Multiple sequence alignment - TraesCS1D01G029700

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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 TraesCS1D01G029700 chr1D 100.000 3431 0 0 1 3431 11637843 11641273 0.000000e+00 6336.0
1 TraesCS1D01G029700 chr1D 81.892 740 124 9 1672 2409 383363821 383363090 1.750000e-172 616.0
2 TraesCS1D01G029700 chr1D 94.510 255 14 0 3177 3431 14148592 14148846 8.920000e-106 394.0
3 TraesCS1D01G029700 chr1A 93.756 2034 84 14 626 2635 13804941 13806955 0.000000e+00 3013.0
4 TraesCS1D01G029700 chr1A 89.273 578 35 14 1 574 13804309 13804863 0.000000e+00 699.0
5 TraesCS1D01G029700 chr1A 81.003 758 132 11 1658 2412 483134138 483133390 2.950000e-165 592.0
6 TraesCS1D01G029700 chr1A 80.713 757 134 10 1658 2412 483196246 483195500 2.300000e-161 579.0
7 TraesCS1D01G029700 chr1A 94.355 124 2 2 2513 2635 13806982 13807101 5.850000e-43 185.0
8 TraesCS1D01G029700 chr1A 89.655 87 5 1 2549 2635 13816991 13817073 1.300000e-19 108.0
9 TraesCS1D01G029700 chr1B 93.702 1699 49 9 905 2572 17537978 17536307 0.000000e+00 2492.0
10 TraesCS1D01G029700 chr1B 92.902 634 39 3 1 633 17539334 17538706 0.000000e+00 917.0
11 TraesCS1D01G029700 chr1B 81.662 758 127 11 1658 2412 514077179 514076431 1.350000e-173 619.0
12 TraesCS1D01G029700 chr1B 80.871 758 133 11 1658 2412 513674444 513673696 1.370000e-163 586.0
13 TraesCS1D01G029700 chr1B 87.543 289 22 2 635 909 17538645 17538357 4.270000e-84 322.0
14 TraesCS1D01G029700 chr7A 93.424 806 41 5 2632 3431 189433129 189432330 0.000000e+00 1184.0
15 TraesCS1D01G029700 chr7A 94.510 255 14 0 3177 3431 422485745 422485491 8.920000e-106 394.0
16 TraesCS1D01G029700 chr7A 95.556 45 2 0 831 875 712339652 712339608 4.750000e-09 73.1
17 TraesCS1D01G029700 chr3A 83.899 795 97 13 2636 3413 698743068 698743848 0.000000e+00 730.0
18 TraesCS1D01G029700 chr3A 90.573 541 45 5 2632 3169 665968825 665969362 0.000000e+00 712.0
19 TraesCS1D01G029700 chr3A 94.118 255 15 0 3177 3431 715408738 715408484 4.150000e-104 388.0
20 TraesCS1D01G029700 chr3A 88.789 223 23 2 3063 3285 665969294 665969514 4.360000e-69 272.0
21 TraesCS1D01G029700 chr5D 81.955 798 98 22 2634 3414 113490885 113490117 4.830000e-178 634.0
22 TraesCS1D01G029700 chr5D 76.289 291 58 8 1293 1579 542632004 542631721 9.920000e-31 145.0
23 TraesCS1D01G029700 chr5D 71.936 563 126 27 1036 1579 540079294 540079843 5.970000e-28 135.0
24 TraesCS1D01G029700 chr5D 82.292 96 15 2 1086 1180 542632256 542632162 7.890000e-12 82.4
