Multiple sequence alignment - TraesCS1B01G400000

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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 TraesCS1B01G400000 chr1B 100.000 2198 0 0 1 2198 630743054 630740857 0.000000e+00 4060.0
1 TraesCS1B01G400000 chr1B 84.607 916 132 3 549 1455 630821342 630820427 0.000000e+00 902.0
2 TraesCS1B01G400000 chr1A 95.207 918 41 1 538 1455 551308587 551307673 0.000000e+00 1448.0
3 TraesCS1B01G400000 chr1A 88.786 758 53 19 1454 2198 23094379 23093641 0.000000e+00 900.0
4 TraesCS1B01G400000 chr1A 84.004 919 132 8 549 1455 551312517 551311602 0.000000e+00 869.0
5 TraesCS1B01G400000 chr1D 93.580 919 44 1 537 1455 458873471 458872568 0.000000e+00 1356.0
6 TraesCS1B01G400000 chr1D 84.498 916 133 3 549 1455 458877050 458876135 0.000000e+00 896.0
7 TraesCS1B01G400000 chr4B 97.027 740 20 1 1456 2193 44369286 44368547 0.000000e+00 1243.0
8 TraesCS1B01G400000 chr4B 97.417 542 14 0 1 542 184138273 184137732 0.000000e+00 924.0
9 TraesCS1B01G400000 chr3A 94.511 747 31 6 1455 2193 552539228 552539972 0.000000e+00 1144.0
10 TraesCS1B01G400000 chr3A 90.972 576 26 13 1454 2021 615645 616202 0.000000e+00 752.0
11 TraesCS1B01G400000 chr6B 91.914 742 50 7 1455 2193 688064603 688065337 0.000000e+00 1029.0
12 TraesCS1B01G400000 chr6B 97.258 547 13 2 1 547 473274040 473273496 0.000000e+00 926.0
13 TraesCS1B01G400000 chr3D 89.761 752 62 9 1455 2193 96440348 96441097 0.000000e+00 948.0
14 TraesCS1B01G400000 chr3B 98.324 537 9 0 1 537 119343597 119344133 0.000000e+00 942.0
15 TraesCS1B01G400000 chr3B 97.948 536 11 0 1 536 719203658 719204193 0.000000e+00 929.0
16 TraesCS1B01G400000 chr5B 97.778 540 11 1 1 540 33349361 33349899 0.000000e+00 929.0
17 TraesCS1B01G400000 chr5B 97.948 536 11 0 2 537 410406020 410406555 0.000000e+00 929.0
18 TraesCS1B01G400000 chr5B 96.250 560 18 3 1 557 13470751 13470192 0.000000e+00 915.0
19 TraesCS1B01G400000 chr2B 97.948 536 11 0 1 536 606452209 606452744 0.000000e+00 929.0
20 TraesCS1B01G400000 chr7B 97.593 540 13 0 1 540 122580959 122580420 0.000000e+00 926.0
21 TraesCS1B01G400000 chr7B 96.578 526 14 2 1672 2193 559525170 559524645 0.000000e+00 869.0
22 TraesCS1B01G400000 chr7B 81.683 404 62 4 556 947 620677824 620678227 2.100000e-85 326.0
23 TraesCS1B01G400000 chr7B 89.956 229 16 7 1451 1676 559527133 559526909 2.760000e-74 289.0
24 TraesCS1B01G400000 chr5D 88.142 759 68 15 1455 2198 407700489 407701240 0.000000e+00 883.0
25 TraesCS1B01G400000 chr5D 87.648 761 68 20 1450 2193 565268280 565269031 0.000000e+00 861.0
26 TraesCS1B01G400000 chr5D 80.349 458 71 13 897 1343 423534436 423534885 1.630000e-86 329.0
27 TraesCS1B01G400000 chr6D 88.196 754 68 15 1454 2193 448898841 448898095 0.000000e+00 880.0
28 TraesCS1B01G400000 chr6D 83.735 332 49 3 915 1242 472925849 472925519 2.120000e-80 309.0
29 TraesCS1B01G400000 chr6D 82.955 88 15 0 1273 1360 460576801 460576888 1.810000e-11 80.5
