Multiple sequence alignment - TraesCS6D01G139000

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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 TraesCS6D01G139000 chr6D 100.000 3281 0 0 1 3281 108221712 108224992 0.000000e+00 6059.0
1 TraesCS6D01G139000 chr6A 94.480 3297 106 27 1 3278 133304942 133308181 0.000000e+00 5011.0
2 TraesCS6D01G139000 chr6A 84.821 112 16 1 2658 2769 393957284 393957394 9.620000e-21 111.0
3 TraesCS6D01G139000 chr6B 96.098 1922 58 6 653 2568 195489574 195491484 0.000000e+00 3118.0
4 TraesCS6D01G139000 chr6B 94.848 427 17 3 1 423 195489155 195489580 0.000000e+00 662.0
5 TraesCS6D01G139000 chr7B 84.937 239 34 2 418 654 414077181 414077419 1.180000e-59 241.0
6 TraesCS6D01G139000 chr7B 84.956 113 14 3 2658 2769 81695795 81695905 9.620000e-21 111.0
7 TraesCS6D01G139000 chr4A 84.426 244 34 4 418 658 497025343 497025101 1.520000e-58 237.0
8 TraesCS6D01G139000 chr4A 100.000 34 0 0 1307 1340 590945000 590944967 2.730000e-06 63.9
9 TraesCS6D01G139000 chr1A 83.740 246 36 4 412 654 542141710 542141954 2.550000e-56 230.0
10 TraesCS6D01G139000 chr1A 83.682 239 36 3 418 654 64940433 64940196 4.260000e-54 222.0
11 TraesCS6D01G139000 chr1B 83.402 241 35 5 418 654 650478874 650478635 5.510000e-53 219.0
12 TraesCS6D01G139000 chr7D 82.787 244 36 5 415 654 8184543 8184784 2.560000e-51 213.0
13 TraesCS6D01G139000 chr7D 83.178 107 17 1 2658 2764 595687890 595687995 2.690000e-16 97.1
14 TraesCS6D01G139000 chr3D 82.329 249 40 3 411 655 312549864 312550112 2.560000e-51 213.0
15 TraesCS6D01G139000 chr3D 83.036 112 17 2 2658 2769 15411415 15411524 2.080000e-17 100.0
16 TraesCS6D01G139000 chr3D 83.721 86 14 0 2681 2766 525642812 525642897 7.550000e-12 82.4
17 TraesCS6D01G139000 chr2B 82.258 248 41 3 411 655 557731916 557731669 9.220000e-51 211.0
18 TraesCS6D01G139000 chr2B 81.034 116 20 1 2654 2769 659028917 659028804 1.250000e-14 91.6
19 TraesCS6D01G139000 chr5B 83.333 120 20 0 1928 2047 394571852 394571733 9.620000e-21 111.0
20 TraesCS6D01G139000 chr5D 81.250 112 18 3 2658 2768 487218187 487218078 1.620000e-13 87.9
21 TraesCS6D01G139000 chr3B 80.198 101 18 2 2663 2763 141119617 141119519 1.260000e-09 75.0
22 TraesCS6D01G139000 chr4D 97.297 37 1 0 1304 1340 11506914 11506950 2.730000e-06 63.9
23 TraesCS6D01G139000 chr4B 97.297 37 1 0 1304 1340 21216004 21216040 2.730000e-06 63.9


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 TraesCS6D01G139000 chr6D 108221712 108224992 3280 False 6059 6059 100.000 1 3281 1 chr6D.!!$F1 3280
1 TraesCS6D01G139000 chr6A 133304942 133308181 3239 False 5011 5011 94.480 1 3278 1 chr6A.!!$F1 3277
2 TraesCS6D01G139000 chr6B 195489155 195491484 2329 False 1890 3118 95.473 1 2568 2 chr6B.!!$F1 2567

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
418 422 0.250727 GGCCAGTGGTCACTTTGCTA 60.251 55.0 9.48 0.0 40.20 3.49 F
419 423 0.875059 GCCAGTGGTCACTTTGCTAC 59.125 55.0 11.74 0.0 40.20 3.58 F
