Multiple sequence alignment - TraesCS7B01G007900

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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 TraesCS7B01G007900 chr7B 100.000 2714 0 0 1 2714 4613023 4615736 0.000000e+00 5012.0
1 TraesCS7B01G007900 chr7B 95.279 1991 64 6 738 2714 4802225 4804199 0.000000e+00 3129.0
2 TraesCS7B01G007900 chr7B 82.231 1587 207 39 746 2286 4826589 4828146 0.000000e+00 1299.0
3 TraesCS7B01G007900 chr7B 90.628 939 56 7 1758 2678 4629516 4630440 0.000000e+00 1218.0
4 TraesCS7B01G007900 chr7B 83.958 1041 129 21 1020 2036 4813654 4814680 0.000000e+00 963.0
5 TraesCS7B01G007900 chr7B 90.712 323 26 4 1 322 4801692 4802011 6.940000e-116 427.0
6 TraesCS7B01G007900 chr7B 92.135 89 6 1 2626 2714 4828467 4828554 1.020000e-24 124.0
7 TraesCS7B01G007900 chr7B 75.984 254 43 14 2345 2594 4828143 4828382 6.140000e-22 115.0
8 TraesCS7B01G007900 chr7B 82.482 137 9 7 371 493 4802019 4802154 3.700000e-19 106.0
9 TraesCS7B01G007900 chr7A 95.114 2067 81 7 1 2050 67000331 67002394 0.000000e+00 3240.0
10 TraesCS7B01G007900 chr7A 95.065 2067 82 7 1 2050 66984533 66986596 0.000000e+00 3234.0
11 TraesCS7B01G007900 chr7A 94.969 2067 84 7 1 2050 67279373 67281436 0.000000e+00 3223.0
12 TraesCS7B01G007900 chr7A 94.869 2066 86 7 1 2050 67015907 67017968 0.000000e+00 3210.0
13 TraesCS7B01G007900 chr7A 94.795 2075 80 7 1 2050 67263739 67265810 0.000000e+00 3208.0
14 TraesCS7B01G007900 chr7A 91.293 1941 121 15 750 2659 67148086 67150009 0.000000e+00 2604.0
15 TraesCS7B01G007900 chr7A 91.128 1950 125 15 750 2668 67384249 67386181 0.000000e+00 2599.0
16 TraesCS7B01G007900 chr7A 83.834 1565 199 34 738 2285 67463264 67464791 0.000000e+00 1439.0
17 TraesCS7B01G007900 chr7A 83.268 508 42 15 1 493 67383696 67384175 6.940000e-116 427.0
18 TraesCS7B01G007900 chr7A 87.834 337 38 3 1 336 67147532 67147866 2.530000e-105 392.0
19 TraesCS7B01G007900 chr7A 81.432 377 37 16 2361 2704 67191909 67191533 7.400000e-71 278.0
20 TraesCS7B01G007900 chr7A 81.432 377 37 15 2361 2704 67217015 67216639 7.400000e-71 278.0
21 TraesCS7B01G007900 chr7A 80.371 377 41 15 2361 2704 66961519 66961143 3.470000e-64 255.0
22 TraesCS7B01G007900 chr7A 86.842 228 20 5 2493 2714 67465130 67465353 2.090000e-61 246.0
23 TraesCS7B01G007900 chr7A 91.304 46 2 1 523 568 67463101 67463144 8.110000e-06 62.1
24 TraesCS7B01G007900 chr7D 82.683 1588 212 33 738 2286 63878620 63880183 0.000000e+00 1351.0
25 TraesCS7B01G007900 chr7D 94.438 827 21 10 1 812 63927772 63928588 0.000000e+00 1249.0
26 TraesCS7B01G007900 chr7D 80.440 409 39 21 2345 2714 63880180 63880586 9.570000e-70 274.0
27 TraesCS7B01G007900 chr4B 95.556 90 4 0 658 747 670388388 670388299 7.830000e-31 145.0
28 TraesCS7B01G007900 chr6B 92.708 96 7 0 652 747 713960616 713960521 3.640000e-29 139.0
29 TraesCS7B01G007900 chr1B 90.291 103 9 1 640 742 593927060 593927161 1.700000e-27 134.0


