Multiple sequence alignment - TraesCS2B01G531100

Loading Multiple Alignment...

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 TraesCS2B01G531100 chr2B 100.000 2607 0 0 1 2607 726544793 726547399 0.000000e+00 4815.0
1 TraesCS2B01G531100 chr2B 82.500 600 65 18 1001 1595 726135846 726136410 8.380000e-135 490.0
2 TraesCS2B01G531100 chr2D 91.065 2675 100 56 1 2607 598711719 598714322 0.000000e+00 3487.0
3 TraesCS2B01G531100 chr2D 78.757 692 92 32 1001 1680 597322519 597323167 1.870000e-111 412.0
4 TraesCS2B01G531100 chr2A 89.492 2636 118 58 1 2550 732579316 732581878 0.000000e+00 3186.0
5 TraesCS2B01G531100 chr2A 80.602 665 84 23 1001 1658 731379423 731380049 3.040000e-129 472.0
6 TraesCS2B01G531100 chr7D 89.474 76 8 0 1012 1087 93949371 93949296 2.140000e-16 97.1
7 TraesCS2B01G531100 chr7D 89.474 76 8 0 1012 1087 94005564 94005639 2.140000e-16 97.1
8 TraesCS2B01G531100 chr7B 89.474 76 8 0 1012 1087 47737281 47737356 2.140000e-16 97.1
9 TraesCS2B01G531100 chr6D 88.000 75 9 0 1012 1086 443741338 443741264 3.570000e-14 89.8


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 TraesCS2B01G531100 chr2B 726544793 726547399 2606 False 4815 4815 100.000 1 2607 1 chr2B.!!$F2 2606
1 TraesCS2B01G531100 chr2B 726135846 726136410 564 False 490 490 82.500 1001 1595 1 chr2B.!!$F1 594
2 TraesCS2B01G531100 chr2D 598711719 598714322 2603 False 3487 3487 91.065 1 2607 1 chr2D.!!$F2 2606
3 TraesCS2B01G531100 chr2D 597322519 597323167 648 False 412 412 78.757 1001 1680 1 chr2D.!!$F1 679
4 TraesCS2B01G531100 chr2A 732579316 732581878 2562 False 3186 3186 89.492 1 2550 1 chr2A.!!$F2 2549
5 TraesCS2B01G531100 chr2A 731379423 731380049 626 False 472 472 80.602 1001 1658 1 chr2A.!!$F1 657

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
594 639 0.029834 CTGCTGTGTGTTGACCTTGC 59.97 55.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 2533 0.179119 GATGCCATGTTCAAGCTGCC 60.179 55.0 0.0 0.0 0.0 4.85 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 38 3.525199 AGAGGCACCACCAATCTAGAAAT 59.475 43.478 0.00 0.00 43.14 2.17
81 82 6.712998 TCCGAGTGATTTGTAGGAAATTTCAA 59.287 34.615 19.49 5.53 0.00 2.69
82 83 6.801862 CCGAGTGATTTGTAGGAAATTTCAAC 59.198 38.462 19.49 16.01 0.00 3.18
89 90 7.873719 TTTGTAGGAAATTTCAACTGAGTGA 57.126 32.000 19.49 0.00 0.00 3.41
