Multiple sequence alignment - TraesCS7A01G219200

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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 TraesCS7A01G219200 chr7A 100.000 3326 0 0 1 3326 186530331 186533656 0.000000e+00 6143.0
1 TraesCS7A01G219200 chr7A 97.810 137 3 0 2615 2751 357351424 357351560 1.540000e-58 237.0
2 TraesCS7A01G219200 chr7B 96.139 2616 77 15 1 2608 153439389 153436790 0.000000e+00 4250.0
3 TraesCS7A01G219200 chr7B 94.273 454 23 1 2873 3326 153436802 153436352 0.000000e+00 691.0
4 TraesCS7A01G219200 chr7B 97.794 136 3 0 2615 2750 316232847 316232712 5.550000e-58 235.0
5 TraesCS7A01G219200 chr7D 94.104 2629 102 27 1 2608 184188330 184185734 0.000000e+00 3947.0
6 TraesCS7A01G219200 chr7D 95.595 454 17 1 2873 3326 184185746 184185296 0.000000e+00 725.0
7 TraesCS7A01G219200 chr2D 94.118 221 10 1 2634 2854 392364101 392364318 1.910000e-87 333.0
8 TraesCS7A01G219200 chr1A 97.163 141 4 0 2605 2745 203320545 203320685 4.290000e-59 239.0
9 TraesCS7A01G219200 chr1B 97.794 136 3 0 2615 2750 320780964 320780829 5.550000e-58 235.0
10 TraesCS7A01G219200 chr1B 100.000 32 0 0 3270 3301 97507412 97507443 3.580000e-05 60.2
11 TraesCS7A01G219200 chr4B 97.122 139 3 1 2615 2753 187174106 187173969 2.000000e-57 233.0
12 TraesCS7A01G219200 chrUn 98.462 130 1 1 2750 2878 466082312 466082183 9.280000e-56 228.0
13 TraesCS7A01G219200 chrUn 94.000 150 8 1 2615 2764 17585271 17585419 3.340000e-55 226.0
14 TraesCS7A01G219200 chrUn 98.450 129 1 1 2751 2878 191968449 191968577 3.340000e-55 226.0
15 TraesCS7A01G219200 chrUn 98.450 129 1 1 2751 2878 191968935 191969063 3.340000e-55 226.0
16 TraesCS7A01G219200 chrUn 98.450 129 1 1 2751 2878 191974280 191974408 3.340000e-55 226.0
17 TraesCS7A01G219200 chr5B 98.462 130 1 1 2750 2878 83405347 83405476 9.280000e-56 228.0
18 TraesCS7A01G219200 chr5B 98.462 130 1 1 2750 2878 83416465 83416594 9.280000e-56 228.0
19 TraesCS7A01G219200 chr5B 94.545 55 3 0 3270 3324 419998058 419998004 5.910000e-13 86.1
20 TraesCS7A01G219200 chr5A 98.462 130 0 2 2751 2878 61644982 61645111 9.280000e-56 228.0
21 TraesCS7A01G219200 chr5A 98.462 130 0 2 2751 2878 61646917 61647046 9.280000e-56 228.0
22 TraesCS7A01G219200 chr2A 94.079 152 6 3 2615 2764 131001901 131001751 9.280000e-56 228.0
23 TraesCS7A01G219200 chr5D 92.405 158 8 3 2615 2769 150825680 150825524 4.320000e-54 222.0
24 TraesCS7A01G219200 chr2B 94.737 57 1 2 3271 3326 399832554 399832609 1.640000e-13 87.9
25 TraesCS7A01G219200 chr2B 88.889 54 3 3 3256 3308 526880951 526880900 2.770000e-06 63.9
26 TraesCS7A01G219200 chr6A 87.273 55 4 1 3271 3322 477168527 477168581 3.580000e-05 60.2


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 TraesCS7A01G219200 chr7A 186530331 186533656 3325 False 6143.0 6143 100.0000 1 3326 1 chr7A.!!$F1 3325
1 TraesCS7A01G219200 chr7B 153436352 153439389 3037 True 2470.5 4250 95.2060 1 3326 2 chr7B.!!$R2 3325
2 TraesCS7A01G219200 chr7D 184185296 184188330 3034 True 2336.0 3947 94.8495 1 3326 2 chr7D.!!$R1 3325
3 TraesCS7A01G219200 chrUn 191968449 191969063 614 False 226.0 226 98.4500 2751 2878 2 chrUn.!!$F3 127
4 TraesCS7A01G219200 chr5A 61644982 61647046 2064 False 228.0 228 98.4620 2751 2878 2 chr5A.!!$F1 127

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
318 323 1.066002 CCCTAAGTCGCCGAATTACGA 59.934 52.381 2.51 0.0 45.77 3.43 F
1155 1179 0.107703 TTGCCTCCTAACCAGCGATG 60.108 55.000 0.00 0.0 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1363 0.684535 TCCATTCTGCTTCGTGTCCA 59.315 50.0 0.0 0.0 0.0 4.02 R
