Multiple sequence alignment - TraesCS2D01G342900

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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 TraesCS2D01G342900 chr2D 100.000 3747 0 0 1 3747 439436193 439439939 0.000000e+00 6920
1 TraesCS2D01G342900 chr2A 94.638 3618 112 18 1 3567 549684577 549680991 0.000000e+00 5531
2 TraesCS2D01G342900 chr2B 90.928 3814 205 63 2 3741 517377667 517381413 0.000000e+00 4996
3 TraesCS2D01G342900 chr4D 98.684 76 1 0 1064 1139 482965416 482965491 6.530000e-28 135
4 TraesCS2D01G342900 chr4D 84.466 103 14 2 3036 3138 4680233 4680133 2.380000e-17 100
5 TraesCS2D01G342900 chrUn 85.714 105 14 1 3036 3140 100775675 100775572 3.960000e-20 110


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 TraesCS2D01G342900 chr2D 439436193 439439939 3746 False 6920 6920 100.000 1 3747 1 chr2D.!!$F1 3746
1 TraesCS2D01G342900 chr2A 549680991 549684577 3586 True 5531 5531 94.638 1 3567 1 chr2A.!!$R1 3566
2 TraesCS2D01G342900 chr2B 517377667 517381413 3746 False 4996 4996 90.928 2 3741 1 chr2B.!!$F1 3739

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
845 888 0.791422 CGTGCGACCGTTGGATAAAA 59.209 50.0 0.0 0.0 0.00 1.52 F
1424 1473 0.608130 ACAAGGCTCGCACAGTATCA 59.392 50.0 0.0 0.0 0.00 2.15 F
1987 2055 0.325933 CTTCAGCCCTCATGGTGTCA 59.674 55.0 0.0 0.0 35.31 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1905 0.034337 ATGGAGTTAACCGCACACGT 59.966 50.0 0.88 0.0 37.70 4.49 R
2611 2679 0.740868 CAAAAGATCTCGCCTCGGCA 60.741 55.0 8.87 0.0 42.06 5.69 R
3656 3746 0.958822 GCCCCCAATAATGTAAGCGG 59.041 55.0 0.00 0.0 0.00 5.52 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
107 109 3.392947 TGTAACAAGAACACCCTCATCCA 59.607 43.478 0.00 0.00 0.00 3.41
167 180 9.073475 ACTGTAGATCTTTCAGGTATCTCATAC 57.927 37.037 22.61 4.11 32.39 2.39
220 233 7.724305 TGTACCATCTTAACTTCTTCAACAC 57.276 36.000 0.00 0.00 0.00 3.32
387 422 3.125316 ACGCTCTCTACTAAGCTCGTAG 58.875 50.000 14.03 14.03 36.35 3.51
685 722 3.735181 CGAGTCTAAAACCCTCGGG 57.265 57.895 0.00 0.00 43.20 5.14
788 831 4.951963 CTCCGATCGCTTCCCCGC 62.952 72.222 10.32 0.00 0.00 6.13
804 847 4.475135 GCCCCCACCTCTTCGCTC 62.475 72.222 0.00 0.00 0.00 5.03
834 877 4.803426 CTCCCTGCTCGTGCGACC 62.803 72.222 4.84 0.00 43.34 4.79
845 888 0.791422 CGTGCGACCGTTGGATAAAA 59.209 50.000 0.00 0.00 0.00 1.52
866 909 7.787725 AAAATCCACCTGAATCGTATACTTC 57.212 36.000 0.56 0.00 0.00 3.01
