Multiple sequence alignment - TraesCS1B01G278200

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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 TraesCS1B01G278200 chr1B 100.000 4042 0 0 1 4042 486547513 486543472 0.000000e+00 7465.0
1 TraesCS1B01G278200 chr1D 92.050 2654 148 27 1388 4016 363282424 363279809 0.000000e+00 3674.0
2 TraesCS1B01G278200 chr1D 92.967 1365 74 8 1 1345 363283791 363282429 0.000000e+00 1969.0
3 TraesCS1B01G278200 chr1D 92.157 102 7 1 2049 2149 363281864 363281763 4.210000e-30 143.0
4 TraesCS1B01G278200 chr1A 93.002 2072 117 13 1817 3874 462436820 462434763 0.000000e+00 2998.0
5 TraesCS1B01G278200 chr1A 86.246 1316 133 25 4 1284 462439020 462437718 0.000000e+00 1384.0
6 TraesCS1B01G278200 chr1A 92.487 386 23 3 1389 1772 462437204 462436823 7.640000e-152 547.0
7 TraesCS1B01G278200 chr3B 91.433 1354 82 19 1388 2733 80774198 80772871 0.000000e+00 1827.0
8 TraesCS1B01G278200 chr6B 90.768 1354 92 18 1388 2733 44469237 44467909 0.000000e+00 1777.0
9 TraesCS1B01G278200 chr7B 91.815 843 52 9 1892 2733 478084504 478083678 0.000000e+00 1158.0
10 TraesCS1B01G278200 chr7B 91.473 516 27 10 1388 1896 478085346 478084841 0.000000e+00 693.0
11 TraesCS1B01G278200 chr7B 91.279 516 28 10 1388 1896 478092017 478091512 0.000000e+00 688.0
12 TraesCS1B01G278200 chr7B 92.934 467 25 4 1892 2358 478086479 478086021 0.000000e+00 673.0
13 TraesCS1B01G278200 chrUn 92.934 467 25 4 1892 2358 377558579 377559037 0.000000e+00 673.0
14 TraesCS1B01G278200 chr3A 83.019 265 37 8 2169 2429 638203830 638203570 2.430000e-57 233.0
15 TraesCS1B01G278200 chr3D 82.197 264 41 6 2169 2429 496679910 496680170 5.260000e-54 222.0
16 TraesCS1B01G278200 chr7D 82.105 95 17 0 284 378 119558239 119558333 9.310000e-12 82.4


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 TraesCS1B01G278200 chr1B 486543472 486547513 4041 True 7465.000000 7465 100.000000 1 4042 1 chr1B.!!$R1 4041
1 TraesCS1B01G278200 chr1D 363279809 363283791 3982 True 1928.666667 3674 92.391333 1 4016 3 chr1D.!!$R1 4015
2 TraesCS1B01G278200 chr1A 462434763 462439020 4257 True 1643.000000 2998 90.578333 4 3874 3 chr1A.!!$R1 3870
3 TraesCS1B01G278200 chr3B 80772871 80774198 1327 True 1827.000000 1827 91.433000 1388 2733 1 chr3B.!!$R1 1345
4 TraesCS1B01G278200 chr6B 44467909 44469237 1328 True 1777.000000 1777 90.768000 1388 2733 1 chr6B.!!$R1 1345
5 TraesCS1B01G278200 chr7B 478083678 478086479 2801 True 841.333333 1158 92.074000 1388 2733 3 chr7B.!!$R2 1345
6 TraesCS1B01G278200 chr7B 478091512 478092017 505 True 688.000000 688 91.279000 1388 1896 1 chr7B.!!$R1 508

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
502 507 0.036306 GGTCGTCCAACCCATTCACT 59.964 55.0 0.00 0.00 32.82 3.41 F
1154 1202 0.031043 TCGCTCTGTTTCGTCCGAAA 59.969 50.0 10.55 10.55 41.22 3.46 F
1308 1360 0.108662 CCCTTTTCGATTTGGCTGGC 60.109 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2207 0.852842 ATGGCTAGCCCCATAAAGCA 59.147 50.000 30.81 9.3 43.65 3.91 R
2767 3588 1.149174 ATGGCCTGCAATCCTACCG 59.851 57.895 3.32 0.0 0.00 4.02 R
3195 4019 0.755698 GACAGGCCTCCCTACGATGA 60.756 60.000 0.00 0.0 40.33 2.92 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
160 162 0.107410 TATGGTGGTGATGGCGGAAC 60.107 55.000 0.00 0.00 0.00 3.62
