Multiple sequence alignment - TraesCS2D01G233000

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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 TraesCS2D01G233000 chr2D 100.000 3288 0 0 1 3288 207006894 207003607 0 6072
1 TraesCS2D01G233000 chr2D 96.727 2658 57 4 633 3288 535662318 535664947 0 4399
2 TraesCS2D01G233000 chr2D 93.679 2658 107 16 633 3288 633747075 633749673 0 3921
3 TraesCS2D01G233000 chr2D 98.107 634 10 2 1 632 165617004 165616371 0 1103
4 TraesCS2D01G233000 chr3D 96.617 2660 58 6 632 3288 374010879 374008249 0 4385
5 TraesCS2D01G233000 chr3D 96.502 2659 63 3 632 3288 155675846 155678476 0 4368
6 TraesCS2D01G233000 chr3D 96.337 1911 50 3 1398 3288 580651490 580649580 0 3123
7 TraesCS2D01G233000 chr3D 97.030 1515 44 1 1377 2890 609770569 609769055 0 2547
8 TraesCS2D01G233000 chr1D 96.504 2660 62 5 633 3288 422850795 422848163 0 4368
9 TraesCS2D01G233000 chr1D 98.104 633 11 1 1 632 327505832 327505200 0 1101
10 TraesCS2D01G233000 chr5D 96.202 2659 70 13 632 3288 504761413 504764042 0 4322
11 TraesCS2D01G233000 chr5D 98.104 633 10 2 1 632 244454206 244454837 0 1101
12 TraesCS2D01G233000 chr6D 95.980 2662 76 5 629 3288 445278104 445275472 0 4294
13 TraesCS2D01G233000 chr6D 96.865 1914 37 3 1377 3288 387623981 387622089 0 3181
14 TraesCS2D01G233000 chr6D 96.885 1894 54 3 1398 3286 445209271 445207378 0 3166
15 TraesCS2D01G233000 chr6D 98.107 634 9 3 1 632 359487378 359486746 0 1101
16 TraesCS2D01G233000 chr6D 98.104 633 11 1 1 632 453972679 453973311 0 1101
17 TraesCS2D01G233000 chr5B 90.640 2703 157 38 626 3280 547624689 547622035 0 3502
18 TraesCS2D01G233000 chr7B 94.614 1968 89 11 633 2587 11701556 11699593 0 3031
19 TraesCS2D01G233000 chr7D 98.257 631 9 2 1 630 459118365 459118994 0 1103
20 TraesCS2D01G233000 chr7D 98.104 633 11 1 1 632 194299801 194300433 0 1101
21 TraesCS2D01G233000 chr7D 98.104 633 11 1 1 632 434771745 434772377 0 1101
22 TraesCS2D01G233000 chr4D 98.104 633 11 1 1 632 111157615 111158247 0 1101


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 TraesCS2D01G233000 chr2D 207003607 207006894 3287 True 6072 6072 100.000 1 3288 1 chr2D.!!$R2 3287
1 TraesCS2D01G233000 chr2D 535662318 535664947 2629 False 4399 4399 96.727 633 3288 1 chr2D.!!$F1 2655
2 TraesCS2D01G233000 chr2D 633747075 633749673 2598 False 3921 3921 93.679 633 3288 1 chr2D.!!$F2 2655
3 TraesCS2D01G233000 chr2D 165616371 165617004 633 True 1103 1103 98.107 1 632 1 chr2D.!!$R1 631
4 TraesCS2D01G233000 chr3D 374008249 374010879 2630 True 4385 4385 96.617 632 3288 1 chr3D.!!$R1 2656
