Multiple sequence alignment - TraesCS6B01G045600

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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 TraesCS6B01G045600 chr6B 100.000 3527 0 0 1 3527 27125387 27121861 0.000000e+00 6514
1 TraesCS6B01G045600 chr6B 92.746 1861 120 9 797 2655 27171441 27169594 0.000000e+00 2675
2 TraesCS6B01G045600 chr6B 90.872 1490 128 6 1071 2558 27181753 27180270 0.000000e+00 1991
3 TraesCS6B01G045600 chr6B 85.590 1610 217 10 977 2579 27779803 27778202 0.000000e+00 1674
4 TraesCS6B01G045600 chr6B 85.128 585 60 11 2952 3526 27169319 27168752 1.100000e-159 573
5 TraesCS6B01G045600 chr6B 86.364 176 18 2 2753 2927 27169542 27169372 1.670000e-43 187
6 TraesCS6B01G045600 chr6B 80.905 199 21 7 372 553 27171820 27171622 1.320000e-29 141
7 TraesCS6B01G045600 chr6D 93.165 2297 109 23 653 2906 15385514 15383223 0.000000e+00 3328
8 TraesCS6B01G045600 chr6D 93.711 1924 105 10 806 2726 15419808 15417898 0.000000e+00 2868
9 TraesCS6B01G045600 chr6D 85.651 1582 218 7 983 2559 15747993 15746416 0.000000e+00 1655
10 TraesCS6B01G045600 chr6D 95.674 601 26 0 2927 3527 15383144 15382544 0.000000e+00 966
11 TraesCS6B01G045600 chr6D 90.391 562 34 7 4 553 15386068 15385515 0.000000e+00 721
12 TraesCS6B01G045600 chr6D 82.058 758 87 20 2796 3526 15417895 15417160 5.040000e-168 601
13 TraesCS6B01G045600 chr6D 90.066 151 12 3 653 802 15419996 15419848 3.590000e-45 193
14 TraesCS6B01G045600 chr6D 78.680 197 26 9 372 553 15420192 15419997 2.220000e-22 117
15 TraesCS6B01G045600 chr6A 93.472 2160 128 12 653 2802 15953761 15951605 0.000000e+00 3195
16 TraesCS6B01G045600 chr6A 92.034 2134 149 11 798 2927 16100366 16098250 0.000000e+00 2979
17 TraesCS6B01G045600 chr6A 85.906 1568 212 8 982 2543 16376130 16374566 0.000000e+00 1663
18 TraesCS6B01G045600 chr6A 88.027 593 48 14 2927 3517 15951388 15950817 0.000000e+00 680
19 TraesCS6B01G045600 chr6A 88.730 559 43 9 1 553 15954306 15953762 0.000000e+00 665
20 TraesCS6B01G045600 chr6A 85.191 601 61 13 2936 3527 16088873 16088292 3.030000e-165 592
21 TraesCS6B01G045600 chr6A 92.000 150 11 1 653 802 16100546 16100398 3.570000e-50 209
22 TraesCS6B01G045600 chr6A 80.928 194 19 8 378 553 16100740 16100547 1.710000e-28 137
23 TraesCS6B01G045600 chr6A 85.714 105 7 3 2808 2904 15951573 15951469 1.730000e-18 104
24 TraesCS6B01G045600 chr5D 93.269 104 7 0 554 657 228447059 228446956 1.700000e-33 154
25 TraesCS6B01G045600 chr4D 93.878 98 6 0 554 651 494042469 494042372 7.890000e-32 148
26 TraesCS6B01G045600 chr1D 93.878 98 6 0 555 652 220408740 220408837 7.890000e-32 148
27 TraesCS6B01G045600 chr3A 93.000 100 7 0 555 654 109150960 109150861 2.840000e-31 147
28 TraesCS6B01G045600 chr5B 92.929 99 7 0 554 652 537533245 537533147 1.020000e-30 145
29 TraesCS6B01G045600 chr5B 92.929 99 7 0 554 652 681819315 681819413 1.020000e-30 145
30 TraesCS6B01G045600 chr5B 87.603 121 13 2 535 654 78959473 78959592 4.750000e-29 139
