Multiple sequence alignment - TraesCS3A01G123200

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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 TraesCS3A01G123200 chr3A 100.000 3168 0 0 1 3168 99270475 99267308 0.000000e+00 5851
1 TraesCS3A01G123200 chr3A 94.556 845 40 4 2326 3168 53892066 53892906 0.000000e+00 1301
2 TraesCS3A01G123200 chr3A 93.140 860 51 5 2311 3168 342072861 342073714 0.000000e+00 1254
3 TraesCS3A01G123200 chr3A 96.398 472 17 0 1 472 737109263 737108792 0.000000e+00 778
4 TraesCS3A01G123200 chr3A 95.763 472 20 0 1 472 733962914 733963385 0.000000e+00 761
5 TraesCS3A01G123200 chr3A 96.522 115 4 0 469 583 30404212 30404098 1.160000e-44 191
6 TraesCS3A01G123200 chr3A 96.522 115 4 0 469 583 113400442 113400556 1.160000e-44 191
7 TraesCS3A01G123200 chr3A 96.522 115 4 0 469 583 603241977 603241863 1.160000e-44 191
8 TraesCS3A01G123200 chr3B 92.961 1449 57 23 876 2307 130112141 130113561 0.000000e+00 2069
9 TraesCS3A01G123200 chr2A 95.621 845 33 4 2326 3168 100844859 100845701 0.000000e+00 1352
10 TraesCS3A01G123200 chr2A 95.266 845 34 5 2328 3168 680503594 680504436 0.000000e+00 1334
11 TraesCS3A01G123200 chr2A 95.763 472 20 0 1 472 10555091 10554620 0.000000e+00 761
12 TraesCS3A01G123200 chr2A 85.440 364 34 13 469 815 10554588 10554227 8.350000e-96 361
13 TraesCS3A01G123200 chr5A 95.261 844 35 4 2328 3168 489655439 489656280 0.000000e+00 1332
14 TraesCS3A01G123200 chr5A 94.083 845 44 5 2326 3168 510439139 510438299 0.000000e+00 1279
15 TraesCS3A01G123200 chr5A 95.652 115 5 0 469 583 14282228 14282342 5.400000e-43 185
16 TraesCS3A01G123200 chr7A 94.320 845 43 4 2326 3168 669490978 669491819 0.000000e+00 1290
17 TraesCS3A01G123200 chr7A 97.034 472 14 0 1 472 552553573 552553102 0.000000e+00 795
18 TraesCS3A01G123200 chr7A 95.763 472 20 0 1 472 721729978 721730449 0.000000e+00 761
19 TraesCS3A01G123200 chr7A 95.579 475 18 2 1 472 552559165 552558691 0.000000e+00 758
20 TraesCS3A01G123200 chr1A 94.201 845 41 5 2326 3168 590564791 590563953 0.000000e+00 1282
21 TraesCS3A01G123200 chr1A 95.339 472 22 0 1 472 513563486 513563957 0.000000e+00 750
22 TraesCS3A01G123200 chr1A 91.667 312 18 5 586 889 14558992 14558681 2.920000e-115 425
23 TraesCS3A01G123200 chr6A 93.964 845 45 4 2326 3168 98303465 98302625 0.000000e+00 1273
24 TraesCS3A01G123200 chr6A 95.127 472 23 0 1 472 563717400 563716929 0.000000e+00 745
25 TraesCS3A01G123200 chr6A 92.834 307 18 4 584 888 591230843 591231147 2.900000e-120 442
26 TraesCS3A01G123200 chr6A 92.642 299 19 2 584 879 602931267 602931565 8.120000e-116 427
27 TraesCS3A01G123200 chr6A 96.522 115 4 0 469 583 14225609 14225723 1.160000e-44 191
28 TraesCS3A01G123200 chr4A 94.947 475 24 0 1 475 581318760 581318286 0.000000e+00 745
29 TraesCS3A01G123200 chr4A 92.131 305 21 2 584 885 714079864 714080168 8.120000e-116 427
30 TraesCS3A01G123200 chr4A 96.522 115 4 0 469 583 591928407 591928521 1.160000e-44 191
31 TraesCS3A01G123200 chr3D 97.128 383 9 1 1775 2155 83487038 83487420 0.000000e+00 645
32 TraesCS3A01G123200 chr3D 91.741 448 26 7 876 1319 83466699 83467139 2.090000e-171 612
33 TraesCS3A01G123200 chr3D 88.771 472 41 5 1311 1782 83468870 83469329 4.590000e-158 568
34 TraesCS3A01G123200 chr3D 92.208 308 17 5 585 885 614035154 614035461 2.260000e-116 429
35 TraesCS3A01G123200 chr3D 88.506 174 6 5 2147 2312 83490584 83490751 6.930000e-47 198
36 TraesCS3A01G123200 chr6D 87.119 427 35 11 469 885 35465515 35465931 1.720000e-127 466