235 237 2.913060 GTCGGCGGCCTAGAGGAT 60.913 66.667 18.34 0.00 37.39 3.24
265 267 3.644884 AGTCCAGTCACTGTTCTTACG 57.355 47.619 3.56 0.00 0.00 3.18
281 283 5.050126 TCTTACGGAGTAGTGGATCTGAT 57.950 43.478 0.00 0.00 46.93 2.90
328 330 4.322499 GGTCTTCAAAGGTGTCTTCCGATA 60.322 45.833 0.00 0.00 31.82 2.92
339 341 2.625790 GTCTTCCGATAGAGTGGATGCT 59.374 50.000 0.00 0.00 39.76 3.79
341 343 2.073252 TCCGATAGAGTGGATGCTGT 57.927 50.000 0.00 0.00 39.76 4.40
439 441 5.982356 TGTCAGGTTATCTCTCCTTGAATG 58.018 41.667 0.00 0.00 30.91 2.67
502 507 0.036306 GGTCGTCCAACCCATTCACT 59.964 55.000 0.00 0.00 32.82 3.41
503 508 1.276989 GGTCGTCCAACCCATTCACTA 59.723 52.381 0.00 0.00 32.82 2.74
508 513 3.344515 GTCCAACCCATTCACTACCTTC 58.655 50.000 0.00 0.00 0.00 3.46
559 565 1.067425 CGTTGTCCCCGACATGTTCTA 60.067 52.381 0.00 0.00 42.40 2.10
585 603 0.321653 GCCGACTCCCTGACAACAAT 60.322 55.000 0.00 0.00 0.00 2.71
599 617 5.380900 TGACAACAATGTGTCCTTGGATAA 58.619 37.500 11.41 0.00 46.13 1.75
623 641 2.224281 TGATGTATCGGAGGTCCAATGC 60.224 50.000 0.00 0.00 35.14 3.56
1154 1202 0.031043 TCGCTCTGTTTCGTCCGAAA 59.969 50.000 10.55 10.55 41.22 3.46
1203 1251 3.508845 ACTGATGTGCCCTAAGTTGTT 57.491 42.857 0.00 0.00 0.00 2.83
1205 1253 4.324267 ACTGATGTGCCCTAAGTTGTTAC 58.676 43.478 0.00 0.00 0.00 2.50
1244 1292 2.597217 CCCCGCAAGCAGGTTCAA 60.597 61.111 0.00 0.00 0.00 2.69
1308 1360 0.108662 CCCTTTTCGATTTGGCTGGC 60.109 55.000 0.00 0.00 0.00 4.85
1330 1382 4.149617 CGTAGATTTACGCTCTATCACCG 58.850 47.826 2.58 0.00 45.21 4.94
1334 1386 3.344904 TTTACGCTCTATCACCGTAGC 57.655 47.619 0.00 0.00 38.48 3.58
1345 1397 7.201548 GCTCTATCACCGTAGCTTAGATAGTAC 60.202 44.444 0.00 0.00 39.27 2.73
1346 1398 7.905265 TCTATCACCGTAGCTTAGATAGTACT 58.095 38.462 0.00 0.00 39.27 2.73
1347 1399 8.034215 TCTATCACCGTAGCTTAGATAGTACTC 58.966 40.741 0.00 0.00 39.27 2.59
1348 1400 5.922053 TCACCGTAGCTTAGATAGTACTCA 58.078 41.667 0.00 0.00 0.00 3.41
1349 1401 6.531923 TCACCGTAGCTTAGATAGTACTCAT 58.468 40.000 0.00 0.00 0.00 2.90
1350 1402 6.427242 TCACCGTAGCTTAGATAGTACTCATG 59.573 42.308 0.00 0.00 0.00 3.07
1351 1403 6.205076 CACCGTAGCTTAGATAGTACTCATGT 59.795 42.308 0.00 0.00 0.00 3.21
1352 1404 6.205076 ACCGTAGCTTAGATAGTACTCATGTG 59.795 42.308 0.00 0.00 0.00 3.21
1353 1405 6.205076 CCGTAGCTTAGATAGTACTCATGTGT 59.795 42.308 0.00 5.63 0.00 3.72
1354 1406 7.255173 CCGTAGCTTAGATAGTACTCATGTGTT 60.255 40.741 5.63 0.00 0.00 3.32
1355 1407 7.588123 CGTAGCTTAGATAGTACTCATGTGTTG 59.412 40.741 5.63 0.00 0.00 3.33
1356 1408 7.646548 AGCTTAGATAGTACTCATGTGTTGA 57.353 36.000 5.63 0.00 0.00 3.18
1357 1409 8.243961 AGCTTAGATAGTACTCATGTGTTGAT 57.756 34.615 5.63 0.00 32.72 2.57
1358 1410 9.355916 AGCTTAGATAGTACTCATGTGTTGATA 57.644 33.333 5.63 0.00 32.72 2.15
1359 1411 9.400638 GCTTAGATAGTACTCATGTGTTGATAC 57.599 37.037 5.63 0.00 32.72 2.24
1362 1414 8.172352 AGATAGTACTCATGTGTTGATACTCC 57.828 38.462 5.63 0.66 33.98 3.85
1363 1415 7.780271 AGATAGTACTCATGTGTTGATACTCCA 59.220 37.037 5.63 0.00 33.98 3.86
1364 1416 6.214191 AGTACTCATGTGTTGATACTCCAG 57.786 41.667 5.63 0.00 32.72 3.86
1365 1417 3.866651 ACTCATGTGTTGATACTCCAGC 58.133 45.455 0.00 0.00 32.72 4.85
1366 1418 3.517100 ACTCATGTGTTGATACTCCAGCT 59.483 43.478 0.00 0.00 32.72 4.24
1367 1419 4.019860 ACTCATGTGTTGATACTCCAGCTT 60.020 41.667 0.00 0.00 32.72 3.74
