Multiple sequence alignment - TraesCS5B01G227700

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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 TraesCS5B01G227700 chr5B 100.000 2687 0 0 1 2687 404182373 404185059 0.000000e+00 4963.0
1 TraesCS5B01G227700 chr5B 92.874 856 54 5 1833 2687 284157768 284158617 0.000000e+00 1236.0
2 TraesCS5B01G227700 chr5B 94.565 736 34 6 1956 2687 64718819 64718086 0.000000e+00 1133.0
3 TraesCS5B01G227700 chr5B 93.758 737 38 7 1956 2685 596981287 596980552 0.000000e+00 1099.0
4 TraesCS5B01G227700 chr5D 89.386 1140 59 26 668 1793 346689846 346688755 0.000000e+00 1378.0
5 TraesCS5B01G227700 chr5D 92.941 85 6 0 534 618 346689928 346689844 1.010000e-24 124.0
6 TraesCS5B01G227700 chr6B 94.166 857 45 3 1835 2687 712097942 712098797 0.000000e+00 1301.0
7 TraesCS5B01G227700 chr6B 92.075 858 46 11 1833 2687 93914146 93914984 0.000000e+00 1188.0
8 TraesCS5B01G227700 chr2B 94.159 856 45 4 1833 2687 105380180 105381031 0.000000e+00 1299.0
9 TraesCS5B01G227700 chr2B 94.966 735 30 6 1956 2687 545166768 545166038 0.000000e+00 1146.0
10 TraesCS5B01G227700 chr2B 83.485 551 52 17 1 517 762594512 762593967 6.730000e-131 477.0
11 TraesCS5B01G227700 chr1B 94.042 856 48 3 1833 2687 562617889 562617036 0.000000e+00 1295.0
12 TraesCS5B01G227700 chr4B 93.466 857 50 6 1833 2687 422783869 422783017 0.000000e+00 1267.0
13 TraesCS5B01G227700 chr7B 92.816 863 42 11 1829 2687 648162607 648163453 0.000000e+00 1232.0
14 TraesCS5B01G227700 chr7B 85.638 564 48 14 1 532 34054331 34053769 1.810000e-156 562.0
15 TraesCS5B01G227700 chr3B 91.920 854 48 11 1835 2681 776548858 776549697 0.000000e+00 1175.0
16 TraesCS5B01G227700 chr3B 91.589 856 54 8 1835 2687 431990305 431991145 0.000000e+00 1166.0
17 TraesCS5B01G227700 chr3B 84.698 281 37 3 253 528 817342003 817341724 2.640000e-70 276.0
18 TraesCS5B01G227700 chr5A 89.441 805 49 22 995 1793 444890956 444891730 0.000000e+00 983.0
19 TraesCS5B01G227700 chr5A 93.678 174 11 0 1618 1791 444894592 444894765 7.380000e-66 261.0
20 TraesCS5B01G227700 chrUn 89.484 504 31 14 1835 2330 7149124 7148635 3.800000e-173 617.0
21 TraesCS5B01G227700 chr2D 93.662 142 8 1 1 142 635248103 635247963 7.540000e-51 211.0
22 TraesCS5B01G227700 chr2D 83.486 109 5 1 356 464 635247890 635247795 3.680000e-14 89.8
23 TraesCS5B01G227700 chr2A 100.000 29 0 0 1269 1297 22887788 22887816 1.000000e-03 54.7


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 TraesCS5B01G227700 chr5B 404182373 404185059 2686 False 4963 4963 100.0000 1 2687 1 chr5B.!!$F2 2686
1 TraesCS5B01G227700 chr5B 284157768 284158617 849 False 1236 1236 92.8740 1833 2687 1 chr5B.!!$F1 854
2 TraesCS5B01G227700 chr5B 64718086 64718819 733 True 1133 1133 94.5650 1956 2687 1 chr5B.!!$R1 731
3 TraesCS5B01G227700 chr5B 596980552 596981287 735 True 1099 1099 93.7580 1956 2685 1 chr5B.!!$R2 729
4 TraesCS5B01G227700 chr5D 346688755 346689928 1173 True 751 1378 91.1635 534 1793 2 chr5D.!!$R1 1259