2672 2702 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.0 0.0 0.0 0.0 4.52 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
55 56 1.646189 GGTTCTCTCGTGGAAGCATC 58.354 55.000 10.78 0.00 39.88 3.91
64 65 6.258727 TCTCTCGTGGAAGCATCATTAATTTC 59.741 38.462 0.00 0.00 0.00 2.17
96 98 3.706594 TGTTATTTTGTCCAACCCAGCAA 59.293 39.130 0.00 0.00 0.00 3.91
155 157 3.443045 CTGCCACAATCGCCACCC 61.443 66.667 0.00 0.00 0.00 4.61
158 160 2.350895 CCACAATCGCCACCCTCA 59.649 61.111 0.00 0.00 0.00 3.86
272 274 6.259550 AGTTAAACTGATTCCATGAACTGC 57.740 37.500 0.00 0.00 0.00 4.40
288 291 2.151202 ACTGCCTACAAAATGACGTGG 58.849 47.619 0.00 0.00 0.00 4.94
318 323 1.066002 CCCTAAGTCGCCGAATTACGA 59.934 52.381 2.51 0.00 45.77 3.43
526 549 1.841302 AAGAGGGGAGCAATGCGACA 61.841 55.000 0.00 0.00 0.00 4.35
683 706 2.360852 ACCTGGACGACGACGGAT 60.361 61.111 12.58 0.00 44.46 4.18
869 892 1.836999 TAGCAGACGTGTGGCCCATT 61.837 55.000 15.19 0.00 0.00 3.16
900 923 3.032459 TCCAAGGTTTTACCAACCAACC 58.968 45.455 6.53 0.00 41.95 3.77
901 924 2.766828 CCAAGGTTTTACCAACCAACCA 59.233 45.455 6.53 0.00 41.95 3.67
995 1019 2.811317 CGCCTTCACTGCTCGGTC 60.811 66.667 0.00 0.00 0.00 4.79
1075 1099 0.607217 TCTACGCTCTCCACGGTTCA 60.607 55.000 0.00 0.00 34.00 3.18
1077 1101 0.454600 TACGCTCTCCACGGTTCATC 59.545 55.000 0.00 0.00 34.00 2.92
1090 1114 1.112113 GTTCATCGCCACTCCTCCTA 58.888 55.000 0.00 0.00 0.00 2.94
1155 1179 0.107703 TTGCCTCCTAACCAGCGATG 60.108 55.000 0.00 0.00 0.00 3.84
1236 1260 3.585990 GGGTTGATGGATGCGCGG 61.586 66.667 8.83 0.00 0.00 6.46
1310 1334 3.836176 GACGCTGAACACGGACGGT 62.836 63.158 0.00 0.00 34.00 4.83
1342 1366 1.912971 TCTCGGTCGGAGATCTGGA 59.087 57.895 0.00 0.00 46.80 3.86
1349 1373 1.095600 TCGGAGATCTGGACACGAAG 58.904 55.000 0.00 0.00 0.00 3.79
1358 1382 0.684535 TGGACACGAAGCAGAATGGA 59.315 50.000 0.00 0.00 35.86 3.41
1360 1384 1.338200 GGACACGAAGCAGAATGGAGT 60.338 52.381 0.00 0.00 35.86 3.85
1557 1584 7.788026 TGTTCCCTTTCGTATGTATAGTTGAT 58.212 34.615 0.00 0.00 0.00 2.57
1594 1624 5.900865 TGCTGCATTGTCAATTTCTCATA 57.099 34.783 0.00 0.00 0.00 2.15
2057 2087 3.055819 TCTGCTTGTTCTCATGGTACTCC 60.056 47.826 0.00 0.00 0.00 3.85
2088 2118 9.900710 CTATCTGAGCATACTATCGTTTAGTTT 57.099 33.333 6.20 0.00 0.00 2.66
2366 2396 5.022282 TGACATCTCATATTCTTTCCGCA 57.978 39.130 0.00 0.00 0.00 5.69
2542 2572 8.980481 ATCATAGACCTTTATTTACCCAAGTG 57.020 34.615 0.00 0.00 0.00 3.16
2610 2640 1.614996 CCATACCTGTGGCACAACAA 58.385 50.000 22.31 9.71 44.16 2.83
2611 2641 1.269448 CCATACCTGTGGCACAACAAC 59.731 52.381 22.31 0.00 44.16 3.32
2612 2642 1.952990 CATACCTGTGGCACAACAACA 59.047 47.619 22.31 5.71 44.16 3.33
2613 2643 2.130272 TACCTGTGGCACAACAACAA 57.870 45.000 22.31 1.39 44.16 2.83
2614 2644 0.530288 ACCTGTGGCACAACAACAAC 59.470 50.000 22.31 0.00 44.16 3.32
2615 2645 0.529833 CCTGTGGCACAACAACAACA 59.470 50.000 22.31 0.00 44.16 3.33
2616 2646 1.067283 CCTGTGGCACAACAACAACAA 60.067 47.619 22.31 0.00 44.16 2.83
2617 2647 1.991965 CTGTGGCACAACAACAACAAC 59.008 47.619 22.31 0.00 44.16 3.32
2618 2648 1.341209 TGTGGCACAACAACAACAACA 59.659 42.857 19.74 0.00 44.16 3.33
2619 2649 2.224042 TGTGGCACAACAACAACAACAA 60.224 40.909 19.74 0.00 44.16 2.83
2620 2650 2.802816 GTGGCACAACAACAACAACAAA 59.197 40.909 13.86 0.00 44.16 2.83
2621 2651 3.248602 GTGGCACAACAACAACAACAAAA 59.751 39.130 13.86 0.00 44.16 2.44
2622 2652 3.876914 TGGCACAACAACAACAACAAAAA 59.123 34.783 0.00 0.00 31.92 1.94
