Multiple sequence alignment - TraesCS4D01G313100

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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 TraesCS4D01G313100 chr4D 100.000 3716 0 0 1587 5302 479363633 479367348 0.000000e+00 6863
1 TraesCS4D01G313100 chr4D 100.000 1146 0 0 1 1146 479362047 479363192 0.000000e+00 2117
2 TraesCS4D01G313100 chr4A 93.907 1986 91 5 1600 3573 685749129 685751096 0.000000e+00 2970
3 TraesCS4D01G313100 chr4A 93.034 847 47 4 3576 4413 685751179 685752022 0.000000e+00 1227
4 TraesCS4D01G313100 chr4A 83.916 429 46 12 4656 5063 685752195 685752621 6.440000e-104 388
5 TraesCS4D01G313100 chr4A 85.673 342 30 8 814 1146 685748444 685748775 5.080000e-90 342
6 TraesCS4D01G313100 chr4A 89.604 202 11 5 4429 4627 685752007 685752201 1.140000e-61 248
7 TraesCS4D01G313100 chr4B 95.712 1819 71 3 1591 3403 605939883 605941700 0.000000e+00 2920
8 TraesCS4D01G313100 chr4B 96.154 1560 43 6 3389 4943 605941728 605943275 0.000000e+00 2532
9 TraesCS4D01G313100 chr4B 89.354 263 15 6 814 1076 605939091 605939340 8.570000e-83 318
10 TraesCS4D01G313100 chr4B 94.400 125 5 2 5180 5302 605943516 605943640 1.950000e-44 191
11 TraesCS4D01G313100 chr4B 89.116 147 16 0 5035 5181 605943287 605943433 3.260000e-42 183
12 TraesCS4D01G313100 chr1B 78.049 738 99 39 2 718 642113831 642113136 1.780000e-109 407
13 TraesCS4D01G313100 chr1B 79.365 315 50 15 144 452 582338850 582339155 1.940000e-49 207
14 TraesCS4D01G313100 chr2A 81.743 482 66 19 200 670 135170792 135170322 3.000000e-102 383
15 TraesCS4D01G313100 chr1A 80.370 540 47 30 2 530 465214719 465214228 6.530000e-94 355
16 TraesCS4D01G313100 chr1A 79.286 280 37 21 184 452 341484380 341484649 5.460000e-40 176
17 TraesCS4D01G313100 chr1A 87.786 131 14 2 593 722 465214216 465214087 9.200000e-33 152
18 TraesCS4D01G313100 chr6A 80.185 540 47 26 2 530 272974566 272975056 3.040000e-92 350
19 TraesCS4D01G313100 chr6A 85.315 143 19 2 580 722 272975057 272975197 4.280000e-31 147
20 TraesCS4D01G313100 chr5A 79.800 401 59 17 26 414 293439207 293439597 6.770000e-69 272
21 TraesCS4D01G313100 chr5A 84.615 143 20 2 580 722 136979320 136979460 1.990000e-29 141
22 TraesCS4D01G313100 chr5B 77.190 548 70 32 186 722 17994528 17995031 8.750000e-68 268
23 TraesCS4D01G313100 chr5D 76.882 558 73 29 179 722 274901997 274901482 1.130000e-66 265
24 TraesCS4D01G313100 chr6D 79.941 339 50 16 143 472 397626972 397627301 3.190000e-57 233
25 TraesCS4D01G313100 chr3A 76.161 323 56 17 139 452 658311681 658311371 3.310000e-32 150


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 TraesCS4D01G313100 chr4D 479362047 479367348 5301 False 4490.0 6863 100.0000 1 5302 2 chr4D.!!$F1 5301
1 TraesCS4D01G313100 chr4A 685748444 685752621 4177 False 1035.0 2970 89.2268 814 5063 5 chr4A.!!$F1 4249
2 TraesCS4D01G313100 chr4B 605939091 605943640 4549 False 1228.8 2920 92.9472 814 5302 5 chr4B.!!$F1 4488
3 TraesCS4D01G313100 chr1B 642113136 642113831 695 True 407.0 407 78.0490 2 718 1 chr1B.!!$R1 716
4 TraesCS4D01G313100 chr1A 465214087 465214719 632 True 253.5 355 84.0780 2 722 2 chr1A.!!$R1 720
5 TraesCS4D01G313100 chr6A 272974566 272975197 631 False 248.5 350 82.7500 2 722 2 chr6A.!!$F1 720
6 TraesCS4D01G313100 chr5B 17994528 17995031 503 False 268.0 268 77.1900 186 722 1 chr5B.!!$F1 536
7 TraesCS4D01G313100 chr5D 274901482 274901997 515 True 265.0 265 76.8820 179 722 1 chr5D.!!$R1 543

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
747 877 0.031111 AGGATTCCCCGAGGATCACA 60.031 55.0 0.00 0.00 43.54 3.58 F
