Multiple sequence alignment - TraesCS7D01G481300

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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 TraesCS7D01G481300 chr7D 100.000 6661 0 0 1 6661 591729578 591736238 0.000000e+00 12301.0
1 TraesCS7D01G481300 chr7D 83.166 897 128 20 3920 4810 591591675 591592554 0.000000e+00 798.0
2 TraesCS7D01G481300 chr7D 82.839 775 100 16 2426 3172 591588475 591589244 0.000000e+00 664.0
3 TraesCS7D01G481300 chr7D 77.530 494 98 10 6171 6661 591594078 591594561 1.090000e-72 285.0
4 TraesCS7D01G481300 chr7D 87.421 159 13 6 2144 2297 591588133 591588289 6.870000e-40 176.0
5 TraesCS7D01G481300 chr7B 95.472 2805 117 7 3863 6661 671822570 671819770 0.000000e+00 4468.0
6 TraesCS7D01G481300 chr7B 91.916 2004 114 13 662 2625 671826244 671824249 0.000000e+00 2760.0
7 TraesCS7D01G481300 chr7B 94.012 668 23 6 2624 3276 671824012 671823347 0.000000e+00 996.0
8 TraesCS7D01G481300 chr7B 91.988 649 35 6 32 668 126185047 126184404 0.000000e+00 894.0
9 TraesCS7D01G481300 chr7B 82.435 928 123 30 3905 4810 672171919 672171010 0.000000e+00 774.0
10 TraesCS7D01G481300 chr7B 95.274 402 18 1 3405 3805 671823357 671822956 2.620000e-178 636.0
11 TraesCS7D01G481300 chr7B 81.281 796 108 29 2406 3172 672173526 672172743 2.050000e-169 606.0
12 TraesCS7D01G481300 chr7A 94.419 2598 140 4 4038 6634 682523561 682526154 0.000000e+00 3989.0
13 TraesCS7D01G481300 chr7A 93.703 1064 54 5 966 2020 682511034 682512093 0.000000e+00 1581.0
14 TraesCS7D01G481300 chr7A 95.116 778 25 5 2148 2913 682512222 682512998 0.000000e+00 1214.0
15 TraesCS7D01G481300 chr7A 89.899 891 83 7 3926 4811 682771907 682772795 0.000000e+00 1140.0
16 TraesCS7D01G481300 chr7A 87.866 923 100 10 5743 6661 682774320 682775234 0.000000e+00 1074.0
17 TraesCS7D01G481300 chr7A 81.541 1181 172 29 5278 6436 682220033 682221189 0.000000e+00 931.0
18 TraesCS7D01G481300 chr7A 90.187 642 45 7 29 668 92090765 92091390 0.000000e+00 821.0
19 TraesCS7D01G481300 chr7A 83.204 899 132 18 3920 4810 682191950 682192837 0.000000e+00 806.0
20 TraesCS7D01G481300 chr7A 85.031 648 83 11 4815 5454 682773330 682773971 0.000000e+00 647.0
21 TraesCS7D01G481300 chr7A 82.323 775 103 24 2427 3172 682190336 682191105 5.630000e-180 641.0
22 TraesCS7D01G481300 chr7A 87.912 546 43 8 2402 2937 682768515 682769047 7.340000e-174 621.0
23 TraesCS7D01G481300 chr7A 88.591 447 15 6 3600 4046 682522202 682522612 1.660000e-140 510.0
24 TraesCS7D01G481300 chr7A 86.335 483 42 11 3354 3815 682771332 682771811 7.710000e-139 505.0
25 TraesCS7D01G481300 chr7A 92.722 316 18 5 662 973 682504814 682505128 1.020000e-122 451.0
26 TraesCS7D01G481300 chr7A 89.640 222 21 2 5451 5672 682774093 682774312 1.410000e-71 281.0
