Multiple sequence alignment - TraesCS1B01G214200

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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 TraesCS1B01G214200 chr1B 100.000 2880 0 0 1 2880 389006625 389009504 0.000000e+00 5319.0
1 TraesCS1B01G214200 chr1B 95.760 2052 66 14 1 2045 389088837 389090874 0.000000e+00 3288.0
2 TraesCS1B01G214200 chr1B 91.610 584 45 4 1 581 319161911 319161329 0.000000e+00 804.0
3 TraesCS1B01G214200 chr1B 92.135 534 38 4 1 531 118173242 118173774 0.000000e+00 750.0
4 TraesCS1B01G214200 chr1B 76.758 512 95 20 2352 2849 660726906 660727407 6.120000e-67 265.0
5 TraesCS1B01G214200 chr1B 97.143 35 0 1 546 579 68132508 68132474 1.110000e-04 58.4
6 TraesCS1B01G214200 chr1A 95.756 1461 47 6 591 2045 358151112 358152563 0.000000e+00 2340.0
7 TraesCS1B01G214200 chr1A 95.483 1461 48 7 591 2045 358174586 358176034 0.000000e+00 2316.0
8 TraesCS1B01G214200 chr1A 94.160 839 39 6 2044 2880 358152704 358153534 0.000000e+00 1269.0
9 TraesCS1B01G214200 chr1D 97.048 1321 32 2 591 1911 286749702 286751015 0.000000e+00 2217.0
10 TraesCS1B01G214200 chr1D 77.987 636 103 25 2271 2880 413727408 413726784 5.860000e-97 364.0
11 TraesCS1B01G214200 chrUn 93.186 587 33 5 1 581 347152999 347152414 0.000000e+00 856.0
12 TraesCS1B01G214200 chr5D 93.151 584 33 6 1 579 92442736 92442155 0.000000e+00 850.0
13 TraesCS1B01G214200 chr5D 92.479 585 37 6 1 581 554386888 554387469 0.000000e+00 830.0
14 TraesCS1B01G214200 chr5D 79.077 607 107 14 2254 2849 205565264 205564667 1.610000e-107 399.0
15 TraesCS1B01G214200 chr5D 79.478 575 100 15 2286 2849 420465742 420466309 2.690000e-105 392.0
16 TraesCS1B01G214200 chr2D 92.955 582 36 4 1 579 648655023 648655602 0.000000e+00 843.0
17 TraesCS1B01G214200 chr2D 88.462 52 5 1 2090 2140 138364987 138364936 8.620000e-06 62.1
18 TraesCS1B01G214200 chr2B 90.706 581 51 3 1 581 407148466 407149043 0.000000e+00 771.0
19 TraesCS1B01G214200 chr2B 90.361 581 55 1 1 581 407103152 407103731 0.000000e+00 761.0
20 TraesCS1B01G214200 chr4A 82.660 594 87 13 2262 2849 31786205 31785622 1.980000e-141 512.0
21 TraesCS1B01G214200 chr4A 84.783 92 14 0 1405 1496 26413651 26413560 3.060000e-15 93.5
22 TraesCS1B01G214200 chr5A 79.104 670 119 16 2193 2849 245434055 245433394 2.630000e-120 442.0
23 TraesCS1B01G214200 chr7B 79.934 608 102 16 2255 2849 544452166 544452766 2.050000e-116 429.0
24 TraesCS1B01G214200 chr3B 78.783 608 110 16 2254 2849 40143816 40144416 9.680000e-105 390.0
25 TraesCS1B01G214200 chr3D 73.852 283 70 4 1405 1685 157443215 157442935 3.030000e-20 110.0
