Multiple sequence alignment - TraesCS1D01G351900

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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 TraesCS1D01G351900 chr1D 100.000 2474 0 0 1 2474 437294007 437291534 0.000000e+00 4569.0
1 TraesCS1D01G351900 chr1D 80.533 1351 224 31 968 2295 7371994 7373328 0.000000e+00 1002.0
2 TraesCS1D01G351900 chr1B 95.038 2499 79 17 1 2474 592368237 592365759 0.000000e+00 3886.0
3 TraesCS1D01G351900 chr1B 80.710 1353 218 34 968 2295 9647338 9648672 0.000000e+00 1013.0
4 TraesCS1D01G351900 chr1A 94.602 2297 64 18 193 2474 534274452 534276703 0.000000e+00 3500.0
5 TraesCS1D01G351900 chr1A 79.874 1431 240 34 897 2295 9533173 9531759 0.000000e+00 1003.0
6 TraesCS1D01G351900 chr1A 96.154 78 3 0 2 79 534274375 534274452 7.180000e-26 128.0
7 TraesCS1D01G351900 chr5D 75.131 957 199 32 1030 1962 41878416 41877475 1.770000e-111 412.0
8 TraesCS1D01G351900 chr5D 71.984 257 61 11 1712 1961 375586275 375586527 5.710000e-07 65.8
9 TraesCS1D01G351900 chr2B 80.934 514 81 11 994 1503 785984561 785984061 8.300000e-105 390.0
10 TraesCS1D01G351900 chr2B 77.844 501 95 13 1030 1522 775385775 775386267 1.860000e-76 296.0
11 TraesCS1D01G351900 chr2B 84.351 262 28 7 465 716 93790534 93790792 6.830000e-61 244.0
12 TraesCS1D01G351900 chr2B 79.620 368 45 17 76 420 772594252 772593892 1.140000e-58 237.0
13 TraesCS1D01G351900 chr2B 88.325 197 18 2 520 716 477510765 477510574 5.320000e-57 231.0
14 TraesCS1D01G351900 chr2B 79.348 368 46 17 76 420 477511187 477510827 5.320000e-57 231.0
15 TraesCS1D01G351900 chr2B 88.083 193 21 2 524 716 239881992 239881802 6.880000e-56 228.0
16 TraesCS1D01G351900 chr2D 76.291 523 106 13 1009 1522 631983067 631983580 1.890000e-66 263.0
17 TraesCS1D01G351900 chr2D 84.030 263 27 9 466 716 100362514 100362773 3.180000e-59 239.0
18 TraesCS1D01G351900 chr4B 83.624 287 28 13 465 739 42272387 42272108 4.080000e-63 252.0
19 TraesCS1D01G351900 chr7B 84.733 262 27 7 465 716 745362801 745362543 1.470000e-62 250.0
20 TraesCS1D01G351900 chr2A 83.650 263 30 8 466 716 664977633 664977894 4.110000e-58 235.0
21 TraesCS1D01G351900 chr2A 75.551 499 106 13 1030 1520 759795198 759794708 5.320000e-57 231.0
22 TraesCS1D01G351900 chr3D 78.151 238 42 8 1730 1962 514680439 514680207 2.560000e-30 143.0
23 TraesCS1D01G351900 chr3B 91.228 57 5 0 2160 2216 676966922 676966866 7.340000e-11 78.7
24 TraesCS1D01G351900 chr5B 72.481 258 58 8 1712 1961 448314635 448314887 1.230000e-08 71.3