5 TraesCS5B01G227700 chr6B 712097942 712098797 855 False 1301 1301 94.1660 1835 2687 1 chr6B.!!$F2 852
6 TraesCS5B01G227700 chr6B 93914146 93914984 838 False 1188 1188 92.0750 1833 2687 1 chr6B.!!$F1 854
7 TraesCS5B01G227700 chr2B 105380180 105381031 851 False 1299 1299 94.1590 1833 2687 1 chr2B.!!$F1 854
8 TraesCS5B01G227700 chr2B 545166038 545166768 730 True 1146 1146 94.9660 1956 2687 1 chr2B.!!$R1 731
9 TraesCS5B01G227700 chr2B 762593967 762594512 545 True 477 477 83.4850 1 517 1 chr2B.!!$R2 516
10 TraesCS5B01G227700 chr1B 562617036 562617889 853 True 1295 1295 94.0420 1833 2687 1 chr1B.!!$R1 854
11 TraesCS5B01G227700 chr4B 422783017 422783869 852 True 1267 1267 93.4660 1833 2687 1 chr4B.!!$R1 854
12 TraesCS5B01G227700 chr7B 648162607 648163453 846 False 1232 1232 92.8160 1829 2687 1 chr7B.!!$F1 858
13 TraesCS5B01G227700 chr7B 34053769 34054331 562 True 562 562 85.6380 1 532 1 chr7B.!!$R1 531
14 TraesCS5B01G227700 chr3B 776548858 776549697 839 False 1175 1175 91.9200 1835 2681 1 chr3B.!!$F2 846
15 TraesCS5B01G227700 chr3B 431990305 431991145 840 False 1166 1166 91.5890 1835 2687 1 chr3B.!!$F1 852
16 TraesCS5B01G227700 chr5A 444890956 444894765 3809 False 622 983 91.5595 995 1793 2 chr5A.!!$F1 798

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
803 846 0.031585 GAAACCCGCTGAAAACCACC 59.968 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2500 4805 1.531578 CTCTGTCTCGTCTGAACACGA 59.468 52.381 0.0 0.0 46.42 4.35 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
40 41 6.773976 TTCTCCATATTTGTTTGCCCTTAG 57.226 37.500 0.00 0.00 0.00 2.18
67 68 7.737525 ATGTTTCTTCTAATCTCGACGTTAC 57.262 36.000 0.00 0.00 0.00 2.50
68 69 6.671190 TGTTTCTTCTAATCTCGACGTTACA 58.329 36.000 0.00 0.00 0.00 2.41
98 99 4.936411 TGTTAAATATTTCGGGCGTCTCAA 59.064 37.500 3.39 0.00 0.00 3.02
103 104 7.972832 AAATATTTCGGGCGTCTCAATATAA 57.027 32.000 0.00 0.00 0.00 0.98
105 106 3.804786 TTCGGGCGTCTCAATATAACA 57.195 42.857 0.00 0.00 0.00 2.41
196 211 3.310227 TGTGTTGTCTATTTTTGCGTCGT 59.690 39.130 0.00 0.00 0.00 4.34
207 229 4.925786 GCGTCGTGCGTTATGAAG 57.074 55.556 0.00 0.00 43.66 3.02
221 243 5.915196 GCGTTATGAAGAAAGAACTTGCTTT 59.085 36.000 8.90 0.00 38.52 3.51
233 255 3.423162 TTGCTTTGCACGTGGTGGC 62.423 57.895 18.88 2.69 38.71 5.01
326 369 7.602644 GGGAAAATAAAAAGGAAATCTCGCTTT 59.397 33.333 0.00 0.00 0.00 3.51
373 416 1.671054 CGCAATGAACAGTCCCGGT 60.671 57.895 0.00 0.00 0.00 5.28
419 462 1.608590 CTGTTTGGGAACGCACTCAAT 59.391 47.619 0.00 0.00 38.65 2.57
441 484 3.055675 TGTTCAAAATAGACCGGGATCGT 60.056 43.478 6.32 0.00 33.95 3.73
466 509 2.622942 GTTTGGTGTGCTCATTTCAGGA 59.377 45.455 0.00 0.00 0.00 3.86
469 512 2.821378 TGGTGTGCTCATTTCAGGAATG 59.179 45.455 0.00 0.00 45.31 2.67
471 514 2.165030 GTGTGCTCATTTCAGGAATGGG 59.835 50.000 1.24 0.00 46.97 4.00
491 534 3.118000 GGGAAGTTCAGGGGTCGATTTAT 60.118 47.826 5.01 0.00 0.00 1.40
494 537 4.674281 AGTTCAGGGGTCGATTTATCTC 57.326 45.455 0.00 0.00 0.00 2.75
508 551 9.021863 GTCGATTTATCTCTCGTCTACAAATTT 57.978 33.333 0.00 0.00 36.33 1.82
