Multiple sequence alignment - TraesCS7D01G394900

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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 TraesCS7D01G394900 chr7D 100.000 4536 0 0 1 4536 509913494 509908959 0.000000e+00 8377.0
1 TraesCS7D01G394900 chr7D 94.318 264 15 0 3714 3977 162188472 162188735 5.460000e-109 405.0
2 TraesCS7D01G394900 chr7D 96.602 206 7 0 3969 4174 501019044 501018839 4.350000e-90 342.0
3 TraesCS7D01G394900 chr7D 90.476 168 15 1 3982 4148 587258735 587258902 2.120000e-53 220.0
4 TraesCS7D01G394900 chr4D 98.792 4222 39 4 1 4220 40831631 40835842 0.000000e+00 7504.0
5 TraesCS7D01G394900 chr4D 95.882 170 6 1 4235 4404 459416551 459416719 1.610000e-69 274.0
6 TraesCS7D01G394900 chr5D 98.483 4088 35 4 1 4085 254532856 254528793 0.000000e+00 7180.0
7 TraesCS7D01G394900 chr5D 97.676 4087 82 8 1 4085 551019609 551015534 0.000000e+00 7009.0
8 TraesCS7D01G394900 chr5D 99.429 175 1 0 4045 4219 254528781 254528607 7.320000e-83 318.0
9 TraesCS7D01G394900 chr5D 95.906 171 7 0 4235 4405 46617628 46617458 1.240000e-70 278.0
10 TraesCS7D01G394900 chr5D 98.684 152 2 0 4251 4402 133250025 133249874 2.080000e-68 270.0
11 TraesCS7D01G394900 chr5D 94.675 169 6 3 4235 4402 326746552 326746386 4.500000e-65 259.0
12 TraesCS7D01G394900 chr5D 98.462 130 2 0 4045 4174 551015522 551015393 3.530000e-56 230.0
13 TraesCS7D01G394900 chr7A 98.323 1849 27 3 923 2771 678171401 678169557 0.000000e+00 3240.0
14 TraesCS7D01G394900 chr7A 92.329 1434 36 10 2741 4174 678169557 678168198 0.000000e+00 1971.0
15 TraesCS7D01G394900 chr1B 97.613 1843 40 2 923 2765 154148262 154150100 0.000000e+00 3157.0
16 TraesCS7D01G394900 chr1B 94.984 1216 39 7 2741 3955 154150104 154151298 0.000000e+00 1888.0
17 TraesCS7D01G394900 chr1B 84.716 229 9 1 3946 4174 154151259 154151461 5.950000e-49 206.0
18 TraesCS7D01G394900 chr1B 87.387 111 9 4 1 111 55535554 55535449 6.160000e-24 122.0
19 TraesCS7D01G394900 chr1B 97.500 40 1 0 4175 4214 416586759 416586798 8.140000e-08 69.4
20 TraesCS7D01G394900 chr2A 97.450 1843 43 3 923 2765 195113158 195114996 0.000000e+00 3140.0
21 TraesCS7D01G394900 chr2A 97.889 1563 28 4 1203 2765 721735602 721737159 0.000000e+00 2699.0
22 TraesCS7D01G394900 chr2A 93.305 1434 46 4 2741 4174 721737165 721738548 0.000000e+00 2071.0
23 TraesCS7D01G394900 chr2A 94.819 1216 41 2 2741 3955 195115000 195116194 0.000000e+00 1877.0
24 TraesCS7D01G394900 chr2A 96.382 304 5 2 923 1226 721735274 721735571 3.150000e-136 496.0
25 TraesCS7D01G394900 chr2A 84.279 229 10 1 3946 4174 195116155 195116357 2.770000e-47 200.0
26 TraesCS7D01G394900 chr1A 96.755 1849 35 7 923 2771 14528458 14526635 0.000000e+00 3059.0
27 TraesCS7D01G394900 chr1A 95.312 1216 34 3 2741 3955 14526635 14525442 0.000000e+00 1908.0
28 TraesCS7D01G394900 chr1A 92.938 354 10 10 3379 3717 13765077 13764724 6.770000e-138 501.0
29 TraesCS7D01G394900 chr1A 85.202 223 7 1 3952 4174 14525475 14525279 5.950000e-49 206.0
30 TraesCS7D01G394900 chr6D 97.513 563 12 1 1732 2294 39581154 39580594 0.000000e+00 961.0
31 TraesCS7D01G394900 chr6D 96.820 566 18 0 2622 3187 39577883 39577318 0.000000e+00 946.0
32 TraesCS7D01G394900 chr6D 96.716 335 9 1 2287 2619 39578443 39578109 1.430000e-154 556.0
33 TraesCS7D01G394900 chr6D 97.619 168 4 0 4235 4402 56195221 56195054 5.740000e-74 289.0
34 TraesCS7D01G394900 chrUn 99.270 411 3 0 1309 1719 477629048 477629458 0.000000e+00 743.0
