Multiple sequence alignment - TraesCS5D01G055000

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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 TraesCS5D01G055000 chr5D 100.000 2312 0 0 1 2312 51860019 51862330 0.000000e+00 4270.0
1 TraesCS5D01G055000 chr5D 83.290 1544 164 54 1 1492 51891996 51893497 0.000000e+00 1336.0
2 TraesCS5D01G055000 chr5D 88.158 912 57 24 576 1446 51851867 51852768 0.000000e+00 1038.0
3 TraesCS5D01G055000 chr5D 89.873 790 48 18 577 1340 51674860 51675643 0.000000e+00 987.0
4 TraesCS5D01G055000 chr5D 86.652 884 64 33 635 1483 51637161 51638025 0.000000e+00 929.0
5 TraesCS5D01G055000 chr5D 86.405 765 69 18 591 1340 51697934 51698678 0.000000e+00 804.0
6 TraesCS5D01G055000 chr5D 83.850 452 49 8 1748 2194 51853081 51853513 2.140000e-110 409.0
7 TraesCS5D01G055000 chr5A 93.980 1495 82 4 1 1492 40933811 40935300 0.000000e+00 2255.0
8 TraesCS5D01G055000 chr5A 93.980 1495 82 4 1 1492 40967694 40969183 0.000000e+00 2255.0
9 TraesCS5D01G055000 chr5A 93.846 1495 84 4 1 1492 41004576 41006065 0.000000e+00 2244.0
10 TraesCS5D01G055000 chr5A 85.273 1521 121 45 1 1492 41045308 41046754 0.000000e+00 1472.0
11 TraesCS5D01G055000 chr5A 92.972 811 45 8 1505 2310 40969166 40969969 0.000000e+00 1171.0
12 TraesCS5D01G055000 chr5A 92.725 811 47 8 1505 2310 41006048 41006851 0.000000e+00 1160.0
13 TraesCS5D01G055000 chr5A 92.365 812 49 8 1505 2310 40935283 40936087 0.000000e+00 1144.0
14 TraesCS5D01G055000 chr5A 92.135 445 33 2 1505 1949 41046737 41047179 5.420000e-176 627.0
15 TraesCS5D01G055000 chr5A 93.176 381 18 4 1936 2312 41047835 41048211 9.330000e-154 553.0
16 TraesCS5D01G055000 chr5B 94.177 1082 54 3 406 1480 54859682 54860761 0.000000e+00 1640.0
17 TraesCS5D01G055000 chr5B 83.074 1542 172 46 1 1492 55027506 55029008 0.000000e+00 1319.0
18 TraesCS5D01G055000 chr5B 88.189 762 54 25 591 1340 54709897 54710634 0.000000e+00 876.0
19 TraesCS5D01G055000 chr5B 84.245 914 76 41 642 1492 54508308 54509216 0.000000e+00 828.0
20 TraesCS5D01G055000 chr5B 88.866 476 38 9 1844 2312 54866909 54867376 2.580000e-159 571.0
21 TraesCS5D01G055000 chr5B 89.977 429 32 5 1 422 54857031 54857455 5.620000e-151 544.0
22 TraesCS5D01G055000 chr5B 83.471 484 62 15 1743 2220 54850976 54851447 3.530000e-118 435.0
23 TraesCS5D01G055000 chr5B 80.780 359 39 14 609 938 54830703 54831060 1.060000e-63 254.0
