Multiple sequence alignment - TraesCS2B01G100800

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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 TraesCS2B01G100800 chr2B 100.000 3278 0 0 1 3278 61341093 61337816 0.000000e+00 6054.0
1 TraesCS2B01G100800 chr2B 94.925 1458 39 5 436 1890 61285497 61284072 0.000000e+00 2250.0
2 TraesCS2B01G100800 chr2B 83.812 766 101 18 889 1640 23597882 23597126 0.000000e+00 706.0
3 TraesCS2B01G100800 chr2B 82.254 834 111 25 1701 2527 23597031 23596228 0.000000e+00 686.0
4 TraesCS2B01G100800 chr2B 90.338 414 20 6 1 400 61285908 61285501 2.900000e-145 525.0
5 TraesCS2B01G100800 chr2B 82.902 193 25 7 565 751 61286041 61285851 2.020000e-37 167.0
6 TraesCS2B01G100800 chr2D 93.712 2290 107 9 702 2976 36112390 36114657 0.000000e+00 3397.0
7 TraesCS2B01G100800 chr2D 94.439 953 51 2 1370 2321 36123887 36122936 0.000000e+00 1465.0
8 TraesCS2B01G100800 chr2D 90.144 416 20 4 1 401 36111748 36112157 3.750000e-144 521.0
9 TraesCS2B01G100800 chr2D 91.003 289 24 2 2975 3262 36118438 36118725 3.970000e-104 388.0
10 TraesCS2B01G100800 chr2D 90.756 238 18 1 436 673 36112160 36112393 6.830000e-82 315.0
11 TraesCS2B01G100800 chr2D 82.383 193 30 3 547 736 36111597 36111788 7.280000e-37 165.0
12 TraesCS2B01G100800 chr2D 94.366 71 4 0 1300 1370 36152093 36152023 3.460000e-20 110.0
13 TraesCS2B01G100800 chr3D 96.051 1418 49 5 780 2193 380046410 380044996 0.000000e+00 2302.0
14 TraesCS2B01G100800 chr3D 94.645 691 34 1 2186 2876 380032050 380031363 0.000000e+00 1068.0
15 TraesCS2B01G100800 chr3D 93.666 521 23 6 1 512 380047365 380046846 0.000000e+00 771.0
16 TraesCS2B01G100800 chr3D 92.690 342 24 1 2922 3262 380031363 380031022 2.940000e-135 492.0
17 TraesCS2B01G100800 chr3D 93.860 228 9 2 523 750 380046630 380046408 4.050000e-89 339.0
18 TraesCS2B01G100800 chr3D 95.349 43 2 0 422 464 28747701 28747743 5.870000e-08 69.4
19 TraesCS2B01G100800 chr2A 93.481 1396 57 5 1411 2806 39468942 39470303 0.000000e+00 2043.0
20 TraesCS2B01G100800 chr2A 94.949 990 45 4 436 1425 39467929 39468913 0.000000e+00 1546.0
21 TraesCS2B01G100800 chr2A 81.633 833 111 25 1701 2523 15011957 15011157 0.000000e+00 652.0
22 TraesCS2B01G100800 chr2A 91.912 408 21 3 1 402 39467526 39467927 7.940000e-156 560.0
23 TraesCS2B01G100800 chr2A 84.086 421 59 7 883 1302 15012960 15012547 1.830000e-107 399.0
24 TraesCS2B01G100800 chr2A 85.586 111 16 0 626 736 39467456 39467566 2.070000e-22 117.0
