Multiple sequence alignment - TraesCS3B01G251200

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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 TraesCS3B01G251200 chr3B 100.000 7981 0 0 1 7981 401810989 401803009 0.000000e+00 14739.0
1 TraesCS3B01G251200 chr3B 80.067 898 161 15 1333 2222 406649934 406650821 0.000000e+00 651.0
2 TraesCS3B01G251200 chr3B 85.425 247 26 7 5008 5247 45269348 45269591 1.720000e-61 248.0
3 TraesCS3B01G251200 chr3B 85.185 243 30 5 5012 5249 44856251 44856492 2.220000e-60 244.0
4 TraesCS3B01G251200 chr3A 97.307 3713 77 9 2807 6501 410112596 410108889 0.000000e+00 6281.0
5 TraesCS3B01G251200 chr3A 96.892 2188 51 9 633 2808 410114969 410112787 0.000000e+00 3648.0
6 TraesCS3B01G251200 chr3A 95.026 965 34 7 7022 7981 410108247 410107292 0.000000e+00 1504.0
7 TraesCS3B01G251200 chr3A 98.102 527 8 1 6500 7024 410108831 410108305 0.000000e+00 917.0
8 TraesCS3B01G251200 chr3A 80.132 906 146 24 1333 2222 419332826 419333713 0.000000e+00 645.0
9 TraesCS3B01G251200 chr3A 83.780 635 101 2 4 637 436432615 436431982 1.150000e-167 601.0
10 TraesCS3B01G251200 chr3D 94.238 2204 85 10 631 2808 317198435 317200622 0.000000e+00 3328.0
11 TraesCS3B01G251200 chr3D 93.491 1352 56 12 2809 4141 317200814 317202152 0.000000e+00 1980.0
12 TraesCS3B01G251200 chr3D 95.223 1256 38 10 5251 6501 317203597 317204835 0.000000e+00 1967.0
13 TraesCS3B01G251200 chr3D 97.322 859 21 1 4152 5010 317202542 317203398 0.000000e+00 1458.0
14 TraesCS3B01G251200 chr3D 96.038 530 16 2 6500 7024 317204889 317205418 0.000000e+00 857.0
15 TraesCS3B01G251200 chr3D 90.909 462 19 6 7243 7692 317205870 317206320 4.120000e-167 599.0
16 TraesCS3B01G251200 chr3D 87.903 248 23 6 5008 5249 26639810 26640056 1.310000e-72 285.0
17 TraesCS3B01G251200 chr3D 85.398 226 11 8 7024 7230 317205463 317205685 1.740000e-51 215.0
18 TraesCS3B01G251200 chr4D 81.655 2055 230 75 840 2807 96912136 96910142 0.000000e+00 1570.0
19 TraesCS3B01G251200 chr4D 89.942 855 81 4 4162 5012 96908425 96907572 0.000000e+00 1098.0
20 TraesCS3B01G251200 chr4D 79.359 998 137 30 5544 6501 96907228 96906260 8.730000e-179 638.0
21 TraesCS3B01G251200 chr4D 78.595 612 80 34 2810 3405 96909948 96909372 2.740000e-94 357.0
22 TraesCS3B01G251200 chr4A 84.052 1624 171 50 1255 2807 479412044 479413650 0.000000e+00 1483.0
23 TraesCS3B01G251200 chr4A 90.158 823 76 4 4194 5012 479416367 479417188 0.000000e+00 1066.0
24 TraesCS3B01G251200 chr4A 86.536 869 92 10 4155 5012 497815650 497814796 0.000000e+00 933.0
25 TraesCS3B01G251200 chr4A 79.379 999 135 32 5544 6501 479417532 479418500 8.730000e-179 638.0
26 TraesCS3B01G251200 chr4A 78.454 608 79 37 2810 3399 479413844 479414417 4.580000e-92 350.0
27 TraesCS3B01G251200 chr4A 77.670 618 79 39 2810 3405 497819798 497819218 9.990000e-84 322.0
28 TraesCS3B01G251200 chr4A 76.952 538 114 8 95 627 697811984 697812516 1.680000e-76 298.0
