Multiple sequence alignment - TraesCS6B01G047700

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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 TraesCS6B01G047700 chr6B 100.000 2636 0 0 1 2636 27993364 27990729 0.000000e+00 4868.0
1 TraesCS6B01G047700 chr6B 84.584 1239 186 5 913 2149 35529359 35528124 0.000000e+00 1225.0
2 TraesCS6B01G047700 chr6B 81.090 1248 210 22 904 2137 34341462 34340227 0.000000e+00 974.0
3 TraesCS6B01G047700 chr6B 94.178 584 31 2 1 582 526123144 526123726 0.000000e+00 887.0
4 TraesCS6B01G047700 chr6B 82.902 193 28 4 713 901 35529589 35529398 4.510000e-38 169.0
5 TraesCS6B01G047700 chr6D 93.319 1362 87 3 903 2263 16242883 16244241 0.000000e+00 2008.0
6 TraesCS6B01G047700 chr6D 84.054 1248 194 5 904 2149 20602627 20601383 0.000000e+00 1197.0
7 TraesCS6B01G047700 chr6D 80.998 1242 218 15 907 2138 20312250 20311017 0.000000e+00 970.0
8 TraesCS6B01G047700 chr6D 91.053 190 14 2 716 905 16242667 16242853 1.210000e-63 254.0
9 TraesCS6B01G047700 chr6D 88.618 123 13 1 2470 2591 427022462 427022584 5.880000e-32 148.0
10 TraesCS6B01G047700 chr6A 92.952 1362 92 3 903 2263 16531214 16532572 0.000000e+00 1980.0
11 TraesCS6B01G047700 chr6A 83.005 1471 211 19 711 2149 20522586 20521123 0.000000e+00 1295.0
12 TraesCS6B01G047700 chr6A 87.437 199 18 5 713 905 16530987 16531184 3.410000e-54 222.0
13 TraesCS6B01G047700 chr6A 92.969 128 8 1 2264 2390 16532733 16532860 4.480000e-43 185.0
14 TraesCS6B01G047700 chr6A 91.463 82 7 0 2401 2482 16532959 16533040 2.140000e-21 113.0
15 TraesCS6B01G047700 chrUn 81.220 1246 212 19 904 2137 273854779 273856014 0.000000e+00 985.0
16 TraesCS6B01G047700 chr1B 94.863 584 27 2 1 582 45814179 45814761 0.000000e+00 909.0
17 TraesCS6B01G047700 chr2B 90.698 688 48 10 1 684 6519130 6518455 0.000000e+00 902.0
18 TraesCS6B01G047700 chr3B 94.590 573 29 1 1 571 529806328 529805756 0.000000e+00 885.0
19 TraesCS6B01G047700 chr5B 93.878 588 31 2 1 583 441102106 441102693 0.000000e+00 881.0
20 TraesCS6B01G047700 chr4B 94.118 578 32 2 1 576 569737439 569738016 0.000000e+00 878.0
21 TraesCS6B01G047700 chr4B 93.471 582 36 1 3 582 219447126 219447707 0.000000e+00 863.0
22 TraesCS6B01G047700 chr4B 88.430 121 12 2 2473 2591 201916071 201915951 7.600000e-31 145.0
23 TraesCS6B01G047700 chr7D 79.967 1198 215 18 914 2097 632406507 632405321 0.000000e+00 859.0
24 TraesCS6B01G047700 chr1A 92.734 578 37 4 7 579 490136597 490137174 0.000000e+00 830.0
25 TraesCS6B01G047700 chr1D 91.667 588 37 9 1 582 490442025 490441444 0.000000e+00 804.0
26 TraesCS6B01G047700 chr1D 88.618 123 13 1 2470 2591 347057872 347057994 5.880000e-32 148.0
27 TraesCS6B01G047700 chr1D 88.618 123 13 1 2470 2591 347075419 347075541 5.880000e-32 148.0
28 TraesCS6B01G047700 chr7B 79.335 1142 218 15 967 2096 744570681 744569546 0.000000e+00 785.0
29 TraesCS6B01G047700 chr7B 89.167 120 12 1 2473 2591 570554246 570554127 5.880000e-32 148.0
30 TraesCS6B01G047700 chr5A 83.537 164 24 3 2475 2636 567285786 567285624 1.630000e-32 150.0
31 TraesCS6B01G047700 chr5D 88.618 123 13 1 2470 2591 250193794 250193916 5.880000e-32 148.0
32 TraesCS6B01G047700 chr5D 92.453 53 4 0 627 679 420965163 420965111 2.810000e-10 76.8
33 TraesCS6B01G047700 chr4D 89.167 120 12 1 2473 2591 269530182 269530063 5.880000e-32 148.0
34 TraesCS6B01G047700 chr4D 88.618 123 13 1 2470 2591 404790866 404790988 5.880000e-32 148.0
