Multiple sequence alignment - TraesCS2B01G413500

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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 TraesCS2B01G413500 chr2B 100.000 3896 0 0 1 3896 589210752 589214647 0.000000e+00 7195.0
1 TraesCS2B01G413500 chr2A 91.940 3970 160 56 1 3896 647344276 647348159 0.000000e+00 5411.0
2 TraesCS2B01G413500 chr2D 95.097 3080 102 19 833 3896 502108896 502111942 0.000000e+00 4806.0
3 TraesCS2B01G413500 chr2D 88.567 621 27 25 1 592 502108051 502108656 0.000000e+00 713.0
4 TraesCS2B01G413500 chr1D 95.849 530 22 0 2692 3221 215044106 215043577 0.000000e+00 857.0
5 TraesCS2B01G413500 chr1D 90.551 127 11 1 2727 2853 113492871 113492996 2.410000e-37 167.0
6 TraesCS2B01G413500 chr1D 98.148 54 1 0 3346 3399 215043579 215043526 1.150000e-15 95.3
7 TraesCS2B01G413500 chr5D 96.800 125 4 0 2727 2851 321681930 321682054 3.940000e-50 209.0
8 TraesCS2B01G413500 chr4D 93.701 127 8 0 2727 2853 227830190 227830064 1.430000e-44 191.0
9 TraesCS2B01G413500 chr6D 92.800 125 9 0 2692 2816 101397236 101397360 8.600000e-42 182.0
10 TraesCS2B01G413500 chr3A 92.126 127 10 0 2727 2853 58310019 58309893 3.090000e-41 180.0
11 TraesCS2B01G413500 chr1A 90.551 127 11 1 2727 2853 234658250 234658375 2.410000e-37 167.0


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 TraesCS2B01G413500 chr2B 589210752 589214647 3895 False 7195.00 7195 100.0000 1 3896 1 chr2B.!!$F1 3895
1 TraesCS2B01G413500 chr2A 647344276 647348159 3883 False 5411.00 5411 91.9400 1 3896 1 chr2A.!!$F1 3895
2 TraesCS2B01G413500 chr2D 502108051 502111942 3891 False 2759.50 4806 91.8320 1 3896 2 chr2D.!!$F1 3895
3 TraesCS2B01G413500 chr1D 215043526 215044106 580 True 476.15 857 96.9985 2692 3399 2 chr1D.!!$R1 707

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
368 425 0.242825 GTGAGTGCTGTGCCGTAGTA 59.757 55.0 0.0 0.0 0.00 1.82 F
1533 1624 0.473755 TGCAGGACTTGGAGAAGCAA 59.526 50.0 0.0 0.0 31.68 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1708 0.035317 TGATTGAGTTGAGCCGCTGT 59.965 50.0 0.00 0.0 0.0 4.40 R
3512 3636 0.247460 CGTGCACCATCTCTCTTCCA 59.753 55.0 12.15 0.0 0.0 3.53 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
134 171 2.348666 CGCTAGTACACCAATCTGTTGC 59.651 50.000 0.00 0.00 33.90 4.17
163 200 1.000843 TGATATCCCGCCATCTGTTCG 59.999 52.381 0.00 0.00 0.00 3.95
217 254 1.760613 TCTAGAAATCGCAATCGGGGT 59.239 47.619 0.00 0.00 36.13 4.95
323 367 4.585581 TGTTGTAGTGCCAGTACTAGTTCA 59.414 41.667 10.85 0.00 34.05 3.18
339 383 0.662970 TTCAAAATTCACGCGCCTGC 60.663 50.000 5.73 0.00 37.91 4.85
365 422 2.207229 AGGTGAGTGCTGTGCCGTA 61.207 57.895 0.00 0.00 0.00 4.02