31 TraesCS6B01G045600 chr2B 90.090 111 9 1 542 652 601206836 601206944 3.670000e-30 143
32 TraesCS6B01G045600 chr2A 89.189 111 11 1 541 651 686781506 686781615 1.710000e-28 137


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 TraesCS6B01G045600 chr6B 27121861 27125387 3526 True 6514.000000 6514 100.000000 1 3527 1 chr6B.!!$R1 3526
1 TraesCS6B01G045600 chr6B 27180270 27181753 1483 True 1991.000000 1991 90.872000 1071 2558 1 chr6B.!!$R2 1487
2 TraesCS6B01G045600 chr6B 27778202 27779803 1601 True 1674.000000 1674 85.590000 977 2579 1 chr6B.!!$R3 1602
3 TraesCS6B01G045600 chr6B 27168752 27171820 3068 True 894.000000 2675 86.285750 372 3526 4 chr6B.!!$R4 3154
4 TraesCS6B01G045600 chr6D 15382544 15386068 3524 True 1671.666667 3328 93.076667 4 3527 3 chr6D.!!$R2 3523
5 TraesCS6B01G045600 chr6D 15746416 15747993 1577 True 1655.000000 1655 85.651000 983 2559 1 chr6D.!!$R1 1576
6 TraesCS6B01G045600 chr6D 15417160 15420192 3032 True 944.750000 2868 86.128750 372 3526 4 chr6D.!!$R3 3154
7 TraesCS6B01G045600 chr6A 16374566 16376130 1564 True 1663.000000 1663 85.906000 982 2543 1 chr6A.!!$R2 1561
8 TraesCS6B01G045600 chr6A 15950817 15954306 3489 True 1161.000000 3195 88.985750 1 3517 4 chr6A.!!$R3 3516
9 TraesCS6B01G045600 chr6A 16098250 16100740 2490 True 1108.333333 2979 88.320667 378 2927 3 chr6A.!!$R4 2549
10 TraesCS6B01G045600 chr6A 16088292 16088873 581 True 592.000000 592 85.191000 2936 3527 1 chr6A.!!$R1 591

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
569 609 0.540365 AACGTACTCCCTCCGTTCCA 60.540 55.0 0.00 0.0 40.46 3.53 F
1215 1303 0.249120 TCATCCGCGACAACCTCAAT 59.751 50.0 8.23 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2203 1.202698 GGGATGACACCATAGACAGCC 60.203 57.143 0.0 0.0 37.97 4.85 R
2594 2689 0.106719 CGGACAAATGGGGTGCCTAT 60.107 55.000 0.0 0.0 0.00 2.57 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
46 47 8.550376 GTGTTTGCAAAGTTTCATCATGTAATT 58.450 29.630 13.26 0.00 0.00 1.40
47 48 9.755804 TGTTTGCAAAGTTTCATCATGTAATTA 57.244 25.926 13.26 0.00 0.00 1.40
51 52 8.871862 TGCAAAGTTTCATCATGTAATTAATGC 58.128 29.630 0.00 4.40 0.00 3.56
52 53 8.330302 GCAAAGTTTCATCATGTAATTAATGCC 58.670 33.333 0.00 0.00 0.00 4.40
53 54 9.368674 CAAAGTTTCATCATGTAATTAATGCCA 57.631 29.630 0.00 0.00 0.00 4.92
54 55 9.590451 AAAGTTTCATCATGTAATTAATGCCAG 57.410 29.630 0.00 0.00 0.00 4.85
75 76 3.809832 AGACATTTGTGGAAGTCGTGAAG 59.190 43.478 0.00 0.00 36.18 3.02
86 90 4.991687 GGAAGTCGTGAAGAAAATCAGAGT 59.008 41.667 0.00 0.00 0.00 3.24
100 104 7.654923 AGAAAATCAGAGTTCCAAAATGCTTTC 59.345 33.333 0.00 0.00 0.00 2.62
109 113 6.918022 AGTTCCAAAATGCTTTCGAAAGTAAG 59.082 34.615 32.32 20.75 40.89 2.34
116 120 9.528018 AAAATGCTTTCGAAAGTAAGATTTTCA 57.472 25.926 32.32 20.86 40.45 2.69
123 127 7.672983 TCGAAAGTAAGATTTTCAGAGCATT 57.327 32.000 0.00 0.00 34.90 3.56
124 128 7.521529 TCGAAAGTAAGATTTTCAGAGCATTG 58.478 34.615 0.00 0.00 34.90 2.82
181 185 7.660112 TGATTACATCATGAAACTTTGCAAGT 58.340 30.769 0.00 0.00 37.62 3.16