90 91 8.463930 TTTGTAGGAAATTTCAACTGAGTGAT 57.536 30.769 19.49 0.00 0.00 3.06
122 123 5.293324 AGCAAATCTTAAATATCGCACGTCA 59.707 36.000 0.00 0.00 0.00 4.35
123 124 5.963004 GCAAATCTTAAATATCGCACGTCAA 59.037 36.000 0.00 0.00 0.00 3.18
124 125 6.467682 GCAAATCTTAAATATCGCACGTCAAA 59.532 34.615 0.00 0.00 0.00 2.69
232 237 2.973420 CGACCATCGGCTCTAAACC 58.027 57.895 0.00 0.00 36.00 3.27
233 238 0.460311 CGACCATCGGCTCTAAACCT 59.540 55.000 0.00 0.00 36.00 3.50
234 239 1.679680 CGACCATCGGCTCTAAACCTA 59.320 52.381 0.00 0.00 36.00 3.08
235 240 2.287668 CGACCATCGGCTCTAAACCTAG 60.288 54.545 0.00 0.00 36.00 3.02
245 250 3.705072 GCTCTAAACCTAGCTAACTCCCA 59.295 47.826 0.00 0.00 35.80 4.37
247 252 4.287552 TCTAAACCTAGCTAACTCCCAGG 58.712 47.826 0.00 0.00 0.00 4.45
294 299 3.066814 GCAGTCGGGTACTCGGGT 61.067 66.667 16.55 0.00 35.76 5.28
352 357 2.226437 CCACACCACATCAAGTAACTGC 59.774 50.000 0.00 0.00 0.00 4.40
360 365 1.636148 TCAAGTAACTGCCCTACGGT 58.364 50.000 0.00 0.00 40.66 4.83
365 370 0.832983 TAACTGCCCTACGGTGTGGT 60.833 55.000 0.00 0.00 38.15 4.16
393 399 4.988716 ACCCTCGCCGACACCTCA 62.989 66.667 0.00 0.00 0.00 3.86
415 453 5.007626 TCAAAACATCACTGCTGTACAACTC 59.992 40.000 0.00 0.00 0.00 3.01
459 497 4.704103 AGGCCCAGAGCTCGACCA 62.704 66.667 8.37 0.00 43.05 4.02
526 564 0.928229 GCCATGCGACCTTAACTACG 59.072 55.000 0.00 0.00 0.00 3.51
527 565 1.738030 GCCATGCGACCTTAACTACGT 60.738 52.381 0.00 0.00 0.00 3.57
593 638 1.382522 ACTGCTGTGTGTTGACCTTG 58.617 50.000 0.00 0.00 0.00 3.61
594 639 0.029834 CTGCTGTGTGTTGACCTTGC 59.970 55.000 0.00 0.00 0.00 4.01
595 640 0.394216 TGCTGTGTGTTGACCTTGCT 60.394 50.000 0.00 0.00 0.00 3.91
596 641 0.029834 GCTGTGTGTTGACCTTGCTG 59.970 55.000 0.00 0.00 0.00 4.41
597 642 1.382522 CTGTGTGTTGACCTTGCTGT 58.617 50.000 0.00 0.00 0.00 4.40
598 643 2.560504 CTGTGTGTTGACCTTGCTGTA 58.439 47.619 0.00 0.00 0.00 2.74
599 644 2.285083 TGTGTGTTGACCTTGCTGTAC 58.715 47.619 0.00 0.00 0.00 2.90
650 699 4.961099 CCATCCATCTATCTATCTGCAGGA 59.039 45.833 15.13 3.44 0.00 3.86
659 708 0.380733 TATCTGCAGGACGTACGCTG 59.619 55.000 16.72 16.21 0.00 5.18
667 716 0.921347 GGACGTACGCTGCACTAATG 59.079 55.000 16.72 0.00 0.00 1.90
734 786 3.959293 TGAACCATCATCAATCTGCACT 58.041 40.909 0.00 0.00 0.00 4.40
