Multiple sequence alignment - TraesCS7A01G187800

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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 TraesCS7A01G187800 chr7A 100.000 5109 0 0 1 5109 143143674 143148782 0.000000e+00 9435.0
1 TraesCS7A01G187800 chr7A 85.525 753 60 21 1299 2035 182095111 182094392 0.000000e+00 741.0
2 TraesCS7A01G187800 chr7A 81.884 690 89 20 4394 5062 143182700 143183374 2.690000e-152 549.0
3 TraesCS7A01G187800 chr7A 87.332 371 28 10 4034 4388 143181813 143182180 1.710000e-109 407.0
4 TraesCS7A01G187800 chr7D 91.854 3106 116 50 533 3593 141189143 141186130 0.000000e+00 4207.0
5 TraesCS7A01G187800 chr7D 92.885 1518 66 16 3583 5087 141186096 141184608 0.000000e+00 2167.0
6 TraesCS7A01G187800 chr7D 93.017 401 19 4 1 401 141190130 141189739 1.230000e-160 577.0
7 TraesCS7A01G187800 chr7D 80.882 612 77 23 4384 4972 141343164 141343758 3.630000e-121 446.0
8 TraesCS7A01G187800 chr7D 88.197 305 29 5 127 431 141189503 141189206 1.750000e-94 357.0
9 TraesCS7A01G187800 chr7D 84.681 235 13 7 4328 4553 141136524 141136304 4.010000e-51 213.0
10 TraesCS7A01G187800 chr7D 91.429 70 6 0 438 507 76929619 76929550 4.210000e-16 97.1
11 TraesCS7A01G187800 chr7B 91.600 3107 113 46 543 3593 106339386 106342400 0.000000e+00 4156.0
12 TraesCS7A01G187800 chr7B 92.303 1520 68 20 3583 5068 106342434 106343938 0.000000e+00 2113.0
13 TraesCS7A01G187800 chr7B 84.758 433 41 13 1 428 106336929 106337341 1.320000e-110 411.0
14 TraesCS7A01G187800 chr7B 86.933 375 36 7 4319 4683 106576752 106577123 4.760000e-110 409.0
15 TraesCS7A01G187800 chr7B 89.667 300 25 6 4256 4553 106541633 106541928 1.340000e-100 377.0
16 TraesCS7A01G187800 chr7B 82.584 178 25 4 4907 5083 106577226 106577398 8.860000e-33 152.0
17 TraesCS7A01G187800 chr2A 86.148 758 57 17 1299 2035 21408688 21409418 0.000000e+00 774.0
18 TraesCS7A01G187800 chr2A 84.477 612 53 18 1439 2035 282967507 282968091 2.670000e-157 566.0
19 TraesCS7A01G187800 chr2A 86.667 405 32 8 1299 1694 64490597 64490988 3.650000e-116 429.0
20 TraesCS7A01G187800 chr2A 75.733 375 60 17 4731 5081 754393951 754393584 5.290000e-35 159.0
21 TraesCS7A01G187800 chr2A 89.474 76 6 2 435 508 622261239 622261314 1.510000e-15 95.3
22 TraesCS7A01G187800 chr2B 87.160 405 30 8 1299 1694 171091320 171091711 1.690000e-119 440.0
23 TraesCS7A01G187800 chr2B 86.301 73 9 1 437 508 738679177 738679249 1.530000e-10 78.7
24 TraesCS7A01G187800 chr5B 86.914 405 31 8 1299 1694 685116694 685117085 7.860000e-118 435.0
25 TraesCS7A01G187800 chr4A 86.914 405 31 8 1299 1694 599536024 599535633 7.860000e-118 435.0
26 TraesCS7A01G187800 chr4A 81.319 91 11 5 434 523 82260024 82260109 9.180000e-08 69.4
27 TraesCS7A01G187800 chr3A 86.667 405 32 8 1299 1694 700004683 700004292 3.650000e-116 429.0
28 TraesCS7A01G187800 chr3A 86.250 80 10 1 429 507 354424269 354424190 9.110000e-13 86.1
29 TraesCS7A01G187800 chr3A 87.671 73 7 2 438 508 264954401 264954329 3.280000e-12 84.2
30 TraesCS7A01G187800 chr1D 88.679 212 23 1 3036 3247 398049933 398049723 1.830000e-64 257.0
31 TraesCS7A01G187800 chr1D 87.264 212 26 1 3036 3247 398053123 398052913 1.840000e-59 241.0
