Multiple sequence alignment - TraesCS5D01G438500

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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 TraesCS5D01G438500 chr5D 100.000 2471 0 0 1 2471 491806812 491804342 0.000000e+00 4564.0
1 TraesCS5D01G438500 chr5D 93.217 1091 50 11 3 1091 491869186 491868118 0.000000e+00 1583.0
2 TraesCS5D01G438500 chr5D 96.044 910 27 8 1565 2471 400246633 400245730 0.000000e+00 1472.0
3 TraesCS5D01G438500 chr5D 95.267 486 15 4 1087 1564 491859940 491859455 0.000000e+00 763.0
4 TraesCS5D01G438500 chr5A 90.774 1344 69 22 268 1565 614379039 614377705 0.000000e+00 1744.0
5 TraesCS5D01G438500 chr5A 90.441 136 13 0 82 217 614379196 614379061 1.950000e-41 180.0
6 TraesCS5D01G438500 chr5A 98.148 54 1 0 215 268 238822784 238822837 7.270000e-16 95.3
7 TraesCS5D01G438500 chr1D 96.272 912 28 5 1565 2471 29817802 29818712 0.000000e+00 1491.0
8 TraesCS5D01G438500 chr4D 95.829 911 32 6 1565 2471 26284028 26284936 0.000000e+00 1467.0
9 TraesCS5D01G438500 chr4D 95.609 911 32 6 1565 2471 23869059 23869965 0.000000e+00 1454.0
10 TraesCS5D01G438500 chr3D 95.714 910 32 4 1565 2471 93179162 93180067 0.000000e+00 1458.0
11 TraesCS5D01G438500 chr7D 95.301 915 33 8 1564 2471 63091698 63092609 0.000000e+00 1443.0
12 TraesCS5D01G438500 chr2D 94.962 913 32 11 1565 2471 423218185 423217281 0.000000e+00 1419.0
13 TraesCS5D01G438500 chr2D 93.939 924 26 14 1564 2471 582021836 582022745 0.000000e+00 1369.0
14 TraesCS5D01G438500 chr2D 93.509 909 34 8 1565 2471 636157979 636157094 0.000000e+00 1328.0
15 TraesCS5D01G438500 chr2D 93.399 909 28 18 1565 2471 636578346 636579224 0.000000e+00 1317.0
16 TraesCS5D01G438500 chr5B 88.814 894 79 11 268 1151 606857148 606856266 0.000000e+00 1077.0
17 TraesCS5D01G438500 chr5B 94.118 357 17 1 1143 1499 606854984 606854632 7.770000e-150 540.0


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 TraesCS5D01G438500 chr5D 491804342 491806812 2470 True 4564.0 4564 100.0000 1 2471 1 chr5D.!!$R2 2470
1 TraesCS5D01G438500 chr5D 491868118 491869186 1068 True 1583.0 1583 93.2170 3 1091 1 chr5D.!!$R4 1088
2 TraesCS5D01G438500 chr5D 400245730 400246633 903 True 1472.0 1472 96.0440 1565 2471 1 chr5D.!!$R1 906
3 TraesCS5D01G438500 chr5A 614377705 614379196 1491 True 962.0 1744 90.6075 82 1565 2 chr5A.!!$R1 1483
4 TraesCS5D01G438500 chr1D 29817802 29818712 910 False 1491.0 1491 96.2720 1565 2471 1 chr1D.!!$F1 906
5 TraesCS5D01G438500 chr4D 26284028 26284936 908 False 1467.0 1467 95.8290 1565 2471 1 chr4D.!!$F2 906
6 TraesCS5D01G438500 chr4D 23869059 23869965 906 False 1454.0 1454 95.6090 1565 2471 1 chr4D.!!$F1 906
