Multiple sequence alignment - TraesCS2A01G407000

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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 TraesCS2A01G407000 chr2A 100.000 4998 0 0 1 4998 662748612 662743615 0.000000e+00 9230
1 TraesCS2A01G407000 chr2B 95.422 3517 120 13 739 4242 610695466 610691978 0.000000e+00 5565
2 TraesCS2A01G407000 chr2B 91.957 746 55 3 4255 4998 610691723 610690981 0.000000e+00 1040
3 TraesCS2A01G407000 chr2B 91.398 93 7 1 605 696 610695555 610695463 5.250000e-25 126
4 TraesCS2A01G407000 chr2D 94.584 2345 75 15 605 2936 518601873 518599568 0.000000e+00 3579
5 TraesCS2A01G407000 chr2D 93.962 1706 74 10 3313 4996 518599096 518597398 0.000000e+00 2553
6 TraesCS2A01G407000 chr2D 96.774 341 6 3 2984 3324 518599495 518599160 9.390000e-157 564
7 TraesCS2A01G407000 chr3B 99.675 616 1 1 1 616 59702450 59701836 0.000000e+00 1125
8 TraesCS2A01G407000 chr3B 99.836 611 0 1 1 611 806065071 806065680 0.000000e+00 1122
9 TraesCS2A01G407000 chr6B 99.836 610 0 1 1 610 119097671 119098279 0.000000e+00 1120
10 TraesCS2A01G407000 chr6B 78.110 635 109 21 1742 2367 492190531 492191144 4.720000e-100 375
11 TraesCS2A01G407000 chr6A 99.836 610 0 1 1 610 588225718 588226326 0.000000e+00 1120
12 TraesCS2A01G407000 chr6A 78.459 636 111 18 1742 2370 467043963 467044579 4.690000e-105 392
13 TraesCS2A01G407000 chr5B 99.836 610 0 1 1 610 13365651 13365043 0.000000e+00 1120
14 TraesCS2A01G407000 chr5B 99.836 610 0 1 1 610 701395820 701396428 0.000000e+00 1120
15 TraesCS2A01G407000 chr5B 81.384 838 122 27 1547 2364 439067172 439067995 0.000000e+00 652
16 TraesCS2A01G407000 chr5B 80.217 460 56 18 2489 2915 439068216 439068673 3.760000e-81 313
17 TraesCS2A01G407000 chr4B 99.836 610 0 1 1 610 613286131 613285523 0.000000e+00 1120
18 TraesCS2A01G407000 chr3D 99.836 610 0 1 1 610 245586600 245585992 0.000000e+00 1120
19 TraesCS2A01G407000 chr1D 99.836 610 0 1 1 610 487888875 487888267 0.000000e+00 1120
20 TraesCS2A01G407000 chr5A 81.425 856 121 28 1540 2373 472284059 472284898 0.000000e+00 665
21 TraesCS2A01G407000 chr5A 81.153 451 58 17 2489 2915 472285113 472285560 2.230000e-88 337
22 TraesCS2A01G407000 chr5D 81.317 835 128 21 1547 2364 369725213 369726036 0.000000e+00 652
23 TraesCS2A01G407000 chr5D 80.624 449 64 15 2489 2915 369726254 369726701 4.830000e-85 326
24 TraesCS2A01G407000 chr4D 78.738 602 111 11 1776 2376 494513395 494512810 2.180000e-103 387
25 TraesCS2A01G407000 chr6D 78.076 634 111 20 1742 2367 328330076 328330689 4.720000e-100 375


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 TraesCS2A01G407000 chr2A 662743615 662748612 4997 True 9230.000000 9230 100.000000 1 4998 1 chr2A.!!$R1 4997
1 TraesCS2A01G407000 chr2B 610690981 610695555 4574 True 2243.666667 5565 92.925667 605 4998 3 chr2B.!!$R1 4393
