Multiple sequence alignment - TraesCS3D01G030100

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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 TraesCS3D01G030100 chr3D 100.000 2729 0 0 1 2729 10899239 10896511 0.000000e+00 5040
1 TraesCS3D01G030100 chr3D 82.536 418 55 11 9 420 10798002 10798407 4.320000e-93 351
2 TraesCS3D01G030100 chr3A 94.567 1583 54 7 1 1571 17432371 17433933 0.000000e+00 2418
3 TraesCS3D01G030100 chr3B 94.397 1160 47 6 423 1571 26042857 26044009 0.000000e+00 1766
4 TraesCS3D01G030100 chr3B 94.397 1160 47 6 423 1571 26385051 26386203 0.000000e+00 1766
5 TraesCS3D01G030100 chr3B 94.682 1147 43 6 436 1571 26190565 26191704 0.000000e+00 1764
6 TraesCS3D01G030100 chr3B 94.310 1160 48 5 423 1571 26002953 26004105 0.000000e+00 1760
7 TraesCS3D01G030100 chr3B 94.224 1160 49 6 423 1571 25906399 25907551 0.000000e+00 1755
8 TraesCS3D01G030100 chr3B 94.224 1160 49 5 423 1571 26341448 26342600 0.000000e+00 1755
9 TraesCS3D01G030100 chr3B 94.138 1160 50 6 423 1571 25869905 25871057 0.000000e+00 1749
10 TraesCS3D01G030100 chr3B 94.052 1160 51 6 423 1571 26231834 26232986 0.000000e+00 1744
11 TraesCS3D01G030100 chr3B 94.052 1160 51 6 423 1571 26300712 26301864 0.000000e+00 1744
12 TraesCS3D01G030100 chr3B 94.011 1052 51 3 1570 2620 26386784 26387824 0.000000e+00 1583
13 TraesCS3D01G030100 chr3B 93.916 1052 52 3 1570 2620 25871638 25872678 0.000000e+00 1578
14 TraesCS3D01G030100 chr3B 93.916 1052 52 3 1570 2620 26044590 26045630 0.000000e+00 1578
15 TraesCS3D01G030100 chr3B 93.916 1052 52 3 1570 2620 26343181 26344221 0.000000e+00 1578
16 TraesCS3D01G030100 chr3B 93.821 1052 53 3 1570 2620 25908132 25909172 0.000000e+00 1572
17 TraesCS3D01G030100 chr3B 93.821 1052 53 3 1570 2620 26004686 26005726 0.000000e+00 1572
18 TraesCS3D01G030100 chr3B 93.744 1055 54 3 1570 2623 26302359 26303402 0.000000e+00 1572
19 TraesCS3D01G030100 chr3B 93.631 1052 55 3 1570 2620 26233567 26234607 0.000000e+00 1561
20 TraesCS3D01G030100 chr3B 91.730 1052 53 4 1570 2620 26192285 26193303 0.000000e+00 1430
21 TraesCS3D01G030100 chr3B 92.925 735 50 2 1886 2620 26420083 26420815 0.000000e+00 1068
22 TraesCS3D01G030100 chr3B 89.450 436 30 8 1 422 25906021 25906454 1.110000e-148 536
23 TraesCS3D01G030100 chr3B 88.864 440 30 7 1 422 26384668 26385106 8.660000e-145 523
24 TraesCS3D01G030100 chr3B 87.173 382 28 8 61 422 25869580 25869960 5.440000e-112 414
25 TraesCS3D01G030100 chr3B 87.988 333 25 6 1 319 26190238 26190569 1.980000e-101 379
26 TraesCS3D01G030100 chr3B 90.378 291 21 4 138 422 26231600 26231889 2.570000e-100 375
27 TraesCS3D01G030100 chr3B 89.667 300 24 4 129 422 26341205 26341503 2.570000e-100 375
28 TraesCS3D01G030100 chr3B 89.632 299 24 4 130 422 26300470 26300767 9.230000e-100 374
29 TraesCS3D01G030100 chr3B 89.324 281 22 5 148 422 26042634 26042912 2.010000e-91 346
30 TraesCS3D01G030100 chr3B 94.286 105 6 0 1 105 26300120 26300224 7.820000e-36 161
31 TraesCS3D01G030100 chr3B 92.035 113 9 0 1 113 26002447 26002559 2.810000e-35 159
32 TraesCS3D01G030100 chr3B 92.035 113 9 0 1 113 26190015 26190127 2.810000e-35 159
33 TraesCS3D01G030100 chr3B 93.617 94 6 0 1 94 26231445 26231538 1.020000e-29 141