37 TraesCS3A01G123200 chr1D 93.485 307 15 1 584 885 269375466 269375772 4.820000e-123 451
38 TraesCS3A01G123200 chr1D 91.961 311 20 3 584 894 269393076 269393381 6.280000e-117 431
39 TraesCS3A01G123200 chr1B 91.586 309 22 3 582 887 435133097 435132790 1.050000e-114 424
40 TraesCS3A01G123200 chr5B 84.018 438 45 19 470 885 708213839 708214273 6.370000e-107 398


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 TraesCS3A01G123200 chr3A 99267308 99270475 3167 True 5851.0 5851 100.0000 1 3168 1 chr3A.!!$R2 3167
1 TraesCS3A01G123200 chr3A 53892066 53892906 840 False 1301.0 1301 94.5560 2326 3168 1 chr3A.!!$F1 842
2 TraesCS3A01G123200 chr3A 342072861 342073714 853 False 1254.0 1254 93.1400 2311 3168 1 chr3A.!!$F3 857
3 TraesCS3A01G123200 chr3B 130112141 130113561 1420 False 2069.0 2069 92.9610 876 2307 1 chr3B.!!$F1 1431
4 TraesCS3A01G123200 chr2A 100844859 100845701 842 False 1352.0 1352 95.6210 2326 3168 1 chr2A.!!$F1 842
5 TraesCS3A01G123200 chr2A 680503594 680504436 842 False 1334.0 1334 95.2660 2328 3168 1 chr2A.!!$F2 840
6 TraesCS3A01G123200 chr2A 10554227 10555091 864 True 561.0 761 90.6015 1 815 2 chr2A.!!$R1 814
7 TraesCS3A01G123200 chr5A 489655439 489656280 841 False 1332.0 1332 95.2610 2328 3168 1 chr5A.!!$F2 840
8 TraesCS3A01G123200 chr5A 510438299 510439139 840 True 1279.0 1279 94.0830 2326 3168 1 chr5A.!!$R1 842
9 TraesCS3A01G123200 chr7A 669490978 669491819 841 False 1290.0 1290 94.3200 2326 3168 1 chr7A.!!$F1 842
10 TraesCS3A01G123200 chr1A 590563953 590564791 838 True 1282.0 1282 94.2010 2326 3168 1 chr1A.!!$R2 842
11 TraesCS3A01G123200 chr6A 98302625 98303465 840 True 1273.0 1273 93.9640 2326 3168 1 chr6A.!!$R1 842
12 TraesCS3A01G123200 chr3D 83466699 83469329 2630 False 590.0 612 90.2560 876 1782 2 chr3D.!!$F2 906
13 TraesCS3A01G123200 chr3D 83487038 83490751 3713 False 421.5 645 92.8170 1775 2312 2 chr3D.!!$F3 537

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
818 898 0.035439 CAAATGGGCTACGTGGACCT 60.035 55.0 25.66 7.67 34.9 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 7326 0.110419 TTGCACGTGCTCGCATTTAC 60.11 50.0 37.59 8.73 42.66 2.01 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
62 63 7.450634 TGAACCGTAGCCTATCATATCTAAAGT 59.549 37.037 0.00 0.00 0.00 2.66
135 136 4.409247 ACAAGGACTAGAACAAGGAACTGT 59.591 41.667 0.00 0.00 40.86 3.55
152 153 3.214328 ACTGTGGCAGAACCTTTAACAG 58.786 45.455 2.91 0.00 42.03 3.16
178 179 1.134226 CAAGAACACGTACGGGACAC 58.866 55.000 27.01 14.25 0.00 3.67
187 188 2.512355 TACGGGACACCAGCAGCAA 61.512 57.895 0.00 0.00 36.13 3.91
193 194 2.063541 GACACCAGCAGCAAAAGCGT 62.064 55.000 0.00 0.00 37.01 5.07
257 258 2.260743 GTGGACGTCGGGGAAGTC 59.739 66.667 9.92 3.55 39.59 3.01
260 261 2.177778 GACGTCGGGGAAGTCGTC 59.822 66.667 0.00 0.00 42.85 4.20
263 264 2.177778 GTCGGGGAAGTCGTCGTC 59.822 66.667 0.00 0.00 0.00 4.20
322 323 1.581447 CTGAGCGCTCCCCAAAAAC 59.419 57.895 33.23 7.51 0.00 2.43
361 362 0.468226 ACAGGACTCAAAAGGTGCGA 59.532 50.000 0.00 0.00 0.00 5.10
366 367 2.552315 GGACTCAAAAGGTGCGATTTCA 59.448 45.455 0.00 0.00 0.00 2.69
384 385 1.380112 AGAGGCCTACTGTCCCGAC 60.380 63.158 4.42 0.00 0.00 4.79
420 421 0.401395 AAGCCGGGATGGGGAAGATA 60.401 55.000 2.18 0.00 38.63 1.98
489 525 6.213600 GGGATCTTATATAGGCACAGGAGAAA 59.786 42.308 0.00 0.00 0.00 2.52
510 546 2.176055 GCGAAGAGTCTGCGACGA 59.824 61.111 25.13 0.00 33.75 4.20
546 582 2.095252 GGAGACGAAGCGAACAGGC 61.095 63.158 0.00 0.00 0.00 4.85
549 585 1.664965 GACGAAGCGAACAGGCAGT 60.665 57.895 0.00 0.00 34.64 4.40
594 666 2.408271 TCAGTGTCTCGTATACCCGT 57.592 50.000 0.00 0.00 0.00 5.28
