Multiple sequence alignment - TraesCS6B01G256100

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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 TraesCS6B01G256100 chr6B 100.000 2906 0 0 1 2906 460093123 460090218 0.000000e+00 5367
1 TraesCS6B01G256100 chr6D 94.693 2299 71 23 639 2906 296860407 296862685 0.000000e+00 3522
2 TraesCS6B01G256100 chr6D 84.649 228 33 1 283 510 6178564 6178339 2.910000e-55 226
3 TraesCS6B01G256100 chr6D 84.000 150 17 3 281 423 6178414 6178265 1.400000e-28 137
4 TraesCS6B01G256100 chr6A 94.998 2159 65 22 617 2755 424087116 424089251 0.000000e+00 3349
5 TraesCS6B01G256100 chr6A 83.673 196 23 4 329 517 594521200 594521393 2.980000e-40 176
6 TraesCS6B01G256100 chr6A 92.308 117 8 1 2791 2906 424089481 424089597 6.440000e-37 165
7 TraesCS6B01G256100 chr4B 90.972 432 15 8 208 615 258739892 258739461 7.030000e-156 560
8 TraesCS6B01G256100 chr4B 97.872 188 4 0 1849 2036 241353741 241353928 2.790000e-85 326
9 TraesCS6B01G256100 chr4B 86.603 209 28 0 53 261 87708865 87709073 6.260000e-57 231
10 TraesCS6B01G256100 chr4B 90.419 167 7 1 1 158 258740058 258739892 8.160000e-51 211
11 TraesCS6B01G256100 chr4B 94.030 134 6 1 384 517 87710465 87710596 4.910000e-48 202
12 TraesCS6B01G256100 chr4B 85.052 194 20 4 331 517 87710458 87710649 3.820000e-44 189
13 TraesCS6B01G256100 chr4B 91.045 134 10 1 384 517 87709401 87709532 2.300000e-41 180
14 TraesCS6B01G256100 chr4B 87.500 152 12 2 279 423 87710512 87710663 4.980000e-38 169
15 TraesCS6B01G256100 chr4D 81.498 654 62 12 1 615 418564748 418565381 1.570000e-132 483
16 TraesCS6B01G256100 chr4D 85.366 205 20 4 279 476 418565071 418565272 1.370000e-48 204
17 TraesCS6B01G256100 chr3A 84.534 472 63 4 53 517 550135179 550134711 2.640000e-125 459
18 TraesCS6B01G256100 chr1D 81.695 590 62 20 61 622 370310199 370309628 1.590000e-122 449
19 TraesCS6B01G256100 chr1D 91.729 133 9 2 384 516 370309991 370309861 1.780000e-42 183
20 TraesCS6B01G256100 chr3B 98.374 246 4 0 1791 2036 242897783 242897538 1.600000e-117 433
21 TraesCS6B01G256100 chr7A 80.830 506 69 10 1 480 676426507 676426004 3.540000e-99 372
22 TraesCS6B01G256100 chr2A 97.872 188 4 0 1849 2036 135190494 135190307 2.790000e-85 326
23 TraesCS6B01G256100 chr2A 97.872 188 4 0 1849 2036 160160122 160160309 2.790000e-85 326
24 TraesCS6B01G256100 chr2A 98.895 181 2 0 1856 2036 135189494 135189314 1.000000e-84 324
25 TraesCS6B01G256100 chr2A 94.667 75 3 1 1962 2036 159927832 159927905 6.580000e-22 115
26 TraesCS6B01G256100 chr3D 78.850 539 69 14 1 517 494644991 494645506 3.610000e-84 322
27 TraesCS6B01G256100 chr7D 88.083 193 22 1 53 245 566561786 566561977 8.100000e-56 228
28 TraesCS6B01G256100 chr1A 79.100 311 35 10 333 615 297256760 297256452 1.370000e-43 187
