Multiple sequence alignment - TraesCS6A01G032400

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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 TraesCS6A01G032400 chr6A 100.000 3527 0 0 1 3527 15954413 15950887 0.000000e+00 6514
1 TraesCS6A01G032400 chr6A 91.763 2246 123 20 798 3042 16100366 16098182 0.000000e+00 3066
2 TraesCS6A01G032400 chr6A 85.303 1735 243 8 799 2526 16400901 16399172 0.000000e+00 1781
3 TraesCS6A01G032400 chr6A 85.385 520 43 17 3033 3527 16088875 16088364 3.140000e-140 508
4 TraesCS6A01G032400 chr6A 85.756 344 29 9 478 802 16100740 16100398 2.610000e-91 346
5 TraesCS6A01G032400 chr6D 92.787 3577 183 34 1 3527 15386175 15382624 0.000000e+00 5107
6 TraesCS6A01G032400 chr6D 94.821 1931 77 12 806 2733 15419808 15417898 0.000000e+00 2990
7 TraesCS6A01G032400 chr6D 85.418 1735 241 8 799 2526 15799469 15797740 0.000000e+00 1792
8 TraesCS6A01G032400 chr6D 85.672 1689 228 11 820 2500 15809028 15807346 0.000000e+00 1766
9 TraesCS6A01G032400 chr6D 81.726 197 18 9 2837 3033 15417887 15417709 7.890000e-32 148
10 TraesCS6A01G032400 chr6B 93.472 2160 128 12 653 2809 27124735 27122586 0.000000e+00 3195
11 TraesCS6A01G032400 chr6B 93.022 1863 113 8 797 2657 27171441 27169594 0.000000e+00 2704
12 TraesCS6A01G032400 chr6B 89.549 1598 147 17 1071 2655 27181753 27180163 0.000000e+00 2008
13 TraesCS6A01G032400 chr6B 88.156 667 57 11 1 652 27125494 27124835 0.000000e+00 774
14 TraesCS6A01G032400 chr6B 87.380 523 43 14 3026 3527 27122461 27121941 2.360000e-161 579
15 TraesCS6A01G032400 chr6B 80.595 706 62 39 2848 3527 27169480 27168824 3.190000e-130 475
16 TraesCS6A01G032400 chr6B 85.714 105 7 3 2841 2945 27122580 27122484 1.730000e-18 104
17 TraesCS6A01G032400 chr5B 77.215 237 36 12 63 287 471384474 471384704 4.780000e-24 122


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 TraesCS6A01G032400 chr6A 15950887 15954413 3526 True 6514.0 6514 100.0000 1 3527 1 chr6A.!!$R1 3526
1 TraesCS6A01G032400 chr6A 16399172 16400901 1729 True 1781.0 1781 85.3030 799 2526 1 chr6A.!!$R3 1727
2 TraesCS6A01G032400 chr6A 16098182 16100740 2558 True 1706.0 3066 88.7595 478 3042 2 chr6A.!!$R4 2564
3 TraesCS6A01G032400 chr6A 16088364 16088875 511 True 508.0 508 85.3850 3033 3527 1 chr6A.!!$R2 494
4 TraesCS6A01G032400 chr6D 15382624 15386175 3551 True 5107.0 5107 92.7870 1 3527 1 chr6D.!!$R1 3526
5 TraesCS6A01G032400 chr6D 15797740 15799469 1729 True 1792.0 1792 85.4180 799 2526 1 chr6D.!!$R2 1727
6 TraesCS6A01G032400 chr6D 15807346 15809028 1682 True 1766.0 1766 85.6720 820 2500 1 chr6D.!!$R3 1680
7 TraesCS6A01G032400 chr6D 15417709 15419808 2099 True 1569.0 2990 88.2735 806 3033 2 chr6D.!!$R4 2227