35 TraesCS7D01G394900 chrUn 88.288 111 8 4 1 111 315664035 315663930 1.320000e-25 128.0
36 TraesCS7D01G394900 chrUn 86.486 111 10 3 1 111 260014721 260014616 2.870000e-22 117.0
37 TraesCS7D01G394900 chrUn 86.486 111 10 3 1 111 262118921 262118816 2.870000e-22 117.0
38 TraesCS7D01G394900 chr1D 93.447 351 8 9 3382 3717 11620623 11620273 1.460000e-139 507.0
39 TraesCS7D01G394900 chr1D 93.939 264 16 0 3714 3977 202975768 202976031 2.540000e-107 399.0
40 TraesCS7D01G394900 chr1D 93.561 264 17 0 3714 3977 12258622 12258359 1.180000e-105 394.0
41 TraesCS7D01G394900 chr1D 96.429 168 5 1 4235 4402 485942387 485942553 4.470000e-70 276.0
42 TraesCS7D01G394900 chr1D 95.833 168 6 1 4235 4402 485941704 485941870 2.080000e-68 270.0
43 TraesCS7D01G394900 chr1D 91.837 49 4 0 4172 4220 406729356 406729404 8.140000e-08 69.4
44 TraesCS7D01G394900 chr4B 93.893 262 16 0 3714 3975 566613061 566613322 3.290000e-106 396.0
45 TraesCS7D01G394900 chr4B 95.000 40 2 0 4175 4214 629897719 629897680 3.790000e-06 63.9
46 TraesCS7D01G394900 chr4B 94.737 38 2 0 4177 4214 629891887 629891850 4.900000e-05 60.2
47 TraesCS7D01G394900 chr2B 93.156 263 16 2 3714 3975 145378319 145378580 7.120000e-103 385.0
48 TraesCS7D01G394900 chr3A 96.237 186 7 0 803 988 365952930 365952745 5.700000e-79 305.0
49 TraesCS7D01G394900 chr3A 90.594 202 11 3 3980 4174 329532653 329532453 1.250000e-65 261.0
50 TraesCS7D01G394900 chr3A 87.387 111 9 4 1 111 568015174 568015069 6.160000e-24 122.0
51 TraesCS7D01G394900 chr3D 95.808 167 6 1 4236 4402 390106088 390106253 7.480000e-68 268.0
52 TraesCS7D01G394900 chr3D 93.827 81 2 2 3303 3380 535396261 535396181 7.970000e-23 119.0
53 TraesCS7D01G394900 chr2D 95.808 167 6 1 4236 4402 592575477 592575312 7.480000e-68 268.0
54 TraesCS7D01G394900 chr5B 90.909 110 9 1 1 110 557300162 557300270 3.660000e-31 147.0
55 TraesCS7D01G394900 chr6B 91.837 49 4 0 4172 4220 222004800 222004848 8.140000e-08 69.4
56 TraesCS7D01G394900 chr4A 91.837 49 4 0 4172 4220 17800117 17800165 8.140000e-08 69.4
57 TraesCS7D01G394900 chr3B 95.000 40 2 0 4175 4214 114172900 114172861 3.790000e-06 63.9


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 TraesCS7D01G394900 chr7D 509908959 509913494 4535 True 8377.000000 8377 100.000000 1 4536 1 chr7D.!!$R2 4535
1 TraesCS7D01G394900 chr4D 40831631 40835842 4211 False 7504.000000 7504 98.792000 1 4220 1 chr4D.!!$F1 4219
2 TraesCS7D01G394900 chr5D 254528607 254532856 4249 True 3749.000000 7180 98.956000 1 4219 2 chr5D.!!$R4 4218
3 TraesCS7D01G394900 chr5D 551015393 551019609 4216 True 3619.500000 7009 98.069000 1 4174 2 chr5D.!!$R5 4173
4 TraesCS7D01G394900 chr7A 678168198 678171401 3203 True 2605.500000 3240 95.326000 923 4174 2 chr7A.!!$R1 3251
5 TraesCS7D01G394900 chr1B 154148262 154151461 3199 False 1750.333333 3157 92.437667 923 4174 3 chr1B.!!$F2 3251
6 TraesCS7D01G394900 chr2A 721735274 721738548 3274 False 1755.333333 2699 95.858667 923 4174 3 chr2A.!!$F2 3251
7 TraesCS7D01G394900 chr2A 195113158 195116357 3199 False 1739.000000 3140 92.182667 923 4174 3 chr2A.!!$F1 3251
8 TraesCS7D01G394900 chr1A 14525279 14528458 3179 True 1724.333333 3059 92.423000 923 4174 3 chr1A.!!$R2 3251
9 TraesCS7D01G394900 chr6D 39577318 39581154 3836 True 821.000000 961 97.016333 1732 3187 3 chr6D.!!$R2 1455
10 TraesCS7D01G394900 chr1D 485941704 485942553 849 False 273.000000 276 96.131000 4235 4402 2 chr1D.!!$F3 167

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
