Multiple sequence alignment - TraesCS3B01G456300

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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 TraesCS3B01G456300 chr3B 100.000 4925 0 0 1 4925 697898360 697903284 0.000000e+00 9095.0
1 TraesCS3B01G456300 chr3B 81.384 795 148 0 3116 3910 71119782 71120576 0.000000e+00 649.0
2 TraesCS3B01G456300 chr3B 81.132 795 150 0 3116 3910 71143521 71144315 5.380000e-179 638.0
3 TraesCS3B01G456300 chr3B 88.821 492 37 9 746 1221 697856205 697856694 5.490000e-164 588.0
4 TraesCS3B01G456300 chr3B 86.082 194 17 3 128 321 697855975 697856158 3.010000e-47 200.0
5 TraesCS3B01G456300 chr3B 90.625 96 6 3 1208 1303 697858065 697858157 1.860000e-24 124.0
6 TraesCS3B01G456300 chr3B 92.982 57 3 1 2829 2884 748777138 748777082 1.140000e-11 82.4
7 TraesCS3B01G456300 chr3A 94.893 2565 56 10 1 2519 662393770 662396305 0.000000e+00 3941.0
8 TraesCS3B01G456300 chr3A 96.589 1964 40 6 2524 4464 662396406 662398365 0.000000e+00 3230.0
9 TraesCS3B01G456300 chr3A 81.807 797 141 4 3116 3910 57199536 57200330 0.000000e+00 665.0
10 TraesCS3B01G456300 chr3A 86.916 214 22 3 4444 4656 662401451 662401659 8.240000e-58 235.0
11 TraesCS3B01G456300 chr3A 92.500 160 5 3 4645 4803 662406894 662407047 6.420000e-54 222.0
12 TraesCS3B01G456300 chr3A 97.980 99 2 0 2566 2664 662396298 662396396 6.550000e-39 172.0
13 TraesCS3B01G456300 chr3A 93.506 77 5 0 4836 4912 662407047 662407123 1.120000e-21 115.0
14 TraesCS3B01G456300 chr3D 95.978 2337 63 13 2342 4656 527666970 527669297 0.000000e+00 3766.0
15 TraesCS3B01G456300 chr3D 98.351 1395 23 0 899 2293 527665576 527666970 0.000000e+00 2449.0
16 TraesCS3B01G456300 chr3D 80.300 868 163 5 3045 3910 45410039 45410900 0.000000e+00 649.0
17 TraesCS3B01G456300 chr3D 92.424 198 12 2 128 325 527588074 527588268 3.750000e-71 279.0
18 TraesCS3B01G456300 chr3D 92.262 168 7 4 4638 4803 527670200 527670363 2.960000e-57 233.0
19 TraesCS3B01G456300 chr3D 86.364 154 6 1 746 884 527588319 527588472 2.370000e-33 154.0
20 TraesCS3B01G456300 chr3D 93.506 77 5 0 4836 4912 527670363 527670439 1.120000e-21 115.0
21 TraesCS3B01G456300 chr3D 97.619 42 0 1 2611 2652 149236000 149236040 2.460000e-08 71.3
22 TraesCS3B01G456300 chr6B 91.546 414 31 1 330 743 579922819 579923228 7.150000e-158 568.0
23 TraesCS3B01G456300 chr6B 91.437 327 24 1 420 746 579888850 579889172 3.500000e-121 446.0
24 TraesCS3B01G456300 chr6B 90.566 53 3 2 2602 2652 79946898 79946950 8.850000e-08 69.4
25 TraesCS3B01G456300 chr6B 90.566 53 3 2 2602 2652 80000974 80001026 8.850000e-08 69.4
26 TraesCS3B01G456300 chr1D 92.331 326 21 2 421 746 491975060 491975381 1.250000e-125 460.0
27 TraesCS3B01G456300 chr1D 93.750 48 2 1 2606 2652 10536557 10536604 2.460000e-08 71.3
28 TraesCS3B01G456300 chr1D 92.000 50 3 1 2603 2652 461081984 461082032 8.850000e-08 69.4
29 TraesCS3B01G456300 chr4B 89.266 354 32 4 391 744 27863236 27863583 5.850000e-119 438.0
30 TraesCS3B01G456300 chr4B 86.478 318 36 3 432 746 27838112 27838425 4.720000e-90 342.0
31 TraesCS3B01G456300 chr4B 90.000 60 6 0 2812 2871 462218877 462218936 1.470000e-10 78.7
32 TraesCS3B01G456300 chr2B 94.828 116 5 1 11 126 638012827 638012713 3.920000e-41 180.0
33 TraesCS3B01G456300 chr7D 90.476 126 12 0 1 126 184210272 184210397 3.050000e-37 167.0
34 TraesCS3B01G456300 chr7D 87.903 124 14 1 1 124 436874626 436874504 1.430000e-30 145.0
35 TraesCS3B01G456300 chr7D 95.455 44 1 1 2609 2652 40006504 40006546 8.850000e-08 69.4
