Multiple sequence alignment - TraesCS2D01G122100

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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 TraesCS2D01G122100 chr2D 100.000 2784 0 0 1 2784 71256907 71259690 0.000000e+00 5142
1 TraesCS2D01G122100 chr2D 95.720 2804 82 15 5 2784 71383058 71385847 0.000000e+00 4479
2 TraesCS2D01G122100 chr2D 92.699 1082 49 12 1480 2541 71204483 71205554 0.000000e+00 1533
3 TraesCS2D01G122100 chr2D 88.845 502 41 7 962 1450 71203996 71204495 1.100000e-168 603
4 TraesCS2D01G122100 chr2D 83.756 197 25 6 2341 2533 70820256 70820063 2.200000e-41 180
5 TraesCS2D01G122100 chr2B 91.252 1086 62 15 1480 2541 107525541 107526617 0.000000e+00 1448
6 TraesCS2D01G122100 chr2B 84.416 770 88 17 1480 2233 107499210 107499963 0.000000e+00 728
7 TraesCS2D01G122100 chr2B 90.121 496 44 3 962 1453 107525062 107525556 8.410000e-180 640
8 TraesCS2D01G122100 chr2B 82.988 676 94 13 10 676 20279266 20278603 2.390000e-165 592
9 TraesCS2D01G122100 chr2B 80.447 716 104 19 1643 2338 107117789 107117090 5.320000e-142 514
10 TraesCS2D01G122100 chr2B 89.968 309 30 1 2234 2541 107500115 107500423 5.590000e-107 398
11 TraesCS2D01G122100 chr2B 83.673 196 25 6 2341 2532 107117131 107116939 7.920000e-41 178
12 TraesCS2D01G122100 chr2A 86.011 1108 95 21 1480 2541 70187133 70188226 0.000000e+00 1133
13 TraesCS2D01G122100 chr2A 79.556 675 99 17 2 652 568996294 568995635 1.970000e-121 446
14 TraesCS2D01G122100 chr2A 76.481 557 65 27 923 1452 70186630 70187147 2.770000e-60 243
15 TraesCS2D01G122100 chr3B 83.828 674 93 7 2 670 228738243 228737581 6.550000e-176 627
16 TraesCS2D01G122100 chr7D 84.332 651 89 9 3 646 127648095 127648739 2.350000e-175 625
17 TraesCS2D01G122100 chr7D 83.676 680 94 8 2 678 206847294 206847959 2.350000e-175 625
18 TraesCS2D01G122100 chr7D 83.113 681 100 10 1 675 162199171 162199842 8.530000e-170 606
19 TraesCS2D01G122100 chr7D 80.310 452 65 12 2 443 14914692 14915129 1.240000e-83 320
20 TraesCS2D01G122100 chr3A 83.861 663 94 9 2 662 398887711 398888362 1.100000e-173 619
21 TraesCS2D01G122100 chr1D 83.056 661 85 20 5 656 449488319 449488961 2.400000e-160 575
22 TraesCS2D01G122100 chr7B 82.362 652 89 13 4 645 89504281 89504916 6.780000e-151 544
23 TraesCS2D01G122100 chr7B 80.422 664 103 15 2 654 104256259 104256906 5.390000e-132 481
24 TraesCS2D01G122100 chr6D 80.884 701 115 10 2 696 91040631 91039944 4.080000e-148 534
25 TraesCS2D01G122100 chr1B 76.638 702 134 24 3 693 427598485 427599167 7.330000e-96 361


