Multiple sequence alignment - TraesCS4A01G136900

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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 TraesCS4A01G136900 chr4A 100.000 2865 0 0 1 2865 195314546 195311682 0.000000e+00 5291.0
1 TraesCS4A01G136900 chr4A 97.101 1311 24 1 2 1298 225578828 225580138 0.000000e+00 2198.0
2 TraesCS4A01G136900 chr4A 95.077 1300 34 6 1378 2673 225582460 225583733 0.000000e+00 2019.0
3 TraesCS4A01G136900 chr4A 97.753 89 2 0 1299 1387 225580184 225580272 1.370000e-33 154.0
4 TraesCS4A01G136900 chr4A 92.381 105 8 0 2569 2673 638482054 638481950 1.780000e-32 150.0
5 TraesCS4A01G136900 chr5D 95.418 1375 41 5 1302 2674 437571793 437570439 0.000000e+00 2170.0
6 TraesCS4A01G136900 chr5D 93.821 1327 47 7 2 1301 437573157 437571839 0.000000e+00 1964.0
7 TraesCS4A01G136900 chr5B 93.419 1322 65 7 2 1301 261376465 261375144 0.000000e+00 1940.0
8 TraesCS4A01G136900 chr5B 89.293 1401 74 19 1302 2673 261375098 261373745 0.000000e+00 1687.0
9 TraesCS4A01G136900 chr3B 88.031 1153 85 27 173 1297 527299605 527298478 0.000000e+00 1315.0
10 TraesCS4A01G136900 chr3B 86.275 1122 80 29 1429 2529 527298132 527297064 0.000000e+00 1151.0
11 TraesCS4A01G136900 chr3B 91.406 128 9 2 1302 1428 527298409 527298283 1.060000e-39 174.0
12 TraesCS4A01G136900 chr3A 85.509 1042 90 23 1429 2446 522178154 522177150 0.000000e+00 1031.0
13 TraesCS4A01G136900 chr3A 93.095 391 27 0 911 1301 522179061 522178671 8.900000e-160 573.0
14 TraesCS4A01G136900 chr3A 82.773 476 31 14 478 925 522179556 522179104 7.490000e-101 377.0
15 TraesCS4A01G136900 chr3A 90.043 231 17 3 133 358 522179795 522179566 7.760000e-76 294.0
16 TraesCS4A01G136900 chr3A 92.126 127 10 0 1302 1428 522178625 522178499 2.270000e-41 180.0
17 TraesCS4A01G136900 chr3D 84.044 1009 85 28 1473 2449 401875217 401874253 0.000000e+00 902.0
18 TraesCS4A01G136900 chr3D 89.344 732 33 21 602 1301 401876260 401875542 0.000000e+00 878.0
19 TraesCS4A01G136900 chr3D 87.750 400 38 8 133 523 401876657 401876260 9.360000e-125 457.0
20 TraesCS4A01G136900 chr3D 92.126 127 5 2 1 126 404855390 404855268 1.060000e-39 174.0
21 TraesCS4A01G136900 chr3D 93.478 92 6 0 2582 2673 404851641 404851550 1.380000e-28 137.0
22 TraesCS4A01G136900 chr3D 96.774 62 2 0 1302 1363 401875496 401875435 1.400000e-18 104.0
23 TraesCS4A01G136900 chr4D 90.751 173 15 1 2673 2844 296268511 296268683 2.220000e-56 230.0
24 TraesCS4A01G136900 chr1A 97.037 135 3 1 1 134 563805438 563805304 2.870000e-55 226.0
25 TraesCS4A01G136900 chr1A 96.124 129 5 0 6 134 559362887 559362759 8.040000e-51 211.0
26 TraesCS4A01G136900 chr1A 92.437 119 8 1 2566 2684 563801651 563801534 4.910000e-38 169.0
27 TraesCS4A01G136900 chr1A 90.833 120 10 1 2566 2684 559359104 559358985 2.950000e-35 159.0
28 TraesCS4A01G136900 chr5A 96.296 135 4 1 1 134 45451686 45451820 1.340000e-53 220.0
29 TraesCS4A01G136900 chr5A 94.815 135 6 1 1 134 702768129 702768263 2.890000e-50 209.0
30 TraesCS4A01G136900 chr7A 92.188 64 5 0 5 68 299530066 299530003 1.090000e-14 91.6


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 TraesCS4A01G136900 chr4A 195311682 195314546 2864 True 5291.00 5291 100.000000 1 2865 1 chr4A.!!$R1 2864
1 TraesCS4A01G136900 chr4A 225578828 225583733 4905 False 1457.00 2198 96.643667 2 2673 3 chr4A.!!$F1 2671
2 TraesCS4A01G136900 chr5D 437570439 437573157 2718 True 2067.00 2170 94.619500 2 2674 2 chr5D.!!$R1 2672
3 TraesCS4A01G136900 chr5B 261373745 261376465 2720 True 1813.50 1940 91.356000 2 2673 2 chr5B.!!$R1 2671
