Multiple sequence alignment - TraesCS4D01G241100

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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 TraesCS4D01G241100 chr4D 100.000 5035 0 0 1 5035 403400287 403395253 0.000000e+00 9299.0
1 TraesCS4D01G241100 chr4D 100.000 118 0 0 4918 5035 14973469 14973352 8.490000e-53 219.0
2 TraesCS4D01G241100 chr4D 77.869 244 52 2 3676 3918 301299570 301299328 3.140000e-32 150.0
3 TraesCS4D01G241100 chr4B 91.273 3873 144 67 24 3788 500258125 500254339 0.000000e+00 5101.0
4 TraesCS4D01G241100 chr4B 88.983 826 30 13 3780 4552 500253407 500252590 0.000000e+00 965.0
5 TraesCS4D01G241100 chr4A 92.417 1899 81 23 719 2596 60929234 60927378 0.000000e+00 2651.0
6 TraesCS4D01G241100 chr4A 86.446 1387 71 54 2707 4051 60927293 60925982 0.000000e+00 1411.0
7 TraesCS4D01G241100 chr4A 82.582 643 48 26 40 634 60929857 60929231 4.500000e-140 508.0
8 TraesCS4D01G241100 chr4A 89.344 244 7 6 4054 4278 60925949 60925706 6.380000e-74 289.0
9 TraesCS4D01G241100 chr4A 77.419 248 54 2 3667 3913 180397865 180398111 4.060000e-31 147.0
10 TraesCS4D01G241100 chr4A 85.714 56 8 0 3665 3720 737868611 737868556 5.440000e-05 60.2
11 TraesCS4D01G241100 chr4A 85.714 56 8 0 3665 3720 738053546 738053601 5.440000e-05 60.2
12 TraesCS4D01G241100 chr5D 95.479 376 6 8 4551 4922 13914723 13915091 1.560000e-164 590.0
13 TraesCS4D01G241100 chr5D 98.347 121 2 0 4915 5035 407016535 407016655 3.950000e-51 213.0
14 TraesCS4D01G241100 chr5D 79.021 286 52 8 2105 2386 33025526 33025245 6.650000e-44 189.0
15 TraesCS4D01G241100 chr5D 100.000 36 0 0 3672 3707 417626599 417626564 3.250000e-07 67.6
16 TraesCS4D01G241100 chrUn 95.405 370 11 4 4551 4919 420333676 420334040 7.260000e-163 584.0
17 TraesCS4D01G241100 chrUn 95.405 370 11 4 4551 4919 420364925 420364561 7.260000e-163 584.0
18 TraesCS4D01G241100 chrUn 95.405 370 10 5 4551 4919 363159617 363159980 2.610000e-162 582.0
19 TraesCS4D01G241100 chrUn 94.638 373 13 4 4551 4922 440550681 440551047 5.660000e-159 571.0
20 TraesCS4D01G241100 chrUn 99.153 118 1 0 4918 5035 420334116 420334233 3.950000e-51 213.0
21 TraesCS4D01G241100 chrUn 99.153 118 1 0 4918 5035 420364485 420364368 3.950000e-51 213.0
22 TraesCS4D01G241100 chr3D 95.405 370 11 4 4551 4919 16540517 16540881 7.260000e-163 584.0
23 TraesCS4D01G241100 chr3D 95.405 370 11 4 4551 4919 16545322 16545686 7.260000e-163 584.0
24 TraesCS4D01G241100 chr3D 95.405 370 10 5 4551 4919 16537256 16537619 2.610000e-162 582.0
25 TraesCS4D01G241100 chr3D 79.443 287 49 9 2105 2386 323693510 323693791 1.430000e-45 195.0
26 TraesCS4D01G241100 chr7D 94.920 374 9 8 4551 4919 576654454 576654822 1.220000e-160 577.0
27 TraesCS4D01G241100 chr7D 100.000 118 0 0 4918 5035 628444607 628444490 8.490000e-53 219.0
28 TraesCS4D01G241100 chr7D 85.714 56 8 0 3665 3720 5018167 5018222 5.440000e-05 60.2
29 TraesCS4D01G241100 chr6D 100.000 118 0 0 4918 5035 446861280 446861397 8.490000e-53 219.0
30 TraesCS4D01G241100 chr6D 97.778 45 1 0 3673 3717 470961823 470961779 1.500000e-10 78.7
31 TraesCS4D01G241100 chr6D 90.244 41 4 0 3665 3705 308330434 308330394 3.000000e-03 54.7
32 TraesCS4D01G241100 chr1D 94.928 138 6 1 4898 5035 7921970 7922106 1.100000e-51 215.0
33 TraesCS4D01G241100 chr1D 98.347 121 1 1 4915 5035 464854653 464854534 1.420000e-50 211.0
34 TraesCS4D01G241100 chr5B 80.351 285 50 6 2105 2386 24115387 24115106 1.420000e-50 211.0
