Multiple sequence alignment - TraesCS3D01G213500

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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 TraesCS3D01G213500 chr3D 100.000 2134 0 0 1 2134 287301927 287304060 0.000000e+00 3941
1 TraesCS3D01G213500 chr3D 96.262 2140 51 10 1 2134 405843498 405845614 0.000000e+00 3482
2 TraesCS3D01G213500 chr3D 96.670 1952 31 11 4 1949 367348029 367349952 0.000000e+00 3214
3 TraesCS3D01G213500 chr3D 95.060 1761 44 12 391 2134 94447180 94448914 0.000000e+00 2730
4 TraesCS3D01G213500 chr3D 96.046 784 8 5 1171 1949 210993195 210993960 0.000000e+00 1254
5 TraesCS3D01G213500 chr3D 97.709 611 8 1 1 605 210992071 210992681 0.000000e+00 1046
6 TraesCS3D01G213500 chr3D 97.862 608 7 1 4 605 502027903 502027296 0.000000e+00 1046
7 TraesCS3D01G213500 chr3D 100.000 393 0 0 2235 2627 287304161 287304553 0.000000e+00 726
8 TraesCS3D01G213500 chr3D 93.333 300 20 0 2235 2534 405845626 405845925 6.670000e-121 444
9 TraesCS3D01G213500 chr3D 92.283 311 12 6 2235 2534 94450015 94450324 5.190000e-117 431
10 TraesCS3D01G213500 chr3D 87.402 254 26 4 1878 2126 590684362 590684110 1.190000e-73 287
11 TraesCS3D01G213500 chr4D 95.603 2138 48 20 4 2134 480148402 480146304 0.000000e+00 3386
12 TraesCS3D01G213500 chr4D 95.540 2130 49 20 4 2126 41949465 41947375 0.000000e+00 3365
13 TraesCS3D01G213500 chr4D 93.980 299 16 2 2235 2532 508996397 508996100 3.990000e-123 451
14 TraesCS3D01G213500 chr4D 92.652 313 10 2 2235 2534 7011107 7010795 3.100000e-119 438
15 TraesCS3D01G213500 chr4D 92.357 314 10 3 2235 2534 508997540 508997227 4.020000e-118 435
16 TraesCS3D01G213500 chr4D 90.096 313 17 3 2235 2534 61992398 61992709 6.810000e-106 394
17 TraesCS3D01G213500 chr4D 97.790 181 3 1 2355 2534 61993807 61993987 7.060000e-81 311
18 TraesCS3D01G213500 chr4D 100.000 97 0 0 2531 2627 7010761 7010665 2.080000e-41 180
19 TraesCS3D01G213500 chr4D 100.000 97 0 0 2531 2627 41945428 41945332 2.080000e-41 180
20 TraesCS3D01G213500 chr4D 100.000 97 0 0 2531 2627 61992743 61992839 2.080000e-41 180
21 TraesCS3D01G213500 chr4D 100.000 97 0 0 2531 2627 61994021 61994117 2.080000e-41 180
22 TraesCS3D01G213500 chr4D 100.000 97 0 0 2531 2627 480144793 480144697 2.080000e-41 180
23 TraesCS3D01G213500 chr4D 100.000 97 0 0 2531 2627 508997193 508997097 2.080000e-41 180
24 TraesCS3D01G213500 chr2D 94.923 2147 67 20 1 2134 537201197 537203314 0.000000e+00 3323
25 TraesCS3D01G213500 chr2D 94.860 2140 61 22 4 2134 601044618 601042519 0.000000e+00 3297
26 TraesCS3D01G213500 chr2D 96.675 1955 36 10 1 1949 158254602 158256533 0.000000e+00 3223
27 TraesCS3D01G213500 chr5D 96.726 1955 35 10 1 1949 156737593 156739524 0.000000e+00 3229
28 TraesCS3D01G213500 chr5D 93.377 302 18 2 2235 2534 156741057 156741358 1.860000e-121 446
