Multiple sequence alignment - TraesCS2B01G372100

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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 TraesCS2B01G372100 chr2B 100.000 3845 0 0 1 3845 530410167 530414011 0.000000e+00 7101.0
1 TraesCS2B01G372100 chr2D 92.866 3869 199 41 1 3844 450369559 450373375 0.000000e+00 5544.0
2 TraesCS2B01G372100 chr2A 94.569 2633 111 9 1225 3844 599167672 599165059 0.000000e+00 4041.0
3 TraesCS2B01G372100 chr2A 93.909 394 15 5 827 1219 599168369 599167984 1.540000e-163 586.0
4 TraesCS2B01G372100 chr7D 74.888 669 131 27 69 710 89871651 89870993 1.760000e-68 270.0
5 TraesCS2B01G372100 chr1D 74.164 658 130 27 69 707 383167100 383167736 1.790000e-58 237.0
6 TraesCS2B01G372100 chr6D 74.144 584 109 33 69 632 266440811 266440250 1.810000e-48 204.0
7 TraesCS2B01G372100 chr6B 74.940 419 89 13 71 474 116112555 116112138 1.100000e-40 178.0
8 TraesCS2B01G372100 chr6B 73.032 597 116 27 69 642 413947549 413946975 6.610000e-38 169.0
9 TraesCS2B01G372100 chr3B 75.202 371 73 16 129 486 578978244 578977880 1.430000e-34 158.0
10 TraesCS2B01G372100 chr3B 92.308 39 3 0 185 223 554540796 554540834 5.370000e-04 56.5
11 TraesCS2B01G372100 chr7A 74.054 370 74 18 182 534 244598848 244598484 8.670000e-27 132.0


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 TraesCS2B01G372100 chr2B 530410167 530414011 3844 False 7101.0 7101 100.000 1 3845 1 chr2B.!!$F1 3844
1 TraesCS2B01G372100 chr2D 450369559 450373375 3816 False 5544.0 5544 92.866 1 3844 1 chr2D.!!$F1 3843
2 TraesCS2B01G372100 chr2A 599165059 599168369 3310 True 2313.5 4041 94.239 827 3844 2 chr2A.!!$R1 3017
3 TraesCS2B01G372100 chr7D 89870993 89871651 658 True 270.0 270 74.888 69 710 1 chr7D.!!$R1 641
4 TraesCS2B01G372100 chr1D 383167100 383167736 636 False 237.0 237 74.164 69 707 1 chr1D.!!$F1 638
5 TraesCS2B01G372100 chr6D 266440250 266440811 561 True 204.0 204 74.144 69 632 1 chr6D.!!$R1 563

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
930 997 0.532573 CCATCTCGCACAGTAGTGGT 59.467 55.000 1.92 0.00 45.98 4.16 F
932 999 1.202348 CATCTCGCACAGTAGTGGTGA 59.798 52.381 1.92 2.79 45.98 4.02 F
1746 2119 0.459899 ACGAGCTCAATGATGCCGTA 59.540 50.000 15.40 0.00 35.55 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 2119 0.686769 CCCAGTAGTACCGGAAGCCT 60.687 60.000 9.46 0.00 0.0 4.58 R