32 TraesCS7A01G187800 chr1A 87.363 182 22 1 4887 5067 562965706 562965887 1.860000e-49 207.0
33 TraesCS7A01G187800 chr6D 84.058 207 31 2 3001 3206 394921086 394920881 1.120000e-46 198.0
34 TraesCS7A01G187800 chr2D 77.344 384 53 20 4726 5083 622935654 622935279 4.040000e-46 196.0
35 TraesCS7A01G187800 chr6A 91.667 72 5 1 437 507 552997030 552996959 1.170000e-16 99.0
36 TraesCS7A01G187800 chr3D 88.889 72 6 2 437 507 353233200 353233130 2.530000e-13 87.9
37 TraesCS7A01G187800 chr1B 86.486 74 9 1 438 511 622608085 622608013 4.240000e-11 80.5


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 TraesCS7A01G187800 chr7A 143143674 143148782 5108 False 9435.000000 9435 100.000000 1 5109 1 chr7A.!!$F1 5108
1 TraesCS7A01G187800 chr7A 182094392 182095111 719 True 741.000000 741 85.525000 1299 2035 1 chr7A.!!$R1 736
2 TraesCS7A01G187800 chr7A 143181813 143183374 1561 False 478.000000 549 84.608000 4034 5062 2 chr7A.!!$F2 1028
3 TraesCS7A01G187800 chr7D 141184608 141190130 5522 True 1827.000000 4207 91.488250 1 5087 4 chr7D.!!$R3 5086
4 TraesCS7A01G187800 chr7D 141343164 141343758 594 False 446.000000 446 80.882000 4384 4972 1 chr7D.!!$F1 588
5 TraesCS7A01G187800 chr7B 106336929 106343938 7009 False 2226.666667 4156 89.553667 1 5068 3 chr7B.!!$F2 5067
6 TraesCS7A01G187800 chr7B 106576752 106577398 646 False 280.500000 409 84.758500 4319 5083 2 chr7B.!!$F3 764
7 TraesCS7A01G187800 chr2A 21408688 21409418 730 False 774.000000 774 86.148000 1299 2035 1 chr2A.!!$F1 736
8 TraesCS7A01G187800 chr2A 282967507 282968091 584 False 566.000000 566 84.477000 1439 2035 1 chr2A.!!$F3 596
9 TraesCS7A01G187800 chr1D 398049723 398053123 3400 True 249.000000 257 87.971500 3036 3247 2 chr1D.!!$R1 211

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
255 258 0.179181 TCGTCGAACATACTCCGTGC 60.179 55.0 0.00 0.00 0.00 5.34 F
258 261 0.455464 TCGAACATACTCCGTGCACG 60.455 55.0 31.77 31.77 39.44 5.34 F
878 3359 0.671251 GCTGTATGTAGAGCGAGCCT 59.329 55.0 0.00 0.00 32.78 4.58 F
2585 5101 0.178970 ATCAATCTCCATGCCAGGCC 60.179 55.0 9.64 0.00 0.00 5.19 F
3451 6015 0.255033 GGAGTCGTTGGGGGCTTAAT 59.745 55.0 0.00 0.00 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 4752 1.663695 ATTAGCGAATGTCAACCCCG 58.336 50.000 0.00 0.00 0.0 5.73 R
2335 4851 4.946157 CCATGTTCTAAGAAACTCCAGCAT 59.054 41.667 0.00 0.00 0.0 3.79 R
2731 5247 0.677842 GCAAATGGATGGATGGAGGC 59.322 55.000 0.00 0.00 0.0 4.70 R
3757 6366 0.387929 CTGGTCCTACGTGTGTGTGT 59.612 55.000 0.00 0.00 0.0 3.72 R
4324 6953 0.786581 CACACACACGAAGCTAGCTG 59.213 55.000 20.16 9.46 0.0 4.24 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
40 41 0.593008 TACGTGTGAGTGTGTGACGC 60.593 55.000 0.00 0.00 33.34 5.19
41 42 2.916556 CGTGTGAGTGTGTGACGCG 61.917 63.158 3.53 3.53 37.28 6.01
42 43 1.587876 GTGTGAGTGTGTGACGCGA 60.588 57.895 15.93 0.00 33.01 5.87
63 64 1.615392 TCGATGCTCATGTGATCCGAT 59.385 47.619 0.00 0.00 0.00 4.18
86 87 8.555361 CGATTAAGACCTACTACTGGTTACTAC 58.445 40.741 0.00 0.00 38.03 2.73
166 169 4.596180 CAGCCAATAAGCGCGCCG 62.596 66.667 30.33 11.33 38.01 6.46
238 241 7.067008 ACCAACTAAAATACCTGGATTTCATCG 59.933 37.037 0.00 0.00 0.00 3.84
241 244 5.734855 AAAATACCTGGATTTCATCGTCG 57.265 39.130 0.00 0.00 0.00 5.12