25 TraesCS1D01G029700 chr3D 81.414 764 120 18 1664 2420 510647373 510648121 3.790000e-169 604.0
26 TraesCS1D01G029700 chr3D 82.862 566 86 8 1033 1588 511060728 511061292 6.610000e-137 497.0
27 TraesCS1D01G029700 chr3D 85.987 471 54 8 1641 2108 511061312 511061773 8.550000e-136 494.0
28 TraesCS1D01G029700 chr3D 94.510 255 14 0 3177 3431 571692039 571691785 8.920000e-106 394.0
29 TraesCS1D01G029700 chr3B 81.591 641 103 8 1641 2275 672706031 672706662 1.830000e-142 516.0
30 TraesCS1D01G029700 chr3B 83.983 462 63 7 1641 2100 672608876 672609328 1.890000e-117 433.0
31 TraesCS1D01G029700 chr3B 83.217 286 33 10 2634 2918 546205225 546204954 7.350000e-62 248.0
32 TraesCS1D01G029700 chr3B 88.679 53 5 1 824 876 685630147 685630198 2.860000e-06 63.9
33 TraesCS1D01G029700 chr3B 88.679 53 5 1 824 876 685658642 685658693 2.860000e-06 63.9
34 TraesCS1D01G029700 chr4A 85.327 443 63 2 1006 1447 728535028 728535469 1.120000e-124 457.0
35 TraesCS1D01G029700 chr6D 95.294 255 12 0 3177 3431 454585703 454585449 4.120000e-109 405.0
36 TraesCS1D01G029700 chr6D 78.972 214 25 9 634 840 315980261 315980461 9.990000e-26 128.0
37 TraesCS1D01G029700 chr6A 94.902 255 13 0 3177 3431 524317906 524317652 1.920000e-107 399.0
38 TraesCS1D01G029700 chr6A 93.725 255 16 0 3177 3431 521552640 521552386 1.930000e-102 383.0
39 TraesCS1D01G029700 chr2D 94.510 255 14 0 3177 3431 524270111 524269857 8.920000e-106 394.0
40 TraesCS1D01G029700 chr2D 72.289 581 110 32 1041 1582 572404260 572404828 2.150000e-27 134.0
41 TraesCS1D01G029700 chr2D 71.543 499 106 24 1104 1581 2770549 2770066 6.060000e-18 102.0
42 TraesCS1D01G029700 chr2D 81.905 105 19 0 1477 1581 630010737 630010633 4.720000e-14 89.8
43 TraesCS1D01G029700 chr5B 83.172 309 36 10 2628 2932 458926320 458926616 5.640000e-68 268.0
44 TraesCS1D01G029700 chr5B 72.291 563 124 27 1036 1579 682398511 682399060 2.760000e-31 147.0
45 TraesCS1D01G029700 chr5A 83.688 282 42 4 2636 2915 638815031 638815310 2.630000e-66 263.0
46 TraesCS1D01G029700 chr5A 95.238 42 2 0 831 872 113726680 113726639 2.210000e-07 67.6
47 TraesCS1D01G029700 chr7D 82.609 276 43 4 2636 2911 180972284 180972014 4.430000e-59 239.0
48 TraesCS1D01G029700 chr7D 91.667 48 4 0 828 875 478366711 478366664 2.210000e-07 67.6
49 TraesCS1D01G029700 chr4D 82.168 286 42 8 2636 2917 196878429 196878149 1.590000e-58 237.0
50 TraesCS1D01G029700 chr7B 82.014 278 44 5 2636 2911 192018789 192018516 7.400000e-57 231.0
