Multiple sequence alignment - TraesCS5B01G318900

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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 TraesCS5B01G318900 chr5B 100.000 4450 0 0 768 5217 503213226 503217675 0.000000e+00 8218.0
1 TraesCS5B01G318900 chr5B 87.243 972 90 25 1840 2794 667673502 667674456 0.000000e+00 1077.0
2 TraesCS5B01G318900 chr5B 84.274 992 91 29 3413 4356 667675376 667676350 0.000000e+00 907.0
3 TraesCS5B01G318900 chr5B 100.000 381 0 0 1 381 503212459 503212839 0.000000e+00 704.0
4 TraesCS5B01G318900 chr5B 88.608 316 30 5 3106 3418 667674894 667675206 3.810000e-101 379.0
5 TraesCS5B01G318900 chr5B 85.714 294 31 5 2871 3163 667674601 667674884 3.050000e-77 300.0
6 TraesCS5B01G318900 chr5B 76.591 487 61 28 999 1467 667672240 667672691 8.800000e-53 219.0
7 TraesCS5B01G318900 chr5B 84.071 113 14 4 4651 4759 667676899 667677011 7.140000e-19 106.0
8 TraesCS5B01G318900 chr5B 79.389 131 18 4 2015 2136 673452536 673452406 3.350000e-12 84.2
9 TraesCS5B01G318900 chr5B 78.626 131 19 2 2015 2136 673422992 673422862 1.560000e-10 78.7
10 TraesCS5B01G318900 chr5B 93.878 49 3 0 2088 2136 673353079 673353031 2.010000e-09 75.0
11 TraesCS5B01G318900 chr5D 91.445 4512 194 61 780 5189 416412188 416416609 0.000000e+00 6017.0
12 TraesCS5B01G318900 chr5D 86.130 1031 105 27 1784 2794 529216487 529217499 0.000000e+00 1077.0
13 TraesCS5B01G318900 chr5D 84.686 986 87 32 3413 4352 529218344 529219311 0.000000e+00 926.0
14 TraesCS5B01G318900 chr5D 95.932 295 9 3 1 293 416411749 416412042 4.730000e-130 475.0
15 TraesCS5B01G318900 chr5D 76.434 488 58 33 999 1467 529215469 529215918 1.470000e-50 211.0
16 TraesCS5B01G318900 chr5D 86.131 137 15 3 4651 4783 529219905 529220041 1.510000e-30 145.0
17 TraesCS5B01G318900 chr5D 94.444 90 4 1 293 381 416412092 416412181 2.530000e-28 137.0
18 TraesCS5B01G318900 chr5D 80.916 131 16 2 2015 2136 533283991 533283861 1.550000e-15 95.3
19 TraesCS5B01G318900 chr5A 94.950 1307 48 3 3113 4409 529085722 529087020 0.000000e+00 2032.0
20 TraesCS5B01G318900 chr5A 90.214 981 62 11 778 1731 529083979 529084952 0.000000e+00 1249.0
21 TraesCS5B01G318900 chr5A 95.850 771 28 2 1954 2720 529084956 529085726 0.000000e+00 1243.0
22 TraesCS5B01G318900 chr5A 81.944 1523 176 45 1490 2974 657379186 657380647 0.000000e+00 1197.0
23 TraesCS5B01G318900 chr5A 83.581 1145 102 51 3132 4237 657380658 657381755 0.000000e+00 994.0
24 TraesCS5B01G318900 chr5A 85.065 462 29 10 4521 4958 529087252 529087697 8.020000e-118 435.0
25 TraesCS5B01G318900 chr5A 79.461 297 35 17 999 1286 657378658 657378937 2.480000e-43 187.0
26 TraesCS5B01G318900 chr5A 88.321 137 14 1 4650 4784 657382435 657382571 4.180000e-36 163.0
27 TraesCS5B01G318900 chr5A 96.629 89 3 0 293 381 529083889 529083977 1.170000e-31 148.0
28 TraesCS5B01G318900 chr5A 92.537 67 5 0 4966 5032 529087687 529087753 4.300000e-16 97.1
29 TraesCS5B01G318900 chr5A 94.595 37 2 0 4487 4523 529087058 529087094 2.030000e-04 58.4
30 TraesCS5B01G318900 chr4D 79.730 148 24 6 47 191 134122678 134122822 9.240000e-18 102.0
31 TraesCS5B01G318900 chr1D 94.118 51 2 1 3198 3248 37516654 37516703 5.600000e-10 76.8
32 TraesCS5B01G318900 chr1D 93.878 49 3 0 3200 3248 37528644 37528692 2.010000e-09 75.0
