Multiple sequence alignment - TraesCS1D01G283700

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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 TraesCS1D01G283700 chr1D 100.000 3383 0 0 1 3383 381972950 381976332 0.000000e+00 6248
1 TraesCS1D01G283700 chr1D 82.812 2304 307 53 830 3073 114366058 114363784 0.000000e+00 1978
2 TraesCS1D01G283700 chr1B 93.109 3091 139 40 1 3044 511972275 511975338 0.000000e+00 4460
3 TraesCS1D01G283700 chr1B 82.807 2280 299 55 859 3075 175429798 175427549 0.000000e+00 1953
4 TraesCS1D01G283700 chr1B 95.918 343 9 2 3041 3383 511977563 511977900 4.930000e-153 551
5 TraesCS1D01G283700 chr1A 92.374 2793 147 21 621 3383 482248251 482251007 0.000000e+00 3917
6 TraesCS1D01G283700 chr1A 82.422 2304 318 50 830 3075 124897914 124895640 0.000000e+00 1930
7 TraesCS1D01G283700 chr1A 90.040 743 40 21 1 723 482247595 482248323 0.000000e+00 931
8 TraesCS1D01G283700 chr5D 79.131 1519 252 32 889 2358 40929126 40927624 0.000000e+00 989


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 TraesCS1D01G283700 chr1D 381972950 381976332 3382 False 6248.0 6248 100.0000 1 3383 1 chr1D.!!$F1 3382
1 TraesCS1D01G283700 chr1D 114363784 114366058 2274 True 1978.0 1978 82.8120 830 3073 1 chr1D.!!$R1 2243
2 TraesCS1D01G283700 chr1B 511972275 511977900 5625 False 2505.5 4460 94.5135 1 3383 2 chr1B.!!$F1 3382
3 TraesCS1D01G283700 chr1B 175427549 175429798 2249 True 1953.0 1953 82.8070 859 3075 1 chr1B.!!$R1 2216
4 TraesCS1D01G283700 chr1A 482247595 482251007 3412 False 2424.0 3917 91.2070 1 3383 2 chr1A.!!$F1 3382
5 TraesCS1D01G283700 chr1A 124895640 124897914 2274 True 1930.0 1930 82.4220 830 3075 1 chr1A.!!$R1 2245
6 TraesCS1D01G283700 chr5D 40927624 40929126 1502 True 989.0 989 79.1310 889 2358 1 chr5D.!!$R1 1469