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 TraesCS2D01G122100 chr2D 71256907 71259690 2783 False 5142 5142 100.0000 1 2784 1 chr2D.!!$F1 2783
1 TraesCS2D01G122100 chr2D 71383058 71385847 2789 False 4479 4479 95.7200 5 2784 1 chr2D.!!$F2 2779
2 TraesCS2D01G122100 chr2D 71203996 71205554 1558 False 1068 1533 90.7720 962 2541 2 chr2D.!!$F3 1579
3 TraesCS2D01G122100 chr2B 107525062 107526617 1555 False 1044 1448 90.6865 962 2541 2 chr2B.!!$F2 1579
4 TraesCS2D01G122100 chr2B 20278603 20279266 663 True 592 592 82.9880 10 676 1 chr2B.!!$R1 666
5 TraesCS2D01G122100 chr2B 107499210 107500423 1213 False 563 728 87.1920 1480 2541 2 chr2B.!!$F1 1061
6 TraesCS2D01G122100 chr2B 107116939 107117789 850 True 346 514 82.0600 1643 2532 2 chr2B.!!$R2 889
7 TraesCS2D01G122100 chr2A 70186630 70188226 1596 False 688 1133 81.2460 923 2541 2 chr2A.!!$F1 1618
8 TraesCS2D01G122100 chr2A 568995635 568996294 659 True 446 446 79.5560 2 652 1 chr2A.!!$R1 650
9 TraesCS2D01G122100 chr3B 228737581 228738243 662 True 627 627 83.8280 2 670 1 chr3B.!!$R1 668
10 TraesCS2D01G122100 chr7D 127648095 127648739 644 False 625 625 84.3320 3 646 1 chr7D.!!$F2 643
11 TraesCS2D01G122100 chr7D 206847294 206847959 665 False 625 625 83.6760 2 678 1 chr7D.!!$F4 676
12 TraesCS2D01G122100 chr7D 162199171 162199842 671 False 606 606 83.1130 1 675 1 chr7D.!!$F3 674
13 TraesCS2D01G122100 chr3A 398887711 398888362 651 False 619 619 83.8610 2 662 1 chr3A.!!$F1 660
14 TraesCS2D01G122100 chr1D 449488319 449488961 642 False 575 575 83.0560 5 656 1 chr1D.!!$F1 651
15 TraesCS2D01G122100 chr7B 89504281 89504916 635 False 544 544 82.3620 4 645 1 chr7B.!!$F1 641
16 TraesCS2D01G122100 chr7B 104256259 104256906 647 False 481 481 80.4220 2 654 1 chr7B.!!$F2 652
17 TraesCS2D01G122100 chr6D 91039944 91040631 687 True 534 534 80.8840 2 696 1 chr6D.!!$R1 694
18 TraesCS2D01G122100 chr1B 427598485 427599167 682 False 361 361 76.6380 3 693 1 chr1B.!!$F1 690

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
681 744 0.722469 TTACAGCGACGACGACGAAC 60.722 55.0 22.94 6.57 42.66 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 2947 0.03601 AAACATGTCAGAGCCGGGAG 60.036 55.0 2.18 0.0 0.0 4.3 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
84 90 1.330521 CATACGGGCTACACAATGTGC 59.669 52.381 14.01 0.00 36.98 4.57
236 250 1.699083 TGATGATGGTATGGATGGCGT 59.301 47.619 0.00 0.00 0.00 5.68
237 251 2.903135 TGATGATGGTATGGATGGCGTA 59.097 45.455 0.00 0.00 0.00 4.42
238 252 3.519107 TGATGATGGTATGGATGGCGTAT 59.481 43.478 0.00 0.00 0.00 3.06
356 409 1.077429 CTTGCTACCAGAAGGCCCC 60.077 63.158 0.00 0.00 39.06 5.80
