Multiple sequence alignment - TraesCS7A01G092100

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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 TraesCS7A01G092100 chr7A 100.000 3089 0 0 1 3089 56071586 56074674 0 5705
1 TraesCS7A01G092100 chr5B 96.702 3093 97 3 1 3089 56333905 56336996 0 5142
2 TraesCS7A01G092100 chr5B 95.382 2837 102 12 105 2914 209178512 209175678 0 4486
3 TraesCS7A01G092100 chr2A 96.798 2998 89 5 97 3089 610787022 610790017 0 4998
4 TraesCS7A01G092100 chr4D 95.635 3093 108 11 22 3089 125888976 125892066 0 4939
5 TraesCS7A01G092100 chr4D 95.310 3092 121 8 22 3089 125841301 125838210 0 4885
6 TraesCS7A01G092100 chr4D 95.310 3092 120 9 22 3089 125920286 125917196 0 4883
7 TraesCS7A01G092100 chr3A 96.914 2916 88 2 1 2914 153247276 153244361 0 4885
8 TraesCS7A01G092100 chr3A 91.554 1705 66 18 22 1698 702235193 702236847 0 2279
9 TraesCS7A01G092100 chr6D 94.951 3090 120 11 27 3089 297173803 297170723 0 4809
10 TraesCS7A01G092100 chr6D 95.244 2334 86 13 768 3089 446365950 446363630 0 3672
11 TraesCS7A01G092100 chr3D 94.570 3094 133 16 22 3089 229430042 229426958 0 4750
12 TraesCS7A01G092100 chr1A 94.084 3127 123 26 22 3089 340068665 340071788 0 4693
13 TraesCS7A01G092100 chr5A 95.235 2917 98 5 1 2914 596912104 596914982 0 4578
14 TraesCS7A01G092100 chr6B 93.210 3019 170 13 105 3089 238424487 238421470 0 4407
15 TraesCS7A01G092100 chr5D 95.326 2503 90 10 22 2499 140955183 140952683 0 3949
16 TraesCS7A01G092100 chr5D 94.529 2577 103 16 547 3089 384513915 384511343 0 3943
17 TraesCS7A01G092100 chr4B 92.515 1376 63 12 10 1360 343792679 343794039 0 1934
18 TraesCS7A01G092100 chr4A 97.023 974 27 2 1 974 404405849 404404878 0 1637


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 TraesCS7A01G092100 chr7A 56071586 56074674 3088 False 5705 5705 100.000 1 3089 1 chr7A.!!$F1 3088
1 TraesCS7A01G092100 chr5B 56333905 56336996 3091 False 5142 5142 96.702 1 3089 1 chr5B.!!$F1 3088
2 TraesCS7A01G092100 chr5B 209175678 209178512 2834 True 4486 4486 95.382 105 2914 1 chr5B.!!$R1 2809
3 TraesCS7A01G092100 chr2A 610787022 610790017 2995 False 4998 4998 96.798 97 3089 1 chr2A.!!$F1 2992
4 TraesCS7A01G092100 chr4D 125888976 125892066 3090 False 4939 4939 95.635 22 3089 1 chr4D.!!$F1 3067
5 TraesCS7A01G092100 chr4D 125838210 125841301 3091 True 4885 4885 95.310 22 3089 1 chr4D.!!$R1 3067
6 TraesCS7A01G092100 chr4D 125917196 125920286 3090 True 4883 4883 95.310 22 3089 1 chr4D.!!$R2 3067
7 TraesCS7A01G092100 chr3A 153244361 153247276 2915 True 4885 4885 96.914 1 2914 1 chr3A.!!$R1 2913
8 TraesCS7A01G092100 chr3A 702235193 702236847 1654 False 2279 2279 91.554 22 1698 1 chr3A.!!$F1 1676
9 TraesCS7A01G092100 chr6D 297170723 297173803 3080 True 4809 4809 94.951 27 3089 1 chr6D.!!$R1 3062
10 TraesCS7A01G092100 chr6D 446363630 446365950 2320 True 3672 3672 95.244 768 3089 1 chr6D.!!$R2 2321
11 TraesCS7A01G092100 chr3D 229426958 229430042 3084 True 4750 4750 94.570 22 3089 1 chr3D.!!$R1 3067
12 TraesCS7A01G092100 chr1A 340068665 340071788 3123 False 4693 4693 94.084 22 3089 1 chr1A.!!$F1 3067
13 TraesCS7A01G092100 chr5A 596912104 596914982 2878 False 4578 4578 95.235 1 2914 1 chr5A.!!$F1 2913
14 TraesCS7A01G092100 chr6B 238421470 238424487 3017 True 4407 4407 93.210 105 3089 1 chr6B.!!$R1 2984
15 TraesCS7A01G092100 chr5D 140952683 140955183 2500 True 3949 3949 95.326 22 2499 1 chr5D.!!$R1 2477
16 TraesCS7A01G092100 chr5D 384511343 384513915 2572 True 3943 3943 94.529 547 3089 1 chr5D.!!$R2 2542
17 TraesCS7A01G092100 chr4B 343792679 343794039 1360 False 1934 1934 92.515 10 1360 1 chr4B.!!$F1 1350
18 TraesCS7A01G092100 chr4A 404404878 404405849 971 True 1637 1637 97.023 1 974 1 chr4A.!!$R1 973