2623 2653 4.516698 TGGCACAACAACAACAACAAAAAT 59.483 33.333 0.00 0.00 31.92 1.82
2624 2654 5.085390 GGCACAACAACAACAACAAAAATC 58.915 37.500 0.00 0.00 0.00 2.17
2625 2655 5.106752 GGCACAACAACAACAACAAAAATCT 60.107 36.000 0.00 0.00 0.00 2.40
2626 2656 6.369799 GCACAACAACAACAACAAAAATCTT 58.630 32.000 0.00 0.00 0.00 2.40
2627 2657 6.855403 GCACAACAACAACAACAAAAATCTTT 59.145 30.769 0.00 0.00 0.00 2.52
2628 2658 7.378194 GCACAACAACAACAACAAAAATCTTTT 59.622 29.630 0.00 0.00 0.00 2.27
2629 2659 8.680261 CACAACAACAACAACAAAAATCTTTTG 58.320 29.630 9.70 9.70 35.64 2.44
2630 2660 8.616076 ACAACAACAACAACAAAAATCTTTTGA 58.384 25.926 16.56 0.00 33.83 2.69
2631 2661 9.105206 CAACAACAACAACAAAAATCTTTTGAG 57.895 29.630 16.56 11.29 33.83 3.02
2632 2662 8.376889 ACAACAACAACAAAAATCTTTTGAGT 57.623 26.923 16.56 11.79 33.83 3.41
2633 2663 8.835439 ACAACAACAACAAAAATCTTTTGAGTT 58.165 25.926 16.56 15.71 38.49 3.01
2634 2664 9.662545 CAACAACAACAAAAATCTTTTGAGTTT 57.337 25.926 16.56 0.00 46.89 2.66
2635 2665 9.877137 AACAACAACAAAAATCTTTTGAGTTTC 57.123 25.926 16.56 0.00 44.59 2.78
2636 2666 9.050601 ACAACAACAAAAATCTTTTGAGTTTCA 57.949 25.926 16.56 0.00 44.59 2.69
2639 2669 9.657419 ACAACAAAAATCTTTTGAGTTTCATCT 57.343 25.926 16.56 0.00 44.59 2.90
2641 2671 8.877808 ACAAAAATCTTTTGAGTTTCATCTCC 57.122 30.769 16.56 0.00 44.59 3.71
2642 2672 8.477256 ACAAAAATCTTTTGAGTTTCATCTCCA 58.523 29.630 16.56 0.00 44.59 3.86
2643 2673 9.485206 CAAAAATCTTTTGAGTTTCATCTCCAT 57.515 29.630 6.07 0.00 44.59 3.41
2647 2677 9.745018 AATCTTTTGAGTTTCATCTCCATAAGA 57.255 29.630 0.00 0.00 38.72 2.10
2648 2678 8.783833 TCTTTTGAGTTTCATCTCCATAAGAG 57.216 34.615 0.00 0.00 44.75 2.85
2649 2679 8.378565 TCTTTTGAGTTTCATCTCCATAAGAGT 58.621 33.333 0.00 0.00 43.71 3.24
2650 2680 7.912056 TTTGAGTTTCATCTCCATAAGAGTG 57.088 36.000 0.00 0.00 43.71 3.51
2651 2681 5.982356 TGAGTTTCATCTCCATAAGAGTGG 58.018 41.667 0.00 0.00 43.71 4.00
2652 2682 4.775236 AGTTTCATCTCCATAAGAGTGGC 58.225 43.478 0.00 0.00 43.71 5.01
2653 2683 4.472833 AGTTTCATCTCCATAAGAGTGGCT 59.527 41.667 0.00 0.00 43.71 4.75
2654 2684 4.412796 TTCATCTCCATAAGAGTGGCTG 57.587 45.455 0.00 0.00 43.71 4.85
2655 2685 3.646534 TCATCTCCATAAGAGTGGCTGA 58.353 45.455 0.00 0.00 43.71 4.26
2656 2686 3.640498 TCATCTCCATAAGAGTGGCTGAG 59.360 47.826 0.00 0.00 43.71 3.35
2657 2687 3.107402 TCTCCATAAGAGTGGCTGAGT 57.893 47.619 0.00 0.00 43.71 3.41
2658 2688 3.445008 TCTCCATAAGAGTGGCTGAGTT 58.555 45.455 0.00 0.00 43.71 3.01
2659 2689 3.840666 TCTCCATAAGAGTGGCTGAGTTT 59.159 43.478 0.00 0.00 43.71 2.66
2660 2690 4.287067 TCTCCATAAGAGTGGCTGAGTTTT 59.713 41.667 0.00 0.00 43.71 2.43
2661 2691 4.985538 TCCATAAGAGTGGCTGAGTTTTT 58.014 39.130 0.00 0.00 39.19 1.94
2662 2692 6.013725 TCTCCATAAGAGTGGCTGAGTTTTTA 60.014 38.462 0.00 0.00 43.71 1.52
2663 2693 6.721318 TCCATAAGAGTGGCTGAGTTTTTAT 58.279 36.000 0.00 0.00 39.19 1.40
2664 2694 6.599244 TCCATAAGAGTGGCTGAGTTTTTATG 59.401 38.462 0.00 0.00 39.19 1.90
2665 2695 6.375455 CCATAAGAGTGGCTGAGTTTTTATGT 59.625 38.462 0.00 0.00 31.43 2.29
2666 2696 7.094205 CCATAAGAGTGGCTGAGTTTTTATGTT 60.094 37.037 0.00 0.00 31.43 2.71
2667 2697 5.695851 AGAGTGGCTGAGTTTTTATGTTG 57.304 39.130 0.00 0.00 0.00 3.33
2668 2698 4.520492 AGAGTGGCTGAGTTTTTATGTTGG 59.480 41.667 0.00 0.00 0.00 3.77
2669 2699 3.005791 AGTGGCTGAGTTTTTATGTTGGC 59.994 43.478 0.00 0.00 0.00 4.52
2670 2700 3.005791 GTGGCTGAGTTTTTATGTTGGCT 59.994 43.478 0.00 0.00 0.00 4.75
2671 2701 3.255642 TGGCTGAGTTTTTATGTTGGCTC 59.744 43.478 0.00 0.00 0.00 4.70