1368 1420 4.910195 TCATGTGTTGATACTCCAGCTTT 58.090 39.130 0.00 0.00 0.00 3.51
1369 1421 5.316167 TCATGTGTTGATACTCCAGCTTTT 58.684 37.500 0.00 0.00 0.00 2.27
1370 1422 6.472016 TCATGTGTTGATACTCCAGCTTTTA 58.528 36.000 0.00 0.00 0.00 1.52
1371 1423 6.595326 TCATGTGTTGATACTCCAGCTTTTAG 59.405 38.462 0.00 0.00 0.00 1.85
1372 1424 6.109156 TGTGTTGATACTCCAGCTTTTAGA 57.891 37.500 0.00 0.00 0.00 2.10
1373 1425 6.711277 TGTGTTGATACTCCAGCTTTTAGAT 58.289 36.000 0.00 0.00 0.00 1.98
1374 1426 7.847096 TGTGTTGATACTCCAGCTTTTAGATA 58.153 34.615 0.00 0.00 0.00 1.98
1375 1427 7.981789 TGTGTTGATACTCCAGCTTTTAGATAG 59.018 37.037 0.00 0.00 0.00 2.08
1376 1428 7.982354 GTGTTGATACTCCAGCTTTTAGATAGT 59.018 37.037 0.00 0.00 0.00 2.12
1377 1429 9.197306 TGTTGATACTCCAGCTTTTAGATAGTA 57.803 33.333 0.00 0.00 0.00 1.82
1378 1430 9.465985 GTTGATACTCCAGCTTTTAGATAGTAC 57.534 37.037 0.00 0.00 0.00 2.73
1379 1431 8.998277 TGATACTCCAGCTTTTAGATAGTACT 57.002 34.615 0.00 0.00 0.00 2.73
1380 1432 9.069082 TGATACTCCAGCTTTTAGATAGTACTC 57.931 37.037 0.00 0.00 0.00 2.59
1381 1433 9.292195 GATACTCCAGCTTTTAGATAGTACTCT 57.708 37.037 0.00 0.00 0.00 3.24
1384 1436 9.073475 ACTCCAGCTTTTAGATAGTACTCTATG 57.927 37.037 0.00 0.00 37.05 2.23
1385 1437 8.410673 TCCAGCTTTTAGATAGTACTCTATGG 57.589 38.462 0.00 0.90 37.05 2.74
1386 1438 8.225416 TCCAGCTTTTAGATAGTACTCTATGGA 58.775 37.037 0.00 3.29 37.05 3.41
1425 1886 1.067142 TGTACAGTCGGTGATTGCCTC 60.067 52.381 0.00 0.00 0.00 4.70
1501 1962 8.677148 ACTATGTTTACTTGTATATTGGCAGG 57.323 34.615 0.00 0.00 0.00 4.85
1555 2017 5.982516 GTGCAACAATCATTTCTTGGTGTTA 59.017 36.000 3.35 0.00 42.13 2.41
1561 2023 3.096092 TCATTTCTTGGTGTTATGGGCC 58.904 45.455 0.00 0.00 0.00 5.80
1587 2049 6.577103 TGTGTGGTGCTTTCAATTGAAATTA 58.423 32.000 28.86 19.39 42.44 1.40
1703 2168 6.947733 TCAAGGGTTTAGATGTGTGAATGATT 59.052 34.615 0.00 0.00 0.00 2.57
1721 2189 9.012161 TGAATGATTGTTGTGAGATTTATGACA 57.988 29.630 0.00 0.00 0.00 3.58
1742 2210 8.467963 TGACAATCATGGATTAATGTTATGCT 57.532 30.769 0.00 0.00 30.44 3.79
1831 2301 4.184629 CCACAGCTTCACTAACTATGGTC 58.815 47.826 0.00 0.00 0.00 4.02
1896 2708 6.428295 TGTATCAGGGTATTTAGGGGTTTTG 58.572 40.000 0.00 0.00 0.00 2.44
1984 2796 3.246619 GACACTGTTGCAGTACTCTAGC 58.753 50.000 1.16 0.00 43.43 3.42
2012 2824 9.109533 CTGCTATTTTTCAATGATTGTTTTTGC 57.890 29.630 4.93 3.85 0.00 3.68
2017 2829 4.637387 TCAATGATTGTTTTTGCCCCAT 57.363 36.364 4.93 0.00 0.00 4.00
2026 2838 0.399833 TTTTGCCCCATTTTGCCTCC 59.600 50.000 0.00 0.00 0.00 4.30
2083 2895 5.987347 GGTTTACACTGTTGCAGTACTCTAA 59.013 40.000 1.16 0.00 43.43 2.10
2087 2899 8.671384 TTACACTGTTGCAGTACTCTAATTTT 57.329 30.769 1.16 0.00 43.43 1.82
2096 2908 9.840427 TTGCAGTACTCTAATTTTGCTATTTTC 57.160 29.630 0.00 0.00 33.00 2.29
2491 3304 5.703592 TGTGTTGTTCTTATGGTATGGTGAC 59.296 40.000 0.00 0.00 0.00 3.67
2522 3335 4.517285 TCTGTGAATAGTTGATTCTGGGC 58.483 43.478 0.00 0.00 43.90 5.36
2548 3361 2.642311 TCCAATACCTGAGGTTCTTGCA 59.358 45.455 10.53 0.00 37.09 4.08
2549 3362 3.012518 CCAATACCTGAGGTTCTTGCAG 58.987 50.000 10.53 0.00 37.09 4.41
2601 3422 2.091277 CGAAGCAGTAGCAAAAGACTCG 59.909 50.000 0.00 0.00 45.49 4.18
2624 3445 5.278463 CGACCCTGAAATTATGCCCTTTATG 60.278 44.000 0.00 0.00 0.00 1.90
2720 3541 5.456921 ACCACTATCAAATCCACCTCAAT 57.543 39.130 0.00 0.00 0.00 2.57
