Multiple sequence alignment - TraesCS6D01G202200

Loading Multiple Alignment...

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 TraesCS6D01G202200 chr6D 100.000 5202 0 0 1 5202 285185247 285180046 0.000000e+00 9607.0
1 TraesCS6D01G202200 chr6D 77.855 289 39 16 2854 3123 470142765 470142483 6.970000e-34 156.0
2 TraesCS6D01G202200 chr6D 77.170 311 38 15 2841 3120 9961356 9961664 3.240000e-32 150.0
3 TraesCS6D01G202200 chr6D 76.972 317 39 16 2844 3128 450085579 450085265 3.240000e-32 150.0
4 TraesCS6D01G202200 chr6D 97.561 41 1 0 4392 4432 405119632 405119592 2.600000e-08 71.3
5 TraesCS6D01G202200 chr6A 95.318 3353 121 13 1414 4745 405663924 405660587 0.000000e+00 5289.0
6 TraesCS6D01G202200 chr6A 94.290 1366 36 12 1 1325 405665315 405663951 0.000000e+00 2052.0
7 TraesCS6D01G202200 chr6A 94.540 348 19 0 4737 5084 405660560 405660213 5.930000e-149 538.0
8 TraesCS6D01G202200 chr6A 92.623 122 6 2 5081 5202 405486717 405486599 6.930000e-39 172.0
9 TraesCS6D01G202200 chr6B 95.961 3169 106 13 1557 4714 446053660 446050503 0.000000e+00 5123.0
10 TraesCS6D01G202200 chr6B 93.787 1368 37 10 1 1328 446055217 446053858 0.000000e+00 2012.0
11 TraesCS6D01G202200 chr6B 92.505 467 19 3 4737 5202 446050429 446049978 0.000000e+00 654.0
12 TraesCS6D01G202200 chr6B 94.444 162 6 1 1414 1572 446053838 446053677 4.020000e-61 246.0
13 TraesCS6D01G202200 chr6B 92.000 50 2 2 4383 4432 480240012 480240059 9.350000e-08 69.4
14 TraesCS6D01G202200 chr1D 82.584 178 26 5 2841 3014 246041961 246042137 9.020000e-33 152.0
15 TraesCS6D01G202200 chr1D 81.548 168 25 6 2844 3006 393760268 393760102 3.270000e-27 134.0
16 TraesCS6D01G202200 chr4B 95.604 91 4 0 1325 1415 104746608 104746518 4.200000e-31 147.0
17 TraesCS6D01G202200 chr1B 76.603 312 43 18 2834 3117 26466615 26466306 1.510000e-30 145.0
18 TraesCS6D01G202200 chr4D 76.797 306 38 15 2841 3115 379345301 379345604 1.950000e-29 141.0
19 TraesCS6D01G202200 chr2D 88.073 109 13 0 4631 4739 81632492 81632600 4.230000e-26 130.0
20 TraesCS6D01G202200 chr2D 92.308 91 5 2 1326 1415 484048826 484048737 1.520000e-25 128.0
21 TraesCS6D01G202200 chr2D 95.455 44 1 1 4400 4443 262457421 262457379 9.350000e-08 69.4
22 TraesCS6D01G202200 chr5B 77.406 239 29 15 4530 4745 311849502 311849266 9.150000e-23 119.0
23 TraesCS6D01G202200 chr5B 83.784 111 15 2 3016 3123 690981216 690981106 9.220000e-18 102.0
24 TraesCS6D01G202200 chr2A 77.637 237 24 11 4530 4739 310410046 310410280 3.290000e-22 117.0
25 TraesCS6D01G202200 chr3A 84.071 113 14 1 4631 4739 639495034 639495146 7.120000e-19 106.0
26 TraesCS6D01G202200 chr3A 96.491 57 2 0 1359 1415 83952773 83952829 1.540000e-15 95.3
27 TraesCS6D01G202200 chr3A 92.727 55 2 1 1363 1415 689506741 689506795 1.550000e-10 78.7
28 TraesCS6D01G202200 chr3A 92.157 51 4 0 4382 4432 599863912 599863862 7.230000e-09 73.1
29 TraesCS6D01G202200 chrUn 87.778 90 8 2 4659 4745 2744953 2744864 9.220000e-18 102.0
30 TraesCS6D01G202200 chrUn 88.095 84 7 2 4659 4739 333448462 333448545 4.290000e-16 97.1
31 TraesCS6D01G202200 chr4A 76.569 239 25 11 4530 4739 632636557 632636793 9.220000e-18 102.0