249 250 1.552337 CACCAGCACTCACCTCAGTAT 59.448 52.381 0.0 0.0 0.00 2.12 F
1009 1012 8.322906 TCTTATTTATTAGAACATGCCGATGG 57.677 34.615 0.0 0.0 33.39 3.51 F
1121 1124 1.122019 CCCTACCTGATTCCCCTCGG 61.122 65.000 0.0 0.0 0.00 4.63 F
1749 1801 6.351117 GGCAGTACTACAGACAAATAGGAGTT 60.351 42.308 0.0 0.0 0.00 3.01 F
3158 5628 1.409381 GGAGGAAAATGAGAGCAGGGG 60.409 57.143 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1121 1124 4.261656 CCCTGTAGGTTCTGATCATACGTC 60.262 50.000 0.00 0.00 0.00 4.34 R
2765 5232 0.337428 AAATCCAAGAGCAGGGGCAT 59.663 50.000 0.00 0.00 44.61 4.40 R
3158 5628 3.567797 GGATGTTCGGCTCGCAGC 61.568 66.667 0.11 0.11 41.46 5.25 R
3170 5640 4.552365 CGCCAGCGATGGGGATGT 62.552 66.667 30.84 0.00 43.67 3.06 R
4486 7691 0.027586 GTGCTCAAACACGCGACTTT 59.972 50.000 15.93 6.52 0.00 2.66 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
165 166 1.819753 CCCCCTTCCAGACCATATCA 58.180 55.000 0.00 0.00 0.00 2.15
171 172 2.262266 TCCAGACCATATCACCACCA 57.738 50.000 0.00 0.00 0.00 4.17
249 250 1.552337 CACCAGCACTCACCTCAGTAT 59.448 52.381 0.00 0.00 0.00 2.12
868 871 9.671279 AATACATATGCTTGCAGCTACATATAA 57.329 29.630 1.58 7.05 42.97 0.98
1009 1012 8.322906 TCTTATTTATTAGAACATGCCGATGG 57.677 34.615 0.00 0.00 33.39 3.51
1121 1124 1.122019 CCCTACCTGATTCCCCTCGG 61.122 65.000 0.00 0.00 0.00 4.63
1749 1801 6.351117 GGCAGTACTACAGACAAATAGGAGTT 60.351 42.308 0.00 0.00 0.00 3.01
2681 5117 7.682787 AGGAAAGAGAGAAAATATGCCTAGA 57.317 36.000 0.00 0.00 0.00 2.43
2961 5429 7.084486 GGAAAACCACATTTGTGTATCTTCTC 58.916 38.462 9.66 0.00 44.21 2.87
3158 5628 1.409381 GGAGGAAAATGAGAGCAGGGG 60.409 57.143 0.00 0.00 0.00 4.79
3297 5768 1.004862 GACCTTTCCTTCTTCCTGGGG 59.995 57.143 0.00 0.00 0.00 4.96
3842 6313 2.192263 GATGAACCTGAGGGAGGAAGT 58.808 52.381 2.38 0.00 46.33 3.01
4220 6743 2.261671 GCGAACGAGGGCAGAGAA 59.738 61.111 0.00 0.00 0.00 2.87
4221 6744 1.374252 GCGAACGAGGGCAGAGAAA 60.374 57.895 0.00 0.00 0.00 2.52
4222 6745 0.949105 GCGAACGAGGGCAGAGAAAA 60.949 55.000 0.00 0.00 0.00 2.29
4223 6746 1.508632 CGAACGAGGGCAGAGAAAAA 58.491 50.000 0.00 0.00 0.00 1.94
4314 7519 1.338136 CGGGAGGTGGGAGCAAGTAT 61.338 60.000 0.00 0.00 0.00 2.12
4365 7570 2.095110 GTGGGACGAAAATAAAACCCGG 60.095 50.000 0.00 0.00 40.08 5.73
4393 7598 4.398358 CGGACTACCAACTGAGACATTAGA 59.602 45.833 0.00 0.00 35.59 2.10
4402 7607 7.094118 ACCAACTGAGACATTAGAAGTAGAGAC 60.094 40.741 0.00 0.00 0.00 3.36
4403 7608 7.122055 CCAACTGAGACATTAGAAGTAGAGACT 59.878 40.741 0.00 0.00 37.59 3.24
4404 7609 9.168451 CAACTGAGACATTAGAAGTAGAGACTA 57.832 37.037 0.00 0.00 33.58 2.59
4405 7610 8.958119 ACTGAGACATTAGAAGTAGAGACTAG 57.042 38.462 0.00 0.00 33.58 2.57
4406 7611 7.990886 ACTGAGACATTAGAAGTAGAGACTAGG 59.009 40.741 0.00 0.00 33.58 3.02
4407 7612 6.768861 TGAGACATTAGAAGTAGAGACTAGGC 59.231 42.308 0.00 0.00 33.58 3.93
4408 7613 6.066032 AGACATTAGAAGTAGAGACTAGGCC 58.934 44.000 0.00 0.00 33.58 5.19
4409 7614 5.141910 ACATTAGAAGTAGAGACTAGGCCC 58.858 45.833 0.00 0.00 33.58 5.80
4410 7615 5.103430 ACATTAGAAGTAGAGACTAGGCCCT 60.103 44.000 0.00 0.00 33.58 5.19
4411 7616 3.588210 AGAAGTAGAGACTAGGCCCTC 57.412 52.381 0.00 0.00 33.58 4.30
4412 7617 3.128049 AGAAGTAGAGACTAGGCCCTCT 58.872 50.000 13.05 13.05 42.02 3.69
4413 7618 3.137728 AGAAGTAGAGACTAGGCCCTCTC 59.862 52.174 12.01 12.43 40.06 3.20
4414 7619 1.778484 AGTAGAGACTAGGCCCTCTCC 59.222 57.143 12.01 2.26 40.06 3.71
4415 7620 1.495574 GTAGAGACTAGGCCCTCTCCA 59.504 57.143 12.01 0.22 40.06 3.86
