Multiple sequence alignment - TraesCS1D01G058400

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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 TraesCS1D01G058400 chr1D 100.000 4166 0 0 1 4166 38560581 38556416 0.000000e+00 7694.0
1 TraesCS1D01G058400 chr1D 92.197 1807 135 4 923 2728 38583368 38581567 0.000000e+00 2551.0
2 TraesCS1D01G058400 chr1D 90.996 1877 165 3 909 2783 38367399 38365525 0.000000e+00 2527.0
3 TraesCS1D01G058400 chr1D 85.884 2104 256 17 909 3001 38259056 38256983 0.000000e+00 2202.0
4 TraesCS1D01G058400 chr1D 86.918 1804 229 7 922 2722 36623965 36622166 0.000000e+00 2017.0
5 TraesCS1D01G058400 chr1D 85.691 1838 257 6 910 2744 37424466 37426300 0.000000e+00 1932.0
6 TraesCS1D01G058400 chr1D 88.295 880 70 17 64 915 38584282 38583408 0.000000e+00 1024.0
7 TraesCS1D01G058400 chr1D 85.697 818 99 15 107 915 38259890 38259082 0.000000e+00 846.0
8 TraesCS1D01G058400 chr1D 84.595 753 90 13 181 915 37423695 37424439 0.000000e+00 725.0
9 TraesCS1D01G058400 chr1A 95.570 4176 85 32 71 4165 37505567 37501411 0.000000e+00 6595.0
10 TraesCS1D01G058400 chr1A 86.485 1835 240 8 910 2741 36613816 36615645 0.000000e+00 2008.0
11 TraesCS1D01G058400 chr1A 83.668 747 96 16 187 915 36605013 36605751 0.000000e+00 680.0
12 TraesCS1D01G058400 chr1A 95.745 47 2 0 1 47 37505684 37505638 4.470000e-10 76.8
13 TraesCS1D01G058400 chr1B 94.672 1952 103 1 909 2859 58328050 58326099 0.000000e+00 3027.0
14 TraesCS1D01G058400 chr1B 85.124 2104 270 19 909 3001 57791012 57788941 0.000000e+00 2111.0
15 TraesCS1D01G058400 chr1B 89.571 863 69 10 64 914 58328930 58328077 0.000000e+00 1075.0
16 TraesCS1D01G058400 chr1B 85.199 804 95 12 124 915 57791829 57791038 0.000000e+00 804.0
17 TraesCS1D01G058400 chr1B 85.581 749 84 13 184 915 56501936 56501195 0.000000e+00 763.0
18 TraesCS1D01G058400 chr1B 87.960 598 69 3 320 915 57130238 57130834 0.000000e+00 702.0
19 TraesCS1D01G058400 chr1B 87.879 429 40 6 3585 4002 58326094 58325667 1.040000e-135 494.0
20 TraesCS1D01G058400 chr1B 81.216 559 95 7 2517 3070 58048777 58048224 3.820000e-120 442.0
21 TraesCS1D01G058400 chr1B 81.216 559 95 7 2517 3070 58087711 58087158 3.820000e-120 442.0
22 TraesCS1D01G058400 chr1B 81.071 560 94 9 2517 3070 58114356 58113803 1.780000e-118 436.0
23 TraesCS1D01G058400 chr7B 96.970 33 0 1 2992 3023 537732607 537732639 2.000000e-03 54.7


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 TraesCS1D01G058400 chr1D 38556416 38560581 4165 True 7694.0 7694 100.000000 1 4166 1 chr1D.!!$R3 4165