735 787 5.101648 TGAACCATCATCAATCTGCACTA 57.898 39.130 0.00 0.00 0.00 2.74
736 788 5.121105 TGAACCATCATCAATCTGCACTAG 58.879 41.667 0.00 0.00 0.00 2.57
763 815 0.108585 TTTGGCCTCACTGAGACACC 59.891 55.000 3.32 6.69 0.00 4.16
807 859 5.285651 TGTCACGATATCGCATGTTGATTA 58.714 37.500 24.59 10.66 44.43 1.75
837 889 1.205485 CGAGAAAGATCGCGCCTGAG 61.205 60.000 0.00 0.00 41.79 3.35
838 890 1.486644 GAGAAAGATCGCGCCTGAGC 61.487 60.000 0.00 0.00 0.00 4.26
839 891 2.512515 AAAGATCGCGCCTGAGCC 60.513 61.111 0.00 0.00 34.57 4.70
840 892 2.914777 GAAAGATCGCGCCTGAGCCT 62.915 60.000 0.00 0.00 34.57 4.58
841 893 3.729965 AAGATCGCGCCTGAGCCTG 62.730 63.158 0.00 0.00 34.57 4.85
842 894 4.212913 GATCGCGCCTGAGCCTGA 62.213 66.667 0.00 0.00 34.57 3.86
898 950 4.715130 CCCTGACCCTGACCCCGA 62.715 72.222 0.00 0.00 0.00 5.14
929 981 1.917955 CGATATATAAGCCGGTGTGCG 59.082 52.381 1.90 0.00 36.02 5.34
1089 1171 1.327690 ACCCGCTCATGTACGTCCAT 61.328 55.000 0.00 0.00 0.00 3.41
1140 1222 2.213499 CTCTGTCGGTGCAGTTTTCTT 58.787 47.619 0.00 0.00 37.70 2.52
1333 1425 1.843421 CACCAACTTCCCCTCCACA 59.157 57.895 0.00 0.00 0.00 4.17
1403 1501 0.815734 GCTGGAGAAATGCTGCATGT 59.184 50.000 17.00 11.10 44.42 3.21
1409 1507 0.858961 GAAATGCTGCATGTCGACGC 60.859 55.000 17.00 9.80 0.00 5.19
1436 1534 3.342627 TGCAAAACGTCGAGGCGG 61.343 61.111 4.75 0.00 35.98 6.13
1670 1779 1.227793 GCTAGCCAGCCAGTCCATC 60.228 63.158 2.29 0.00 42.37 3.51
1706 1815 0.902531 TCAGAACATCCCCTTCGTCC 59.097 55.000 0.00 0.00 0.00 4.79
1733 1843 6.038492 TCCCGACTTGTTTTTGTTAGGTAAAG 59.962 38.462 0.00 0.00 0.00 1.85
1804 1914 1.162698 CATTAGCCGCCATGGATCAG 58.837 55.000 18.40 2.76 42.00 2.90
1816 1926 0.758123 TGGATCAGCATCGGCACATA 59.242 50.000 0.00 0.00 44.61 2.29
1893 2005 3.867226 CTTGTCGTCGTCGTCGGCA 62.867 63.158 14.81 14.81 42.21 5.69
2083 2196 2.837591 GGAGCCTCCTCTCTTTTCTCTT 59.162 50.000 2.64 0.00 38.21 2.85
2087 2200 4.841246 AGCCTCCTCTCTTTTCTCTTGTTA 59.159 41.667 0.00 0.00 0.00 2.41
2088 2201 5.487131 AGCCTCCTCTCTTTTCTCTTGTTAT 59.513 40.000 0.00 0.00 0.00 1.89
2089 2202 6.670027 AGCCTCCTCTCTTTTCTCTTGTTATA 59.330 38.462 0.00 0.00 0.00 0.98
2090 2203 6.759356 GCCTCCTCTCTTTTCTCTTGTTATAC 59.241 42.308 0.00 0.00 0.00 1.47
2117 2230 2.116736 TTTGCTCTGGAAACTGCGCG 62.117 55.000 0.00 0.00 42.20 6.86