36 TraesCS3B01G456300 chr4D 89.516 124 13 0 1 124 421316830 421316707 1.840000e-34 158.0
37 TraesCS3B01G456300 chr4D 87.903 124 15 0 1 124 320191944 320191821 3.970000e-31 147.0
38 TraesCS3B01G456300 chr1B 93.396 106 7 0 1 106 61648922 61648817 1.840000e-34 158.0
39 TraesCS3B01G456300 chr1B 93.333 60 2 2 2828 2886 621061911 621061969 2.440000e-13 87.9
40 TraesCS3B01G456300 chr6D 91.509 106 9 0 1 106 324755205 324755310 3.970000e-31 147.0
41 TraesCS3B01G456300 chr6D 100.000 28 0 0 2806 2833 405119640 405119613 9.000000e-03 52.8
42 TraesCS3B01G456300 chr2A 91.509 106 9 0 1 106 667953124 667953229 3.970000e-31 147.0
43 TraesCS3B01G456300 chr2A 86.957 69 6 3 2818 2885 742692562 742692628 1.900000e-09 75.0
44 TraesCS3B01G456300 chr7B 95.604 91 1 1 603 693 115194516 115194429 5.140000e-30 143.0
45 TraesCS3B01G456300 chr5D 90.909 66 1 1 2814 2879 354697320 354697380 3.160000e-12 84.2
46 TraesCS3B01G456300 chr5B 90.909 66 1 1 2814 2879 419395704 419395764 3.160000e-12 84.2
47 TraesCS3B01G456300 chr5A 90.909 66 1 1 2814 2879 456599630 456599690 3.160000e-12 84.2


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 TraesCS3B01G456300 chr3B 697898360 697903284 4924 False 9095.00 9095 100.000000 1 4925 1 chr3B.!!$F3 4924
1 TraesCS3B01G456300 chr3B 71119782 71120576 794 False 649.00 649 81.384000 3116 3910 1 chr3B.!!$F1 794
2 TraesCS3B01G456300 chr3B 71143521 71144315 794 False 638.00 638 81.132000 3116 3910 1 chr3B.!!$F2 794
3 TraesCS3B01G456300 chr3B 697855975 697858157 2182 False 304.00 588 88.509333 128 1303 3 chr3B.!!$F4 1175
4 TraesCS3B01G456300 chr3A 662393770 662401659 7889 False 1894.50 3941 94.094500 1 4656 4 chr3A.!!$F2 4655
5 TraesCS3B01G456300 chr3A 57199536 57200330 794 False 665.00 665 81.807000 3116 3910 1 chr3A.!!$F1 794
6 TraesCS3B01G456300 chr3D 527665576 527670439 4863 False 1640.75 3766 95.024250 899 4912 4 chr3D.!!$F4 4013
7 TraesCS3B01G456300 chr3D 45410039 45410900 861 False 649.00 649 80.300000 3045 3910 1 chr3D.!!$F1 865

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
390 391 0.107703 TTCCATCTACAGCGCCTTGG 60.108 55.000 2.29 2.46 0.00 3.61 F
557 558 0.531090 GTGCGTGTGTGGGTTGAGTA 60.531 55.000 0.00 0.00 0.00 2.59 F
1647 3076 0.179084 TTCGATTCATCTGGGGCGTC 60.179 55.000 0.00 0.00 0.00 5.19 F
3228 4774 1.946768 TCTGCTTGGTTAGTGCACAAC 59.053 47.619 21.04 19.29 32.91 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 2732 0.034896 GACCCCTCGCTTGAGTTGAA 59.965 55.000 0.0 0.0 38.10 2.69 R
2090 3522 2.095853 GCCATTGTCCACACATAAGTCG 59.904 50.000 0.0 0.0 30.55 4.18 R
3389 4935 1.376942 CAGAGCTGCCCTCCAACAG 60.377 63.158 0.0 0.0 41.74 3.16 R
4804 10402 0.036732 GGTGACCTGATGTTGCTGGA 59.963 55.000 0.0 0.0 0.00 3.86 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
88 89 6.017109 CACATAAGTGCCTAAAACAGTCACTT 60.017 38.462 10.22 10.22 46.09 3.16
109 110 0.918258 TATCTGCTCCCACCATTGCA 59.082 50.000 0.00 0.00 0.00 4.08
110 111 0.260816 ATCTGCTCCCACCATTGCAT 59.739 50.000 0.00 0.00 34.79 3.96
126 127 3.226682 TGCATGCAGGCCAAGATATTA 57.773 42.857 22.16 0.00 0.00 0.98
202 203 3.569701 AGATGAATGTGCCGTTCAAACTT 59.430 39.130 12.06 0.00 41.73 2.66
254 255 1.022735 GCGAACTCGGATCTACCTGA 58.977 55.000 0.69 0.00 40.23 3.86
316 317 0.409876 GCCTTCCTTTCCCCTTCCTT 59.590 55.000 0.00 0.00 0.00 3.36
350 351 2.713967 TGGCAACATGGGAGGATCT 58.286 52.632 0.00 0.00 46.17 2.75
360 361 1.663173 GGAGGATCTAGTGGCGCTC 59.337 63.158 7.64 0.45 33.73 5.03
382 383 3.744942 CCATCGCTGATTTCCATCTACAG 59.255 47.826 0.00 0.00 0.00 2.74