2 TraesCS2A01G407000 chr2D 518597398 518601873 4475 True 2232.000000 3579 95.106667 605 4996 3 chr2D.!!$R1 4391
3 TraesCS2A01G407000 chr3B 59701836 59702450 614 True 1125.000000 1125 99.675000 1 616 1 chr3B.!!$R1 615
4 TraesCS2A01G407000 chr3B 806065071 806065680 609 False 1122.000000 1122 99.836000 1 611 1 chr3B.!!$F1 610
5 TraesCS2A01G407000 chr6B 119097671 119098279 608 False 1120.000000 1120 99.836000 1 610 1 chr6B.!!$F1 609
6 TraesCS2A01G407000 chr6B 492190531 492191144 613 False 375.000000 375 78.110000 1742 2367 1 chr6B.!!$F2 625
7 TraesCS2A01G407000 chr6A 588225718 588226326 608 False 1120.000000 1120 99.836000 1 610 1 chr6A.!!$F2 609
8 TraesCS2A01G407000 chr6A 467043963 467044579 616 False 392.000000 392 78.459000 1742 2370 1 chr6A.!!$F1 628
9 TraesCS2A01G407000 chr5B 13365043 13365651 608 True 1120.000000 1120 99.836000 1 610 1 chr5B.!!$R1 609
10 TraesCS2A01G407000 chr5B 701395820 701396428 608 False 1120.000000 1120 99.836000 1 610 1 chr5B.!!$F1 609
11 TraesCS2A01G407000 chr5B 439067172 439068673 1501 False 482.500000 652 80.800500 1547 2915 2 chr5B.!!$F2 1368
12 TraesCS2A01G407000 chr4B 613285523 613286131 608 True 1120.000000 1120 99.836000 1 610 1 chr4B.!!$R1 609
13 TraesCS2A01G407000 chr3D 245585992 245586600 608 True 1120.000000 1120 99.836000 1 610 1 chr3D.!!$R1 609
14 TraesCS2A01G407000 chr1D 487888267 487888875 608 True 1120.000000 1120 99.836000 1 610 1 chr1D.!!$R1 609
15 TraesCS2A01G407000 chr5A 472284059 472285560 1501 False 501.000000 665 81.289000 1540 2915 2 chr5A.!!$F1 1375
16 TraesCS2A01G407000 chr5D 369725213 369726701 1488 False 489.000000 652 80.970500 1547 2915 2 chr5D.!!$F1 1368
17 TraesCS2A01G407000 chr4D 494512810 494513395 585 True 387.000000 387 78.738000 1776 2376 1 chr4D.!!$R1 600
18 TraesCS2A01G407000 chr6D 328330076 328330689 613 False 375.000000 375 78.076000 1742 2367 1 chr6D.!!$F1 625

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
706 707 0.444260 GCTGCTTTTAGCTCGGTCAC 59.556 55.0 0.0 0.0 42.97 3.67 F
1452 1453 0.250234 TCTCGTTCCAAGATGCCCAG 59.750 55.0 0.0 0.0 0.00 4.45 F
2739 2861 0.478072 TCCCAGACATTGGTGTTGCT 59.522 50.0 0.0 0.0 46.25 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2155 0.313043 GGTCACCGTTGTCGAAGAGA 59.687 55.0 0.0 0.0 36.95 3.10 R
3366 3626 0.246635 ACGACCACCTGAAAGATCCG 59.753 55.0 0.0 0.0 34.07 4.18 R
4452 4972 0.686441 TAGTGCGGATAGTGGGTGCT 60.686 55.0 0.0 0.0 0.00 4.40 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
630 631 2.527875 ATGAGGCTCCCGGGATCC 60.528 66.667 32.45 32.45 0.00 3.36
644 645 1.226888 GATCCCGTAGCCACACGTC 60.227 63.158 0.00 0.00 40.31 4.34
663 664 0.745845 CCAGAATTCTCCACCTGCCG 60.746 60.000 4.57 0.00 0.00 5.69
705 706 1.014044 CGCTGCTTTTAGCTCGGTCA 61.014 55.000 0.00 0.00 42.97 4.02
706 707 0.444260 GCTGCTTTTAGCTCGGTCAC 59.556 55.000 0.00 0.00 42.97 3.67