51 TraesCS1D01G029700 chr7B 91.837 49 3 1 824 872 123036658 123036705 2.210000e-07 67.6
52 TraesCS1D01G029700 chr6B 80.727 275 43 6 2989 3256 235608281 235608552 4.490000e-49 206.0
53 TraesCS1D01G029700 chr2B 71.821 582 111 34 1041 1582 687634074 687634642 2.160000e-22 117.0
54 TraesCS1D01G029700 chr2B 82.692 104 18 0 1478 1581 8507547 8507650 3.650000e-15 93.5
55 TraesCS1D01G029700 chr2B 80.952 105 20 0 1477 1581 772981779 772981675 2.190000e-12 84.2
56 TraesCS1D01G029700 chr2A 80.147 136 24 2 1041 1176 711855899 711856031 7.840000e-17 99.0
57 TraesCS1D01G029700 chr2A 81.731 104 19 0 1478 1581 2839594 2839697 1.700000e-13 87.9
58 TraesCS1D01G029700 chr4B 94.286 35 1 1 824 858 15359637 15359670 6.000000e-03 52.8


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 TraesCS1D01G029700 chr1D 11637843 11641273 3430 False 6336.000000 6336 100.000000 1 3431 1 chr1D.!!$F1 3430
1 TraesCS1D01G029700 chr1D 383363090 383363821 731 True 616.000000 616 81.892000 1672 2409 1 chr1D.!!$R1 737
2 TraesCS1D01G029700 chr1A 13804309 13807101 2792 False 1299.000000 3013 92.461333 1 2635 3 chr1A.!!$F2 2634
3 TraesCS1D01G029700 chr1A 483133390 483134138 748 True 592.000000 592 81.003000 1658 2412 1 chr1A.!!$R1 754
4 TraesCS1D01G029700 chr1A 483195500 483196246 746 True 579.000000 579 80.713000 1658 2412 1 chr1A.!!$R2 754
5 TraesCS1D01G029700 chr1B 17536307 17539334 3027 True 1243.666667 2492 91.382333 1 2572 3 chr1B.!!$R3 2571
6 TraesCS1D01G029700 chr1B 514076431 514077179 748 True 619.000000 619 81.662000 1658 2412 1 chr1B.!!$R2 754
7 TraesCS1D01G029700 chr1B 513673696 513674444 748 True 586.000000 586 80.871000 1658 2412 1 chr1B.!!$R1 754
8 TraesCS1D01G029700 chr7A 189432330 189433129 799 True 1184.000000 1184 93.424000 2632 3431 1 chr7A.!!$R1 799
9 TraesCS1D01G029700 chr3A 698743068 698743848 780 False 730.000000 730 83.899000 2636 3413 1 chr3A.!!$F1 777
10 TraesCS1D01G029700 chr3A 665968825 665969514 689 False 492.000000 712 89.681000 2632 3285 2 chr3A.!!$F2 653
11 TraesCS1D01G029700 chr5D 113490117 113490885 768 True 634.000000 634 81.955000 2634 3414 1 chr5D.!!$R1 780
12 TraesCS1D01G029700 chr3D 510647373 510648121 748 False 604.000000 604 81.414000 1664 2420 1 chr3D.!!$F1 756
13 TraesCS1D01G029700 chr3D 511060728 511061773 1045 False 495.500000 497 84.424500 1033 2108 2 chr3D.!!$F2 1075
14 TraesCS1D01G029700 chr3B 672706031 672706662 631 False 516.000000 516 81.591000 1641 2275 1 chr3B.!!$F2 634