7 TraesCS5D01G438500 chr3D 93179162 93180067 905 False 1458.0 1458 95.7140 1565 2471 1 chr3D.!!$F1 906
8 TraesCS5D01G438500 chr7D 63091698 63092609 911 False 1443.0 1443 95.3010 1564 2471 1 chr7D.!!$F1 907
9 TraesCS5D01G438500 chr2D 423217281 423218185 904 True 1419.0 1419 94.9620 1565 2471 1 chr2D.!!$R1 906
10 TraesCS5D01G438500 chr2D 582021836 582022745 909 False 1369.0 1369 93.9390 1564 2471 1 chr2D.!!$F1 907
11 TraesCS5D01G438500 chr2D 636157094 636157979 885 True 1328.0 1328 93.5090 1565 2471 1 chr2D.!!$R2 906
12 TraesCS5D01G438500 chr2D 636578346 636579224 878 False 1317.0 1317 93.3990 1565 2471 1 chr2D.!!$F2 906
13 TraesCS5D01G438500 chr5B 606854632 606857148 2516 True 808.5 1077 91.4660 268 1499 2 chr5B.!!$R1 1231

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
933 959 0.878416 ACACAAACACACACAACGCT 59.122 45.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 3350 1.202663 GGGAGAATAGAACCCGGAAGC 60.203 57.143 0.73 0.0 34.03 3.86 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
39 40 1.001393 GCAATTCGAGGACCCCCAA 60.001 57.895 0.00 0.00 33.88 4.12
202 205 3.936564 TGCCAACTTTGCAAAAGAGTTT 58.063 36.364 13.84 0.00 35.40 2.66
235 238 3.559655 CGCAGAAACGATCCAATCCATTA 59.440 43.478 0.00 0.00 34.06 1.90
448 451 2.663602 CGTCTTGAGATGTCTGAAACGG 59.336 50.000 0.00 0.00 0.00 4.44
461 464 1.001520 TGAAACGGGAGAAATGCTCGA 59.998 47.619 0.00 0.00 44.91 4.04
483 486 5.470047 AGTCTTTCGAAACATCTACACCT 57.530 39.130 6.47 0.00 0.00 4.00
484 487 5.855045 AGTCTTTCGAAACATCTACACCTT 58.145 37.500 6.47 0.00 0.00 3.50
501 504 2.676342 ACCTTTTGCCAACGACGATATC 59.324 45.455 0.00 0.00 0.00 1.63
521 524 1.884464 GCCATCATCAAGCGCGAGA 60.884 57.895 12.10 4.18 0.00 4.04
571 574 4.558226 ACACTTGAGGTTGATCATGCTA 57.442 40.909 0.00 0.00 0.00 3.49
586 589 4.476297 TCATGCTACGAGGGTAATTCCTA 58.524 43.478 0.00 0.00 37.25 2.94
587 590 4.523173 TCATGCTACGAGGGTAATTCCTAG 59.477 45.833 0.00 0.00 37.25 3.02
591 594 4.262506 GCTACGAGGGTAATTCCTAGCATT 60.263 45.833 0.00 0.00 36.71 3.56
628 631 6.014840 TCGGGTGAGAGTTGTAATTCTAAACT 60.015 38.462 1.20 1.20 36.87 2.66
673 682 2.220313 CCAAACTTTGGCCCATGTTTG 58.780 47.619 28.13 28.13 45.17 2.93
758 771 1.374947 CTCCTTCCTTGCCACCGAA 59.625 57.895 0.00 0.00 0.00 4.30
811 824 1.916000 GGCTGTACGTACGTGCTTTAG 59.084 52.381 31.45 22.93 0.00 1.85
877 899 1.228124 CAAAGTCACCGGCTCCCAA 60.228 57.895 0.00 0.00 0.00 4.12
932 958 2.529136 TACACAAACACACACAACGC 57.471 45.000 0.00 0.00 0.00 4.84
933 959 0.878416 ACACAAACACACACAACGCT 59.122 45.000 0.00 0.00 0.00 5.07
934 960 1.135803 ACACAAACACACACAACGCTC 60.136 47.619 0.00 0.00 0.00 5.03