183 187 9.624697 GATTACATCATGAAACTTTGCAAGTAA 57.375 29.630 0.00 0.77 41.91 2.24
194 199 5.897050 ACTTTGCAAGTAACCGAAAAATCA 58.103 33.333 0.00 0.00 40.69 2.57
265 278 4.759516 ATGCGTTCGAAAGTACCATTTT 57.240 36.364 12.65 0.00 0.00 1.82
266 279 5.866335 ATGCGTTCGAAAGTACCATTTTA 57.134 34.783 12.65 0.00 0.00 1.52
270 283 7.140048 TGCGTTCGAAAGTACCATTTTATTTT 58.860 30.769 12.65 0.00 0.00 1.82
331 351 7.883391 TCCTTTACTTGGTACATTTGAAACA 57.117 32.000 0.00 0.00 39.30 2.83
461 484 6.819146 GGAAAACAAATTCTTGGGTACAACAA 59.181 34.615 0.00 0.00 36.82 2.83
486 509 7.110155 ACTCCAGGAAAATCGTATTTACATGT 58.890 34.615 2.69 2.69 0.00 3.21
559 599 9.591792 AATGGACTTAGTTTTATAACGTACTCC 57.408 33.333 0.00 0.00 39.31 3.85
560 600 7.547227 TGGACTTAGTTTTATAACGTACTCCC 58.453 38.462 0.00 0.00 39.31 4.30
561 601 7.397192 TGGACTTAGTTTTATAACGTACTCCCT 59.603 37.037 0.00 0.00 39.31 4.20
562 602 7.918033 GGACTTAGTTTTATAACGTACTCCCTC 59.082 40.741 0.00 0.00 39.31 4.30
563 603 7.776107 ACTTAGTTTTATAACGTACTCCCTCC 58.224 38.462 0.00 0.00 39.31 4.30
564 604 5.254339 AGTTTTATAACGTACTCCCTCCG 57.746 43.478 0.00 0.00 39.31 4.63
565 605 4.706962 AGTTTTATAACGTACTCCCTCCGT 59.293 41.667 0.00 0.00 39.31 4.69
566 606 5.185828 AGTTTTATAACGTACTCCCTCCGTT 59.814 40.000 0.00 0.00 45.65 4.44
567 607 4.900635 TTATAACGTACTCCCTCCGTTC 57.099 45.455 0.00 0.00 43.09 3.95
568 608 1.463674 TAACGTACTCCCTCCGTTCC 58.536 55.000 0.00 0.00 43.09 3.62
569 609 0.540365 AACGTACTCCCTCCGTTCCA 60.540 55.000 0.00 0.00 40.46 3.53
570 610 0.540365 ACGTACTCCCTCCGTTCCAA 60.540 55.000 0.00 0.00 0.00 3.53
571 611 0.604578 CGTACTCCCTCCGTTCCAAA 59.395 55.000 0.00 0.00 0.00 3.28
572 612 1.001181 CGTACTCCCTCCGTTCCAAAA 59.999 52.381 0.00 0.00 0.00 2.44
573 613 2.354403 CGTACTCCCTCCGTTCCAAAAT 60.354 50.000 0.00 0.00 0.00 1.82
574 614 3.119029 CGTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
575 615 4.621274 CGTACTCCCTCCGTTCCAAAATAA 60.621 45.833 0.00 0.00 0.00 1.40
576 616 3.951663 ACTCCCTCCGTTCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
577 617 3.329814 ACTCCCTCCGTTCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
578 618 3.681593 TCCCTCCGTTCCAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
579 619 3.073356 TCCCTCCGTTCCAAAATAAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
580 620 3.439129 CCCTCCGTTCCAAAATAAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
581 621 4.324267 CCTCCGTTCCAAAATAAGTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
582 622 4.392138 CCTCCGTTCCAAAATAAGTGTCTC 59.608 45.833 0.00 0.00 0.00 3.36
583 623 4.963373 TCCGTTCCAAAATAAGTGTCTCA 58.037 39.130 0.00 0.00 0.00 3.27
584 624 5.369833 TCCGTTCCAAAATAAGTGTCTCAA 58.630 37.500 0.00 0.00 0.00 3.02
585 625 6.001460 TCCGTTCCAAAATAAGTGTCTCAAT 58.999 36.000 0.00 0.00 0.00 2.57
586 626 6.488683 TCCGTTCCAAAATAAGTGTCTCAATT 59.511 34.615 0.00 0.00 0.00 2.32
587 627 7.013846 TCCGTTCCAAAATAAGTGTCTCAATTT 59.986 33.333 0.00 0.00 0.00 1.82
588 628 7.651704 CCGTTCCAAAATAAGTGTCTCAATTTT 59.348 33.333 0.00 0.00 33.07 1.82