35 TraesCS4D01G241100 chr5B 78.358 134 20 6 3684 3817 354785119 354785243 1.500000e-10 78.7
36 TraesCS4D01G241100 chr2D 97.581 124 2 1 4912 5035 95664976 95665098 1.420000e-50 211.0
37 TraesCS4D01G241100 chr5A 80.139 287 47 9 2105 2386 21433394 21433113 6.610000e-49 206.0
38 TraesCS4D01G241100 chr5A 78.358 134 20 6 3684 3817 402907607 402907731 1.500000e-10 78.7
39 TraesCS4D01G241100 chr3A 80.139 287 47 9 2105 2386 398884963 398884682 6.610000e-49 206.0
40 TraesCS4D01G241100 chr3A 79.545 220 38 7 3664 3878 589395278 589395495 3.140000e-32 150.0
41 TraesCS4D01G241100 chr3A 84.821 112 17 0 3767 3878 131406670 131406781 4.120000e-21 113.0
42 TraesCS4D01G241100 chr3B 79.791 287 48 9 2105 2386 395384251 395383970 3.070000e-47 200.0
43 TraesCS4D01G241100 chr3B 91.071 56 5 0 3665 3720 76433068 76433013 5.410000e-10 76.8
44 TraesCS4D01G241100 chr7B 88.710 62 5 2 3660 3720 57633400 57633340 1.940000e-09 75.0
45 TraesCS4D01G241100 chr7B 97.059 34 1 0 2191 2224 577205266 577205233 1.960000e-04 58.4
46 TraesCS4D01G241100 chr7A 84.746 59 9 0 3662 3720 5600389 5600447 5.440000e-05 60.2
47 TraesCS4D01G241100 chr7A 97.059 34 1 0 2191 2224 618241810 618241843 1.960000e-04 58.4
48 TraesCS4D01G241100 chr2B 100.000 28 0 0 1510 1537 775127303 775127330 9.000000e-03 52.8


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 TraesCS4D01G241100 chr4D 403395253 403400287 5034 True 9299.00 9299 100.00000 1 5035 1 chr4D.!!$R3 5034
1 TraesCS4D01G241100 chr4B 500252590 500258125 5535 True 3033.00 5101 90.12800 24 4552 2 chr4B.!!$R1 4528
2 TraesCS4D01G241100 chr4A 60925706 60929857 4151 True 1214.75 2651 87.69725 40 4278 4 chr4A.!!$R2 4238
3 TraesCS4D01G241100 chrUn 420333676 420334233 557 False 398.50 584 97.27900 4551 5035 2 chrUn.!!$F3 484
4 TraesCS4D01G241100 chrUn 420364368 420364925 557 True 398.50 584 97.27900 4551 5035 2 chrUn.!!$R1 484
5 TraesCS4D01G241100 chr3D 16537256 16540881 3625 False 583.00 584 95.40500 4551 4919 2 chr3D.!!$F3 368

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
20 21 0.106519 GCCACTGGCCACCATTCTAT 60.107 55.000 9.13 0.0 44.06 1.98 F
657 720 0.543749 AATCTGCCTTTCTCCCCTCG 59.456 55.000 0.00 0.0 0.00 4.63 F
900 968 1.000283 CACCACACAGAGAGAGTGTCC 60.000 57.143 0.00 0.0 46.57 4.02 F
1083 1173 1.442184 CTCCGACGACCTCAACACG 60.442 63.158 0.00 0.0 0.00 4.49 F
2605 2723 1.550130 TTAACCAGTGCTCCCTCGGG 61.550 60.000 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1493 0.249868 CACCAGGTTCTTGAGCGTGA 60.250 55.0 8.35 0.00 0.00 4.35 R
2485 2603 0.546122 TATCGCCAGCCTGTTTGGAT 59.454 50.0 0.00 0.00 37.96 3.41 R
2662 2781 0.041090 AAAGAAACCGGGCCATGGAT 59.959 50.0 18.40 5.22 0.00 3.41 R
2793 2946 0.981183 ATTAGACCCCACGCAACTCA 59.019 50.0 0.00 0.00 0.00 3.41 R
4365 5618 0.039256 TAGGCAAGCAAAGCAAAGCG 60.039 50.0 0.00 0.00 35.48 4.68 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
18 19 2.036256 GCCACTGGCCACCATTCT 59.964 61.111 9.13 0.00 44.06 2.40
19 20 1.302949 GCCACTGGCCACCATTCTA 59.697 57.895 9.13 0.00 44.06 2.10
20 21 0.106519 GCCACTGGCCACCATTCTAT 60.107 55.000 9.13 0.00 44.06 1.98
21 22 1.142870 GCCACTGGCCACCATTCTATA 59.857 52.381 9.13 0.00 44.06 1.31
22 23 2.224867 GCCACTGGCCACCATTCTATAT 60.225 50.000 9.13 0.00 44.06 0.86
23 24 3.751893 GCCACTGGCCACCATTCTATATT 60.752 47.826 9.13 0.00 44.06 1.28
24 25 4.473444 CCACTGGCCACCATTCTATATTT 58.527 43.478 0.00 0.00 30.82 1.40