4 TraesCS4A01G136900 chr3B 527297064 527299605 2541 True 880.00 1315 88.570667 173 2529 3 chr3B.!!$R1 2356
5 TraesCS4A01G136900 chr3A 522177150 522179795 2645 True 491.00 1031 88.709200 133 2446 5 chr3A.!!$R1 2313
6 TraesCS4A01G136900 chr3D 401874253 401876657 2404 True 585.25 902 89.478000 133 2449 4 chr3D.!!$R1 2316

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
677 705 2.476619 CGTTACTTCTTGCTGACAGTGG 59.523 50.0 3.99 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 5425 0.251033 GGTTCTTTGGTTAGGCGGGT 60.251 55.0 0.0 0.0 0.0 5.28 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
281 295 9.528489 ACTGGTTAATTATAAGTTGGTGACATT 57.472 29.630 0.00 0.00 42.32 2.71
310 324 6.603237 TCTGATATGTCGCAAAATCGAATT 57.397 33.333 0.00 0.00 40.43 2.17
442 457 5.627499 TGCCAATGTAGTTTGATTCAGAC 57.373 39.130 0.00 0.00 0.00 3.51
677 705 2.476619 CGTTACTTCTTGCTGACAGTGG 59.523 50.000 3.99 0.00 0.00 4.00
743 792 5.105351 TGTCGTGAAGGACATAGATGTGAAT 60.105 40.000 0.00 0.00 41.76 2.57
885 948 8.579850 AGAATTACAAATTTGGATGCACTCTA 57.420 30.769 21.74 0.00 0.00 2.43
1067 1192 4.195416 CCCCTGAATGAAGAGAAAGCTAC 58.805 47.826 0.00 0.00 0.00 3.58
1170 1295 4.644103 ACAGCTTTCCATTATGCACATC 57.356 40.909 0.00 0.00 0.00 3.06
1615 4406 5.172687 TGCCCTACATACAATCTTGTCAA 57.827 39.130 0.00 0.00 42.35 3.18
1717 4509 0.687354 AGCTCGAGAGGGAAAAGCAA 59.313 50.000 18.75 0.00 35.42 3.91
1809 4601 4.699522 GGCCTTCACTTCCGGCGT 62.700 66.667 6.01 0.00 44.68 5.68
2024 4834 8.696374 GTCGATGGAGGATGATATATTCCTTTA 58.304 37.037 7.30 1.72 42.48 1.85
2083 4905 3.641906 CTGGTAGTAATGAGGTACCTGGG 59.358 52.174 22.10 0.00 37.66 4.45
2084 4906 3.013188 TGGTAGTAATGAGGTACCTGGGT 59.987 47.826 22.10 6.08 37.66 4.51
2098 4920 4.362470 ACCTGGGTTTGTAGTTACTTCC 57.638 45.455 0.00 0.00 0.00 3.46
2309 5158 1.133199 TGGTGGGAGAAAATGCACCTT 60.133 47.619 0.00 0.00 34.12 3.50
2674 5543 2.422127 GCGCAGGCAATTTTCCTAGTAA 59.578 45.455 0.30 0.00 39.62 2.24
2675 5544 3.487544 GCGCAGGCAATTTTCCTAGTAAG 60.488 47.826 0.30 0.00 39.62 2.34
2676 5545 3.938963 CGCAGGCAATTTTCCTAGTAAGA 59.061 43.478 0.00 0.00 31.52 2.10
2677 5546 4.034510 CGCAGGCAATTTTCCTAGTAAGAG 59.965 45.833 0.00 0.00 31.52 2.85
2678 5547 4.944317 GCAGGCAATTTTCCTAGTAAGAGT 59.056 41.667 0.00 0.00 31.52 3.24
2679 5548 6.113411 GCAGGCAATTTTCCTAGTAAGAGTA 58.887 40.000 0.00 0.00 31.52 2.59
2680 5549 6.598064 GCAGGCAATTTTCCTAGTAAGAGTAA 59.402 38.462 0.00 0.00 31.52 2.24
2681 5550 7.120726 GCAGGCAATTTTCCTAGTAAGAGTAAA 59.879 37.037 0.00 0.00 31.52 2.01
2682 5551 9.010029 CAGGCAATTTTCCTAGTAAGAGTAAAA 57.990 33.333 0.00 0.00 31.52 1.52
2683 5552 9.755122 AGGCAATTTTCCTAGTAAGAGTAAAAT 57.245 29.630 0.00 0.00 30.79 1.82
2698 5567 8.990163 AAGAGTAAAATTTTGGTCTTACTCCA 57.010 30.769 20.05 0.00 45.96 3.86
2699 5568 8.392372 AGAGTAAAATTTTGGTCTTACTCCAC 57.608 34.615 18.87 5.26 45.96 4.02
2700 5569 8.218488 AGAGTAAAATTTTGGTCTTACTCCACT 58.782 33.333 18.87 9.05 45.96 4.00
2701 5570 9.498176 GAGTAAAATTTTGGTCTTACTCCACTA 57.502 33.333 13.76 0.00 42.01 2.74
2702 5571 9.856162 AGTAAAATTTTGGTCTTACTCCACTAA 57.144 29.630 13.76 0.00 30.57 2.24
2705 5574 7.611213 AATTTTGGTCTTACTCCACTAATCG 57.389 36.000 0.00 0.00 34.45 3.34
2706 5575 5.988310 TTTGGTCTTACTCCACTAATCGA 57.012 39.130 0.00 0.00 34.45 3.59
2707 5576 4.978083 TGGTCTTACTCCACTAATCGAC 57.022 45.455 0.00 0.00 0.00 4.20
2708 5577 4.338012 TGGTCTTACTCCACTAATCGACA 58.662 43.478 0.00 0.00 0.00 4.35
2709 5578 4.157289 TGGTCTTACTCCACTAATCGACAC 59.843 45.833 0.00 0.00 0.00 3.67
2710 5579 4.398673 GGTCTTACTCCACTAATCGACACT 59.601 45.833 0.00 0.00 0.00 3.55