366 423 1.738099 GGTGAGTGCTGTGCCGTAG 60.738 63.158 0.00 0.00 0.00 3.51
367 424 1.006102 GTGAGTGCTGTGCCGTAGT 60.006 57.895 0.00 0.00 0.00 2.73
368 425 0.242825 GTGAGTGCTGTGCCGTAGTA 59.757 55.000 0.00 0.00 0.00 1.82
576 647 2.019249 CCATCGCTTCACACCATTCAT 58.981 47.619 0.00 0.00 0.00 2.57
584 655 2.513753 TCACACCATTCATTCACCACC 58.486 47.619 0.00 0.00 0.00 4.61
585 656 2.158549 TCACACCATTCATTCACCACCA 60.159 45.455 0.00 0.00 0.00 4.17
586 657 2.030007 CACACCATTCATTCACCACCAC 60.030 50.000 0.00 0.00 0.00 4.16
587 658 2.237643 CACCATTCATTCACCACCACA 58.762 47.619 0.00 0.00 0.00 4.17
588 659 2.030007 CACCATTCATTCACCACCACAC 60.030 50.000 0.00 0.00 0.00 3.82
589 660 1.545582 CCATTCATTCACCACCACACC 59.454 52.381 0.00 0.00 0.00 4.16
590 661 1.199789 CATTCATTCACCACCACACCG 59.800 52.381 0.00 0.00 0.00 4.94
591 662 1.169661 TTCATTCACCACCACACCGC 61.170 55.000 0.00 0.00 0.00 5.68
592 663 1.600636 CATTCACCACCACACCGCT 60.601 57.895 0.00 0.00 0.00 5.52
593 664 1.600636 ATTCACCACCACACCGCTG 60.601 57.895 0.00 0.00 0.00 5.18
594 665 4.927782 TCACCACCACACCGCTGC 62.928 66.667 0.00 0.00 0.00 5.25
595 666 4.935495 CACCACCACACCGCTGCT 62.935 66.667 0.00 0.00 0.00 4.24
596 667 4.626081 ACCACCACACCGCTGCTC 62.626 66.667 0.00 0.00 0.00 4.26
618 689 2.384382 CCCGCGCATTTATTTTAGCAG 58.616 47.619 8.75 0.00 0.00 4.24
621 692 4.290155 CCGCGCATTTATTTTAGCAGAAT 58.710 39.130 8.75 0.00 0.00 2.40
677 752 6.500910 CAGGTAAGTTCAAGGTAAACAAACC 58.499 40.000 0.00 0.00 40.06 3.27
680 755 3.623703 AGTTCAAGGTAAACAAACCCGT 58.376 40.909 0.00 0.00 40.71 5.28
681 756 3.628942 AGTTCAAGGTAAACAAACCCGTC 59.371 43.478 0.00 0.00 40.71 4.79
751 826 2.826702 CTGTATACGGGTGGGGGC 59.173 66.667 3.55 0.00 0.00 5.80
752 827 3.155861 TGTATACGGGTGGGGGCG 61.156 66.667 0.00 0.00 0.00 6.13
753 828 3.932483 GTATACGGGTGGGGGCGG 61.932 72.222 0.00 0.00 0.00 6.13
789 864 3.792712 GCTTTATAACAGCGGGGGA 57.207 52.632 4.59 0.00 0.00 4.81
831 906 2.925966 AGGGGAAGCAATTGAATGGA 57.074 45.000 10.34 0.00 0.00 3.41
902 989 1.337387 GCGTTCGGAGCTAGTATTCCT 59.663 52.381 0.00 0.00 0.00 3.36
956 1047 0.551879 TACCTCCTCTTCCCTCCTCG 59.448 60.000 0.00 0.00 0.00 4.63
957 1048 1.308326 CCTCCTCTTCCCTCCTCGT 59.692 63.158 0.00 0.00 0.00 4.18
958 1049 0.753848 CCTCCTCTTCCCTCCTCGTC 60.754 65.000 0.00 0.00 0.00 4.20
959 1050 1.077644 TCCTCTTCCCTCCTCGTCG 60.078 63.158 0.00 0.00 0.00 5.12
1044 1135 4.910585 CCGCGCCAGGGGTACATC 62.911 72.222 0.00 0.00 44.60 3.06
1242 1333 4.867599 GCCGTCTCCCCGCTTACG 62.868 72.222 0.00 0.00 39.67 3.18
1533 1624 0.473755 TGCAGGACTTGGAGAAGCAA 59.526 50.000 0.00 0.00 31.68 3.91
1617 1708 0.106167 CCGAGTGGGAGGAGACCATA 60.106 60.000 0.00 0.00 40.70 2.74
1632 1723 0.108186 CCATACAGCGGCTCAACTCA 60.108 55.000 0.00 0.00 0.00 3.41