33 TraesCS5B01G318900 chr1A 94.118 51 2 1 3198 3248 36765343 36765392 5.600000e-10 76.8


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 TraesCS5B01G318900 chr5B 503212459 503217675 5216 False 4461.000000 8218 100.000000 1 5217 2 chr5B.!!$F1 5216
1 TraesCS5B01G318900 chr5B 667672240 667677011 4771 False 498.000000 1077 84.416833 999 4759 6 chr5B.!!$F2 3760
2 TraesCS5B01G318900 chr5D 416411749 416416609 4860 False 2209.666667 6017 93.940333 1 5189 3 chr5D.!!$F1 5188
3 TraesCS5B01G318900 chr5D 529215469 529220041 4572 False 589.750000 1077 83.345250 999 4783 4 chr5D.!!$F2 3784
4 TraesCS5B01G318900 chr5A 529083889 529087753 3864 False 751.785714 2032 92.834286 293 5032 7 chr5A.!!$F1 4739
5 TraesCS5B01G318900 chr5A 657378658 657382571 3913 False 635.250000 1197 83.326750 999 4784 4 chr5A.!!$F2 3785

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
380 433 0.250727 CTCTGCCGACCCCTCAAAAA 60.251 55.000 0.00 0.0 0.00 1.94 F
792 845 0.251742 AGAGAGACTGCTCCTGTGCT 60.252 55.000 0.00 0.0 42.30 4.40 F
1299 1408 0.443869 CTTGGGCGTTGACAGAATCG 59.556 55.000 0.00 0.0 0.00 3.34 F
1707 2313 0.178861 ACCCTGGATGACCTTCACCT 60.179 55.000 0.00 0.0 37.04 4.00 F
2710 3350 1.003003 GAAACTGGAAGGAGCTCTGCT 59.997 52.381 14.64 0.0 38.77 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1464 1.129811 GGCGTGTTATACAGTTGCACC 59.870 52.381 0.00 0.0 0.00 5.01 R
1693 2299 2.027192 TGCACTAAGGTGAAGGTCATCC 60.027 50.000 0.00 0.0 45.61 3.51 R
3278 4103 1.117150 GCTACTACCATCCCGGAACA 58.883 55.000 0.73 0.0 38.63 3.18 R
3327 4152 0.846427 TGGGGGAAATGGCTCAGAGT 60.846 55.000 0.00 0.0 0.00 3.24 R
4428 5498 0.033109 ATTCCCCCAAGGTAGCAAGC 60.033 55.000 0.00 0.0 36.75 4.01 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
138 141 2.603075 TGGAAGGTTTTCATGAGGGG 57.397 50.000 0.00 0.00 34.90 4.79
376 429 3.965026 CTCCTCTGCCGACCCCTCA 62.965 68.421 0.00 0.00 0.00 3.86
377 430 3.003173 CCTCTGCCGACCCCTCAA 61.003 66.667 0.00 0.00 0.00 3.02
378 431 2.592993 CCTCTGCCGACCCCTCAAA 61.593 63.158 0.00 0.00 0.00 2.69
379 432 1.374947 CTCTGCCGACCCCTCAAAA 59.625 57.895 0.00 0.00 0.00 2.44
380 433 0.250727 CTCTGCCGACCCCTCAAAAA 60.251 55.000 0.00 0.00 0.00 1.94
788 841 3.959535 AAAAGAGAGAGACTGCTCCTG 57.040 47.619 0.00 0.00 42.30 3.86
792 845 0.251742 AGAGAGACTGCTCCTGTGCT 60.252 55.000 0.00 0.00 42.30 4.40
973 1036 2.305607 CCCGAATCCTGGGTGGGAA 61.306 63.158 0.00 0.00 42.77 3.97
990 1053 2.076622 GAAGGAGATCTGCCGCGCTA 62.077 60.000 11.06 0.00 0.00 4.26
1183 1279 1.682323 CTTCTACTTCTCCCGGTAGGC 59.318 57.143 0.00 0.00 36.86 3.93
1193 1289 0.541863 CCCGGTAGGCAGTTGAGATT 59.458 55.000 0.00 0.00 35.76 2.40
1248 1344 6.500589 TCCAGAATTCCAGATAGGTTTAGG 57.499 41.667 0.65 0.00 39.02 2.69
1299 1408 0.443869 CTTGGGCGTTGACAGAATCG 59.556 55.000 0.00 0.00 0.00 3.34
1319 1428 5.398176 TCGTTGTTTACAAGTTACTGCTG 57.602 39.130 0.00 0.00 36.39 4.41
1322 1431 6.924612 TCGTTGTTTACAAGTTACTGCTGATA 59.075 34.615 0.00 0.00 36.39 2.15
1354 1464 0.613260 TCCAATTCTCCACTCCCACG 59.387 55.000 0.00 0.00 0.00 4.94
1376 1486 2.073056 TGCAACTGTATAACACGCCTG 58.927 47.619 0.00 0.00 0.00 4.85
1433 1560 3.615834 GCCATGAGATATGATCGCTGTCA 60.616 47.826 0.00 0.00 0.00 3.58
1470 1597 1.825090 CTGCCAAATGCTAGTGGTGA 58.175 50.000 0.00 0.00 42.00 4.02