2711 5580 5.105837 GGTCTTACTCCACTAATCGACACTT 60.106 44.000 0.00 0.00 0.00 3.16
2712 5581 6.094603 GGTCTTACTCCACTAATCGACACTTA 59.905 42.308 0.00 0.00 0.00 2.24
2713 5582 7.188157 GTCTTACTCCACTAATCGACACTTAG 58.812 42.308 3.30 3.30 33.36 2.18
2714 5583 4.373348 ACTCCACTAATCGACACTTAGC 57.627 45.455 4.54 0.00 30.80 3.09
2715 5584 3.130693 ACTCCACTAATCGACACTTAGCC 59.869 47.826 4.54 0.00 30.80 3.93
2716 5585 3.093814 TCCACTAATCGACACTTAGCCA 58.906 45.455 4.54 0.00 30.80 4.75
2717 5586 3.512329 TCCACTAATCGACACTTAGCCAA 59.488 43.478 4.54 0.00 30.80 4.52
2718 5587 4.161565 TCCACTAATCGACACTTAGCCAAT 59.838 41.667 4.54 0.00 30.80 3.16
2719 5588 4.508124 CCACTAATCGACACTTAGCCAATC 59.492 45.833 4.54 0.00 30.80 2.67
2720 5589 5.352284 CACTAATCGACACTTAGCCAATCT 58.648 41.667 4.54 0.00 30.80 2.40
2721 5590 5.460419 CACTAATCGACACTTAGCCAATCTC 59.540 44.000 4.54 0.00 30.80 2.75
2722 5591 4.744795 AATCGACACTTAGCCAATCTCT 57.255 40.909 0.00 0.00 0.00 3.10
2723 5592 4.744795 ATCGACACTTAGCCAATCTCTT 57.255 40.909 0.00 0.00 0.00 2.85
2724 5593 5.854010 ATCGACACTTAGCCAATCTCTTA 57.146 39.130 0.00 0.00 0.00 2.10
2725 5594 5.654603 TCGACACTTAGCCAATCTCTTAA 57.345 39.130 0.00 0.00 0.00 1.85
2726 5595 6.032956 TCGACACTTAGCCAATCTCTTAAA 57.967 37.500 0.00 0.00 0.00 1.52
2727 5596 5.867716 TCGACACTTAGCCAATCTCTTAAAC 59.132 40.000 0.00 0.00 0.00 2.01
2728 5597 5.063564 CGACACTTAGCCAATCTCTTAAACC 59.936 44.000 0.00 0.00 0.00 3.27
2729 5598 4.935808 ACACTTAGCCAATCTCTTAAACCG 59.064 41.667 0.00 0.00 0.00 4.44
2730 5599 4.332819 CACTTAGCCAATCTCTTAAACCGG 59.667 45.833 0.00 0.00 0.00 5.28
2731 5600 4.019591 ACTTAGCCAATCTCTTAAACCGGT 60.020 41.667 0.00 0.00 0.00 5.28
2732 5601 3.434940 AGCCAATCTCTTAAACCGGTT 57.565 42.857 15.86 15.86 0.00 4.44
2733 5602 4.563140 AGCCAATCTCTTAAACCGGTTA 57.437 40.909 22.60 4.69 0.00 2.85
2734 5603 4.514401 AGCCAATCTCTTAAACCGGTTAG 58.486 43.478 22.60 15.72 0.00 2.34
2735 5604 4.224370 AGCCAATCTCTTAAACCGGTTAGA 59.776 41.667 22.60 19.66 0.00 2.10
2736 5605 4.571176 GCCAATCTCTTAAACCGGTTAGAG 59.429 45.833 29.70 29.70 0.00 2.43
2737 5606 5.626116 GCCAATCTCTTAAACCGGTTAGAGA 60.626 44.000 35.38 35.38 33.91 3.10
2738 5607 6.403878 CCAATCTCTTAAACCGGTTAGAGAA 58.596 40.000 36.23 25.56 33.50 2.87
2739 5608 6.313164 CCAATCTCTTAAACCGGTTAGAGAAC 59.687 42.308 36.23 0.00 33.50 3.01
2740 5609 6.854091 ATCTCTTAAACCGGTTAGAGAACT 57.146 37.500 36.23 25.43 33.50 3.01
2741 5610 7.951347 ATCTCTTAAACCGGTTAGAGAACTA 57.049 36.000 36.23 22.94 33.50 2.24
2742 5611 7.765695 TCTCTTAAACCGGTTAGAGAACTAA 57.234 36.000 33.20 20.60 35.74 2.24
2743 5612 7.824672 TCTCTTAAACCGGTTAGAGAACTAAG 58.175 38.462 33.20 26.53 38.97 2.18
2744 5613 6.928520 TCTTAAACCGGTTAGAGAACTAAGG 58.071 40.000 22.60 7.76 38.97 2.69
2745 5614 6.721208 TCTTAAACCGGTTAGAGAACTAAGGA 59.279 38.462 22.60 9.71 38.97 3.36
2746 5615 5.813513 AAACCGGTTAGAGAACTAAGGAA 57.186 39.130 22.60 0.00 38.97 3.36
2747 5616 6.370186 AAACCGGTTAGAGAACTAAGGAAT 57.630 37.500 22.60 0.00 38.97 3.01
2748 5617 6.370186 AACCGGTTAGAGAACTAAGGAATT 57.630 37.500 20.78 0.00 38.97 2.17
2749 5618 6.370186 ACCGGTTAGAGAACTAAGGAATTT 57.630 37.500 0.00 0.00 38.97 1.82
2750 5619 7.486407 ACCGGTTAGAGAACTAAGGAATTTA 57.514 36.000 0.00 0.00 38.97 1.40
2751 5620 7.910584 ACCGGTTAGAGAACTAAGGAATTTAA 58.089 34.615 0.00 0.00 38.97 1.52
2752 5621 8.546322 ACCGGTTAGAGAACTAAGGAATTTAAT 58.454 33.333 0.00 0.00 38.97 1.40
2753 5622 9.392259 CCGGTTAGAGAACTAAGGAATTTAATT 57.608 33.333 0.00 0.00 38.97 1.40
2763 5632 9.642343 AACTAAGGAATTTAATTATCACCCTCC 57.358 33.333 0.00 0.00 0.00 4.30