1644 1735 2.034879 CAACTCAATCACGGCCGCT 61.035 57.895 28.58 10.12 0.00 5.52
1645 1736 1.302511 AACTCAATCACGGCCGCTT 60.303 52.632 28.58 14.08 0.00 4.68
1800 1891 0.638746 CCACGTCGCGTCAATTACTC 59.361 55.000 5.77 0.00 38.32 2.59
1872 1963 0.322975 ATCTGGCAACTCTCAAGCGT 59.677 50.000 0.00 0.00 37.61 5.07
1875 1966 1.963338 GGCAACTCTCAAGCGTGCT 60.963 57.895 0.00 0.00 37.15 4.40
1974 2065 4.147449 TCGGCATCGTCCCAGCAG 62.147 66.667 0.00 0.00 37.69 4.24
2202 2293 2.359107 ACATGCCTGCAGGTGACG 60.359 61.111 32.81 20.67 39.60 4.35
2826 2917 2.342279 CCAGGCCTCGTCGTGAAA 59.658 61.111 0.00 0.00 0.00 2.69
2937 3034 2.268076 GCCGGCACCAGACAATTGT 61.268 57.895 24.80 11.78 0.00 2.71
3008 3108 1.608055 TGGCAAGGTGTGATGAGTTG 58.392 50.000 0.00 0.00 0.00 3.16
3099 3200 7.595502 AGAGTACATTATTACGCTACTGATTGC 59.404 37.037 0.00 0.00 31.12 3.56
3179 3280 2.742372 ACCGCGTGATTGTGGCTC 60.742 61.111 4.92 0.00 43.47 4.70
3267 3371 4.142687 CCGCCTTTCTTGTCGATTAATGTT 60.143 41.667 0.00 0.00 0.00 2.71
3284 3388 1.292992 GTTTGTTTCCTCACGTCGGT 58.707 50.000 0.00 0.00 0.00 4.69
3325 3429 1.547372 ACGTGCTACTTTCGGGTGTAT 59.453 47.619 0.00 0.00 0.00 2.29
3326 3430 2.754552 ACGTGCTACTTTCGGGTGTATA 59.245 45.455 0.00 0.00 0.00 1.47
3328 3432 3.181493 CGTGCTACTTTCGGGTGTATACT 60.181 47.826 4.17 0.00 0.00 2.12
3329 3433 4.357996 GTGCTACTTTCGGGTGTATACTC 58.642 47.826 4.17 0.00 0.00 2.59
3338 3442 3.945179 CGGGTGTATACTCGTCAGTAAC 58.055 50.000 3.37 0.00 45.61 2.50
3340 3444 4.095483 CGGGTGTATACTCGTCAGTAACTT 59.905 45.833 3.37 0.00 45.61 2.66
3341 3445 5.576895 GGGTGTATACTCGTCAGTAACTTC 58.423 45.833 4.17 0.00 38.66 3.01
3556 3680 2.428530 TGACATGCTACTACTCCTGCTG 59.571 50.000 0.00 0.00 0.00 4.41
3590 3714 6.437755 TGGCCTCAAAAGTATCCTACTACTA 58.562 40.000 3.32 0.00 38.26 1.82
3596 3720 9.339850 CTCAAAAGTATCCTACTACTACTGCTA 57.660 37.037 0.00 0.00 38.26 3.49
3844 3968 3.501828 TCGAACTTGTGGATTGTGATTGG 59.498 43.478 0.00 0.00 0.00 3.16
3875 4001 1.941812 CCCATTACGGATTCGCTGC 59.058 57.895 0.00 0.00 40.63 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 171 7.554118 ACAGATGGCGGGATATCAATATTTTAG 59.446 37.037 4.83 0.00 0.00 1.85
163 200 0.675522 TCCATTCGGCGAAAGGGAAC 60.676 55.000 34.85 0.00 32.10 3.62
309 350 5.618561 CGTGAATTTTGAACTAGTACTGGC 58.381 41.667 5.39 0.00 0.00 4.85
348 392 1.738099 CTACGGCACAGCACTCACC 60.738 63.158 0.00 0.00 0.00 4.02
349 393 0.242825 TACTACGGCACAGCACTCAC 59.757 55.000 0.00 0.00 0.00 3.51
350 394 0.526211 CTACTACGGCACAGCACTCA 59.474 55.000 0.00 0.00 0.00 3.41
351 395 0.809385 TCTACTACGGCACAGCACTC 59.191 55.000 0.00 0.00 0.00 3.51
365 422 0.526662 CGGTTTCGTGGAGCTCTACT 59.473 55.000 25.42 0.00 0.00 2.57