589 629 9.672086 CGTTCCAAAATAAGTGTCTCAATTTTA 57.328 29.630 0.00 0.00 31.97 1.52
626 666 9.635520 TGTGTAAAGTTATACTAAGCTTGAGAC 57.364 33.333 9.86 0.00 0.00 3.36
627 667 9.635520 GTGTAAAGTTATACTAAGCTTGAGACA 57.364 33.333 9.86 0.00 0.00 3.41
628 668 9.635520 TGTAAAGTTATACTAAGCTTGAGACAC 57.364 33.333 9.86 0.00 0.00 3.67
629 669 9.857957 GTAAAGTTATACTAAGCTTGAGACACT 57.142 33.333 9.86 1.30 0.00 3.55
637 677 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
638 678 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
639 679 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
640 680 4.762251 AGCTTGAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
641 681 4.378459 GCTTGAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
642 682 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
643 683 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
644 684 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
645 685 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
646 686 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
647 687 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
648 688 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
649 689 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
650 690 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
651 691 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
747 795 5.107259 CGAGACAGATGGACGATCTTACTAG 60.107 48.000 0.00 0.00 39.64 2.57
831 915 5.041940 AGAGAACGTGTCAAACTGAAGTAC 58.958 41.667 0.00 0.00 0.00 2.73
860 944 7.606073 TCCGTGCATGCTATAAATACATGTATT 59.394 33.333 22.70 22.70 42.50 1.89
1021 1109 0.938008 GGAAATGGAGATCGGTTCGC 59.062 55.000 0.00 0.00 0.00 4.70
1053 1141 1.612726 GCAGCATCCACCAACTTCTCT 60.613 52.381 0.00 0.00 0.00 3.10
1215 1303 0.249120 TCATCCGCGACAACCTCAAT 59.751 50.000 8.23 0.00 0.00 2.57
1266 1354 1.699054 TTGCCTCTGTGTCTGGTGCT 61.699 55.000 0.00 0.00 0.00 4.40
1311 1399 0.250234 CCATCTGCGACCTTCTTGGA 59.750 55.000 0.00 0.00 39.71 3.53
1422 1510 2.411701 CGCTTCCTCATCGGCGTA 59.588 61.111 6.85 0.00 42.23 4.42
1491 1579 3.643320 TCAATAGCAAGATCATCGGGACT 59.357 43.478 0.00 0.00 0.00 3.85
1647 1735 4.525996 CAGGAATGATGTTGGTGGTGATA 58.474 43.478 0.00 0.00 0.00 2.15
1668 1756 0.670546 GCTTGCTCGTGCTCACCTTA 60.671 55.000 11.19 0.00 40.48 2.69
2083 2171 1.073444 CCTCCATAGCATGCATGGTCT 59.927 52.381 33.01 21.79 43.03 3.85
2248 2336 0.033642 TTCGTCGCAATACACCACCA 59.966 50.000 0.00 0.00 0.00 4.17
2316 2404 1.148310 CCGTCATTCTCGTGCACTTT 58.852 50.000 16.19 0.00 0.00 2.66
2463 2552 1.665916 CAGCATATCCGAGCGTGGG 60.666 63.158 0.00 0.00 35.48 4.61
2484 2573 4.303603 CGCAATGCCATCCTCGCG 62.304 66.667 0.00 0.00 36.47 5.87
2529 2618 1.083015 GCCACAACACGTGTAAGCG 60.083 57.895 23.69 13.21 44.78 4.68
2532 2621 1.859703 CCACAACACGTGTAAGCGTTA 59.140 47.619 23.69 0.00 44.78 3.18
2584 2679 2.853963 CGTATACATACATACGCGCCA 58.146 47.619 5.73 0.00 44.96 5.69
2585 2680 3.431856 CGTATACATACATACGCGCCAT 58.568 45.455 5.73 0.00 44.96 4.40