1472 1882 1.202867 TGCCAAATGCTAGTGGTGACA 60.203 47.619 0.00 0.00 42.00 3.58
1486 1896 1.669779 GGTGACATGCTCAGCTGAATC 59.330 52.381 18.85 12.83 43.11 2.52
1507 1926 3.584406 TCCAGTCCACTTGATCTTGTGAT 59.416 43.478 16.45 3.88 36.38 3.06
1542 1961 6.678568 AAGGACATAGATAGATCAAGGTGG 57.321 41.667 0.00 0.00 0.00 4.61
1548 1967 0.469917 ATAGATCAAGGTGGCCGTGG 59.530 55.000 0.00 0.00 33.92 4.94
1552 1971 3.751246 CAAGGTGGCCGTGGCATG 61.751 66.667 13.76 0.00 44.11 4.06
1693 2299 4.332819 GCACTTAGCACTGTTTATACCCTG 59.667 45.833 0.00 0.00 44.79 4.45
1705 2311 5.123936 GTTTATACCCTGGATGACCTTCAC 58.876 45.833 0.00 0.00 37.04 3.18
1707 2313 0.178861 ACCCTGGATGACCTTCACCT 60.179 55.000 0.00 0.00 37.04 4.00
1747 2353 1.317613 TTGACCGATTGCTGCAAACT 58.682 45.000 20.06 3.30 0.00 2.66
1833 2452 4.578928 ACCTAATTTTATGTAGGGCTTGCG 59.421 41.667 2.04 0.00 41.16 4.85
1862 2481 2.132740 TCGTTTTGCATTCACCTTGC 57.867 45.000 0.00 0.00 40.55 4.01
1961 2580 4.632538 ACTTGTAGTTTTTGGTCAGCAC 57.367 40.909 0.00 0.00 0.00 4.40
1992 2611 2.046283 TCGTTGCTTCTGTGTACTCG 57.954 50.000 0.00 0.00 0.00 4.18
1996 2615 3.542704 CGTTGCTTCTGTGTACTCGTATC 59.457 47.826 0.00 0.00 0.00 2.24
2011 2630 6.804770 ACTCGTATCATCTCGTTAGCTTAT 57.195 37.500 0.00 0.00 0.00 1.73
2482 3121 9.602568 GCAGATCTATCTCATCATGTATGATTT 57.397 33.333 4.66 3.36 43.70 2.17
2710 3350 1.003003 GAAACTGGAAGGAGCTCTGCT 59.997 52.381 14.64 0.00 38.77 4.24
2719 3359 4.370917 GAAGGAGCTCTGCTTATTCTCTG 58.629 47.826 14.64 0.00 41.41 3.35
2758 3398 4.755123 ACCATAATTATAGTGGTTGCTCGC 59.245 41.667 3.78 0.00 43.44 5.03
2865 3505 3.019564 GGGGTCAATCAAGTCCTCATTG 58.980 50.000 0.00 0.00 0.00 2.82
2982 3745 9.672673 CTTATTCACTATTCTCTTTTTCCTGGA 57.327 33.333 0.00 0.00 0.00 3.86
3177 4001 2.845967 GTGTTCTCGTGTGCTTTGTTTG 59.154 45.455 0.00 0.00 0.00 2.93
3327 4152 5.235616 GTGATATGATTCGGCGAAAGGTTTA 59.764 40.000 27.40 13.74 0.00 2.01
3484 4495 6.582672 GTCTTAATTAACCAGTTTGCTCTTGC 59.417 38.462 0.00 0.00 40.20 4.01
3503 4514 5.428457 TCTTGCCAGGTCTAGAAATGGAATA 59.572 40.000 22.79 9.40 34.60 1.75
3592 4617 4.285863 AGTTTGGTATAGCTGAGCTCTCT 58.714 43.478 11.68 13.98 40.44 3.10
3662 4687 7.433680 AGCTTTTCTTTTAATCATGTTCCGTT 58.566 30.769 0.00 0.00 0.00 4.44
3663 4688 7.926018 AGCTTTTCTTTTAATCATGTTCCGTTT 59.074 29.630 0.00 0.00 0.00 3.60
3840 4865 2.094182 TCTGACTGGATCGTTTAGGTGC 60.094 50.000 0.00 0.00 0.00 5.01
4247 5314 3.367932 CACGGTAGATGCTTGTTAGTGTG 59.632 47.826 0.00 0.00 0.00 3.82
4248 5315 3.006537 ACGGTAGATGCTTGTTAGTGTGT 59.993 43.478 0.00 0.00 0.00 3.72
4249 5316 3.367932 CGGTAGATGCTTGTTAGTGTGTG 59.632 47.826 0.00 0.00 0.00 3.82
4250 5317 4.315803 GGTAGATGCTTGTTAGTGTGTGT 58.684 43.478 0.00 0.00 0.00 3.72
4381 5451 0.517316 GCATCTTGTGTTCCGTGACC 59.483 55.000 0.00 0.00 0.00 4.02
4398 5468 4.091509 CGTGACCTGTAATTACTCAACTGC 59.908 45.833 16.33 0.80 0.00 4.40
4399 5469 5.238583 GTGACCTGTAATTACTCAACTGCT 58.761 41.667 16.33 0.00 0.00 4.24
4400 5470 5.701290 GTGACCTGTAATTACTCAACTGCTT 59.299 40.000 16.33 0.00 0.00 3.91
4401 5471 5.700832 TGACCTGTAATTACTCAACTGCTTG 59.299 40.000 16.33 0.00 0.00 4.01
4402 5472 4.455877 ACCTGTAATTACTCAACTGCTTGC 59.544 41.667 16.33 0.00 0.00 4.01
4405 5475 6.183360 CCTGTAATTACTCAACTGCTTGCTAC 60.183 42.308 16.33 0.00 0.00 3.58