962 963 1.153549 CCGTCTAGGAGTTGCTGGC 60.154 63.158 0.00 0.00 45.00 4.85
985 986 4.452733 CGCCGGGTGGTTCTCTCC 62.453 72.222 2.18 0.00 37.67 3.71
1021 1022 0.883814 GGATCATCAGCAGAAGGCCG 60.884 60.000 0.00 0.00 46.50 6.13
1204 1205 2.095252 GGCGAGACGTTCAGCTTCC 61.095 63.158 9.32 0.00 0.00 3.46
1210 1211 1.149148 GACGTTCAGCTTCCAGAACC 58.851 55.000 8.58 0.00 40.69 3.62
1217 1218 2.747855 CTTCCAGAACCGCCAGCC 60.748 66.667 0.00 0.00 0.00 4.85
1361 1362 2.625790 CCGACCTGGAAATAGAGGAGAG 59.374 54.545 0.00 0.00 42.00 3.20
1447 1448 1.413767 CCGCGTCTCGTTCCAAGATG 61.414 60.000 4.92 0.00 36.19 2.90
1452 1453 0.250234 TCTCGTTCCAAGATGCCCAG 59.750 55.000 0.00 0.00 0.00 4.45
1514 1515 1.963855 CCACCGCCGACAACAATCA 60.964 57.895 0.00 0.00 0.00 2.57
1703 1710 2.452813 CGTTCGTCATGAAGGGGCG 61.453 63.158 8.84 2.58 38.50 6.13
2148 2155 1.606531 GCTCATCTCCTGGCACCTT 59.393 57.895 0.00 0.00 0.00 3.50
2716 2834 2.492088 GCCAAACCTGGATCCAAGTAAC 59.508 50.000 16.48 3.24 46.92 2.50
2719 2837 4.941873 CCAAACCTGGATCCAAGTAACTAC 59.058 45.833 16.48 0.00 46.92 2.73
2720 2838 5.280521 CCAAACCTGGATCCAAGTAACTACT 60.281 44.000 16.48 0.00 46.92 2.57
2724 2846 4.030913 CTGGATCCAAGTAACTACTCCCA 58.969 47.826 17.00 0.00 34.99 4.37
2725 2847 4.030913 TGGATCCAAGTAACTACTCCCAG 58.969 47.826 13.46 0.00 34.99 4.45
2728 2850 4.122337 TCCAAGTAACTACTCCCAGACA 57.878 45.455 0.00 0.00 34.99 3.41
2739 2861 0.478072 TCCCAGACATTGGTGTTGCT 59.522 50.000 0.00 0.00 46.25 3.91
2742 2893 1.682854 CCAGACATTGGTGTTGCTGTT 59.317 47.619 0.00 0.00 42.41 3.16
2745 2896 3.023119 AGACATTGGTGTTGCTGTTGAA 58.977 40.909 0.00 0.00 39.09 2.69
2753 2904 3.245990 GGTGTTGCTGTTGAAAAATGCTC 59.754 43.478 0.00 0.00 0.00 4.26
2757 2908 4.587584 TGCTGTTGAAAAATGCTCATCA 57.412 36.364 0.00 0.00 0.00 3.07
2779 2930 5.473162 TCAAATTCTTGATGGTGAACGATGT 59.527 36.000 0.00 0.00 36.62 3.06
2781 2932 4.747540 TTCTTGATGGTGAACGATGTTG 57.252 40.909 0.00 0.00 0.00 3.33
2978 3163 3.283751 TGTGGTGTGGGTTCTAAACTTG 58.716 45.455 0.00 0.00 0.00 3.16
3290 3475 3.200593 GGCATGCAGGTCGCTCAG 61.201 66.667 21.36 0.00 43.06 3.35
3305 3490 0.758685 CTCAGAGATTCTCCCCGCCT 60.759 60.000 10.09 0.00 0.00 5.52
3337 3597 3.183172 CACTGAGTTGACACACGAGATTG 59.817 47.826 0.00 0.00 0.00 2.67
3341 3601 2.794910 AGTTGACACACGAGATTGTTCG 59.205 45.455 0.00 0.00 45.70 3.95
3366 3626 2.279582 ACTGATCGACGTGGATGAAC 57.720 50.000 18.34 4.37 0.00 3.18
3512 3772 1.609210 TCCTGACATGGGAGACGCA 60.609 57.895 0.00 0.00 0.00 5.24
3847 4107 4.570926 TCCAGGACATAGGGATGAGATTT 58.429 43.478 0.00 0.00 36.48 2.17
4120 4381 4.472691 TTTTGATCGACAACTTGCTGAG 57.527 40.909 0.00 0.00 38.29 3.35
4133 4394 2.034104 TGCTGAGGAGAACATGATGC 57.966 50.000 0.00 0.00 0.00 3.91
4148 4409 5.106442 ACATGATGCGTTATCGAGTAACAA 58.894 37.500 0.00 5.95 42.29 2.83
4246 4524 4.746535 TGGAGTTAAGTGCAATATCGGA 57.253 40.909 1.46 0.00 0.00 4.55