944 992 1.446272 CAGACCGAGACCTTTCGCC 60.446 63.158 0.00 0.00 39.19 5.54
1181 1229 2.421424 GCTGCTCTATGGTTTCACCTTG 59.579 50.000 0.00 0.00 39.58 3.61
1200 1248 1.621317 TGAGTGTCAATCGCAACCCTA 59.379 47.619 0.00 0.00 0.00 3.53
1312 1360 4.961438 AGTCCGGTTTAGTTTCAGGTTA 57.039 40.909 0.00 0.00 0.00 2.85
1388 1437 6.322491 TCGATTCTGTGTGTAATGTCTGTAG 58.678 40.000 0.00 0.00 0.00 2.74
1401 1450 8.321353 TGTAATGTCTGTAGATGTTGGAATCTT 58.679 33.333 0.00 0.00 37.98 2.40
1415 1464 3.124560 GGAATCTTAGTACAAGGCTCGC 58.875 50.000 0.00 0.00 0.00 5.03
1424 1473 0.608130 ACAAGGCTCGCACAGTATCA 59.392 50.000 0.00 0.00 0.00 2.15
1486 1549 6.018180 CAGTTACCTAGAGTTTGCTTTCGTTT 60.018 38.462 0.00 0.00 0.00 3.60
1530 1593 5.215160 CACCTGTCAGAAATGTTTACTTGC 58.785 41.667 0.00 0.00 0.00 4.01
1599 1662 1.269448 GGTTGCTTGCGAAATTCCTCA 59.731 47.619 0.00 0.00 0.00 3.86
1837 1905 1.612950 ACGGCATTTTGCTCAACATCA 59.387 42.857 0.00 0.00 44.28 3.07
1930 1998 0.920664 CGCGTTCATCGTTGCAGATA 59.079 50.000 0.00 0.00 42.13 1.98
1987 2055 0.325933 CTTCAGCCCTCATGGTGTCA 59.674 55.000 0.00 0.00 35.31 3.58
2013 2081 2.016393 CTTCCGCCGGCTGATGTAGA 62.016 60.000 26.68 6.96 0.00 2.59
2014 2082 2.016393 TTCCGCCGGCTGATGTAGAG 62.016 60.000 26.68 4.88 0.00 2.43
2209 2277 4.646492 GGAACCAATCATGAAAGTATGGCT 59.354 41.667 0.00 0.00 0.00 4.75
2281 2349 1.016130 CAGTGCACACCGAGGCTAAG 61.016 60.000 21.04 0.00 0.00 2.18
2422 2490 2.223947 CGTGCCATACTACTACATGCCA 60.224 50.000 0.00 0.00 0.00 4.92
2482 2550 0.680280 TCGACCTCTACTGCTGGACC 60.680 60.000 0.00 0.00 0.00 4.46
2611 2679 1.000396 GGTGCTGCTTGGGAAGGAT 60.000 57.895 0.00 0.00 0.00 3.24
2629 2697 0.179000 ATGCCGAGGCGAGATCTTTT 59.821 50.000 9.78 0.00 45.51 2.27
2635 2703 0.615331 AGGCGAGATCTTTTGAGCCA 59.385 50.000 20.90 0.00 46.34 4.75
2650 2718 4.641645 CCACAGCCCAAGCACCGA 62.642 66.667 0.00 0.00 43.56 4.69
2979 3050 2.110578 GGGGGTCATCCAAAGAAATGG 58.889 52.381 0.00 0.00 42.12 3.16
2985 3056 3.196254 GTCATCCAAAGAAATGGGCACAT 59.804 43.478 0.00 0.00 41.05 3.21
3072 3156 3.658725 AGCTACCCTGATGATGTAACCT 58.341 45.455 0.00 0.00 0.00 3.50
3077 3161 2.356022 CCCTGATGATGTAACCTGTGCA 60.356 50.000 0.00 0.00 0.00 4.57
3084 3168 3.071747 TGATGTAACCTGTGCAGTAACCA 59.928 43.478 0.00 0.00 0.00 3.67
3093 3177 2.553602 TGTGCAGTAACCAGCAATCTTG 59.446 45.455 0.00 0.00 43.20 3.02
3121 3210 6.001460 TGTCTTAAATGGAATCCGAGTGTTT 58.999 36.000 0.00 0.00 0.00 2.83