595 667 2.283298 TCAGTGTCTCGTATACCCGTC 58.717 52.381 0.00 0.00 0.00 4.79
596 668 1.004185 CAGTGTCTCGTATACCCGTCG 60.004 57.143 0.00 0.00 0.00 5.12
597 669 1.009829 GTGTCTCGTATACCCGTCGT 58.990 55.000 0.00 0.00 0.00 4.34
598 670 1.009078 TGTCTCGTATACCCGTCGTG 58.991 55.000 0.00 0.00 0.00 4.35
599 671 0.316524 GTCTCGTATACCCGTCGTGC 60.317 60.000 0.00 0.00 0.00 5.34
600 672 1.368493 CTCGTATACCCGTCGTGCG 60.368 63.158 0.00 0.00 40.95 5.34
601 673 2.040213 CTCGTATACCCGTCGTGCGT 62.040 60.000 0.00 0.00 39.32 5.24
602 674 1.935917 CGTATACCCGTCGTGCGTG 60.936 63.158 0.00 0.00 39.32 5.34
603 675 1.587088 GTATACCCGTCGTGCGTGG 60.587 63.158 0.00 5.25 39.32 4.94
604 676 3.414343 TATACCCGTCGTGCGTGGC 62.414 63.158 0.00 0.00 39.32 5.01
608 680 3.943034 CCGTCGTGCGTGGCAAAA 61.943 61.111 0.00 0.00 41.47 2.44
609 681 2.023461 CGTCGTGCGTGGCAAAAA 59.977 55.556 0.00 0.00 41.47 1.94
610 682 1.369930 CGTCGTGCGTGGCAAAAAT 60.370 52.632 0.00 0.00 41.47 1.82
611 683 0.932585 CGTCGTGCGTGGCAAAAATT 60.933 50.000 0.00 0.00 41.47 1.82
612 684 1.204792 GTCGTGCGTGGCAAAAATTT 58.795 45.000 0.00 0.00 41.47 1.82
613 685 2.386249 GTCGTGCGTGGCAAAAATTTA 58.614 42.857 0.00 0.00 41.47 1.40
614 686 2.403698 GTCGTGCGTGGCAAAAATTTAG 59.596 45.455 0.00 0.00 41.47 1.85
615 687 2.290916 TCGTGCGTGGCAAAAATTTAGA 59.709 40.909 0.00 0.00 41.47 2.10
616 688 2.403698 CGTGCGTGGCAAAAATTTAGAC 59.596 45.455 0.00 0.00 41.47 2.59
617 689 3.376540 GTGCGTGGCAAAAATTTAGACA 58.623 40.909 0.00 0.00 41.47 3.41
618 690 3.987220 GTGCGTGGCAAAAATTTAGACAT 59.013 39.130 2.78 0.00 41.47 3.06
619 691 4.089923 GTGCGTGGCAAAAATTTAGACATC 59.910 41.667 2.78 0.39 41.47 3.06
620 692 3.300590 GCGTGGCAAAAATTTAGACATCG 59.699 43.478 2.78 8.77 0.00 3.84
621 693 3.851403 CGTGGCAAAAATTTAGACATCGG 59.149 43.478 2.78 0.00 0.00 4.18
622 694 3.612423 GTGGCAAAAATTTAGACATCGGC 59.388 43.478 2.78 0.00 0.00 5.54
636 708 4.161295 CGGCTCGGCTCATTCCCA 62.161 66.667 0.00 0.00 0.00 4.37
692 772 0.535335 GCGTGTGGATGTCCCTCTTA 59.465 55.000 0.00 0.00 35.38 2.10
695 775 3.873910 CGTGTGGATGTCCCTCTTATTT 58.126 45.455 0.00 0.00 35.38 1.40
753 833 6.713731 ATAAAAAGGTCCAACTCCCTCTAA 57.286 37.500 0.00 0.00 0.00 2.10
763 843 5.962031 TCCAACTCCCTCTAAACTAGCAATA 59.038 40.000 0.00 0.00 0.00 1.90
809 889 0.541530 TGCCTTGCACAAATGGGCTA 60.542 50.000 9.34 0.00 46.62 3.93
815 895 0.958382 GCACAAATGGGCTACGTGGA 60.958 55.000 1.81 0.00 42.27 4.02
816 896 0.802494 CACAAATGGGCTACGTGGAC 59.198 55.000 1.81 0.00 0.00 4.02
817 897 0.322187 ACAAATGGGCTACGTGGACC 60.322 55.000 18.56 18.56 34.27 4.46
818 898 0.035439 CAAATGGGCTACGTGGACCT 60.035 55.000 25.66 7.67 34.90 3.85
819 899 0.696501 AAATGGGCTACGTGGACCTT 59.303 50.000 25.66 16.37 34.90 3.50
820 900 0.696501 AATGGGCTACGTGGACCTTT 59.303 50.000 25.66 21.56 34.90 3.11
821 901 1.575419 ATGGGCTACGTGGACCTTTA 58.425 50.000 25.66 4.86 34.90 1.85
822 902 0.899720 TGGGCTACGTGGACCTTTAG 59.100 55.000 25.66 0.00 34.90 1.85
823 903 0.177373 GGGCTACGTGGACCTTTAGG 59.823 60.000 18.07 0.00 42.17 2.69
824 904 1.188863 GGCTACGTGGACCTTTAGGA 58.811 55.000 1.81 0.00 38.94 2.94
825 905 1.761198 GGCTACGTGGACCTTTAGGAT 59.239 52.381 1.81 0.00 38.94 3.24
826 906 2.169978 GGCTACGTGGACCTTTAGGATT 59.830 50.000 1.81 0.00 38.94 3.01
827 907 3.370209 GGCTACGTGGACCTTTAGGATTT 60.370 47.826 1.81 0.00 38.94 2.17
828 908 4.141869 GGCTACGTGGACCTTTAGGATTTA 60.142 45.833 1.81 0.00 38.94 1.40
829 909 5.454329 GGCTACGTGGACCTTTAGGATTTAT 60.454 44.000 1.81 0.00 38.94 1.40
830 910 6.053650 GCTACGTGGACCTTTAGGATTTATT 58.946 40.000 1.81 0.00 38.94 1.40
