Multiple sequence alignment - TraesCS2B01G259900

Loading Multiple Alignment...

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 TraesCS2B01G259900 chr2B 100.000 2530 0 0 891 3420 325632237 325634766 0.000000e+00 4673
1 TraesCS2B01G259900 chr2B 100.000 689 0 0 1 689 325631347 325632035 0.000000e+00 1273
2 TraesCS2B01G259900 chr2B 96.006 651 26 0 38 688 484091056 484091706 0.000000e+00 1059
3 TraesCS2B01G259900 chr2A 96.295 2510 86 3 912 3420 382861182 382858679 0.000000e+00 4113
4 TraesCS2B01G259900 chr2A 95.581 2512 96 8 912 3420 77797278 77799777 0.000000e+00 4010
5 TraesCS2B01G259900 chr2A 95.646 689 30 0 1 689 382861882 382861194 0.000000e+00 1107
6 TraesCS2B01G259900 chr2A 95.461 661 30 0 3 663 77796324 77796984 0.000000e+00 1055
7 TraesCS2B01G259900 chr1D 94.146 2511 138 5 912 3420 176355602 176358105 0.000000e+00 3814
8 TraesCS2B01G259900 chr1D 93.713 2513 131 5 912 3420 356876064 356878553 0.000000e+00 3740
9 TraesCS2B01G259900 chr1D 94.898 686 35 0 1 686 176354908 176355593 0.000000e+00 1074
10 TraesCS2B01G259900 chr1D 95.489 665 30 0 1 665 356875003 356875667 0.000000e+00 1062
11 TraesCS2B01G259900 chr6D 94.126 2247 122 5 1179 3420 452076331 452074090 0.000000e+00 3410
12 TraesCS2B01G259900 chr6A 95.315 1793 75 8 916 2699 359014226 359012434 0.000000e+00 2837
13 TraesCS2B01G259900 chr6A 96.348 575 21 0 77 651 359015081 359014507 0.000000e+00 946
14 TraesCS2B01G259900 chr6B 85.461 2421 331 15 925 3337 583179655 583182062 0.000000e+00 2501
15 TraesCS2B01G259900 chr4B 84.509 2466 356 17 912 3365 460993615 460996066 0.000000e+00 2414
16 TraesCS2B01G259900 chr4B 85.294 2346 303 24 925 3256 245677509 245675192 0.000000e+00 2383
17 TraesCS2B01G259900 chr4B 84.761 689 99 5 1 689 460992921 460993603 0.000000e+00 686
18 TraesCS2B01G259900 chr4B 82.779 691 108 11 1 687 245678244 245677561 1.050000e-169 606
19 TraesCS2B01G259900 chr7A 94.032 687 41 0 3 689 439780298 439780984 0.000000e+00 1042


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 TraesCS2B01G259900 chr2B 325631347 325634766 3419 False 2973.0 4673 100.0000 1 3420 2 chr2B.!!$F2 3419
1 TraesCS2B01G259900 chr2B 484091056 484091706 650 False 1059.0 1059 96.0060 38 688 1 chr2B.!!$F1 650
2 TraesCS2B01G259900 chr2A 382858679 382861882 3203 True 2610.0 4113 95.9705 1 3420 2 chr2A.!!$R1 3419
3 TraesCS2B01G259900 chr2A 77796324 77799777 3453 False 2532.5 4010 95.5210 3 3420 2 chr2A.!!$F1 3417
4 TraesCS2B01G259900 chr1D 176354908 176358105 3197 False 2444.0 3814 94.5220 1 3420 2 chr1D.!!$F1 3419
5 TraesCS2B01G259900 chr1D 356875003 356878553 3550 False 2401.0 3740 94.6010 1 3420 2 chr1D.!!$F2 3419
6 TraesCS2B01G259900 chr6D 452074090 452076331 2241 True 3410.0 3410 94.1260 1179 3420 1 chr6D.!!$R1 2241
7 TraesCS2B01G259900 chr6A 359012434 359015081 2647 True 1891.5 2837 95.8315 77 2699 2 chr6A.!!$R1 2622
8 TraesCS2B01G259900 chr6B 583179655 583182062 2407 False 2501.0 2501 85.4610 925 3337 1 chr6B.!!$F1 2412
9 TraesCS2B01G259900 chr4B 460992921 460996066 3145 False 1550.0 2414 84.6350 1 3365 2 chr4B.!!$F1 3364
10 TraesCS2B01G259900 chr4B 245675192 245678244 3052 True 1494.5 2383 84.0365 1 3256 2 chr4B.!!$R1 3255
11 TraesCS2B01G259900 chr7A 439780298 439780984 686 False 1042.0 1042 94.0320 3 689 1 chr7A.!!$F1 686