32 TraesCS6D01G202200 chr4A 83.178 107 12 5 3016 3120 646855617 646855719 5.550000e-15 93.5
33 TraesCS6D01G202200 chr7D 84.884 86 11 1 3016 3099 638569946 638569861 9.280000e-13 86.1
34 TraesCS6D01G202200 chr7D 95.745 47 2 0 4392 4438 204247188 204247234 5.590000e-10 76.8
35 TraesCS6D01G202200 chr3D 89.062 64 5 2 4374 4435 79511704 79511641 1.550000e-10 78.7
36 TraesCS6D01G202200 chr7A 95.745 47 2 0 4392 4438 216344334 216344380 5.590000e-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 TraesCS6D01G202200 chr6D 285180046 285185247 5201 True 9607.000000 9607 100.00000 1 5202 1 chr6D.!!$R1 5201
1 TraesCS6D01G202200 chr6A 405660213 405665315 5102 True 2626.333333 5289 94.71600 1 5084 3 chr6A.!!$R2 5083
2 TraesCS6D01G202200 chr6B 446049978 446055217 5239 True 2008.750000 5123 94.17425 1 5202 4 chr6B.!!$R1 5201

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
790 819 1.003545 CGCCAGTTGAGTTCACACAAG 60.004 52.381 0.00 0.0 0.00 3.16 F
1342 1400 0.035739 TACTTTCCGGCCACTTGGTC 59.964 55.000 2.24 0.0 37.57 4.02 F
1760 1853 0.034089 AGCCAAGCACTAACCATCCC 60.034 55.000 0.00 0.0 0.00 3.85 F
2898 3006 0.107410 GGTTGGTGCGGATATGGTCA 60.107 55.000 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 1814 5.109903 GGCTGAAGCGTTCTTAATAGAGAA 58.890 41.667 0.00 0.0 43.26 2.87 R
2958 3067 0.106167 ACCGGAGCTATGCCTAGACA 60.106 55.000 9.46 0.0 0.00 3.41 R
2963 3072 0.978146 ACAAGACCGGAGCTATGCCT 60.978 55.000 9.46 0.0 0.00 4.75 R
4225 4339 0.101939 GACCGGTGGATCGAACTACC 59.898 60.000 14.63 16.9 37.92 3.18 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
23 24 2.087009 GTCGCCGAAGAGGTTGTCG 61.087 63.158 0.00 0.00 43.70 4.35
201 202 2.839632 AGGCGCGGGAGATGATGA 60.840 61.111 8.83 0.00 0.00 2.92
605 624 3.145551 GCCGGGACTAAGAGGCGA 61.146 66.667 2.18 0.00 40.17 5.54
607 626 2.029307 GCCGGGACTAAGAGGCGATT 62.029 60.000 2.18 0.00 40.17 3.34
783 812 4.090057 GCGGCGCCAGTTGAGTTC 62.090 66.667 28.98 0.81 0.00 3.01
784 813 2.664851 CGGCGCCAGTTGAGTTCA 60.665 61.111 28.98 0.00 0.00 3.18
785 814 2.946762 GGCGCCAGTTGAGTTCAC 59.053 61.111 24.80 0.00 0.00 3.18
786 815 1.891919 GGCGCCAGTTGAGTTCACA 60.892 57.895 24.80 0.00 0.00 3.58
788 817 1.436195 GCGCCAGTTGAGTTCACACA 61.436 55.000 0.00 0.00 0.00 3.72
789 818 1.013596 CGCCAGTTGAGTTCACACAA 58.986 50.000 0.00 0.00 0.00 3.33
790 819 1.003545 CGCCAGTTGAGTTCACACAAG 60.004 52.381 0.00 0.00 0.00 3.16
791 820 1.334869 GCCAGTTGAGTTCACACAAGG 59.665 52.381 0.00 0.00 0.00 3.61
795 826 3.689161 CAGTTGAGTTCACACAAGGACAA 59.311 43.478 0.00 0.00 0.00 3.18
1186 1235 1.986575 GCTCTGCTTCGGGTTCATGC 61.987 60.000 0.00 0.00 0.00 4.06
1240 1289 4.722700 CACTGAAGGCCGGGGTGG 62.723 72.222 2.18 0.00 42.50 4.61
1329 1387 9.233232 ACAAGAAAATCGTTTTGTGATACTTTC 57.767 29.630 1.33 0.00 32.90 2.62
1331 1389 7.075741 AGAAAATCGTTTTGTGATACTTTCCG 58.924 34.615 1.33 0.00 31.94 4.30
1333 1391 2.481185 TCGTTTTGTGATACTTTCCGGC 59.519 45.455 0.00 0.00 0.00 6.13
1335 1393 2.554893 GTTTTGTGATACTTTCCGGCCA 59.445 45.455 2.24 0.00 0.00 5.36
1336 1394 1.816074 TTGTGATACTTTCCGGCCAC 58.184 50.000 2.24 0.00 0.00 5.01
1338 1396 1.349688 TGTGATACTTTCCGGCCACTT 59.650 47.619 2.24 0.00 0.00 3.16