29 TraesCS6B01G256100 chr2D 91.000 100 9 0 279 378 75654787 75654886 5.050000e-28 135


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 TraesCS6B01G256100 chr6B 460090218 460093123 2905 True 5367.0 5367 100.0000 1 2906 1 chr6B.!!$R1 2905
1 TraesCS6B01G256100 chr6D 296860407 296862685 2278 False 3522.0 3522 94.6930 639 2906 1 chr6D.!!$F1 2267
2 TraesCS6B01G256100 chr6A 424087116 424089597 2481 False 1757.0 3349 93.6530 617 2906 2 chr6A.!!$F2 2289
3 TraesCS6B01G256100 chr4B 258739461 258740058 597 True 385.5 560 90.6955 1 615 2 chr4B.!!$R1 614
4 TraesCS6B01G256100 chr4D 418564748 418565381 633 False 343.5 483 83.4320 1 615 2 chr4D.!!$F1 614
5 TraesCS6B01G256100 chr1D 370309628 370310199 571 True 316.0 449 86.7120 61 622 2 chr1D.!!$R1 561
6 TraesCS6B01G256100 chr7A 676426004 676426507 503 True 372.0 372 80.8300 1 480 1 chr7A.!!$R1 479
7 TraesCS6B01G256100 chr2A 135189314 135190494 1180 True 325.0 326 98.3835 1849 2036 2 chr2A.!!$R1 187
8 TraesCS6B01G256100 chr3D 494644991 494645506 515 False 322.0 322 78.8500 1 517 1 chr3D.!!$F1 516

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
379 453 0.036164 AAGTAACGAGGTGGCATGCA 59.964 50.0 21.36 2.54 0.00 3.96 F
1006 1170 0.249657 GTAGCGAGGAGGCATGAAGG 60.250 60.0 0.00 0.00 34.64 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2018 0.105349 CATCCCAGGGGCCATTGATT 60.105 55.0 5.33 0.0 34.68 2.57 R
2761 3232 0.257039 CTGGGGTAGCAAATGAGGCT 59.743 55.0 0.00 0.0 45.18 4.58 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
140 160 1.144496 GGGCTTATCCAACGCGGTA 59.856 57.895 12.47 0.00 36.21 4.02
190 220 2.034879 CCGGCGACAACTCAAGCAT 61.035 57.895 9.30 0.00 0.00 3.79
324 398 1.483415 GGGAAGTAACGAGTGGGCATA 59.517 52.381 0.00 0.00 0.00 3.14
327 401 1.466856 AGTAACGAGTGGGCATACGA 58.533 50.000 0.00 0.00 0.00 3.43
348 422 3.811722 TCTTGTTTCTGCAACATAGCG 57.188 42.857 0.00 0.00 45.17 4.26
351 425 3.536158 TGTTTCTGCAACATAGCGTTC 57.464 42.857 0.00 0.00 40.71 3.95
379 453 0.036164 AAGTAACGAGGTGGCATGCA 59.964 50.000 21.36 2.54 0.00 3.96
534 687 3.270877 GAAGGCGGACACTACATCAAAT 58.729 45.455 0.00 0.00 0.00 2.32
615 768 4.473520 GGAAGCCTAGCAGCGCCA 62.474 66.667 2.29 0.00 38.01 5.69
770 933 2.854420 ATTCTCCTCCCTGCCCTGCT 62.854 60.000 0.00 0.00 0.00 4.24
771 934 3.795041 CTCCTCCCTGCCCTGCTG 61.795 72.222 0.00 0.00 0.00 4.41
1006 1170 0.249657 GTAGCGAGGAGGCATGAAGG 60.250 60.000 0.00 0.00 34.64 3.46
1010 1174 3.011517 AGGAGGCATGAAGGGCGT 61.012 61.111 0.00 0.00 38.57 5.68
1011 1175 2.514824 GGAGGCATGAAGGGCGTC 60.515 66.667 0.00 0.00 43.41 5.19
1170 1334 0.251608 TGAGGGTGATGGTCGACTCA 60.252 55.000 16.46 12.14 33.05 3.41
1179 1343 1.924731 TGGTCGACTCAGTCTCCATT 58.075 50.000 16.46 0.00 32.68 3.16
1261 1425 2.217750 CCATCGACGAGATCACTCTCT 58.782 52.381 3.01 0.00 44.92 3.10
