Multiple sequence alignment - TraesCS1B01G457400

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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 TraesCS1B01G457400 chr1B 100.000 6255 0 0 1 6255 671830317 671836571 0.000000e+00 11551
1 TraesCS1B01G457400 chr1B 85.595 840 104 11 1 829 127614760 127613927 0.000000e+00 865
2 TraesCS1B01G457400 chr7D 95.199 5520 146 37 1 5447 158647631 158642158 0.000000e+00 8615
3 TraesCS1B01G457400 chr7D 92.826 2495 89 26 1 2441 577333913 577331455 0.000000e+00 3533
4 TraesCS1B01G457400 chr7D 92.655 2505 95 22 1 2441 435178694 435181173 0.000000e+00 3524
5 TraesCS1B01G457400 chr7D 93.886 1750 66 17 4 1724 65768256 65766519 0.000000e+00 2601
6 TraesCS1B01G457400 chr7D 96.039 1136 29 4 4320 5447 139200516 139199389 0.000000e+00 1834
7 TraesCS1B01G457400 chr7D 93.776 723 9 9 1755 2441 65766525 65765803 0.000000e+00 1053
8 TraesCS1B01G457400 chr7D 85.663 837 101 15 1 829 593566195 593567020 0.000000e+00 863
9 TraesCS1B01G457400 chr7D 90.411 584 56 0 1087 1670 609066624 609066041 0.000000e+00 769
10 TraesCS1B01G457400 chr7D 88.144 582 56 8 5448 6022 348987255 348986680 0.000000e+00 680
11 TraesCS1B01G457400 chr1A 94.499 5035 198 36 1 4966 503679155 503674131 0.000000e+00 7690
12 TraesCS1B01G457400 chr1A 91.507 836 44 13 5447 6255 473566485 473565650 0.000000e+00 1125
13 TraesCS1B01G457400 chr1A 90.909 836 49 13 5447 6255 473511038 473510203 0.000000e+00 1098
14 TraesCS1B01G457400 chr1A 92.982 684 43 4 5447 6128 183435460 183436140 0.000000e+00 992
15 TraesCS1B01G457400 chr1A 85.731 841 106 9 1 829 530576076 530576914 0.000000e+00 876
16 TraesCS1B01G457400 chr1A 86.757 370 15 2 3439 3799 177381466 177381810 1.270000e-101 381
17 TraesCS1B01G457400 chr1A 85.676 370 19 2 3439 3799 98349287 98348943 5.960000e-95 359
18 TraesCS1B01G457400 chr1A 85.255 373 21 2 3439 3802 270719118 270718771 2.770000e-93 353
19 TraesCS1B01G457400 chr6A 93.755 5044 221 37 1 4966 385573375 385568348 0.000000e+00 7483
20 TraesCS1B01G457400 chr6A 97.198 2391 49 7 2587 4960 580785524 580787913 0.000000e+00 4028
21 TraesCS1B01G457400 chr6A 85.249 583 54 11 5448 6022 173272107 173271549 7.030000e-159 571
22 TraesCS1B01G457400 chr3A 93.550 3442 154 23 1 3389 734237813 734241239 0.000000e+00 5064
23 TraesCS1B01G457400 chr3A 86.326 841 99 10 1 829 588380910 588381746 0.000000e+00 902
24 TraesCS1B01G457400 chr4D 96.715 2679 72 4 2448 5110 251092894 251090216 0.000000e+00 4446
25 TraesCS1B01G457400 chr4D 89.384 1997 143 29 1 1962 347176375 347174413 0.000000e+00 2449
