Multiple sequence alignment - TraesCS7D01G269700

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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 TraesCS7D01G269700 chr7D 100.000 4037 0 0 1 4037 254900652 254896616 0.000000e+00 7456.0
1 TraesCS7D01G269700 chr7D 92.078 669 30 9 1 648 349949322 349949988 0.000000e+00 920.0
2 TraesCS7D01G269700 chr7D 91.195 636 43 6 1 627 618385258 618384627 0.000000e+00 852.0
3 TraesCS7D01G269700 chr7A 96.566 2679 67 12 648 3303 273516439 273513763 0.000000e+00 4414.0
4 TraesCS7D01G269700 chr7A 81.651 109 6 8 3301 3395 167845632 167845740 1.200000e-10 78.7
5 TraesCS7D01G269700 chr7B 96.592 2670 65 10 648 3297 232270604 232267941 0.000000e+00 4403.0
6 TraesCS7D01G269700 chr7B 86.154 325 30 11 3725 4036 355864899 355864577 1.800000e-88 337.0
7 TraesCS7D01G269700 chr7B 85.583 326 32 11 3722 4034 633844876 633845199 1.080000e-85 327.0
8 TraesCS7D01G269700 chr7B 81.879 149 11 10 3585 3731 355865082 355864948 1.190000e-20 111.0
9 TraesCS7D01G269700 chr7B 81.081 148 14 12 3585 3731 633844696 633844830 5.520000e-19 106.0
10 TraesCS7D01G269700 chr1D 90.504 674 40 11 1 650 320980709 320980036 0.000000e+00 869.0
11 TraesCS7D01G269700 chr1D 87.835 411 25 12 3304 3700 453102148 453101749 3.680000e-125 459.0
12 TraesCS7D01G269700 chr1D 92.381 210 15 1 3828 4037 453101752 453101544 8.480000e-77 298.0
13 TraesCS7D01G269700 chr6D 90.555 667 32 9 1 648 428424502 428425156 0.000000e+00 854.0
14 TraesCS7D01G269700 chr6D 85.588 451 43 19 3311 3747 400542130 400541688 1.710000e-123 453.0
15 TraesCS7D01G269700 chr6D 90.175 285 21 3 3754 4037 400541622 400541344 8.250000e-97 364.0
16 TraesCS7D01G269700 chr3D 90.149 670 44 6 1 648 556937432 556936763 0.000000e+00 852.0
17 TraesCS7D01G269700 chr3D 90.032 622 42 6 50 651 580086496 580085875 0.000000e+00 787.0
18 TraesCS7D01G269700 chr3D 86.650 412 20 12 3299 3697 7310819 7311208 1.340000e-114 424.0
19 TraesCS7D01G269700 chr2D 89.851 670 35 9 1 650 74973120 74972464 0.000000e+00 830.0
20 TraesCS7D01G269700 chr2D 88.535 471 23 20 3304 3754 379719578 379720037 3.550000e-150 542.0
21 TraesCS7D01G269700 chr2D 94.059 303 15 3 3737 4037 379720053 379720354 1.320000e-124 457.0
22 TraesCS7D01G269700 chr5D 90.078 645 37 12 1 629 381788355 381787722 0.000000e+00 811.0
23 TraesCS7D01G269700 chr5D 89.004 673 43 17 1 645 368296932 368297601 0.000000e+00 804.0
24 TraesCS7D01G269700 chr5D 83.878 459 28 25 3304 3747 412050244 412049817 2.920000e-106 396.0
25 TraesCS7D01G269700 chr4B 85.376 465 33 24 3311 3747 527648078 527647621 2.210000e-122 449.0
26 TraesCS7D01G269700 chr4B 89.655 290 23 3 3754 4037 527647555 527647267 2.970000e-96 363.0