4408 5478 2.938956 ACTCAACTGCTTGCTACCTT 57.061 45.000 0.00 0.00 0.00 3.50
4411 5481 3.954258 ACTCAACTGCTTGCTACCTTTTT 59.046 39.130 0.00 0.00 0.00 1.94
4447 5604 0.033109 GCTTGCTACCTTGGGGGAAT 60.033 55.000 0.00 0.00 38.76 3.01
4461 5618 7.075009 ACCTTGGGGGAATTATATGACTGTATT 59.925 37.037 0.00 0.00 38.76 1.89
4463 5620 7.640577 TGGGGGAATTATATGACTGTATTGA 57.359 36.000 0.00 0.00 0.00 2.57
4464 5621 8.230848 TGGGGGAATTATATGACTGTATTGAT 57.769 34.615 0.00 0.00 0.00 2.57
4465 5622 8.108999 TGGGGGAATTATATGACTGTATTGATG 58.891 37.037 0.00 0.00 0.00 3.07
4466 5623 7.557719 GGGGGAATTATATGACTGTATTGATGG 59.442 40.741 0.00 0.00 0.00 3.51
4493 5661 4.637483 AGTTGGTCACTTGTGAACATTG 57.363 40.909 20.25 0.00 35.21 2.82
4617 5945 8.803397 AGTAAAAATACTCCAGGGAATAACAC 57.197 34.615 0.00 0.00 0.00 3.32
4727 6308 5.034554 AGAAGTTGCACAATGACAATACG 57.965 39.130 0.00 0.00 0.00 3.06
4829 6431 3.371965 CACAGTTAGCCCCTAGGACTTA 58.628 50.000 11.48 0.00 33.47 2.24
4847 6449 8.777578 AGGACTTAGATTTGTTAAAAAGGGTT 57.222 30.769 0.00 0.00 0.00 4.11
4857 6459 9.764363 ATTTGTTAAAAAGGGTTGAAGAGAATC 57.236 29.630 0.00 0.00 0.00 2.52
4858 6460 7.889873 TGTTAAAAAGGGTTGAAGAGAATCA 57.110 32.000 0.00 0.00 37.82 2.57
4874 6476 6.582636 AGAGAATCACTTGGTTAATATGCGA 58.417 36.000 0.00 0.00 37.82 5.10
4875 6477 7.047891 AGAGAATCACTTGGTTAATATGCGAA 58.952 34.615 0.00 0.00 37.82 4.70
4876 6478 7.552687 AGAGAATCACTTGGTTAATATGCGAAA 59.447 33.333 0.00 0.00 37.82 3.46
4877 6479 8.050778 AGAATCACTTGGTTAATATGCGAAAA 57.949 30.769 0.00 0.00 0.00 2.29
4878 6480 8.686334 AGAATCACTTGGTTAATATGCGAAAAT 58.314 29.630 0.00 0.00 0.00 1.82
4879 6481 8.856490 AATCACTTGGTTAATATGCGAAAATC 57.144 30.769 0.00 0.00 0.00 2.17
4880 6482 6.791303 TCACTTGGTTAATATGCGAAAATCC 58.209 36.000 0.00 0.00 0.00 3.01
4881 6483 5.681105 CACTTGGTTAATATGCGAAAATCCG 59.319 40.000 0.00 0.00 0.00 4.18
4882 6484 4.822036 TGGTTAATATGCGAAAATCCGG 57.178 40.909 0.00 0.00 0.00 5.14
4883 6485 4.452825 TGGTTAATATGCGAAAATCCGGA 58.547 39.130 6.61 6.61 0.00 5.14
4884 6486 4.273969 TGGTTAATATGCGAAAATCCGGAC 59.726 41.667 6.12 0.00 31.57 4.79
4885 6487 4.273969 GGTTAATATGCGAAAATCCGGACA 59.726 41.667 6.12 0.00 31.57 4.02
4951 6564 0.618458 GGCTACCCACAAGATCCACA 59.382 55.000 0.00 0.00 0.00 4.17
4952 6565 1.679032 GGCTACCCACAAGATCCACAC 60.679 57.143 0.00 0.00 0.00 3.82
4953 6566 1.003118 GCTACCCACAAGATCCACACA 59.997 52.381 0.00 0.00 0.00 3.72
4954 6567 2.699954 CTACCCACAAGATCCACACAC 58.300 52.381 0.00 0.00 0.00 3.82
4955 6568 0.843309 ACCCACAAGATCCACACACA 59.157 50.000 0.00 0.00 0.00 3.72
4956 6569 1.238439 CCCACAAGATCCACACACAC 58.762 55.000 0.00 0.00 0.00 3.82
4957 6570 1.238439 CCACAAGATCCACACACACC 58.762 55.000 0.00 0.00 0.00 4.16
4958 6571 1.476652 CCACAAGATCCACACACACCA 60.477 52.381 0.00 0.00 0.00 4.17
4959 6572 1.603802 CACAAGATCCACACACACCAC 59.396 52.381 0.00 0.00 0.00 4.16
4960 6573 1.211703 ACAAGATCCACACACACCACA 59.788 47.619 0.00 0.00 0.00 4.17
4961 6574 2.296792 CAAGATCCACACACACCACAA 58.703 47.619 0.00 0.00 0.00 3.33
4962 6575 2.260844 AGATCCACACACACCACAAG 57.739 50.000 0.00 0.00 0.00 3.16
4963 6576 1.768275 AGATCCACACACACCACAAGA 59.232 47.619 0.00 0.00 0.00 3.02
4964 6577 2.172505 AGATCCACACACACCACAAGAA 59.827 45.455 0.00 0.00 0.00 2.52
4965 6578 1.745232 TCCACACACACCACAAGAAC 58.255 50.000 0.00 0.00 0.00 3.01