25 26 4.520492 CCACTGGCCACCATTCTATATTTC 59.480 45.833 0.00 0.00 30.82 2.17
26 27 5.380043 CACTGGCCACCATTCTATATTTCT 58.620 41.667 0.00 0.00 30.82 2.52
27 28 5.829924 CACTGGCCACCATTCTATATTTCTT 59.170 40.000 0.00 0.00 30.82 2.52
28 29 6.322201 CACTGGCCACCATTCTATATTTCTTT 59.678 38.462 0.00 0.00 30.82 2.52
29 30 6.897413 ACTGGCCACCATTCTATATTTCTTTT 59.103 34.615 0.00 0.00 30.82 2.27
30 31 8.058847 ACTGGCCACCATTCTATATTTCTTTTA 58.941 33.333 0.00 0.00 30.82 1.52
31 32 9.082313 CTGGCCACCATTCTATATTTCTTTTAT 57.918 33.333 0.00 0.00 30.82 1.40
32 33 9.077885 TGGCCACCATTCTATATTTCTTTTATC 57.922 33.333 0.00 0.00 0.00 1.75
33 34 9.301897 GGCCACCATTCTATATTTCTTTTATCT 57.698 33.333 0.00 0.00 0.00 1.98
150 152 5.236263 CCCAGTTAAATTTGCCTTTTCACAC 59.764 40.000 0.00 0.00 0.00 3.82
184 190 2.063266 CCGAGTTTTACTGCTGCGTTA 58.937 47.619 0.00 0.00 0.00 3.18
220 230 3.451250 CGTACGTACGTGTTGCCC 58.549 61.111 33.95 9.95 44.13 5.36
231 241 2.428890 ACGTGTTGCCCAAAATTCAAGA 59.571 40.909 0.00 0.00 0.00 3.02
251 261 7.220740 TCAAGATTATGTACACCAACACAAGA 58.779 34.615 0.00 0.00 30.75 3.02
364 374 3.390521 CCCGAGTGGCCAGCAGTA 61.391 66.667 5.11 0.00 0.00 2.74
366 376 2.650116 CCGAGTGGCCAGCAGTACT 61.650 63.158 5.11 0.00 0.00 2.73
367 377 1.153745 CGAGTGGCCAGCAGTACTC 60.154 63.158 5.11 7.27 36.95 2.59
368 378 1.153745 GAGTGGCCAGCAGTACTCG 60.154 63.158 5.11 0.00 31.39 4.18
369 379 2.815647 GTGGCCAGCAGTACTCGC 60.816 66.667 5.11 8.67 0.00 5.03
370 380 3.310307 TGGCCAGCAGTACTCGCA 61.310 61.111 0.00 0.00 33.55 5.10
383 409 1.388547 ACTCGCAAACCTTTTGCTCA 58.611 45.000 18.68 6.92 42.87 4.26
448 498 1.746171 GCGGTGGGTAGGAATTTCTCC 60.746 57.143 0.00 0.00 45.81 3.71
450 500 1.920351 GGTGGGTAGGAATTTCTCCCA 59.080 52.381 16.09 16.09 46.81 4.37
608 671 2.464459 CCGCGTCCAGCCTTTCATC 61.464 63.158 4.92 0.00 44.76 2.92
649 712 2.019984 CCACCTGCTAATCTGCCTTTC 58.980 52.381 0.00 0.00 0.00 2.62
657 720 0.543749 AATCTGCCTTTCTCCCCTCG 59.456 55.000 0.00 0.00 0.00 4.63
758 824 5.680594 TCATTAAAGCAATCAAGCCCATT 57.319 34.783 0.00 0.00 34.23 3.16
866 932 3.181461 CCCTGCCCACTCTATTTCTACTG 60.181 52.174 0.00 0.00 0.00 2.74
894 962 2.677542 ACTACCACCACACAGAGAGA 57.322 50.000 0.00 0.00 0.00 3.10
897 965 1.043816 ACCACCACACAGAGAGAGTG 58.956 55.000 0.00 0.00 42.56 3.51
900 968 1.000283 CACCACACAGAGAGAGTGTCC 60.000 57.143 0.00 0.00 46.57 4.02
1041 1131 2.281761 CTTGCGGTGCTGGTCCTT 60.282 61.111 0.00 0.00 0.00 3.36
1043 1133 3.414136 TTGCGGTGCTGGTCCTTGT 62.414 57.895 0.00 0.00 0.00 3.16
1083 1173 1.442184 CTCCGACGACCTCAACACG 60.442 63.158 0.00 0.00 0.00 4.49
1389 1479 4.516195 GCCTTCTCCGGCGAGGTC 62.516 72.222 9.30 0.00 40.79 3.85
2419 2527 5.986004 AAAACCTTCTCTTTCACAGTACG 57.014 39.130 0.00 0.00 0.00 3.67
2435 2549 4.751600 ACAGTACGGTAACTTTTTACAGGC 59.248 41.667 0.00 0.00 39.64 4.85
2484 2602 4.873129 CGCCCTGTCGGTGGATCG 62.873 72.222 0.00 0.00 38.61 3.69
2485 2603 3.458163 GCCCTGTCGGTGGATCGA 61.458 66.667 0.00 0.00 36.76 3.59
2486 2604 2.797278 GCCCTGTCGGTGGATCGAT 61.797 63.158 0.00 0.00 41.40 3.59
2605 2723 1.550130 TTAACCAGTGCTCCCTCGGG 61.550 60.000 0.00 0.00 0.00 5.14
2626 2745 1.561730 CGATCAATTCGCTGGCTCG 59.438 57.895 0.00 0.00 41.69 5.03
2744 2886 5.164031 CGAACTGCAATTTGTACGCTAGTAA 60.164 40.000 0.00 0.00 34.16 2.24
2745 2887 6.455113 CGAACTGCAATTTGTACGCTAGTAAT 60.455 38.462 0.00 0.00 34.16 1.89
2793 2946 3.360340 GCTCAGCGTTTGCCAGCT 61.360 61.111 2.47 0.00 45.74 4.24