27 TraesCS7D01G481300 chr7A 92.405 79 5 1 2932 3010 682769090 682769167 1.960000e-20 111.0
28 TraesCS7D01G481300 chr7A 92.857 56 3 1 3853 3907 682771811 682771866 5.540000e-11 80.5
29 TraesCS7D01G481300 chr6B 88.975 1805 185 11 4868 6661 78380141 78381942 0.000000e+00 2218.0
30 TraesCS7D01G481300 chr6B 89.789 901 85 6 3910 4808 78378536 78379431 0.000000e+00 1147.0
31 TraesCS7D01G481300 chr6B 89.924 655 35 12 32 674 70679209 70679844 0.000000e+00 815.0
32 TraesCS7D01G481300 chr6B 86.931 505 55 8 2420 2917 78377410 78377910 2.100000e-154 556.0
33 TraesCS7D01G481300 chr6B 81.563 499 62 13 995 1477 78376060 78376544 1.050000e-102 385.0
34 TraesCS7D01G481300 chr6B 90.690 290 24 3 3209 3497 78378206 78378493 3.770000e-102 383.0
35 TraesCS7D01G481300 chr6B 93.450 229 9 4 2932 3155 78377978 78378205 1.070000e-87 335.0
36 TraesCS7D01G481300 chr6B 92.778 180 8 5 784 960 78375546 78375723 8.570000e-64 255.0
37 TraesCS7D01G481300 chr6B 91.971 137 7 4 662 796 78375351 78375485 8.820000e-44 189.0
38 TraesCS7D01G481300 chr3B 94.012 668 29 3 1 668 710169181 710169837 0.000000e+00 1002.0
39 TraesCS7D01G481300 chrUn 91.912 680 39 4 4 672 113112591 113111917 0.000000e+00 937.0
40 TraesCS7D01G481300 chr5B 93.071 635 33 5 29 661 592439944 592439319 0.000000e+00 918.0
41 TraesCS7D01G481300 chr5B 92.296 649 41 6 29 675 702362815 702362174 0.000000e+00 913.0
42 TraesCS7D01G481300 chr2B 91.220 672 44 10 1 668 40923468 40924128 0.000000e+00 900.0
43 TraesCS7D01G481300 chr2B 91.638 574 39 4 32 601 609960182 609959614 0.000000e+00 785.0
44 TraesCS7D01G481300 chr2B 79.898 786 121 27 2430 3185 11308232 11307454 5.880000e-150 542.0
45 TraesCS7D01G481300 chr2B 78.926 503 88 12 6170 6661 11303979 11303484 6.440000e-85 326.0
46 TraesCS7D01G481300 chr2B 76.160 625 110 31 3192 3791 11307367 11306757 6.530000e-75 292.0
47 TraesCS7D01G481300 chr1A 91.837 637 40 5 33 668 812979 812354 0.000000e+00 878.0
48 TraesCS7D01G481300 chr2A 80.282 852 145 15 3920 4753 7558427 7557581 7.340000e-174 621.0
49 TraesCS7D01G481300 chr2A 80.025 791 101 31 2427 3185 7560051 7559286 3.540000e-147 532.0
50 TraesCS7D01G481300 chr2A 85.075 134 16 4 3660 3791 7558638 7558507 4.190000e-27 134.0
51 TraesCS7D01G481300 chr2A 100.000 31 0 0 5277 5307 29326061 29326031 2.590000e-04 58.4
52 TraesCS7D01G481300 chr2D 82.444 712 119 6 4045 4753 8508721 8508013 9.490000e-173 617.0
53 TraesCS7D01G481300 chr2D 79.825 798 95 28 2428 3185 8510417 8509646 7.650000e-144 521.0
54 TraesCS7D01G481300 chr2D 74.682 628 114 36 3192 3791 8509558 8508948 3.100000e-58 237.0


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 TraesCS7D01G481300 chr7D 591729578 591736238 6660 False 12301.000000 12301 100.000000 1 6661 1 chr7D.!!$F1 6660