533 576 9.594936 TTAAGATTTATTTTGGACTTTCTCCCA 57.405 29.630 0.00 0.00 38.49 4.37
534 577 8.670521 AAGATTTATTTTGGACTTTCTCCCAT 57.329 30.769 0.00 0.00 38.49 4.00
535 578 9.768215 AAGATTTATTTTGGACTTTCTCCCATA 57.232 29.630 0.00 0.00 38.49 2.74
536 579 9.942526 AGATTTATTTTGGACTTTCTCCCATAT 57.057 29.630 0.00 0.00 38.49 1.78
567 610 7.358270 CGAAATCAAATCAAAATTCAGTCGCAA 60.358 33.333 0.00 0.00 0.00 4.85
570 613 7.712264 TCAAATCAAAATTCAGTCGCAAAAT 57.288 28.000 0.00 0.00 0.00 1.82
585 628 3.432933 CGCAAAATGAAAATCAACCAGGG 59.567 43.478 0.00 0.00 0.00 4.45
586 629 4.640364 GCAAAATGAAAATCAACCAGGGA 58.360 39.130 0.00 0.00 0.00 4.20
618 661 1.227118 GGAAGAGTAGCAGGCGAGC 60.227 63.158 0.00 0.00 0.00 5.03
619 662 1.587613 GAAGAGTAGCAGGCGAGCG 60.588 63.158 0.00 0.00 40.15 5.03
620 663 2.945398 GAAGAGTAGCAGGCGAGCGG 62.945 65.000 0.00 0.00 40.15 5.52
621 664 3.518998 GAGTAGCAGGCGAGCGGA 61.519 66.667 0.00 0.00 40.15 5.54
622 665 2.835431 AGTAGCAGGCGAGCGGAT 60.835 61.111 0.00 0.00 40.15 4.18
623 666 2.659897 GTAGCAGGCGAGCGGATG 60.660 66.667 0.00 0.00 40.15 3.51
624 667 4.592192 TAGCAGGCGAGCGGATGC 62.592 66.667 9.52 9.52 40.15 3.91
630 673 4.819761 GCGAGCGGATGCACCAGA 62.820 66.667 0.00 0.00 46.23 3.86
631 674 2.584418 CGAGCGGATGCACCAGAG 60.584 66.667 0.00 0.00 46.23 3.35
632 675 2.895680 GAGCGGATGCACCAGAGA 59.104 61.111 0.00 0.00 46.23 3.10
633 676 1.227205 GAGCGGATGCACCAGAGAG 60.227 63.158 0.00 0.00 46.23 3.20
634 677 2.202987 GCGGATGCACCAGAGAGG 60.203 66.667 0.00 0.00 45.67 3.69
635 678 2.725312 GCGGATGCACCAGAGAGGA 61.725 63.158 0.00 0.00 39.82 3.71
636 679 1.440893 CGGATGCACCAGAGAGGAG 59.559 63.158 0.00 0.00 41.22 3.69
637 680 1.039785 CGGATGCACCAGAGAGGAGA 61.040 60.000 0.00 0.00 41.22 3.71
638 681 0.463620 GGATGCACCAGAGAGGAGAC 59.536 60.000 0.00 0.00 41.22 3.36
639 682 0.102120 GATGCACCAGAGAGGAGACG 59.898 60.000 0.00 0.00 41.22 4.18
640 683 0.323816 ATGCACCAGAGAGGAGACGA 60.324 55.000 0.00 0.00 41.22 4.20
641 684 0.539669 TGCACCAGAGAGGAGACGAA 60.540 55.000 0.00 0.00 41.22 3.85
642 685 0.603569 GCACCAGAGAGGAGACGAAA 59.396 55.000 0.00 0.00 41.22 3.46
643 686 1.403514 GCACCAGAGAGGAGACGAAAG 60.404 57.143 0.00 0.00 41.22 2.62
644 687 0.892063 ACCAGAGAGGAGACGAAAGC 59.108 55.000 0.00 0.00 41.22 3.51
645 688 0.179150 CCAGAGAGGAGACGAAAGCG 60.179 60.000 0.00 0.00 41.22 4.68
646 689 0.805614 CAGAGAGGAGACGAAAGCGA 59.194 55.000 0.00 0.00 41.64 4.93
647 690 0.806241 AGAGAGGAGACGAAAGCGAC 59.194 55.000 0.00 0.00 41.64 5.19
648 691 0.521659 GAGAGGAGACGAAAGCGACG 60.522 60.000 0.00 0.00 41.64 5.12
649 692 1.209640 GAGGAGACGAAAGCGACGT 59.790 57.895 5.69 5.69 46.58 4.34
650 693 1.066114 GAGGAGACGAAAGCGACGTG 61.066 60.000 10.10 0.00 43.97 4.49
651 694 2.717809 GGAGACGAAAGCGACGTGC 61.718 63.158 10.10 0.00 43.97 5.34
661 704 3.117589 GCGACGTGCTAGGAAAAGA 57.882 52.632 0.00 0.00 41.73 2.52
662 705 0.992802 GCGACGTGCTAGGAAAAGAG 59.007 55.000 0.00 0.00 41.73 2.85
663 706 1.630148 CGACGTGCTAGGAAAAGAGG 58.370 55.000 0.00 0.00 0.00 3.69