34 TraesCS3D01G030100 chr7A 100.000 106 0 0 2624 2729 620773846 620773741 2.140000e-46 196
35 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 84703455 84703560 9.970000e-45 191
36 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 92123046 92123151 9.970000e-45 191
37 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 122346695 122346590 9.970000e-45 191
38 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 165030098 165029993 9.970000e-45 191
39 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 295065400 295065505 9.970000e-45 191
40 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 309452615 309452720 9.970000e-45 191
41 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 322808436 322808541 9.970000e-45 191
42 TraesCS3D01G030100 chr4D 99.057 106 1 0 2624 2729 334128701 334128806 9.970000e-45 191


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 TraesCS3D01G030100 chr3D 10896511 10899239 2728 True 5040.000000 5040 100.000000 1 2729 1 chr3D.!!$R1 2728
1 TraesCS3D01G030100 chr3A 17432371 17433933 1562 False 2418.000000 2418 94.567000 1 1571 1 chr3A.!!$F1 1570
2 TraesCS3D01G030100 chr3B 26384668 26387824 3156 False 1290.666667 1766 92.424000 1 2620 3 chr3B.!!$F10 2619
3 TraesCS3D01G030100 chr3B 25906021 25909172 3151 False 1287.666667 1755 92.498333 1 2620 3 chr3B.!!$F3 2619
4 TraesCS3D01G030100 chr3B 25869580 25872678 3098 False 1247.000000 1749 91.742333 61 2620 3 chr3B.!!$F2 2559
5 TraesCS3D01G030100 chr3B 26341205 26344221 3016 False 1236.000000 1755 92.602333 129 2620 3 chr3B.!!$F9 2491
6 TraesCS3D01G030100 chr3B 26042634 26045630 2996 False 1230.000000 1766 92.545667 148 2620 3 chr3B.!!$F5 2472
7 TraesCS3D01G030100 chr3B 26002447 26005726 3279 False 1163.666667 1760 93.388667 1 2620 3 chr3B.!!$F4 2619
8 TraesCS3D01G030100 chr3B 26420083 26420815 732 False 1068.000000 1068 92.925000 1886 2620 1 chr3B.!!$F1 734
9 TraesCS3D01G030100 chr3B 26300120 26303402 3282 False 962.750000 1744 92.928500 1 2623 4 chr3B.!!$F8 2622
10 TraesCS3D01G030100 chr3B 26231445 26234607 3162 False 955.250000 1744 92.919500 1 2620 4 chr3B.!!$F7 2619
11 TraesCS3D01G030100 chr3B 26190015 26193303 3288 False 933.000000 1764 91.608750 1 2620 4 chr3B.!!$F6 2619

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
496 950 0.100503 ACACCAAAGCAACGTCAAGC 59.899 50.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2960 0.944999 AGGATGGCCTCTCCCTTCTA 59.055 55.0 18.18 0.0 42.19 2.1 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
58 59 2.661718 TCCAAAACCAAGGAGAACCAC 58.338 47.619 0.00 0.00 38.94 4.16
76 79 1.255084 CACGCAAAAACTGAAAAGCCG 59.745 47.619 0.00 0.00 0.00 5.52
105 331 3.857093 CCCATCTAAAATCCAAAAACGCG 59.143 43.478 3.53 3.53 0.00 6.01
173 620 0.378257 GGATGCATCATTTGACGCGT 59.622 50.000 27.25 13.85 35.80 6.01
188 635 1.265905 ACGCGTTCTAAGGCCAAAAAG 59.734 47.619 5.58 0.00 36.51 2.27
411 865 3.057526 GCCTGGTTTAATGTCCACAGAAC 60.058 47.826 0.00 0.00 0.00 3.01
496 950 0.100503 ACACCAAAGCAACGTCAAGC 59.899 50.000 0.00 0.00 0.00 4.01
625 1080 7.412672 GGTTTCTTCACGACCTAATTATCACAC 60.413 40.741 0.00 0.00 0.00 3.82
626 1081 5.337554 TCTTCACGACCTAATTATCACACG 58.662 41.667 0.00 0.00 0.00 4.49
627 1082 3.441163 TCACGACCTAATTATCACACGC 58.559 45.455 0.00 0.00 0.00 5.34