1942 1962 0.252513 TAAGGTGCTGGCCTACTCCA 60.253 55.0 3.32 0.0 38.03 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 1943 0.252513 TGGAGTAGGCCAGCACCTTA 60.253 55.000 5.01 0.0 41.5 2.69 R
2025 2045 1.227853 GCGGTTGGTGAGGTTGAGT 60.228 57.895 0.00 0.0 0.0 3.41 R
2750 2771 2.095466 TCACATCGCCGGAAATTTTGAC 60.095 45.455 5.05 0.0 0.0 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
85 86 0.537143 TTCACCATGCTTCCTTGCGT 60.537 50.000 0.00 0.00 35.36 5.24
325 326 1.268794 TGTTTTGCCATTTCCGTGTCG 60.269 47.619 0.00 0.00 0.00 4.35
408 412 3.686016 CACTAAACTAATGGCCAGTGGT 58.314 45.455 17.16 17.16 31.83 4.16
416 420 1.181098 ATGGCCAGTGGTCACTTTGC 61.181 55.000 21.13 11.68 41.42 3.68
417 421 1.529244 GGCCAGTGGTCACTTTGCT 60.529 57.895 9.48 0.00 40.20 3.91
418 422 0.250727 GGCCAGTGGTCACTTTGCTA 60.251 55.000 9.48 0.00 40.20 3.49
419 423 0.875059 GCCAGTGGTCACTTTGCTAC 59.125 55.000 11.74 0.00 40.20 3.58
420 424 1.543429 GCCAGTGGTCACTTTGCTACT 60.543 52.381 11.74 0.00 40.20 2.57
421 425 2.289444 GCCAGTGGTCACTTTGCTACTA 60.289 50.000 11.74 0.00 40.20 1.82
422 426 3.326747 CCAGTGGTCACTTTGCTACTAC 58.673 50.000 0.00 0.00 40.20 2.73
423 427 3.326747 CAGTGGTCACTTTGCTACTACC 58.673 50.000 0.20 0.00 40.20 3.18
424 428 3.006967 CAGTGGTCACTTTGCTACTACCT 59.993 47.826 0.20 0.00 40.20 3.08
425 429 3.258622 AGTGGTCACTTTGCTACTACCTC 59.741 47.826 0.00 0.00 38.83 3.85
426 430 2.565834 TGGTCACTTTGCTACTACCTCC 59.434 50.000 0.00 0.00 0.00 4.30
427 431 2.416972 GGTCACTTTGCTACTACCTCCG 60.417 54.545 0.00 0.00 0.00 4.63
428 432 2.230750 GTCACTTTGCTACTACCTCCGT 59.769 50.000 0.00 0.00 0.00 4.69
429 433 2.895404 TCACTTTGCTACTACCTCCGTT 59.105 45.455 0.00 0.00 0.00 4.44
430 434 3.057033 TCACTTTGCTACTACCTCCGTTC 60.057 47.826 0.00 0.00 0.00 3.95
431 435 3.056749 CACTTTGCTACTACCTCCGTTCT 60.057 47.826 0.00 0.00 0.00 3.01
432 436 4.157289 CACTTTGCTACTACCTCCGTTCTA 59.843 45.833 0.00 0.00 0.00 2.10
444 448 8.925338 ACTACCTCCGTTCTAATTTATTGATCT 58.075 33.333 0.00 0.00 0.00 2.75
508 515 9.801873 ACTAACAAAATAATAATGCATGTCACC 57.198 29.630 0.00 0.00 0.00 4.02
525 532 9.531942 GCATGTCACCAAAAATTATATCATTGA 57.468 29.630 0.00 0.00 0.00 2.57
650 658 8.388656 AGAACTAATAAACCAGGATGAAGGTA 57.611 34.615 0.00 0.00 39.69 3.08
666 674 7.147983 GGATGAAGGTAGTAGCTACTATGATGG 60.148 44.444 31.04 0.00 40.55 3.51
668 676 5.602291 AGGTAGTAGCTACTATGATGGGT 57.398 43.478 31.04 9.00 40.55 4.51
886 895 1.889105 CGCAACAGAGCACACTGGT 60.889 57.895 9.61 1.25 41.59 4.00
925 934 4.023365 GGTATACCTACACTTGTAGCCTCG 60.023 50.000 15.09 0.89 44.97 4.63
1297 1309 4.289101 TCCTCCGGACCGTCCACA 62.289 66.667 17.87 1.98 35.91 4.17
1374 1386 4.916314 GGCGGGAGGATCGGGAGA 62.916 72.222 0.00 0.00 46.90 3.71
1752 1768 3.049912 GTTGGGATTTGACTTTTGACGC 58.950 45.455 0.00 0.00 0.00 5.19
1942 1962 0.252513 TAAGGTGCTGGCCTACTCCA 60.253 55.000 3.32 0.00 38.03 3.86
2025 2045 2.756760 GGAGTACACCAACGACATCCTA 59.243 50.000 4.24 0.00 0.00 2.94
