Multiple sequence alignment - TraesCS3D01G496000

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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 TraesCS3D01G496000 chr3D 100.000 2402 0 0 1 2402 587906522 587908923 0.000000e+00 4436.0
1 TraesCS3D01G496000 chr3D 86.617 538 55 14 1875 2402 11298875 11299405 1.600000e-161 579.0
2 TraesCS3D01G496000 chr3B 95.412 1177 52 2 667 1843 785312698 785313872 0.000000e+00 1873.0
3 TraesCS3D01G496000 chr3B 96.318 679 14 4 1 669 785311974 785312651 0.000000e+00 1105.0
4 TraesCS3D01G496000 chr3B 85.435 563 68 12 1847 2402 690121958 690121403 7.450000e-160 573.0
5 TraesCS3D01G496000 chr3B 82.697 445 64 8 1293 1726 785312702 785313144 1.350000e-102 383.0
6 TraesCS3D01G496000 chr3B 93.048 187 13 0 1185 1371 785314408 785314594 8.460000e-70 274.0
7 TraesCS3D01G496000 chr3A 84.921 1008 127 15 669 1665 717526482 717527475 0.000000e+00 996.0
8 TraesCS3D01G496000 chr3A 85.315 572 64 18 1841 2402 117605470 117604909 7.450000e-160 573.0
9 TraesCS3D01G496000 chr3A 81.455 550 85 13 1189 1730 717526380 717526920 3.670000e-118 435.0
10 TraesCS3D01G496000 chr3A 84.555 382 57 2 671 1051 717527097 717527477 6.270000e-101 377.0
11 TraesCS3D01G496000 chr3A 82.692 312 44 7 364 667 717526081 717526390 3.940000e-68 268.0
12 TraesCS3D01G496000 chr3A 88.889 189 20 1 171 359 717493200 717493387 5.160000e-57 231.0
13 TraesCS3D01G496000 chr3A 88.889 162 4 4 1 157 717493065 717493217 1.130000e-43 187.0
14 TraesCS3D01G496000 chr7D 89.165 563 51 5 1841 2402 535895183 535894630 0.000000e+00 693.0
15 TraesCS3D01G496000 chr1D 87.900 562 56 10 1841 2397 420253565 420253011 0.000000e+00 651.0
16 TraesCS3D01G496000 chr1D 77.632 152 33 1 1235 1386 387330963 387330813 9.140000e-15 91.6
17 TraesCS3D01G496000 chr4D 90.543 497 37 7 1915 2402 234372785 234372290 0.000000e+00 649.0
18 TraesCS3D01G496000 chr5A 88.668 503 51 4 1902 2402 35876245 35875747 2.040000e-170 608.0
19 TraesCS3D01G496000 chr5B 85.794 535 59 15 1844 2369 555926135 555925609 3.490000e-153 551.0
20 TraesCS3D01G496000 chr6B 84.127 567 75 11 1841 2402 35467302 35466746 3.510000e-148 534.0
21 TraesCS3D01G496000 chr1B 81.720 93 17 0 1235 1327 520687711 520687619 7.120000e-11 78.7
22 TraesCS3D01G496000 chr1A 77.778 126 18 3 1210 1327 487080457 487080334 4.280000e-08 69.4


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 TraesCS3D01G496000 chr3D 587906522 587908923 2401 False 4436.00 4436 100.00000 1 2402 1 chr3D.!!$F2 2401
1 TraesCS3D01G496000 chr3D 11298875 11299405 530 False 579.00 579 86.61700 1875 2402 1 chr3D.!!$F1 527
2 TraesCS3D01G496000 chr3B 785311974 785314594 2620 False 908.75 1873 91.86875 1 1843 4 chr3B.!!$F1 1842
3 TraesCS3D01G496000 chr3B 690121403 690121958 555 True 573.00 573 85.43500 1847 2402 1 chr3B.!!$R1 555
4 TraesCS3D01G496000 chr3A 117604909 117605470 561 True 573.00 573 85.31500 1841 2402 1 chr3A.!!$R1 561
5 TraesCS3D01G496000 chr3A 717526081 717527477 1396 False 519.00 996 83.40575 364 1730 4 chr3A.!!$F2 1366