4416 7621 0.260523 AGAGACTAGGCCCTCTCCAC 59.739 60.000 15.83 0.00 34.94 4.02
4417 7622 0.757561 GAGACTAGGCCCTCTCCACC 60.758 65.000 0.00 0.00 0.00 4.61
4418 7623 1.001760 GACTAGGCCCTCTCCACCA 59.998 63.158 0.00 0.00 0.00 4.17
4419 7624 0.399233 GACTAGGCCCTCTCCACCAT 60.399 60.000 0.00 0.00 0.00 3.55
4420 7625 0.399233 ACTAGGCCCTCTCCACCATC 60.399 60.000 0.00 0.00 0.00 3.51
4421 7626 1.457643 TAGGCCCTCTCCACCATCG 60.458 63.158 0.00 0.00 0.00 3.84
4422 7627 2.946988 TAGGCCCTCTCCACCATCGG 62.947 65.000 0.00 0.00 0.00 4.18
4423 7628 3.083997 GCCCTCTCCACCATCGGT 61.084 66.667 0.00 0.00 35.62 4.69
4424 7629 3.095347 GCCCTCTCCACCATCGGTC 62.095 68.421 0.00 0.00 31.02 4.79
4425 7630 1.685765 CCCTCTCCACCATCGGTCA 60.686 63.158 0.00 0.00 31.02 4.02
4426 7631 1.517832 CCTCTCCACCATCGGTCAC 59.482 63.158 0.00 0.00 31.02 3.67
4427 7632 1.517832 CTCTCCACCATCGGTCACC 59.482 63.158 0.00 0.00 31.02 4.02
4428 7633 1.229051 TCTCCACCATCGGTCACCA 60.229 57.895 0.00 0.00 31.02 4.17
4429 7634 1.219124 CTCCACCATCGGTCACCAG 59.781 63.158 0.00 0.00 31.02 4.00
4430 7635 1.229051 TCCACCATCGGTCACCAGA 60.229 57.895 0.00 0.00 31.02 3.86
4431 7636 1.219124 CCACCATCGGTCACCAGAG 59.781 63.158 0.00 0.00 31.02 3.35
4432 7637 1.448540 CACCATCGGTCACCAGAGC 60.449 63.158 0.00 0.00 38.87 4.09
4438 7643 4.285851 GGTCACCAGAGCGAAAGG 57.714 61.111 0.00 0.00 31.89 3.11
4439 7644 2.035442 GGTCACCAGAGCGAAAGGC 61.035 63.158 0.00 0.00 44.05 4.35
4448 7653 3.787458 GCGAAAGGCGAAGAGGAG 58.213 61.111 0.00 0.00 44.57 3.69
4449 7654 1.215647 GCGAAAGGCGAAGAGGAGA 59.784 57.895 0.00 0.00 44.57 3.71
4450 7655 1.079317 GCGAAAGGCGAAGAGGAGAC 61.079 60.000 0.00 0.00 44.57 3.36
4451 7656 0.798771 CGAAAGGCGAAGAGGAGACG 60.799 60.000 0.00 0.00 44.57 4.18
4452 7657 0.526662 GAAAGGCGAAGAGGAGACGA 59.473 55.000 0.00 0.00 0.00 4.20
4453 7658 1.135333 GAAAGGCGAAGAGGAGACGAT 59.865 52.381 0.00 0.00 0.00 3.73
4454 7659 0.741915 AAGGCGAAGAGGAGACGATC 59.258 55.000 0.00 0.00 0.00 3.69
4464 7669 1.433879 GAGACGATCCACAGACCCG 59.566 63.158 0.00 0.00 0.00 5.28
4465 7670 1.304217 AGACGATCCACAGACCCGT 60.304 57.895 0.00 0.00 37.35 5.28
4466 7671 1.139095 GACGATCCACAGACCCGTC 59.861 63.158 0.00 0.00 41.23 4.79
4467 7672 2.102357 CGATCCACAGACCCGTCG 59.898 66.667 0.00 0.00 34.09 5.12
4468 7673 2.404186 CGATCCACAGACCCGTCGA 61.404 63.158 0.00 0.00 34.09 4.20
4469 7674 1.725557 CGATCCACAGACCCGTCGAT 61.726 60.000 0.00 0.00 34.09 3.59
4470 7675 0.249073 GATCCACAGACCCGTCGATG 60.249 60.000 0.00 0.00 34.09 3.84
4471 7676 1.676678 ATCCACAGACCCGTCGATGG 61.677 60.000 17.27 17.27 39.40 3.51
4472 7677 2.348104 CCACAGACCCGTCGATGGA 61.348 63.158 25.65 0.00 40.02 3.41
4473 7678 1.139734 CACAGACCCGTCGATGGAG 59.860 63.158 25.65 16.69 34.09 3.86
4474 7679 1.001269 ACAGACCCGTCGATGGAGA 60.001 57.895 25.65 0.00 34.09 3.71
4475 7680 0.395862 ACAGACCCGTCGATGGAGAT 60.396 55.000 25.65 9.93 34.09 2.75
4476 7681 0.747255 CAGACCCGTCGATGGAGATT 59.253 55.000 25.65 6.01 34.09 2.40
4477 7682 1.954382 CAGACCCGTCGATGGAGATTA 59.046 52.381 25.65 0.00 34.09 1.75
4478 7683 2.361119 CAGACCCGTCGATGGAGATTAA 59.639 50.000 25.65 0.00 34.09 1.40
4479 7684 2.623889 AGACCCGTCGATGGAGATTAAG 59.376 50.000 25.65 8.69 34.09 1.85
4480 7685 1.687123 ACCCGTCGATGGAGATTAAGG 59.313 52.381 25.65 7.94 0.00 2.69
4481 7686 1.605712 CCCGTCGATGGAGATTAAGGC 60.606 57.143 25.65 0.00 0.00 4.35
4482 7687 1.409412 CGTCGATGGAGATTAAGGCG 58.591 55.000 0.00 0.00 0.00 5.52
4483 7688 1.001706 CGTCGATGGAGATTAAGGCGA 60.002 52.381 0.00 0.00 0.00 5.54
