Multiple sequence alignment - TraesCS6B01G140500

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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 TraesCS6B01G140500 chr6B 100.000 4543 0 0 1 4543 139882785 139887327 0.000000e+00 8390.0
1 TraesCS6B01G140500 chr6B 93.638 1902 76 13 823 2688 140367437 140365545 0.000000e+00 2800.0
2 TraesCS6B01G140500 chr6B 85.057 1499 161 24 966 2433 140333532 140332066 0.000000e+00 1469.0
3 TraesCS6B01G140500 chr6B 85.145 1306 158 23 968 2255 140097446 140096159 0.000000e+00 1304.0
4 TraesCS6B01G140500 chr6B 85.066 837 85 22 1 801 140368254 140367422 0.000000e+00 817.0
5 TraesCS6B01G140500 chr6B 77.024 1062 175 48 2817 3849 140094804 140093783 3.090000e-151 545.0
6 TraesCS6B01G140500 chr6B 82.812 320 26 17 4064 4363 140354589 140354279 4.510000e-65 259.0
7 TraesCS6B01G140500 chr6B 92.157 102 6 2 3885 3985 13827619 13827519 4.740000e-30 143.0
8 TraesCS6B01G140500 chr6B 94.318 88 4 1 3891 3977 179236253 179236340 2.850000e-27 134.0
9 TraesCS6B01G140500 chr6D 97.999 4547 76 8 2 4543 65050680 65055216 0.000000e+00 7878.0
10 TraesCS6B01G140500 chr6D 92.430 3329 170 38 614 3895 65361424 65358131 0.000000e+00 4676.0
11 TraesCS6B01G140500 chr6D 85.202 1507 161 28 957 2431 65343459 65341983 0.000000e+00 1491.0
12 TraesCS6B01G140500 chr6D 84.986 1412 177 17 968 2354 65095181 65093780 0.000000e+00 1400.0
13 TraesCS6B01G140500 chr6D 82.476 1381 182 38 999 2352 63817296 63815949 0.000000e+00 1155.0
14 TraesCS6B01G140500 chr6D 77.291 1004 173 36 2866 3849 65093658 65092690 1.440000e-149 540.0
15 TraesCS6B01G140500 chr6D 82.820 617 54 19 3249 3836 65341677 65341084 5.250000e-139 505.0
16 TraesCS6B01G140500 chr6D 90.991 333 29 1 127 459 65363301 65362970 8.970000e-122 448.0
17 TraesCS6B01G140500 chr6D 84.101 434 48 16 3974 4388 65358134 65357703 2.550000e-107 399.0
18 TraesCS6B01G140500 chr6D 82.313 441 42 20 3976 4391 65352075 65351646 2.600000e-92 350.0
19 TraesCS6B01G140500 chr6D 87.671 146 15 2 2545 2689 10312267 10312410 2.810000e-37 167.0
20 TraesCS6B01G140500 chr6D 91.803 122 5 3 3719 3835 65357577 65357456 1.010000e-36 165.0
21 TraesCS6B01G140500 chr6D 90.909 99 7 2 3883 3980 427344949 427344852 1.030000e-26 132.0
22 TraesCS6B01G140500 chr6A 89.650 2000 134 23 458 2437 83434564 83436510 0.000000e+00 2479.0
23 TraesCS6B01G140500 chr6A 93.344 1247 66 11 2760 3994 83436988 83438229 0.000000e+00 1827.0
24 TraesCS6B01G140500 chr6A 84.697 1503 170 28 957 2433 83599489 83600957 0.000000e+00 1447.0
25 TraesCS6B01G140500 chr6A 84.817 1449 176 24 957 2373 83644506 83645942 0.000000e+00 1417.0