366 423 1.077089 GCGGTTTCGTGGAGCTCTAC 61.077 60.000 19.57 19.57 38.89 2.59
367 424 1.214589 GCGGTTTCGTGGAGCTCTA 59.785 57.895 14.64 4.15 38.89 2.43
368 425 2.048127 GCGGTTTCGTGGAGCTCT 60.048 61.111 14.64 0.00 38.89 4.09
405 462 3.291383 CGCCTGGTTTTCGCCCAA 61.291 61.111 0.00 0.00 0.00 4.12
576 647 2.203139 CAGCGGTGTGGTGGTGAA 60.203 61.111 6.41 0.00 42.42 3.18
593 664 1.734388 AAATAAATGCGCGGGGGAGC 61.734 55.000 8.83 0.00 0.00 4.70
594 665 0.744281 AAAATAAATGCGCGGGGGAG 59.256 50.000 8.83 0.00 0.00 4.30
595 666 1.950909 CTAAAATAAATGCGCGGGGGA 59.049 47.619 8.83 0.00 0.00 4.81
596 667 1.601914 GCTAAAATAAATGCGCGGGGG 60.602 52.381 8.83 0.00 0.00 5.40
597 668 1.066303 TGCTAAAATAAATGCGCGGGG 59.934 47.619 8.83 0.00 0.00 5.73
651 722 3.810941 TGTTTACCTTGAACTTACCTGCG 59.189 43.478 0.00 0.00 0.00 5.18
652 723 5.761165 TTGTTTACCTTGAACTTACCTGC 57.239 39.130 0.00 0.00 0.00 4.85
664 739 2.300433 GTGGACGGGTTTGTTTACCTT 58.700 47.619 0.00 0.00 38.30 3.50
669 744 1.824760 CGGGTGGACGGGTTTGTTT 60.825 57.895 0.00 0.00 0.00 2.83
716 791 0.606604 AGCATTACCTATACGGCGGG 59.393 55.000 13.24 4.90 35.61 6.13
725 800 3.575256 CCACCCGTATACAGCATTACCTA 59.425 47.826 3.32 0.00 0.00 3.08
763 838 1.578583 CTGTTATAAAGCGACCCCCG 58.421 55.000 0.00 0.00 42.21 5.73
764 839 1.306148 GCTGTTATAAAGCGACCCCC 58.694 55.000 0.00 0.00 0.00 5.40
831 906 3.317993 GCTATAAACGGGTGCCATTCATT 59.682 43.478 0.00 0.00 0.00 2.57
902 989 4.739356 TAGGCAGGCAGGGGCAGA 62.739 66.667 0.00 0.00 43.71 4.26
927 1014 0.256464 AGAGGAGGTAGACGGAGGTG 59.744 60.000 0.00 0.00 0.00 4.00
928 1015 1.001282 AAGAGGAGGTAGACGGAGGT 58.999 55.000 0.00 0.00 0.00 3.85
985 1076 3.570638 CATGCAGGCGAGGCGAAG 61.571 66.667 0.00 0.00 0.00 3.79
1101 1192 4.344865 TTGAGAACCCCGCCAGCC 62.345 66.667 0.00 0.00 0.00 4.85
1326 1417 2.432628 GACAGCGTGGACGAAGGG 60.433 66.667 2.73 0.00 43.02 3.95
1389 1480 2.816360 CGTCTGCCGATGCACATGG 61.816 63.158 0.00 0.00 44.23 3.66
1493 1584 2.244117 GATGGACAGCTCGCTCCCAA 62.244 60.000 11.89 0.05 32.20 4.12
1584 1675 2.034532 TCGGAGCTGGTGACCGTA 59.965 61.111 10.26 0.00 45.71 4.02
1590 1681 2.997315 TCCCACTCGGAGCTGGTG 60.997 66.667 18.79 13.06 34.86 4.17
1617 1708 0.035317 TGATTGAGTTGAGCCGCTGT 59.965 50.000 0.00 0.00 0.00 4.40
1632 1723 2.813908 GACGAAGCGGCCGTGATT 60.814 61.111 28.70 19.10 40.67 2.57
1644 1735 1.735386 CGTAGAGTGGAGGAGACGAA 58.265 55.000 0.00 0.00 32.20 3.85
1645 1736 0.743701 GCGTAGAGTGGAGGAGACGA 60.744 60.000 0.00 0.00 32.20 4.20
1719 1810 1.067776 GTGGAAGTGGACGAGTTCGAT 60.068 52.381 8.72 0.00 43.02 3.59
2202 2293 1.153229 GGTGGGATCGGTTACAGCC 60.153 63.158 0.00 0.00 0.00 4.85
2205 2296 0.899720 GTGAGGTGGGATCGGTTACA 59.100 55.000 0.00 0.00 0.00 2.41