27 TraesCS7D01G269700 chr3A 83.890 509 43 19 1 509 609825524 609825055 2.210000e-122 449.0
28 TraesCS7D01G269700 chr3A 84.783 92 7 2 568 652 32127923 32127832 7.190000e-13 86.1
29 TraesCS7D01G269700 chr6A 86.124 418 35 19 3343 3747 48681748 48681341 2.880000e-116 429.0
30 TraesCS7D01G269700 chr2A 84.667 450 44 18 3311 3747 617762305 617761868 3.730000e-115 425.0
31 TraesCS7D01G269700 chr2A 85.646 418 35 19 3343 3747 581564845 581564440 2.240000e-112 416.0
32 TraesCS7D01G269700 chr2A 86.111 324 33 5 3726 4037 581564426 581564103 5.000000e-89 339.0
33 TraesCS7D01G269700 chr2A 88.492 252 20 5 3754 3999 617761808 617761560 3.050000e-76 296.0
34 TraesCS7D01G269700 chr2B 80.973 452 61 16 3297 3731 301729853 301730296 6.470000e-88 335.0
35 TraesCS7D01G269700 chr1B 90.610 213 14 2 3753 3959 531195952 531196164 1.110000e-70 278.0
36 TraesCS7D01G269700 chr1B 83.420 193 20 12 3561 3747 531195705 531195891 6.940000e-38 169.0
37 TraesCS7D01G269700 chr5A 81.742 356 24 15 294 626 16416657 16416320 4.000000e-65 259.0
38 TraesCS7D01G269700 chr1A 84.694 196 12 10 3300 3481 23415001 23414810 3.210000e-41 180.0


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 TraesCS7D01G269700 chr7D 254896616 254900652 4036 True 7456.0 7456 100.0000 1 4037 1 chr7D.!!$R1 4036
1 TraesCS7D01G269700 chr7D 349949322 349949988 666 False 920.0 920 92.0780 1 648 1 chr7D.!!$F1 647
2 TraesCS7D01G269700 chr7D 618384627 618385258 631 True 852.0 852 91.1950 1 627 1 chr7D.!!$R2 626
3 TraesCS7D01G269700 chr7A 273513763 273516439 2676 True 4414.0 4414 96.5660 648 3303 1 chr7A.!!$R1 2655
4 TraesCS7D01G269700 chr7B 232267941 232270604 2663 True 4403.0 4403 96.5920 648 3297 1 chr7B.!!$R1 2649
5 TraesCS7D01G269700 chr7B 355864577 355865082 505 True 224.0 337 84.0165 3585 4036 2 chr7B.!!$R2 451
6 TraesCS7D01G269700 chr7B 633844696 633845199 503 False 216.5 327 83.3320 3585 4034 2 chr7B.!!$F1 449
7 TraesCS7D01G269700 chr1D 320980036 320980709 673 True 869.0 869 90.5040 1 650 1 chr1D.!!$R1 649
8 TraesCS7D01G269700 chr1D 453101544 453102148 604 True 378.5 459 90.1080 3304 4037 2 chr1D.!!$R2 733
9 TraesCS7D01G269700 chr6D 428424502 428425156 654 False 854.0 854 90.5550 1 648 1 chr6D.!!$F1 647
10 TraesCS7D01G269700 chr6D 400541344 400542130 786 True 408.5 453 87.8815 3311 4037 2 chr6D.!!$R1 726
11 TraesCS7D01G269700 chr3D 556936763 556937432 669 True 852.0 852 90.1490 1 648 1 chr3D.!!$R1 647
12 TraesCS7D01G269700 chr3D 580085875 580086496 621 True 787.0 787 90.0320 50 651 1 chr3D.!!$R2 601
13 TraesCS7D01G269700 chr2D 74972464 74973120 656 True 830.0 830 89.8510 1 650 1 chr2D.!!$R1 649
14 TraesCS7D01G269700 chr2D 379719578 379720354 776 False 499.5 542 91.2970 3304 4037 2 chr2D.!!$F1 733