29 TraesCS3B01G251200 chr4A 81.792 346 46 7 6672 7000 497814396 497814051 2.840000e-69 274.0
30 TraesCS3B01G251200 chr4A 86.087 115 14 2 3286 3399 479415141 479415254 1.090000e-23 122.0
31 TraesCS3B01G251200 chr4A 84.404 109 17 0 7744 7852 690218473 690218365 3.050000e-19 108.0
32 TraesCS3B01G251200 chr4B 89.899 792 75 4 4225 5012 138302844 138302054 0.000000e+00 1014.0
33 TraesCS3B01G251200 chr4B 81.429 1120 127 45 840 1928 138306621 138305552 0.000000e+00 841.0
34 TraesCS3B01G251200 chr4B 81.951 892 101 29 1970 2805 138305553 138304666 0.000000e+00 701.0
35 TraesCS3B01G251200 chr4B 81.669 791 102 26 1069 1845 119858766 119859527 1.140000e-172 617.0
36 TraesCS3B01G251200 chr4B 85.824 522 59 10 1837 2348 119866772 119867288 2.530000e-149 540.0
37 TraesCS3B01G251200 chr4B 82.003 639 84 20 5873 6501 138301117 138300500 1.540000e-141 514.0
38 TraesCS3B01G251200 chr4B 78.103 580 82 33 2844 3405 138304446 138303894 7.720000e-85 326.0
39 TraesCS3B01G251200 chr6B 92.516 628 47 0 3 630 52377376 52378003 0.000000e+00 900.0
40 TraesCS3B01G251200 chr6B 76.263 594 133 6 37 626 118083983 118084572 7.780000e-80 309.0
41 TraesCS3B01G251200 chr6B 84.328 268 11 13 5010 5256 147680294 147680037 4.820000e-57 233.0
42 TraesCS3B01G251200 chr6B 84.404 109 17 0 7744 7852 659568084 659567976 3.050000e-19 108.0
43 TraesCS3B01G251200 chr7B 85.069 864 116 11 4156 5012 665542936 665542079 0.000000e+00 869.0
44 TraesCS3B01G251200 chr7B 83.333 66 9 1 5651 5716 23255548 23255611 8.650000e-05 60.2
45 TraesCS3B01G251200 chr5B 83.282 969 128 23 4066 5012 93459236 93460192 0.000000e+00 861.0
46 TraesCS3B01G251200 chr2B 90.047 633 62 1 1 632 768594044 768593412 0.000000e+00 819.0
47 TraesCS3B01G251200 chr2B 76.723 537 113 10 98 628 458092345 458091815 1.010000e-73 289.0
48 TraesCS3B01G251200 chr2B 88.000 250 20 8 5010 5252 653963248 653963002 3.640000e-73 287.0
49 TraesCS3B01G251200 chr5A 83.044 519 75 9 4164 4672 684629502 684628987 7.300000e-125 459.0
50 TraesCS3B01G251200 chr5A 80.070 286 32 17 4986 5252 477725799 477725520 1.060000e-43 189.0
51 TraesCS3B01G251200 chr5A 81.538 130 23 1 7723 7852 693495241 693495113 1.100000e-18 106.0
52 TraesCS3B01G251200 chr5D 85.075 268 16 7 5008 5252 538708183 538708449 1.330000e-62 252.0
53 TraesCS3B01G251200 chrUn 85.425 247 26 7 5008 5247 345547250 345547493 1.720000e-61 248.0
54 TraesCS3B01G251200 chrUn 85.425 247 26 7 5008 5247 362558895 362559138 1.720000e-61 248.0
55 TraesCS3B01G251200 chrUn 84.615 247 32 5 5008 5249 38772130 38771885 2.880000e-59 241.0
56 TraesCS3B01G251200 chr1A 73.201 653 109 34 5544 6155 23454124 23453497 8.230000e-40 176.0
57 TraesCS3B01G251200 chr2D 87.143 140 17 1 4156 4295 427946828 427946966 2.980000e-34 158.0
58 TraesCS3B01G251200 chr7D 80.000 205 35 5 5621 5823 590656940 590656740 6.450000e-31 147.0
59 TraesCS3B01G251200 chr6A 86.667 75 10 0 7778 7852 51608010 51607936 5.130000e-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 TraesCS3B01G251200 chr3B 401803009 401810989 7980 True 14739.000000 14739 100.000000 1 7981 1 chr3B.!!$R1 7980