2890 3051 0.667184 CATTTGCGACCAACTTGCCC 60.667 55.000 0.00 0.00 0.00 5.36
2891 3052 0.827507 ATTTGCGACCAACTTGCCCT 60.828 50.000 0.00 0.00 0.00 5.19
2893 3054 2.594592 GCGACCAACTTGCCCTGT 60.595 61.111 0.00 0.00 0.00 4.00
2895 3056 1.949257 CGACCAACTTGCCCTGTTC 59.051 57.895 0.00 0.00 0.00 3.18
2896 3057 0.535102 CGACCAACTTGCCCTGTTCT 60.535 55.000 0.00 0.00 0.00 3.01
2897 3058 0.954452 GACCAACTTGCCCTGTTCTG 59.046 55.000 0.00 0.00 0.00 3.02
2898 3059 0.550914 ACCAACTTGCCCTGTTCTGA 59.449 50.000 0.00 0.00 0.00 3.27
2899 3060 1.242076 CCAACTTGCCCTGTTCTGAG 58.758 55.000 0.00 0.00 0.00 3.35
2900 3061 1.242076 CAACTTGCCCTGTTCTGAGG 58.758 55.000 0.00 0.00 0.00 3.86
2904 3065 2.435059 GCCCTGTTCTGAGGCGAC 60.435 66.667 0.00 0.00 36.84 5.19
2907 3081 0.970937 CCCTGTTCTGAGGCGACCTA 60.971 60.000 0.00 0.00 31.76 3.08
2919 3096 4.254492 GAGGCGACCTAGTTTTGAAATCT 58.746 43.478 0.00 0.00 31.76 2.40
2920 3097 4.652822 AGGCGACCTAGTTTTGAAATCTT 58.347 39.130 0.00 0.00 28.47 2.40
2922 3099 4.379499 GGCGACCTAGTTTTGAAATCTTGG 60.379 45.833 12.73 12.73 0.00 3.61
2924 3101 5.123979 GCGACCTAGTTTTGAAATCTTGGAT 59.876 40.000 18.72 7.15 0.00 3.41
2925 3102 6.546395 CGACCTAGTTTTGAAATCTTGGATG 58.454 40.000 18.72 9.49 0.00 3.51
2926 3103 6.272822 ACCTAGTTTTGAAATCTTGGATGC 57.727 37.500 18.72 0.00 0.00 3.91
2928 3105 5.185635 CCTAGTTTTGAAATCTTGGATGCCA 59.814 40.000 9.83 0.00 0.00 4.92
2929 3106 5.750352 AGTTTTGAAATCTTGGATGCCAT 57.250 34.783 0.00 0.00 31.53 4.40
2930 3107 6.855763 AGTTTTGAAATCTTGGATGCCATA 57.144 33.333 0.00 0.00 31.53 2.74
2932 3109 6.438425 AGTTTTGAAATCTTGGATGCCATACT 59.562 34.615 0.00 0.00 31.53 2.12
2933 3110 5.840243 TTGAAATCTTGGATGCCATACTG 57.160 39.130 0.00 0.00 31.53 2.74
2934 3111 4.858850 TGAAATCTTGGATGCCATACTGT 58.141 39.130 0.00 0.00 31.53 3.55
2935 3112 4.641541 TGAAATCTTGGATGCCATACTGTG 59.358 41.667 0.00 0.00 31.53 3.66
2936 3113 2.042686 TCTTGGATGCCATACTGTGC 57.957 50.000 0.00 0.00 31.53 4.57
2937 3114 1.561076 TCTTGGATGCCATACTGTGCT 59.439 47.619 0.00 0.00 31.53 4.40
2938 3115 2.771372 TCTTGGATGCCATACTGTGCTA 59.229 45.455 0.00 0.00 31.53 3.49
2939 3116 2.916702 TGGATGCCATACTGTGCTAG 57.083 50.000 0.00 0.00 0.00 3.42
2940 3117 1.202687 TGGATGCCATACTGTGCTAGC 60.203 52.381 8.10 8.10 0.00 3.42
2941 3118 1.143305 GATGCCATACTGTGCTAGCG 58.857 55.000 10.77 0.00 0.00 4.26
2942 3119 0.465705 ATGCCATACTGTGCTAGCGT 59.534 50.000 10.77 4.54 0.00 5.07
2943 3120 1.107945 TGCCATACTGTGCTAGCGTA 58.892 50.000 10.77 6.83 0.00 4.42
2944 3121 1.067060 TGCCATACTGTGCTAGCGTAG 59.933 52.381 10.77 12.94 0.00 3.51
2945 3122 1.067212 GCCATACTGTGCTAGCGTAGT 59.933 52.381 22.26 22.26 0.00 2.73
2946 3123 2.732366 CCATACTGTGCTAGCGTAGTG 58.268 52.381 25.38 14.31 0.00 2.74
2947 3124 2.099263 CCATACTGTGCTAGCGTAGTGT 59.901 50.000 25.38 19.22 0.00 3.55
2948 3125 3.314357 CCATACTGTGCTAGCGTAGTGTA 59.686 47.826 25.38 16.69 0.00 2.90
2992 3172 6.040247 CGTACATGGAGTTATTAGTTGCAGA 58.960 40.000 0.00 0.00 0.00 4.26
2993 3173 6.701841 CGTACATGGAGTTATTAGTTGCAGAT 59.298 38.462 0.00 0.00 0.00 2.90
2994 3174 7.224753 CGTACATGGAGTTATTAGTTGCAGATT 59.775 37.037 0.00 0.00 0.00 2.40
2995 3175 7.325660 ACATGGAGTTATTAGTTGCAGATTG 57.674 36.000 0.00 0.00 0.00 2.67
2996 3176 6.319658 ACATGGAGTTATTAGTTGCAGATTGG 59.680 38.462 0.00 0.00 0.00 3.16
3014 3194 6.933521 CAGATTGGATTGATTCCTGGTAGTAG 59.066 42.308 0.00 0.00 45.68 2.57