2762 3583 3.895041 TCCTGTGTCACAACATAGAGTGA 59.105 43.478 7.18 0.00 44.85 3.41
2767 3588 7.148573 CCTGTGTCACAACATAGAGTGATAAAC 60.149 40.741 7.18 0.00 44.85 2.01
2853 3675 6.430007 AGAGAGTTTCTTTGGCCATATGAAT 58.570 36.000 6.09 0.00 29.61 2.57
2942 3766 5.104652 TGGGGTAGCAAGTAGAGGATTAAAC 60.105 44.000 0.00 0.00 0.00 2.01
3048 3872 5.494724 CATACCCGTCCTACTAGCATACTA 58.505 45.833 0.00 0.00 0.00 1.82
3159 3983 5.063204 TGTAAATATGGCTGATGGTAGTGC 58.937 41.667 0.00 0.00 0.00 4.40
3168 3992 1.205893 TGATGGTAGTGCATGTGCGTA 59.794 47.619 0.00 0.00 45.83 4.42
3195 4019 5.242838 TGTCTGGTTGTTCTGTTGTTTTCTT 59.757 36.000 0.00 0.00 0.00 2.52
3203 4027 6.943981 TGTTCTGTTGTTTTCTTCATCGTAG 58.056 36.000 0.00 0.00 0.00 3.51
3215 4039 1.043116 CATCGTAGGGAGGCCTGTCA 61.043 60.000 12.00 0.00 0.00 3.58
3285 4109 5.035443 CCACTAATGTCGCTGTAGTACTTC 58.965 45.833 0.00 0.00 0.00 3.01
3286 4110 5.163642 CCACTAATGTCGCTGTAGTACTTCT 60.164 44.000 0.00 0.00 0.00 2.85
3310 4134 0.550914 GTCATAGGGATGGGGTTGCA 59.449 55.000 0.00 0.00 33.49 4.08
3328 4161 6.460953 GGGTTGCAGTATTCTCAGTTCAAAAA 60.461 38.462 0.00 0.00 0.00 1.94
3390 4223 5.304686 TGGATCTGTATTATGTTGGGACC 57.695 43.478 0.00 0.00 0.00 4.46
3395 4228 8.164070 GGATCTGTATTATGTTGGGACCTAAAT 58.836 37.037 0.00 0.00 0.00 1.40
3396 4229 8.924511 ATCTGTATTATGTTGGGACCTAAATG 57.075 34.615 0.00 0.00 0.00 2.32
3424 4257 3.512724 AGAAACCCAAGAAATCTGCCATG 59.487 43.478 0.00 0.00 0.00 3.66
3499 4335 2.223572 GCAGTATTTGTATGGCAGCCAC 60.224 50.000 19.10 5.54 35.80 5.01
3500 4336 3.016031 CAGTATTTGTATGGCAGCCACA 58.984 45.455 19.10 8.73 35.80 4.17
3544 4380 2.872408 GCATTGGCTACCTCTTGCA 58.128 52.632 0.00 0.00 36.96 4.08
3546 4382 1.098050 CATTGGCTACCTCTTGCACC 58.902 55.000 0.00 0.00 0.00 5.01
3547 4383 0.995024 ATTGGCTACCTCTTGCACCT 59.005 50.000 0.00 0.00 0.00 4.00
3570 4406 5.779922 TGAGTAGTCGAGCTGTACATTTTT 58.220 37.500 0.00 0.00 0.00 1.94
3576 4412 7.849804 AGTCGAGCTGTACATTTTTGATTAT 57.150 32.000 0.00 0.00 0.00 1.28
3595 4431 0.752743 TTTGCTGCTGAGGTGCAACT 60.753 50.000 2.34 2.34 44.81 3.16
3619 4455 4.780815 CTGTGATTTCCTGGTATGGCTTA 58.219 43.478 0.00 0.00 0.00 3.09
3633 4469 3.290948 TGGCTTACTGTTCTTGTTGGT 57.709 42.857 0.00 0.00 0.00 3.67
3671 4508 8.034804 AGTTTTGCTACTTGATTTTTCAACTGT 58.965 29.630 0.00 0.00 0.00 3.55
3706 4543 3.965379 TTCATTGATGGTGCATTTGCT 57.035 38.095 3.94 0.00 42.66 3.91
3776 4615 3.651803 ATACGAGAACCATCTGCTAGC 57.348 47.619 8.10 8.10 35.54 3.42
3788 4629 3.189618 TCTGCTAGCCACATCATTCAG 57.810 47.619 13.29 0.00 0.00 3.02
3817 4658 0.689055 AGCTGTGGCATTGAGTCAGA 59.311 50.000 4.87 0.00 41.70 3.27
3821 4662 0.737219 GTGGCATTGAGTCAGATGGC 59.263 55.000 23.04 23.04 45.82 4.40
3822 4663 0.622136 TGGCATTGAGTCAGATGGCT 59.378 50.000 26.51 0.00 45.81 4.75
3824 4665 2.239402 TGGCATTGAGTCAGATGGCTTA 59.761 45.455 26.51 14.78 45.81 3.09
3829 4670 5.105997 GCATTGAGTCAGATGGCTTAAAACT 60.106 40.000 13.61 0.00 29.10 2.66
3843 4684 8.911918 TGGCTTAAAACTACTGAAGATGTTAA 57.088 30.769 0.00 0.00 0.00 2.01
3846 4687 9.000486 GCTTAAAACTACTGAAGATGTTAACCT 58.000 33.333 2.48 0.00 0.00 3.50
3851 4692 7.964604 ACTACTGAAGATGTTAACCTTGTTC 57.035 36.000 2.48 5.96 0.00 3.18
3875 4716 4.614535 GCTTGTGTAGCTTGTTCATGGAAG 60.615 45.833 0.00 0.00 46.77 3.46
