Multiple sequence alignment - TraesCS5D01G246400

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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 TraesCS5D01G246400 chr5D 100.000 4789 0 0 1 4789 354505227 354500439 0.000000e+00 8844.0
1 TraesCS5D01G246400 chr5D 100.000 254 0 0 4964 5217 354500264 354500011 2.200000e-128 470.0
2 TraesCS5D01G246400 chr5A 94.444 1908 90 13 2877 4772 455465250 455463347 0.000000e+00 2922.0
3 TraesCS5D01G246400 chr5A 96.025 1585 47 6 1 1571 455468387 455466805 0.000000e+00 2564.0
4 TraesCS5D01G246400 chr5A 96.016 1029 16 5 1567 2588 455466763 455465753 0.000000e+00 1650.0
5 TraesCS5D01G246400 chr5A 98.354 243 4 0 2609 2851 455465490 455465248 1.340000e-115 427.0
6 TraesCS5D01G246400 chr5B 98.318 1605 20 2 1567 3171 418814225 418812628 0.000000e+00 2808.0
7 TraesCS5D01G246400 chr5B 97.403 1579 32 2 1 1571 418815844 418814267 0.000000e+00 2680.0
8 TraesCS5D01G246400 chr5B 93.379 876 35 10 3524 4395 418812149 418811293 0.000000e+00 1275.0
9 TraesCS5D01G246400 chr5B 98.722 313 3 1 3225 3537 418812630 418812319 5.900000e-154 555.0
10 TraesCS5D01G246400 chr5B 95.238 84 4 0 4396 4479 418811259 418811176 3.280000e-27 134.0
11 TraesCS5D01G246400 chr5B 82.558 86 13 2 4457 4542 563917192 563917275 2.010000e-09 75.0
12 TraesCS5D01G246400 chr6A 88.973 1061 78 12 2122 3170 42924611 42925644 0.000000e+00 1275.0
13 TraesCS5D01G246400 chr6A 86.445 723 48 26 3373 4083 42925852 42926536 0.000000e+00 747.0
14 TraesCS5D01G246400 chr6A 87.263 581 45 8 1567 2120 42923293 42923871 2.050000e-178 636.0
15 TraesCS5D01G246400 chr6A 83.788 586 64 15 993 1571 42922690 42923251 1.290000e-145 527.0
16 TraesCS5D01G246400 chr6A 88.169 355 24 8 4007 4347 42926536 42926886 1.750000e-109 407.0
17 TraesCS5D01G246400 chr6B 88.889 1062 75 17 2125 3170 76858810 76859844 0.000000e+00 1267.0
18 TraesCS5D01G246400 chr6B 88.088 999 85 17 3373 4347 76860062 76861050 0.000000e+00 1155.0
19 TraesCS5D01G246400 chr6B 86.348 586 46 10 1567 2120 76857189 76857772 4.470000e-170 608.0
20 TraesCS5D01G246400 chr6B 86.905 84 11 0 3177 3260 664257850 664257767 1.550000e-15 95.3
21 TraesCS5D01G246400 chr6B 77.358 159 28 7 4555 4708 126634300 126634455 2.590000e-13 87.9
22 TraesCS5D01G246400 chr6B 87.671 73 5 2 3907 3975 645555966 645556038 1.200000e-11 82.4
23 TraesCS5D01G246400 chrUn 88.542 1056 74 20 2131 3170 104868374 104867350 0.000000e+00 1236.0
24 TraesCS5D01G246400 chrUn 89.211 1001 72 16 3373 4347 104867145 104866155 0.000000e+00 1218.0
25 TraesCS5D01G246400 chrUn 88.075 587 35 12 1567 2120 104869910 104869326 0.000000e+00 664.0
26 TraesCS5D01G246400 chrUn 76.538 260 49 9 4456 4709 436992336 436992589 1.180000e-26 132.0
27 TraesCS5D01G246400 chrUn 76.613 248 46 9 4468 4709 295799026 295798785 5.480000e-25 126.0
28 TraesCS5D01G246400 chr7D 85.856 403 46 8 56 455 11676438 11676044 8.080000e-113 418.0
29 TraesCS5D01G246400 chr7A 84.091 264 38 1 50 309 11104831 11104568 8.670000e-63 252.0
30 TraesCS5D01G246400 chr7A 90.667 75 6 1 3169 3243 651087959 651088032 1.200000e-16 99.0