2764 5633 8.225416 ACTAAGGAATTTAATTATCACCCTCCC 58.775 37.037 0.00 0.00 0.00 4.30
2765 5634 6.606241 AGGAATTTAATTATCACCCTCCCA 57.394 37.500 0.00 0.00 0.00 4.37
2766 5635 6.614657 AGGAATTTAATTATCACCCTCCCAG 58.385 40.000 0.00 0.00 0.00 4.45
2767 5636 6.392842 AGGAATTTAATTATCACCCTCCCAGA 59.607 38.462 0.00 0.00 0.00 3.86
2768 5637 6.490381 GGAATTTAATTATCACCCTCCCAGAC 59.510 42.308 0.00 0.00 0.00 3.51
2769 5638 4.682778 TTAATTATCACCCTCCCAGACG 57.317 45.455 0.00 0.00 0.00 4.18
2770 5639 2.471815 ATTATCACCCTCCCAGACGA 57.528 50.000 0.00 0.00 0.00 4.20
2771 5640 1.776662 TTATCACCCTCCCAGACGAG 58.223 55.000 0.00 0.00 0.00 4.18
2772 5641 0.629596 TATCACCCTCCCAGACGAGT 59.370 55.000 0.00 0.00 0.00 4.18
2773 5642 0.972983 ATCACCCTCCCAGACGAGTG 60.973 60.000 0.00 0.00 0.00 3.51
2774 5643 1.606601 CACCCTCCCAGACGAGTGA 60.607 63.158 0.00 0.00 0.00 3.41
2775 5644 1.155390 ACCCTCCCAGACGAGTGAA 59.845 57.895 0.00 0.00 0.00 3.18
2776 5645 0.252284 ACCCTCCCAGACGAGTGAAT 60.252 55.000 0.00 0.00 0.00 2.57
2777 5646 1.006758 ACCCTCCCAGACGAGTGAATA 59.993 52.381 0.00 0.00 0.00 1.75
2778 5647 2.320781 CCCTCCCAGACGAGTGAATAT 58.679 52.381 0.00 0.00 0.00 1.28
2779 5648 3.117246 ACCCTCCCAGACGAGTGAATATA 60.117 47.826 0.00 0.00 0.00 0.86
2780 5649 3.256136 CCCTCCCAGACGAGTGAATATAC 59.744 52.174 0.00 0.00 0.00 1.47
2781 5650 4.145807 CCTCCCAGACGAGTGAATATACT 58.854 47.826 0.00 0.00 0.00 2.12
2782 5651 4.585162 CCTCCCAGACGAGTGAATATACTT 59.415 45.833 0.00 0.00 0.00 2.24
2783 5652 5.508153 CCTCCCAGACGAGTGAATATACTTG 60.508 48.000 0.00 0.00 37.94 3.16
2784 5653 5.198207 TCCCAGACGAGTGAATATACTTGA 58.802 41.667 0.00 0.00 35.93 3.02
2785 5654 5.833667 TCCCAGACGAGTGAATATACTTGAT 59.166 40.000 0.00 0.00 35.93 2.57
2786 5655 5.923114 CCCAGACGAGTGAATATACTTGATG 59.077 44.000 0.00 0.00 35.93 3.07
2787 5656 6.239036 CCCAGACGAGTGAATATACTTGATGA 60.239 42.308 0.00 0.00 35.93 2.92
2788 5657 6.638873 CCAGACGAGTGAATATACTTGATGAC 59.361 42.308 0.00 0.00 35.93 3.06
2789 5658 7.196331 CAGACGAGTGAATATACTTGATGACA 58.804 38.462 0.00 0.00 35.93 3.58
2790 5659 7.378194 CAGACGAGTGAATATACTTGATGACAG 59.622 40.741 0.00 0.00 35.93 3.51
2791 5660 6.507900 ACGAGTGAATATACTTGATGACAGG 58.492 40.000 0.00 0.00 35.93 4.00
2792 5661 5.403766 CGAGTGAATATACTTGATGACAGGC 59.596 44.000 0.00 0.00 34.59 4.85
2793 5662 6.239217 AGTGAATATACTTGATGACAGGCA 57.761 37.500 0.00 0.00 0.00 4.75
2794 5663 6.286758 AGTGAATATACTTGATGACAGGCAG 58.713 40.000 0.00 0.00 0.00 4.85
2795 5664 6.051717 GTGAATATACTTGATGACAGGCAGT 58.948 40.000 0.00 0.00 0.00 4.40
2796 5665 7.069950 AGTGAATATACTTGATGACAGGCAGTA 59.930 37.037 0.00 0.00 0.00 2.74
2797 5666 7.710907 GTGAATATACTTGATGACAGGCAGTAA 59.289 37.037 0.00 0.00 0.00 2.24
2798 5667 8.264347 TGAATATACTTGATGACAGGCAGTAAA 58.736 33.333 0.00 0.00 0.00 2.01
2799 5668 9.109393 GAATATACTTGATGACAGGCAGTAAAA 57.891 33.333 0.00 0.00 0.00 1.52
2800 5669 9.461312 AATATACTTGATGACAGGCAGTAAAAA 57.539 29.630 0.00 0.00 0.00 1.94
2801 5670 7.944729 ATACTTGATGACAGGCAGTAAAAAT 57.055 32.000 0.00 0.00 0.00 1.82
2802 5671 6.655078 ACTTGATGACAGGCAGTAAAAATT 57.345 33.333 0.00 0.00 0.00 1.82
2803 5672 7.054491 ACTTGATGACAGGCAGTAAAAATTT 57.946 32.000 0.00 0.00 0.00 1.82
2804 5673 6.925165 ACTTGATGACAGGCAGTAAAAATTTG 59.075 34.615 0.00 0.00 0.00 2.32
2805 5674 5.782047 TGATGACAGGCAGTAAAAATTTGG 58.218 37.500 0.00 0.00 0.00 3.28
2806 5675 5.304101 TGATGACAGGCAGTAAAAATTTGGT 59.696 36.000 0.00 0.00 0.00 3.67
2807 5676 5.195001 TGACAGGCAGTAAAAATTTGGTC 57.805 39.130 0.00 0.00 0.00 4.02
2808 5677 4.226761 GACAGGCAGTAAAAATTTGGTCG 58.773 43.478 0.00 0.00 0.00 4.79