1 TraesCS7D01G481300 chr7D 591588133 591594561 6428 False 480.750000 798 82.739000 2144 6661 4 chr7D.!!$F2 4517
2 TraesCS7D01G481300 chr7B 671819770 671826244 6474 True 2215.000000 4468 94.168500 662 6661 4 chr7B.!!$R2 5999
3 TraesCS7D01G481300 chr7B 126184404 126185047 643 True 894.000000 894 91.988000 32 668 1 chr7B.!!$R1 636
4 TraesCS7D01G481300 chr7B 672171010 672173526 2516 True 690.000000 774 81.858000 2406 4810 2 chr7B.!!$R3 2404
5 TraesCS7D01G481300 chr7A 682522202 682526154 3952 False 2249.500000 3989 91.505000 3600 6634 2 chr7A.!!$F6 3034
6 TraesCS7D01G481300 chr7A 682511034 682512998 1964 False 1397.500000 1581 94.409500 966 2913 2 chr7A.!!$F5 1947
7 TraesCS7D01G481300 chr7A 682220033 682221189 1156 False 931.000000 931 81.541000 5278 6436 1 chr7A.!!$F2 1158
8 TraesCS7D01G481300 chr7A 92090765 92091390 625 False 821.000000 821 90.187000 29 668 1 chr7A.!!$F1 639
9 TraesCS7D01G481300 chr7A 682190336 682192837 2501 False 723.500000 806 82.763500 2427 4810 2 chr7A.!!$F4 2383
10 TraesCS7D01G481300 chr7A 682768515 682775234 6719 False 557.437500 1140 88.993125 2402 6661 8 chr7A.!!$F7 4259
11 TraesCS7D01G481300 chr6B 70679209 70679844 635 False 815.000000 815 89.924000 32 674 1 chr6B.!!$F1 642
12 TraesCS7D01G481300 chr6B 78375351 78381942 6591 False 683.500000 2218 89.518375 662 6661 8 chr6B.!!$F2 5999
13 TraesCS7D01G481300 chr3B 710169181 710169837 656 False 1002.000000 1002 94.012000 1 668 1 chr3B.!!$F1 667
14 TraesCS7D01G481300 chrUn 113111917 113112591 674 True 937.000000 937 91.912000 4 672 1 chrUn.!!$R1 668
15 TraesCS7D01G481300 chr5B 592439319 592439944 625 True 918.000000 918 93.071000 29 661 1 chr5B.!!$R1 632
16 TraesCS7D01G481300 chr5B 702362174 702362815 641 True 913.000000 913 92.296000 29 675 1 chr5B.!!$R2 646
17 TraesCS7D01G481300 chr2B 40923468 40924128 660 False 900.000000 900 91.220000 1 668 1 chr2B.!!$F1 667
18 TraesCS7D01G481300 chr2B 609959614 609960182 568 True 785.000000 785 91.638000 32 601 1 chr2B.!!$R1 569
19 TraesCS7D01G481300 chr2B 11303484 11308232 4748 True 386.666667 542 78.328000 2430 6661 3 chr2B.!!$R2 4231
20 TraesCS7D01G481300 chr1A 812354 812979 625 True 878.000000 878 91.837000 33 668 1 chr1A.!!$R1 635
21 TraesCS7D01G481300 chr2A 7557581 7560051 2470 True 429.000000 621 81.794000 2427 4753 3 chr2A.!!$R2 2326
22 TraesCS7D01G481300 chr2D 8508013 8510417 2404 True 458.333333 617 78.983667 2428 4753 3 chr2D.!!$R1 2325

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
654 690 1.677820 GGGCCTAAAAGCTTGCTCGTA 60.678 52.381 0.84 0.0 0.00 3.43 F
1393 1811 0.387929 TACACGCGATTCCTGGATCC 59.612 55.000 15.93 4.2 0.00 3.36 F
1627 2094 0.957395 TACCTGTCGAGTCCCGTCAC 60.957 60.000 0.00 0.0 39.75 3.67 F