26 TraesCS1B01G457400 chr4D 96.491 342 9 1 5109 5447 447218436 447218095 4.230000e-156 562
27 TraesCS1B01G457400 chr2B 95.750 2706 84 7 2448 5137 733356174 733353484 0.000000e+00 4331
28 TraesCS1B01G457400 chr2B 86.326 841 97 10 1 829 88451107 88450273 0.000000e+00 900
29 TraesCS1B01G457400 chr2B 86.094 827 95 11 2 815 88451767 88450948 0.000000e+00 872
30 TraesCS1B01G457400 chr7A 96.204 2397 65 7 2587 4966 26227543 26225156 0.000000e+00 3899
31 TraesCS1B01G457400 chr7A 93.767 1877 64 18 588 2435 69160776 69158924 0.000000e+00 2769
32 TraesCS1B01G457400 chr7A 92.237 1855 66 25 713 2511 26229370 26227538 0.000000e+00 2556
33 TraesCS1B01G457400 chr7A 90.960 354 18 4 3511 3854 107342710 107342361 1.230000e-126 464
34 TraesCS1B01G457400 chr3D 94.342 2492 78 22 1 2441 584383160 584380681 0.000000e+00 3762
35 TraesCS1B01G457400 chr3D 94.996 1319 48 10 3803 5110 214436427 214435116 0.000000e+00 2054
36 TraesCS1B01G457400 chr3D 95.614 342 12 1 5109 5447 250989201 250989542 4.260000e-151 545
37 TraesCS1B01G457400 chr3D 90.877 285 16 2 3517 3792 281245619 281245336 2.130000e-99 374
38 TraesCS1B01G457400 chr3D 89.931 288 20 1 3514 3792 555075430 555075717 4.610000e-96 363
39 TraesCS1B01G457400 chr3D 96.970 99 3 0 5448 5546 396621817 396621719 3.880000e-37 167
40 TraesCS1B01G457400 chr3D 94.737 95 3 1 3517 3611 214437001 214436909 5.050000e-31 147
41 TraesCS1B01G457400 chr2A 91.401 2477 129 17 1 2412 731834190 731836647 0.000000e+00 3317
42 TraesCS1B01G457400 chr2A 96.674 1714 44 3 2405 4107 731836804 731838515 0.000000e+00 2837
43 TraesCS1B01G457400 chr2A 92.043 1219 47 6 1049 2236 21732238 21731039 0.000000e+00 1668
44 TraesCS1B01G457400 chr2A 92.575 835 35 12 5447 6255 506754563 506755396 0.000000e+00 1173
45 TraesCS1B01G457400 chr2A 91.647 838 44 11 5444 6255 331637266 331638103 0.000000e+00 1136
46 TraesCS1B01G457400 chr2A 91.487 834 44 12 5448 6255 311414852 311414020 0.000000e+00 1122
47 TraesCS1B01G457400 chr2A 91.007 834 49 13 5448 6255 242904064 242904897 0.000000e+00 1101
48 TraesCS1B01G457400 chr2A 86.165 824 96 12 1 815 731832210 731833024 0.000000e+00 874
49 TraesCS1B01G457400 chr2A 94.922 256 11 2 2448 2703 774083631 774083378 3.510000e-107 399
50 TraesCS1B01G457400 chr7B 93.603 1876 83 20 3242 5110 646690595 646688750 0.000000e+00 2765
51 TraesCS1B01G457400 chr7B 92.440 754 22 10 3232 3975 695979218 695978490 0.000000e+00 1044
52 TraesCS1B01G457400 chr7B 91.910 754 26 3 3232 3975 532492090 532491362 0.000000e+00 1022
53 TraesCS1B01G457400 chr7B 91.512 754 22 4 3232 3975 601136727 601136006 0.000000e+00 1000
54 TraesCS1B01G457400 chr7B 86.490 829 92 14 1 815 27770533 27769711 0.000000e+00 893