4966 6579 0.738389 CCACACACACCACAAGAACC 59.262 55.000 0.00 0.00 0.00 3.62
4967 6580 1.458398 CACACACACCACAAGAACCA 58.542 50.000 0.00 0.00 0.00 3.67
4968 6581 1.132262 CACACACACCACAAGAACCAC 59.868 52.381 0.00 0.00 0.00 4.16
4994 6607 1.302511 GCCAAGGAGAGAAACGCCA 60.303 57.895 0.00 0.00 40.96 5.69
5019 6632 5.825507 TGAGATTGTCTACGATCTGTCATG 58.174 41.667 16.00 0.00 44.86 3.07
5047 6673 0.824595 TTCTCCGACTTCACCGTGGA 60.825 55.000 0.00 0.00 0.00 4.02
5077 6703 4.646492 ACCAAGAGTCTCAAAACAAATGCT 59.354 37.500 1.94 0.00 0.00 3.79
5079 6705 4.234530 AGAGTCTCAAAACAAATGCTGC 57.765 40.909 1.94 0.00 0.00 5.25
5089 6715 3.523606 ACAAATGCTGCACAAGAAACA 57.476 38.095 3.57 0.00 0.00 2.83
5093 6719 2.780065 TGCTGCACAAGAAACATGTC 57.220 45.000 0.00 0.00 0.00 3.06
5096 6722 1.603802 CTGCACAAGAAACATGTCGGT 59.396 47.619 0.00 0.00 0.00 4.69
5118 6745 6.365520 GGTATATCCAAGAAATCCACCAACT 58.634 40.000 0.00 0.00 35.97 3.16
5150 6778 0.802607 GGCAGCTCCGACTTCGTTAG 60.803 60.000 0.00 0.00 37.74 2.34
5171 6799 2.737039 GCAAGCCTCGTAGGAGAAAGAG 60.737 54.545 13.99 0.00 43.27 2.85
5189 6817 2.339712 GCGCACCTTGCACCAATT 59.660 55.556 0.30 0.00 45.36 2.32
5190 6818 1.583986 GCGCACCTTGCACCAATTA 59.416 52.632 0.30 0.00 45.36 1.40
5191 6819 0.038709 GCGCACCTTGCACCAATTAA 60.039 50.000 0.30 0.00 45.36 1.40
5192 6820 1.696988 CGCACCTTGCACCAATTAAC 58.303 50.000 0.00 0.00 45.36 2.01
5193 6821 1.668628 CGCACCTTGCACCAATTAACC 60.669 52.381 0.00 0.00 45.36 2.85
5194 6822 1.342819 GCACCTTGCACCAATTAACCA 59.657 47.619 0.00 0.00 44.26 3.67
5195 6823 2.224161 GCACCTTGCACCAATTAACCAA 60.224 45.455 0.00 0.00 44.26 3.67
5196 6824 3.556843 GCACCTTGCACCAATTAACCAAT 60.557 43.478 0.00 0.00 44.26 3.16
5197 6825 4.322349 GCACCTTGCACCAATTAACCAATA 60.322 41.667 0.00 0.00 44.26 1.90
5198 6826 5.626578 GCACCTTGCACCAATTAACCAATAT 60.627 40.000 0.00 0.00 44.26 1.28
5199 6827 6.042143 CACCTTGCACCAATTAACCAATATC 58.958 40.000 0.00 0.00 0.00 1.63
5200 6828 5.163561 ACCTTGCACCAATTAACCAATATCG 60.164 40.000 0.00 0.00 0.00 2.92
5201 6829 4.909696 TGCACCAATTAACCAATATCGG 57.090 40.909 0.00 0.00 0.00 4.18
5202 6830 4.274147 TGCACCAATTAACCAATATCGGT 58.726 39.130 0.00 0.00 42.71 4.69
5203 6831 5.437946 TGCACCAATTAACCAATATCGGTA 58.562 37.500 0.00 0.00 38.76 4.02
5204 6832 5.886474 TGCACCAATTAACCAATATCGGTAA 59.114 36.000 0.00 0.00 38.76 2.85
5205 6833 6.183360 TGCACCAATTAACCAATATCGGTAAC 60.183 38.462 0.00 0.00 38.76 2.50
5206 6834 6.183360 GCACCAATTAACCAATATCGGTAACA 60.183 38.462 0.00 0.00 38.76 2.41
5207 6835 7.628794 GCACCAATTAACCAATATCGGTAACAA 60.629 37.037 0.00 0.00 38.76 2.83
5208 6836 7.913297 CACCAATTAACCAATATCGGTAACAAG 59.087 37.037 0.00 0.00 38.76 3.16
5209 6837 6.915843 CCAATTAACCAATATCGGTAACAAGC 59.084 38.462 0.00 0.00 38.76 4.01
5210 6838 6.628919 ATTAACCAATATCGGTAACAAGCC 57.371 37.500 0.00 0.00 38.76 4.35
5211 6839 2.927028 ACCAATATCGGTAACAAGCCC 58.073 47.619 0.00 0.00 37.57 5.19
5212 6840 2.227194 CCAATATCGGTAACAAGCCCC 58.773 52.381 0.00 0.00 0.00 5.80
5213 6841 1.871039 CAATATCGGTAACAAGCCCCG 59.129 52.381 0.00 0.00 0.00 5.73
5214 6842 1.125633 ATATCGGTAACAAGCCCCGT 58.874 50.000 0.00 0.00 0.00 5.28
5215 6843 1.774110 TATCGGTAACAAGCCCCGTA 58.226 50.000 0.00 0.00 0.00 4.02