1 TraesCS3B01G251200 chr3B 406649934 406650821 887 False 651.000000 651 80.067000 1333 2222 1 chr3B.!!$F3 889
2 TraesCS3B01G251200 chr3A 410107292 410114969 7677 True 3087.500000 6281 96.831750 633 7981 4 chr3A.!!$R2 7348
3 TraesCS3B01G251200 chr3A 419332826 419333713 887 False 645.000000 645 80.132000 1333 2222 1 chr3A.!!$F1 889
4 TraesCS3B01G251200 chr3A 436431982 436432615 633 True 601.000000 601 83.780000 4 637 1 chr3A.!!$R1 633
5 TraesCS3B01G251200 chr3D 317198435 317206320 7885 False 1486.285714 3328 93.231286 631 7692 7 chr3D.!!$F2 7061
6 TraesCS3B01G251200 chr4D 96906260 96912136 5876 True 915.750000 1570 82.387750 840 6501 4 chr4D.!!$R1 5661
7 TraesCS3B01G251200 chr4A 479412044 479418500 6456 False 731.800000 1483 83.626000 1255 6501 5 chr4A.!!$F2 5246
8 TraesCS3B01G251200 chr4A 497814051 497819798 5747 True 509.666667 933 81.999333 2810 7000 3 chr4A.!!$R2 4190
9 TraesCS3B01G251200 chr4A 697811984 697812516 532 False 298.000000 298 76.952000 95 627 1 chr4A.!!$F1 532
10 TraesCS3B01G251200 chr4B 138300500 138306621 6121 True 679.200000 1014 82.677000 840 6501 5 chr4B.!!$R1 5661
11 TraesCS3B01G251200 chr4B 119858766 119859527 761 False 617.000000 617 81.669000 1069 1845 1 chr4B.!!$F1 776
12 TraesCS3B01G251200 chr4B 119866772 119867288 516 False 540.000000 540 85.824000 1837 2348 1 chr4B.!!$F2 511
13 TraesCS3B01G251200 chr6B 52377376 52378003 627 False 900.000000 900 92.516000 3 630 1 chr6B.!!$F1 627
14 TraesCS3B01G251200 chr6B 118083983 118084572 589 False 309.000000 309 76.263000 37 626 1 chr6B.!!$F2 589
15 TraesCS3B01G251200 chr7B 665542079 665542936 857 True 869.000000 869 85.069000 4156 5012 1 chr7B.!!$R1 856
16 TraesCS3B01G251200 chr5B 93459236 93460192 956 False 861.000000 861 83.282000 4066 5012 1 chr5B.!!$F1 946
17 TraesCS3B01G251200 chr2B 768593412 768594044 632 True 819.000000 819 90.047000 1 632 1 chr2B.!!$R3 631
18 TraesCS3B01G251200 chr2B 458091815 458092345 530 True 289.000000 289 76.723000 98 628 1 chr2B.!!$R1 530
19 TraesCS3B01G251200 chr5A 684628987 684629502 515 True 459.000000 459 83.044000 4164 4672 1 chr5A.!!$R2 508

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
200 201 0.976073 TGGCTAGGGACGAAGAAGGG 60.976 60.000 0.00 0.00 0.00 3.95 F
901 918 1.236708 CCCTCCTCCTCCCTCTTCTA 58.763 60.000 0.00 0.00 0.00 2.10 F
1043 1063 1.298667 GGTACGTCATGCCCAACCT 59.701 57.895 0.00 0.00 0.00 3.50 F
1051 1071 1.988107 TCATGCCCAACCTCTCTTTCT 59.012 47.619 0.00 0.00 0.00 2.52 F
1325 1361 2.113986 GGCTCAAGGCTGTGGTGT 59.886 61.111 0.00 0.00 41.46 4.16 F
2640 2768 2.430465 CCAGTTCTCCACCATCAAGTG 58.570 52.381 0.00 0.00 37.51 3.16 F
4143 7909 1.669265 GGTACAAAATGTAGGCGCCTC 59.331 52.381 36.73 24.38 32.84 4.70 F
4656 8818 1.002430 TGCAAGATGCTCGGAAGAAGT 59.998 47.619 3.78 0.00 45.31 3.01 F