801 931 0.107214 GAGTCCAATGGGCCATTCGA 60.107 55.0 28.54 24.44 31.05 3.71 F
1990 2597 0.250295 CTGAAGTGCCGGTTCCTGAA 60.250 55.0 1.90 0.00 0.00 3.02 F
2805 3412 0.250081 GGGTCAGCCGGAATCATCTC 60.250 60.0 5.05 0.00 34.97 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2661 0.248377 GCAGCGCCTTATCAAAGCAG 60.248 55.000 2.29 0.0 0.00 4.24 R
2431 3038 0.957395 AGCAATCTCCAAGCACCGTG 60.957 55.000 0.00 0.0 0.00 4.94 R
2890 3497 2.431454 TCAGTCCATACGCATTTGCAA 58.569 42.857 0.00 0.0 42.21 4.08 R
4747 5515 1.362224 ATAGTCACAGCACCCAACCT 58.638 50.000 0.00 0.0 0.00 3.50 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
19 20 2.425143 CATGACCCCATGTGCTACTT 57.575 50.000 0.00 0.00 43.90 2.24
20 21 2.292267 CATGACCCCATGTGCTACTTC 58.708 52.381 0.00 0.00 43.90 3.01
61 67 8.728337 TTTATATAAATGCAAAAATGGCAGCA 57.272 26.923 3.71 0.61 45.68 4.41
161 178 6.686253 GCGAAATTTTTGCAAAATCAGTGAAA 59.314 30.769 24.39 8.19 0.00 2.69
162 179 7.097329 GCGAAATTTTTGCAAAATCAGTGAAAG 60.097 33.333 24.39 11.22 0.00 2.62
223 279 7.254084 GCGAACTGTTTTTCAAATTGATGAACT 60.254 33.333 17.02 4.02 38.95 3.01
224 280 8.594687 CGAACTGTTTTTCAAATTGATGAACTT 58.405 29.630 17.02 8.65 38.95 2.66
227 283 9.657419 ACTGTTTTTCAAATTGATGAACTTTCT 57.343 25.926 17.02 2.22 38.95 2.52
229 285 9.650539 TGTTTTTCAAATTGATGAACTTTCTCA 57.349 25.926 17.02 0.00 38.95 3.27
241 297 9.467258 TGATGAACTTTCTCAAATTCAATGAAC 57.533 29.630 0.00 0.00 34.88 3.18
242 298 9.688592 GATGAACTTTCTCAAATTCAATGAACT 57.311 29.630 0.00 0.00 34.88 3.01
297 376 8.664211 ACTCGATGAACTTCTTTTTAAACTCT 57.336 30.769 0.00 0.00 0.00 3.24
414 539 9.748708 ATTTTCAAAATCGATGAACTCTTTTCA 57.251 25.926 0.00 0.00 36.57 2.69
415 540 8.786937 TTTCAAAATCGATGAACTCTTTTCAG 57.213 30.769 0.00 0.00 36.57 3.02
416 541 7.728847 TCAAAATCGATGAACTCTTTTCAGA 57.271 32.000 0.00 0.00 0.00 3.27
417 542 8.153479 TCAAAATCGATGAACTCTTTTCAGAA 57.847 30.769 0.00 0.00 0.00 3.02
418 543 8.786898 TCAAAATCGATGAACTCTTTTCAGAAT 58.213 29.630 0.00 0.00 0.00 2.40
419 544 9.059485 CAAAATCGATGAACTCTTTTCAGAATC 57.941 33.333 0.00 0.00 0.00 2.52
420 545 6.580963 ATCGATGAACTCTTTTCAGAATCG 57.419 37.500 0.00 0.00 32.74 3.34
421 546 5.709966 TCGATGAACTCTTTTCAGAATCGA 58.290 37.500 6.96 6.96 36.05 3.59
422 547 6.333416 TCGATGAACTCTTTTCAGAATCGAT 58.667 36.000 6.96 0.00 34.54 3.59
423 548 6.813649 TCGATGAACTCTTTTCAGAATCGATT 59.186 34.615 11.20 11.20 34.54 3.34
424 549 7.973944 TCGATGAACTCTTTTCAGAATCGATTA 59.026 33.333 11.38 0.00 34.54 1.75
425 550 8.595533 CGATGAACTCTTTTCAGAATCGATTAA 58.404 33.333 11.38 0.00 33.04 1.40
426 551 9.695884 GATGAACTCTTTTCAGAATCGATTAAC 57.304 33.333 11.38 0.00 0.00 2.01
427 552 8.029642 TGAACTCTTTTCAGAATCGATTAACC 57.970 34.615 11.38 0.00 0.00 2.85
457 582 9.964303 TTTCAAATCGATGATCTTTTTCTTTCA 57.036 25.926 0.00 0.00 0.00 2.69
475 600 9.664332 TTTCTTTCAAAAATCAATGAACTTGGA 57.336 25.926 0.00 0.00 35.42 3.53
530 657 3.708563 TTTTTGAGGGAGTTTCGCAAG 57.291 42.857 0.00 0.00 0.00 4.01
549 679 5.500771 CGCAAGAAAAACTTTTTGAGGAAGC 60.501 40.000 4.17 0.51 43.02 3.86
555 685 4.756084 AACTTTTTGAGGAAGCTCGATG 57.244 40.909 0.00 0.00 0.00 3.84
577 707 2.048503 GCGAAGGTACCTGTGCGT 60.049 61.111 17.14 0.00 0.00 5.24
584 714 0.801067 GGTACCTGTGCGTGATCGAC 60.801 60.000 4.06 0.00 39.71 4.20
591 721 1.336795 TGTGCGTGATCGACAGTGATT 60.337 47.619 0.00 0.00 39.71 2.57
614 744 1.010580 TTTCTTTTCGAGCGTGTGCA 58.989 45.000 0.00 0.00 46.23 4.57
623 753 1.005037 AGCGTGTGCAAATCGAGGA 60.005 52.632 9.93 0.00 46.23 3.71
734 864 4.359434 GGAGGTCTCCCAAATAGGATTC 57.641 50.000 5.73 0.00 43.94 2.52