26 TraesCS1B01G214200 chr3D 72.590 332 73 14 1405 1727 157540410 157540088 3.060000e-15 93.5
27 TraesCS1B01G214200 chr3A 73.519 287 67 8 1405 1685 170811852 170812135 1.830000e-17 100.0
28 TraesCS1B01G214200 chr4B 85.870 92 13 0 1405 1496 547205194 547205285 6.570000e-17 99.0
29 TraesCS1B01G214200 chr5B 77.576 165 33 3 1405 1567 700997746 700997908 2.360000e-16 97.1
30 TraesCS1B01G214200 chr2A 88.462 52 5 1 2090 2140 163486914 163486965 8.620000e-06 62.1


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 TraesCS1B01G214200 chr1B 389006625 389009504 2879 False 5319.0 5319 100.000 1 2880 1 chr1B.!!$F2 2879
1 TraesCS1B01G214200 chr1B 389088837 389090874 2037 False 3288.0 3288 95.760 1 2045 1 chr1B.!!$F3 2044
2 TraesCS1B01G214200 chr1B 319161329 319161911 582 True 804.0 804 91.610 1 581 1 chr1B.!!$R2 580
3 TraesCS1B01G214200 chr1B 118173242 118173774 532 False 750.0 750 92.135 1 531 1 chr1B.!!$F1 530
4 TraesCS1B01G214200 chr1B 660726906 660727407 501 False 265.0 265 76.758 2352 2849 1 chr1B.!!$F4 497
5 TraesCS1B01G214200 chr1A 358174586 358176034 1448 False 2316.0 2316 95.483 591 2045 1 chr1A.!!$F1 1454
6 TraesCS1B01G214200 chr1A 358151112 358153534 2422 False 1804.5 2340 94.958 591 2880 2 chr1A.!!$F2 2289
7 TraesCS1B01G214200 chr1D 286749702 286751015 1313 False 2217.0 2217 97.048 591 1911 1 chr1D.!!$F1 1320
8 TraesCS1B01G214200 chr1D 413726784 413727408 624 True 364.0 364 77.987 2271 2880 1 chr1D.!!$R1 609
9 TraesCS1B01G214200 chrUn 347152414 347152999 585 True 856.0 856 93.186 1 581 1 chrUn.!!$R1 580
10 TraesCS1B01G214200 chr5D 92442155 92442736 581 True 850.0 850 93.151 1 579 1 chr5D.!!$R1 578
11 TraesCS1B01G214200 chr5D 554386888 554387469 581 False 830.0 830 92.479 1 581 1 chr5D.!!$F2 580
12 TraesCS1B01G214200 chr5D 205564667 205565264 597 True 399.0 399 79.077 2254 2849 1 chr5D.!!$R2 595
13 TraesCS1B01G214200 chr5D 420465742 420466309 567 False 392.0 392 79.478 2286 2849 1 chr5D.!!$F1 563
14 TraesCS1B01G214200 chr2D 648655023 648655602 579 False 843.0 843 92.955 1 579 1 chr2D.!!$F1 578
15 TraesCS1B01G214200 chr2B 407148466 407149043 577 False 771.0 771 90.706 1 581 1 chr2B.!!$F2 580
16 TraesCS1B01G214200 chr2B 407103152 407103731 579 False 761.0 761 90.361 1 581 1 chr2B.!!$F1 580
17 TraesCS1B01G214200 chr4A 31785622 31786205 583 True 512.0 512 82.660 2262 2849 1 chr4A.!!$R2 587
18 TraesCS1B01G214200 chr5A 245433394 245434055 661 True 442.0 442 79.104 2193 2849 1 chr5A.!!$R1 656