8 TraesCS6A01G032400 chr6B 27180163 27181753 1590 True 2008.0 2008 89.5490 1071 2655 1 chr6B.!!$R1 1584
9 TraesCS6A01G032400 chr6B 27168824 27171441 2617 True 1589.5 2704 86.8085 797 3527 2 chr6B.!!$R3 2730
10 TraesCS6A01G032400 chr6B 27121941 27125494 3553 True 1163.0 3195 88.6805 1 3527 4 chr6B.!!$R2 3526

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
713 859 0.389025 GTTCAACCAAACAGCCCTGG 59.611 55.0 0.00 0.0 38.77 4.45 F
1149 1345 2.291800 CCACCTTGGATGGATGTCCTTT 60.292 50.0 0.09 0.0 40.96 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1882 1.376037 GAGGTTCCTCAGGTTGCCG 60.376 63.158 13.31 0.0 33.58 5.69 R
3126 3337 0.385473 CACCGCCATCGTTGTTGTTC 60.385 55.000 0.00 0.0 0.00 3.18 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
60 63 7.944729 ATGCTCTGGTATGAACAGTAAAATT 57.055 32.000 0.00 0.00 37.25 1.82
147 150 4.978580 GGAGTTCTTGCAAAGTTTCATCAC 59.021 41.667 0.00 0.00 46.34 3.06
164 175 4.394610 TCATCACGTAATCACATTTGTGGG 59.605 41.667 10.60 0.00 45.65 4.61
168 179 4.215399 CACGTAATCACATTTGTGGGAGTT 59.785 41.667 10.60 4.46 45.65 3.01
169 180 4.825085 ACGTAATCACATTTGTGGGAGTTT 59.175 37.500 10.60 1.45 45.65 2.66
207 222 9.744468 GAACTCCTAAATGCTTTTGAAAGTAAA 57.256 29.630 7.78 0.00 38.28 2.01
217 232 8.130307 TGCTTTTGAAAGTAAAATTTCAGAGC 57.870 30.769 22.47 22.47 46.70 4.09
218 233 8.130307 GCTTTTGAAAGTAAAATTTCAGAGCA 57.870 30.769 23.37 5.29 46.70 4.26
219 234 8.768019 GCTTTTGAAAGTAAAATTTCAGAGCAT 58.232 29.630 23.37 0.00 46.70 3.79
253 270 4.746535 TGCCACTAATTCCACGAATCTA 57.253 40.909 0.00 0.00 30.29 1.98
262 279 9.193133 ACTAATTCCACGAATCTAATTACATCG 57.807 33.333 0.00 7.77 39.30 3.84
279 296 2.473530 TCGTGAAACTTTGCAAGCAG 57.526 45.000 0.00 0.00 31.75 4.24
320 337 9.807649 ACTGCTTATCACCATTTTATTGAATTC 57.192 29.630 0.00 0.00 0.00 2.17
321 338 9.806203 CTGCTTATCACCATTTTATTGAATTCA 57.194 29.630 3.38 3.38 0.00 2.57
336 353 6.582677 TTGAATTCAATTTACCATCCGTGT 57.417 33.333 16.91 0.00 0.00 4.49
337 354 6.582677 TGAATTCAATTTACCATCCGTGTT 57.417 33.333 5.45 0.00 0.00 3.32
340 357 4.022413 TCAATTTACCATCCGTGTTCCA 57.978 40.909 0.00 0.00 0.00 3.53
359 376 5.614923 TCCAATTAAATGCGTTCGAAAGA 57.385 34.783 15.53 0.78 39.20 2.52
421 448 5.221783 ACTCCACGTTTCCTTTACTTGGTAT 60.222 40.000 0.00 0.00 36.57 2.73
422 449 4.998672 TCCACGTTTCCTTTACTTGGTATG 59.001 41.667 0.00 0.00 36.57 2.39
432 459 5.627780 CCTTTACTTGGTATGTTTGAAACGC 59.372 40.000 3.37 0.00 0.00 4.84
710 856 3.572255 TGATAAGTTCAACCAAACAGCCC 59.428 43.478 0.00 0.00 0.00 5.19
711 857 2.159179 AAGTTCAACCAAACAGCCCT 57.841 45.000 0.00 0.00 0.00 5.19
712 858 1.402787 AGTTCAACCAAACAGCCCTG 58.597 50.000 0.00 0.00 0.00 4.45
713 859 0.389025 GTTCAACCAAACAGCCCTGG 59.611 55.000 0.00 0.00 38.77 4.45
1149 1345 2.291800 CCACCTTGGATGGATGTCCTTT 60.292 50.000 0.09 0.00 40.96 3.11