31 TraesCS5D01G246400 chr2D 77.308 260 47 9 4456 4709 30234009 30234262 5.450000e-30 143.0
32 TraesCS5D01G246400 chr2D 76.538 260 49 9 4456 4709 30162000 30162253 1.180000e-26 132.0
33 TraesCS5D01G246400 chr2D 75.385 260 52 9 4456 4709 30100774 30101027 1.190000e-21 115.0
34 TraesCS5D01G246400 chr2D 88.043 92 11 0 3169 3260 595166398 595166489 5.520000e-20 110.0
35 TraesCS5D01G246400 chr4D 92.135 89 7 0 3176 3264 298540016 298539928 5.480000e-25 126.0
36 TraesCS5D01G246400 chr4A 93.023 86 6 0 3176 3261 187263717 187263802 5.480000e-25 126.0
37 TraesCS5D01G246400 chr2B 74.510 306 63 11 4435 4730 49143726 49143426 9.180000e-23 119.0
38 TraesCS5D01G246400 chr2B 73.759 282 52 16 4435 4705 565186784 565187054 2.000000e-14 91.6
39 TraesCS5D01G246400 chr3D 87.879 99 9 3 3163 3260 372318740 372318644 4.270000e-21 113.0
40 TraesCS5D01G246400 chr3D 89.412 85 9 0 3176 3260 372318644 372318728 1.990000e-19 108.0
41 TraesCS5D01G246400 chr3B 84.848 99 12 3 3163 3260 486382322 486382226 4.300000e-16 97.1
42 TraesCS5D01G246400 chr7B 79.070 86 16 2 4457 4542 131066284 131066201 2.030000e-04 58.4


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 TraesCS5D01G246400 chr5D 354500011 354505227 5216 True 4657.000000 8844 100.000000 1 5217 2 chr5D.!!$R1 5216
1 TraesCS5D01G246400 chr5A 455463347 455468387 5040 True 1890.750000 2922 96.209750 1 4772 4 chr5A.!!$R1 4771
2 TraesCS5D01G246400 chr5B 418811176 418815844 4668 True 1490.400000 2808 96.612000 1 4479 5 chr5B.!!$R1 4478
3 TraesCS5D01G246400 chr6A 42922690 42926886 4196 False 718.400000 1275 86.927600 993 4347 5 chr6A.!!$F1 3354
4 TraesCS5D01G246400 chr6B 76857189 76861050 3861 False 1010.000000 1267 87.775000 1567 4347 3 chr6B.!!$F3 2780
5 TraesCS5D01G246400 chrUn 104866155 104869910 3755 True 1039.333333 1236 88.609333 1567 4347 3 chrUn.!!$R2 2780

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
168 169 0.390340 CAGGTGTCCGTGTCATGGAG 60.390 60.000 14.40 0.00 33.08 3.86 F
906 920 1.338337 CGTGATCCAGCTACTACCCTG 59.662 57.143 0.00 0.00 0.00 4.45 F
1111 1125 1.134220 TCGCCAAGGTCTTGTTCTTGT 60.134 47.619 9.51 0.00 38.83 3.16 F
1217 1231 1.137479 CCGCATTTGGCTCATTGGATT 59.863 47.619 0.00 0.00 41.67 3.01 F
1457 1478 2.376518 CACCACCTGAGGGGCATATATT 59.623 50.000 2.38 0.00 39.10 1.28 F
3170 4632 1.610522 GGGCCACAGTAATGATCATGC 59.389 52.381 9.46 6.18 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 1125 0.401395 GACATGGGGAGGATGGGGTA 60.401 60.000 0.00 0.0 0.00 3.69 R
2658 4119 1.213296 AGTTGAGTGTGTCCCCTGTT 58.787 50.000 0.00 0.0 0.00 3.16 R
2708 4169 3.735746 CCTTTTTGCTTGTAAGGCTTTCG 59.264 43.478 4.45 0.0 32.73 3.46 R
3021 4482 6.769822 ACATCCAGGAAGATACACAATGATTC 59.230 38.462 0.00 0.0 0.00 2.52 R
3410 4972 5.845734 TCCATTAGAACTAGGGGTAAGTGA 58.154 41.667 0.00 0.0 0.00 3.41 R
4695 6577 0.179004 GGACATCACAACCACCACCA 60.179 55.000 0.00 0.0 0.00 4.17 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
32 33 3.637273 GGGGCTTGGACCACTCGT 61.637 66.667 0.00 0.00 27.52 4.18
168 169 0.390340 CAGGTGTCCGTGTCATGGAG 60.390 60.000 14.40 0.00 33.08 3.86