4484 7689 2.667137 GTCGATGGAGATTAAGGCGAG 58.333 52.381 0.00 0.00 0.00 5.03
4485 7690 1.613925 TCGATGGAGATTAAGGCGAGG 59.386 52.381 0.00 0.00 0.00 4.63
4486 7691 1.613925 CGATGGAGATTAAGGCGAGGA 59.386 52.381 0.00 0.00 0.00 3.71
4487 7692 2.035961 CGATGGAGATTAAGGCGAGGAA 59.964 50.000 0.00 0.00 0.00 3.36
4488 7693 3.492656 CGATGGAGATTAAGGCGAGGAAA 60.493 47.826 0.00 0.00 0.00 3.13
4489 7694 3.543680 TGGAGATTAAGGCGAGGAAAG 57.456 47.619 0.00 0.00 0.00 2.62
4490 7695 2.838202 TGGAGATTAAGGCGAGGAAAGT 59.162 45.455 0.00 0.00 0.00 2.66
4491 7696 3.118738 TGGAGATTAAGGCGAGGAAAGTC 60.119 47.826 0.00 0.00 0.00 3.01
4492 7697 3.117046 GAGATTAAGGCGAGGAAAGTCG 58.883 50.000 0.00 0.00 43.08 4.18
4498 7703 3.932289 CGAGGAAAGTCGCGTGTT 58.068 55.556 5.77 0.00 32.22 3.32
4499 7704 2.222592 CGAGGAAAGTCGCGTGTTT 58.777 52.632 5.77 7.10 32.22 2.83
4500 7705 0.111266 CGAGGAAAGTCGCGTGTTTG 60.111 55.000 5.77 0.00 32.22 2.93
4501 7706 1.214367 GAGGAAAGTCGCGTGTTTGA 58.786 50.000 5.77 0.00 0.00 2.69
4502 7707 1.192534 GAGGAAAGTCGCGTGTTTGAG 59.807 52.381 5.77 0.00 0.00 3.02
4503 7708 0.384353 GGAAAGTCGCGTGTTTGAGC 60.384 55.000 5.77 0.00 0.00 4.26
4504 7709 0.303493 GAAAGTCGCGTGTTTGAGCA 59.697 50.000 5.77 0.00 0.00 4.26
4505 7710 0.027586 AAAGTCGCGTGTTTGAGCAC 59.972 50.000 5.77 0.00 36.12 4.40
4506 7711 1.772063 AAGTCGCGTGTTTGAGCACC 61.772 55.000 5.77 0.00 36.08 5.01
4507 7712 2.108157 TCGCGTGTTTGAGCACCT 59.892 55.556 5.77 0.00 36.08 4.00
4508 7713 1.522806 TCGCGTGTTTGAGCACCTT 60.523 52.632 5.77 0.00 36.08 3.50
4509 7714 1.369209 CGCGTGTTTGAGCACCTTG 60.369 57.895 0.00 0.00 36.08 3.61
4510 7715 1.727467 GCGTGTTTGAGCACCTTGT 59.273 52.632 0.00 0.00 36.08 3.16
4511 7716 0.941542 GCGTGTTTGAGCACCTTGTA 59.058 50.000 0.00 0.00 36.08 2.41
4512 7717 1.332375 GCGTGTTTGAGCACCTTGTAA 59.668 47.619 0.00 0.00 36.08 2.41
4513 7718 2.602217 GCGTGTTTGAGCACCTTGTAAG 60.602 50.000 0.00 0.00 36.08 2.34
4514 7719 2.612212 CGTGTTTGAGCACCTTGTAAGT 59.388 45.455 0.00 0.00 36.08 2.24
4515 7720 3.805422 CGTGTTTGAGCACCTTGTAAGTA 59.195 43.478 0.00 0.00 36.08 2.24
4516 7721 4.451096 CGTGTTTGAGCACCTTGTAAGTAT 59.549 41.667 0.00 0.00 36.08 2.12
4517 7722 5.049680 CGTGTTTGAGCACCTTGTAAGTATT 60.050 40.000 0.00 0.00 36.08 1.89
4518 7723 6.371389 GTGTTTGAGCACCTTGTAAGTATTC 58.629 40.000 0.00 0.00 33.53 1.75
4519 7724 5.472137 TGTTTGAGCACCTTGTAAGTATTCC 59.528 40.000 0.00 0.00 0.00 3.01
4520 7725 4.216411 TGAGCACCTTGTAAGTATTCCC 57.784 45.455 0.00 0.00 0.00 3.97
4521 7726 3.585289 TGAGCACCTTGTAAGTATTCCCA 59.415 43.478 0.00 0.00 0.00 4.37
4522 7727 3.939592 GAGCACCTTGTAAGTATTCCCAC 59.060 47.826 0.00 0.00 0.00 4.61
4523 7728 3.587506 AGCACCTTGTAAGTATTCCCACT 59.412 43.478 0.00 0.00 0.00 4.00
4524 7729 4.781087 AGCACCTTGTAAGTATTCCCACTA 59.219 41.667 0.00 0.00 0.00 2.74
4525 7730 5.104900 AGCACCTTGTAAGTATTCCCACTAG 60.105 44.000 0.00 0.00 0.00 2.57
4526 7731 5.338137 GCACCTTGTAAGTATTCCCACTAGT 60.338 44.000 0.00 0.00 0.00 2.57
4527 7732 6.106673 CACCTTGTAAGTATTCCCACTAGTG 58.893 44.000 16.34 16.34 0.00 2.74
4528 7733 6.021030 ACCTTGTAAGTATTCCCACTAGTGA 58.979 40.000 24.68 4.71 0.00 3.41
4529 7734 6.499350 ACCTTGTAAGTATTCCCACTAGTGAA 59.501 38.462 24.68 11.80 0.00 3.18
4530 7735 7.182206 ACCTTGTAAGTATTCCCACTAGTGAAT 59.818 37.037 24.68 17.81 35.48 2.57
4531 7736 8.047310 CCTTGTAAGTATTCCCACTAGTGAATT 58.953 37.037 24.68 11.41 33.46 2.17
4532 7737 8.786826 TTGTAAGTATTCCCACTAGTGAATTG 57.213 34.615 24.68 7.15 33.46 2.32