935 961 1.135831 CACAAACACACACAACGCTCA 60.136 47.619 0.00 0.00 0.00 4.26
936 962 1.537638 ACAAACACACACAACGCTCAA 59.462 42.857 0.00 0.00 0.00 3.02
937 963 1.910819 CAAACACACACAACGCTCAAC 59.089 47.619 0.00 0.00 0.00 3.18
967 993 1.481871 ACATACCGATCGAACCACCT 58.518 50.000 18.66 0.00 0.00 4.00
1213 2533 1.665599 GCACCAACCTTGCATGCAC 60.666 57.895 22.58 0.98 39.93 4.57
1281 2621 3.938289 GAGTTTCTCTACTCGTTGGGT 57.062 47.619 0.00 0.00 35.62 4.51
1422 2762 1.098050 GGTTCTTCATCTGCGGCATT 58.902 50.000 1.75 0.00 0.00 3.56
1481 2825 1.676529 CGTCCACTGATCCACTATCGT 59.323 52.381 0.00 0.00 37.42 3.73
1518 2862 1.062002 CTGCGACCGTGCGAATAAAAT 59.938 47.619 0.00 0.00 37.81 1.82
1519 2863 1.061421 TGCGACCGTGCGAATAAAATC 59.939 47.619 0.00 0.00 37.81 2.17
1520 2864 1.326548 GCGACCGTGCGAATAAAATCT 59.673 47.619 0.00 0.00 0.00 2.40
1522 2866 3.342269 CGACCGTGCGAATAAAATCTTG 58.658 45.455 0.00 0.00 0.00 3.02
1523 2867 3.061563 CGACCGTGCGAATAAAATCTTGA 59.938 43.478 0.00 0.00 0.00 3.02
1524 2868 4.578601 GACCGTGCGAATAAAATCTTGAG 58.421 43.478 0.00 0.00 0.00 3.02
1525 2869 4.250464 ACCGTGCGAATAAAATCTTGAGA 58.750 39.130 0.00 0.00 0.00 3.27
1526 2870 4.330074 ACCGTGCGAATAAAATCTTGAGAG 59.670 41.667 0.00 0.00 0.00 3.20
1527 2871 4.330074 CCGTGCGAATAAAATCTTGAGAGT 59.670 41.667 0.00 0.00 0.00 3.24
1659 3010 1.760613 TCGTTACTAATGCCTCCCCTG 59.239 52.381 0.00 0.00 0.00 4.45
1693 3044 1.331214 ACACGAACCGGGACTAAAGA 58.669 50.000 6.32 0.00 32.98 2.52
1734 3085 1.331399 GGAGCTCCGCCTTTAGTCCT 61.331 60.000 19.06 0.00 0.00 3.85
1901 3268 8.489489 TCACTGCTCAATTTATCCTCTAATCTT 58.511 33.333 0.00 0.00 0.00 2.40
1974 3341 2.451490 CTCTCACTACTCCAGCCTGAA 58.549 52.381 0.00 0.00 0.00 3.02
1983 3350 0.037326 TCCAGCCTGAACACGCTTAG 60.037 55.000 0.00 0.00 31.40 2.18
2306 3688 9.617975 TTGTTTGACCACAATTTGAAATTTTTC 57.382 25.926 2.79 0.00 35.85 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.429881 GCTTTTTATTTGCAGTGCCAGAC 59.570 43.478 13.72 0.00 0.00 3.51
1 2 3.069300 TGCTTTTTATTTGCAGTGCCAGA 59.931 39.130 13.72 0.00 32.55 3.86
39 40 1.072143 AAGGTTGAGGGAAGGGGGT 60.072 57.895 0.00 0.00 0.00 4.95
97 99 5.987347 CAGGATTAGCCAGCCAAATAATTTG 59.013 40.000 0.00 0.00 40.02 2.32
438 441 2.416893 GAGCATTTCTCCCGTTTCAGAC 59.583 50.000 0.00 0.00 35.77 3.51
461 464 5.470047 AGGTGTAGATGTTTCGAAAGACT 57.530 39.130 11.66 12.71 41.84 3.24
483 486 1.661617 CGGATATCGTCGTTGGCAAAA 59.338 47.619 0.00 0.00 0.00 2.44
484 487 1.282817 CGGATATCGTCGTTGGCAAA 58.717 50.000 0.00 0.00 0.00 3.68
521 524 1.805428 GCAATGCCCCAAAGTGACGT 61.805 55.000 0.00 0.00 0.00 4.34
571 574 4.772886 AAATGCTAGGAATTACCCTCGT 57.227 40.909 0.00 0.00 40.05 4.18