30 TraesCS1B01G400000 chr2D 84.503 755 95 15 1452 2198 68800226 68800966 0.000000e+00 726.0
31 TraesCS1B01G400000 chr7D 78.934 807 138 16 556 1336 566521158 566520358 8.990000e-144 520.0
32 TraesCS1B01G400000 chr7D 80.172 464 70 11 897 1339 549835258 549834796 5.850000e-86 327.0
33 TraesCS1B01G400000 chr7D 79.333 300 58 4 554 851 602293035 602292738 7.950000e-50 207.0
34 TraesCS1B01G400000 chr5A 80.045 441 74 11 897 1330 537124080 537124513 4.560000e-82 315.0
35 TraesCS1B01G400000 chr7A 79.126 206 34 2 751 947 652702497 652702292 1.370000e-27 134.0


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 TraesCS1B01G400000 chr1B 630740857 630743054 2197 True 4060.0 4060 100.0000 1 2198 1 chr1B.!!$R1 2197
1 TraesCS1B01G400000 chr1B 630820427 630821342 915 True 902.0 902 84.6070 549 1455 1 chr1B.!!$R2 906
2 TraesCS1B01G400000 chr1A 551307673 551312517 4844 True 1158.5 1448 89.6055 538 1455 2 chr1A.!!$R2 917
3 TraesCS1B01G400000 chr1A 23093641 23094379 738 True 900.0 900 88.7860 1454 2198 1 chr1A.!!$R1 744
4 TraesCS1B01G400000 chr1D 458872568 458877050 4482 True 1126.0 1356 89.0390 537 1455 2 chr1D.!!$R1 918
5 TraesCS1B01G400000 chr4B 44368547 44369286 739 True 1243.0 1243 97.0270 1456 2193 1 chr4B.!!$R1 737
6 TraesCS1B01G400000 chr4B 184137732 184138273 541 True 924.0 924 97.4170 1 542 1 chr4B.!!$R2 541
7 TraesCS1B01G400000 chr3A 552539228 552539972 744 False 1144.0 1144 94.5110 1455 2193 1 chr3A.!!$F2 738
8 TraesCS1B01G400000 chr3A 615645 616202 557 False 752.0 752 90.9720 1454 2021 1 chr3A.!!$F1 567
9 TraesCS1B01G400000 chr6B 688064603 688065337 734 False 1029.0 1029 91.9140 1455 2193 1 chr6B.!!$F1 738
10 TraesCS1B01G400000 chr6B 473273496 473274040 544 True 926.0 926 97.2580 1 547 1 chr6B.!!$R1 546
11 TraesCS1B01G400000 chr3D 96440348 96441097 749 False 948.0 948 89.7610 1455 2193 1 chr3D.!!$F1 738
12 TraesCS1B01G400000 chr3B 119343597 119344133 536 False 942.0 942 98.3240 1 537 1 chr3B.!!$F1 536
13 TraesCS1B01G400000 chr3B 719203658 719204193 535 False 929.0 929 97.9480 1 536 1 chr3B.!!$F2 535
14 TraesCS1B01G400000 chr5B 33349361 33349899 538 False 929.0 929 97.7780 1 540 1 chr5B.!!$F1 539
15 TraesCS1B01G400000 chr5B 410406020 410406555 535 False 929.0 929 97.9480 2 537 1 chr5B.!!$F2 535
16 TraesCS1B01G400000 chr5B 13470192 13470751 559 True 915.0 915 96.2500 1 557 1 chr5B.!!$R1 556
17 TraesCS1B01G400000 chr2B 606452209 606452744 535 False 929.0 929 97.9480 1 536 1 chr2B.!!$F1 535
18 TraesCS1B01G400000 chr7B 122580420 122580959 539 True 926.0 926 97.5930 1 540 1 chr7B.!!$R1 539
19 TraesCS1B01G400000 chr7B 559524645 559527133 2488 True 579.0 869 93.2670 1451 2193 2 chr7B.!!$R2 742
20 TraesCS1B01G400000 chr5D 407700489 407701240 751 False 883.0 883 88.1420 1455 2198 1 chr5D.!!$F1 743
21 TraesCS1B01G400000 chr5D 565268280 565269031 751 False 861.0 861 87.6480 1450 2193 1 chr5D.!!$F3 743
22 TraesCS1B01G400000 chr6D 448898095 448898841 746 True 880.0 880 88.1960 1454 2193 1 chr6D.!!$R1 739
