Multiple sequence alignment - TraesCS4A01G206000

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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 TraesCS4A01G206000 chr4A 100.000 5144 0 0 1 5144 498989773 498984630 0.000000e+00 9500.0
1 TraesCS4A01G206000 chr4B 95.293 4865 154 26 1 4819 122301286 122296451 0.000000e+00 7646.0
2 TraesCS4A01G206000 chr4B 87.898 314 23 6 4841 5144 122296252 122295944 6.340000e-94 355.0
3 TraesCS4A01G206000 chr4B 100.000 29 0 0 4818 4846 122296288 122296260 3.000000e-03 54.7
4 TraesCS4A01G206000 chr4D 96.695 4176 124 9 1 4165 85176561 85172389 0.000000e+00 6935.0
5 TraesCS4A01G206000 chr4D 94.329 4267 212 17 120 4370 85263725 85259473 0.000000e+00 6512.0
6 TraesCS4A01G206000 chr4D 87.089 790 52 18 4402 5144 85166904 85166118 0.000000e+00 848.0
7 TraesCS4A01G206000 chr4D 86.456 790 57 20 4402 5144 84990223 84991009 0.000000e+00 821.0
8 TraesCS4A01G206000 chr4D 72.692 2329 564 63 1377 3674 84797506 84795219 0.000000e+00 712.0
9 TraesCS4A01G206000 chr4D 88.538 506 39 12 4531 5031 85259325 85258834 3.430000e-166 595.0
10 TraesCS4A01G206000 chr4D 95.028 181 8 1 4152 4332 85172369 85172190 3.030000e-72 283.0
11 TraesCS4A01G206000 chr4D 96.078 51 2 0 5094 5144 85258838 85258788 3.300000e-12 84.2
12 TraesCS4A01G206000 chr4D 100.000 42 0 0 4404 4445 85259411 85259370 1.540000e-10 78.7
13 TraesCS4A01G206000 chr3A 75.341 2640 574 67 1074 3676 36300277 36302876 0.000000e+00 1197.0
14 TraesCS4A01G206000 chr3A 79.245 159 28 4 3518 3675 36286067 36286221 7.040000e-19 106.0
15 TraesCS4A01G206000 chr3D 75.254 2558 558 62 1074 3590 26300877 26303400 0.000000e+00 1147.0
16 TraesCS4A01G206000 chrUn 74.832 2674 584 79 1073 3700 245875138 245872508 0.000000e+00 1127.0
17 TraesCS4A01G206000 chrUn 74.813 2680 586 78 1067 3700 260283775 260286411 0.000000e+00 1127.0
18 TraesCS4A01G206000 chr6D 74.235 2678 604 75 1067 3700 387397 390032 0.000000e+00 1044.0
19 TraesCS4A01G206000 chr6D 81.867 1114 176 15 3010 4102 473271868 473270760 0.000000e+00 915.0
20 TraesCS4A01G206000 chr3B 75.746 1641 362 34 2084 3708 44038657 44040277 0.000000e+00 793.0


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 TraesCS4A01G206000 chr4A 498984630 498989773 5143 True 9500.000000 9500 100.00000 1 5144 1 chr4A.!!$R1 5143
1 TraesCS4A01G206000 chr4B 122295944 122301286 5342 True 2685.233333 7646 94.39700 1 5144 3 chr4B.!!$R1 5143
2 TraesCS4A01G206000 chr4D 85172190 85176561 4371 True 3609.000000 6935 95.86150 1 4332 2 chr4D.!!$R3 4331
3 TraesCS4A01G206000 chr4D 85258788 85263725 4937 True 1817.475000 6512 94.73625 120 5144 4 chr4D.!!$R4 5024