390 391 0.107703 TTCCATCTACAGCGCCTTGG 60.108 55.000 2.29 2.46 0.00 3.61
395 396 2.925706 TACAGCGCCTTGGGGACA 60.926 61.111 2.29 0.00 39.83 4.02
422 423 1.379642 GCTCAAGAAGGGGCGAATGG 61.380 60.000 0.00 0.00 0.00 3.16
456 457 1.673665 GGCTCCACCTGCAGACAAG 60.674 63.158 17.39 8.08 34.51 3.16
465 466 1.584380 CTGCAGACAAGCAAGAGGGC 61.584 60.000 8.42 0.00 45.13 5.19
557 558 0.531090 GTGCGTGTGTGGGTTGAGTA 60.531 55.000 0.00 0.00 0.00 2.59
561 562 1.821216 GTGTGTGGGTTGAGTATGGG 58.179 55.000 0.00 0.00 0.00 4.00
570 571 3.264897 GAGTATGGGCTGCGTGCG 61.265 66.667 0.00 0.00 44.05 5.34
650 652 3.816524 CGAACCGAGAGCGAGGCT 61.817 66.667 0.00 0.00 43.88 4.58
652 654 2.676822 AACCGAGAGCGAGGCTGA 60.677 61.111 0.00 0.00 39.88 4.26
653 655 2.010582 GAACCGAGAGCGAGGCTGAT 62.011 60.000 0.00 0.00 39.88 2.90
654 656 2.010582 AACCGAGAGCGAGGCTGATC 62.011 60.000 0.00 0.00 39.88 2.92
655 657 2.334653 CGAGAGCGAGGCTGATCC 59.665 66.667 0.00 0.00 39.88 3.36
664 666 3.238987 AGGCTGATCCTCCTCCTTC 57.761 57.895 0.00 0.00 43.20 3.46
665 667 0.641601 AGGCTGATCCTCCTCCTTCT 59.358 55.000 0.00 0.00 43.20 2.85
666 668 1.862911 AGGCTGATCCTCCTCCTTCTA 59.137 52.381 0.00 0.00 43.20 2.10
667 669 2.454381 AGGCTGATCCTCCTCCTTCTAT 59.546 50.000 0.00 0.00 43.20 1.98
668 670 2.831526 GGCTGATCCTCCTCCTTCTATC 59.168 54.545 0.00 0.00 0.00 2.08
669 671 2.831526 GCTGATCCTCCTCCTTCTATCC 59.168 54.545 0.00 0.00 0.00 2.59
670 672 3.502119 GCTGATCCTCCTCCTTCTATCCT 60.502 52.174 0.00 0.00 0.00 3.24
671 673 4.344104 CTGATCCTCCTCCTTCTATCCTC 58.656 52.174 0.00 0.00 0.00 3.71
672 674 3.729524 TGATCCTCCTCCTTCTATCCTCA 59.270 47.826 0.00 0.00 0.00 3.86
673 675 3.603965 TCCTCCTCCTTCTATCCTCAC 57.396 52.381 0.00 0.00 0.00 3.51
674 676 2.178106 TCCTCCTCCTTCTATCCTCACC 59.822 54.545 0.00 0.00 0.00 4.02
675 677 2.091055 CCTCCTCCTTCTATCCTCACCA 60.091 54.545 0.00 0.00 0.00 4.17
742 744 7.122048 TCCAGAAGAGAGAATTGAGTAGATCA 58.878 38.462 0.00 0.00 35.62 2.92
743 745 7.285172 TCCAGAAGAGAGAATTGAGTAGATCAG 59.715 40.741 0.00 0.00 39.68 2.90
744 746 7.428020 CAGAAGAGAGAATTGAGTAGATCAGG 58.572 42.308 0.00 0.00 39.68 3.86
977 1022 2.489722 GCCCTTGGAGAAATCACTTGAC 59.510 50.000 0.00 0.00 0.00 3.18
1229 2658 3.378339 GCAAGAATGATATTGCCACTGC 58.622 45.455 4.45 0.00 45.71 4.40
1303 2732 0.527565 CAGCGCCCAAAATGCTACTT 59.472 50.000 2.29 0.00 37.15 2.24
1342 2771 5.394773 GGGTCTCTGAATACAAGAGAGGTTC 60.395 48.000 3.44 0.00 39.09 3.62
1537 2966 0.464036 TTCCCGCTGCACTATACTGG 59.536 55.000 0.00 0.00 0.00 4.00
1647 3076 0.179084 TTCGATTCATCTGGGGCGTC 60.179 55.000 0.00 0.00 0.00 5.19
1935 3364 5.500234 TCACTGCAATTTGCCTAAGTAGAT 58.500 37.500 18.27 0.00 44.23 1.98
2090 3522 5.240121 TGGTCCGAGTTAAGGTGTTATTTC 58.760 41.667 0.00 0.00 0.00 2.17
2239 3671 8.573035 GTTCCTGTAAACTGGTGAAAATTATCA 58.427 33.333 6.00 0.00 36.48 2.15
2491 3938 6.716628 TGGGATGAAATTGTAATATCAGCTCC 59.283 38.462 0.00 0.00 27.76 4.70
2664 4210 3.369471 GGCCTCTGCAACTTCACTATACA 60.369 47.826 0.00 0.00 40.13 2.29
2834 4380 6.854091 AAGTACTCCCTCTGTAAACTAAGG 57.146 41.667 0.00 0.00 0.00 2.69
3027 4573 4.574013 GCTGGAATGTTCAGATCAACCTAG 59.426 45.833 0.00 0.00 34.36 3.02
3189 4735 3.058224 GGATCTTCAGGTCAACCAAAACG 60.058 47.826 1.33 0.00 38.89 3.60
3196 4742 4.513692 TCAGGTCAACCAAAACGACTATTG 59.486 41.667 1.33 0.00 38.89 1.90
3228 4774 1.946768 TCTGCTTGGTTAGTGCACAAC 59.053 47.619 21.04 19.29 32.91 3.32
3296 4842 3.646534 TCCTGGATGTAGCAGATGAGAA 58.353 45.455 0.00 0.00 0.00 2.87
