Multiple sequence alignment - TraesCS4D01G114900

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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 TraesCS4D01G114900 chr4D 100.000 2941 0 0 1 2941 95780089 95783029 0.000000e+00 5432.0
1 TraesCS4D01G114900 chr4A 96.048 2986 56 16 1 2941 483952418 483949450 0.000000e+00 4804.0
2 TraesCS4D01G114900 chr4A 91.593 226 15 2 852 1077 373804806 373805027 2.850000e-80 309.0
3 TraesCS4D01G114900 chr4A 91.593 226 15 2 852 1077 606355196 606355417 2.850000e-80 309.0
4 TraesCS4D01G114900 chr4A 98.214 168 3 0 516 683 624286536 624286703 7.970000e-76 294.0
5 TraesCS4D01G114900 chr4A 100.000 30 0 0 752 781 624286702 624286731 4.090000e-04 56.5
6 TraesCS4D01G114900 chr4B 94.886 2679 70 18 300 2941 135210692 135213340 0.000000e+00 4126.0
7 TraesCS4D01G114900 chr4B 97.628 253 1 3 1 250 135210443 135210693 2.090000e-116 429.0
8 TraesCS4D01G114900 chr4B 96.471 170 4 1 516 683 211593425 211593256 2.230000e-71 279.0
9 TraesCS4D01G114900 chr4B 96.471 170 4 1 516 683 286753629 286753460 2.230000e-71 279.0
10 TraesCS4D01G114900 chr5A 82.915 597 73 20 846 1428 282588085 282587504 7.270000e-141 510.0
11 TraesCS4D01G114900 chr5A 92.478 226 13 2 852 1077 598933355 598933576 1.320000e-83 320.0
12 TraesCS4D01G114900 chr5D 82.667 600 74 21 846 1428 214919830 214919244 3.380000e-139 505.0
13 TraesCS4D01G114900 chr2A 82.558 602 73 24 847 1426 706995025 706995616 4.380000e-138 501.0
14 TraesCS4D01G114900 chr2A 78.529 340 65 7 1093 1428 645311418 645311753 1.770000e-52 217.0
15 TraesCS4D01G114900 chr2A 87.234 141 13 4 475 614 706994574 706994710 3.920000e-34 156.0
16 TraesCS4D01G114900 chr5B 82.412 597 77 20 846 1428 230248676 230248094 2.040000e-136 496.0
17 TraesCS4D01G114900 chr5B 96.471 170 4 1 516 683 36727182 36727351 2.230000e-71 279.0
18 TraesCS4D01G114900 chr2D 81.924 603 77 25 847 1428 567477118 567477709 5.700000e-132 481.0
19 TraesCS4D01G114900 chr2B 83.865 502 58 16 941 1428 680193883 680194375 9.610000e-125 457.0
20 TraesCS4D01G114900 chr7D 92.070 227 14 3 852 1078 548559393 548559615 1.700000e-82 316.0
21 TraesCS4D01G114900 chr7A 92.035 226 14 2 852 1077 663752276 663752055 6.120000e-82 315.0
22 TraesCS4D01G114900 chr7A 97.059 170 3 1 516 683 169392764 169392933 4.800000e-73 285.0
23 TraesCS4D01G114900 chr6B 92.070 227 13 2 852 1077 60485158 60484936 6.120000e-82 315.0
24 TraesCS4D01G114900 chr1B 91.593 226 15 2 852 1077 258836430 258836651 2.850000e-80 309.0
25 TraesCS4D01G114900 chr3B 97.059 170 3 1 516 683 327795860 327795691 4.800000e-73 285.0
26 TraesCS4D01G114900 chr1D 96.951 164 4 1 549 712 12646754 12646592 1.040000e-69 274.0
27 TraesCS4D01G114900 chr1D 97.368 38 1 0 713 750 12646573 12646536 6.800000e-07 65.8


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 TraesCS4D01G114900 chr4D 95780089 95783029 2940 False 5432.0 5432 100.000 1 2941 1 chr4D.!!$F1 2940
1 TraesCS4D01G114900 chr4A 483949450 483952418 2968 True 4804.0 4804 96.048 1 2941 1 chr4A.!!$R1 2940
2 TraesCS4D01G114900 chr4B 135210443 135213340 2897 False 2277.5 4126 96.257 1 2941 2 chr4B.!!$F1 2940
3 TraesCS4D01G114900 chr5A 282587504 282588085 581 True 510.0 510 82.915 846 1428 1 chr5A.!!$R1 582
4 TraesCS4D01G114900 chr5D 214919244 214919830 586 True 505.0 505 82.667 846 1428 1 chr5D.!!$R1 582
5 TraesCS4D01G114900 chr2A 706994574 706995616 1042 False 328.5 501 84.896 475 1426 2 chr2A.!!$F2 951
6 TraesCS4D01G114900 chr5B 230248094 230248676 582 True 496.0 496 82.412 846 1428 1 chr5B.!!$R1 582
7 TraesCS4D01G114900 chr2D 567477118 567477709 591 False 481.0 481 81.924 847 1428 1 chr2D.!!$F1 581

