Multiple sequence alignment - TraesCS2D01G503900

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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 TraesCS2D01G503900 chr2D 100.000 2614 0 0 1 2614 598711682 598714295 0.000000e+00 4828.0
1 TraesCS2D01G503900 chr2D 79.562 685 87 24 924 1602 597322441 597323078 8.590000e-120 440.0
2 TraesCS2D01G503900 chr2B 91.651 2635 97 48 1 2564 726544756 726547338 0.000000e+00 3533.0
3 TraesCS2D01G503900 chr2B 81.659 687 74 21 924 1602 726135768 726136410 8.290000e-145 523.0
4 TraesCS2D01G503900 chr2A 90.305 2692 116 57 1 2602 732579279 732581915 0.000000e+00 3391.0
5 TraesCS2D01G503900 chr2A 79.898 781 101 36 924 1696 731379345 731380077 2.980000e-144 521.0
6 TraesCS2D01G503900 chr7D 88.158 76 9 0 1012 1087 93949371 93949296 9.960000e-15 91.6
7 TraesCS2D01G503900 chr7D 88.158 76 9 0 1012 1087 94005564 94005639 9.960000e-15 91.6
8 TraesCS2D01G503900 chr7B 88.158 76 9 0 1012 1087 47737281 47737356 9.960000e-15 91.6
9 TraesCS2D01G503900 chr6D 86.667 75 10 0 1012 1086 443741338 443741264 1.670000e-12 84.2


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 TraesCS2D01G503900 chr2D 598711682 598714295 2613 False 4828 4828 100.000 1 2614 1 chr2D.!!$F2 2613
1 TraesCS2D01G503900 chr2D 597322441 597323078 637 False 440 440 79.562 924 1602 1 chr2D.!!$F1 678
2 TraesCS2D01G503900 chr2B 726544756 726547338 2582 False 3533 3533 91.651 1 2564 1 chr2B.!!$F2 2563
3 TraesCS2D01G503900 chr2B 726135768 726136410 642 False 523 523 81.659 924 1602 1 chr2B.!!$F1 678
4 TraesCS2D01G503900 chr2A 732579279 732581915 2636 False 3391 3391 90.305 1 2602 1 chr2A.!!$F2 2601
5 TraesCS2D01G503900 chr2A 731379345 731380077 732 False 521 521 79.898 924 1696 1 chr2A.!!$F1 772

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
708 775 0.471191 TATCCATCCACAGGCTGCTG 59.529 55.0 15.89 11.87 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 2282 0.250597 AAGATCTGCACTGCACTGCA 60.251 50.0 18.27 18.27 45.06 4.41 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
86 87 8.660373 CACCAATCTAGAAACAAATCACTCTAC 58.340 37.037 0.00 0.00 0.00 2.59
95 96 8.091449 AGAAACAAATCACTCTACTCGAAATCT 58.909 33.333 0.00 0.00 0.00 2.40
118 119 8.327941 TCTGAGTGATTTGTAGGAAATTTCAG 57.672 34.615 19.49 4.35 31.58 3.02
380 403 1.229272 TAACTGGCCTACGGGGTGT 60.229 57.895 3.32 0.00 37.43 4.16
381 404 1.546589 TAACTGGCCTACGGGGTGTG 61.547 60.000 3.32 0.00 37.43 3.82
383 406 4.966274 TGGCCTACGGGGTGTGGT 62.966 66.667 3.32 0.00 37.43 4.16
406 429 4.680237 CTGCACCCTCGCCGACAA 62.680 66.667 0.00 0.00 0.00 3.18
431 455 5.606505 TCAAACATCACTGCTGTACAACTA 58.393 37.500 0.00 0.00 0.00 2.24
502 559 1.076632 TTCCAAACCCAACAGCGGT 60.077 52.632 0.00 0.00 34.07 5.68