3774 5320 2.044492 TCCTGGTCCATACAGAAGTCCT 59.956 50.000 0.00 0.00 38.20 3.85
3898 5444 2.673368 CTGTTTGAGACCATACGAAGCC 59.327 50.000 0.00 0.00 0.00 4.35
4019 5568 8.087136 CAGTGTATATCAGAGTGCTTATGATGT 58.913 37.037 8.53 5.45 35.39 3.06
4020 5569 8.646004 AGTGTATATCAGAGTGCTTATGATGTT 58.354 33.333 8.53 1.36 35.39 2.71
4021 5570 8.706936 GTGTATATCAGAGTGCTTATGATGTTG 58.293 37.037 8.53 0.00 35.39 3.33
4097 5646 4.596643 AGTTGAGATAGGGAATGGGAGATG 59.403 45.833 0.00 0.00 0.00 2.90
4114 5663 5.488341 GGAGATGTCTTTTAGCACCTAACA 58.512 41.667 0.00 0.00 0.00 2.41
4148 5708 1.002069 AGAGGGATGGAAATGCACCA 58.998 50.000 0.00 0.00 41.83 4.17
4415 5984 2.036604 GGTCTAGCTTAGGCATGTCTCC 59.963 54.545 1.25 0.00 41.70 3.71
4465 9141 3.986277 AGAAACGGTCTATCAAACACGT 58.014 40.909 0.00 0.00 33.56 4.49
4466 9142 3.739300 AGAAACGGTCTATCAAACACGTG 59.261 43.478 15.48 15.48 33.56 4.49
4501 9177 8.055279 CTTCCTTGAGAAGCATTTTATTACCA 57.945 34.615 0.00 0.00 45.38 3.25
4504 9180 7.121168 TCCTTGAGAAGCATTTTATTACCACTG 59.879 37.037 0.00 0.00 0.00 3.66
4525 9201 3.630312 TGTCAGCTTTGGTTTGGTTACTC 59.370 43.478 0.00 0.00 0.00 2.59
4529 9205 4.020543 AGCTTTGGTTTGGTTACTCAACA 58.979 39.130 0.00 0.00 36.29 3.33
4585 9261 1.734465 GCTAGCAGCAAGGTTGTGTAG 59.266 52.381 10.63 0.00 41.89 2.74
4586 9262 1.734465 CTAGCAGCAAGGTTGTGTAGC 59.266 52.381 0.00 0.00 0.00 3.58
4587 9263 0.109342 AGCAGCAAGGTTGTGTAGCT 59.891 50.000 0.00 0.00 35.72 3.32
4588 9264 1.347707 AGCAGCAAGGTTGTGTAGCTA 59.652 47.619 0.00 0.00 33.29 3.32
4589 9265 1.734465 GCAGCAAGGTTGTGTAGCTAG 59.266 52.381 0.00 0.00 33.29 3.42
4590 9266 2.350522 CAGCAAGGTTGTGTAGCTAGG 58.649 52.381 0.00 0.00 33.29 3.02
4620 9296 8.361889 GGCCTTTGTTAAACAAACCTTTATAGA 58.638 33.333 0.00 0.00 42.55 1.98
4621 9297 9.752961 GCCTTTGTTAAACAAACCTTTATAGAA 57.247 29.630 0.00 0.00 42.55 2.10
4631 9307 8.950007 ACAAACCTTTATAGAATTGAAGGGAA 57.050 30.769 6.02 0.00 42.30 3.97
4633 9309 8.802267 CAAACCTTTATAGAATTGAAGGGAACA 58.198 33.333 6.02 0.00 42.30 3.18
4643 9319 8.893563 AGAATTGAAGGGAACATATAAAACCA 57.106 30.769 0.00 0.00 0.00 3.67
4650 9326 5.650703 AGGGAACATATAAAACCAAAGGTCG 59.349 40.000 0.00 0.00 33.12 4.79
4698 10296 1.929038 GCCTTTCTTTTTCGCGGGAAC 60.929 52.381 15.20 0.00 0.00 3.62
4714 10312 2.418334 GGGAACGATGGAAGTGACCTAC 60.418 54.545 0.00 0.00 0.00 3.18
4716 10314 2.233305 ACGATGGAAGTGACCTACCT 57.767 50.000 0.00 0.00 0.00 3.08
4717 10315 3.377253 ACGATGGAAGTGACCTACCTA 57.623 47.619 0.00 0.00 0.00 3.08
4718 10316 3.705051 ACGATGGAAGTGACCTACCTAA 58.295 45.455 0.00 0.00 0.00 2.69
4719 10317 3.446516 ACGATGGAAGTGACCTACCTAAC 59.553 47.826 0.00 0.00 0.00 2.34
4720 10318 3.181478 CGATGGAAGTGACCTACCTAACC 60.181 52.174 0.00 0.00 0.00 2.85
4721 10319 3.555117 TGGAAGTGACCTACCTAACCT 57.445 47.619 0.00 0.00 0.00 3.50
4722 10320 3.865571 TGGAAGTGACCTACCTAACCTT 58.134 45.455 0.00 0.00 0.00 3.50
4723 10321 5.014534 TGGAAGTGACCTACCTAACCTTA 57.985 43.478 0.00 0.00 0.00 2.69
4724 10322 5.405279 TGGAAGTGACCTACCTAACCTTAA 58.595 41.667 0.00 0.00 0.00 1.85
4725 10323 5.482878 TGGAAGTGACCTACCTAACCTTAAG 59.517 44.000 0.00 0.00 0.00 1.85
4726 10324 5.718607 GGAAGTGACCTACCTAACCTTAAGA 59.281 44.000 3.36 0.00 0.00 2.10
4756 10354 2.421424 CAGATGCCTTCCTGCTGTAAAC 59.579 50.000 0.00 0.00 0.00 2.01
4777 10375 3.113322 CGGATATTCTTTCTGCGTTCGA 58.887 45.455 0.00 0.00 0.00 3.71
4799 10397 2.727123 TTCTTCTGGTGCCTTGTCAA 57.273 45.000 0.00 0.00 0.00 3.18
4802 10400 4.365514 TCTTCTGGTGCCTTGTCAATTA 57.634 40.909 0.00 0.00 0.00 1.40