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
910 911 0.322816 TCATTGACTTGGAGGCTGCC 60.323 55.0 11.65 11.65 0.00 4.85 F
1893 2075 0.396435 TCAAGTTGACACTCGGCCAT 59.604 50.0 2.24 0.00 30.45 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2232 2423 0.112412 ATTTTCTGGGTCGCCACCTT 59.888 50.0 0.0 0.0 43.22 3.50 R
3336 3532 0.324943 AATCCGTGTCCAAGACCAGG 59.675 55.0 0.0 0.0 32.24 4.45 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
79 80 3.766051 GAGTGGGAGCAAATCAAGGAAAT 59.234 43.478 0.00 0.00 0.00 2.17
272 273 1.830847 GGGGGTGAGCGTGGTTTTT 60.831 57.895 0.00 0.00 0.00 1.94
282 283 0.593773 CGTGGTTTTTGCCGGTTCTG 60.594 55.000 1.90 0.00 0.00 3.02
385 386 2.147436 TCAATTTTGTTTCCTGCCGC 57.853 45.000 0.00 0.00 0.00 6.53
416 417 3.739401 TTTGAGGGAAAGGGAGGAATC 57.261 47.619 0.00 0.00 0.00 2.52
909 910 0.807496 GTCATTGACTTGGAGGCTGC 59.193 55.000 9.59 0.00 0.00 5.25
910 911 0.322816 TCATTGACTTGGAGGCTGCC 60.323 55.000 11.65 11.65 0.00 4.85
1213 1389 3.423154 GCGCAGACGGGAGGTTTG 61.423 66.667 0.30 0.00 40.57 2.93
1300 1476 0.684535 TGACGGTCTCATCTTTGCCA 59.315 50.000 9.88 0.00 0.00 4.92
1679 1855 8.607713 TGATAAGAGGGTTGTTTGTTATCCTAA 58.392 33.333 0.00 0.00 0.00 2.69
1863 2045 2.747686 GTCTCGGACAAAGGGGCA 59.252 61.111 0.00 0.00 32.09 5.36
1893 2075 0.396435 TCAAGTTGACACTCGGCCAT 59.604 50.000 2.24 0.00 30.45 4.40
1993 2175 1.372997 GTTTCTGGCGAGCGAGACA 60.373 57.895 9.27 0.59 30.70 3.41
2162 2353 2.589720 CCAAATCATGGGCTGATGCTA 58.410 47.619 0.00 0.00 44.03 3.49
2165 2356 4.768448 CCAAATCATGGGCTGATGCTAATA 59.232 41.667 0.00 0.00 44.03 0.98
2180 2371 9.118300 CTGATGCTAATAGATTTCTTTTCCAGT 57.882 33.333 0.00 0.00 0.00 4.00
2190 2381 1.515521 CTTTTCCAGTCGGGTGTGCC 61.516 60.000 0.00 0.00 38.11 5.01
2232 2423 0.392461 GCTGCAAGAATGGGTACGGA 60.392 55.000 0.00 0.00 34.07 4.69
2340 2534 2.470057 AAGAAAGGGGGAGCAAACAA 57.530 45.000 0.00 0.00 0.00 2.83
2660 2856 1.610327 CTCTGAGGAGGAGGACCGA 59.390 63.158 0.00 0.00 41.83 4.69
2664 2860 3.336568 AGGAGGAGGACCGACGGA 61.337 66.667 23.38 0.00 41.83 4.69
2789 2985 6.780457 TCCTTTCTGAATCCCATTTGAATC 57.220 37.500 0.00 0.00 0.00 2.52
2790 2986 5.658190 TCCTTTCTGAATCCCATTTGAATCC 59.342 40.000 0.00 0.00 0.00 3.01
2791 2987 5.163374 CCTTTCTGAATCCCATTTGAATCCC 60.163 44.000 0.00 0.00 0.00 3.85
2792 2988 4.606476 TCTGAATCCCATTTGAATCCCA 57.394 40.909 0.00 0.00 0.00 4.37
2793 2989 4.280819 TCTGAATCCCATTTGAATCCCAC 58.719 43.478 0.00 0.00 0.00 4.61
2981 3177 4.096382 GGATGTTGTAAAGTGGCGATTCAT 59.904 41.667 0.00 0.00 0.00 2.57
2986 3182 0.611618 AAAGTGGCGATTCATGGGCA 60.612 50.000 0.00 0.00 38.65 5.36
3205 3401 3.200165 GGAAGACTTAGGTTACATGGGCT 59.800 47.826 0.00 0.00 0.00 5.19
3336 3532 0.397941 TCCATTCTGATCATCGGCCC 59.602 55.000 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 1.070134 CCCAAAAGATCCGCCTCGATA 59.930 52.381 0.00 0.00 0.00 2.92