4 TraesCS4A01G206000 chr4D 85166118 85166904 786 True 848.000000 848 87.08900 4402 5144 1 chr4D.!!$R2 742
5 TraesCS4A01G206000 chr4D 84990223 84991009 786 False 821.000000 821 86.45600 4402 5144 1 chr4D.!!$F1 742
6 TraesCS4A01G206000 chr4D 84795219 84797506 2287 True 712.000000 712 72.69200 1377 3674 1 chr4D.!!$R1 2297
7 TraesCS4A01G206000 chr3A 36300277 36302876 2599 False 1197.000000 1197 75.34100 1074 3676 1 chr3A.!!$F2 2602
8 TraesCS4A01G206000 chr3D 26300877 26303400 2523 False 1147.000000 1147 75.25400 1074 3590 1 chr3D.!!$F1 2516
9 TraesCS4A01G206000 chrUn 245872508 245875138 2630 True 1127.000000 1127 74.83200 1073 3700 1 chrUn.!!$R1 2627
10 TraesCS4A01G206000 chrUn 260283775 260286411 2636 False 1127.000000 1127 74.81300 1067 3700 1 chrUn.!!$F1 2633
11 TraesCS4A01G206000 chr6D 387397 390032 2635 False 1044.000000 1044 74.23500 1067 3700 1 chr6D.!!$F1 2633
12 TraesCS4A01G206000 chr6D 473270760 473271868 1108 True 915.000000 915 81.86700 3010 4102 1 chr6D.!!$R1 1092
13 TraesCS4A01G206000 chr3B 44038657 44040277 1620 False 793.000000 793 75.74600 2084 3708 1 chr3B.!!$F1 1624

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
456 464 0.535102 GTATGCCCGGATGGTGGAAG 60.535 60.000 0.73 0.00 36.04 3.46 F
852 866 3.556004 GCAGAAAGACAGTAGGCAAGTCT 60.556 47.826 0.00 0.00 43.98 3.24 F
933 947 5.666462 TCGCTAACATCAACTATTGGCTAA 58.334 37.500 0.00 0.00 0.00 3.09 F
934 948 6.288294 TCGCTAACATCAACTATTGGCTAAT 58.712 36.000 0.00 0.00 0.00 1.73 F
1640 1670 6.317088 CGAATGAGATTGCAAAGTTACATGT 58.683 36.000 1.71 2.69 0.00 3.21 F
3361 3402 0.534412 CATGCCTCGAGGAGACTTGT 59.466 55.000 35.69 8.59 44.43 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1670 2.419990 CCCACGTTCAGAATATGGAGCA 60.420 50.000 14.58 0.0 31.69 4.26 R
2325 2361 4.583489 ACAAACTGGTTCGAGTCTAGAAGA 59.417 41.667 0.00 0.0 0.00 2.87 R
2916 2954 6.373216 ACACTTTGAGTACAGCAAACAGTTTA 59.627 34.615 9.12 0.0 32.35 2.01 R
2953 2991 1.072806 AGCAAGTGAGACCATGCAAGA 59.927 47.619 0.00 0.0 41.18 3.02 R
3511 3555 4.773323 AAAGAATGTTGCTAGGCTTCAC 57.227 40.909 0.00 0.0 0.00 3.18 R
4528 4660 0.182775 GGCCTGATTGACCGGGTATT 59.817 55.000 6.32 0.0 35.02 1.89 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
131 133 2.634815 AGCTATGGCAGTTCAGATGG 57.365 50.000 3.10 0.00 41.70 3.51
300 307 4.039124 CCAAGTGTTTTAGGTGGCTCATTT 59.961 41.667 0.00 0.00 0.00 2.32
359 366 4.419282 ACAACAAGGATGATTCCCACAAT 58.581 39.130 0.00 0.00 43.76 2.71
453 461 1.227943 CTGTATGCCCGGATGGTGG 60.228 63.158 0.73 0.00 36.04 4.61
456 464 0.535102 GTATGCCCGGATGGTGGAAG 60.535 60.000 0.73 0.00 36.04 3.46
638 647 4.688879 CGCGTAACATATTGGTCCATATGT 59.311 41.667 15.62 15.62 43.50 2.29