1686 1882 2.657066 GGGACAGGACCTTCCCGAC 61.657 68.421 19.83 4.67 42.35 4.79
2465 2662 0.178767 AGCATATCTGAGCGTGGCAA 59.821 50.000 0.00 0.00 35.48 4.52
2481 2678 1.079875 GCAAACGCAATGCCATCCTG 61.080 55.000 0.00 0.00 37.85 3.86
2526 2723 4.021650 ACGCCACAACACGTGTAG 57.978 55.556 23.69 14.64 44.78 2.74
2671 2881 6.628398 GCGCTTATCTAGGCCTTAGTCAATAT 60.628 42.308 12.58 0.00 0.00 1.28
2672 2882 7.416438 GCGCTTATCTAGGCCTTAGTCAATATA 60.416 40.741 12.58 0.00 0.00 0.86
2673 2883 8.634444 CGCTTATCTAGGCCTTAGTCAATATAT 58.366 37.037 12.58 0.00 0.00 0.86
2857 3067 7.599054 CATATATGCCATGCGATTAATTTCG 57.401 36.000 0.00 0.00 41.99 3.46
2890 3100 6.757947 TGTAAGGGCTTGTAATATGTTACGAC 59.242 38.462 7.72 0.00 42.50 4.34
2891 3101 5.609533 AGGGCTTGTAATATGTTACGACT 57.390 39.130 7.72 0.00 42.50 4.18
2892 3102 5.985911 AGGGCTTGTAATATGTTACGACTT 58.014 37.500 7.72 0.00 42.50 3.01
2893 3103 7.116075 AGGGCTTGTAATATGTTACGACTTA 57.884 36.000 7.72 0.00 42.50 2.24
2894 3104 6.982724 AGGGCTTGTAATATGTTACGACTTAC 59.017 38.462 7.72 0.00 42.50 2.34
2895 3105 6.074676 GGGCTTGTAATATGTTACGACTTACG 60.075 42.308 7.72 0.00 42.50 3.18
2896 3106 6.692681 GGCTTGTAATATGTTACGACTTACGA 59.307 38.462 7.72 0.00 42.50 3.43
2987 3197 0.028242 CACGCCAAAGTACAAACGCA 59.972 50.000 0.00 0.00 0.00 5.24
2989 3199 1.326576 CGCCAAAGTACAAACGCATG 58.673 50.000 0.00 0.00 0.00 4.06
3080 3291 1.204062 CGTGATGCGAACTTGCGTT 59.796 52.632 0.00 0.00 44.77 4.84
3114 3325 6.153680 ACACCAAAGTACAGAACCATTCAAAA 59.846 34.615 0.00 0.00 0.00 2.44
3115 3326 6.697019 CACCAAAGTACAGAACCATTCAAAAG 59.303 38.462 0.00 0.00 0.00 2.27
3126 3337 3.941483 ACCATTCAAAAGGCGACTCTATG 59.059 43.478 0.00 0.00 42.68 2.23
3256 3477 9.616156 TCTAACCAAGTCAATAAAGTTGTTGTA 57.384 29.630 1.20 0.00 32.07 2.41
3299 3520 3.633986 AGTTTGCCAAAAGAACAGGAGAG 59.366 43.478 0.00 0.00 0.00 3.20
3303 3525 4.277476 TGCCAAAAGAACAGGAGAGAAAA 58.723 39.130 0.00 0.00 0.00 2.29
3304 3526 4.895297 TGCCAAAAGAACAGGAGAGAAAAT 59.105 37.500 0.00 0.00 0.00 1.82
3343 3565 4.874396 GTGGTCCGAATTTCTACCTTTAGG 59.126 45.833 15.01 0.00 42.17 2.69
3403 3625 1.154357 TCGATCGACACGTGGTTCG 60.154 57.895 21.57 20.23 46.00 3.95
3439 3661 7.149973 ACTGTTTACTAGCTATTTTGACGACA 58.850 34.615 0.00 0.00 0.00 4.35
3442 3664 8.995220 TGTTTACTAGCTATTTTGACGACAAAT 58.005 29.630 13.54 7.09 43.99 2.32
3446 3668 8.997621 ACTAGCTATTTTGACGACAAATAAGA 57.002 30.769 13.54 0.00 43.99 2.10
3447 3669 8.870879 ACTAGCTATTTTGACGACAAATAAGAC 58.129 33.333 13.54 9.86 43.99 3.01
3448 3670 6.762108 AGCTATTTTGACGACAAATAAGACG 58.238 36.000 13.54 0.00 43.99 4.18
3449 3671 6.367969 AGCTATTTTGACGACAAATAAGACGT 59.632 34.615 13.54 0.00 43.99 4.34