424 425 3.211045 CACCTCTTTTTCTTGGTCCGAA 58.789 45.455 0.00 0.00 0.00 4.30
703 717 8.229811 CCATAGTTAAACCCTTGTAACGTAAAC 58.770 37.037 0.00 0.00 35.73 2.01
901 915 2.158652 ACCTAGCGTGATCCAGCTACTA 60.159 50.000 13.24 0.00 44.15 1.82
906 920 1.338337 CGTGATCCAGCTACTACCCTG 59.662 57.143 0.00 0.00 0.00 4.45
1111 1125 1.134220 TCGCCAAGGTCTTGTTCTTGT 60.134 47.619 9.51 0.00 38.83 3.16
1217 1231 1.137479 CCGCATTTGGCTCATTGGATT 59.863 47.619 0.00 0.00 41.67 3.01
1228 1242 3.769300 GCTCATTGGATTGGTAGGGTTTT 59.231 43.478 0.00 0.00 0.00 2.43
1372 1387 7.615403 TCCTGATATATGGAAGAAGAAATCGG 58.385 38.462 0.00 0.00 0.00 4.18
1457 1478 2.376518 CACCACCTGAGGGGCATATATT 59.623 50.000 2.38 0.00 39.10 1.28
1924 2071 3.601443 TTCTAGTTCTGCCTTCTCAGC 57.399 47.619 0.00 0.00 34.19 4.26
2282 3482 7.725397 TGTATCATAATTGGCTAATGGAAAGCT 59.275 33.333 0.00 0.00 39.97 3.74
2283 3483 9.231297 GTATCATAATTGGCTAATGGAAAGCTA 57.769 33.333 0.00 0.00 39.97 3.32
2284 3484 8.890410 ATCATAATTGGCTAATGGAAAGCTAT 57.110 30.769 0.00 0.00 39.97 2.97
2285 3485 9.979897 ATCATAATTGGCTAATGGAAAGCTATA 57.020 29.630 0.00 0.00 39.97 1.31
2286 3486 9.979897 TCATAATTGGCTAATGGAAAGCTATAT 57.020 29.630 0.00 0.00 39.97 0.86
2581 3800 8.271458 TGTGATCTGTATGTTGGGTGTAATATT 58.729 33.333 0.00 0.00 0.00 1.28
2633 4094 7.907214 AGTTCTATCTTTCTAATGCACGTTT 57.093 32.000 0.00 0.00 0.00 3.60
2658 4119 5.220835 CGATAATTGCATGCACCTGTCTTTA 60.221 40.000 22.58 1.96 0.00 1.85
2850 4311 5.598417 TCCGGAGATATCTCATCTTGTTTGA 59.402 40.000 29.33 11.72 44.60 2.69
3021 4482 3.550437 AAGGTATCTGCTGCCTTACTG 57.450 47.619 0.00 0.00 46.93 2.74
3075 4537 4.838986 TGTAGAGTTAGCTCCTTCCTTGTT 59.161 41.667 2.55 0.00 42.59 2.83
3170 4632 1.610522 GGGCCACAGTAATGATCATGC 59.389 52.381 9.46 6.18 0.00 4.06
3191 4653 7.509318 TCATGCTTATTACTACCTCTGTACCAT 59.491 37.037 0.00 0.00 0.00 3.55
3566 5310 5.818136 ACATTGAGATGGTATTGTTTCCG 57.182 39.130 0.00 0.00 37.60 4.30
3615 5359 4.176271 TGAAATCTATCGAGCAGTGTGTG 58.824 43.478 0.00 0.00 0.00 3.82
3621 5365 3.592898 ATCGAGCAGTGTGTGACAATA 57.407 42.857 0.00 0.00 0.00 1.90
3710 5456 5.420421 TGACAAAGGAAAAACTTGACCATCA 59.580 36.000 0.00 0.00 0.00 3.07
3715 5461 6.635030 AGGAAAAACTTGACCATCAGTTAC 57.365 37.500 0.00 0.00 0.00 2.50
4058 5811 3.025322 ACAGTCCCATTGTGGTTTTCA 57.975 42.857 0.00 0.00 35.17 2.69
4099 5928 4.645956 GAGAAGATTGTGCTGATGTTTCG 58.354 43.478 0.00 0.00 0.00 3.46
4168 5997 1.108776 CCCTCGTAATGACTCGGGAA 58.891 55.000 0.00 0.00 35.67 3.97
4288 6131 2.264005 TTTGGTACAGCCGTTCATGT 57.736 45.000 0.00 0.00 42.39 3.21
4336 6183 8.802267 CCCTTTGATTATCTGTTGTAAGGAAAA 58.198 33.333 0.00 0.00 34.26 2.29
4410 6290 1.738099 GCGTCCATCAGCAGTCGTT 60.738 57.895 0.00 0.00 0.00 3.85
4418 6298 1.295792 TCAGCAGTCGTTCGCTTTTT 58.704 45.000 0.00 0.00 35.96 1.94
4479 6359 3.479269 CCGCGCCGTTCTTCACTC 61.479 66.667 0.00 0.00 0.00 3.51
4495 6375 3.888583 TCACTCGTGGGGTTAACTTTTT 58.111 40.909 5.42 0.00 0.00 1.94
4542 6422 9.437045 GTGGATGATTGTTTTGTTTTGATTTTC 57.563 29.630 0.00 0.00 0.00 2.29
4543 6423 8.619546 TGGATGATTGTTTTGTTTTGATTTTCC 58.380 29.630 0.00 0.00 0.00 3.13