2586 2681 4.590226 CGTATACATACATACGCGCCATA 58.410 43.478 5.73 0.00 44.96 2.74
2587 2682 4.669283 CGTATACATACATACGCGCCATAG 59.331 45.833 5.73 0.00 44.96 2.23
2590 2685 4.976224 ACATACATACGCGCCATAGATA 57.024 40.909 5.73 0.00 0.00 1.98
2591 2686 5.515797 ACATACATACGCGCCATAGATAT 57.484 39.130 5.73 0.00 0.00 1.63
2593 2688 7.215719 ACATACATACGCGCCATAGATATAT 57.784 36.000 5.73 0.00 0.00 0.86
2594 2689 8.331730 ACATACATACGCGCCATAGATATATA 57.668 34.615 5.73 0.00 0.00 0.86
2595 2690 8.957466 ACATACATACGCGCCATAGATATATAT 58.043 33.333 5.73 0.00 0.00 0.86
2609 2706 9.730705 CATAGATATATATAGGCACCCCATTTG 57.269 37.037 0.00 0.00 0.00 2.32
2610 2707 7.771506 AGATATATATAGGCACCCCATTTGT 57.228 36.000 0.00 0.00 0.00 2.83
2629 2726 1.149627 CCGGTGTGGTTTCCCAGAA 59.850 57.895 0.00 0.00 42.94 3.02
2655 2752 3.287222 TGCTTTTTGGGCGCTTATCTAT 58.713 40.909 7.64 0.00 0.00 1.98
2678 2780 7.574021 ATGCCTTAGTCAATAATATCTGGGA 57.426 36.000 0.00 0.00 0.00 4.37
2698 2801 7.125659 TCTGGGACTTGTATCATGTATGAGAAA 59.874 37.037 0.74 0.00 40.64 2.52
2757 2860 9.730705 CCTTGCATATCTCTCCTTAATTTCATA 57.269 33.333 0.00 0.00 0.00 2.15
2806 2935 6.474140 TTTCCGAGATAGCTTACCACATAA 57.526 37.500 0.00 0.00 0.00 1.90
2855 2985 6.050432 TGTAAGGGCTTGTAATATGTTACGG 58.950 40.000 7.72 4.80 42.50 4.02
2871 3008 7.730364 ATGTTACGGGAAAGATCAATATGAC 57.270 36.000 0.00 0.00 0.00 3.06
2888 3025 1.180029 GACAGCATTGGTCAATGGCT 58.820 50.000 20.88 15.98 46.14 4.75
2906 3043 6.982160 ATGGCTTATTCTTGCATAATGGAA 57.018 33.333 5.32 0.00 0.00 3.53
2908 3045 5.221303 TGGCTTATTCTTGCATAATGGAAGC 60.221 40.000 15.15 15.15 44.16 3.86
2913 3050 3.609853 TCTTGCATAATGGAAGCGAACT 58.390 40.909 0.00 0.00 44.16 3.01
2963 3159 4.863131 GTGCGCTTGTGTACTTATTCTAGT 59.137 41.667 9.73 0.00 0.00 2.57
2971 3167 6.338146 TGTGTACTTATTCTAGTGTGATGCC 58.662 40.000 0.00 0.00 0.00 4.40
2988 3184 2.582052 TGCCAACTTGGGTACTTCTTG 58.418 47.619 9.95 0.00 38.19 3.02
2997 3193 1.607148 GGGTACTTCTTGCACACCAAC 59.393 52.381 0.00 0.00 0.00 3.77
3195 3395 5.861222 AAAAAGTGTCAAGTTTGCCAAAG 57.139 34.783 0.00 0.00 0.00 2.77
3232 3436 0.748450 TTCAAACGAGTCGGTGGTCT 59.252 50.000 18.30 0.00 0.00 3.85
3279 3483 1.670811 CACGCAAAGAGTTTGACCTGT 59.329 47.619 3.56 0.00 43.26 4.00
3300 3504 1.258458 GAGAGTACTGGTCGATCGACG 59.742 57.143 34.69 26.19 45.41 5.12
3402 3606 0.609131 TCTTAACCTTGGGCAGCTGC 60.609 55.000 30.88 30.88 41.14 5.25
3449 3658 4.957296 TCGGCCTCCTTCAGTATATTTTC 58.043 43.478 0.00 0.00 0.00 2.29
3468 3677 9.918630 ATATTTTCTGATTTTATGCTATGCACC 57.081 29.630 0.00 0.00 43.04 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.406456 ACTTCCACAAATGTCTGGCATTA 58.594 39.130 8.06 0.00 46.29 1.90
48 49 2.821969 GACTTCCACAAATGTCTGGCAT 59.178 45.455 0.00 0.00 40.03 4.40
49 50 2.229792 GACTTCCACAAATGTCTGGCA 58.770 47.619 0.00 0.00 0.00 4.92
50 51 1.197721 CGACTTCCACAAATGTCTGGC 59.802 52.381 0.00 0.00 0.00 4.85
51 52 2.224079 CACGACTTCCACAAATGTCTGG 59.776 50.000 0.00 0.00 0.00 3.86