3452 3688 5.721876 TTTGACGACAAATAAGACGTGTT 57.278 34.783 8.97 2.58 40.47 3.32
3457 3693 3.428870 CGACAAATAAGACGTGTTGCTCT 59.571 43.478 8.42 0.00 0.00 4.09
3476 3712 5.481824 TGCTCTGAGATTCTTAACCTTGAGA 59.518 40.000 9.28 0.00 0.00 3.27
3485 3721 6.867662 TTCTTAACCTTGAGAAGCTCTTTG 57.132 37.500 0.00 0.00 30.50 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.176680 AGCATTTGAGCTCGATCCGT 59.823 50.000 9.64 0.00 42.18 4.69
114 117 4.998671 TGCAAGAACTCCAAACATTTCA 57.001 36.364 0.00 0.00 0.00 2.69
129 132 5.743026 TTACGTGATGAAACTTTGCAAGA 57.257 34.783 0.00 0.00 0.00 3.02
179 190 8.011844 ACTTTCAAAAGCATTTAGGAGTTCTT 57.988 30.769 2.43 0.00 37.28 2.52
240 257 7.207383 TCACGATGTAATTAGATTCGTGGAAT 58.793 34.615 27.17 0.00 46.08 3.01
253 270 6.991485 CTTGCAAAGTTTCACGATGTAATT 57.009 33.333 0.00 0.00 39.70 1.40
290 307 9.461312 TCAATAAAATGGTGATAAGCAGTAAGT 57.539 29.630 0.00 0.00 0.00 2.24
295 312 9.806203 TGAATTCAATAAAATGGTGATAAGCAG 57.194 29.630 5.45 0.00 0.00 4.24
320 337 4.775058 TTGGAACACGGATGGTAAATTG 57.225 40.909 0.00 0.00 39.29 2.32
321 338 5.993748 AATTGGAACACGGATGGTAAATT 57.006 34.783 0.00 0.00 39.29 1.82
322 339 7.469537 TTTAATTGGAACACGGATGGTAAAT 57.530 32.000 0.00 0.00 39.29 1.40
323 340 6.896021 TTTAATTGGAACACGGATGGTAAA 57.104 33.333 0.00 0.00 39.29 2.01
324 341 6.626181 GCATTTAATTGGAACACGGATGGTAA 60.626 38.462 0.00 0.00 39.29 2.85
336 353 6.003234 TCTTTCGAACGCATTTAATTGGAA 57.997 33.333 0.00 0.00 0.00 3.53
337 354 5.614923 TCTTTCGAACGCATTTAATTGGA 57.385 34.783 0.00 0.00 0.00 3.53
421 448 1.946768 CCCTCTCAAGCGTTTCAAACA 59.053 47.619 0.22 0.00 0.00 2.83
422 449 1.266989 CCCCTCTCAAGCGTTTCAAAC 59.733 52.381 0.00 0.00 0.00 2.93
432 459 1.065126 CAACCTTAGGCCCCTCTCAAG 60.065 57.143 0.00 0.00 0.00 3.02
533 561 6.375377 TGTACGCTACAATTTGTTTTCCATC 58.625 36.000 7.45 0.00 35.38 3.51
550 578 1.185618 TCCTGGAGCTGTTGTACGCT 61.186 55.000 0.00 0.00 39.61 5.07
710 856 4.238761 TCTGTCTCGTTGAACTTACCAG 57.761 45.455 0.00 0.00 0.00 4.00
711 857 4.556233 CATCTGTCTCGTTGAACTTACCA 58.444 43.478 0.00 0.00 0.00 3.25
712 858 3.927142 CCATCTGTCTCGTTGAACTTACC 59.073 47.826 0.00 0.00 0.00 2.85
713 859 4.621886 GTCCATCTGTCTCGTTGAACTTAC 59.378 45.833 0.00 0.00 0.00 2.34
1149 1345 0.179234 TGGAGACAACGCAGGTGAAA 59.821 50.000 0.61 0.00 37.44 2.69
1686 1882 1.376037 GAGGTTCCTCAGGTTGCCG 60.376 63.158 13.31 0.00 33.58 5.69
2526 2723 9.448294 CATTGAGGTAAGAAGATACTAACGTAC 57.552 37.037 0.00 0.00 0.00 3.67
2671 2881 5.082633 TGATACAAGCCCCAGGTACTATA 57.917 43.478 0.00 0.00 36.02 1.31
2672 2882 3.936461 TGATACAAGCCCCAGGTACTAT 58.064 45.455 0.00 0.00 36.02 2.12
2673 2883 3.408157 TGATACAAGCCCCAGGTACTA 57.592 47.619 0.00 0.00 36.02 1.82
2674 2884 2.263895 TGATACAAGCCCCAGGTACT 57.736 50.000 0.00 0.00 43.88 2.73