2238 2258 2.404995 GCTTAGCTGCAGCCACCAG 61.405 63.158 34.39 23.86 43.38 4.00
2312 2332 2.590575 ACGGACCGGCTGTTGTTG 60.591 61.111 20.00 0.00 29.75 3.33
2697 2718 7.437713 TTGATGATTAGAGGGACAGTGTTAT 57.562 36.000 0.00 0.00 0.00 1.89
2706 2727 3.382048 GGACAGTGTTATCCCCGATAC 57.618 52.381 0.00 0.00 0.00 2.24
2707 2728 2.696707 GGACAGTGTTATCCCCGATACA 59.303 50.000 0.00 0.00 0.00 2.29
2708 2729 3.323979 GGACAGTGTTATCCCCGATACAT 59.676 47.826 0.00 0.00 0.00 2.29
2709 2730 4.557205 GACAGTGTTATCCCCGATACATC 58.443 47.826 0.00 0.00 0.00 3.06
2710 2731 3.964688 ACAGTGTTATCCCCGATACATCA 59.035 43.478 0.00 0.00 0.00 3.07
2712 2733 5.104693 ACAGTGTTATCCCCGATACATCAAA 60.105 40.000 0.00 0.00 0.00 2.69
2713 2734 5.466728 CAGTGTTATCCCCGATACATCAAAG 59.533 44.000 0.00 0.00 0.00 2.77
2716 2737 6.018180 GTGTTATCCCCGATACATCAAAGTTC 60.018 42.308 0.00 0.00 0.00 3.01
2732 2753 0.249911 GTTCAAGTCCTGGTGCTCGT 60.250 55.000 0.00 0.00 0.00 4.18
2750 2771 7.276658 GGTGCTCGTATTATTCCTGAATCTATG 59.723 40.741 0.00 0.00 32.50 2.23
2786 2807 3.543889 CGATGTGATAATATGACGGCTCG 59.456 47.826 0.00 0.00 0.00 5.03
2802 2823 1.363744 CTCGGTCTCTCAAATGTGCC 58.636 55.000 0.00 0.00 0.00 5.01
2823 2844 2.104792 CCATAGGGGTAGGATGTGTGTG 59.895 54.545 0.00 0.00 0.00 3.82
2854 2875 7.780271 TCATAGGATAAGTGAGTGAGTGTATGT 59.220 37.037 0.00 0.00 0.00 2.29
3245 3269 2.014594 GCGGGAAGCGGTTGATAAG 58.985 57.895 3.70 0.00 35.41 1.73
3253 3277 5.008712 GGGAAGCGGTTGATAAGAATTTAGG 59.991 44.000 3.70 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
408 412 2.522185 ACGGAGGTAGTAGCAAAGTGA 58.478 47.619 1.58 0.00 0.00 3.41
418 422 8.925338 AGATCAATAAATTAGAACGGAGGTAGT 58.075 33.333 0.00 0.00 0.00 2.73
419 423 9.765795 AAGATCAATAAATTAGAACGGAGGTAG 57.234 33.333 0.00 0.00 0.00 3.18
420 424 9.760077 GAAGATCAATAAATTAGAACGGAGGTA 57.240 33.333 0.00 0.00 0.00 3.08
421 425 8.487028 AGAAGATCAATAAATTAGAACGGAGGT 58.513 33.333 0.00 0.00 0.00 3.85
422 426 8.894768 AGAAGATCAATAAATTAGAACGGAGG 57.105 34.615 0.00 0.00 0.00 4.30
424 428 9.031360 CGAAGAAGATCAATAAATTAGAACGGA 57.969 33.333 0.00 0.00 0.00 4.69
425 429 8.818057 ACGAAGAAGATCAATAAATTAGAACGG 58.182 33.333 0.00 0.00 0.00 4.44
562 569 9.585099 ACGAATAAAATGTTAATGCATGTCAAT 57.415 25.926 0.00 0.00 0.00 2.57
564 571 8.978564 AACGAATAAAATGTTAATGCATGTCA 57.021 26.923 0.00 0.14 0.00 3.58
621 628 9.454859 CTTCATCCTGGTTTATTAGTTCTCTTT 57.545 33.333 0.00 0.00 0.00 2.52
638 646 6.943146 TCATAGTAGCTACTACCTTCATCCTG 59.057 42.308 31.06 22.00 41.18 3.86
643 651 6.010850 CCCATCATAGTAGCTACTACCTTCA 58.989 44.000 31.06 14.19 41.18 3.02
644 652 6.011481 ACCCATCATAGTAGCTACTACCTTC 58.989 44.000 31.06 1.40 41.18 3.46
645 653 5.966684 ACCCATCATAGTAGCTACTACCTT 58.033 41.667 31.06 16.17 41.18 3.50
650 658 5.597182 TCGAAAACCCATCATAGTAGCTACT 59.403 40.000 28.50 28.50 40.24 2.57
666 674 1.347320 AGCGAATCGACTCGAAAACC 58.653 50.000 21.77 1.21 41.44 3.27