628 1083 2.538449 CACGACCTAATTATCACACGCC 59.462 50.000 0.00 0.00 0.00 5.68
629 1084 1.784856 CGACCTAATTATCACACGCCG 59.215 52.381 0.00 0.00 0.00 6.46
630 1085 2.542205 CGACCTAATTATCACACGCCGA 60.542 50.000 0.00 0.00 0.00 5.54
631 1086 2.793232 GACCTAATTATCACACGCCGAC 59.207 50.000 0.00 0.00 0.00 4.79
836 1307 3.250521 GCTTAATCCTCTAGCGACGTACT 59.749 47.826 0.00 0.00 0.00 2.73
837 1308 4.450419 GCTTAATCCTCTAGCGACGTACTA 59.550 45.833 0.00 0.00 0.00 1.82
838 1309 5.389725 GCTTAATCCTCTAGCGACGTACTAG 60.390 48.000 15.70 15.70 38.79 2.57
839 1310 3.749665 ATCCTCTAGCGACGTACTAGT 57.250 47.619 19.30 0.00 38.60 2.57
840 1311 4.862902 ATCCTCTAGCGACGTACTAGTA 57.137 45.455 19.30 0.00 38.60 1.82
841 1312 4.235939 TCCTCTAGCGACGTACTAGTAG 57.764 50.000 19.30 15.54 38.60 2.57
901 1372 1.904537 TCATCAGATCACCACAGCAGT 59.095 47.619 0.00 0.00 0.00 4.40
1059 1530 1.520342 GATCGCCTGTGTGCTCTCC 60.520 63.158 0.00 0.00 0.00 3.71
1159 1630 0.678950 TGACGCCTCTGACACAATGA 59.321 50.000 0.00 0.00 0.00 2.57
1182 1660 4.631813 AGTAATCAATTCAACTCACGCCTC 59.368 41.667 0.00 0.00 0.00 4.70
1208 1686 0.752658 TATCTACTGCGTGCATGCCT 59.247 50.000 27.43 15.08 0.00 4.75
1227 1705 4.041567 TGCCTGGTTGATCTTGTTCTTCTA 59.958 41.667 0.00 0.00 0.00 2.10
1677 2738 7.380536 TGGTAACTCACGCTTATAAGAAAGAA 58.619 34.615 16.85 0.00 37.61 2.52
1727 2788 3.002862 GTGTTGTTGAATGGTCGCAAGTA 59.997 43.478 0.00 0.00 39.48 2.24
1731 2792 1.271856 TGAATGGTCGCAAGTAGGGA 58.728 50.000 0.00 0.00 36.77 4.20
1818 2879 2.542595 GGGCGTCTGGTTATGAATAACG 59.457 50.000 7.02 0.00 42.66 3.18
1915 2976 1.485978 GGGATAGAAGGGAGAGGCCAT 60.486 57.143 5.01 0.00 38.95 4.40
1952 3013 1.464734 TTTTTGTGTTCAGCGGGTCA 58.535 45.000 0.00 0.00 0.00 4.02
2050 3111 0.693622 TCACGCCCCCAATCTGTTTA 59.306 50.000 0.00 0.00 0.00 2.01
2075 3136 8.911247 ATTCTGCGTTAATTTTCCTATCAAAC 57.089 30.769 0.00 0.00 0.00 2.93
2159 3220 6.402222 AGGAGATAGATTGAACCGAATATGC 58.598 40.000 0.00 0.00 0.00 3.14
2217 3278 5.353123 GTCTACAAATTGAAATAGGCACGGA 59.647 40.000 0.00 0.00 0.00 4.69
2229 3290 1.152963 GCACGGAGCCCCATACATT 60.153 57.895 0.00 0.00 37.23 2.71
2316 3377 6.073222 AGGTGATGTTTTTCATTCGACACTAC 60.073 38.462 0.00 0.00 36.83 2.73
2438 3499 5.888161 ACTTGTTGTTCCTTGACTCTTGATT 59.112 36.000 0.00 0.00 0.00 2.57
2609 3670 3.020984 ACAAATGTCAACAACCCTTCGT 58.979 40.909 0.00 0.00 0.00 3.85
2623 3684 1.068474 CTTCGTTGTACCCAAGAGCG 58.932 55.000 0.00 0.00 0.00 5.03
2624 3685 0.390124 TTCGTTGTACCCAAGAGCGT 59.610 50.000 0.00 0.00 0.00 5.07
2625 3686 0.390124 TCGTTGTACCCAAGAGCGTT 59.610 50.000 0.00 0.00 0.00 4.84
2626 3687 0.511221 CGTTGTACCCAAGAGCGTTG 59.489 55.000 0.00 0.00 0.00 4.10
2627 3688 1.870580 CGTTGTACCCAAGAGCGTTGA 60.871 52.381 3.62 0.00 0.00 3.18
2628 3689 1.529865 GTTGTACCCAAGAGCGTTGAC 59.470 52.381 3.62 0.00 0.00 3.18
2629 3690 0.034337 TGTACCCAAGAGCGTTGACC 59.966 55.000 3.62 0.00 0.00 4.02
2630 3691 0.320697 GTACCCAAGAGCGTTGACCT 59.679 55.000 3.62 0.00 0.00 3.85
2631 3692 1.547372 GTACCCAAGAGCGTTGACCTA 59.453 52.381 3.62 0.00 0.00 3.08
2632 3693 1.053424 ACCCAAGAGCGTTGACCTAA 58.947 50.000 3.62 0.00 0.00 2.69
2633 3694 1.002087 ACCCAAGAGCGTTGACCTAAG 59.998 52.381 3.62 0.00 0.00 2.18
2634 3695 1.275291 CCCAAGAGCGTTGACCTAAGA 59.725 52.381 3.62 0.00 0.00 2.10
