Multiple sequence alignment - TraesCS3D01G244900

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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 TraesCS3D01G244900 chr3D 100.000 2738 0 0 1 2738 340416818 340414081 0.000000e+00 5057
1 TraesCS3D01G244900 chr3D 71.552 464 114 15 1092 1546 58080799 58081253 2.880000e-20 110
2 TraesCS3D01G244900 chr3A 94.221 2215 78 19 563 2738 464319297 464321500 0.000000e+00 3336
3 TraesCS3D01G244900 chr3A 88.850 565 42 7 1 563 696272813 696272268 0.000000e+00 675
4 TraesCS3D01G244900 chr3A 88.050 159 19 0 399 557 696273416 696273574 3.600000e-44 189
5 TraesCS3D01G244900 chr3A 71.274 463 114 15 1093 1546 66907967 66908419 1.730000e-17 100
6 TraesCS3D01G244900 chr3B 93.954 2051 77 16 715 2738 439334107 439332077 0.000000e+00 3057
7 TraesCS3D01G244900 chr3B 88.632 563 48 6 1 557 451357960 451358512 0.000000e+00 671
8 TraesCS3D01G244900 chr3B 86.957 437 42 6 126 557 397415149 397415575 6.860000e-131 477
9 TraesCS3D01G244900 chr3B 71.183 465 114 16 1092 1546 90858382 90858836 6.240000e-17 99
10 TraesCS3D01G244900 chr6D 96.986 564 16 1 1 563 14257013 14257576 0.000000e+00 946
11 TraesCS3D01G244900 chr6D 91.607 560 29 9 1 557 53146300 53146844 0.000000e+00 758
12 TraesCS3D01G244900 chr1D 92.857 560 28 8 1 557 383366991 383367541 0.000000e+00 802
13 TraesCS3D01G244900 chr1D 78.131 503 90 15 1095 1589 469587034 469587524 4.430000e-78 302
14 TraesCS3D01G244900 chr4A 87.698 569 48 8 1 557 740642927 740643485 0.000000e+00 643
15 TraesCS3D01G244900 chr4A 90.682 440 27 8 1 437 219191768 219191340 8.500000e-160 573
16 TraesCS3D01G244900 chr4A 88.679 159 18 0 399 557 219192383 219192541 7.740000e-46 195
17 TraesCS3D01G244900 chr4D 94.667 375 17 2 1 372 381551770 381551396 1.830000e-161 579
18 TraesCS3D01G244900 chr4D 83.304 575 75 17 1 557 147516478 147517049 6.760000e-141 510
19 TraesCS3D01G244900 chr7D 82.935 586 68 17 1 557 448935740 448935158 1.460000e-137 499
20 TraesCS3D01G244900 chr5B 83.957 561 47 19 1 557 490729617 490729096 5.270000e-137 497
21 TraesCS3D01G244900 chr5B 90.361 166 14 2 399 562 693121749 693121584 1.650000e-52 217
22 TraesCS3D01G244900 chr1B 79.482 502 85 13 1095 1589 649368730 649369220 9.390000e-90 340
23 TraesCS3D01G244900 chr1A 78.905 493 86 13 1104 1589 562784804 562785285 4.400000e-83 318


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 TraesCS3D01G244900 chr3D 340414081 340416818 2737 True 5057 5057 100.000 1 2738 1 chr3D.!!$R1 2737
1 TraesCS3D01G244900 chr3A 464319297 464321500 2203 False 3336 3336 94.221 563 2738 1 chr3A.!!$F2 2175
2 TraesCS3D01G244900 chr3A 696272268 696272813 545 True 675 675 88.850 1 563 1 chr3A.!!$R1 562
3 TraesCS3D01G244900 chr3B 439332077 439334107 2030 True 3057 3057 93.954 715 2738 1 chr3B.!!$R1 2023
4 TraesCS3D01G244900 chr3B 451357960 451358512 552 False 671 671 88.632 1 557 1 chr3B.!!$F3 556