5216 6844 0.462789 ATCGGTAACAAGCCCCGTAG 59.537 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.862149 AGAAGGATAGGAAAACTACAAAAGAAA 57.138 29.630 0.00 0.00 33.70 2.52
124 127 1.075536 AGTGACCCCCTCATGAAAACC 59.924 52.381 0.00 0.00 0.00 3.27
223 226 5.474825 TGGCCCAAATACTTCGAATTTTTC 58.525 37.500 0.00 0.00 0.00 2.29
229 232 4.582656 CCATTATGGCCCAAATACTTCGAA 59.417 41.667 0.00 0.00 0.00 3.71
310 363 1.219213 ACCCAAACCTGACCAATTGGA 59.781 47.619 31.22 8.67 44.01 3.53
767 820 3.645687 ACAGGAGCAGTCTCTCTCTTTTT 59.354 43.478 0.00 0.00 39.31 1.94
772 825 0.173255 GCACAGGAGCAGTCTCTCTC 59.827 60.000 0.00 0.00 39.31 3.20
774 827 0.108709 CAGCACAGGAGCAGTCTCTC 60.109 60.000 0.00 0.00 39.31 3.20
776 829 1.741032 GCAGCACAGGAGCAGTCTC 60.741 63.158 0.00 0.00 38.62 3.36
792 845 2.680352 GAGAGTGGAGGTCCGGCA 60.680 66.667 0.00 0.00 39.43 5.69
908 971 2.190488 GACAGGGGAGAGCTTGGGTG 62.190 65.000 0.00 0.00 0.00 4.61
913 976 2.654079 CGCAGACAGGGGAGAGCTT 61.654 63.158 0.00 0.00 0.00 3.74
973 1036 2.519541 TAGCGCGGCAGATCTCCT 60.520 61.111 8.83 0.00 0.00 3.69
990 1053 1.102154 CAGTCTCCATCGAGCAGAGT 58.898 55.000 8.48 1.87 35.94 3.24
1029 1099 0.396556 TGATGCTGTACTCCGGCCTA 60.397 55.000 0.00 0.00 45.48 3.93
1193 1289 2.307768 CTCCGCCCTACAGAGATAACA 58.692 52.381 0.00 0.00 0.00 2.41
1248 1344 2.472909 CGGAAAATCTGAGCCGGCC 61.473 63.158 26.15 15.80 40.08 6.13
1299 1408 7.015877 GCTATCAGCAGTAACTTGTAAACAAC 58.984 38.462 0.00 0.00 41.89 3.32
1354 1464 1.129811 GGCGTGTTATACAGTTGCACC 59.870 52.381 0.00 0.00 0.00 5.01
1389 1499 6.829298 TGGCCTCAATCCAACGTAATAATTAA 59.171 34.615 3.32 0.00 0.00 1.40
1408 1521 2.168106 AGCGATCATATCTCATGGCCTC 59.832 50.000 3.32 0.00 0.00 4.70
1433 1560 2.289565 CAGCTGCACATGATGAGATGT 58.710 47.619 0.00 0.00 37.01 3.06
1470 1597 1.281287 ACTGGATTCAGCTGAGCATGT 59.719 47.619 17.43 10.53 44.59 3.21
1472 1882 1.134159 GGACTGGATTCAGCTGAGCAT 60.134 52.381 17.43 8.69 44.59 3.79
1486 1896 3.407424 TCACAAGATCAAGTGGACTGG 57.593 47.619 14.98 0.00 36.43 4.00
1542 1961 2.063541 GAATAGCCACATGCCACGGC 62.064 60.000 0.00 0.00 46.62 5.68
1693 2299 2.027192 TGCACTAAGGTGAAGGTCATCC 60.027 50.000 0.00 0.00 45.61 3.51
1705 2311 2.169352 ACTAGCCACAGATGCACTAAGG 59.831 50.000 0.00 0.00 0.00 2.69
1707 2313 3.981071 AACTAGCCACAGATGCACTAA 57.019 42.857 0.00 0.00 0.00 2.24
1766 2384 4.753107 CGGTGTACTGTTATCAACCAGTTT 59.247 41.667 0.00 0.00 0.00 2.66
1833 2452 3.626028 ATGCAAAACGAACCAACTCTC 57.374 42.857 0.00 0.00 0.00 3.20
1862 2481 8.980481 ATGGATTCTAAAATAACCACTACAGG 57.020 34.615 0.00 0.00 0.00 4.00
1961 2580 3.560068 AGAAGCAACGAAACAGGTTGTAG 59.440 43.478 6.54 0.00 45.01 2.74
1992 2611 8.827677 ACCAAAAATAAGCTAACGAGATGATAC 58.172 33.333 0.00 0.00 0.00 2.24
1996 2615 6.842163 ACACCAAAAATAAGCTAACGAGATG 58.158 36.000 0.00 0.00 0.00 2.90
2011 2630 6.261826 CCTTGCCATTTGAAATACACCAAAAA 59.738 34.615 0.00 0.00 36.10 1.94
2482 3121 7.962964 ATAACAGAGAGACGAAAATGTGAAA 57.037 32.000 0.00 0.00 0.00 2.69
2494 3133 8.718102 TTAACTATGCCAAATAACAGAGAGAC 57.282 34.615 0.00 0.00 0.00 3.36
2621 3260 7.982919 TCTGGATAAATTCAAAAGCATCATTGG 59.017 33.333 0.00 0.00 0.00 3.16
2736 3376 4.997395 AGCGAGCAACCACTATAATTATGG 59.003 41.667 8.28 7.74 39.57 2.74
2758 3398 5.354234 ACTCTGTGGTGTTACTGTTGAAAAG 59.646 40.000 0.00 0.00 0.00 2.27