4548 6430 6.129053 TGTTTTGTTTTGATTTTCCATGGC 57.871 33.333 6.96 0.00 0.00 4.40
4569 6451 9.381033 CATGGCTTGGATTTTAATTATGTTTGA 57.619 29.630 0.00 0.00 0.00 2.69
4571 6453 9.381033 TGGCTTGGATTTTAATTATGTTTGATG 57.619 29.630 0.00 0.00 0.00 3.07
4573 6455 9.382275 GCTTGGATTTTAATTATGTTTGATGGT 57.618 29.630 0.00 0.00 0.00 3.55
4667 6549 1.668751 TCAGCTCGTGTTTGTGGTTTC 59.331 47.619 0.00 0.00 0.00 2.78
4679 6561 7.452231 GTGTTTGTGGTTTCTTTACATGTTTG 58.548 34.615 2.30 0.00 0.00 2.93
4690 6572 1.603455 CATGTTTGGGCCTCGGTGT 60.603 57.895 4.53 0.00 0.00 4.16
4695 6577 1.990160 TTTGGGCCTCGGTGTCAGTT 61.990 55.000 4.53 0.00 0.00 3.16
4716 6598 1.238439 GTGGTGGTTGTGATGTCCTG 58.762 55.000 0.00 0.00 0.00 3.86
4730 6612 2.562296 TGTCCTGGGGAGCTCTTATTT 58.438 47.619 14.64 0.00 29.39 1.40
4733 6615 1.587547 CTGGGGAGCTCTTATTTCGC 58.412 55.000 14.64 4.63 0.00 4.70
4735 6617 0.179081 GGGGAGCTCTTATTTCGCGT 60.179 55.000 14.64 0.00 0.00 6.01
4737 6619 0.931005 GGAGCTCTTATTTCGCGTGG 59.069 55.000 14.64 0.00 0.00 4.94
4772 6654 3.244875 TGTTGACATACATTGGCTGACCT 60.245 43.478 0.00 0.00 32.91 3.85
4773 6655 3.719268 TGACATACATTGGCTGACCTT 57.281 42.857 0.00 0.00 32.91 3.50
4774 6656 4.032960 TGACATACATTGGCTGACCTTT 57.967 40.909 0.00 0.00 32.91 3.11
4775 6657 4.406456 TGACATACATTGGCTGACCTTTT 58.594 39.130 0.00 0.00 32.91 2.27
4776 6658 4.832266 TGACATACATTGGCTGACCTTTTT 59.168 37.500 0.00 0.00 32.91 1.94
4982 6864 1.620822 CTTGCCCCACACTTTAAGCT 58.379 50.000 0.00 0.00 0.00 3.74
4983 6865 2.790433 CTTGCCCCACACTTTAAGCTA 58.210 47.619 0.00 0.00 0.00 3.32
4984 6866 2.489938 TGCCCCACACTTTAAGCTAG 57.510 50.000 0.00 0.00 0.00 3.42
4985 6867 1.982226 TGCCCCACACTTTAAGCTAGA 59.018 47.619 0.00 0.00 0.00 2.43
4986 6868 2.373836 TGCCCCACACTTTAAGCTAGAA 59.626 45.455 0.00 0.00 0.00 2.10
4987 6869 3.010420 GCCCCACACTTTAAGCTAGAAG 58.990 50.000 0.00 7.29 0.00 2.85
4988 6870 3.307480 GCCCCACACTTTAAGCTAGAAGA 60.307 47.826 14.05 0.00 0.00 2.87
4989 6871 4.806286 GCCCCACACTTTAAGCTAGAAGAA 60.806 45.833 14.05 0.00 0.00 2.52
4990 6872 5.313712 CCCCACACTTTAAGCTAGAAGAAA 58.686 41.667 14.05 0.00 0.00 2.52
4991 6873 5.181433 CCCCACACTTTAAGCTAGAAGAAAC 59.819 44.000 14.05 0.00 0.00 2.78
4992 6874 5.763204 CCCACACTTTAAGCTAGAAGAAACA 59.237 40.000 14.05 0.00 0.00 2.83
4993 6875 6.073003 CCCACACTTTAAGCTAGAAGAAACAG 60.073 42.308 14.05 0.00 0.00 3.16
4994 6876 6.366630 CACACTTTAAGCTAGAAGAAACAGC 58.633 40.000 14.05 0.00 35.49 4.40
4996 6878 7.385205 CACACTTTAAGCTAGAAGAAACAGCTA 59.615 37.037 14.05 0.00 44.70 3.32
4997 6879 8.097662 ACACTTTAAGCTAGAAGAAACAGCTAT 58.902 33.333 14.05 0.00 44.70 2.97
4998 6880 8.599774 CACTTTAAGCTAGAAGAAACAGCTATC 58.400 37.037 14.05 0.00 44.70 2.08
4999 6881 8.314751 ACTTTAAGCTAGAAGAAACAGCTATCA 58.685 33.333 14.05 0.00 44.70 2.15
5000 6882 9.323985 CTTTAAGCTAGAAGAAACAGCTATCAT 57.676 33.333 0.00 0.00 44.70 2.45
5002 6884 9.751542 TTAAGCTAGAAGAAACAGCTATCATAC 57.248 33.333 0.00 0.00 44.70 2.39
5003 6885 7.595819 AGCTAGAAGAAACAGCTATCATACT 57.404 36.000 0.00 0.00 43.67 2.12
5004 6886 8.017418 AGCTAGAAGAAACAGCTATCATACTT 57.983 34.615 0.00 0.00 43.67 2.24