242 245 4.665833 AATACCTGGATTTCATCGTCGA 57.334 40.909 0.00 0.00 0.00 4.20
255 258 0.179181 TCGTCGAACATACTCCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
258 261 0.455464 TCGAACATACTCCGTGCACG 60.455 55.000 31.77 31.77 39.44 5.34
332 335 2.143122 TCCAGCAACAACTCAATCGAC 58.857 47.619 0.00 0.00 0.00 4.20
392 395 6.352016 AGATCTGAAGCAATATGGACGTAT 57.648 37.500 0.00 0.00 0.00 3.06
417 922 8.552469 TCGTATACTAGTTTATTTTCTGCGAC 57.448 34.615 0.00 0.00 0.00 5.19
443 948 5.956642 GCATACTTGCTATCTAGTACTCCC 58.043 45.833 0.00 0.00 45.77 4.30
446 951 7.576098 GCATACTTGCTATCTAGTACTCCCTTC 60.576 44.444 0.00 0.00 45.77 3.46
447 952 4.822896 ACTTGCTATCTAGTACTCCCTTCG 59.177 45.833 0.00 0.00 0.00 3.79
448 953 4.434545 TGCTATCTAGTACTCCCTTCGT 57.565 45.455 0.00 0.00 0.00 3.85
449 954 5.557576 TGCTATCTAGTACTCCCTTCGTA 57.442 43.478 0.00 0.00 0.00 3.43
452 957 7.002879 TGCTATCTAGTACTCCCTTCGTAAAT 58.997 38.462 0.00 0.00 0.00 1.40
480 985 9.680315 AATATAAGAGTGTTTAGATCACTACGC 57.320 33.333 0.00 0.00 44.68 4.42
481 986 5.646577 AAGAGTGTTTAGATCACTACGCT 57.353 39.130 0.00 1.13 44.68 5.07
482 987 5.646577 AGAGTGTTTAGATCACTACGCTT 57.353 39.130 0.00 0.00 44.68 4.68
484 989 6.456501 AGAGTGTTTAGATCACTACGCTTTT 58.543 36.000 0.00 0.00 44.68 2.27
485 990 7.600065 AGAGTGTTTAGATCACTACGCTTTTA 58.400 34.615 0.00 0.00 44.68 1.52
503 1008 8.480501 ACGCTTTTATATTAGTTTACAGAGGGA 58.519 33.333 0.00 0.00 0.00 4.20
504 1009 8.979574 CGCTTTTATATTAGTTTACAGAGGGAG 58.020 37.037 0.00 0.00 0.00 4.30
505 1010 9.833917 GCTTTTATATTAGTTTACAGAGGGAGT 57.166 33.333 0.00 0.00 0.00 3.85
528 1033 8.537049 AGTACTGTACTATTCTAGTAGCATCG 57.463 38.462 18.42 0.00 41.59 3.84
531 1036 6.205076 ACTGTACTATTCTAGTAGCATCGGTG 59.795 42.308 0.00 0.00 41.59 4.94
540 1045 3.840991 AGTAGCATCGGTGGTAGGATTA 58.159 45.455 8.06 0.00 38.86 1.75
717 3197 3.700350 CCCTCCCTCCCTCCACCT 61.700 72.222 0.00 0.00 0.00 4.00
878 3359 0.671251 GCTGTATGTAGAGCGAGCCT 59.329 55.000 0.00 0.00 32.78 4.58
879 3360 1.880675 GCTGTATGTAGAGCGAGCCTA 59.119 52.381 0.00 0.00 32.78 3.93
884 3366 1.035932 TGTAGAGCGAGCCTACCACC 61.036 60.000 15.77 0.00 36.54 4.61
897 3379 1.601419 TACCACCGCTAGCTGACACC 61.601 60.000 13.57 0.00 0.00 4.16
1652 4150 6.042781 TGTTCAGTAGGACTTGGTTATCAACT 59.957 38.462 0.00 0.00 0.00 3.16
1665 4163 4.439776 GGTTATCAACTTGAACGTGCAAAC 59.560 41.667 10.87 3.45 0.00 2.93
1687 4185 6.084326 ACAAGAAATTGTCACGGCTTAATT 57.916 33.333 0.00 0.00 0.00 1.40
1689 4187 7.653647 ACAAGAAATTGTCACGGCTTAATTAA 58.346 30.769 0.00 0.00 0.00 1.40
1701 4209 9.997482 TCACGGCTTAATTAATTAAGTGATTTC 57.003 29.630 33.13 21.83 46.78 2.17
1716 4224 7.964604 AAGTGATTTCGAGCCTAATATAACC 57.035 36.000 0.00 0.00 0.00 2.85
1781 4289 7.572168 GCAGCAGATAATTAGTTAAGCTTAGCC 60.572 40.741 15.82 6.88 29.65 3.93
1989 4498 4.820894 TGGAGTAGCTAAAAGACTTCCC 57.179 45.455 0.00 0.00 0.00 3.97
1990 4499 4.426704 TGGAGTAGCTAAAAGACTTCCCT 58.573 43.478 0.00 0.00 0.00 4.20
1991 4500 4.223032 TGGAGTAGCTAAAAGACTTCCCTG 59.777 45.833 0.00 0.00 0.00 4.45
1992 4501 4.383226 GGAGTAGCTAAAAGACTTCCCTGG 60.383 50.000 0.00 0.00 0.00 4.45
2063 4572 6.582636 TGTAGCACTAGCAGCAAAGTAATAT 58.417 36.000 10.05 0.00 45.49 1.28
2064 4573 7.722363 TGTAGCACTAGCAGCAAAGTAATATA 58.278 34.615 10.05 0.00 45.49 0.86