272 273 1.968493 ACTTTCTCTACAGAACCGGCA 59.032 47.619 0.00 0.00 38.44 5.69
282 283 8.471609 AGCCTTATCTACTGAAACTTTCTCTAC 58.528 37.037 3.22 0.00 0.00 2.59
319 320 5.620738 TCTGATTCTACAATCCTGAAGGG 57.379 43.478 0.00 0.00 38.14 3.95
385 386 3.386932 TTCCCTCAAATGAATCCCCAG 57.613 47.619 0.00 0.00 0.00 4.45
416 417 5.355350 CAGTTTCCTAATAACTGCTCCAAGG 59.645 44.000 0.00 0.00 44.02 3.61
890 891 0.807496 GCAGCCTCCAAGTCAATGAC 59.193 55.000 5.02 5.02 0.00 3.06
891 892 0.322816 GGCAGCCTCCAAGTCAATGA 60.323 55.000 3.29 0.00 0.00 2.57
892 893 1.318158 GGGCAGCCTCCAAGTCAATG 61.318 60.000 12.43 0.00 0.00 2.82
893 894 1.000396 GGGCAGCCTCCAAGTCAAT 60.000 57.895 12.43 0.00 0.00 2.57
894 895 2.436109 GGGCAGCCTCCAAGTCAA 59.564 61.111 12.43 0.00 0.00 3.18
895 896 4.020617 CGGGCAGCCTCCAAGTCA 62.021 66.667 12.43 0.00 0.00 3.41
896 897 4.785453 CCGGGCAGCCTCCAAGTC 62.785 72.222 12.43 0.00 0.00 3.01
1213 1389 0.174389 TCAGCAGCGAGATTCAGGAC 59.826 55.000 0.00 0.00 0.00 3.85
1218 1394 0.997932 CACTGTCAGCAGCGAGATTC 59.002 55.000 0.00 0.00 46.30 2.52
1300 1476 1.000896 CCCCCTTGCCATCGAACTT 60.001 57.895 0.00 0.00 0.00 2.66
1679 1855 6.295916 CCAGTAGGGTTCTACACTCAGATTTT 60.296 42.308 6.37 0.00 46.23 1.82
1863 2045 3.252974 GTCAACTTGACGGATGAGGAT 57.747 47.619 6.16 0.00 37.67 3.24
1922 2104 2.031919 TTGCGTCAGCCGGAACAT 59.968 55.556 5.05 0.00 42.27 2.71
1970 2152 2.669569 GCTCGCCAGAAACAGCCA 60.670 61.111 0.00 0.00 0.00 4.75
2162 2353 5.648092 CACCCGACTGGAAAAGAAATCTATT 59.352 40.000 0.00 0.00 37.49 1.73
2165 2356 3.181443 ACACCCGACTGGAAAAGAAATCT 60.181 43.478 0.00 0.00 37.49 2.40
2190 2381 0.802494 AGCGTTTGTTAATGCCTCCG 59.198 50.000 0.00 0.00 45.49 4.63
2232 2423 0.112412 ATTTTCTGGGTCGCCACCTT 59.888 50.000 0.00 0.00 43.22 3.50
2340 2534 2.103373 TCTTACGAGCATCCTCAGCTT 58.897 47.619 0.00 0.00 43.58 3.74
2660 2856 4.018779 TCCTAGGATTTTCATTTGGTCCGT 60.019 41.667 7.62 0.00 34.19 4.69
2664 2860 6.091076 TCCATCCTAGGATTTTCATTTGGT 57.909 37.500 22.29 0.00 31.23 3.67
2789 2985 1.468520 CATCGGCTTTACACTTGTGGG 59.531 52.381 5.72 0.00 0.00 4.61
2790 2986 2.416547 CTCATCGGCTTTACACTTGTGG 59.583 50.000 5.72 0.00 0.00 4.17
2791 2987 2.159653 GCTCATCGGCTTTACACTTGTG 60.160 50.000 0.00 0.00 0.00 3.33
2792 2988 2.076863 GCTCATCGGCTTTACACTTGT 58.923 47.619 0.00 0.00 0.00 3.16
2793 2989 2.350522 AGCTCATCGGCTTTACACTTG 58.649 47.619 0.00 0.00 39.86 3.16
2981 3177 1.492599 TCGGATGACCATAAATGCCCA 59.507 47.619 0.00 0.00 35.59 5.36
2986 3182 4.771114 TCCAGTTCGGATGACCATAAAT 57.229 40.909 0.00 0.00 39.64 1.40
3205 3401 7.186972 TCACCTCTACTCCAAGTAAAAGGATA 58.813 38.462 16.40 6.36 32.53 2.59
3336 3532 0.324943 AATCCGTGTCCAAGACCAGG 59.675 55.000 0.00 0.00 32.24 4.45
3394 3590 4.159135 CCACCTAGCTTCAAATTGCTTCAT 59.841 41.667 0.00 0.00 40.35 2.57


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

AutoCloner maintained by Alex Coulton.