Multiple sequence alignment - TraesCS2A01G249500

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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 TraesCS2A01G249500 chr2A 100.000 2550 0 0 1 2550 376077455 376074906 0.000000e+00 4710
1 TraesCS2A01G249500 chr2D 95.511 1537 47 10 1 1523 299888781 299887253 0.000000e+00 2436
2 TraesCS2A01G249500 chr2D 94.326 987 25 11 1581 2550 299886930 299885958 0.000000e+00 1483
3 TraesCS2A01G249500 chr2B 94.836 1433 44 7 710 2123 371167486 371168907 0.000000e+00 2209
4 TraesCS2A01G249500 chr2B 96.667 690 21 1 1 690 371166812 371167499 0.000000e+00 1146
5 TraesCS2A01G249500 chr2B 90.508 295 14 9 2263 2550 371168914 371169201 6.660000e-101 377
6 TraesCS2A01G249500 chr5B 87.447 1649 104 35 710 2323 689486902 689488482 0.000000e+00 1803
7 TraesCS2A01G249500 chr5B 87.874 701 62 12 1 692 689486231 689486917 0.000000e+00 802
8 TraesCS2A01G249500 chr5D 87.140 1283 86 30 625 1897 546365538 546366751 0.000000e+00 1382
9 TraesCS2A01G249500 chr5D 92.435 423 29 3 156 576 546358614 546359035 3.630000e-168 601
10 TraesCS2A01G249500 chr5D 91.176 374 28 3 1947 2317 546371708 546372079 1.050000e-138 503
11 TraesCS2A01G249500 chr5D 96.923 65 2 0 574 638 546361501 546361565 2.680000e-20 110
12 TraesCS2A01G249500 chr3A 85.434 611 62 20 736 1335 724300309 724300903 6.030000e-171 610
13 TraesCS2A01G249500 chr3A 83.164 493 41 14 1462 1947 724301051 724301508 1.830000e-111 412
14 TraesCS2A01G249500 chr3A 82.127 442 46 17 1969 2393 724303069 724303494 5.220000e-92 348


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 TraesCS2A01G249500 chr2A 376074906 376077455 2549 True 4710.000000 4710 100.000000 1 2550 1 chr2A.!!$R1 2549
1 TraesCS2A01G249500 chr2D 299885958 299888781 2823 True 1959.500000 2436 94.918500 1 2550 2 chr2D.!!$R1 2549
2 TraesCS2A01G249500 chr2B 371166812 371169201 2389 False 1244.000000 2209 94.003667 1 2550 3 chr2B.!!$F1 2549
3 TraesCS2A01G249500 chr5B 689486231 689488482 2251 False 1302.500000 1803 87.660500 1 2323 2 chr5B.!!$F1 2322
4 TraesCS2A01G249500 chr5D 546358614 546366751 8137 False 697.666667 1382 92.166000 156 1897 3 chr5D.!!$F2 1741
5 TraesCS2A01G249500 chr3A 724300309 724303494 3185 False 456.666667 610 83.575000 736 2393 3 chr3A.!!$F1 1657

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
103 105 1.093496 TCTGCAGGAGCGCAATCATG 61.093 55.000 15.13 8.75 46.23 3.07 F
1501 8108 1.521681 CGCCGAGGGGATGAAGAAC 60.522 63.158 0.00 0.00 34.06 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 8120 0.827925 AGGACTCTGCCTTGTCGACA 60.828 55.0 15.76 15.76 33.46 4.35 R
2490 10938 1.655484 TCACATTCATAGCGGCAGTG 58.345 50.0 1.45 0.00 0.00 3.66 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