735 865 3.073209 GGAGGTCTCCCAAATAGGATTCC 59.927 52.174 5.73 0.00 43.94 3.01
736 866 3.056832 AGGTCTCCCAAATAGGATTCCC 58.943 50.000 0.00 0.00 41.22 3.97
737 867 2.108425 GGTCTCCCAAATAGGATTCCCC 59.892 54.545 0.00 0.00 41.22 4.81
738 868 2.054799 TCTCCCAAATAGGATTCCCCG 58.945 52.381 0.00 0.00 41.22 5.73
739 869 2.054799 CTCCCAAATAGGATTCCCCGA 58.945 52.381 0.00 0.00 41.22 5.14
740 870 2.039084 CTCCCAAATAGGATTCCCCGAG 59.961 54.545 0.00 0.00 41.22 4.63
741 871 1.073923 CCCAAATAGGATTCCCCGAGG 59.926 57.143 0.00 0.00 41.22 4.63
742 872 2.054799 CCAAATAGGATTCCCCGAGGA 58.945 52.381 0.00 0.00 41.22 3.71
743 873 2.644798 CCAAATAGGATTCCCCGAGGAT 59.355 50.000 0.00 0.00 40.57 3.24
744 874 3.307762 CCAAATAGGATTCCCCGAGGATC 60.308 52.174 0.00 0.00 40.57 3.36
745 875 3.275848 AATAGGATTCCCCGAGGATCA 57.724 47.619 0.00 0.00 43.54 2.92
746 876 2.011122 TAGGATTCCCCGAGGATCAC 57.989 55.000 0.00 0.00 43.54 3.06
747 877 0.031111 AGGATTCCCCGAGGATCACA 60.031 55.000 0.00 0.00 43.54 3.58
748 878 0.394565 GGATTCCCCGAGGATCACAG 59.605 60.000 0.00 0.00 43.54 3.66
749 879 0.250081 GATTCCCCGAGGATCACAGC 60.250 60.000 0.00 0.00 43.54 4.40
750 880 2.032860 ATTCCCCGAGGATCACAGCG 62.033 60.000 0.00 0.00 43.54 5.18
751 881 3.461773 CCCCGAGGATCACAGCGT 61.462 66.667 0.00 0.00 33.47 5.07
752 882 2.202797 CCCGAGGATCACAGCGTG 60.203 66.667 0.00 2.79 33.17 5.34
753 883 2.202797 CCGAGGATCACAGCGTGG 60.203 66.667 8.46 0.00 33.87 4.94
754 884 2.710902 CCGAGGATCACAGCGTGGA 61.711 63.158 8.46 0.00 33.87 4.02
755 885 1.439228 CGAGGATCACAGCGTGGAT 59.561 57.895 8.46 0.00 33.87 3.41
756 886 0.873312 CGAGGATCACAGCGTGGATG 60.873 60.000 8.46 0.00 33.87 3.51
757 887 0.531532 GAGGATCACAGCGTGGATGG 60.532 60.000 8.46 0.00 33.87 3.51
758 888 0.977627 AGGATCACAGCGTGGATGGA 60.978 55.000 8.46 0.00 33.87 3.41
759 889 0.531532 GGATCACAGCGTGGATGGAG 60.532 60.000 8.46 0.00 33.87 3.86
760 890 0.176680 GATCACAGCGTGGATGGAGT 59.823 55.000 8.46 0.00 33.87 3.85
761 891 0.107993 ATCACAGCGTGGATGGAGTG 60.108 55.000 8.46 0.00 33.87 3.51
762 892 1.184970 TCACAGCGTGGATGGAGTGA 61.185 55.000 8.46 0.00 33.87 3.41
763 893 1.016130 CACAGCGTGGATGGAGTGAC 61.016 60.000 1.40 0.00 0.00 3.67
764 894 1.807165 CAGCGTGGATGGAGTGACG 60.807 63.158 0.00 0.00 34.93 4.35
766 896 2.261361 CGTGGATGGAGTGACGCA 59.739 61.111 0.00 0.00 0.00 5.24
767 897 1.807165 CGTGGATGGAGTGACGCAG 60.807 63.158 0.00 0.00 0.00 5.18
782 912 2.436646 CAGTGGCCTGCTAACCCG 60.437 66.667 3.32 0.00 0.00 5.28
783 913 2.606519 AGTGGCCTGCTAACCCGA 60.607 61.111 3.32 0.00 0.00 5.14
784 914 2.125106 GTGGCCTGCTAACCCGAG 60.125 66.667 3.32 0.00 0.00 4.63
785 915 2.606519 TGGCCTGCTAACCCGAGT 60.607 61.111 3.32 0.00 0.00 4.18
786 916 2.187163 GGCCTGCTAACCCGAGTC 59.813 66.667 0.00 0.00 0.00 3.36
787 917 2.187163 GCCTGCTAACCCGAGTCC 59.813 66.667 0.00 0.00 0.00 3.85
788 918 2.656069 GCCTGCTAACCCGAGTCCA 61.656 63.158 0.00 0.00 0.00 4.02
789 919 1.980052 CCTGCTAACCCGAGTCCAA 59.020 57.895 0.00 0.00 0.00 3.53
790 920 0.541863 CCTGCTAACCCGAGTCCAAT 59.458 55.000 0.00 0.00 0.00 3.16
791 921 1.656652 CTGCTAACCCGAGTCCAATG 58.343 55.000 0.00 0.00 0.00 2.82
792 922 0.251916 TGCTAACCCGAGTCCAATGG 59.748 55.000 0.00 0.00 0.00 3.16
796 926 3.727258 CCCGAGTCCAATGGGCCA 61.727 66.667 9.61 9.61 35.82 5.36
797 927 2.597340 CCGAGTCCAATGGGCCAT 59.403 61.111 14.78 14.78 0.00 4.40
798 928 1.076777 CCGAGTCCAATGGGCCATT 60.077 57.895 25.94 25.94 34.04 3.16
799 929 1.103398 CCGAGTCCAATGGGCCATTC 61.103 60.000 28.54 17.54 31.05 2.67
800 930 1.439353 CGAGTCCAATGGGCCATTCG 61.439 60.000 28.54 23.56 31.05 3.34