29 TraesCS3D01G213500 chr2A 89.351 1371 93 22 814 2134 445750816 445749449 0.000000e+00 1674
30 TraesCS3D01G213500 chr2A 89.305 1309 87 22 876 2134 628679972 628681277 0.000000e+00 1592
31 TraesCS3D01G213500 chr6A 89.338 1360 93 33 814 2124 105156525 105155169 0.000000e+00 1661
32 TraesCS3D01G213500 chr3A 89.108 1368 96 30 814 2131 19598082 19599446 0.000000e+00 1652
33 TraesCS3D01G213500 chr1D 97.709 611 8 1 1 605 318137190 318137800 0.000000e+00 1046
34 TraesCS3D01G213500 chr1D 97.862 608 7 1 4 605 485468457 485467850 0.000000e+00 1046
35 TraesCS3D01G213500 chr1D 95.017 301 14 1 2235 2534 318140100 318140400 3.060000e-129 472
36 TraesCS3D01G213500 chr1D 92.357 314 10 3 2235 2534 485466040 485465727 4.020000e-118 435
37 TraesCS3D01G213500 chr1D 85.762 302 32 9 2235 2534 485447430 485447138 2.540000e-80 309
38 TraesCS3D01G213500 chr1D 100.000 97 0 0 2531 2627 318140434 318140530 2.080000e-41 180
39 TraesCS3D01G213500 chr1D 100.000 97 0 0 2531 2627 485465693 485465597 2.080000e-41 180
40 TraesCS3D01G213500 chr6D 97.553 613 7 2 1 605 400558319 400558931 0.000000e+00 1042
41 TraesCS3D01G213500 chr6D 100.000 97 0 0 2531 2627 400560786 400560882 2.080000e-41 180
42 TraesCS3D01G213500 chr4B 81.775 417 43 21 2235 2627 416148986 416148579 4.220000e-83 318
43 TraesCS3D01G213500 chr7B 88.889 261 23 4 1878 2134 197006351 197006609 1.520000e-82 316
44 TraesCS3D01G213500 chr7D 88.142 253 20 7 1878 2126 53446223 53446469 2.560000e-75 292
45 TraesCS3D01G213500 chr5B 86.538 260 25 7 1884 2134 594884866 594884608 7.160000e-71 278


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 TraesCS3D01G213500 chr3D 287301927 287304553 2626 False 2333.500000 3941 100.000000 1 2627 2 chr3D.!!$F4 2626
1 TraesCS3D01G213500 chr3D 367348029 367349952 1923 False 3214.000000 3214 96.670000 4 1949 1 chr3D.!!$F1 1945
2 TraesCS3D01G213500 chr3D 405843498 405845925 2427 False 1963.000000 3482 94.797500 1 2534 2 chr3D.!!$F5 2533
3 TraesCS3D01G213500 chr3D 94447180 94450324 3144 False 1580.500000 2730 93.671500 391 2534 2 chr3D.!!$F2 2143
4 TraesCS3D01G213500 chr3D 210992071 210993960 1889 False 1150.000000 1254 96.877500 1 1949 2 chr3D.!!$F3 1948
5 TraesCS3D01G213500 chr3D 502027296 502027903 607 True 1046.000000 1046 97.862000 4 605 1 chr3D.!!$R1 601
6 TraesCS3D01G213500 chr4D 480144697 480148402 3705 True 1783.000000 3386 97.801500 4 2627 2 chr4D.!!$R3 2623
7 TraesCS3D01G213500 chr4D 41945332 41949465 4133 True 1772.500000 3365 97.770000 4 2627 2 chr4D.!!$R2 2623
8 TraesCS3D01G213500 chr4D 508996100 508997540 1440 True 355.333333 451 95.445667 2235 2627 3 chr4D.!!$R4 392
9 TraesCS3D01G213500 chr4D 61992398 61994117 1719 False 266.250000 394 96.971500 2235 2627 4 chr4D.!!$F1 392