2809 5678 2.986479 CAGGCAGTAAAAATTTGGTCGC 59.014 45.455 0.00 0.00 0.00 5.19
2810 5679 2.890945 AGGCAGTAAAAATTTGGTCGCT 59.109 40.909 0.00 0.00 0.00 4.93
2811 5680 3.057526 AGGCAGTAAAAATTTGGTCGCTC 60.058 43.478 0.00 0.00 0.00 5.03
2812 5681 3.242518 GCAGTAAAAATTTGGTCGCTCC 58.757 45.455 0.00 0.00 0.00 4.70
2813 5682 3.305064 GCAGTAAAAATTTGGTCGCTCCA 60.305 43.478 0.00 0.00 45.60 3.86
2837 5706 1.442148 CCCCCTTCGTCTCGAATCC 59.558 63.158 5.10 0.00 44.85 3.01
2838 5707 1.327690 CCCCCTTCGTCTCGAATCCA 61.328 60.000 5.10 0.00 44.85 3.41
2839 5708 0.179108 CCCCTTCGTCTCGAATCCAC 60.179 60.000 5.10 0.00 44.85 4.02
2840 5709 0.818296 CCCTTCGTCTCGAATCCACT 59.182 55.000 5.10 0.00 44.85 4.00
2841 5710 2.022195 CCCTTCGTCTCGAATCCACTA 58.978 52.381 5.10 0.00 44.85 2.74
2842 5711 2.223525 CCCTTCGTCTCGAATCCACTAC 60.224 54.545 5.10 0.00 44.85 2.73
2843 5712 2.223525 CCTTCGTCTCGAATCCACTACC 60.224 54.545 5.10 0.00 44.85 3.18
2844 5713 1.386533 TCGTCTCGAATCCACTACCC 58.613 55.000 0.00 0.00 31.06 3.69
2845 5714 0.384669 CGTCTCGAATCCACTACCCC 59.615 60.000 0.00 0.00 0.00 4.95
2846 5715 0.751452 GTCTCGAATCCACTACCCCC 59.249 60.000 0.00 0.00 0.00 5.40
2847 5716 0.337082 TCTCGAATCCACTACCCCCA 59.663 55.000 0.00 0.00 0.00 4.96
2848 5717 0.464452 CTCGAATCCACTACCCCCAC 59.536 60.000 0.00 0.00 0.00 4.61
2849 5718 0.979187 TCGAATCCACTACCCCCACC 60.979 60.000 0.00 0.00 0.00 4.61
2850 5719 1.920532 GAATCCACTACCCCCACCC 59.079 63.158 0.00 0.00 0.00 4.61
2851 5720 0.917333 GAATCCACTACCCCCACCCA 60.917 60.000 0.00 0.00 0.00 4.51
2852 5721 0.919289 AATCCACTACCCCCACCCAG 60.919 60.000 0.00 0.00 0.00 4.45
2853 5722 2.132946 ATCCACTACCCCCACCCAGT 62.133 60.000 0.00 0.00 0.00 4.00
2854 5723 2.602676 CCACTACCCCCACCCAGTG 61.603 68.421 0.00 0.00 38.48 3.66
2855 5724 1.846124 CACTACCCCCACCCAGTGT 60.846 63.158 0.00 0.00 34.91 3.55
2856 5725 0.545787 CACTACCCCCACCCAGTGTA 60.546 60.000 0.00 0.00 34.91 2.90
2857 5726 0.420272 ACTACCCCCACCCAGTGTAT 59.580 55.000 0.00 0.00 0.00 2.29
2858 5727 0.837272 CTACCCCCACCCAGTGTATG 59.163 60.000 0.00 0.00 0.00 2.39
2859 5728 1.276140 TACCCCCACCCAGTGTATGC 61.276 60.000 0.00 0.00 0.00 3.14
2860 5729 2.124736 CCCCACCCAGTGTATGCG 60.125 66.667 0.00 0.00 0.00 4.73
2861 5730 2.665089 CCCCACCCAGTGTATGCGA 61.665 63.158 0.00 0.00 0.00 5.10
2862 5731 1.449601 CCCACCCAGTGTATGCGAC 60.450 63.158 0.00 0.00 0.00 5.19
2863 5732 1.295101 CCACCCAGTGTATGCGACA 59.705 57.895 0.00 0.00 34.94 4.35
2864 5733 0.107703 CCACCCAGTGTATGCGACAT 60.108 55.000 0.00 0.00 41.14 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.329889 ATGGTTGAGCCTGCGGGA 61.330 61.111 18.31 0.00 38.35 5.14
281 295 6.346838 CGATTTTGCGACATATCAGAGCAATA 60.347 38.462 1.98 0.00 45.47 1.90
310 324 0.527113 CACGCCCAAGCATGAAATCA 59.473 50.000 0.00 0.00 32.75 2.57
385 400 0.256464 TTCCCCCGAAACAACAGTGT 59.744 50.000 0.00 0.00 40.75 3.55
420 435 5.181811 CAGTCTGAATCAAACTACATTGGCA 59.818 40.000 0.00 0.00 0.00 4.92
442 457 4.142902 CGTTAGATAAGGTTGCACCAACAG 60.143 45.833 9.93 0.00 45.11 3.16
743 792 9.192642 AGGATTGAACATCATCATCAACAATAA 57.807 29.630 0.00 0.00 36.03 1.40
1067 1192 4.389890 AGAAGATCTGTAGCAGCTTGAG 57.610 45.455 0.00 0.00 0.00 3.02
1170 1295 4.271776 ACTTGTCGGGTTTTTAGTTCTTCG 59.728 41.667 0.00 0.00 0.00 3.79
1615 4406 1.672881 GCACAACTCTTGCACAACTCT 59.327 47.619 0.00 0.00 39.93 3.24
1717 4509 2.641305 GCCACTCTCAGCTTCATCATT 58.359 47.619 0.00 0.00 0.00 2.57
2083 4905 7.964604 ATCTGAACAGGAAGTAACTACAAAC 57.035 36.000 1.93 0.00 0.00 2.93
2084 4906 8.974060 AAATCTGAACAGGAAGTAACTACAAA 57.026 30.769 1.93 0.00 0.00 2.83