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 TraesCS1D01G351900 chr1D 437291534 437294007 2473 True 4569 4569 100.0000 1 2474 1 chr1D.!!$R1 2473
1 TraesCS1D01G351900 chr1D 7371994 7373328 1334 False 1002 1002 80.5330 968 2295 1 chr1D.!!$F1 1327
2 TraesCS1D01G351900 chr1B 592365759 592368237 2478 True 3886 3886 95.0380 1 2474 1 chr1B.!!$R1 2473
3 TraesCS1D01G351900 chr1B 9647338 9648672 1334 False 1013 1013 80.7100 968 2295 1 chr1B.!!$F1 1327
4 TraesCS1D01G351900 chr1A 534274375 534276703 2328 False 1814 3500 95.3780 2 2474 2 chr1A.!!$F1 2472
5 TraesCS1D01G351900 chr1A 9531759 9533173 1414 True 1003 1003 79.8740 897 2295 1 chr1A.!!$R1 1398
6 TraesCS1D01G351900 chr5D 41877475 41878416 941 True 412 412 75.1310 1030 1962 1 chr5D.!!$R1 932
7 TraesCS1D01G351900 chr2B 785984061 785984561 500 True 390 390 80.9340 994 1503 1 chr2B.!!$R3 509
8 TraesCS1D01G351900 chr2B 477510574 477511187 613 True 231 231 83.8365 76 716 2 chr2B.!!$R4 640
9 TraesCS1D01G351900 chr2D 631983067 631983580 513 False 263 263 76.2910 1009 1522 1 chr2D.!!$F2 513