5 TraesCS3D01G244900 chr6D 14257013 14257576 563 False 946 946 96.986 1 563 1 chr6D.!!$F1 562
6 TraesCS3D01G244900 chr6D 53146300 53146844 544 False 758 758 91.607 1 557 1 chr6D.!!$F2 556
7 TraesCS3D01G244900 chr1D 383366991 383367541 550 False 802 802 92.857 1 557 1 chr1D.!!$F1 556
8 TraesCS3D01G244900 chr4A 740642927 740643485 558 False 643 643 87.698 1 557 1 chr4A.!!$F2 556
9 TraesCS3D01G244900 chr4D 147516478 147517049 571 False 510 510 83.304 1 557 1 chr4D.!!$F1 556
10 TraesCS3D01G244900 chr7D 448935158 448935740 582 True 499 499 82.935 1 557 1 chr7D.!!$R1 556
11 TraesCS3D01G244900 chr5B 490729096 490729617 521 True 497 497 83.957 1 557 1 chr5B.!!$R1 556

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
937 1017 0.530744 ACCGATCACACGCACTACAT 59.469 50.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2074 0.250793 AATCGCAACGGGACCATGTA 59.749 50.0 0.0 0.0 0.0 2.29 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
317 335 1.270147 GGTATGGGGTTCGAATCCTCG 60.270 57.143 26.15 0.00 46.87 4.63
394 449 1.700523 CACGCCATGTGGATTGTTTG 58.299 50.000 2.55 0.00 45.21 2.93
395 450 1.269174 CACGCCATGTGGATTGTTTGA 59.731 47.619 2.55 0.00 45.21 2.69
396 451 1.269448 ACGCCATGTGGATTGTTTGAC 59.731 47.619 2.55 0.00 37.39 3.18
397 452 1.402720 CGCCATGTGGATTGTTTGACC 60.403 52.381 2.55 0.00 37.39 4.02
398 453 1.895131 GCCATGTGGATTGTTTGACCT 59.105 47.619 2.55 0.00 37.39 3.85
399 454 2.353011 GCCATGTGGATTGTTTGACCTG 60.353 50.000 2.55 0.00 37.39 4.00
400 455 2.892852 CCATGTGGATTGTTTGACCTGT 59.107 45.455 0.00 0.00 37.39 4.00
401 456 3.321682 CCATGTGGATTGTTTGACCTGTT 59.678 43.478 0.00 0.00 37.39 3.16
402 457 4.202243 CCATGTGGATTGTTTGACCTGTTT 60.202 41.667 0.00 0.00 37.39 2.83
548 612 6.525578 ACGATAAGTTCAATGACCACTAGA 57.474 37.500 0.00 0.00 0.00 2.43
557 621 7.831193 AGTTCAATGACCACTAGAGCATTTTAT 59.169 33.333 0.00 0.00 0.00 1.40
559 623 8.579850 TCAATGACCACTAGAGCATTTTATTT 57.420 30.769 0.00 0.00 0.00 1.40
585 649 1.276421 TCTTGCTTCTCACCTGCTACC 59.724 52.381 0.00 0.00 0.00 3.18
595 659 1.798813 CACCTGCTACCGACTTTTCAC 59.201 52.381 0.00 0.00 0.00 3.18
755 834 1.226295 CGCACAGCATCGTCTCGTA 60.226 57.895 0.00 0.00 0.00 3.43
803 882 3.060272 CCACGCGCAGAGAATAACATAAG 60.060 47.826 5.73 0.00 0.00 1.73
936 1016 1.135603 GTACCGATCACACGCACTACA 60.136 52.381 0.00 0.00 0.00 2.74
937 1017 0.530744 ACCGATCACACGCACTACAT 59.469 50.000 0.00 0.00 0.00 2.29
938 1018 1.746787 ACCGATCACACGCACTACATA 59.253 47.619 0.00 0.00 0.00 2.29
942 1022 2.357327 TCACACGCACTACATACACC 57.643 50.000 0.00 0.00 0.00 4.16
943 1023 1.614413 TCACACGCACTACATACACCA 59.386 47.619 0.00 0.00 0.00 4.17
950 1030 0.822164 ACTACATACACCACCGCTCC 59.178 55.000 0.00 0.00 0.00 4.70
982 1062 0.882042 CCGTTGTTCAGAGCAGCACT 60.882 55.000 0.00 0.00 0.00 4.40