2635 3696 2.611518 CCAAGAGCGTTGACCTAAGAG 58.388 52.381 3.62 0.00 0.00 2.85
2636 3697 2.611518 CAAGAGCGTTGACCTAAGAGG 58.388 52.381 0.00 0.00 42.49 3.69
2650 3711 5.911378 CCTAAGAGGTTCGGTAGTAACTT 57.089 43.478 0.00 0.00 0.00 2.66
2651 3712 5.648572 CCTAAGAGGTTCGGTAGTAACTTG 58.351 45.833 0.00 0.00 0.00 3.16
2652 3713 5.416952 CCTAAGAGGTTCGGTAGTAACTTGA 59.583 44.000 0.00 0.00 0.00 3.02
2653 3714 5.997384 AAGAGGTTCGGTAGTAACTTGAT 57.003 39.130 0.00 0.00 0.00 2.57
2654 3715 5.579564 AGAGGTTCGGTAGTAACTTGATC 57.420 43.478 0.00 0.00 0.00 2.92
2655 3716 5.262804 AGAGGTTCGGTAGTAACTTGATCT 58.737 41.667 0.00 0.00 0.00 2.75
2656 3717 5.125739 AGAGGTTCGGTAGTAACTTGATCTG 59.874 44.000 0.00 0.00 0.00 2.90
2657 3718 5.014858 AGGTTCGGTAGTAACTTGATCTGA 58.985 41.667 0.00 0.00 0.00 3.27
2658 3719 5.479375 AGGTTCGGTAGTAACTTGATCTGAA 59.521 40.000 0.00 0.00 0.00 3.02
2659 3720 5.805994 GGTTCGGTAGTAACTTGATCTGAAG 59.194 44.000 0.00 0.00 0.00 3.02
2660 3721 6.388278 GTTCGGTAGTAACTTGATCTGAAGT 58.612 40.000 0.00 0.00 37.81 3.01
2661 3722 6.585695 TCGGTAGTAACTTGATCTGAAGTT 57.414 37.500 13.79 13.79 45.87 2.66
2662 3723 6.989659 TCGGTAGTAACTTGATCTGAAGTTT 58.010 36.000 14.35 3.30 42.33 2.66
2663 3724 7.088905 TCGGTAGTAACTTGATCTGAAGTTTC 58.911 38.462 14.35 10.48 42.33 2.78
2664 3725 6.866770 CGGTAGTAACTTGATCTGAAGTTTCA 59.133 38.462 14.35 0.00 42.33 2.69
2665 3726 7.545965 CGGTAGTAACTTGATCTGAAGTTTCAT 59.454 37.037 14.35 6.08 42.33 2.57
2666 3727 8.660373 GGTAGTAACTTGATCTGAAGTTTCATG 58.340 37.037 14.35 0.00 42.33 3.07
2667 3728 9.424319 GTAGTAACTTGATCTGAAGTTTCATGA 57.576 33.333 14.35 0.00 42.33 3.07
2669 3730 9.160496 AGTAACTTGATCTGAAGTTTCATGATC 57.840 33.333 14.35 17.74 42.33 2.92
2670 3731 7.991084 AACTTGATCTGAAGTTTCATGATCA 57.009 32.000 20.55 20.55 42.33 2.92
2671 3732 8.577048 AACTTGATCTGAAGTTTCATGATCAT 57.423 30.769 22.69 1.18 42.33 2.45
2672 3733 8.211116 ACTTGATCTGAAGTTTCATGATCATC 57.789 34.615 22.69 0.00 43.24 2.92
2673 3734 7.827729 ACTTGATCTGAAGTTTCATGATCATCA 59.172 33.333 22.69 15.09 43.24 3.07
2674 3735 8.747538 TTGATCTGAAGTTTCATGATCATCAT 57.252 30.769 22.69 0.00 43.24 2.45
2675 3736 8.379457 TGATCTGAAGTTTCATGATCATCATC 57.621 34.615 20.55 3.27 41.42 2.92
2676 3737 7.990886 TGATCTGAAGTTTCATGATCATCATCA 59.009 33.333 20.55 5.65 41.42 3.07
2678 3739 8.747538 TCTGAAGTTTCATGATCATCATCATT 57.252 30.769 4.86 0.00 46.07 2.57
2679 3740 9.841295 TCTGAAGTTTCATGATCATCATCATTA 57.159 29.630 4.86 0.00 46.07 1.90
2681 3742 8.565416 TGAAGTTTCATGATCATCATCATTAGC 58.435 33.333 4.86 0.00 46.07 3.09
2682 3743 8.693120 AAGTTTCATGATCATCATCATTAGCT 57.307 30.769 4.86 0.00 46.07 3.32
2683 3744 8.693120 AGTTTCATGATCATCATCATTAGCTT 57.307 30.769 4.86 0.00 46.07 3.74
2684 3745 8.784994 AGTTTCATGATCATCATCATTAGCTTC 58.215 33.333 4.86 0.00 46.07 3.86
2685 3746 7.683437 TTCATGATCATCATCATTAGCTTCC 57.317 36.000 4.86 0.00 46.07 3.46
2686 3747 7.017319 TCATGATCATCATCATTAGCTTCCT 57.983 36.000 4.86 0.00 46.07 3.36
2687 3748 7.104290 TCATGATCATCATCATTAGCTTCCTC 58.896 38.462 4.86 0.00 46.07 3.71
2688 3749 6.429521 TGATCATCATCATTAGCTTCCTCA 57.570 37.500 0.00 0.00 33.80 3.86
2689 3750 6.228995 TGATCATCATCATTAGCTTCCTCAC 58.771 40.000 0.00 0.00 33.80 3.51
2690 3751 5.883685 TCATCATCATTAGCTTCCTCACT 57.116 39.130 0.00 0.00 0.00 3.41