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
578 582 1.210155 CCAAAAGAGGAAAGCGCGG 59.790 57.895 8.83 0.0 0.00 6.46 F
810 887 1.213430 CCGGCCCAAAATACCTTCCTA 59.787 52.381 0.00 0.0 0.00 2.94 F
1617 2094 0.320334 ACGTCAATGGCGTCATCACA 60.320 50.000 7.21 0.0 38.23 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 2086 0.320771 AGGCCGTTGTCTGTGATGAC 60.321 55.0 0.0 0.0 37.47 3.06 R
1701 2178 0.988832 TGCTGAACGGTAAGGGGATT 59.011 50.0 0.0 0.0 0.00 3.01 R
2585 3244 2.924290 CACACGCCTTAGCTAGAAGTTC 59.076 50.0 0.0 0.0 36.60 3.01 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
64 65 4.020218 CCAATACCCATCGACCATGTAGAT 60.020 45.833 0.00 0.00 0.00 1.98
269 273 2.366916 CGGAGGCTAAGATGATCTTGGT 59.633 50.000 17.50 0.00 37.31 3.67
283 287 3.889196 TCTTGGTTCGAATTTGTTCCG 57.111 42.857 0.00 0.00 0.00 4.30
284 288 3.207778 TCTTGGTTCGAATTTGTTCCGT 58.792 40.909 0.00 0.00 0.00 4.69
392 396 1.721804 GCGCGCTAGACTTGTGTTTTC 60.722 52.381 26.67 0.00 0.00 2.29
426 430 1.534805 CGACTCGACATCACTCATGGG 60.535 57.143 0.00 0.00 36.72 4.00
451 455 2.118513 ACTCGGACTCACCAGGCT 59.881 61.111 0.00 0.00 38.90 4.58
460 464 4.514577 CACCAGGCTAGCGGTCCG 62.515 72.222 11.00 6.99 31.41 4.79
499 503 3.629058 AGCGCGTACAATCACATAGTAG 58.371 45.455 8.43 0.00 0.00 2.57
507 511 7.193595 CGTACAATCACATAGTAGTCACATCA 58.806 38.462 0.00 0.00 0.00 3.07
511 515 9.102757 ACAATCACATAGTAGTCACATCATTTC 57.897 33.333 0.00 0.00 0.00 2.17
534 538 9.612066 TTTCTTGAAAGCCTGAAATACAATTTT 57.388 25.926 0.00 0.00 0.00 1.82
578 582 1.210155 CCAAAAGAGGAAAGCGCGG 59.790 57.895 8.83 0.00 0.00 6.46
587 591 3.912745 GAAAGCGCGGGGAAGGGAA 62.913 63.158 8.83 0.00 0.00 3.97
594 598 1.595993 GCGGGGAAGGGAAAGCTTTC 61.596 60.000 27.68 27.68 36.46 2.62
607 611 4.513442 GAAAGCTTTCCCAAAACAGGTTT 58.487 39.130 25.80 0.00 0.00 3.27
662 725 5.190677 GCCTTAAGCCCAAAATACACTCTA 58.809 41.667 0.00 0.00 34.35 2.43
697 766 2.517166 GGATCAAGCCCGAAGCCC 60.517 66.667 0.00 0.00 45.47 5.19
698 767 2.272146 GATCAAGCCCGAAGCCCA 59.728 61.111 0.00 0.00 45.47 5.36
810 887 1.213430 CCGGCCCAAAATACCTTCCTA 59.787 52.381 0.00 0.00 0.00 2.94
932 1392 3.296854 TCGTGTTAGGATGGATGCTACT 58.703 45.455 0.00 0.00 30.09 2.57
933 1393 4.466827 TCGTGTTAGGATGGATGCTACTA 58.533 43.478 0.00 0.00 30.09 1.82
1246 1723 2.683933 CCCTGGACCGGTACTGCT 60.684 66.667 19.95 0.00 0.00 4.24
1290 1767 4.500116 GAGCTCGGCGACAGGACC 62.500 72.222 4.99 0.00 0.00 4.46