4803 10401 4.072131 TCTTCTGGTGCCTTGTCAATTAC 58.928 43.478 0.00 0.00 0.00 1.89
4804 10402 3.788227 TCTGGTGCCTTGTCAATTACT 57.212 42.857 0.00 0.00 0.00 2.24
4805 10403 3.674997 TCTGGTGCCTTGTCAATTACTC 58.325 45.455 0.00 0.00 0.00 2.59
4806 10404 2.749621 CTGGTGCCTTGTCAATTACTCC 59.250 50.000 0.00 0.00 0.00 3.85
4807 10405 2.107378 TGGTGCCTTGTCAATTACTCCA 59.893 45.455 0.00 0.00 0.00 3.86
4808 10406 2.749621 GGTGCCTTGTCAATTACTCCAG 59.250 50.000 0.00 0.00 0.00 3.86
4809 10407 2.162408 GTGCCTTGTCAATTACTCCAGC 59.838 50.000 0.00 0.00 0.00 4.85
4810 10408 2.224744 TGCCTTGTCAATTACTCCAGCA 60.225 45.455 0.00 0.00 0.00 4.41
4811 10409 2.819608 GCCTTGTCAATTACTCCAGCAA 59.180 45.455 0.00 0.00 0.00 3.91
4812 10410 3.366374 GCCTTGTCAATTACTCCAGCAAC 60.366 47.826 0.00 0.00 0.00 4.17
4813 10411 3.820467 CCTTGTCAATTACTCCAGCAACA 59.180 43.478 0.00 0.00 0.00 3.33
4814 10412 4.460382 CCTTGTCAATTACTCCAGCAACAT 59.540 41.667 0.00 0.00 0.00 2.71
4815 10413 5.392380 CCTTGTCAATTACTCCAGCAACATC 60.392 44.000 0.00 0.00 0.00 3.06
4816 10414 4.650734 TGTCAATTACTCCAGCAACATCA 58.349 39.130 0.00 0.00 0.00 3.07
4817 10415 4.696877 TGTCAATTACTCCAGCAACATCAG 59.303 41.667 0.00 0.00 0.00 2.90
4818 10416 4.095483 GTCAATTACTCCAGCAACATCAGG 59.905 45.833 0.00 0.00 0.00 3.86
4819 10417 4.012374 CAATTACTCCAGCAACATCAGGT 58.988 43.478 0.00 0.00 0.00 4.00
4820 10418 3.334583 TTACTCCAGCAACATCAGGTC 57.665 47.619 0.00 0.00 0.00 3.85
4821 10419 1.059098 ACTCCAGCAACATCAGGTCA 58.941 50.000 0.00 0.00 0.00 4.02
4822 10420 1.271054 ACTCCAGCAACATCAGGTCAC 60.271 52.381 0.00 0.00 0.00 3.67
4823 10421 0.036732 TCCAGCAACATCAGGTCACC 59.963 55.000 0.00 0.00 0.00 4.02
4824 10422 0.962356 CCAGCAACATCAGGTCACCC 60.962 60.000 0.00 0.00 0.00 4.61
4825 10423 0.037303 CAGCAACATCAGGTCACCCT 59.963 55.000 0.00 0.00 44.02 4.34
4826 10424 0.326264 AGCAACATCAGGTCACCCTC 59.674 55.000 0.00 0.00 39.89 4.30
4827 10425 0.678048 GCAACATCAGGTCACCCTCC 60.678 60.000 0.00 0.00 39.89 4.30
4828 10426 0.692476 CAACATCAGGTCACCCTCCA 59.308 55.000 0.00 0.00 39.89 3.86
4829 10427 0.987294 AACATCAGGTCACCCTCCAG 59.013 55.000 0.00 0.00 39.89 3.86
4830 10428 0.178891 ACATCAGGTCACCCTCCAGT 60.179 55.000 0.00 0.00 39.89 4.00
4831 10429 1.078823 ACATCAGGTCACCCTCCAGTA 59.921 52.381 0.00 0.00 39.89 2.74
4832 10430 2.187958 CATCAGGTCACCCTCCAGTAA 58.812 52.381 0.00 0.00 39.89 2.24
4833 10431 1.640917 TCAGGTCACCCTCCAGTAAC 58.359 55.000 0.00 0.00 39.89 2.50
4834 10432 1.132977 TCAGGTCACCCTCCAGTAACA 60.133 52.381 0.00 0.00 39.89 2.41
4869 10467 3.558931 TGATGTGGTCAGTTGTTCTGT 57.441 42.857 0.00 0.00 43.97 3.41
4871 10469 5.227569 TGATGTGGTCAGTTGTTCTGTAT 57.772 39.130 0.00 0.00 43.97 2.29
4872 10470 5.620206 TGATGTGGTCAGTTGTTCTGTATT 58.380 37.500 0.00 0.00 43.97 1.89
4876 10474 4.452455 GTGGTCAGTTGTTCTGTATTCCAG 59.548 45.833 0.00 0.00 43.97 3.86
4887 10485 7.500992 TGTTCTGTATTCCAGTTGATATCTCC 58.499 38.462 3.98 0.00 42.19 3.71
4912 10510 0.471617 CATCAGGTCACCCTCCCATC 59.528 60.000 0.00 0.00 39.89 3.51
4913 10511 0.695803 ATCAGGTCACCCTCCCATCC 60.696 60.000 0.00 0.00 39.89 3.51
4914 10512 2.042930 AGGTCACCCTCCCATCCC 59.957 66.667 0.00 0.00 35.62 3.85
4915 10513 2.286121 GGTCACCCTCCCATCCCA 60.286 66.667 0.00 0.00 0.00 4.37
4916 10514 1.697754 GGTCACCCTCCCATCCCAT 60.698 63.158 0.00 0.00 0.00 4.00
4917 10515 1.289244 GGTCACCCTCCCATCCCATT 61.289 60.000 0.00 0.00 0.00 3.16
4918 10516 0.631212 GTCACCCTCCCATCCCATTT 59.369 55.000 0.00 0.00 0.00 2.32
4919 10517 1.850345 GTCACCCTCCCATCCCATTTA 59.150 52.381 0.00 0.00 0.00 1.40