23 TraesCS1B01G400000 chr2D 68800226 68800966 740 False 726.0 726 84.5030 1452 2198 1 chr2D.!!$F1 746
24 TraesCS1B01G400000 chr7D 566520358 566521158 800 True 520.0 520 78.9340 556 1336 1 chr7D.!!$R2 780

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
588 592 1.271656 GCAAACATGGCAAAGAGCTCT 59.728 47.619 11.45 11.45 44.79 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 5403 1.749638 ATCGACGAGGCGGAGAAGT 60.75 57.895 3.01 0.0 0.0 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
193 194 4.226620 TCTTGATGGAGGTAAAACCCTACC 59.773 45.833 0.00 0.00 39.75 3.18
544 545 3.576861 CAGGACTCCCTCACATACCATA 58.423 50.000 0.00 0.00 42.02 2.74
545 546 4.163427 CAGGACTCCCTCACATACCATAT 58.837 47.826 0.00 0.00 42.02 1.78
546 547 4.020751 CAGGACTCCCTCACATACCATATG 60.021 50.000 0.00 0.00 42.02 1.78
547 548 4.140686 AGGACTCCCTCACATACCATATGA 60.141 45.833 3.65 0.00 38.86 2.15
581 585 2.941720 GGTTCAAAGCAAACATGGCAAA 59.058 40.909 0.00 0.00 0.00 3.68
588 592 1.271656 GCAAACATGGCAAAGAGCTCT 59.728 47.619 11.45 11.45 44.79 4.09
606 4585 6.950619 AGAGCTCTTTCAAAACAAAGGGATAT 59.049 34.615 11.45 0.00 36.09 1.63
637 4616 2.268920 GCTCCCAGCAATCGGTCA 59.731 61.111 0.00 0.00 41.89 4.02
656 4635 5.092781 GGTCACCATTACTATTTGCAAACG 58.907 41.667 15.41 11.21 0.00 3.60
705 4684 2.417257 GCATGCCGCCTTCAATGGA 61.417 57.895 6.36 0.00 32.94 3.41
706 4685 1.741327 GCATGCCGCCTTCAATGGAT 61.741 55.000 6.36 0.00 32.94 3.41
784 4763 1.615392 GCAAGGACAACTGCCTTTCAT 59.385 47.619 0.00 0.00 42.99 2.57
793 4772 6.374333 GGACAACTGCCTTTCATAGATAAACA 59.626 38.462 0.00 0.00 0.00 2.83
940 4919 4.444876 CCTCTTCTTGTCCTTCTTCCACAA 60.445 45.833 0.00 0.00 0.00 3.33
963 4942 1.550524 TCTGTTTCGTCCTCCTCCATG 59.449 52.381 0.00 0.00 0.00 3.66
1033 5012 1.268079 GAGCCCTGAACACTTTTGCTC 59.732 52.381 0.00 0.00 37.24 4.26
1104 5089 0.681175 GGCCAAAGAGTTGTGCCATT 59.319 50.000 0.00 0.00 44.31 3.16
1107 5092 3.244044 GGCCAAAGAGTTGTGCCATTAAA 60.244 43.478 0.00 0.00 44.31 1.52
1109 5094 4.448732 GCCAAAGAGTTGTGCCATTAAAAG 59.551 41.667 0.00 0.00 32.40 2.27
1167 5152 2.755876 ATCTCGCCGCTGACCTCA 60.756 61.111 0.00 0.00 0.00 3.86
1285 5270 3.251729 GCTGAACAACATGATGTCACACT 59.748 43.478 9.25 0.00 31.81 3.55
1361 5346 3.966979 TCATGAACATGTTGTAGCCCAT 58.033 40.909 17.58 9.03 39.72 4.00
1378 5363 1.140452 CCATCATGGACTCAGAGTGGG 59.860 57.143 8.15 0.00 40.96 4.61
1390 5375 5.006386 ACTCAGAGTGGGAATTGAATGTTC 58.994 41.667 0.91 0.00 0.00 3.18
1417 5402 2.163412 TCCGAAATGTACATTGGCTTGC 59.837 45.455 21.46 6.77 0.00 4.01
1418 5403 2.094803 CCGAAATGTACATTGGCTTGCA 60.095 45.455 21.46 0.00 0.00 4.08
1555 5545 1.478916 GGAGAGGTTTTAGCGCTCTCT 59.521 52.381 21.61 21.61 41.30 3.10
1613 5615 4.399618 TCATACACTCTCCAGCTACTCAAC 59.600 45.833 0.00 0.00 0.00 3.18
1994 7747 3.153919 CTCCAGATAGCCCAGAGAGTAC 58.846 54.545 0.00 0.00 0.00 2.73
2194 7949 9.757227 ATAAGCAACTAAGATCATCTAAGTGTC 57.243 33.333 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.759183 GCTTTCATTGAGAGTTCCTCTGTT 59.241 41.667 6.13 0.00 41.35 3.16