1401 1565 2.223572 CCTTTATGTTCTGGCGCCAATC 60.224 50.000 32.09 22.26 0.00 2.67
1662 1826 1.896660 GGTCTTCCTGTTTGCGCCA 60.897 57.895 4.18 0.00 0.00 5.69
1718 1882 7.957002 TGTAGACTCCATTTGATATTCTCCTC 58.043 38.462 0.00 0.00 0.00 3.71
1794 1958 0.819259 TTTTGCTGCTGGCTCTCGTT 60.819 50.000 0.00 0.00 42.39 3.85
1854 2018 5.997746 CAGGATTCAGGAGTACAAGTTTGAA 59.002 40.000 0.00 0.00 0.00 2.69
2030 2194 6.701841 CCATGTGTATGTACATACTCTTGACC 59.298 42.308 36.02 22.10 43.04 4.02
2232 2437 6.428159 AGCAACACTGATTATTTTCTCTCGTT 59.572 34.615 0.00 0.00 0.00 3.85
2234 2439 6.727824 ACACTGATTATTTTCTCTCGTTGG 57.272 37.500 0.00 0.00 0.00 3.77
2339 2795 0.535780 TGAACTGCAACTCAGCCCTG 60.536 55.000 0.00 0.00 46.76 4.45
2357 2813 1.732809 CTGCTCTGCACTCTGTTGATG 59.267 52.381 0.00 0.00 33.79 3.07
2366 2823 1.985159 ACTCTGTTGATGGGTTGGCTA 59.015 47.619 0.00 0.00 0.00 3.93
2401 2858 1.815003 CTCAATCAGTTGGGGCACTTC 59.185 52.381 0.00 0.00 35.99 3.01
2420 2879 8.138074 GGCACTTCTTTTTCTTAGATCAAAAGT 58.862 33.333 14.86 5.74 38.26 2.66
2513 2977 2.599408 AACCTAAGACAGGGTCGAGA 57.401 50.000 0.00 0.00 42.61 4.04
2514 2978 2.169330 AACCTAAGACAGGGTCGAGAC 58.831 52.381 0.00 0.00 42.61 3.36
2515 2979 1.835494 CCTAAGACAGGGTCGAGACA 58.165 55.000 5.55 0.00 41.26 3.41
2516 2980 1.746220 CCTAAGACAGGGTCGAGACAG 59.254 57.143 5.55 0.00 41.26 3.51
2517 2981 2.438411 CTAAGACAGGGTCGAGACAGT 58.562 52.381 5.55 0.76 37.67 3.55
2518 2982 0.962489 AAGACAGGGTCGAGACAGTG 59.038 55.000 5.55 4.36 37.67 3.66
2519 2983 0.178987 AGACAGGGTCGAGACAGTGT 60.179 55.000 0.00 0.00 37.67 3.55
2829 3555 5.973899 TGCTCCAATTGCACATTAGTTTA 57.026 34.783 0.00 0.00 35.31 2.01
2845 3571 6.753107 TTAGTTTAACAAGCATCTTAGGGC 57.247 37.500 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.175962 TGAAAGACCCCTTCTGTTATCCT 58.824 43.478 0.00 0.00 33.46 3.24
102 122 3.372730 GTCGCCCAATGCCTTGCA 61.373 61.111 0.00 0.00 44.86 4.08
140 160 4.104417 GAGCCAGTCGTCGACGCT 62.104 66.667 32.19 26.98 37.67 5.07
180 210 3.195610 TCTGATCCGTACATGCTTGAGTT 59.804 43.478 6.60 0.00 0.00 3.01
190 220 3.223435 GAAGGGATCTCTGATCCGTACA 58.777 50.000 18.31 0.00 39.07 2.90
348 422 2.572173 CGTTACTTCCTGCAACGAAC 57.428 50.000 0.00 0.00 45.43 3.95
351 425 1.068474 CCTCGTTACTTCCTGCAACG 58.932 55.000 0.00 0.00 44.33 4.10
379 453 0.179113 CAAACGCCCTGTTGCAAAGT 60.179 50.000 0.00 0.00 40.84 2.66
534 687 0.676184 GATGCCCGAGCTGATAGTCA 59.324 55.000 0.00 0.00 40.80 3.41
625 778 5.726688 GCGGCACTTTTTCCTTTTTCTTTTC 60.727 40.000 0.00 0.00 0.00 2.29
629 782 2.430694 AGCGGCACTTTTTCCTTTTTCT 59.569 40.909 1.45 0.00 0.00 2.52
645 800 3.978063 GCTTAAGAGTTTGAGCGGC 57.022 52.632 6.67 0.00 36.39 6.53
691 846 1.413812 CAGGGCTGCCTCAAACTTTTT 59.586 47.619 19.68 0.00 0.00 1.94