801 931 0.107214 GAGTCCAATGGGCCATTCGA 60.107 55.000 28.54 24.44 31.05 3.71
802 932 0.394352 AGTCCAATGGGCCATTCGAC 60.394 55.000 35.57 35.57 40.48 4.20
803 933 1.077068 TCCAATGGGCCATTCGACC 60.077 57.895 28.54 0.00 31.05 4.79
804 934 2.480610 CCAATGGGCCATTCGACCG 61.481 63.158 28.54 16.60 31.05 4.79
805 935 2.124320 AATGGGCCATTCGACCGG 60.124 61.111 25.94 0.00 26.27 5.28
806 936 3.714487 AATGGGCCATTCGACCGGG 62.714 63.158 25.94 0.00 26.27 5.73
811 941 2.124736 CCATTCGACCGGGCACAT 60.125 61.111 8.76 0.00 0.00 3.21
812 942 2.180204 CCATTCGACCGGGCACATC 61.180 63.158 8.76 0.00 0.00 3.06
813 943 1.153369 CATTCGACCGGGCACATCT 60.153 57.895 8.76 0.00 0.00 2.90
814 944 1.144057 ATTCGACCGGGCACATCTC 59.856 57.895 8.76 0.00 0.00 2.75
815 945 2.629050 ATTCGACCGGGCACATCTCG 62.629 60.000 8.76 4.84 0.00 4.04
829 959 4.278513 CTCGGCCCCAACCCAACA 62.279 66.667 0.00 0.00 0.00 3.33
901 1031 1.376812 TCGCTGCTCACTCGGACTA 60.377 57.895 0.00 0.00 0.00 2.59
993 1123 2.033448 CCACAGCCGCTAAACCCA 59.967 61.111 0.00 0.00 0.00 4.51
1089 1696 2.443016 CCTCTCCCTCTCCACCGG 60.443 72.222 0.00 0.00 0.00 5.28
1989 2596 1.371183 CTGAAGTGCCGGTTCCTGA 59.629 57.895 1.90 0.00 0.00 3.86
1990 2597 0.250295 CTGAAGTGCCGGTTCCTGAA 60.250 55.000 1.90 0.00 0.00 3.02
2054 2661 3.851128 GCCTACGAGGGGGTGCTC 61.851 72.222 0.00 0.00 35.37 4.26
2171 2778 3.069729 GGATCCTCGTGGTTGCTTATACT 59.930 47.826 3.84 0.00 34.23 2.12
2175 2782 2.167693 CTCGTGGTTGCTTATACTGGGA 59.832 50.000 0.00 0.00 0.00 4.37
2183 2790 1.002087 GCTTATACTGGGATGGGTCGG 59.998 57.143 0.00 0.00 0.00 4.79
2303 2910 0.251916 TGCGTATTCTGTTGGGGAGG 59.748 55.000 0.00 0.00 0.00 4.30
2414 3021 3.274288 GAAGATTTTGTGCTCCGAGGAT 58.726 45.455 0.00 0.00 0.00 3.24
2730 3337 2.297701 TGAAGAACTGCTTTGGACCAC 58.702 47.619 0.00 0.00 36.83 4.16
2789 3396 4.344968 GGCAAGGCTTATATTGAAATGGGT 59.655 41.667 0.00 0.00 0.00 4.51
2792 3399 6.736794 GCAAGGCTTATATTGAAATGGGTCAG 60.737 42.308 0.00 0.00 0.00 3.51
2805 3412 0.250081 GGGTCAGCCGGAATCATCTC 60.250 60.000 5.05 0.00 34.97 2.75
2890 3497 4.788679 TCCATTGAGATCATTCAGTGCAT 58.211 39.130 0.00 0.00 34.53 3.96
2981 3598 7.442364 TGAAATAAAGATGCTGCTATCCTGTAC 59.558 37.037 0.00 0.00 0.00 2.90
3108 3730 3.393089 ACTGACTGAGCGATTTTGAGT 57.607 42.857 0.00 0.00 0.00 3.41
3179 3801 8.638685 AGCACATTCAATAGTATTTCATTTGC 57.361 30.769 11.23 11.23 0.00 3.68
3405 4076 9.868277 GTGGTCTCATAGATGAAATATAGGAAG 57.132 37.037 0.00 0.00 29.89 3.46
3406 4077 9.828691 TGGTCTCATAGATGAAATATAGGAAGA 57.171 33.333 0.00 0.00 29.89 2.87
3465 4136 5.923204 ACAGCCCTACATTGAGATAGAAAG 58.077 41.667 0.00 0.00 0.00 2.62
3525 4196 5.413523 AGCACAGTTTAACCTTATAAACCCG 59.586 40.000 6.37 2.30 43.57 5.28
3628 4379 6.874134 AGTCGTGACAGCTTAAGAATTGTAAT 59.126 34.615 6.67 0.00 0.00 1.89
3950 4707 3.037833 TGCGCTGTTGAGCAGTCG 61.038 61.111 9.73 8.25 46.62 4.18
4036 4793 6.839124 TGCAATTTTCTGACCATGTTCTAT 57.161 33.333 0.00 0.00 0.00 1.98
4055 4812 9.472361 TGTTCTATCGATTTATAGTAAAGCACC 57.528 33.333 1.71 0.00 32.31 5.01
4125 4882 4.326826 TGCTTCTTATTGCAGCTACAAGT 58.673 39.130 5.46 0.00 35.93 3.16
4421 5181 8.584157 GCCCAATGTCATTATATGGTTCATTTA 58.416 33.333 0.00 0.00 30.69 1.40
4537 5299 5.534654 AGCATGTATGGTTGTACACAGTTTT 59.465 36.000 0.00 0.00 37.40 2.43
4538 5300 5.856455 GCATGTATGGTTGTACACAGTTTTC 59.144 40.000 0.00 0.00 37.40 2.29
4539 5301 6.514212 GCATGTATGGTTGTACACAGTTTTCA 60.514 38.462 0.00 0.00 37.40 2.69
4669 5436 3.226346 CCATTGTGGTTGAATCAGCTG 57.774 47.619 7.63 7.63 31.35 4.24
4747 5515 3.704566 AGATAAACATCACTCACGGGCTA 59.295 43.478 0.00 0.00 0.00 3.93
