Multiple sequence alignment - TraesCS1D01G213200

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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 TraesCS1D01G213200 chr1D 100.000 2699 0 0 1 2699 298607496 298604798 0.000000e+00 4985
1 TraesCS1D01G213200 chr1D 88.636 572 56 4 763 1326 385053035 385052465 0.000000e+00 688
2 TraesCS1D01G213200 chr1D 89.452 493 27 4 1327 1798 385052341 385051853 1.380000e-167 599
3 TraesCS1D01G213200 chr1D 84.842 442 56 3 199 632 47928814 47928376 4.130000e-118 435
4 TraesCS1D01G213200 chr1D 86.869 297 30 2 8 296 224518251 224517956 9.320000e-85 324
5 TraesCS1D01G213200 chr1B 97.733 838 10 4 1646 2483 402041903 402041075 0.000000e+00 1434
6 TraesCS1D01G213200 chr1B 88.082 881 60 14 1 869 402048670 402047823 0.000000e+00 1003
7 TraesCS1D01G213200 chr1B 96.739 460 15 0 867 1326 402044428 402043969 0.000000e+00 767
8 TraesCS1D01G213200 chr1B 89.336 572 53 3 763 1326 517508027 517507456 0.000000e+00 712
9 TraesCS1D01G213200 chr1B 89.249 493 28 4 1327 1798 517507340 517506852 6.430000e-166 593
10 TraesCS1D01G213200 chr1B 92.135 356 6 2 1327 1661 402043845 402043491 1.450000e-132 483
11 TraesCS1D01G213200 chr1B 98.222 225 4 0 2475 2699 402040168 402039944 7.000000e-106 394
12 TraesCS1D01G213200 chr1B 93.684 95 6 0 2605 2699 401992893 401992799 2.800000e-30 143
13 TraesCS1D01G213200 chr1B 93.617 94 6 0 2606 2699 401764159 401764066 1.010000e-29 141
14 TraesCS1D01G213200 chr1A 86.509 719 59 11 2011 2699 372317278 372316568 0.000000e+00 756
15 TraesCS1D01G213200 chr1A 89.161 572 54 2 763 1326 485215677 485215106 0.000000e+00 706
16 TraesCS1D01G213200 chr1A 86.538 572 65 5 636 1195 372464978 372464407 1.060000e-173 619
17 TraesCS1D01G213200 chr1A 88.452 407 26 3 1327 1712 485214982 485214576 3.150000e-129 472
18 TraesCS1D01G213200 chr1A 86.423 383 40 4 6 380 41149550 41149928 2.500000e-110 409
19 TraesCS1D01G213200 chr1A 87.755 294 15 10 1327 1600 372395985 372395693 9.320000e-85 324
20 TraesCS1D01G213200 chr1A 92.086 139 11 0 1188 1326 372396247 372396109 2.120000e-46 196
21 TraesCS1D01G213200 chr1A 86.667 180 19 4 2524 2699 372288274 372288096 7.620000e-46 195
22 TraesCS1D01G213200 chr7D 87.850 642 63 7 6 638 223095752 223095117 0.000000e+00 739
23 TraesCS1D01G213200 chr7D 85.034 441 49 12 199 629 615930830 615931263 1.480000e-117 433
24 TraesCS1D01G213200 chr7D 93.258 89 4 2 1703 1790 168811102 168811015 2.180000e-26 130
25 TraesCS1D01G213200 chr7D 87.879 66 5 3 738 800 169041011 169040946 1.040000e-09 75