4288 4808 9.237706 TCCTCATTTAGTCTTTAGGGGATTTAT 57.762 33.333 0.00 0.00 0.00 1.40
4341 4861 8.504005 CAACTAAAAGAATCCGCGGATAATTAT 58.496 33.333 39.08 24.48 33.97 1.28
4389 4909 3.304659 CGTATGAAAAGCACACTGCCTTT 60.305 43.478 0.00 0.00 46.52 3.11
4393 4913 3.261580 GAAAAGCACACTGCCTTTGTTT 58.738 40.909 0.00 0.00 46.52 2.83
4452 4972 3.142162 CCCATTGGCATGCTCGCA 61.142 61.111 18.92 4.09 0.00 5.10
4465 4985 1.227380 CTCGCAGCACCCACTATCC 60.227 63.158 0.00 0.00 0.00 2.59
4466 4986 2.586079 CGCAGCACCCACTATCCG 60.586 66.667 0.00 0.00 0.00 4.18
4470 4990 1.990060 AGCACCCACTATCCGCACT 60.990 57.895 0.00 0.00 0.00 4.40
4471 4991 0.686441 AGCACCCACTATCCGCACTA 60.686 55.000 0.00 0.00 0.00 2.74
4500 5020 1.696063 ATGTATGTTGCTGCATCCCC 58.304 50.000 1.84 0.00 0.00 4.81
4505 5025 3.588511 TTGCTGCATCCCCACCCA 61.589 61.111 1.84 0.00 0.00 4.51
4506 5026 3.884704 TTGCTGCATCCCCACCCAC 62.885 63.158 1.84 0.00 0.00 4.61
4550 5070 5.414454 TGTGTTACATTGTAATCAAGAGGGC 59.586 40.000 12.16 0.00 36.97 5.19
4697 5219 5.163663 GGAATGTGTTGTCTTTGACTTCACA 60.164 40.000 20.18 20.18 43.63 3.58
4722 5244 8.450964 CAATGATTATCCCACGGAAATATACAC 58.549 37.037 0.00 0.00 34.34 2.90
4889 5412 3.504520 GGTGTCTAGCTCACTATCTAGCC 59.495 52.174 14.30 0.00 39.64 3.93
4916 5439 4.097418 ACTTGATTAGGAGTGGTAGCACT 58.903 43.478 26.83 26.83 38.26 4.40
4964 5488 4.164413 GCCCCTAGTTTAGGTCTTCTCATT 59.836 45.833 1.76 0.00 44.73 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
644 645 0.745845 CGGCAGGTGGAGAATTCTGG 60.746 60.000 14.00 0.00 0.00 3.86
919 920 3.499737 CGCTGATCACCAACGGCC 61.500 66.667 0.00 0.00 35.28 6.13
1041 1042 1.567504 CCGACTGTGACGACTTGTTT 58.432 50.000 0.00 0.00 0.00 2.83
1242 1243 3.257561 CATTCCGCTCTGACGCCG 61.258 66.667 0.00 0.00 0.00 6.46
1249 1250 1.748122 CTTGGCTGCATTCCGCTCT 60.748 57.895 0.50 0.00 43.06 4.09
1361 1362 1.469308 ACGTCTCGTGATTCTCCTGAC 59.531 52.381 0.00 0.00 39.18 3.51
1452 1453 2.517450 CGATTGGCCGAGACGCTTC 61.517 63.158 8.99 0.00 0.00 3.86
1514 1515 1.169661 TGCGTTCGCATCCTGGTTTT 61.170 50.000 15.82 0.00 36.09 2.43
1788 1795 1.505353 GTCGATGAACGGGTCGTCT 59.495 57.895 13.06 0.00 39.99 4.18
2148 2155 0.313043 GGTCACCGTTGTCGAAGAGA 59.687 55.000 0.00 0.00 36.95 3.10
2724 2846 2.653726 TCAACAGCAACACCAATGTCT 58.346 42.857 0.00 0.00 38.45 3.41
2725 2847 3.435105 TTCAACAGCAACACCAATGTC 57.565 42.857 0.00 0.00 38.45 3.06
2728 2850 4.035441 GCATTTTTCAACAGCAACACCAAT 59.965 37.500 0.00 0.00 0.00 3.16
2739 2861 8.552865 CAAGAATTTGATGAGCATTTTTCAACA 58.447 29.630 0.00 0.00 36.36 3.33
2757 2908 5.964958 ACATCGTTCACCATCAAGAATTT 57.035 34.783 0.00 0.00 0.00 1.82
2779 2930 2.934887 AGTATATGTGCCTGCATGCAA 58.065 42.857 22.88 6.66 44.11 4.08
2781 2932 2.620115 ACAAGTATATGTGCCTGCATGC 59.380 45.455 11.82 11.82 30.82 4.06
2978 3163 1.154413 CGCGTTCACCTGCAATCAC 60.154 57.895 0.00 0.00 0.00 3.06