6 TraesCS3D01G496000 chr7D 535894630 535895183 553 True 693.00 693 89.16500 1841 2402 1 chr7D.!!$R1 561
7 TraesCS3D01G496000 chr1D 420253011 420253565 554 True 651.00 651 87.90000 1841 2397 1 chr1D.!!$R2 556
8 TraesCS3D01G496000 chr5B 555925609 555926135 526 True 551.00 551 85.79400 1844 2369 1 chr5B.!!$R1 525
9 TraesCS3D01G496000 chr6B 35466746 35467302 556 True 534.00 534 84.12700 1841 2402 1 chr6B.!!$R1 561

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
580 599 1.000955 CCTGCTAGACCTCGTTGTGTT 59.999 52.381 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2492 0.251386 ACTCCGAGCTCCTCTCAACA 60.251 55.0 8.47 0.0 41.98 3.33 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
74 76 1.627297 ATTCGGCCCAGTTCTCTCCC 61.627 60.000 0.00 0.00 0.00 4.30
436 447 1.026718 GTCCTGTGTGTATGCTGCCC 61.027 60.000 0.00 0.00 0.00 5.36
548 564 5.704053 TGCTATGATTCAAGTGCCTGATATG 59.296 40.000 0.00 0.00 0.00 1.78
580 599 1.000955 CCTGCTAGACCTCGTTGTGTT 59.999 52.381 0.00 0.00 0.00 3.32
675 784 7.073342 AGTGCAAAATAGACCGATAAACTTC 57.927 36.000 0.00 0.00 0.00 3.01
762 871 3.523157 TGGATGGCTTAAGAGGACATGAA 59.477 43.478 6.67 0.00 0.00 2.57
865 974 7.994425 ATGTGTTATGAACTTGTACCATTGA 57.006 32.000 0.00 0.00 0.00 2.57
1131 1240 0.834687 TACACCTTTCGCCAGGTCCT 60.835 55.000 2.51 0.00 44.63 3.85
1148 1257 2.480802 GTCCTGAAGAAAAAGAGACCGC 59.519 50.000 0.00 0.00 0.00 5.68
1203 1312 3.064207 CCAAGAAAAACAGATCGTCGGA 58.936 45.455 0.00 0.00 0.00 4.55
1386 1495 4.104738 GGATGGATTAAGAGGACATGGGAA 59.895 45.833 0.00 0.00 0.00 3.97
1389 1498 4.080356 TGGATTAAGAGGACATGGGAACTG 60.080 45.833 0.00 0.00 0.00 3.16
1461 1571 4.940463 TGCTATGTATCGTGTTAACCTCC 58.060 43.478 2.48 0.00 0.00 4.30
1545 1655 8.721478 GCCATTTATGTACTTGTACTATCATGG 58.279 37.037 18.03 18.03 0.00 3.66
1609 1720 7.270757 TGTAACATTGTGTTTGCTATCTTGT 57.729 32.000 0.20 0.00 41.45 3.16
1683 1800 5.372373 TGCCAAGGTAAAATTTTCTTTGGG 58.628 37.500 26.54 18.23 0.00 4.12
1726 1843 4.793071 TGTCGTATGCACCAAGAAAATTG 58.207 39.130 0.00 0.00 0.00 2.32
1732 1849 7.116090 TCGTATGCACCAAGAAAATTGAAAATG 59.884 33.333 0.00 0.00 0.00 2.32
1744 1861 2.933495 TGAAAATGAGCATGAGCAGC 57.067 45.000 0.00 0.00 45.49 5.25
1745 1862 1.131693 TGAAAATGAGCATGAGCAGCG 59.868 47.619 0.00 0.00 45.49 5.18
1779 1896 3.641437 GTTGTGAGCAAGCATACCAAA 57.359 42.857 0.00 0.00 34.94 3.28
1784 1901 1.745653 GAGCAAGCATACCAAACTCCC 59.254 52.381 0.00 0.00 0.00 4.30
1797 1914 4.264172 ACCAAACTCCCATGTAATAAGCCA 60.264 41.667 0.00 0.00 0.00 4.75
1835 1952 4.746535 TGTCCTATACGAGGCATCAAAA 57.253 40.909 0.00 0.00 46.25 2.44
1871 2309 2.046217 GGCGGGAAACAGAGACCC 60.046 66.667 0.00 0.00 40.17 4.46
1927 2366 1.076549 GGGCATTGGTCCAGGTTGA 59.923 57.895 0.00 0.00 39.19 3.18
1937 2376 0.327924 TCCAGGTTGATGCCACGAAT 59.672 50.000 0.00 0.00 0.00 3.34
2034 2492 2.435203 AGTTTAGTCCCACCTCCCTT 57.565 50.000 0.00 0.00 0.00 3.95
2071 2529 2.118313 GTGGTTTATAAGCCCCACGT 57.882 50.000 15.03 0.00 38.14 4.49