26 TraesCS6B01G140500 chr6A 82.675 1443 206 27 999 2431 81191957 81190549 0.000000e+00 1240.0
27 TraesCS6B01G140500 chr6A 83.528 771 117 6 2779 3543 83600874 83601640 0.000000e+00 712.0
28 TraesCS6B01G140500 chr6A 77.195 1105 179 47 2819 3888 83645988 83647054 1.100000e-160 577.0
29 TraesCS6B01G140500 chr6A 88.528 462 47 5 1 459 83434036 83434494 5.130000e-154 555.0
30 TraesCS6B01G140500 chr6A 86.427 501 41 14 4051 4541 83438235 83438718 1.450000e-144 523.0
31 TraesCS6B01G140500 chr6A 82.097 391 31 18 3460 3832 83439331 83439700 9.550000e-77 298.0
32 TraesCS6B01G140500 chr6A 93.277 119 6 2 3719 3835 83440281 83440399 1.680000e-39 174.0
33 TraesCS6B01G140500 chr6A 93.478 92 5 1 3887 3977 508000855 508000946 7.930000e-28 135.0
34 TraesCS6B01G140500 chr6A 80.000 115 9 12 831 942 83599394 83599497 6.300000e-09 73.1
35 TraesCS6B01G140500 chrUn 94.850 1165 47 10 2738 3890 388715148 388713985 0.000000e+00 1807.0
36 TraesCS6B01G140500 chrUn 88.202 178 8 3 2635 2799 388715305 388715128 2.770000e-47 200.0
37 TraesCS6B01G140500 chr5B 79.825 1031 155 27 2782 3792 261675472 261674475 0.000000e+00 702.0
38 TraesCS6B01G140500 chr5B 92.708 96 2 5 3891 3982 554776750 554776656 2.850000e-27 134.0
39 TraesCS6B01G140500 chr7D 98.864 88 1 0 2430 2517 165657947 165657860 1.690000e-34 158.0
40 TraesCS6B01G140500 chr1A 97.802 91 1 1 2428 2518 27361940 27362029 6.090000e-34 156.0
41 TraesCS6B01G140500 chr1A 94.565 92 4 1 3887 3977 527084022 527083931 1.700000e-29 141.0
42 TraesCS6B01G140500 chr3D 84.076 157 22 1 2533 2689 187220266 187220113 1.020000e-31 148.0
43 TraesCS6B01G140500 chr3D 89.815 108 6 5 3878 3984 302930484 302930381 2.850000e-27 134.0
44 TraesCS6B01G140500 chr3D 86.441 59 8 0 382 440 405441974 405442032 1.050000e-06 65.8
45 TraesCS6B01G140500 chr5D 97.561 82 2 0 2435 2516 294637753 294637672 1.700000e-29 141.0
46 TraesCS6B01G140500 chr5D 92.857 84 5 1 2437 2519 294637677 294637760 2.220000e-23 121.0
47 TraesCS6B01G140500 chr5A 93.478 92 5 1 3887 3977 560883484 560883393 7.930000e-28 135.0
48 TraesCS6B01G140500 chr5A 95.122 82 4 0 2435 2516 387927543 387927462 3.690000e-26 130.0
49 TraesCS6B01G140500 chr2D 93.827 81 4 1 2435 2514 579535336 579535256 2.220000e-23 121.0
50 TraesCS6B01G140500 chr3B 100.000 32 0 0 253 284 416509443 416509412 4.910000e-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 TraesCS6B01G140500 chr6B 139882785 139887327 4542 False 8390.000000 8390 100.000000 1 4543 1 chr6B.!!$F1 4542
1 TraesCS6B01G140500 chr6B 140365545 140368254 2709 True 1808.500000 2800 89.352000 1 2688 2 chr6B.!!$R5 2687