4770 5538 3.123804 GTTGGGTGCTGTGACTATATCG 58.876 50.000 0.00 0.00 0.00 2.92
4799 5568 2.886523 CTGCCCTGTGAATTTTCTGTCA 59.113 45.455 0.00 0.00 0.00 3.58
4803 5572 4.925646 GCCCTGTGAATTTTCTGTCATTTC 59.074 41.667 0.00 0.00 0.00 2.17
4883 5653 4.454161 TGTGTATTAGGTTGTGCATCACAC 59.546 41.667 0.00 0.00 44.47 3.82
4962 5748 5.066593 GGAAAGTGAGGACTGTTTGATTCT 58.933 41.667 0.00 0.00 30.61 2.40
4970 5756 3.550842 GGACTGTTTGATTCTTGTGGTGC 60.551 47.826 0.00 0.00 0.00 5.01
4971 5757 3.290710 ACTGTTTGATTCTTGTGGTGCT 58.709 40.909 0.00 0.00 0.00 4.40
4985 5771 3.004629 TGTGGTGCTTTCACTATTTGCTG 59.995 43.478 0.00 0.00 42.72 4.41
5002 5788 0.100325 CTGCTGAGCGTCGAGATTCT 59.900 55.000 0.00 0.00 0.00 2.40
5008 5794 4.166523 CTGAGCGTCGAGATTCTGTTTTA 58.833 43.478 0.00 0.00 0.00 1.52
5010 5796 5.168569 TGAGCGTCGAGATTCTGTTTTATT 58.831 37.500 0.00 0.00 0.00 1.40
5011 5797 5.062183 TGAGCGTCGAGATTCTGTTTTATTG 59.938 40.000 0.00 0.00 0.00 1.90
5014 5800 5.898606 GCGTCGAGATTCTGTTTTATTGATG 59.101 40.000 0.00 0.00 0.00 3.07
5015 5801 6.237835 GCGTCGAGATTCTGTTTTATTGATGA 60.238 38.462 0.00 0.00 0.00 2.92
5016 5802 7.517417 GCGTCGAGATTCTGTTTTATTGATGAT 60.517 37.037 0.00 0.00 0.00 2.45
5017 5803 8.000991 CGTCGAGATTCTGTTTTATTGATGATC 58.999 37.037 0.00 0.00 0.00 2.92
5018 5804 8.820933 GTCGAGATTCTGTTTTATTGATGATCA 58.179 33.333 0.00 0.00 0.00 2.92
5019 5805 9.551734 TCGAGATTCTGTTTTATTGATGATCAT 57.448 29.630 8.25 8.25 0.00 2.45
5020 5806 9.808808 CGAGATTCTGTTTTATTGATGATCATC 57.191 33.333 25.91 25.91 38.29 2.92
5023 5809 9.894783 GATTCTGTTTTATTGATGATCATCTGG 57.105 33.333 30.65 13.19 38.60 3.86
5033 5820 6.688637 TGATGATCATCTGGAAAATGACAC 57.311 37.500 30.65 5.89 36.04 3.67
5064 5851 5.011090 TCTGGATGCTGAGTTACATGTAC 57.989 43.478 4.68 1.30 0.00 2.90
5083 5870 4.836175 TGTACAATAGTGTCCAAGTCAGGA 59.164 41.667 0.00 0.00 39.30 3.86
5099 5886 3.981051 GGAGTTTTTCCTCCCCTCC 57.019 57.895 0.00 0.00 44.49 4.30
5109 5896 1.501170 TCCTCCCCTCCTGAGTAGATG 59.499 57.143 0.00 0.00 0.00 2.90
5111 5898 1.501170 CTCCCCTCCTGAGTAGATGGA 59.499 57.143 0.00 0.00 0.00 3.41
5115 5902 4.172041 TCCCCTCCTGAGTAGATGGAAATA 59.828 45.833 0.00 0.00 0.00 1.40
5123 5910 6.599244 CCTGAGTAGATGGAAATAACAAAGCA 59.401 38.462 0.00 0.00 0.00 3.91
5125 5912 8.044060 TGAGTAGATGGAAATAACAAAGCAAG 57.956 34.615 0.00 0.00 0.00 4.01
5130 5917 4.479158 TGGAAATAACAAAGCAAGGTCCT 58.521 39.130 0.00 0.00 0.00 3.85
5144 5931 2.924757 GGTCCTATAAAAGGTCCCCG 57.075 55.000 0.00 0.00 45.20 5.73
5149 5936 2.701951 CCTATAAAAGGTCCCCGCACTA 59.298 50.000 0.00 0.00 40.94 2.74
5152 5939 0.475044 AAAAGGTCCCCGCACTAACA 59.525 50.000 0.00 0.00 0.00 2.41
5237 6109 4.081697 TCACATGTACATATATGAGGCCCG 60.082 45.833 19.63 5.66 0.00 6.13
5278 6150 3.451526 CTCAGTTGAAGCTCATATGCGA 58.548 45.455 0.00 0.00 38.13 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.514458 AAAGGGAAGTAGCACATGGG 57.486 50.000 0.00 0.00 0.00 4.00
61 67 4.265856 AGGAAAGGAAACAGGGAAAACT 57.734 40.909 0.00 0.00 0.00 2.66
122 139 2.517650 TTTCGCCGCCTTTGAAAAAT 57.482 40.000 0.00 0.00 0.00 1.82
136 153 5.736338 TCACTGATTTTGCAAAAATTTCGC 58.264 33.333 27.10 13.09 0.00 4.70
197 253 6.509317 TCATCAATTTGAAAAACAGTTCGC 57.491 33.333 2.68 0.00 0.00 4.70
198 254 8.118893 AGTTCATCAATTTGAAAAACAGTTCG 57.881 30.769 20.38 0.00 37.36 3.95
388 513 9.748708 TGAAAAGAGTTCATCGATTTTGAAAAT 57.251 25.926 2.27 2.27 35.03 1.82
530 657 5.578776 TCGAGCTTCCTCAAAAAGTTTTTC 58.421 37.500 10.66 0.00 38.00 2.29
549 679 1.002251 GTACCTTCGCTCTCCATCGAG 60.002 57.143 0.00 0.00 36.02 4.04