2691 3752 6.983906 TCATCATCATTAGCTTCCTCACTA 57.016 37.500 0.00 0.00 0.00 2.74
2692 3753 7.365497 TCATCATCATTAGCTTCCTCACTAA 57.635 36.000 0.00 0.00 33.17 2.24
2693 3754 7.971201 TCATCATCATTAGCTTCCTCACTAAT 58.029 34.615 0.00 0.00 39.17 1.73
2694 3755 8.435187 TCATCATCATTAGCTTCCTCACTAATT 58.565 33.333 0.00 0.00 37.05 1.40
2695 3756 8.504815 CATCATCATTAGCTTCCTCACTAATTG 58.495 37.037 0.00 0.00 37.05 2.32
2696 3757 6.994496 TCATCATTAGCTTCCTCACTAATTGG 59.006 38.462 0.00 0.00 37.05 3.16
2697 3758 6.313519 TCATTAGCTTCCTCACTAATTGGT 57.686 37.500 0.00 0.00 37.05 3.67
2698 3759 6.115446 TCATTAGCTTCCTCACTAATTGGTG 58.885 40.000 15.31 15.31 37.05 4.17
2699 3760 5.499004 TTAGCTTCCTCACTAATTGGTGT 57.501 39.130 19.91 3.41 38.28 4.16
2700 3761 6.614694 TTAGCTTCCTCACTAATTGGTGTA 57.385 37.500 19.91 7.65 38.28 2.90
2701 3762 5.091261 AGCTTCCTCACTAATTGGTGTAG 57.909 43.478 19.91 15.21 38.28 2.74
2702 3763 4.080863 AGCTTCCTCACTAATTGGTGTAGG 60.081 45.833 22.83 22.83 38.28 3.18
2703 3764 4.081087 GCTTCCTCACTAATTGGTGTAGGA 60.081 45.833 25.27 25.27 39.41 2.94
2704 3765 5.570844 GCTTCCTCACTAATTGGTGTAGGAA 60.571 44.000 30.65 30.65 43.06 3.36
2705 3766 6.636454 TTCCTCACTAATTGGTGTAGGAAT 57.364 37.500 29.99 0.00 41.98 3.01
2706 3767 6.235231 TCCTCACTAATTGGTGTAGGAATC 57.765 41.667 26.10 0.00 38.86 2.52
2707 3768 5.724370 TCCTCACTAATTGGTGTAGGAATCA 59.276 40.000 26.10 13.50 38.86 2.57
2708 3769 5.817816 CCTCACTAATTGGTGTAGGAATCAC 59.182 44.000 23.72 0.00 37.03 3.06
2709 3770 6.352222 CCTCACTAATTGGTGTAGGAATCACT 60.352 42.308 23.72 0.00 37.03 3.41
2710 3771 6.406370 TCACTAATTGGTGTAGGAATCACTG 58.594 40.000 19.91 0.00 38.28 3.66
2711 3772 5.586243 CACTAATTGGTGTAGGAATCACTGG 59.414 44.000 13.42 0.00 36.25 4.00
2712 3773 4.927267 AATTGGTGTAGGAATCACTGGA 57.073 40.909 0.00 0.00 36.25 3.86
2713 3774 4.927267 ATTGGTGTAGGAATCACTGGAA 57.073 40.909 0.00 0.00 36.25 3.53
2714 3775 3.695830 TGGTGTAGGAATCACTGGAAC 57.304 47.619 0.00 0.00 36.25 3.62
2715 3776 3.248024 TGGTGTAGGAATCACTGGAACT 58.752 45.455 0.00 0.00 36.25 3.01
2716 3777 3.007940 TGGTGTAGGAATCACTGGAACTG 59.992 47.826 0.00 0.00 36.25 3.16
2717 3778 3.260884 GGTGTAGGAATCACTGGAACTGA 59.739 47.826 0.00 0.00 36.25 3.41
2718 3779 4.080863 GGTGTAGGAATCACTGGAACTGAT 60.081 45.833 0.00 0.00 36.25 2.90
2719 3780 5.491982 GTGTAGGAATCACTGGAACTGATT 58.508 41.667 0.00 0.00 40.38 2.57
2720 3781 5.940470 GTGTAGGAATCACTGGAACTGATTT 59.060 40.000 0.00 0.00 38.27 2.17
2721 3782 6.092807 GTGTAGGAATCACTGGAACTGATTTC 59.907 42.308 0.00 0.00 38.27 2.17
2722 3783 5.511386 AGGAATCACTGGAACTGATTTCT 57.489 39.130 0.00 0.00 38.61 2.52
2723 3784 5.251764 AGGAATCACTGGAACTGATTTCTG 58.748 41.667 1.81 0.00 40.90 3.02
2724 3785 5.006386 GGAATCACTGGAACTGATTTCTGT 58.994 41.667 0.00 0.00 38.27 3.41
2725 3786 5.106396 GGAATCACTGGAACTGATTTCTGTG 60.106 44.000 0.00 0.23 38.27 3.66
2726 3787 4.687901 TCACTGGAACTGATTTCTGTGA 57.312 40.909 4.45 4.45 41.17 3.58
2727 3788 5.233083 TCACTGGAACTGATTTCTGTGAT 57.767 39.130 4.45 0.00 39.92 3.06
2728 3789 4.999311 TCACTGGAACTGATTTCTGTGATG 59.001 41.667 4.45 0.00 39.92 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.833860 TCGGCTTTTCAGTTTTTGCG 58.166 45.000 0.00 0.00 0.00 4.85
173 620 6.725834 AGGATCAATTCTTTTTGGCCTTAGAA 59.274 34.615 3.32 8.02 31.88 2.10