10 TraesCS3D01G213500 chr2D 537201197 537203314 2117 False 3323.000000 3323 94.923000 1 2134 1 chr2D.!!$F2 2133
11 TraesCS3D01G213500 chr2D 601042519 601044618 2099 True 3297.000000 3297 94.860000 4 2134 1 chr2D.!!$R1 2130
12 TraesCS3D01G213500 chr2D 158254602 158256533 1931 False 3223.000000 3223 96.675000 1 1949 1 chr2D.!!$F1 1948
13 TraesCS3D01G213500 chr5D 156737593 156741358 3765 False 1837.500000 3229 95.051500 1 2534 2 chr5D.!!$F1 2533
14 TraesCS3D01G213500 chr2A 445749449 445750816 1367 True 1674.000000 1674 89.351000 814 2134 1 chr2A.!!$R1 1320
15 TraesCS3D01G213500 chr2A 628679972 628681277 1305 False 1592.000000 1592 89.305000 876 2134 1 chr2A.!!$F1 1258
16 TraesCS3D01G213500 chr6A 105155169 105156525 1356 True 1661.000000 1661 89.338000 814 2124 1 chr6A.!!$R1 1310
17 TraesCS3D01G213500 chr3A 19598082 19599446 1364 False 1652.000000 1652 89.108000 814 2131 1 chr3A.!!$F1 1317
18 TraesCS3D01G213500 chr1D 318137190 318140530 3340 False 566.000000 1046 97.575333 1 2627 3 chr1D.!!$F1 2626
19 TraesCS3D01G213500 chr1D 485465597 485468457 2860 True 553.666667 1046 96.739667 4 2627 3 chr1D.!!$R2 2623
20 TraesCS3D01G213500 chr6D 400558319 400560882 2563 False 611.000000 1042 98.776500 1 2627 2 chr6D.!!$F1 2626

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
609 618 2.091555 AGGTGGGCAAAGTAGTTTTGGA 60.092 45.455 0.0 0.0 45.09 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 4201 2.031465 GCTCGGGGTGGACGAAAA 59.969 61.111 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
93 94 7.432869 AGGATTTCGTTTGATTTGATTTGTCA 58.567 30.769 0.00 0.00 0.00 3.58
605 614 6.208007 GTGTATTTAGGTGGGCAAAGTAGTTT 59.792 38.462 0.00 0.00 0.00 2.66
606 615 6.778559 TGTATTTAGGTGGGCAAAGTAGTTTT 59.221 34.615 0.00 0.00 0.00 2.43
608 617 2.316108 AGGTGGGCAAAGTAGTTTTGG 58.684 47.619 0.00 0.00 45.09 3.28
609 618 2.091555 AGGTGGGCAAAGTAGTTTTGGA 60.092 45.455 0.00 0.00 45.09 3.53
613 622 3.964031 TGGGCAAAGTAGTTTTGGATGTT 59.036 39.130 0.00 0.00 45.09 2.71
614 623 5.010213 GTGGGCAAAGTAGTTTTGGATGTTA 59.990 40.000 0.00 0.00 45.09 2.41
615 624 5.598830 TGGGCAAAGTAGTTTTGGATGTTAA 59.401 36.000 0.00 0.00 45.09 2.01
616 625 5.924254 GGGCAAAGTAGTTTTGGATGTTAAC 59.076 40.000 0.00 0.00 45.09 2.01
617 626 6.461788 GGGCAAAGTAGTTTTGGATGTTAACA 60.462 38.462 11.41 11.41 45.09 2.41
619 628 8.301002 GGCAAAGTAGTTTTGGATGTTAACATA 58.699 33.333 20.83 3.97 45.09 2.29
620 629 9.855021 GCAAAGTAGTTTTGGATGTTAACATAT 57.145 29.630 20.83 0.64 45.09 1.78
627 636 9.174166 AGTTTTGGATGTTAACATATACCACTC 57.826 33.333 20.83 14.59 36.57 3.51
628 637 8.403236 GTTTTGGATGTTAACATATACCACTCC 58.597 37.037 20.83 15.75 36.57 3.85
629 638 7.446106 TTGGATGTTAACATATACCACTCCT 57.554 36.000 20.83 0.00 36.57 3.69