5256 9425 1.063492 TGGAACGGAGGGAGTAGCATA 60.063 52.381 0.00 0.00 0.00 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1071 5.747197 GGTTTCGCGAAATAGAGAAGATACA 59.253 40.000 34.19 6.78 31.96 2.29 R
2848 3177 3.457380 ACAAGACATGGATGCTATCAGGT 59.543 43.478 0.00 0.00 0.00 4.00 R
2950 3285 1.600636 ATGTATGGATTGGCGGCCG 60.601 57.895 24.05 24.05 0.00 6.13 R
3128 3480 9.403110 GATGGCTTTGTAGATTAATTTATGCAG 57.597 33.333 0.00 0.00 0.00 4.41 R
3148 3500 5.895534 ACACAGATTATTTTGATGGATGGCT 59.104 36.000 0.00 0.00 0.00 4.75 R
4175 8320 4.720046 TGTATAAACCACAACAGCCTGAA 58.280 39.130 0.00 0.00 0.00 3.02 R
5236 9405 0.325296 ATGCTACTCCCTCCGTTCCA 60.325 55.000 0.00 0.00 0.00 3.53 R
6734 11314 0.726827 CCTAACGTCAATGCACGCAT 59.273 50.000 0.00 0.00 43.93 4.73 R
7024 11619 0.692476 TGTCAATGCTACACCAGGCT 59.308 50.000 0.00 0.00 0.00 4.58 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
29 30 4.415150 TCCGAGGTAGTCCGGCGT 62.415 66.667 6.01 0.00 44.96 5.68
113 114 2.616458 ATGGGTCCCTCCTGCCAAC 61.616 63.158 10.00 0.00 36.25 3.77
139 140 7.308049 CGACGAGATTAAGATCAACCTAGATGA 60.308 40.741 0.00 0.00 34.60 2.92
176 177 1.309013 AAGCATGGGAGGATGGGGA 60.309 57.895 0.00 0.00 0.00 4.81
200 201 0.976073 TGGCTAGGGACGAAGAAGGG 60.976 60.000 0.00 0.00 0.00 3.95
270 271 4.598894 CGGCTGAGATCGGGGCAG 62.599 72.222 8.55 6.43 0.00 4.85
364 365 1.508088 CCGAGGCTTTGGACATTGC 59.492 57.895 0.00 0.00 0.00 3.56
377 378 1.529438 GACATTGCGAAAACGGACTCA 59.471 47.619 0.00 0.00 0.00 3.41
411 412 3.019564 GCAGCCATTGAGGACATTAAGT 58.980 45.455 0.00 0.00 41.22 2.24
423 424 8.918202 TGAGGACATTAAGTTACAACTCAAAT 57.082 30.769 0.00 0.00 38.57 2.32
440 441 5.357032 ACTCAAATTGTGGTTCTCGAAGTTT 59.643 36.000 0.05 0.00 0.00 2.66
443 444 5.684550 AATTGTGGTTCTCGAAGTTTACC 57.315 39.130 0.00 0.00 0.00 2.85
461 462 2.974698 ATTAGAGCATGCCGGCGC 60.975 61.111 23.90 20.42 39.27 6.53
485 486 3.693085 AGGCAAATTCTGTAGCACATGAG 59.307 43.478 0.00 0.00 0.00 2.90
488 489 4.730035 GCAAATTCTGTAGCACATGAGCTC 60.730 45.833 21.36 6.82 45.26 4.09
521 522 4.421058 GTCGTATGTGCTTGTCAGACATA 58.579 43.478 3.45 0.00 32.59 2.29
528 529 5.976458 TGTGCTTGTCAGACATATGTATGA 58.024 37.500 25.41 25.41 43.12 2.15
553 554 1.985460 AACACCACTGTACCGCCCAA 61.985 55.000 0.00 0.00 0.00 4.12
688 689 2.501610 GGAGCAGAACGCCTAGGG 59.498 66.667 11.72 3.13 44.04 3.53
881 897 1.519455 GCTTCCTCATCCGTGGACG 60.519 63.158 0.00 0.00 34.53 4.79
883 899 2.907897 CTTCCTCATCCGTGGACGCC 62.908 65.000 0.00 0.00 34.53 5.68
895 912 4.467107 GACGCCCTCCTCCTCCCT 62.467 72.222 0.00 0.00 0.00 4.20
901 918 1.236708 CCCTCCTCCTCCCTCTTCTA 58.763 60.000 0.00 0.00 0.00 2.10
1043 1063 1.298667 GGTACGTCATGCCCAACCT 59.701 57.895 0.00 0.00 0.00 3.50
1051 1071 1.988107 TCATGCCCAACCTCTCTTTCT 59.012 47.619 0.00 0.00 0.00 2.52
1325 1361 2.113986 GGCTCAAGGCTGTGGTGT 59.886 61.111 0.00 0.00 41.46 4.16
2241 2316 3.096092 GTGCCCAATGTCTCCCATAAAA 58.904 45.455 0.00 0.00 31.97 1.52
2391 2492 7.890655 AGCATTATATTGGTATTTTCCTCTCCC 59.109 37.037 0.00 0.00 0.00 4.30