2672 2702 3.492313 GCTGAGTTTTTATGTTGGCTCG 58.508 45.455 0.00 0.00 0.00 5.03
2673 2703 3.492313 CTGAGTTTTTATGTTGGCTCGC 58.508 45.455 0.00 0.00 0.00 5.03
2674 2704 2.227865 TGAGTTTTTATGTTGGCTCGCC 59.772 45.455 0.00 0.00 0.00 5.54
2675 2705 2.227865 GAGTTTTTATGTTGGCTCGCCA 59.772 45.455 6.52 6.52 45.63 5.69
2685 2715 3.724494 GCTCGCCAAGCCTATCAC 58.276 61.111 0.00 0.00 45.92 3.06
2686 2716 1.153369 GCTCGCCAAGCCTATCACA 60.153 57.895 0.00 0.00 45.92 3.58
2687 2717 0.744414 GCTCGCCAAGCCTATCACAA 60.744 55.000 0.00 0.00 45.92 3.33
2688 2718 1.009829 CTCGCCAAGCCTATCACAAC 58.990 55.000 0.00 0.00 0.00 3.32
2689 2719 0.392461 TCGCCAAGCCTATCACAACC 60.392 55.000 0.00 0.00 0.00 3.77
2690 2720 1.376609 CGCCAAGCCTATCACAACCC 61.377 60.000 0.00 0.00 0.00 4.11
2691 2721 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.00 0.00 4.34
2692 2722 2.019156 GCCAAGCCTATCACAACCCTC 61.019 57.143 0.00 0.00 0.00 4.30
2693 2723 1.408822 CCAAGCCTATCACAACCCTCC 60.409 57.143 0.00 0.00 0.00 4.30
2694 2724 1.561542 CAAGCCTATCACAACCCTCCT 59.438 52.381 0.00 0.00 0.00 3.69
2695 2725 1.501582 AGCCTATCACAACCCTCCTC 58.498 55.000 0.00 0.00 0.00 3.71
2696 2726 0.470341 GCCTATCACAACCCTCCTCC 59.530 60.000 0.00 0.00 0.00 4.30
2697 2727 1.972207 GCCTATCACAACCCTCCTCCT 60.972 57.143 0.00 0.00 0.00 3.69
2698 2728 2.482494 CCTATCACAACCCTCCTCCTT 58.518 52.381 0.00 0.00 0.00 3.36
2699 2729 2.846827 CCTATCACAACCCTCCTCCTTT 59.153 50.000 0.00 0.00 0.00 3.11
2700 2730 4.037927 CCTATCACAACCCTCCTCCTTTA 58.962 47.826 0.00 0.00 0.00 1.85
2701 2731 4.141688 CCTATCACAACCCTCCTCCTTTAC 60.142 50.000 0.00 0.00 0.00 2.01
2702 2732 1.982958 TCACAACCCTCCTCCTTTACC 59.017 52.381 0.00 0.00 0.00 2.85
2703 2733 1.004394 CACAACCCTCCTCCTTTACCC 59.996 57.143 0.00 0.00 0.00 3.69
2704 2734 0.252197 CAACCCTCCTCCTTTACCCG 59.748 60.000 0.00 0.00 0.00 5.28
2705 2735 0.912968 AACCCTCCTCCTTTACCCGG 60.913 60.000 0.00 0.00 0.00 5.73
2706 2736 2.070650 CCCTCCTCCTTTACCCGGG 61.071 68.421 22.25 22.25 0.00 5.73
2707 2737 2.743179 CCTCCTCCTTTACCCGGGC 61.743 68.421 24.08 0.00 0.00 6.13
2708 2738 1.689582 CTCCTCCTTTACCCGGGCT 60.690 63.158 24.08 10.93 0.00 5.19
2709 2739 1.229723 TCCTCCTTTACCCGGGCTT 60.230 57.895 24.08 4.08 0.00 4.35
2710 2740 1.077716 CCTCCTTTACCCGGGCTTG 60.078 63.158 24.08 8.51 0.00 4.01
2711 2741 1.077716 CTCCTTTACCCGGGCTTGG 60.078 63.158 24.08 17.99 0.00 3.61
2721 2751 3.489513 GGGCTTGGGACCGGCTAT 61.490 66.667 0.00 0.00 0.00 2.97
2722 2752 2.203209 GGCTTGGGACCGGCTATG 60.203 66.667 0.00 0.00 0.00 2.23
2723 2753 2.590092 GCTTGGGACCGGCTATGT 59.410 61.111 0.00 0.00 0.00 2.29
2724 2754 1.077716 GCTTGGGACCGGCTATGTT 60.078 57.895 0.00 0.00 0.00 2.71
2725 2755 1.376609 GCTTGGGACCGGCTATGTTG 61.377 60.000 0.00 0.00 0.00 3.33
2726 2756 0.251916 CTTGGGACCGGCTATGTTGA 59.748 55.000 0.00 0.00 0.00 3.18
2727 2757 0.251916 TTGGGACCGGCTATGTTGAG 59.748 55.000 0.00 0.00 0.00 3.02
2728 2758 0.616395 TGGGACCGGCTATGTTGAGA 60.616 55.000 0.00 0.00 0.00 3.27
2729 2759 0.179081 GGGACCGGCTATGTTGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
2730 2760 0.535335 GGACCGGCTATGTTGAGACA 59.465 55.000 0.00 0.00 40.71 3.41
2731 2761 1.066430 GGACCGGCTATGTTGAGACAA 60.066 52.381 0.00 0.00 39.66 3.18
2732 2762 2.000447 GACCGGCTATGTTGAGACAAC 59.000 52.381 0.00 7.55 39.66 3.32
2733 2763 1.346395 ACCGGCTATGTTGAGACAACA 59.654 47.619 17.39 17.39 39.66 3.33
2734 2764 2.027192 ACCGGCTATGTTGAGACAACAT 60.027 45.455 25.70 25.70 42.82 2.71
2735 2765 3.196901 ACCGGCTATGTTGAGACAACATA 59.803 43.478 25.32 25.32 40.87 2.29