3877 4718 5.222079 TGTGTAGCTTGTTCATGGAAGTA 57.778 39.130 0.00 0.00 0.00 2.24
3880 4721 6.014925 TGTGTAGCTTGTTCATGGAAGTACTA 60.015 38.462 0.00 0.00 0.00 1.82
3893 4737 8.082852 TCATGGAAGTACTAGAATTTATCGAGC 58.917 37.037 0.00 0.00 34.41 5.03
3901 4745 6.821388 ACTAGAATTTATCGAGCCATGAAGT 58.179 36.000 0.00 0.00 34.41 3.01
3902 4746 5.998454 AGAATTTATCGAGCCATGAAGTG 57.002 39.130 0.00 0.00 0.00 3.16
3904 4748 1.570813 TTATCGAGCCATGAAGTGCG 58.429 50.000 0.00 0.00 0.00 5.34
3905 4749 0.249447 TATCGAGCCATGAAGTGCGG 60.249 55.000 0.00 0.00 0.00 5.69
3906 4750 2.244117 ATCGAGCCATGAAGTGCGGT 62.244 55.000 0.00 0.00 0.00 5.68
3907 4751 2.743752 CGAGCCATGAAGTGCGGTG 61.744 63.158 0.00 0.00 0.00 4.94
3908 4752 1.672356 GAGCCATGAAGTGCGGTGT 60.672 57.895 0.00 0.00 0.00 4.16
3909 4753 0.391130 GAGCCATGAAGTGCGGTGTA 60.391 55.000 0.00 0.00 0.00 2.90
3910 4754 0.673644 AGCCATGAAGTGCGGTGTAC 60.674 55.000 0.00 0.00 0.00 2.90
3911 4755 0.673644 GCCATGAAGTGCGGTGTACT 60.674 55.000 0.00 0.00 0.00 2.73
3914 4758 1.464608 CATGAAGTGCGGTGTACTTGG 59.535 52.381 5.01 0.00 38.49 3.61
3933 4777 3.507597 GGTGCGGAACCCAAATTTC 57.492 52.632 0.00 0.00 44.02 2.17
3936 4780 0.965439 TGCGGAACCCAAATTTCAGG 59.035 50.000 2.76 2.76 0.00 3.86
3957 4801 4.835056 AGGAAGTGGCTAATTTTGAAAGCT 59.165 37.500 0.00 0.00 36.48 3.74
3971 4815 8.763049 ATTTTGAAAGCTAGCTGATTTAAACC 57.237 30.769 20.16 0.00 34.06 3.27
3972 4816 6.892658 TTGAAAGCTAGCTGATTTAAACCA 57.107 33.333 20.16 0.78 34.06 3.67
3973 4817 6.892658 TGAAAGCTAGCTGATTTAAACCAA 57.107 33.333 20.16 0.00 34.06 3.67
3974 4818 6.677913 TGAAAGCTAGCTGATTTAAACCAAC 58.322 36.000 20.16 0.00 34.06 3.77
3975 4819 5.644977 AAGCTAGCTGATTTAAACCAACC 57.355 39.130 20.16 0.00 0.00 3.77
4016 4860 1.470285 GCCATTGCATTGCTGTAGGTG 60.470 52.381 10.49 0.32 37.47 4.00
4017 4861 2.093890 CCATTGCATTGCTGTAGGTGA 58.906 47.619 10.49 0.00 0.00 4.02
4018 4862 2.691526 CCATTGCATTGCTGTAGGTGAT 59.308 45.455 10.49 0.00 0.00 3.06
4019 4863 3.131577 CCATTGCATTGCTGTAGGTGATT 59.868 43.478 10.49 0.00 0.00 2.57
4020 4864 4.382254 CCATTGCATTGCTGTAGGTGATTT 60.382 41.667 10.49 0.00 0.00 2.17
4021 4865 5.163530 CCATTGCATTGCTGTAGGTGATTTA 60.164 40.000 10.49 0.00 0.00 1.40
4022 4866 5.565592 TTGCATTGCTGTAGGTGATTTAG 57.434 39.130 10.49 0.00 0.00 1.85
4023 4867 4.842574 TGCATTGCTGTAGGTGATTTAGA 58.157 39.130 10.49 0.00 0.00 2.10
4024 4868 5.439721 TGCATTGCTGTAGGTGATTTAGAT 58.560 37.500 10.49 0.00 0.00 1.98
4025 4869 5.297527 TGCATTGCTGTAGGTGATTTAGATG 59.702 40.000 10.49 0.00 0.00 2.90
4026 4870 5.297776 GCATTGCTGTAGGTGATTTAGATGT 59.702 40.000 0.16 0.00 0.00 3.06
4027 4871 6.483307 GCATTGCTGTAGGTGATTTAGATGTA 59.517 38.462 0.16 0.00 0.00 2.29
4028 4872 7.012327 GCATTGCTGTAGGTGATTTAGATGTAA 59.988 37.037 0.16 0.00 0.00 2.41
4029 4873 8.554528 CATTGCTGTAGGTGATTTAGATGTAAG 58.445 37.037 0.00 0.00 0.00 2.34
4030 4874 6.049149 TGCTGTAGGTGATTTAGATGTAAGC 58.951 40.000 0.00 0.00 0.00 3.09
4031 4875 6.049149 GCTGTAGGTGATTTAGATGTAAGCA 58.951 40.000 0.00 0.00 0.00 3.91
4032 4876 6.018669 GCTGTAGGTGATTTAGATGTAAGCAC 60.019 42.308 8.35 8.35 0.00 4.40
4033 4877 7.182817 TGTAGGTGATTTAGATGTAAGCACT 57.817 36.000 13.58 6.41 31.20 4.40
4034 4878 7.041721 TGTAGGTGATTTAGATGTAAGCACTG 58.958 38.462 13.58 0.00 31.20 3.66
4035 4879 6.054860 AGGTGATTTAGATGTAAGCACTGT 57.945 37.500 13.58 3.99 31.20 3.55
