Multiple sequence alignment - TraesCS1D01G189400

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 TraesCS1D01G189400 chr1D 100.000 4268 0 0 1 4268 261842882 261838615 0.000000e+00 7882
1 TraesCS1D01G189400 chr1A 92.255 3680 168 41 1 3609 338213784 338217417 0.000000e+00 5108
2 TraesCS1D01G189400 chr1A 93.539 681 35 5 3593 4268 338217432 338218108 0.000000e+00 1005
3 TraesCS1D01G189400 chr1B 96.942 2714 67 9 912 3609 350025786 350028499 0.000000e+00 4538
4 TraesCS1D01G189400 chr1B 96.840 1234 37 2 1871 3103 570299139 570300371 0.000000e+00 2061
5 TraesCS1D01G189400 chr1B 98.169 710 13 0 1433 2142 350053822 350054531 0.000000e+00 1240
6 TraesCS1D01G189400 chr1B 95.883 583 20 2 3031 3609 350055882 350056464 0.000000e+00 941
7 TraesCS1D01G189400 chr1B 90.789 684 50 8 3593 4266 350028514 350029194 0.000000e+00 902
8 TraesCS1D01G189400 chr1B 90.789 684 50 8 3593 4266 350056479 350057159 0.000000e+00 902
9 TraesCS1D01G189400 chr1B 93.392 454 29 1 3114 3566 570300560 570301013 0.000000e+00 671
10 TraesCS1D01G189400 chr1B 84.814 619 40 27 273 867 350024854 350025442 1.330000e-159 573
11 TraesCS1D01G189400 chr1B 92.163 319 20 4 1003 1321 570298828 570299141 3.030000e-121 446
12 TraesCS1D01G189400 chr1B 95.402 261 8 2 1 261 350024616 350024872 3.070000e-111 412
13 TraesCS1D01G189400 chr1B 92.105 152 5 4 4123 4268 350029102 350029252 1.560000e-49 207
14 TraesCS1D01G189400 chr1B 92.105 152 5 4 4123 4268 350057067 350057217 1.560000e-49 207
15 TraesCS1D01G189400 chr7B 95.995 1698 65 3 1871 3566 516800388 516798692 0.000000e+00 2756
16 TraesCS1D01G189400 chr7B 95.583 1698 67 4 1871 3566 656196068 656197759 0.000000e+00 2713
17 TraesCS1D01G189400 chr7B 92.163 319 21 3 1003 1321 656195756 656196070 8.420000e-122 448
18 TraesCS1D01G189400 chr7B 91.850 319 22 3 1003 1321 516800700 516800386 3.920000e-120 442
19 TraesCS1D01G189400 chr2B 96.532 1557 52 2 1871 3426 467877234 467875679 0.000000e+00 2575
20 TraesCS1D01G189400 chr2B 92.476 319 20 3 1003 1321 467877546 467877232 1.810000e-123 453
21 TraesCS1D01G189400 chr4D 80.797 2208 361 47 1071 3249 500468029 500470202 0.000000e+00 1670
22 TraesCS1D01G189400 chr4B 80.609 2202 366 48 1077 3249 644094525 644096694 0.000000e+00 1644
23 TraesCS1D01G189400 chr5A 80.159 2258 383 50 1023 3249 681384767 681386990 0.000000e+00 1628


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 TraesCS1D01G189400 chr1D 261838615 261842882 4267 True 7882.000000 7882 100.000000 1 4268 1 chr1D.!!$R1 4267
1 TraesCS1D01G189400 chr1A 338213784 338218108 4324 False 3056.500000 5108 92.897000 1 4268 2 chr1A.!!$F1 4267
2 TraesCS1D01G189400 chr1B 350024616 350029252 4636 False 1326.400000 4538 92.010400 1 4268 5 chr1B.!!$F1 4267
3 TraesCS1D01G189400 chr1B 570298828 570301013 2185 False 1059.333333 2061 94.131667 1003 3566 3 chr1B.!!$F3 2563
4 TraesCS1D01G189400 chr1B 350053822 350057217 3395 False 822.500000 1240 94.236500 1433 4268 4 chr1B.!!$F2 2835
5 TraesCS1D01G189400 chr7B 516798692 516800700 2008 True 1599.000000 2756 93.922500 1003 3566 2 chr7B.!!$R1 2563
6 TraesCS1D01G189400 chr7B 656195756 656197759 2003 False 1580.500000 2713 93.873000 1003 3566 2 chr7B.!!$F1 2563