2740 2770 2.093306 TGTTGAGACAACATAGGCGG 57.907 50.000 12.32 0.00 31.49 6.13
2741 2771 1.621317 TGTTGAGACAACATAGGCGGA 59.379 47.619 12.32 0.00 31.49 5.54
2742 2772 2.271800 GTTGAGACAACATAGGCGGAG 58.728 52.381 9.32 0.00 0.00 4.63
2743 2773 1.557099 TGAGACAACATAGGCGGAGT 58.443 50.000 0.00 0.00 0.00 3.85
2744 2774 1.899814 TGAGACAACATAGGCGGAGTT 59.100 47.619 0.00 0.00 0.00 3.01
2745 2775 2.301870 TGAGACAACATAGGCGGAGTTT 59.698 45.455 0.00 0.00 0.00 2.66
2746 2776 2.930682 GAGACAACATAGGCGGAGTTTC 59.069 50.000 0.00 0.00 0.00 2.78
2747 2777 2.567615 AGACAACATAGGCGGAGTTTCT 59.432 45.455 0.00 0.00 0.00 2.52
2748 2778 3.008049 AGACAACATAGGCGGAGTTTCTT 59.992 43.478 0.00 0.00 0.00 2.52
2749 2779 3.751518 ACAACATAGGCGGAGTTTCTTT 58.248 40.909 0.00 0.00 0.00 2.52
2872 2902 0.758123 TGCTGGTATGATCGCATCCA 59.242 50.000 0.00 0.00 35.94 3.41
2873 2903 1.151668 GCTGGTATGATCGCATCCAC 58.848 55.000 0.00 0.00 35.94 4.02
2875 2905 1.345741 CTGGTATGATCGCATCCACCT 59.654 52.381 13.27 0.00 35.51 4.00
2876 2906 1.070601 TGGTATGATCGCATCCACCTG 59.929 52.381 13.27 0.00 35.51 4.00
2877 2907 1.070758 GGTATGATCGCATCCACCTGT 59.929 52.381 0.00 0.00 35.94 4.00
2878 2908 2.138320 GTATGATCGCATCCACCTGTG 58.862 52.381 0.00 0.00 35.94 3.66
2949 3462 8.774890 AGATGCAGAGCTTAATATTCATACTG 57.225 34.615 0.00 0.00 0.00 2.74
2968 3481 4.734266 ACTGAATTGAGAAGCTTTCCCTT 58.266 39.130 0.00 0.00 0.00 3.95
3009 4744 0.953727 AAACAGCGCTTCAATGCTCA 59.046 45.000 7.50 0.00 40.03 4.26
3053 4788 6.049149 CGGTAGCATATTCAGGGGTATTATG 58.951 44.000 0.00 0.00 0.00 1.90
3057 4792 7.270832 AGCATATTCAGGGGTATTATGCTTA 57.729 36.000 9.32 0.00 44.36 3.09
3128 4863 5.432645 TGTTTGTGTCTTGATGTGGTCTTA 58.567 37.500 0.00 0.00 0.00 2.10
3138 4873 9.553064 GTCTTGATGTGGTCTTAGATTTGATAT 57.447 33.333 0.00 0.00 0.00 1.63
3317 5052 2.303175 GTGTCCCACTAAGTTTTGCCA 58.697 47.619 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 9.139174 GGTTGGACAAAATAACATTTCACATAG 57.861 33.333 0.00 0.00 0.00 2.23
155 157 3.827898 GGGCTCCGAGACCGTGAG 61.828 72.222 3.94 0.00 30.77 3.51
272 274 1.737793 GCTCCCACGTCATTTTGTAGG 59.262 52.381 0.00 0.00 0.00 3.18
288 291 1.807495 CGACTTAGGGGATCGGCTCC 61.807 65.000 0.00 0.00 44.11 4.70
318 323 1.357907 TTCGTTTCGTCGTTGTGGTT 58.642 45.000 0.00 0.00 0.00 3.67
422 444 2.015736 ACTTTGATCTTCGAGCGCAT 57.984 45.000 11.47 0.00 0.00 4.73
455 477 3.502191 TTTTCTGCTGCAACTTTTCGT 57.498 38.095 3.02 0.00 0.00 3.85
779 802 0.459585 CCACCGTCCGATCACGAATT 60.460 55.000 7.13 0.00 42.69 2.17
869 892 5.044030 TGGTAAAACCTTGGATGGGCTTATA 60.044 40.000 0.00 0.00 39.58 0.98
971 995 4.379243 CAGTGAAGGCGCTCCGGT 62.379 66.667 7.64 0.00 37.47 5.28
1075 1099 3.307059 GCATTAATAGGAGGAGTGGCGAT 60.307 47.826 0.00 0.00 0.00 4.58
1077 1101 2.417719 GCATTAATAGGAGGAGTGGCG 58.582 52.381 0.00 0.00 0.00 5.69
1134 1158 1.003839 CGCTGGTTAGGAGGCAACA 60.004 57.895 0.00 0.00 41.41 3.33
1310 1334 3.353836 GAGAACCGCGCAAAGCCA 61.354 61.111 8.75 0.00 44.76 4.75
1339 1363 0.684535 TCCATTCTGCTTCGTGTCCA 59.315 50.000 0.00 0.00 0.00 4.02
1342 1366 1.800805 CACTCCATTCTGCTTCGTGT 58.199 50.000 0.00 0.00 0.00 4.49
1349 1373 2.355132 CTGATTCTGCACTCCATTCTGC 59.645 50.000 0.00 0.00 0.00 4.26
1358 1382 2.437359 GGCGGCTGATTCTGCACT 60.437 61.111 16.12 0.00 40.04 4.40
1522 1549 3.326880 ACGAAAGGGAACAGAGTGGTAAT 59.673 43.478 0.00 0.00 0.00 1.89
1557 1584 2.559231 TGCAGCATTTCAGCATTTCTCA 59.441 40.909 0.00 0.00 36.85 3.27
1594 1624 3.744940 TTCCTCTTGGCCTGAATTCAT 57.255 42.857 8.96 0.00 0.00 2.57