2377 5226 9.507280 CAGGATTTAGTGTAAATGCAGTAAATG 57.493 33.333 21.35 10.66 46.50 2.32
2418 5267 4.161942 TGCTCGTTCTCTAGGTAGTACTCT 59.838 45.833 0.00 0.00 0.00 3.24
2556 5425 0.251033 GGTTCTTTGGTTAGGCGGGT 60.251 55.000 0.00 0.00 0.00 5.28
2655 5524 4.944317 ACTCTTACTAGGAAAATTGCCTGC 59.056 41.667 1.88 0.00 36.96 4.85
2674 5543 8.218488 AGTGGAGTAAGACCAAAATTTTACTCT 58.782 33.333 20.53 13.29 45.62 3.24
2675 5544 8.392372 AGTGGAGTAAGACCAAAATTTTACTC 57.608 34.615 16.03 16.03 45.61 2.59
2676 5545 9.856162 TTAGTGGAGTAAGACCAAAATTTTACT 57.144 29.630 2.44 2.31 39.22 2.24
2679 5548 8.512138 CGATTAGTGGAGTAAGACCAAAATTTT 58.488 33.333 0.00 0.00 39.22 1.82
2680 5549 7.881232 TCGATTAGTGGAGTAAGACCAAAATTT 59.119 33.333 0.00 0.00 39.22 1.82
2681 5550 7.333672 GTCGATTAGTGGAGTAAGACCAAAATT 59.666 37.037 0.00 0.00 39.22 1.82
2682 5551 6.817140 GTCGATTAGTGGAGTAAGACCAAAAT 59.183 38.462 0.00 0.00 39.22 1.82
2683 5552 6.161381 GTCGATTAGTGGAGTAAGACCAAAA 58.839 40.000 0.00 0.00 39.22 2.44
2684 5553 5.244402 TGTCGATTAGTGGAGTAAGACCAAA 59.756 40.000 0.00 0.00 39.22 3.28
2685 5554 4.768448 TGTCGATTAGTGGAGTAAGACCAA 59.232 41.667 0.00 0.00 39.22 3.67
2686 5555 4.157289 GTGTCGATTAGTGGAGTAAGACCA 59.843 45.833 0.00 0.00 34.84 4.02
2687 5556 4.398673 AGTGTCGATTAGTGGAGTAAGACC 59.601 45.833 0.00 0.00 0.00 3.85
2688 5557 5.564048 AGTGTCGATTAGTGGAGTAAGAC 57.436 43.478 0.00 0.00 0.00 3.01
2689 5558 6.183360 GCTAAGTGTCGATTAGTGGAGTAAGA 60.183 42.308 6.24 0.00 33.60 2.10
2690 5559 5.972382 GCTAAGTGTCGATTAGTGGAGTAAG 59.028 44.000 6.24 0.00 33.60 2.34
2691 5560 5.163581 GGCTAAGTGTCGATTAGTGGAGTAA 60.164 44.000 6.24 0.00 33.60 2.24
2692 5561 4.337555 GGCTAAGTGTCGATTAGTGGAGTA 59.662 45.833 6.24 0.00 33.60 2.59
2693 5562 3.130693 GGCTAAGTGTCGATTAGTGGAGT 59.869 47.826 6.24 0.00 33.60 3.85
2694 5563 3.130516 TGGCTAAGTGTCGATTAGTGGAG 59.869 47.826 6.24 0.00 33.60 3.86
2695 5564 3.093814 TGGCTAAGTGTCGATTAGTGGA 58.906 45.455 6.24 0.00 33.60 4.02
2696 5565 3.520290 TGGCTAAGTGTCGATTAGTGG 57.480 47.619 6.24 0.00 33.60 4.00
2697 5566 5.352284 AGATTGGCTAAGTGTCGATTAGTG 58.648 41.667 6.24 0.00 33.60 2.74
2698 5567 5.361285 AGAGATTGGCTAAGTGTCGATTAGT 59.639 40.000 6.24 0.00 33.60 2.24
2699 5568 5.837437 AGAGATTGGCTAAGTGTCGATTAG 58.163 41.667 0.00 0.00 34.09 1.73
2700 5569 5.854010 AGAGATTGGCTAAGTGTCGATTA 57.146 39.130 0.00 0.00 0.00 1.75
2701 5570 4.744795 AGAGATTGGCTAAGTGTCGATT 57.255 40.909 0.00 0.00 0.00 3.34
2702 5571 4.744795 AAGAGATTGGCTAAGTGTCGAT 57.255 40.909 0.00 0.00 0.00 3.59
2703 5572 5.654603 TTAAGAGATTGGCTAAGTGTCGA 57.345 39.130 0.00 0.00 0.00 4.20
2704 5573 5.063564 GGTTTAAGAGATTGGCTAAGTGTCG 59.936 44.000 0.00 0.00 0.00 4.35
2705 5574 5.063564 CGGTTTAAGAGATTGGCTAAGTGTC 59.936 44.000 0.00 0.00 0.00 3.67
2706 5575 4.935808 CGGTTTAAGAGATTGGCTAAGTGT 59.064 41.667 0.00 0.00 0.00 3.55
2707 5576 4.332819 CCGGTTTAAGAGATTGGCTAAGTG 59.667 45.833 0.00 0.00 0.00 3.16
2708 5577 4.019591 ACCGGTTTAAGAGATTGGCTAAGT 60.020 41.667 0.00 0.00 0.00 2.24
2709 5578 4.514401 ACCGGTTTAAGAGATTGGCTAAG 58.486 43.478 0.00 0.00 0.00 2.18
2710 5579 4.563140 ACCGGTTTAAGAGATTGGCTAA 57.437 40.909 0.00 0.00 0.00 3.09
2711 5580 4.563140 AACCGGTTTAAGAGATTGGCTA 57.437 40.909 15.86 0.00 0.00 3.93
2712 5581 3.434940 AACCGGTTTAAGAGATTGGCT 57.565 42.857 15.86 0.00 0.00 4.75
2713 5582 4.510571 TCTAACCGGTTTAAGAGATTGGC 58.489 43.478 27.64 0.00 0.00 4.52
2714 5583 5.974108 TCTCTAACCGGTTTAAGAGATTGG 58.026 41.667 32.29 16.93 0.00 3.16
2715 5584 7.097834 AGTTCTCTAACCGGTTTAAGAGATTG 58.902 38.462 34.52 18.70 36.15 2.67
2716 5585 7.242322 AGTTCTCTAACCGGTTTAAGAGATT 57.758 36.000 34.52 26.50 36.15 2.40