4036 4880 6.476378 AGGTGATTTAGATGTAAGCACTGTT 58.524 36.000 13.58 3.07 31.20 3.16
4037 4881 6.942576 AGGTGATTTAGATGTAAGCACTGTTT 59.057 34.615 13.58 0.00 31.20 2.83
4038 4882 7.023575 GGTGATTTAGATGTAAGCACTGTTTG 58.976 38.462 13.58 0.00 31.20 2.93
4039 4883 7.094805 GGTGATTTAGATGTAAGCACTGTTTGA 60.095 37.037 13.58 0.00 31.20 2.69
4040 4884 8.454106 GTGATTTAGATGTAAGCACTGTTTGAT 58.546 33.333 9.18 0.00 0.00 2.57
4041 4885 8.453320 TGATTTAGATGTAAGCACTGTTTGATG 58.547 33.333 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.506255 GGCAATCGGTGGAGGGGG 62.506 72.222 0.00 0.00 0.00 5.40
68 69 1.418334 CAATGGAGATCTCGGGTCCT 58.582 55.000 16.46 0.00 0.00 3.85
75 76 3.341823 ACAGTGTTGCAATGGAGATCTC 58.658 45.455 14.75 14.75 33.50 2.75
160 162 7.094032 GGGGAAATCTTATTTGGATCTGCATAG 60.094 40.741 0.00 0.00 0.00 2.23
235 237 0.415830 TGACTGGACTATCCCCACCA 59.584 55.000 0.00 0.00 35.03 4.17
265 267 5.091261 ACACAAATCAGATCCACTACTCC 57.909 43.478 0.00 0.00 0.00 3.85
281 283 3.743911 CCTACATAACACGCAGACACAAA 59.256 43.478 0.00 0.00 0.00 2.83
351 353 3.787001 GGAGCCCGAGGACCAAGG 61.787 72.222 0.00 0.00 0.00 3.61
439 441 5.871396 TTCAGGGAGATATAACCAGACAC 57.129 43.478 0.00 0.00 0.00 3.67
502 507 4.245660 CAATCGTTGCAGAGAAGAAGGTA 58.754 43.478 0.00 0.00 0.00 3.08
503 508 3.070018 CAATCGTTGCAGAGAAGAAGGT 58.930 45.455 0.00 0.00 0.00 3.50
508 513 3.062763 ACAGACAATCGTTGCAGAGAAG 58.937 45.455 0.00 0.00 0.00 2.85
585 603 5.698741 ACATCATCTTATCCAAGGACACA 57.301 39.130 0.00 0.00 32.22 3.72
599 617 3.244887 TGGACCTCCGATACATCATCT 57.755 47.619 0.00 0.00 39.43 2.90
623 641 1.576421 GAGTGAAGCTTGTTGCCGG 59.424 57.895 2.10 0.00 44.23 6.13
659 683 0.826715 CATCTTCCTCCTCCGCTTGA 59.173 55.000 0.00 0.00 0.00 3.02
661 685 0.827368 GACATCTTCCTCCTCCGCTT 59.173 55.000 0.00 0.00 0.00 4.68
664 688 1.069823 CCATGACATCTTCCTCCTCCG 59.930 57.143 0.00 0.00 0.00 4.63
828 856 0.321034 GGTGGTTTGGAGACGGTACC 60.321 60.000 0.16 0.16 0.00 3.34
943 971 2.676471 CCAACCGGGGGAAGCAAG 60.676 66.667 6.32 0.00 0.00 4.01
1184 1232 4.579869 AGTAACAACTTAGGGCACATCAG 58.420 43.478 0.00 0.00 0.00 2.90
1203 1251 3.395639 ACGACAGCAATTCCGAAAAGTA 58.604 40.909 0.00 0.00 0.00 2.24
1205 1253 2.969443 ACGACAGCAATTCCGAAAAG 57.031 45.000 0.00 0.00 0.00 2.27
1244 1292 1.811266 CTACAGCGCGCAATCTGGT 60.811 57.895 35.10 21.32 34.76 4.00
1330 1382 8.622157 TCAACACATGAGTACTATCTAAGCTAC 58.378 37.037 0.00 0.00 33.04 3.58
1345 1397 4.134379 AGCTGGAGTATCAACACATGAG 57.866 45.455 0.00 0.00 42.53 2.90
1346 1398 4.558226 AAGCTGGAGTATCAACACATGA 57.442 40.909 0.00 0.00 43.67 3.07
1347 1399 5.633830 AAAAGCTGGAGTATCAACACATG 57.366 39.130 0.00 0.00 36.25 3.21
1348 1400 6.711277 TCTAAAAGCTGGAGTATCAACACAT 58.289 36.000 0.00 0.00 36.25 3.21
1349 1401 6.109156 TCTAAAAGCTGGAGTATCAACACA 57.891 37.500 0.00 0.00 36.25 3.72
1350 1402 7.982354 ACTATCTAAAAGCTGGAGTATCAACAC 59.018 37.037 0.00 0.00 36.25 3.32
1351 1403 8.079211 ACTATCTAAAAGCTGGAGTATCAACA 57.921 34.615 0.00 0.00 36.25 3.33
1352 1404 9.465985 GTACTATCTAAAAGCTGGAGTATCAAC 57.534 37.037 0.00 0.00 36.25 3.18
1353 1405 9.422681 AGTACTATCTAAAAGCTGGAGTATCAA 57.577 33.333 0.00 0.00 36.25 2.57
1354 1406 8.998277 AGTACTATCTAAAAGCTGGAGTATCA 57.002 34.615 0.00 0.00 36.25 2.15
1355 1407 9.292195 AGAGTACTATCTAAAAGCTGGAGTATC 57.708 37.037 0.00 0.00 0.00 2.24