15 TraesCS7D01G269700 chr5D 381787722 381788355 633 True 811.0 811 90.0780 1 629 1 chr5D.!!$R1 628
16 TraesCS7D01G269700 chr5D 368296932 368297601 669 False 804.0 804 89.0040 1 645 1 chr5D.!!$F1 644
17 TraesCS7D01G269700 chr4B 527647267 527648078 811 True 406.0 449 87.5155 3311 4037 2 chr4B.!!$R1 726
18 TraesCS7D01G269700 chr2A 581564103 581564845 742 True 377.5 416 85.8785 3343 4037 2 chr2A.!!$R1 694
19 TraesCS7D01G269700 chr2A 617761560 617762305 745 True 360.5 425 86.5795 3311 3999 2 chr2A.!!$R2 688

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
502 515 0.249953 TGTTTAGCCGAACTTCGCCA 60.250 50.0 5.61 0.0 38.82 5.69 F
711 776 0.393537 CCAGCCTCCATGAACCAGAC 60.394 60.0 0.00 0.0 0.00 3.51 F
2453 2531 0.038526 TCCGAAGCCGAAGAAGACAC 60.039 55.0 0.00 0.0 38.22 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 2484 0.168128 GGTCCACCTCGCAAATTTCG 59.832 55.000 0.0 0.0 0.00 3.46 R
2774 2852 2.202987 CGCAGGTGAGGGAGATGC 60.203 66.667 0.0 0.0 0.00 3.91 R
3642 3754 0.531974 CTTGCCGTATGCCCGTATGT 60.532 55.000 0.0 0.0 40.16 2.29 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
78 79 4.011517 GGTCTCCCCGCCGTGAAA 62.012 66.667 0.00 0.00 0.00 2.69
337 347 1.229209 AAGGAGGAGAAGGCCGACA 60.229 57.895 0.00 0.00 0.00 4.35
463 476 5.063944 GCGAACATGTCTAATATATGCCCAG 59.936 44.000 0.00 0.00 30.12 4.45
465 478 5.441718 ACATGTCTAATATATGCCCAGGG 57.558 43.478 0.00 0.00 30.12 4.45
502 515 0.249953 TGTTTAGCCGAACTTCGCCA 60.250 50.000 5.61 0.00 38.82 5.69
509 522 1.264826 GCCGAACTTCGCCAAACTTTA 59.735 47.619 5.61 0.00 38.82 1.85
548 578 2.416901 TTTTTAAACGCGCCTGGGT 58.583 47.368 5.73 0.00 44.11 4.51
602 659 4.947147 TTTTGCGCCGGCTCACCT 62.947 61.111 26.68 0.00 40.82 4.00
711 776 0.393537 CCAGCCTCCATGAACCAGAC 60.394 60.000 0.00 0.00 0.00 3.51
803 868 7.469318 GCTCAAGGAGAAACTAAAAGCTTTTCT 60.469 37.037 27.03 17.77 41.29 2.52
874 939 1.581447 GAAGCAAACAAGGAGCCCG 59.419 57.895 0.00 0.00 0.00 6.13
1331 1409 1.001145 AGGCCTACTCGGAGTTCGT 60.001 57.895 16.95 5.23 40.32 3.85
2167 2245 1.667830 TTCGTCAAGAAGGCCAGCG 60.668 57.895 5.01 0.00 34.26 5.18
2337 2415 2.565841 GATGTTGATACCACCTGCTCC 58.434 52.381 0.00 0.00 0.00 4.70
2346 2424 1.073199 CACCTGCTCCTTTTCCGGT 59.927 57.895 0.00 0.00 0.00 5.28
2453 2531 0.038526 TCCGAAGCCGAAGAAGACAC 60.039 55.000 0.00 0.00 38.22 3.67
2815 2893 1.236616 CCTGCGCAACATCTGGTTCA 61.237 55.000 13.05 0.00 37.72 3.18
3072 3165 1.660575 CGCCGCTGGGTATAGTTCG 60.661 63.158 0.00 0.00 34.97 3.95
3090 3183 0.586319 CGGTTCACTGCGTCATTTGT 59.414 50.000 0.00 0.00 0.00 2.83
3092 3185 2.384382 GGTTCACTGCGTCATTTGTTG 58.616 47.619 0.00 0.00 0.00 3.33
3130 3223 2.343163 GATCAGCTCGACCGGACTGG 62.343 65.000 9.46 0.00 46.41 4.00
