Multiple sequence alignment - TraesCS2D01G392700

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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 TraesCS2D01G392700 chr2D 100.000 2718 0 0 1 2718 500667776 500665059 0.000000e+00 5020.0
1 TraesCS2D01G392700 chr2D 94.236 2186 88 13 564 2718 603142396 603144574 0.000000e+00 3304.0
2 TraesCS2D01G392700 chr7D 94.785 2186 75 14 560 2718 85019317 85021490 0.000000e+00 3369.0
3 TraesCS2D01G392700 chr5D 94.482 2193 89 12 552 2718 426404716 426402530 0.000000e+00 3350.0
4 TraesCS2D01G392700 chr5D 93.991 1947 65 9 796 2718 544615481 544617399 0.000000e+00 2900.0
5 TraesCS2D01G392700 chr4D 94.419 2186 70 16 555 2714 119369769 119367610 0.000000e+00 3314.0
6 TraesCS2D01G392700 chr7B 94.249 2191 83 16 560 2718 442357632 442359811 0.000000e+00 3308.0
7 TraesCS2D01G392700 chr7B 77.907 172 32 5 181 348 393637500 393637331 4.790000e-18 102.0
8 TraesCS2D01G392700 chr6D 94.353 2178 83 16 565 2718 347439904 347437743 0.000000e+00 3304.0
9 TraesCS2D01G392700 chr6D 93.853 2180 89 10 563 2718 430885510 430883352 0.000000e+00 3241.0
10 TraesCS2D01G392700 chr6D 95.370 1123 35 4 563 1669 41924609 41923488 0.000000e+00 1770.0
11 TraesCS2D01G392700 chr6D 76.966 178 35 5 199 372 388549438 388549263 2.230000e-16 97.1
12 TraesCS2D01G392700 chr5A 94.045 2183 91 16 563 2718 375292317 375290147 0.000000e+00 3275.0
13 TraesCS2D01G392700 chr5A 93.931 2142 91 18 604 2718 581623297 581625426 0.000000e+00 3199.0
14 TraesCS2D01G392700 chr5A 91.872 2190 120 28 556 2718 590663665 590661507 0.000000e+00 3005.0
15 TraesCS2D01G392700 chr6B 93.756 2194 95 13 564 2718 689112992 689110802 0.000000e+00 3254.0
16 TraesCS2D01G392700 chr6B 93.576 2195 98 14 564 2718 689092931 689090740 0.000000e+00 3232.0
17 TraesCS2D01G392700 chrUn 95.205 2044 71 7 565 2591 105335964 105333931 0.000000e+00 3206.0
18 TraesCS2D01G392700 chrUn 95.422 1376 43 9 1351 2718 108804449 108805812 0.000000e+00 2174.0
19 TraesCS2D01G392700 chrUn 92.308 143 2 2 2585 2718 105325918 105325776 7.680000e-46 195.0
20 TraesCS2D01G392700 chr4B 92.893 2181 99 11 563 2718 671183085 671185234 0.000000e+00 3118.0
21 TraesCS2D01G392700 chr4B 86.466 1064 115 18 561 1602 3213136 3214192 0.000000e+00 1140.0
22 TraesCS2D01G392700 chr3D 91.923 2179 86 23 565 2718 162857494 162855381 0.000000e+00 2966.0
23 TraesCS2D01G392700 chr3D 95.447 1801 57 6 928 2718 515672391 515674176 0.000000e+00 2848.0
24 TraesCS2D01G392700 chr3D 91.990 387 14 5 563 935 515671974 515672357 6.670000e-146 527.0
25 TraesCS2D01G392700 chr3D 81.319 91 15 2 144 233 81183602 81183513 3.750000e-09 73.1
26 TraesCS2D01G392700 chr2B 94.644 1923 79 11 564 2465 441885059 441886978 0.000000e+00 2959.0
27 TraesCS2D01G392700 chr2B 90.791 923 63 9 529 1433 496635525 496634607 0.000000e+00 1214.0
28 TraesCS2D01G392700 chr2B 92.389 565 35 5 2 565 588735976 588736533 0.000000e+00 798.0