2106 2479 1.888512 GCCTTCACAATCCTGCAAAGA 59.111 47.619 0.00 0.00 0.0 2.52 R
3256 3656 0.107508 GATGCCCAGCTTGCTGTAGA 60.108 55.000 19.49 4.84 0.0 2.59 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
274 294 9.471084 AATCCTTGAACACCTTTTAATTTAACG 57.529 29.630 0.00 0.00 0.00 3.18
320 343 3.120373 GCAACTTTTCTGAGCTAGCAGTC 60.120 47.826 18.83 7.30 37.20 3.51
329 353 2.718731 CTAGCAGTCGGGAGAGCG 59.281 66.667 0.00 0.00 41.26 5.03
334 358 1.355066 GCAGTCGGGAGAGCGAAAAG 61.355 60.000 0.00 0.00 41.26 2.27
412 439 3.643763 CTCCTCTTGCGAGCGTTATAAT 58.356 45.455 0.00 0.00 35.90 1.28
475 502 1.002142 GCTTAAACAACCACCACCGAC 60.002 52.381 0.00 0.00 0.00 4.79
477 504 0.545171 TAAACAACCACCACCGACCA 59.455 50.000 0.00 0.00 0.00 4.02
499 527 0.963962 ACCGAGGTCACAACGTGTAT 59.036 50.000 0.00 0.00 34.79 2.29
522 552 1.136872 CACCACAAACGCACCAAACG 61.137 55.000 0.00 0.00 0.00 3.60
536 566 1.470098 CCAAACGGCTCCATTCTCTTG 59.530 52.381 0.00 0.00 0.00 3.02
538 568 2.554032 CAAACGGCTCCATTCTCTTGTT 59.446 45.455 0.00 0.00 0.00 2.83
694 732 4.163078 AGAATCAATCCCACGAGTGAAGAT 59.837 41.667 4.59 4.14 45.48 2.40
700 738 1.154016 CACGAGTGAAGATCGGCGT 60.154 57.895 6.85 0.00 44.36 5.68
725 763 3.992427 CGAAACCAGTGTTACCCTTCTAC 59.008 47.826 0.00 0.00 33.30 2.59
726 764 4.501915 CGAAACCAGTGTTACCCTTCTACA 60.502 45.833 0.00 0.00 33.30 2.74
727 765 4.618920 AACCAGTGTTACCCTTCTACAG 57.381 45.455 0.00 0.00 31.36 2.74
743 781 9.930693 CCCTTCTACAGTAGTAATAAATGATCC 57.069 37.037 7.50 0.00 0.00 3.36
750 788 9.920946 ACAGTAGTAATAAATGATCCATGGTTT 57.079 29.630 12.58 7.46 0.00 3.27
795 833 4.340617 TCCATGGTTTTATCTTGTCCACC 58.659 43.478 12.58 0.00 0.00 4.61
800 838 3.686241 GGTTTTATCTTGTCCACCGTACC 59.314 47.826 0.00 0.00 0.00 3.34
805 843 2.841215 TCTTGTCCACCGTACCAAAAG 58.159 47.619 0.00 0.00 0.00 2.27
866 933 3.976704 CCATCTGGTGGTAAAGCCA 57.023 52.632 0.00 0.00 46.95 4.75
882 949 1.680338 GCCAAATCTTCGTGGGCTAT 58.320 50.000 0.00 0.00 41.39 2.97
925 992 0.817654 CCAGTCCATCTCGCACAGTA 59.182 55.000 0.00 0.00 0.00 2.74
926 993 1.202348 CCAGTCCATCTCGCACAGTAG 60.202 57.143 0.00 0.00 0.00 2.57
927 994 1.474478 CAGTCCATCTCGCACAGTAGT 59.526 52.381 0.00 0.00 0.00 2.73
929 996 0.817654 TCCATCTCGCACAGTAGTGG 59.182 55.000 1.92 0.00 45.98 4.00