1340 1398 1.339631 TGATACTTTCCGGCCACTTGG 60.340 52.381 2.24 0.00 38.53 3.61
1341 1399 0.696501 ATACTTTCCGGCCACTTGGT 59.303 50.000 2.24 0.00 37.57 3.67
1342 1400 0.035739 TACTTTCCGGCCACTTGGTC 59.964 55.000 2.24 0.00 37.57 4.02
1344 1402 1.228124 TTTCCGGCCACTTGGTCTG 60.228 57.895 2.24 0.00 37.76 3.51
1345 1403 1.701031 TTTCCGGCCACTTGGTCTGA 61.701 55.000 2.24 0.00 37.76 3.27
1347 1405 2.583441 CCGGCCACTTGGTCTGAGA 61.583 63.158 2.24 0.00 37.76 3.27
1348 1406 1.079543 CGGCCACTTGGTCTGAGAG 60.080 63.158 2.24 0.00 37.76 3.20
1349 1407 1.536073 CGGCCACTTGGTCTGAGAGA 61.536 60.000 2.24 0.00 37.76 3.10
1351 1409 0.972883 GCCACTTGGTCTGAGAGACT 59.027 55.000 3.85 0.00 44.46 3.24
1352 1410 1.346068 GCCACTTGGTCTGAGAGACTT 59.654 52.381 3.85 0.00 44.46 3.01
1353 1411 2.224402 GCCACTTGGTCTGAGAGACTTT 60.224 50.000 3.85 0.00 44.46 2.66
1354 1412 3.745797 GCCACTTGGTCTGAGAGACTTTT 60.746 47.826 3.85 0.00 44.46 2.27
1355 1413 4.455606 CCACTTGGTCTGAGAGACTTTTT 58.544 43.478 3.85 0.00 44.46 1.94
1356 1414 4.274459 CCACTTGGTCTGAGAGACTTTTTG 59.726 45.833 3.85 0.00 44.46 2.44
1357 1415 4.878397 CACTTGGTCTGAGAGACTTTTTGT 59.122 41.667 3.85 0.00 44.46 2.83
1358 1416 6.049149 CACTTGGTCTGAGAGACTTTTTGTA 58.951 40.000 3.85 0.00 44.46 2.41
1359 1417 6.538742 CACTTGGTCTGAGAGACTTTTTGTAA 59.461 38.462 3.85 0.00 44.46 2.41
1360 1418 7.227512 CACTTGGTCTGAGAGACTTTTTGTAAT 59.772 37.037 3.85 0.00 44.46 1.89
1361 1419 7.442666 ACTTGGTCTGAGAGACTTTTTGTAATC 59.557 37.037 3.85 0.00 44.46 1.75
1362 1420 6.231211 TGGTCTGAGAGACTTTTTGTAATCC 58.769 40.000 3.85 0.00 44.46 3.01
1363 1421 6.043243 TGGTCTGAGAGACTTTTTGTAATCCT 59.957 38.462 3.85 0.00 44.46 3.24
1364 1422 6.592220 GGTCTGAGAGACTTTTTGTAATCCTC 59.408 42.308 3.85 0.00 44.46 3.71
1365 1423 7.382898 GTCTGAGAGACTTTTTGTAATCCTCT 58.617 38.462 0.00 0.00 41.88 3.69
1366 1424 7.875554 GTCTGAGAGACTTTTTGTAATCCTCTT 59.124 37.037 0.00 0.00 41.88 2.85
1367 1425 8.091449 TCTGAGAGACTTTTTGTAATCCTCTTC 58.909 37.037 0.00 0.00 30.59 2.87
1368 1426 7.967908 TGAGAGACTTTTTGTAATCCTCTTCT 58.032 34.615 0.00 0.00 30.59 2.85
1369 1427 7.875041 TGAGAGACTTTTTGTAATCCTCTTCTG 59.125 37.037 0.00 0.00 30.59 3.02
1370 1428 6.652900 AGAGACTTTTTGTAATCCTCTTCTGC 59.347 38.462 0.00 0.00 0.00 4.26
1371 1429 6.538263 AGACTTTTTGTAATCCTCTTCTGCT 58.462 36.000 0.00 0.00 0.00 4.24
1372 1430 7.680730 AGACTTTTTGTAATCCTCTTCTGCTA 58.319 34.615 0.00 0.00 0.00 3.49
1373 1431 8.157476 AGACTTTTTGTAATCCTCTTCTGCTAA 58.843 33.333 0.00 0.00 0.00 3.09
1374 1432 8.691661 ACTTTTTGTAATCCTCTTCTGCTAAA 57.308 30.769 0.00 0.00 0.00 1.85
1375 1433 9.301897 ACTTTTTGTAATCCTCTTCTGCTAAAT 57.698 29.630 0.00 0.00 0.00 1.40
1376 1434 9.780413 CTTTTTGTAATCCTCTTCTGCTAAATC 57.220 33.333 0.00 0.00 0.00 2.17
1377 1435 8.862325 TTTTGTAATCCTCTTCTGCTAAATCA 57.138 30.769 0.00 0.00 0.00 2.57
1378 1436 8.862325 TTTGTAATCCTCTTCTGCTAAATCAA 57.138 30.769 0.00 0.00 0.00 2.57
1379 1437 9.466497 TTTGTAATCCTCTTCTGCTAAATCAAT 57.534 29.630 0.00 0.00 0.00 2.57
1380 1438 9.466497 TTGTAATCCTCTTCTGCTAAATCAATT 57.534 29.630 0.00 0.00 0.00 2.32
1381 1439 8.896744 TGTAATCCTCTTCTGCTAAATCAATTG 58.103 33.333 0.00 0.00 0.00 2.32