4533 7738 7.913789 TGTAAGTATTCCCACTAGTGAATTGT 58.086 34.615 24.68 8.45 33.46 2.71
4534 7739 8.380099 TGTAAGTATTCCCACTAGTGAATTGTT 58.620 33.333 24.68 14.02 33.46 2.83
4535 7740 7.923414 AAGTATTCCCACTAGTGAATTGTTC 57.077 36.000 24.68 8.69 33.46 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 166 2.108075 TGTGGTTTGATGAGATGGTGGT 59.892 45.455 0.00 0.00 0.00 4.16
171 172 4.371624 TCTTGGTGTGGTTTGATGAGAT 57.628 40.909 0.00 0.00 0.00 2.75
249 250 2.794103 CATGTCCTTTGTCATGGGTCA 58.206 47.619 0.00 0.00 38.10 4.02
625 628 5.106157 GGTATGTGCAGCAACATCTTTTAGT 60.106 40.000 12.13 0.00 41.09 2.24
746 749 3.019964 TGTGATGAGCCACACAACC 57.980 52.632 0.00 0.00 42.72 3.77
868 871 6.183361 GGGACTGTGGTGGATTAGAAGATATT 60.183 42.308 0.00 0.00 0.00 1.28
887 890 5.413309 ACATAGTCAGAAAAGAGGGACTG 57.587 43.478 0.00 0.00 41.55 3.51
1121 1124 4.261656 CCCTGTAGGTTCTGATCATACGTC 60.262 50.000 0.00 0.00 0.00 4.34
2681 5117 7.005709 AGCAACAGTTGTAGTAAGAACCTAT 57.994 36.000 14.88 0.00 29.18 2.57
2765 5232 0.337428 AAATCCAAGAGCAGGGGCAT 59.663 50.000 0.00 0.00 44.61 4.40
3158 5628 3.567797 GGATGTTCGGCTCGCAGC 61.568 66.667 0.11 0.11 41.46 5.25
3170 5640 4.552365 CGCCAGCGATGGGGATGT 62.552 66.667 30.84 0.00 43.67 3.06
3934 6405 2.721167 CCGCCATCGACCTCCAAGA 61.721 63.158 0.00 0.00 38.10 3.02
4222 6745 4.871822 CCTAACCTCCCTCCATCATTTTT 58.128 43.478 0.00 0.00 0.00 1.94
4223 6746 3.373110 GCCTAACCTCCCTCCATCATTTT 60.373 47.826 0.00 0.00 0.00 1.82
4224 6747 2.175715 GCCTAACCTCCCTCCATCATTT 59.824 50.000 0.00 0.00 0.00 2.32
4225 6748 1.777272 GCCTAACCTCCCTCCATCATT 59.223 52.381 0.00 0.00 0.00 2.57
4226 6749 1.439543 GCCTAACCTCCCTCCATCAT 58.560 55.000 0.00 0.00 0.00 2.45
4227 6750 1.048724 CGCCTAACCTCCCTCCATCA 61.049 60.000 0.00 0.00 0.00 3.07
4228 6751 1.049289 ACGCCTAACCTCCCTCCATC 61.049 60.000 0.00 0.00 0.00 3.51
4229 6752 1.003051 ACGCCTAACCTCCCTCCAT 59.997 57.895 0.00 0.00 0.00 3.41
4230 6753 1.684734 GACGCCTAACCTCCCTCCA 60.685 63.158 0.00 0.00 0.00 3.86
4231 6754 2.433146 GGACGCCTAACCTCCCTCC 61.433 68.421 0.00 0.00 0.00 4.30
4232 6755 2.783288 CGGACGCCTAACCTCCCTC 61.783 68.421 0.00 0.00 0.00 4.30
4233 6756 2.758737 CGGACGCCTAACCTCCCT 60.759 66.667 0.00 0.00 0.00 4.20
4234 6757 4.525949 GCGGACGCCTAACCTCCC 62.526 72.222 5.20 0.00 34.56 4.30
4235 6758 4.867599 CGCGGACGCCTAACCTCC 62.868 72.222 11.42 0.00 37.98 4.30
4236 6759 4.867599 CCGCGGACGCCTAACCTC 62.868 72.222 24.07 0.00 38.22 3.85
4365 7570 0.038892 TCAGTTGGTAGTCCGCGTTC 60.039 55.000 4.92 0.00 36.30 3.95
4393 7598 2.176148 GGAGAGGGCCTAGTCTCTACTT 59.824 54.545 21.92 0.00 40.12 2.24
4402 7607 1.467678 CGATGGTGGAGAGGGCCTAG 61.468 65.000 5.73 0.00 0.00 3.02
4403 7608 1.457643 CGATGGTGGAGAGGGCCTA 60.458 63.158 5.73 0.00 0.00 3.93
4404 7609 2.765807 CGATGGTGGAGAGGGCCT 60.766 66.667 5.25 5.25 0.00 5.19
4405 7610 3.866582 CCGATGGTGGAGAGGGCC 61.867 72.222 0.00 0.00 0.00 5.80
4406 7611 3.083997 ACCGATGGTGGAGAGGGC 61.084 66.667 0.00 0.00 32.98 5.19
4407 7612 1.685765 TGACCGATGGTGGAGAGGG 60.686 63.158 0.00 0.00 35.25 4.30
4408 7613 1.517832 GTGACCGATGGTGGAGAGG 59.482 63.158 0.00 0.00 35.25 3.69
4409 7614 1.257750 TGGTGACCGATGGTGGAGAG 61.258 60.000 0.00 0.00 35.25 3.20
4410 7615 1.229051 TGGTGACCGATGGTGGAGA 60.229 57.895 0.00 0.00 35.25 3.71
4411 7616 1.219124 CTGGTGACCGATGGTGGAG 59.781 63.158 0.00 0.00 35.25 3.86
4412 7617 1.229051 TCTGGTGACCGATGGTGGA 60.229 57.895 0.00 0.00 35.25 4.02
4413 7618 1.219124 CTCTGGTGACCGATGGTGG 59.781 63.158 0.00 0.00 35.25 4.61