783 797 9.019656 AGACTATGGTTATTGTGTAAATTTGCA 57.980 29.630 4.71 4.71 0.00 4.08
852 866 3.556004 GCAGAAAGACAGTAGGCAAGTCT 60.556 47.826 0.00 0.00 43.98 3.24
933 947 5.666462 TCGCTAACATCAACTATTGGCTAA 58.334 37.500 0.00 0.00 0.00 3.09
934 948 6.288294 TCGCTAACATCAACTATTGGCTAAT 58.712 36.000 0.00 0.00 0.00 1.73
935 949 6.423905 TCGCTAACATCAACTATTGGCTAATC 59.576 38.462 0.00 0.00 0.00 1.75
936 950 6.425114 CGCTAACATCAACTATTGGCTAATCT 59.575 38.462 0.00 0.00 0.00 2.40
937 951 7.598869 CGCTAACATCAACTATTGGCTAATCTA 59.401 37.037 0.00 0.00 0.00 1.98
1640 1670 6.317088 CGAATGAGATTGCAAAGTTACATGT 58.683 36.000 1.71 2.69 0.00 3.21
2009 2042 7.836183 AGATTGGGAGTTTATGAACAGCTTAAT 59.164 33.333 2.93 0.00 38.26 1.40
2292 2328 7.643123 ACATCTTTACAGGGTTTATTCCATCT 58.357 34.615 0.00 0.00 0.00 2.90
2916 2954 9.374838 GTTATGCCTTCAAATTCAAGAAATCAT 57.625 29.630 0.00 0.00 0.00 2.45
3361 3402 0.534412 CATGCCTCGAGGAGACTTGT 59.466 55.000 35.69 8.59 44.43 3.16
3583 3628 2.341846 TTTCGGTCTTGCAAGGTTCT 57.658 45.000 25.73 0.00 0.00 3.01
3591 3636 4.214332 GGTCTTGCAAGGTTCTTAGTTGAG 59.786 45.833 25.73 0.00 0.00 3.02
3736 3788 7.282224 ACTGAGAGTAACTTCTGCTCATACTAG 59.718 40.741 0.00 0.00 39.14 2.57
3748 3800 4.628074 GCTCATACTAGCACCGGAATTAA 58.372 43.478 9.46 0.00 42.30 1.40
3978 4036 2.639347 TCAAGATCAGCCTGAGTTTCCA 59.361 45.455 0.00 0.00 0.00 3.53
3995 4053 5.888982 TTTCCAGAAGAAACTCTAGTGGT 57.111 39.130 0.00 0.00 39.60 4.16
4059 4119 3.294493 GGGCTTCGCTGCACCAAA 61.294 61.111 0.00 0.00 34.04 3.28
4195 4288 8.038351 TGCTGCAGTGTTATTTATAGTCTACAA 58.962 33.333 16.64 0.00 0.00 2.41
4258 4351 5.324832 TGGAGTTTTCAGAGAATCCCTTT 57.675 39.130 1.28 0.00 33.66 3.11
4261 4354 5.414144 GGAGTTTTCAGAGAATCCCTTTCTG 59.586 44.000 0.00 0.00 44.88 3.02
4356 4451 4.282703 ACCGTAGTATTCCTGAAAGTGTGT 59.717 41.667 0.00 0.00 0.00 3.72
4465 4589 2.829206 CGCCGTGTCACCTGCAAAA 61.829 57.895 11.45 0.00 0.00 2.44
4484 4609 8.613060 TGCAAAACCATTAGCATAATTTTTCA 57.387 26.923 0.00 0.00 31.05 2.69
4502 4634 6.817765 TTTTCAAGTGAGGTATCCAATCAC 57.182 37.500 0.00 0.00 42.91 3.06
4566 4698 3.655276 CCCATCAGGCATTAGCAAATC 57.345 47.619 0.00 0.00 44.61 2.17
4572 4704 2.696707 CAGGCATTAGCAAATCCCATGT 59.303 45.455 0.00 0.00 44.61 3.21
4588 4720 0.174845 ATGTGCGCGTAGTGTGGTAT 59.825 50.000 8.43 0.00 41.96 2.73
4663 4795 0.912486 CCGGATTTCCTCTTCCCACT 59.088 55.000 0.00 0.00 0.00 4.00
4709 4841 4.002982 GCACACATACTTCACATCCTTCA 58.997 43.478 0.00 0.00 0.00 3.02
4891 5201 3.997021 CTGATTAATCGGGTCATGTAGCC 59.003 47.826 15.47 0.00 42.76 3.93
4907 5217 0.974383 AGCCCGTTAAGTGTAGCTGT 59.026 50.000 0.00 0.00 0.00 4.40
4908 5218 1.067071 AGCCCGTTAAGTGTAGCTGTC 60.067 52.381 0.00 0.00 0.00 3.51