2392 2493 7.890655 GCATTATATTGGTATTTTCCTCTCCCT 59.109 37.037 0.00 0.00 0.00 4.20
2640 2768 2.430465 CCAGTTCTCCACCATCAAGTG 58.570 52.381 0.00 0.00 37.51 3.16
2847 3176 5.407407 ACATCGATCTACCAGTTGTTCTT 57.593 39.130 0.00 0.00 0.00 2.52
2848 3177 6.525578 ACATCGATCTACCAGTTGTTCTTA 57.474 37.500 0.00 0.00 0.00 2.10
2849 3178 6.331061 ACATCGATCTACCAGTTGTTCTTAC 58.669 40.000 0.00 0.00 0.00 2.34
2850 3179 5.320549 TCGATCTACCAGTTGTTCTTACC 57.679 43.478 0.00 0.00 0.00 2.85
2851 3180 5.014858 TCGATCTACCAGTTGTTCTTACCT 58.985 41.667 0.00 0.00 0.00 3.08
2950 3285 9.387123 CTGTCTTTTTATCTGCTGTAAACTTTC 57.613 33.333 0.00 0.00 0.00 2.62
3467 4613 3.483196 CGCTTTCTTGTGTTTGATGTGTG 59.517 43.478 0.00 0.00 0.00 3.82
3559 4708 6.598457 TCTGCTCAAAGTTCTACGAGTAGTAT 59.402 38.462 9.75 0.00 38.76 2.12
3652 4808 2.418368 ACGGGCTCTGATTATTTGCA 57.582 45.000 0.00 0.00 0.00 4.08
3854 5011 4.043435 AGCTGGAATTGGTCTAAGGTTTCT 59.957 41.667 0.00 0.00 0.00 2.52
3856 5013 5.243954 GCTGGAATTGGTCTAAGGTTTCTTT 59.756 40.000 0.00 0.00 34.59 2.52
3857 5014 6.433093 GCTGGAATTGGTCTAAGGTTTCTTTA 59.567 38.462 0.00 0.00 34.59 1.85
3910 5078 9.848710 AGTTGATGTTGATGAATCTCTATCAAT 57.151 29.630 14.04 0.00 43.03 2.57
4143 7909 1.669265 GGTACAAAATGTAGGCGCCTC 59.331 52.381 36.73 24.38 32.84 4.70
4175 8320 6.029346 CAGGTTTCCTGCATAAAACTCATT 57.971 37.500 18.22 5.30 45.13 2.57
4554 8716 1.795768 TGAACTTAGTGCCGAGCTTG 58.204 50.000 0.00 0.00 0.00 4.01
4656 8818 1.002430 TGCAAGATGCTCGGAAGAAGT 59.998 47.619 3.78 0.00 45.31 3.01
4702 8864 7.801716 TTAATTGAGTACTTGCACTTGTCTT 57.198 32.000 0.00 0.00 0.00 3.01
4999 9168 4.580167 TCACTCTTGCTTTTATGCACTTGT 59.420 37.500 0.00 0.00 43.20 3.16
5218 9387 1.686355 TGTTTGACTTGCACGGGAAT 58.314 45.000 0.00 0.00 0.00 3.01
5236 9405 7.878127 CACGGGAATCAATACACCTTATATTCT 59.122 37.037 0.00 0.00 0.00 2.40
5256 9425 1.063492 TGGAACGGAGGGAGTAGCATA 60.063 52.381 0.00 0.00 0.00 3.14
5526 9718 5.810587 GCATTGTGGACTTATCGAGTTAAGA 59.189 40.000 11.77 0.00 39.19 2.10
5576 9805 7.762615 AGTTGCATTAACAATTCAGATCCATTG 59.237 33.333 7.88 7.88 41.88 2.82
5617 9847 3.104519 TCCTTGGTCCTCCATTACGTA 57.895 47.619 0.00 0.00 43.91 3.57
5776 10014 3.181479 GGATGTAAGCTACCACATGACGA 60.181 47.826 11.93 0.00 35.55 4.20
6042 10544 7.006865 AGCTGCTCTTGATTGAGATGTATAT 57.993 36.000 0.00 0.00 36.23 0.86
6136 10638 6.552445 AAAGCTGATGGTGAGTTCTATACT 57.448 37.500 0.00 0.00 40.71 2.12
6163 10667 8.947115 AGTTAAGTTATGTAATTCACCAGCTTC 58.053 33.333 0.00 0.00 0.00 3.86
6994 11586 1.273606 GCGCTGAGCCCAGATATCTAA 59.726 52.381 4.54 0.00 43.02 2.10
7024 11619 4.054780 AGTGAACTAGAAGTGCGTTTCA 57.945 40.909 0.00 0.00 0.00 2.69
7026 11621 2.800544 TGAACTAGAAGTGCGTTTCAGC 59.199 45.455 0.00 0.00 37.71 4.26
7027 11622 1.797025 ACTAGAAGTGCGTTTCAGCC 58.203 50.000 0.00 0.00 36.02 4.85
7071 11726 6.299805 TGCTAGTACTTGGAGATTGTGAAT 57.700 37.500 0.00 0.00 0.00 2.57