4920 10518 1.850345 TCACCCTCCCATCCCATTTAC 59.150 52.381 0.00 0.00 0.00 2.01
4921 10519 1.568597 CACCCTCCCATCCCATTTACA 59.431 52.381 0.00 0.00 0.00 2.41
4922 10520 1.852965 ACCCTCCCATCCCATTTACAG 59.147 52.381 0.00 0.00 0.00 2.74
4923 10521 1.479389 CCCTCCCATCCCATTTACAGC 60.479 57.143 0.00 0.00 0.00 4.40
4924 10522 1.479389 CCTCCCATCCCATTTACAGCC 60.479 57.143 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.141657 GCAATGGTGGGAGCAGATAGA 59.858 52.381 0.00 0.00 0.00 1.98
109 110 6.736110 ACATTTTAATATCTTGGCCTGCAT 57.264 33.333 3.32 0.00 0.00 3.96
110 111 6.833416 AGTACATTTTAATATCTTGGCCTGCA 59.167 34.615 3.32 0.00 0.00 4.41
152 153 9.226345 GATGTTTTTGTTTTCACTCTACTCTTG 57.774 33.333 0.00 0.00 0.00 3.02
202 203 3.827722 CCAGAGGGTTAAACCAACTCAA 58.172 45.455 13.24 0.00 40.41 3.02
316 317 4.586421 TGTTGCCAATGTTGTAGATGGAAA 59.414 37.500 0.00 0.00 34.82 3.13
360 361 3.732212 TGTAGATGGAAATCAGCGATGG 58.268 45.455 0.00 0.00 36.78 3.51
367 368 1.486310 AGGCGCTGTAGATGGAAATCA 59.514 47.619 7.64 0.00 0.00 2.57
397 398 3.130160 CCCTTCTTGAGCAGCGGC 61.130 66.667 0.00 0.00 41.61 6.53
422 423 3.357079 CCCACCTGACAAGCGTGC 61.357 66.667 0.00 0.00 0.00 5.34
456 457 3.123620 CAGCTCACGCCCTCTTGC 61.124 66.667 0.00 0.00 36.60 4.01
474 475 2.910737 ATCAGTGGTGGTGGCAGGG 61.911 63.158 0.00 0.00 0.00 4.45
481 482 2.532715 AGGCCCATCAGTGGTGGT 60.533 61.111 21.14 0.00 44.48 4.16
561 562 0.731514 TAACTAGTCACGCACGCAGC 60.732 55.000 0.00 0.00 40.87 5.25
570 571 1.547372 TCGCACCCCTTAACTAGTCAC 59.453 52.381 0.00 0.00 0.00 3.67
575 576 1.822990 CAGTCTCGCACCCCTTAACTA 59.177 52.381 0.00 0.00 0.00 2.24
650 652 3.729524 TGAGGATAGAAGGAGGAGGATCA 59.270 47.826 0.00 0.00 36.25 2.92
652 654 3.181412 GGTGAGGATAGAAGGAGGAGGAT 60.181 52.174 0.00 0.00 0.00 3.24
653 655 2.178106 GGTGAGGATAGAAGGAGGAGGA 59.822 54.545 0.00 0.00 0.00 3.71
654 656 2.091055 TGGTGAGGATAGAAGGAGGAGG 60.091 54.545 0.00 0.00 0.00 4.30
655 657 3.320610 TGGTGAGGATAGAAGGAGGAG 57.679 52.381 0.00 0.00 0.00 3.69
656 658 3.375699 GTTGGTGAGGATAGAAGGAGGA 58.624 50.000 0.00 0.00 0.00 3.71
657 659 2.436173 GGTTGGTGAGGATAGAAGGAGG 59.564 54.545 0.00 0.00 0.00 4.30
658 660 2.436173 GGGTTGGTGAGGATAGAAGGAG 59.564 54.545 0.00 0.00 0.00 3.69
659 661 2.478292 GGGTTGGTGAGGATAGAAGGA 58.522 52.381 0.00 0.00 0.00 3.36
660 662 1.490910 GGGGTTGGTGAGGATAGAAGG 59.509 57.143 0.00 0.00 0.00 3.46
661 663 1.490910 GGGGGTTGGTGAGGATAGAAG 59.509 57.143 0.00 0.00 0.00 2.85
662 664 1.082194 AGGGGGTTGGTGAGGATAGAA 59.918 52.381 0.00 0.00 0.00 2.10
663 665 0.722676 AGGGGGTTGGTGAGGATAGA 59.277 55.000 0.00 0.00 0.00 1.98
664 666 1.132500 GAGGGGGTTGGTGAGGATAG 58.868 60.000 0.00 0.00 0.00 2.08
665 667 0.722676 AGAGGGGGTTGGTGAGGATA 59.277 55.000 0.00 0.00 0.00 2.59
666 668 0.916358 CAGAGGGGGTTGGTGAGGAT 60.916 60.000 0.00 0.00 0.00 3.24
667 669 1.538876 CAGAGGGGGTTGGTGAGGA 60.539 63.158 0.00 0.00 0.00 3.71
668 670 3.081554 CAGAGGGGGTTGGTGAGG 58.918 66.667 0.00 0.00 0.00 3.86
669 671 1.783250 AAGCAGAGGGGGTTGGTGAG 61.783 60.000 0.00 0.00 0.00 3.51
670 672 1.774217 AAGCAGAGGGGGTTGGTGA 60.774 57.895 0.00 0.00 0.00 4.02
671 673 1.303643 GAAGCAGAGGGGGTTGGTG 60.304 63.158 0.00 0.00 0.00 4.17
672 674 2.539081 GGAAGCAGAGGGGGTTGGT 61.539 63.158 0.00 0.00 0.00 3.67
673 675 1.793820 AAGGAAGCAGAGGGGGTTGG 61.794 60.000 0.00 0.00 0.00 3.77
674 676 0.113190 AAAGGAAGCAGAGGGGGTTG 59.887 55.000 0.00 0.00 0.00 3.77
675 677 1.354705 GTAAAGGAAGCAGAGGGGGTT 59.645 52.381 0.00 0.00 0.00 4.11
977 1022 2.885644 CATCCGAGACCCGCAACG 60.886 66.667 0.00 0.00 36.84 4.10