831 911 7.212274 GCTACGTGGACCTTTAGGATTTATTA 58.788 38.462 1.81 0.00 38.94 0.98
832 912 7.384387 GCTACGTGGACCTTTAGGATTTATTAG 59.616 40.741 1.81 0.00 38.94 1.73
833 913 6.589135 ACGTGGACCTTTAGGATTTATTAGG 58.411 40.000 2.06 0.00 38.94 2.69
834 914 6.384886 ACGTGGACCTTTAGGATTTATTAGGA 59.615 38.462 2.06 0.00 38.94 2.94
835 915 7.092757 ACGTGGACCTTTAGGATTTATTAGGAA 60.093 37.037 2.06 0.00 38.94 3.36
836 916 7.937394 CGTGGACCTTTAGGATTTATTAGGAAT 59.063 37.037 2.06 0.00 38.94 3.01
837 917 9.642343 GTGGACCTTTAGGATTTATTAGGAATT 57.358 33.333 2.06 0.00 38.94 2.17
848 928 9.521503 GGATTTATTAGGAATTTCTGAAACTGC 57.478 33.333 4.73 0.00 0.00 4.40
854 934 6.521151 AGGAATTTCTGAAACTGCTATTGG 57.479 37.500 3.77 0.00 0.00 3.16
855 935 5.420104 AGGAATTTCTGAAACTGCTATTGGG 59.580 40.000 3.77 0.00 0.00 4.12
856 936 4.725790 ATTTCTGAAACTGCTATTGGGC 57.274 40.909 4.73 0.00 0.00 5.36
857 937 3.439857 TTCTGAAACTGCTATTGGGCT 57.560 42.857 0.00 0.00 0.00 5.19
858 938 4.568072 TTCTGAAACTGCTATTGGGCTA 57.432 40.909 0.00 0.00 0.00 3.93
859 939 4.142609 TCTGAAACTGCTATTGGGCTAG 57.857 45.455 0.00 0.00 0.00 3.42
860 940 3.118261 TCTGAAACTGCTATTGGGCTAGG 60.118 47.826 0.00 0.00 0.00 3.02
861 941 1.950216 GAAACTGCTATTGGGCTAGGC 59.050 52.381 8.00 8.00 0.00 3.93
873 953 2.729028 GGCTAGGCCCAAAATAGACA 57.271 50.000 4.61 0.00 44.06 3.41
874 954 3.012934 GGCTAGGCCCAAAATAGACAA 57.987 47.619 4.61 0.00 44.06 3.18
875 955 3.361786 GGCTAGGCCCAAAATAGACAAA 58.638 45.455 4.61 0.00 44.06 2.83
876 956 3.767131 GGCTAGGCCCAAAATAGACAAAA 59.233 43.478 4.61 0.00 44.06 2.44
877 957 4.405680 GGCTAGGCCCAAAATAGACAAAAT 59.594 41.667 4.61 0.00 44.06 1.82
878 958 5.104941 GGCTAGGCCCAAAATAGACAAAATT 60.105 40.000 4.61 0.00 44.06 1.82
879 959 6.042777 GCTAGGCCCAAAATAGACAAAATTC 58.957 40.000 0.00 0.00 0.00 2.17
880 960 5.072040 AGGCCCAAAATAGACAAAATTCG 57.928 39.130 0.00 0.00 0.00 3.34
881 961 4.770010 AGGCCCAAAATAGACAAAATTCGA 59.230 37.500 0.00 0.00 0.00 3.71
882 962 5.102313 GGCCCAAAATAGACAAAATTCGAG 58.898 41.667 0.00 0.00 0.00 4.04
883 963 4.562789 GCCCAAAATAGACAAAATTCGAGC 59.437 41.667 0.00 0.00 0.00 5.03
884 964 5.708948 CCCAAAATAGACAAAATTCGAGCA 58.291 37.500 0.00 0.00 0.00 4.26
890 970 8.723942 AAATAGACAAAATTCGAGCAGATACT 57.276 30.769 0.00 0.00 0.00 2.12
939 1019 9.712305 CTCCATTCTTTTCGACCATACTATAAT 57.288 33.333 0.00 0.00 0.00 1.28
961 1041 0.178873 AAGGTGGAGGTAGGGAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
968 1048 3.282885 GGAGGTAGGGAAGCAGATTTTG 58.717 50.000 0.00 0.00 0.00 2.44
969 1049 3.308473 GGAGGTAGGGAAGCAGATTTTGT 60.308 47.826 0.00 0.00 0.00 2.83
970 1050 3.942115 GAGGTAGGGAAGCAGATTTTGTC 59.058 47.826 0.00 0.00 0.00 3.18
971 1051 3.589288 AGGTAGGGAAGCAGATTTTGTCT 59.411 43.478 0.00 0.00 37.80 3.41
972 1052 3.942115 GGTAGGGAAGCAGATTTTGTCTC 59.058 47.826 0.00 0.00 34.00 3.36
973 1053 2.704572 AGGGAAGCAGATTTTGTCTCG 58.295 47.619 0.00 0.00 34.00 4.04
974 1054 1.131315 GGGAAGCAGATTTTGTCTCGC 59.869 52.381 0.00 0.00 34.00 5.03
975 1055 1.131315 GGAAGCAGATTTTGTCTCGCC 59.869 52.381 0.00 0.00 34.00 5.54
976 1056 2.079925 GAAGCAGATTTTGTCTCGCCT 58.920 47.619 0.00 0.00 34.00 5.52
977 1057 2.191128 AGCAGATTTTGTCTCGCCTT 57.809 45.000 0.00 0.00 34.00 4.35
978 1058 3.334583 AGCAGATTTTGTCTCGCCTTA 57.665 42.857 0.00 0.00 34.00 2.69
981 1061 2.993899 CAGATTTTGTCTCGCCTTACGT 59.006 45.455 0.00 0.00 44.19 3.57
982 1062 2.993899 AGATTTTGTCTCGCCTTACGTG 59.006 45.455 0.00 0.00 44.19 4.49
1041 1124 2.286523 CCTTGTGAGCCCTCCTCGT 61.287 63.158 0.00 0.00 43.82 4.18