2717 5586 6.854091 AGTTCTCTAACCGGTTTAAGAGAT 57.146 37.500 34.52 24.48 36.15 2.75
2718 5587 7.094032 CCTTAGTTCTCTAACCGGTTTAAGAGA 60.094 40.741 32.29 32.29 36.15 3.10
2719 5588 7.034397 CCTTAGTTCTCTAACCGGTTTAAGAG 58.966 42.308 29.70 29.70 36.15 2.85
2720 5589 6.721208 TCCTTAGTTCTCTAACCGGTTTAAGA 59.279 38.462 27.64 23.66 36.15 2.10
2721 5590 6.928520 TCCTTAGTTCTCTAACCGGTTTAAG 58.071 40.000 27.64 22.29 36.15 1.85
2722 5591 6.916360 TCCTTAGTTCTCTAACCGGTTTAA 57.084 37.500 27.64 14.54 36.15 1.52
2723 5592 6.916360 TTCCTTAGTTCTCTAACCGGTTTA 57.084 37.500 27.64 13.44 36.15 2.01
2724 5593 5.813513 TTCCTTAGTTCTCTAACCGGTTT 57.186 39.130 27.64 8.02 36.15 3.27
2725 5594 6.370186 AATTCCTTAGTTCTCTAACCGGTT 57.630 37.500 25.64 25.64 36.15 4.44
2726 5595 6.370186 AAATTCCTTAGTTCTCTAACCGGT 57.630 37.500 0.00 0.00 36.15 5.28
2727 5596 8.959705 ATTAAATTCCTTAGTTCTCTAACCGG 57.040 34.615 0.00 0.00 36.15 5.28
2737 5606 9.642343 GGAGGGTGATAATTAAATTCCTTAGTT 57.358 33.333 0.00 0.00 0.00 2.24
2738 5607 8.225416 GGGAGGGTGATAATTAAATTCCTTAGT 58.775 37.037 0.00 0.00 0.00 2.24
2739 5608 8.224720 TGGGAGGGTGATAATTAAATTCCTTAG 58.775 37.037 0.00 0.00 0.00 2.18
2740 5609 8.120256 TGGGAGGGTGATAATTAAATTCCTTA 57.880 34.615 0.00 0.00 0.00 2.69
2741 5610 6.992235 TGGGAGGGTGATAATTAAATTCCTT 58.008 36.000 0.00 0.00 0.00 3.36
2742 5611 6.392842 TCTGGGAGGGTGATAATTAAATTCCT 59.607 38.462 0.00 0.00 0.00 3.36
2743 5612 6.490381 GTCTGGGAGGGTGATAATTAAATTCC 59.510 42.308 0.00 0.00 0.00 3.01
2744 5613 6.204882 CGTCTGGGAGGGTGATAATTAAATTC 59.795 42.308 0.00 0.00 0.00 2.17
2745 5614 6.062095 CGTCTGGGAGGGTGATAATTAAATT 58.938 40.000 0.00 0.00 0.00 1.82
2746 5615 5.368523 TCGTCTGGGAGGGTGATAATTAAAT 59.631 40.000 0.00 0.00 0.00 1.40
2747 5616 4.717778 TCGTCTGGGAGGGTGATAATTAAA 59.282 41.667 0.00 0.00 0.00 1.52
2748 5617 4.291792 TCGTCTGGGAGGGTGATAATTAA 58.708 43.478 0.00 0.00 0.00 1.40
2749 5618 3.895656 CTCGTCTGGGAGGGTGATAATTA 59.104 47.826 0.00 0.00 0.00 1.40
2750 5619 2.700897 CTCGTCTGGGAGGGTGATAATT 59.299 50.000 0.00 0.00 0.00 1.40
2751 5620 2.320781 CTCGTCTGGGAGGGTGATAAT 58.679 52.381 0.00 0.00 0.00 1.28
2752 5621 1.006758 ACTCGTCTGGGAGGGTGATAA 59.993 52.381 0.00 0.00 38.39 1.75
2753 5622 0.629596 ACTCGTCTGGGAGGGTGATA 59.370 55.000 0.00 0.00 38.39 2.15
2754 5623 0.972983 CACTCGTCTGGGAGGGTGAT 60.973 60.000 0.00 0.00 38.39 3.06
2755 5624 1.606601 CACTCGTCTGGGAGGGTGA 60.607 63.158 0.00 0.00 38.39 4.02
2756 5625 1.185618 TTCACTCGTCTGGGAGGGTG 61.186 60.000 0.00 0.00 38.61 4.61
2757 5626 0.252284 ATTCACTCGTCTGGGAGGGT 60.252 55.000 0.00 0.00 38.61 4.34
2758 5627 1.776662 TATTCACTCGTCTGGGAGGG 58.223 55.000 0.00 0.00 38.86 4.30
2759 5628 4.145807 AGTATATTCACTCGTCTGGGAGG 58.854 47.826 0.00 0.00 38.39 4.30
2760 5629 5.299531 TCAAGTATATTCACTCGTCTGGGAG 59.700 44.000 0.00 0.00 39.97 4.30
2761 5630 5.198207 TCAAGTATATTCACTCGTCTGGGA 58.802 41.667 0.00 0.00 0.00 4.37
2762 5631 5.515797 TCAAGTATATTCACTCGTCTGGG 57.484 43.478 0.00 0.00 0.00 4.45
2763 5632 6.638873 GTCATCAAGTATATTCACTCGTCTGG 59.361 42.308 0.00 0.00 0.00 3.86
2764 5633 7.196331 TGTCATCAAGTATATTCACTCGTCTG 58.804 38.462 0.00 0.00 0.00 3.51
2765 5634 7.334844 TGTCATCAAGTATATTCACTCGTCT 57.665 36.000 0.00 0.00 0.00 4.18
2766 5635 6.638873 CCTGTCATCAAGTATATTCACTCGTC 59.361 42.308 0.00 0.00 0.00 4.20
2767 5636 6.507900 CCTGTCATCAAGTATATTCACTCGT 58.492 40.000 0.00 0.00 0.00 4.18
2768 5637 5.403766 GCCTGTCATCAAGTATATTCACTCG 59.596 44.000 0.00 0.00 0.00 4.18
2769 5638 6.283694 TGCCTGTCATCAAGTATATTCACTC 58.716 40.000 0.00 0.00 0.00 3.51