188 635 2.224892 GGGCTCCCCTAAGGATCAATTC 60.225 54.545 0.00 0.00 46.33 2.17
236 689 9.720769 ATTCGAGTTTGGTTTCTATTTCTAAGA 57.279 29.630 0.00 0.00 0.00 2.10
282 735 5.719173 TGTTTGTTGTTTCTCCCTTTTCAG 58.281 37.500 0.00 0.00 0.00 3.02
411 865 1.926511 GCAAGTTGCTGGGTGGATCG 61.927 60.000 20.71 0.00 40.96 3.69
496 950 1.068474 CGGTTGGTCTTGCGAAGTAG 58.932 55.000 0.00 0.00 0.00 2.57
836 1307 3.016031 TGCGGTCAATTCGTACCTACTA 58.984 45.455 0.00 0.00 33.34 1.82
837 1308 1.820519 TGCGGTCAATTCGTACCTACT 59.179 47.619 0.00 0.00 33.34 2.57
838 1309 2.190981 CTGCGGTCAATTCGTACCTAC 58.809 52.381 0.00 0.00 33.34 3.18
839 1310 1.820519 ACTGCGGTCAATTCGTACCTA 59.179 47.619 0.00 0.00 33.34 3.08
840 1311 0.606604 ACTGCGGTCAATTCGTACCT 59.393 50.000 0.00 0.00 33.34 3.08
841 1312 0.719465 CACTGCGGTCAATTCGTACC 59.281 55.000 0.00 0.00 0.00 3.34
883 1354 2.303890 TGAACTGCTGTGGTGATCTGAT 59.696 45.455 0.00 0.00 0.00 2.90
901 1372 1.013596 CTGTTGCTGACGGTTGTGAA 58.986 50.000 0.00 0.00 0.00 3.18
1046 1517 2.047844 CCACGGAGAGCACACAGG 60.048 66.667 0.00 0.00 0.00 4.00
1086 1557 1.376037 GACGAAGGGTTGCTGGGAG 60.376 63.158 0.00 0.00 0.00 4.30
1091 1562 2.032681 GCCAGACGAAGGGTTGCT 59.967 61.111 0.00 0.00 0.00 3.91
1159 1630 4.579869 AGGCGTGAGTTGAATTGATTACT 58.420 39.130 0.00 0.00 0.00 2.24
1182 1660 4.489679 TGCACGCAGTAGATAGATGTAG 57.510 45.455 0.00 0.00 41.61 2.74
1227 1705 4.523083 ACCCATCGCAAGTGTTAATACAT 58.477 39.130 5.08 0.00 36.50 2.29
1440 1918 1.593209 GAAGTTCGTGGCCGTGACA 60.593 57.895 0.00 0.00 35.01 3.58
1539 2017 1.002274 ACCGATCTTCTCCCAGGCT 59.998 57.895 0.00 0.00 0.00 4.58
1602 2662 7.876936 ATTCACAGAATGCATGATAGAAGTT 57.123 32.000 0.00 0.00 42.53 2.66
1609 2669 9.163899 GACATATCTATTCACAGAATGCATGAT 57.836 33.333 0.00 0.00 42.53 2.45
1611 2671 8.319143 TGACATATCTATTCACAGAATGCATG 57.681 34.615 0.00 0.00 42.53 4.06
1677 2738 6.645415 ACTTGAGTTTCGATTCGAATAGTGTT 59.355 34.615 21.09 4.98 45.28 3.32
1691 2752 5.150683 TCAACAACACAAACTTGAGTTTCG 58.849 37.500 6.16 4.11 45.54 3.46
1727 2788 2.733956 TCAGTTGTGCAGTTTTTCCCT 58.266 42.857 0.00 0.00 0.00 4.20
1731 2792 8.770438 TTAGAATTTTCAGTTGTGCAGTTTTT 57.230 26.923 0.00 0.00 0.00 1.94
1818 2879 6.694411 ACCGTATTAATCGTGTTCATAGTCAC 59.306 38.462 0.00 0.00 0.00 3.67
1899 2960 0.944999 AGGATGGCCTCTCCCTTCTA 59.055 55.000 18.18 0.00 42.19 2.10
1952 3013 4.458397 CCCTAATGCACATGATCAGAACT 58.542 43.478 0.00 0.00 0.00 3.01
2026 3087 1.881973 CAGATTGGGGGCGTGAATATG 59.118 52.381 0.00 0.00 0.00 1.78
2035 3096 2.101415 GCAGAATAAACAGATTGGGGGC 59.899 50.000 0.00 0.00 0.00 5.80
2036 3097 2.358898 CGCAGAATAAACAGATTGGGGG 59.641 50.000 0.00 0.00 0.00 5.40
2050 3111 8.519526 TGTTTGATAGGAAAATTAACGCAGAAT 58.480 29.630 0.00 0.00 0.00 2.40
2075 3136 9.552114 CTCTTTCAGCAAGATGTTAACTATTTG 57.448 33.333 7.22 9.14 40.95 2.32
2186 3247 9.294030 GCCTATTTCAATTTGTAGACAAGAATG 57.706 33.333 0.00 0.00 37.15 2.67
2217 3278 3.644966 TTTTCTCGAATGTATGGGGCT 57.355 42.857 0.00 0.00 0.00 5.19
2229 3290 7.411486 ACTCCTTCAGAGATTATTTTCTCGA 57.589 36.000 0.00 0.00 46.50 4.04
2304 3365 7.421599 AGATCATAGTCTTGTAGTGTCGAATG 58.578 38.462 0.00 0.00 0.00 2.67
2316 3377 7.925483 AGAAAATCCTTCGAGATCATAGTCTTG 59.075 37.037 0.00 0.00 0.00 3.02
2438 3499 3.069443 GGTCTTTTTCCATTTGCTGGTCA 59.931 43.478 0.00 0.00 46.08 4.02