930 997 0.532573 CCATCTCGCACAGTAGTGGT 59.467 55.000 1.92 0.00 45.98 4.16
931 998 1.633561 CATCTCGCACAGTAGTGGTG 58.366 55.000 1.92 0.00 45.98 4.17
932 999 1.202348 CATCTCGCACAGTAGTGGTGA 59.798 52.381 1.92 2.79 45.98 4.02
1132 1199 2.378634 CCCTTCCGCCCAGATTCCT 61.379 63.158 0.00 0.00 0.00 3.36
1197 1264 3.160047 CATGCCGCCTCCTCCTCT 61.160 66.667 0.00 0.00 0.00 3.69
1488 1861 3.765051 GAGATGATCGGCCTCGGA 58.235 61.111 0.00 0.00 36.95 4.55
1746 2119 0.459899 ACGAGCTCAATGATGCCGTA 59.540 50.000 15.40 0.00 35.55 4.02
1900 2273 1.676303 ATGGGCCGGTTTGGTAACG 60.676 57.895 1.90 0.00 41.21 3.18
1920 2293 0.523546 CGACACGCGAGCTAATCACT 60.524 55.000 15.93 0.00 44.57 3.41
1956 2329 1.080025 GCGCCCCGACATCCTATAC 60.080 63.158 0.00 0.00 0.00 1.47
1965 2338 2.662700 GACATCCTATACGTCAAGCGG 58.337 52.381 0.00 0.00 46.52 5.52
2052 2425 2.777692 TCCCTCAACAGAGAACCAGTTT 59.222 45.455 0.00 0.00 0.00 2.66
2106 2479 0.178912 AGACGACCTACTTTGGGGGT 60.179 55.000 0.00 0.00 35.89 4.95
2298 2671 1.303561 GGAGCTTGGGTGTGATGCA 60.304 57.895 0.00 0.00 0.00 3.96
2367 2740 4.706476 GTCATTGATTGGGTTGAGGATGAA 59.294 41.667 0.00 0.00 0.00 2.57
2430 2812 2.550208 GGATGAGGAAGTGGTTGACGTT 60.550 50.000 0.00 0.00 0.00 3.99
2549 2931 5.774498 AAAATGGAGAAACTGGTCAAGAC 57.226 39.130 0.00 0.00 0.00 3.01
2677 3059 1.479709 CGAGGAGGATGAGGTGAAGT 58.520 55.000 0.00 0.00 0.00 3.01
2685 3067 3.846588 AGGATGAGGTGAAGTTGGTACAT 59.153 43.478 0.00 0.00 39.30 2.29
2730 3112 1.005630 GCTGGTCAGAGTGAAGCGT 60.006 57.895 1.65 0.00 0.00 5.07
2734 3116 0.315568 GGTCAGAGTGAAGCGTGAGT 59.684 55.000 0.00 0.00 0.00 3.41
2952 3334 3.262420 AGCTGTATTTAGAGCGTGTTGG 58.738 45.455 1.56 0.00 46.12 3.77
3101 3499 8.978472 AGTTTAGTATGGCTTAGTTCATGTCTA 58.022 33.333 0.00 0.00 0.00 2.59
3175 3575 7.051623 TCTAATGTGGCGTATGGAGTTATTTT 58.948 34.615 0.00 0.00 0.00 1.82
3177 3577 3.942748 TGTGGCGTATGGAGTTATTTTCC 59.057 43.478 0.00 0.00 35.20 3.13
3233 3633 0.784778 GACTGCTCAACCGAAACTCG 59.215 55.000 0.00 0.00 40.07 4.18
3247 3647 0.317479 AACTCGGAAGAACGGACAGG 59.683 55.000 0.00 0.00 41.32 4.00
3256 3656 0.818040 GAACGGACAGGCACAAAGGT 60.818 55.000 0.00 0.00 0.00 3.50
3280 3680 1.679977 GCAAGCTGGGCATCAAGGA 60.680 57.895 5.80 0.00 0.00 3.36
3301 3701 4.249661 GAGATGCTGCTAAACTATAGGGC 58.750 47.826 4.43 3.83 0.00 5.19