3015 3195 6.617371 AGATTGGATTGATTCCTGGTAGTAGT 59.383 38.462 0.00 0.00 45.68 2.73
3019 3206 8.153221 TGGATTGATTCCTGGTAGTAGTAAAA 57.847 34.615 0.00 0.00 45.68 1.52
3037 3224 2.888834 AATTTCTTGGCAAGTTGCGT 57.111 40.000 25.39 7.17 46.21 5.24
3178 3369 2.867368 CAATAATGGCTGGCGTACGTAA 59.133 45.455 17.90 4.47 0.00 3.18
3188 3379 0.159345 GCGTACGTAAACACACACGG 59.841 55.000 17.90 0.00 42.35 4.94
3285 3498 2.595124 AAACCAACGGAAGCCAAAAG 57.405 45.000 0.00 0.00 0.00 2.27
3312 3525 3.883180 AACCGTGTTGCACCGTGC 61.883 61.111 16.93 16.93 45.29 5.34
3348 3561 5.505159 CGCGGTAACTAACTGTGATGAGATA 60.505 44.000 0.00 0.00 46.18 1.98
3349 3562 6.448006 GCGGTAACTAACTGTGATGAGATAT 58.552 40.000 0.00 0.00 36.77 1.63
3350 3563 6.363626 GCGGTAACTAACTGTGATGAGATATG 59.636 42.308 0.00 0.00 36.77 1.78
3351 3564 7.426410 CGGTAACTAACTGTGATGAGATATGT 58.574 38.462 0.00 0.00 0.00 2.29
3352 3565 8.565416 CGGTAACTAACTGTGATGAGATATGTA 58.435 37.037 0.00 0.00 0.00 2.29
3353 3566 9.680315 GGTAACTAACTGTGATGAGATATGTAC 57.320 37.037 0.00 0.00 0.00 2.90
3380 3593 7.810658 ACTGTGTTAACAATCTTCATGTGATC 58.189 34.615 10.51 0.00 35.37 2.92
3387 3604 2.453983 TCTTCATGTGATCGTGTGCA 57.546 45.000 0.00 0.00 32.85 4.57
3713 3930 2.814341 CTGCTGGAGCTGCTCACG 60.814 66.667 28.95 19.69 42.66 4.35
4051 5229 0.179067 TAACCGACCGGCATTGATCC 60.179 55.000 8.55 0.00 39.32 3.36
4052 5230 2.591715 CCGACCGGCATTGATCCC 60.592 66.667 0.00 0.00 0.00 3.85
4327 5580 5.107104 GCTTGCTTGCTTATTTAAAACACCC 60.107 40.000 0.00 0.00 0.00 4.61
4338 5591 5.344743 TTTAAAACACCCAGTGATTTGCA 57.655 34.783 11.75 0.00 38.57 4.08
4384 5637 0.039256 CGCTTTGCTTTGCTTGCCTA 60.039 50.000 0.00 0.00 0.00 3.93
4388 5641 0.247185 TTGCTTTGCTTGCCTATGCC 59.753 50.000 0.00 0.00 36.33 4.40
4389 5642 0.899253 TGCTTTGCTTGCCTATGCCA 60.899 50.000 0.00 0.00 36.33 4.92
4394 5647 4.154296 CTTGCCTATGCCAGCTCC 57.846 61.111 0.00 0.00 36.33 4.70
4396 5649 2.972892 CTTGCCTATGCCAGCTCCCC 62.973 65.000 0.00 0.00 36.33 4.81
4397 5650 3.174265 GCCTATGCCAGCTCCCCT 61.174 66.667 0.00 0.00 0.00 4.79
4400 5653 2.448542 TATGCCAGCTCCCCTCCC 60.449 66.667 0.00 0.00 0.00 4.30
4401 5654 2.979990 CTATGCCAGCTCCCCTCCCT 62.980 65.000 0.00 0.00 0.00 4.20
4407 5660 4.095400 GCTCCCCTCCCTCCCTCA 62.095 72.222 0.00 0.00 0.00 3.86
4421 5674 2.370189 CTCCCTCACTCACTTTCACCTT 59.630 50.000 0.00 0.00 0.00 3.50
4431 5684 5.010719 ACTCACTTTCACCTTGTCTAATCGA 59.989 40.000 0.00 0.00 0.00 3.59
4439 5692 3.700038 ACCTTGTCTAATCGACCGATCTT 59.300 43.478 5.32 0.00 42.13 2.40
4463 5716 1.967066 TGTTAATGGTTGTTGGGCTGG 59.033 47.619 0.00 0.00 0.00 4.85
4497 5750 0.323725 TGATGAGCCTCCTTTTGCCC 60.324 55.000 0.00 0.00 0.00 5.36
4503 5756 1.971695 CCTCCTTTTGCCCGTCACC 60.972 63.158 0.00 0.00 0.00 4.02
4504 5757 1.073199 CTCCTTTTGCCCGTCACCT 59.927 57.895 0.00 0.00 0.00 4.00
4814 6068 0.321122 CTTGCTGAAGGCCGAGAAGT 60.321 55.000 0.00 0.00 40.92 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.380043 AGAAATATAGAATGGTGGCCAGTG 58.620 41.667 5.11 0.00 36.75 3.66
4 5 5.653255 AGAAATATAGAATGGTGGCCAGT 57.347 39.130 5.11 0.00 36.75 4.00
5 6 6.966534 AAAGAAATATAGAATGGTGGCCAG 57.033 37.500 5.11 0.00 36.75 4.85
7 8 9.301897 AGATAAAAGAAATATAGAATGGTGGCC 57.698 33.333 0.00 0.00 0.00 5.36
17 18 9.279904 CGGCTACTCGAGATAAAAGAAATATAG 57.720 37.037 21.68 6.47 0.00 1.31
18 19 9.006839 TCGGCTACTCGAGATAAAAGAAATATA 57.993 33.333 21.68 0.00 34.82 0.86
19 20 7.883217 TCGGCTACTCGAGATAAAAGAAATAT 58.117 34.615 21.68 0.00 34.82 1.28
