Multiple sequence alignment - TraesCS4D01G048200

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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 TraesCS4D01G048200 chr4D 100.000 3128 0 0 1 3128 24109458 24112585 0.000000e+00 5777.0
1 TraesCS4D01G048200 chr4A 95.655 2739 76 7 430 3128 527956989 527959724 0.000000e+00 4359.0
2 TraesCS4D01G048200 chr4A 95.667 2700 74 9 469 3128 426664461 426661765 0.000000e+00 4298.0
3 TraesCS4D01G048200 chr4A 97.019 1476 42 2 1654 3128 112246106 112244632 0.000000e+00 2481.0
4 TraesCS4D01G048200 chr4A 93.209 1237 44 4 469 1667 112249055 112247821 0.000000e+00 1783.0
5 TraesCS4D01G048200 chr4A 97.163 141 4 0 2598 2738 426662436 426662296 4.030000e-59 239.0
6 TraesCS4D01G048200 chr4A 90.526 95 6 3 464 557 615024566 615024658 4.240000e-24 122.0
7 TraesCS4D01G048200 chr7D 98.023 2478 35 2 653 3128 623596353 623593888 0.000000e+00 4292.0
8 TraesCS4D01G048200 chr7D 97.482 278 7 0 1 278 90993839 90994116 2.820000e-130 475.0
9 TraesCS4D01G048200 chr7D 80.727 275 27 18 476 740 623596493 623596235 1.150000e-44 191.0
10 TraesCS4D01G048200 chr7A 95.652 2185 56 3 983 3128 730253206 730251022 0.000000e+00 3472.0
11 TraesCS4D01G048200 chr6B 92.725 1347 84 7 1786 3128 334481852 334480516 0.000000e+00 1932.0
12 TraesCS4D01G048200 chr6B 91.453 468 35 5 1321 1787 334482474 334482011 3.400000e-179 638.0
13 TraesCS4D01G048200 chr6B 89.450 436 36 5 45 474 598007679 598008110 2.740000e-150 542.0
14 TraesCS4D01G048200 chr3D 95.697 1069 20 2 1178 2221 519300247 519301314 0.000000e+00 1696.0
15 TraesCS4D01G048200 chr3D 98.463 911 14 0 2217 3127 519301766 519302676 0.000000e+00 1605.0
16 TraesCS4D01G048200 chr3D 98.514 471 6 1 1 470 351924690 351924220 0.000000e+00 830.0
17 TraesCS4D01G048200 chr3D 95.079 508 8 4 691 1181 519299697 519300204 0.000000e+00 784.0
18 TraesCS4D01G048200 chr3D 96.296 297 11 0 487 783 519299454 519299750 3.630000e-134 488.0
19 TraesCS4D01G048200 chr2A 95.634 962 32 3 2168 3128 20351354 20350402 0.000000e+00 1535.0
20 TraesCS4D01G048200 chr2A 93.777 707 29 4 1331 2022 20352226 20351520 0.000000e+00 1048.0
21 TraesCS4D01G048200 chr2A 91.667 72 3 3 487 557 2933868 2933937 2.570000e-16 97.1
22 TraesCS4D01G048200 chr2D 92.416 778 50 6 1321 2098 254331450 254332218 0.000000e+00 1101.0
23 TraesCS4D01G048200 chr2D 97.021 470 11 2 1 469 48049851 48050318 0.000000e+00 787.0
24 TraesCS4D01G048200 chr2D 94.079 456 24 2 2676 3128 164135480 164135935 0.000000e+00 689.0
25 TraesCS4D01G048200 chr2D 95.874 412 14 1 2235 2646 164135071 164135479 0.000000e+00 664.0
26 TraesCS4D01G048200 chr2D 88.694 513 57 1 2023 2534 254332289 254332801 2.650000e-175 625.0
27 TraesCS4D01G048200 chr2D 91.379 58 5 0 851 908 254331088 254331145 2.590000e-11 80.5
28 TraesCS4D01G048200 chr7B 95.532 470 15 5 1 469 363245240 363245704 0.000000e+00 747.0
29 TraesCS4D01G048200 chr7B 95.437 263 9 2 1 262 674177957 674178217 1.740000e-112 416.0