3323 3723 1.015109 CTGTGCTAGGCAATCTGCTG 58.985 55.000 0.00 0.00 44.28 4.41
3402 3804 8.220755 AGTGTTTAACTGAGCTAAAACAATGA 57.779 30.769 8.53 0.00 41.85 2.57
3406 3808 5.695851 AACTGAGCTAAAACAATGACTGG 57.304 39.130 0.00 0.00 0.00 4.00
3483 3888 4.517285 GAAGACATTCTGAACATGCCCTA 58.483 43.478 0.00 0.00 32.33 3.53
3501 3906 3.574614 CCTAAAAATTGTCCAGCAACCG 58.425 45.455 0.00 0.00 40.28 4.44
3694 4099 0.625849 ATGATCGAAAGGGCCCTTGT 59.374 50.000 37.80 25.79 36.26 3.16
3696 4101 0.748367 GATCGAAAGGGCCCTTGTCC 60.748 60.000 37.80 25.95 36.26 4.02
3819 4224 2.415625 GCTTCAGCTGGAATGCTCTTTG 60.416 50.000 15.13 0.00 41.98 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
300 321 3.321497 CGACTGCTAGCTCAGAAAAGTT 58.679 45.455 17.23 0.00 37.51 2.66
320 343 4.648970 GTTTAATTCTTTTCGCTCTCCCG 58.351 43.478 0.00 0.00 0.00 5.14
329 353 7.113704 TCCTCTCGTTCGTTTAATTCTTTTC 57.886 36.000 0.00 0.00 0.00 2.29
334 358 3.924686 TGCTCCTCTCGTTCGTTTAATTC 59.075 43.478 0.00 0.00 0.00 2.17
412 439 5.180492 CCAAGCTGAAACCGTAGAATTGTTA 59.820 40.000 0.00 0.00 0.00 2.41
475 502 1.495584 CGTTGTGACCTCGGTGTTGG 61.496 60.000 0.00 0.00 0.00 3.77
477 504 0.808453 CACGTTGTGACCTCGGTGTT 60.808 55.000 0.00 0.00 35.23 3.32
499 527 0.178301 TGGTGCGTTTGTGGTGTCTA 59.822 50.000 0.00 0.00 0.00 2.59
522 552 3.149196 TGTTCAACAAGAGAATGGAGCC 58.851 45.455 0.00 0.00 0.00 4.70
536 566 6.798959 GCTGTCAGAGACAATATTTGTTCAAC 59.201 38.462 3.32 0.00 45.52 3.18
538 568 5.997129 TGCTGTCAGAGACAATATTTGTTCA 59.003 36.000 3.32 0.00 45.52 3.18
662 700 7.661847 ACTCGTGGGATTGATTCTTTTATATCC 59.338 37.037 0.00 0.00 0.00 2.59
676 714 2.196749 CGATCTTCACTCGTGGGATTG 58.803 52.381 0.00 2.96 0.00 2.67
700 738 0.535553 GGGTAACACTGGTTTCGCCA 60.536 55.000 0.00 0.00 42.31 5.69
764 802 9.699410 ACAAGATAAAACCATGGATGATTCTAA 57.301 29.630 21.47 0.00 0.00 2.10
765 803 9.342308 GACAAGATAAAACCATGGATGATTCTA 57.658 33.333 21.47 0.00 0.00 2.10
766 804 7.286316 GGACAAGATAAAACCATGGATGATTCT 59.714 37.037 21.47 11.69 0.00 2.40
767 805 7.068593 TGGACAAGATAAAACCATGGATGATTC 59.931 37.037 21.47 9.52 0.00 2.52
768 806 6.896860 TGGACAAGATAAAACCATGGATGATT 59.103 34.615 21.47 9.78 0.00 2.57
769 807 6.322201 GTGGACAAGATAAAACCATGGATGAT 59.678 38.462 21.47 5.22 33.19 2.45
770 808 5.652014 GTGGACAAGATAAAACCATGGATGA 59.348 40.000 21.47 0.00 33.19 2.92
