Multiple sequence alignment - TraesCS2B01G339000

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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 TraesCS2B01G339000 chr2B 100.000 3052 0 0 1 3052 484489700 484492751 0.000000e+00 5637.0
1 TraesCS2B01G339000 chr2D 95.029 3058 115 19 1 3035 409285575 409282532 0.000000e+00 4771.0
2 TraesCS2B01G339000 chr2D 92.481 133 8 2 462 592 524963664 524963796 4.020000e-44 189.0
3 TraesCS2B01G339000 chr2A 95.894 2119 71 7 938 3052 577213657 577211551 0.000000e+00 3417.0
4 TraesCS2B01G339000 chr2A 91.822 538 34 5 351 879 577214189 577213653 0.000000e+00 741.0
5 TraesCS2B01G339000 chr2A 90.883 351 25 5 1 347 577215025 577214678 5.960000e-127 464.0
6 TraesCS2B01G339000 chr6D 92.308 130 8 2 464 592 431160696 431160824 1.870000e-42 183.0
7 TraesCS2B01G339000 chr6B 92.623 122 9 0 464 585 650598568 650598689 3.130000e-40 176.0
8 TraesCS2B01G339000 chr6B 87.671 146 13 4 464 604 489430821 489430676 6.770000e-37 165.0
9 TraesCS2B01G339000 chr1D 90.076 131 11 2 464 592 317387936 317388066 5.230000e-38 169.0
10 TraesCS2B01G339000 chr1D 89.394 132 13 1 462 592 103408744 103408875 6.770000e-37 165.0
11 TraesCS2B01G339000 chr5B 90.551 127 9 3 463 586 679113963 679114089 6.770000e-37 165.0
12 TraesCS2B01G339000 chr1B 83.969 131 18 2 2315 2444 49864499 49864627 4.130000e-24 122.0
13 TraesCS2B01G339000 chr1A 88.235 51 4 1 2397 2445 476908337 476908287 3.290000e-05 60.2


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 TraesCS2B01G339000 chr2B 484489700 484492751 3051 False 5637.000000 5637 100.000000 1 3052 1 chr2B.!!$F1 3051
1 TraesCS2B01G339000 chr2D 409282532 409285575 3043 True 4771.000000 4771 95.029000 1 3035 1 chr2D.!!$R1 3034
2 TraesCS2B01G339000 chr2A 577211551 577215025 3474 True 1540.666667 3417 92.866333 1 3052 3 chr2A.!!$R1 3051