35 TraesCS6B01G047700 chr3A 86.885 61 8 0 624 684 733495633 733495693 4.710000e-08 69.4


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 TraesCS6B01G047700 chr6B 27990729 27993364 2635 True 4868 4868 100.00000 1 2636 1 chr6B.!!$R1 2635
1 TraesCS6B01G047700 chr6B 34340227 34341462 1235 True 974 974 81.09000 904 2137 1 chr6B.!!$R2 1233
2 TraesCS6B01G047700 chr6B 526123144 526123726 582 False 887 887 94.17800 1 582 1 chr6B.!!$F1 581
3 TraesCS6B01G047700 chr6B 35528124 35529589 1465 True 697 1225 83.74300 713 2149 2 chr6B.!!$R3 1436
4 TraesCS6B01G047700 chr6D 20601383 20602627 1244 True 1197 1197 84.05400 904 2149 1 chr6D.!!$R2 1245
5 TraesCS6B01G047700 chr6D 16242667 16244241 1574 False 1131 2008 92.18600 716 2263 2 chr6D.!!$F2 1547
6 TraesCS6B01G047700 chr6D 20311017 20312250 1233 True 970 970 80.99800 907 2138 1 chr6D.!!$R1 1231
7 TraesCS6B01G047700 chr6A 20521123 20522586 1463 True 1295 1295 83.00500 711 2149 1 chr6A.!!$R1 1438
8 TraesCS6B01G047700 chr6A 16530987 16533040 2053 False 625 1980 91.20525 713 2482 4 chr6A.!!$F1 1769
9 TraesCS6B01G047700 chrUn 273854779 273856014 1235 False 985 985 81.22000 904 2137 1 chrUn.!!$F1 1233
10 TraesCS6B01G047700 chr1B 45814179 45814761 582 False 909 909 94.86300 1 582 1 chr1B.!!$F1 581
11 TraesCS6B01G047700 chr2B 6518455 6519130 675 True 902 902 90.69800 1 684 1 chr2B.!!$R1 683
12 TraesCS6B01G047700 chr3B 529805756 529806328 572 True 885 885 94.59000 1 571 1 chr3B.!!$R1 570
13 TraesCS6B01G047700 chr5B 441102106 441102693 587 False 881 881 93.87800 1 583 1 chr5B.!!$F1 582
14 TraesCS6B01G047700 chr4B 569737439 569738016 577 False 878 878 94.11800 1 576 1 chr4B.!!$F2 575
15 TraesCS6B01G047700 chr4B 219447126 219447707 581 False 863 863 93.47100 3 582 1 chr4B.!!$F1 579
16 TraesCS6B01G047700 chr7D 632405321 632406507 1186 True 859 859 79.96700 914 2097 1 chr7D.!!$R1 1183
17 TraesCS6B01G047700 chr1A 490136597 490137174 577 False 830 830 92.73400 7 579 1 chr1A.!!$F1 572
18 TraesCS6B01G047700 chr1D 490441444 490442025 581 True 804 804 91.66700 1 582 1 chr1D.!!$R1 581
19 TraesCS6B01G047700 chr7B 744569546 744570681 1135 True 785 785 79.33500 967 2096 1 chr7B.!!$R2 1129

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
708 723 0.391395 CCAAGGCTCTCTCTGCACAG 60.391 60.0 0.0 0.0 0.0 3.66 F
1084 1157 0.250684 ACACGCCATGGACATCACAA 60.251 50.0 18.4 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 1600 0.469331 TGACACCAGGTTCCTCGTCT 60.469 55.0 8.17 0.0 0.00 4.18 R
2324 2564 1.339097 GGTGTAGGGTGAGACACTGT 58.661 55.0 5.25 0.0 44.39 3.55 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
584 598 4.755507 GACTCGGGGGTCGGGACT 62.756 72.222 0.00 0.00 43.26 3.85
585 599 4.755507 ACTCGGGGGTCGGGACTC 62.756 72.222 0.00 0.00 43.26 3.36
590 604 4.828296 GGGGTCGGGACTCGGCTA 62.828 72.222 0.00 0.00 44.01 3.93
591 605 2.757099 GGGTCGGGACTCGGCTAA 60.757 66.667 0.00 0.00 44.01 3.09
593 607 2.783288 GGTCGGGACTCGGCTAAGG 61.783 68.421 0.00 0.00 44.01 2.69
595 609 2.441532 CGGGACTCGGCTAAGGGA 60.442 66.667 0.00 0.00 34.75 4.20
598 612 1.393487 GGGACTCGGCTAAGGGACTC 61.393 65.000 0.00 0.00 38.49 3.36
599 613 1.726533 GGACTCGGCTAAGGGACTCG 61.727 65.000 0.00 0.00 38.49 4.18
600 614 0.747283 GACTCGGCTAAGGGACTCGA 60.747 60.000 0.00 0.00 38.49 4.04
602 616 2.065906 CTCGGCTAAGGGACTCGAGC 62.066 65.000 13.61 5.26 43.88 5.03