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
187 202 0.171231 TCGACTTCGACAGCATCCAG 59.829 55.0 0.0 0.0 44.22 3.86 F
683 736 1.029681 AAACCCGAACAGCAGAAACC 58.970 50.0 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1012 1075 2.132762 CCACCCGCTGTATAATTCGAC 58.867 52.381 0.00 0.00 0.00 4.20 R
2007 2088 2.668556 CGTCCTTGGATATCCGATGTCG 60.669 54.545 17.04 16.16 39.43 4.35 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
21 22 1.571773 ATTACTCCCCCACCAGGCAC 61.572 60.000 0.00 0.00 0.00 5.01
118 120 1.953686 GAAGGAGAGAGGACCAGATCG 59.046 57.143 0.00 0.00 0.00 3.69
187 202 0.171231 TCGACTTCGACAGCATCCAG 59.829 55.000 0.00 0.00 44.22 3.86
368 410 2.579207 TTCTTCGTCCGCTATTCTGG 57.421 50.000 0.00 0.00 0.00 3.86
403 445 1.909700 TGGCAAGTTGGATCTTGGAC 58.090 50.000 4.75 0.00 43.26 4.02
420 462 3.645884 TGGACGCACTGTTCTTTAGTAC 58.354 45.455 0.00 0.00 0.00 2.73
421 463 3.319972 TGGACGCACTGTTCTTTAGTACT 59.680 43.478 0.00 0.00 0.00 2.73
422 464 4.520111 TGGACGCACTGTTCTTTAGTACTA 59.480 41.667 0.00 0.00 0.00 1.82
490 535 7.763172 TTTTTCGTTGTTATGCTGTCAAAAT 57.237 28.000 0.00 0.00 0.00 1.82
554 600 7.065803 AGTGCATTTTCTGTACATGGTACATAC 59.934 37.037 9.42 0.00 42.39 2.39
650 696 2.028876 CGGTTTCCACTTTCCCAAACT 58.971 47.619 0.00 0.00 0.00 2.66
683 736 1.029681 AAACCCGAACAGCAGAAACC 58.970 50.000 0.00 0.00 0.00 3.27
789 844 5.411361 TGTTTCTCTTTCCATTCCACATACG 59.589 40.000 0.00 0.00 0.00 3.06
790 845 5.414789 TTCTCTTTCCATTCCACATACGA 57.585 39.130 0.00 0.00 0.00 3.43
862 917 9.689976 TGTCATAAACAAAACATTGGATACTTG 57.310 29.630 0.00 0.00 34.03 3.16
867 922 4.990426 ACAAAACATTGGATACTTGCTTGC 59.010 37.500 0.00 0.00 37.61 4.01
893 948 7.590279 TGAACATGCCTAGTTAAAGCTAAAAC 58.410 34.615 0.00 3.47 0.00 2.43
1225 1294 3.479006 GATGTCACCATTGAAACGAACG 58.521 45.455 0.00 0.00 31.90 3.95
1374 1443 1.542915 CTGGTGATGCAAGTTTCCCTG 59.457 52.381 0.00 0.00 0.00 4.45
1653 1725 0.460311 ACTTACTTGATCTCGGCCGG 59.540 55.000 27.83 16.54 0.00 6.13
1966 2044 2.290896 TGGGCATGGTTGAAGGTTAGAG 60.291 50.000 0.00 0.00 0.00 2.43
2007 2088 3.535280 TTGTGGGTTTTCTTTTGCTCC 57.465 42.857 0.00 0.00 0.00 4.70
2154 2247 2.611225 TGTTTGTGGATTTGTTGGGC 57.389 45.000 0.00 0.00 0.00 5.36
2201 2294 1.861575 GAGCAAGCTATTAGACACCGC 59.138 52.381 0.00 0.00 0.00 5.68
2249 2342 2.139118 GGAGTGTGTTGCAGAAGAGAC 58.861 52.381 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 0.242825 TTCCTTGTGTACGGCGAGAG 59.757 55.000 16.62 1.46 0.00 3.20
187 202 2.467826 GCTTGGCGATGTGGAGAGC 61.468 63.158 0.00 0.00 0.00 4.09
259 278 2.317609 CGTTGTGGCGAAGTGGAGG 61.318 63.158 0.00 0.00 0.00 4.30
359 401 9.526713 CATGTACATATAGTCATCCAGAATAGC 57.473 37.037 8.32 0.00 29.25 2.97
368 410 7.095060 CCAACTTGCCATGTACATATAGTCATC 60.095 40.741 8.32 0.00 0.00 2.92
403 445 7.347508 ACAAATAGTACTAAAGAACAGTGCG 57.652 36.000 6.70 0.00 34.26 5.34
420 462 9.221775 GCGTCCAATAAAATCAGTAACAAATAG 57.778 33.333 0.00 0.00 0.00 1.73
421 463 8.731605 TGCGTCCAATAAAATCAGTAACAAATA 58.268 29.630 0.00 0.00 0.00 1.40
422 464 7.598278 TGCGTCCAATAAAATCAGTAACAAAT 58.402 30.769 0.00 0.00 0.00 2.32
444 488 5.725110 ATTCTTCTATACTTGCAGTTGCG 57.275 39.130 0.00 0.00 45.83 4.85
470 515 7.199766 AGAAAATTTTGACAGCATAACAACGA 58.800 30.769 8.47 0.00 0.00 3.85
490 535 9.486497 TTGACAGCATGCATATTTTAAAGAAAA 57.514 25.926 21.98 0.00 42.53 2.29
620 666 4.568152 AAGTGGAAACCGAATTTGACAG 57.432 40.909 0.00 0.00 0.00 3.51
668 714 0.941542 TTTCGGTTTCTGCTGTTCGG 59.058 50.000 0.00 0.00 0.00 4.30
669 715 2.969443 ATTTCGGTTTCTGCTGTTCG 57.031 45.000 0.00 0.00 0.00 3.95
670 716 4.209080 CCAAAATTTCGGTTTCTGCTGTTC 59.791 41.667 0.00 0.00 0.00 3.18
683 736 5.115021 GCGTTCTGTAGAAACCAAAATTTCG 59.885 40.000 0.00 0.00 42.37 3.46
789 844 7.088589 ACAGCAAAGACCAAACATATATGTC 57.911 36.000 18.52 6.15 40.80 3.06
790 845 8.752005 ATACAGCAAAGACCAAACATATATGT 57.248 30.769 12.75 12.75 44.20 2.29
862 917 1.457346 ACTAGGCATGTTCAGCAAGC 58.543 50.000 0.00 0.00 40.72 4.01
867 922 6.985188 TTAGCTTTAACTAGGCATGTTCAG 57.015 37.500 0.00 0.00 0.00 3.02
1012 1075 2.132762 CCACCCGCTGTATAATTCGAC 58.867 52.381 0.00 0.00 0.00 4.20
1225 1294 4.711399 AGTGGTTGGGTTCTTGTAAGTAC 58.289 43.478 0.00 0.00 0.00 2.73
1471 1543 5.991606 CACACTTGAGAGACCATGTTCTTTA 59.008 40.000 0.00 0.00 0.00 1.85
2007 2088 2.668556 CGTCCTTGGATATCCGATGTCG 60.669 54.545 17.04 16.16 39.43 4.35
2249 2342 8.824159 ATATCGGAATCAAATGTCAAGAGTAG 57.176 34.615 0.00 0.00 0.00 2.57
2415 2510 6.844388 ACTTGTACCATGAACCTCTATATCCA 59.156 38.462 0.00 0.00 0.00 3.41



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

AutoCloner maintained by Alex Coulton.