1382 1440 9.113838 GTAATCCTCTTCTGCTAAATCAATTGA 57.886 33.333 11.26 11.26 0.00 2.57
1383 1441 8.585471 AATCCTCTTCTGCTAAATCAATTGAA 57.415 30.769 13.09 0.00 0.00 2.69
1384 1442 7.383102 TCCTCTTCTGCTAAATCAATTGAAC 57.617 36.000 13.09 0.88 0.00 3.18
1385 1443 6.092670 TCCTCTTCTGCTAAATCAATTGAACG 59.907 38.462 13.09 2.53 0.00 3.95
1386 1444 5.631026 TCTTCTGCTAAATCAATTGAACGC 58.369 37.500 13.09 12.44 0.00 4.84
1387 1445 4.355543 TCTGCTAAATCAATTGAACGCC 57.644 40.909 13.09 1.26 0.00 5.68
1388 1446 3.755905 TCTGCTAAATCAATTGAACGCCA 59.244 39.130 13.09 5.74 0.00 5.69
1389 1447 4.095410 TGCTAAATCAATTGAACGCCAG 57.905 40.909 13.09 6.85 0.00 4.85
1390 1448 2.854185 GCTAAATCAATTGAACGCCAGC 59.146 45.455 13.09 12.54 0.00 4.85
1391 1449 3.673052 GCTAAATCAATTGAACGCCAGCA 60.673 43.478 13.09 0.00 0.00 4.41
1392 1450 3.383620 AAATCAATTGAACGCCAGCAA 57.616 38.095 13.09 0.00 0.00 3.91
1393 1451 3.598019 AATCAATTGAACGCCAGCAAT 57.402 38.095 13.09 0.00 36.35 3.56
1394 1452 2.350899 TCAATTGAACGCCAGCAATG 57.649 45.000 5.45 0.00 35.11 2.82
1395 1453 0.717224 CAATTGAACGCCAGCAATGC 59.283 50.000 0.00 0.00 35.11 3.56
1396 1454 0.604578 AATTGAACGCCAGCAATGCT 59.395 45.000 0.00 0.00 40.77 3.79
1409 1467 4.877378 AGCAATGCTGGATCTTTCAAAA 57.123 36.364 7.07 0.00 37.57 2.44
1410 1468 5.217978 AGCAATGCTGGATCTTTCAAAAA 57.782 34.783 7.07 0.00 37.57 1.94
1576 1669 2.397597 TGTAGAGTGATATGCTGGCCA 58.602 47.619 4.71 4.71 0.00 5.36
1594 1687 2.893489 GCCACCACTTTCCTCTTTTGAT 59.107 45.455 0.00 0.00 0.00 2.57
1721 1814 4.280929 GCCCATCCTTTCTGTAACAGTTTT 59.719 41.667 0.00 0.00 32.61 2.43
1760 1853 0.034089 AGCCAAGCACTAACCATCCC 60.034 55.000 0.00 0.00 0.00 3.85
1845 1949 5.702670 ACTGTATCAGTGTTCCAATGACTTG 59.297 40.000 1.44 0.00 43.63 3.16
1896 2000 7.920160 TCAATAGTATTTGCTGATGTGTCAA 57.080 32.000 0.00 0.00 33.05 3.18
1915 2019 5.470437 TGTCAATTACACGCCTTTGTATTCA 59.530 36.000 0.00 0.00 31.98 2.57
2711 2815 6.564499 GCCATACAAACAGAAATTTTGTGCAG 60.564 38.462 10.06 0.18 44.86 4.41
2811 2915 7.309770 AGGGGATGCAAACTAACAAAAATAA 57.690 32.000 0.00 0.00 0.00 1.40
2898 3006 0.107410 GGTTGGTGCGGATATGGTCA 60.107 55.000 0.00 0.00 0.00 4.02
2907 3015 4.334203 GTGCGGATATGGTCATTGTTGTAA 59.666 41.667 0.00 0.00 0.00 2.41
2917 3025 7.389803 TGGTCATTGTTGTAATTCATCGATT 57.610 32.000 0.00 0.00 0.00 3.34
2933 3042 2.094258 TCGATTGCTGTTTCATCGCTTC 59.906 45.455 0.00 0.00 35.05 3.86
2958 3067 7.122204 TCGGAGTTTTTCTTTTCTTTTTCCTCT 59.878 33.333 0.00 0.00 0.00 3.69
2973 3082 2.870175 TCCTCTGTCTAGGCATAGCTC 58.130 52.381 0.00 0.00 36.51 4.09
2975 3084 1.539388 CTCTGTCTAGGCATAGCTCCG 59.461 57.143 0.00 0.00 0.00 4.63
3003 3112 2.497107 TGACTTTGCTCTTTGCTTGC 57.503 45.000 0.00 0.00 43.37 4.01
3045 3154 2.565841 CTAGTTATGCAGAGGTTGGGC 58.434 52.381 0.00 0.00 0.00 5.36
3082 3192 7.611467 TGTGTTTGTATCTCCTTTATGCTTCAT 59.389 33.333 0.00 0.00 0.00 2.57
3101 3213 8.587608 TGCTTCATTTTGAGAATAAAATCCAGT 58.412 29.630 0.00 0.00 37.97 4.00
3111 3223 9.958180 TGAGAATAAAATCCAGTATTTGTCAGA 57.042 29.630 0.00 0.00 37.85 3.27
3157 3269 5.372661 ACATGGCTTTCCCCTAGTTATATGT 59.627 40.000 0.00 0.00 0.00 2.29
3166 3278 8.626917 TTCCCCTAGTTATATGTGGTTCTTTA 57.373 34.615 0.00 0.00 0.00 1.85