5005 6887 8.482128 AGCTAGAAGAAACAGCTATCATACTTT 58.518 33.333 0.00 0.00 43.67 2.66
5006 6888 9.103861 GCTAGAAGAAACAGCTATCATACTTTT 57.896 33.333 0.00 0.00 32.46 2.27
5043 6925 9.893305 AGTCCATTTAATCAAAAGAAGTTAACG 57.107 29.630 0.00 0.00 0.00 3.18
5044 6926 9.673454 GTCCATTTAATCAAAAGAAGTTAACGT 57.327 29.630 0.00 0.00 0.00 3.99
5086 6968 9.932699 TTCGAGAAAACGTTTAAAATATTGTGA 57.067 25.926 15.03 0.00 34.70 3.58
5087 6969 9.932699 TCGAGAAAACGTTTAAAATATTGTGAA 57.067 25.926 15.03 0.00 34.70 3.18
5171 7053 6.843069 ATTTGTGAATTTGAAAAAGGTCCG 57.157 33.333 0.00 0.00 0.00 4.79
5172 7054 3.712187 TGTGAATTTGAAAAAGGTCCGC 58.288 40.909 0.00 0.00 0.00 5.54
5173 7055 3.131223 TGTGAATTTGAAAAAGGTCCGCA 59.869 39.130 0.00 0.00 0.00 5.69
5174 7056 3.735746 GTGAATTTGAAAAAGGTCCGCAG 59.264 43.478 0.00 0.00 0.00 5.18
5175 7057 3.634448 TGAATTTGAAAAAGGTCCGCAGA 59.366 39.130 0.00 0.00 0.00 4.26
5176 7058 4.280677 TGAATTTGAAAAAGGTCCGCAGAT 59.719 37.500 0.00 0.00 0.00 2.90
5177 7059 4.871933 ATTTGAAAAAGGTCCGCAGATT 57.128 36.364 0.00 0.00 0.00 2.40
5178 7060 5.975693 ATTTGAAAAAGGTCCGCAGATTA 57.024 34.783 0.00 0.00 0.00 1.75
5179 7061 5.776173 TTTGAAAAAGGTCCGCAGATTAA 57.224 34.783 0.00 0.00 0.00 1.40
5180 7062 5.776173 TTGAAAAAGGTCCGCAGATTAAA 57.224 34.783 0.00 0.00 0.00 1.52
5181 7063 5.776173 TGAAAAAGGTCCGCAGATTAAAA 57.224 34.783 0.00 0.00 0.00 1.52
5182 7064 6.150396 TGAAAAAGGTCCGCAGATTAAAAA 57.850 33.333 0.00 0.00 0.00 1.94
5183 7065 6.754193 TGAAAAAGGTCCGCAGATTAAAAAT 58.246 32.000 0.00 0.00 0.00 1.82
5184 7066 7.213678 TGAAAAAGGTCCGCAGATTAAAAATT 58.786 30.769 0.00 0.00 0.00 1.82
5185 7067 7.170658 TGAAAAAGGTCCGCAGATTAAAAATTG 59.829 33.333 0.00 0.00 0.00 2.32
5186 7068 5.975693 AAGGTCCGCAGATTAAAAATTGA 57.024 34.783 0.00 0.00 0.00 2.57
5187 7069 6.530019 AAGGTCCGCAGATTAAAAATTGAT 57.470 33.333 0.00 0.00 0.00 2.57
5188 7070 6.136541 AGGTCCGCAGATTAAAAATTGATC 57.863 37.500 0.00 0.00 0.00 2.92
5189 7071 5.067805 AGGTCCGCAGATTAAAAATTGATCC 59.932 40.000 0.00 0.00 0.00 3.36
5190 7072 5.067805 GGTCCGCAGATTAAAAATTGATCCT 59.932 40.000 0.00 0.00 0.00 3.24
5191 7073 6.405842 GGTCCGCAGATTAAAAATTGATCCTT 60.406 38.462 0.00 0.00 0.00 3.36
5192 7074 7.035612 GTCCGCAGATTAAAAATTGATCCTTT 58.964 34.615 0.00 0.00 0.00 3.11
5193 7075 7.009540 GTCCGCAGATTAAAAATTGATCCTTTG 59.990 37.037 0.00 0.00 0.00 2.77
5194 7076 6.237915 CCGCAGATTAAAAATTGATCCTTTGC 60.238 38.462 0.00 0.00 0.00 3.68
5195 7077 6.310956 CGCAGATTAAAAATTGATCCTTTGCA 59.689 34.615 0.00 0.00 0.00 4.08
5196 7078 7.463648 CGCAGATTAAAAATTGATCCTTTGCAG 60.464 37.037 0.00 0.00 0.00 4.41
5197 7079 7.201582 GCAGATTAAAAATTGATCCTTTGCAGG 60.202 37.037 0.00 0.00 42.50 4.85
5198 7080 7.820872 CAGATTAAAAATTGATCCTTTGCAGGT 59.179 33.333 0.00 0.00 41.69 4.00
5199 7081 8.377799 AGATTAAAAATTGATCCTTTGCAGGTT 58.622 29.630 0.00 0.00 41.69 3.50
5200 7082 8.922931 ATTAAAAATTGATCCTTTGCAGGTTT 57.077 26.923 0.00 0.00 41.69 3.27
5202 7084 9.838339 TTAAAAATTGATCCTTTGCAGGTTTAA 57.162 25.926 0.00 0.00 41.69 1.52
5203 7085 8.922931 AAAAATTGATCCTTTGCAGGTTTAAT 57.077 26.923 0.00 0.00 41.69 1.40