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
462 963 0.531200 CTTACAGGAGACACGGTCCC 59.469 60.0 1.06 3.05 34.21 4.46 F
1013 1515 0.842635 ACCAAGATGGATCCTCTGGC 59.157 55.0 14.23 0.00 40.96 4.85 F
1416 1918 0.676466 TATTCCTGTGCAACCCAGCG 60.676 55.0 0.00 0.00 37.31 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1918 0.733223 GCTCGACGAACTCCTTGGTC 60.733 60.000 0.00 0.00 33.06 4.02 R
2019 2527 1.105167 ACAACCTCTGGTCGACGTCA 61.105 55.000 17.16 1.62 33.12 4.35 R
2521 3029 6.208797 AGCCCAGTTTTAGAGAAAATTACACC 59.791 38.462 0.00 0.00 36.92 4.16 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
37 40 5.954150 ACTTCTACAATTGGGATGCAGATTT 59.046 36.000 10.83 0.00 0.00 2.17
99 102 2.369983 TAGTGGATTCCGGACGGTAT 57.630 50.000 1.83 6.61 36.47 2.73
104 107 2.904697 GATTCCGGACGGTATCCTTT 57.095 50.000 16.52 0.00 46.69 3.11
105 108 3.189618 GATTCCGGACGGTATCCTTTT 57.810 47.619 16.52 0.00 46.69 2.27
114 117 3.943381 GACGGTATCCTTTTAACCCAAGG 59.057 47.826 0.00 0.00 42.16 3.61
189 196 4.081420 ACTTTGACTCATGCTATCTTCCGT 60.081 41.667 0.00 0.00 0.00 4.69
202 209 5.989777 GCTATCTTCCGTTGTGGTAATGTAT 59.010 40.000 0.00 0.00 39.52 2.29
213 220 3.375922 GTGGTAATGTATTGTTGGACCGG 59.624 47.826 0.00 0.00 0.00 5.28
216 223 2.038387 ATGTATTGTTGGACCGGCTC 57.962 50.000 0.00 0.00 0.00 4.70
462 963 0.531200 CTTACAGGAGACACGGTCCC 59.469 60.000 1.06 3.05 34.21 4.46
483 984 8.841300 GGTCCCTTTTAGAGATTCAAATATGAC 58.159 37.037 0.00 0.00 34.61 3.06
729 1231 9.809096 TGTGAACAAGATAACAAGCAAAATTAA 57.191 25.926 0.00 0.00 0.00 1.40
778 1280 6.142818 TGCTTCCAATTATATTGTTTCGGG 57.857 37.500 0.00 0.00 0.00 5.14
873 1375 6.435904 TGAACCAAATCGGGAAGTGAAATATT 59.564 34.615 0.00 0.00 40.22 1.28
911 1413 9.946418 GTACAATTTTAAAACGGATTAATGTGC 57.054 29.630 1.97 0.12 0.00 4.57
912 1414 8.594881 ACAATTTTAAAACGGATTAATGTGCA 57.405 26.923 1.97 0.00 0.00 4.57
913 1415 9.213799 ACAATTTTAAAACGGATTAATGTGCAT 57.786 25.926 1.97 0.00 0.00 3.96
917 1419 9.562583 TTTTAAAACGGATTAATGTGCATAGTC 57.437 29.630 0.00 0.00 0.00 2.59
920 1422 4.883083 ACGGATTAATGTGCATAGTCGAT 58.117 39.130 0.00 0.00 0.00 3.59
1013 1515 0.842635 ACCAAGATGGATCCTCTGGC 59.157 55.000 14.23 0.00 40.96 4.85
1045 1547 4.393680 CCGACGACCTAATTTTCATGGAAA 59.606 41.667 0.54 0.54 0.00 3.13
1065 1567 4.980805 TTGGTGCGACTGCCCGTC 62.981 66.667 0.00 0.00 41.78 4.79
1416 1918 0.676466 TATTCCTGTGCAACCCAGCG 60.676 55.000 0.00 0.00 37.31 5.18
1629 2134 3.688553 CGGGAATAACTCCTGCTCC 57.311 57.895 0.00 0.00 43.90 4.70
1630 2135 1.123928 CGGGAATAACTCCTGCTCCT 58.876 55.000 0.00 0.00 43.90 3.69
1861 2366 2.186826 AAGCTGTGCCACGTCAACC 61.187 57.895 0.00 0.00 0.00 3.77
1942 2447 3.576356 CGCGCTGCCGGATTGATT 61.576 61.111 5.05 0.00 34.32 2.57
2019 2527 0.176680 GGATGCTGACGATGGTGTCT 59.823 55.000 0.00 0.00 39.64 3.41
2067 2575 1.269448 GATGAGAGGAGCGGAGATGTC 59.731 57.143 0.00 0.00 0.00 3.06
2082 2590 5.445142 CGGAGATGTCGAAAAAGTGATGAAG 60.445 44.000 0.00 0.00 0.00 3.02
2395 2903 7.430441 TCTTCCAGTTACCAAAAATACTTTGC 58.570 34.615 0.00 0.00 0.00 3.68
2417 2925 6.345298 TGCATTTCCGTTATGAGAGTAATGA 58.655 36.000 0.00 0.00 0.00 2.57
2555 3063 7.304497 TCTCTAAAACTGGGCTAGAATATCC 57.696 40.000 4.33 0.00 0.00 2.59
2619 3127 3.857157 AAGAGAAGTGCTTTGGTACCA 57.143 42.857 11.60 11.60 0.00 3.25
2952 3464 1.133025 CAAGCACGCCTCCCATAAAAG 59.867 52.381 0.00 0.00 0.00 2.27
2964 3476 5.235850 TCCCATAAAAGCTCAAGTGTGTA 57.764 39.130 0.00 0.00 0.00 2.90
3040 3552 3.322211 TCCTTTTGAATTAGCGGACGA 57.678 42.857 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 40 6.805713 TCGAAGTCAACATAATAGCATCTGA 58.194 36.000 0.00 0.00 0.00 3.27