538 595 1.553248 TGCCATGCGACCTTAACTACT 59.447 47.619 0.00 0.00 0.00 2.57
539 596 2.202566 GCCATGCGACCTTAACTACTC 58.797 52.381 0.00 0.00 0.00 2.59
543 600 4.499357 CCATGCGACCTTAACTACTCCTAC 60.499 50.000 0.00 0.00 0.00 3.18
546 603 3.127721 GCGACCTTAACTACTCCTACGTT 59.872 47.826 0.00 0.00 0.00 3.99
564 621 4.465512 GCATGCACCAAGGTCGCG 62.466 66.667 14.21 0.00 0.00 5.87
664 728 5.287042 ACCCATCCATCTATCTATCTGCAT 58.713 41.667 0.00 0.00 0.00 3.96
672 736 4.079253 TCTATCTATCTGCATGGCGTACA 58.921 43.478 0.00 0.00 0.00 2.90
707 774 0.471617 GTATCCATCCACAGGCTGCT 59.528 55.000 15.89 0.00 0.00 4.24
708 775 0.471191 TATCCATCCACAGGCTGCTG 59.529 55.000 15.89 11.87 0.00 4.41
846 916 3.323136 CCCGAGAAAGATCGCGCG 61.323 66.667 26.76 26.76 45.92 6.86
1155 1273 3.290948 TTTCTGTTAGTGGCAAGGTGT 57.709 42.857 0.00 0.00 0.00 4.16
1157 1275 3.290948 TCTGTTAGTGGCAAGGTGTTT 57.709 42.857 0.00 0.00 0.00 2.83
1162 1280 4.096682 TGTTAGTGGCAAGGTGTTTGTTAC 59.903 41.667 0.00 0.00 39.08 2.50
1163 1281 3.012934 AGTGGCAAGGTGTTTGTTACT 57.987 42.857 0.00 0.00 39.08 2.24
1164 1282 2.687935 AGTGGCAAGGTGTTTGTTACTG 59.312 45.455 0.00 0.00 39.08 2.74
1813 1943 1.357137 TCCATTAGCCGCCATGGATA 58.643 50.000 18.40 0.00 43.44 2.59
1902 2034 2.250485 CCTTGTCGTCGTCGTCGT 59.750 61.111 11.41 0.00 38.33 4.34
1953 2085 1.227380 CCTAGGATCGTGCTGTGCC 60.227 63.158 1.05 0.00 0.00 5.01
2003 2135 3.056832 GGGATCTTTCAGGATAAGGGGT 58.943 50.000 0.00 0.00 0.00 4.95
2005 2137 3.244249 GGATCTTTCAGGATAAGGGGTCG 60.244 52.174 0.00 0.00 0.00 4.79
2133 2271 2.286418 GGAAACTGCGCAAGATATTCCG 60.286 50.000 13.05 0.00 43.02 4.30
2135 2273 0.178068 ACTGCGCAAGATATTCCGGT 59.822 50.000 13.05 0.00 43.02 5.28
2136 2274 1.411246 ACTGCGCAAGATATTCCGGTA 59.589 47.619 13.05 0.00 43.02 4.02
2137 2275 2.037251 ACTGCGCAAGATATTCCGGTAT 59.963 45.455 13.05 0.00 43.02 2.73
2138 2276 2.412870 TGCGCAAGATATTCCGGTATG 58.587 47.619 8.16 0.00 43.02 2.39
2139 2277 2.036604 TGCGCAAGATATTCCGGTATGA 59.963 45.455 8.16 0.00 43.02 2.15
2140 2278 2.668457 GCGCAAGATATTCCGGTATGAG 59.332 50.000 0.30 0.00 43.02 2.90
2141 2279 2.668457 CGCAAGATATTCCGGTATGAGC 59.332 50.000 0.00 0.00 43.02 4.26
2142 2280 3.664107 GCAAGATATTCCGGTATGAGCA 58.336 45.455 0.00 0.00 0.00 4.26
2143 2281 3.681897 GCAAGATATTCCGGTATGAGCAG 59.318 47.826 0.00 0.00 0.00 4.24
2144 2282 4.800914 GCAAGATATTCCGGTATGAGCAGT 60.801 45.833 0.00 0.00 0.00 4.40
2149 2287 1.219124 CCGGTATGAGCAGTGCAGT 59.781 57.895 19.20 4.99 0.00 4.40
2150 2288 1.086067 CCGGTATGAGCAGTGCAGTG 61.086 60.000 19.20 17.56 0.00 3.66
2169 2307 2.071540 TGCAGTGCAGATCTTTTCTCG 58.928 47.619 15.37 0.00 33.32 4.04
2277 2419 3.262660 TGAGCAGTCAAGATGGACAGATT 59.737 43.478 0.00 0.00 40.29 2.40