1436 1516 2.444624 CGGTCAACATCGTCGCCAG 61.445 63.158 0.00 0.00 0.00 4.85
1542 1622 1.446966 GCTCGACAAGGTGCTCCTC 60.447 63.158 7.99 0.00 44.35 3.71
1656 1736 2.504244 GGGTCAGACGACGAAGCG 60.504 66.667 0.00 0.00 43.61 4.68
1805 1886 5.221185 GCCATCAATCAATGTGCATAGACTT 60.221 40.000 0.00 0.00 0.00 3.01
1880 1961 5.529581 TTCCTTTGTTCCATTCTTGTTCC 57.470 39.130 0.00 0.00 0.00 3.62
1889 1970 2.229784 CCATTCTTGTTCCTGCCTTGTC 59.770 50.000 0.00 0.00 0.00 3.18
1993 2074 1.065709 ACCCGGTAGTGCGATTGAAAT 60.066 47.619 0.00 0.00 0.00 2.17
2102 2207 3.579709 ACTCACGTTAGTTGAGCTGATG 58.420 45.455 0.00 0.00 32.51 3.07
2190 2295 4.529897 TCTCTGGTCAAAATGGGATGATG 58.470 43.478 0.00 0.00 0.00 3.07
2283 2397 4.432741 GAGCAGGGAGGGGCCAAC 62.433 72.222 4.39 0.00 38.95 3.77
2323 2437 1.062685 CTCGTCCGGTGATGAGTCG 59.937 63.158 0.00 0.00 45.67 4.18
2324 2438 1.366854 CTCGTCCGGTGATGAGTCGA 61.367 60.000 0.00 0.05 45.67 4.20
2326 2440 0.100682 CGTCCGGTGATGAGTCGATT 59.899 55.000 0.00 0.00 0.00 3.34
2327 2441 1.841450 GTCCGGTGATGAGTCGATTC 58.159 55.000 0.00 0.13 0.00 2.52
2328 2442 1.405821 GTCCGGTGATGAGTCGATTCT 59.594 52.381 9.50 0.00 0.00 2.40
2329 2443 2.617308 GTCCGGTGATGAGTCGATTCTA 59.383 50.000 9.50 0.00 0.00 2.10
2330 2444 2.617308 TCCGGTGATGAGTCGATTCTAC 59.383 50.000 9.50 5.88 0.00 2.59
2331 2445 2.619177 CCGGTGATGAGTCGATTCTACT 59.381 50.000 9.50 0.00 0.00 2.57
2332 2446 3.813724 CCGGTGATGAGTCGATTCTACTA 59.186 47.826 9.50 0.00 0.00 1.82
2333 2447 4.083749 CCGGTGATGAGTCGATTCTACTAG 60.084 50.000 9.50 0.00 0.00 2.57
2335 2449 5.695363 CGGTGATGAGTCGATTCTACTAGTA 59.305 44.000 9.50 1.89 0.00 1.82
2336 2450 6.369340 CGGTGATGAGTCGATTCTACTAGTAT 59.631 42.308 9.50 0.00 0.00 2.12
2337 2451 7.095144 CGGTGATGAGTCGATTCTACTAGTATT 60.095 40.741 9.50 0.00 0.00 1.89
2478 2604 1.620819 ACTTCACAGCCTACTCACAGG 59.379 52.381 0.00 0.00 38.86 4.00
2572 2698 1.279271 CCAGTAGCTTGTAGCCCTGTT 59.721 52.381 0.00 0.00 43.77 3.16
2600 2726 5.794507 CTGTTGGCAAAGAGCATAACATTGT 60.795 40.000 0.00 0.00 44.90 2.71
2626 2752 4.465040 AGCTTCGTACTACGTATAGCAC 57.535 45.455 22.60 0.00 43.14 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 249 6.724441 TCCAATCTTGTGTCTAGTTAGAGGAA 59.276 38.462 0.00 0.00 32.01 3.36
317 335 4.256110 AGGGAAAATAAAAATGCTGCTGC 58.744 39.130 8.89 8.89 40.20 5.25
353 376 1.296715 CCCTACCTGTCAGTGGTGC 59.703 63.158 0.00 0.00 38.42 5.01
401 456 3.805066 TCCATCCATTTGACTGGTCAA 57.195 42.857 11.53 11.53 46.72 3.18
402 457 3.805066 TTCCATCCATTTGACTGGTCA 57.195 42.857 0.00 0.00 37.57 4.02
557 621 6.040842 AGCAGGTGAGAAGCAAGAAAATAAAA 59.959 34.615 0.00 0.00 0.00 1.52
559 623 5.072741 AGCAGGTGAGAAGCAAGAAAATAA 58.927 37.500 0.00 0.00 0.00 1.40
585 649 1.014564 GCCGAGGGAGTGAAAAGTCG 61.015 60.000 0.00 0.00 0.00 4.18
595 659 1.681793 TCGATTAGAAAGCCGAGGGAG 59.318 52.381 0.00 0.00 0.00 4.30
632 696 1.557443 GCAGAACTACTTGTGCGCGT 61.557 55.000 8.43 0.00 36.97 6.01