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
224 225 0.250553 CCAAGCGGACCACAGGTTTA 60.251 55.000 0.0 0.0 35.25 2.01 F
391 393 1.102978 CAGGTAAAAATGGGAGGCCG 58.897 55.000 0.0 0.0 0.00 6.13 F
1350 1555 1.078143 GAAGCATCTGGAAGCCGGT 60.078 57.895 1.9 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1555 0.101579 TCTCAAAGTGCACGACGTCA 59.898 50.000 17.16 0.0 0.00 4.35 R
1398 1603 1.220206 CCTGCAGCCGATGAAGAGT 59.780 57.895 8.66 0.0 36.54 3.24 R
2397 2615 0.321122 CCCCACTGAAGCACTCACTC 60.321 60.000 0.00 0.0 0.00 3.51 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
222 223 1.990160 TTCCAAGCGGACCACAGGTT 61.990 55.000 0.00 0.00 42.67 3.50
223 224 1.528309 CCAAGCGGACCACAGGTTT 60.528 57.895 0.00 0.00 35.25 3.27
224 225 0.250553 CCAAGCGGACCACAGGTTTA 60.251 55.000 0.00 0.00 35.25 2.01
226 227 1.950909 CAAGCGGACCACAGGTTTAAA 59.049 47.619 0.00 0.00 35.25 1.52
227 228 1.601166 AGCGGACCACAGGTTTAAAC 58.399 50.000 9.98 9.98 35.25 2.01
292 294 6.347725 GCTAATCCATCATGTCGGTCAATTAC 60.348 42.308 0.00 0.00 0.00 1.89
293 295 4.753516 TCCATCATGTCGGTCAATTACT 57.246 40.909 0.00 0.00 0.00 2.24
294 296 5.862678 TCCATCATGTCGGTCAATTACTA 57.137 39.130 0.00 0.00 0.00 1.82
295 297 5.597806 TCCATCATGTCGGTCAATTACTAC 58.402 41.667 0.00 0.00 0.00 2.73
296 298 5.362717 TCCATCATGTCGGTCAATTACTACT 59.637 40.000 0.00 0.00 0.00 2.57
297 299 6.548251 TCCATCATGTCGGTCAATTACTACTA 59.452 38.462 0.00 0.00 0.00 1.82
298 300 6.641314 CCATCATGTCGGTCAATTACTACTAC 59.359 42.308 0.00 0.00 0.00 2.73
299 301 7.426410 CATCATGTCGGTCAATTACTACTACT 58.574 38.462 0.00 0.00 0.00 2.57
300 302 8.565416 CATCATGTCGGTCAATTACTACTACTA 58.435 37.037 0.00 0.00 0.00 1.82
391 393 1.102978 CAGGTAAAAATGGGAGGCCG 58.897 55.000 0.00 0.00 0.00 6.13
796 948 2.113433 GCTGCTGAGCCCTCATGTG 61.113 63.158 0.23 0.00 39.57 3.21
1182 1381 3.684990 AAGCAGCACGCCGAGAGA 61.685 61.111 0.00 0.00 44.04 3.10
1350 1555 1.078143 GAAGCATCTGGAAGCCGGT 60.078 57.895 1.90 0.00 0.00 5.28
1365 1570 3.713963 GGTGACGTCGTGCACTTT 58.286 55.556 16.19 0.00 35.43 2.66
1380 1585 3.883744 CTTTGAGAGGGTGCGCGGT 62.884 63.158 8.83 0.00 0.00 5.68
2113 2326 1.354101 TTACTACCACCACCACCAGG 58.646 55.000 0.00 0.00 42.21 4.45
2257 2473 3.726291 TCGCCCCTTTTCTTTTTCTTG 57.274 42.857 0.00 0.00 0.00 3.02
2397 2615 5.868801 TGTGTATGTATGTGTCATGTCTGTG 59.131 40.000 0.00 0.00 0.00 3.66
2500 2718 3.371059 GGGATTTTGTTCTCTCCCCTCTC 60.371 52.174 0.00 0.00 41.35 3.20
2501 2719 3.521531 GGATTTTGTTCTCTCCCCTCTCT 59.478 47.826 0.00 0.00 0.00 3.10
2507 2725 5.011982 TGTTCTCTCCCCTCTCTCTTTTA 57.988 43.478 0.00 0.00 0.00 1.52