668 676 2.159421 AGCTAGCGAATCGACTCGAAAA 60.159 45.455 21.77 2.96 41.44 2.29
693 702 1.951130 CGATCGAGATGGGCAACGG 60.951 63.158 10.26 0.00 37.60 4.44
785 794 0.948678 ACGAACGTGGAATTGGGTTG 59.051 50.000 0.00 0.00 0.00 3.77
886 895 0.252057 TACCTGCCACTGCCACTCTA 60.252 55.000 0.00 0.00 36.33 2.43
925 934 1.098050 CTGGCACTGGCAAGATAACC 58.902 55.000 6.75 0.00 44.40 2.85
1297 1309 4.778143 GACGCGCTTCCCCATGGT 62.778 66.667 11.73 0.00 0.00 3.55
1693 1709 0.541392 ATTAGATGACACAGCGGCCA 59.459 50.000 2.24 0.00 0.00 5.36
1752 1768 4.145997 GCAAGTGACGTGGTTTATTAACG 58.854 43.478 0.00 0.00 42.82 3.18
1815 1835 4.530710 AACTTACGAACATACTGGAGCA 57.469 40.909 0.00 0.00 0.00 4.26
1923 1943 0.252513 TGGAGTAGGCCAGCACCTTA 60.253 55.000 5.01 0.00 41.50 2.69
1942 1962 2.765250 ATCTCCACGCGCGTCTTGTT 62.765 55.000 35.61 15.53 0.00 2.83
2025 2045 1.227853 GCGGTTGGTGAGGTTGAGT 60.228 57.895 0.00 0.00 0.00 3.41
2238 2258 2.435059 GCAGGGAAGTGAGCGACC 60.435 66.667 0.00 0.00 0.00 4.79
2291 2311 4.555709 AACAGCCGGTCCGTGCAA 62.556 61.111 21.73 0.00 0.00 4.08
2312 2332 3.814268 ACATGCATGCGCCGAACC 61.814 61.111 26.53 0.00 37.32 3.62
2697 2718 4.019681 ACTTGAACTTTGATGTATCGGGGA 60.020 41.667 0.00 0.00 0.00 4.81
2701 2722 5.063944 CCAGGACTTGAACTTTGATGTATCG 59.936 44.000 0.00 0.00 0.00 2.92
2703 2724 5.707298 CACCAGGACTTGAACTTTGATGTAT 59.293 40.000 0.00 0.00 0.00 2.29
2704 2725 5.063204 CACCAGGACTTGAACTTTGATGTA 58.937 41.667 0.00 0.00 0.00 2.29
2705 2726 3.885297 CACCAGGACTTGAACTTTGATGT 59.115 43.478 0.00 0.00 0.00 3.06
2706 2727 3.304928 GCACCAGGACTTGAACTTTGATG 60.305 47.826 0.00 0.00 0.00 3.07
2707 2728 2.887152 GCACCAGGACTTGAACTTTGAT 59.113 45.455 0.00 0.00 0.00 2.57
2708 2729 2.092429 AGCACCAGGACTTGAACTTTGA 60.092 45.455 0.00 0.00 0.00 2.69
2709 2730 2.291741 GAGCACCAGGACTTGAACTTTG 59.708 50.000 0.00 0.00 0.00 2.77
2710 2731 2.576615 GAGCACCAGGACTTGAACTTT 58.423 47.619 0.00 0.00 0.00 2.66
2712 2733 0.034059 CGAGCACCAGGACTTGAACT 59.966 55.000 0.00 0.00 0.00 3.01
2713 2734 0.249911 ACGAGCACCAGGACTTGAAC 60.250 55.000 0.00 0.00 0.00 3.18
2716 2737 2.386661 AATACGAGCACCAGGACTTG 57.613 50.000 0.00 0.00 0.00 3.16
2750 2771 2.095466 TCACATCGCCGGAAATTTTGAC 60.095 45.455 5.05 0.00 0.00 3.18
2760 2781 2.598637 CGTCATATTATCACATCGCCGG 59.401 50.000 0.00 0.00 0.00 6.13
2786 2807 2.134789 ATGGGCACATTTGAGAGACC 57.865 50.000 0.00 0.00 32.00 3.85
2802 2823 2.104792 CACACACATCCTACCCCTATGG 59.895 54.545 0.00 0.00 41.37 2.74
2813 2834 2.615447 CCTATGATGCACACACACATCC 59.385 50.000 0.00 0.00 41.63 3.51
2814 2835 3.534554 TCCTATGATGCACACACACATC 58.465 45.455 0.00 0.00 42.46 3.06
2823 2844 5.847304 TCACTCACTTATCCTATGATGCAC 58.153 41.667 0.00 0.00 32.18 4.57
2854 2875 5.661056 ACTTAAGCGCTCATATATAGGCA 57.339 39.130 12.06 0.00 0.00 4.75
3168 3191 5.131977 TCCTATTTCTTAAGGCTATGGCACA 59.868 40.000 2.58 0.00 40.87 4.57


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

AutoCloner maintained by Alex Coulton.