1358 1410 9.073475 CATAGAGTACTATCTAAAAGCTGGAGT 57.927 37.037 0.00 0.00 37.24 3.85
1359 1411 8.519526 CCATAGAGTACTATCTAAAAGCTGGAG 58.480 40.741 0.00 0.00 37.24 3.86
1360 1412 8.225416 TCCATAGAGTACTATCTAAAAGCTGGA 58.775 37.037 0.00 1.77 37.24 3.86
1361 1413 8.410673 TCCATAGAGTACTATCTAAAAGCTGG 57.589 38.462 0.00 0.00 37.24 4.85
1425 1886 2.932614 GAGCTAGGTACAGCAACACATG 59.067 50.000 7.83 0.00 44.35 3.21
1555 2017 4.684134 GCACCACACAGGGCCCAT 62.684 66.667 27.56 9.08 43.89 4.00
1561 2023 2.361757 TCAATTGAAAGCACCACACAGG 59.638 45.455 5.45 0.00 45.67 4.00
1587 2049 6.513806 TTTTCACTATGTGCATGCTTACAT 57.486 33.333 22.68 22.68 40.39 2.29
1629 2093 6.942886 TTTGCTATTAGATTTGGTTTTGCG 57.057 33.333 0.00 0.00 0.00 4.85
1703 2168 7.611079 TCCATGATTGTCATAAATCTCACAACA 59.389 33.333 0.00 0.00 34.28 3.33
1739 2207 0.852842 ATGGCTAGCCCCATAAAGCA 59.147 50.000 30.81 9.30 43.65 3.91
1742 2210 2.912956 CCTCTATGGCTAGCCCCATAAA 59.087 50.000 30.81 11.72 44.83 1.40
1807 2275 5.339008 CCATAGTTAGTGAAGCTGTGGTA 57.661 43.478 0.00 0.00 36.95 3.25
1831 2301 9.219603 TCTATCTTACAACAATGTCTTTCAAGG 57.780 33.333 0.00 0.00 41.05 3.61
1896 2708 3.813166 TCTGCAACAGCCTAACAGTAAAC 59.187 43.478 0.00 0.00 0.00 2.01
2012 2824 1.361204 AAAAGGGAGGCAAAATGGGG 58.639 50.000 0.00 0.00 0.00 4.96
2063 2875 7.307751 GCAAAATTAGAGTACTGCAACAGTGTA 60.308 37.037 10.42 0.00 45.01 2.90
2087 2899 9.941325 AACAATAACAATCATTGGAAAATAGCA 57.059 25.926 1.58 0.00 37.64 3.49
2096 2908 7.360269 GCAAAGTGGAACAATAACAATCATTGG 60.360 37.037 1.58 0.00 44.16 3.16
2451 3264 8.260818 AGAACAACACACTGCAATCTATACTAT 58.739 33.333 0.00 0.00 0.00 2.12
2522 3335 3.203040 AGAACCTCAGGTATTGGATTGGG 59.797 47.826 0.00 0.00 33.12 4.12
2579 3400 1.801178 AGTCTTTTGCTACTGCTTCGC 59.199 47.619 0.00 0.00 40.48 4.70
2601 3422 5.598417 ACATAAAGGGCATAATTTCAGGGTC 59.402 40.000 0.00 0.00 0.00 4.46
2624 3445 3.569701 TCTTGCCCAGAAATCTGTCAAAC 59.430 43.478 9.43 0.00 42.27 2.93
2720 3541 6.070021 ACAGGAGTATCACCAAATCTCATTGA 60.070 38.462 0.00 0.00 36.25 2.57
2762 3583 2.572290 GCCTGCAATCCTACCGTTTAT 58.428 47.619 0.00 0.00 0.00 1.40
2767 3588 1.149174 ATGGCCTGCAATCCTACCG 59.851 57.895 3.32 0.00 0.00 4.02
2942 3766 8.541312 CGTCTACTATACTCATATGTACCATCG 58.459 40.741 1.90 0.00 0.00 3.84
3048 3872 4.142315 CCGATGTTTCATTCATTGGAGCTT 60.142 41.667 6.38 0.00 45.06 3.74
3149 3973 1.934589 TACGCACATGCACTACCATC 58.065 50.000 4.49 0.00 42.21 3.51
3159 3983 2.299993 ACCAGACAGATACGCACATG 57.700 50.000 0.00 0.00 0.00 3.21
3168 3992 4.156455 ACAACAGAACAACCAGACAGAT 57.844 40.909 0.00 0.00 0.00 2.90
3195 4019 0.755698 GACAGGCCTCCCTACGATGA 60.756 60.000 0.00 0.00 40.33 2.92
3203 4027 1.222936 CATCAGTGACAGGCCTCCC 59.777 63.158 0.00 0.00 0.00 4.30
3215 4039 2.357154 GGCATGGAACCTAACCATCAGT 60.357 50.000 0.00 0.00 45.00 3.41
3285 4109 2.112691 ACCCCATCCCTATGACTAGGAG 59.887 54.545 0.14 0.00 46.66 3.69
3286 4110 2.161624 ACCCCATCCCTATGACTAGGA 58.838 52.381 0.14 0.00 46.66 2.94
3357 4190 7.930325 ACATAATACAGATCCAACTGACATGAG 59.070 37.037 0.00 0.00 40.63 2.90
3410 4243 9.247861 AGTTTAAAGATACATGGCAGATTTCTT 57.752 29.630 0.00 0.00 0.00 2.52
3451 4287 5.772521 AGCAAACAAGTCATATCAACAACC 58.227 37.500 0.00 0.00 0.00 3.77
3499 4335 2.361119 CCAAAGTGAGGATGGATGCATG 59.639 50.000 2.46 0.00 36.27 4.06