4414 7619 1.448540 GCTCTGGTGACCGATGGTG 60.449 63.158 0.00 0.00 35.25 4.17
4415 7620 2.982130 GCTCTGGTGACCGATGGT 59.018 61.111 0.00 0.00 39.44 3.55
4416 7621 2.202797 CGCTCTGGTGACCGATGG 60.203 66.667 0.00 0.00 0.00 3.51
4417 7622 0.389817 TTTCGCTCTGGTGACCGATG 60.390 55.000 0.00 0.00 31.43 3.84
4418 7623 0.108615 CTTTCGCTCTGGTGACCGAT 60.109 55.000 0.00 0.00 31.43 4.18
4419 7624 1.289066 CTTTCGCTCTGGTGACCGA 59.711 57.895 0.00 0.00 0.00 4.69
4420 7625 1.738099 CCTTTCGCTCTGGTGACCG 60.738 63.158 0.00 0.00 0.00 4.79
4421 7626 2.035442 GCCTTTCGCTCTGGTGACC 61.035 63.158 0.00 0.00 0.00 4.02
4422 7627 2.383527 CGCCTTTCGCTCTGGTGAC 61.384 63.158 0.00 0.00 33.56 3.67
4423 7628 2.048222 CGCCTTTCGCTCTGGTGA 60.048 61.111 0.00 0.00 33.56 4.02
4424 7629 1.630244 CTTCGCCTTTCGCTCTGGTG 61.630 60.000 0.00 0.00 38.27 4.17
4425 7630 1.374758 CTTCGCCTTTCGCTCTGGT 60.375 57.895 0.00 0.00 38.27 4.00
4426 7631 1.079819 TCTTCGCCTTTCGCTCTGG 60.080 57.895 0.00 0.00 38.27 3.86
4427 7632 1.080995 CCTCTTCGCCTTTCGCTCTG 61.081 60.000 0.00 0.00 38.27 3.35
4428 7633 1.216710 CCTCTTCGCCTTTCGCTCT 59.783 57.895 0.00 0.00 38.27 4.09
4429 7634 0.804156 CTCCTCTTCGCCTTTCGCTC 60.804 60.000 0.00 0.00 38.27 5.03
4430 7635 1.216710 CTCCTCTTCGCCTTTCGCT 59.783 57.895 0.00 0.00 38.27 4.93
4431 7636 1.079317 GTCTCCTCTTCGCCTTTCGC 61.079 60.000 0.00 0.00 38.27 4.70
4432 7637 0.798771 CGTCTCCTCTTCGCCTTTCG 60.799 60.000 0.00 0.00 40.15 3.46
4433 7638 0.526662 TCGTCTCCTCTTCGCCTTTC 59.473 55.000 0.00 0.00 0.00 2.62
4434 7639 1.135333 GATCGTCTCCTCTTCGCCTTT 59.865 52.381 0.00 0.00 0.00 3.11
4435 7640 0.741915 GATCGTCTCCTCTTCGCCTT 59.258 55.000 0.00 0.00 0.00 4.35
4436 7641 1.104577 GGATCGTCTCCTCTTCGCCT 61.105 60.000 0.32 0.00 41.29 5.52
4437 7642 1.360911 GGATCGTCTCCTCTTCGCC 59.639 63.158 0.32 0.00 41.29 5.54
4438 7643 0.248702 GTGGATCGTCTCCTCTTCGC 60.249 60.000 8.01 0.00 45.21 4.70
4439 7644 1.064803 CTGTGGATCGTCTCCTCTTCG 59.935 57.143 8.01 0.00 45.21 3.79
4440 7645 2.098443 GTCTGTGGATCGTCTCCTCTTC 59.902 54.545 8.01 0.00 45.21 2.87
4441 7646 2.096248 GTCTGTGGATCGTCTCCTCTT 58.904 52.381 8.01 0.00 45.21 2.85
4442 7647 1.683629 GGTCTGTGGATCGTCTCCTCT 60.684 57.143 8.01 0.00 45.21 3.69
4443 7648 0.741915 GGTCTGTGGATCGTCTCCTC 59.258 60.000 8.01 5.45 45.21 3.71
4444 7649 0.684805 GGGTCTGTGGATCGTCTCCT 60.685 60.000 8.01 0.00 45.21 3.69
4445 7650 1.817209 GGGTCTGTGGATCGTCTCC 59.183 63.158 0.53 0.53 45.19 3.71
4446 7651 1.313812 ACGGGTCTGTGGATCGTCTC 61.314 60.000 0.00 0.00 32.17 3.36
4447 7652 1.304217 ACGGGTCTGTGGATCGTCT 60.304 57.895 0.00 0.00 32.17 4.18
4448 7653 1.139095 GACGGGTCTGTGGATCGTC 59.861 63.158 0.00 0.00 40.54 4.20
4449 7654 2.697761 CGACGGGTCTGTGGATCGT 61.698 63.158 0.00 0.00 37.10 3.73
4450 7655 1.725557 ATCGACGGGTCTGTGGATCG 61.726 60.000 0.00 0.00 32.69 3.69
4451 7656 0.249073 CATCGACGGGTCTGTGGATC 60.249 60.000 4.77 0.00 35.46 3.36
4452 7657 1.676678 CCATCGACGGGTCTGTGGAT 61.677 60.000 11.61 2.27 37.74 3.41
4453 7658 2.348104 CCATCGACGGGTCTGTGGA 61.348 63.158 11.61 0.00 35.27 4.02
4454 7659 2.184322 CCATCGACGGGTCTGTGG 59.816 66.667 0.00 5.38 0.00 4.17
4455 7660 1.139734 CTCCATCGACGGGTCTGTG 59.860 63.158 0.00 0.00 0.00 3.66
4456 7661 0.395862 ATCTCCATCGACGGGTCTGT 60.396 55.000 0.00 0.00 0.00 3.41
4457 7662 0.747255 AATCTCCATCGACGGGTCTG 59.253 55.000 0.00 0.00 0.00 3.51
4458 7663 2.359981 TAATCTCCATCGACGGGTCT 57.640 50.000 0.00 0.00 0.00 3.85
4459 7664 2.288273 CCTTAATCTCCATCGACGGGTC 60.288 54.545 0.00 0.00 0.00 4.46