7 TraesCS1D01G189400 chr2B 467875679 467877546 1867 True 1514.000000 2575 94.504000 1003 3426 2 chr2B.!!$R1 2423
8 TraesCS1D01G189400 chr4D 500468029 500470202 2173 False 1670.000000 1670 80.797000 1071 3249 1 chr4D.!!$F1 2178
9 TraesCS1D01G189400 chr4B 644094525 644096694 2169 False 1644.000000 1644 80.609000 1077 3249 1 chr4B.!!$F1 2172
10 TraesCS1D01G189400 chr5A 681384767 681386990 2223 False 1628.000000 1628 80.159000 1023 3249 1 chr5A.!!$F1 2226

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
811 916 0.105964 TTTACACCAGTGACGCAGCT 59.894 50.000 4.48 0.00 0.0 4.24 F
812 917 0.599991 TTACACCAGTGACGCAGCTG 60.600 55.000 10.11 10.11 0.0 4.24 F
1230 1659 1.564622 CCCGCGCATCATTTACTCG 59.435 57.895 8.75 0.00 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 3100 3.311110 GACCAGTCCGGGTGCAGA 61.311 66.667 0.0 0.0 42.53 4.26 R
3080 3974 2.126965 CCGTCACCGACACGTCTC 60.127 66.667 0.0 0.0 35.39 3.36 R
3341 4424 1.286570 CGCTCCAGTTTGCATGCAA 59.713 52.632 28.8 28.8 0.00 4.08 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
48 54 2.027192 TGGGGCAGTATGTTTGAGACTC 60.027 50.000 0.00 0.00 39.31 3.36
49 55 2.237392 GGGGCAGTATGTTTGAGACTCT 59.763 50.000 3.68 0.00 39.31 3.24
80 86 3.257933 CCAAACGAGCTCTGTGGC 58.742 61.111 12.85 0.00 0.00 5.01
134 141 4.144108 CGAATTTGTTACTTTTGTGCGACG 60.144 41.667 0.00 0.00 0.00 5.12
187 202 6.217294 GGTTCAAAATTCAAAATACGGGTGA 58.783 36.000 0.00 0.00 0.00 4.02
241 269 4.094442 GGGAGTGAACACGAATAAATGGTC 59.906 45.833 0.00 0.00 36.20 4.02
242 270 4.693566 GGAGTGAACACGAATAAATGGTCA 59.306 41.667 0.00 0.00 40.23 4.02
272 300 6.935741 TTCCATATTTCCGTGTTTATGGAG 57.064 37.500 9.68 0.00 46.50 3.86
479 535 3.580319 AAAAGGCGGGCCCTGTCT 61.580 61.111 22.43 17.66 45.62 3.41
497 553 2.587753 CTGCACGTGTCAACCGGT 60.588 61.111 18.38 0.00 0.00 5.28
681 763 3.246112 CACGGGACAGGGGTTGGA 61.246 66.667 0.00 0.00 0.00 3.53
688 770 3.717294 CAGGGGTTGGAGGTCCCG 61.717 72.222 0.00 0.00 45.13 5.14
768 861 1.039233 TACTAGTACTGCGCCCCACC 61.039 60.000 4.18 0.00 0.00 4.61
811 916 0.105964 TTTACACCAGTGACGCAGCT 59.894 50.000 4.48 0.00 0.00 4.24
812 917 0.599991 TTACACCAGTGACGCAGCTG 60.600 55.000 10.11 10.11 0.00 4.24
813 918 3.720193 CACCAGTGACGCAGCTGC 61.720 66.667 29.12 29.12 37.78 5.25
1186 1615 2.190578 CCGAATGGGAGGTGGAGC 59.809 66.667 0.00 0.00 38.47 4.70
1230 1659 1.564622 CCCGCGCATCATTTACTCG 59.435 57.895 8.75 0.00 0.00 4.18
1242 1671 2.232239 TTTACTCGTACAGCGACGTC 57.768 50.000 5.18 5.18 45.68 4.34
1752 2184 2.745152 GCACCTGGCGATATACAAGGTT 60.745 50.000 2.09 0.00 0.00 3.50
3080 3974 2.747460 CGTGGTGGACATGCCCAG 60.747 66.667 0.00 0.00 36.78 4.45
3222 4297 0.611062 TGAAGTGGGTCTCCGACGAT 60.611 55.000 0.00 0.00 35.24 3.73
3252 4327 1.076549 GAGCCCCATTGTGGTTCCA 59.923 57.895 0.00 0.00 35.17 3.53
3341 4424 1.112315 TTCCATGGTTTTGCGCAGGT 61.112 50.000 11.31 0.00 0.00 4.00
3360 4443 2.144833 TTGCATGCAAACTGGAGCGG 62.145 55.000 30.19 0.00 32.44 5.52
3426 4510 4.216257 AGAACATCTGGTCGTCCAAAAATG 59.784 41.667 2.32 9.27 43.81 2.32
3513 4598 3.819564 AGTTGACTACACTCACTGCAA 57.180 42.857 0.00 0.00 0.00 4.08
3514 4599 3.458189 AGTTGACTACACTCACTGCAAC 58.542 45.455 0.00 0.00 35.61 4.17
3520 4605 1.597742 ACACTCACTGCAACCATGAC 58.402 50.000 0.00 0.00 0.00 3.06