5 TraesCS2D01G233000 chr3D 155675846 155678476 2630 False 4368 4368 96.502 632 3288 1 chr3D.!!$F1 2656
6 TraesCS2D01G233000 chr3D 580649580 580651490 1910 True 3123 3123 96.337 1398 3288 1 chr3D.!!$R2 1890
7 TraesCS2D01G233000 chr3D 609769055 609770569 1514 True 2547 2547 97.030 1377 2890 1 chr3D.!!$R3 1513
8 TraesCS2D01G233000 chr1D 422848163 422850795 2632 True 4368 4368 96.504 633 3288 1 chr1D.!!$R2 2655
9 TraesCS2D01G233000 chr1D 327505200 327505832 632 True 1101 1101 98.104 1 632 1 chr1D.!!$R1 631
10 TraesCS2D01G233000 chr5D 504761413 504764042 2629 False 4322 4322 96.202 632 3288 1 chr5D.!!$F2 2656
11 TraesCS2D01G233000 chr5D 244454206 244454837 631 False 1101 1101 98.104 1 632 1 chr5D.!!$F1 631
12 TraesCS2D01G233000 chr6D 445275472 445278104 2632 True 4294 4294 95.980 629 3288 1 chr6D.!!$R4 2659
13 TraesCS2D01G233000 chr6D 387622089 387623981 1892 True 3181 3181 96.865 1377 3288 1 chr6D.!!$R2 1911
14 TraesCS2D01G233000 chr6D 445207378 445209271 1893 True 3166 3166 96.885 1398 3286 1 chr6D.!!$R3 1888
15 TraesCS2D01G233000 chr6D 359486746 359487378 632 True 1101 1101 98.107 1 632 1 chr6D.!!$R1 631
16 TraesCS2D01G233000 chr6D 453972679 453973311 632 False 1101 1101 98.104 1 632 1 chr6D.!!$F1 631
17 TraesCS2D01G233000 chr5B 547622035 547624689 2654 True 3502 3502 90.640 626 3280 1 chr5B.!!$R1 2654
18 TraesCS2D01G233000 chr7B 11699593 11701556 1963 True 3031 3031 94.614 633 2587 1 chr7B.!!$R1 1954
19 TraesCS2D01G233000 chr7D 459118365 459118994 629 False 1103 1103 98.257 1 630 1 chr7D.!!$F3 629
20 TraesCS2D01G233000 chr7D 194299801 194300433 632 False 1101 1101 98.104 1 632 1 chr7D.!!$F1 631
21 TraesCS2D01G233000 chr7D 434771745 434772377 632 False 1101 1101 98.104 1 632 1 chr7D.!!$F2 631
22 TraesCS2D01G233000 chr4D 111157615 111158247 632 False 1101 1101 98.104 1 632 1 chr4D.!!$F1 631

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
194 196 0.107410 TCAAAGTTCGCCACCAGTGT 60.107 50.0 0.0 0.0 0.00 3.55 F
552 557 0.325296 ACCTTGGGGTCATCTCGCTA 60.325 55.0 0.0 0.0 43.38 4.26 F
1061 1068 0.031449 GCGCAGTACATCTCCTCCTC 59.969 60.0 0.3 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1067 1.000486 CCTTGAGAGGGGAGTCGGA 60.000 63.158 0.00 0.00 39.55 4.55 R
2247 2366 3.265479 AGCCTTAATCTGGTGAAGCTTCT 59.735 43.478 26.09 7.63 0.00 2.85 R
2876 3101 4.141181 AGCCCAATTGATGTGGATAAGCTA 60.141 41.667 7.12 0.00 38.54 3.32 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
24 26 5.833131 CCATGGTTATTGTGGCCTAGTTTAT 59.167 40.000 3.32 0.00 0.00 1.40
194 196 0.107410 TCAAAGTTCGCCACCAGTGT 60.107 50.000 0.00 0.00 0.00 3.55