664 707 1.201647 CGACGTGCTAGGAAAAGAGGA 59.798 52.381 0.00 0.00 0.00 3.71
665 708 2.732597 CGACGTGCTAGGAAAAGAGGAG 60.733 54.545 0.00 0.00 0.00 3.69
666 709 2.492484 GACGTGCTAGGAAAAGAGGAGA 59.508 50.000 0.00 0.00 0.00 3.71
667 710 2.494073 ACGTGCTAGGAAAAGAGGAGAG 59.506 50.000 0.00 0.00 0.00 3.20
668 711 2.755655 CGTGCTAGGAAAAGAGGAGAGA 59.244 50.000 0.00 0.00 0.00 3.10
669 712 3.181491 CGTGCTAGGAAAAGAGGAGAGAG 60.181 52.174 0.00 0.00 0.00 3.20
676 719 2.237534 AAAGAGGAGAGAGGCTGCGC 62.238 60.000 0.00 0.00 40.35 6.09
794 837 4.778143 CTCCCCCGAAACCCGCTG 62.778 72.222 0.00 0.00 36.84 5.18
796 839 4.338710 CCCCCGAAACCCGCTGAA 62.339 66.667 0.00 0.00 36.84 3.02
797 840 2.281900 CCCCGAAACCCGCTGAAA 60.282 61.111 0.00 0.00 36.84 2.69
798 841 1.899534 CCCCGAAACCCGCTGAAAA 60.900 57.895 0.00 0.00 36.84 2.29
799 842 1.284715 CCCGAAACCCGCTGAAAAC 59.715 57.895 0.00 0.00 36.84 2.43
800 843 1.284715 CCGAAACCCGCTGAAAACC 59.715 57.895 0.00 0.00 36.84 3.27
801 844 1.448922 CCGAAACCCGCTGAAAACCA 61.449 55.000 0.00 0.00 36.84 3.67
802 845 0.317519 CGAAACCCGCTGAAAACCAC 60.318 55.000 0.00 0.00 0.00 4.16
803 846 0.031585 GAAACCCGCTGAAAACCACC 59.968 55.000 0.00 0.00 0.00 4.61
829 872 1.793581 GCGCACGACAATTCCATCA 59.206 52.632 0.30 0.00 0.00 3.07
837 880 2.600420 CGACAATTCCATCACTCTCACG 59.400 50.000 0.00 0.00 0.00 4.35
882 925 3.351416 GTCCGGCGTTTCCACCAC 61.351 66.667 6.01 0.00 34.01 4.16
928 971 2.125106 CTCCCGGCTTTCTTCCCG 60.125 66.667 0.00 0.00 43.97 5.14
965 1013 1.534729 CCCTTCCAACTTCTTTCCCG 58.465 55.000 0.00 0.00 0.00 5.14
984 1032 1.654954 GCCTTCTCGCGAGTCTACCA 61.655 60.000 33.33 12.48 0.00 3.25
986 1034 1.370609 CTTCTCGCGAGTCTACCAGA 58.629 55.000 33.33 11.17 0.00 3.86
987 1035 1.329292 CTTCTCGCGAGTCTACCAGAG 59.671 57.143 33.33 15.67 0.00 3.35
988 1036 0.535797 TCTCGCGAGTCTACCAGAGA 59.464 55.000 33.33 9.62 33.02 3.10
1071 1119 3.067883 CGAGAATTCTCATCTCAGAGGCA 59.932 47.826 29.93 0.00 42.79 4.75
1106 1158 1.163554 GGCAACAAGAGCAGAGGAAG 58.836 55.000 0.00 0.00 0.00 3.46
1108 1160 1.888215 CAACAAGAGCAGAGGAAGCA 58.112 50.000 0.00 0.00 0.00 3.91
1109 1161 1.805345 CAACAAGAGCAGAGGAAGCAG 59.195 52.381 0.00 0.00 0.00 4.24
1110 1162 1.346062 ACAAGAGCAGAGGAAGCAGA 58.654 50.000 0.00 0.00 0.00 4.26
1111 1163 1.001860 ACAAGAGCAGAGGAAGCAGAC 59.998 52.381 0.00 0.00 0.00 3.51
1112 1164 1.001746 CAAGAGCAGAGGAAGCAGACA 59.998 52.381 0.00 0.00 0.00 3.41
1113 1165 0.896923 AGAGCAGAGGAAGCAGACAG 59.103 55.000 0.00 0.00 0.00 3.51
1114 1166 0.894141 GAGCAGAGGAAGCAGACAGA 59.106 55.000 0.00 0.00 0.00 3.41
1115 1167 0.896923 AGCAGAGGAAGCAGACAGAG 59.103 55.000 0.00 0.00 0.00 3.35
1116 1168 0.894141 GCAGAGGAAGCAGACAGAGA 59.106 55.000 0.00 0.00 0.00 3.10
1117 1169 1.274728 GCAGAGGAAGCAGACAGAGAA 59.725 52.381 0.00 0.00 0.00 2.87
1137 1190 2.238084 AGGCACAGACAGAGGACATA 57.762 50.000 0.00 0.00 0.00 2.29
1146 1199 3.957497 AGACAGAGGACATAGACATGGAC 59.043 47.826 0.00 0.00 36.39 4.02
1150 1203 3.645212 AGAGGACATAGACATGGACATGG 59.355 47.826 15.94 1.34 42.91 3.66