52 53 3.130633 TCACGACTTCCACAAATGTCTG 58.869 45.455 0.00 0.00 0.00 3.51
53 54 3.469008 TCACGACTTCCACAAATGTCT 57.531 42.857 0.00 0.00 0.00 3.41
54 55 3.807622 TCTTCACGACTTCCACAAATGTC 59.192 43.478 0.00 0.00 0.00 3.06
75 76 7.358683 CGAAAGCATTTTGGAACTCTGATTTTC 60.359 37.037 0.00 0.00 39.27 2.29
86 90 7.033530 TCTTACTTTCGAAAGCATTTTGGAA 57.966 32.000 32.49 12.20 39.27 3.53
100 104 7.521529 TCAATGCTCTGAAAATCTTACTTTCG 58.478 34.615 0.00 0.00 35.88 3.46
183 187 9.581099 GGTGATAAACATTAATGATTTTTCGGT 57.419 29.630 22.16 3.16 0.00 4.69
266 279 8.413229 CCTCGTGGATGAATGGTAAATTAAAAT 58.587 33.333 0.00 0.00 34.57 1.82
270 283 6.099125 TCTCCTCGTGGATGAATGGTAAATTA 59.901 38.462 6.68 0.00 42.29 1.40
331 351 0.119358 ACCTTAGGCCCCTCTCAACT 59.881 55.000 0.00 0.00 0.00 3.16
432 455 8.251383 TGTACCCAAGAATTTGTTTTCCATTA 57.749 30.769 0.00 0.00 32.21 1.90
448 471 2.105821 TCCTGGAGTTGTTGTACCCAAG 59.894 50.000 0.00 0.00 0.00 3.61
452 475 4.083484 CGATTTTCCTGGAGTTGTTGTACC 60.083 45.833 0.00 0.00 0.00 3.34
461 484 7.110155 ACATGTAAATACGATTTTCCTGGAGT 58.890 34.615 0.00 0.00 0.00 3.85
542 582 4.706962 ACGGAGGGAGTACGTTATAAAACT 59.293 41.667 0.00 0.00 37.61 2.66
553 593 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
554 594 4.533311 ACTTATTTTGGAACGGAGGGAGTA 59.467 41.667 0.00 0.00 0.00 2.59
555 595 3.329814 ACTTATTTTGGAACGGAGGGAGT 59.670 43.478 0.00 0.00 0.00 3.85
556 596 3.689649 CACTTATTTTGGAACGGAGGGAG 59.310 47.826 0.00 0.00 0.00 4.30
557 597 3.073356 ACACTTATTTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
558 598 3.418047 ACACTTATTTTGGAACGGAGGG 58.582 45.455 0.00 0.00 0.00 4.30
559 599 4.324267 AGACACTTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
560 600 4.994852 TGAGACACTTATTTTGGAACGGAG 59.005 41.667 0.00 0.00 0.00 4.63
561 601 4.963373 TGAGACACTTATTTTGGAACGGA 58.037 39.130 0.00 0.00 0.00 4.69
562 602 5.682943 TTGAGACACTTATTTTGGAACGG 57.317 39.130 0.00 0.00 0.00 4.44
563 603 8.574196 AAAATTGAGACACTTATTTTGGAACG 57.426 30.769 0.00 0.00 31.14 3.95
600 640 9.635520 GTCTCAAGCTTAGTATAACTTTACACA 57.364 33.333 0.00 0.00 0.00 3.72
601 641 9.635520 TGTCTCAAGCTTAGTATAACTTTACAC 57.364 33.333 0.00 0.00 0.00 2.90
602 642 9.635520 GTGTCTCAAGCTTAGTATAACTTTACA 57.364 33.333 0.00 0.00 0.00 2.41
603 643 9.857957 AGTGTCTCAAGCTTAGTATAACTTTAC 57.142 33.333 0.00 0.00 0.00 2.01
611 651 9.167311 CCAAAATAAGTGTCTCAAGCTTAGTAT 57.833 33.333 0.00 0.00 0.00 2.12
612 652 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
613 653 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
614 654 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
615 655 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
616 656 5.241728 GTCCCAAAATAAGTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
617 657 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
618 658 4.378459 CGTCCCAAAATAAGTGTCTCAAGC 60.378 45.833 0.00 0.00 0.00 4.01
619 659 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
620 660 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