2065 4574 8.367911 TGTAGCACTAGCAGCAAAGTAATATAT 58.632 33.333 10.05 0.00 45.49 0.86
2066 4575 9.856488 GTAGCACTAGCAGCAAAGTAATATATA 57.144 33.333 10.05 0.00 45.49 0.86
2140 4653 9.692325 ATTAAAATAGATGGATAAGGCATCTCC 57.308 33.333 0.00 0.00 37.01 3.71
2186 4702 3.274288 GAAGAACATGGCTTACCCTGAG 58.726 50.000 0.00 0.00 35.30 3.35
2318 4834 1.247567 GGGCATCCGTCCCAATTATG 58.752 55.000 0.00 0.00 43.37 1.90
2319 4835 1.202879 GGGCATCCGTCCCAATTATGA 60.203 52.381 0.00 0.00 43.37 2.15
2334 4850 7.833682 TCCCAATTATGACGGCATATGAATAAT 59.166 33.333 12.78 0.00 36.89 1.28
2335 4851 9.119418 CCCAATTATGACGGCATATGAATAATA 57.881 33.333 12.78 0.00 36.89 0.98
2360 4876 4.393371 GCTGGAGTTTCTTAGAACATGGTC 59.607 45.833 1.26 1.26 31.94 4.02
2361 4877 5.799213 CTGGAGTTTCTTAGAACATGGTCT 58.201 41.667 19.12 19.12 31.94 3.85
2362 4878 6.574465 GCTGGAGTTTCTTAGAACATGGTCTA 60.574 42.308 16.71 16.71 31.94 2.59
2363 4879 6.936279 TGGAGTTTCTTAGAACATGGTCTAG 58.064 40.000 19.51 13.93 31.80 2.43
2493 5009 1.811965 CGATCACAAATCAACCAGCCA 59.188 47.619 0.00 0.00 0.00 4.75
2524 5040 1.798079 GCCAGTAGTAGTCTTTCGGCG 60.798 57.143 0.00 0.00 0.00 6.46
2563 5079 2.123854 CCTGCATGCTCCAGCCAT 60.124 61.111 20.33 0.00 41.18 4.40
2577 5093 2.225041 CCAGCCATCCATCAATCTCCAT 60.225 50.000 0.00 0.00 0.00 3.41
2578 5094 2.820197 CAGCCATCCATCAATCTCCATG 59.180 50.000 0.00 0.00 0.00 3.66
2579 5095 1.544691 GCCATCCATCAATCTCCATGC 59.455 52.381 0.00 0.00 0.00 4.06
2580 5096 2.168496 CCATCCATCAATCTCCATGCC 58.832 52.381 0.00 0.00 0.00 4.40
2581 5097 2.490168 CCATCCATCAATCTCCATGCCA 60.490 50.000 0.00 0.00 0.00 4.92
2582 5098 2.651382 TCCATCAATCTCCATGCCAG 57.349 50.000 0.00 0.00 0.00 4.85
2583 5099 1.144298 TCCATCAATCTCCATGCCAGG 59.856 52.381 0.00 0.00 0.00 4.45
2584 5100 0.959553 CATCAATCTCCATGCCAGGC 59.040 55.000 3.66 3.66 0.00 4.85
2585 5101 0.178970 ATCAATCTCCATGCCAGGCC 60.179 55.000 9.64 0.00 0.00 5.19
2586 5102 1.229359 CAATCTCCATGCCAGGCCT 59.771 57.895 9.64 0.00 0.00 5.19
2587 5103 1.107538 CAATCTCCATGCCAGGCCTG 61.108 60.000 26.87 26.87 0.00 4.85
2722 5238 2.355756 TCGTACGATCTTTTCCCCGTAG 59.644 50.000 15.28 0.00 38.04 3.51
2764 5288 1.064505 CATTTGCTGGCCATAGACGTG 59.935 52.381 5.51 0.00 0.00 4.49
2845 5372 0.685097 GGGGGTCAAAAGAAAAGGCC 59.315 55.000 0.00 0.00 0.00 5.19
3103 5651 4.736896 GTGCTGGGGACGACGACC 62.737 72.222 7.89 7.89 0.00 4.79
3224 5772 1.398390 GTTCATTGATCCGCCACAGAC 59.602 52.381 0.00 0.00 0.00 3.51
3228 5776 4.176752 GATCCGCCACAGACCCCC 62.177 72.222 0.00 0.00 0.00 5.40
3261 5818 5.590530 TCTTGATTGGAGTTCTAGCTCTC 57.409 43.478 0.00 0.00 35.89 3.20
3262 5819 4.097135 TCTTGATTGGAGTTCTAGCTCTCG 59.903 45.833 0.00 0.00 35.89 4.04
3263 5820 2.690497 TGATTGGAGTTCTAGCTCTCGG 59.310 50.000 0.00 0.00 35.89 4.63
3264 5821 2.217510 TTGGAGTTCTAGCTCTCGGT 57.782 50.000 0.00 0.00 35.89 4.69
3266 5823 2.093106 TGGAGTTCTAGCTCTCGGTTC 58.907 52.381 0.00 0.00 35.89 3.62
3267 5824 2.291024 TGGAGTTCTAGCTCTCGGTTCT 60.291 50.000 0.00 0.00 35.89 3.01
3269 5826 3.181494 GGAGTTCTAGCTCTCGGTTCTTC 60.181 52.174 0.00 0.00 35.89 2.87
3270 5827 3.422796 AGTTCTAGCTCTCGGTTCTTCA 58.577 45.455 0.00 0.00 0.00 3.02
3271 5828 4.020543 AGTTCTAGCTCTCGGTTCTTCAT 58.979 43.478 0.00 0.00 0.00 2.57