1 TraesCS1D01G058400 chr1D 38365525 38367399 1874 True 2527.0 2527 90.996000 909 2783 1 chr1D.!!$R2 1874
2 TraesCS1D01G058400 chr1D 36622166 36623965 1799 True 2017.0 2017 86.918000 922 2722 1 chr1D.!!$R1 1800
3 TraesCS1D01G058400 chr1D 38581567 38584282 2715 True 1787.5 2551 90.246000 64 2728 2 chr1D.!!$R5 2664
4 TraesCS1D01G058400 chr1D 38256983 38259890 2907 True 1524.0 2202 85.790500 107 3001 2 chr1D.!!$R4 2894
5 TraesCS1D01G058400 chr1D 37423695 37426300 2605 False 1328.5 1932 85.143000 181 2744 2 chr1D.!!$F1 2563
6 TraesCS1D01G058400 chr1A 37501411 37505684 4273 True 3335.9 6595 95.657500 1 4165 2 chr1A.!!$R1 4164
7 TraesCS1D01G058400 chr1A 36613816 36615645 1829 False 2008.0 2008 86.485000 910 2741 1 chr1A.!!$F2 1831
8 TraesCS1D01G058400 chr1A 36605013 36605751 738 False 680.0 680 83.668000 187 915 1 chr1A.!!$F1 728
9 TraesCS1D01G058400 chr1B 58325667 58328930 3263 True 1532.0 3027 90.707333 64 4002 3 chr1B.!!$R6 3938
10 TraesCS1D01G058400 chr1B 57788941 57791829 2888 True 1457.5 2111 85.161500 124 3001 2 chr1B.!!$R5 2877
11 TraesCS1D01G058400 chr1B 56501195 56501936 741 True 763.0 763 85.581000 184 915 1 chr1B.!!$R1 731
12 TraesCS1D01G058400 chr1B 57130238 57130834 596 False 702.0 702 87.960000 320 915 1 chr1B.!!$F1 595
13 TraesCS1D01G058400 chr1B 58048224 58048777 553 True 442.0 442 81.216000 2517 3070 1 chr1B.!!$R2 553
14 TraesCS1D01G058400 chr1B 58087158 58087711 553 True 442.0 442 81.216000 2517 3070 1 chr1B.!!$R3 553
15 TraesCS1D01G058400 chr1B 58113803 58114356 553 True 436.0 436 81.071000 2517 3070 1 chr1B.!!$R4 553

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
748 922 0.036952 ACAGAACAGATCACCGCCAG 60.037 55.00 0.0 0.0 0.0 4.85 F
1770 1977 0.684535 TTCCTCGTCCTGACATTGCA 59.315 50.00 0.0 0.0 0.0 4.08 F
2287 2495 4.660168 AGGAGCAATGAATGTCAAGTTCT 58.340 39.13 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 2694 1.220206 CGAGAGCTGGGAGCACAAT 59.780 57.895 0.0 0.0 45.56 2.71 R
3163 3380 1.003118 CGTTCTTCCAGGACCCATTCA 59.997 52.381 0.0 0.0 0.00 2.57 R
3951 4203 0.030638 CCTTTTGCGACAACCACCTG 59.969 55.000 0.0 0.0 0.00 4.00 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 7.604164 TGTCAAAGTTTGGCACAGAAAAATTTA 59.396 29.630 18.71 0.00 40.96 1.40
41 42 8.785329 AAGTTTGGCACAGAAAAATTTAAGAA 57.215 26.923 0.00 0.00 42.39 2.52
126 175 3.138930 GAGCCAGAGCACGCCGATA 62.139 63.158 0.00 0.00 43.56 2.92
136 196 2.261361 CGCCGATATCCCGCATCA 59.739 61.111 9.44 0.00 0.00 3.07
137 197 1.374125 CGCCGATATCCCGCATCAA 60.374 57.895 9.44 0.00 0.00 2.57