3122 3211 6.072728 TGTCTTAAATGGAATCCGAGTGTTTG 60.073 38.462 0.00 0.00 0.00 2.93
3167 3256 6.017687 ACGTAAATAACAGACACCAAAAGGAC 60.018 38.462 0.00 0.00 0.00 3.85
3228 3317 5.720371 TTCACATATGAAACAAGGGGTTG 57.280 39.130 10.38 0.00 41.99 3.77
3321 3410 2.021208 GCTCCCTTGCTTGATCCTTCC 61.021 57.143 0.00 0.00 0.00 3.46
3388 3478 1.339291 GGCAAGAAAAGCAGAGCAACT 59.661 47.619 0.00 0.00 0.00 3.16
3398 3488 0.668706 CAGAGCAACTCGACAGGTGG 60.669 60.000 0.00 0.00 37.87 4.61
3406 3496 3.716006 CGACAGGTGGTGCTTGCG 61.716 66.667 0.00 0.00 0.00 4.85
3543 3633 0.741221 GACAAGCAAGCGAGGTAGGG 60.741 60.000 0.00 0.00 0.00 3.53
3600 3690 3.006110 CCTCACATTTGTTGCATGACCTT 59.994 43.478 0.00 0.00 0.00 3.50
3606 3696 4.462508 TTTGTTGCATGACCTTTTCACA 57.537 36.364 0.00 0.00 36.92 3.58
3607 3697 4.462508 TTGTTGCATGACCTTTTCACAA 57.537 36.364 0.00 0.00 36.92 3.33
3615 3705 2.869801 TGACCTTTTCACAAGCTACGTG 59.130 45.455 9.42 9.42 35.63 4.49
3618 3708 3.131396 CCTTTTCACAAGCTACGTGACT 58.869 45.455 16.31 0.00 42.88 3.41
3625 3715 3.798878 CACAAGCTACGTGACTCCATATG 59.201 47.826 10.02 0.00 36.43 1.78
3633 3723 2.736978 GTGACTCCATATGCTCTCGTG 58.263 52.381 0.00 0.00 0.00 4.35
3635 3725 1.957177 GACTCCATATGCTCTCGTGGA 59.043 52.381 0.00 0.00 38.37 4.02
3636 3726 2.362397 GACTCCATATGCTCTCGTGGAA 59.638 50.000 0.00 0.00 40.03 3.53
3646 3736 5.219343 TGCTCTCGTGGAATATCATGATT 57.781 39.130 14.65 0.00 32.89 2.57
3648 3738 4.993584 GCTCTCGTGGAATATCATGATTGT 59.006 41.667 14.65 1.70 32.89 2.71
3653 3743 4.512571 CGTGGAATATCATGATTGTCTGCA 59.487 41.667 14.65 4.98 0.00 4.41
3654 3744 5.007921 CGTGGAATATCATGATTGTCTGCAA 59.992 40.000 14.65 0.00 39.16 4.08
3656 3746 6.694411 GTGGAATATCATGATTGTCTGCAAAC 59.306 38.462 14.65 0.00 38.21 2.93
3663 3753 2.225491 TGATTGTCTGCAAACCGCTTAC 59.775 45.455 0.00 0.00 43.06 2.34
3673 3763 3.736740 GCAAACCGCTTACATTATTGGGG 60.737 47.826 0.00 0.00 37.77 4.96
3705 3795 1.106285 GGGCGAGCTTTGGATGAATT 58.894 50.000 0.00 0.00 0.00 2.17
3717 3807 8.944029 AGCTTTGGATGAATTGATCTATTATCG 58.056 33.333 4.85 0.00 0.00 2.92
3734 3824 0.690192 TCGGGCAATCTTGACAAGGA 59.310 50.000 15.13 2.90 38.18 3.36
3736 3826 1.177401 GGGCAATCTTGACAAGGACC 58.823 55.000 15.13 7.18 38.18 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 180 3.738282 GCGGTCTGATATGCACTAGAAAG 59.262 47.826 0.00 0.00 0.00 2.62
253 266 4.520111 TGCATGCTTTCTCTGTGTACAAAT 59.480 37.500 20.33 0.00 0.00 2.32
387 422 7.167468 CAGGTTTTTATTGTTGTTACAGCTGAC 59.833 37.037 23.35 9.91 35.28 3.51