2088 2118 5.125356 ACATGATGTCAAGTCAACTGAACA 58.875 37.500 0.00 1.70 0.00 3.18
2121 2151 1.679977 CAAGGCCTGTGGACATGGG 60.680 63.158 5.69 0.00 29.21 4.00
2366 2396 4.633565 GCGAGATCTTCTCAAACCTTCATT 59.366 41.667 0.00 0.00 43.55 2.57
2435 2465 0.318107 CGTTTCTTGCACCTGCCAAG 60.318 55.000 0.00 0.00 41.18 3.61
2481 2511 9.733556 ATAAATACAATGTTAGACAAGTGTGGA 57.266 29.630 0.00 0.00 33.95 4.02
2608 2638 9.662545 AAACTCAAAAGATTTTTGTTGTTGTTG 57.337 25.926 18.51 0.00 32.54 3.33
2610 2640 9.050601 TGAAACTCAAAAGATTTTTGTTGTTGT 57.949 25.926 18.51 13.08 32.54 3.32
2613 2643 9.657419 AGATGAAACTCAAAAGATTTTTGTTGT 57.343 25.926 12.44 10.27 30.18 3.32
2615 2645 9.317936 GGAGATGAAACTCAAAAGATTTTTGTT 57.682 29.630 12.44 6.25 38.51 2.83
2616 2646 8.477256 TGGAGATGAAACTCAAAAGATTTTTGT 58.523 29.630 12.44 1.25 38.51 2.83
2617 2647 8.876275 TGGAGATGAAACTCAAAAGATTTTTG 57.124 30.769 7.73 7.73 38.51 2.44
2621 2651 9.745018 TCTTATGGAGATGAAACTCAAAAGATT 57.255 29.630 0.00 0.00 38.51 2.40
2622 2652 9.393512 CTCTTATGGAGATGAAACTCAAAAGAT 57.606 33.333 0.00 0.00 44.45 2.40
2623 2653 8.378565 ACTCTTATGGAGATGAAACTCAAAAGA 58.621 33.333 0.00 0.00 44.45 2.52
2624 2654 8.449397 CACTCTTATGGAGATGAAACTCAAAAG 58.551 37.037 0.00 0.00 44.45 2.27
2625 2655 7.391554 CCACTCTTATGGAGATGAAACTCAAAA 59.608 37.037 0.00 0.00 44.45 2.44
2626 2656 6.881065 CCACTCTTATGGAGATGAAACTCAAA 59.119 38.462 0.00 0.00 44.45 2.69
2627 2657 6.409704 CCACTCTTATGGAGATGAAACTCAA 58.590 40.000 0.00 0.00 44.45 3.02
2628 2658 5.627735 GCCACTCTTATGGAGATGAAACTCA 60.628 44.000 0.00 0.00 44.45 3.41
2629 2659 4.813697 GCCACTCTTATGGAGATGAAACTC 59.186 45.833 0.00 0.00 44.45 3.01
2630 2660 4.472833 AGCCACTCTTATGGAGATGAAACT 59.527 41.667 0.00 0.00 44.45 2.66
2631 2661 4.574013 CAGCCACTCTTATGGAGATGAAAC 59.426 45.833 0.00 0.00 44.45 2.78
2632 2662 4.471025 TCAGCCACTCTTATGGAGATGAAA 59.529 41.667 0.00 0.00 44.45 2.69
2633 2663 4.033009 TCAGCCACTCTTATGGAGATGAA 58.967 43.478 0.00 0.00 44.45 2.57
2634 2664 3.640498 CTCAGCCACTCTTATGGAGATGA 59.360 47.826 0.00 0.00 44.45 2.92
2635 2665 3.387374 ACTCAGCCACTCTTATGGAGATG 59.613 47.826 0.00 0.00 44.45 2.90
2636 2666 3.652055 ACTCAGCCACTCTTATGGAGAT 58.348 45.455 0.00 0.00 44.45 2.75
2637 2667 3.107402 ACTCAGCCACTCTTATGGAGA 57.893 47.619 0.00 0.00 44.45 3.71
2638 2668 3.902881 AACTCAGCCACTCTTATGGAG 57.097 47.619 0.00 0.00 43.02 3.86
2639 2669 4.640771 AAAACTCAGCCACTCTTATGGA 57.359 40.909 0.00 0.00 43.02 3.41
2640 2670 6.375455 ACATAAAAACTCAGCCACTCTTATGG 59.625 38.462 0.00 0.00 43.26 2.74
2641 2671 7.383102 ACATAAAAACTCAGCCACTCTTATG 57.617 36.000 0.00 0.00 33.66 1.90
2642 2672 7.094205 CCAACATAAAAACTCAGCCACTCTTAT 60.094 37.037 0.00 0.00 0.00 1.73
2643 2673 6.206634 CCAACATAAAAACTCAGCCACTCTTA 59.793 38.462 0.00 0.00 0.00 2.10
2644 2674 5.010012 CCAACATAAAAACTCAGCCACTCTT 59.990 40.000 0.00 0.00 0.00 2.85
2645 2675 4.520492 CCAACATAAAAACTCAGCCACTCT 59.480 41.667 0.00 0.00 0.00 3.24
2646 2676 4.798574 CCAACATAAAAACTCAGCCACTC 58.201 43.478 0.00 0.00 0.00 3.51
2647 2677 3.005791 GCCAACATAAAAACTCAGCCACT 59.994 43.478 0.00 0.00 0.00 4.00
2648 2678 3.005791 AGCCAACATAAAAACTCAGCCAC 59.994 43.478 0.00 0.00 0.00 5.01
2649 2679 3.230134 AGCCAACATAAAAACTCAGCCA 58.770 40.909 0.00 0.00 0.00 4.75
2650 2680 3.670627 CGAGCCAACATAAAAACTCAGCC 60.671 47.826 0.00 0.00 0.00 4.85
2651 2681 3.492313 CGAGCCAACATAAAAACTCAGC 58.508 45.455 0.00 0.00 0.00 4.26
2652 2682 3.492313 GCGAGCCAACATAAAAACTCAG 58.508 45.455 0.00 0.00 0.00 3.35