3272 5829 5.194432 AGTTCTAGCTCTCGGTTCTTCATA 58.806 41.667 0.00 0.00 0.00 2.15
3273 5830 5.830991 AGTTCTAGCTCTCGGTTCTTCATAT 59.169 40.000 0.00 0.00 0.00 1.78
3274 5831 6.322712 AGTTCTAGCTCTCGGTTCTTCATATT 59.677 38.462 0.00 0.00 0.00 1.28
3275 5832 7.502895 AGTTCTAGCTCTCGGTTCTTCATATTA 59.497 37.037 0.00 0.00 0.00 0.98
3276 5833 8.301002 GTTCTAGCTCTCGGTTCTTCATATTAT 58.699 37.037 0.00 0.00 0.00 1.28
3277 5834 7.821652 TCTAGCTCTCGGTTCTTCATATTATG 58.178 38.462 0.00 0.00 0.00 1.90
3278 5835 5.233988 AGCTCTCGGTTCTTCATATTATGC 58.766 41.667 0.00 0.00 0.00 3.14
3279 5836 5.011533 AGCTCTCGGTTCTTCATATTATGCT 59.988 40.000 0.00 0.00 0.00 3.79
3280 5837 6.209589 AGCTCTCGGTTCTTCATATTATGCTA 59.790 38.462 0.00 0.00 0.00 3.49
3281 5838 6.309251 GCTCTCGGTTCTTCATATTATGCTAC 59.691 42.308 0.00 0.00 0.00 3.58
3282 5839 7.526142 TCTCGGTTCTTCATATTATGCTACT 57.474 36.000 0.00 0.00 0.00 2.57
3283 5840 8.631480 TCTCGGTTCTTCATATTATGCTACTA 57.369 34.615 0.00 0.00 0.00 1.82
3284 5841 9.244292 TCTCGGTTCTTCATATTATGCTACTAT 57.756 33.333 0.00 0.00 0.00 2.12
3450 6014 0.838987 AGGAGTCGTTGGGGGCTTAA 60.839 55.000 0.00 0.00 0.00 1.85
3451 6015 0.255033 GGAGTCGTTGGGGGCTTAAT 59.745 55.000 0.00 0.00 0.00 1.40
3452 6016 1.340697 GGAGTCGTTGGGGGCTTAATT 60.341 52.381 0.00 0.00 0.00 1.40
3453 6017 2.092807 GGAGTCGTTGGGGGCTTAATTA 60.093 50.000 0.00 0.00 0.00 1.40
3599 6207 2.338785 GGACCCAGCTTGCAAGAGC 61.339 63.158 30.39 16.76 43.02 4.09
3658 6266 7.550551 ACCTTACAAACAGATAGATGACACATG 59.449 37.037 0.00 0.00 0.00 3.21
4048 6657 0.248843 CGCAGAAGCTCTCCTCCTTT 59.751 55.000 0.00 0.00 39.10 3.11
4096 6705 1.736645 CATGGCCGTCGACGAGTTT 60.737 57.895 37.65 17.33 43.02 2.66
4214 6843 2.426425 CGTATACGAGCGCGGGAC 60.426 66.667 20.58 7.83 43.17 4.46
4322 6951 5.725325 AAGGAACTGAAGTAGTACTGGAC 57.275 43.478 5.39 0.00 40.86 4.02
4324 6953 3.500014 GAACTGAAGTAGTACTGGACGC 58.500 50.000 5.39 0.00 39.18 5.19
4347 6978 2.345641 GCTAGCTTCGTGTGTGTGTATG 59.654 50.000 7.70 0.00 0.00 2.39
4367 6998 1.067071 GCCATGGGTACGTAGATAGCC 60.067 57.143 15.13 0.00 42.14 3.93
4437 7588 1.142965 TGCCTACGCGCATGTGTAT 59.857 52.632 5.73 0.00 40.13 2.29
4483 7634 2.076100 CTGCGTCAGAGGTTGCATAAA 58.924 47.619 1.18 0.00 36.64 1.40
4488 7639 5.356751 TGCGTCAGAGGTTGCATAAATTTAT 59.643 36.000 4.81 4.81 31.31 1.40
4489 7640 6.540551 TGCGTCAGAGGTTGCATAAATTTATA 59.459 34.615 10.34 0.00 31.31 0.98
4590 7756 3.703001 AAAACTCGTGAGGTCATGGAT 57.297 42.857 1.43 0.00 33.80 3.41
4862 8060 2.704572 GCTAGAGCAAATCCACACACT 58.295 47.619 0.00 0.00 41.59 3.55
4873 8071 8.537016 AGCAAATCCACACACTAACTAGTAATA 58.463 33.333 0.00 0.00 34.13 0.98
4899 8111 6.594788 AGTTGATTTGATAGGCAACAATGT 57.405 33.333 0.00 0.00 42.16 2.71
4920 8132 2.969950 TGTTTAGTGAGCCTACCAGTGT 59.030 45.455 0.00 0.00 0.00 3.55
4921 8133 3.006537 TGTTTAGTGAGCCTACCAGTGTC 59.993 47.826 0.00 0.00 0.00 3.67
4933 8147 3.474798 ACCAGTGTCTCTCCCATAGAA 57.525 47.619 0.00 0.00 32.46 2.10
4935 8149 3.011821 ACCAGTGTCTCTCCCATAGAAGA 59.988 47.826 0.00 0.00 32.46 2.87
4947 8161 9.443246 CTCTCCCATAGAAGAGTGACAAGTCAC 62.443 48.148 22.30 22.30 45.76 3.67
4989 8204 6.937436 AGATTTCCTTGTTTAGTTTCGTGT 57.063 33.333 0.00 0.00 0.00 4.49