630 639 7.062749 TGGATGTTAACATATACCACTCCTC 57.937 40.000 20.83 5.11 36.57 3.71
631 640 6.613679 TGGATGTTAACATATACCACTCCTCA 59.386 38.462 20.83 0.00 36.57 3.86
632 641 7.126573 TGGATGTTAACATATACCACTCCTCAA 59.873 37.037 20.83 0.00 36.57 3.02
633 642 7.441458 GGATGTTAACATATACCACTCCTCAAC 59.559 40.741 20.83 3.05 36.57 3.18
634 643 7.247456 TGTTAACATATACCACTCCTCAACA 57.753 36.000 3.59 0.00 0.00 3.33
635 644 7.327975 TGTTAACATATACCACTCCTCAACAG 58.672 38.462 3.59 0.00 0.00 3.16
636 645 7.038587 TGTTAACATATACCACTCCTCAACAGT 60.039 37.037 3.59 0.00 0.00 3.55
637 646 8.472413 GTTAACATATACCACTCCTCAACAGTA 58.528 37.037 0.00 0.00 0.00 2.74
638 647 7.490657 AACATATACCACTCCTCAACAGTAA 57.509 36.000 0.00 0.00 0.00 2.24
639 648 7.676683 ACATATACCACTCCTCAACAGTAAT 57.323 36.000 0.00 0.00 0.00 1.89
640 649 8.777578 ACATATACCACTCCTCAACAGTAATA 57.222 34.615 0.00 0.00 0.00 0.98
641 650 9.209048 ACATATACCACTCCTCAACAGTAATAA 57.791 33.333 0.00 0.00 0.00 1.40
644 653 6.182507 ACCACTCCTCAACAGTAATAAACA 57.817 37.500 0.00 0.00 0.00 2.83
645 654 6.231211 ACCACTCCTCAACAGTAATAAACAG 58.769 40.000 0.00 0.00 0.00 3.16
646 655 6.042781 ACCACTCCTCAACAGTAATAAACAGA 59.957 38.462 0.00 0.00 0.00 3.41
647 656 6.591834 CCACTCCTCAACAGTAATAAACAGAG 59.408 42.308 0.00 0.00 0.00 3.35
648 657 6.091441 CACTCCTCAACAGTAATAAACAGAGC 59.909 42.308 0.00 0.00 0.00 4.09
649 658 5.488341 TCCTCAACAGTAATAAACAGAGCC 58.512 41.667 0.00 0.00 0.00 4.70
650 659 5.248477 TCCTCAACAGTAATAAACAGAGCCT 59.752 40.000 0.00 0.00 0.00 4.58
651 660 5.352569 CCTCAACAGTAATAAACAGAGCCTG 59.647 44.000 1.16 1.16 37.52 4.85
652 661 4.695455 TCAACAGTAATAAACAGAGCCTGC 59.305 41.667 2.50 0.00 34.37 4.85
887 897 7.125204 ACATTAGGTACTGCCATGAACTAACTA 59.875 37.037 0.00 0.00 41.52 2.24
1100 1110 7.790027 AGTGCTCTAACTATTCATCAGTTGAT 58.210 34.615 0.00 0.00 36.88 2.57
1548 1558 3.598299 AGAGAAGCAGATGCAAGAGTTC 58.402 45.455 7.68 1.88 45.16 3.01
2014 4209 5.240121 TGATAGGTTTAGGTGTTTTCGTCC 58.760 41.667 0.00 0.00 0.00 4.79
2038 4233 0.396695 CGAGCCACCCTAGACCCTAA 60.397 60.000 0.00 0.00 0.00 2.69
2087 5690 0.396695 CGAGCCACCCTAGACCCTAA 60.397 60.000 0.00 0.00 0.00 2.69
2407 7343 5.844004 AGCCTAGACCTTAACAACATATCG 58.156 41.667 0.00 0.00 0.00 2.92
2443 8669 7.564793 ACAACAATATATCCAGCAACAGAGTA 58.435 34.615 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.591085 ACCTAACCCTAACCCTAGCTCT 59.409 50.000 0.00 0.00 0.00 4.09
93 94 1.202615 CCATCATGTGCAGAGGACGAT 60.203 52.381 0.00 0.00 0.00 3.73
418 427 7.012327 GCACACAACAGGAGCATATATTTTCTA 59.988 37.037 0.00 0.00 0.00 2.10
419 428 6.183360 GCACACAACAGGAGCATATATTTTCT 60.183 38.462 0.00 0.00 0.00 2.52
420 429 5.973565 GCACACAACAGGAGCATATATTTTC 59.026 40.000 0.00 0.00 0.00 2.29
605 614 7.126573 TGAGGAGTGGTATATGTTAACATCCAA 59.873 37.037 24.00 8.15 37.76 3.53