1187 1240 2.499685 GGGCGCGTCCTACTTCAT 59.500 61.111 25.46 0.00 34.39 2.57
1188 1241 1.591863 GGGCGCGTCCTACTTCATC 60.592 63.158 25.46 0.00 34.39 2.92
1189 1242 1.437986 GGCGCGTCCTACTTCATCT 59.562 57.895 8.43 0.00 0.00 2.90
1190 1243 0.179108 GGCGCGTCCTACTTCATCTT 60.179 55.000 8.43 0.00 0.00 2.40
1191 1244 1.201343 GCGCGTCCTACTTCATCTTC 58.799 55.000 8.43 0.00 0.00 2.87
1192 1245 1.469251 GCGCGTCCTACTTCATCTTCA 60.469 52.381 8.43 0.00 0.00 3.02
1208 1261 3.423154 CAACTTCTCCGTGGCGCC 61.423 66.667 22.73 22.73 0.00 6.53
1273 1326 1.985116 GCCCTCGTCAAGTCCTCCT 60.985 63.158 0.00 0.00 0.00 3.69
1278 1331 0.404426 TCGTCAAGTCCTCCTCCTCA 59.596 55.000 0.00 0.00 0.00 3.86
1284 1337 1.619298 AGTCCTCCTCCTCATCCTCT 58.381 55.000 0.00 0.00 0.00 3.69
1285 1338 1.936631 AGTCCTCCTCCTCATCCTCTT 59.063 52.381 0.00 0.00 0.00 2.85
1286 1339 2.091333 AGTCCTCCTCCTCATCCTCTTC 60.091 54.545 0.00 0.00 0.00 2.87
1287 1340 2.091333 GTCCTCCTCCTCATCCTCTTCT 60.091 54.545 0.00 0.00 0.00 2.85
1288 1341 2.589664 TCCTCCTCCTCATCCTCTTCTT 59.410 50.000 0.00 0.00 0.00 2.52
1289 1342 2.965147 CCTCCTCCTCATCCTCTTCTTC 59.035 54.545 0.00 0.00 0.00 2.87
1290 1343 2.622942 CTCCTCCTCATCCTCTTCTTCG 59.377 54.545 0.00 0.00 0.00 3.79
1297 1350 2.103373 CATCCTCTTCTTCGTCCTCCA 58.897 52.381 0.00 0.00 0.00 3.86
1445 1498 4.162690 GTTCGAGGAGGCGGCCAT 62.163 66.667 23.09 6.44 0.00 4.40
1446 1499 3.849951 TTCGAGGAGGCGGCCATC 61.850 66.667 23.09 15.03 0.00 3.51
1557 1610 3.443925 CTCCGGAGCGTGCTGAGA 61.444 66.667 20.67 0.00 0.00 3.27
1633 1686 2.094182 GCCTATGACGAGAACAAGGACA 60.094 50.000 0.00 0.00 0.00 4.02
1723 1776 0.572590 GACGACCGATGATTTGCTCG 59.427 55.000 0.00 0.00 34.73 5.03
1728 1781 2.866156 GACCGATGATTTGCTCGATTCA 59.134 45.455 0.00 0.00 37.05 2.57
1793 1850 2.435234 GCCGAATGGTGCACCGTA 60.435 61.111 30.52 15.10 39.43 4.02
1794 1851 1.817941 GCCGAATGGTGCACCGTAT 60.818 57.895 30.52 19.75 39.43 3.06
1795 1852 2.013807 CCGAATGGTGCACCGTATG 58.986 57.895 30.52 23.49 39.43 2.39
1796 1853 0.742990 CCGAATGGTGCACCGTATGT 60.743 55.000 30.52 15.86 39.43 2.29
1802 1874 5.557514 CGAATGGTGCACCGTATGTATTTAC 60.558 44.000 30.52 11.08 39.43 2.01
1815 1887 8.909671 CCGTATGTATTTACTCCGATTCTTTAC 58.090 37.037 0.00 0.00 0.00 2.01
1949 2591 2.793946 CAGCCGCGCTAAAATGCT 59.206 55.556 5.56 0.00 36.40 3.79
1954 2596 1.135315 CGCGCTAAAATGCTGCTGT 59.865 52.632 5.56 0.00 33.07 4.40
1956 2598 1.408474 GCGCTAAAATGCTGCTGTGC 61.408 55.000 0.00 0.00 32.72 4.57
1957 2599 1.129879 CGCTAAAATGCTGCTGTGCG 61.130 55.000 0.00 5.07 36.41 5.34
1958 2600 1.408474 GCTAAAATGCTGCTGTGCGC 61.408 55.000 0.00 0.00 39.77 6.09
1959 2601 1.129879 CTAAAATGCTGCTGTGCGCG 61.130 55.000 0.00 0.00 43.27 6.86
2251 4357 2.180769 CCACCGCTCATCGTTCGA 59.819 61.111 0.00 0.00 36.19 3.71
2326 4631 1.080093 CCTTCCGCTGACGCTTGTA 60.080 57.895 0.00 0.00 38.22 2.41
2359 4664 2.260434 GCGCCTTCGTGTGTCCTA 59.740 61.111 0.00 0.00 38.14 2.94
2523 4828 1.202891 TGTTCAGACGAGACAGAGGGA 60.203 52.381 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.773976 TTCTAAGGGCAAACAAATATGGAG 57.226 37.500 0.00 0.00 0.00 3.86
