Multiple sequence alignment - TraesCS1D01G228000

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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 TraesCS1D01G228000 chr1D 100.000 2462 0 0 1 2462 316204441 316206902 0.000000e+00 4547.0
1 TraesCS1D01G228000 chr1A 95.554 2429 91 7 1 2420 397052249 397054669 0.000000e+00 3871.0
2 TraesCS1D01G228000 chr1A 100.000 38 0 0 2425 2462 397054702 397054739 1.220000e-08 71.3
3 TraesCS1D01G228000 chr1B 94.454 2362 96 22 66 2420 428535119 428537452 0.000000e+00 3603.0
4 TraesCS1D01G228000 chr1B 95.556 45 1 1 2419 2462 428537477 428537521 1.220000e-08 71.3
5 TraesCS1D01G228000 chr2A 96.875 64 2 0 1 64 143038455 143038518 9.310000e-20 108.0
6 TraesCS1D01G228000 chr7D 93.151 73 3 2 1 73 209025301 209025231 3.350000e-19 106.0
7 TraesCS1D01G228000 chr4B 95.385 65 3 0 1 65 354667831 354667895 1.200000e-18 104.0
8 TraesCS1D01G228000 chr7B 91.781 73 6 0 1 73 228968520 228968448 4.330000e-18 102.0
9 TraesCS1D01G228000 chr5A 90.789 76 5 2 1 74 49701724 49701799 1.560000e-17 100.0
10 TraesCS1D01G228000 chr5A 89.024 82 7 2 1 82 228883915 228883994 1.560000e-17 100.0
11 TraesCS1D01G228000 chr3D 90.667 75 5 2 1 74 558212068 558212141 5.600000e-17 99.0
12 TraesCS1D01G228000 chr2B 90.667 75 5 1 1 73 12372234 12372308 5.600000e-17 99.0


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 TraesCS1D01G228000 chr1D 316204441 316206902 2461 False 4547.00 4547 100.000 1 2462 1 chr1D.!!$F1 2461
1 TraesCS1D01G228000 chr1A 397052249 397054739 2490 False 1971.15 3871 97.777 1 2462 2 chr1A.!!$F1 2461
2 TraesCS1D01G228000 chr1B 428535119 428537521 2402 False 1837.15 3603 95.005 66 2462 2 chr1B.!!$F1 2396