30 TraesCS4D01G048200 chr4B 93.037 517 22 10 1 508 150983419 150983930 0.000000e+00 743.0
31 TraesCS4D01G048200 chr5B 89.510 429 29 4 44 471 102907775 102907362 2.140000e-146 529.0
32 TraesCS4D01G048200 chr5B 97.727 44 1 0 1 44 102912827 102912784 3.350000e-10 76.8
33 TraesCS4D01G048200 chr3A 91.209 91 4 4 469 557 235835110 235835198 1.520000e-23 121.0
34 TraesCS4D01G048200 chr6A 93.333 75 5 0 439 513 194461632 194461706 9.170000e-21 111.0
35 TraesCS4D01G048200 chr5A 87.500 88 6 2 397 479 470974672 470974585 2.570000e-16 97.1
36 TraesCS4D01G048200 chr3B 93.023 43 3 0 798 840 272541014 272541056 2.600000e-06 63.9
37 TraesCS4D01G048200 chr1A 94.737 38 2 0 798 835 36601226 36601263 3.370000e-05 60.2


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 TraesCS4D01G048200 chr4D 24109458 24112585 3127 False 5777.000000 5777 100.000000 1 3128 1 chr4D.!!$F1 3127
1 TraesCS4D01G048200 chr4A 527956989 527959724 2735 False 4359.000000 4359 95.655000 430 3128 1 chr4A.!!$F1 2698
2 TraesCS4D01G048200 chr4A 426661765 426664461 2696 True 2268.500000 4298 96.415000 469 3128 2 chr4A.!!$R2 2659
3 TraesCS4D01G048200 chr4A 112244632 112249055 4423 True 2132.000000 2481 95.114000 469 3128 2 chr4A.!!$R1 2659
4 TraesCS4D01G048200 chr7D 623593888 623596493 2605 True 2241.500000 4292 89.375000 476 3128 2 chr7D.!!$R1 2652
5 TraesCS4D01G048200 chr7A 730251022 730253206 2184 True 3472.000000 3472 95.652000 983 3128 1 chr7A.!!$R1 2145
6 TraesCS4D01G048200 chr6B 334480516 334482474 1958 True 1285.000000 1932 92.089000 1321 3128 2 chr6B.!!$R1 1807
7 TraesCS4D01G048200 chr3D 519299454 519302676 3222 False 1143.250000 1696 96.383750 487 3127 4 chr3D.!!$F1 2640
8 TraesCS4D01G048200 chr2A 20350402 20352226 1824 True 1291.500000 1535 94.705500 1331 3128 2 chr2A.!!$R1 1797
9 TraesCS4D01G048200 chr2D 164135071 164135935 864 False 676.500000 689 94.976500 2235 3128 2 chr2D.!!$F2 893
10 TraesCS4D01G048200 chr2D 254331088 254332801 1713 False 602.166667 1101 90.829667 851 2534 3 chr2D.!!$F3 1683
11 TraesCS4D01G048200 chr4B 150983419 150983930 511 False 743.000000 743 93.037000 1 508 1 chr4B.!!$F1 507

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
925 977 0.108329 CACGTCCTTATCCAACGCCT 60.108 55.0 0.0 0.0 39.93 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 5236 1.46852 AGGCACATACAATCGCAACAC 59.531 47.619 0.0 0.0 0.0 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
96 97 3.242518 CTGCATGCAGTTTTGACATCAG 58.757 45.455 34.76 9.76 39.10 2.90
145 146 6.577103 TGATTTGTGTTTTTCATTAGTGCCA 58.423 32.000 0.00 0.00 0.00 4.92
153 154 3.998913 TTCATTAGTGCCACATCTCCA 57.001 42.857 0.00 0.00 0.00 3.86
168 169 8.362639 GCCACATCTCCAACATTTTATATTCAT 58.637 33.333 0.00 0.00 0.00 2.57
193 194 5.642063 AGAATAATTACACACACCGGTCTTG 59.358 40.000 2.59 7.80 0.00 3.02
195 196 0.831966 TTACACACACCGGTCTTGGT 59.168 50.000 2.59 7.97 45.21 3.67