1642 2109 1.404181 CGTCACCCATCGTTGACTGAT 60.404 52.381 0.00 0.0 0.00 2.90 F
2610 3220 1.458398 CCAATGTGGCGACAATGGTA 58.542 50.000 23.66 0.0 45.05 3.25 F
3859 8702 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.0 0.00 3.67 F
3861 9023 1.393539 GTGTGTGTGTGTGTGTGTCTC 59.606 52.381 0.00 0.0 0.00 3.36 F
5427 12424 2.762535 TTCTTAAGTTCCTCCAGCCG 57.237 50.000 1.63 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2503 0.527600 TGCGATTGTACTAGCAGCGG 60.528 55.000 0.00 0.00 34.39 5.52 R
2595 3205 0.973632 AGAGTACCATTGTCGCCACA 59.026 50.000 0.00 0.00 0.00 4.17 R
2820 3678 2.239681 AGGTAGTTCAGGACCTCAGG 57.760 55.000 0.00 0.00 42.69 3.86 R
3302 6420 5.385198 TGAGGAAAGCTATGTGAACCTTTT 58.615 37.500 0.00 0.00 0.00 2.27 R
4150 10336 0.792640 CGAGAGCTTGTGTCGCATTT 59.207 50.000 0.00 0.00 34.82 2.32 R
5338 12331 2.724454 TCTAGGTCTCGAAGGACTTGG 58.276 52.381 4.97 0.24 36.55 3.61 R
5456 12578 7.383102 AGGAAAACAATATGTGTGAGACATC 57.617 36.000 0.00 0.00 41.91 3.06 R
6399 13755 9.635404 TTTTCACCACCTATTCTTCTTTCTTAA 57.365 29.630 0.00 0.00 0.00 1.85 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
102 113 6.625873 ACCAACTGAAGAAAATTCAGAGAC 57.374 37.500 21.08 0.00 46.57 3.36
288 300 3.911698 AGCCGTGCAGACGTGACA 61.912 61.111 0.00 0.00 44.54 3.58
339 351 1.873270 ATCGCGTACAGGTGCAGACA 61.873 55.000 5.77 0.00 0.00 3.41
409 437 2.045536 CCCTTCTGCAGCCAGGAC 60.046 66.667 25.87 0.00 39.61 3.85
491 527 2.494677 CTAGCGACTACTGCTGGGT 58.505 57.895 0.00 0.00 43.85 4.51
516 552 4.570663 CATCGGTCCGCTCGGTCC 62.571 72.222 6.34 13.33 39.56 4.46
654 690 1.677820 GGGCCTAAAAGCTTGCTCGTA 60.678 52.381 0.84 0.00 0.00 3.43
658 694 2.540101 CCTAAAAGCTTGCTCGTATCGG 59.460 50.000 0.00 0.00 0.00 4.18
705 741 8.918961 AAACAACACGAATAATTTGTTTCTGA 57.081 26.923 5.65 0.00 44.82 3.27
739 775 5.503634 TTCCATGACCTCTCATTTCTTCA 57.496 39.130 0.00 0.00 34.65 3.02
785 821 7.614583 AGCTGAATATAATAGCCATGCATCTTT 59.385 33.333 0.00 0.00 38.18 2.52
891 1001 2.125326 GGCCCGCCCTTACCATTTC 61.125 63.158 0.00 0.00 0.00 2.17
898 1008 3.932089 CCGCCCTTACCATTTCAAAATTG 59.068 43.478 0.00 0.00 0.00 2.32
920 1030 2.817844 CAACCACCTACCTAGTTTTGGC 59.182 50.000 0.00 0.00 0.00 4.52
961 1071 2.282180 CCACCAACCCCTTCCACG 60.282 66.667 0.00 0.00 0.00 4.94
978 1090 6.696148 CCTTCCACGAAATATATATACCGCTC 59.304 42.308 13.40 0.23 0.00 5.03
1053 1469 2.488355 CTTTAGTCGCCTCGCCGA 59.512 61.111 0.00 0.00 34.40 5.54
1085 1501 1.671979 GTTTACCGGTGGAATAGCCC 58.328 55.000 19.93 0.00 34.97 5.19
1087 1503 0.687098 TTACCGGTGGAATAGCCCGA 60.687 55.000 19.93 0.00 44.41 5.14
1281 1697 1.638529 AAATGGGTTTGGCGATGGAA 58.361 45.000 0.00 0.00 0.00 3.53
1295 1711 4.226761 GCGATGGAAATTCGTTTGTTTCT 58.773 39.130 0.00 0.00 38.81 2.52