55 TraesCS1B01G457400 chr7B 80.000 210 33 7 741 948 439176134 439175932 5.050000e-31 147
56 TraesCS1B01G457400 chr5D 91.124 1735 110 21 1 1699 556291022 556289296 0.000000e+00 2311
57 TraesCS1B01G457400 chr5D 95.965 347 10 2 5109 5451 398038048 398038394 1.520000e-155 560
58 TraesCS1B01G457400 chr1D 95.737 1431 47 3 3511 4927 408983393 408984823 0.000000e+00 2292
59 TraesCS1B01G457400 chr1D 87.831 189 20 3 3418 3605 385627120 385626934 1.060000e-52 219
60 TraesCS1B01G457400 chr3B 94.058 791 32 8 990 1770 801612531 801611746 0.000000e+00 1186
61 TraesCS1B01G457400 chr3B 96.053 608 9 10 2059 2651 801611728 801611121 0.000000e+00 976
62 TraesCS1B01G457400 chr3B 94.595 592 24 7 4861 5447 801608813 801608225 0.000000e+00 909
63 TraesCS1B01G457400 chr3B 79.667 300 25 14 838 1104 219331855 219332151 3.850000e-42 183
64 TraesCS1B01G457400 chr3B 79.333 300 26 14 838 1104 220619271 220619567 1.790000e-40 178
65 TraesCS1B01G457400 chr4A 92.206 834 40 11 5447 6255 531652399 531651566 0.000000e+00 1157
66 TraesCS1B01G457400 chr4A 91.340 843 39 18 5447 6255 391091745 391092587 0.000000e+00 1122
67 TraesCS1B01G457400 chr4A 90.442 837 51 14 5447 6255 130319907 130320742 0.000000e+00 1075
68 TraesCS1B01G457400 chr5A 88.738 808 67 7 5450 6255 346505596 346504811 0.000000e+00 966
69 TraesCS1B01G457400 chr5A 90.014 711 51 11 5436 6128 227291057 227291765 0.000000e+00 902
70 TraesCS1B01G457400 chr5A 83.509 285 16 15 830 1085 121945178 121944896 2.910000e-58 237
71 TraesCS1B01G457400 chr6D 86.873 777 52 29 5434 6171 73285927 73285162 0.000000e+00 824
72 TraesCS1B01G457400 chr6D 87.459 606 42 15 5448 6022 85502926 85502324 0.000000e+00 667
73 TraesCS1B01G457400 chr6D 94.924 197 10 0 3415 3611 21353992 21354188 6.090000e-80 309
74 TraesCS1B01G457400 chr6B 89.376 593 50 8 5448 6028 391806688 391807279 0.000000e+00 734
75 TraesCS1B01G457400 chr4B 94.799 423 12 2 3242 3654 165701722 165702144 0.000000e+00 651
76 TraesCS1B01G457400 chr2D 95.614 342 12 1 5109 5447 415157293 415157634 4.260000e-151 545
77 TraesCS1B01G457400 chrUn 95.588 340 14 1 5109 5447 331572939 331573278 1.530000e-150 544
78 TraesCS1B01G457400 chrUn 95.588 340 14 1 5109 5447 331601311 331601650 1.530000e-150 544
79 TraesCS1B01G457400 chr5B 83.065 124 17 4 838 959 627291137 627291258 6.630000e-20 110


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 TraesCS1B01G457400 chr1B 671830317 671836571 6254 False 11551.000000 11551 100.000000 1 6255 1 chr1B.!!$F1 6254
1 TraesCS1B01G457400 chr1B 127613927 127614760 833 True 865.000000 865 85.595000 1 829 1 chr1B.!!$R1 828