5204 7086 8.552083 AAAATTGATCCTTTGCAGGTTTAATC 57.448 30.769 0.00 0.00 41.69 1.75
5205 7087 7.486407 AATTGATCCTTTGCAGGTTTAATCT 57.514 32.000 0.00 0.00 41.69 2.40
5206 7088 6.916360 TTGATCCTTTGCAGGTTTAATCTT 57.084 33.333 0.00 0.00 41.69 2.40
5207 7089 6.916360 TGATCCTTTGCAGGTTTAATCTTT 57.084 33.333 0.00 0.00 41.69 2.52
5208 7090 7.301868 TGATCCTTTGCAGGTTTAATCTTTT 57.698 32.000 0.00 0.00 41.69 2.27
5209 7091 7.734942 TGATCCTTTGCAGGTTTAATCTTTTT 58.265 30.769 0.00 0.00 41.69 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.447140 CTGTACCTAAAGGCGCGCA 60.447 57.895 34.42 11.59 39.32 6.09
168 169 1.002502 GGAGTAACACACCTGCCCC 60.003 63.158 0.00 0.00 0.00 5.80
400 401 2.959030 GGACCAAGAAAAAGAGGTGCTT 59.041 45.455 0.00 0.00 39.13 3.91
402 403 1.266989 CGGACCAAGAAAAAGAGGTGC 59.733 52.381 0.00 0.00 38.88 5.01
703 717 1.966451 GTGTCAAACCTCCCCAGCG 60.966 63.158 0.00 0.00 0.00 5.18
901 915 2.623450 TACGAGAGAGGGGCAGGGT 61.623 63.158 0.00 0.00 0.00 4.34
906 920 0.680280 TGACAGTACGAGAGAGGGGC 60.680 60.000 0.00 0.00 0.00 5.80
1020 1034 4.147449 CGACGCAGGAGGGATGCA 62.147 66.667 0.00 0.00 44.05 3.96
1111 1125 0.401395 GACATGGGGAGGATGGGGTA 60.401 60.000 0.00 0.00 0.00 3.69
1217 1231 2.136974 ACCCCTGTAAAACCCTACCA 57.863 50.000 0.00 0.00 0.00 3.25
1228 1242 6.956102 TCCATAGTTTCTAAAACCCCTGTA 57.044 37.500 0.00 0.00 0.00 2.74
1457 1478 3.838244 ACTTGTGGAAGCTGTTCAGTA 57.162 42.857 0.00 0.00 33.93 2.74
1924 2071 7.950236 CAAAATCTGCAAATGAAGAAAGCTAG 58.050 34.615 0.00 0.00 32.47 3.42
2633 4094 2.613595 GACAGGTGCATGCAATTATCGA 59.386 45.455 24.58 0.00 0.00 3.59
2658 4119 1.213296 AGTTGAGTGTGTCCCCTGTT 58.787 50.000 0.00 0.00 0.00 3.16
2708 4169 3.735746 CCTTTTTGCTTGTAAGGCTTTCG 59.264 43.478 4.45 0.00 32.73 3.46
2850 4311 9.301897 AGTTTGAATCTTAAATTAGTTGGAGCT 57.698 29.630 0.00 0.00 0.00 4.09
3021 4482 6.769822 ACATCCAGGAAGATACACAATGATTC 59.230 38.462 0.00 0.00 0.00 2.52
3410 4972 5.845734 TCCATTAGAACTAGGGGTAAGTGA 58.154 41.667 0.00 0.00 0.00 3.41
3566 5310 4.467735 CTTTTACTCTTTCAAGAAGCCGC 58.532 43.478 0.00 0.00 34.03 6.53
3710 5456 2.997986 CGTATTTGCGTTCAGGGTAACT 59.002 45.455 0.00 0.00 0.00 2.24
3715 5461 6.809689 TCATATATACGTATTTGCGTTCAGGG 59.190 38.462 14.33 0.00 43.04 4.45
3736 5484 3.497048 GGAGAGATCCAGACCGACTCATA 60.497 52.174 0.00 0.00 0.00 2.15
3903 5656 3.434637 CACCAACAAAACCTTCTTCGTG 58.565 45.455 0.00 0.00 0.00 4.35
4058 5811 3.197766 TCTCGGGTCAAAATATCTGCTGT 59.802 43.478 0.00 0.00 0.00 4.40
4234 6063 4.394439 TGTCGTATGCATAGCAAGGTTA 57.606 40.909 6.67 0.00 43.62 2.85
4288 6131 1.671054 GGCTGCACTTTCGCCTACA 60.671 57.895 6.66 0.00 40.62 2.74
4336 6183 3.001939 GCAACAAAACACTAGTGCTACGT 59.998 43.478 22.90 12.16 0.00 3.57
4410 6290 3.008594 TGAAGGGGATGTAGAAAAAGCGA 59.991 43.478 0.00 0.00 0.00 4.93
4418 6298 8.453681 TCTAGTGTATTATGAAGGGGATGTAGA 58.546 37.037 0.00 0.00 0.00 2.59
4497 6377 6.121776 TCCACAATAACCTGCTAGAGAAAA 57.878 37.500 0.00 0.00 0.00 2.29
4502 6382 5.894298 ATCATCCACAATAACCTGCTAGA 57.106 39.130 0.00 0.00 0.00 2.43
4504 6384 5.754782 ACAATCATCCACAATAACCTGCTA 58.245 37.500 0.00 0.00 0.00 3.49