40 41 7.279470 ACGTCGAGATTAGAAGAAACATTTC 57.721 36.000 0.00 0.00 37.45 2.17
67 68 6.027749 GCCCGAAATATTTAACAACAGACTG 58.972 40.000 0.00 0.00 0.00 3.51
68 69 5.163794 CGCCCGAAATATTTAACAACAGACT 60.164 40.000 0.00 0.00 0.00 3.24
98 99 6.830324 ACAACAGATGGCAGTCATTGTTATAT 59.170 34.615 12.38 3.38 36.40 0.86
103 104 2.867624 ACAACAGATGGCAGTCATTGT 58.132 42.857 0.00 0.00 35.97 2.71
105 106 3.012518 GCTACAACAGATGGCAGTCATT 58.987 45.455 0.00 0.00 35.97 2.57
196 211 4.515191 AGCAAGTTCTTTCTTCATAACGCA 59.485 37.500 0.00 0.00 0.00 5.24
233 255 2.081462 GACAACTGTTATTGGACCGGG 58.919 52.381 6.32 0.00 33.63 5.73
300 343 6.631016 AGCGAGATTTCCTTTTTATTTTCCC 58.369 36.000 0.00 0.00 0.00 3.97
359 402 4.520179 GGTTTAATACCGGGACTGTTCAT 58.480 43.478 6.32 0.00 37.12 2.57
373 416 6.719370 GGATTATGGATGTGGCAGGTTTAATA 59.281 38.462 0.00 0.00 0.00 0.98
419 462 3.055675 ACGATCCCGGTCTATTTTGAACA 60.056 43.478 0.00 0.00 40.78 3.18
441 484 3.698539 TGAAATGAGCACACCAAACTTGA 59.301 39.130 0.00 0.00 0.00 3.02
466 509 0.328258 CGACCCCTGAACTTCCCATT 59.672 55.000 0.00 0.00 0.00 3.16
469 512 0.618981 AATCGACCCCTGAACTTCCC 59.381 55.000 0.00 0.00 0.00 3.97
471 514 5.024785 AGATAAATCGACCCCTGAACTTC 57.975 43.478 0.00 0.00 0.00 3.01
521 564 8.622948 ATTTCGATAAATATGGGAGAAAGTCC 57.377 34.615 0.00 0.00 37.83 3.85
527 570 9.791801 TGATTTGATTTCGATAAATATGGGAGA 57.208 29.630 0.00 0.00 35.41 3.71
567 610 5.012046 GGTTCTCCCTGGTTGATTTTCATTT 59.988 40.000 0.00 0.00 0.00 2.32
570 613 3.496331 GGTTCTCCCTGGTTGATTTTCA 58.504 45.455 0.00 0.00 0.00 2.69
601 644 1.587613 CGCTCGCCTGCTACTCTTC 60.588 63.158 0.00 0.00 0.00 2.87
618 661 1.039785 TCTCCTCTCTGGTGCATCCG 61.040 60.000 0.00 0.00 39.52 4.18
619 662 0.463620 GTCTCCTCTCTGGTGCATCC 59.536 60.000 0.00 0.00 37.07 3.51
620 663 0.102120 CGTCTCCTCTCTGGTGCATC 59.898 60.000 0.00 0.00 37.07 3.91
621 664 0.323816 TCGTCTCCTCTCTGGTGCAT 60.324 55.000 0.00 0.00 37.07 3.96
622 665 0.539669 TTCGTCTCCTCTCTGGTGCA 60.540 55.000 0.00 0.00 37.07 4.57
623 666 0.603569 TTTCGTCTCCTCTCTGGTGC 59.396 55.000 0.00 0.00 37.07 5.01
624 667 1.403514 GCTTTCGTCTCCTCTCTGGTG 60.404 57.143 0.00 0.00 37.07 4.17
625 668 0.892063 GCTTTCGTCTCCTCTCTGGT 59.108 55.000 0.00 0.00 37.07 4.00
626 669 0.179150 CGCTTTCGTCTCCTCTCTGG 60.179 60.000 0.00 0.00 37.10 3.86
627 670 0.805614 TCGCTTTCGTCTCCTCTCTG 59.194 55.000 0.00 0.00 36.96 3.35
628 671 0.806241 GTCGCTTTCGTCTCCTCTCT 59.194 55.000 0.00 0.00 36.96 3.10
629 672 0.521659 CGTCGCTTTCGTCTCCTCTC 60.522 60.000 0.00 0.00 36.96 3.20
630 673 1.235948 ACGTCGCTTTCGTCTCCTCT 61.236 55.000 0.00 0.00 36.85 3.69
631 674 1.066114 CACGTCGCTTTCGTCTCCTC 61.066 60.000 0.00 0.00 39.55 3.71
632 675 1.081376 CACGTCGCTTTCGTCTCCT 60.081 57.895 0.00 0.00 39.55 3.69
633 676 2.717809 GCACGTCGCTTTCGTCTCC 61.718 63.158 0.00 0.00 39.55 3.71
634 677 2.763881 GCACGTCGCTTTCGTCTC 59.236 61.111 0.00 0.00 39.55 3.36
643 686 0.992802 CTCTTTTCCTAGCACGTCGC 59.007 55.000 0.00 2.28 42.91 5.19