1303 2732 0.034896 GACCCCTCGCTTGAGTTGAA 59.965 55.000 0.00 0.00 38.10 2.69
1342 2771 1.480545 TGGATCCGGTACTGTGTCATG 59.519 52.381 7.39 0.00 0.00 3.07
1537 2966 7.072030 CAGCTACGCCTTTATCATGAATAAAC 58.928 38.462 0.00 0.00 35.38 2.01
1647 3076 2.286772 GGGCAAGAGTTGTTTGTGTACG 60.287 50.000 0.00 0.00 0.00 3.67
1918 3347 6.058183 AGCTACCATCTACTTAGGCAAATTG 58.942 40.000 0.00 0.00 0.00 2.32
1935 3364 6.043822 TGGATAGTATAATTGGCAAGCTACCA 59.956 38.462 5.96 4.29 34.65 3.25
2090 3522 2.095853 GCCATTGTCCACACATAAGTCG 59.904 50.000 0.00 0.00 30.55 4.18
2239 3671 9.877178 AACTGACAATAAATCTTCTACGAGATT 57.123 29.630 0.00 0.00 45.75 2.40
2664 4210 5.957842 TCAACCGCTAAAATCAACAATCT 57.042 34.783 0.00 0.00 0.00 2.40
2810 4356 6.786461 ACCTTAGTTTACAGAGGGAGTACTTT 59.214 38.462 0.00 0.00 33.51 2.66
3027 4573 6.456501 ACAAGTACAGGATCACTAAGTTGAC 58.543 40.000 0.00 0.00 32.78 3.18
3189 4735 2.101582 AGACCAGATGCGGACAATAGTC 59.898 50.000 0.00 0.00 44.21 2.59
3228 4774 1.915141 ACCCCACAGCTTCAATTGAG 58.085 50.000 8.41 4.57 0.00 3.02
3296 4842 5.824904 AGAAGCGATAAATTGCATGAACT 57.175 34.783 0.00 0.00 39.70 3.01
3389 4935 1.376942 CAGAGCTGCCCTCCAACAG 60.377 63.158 0.00 0.00 41.74 3.16
3774 5320 3.924114 TGAGTCTTCTTGTTTGGGTCA 57.076 42.857 0.00 0.00 0.00 4.02
3898 5444 1.134848 GCTGCTGTCTCCCTCTAGTTG 60.135 57.143 0.00 0.00 0.00 3.16
4019 5568 3.833650 TCTTCCTATCCGTGGTACAACAA 59.166 43.478 0.35 0.00 44.16 2.83
4020 5569 3.433343 TCTTCCTATCCGTGGTACAACA 58.567 45.455 0.35 0.00 44.16 3.33
4021 5570 4.081807 AGTTCTTCCTATCCGTGGTACAAC 60.082 45.833 0.00 0.00 44.16 3.32
4097 5646 5.106277 GGATTGGTGTTAGGTGCTAAAAGAC 60.106 44.000 0.00 0.00 0.00 3.01
4114 5663 0.040204 CCTCTTGCCAAGGGATTGGT 59.960 55.000 5.72 0.00 43.90 3.67
4148 5708 3.829026 TGCAGCGAATATCTCCAGATACT 59.171 43.478 0.00 0.00 39.57 2.12
4329 5898 1.887854 CACATCACAATGGTGGCAAGA 59.112 47.619 0.00 0.00 45.32 3.02
4415 5984 4.202233 ACAGTGCAGGATCATCATAGACTG 60.202 45.833 7.88 7.88 35.50 3.51
4465 9141 1.902508 CTCAAGGAAGTAGGACCAGCA 59.097 52.381 0.00 0.00 0.00 4.41
4466 9142 2.180276 TCTCAAGGAAGTAGGACCAGC 58.820 52.381 0.00 0.00 0.00 4.85
4500 9176 1.750778 ACCAAACCAAAGCTGACAGTG 59.249 47.619 3.99 0.00 0.00 3.66
4501 9177 2.143876 ACCAAACCAAAGCTGACAGT 57.856 45.000 3.99 0.00 0.00 3.55
4504 9180 3.630312 TGAGTAACCAAACCAAAGCTGAC 59.370 43.478 0.00 0.00 0.00 3.51
4525 9201 1.019673 ACTGCACAGCTTCAGTGTTG 58.980 50.000 11.07 4.57 41.53 3.33
4529 9205 1.446907 GCATACTGCACAGCTTCAGT 58.553 50.000 14.94 14.94 44.26 3.41
4577 9253 1.202545 GGCCTAGCCTAGCTACACAAC 60.203 57.143 0.00 0.00 46.69 3.32
4579 9255 2.822215 GGCCTAGCCTAGCTACACA 58.178 57.895 0.00 0.00 46.69 3.72
4589 9265 4.594123 TTTGTTTAACAAAGGCCTAGCC 57.406 40.909 17.93 0.00 42.55 3.93
4606 9282 8.803235 GTTCCCTTCAATTCTATAAAGGTTTGT 58.197 33.333 0.00 0.00 37.22 2.83
4607 9283 8.802267 TGTTCCCTTCAATTCTATAAAGGTTTG 58.198 33.333 0.00 0.00 37.22 2.93
4608 9284 8.950007 TGTTCCCTTCAATTCTATAAAGGTTT 57.050 30.769 0.00 0.00 37.22 3.27
4620 9296 9.942850 CTTTGGTTTTATATGTTCCCTTCAATT 57.057 29.630 0.00 0.00 0.00 2.32
4621 9297 8.539544 CCTTTGGTTTTATATGTTCCCTTCAAT 58.460 33.333 0.00 0.00 0.00 2.57
4628 9304 6.746745 TCGACCTTTGGTTTTATATGTTCC 57.253 37.500 0.00 0.00 35.25 3.62
4631 9307 8.026607 CACAATTCGACCTTTGGTTTTATATGT 58.973 33.333 6.82 0.00 35.25 2.29
4633 9309 8.117813 ACACAATTCGACCTTTGGTTTTATAT 57.882 30.769 6.82 0.00 35.25 0.86
4643 9319 3.945285 ACACTTGACACAATTCGACCTTT 59.055 39.130 0.00 0.00 0.00 3.11