2 TraesCS6B01G140500 chr6B 140332066 140333532 1466 True 1469.000000 1469 85.057000 966 2433 1 chr6B.!!$R2 1467
3 TraesCS6B01G140500 chr6B 140093783 140097446 3663 True 924.500000 1304 81.084500 968 3849 2 chr6B.!!$R4 2881
4 TraesCS6B01G140500 chr6D 65050680 65055216 4536 False 7878.000000 7878 97.999000 2 4543 1 chr6D.!!$F2 4541
5 TraesCS6B01G140500 chr6D 65357456 65363301 5845 True 1422.000000 4676 89.831250 127 4388 4 chr6D.!!$R6 4261
6 TraesCS6B01G140500 chr6D 63815949 63817296 1347 True 1155.000000 1155 82.476000 999 2352 1 chr6D.!!$R1 1353
7 TraesCS6B01G140500 chr6D 65341084 65343459 2375 True 998.000000 1491 84.011000 957 3836 2 chr6D.!!$R5 2879
8 TraesCS6B01G140500 chr6D 65092690 65095181 2491 True 970.000000 1400 81.138500 968 3849 2 chr6D.!!$R4 2881
9 TraesCS6B01G140500 chr6A 81190549 81191957 1408 True 1240.000000 1240 82.675000 999 2431 1 chr6A.!!$R1 1432
10 TraesCS6B01G140500 chr6A 83644506 83647054 2548 False 997.000000 1417 81.006000 957 3888 2 chr6A.!!$F4 2931
11 TraesCS6B01G140500 chr6A 83434036 83440399 6363 False 976.000000 2479 88.887167 1 4541 6 chr6A.!!$F2 4540
12 TraesCS6B01G140500 chr6A 83599394 83601640 2246 False 744.033333 1447 82.741667 831 3543 3 chr6A.!!$F3 2712
13 TraesCS6B01G140500 chrUn 388713985 388715305 1320 True 1003.500000 1807 91.526000 2635 3890 2 chrUn.!!$R1 1255
14 TraesCS6B01G140500 chr5B 261674475 261675472 997 True 702.000000 702 79.825000 2782 3792 1 chr5B.!!$R1 1010

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
133 135 0.439985 CACGACGAGCAACTTCCATG 59.560 55.000 0.00 0.0 0.0 3.66 F
380 382 1.000506 TCTGAGGCCAAAGACGTACAC 59.999 52.381 5.01 0.0 0.0 2.90 F
1911 3409 0.925558 TGGAATGGGGATGCAGCTTA 59.074 50.000 0.22 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 3148 1.684734 GTAGAGGCGGGTGAGGGAA 60.685 63.158 0.0 0.0 0.0 3.97 R
2180 3695 1.579698 CTCTCACATTCATCCCAGCG 58.420 55.000 0.0 0.0 0.0 5.18 R
3950 7305 8.252624 ACTCCCTCTGTAAAGAAATATAGGAC 57.747 38.462 0.0 0.0 0.0 3.85 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
133 135 0.439985 CACGACGAGCAACTTCCATG 59.560 55.000 0.00 0.00 0.00 3.66
380 382 1.000506 TCTGAGGCCAAAGACGTACAC 59.999 52.381 5.01 0.00 0.00 2.90
859 2273 5.092554 TCACAACACTAGTCAGACCAAAA 57.907 39.130 0.00 0.00 0.00 2.44
860 2274 5.492895 TCACAACACTAGTCAGACCAAAAA 58.507 37.500 0.00 0.00 0.00 1.94
1659 3148 2.498167 GACAACATCCTCAACTGTGCT 58.502 47.619 0.00 0.00 0.00 4.40
1707 3202 2.109799 CGATGGCGCTTCCCAGAT 59.890 61.111 7.64 0.00 38.50 2.90
