Multiple sequence alignment - TraesCS4B01G394200

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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 TraesCS4B01G394200 chr4B 100.000 3787 0 0 1 3787 668303073 668306859 0.000000e+00 6994.0
1 TraesCS4B01G394200 chr4B 97.158 2252 62 2 1537 3787 669428307 669430557 0.000000e+00 3803.0
2 TraesCS4B01G394200 chr4B 96.980 2252 66 2 1537 3787 669205695 669203445 0.000000e+00 3781.0
3 TraesCS4B01G394200 chr4B 96.847 2252 70 1 1537 3787 669394378 669392127 0.000000e+00 3764.0
4 TraesCS4B01G394200 chr4B 97.479 1547 36 1 1 1544 669215921 669214375 0.000000e+00 2638.0
5 TraesCS4B01G394200 chr4B 97.343 1543 40 1 1 1542 669064866 669066408 0.000000e+00 2621.0
6 TraesCS4B01G394200 chr4B 97.156 1547 40 2 1 1544 669409531 669411076 0.000000e+00 2610.0
7 TraesCS4B01G394200 chr4B 92.506 387 27 2 3370 3754 524147647 524147261 1.540000e-153 553.0
8 TraesCS4B01G394200 chr6B 96.484 1934 66 2 870 2802 55638959 55637027 0.000000e+00 3193.0
9 TraesCS4B01G394200 chr6B 94.724 417 21 1 3370 3786 55636858 55636443 0.000000e+00 647.0
10 TraesCS4B01G394200 chr2D 97.191 1780 46 4 1024 2802 82249542 82247766 0.000000e+00 3007.0
11 TraesCS4B01G394200 chr4D 97.135 1780 47 4 1024 2802 502619827 502621603 0.000000e+00 3001.0
12 TraesCS4B01G394200 chr4D 95.174 1036 48 2 1 1034 505475418 505474383 0.000000e+00 1635.0
13 TraesCS4B01G394200 chrUn 97.022 1780 49 4 1024 2802 134332682 134330906 0.000000e+00 2990.0
14 TraesCS4B01G394200 chrUn 97.537 1543 37 1 1 1542 291296780 291295238 0.000000e+00 2638.0
15 TraesCS4B01G394200 chr3D 96.966 1780 50 4 1024 2802 579345692 579347468 0.000000e+00 2985.0
16 TraesCS4B01G394200 chr3B 96.740 1779 56 2 1024 2802 728852370 728854146 0.000000e+00 2963.0
17 TraesCS4B01G394200 chr3B 91.885 382 29 2 3370 3749 685955662 685955281 2.000000e-147 532.0
18 TraesCS4B01G394200 chr3B 95.833 48 2 0 3739 3786 685954590 685954543 1.130000e-10 78.7
19 TraesCS4B01G394200 chr1D 95.279 1038 45 3 1 1034 26581532 26582569 0.000000e+00 1642.0
20 TraesCS4B01G394200 chr1D 95.178 1037 47 3 1 1034 46658521 46659557 0.000000e+00 1635.0
21 TraesCS4B01G394200 chr1D 94.986 1037 49 3 1 1034 288336247 288335211 0.000000e+00 1624.0
22 TraesCS4B01G394200 chr5D 95.077 1036 49 2 1 1034 449314540 449313505 0.000000e+00 1629.0
23 TraesCS4B01G394200 chr4A 92.782 762 55 0 3025 3786 687958390 687957629 0.000000e+00 1103.0
24 TraesCS4B01G394200 chr4A 95.652 184 6 2 2801 2983 687958576 687958394 1.030000e-75 294.0
25 TraesCS4B01G394200 chr1B 92.889 675 47 1 3112 3786 51343939 51343266 0.000000e+00 979.0