7080 11735 3.682372 GAGATTGTGAATCGCCCTTTC 57.318 47.619 0.00 0.00 42.75 2.62
7091 11746 4.713792 ATCGCCCTTTCAGGATAATCTT 57.286 40.909 0.00 0.00 37.67 2.40
7171 11844 0.694771 ATGTGATGCCTGGTGACTGT 59.305 50.000 0.00 0.00 0.00 3.55
7188 11861 0.534877 TGTTTGGTGCTCGACATGCT 60.535 50.000 0.00 0.00 0.00 3.79
7263 12108 8.202137 TGTACTAGTTATAGCAGGAAAACCATC 58.798 37.037 0.00 0.00 31.66 3.51
7418 12274 0.804989 CCCGGCTGTCACAATTCTTC 59.195 55.000 0.00 0.00 0.00 2.87
7478 12344 5.432390 TGTACAGGAGGAAGGAGACTATACT 59.568 44.000 0.00 0.00 42.68 2.12
7479 12345 6.618610 TGTACAGGAGGAAGGAGACTATACTA 59.381 42.308 0.00 0.00 42.68 1.82
7480 12346 5.944135 ACAGGAGGAAGGAGACTATACTAC 58.056 45.833 0.00 0.00 42.68 2.73
7481 12347 5.673113 ACAGGAGGAAGGAGACTATACTACT 59.327 44.000 0.00 0.00 42.68 2.57
7482 12348 6.183361 ACAGGAGGAAGGAGACTATACTACTC 60.183 46.154 0.00 0.00 42.68 2.59
7483 12349 6.043938 CAGGAGGAAGGAGACTATACTACTCT 59.956 46.154 0.00 0.00 42.68 3.24
7484 12350 6.043938 AGGAGGAAGGAGACTATACTACTCTG 59.956 46.154 0.00 0.00 42.68 3.35
7485 12351 5.627135 AGGAAGGAGACTATACTACTCTGC 58.373 45.833 0.00 0.00 42.68 4.26
7486 12352 4.453136 GGAAGGAGACTATACTACTCTGCG 59.547 50.000 0.00 0.00 42.68 5.18
7487 12353 3.404899 AGGAGACTATACTACTCTGCGC 58.595 50.000 0.00 0.00 40.61 6.09
7505 12371 0.809241 GCAGCTCAGCTCAGCGTAAT 60.809 55.000 3.13 0.00 44.82 1.89
7525 12391 5.435686 AATAGTGTTCACCTGCCAAGATA 57.564 39.130 0.00 0.00 0.00 1.98
7587 12454 1.649321 TGCATCTCTCACTTCACCCT 58.351 50.000 0.00 0.00 0.00 4.34
7676 12543 3.138884 TGCAAATAGCTCTTGGTCACA 57.861 42.857 9.77 0.00 45.94 3.58
7734 12601 7.548780 CCCAATGATAACACCCTACAAAAATTG 59.451 37.037 0.00 0.00 0.00 2.32
7760 12627 7.780008 ATTGTCAATGGATTAAATACGACGA 57.220 32.000 0.00 0.00 0.00 4.20
7761 12628 6.822073 TGTCAATGGATTAAATACGACGAG 57.178 37.500 0.00 0.00 0.00 4.18
7781 12648 5.750547 ACGAGACGTCTATACAGTTCGATTA 59.249 40.000 20.09 0.00 33.69 1.75
7897 12764 0.984109 GGATGCACGCAAATGAAACG 59.016 50.000 0.00 0.00 0.00 3.60
7905 12772 4.222886 CACGCAAATGAAACGTTCCATAA 58.777 39.130 0.00 0.00 38.09 1.90
7919 12786 5.708230 ACGTTCCATAAGCTTATTGAAACCA 59.292 36.000 26.16 9.26 29.86 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 3.017581 GGCAGGAGGGACCCATGT 61.018 66.667 14.60 0.00 40.05 3.21
113 114 6.301687 TCTAGGTTGATCTTAATCTCGTCG 57.698 41.667 0.00 0.00 32.75 5.12
176 177 1.229082 TTCGTCCCTAGCCACCACT 60.229 57.895 0.00 0.00 0.00 4.00
200 201 2.105006 ATCGGGCTATGATCACATGC 57.895 50.000 0.00 2.49 37.87 4.06
257 258 1.305297 ACTCACTGCCCCGATCTCA 60.305 57.895 0.00 0.00 0.00 3.27
270 271 3.181967 CGCTACTGCCGCACTCAC 61.182 66.667 0.00 0.00 35.36 3.51
320 321 3.803555 CAGCATTGAGTCTGTTTCGAAC 58.196 45.455 0.00 0.00 0.00 3.95
364 365 0.713883 CGGTGATGAGTCCGTTTTCG 59.286 55.000 0.00 0.00 41.58 3.46
377 378 2.509336 GCTGCAGCGTACGGTGAT 60.509 61.111 42.02 0.85 45.42 3.06
386 387 2.437180 TCCTCAATGGCTGCAGCG 60.437 61.111 31.19 18.10 43.26 5.18
