Multiple sequence alignment - TraesCS7D01G135700

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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 TraesCS7D01G135700 chr7D 100.000 4108 0 0 1 4108 87212858 87208751 0 7587
1 TraesCS7D01G135700 chr7D 93.029 3988 218 20 1 3964 86768912 86764961 0 5770
2 TraesCS7D01G135700 chr7D 92.807 3712 202 24 428 4108 86924515 86920838 0 5315
3 TraesCS7D01G135700 chr7D 90.745 3771 274 45 360 4108 86801001 86797284 0 4961
4 TraesCS7D01G135700 chr7D 92.660 2425 126 14 1 2411 86927683 86925297 0 3445
5 TraesCS7D01G135700 chr7D 87.401 2262 217 31 117 2346 86298583 86296358 0 2536
6 TraesCS7D01G135700 chr7A 96.766 4113 117 12 1 4108 88442289 88438188 0 6844
7 TraesCS7D01G135700 chr7A 93.481 4142 197 32 1 4108 88014779 88010677 0 6085
8 TraesCS7D01G135700 chr7A 93.480 4126 205 25 1 4108 88128036 88123957 0 6071
9 TraesCS7D01G135700 chr7A 92.611 4128 220 28 1 4108 88178787 88174725 0 5854
10 TraesCS7D01G135700 chr7A 90.949 3458 232 40 700 4108 87456919 87453494 0 4577
11 TraesCS7D01G135700 chr7A 94.933 2546 97 18 1 2543 88324087 88321571 0 3958
12 TraesCS7D01G135700 chr7A 95.851 1446 47 9 2553 3989 88320596 88319155 0 2326
13 TraesCS7D01G135700 chr7B 91.121 3942 262 39 196 4090 35313792 35309892 0 5260
14 TraesCS7D01G135700 chr7B 90.796 3303 190 46 2 3264 35513671 35510443 0 4311
15 TraesCS7D01G135700 chr7B 82.649 2363 293 65 117 2437 35257603 35255316 0 1984


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 TraesCS7D01G135700 chr7D 87208751 87212858 4107 True 7587 7587 100.0000 1 4108 1 chr7D.!!$R4 4107
1 TraesCS7D01G135700 chr7D 86764961 86768912 3951 True 5770 5770 93.0290 1 3964 1 chr7D.!!$R2 3963
2 TraesCS7D01G135700 chr7D 86797284 86801001 3717 True 4961 4961 90.7450 360 4108 1 chr7D.!!$R3 3748
3 TraesCS7D01G135700 chr7D 86920838 86927683 6845 True 4380 5315 92.7335 1 4108 2 chr7D.!!$R5 4107
4 TraesCS7D01G135700 chr7D 86296358 86298583 2225 True 2536 2536 87.4010 117 2346 1 chr7D.!!$R1 2229
5 TraesCS7D01G135700 chr7A 88438188 88442289 4101 True 6844 6844 96.7660 1 4108 1 chr7A.!!$R5 4107
6 TraesCS7D01G135700 chr7A 88010677 88014779 4102 True 6085 6085 93.4810 1 4108 1 chr7A.!!$R2 4107
7 TraesCS7D01G135700 chr7A 88123957 88128036 4079 True 6071 6071 93.4800 1 4108 1 chr7A.!!$R3 4107
8 TraesCS7D01G135700 chr7A 88174725 88178787 4062 True 5854 5854 92.6110 1 4108 1 chr7A.!!$R4 4107
9 TraesCS7D01G135700 chr7A 87453494 87456919 3425 True 4577 4577 90.9490 700 4108 1 chr7A.!!$R1 3408
10 TraesCS7D01G135700 chr7A 88319155 88324087 4932 True 3142 3958 95.3920 1 3989 2 chr7A.!!$R6 3988
11 TraesCS7D01G135700 chr7B 35309892 35313792 3900 True 5260 5260 91.1210 196 4090 1 chr7B.!!$R2 3894
12 TraesCS7D01G135700 chr7B 35510443 35513671 3228 True 4311 4311 90.7960 2 3264 1 chr7B.!!$R3 3262
13 TraesCS7D01G135700 chr7B 35255316 35257603 2287 True 1984 1984 82.6490 117 2437 1 chr7B.!!$R1 2320