693 848 2.737503 CAGGGCTGCCTCAAACTTT 58.262 52.632 19.68 0.00 0.00 2.66
694 849 4.507969 CAGGGCTGCCTCAAACTT 57.492 55.556 19.68 0.00 0.00 2.66
836 1000 0.106569 TATGCTTGGGTGGATGGCTG 60.107 55.000 0.00 0.00 0.00 4.85
951 1115 1.490693 CCACCGGATTTGATCGAGCG 61.491 60.000 9.46 0.00 0.00 5.03
953 1117 0.461870 TGCCACCGGATTTGATCGAG 60.462 55.000 9.46 0.00 0.00 4.04
1170 1334 4.653341 CAGAGATACTGGGAAATGGAGACT 59.347 45.833 0.00 0.00 42.39 3.24
1179 1343 2.362397 GACGATGCAGAGATACTGGGAA 59.638 50.000 0.00 0.00 45.82 3.97
1261 1425 3.820467 AGCAGACCAATGTCGAATTTCAA 59.180 39.130 0.00 0.00 46.51 2.69
1401 1565 1.274703 ACCTGGTGAGGGTATGGCAG 61.275 60.000 0.00 0.00 44.84 4.85
1662 1826 6.772716 ACTTCTTGATACAAAATGTGACCAGT 59.227 34.615 0.00 0.00 0.00 4.00
1794 1958 3.371168 GCAAACAAGCGAGATGAAAACA 58.629 40.909 0.00 0.00 0.00 2.83
1854 2018 0.105349 CATCCCAGGGGCCATTGATT 60.105 55.000 5.33 0.00 34.68 2.57
2030 2194 5.971202 CCACAGTAGCAAAACAAGTTAACAG 59.029 40.000 8.61 2.39 0.00 3.16
2334 2790 2.436292 CAGAGTGCAGAGCAGGGC 60.436 66.667 0.00 0.00 40.08 5.19
2339 2795 1.085091 CCATCAACAGAGTGCAGAGC 58.915 55.000 0.00 0.00 0.00 4.09
2357 2813 1.282157 AGGAGATTGTGTAGCCAACCC 59.718 52.381 0.00 0.00 0.00 4.11
2401 2858 7.087007 GGCCTCACTTTTGATCTAAGAAAAAG 58.913 38.462 13.01 12.30 43.39 2.27
2506 2970 3.637998 TTTGTCTACACTGTCTCGACC 57.362 47.619 0.00 0.00 0.00 4.79
2507 2971 6.147581 TGTAATTTGTCTACACTGTCTCGAC 58.852 40.000 0.00 0.00 0.00 4.20
2508 2972 6.206048 TCTGTAATTTGTCTACACTGTCTCGA 59.794 38.462 0.00 0.00 0.00 4.04
2509 2973 6.305877 GTCTGTAATTTGTCTACACTGTCTCG 59.694 42.308 0.00 0.00 0.00 4.04
2510 2974 6.586844 GGTCTGTAATTTGTCTACACTGTCTC 59.413 42.308 0.00 0.00 0.00 3.36
2511 2975 6.041637 TGGTCTGTAATTTGTCTACACTGTCT 59.958 38.462 0.00 0.00 0.00 3.41
2512 2976 6.220930 TGGTCTGTAATTTGTCTACACTGTC 58.779 40.000 0.00 0.00 0.00 3.51
2513 2977 6.169557 TGGTCTGTAATTTGTCTACACTGT 57.830 37.500 0.00 0.00 0.00 3.55
2514 2978 5.639506 CCTGGTCTGTAATTTGTCTACACTG 59.360 44.000 0.00 0.00 0.00 3.66
2515 2979 5.280011 CCCTGGTCTGTAATTTGTCTACACT 60.280 44.000 0.00 0.00 0.00 3.55
2516 2980 4.935808 CCCTGGTCTGTAATTTGTCTACAC 59.064 45.833 0.00 0.00 0.00 2.90
2517 2981 4.019681 CCCCTGGTCTGTAATTTGTCTACA 60.020 45.833 0.00 0.00 0.00 2.74
2518 2982 4.514401 CCCCTGGTCTGTAATTTGTCTAC 58.486 47.826 0.00 0.00 0.00 2.59
2519 2983 3.054655 GCCCCTGGTCTGTAATTTGTCTA 60.055 47.826 0.00 0.00 0.00 2.59
2552 3016 4.439700 CCGGTAGACTCTTTAAGATTCGCA 60.440 45.833 6.67 0.00 30.23 5.10
2756 3227 1.940613 GGTAGCAAATGAGGCTTACCG 59.059 52.381 0.00 0.00 42.62 4.02
2761 3232 0.257039 CTGGGGTAGCAAATGAGGCT 59.743 55.000 0.00 0.00 45.18 4.58
2829 3555 1.075374 TGTGGCCCTAAGATGCTTGTT 59.925 47.619 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.