603 617 2.413765 GGCTAAGGGACTCGAGCG 59.586 66.667 13.61 0.00 45.06 5.03
604 618 2.278923 GCTAAGGGACTCGAGCGC 60.279 66.667 13.61 13.50 38.49 5.92
606 620 3.140225 CTAAGGGACTCGAGCGCCC 62.140 68.421 28.09 28.09 38.49 6.13
614 628 3.200593 TCGAGCGCCCGAGTACTC 61.201 66.667 10.91 13.18 34.19 2.59
625 639 1.434622 CGAGTACTCGCCTCGCCTTA 61.435 60.000 30.44 0.00 46.50 2.69
631 645 2.433436 ACTCGCCTCGCCTTAAAAATT 58.567 42.857 0.00 0.00 0.00 1.82
639 653 3.976015 TCGCCTTAAAAATTGGGGAGAT 58.024 40.909 0.00 0.00 37.79 2.75
658 673 3.846588 AGATTTTCACTTCCCAGCCTCTA 59.153 43.478 0.00 0.00 0.00 2.43
668 683 1.906574 CCCAGCCTCTACACCAACTAA 59.093 52.381 0.00 0.00 0.00 2.24
670 685 2.832129 CCAGCCTCTACACCAACTAAGA 59.168 50.000 0.00 0.00 0.00 2.10
680 695 3.938963 ACACCAACTAAGAATGCATACGG 59.061 43.478 0.00 0.00 0.00 4.02
684 699 2.561569 ACTAAGAATGCATACGGCCAC 58.438 47.619 2.24 0.00 43.89 5.01
685 700 2.170607 ACTAAGAATGCATACGGCCACT 59.829 45.455 2.24 0.00 43.89 4.00
686 701 1.382522 AAGAATGCATACGGCCACTG 58.617 50.000 2.24 0.00 43.89 3.66
687 702 0.541392 AGAATGCATACGGCCACTGA 59.459 50.000 2.24 0.00 43.89 3.41
688 703 0.940126 GAATGCATACGGCCACTGAG 59.060 55.000 2.24 0.00 43.89 3.35
689 704 1.097547 AATGCATACGGCCACTGAGC 61.098 55.000 2.24 0.00 43.89 4.26
705 720 2.667418 GCCAAGGCTCTCTCTGCA 59.333 61.111 3.29 0.00 38.26 4.41
706 721 1.744741 GCCAAGGCTCTCTCTGCAC 60.745 63.158 3.29 0.00 38.26 4.57
707 722 1.675801 CCAAGGCTCTCTCTGCACA 59.324 57.895 0.00 0.00 0.00 4.57
708 723 0.391395 CCAAGGCTCTCTCTGCACAG 60.391 60.000 0.00 0.00 0.00 3.66
709 724 0.391395 CAAGGCTCTCTCTGCACAGG 60.391 60.000 0.00 0.00 0.00 4.00
727 750 9.625747 CTGCACAGGAGATAGATAGATAGATAA 57.374 37.037 0.00 0.00 0.00 1.75
768 793 4.098155 AGATGGAGATGGAGATGGAGATG 58.902 47.826 0.00 0.00 0.00 2.90
774 799 4.098155 AGATGGAGATGGAGATGGAGATG 58.902 47.826 0.00 0.00 0.00 2.90
777 802 2.833338 GGAGATGGAGATGGAGATGGAG 59.167 54.545 0.00 0.00 0.00 3.86
779 804 4.355549 GAGATGGAGATGGAGATGGAGAT 58.644 47.826 0.00 0.00 0.00 2.75
784 812 7.951806 AGATGGAGATGGAGATGGAGATATATC 59.048 40.741 4.42 4.42 0.00 1.63
897 934 4.034510 CCACTATTTCAGCATTTCCGAGTC 59.965 45.833 0.00 0.00 0.00 3.36
910 979 6.470160 CATTTCCGAGTCAACTAAGAATTCG 58.530 40.000 0.00 0.00 0.00 3.34
921 990 9.694137 GTCAACTAAGAATTCGGCTATATAAGT 57.306 33.333 0.00 0.00 0.00 2.24
1084 1157 0.250684 ACACGCCATGGACATCACAA 60.251 50.000 18.40 0.00 0.00 3.33
1089 1162 2.945008 CGCCATGGACATCACAAATAGT 59.055 45.455 18.40 0.00 0.00 2.12
1131 1204 1.810755 CTATGGGCACTATACGAGCGA 59.189 52.381 0.00 0.00 0.00 4.93
1142 1215 4.214383 CGAGCGATGGTGCAAGCG 62.214 66.667 0.00 0.00 36.92 4.68
1212 1285 2.839486 TCAAGGAGAACACTCGCATT 57.161 45.000 0.00 0.00 0.00 3.56
1527 1600 2.425143 GAGGGCATCAACTCCATCAA 57.575 50.000 0.00 0.00 33.69 2.57
1555 1628 0.473755 ACCTGGTGTCATTGTCTGCA 59.526 50.000 0.00 0.00 0.00 4.41
1577 1650 0.099613 ACAGCTCATAGACTGCGACG 59.900 55.000 0.00 0.00 37.42 5.12
1626 1699 3.259902 GCGCACTAGTAGCCTTAAAGTT 58.740 45.455 0.30 0.00 0.00 2.66
1897 1973 0.178964 ACTCAATGTTGGTGGTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
1924 2000 1.626356 CCACCGATGACCATGACCCT 61.626 60.000 0.00 0.00 0.00 4.34
2155 2235 5.516339 GCAAACTAATGCACATGTATCCAAC 59.484 40.000 0.00 0.00 45.70 3.77
2158 2238 4.570772 ACTAATGCACATGTATCCAACGAC 59.429 41.667 0.00 0.00 0.00 4.34