19 TraesCS1B01G214200 chr7B 544452166 544452766 600 False 429.0 429 79.934 2255 2849 1 chr7B.!!$F1 594
20 TraesCS1B01G214200 chr3B 40143816 40144416 600 False 390.0 390 78.783 2254 2849 1 chr3B.!!$F1 595

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
524 539 0.676466 CATAGTTGCTTGACCCGGCA 60.676 55.0 0.0 0.0 36.62 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 1994 0.611714 AACGGTAGAGGGCAACGATT 59.388 50.0 0.0 0.0 37.6 3.34 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
33 34 9.829507 CATAGGAAGTAACATGAGAGAGAATTT 57.170 33.333 0.00 0.00 0.00 1.82
79 82 9.216117 AGGGTATCGAGCATATATTTTACAAAC 57.784 33.333 0.00 0.00 0.00 2.93
149 154 9.241317 GGAAGCATCAAACATGTTAATATGAAG 57.759 33.333 22.30 15.86 0.00 3.02
166 171 8.517062 AATATGAAGTCCTCCAAGAAAAGATG 57.483 34.615 0.00 0.00 0.00 2.90
303 317 6.266323 AGATACTTACTGCAACTATCACACG 58.734 40.000 0.00 0.00 0.00 4.49
322 336 1.806542 CGTGATTGGTTAGCTTGCTGT 59.193 47.619 5.26 0.00 0.00 4.40
483 498 6.377712 TCATAACAATGCATGTCCTGATCAAA 59.622 34.615 0.00 0.00 42.99 2.69
524 539 0.676466 CATAGTTGCTTGACCCGGCA 60.676 55.000 0.00 0.00 36.62 5.69
537 552 3.013921 GACCCGGCACATTCATAGAAAA 58.986 45.455 0.00 0.00 0.00 2.29
542 557 3.845775 CGGCACATTCATAGAAAACGTTG 59.154 43.478 0.00 0.00 0.00 4.10
543 558 4.612712 CGGCACATTCATAGAAAACGTTGT 60.613 41.667 0.00 0.00 0.00 3.32
544 559 4.851558 GGCACATTCATAGAAAACGTTGTC 59.148 41.667 10.66 10.66 0.00 3.18
846 868 5.186215 TGGCCCGAAGATTGAACGATATATA 59.814 40.000 0.00 0.00 0.00 0.86
875 897 1.871676 CAATCATCACCGGCTGATCTG 59.128 52.381 14.28 8.31 37.53 2.90
1687 1719 2.036256 ATGTGGGTGAAGGGCAGC 59.964 61.111 0.00 0.00 44.17 5.25
1937 1969 1.696336 AGGAGCTGTGACACTGACAAT 59.304 47.619 15.90 0.00 0.00 2.71
1943 1975 2.735663 CTGTGACACTGACAATGCTCTC 59.264 50.000 7.20 0.00 0.00 3.20
1961 1994 2.434843 CCGGTGCTCTGCTGGGATA 61.435 63.158 0.00 0.00 0.00 2.59
2088 2264 3.314541 AGACTAAAGTTGGTACAGCCG 57.685 47.619 0.00 0.00 41.77 5.52
2112 2288 3.047877 CAACTCCAACCGGCCGAC 61.048 66.667 30.73 0.00 0.00 4.79
2145 2322 5.064198 CGTTGGATTTGTCCGCTTTCTATTA 59.936 40.000 0.00 0.00 0.00 0.98
2151 2328 8.837389 GGATTTGTCCGCTTTCTATTAGTTTAT 58.163 33.333 0.00 0.00 0.00 1.40
2160 2337 9.915629 CGCTTTCTATTAGTTTATAGATGGTCT 57.084 33.333 0.00 0.00 37.08 3.85
2177 2354 1.762460 CTGGAGGGGCGGTGTCTAT 60.762 63.158 0.00 0.00 0.00 1.98
2229 2407 4.401202 GTCCAACGGGTAATCCATTTGATT 59.599 41.667 0.00 0.00 45.64 2.57
2235 2413 4.261572 CGGGTAATCCATTTGATTCGCATT 60.262 41.667 0.00 0.00 42.75 3.56
2252 2431 7.561237 TTCGCATTGCTGTTTTTATCTAAAC 57.439 32.000 7.12 0.00 38.26 2.01