2123 2581 1.746470 GCTTACGGGCCTAAACACAT 58.254 50.000 0.84 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 76 2.895372 GGCGTATTGGTGGGCTCG 60.895 66.667 0.00 0.00 0.00 5.03
194 197 2.325166 GACTAGAGCTCGGTCGCG 59.675 66.667 20.85 0.00 34.40 5.87
195 198 1.778027 GAGGACTAGAGCTCGGTCGC 61.778 65.000 25.23 20.26 0.00 5.19
357 368 1.379309 GGCGAGACAGAGAGGAGGT 60.379 63.158 0.00 0.00 0.00 3.85
436 447 6.057533 TCAAGCAGTACCAATATCAATCAGG 58.942 40.000 0.00 0.00 0.00 3.86
548 564 1.212935 TCTAGCAGGAAAATGAGGGCC 59.787 52.381 0.00 0.00 0.00 5.80
675 784 3.441222 TCACCATATTTCTGCTGCAACAG 59.559 43.478 10.97 10.97 39.12 3.16
865 974 9.464714 CGATACATAGCACATAAACTTAGTTCT 57.535 33.333 0.00 0.00 0.00 3.01
934 1043 1.391485 GCACGAGTTCATAGCACACAG 59.609 52.381 0.00 0.00 0.00 3.66
1027 1136 5.449588 CCATGACCGATTCAAATTCCTCTTG 60.450 44.000 0.00 0.00 37.92 3.02
1029 1138 4.202441 CCATGACCGATTCAAATTCCTCT 58.798 43.478 0.00 0.00 37.92 3.69
1131 1240 3.469008 TCAGCGGTCTCTTTTTCTTCA 57.531 42.857 0.00 0.00 0.00 3.02
1148 1257 7.706179 ACACAAGGTGTAATTTTGTCAAATCAG 59.294 33.333 0.00 0.00 45.56 2.90
1231 1340 0.966875 TCTGCAATGACCATGGCCAC 60.967 55.000 8.16 4.34 36.93 5.01
1508 1618 7.553881 AGTACATAAATGGCTCATACAACAC 57.446 36.000 0.00 0.00 0.00 3.32
1519 1629 8.721478 CCATGATAGTACAAGTACATAAATGGC 58.279 37.037 12.43 0.00 38.48 4.40
1676 1793 1.746322 TACGACGCCACACCCAAAGA 61.746 55.000 0.00 0.00 0.00 2.52
1683 1800 1.136984 CTCTCCTACGACGCCACAC 59.863 63.158 0.00 0.00 0.00 3.82
1726 1843 1.533338 CCGCTGCTCATGCTCATTTTC 60.533 52.381 0.00 0.00 40.48 2.29
1744 1861 2.045340 AACCGATTCCAAGGGCCG 60.045 61.111 0.00 0.00 0.00 6.13
1745 1862 1.304134 ACAACCGATTCCAAGGGCC 60.304 57.895 0.00 0.00 0.00 5.80
1775 1892 4.277476 TGGCTTATTACATGGGAGTTTGG 58.723 43.478 0.00 0.00 0.00 3.28
1779 1896 4.683400 CGAGTTGGCTTATTACATGGGAGT 60.683 45.833 0.00 0.00 0.00 3.85
1784 1901 3.248602 GCCTCGAGTTGGCTTATTACATG 59.751 47.826 12.31 0.00 46.38 3.21
1797 1914 0.677842 ACAAGTAACCGCCTCGAGTT 59.322 50.000 12.31 2.15 0.00 3.01
1835 1952 1.302033 CTTTGGGCTGCTGACGACT 60.302 57.895 0.00 0.00 0.00 4.18
1871 2309 2.282180 CCACCAACCGGGACCAAG 60.282 66.667 6.32 0.00 41.15 3.61
1921 2360 0.744414 CCGATTCGTGGCATCAACCT 60.744 55.000 5.20 0.00 0.00 3.50
1927 2366 2.189521 GGTCCCGATTCGTGGCAT 59.810 61.111 5.20 0.00 0.00 4.40
1937 2376 0.548197 ATACCCACCTTTGGTCCCGA 60.548 55.000 0.00 0.00 42.10 5.14
2003 2460 1.443702 CTAAACTTTTGGCCGCGGC 60.444 57.895 41.63 41.63 41.06 6.53
2034 2492 0.251386 ACTCCGAGCTCCTCTCAACA 60.251 55.000 8.47 0.00 41.98 3.33
2070 2528 2.125350 CTCAAGAGGGCAGCGGAC 60.125 66.667 0.00 0.00 0.00 4.79
2071 2529 4.087892 GCTCAAGAGGGCAGCGGA 62.088 66.667 0.00 0.00 0.00 5.54
2153 2612 2.825836 CAGGATTCAGGCCCGCAC 60.826 66.667 0.00 0.00 0.00 5.34
2177 2637 5.514136 CCTGAATACAACTAGAAACCCACCA 60.514 44.000 0.00 0.00 0.00 4.17
2192 2652 3.901087 CCACCATGGCCTGAATACA 57.099 52.632 13.04 0.00 0.00 2.29
2335 2848 7.422399 TGAAAACTATTGGCACTAACAGAAAC 58.578 34.615 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.