2179 2259 6.147821 ACGACGTCTTCTTTCATTTGATTCAT 59.852 34.615 14.70 0.00 0.00 2.57
2181 2261 7.439157 ACGTCTTCTTTCATTTGATTCATCA 57.561 32.000 0.00 0.00 34.44 3.07
2197 2277 7.997482 TGATTCATCACTACCTCAACTACTAC 58.003 38.462 0.00 0.00 0.00 2.73
2198 2278 7.834681 TGATTCATCACTACCTCAACTACTACT 59.165 37.037 0.00 0.00 0.00 2.57
2202 2282 7.769507 TCATCACTACCTCAACTACTACTACTG 59.230 40.741 0.00 0.00 0.00 2.74
2315 2555 3.446442 AATGAACTGAGCCATCCAACT 57.554 42.857 0.00 0.00 0.00 3.16
2324 2564 6.562228 ACTGAGCCATCCAACTACCTATATA 58.438 40.000 0.00 0.00 0.00 0.86
2328 2568 6.323737 AGCCATCCAACTACCTATATACAGT 58.676 40.000 0.00 0.00 0.00 3.55
2343 2583 1.339097 ACAGTGTCTCACCCTACACC 58.661 55.000 0.00 0.00 45.70 4.16
2397 2638 7.556733 TGGAAATATGTTAATTACACGGACC 57.443 36.000 0.00 0.00 40.19 4.46
2398 2639 7.110810 TGGAAATATGTTAATTACACGGACCA 58.889 34.615 0.00 0.00 40.19 4.02
2399 2640 7.066043 TGGAAATATGTTAATTACACGGACCAC 59.934 37.037 0.00 0.00 40.19 4.16
2410 2739 8.943909 AATTACACGGACCACAATTTTAAAAA 57.056 26.923 4.44 0.00 0.00 1.94
2413 2742 6.631962 ACACGGACCACAATTTTAAAAAGAA 58.368 32.000 4.44 0.00 0.00 2.52
2473 2802 8.361889 TCAACATTATTTGCAGATAATCATGGG 58.638 33.333 17.24 9.99 31.52 4.00
2507 2836 8.337118 AGGAATAGGAAAATGATAGGAAGTGA 57.663 34.615 0.00 0.00 0.00 3.41
2508 2837 8.435982 AGGAATAGGAAAATGATAGGAAGTGAG 58.564 37.037 0.00 0.00 0.00 3.51
2509 2838 8.432805 GGAATAGGAAAATGATAGGAAGTGAGA 58.567 37.037 0.00 0.00 0.00 3.27
2511 2840 9.790344 AATAGGAAAATGATAGGAAGTGAGATG 57.210 33.333 0.00 0.00 0.00 2.90
2512 2841 7.443302 AGGAAAATGATAGGAAGTGAGATGA 57.557 36.000 0.00 0.00 0.00 2.92
2513 2842 7.278875 AGGAAAATGATAGGAAGTGAGATGAC 58.721 38.462 0.00 0.00 0.00 3.06
2514 2843 7.050377 GGAAAATGATAGGAAGTGAGATGACA 58.950 38.462 0.00 0.00 0.00 3.58
2515 2844 7.718753 GGAAAATGATAGGAAGTGAGATGACAT 59.281 37.037 0.00 0.00 0.00 3.06
2516 2845 8.447924 AAAATGATAGGAAGTGAGATGACATG 57.552 34.615 0.00 0.00 0.00 3.21
2517 2846 4.953667 TGATAGGAAGTGAGATGACATGC 58.046 43.478 0.00 0.00 0.00 4.06
2518 2847 4.406649 TGATAGGAAGTGAGATGACATGCA 59.593 41.667 0.00 0.00 0.00 3.96
2519 2848 3.928005 AGGAAGTGAGATGACATGCAT 57.072 42.857 0.00 0.00 40.77 3.96
2520 2849 4.232188 AGGAAGTGAGATGACATGCATT 57.768 40.909 0.00 0.00 37.34 3.56
2521 2850 4.597004 AGGAAGTGAGATGACATGCATTT 58.403 39.130 0.00 0.00 37.34 2.32
2522 2851 4.639310 AGGAAGTGAGATGACATGCATTTC 59.361 41.667 5.88 5.88 37.34 2.17
2523 2852 4.397103 GGAAGTGAGATGACATGCATTTCA 59.603 41.667 17.40 17.40 43.49 2.69
2524 2853 5.106038 GGAAGTGAGATGACATGCATTTCAA 60.106 40.000 18.83 0.34 46.07 2.69
2525 2854 5.970317 AGTGAGATGACATGCATTTCAAA 57.030 34.783 18.83 3.67 46.07 2.69
2526 2855 6.525578 AGTGAGATGACATGCATTTCAAAT 57.474 33.333 18.83 10.66 46.07 2.32
2527 2856 6.561614 AGTGAGATGACATGCATTTCAAATC 58.438 36.000 18.83 17.99 46.07 2.17
2528 2857 6.152154 AGTGAGATGACATGCATTTCAAATCA 59.848 34.615 18.83 19.98 46.07 2.57
2529 2858 6.978659 GTGAGATGACATGCATTTCAAATCAT 59.021 34.615 24.45 15.18 46.07 2.45
2530 2859 8.132995 GTGAGATGACATGCATTTCAAATCATA 58.867 33.333 24.45 10.45 46.07 2.15
2531 2860 8.856103 TGAGATGACATGCATTTCAAATCATAT 58.144 29.630 18.83 8.25 42.96 1.78
2536 2865 9.563748 TGACATGCATTTCAAATCATATAGAGA 57.436 29.630 13.07 0.00 0.00 3.10
2546 2875 9.499479 TTCAAATCATATAGAGAAAGAGATGCC 57.501 33.333 0.00 0.00 0.00 4.40
2547 2876 8.654094 TCAAATCATATAGAGAAAGAGATGCCA 58.346 33.333 0.00 0.00 0.00 4.92