2 TraesCS1B01G457400 chr7D 158642158 158647631 5473 True 8615.000000 8615 95.199000 1 5447 1 chr7D.!!$R2 5446
3 TraesCS1B01G457400 chr7D 577331455 577333913 2458 True 3533.000000 3533 92.826000 1 2441 1 chr7D.!!$R4 2440
4 TraesCS1B01G457400 chr7D 435178694 435181173 2479 False 3524.000000 3524 92.655000 1 2441 1 chr7D.!!$F1 2440
5 TraesCS1B01G457400 chr7D 139199389 139200516 1127 True 1834.000000 1834 96.039000 4320 5447 1 chr7D.!!$R1 1127
6 TraesCS1B01G457400 chr7D 65765803 65768256 2453 True 1827.000000 2601 93.831000 4 2441 2 chr7D.!!$R6 2437
7 TraesCS1B01G457400 chr7D 593566195 593567020 825 False 863.000000 863 85.663000 1 829 1 chr7D.!!$F2 828
8 TraesCS1B01G457400 chr7D 609066041 609066624 583 True 769.000000 769 90.411000 1087 1670 1 chr7D.!!$R5 583
9 TraesCS1B01G457400 chr7D 348986680 348987255 575 True 680.000000 680 88.144000 5448 6022 1 chr7D.!!$R3 574
10 TraesCS1B01G457400 chr1A 503674131 503679155 5024 True 7690.000000 7690 94.499000 1 4966 1 chr1A.!!$R5 4965
11 TraesCS1B01G457400 chr1A 473565650 473566485 835 True 1125.000000 1125 91.507000 5447 6255 1 chr1A.!!$R4 808
12 TraesCS1B01G457400 chr1A 473510203 473511038 835 True 1098.000000 1098 90.909000 5447 6255 1 chr1A.!!$R3 808
13 TraesCS1B01G457400 chr1A 183435460 183436140 680 False 992.000000 992 92.982000 5447 6128 1 chr1A.!!$F2 681
14 TraesCS1B01G457400 chr1A 530576076 530576914 838 False 876.000000 876 85.731000 1 829 1 chr1A.!!$F3 828
15 TraesCS1B01G457400 chr6A 385568348 385573375 5027 True 7483.000000 7483 93.755000 1 4966 1 chr6A.!!$R2 4965
16 TraesCS1B01G457400 chr6A 580785524 580787913 2389 False 4028.000000 4028 97.198000 2587 4960 1 chr6A.!!$F1 2373
17 TraesCS1B01G457400 chr6A 173271549 173272107 558 True 571.000000 571 85.249000 5448 6022 1 chr6A.!!$R1 574
18 TraesCS1B01G457400 chr3A 734237813 734241239 3426 False 5064.000000 5064 93.550000 1 3389 1 chr3A.!!$F2 3388
19 TraesCS1B01G457400 chr3A 588380910 588381746 836 False 902.000000 902 86.326000 1 829 1 chr3A.!!$F1 828
20 TraesCS1B01G457400 chr4D 251090216 251092894 2678 True 4446.000000 4446 96.715000 2448 5110 1 chr4D.!!$R1 2662
21 TraesCS1B01G457400 chr4D 347174413 347176375 1962 True 2449.000000 2449 89.384000 1 1962 1 chr4D.!!$R2 1961
22 TraesCS1B01G457400 chr2B 733353484 733356174 2690 True 4331.000000 4331 95.750000 2448 5137 1 chr2B.!!$R1 2689
23 TraesCS1B01G457400 chr2B 88450273 88451767 1494 True 886.000000 900 86.210000 1 829 2 chr2B.!!$R2 828
24 TraesCS1B01G457400 chr7A 26225156 26229370 4214 True 3227.500000 3899 94.220500 713 4966 2 chr7A.!!$R3 4253