771 809 5.163519 GGTGGACAAGATAAAACCATGGATG 60.164 44.000 21.47 6.40 33.19 3.51
772 810 4.956075 GGTGGACAAGATAAAACCATGGAT 59.044 41.667 21.47 2.68 33.19 3.41
773 811 4.340617 GGTGGACAAGATAAAACCATGGA 58.659 43.478 21.47 0.00 33.19 3.41
774 812 3.128589 CGGTGGACAAGATAAAACCATGG 59.871 47.826 11.19 11.19 33.19 3.66
778 816 3.686241 GGTACGGTGGACAAGATAAAACC 59.314 47.826 0.00 0.00 0.00 3.27
866 933 3.864921 GCCGATATAGCCCACGAAGATTT 60.865 47.826 0.00 0.00 0.00 2.17
938 1005 7.703058 TGGAGATTTTCCTTACCTTCATTTC 57.297 36.000 0.00 0.00 46.92 2.17
951 1018 3.691609 CCTGTAGCAGTTGGAGATTTTCC 59.308 47.826 0.00 0.00 46.98 3.13
1183 1250 3.844090 GTCAGAGGAGGAGGCGGC 61.844 72.222 0.00 0.00 0.00 6.53
1184 1251 3.151022 GGTCAGAGGAGGAGGCGG 61.151 72.222 0.00 0.00 0.00 6.13
1185 1252 3.151022 GGGTCAGAGGAGGAGGCG 61.151 72.222 0.00 0.00 0.00 5.52
1197 1264 1.764854 GGAATAGAGGGCGGGGTCA 60.765 63.158 0.00 0.00 0.00 4.02
1488 1861 3.580193 CGGACGGAGCGGTCGTAT 61.580 66.667 8.77 0.00 41.22 3.06
1620 1993 4.099170 CGGTCGTCGGAGAAGCGT 62.099 66.667 0.00 0.00 39.69 5.07
1746 2119 0.686769 CCCAGTAGTACCGGAAGCCT 60.687 60.000 9.46 0.00 0.00 4.58
1944 2317 2.307929 CGCTTGACGTATAGGATGTCG 58.692 52.381 0.00 0.00 45.75 4.35
2040 2413 5.016831 AGGTCAAACAAAAACTGGTTCTCT 58.983 37.500 0.00 0.00 30.20 3.10
2106 2479 1.888512 GCCTTCACAATCCTGCAAAGA 59.111 47.619 0.00 0.00 0.00 2.52
2298 2671 2.687425 CTCATCGTCACTCTCATCAGGT 59.313 50.000 0.00 0.00 0.00 4.00
2367 2740 6.990939 CAGTATCATCAATCACATCAACCTCT 59.009 38.462 0.00 0.00 0.00 3.69
2430 2812 2.889512 TCTGCTTCCACCTCTTCACTA 58.110 47.619 0.00 0.00 0.00 2.74
2549 2931 5.688807 ACTCATATGATTTCTCAACCCTGG 58.311 41.667 5.72 0.00 34.37 4.45
2677 3059 3.500448 TGCACTTTCCTGATGTACCAA 57.500 42.857 0.00 0.00 0.00 3.67
2685 3067 3.329300 GCTCCTTGCACTTTCCTGA 57.671 52.632 0.00 0.00 42.31 3.86
2913 3295 9.997482 AATACAGCTAAACATTGTAAATAACCG 57.003 29.630 0.00 0.00 31.72 4.44
2943 3325 2.038387 ACAAAGAAGACCAACACGCT 57.962 45.000 0.00 0.00 0.00 5.07
2952 3334 6.869388 CCTAGGTTCAGAACTACAAAGAAGAC 59.131 42.308 13.13 0.00 0.00 3.01
3042 3430 9.814899 GGGAGAACTCAATATATCAGACATATG 57.185 37.037 0.00 0.00 0.00 1.78
3045 3433 6.789457 TGGGGAGAACTCAATATATCAGACAT 59.211 38.462 4.23 0.00 0.00 3.06
3047 3435 6.672266 TGGGGAGAACTCAATATATCAGAC 57.328 41.667 4.23 0.00 0.00 3.51