2548 2877 9.451002 CAAATCATATAGAGAAAGAGATGCCAT 57.549 33.333 0.00 0.00 0.00 4.40
2551 2880 8.843885 TCATATAGAGAAAGAGATGCCATTTG 57.156 34.615 0.00 0.00 0.00 2.32
2552 2881 8.654094 TCATATAGAGAAAGAGATGCCATTTGA 58.346 33.333 0.00 0.00 0.00 2.69
2553 2882 9.451002 CATATAGAGAAAGAGATGCCATTTGAT 57.549 33.333 0.00 0.00 0.00 2.57
2554 2883 7.747155 ATAGAGAAAGAGATGCCATTTGATG 57.253 36.000 0.00 0.00 0.00 3.07
2555 2884 4.338682 AGAGAAAGAGATGCCATTTGATGC 59.661 41.667 0.00 0.00 0.00 3.91
2556 2885 3.066342 AGAAAGAGATGCCATTTGATGCG 59.934 43.478 0.00 0.00 0.00 4.73
2557 2886 2.048444 AGAGATGCCATTTGATGCGT 57.952 45.000 0.00 0.00 0.00 5.24
2558 2887 3.198409 AGAGATGCCATTTGATGCGTA 57.802 42.857 0.00 0.00 0.00 4.42
2559 2888 3.136763 AGAGATGCCATTTGATGCGTAG 58.863 45.455 0.00 0.00 0.00 3.51
2560 2889 3.133691 GAGATGCCATTTGATGCGTAGA 58.866 45.455 0.00 0.00 0.00 2.59
2561 2890 3.748083 AGATGCCATTTGATGCGTAGAT 58.252 40.909 0.00 0.00 0.00 1.98
2562 2891 4.898320 AGATGCCATTTGATGCGTAGATA 58.102 39.130 0.00 0.00 0.00 1.98
2563 2892 4.934001 AGATGCCATTTGATGCGTAGATAG 59.066 41.667 0.00 0.00 0.00 2.08
2564 2893 3.402110 TGCCATTTGATGCGTAGATAGG 58.598 45.455 0.00 0.00 0.00 2.57
2565 2894 2.744202 GCCATTTGATGCGTAGATAGGG 59.256 50.000 0.00 0.00 0.00 3.53
2566 2895 3.557054 GCCATTTGATGCGTAGATAGGGA 60.557 47.826 0.00 0.00 0.00 4.20
2567 2896 4.836825 CCATTTGATGCGTAGATAGGGAT 58.163 43.478 0.00 0.00 0.00 3.85
2568 2897 5.248640 CCATTTGATGCGTAGATAGGGATT 58.751 41.667 0.00 0.00 0.00 3.01
2569 2898 5.707298 CCATTTGATGCGTAGATAGGGATTT 59.293 40.000 0.00 0.00 0.00 2.17
2570 2899 6.207417 CCATTTGATGCGTAGATAGGGATTTT 59.793 38.462 0.00 0.00 0.00 1.82
2571 2900 7.255590 CCATTTGATGCGTAGATAGGGATTTTT 60.256 37.037 0.00 0.00 0.00 1.94
2632 2961 9.471702 AATATGAATGATTGATTCCTATCCCAC 57.528 33.333 0.00 0.00 40.00 4.61
2633 2962 6.264771 TGAATGATTGATTCCTATCCCACA 57.735 37.500 0.00 0.00 40.00 4.17
2634 2963 6.855667 TGAATGATTGATTCCTATCCCACAT 58.144 36.000 0.00 0.00 40.00 3.21
2635 2964 7.987820 TGAATGATTGATTCCTATCCCACATA 58.012 34.615 0.00 0.00 40.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.898326 GGGATTCGTTGGGGCTTGTT 60.898 55.000 0.00 0.00 0.00 2.83
57 58 1.819632 GCGAGGCATGGGATTCGTT 60.820 57.895 0.00 0.00 35.61 3.85
584 598 2.119655 GCTCGAGTCCCTTAGCCGA 61.120 63.158 15.13 0.00 0.00 5.54
585 599 2.413765 GCTCGAGTCCCTTAGCCG 59.586 66.667 15.13 0.00 0.00 5.52
586 600 2.413765 CGCTCGAGTCCCTTAGCC 59.586 66.667 15.13 0.00 0.00 3.93
588 602 2.413765 GGCGCTCGAGTCCCTTAG 59.586 66.667 15.13 0.00 0.00 2.18
589 603 3.145551 GGGCGCTCGAGTCCCTTA 61.146 66.667 27.30 0.00 37.08 2.69
597 611 3.200593 GAGTACTCGGGCGCTCGA 61.201 66.667 32.87 32.87 37.60 4.04
607 621 0.737219 TTAAGGCGAGGCGAGTACTC 59.263 55.000 13.18 13.18 0.00 2.59
608 622 1.180029 TTTAAGGCGAGGCGAGTACT 58.820 50.000 0.00 0.00 0.00 2.73
609 623 2.000429 TTTTAAGGCGAGGCGAGTAC 58.000 50.000 0.00 0.00 0.00 2.73
610 624 2.747396 TTTTTAAGGCGAGGCGAGTA 57.253 45.000 0.00 0.00 0.00 2.59
611 625 2.109425 ATTTTTAAGGCGAGGCGAGT 57.891 45.000 0.00 0.00 0.00 4.18
612 626 2.477863 CCAATTTTTAAGGCGAGGCGAG 60.478 50.000 0.00 0.00 0.00 5.03
613 627 1.470890 CCAATTTTTAAGGCGAGGCGA 59.529 47.619 0.00 0.00 0.00 5.54
614 628 1.469079 CCCAATTTTTAAGGCGAGGCG 60.469 52.381 0.00 0.00 0.00 5.52
615 629 1.134818 CCCCAATTTTTAAGGCGAGGC 60.135 52.381 0.00 0.00 0.00 4.70