2291 2433 0.099968 CAGATTGATTGCAGGGCGTG 59.900 55.000 2.14 2.14 0.00 5.34
2345 2504 0.609406 GGCCAGGGGAGAAGAACAAC 60.609 60.000 0.00 0.00 0.00 3.32
2492 2655 5.885230 TCATAGAATGCCAAAACAGACAG 57.115 39.130 0.00 0.00 0.00 3.51
2493 2656 5.559770 TCATAGAATGCCAAAACAGACAGA 58.440 37.500 0.00 0.00 0.00 3.41
2494 2657 5.412594 TCATAGAATGCCAAAACAGACAGAC 59.587 40.000 0.00 0.00 0.00 3.51
2495 2658 3.554934 AGAATGCCAAAACAGACAGACA 58.445 40.909 0.00 0.00 0.00 3.41
2496 2659 3.567164 AGAATGCCAAAACAGACAGACAG 59.433 43.478 0.00 0.00 0.00 3.51
2497 2660 2.708216 TGCCAAAACAGACAGACAGA 57.292 45.000 0.00 0.00 0.00 3.41
2498 2661 3.213206 TGCCAAAACAGACAGACAGAT 57.787 42.857 0.00 0.00 0.00 2.90
2506 2669 8.200120 CCAAAACAGACAGACAGATAGATATGA 58.800 37.037 0.00 0.00 0.00 2.15
2507 2670 9.761504 CAAAACAGACAGACAGATAGATATGAT 57.238 33.333 0.00 0.00 0.00 2.45
2512 2675 9.406113 CAGACAGACAGATAGATATGATATGGA 57.594 37.037 0.00 0.00 0.00 3.41
2567 2733 3.861276 ACATGCACTGTCAATCAATGG 57.139 42.857 0.00 0.00 29.94 3.16
2602 2768 8.969260 ATACAATCAAATAGCAGTGATGAAGA 57.031 30.769 0.00 0.00 34.70 2.87
2603 2769 7.692460 ACAATCAAATAGCAGTGATGAAGAA 57.308 32.000 0.00 0.00 34.70 2.52
2604 2770 7.759465 ACAATCAAATAGCAGTGATGAAGAAG 58.241 34.615 0.00 0.00 34.70 2.85
2605 2771 7.392673 ACAATCAAATAGCAGTGATGAAGAAGT 59.607 33.333 0.00 0.00 34.70 3.01
2606 2772 7.934855 ATCAAATAGCAGTGATGAAGAAGTT 57.065 32.000 0.00 0.00 33.21 2.66
2607 2773 7.137490 TCAAATAGCAGTGATGAAGAAGTTG 57.863 36.000 0.00 0.00 0.00 3.16
2608 2774 6.712095 TCAAATAGCAGTGATGAAGAAGTTGT 59.288 34.615 0.00 0.00 0.00 3.32
2609 2775 7.229306 TCAAATAGCAGTGATGAAGAAGTTGTT 59.771 33.333 0.00 0.00 0.00 2.83
2610 2776 6.734104 ATAGCAGTGATGAAGAAGTTGTTC 57.266 37.500 5.82 5.82 0.00 3.18
2611 2777 4.712476 AGCAGTGATGAAGAAGTTGTTCT 58.288 39.130 13.36 0.28 45.56 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 8.352201 CAACTGAAATTTCCTACAAATCACTCA 58.648 33.333 15.48 0.00 0.00 3.41
239 250 1.767088 GGAGTTAGGTTTAGGGCCGAT 59.233 52.381 0.00 0.00 0.00 4.18
381 404 4.416738 GAGGGTGCAGAGGCCACC 62.417 72.222 5.01 2.31 40.13 4.61
406 429 4.071961 TGTACAGCAGTGATGTTTGAGT 57.928 40.909 20.62 0.00 33.09 3.41
502 559 0.250727 GGCAGTTTCTGTGGCCACTA 60.251 55.000 34.75 21.08 45.70 2.74
538 595 0.250510 TTGGTGCATGCAACGTAGGA 60.251 50.000 29.46 10.04 36.20 2.94
539 596 0.168788 CTTGGTGCATGCAACGTAGG 59.831 55.000 29.46 15.49 36.20 3.18
543 600 1.081242 GACCTTGGTGCATGCAACG 60.081 57.895 29.46 18.31 36.20 4.10
546 603 3.364441 GCGACCTTGGTGCATGCA 61.364 61.111 18.46 18.46 0.00 3.96
564 621 4.519437 GTGGGGCCTACGTACGGC 62.519 72.222 21.06 21.03 46.83 5.68
642 702 5.612351 CATGCAGATAGATAGATGGATGGG 58.388 45.833 0.00 0.00 37.71 4.00