211 212 5.805994 GGTCTTGGTCTACATAAAACTCGAG 59.194 44.000 11.84 11.84 0.00 4.04
352 353 4.864704 AGAGTCTTCTGAGGTCAAAGTC 57.135 45.455 0.00 0.00 30.72 3.01
354 355 2.297597 AGTCTTCTGAGGTCAAAGTCCG 59.702 50.000 0.00 0.00 0.00 4.79
355 356 1.618837 TCTTCTGAGGTCAAAGTCCGG 59.381 52.381 0.00 0.00 0.00 5.14
397 399 0.236711 CACAAGGCAACGAGAAGCAG 59.763 55.000 0.00 0.00 46.39 4.24
405 407 2.157863 GCAACGAGAAGCAGGTAAACTC 59.842 50.000 0.00 0.00 0.00 3.01
458 460 4.322385 GTTGCAACGCACGGACCC 62.322 66.667 14.90 0.00 38.71 4.46
463 465 1.008995 CAACGCACGGACCCTTTTG 60.009 57.895 0.00 0.00 0.00 2.44
478 487 8.895737 CGGACCCTTTTGCTAGTAATAATAAAA 58.104 33.333 0.00 0.00 0.00 1.52
559 568 6.153067 TGTTTTAGTTATTCAACCCGCAATG 58.847 36.000 0.00 0.00 35.05 2.82
628 637 2.348104 ACCCGTACGCATCTGCTCA 61.348 57.895 10.49 0.00 39.32 4.26
925 977 0.108329 CACGTCCTTATCCAACGCCT 60.108 55.000 0.00 0.00 39.93 5.52
1817 3873 5.540911 ACAATAACATGCCAACCTTCTTTG 58.459 37.500 0.00 0.00 0.00 2.77
2157 4407 9.739276 AGGAATACACAATGTTTCTTCAGAATA 57.261 29.630 1.22 0.00 33.54 1.75
2221 4927 5.336690 CCATGGAATAAAACTGACTTGTGGG 60.337 44.000 5.56 0.00 0.00 4.61
2526 5236 4.240881 TGGAGATGGATTTCTTTCCTGG 57.759 45.455 0.00 0.00 36.68 4.45
3017 5730 6.676950 TGAACATAAATTTCGTTCTGCACAT 58.323 32.000 23.43 0.00 39.77 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.015327 ACGACACCTGAGTACCTATGAC 58.985 50.000 0.00 0.00 0.00 3.06
96 97 5.877564 ACTTGAAGTCCTAGCTCAAATAAGC 59.122 40.000 0.00 0.00 42.82 3.09
116 117 9.904647 CACTAATGAAAAACACAAATCAACTTG 57.095 29.630 0.00 0.00 0.00 3.16
168 169 6.534475 AGACCGGTGTGTGTAATTATTCTA 57.466 37.500 14.63 0.00 0.00 2.10
170 171 5.163794 CCAAGACCGGTGTGTGTAATTATTC 60.164 44.000 14.63 0.00 0.00 1.75
193 194 5.579564 AGACCTCGAGTTTTATGTAGACC 57.420 43.478 12.31 0.00 0.00 3.85
195 196 6.182627 TGGTAGACCTCGAGTTTTATGTAGA 58.817 40.000 12.31 0.00 36.82 2.59
211 212 8.638629 ACAGATATACTTAGTCATGGTAGACC 57.361 38.462 0.00 0.00 39.34 3.85
341 342 1.619332 AGAACTCCGGACTTTGACCTC 59.381 52.381 0.00 0.00 0.00 3.85
352 353 2.501610 GGCTAGGCAGAACTCCGG 59.498 66.667 12.16 0.00 0.00 5.14
354 355 1.142097 GACGGCTAGGCAGAACTCC 59.858 63.158 17.45 0.00 0.00 3.85
355 356 1.890894 TGACGGCTAGGCAGAACTC 59.109 57.895 17.45 2.94 31.44 3.01
387 389 2.891580 TGAGAGTTTACCTGCTTCTCGT 59.108 45.455 0.00 0.00 0.00 4.18
397 399 4.081322 TCCAGGTGTTTGAGAGTTTACC 57.919 45.455 0.00 0.00 0.00 2.85
478 487 0.811915 CCGAGAGACTCAATCCGTGT 59.188 55.000 5.02 0.00 0.00 4.49
559 568 2.009774 AGTGTGCCAGATTAACGATGC 58.990 47.619 0.00 0.00 0.00 3.91
1572 1740 9.374838 TCACTGCTGCATATATCAATACTAATG 57.625 33.333 1.31 0.00 0.00 1.90
2157 4407 1.813513 CCTCGATTTGGTGCTCTGTT 58.186 50.000 0.00 0.00 0.00 3.16
2526 5236 1.468520 AGGCACATACAATCGCAACAC 59.531 47.619 0.00 0.00 0.00 3.32
3017 5730 5.069318 TCATTGCACTGTAGTTTGAATCCA 58.931 37.500 3.77 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.