29 TraesCS2D01G392700 chr5B 94.000 1800 91 7 932 2718 576995504 576993709 0.000000e+00 2710.0
30 TraesCS2D01G392700 chr6A 89.050 1105 66 26 1628 2718 508054800 508055863 0.000000e+00 1319.0
31 TraesCS2D01G392700 chr2A 92.007 538 42 1 2 538 646646166 646646703 0.000000e+00 754.0
32 TraesCS2D01G392700 chr2A 100.000 34 0 0 532 565 646725957 646725990 2.260000e-06 63.9
33 TraesCS2D01G392700 chr1D 78.049 205 39 5 169 369 405758213 405758415 1.020000e-24 124.0
34 TraesCS2D01G392700 chr1D 75.419 179 36 6 144 317 403327414 403327589 2.240000e-11 80.5
35 TraesCS2D01G392700 chr3B 76.699 206 40 4 169 369 187545279 187545481 1.030000e-19 108.0
36 TraesCS2D01G392700 chr4A 79.470 151 24 6 169 315 133376230 133376377 1.720000e-17 100.0


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 TraesCS2D01G392700 chr2D 500665059 500667776 2717 True 5020.0 5020 100.0000 1 2718 1 chr2D.!!$R1 2717
1 TraesCS2D01G392700 chr2D 603142396 603144574 2178 False 3304.0 3304 94.2360 564 2718 1 chr2D.!!$F1 2154
2 TraesCS2D01G392700 chr7D 85019317 85021490 2173 False 3369.0 3369 94.7850 560 2718 1 chr7D.!!$F1 2158
3 TraesCS2D01G392700 chr5D 426402530 426404716 2186 True 3350.0 3350 94.4820 552 2718 1 chr5D.!!$R1 2166
4 TraesCS2D01G392700 chr5D 544615481 544617399 1918 False 2900.0 2900 93.9910 796 2718 1 chr5D.!!$F1 1922
5 TraesCS2D01G392700 chr4D 119367610 119369769 2159 True 3314.0 3314 94.4190 555 2714 1 chr4D.!!$R1 2159
6 TraesCS2D01G392700 chr7B 442357632 442359811 2179 False 3308.0 3308 94.2490 560 2718 1 chr7B.!!$F1 2158
7 TraesCS2D01G392700 chr6D 347437743 347439904 2161 True 3304.0 3304 94.3530 565 2718 1 chr6D.!!$R2 2153
8 TraesCS2D01G392700 chr6D 430883352 430885510 2158 True 3241.0 3241 93.8530 563 2718 1 chr6D.!!$R4 2155
9 TraesCS2D01G392700 chr6D 41923488 41924609 1121 True 1770.0 1770 95.3700 563 1669 1 chr6D.!!$R1 1106
10 TraesCS2D01G392700 chr5A 375290147 375292317 2170 True 3275.0 3275 94.0450 563 2718 1 chr5A.!!$R1 2155
11 TraesCS2D01G392700 chr5A 581623297 581625426 2129 False 3199.0 3199 93.9310 604 2718 1 chr5A.!!$F1 2114
12 TraesCS2D01G392700 chr5A 590661507 590663665 2158 True 3005.0 3005 91.8720 556 2718 1 chr5A.!!$R2 2162
13 TraesCS2D01G392700 chr6B 689110802 689112992 2190 True 3254.0 3254 93.7560 564 2718 1 chr6B.!!$R2 2154
14 TraesCS2D01G392700 chr6B 689090740 689092931 2191 True 3232.0 3232 93.5760 564 2718 1 chr6B.!!$R1 2154
15 TraesCS2D01G392700 chrUn 105333931 105335964 2033 True 3206.0 3206 95.2050 565 2591 1 chrUn.!!$R2 2026
16 TraesCS2D01G392700 chrUn 108804449 108805812 1363 False 2174.0 2174 95.4220 1351 2718 1 chrUn.!!$F1 1367
17 TraesCS2D01G392700 chr4B 671183085 671185234 2149 False 3118.0 3118 92.8930 563 2718 1 chr4B.!!$F2 2155
18 TraesCS2D01G392700 chr4B 3213136 3214192 1056 False 1140.0 1140 86.4660 561 1602 1 chr4B.!!$F1 1041
19 TraesCS2D01G392700 chr3D 162855381 162857494 2113 True 2966.0 2966 91.9230 565 2718 1 chr3D.!!$R2 2153