22 23 4.811364 GCCTTGGCAGCCTCCTCC 62.811 72.222 14.15 0.00 0.00 4.30
103 105 1.093496 TCTGCAGGAGCGCAATCATG 61.093 55.000 15.13 8.75 46.23 3.07
318 334 2.739132 GGGGGATAGTAACCGCGG 59.261 66.667 26.86 26.86 40.53 6.46
348 364 2.683933 TCGGGTTCTGCCTCCTCC 60.684 66.667 0.00 0.00 37.43 4.30
351 367 2.285743 GGTTCTGCCTCCTCCCCT 60.286 66.667 0.00 0.00 0.00 4.79
392 414 2.697751 CTGGACCCTCCTCAGAGTAATG 59.302 54.545 0.00 0.00 38.58 1.90
648 7136 1.645455 GTGCTGTGCTGTGTCAGTG 59.355 57.895 0.00 0.00 33.43 3.66
649 7137 1.524393 TGCTGTGCTGTGTCAGTGG 60.524 57.895 0.00 0.00 33.43 4.00
692 7180 6.013553 GGTAATTTCCTTATCCCCTACTCCTC 60.014 46.154 0.00 0.00 0.00 3.71
698 7186 5.666265 TCCTTATCCCCTACTCCTCTTTTTC 59.334 44.000 0.00 0.00 0.00 2.29
699 7187 5.163184 CCTTATCCCCTACTCCTCTTTTTCC 60.163 48.000 0.00 0.00 0.00 3.13
700 7188 3.579742 TCCCCTACTCCTCTTTTTCCT 57.420 47.619 0.00 0.00 0.00 3.36
701 7189 3.883135 TCCCCTACTCCTCTTTTTCCTT 58.117 45.455 0.00 0.00 0.00 3.36
703 7191 3.587506 CCCCTACTCCTCTTTTTCCTTGA 59.412 47.826 0.00 0.00 0.00 3.02
1071 7609 3.444805 GAGGAGTCGTCCAGCGCT 61.445 66.667 2.64 2.64 46.80 5.92
1185 7729 2.359900 GGGTTCTGCCTGTACATGAAG 58.640 52.381 0.00 0.77 37.43 3.02
1370 7917 4.452733 CCGTCTCCGACCAAGCCC 62.453 72.222 0.00 0.00 35.63 5.19
1455 8062 1.676968 CGGACACTGATTGGGTGGA 59.323 57.895 0.00 0.00 38.83 4.02
1501 8108 1.521681 CGCCGAGGGGATGAAGAAC 60.522 63.158 0.00 0.00 34.06 3.01
1513 8120 4.156739 GGGATGAAGAACGAAGAAGCAATT 59.843 41.667 0.00 0.00 0.00 2.32
1553 8160 7.881751 AGTCCTTGTCTTTGGGTAACTAATAAC 59.118 37.037 0.00 0.00 36.70 1.89
1554 8161 7.120285 GTCCTTGTCTTTGGGTAACTAATAACC 59.880 40.741 0.00 0.00 42.26 2.85
1589 8461 7.066374 AGATTTTTCAGCTCGTGATAACTTC 57.934 36.000 0.00 0.00 34.17 3.01
1674 8547 6.013725 GGGGAAATAAGGTTGTTCTTCCAATT 60.014 38.462 0.00 0.00 35.13 2.32
1804 8682 2.826488 AGAACTACTCCTGGTGAGCAT 58.174 47.619 2.23 0.00 45.61 3.79
1974 8867 2.239402 TGGATCTGCCATGCTGAGTAAA 59.761 45.455 0.00 0.00 43.33 2.01
1979 8872 3.444742 TCTGCCATGCTGAGTAAATTTGG 59.555 43.478 0.00 0.00 32.96 3.28
1997 10418 3.350219 TGGAATAGGTTTCAGCTGGTC 57.650 47.619 15.13 4.57 0.00 4.02
1998 10419 2.026262 TGGAATAGGTTTCAGCTGGTCC 60.026 50.000 15.13 13.52 33.31 4.46
2218 10652 8.621286 GTTATTTACATTGTCTTATGTGAGGGG 58.379 37.037 0.00 0.00 39.06 4.79
2350 10795 6.722328 AGTCATCATCATCATGGCAAGATAT 58.278 36.000 4.72 0.00 0.00 1.63
2351 10796 7.858498 AGTCATCATCATCATGGCAAGATATA 58.142 34.615 4.72 0.00 0.00 0.86
2466 10914 5.856126 TCATTCGTTCCACTATTGTGAAC 57.144 39.130 8.98 9.81 46.55 3.18