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
883 986 0.107945 AAATCAGTCTCTCTGCCGCC 60.108 55.0 0.0 0.0 43.32 6.13 F
1506 1666 0.968901 ACTCCACGCTTATCACGGGA 60.969 55.0 0.0 0.0 35.45 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 2441 0.809385 CCTGCTGCCATGTCAGAAAG 59.191 55.000 8.18 4.01 36.19 2.62 R
3354 5761 2.518949 CAAACCTTGGATCGAATTGCG 58.481 47.619 0.00 0.00 42.69 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
36 37 5.866633 GGTATGACTCTTCTGTTCTTGTCTG 59.133 44.000 0.00 0.00 0.00 3.51
148 149 8.613922 ATGAAATAATGATCCCCAGTTTCTTT 57.386 30.769 0.00 0.00 31.51 2.52
170 171 2.162681 CTGATGTGTCAAAAGGGGGAC 58.837 52.381 0.00 0.00 33.05 4.46
191 192 3.641436 ACGAGTTGCAGATATATGACCCA 59.359 43.478 0.39 0.00 0.00 4.51
197 198 7.749666 AGTTGCAGATATATGACCCAACTATT 58.250 34.615 15.72 0.00 39.45 1.73
208 209 6.636454 TGACCCAACTATTATGAGTTTCCT 57.364 37.500 0.00 0.00 37.57 3.36
209 210 7.743116 TGACCCAACTATTATGAGTTTCCTA 57.257 36.000 0.00 0.00 37.57 2.94
210 211 7.792032 TGACCCAACTATTATGAGTTTCCTAG 58.208 38.462 0.00 0.00 37.57 3.02
258 259 6.994868 TTTTCCATGAAATTTACGGTTTCG 57.005 33.333 0.00 0.00 38.18 3.46
280 281 8.969121 TTCGAGTTCACGTATTTGTTATTCTA 57.031 30.769 0.00 0.00 34.70 2.10
417 420 5.332743 TCCACAAGGAGCATTTTTAGGATT 58.667 37.500 0.00 0.00 39.61 3.01
426 429 9.075678 AGGAGCATTTTTAGGATTGATAATGAG 57.924 33.333 0.00 0.00 0.00 2.90
510 521 8.848474 ACATGAGCTTGTGTTTACTAATTACT 57.152 30.769 0.00 0.00 0.00 2.24
607 620 6.870439 TCAAATCTCTATTGGATATGCTCGTG 59.130 38.462 0.00 0.00 0.00 4.35
626 639 4.342951 TCGTGTTTCTTCTGAGGGAGTAAA 59.657 41.667 0.00 0.00 0.00 2.01
817 914 2.907917 CGGCCCACGTTCCCAAAA 60.908 61.111 0.00 0.00 37.93 2.44
821 918 1.455959 CCCACGTTCCCAAAACCCA 60.456 57.895 0.00 0.00 0.00 4.51
852 949 3.508840 CGCCGTTTCAGCCCATCC 61.509 66.667 0.00 0.00 0.00 3.51
856 953 1.604378 CGTTTCAGCCCATCCTCCT 59.396 57.895 0.00 0.00 0.00 3.69
877 975 5.966935 TCCTTATCCCAAAATCAGTCTCTCT 59.033 40.000 0.00 0.00 0.00 3.10
879 982 3.340814 TCCCAAAATCAGTCTCTCTGC 57.659 47.619 0.00 0.00 43.32 4.26
881 984 2.005451 CCAAAATCAGTCTCTCTGCCG 58.995 52.381 0.00 0.00 43.32 5.69
883 986 0.107945 AAATCAGTCTCTCTGCCGCC 60.108 55.000 0.00 0.00 43.32 6.13
884 987 2.290122 AATCAGTCTCTCTGCCGCCG 62.290 60.000 0.00 0.00 43.32 6.46
1271 1428 4.459089 GACCCCCAGCGTGCTCTC 62.459 72.222 0.00 0.00 0.00 3.20
1389 1546 1.078759 CGTCGTCCTGCAACATCCTC 61.079 60.000 0.00 0.00 0.00 3.71
1438 1598 1.073964 CGACGACTCTCCGTACAAGA 58.926 55.000 0.00 0.00 43.49 3.02
1506 1666 0.968901 ACTCCACGCTTATCACGGGA 60.969 55.000 0.00 0.00 35.45 5.14
1563 1723 2.172372 GCTCGAGTGCATGCTGGAG 61.172 63.158 20.33 18.62 42.02 3.86
1658 1818 1.540166 CCATGGACCTGATGGCCAT 59.460 57.895 20.96 20.96 44.96 4.40
1667 1827 2.292389 ACCTGATGGCCATGATGGAAAA 60.292 45.455 26.56 0.00 39.92 2.29
1668 1828 2.767394 CCTGATGGCCATGATGGAAAAA 59.233 45.455 26.56 0.00 40.96 1.94
1669 1829 3.389983 CCTGATGGCCATGATGGAAAAAT 59.610 43.478 26.56 1.92 40.96 1.82
1893 2053 2.574018 GCTGGGCAAAGGGTTGGAC 61.574 63.158 0.00 0.00 35.10 4.02
2079 2242 2.565841 GGTGTTCTGAAGCTGTTGACT 58.434 47.619 0.00 0.00 0.00 3.41