3205 3317 6.660521 TGCCATTTTCATGTCTACTTCATCTT 59.339 34.615 0.00 0.00 0.00 2.40
3301 3413 3.515104 GACATTCACATGGACCCCAATTT 59.485 43.478 0.00 0.00 36.95 1.82
3303 3415 4.711355 ACATTCACATGGACCCCAATTTAG 59.289 41.667 0.00 0.00 36.95 1.85
3332 3444 2.428071 GCAACGCTTCAGTGCTGC 60.428 61.111 0.26 0.26 39.86 5.25
3350 3462 7.117236 CAGTGCTGCATGTATGATTTTCTTTTT 59.883 33.333 5.27 0.00 0.00 1.94
3519 3631 4.216411 TCTGTTGTATGCCCCTCTAAAC 57.784 45.455 0.00 0.00 0.00 2.01
3544 3656 4.560035 GCACAATCAGCACACATTTGATAC 59.440 41.667 0.00 0.00 31.64 2.24
3584 3696 9.528018 TCTTTCATTTCTTTTACCACAACATTC 57.472 29.630 0.00 0.00 0.00 2.67
3676 3788 3.355378 CTGCATTGGTATTGGAAGGTCA 58.645 45.455 0.00 0.00 0.00 4.02
3693 3805 3.108376 GGTCAGACAGGAAAGGGTATCT 58.892 50.000 2.17 0.00 0.00 1.98
3698 3810 1.923148 ACAGGAAAGGGTATCTTGGGG 59.077 52.381 0.00 0.00 35.55 4.96
3802 3916 4.019792 TCCAGAGAAATGCTGCAACTAA 57.980 40.909 6.36 0.00 32.06 2.24
3822 3936 8.670135 CAACTAATTTATGTGTTATCCACCGAA 58.330 33.333 0.00 0.00 43.85 4.30
3862 3976 7.483691 GCTTACCAGAACGTTAAATAATGGTTG 59.516 37.037 17.33 13.33 40.03 3.77
3864 3978 6.674066 ACCAGAACGTTAAATAATGGTTGTG 58.326 36.000 0.00 8.76 36.16 3.33
3877 3991 3.918294 TGGTTGTGCCCTACTAATACC 57.082 47.619 0.00 0.00 36.04 2.73
4064 4178 3.623060 AGCTGGATGTACAATAACGCTTG 59.377 43.478 0.00 0.00 0.00 4.01
4103 4217 6.971726 TGATCTACTCGGCTATTTTTCCTA 57.028 37.500 0.00 0.00 0.00 2.94
4183 4297 6.246163 ACGTATTCCCTTCCTTCTGAAAAAT 58.754 36.000 0.00 0.00 31.06 1.82
4225 4339 6.457934 CCATGATTCTGTTTAGCAGCTTAGTG 60.458 42.308 0.00 0.00 44.66 2.74
4331 4445 9.999009 GTTAATTTTGGTAGCTCAGGTATAAAC 57.001 33.333 0.00 0.00 0.00 2.01
4564 4678 2.231529 GGCCGCTGAGATAGAGAACTA 58.768 52.381 0.00 0.00 0.00 2.24
4610 4724 1.064906 GTTAGGGTTTCTGTAGGGGGC 60.065 57.143 0.00 0.00 0.00 5.80
4668 4783 4.794241 GCCTAAAGCGCGCACACG 62.794 66.667 35.10 18.03 44.07 4.49
4681 4796 1.720894 CACACGCACTGAAGCACAA 59.279 52.632 0.00 0.00 0.00 3.33
4745 4874 6.013379 AGATATCTATCATGTCCACCTCGTT 58.987 40.000 2.53 0.00 35.17 3.85
4821 4985 0.036010 CTGGCACCTCTGGAAACGAT 60.036 55.000 0.00 0.00 0.00 3.73
4861 5025 1.381872 ATGCCACGCCCTCTCTAGT 60.382 57.895 0.00 0.00 0.00 2.57
4949 5113 1.167851 CCACATCGATGTTTGGCTGT 58.832 50.000 28.04 2.95 39.39 4.40
5022 5186 8.347004 TCTTGATCAGGAGCTATAGTTCTATG 57.653 38.462 15.24 13.82 0.00 2.23
5098 5262 4.575236 GGTCGACCCCTCTTTTATGAAATC 59.425 45.833 24.75 0.00 0.00 2.17
5109 5273 4.396357 TTTATGAAATCCAGGTGGGTGT 57.604 40.909 0.00 0.00 38.11 4.16
5142 5306 6.237901 CCTCCCCCTTAAAAATTCAAAAAGG 58.762 40.000 0.00 0.00 37.13 3.11
5184 5348 1.546029 GCTCCCAAGCCTTTTGTTAGG 59.454 52.381 0.00 0.00 43.10 2.69
5192 5356 2.438868 CCTTTTGTTAGGCAGTTGGC 57.561 50.000 0.00 0.00 43.74 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.966787 TTCGCCACCAACCTGCCC 62.967 66.667 0.00 0.00 0.00 5.36
201 202 1.960040 TTCCGGTCGCAGATGCAGAT 61.960 55.000 0.00 0.00 40.67 2.90
782 811 2.485479 GCTTCTCCTTGTCCTTGTGTGA 60.485 50.000 0.00 0.00 0.00 3.58
783 812 1.876156 GCTTCTCCTTGTCCTTGTGTG 59.124 52.381 0.00 0.00 0.00 3.82
784 813 1.490490 TGCTTCTCCTTGTCCTTGTGT 59.510 47.619 0.00 0.00 0.00 3.72