2504 3565 8.691661 TTTAGCTGAATTCTTTCCTGTTAAGT 57.308 30.769 7.05 0.00 0.00 2.24
2609 3670 1.541670 GGTCAACGCTCTTGGGTACAA 60.542 52.381 0.00 0.00 38.46 2.41
2628 3689 5.416952 TCAAGTTACTACCGAACCTCTTAGG 59.583 44.000 0.00 0.00 42.49 2.69
2629 3690 6.506500 TCAAGTTACTACCGAACCTCTTAG 57.493 41.667 0.00 0.00 0.00 2.18
2630 3691 6.888632 AGATCAAGTTACTACCGAACCTCTTA 59.111 38.462 0.00 0.00 0.00 2.10
2631 3692 5.715753 AGATCAAGTTACTACCGAACCTCTT 59.284 40.000 0.00 0.00 0.00 2.85
2632 3693 5.125739 CAGATCAAGTTACTACCGAACCTCT 59.874 44.000 0.00 0.00 0.00 3.69
2633 3694 5.125097 TCAGATCAAGTTACTACCGAACCTC 59.875 44.000 0.00 0.00 0.00 3.85
2634 3695 5.014858 TCAGATCAAGTTACTACCGAACCT 58.985 41.667 0.00 0.00 0.00 3.50
2635 3696 5.320549 TCAGATCAAGTTACTACCGAACC 57.679 43.478 0.00 0.00 0.00 3.62
2636 3697 6.388278 ACTTCAGATCAAGTTACTACCGAAC 58.612 40.000 0.00 0.00 32.34 3.95
2637 3698 6.585695 ACTTCAGATCAAGTTACTACCGAA 57.414 37.500 0.00 0.00 32.34 4.30
2638 3699 6.585695 AACTTCAGATCAAGTTACTACCGA 57.414 37.500 8.92 0.00 43.43 4.69
2639 3700 6.866770 TGAAACTTCAGATCAAGTTACTACCG 59.133 38.462 10.61 0.00 44.28 4.02
2640 3701 8.660373 CATGAAACTTCAGATCAAGTTACTACC 58.340 37.037 10.61 1.98 44.28 3.18
2641 3702 9.424319 TCATGAAACTTCAGATCAAGTTACTAC 57.576 33.333 10.61 5.45 44.28 2.73
2643 3704 9.160496 GATCATGAAACTTCAGATCAAGTTACT 57.840 33.333 10.61 0.00 44.28 2.24
2644 3705 8.939929 TGATCATGAAACTTCAGATCAAGTTAC 58.060 33.333 20.35 5.60 44.28 2.50
2645 3706 9.676861 ATGATCATGAAACTTCAGATCAAGTTA 57.323 29.630 23.30 11.18 44.28 2.24
2646 3707 7.991084 TGATCATGAAACTTCAGATCAAGTT 57.009 32.000 20.35 5.56 46.51 2.66
2647 3708 7.827729 TGATGATCATGAAACTTCAGATCAAGT 59.172 33.333 23.30 15.45 44.71 3.16
2648 3709 8.209917 TGATGATCATGAAACTTCAGATCAAG 57.790 34.615 23.30 0.00 44.71 3.02
2649 3710 8.747538 ATGATGATCATGAAACTTCAGATCAA 57.252 30.769 23.30 15.61 44.71 2.57
2650 3711 7.990886 TGATGATGATCATGAAACTTCAGATCA 59.009 33.333 14.30 22.53 45.09 2.92
2651 3712 8.379457 TGATGATGATCATGAAACTTCAGATC 57.621 34.615 14.30 16.66 41.08 2.75
2652 3713 8.926092 ATGATGATGATCATGAAACTTCAGAT 57.074 30.769 14.30 13.50 45.90 2.90
2653 3714 8.747538 AATGATGATGATCATGAAACTTCAGA 57.252 30.769 14.30 12.45 46.79 3.27
2655 3716 8.565416 GCTAATGATGATGATCATGAAACTTCA 58.435 33.333 14.30 12.15 46.79 3.02
2656 3717 8.784994 AGCTAATGATGATGATCATGAAACTTC 58.215 33.333 14.30 6.96 46.79 3.01
2657 3718 8.693120 AGCTAATGATGATGATCATGAAACTT 57.307 30.769 14.30 0.00 46.79 2.66
2658 3719 8.693120 AAGCTAATGATGATGATCATGAAACT 57.307 30.769 14.30 2.06 46.79 2.66
2659 3720 8.021973 GGAAGCTAATGATGATGATCATGAAAC 58.978 37.037 14.30 4.43 46.79 2.78
2660 3721 7.942894 AGGAAGCTAATGATGATGATCATGAAA 59.057 33.333 14.30 0.00 46.79 2.69
2661 3722 7.459234 AGGAAGCTAATGATGATGATCATGAA 58.541 34.615 14.30 1.09 46.79 2.57
2662 3723 7.017319 AGGAAGCTAATGATGATGATCATGA 57.983 36.000 14.30 4.76 46.79 3.07
2663 3724 6.879458 TGAGGAAGCTAATGATGATGATCATG 59.121 38.462 14.30 0.00 46.79 3.07
2665 3726 6.042897 AGTGAGGAAGCTAATGATGATGATCA 59.957 38.462 0.00 0.00 42.92 2.92
2666 3727 6.465948 AGTGAGGAAGCTAATGATGATGATC 58.534 40.000 0.00 0.00 0.00 2.92
2667 3728 6.436738 AGTGAGGAAGCTAATGATGATGAT 57.563 37.500 0.00 0.00 0.00 2.45