555 685 0.173708 CACAGGTACCTTCGCTCTCC 59.826 60.000 13.15 0.00 0.00 3.71
565 695 0.801067 GTCGATCACGCACAGGTACC 60.801 60.000 2.73 2.73 39.58 3.34
597 727 1.010580 TTTGCACACGCTCGAAAAGA 58.989 45.000 0.00 0.00 39.64 2.52
646 776 1.508088 GAACAATTGGGCAGGCTCG 59.492 57.895 10.83 0.00 0.00 5.03
648 778 1.228552 ACGAACAATTGGGCAGGCT 60.229 52.632 10.83 0.00 0.00 4.58
652 782 2.190170 ACGCACGAACAATTGGGCA 61.190 52.632 10.83 0.00 39.55 5.36
705 835 2.043852 GGAGACCTCCTCGCCAGA 60.044 66.667 8.76 0.00 46.16 3.86
722 852 2.054799 TCCTCGGGGAATCCTATTTGG 58.945 52.381 0.00 0.00 38.93 3.28
723 853 3.327757 TGATCCTCGGGGAATCCTATTTG 59.672 47.826 8.88 0.00 45.78 2.32
724 854 3.328050 GTGATCCTCGGGGAATCCTATTT 59.672 47.826 8.88 0.00 45.78 1.40
725 855 2.907042 GTGATCCTCGGGGAATCCTATT 59.093 50.000 8.88 0.00 45.78 1.73
726 856 2.158158 TGTGATCCTCGGGGAATCCTAT 60.158 50.000 8.88 0.00 45.78 2.57
727 857 1.219469 TGTGATCCTCGGGGAATCCTA 59.781 52.381 8.88 0.00 45.78 2.94
728 858 0.031111 TGTGATCCTCGGGGAATCCT 60.031 55.000 8.88 0.00 45.78 3.24
729 859 0.394565 CTGTGATCCTCGGGGAATCC 59.605 60.000 8.88 0.66 45.78 3.01
730 860 0.250081 GCTGTGATCCTCGGGGAATC 60.250 60.000 8.88 7.51 45.78 2.52
731 861 1.832912 GCTGTGATCCTCGGGGAAT 59.167 57.895 8.88 0.00 45.78 3.01
732 862 2.721167 CGCTGTGATCCTCGGGGAA 61.721 63.158 8.88 0.00 45.78 3.97
733 863 3.147595 CGCTGTGATCCTCGGGGA 61.148 66.667 6.42 6.42 46.81 4.81
734 864 3.461773 ACGCTGTGATCCTCGGGG 61.462 66.667 0.00 0.00 0.00 5.73
735 865 2.202797 CACGCTGTGATCCTCGGG 60.203 66.667 3.04 0.00 35.23 5.14
736 866 2.021068 ATCCACGCTGTGATCCTCGG 62.021 60.000 9.75 0.00 35.23 4.63
737 867 0.873312 CATCCACGCTGTGATCCTCG 60.873 60.000 9.75 0.00 35.23 4.63
738 868 0.531532 CCATCCACGCTGTGATCCTC 60.532 60.000 9.75 0.00 35.23 3.71
739 869 0.977627 TCCATCCACGCTGTGATCCT 60.978 55.000 9.75 0.00 35.23 3.24
740 870 0.531532 CTCCATCCACGCTGTGATCC 60.532 60.000 9.75 0.00 35.23 3.36
741 871 0.176680 ACTCCATCCACGCTGTGATC 59.823 55.000 9.75 0.00 35.23 2.92
742 872 0.107993 CACTCCATCCACGCTGTGAT 60.108 55.000 9.75 0.80 35.23 3.06
743 873 1.184970 TCACTCCATCCACGCTGTGA 61.185 55.000 9.75 0.00 35.23 3.58
744 874 1.016130 GTCACTCCATCCACGCTGTG 61.016 60.000 2.27 2.27 0.00 3.66
745 875 1.293498 GTCACTCCATCCACGCTGT 59.707 57.895 0.00 0.00 0.00 4.40
746 876 1.807165 CGTCACTCCATCCACGCTG 60.807 63.158 0.00 0.00 0.00 5.18
747 877 2.573869 CGTCACTCCATCCACGCT 59.426 61.111 0.00 0.00 0.00 5.07
749 879 1.807165 CTGCGTCACTCCATCCACG 60.807 63.158 0.00 0.00 35.32 4.94
750 880 1.016130 CACTGCGTCACTCCATCCAC 61.016 60.000 0.00 0.00 0.00 4.02
751 881 1.293179 CACTGCGTCACTCCATCCA 59.707 57.895 0.00 0.00 0.00 3.41
752 882 1.448540 CCACTGCGTCACTCCATCC 60.449 63.158 0.00 0.00 0.00 3.51
753 883 2.103042 GCCACTGCGTCACTCCATC 61.103 63.158 0.00 0.00 0.00 3.51
754 884 2.046892 GCCACTGCGTCACTCCAT 60.047 61.111 0.00 0.00 0.00 3.41
755 885 4.314440 GGCCACTGCGTCACTCCA 62.314 66.667 0.00 0.00 38.85 3.86
756 886 4.008933 AGGCCACTGCGTCACTCC 62.009 66.667 5.01 0.00 38.85 3.85
757 887 2.740055 CAGGCCACTGCGTCACTC 60.740 66.667 5.01 0.00 38.01 3.51
766 896 2.606519 TCGGGTTAGCAGGCCACT 60.607 61.111 5.01 4.14 0.00 4.00
767 897 2.125106 CTCGGGTTAGCAGGCCAC 60.125 66.667 5.01 0.00 0.00 5.01
768 898 2.606519 ACTCGGGTTAGCAGGCCA 60.607 61.111 5.01 0.00 0.00 5.36
769 899 2.187163 GACTCGGGTTAGCAGGCC 59.813 66.667 0.00 0.00 0.00 5.19
770 900 2.180159 TTGGACTCGGGTTAGCAGGC 62.180 60.000 0.00 0.00 0.00 4.85
771 901 0.541863 ATTGGACTCGGGTTAGCAGG 59.458 55.000 0.00 0.00 0.00 4.85