2770 5639 6.126940 ACTGCCTGTCATCAAGTATATTCACT 60.127 38.462 0.00 0.00 0.00 3.41
2771 5640 6.051717 ACTGCCTGTCATCAAGTATATTCAC 58.948 40.000 0.00 0.00 0.00 3.18
2772 5641 6.239217 ACTGCCTGTCATCAAGTATATTCA 57.761 37.500 0.00 0.00 0.00 2.57
2773 5642 8.662781 TTTACTGCCTGTCATCAAGTATATTC 57.337 34.615 0.00 0.00 0.00 1.75
2774 5643 9.461312 TTTTTACTGCCTGTCATCAAGTATATT 57.539 29.630 0.00 0.00 0.00 1.28
2775 5644 9.632638 ATTTTTACTGCCTGTCATCAAGTATAT 57.367 29.630 0.00 0.00 0.00 0.86
2776 5645 9.461312 AATTTTTACTGCCTGTCATCAAGTATA 57.539 29.630 0.00 0.00 0.00 1.47
2777 5646 7.944729 ATTTTTACTGCCTGTCATCAAGTAT 57.055 32.000 0.00 0.00 0.00 2.12
2778 5647 7.759489 AATTTTTACTGCCTGTCATCAAGTA 57.241 32.000 0.00 0.00 0.00 2.24
2779 5648 6.655078 AATTTTTACTGCCTGTCATCAAGT 57.345 33.333 0.00 0.00 0.00 3.16
2780 5649 6.366877 CCAAATTTTTACTGCCTGTCATCAAG 59.633 38.462 0.00 0.00 0.00 3.02
2781 5650 6.183360 ACCAAATTTTTACTGCCTGTCATCAA 60.183 34.615 0.00 0.00 0.00 2.57
2782 5651 5.304101 ACCAAATTTTTACTGCCTGTCATCA 59.696 36.000 0.00 0.00 0.00 3.07
2783 5652 5.783111 ACCAAATTTTTACTGCCTGTCATC 58.217 37.500 0.00 0.00 0.00 2.92
2784 5653 5.564651 CGACCAAATTTTTACTGCCTGTCAT 60.565 40.000 0.00 0.00 0.00 3.06
2785 5654 4.261405 CGACCAAATTTTTACTGCCTGTCA 60.261 41.667 0.00 0.00 0.00 3.58
2786 5655 4.226761 CGACCAAATTTTTACTGCCTGTC 58.773 43.478 0.00 0.00 0.00 3.51
2787 5656 3.552068 GCGACCAAATTTTTACTGCCTGT 60.552 43.478 0.00 0.00 0.00 4.00
2788 5657 2.986479 GCGACCAAATTTTTACTGCCTG 59.014 45.455 0.00 0.00 0.00 4.85
2789 5658 2.890945 AGCGACCAAATTTTTACTGCCT 59.109 40.909 0.00 0.00 0.00 4.75
2790 5659 3.242518 GAGCGACCAAATTTTTACTGCC 58.757 45.455 0.00 0.00 0.00 4.85
2791 5660 3.242518 GGAGCGACCAAATTTTTACTGC 58.757 45.455 0.00 0.00 38.79 4.40
2792 5661 4.497473 TGGAGCGACCAAATTTTTACTG 57.503 40.909 3.31 0.00 46.75 2.74
2825 5694 1.386533 GGGTAGTGGATTCGAGACGA 58.613 55.000 0.00 0.00 0.00 4.20
2826 5695 0.384669 GGGGTAGTGGATTCGAGACG 59.615 60.000 0.00 0.00 0.00 4.18
2827 5696 0.751452 GGGGGTAGTGGATTCGAGAC 59.249 60.000 0.00 0.00 0.00 3.36
2828 5697 0.337082 TGGGGGTAGTGGATTCGAGA 59.663 55.000 0.00 0.00 0.00 4.04
2829 5698 0.464452 GTGGGGGTAGTGGATTCGAG 59.536 60.000 0.00 0.00 0.00 4.04
2830 5699 0.979187 GGTGGGGGTAGTGGATTCGA 60.979 60.000 0.00 0.00 0.00 3.71
2831 5700 1.525442 GGTGGGGGTAGTGGATTCG 59.475 63.158 0.00 0.00 0.00 3.34
2832 5701 0.917333 TGGGTGGGGGTAGTGGATTC 60.917 60.000 0.00 0.00 0.00 2.52
2833 5702 0.919289 CTGGGTGGGGGTAGTGGATT 60.919 60.000 0.00 0.00 0.00 3.01
2834 5703 1.307866 CTGGGTGGGGGTAGTGGAT 60.308 63.158 0.00 0.00 0.00 3.41
2835 5704 2.124085 CTGGGTGGGGGTAGTGGA 59.876 66.667 0.00 0.00 0.00 4.02
2836 5705 2.204090 ACTGGGTGGGGGTAGTGG 60.204 66.667 0.00 0.00 0.00 4.00
2837 5706 0.545787 TACACTGGGTGGGGGTAGTG 60.546 60.000 0.00 0.00 44.52 2.74
2838 5707 0.420272 ATACACTGGGTGGGGGTAGT 59.580 55.000 0.00 0.00 37.94 2.73
2839 5708 0.837272 CATACACTGGGTGGGGGTAG 59.163 60.000 0.00 0.00 37.94 3.18
2840 5709 1.276140 GCATACACTGGGTGGGGGTA 61.276 60.000 0.00 0.00 37.94 3.69
2841 5710 2.612493 GCATACACTGGGTGGGGGT 61.612 63.158 0.00 0.00 37.94 4.95
2842 5711 2.275418 GCATACACTGGGTGGGGG 59.725 66.667 0.00 0.00 37.94 5.40
2843 5712 2.124736 CGCATACACTGGGTGGGG 60.125 66.667 0.00 0.00 37.94 4.96
2844 5713 1.449601 GTCGCATACACTGGGTGGG 60.450 63.158 0.00 0.00 37.94 4.61
2845 5714 0.107703 ATGTCGCATACACTGGGTGG 60.108 55.000 0.00 0.00 42.09 4.61
2846 5715 3.458872 ATGTCGCATACACTGGGTG 57.541 52.632 0.00 0.00 42.09 4.61


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

AutoCloner maintained by Alex Coulton.