24 TraesCS5D01G055000 chr2B 81.667 180 24 4 1571 1743 248457315 248457492 8.610000e-30 141.0
25 TraesCS5D01G055000 chr3B 77.982 218 34 6 1531 1741 719434131 719433921 8.670000e-25 124.0
26 TraesCS5D01G055000 chr3A 78.082 219 30 11 1536 1743 487365560 487365771 3.120000e-24 122.0
27 TraesCS5D01G055000 chr7D 87.368 95 11 1 1647 1740 60454935 60455029 8.730000e-20 108.0
28 TraesCS5D01G055000 chr7D 75.983 229 37 10 1528 1743 69951410 69951633 4.060000e-18 102.0
29 TraesCS5D01G055000 chr4B 79.355 155 25 4 1593 1740 605949202 605949356 4.060000e-18 102.0
30 TraesCS5D01G055000 chr2D 78.846 156 22 7 1597 1743 422825816 422825663 6.800000e-16 95.3


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 TraesCS5D01G055000 chr5D 51860019 51862330 2311 False 4270.0 4270 100.000000 1 2312 1 chr5D.!!$F4 2311
1 TraesCS5D01G055000 chr5D 51891996 51893497 1501 False 1336.0 1336 83.290000 1 1492 1 chr5D.!!$F5 1491
2 TraesCS5D01G055000 chr5D 51674860 51675643 783 False 987.0 987 89.873000 577 1340 1 chr5D.!!$F2 763
3 TraesCS5D01G055000 chr5D 51637161 51638025 864 False 929.0 929 86.652000 635 1483 1 chr5D.!!$F1 848
4 TraesCS5D01G055000 chr5D 51697934 51698678 744 False 804.0 804 86.405000 591 1340 1 chr5D.!!$F3 749
5 TraesCS5D01G055000 chr5D 51851867 51853513 1646 False 723.5 1038 86.004000 576 2194 2 chr5D.!!$F6 1618
6 TraesCS5D01G055000 chr5A 40967694 40969969 2275 False 1713.0 2255 93.476000 1 2310 2 chr5A.!!$F2 2309
7 TraesCS5D01G055000 chr5A 41004576 41006851 2275 False 1702.0 2244 93.285500 1 2310 2 chr5A.!!$F3 2309
8 TraesCS5D01G055000 chr5A 40933811 40936087 2276 False 1699.5 2255 93.172500 1 2310 2 chr5A.!!$F1 2309
9 TraesCS5D01G055000 chr5A 41045308 41048211 2903 False 884.0 1472 90.194667 1 2312 3 chr5A.!!$F4 2311
10 TraesCS5D01G055000 chr5B 55027506 55029008 1502 False 1319.0 1319 83.074000 1 1492 1 chr5B.!!$F6 1491
11 TraesCS5D01G055000 chr5B 54857031 54860761 3730 False 1092.0 1640 92.077000 1 1480 2 chr5B.!!$F7 1479
12 TraesCS5D01G055000 chr5B 54709897 54710634 737 False 876.0 876 88.189000 591 1340 1 chr5B.!!$F2 749
13 TraesCS5D01G055000 chr5B 54508308 54509216 908 False 828.0 828 84.245000 642 1492 1 chr5B.!!$F1 850

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
182 199 1.003355 CCATGACAAGGCCACTCGT 60.003 57.895 5.01 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 4231 1.022735 CATCGCTAGGTGGTCTACGT 58.977 55.0 0.0 0.0 0.0 3.57 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