1393 1811 0.387929 TACACGCGATTCCTGGATCC 59.612 55.000 15.93 4.20 0.00 3.36
1434 1864 7.513505 CGTTTGTTTTTGTGATCTGTGTTGATC 60.514 37.037 0.00 0.00 42.19 2.92
1449 1879 5.179368 TGTGTTGATCTTTTCGAAGTGGATC 59.821 40.000 20.28 20.28 34.96 3.36
1512 1971 2.034104 TTGCTGATCTGATCTGTGCC 57.966 50.000 20.92 9.12 0.00 5.01
1543 2006 6.304882 GTGAAGTTTGTATTAGAGTTTCCGC 58.695 40.000 0.00 0.00 0.00 5.54
1548 2011 7.156673 AGTTTGTATTAGAGTTTCCGCTGTTA 58.843 34.615 0.00 0.00 0.00 2.41
1572 2035 1.338105 TGCTCTTCCGTCAGTTGGATG 60.338 52.381 0.00 0.00 34.91 3.51
1609 2076 3.258372 ACTCGATTCAGTTCTTGGCTGTA 59.742 43.478 0.00 0.00 35.60 2.74
1627 2094 0.957395 TACCTGTCGAGTCCCGTCAC 60.957 60.000 0.00 0.00 39.75 3.67
1642 2109 1.404181 CGTCACCCATCGTTGACTGAT 60.404 52.381 0.00 0.00 0.00 2.90
1670 2137 3.830192 CATGCCCTTTGCCTCGCC 61.830 66.667 0.00 0.00 40.16 5.54
1921 2404 2.590007 CATCCACTGCCTAGCGCC 60.590 66.667 2.29 0.00 36.24 6.53
1956 2439 4.787280 AGCCTGGGTCTCCTCCGG 62.787 72.222 0.00 0.00 0.00 5.14
2011 2503 6.365247 TGACTTTCGAAACTGTAGACAATAGC 59.635 38.462 6.47 0.00 0.00 2.97
2039 2531 5.047847 GCTAGTACAATCGCAATGGTAGAA 58.952 41.667 0.00 0.00 0.00 2.10
2105 2597 2.327325 ATCATCCGGGCCTACACTAT 57.673 50.000 0.84 0.00 0.00 2.12
2142 2634 8.668510 ACCTGCTGTATATTTGATTTAGTGAG 57.331 34.615 0.00 0.00 0.00 3.51
2304 2879 8.047911 CCTTCATGCTTCATCATAAGGATATCT 58.952 37.037 2.05 0.00 35.59 1.98
2387 2963 4.742440 GCATATCGTTTCCATGGGAGTGTA 60.742 45.833 13.02 0.00 31.21 2.90
2610 3220 1.458398 CCAATGTGGCGACAATGGTA 58.542 50.000 23.66 0.00 45.05 3.25
3074 6098 4.425180 TGTACAAGGTAGCTTTTCACCA 57.575 40.909 3.96 0.00 37.28 4.17
3294 6411 8.893219 TTGTCTATAAGCATGGTGATAAAGAG 57.107 34.615 0.00 0.00 0.00 2.85
3328 6446 3.629398 GGTTCACATAGCTTTCCTCATGG 59.371 47.826 0.00 0.00 0.00 3.66
3545 8270 4.785341 GCGATTAACGGTCACATGGATTTC 60.785 45.833 0.00 0.00 42.83 2.17
3639 8467 7.944000 TGTGGCCAACTGTTGATATATGATAAT 59.056 33.333 21.49 0.00 0.00 1.28
3828 8671 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3829 8672 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3830 8673 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3831 8674 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3832 8675 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3833 8676 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
3834 8677 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
3835 8678 4.403752 TCTCTCTCTCTCTCTCTCTCTGTG 59.596 50.000 0.00 0.00 0.00 3.66
3836 8679 4.096681 TCTCTCTCTCTCTCTCTCTGTGT 58.903 47.826 0.00 0.00 0.00 3.72
3837 8680 4.081476 TCTCTCTCTCTCTCTCTCTGTGTG 60.081 50.000 0.00 0.00 0.00 3.82
3838 8681 3.582647 TCTCTCTCTCTCTCTCTGTGTGT 59.417 47.826 0.00 0.00 0.00 3.72