4909 5219 2.005560 GCCCGTTAAGTGTAGCTGTCC 61.006 57.143 0.00 0.00 0.00 4.02
4910 5220 1.274167 CCCGTTAAGTGTAGCTGTCCA 59.726 52.381 0.00 0.00 0.00 4.02
4911 5221 2.093658 CCCGTTAAGTGTAGCTGTCCAT 60.094 50.000 0.00 0.00 0.00 3.41
4913 5223 2.348666 CGTTAAGTGTAGCTGTCCATGC 59.651 50.000 0.00 0.00 0.00 4.06
4914 5224 2.678336 GTTAAGTGTAGCTGTCCATGCC 59.322 50.000 0.00 0.00 0.00 4.40
4915 5225 0.391661 AAGTGTAGCTGTCCATGCCG 60.392 55.000 0.00 0.00 0.00 5.69
4922 5242 4.737177 TGTCCATGCCGCCATGCA 62.737 61.111 0.00 0.00 45.97 3.96
4939 5259 5.617751 GCCATGCATATCTATCGGTCAAAAC 60.618 44.000 0.00 0.00 0.00 2.43
4941 5261 6.205464 CCATGCATATCTATCGGTCAAAACTT 59.795 38.462 0.00 0.00 0.00 2.66
5016 5351 5.659048 AGTGACAGTTTTGAGAAATCGAC 57.341 39.130 0.00 0.00 0.00 4.20
5018 5353 3.059868 TGACAGTTTTGAGAAATCGACGC 60.060 43.478 0.00 0.00 0.00 5.19
5020 5355 3.498397 ACAGTTTTGAGAAATCGACGCAT 59.502 39.130 0.00 0.00 0.00 4.73
5021 5356 4.024048 ACAGTTTTGAGAAATCGACGCATT 60.024 37.500 0.00 0.00 0.00 3.56
5022 5357 4.551126 CAGTTTTGAGAAATCGACGCATTC 59.449 41.667 0.00 4.80 0.00 2.67
5023 5358 4.213270 AGTTTTGAGAAATCGACGCATTCA 59.787 37.500 12.78 0.87 0.00 2.57
5024 5359 4.944962 TTTGAGAAATCGACGCATTCAT 57.055 36.364 12.78 1.68 0.00 2.57
5052 5392 2.280708 CGCGTTGGAATACCTAAGTTCG 59.719 50.000 0.00 0.00 37.04 3.95
5054 5394 3.676873 GCGTTGGAATACCTAAGTTCGGA 60.677 47.826 0.00 0.00 37.04 4.55
5071 5411 3.724374 TCGGAAGTACTGTGGTTTTGAG 58.276 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.889589 ATCAAACTTTAGCCTTTTAACATGC 57.110 32.000 0.00 0.00 0.00 4.06
17 18 9.353999 GGTATCAAACTTTAGCCTTTTAACATG 57.646 33.333 0.00 0.00 0.00 3.21
66 68 6.075315 GGTTACCCCTTGATTTATAGGCAAT 58.925 40.000 0.00 0.00 0.00 3.56
67 69 5.044030 TGGTTACCCCTTGATTTATAGGCAA 60.044 40.000 0.00 0.00 0.00 4.52
79 81 0.251341 AGCTGCTTGGTTACCCCTTG 60.251 55.000 0.00 0.00 0.00 3.61
131 133 0.798009 CCAAAACGGCGTGATCATGC 60.798 55.000 28.35 28.35 42.40 4.06
300 307 1.065926 CAAGCACCATGTAGCTCCTCA 60.066 52.381 9.27 0.00 40.90 3.86
359 366 7.120138 GGAGAAATACGACCCATAAAAAGTTGA 59.880 37.037 0.00 0.00 0.00 3.18
480 489 7.927629 CCAAATTGTGATTAGGATTGGTTATGG 59.072 37.037 0.00 0.00 33.00 2.74
638 647 3.696051 GCAGATGCTAGAAAACCCAATCA 59.304 43.478 0.00 0.00 38.21 2.57
783 797 5.183904 GTGAAATTACAGACTTCCAGCCAAT 59.816 40.000 0.00 0.00 0.00 3.16
852 866 7.290061 CAATTATACTTCAATCCCTCCCTCAA 58.710 38.462 0.00 0.00 0.00 3.02
1640 1670 2.419990 CCCACGTTCAGAATATGGAGCA 60.420 50.000 14.58 0.00 31.69 4.26
2009 2042 7.829211 AGAAGGCATTTAGCTTAGTACAATTGA 59.171 33.333 13.59 0.00 44.79 2.57
2325 2361 4.583489 ACAAACTGGTTCGAGTCTAGAAGA 59.417 41.667 0.00 0.00 0.00 2.87