2213 2330 3.111853 TCGGATGCATCTCCATGTTAC 57.888 47.619 25.28 5.29 34.78 2.50
2335 2473 0.322906 GGCCAGGGGAGAAGAACAAG 60.323 60.000 0.00 0.00 0.00 3.16
2336 2474 0.322906 GCCAGGGGAGAAGAACAAGG 60.323 60.000 0.00 0.00 0.00 3.61
2337 2475 0.329596 CCAGGGGAGAAGAACAAGGG 59.670 60.000 0.00 0.00 0.00 3.95
2459 2602 7.353525 AGATGGATAGATAGATACAGGACCAG 58.646 42.308 0.00 0.00 0.00 4.00
2509 2659 1.837947 TGGCTGGTGGCAATGCTTT 60.838 52.632 4.82 0.00 46.03 3.51
2515 2665 1.229975 GGTGGCAATGCTTTTGTGGC 61.230 55.000 4.82 0.00 38.26 5.01
2550 2700 5.456548 AACATGCACTGTCAATCATCAAA 57.543 34.783 0.00 0.00 36.98 2.69
2551 2701 5.654603 ACATGCACTGTCAATCATCAAAT 57.345 34.783 0.00 0.00 29.94 2.32
2552 2702 6.762702 ACATGCACTGTCAATCATCAAATA 57.237 33.333 0.00 0.00 29.94 1.40
2553 2703 6.792326 ACATGCACTGTCAATCATCAAATAG 58.208 36.000 0.00 0.00 29.94 1.73
2554 2704 6.376299 ACATGCACTGTCAATCATCAAATAGT 59.624 34.615 0.00 0.00 29.94 2.12
2555 2705 7.553760 ACATGCACTGTCAATCATCAAATAGTA 59.446 33.333 0.00 0.00 29.94 1.82
2556 2706 7.543947 TGCACTGTCAATCATCAAATAGTAG 57.456 36.000 0.00 0.00 0.00 2.57
2557 2707 7.105588 TGCACTGTCAATCATCAAATAGTAGT 58.894 34.615 0.00 0.00 0.00 2.73
2578 2744 9.298250 AGTAGTAGTGATGAAGAAGTTGTTCTA 57.702 33.333 13.36 1.70 42.59 2.10
2598 2764 3.832615 ACCGTCTTTCACAAACTACCT 57.167 42.857 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 155 3.006859 CGGCCACAAGAGTCATCCATATA 59.993 47.826 2.24 0.00 0.00 0.86
151 156 2.224378 CGGCCACAAGAGTCATCCATAT 60.224 50.000 2.24 0.00 0.00 1.78
152 157 1.138859 CGGCCACAAGAGTCATCCATA 59.861 52.381 2.24 0.00 0.00 2.74
214 219 0.460311 AGGTTTAGAGCCGATGGTCG 59.540 55.000 0.00 0.00 43.79 4.79
216 221 1.413077 GCTAGGTTTAGAGCCGATGGT 59.587 52.381 0.00 0.00 32.25 3.55
219 224 4.216708 AGTTAGCTAGGTTTAGAGCCGAT 58.783 43.478 0.00 0.00 39.65 4.18
220 225 3.629087 AGTTAGCTAGGTTTAGAGCCGA 58.371 45.455 0.00 0.00 39.65 5.54
221 226 3.243468 GGAGTTAGCTAGGTTTAGAGCCG 60.243 52.174 0.00 0.00 39.65 5.52
222 227 3.069872 GGGAGTTAGCTAGGTTTAGAGCC 59.930 52.174 0.00 0.00 39.65 4.70
223 228 3.705072 TGGGAGTTAGCTAGGTTTAGAGC 59.295 47.826 0.00 0.00 39.08 4.09
224 229 4.342665 CCTGGGAGTTAGCTAGGTTTAGAG 59.657 50.000 0.00 0.00 0.00 2.43
225 230 4.264713 ACCTGGGAGTTAGCTAGGTTTAGA 60.265 45.833 0.00 0.00 38.56 2.10