586 589 0.248054 CGACGGCGCAAATAAATGCT 60.248 50.000 10.83 0.00 44.21 3.79
587 590 1.199852 CCGACGGCGCAAATAAATGC 61.200 55.000 4.27 0.00 42.94 3.56
591 594 2.047083 ACCCGACGGCGCAAATAA 60.047 55.556 4.27 0.00 35.83 1.40
628 631 8.447053 GGCCGCATTTTATTGATTAAAAAGAAA 58.553 29.630 0.00 0.00 41.76 2.52
634 637 6.876257 AGTTTGGCCGCATTTTATTGATTAAA 59.124 30.769 0.00 0.00 0.00 1.52
673 682 3.121738 TGGTTTCGTCCTCCTTTTCTC 57.878 47.619 0.00 0.00 0.00 2.87
811 824 0.647410 CGGTGTGATCGATGCAGAAC 59.353 55.000 0.54 1.24 0.00 3.01
844 866 2.365293 GACTTTGGCTGGTTTGGAACAT 59.635 45.455 0.00 0.00 39.30 2.71
877 899 4.340097 TGCGTGTACATATAGTGGTAGCTT 59.660 41.667 0.00 0.00 0.00 3.74
881 903 3.952967 TGGTGCGTGTACATATAGTGGTA 59.047 43.478 0.00 0.00 0.00 3.25
932 958 1.238439 ATGTTGGAGGTTGCGTTGAG 58.762 50.000 0.00 0.00 0.00 3.02
933 959 2.147958 GTATGTTGGAGGTTGCGTTGA 58.852 47.619 0.00 0.00 0.00 3.18
934 960 1.199097 GGTATGTTGGAGGTTGCGTTG 59.801 52.381 0.00 0.00 0.00 4.10
935 961 1.530323 GGTATGTTGGAGGTTGCGTT 58.470 50.000 0.00 0.00 0.00 4.84
936 962 0.672401 CGGTATGTTGGAGGTTGCGT 60.672 55.000 0.00 0.00 0.00 5.24
937 963 0.390603 TCGGTATGTTGGAGGTTGCG 60.391 55.000 0.00 0.00 0.00 4.85
938 964 1.940613 GATCGGTATGTTGGAGGTTGC 59.059 52.381 0.00 0.00 0.00 4.17
967 993 1.302192 GGGAGGCGTGCACAAGTAA 60.302 57.895 18.64 0.00 0.00 2.24
996 1026 3.039011 GACCTTAGGAGAGGCCATTACA 58.961 50.000 4.77 0.00 40.65 2.41
1077 1107 4.712425 ACTGTGTACGACGCCGCC 62.712 66.667 0.00 0.00 39.95 6.13
1213 2533 0.300491 CAATGTACCAACGCCGATCG 59.700 55.000 8.51 8.51 45.38 3.69
1281 2621 3.923864 ACGTTGTGCTCGGCCTCA 61.924 61.111 0.00 0.00 0.00 3.86
1481 2825 0.602638 CAGCGGCTACACCAGTTGAA 60.603 55.000 0.26 0.00 39.03 2.69
1524 2868 7.982663 CGAATTGCGTAATGGTACAATGTACTC 60.983 40.741 21.17 12.75 37.21 2.59
1525 2869 6.237996 CGAATTGCGTAATGGTACAATGTACT 60.238 38.462 21.17 6.30 37.21 2.73
1526 2870 5.899696 CGAATTGCGTAATGGTACAATGTAC 59.100 40.000 14.73 14.73 37.21 2.90
1527 2871 5.006844 CCGAATTGCGTAATGGTACAATGTA 59.993 40.000 0.00 0.00 39.83 2.29
1631 2980 5.422145 GAGGCATTAGTAACGACCCTTTAA 58.578 41.667 0.00 0.00 0.00 1.52
1659 3010 1.812571 TCGTGTAAGAACCGGGACTAC 59.187 52.381 6.32 2.24 0.00 2.73
1723 3074 1.202891 ACACCAACCAGGACTAAAGGC 60.203 52.381 0.00 0.00 41.22 4.35
1901 3268 5.464588 TTGGAATGATGAGGGGTGATTAA 57.535 39.130 0.00 0.00 0.00 1.40
1974 3341 2.108278 AACCCGGAAGCTAAGCGTGT 62.108 55.000 0.73 0.00 0.00 4.49
1983 3350 1.202663 GGGAGAATAGAACCCGGAAGC 60.203 57.143 0.73 0.00 34.03 3.86
2325 3707 4.353383 AGATACGGGGCTTTTAAGATCC 57.647 45.455 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.