621 661 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
622 662 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
623 663 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
624 664 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
625 665 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
626 666 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
627 667 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
628 668 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
629 669 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
630 670 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
631 671 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
632 672 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
633 673 1.007963 AGATACTCCCTCCGTCCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
634 674 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
635 675 0.106167 CAGATACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
636 676 0.106116 ACAGATACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
637 677 1.777941 AACAGATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
638 678 4.737055 GCTTTAACAGATACTCCCTCCGTC 60.737 50.000 0.00 0.00 0.00 4.79
639 679 3.132467 GCTTTAACAGATACTCCCTCCGT 59.868 47.826 0.00 0.00 0.00 4.69
640 680 3.385111 AGCTTTAACAGATACTCCCTCCG 59.615 47.826 0.00 0.00 0.00 4.63
641 681 4.406003 TGAGCTTTAACAGATACTCCCTCC 59.594 45.833 0.00 0.00 0.00 4.30
642 682 5.599999 TGAGCTTTAACAGATACTCCCTC 57.400 43.478 0.00 0.00 0.00 4.30
643 683 6.174049 GTTTGAGCTTTAACAGATACTCCCT 58.826 40.000 6.93 0.00 0.00 4.20
644 684 5.938125 TGTTTGAGCTTTAACAGATACTCCC 59.062 40.000 9.69 0.00 31.15 4.30
645 685 7.617041 ATGTTTGAGCTTTAACAGATACTCC 57.383 36.000 16.46 0.00 37.64 3.85
646 686 9.372369 ACTATGTTTGAGCTTTAACAGATACTC 57.628 33.333 16.46 0.00 37.64 2.59
647 687 9.726438 AACTATGTTTGAGCTTTAACAGATACT 57.274 29.630 16.46 5.80 37.64 2.12
650 690 9.899226 GAAAACTATGTTTGAGCTTTAACAGAT 57.101 29.630 16.46 6.87 37.64 2.90
651 691 8.898761 TGAAAACTATGTTTGAGCTTTAACAGA 58.101 29.630 16.46 12.48 37.64 3.41
747 795 7.316544 TGTTTGACCTCTTCTGTTTCTTAAC 57.683 36.000 0.00 0.00 34.75 2.01
831 915 1.577468 TTTATAGCATGCACGGACCG 58.423 50.000 21.98 13.61 0.00 4.79
860 944 2.567615 GGGTGCTCAAGAGGTTAGAAGA 59.432 50.000 0.00 0.00 0.00 2.87
1031 1119 1.630369 AGAAGTTGGTGGATGCTGCTA 59.370 47.619 0.00 0.00 0.00 3.49
1053 1141 1.979155 CTCAGAGTCCACCGGCAGA 60.979 63.158 0.00 0.00 0.00 4.26
1215 1303 1.833630 CCTATGTCAGCCTTGGTGAGA 59.166 52.381 0.00 0.00 40.79 3.27
1266 1354 1.583556 TGGCCAGCCTTGAGAAGATA 58.416 50.000 0.00 0.00 36.94 1.98
1647 1735 2.358003 GTGAGCACGAGCAAGCCT 60.358 61.111 7.77 0.00 45.49 4.58
2083 2171 2.492088 CCTCGACACAGATGGAGTACAA 59.508 50.000 0.00 0.00 0.00 2.41
2115 2203 1.202698 GGGATGACACCATAGACAGCC 60.203 57.143 0.00 0.00 37.97 4.85
2271 2359 2.030274 CGTGCATGCCATGATCATGATT 60.030 45.455 32.71 16.10 42.84 2.57