644 687 1.201647 TCCTCTTTTCCTAGCACGTCG 59.798 52.381 0.00 0.00 0.00 5.12
645 688 2.492484 TCTCCTCTTTTCCTAGCACGTC 59.508 50.000 0.00 0.00 0.00 4.34
646 689 2.494073 CTCTCCTCTTTTCCTAGCACGT 59.506 50.000 0.00 0.00 0.00 4.49
647 690 2.755655 TCTCTCCTCTTTTCCTAGCACG 59.244 50.000 0.00 0.00 0.00 5.34
648 691 3.132111 CCTCTCTCCTCTTTTCCTAGCAC 59.868 52.174 0.00 0.00 0.00 4.40
649 692 3.370104 CCTCTCTCCTCTTTTCCTAGCA 58.630 50.000 0.00 0.00 0.00 3.49
650 693 2.102420 GCCTCTCTCCTCTTTTCCTAGC 59.898 54.545 0.00 0.00 0.00 3.42
651 694 3.384467 CAGCCTCTCTCCTCTTTTCCTAG 59.616 52.174 0.00 0.00 0.00 3.02
652 695 3.370104 CAGCCTCTCTCCTCTTTTCCTA 58.630 50.000 0.00 0.00 0.00 2.94
653 696 2.187100 CAGCCTCTCTCCTCTTTTCCT 58.813 52.381 0.00 0.00 0.00 3.36
654 697 1.406751 GCAGCCTCTCTCCTCTTTTCC 60.407 57.143 0.00 0.00 0.00 3.13
655 698 1.738700 CGCAGCCTCTCTCCTCTTTTC 60.739 57.143 0.00 0.00 0.00 2.29
656 699 0.248843 CGCAGCCTCTCTCCTCTTTT 59.751 55.000 0.00 0.00 0.00 2.27
657 700 1.896694 CGCAGCCTCTCTCCTCTTT 59.103 57.895 0.00 0.00 0.00 2.52
658 701 3.614806 CGCAGCCTCTCTCCTCTT 58.385 61.111 0.00 0.00 0.00 2.85
685 728 4.629523 TCGGTTGGGGTTGGCGTC 62.630 66.667 0.00 0.00 0.00 5.19
727 770 1.440023 GTCGGTCGTCTCGTCACAC 60.440 63.158 0.00 0.00 0.00 3.82
728 771 2.941333 GTCGGTCGTCTCGTCACA 59.059 61.111 0.00 0.00 0.00 3.58
782 825 1.284715 GGTTTTCAGCGGGTTTCGG 59.715 57.895 0.00 0.00 39.69 4.30
815 858 3.589988 GTGAGAGTGATGGAATTGTCGT 58.410 45.455 0.00 0.00 0.00 4.34
965 1013 1.064458 GGTAGACTCGCGAGAAGGC 59.936 63.158 40.58 25.15 41.32 4.35
978 1026 0.851469 ATAGCCGGGTCTCTGGTAGA 59.149 55.000 10.79 0.00 41.53 2.59
980 1028 4.533815 CATATATAGCCGGGTCTCTGGTA 58.466 47.826 10.79 0.00 41.53 3.25
984 1032 2.389715 GGCATATATAGCCGGGTCTCT 58.610 52.381 10.79 0.00 43.15 3.10
1005 1053 1.484038 TTTGCAGAGCACCAAGGTTT 58.516 45.000 0.00 0.00 38.71 3.27
1007 1055 2.440409 CTATTTGCAGAGCACCAAGGT 58.560 47.619 0.00 0.00 38.71 3.50
1046 1094 4.292599 CTCTGAGATGAGAATTCTCGCTG 58.707 47.826 26.16 19.24 45.72 5.18
1047 1095 3.318839 CCTCTGAGATGAGAATTCTCGCT 59.681 47.826 26.32 24.58 45.72 4.93
1048 1096 3.641648 CCTCTGAGATGAGAATTCTCGC 58.358 50.000 26.32 21.01 45.72 5.03
1049 1097 3.067883 TGCCTCTGAGATGAGAATTCTCG 59.932 47.826 26.32 13.60 45.72 4.04
1050 1098 4.669206 TGCCTCTGAGATGAGAATTCTC 57.331 45.455 25.68 25.68 43.15 2.87
1051 1099 4.683942 GCTTGCCTCTGAGATGAGAATTCT 60.684 45.833 7.95 7.95 36.23 2.40
1052 1100 3.560896 GCTTGCCTCTGAGATGAGAATTC 59.439 47.826 6.17 0.00 36.23 2.17
1071 1119 0.756442 TGCCTTGGTGCTTCTTGCTT 60.756 50.000 0.00 0.00 43.37 3.91
1106 1158 1.155042 CTGTGCCTTTCTCTGTCTGC 58.845 55.000 0.00 0.00 0.00 4.26
1108 1160 2.036992 CTGTCTGTGCCTTTCTCTGTCT 59.963 50.000 0.00 0.00 0.00 3.41
1109 1161 2.036475 TCTGTCTGTGCCTTTCTCTGTC 59.964 50.000 0.00 0.00 0.00 3.51
1110 1162 2.036992 CTCTGTCTGTGCCTTTCTCTGT 59.963 50.000 0.00 0.00 0.00 3.41
1111 1163 2.612471 CCTCTGTCTGTGCCTTTCTCTG 60.612 54.545 0.00 0.00 0.00 3.35
1112 1164 1.622811 CCTCTGTCTGTGCCTTTCTCT 59.377 52.381 0.00 0.00 0.00 3.10