616 630 2.427095 CTCCCCAATTTTTAAGGCGAGG 59.573 50.000 0.00 0.00 0.00 4.63
617 631 3.352648 TCTCCCCAATTTTTAAGGCGAG 58.647 45.455 0.00 0.00 0.00 5.03
618 632 3.443145 TCTCCCCAATTTTTAAGGCGA 57.557 42.857 0.00 0.00 0.00 5.54
619 633 4.736126 AATCTCCCCAATTTTTAAGGCG 57.264 40.909 0.00 0.00 0.00 5.52
622 636 9.208022 GAAGTGAAAATCTCCCCAATTTTTAAG 57.792 33.333 0.00 0.00 36.66 1.85
625 639 6.465751 GGGAAGTGAAAATCTCCCCAATTTTT 60.466 38.462 0.00 0.00 36.66 1.94
631 645 2.041620 CTGGGAAGTGAAAATCTCCCCA 59.958 50.000 3.58 0.00 39.81 4.96
639 653 2.708861 TGTAGAGGCTGGGAAGTGAAAA 59.291 45.455 0.00 0.00 0.00 2.29
651 665 4.624125 GCATTCTTAGTTGGTGTAGAGGCT 60.624 45.833 0.00 0.00 0.00 4.58
658 673 3.938963 CCGTATGCATTCTTAGTTGGTGT 59.061 43.478 3.54 0.00 0.00 4.16
668 683 0.541392 TCAGTGGCCGTATGCATTCT 59.459 50.000 3.54 0.00 43.89 2.40
670 685 1.097547 GCTCAGTGGCCGTATGCATT 61.098 55.000 3.54 0.00 43.89 3.56
680 695 2.749441 GAGCCTTGGCTCAGTGGC 60.749 66.667 30.25 8.19 45.21 5.01
684 699 0.176219 CAGAGAGAGCCTTGGCTCAG 59.824 60.000 34.40 18.91 39.13 3.35
685 700 1.897225 GCAGAGAGAGCCTTGGCTCA 61.897 60.000 34.40 0.00 39.13 4.26
686 701 1.153389 GCAGAGAGAGCCTTGGCTC 60.153 63.158 28.67 28.67 37.11 4.70
687 702 1.917282 TGCAGAGAGAGCCTTGGCT 60.917 57.895 14.69 14.69 0.00 4.75
688 703 1.744741 GTGCAGAGAGAGCCTTGGC 60.745 63.158 2.97 2.97 0.00 4.52
689 704 0.391395 CTGTGCAGAGAGAGCCTTGG 60.391 60.000 4.50 0.00 0.00 3.61
690 705 0.391395 CCTGTGCAGAGAGAGCCTTG 60.391 60.000 13.38 0.00 0.00 3.61
691 706 0.543883 TCCTGTGCAGAGAGAGCCTT 60.544 55.000 13.38 0.00 0.00 4.35
692 707 0.971959 CTCCTGTGCAGAGAGAGCCT 60.972 60.000 13.38 0.00 31.59 4.58
693 708 0.969917 TCTCCTGTGCAGAGAGAGCC 60.970 60.000 13.38 0.00 33.15 4.70
694 709 1.113788 ATCTCCTGTGCAGAGAGAGC 58.886 55.000 13.38 0.00 37.80 4.09
695 710 3.819368 TCTATCTCCTGTGCAGAGAGAG 58.181 50.000 13.38 15.08 37.80 3.20
696 711 3.941704 TCTATCTCCTGTGCAGAGAGA 57.058 47.619 13.38 12.27 36.17 3.10
697 712 5.559770 TCTATCTATCTCCTGTGCAGAGAG 58.440 45.833 13.38 6.83 31.54 3.20
698 713 5.574970 TCTATCTATCTCCTGTGCAGAGA 57.425 43.478 13.38 9.59 0.00 3.10
699 714 7.337938 TCTATCTATCTATCTCCTGTGCAGAG 58.662 42.308 3.32 3.32 0.00 3.35
700 715 7.264294 TCTATCTATCTATCTCCTGTGCAGA 57.736 40.000 0.02 0.00 0.00 4.26
701 716 9.625747 TTATCTATCTATCTATCTCCTGTGCAG 57.374 37.037 0.00 0.00 0.00 4.41
702 717 9.981460 TTTATCTATCTATCTATCTCCTGTGCA 57.019 33.333 0.00 0.00 0.00 4.57
744 767 2.833338 CTCCATCTCCATCTCCATCTCC 59.167 54.545 0.00 0.00 0.00 3.71
749 774 2.180751 TCCATCTCCATCTCCATCTCCA 59.819 50.000 0.00 0.00 0.00 3.86
750 775 2.833338 CTCCATCTCCATCTCCATCTCC 59.167 54.545 0.00 0.00 0.00 3.71
751 776 3.777087 TCTCCATCTCCATCTCCATCTC 58.223 50.000 0.00 0.00 0.00 2.75
752 777 3.919304 TCTCCATCTCCATCTCCATCT 57.081 47.619 0.00 0.00 0.00 2.90
753 778 3.198200 CCATCTCCATCTCCATCTCCATC 59.802 52.174 0.00 0.00 0.00 3.51
754 779 3.181398 TCCATCTCCATCTCCATCTCCAT 60.181 47.826 0.00 0.00 0.00 3.41
756 781 2.833338 CTCCATCTCCATCTCCATCTCC 59.167 54.545 0.00 0.00 0.00 3.71
768 793 9.189156 GCATATCTAGGATATATCTCCATCTCC 57.811 40.741 12.42 0.00 37.81 3.71
784 812 7.814587 TGTTCGAGATATTTGTGCATATCTAGG 59.185 37.037 7.40 4.23 43.67 3.02
910 979 6.361768 AGCTTTGGTCCTACTTATATAGCC 57.638 41.667 0.00 0.00 0.00 3.93
1084 1157 5.104193 ACTCCTCAGATGCCAAATCACTATT 60.104 40.000 0.00 0.00 0.00 1.73