785 814 2.260844 TGCTTCTCCTTGTCCTTGTG 57.739 50.000 0.00 0.00 0.00 3.33
786 815 3.297134 TTTGCTTCTCCTTGTCCTTGT 57.703 42.857 0.00 0.00 0.00 3.16
788 817 3.077359 CGATTTGCTTCTCCTTGTCCTT 58.923 45.455 0.00 0.00 0.00 3.36
789 818 2.616510 CCGATTTGCTTCTCCTTGTCCT 60.617 50.000 0.00 0.00 0.00 3.85
790 819 1.740025 CCGATTTGCTTCTCCTTGTCC 59.260 52.381 0.00 0.00 0.00 4.02
791 820 1.131315 GCCGATTTGCTTCTCCTTGTC 59.869 52.381 0.00 0.00 0.00 3.18
795 826 0.460987 CGAGCCGATTTGCTTCTCCT 60.461 55.000 0.00 0.00 42.95 3.69
979 1010 4.869440 CGCCTCTCCTGCGCAGAG 62.869 72.222 38.06 29.15 46.01 3.35
1054 1098 1.134175 GAGAGCAACGGAGAAGAGGAG 59.866 57.143 0.00 0.00 0.00 3.69
1186 1235 0.304705 GAACATACTGCGCAATCGGG 59.695 55.000 13.05 0.79 35.95 5.14
1240 1289 3.869272 CGGCGTCATGAAGCAGCC 61.869 66.667 30.28 23.47 44.00 4.85
1328 1386 2.525629 TCAGACCAAGTGGCCGGA 60.526 61.111 5.05 0.00 39.32 5.14
1329 1387 2.046892 CTCAGACCAAGTGGCCGG 60.047 66.667 0.00 0.00 39.32 6.13
1331 1389 0.036858 GTCTCTCAGACCAAGTGGCC 60.037 60.000 0.00 0.00 39.28 5.36
1333 1391 3.760580 AAAGTCTCTCAGACCAAGTGG 57.239 47.619 0.00 0.00 46.18 4.00
1335 1393 5.104259 ACAAAAAGTCTCTCAGACCAAGT 57.896 39.130 0.00 0.00 46.18 3.16
1336 1394 7.095017 GGATTACAAAAAGTCTCTCAGACCAAG 60.095 40.741 0.00 0.00 46.18 3.61
1338 1396 6.043243 AGGATTACAAAAAGTCTCTCAGACCA 59.957 38.462 0.00 0.00 46.18 4.02
1340 1398 7.382898 AGAGGATTACAAAAAGTCTCTCAGAC 58.617 38.462 0.00 0.00 45.38 3.51
1341 1399 7.546250 AGAGGATTACAAAAAGTCTCTCAGA 57.454 36.000 0.00 0.00 0.00 3.27
1342 1400 8.093927 AGAAGAGGATTACAAAAAGTCTCTCAG 58.906 37.037 0.00 0.00 30.81 3.35
1344 1402 7.148490 GCAGAAGAGGATTACAAAAAGTCTCTC 60.148 40.741 0.00 0.00 30.81 3.20
1345 1403 6.652900 GCAGAAGAGGATTACAAAAAGTCTCT 59.347 38.462 0.00 0.00 0.00 3.10
1347 1405 6.538263 AGCAGAAGAGGATTACAAAAAGTCT 58.462 36.000 0.00 0.00 0.00 3.24
1348 1406 6.809630 AGCAGAAGAGGATTACAAAAAGTC 57.190 37.500 0.00 0.00 0.00 3.01
1349 1407 8.691661 TTTAGCAGAAGAGGATTACAAAAAGT 57.308 30.769 0.00 0.00 0.00 2.66
1351 1409 9.295825 TGATTTAGCAGAAGAGGATTACAAAAA 57.704 29.630 0.00 0.00 0.00 1.94
1352 1410 8.862325 TGATTTAGCAGAAGAGGATTACAAAA 57.138 30.769 0.00 0.00 0.00 2.44
1353 1411 8.862325 TTGATTTAGCAGAAGAGGATTACAAA 57.138 30.769 0.00 0.00 0.00 2.83
1354 1412 9.466497 AATTGATTTAGCAGAAGAGGATTACAA 57.534 29.630 0.00 0.00 0.00 2.41
1355 1413 8.896744 CAATTGATTTAGCAGAAGAGGATTACA 58.103 33.333 0.00 0.00 0.00 2.41
1356 1414 9.113838 TCAATTGATTTAGCAGAAGAGGATTAC 57.886 33.333 3.38 0.00 0.00 1.89
1357 1415 9.685276 TTCAATTGATTTAGCAGAAGAGGATTA 57.315 29.630 9.40 0.00 0.00 1.75
1358 1416 8.465201 GTTCAATTGATTTAGCAGAAGAGGATT 58.535 33.333 9.40 0.00 0.00 3.01
1359 1417 7.201679 CGTTCAATTGATTTAGCAGAAGAGGAT 60.202 37.037 9.40 0.00 0.00 3.24
1360 1418 6.092670 CGTTCAATTGATTTAGCAGAAGAGGA 59.907 38.462 9.40 0.00 0.00 3.71
1361 1419 6.253746 CGTTCAATTGATTTAGCAGAAGAGG 58.746 40.000 9.40 0.00 0.00 3.69
1362 1420 5.736358 GCGTTCAATTGATTTAGCAGAAGAG 59.264 40.000 9.40 0.00 0.00 2.85
1363 1421 5.391950 GGCGTTCAATTGATTTAGCAGAAGA 60.392 40.000 9.40 0.00 0.00 2.87
1364 1422 4.795278 GGCGTTCAATTGATTTAGCAGAAG 59.205 41.667 9.40 0.00 0.00 2.85