3839 8682 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
3840 8683 3.072330 TCTCTCTCTCTCTCTGTGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
3841 8684 3.145286 TCTCTCTCTCTCTGTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
3842 8685 2.884012 CTCTCTCTCTCTGTGTGTGTGT 59.116 50.000 0.00 0.00 0.00 3.72
3843 8686 2.620585 TCTCTCTCTCTGTGTGTGTGTG 59.379 50.000 0.00 0.00 0.00 3.82
3844 8687 2.360483 CTCTCTCTCTGTGTGTGTGTGT 59.640 50.000 0.00 0.00 0.00 3.72
3845 8688 2.099756 TCTCTCTCTGTGTGTGTGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
3846 8689 1.824852 TCTCTCTGTGTGTGTGTGTGT 59.175 47.619 0.00 0.00 0.00 3.72
3847 8690 1.929169 CTCTCTGTGTGTGTGTGTGTG 59.071 52.381 0.00 0.00 0.00 3.82
3859 8702 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
3861 9023 1.393539 GTGTGTGTGTGTGTGTGTCTC 59.606 52.381 0.00 0.00 0.00 3.36
4150 10336 3.550820 CCGGAATGTGATACAAATGGGA 58.449 45.455 0.00 0.00 0.00 4.37
4723 10916 8.383318 ACATGCAGTGGTATAGCTATTAAAAG 57.617 34.615 12.39 0.00 0.00 2.27
4969 11957 5.727515 GCATTGTTTGGTTTCTTTCACAAGC 60.728 40.000 0.00 0.00 0.00 4.01
4974 11962 3.271729 TGGTTTCTTTCACAAGCGTGTA 58.728 40.909 4.57 0.00 44.02 2.90
5003 11991 8.589701 TTTCTTAGGAAACTTTGAAGAGGTTT 57.410 30.769 0.00 0.00 43.67 3.27
5427 12424 2.762535 TTCTTAAGTTCCTCCAGCCG 57.237 50.000 1.63 0.00 0.00 5.52
5456 12578 9.831737 GCTGCTGTGATATTTATTTATACTTGG 57.168 33.333 0.00 0.00 0.00 3.61
5737 12886 8.410673 TCTGAGGATGTCCATTAGTTAGATAC 57.589 38.462 1.30 0.00 38.89 2.24
5945 13095 5.399892 GTCAATTTTGCATTTTTGCACATGG 59.600 36.000 0.00 0.00 45.32 3.66
5965 13115 7.639850 CACATGGACATTCACGTATATTTTCAC 59.360 37.037 0.00 0.00 0.00 3.18
6379 13735 0.606604 GACCACCCAAAGTAGCGAGA 59.393 55.000 0.00 0.00 0.00 4.04
6399 13755 6.102663 CGAGACAAACTGAGGAAGACATAAT 58.897 40.000 0.00 0.00 0.00 1.28
6494 13851 5.303165 AGGTAACGAAGAAAGGGTTGTTAG 58.697 41.667 0.00 0.00 46.39 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 113 4.260620 CCGACAGTTTGTACTTGTTCCTTG 60.261 45.833 0.00 0.00 30.26 3.61
288 300 1.306568 GAGGAGCCAAGGAGGGAGT 60.307 63.158 0.00 0.00 38.09 3.85
339 351 2.571216 CGTCGACCACCACCTCCTT 61.571 63.158 10.58 0.00 0.00 3.36
381 409 2.762043 AGAAGGGAGGGAGCGCTC 60.762 66.667 29.38 29.38 0.00 5.03
409 437 0.182775 AATTCCCCGATCCCCTTTCG 59.817 55.000 0.00 0.00 36.38 3.46
454 490 4.247612 GGCCGATACGACGACGCT 62.248 66.667 7.30 0.00 43.96 5.07
491 527 3.781307 CGGACCGATGGCCCAAGA 61.781 66.667 8.64 0.00 0.00 3.02
654 690 1.224592 GTGATTCAGGGTGGCCGAT 59.775 57.895 0.00 0.00 0.00 4.18
658 694 1.271597 ACTCTTGTGATTCAGGGTGGC 60.272 52.381 0.00 0.00 0.00 5.01
705 741 4.536765 AGGTCATGGAAAAATAGGCGATT 58.463 39.130 0.00 0.00 0.00 3.34