411 412 5.818336 TCGAGAACCACAATTTGAGTTGTAA 59.182 36.000 2.79 0.00 40.17 2.41
423 424 4.139859 TGGTAAACTTCGAGAACCACAA 57.860 40.909 3.26 0.00 35.34 3.33
440 441 0.250295 GCCGGCATGCTCTAATGGTA 60.250 55.000 24.80 0.00 0.00 3.25
443 444 2.941333 CGCCGGCATGCTCTAATG 59.059 61.111 28.98 0.98 0.00 1.90
461 462 2.076100 TGTGCTACAGAATTTGCCTCG 58.924 47.619 0.00 0.00 0.00 4.63
553 554 1.881973 CTAACACACAAGCAGCCACAT 59.118 47.619 0.00 0.00 0.00 3.21
688 689 4.115199 ATTGAGCAGGCCGGACCC 62.115 66.667 1.76 0.00 40.58 4.46
731 732 1.330655 ACGTGATGGAGGAGGCGAAT 61.331 55.000 0.00 0.00 0.00 3.34
881 897 1.764454 GAAGAGGGAGGAGGAGGGC 60.764 68.421 0.00 0.00 0.00 5.19
883 899 2.554344 CGATAGAAGAGGGAGGAGGAGG 60.554 59.091 0.00 0.00 39.76 4.30
901 918 1.866015 TCAGTCCAATGTCCCTCGAT 58.134 50.000 0.00 0.00 0.00 3.59
1043 1063 8.132362 GCGAAATAGAGAAGATACAGAAAGAGA 58.868 37.037 0.00 0.00 0.00 3.10
1051 1071 5.747197 GGTTTCGCGAAATAGAGAAGATACA 59.253 40.000 34.19 6.78 31.96 2.29
2391 2492 6.201806 GGATCGTTCATTCACAAATAGGAGAG 59.798 42.308 0.00 0.00 0.00 3.20
2392 2493 6.049149 GGATCGTTCATTCACAAATAGGAGA 58.951 40.000 0.00 0.00 0.00 3.71
2640 2768 5.959618 ACTAGCAACCCACATTTAAAGTC 57.040 39.130 0.00 0.00 0.00 3.01
2847 3176 4.655649 ACAAGACATGGATGCTATCAGGTA 59.344 41.667 0.00 0.00 0.00 3.08
2848 3177 3.457380 ACAAGACATGGATGCTATCAGGT 59.543 43.478 0.00 0.00 0.00 4.00
2849 3178 4.082665 ACAAGACATGGATGCTATCAGG 57.917 45.455 0.00 0.00 0.00 3.86
2850 3179 6.723131 CATACAAGACATGGATGCTATCAG 57.277 41.667 0.00 0.00 43.33 2.90
2950 3285 1.600636 ATGTATGGATTGGCGGCCG 60.601 57.895 24.05 24.05 0.00 6.13
3128 3480 9.403110 GATGGCTTTGTAGATTAATTTATGCAG 57.597 33.333 0.00 0.00 0.00 4.41
3148 3500 5.895534 ACACAGATTATTTTGATGGATGGCT 59.104 36.000 0.00 0.00 0.00 4.75
3467 4613 7.671495 AAATAAAACCATGCATCTCAAAACC 57.329 32.000 0.00 0.00 0.00 3.27
3559 4708 5.554437 TGTACCACACATCAACTTTAGGA 57.446 39.130 0.00 0.00 30.04 2.94
3687 4843 5.547631 AGGAATCCGGATAGGGATAAGTA 57.452 43.478 19.48 0.00 46.08 2.24
4175 8320 4.720046 TGTATAAACCACAACAGCCTGAA 58.280 39.130 0.00 0.00 0.00 3.02
4448 8610 8.593945 TTCCCTGCATCTGTTTTATTTCTAAT 57.406 30.769 0.00 0.00 0.00 1.73
4554 8716 6.293845 GCATCCATTTCATCATACTTGTCCTC 60.294 42.308 0.00 0.00 0.00 3.71
4702 8864 7.541783 GCTCTGCAATGTAATTCAAACATAACA 59.458 33.333 0.00 0.00 36.56 2.41
4999 9168 4.607239 ACGGAGGGAGTATTAGAGAACAA 58.393 43.478 0.00 0.00 0.00 2.83
5054 9223 2.038387 AAACAGGCACTCGTTTGACT 57.962 45.000 0.00 0.00 37.92 3.41
5135 9304 9.331282 ACATCTGCAATACCTAATAGAGAAAAC 57.669 33.333 0.00 0.00 0.00 2.43
5140 9309 8.668510 AACAACATCTGCAATACCTAATAGAG 57.331 34.615 0.00 0.00 0.00 2.43
5218 9387 7.070198 TCCGTTCCAGAATATAAGGTGTATTGA 59.930 37.037 0.00 0.00 0.00 2.57
5236 9405 0.325296 ATGCTACTCCCTCCGTTCCA 60.325 55.000 0.00 0.00 0.00 3.53
5256 9425 7.039504 ACTGTGAAATTGATTGCTCAAGGTTAT 60.040 33.333 0.00 0.00 44.32 1.89
5526 9718 9.520515 ACTAATGTTTGTCAGATTATTTGGAGT 57.479 29.630 0.00 0.00 0.00 3.85