664 728 2.732912 CGCATTAGTGTAGTGTACGCCA 60.733 50.000 1.98 0.00 39.94 5.69
672 736 2.288030 GGATACGCCGCATTAGTGTAGT 60.288 50.000 0.00 0.00 33.98 2.73
846 916 1.519455 CGGCAAGAGATGGACGGAC 60.519 63.158 0.00 0.00 0.00 4.79
892 990 3.832490 TGCACACCGGCTTATATATCTCT 59.168 43.478 0.00 0.00 34.04 3.10
894 992 3.055819 CCTGCACACCGGCTTATATATCT 60.056 47.826 0.00 0.00 34.04 1.98
1162 1280 3.599938 CAGAACATATCGATCGTACGCAG 59.400 47.826 15.94 4.23 0.00 5.18
1163 1281 3.249080 TCAGAACATATCGATCGTACGCA 59.751 43.478 15.94 0.00 0.00 5.24
1164 1282 3.806958 TCAGAACATATCGATCGTACGC 58.193 45.455 15.94 0.00 0.00 4.42
1745 1875 8.512138 ACTGGTTTACTGCTACATGTTATTTTC 58.488 33.333 2.30 0.00 0.00 2.29
1813 1943 2.646930 ACATGACATGTGCCGATGATT 58.353 42.857 20.21 0.00 43.01 2.57
1902 2034 1.999071 GCCGGTTATTGCAATGCCGA 61.999 55.000 36.79 15.06 39.17 5.54
1953 2085 3.767230 CCGTTGCAGACAGACGCG 61.767 66.667 3.53 3.53 35.60 6.01
2003 2135 1.298602 CATCATGACCCAAATCGCGA 58.701 50.000 13.09 13.09 0.00 5.87
2005 2137 2.016318 TCACATCATGACCCAAATCGC 58.984 47.619 0.00 0.00 29.99 4.58
2133 2271 0.674581 TGCACTGCACTGCTCATACC 60.675 55.000 17.53 0.00 38.07 2.73
2135 2273 0.322648 ACTGCACTGCACTGCTCATA 59.677 50.000 17.53 0.00 38.07 2.15
2136 2274 1.072678 ACTGCACTGCACTGCTCAT 59.927 52.632 17.53 2.66 38.07 2.90
2137 2275 1.890510 CACTGCACTGCACTGCTCA 60.891 57.895 17.53 0.00 38.07 4.26
2138 2276 2.944429 CACTGCACTGCACTGCTC 59.056 61.111 17.53 0.00 38.07 4.26
2139 2277 3.285215 GCACTGCACTGCACTGCT 61.285 61.111 21.70 0.00 42.21 4.24
2140 2278 3.538028 CTGCACTGCACTGCACTGC 62.538 63.158 22.02 22.02 44.42 4.40
2141 2279 1.235281 ATCTGCACTGCACTGCACTG 61.235 55.000 15.89 8.67 42.36 3.66
2142 2280 0.954449 GATCTGCACTGCACTGCACT 60.954 55.000 15.89 7.47 42.36 4.40
2143 2281 0.954449 AGATCTGCACTGCACTGCAC 60.954 55.000 15.89 7.87 42.36 4.57
2144 2282 0.250597 AAGATCTGCACTGCACTGCA 60.251 50.000 18.27 18.27 45.06 4.41
2149 2287 2.071540 CGAGAAAAGATCTGCACTGCA 58.928 47.619 3.11 3.11 38.96 4.41
2150 2288 1.396301 CCGAGAAAAGATCTGCACTGC 59.604 52.381 0.00 0.00 38.96 4.40
2169 2307 0.320771 AAGCGTCACATCAGTCCACC 60.321 55.000 0.00 0.00 0.00 4.61
2277 2419 1.750018 CCATCACGCCCTGCAATCA 60.750 57.895 0.00 0.00 0.00 2.57
2345 2504 3.262420 CTCGTATGGGTCAAACTCTTGG 58.738 50.000 0.00 0.00 33.01 3.61
2493 2656 9.087871 GCCACTATCCATATCATATCTATCTGT 57.912 37.037 0.00 0.00 0.00 3.41
2494 2657 9.086758 TGCCACTATCCATATCATATCTATCTG 57.913 37.037 0.00 0.00 0.00 2.90
2495 2658 9.666191 TTGCCACTATCCATATCATATCTATCT 57.334 33.333 0.00 0.00 0.00 1.98
2498 2661 8.152898 GCATTGCCACTATCCATATCATATCTA 58.847 37.037 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.