1458 3280 0.821301 TTTGCTGTGATGTGGCCGAA 60.821 50.000 0.00 0.00 0.00 4.30
1459 3281 1.236616 TTGCTGTGATGTGGCCGAAG 61.237 55.000 0.00 0.00 0.00 3.79
1460 3282 1.672356 GCTGTGATGTGGCCGAAGT 60.672 57.895 0.00 0.00 0.00 3.01
1461 3283 0.391130 GCTGTGATGTGGCCGAAGTA 60.391 55.000 0.00 0.00 0.00 2.24
1462 3284 1.359848 CTGTGATGTGGCCGAAGTAC 58.640 55.000 0.00 0.00 0.00 2.73
1463 3285 0.973632 TGTGATGTGGCCGAAGTACT 59.026 50.000 0.00 0.00 0.00 2.73
1464 3286 2.165641 CTGTGATGTGGCCGAAGTACTA 59.834 50.000 0.00 0.00 0.00 1.82
1465 3287 2.563620 TGTGATGTGGCCGAAGTACTAA 59.436 45.455 0.00 0.00 0.00 2.24
1482 3309 9.530633 GAAGTACTAATAATCATTTCTCCACGT 57.469 33.333 0.00 0.00 0.00 4.49
1485 3312 7.016361 ACTAATAATCATTTCTCCACGTTGC 57.984 36.000 0.00 0.00 0.00 4.17
1563 3390 4.470170 TCGCCATGGTCGTCGACG 62.470 66.667 31.30 31.30 41.45 5.12
1645 3472 1.539496 GCTCAGGTACCACAACGACAA 60.539 52.381 15.94 0.00 0.00 3.18
1752 3579 2.974489 GACGTGGACGGCTTCGAGA 61.974 63.158 11.90 0.00 45.57 4.04
1761 3588 1.066587 GGCTTCGAGATGAGGACGG 59.933 63.158 0.00 0.00 0.00 4.79
2020 3849 0.884704 GCGTGTTCCTGCTTCCAAGA 60.885 55.000 0.00 0.00 0.00 3.02
2022 3851 1.532868 CGTGTTCCTGCTTCCAAGAAG 59.467 52.381 0.00 0.00 0.00 2.85
2181 7182 5.406649 TGGGATTTGATACGTTGCATTTTC 58.593 37.500 0.00 0.00 0.00 2.29
2216 7219 2.559330 GCCCCTTGCACGTTAACG 59.441 61.111 25.68 25.68 46.33 3.18
2218 7221 1.508808 GCCCCTTGCACGTTAACGAA 61.509 55.000 33.06 16.50 43.39 3.85
2267 7278 5.177374 GCACGTTGCATTTGACTAATTTC 57.823 39.130 5.30 0.00 44.26 2.17
2268 7279 4.917415 GCACGTTGCATTTGACTAATTTCT 59.083 37.500 5.30 0.00 44.26 2.52
2269 7280 6.083630 GCACGTTGCATTTGACTAATTTCTA 58.916 36.000 5.30 0.00 44.26 2.10
2315 7326 8.500753 TTACTTTACTTGCATATGGGTACAAG 57.499 34.615 15.27 15.27 43.99 3.16
2322 7333 5.766150 TGCATATGGGTACAAGTAAATGC 57.234 39.130 4.56 2.99 39.08 3.56
2323 7334 4.274705 TGCATATGGGTACAAGTAAATGCG 59.725 41.667 4.56 0.00 40.96 4.73
2324 7335 4.513692 GCATATGGGTACAAGTAAATGCGA 59.486 41.667 4.56 0.00 30.42 5.10
2385 7396 4.318475 GCATATGCAACACGCGTCTATTTA 60.318 41.667 22.84 0.00 46.97 1.40
2387 7398 1.996898 TGCAACACGCGTCTATTTAGG 59.003 47.619 9.86 0.00 46.97 2.69
2544 7556 5.311121 TCTCCTGTATTAAAAGACCACCCAA 59.689 40.000 0.00 0.00 0.00 4.12
2555 7567 4.396357 AGACCACCCAATGTTTCCAATA 57.604 40.909 0.00 0.00 0.00 1.90
2671 7683 5.362263 ACAAGCTAAGAAACCGTTTCAGTA 58.638 37.500 22.84 14.24 42.10 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.445402 ACGGTTCATATATGCAGAAGCTATTTT 59.555 33.333 7.92 0.00 42.74 1.82
152 153 2.473984 CCGTACGTGTTCTTGTCTTTCC 59.526 50.000 15.21 0.00 0.00 3.13
178 179 1.662446 CCAACGCTTTTGCTGCTGG 60.662 57.895 0.00 0.00 44.80 4.85
187 188 0.822121 GACCCCAAGTCCAACGCTTT 60.822 55.000 0.00 0.00 39.84 3.51
193 194 2.047213 GACACCGACCCCAAGTCCAA 62.047 60.000 0.00 0.00 43.08 3.53
276 277 0.463295 CTGGCTGCTTCATCACGGAT 60.463 55.000 0.00 0.00 0.00 4.18
322 323 1.497161 ACGGGAGAAGGGTGATAAGG 58.503 55.000 0.00 0.00 0.00 2.69
361 362 1.840635 GGGACAGTAGGCCTCTGAAAT 59.159 52.381 28.29 13.54 36.81 2.17
366 367 1.380112 GTCGGGACAGTAGGCCTCT 60.380 63.158 9.68 3.20 0.00 3.69
407 408 2.027653 GCTGCTACTATCTTCCCCATCC 60.028 54.545 0.00 0.00 0.00 3.51
420 421 2.433838 CACTGCGCTGCTGCTACT 60.434 61.111 14.80 0.00 36.97 2.57
441 442 1.291877 CCTCTCGCCACAAAGTTCCG 61.292 60.000 0.00 0.00 0.00 4.30
489 525 2.177038 CGCAGACTCTTCGCGTCT 59.823 61.111 5.77 0.00 42.17 4.18
501 537 1.876664 CTTCACCTCTCGTCGCAGA 59.123 57.895 0.00 0.00 0.00 4.26
507 543 0.387929 TTCGTTGCTTCACCTCTCGT 59.612 50.000 0.00 0.00 0.00 4.18