26 TraesCS1D01G213200 chr6B 87.461 638 65 9 10 639 211812963 211812333 0.000000e+00 721
27 TraesCS1D01G213200 chr6A 86.739 641 69 6 9 639 147985201 147984567 0.000000e+00 699
28 TraesCS1D01G213200 chr6A 84.929 637 68 19 6 638 555937718 555937106 1.060000e-173 619
29 TraesCS1D01G213200 chr6A 88.538 253 25 4 4 255 594403165 594402916 1.210000e-78 303
30 TraesCS1D01G213200 chr6D 86.772 635 61 18 9 639 119819078 119818463 0.000000e+00 686
31 TraesCS1D01G213200 chr6D 85.248 644 86 7 6 644 454579068 454579707 0.000000e+00 654
32 TraesCS1D01G213200 chr3B 84.418 661 60 27 6 632 109032740 109032089 6.390000e-171 610
33 TraesCS1D01G213200 chr5A 84.258 667 56 17 6 629 368182958 368183618 2.970000e-169 604
34 TraesCS1D01G213200 chr4D 82.982 617 80 15 43 638 508594879 508594267 3.960000e-148 534
35 TraesCS1D01G213200 chr3D 87.443 438 43 6 199 629 506116437 506116869 6.710000e-136 494
36 TraesCS1D01G213200 chr7B 75.817 612 109 19 752 1326 134304990 134304381 9.520000e-70 274
37 TraesCS1D01G213200 chr7B 93.258 89 4 2 1703 1790 134303637 134303550 2.180000e-26 130
38 TraesCS1D01G213200 chr7A 85.398 226 29 4 1565 1788 171273746 171273523 5.810000e-57 231
39 TraesCS1D01G213200 chr3A 79.412 272 48 8 1475 1741 647802503 647802235 4.590000e-43 185


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 TraesCS1D01G213200 chr1D 298604798 298607496 2698 True 4985.0 4985 100.0000 1 2699 1 chr1D.!!$R3 2698
1 TraesCS1D01G213200 chr1D 385051853 385053035 1182 True 643.5 688 89.0440 763 1798 2 chr1D.!!$R4 1035
2 TraesCS1D01G213200 chr1B 402039944 402048670 8726 True 816.2 1434 94.5822 1 2699 5 chr1B.!!$R3 2698
3 TraesCS1D01G213200 chr1B 517506852 517508027 1175 True 652.5 712 89.2925 763 1798 2 chr1B.!!$R4 1035
4 TraesCS1D01G213200 chr1A 372316568 372317278 710 True 756.0 756 86.5090 2011 2699 1 chr1A.!!$R2 688
5 TraesCS1D01G213200 chr1A 372464407 372464978 571 True 619.0 619 86.5380 636 1195 1 chr1A.!!$R3 559
6 TraesCS1D01G213200 chr1A 485214576 485215677 1101 True 589.0 706 88.8065 763 1712 2 chr1A.!!$R5 949
7 TraesCS1D01G213200 chr1A 372395693 372396247 554 True 260.0 324 89.9205 1188 1600 2 chr1A.!!$R4 412
8 TraesCS1D01G213200 chr7D 223095117 223095752 635 True 739.0 739 87.8500 6 638 1 chr7D.!!$R3 632
9 TraesCS1D01G213200 chr6B 211812333 211812963 630 True 721.0 721 87.4610 10 639 1 chr6B.!!$R1 629
10 TraesCS1D01G213200 chr6A 147984567 147985201 634 True 699.0 699 86.7390 9 639 1 chr6A.!!$R1 630
11 TraesCS1D01G213200 chr6A 555937106 555937718 612 True 619.0 619 84.9290 6 638 1 chr6A.!!$R2 632