772 902 1.656652 CATTGGACTCGGGTTAGCAG 58.343 55.000 0.00 0.00 0.00 4.24
773 903 0.251916 CCATTGGACTCGGGTTAGCA 59.748 55.000 0.00 0.00 0.00 3.49
774 904 0.463833 CCCATTGGACTCGGGTTAGC 60.464 60.000 3.62 0.00 35.03 3.09
775 905 0.463833 GCCCATTGGACTCGGGTTAG 60.464 60.000 3.62 0.00 42.44 2.34
776 906 1.605453 GCCCATTGGACTCGGGTTA 59.395 57.895 3.62 0.00 42.44 2.85
777 907 2.355115 GCCCATTGGACTCGGGTT 59.645 61.111 3.62 0.00 42.44 4.11
778 908 3.728373 GGCCCATTGGACTCGGGT 61.728 66.667 3.62 0.00 42.44 5.28
779 909 2.572333 AATGGCCCATTGGACTCGGG 62.572 60.000 8.51 0.00 42.00 5.14
780 910 1.076777 AATGGCCCATTGGACTCGG 60.077 57.895 8.51 0.00 42.00 4.63
781 911 1.439353 CGAATGGCCCATTGGACTCG 61.439 60.000 15.10 7.05 42.00 4.18
782 912 0.107214 TCGAATGGCCCATTGGACTC 60.107 55.000 15.10 0.00 42.00 3.36
783 913 1.998530 TCGAATGGCCCATTGGACT 59.001 52.632 15.10 0.00 42.00 3.85
784 914 2.106844 GTCGAATGGCCCATTGGAC 58.893 57.895 28.38 28.38 46.21 4.02
785 915 1.077068 GGTCGAATGGCCCATTGGA 60.077 57.895 15.10 15.73 36.52 3.53
786 916 2.480610 CGGTCGAATGGCCCATTGG 61.481 63.158 15.10 13.31 33.90 3.16
787 917 2.480610 CCGGTCGAATGGCCCATTG 61.481 63.158 15.10 6.63 33.90 2.82
788 918 2.124320 CCGGTCGAATGGCCCATT 60.124 61.111 9.17 9.17 36.72 3.16
789 919 4.189580 CCCGGTCGAATGGCCCAT 62.190 66.667 0.00 0.00 0.00 4.00
794 924 2.124736 ATGTGCCCGGTCGAATGG 60.125 61.111 0.00 0.00 0.00 3.16
795 925 1.153369 AGATGTGCCCGGTCGAATG 60.153 57.895 0.00 0.00 0.00 2.67
796 926 1.144057 GAGATGTGCCCGGTCGAAT 59.856 57.895 0.00 0.00 0.00 3.34
797 927 2.577059 GAGATGTGCCCGGTCGAA 59.423 61.111 0.00 0.00 0.00 3.71
798 928 3.822192 CGAGATGTGCCCGGTCGA 61.822 66.667 0.00 0.00 32.32 4.20
799 929 4.873129 CCGAGATGTGCCCGGTCG 62.873 72.222 0.00 0.23 38.55 4.79
806 936 3.134127 GTTGGGGCCGAGATGTGC 61.134 66.667 0.00 0.00 0.00 4.57
807 937 2.438434 GGTTGGGGCCGAGATGTG 60.438 66.667 0.00 0.00 0.00 3.21
808 938 3.728373 GGGTTGGGGCCGAGATGT 61.728 66.667 0.00 0.00 0.00 3.06
809 939 3.280938 TTGGGTTGGGGCCGAGATG 62.281 63.158 0.00 0.00 0.00 2.90
810 940 2.938798 TTGGGTTGGGGCCGAGAT 60.939 61.111 0.00 0.00 0.00 2.75
811 941 3.961414 GTTGGGTTGGGGCCGAGA 61.961 66.667 0.00 0.00 0.00 4.04
812 942 4.278513 TGTTGGGTTGGGGCCGAG 62.279 66.667 0.00 0.00 0.00 4.63
813 943 4.278513 CTGTTGGGTTGGGGCCGA 62.279 66.667 0.00 0.00 0.00 5.54
821 951 2.912025 CTTGGGCGCTGTTGGGTT 60.912 61.111 7.64 0.00 0.00 4.11
878 1008 2.659610 GAGTGAGCAGCGACCCTT 59.340 61.111 0.00 0.00 0.00 3.95
882 1012 1.645704 TAGTCCGAGTGAGCAGCGAC 61.646 60.000 0.00 0.00 0.00 5.19
2033 2640 4.477119 ACCCCCTCGTAGGCCTCC 62.477 72.222 9.68 0.00 32.73 4.30
2044 2651 1.504275 ATCAAAGCAGAGCACCCCCT 61.504 55.000 0.00 0.00 0.00 4.79
2054 2661 0.248377 GCAGCGCCTTATCAAAGCAG 60.248 55.000 2.29 0.00 0.00 4.24
2102 2709 3.685214 CTCACCGGACCGCTTCTCG 62.685 68.421 9.46 0.00 38.08 4.04
2171 2778 2.284039 TCGTTCCGACCCATCCCA 60.284 61.111 0.00 0.00 0.00 4.37
2175 2782 2.058595 CCTCCTCGTTCCGACCCAT 61.059 63.158 0.00 0.00 0.00 4.00
2303 2910 1.202302 TCATTCATCGCGTCCTCTGTC 60.202 52.381 5.77 0.00 0.00 3.51
2414 3021 2.617276 CCGTGTAGAGTCACTGGACCTA 60.617 54.545 0.00 0.00 45.48 3.08
2429 3036 1.943968 GCAATCTCCAAGCACCGTGTA 60.944 52.381 0.00 0.00 0.00 2.90
2431 3038 0.957395 AGCAATCTCCAAGCACCGTG 60.957 55.000 0.00 0.00 0.00 4.94
2581 3188 1.671742 GAGGCACCCTCGAGAAACA 59.328 57.895 15.71 0.00 41.08 2.83
2730 3337 3.934579 GCAAATCCTAACCCAAAATGCAG 59.065 43.478 0.00 0.00 0.00 4.41
2769 3376 5.302823 GCTGACCCATTTCAATATAAGCCTT 59.697 40.000 0.00 0.00 0.00 4.35