2785 2997 3.578282 CCCTTGTTCTTTGGCAAACCTAT 59.422 43.478 8.93 0.00 36.63 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 6.017192 ACCCTGAACTGAAGTTATGACTCTA 58.983 40.000 0.00 0.00 38.56 2.43
43 46 2.166664 GCTCGATACCCTGAACTGAAGT 59.833 50.000 0.00 0.00 0.00 3.01
149 154 4.646572 ACACTCATCTTTTCTTGGAGGAC 58.353 43.478 0.00 0.00 0.00 3.85
283 297 3.987868 CACGTGTGATAGTTGCAGTAAGT 59.012 43.478 7.58 0.00 0.00 2.24
303 317 3.568538 CAACAGCAAGCTAACCAATCAC 58.431 45.455 0.00 0.00 0.00 3.06
463 477 4.338012 TCTTTGATCAGGACATGCATTGT 58.662 39.130 0.00 0.00 42.79 2.71
465 479 4.583489 GGATCTTTGATCAGGACATGCATT 59.417 41.667 0.00 0.00 0.00 3.56
520 535 3.740044 ACGTTTTCTATGAATGTGCCG 57.260 42.857 0.00 0.00 0.00 5.69
603 625 4.292571 TCTGGGAGAGATCGGATAGGTTAT 59.707 45.833 0.00 0.00 0.00 1.89
846 868 2.105477 CCGGTGATGATTGAGGAGGAAT 59.895 50.000 0.00 0.00 0.00 3.01
875 897 2.290260 TGGATCAATCAGTGTGGTGGTC 60.290 50.000 0.00 0.00 0.00 4.02
1729 1761 2.493030 CCGAACGCCTGGTACGAT 59.507 61.111 0.64 0.00 0.00 3.73
1937 1969 4.074526 GCAGAGCACCGGAGAGCA 62.075 66.667 9.46 0.00 0.00 4.26
1943 1975 1.971505 TTATCCCAGCAGAGCACCGG 61.972 60.000 0.00 0.00 0.00 5.28
1961 1994 0.611714 AACGGTAGAGGGCAACGATT 59.388 50.000 0.00 0.00 37.60 3.34
2088 2264 0.958876 CCGGTTGGAGTTGGCCTTAC 60.959 60.000 3.32 1.81 37.49 2.34
2145 2322 4.235372 CCCCTCCAGACCATCTATAAACT 58.765 47.826 0.00 0.00 0.00 2.66
2151 2328 1.457643 CGCCCCTCCAGACCATCTA 60.458 63.158 0.00 0.00 0.00 1.98
2152 2329 2.765807 CGCCCCTCCAGACCATCT 60.766 66.667 0.00 0.00 0.00 2.90
2153 2330 3.866582 CCGCCCCTCCAGACCATC 61.867 72.222 0.00 0.00 0.00 3.51
2154 2331 4.741239 ACCGCCCCTCCAGACCAT 62.741 66.667 0.00 0.00 0.00 3.55
2160 2337 1.760875 GATAGACACCGCCCCTCCA 60.761 63.158 0.00 0.00 0.00 3.86
2177 2354 2.483876 CAGAAAAGAGCTGACAACGGA 58.516 47.619 0.00 0.00 35.39 4.69
2180 2357 1.268079 GGCCAGAAAAGAGCTGACAAC 59.732 52.381 0.00 0.00 35.39 3.32
2186 2363 1.302832 CACCGGCCAGAAAAGAGCT 60.303 57.895 0.00 0.00 0.00 4.09
2229 2407 6.908825 AGTTTAGATAAAAACAGCAATGCGA 58.091 32.000 0.00 0.00 40.97 5.10
2445 2647 3.555956 GGTTAAGCATATGTGGACTCACG 59.444 47.826 4.29 0.00 46.42 4.35
2463 2665 9.258826 CACATTCAACTTCAAATGATTTGGTTA 57.741 29.630 17.01 2.47 40.98 2.85
2547 2751 0.967887 TGGTTGAGCTCGAGGGAGAG 60.968 60.000 15.58 0.00 43.27 3.20
2785 2997 0.043334 CCCCAAGGAGAGAAGAGGGA 59.957 60.000 0.00 0.00 38.60 4.20


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

AutoCloner maintained by Alex Coulton.