4460 7665 1.687123 CCTTAATCTCCATCGACGGGT 59.313 52.381 0.00 0.00 0.00 5.28
4461 7666 1.605712 GCCTTAATCTCCATCGACGGG 60.606 57.143 0.00 0.00 0.00 5.28
4462 7667 1.784525 GCCTTAATCTCCATCGACGG 58.215 55.000 0.00 0.00 0.00 4.79
4463 7668 1.001706 TCGCCTTAATCTCCATCGACG 60.002 52.381 0.00 0.00 0.00 5.12
4464 7669 2.608261 CCTCGCCTTAATCTCCATCGAC 60.608 54.545 0.00 0.00 0.00 4.20
4465 7670 1.613925 CCTCGCCTTAATCTCCATCGA 59.386 52.381 0.00 0.00 0.00 3.59
4466 7671 1.613925 TCCTCGCCTTAATCTCCATCG 59.386 52.381 0.00 0.00 0.00 3.84
4467 7672 3.753294 TTCCTCGCCTTAATCTCCATC 57.247 47.619 0.00 0.00 0.00 3.51
4468 7673 3.456277 ACTTTCCTCGCCTTAATCTCCAT 59.544 43.478 0.00 0.00 0.00 3.41
4469 7674 2.838202 ACTTTCCTCGCCTTAATCTCCA 59.162 45.455 0.00 0.00 0.00 3.86
4470 7675 3.459145 GACTTTCCTCGCCTTAATCTCC 58.541 50.000 0.00 0.00 0.00 3.71
4471 7676 3.117046 CGACTTTCCTCGCCTTAATCTC 58.883 50.000 0.00 0.00 0.00 2.75
4472 7677 3.166489 CGACTTTCCTCGCCTTAATCT 57.834 47.619 0.00 0.00 0.00 2.40
4481 7686 0.111266 CAAACACGCGACTTTCCTCG 60.111 55.000 15.93 0.00 36.70 4.63
4482 7687 1.192534 CTCAAACACGCGACTTTCCTC 59.807 52.381 15.93 0.00 0.00 3.71
4483 7688 1.217882 CTCAAACACGCGACTTTCCT 58.782 50.000 15.93 0.00 0.00 3.36
4484 7689 0.384353 GCTCAAACACGCGACTTTCC 60.384 55.000 15.93 0.00 0.00 3.13
4485 7690 0.303493 TGCTCAAACACGCGACTTTC 59.697 50.000 15.93 0.00 0.00 2.62
4486 7691 0.027586 GTGCTCAAACACGCGACTTT 59.972 50.000 15.93 6.52 0.00 2.66
4487 7692 1.641677 GTGCTCAAACACGCGACTT 59.358 52.632 15.93 0.00 0.00 3.01
4488 7693 2.244651 GGTGCTCAAACACGCGACT 61.245 57.895 15.93 0.00 41.65 4.18
4489 7694 1.772063 AAGGTGCTCAAACACGCGAC 61.772 55.000 15.93 0.00 41.65 5.19
4490 7695 1.522806 AAGGTGCTCAAACACGCGA 60.523 52.632 15.93 0.00 41.65 5.87
4491 7696 1.369209 CAAGGTGCTCAAACACGCG 60.369 57.895 3.53 3.53 41.65 6.01
4492 7697 0.941542 TACAAGGTGCTCAAACACGC 59.058 50.000 0.00 0.00 41.65 5.34
4493 7698 2.612212 ACTTACAAGGTGCTCAAACACG 59.388 45.455 0.00 0.00 41.65 4.49
4494 7699 5.941948 ATACTTACAAGGTGCTCAAACAC 57.058 39.130 0.00 0.00 39.94 3.32
4495 7700 5.472137 GGAATACTTACAAGGTGCTCAAACA 59.528 40.000 0.00 0.00 0.00 2.83
4496 7701 5.106277 GGGAATACTTACAAGGTGCTCAAAC 60.106 44.000 0.00 0.00 0.00 2.93
4497 7702 5.007682 GGGAATACTTACAAGGTGCTCAAA 58.992 41.667 0.00 0.00 0.00 2.69
4498 7703 4.042311 TGGGAATACTTACAAGGTGCTCAA 59.958 41.667 0.00 0.00 0.00 3.02
4499 7704 3.585289 TGGGAATACTTACAAGGTGCTCA 59.415 43.478 0.00 0.00 0.00 4.26
4500 7705 3.939592 GTGGGAATACTTACAAGGTGCTC 59.060 47.826 0.00 0.00 0.00 4.26
4501 7706 3.587506 AGTGGGAATACTTACAAGGTGCT 59.412 43.478 0.00 0.00 0.00 4.40
4502 7707 3.951663 AGTGGGAATACTTACAAGGTGC 58.048 45.455 0.00 0.00 0.00 5.01
4503 7708 6.070995 TCACTAGTGGGAATACTTACAAGGTG 60.071 42.308 22.48 0.00 32.19 4.00
4504 7709 6.021030 TCACTAGTGGGAATACTTACAAGGT 58.979 40.000 22.48 0.00 32.19 3.50
4505 7710 6.540438 TCACTAGTGGGAATACTTACAAGG 57.460 41.667 22.48 0.00 32.19 3.61
4506 7711 8.883731 CAATTCACTAGTGGGAATACTTACAAG 58.116 37.037 22.48 0.00 33.57 3.16
4507 7712 8.380099 ACAATTCACTAGTGGGAATACTTACAA 58.620 33.333 22.48 5.45 33.57 2.41
4508 7713 7.913789 ACAATTCACTAGTGGGAATACTTACA 58.086 34.615 22.48 0.00 33.57 2.41
4509 7714 8.788325 AACAATTCACTAGTGGGAATACTTAC 57.212 34.615 22.48 0.00 33.57 2.34
4511 7716 7.923414 GAACAATTCACTAGTGGGAATACTT 57.077 36.000 22.48 10.04 33.57 2.24


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

AutoCloner maintained by Alex Coulton.