3812 4962 3.631686 TCCACTCCAGTGTTTTGATTGTG 59.368 43.478 5.99 0.00 44.21 3.33
3825 4975 1.270274 TGATTGTGTTGCACATGGCTC 59.730 47.619 2.65 0.30 44.16 4.70
3827 4977 0.754587 TTGTGTTGCACATGGCTCCA 60.755 50.000 2.65 0.00 44.16 3.86
3835 4985 1.825090 CACATGGCTCCAGCAACTTA 58.175 50.000 0.03 0.00 44.36 2.24
3955 5107 6.055588 AGTGAGTTTCCTCTTCGATTTTCAA 58.944 36.000 0.00 0.00 38.61 2.69
4096 5249 5.633830 ATGTTGAAGATGATGTTGTGGAC 57.366 39.130 0.00 0.00 0.00 4.02
4121 5274 7.702348 ACGTACAACCTATCGACCTTTAAATAC 59.298 37.037 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 86 4.778143 GCGTGGGGTAGCCACAGG 62.778 72.222 14.06 14.11 44.63 4.00
134 141 2.024941 ACCAAGGGACAATCAATCCTCC 60.025 50.000 0.00 0.00 36.40 4.30
187 202 1.153489 ATCTCGCATCTGCAACGCT 60.153 52.632 2.72 0.00 42.21 5.07
321 349 2.108976 ACGCACGCATATCTGGGG 59.891 61.111 0.27 0.00 39.53 4.96
479 535 2.279851 CCGGTTGACACGTGCAGA 60.280 61.111 17.22 0.00 0.00 4.26
497 553 0.106708 GGCGCTATCAGGGTCAATGA 59.893 55.000 7.64 0.00 32.53 2.57
599 678 2.421314 GGTGCCACCTTTGGTTGC 59.579 61.111 6.63 5.94 45.98 4.17
668 750 2.603652 GGACCTCCAACCCCTGTCC 61.604 68.421 0.00 0.00 38.78 4.02
688 770 3.418068 GCTGACTGCTGTCCGTGC 61.418 66.667 19.64 16.46 42.28 5.34
731 824 0.532573 TACTGCTGCTCCTACTGTGC 59.467 55.000 0.00 0.00 0.00 4.57
768 861 1.226660 GGCGTTTCATTGCATCCGG 60.227 57.895 0.00 0.00 0.00 5.14
770 863 1.134753 TGATGGCGTTTCATTGCATCC 59.865 47.619 0.00 0.00 0.00 3.51
822 927 4.792804 GAGCTGGAGGGCAGTGGC 62.793 72.222 8.47 8.47 40.13 5.01
823 928 3.324930 TGAGCTGGAGGGCAGTGG 61.325 66.667 0.00 0.00 34.17 4.00
824 929 2.046507 GTGAGCTGGAGGGCAGTG 60.047 66.667 0.00 0.00 34.17 3.66
1230 1659 1.063951 CGGTGAAGACGTCGCTGTAC 61.064 60.000 10.46 6.44 38.19 2.90
1419 1848 1.217057 AGATGCCAATCACCACCCCT 61.217 55.000 0.00 0.00 35.03 4.79
2592 3025 3.504134 CAGACTCCACGAAGAAAGAGAGA 59.496 47.826 0.00 0.00 0.00 3.10
2667 3100 3.311110 GACCAGTCCGGGTGCAGA 61.311 66.667 0.00 0.00 42.53 4.26
3080 3974 2.126965 CCGTCACCGACACGTCTC 60.127 66.667 0.00 0.00 35.39 3.36
3222 4297 4.451150 GGGCTCCGCACGATGTGA 62.451 66.667 0.24 0.00 35.23 3.58
3252 4327 1.619807 ATTACTACGCGGCCTTGGGT 61.620 55.000 12.47 3.03 38.66 4.51
3341 4424 1.286570 CGCTCCAGTTTGCATGCAA 59.713 52.632 28.80 28.80 0.00 4.08
3360 4443 4.704457 TCGCGCTATTTACAGAACAAAAC 58.296 39.130 5.56 0.00 0.00 2.43
3426 4510 1.325355 CACATGCATGGATTCCCTCC 58.675 55.000 29.41 0.00 45.19 4.30
3520 4605 1.268184 CGATGTTTGCATGATCCACCG 60.268 52.381 0.00 0.00 35.07 4.94
3704 4851 3.688694 AACATGCTGGAAACGGTAGTA 57.311 42.857 0.00 0.00 39.64 1.82
3705 4852 2.561478 AACATGCTGGAAACGGTAGT 57.439 45.000 0.00 0.00 39.64 2.73
3812 4962 1.808531 TTGCTGGAGCCATGTGCAAC 61.809 55.000 9.72 2.26 44.83 4.17
3825 4975 2.636830 CAGTGGGAGATAAGTTGCTGG 58.363 52.381 0.00 0.00 0.00 4.85
3827 4977 2.269940 ACCAGTGGGAGATAAGTTGCT 58.730 47.619 15.21 0.00 38.05 3.91
3835 4985 1.617947 GGCGAGAACCAGTGGGAGAT 61.618 60.000 15.21 0.00 38.05 2.75
3869 5019 7.704789 AAACTGAAGAGATGCAAATCAAAAC 57.295 32.000 0.00 0.00 0.00 2.43
3916 5066 7.545615 AGGAAACTCACTTGATCAAACAAAAAC 59.454 33.333 9.88 0.00 32.90 2.43
4096 5249 7.701924 TGTATTTAAAGGTCGATAGGTTGTACG 59.298 37.037 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.