2789 3396 3.706594 ACTTAAGAGATGATTCCGGCTGA 59.293 43.478 10.09 0.00 0.00 4.26
2792 3399 4.698575 AGAACTTAAGAGATGATTCCGGC 58.301 43.478 10.09 0.00 0.00 6.13
2805 3412 5.973565 CACTTGCAAGACCAAAGAACTTAAG 59.026 40.000 32.50 0.00 0.00 1.85
2890 3497 2.431454 TCAGTCCATACGCATTTGCAA 58.569 42.857 0.00 0.00 42.21 4.08
3108 3730 8.771920 AATGTTGACGATATTTCTGACACTAA 57.228 30.769 0.00 0.00 0.00 2.24
3153 3775 9.734620 GCAAATGAAATACTATTGAATGTGCTA 57.265 29.630 9.78 0.00 0.00 3.49
3415 4086 7.148239 CCCTTGCTGTATTAGGAAACAACTAAG 60.148 40.741 0.00 0.00 36.22 2.18
3465 4136 8.611654 TTTCCCTTCTAATTGTGTACAGTTAC 57.388 34.615 0.00 0.00 0.00 2.50
3525 4196 5.220381 GGCCAAGCTTAAGTTTACACTTTC 58.780 41.667 4.08 0.00 40.66 2.62
3649 4400 2.920490 GAGTGTGCTCGAGAAAGATCAC 59.080 50.000 18.75 13.75 37.66 3.06
3738 4489 2.762327 GCACCAAACATGGGATCTTCAT 59.238 45.455 0.00 0.00 0.00 2.57
3788 4539 8.888579 ATAGTTCAACTTGGATATAGTTTCGG 57.111 34.615 0.00 0.00 33.73 4.30
4055 4812 6.834451 AGGGGTATCCACGACATATATAAGAG 59.166 42.308 0.00 0.00 38.24 2.85
4125 4882 4.460731 TCGTTGTTGAAAATCCATGGCATA 59.539 37.500 6.96 0.00 0.00 3.14
4669 5436 3.189702 TGTTCGGCAAAGTAGTTAATGGC 59.810 43.478 0.00 0.00 35.24 4.40
4747 5515 1.362224 ATAGTCACAGCACCCAACCT 58.638 50.000 0.00 0.00 0.00 3.50
4817 5586 5.806654 AGTTGTATTGCCATTTGGAACTT 57.193 34.783 0.00 0.00 37.39 2.66
4883 5653 0.179156 GGGCACAGCGAATCAACATG 60.179 55.000 0.00 0.00 0.00 3.21
4962 5748 3.636300 AGCAAATAGTGAAAGCACCACAA 59.364 39.130 0.00 0.00 46.32 3.33
4970 5756 3.756069 GCTCAGCAGCAAATAGTGAAAG 58.244 45.455 0.00 0.00 46.06 2.62
4971 5757 3.837213 GCTCAGCAGCAAATAGTGAAA 57.163 42.857 0.00 0.00 46.06 2.69
4985 5771 0.179150 ACAGAATCTCGACGCTCAGC 60.179 55.000 0.00 0.00 0.00 4.26
4993 5779 8.947055 TGATCATCAATAAAACAGAATCTCGA 57.053 30.769 0.00 0.00 0.00 4.04
4994 5780 9.808808 GATGATCATCAATAAAACAGAATCTCG 57.191 33.333 27.30 0.00 37.74 4.04
4998 5784 9.636789 TCCAGATGATCATCAATAAAACAGAAT 57.363 29.630 31.99 8.65 40.22 2.40
5008 5794 7.560262 AGTGTCATTTTCCAGATGATCATCAAT 59.440 33.333 31.99 20.88 40.22 2.57
5010 5796 6.420638 AGTGTCATTTTCCAGATGATCATCA 58.579 36.000 31.99 14.69 40.22 3.07
5011 5797 6.939132 AGTGTCATTTTCCAGATGATCATC 57.061 37.500 25.42 25.42 36.07 2.92
5014 5800 7.373493 ACAAAAGTGTCATTTTCCAGATGATC 58.627 34.615 0.00 0.00 36.07 2.92
5015 5801 7.294017 ACAAAAGTGTCATTTTCCAGATGAT 57.706 32.000 0.00 0.00 36.07 2.45
5016 5802 6.713762 ACAAAAGTGTCATTTTCCAGATGA 57.286 33.333 0.00 0.00 29.49 2.92
5033 5820 3.008330 CTCAGCATCCAGAGGACAAAAG 58.992 50.000 0.00 0.00 32.98 2.27
5064 5851 4.543590 ACTCCTGACTTGGACACTATTG 57.456 45.455 0.00 0.00 31.94 1.90
5083 5870 1.988846 CTCAGGAGGGGAGGAAAAACT 59.011 52.381 0.00 0.00 0.00 2.66
5094 5881 5.366768 TGTTATTTCCATCTACTCAGGAGGG 59.633 44.000 0.83 0.00 36.16 4.30
5097 5884 6.823689 GCTTTGTTATTTCCATCTACTCAGGA 59.176 38.462 0.00 0.00 0.00 3.86
5099 5886 7.615582 TGCTTTGTTATTTCCATCTACTCAG 57.384 36.000 0.00 0.00 0.00 3.35
5109 5896 6.775594 ATAGGACCTTGCTTTGTTATTTCC 57.224 37.500 0.00 0.00 0.00 3.13
5130 5917 8.744465 CACTGTTAGTGCGGGGACCTTTTATA 62.744 46.154 0.00 0.00 42.45 0.98
5149 5936 2.034124 AGAAACATTGCCAGCACTGTT 58.966 42.857 19.10 19.10 46.74 3.16
5152 5939 3.947834 GGTATAGAAACATTGCCAGCACT 59.052 43.478 0.00 0.00 0.00 4.40
5206 6077 9.201127 CTCATATATGTACATGTGAGTGAAAGG 57.799 37.037 24.74 6.94 0.00 3.11
5215 6087 4.183865 CGGGCCTCATATATGTACATGTG 58.816 47.826 18.81 13.58 0.00 3.21
5266 6138 3.988976 ATTGGGTATCGCATATGAGCT 57.011 42.857 6.97 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.