20 21 7.268199 TCGGCTACTCGAGATAAAAGAAATA 57.732 36.000 21.68 0.00 34.82 1.40
21 22 6.145338 TCGGCTACTCGAGATAAAAGAAAT 57.855 37.500 21.68 0.00 34.82 2.17
22 23 5.571784 TCGGCTACTCGAGATAAAAGAAA 57.428 39.130 21.68 0.00 34.82 2.52
150 152 2.280524 TCGGCAGGTTCACGGTTG 60.281 61.111 0.00 0.00 0.00 3.77
184 190 1.229820 TACCCACCCAGTGCCTGAT 60.230 57.895 4.00 0.00 32.44 2.90
220 230 9.689976 TGTTGGTGTACATAATCTTGAATTTTG 57.310 29.630 0.00 0.00 0.00 2.44
231 241 4.693566 CGGTCTTGTGTTGGTGTACATAAT 59.306 41.667 0.00 0.00 30.35 1.28
251 261 4.235762 AAGGCACACGAGCACGGT 62.236 61.111 8.74 0.00 44.46 4.83
357 367 1.512926 AAGGTTTGCGAGTACTGCTG 58.487 50.000 0.00 0.00 0.00 4.41
358 368 2.256117 AAAGGTTTGCGAGTACTGCT 57.744 45.000 0.00 0.00 0.00 4.24
359 369 2.650608 CAAAAGGTTTGCGAGTACTGC 58.349 47.619 0.00 5.18 0.00 4.40
368 378 2.531522 ACCATGAGCAAAAGGTTTGC 57.468 45.000 16.08 16.08 45.22 3.68
369 379 3.132925 CCAACCATGAGCAAAAGGTTTG 58.867 45.455 0.00 0.00 42.15 2.93
370 380 3.037549 TCCAACCATGAGCAAAAGGTTT 58.962 40.909 0.00 0.00 42.15 3.27
383 409 3.259123 GTGAATTCCAAGCTTCCAACCAT 59.741 43.478 2.27 0.00 0.00 3.55
448 498 1.846007 TTCACCCGGAATTCCATTGG 58.154 50.000 24.09 20.96 35.14 3.16
450 500 1.824852 GCTTTCACCCGGAATTCCATT 59.175 47.619 24.09 4.51 34.91 3.16
483 535 3.357203 AGGAAATCGTGAGCTAGACAGA 58.643 45.455 0.00 0.00 0.00 3.41
485 537 5.047590 TGTTTAGGAAATCGTGAGCTAGACA 60.048 40.000 0.00 0.00 0.00 3.41
608 671 1.065854 AGTCTTTTGAGGCCCGATGAG 60.066 52.381 0.00 0.00 0.00 2.90
657 720 2.604046 TCTAATCCAAAGCTCGCTCC 57.396 50.000 0.00 0.00 0.00 4.70
793 859 9.196139 TGAATTATAATGGAAGGTTTGGTTAGG 57.804 33.333 0.00 0.00 0.00 2.69
842 908 0.466372 GAAATAGAGTGGGCAGGGGC 60.466 60.000 0.00 0.00 40.13 5.80
866 932 0.391263 GTGGTGGTAGTACTGGCAGC 60.391 60.000 15.89 0.00 0.00 5.25
894 962 2.660064 GGCCATGGAGACGGACACT 61.660 63.158 18.40 0.00 0.00 3.55
897 965 1.524621 CATGGCCATGGAGACGGAC 60.525 63.158 34.31 0.00 35.24 4.79
966 1047 4.465446 TGAGAGAGGGCGGGAGGG 62.465 72.222 0.00 0.00 0.00 4.30
1023 1113 3.120086 AAGGACCAGCACCGCAAGT 62.120 57.895 0.00 0.00 0.00 3.16
1038 1128 2.358737 GGGAGCACCGACACAAGG 60.359 66.667 0.00 0.00 36.97 3.61
1397 1487 0.793250 GTTCTTGAGCGTGAAGAGCC 59.207 55.000 0.00 0.00 31.17 4.70
1403 1493 0.249868 CACCAGGTTCTTGAGCGTGA 60.250 55.000 8.35 0.00 0.00 4.35
2394 2502 7.172703 CCGTACTGTGAAAGAGAAGGTTTTTAT 59.827 37.037 0.00 0.00 0.00 1.40
2414 2522 5.219343 AGCCTGTAAAAAGTTACCGTACT 57.781 39.130 0.00 0.00 39.16 2.73
2419 2527 2.159747 CGCGAGCCTGTAAAAAGTTACC 60.160 50.000 0.00 0.00 39.16 2.85
2483 2601 2.753966 CGCCAGCCTGTTTGGATCG 61.754 63.158 0.00 0.00 37.96 3.69
2484 2602 0.749454 ATCGCCAGCCTGTTTGGATC 60.749 55.000 0.00 0.00 37.96 3.36
2485 2603 0.546122 TATCGCCAGCCTGTTTGGAT 59.454 50.000 0.00 0.00 37.96 3.41
2486 2604 0.546122 ATATCGCCAGCCTGTTTGGA 59.454 50.000 0.00 0.00 37.96 3.53
2635 2754 3.000819 TAGGTCAGGCGTGGGTGG 61.001 66.667 6.56 0.00 0.00 4.61
2636 2755 2.264794 GTAGGTCAGGCGTGGGTG 59.735 66.667 6.56 0.00 0.00 4.61
2637 2756 3.001406 GGTAGGTCAGGCGTGGGT 61.001 66.667 6.56 0.00 0.00 4.51
2638 2757 3.782443 GGGTAGGTCAGGCGTGGG 61.782 72.222 6.56 0.00 0.00 4.61
2662 2781 0.041090 AAAGAAACCGGGCCATGGAT 59.959 50.000 18.40 5.22 0.00 3.41
2744 2886 8.006298 ACTCTACTACTGTAGTCGTAGTACAT 57.994 38.462 22.79 0.00 44.10 2.29
2745 2887 7.397892 ACTCTACTACTGTAGTCGTAGTACA 57.602 40.000 22.79 3.47 44.10 2.90