25 TraesCS2B01G100800 chr2A 91.837 49 2 1 456 504 653298548 653298594 2.110000e-07 67.6
26 TraesCS2B01G100800 chr6D 95.349 43 2 0 423 465 63729747 63729789 5.870000e-08 69.4
27 TraesCS2B01G100800 chr1D 95.349 43 2 0 422 464 406839759 406839717 5.870000e-08 69.4
28 TraesCS2B01G100800 chr3B 95.238 42 2 0 423 464 445147273 445147232 2.110000e-07 67.6
29 TraesCS2B01G100800 chr3B 95.238 42 2 0 423 464 641661757 641661716 2.110000e-07 67.6
30 TraesCS2B01G100800 chr3B 90.244 41 4 0 464 504 56061839 56061799 2.000000e-03 54.7
31 TraesCS2B01G100800 chr7D 95.238 42 0 2 385 424 210076991 210077032 7.590000e-07 65.8
32 TraesCS2B01G100800 chr7D 88.235 51 4 2 464 512 53506124 53506074 3.530000e-05 60.2
33 TraesCS2B01G100800 chr5B 89.362 47 5 0 467 513 704891353 704891307 3.530000e-05 60.2
34 TraesCS2B01G100800 chr7A 90.909 44 2 2 384 425 736420836 736420793 1.270000e-04 58.4
35 TraesCS2B01G100800 chr1B 90.244 41 4 0 464 504 565684545 565684585 2.000000e-03 54.7


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 TraesCS2B01G100800 chr2B 61337816 61341093 3277 True 6054.000000 6054 100.000000 1 3278 1 chr2B.!!$R1 3277
1 TraesCS2B01G100800 chr2B 61284072 61286041 1969 True 980.666667 2250 89.388333 1 1890 3 chr2B.!!$R3 1889
2 TraesCS2B01G100800 chr2B 23596228 23597882 1654 True 696.000000 706 83.033000 889 2527 2 chr2B.!!$R2 1638
3 TraesCS2B01G100800 chr2D 36122936 36123887 951 True 1465.000000 1465 94.439000 1370 2321 1 chr2D.!!$R1 951
4 TraesCS2B01G100800 chr2D 36111597 36118725 7128 False 957.200000 3397 89.599600 1 3262 5 chr2D.!!$F1 3261
5 TraesCS2B01G100800 chr3D 380044996 380047365 2369 True 1137.333333 2302 94.525667 1 2193 3 chr3D.!!$R2 2192
6 TraesCS2B01G100800 chr3D 380031022 380032050 1028 True 780.000000 1068 93.667500 2186 3262 2 chr3D.!!$R1 1076
7 TraesCS2B01G100800 chr2A 39467456 39470303 2847 False 1066.500000 2043 91.482000 1 2806 4 chr2A.!!$F2 2805
8 TraesCS2B01G100800 chr2A 15011157 15012960 1803 True 525.500000 652 82.859500 883 2523 2 chr2A.!!$R1 1640

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
690 1069 0.322975 CTTACTGCCACCAGAGCTGT 59.677 55.000 0.0 0.0 41.77 4.40 F
1719 2389 7.309920 TGCGTCCCTTTTATTCAAGAAAATAC 58.690 34.615 0.0 0.0 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 2423 0.318120 CCATGGTCCAACCTTTGTGC 59.682 55.0 2.57 0.0 39.58 4.57 R
2609 3298 0.394625 GGACGAGGAGTAGGAGCACT 60.395 60.0 0.00 0.0 0.00 4.40 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