25 TraesCS1B01G457400 chr7A 69158924 69160776 1852 True 2769.000000 2769 93.767000 588 2435 1 chr7A.!!$R1 1847
26 TraesCS1B01G457400 chr3D 584380681 584383160 2479 True 3762.000000 3762 94.342000 1 2441 1 chr3D.!!$R3 2440
27 TraesCS1B01G457400 chr3D 214435116 214437001 1885 True 1100.500000 2054 94.866500 3517 5110 2 chr3D.!!$R4 1593
28 TraesCS1B01G457400 chr2A 731832210 731838515 6305 False 2342.666667 3317 91.413333 1 4107 3 chr2A.!!$F4 4106
29 TraesCS1B01G457400 chr2A 21731039 21732238 1199 True 1668.000000 1668 92.043000 1049 2236 1 chr2A.!!$R1 1187
30 TraesCS1B01G457400 chr2A 506754563 506755396 833 False 1173.000000 1173 92.575000 5447 6255 1 chr2A.!!$F3 808
31 TraesCS1B01G457400 chr2A 331637266 331638103 837 False 1136.000000 1136 91.647000 5444 6255 1 chr2A.!!$F2 811
32 TraesCS1B01G457400 chr2A 311414020 311414852 832 True 1122.000000 1122 91.487000 5448 6255 1 chr2A.!!$R2 807
33 TraesCS1B01G457400 chr2A 242904064 242904897 833 False 1101.000000 1101 91.007000 5448 6255 1 chr2A.!!$F1 807
34 TraesCS1B01G457400 chr7B 646688750 646690595 1845 True 2765.000000 2765 93.603000 3242 5110 1 chr7B.!!$R5 1868
35 TraesCS1B01G457400 chr7B 695978490 695979218 728 True 1044.000000 1044 92.440000 3232 3975 1 chr7B.!!$R6 743
36 TraesCS1B01G457400 chr7B 532491362 532492090 728 True 1022.000000 1022 91.910000 3232 3975 1 chr7B.!!$R3 743
37 TraesCS1B01G457400 chr7B 601136006 601136727 721 True 1000.000000 1000 91.512000 3232 3975 1 chr7B.!!$R4 743
38 TraesCS1B01G457400 chr7B 27769711 27770533 822 True 893.000000 893 86.490000 1 815 1 chr7B.!!$R1 814
39 TraesCS1B01G457400 chr5D 556289296 556291022 1726 True 2311.000000 2311 91.124000 1 1699 1 chr5D.!!$R1 1698
40 TraesCS1B01G457400 chr1D 408983393 408984823 1430 False 2292.000000 2292 95.737000 3511 4927 1 chr1D.!!$F1 1416
41 TraesCS1B01G457400 chr3B 801608225 801612531 4306 True 1023.666667 1186 94.902000 990 5447 3 chr3B.!!$R1 4457
42 TraesCS1B01G457400 chr4A 531651566 531652399 833 True 1157.000000 1157 92.206000 5447 6255 1 chr4A.!!$R1 808
43 TraesCS1B01G457400 chr4A 391091745 391092587 842 False 1122.000000 1122 91.340000 5447 6255 1 chr4A.!!$F2 808
44 TraesCS1B01G457400 chr4A 130319907 130320742 835 False 1075.000000 1075 90.442000 5447 6255 1 chr4A.!!$F1 808
45 TraesCS1B01G457400 chr5A 346504811 346505596 785 True 966.000000 966 88.738000 5450 6255 1 chr5A.!!$R2 805
46 TraesCS1B01G457400 chr5A 227291057 227291765 708 False 902.000000 902 90.014000 5436 6128 1 chr5A.!!$F1 692
47 TraesCS1B01G457400 chr6D 73285162 73285927 765 True 824.000000 824 86.873000 5434 6171 1 chr6D.!!$R1 737