510 546 0.035458 CCCTTCGTTGCTTCACCTCT 59.965 55.000 0.00 0.00 0.00 3.69
594 666 2.290916 TCTAAATTTTTGCCACGCACGA 59.709 40.909 0.00 0.00 38.71 4.35
595 667 2.403698 GTCTAAATTTTTGCCACGCACG 59.596 45.455 0.00 0.00 38.71 5.34
596 668 3.376540 TGTCTAAATTTTTGCCACGCAC 58.623 40.909 0.00 0.00 38.71 5.34
597 669 3.717400 TGTCTAAATTTTTGCCACGCA 57.283 38.095 0.00 0.00 36.47 5.24
598 670 3.300590 CGATGTCTAAATTTTTGCCACGC 59.699 43.478 0.00 0.00 0.00 5.34
599 671 3.851403 CCGATGTCTAAATTTTTGCCACG 59.149 43.478 0.00 0.00 0.00 4.94
600 672 3.612423 GCCGATGTCTAAATTTTTGCCAC 59.388 43.478 0.00 0.00 0.00 5.01
601 673 3.509575 AGCCGATGTCTAAATTTTTGCCA 59.490 39.130 0.00 0.00 0.00 4.92
602 674 4.105486 GAGCCGATGTCTAAATTTTTGCC 58.895 43.478 0.00 0.00 0.00 4.52
603 675 3.786048 CGAGCCGATGTCTAAATTTTTGC 59.214 43.478 0.00 0.00 0.00 3.68
604 676 4.342772 CCGAGCCGATGTCTAAATTTTTG 58.657 43.478 0.00 0.00 0.00 2.44
605 677 3.181500 GCCGAGCCGATGTCTAAATTTTT 60.181 43.478 0.00 0.00 0.00 1.94
606 678 2.354821 GCCGAGCCGATGTCTAAATTTT 59.645 45.455 0.00 0.00 0.00 1.82
607 679 1.940613 GCCGAGCCGATGTCTAAATTT 59.059 47.619 0.00 0.00 0.00 1.82
608 680 1.139058 AGCCGAGCCGATGTCTAAATT 59.861 47.619 0.00 0.00 0.00 1.82
609 681 0.753262 AGCCGAGCCGATGTCTAAAT 59.247 50.000 0.00 0.00 0.00 1.40
610 682 0.102481 GAGCCGAGCCGATGTCTAAA 59.898 55.000 0.00 0.00 0.00 1.85
611 683 1.035385 TGAGCCGAGCCGATGTCTAA 61.035 55.000 0.00 0.00 0.00 2.10
612 684 0.823769 ATGAGCCGAGCCGATGTCTA 60.824 55.000 0.00 0.00 0.00 2.59
613 685 1.680522 AATGAGCCGAGCCGATGTCT 61.681 55.000 0.00 0.00 0.00 3.41
614 686 1.218230 GAATGAGCCGAGCCGATGTC 61.218 60.000 0.00 0.00 0.00 3.06
615 687 1.227380 GAATGAGCCGAGCCGATGT 60.227 57.895 0.00 0.00 0.00 3.06
616 688 1.958205 GGAATGAGCCGAGCCGATG 60.958 63.158 0.00 0.00 0.00 3.84
617 689 2.423446 GGAATGAGCCGAGCCGAT 59.577 61.111 0.00 0.00 0.00 4.18
618 690 3.849951 GGGAATGAGCCGAGCCGA 61.850 66.667 0.00 0.00 0.00 5.54
619 691 4.161295 TGGGAATGAGCCGAGCCG 62.161 66.667 0.00 0.00 0.00 5.52
620 692 2.514824 GTGGGAATGAGCCGAGCC 60.515 66.667 0.00 0.00 0.00 4.70
621 693 1.377202 TTGTGGGAATGAGCCGAGC 60.377 57.895 0.00 0.00 0.00 5.03
622 694 1.026718 GGTTGTGGGAATGAGCCGAG 61.027 60.000 0.00 0.00 0.00 4.63
664 744 3.989698 ATCCACACGCGCTCCTTCG 62.990 63.158 5.73 0.00 0.00 3.79
666 746 2.434884 CATCCACACGCGCTCCTT 60.435 61.111 5.73 0.00 0.00 3.36
676 756 5.512942 TGAAAATAAGAGGGACATCCACA 57.487 39.130 0.00 0.00 38.24 4.17
692 772 4.342951 CCCCACATGTATGAGCATGAAAAT 59.657 41.667 12.27 0.00 46.65 1.82
695 775 2.509131 TCCCCACATGTATGAGCATGAA 59.491 45.455 12.27 0.00 46.65 2.57
735 815 3.599348 AGTTTAGAGGGAGTTGGACCTT 58.401 45.455 0.00 0.00 37.18 3.50
753 833 8.739972 CAAAAGTTTAGTCCCATATTGCTAGTT 58.260 33.333 0.00 0.00 0.00 2.24
763 843 5.897250 AGGTGAAACAAAAGTTTAGTCCCAT 59.103 36.000 0.00 0.00 39.98 4.00
782 862 0.106769 TTGTGCAAGGCAAGAGGTGA 60.107 50.000 0.00 0.00 41.47 4.02
809 889 6.384886 TCCTAATAAATCCTAAAGGTCCACGT 59.615 38.462 0.00 0.00 36.34 4.49
822 902 9.521503 GCAGTTTCAGAAATTCCTAATAAATCC 57.478 33.333 0.00 0.00 0.00 3.01
828 908 8.689972 CCAATAGCAGTTTCAGAAATTCCTAAT 58.310 33.333 0.00 0.00 0.00 1.73
829 909 7.122650 CCCAATAGCAGTTTCAGAAATTCCTAA 59.877 37.037 0.00 0.00 0.00 2.69
830 910 6.603201 CCCAATAGCAGTTTCAGAAATTCCTA 59.397 38.462 0.00 0.00 0.00 2.94
831 911 5.420104 CCCAATAGCAGTTTCAGAAATTCCT 59.580 40.000 0.00 0.00 0.00 3.36
832 912 5.654497 CCCAATAGCAGTTTCAGAAATTCC 58.346 41.667 0.00 0.00 0.00 3.01