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
390 425 2.710377 GCTGGTAATGTGTGTGGATCA 58.290 47.619 0.00 0.00 0.00 2.92 F
391 426 3.282021 GCTGGTAATGTGTGTGGATCAT 58.718 45.455 0.00 0.00 0.00 2.45 F
1230 4043 4.356405 AATGCATATGATCCAACGGAGA 57.644 40.909 6.97 0.00 34.05 3.71 F
1906 4739 0.032615 AGGAAGACGGATGAGGCTCT 60.033 55.000 16.72 0.75 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 4043 2.318207 ACTAGTAACATGGGTCCCCTCT 59.682 50.0 5.13 0.0 36.94 3.69 R
1898 4731 2.961741 GTCTACCATCATCAGAGCCTCA 59.038 50.0 0.00 0.0 0.00 3.86 R
3039 6884 2.355412 GCACATAGTTTCCTACCCCGTT 60.355 50.0 0.00 0.0 0.00 4.44 R
3321 7192 2.206576 AGGGAGATGGCAAACACTTC 57.793 50.0 0.00 0.0 0.00 3.01 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
348 378 6.327626 TGGGAAGAATGGTCACCAAAATTAAA 59.672 34.615 0.00 0.00 36.95 1.52
390 425 2.710377 GCTGGTAATGTGTGTGGATCA 58.290 47.619 0.00 0.00 0.00 2.92
391 426 3.282021 GCTGGTAATGTGTGTGGATCAT 58.718 45.455 0.00 0.00 0.00 2.45
862 3668 7.026562 CGACAAACTATCAATGTGCCAAATTA 58.973 34.615 0.00 0.00 0.00 1.40
969 3779 8.034215 CCATCTTCATAGTTCATACTCCTCATC 58.966 40.741 0.00 0.00 35.78 2.92
1230 4043 4.356405 AATGCATATGATCCAACGGAGA 57.644 40.909 6.97 0.00 34.05 3.71
1898 4731 5.221541 GGATACAAGAATCAGGAAGACGGAT 60.222 44.000 0.00 0.00 35.41 4.18
1906 4739 0.032615 AGGAAGACGGATGAGGCTCT 60.033 55.000 16.72 0.75 0.00 4.09
2036 4869 9.828852 CACAAGTTAGTCGATACCTATATTCTC 57.171 37.037 0.00 0.00 0.00 2.87
2433 5313 9.820229 TTGTCAATATGTTAGAAAATGTTCGTC 57.180 29.630 0.00 0.00 38.90 4.20
2586 6431 8.910666 TCAATAAAACAACTGCACAATTTATCG 58.089 29.630 0.00 0.00 0.00 2.92
2596 6441 7.298122 ACTGCACAATTTATCGTTCAGTAAAG 58.702 34.615 0.00 0.00 37.75 1.85
3039 6884 2.813754 GGTTCTGTTGCAGCTGTAATGA 59.186 45.455 20.46 17.40 0.00 2.57
3101 6949 6.531594 GGTCAGCTTATTTTTATCTTGGCAAC 59.468 38.462 0.00 0.00 0.00 4.17
3291 7161 7.033530 AGTATTTCACCTTCGATAGTCTCAG 57.966 40.000 0.00 0.00 37.40 3.35
3922 7821 7.379529 CACGATTGGCATTTATTGAGGTATTTC 59.620 37.037 0.00 0.00 0.00 2.17
3975 7874 0.766131 TTGGGACGTAGGCTTGGAAA 59.234 50.000 0.00 0.00 0.00 3.13
4021 7920 6.834168 TGGCCAAAAGAAGAAATTAGTAGG 57.166 37.500 0.61 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 378 4.816925 GCGAAGGTAAGCATATCCTTTCTT 59.183 41.667 0.00 0.00 41.00 2.52
391 426 8.713971 CCCCATGATAACTTGGCTACATATATA 58.286 37.037 0.00 0.00 39.20 0.86
729 784 4.202151 ACCTTGACATTGTGGCTTTCTTTC 60.202 41.667 0.00 0.00 0.00 2.62
862 3668 4.392138 GTGCAGTCCTACTTTCGCTAATTT 59.608 41.667 0.00 0.00 0.00 1.82
969 3779 5.462398 GTGGGTAGTTGAACGCTATAGAATG 59.538 44.000 3.21 0.00 33.71 2.67
1075 3885 3.120477 TCGTCGTACATGATTTTGTTGGC 60.120 43.478 0.00 0.00 0.00 4.52
1230 4043 2.318207 ACTAGTAACATGGGTCCCCTCT 59.682 50.000 5.13 0.00 36.94 3.69
1289 4102 3.714391 GGTAGCTCATAGTTACCGTTGG 58.286 50.000 4.50 0.00 41.19 3.77
1898 4731 2.961741 GTCTACCATCATCAGAGCCTCA 59.038 50.000 0.00 0.00 0.00 3.86
1906 4739 6.358974 TCTTGTTCTTGTCTACCATCATCA 57.641 37.500 0.00 0.00 0.00 3.07
2036 4869 6.877611 ACAACTAAAACTACATGACAAGGG 57.122 37.500 0.00 0.00 0.00 3.95
2392 5272 8.332464 ACATATTGACAACCGAAACATATTACG 58.668 33.333 0.00 0.00 0.00 3.18
3039 6884 2.355412 GCACATAGTTTCCTACCCCGTT 60.355 50.000 0.00 0.00 0.00 4.44
3101 6949 7.353497 ACGATCTACTACATCTTGTTCATACG 58.647 38.462 0.00 0.00 0.00 3.06
3321 7192 2.206576 AGGGAGATGGCAAACACTTC 57.793 50.000 0.00 0.00 0.00 3.01
3746 7645 6.700081 GTGACAAACTGTGAACTATAGTGACA 59.300 38.462 6.06 11.34 30.41 3.58
3922 7821 3.997021 AGAGCAAGAAGAACGTAACATGG 59.003 43.478 0.00 0.00 0.00 3.66
3975 7874 8.910944 GCCATCTCTGCCATTTCATATATAATT 58.089 33.333 0.00 0.00 0.00 1.40
4021 7920 6.713762 TGACCCATTCCAATAAATGATCAC 57.286 37.500 0.00 0.00 38.64 3.06
4033 7932 7.234371 TGTTTCTTTATGAAATGACCCATTCCA 59.766 33.333 0.00 0.00 45.19 3.53


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

AutoCloner maintained by Alex Coulton.