5000 8215 8.450385 TGTTTAGTTTCGTGTAAAACCTTTTG 57.550 30.769 0.00 0.00 39.46 2.44
5089 8305 9.847706 AAAAACGAATTATATGTATGTGCACAA 57.152 25.926 25.72 8.09 30.84 3.33
5090 8306 8.835467 AAACGAATTATATGTATGTGCACAAC 57.165 30.769 25.72 21.57 30.84 3.32
5091 8307 7.786178 ACGAATTATATGTATGTGCACAACT 57.214 32.000 25.72 11.27 30.84 3.16
5092 8308 8.880878 ACGAATTATATGTATGTGCACAACTA 57.119 30.769 25.72 10.09 30.84 2.24
5093 8309 9.320352 ACGAATTATATGTATGTGCACAACTAA 57.680 29.630 25.72 16.01 30.84 2.24
5100 8316 9.830975 ATATGTATGTGCACAACTAATAACAGA 57.169 29.630 25.72 15.52 30.84 3.41
5101 8317 7.971183 TGTATGTGCACAACTAATAACAGAA 57.029 32.000 25.72 0.00 0.00 3.02
5102 8318 8.384607 TGTATGTGCACAACTAATAACAGAAA 57.615 30.769 25.72 0.00 0.00 2.52
5103 8319 8.503196 TGTATGTGCACAACTAATAACAGAAAG 58.497 33.333 25.72 0.00 0.00 2.62
5104 8320 5.757886 TGTGCACAACTAATAACAGAAAGC 58.242 37.500 19.28 0.00 0.00 3.51
5105 8321 5.298026 TGTGCACAACTAATAACAGAAAGCA 59.702 36.000 19.28 0.00 0.00 3.91
5106 8322 5.625311 GTGCACAACTAATAACAGAAAGCAC 59.375 40.000 13.17 0.00 40.26 4.40
5107 8323 5.530915 TGCACAACTAATAACAGAAAGCACT 59.469 36.000 0.00 0.00 0.00 4.40
5108 8324 6.708502 TGCACAACTAATAACAGAAAGCACTA 59.291 34.615 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.991264 GGATCACATGAGCATCGATCG 59.009 52.381 9.36 9.36 38.61 3.69
41 42 1.991264 CGGATCACATGAGCATCGATC 59.009 52.381 0.00 9.40 38.61 3.69
42 43 1.615392 TCGGATCACATGAGCATCGAT 59.385 47.619 0.00 0.00 38.61 3.59
86 87 0.745845 GGGAGTACATGCTGCAGTGG 60.746 60.000 16.64 7.70 0.00 4.00
166 169 1.152673 GATTGGGTCCAGGGCATCC 60.153 63.158 0.00 0.00 0.00 3.51
206 209 3.694566 CAGGTATTTTAGTTGGTCCCAGC 59.305 47.826 0.00 0.00 0.00 4.85
211 214 7.696992 TGAAATCCAGGTATTTTAGTTGGTC 57.303 36.000 0.00 0.00 0.00 4.02
214 217 7.985476 ACGATGAAATCCAGGTATTTTAGTTG 58.015 34.615 0.00 0.00 41.39 3.16
216 219 6.479001 CGACGATGAAATCCAGGTATTTTAGT 59.521 38.462 0.00 0.00 41.39 2.24
238 241 0.989890 GTGCACGGAGTATGTTCGAC 59.010 55.000 0.00 0.00 41.61 4.20
241 244 1.708027 GCGTGCACGGAGTATGTTC 59.292 57.895 37.47 15.93 41.61 3.18
242 245 2.092291 CGCGTGCACGGAGTATGTT 61.092 57.895 37.47 0.00 41.61 2.71
255 258 2.951745 GAGATGCTCCGTCGCGTG 60.952 66.667 5.77 0.00 0.00 5.34
316 319 1.234821 TGGGTCGATTGAGTTGTTGC 58.765 50.000 0.00 0.00 0.00 4.17
322 325 2.218603 GTTGTGTTGGGTCGATTGAGT 58.781 47.619 0.00 0.00 0.00 3.41
325 328 1.222300 TCGTTGTGTTGGGTCGATTG 58.778 50.000 0.00 0.00 0.00 2.67
332 335 4.177026 TGTTTTTCATTCGTTGTGTTGGG 58.823 39.130 0.00 0.00 0.00 4.12
392 395 8.400947 AGTCGCAGAAAATAAACTAGTATACGA 58.599 33.333 0.00 0.00 39.69 3.43
458 963 6.754702 AGCGTAGTGATCTAAACACTCTTA 57.245 37.500 0.00 0.00 45.58 2.10
459 964 5.646577 AGCGTAGTGATCTAAACACTCTT 57.353 39.130 0.00 0.00 45.58 2.85
477 982 8.480501 TCCCTCTGTAAACTAATATAAAAGCGT 58.519 33.333 0.00 0.00 0.00 5.07
478 983 8.882415 TCCCTCTGTAAACTAATATAAAAGCG 57.118 34.615 0.00 0.00 0.00 4.68
479 984 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
488 993 7.465116 AGTACAGTACTCCCTCTGTAAACTAA 58.535 38.462 7.48 0.00 44.90 2.24
489 994 7.025520 AGTACAGTACTCCCTCTGTAAACTA 57.974 40.000 7.48 0.00 44.90 2.24
490 995 5.890049 AGTACAGTACTCCCTCTGTAAACT 58.110 41.667 7.48 1.89 44.90 2.66