2291 2382 1.454295 TGGTACTCTATGCCGGCGA 60.454 57.895 23.90 12.42 35.35 5.54
2336 2427 1.473965 GCTTGGATGCCTCAATCTCGA 60.474 52.381 0.00 0.00 0.00 4.04
2337 2428 0.942962 GCTTGGATGCCTCAATCTCG 59.057 55.000 0.00 0.00 0.00 4.04
2937 3034 4.263435 AGGACGGGTGCGAATTAATTAAA 58.737 39.130 1.21 0.00 0.00 1.52
3008 3108 9.738832 CTAAGCTTTACTACTAGATCAAGAACC 57.261 37.037 3.20 0.00 0.00 3.62
3099 3200 2.920490 CAGGTGACAAAAACAACAACGG 59.080 45.455 0.00 0.00 0.00 4.44
3179 3280 3.250744 CGACCTGTGTACAAGTGTATGG 58.749 50.000 0.00 0.00 32.54 2.74
3267 3371 1.574134 GAACCGACGTGAGGAAACAA 58.426 50.000 13.03 0.00 0.00 2.83
3291 3395 0.935196 GCACGTCACGAAGGAAAACT 59.065 50.000 2.91 0.00 0.00 2.66
3325 3429 4.581824 ACCAACTGAAGTTACTGACGAGTA 59.418 41.667 0.00 0.00 36.32 2.59
3326 3430 3.383825 ACCAACTGAAGTTACTGACGAGT 59.616 43.478 0.00 0.00 36.32 4.18
3328 3432 3.382227 TGACCAACTGAAGTTACTGACGA 59.618 43.478 0.00 0.00 36.32 4.20
3329 3433 3.713288 TGACCAACTGAAGTTACTGACG 58.287 45.455 0.00 0.00 36.32 4.35
3330 3434 4.083802 GCATGACCAACTGAAGTTACTGAC 60.084 45.833 0.00 0.00 36.32 3.51
3331 3435 4.065088 GCATGACCAACTGAAGTTACTGA 58.935 43.478 0.00 0.00 36.32 3.41
3332 3436 4.067896 AGCATGACCAACTGAAGTTACTG 58.932 43.478 0.00 0.00 36.32 2.74
3333 3437 4.357918 AGCATGACCAACTGAAGTTACT 57.642 40.909 0.00 0.00 36.32 2.24
3334 3438 4.275936 ACAAGCATGACCAACTGAAGTTAC 59.724 41.667 0.00 0.00 36.32 2.50
3335 3439 4.460263 ACAAGCATGACCAACTGAAGTTA 58.540 39.130 0.00 0.00 36.32 2.24
3338 3442 3.120546 CGTACAAGCATGACCAACTGAAG 60.121 47.826 0.00 0.00 0.00 3.02
3340 3444 2.224185 ACGTACAAGCATGACCAACTGA 60.224 45.455 0.00 0.00 0.00 3.41
3341 3445 2.143122 ACGTACAAGCATGACCAACTG 58.857 47.619 0.00 0.00 0.00 3.16
3510 3634 0.907486 TGCACCATCTCTCTTCCAGG 59.093 55.000 0.00 0.00 0.00 4.45
3511 3635 1.738365 CGTGCACCATCTCTCTTCCAG 60.738 57.143 12.15 0.00 0.00 3.86
3512 3636 0.247460 CGTGCACCATCTCTCTTCCA 59.753 55.000 12.15 0.00 0.00 3.53
3513 3637 0.532573 TCGTGCACCATCTCTCTTCC 59.467 55.000 12.15 0.00 0.00 3.46
3514 3638 2.370281 TTCGTGCACCATCTCTCTTC 57.630 50.000 12.15 0.00 0.00 2.87
3515 3639 2.839486 TTTCGTGCACCATCTCTCTT 57.161 45.000 12.15 0.00 0.00 2.85
3516 3640 2.234661 TCATTTCGTGCACCATCTCTCT 59.765 45.455 12.15 0.00 0.00 3.10
3517 3641 2.349886 GTCATTTCGTGCACCATCTCTC 59.650 50.000 12.15 0.00 0.00 3.20
3556 3680 4.648626 TGAGGCCAGCCAGTGCAC 62.649 66.667 9.40 9.40 41.13 4.57
3590 3714 4.767255 GCAGCCGGCAGTAGCAGT 62.767 66.667 31.54 0.76 44.61 4.40
3844 3968 1.022451 TAATGGGCGACGCAGGAAAC 61.022 55.000 23.09 2.24 0.00 2.78


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

AutoCloner maintained by Alex Coulton.