637 701 0.512952 GCCGTGCAGAACTACTTGTG 59.487 55.000 0.00 0.00 0.00 3.33
664 728 1.057822 CACACGAGAATCTTGCGCG 59.942 57.895 0.00 0.00 38.00 6.86
713 777 2.736081 GCAATGAAATGAGCCGCAATGA 60.736 45.455 0.00 0.00 0.00 2.57
755 834 1.153628 GGAATGTGCGCTACGACCT 60.154 57.895 9.73 0.00 0.00 3.85
936 1016 2.064581 GGAGGGAGCGGTGGTGTAT 61.065 63.158 0.00 0.00 0.00 2.29
937 1017 2.682494 GGAGGGAGCGGTGGTGTA 60.682 66.667 0.00 0.00 0.00 2.90
938 1018 4.640690 AGGAGGGAGCGGTGGTGT 62.641 66.667 0.00 0.00 0.00 4.16
942 1022 4.020617 TTGCAGGAGGGAGCGGTG 62.021 66.667 0.00 0.00 0.00 4.94
943 1023 4.021925 GTTGCAGGAGGGAGCGGT 62.022 66.667 0.00 0.00 0.00 5.68
950 1030 1.672356 CAACGGAGGTTGCAGGAGG 60.672 63.158 0.00 0.00 46.22 4.30
982 1062 0.329261 ATTGCTTGTGGCTCTGGCTA 59.671 50.000 0.00 0.00 42.39 3.93
1436 1516 0.028902 GACGTTGACCTGGTTGTTGC 59.971 55.000 0.00 0.00 0.00 4.17
1491 1571 4.742201 GGCTTGACGGCGCTGAGA 62.742 66.667 25.98 5.42 0.00 3.27
1805 1886 3.230134 CCAAAGACAAGGAAACCCATCA 58.770 45.455 0.00 0.00 0.00 3.07
1889 1970 2.482721 ACTCAATCTTAACAAACCGCCG 59.517 45.455 0.00 0.00 0.00 6.46
1993 2074 0.250793 AATCGCAACGGGACCATGTA 59.749 50.000 0.00 0.00 0.00 2.29
2102 2207 5.975693 AGTACCAGCTAGCTCTGATTATC 57.024 43.478 16.15 0.55 36.19 1.75
2190 2295 3.288809 ACCGAAAACTAGACGTGTACC 57.711 47.619 0.00 0.00 0.00 3.34
2303 2417 2.105128 CTCATCACCGGACGAGCC 59.895 66.667 9.46 0.00 0.00 4.70
2306 2420 0.746923 ATCGACTCATCACCGGACGA 60.747 55.000 9.46 4.22 0.00 4.20
2326 2440 9.499479 GCAGTACCACTATGTAATACTAGTAGA 57.501 37.037 8.85 0.00 0.00 2.59
2327 2441 9.281371 TGCAGTACCACTATGTAATACTAGTAG 57.719 37.037 8.85 0.00 0.00 2.57
2328 2442 9.803507 ATGCAGTACCACTATGTAATACTAGTA 57.196 33.333 4.77 4.77 0.00 1.82
2329 2443 8.707796 ATGCAGTACCACTATGTAATACTAGT 57.292 34.615 0.00 0.00 0.00 2.57
2330 2444 9.411801 CAATGCAGTACCACTATGTAATACTAG 57.588 37.037 0.00 0.00 0.00 2.57
2331 2445 8.920174 ACAATGCAGTACCACTATGTAATACTA 58.080 33.333 0.00 0.00 0.00 1.82
2332 2446 7.792032 ACAATGCAGTACCACTATGTAATACT 58.208 34.615 0.00 0.00 0.00 2.12
2333 2447 8.975439 GTACAATGCAGTACCACTATGTAATAC 58.025 37.037 5.20 0.00 38.70 1.89
2335 2449 6.700081 CGTACAATGCAGTACCACTATGTAAT 59.300 38.462 9.86 0.00 40.94 1.89
2336 2450 6.037726 CGTACAATGCAGTACCACTATGTAA 58.962 40.000 9.86 0.00 40.94 2.41
2337 2451 5.357596 TCGTACAATGCAGTACCACTATGTA 59.642 40.000 9.86 0.00 40.94 2.29
2339 2453 4.678622 TCGTACAATGCAGTACCACTATG 58.321 43.478 9.86 0.00 40.94 2.23
2478 2604 1.312815 GGAAGGCCATGCTATCACAC 58.687 55.000 5.01 0.00 0.00 3.82
2555 2681 3.447944 AGAGTAACAGGGCTACAAGCTAC 59.552 47.826 0.00 0.00 41.99 3.58
2572 2698 2.928801 TGCTCTTTGCCAACAGAGTA 57.071 45.000 14.09 9.46 39.10 2.59
2626 2752 6.459066 ACAACGATGAATCCCTGTATGATAG 58.541 40.000 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.