3289 3474 0.758685 CAGAGGCGGGGAGAATCTCT 60.759 60.000 10.38 0.00 34.46 3.10
3290 3475 1.745264 CAGAGGCGGGGAGAATCTC 59.255 63.158 0.71 0.71 33.73 2.75
3305 3490 1.413812 TCAACTCAGTGAAGCAGCAGA 59.586 47.619 0.00 0.00 0.00 4.26
3315 3500 2.492019 TCTCGTGTGTCAACTCAGTG 57.508 50.000 0.00 0.00 0.00 3.66
3337 3597 2.223433 ACGTCGATCAGTTATCCCGAAC 60.223 50.000 0.00 0.00 32.55 3.95
3341 3601 1.679680 TCCACGTCGATCAGTTATCCC 59.320 52.381 0.00 0.00 0.00 3.85
3366 3626 0.246635 ACGACCACCTGAAAGATCCG 59.753 55.000 0.00 0.00 34.07 4.18
3465 3725 3.878778 AGTAGTTCATGATGGGCAAGAC 58.121 45.455 0.00 0.00 0.00 3.01
3512 3772 3.636381 GACGTTAACGGAGAAGTCAACT 58.364 45.455 29.81 6.02 44.95 3.16
3677 3937 7.220108 CGAAACAAAGTAAAAGGGAAACTCAAG 59.780 37.037 0.00 0.00 0.00 3.02
3847 4107 1.290431 AGAATCAGCTCCCTCCTCTCA 59.710 52.381 0.00 0.00 0.00 3.27
3945 4205 4.111577 CCTATTAGAATGGATAGGGGGCA 58.888 47.826 2.20 0.00 40.70 5.36
4120 4381 3.381045 TCGATAACGCATCATGTTCTCC 58.619 45.455 0.00 0.00 39.58 3.71
4133 4394 5.004440 CCTCATGTGTTGTTACTCGATAACG 59.996 44.000 10.88 0.00 45.45 3.18
4148 4409 3.007614 AGCGTAAAACCTACCTCATGTGT 59.992 43.478 0.00 0.00 0.00 3.72
4288 4808 1.284785 CTCCAACAAGAGCCCCCATTA 59.715 52.381 0.00 0.00 0.00 1.90
4327 4847 8.441312 AAAACTAAGAAATAATTATCCGCGGA 57.559 30.769 33.12 33.12 0.00 5.54
4341 4861 8.947055 AACTAGTGGTTACGAAAACTAAGAAA 57.053 30.769 0.00 0.00 36.23 2.52
4360 4880 5.405571 CAGTGTGCTTTTCATACGAACTAGT 59.594 40.000 0.00 0.00 41.10 2.57
4389 4909 0.865111 CAGCGTTCATGGACGAAACA 59.135 50.000 30.47 0.00 45.47 2.83
4393 4913 2.434185 GGCAGCGTTCATGGACGA 60.434 61.111 30.47 0.00 45.47 4.20
4452 4972 0.686441 TAGTGCGGATAGTGGGTGCT 60.686 55.000 0.00 0.00 0.00 4.40
4465 4985 7.358765 GCAACATACATAGAGAAAGATAGTGCG 60.359 40.741 0.00 0.00 0.00 5.34
4466 4986 7.655328 AGCAACATACATAGAGAAAGATAGTGC 59.345 37.037 0.00 0.00 0.00 4.40
4470 4990 7.500141 TGCAGCAACATACATAGAGAAAGATA 58.500 34.615 0.00 0.00 0.00 1.98
4471 4991 6.351711 TGCAGCAACATACATAGAGAAAGAT 58.648 36.000 0.00 0.00 0.00 2.40
4500 5020 2.118404 AAGCCAACACGTGTGGGTG 61.118 57.895 36.49 24.28 41.33 4.61
4505 5025 0.885196 AACAACAAGCCAACACGTGT 59.115 45.000 17.22 17.22 33.50 4.49
4506 5026 2.834574 TAACAACAAGCCAACACGTG 57.165 45.000 15.48 15.48 0.00 4.49
4550 5070 5.583854 CCGCTCTTATAATTCATGGATCCAG 59.416 44.000 21.33 12.25 0.00 3.86
4661 5181 7.035612 AGACAACACATTCCTTTTTGAAGAAC 58.964 34.615 0.00 0.00 0.00 3.01
4697 5219 8.160765 TGTGTATATTTCCGTGGGATAATCATT 58.839 33.333 0.00 0.00 0.00 2.57
4747 5269 7.325660 TGAGTTATACTACTACCTCCGTTTG 57.674 40.000 0.00 0.00 0.00 2.93
4889 5412 4.392921 ACCACTCCTAATCAAGTCGATG 57.607 45.455 0.00 0.00 33.40 3.84
4916 5439 4.648762 CACCTCCCCATTAATGTTAATGCA 59.351 41.667 14.25 0.00 45.36 3.96
4964 5488 2.692368 GATCCCCTGCCTCACCCA 60.692 66.667 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.