTGTACATCTAGCTTTTGTT 57.498 29.630 0.00 0.00 0.00 2.83
960 1011 8.936864 GTGAATAAGTGTACATCTAGCTTTTGT 58.063 33.333 0.00 0.00 0.00 2.83
961 1012 8.110612 CGTGAATAAGTGTACATCTAGCTTTTG 58.889 37.037 0.00 0.00 0.00 2.44
962 1013 7.277981 CCGTGAATAAGTGTACATCTAGCTTTT 59.722 37.037 0.00 0.00 0.00 2.27
963 1014 6.757010 CCGTGAATAAGTGTACATCTAGCTTT 59.243 38.462 0.00 0.00 0.00 3.51
964 1015 6.096423 TCCGTGAATAAGTGTACATCTAGCTT 59.904 38.462 0.00 0.00 0.00 3.74
965 1016 5.593095 TCCGTGAATAAGTGTACATCTAGCT 59.407 40.000 0.00 0.00 0.00 3.32
966 1017 5.686397 GTCCGTGAATAAGTGTACATCTAGC 59.314 44.000 0.00 0.00 0.00 3.42
967 1018 5.907945 CGTCCGTGAATAAGTGTACATCTAG 59.092 44.000 0.00 0.00 0.00 2.43
968 1019 5.220912 CCGTCCGTGAATAAGTGTACATCTA 60.221 44.000 0.00 0.00 0.00 1.98
969 1020 4.439700 CCGTCCGTGAATAAGTGTACATCT 60.440 45.833 0.00 0.00 0.00 2.90
970 1021 3.795101 CCGTCCGTGAATAAGTGTACATC 59.205 47.826 0.00 0.00 0.00 3.06
971 1022 3.444742 TCCGTCCGTGAATAAGTGTACAT 59.555 43.478 0.00 0.00 0.00 2.29
972 1023 2.819019 TCCGTCCGTGAATAAGTGTACA 59.181 45.455 0.00 0.00 0.00 2.90
973 1024 3.492421 TCCGTCCGTGAATAAGTGTAC 57.508 47.619 0.00 0.00 0.00 2.90
974 1025 3.119388 CCTTCCGTCCGTGAATAAGTGTA 60.119 47.826 0.00 0.00 0.00 2.90
975 1026 2.353406 CCTTCCGTCCGTGAATAAGTGT 60.353 50.000 0.00 0.00 0.00 3.55
976 1027 2.094390 TCCTTCCGTCCGTGAATAAGTG 60.094 50.000 0.00 0.00 0.00 3.16
977 1028 2.165845 CTCCTTCCGTCCGTGAATAAGT 59.834 50.000 0.00 0.00 0.00 2.24
978 1029 2.165845 ACTCCTTCCGTCCGTGAATAAG 59.834 50.000 0.00 0.00 0.00 1.73
979 1030 2.173519 ACTCCTTCCGTCCGTGAATAA 58.826 47.619 0.00 0.00 0.00 1.40
980 1031 1.843368 ACTCCTTCCGTCCGTGAATA 58.157 50.000 0.00 0.00 0.00 1.75
981 1032 1.843368 TACTCCTTCCGTCCGTGAAT 58.157 50.000 0.00 0.00 0.00 2.57
982 1033 1.475280 CATACTCCTTCCGTCCGTGAA 59.525 52.381 0.00 0.00 0.00 3.18
983 1034 1.100510 CATACTCCTTCCGTCCGTGA 58.899 55.000 0.00 0.00 0.00 4.35
984 1035 0.527817 GCATACTCCTTCCGTCCGTG 60.528 60.000 0.00 0.00 0.00 4.94
985 1036 0.968901 TGCATACTCCTTCCGTCCGT 60.969 55.000 0.00 0.00 0.00 4.69
986 1037 0.389391 ATGCATACTCCTTCCGTCCG 59.611 55.000 0.00 0.00 0.00 4.79
987 1038 1.139058 ACATGCATACTCCTTCCGTCC 59.861 52.381 0.00 0.00 0.00 4.79
988 1039 2.205074 CACATGCATACTCCTTCCGTC 58.795 52.381 0.00 0.00 0.00 4.79
989 1040 1.555075 ACACATGCATACTCCTTCCGT 59.445 47.619 0.00 0.00 0.00 4.69
990 1041 1.935873 CACACATGCATACTCCTTCCG 59.064 52.381 0.00 0.00 0.00 4.30
1048 1099 1.936547 GCTAGCTGTACATTGCTGACC 59.063 52.381 17.41 4.46 40.08 4.02
1073 1124 5.059833 GGCTGAGAACCACATAAATAGGAG 58.940 45.833 0.00 0.00 0.00 3.69
1074 1125 4.721776 AGGCTGAGAACCACATAAATAGGA 59.278 41.667 0.00 0.00 0.00 2.94
1079 1130 2.642311 TGGAGGCTGAGAACCACATAAA 59.358 45.455 0.00 0.00 0.00 1.40
1084 1135 4.703703 GTGGAGGCTGAGAACCAC 57.296 61.111 6.57 6.57 44.23 4.16
1139 1213 2.226674 GGCTGAGCTAGTTGGTTTTGAC 59.773 50.000 3.72 0.00 0.00 3.18
1140 1214 2.106511 AGGCTGAGCTAGTTGGTTTTGA 59.893 45.455 3.72 0.00 0.00 2.69
1141 1215 2.485814 GAGGCTGAGCTAGTTGGTTTTG 59.514 50.000 3.72 0.00 0.00 2.44