2350 2438 4.135153 CTCCTCAGTGGCGTCGGG 62.135 72.222 0.00 0.00 35.26 5.14
2463 2552 1.493950 CGAGGATGGCATTGCGTCTC 61.494 60.000 0.00 5.95 0.00 3.36
2580 2675 5.105310 GGGGTGCCTATATATATCTATGGCG 60.105 48.000 16.87 0.00 41.51 5.69
2581 2676 5.785423 TGGGGTGCCTATATATATCTATGGC 59.215 44.000 15.93 15.93 39.33 4.40
2583 2678 9.730705 CAAATGGGGTGCCTATATATATCTATG 57.269 37.037 0.00 0.00 0.00 2.23
2584 2679 9.465704 ACAAATGGGGTGCCTATATATATCTAT 57.534 33.333 0.00 0.00 0.00 1.98
2585 2680 8.869986 ACAAATGGGGTGCCTATATATATCTA 57.130 34.615 0.00 0.00 0.00 1.98
2586 2681 7.147302 GGACAAATGGGGTGCCTATATATATCT 60.147 40.741 0.00 0.00 0.00 1.98
2587 2682 6.998673 GGACAAATGGGGTGCCTATATATATC 59.001 42.308 0.00 0.00 0.00 1.63
2590 2685 4.324254 CGGACAAATGGGGTGCCTATATAT 60.324 45.833 0.00 0.00 0.00 0.86
2591 2686 3.008594 CGGACAAATGGGGTGCCTATATA 59.991 47.826 0.00 0.00 0.00 0.86
2593 2688 1.142060 CGGACAAATGGGGTGCCTATA 59.858 52.381 0.00 0.00 0.00 1.31
2594 2689 0.106719 CGGACAAATGGGGTGCCTAT 60.107 55.000 0.00 0.00 0.00 2.57
2595 2690 1.301623 CGGACAAATGGGGTGCCTA 59.698 57.895 0.00 0.00 0.00 3.93
2596 2691 2.035626 CGGACAAATGGGGTGCCT 59.964 61.111 0.00 0.00 0.00 4.75
2629 2726 3.128375 CGCCCAAAAAGCAGGTGT 58.872 55.556 0.00 0.00 0.00 4.16
2655 2752 6.558775 AGTCCCAGATATTATTGACTAAGGCA 59.441 38.462 0.00 0.00 31.70 4.75
2672 2774 6.136155 TCTCATACATGATACAAGTCCCAGA 58.864 40.000 0.00 0.00 36.02 3.86
2774 2877 8.837389 GGTAAGCTATCTCGGAAAATACAAATT 58.163 33.333 0.00 0.00 0.00 1.82
2806 2935 6.418101 AGTACACTGAAATAATCACATGGCT 58.582 36.000 0.00 0.00 33.47 4.75
2824 2954 7.551617 ACATATTACAAGCCCTTACAAGTACAC 59.448 37.037 0.00 0.00 0.00 2.90
2855 2985 6.040166 ACCAATGCTGTCATATTGATCTTTCC 59.960 38.462 10.11 0.00 36.61 3.13
2871 3008 4.098960 AGAATAAGCCATTGACCAATGCTG 59.901 41.667 15.29 6.07 45.06 4.41
2888 3025 6.318648 AGTTCGCTTCCATTATGCAAGAATAA 59.681 34.615 0.00 0.00 0.00 1.40
2906 3043 2.607282 CGTGTGGAAGAGTAAGTTCGCT 60.607 50.000 0.00 0.00 0.00 4.93
2908 3045 3.009301 ACGTGTGGAAGAGTAAGTTCG 57.991 47.619 0.00 0.00 0.00 3.95
2913 3050 1.068333 GCCGTACGTGTGGAAGAGTAA 60.068 52.381 15.21 0.00 0.00 2.24
2934 3129 1.373246 TACACAAGCGCACCGTACC 60.373 57.895 11.47 0.00 0.00 3.34
2963 3159 1.423541 AGTACCCAAGTTGGCATCACA 59.576 47.619 17.07 0.00 35.79 3.58
2971 3167 2.948979 TGTGCAAGAAGTACCCAAGTTG 59.051 45.455 0.00 0.00 31.00 3.16
2988 3184 0.584876 GGTTCTGTACGTTGGTGTGC 59.415 55.000 0.00 0.00 0.00 4.57
2997 3193 2.729882 CCTCTTTGAACGGTTCTGTACG 59.270 50.000 20.53 7.52 0.00 3.67
3097 3293 1.376942 CTGTTGAGAGGCCAGGCTG 60.377 63.158 12.43 7.75 0.00 4.85
3195 3395 6.019881 CGTTTGAATTTTGTTTCTCCTGTTCC 60.020 38.462 0.00 0.00 0.00 3.62
3279 3483 2.277969 GTCGATCGACCAGTACTCTCA 58.722 52.381 33.06 0.00 39.08 3.27
3300 3504 0.650512 CATGTCCGTATGAACCACGC 59.349 55.000 0.00 0.00 38.07 5.34
3449 3658 9.778993 GTATATTGGTGCATAGCATAAAATCAG 57.221 33.333 0.00 0.00 41.91 2.90


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

AutoCloner maintained by Alex Coulton.