365 539 7.838771 CCATTCAGAGGGAAATTTCATTTTC 57.161 36.000 19.49 10.47 39.39 2.29
366 540 7.388437 CCATTCAGAGGGAAATTTCATTTTCA 58.612 34.615 19.49 0.00 39.39 2.69
367 541 8.044908 CCATTCAGAGGGAAATTTCATTTTCAT 58.955 33.333 19.49 0.00 39.39 2.57
402 576 7.822822 TGAATCATATATACTCTCTTCGTCCGA 59.177 37.037 0.00 0.00 0.00 4.55
475 649 6.944234 AGTATTTTCGGATCCATTTCTTCC 57.056 37.500 13.41 0.00 0.00 3.46
493 667 1.894466 TCCACAAGTATTTCCGGACGA 59.106 47.619 1.83 0.00 0.00 4.20
504 678 2.768492 CCGGACGAAGGGAGTACCG 61.768 68.421 0.00 0.00 46.96 4.02
519 693 6.438425 AGGGAGTACCGAATTACTAACAAGAA 59.562 38.462 0.00 0.00 46.96 2.52
537 916 1.666189 GAAGCACCTAAGGATCGTTGC 59.334 52.381 10.86 6.33 0.00 4.17
541 920 3.071602 AGCACCTAAGGATCGTTGCATAT 59.928 43.478 10.86 0.00 0.00 1.78
542 921 4.283467 AGCACCTAAGGATCGTTGCATATA 59.717 41.667 10.86 0.00 0.00 0.86
543 922 5.046304 AGCACCTAAGGATCGTTGCATATAT 60.046 40.000 10.86 0.00 0.00 0.86
544 923 6.154534 AGCACCTAAGGATCGTTGCATATATA 59.845 38.462 10.86 0.00 0.00 0.86
643 1022 4.246458 ACGTCCTTAGTCAAGAAAGCATC 58.754 43.478 0.00 0.00 33.20 3.91
684 1063 4.142381 GCCTTTATTTCTTACTGCCACCAG 60.142 45.833 0.00 0.00 44.80 4.00
690 1069 0.322975 CTTACTGCCACCAGAGCTGT 59.677 55.000 0.00 0.00 41.77 4.40
1719 2389 7.309920 TGCGTCCCTTTTATTCAAGAAAATAC 58.690 34.615 0.00 0.00 0.00 1.89
1753 2423 7.371159 TGTCTTATCATATTGTAGAGCCTTCG 58.629 38.462 0.00 0.00 0.00 3.79
2025 2701 5.687285 ACAAGCACTTCTTTATTCTTTTGCG 59.313 36.000 0.00 0.00 33.90 4.85
2190 2866 3.149005 GGAACCACTTTCACCATACCA 57.851 47.619 0.00 0.00 35.70 3.25
2250 2926 3.118992 GCAGTGGGATATATCTCGATGCA 60.119 47.826 25.69 0.00 39.65 3.96
2303 2982 2.820986 GCTAGCGGCTAATGCTCTC 58.179 57.895 11.39 0.00 42.85 3.20
2482 3171 7.805071 GTGATTTGCTTATATATGTGTCTTGCC 59.195 37.037 0.00 0.00 0.00 4.52
2609 3298 4.984295 TCAAGGAGGTTGTTTCATCATCA 58.016 39.130 0.00 0.00 37.43 3.07
2618 3307 4.824479 TGTTTCATCATCAGTGCTCCTA 57.176 40.909 0.00 0.00 0.00 2.94
2720 3409 1.537202 GTGTGCTCACCATTTCTCACC 59.463 52.381 7.70 0.00 38.51 4.02
2743 3432 7.238710 ACCAGAGATTGTGGTAAATAAAAGGT 58.761 34.615 0.00 0.00 46.96 3.50
2832 3521 5.486526 CAGTAGCTCTTTCTTCTGTGGAAT 58.513 41.667 0.00 0.00 30.06 3.01
2857 3546 6.317642 TGGATCCTACAATAATTTTGGACACG 59.682 38.462 14.23 0.00 0.00 4.49
2871 3560 1.539496 GGACACGTGCTTGTTACCTCA 60.539 52.381 17.22 0.00 0.00 3.86
2883 3572 5.665459 CTTGTTACCTCAAGGATCGAATCT 58.335 41.667 2.30 0.00 40.49 2.40
2887 3576 2.697751 ACCTCAAGGATCGAATCTGGAG 59.302 50.000 13.06 13.06 38.94 3.86