4650 9326 4.756642 TCCATCAGACACTTGACACAATTC 59.243 41.667 0.00 0.00 0.00 2.17
4698 10296 3.181478 GGTTAGGTAGGTCACTTCCATCG 60.181 52.174 0.00 0.00 36.68 3.84
4714 10312 6.472887 TCTGGTGTCAAATCTTAAGGTTAGG 58.527 40.000 0.30 0.00 0.00 2.69
4716 10314 6.374333 GCATCTGGTGTCAAATCTTAAGGTTA 59.626 38.462 0.30 0.00 0.00 2.85
4717 10315 5.183904 GCATCTGGTGTCAAATCTTAAGGTT 59.816 40.000 1.85 0.00 0.00 3.50
4718 10316 4.702131 GCATCTGGTGTCAAATCTTAAGGT 59.298 41.667 1.85 0.00 0.00 3.50
4719 10317 4.096984 GGCATCTGGTGTCAAATCTTAAGG 59.903 45.833 1.85 0.00 30.99 2.69
4720 10318 4.946157 AGGCATCTGGTGTCAAATCTTAAG 59.054 41.667 0.00 0.00 33.88 1.85
4721 10319 4.922206 AGGCATCTGGTGTCAAATCTTAA 58.078 39.130 0.00 0.00 33.88 1.85
4722 10320 4.574674 AGGCATCTGGTGTCAAATCTTA 57.425 40.909 0.00 0.00 33.88 2.10
4723 10321 3.446442 AGGCATCTGGTGTCAAATCTT 57.554 42.857 0.00 0.00 33.88 2.40
4724 10322 3.350833 GAAGGCATCTGGTGTCAAATCT 58.649 45.455 0.00 0.00 33.88 2.40
4725 10323 2.424956 GGAAGGCATCTGGTGTCAAATC 59.575 50.000 0.00 0.00 33.88 2.17
4726 10324 2.042162 AGGAAGGCATCTGGTGTCAAAT 59.958 45.455 0.00 0.00 33.88 2.32
4756 10354 3.113322 TCGAACGCAGAAAGAATATCCG 58.887 45.455 0.00 0.00 0.00 4.18
4777 10375 3.565307 TGACAAGGCACCAGAAGAATTT 58.435 40.909 0.00 0.00 0.00 1.82
4799 10397 3.264193 TGACCTGATGTTGCTGGAGTAAT 59.736 43.478 0.00 0.00 0.00 1.89
4802 10400 1.059098 TGACCTGATGTTGCTGGAGT 58.941 50.000 0.00 0.00 0.00 3.85
4803 10401 1.446907 GTGACCTGATGTTGCTGGAG 58.553 55.000 0.00 0.00 0.00 3.86
4804 10402 0.036732 GGTGACCTGATGTTGCTGGA 59.963 55.000 0.00 0.00 0.00 3.86
4805 10403 2.559785 GGTGACCTGATGTTGCTGG 58.440 57.895 0.00 0.00 0.00 4.85
4818 10416 3.202829 TGTTTGTTACTGGAGGGTGAC 57.797 47.619 0.00 0.00 0.00 3.67
4819 10417 3.935818 TTGTTTGTTACTGGAGGGTGA 57.064 42.857 0.00 0.00 0.00 4.02
4820 10418 4.795962 GCAATTGTTTGTTACTGGAGGGTG 60.796 45.833 7.40 0.00 35.17 4.61
4821 10419 3.320826 GCAATTGTTTGTTACTGGAGGGT 59.679 43.478 7.40 0.00 35.17 4.34
4822 10420 3.320541 TGCAATTGTTTGTTACTGGAGGG 59.679 43.478 7.40 0.00 35.17 4.30
4823 10421 4.582701 TGCAATTGTTTGTTACTGGAGG 57.417 40.909 7.40 0.00 35.17 4.30
4824 10422 5.809562 TGTTTGCAATTGTTTGTTACTGGAG 59.190 36.000 7.40 0.00 35.17 3.86
4825 10423 5.724328 TGTTTGCAATTGTTTGTTACTGGA 58.276 33.333 7.40 0.00 35.17 3.86
4826 10424 6.257411 TCATGTTTGCAATTGTTTGTTACTGG 59.743 34.615 7.40 0.00 35.17 4.00
4827 10425 7.231705 TCATGTTTGCAATTGTTTGTTACTG 57.768 32.000 7.40 0.00 35.17 2.74
4828 10426 7.495279 ACATCATGTTTGCAATTGTTTGTTACT 59.505 29.630 7.40 0.00 35.17 2.24
4829 10427 7.583401 CACATCATGTTTGCAATTGTTTGTTAC 59.417 33.333 7.40 0.00 35.17 2.50
4830 10428 7.254692 CCACATCATGTTTGCAATTGTTTGTTA 60.255 33.333 7.40 0.00 35.17 2.41
4831 10429 6.458478 CCACATCATGTTTGCAATTGTTTGTT 60.458 34.615 7.40 0.00 35.17 2.83
4832 10430 5.007823 CCACATCATGTTTGCAATTGTTTGT 59.992 36.000 7.40 5.31 35.17 2.83
4833 10431 5.007823 ACCACATCATGTTTGCAATTGTTTG 59.992 36.000 7.40 4.76 35.85 2.93
4834 10432 5.124645 ACCACATCATGTTTGCAATTGTTT 58.875 33.333 7.40 0.00 0.00 2.83
4869 10467 6.126796 TGTTGCTGGAGATATCAACTGGAATA 60.127 38.462 5.32 4.71 39.44 1.75
4871 10469 4.019411 TGTTGCTGGAGATATCAACTGGAA 60.019 41.667 5.32 6.04 39.44 3.53
4872 10470 3.519107 TGTTGCTGGAGATATCAACTGGA 59.481 43.478 5.32 0.00 39.44 3.86
4876 10474 4.514441 CCTGATGTTGCTGGAGATATCAAC 59.486 45.833 5.32 0.81 39.23 3.18


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

AutoCloner maintained by Alex Coulton.