1798 3296 1.092345 GGAAGTCGATGCCTTGCTCC 61.092 60.000 0.00 0.00 0.00 4.70
1911 3409 0.925558 TGGAATGGGGATGCAGCTTA 59.074 50.000 0.22 0.00 0.00 3.09
2097 3598 6.972901 GGGTAACTGCTTATTGTAATTTCTGC 59.027 38.462 0.00 0.00 0.00 4.26
2556 5345 5.589050 CGATGATACTAGATTCACGGGGATA 59.411 44.000 0.00 0.00 0.00 2.59
2588 5377 2.819550 ACGGGCTGAAGAACGTGT 59.180 55.556 0.00 0.00 38.24 4.49
3994 7349 5.104485 GGGAGTAACATAGTTCCTGGAATGT 60.104 44.000 13.07 10.23 34.11 2.71
4086 7444 3.241067 TGTTGTTGATCCGGTAGCTAC 57.759 47.619 15.88 15.88 0.00 3.58
4135 7493 4.083802 GCTGCGTTCAGAATTTGTAGTTCT 60.084 41.667 0.00 0.00 42.95 3.01
4309 7678 4.508124 GTCGAAACCAATAGCTATGGAGTG 59.492 45.833 21.77 11.28 40.56 3.51
4377 7758 3.062639 CACGTACCACATGAGCAGAATTC 59.937 47.826 0.00 0.00 0.00 2.17
4434 7815 2.047560 GACTACGGGTGTGTGGCC 60.048 66.667 0.00 0.00 0.00 5.36
4455 7837 1.811359 CGATAGAGGACCCCGTGTATC 59.189 57.143 0.00 0.00 39.76 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.350522 CTGCCTTCTGCTTCGTGTAAT 58.649 47.619 0.00 0.0 42.00 1.89
133 135 3.119280 GCTGACTACCTGACTCTTCTTCC 60.119 52.174 0.00 0.0 0.00 3.46
145 147 1.273267 TGACTCCCATGCTGACTACCT 60.273 52.381 0.00 0.0 0.00 3.08
380 382 4.800993 GGTGAGTGAGTTTCGTAGATCATG 59.199 45.833 0.00 0.0 35.04 3.07
621 2014 4.222588 GGGACCATCACATGAAAATTCCAA 59.777 41.667 0.00 0.0 0.00 3.53
859 2273 2.606519 TGGCTGTACGGGGCTCTT 60.607 61.111 3.34 0.0 0.00 2.85
860 2274 3.077556 CTGGCTGTACGGGGCTCT 61.078 66.667 3.34 0.0 0.00 4.09
1659 3148 1.684734 GTAGAGGCGGGTGAGGGAA 60.685 63.158 0.00 0.0 0.00 3.97
1707 3202 4.424566 GGCGAGTTGGCGGTCGTA 62.425 66.667 5.11 0.0 38.48 3.43
1911 3409 4.514441 GCATCCTCGACAATGATTTCATCT 59.486 41.667 6.48 0.0 35.10 2.90
2180 3695 1.579698 CTCTCACATTCATCCCAGCG 58.420 55.000 0.00 0.0 0.00 5.18
2556 5345 1.265905 GCCCGTGAAGTTCGTTGAAAT 59.734 47.619 0.00 0.0 0.00 2.17
3950 7305 8.252624 ACTCCCTCTGTAAAGAAATATAGGAC 57.747 38.462 0.00 0.0 0.00 3.85
3994 7349 5.348986 GGCGAGAATCAGTCAACTACATTA 58.651 41.667 0.00 0.0 33.17 1.90
4086 7444 0.525761 ATGTGTGGATTTTTCCGCCG 59.474 50.000 3.30 0.0 39.42 6.46
4135 7493 7.172875 CACAAGCATAATTTTGGGAAACAATGA 59.827 33.333 0.00 0.0 39.21 2.57
4309 7678 1.475403 TACTGTGAGCTCCAGTAGGC 58.525 55.000 27.45 7.5 42.83 3.93
4434 7815 0.179009 TACACGGGGTCCTCTATCGG 60.179 60.000 0.00 0.0 0.00 4.18
4455 7837 1.151668 CCAACAGCAAGAGTTCCTCG 58.848 55.000 0.00 0.0 35.36 4.63
4472 7854 6.214278 TCCTAAAGGATAGGGTTACAATCCA 58.786 40.000 11.41 0.0 41.44 3.41


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

AutoCloner maintained by Alex Coulton.