5560 9789 5.776716 AGGAAACACAATGGATCTGAATTGT 59.223 36.000 12.98 12.98 45.54 2.71
5576 9805 4.636206 GGATGTAACAGATGGAGGAAACAC 59.364 45.833 0.00 0.00 0.00 3.32
5617 9847 3.496337 GGTTTCCTCCTCTCCTTTTTCGT 60.496 47.826 0.00 0.00 0.00 3.85
5798 10036 2.224744 TGGCACAGCTTAATTGACTGGA 60.225 45.455 8.48 0.00 35.70 3.86
6136 10638 9.953565 AAGCTGGTGAATTACATAACTTAACTA 57.046 29.630 0.00 0.00 0.00 2.24
6163 10667 7.969536 AGATGTATTATGTTCTGATTTCCGG 57.030 36.000 0.00 0.00 0.00 5.14
6198 10702 1.057275 TGCCCCACACACTACTCCAA 61.057 55.000 0.00 0.00 0.00 3.53
6657 11230 3.730715 GCTTCAAAATTTCACACTCCACG 59.269 43.478 0.00 0.00 0.00 4.94
6734 11314 0.726827 CCTAACGTCAATGCACGCAT 59.273 50.000 0.00 0.00 43.93 4.73
6994 11586 6.166982 GCACTTCTAGTTCACTACAGGAATT 58.833 40.000 0.00 0.00 0.00 2.17
7024 11619 0.692476 TGTCAATGCTACACCAGGCT 59.308 50.000 0.00 0.00 0.00 4.58
7026 11621 2.989909 TCATGTCAATGCTACACCAGG 58.010 47.619 0.00 0.00 33.47 4.45
7027 11622 4.916870 CATTCATGTCAATGCTACACCAG 58.083 43.478 0.00 0.00 33.47 4.00
7080 11735 4.963276 TGGCACGAAAAAGATTATCCTG 57.037 40.909 0.00 0.00 0.00 3.86
7091 11746 1.068610 GCACATAGCTTGGCACGAAAA 60.069 47.619 0.00 0.00 41.15 2.29
7171 11844 2.177394 TAAGCATGTCGAGCACCAAA 57.823 45.000 0.00 0.00 0.00 3.28
7263 12108 5.097529 ACAAGATAAAATCATGTGCTTGCG 58.902 37.500 0.00 0.00 39.48 4.85
7294 12142 7.676683 ATCCTAGAAATAAGTACAAGCCTGA 57.323 36.000 0.00 0.00 0.00 3.86
7343 12191 4.080356 TGAACCAGGAGTGATTATTCCAGG 60.080 45.833 8.60 8.60 42.75 4.45
7418 12274 5.583457 GGATTTTGGATGCATTCTTTTCCAG 59.417 40.000 6.53 0.00 39.33 3.86
7478 12344 2.182791 GCTGAGCTGCGCAGAGTA 59.817 61.111 40.21 22.37 33.20 2.59
7479 12345 3.646023 GAGCTGAGCTGCGCAGAGT 62.646 63.158 40.21 26.04 39.88 3.24
7480 12346 2.886604 GAGCTGAGCTGCGCAGAG 60.887 66.667 40.21 28.07 39.88 3.35
7481 12347 3.688159 TGAGCTGAGCTGCGCAGA 61.688 61.111 40.21 19.26 39.88 4.26
7486 12352 0.809241 ATTACGCTGAGCTGAGCTGC 60.809 55.000 23.02 9.51 39.88 5.25
7487 12353 2.223688 ACTATTACGCTGAGCTGAGCTG 60.224 50.000 23.02 17.69 39.88 4.24
7505 12371 4.901197 TTATCTTGGCAGGTGAACACTA 57.099 40.909 4.96 0.00 0.00 2.74
7525 12391 0.689055 GAGACGGGGTAGGGTTGTTT 59.311 55.000 0.00 0.00 0.00 2.83
7587 12454 4.869861 GCTGCAGGAAAGAAAGAAACAAAA 59.130 37.500 17.12 0.00 0.00 2.44
7700 12567 6.078664 AGGGTGTTATCATTGGGTAAAACAA 58.921 36.000 0.00 0.00 0.00 2.83
7701 12568 5.646215 AGGGTGTTATCATTGGGTAAAACA 58.354 37.500 0.00 0.00 0.00 2.83
7734 12601 8.332464 TCGTCGTATTTAATCCATTGACAATTC 58.668 33.333 0.00 0.00 0.00 2.17
7897 12764 7.391148 TCTGGTTTCAATAAGCTTATGGAAC 57.609 36.000 28.52 24.01 33.85 3.62
7905 12772 7.071698 TGGATAGAGATCTGGTTTCAATAAGCT 59.928 37.037 0.00 0.00 32.15 3.74
7919 12786 6.566079 TGTTGTTTCCATGGATAGAGATCT 57.434 37.500 17.06 0.00 32.15 2.75
7950 12817 8.012241 GCAAAATATGTTGTTATTCCGCAAAAA 58.988 29.630 7.46 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.