833 913 5.105063 GCCCAATAGCAGTTTCAGAAATTC 58.895 41.667 0.00 0.00 0.00 2.17
834 914 4.774200 AGCCCAATAGCAGTTTCAGAAATT 59.226 37.500 0.00 0.00 34.23 1.82
835 915 4.347607 AGCCCAATAGCAGTTTCAGAAAT 58.652 39.130 0.00 0.00 34.23 2.17
836 916 3.766545 AGCCCAATAGCAGTTTCAGAAA 58.233 40.909 0.00 0.00 34.23 2.52
837 917 3.439857 AGCCCAATAGCAGTTTCAGAA 57.560 42.857 0.00 0.00 34.23 3.02
838 918 3.118261 CCTAGCCCAATAGCAGTTTCAGA 60.118 47.826 0.00 0.00 34.23 3.27
839 919 3.209410 CCTAGCCCAATAGCAGTTTCAG 58.791 50.000 0.00 0.00 34.23 3.02
840 920 2.683742 GCCTAGCCCAATAGCAGTTTCA 60.684 50.000 0.00 0.00 34.23 2.69
841 921 1.950216 GCCTAGCCCAATAGCAGTTTC 59.050 52.381 0.00 0.00 34.23 2.78
842 922 1.410224 GGCCTAGCCCAATAGCAGTTT 60.410 52.381 0.00 0.00 44.06 2.66
843 923 0.183731 GGCCTAGCCCAATAGCAGTT 59.816 55.000 0.00 0.00 44.06 3.16
844 924 1.839894 GGCCTAGCCCAATAGCAGT 59.160 57.895 0.00 0.00 44.06 4.40
845 925 4.809070 GGCCTAGCCCAATAGCAG 57.191 61.111 0.00 0.00 44.06 4.24
855 935 5.598416 ATTTTGTCTATTTTGGGCCTAGC 57.402 39.130 4.53 0.00 0.00 3.42
856 936 6.094881 TCGAATTTTGTCTATTTTGGGCCTAG 59.905 38.462 4.53 0.00 0.00 3.02
857 937 5.946972 TCGAATTTTGTCTATTTTGGGCCTA 59.053 36.000 4.53 0.00 0.00 3.93
858 938 4.770010 TCGAATTTTGTCTATTTTGGGCCT 59.230 37.500 4.53 0.00 0.00 5.19
859 939 5.066968 TCGAATTTTGTCTATTTTGGGCC 57.933 39.130 0.00 0.00 0.00 5.80
860 940 4.562789 GCTCGAATTTTGTCTATTTTGGGC 59.437 41.667 0.00 0.00 0.00 5.36
861 941 5.708948 TGCTCGAATTTTGTCTATTTTGGG 58.291 37.500 0.00 0.00 0.00 4.12
862 942 6.611381 TCTGCTCGAATTTTGTCTATTTTGG 58.389 36.000 0.00 0.00 0.00 3.28
863 943 9.214953 GTATCTGCTCGAATTTTGTCTATTTTG 57.785 33.333 0.00 0.00 0.00 2.44
864 944 9.167311 AGTATCTGCTCGAATTTTGTCTATTTT 57.833 29.630 0.00 0.00 0.00 1.82
865 945 8.723942 AGTATCTGCTCGAATTTTGTCTATTT 57.276 30.769 0.00 0.00 0.00 1.40
866 946 9.250624 GTAGTATCTGCTCGAATTTTGTCTATT 57.749 33.333 0.00 0.00 0.00 1.73
867 947 7.868415 GGTAGTATCTGCTCGAATTTTGTCTAT 59.132 37.037 0.00 0.00 0.00 1.98
868 948 7.147966 TGGTAGTATCTGCTCGAATTTTGTCTA 60.148 37.037 0.00 0.00 0.00 2.59
869 949 6.043411 GGTAGTATCTGCTCGAATTTTGTCT 58.957 40.000 0.00 0.00 0.00 3.41
870 950 5.810587 TGGTAGTATCTGCTCGAATTTTGTC 59.189 40.000 0.00 0.00 0.00 3.18
871 951 5.730550 TGGTAGTATCTGCTCGAATTTTGT 58.269 37.500 0.00 0.00 0.00 2.83
872 952 6.662414 TTGGTAGTATCTGCTCGAATTTTG 57.338 37.500 0.00 0.00 0.00 2.44
873 953 6.260936 CCATTGGTAGTATCTGCTCGAATTTT 59.739 38.462 0.00 0.00 0.00 1.82
874 954 5.760253 CCATTGGTAGTATCTGCTCGAATTT 59.240 40.000 0.00 0.00 0.00 1.82
875 955 5.300752 CCATTGGTAGTATCTGCTCGAATT 58.699 41.667 0.00 0.00 0.00 2.17
876 956 4.800914 GCCATTGGTAGTATCTGCTCGAAT 60.801 45.833 4.26 0.00 0.00 3.34
877 957 3.492656 GCCATTGGTAGTATCTGCTCGAA 60.493 47.826 4.26 0.00 0.00 3.71
878 958 2.035961 GCCATTGGTAGTATCTGCTCGA 59.964 50.000 4.26 0.00 0.00 4.04
879 959 2.408050 GCCATTGGTAGTATCTGCTCG 58.592 52.381 4.26 0.00 0.00 5.03
880 960 2.408050 CGCCATTGGTAGTATCTGCTC 58.592 52.381 4.26 0.00 0.00 4.26
881 961 1.070758 CCGCCATTGGTAGTATCTGCT 59.929 52.381 4.26 0.00 0.00 4.24
882 962 1.202651 ACCGCCATTGGTAGTATCTGC 60.203 52.381 4.26 0.00 41.55 4.26
883 963 2.158957 ACACCGCCATTGGTAGTATCTG 60.159 50.000 4.26 0.00 41.38 2.90
884 964 2.116238 ACACCGCCATTGGTAGTATCT 58.884 47.619 4.26 0.00 41.38 1.98
890 970 0.173935 CGACTACACCGCCATTGGTA 59.826 55.000 4.26 0.00 41.38 3.25
939 1019 3.051650 TGCTTCCCTACCTCCACCTTATA 60.052 47.826 0.00 0.00 0.00 0.98
940 1020 2.293586 TGCTTCCCTACCTCCACCTTAT 60.294 50.000 0.00 0.00 0.00 1.73