26 TraesCS4B01G394200 chr1B 89.511 696 51 8 3112 3786 51365964 51365270 0.000000e+00 861.0
27 TraesCS4B01G394200 chr2B 93.282 387 24 2 3370 3754 651657962 651657576 1.530000e-158 569.0
28 TraesCS4B01G394200 chr2B 100.000 31 0 0 3756 3786 651656889 651656859 1.470000e-04 58.4


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 TraesCS4B01G394200 chr4B 668303073 668306859 3786 False 6994.00 6994 100.000 1 3787 1 chr4B.!!$F1 3786
1 TraesCS4B01G394200 chr4B 669428307 669430557 2250 False 3803.00 3803 97.158 1537 3787 1 chr4B.!!$F4 2250
2 TraesCS4B01G394200 chr4B 669203445 669205695 2250 True 3781.00 3781 96.980 1537 3787 1 chr4B.!!$R2 2250
3 TraesCS4B01G394200 chr4B 669392127 669394378 2251 True 3764.00 3764 96.847 1537 3787 1 chr4B.!!$R4 2250
4 TraesCS4B01G394200 chr4B 669214375 669215921 1546 True 2638.00 2638 97.479 1 1544 1 chr4B.!!$R3 1543
5 TraesCS4B01G394200 chr4B 669064866 669066408 1542 False 2621.00 2621 97.343 1 1542 1 chr4B.!!$F2 1541
6 TraesCS4B01G394200 chr4B 669409531 669411076 1545 False 2610.00 2610 97.156 1 1544 1 chr4B.!!$F3 1543
7 TraesCS4B01G394200 chr6B 55636443 55638959 2516 True 1920.00 3193 95.604 870 3786 2 chr6B.!!$R1 2916
8 TraesCS4B01G394200 chr2D 82247766 82249542 1776 True 3007.00 3007 97.191 1024 2802 1 chr2D.!!$R1 1778
9 TraesCS4B01G394200 chr4D 502619827 502621603 1776 False 3001.00 3001 97.135 1024 2802 1 chr4D.!!$F1 1778
10 TraesCS4B01G394200 chr4D 505474383 505475418 1035 True 1635.00 1635 95.174 1 1034 1 chr4D.!!$R1 1033
11 TraesCS4B01G394200 chrUn 134330906 134332682 1776 True 2990.00 2990 97.022 1024 2802 1 chrUn.!!$R1 1778
12 TraesCS4B01G394200 chrUn 291295238 291296780 1542 True 2638.00 2638 97.537 1 1542 1 chrUn.!!$R2 1541
13 TraesCS4B01G394200 chr3D 579345692 579347468 1776 False 2985.00 2985 96.966 1024 2802 1 chr3D.!!$F1 1778
14 TraesCS4B01G394200 chr3B 728852370 728854146 1776 False 2963.00 2963 96.740 1024 2802 1 chr3B.!!$F1 1778
15 TraesCS4B01G394200 chr3B 685954543 685955662 1119 True 305.35 532 93.859 3370 3786 2 chr3B.!!$R1 416
16 TraesCS4B01G394200 chr1D 26581532 26582569 1037 False 1642.00 1642 95.279 1 1034 1 chr1D.!!$F1 1033
17 TraesCS4B01G394200 chr1D 46658521 46659557 1036 False 1635.00 1635 95.178 1 1034 1 chr1D.!!$F2 1033
18 TraesCS4B01G394200 chr1D 288335211 288336247 1036 True 1624.00 1624 94.986 1 1034 1 chr1D.!!$R1 1033
19 TraesCS4B01G394200 chr5D 449313505 449314540 1035 True 1629.00 1629 95.077 1 1034 1 chr5D.!!$R1 1033
20 TraesCS4B01G394200 chr4A 687957629 687958576 947 True 698.50 1103 94.217 2801 3786 2 chr4A.!!$R1 985