2490 10938 7.988547 ACGAACAAAACAGCGATTATTTAAAC 58.011 30.769 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 3.064931 CTGGTCTTCCTGTAACGGTTTC 58.935 50.000 0.00 0.00 34.23 2.78
318 334 3.775654 CCCGAGGTCCAGGCAGTC 61.776 72.222 0.00 0.00 0.00 3.51
348 364 1.477295 GAGTACGTGGAGGAAGAAGGG 59.523 57.143 0.00 0.00 0.00 3.95
351 367 2.041350 AGAGGAGTACGTGGAGGAAGAA 59.959 50.000 0.00 0.00 0.00 2.52
473 495 3.878358 GGCTCCGCCTATTCTCCT 58.122 61.111 0.00 0.00 46.69 3.69
638 3132 0.600255 GACCGAACCCACTGACACAG 60.600 60.000 0.00 0.00 37.52 3.66
648 7136 2.027625 CACAAGAGCGACCGAACCC 61.028 63.158 0.00 0.00 0.00 4.11
649 7137 2.027625 CCACAAGAGCGACCGAACC 61.028 63.158 0.00 0.00 0.00 3.62
805 7323 0.035739 TTTAGTGGGCCGGTGTCTTC 59.964 55.000 1.90 0.00 0.00 2.87
811 7329 2.599757 GGGTCTTTAGTGGGCCGGT 61.600 63.158 1.90 0.00 0.00 5.28
1071 7609 4.382541 TCCTCTCGGCTGCCTCCA 62.383 66.667 17.92 0.00 0.00 3.86
1185 7729 3.373565 CCTTTGCAACCTCCGGCC 61.374 66.667 0.00 0.00 0.00 6.13
1198 7742 1.663702 CGACACGAACGCCTCCTTT 60.664 57.895 0.00 0.00 0.00 3.11
1396 7943 5.361427 TCTCCGTTGTTCTTGTTTGTATCA 58.639 37.500 0.00 0.00 0.00 2.15
1455 8062 1.079658 AGGAAGTAGCCTCCTCAACCT 59.920 52.381 0.00 0.00 30.76 3.50
1493 8100 5.615544 CGACAATTGCTTCTTCGTTCTTCAT 60.616 40.000 5.05 0.00 0.00 2.57
1501 8108 3.473367 CTTGTCGACAATTGCTTCTTCG 58.527 45.455 29.79 11.44 35.02 3.79
1513 8120 0.827925 AGGACTCTGCCTTGTCGACA 60.828 55.000 15.76 15.76 33.46 4.35
1553 8160 2.025699 TGAAAAATCTAACCCTCCCCGG 60.026 50.000 0.00 0.00 0.00 5.73
1554 8161 3.279434 CTGAAAAATCTAACCCTCCCCG 58.721 50.000 0.00 0.00 0.00 5.73
1674 8547 5.408880 TTCGGTATCATGTCCAACAGTTA 57.591 39.130 0.00 0.00 0.00 2.24
1804 8682 6.620518 GCAAATTGTGTATCTTGTCGTCATCA 60.621 38.462 0.00 0.00 0.00 3.07
1974 8867 4.677182 ACCAGCTGAAACCTATTCCAAAT 58.323 39.130 17.39 0.00 0.00 2.32
1979 8872 2.239907 AGGGACCAGCTGAAACCTATTC 59.760 50.000 17.39 2.94 0.00 1.75
1997 10418 5.135383 ACCATATTGATGTCAATGACAGGG 58.865 41.667 21.23 14.38 46.04 4.45
1998 10419 6.704289 AACCATATTGATGTCAATGACAGG 57.296 37.500 21.23 16.26 46.04 4.00
2218 10652 6.633634 TCACGTCCAACAATTATTCGAAAAAC 59.366 34.615 0.00 0.00 0.00 2.43
2289 10734 6.124340 AGATACAATGTCAATCCATCAAGCA 58.876 36.000 0.00 0.00 0.00 3.91
2350 10795 4.098807 TGTACAAGACAGTCACTGCAAGTA 59.901 41.667 4.13 0.29 38.34 2.24
2351 10796 3.118775 TGTACAAGACAGTCACTGCAAGT 60.119 43.478 4.13 1.31 40.28 3.16
2456 10904 4.375698 CGCTGTTTTGTTCGTTCACAATAG 59.624 41.667 0.00 1.51 36.54 1.73
2466 10914 7.937294 GTGTTTAAATAATCGCTGTTTTGTTCG 59.063 33.333 0.00 0.00 0.00 3.95
2490 10938 1.655484 TCACATTCATAGCGGCAGTG 58.345 50.000 1.45 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.