2865 3505 2.032681 GGTCTGTGGAGTGTGCCC 59.967 66.667 0.00 0.00 0.00 5.36
2992 3755 1.304282 CTGCACCTTGGGCCTGTAT 59.696 57.895 4.53 0.00 0.00 2.29
3278 4103 1.117150 GCTACTACCATCCCGGAACA 58.883 55.000 0.73 0.00 38.63 3.18
3327 4152 0.846427 TGGGGGAAATGGCTCAGAGT 60.846 55.000 0.00 0.00 0.00 3.24
3484 4495 5.474876 GCCAATATTCCATTTCTAGACCTGG 59.525 44.000 11.92 11.92 0.00 4.45
3527 4538 9.332502 TCAAACAACTAACACACAAGTACATAT 57.667 29.630 0.00 0.00 0.00 1.78
3528 4539 8.719560 TCAAACAACTAACACACAAGTACATA 57.280 30.769 0.00 0.00 0.00 2.29
3660 4685 6.584185 TCCTTTTGCTTCCTGGTAATAAAC 57.416 37.500 0.00 0.00 0.00 2.01
3662 4687 6.014925 GGTTTCCTTTTGCTTCCTGGTAATAA 60.015 38.462 0.00 0.00 0.00 1.40
3663 4688 5.479027 GGTTTCCTTTTGCTTCCTGGTAATA 59.521 40.000 0.00 0.00 0.00 0.98
3666 4691 3.227614 GGTTTCCTTTTGCTTCCTGGTA 58.772 45.455 0.00 0.00 0.00 3.25
4227 5270 3.367932 CACACACTAACAAGCATCTACCG 59.632 47.826 0.00 0.00 0.00 4.02
4322 5392 7.244192 GGATACTCATAGACAAAAACTTGTGC 58.756 38.462 0.00 0.00 34.90 4.57
4357 5427 1.167851 CGGAACACAAGATGCCACAT 58.832 50.000 0.00 0.00 0.00 3.21
4381 5451 5.869753 AGCAAGCAGTTGAGTAATTACAG 57.130 39.130 17.65 1.98 35.46 2.74
4412 5482 0.820871 AAGCAGTTCACCCGCAAAAA 59.179 45.000 0.00 0.00 0.00 1.94
4413 5483 0.102120 CAAGCAGTTCACCCGCAAAA 59.898 50.000 0.00 0.00 0.00 2.44
4414 5484 1.732917 CAAGCAGTTCACCCGCAAA 59.267 52.632 0.00 0.00 0.00 3.68
4415 5485 2.844451 GCAAGCAGTTCACCCGCAA 61.844 57.895 0.00 0.00 0.00 4.85
4416 5486 2.390306 TAGCAAGCAGTTCACCCGCA 62.390 55.000 0.00 0.00 0.00 5.69
4417 5487 1.671054 TAGCAAGCAGTTCACCCGC 60.671 57.895 0.00 0.00 0.00 6.13
4418 5488 1.298859 GGTAGCAAGCAGTTCACCCG 61.299 60.000 0.00 0.00 0.00 5.28
4419 5489 0.036875 AGGTAGCAAGCAGTTCACCC 59.963 55.000 0.00 0.00 0.00 4.61
4420 5490 1.537202 CAAGGTAGCAAGCAGTTCACC 59.463 52.381 0.00 0.00 0.00 4.02
4422 5492 1.545428 CCCAAGGTAGCAAGCAGTTCA 60.545 52.381 0.00 0.00 0.00 3.18
4423 5493 1.168714 CCCAAGGTAGCAAGCAGTTC 58.831 55.000 0.00 0.00 0.00 3.01
4424 5494 0.251341 CCCCAAGGTAGCAAGCAGTT 60.251 55.000 0.00 0.00 0.00 3.16
4426 5496 1.379044 CCCCCAAGGTAGCAAGCAG 60.379 63.158 0.00 0.00 0.00 4.24
4427 5497 1.431195 TTCCCCCAAGGTAGCAAGCA 61.431 55.000 0.00 0.00 36.75 3.91
4428 5498 0.033109 ATTCCCCCAAGGTAGCAAGC 60.033 55.000 0.00 0.00 36.75 4.01
4461 5618 4.974645 AGTGACCAACTAGTTTCCATCA 57.025 40.909 5.07 4.72 37.36 3.07
4463 5620 4.821805 CACAAGTGACCAACTAGTTTCCAT 59.178 41.667 5.07 0.00 38.56 3.41
4464 5621 4.080807 TCACAAGTGACCAACTAGTTTCCA 60.081 41.667 5.07 1.39 38.56 3.53
4465 5622 4.448210 TCACAAGTGACCAACTAGTTTCC 58.552 43.478 5.07 0.00 38.56 3.13
4466 5623 5.353123 TGTTCACAAGTGACCAACTAGTTTC 59.647 40.000 5.07 2.71 38.56 2.78
4592 5920 7.832685 GGTGTTATTCCCTGGAGTATTTTTACT 59.167 37.037 0.00 0.00 0.00 2.24
4617 5945 9.449719 GGTAGTTCCTTTGATGTAATATATGGG 57.550 37.037 0.00 0.00 0.00 4.00
4669 6241 5.197451 TCTAACTTCTTTTGGGTGCTTTGA 58.803 37.500 0.00 0.00 0.00 2.69
4670 6242 5.514274 TCTAACTTCTTTTGGGTGCTTTG 57.486 39.130 0.00 0.00 0.00 2.77
4727 6308 4.451096 TCGTTTTGCTCTCTGGTATTTGTC 59.549 41.667 0.00 0.00 0.00 3.18
4829 6431 8.533569 TCTCTTCAACCCTTTTTAACAAATCT 57.466 30.769 0.00 0.00 0.00 2.40
4847 6449 7.011389 CGCATATTAACCAAGTGATTCTCTTCA 59.989 37.037 0.00 0.00 0.00 3.02