2793 2946 0.981183 ATTAGACCCCACGCAACTCA 59.019 50.000 0.00 0.00 0.00 3.41
2890 3051 1.178276 ACTAGGTCGCCTCAGAACAG 58.822 55.000 1.46 0.00 34.61 3.16
2891 3052 1.629043 AACTAGGTCGCCTCAGAACA 58.371 50.000 1.46 0.00 34.61 3.18
2893 3054 2.631062 TCAAAACTAGGTCGCCTCAGAA 59.369 45.455 1.46 0.00 34.61 3.02
2895 3056 2.743636 TCAAAACTAGGTCGCCTCAG 57.256 50.000 1.46 2.42 34.61 3.35
2896 3057 3.478857 TTTCAAAACTAGGTCGCCTCA 57.521 42.857 1.46 0.00 34.61 3.86
2897 3058 4.254492 AGATTTCAAAACTAGGTCGCCTC 58.746 43.478 1.46 0.00 34.61 4.70
2898 3059 4.287766 AGATTTCAAAACTAGGTCGCCT 57.712 40.909 3.87 3.87 37.71 5.52
2899 3060 4.379499 CCAAGATTTCAAAACTAGGTCGCC 60.379 45.833 0.00 0.00 0.00 5.54
2900 3061 4.454504 TCCAAGATTTCAAAACTAGGTCGC 59.545 41.667 0.00 0.00 0.00 5.19
2903 3064 5.185828 GGCATCCAAGATTTCAAAACTAGGT 59.814 40.000 0.00 0.00 0.00 3.08
2904 3065 5.185635 TGGCATCCAAGATTTCAAAACTAGG 59.814 40.000 0.00 0.00 0.00 3.02
2907 3081 5.750352 ATGGCATCCAAGATTTCAAAACT 57.250 34.783 0.00 0.00 36.95 2.66
2919 3096 2.746142 GCTAGCACAGTATGGCATCCAA 60.746 50.000 10.63 0.00 43.62 3.53
2920 3097 1.202687 GCTAGCACAGTATGGCATCCA 60.203 52.381 10.63 0.00 43.62 3.41
2922 3099 1.143305 CGCTAGCACAGTATGGCATC 58.857 55.000 16.45 0.00 43.62 3.91
2924 3101 1.067060 CTACGCTAGCACAGTATGGCA 59.933 52.381 16.45 0.00 43.62 4.92
2925 3102 1.067212 ACTACGCTAGCACAGTATGGC 59.933 52.381 16.45 0.00 43.62 4.40
2926 3103 2.099263 ACACTACGCTAGCACAGTATGG 59.901 50.000 16.45 7.59 43.62 2.74
2928 3105 3.002042 CGTACACTACGCTAGCACAGTAT 59.998 47.826 16.45 8.55 45.81 2.12
2929 3106 2.349580 CGTACACTACGCTAGCACAGTA 59.650 50.000 16.45 8.09 45.81 2.74
2930 3107 1.129998 CGTACACTACGCTAGCACAGT 59.870 52.381 16.45 13.62 45.81 3.55
2932 3109 3.982213 CGTACACTACGCTAGCACA 57.018 52.632 16.45 0.00 45.81 4.57
2941 3118 5.741425 TCGCATAGTTGTATCGTACACTAC 58.259 41.667 0.00 0.00 38.63 2.73
2942 3119 5.559608 GCTCGCATAGTTGTATCGTACACTA 60.560 44.000 0.00 0.00 38.63 2.74
2943 3120 4.788840 GCTCGCATAGTTGTATCGTACACT 60.789 45.833 0.00 0.00 38.63 3.55
2944 3121 3.421231 GCTCGCATAGTTGTATCGTACAC 59.579 47.826 0.00 0.00 38.63 2.90
2945 3122 3.065648 TGCTCGCATAGTTGTATCGTACA 59.934 43.478 0.00 0.00 36.79 2.90
2946 3123 3.421231 GTGCTCGCATAGTTGTATCGTAC 59.579 47.826 0.00 0.00 0.00 3.67
2947 3124 3.624900 GTGCTCGCATAGTTGTATCGTA 58.375 45.455 0.00 0.00 0.00 3.43
2948 3125 2.460918 GTGCTCGCATAGTTGTATCGT 58.539 47.619 0.00 0.00 0.00 3.73
3014 3194 4.506288 ACGCAACTTGCCAAGAAATTTTAC 59.494 37.500 12.25 0.00 41.12 2.01
3015 3195 4.505922 CACGCAACTTGCCAAGAAATTTTA 59.494 37.500 12.25 0.00 41.12 1.52
3019 3206 1.869342 GCACGCAACTTGCCAAGAAAT 60.869 47.619 12.25 0.00 41.12 2.17
3022 3209 2.721231 GCACGCAACTTGCCAAGA 59.279 55.556 12.25 0.00 41.12 3.02
3037 3224 3.549900 TTCCCTGCTCACATGCGCA 62.550 57.895 14.96 14.96 34.31 6.09
3128 3319 3.552219 GGGAGGAATCCCGAGGAC 58.448 66.667 0.00 0.00 40.59 3.85
3178 3369 5.238650 CCTTTTAAATCTCTCCGTGTGTGTT 59.761 40.000 0.00 0.00 0.00 3.32
3188 3379 8.425577 TCACGAATGATCCTTTTAAATCTCTC 57.574 34.615 0.00 0.00 0.00 3.20
3285 3498 2.190161 GCAACACGGTTGTTTCTTTCC 58.810 47.619 15.22 0.00 43.89 3.13
3319 3532 1.447314 AGTTAGTTACCGCGCTGGC 60.447 57.895 16.48 2.93 43.94 4.85
3320 3533 0.389426 ACAGTTAGTTACCGCGCTGG 60.389 55.000 15.25 15.25 46.41 4.85
3321 3534 0.713883 CACAGTTAGTTACCGCGCTG 59.286 55.000 5.56 0.00 0.00 5.18