941 1021 1.079825 TGCTTCCCTACCTCCACCTTA 59.920 52.381 0.00 0.00 0.00 2.69
942 1022 0.178873 TGCTTCCCTACCTCCACCTT 60.179 55.000 0.00 0.00 0.00 3.50
943 1023 0.618968 CTGCTTCCCTACCTCCACCT 60.619 60.000 0.00 0.00 0.00 4.00
961 1041 2.993899 CACGTAAGGCGAGACAAAATCT 59.006 45.455 0.00 0.00 44.77 2.40
968 1048 0.454600 TGATCCACGTAAGGCGAGAC 59.545 55.000 0.00 0.00 44.77 3.36
969 1049 0.738975 CTGATCCACGTAAGGCGAGA 59.261 55.000 0.00 0.00 44.77 4.04
970 1050 0.738975 TCTGATCCACGTAAGGCGAG 59.261 55.000 0.00 0.00 44.77 5.03
971 1051 0.738975 CTCTGATCCACGTAAGGCGA 59.261 55.000 0.00 0.00 44.77 5.54
973 1053 0.872021 CGCTCTGATCCACGTAAGGC 60.872 60.000 0.00 0.00 46.39 4.35
974 1054 0.738975 TCGCTCTGATCCACGTAAGG 59.261 55.000 0.00 0.00 46.39 2.69
976 1056 0.100682 GCTCGCTCTGATCCACGTAA 59.899 55.000 0.00 0.00 0.00 3.18
977 1057 1.029947 TGCTCGCTCTGATCCACGTA 61.030 55.000 0.00 0.00 0.00 3.57
978 1058 1.877576 TTGCTCGCTCTGATCCACGT 61.878 55.000 0.00 0.00 0.00 4.49
981 1061 0.321346 TGTTTGCTCGCTCTGATCCA 59.679 50.000 0.00 0.00 0.00 3.41
982 1062 1.329906 CATGTTTGCTCGCTCTGATCC 59.670 52.381 0.00 0.00 0.00 3.36
1014 1097 1.733399 GCTCACAAGGGTCGACGAC 60.733 63.158 19.70 19.70 0.00 4.34
1017 1100 2.047179 GGGCTCACAAGGGTCGAC 60.047 66.667 7.13 7.13 0.00 4.20
1041 1124 2.203523 TCCCCGTCGAGGTCAACA 60.204 61.111 4.18 0.00 38.74 3.33
1413 3235 1.293498 TCTGAACGGCCAGAGCTTC 59.707 57.895 2.24 0.00 38.18 3.86
1414 3236 3.471620 TCTGAACGGCCAGAGCTT 58.528 55.556 2.24 0.00 38.18 3.74
1458 3280 9.314321 CAACGTGGAGAAATGATTATTAGTACT 57.686 33.333 0.00 0.00 0.00 2.73
1459 3281 8.062448 GCAACGTGGAGAAATGATTATTAGTAC 58.938 37.037 0.00 0.00 0.00 2.73
1460 3282 7.225931 GGCAACGTGGAGAAATGATTATTAGTA 59.774 37.037 0.00 0.00 0.00 1.82
1461 3283 6.038271 GGCAACGTGGAGAAATGATTATTAGT 59.962 38.462 0.00 0.00 0.00 2.24
1462 3284 6.038161 TGGCAACGTGGAGAAATGATTATTAG 59.962 38.462 0.00 0.00 42.51 1.73
1463 3285 5.883115 TGGCAACGTGGAGAAATGATTATTA 59.117 36.000 0.00 0.00 42.51 0.98
1464 3286 4.704540 TGGCAACGTGGAGAAATGATTATT 59.295 37.500 0.00 0.00 42.51 1.40
1465 3287 4.269183 TGGCAACGTGGAGAAATGATTAT 58.731 39.130 0.00 0.00 42.51 1.28
1482 3309 2.989639 CGTCTCCCTGGATGGCAA 59.010 61.111 0.00 0.00 0.00 4.52
1485 3312 2.060383 TCAGCGTCTCCCTGGATGG 61.060 63.158 0.00 0.00 0.00 3.51
1868 3697 3.863142 ACCAAGAGATGCAATTGAAGC 57.137 42.857 10.34 0.10 0.00 3.86
2020 3849 4.069869 TCGACGACGAGGTTCCTT 57.930 55.556 5.75 0.00 43.81 3.36
2290 7301 8.500753 CTTGTACCCATATGCAAGTAAAGTAA 57.499 34.615 10.84 2.05 37.48 2.24
2312 7323 1.869503 CACGTGCTCGCATTTACTTG 58.130 50.000 0.82 0.00 41.18 3.16
2313 7324 0.165944 GCACGTGCTCGCATTTACTT 59.834 50.000 32.55 0.00 41.18 2.24
2314 7325 0.948623 TGCACGTGCTCGCATTTACT 60.949 50.000 37.59 0.00 42.66 2.24
2315 7326 0.110419 TTGCACGTGCTCGCATTTAC 60.110 50.000 37.59 8.73 42.66 2.01
2316 7327 0.801872 ATTGCACGTGCTCGCATTTA 59.198 45.000 37.59 15.28 42.66 1.40
2317 7328 0.730155 CATTGCACGTGCTCGCATTT 60.730 50.000 37.59 13.98 42.66 2.32
2318 7329 1.154169 CATTGCACGTGCTCGCATT 60.154 52.632 37.59 13.86 42.66 3.56
2319 7330 2.481919 CATTGCACGTGCTCGCAT 59.518 55.556 37.59 22.12 42.66 4.73
2320 7331 4.388080 GCATTGCACGTGCTCGCA 62.388 61.111 37.59 20.95 42.66 5.10
2321 7332 4.388080 TGCATTGCACGTGCTCGC 62.388 61.111 37.59 33.10 42.92 5.03
2365 7376 3.799963 CCTAAATAGACGCGTGTTGCATA 59.200 43.478 20.70 0.00 46.97 3.14
2671 7683 3.644966 TCTTGACTGGAGTTTGTTGGT 57.355 42.857 0.00 0.00 0.00 3.67
3122 8138 4.320608 ACGCATGTTGAAGACCATTTTT 57.679 36.364 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.