4543 6423 9.381033 TCAAACATAATTAAAATCCAAGCCATG 57.619 29.630 0.00 0.00 0.00 3.66
4593 6475 0.931702 TCTAACGGCAACACAACACG 59.068 50.000 0.00 0.00 0.00 4.49
4630 6512 0.472471 TGAACAACCCCACACTCCTC 59.528 55.000 0.00 0.00 0.00 3.71
4631 6513 0.474184 CTGAACAACCCCACACTCCT 59.526 55.000 0.00 0.00 0.00 3.69
4632 6514 1.172812 GCTGAACAACCCCACACTCC 61.173 60.000 0.00 0.00 0.00 3.85
4635 6517 1.507141 CGAGCTGAACAACCCCACAC 61.507 60.000 0.00 0.00 0.00 3.82
4667 6549 1.472480 CCGAGGCCCAAACATGTAAAG 59.528 52.381 0.00 0.00 0.00 1.85
4679 6561 2.358737 CAACTGACACCGAGGCCC 60.359 66.667 0.00 0.00 0.00 5.80
4690 6572 0.621082 TCACAACCACCACCAACTGA 59.379 50.000 0.00 0.00 0.00 3.41
4695 6577 0.179004 GGACATCACAACCACCACCA 60.179 55.000 0.00 0.00 0.00 4.17
4716 6598 0.179081 ACGCGAAATAAGAGCTCCCC 60.179 55.000 15.93 0.00 0.00 4.81
4730 6612 0.671163 GTTACATGGTTCCCACGCGA 60.671 55.000 15.93 0.00 35.80 5.87
4733 6615 2.178912 ACAGTTACATGGTTCCCACG 57.821 50.000 0.00 0.00 35.80 4.94
4735 6617 3.117851 TGTCAACAGTTACATGGTTCCCA 60.118 43.478 0.00 0.00 38.19 4.37
4737 6619 5.703592 TGTATGTCAACAGTTACATGGTTCC 59.296 40.000 14.07 0.00 36.96 3.62
4745 6627 5.411361 TCAGCCAATGTATGTCAACAGTTAC 59.589 40.000 0.00 0.00 31.70 2.50
4746 6628 5.411361 GTCAGCCAATGTATGTCAACAGTTA 59.589 40.000 0.00 0.00 31.70 2.24
4749 6631 3.127548 GGTCAGCCAATGTATGTCAACAG 59.872 47.826 0.00 0.00 31.32 3.16
4963 6845 1.620822 AGCTTAAAGTGTGGGGCAAG 58.379 50.000 0.00 0.00 0.00 4.01
4964 6846 2.373836 TCTAGCTTAAAGTGTGGGGCAA 59.626 45.455 0.00 0.00 0.00 4.52
4965 6847 1.982226 TCTAGCTTAAAGTGTGGGGCA 59.018 47.619 0.00 0.00 0.00 5.36
4966 6848 2.781681 TCTAGCTTAAAGTGTGGGGC 57.218 50.000 0.00 0.00 0.00 5.80
4967 6849 4.553330 TCTTCTAGCTTAAAGTGTGGGG 57.447 45.455 0.00 0.00 0.00 4.96
4968 6850 5.763204 TGTTTCTTCTAGCTTAAAGTGTGGG 59.237 40.000 0.00 0.00 0.00 4.61
4969 6851 6.566753 GCTGTTTCTTCTAGCTTAAAGTGTGG 60.567 42.308 0.00 0.00 34.70 4.17
4970 6852 6.203723 AGCTGTTTCTTCTAGCTTAAAGTGTG 59.796 38.462 0.00 0.00 44.87 3.82
4971 6853 6.292150 AGCTGTTTCTTCTAGCTTAAAGTGT 58.708 36.000 0.00 0.00 44.87 3.55
4972 6854 6.793492 AGCTGTTTCTTCTAGCTTAAAGTG 57.207 37.500 0.00 0.00 44.87 3.16
4973 6855 8.314751 TGATAGCTGTTTCTTCTAGCTTAAAGT 58.685 33.333 0.00 0.00 44.87 2.66
4974 6856 8.709386 TGATAGCTGTTTCTTCTAGCTTAAAG 57.291 34.615 0.00 0.00 44.87 1.85
4976 6858 9.751542 GTATGATAGCTGTTTCTTCTAGCTTAA 57.248 33.333 0.00 0.00 44.87 1.85
4977 6859 9.137459 AGTATGATAGCTGTTTCTTCTAGCTTA 57.863 33.333 0.00 0.00 44.87 3.09
4978 6860 8.017418 AGTATGATAGCTGTTTCTTCTAGCTT 57.983 34.615 0.00 0.00 44.87 3.74
4980 6862 8.655651 AAAGTATGATAGCTGTTTCTTCTAGC 57.344 34.615 0.00 0.00 37.71 3.42
5017 6899 9.893305 CGTTAACTTCTTTTGATTAAATGGACT 57.107 29.630 3.71 0.00 0.00 3.85
5018 6900 9.673454 ACGTTAACTTCTTTTGATTAAATGGAC 57.327 29.630 3.71 0.00 0.00 4.02
5060 6942 9.932699 TCACAATATTTTAAACGTTTTCTCGAA 57.067 25.926 20.19 3.82 34.70 3.71
5061 6943 9.932699 TTCACAATATTTTAAACGTTTTCTCGA 57.067 25.926 20.19 3.04 34.70 4.04
5145 7027 8.987890 CGGACCTTTTTCAAATTCACAAATATT 58.012 29.630 0.00 0.00 0.00 1.28