99 102 1.714217 CCCTCCCTTGGGTTAAAAGGA 59.286 52.381 10.86 0.00 46.08 3.36
114 117 3.744660 AGATAAAACATGCGATCCCTCC 58.255 45.455 0.00 0.00 0.00 4.30
165 172 4.872691 CGGAAGATAGCATGAGTCAAAGTT 59.127 41.667 0.00 0.00 0.00 2.66
189 196 4.456222 CGGTCCAACAATACATTACCACAA 59.544 41.667 0.00 0.00 0.00 3.33
202 209 2.029964 GACGAGCCGGTCCAACAA 59.970 61.111 1.90 0.00 0.00 2.83
213 220 8.328864 CCTAATTTGTTACAATTAGAGACGAGC 58.671 37.037 19.18 0.00 39.92 5.03
286 294 7.768582 TGAATATCATAACAACACCACTACAGG 59.231 37.037 0.00 0.00 0.00 4.00
325 333 4.950744 GCATTGTCATATGCCGCC 57.049 55.556 0.00 0.00 44.01 6.13
347 355 5.621197 TGTAACACATGGCTTCATAACAC 57.379 39.130 0.00 0.00 0.00 3.32
483 984 9.979270 GATTCACTCATTTTGTTCTGTATGTAG 57.021 33.333 0.00 0.00 0.00 2.74
485 986 8.627208 AGATTCACTCATTTTGTTCTGTATGT 57.373 30.769 0.00 0.00 0.00 2.29
486 987 9.979270 GTAGATTCACTCATTTTGTTCTGTATG 57.021 33.333 0.00 0.00 0.00 2.39
487 988 9.725019 TGTAGATTCACTCATTTTGTTCTGTAT 57.275 29.630 0.00 0.00 0.00 2.29
488 989 8.988934 GTGTAGATTCACTCATTTTGTTCTGTA 58.011 33.333 0.00 0.00 35.68 2.74
489 990 7.716998 AGTGTAGATTCACTCATTTTGTTCTGT 59.283 33.333 0.00 0.00 44.07 3.41
490 991 8.092521 AGTGTAGATTCACTCATTTTGTTCTG 57.907 34.615 0.00 0.00 44.07 3.02
491 992 9.950496 ATAGTGTAGATTCACTCATTTTGTTCT 57.050 29.630 2.59 0.00 45.79 3.01
587 1089 9.736023 CGAAATATAGTACGTTAACTTACCCTT 57.264 33.333 16.28 6.55 0.00 3.95
703 1205 9.809096 TTAATTTTGCTTGTTATCTTGTTCACA 57.191 25.926 0.00 0.00 0.00 3.58
770 1272 4.620589 TTATAACACACCTCCCGAAACA 57.379 40.909 0.00 0.00 0.00 2.83
771 1273 5.945466 TTTTATAACACACCTCCCGAAAC 57.055 39.130 0.00 0.00 0.00 2.78
911 1413 1.596703 CTCGCTACGCATCGACTATG 58.403 55.000 0.00 0.00 38.74 2.23
912 1414 0.517755 CCTCGCTACGCATCGACTAT 59.482 55.000 0.00 0.00 0.00 2.12
913 1415 1.504647 CCCTCGCTACGCATCGACTA 61.505 60.000 0.00 0.00 0.00 2.59
914 1416 2.716244 CCTCGCTACGCATCGACT 59.284 61.111 0.00 0.00 0.00 4.18
915 1417 2.353607 CCCTCGCTACGCATCGAC 60.354 66.667 0.00 0.00 0.00 4.20
916 1418 2.332362 GAACCCTCGCTACGCATCGA 62.332 60.000 0.00 0.00 0.00 3.59
917 1419 1.944676 GAACCCTCGCTACGCATCG 60.945 63.158 0.00 0.00 0.00 3.84
920 1422 4.124351 CCGAACCCTCGCTACGCA 62.124 66.667 0.00 0.00 44.04 5.24
1045 1547 2.045926 GGGCAGTCGCACCAAGAT 60.046 61.111 0.00 0.00 41.24 2.40
1065 1567 3.176578 CAGCGCGCAAGGCATTTG 61.177 61.111 35.10 16.38 43.84 2.32
1278 1780 1.815196 CATCAGCTCTGCCTCGTCT 59.185 57.895 0.00 0.00 0.00 4.18
1300 1802 2.267961 GGGTGGGTACGCCTTCTG 59.732 66.667 7.55 0.00 46.67 3.02
1416 1918 0.733223 GCTCGACGAACTCCTTGGTC 60.733 60.000 0.00 0.00 33.06 4.02
1625 2130 4.785453 CGGTGGCTTCCCAGGAGC 62.785 72.222 0.00 0.00 43.18 4.70
1861 2366 1.801913 CCGTCTTCGAGGTCGCAAG 60.802 63.158 8.57 0.60 39.71 4.01
1942 2447 2.301870 AGCCGAAACTAACATCACCTGA 59.698 45.455 0.00 0.00 0.00 3.86
2019 2527 1.105167 ACAACCTCTGGTCGACGTCA 61.105 55.000 17.16 1.62 33.12 4.35
2067 2575 4.214119 TCTTCCAGCTTCATCACTTTTTCG 59.786 41.667 0.00 0.00 0.00 3.46
2170 2678 4.455877 GCAGCATTACACCATATAGTTCCC 59.544 45.833 0.00 0.00 0.00 3.97
2217 2725 8.685838 AACCTAGCTACTAATGAACAAAACAA 57.314 30.769 0.00 0.00 0.00 2.83
2395 2903 9.708222 CTTTTCATTACTCTCATAACGGAAATG 57.292 33.333 0.00 0.00 0.00 2.32
2514 3022 9.281371 GTTTTAGAGAAAATTACACCACTACCT 57.719 33.333 0.00 0.00 36.92 3.08
2521 3029 6.208797 AGCCCAGTTTTAGAGAAAATTACACC 59.791 38.462 0.00 0.00 36.92 4.16
2629 3137 9.898152 ATAAGAAACCTTTTCAATGTTTTTGGA 57.102 25.926 1.72 0.00 32.67 3.53


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

AutoCloner maintained by Alex Coulton.