564 625 5.667626 AGATTGATGAAGTGTACCTGGGTAT 59.332 40.000 2.63 0.00 32.82 2.73
577 639 4.864726 ACCTGGGTATAAACGACTCTAGT 58.135 43.478 0.00 0.00 0.00 2.57
657 720 2.419011 AATACCTGTGTGGCGGCCAA 62.419 55.000 25.70 11.51 40.22 4.52
681 744 0.722469 TTACAGCGACGACGACGAAC 60.722 55.000 22.94 6.57 42.66 3.95
696 759 0.994995 CGAACGTGAAGGATGCAGAG 59.005 55.000 0.00 0.00 0.00 3.35
705 779 4.096081 GTGAAGGATGCAGAGGAAGAAATG 59.904 45.833 0.00 0.00 0.00 2.32
727 801 4.278170 TGGTGAAGTGCAACAAAATAGAGG 59.722 41.667 0.00 0.00 42.37 3.69
741 819 1.789523 TAGAGGCGGGCAGATTTAGT 58.210 50.000 3.78 0.00 0.00 2.24
793 871 6.391227 ACTCTCACAACCTACCAAATTTTG 57.609 37.500 1.99 1.99 0.00 2.44
816 894 2.666508 CTCTACGTTGGATGGTTTCACG 59.333 50.000 0.00 0.00 0.00 4.35
891 969 1.374252 CGACCACTTCACTTCCCGG 60.374 63.158 0.00 0.00 0.00 5.73
1453 1572 3.417101 TCCTGAATTCAAAAGCGGCTAA 58.583 40.909 9.88 0.00 0.00 3.09
1682 1813 3.044894 GTGGAAGGATCTCAGAGGGAAT 58.955 50.000 0.00 0.00 0.00 3.01
1701 1832 4.406649 GGAATGGATTGGTTCAATGGTGAT 59.593 41.667 0.00 0.00 33.90 3.06
2095 2247 7.131498 TGCATTTAACATTGATTTCTTTGGC 57.869 32.000 0.00 0.00 0.00 4.52
2589 2917 3.081061 GTTGTGCCCACATCTGACAATA 58.919 45.455 1.46 0.00 41.52 1.90
2595 2923 3.873801 GCCCACATCTGACAATAACCAGT 60.874 47.826 0.00 0.00 0.00 4.00
2598 2926 4.572389 CCACATCTGACAATAACCAGTAGC 59.428 45.833 0.00 0.00 0.00 3.58
2601 2929 4.106029 TCTGACAATAACCAGTAGCGAC 57.894 45.455 0.00 0.00 0.00 5.19
2639 2967 0.321564 TCCCGGCTCTGACATGTTTG 60.322 55.000 0.00 0.00 0.00 2.93
2640 2968 0.321564 CCCGGCTCTGACATGTTTGA 60.322 55.000 0.00 0.43 0.00 2.69
2641 2969 1.679944 CCCGGCTCTGACATGTTTGAT 60.680 52.381 0.00 0.00 0.00 2.57
2665 2994 5.869344 TGATATGAGCCGTCTGCATAATTAC 59.131 40.000 0.00 0.00 44.83 1.89
2680 3009 5.527582 GCATAATTACTCTGTTCCCAACGAT 59.472 40.000 0.00 0.00 0.00 3.73
2684 3013 1.971357 ACTCTGTTCCCAACGATGTCT 59.029 47.619 0.00 0.00 0.00 3.41
2685 3014 2.028930 ACTCTGTTCCCAACGATGTCTC 60.029 50.000 0.00 0.00 0.00 3.36
2698 3027 3.075641 GTCTCTCCACGGGGTCCC 61.076 72.222 2.12 0.00 34.93 4.46
2709 3038 1.064979 ACGGGGTCCCATTTATGACAC 60.065 52.381 10.98 0.00 34.08 3.67
2711 3040 2.067365 GGGTCCCATTTATGACACCC 57.933 55.000 1.78 11.22 40.20 4.61
2743 3072 4.079253 GACCTGCTTACTTTTCCCATTCA 58.921 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 90 2.497138 TGTCCACTCAATGTTGCTCTG 58.503 47.619 0.00 0.00 0.00 3.35
356 409 2.502295 GATTTCATAGGCAGGAGCAGG 58.498 52.381 0.00 0.00 44.61 4.85
564 625 3.057736 GCTGTCCACACTAGAGTCGTTTA 60.058 47.826 0.00 0.00 0.00 2.01
577 639 0.812549 TTACGATAGCGCTGTCCACA 59.187 50.000 25.90 10.25 42.48 4.17