2916 2954 6.373216 ACACTTTGAGTACAGCAAACAGTTTA 59.627 34.615 9.12 0.00 32.35 2.01
2953 2991 1.072806 AGCAAGTGAGACCATGCAAGA 59.927 47.619 0.00 0.00 41.18 3.02
3361 3402 9.339850 GTCTTGAGTTGAGTATAGTAGTCCATA 57.660 37.037 0.00 0.00 0.00 2.74
3406 3447 9.935241 CCTTTGAGCTACTGTAATATGTATCAT 57.065 33.333 0.00 0.00 0.00 2.45
3511 3555 4.773323 AAAGAATGTTGCTAGGCTTCAC 57.227 40.909 0.00 0.00 0.00 3.18
3583 3628 6.275494 TGATGATACCGTTGACTCAACTAA 57.725 37.500 17.81 5.53 41.62 2.24
3736 3788 5.578727 TGCAACAATAATTTAATTCCGGTGC 59.421 36.000 13.48 13.48 0.00 5.01
3748 3800 8.109705 TCTGTAGTTCACATGCAACAATAATT 57.890 30.769 10.04 0.00 36.29 1.40
3780 3838 3.865745 CAGTCGAAATATGACCACCTGTC 59.134 47.826 0.00 0.00 44.72 3.51
3978 4036 4.142790 TCACGACCACTAGAGTTTCTTCT 58.857 43.478 0.00 0.00 0.00 2.85
3995 4053 2.370519 TCCAGGTCATTTTCCTTCACGA 59.629 45.455 0.00 0.00 32.37 4.35
4059 4119 2.493030 CGCTCGTTCGGGTATGGT 59.507 61.111 0.00 0.00 0.00 3.55
4195 4288 8.522830 CCAAATGTAGTGAGTGATAAAACCATT 58.477 33.333 0.00 0.00 0.00 3.16
4197 4290 6.072175 GCCAAATGTAGTGAGTGATAAAACCA 60.072 38.462 0.00 0.00 0.00 3.67
4465 4589 8.253113 CCTCACTTGAAAAATTATGCTAATGGT 58.747 33.333 0.00 0.00 0.00 3.55
4523 4655 3.118408 CCTGATTGACCGGGTATTTCTCA 60.118 47.826 6.32 0.00 0.00 3.27
4528 4660 0.182775 GGCCTGATTGACCGGGTATT 59.817 55.000 6.32 0.00 35.02 1.89
4566 4698 2.434185 ACACTACGCGCACATGGG 60.434 61.111 5.73 0.00 0.00 4.00
4572 4704 0.458260 ATCATACCACACTACGCGCA 59.542 50.000 5.73 0.00 0.00 6.09
4663 4795 3.147595 CGATGGTCGAGGGCTCCA 61.148 66.667 0.00 0.00 43.74 3.86
4813 4946 7.846101 ATGTCAACACATCCTCATCTAGATA 57.154 36.000 4.54 0.00 39.15 1.98
4891 5201 2.736144 TGGACAGCTACACTTAACGG 57.264 50.000 0.00 0.00 0.00 4.44
4911 5221 1.740043 CGATAGATATGCATGGCGGCA 60.740 52.381 16.34 16.34 44.54 5.69
4913 5223 1.134699 ACCGATAGATATGCATGGCGG 60.135 52.381 10.16 14.38 42.85 6.13
4914 5224 2.196749 GACCGATAGATATGCATGGCG 58.803 52.381 10.16 3.80 39.76 5.69
4915 5225 3.251479 TGACCGATAGATATGCATGGC 57.749 47.619 10.16 0.47 39.76 4.40
4922 5242 4.989168 GCCGAAGTTTTGACCGATAGATAT 59.011 41.667 0.00 0.00 39.76 1.63
4928 5248 1.535462 CTTGCCGAAGTTTTGACCGAT 59.465 47.619 0.00 0.00 0.00 4.18
4995 5330 4.446234 CGTCGATTTCTCAAAACTGTCAC 58.554 43.478 0.00 0.00 0.00 3.67
5018 5353 3.681961 AACGCGCGGGCAATGAATG 62.682 57.895 35.22 8.45 39.92 2.67
5020 5355 4.397090 CAACGCGCGGGCAATGAA 62.397 61.111 35.22 0.00 39.92 2.57
5052 5392 6.263344 GTTTTCTCAAAACCACAGTACTTCC 58.737 40.000 0.00 0.00 43.78 3.46
5071 5411 4.320275 GCCTAGTTTGGTAGCACAGTTTTC 60.320 45.833 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.