225 227 4.154375 TGCGCCGACAAAAGAATATACAAA 59.846 37.500 4.18 0.00 0.00 2.83
552 557 0.325296 ACCTTGGGGTCATCTCGCTA 60.325 55.000 0.00 0.00 43.38 4.26
650 655 3.837355 AGGGAGTGAATTGCAAGAAACT 58.163 40.909 4.94 7.82 0.00 2.66
712 717 3.674753 CCTAATCTTTTGCAAAAGCCACG 59.325 43.478 36.33 25.59 43.85 4.94
787 792 2.280592 GGCGTTTCCGACAGGTGT 60.281 61.111 0.00 0.00 43.43 4.16
945 952 4.749310 CTGCTCCCACGCTCGCTT 62.749 66.667 0.00 0.00 0.00 4.68
974 981 1.563410 CCCATTTGCTCCTCTCCTCTT 59.437 52.381 0.00 0.00 0.00 2.85
1060 1067 1.729470 CGCGCAGTACATCTCCTCCT 61.729 60.000 8.75 0.00 0.00 3.69
1061 1068 0.031449 GCGCAGTACATCTCCTCCTC 59.969 60.000 0.30 0.00 0.00 3.71
1207 1214 1.285023 CGTCGTTCGAGGGTCTTGT 59.715 57.895 6.96 0.00 42.86 3.16
1327 1334 7.553402 TGCCACTGAAGTAAGTTTTAAGTTGTA 59.447 33.333 0.00 0.00 0.00 2.41
1387 1394 7.514721 AGTTACTGTTCATTTTCTAGGGTTCA 58.485 34.615 0.00 0.00 0.00 3.18
1388 1395 8.164070 AGTTACTGTTCATTTTCTAGGGTTCAT 58.836 33.333 0.00 0.00 0.00 2.57
1389 1396 9.444600 GTTACTGTTCATTTTCTAGGGTTCATA 57.555 33.333 0.00 0.00 0.00 2.15
1390 1397 9.667107 TTACTGTTCATTTTCTAGGGTTCATAG 57.333 33.333 0.00 0.00 0.00 2.23
1391 1398 7.690256 ACTGTTCATTTTCTAGGGTTCATAGT 58.310 34.615 0.00 0.00 0.00 2.12
1392 1399 8.164070 ACTGTTCATTTTCTAGGGTTCATAGTT 58.836 33.333 0.00 0.00 0.00 2.24
1393 1400 9.667107 CTGTTCATTTTCTAGGGTTCATAGTTA 57.333 33.333 0.00 0.00 0.00 2.24
1394 1401 9.444600 TGTTCATTTTCTAGGGTTCATAGTTAC 57.555 33.333 0.00 0.00 0.00 2.50
1395 1402 9.668497 GTTCATTTTCTAGGGTTCATAGTTACT 57.332 33.333 0.00 0.00 0.00 2.24
1396 1403 9.667107 TTCATTTTCTAGGGTTCATAGTTACTG 57.333 33.333 0.00 0.00 0.00 2.74
1400 1407 7.786046 TTCTAGGGTTCATAGTTACTGTTCA 57.214 36.000 0.00 0.00 0.00 3.18
2102 2173 3.005554 TGCTATGCTGAGCTGAAGAAAC 58.994 45.455 5.83 0.00 43.27 2.78
2247 2366 3.076621 CAGCAGGTGATAGCAACAAGAA 58.923 45.455 0.00 0.00 32.84 2.52
2435 2554 8.677148 ATTGTATGTTGTTTGTGAGAGTACTT 57.323 30.769 0.00 0.00 0.00 2.24
2867 3092 3.240134 GAGCTCTGGGTTGTCGGCA 62.240 63.158 6.43 0.00 0.00 5.69
2876 3101 1.227853 GTTGTCGGCAACCTCCAGT 60.228 57.895 22.14 0.00 46.81 4.00
2903 3128 1.894466 TCCACATCAATTGGGCTGTTG 59.106 47.619 5.42 3.98 34.56 3.33
3020 3245 1.549620 TCGTCGTCAGAGGAGTAGTCT 59.450 52.381 0.00 0.00 36.48 3.24
3069 3301 1.604023 ACTCGGCGTCAGAGTCCTT 60.604 57.895 6.85 0.00 44.87 3.36
3160 3392 1.141881 GGCGTCGGTGATGTCATCT 59.858 57.895 13.90 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 7.201785 GCTAGTGGCTGCAATAACCTATTTTTA 60.202 37.037 0.50 0.00 38.06 1.52