43 44 3.441572 GCATGTATGAGAAACTTGCAGGT 59.558 43.478 0.00 0.00 43.65 4.00
99 100 8.918961 TGCCGATGTAAAATTCGATAAAAATT 57.081 26.923 0.00 0.00 37.55 1.82
182 199 1.003355 CCATGACAAGGCCACTCGT 60.003 57.895 5.01 0.00 0.00 4.18
254 271 3.428589 GGTAACCACTATGGACTCGTCAC 60.429 52.174 0.84 0.00 40.96 3.67
287 310 9.874205 ATTTTTCTTCACATGAGTTTTCTTTCA 57.126 25.926 0.00 0.00 0.00 2.69
369 392 4.719026 ATATGAAGTCACCATCAGGCAT 57.281 40.909 0.00 0.00 39.06 4.40
410 2673 6.237755 GGCACGTAGTTCAACAATACTCATAC 60.238 42.308 0.00 0.00 41.61 2.39
453 2716 3.378512 TGGCATCACCTATGAGTTCTCT 58.621 45.455 1.53 0.00 38.57 3.10
478 2741 5.790593 CGGCTTATACTCCCTAGCAAAATA 58.209 41.667 0.00 0.00 35.36 1.40
532 2799 4.848562 AAGATGGTATGCATCATGCTTG 57.151 40.909 11.84 0.00 45.31 4.01
561 2828 4.880120 TGCAAAACCTCAATGCAATTTTGA 59.120 33.333 16.84 10.81 46.23 2.69
600 2867 2.032620 GGACCGTATGATCTCACCAGT 58.967 52.381 0.00 0.00 0.00 4.00
606 2873 4.156922 CCGTATGATCTCACCAGTATCTCC 59.843 50.000 0.00 0.00 0.00 3.71
951 3279 4.273148 ACTCAAAGTCAAAGCCTCGTAT 57.727 40.909 0.00 0.00 0.00 3.06
1390 3754 6.160684 TGTAATGTGTACGTGCTCTGTTATT 58.839 36.000 4.97 0.35 0.00 1.40
1449 3813 4.549458 CCATGCAGGTCTTTTTACTGTTG 58.451 43.478 0.00 0.00 34.79 3.33
1450 3814 4.278170 CCATGCAGGTCTTTTTACTGTTGA 59.722 41.667 0.00 0.00 34.79 3.18
1493 4109 9.826574 TCCTATCAAAGTGTTACACATTATACC 57.173 33.333 18.19 0.00 36.74 2.73
1498 4114 9.562408 TCAAAGTGTTACACATTATACCTTTCA 57.438 29.630 18.19 0.00 36.74 2.69
1557 4173 7.276658 TGCGAGAGAACTTTCATTCTATTTCTC 59.723 37.037 0.00 0.00 39.08 2.87
1570 4186 5.801350 TCTATTTCTCAATTGTCAAGCGG 57.199 39.130 5.13 0.00 0.00 5.52
1575 4191 2.037902 TCTCAATTGTCAAGCGGGTACA 59.962 45.455 5.13 0.00 0.00 2.90
1583 4199 2.032290 GTCAAGCGGGTACAAAGAACAC 60.032 50.000 0.00 0.00 0.00 3.32
1591 4207 4.204799 GGGTACAAAGAACACCAGAAGTT 58.795 43.478 0.00 0.00 33.78 2.66
1627 4245 3.614092 TCCAAGTACGTAGACCACCTAG 58.386 50.000 0.00 0.00 0.00 3.02
1654 4272 4.430423 CAAGTGCGCGCCGAAGAC 62.430 66.667 30.77 19.77 0.00 3.01
1655 4273 4.961511 AAGTGCGCGCCGAAGACA 62.962 61.111 30.77 4.37 0.00 3.41
1684 4302 3.157217 ATCGCCACTCCCTCATCGC 62.157 63.158 0.00 0.00 0.00 4.58
1691 4309 1.227205 CTCCCTCATCGCTGTCAGC 60.227 63.158 15.22 15.22 38.02 4.26
1716 4334 5.864418 AACCTTGTTGTAGTAGACAGTCA 57.136 39.130 2.66 0.00 39.88 3.41