12 TraesCS1D01G213200 chr6D 119818463 119819078 615 True 686.0 686 86.7720 9 639 1 chr6D.!!$R1 630
13 TraesCS1D01G213200 chr6D 454579068 454579707 639 False 654.0 654 85.2480 6 644 1 chr6D.!!$F1 638
14 TraesCS1D01G213200 chr3B 109032089 109032740 651 True 610.0 610 84.4180 6 632 1 chr3B.!!$R1 626
15 TraesCS1D01G213200 chr5A 368182958 368183618 660 False 604.0 604 84.2580 6 629 1 chr5A.!!$F1 623
16 TraesCS1D01G213200 chr4D 508594267 508594879 612 True 534.0 534 82.9820 43 638 1 chr4D.!!$R1 595
17 TraesCS1D01G213200 chr7B 134303550 134304990 1440 True 202.0 274 84.5375 752 1790 2 chr7B.!!$R1 1038

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
464 564 0.104855 GACACCATAGATGCGAGGCA 59.895 55.0 0.0 0.0 44.86 4.75 F
620 720 0.538118 TCGCAGCTTTATACGGGGTT 59.462 50.0 0.0 0.0 0.00 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 5178 1.362355 GGCAAAACCTGGTGTTCCG 59.638 57.895 0.0 0.0 35.67 4.30 R
2270 7809 3.074538 ACCACTTAGGCTCCACAGATTTT 59.925 43.478 0.0 0.0 43.14 1.82 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
329 427 0.886490 ATTCCGCCCGCAGATCATTC 60.886 55.000 0.00 0.00 0.00 2.67
418 518 1.021390 CGCGGGCTGAAATGTCTCTT 61.021 55.000 0.00 0.00 0.00 2.85
455 555 1.218450 TGGGATACGGGACACCATAGA 59.782 52.381 0.00 0.00 36.13 1.98
464 564 0.104855 GACACCATAGATGCGAGGCA 59.895 55.000 0.00 0.00 44.86 4.75
524 624 3.550030 CCGCGCCCCTCAAAAATATTTAG 60.550 47.826 0.00 0.00 0.00 1.85
620 720 0.538118 TCGCAGCTTTATACGGGGTT 59.462 50.000 0.00 0.00 0.00 4.11
629 729 4.377897 CTTTATACGGGGTTTGCTAGAGG 58.622 47.826 0.00 0.00 0.00 3.69
634 734 1.534729 GGGGTTTGCTAGAGGTGTTG 58.465 55.000 0.00 0.00 0.00 3.33
693 793 3.950397 TCAGACCTGTCTTGTTGTGTTT 58.050 40.909 0.00 0.00 37.98 2.83
1107 4631 3.483869 GCCATCGGCCCTCCTCTT 61.484 66.667 0.00 0.00 44.06 2.85
1291 4827 2.435586 CAAGCGTGCCCTCTCCAG 60.436 66.667 0.00 0.00 0.00 3.86
1458 5120 2.637383 GCCGGACTGGAAGACGACT 61.637 63.158 5.05 0.00 42.00 4.18
1486 5178 4.213482 AGAAACTTTTCCTCACGTACATGC 59.787 41.667 0.00 0.00 37.92 4.06
1529 5221 3.258372 GTGGAGAGTGTGGTATGTGAAGA 59.742 47.826 0.00 0.00 0.00 2.87
1871 7408 1.167851 CCCACGACACTACGGAGTTA 58.832 55.000 0.00 0.00 37.78 2.24
1981 7518 8.142994 ACATATGTGAACTCCGAAAATATGTC 57.857 34.615 7.78 0.00 35.78 3.06
2001 7538 5.972935 TGTCCGAGCACATTTCTCTATTTA 58.027 37.500 0.00 0.00 0.00 1.40
2005 7542 8.398665 GTCCGAGCACATTTCTCTATTTATTTT 58.601 33.333 0.00 0.00 0.00 1.82