48 TraesCS1B01G457400 chr6D 85502324 85502926 602 True 667.000000 667 87.459000 5448 6022 1 chr6D.!!$R2 574
49 TraesCS1B01G457400 chr6B 391806688 391807279 591 False 734.000000 734 89.376000 5448 6028 1 chr6B.!!$F1 580

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
34 35 1.019278 GCTTCCAACTGAATCGGCGA 61.019 55.000 13.87 13.87 31.06 5.54 F
1029 3067 0.766288 CTCCCTCCCCCTTCCAGATC 60.766 65.000 0.00 0.00 0.00 2.75 F
1591 3678 1.218047 CGTTCTTCGATCCCAGGCA 59.782 57.895 0.00 0.00 42.86 4.75 F
1948 4044 2.117156 ATGCGTGAGGAATGGCTGC 61.117 57.895 0.00 0.00 32.68 5.25 F
3664 6263 0.911769 TGTCCATTCGCCTGATTCCT 59.088 50.000 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 3691 1.673920 AGACACGAACGCACCAAAAAT 59.326 42.857 0.00 0.00 0.00 1.82 R
1948 4044 1.922570 AGAGCTATAACCGCACAACG 58.077 50.000 0.00 0.00 43.15 4.10 R
2825 5246 3.563808 TCCACTGTCATGTACTTGTTTGC 59.436 43.478 8.46 0.32 0.00 3.68 R
3667 6266 0.322546 GGAGGCGTTTGGAATCAGGT 60.323 55.000 0.00 0.00 0.00 4.00 R
5591 8393 0.527817 AAGTGTAGTATCGCAGGCGC 60.528 55.000 9.11 0.00 39.59 6.53 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
34 35 1.019278 GCTTCCAACTGAATCGGCGA 61.019 55.000 13.87 13.87 31.06 5.54
78 80 6.833933 AGAGGTGGATCAAAACTTTTTACACT 59.166 34.615 0.00 0.00 0.00 3.55
211 869 4.524714 TGGGCACTCGAAAAATGGAAAATA 59.475 37.500 0.00 0.00 0.00 1.40
212 870 5.186797 TGGGCACTCGAAAAATGGAAAATAT 59.813 36.000 0.00 0.00 0.00 1.28
368 1026 6.111768 CTTGAAAGCTATGCATCTTTACGT 57.888 37.500 0.19 0.00 33.14 3.57
393 1051 2.890808 AGCTCGTTTCTGAGAACACA 57.109 45.000 0.00 0.00 38.28 3.72
470 1129 7.355017 GTCACATATAATGACACAATGCGAAT 58.645 34.615 13.14 0.00 44.87 3.34
569 1248 4.937201 AGTGGTTGAATCTTGGAAAACC 57.063 40.909 0.00 0.00 40.59 3.27
656 2661 1.821753 CAAATTGTGCGATGGGGGTAA 59.178 47.619 0.00 0.00 0.00 2.85
719 2724 5.328565 TGTCAATTTGATGGGTGGTTGATA 58.671 37.500 1.78 0.00 0.00 2.15
761 2767 8.686334 ACAATCATCTGGTTAATTGGACATAAC 58.314 33.333 0.00 0.00 34.23 1.89
766 2772 9.559732 CATCTGGTTAATTGGACATAACTATGA 57.440 33.333 3.73 0.00 37.15 2.15
957 2968 3.182976 CATCCATCCATCTCCTCATCCT 58.817 50.000 0.00 0.00 0.00 3.24
1029 3067 0.766288 CTCCCTCCCCCTTCCAGATC 60.766 65.000 0.00 0.00 0.00 2.75
1030 3068 2.143419 CCCTCCCCCTTCCAGATCG 61.143 68.421 0.00 0.00 0.00 3.69
1031 3069 2.812619 CCTCCCCCTTCCAGATCGC 61.813 68.421 0.00 0.00 0.00 4.58
1085 3134 2.989639 CCCTTCCTCACCGCATCA 59.010 61.111 0.00 0.00 0.00 3.07
1540 3621 1.273896 CCAACCCTACCTCTCCCTCTT 60.274 57.143 0.00 0.00 0.00 2.85
1591 3678 1.218047 CGTTCTTCGATCCCAGGCA 59.782 57.895 0.00 0.00 42.86 4.75