1365 1423 4.217334 TGGCGTTCAATTGATTTAGCAGAA 59.783 37.500 9.40 0.81 0.00 3.02
1366 1424 3.755905 TGGCGTTCAATTGATTTAGCAGA 59.244 39.130 9.40 1.41 0.00 4.26
1367 1425 4.095410 TGGCGTTCAATTGATTTAGCAG 57.905 40.909 9.40 0.00 0.00 4.24
1368 1426 3.673052 GCTGGCGTTCAATTGATTTAGCA 60.673 43.478 9.40 0.00 0.00 3.49
1369 1427 2.854185 GCTGGCGTTCAATTGATTTAGC 59.146 45.455 9.40 11.82 0.00 3.09
1370 1428 4.095410 TGCTGGCGTTCAATTGATTTAG 57.905 40.909 9.40 5.35 0.00 1.85
1371 1429 4.511617 TTGCTGGCGTTCAATTGATTTA 57.488 36.364 9.40 0.00 0.00 1.40
1372 1430 3.383620 TTGCTGGCGTTCAATTGATTT 57.616 38.095 9.40 0.00 0.00 2.17
1373 1431 3.255725 CATTGCTGGCGTTCAATTGATT 58.744 40.909 9.40 0.00 31.15 2.57
1374 1432 2.883574 CATTGCTGGCGTTCAATTGAT 58.116 42.857 9.40 0.00 31.15 2.57
1375 1433 1.669502 GCATTGCTGGCGTTCAATTGA 60.670 47.619 3.38 3.38 31.15 2.57
1376 1434 0.717224 GCATTGCTGGCGTTCAATTG 59.283 50.000 0.16 0.00 31.15 2.32
1377 1435 0.604578 AGCATTGCTGGCGTTCAATT 59.395 45.000 11.09 0.00 37.57 2.32
1378 1436 2.269978 AGCATTGCTGGCGTTCAAT 58.730 47.368 11.09 0.00 37.57 2.57
1379 1437 3.762293 AGCATTGCTGGCGTTCAA 58.238 50.000 11.09 0.00 37.57 2.69
1388 1446 4.877378 TTTTGAAAGATCCAGCATTGCT 57.123 36.364 5.03 5.03 40.77 3.91
1489 1550 2.287909 GCAGCTTATCTCGGAGTAGGTG 60.288 54.545 21.06 21.06 37.39 4.00
1576 1669 5.634118 TCATGATCAAAAGAGGAAAGTGGT 58.366 37.500 0.00 0.00 0.00 4.16
1594 1687 9.356433 CAACATGCTGTACAATTTATTTCATGA 57.644 29.630 0.00 0.00 34.56 3.07
1721 1814 5.109903 GGCTGAAGCGTTCTTAATAGAGAA 58.890 41.667 0.00 0.00 43.26 2.87
1760 1853 6.382869 AACTCTCACCAAATCAGAACTTTG 57.617 37.500 0.00 0.00 34.17 2.77
1870 1974 8.510243 TGACACATCAGCAAATACTATTGATT 57.490 30.769 0.00 0.00 31.84 2.57
1896 2000 7.173218 CCATCTATGAATACAAAGGCGTGTAAT 59.827 37.037 7.94 0.72 37.52 1.89
2687 2791 6.479660 ACTGCACAAAATTTCTGTTTGTATGG 59.520 34.615 2.48 0.01 45.16 2.74
2701 2805 9.836864 TGATCTGTATAGATTACTGCACAAAAT 57.163 29.630 3.24 0.00 43.63 1.82
2829 2933 7.505585 TGAAAAAGGTTCTCCAGTAACAATCAT 59.494 33.333 0.00 0.00 35.89 2.45
2898 3006 6.855836 ACAGCAATCGATGAATTACAACAAT 58.144 32.000 0.00 0.00 31.28 2.71
2907 3015 4.787563 GCGATGAAACAGCAATCGATGAAT 60.788 41.667 0.00 0.00 36.95 2.57
2917 3025 0.320334 TCCGAAGCGATGAAACAGCA 60.320 50.000 0.00 0.00 0.00 4.41
2933 3042 7.220875 CAGAGGAAAAAGAAAAGAAAAACTCCG 59.779 37.037 0.00 0.00 0.00 4.63
2958 3067 0.106167 ACCGGAGCTATGCCTAGACA 60.106 55.000 9.46 0.00 0.00 3.41
2963 3072 0.978146 ACAAGACCGGAGCTATGCCT 60.978 55.000 9.46 0.00 0.00 4.75
2973 3082 2.673368 GAGCAAAGTCATACAAGACCGG 59.327 50.000 0.00 0.00 39.34 5.28
2975 3084 5.693814 CAAAGAGCAAAGTCATACAAGACC 58.306 41.667 0.00 0.00 39.34 3.85
3003 3112 3.059188 GGATGTACACACAAAGAACCACG 60.059 47.826 0.00 0.00 38.42 4.94
3045 3154 2.473530 ACAAACACAATGAGCACACG 57.526 45.000 0.00 0.00 0.00 4.49
3119 3231 7.093945 GGGAAAGCCATGTTTTGATTCTAGTTA 60.094 37.037 0.00 0.00 35.15 2.24
3124 3236 3.261643 GGGGAAAGCCATGTTTTGATTCT 59.738 43.478 0.00 0.00 35.15 2.40
3157 3269 7.440856 GGCAAATCAAGACAAAATAAAGAACCA 59.559 33.333 0.00 0.00 0.00 3.67