2851 3061 5.067954 AGCCCTTACAAGTACAACGAAATT 58.932 37.500 0.00 0.00 0.00 1.82
2857 3067 6.812879 ATTACAAGCCCTTACAAGTACAAC 57.187 37.500 0.00 0.00 0.00 3.32
2890 3100 7.864882 TGCTCTCATATTGATCTTTCTCGTAAG 59.135 37.037 0.00 0.00 0.00 2.34
2891 3101 7.716612 TGCTCTCATATTGATCTTTCTCGTAA 58.283 34.615 0.00 0.00 0.00 3.18
2892 3102 7.277174 TGCTCTCATATTGATCTTTCTCGTA 57.723 36.000 0.00 0.00 0.00 3.43
2893 3103 6.154203 TGCTCTCATATTGATCTTTCTCGT 57.846 37.500 0.00 0.00 0.00 4.18
2894 3104 7.360185 CCAATGCTCTCATATTGATCTTTCTCG 60.360 40.741 0.00 0.00 36.61 4.04
2895 3105 7.444792 ACCAATGCTCTCATATTGATCTTTCTC 59.555 37.037 0.00 0.00 36.61 2.87
2896 3106 7.288560 ACCAATGCTCTCATATTGATCTTTCT 58.711 34.615 0.00 0.00 36.61 2.52
2953 3163 1.137513 GCGTGCAAGAAGTTCGTACT 58.862 50.000 2.99 0.00 35.68 2.73
3077 3288 2.943033 ACTTTGGTGTGGAAGAAGAACG 59.057 45.455 0.00 0.00 0.00 3.95
3080 3291 4.407621 TCTGTACTTTGGTGTGGAAGAAGA 59.592 41.667 0.00 0.00 0.00 2.87
3114 3325 3.326747 GTTGTTGTTCATAGAGTCGCCT 58.673 45.455 0.00 0.00 0.00 5.52
3115 3326 2.092211 CGTTGTTGTTCATAGAGTCGCC 59.908 50.000 0.00 0.00 0.00 5.54
3126 3337 0.385473 CACCGCCATCGTTGTTGTTC 60.385 55.000 0.00 0.00 0.00 3.18
3149 3365 2.159282 AGTACTCCGTACGCTTTCATGG 60.159 50.000 10.49 0.00 43.05 3.66
3272 3493 3.506810 TGTTCTTTTGGCAAACTTGACG 58.493 40.909 13.10 0.00 39.74 4.35
3299 3520 5.793457 CCACCGACTCGTTTGATTTATTTTC 59.207 40.000 0.00 0.00 0.00 2.29
3303 3525 3.930848 GACCACCGACTCGTTTGATTTAT 59.069 43.478 0.00 0.00 0.00 1.40
3304 3526 3.319755 GACCACCGACTCGTTTGATTTA 58.680 45.455 0.00 0.00 0.00 1.40
3343 3565 2.480419 ACTCTTTGCGTGCTGAATGTAC 59.520 45.455 0.00 0.00 0.00 2.90
3403 3625 5.127356 AGCTAGTAAACAGTCCTGTCCATAC 59.873 44.000 0.00 5.42 44.13 2.39
3406 3628 3.507411 AGCTAGTAAACAGTCCTGTCCA 58.493 45.455 0.00 0.00 44.13 4.02
3439 3661 4.883083 TCTCAGAGCAACACGTCTTATTT 58.117 39.130 0.00 0.00 0.00 1.40
3442 3664 4.218635 AGAATCTCAGAGCAACACGTCTTA 59.781 41.667 0.00 0.00 0.00 2.10
3444 3666 2.560542 AGAATCTCAGAGCAACACGTCT 59.439 45.455 0.00 0.00 0.00 4.18
3445 3667 2.953020 AGAATCTCAGAGCAACACGTC 58.047 47.619 0.00 0.00 0.00 4.34
3446 3668 3.393089 AAGAATCTCAGAGCAACACGT 57.607 42.857 0.00 0.00 0.00 4.49
3447 3669 4.092091 GGTTAAGAATCTCAGAGCAACACG 59.908 45.833 0.00 0.00 0.00 4.49
3448 3670 5.241662 AGGTTAAGAATCTCAGAGCAACAC 58.758 41.667 0.00 0.00 0.00 3.32
3449 3671 5.489792 AGGTTAAGAATCTCAGAGCAACA 57.510 39.130 0.00 0.00 0.00 3.33
3452 3688 5.481824 TCTCAAGGTTAAGAATCTCAGAGCA 59.518 40.000 0.00 0.00 0.00 4.26
3457 3693 6.212388 AGAGCTTCTCAAGGTTAAGAATCTCA 59.788 38.462 14.69 0.00 42.81 3.27
3485 3721 9.218359 GCCGAAAAGCTAGTAAACATAAAATAC 57.782 33.333 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.