5146 7028 7.117667 GCGGACCTTTTTCAAATTCACAAATAT 59.882 33.333 0.00 0.00 0.00 1.28
5147 7029 6.422400 GCGGACCTTTTTCAAATTCACAAATA 59.578 34.615 0.00 0.00 0.00 1.40
5148 7030 5.236263 GCGGACCTTTTTCAAATTCACAAAT 59.764 36.000 0.00 0.00 0.00 2.32
5149 7031 4.568760 GCGGACCTTTTTCAAATTCACAAA 59.431 37.500 0.00 0.00 0.00 2.83
5150 7032 4.116238 GCGGACCTTTTTCAAATTCACAA 58.884 39.130 0.00 0.00 0.00 3.33
5151 7033 3.131223 TGCGGACCTTTTTCAAATTCACA 59.869 39.130 0.00 0.00 0.00 3.58
5152 7034 3.712187 TGCGGACCTTTTTCAAATTCAC 58.288 40.909 0.00 0.00 0.00 3.18
5153 7035 3.634448 TCTGCGGACCTTTTTCAAATTCA 59.366 39.130 0.00 0.00 0.00 2.57
5154 7036 4.237349 TCTGCGGACCTTTTTCAAATTC 57.763 40.909 0.00 0.00 0.00 2.17
5155 7037 4.871933 ATCTGCGGACCTTTTTCAAATT 57.128 36.364 0.00 0.00 0.00 1.82
5156 7038 4.871933 AATCTGCGGACCTTTTTCAAAT 57.128 36.364 0.00 0.00 0.00 2.32
5157 7039 5.776173 TTAATCTGCGGACCTTTTTCAAA 57.224 34.783 0.00 0.00 0.00 2.69
5158 7040 5.776173 TTTAATCTGCGGACCTTTTTCAA 57.224 34.783 0.00 0.00 0.00 2.69
5159 7041 5.776173 TTTTAATCTGCGGACCTTTTTCA 57.224 34.783 0.00 0.00 0.00 2.69
5160 7042 7.383843 TCAATTTTTAATCTGCGGACCTTTTTC 59.616 33.333 0.00 0.00 0.00 2.29
5161 7043 7.213678 TCAATTTTTAATCTGCGGACCTTTTT 58.786 30.769 0.00 0.00 0.00 1.94
5162 7044 6.754193 TCAATTTTTAATCTGCGGACCTTTT 58.246 32.000 0.00 0.00 0.00 2.27
5163 7045 6.339587 TCAATTTTTAATCTGCGGACCTTT 57.660 33.333 0.00 0.00 0.00 3.11
5164 7046 5.975693 TCAATTTTTAATCTGCGGACCTT 57.024 34.783 0.00 0.00 0.00 3.50
5165 7047 5.067805 GGATCAATTTTTAATCTGCGGACCT 59.932 40.000 0.00 0.00 0.00 3.85
5166 7048 5.067805 AGGATCAATTTTTAATCTGCGGACC 59.932 40.000 0.00 0.00 0.00 4.46
5167 7049 6.136541 AGGATCAATTTTTAATCTGCGGAC 57.863 37.500 0.00 0.00 0.00 4.79
5168 7050 6.773976 AAGGATCAATTTTTAATCTGCGGA 57.226 33.333 0.00 0.00 0.00 5.54
5169 7051 6.237915 GCAAAGGATCAATTTTTAATCTGCGG 60.238 38.462 0.00 0.00 0.00 5.69
5170 7052 6.310956 TGCAAAGGATCAATTTTTAATCTGCG 59.689 34.615 0.00 0.00 0.00 5.18
5171 7053 7.201582 CCTGCAAAGGATCAATTTTTAATCTGC 60.202 37.037 0.00 0.00 0.00 4.26
5172 7054 7.820872 ACCTGCAAAGGATCAATTTTTAATCTG 59.179 33.333 0.00 0.00 0.00 2.90
5173 7055 7.910584 ACCTGCAAAGGATCAATTTTTAATCT 58.089 30.769 0.00 0.00 0.00 2.40
5174 7056 8.552083 AACCTGCAAAGGATCAATTTTTAATC 57.448 30.769 0.00 0.00 0.00 1.75
5175 7057 8.922931 AAACCTGCAAAGGATCAATTTTTAAT 57.077 26.923 0.00 0.00 0.00 1.40
5176 7058 9.838339 TTAAACCTGCAAAGGATCAATTTTTAA 57.162 25.926 0.00 0.00 0.00 1.52
5178 7060 8.922931 ATTAAACCTGCAAAGGATCAATTTTT 57.077 26.923 0.00 0.00 0.00 1.94
5179 7061 8.377799 AGATTAAACCTGCAAAGGATCAATTTT 58.622 29.630 0.00 0.00 0.00 1.82
5180 7062 7.910584 AGATTAAACCTGCAAAGGATCAATTT 58.089 30.769 0.00 0.00 0.00 1.82
5181 7063 7.486407 AGATTAAACCTGCAAAGGATCAATT 57.514 32.000 0.00 0.00 0.00 2.32
5182 7064 7.486407 AAGATTAAACCTGCAAAGGATCAAT 57.514 32.000 0.00 0.00 0.00 2.57
5183 7065 6.916360 AAGATTAAACCTGCAAAGGATCAA 57.084 33.333 0.00 0.00 0.00 2.57
5184 7066 6.916360 AAAGATTAAACCTGCAAAGGATCA 57.084 33.333 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.