2888 3577 2.036992 CCTCAAGGATCGAATCTGGAGG 59.963 54.545 20.56 20.56 37.39 4.30
2938 3630 5.390991 GGACAGTAATTTGTGCTGCTCTAAC 60.391 44.000 0.00 0.00 43.33 2.34
2940 3632 4.152402 CAGTAATTTGTGCTGCTCTAACGT 59.848 41.667 0.00 0.00 32.85 3.99
3008 7482 2.597217 ACACCATGCCCAACACGG 60.597 61.111 0.00 0.00 0.00 4.94
3050 7524 0.744414 CCGCGACCCTGATCACAAAT 60.744 55.000 8.23 0.00 0.00 2.32
3184 7659 2.169832 ACAAGGACTCACATTCACCG 57.830 50.000 0.00 0.00 0.00 4.94
3206 7682 4.190772 GCCCCAAAACACATAATCATTGG 58.809 43.478 0.00 0.00 37.61 3.16
3214 7690 9.345517 CAAAACACATAATCATTGGTACTCAAG 57.654 33.333 0.00 0.00 38.95 3.02
3237 7713 2.749800 GCCTTCACTCCAAACCTCTTGT 60.750 50.000 0.00 0.00 0.00 3.16
3247 7723 3.307691 CCAAACCTCTTGTGCATCTCCTA 60.308 47.826 0.00 0.00 0.00 2.94
3262 7738 3.039011 TCTCCTAGAAATTCCCCCTTCG 58.961 50.000 0.00 0.00 0.00 3.79
3263 7739 2.104963 CTCCTAGAAATTCCCCCTTCGG 59.895 54.545 0.00 0.00 0.00 4.30
3264 7740 2.124411 CCTAGAAATTCCCCCTTCGGA 58.876 52.381 0.00 0.00 0.00 4.55
3265 7741 2.508300 CCTAGAAATTCCCCCTTCGGAA 59.492 50.000 0.00 0.00 45.87 4.30
3266 7742 3.053917 CCTAGAAATTCCCCCTTCGGAAA 60.054 47.826 0.00 0.00 44.97 3.13
3267 7743 2.803956 AGAAATTCCCCCTTCGGAAAC 58.196 47.619 0.00 0.00 44.97 2.78
3268 7744 2.109304 AGAAATTCCCCCTTCGGAAACA 59.891 45.455 0.00 0.00 44.97 2.83
3269 7745 2.919772 AATTCCCCCTTCGGAAACAT 57.080 45.000 0.00 0.00 44.97 2.71
3270 7746 2.919772 ATTCCCCCTTCGGAAACATT 57.080 45.000 0.00 0.00 44.97 2.71
3271 7747 2.209690 TTCCCCCTTCGGAAACATTC 57.790 50.000 0.00 0.00 39.00 2.67
3272 7748 1.368374 TCCCCCTTCGGAAACATTCT 58.632 50.000 0.00 0.00 0.00 2.40
3273 7749 2.553464 TCCCCCTTCGGAAACATTCTA 58.447 47.619 0.00 0.00 0.00 2.10
3274 7750 2.237893 TCCCCCTTCGGAAACATTCTAC 59.762 50.000 0.00 0.00 0.00 2.59
3275 7751 2.026636 CCCCCTTCGGAAACATTCTACA 60.027 50.000 0.00 0.00 0.00 2.74
3276 7752 3.270877 CCCCTTCGGAAACATTCTACAG 58.729 50.000 0.00 0.00 0.00 2.74
3277 7753 3.055385 CCCCTTCGGAAACATTCTACAGA 60.055 47.826 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 196 3.386486 ACAACGTTTGCTATTCGAGACA 58.614 40.909 0.00 0.00 0.00 3.41
228 397 5.012893 CCTATTTTCAAACTTCAGAGCCCT 58.987 41.667 0.00 0.00 0.00 5.19
392 566 2.664568 CGCAAGTATTTTCGGACGAAGA 59.335 45.455 7.25 3.70 35.38 2.87
402 576 7.624360 TGTATCCATTTCTCGCAAGTATTTT 57.376 32.000 0.00 0.00 39.48 1.82
427 601 4.854173 TCGGAGAAATGGATCAAAATGGA 58.146 39.130 0.00 0.00 0.00 3.41
475 649 2.671396 CCTTCGTCCGGAAATACTTGTG 59.329 50.000 5.23 0.00 33.34 3.33