193 194 7.175119 ACATCATCAATATCAATCAAGCAGGAG 59.825 37.037 0.00 0.00 0.00 3.69
544 545 4.085357 TGAACCAGCAGTAACACTTCAT 57.915 40.909 0.00 0.00 0.00 2.57
545 546 3.552132 TGAACCAGCAGTAACACTTCA 57.448 42.857 0.00 0.00 0.00 3.02
546 547 4.789802 GCTTTGAACCAGCAGTAACACTTC 60.790 45.833 0.00 0.00 37.22 3.01
547 548 3.066760 GCTTTGAACCAGCAGTAACACTT 59.933 43.478 0.00 0.00 37.22 3.16
572 573 2.867624 TGAAAGAGCTCTTTGCCATGT 58.132 42.857 39.32 19.11 45.37 3.21
574 578 4.099881 TGTTTTGAAAGAGCTCTTTGCCAT 59.900 37.500 39.32 20.55 45.37 4.40
581 585 4.536765 TCCCTTTGTTTTGAAAGAGCTCT 58.463 39.130 11.45 11.45 35.30 4.09
588 592 6.642707 ACGACATATCCCTTTGTTTTGAAA 57.357 33.333 0.00 0.00 0.00 2.69
606 4585 3.857052 CTGGGAGCACTTAATTACGACA 58.143 45.455 0.00 0.00 0.00 4.35
629 4608 5.189928 TGCAAATAGTAATGGTGACCGATT 58.810 37.500 0.00 0.93 0.00 3.34
637 4616 3.437395 TCGCGTTTGCAAATAGTAATGGT 59.563 39.130 16.21 0.00 42.97 3.55
656 4635 2.125106 AAGCCCAATCTCCGTCGC 60.125 61.111 0.00 0.00 0.00 5.19
784 4763 4.404394 TCTCCAACGGCTCATGTTTATCTA 59.596 41.667 0.00 0.00 0.00 1.98
793 4772 3.837146 AGATATGATCTCCAACGGCTCAT 59.163 43.478 0.00 0.00 33.42 2.90
843 4822 3.959293 ACCATCAGAGATTGTGCAATGA 58.041 40.909 1.77 0.00 0.00 2.57
853 4832 6.371595 ACAAAGAGAGAAACCATCAGAGAT 57.628 37.500 0.00 0.00 0.00 2.75
860 4839 5.053978 ACAAGGACAAAGAGAGAAACCAT 57.946 39.130 0.00 0.00 0.00 3.55
940 4919 1.550976 GGAGGAGGACGAAACAGATGT 59.449 52.381 0.00 0.00 0.00 3.06
963 4942 3.711704 TCCCTAAGATGGAGGATGACAAC 59.288 47.826 0.00 0.00 35.99 3.32
988 4967 4.803088 GCTTAGCTTCATCTACACAGACTG 59.197 45.833 0.00 0.00 32.25 3.51
1033 5012 5.295292 GTGTCATACAGATCAAAGACATGGG 59.705 44.000 0.00 0.00 38.16 4.00
1104 5089 3.945346 TGCAGCCCGATCTAAACTTTTA 58.055 40.909 0.00 0.00 0.00 1.52
1107 5092 2.359900 CTTGCAGCCCGATCTAAACTT 58.640 47.619 0.00 0.00 0.00 2.66
1109 5094 0.378610 GCTTGCAGCCCGATCTAAAC 59.621 55.000 0.00 0.00 34.48 2.01
1133 5118 1.959899 GATGTTCGCTGCACACCGAG 61.960 60.000 0.00 0.00 34.68 4.63
1167 5152 1.888512 GTGGGTGCTGATGTGACATTT 59.111 47.619 0.00 0.00 0.00 2.32
1285 5270 6.608539 AATGAATGATTGTTTCACCATCCA 57.391 33.333 0.00 0.00 37.11 3.41
1361 5346 2.325661 TTCCCACTCTGAGTCCATGA 57.674 50.000 7.49 0.00 0.00 3.07
1378 5363 5.371115 TCGGAAACTGGAACATTCAATTC 57.629 39.130 0.00 0.00 38.20 2.17
1390 5375 4.732784 CCAATGTACATTTCGGAAACTGG 58.267 43.478 18.50 10.32 0.00 4.00
1417 5402 1.994507 ATCGACGAGGCGGAGAAGTG 61.995 60.000 3.01 0.00 0.00 3.16
1418 5403 1.749638 ATCGACGAGGCGGAGAAGT 60.750 57.895 3.01 0.00 0.00 3.01
1472 5457 4.974438 TGGAACCGGGGCAGGAGT 62.974 66.667 6.32 0.00 34.73 3.85
1555 5545 3.960102 GGTCAGGATGGATTTTTATGCCA 59.040 43.478 0.00 0.00 36.16 4.92
1994 7747 7.524912 CAAGTTGAGAATATGTTTGTCTCAGG 58.475 38.462 0.00 0.00 46.24 3.86


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

AutoCloner maintained by Alex Coulton.