20 TraesCS2D01G392700 chr3D 515671974 515674176 2202 False 1687.5 2848 93.7185 563 2718 2 chr3D.!!$F1 2155
21 TraesCS2D01G392700 chr2B 441885059 441886978 1919 False 2959.0 2959 94.6440 564 2465 1 chr2B.!!$F1 1901
22 TraesCS2D01G392700 chr2B 496634607 496635525 918 True 1214.0 1214 90.7910 529 1433 1 chr2B.!!$R1 904
23 TraesCS2D01G392700 chr2B 588735976 588736533 557 False 798.0 798 92.3890 2 565 1 chr2B.!!$F2 563
24 TraesCS2D01G392700 chr5B 576993709 576995504 1795 True 2710.0 2710 94.0000 932 2718 1 chr5B.!!$R1 1786
25 TraesCS2D01G392700 chr6A 508054800 508055863 1063 False 1319.0 1319 89.0500 1628 2718 1 chr6A.!!$F1 1090
26 TraesCS2D01G392700 chr2A 646646166 646646703 537 False 754.0 754 92.0070 2 538 1 chr2A.!!$F1 536

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
242 244 0.036164 ACTTTGCACATACGAGCCCA 59.964 50.0 0.0 0.0 0.0 5.36 F
243 245 1.164411 CTTTGCACATACGAGCCCAA 58.836 50.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1263 0.393537 AGTGCTGCTGCCTGGATTAC 60.394 55.0 13.47 2.58 38.71 1.89 R
1992 2108 1.266160 TGGAAGAATACCCGGCCGAA 61.266 55.0 30.73 12.51 0.00 4.30 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
43 44 4.099633 TCATAGCTATATGCAGAGCCCTT 58.900 43.478 5.77 0.41 45.94 3.95
167 168 1.736645 CCAAGTCAACGACGCCGAT 60.737 57.895 0.00 0.00 37.67 4.18
239 241 3.125146 TCATCAACTTTGCACATACGAGC 59.875 43.478 0.00 0.00 0.00 5.03
242 244 0.036164 ACTTTGCACATACGAGCCCA 59.964 50.000 0.00 0.00 0.00 5.36
243 245 1.164411 CTTTGCACATACGAGCCCAA 58.836 50.000 0.00 0.00 0.00 4.12
304 306 8.507249 GCGCTTGATTAAATAACCTAAGATCAT 58.493 33.333 0.00 0.00 0.00 2.45
336 338 3.831323 ACTGTCATCATGTTTTGGTCCA 58.169 40.909 0.00 0.00 0.00 4.02
355 357 2.032030 CCAGTAAGTTTGTCACAAGCCG 60.032 50.000 0.00 0.00 0.00 5.52
500 502 7.876068 ACCTGTTTTCTAGTCATTCGAATACAA 59.124 33.333 10.97 0.00 31.57 2.41
507 509 3.446161 AGTCATTCGAATACAACCGAGGA 59.554 43.478 10.97 0.00 36.11 3.71
551 553 3.190327 TGCAATGTTGTCCTATCCAAACG 59.810 43.478 0.00 0.00 0.00 3.60
572 574 2.022764 TGATTCATGTAGGGCGTGTG 57.977 50.000 0.00 0.00 35.64 3.82
829 837 2.828549 CCCGGCGCCAAATTAGCT 60.829 61.111 28.98 0.00 0.00 3.32
837 845 1.555967 GCCAAATTAGCTTCACCCCA 58.444 50.000 0.00 0.00 0.00 4.96
839 848 3.295973 GCCAAATTAGCTTCACCCCATA 58.704 45.455 0.00 0.00 0.00 2.74
847 857 1.541233 GCTTCACCCCATATCACTCGG 60.541 57.143 0.00 0.00 0.00 4.63
1050 1146 2.351276 CCGGTAAGCAGCAACCCT 59.649 61.111 10.55 0.00 31.68 4.34
1075 1181 4.262894 CCCTTTGTTAGCTCAGTGGTTAGA 60.263 45.833 0.00 0.00 0.00 2.10
1157 1263 4.457496 ACGCACGGATGAGGCTGG 62.457 66.667 0.00 0.00 0.00 4.85
1313 1419 7.606456 TCCAAAATCTGAACTACATCTACAACC 59.394 37.037 0.00 0.00 0.00 3.77
1336 1442 0.960861 ATGACGTCGAGGCTCTGTCA 60.961 55.000 25.68 25.68 43.02 3.58
1341 1447 1.086634 GTCGAGGCTCTGTCAATGCC 61.087 60.000 13.50 7.47 46.42 4.40
2075 2191 4.917906 AGGAACTTTTCTAGGACTGCAT 57.082 40.909 0.00 0.00 27.25 3.96