21 TraesCS4B01G394200 chr1B 51343266 51343939 673 True 979.00 979 92.889 3112 3786 1 chr1B.!!$R1 674
22 TraesCS4B01G394200 chr1B 51365270 51365964 694 True 861.00 861 89.511 3112 3786 1 chr1B.!!$R2 674
23 TraesCS4B01G394200 chr2B 651656859 651657962 1103 True 313.70 569 96.641 3370 3786 2 chr2B.!!$R1 416

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
210 212 2.482490 GGTCGTCACTTGTACCACTTGT 60.482 50.000 0.00 0.0 32.04 3.16 F
1158 1166 0.523072 CACCAAGGCATTTCGTGGAG 59.477 55.000 4.01 0.0 38.32 3.86 F
2058 2066 1.926510 CGACGCTGATCAACAATGCTA 59.073 47.619 0.00 0.0 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2192 2.698797 GAGGAATCCGGGATAGACAACA 59.301 50.00 10.54 0.0 0.00 3.33 R
2406 2415 3.692101 ACCGCCGAAAATTGAATGACATA 59.308 39.13 0.00 0.0 0.00 2.29 R
3240 3253 0.030235 TATGACGACTTCGATGGCCG 59.970 55.00 5.47 11.7 43.02 6.13 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
85 87 6.105397 TCGGTAAACTCCAATCAGTACTTT 57.895 37.500 0.00 0.00 0.00 2.66
181 183 6.980051 ACTTTTTATACGCCTAAGTCAAGG 57.020 37.500 0.00 0.00 39.87 3.61
210 212 2.482490 GGTCGTCACTTGTACCACTTGT 60.482 50.000 0.00 0.00 32.04 3.16
251 253 6.146510 TGTTCGAGAAAATTGCAGTTACGTAT 59.853 34.615 0.00 0.00 0.00 3.06
336 338 4.022935 CCCCCGACATTAATGATGATGTTG 60.023 45.833 22.16 3.83 36.04 3.33
583 588 3.906720 TTCCCTCGGTCCTTTTATCTG 57.093 47.619 0.00 0.00 0.00 2.90
625 630 9.500785 TGTATTCACACAGAACAATCATTTCTA 57.499 29.630 0.00 0.00 39.49 2.10
668 673 3.612004 GCTTGTCAACTCTACGTGTAGCT 60.612 47.826 0.00 0.00 33.32 3.32
778 786 7.642669 AGATTGAACTGTAAATATGGCAATCG 58.357 34.615 0.00 0.00 42.91 3.34
961 969 3.627395 TCGACATCCTAATTGCCAAGT 57.373 42.857 0.00 0.00 0.00 3.16
1029 1037 1.215912 CATTGGAAGCAATGCGCCA 59.784 52.632 16.61 16.61 44.04 5.69
1158 1166 0.523072 CACCAAGGCATTTCGTGGAG 59.477 55.000 4.01 0.00 38.32 3.86
1974 1982 7.147655 TGGTTGGAGGAAAACATTATTTTGACA 60.148 33.333 0.00 0.00 0.00 3.58
2058 2066 1.926510 CGACGCTGATCAACAATGCTA 59.073 47.619 0.00 0.00 0.00 3.49
2066 2074 6.238184 CGCTGATCAACAATGCTATTCTACAA 60.238 38.462 0.00 0.00 0.00 2.41
2183 2192 7.889073 TGTTGACCTTCTGTAGTATCTACTTCT 59.111 37.037 8.13 0.00 37.73 2.85
2221 2230 3.959293 TCCTCGTATGGTCTACTTGTGA 58.041 45.455 0.00 0.00 0.00 3.58
2440 2449 9.635520 TCAATTTTCGGCGGTAATTTAATAAAA 57.364 25.926 7.21 2.54 0.00 1.52
2447 2456 9.635520 TCGGCGGTAATTTAATAAAAATTTCAA 57.364 25.926 7.21 0.00 32.64 2.69
2532 2542 5.537674 TCGGGTTTCTTAGTTCTACAAGAGT 59.462 40.000 0.00 0.00 32.62 3.24
2649 2659 2.031157 CCACTTCAGCGTTTAAAGGTGG 60.031 50.000 9.83 4.57 37.66 4.61
3036 3049 9.407380 AGTAATAAGAACAAATGTATGATGGCA 57.593 29.630 0.00 0.00 0.00 4.92