1143 1217 1.003696 GGAGGCTGAGCTAGTTGGTTT 59.996 52.381 3.72 0.00 0.00 3.27
1144 1218 0.615850 GGAGGCTGAGCTAGTTGGTT 59.384 55.000 3.72 0.00 0.00 3.67
1145 1219 0.545309 TGGAGGCTGAGCTAGTTGGT 60.545 55.000 3.72 0.00 0.00 3.67
1146 1220 0.615331 TTGGAGGCTGAGCTAGTTGG 59.385 55.000 3.72 0.00 0.00 3.77
1147 1221 1.002430 TGTTGGAGGCTGAGCTAGTTG 59.998 52.381 3.72 0.00 0.00 3.16
1148 1222 1.352083 TGTTGGAGGCTGAGCTAGTT 58.648 50.000 3.72 0.00 0.00 2.24
1149 1223 1.277557 CTTGTTGGAGGCTGAGCTAGT 59.722 52.381 3.72 0.00 0.00 2.57
1150 1224 1.406614 CCTTGTTGGAGGCTGAGCTAG 60.407 57.143 3.72 0.00 38.35 3.42
1151 1225 0.615331 CCTTGTTGGAGGCTGAGCTA 59.385 55.000 3.72 0.00 38.35 3.32
1152 1226 1.377994 CCTTGTTGGAGGCTGAGCT 59.622 57.895 3.72 0.00 38.35 4.09
1153 1227 3.993535 CCTTGTTGGAGGCTGAGC 58.006 61.111 0.00 0.00 38.35 4.26
1159 1233 2.747855 GGAGCGCCTTGTTGGAGG 60.748 66.667 2.29 0.00 39.93 4.30
1160 1234 2.032528 TGGAGCGCCTTGTTGGAG 59.967 61.111 8.34 0.00 38.35 3.86
1161 1235 2.281484 GTGGAGCGCCTTGTTGGA 60.281 61.111 8.34 0.00 38.35 3.53
1162 1236 3.365265 GGTGGAGCGCCTTGTTGG 61.365 66.667 8.34 0.00 39.35 3.77
1163 1237 2.594303 TGGTGGAGCGCCTTGTTG 60.594 61.111 8.34 0.00 34.70 3.33
1164 1238 2.594592 GTGGTGGAGCGCCTTGTT 60.595 61.111 8.34 0.00 34.70 2.83
1165 1239 4.643387 GGTGGTGGAGCGCCTTGT 62.643 66.667 8.34 0.00 34.70 3.16
1166 1240 3.925630 ATGGTGGTGGAGCGCCTTG 62.926 63.158 8.34 0.00 34.70 3.61
1167 1241 3.650950 ATGGTGGTGGAGCGCCTT 61.651 61.111 8.34 0.86 34.70 4.35
1168 1242 4.415150 CATGGTGGTGGAGCGCCT 62.415 66.667 8.34 0.00 34.70 5.52
1171 1245 3.129502 CTGCATGGTGGTGGAGCG 61.130 66.667 0.00 0.00 30.76 5.03
1173 1247 1.748122 GAGCTGCATGGTGGTGGAG 60.748 63.158 1.02 0.00 40.15 3.86
1174 1248 2.352422 GAGCTGCATGGTGGTGGA 59.648 61.111 1.02 0.00 0.00 4.02
1175 1249 2.034532 TGAGCTGCATGGTGGTGG 59.965 61.111 1.02 0.00 0.00 4.61
1176 1250 2.683859 CGTGAGCTGCATGGTGGTG 61.684 63.158 1.02 0.00 0.00 4.17
1177 1251 2.359107 CGTGAGCTGCATGGTGGT 60.359 61.111 1.02 0.00 0.00 4.16
1178 1252 2.046988 TCGTGAGCTGCATGGTGG 60.047 61.111 1.02 0.00 34.18 4.61
1278 1352 1.170290 TGTCCGACTTGTCGCAGAGA 61.170 55.000 16.59 6.68 36.95 3.10
1783 1857 3.641986 GAACCGGTTGCGCGACAA 61.642 61.111 27.87 11.45 35.33 3.18
2035 2109 3.078836 TGGCCACCGTACCTAGCC 61.079 66.667 0.00 4.37 44.13 3.93
2056 2135 4.374702 CAAGCGGTCACGTGCAGC 62.375 66.667 20.72 20.72 43.45 5.25
2136 2217 2.997315 CCGGCTCACCCTCAGACA 60.997 66.667 0.00 0.00 0.00 3.41
2259 2360 9.161629 GCCATGTTTAGCCAAAATTTAACTATT 57.838 29.630 0.00 0.00 0.00 1.73
2260 2361 8.317679 TGCCATGTTTAGCCAAAATTTAACTAT 58.682 29.630 0.00 0.00 0.00 2.12
2449 2553 1.796355 CGACAGCGACGACAACGAT 60.796 57.895 0.00 0.00 43.06 3.73
2556 2664 1.734137 GATAGAGAAGGCGTGCCGA 59.266 57.895 5.02 0.00 41.95 5.54
2561 2669 1.539065 CCATTGCGATAGAGAAGGCGT 60.539 52.381 0.00 0.00 39.76 5.68
2571 2679 0.106708 GCCAGGACTCCATTGCGATA 59.893 55.000 0.00 0.00 0.00 2.92
2832 2942 0.336737 GGTCCTCCTCCTCCTCTTCA 59.663 60.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.