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
714 792 0.827507 AAGCATGAGGCCAACCGTTT 60.828 50.000 5.01 0.0 46.50 3.60 F
982 1062 2.619147 CTCTCACCGAGTACGAGAAGA 58.381 52.381 0.00 0.0 42.66 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1653 0.179089 GTCTCAGAGTCCATGCGCAT 60.179 55.0 19.28 19.28 0.00 4.73 R
2240 2376 0.747255 CGGTCTTGATGGTCTCCGAT 59.253 55.0 0.00 0.00 40.29 4.18 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
57 58 5.007234 TGTCGAAATGTCTTAACTTGTGTGG 59.993 40.000 0.00 0.00 0.00 4.17
321 362 7.651808 CATACATGCTTAATTAGGGTTTCCAG 58.348 38.462 0.00 0.00 34.83 3.86
450 492 6.519679 TCATTGCTTGCTTGTTTCTATCAT 57.480 33.333 0.00 0.00 0.00 2.45
514 574 3.671459 CAGTGTACATGCATGCTTGTTTG 59.329 43.478 35.25 24.97 36.11 2.93
621 681 8.902806 CAAGTGCATCATTTTACTTTATCCCTA 58.097 33.333 0.00 0.00 31.47 3.53
714 792 0.827507 AAGCATGAGGCCAACCGTTT 60.828 50.000 5.01 0.00 46.50 3.60
982 1062 2.619147 CTCTCACCGAGTACGAGAAGA 58.381 52.381 0.00 0.00 42.66 2.87
1064 1144 6.511121 GCAATAGCGTCGATGATTAGGAAAAA 60.511 38.462 9.31 0.00 0.00 1.94
1136 1216 5.678583 AGTTATCAATGATGACCCAGAGTG 58.321 41.667 13.53 0.00 38.69 3.51
1233 1359 3.399644 TGGAGGGTTGGGTTCTTTTATGA 59.600 43.478 0.00 0.00 0.00 2.15
1521 1653 1.550524 CGGACCATCAGGAAAGTCTGA 59.449 52.381 5.43 0.00 46.32 3.27
1614 1746 1.408683 GCATGGATGGAAGTGGCACTA 60.409 52.381 22.37 5.70 0.00 2.74
1618 1750 2.116238 GGATGGAAGTGGCACTACCTA 58.884 52.381 22.37 14.00 40.22 3.08
1633 1765 5.697067 CACTACCTACCTAGATGAAGGAGT 58.303 45.833 0.00 0.00 39.15 3.85
1734 1866 5.410746 GTCATCAATGAAGAAGAACAGCAGA 59.589 40.000 0.00 0.00 38.75 4.26
1822 1954 6.377712 TGGAATGATCATGTATGCTTTTGTCA 59.622 34.615 9.46 0.00 0.00 3.58
2240 2376 6.040391 AGGAAAATTTTGAGATGAACACGGAA 59.960 34.615 8.47 0.00 0.00 4.30
2260 2396 0.611062 TCGGAGACCATCAAGACCGT 60.611 55.000 0.00 0.00 40.93 4.83
2383 2519 1.115467 GTCCCAGATCTGACGGATGT 58.885 55.000 24.62 0.00 34.33 3.06
2418 2554 1.078823 TGGTGGAGATGTGGTCTACCT 59.921 52.381 7.11 0.00 36.93 3.08
2653 2789 7.069085 ACCTTACCATTTGATCCTCATTGAATG 59.931 37.037 0.00 0.00 0.00 2.67