1089 1162 2.092753 GGACTCCTCAGATGCCAAATCA 60.093 50.000 0.00 0.00 0.00 2.57
1092 1165 0.620556 GGGACTCCTCAGATGCCAAA 59.379 55.000 0.00 0.00 0.00 3.28
1131 1204 0.241749 CATTGTGACGCTTGCACCAT 59.758 50.000 0.00 0.00 35.43 3.55
1142 1215 1.666553 TCGCGTCCCACATTGTGAC 60.667 57.895 18.33 8.30 35.23 3.67
1204 1277 5.009010 GGTTGAATTCATGGATAATGCGAGT 59.991 40.000 9.40 0.00 36.11 4.18
1212 1285 5.652014 GTCACCTTGGTTGAATTCATGGATA 59.348 40.000 9.40 0.00 33.84 2.59
1344 1417 0.304705 CGTGTGTGAACTGGTCTTGC 59.695 55.000 0.00 0.00 0.00 4.01
1471 1544 2.146724 AAAAGCCCAACAAGCCCCC 61.147 57.895 0.00 0.00 0.00 5.40
1527 1600 0.469331 TGACACCAGGTTCCTCGTCT 60.469 55.000 8.17 0.00 0.00 4.18
1555 1628 1.546029 TCGCAGTCTATGAGCTGTTGT 59.454 47.619 0.00 0.00 35.33 3.32
1577 1650 3.139077 CAACACAACCAGTACTTCCCTC 58.861 50.000 0.00 0.00 0.00 4.30
1615 1688 8.621286 CCGTGATTATAAATGAACTTTAAGGCT 58.379 33.333 0.00 0.00 33.15 4.58
1626 1699 2.839975 TGCCGCCGTGATTATAAATGA 58.160 42.857 0.00 0.00 0.00 2.57
1701 1774 1.273455 GACAGGGTGACGTTTCGACG 61.273 60.000 0.00 0.00 39.31 5.12
1712 1788 1.446099 CGATGGTGACGACAGGGTG 60.446 63.158 0.00 0.00 0.00 4.61
1924 2000 6.715264 TGATCCAGTAATCTATGCGTCTCTTA 59.285 38.462 0.00 0.00 0.00 2.10
2155 2235 5.915857 TGAATCAAATGAAAGAAGACGTCG 58.084 37.500 10.46 0.00 0.00 5.12
2158 2238 7.524912 AGTGATGAATCAAATGAAAGAAGACG 58.475 34.615 0.00 0.00 38.75 4.18
2179 2259 5.879223 GCAGTAGTAGTAGTTGAGGTAGTGA 59.121 44.000 0.00 0.00 0.00 3.41
2181 2261 6.064735 AGCAGTAGTAGTAGTTGAGGTAGT 57.935 41.667 0.00 0.00 0.00 2.73
2266 2506 9.490663 GATTCACCAAACTCGTGATTTTATAAG 57.509 33.333 0.00 0.00 39.86 1.73
2275 2515 2.920724 TGGATTCACCAAACTCGTGA 57.079 45.000 0.00 0.00 46.75 4.35
2315 2555 6.526056 AGGGTGAGACACTGTATATAGGTA 57.474 41.667 1.26 0.00 34.40 3.08
2324 2564 1.339097 GGTGTAGGGTGAGACACTGT 58.661 55.000 5.25 0.00 44.39 3.55
2328 2568 2.615391 TCATTGGTGTAGGGTGAGACA 58.385 47.619 0.00 0.00 0.00 3.41
2390 2631 7.527084 TTTCTTTTTAAAATTGTGGTCCGTG 57.473 32.000 0.55 0.00 0.00 4.94
2391 2632 8.725405 AATTTCTTTTTAAAATTGTGGTCCGT 57.275 26.923 0.55 0.00 35.54 4.69
2425 2754 7.377766 TGATTCCAAGATTAGTTGTGCTTAC 57.622 36.000 0.00 0.00 0.00 2.34
2482 2811 8.337118 TCACTTCCTATCATTTTCCTATTCCT 57.663 34.615 0.00 0.00 0.00 3.36
2483 2812 8.432805 TCTCACTTCCTATCATTTTCCTATTCC 58.567 37.037 0.00 0.00 0.00 3.01
2485 2814 9.790344 CATCTCACTTCCTATCATTTTCCTATT 57.210 33.333 0.00 0.00 0.00 1.73
2486 2815 9.163894 TCATCTCACTTCCTATCATTTTCCTAT 57.836 33.333 0.00 0.00 0.00 2.57
2487 2816 8.424918 GTCATCTCACTTCCTATCATTTTCCTA 58.575 37.037 0.00 0.00 0.00 2.94
2488 2817 7.092712 TGTCATCTCACTTCCTATCATTTTCCT 60.093 37.037 0.00 0.00 0.00 3.36
2489 2818 7.050377 TGTCATCTCACTTCCTATCATTTTCC 58.950 38.462 0.00 0.00 0.00 3.13
2490 2819 8.557864 CATGTCATCTCACTTCCTATCATTTTC 58.442 37.037 0.00 0.00 0.00 2.29
2491 2820 7.013083 GCATGTCATCTCACTTCCTATCATTTT 59.987 37.037 0.00 0.00 0.00 1.82
2492 2821 6.485984 GCATGTCATCTCACTTCCTATCATTT 59.514 38.462 0.00 0.00 0.00 2.32
2493 2822 5.996513 GCATGTCATCTCACTTCCTATCATT 59.003 40.000 0.00 0.00 0.00 2.57
2494 2823 5.071384 TGCATGTCATCTCACTTCCTATCAT 59.929 40.000 0.00 0.00 0.00 2.45
2495 2824 4.406649 TGCATGTCATCTCACTTCCTATCA 59.593 41.667 0.00 0.00 0.00 2.15
2496 2825 4.953667 TGCATGTCATCTCACTTCCTATC 58.046 43.478 0.00 0.00 0.00 2.08