1320 1797 4.790962 CTGCGCTGCACAGGGGAT 62.791 66.667 9.73 0.00 40.57 3.85
1616 2093 2.456000 ACGTCAATGGCGTCATCAC 58.544 52.632 7.21 2.15 38.23 3.06
1617 2094 0.320334 ACGTCAATGGCGTCATCACA 60.320 50.000 7.21 0.00 38.23 3.58
1618 2095 0.371301 CGTCAATGGCGTCATCACAG 59.629 55.000 1.37 0.00 32.24 3.66
1619 2096 1.725641 GTCAATGGCGTCATCACAGA 58.274 50.000 1.37 0.00 32.24 3.41
1710 2187 2.685534 CCCCGTGCCAATCCCCTTA 61.686 63.158 0.00 0.00 0.00 2.69
2049 2529 2.646175 CGGCGAGGTCCTGGAGAAA 61.646 63.158 0.00 0.00 0.00 2.52
2458 2966 0.105593 GCTGATGAGGGATTGCTCGA 59.894 55.000 0.00 0.00 0.00 4.04
2480 2988 2.050714 CGGTGTAGTGTCGCGTGT 60.051 61.111 5.77 0.00 0.00 4.49
2582 3241 6.630443 CAGCTGCACGATTTATTTAGAATCAC 59.370 38.462 0.00 0.00 34.02 3.06
2585 3244 7.164826 GCTGCACGATTTATTTAGAATCACAAG 59.835 37.037 0.00 0.00 34.02 3.16
2682 3341 4.846779 TGAAGGTTAGCTTTGCGAAAAT 57.153 36.364 0.00 0.00 0.00 1.82
2694 3353 5.511729 GCTTTGCGAAAATCACTACAATACC 59.488 40.000 0.00 0.00 0.00 2.73
2910 3572 7.221452 CACCTGTCATTGAAACAAAAGAAGAAG 59.779 37.037 0.00 0.00 0.00 2.85
2911 3573 7.122650 ACCTGTCATTGAAACAAAAGAAGAAGA 59.877 33.333 0.00 0.00 0.00 2.87
3360 4082 0.036952 CACTCCAGGACGACTGCATT 60.037 55.000 6.40 0.00 46.14 3.56
3362 4084 0.247460 CTCCAGGACGACTGCATTGA 59.753 55.000 6.40 0.00 46.14 2.57
3392 4114 2.765807 CCTCATCCAGGTCCCGCT 60.766 66.667 0.00 0.00 37.53 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 273 2.214347 TCTGCACGGAACAAATTCGAA 58.786 42.857 0.00 0.00 35.48 3.71
283 287 0.798776 CCGTTGAACAGGATCTGCAC 59.201 55.000 0.00 0.00 34.37 4.57
284 288 0.684535 TCCGTTGAACAGGATCTGCA 59.315 50.000 5.10 0.00 34.37 4.41
336 340 6.623549 CGGACATGCTCAAAAACATCTTGTAT 60.624 38.462 0.00 0.00 0.00 2.29
392 396 1.347817 GAGTCGCCAGTTTCTCGCAG 61.348 60.000 0.00 0.00 0.00 5.18
413 417 2.573009 TGATGACACCCATGAGTGATGT 59.427 45.455 14.98 0.80 40.34 3.06
426 430 1.402984 GGTGAGTCCGAGTGATGACAC 60.403 57.143 0.00 0.00 46.24 3.67
460 464 2.678324 GCTATAGGAATCCAGTGCGAC 58.322 52.381 0.61 0.00 0.00 5.19
499 503 5.048504 TCAGGCTTTCAAGAAATGATGTGAC 60.049 40.000 0.00 0.00 38.03 3.67
507 511 9.783081 AAATTGTATTTCAGGCTTTCAAGAAAT 57.217 25.926 12.57 12.57 41.83 2.17
511 515 9.044150 TCAAAAATTGTATTTCAGGCTTTCAAG 57.956 29.630 0.00 0.00 0.00 3.02
575 579 1.595993 GAAAGCTTTCCCTTCCCCGC 61.596 60.000 25.80 0.00 0.00 6.13
587 591 4.568072 AAAACCTGTTTTGGGAAAGCTT 57.432 36.364 7.18 0.00 40.84 3.74