3322 3535 0.599558 TCACAGTTAGTTACCGCGCT 59.400 50.000 5.56 0.00 0.00 5.92
3323 3536 1.323534 CATCACAGTTAGTTACCGCGC 59.676 52.381 0.00 0.00 0.00 6.86
3324 3537 2.852413 CTCATCACAGTTAGTTACCGCG 59.148 50.000 0.00 0.00 0.00 6.46
3325 3538 4.106029 TCTCATCACAGTTAGTTACCGC 57.894 45.455 0.00 0.00 0.00 5.68
3326 3539 7.426410 ACATATCTCATCACAGTTAGTTACCG 58.574 38.462 0.00 0.00 0.00 4.02
3327 3540 9.680315 GTACATATCTCATCACAGTTAGTTACC 57.320 37.037 0.00 0.00 0.00 2.85
3331 3544 9.854668 AGTAGTACATATCTCATCACAGTTAGT 57.145 33.333 2.52 0.00 0.00 2.24
3348 3561 9.944376 ATGAAGATTGTTAACACAGTAGTACAT 57.056 29.630 8.07 4.68 33.22 2.29
3349 3562 9.203421 CATGAAGATTGTTAACACAGTAGTACA 57.797 33.333 8.07 2.58 33.22 2.90
3350 3563 9.204570 ACATGAAGATTGTTAACACAGTAGTAC 57.795 33.333 8.07 0.00 33.22 2.73
3351 3564 9.203421 CACATGAAGATTGTTAACACAGTAGTA 57.797 33.333 8.07 0.00 33.22 1.82
3352 3565 7.931407 TCACATGAAGATTGTTAACACAGTAGT 59.069 33.333 8.07 1.16 33.22 2.73
3353 3566 8.310406 TCACATGAAGATTGTTAACACAGTAG 57.690 34.615 8.07 0.58 33.22 2.57
3354 3567 8.846943 ATCACATGAAGATTGTTAACACAGTA 57.153 30.769 8.07 0.00 33.22 2.74
3355 3568 7.360353 CGATCACATGAAGATTGTTAACACAGT 60.360 37.037 8.07 0.00 33.22 3.55
3356 3569 6.957635 CGATCACATGAAGATTGTTAACACAG 59.042 38.462 8.07 0.48 33.22 3.66
3365 3578 3.125658 TGCACACGATCACATGAAGATTG 59.874 43.478 0.00 8.97 33.88 2.67
3767 3984 4.295119 ACGACCGACTGCACCCAC 62.295 66.667 0.00 0.00 0.00 4.61
4025 5203 1.111116 TGCCGGTCGGTTATAGGGAG 61.111 60.000 11.25 0.00 37.65 4.30
4051 5229 4.655963 TCCTTTCTTCCAACTGATGAAGG 58.344 43.478 0.00 0.00 38.11 3.46
4052 5230 6.639632 TTTCCTTTCTTCCAACTGATGAAG 57.360 37.500 0.00 0.00 38.11 3.02
4327 5580 0.095245 CTACCGCGTGCAAATCACTG 59.905 55.000 4.92 0.00 43.46 3.66
4338 5591 1.141234 GAAAGCCTAGCTACCGCGT 59.859 57.895 4.92 0.00 38.25 6.01
4364 5617 1.592400 GGCAAGCAAAGCAAAGCGT 60.592 52.632 0.00 0.00 35.48 5.07
4365 5618 0.039256 TAGGCAAGCAAAGCAAAGCG 60.039 50.000 0.00 0.00 35.48 4.68
4384 5637 4.444957 AGGGAGGGGAGCTGGCAT 62.445 66.667 0.00 0.00 0.00 4.40
4388 5641 4.101077 AGGGAGGGAGGGGAGCTG 62.101 72.222 0.00 0.00 0.00 4.24
4389 5642 3.773154 GAGGGAGGGAGGGGAGCT 61.773 72.222 0.00 0.00 0.00 4.09
4392 5645 2.540910 AGTGAGGGAGGGAGGGGA 60.541 66.667 0.00 0.00 0.00 4.81
4393 5646 2.041405 GAGTGAGGGAGGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
4394 5647 1.687493 GTGAGTGAGGGAGGGAGGG 60.687 68.421 0.00 0.00 0.00 4.30
4396 5649 1.552792 GAAAGTGAGTGAGGGAGGGAG 59.447 57.143 0.00 0.00 0.00 4.30
4397 5650 1.132849 TGAAAGTGAGTGAGGGAGGGA 60.133 52.381 0.00 0.00 0.00 4.20
4400 5653 1.974236 AGGTGAAAGTGAGTGAGGGAG 59.026 52.381 0.00 0.00 0.00 4.30
4401 5654 2.103153 AGGTGAAAGTGAGTGAGGGA 57.897 50.000 0.00 0.00 0.00 4.20
4407 5660 5.010719 TCGATTAGACAAGGTGAAAGTGAGT 59.989 40.000 0.00 0.00 0.00 3.41
4431 5684 4.028993 ACCATTAACAACCAAGATCGGT 57.971 40.909 0.00 0.00 42.71 4.69
4439 5692 2.103263 GCCCAACAACCATTAACAACCA 59.897 45.455 0.00 0.00 0.00 3.67
4463 5716 2.614057 CTCATCACGGTAGGAAAATGGC 59.386 50.000 0.00 0.00 0.00 4.40
4522 5775 2.815647 GTGCTAGACGCCACAGGC 60.816 66.667 0.00 0.00 46.75 4.85
4574 5827 2.516225 GCGATTTTAGGCGCCCCT 60.516 61.111 26.15 8.44 46.93 4.79
4695 5949 4.118410 TGACGTGTTTTAGCCGAACTTTA 58.882 39.130 0.00 0.00 0.00 1.85
4835 6089 1.078528 TCAAGGAGGAGAAGGCCGA 59.921 57.895 0.00 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.