226 231 4.031611 ACCTGGGAGTTAGCTAGGTTTAG 58.968 47.826 0.00 0.00 38.56 1.85
227 232 4.070681 ACCTGGGAGTTAGCTAGGTTTA 57.929 45.455 0.00 0.00 38.56 2.01
228 233 2.917205 ACCTGGGAGTTAGCTAGGTTT 58.083 47.619 0.00 0.00 38.56 3.27
229 234 2.644060 ACCTGGGAGTTAGCTAGGTT 57.356 50.000 0.00 0.00 38.56 3.50
230 235 2.359037 GGTACCTGGGAGTTAGCTAGGT 60.359 54.545 4.06 7.25 43.69 3.08
231 236 2.317973 GGTACCTGGGAGTTAGCTAGG 58.682 57.143 4.06 0.00 34.70 3.02
247 252 1.597742 TCACTATCGCGTAGGGGTAC 58.402 55.000 5.77 0.00 42.39 3.34
277 282 3.066814 ACCCGAGTACCCGACTGC 61.067 66.667 0.00 0.00 39.06 4.40
323 328 0.400213 GATGTGGTGTGGACTGGGAA 59.600 55.000 0.00 0.00 0.00 3.97
360 365 4.269523 GTGCAGAGGCCCACCACA 62.270 66.667 0.00 0.00 40.13 4.17
389 395 3.814842 TGTACAGCAGTGATGTTTTGAGG 59.185 43.478 20.62 0.00 33.09 3.86
393 399 4.881273 TGAGTTGTACAGCAGTGATGTTTT 59.119 37.500 20.62 0.00 33.09 2.43
440 478 3.386237 GTCGAGCTCTGGGCCTGT 61.386 66.667 12.85 0.00 43.05 4.00
459 497 0.400213 TTTGGAACATCTGGCCGTCT 59.600 50.000 0.00 0.00 39.30 4.18
526 564 2.690778 GCGACCTTGGTGCATGGAC 61.691 63.158 9.16 9.16 33.58 4.02
527 565 2.359850 GCGACCTTGGTGCATGGA 60.360 61.111 0.00 0.00 33.58 3.41
703 755 3.627123 TGATGATGGTTCATTAACGCAGG 59.373 43.478 0.00 0.00 42.73 4.85
734 786 6.382859 TCTCAGTGAGGCCAAATGTAATACTA 59.617 38.462 19.99 0.00 0.00 1.82
735 787 5.189736 TCTCAGTGAGGCCAAATGTAATACT 59.810 40.000 19.99 0.00 0.00 2.12
736 788 5.294552 GTCTCAGTGAGGCCAAATGTAATAC 59.705 44.000 19.99 2.42 0.00 1.89
807 859 4.201930 GCGATCTTTCTCGGGATATACGAT 60.202 45.833 2.86 0.00 39.89 3.73
837 889 1.520342 GACGGATGCTCAGTCAGGC 60.520 63.158 10.07 0.00 40.52 4.85
838 890 1.142748 GGACGGATGCTCAGTCAGG 59.857 63.158 14.57 0.00 42.18 3.86
839 891 0.463204 ATGGACGGATGCTCAGTCAG 59.537 55.000 14.57 0.24 42.18 3.51
840 892 0.461548 GATGGACGGATGCTCAGTCA 59.538 55.000 14.57 5.53 42.18 3.41
841 893 0.749649 AGATGGACGGATGCTCAGTC 59.250 55.000 7.54 7.54 40.18 3.51
842 894 0.749649 GAGATGGACGGATGCTCAGT 59.250 55.000 0.00 0.00 0.00 3.41
898 950 0.394762 TATATATCGCCGCTCGGGGT 60.395 55.000 21.82 13.27 46.70 4.95
1089 1171 7.337480 TCGCACAGGAATATAGTACAGTTTA 57.663 36.000 0.00 0.00 0.00 2.01
1140 1222 2.031012 CGAGCACCTGCCACTCAA 59.969 61.111 0.00 0.00 43.38 3.02
1357 1452 2.364842 AGGGTCGCTGAGAGGCAT 60.365 61.111 0.00 0.00 0.00 4.40