748 922 0.036952 ACAGAACAGATCACCGCCAG 60.037 55.000 0.00 0.00 0.00 4.85
879 1053 4.397103 CCATTGTTCTGAAGAGCTTATGCA 59.603 41.667 3.16 0.00 42.74 3.96
1055 1262 4.112634 ACGTACAACTCGATCATTGATGG 58.887 43.478 3.32 2.85 0.00 3.51
1443 1650 5.275067 TGAAAAGCAATGGTTTTGTAGCT 57.725 34.783 25.10 2.68 42.14 3.32
1770 1977 0.684535 TTCCTCGTCCTGACATTGCA 59.315 50.000 0.00 0.00 0.00 4.08
2287 2495 4.660168 AGGAGCAATGAATGTCAAGTTCT 58.340 39.130 0.00 0.00 0.00 3.01
2486 2694 6.298361 TGTTTTCATCAATGGAGAAGAGTGA 58.702 36.000 0.00 0.00 0.00 3.41
3163 3380 6.380079 AGATGTTTTCTCTATTGTCAGGGT 57.620 37.500 0.00 0.00 0.00 4.34
3200 3417 2.753966 CGATGTTTGAGCGGGCTGG 61.754 63.158 0.00 0.00 0.00 4.85
3274 3491 1.069765 ACTGGTGGAGTCTGTTGCG 59.930 57.895 0.00 0.00 0.00 4.85
3353 3570 3.295973 TCAACCACTTTCCTTCCCAAAG 58.704 45.455 0.00 0.00 36.97 2.77
3769 4020 2.118403 TTTCTTCCTCAGACCCCAGT 57.882 50.000 0.00 0.00 0.00 4.00
3779 4030 5.074515 TCCTCAGACCCCAGTTTCTTTTTAT 59.925 40.000 0.00 0.00 0.00 1.40
3788 4039 7.881751 ACCCCAGTTTCTTTTTATCTAGTGTAC 59.118 37.037 0.00 0.00 0.00 2.90
3838 4089 2.670414 CCTTCTCACGCTCTTGCTTAAG 59.330 50.000 0.00 0.00 36.97 1.85
3863 4114 2.032860 ATGGACAGCGCCGCTTAGAT 62.033 55.000 9.89 0.00 36.40 1.98
3871 4122 1.258197 GCGCCGCTTAGATGTAAACTC 59.742 52.381 0.00 0.00 0.00 3.01
3905 4157 1.300481 GAGGTGGATTAGAAAGCGCC 58.700 55.000 2.29 0.00 0.00 6.53
3922 4174 2.284417 GCGCCGGTGAATTTACTAGAAG 59.716 50.000 21.76 0.00 0.00 2.85
3940 4192 8.152023 ACTAGAAGTGGAAATATGGAACTCTT 57.848 34.615 0.00 0.00 0.00 2.85
3951 4203 3.045601 TGGAACTCTTGAAGTAGCTGC 57.954 47.619 0.00 0.00 37.17 5.25
3963 4215 1.005037 TAGCTGCAGGTGGTTGTCG 60.005 57.895 28.10 0.00 0.00 4.35
4002 4263 5.347342 TGTATGTTGCTGAAACTTTGGTTG 58.653 37.500 0.00 0.00 39.70 3.77
4062 4324 8.170553 GCATTCAGCCAAATTACTTTTTGTATG 58.829 33.333 0.00 0.00 35.30 2.39
4104 4366 8.879759 ACATGTTTCTCTATACGGTGTTATTTG 58.120 33.333 0.00 0.00 0.00 2.32
4107 4369 5.601583 TCTCTATACGGTGTTATTTGGCA 57.398 39.130 0.00 0.00 0.00 4.92
4110 4372 7.728148 TCTCTATACGGTGTTATTTGGCATTA 58.272 34.615 0.00 0.00 0.00 1.90
4112 4374 9.647797 CTCTATACGGTGTTATTTGGCATTATA 57.352 33.333 0.00 0.00 0.00 0.98
4134 4396 4.872664 AGTCTGTAGTGTTCAGCTGTTAC 58.127 43.478 14.67 13.50 33.48 2.50
4139 4401 1.140852 AGTGTTCAGCTGTTACCTGCA 59.859 47.619 14.67 1.02 37.95 4.41
4140 4402 2.154462 GTGTTCAGCTGTTACCTGCAT 58.846 47.619 14.67 0.00 37.95 3.96
4141 4403 2.554032 GTGTTCAGCTGTTACCTGCATT 59.446 45.455 14.67 0.00 37.95 3.56