683 720 2.038837 GCGAGGGTTTACTGTGCCC 61.039 63.158 8.32 8.32 42.64 5.36
685 722 0.517316 CTTGCGAGGGTTTACTGTGC 59.483 55.000 0.00 0.00 0.00 4.57
788 831 3.787001 GGAGCGAAGAGGTGGGGG 61.787 72.222 0.00 0.00 0.00 5.40
845 888 6.732896 AAGAAGTATACGATTCAGGTGGAT 57.267 37.500 7.40 0.00 0.00 3.41
855 898 6.328641 AGCGTCCATAAAGAAGTATACGAT 57.671 37.500 0.00 0.00 0.00 3.73
866 909 1.135112 GGGGCAAAAGCGTCCATAAAG 60.135 52.381 0.00 0.00 29.64 1.85
1151 1199 4.815108 TAGAGCAGCGGGGCGAGA 62.815 66.667 0.00 0.00 39.27 4.04
1181 1229 2.380084 TAGGGTTGCGATTGACACTC 57.620 50.000 0.00 0.00 30.82 3.51
1339 1388 5.845103 TGCGACCAAATTAGGAACGATATA 58.155 37.500 0.00 0.00 35.44 0.86
1340 1389 4.699637 TGCGACCAAATTAGGAACGATAT 58.300 39.130 0.00 0.00 35.44 1.63
1371 1420 5.931724 CCAACATCTACAGACATTACACACA 59.068 40.000 0.00 0.00 0.00 3.72
1374 1423 7.766278 AGATTCCAACATCTACAGACATTACAC 59.234 37.037 0.00 0.00 31.25 2.90
1388 1437 6.116126 AGCCTTGTACTAAGATTCCAACATC 58.884 40.000 0.00 0.00 0.00 3.06
1401 1450 1.254026 ACTGTGCGAGCCTTGTACTA 58.746 50.000 1.75 0.00 0.00 1.82
1415 1464 3.513912 TCCACTAGTTGGGTGATACTGTG 59.486 47.826 10.33 0.00 46.92 3.66
1424 1473 1.729586 TCTTGCTCCACTAGTTGGGT 58.270 50.000 10.33 0.00 46.92 4.51
1599 1662 4.082026 GCCTCACTTGTTGGATAAAGCATT 60.082 41.667 0.00 0.00 0.00 3.56
1837 1905 0.034337 ATGGAGTTAACCGCACACGT 59.966 50.000 0.88 0.00 37.70 4.49
1930 1998 2.037144 GGTGATGACCGGGTAGTGTAT 58.963 52.381 6.32 0.00 30.61 2.29
1952 2020 3.005261 GCTGAAGATGGCGAGAGAGATAA 59.995 47.826 0.00 0.00 0.00 1.75
2013 2081 2.283532 ACTCCTCTGACCGCTGCT 60.284 61.111 0.00 0.00 0.00 4.24
2014 2082 2.125753 CACTCCTCTGACCGCTGC 60.126 66.667 0.00 0.00 0.00 5.25
2147 2215 2.480555 CGCATCCGCCAACTTGAC 59.519 61.111 0.00 0.00 33.11 3.18
2209 2277 1.530323 TGCTCGTGTACTGCTCTACA 58.470 50.000 0.00 0.00 0.00 2.74
2422 2490 2.937689 ATCAGCCCCTGCACCTGT 60.938 61.111 0.00 0.00 41.13 4.00
2545 2613 1.367471 CCAGAACTCACGCAGGACA 59.633 57.895 0.00 0.00 0.00 4.02
2602 2670 3.797353 GCCTCGGCATCCTTCCCA 61.797 66.667 2.41 0.00 41.49 4.37
2611 2679 0.740868 CAAAAGATCTCGCCTCGGCA 60.741 55.000 8.87 0.00 42.06 5.69
2635 2703 3.560251 AGTCGGTGCTTGGGCTGT 61.560 61.111 0.00 0.00 39.59 4.40
2979 3050 5.708948 TGTAAGAAGCAAATTGTATGTGCC 58.291 37.500 0.00 0.00 39.13 5.01
3093 3177 3.882888 TCGGATTCCATTTAAGACATGGC 59.117 43.478 3.09 0.00 41.10 4.40