891 1001 4.522789 ACTAGGTAGGTGGTTGCAATTTTG 59.477 41.667 0.59 0.00 0.00 2.44
898 1008 2.817844 CCAAAACTAGGTAGGTGGTTGC 59.182 50.000 0.00 0.00 0.00 4.17
920 1030 5.421056 GGAAAGGGGTCTAGGGTTAAAAATG 59.579 44.000 0.00 0.00 0.00 2.32
961 1071 5.533903 TCTCGGGGAGCGGTATATATATTTC 59.466 44.000 0.00 0.00 0.00 2.17
993 1406 4.179579 GCGAGGTGGCGGAATTGC 62.180 66.667 0.00 0.00 0.00 3.56
1053 1469 4.992511 TAAACCACGCGGCGGCTT 62.993 61.111 27.37 15.12 36.88 4.35
1087 1503 2.430367 GAGGGCGACTGGGTTTGT 59.570 61.111 0.00 0.00 0.00 2.83
1168 1584 1.068083 GGCGCCATCGAATCTCTGA 59.932 57.895 24.80 0.00 38.10 3.27
1281 1697 1.000717 CCGGCCAGAAACAAACGAATT 60.001 47.619 2.24 0.00 0.00 2.17
1307 1725 1.079336 GAGCGGACCAAGTACCCAC 60.079 63.158 0.00 0.00 0.00 4.61
1308 1726 1.229082 AGAGCGGACCAAGTACCCA 60.229 57.895 0.00 0.00 0.00 4.51
1368 1786 0.175073 AGGAATCGCGTGTACCTTCC 59.825 55.000 5.77 10.10 36.45 3.46
1393 1811 3.622060 AACGCCGTTCCCCAGATGG 62.622 63.158 0.00 0.00 0.00 3.51
1434 1864 3.060363 CGTTACCGATCCACTTCGAAAAG 59.940 47.826 0.00 0.00 41.62 2.27
1449 1879 0.813184 TAAGACCTCAGCCGTTACCG 59.187 55.000 0.00 0.00 0.00 4.02
1512 1971 1.722011 ATACAAACTTCACCTCCGCG 58.278 50.000 0.00 0.00 0.00 6.46
1543 2006 4.452455 ACTGACGGAAGAGCAAAATAACAG 59.548 41.667 0.00 0.00 0.00 3.16
1548 2011 2.554032 CCAACTGACGGAAGAGCAAAAT 59.446 45.455 0.00 0.00 0.00 1.82
1572 2035 3.655276 TCGAGTTCTTAGACACAACCC 57.345 47.619 0.00 0.00 0.00 4.11
1609 2076 2.114625 TGACGGGACTCGACAGGT 59.885 61.111 0.00 0.00 42.43 4.00
1627 2094 1.280982 CGACATCAGTCAACGATGGG 58.719 55.000 14.73 6.79 45.23 4.00
1642 2109 2.433491 GGGCATGTACACGCGACA 60.433 61.111 15.93 7.50 0.00 4.35
1670 2137 3.032609 GCCGACGATGAGATGGCG 61.033 66.667 0.00 0.00 34.98 5.69
1811 2283 4.758251 CCGCCTGGATGTCGCACA 62.758 66.667 0.00 0.00 37.49 4.57
1895 2370 1.153086 GCAGTGGATGGCGAGGAAT 60.153 57.895 0.00 0.00 0.00 3.01
1937 2420 3.086600 GGAGGAGACCCAGGCTGG 61.087 72.222 27.04 27.04 37.25 4.85
1956 2439 4.119363 TGCATCTGAGCAGGGGCC 62.119 66.667 0.00 0.00 42.56 5.80
2011 2503 0.527600 TGCGATTGTACTAGCAGCGG 60.528 55.000 0.00 0.00 34.39 5.52
2360 2936 2.951642 CCCATGGAAACGATATGCAAGT 59.048 45.455 15.22 0.00 0.00 3.16
2387 2963 1.337118 AACAACGTGAATTGGCCCAT 58.663 45.000 0.00 0.00 33.63 4.00
2595 3205 0.973632 AGAGTACCATTGTCGCCACA 59.026 50.000 0.00 0.00 0.00 4.17
2820 3678 2.239681 AGGTAGTTCAGGACCTCAGG 57.760 55.000 0.00 0.00 42.69 3.86
3074 6098 8.697507 AATGGAGTGAGTACTTTGAAGAAAAT 57.302 30.769 0.00 0.00 37.25 1.82
3173 6204 8.413309 TTCCAATTGAGAAAACTCATGAGAAT 57.587 30.769 29.27 14.23 32.91 2.40
3187 6299 6.657541 GGTGGTACTTTGTATTCCAATTGAGA 59.342 38.462 7.12 0.00 31.81 3.27
3302 6420 5.385198 TGAGGAAAGCTATGTGAACCTTTT 58.615 37.500 0.00 0.00 0.00 2.27