492 997 8.334734 AGAATAGTACAGTACTCCCTCTGTAAA 58.665 37.037 16.91 0.00 44.90 2.01
493 998 7.870027 AGAATAGTACAGTACTCCCTCTGTAA 58.130 38.462 16.91 0.00 44.90 2.41
495 1000 6.330178 AGAATAGTACAGTACTCCCTCTGT 57.670 41.667 16.91 0.00 45.21 3.41
496 1001 7.972832 CTAGAATAGTACAGTACTCCCTCTG 57.027 44.000 16.91 8.36 40.14 3.35
528 1033 2.288886 GGATGCGAGTAATCCTACCACC 60.289 54.545 0.00 0.00 40.50 4.61
540 1045 0.322975 AAAGCTGACAGGATGCGAGT 59.677 50.000 4.26 0.00 42.53 4.18
584 3062 3.570638 CCAATCTGCCTGCGAGCG 61.571 66.667 0.00 0.00 34.65 5.03
585 3063 3.885521 GCCAATCTGCCTGCGAGC 61.886 66.667 0.00 0.00 0.00 5.03
634 3112 1.732917 CTGCCTTTGCGTTTGTGGA 59.267 52.632 0.00 0.00 41.78 4.02
773 3253 0.604780 TTGCTTGCCTGCTCTCTGTC 60.605 55.000 0.00 0.00 0.00 3.51
878 3359 1.601419 GGTGTCAGCTAGCGGTGGTA 61.601 60.000 14.70 0.00 39.09 3.25
879 3360 2.657237 GTGTCAGCTAGCGGTGGT 59.343 61.111 14.70 0.00 39.09 4.16
884 3366 4.175599 CTGTGGTGTCAGCTAGCG 57.824 61.111 9.55 4.60 0.00 4.26
897 3379 5.470437 AGATATGATCAATCAGCAAGCTGTG 59.530 40.000 20.34 13.03 43.96 3.66
1041 3523 3.487209 GGATCTCGTTCGAGTAGTTCACC 60.487 52.174 19.26 10.71 34.19 4.02
1216 3698 3.094058 GATCGATCGACCGCTGCG 61.094 66.667 22.06 16.34 0.00 5.18
1244 3726 2.097791 ACGTCCGAGCTAGCTAGAAAAG 59.902 50.000 25.15 16.06 0.00 2.27
1652 4150 4.926238 ACAATTTCTTGTTTGCACGTTCAA 59.074 33.333 0.00 0.00 43.05 2.69
1665 4163 8.687824 ATTAATTAAGCCGTGACAATTTCTTG 57.312 30.769 3.94 0.00 38.39 3.02
1694 4202 6.369065 CCTGGTTATATTAGGCTCGAAATCAC 59.631 42.308 0.00 0.00 0.00 3.06
1716 4224 2.504681 GCGTTTTGATGCCGCCTG 60.505 61.111 0.00 0.00 41.50 4.85
2116 4629 8.218423 TGGAGATGCCTTATCCATCTATTTTA 57.782 34.615 4.08 0.00 46.88 1.52
2140 4653 8.597167 TCCCTAATCATGGAATAGTTCTACATG 58.403 37.037 0.00 0.00 40.06 3.21
2186 4702 6.635755 AGTGGAGACTAATTAACAAGAGCTC 58.364 40.000 5.27 5.27 0.00 4.09
2236 4752 1.663695 ATTAGCGAATGTCAACCCCG 58.336 50.000 0.00 0.00 0.00 5.73
2334 4850 6.115446 CCATGTTCTAAGAAACTCCAGCATA 58.885 40.000 0.00 0.00 0.00 3.14
2335 4851 4.946157 CCATGTTCTAAGAAACTCCAGCAT 59.054 41.667 0.00 0.00 0.00 3.79
2360 4876 3.190874 GCTAATTATGCCCGCTAGCTAG 58.809 50.000 16.84 16.84 33.68 3.42
2361 4877 2.565391 TGCTAATTATGCCCGCTAGCTA 59.435 45.455 13.93 0.00 36.71 3.32
2362 4878 1.347707 TGCTAATTATGCCCGCTAGCT 59.652 47.619 13.93 0.00 36.71 3.32
2363 4879 1.808411 TGCTAATTATGCCCGCTAGC 58.192 50.000 4.06 4.06 36.38 3.42
2524 5040 3.198872 GAGGGACACATCGGAATCTTTC 58.801 50.000 0.00 0.00 0.00 2.62
2563 5079 1.144298 CCTGGCATGGAGATTGATGGA 59.856 52.381 0.00 0.00 0.00 3.41
2580 5096 1.589716 GCACAAAGTAGCCAGGCCTG 61.590 60.000 26.87 26.87 0.00 4.85
2581 5097 1.303643 GCACAAAGTAGCCAGGCCT 60.304 57.895 8.22 0.00 0.00 5.19
2582 5098 3.278157 GCACAAAGTAGCCAGGCC 58.722 61.111 8.22 0.00 0.00 5.19
2587 5103 1.266989 GTTGTCAGGCACAAAGTAGCC 59.733 52.381 0.00 0.00 46.90 3.93
2588 5104 1.946768 TGTTGTCAGGCACAAAGTAGC 59.053 47.619 0.00 0.00 46.90 3.58
2589 5105 2.290641 GGTGTTGTCAGGCACAAAGTAG 59.709 50.000 10.46 0.00 46.90 2.57
2590 5106 2.294074 GGTGTTGTCAGGCACAAAGTA 58.706 47.619 10.46 0.00 46.90 2.24
2725 5241 1.369321 GATGGATGGAGGCCGTCTC 59.631 63.158 0.00 0.00 39.36 3.36