657 720 0.870393 TCGTCGTCGCTGTAACTCTT 59.130 50.000 0.00 0.00 36.96 2.85
681 744 1.205655 TCTTCCTCTGCATCCTTCACG 59.794 52.381 0.00 0.00 0.00 4.35
696 759 3.068024 TGTTGCACTTCACCATTTCTTCC 59.932 43.478 0.00 0.00 0.00 3.46
705 779 4.798574 CCTCTATTTTGTTGCACTTCACC 58.201 43.478 0.00 0.00 0.00 4.02
727 801 0.679960 AACCCACTAAATCTGCCCGC 60.680 55.000 0.00 0.00 0.00 6.13
793 871 3.678548 GTGAAACCATCCAACGTAGAGAC 59.321 47.826 0.00 0.00 0.00 3.36
816 894 0.652071 CCGCCCGATACGTTTTAACC 59.348 55.000 0.00 0.00 0.00 2.85
891 969 1.956802 CTTTGTGGGTTTCGGCCTC 59.043 57.895 0.00 0.00 0.00 4.70
1047 1126 4.116328 TCGACGCTGGCGAGGAAG 62.116 66.667 21.77 7.58 42.83 3.46
1376 1495 6.810911 TGGCAACTTAATTTAAACAGCAGAA 58.189 32.000 0.00 0.00 37.61 3.02
1471 1590 6.128418 GGCAGCCGCTTTTGATTTTTATTTTA 60.128 34.615 0.00 0.00 38.60 1.52
1475 1594 3.261580 GGCAGCCGCTTTTGATTTTTAT 58.738 40.909 0.00 0.00 38.60 1.40
1476 1595 2.611722 GGGCAGCCGCTTTTGATTTTTA 60.612 45.455 5.00 0.00 38.60 1.52
1477 1596 1.511850 GGCAGCCGCTTTTGATTTTT 58.488 45.000 0.00 0.00 38.60 1.94
1572 1696 2.228059 CCATCATGTCCTTGAGCATCC 58.772 52.381 0.00 0.00 0.00 3.51
1682 1813 3.098377 CCATCACCATTGAACCAATCCA 58.902 45.455 0.00 0.00 34.61 3.41
1701 1832 2.826488 CACCCATTAACCCCAAATCCA 58.174 47.619 0.00 0.00 0.00 3.41
2095 2247 3.937706 TGGTCAAATGGCAACTTGTTTTG 59.062 39.130 11.17 7.42 37.61 2.44
2589 2917 0.249741 AAACAGCGTCGCTACTGGTT 60.250 50.000 21.25 16.52 38.98 3.67
2601 2929 2.243407 GAGTCTAGTCGACAAACAGCG 58.757 52.381 19.50 0.00 45.32 5.18
2619 2947 0.036010 AAACATGTCAGAGCCGGGAG 60.036 55.000 2.18 0.00 0.00 4.30
2639 2967 2.445565 TGCAGACGGCTCATATCATC 57.554 50.000 0.00 0.00 45.15 2.92
2640 2968 4.541973 TTATGCAGACGGCTCATATCAT 57.458 40.909 10.11 2.62 45.15 2.45
2641 2969 4.541973 ATTATGCAGACGGCTCATATCA 57.458 40.909 10.11 0.01 45.15 2.15
2665 2994 2.232452 AGAGACATCGTTGGGAACAGAG 59.768 50.000 0.00 0.00 44.54 3.35
2680 3009 2.283676 GGACCCCGTGGAGAGACA 60.284 66.667 0.00 0.00 34.81 3.41
2684 3013 0.252789 TAAATGGGACCCCGTGGAGA 60.253 55.000 8.45 0.00 39.42 3.71
2685 3014 0.843984 ATAAATGGGACCCCGTGGAG 59.156 55.000 8.45 0.00 39.42 3.86
2698 3027 1.202177 GCTGTGCGGGTGTCATAAATG 60.202 52.381 0.00 0.00 0.00 2.32
2709 3038 2.185350 CAGGTCTAGCTGTGCGGG 59.815 66.667 0.00 0.00 0.00 6.13
2711 3040 0.173481 TAAGCAGGTCTAGCTGTGCG 59.827 55.000 10.58 0.00 42.53 5.34
2743 3072 8.522542 ACACCTTATAGAAAGAGATAAGACGT 57.477 34.615 0.00 0.00 37.70 4.34


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

AutoCloner maintained by Alex Coulton.