2864 3020 6.071221 TGTTTGATTCATAGCCAGCTTTGATT 60.071 34.615 12.58 9.65 34.84 2.57
3056 3231 0.758734 TGATCGGCTCAATCGGGAAT 59.241 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 5.863935 CCAAAAATGGCTACAAACTAGAAGC 59.136 40.000 0.00 0.00 0.00 3.86
514 574 2.712057 AGCAAACATGTAAGTGCAGC 57.288 45.000 23.37 10.76 39.50 5.25
644 704 3.164268 TGAGGTGGTGCTTGCAAAATAT 58.836 40.909 0.00 0.00 0.00 1.28
899 979 2.596346 TGTTTGGAATGCATGGACAGT 58.404 42.857 0.00 0.00 0.00 3.55
982 1062 8.325046 GTTCCTCATGATATTTCTAGCCCTAAT 58.675 37.037 0.00 0.00 0.00 1.73
1064 1144 7.228706 CACTTCTACCTTCTTGTACACCATTTT 59.771 37.037 0.00 0.00 0.00 1.82
1136 1216 4.679373 TCTTCTCCATCATTAGGACTGC 57.321 45.455 0.00 0.00 0.00 4.40
1233 1359 9.578576 AATATGTGAGCACAAGGAATAACATAT 57.421 29.630 7.46 0.00 45.41 1.78
1521 1653 0.179089 GTCTCAGAGTCCATGCGCAT 60.179 55.000 19.28 19.28 0.00 4.73
1614 1746 5.043582 TGGTTACTCCTTCATCTAGGTAGGT 60.044 44.000 0.00 0.00 36.63 3.08
1618 1750 5.600484 CAGATGGTTACTCCTTCATCTAGGT 59.400 44.000 0.00 0.00 42.85 3.08
1633 1765 4.271661 TGCTTCATCAATGCAGATGGTTA 58.728 39.130 14.11 2.59 44.30 2.85
1669 1801 0.835971 TGCAACAGGGCTGAGGTCTA 60.836 55.000 0.00 0.00 34.04 2.59
1822 1954 5.649782 AGAAATCGACAAATGCAGGAATT 57.350 34.783 0.00 0.00 0.00 2.17
1951 2083 3.885297 CCTTCGGCAATTTGGATAGACAT 59.115 43.478 0.00 0.00 0.00 3.06
2240 2376 0.747255 CGGTCTTGATGGTCTCCGAT 59.253 55.000 0.00 0.00 40.29 4.18
2260 2396 5.241285 TGTTTCTGCAGAATATCTTTGCACA 59.759 36.000 28.89 21.99 42.41 4.57
2383 2519 1.250328 CACCAGAGCTTGCCATTCAA 58.750 50.000 0.00 0.00 0.00 2.69
2519 2655 4.493382 CGATTCAACTTGTTCGACACACAA 60.493 41.667 9.75 1.50 33.98 3.33
2535 2671 5.749588 TGTACACGACTTTTTCTCGATTCAA 59.250 36.000 0.00 0.00 35.08 2.69
2653 2789 8.239314 TGTTATTCAGCAAGAATCAGAAATGTC 58.761 33.333 7.57 0.00 43.42 3.06
2864 3020 6.983984 TCAAATCATCAAAGCATCAAACAGA 58.016 32.000 0.00 0.00 0.00 3.41
3056 3231 8.742125 AGAATGGTGGTTCTATATAAGATGGA 57.258 34.615 0.00 0.00 36.71 3.41


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

AutoCloner maintained by Alex Coulton.