3166 3278 7.804843 TGAAAATGGCAAATCAAGACAAAAT 57.195 28.000 0.00 0.00 0.00 1.82
3205 3317 4.219507 ACACACAGTCACATTTTGGTTGAA 59.780 37.500 0.00 0.00 0.00 2.69
3265 3377 6.252967 TGTGAATGTCATTACAATCCACAC 57.747 37.500 10.05 6.97 39.58 3.82
3301 3413 4.829064 AGCGTTGCAATTTGAAAGACTA 57.171 36.364 0.59 0.00 0.00 2.59
3303 3415 3.796178 TGAAGCGTTGCAATTTGAAAGAC 59.204 39.130 0.59 0.00 0.00 3.01
3350 3462 7.768240 ACACGATAAGACACTACATACATGAA 58.232 34.615 0.00 0.00 0.00 2.57
3355 3467 8.965172 CCAATAACACGATAAGACACTACATAC 58.035 37.037 0.00 0.00 0.00 2.39
3420 3532 6.327365 TCATATATGCTCAAGGAAAGAGGACA 59.673 38.462 7.92 0.00 36.26 4.02
3519 3631 2.717580 AATGTGTGCTGATTGTGCAG 57.282 45.000 0.00 0.00 41.41 4.41
3559 3671 9.533253 AGAATGTTGTGGTAAAAGAAATGAAAG 57.467 29.630 0.00 0.00 0.00 2.62
3676 3788 2.846827 CCCAAGATACCCTTTCCTGTCT 59.153 50.000 0.00 0.00 31.42 3.41
3693 3805 2.645297 TCAACTTATGTACCTGCCCCAA 59.355 45.455 0.00 0.00 0.00 4.12
3698 3810 6.538742 TCTTTATGCTCAACTTATGTACCTGC 59.461 38.462 0.00 0.00 0.00 4.85
3822 3936 5.983540 TCTGGTAAGCAATTTTGGTGTTTT 58.016 33.333 0.00 0.00 39.13 2.43
3862 3976 5.070580 ACAAGATCAGGTATTAGTAGGGCAC 59.929 44.000 0.00 0.00 0.00 5.01
3864 3978 5.070580 ACACAAGATCAGGTATTAGTAGGGC 59.929 44.000 0.00 0.00 0.00 5.19
4064 4178 4.361451 AGATCATTTCACGTGCAAATCC 57.639 40.909 11.67 8.98 0.00 3.01
4163 4277 7.730332 AGTACAATTTTTCAGAAGGAAGGGAAT 59.270 33.333 0.00 0.00 36.72 3.01
4225 4339 0.101939 GACCGGTGGATCGAACTACC 59.898 60.000 14.63 16.90 37.92 3.18
4331 4445 6.644181 CCACTAGAGCAACATCATATACACAG 59.356 42.308 0.00 0.00 0.00 3.66
4352 4466 7.640597 AAAAGAAGCAGTAAACTTTACCACT 57.359 32.000 7.89 3.79 33.21 4.00
4432 4546 7.383102 AGCACATGCCATTTATATAAGTAGC 57.617 36.000 0.00 2.20 43.38 3.58
4437 4551 8.306038 GGATCAAAGCACATGCCATTTATATAA 58.694 33.333 0.00 0.00 43.38 0.98
4525 4639 0.105913 CACCCCTCTCTCCCCTACTC 60.106 65.000 0.00 0.00 0.00 2.59
4564 4678 3.876309 AGGAATACAACACCACAGGTT 57.124 42.857 0.00 0.00 31.02 3.50
4610 4724 4.761739 CCCAGCAACCTATATATGTGTTGG 59.238 45.833 21.21 16.86 38.74 3.77
4668 4783 3.911661 ATCTTCTTTGTGCTTCAGTGC 57.088 42.857 0.00 0.00 0.00 4.40
4681 4796 4.506802 GGGAGTGTTGGGTTGTATCTTCTT 60.507 45.833 0.00 0.00 0.00 2.52
4739 4868 4.452733 GGGGAGGCGTCAACGAGG 62.453 72.222 8.91 0.00 43.02 4.63
4742 4871 0.810031 CAATAGGGGAGGCGTCAACG 60.810 60.000 8.91 0.00 43.27 4.10
4745 4874 1.672854 CGACAATAGGGGAGGCGTCA 61.673 60.000 8.91 0.00 0.00 4.35
4779 4943 4.221422 GAGGAGCGCCACGGCATA 62.221 66.667 9.88 0.00 42.06 3.14
4821 4985 1.341852 TCGGAAGACAACGACATTCCA 59.658 47.619 3.93 0.00 41.08 3.53
4861 5025 1.029408 ACACGCTTTCACAGTGGCAA 61.029 50.000 0.00 0.00 39.95 4.52
4949 5113 3.260884 AGCTTTCGGAGAACCAGAATACA 59.739 43.478 0.00 0.00 45.90 2.29
4987 5151 6.424883 AGCTCCTGATCAAGAATCAAGAAAT 58.575 36.000 0.00 0.00 43.78 2.17
5119 5283 7.073457 TCCTTTTTGAATTTTTAAGGGGGAG 57.927 36.000 0.00 0.00 36.77 4.30
5142 5306 7.319142 AGCTAAGAAGAGCAATCTTGATTTC 57.681 36.000 8.42 0.00 45.43 2.17
5184 5348 4.614673 CAACAAGTCGCCAACTGC 57.385 55.556 0.00 0.00 38.58 4.40


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

AutoCloner maintained by Alex Coulton.