194 196 5.298197 TCTTTTGTCGGCGCATTTATTTA 57.702 34.783 10.83 0.00 0.00 1.40
225 227 3.080319 GCCTTCTGAAGTGCTCTCATTT 58.920 45.455 15.72 0.00 0.00 2.32
552 557 2.309755 TGAGCCAAACCATCTTGAGGAT 59.690 45.455 0.00 0.00 34.51 3.24
615 620 5.110814 TCACTCCCTTGTTTCTCTTTCAA 57.889 39.130 0.00 0.00 0.00 2.69
650 655 1.992557 AGAGAAGCCCCAAATGTGGTA 59.007 47.619 0.00 0.00 44.30 3.25
712 717 5.708948 TGCAAAACTATTACTGAATGTGCC 58.291 37.500 0.00 0.00 0.00 5.01
787 792 0.400213 ACGTCAGAGATTTTGGGCCA 59.600 50.000 0.00 0.00 0.00 5.36
884 889 4.357947 GCGAGCGAGGTGTGGTCA 62.358 66.667 0.00 0.00 33.56 4.02
892 897 2.164026 GCAGAAAGAGCGAGCGAGG 61.164 63.158 0.00 0.00 0.00 4.63
945 952 2.215451 GAGCAAATGGGAGGGGAGCA 62.215 60.000 0.00 0.00 0.00 4.26
1060 1067 1.000486 CCTTGAGAGGGGAGTCGGA 60.000 63.158 0.00 0.00 39.55 4.55
1061 1068 3.622514 CCTTGAGAGGGGAGTCGG 58.377 66.667 0.00 0.00 39.55 4.79
1207 1214 5.295540 TCACAAATCACATTCAAGTCGTCAA 59.704 36.000 0.00 0.00 0.00 3.18
1387 1394 7.735326 ACCCTAGAACATGAACAGTAACTAT 57.265 36.000 0.00 0.00 0.00 2.12
1388 1395 7.233962 TGAACCCTAGAACATGAACAGTAACTA 59.766 37.037 0.00 0.00 0.00 2.24
1389 1396 6.042781 TGAACCCTAGAACATGAACAGTAACT 59.957 38.462 0.00 0.00 0.00 2.24
1390 1397 6.228258 TGAACCCTAGAACATGAACAGTAAC 58.772 40.000 0.00 0.00 0.00 2.50
1391 1398 6.428083 TGAACCCTAGAACATGAACAGTAA 57.572 37.500 0.00 0.00 0.00 2.24
1392 1399 6.620877 ATGAACCCTAGAACATGAACAGTA 57.379 37.500 0.00 0.00 0.00 2.74
1393 1400 4.974645 TGAACCCTAGAACATGAACAGT 57.025 40.909 0.00 0.00 0.00 3.55
1394 1401 6.644347 ACTATGAACCCTAGAACATGAACAG 58.356 40.000 0.00 0.00 0.00 3.16
1395 1402 6.620877 ACTATGAACCCTAGAACATGAACA 57.379 37.500 0.00 0.00 0.00 3.18
1396 1403 8.258708 AGTAACTATGAACCCTAGAACATGAAC 58.741 37.037 0.00 0.00 0.00 3.18
1400 1407 7.735326 ACAGTAACTATGAACCCTAGAACAT 57.265 36.000 0.00 0.00 0.00 2.71
2102 2173 5.046735 TCTCTTTCTTCAGGTCATCCTTCTG 60.047 44.000 0.00 0.00 43.07 3.02
2247 2366 3.265479 AGCCTTAATCTGGTGAAGCTTCT 59.735 43.478 26.09 7.63 0.00 2.85
2435 2554 7.660112 ACAAGCTGATAATTCATCACAAACAA 58.340 30.769 0.00 0.00 38.79 2.83
2525 2644 7.598118 CAGACTATCTATGCAGTATGAACTTGG 59.402 40.741 0.00 0.00 39.69 3.61
2874 3099 5.380043 CCCAATTGATGTGGATAAGCTACT 58.620 41.667 7.12 0.00 38.54 2.57
2876 3101 4.141181 AGCCCAATTGATGTGGATAAGCTA 60.141 41.667 7.12 0.00 38.54 3.32
3020 3245 5.640357 ACAACTACAACTTGACGAAACTGAA 59.360 36.000 0.00 0.00 0.00 3.02
3190 3422 1.813753 CGCCCGTTGGTGGATGTAG 60.814 63.158 0.00 0.00 38.56 2.74


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

AutoCloner maintained by Alex Coulton.