3373 6491 7.985184 TGGTAAGAAGATGGACATACAATGTAC 59.015 37.037 0.00 0.00 45.03 2.90
3828 8671 1.275010 ACACACACACACACACAGAGA 59.725 47.619 0.00 0.00 0.00 3.10
3829 8672 1.394572 CACACACACACACACACAGAG 59.605 52.381 0.00 0.00 0.00 3.35
3830 8673 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
3831 8674 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
3832 8675 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3833 8676 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3834 8677 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3835 8678 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3836 8679 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3837 8680 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3838 8681 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3839 8682 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3840 8683 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
3841 8684 1.393539 GAGACACACACACACACACAC 59.606 52.381 0.00 0.00 0.00 3.82
3842 8685 1.275010 AGAGACACACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
3843 8686 2.010145 AGAGACACACACACACACAC 57.990 50.000 0.00 0.00 0.00 3.82
3844 8687 3.430236 CCTTAGAGACACACACACACACA 60.430 47.826 0.00 0.00 0.00 3.72
3845 8688 3.123804 CCTTAGAGACACACACACACAC 58.876 50.000 0.00 0.00 0.00 3.82
3846 8689 2.764010 ACCTTAGAGACACACACACACA 59.236 45.455 0.00 0.00 0.00 3.72
3847 8690 3.454371 ACCTTAGAGACACACACACAC 57.546 47.619 0.00 0.00 0.00 3.82
3859 8702 2.915463 CGTGTGCGAAGTTACCTTAGAG 59.085 50.000 0.00 0.00 41.33 2.43
3861 9023 2.407361 CACGTGTGCGAAGTTACCTTAG 59.593 50.000 7.58 0.00 42.00 2.18
4150 10336 0.792640 CGAGAGCTTGTGTCGCATTT 59.207 50.000 0.00 0.00 34.82 2.32
4624 10816 2.564771 ACGATGTATGGCAATCACTGG 58.435 47.619 0.00 0.00 0.00 4.00
5338 12331 2.724454 TCTAGGTCTCGAAGGACTTGG 58.276 52.381 4.97 0.24 36.55 3.61
5427 12424 8.926710 AGTATAAATAAATATCACAGCAGCGAC 58.073 33.333 0.00 0.00 0.00 5.19
5456 12578 7.383102 AGGAAAACAATATGTGTGAGACATC 57.617 36.000 0.00 0.00 41.91 3.06
5491 12615 9.679661 TGTTTGCTAAATTGACTAGATTGGATA 57.320 29.630 0.00 0.00 0.00 2.59
5516 12640 8.622157 TCTCCTCAATAAGACGAGTAAAGTATG 58.378 37.037 0.00 0.00 32.98 2.39
5595 12720 8.814038 AGTATGCATGAGTATTTCTTTTCCTT 57.186 30.769 10.16 0.00 0.00 3.36
5682 12807 9.167311 AGCAAGAGAAAACAAATCTAATATCGT 57.833 29.630 0.00 0.00 0.00 3.73
5945 13095 5.791589 TGCGTGAAAATATACGTGAATGTC 58.208 37.500 0.00 0.00 41.98 3.06
5965 13115 6.304126 ACTCGAAACTAATTACACAATTGCG 58.696 36.000 5.05 0.00 35.88 4.85
6379 13735 9.793259 TTCTTAATTATGTCTTCCTCAGTTTGT 57.207 29.630 0.00 0.00 0.00 2.83
6399 13755 9.635404 TTTTCACCACCTATTCTTCTTTCTTAA 57.365 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.