3500 4336 2.242965 TCCAAAGTGAGGATGGATGCAT 59.757 45.455 0.00 0.00 38.30 3.96
3544 4380 2.290134 TGTACAGCTCGACTACTCAGGT 60.290 50.000 0.00 0.00 0.00 4.00
3546 4382 4.624336 AATGTACAGCTCGACTACTCAG 57.376 45.455 0.33 0.00 0.00 3.35
3547 4383 5.386958 AAAATGTACAGCTCGACTACTCA 57.613 39.130 0.33 0.00 0.00 3.41
3570 4406 2.424601 GCACCTCAGCAGCAAATAATCA 59.575 45.455 0.00 0.00 0.00 2.57
3576 4412 4.256462 TTGCACCTCAGCAGCAAA 57.744 50.000 0.00 0.00 46.54 3.68
3595 4431 2.945440 GCCATACCAGGAAATCACAGCA 60.945 50.000 0.00 0.00 0.00 4.41
3619 4455 3.864243 TCGTACAACCAACAAGAACAGT 58.136 40.909 0.00 0.00 0.00 3.55
3633 4469 5.362263 AGTAGCAAAACTTTCCTCGTACAA 58.638 37.500 0.00 0.00 0.00 2.41
3693 4530 3.156293 TGTAACTCAGCAAATGCACCAT 58.844 40.909 8.28 0.00 45.16 3.55
3706 4543 5.298276 GGGTCACTGACAAATTTGTAACTCA 59.702 40.000 23.33 15.44 42.43 3.41
3759 4598 0.461548 TGGCTAGCAGATGGTTCTCG 59.538 55.000 18.24 0.00 0.00 4.04
3760 4599 1.208052 TGTGGCTAGCAGATGGTTCTC 59.792 52.381 18.24 0.00 0.00 2.87
3788 4629 4.577693 TCAATGCCACAGCTCTTATCATTC 59.422 41.667 0.00 0.00 40.80 2.67
3805 4646 4.970662 TTTAAGCCATCTGACTCAATGC 57.029 40.909 0.00 0.00 0.00 3.56
3817 4658 9.515226 TTAACATCTTCAGTAGTTTTAAGCCAT 57.485 29.630 0.00 0.00 0.00 4.40
3824 4665 8.747538 ACAAGGTTAACATCTTCAGTAGTTTT 57.252 30.769 8.10 0.00 0.00 2.43
3829 4670 5.407387 GCGAACAAGGTTAACATCTTCAGTA 59.593 40.000 8.10 0.00 0.00 2.74
3843 4684 1.226746 GCTACACAAGCGAACAAGGT 58.773 50.000 0.00 0.00 42.53 3.50
3875 4716 7.868415 ACTTCATGGCTCGATAAATTCTAGTAC 59.132 37.037 0.00 0.00 0.00 2.73
3877 4718 6.703607 CACTTCATGGCTCGATAAATTCTAGT 59.296 38.462 0.00 0.00 0.00 2.57
3880 4721 4.274459 GCACTTCATGGCTCGATAAATTCT 59.726 41.667 0.00 0.00 0.00 2.40
3893 4737 1.464608 CAAGTACACCGCACTTCATGG 59.535 52.381 0.00 0.00 33.99 3.66
3901 4745 2.428187 CACCCCAAGTACACCGCA 59.572 61.111 0.00 0.00 0.00 5.69
3902 4746 3.053896 GCACCCCAAGTACACCGC 61.054 66.667 0.00 0.00 0.00 5.68
3904 4748 2.359478 CCGCACCCCAAGTACACC 60.359 66.667 0.00 0.00 0.00 4.16
3905 4749 1.071814 TTCCGCACCCCAAGTACAC 59.928 57.895 0.00 0.00 0.00 2.90
3906 4750 1.071814 GTTCCGCACCCCAAGTACA 59.928 57.895 0.00 0.00 0.00 2.90
3907 4751 1.673337 GGTTCCGCACCCCAAGTAC 60.673 63.158 0.00 0.00 40.19 2.73
3908 4752 2.751688 GGTTCCGCACCCCAAGTA 59.248 61.111 0.00 0.00 40.19 2.24
3925 4769 5.665916 ATTAGCCACTTCCTGAAATTTGG 57.334 39.130 0.00 0.00 0.00 3.28
3933 4777 4.925646 GCTTTCAAAATTAGCCACTTCCTG 59.074 41.667 0.00 0.00 0.00 3.86
3936 4780 5.802451 GCTAGCTTTCAAAATTAGCCACTTC 59.198 40.000 7.70 0.00 35.53 3.01
3957 4801 4.764823 CCACTGGTTGGTTTAAATCAGCTA 59.235 41.667 14.03 8.05 41.10 3.32
3972 4816 2.492773 GCACTGCAAGCCACTGGTT 61.493 57.895 0.00 0.00 37.60 3.67
3973 4817 2.908940 GCACTGCAAGCCACTGGT 60.909 61.111 0.00 0.00 37.60 4.00
3974 4818 2.908428 TGCACTGCAAGCCACTGG 60.908 61.111 0.00 0.00 37.60 4.00
3975 4819 2.643272 CTGCACTGCAAGCCACTG 59.357 61.111 4.99 0.00 38.41 3.66
3996 4840 0.819582 ACCTACAGCAATGCAATGGC 59.180 50.000 8.35 1.49 46.28 4.40
3998 4842 4.380841 AATCACCTACAGCAATGCAATG 57.619 40.909 8.35 0.00 0.00 2.82
3999 4843 5.887598 TCTAAATCACCTACAGCAATGCAAT 59.112 36.000 8.35 0.00 0.00 3.56
4016 4860 8.832487 CATCAAACAGTGCTTACATCTAAATC 57.168 34.615 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.