2188 2351 1.347707 CCAAGAGCCTGGTCTGTAACA 59.652 52.381 0.00 0.00 0.00 2.41
2298 2464 1.202915 TCTGACATGGCAGCAGGAAAA 60.203 47.619 24.63 1.09 35.86 2.29
2619 2798 2.297701 TGTTGGGAAAGCAGTGAACTC 58.702 47.619 0.00 0.00 0.00 3.01
2739 2919 3.002791 TCACTGCTGAATTCGTCCAATC 58.997 45.455 0.04 0.00 0.00 2.67
2966 3147 3.220940 TCTCAACAATGTTGCATGTCCA 58.779 40.909 20.34 1.54 0.00 4.02
3231 5638 9.573133 GAACCAATCAACCAATACTTTATGAAG 57.427 33.333 0.00 0.00 38.87 3.02
3354 5761 2.234908 ACAATGTCTCCTCTAGCACACC 59.765 50.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 4.800784 TCGTACGATGATTTGACTGACAA 58.199 39.130 15.28 0.00 36.65 3.18
148 149 2.445145 TCCCCCTTTTGACACATCAGAA 59.555 45.455 0.00 0.00 35.83 3.02
170 171 4.257267 TGGGTCATATATCTGCAACTCG 57.743 45.455 0.00 0.00 0.00 4.18
250 251 2.712057 ATACGTGAACTCGAAACCGT 57.288 45.000 0.00 0.00 34.70 4.83
258 259 9.916397 CCATTAGAATAACAAATACGTGAACTC 57.084 33.333 0.00 0.00 0.00 3.01
280 281 3.054287 TGCCATTGCATTCCATTTCCATT 60.054 39.130 0.00 0.00 44.23 3.16
417 420 8.461222 GTCACATTTCATTTCACCTCATTATCA 58.539 33.333 0.00 0.00 0.00 2.15
426 429 5.922544 CAGGAAAGTCACATTTCATTTCACC 59.077 40.000 2.05 0.00 40.29 4.02
471 482 4.097418 AGCTCATGTTCTACCCTAGTTGT 58.903 43.478 0.00 0.00 0.00 3.32
472 483 4.744795 AGCTCATGTTCTACCCTAGTTG 57.255 45.455 0.00 0.00 0.00 3.16
473 484 4.532521 ACAAGCTCATGTTCTACCCTAGTT 59.467 41.667 0.00 0.00 0.00 2.24
741 829 4.455533 CAGCACCAGTTAACAGAGCATAAA 59.544 41.667 16.34 0.00 0.00 1.40
742 830 4.002982 CAGCACCAGTTAACAGAGCATAA 58.997 43.478 16.34 0.00 0.00 1.90
852 949 6.099557 AGAGAGACTGATTTTGGGATAAGGAG 59.900 42.308 0.00 0.00 0.00 3.69
1033 1145 1.614824 AGGAGGAGCAGGTGGGAAG 60.615 63.158 0.00 0.00 0.00 3.46
1271 1428 2.668457 GCGTTCATGAGAGTGTTGTAGG 59.332 50.000 0.00 0.00 0.00 3.18
1389 1546 2.031516 CCACGAGTGCAGCTTGAGG 61.032 63.158 9.64 7.69 33.89 3.86
1448 1608 4.598894 CCCCAGCCTCTCGCATCG 62.599 72.222 0.00 0.00 41.38 3.84
1506 1666 3.941188 CTCCCCACACGGCACAGT 61.941 66.667 0.00 0.00 0.00 3.55
1658 1818 1.626686 ACCGGCACATTTTTCCATCA 58.373 45.000 0.00 0.00 0.00 3.07
1893 2053 3.826157 TGCTCAAAGTAAAATCTGTGGGG 59.174 43.478 0.00 0.00 0.00 4.96
2079 2242 4.971939 TCACACCTTTCTTGATCATGTCA 58.028 39.130 8.33 0.00 34.25 3.58
2188 2351 2.802774 CGACATTTGCAGCAAACCCTTT 60.803 45.455 22.92 3.80 36.13 3.11
2275 2441 0.809385 CCTGCTGCCATGTCAGAAAG 59.191 55.000 8.18 4.01 36.19 2.62
2298 2464 8.936864 GTGTAAGTAACTTCATCTACAGCAATT 58.063 33.333 0.00 0.00 0.00 2.32
2619 2798 4.187694 GCTTCCTAGATCCACAAGAGTTG 58.812 47.826 0.00 0.00 0.00 3.16
2739 2919 5.124297 TGCACAGAACATCCTATTGTCATTG 59.876 40.000 0.00 0.00 0.00 2.82
2852 3033 7.759489 TGGAACCATTGATAATTACATAGCC 57.241 36.000 0.00 0.00 0.00 3.93
2987 3168 5.623596 GCGGCAAATTTTCCTACCAATTAGT 60.624 40.000 5.31 0.00 0.00 2.24
3231 5638 4.561606 ACATCTGTCATACGAAGCGTTTAC 59.438 41.667 0.00 0.00 41.54 2.01
3354 5761 2.518949 CAAACCTTGGATCGAATTGCG 58.481 47.619 0.00 0.00 42.69 4.85


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

AutoCloner maintained by Alex Coulton.