1113 1165 1.620819 TCCTCTGTCTGTGCCTTTCTC 59.379 52.381 0.00 0.00 0.00 2.87
1114 1166 1.346068 GTCCTCTGTCTGTGCCTTTCT 59.654 52.381 0.00 0.00 0.00 2.52
1115 1167 1.070758 TGTCCTCTGTCTGTGCCTTTC 59.929 52.381 0.00 0.00 0.00 2.62
1116 1168 1.131638 TGTCCTCTGTCTGTGCCTTT 58.868 50.000 0.00 0.00 0.00 3.11
1117 1169 1.356124 ATGTCCTCTGTCTGTGCCTT 58.644 50.000 0.00 0.00 0.00 4.35
1137 1190 0.257905 ATGCTGCCATGTCCATGTCT 59.742 50.000 6.53 0.00 37.11 3.41
1146 1199 1.164662 CCGAGGAAGATGCTGCCATG 61.165 60.000 0.00 0.00 29.53 3.66
1150 1203 3.267860 CGCCGAGGAAGATGCTGC 61.268 66.667 0.00 0.00 0.00 5.25
1151 1204 3.267860 GCGCCGAGGAAGATGCTG 61.268 66.667 0.00 0.00 0.00 4.41
1152 1205 4.537433 GGCGCCGAGGAAGATGCT 62.537 66.667 12.58 0.00 0.00 3.79
1172 1225 1.201343 GAAGATGAAGTAGGACGCGC 58.799 55.000 5.73 0.00 0.00 6.86
1173 1226 2.561733 TGAAGATGAAGTAGGACGCG 57.438 50.000 3.53 3.53 0.00 6.01
1187 1240 0.319555 CGCCACGGAGAAGTTGAAGA 60.320 55.000 0.00 0.00 0.00 2.87
1188 1241 1.901650 GCGCCACGGAGAAGTTGAAG 61.902 60.000 0.00 0.00 0.00 3.02
1189 1242 1.959226 GCGCCACGGAGAAGTTGAA 60.959 57.895 0.00 0.00 0.00 2.69
1190 1243 2.357034 GCGCCACGGAGAAGTTGA 60.357 61.111 0.00 0.00 0.00 3.18
1191 1244 3.423154 GGCGCCACGGAGAAGTTG 61.423 66.667 24.80 0.00 0.00 3.16
1208 1261 4.082523 AGATGACCACCACGGCCG 62.083 66.667 26.86 26.86 39.03 6.13
1219 1272 3.126831 GGATGACGTTGATGGAGATGAC 58.873 50.000 0.00 0.00 0.00 3.06
1220 1273 3.033909 AGGATGACGTTGATGGAGATGA 58.966 45.455 0.00 0.00 0.00 2.92
1273 1326 2.024846 AGGACGAAGAAGAGGATGAGGA 60.025 50.000 0.00 0.00 0.00 3.71
1278 1331 2.104170 GTGGAGGACGAAGAAGAGGAT 58.896 52.381 0.00 0.00 0.00 3.24
1284 1337 1.671742 GCTGGTGGAGGACGAAGAA 59.328 57.895 0.00 0.00 0.00 2.52
1285 1338 2.283529 GGCTGGTGGAGGACGAAGA 61.284 63.158 0.00 0.00 0.00 2.87
1286 1339 2.266055 GGCTGGTGGAGGACGAAG 59.734 66.667 0.00 0.00 0.00 3.79
1287 1340 3.691342 CGGCTGGTGGAGGACGAA 61.691 66.667 0.00 0.00 0.00 3.85
1416 1469 2.752640 TCGAACCCGATCGAGGCA 60.753 61.111 18.66 0.00 46.12 4.75
1423 1476 3.528370 CGCCTCCTCGAACCCGAT 61.528 66.667 0.00 0.00 44.62 4.18
1446 1499 0.101399 CCTCGTCATCCTCGAACAGG 59.899 60.000 0.00 0.00 45.15 4.00
1633 1686 2.370445 CCTGGAAGTCCATCCGGCT 61.370 63.158 0.00 0.00 46.46 5.52
1723 1776 4.318332 GCAGAACGAACGAACAAATGAATC 59.682 41.667 0.14 0.00 0.00 2.52
1728 1781 3.963383 AAGCAGAACGAACGAACAAAT 57.037 38.095 0.14 0.00 0.00 2.32
1793 1850 9.661563 TTGTGTAAAGAATCGGAGTAAATACAT 57.338 29.630 0.00 0.00 0.00 2.29
1794 1851 9.661563 ATTGTGTAAAGAATCGGAGTAAATACA 57.338 29.630 0.00 0.00 0.00 2.29
1802 1874 8.223769 GCATATGTATTGTGTAAAGAATCGGAG 58.776 37.037 4.29 0.00 0.00 4.63
2430 4735 4.131088 GGAGGACGAGCGGGTCAC 62.131 72.222 8.06 0.78 38.70 3.67
2500 4805 1.531578 CTCTGTCTCGTCTGAACACGA 59.468 52.381 0.00 0.00 46.42 4.35
2523 4828 2.939022 GCAAGCGCTCAACTTCGT 59.061 55.556 12.06 0.00 34.30 3.85


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

AutoCloner maintained by Alex Coulton.