3171 3264 4.584743 TCTTTGTCAGAGAGAGTTGTAGCA 59.415 41.667 0.00 0.00 0.00 3.49
3281 3377 2.837591 GGCAACCATTGGTAAGGGAAAT 59.162 45.455 9.20 0.00 33.12 2.17
3290 3386 2.912956 TGGTAAGGGAAATGACAGCTCT 59.087 45.455 0.00 0.00 0.00 4.09
3337 3433 2.796651 GGCGACACCGATACGAGT 59.203 61.111 0.00 0.00 38.22 4.18
3339 3435 0.316524 GGCGACACCGATACGAGTAC 60.317 60.000 0.00 0.00 38.22 2.73
3340 3436 0.652751 GCGACACCGATACGAGTACG 60.653 60.000 0.00 0.00 41.03 3.67
3467 3579 6.805713 TGCGTGAGATGAGATCAAAATACTA 58.194 36.000 0.00 0.00 0.00 1.82
3547 3659 2.350522 CTCGTCCATTAGCTTGCTGTT 58.649 47.619 5.26 0.00 0.00 3.16
3632 3744 1.547372 GGAACATCAGCAAGCACCAAT 59.453 47.619 0.00 0.00 0.00 3.16
3640 3752 2.751259 CAGCAAGCACCAATCACATACT 59.249 45.455 0.00 0.00 0.00 2.12
3642 3754 2.749076 GCAAGCACCAATCACATACTGA 59.251 45.455 0.00 0.00 0.00 3.41
3650 3762 4.058124 CCAATCACATACTGACATACGGG 58.942 47.826 0.00 0.00 0.00 5.28
3651 3763 2.882927 TCACATACTGACATACGGGC 57.117 50.000 0.00 0.00 0.00 6.13
3653 3765 2.698274 TCACATACTGACATACGGGCAT 59.302 45.455 0.00 0.00 0.00 4.40
3654 3766 3.892588 TCACATACTGACATACGGGCATA 59.107 43.478 0.00 0.00 0.00 3.14
3655 3767 3.987868 CACATACTGACATACGGGCATAC 59.012 47.826 0.00 0.00 0.00 2.39
3656 3768 3.242518 CATACTGACATACGGGCATACG 58.757 50.000 0.00 0.00 40.31 3.06
3684 3803 1.287815 CACACACATGCCAGCAAGG 59.712 57.895 0.00 0.00 41.84 3.61
3862 4095 4.479993 GGCTCGAGGCTGCATGGT 62.480 66.667 30.02 0.00 41.46 3.55
3865 4098 3.068064 TCGAGGCTGCATGGTCGA 61.068 61.111 9.60 9.60 39.04 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 4.776322 CATTCCAGGGCCGCGTCA 62.776 66.667 4.92 0.00 0.00 4.35
337 347 2.126071 CTCACCGCCGTCGTCATT 60.126 61.111 0.00 0.00 0.00 2.57
421 434 5.583061 TGTTCGCGGATTTTCATTACATAGT 59.417 36.000 6.13 0.00 0.00 2.12
463 476 1.808343 ACGACTAAATTTCGGCAACCC 59.192 47.619 0.00 0.00 40.92 4.11
465 478 3.531262 ACACGACTAAATTTCGGCAAC 57.469 42.857 0.00 0.00 40.92 4.17
571 628 1.540435 GCAAAAATTCGGCCTGGGGA 61.540 55.000 0.00 0.00 0.00 4.81
602 659 0.461339 GCCTAAAATCGTCGCCTGGA 60.461 55.000 0.00 0.00 0.00 3.86
610 668 3.754766 GAGGGACGCCTAAAATCGT 57.245 52.632 0.00 0.00 42.09 3.73
711 776 3.730761 GAAGCAGCACAGCACCCG 61.731 66.667 0.00 0.00 36.85 5.28
1066 1135 2.438075 CTGCCTCTGCCTCTTGCC 60.438 66.667 0.00 0.00 40.16 4.52
1068 1137 1.025647 GCTTCTGCCTCTGCCTCTTG 61.026 60.000 0.00 0.00 36.33 3.02
1331 1409 1.980232 TACTGCGGGAAAGCGGAGA 60.980 57.895 0.00 0.00 45.94 3.71
1623 1701 2.280119 GCCATGATGCGCCTCGTA 60.280 61.111 4.18 0.00 0.00 3.43
1710 1788 3.527641 GAGTAGGACTCCGCCAGG 58.472 66.667 0.00 0.00 39.28 4.45
1929 2007 1.291877 CCAGCGGAAACACGAAGAGG 61.292 60.000 0.00 0.00 35.47 3.69