2668 3729 5.883685 AGTGAGGAAGCTAATGATGATGA 57.116 39.130 0.00 0.00 0.00 2.92
2669 3730 8.504815 CAATTAGTGAGGAAGCTAATGATGATG 58.495 37.037 0.00 0.00 37.79 3.07
2670 3731 7.664731 CCAATTAGTGAGGAAGCTAATGATGAT 59.335 37.037 0.00 0.00 37.79 2.45
2671 3732 6.994496 CCAATTAGTGAGGAAGCTAATGATGA 59.006 38.462 0.00 0.00 37.79 2.92
2672 3733 6.769822 ACCAATTAGTGAGGAAGCTAATGATG 59.230 38.462 0.00 0.00 37.79 3.07
2673 3734 6.769822 CACCAATTAGTGAGGAAGCTAATGAT 59.230 38.462 0.00 0.00 40.34 2.45
2674 3735 6.115446 CACCAATTAGTGAGGAAGCTAATGA 58.885 40.000 0.00 0.00 40.34 2.57
2675 3736 5.882557 ACACCAATTAGTGAGGAAGCTAATG 59.117 40.000 11.13 0.00 40.34 1.90
2676 3737 6.067217 ACACCAATTAGTGAGGAAGCTAAT 57.933 37.500 11.13 0.00 40.34 1.73
2677 3738 5.499004 ACACCAATTAGTGAGGAAGCTAA 57.501 39.130 11.13 0.00 40.34 3.09
2678 3739 5.128827 CCTACACCAATTAGTGAGGAAGCTA 59.871 44.000 11.13 0.00 40.34 3.32
2679 3740 4.080863 CCTACACCAATTAGTGAGGAAGCT 60.081 45.833 11.13 0.00 40.34 3.74
2680 3741 4.081087 TCCTACACCAATTAGTGAGGAAGC 60.081 45.833 11.13 0.00 39.24 3.86
2681 3742 5.677319 TCCTACACCAATTAGTGAGGAAG 57.323 43.478 11.13 3.03 39.24 3.46
2682 3743 6.214615 TGATTCCTACACCAATTAGTGAGGAA 59.785 38.462 24.87 24.87 46.30 3.36
2683 3744 5.724370 TGATTCCTACACCAATTAGTGAGGA 59.276 40.000 11.13 13.97 39.84 3.71
2684 3745 5.817816 GTGATTCCTACACCAATTAGTGAGG 59.182 44.000 11.13 12.14 40.34 3.86
2685 3746 6.536582 CAGTGATTCCTACACCAATTAGTGAG 59.463 42.308 11.13 4.20 40.34 3.51
2686 3747 6.406370 CAGTGATTCCTACACCAATTAGTGA 58.594 40.000 11.13 0.00 40.34 3.41
2687 3748 5.586243 CCAGTGATTCCTACACCAATTAGTG 59.414 44.000 2.21 2.21 43.65 2.74
2688 3749 5.487488 TCCAGTGATTCCTACACCAATTAGT 59.513 40.000 0.00 0.00 38.82 2.24
2689 3750 5.989477 TCCAGTGATTCCTACACCAATTAG 58.011 41.667 0.00 0.00 38.82 1.73
2690 3751 6.012858 AGTTCCAGTGATTCCTACACCAATTA 60.013 38.462 0.00 0.00 38.82 1.40
2691 3752 4.927267 TCCAGTGATTCCTACACCAATT 57.073 40.909 0.00 0.00 38.82 2.32
2692 3753 4.289672 AGTTCCAGTGATTCCTACACCAAT 59.710 41.667 0.00 0.00 38.82 3.16
2693 3754 3.650942 AGTTCCAGTGATTCCTACACCAA 59.349 43.478 0.00 0.00 38.82 3.67
2694 3755 3.007940 CAGTTCCAGTGATTCCTACACCA 59.992 47.826 0.00 0.00 38.82 4.17
2695 3756 3.260884 TCAGTTCCAGTGATTCCTACACC 59.739 47.826 0.00 0.00 38.82 4.16
2696 3757 4.537135 TCAGTTCCAGTGATTCCTACAC 57.463 45.455 0.00 0.00 38.38 2.90
2697 3758 5.762179 AATCAGTTCCAGTGATTCCTACA 57.238 39.130 1.60 0.00 42.84 2.74
2698 3759 6.314896 CAGAAATCAGTTCCAGTGATTCCTAC 59.685 42.308 7.17 1.92 44.92 3.18
2699 3760 6.013379 ACAGAAATCAGTTCCAGTGATTCCTA 60.013 38.462 7.17 0.00 44.92 2.94
2700 3761 5.222007 ACAGAAATCAGTTCCAGTGATTCCT 60.222 40.000 7.17 0.00 44.92 3.36
2701 3762 5.006386 ACAGAAATCAGTTCCAGTGATTCC 58.994 41.667 7.17 0.00 44.92 3.01
2702 3763 5.702670 TCACAGAAATCAGTTCCAGTGATTC 59.297 40.000 6.63 2.86 44.92 2.52
2703 3764 5.624159 TCACAGAAATCAGTTCCAGTGATT 58.376 37.500 6.63 1.60 46.95 2.57
2704 3765 5.233083 TCACAGAAATCAGTTCCAGTGAT 57.767 39.130 6.63 0.00 42.37 3.06
2705 3766 4.687901 TCACAGAAATCAGTTCCAGTGA 57.312 40.909 6.63 6.63 43.76 3.41
2706 3767 5.292671 CATCACAGAAATCAGTTCCAGTG 57.707 43.478 2.52 2.52 41.06 3.66


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

AutoCloner maintained by Alex Coulton.