3094 3178 5.008019 CACTCGGATTCCATTTAAGACATGG 59.992 44.000 3.09 0.00 42.51 3.66
3095 3179 5.586243 ACACTCGGATTCCATTTAAGACATG 59.414 40.000 3.09 0.00 0.00 3.21
3096 3180 5.745227 ACACTCGGATTCCATTTAAGACAT 58.255 37.500 3.09 0.00 0.00 3.06
3140 3229 7.714377 TCCTTTTGGTGTCTGTTATTTACGTAA 59.286 33.333 3.29 3.29 41.38 3.18
3141 3230 7.171337 GTCCTTTTGGTGTCTGTTATTTACGTA 59.829 37.037 0.00 0.00 41.38 3.57
3142 3231 6.017687 GTCCTTTTGGTGTCTGTTATTTACGT 60.018 38.462 0.00 0.00 41.38 3.57
3143 3232 6.368213 GTCCTTTTGGTGTCTGTTATTTACG 58.632 40.000 0.00 0.00 41.38 3.18
3167 3256 1.273327 GACCACTTTGGCCAGAAATGG 59.727 52.381 19.68 19.68 42.67 3.16
3228 3317 1.763545 GGTACCTTGAGTGATCCCTCC 59.236 57.143 4.06 0.00 0.00 4.30
3321 3410 3.576356 CAACCATAGCAGCGGCCG 61.576 66.667 24.05 24.05 42.56 6.13
3388 3478 2.280797 GCAAGCACCACCTGTCGA 60.281 61.111 0.00 0.00 0.00 4.20
3398 3488 4.980805 TGTCCCGGACGCAAGCAC 62.981 66.667 13.02 0.00 45.62 4.40
3406 3496 1.668419 CAAGAATCCATGTCCCGGAC 58.332 55.000 10.96 10.96 34.69 4.79
3543 3633 1.153349 GGGAAGCATGTCGACTCCC 60.153 63.158 20.42 20.42 0.00 4.30
3600 3690 2.101750 TGGAGTCACGTAGCTTGTGAAA 59.898 45.455 19.40 6.78 46.99 2.69
3606 3696 2.695666 AGCATATGGAGTCACGTAGCTT 59.304 45.455 4.56 0.00 0.00 3.74
3607 3697 2.294791 GAGCATATGGAGTCACGTAGCT 59.705 50.000 4.56 0.00 0.00 3.32
3615 3705 1.957177 TCCACGAGAGCATATGGAGTC 59.043 52.381 4.56 0.00 36.30 3.36
3618 3708 4.772100 TGATATTCCACGAGAGCATATGGA 59.228 41.667 4.56 0.00 39.50 3.41
3625 3715 4.993584 ACAATCATGATATTCCACGAGAGC 59.006 41.667 9.04 0.00 0.00 4.09
3633 3723 6.211515 GGTTTGCAGACAATCATGATATTCC 58.788 40.000 9.04 0.00 35.21 3.01
3635 3725 5.734220 GCGGTTTGCAGACAATCATGATATT 60.734 40.000 9.04 0.00 45.45 1.28
3636 3726 4.261322 GCGGTTTGCAGACAATCATGATAT 60.261 41.667 9.04 0.00 45.45 1.63
3653 3743 3.028130 CCCCCAATAATGTAAGCGGTTT 58.972 45.455 4.64 0.00 0.00 3.27
3654 3744 2.661718 CCCCCAATAATGTAAGCGGTT 58.338 47.619 4.76 4.76 0.00 4.44
3656 3746 0.958822 GCCCCCAATAATGTAAGCGG 59.041 55.000 0.00 0.00 0.00 5.52
3663 3753 2.159057 GCTTGTTCTGCCCCCAATAATG 60.159 50.000 0.00 0.00 0.00 1.90
3673 3763 3.741476 CGCCCTGCTTGTTCTGCC 61.741 66.667 0.00 0.00 0.00 4.85
3705 3795 6.166279 GTCAAGATTGCCCGATAATAGATCA 58.834 40.000 0.00 0.00 0.00 2.92
3717 3807 1.177401 GGTCCTTGTCAAGATTGCCC 58.823 55.000 14.42 2.77 0.00 5.36


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

AutoCloner maintained by Alex Coulton.