1737 4355 1.084289 AAAATCGTCGTGCTAAGCCC 58.916 50.000 0.00 0.00 0.00 5.19
1759 4377 8.104566 AGCCCCATAGTTACGCATTATAATTAA 58.895 33.333 0.00 0.00 0.00 1.40
1895 4514 8.868522 AATAGGTATGGTGAATGGTGATATTG 57.131 34.615 0.00 0.00 0.00 1.90
1896 4515 6.266131 AGGTATGGTGAATGGTGATATTGT 57.734 37.500 0.00 0.00 0.00 2.71
1955 5243 9.639601 TGACTTAAGACAACACTATTATGTGAG 57.360 33.333 10.09 0.00 40.12 3.51
2252 5545 1.831736 CTACGGAGGCCCCCTATAATG 59.168 57.143 0.11 0.00 31.76 1.90
2254 5547 1.691823 GGAGGCCCCCTATAATGCC 59.308 63.158 0.00 0.00 44.35 4.40
2264 5557 2.890311 CCCTATAATGCCGGAAATGCAA 59.110 45.455 5.05 0.00 42.92 4.08
2265 5558 3.511146 CCCTATAATGCCGGAAATGCAAT 59.489 43.478 5.05 0.00 42.92 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.963599 TCTCATACATGCATGGCCAT 57.036 45.000 29.41 14.09 0.00 4.40
43 44 4.159321 TGATGTGCTTTTTCTTCACCAACA 59.841 37.500 0.00 0.00 0.00 3.33
99 100 2.628696 CGCATGCACCAAAGAGGCA 61.629 57.895 19.57 0.00 43.14 4.75
182 199 4.621510 CGAAGAGGTCCATGTGAAGAATCA 60.622 45.833 0.00 0.00 0.00 2.57
211 228 3.065648 CCACCGAAGCTAGAGTAGTTCTC 59.934 52.174 0.00 0.00 43.05 2.87
254 271 9.525409 AAACTCATGTGAAGAAAAATCAGAAAG 57.475 29.630 0.94 0.00 0.00 2.62
287 310 5.455872 TCTGGGTTCTAGATTAATCCTCGT 58.544 41.667 11.92 0.00 0.00 4.18
345 368 3.496130 GCCTGATGGTGACTTCATATTCG 59.504 47.826 0.00 0.00 42.83 3.34
369 392 3.880490 ACGTGCCACTTTCACTTTTCATA 59.120 39.130 0.00 0.00 32.54 2.15
410 2673 7.012327 TGCCATAATAATTGAGAAACTCTTCGG 59.988 37.037 0.00 0.00 36.61 4.30
453 2716 0.966920 GCTAGGGAGTATAAGCCGCA 59.033 55.000 0.00 0.00 0.00 5.69
478 2741 5.199982 TGATTCTTCCTCTCCACTACTCT 57.800 43.478 0.00 0.00 0.00 3.24
532 2799 3.248266 GCATTGAGGTTTTGCAGTCATC 58.752 45.455 0.00 0.00 36.40 2.92
537 2804 5.007823 TCAAAATTGCATTGAGGTTTTGCAG 59.992 36.000 0.00 0.00 46.10 4.41
539 2806 5.421212 TCAAAATTGCATTGAGGTTTTGC 57.579 34.783 0.00 0.00 38.79 3.68
561 2828 0.238289 CTTTGTTGATGGCGTTCGCT 59.762 50.000 16.40 0.00 0.00 4.93
600 2867 5.394562 TGAGAGAGACATGAAGGGAGATA 57.605 43.478 0.00 0.00 0.00 1.98
606 2873 4.646040 AGTCAGATGAGAGAGACATGAAGG 59.354 45.833 0.00 0.00 33.56 3.46
666 2933 2.130193 TGGATAAGGCATGGAGCTCTT 58.870 47.619 14.64 0.96 44.79 2.85
951 3279 2.287069 GCTAGAGCGCTTGATTCTCGTA 60.287 50.000 13.26 0.00 32.42 3.43
1227 3567 2.351276 ACCTTGTCGGTGCATCCC 59.649 61.111 0.00 0.00 46.80 3.85