2006 7543 8.612619 TCCGAGCACATTTCTCTATTTATTTTC 58.387 33.333 0.00 0.00 0.00 2.29
2127 7664 6.366061 TCGATGCCATTGATACTTTCTTATCG 59.634 38.462 0.00 0.00 35.28 2.92
2206 7743 1.289109 GAGTTGCTTGCGGTCGCTAA 61.289 55.000 16.36 8.15 42.51 3.09
2258 7797 2.434843 AATCGGAGAGCGCATCCCA 61.435 57.895 21.82 12.75 43.63 4.37
2378 7917 0.898789 TGGTTGACCGTCTCCTCCTC 60.899 60.000 12.23 0.00 39.43 3.71
2379 7918 1.605971 GGTTGACCGTCTCCTCCTCC 61.606 65.000 0.00 0.00 0.00 4.30
2380 7919 0.612453 GTTGACCGTCTCCTCCTCCT 60.612 60.000 0.00 0.00 0.00 3.69
2600 9055 9.632807 GATCTGTAGAAACCATCATACTGTATC 57.367 37.037 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
271 367 2.449967 TACCCTCTTCCACCGAGCCA 62.450 60.000 0.00 0.00 0.00 4.75
455 555 4.308526 CAGGTTTCTGCCTCGCAT 57.691 55.556 0.00 0.00 38.13 4.73
464 564 1.674817 CCCACGAATACGCAGGTTTCT 60.675 52.381 0.00 0.00 43.96 2.52
620 720 2.290071 GGGCTTACAACACCTCTAGCAA 60.290 50.000 0.00 0.00 0.00 3.91
629 729 1.073284 TCTGAAGGGGGCTTACAACAC 59.927 52.381 0.00 0.00 0.00 3.32
634 734 1.120530 TCGATCTGAAGGGGGCTTAC 58.879 55.000 0.00 0.00 0.00 2.34
693 793 0.609957 TCGCAGTCGAGGTTTAGGGA 60.610 55.000 0.00 0.00 40.21 4.20
808 918 3.712907 GCGGCCCCTGTAGTTGGA 61.713 66.667 0.00 0.00 0.00 3.53
1234 4761 4.895297 GCTTGGATTTGAAGAATGGGGATA 59.105 41.667 0.00 0.00 0.00 2.59
1291 4827 1.474077 GTCATCCTTGGTGAATGGCAC 59.526 52.381 0.00 0.00 46.98 5.01
1458 5120 5.286267 ACGTGAGGAAAAGTTTCTCCTTA 57.714 39.130 15.90 11.48 42.34 2.69
1486 5178 1.362355 GGCAAAACCTGGTGTTCCG 59.638 57.895 0.00 0.00 35.67 4.30
1529 5221 4.851639 AAGGCATCATCTAACTCCACTT 57.148 40.909 0.00 0.00 0.00 3.16
1863 7400 8.964476 ATGAATCATAGAAAACATAACTCCGT 57.036 30.769 0.00 0.00 0.00 4.69
1981 7518 8.397906 TGAAAATAAATAGAGAAATGTGCTCGG 58.602 33.333 0.00 0.00 37.46 4.63
2001 7538 7.882271 ACTTAGAGTGCTTTCTCTCATGAAAAT 59.118 33.333 0.00 0.00 42.84 1.82
2005 7542 5.991933 ACTTAGAGTGCTTTCTCTCATGA 57.008 39.130 9.21 0.00 42.84 3.07
2006 7543 7.763528 ACATAACTTAGAGTGCTTTCTCTCATG 59.236 37.037 9.21 0.00 42.84 3.07
2206 7743 3.129988 GTGAGCAGCATTTTTAGAGCCAT 59.870 43.478 0.00 0.00 0.00 4.40
2258 7797 3.571401 CCACAGATTTTCTCCAAGCAGTT 59.429 43.478 0.00 0.00 0.00 3.16
2270 7809 3.074538 ACCACTTAGGCTCCACAGATTTT 59.925 43.478 0.00 0.00 43.14 1.82
2526 8980 9.781834 CTTTAGCTATCGAATGGTAGAGATTAG 57.218 37.037 0.00 0.00 0.00 1.73
2600 9055 8.295288 GGGAGATCAATAATGAACAAGCTTATG 58.705 37.037 0.00 0.00 39.49 1.90


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

AutoCloner maintained by Alex Coulton.