4152 4414 7.176690 AGCTGTTACCTGCATTATTAAAACAGT 59.823 33.333 16.53 7.27 42.71 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 175 1.893808 GCGGATGTTGATGCGGGAT 60.894 57.895 0.00 0.00 43.19 3.85
202 277 0.631753 TAGGTGGAGGAGGAGGAGTG 59.368 60.000 0.00 0.00 0.00 3.51
203 278 0.930726 CTAGGTGGAGGAGGAGGAGT 59.069 60.000 0.00 0.00 0.00 3.85
333 489 1.990614 GGTGGAGGTGGAGGAGGAC 60.991 68.421 0.00 0.00 0.00 3.85
748 922 0.957888 GAGGCACTTGAGGAAGGTGC 60.958 60.000 8.53 8.53 41.55 5.01
879 1053 2.484417 CCCGCTGACTCATGCTATTCTT 60.484 50.000 0.00 0.00 0.00 2.52
1055 1262 1.246056 TGCTCTGGCCTTGCACAATC 61.246 55.000 3.32 0.00 37.74 2.67
1443 1650 2.064434 TGGTGAAAACATGGCAGTCA 57.936 45.000 0.00 0.00 0.00 3.41
2219 2427 6.316140 TGCTTCGTCTGCACAATTATTTCTAT 59.684 34.615 0.00 0.00 35.31 1.98
2486 2694 1.220206 CGAGAGCTGGGAGCACAAT 59.780 57.895 0.00 0.00 45.56 2.71
3144 3361 6.127897 CCATTCACCCTGACAATAGAGAAAAC 60.128 42.308 0.00 0.00 0.00 2.43
3163 3380 1.003118 CGTTCTTCCAGGACCCATTCA 59.997 52.381 0.00 0.00 0.00 2.57
3200 3417 7.819415 TGTATATCCAATACTTGAGCATAGCAC 59.181 37.037 0.00 0.00 0.00 4.40
3788 4039 6.334202 AGCGACCTTCTACTATTTTTCAGAG 58.666 40.000 0.00 0.00 0.00 3.35
3838 4089 3.589881 GGCGCTGTCCATCCATGC 61.590 66.667 7.64 0.00 0.00 4.06
3863 4114 8.846211 CCTCAATTCCTTAAAACAGAGTTTACA 58.154 33.333 0.00 0.00 0.00 2.41
3871 4122 6.840780 ATCCACCTCAATTCCTTAAAACAG 57.159 37.500 0.00 0.00 0.00 3.16
3905 4157 7.611213 ATTTCCACTTCTAGTAAATTCACCG 57.389 36.000 0.00 0.00 0.00 4.94
3922 4174 7.201652 GCTACTTCAAGAGTTCCATATTTCCAC 60.202 40.741 0.00 0.00 39.86 4.02
3940 4192 0.764890 AACCACCTGCAGCTACTTCA 59.235 50.000 8.66 0.00 0.00 3.02
3951 4203 0.030638 CCTTTTGCGACAACCACCTG 59.969 55.000 0.00 0.00 0.00 4.00
3963 4215 5.064441 ACATACAGAATGAAGCCTTTTGC 57.936 39.130 0.00 0.00 39.69 3.68
4018 4280 7.473735 TGAATGCTTAGCTAGATATGCTACT 57.526 36.000 21.92 9.86 41.95 2.57
4062 4324 1.062587 CATGTAACTTACGCCAGCTGC 59.937 52.381 8.66 2.87 0.00 5.25
4075 4337 7.823149 AACACCGTATAGAGAAACATGTAAC 57.177 36.000 0.00 0.00 0.00 2.50
4104 4366 5.463724 GCTGAACACTACAGACTATAATGCC 59.536 44.000 0.00 0.00 37.54 4.40
4107 4369 7.411486 ACAGCTGAACACTACAGACTATAAT 57.589 36.000 23.35 0.00 37.54 1.28
4110 4372 5.730296 AACAGCTGAACACTACAGACTAT 57.270 39.130 23.35 0.00 37.54 2.12
4112 4374 4.262079 GGTAACAGCTGAACACTACAGACT 60.262 45.833 23.35 0.00 37.54 3.24


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

AutoCloner maintained by Alex Coulton.