1390 3754 5.448654 CATCATCCCCAAATACAGGAAAGA 58.551 41.667 0.00 0.00 32.26 2.52
1447 3811 3.199946 GGACAGGTACTCCCATCAATCAA 59.800 47.826 0.00 0.00 34.60 2.57
1449 3813 3.041946 AGGACAGGTACTCCCATCAATC 58.958 50.000 0.00 0.00 34.60 2.67
1450 3814 3.136641 AGGACAGGTACTCCCATCAAT 57.863 47.619 0.00 0.00 34.60 2.57
1507 4123 9.739786 GCAATTTGCTTTTATAATGTGTAACAC 57.260 29.630 14.11 0.00 46.16 3.32
1509 4125 8.855279 TCGCAATTTGCTTTTATAATGTGTAAC 58.145 29.630 18.57 0.00 42.25 2.50
1510 4126 8.972262 TCGCAATTTGCTTTTATAATGTGTAA 57.028 26.923 18.57 0.00 42.25 2.41
1511 4127 8.454894 TCTCGCAATTTGCTTTTATAATGTGTA 58.545 29.630 18.57 0.00 42.25 2.90
1512 4128 7.312154 TCTCGCAATTTGCTTTTATAATGTGT 58.688 30.769 18.57 0.00 42.25 3.72
1513 4129 7.697710 TCTCTCGCAATTTGCTTTTATAATGTG 59.302 33.333 18.57 2.21 42.25 3.21
1515 4131 8.526681 GTTCTCTCGCAATTTGCTTTTATAATG 58.473 33.333 18.57 0.85 42.25 1.90
1517 4133 7.816640 AGTTCTCTCGCAATTTGCTTTTATAA 58.183 30.769 18.57 4.30 42.25 0.98
1518 4134 7.377766 AGTTCTCTCGCAATTTGCTTTTATA 57.622 32.000 18.57 0.00 42.25 0.98
1519 4135 6.259550 AGTTCTCTCGCAATTTGCTTTTAT 57.740 33.333 18.57 0.00 42.25 1.40
1520 4136 5.689383 AGTTCTCTCGCAATTTGCTTTTA 57.311 34.783 18.57 1.86 42.25 1.52
1521 4137 4.574599 AGTTCTCTCGCAATTTGCTTTT 57.425 36.364 18.57 0.00 42.25 2.27
1557 4173 3.252215 TCTTTGTACCCGCTTGACAATTG 59.748 43.478 3.24 3.24 33.33 2.32
1560 4176 2.614983 GTTCTTTGTACCCGCTTGACAA 59.385 45.455 0.00 0.00 0.00 3.18
1570 4186 6.930667 TTAACTTCTGGTGTTCTTTGTACC 57.069 37.500 0.00 0.00 35.05 3.34
1613 4231 1.022735 CATCGCTAGGTGGTCTACGT 58.977 55.000 0.00 0.00 0.00 3.57
1627 4245 1.345176 GCGCACTTGTAGTCATCGC 59.655 57.895 0.30 0.00 33.65 4.58
1684 4302 1.750778 ACAACAAGGTTTGGCTGACAG 59.249 47.619 0.00 0.00 34.12 3.51
1691 4309 5.365619 ACTGTCTACTACAACAAGGTTTGG 58.634 41.667 0.00 0.00 37.74 3.28
1727 4345 2.480845 CGTAACTATGGGGCTTAGCAC 58.519 52.381 6.53 0.77 0.00 4.40
1759 4377 6.469782 ACAAAGTTTGATTGAAGACACCAT 57.530 33.333 22.23 0.00 0.00 3.55
2252 5545 2.057408 TCCCCATTGCATTTCCGGC 61.057 57.895 0.00 0.00 0.00 6.13
2254 5547 2.051334 TAGTCCCCATTGCATTTCCG 57.949 50.000 0.00 0.00 0.00 4.30
2264 5557 5.254032 AGAACAAAAGAGGAATAGTCCCCAT 59.746 40.000 5.39 0.00 46.30 4.00
2265 5558 4.601857 AGAACAAAAGAGGAATAGTCCCCA 59.398 41.667 5.39 0.00 46.30 4.96


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

AutoCloner maintained by Alex Coulton.