493 667 6.438425 TCTTGTTAGTAATTCGGTACTCCCTT 59.562 38.462 0.00 0.00 35.85 3.95
504 678 7.822822 TCCTTAGGTGCTTCTTGTTAGTAATTC 59.177 37.037 0.00 0.00 0.00 2.17
519 693 3.460648 GCAACGATCCTTAGGTGCT 57.539 52.632 0.00 0.00 46.65 4.40
537 916 8.151141 CTGCAAGGCCATCATTAGTATATATG 57.849 38.462 5.01 0.00 0.00 1.78
684 1063 3.114809 CAGAATCACTCGATCACAGCTC 58.885 50.000 0.00 0.00 0.00 4.09
690 1069 2.621338 GGCAACAGAATCACTCGATCA 58.379 47.619 0.00 0.00 0.00 2.92
1530 2164 4.753107 GGAACTTTTTGTAGATGACACCGA 59.247 41.667 0.00 0.00 37.96 4.69
1685 2351 1.757682 AAAGGGACGCAGACACAAAA 58.242 45.000 0.00 0.00 0.00 2.44
1753 2423 0.318120 CCATGGTCCAACCTTTGTGC 59.682 55.000 2.57 0.00 39.58 4.57
1998 2669 7.222611 GCAAAAGAATAAAGAAGTGCTTGTTGA 59.777 33.333 0.00 0.00 36.80 3.18
2005 2677 5.220098 GCATCGCAAAAGAATAAAGAAGTGC 60.220 40.000 0.00 0.00 0.00 4.40
2025 2701 0.457853 TGCCGAGTACGAACTGCATC 60.458 55.000 0.00 0.00 42.66 3.91
2190 2866 3.181503 CGATGCTGCTATTCTTTTGCACT 60.182 43.478 0.00 0.00 33.16 4.40
2250 2926 3.284197 GTGCACGTAGACACCAAGT 57.716 52.632 0.00 0.00 33.45 3.16
2303 2982 7.304735 TGATTGAGAAATACACACCGAAAATG 58.695 34.615 0.00 0.00 0.00 2.32
2482 3171 2.047002 TCACATCACATGCATCCCAG 57.953 50.000 0.00 0.00 0.00 4.45
2581 3270 6.550854 TGATGAAACAACCTCCTTGAGATTTT 59.449 34.615 0.00 0.00 33.59 1.82
2609 3298 0.394625 GGACGAGGAGTAGGAGCACT 60.395 60.000 0.00 0.00 0.00 4.40
2618 3307 0.547553 GTAGGAGGAGGACGAGGAGT 59.452 60.000 0.00 0.00 0.00 3.85
2720 3409 8.335532 TGACCTTTTATTTACCACAATCTCTG 57.664 34.615 0.00 0.00 0.00 3.35
2743 3432 8.192743 TGTTACCACTACAACCTTATACTTGA 57.807 34.615 0.00 0.00 0.00 3.02
2790 3479 0.863144 GCGTCCGTTCTTGTAAGCAA 59.137 50.000 0.00 0.00 0.00 3.91
2832 3521 6.317642 CGTGTCCAAAATTATTGTAGGATCCA 59.682 38.462 15.82 0.00 0.00 3.41
2857 3546 2.673368 CGATCCTTGAGGTAACAAGCAC 59.327 50.000 0.00 0.00 43.83 4.40
2871 3560 1.765314 CCACCTCCAGATTCGATCCTT 59.235 52.381 0.00 0.00 0.00 3.36
2888 3577 6.235664 TCCTTGTTTGATCTAGGTTAACCAC 58.764 40.000 26.26 13.13 38.89 4.16
2907 3596 4.520492 AGCACAAATTACTGTCCTTCCTTG 59.480 41.667 0.00 0.00 0.00 3.61
3184 7659 4.190772 CCAATGATTATGTGTTTTGGGGC 58.809 43.478 0.00 0.00 31.97 5.80
3214 7690 1.202818 AGAGGTTTGGAGTGAAGGCAC 60.203 52.381 0.00 0.00 45.49 5.01
3221 7697 1.679139 TGCACAAGAGGTTTGGAGTG 58.321 50.000 0.00 0.00 0.00 3.51
3237 7713 2.443255 GGGGGAATTTCTAGGAGATGCA 59.557 50.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.