2653 2683 2.227865 GGCGAGCCAACATAAAAACTCA 59.772 45.455 9.58 0.00 35.81 3.41
2654 2684 2.227865 TGGCGAGCCAACATAAAAACTC 59.772 45.455 15.24 0.00 44.12 3.01
2655 2685 2.235016 TGGCGAGCCAACATAAAAACT 58.765 42.857 15.24 0.00 44.12 2.66
2656 2686 2.715737 TGGCGAGCCAACATAAAAAC 57.284 45.000 15.24 0.00 44.12 2.43
2669 2699 1.009829 GTTGTGATAGGCTTGGCGAG 58.990 55.000 0.00 0.00 0.00 5.03
2670 2700 0.392461 GGTTGTGATAGGCTTGGCGA 60.392 55.000 0.00 0.00 0.00 5.54
2671 2701 1.376609 GGGTTGTGATAGGCTTGGCG 61.377 60.000 0.00 0.00 0.00 5.69
2672 2702 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.000 0.00 0.00 0.00 4.52
2673 2703 1.408822 GGAGGGTTGTGATAGGCTTGG 60.409 57.143 0.00 0.00 0.00 3.61
2674 2704 1.561542 AGGAGGGTTGTGATAGGCTTG 59.438 52.381 0.00 0.00 0.00 4.01
2675 2705 1.840635 GAGGAGGGTTGTGATAGGCTT 59.159 52.381 0.00 0.00 0.00 4.35
2676 2706 1.501582 GAGGAGGGTTGTGATAGGCT 58.498 55.000 0.00 0.00 0.00 4.58
2677 2707 0.470341 GGAGGAGGGTTGTGATAGGC 59.530 60.000 0.00 0.00 0.00 3.93
2678 2708 2.182516 AGGAGGAGGGTTGTGATAGG 57.817 55.000 0.00 0.00 0.00 2.57
2679 2709 4.141688 GGTAAAGGAGGAGGGTTGTGATAG 60.142 50.000 0.00 0.00 0.00 2.08
2680 2710 3.778629 GGTAAAGGAGGAGGGTTGTGATA 59.221 47.826 0.00 0.00 0.00 2.15
2681 2711 2.576648 GGTAAAGGAGGAGGGTTGTGAT 59.423 50.000 0.00 0.00 0.00 3.06
2682 2712 1.982958 GGTAAAGGAGGAGGGTTGTGA 59.017 52.381 0.00 0.00 0.00 3.58
2683 2713 1.004394 GGGTAAAGGAGGAGGGTTGTG 59.996 57.143 0.00 0.00 0.00 3.33
2684 2714 1.369403 GGGTAAAGGAGGAGGGTTGT 58.631 55.000 0.00 0.00 0.00 3.32
2685 2715 0.252197 CGGGTAAAGGAGGAGGGTTG 59.748 60.000 0.00 0.00 0.00 3.77
2686 2716 0.912968 CCGGGTAAAGGAGGAGGGTT 60.913 60.000 0.00 0.00 0.00 4.11
2687 2717 1.306739 CCGGGTAAAGGAGGAGGGT 60.307 63.158 0.00 0.00 0.00 4.34
2688 2718 2.070650 CCCGGGTAAAGGAGGAGGG 61.071 68.421 14.18 0.00 0.00 4.30
2689 2719 2.743179 GCCCGGGTAAAGGAGGAGG 61.743 68.421 24.63 0.00 0.00 4.30
2690 2720 1.272554 AAGCCCGGGTAAAGGAGGAG 61.273 60.000 24.63 0.00 0.00 3.69
2691 2721 1.229723 AAGCCCGGGTAAAGGAGGA 60.230 57.895 24.63 0.00 0.00 3.71
2692 2722 1.077716 CAAGCCCGGGTAAAGGAGG 60.078 63.158 24.63 0.00 0.00 4.30
2693 2723 1.077716 CCAAGCCCGGGTAAAGGAG 60.078 63.158 24.63 5.31 0.00 3.69
2694 2724 2.608550 CCCAAGCCCGGGTAAAGGA 61.609 63.158 24.63 0.00 41.83 3.36
2695 2725 2.044352 CCCAAGCCCGGGTAAAGG 60.044 66.667 24.63 18.41 41.83 3.11
2704 2734 3.489513 ATAGCCGGTCCCAAGCCC 61.490 66.667 1.90 0.00 0.00 5.19
2705 2735 2.203209 CATAGCCGGTCCCAAGCC 60.203 66.667 1.90 0.00 0.00 4.35
2706 2736 1.077716 AACATAGCCGGTCCCAAGC 60.078 57.895 1.90 0.00 0.00 4.01
2707 2737 0.251916 TCAACATAGCCGGTCCCAAG 59.748 55.000 1.90 0.00 0.00 3.61
2708 2738 0.251916 CTCAACATAGCCGGTCCCAA 59.748 55.000 1.90 0.00 0.00 4.12
2709 2739 0.616395 TCTCAACATAGCCGGTCCCA 60.616 55.000 1.90 0.00 0.00 4.37
2710 2740 0.179081 GTCTCAACATAGCCGGTCCC 60.179 60.000 1.90 0.00 0.00 4.46
2711 2741 0.535335 TGTCTCAACATAGCCGGTCC 59.465 55.000 1.90 0.00 0.00 4.46
2712 2742 2.000447 GTTGTCTCAACATAGCCGGTC 59.000 52.381 1.90 0.00 34.73 4.79
2713 2743 1.346395 TGTTGTCTCAACATAGCCGGT 59.654 47.619 1.90 0.00 34.73 5.28
2714 2744 2.093306 TGTTGTCTCAACATAGCCGG 57.907 50.000 10.63 0.00 34.73 6.13
2719 2749 3.449377 TCCGCCTATGTTGTCTCAACATA 59.551 43.478 24.21 24.21 40.87 2.29
2720 2750 2.236146 TCCGCCTATGTTGTCTCAACAT 59.764 45.455 24.50 24.50 42.82 2.71
2721 2751 1.621317 TCCGCCTATGTTGTCTCAACA 59.379 47.619 15.83 15.83 34.31 3.33
2722 2752 2.271800 CTCCGCCTATGTTGTCTCAAC 58.728 52.381 5.78 5.78 0.00 3.18