2497 2826 5.563876 ATGCATGTCATCTCACTTCCTAT 57.436 39.130 0.00 0.00 0.00 2.57
2498 2827 5.363562 AATGCATGTCATCTCACTTCCTA 57.636 39.130 0.00 0.00 33.40 2.94
2499 2828 3.928005 ATGCATGTCATCTCACTTCCT 57.072 42.857 0.00 0.00 0.00 3.36
2500 2829 4.397103 TGAAATGCATGTCATCTCACTTCC 59.603 41.667 15.88 0.00 33.40 3.46
2501 2830 5.556355 TGAAATGCATGTCATCTCACTTC 57.444 39.130 15.88 4.60 33.40 3.01
2502 2831 5.970317 TTGAAATGCATGTCATCTCACTT 57.030 34.783 20.25 0.00 32.23 3.16
2503 2832 5.970317 TTTGAAATGCATGTCATCTCACT 57.030 34.783 20.25 0.00 32.23 3.41
2504 2833 6.327154 TGATTTGAAATGCATGTCATCTCAC 58.673 36.000 20.25 10.65 32.23 3.51
2505 2834 6.518208 TGATTTGAAATGCATGTCATCTCA 57.482 33.333 20.25 20.21 30.67 3.27
2510 2839 9.563748 TCTCTATATGATTTGAAATGCATGTCA 57.436 29.630 15.88 15.88 0.00 3.58
2520 2849 9.499479 GGCATCTCTTTCTCTATATGATTTGAA 57.501 33.333 0.00 0.00 0.00 2.69
2521 2850 8.654094 TGGCATCTCTTTCTCTATATGATTTGA 58.346 33.333 0.00 0.00 0.00 2.69
2522 2851 8.843885 TGGCATCTCTTTCTCTATATGATTTG 57.156 34.615 0.00 0.00 0.00 2.32
2525 2854 9.451002 CAAATGGCATCTCTTTCTCTATATGAT 57.549 33.333 0.00 0.00 0.00 2.45
2526 2855 8.654094 TCAAATGGCATCTCTTTCTCTATATGA 58.346 33.333 0.00 0.00 0.00 2.15
2527 2856 8.843885 TCAAATGGCATCTCTTTCTCTATATG 57.156 34.615 0.00 0.00 0.00 1.78
2528 2857 9.451002 CATCAAATGGCATCTCTTTCTCTATAT 57.549 33.333 0.00 0.00 0.00 0.86
2529 2858 7.389884 GCATCAAATGGCATCTCTTTCTCTATA 59.610 37.037 0.00 0.00 0.00 1.31
2530 2859 6.207025 GCATCAAATGGCATCTCTTTCTCTAT 59.793 38.462 0.00 0.00 0.00 1.98
2531 2860 5.530171 GCATCAAATGGCATCTCTTTCTCTA 59.470 40.000 0.00 0.00 0.00 2.43
2532 2861 4.338682 GCATCAAATGGCATCTCTTTCTCT 59.661 41.667 0.00 0.00 0.00 3.10
2533 2862 4.608951 GCATCAAATGGCATCTCTTTCTC 58.391 43.478 0.00 0.00 0.00 2.87
2534 2863 3.066342 CGCATCAAATGGCATCTCTTTCT 59.934 43.478 0.00 0.00 0.00 2.52
2535 2864 3.181493 ACGCATCAAATGGCATCTCTTTC 60.181 43.478 0.00 0.00 0.00 2.62
2536 2865 2.756760 ACGCATCAAATGGCATCTCTTT 59.243 40.909 0.00 0.00 0.00 2.52
2537 2866 2.372264 ACGCATCAAATGGCATCTCTT 58.628 42.857 0.00 0.00 0.00 2.85
2538 2867 2.048444 ACGCATCAAATGGCATCTCT 57.952 45.000 0.00 0.00 0.00 3.10
2539 2868 3.133691 TCTACGCATCAAATGGCATCTC 58.866 45.455 0.00 0.00 0.00 2.75
2540 2869 3.198409 TCTACGCATCAAATGGCATCT 57.802 42.857 0.00 0.00 0.00 2.90
2541 2870 4.093998 CCTATCTACGCATCAAATGGCATC 59.906 45.833 0.00 0.00 0.00 3.91
2542 2871 4.005650 CCTATCTACGCATCAAATGGCAT 58.994 43.478 0.00 0.00 0.00 4.40
2543 2872 3.402110 CCTATCTACGCATCAAATGGCA 58.598 45.455 0.00 0.00 0.00 4.92
2544 2873 2.744202 CCCTATCTACGCATCAAATGGC 59.256 50.000 0.00 0.00 0.00 4.40
2545 2874 4.271696 TCCCTATCTACGCATCAAATGG 57.728 45.455 0.00 0.00 0.00 3.16
2546 2875 6.808008 AAATCCCTATCTACGCATCAAATG 57.192 37.500 0.00 0.00 0.00 2.32
2547 2876 7.823745 AAAAATCCCTATCTACGCATCAAAT 57.176 32.000 0.00 0.00 0.00 2.32
2606 2935 9.471702 GTGGGATAGGAATCAATCATTCATATT 57.528 33.333 3.71 0.00 44.76 1.28
2607 2936 8.617491 TGTGGGATAGGAATCAATCATTCATAT 58.383 33.333 2.07 2.07 46.50 1.78
2608 2937 7.987820 TGTGGGATAGGAATCAATCATTCATA 58.012 34.615 0.00 0.00 42.69 2.15
2609 2938 6.855667 TGTGGGATAGGAATCAATCATTCAT 58.144 36.000 0.00 0.00 42.69 2.57
2610 2939 6.264771 TGTGGGATAGGAATCAATCATTCA 57.735 37.500 0.00 0.00 42.69 2.57


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

AutoCloner maintained by Alex Coulton.