606 615 6.613679 TGAGGAGTGGTATATGTTAACATCCA 59.386 38.462 24.00 20.99 37.76 3.41
607 616 7.062749 TGAGGAGTGGTATATGTTAACATCC 57.937 40.000 24.00 18.80 37.76 3.51
608 617 7.985184 TGTTGAGGAGTGGTATATGTTAACATC 59.015 37.037 24.00 10.78 37.76 3.06
609 618 7.857456 TGTTGAGGAGTGGTATATGTTAACAT 58.143 34.615 23.80 23.80 40.22 2.71
613 622 8.598202 TTACTGTTGAGGAGTGGTATATGTTA 57.402 34.615 0.00 0.00 0.00 2.41
614 623 7.490657 TTACTGTTGAGGAGTGGTATATGTT 57.509 36.000 0.00 0.00 0.00 2.71
615 624 7.676683 ATTACTGTTGAGGAGTGGTATATGT 57.323 36.000 0.00 0.00 0.00 2.29
619 628 7.913789 TGTTTATTACTGTTGAGGAGTGGTAT 58.086 34.615 0.00 0.00 0.00 2.73
620 629 7.233962 TCTGTTTATTACTGTTGAGGAGTGGTA 59.766 37.037 0.00 0.00 0.00 3.25
621 630 6.042781 TCTGTTTATTACTGTTGAGGAGTGGT 59.957 38.462 0.00 0.00 0.00 4.16
622 631 6.464222 TCTGTTTATTACTGTTGAGGAGTGG 58.536 40.000 0.00 0.00 0.00 4.00
623 632 6.091441 GCTCTGTTTATTACTGTTGAGGAGTG 59.909 42.308 0.00 0.00 0.00 3.51
624 633 6.166982 GCTCTGTTTATTACTGTTGAGGAGT 58.833 40.000 0.00 0.00 0.00 3.85
625 634 5.582665 GGCTCTGTTTATTACTGTTGAGGAG 59.417 44.000 0.00 0.00 0.00 3.69
626 635 5.248477 AGGCTCTGTTTATTACTGTTGAGGA 59.752 40.000 0.00 0.00 0.00 3.71
627 636 5.352569 CAGGCTCTGTTTATTACTGTTGAGG 59.647 44.000 0.00 0.00 0.00 3.86
628 637 5.163814 GCAGGCTCTGTTTATTACTGTTGAG 60.164 44.000 4.45 0.00 33.43 3.02
629 638 4.695455 GCAGGCTCTGTTTATTACTGTTGA 59.305 41.667 4.45 0.00 33.43 3.18
630 639 4.436050 CGCAGGCTCTGTTTATTACTGTTG 60.436 45.833 4.45 0.00 33.43 3.33
631 640 3.684788 CGCAGGCTCTGTTTATTACTGTT 59.315 43.478 4.45 0.00 33.43 3.16
632 641 3.262420 CGCAGGCTCTGTTTATTACTGT 58.738 45.455 4.45 0.00 33.43 3.55
633 642 2.609459 CCGCAGGCTCTGTTTATTACTG 59.391 50.000 4.45 0.00 46.14 2.74
634 643 2.906354 CCGCAGGCTCTGTTTATTACT 58.094 47.619 4.45 0.00 46.14 2.24
649 658 8.729756 TGACCATTAATATAATGAAATCCGCAG 58.270 33.333 10.82 0.00 0.00 5.18
650 659 8.628630 TGACCATTAATATAATGAAATCCGCA 57.371 30.769 10.82 0.00 0.00 5.69
933 943 8.534496 CAATTCTGACCTTCCTGGAAAAATTAT 58.466 33.333 10.86 0.00 39.71 1.28
1100 1110 5.182001 GCATCCAGCTTGTTCTTTTCTTCTA 59.818 40.000 0.00 0.00 41.15 2.10
1548 1558 4.272991 GCCTTGATGAGCTCAGTAATCTTG 59.727 45.833 22.96 10.70 34.68 3.02
1736 1779 4.950050 AGAGTTACAACCAGAGTTCACAG 58.050 43.478 0.00 0.00 32.45 3.66
2006 4201 2.031465 GCTCGGGGTGGACGAAAA 59.969 61.111 0.00 0.00 40.16 2.29
2014 4209 3.470888 CTAGGGTGGCTCGGGGTG 61.471 72.222 0.00 0.00 0.00 4.61
2038 4233 3.365472 GGAACCACCTAAAGGCATCATT 58.635 45.455 0.00 0.00 39.32 2.57
2087 5690 3.365472 GGAACCACCTAAAGGCATCATT 58.635 45.455 0.00 0.00 39.32 2.57
2443 8669 6.747414 TGGTGCATACTATTGGATAGAGTT 57.253 37.500 0.00 0.00 36.68 3.01


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

AutoCloner maintained by Alex Coulton.