3123 3136 7.254795 GGCACCTACTACATATGTTGTCAATTC 60.255 40.741 23.30 12.53 39.87 2.17
3199 3212 3.255725 CTGTCCAGTTAATTAACGCCGA 58.744 45.455 19.92 14.24 40.96 5.54
3205 3218 3.305094 CAGTTAATTAACGCCGACACGAT 59.695 43.478 19.92 0.00 40.96 3.73
3248 3261 1.949133 CATACACGACCGGCCATCG 60.949 63.158 21.62 21.62 45.17 3.84
3449 3464 0.465460 TGCTCAAAAAGACGGGCAGT 60.465 50.000 0.00 0.00 0.00 4.40
3535 3571 3.130633 TCGCACCCAAAATCATATCTCG 58.869 45.455 0.00 0.00 0.00 4.04
3646 3682 2.854522 GGTTCCCGATCAGTGTTGG 58.145 57.895 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.810031 CAAATGGACCCGCCGTCTAG 60.810 60.000 0.00 0.00 41.64 2.43
181 183 1.672356 AAGTGACGACCAGCATGCC 60.672 57.895 15.66 0.00 31.97 4.40
210 212 5.525745 TCTCGAACAAATTTTCAGTGCACTA 59.474 36.000 21.20 3.85 0.00 2.74
251 253 3.317455 TCCCTCCGGTTTAGCTGTATA 57.683 47.619 0.00 0.00 0.00 1.47
284 286 4.036518 AGAATGTGCTCTCCCTCATAGTT 58.963 43.478 0.00 0.00 0.00 2.24
625 630 8.034804 ACAAGCAAAAAGAAAACACACTCTAAT 58.965 29.630 0.00 0.00 0.00 1.73
629 634 5.633182 TGACAAGCAAAAAGAAAACACACTC 59.367 36.000 0.00 0.00 0.00 3.51
1974 1982 3.427098 CGTGATTGAGCATGAAACTGCAT 60.427 43.478 0.00 0.00 44.77 3.96
2058 2066 8.798975 TCATATCTAGGAAAGGGTTGTAGAAT 57.201 34.615 0.00 0.00 0.00 2.40
2066 2074 6.386927 TGAACACATCATATCTAGGAAAGGGT 59.613 38.462 0.00 0.00 31.50 4.34
2127 2135 9.129209 GTTAATTGCTATCAGGAAAGAAAACAC 57.871 33.333 0.00 0.00 0.00 3.32
2183 2192 2.698797 GAGGAATCCGGGATAGACAACA 59.301 50.000 10.54 0.00 0.00 3.33
2221 2230 4.235372 ACCCTTCTCCTCATCCGATTTAT 58.765 43.478 0.00 0.00 0.00 1.40
2406 2415 3.692101 ACCGCCGAAAATTGAATGACATA 59.308 39.130 0.00 0.00 0.00 2.29
2649 2659 8.522830 TGGATCCTAGAAACAATGAAACAAATC 58.477 33.333 14.23 0.00 0.00 2.17
3123 3136 3.983344 GCCAACAAAAGCAGTCAGTATTG 59.017 43.478 0.00 0.00 0.00 1.90
3128 3141 5.824904 ATATAGCCAACAAAAGCAGTCAG 57.175 39.130 0.00 0.00 0.00 3.51
3199 3212 1.548719 TGCTAGGTGCTACAATCGTGT 59.451 47.619 0.00 0.00 43.37 4.49
3205 3218 1.616865 ACGAGTTGCTAGGTGCTACAA 59.383 47.619 0.00 0.00 46.97 2.41
3240 3253 0.030235 TATGACGACTTCGATGGCCG 59.970 55.000 5.47 11.70 43.02 6.13
3248 3261 1.751924 AGCCAGTCCTATGACGACTTC 59.248 52.381 0.00 0.00 46.51 3.01
3324 3337 0.669318 AACCGACAACGTGATGCGAT 60.669 50.000 0.00 0.00 44.77 4.58
3535 3571 2.223665 CGGTTGAATCCTCGTAGGGTAC 60.224 54.545 1.76 0.00 35.59 3.34
3615 3651 1.313091 GGGAACCGGAATGTGAAGCC 61.313 60.000 9.46 0.00 40.86 4.35
3646 3682 4.658063 TCTCCCTTATCCTCTCTCGATTC 58.342 47.826 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.