4857 6459 5.681105 CGGATTTTCGCATATTAACCAAGTG 59.319 40.000 0.00 0.00 0.00 3.16
4858 6460 5.220970 CCGGATTTTCGCATATTAACCAAGT 60.221 40.000 0.00 0.00 0.00 3.16
4874 6476 6.163135 TGTAATGGTTTTTGTCCGGATTTT 57.837 33.333 7.81 0.00 0.00 1.82
4875 6477 5.793030 TGTAATGGTTTTTGTCCGGATTT 57.207 34.783 7.81 0.00 0.00 2.17
4876 6478 5.069251 TGTTGTAATGGTTTTTGTCCGGATT 59.931 36.000 7.81 0.00 0.00 3.01
4877 6479 4.585162 TGTTGTAATGGTTTTTGTCCGGAT 59.415 37.500 7.81 0.00 0.00 4.18
4878 6480 3.952323 TGTTGTAATGGTTTTTGTCCGGA 59.048 39.130 0.00 0.00 0.00 5.14
4879 6481 4.045783 GTGTTGTAATGGTTTTTGTCCGG 58.954 43.478 0.00 0.00 0.00 5.14
4880 6482 4.927422 AGTGTTGTAATGGTTTTTGTCCG 58.073 39.130 0.00 0.00 0.00 4.79
4881 6483 5.286438 GGAGTGTTGTAATGGTTTTTGTCC 58.714 41.667 0.00 0.00 0.00 4.02
4882 6484 5.163499 TGGGAGTGTTGTAATGGTTTTTGTC 60.163 40.000 0.00 0.00 0.00 3.18
4883 6485 4.712337 TGGGAGTGTTGTAATGGTTTTTGT 59.288 37.500 0.00 0.00 0.00 2.83
4884 6486 5.047188 GTGGGAGTGTTGTAATGGTTTTTG 58.953 41.667 0.00 0.00 0.00 2.44
4885 6487 4.712337 TGTGGGAGTGTTGTAATGGTTTTT 59.288 37.500 0.00 0.00 0.00 1.94
4951 6564 1.373590 GCGTGGTTCTTGTGGTGTGT 61.374 55.000 0.00 0.00 0.00 3.72
4952 6565 1.355210 GCGTGGTTCTTGTGGTGTG 59.645 57.895 0.00 0.00 0.00 3.82
4953 6566 1.078072 TGCGTGGTTCTTGTGGTGT 60.078 52.632 0.00 0.00 0.00 4.16
4954 6567 1.355210 GTGCGTGGTTCTTGTGGTG 59.645 57.895 0.00 0.00 0.00 4.17
4955 6568 1.078072 TGTGCGTGGTTCTTGTGGT 60.078 52.632 0.00 0.00 0.00 4.16
4956 6569 1.355210 GTGTGCGTGGTTCTTGTGG 59.645 57.895 0.00 0.00 0.00 4.17
4957 6570 1.355210 GGTGTGCGTGGTTCTTGTG 59.645 57.895 0.00 0.00 0.00 3.33
4958 6571 2.177580 CGGTGTGCGTGGTTCTTGT 61.178 57.895 0.00 0.00 0.00 3.16
4959 6572 2.631428 CGGTGTGCGTGGTTCTTG 59.369 61.111 0.00 0.00 0.00 3.02
4960 6573 3.276846 GCGGTGTGCGTGGTTCTT 61.277 61.111 0.00 0.00 0.00 2.52
4994 6607 6.456795 TGACAGATCGTAGACAATCTCAAT 57.543 37.500 0.00 0.00 42.51 2.57
5019 6632 2.231478 TGAAGTCGGAGAAGTGATGACC 59.769 50.000 0.00 0.00 39.69 4.02
5047 6673 3.644966 TTGAGACTCTTGGTTGGTTGT 57.355 42.857 3.68 0.00 0.00 3.32
5058 6684 3.633525 TGCAGCATTTGTTTTGAGACTCT 59.366 39.130 3.68 0.00 0.00 3.24
5061 6687 3.446799 TGTGCAGCATTTGTTTTGAGAC 58.553 40.909 0.00 0.00 0.00 3.36
5062 6688 3.797451 TGTGCAGCATTTGTTTTGAGA 57.203 38.095 0.00 0.00 0.00 3.27
5077 6703 1.674359 ACCGACATGTTTCTTGTGCA 58.326 45.000 0.00 0.00 0.00 4.57
5079 6705 5.815222 TGGATATACCGACATGTTTCTTGTG 59.185 40.000 0.00 0.00 42.61 3.33
5089 6715 6.231211 GTGGATTTCTTGGATATACCGACAT 58.769 40.000 0.00 0.00 42.61 3.06
5093 6719 4.968259 TGGTGGATTTCTTGGATATACCG 58.032 43.478 0.00 0.00 42.61 4.02
5118 6745 0.545309 AGCTGCCTAGTCCTTGACCA 60.545 55.000 0.00 0.00 32.18 4.02
5123 6751 1.000486 TCGGAGCTGCCTAGTCCTT 60.000 57.895 0.00 0.00 0.00 3.36
5150 6778 1.204941 TCTTTCTCCTACGAGGCTTGC 59.795 52.381 0.37 0.00 36.70 4.01
5189 6817 4.453751 GGGCTTGTTACCGATATTGGTTA 58.546 43.478 20.07 8.41 43.56 2.85
5190 6818 3.284617 GGGCTTGTTACCGATATTGGTT 58.715 45.455 20.07 4.80 43.56 3.67
5191 6819 2.422377 GGGGCTTGTTACCGATATTGGT 60.422 50.000 18.90 18.90 46.26 3.67
5192 6820 2.227194 GGGGCTTGTTACCGATATTGG 58.773 52.381 7.52 7.52 0.00 3.16


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

AutoCloner maintained by Alex Coulton.