2723 2753 1.899814 ACTCCGCCTATGTTGTCTCAA 59.100 47.619 0.00 0.00 0.00 3.02
2724 2754 1.557099 ACTCCGCCTATGTTGTCTCA 58.443 50.000 0.00 0.00 0.00 3.27
2725 2755 2.674796 AACTCCGCCTATGTTGTCTC 57.325 50.000 0.00 0.00 0.00 3.36
2726 2756 2.567615 AGAAACTCCGCCTATGTTGTCT 59.432 45.455 0.00 0.00 0.00 3.41
2727 2757 2.973945 AGAAACTCCGCCTATGTTGTC 58.026 47.619 0.00 0.00 0.00 3.18
2728 2758 3.418684 AAGAAACTCCGCCTATGTTGT 57.581 42.857 0.00 0.00 0.00 3.32
2729 2759 5.873179 TTAAAGAAACTCCGCCTATGTTG 57.127 39.130 0.00 0.00 0.00 3.33
2730 2760 5.414765 CCTTTAAAGAAACTCCGCCTATGTT 59.585 40.000 16.98 0.00 0.00 2.71
2731 2761 4.941873 CCTTTAAAGAAACTCCGCCTATGT 59.058 41.667 16.98 0.00 0.00 2.29
2732 2762 5.183228 TCCTTTAAAGAAACTCCGCCTATG 58.817 41.667 16.98 0.00 0.00 2.23
2733 2763 5.431179 TCCTTTAAAGAAACTCCGCCTAT 57.569 39.130 16.98 0.00 0.00 2.57
2734 2764 4.895668 TCCTTTAAAGAAACTCCGCCTA 57.104 40.909 16.98 0.00 0.00 3.93
2735 2765 3.782656 TCCTTTAAAGAAACTCCGCCT 57.217 42.857 16.98 0.00 0.00 5.52
2736 2766 4.733850 CATTCCTTTAAAGAAACTCCGCC 58.266 43.478 16.98 0.00 0.00 6.13
2737 2767 4.166523 GCATTCCTTTAAAGAAACTCCGC 58.833 43.478 16.98 6.06 0.00 5.54
2738 2768 5.371115 TGCATTCCTTTAAAGAAACTCCG 57.629 39.130 16.98 0.00 0.00 4.63
2739 2769 6.420903 GTGTTGCATTCCTTTAAAGAAACTCC 59.579 38.462 16.98 1.54 0.00 3.85
2740 2770 6.142320 CGTGTTGCATTCCTTTAAAGAAACTC 59.858 38.462 16.98 9.90 0.00 3.01
2741 2771 5.977129 CGTGTTGCATTCCTTTAAAGAAACT 59.023 36.000 16.98 0.00 0.00 2.66
2742 2772 5.974751 TCGTGTTGCATTCCTTTAAAGAAAC 59.025 36.000 16.98 10.54 0.00 2.78
2743 2773 6.137794 TCGTGTTGCATTCCTTTAAAGAAA 57.862 33.333 16.98 2.52 0.00 2.52
2744 2774 5.278266 CCTCGTGTTGCATTCCTTTAAAGAA 60.278 40.000 16.98 9.24 0.00 2.52
2745 2775 4.215399 CCTCGTGTTGCATTCCTTTAAAGA 59.785 41.667 16.98 0.00 0.00 2.52
2746 2776 4.215399 TCCTCGTGTTGCATTCCTTTAAAG 59.785 41.667 8.32 8.32 0.00 1.85
2747 2777 4.023536 GTCCTCGTGTTGCATTCCTTTAAA 60.024 41.667 0.00 0.00 0.00 1.52
2748 2778 3.500680 GTCCTCGTGTTGCATTCCTTTAA 59.499 43.478 0.00 0.00 0.00 1.52
2749 2779 3.071479 GTCCTCGTGTTGCATTCCTTTA 58.929 45.455 0.00 0.00 0.00 1.85
2872 2902 2.387757 ACTCAATTTTGTGCCACAGGT 58.612 42.857 0.00 0.00 0.00 4.00
2873 2903 3.457610 AACTCAATTTTGTGCCACAGG 57.542 42.857 0.00 0.00 0.00 4.00
2875 2905 8.986847 CATAAATTAACTCAATTTTGTGCCACA 58.013 29.630 0.00 0.00 42.93 4.17
2876 2906 8.442384 CCATAAATTAACTCAATTTTGTGCCAC 58.558 33.333 0.74 0.00 42.93 5.01
2877 2907 8.370940 TCCATAAATTAACTCAATTTTGTGCCA 58.629 29.630 0.74 0.00 42.93 4.92
2878 2908 8.770438 TCCATAAATTAACTCAATTTTGTGCC 57.230 30.769 0.74 0.00 42.93 5.01
2881 2911 9.382275 GCCATCCATAAATTAACTCAATTTTGT 57.618 29.630 0.74 0.00 42.93 2.83
2883 2913 9.603921 CTGCCATCCATAAATTAACTCAATTTT 57.396 29.630 0.74 0.00 42.93 1.82
2884 2914 7.712205 GCTGCCATCCATAAATTAACTCAATTT 59.288 33.333 0.00 1.12 46.31 1.82
2885 2915 7.212274 GCTGCCATCCATAAATTAACTCAATT 58.788 34.615 0.00 0.00 38.54 2.32
2886 2916 6.239402 GGCTGCCATCCATAAATTAACTCAAT 60.239 38.462 15.17 0.00 0.00 2.57
2887 2917 5.068987 GGCTGCCATCCATAAATTAACTCAA 59.931 40.000 15.17 0.00 0.00 3.02
2949 3462 8.207545 TCTATCTAAGGGAAAGCTTCTCAATTC 58.792 37.037 0.00 0.00 30.58 2.17
3009 4744 4.020128 ACCGCTCTTTTTCTACCTGATTCT 60.020 41.667 0.00 0.00 0.00 2.40
3053 4788 8.880750 CAACTACCCAGACTAGTAATTTTAAGC 58.119 37.037 0.00 0.00 0.00 3.09
3057 4792 7.325725 ACCAACTACCCAGACTAGTAATTTT 57.674 36.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.