3101 3499 4.473196 ACCAAACCAAGAAAAATCAACCCT 59.527 37.500 0.00 0.00 0.00 4.34
3142 3540 6.072119 TCCATACGCCACATTAGATAGTACTG 60.072 42.308 5.39 0.00 0.00 2.74
3143 3541 6.008331 TCCATACGCCACATTAGATAGTACT 58.992 40.000 0.00 0.00 0.00 2.73
3144 3542 6.072064 ACTCCATACGCCACATTAGATAGTAC 60.072 42.308 0.00 0.00 0.00 2.73
3145 3543 6.008331 ACTCCATACGCCACATTAGATAGTA 58.992 40.000 0.00 0.00 0.00 1.82
3146 3544 4.833380 ACTCCATACGCCACATTAGATAGT 59.167 41.667 0.00 0.00 0.00 2.12
3175 3575 0.972134 CAGAGGAGCAAGTGACAGGA 59.028 55.000 0.00 0.00 0.00 3.86
3177 3577 3.883830 ATACAGAGGAGCAAGTGACAG 57.116 47.619 0.00 0.00 0.00 3.51
3233 3633 0.534203 TTGTGCCTGTCCGTTCTTCC 60.534 55.000 0.00 0.00 0.00 3.46
3240 3640 0.320374 TAGACCTTTGTGCCTGTCCG 59.680 55.000 0.00 0.00 0.00 4.79
3241 3641 1.071699 TGTAGACCTTTGTGCCTGTCC 59.928 52.381 0.00 0.00 0.00 4.02
3247 3647 1.068954 GCTTGCTGTAGACCTTTGTGC 60.069 52.381 0.00 0.00 0.00 4.57
3256 3656 0.107508 GATGCCCAGCTTGCTGTAGA 60.108 55.000 19.49 4.84 0.00 2.59
3280 3680 3.306364 CGCCCTATAGTTTAGCAGCATCT 60.306 47.826 0.00 0.00 0.00 2.90
3301 3701 1.284657 CAGATTGCCTAGCACAGTCG 58.715 55.000 0.00 0.00 38.71 4.18
3362 3764 9.736023 CAGTTAAACACTTAATTGCTTCTCTTT 57.264 29.630 0.00 0.00 30.92 2.52
3363 3765 9.120538 TCAGTTAAACACTTAATTGCTTCTCTT 57.879 29.630 0.00 0.00 35.67 2.85
3364 3766 8.677148 TCAGTTAAACACTTAATTGCTTCTCT 57.323 30.769 0.00 0.00 35.67 3.10
3365 3767 7.535599 GCTCAGTTAAACACTTAATTGCTTCTC 59.464 37.037 0.00 0.00 35.67 2.87
3366 3768 7.229506 AGCTCAGTTAAACACTTAATTGCTTCT 59.770 33.333 0.00 0.00 35.67 2.85
3367 3769 7.363431 AGCTCAGTTAAACACTTAATTGCTTC 58.637 34.615 0.00 0.00 35.67 3.86
3368 3770 7.277174 AGCTCAGTTAAACACTTAATTGCTT 57.723 32.000 0.00 0.00 35.67 3.91
3402 3804 2.228545 TCAGCTGAGATCAGACCAGT 57.771 50.000 13.74 0.00 46.59 4.00
3406 3808 4.120792 TCACATTCAGCTGAGATCAGAC 57.879 45.455 17.43 5.27 46.59 3.51
3483 3888 3.453424 GAACGGTTGCTGGACAATTTTT 58.547 40.909 0.00 0.00 41.27 1.94
3501 3906 0.685097 GCTTTTGGGAAAGGGGGAAC 59.315 55.000 1.59 0.00 42.04 3.62
3694 4099 6.157536 TGAGGGGGATTTTTATATCTCAGGA 58.842 40.000 0.00 0.00 0.00 3.86
3696 4101 7.521669 ACTTGAGGGGGATTTTTATATCTCAG 58.478 38.462 0.00 0.00 32.62 3.35


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

AutoCloner maintained by Alex Coulton.