2424 2560 7.559590 TTTGAAGAAGAGGAAGAAGAAACAG 57.440 36.000 0.00 0.00 0.00 3.16
2425 2561 5.615289 TGAAGAAGAGGAAGAAGAAACAGG 58.385 41.667 0.00 0.00 0.00 4.00
2426 2562 5.366768 TGAAGAAGAGGAAGAAGAAACAGGA 59.633 40.000 0.00 0.00 0.00 3.86
2621 2842 6.001460 TGTTTAACTAGCTGGCACTATGTTT 58.999 36.000 0.00 0.00 0.00 2.83
2695 2924 5.012893 TGCAACCAAACACCATGTCATATA 58.987 37.500 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.123186 GCATATAGCTATGAGAGACGACTGT 59.877 44.000 16.77 0.00 37.51 3.55
167 168 9.806203 CATATTCTTGATACCATTTTTCTGCAA 57.194 29.630 0.00 0.00 0.00 4.08
239 241 1.203758 GGCGGTTGGTCTTATTTTGGG 59.796 52.381 0.00 0.00 0.00 4.12
242 244 2.029380 GCTTGGCGGTTGGTCTTATTTT 60.029 45.455 0.00 0.00 0.00 1.82
243 245 1.544246 GCTTGGCGGTTGGTCTTATTT 59.456 47.619 0.00 0.00 0.00 1.40
321 323 6.323739 ACAAACTTACTGGACCAAAACATGAT 59.676 34.615 0.00 0.00 0.00 2.45
324 326 5.654650 TGACAAACTTACTGGACCAAAACAT 59.345 36.000 0.00 0.00 0.00 2.71
336 338 2.218603 CCGGCTTGTGACAAACTTACT 58.781 47.619 0.00 0.00 0.00 2.24
381 383 9.226606 TCCGTGATCAAAACTTACAAGAATTAT 57.773 29.630 0.00 0.00 0.00 1.28
466 468 8.697507 AATGACTAGAAAACAGGTTTGAGAAT 57.302 30.769 0.00 0.00 32.36 2.40
472 474 7.745620 ATTCGAATGACTAGAAAACAGGTTT 57.254 32.000 10.50 0.00 0.00 3.27
551 553 2.545526 CACACGCCCTACATGAATCATC 59.454 50.000 0.00 0.00 0.00 2.92
621 624 2.158827 GGAAAACCAGGCAACCAAACAT 60.159 45.455 0.00 0.00 37.17 2.71
829 837 1.760613 GACCGAGTGATATGGGGTGAA 59.239 52.381 0.00 0.00 0.00 3.18
847 857 1.452108 GGCAGTGGCTATGGGTGAC 60.452 63.158 9.90 0.00 40.87 3.67
1046 1142 0.992695 GAGCTAACAAAGGGGAGGGT 59.007 55.000 0.00 0.00 0.00 4.34
1050 1146 1.351017 CCACTGAGCTAACAAAGGGGA 59.649 52.381 0.00 0.00 35.00 4.81
1075 1181 5.655532 TCGATCCTACACCTAGCTTAAAGTT 59.344 40.000 0.00 0.00 0.00 2.66
1129 1235 0.457035 TCCGTGCGTCCATAACCTAC 59.543 55.000 0.00 0.00 0.00 3.18
1157 1263 0.393537 AGTGCTGCTGCCTGGATTAC 60.394 55.000 13.47 2.58 38.71 1.89
1313 1419 2.507102 AGCCTCGACGTCATTGCG 60.507 61.111 17.16 1.23 37.94 4.85
1336 1442 7.828508 TGATGCTATTTTCATTCTAGGCATT 57.171 32.000 0.00 0.00 38.92 3.56
1366 1472 1.819288 CTGAAGGTCTCGACAAGCCTA 59.181 52.381 0.00 0.00 33.01 3.93
1621 1729 6.042093 TCACCTTGAAGTATGGATACCATCTC 59.958 42.308 6.55 4.11 40.74 2.75
1992 2108 1.266160 TGGAAGAATACCCGGCCGAA 61.266 55.000 30.73 12.51 0.00 4.30
2075 2191 5.717178 AGTGTCTGAGATTAAACAGCTCCTA 59.283 40.000 0.00 0.00 37.08 2.94
2337 2453 4.775253 ACTCCAACCTTTTGTTCTTCCAAA 59.225 37.500 0.00 0.00 34.00 3.28
2424 2560 0.604780 TTCTGTGCTTCTGCTGCTCC 60.605 55.000 0.00 0.00 40.48 4.70
2425 2561 0.797542 CTTCTGTGCTTCTGCTGCTC 59.202 55.000 0.00 0.00 40.48 4.26
2426 2562 0.395686 TCTTCTGTGCTTCTGCTGCT 59.604 50.000 0.00 0.00 40.48 4.24
2621 2842 4.262721 GGTGACCTTACCACACACAATCTA 60.263 45.833 0.00 0.00 40.54 1.98


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

AutoCloner maintained by Alex Coulton.