604 608 3.243134 TGCACGGGTTTAACTAGCAAAAC 60.243 43.478 10.60 10.60 35.34 2.43
607 611 2.257691 TGCACGGGTTTAACTAGCAA 57.742 45.000 0.00 0.00 0.00 3.91
642 705 9.303116 TGAAAATAGAGTGTATTTTGGGCTTAA 57.697 29.630 19.53 0.00 37.28 1.85
643 706 8.871629 TGAAAATAGAGTGTATTTTGGGCTTA 57.128 30.769 19.53 0.97 37.28 3.09
662 725 2.046285 CGGGCTCGGGCTTGAAAAT 61.046 57.895 7.48 0.00 38.73 1.82
697 766 1.059942 GCGTTTCAATCGGCCTTTTG 58.940 50.000 0.00 4.56 0.00 2.44
698 767 0.958822 AGCGTTTCAATCGGCCTTTT 59.041 45.000 0.00 0.00 0.00 2.27
710 779 5.005971 TGTGTACACTAGAAAACAGCGTTTC 59.994 40.000 25.60 5.13 37.70 2.78
800 877 4.301072 TGTTTTGCAGCTAGGAAGGTAT 57.699 40.909 0.00 0.00 0.00 2.73
810 887 1.336632 TTGGGCCTTGTTTTGCAGCT 61.337 50.000 4.53 0.00 0.00 4.24
1458 1935 4.008933 GCAGACAGCACGGGGAGT 62.009 66.667 0.00 0.00 44.79 3.85
1566 2043 1.522092 GTGGATCTCCGACCATGCA 59.478 57.895 0.00 0.00 38.48 3.96
1608 2085 1.626654 GGCCGTTGTCTGTGATGACG 61.627 60.000 0.00 0.00 39.64 4.35
1609 2086 0.320771 AGGCCGTTGTCTGTGATGAC 60.321 55.000 0.00 0.00 37.47 3.06
1610 2087 1.262417 TAGGCCGTTGTCTGTGATGA 58.738 50.000 0.00 0.00 0.00 2.92
1611 2088 2.093306 TTAGGCCGTTGTCTGTGATG 57.907 50.000 0.00 0.00 0.00 3.07
1612 2089 2.224426 TGTTTAGGCCGTTGTCTGTGAT 60.224 45.455 0.00 0.00 0.00 3.06
1613 2090 1.139256 TGTTTAGGCCGTTGTCTGTGA 59.861 47.619 0.00 0.00 0.00 3.58
1614 2091 1.588674 TGTTTAGGCCGTTGTCTGTG 58.411 50.000 0.00 0.00 0.00 3.66
1615 2092 2.158871 TCTTGTTTAGGCCGTTGTCTGT 60.159 45.455 0.00 0.00 0.00 3.41
1616 2093 2.489971 TCTTGTTTAGGCCGTTGTCTG 58.510 47.619 0.00 0.00 0.00 3.51
1617 2094 2.922740 TCTTGTTTAGGCCGTTGTCT 57.077 45.000 0.00 0.00 0.00 3.41
1618 2095 3.071479 TCATCTTGTTTAGGCCGTTGTC 58.929 45.455 0.00 0.00 0.00 3.18
1619 2096 3.134574 TCATCTTGTTTAGGCCGTTGT 57.865 42.857 0.00 0.00 0.00 3.32
1701 2178 0.988832 TGCTGAACGGTAAGGGGATT 59.011 50.000 0.00 0.00 0.00 3.01
1710 2187 2.203195 TGCAGCTTGCTGAACGGT 60.203 55.556 24.67 0.00 45.31 4.83
2458 2966 4.647654 CGACACTACACCGCAAGT 57.352 55.556 0.00 0.00 0.00 3.16
2582 3241 3.614616 CACGCCTTAGCTAGAAGTTCTTG 59.385 47.826 11.40 10.42 36.60 3.02
2585 3244 2.924290 CACACGCCTTAGCTAGAAGTTC 59.076 50.000 0.00 0.00 36.60 3.01
2809 3471 5.593010 TGTAAAATGTTAAGTGTTGCCACC 58.407 37.500 0.00 0.00 42.88 4.61
3360 4082 3.794369 ATGAGGTAGGCGACCCCATCA 62.794 57.143 13.56 11.05 42.86 3.07


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

AutoCloner maintained by Alex Coulton.