2322 2400 2.026262 GGAAAAGGAGCAGGTGGTATCA 60.026 50.000 0.00 0.00 0.00 2.15
2337 2415 2.391389 GCTGAGCGGACCGGAAAAG 61.391 63.158 17.22 0.00 0.00 2.27
2406 2484 0.168128 GGTCCACCTCGCAAATTTCG 59.832 55.000 0.00 0.00 0.00 3.46
2774 2852 2.202987 CGCAGGTGAGGGAGATGC 60.203 66.667 0.00 0.00 0.00 3.91
2815 2893 2.968206 GGCCTCGTACTTGTCGGT 59.032 61.111 0.00 0.00 0.00 4.69
2879 2963 2.252072 ATTCACCACGTGGATCCCCG 62.252 60.000 40.21 15.57 38.94 5.73
3056 3140 0.462789 AACCGAACTATACCCAGCGG 59.537 55.000 0.00 0.00 43.95 5.52
3090 3183 1.268794 CCACAAAAATGGCGTCGTCAA 60.269 47.619 2.47 0.00 31.52 3.18
3092 3185 0.386731 CCCACAAAAATGGCGTCGTC 60.387 55.000 0.00 0.00 38.55 4.20
3171 3264 3.201290 CAGTTCACACAGAAGCAGAAGT 58.799 45.455 0.00 0.00 36.78 3.01
3336 3432 0.598065 ATTACCGTATCCCGCCGTAC 59.402 55.000 0.00 0.00 34.38 3.67
3337 3433 1.327303 AATTACCGTATCCCGCCGTA 58.673 50.000 0.00 0.00 34.38 4.02
3339 3435 1.142474 GAAATTACCGTATCCCGCCG 58.858 55.000 0.00 0.00 34.38 6.46
3340 3436 2.538512 AGAAATTACCGTATCCCGCC 57.461 50.000 0.00 0.00 34.38 6.13
3341 3437 4.510038 TCTAGAAATTACCGTATCCCGC 57.490 45.455 0.00 0.00 34.38 6.13
3434 3546 7.661040 TGATCTCATCTCACGCATTCTATTAA 58.339 34.615 0.00 0.00 0.00 1.40
3632 3744 2.104170 TGCCCGTATGTCAGTATGTGA 58.896 47.619 0.00 0.00 37.40 3.58
3640 3752 1.068417 GCCGTATGCCCGTATGTCA 59.932 57.895 0.00 0.00 0.00 3.58
3642 3754 0.531974 CTTGCCGTATGCCCGTATGT 60.532 55.000 0.00 0.00 40.16 2.29
3650 3762 3.798650 TGTGCGCTTGCCGTATGC 61.799 61.111 9.73 0.00 39.71 3.14
3651 3763 2.098298 GTGTGCGCTTGCCGTATG 59.902 61.111 9.73 0.00 39.71 2.39
3653 3765 3.342627 GTGTGTGCGCTTGCCGTA 61.343 61.111 9.73 0.00 39.71 4.02
3655 3767 4.962122 GTGTGTGTGCGCTTGCCG 62.962 66.667 9.73 0.00 38.03 5.69
3656 3768 3.198236 ATGTGTGTGTGCGCTTGCC 62.198 57.895 9.73 0.00 38.03 4.52
3659 3771 2.332514 GCATGTGTGTGTGCGCTT 59.667 55.556 9.73 0.00 0.00 4.68
3660 3772 3.663176 GGCATGTGTGTGTGCGCT 61.663 61.111 9.73 0.00 42.15 5.92
3684 3803 2.026590 GTGTGTGTGCTTGGCTGC 59.973 61.111 0.00 0.00 0.00 5.25
3685 3804 2.723746 GGTGTGTGTGCTTGGCTG 59.276 61.111 0.00 0.00 0.00 4.85
3686 3805 2.901840 CGGTGTGTGTGCTTGGCT 60.902 61.111 0.00 0.00 0.00 4.75
3687 3806 4.629115 GCGGTGTGTGTGCTTGGC 62.629 66.667 0.00 0.00 0.00 4.52
3797 4019 0.808125 GCTCTCTCGCTCTCTGTTCA 59.192 55.000 0.00 0.00 0.00 3.18
3862 4095 0.832135 GGGATATGGGCAGGACTCGA 60.832 60.000 0.00 0.00 0.00 4.04
3865 4098 0.833834 CTCGGGATATGGGCAGGACT 60.834 60.000 0.00 0.00 0.00 3.85
3943 4177 1.245732 GCGATACTCGTATCCCAGGT 58.754 55.000 10.55 0.00 42.81 4.00


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

AutoCloner maintained by Alex Coulton.