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
222 223 0.458543 ATGCGTGTCGTCTCATGTCC 60.459 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 1960 0.616371 CCGGAACACCCACTCCAATA 59.384 55.0 0.0 0.0 34.14 1.9 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
53 54 8.114102 AGGACTACGATTGATCCCATATACTTA 58.886 37.037 0.00 0.00 30.99 2.24
146 147 3.451178 TGGACTAGGTCTTCATGGTTAGC 59.549 47.826 0.00 0.00 32.47 3.09
150 151 1.065126 AGGTCTTCATGGTTAGCTGGC 60.065 52.381 0.00 0.00 0.00 4.85
159 160 2.511373 TTAGCTGGCGTGCATCCG 60.511 61.111 0.00 0.00 34.99 4.18
222 223 0.458543 ATGCGTGTCGTCTCATGTCC 60.459 55.000 0.00 0.00 0.00 4.02
304 306 5.105473 TCCCTTTAAATGACTAGGACACTCG 60.105 44.000 0.00 0.00 0.00 4.18
453 457 3.548745 TGCATACTCTCATGTCCCTTG 57.451 47.619 0.00 0.00 0.00 3.61
569 574 2.871022 CTGCATGCATGAACTAGACCTC 59.129 50.000 30.64 8.66 0.00 3.85
571 576 2.420547 GCATGCATGAACTAGACCTCCA 60.421 50.000 30.64 0.00 0.00 3.86
599 604 4.834357 AATTAACCGTGCCGTAAACTTT 57.166 36.364 0.00 0.00 0.00 2.66
653 658 3.612860 GCGTTGTCTACTGTCCAATGTAG 59.387 47.826 0.00 0.00 37.92 2.74
693 698 3.821421 AGTCGATACCCATCCAACTTC 57.179 47.619 0.00 0.00 0.00 3.01
705 710 4.326826 CATCCAACTTCAAGGAGTGCTTA 58.673 43.478 0.00 0.00 37.34 3.09
746 751 6.790319 ACTTCCAAGGTTTATATCACCAAGT 58.210 36.000 6.74 4.85 36.67 3.16
761 766 6.554334 TCACCAAGTCACTATTAAAACTGC 57.446 37.500 0.00 0.00 0.00 4.40
777 782 5.796350 AAACTGCGACAAGTAATATGGAC 57.204 39.130 0.00 0.00 0.00 4.02
797 808 7.989947 TGGACTAGAGGAAGTATATGGTTTT 57.010 36.000 0.00 0.00 0.00 2.43
801 812 9.315525 GACTAGAGGAAGTATATGGTTTTTCAC 57.684 37.037 0.00 0.00 0.00 3.18
802 813 9.047947 ACTAGAGGAAGTATATGGTTTTTCACT 57.952 33.333 0.00 0.00 0.00 3.41
872 884 6.695292 CGAAGGAAATGAAAATTCTTGGTG 57.305 37.500 0.00 0.00 0.00 4.17
938 950 6.585389 AAGCTAAACGACTATTCCGAATTC 57.415 37.500 0.00 0.00 0.00 2.17
944 956 2.158871 CGACTATTCCGAATTCCCCCAA 60.159 50.000 0.00 0.00 0.00 4.12
1136 1148 1.437573 CATACTTCTCCTCCGCGCA 59.562 57.895 8.75 0.00 0.00 6.09
1679 1691 7.421599 TGAAATGTTTGTGATGTGTCGTATTT 58.578 30.769 0.00 0.00 0.00 1.40
1948 1960 5.418209 GGTGAAGTGTGTGGTACTACTATCT 59.582 44.000 10.95 3.44 0.00 1.98
2105 2118 6.999153 CTGATTGGCTCAAAATTGTTGCAAAC 60.999 38.462 0.00 0.00 39.59 2.93
2317 2330 1.007038 TCTACGTTCGGTGTGGCAC 60.007 57.895 11.55 11.55 0.00 5.01
2318 2331 1.006571 CTACGTTCGGTGTGGCACT 60.007 57.895 19.83 0.00 34.40 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.963532 AGTCCTTTCAATAAGTAAGAGTGTCA 58.036 34.615 0.00 0.00 0.00 3.58
14 15 9.582431 TCAATCGTAGTCCTTTCAATAAGTAAG 57.418 33.333 0.00 0.00 0.00 2.34
16 17 9.745880 GATCAATCGTAGTCCTTTCAATAAGTA 57.254 33.333 0.00 0.00 0.00 2.24
17 18 7.711339 GGATCAATCGTAGTCCTTTCAATAAGT 59.289 37.037 0.00 0.00 0.00 2.24
53 54 8.489676 AGAACTGTGAAGATATGATGACCTAT 57.510 34.615 0.00 0.00 0.00 2.57
55 56 6.805016 AGAACTGTGAAGATATGATGACCT 57.195 37.500 0.00 0.00 0.00 3.85
146 147 0.514255 CAATATCGGATGCACGCCAG 59.486 55.000 8.07 1.69 0.00 4.85
159 160 8.483307 TTCACTTAAAGGTTACCGACAATATC 57.517 34.615 0.00 0.00 0.00 1.63
241 242 4.080919 TGGATGGAGATCAACTTTGACGAT 60.081 41.667 0.00 0.00 40.49 3.73
282 283 5.962433 TCGAGTGTCCTAGTCATTTAAAGG 58.038 41.667 0.00 0.00 0.00 3.11
533 538 0.317160 TGCAGTCGAGGACAACGAAT 59.683 50.000 0.00 0.00 41.31 3.34
548 553 2.871022 GAGGTCTAGTTCATGCATGCAG 59.129 50.000 26.69 17.32 0.00 4.41
586 591 6.147328 AGTCAATCTCTTAAAGTTTACGGCAC 59.853 38.462 0.00 0.00 0.00 5.01
628 633 3.293311 TTGGACAGTAGACAACGCTAC 57.707 47.619 0.00 0.00 40.78 3.58
632 637 4.082408 TCCTACATTGGACAGTAGACAACG 60.082 45.833 0.00 0.00 40.02 4.10
653 658 4.557205 ACTTTGACGACTCAACTACATCC 58.443 43.478 0.00 0.00 36.06 3.51
693 698 5.010012 ACCTTTCAACAATAAGCACTCCTTG 59.990 40.000 0.00 0.00 34.95 3.61
705 710 5.200483 TGGAAGTTCTGACCTTTCAACAAT 58.800 37.500 2.25 0.00 0.00 2.71
746 751 7.949903 TTACTTGTCGCAGTTTTAATAGTGA 57.050 32.000 5.07 0.00 0.00 3.41
761 766 6.879276 TCCTCTAGTCCATATTACTTGTCG 57.121 41.667 0.00 0.00 0.00 4.35
777 782 9.892130 AAGTGAAAAACCATATACTTCCTCTAG 57.108 33.333 0.00 0.00 0.00 2.43
838 849 1.358152 TTTCCTTCGGGATGTGGAGT 58.642 50.000 0.00 0.00 44.61 3.85
872 884 4.320023 GAGAAAGGGAAAGAAGAGGACAC 58.680 47.826 0.00 0.00 0.00 3.67
938 950 0.409484 AGGAAATGGAGTGTTGGGGG 59.591 55.000 0.00 0.00 0.00 5.40
944 956 1.566231 GATGGGGAGGAAATGGAGTGT 59.434 52.381 0.00 0.00 0.00 3.55
980 992 3.351885 AGAGGAGCGGGAGGAGGT 61.352 66.667 0.00 0.00 0.00 3.85
1136 1148 1.671379 GGGAAAGCGCCGTCTTTCT 60.671 57.895 23.23 1.22 46.76 2.52
1296 1308 3.055719 ATGTTGGCGCTTCCACCG 61.056 61.111 7.64 0.00 46.55 4.94
1679 1691 4.162131 TGCAGATAAATCTACAGAGGTGCA 59.838 41.667 0.00 0.00 34.85 4.57
1948 1960 0.616371 CCGGAACACCCACTCCAATA 59.384 55.000 0.00 0.00 34.14 1.90
2420 2433 6.136155 AGCAAAGGGGCAATTATGTTATACT 58.864 36.000 0.00 0.00 35.83 2.12
2421 2434 6.405278 AGCAAAGGGGCAATTATGTTATAC 57.595 37.500 0.00 0.00 35.83 1.47
2423 2436 5.424895 TCAAGCAAAGGGGCAATTATGTTAT 59.575 36.000 0.00 0.00 35.83 1.89


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

AutoCloner maintained by Alex Coulton.