2604 2822 1.200948 GCTCAATGCTTTCACTCCCAC 59.799 52.381 0.00 0.00 38.95 4.61
2802 3027 5.334802 GGAAAATTTAGCAAATGCCCAACAC 60.335 40.000 0.94 0.00 43.38 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 227 9.956640 TGATAATTTGGCAGAAATTTTTATGGT 57.043 25.926 10.05 0.00 32.64 3.55
230 231 9.225436 GGGTTGATAATTTGGCAGAAATTTTTA 57.775 29.630 10.05 0.00 32.64 1.52
231 232 7.723172 TGGGTTGATAATTTGGCAGAAATTTTT 59.277 29.630 10.05 0.00 32.64 1.94
294 296 9.404848 TGAATAACATGCAGTAGTAGTAGTAGT 57.595 33.333 0.00 0.00 0.00 2.73
295 297 9.885934 CTGAATAACATGCAGTAGTAGTAGTAG 57.114 37.037 0.00 0.00 0.00 2.57
296 298 9.404848 ACTGAATAACATGCAGTAGTAGTAGTA 57.595 33.333 0.00 0.00 40.79 1.82
297 299 8.294954 ACTGAATAACATGCAGTAGTAGTAGT 57.705 34.615 0.00 0.00 40.79 2.73
298 300 9.025020 CAACTGAATAACATGCAGTAGTAGTAG 57.975 37.037 0.16 0.00 41.65 2.57
299 301 8.745590 TCAACTGAATAACATGCAGTAGTAGTA 58.254 33.333 0.16 0.00 41.65 1.82
300 302 7.611770 TCAACTGAATAACATGCAGTAGTAGT 58.388 34.615 0.16 0.00 41.65 2.73
391 393 7.255625 GCTTTCCCATTCTATTTCCAAGTATCC 60.256 40.741 0.00 0.00 0.00 2.59
431 433 3.054065 AGCTTCCCATTTCCTCTAACCAG 60.054 47.826 0.00 0.00 0.00 4.00
954 1140 2.731976 CGTGTTAGGCTCTTGTTGTCTC 59.268 50.000 0.00 0.00 0.00 3.36
1182 1381 2.273449 CCGCCAAGAGGGAAGCAT 59.727 61.111 0.00 0.00 40.01 3.79
1350 1555 0.101579 TCTCAAAGTGCACGACGTCA 59.898 50.000 17.16 0.00 0.00 4.35
1398 1603 1.220206 CCTGCAGCCGATGAAGAGT 59.780 57.895 8.66 0.00 36.54 3.24
1431 1636 2.112928 ACTGCCGTTGATGCACCA 59.887 55.556 0.00 0.00 34.46 4.17
1432 1637 2.562912 CACTGCCGTTGATGCACC 59.437 61.111 0.00 0.00 34.46 5.01
1438 1643 4.182433 TGGTGCCACTGCCGTTGA 62.182 61.111 0.00 0.00 36.33 3.18
1665 1870 5.412526 TGAAATGGTAACGTGTCTTGTTC 57.587 39.130 0.00 0.00 40.79 3.18
1745 1950 2.331132 GCTGCAGCTCCTTGTGTCC 61.331 63.158 31.33 0.00 38.21 4.02
1751 1956 4.737177 GCTGGGCTGCAGCTCCTT 62.737 66.667 34.91 0.00 41.95 3.36
2113 2326 2.131183 GTGCATAGCAGCAGTAGTAGC 58.869 52.381 0.00 0.00 46.69 3.58
2257 2473 4.404394 TGGAAGACAAAAAGGGGAGAAAAC 59.596 41.667 0.00 0.00 0.00 2.43
2397 2615 0.321122 CCCCACTGAAGCACTCACTC 60.321 60.000 0.00 0.00 0.00 3.51
2604 2822 4.762289 ACTTAATCCTTGCACCTCTAGG 57.238 45.455 0.00 0.00 38.78 3.02
2674 2892 3.632333 GCTTATTCCTAACAGGGCCTTT 58.368 45.455 1.32 4.66 35.59 3.11
2675 2893 2.421529 CGCTTATTCCTAACAGGGCCTT 60.422 50.000 1.32 0.00 35.59 4.35
2676 2894 1.141053 CGCTTATTCCTAACAGGGCCT 59.859 52.381 0.00 0.00 35.59 5.19
2838 3063 2.576615 AGATAAGGGAAAATCCGCAGC 58.423 47.619 0.00 0.00 37.43 5.25


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

AutoCloner maintained by Alex Coulton.