2731 5247 0.677842 GCAAATGGATGGATGGAGGC 59.322 55.000 0.00 0.00 0.00 4.70
2764 5288 3.296516 GTGCATGCACGCTAAGTTC 57.703 52.632 33.20 9.23 37.19 3.01
2838 5365 2.343387 GGTGCAATGCGGCCTTTT 59.657 55.556 10.63 0.00 0.00 2.27
2927 5475 1.138047 CACGGATTGAGACGTACGCC 61.138 60.000 16.72 3.66 42.04 5.68
3136 5684 3.258123 TGTTGAAGGTGACGATGATCTCA 59.742 43.478 0.00 0.00 0.00 3.27
3211 5759 4.176752 GGGGGTCTGTGGCGGATC 62.177 72.222 0.00 0.00 0.00 3.36
3224 5772 5.240121 CAATCAAGAAATCAAAACAGGGGG 58.760 41.667 0.00 0.00 0.00 5.40
3228 5776 8.139989 AGAACTCCAATCAAGAAATCAAAACAG 58.860 33.333 0.00 0.00 0.00 3.16
3234 5782 6.715280 AGCTAGAACTCCAATCAAGAAATCA 58.285 36.000 0.00 0.00 0.00 2.57
3261 5818 8.873830 CCAATAGTAGCATAATATGAAGAACCG 58.126 37.037 4.14 0.00 31.44 4.44
3262 5819 9.726438 ACCAATAGTAGCATAATATGAAGAACC 57.274 33.333 4.14 0.00 31.44 3.62
3275 5832 9.799106 AGCAGAAATTAATACCAATAGTAGCAT 57.201 29.630 0.00 0.00 33.42 3.79
3276 5833 9.627123 AAGCAGAAATTAATACCAATAGTAGCA 57.373 29.630 0.00 0.00 33.42 3.49
3309 5869 4.603535 ACCCACCTGCACCAAGCC 62.604 66.667 0.00 0.00 44.83 4.35
3498 6062 8.480501 GGGTTGGTGATCAATTTACTAGTAGTA 58.519 37.037 5.90 5.90 37.73 1.82
3499 6063 7.037873 TGGGTTGGTGATCAATTTACTAGTAGT 60.038 37.037 8.14 8.14 37.73 2.73
3500 6064 7.280205 GTGGGTTGGTGATCAATTTACTAGTAG 59.720 40.741 0.00 0.00 37.73 2.57
3563 6127 2.335011 GGCCGTCACCTTTGCAAC 59.665 61.111 0.00 0.00 0.00 4.17
3658 6266 5.401531 TTGTCTATATACGGCCAGGAATC 57.598 43.478 2.24 0.00 0.00 2.52
3702 6311 9.901172 TCTTTCCTGTCTAGTATTATTTTTCCC 57.099 33.333 0.00 0.00 0.00 3.97
3757 6366 0.387929 CTGGTCCTACGTGTGTGTGT 59.612 55.000 0.00 0.00 0.00 3.72
3758 6367 0.671796 TCTGGTCCTACGTGTGTGTG 59.328 55.000 0.00 0.00 0.00 3.82
3759 6368 1.068127 GTTCTGGTCCTACGTGTGTGT 59.932 52.381 0.00 0.00 0.00 3.72
4096 6705 1.522092 GGCCGATCAGACATGGTCA 59.478 57.895 0.00 0.00 36.23 4.02
4214 6843 3.004315 ACTTTGACTGGTTACAAATGGCG 59.996 43.478 0.00 0.00 35.84 5.69
4278 6907 1.581402 CACAGAGCTCGCTCGTACG 60.581 63.158 9.53 9.53 46.90 3.67
4324 6953 0.786581 CACACACACGAAGCTAGCTG 59.213 55.000 20.16 9.46 0.00 4.24
4347 6978 1.067071 GGCTATCTACGTACCCATGGC 60.067 57.143 6.09 0.00 0.00 4.40
4367 6998 4.166523 CGTTACACCAGACATGTACTCAG 58.833 47.826 0.00 0.00 32.30 3.35
4590 7756 6.432403 AAATCTGCATGGAAAAAGGGTAAA 57.568 33.333 0.00 0.00 0.00 2.01
4654 7820 6.608610 TGTACGTCACTCAATATATCATCCG 58.391 40.000 0.00 0.00 0.00 4.18
4873 8071 8.752187 ACATTGTTGCCTATCAAATCAACTAAT 58.248 29.630 0.00 0.00 39.44 1.73
4899 8111 2.969950 ACACTGGTAGGCTCACTAAACA 59.030 45.455 0.00 0.00 32.37 2.83
4920 8132 4.592997 TGTCACTCTTCTATGGGAGAGA 57.407 45.455 20.61 0.00 34.93 3.10
4921 8133 4.709397 ACTTGTCACTCTTCTATGGGAGAG 59.291 45.833 12.70 12.70 34.93 3.20
4933 8147 7.865706 AAATTTTAGTGTGACTTGTCACTCT 57.134 32.000 28.96 28.96 42.77 3.24
4935 8149 9.120538 ACATAAATTTTAGTGTGACTTGTCACT 57.879 29.630 27.23 15.20 45.21 3.41
5000 8215 5.196695 AGGGCTCCTATCAATTTCTGAAAC 58.803 41.667 4.73 0.00 37.67 2.78
5014 8229 5.658198 TCTAGTGTATACAAGGGCTCCTA 57.342 43.478 7.25 2.34 31.13 2.94
5084 8300 6.002062 AGTGCTTTCTGTTATTAGTTGTGC 57.998 37.500 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.