1604 3691 3.838565 TCCCAGGCAGTGATGTTTTTAA 58.161 40.909 0.00 0.00 0.00 1.52
1948 4044 2.117156 ATGCGTGAGGAATGGCTGC 61.117 57.895 0.00 0.00 32.68 5.25
2109 4222 4.899502 TGAATTCTCTTCTTGTGGGAGTC 58.100 43.478 7.05 0.00 0.00 3.36
2456 4752 2.354821 GCCAGTTACAATAAAGCTCCCG 59.645 50.000 0.00 0.00 0.00 5.14
3145 5568 7.047891 CGGCTTCCCTATGATTATTATTGCTA 58.952 38.462 0.00 0.00 0.00 3.49
3664 6263 0.911769 TGTCCATTCGCCTGATTCCT 59.088 50.000 0.00 0.00 0.00 3.36
3667 6266 1.559219 TCCATTCGCCTGATTCCTTCA 59.441 47.619 0.00 0.00 0.00 3.02
3845 6588 2.170607 TGGTCTAGCTGGGCATTACTTC 59.829 50.000 3.40 0.00 0.00 3.01
3985 6728 2.270923 GCTGTGAATCTGTCGTGCATA 58.729 47.619 0.00 0.00 0.00 3.14
4494 7245 5.649265 AGACTTATCATATCCTCTCTGGCA 58.351 41.667 0.00 0.00 35.26 4.92
4530 7281 5.926542 GCGCATGATAGACTACTAAATGGAA 59.073 40.000 0.30 0.00 32.33 3.53
4859 7626 6.811954 TGTTAGGAGAATGTTATATGCACGA 58.188 36.000 0.00 0.00 0.00 4.35
5008 7777 4.469945 AGGATCTTATGTTTTCGAGGTGGA 59.530 41.667 0.00 0.00 0.00 4.02
5048 7817 0.107312 AGCCTGGAGATGTGCATCAC 60.107 55.000 13.79 7.82 40.22 3.06
5221 7990 6.245115 TGATGTAACAGATTGTTGCTTCTG 57.755 37.500 18.93 0.00 42.86 3.02
5357 8126 1.423921 AGAAACGGACATTTGGGACCT 59.576 47.619 0.00 0.00 0.00 3.85
5414 8186 0.264657 AGGAAAAAGGGCCACAACCT 59.735 50.000 6.18 4.83 40.96 3.50
5478 8250 1.339151 GGCTCAGAGAAACCGGAACAT 60.339 52.381 9.46 0.00 0.00 2.71
5493 8265 0.179056 AACATCCCGTATTCCAGCCG 60.179 55.000 0.00 0.00 0.00 5.52
5558 8357 4.081322 AGAACAAATTACACGGGTCTGT 57.919 40.909 0.00 0.00 0.00 3.41
5989 8802 0.614979 TCTCTCTTGGCTAACCGGCT 60.615 55.000 0.00 0.00 39.70 5.52
6209 9031 1.065926 TCCTGCCAATCTGTACTGCTG 60.066 52.381 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.751888 CACCTCTCGTGAAAAAGACAAATTTT 59.248 34.615 0.00 0.00 46.20 1.82
78 80 9.731723 TTGATGCACAATTGACCAAATGGTTGA 62.732 37.037 13.59 0.00 40.14 3.18
234 892 7.381408 GCAAACAATGTTACCTAAGGAAGTTTC 59.619 37.037 0.00 0.00 0.00 2.78
364 1022 7.719778 TCTCAGAAACGAGCTATTATACGTA 57.280 36.000 0.00 0.00 38.00 3.57
368 1026 7.768240 TGTGTTCTCAGAAACGAGCTATTATA 58.232 34.615 0.00 0.00 32.75 0.98
444 1103 6.048509 TCGCATTGTGTCATTATATGTGACT 58.951 36.000 18.24 2.42 44.80 3.41
496 1156 9.592720 CATTTTGAAACGGACATAAAAATTTCC 57.407 29.630 0.00 0.00 0.00 3.13
500 1160 6.816377 CGCATTTTGAAACGGACATAAAAAT 58.184 32.000 0.00 0.00 0.00 1.82
656 2661 5.773176 AGTAGGAAACGGGTCAAATTTGAAT 59.227 36.000 22.07 6.12 39.21 2.57
711 2716 9.706691 TGTGTGTTAAAAACTTTTTATCAACCA 57.293 25.926 14.97 12.45 0.00 3.67