1358 1453 3.385384 CAGGGTCGCTGAGAGGCA 61.385 66.667 11.37 0.00 0.00 4.75
1670 1779 2.436911 TCTGATGGACATGGACATGGAG 59.563 50.000 15.94 5.52 42.91 3.86
1706 1815 3.252458 CCTAACAAAAACAAGTCGGGAGG 59.748 47.826 0.00 0.00 0.00 4.30
1733 1843 9.341899 CTGGTTTACTGCTACATGTTATTTTTC 57.658 33.333 2.30 0.00 0.00 2.29
1804 1914 3.066380 TGTACATGATATGTGCCGATGC 58.934 45.455 0.00 0.00 43.98 3.91
1816 1926 3.244215 CCGGCTAATGGAGTGTACATGAT 60.244 47.826 0.00 0.00 0.00 2.45
1893 2005 1.815866 GGCCGGTTATTGCAATGCT 59.184 52.632 22.27 0.00 0.00 3.79
2062 2174 2.466846 AGAGAAAAGAGAGGAGGCTCC 58.533 52.381 26.42 26.42 35.49 4.70
2063 2175 3.260632 ACAAGAGAAAAGAGAGGAGGCTC 59.739 47.826 5.78 5.78 35.11 4.70
2087 2200 9.553064 CAGTTTCCAGAGCAAAGATTATAGTAT 57.447 33.333 0.00 0.00 0.00 2.12
2088 2201 7.495934 GCAGTTTCCAGAGCAAAGATTATAGTA 59.504 37.037 0.00 0.00 0.00 1.82
2089 2202 6.317391 GCAGTTTCCAGAGCAAAGATTATAGT 59.683 38.462 0.00 0.00 0.00 2.12
2090 2203 6.510799 CGCAGTTTCCAGAGCAAAGATTATAG 60.511 42.308 0.00 0.00 0.00 1.31
2117 2230 1.884579 TGCTCGTACCGGGAATATCTC 59.115 52.381 6.32 0.00 0.00 2.75
2213 2330 0.248134 GAGGACAGTTCGATCGACCG 60.248 60.000 19.26 11.52 0.00 4.79
2335 2473 0.906775 TCGTATGGGTCAAACTCCCC 59.093 55.000 0.00 0.00 44.00 4.81
2336 2474 1.553704 ACTCGTATGGGTCAAACTCCC 59.446 52.381 0.00 0.00 44.81 4.30
2337 2475 2.734492 CGACTCGTATGGGTCAAACTCC 60.734 54.545 15.24 0.00 33.19 3.85
2394 2533 0.179119 GATGCCATGTTCAAGCTGCC 60.179 55.000 0.00 0.00 0.00 4.85
2509 2659 3.065655 GTTATGCTTGCATTTGCCACAA 58.934 40.909 13.52 0.00 41.18 3.33
2551 2701 9.298250 AGAACAACTTCTTCATCACTACTACTA 57.702 33.333 0.00 0.00 32.29 1.82
2552 2702 8.184304 AGAACAACTTCTTCATCACTACTACT 57.816 34.615 0.00 0.00 32.29 2.57
2553 2703 9.344309 GTAGAACAACTTCTTCATCACTACTAC 57.656 37.037 0.00 0.00 37.87 2.73
2554 2704 8.521176 GGTAGAACAACTTCTTCATCACTACTA 58.479 37.037 0.00 0.00 37.87 1.82
2555 2705 7.379750 GGTAGAACAACTTCTTCATCACTACT 58.620 38.462 0.00 0.00 37.87 2.57
2556 2706 6.308282 CGGTAGAACAACTTCTTCATCACTAC 59.692 42.308 0.00 0.00 37.87 2.73
2557 2707 6.015688 ACGGTAGAACAACTTCTTCATCACTA 60.016 38.462 0.00 0.00 37.87 2.74
2578 2744 3.832615 AGGTAGTTTGTGAAAGACGGT 57.167 42.857 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.