957 2968 2.644299 GGTGGATGGATGGATGGATGTA 59.356 50.000 0.00 0.00 0.00 2.29
1187 3258 2.519780 GAGCGTCGGGGAGAGGAT 60.520 66.667 0.00 0.00 36.91 3.24
1261 3332 3.714078 ATCCGCCCTCCCTGCCTAA 62.714 63.158 0.00 0.00 0.00 2.69
1314 3385 1.925285 ATCTTGGGGATGCGCTTCCA 61.925 55.000 35.03 21.69 37.53 3.53
1452 3526 3.119096 GCGGCGGAACCAGAAGAC 61.119 66.667 9.78 0.00 39.03 3.01
1591 3678 6.536941 ACGCACCAAAAATTAAAAACATCACT 59.463 30.769 0.00 0.00 0.00 3.41
1604 3691 1.673920 AGACACGAACGCACCAAAAAT 59.326 42.857 0.00 0.00 0.00 1.82
1948 4044 1.922570 AGAGCTATAACCGCACAACG 58.077 50.000 0.00 0.00 43.15 4.10
2109 4222 4.379186 CCAAGATACTGCAAGCAAGTTCAG 60.379 45.833 0.00 0.00 37.60 3.02
2456 4752 5.908341 TGACCAATGAAACAAAAGGTTACC 58.092 37.500 0.00 0.00 39.29 2.85
2519 4815 7.278875 TGTATGTGACCATTAGAATGCATACA 58.721 34.615 19.03 19.03 41.22 2.29
2825 5246 3.563808 TCCACTGTCATGTACTTGTTTGC 59.436 43.478 8.46 0.32 0.00 3.68
2833 5254 5.902681 TGCTACTAATCCACTGTCATGTAC 58.097 41.667 0.00 0.00 0.00 2.90
3145 5568 6.482308 CCTATTTACACTAAAACCAGCGCTAT 59.518 38.462 10.99 0.00 0.00 2.97
3664 6263 1.202879 AGGCGTTTGGAATCAGGTGAA 60.203 47.619 0.00 0.00 0.00 3.18
3667 6266 0.322546 GGAGGCGTTTGGAATCAGGT 60.323 55.000 0.00 0.00 0.00 4.00
3726 6350 4.351938 CGCGGTCACCACCTTCGA 62.352 66.667 0.00 0.00 41.17 3.71
3845 6588 5.967469 GTGACAAGCACATATATGAACTCG 58.033 41.667 19.63 7.75 46.91 4.18
4494 7245 4.166888 ATGCGCTCCTGCCATCGT 62.167 61.111 9.73 0.00 35.36 3.73
4530 7281 2.157668 CGCTGAACGTTGCAGATACTTT 59.842 45.455 23.26 0.00 35.39 2.66
4818 7585 5.709631 TCCTAACAATGAAACATAGCTGCAA 59.290 36.000 1.02 0.00 0.00 4.08
4859 7626 8.147244 AGTTAGGGAACATAATCAAGTGTAGT 57.853 34.615 0.00 0.00 38.10 2.73
4896 7663 3.056393 TGAAGGCCAAAATCTGCAGATTG 60.056 43.478 36.16 27.25 43.41 2.67
5008 7777 2.089980 GATCTTTGGTCACAGCAGCAT 58.910 47.619 0.00 0.00 0.00 3.79
5137 7906 6.108687 CAGGTGTACAATATGTCACATGAGT 58.891 40.000 15.75 0.00 39.78 3.41
5357 8126 5.591472 CCCAATTGTCAGATTCTGATAAGCA 59.409 40.000 24.22 13.91 42.85 3.91
5478 8250 1.076559 TCTCGGCTGGAATACGGGA 60.077 57.895 0.00 0.00 34.28 5.14
5493 8265 3.809832 CAGAGACTTCTCCTCGATCTCTC 59.190 52.174 9.04 1.26 43.33 3.20
5558 8357 6.404954 CCATGCTGATGTGATCATTGTAACAA 60.405 38.462 0.00 0.00 38.85 2.83
5589 8391 0.804544 GTGTAGTATCGCAGGCGCAA 60.805 55.000 10.83 0.00 38.40 4.85
5591 8393 0.527817 AAGTGTAGTATCGCAGGCGC 60.528 55.000 9.11 0.00 39.59 6.53
5989 8802 7.896811 AGTTGATCGAGATGGTATATTGCTTA 58.103 34.615 0.00 0.00 0.00 3.09
6042 8855 0.384309 GTCATGGTAGTGATCGCCGA 59.616 55.000 1.76 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.