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 TraesCS7B01G007900 chr7B 4613023 4615736 2713 False 5012.000000 5012 100.000000 1 2714 1 chr7B.!!$F1 2713
1 TraesCS7B01G007900 chr7B 4801692 4804199 2507 False 1220.666667 3129 89.491000 1 2714 3 chr7B.!!$F4 2713
2 TraesCS7B01G007900 chr7B 4629516 4630440 924 False 1218.000000 1218 90.628000 1758 2678 1 chr7B.!!$F2 920
3 TraesCS7B01G007900 chr7B 4813654 4814680 1026 False 963.000000 963 83.958000 1020 2036 1 chr7B.!!$F3 1016
4 TraesCS7B01G007900 chr7B 4826589 4828554 1965 False 512.666667 1299 83.450000 746 2714 3 chr7B.!!$F5 1968
5 TraesCS7B01G007900 chr7A 67000331 67002394 2063 False 3240.000000 3240 95.114000 1 2050 1 chr7A.!!$F2 2049
6 TraesCS7B01G007900 chr7A 66984533 66986596 2063 False 3234.000000 3234 95.065000 1 2050 1 chr7A.!!$F1 2049
7 TraesCS7B01G007900 chr7A 67279373 67281436 2063 False 3223.000000 3223 94.969000 1 2050 1 chr7A.!!$F5 2049
8 TraesCS7B01G007900 chr7A 67015907 67017968 2061 False 3210.000000 3210 94.869000 1 2050 1 chr7A.!!$F3 2049
9 TraesCS7B01G007900 chr7A 67263739 67265810 2071 False 3208.000000 3208 94.795000 1 2050 1 chr7A.!!$F4 2049
10 TraesCS7B01G007900 chr7A 67383696 67386181 2485 False 1513.000000 2599 87.198000 1 2668 2 chr7A.!!$F7 2667
11 TraesCS7B01G007900 chr7A 67147532 67150009 2477 False 1498.000000 2604 89.563500 1 2659 2 chr7A.!!$F6 2658
12 TraesCS7B01G007900 chr7A 67463101 67465353 2252 False 582.366667 1439 87.326667 523 2714 3 chr7A.!!$F8 2191
13 TraesCS7B01G007900 chr7D 63927772 63928588 816 False 1249.000000 1249 94.438000 1 812 1 chr7D.!!$F1 811
14 TraesCS7B01G007900 chr7D 63878620 63880586 1966 False 812.500000 1351 81.561500 738 2714 2 chr7D.!!$F2 1976

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
858 926 0.405198 ATGCCATCAACCTCACCACA 59.595 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2634 3078 1.017387 GGGCGGCAAGATTTCTACAG 58.983 55.0 12.47 0.0 0.0 2.74 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
184 185 4.118093 TGTTTCTTCTCTGTCGTTGACA 57.882 40.909 0.00 0.00 40.50 3.58
483 498 4.878971 GTGCACACCCCAAAACTAAATTTT 59.121 37.500 13.17 0.00 41.38 1.82
604 664 1.094073 CCAAGATTCGAGCAGGGCTG 61.094 60.000 0.00 0.00 39.88 4.85
690 758 9.585099 TCCGTAAAGAAATATAAGAGCGTTTAA 57.415 29.630 0.00 0.00 0.00 1.52
812 880 1.086067 CAGTTCCTCGCGATGCATGT 61.086 55.000 10.36 0.00 0.00 3.21
858 926 0.405198 ATGCCATCAACCTCACCACA 59.595 50.000 0.00 0.00 0.00 4.17
1082 1158 5.355596 CAATGACAGAGTGAGGGAGATTAC 58.644 45.833 0.00 0.00 0.00 1.89
1107 1183 2.487805 GGGTATGCAGAATCTCATGCCA 60.488 50.000 21.18 1.34 44.11 4.92
1186 1262 5.532406 TGCAAAGGATTGGATATGCTCTTAC 59.468 40.000 0.00 0.00 37.02 2.34
1200 1276 1.674441 CTCTTACCTCGACACGGCATA 59.326 52.381 0.00 0.00 0.00 3.14
1428 1527 4.335400 TTGCCTTTTCATGTTCCTTTCC 57.665 40.909 0.00 0.00 0.00 3.13
1557 1657 2.483876 CGCAGAAGTCTTGGTCTTGAA 58.516 47.619 0.00 0.00 0.00 2.69
1854 1982 3.260884 TGTTAGACAGGGACACAATCTCC 59.739 47.826 0.00 0.00 0.00 3.71
1921 2049 0.597118 GCTGTTGAAATTGCGCCACA 60.597 50.000 4.18 0.00 0.00 4.17
2025 2154 5.640732 CAAGTTGACCATACATGTTTAGCC 58.359 41.667 2.30 0.00 0.00 3.93
2121 2274 5.620206 TGGTGAAGACAGTGTATCATGTTT 58.380 37.500 12.81 0.00 0.00 2.83
2150 2320 5.700832 TGCTAATCAGTTCATCGTTGAAGTT 59.299 36.000 12.79 7.31 41.72 2.66
2349 2524 8.818141 TGACGAATATAAGAAATCCTAAGCTG 57.182 34.615 0.00 0.00 0.00 4.24
2530 2916 6.208204 CCTCCTCAAAGTTTTGATGTCTTGAT 59.792 38.462 7.67 0.00 45.26 2.57
2634 3078 7.090173 TGAAAATTTCTAGTTAATGCAGGTGC 58.910 34.615 7.29 0.00 42.50 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 185 1.297364 GGTGCTTGGCAATGGCATT 59.703 52.632 15.91 6.96 41.47 3.56
483 498 1.611491 TGTATCGTGTGTGAGTGCTCA 59.389 47.619 0.00 0.00 37.24 4.26
568 602 3.069872 TCTTGGTTTAACCTACTCACGCA 59.930 43.478 15.68 0.00 39.58 5.24
690 758 9.122779 AGCGTTTAGATCACTACTCTAGTAATT 57.877 33.333 0.00 0.00 37.23 1.40
733 801 8.739972 ACATAAAGCTTGTAAAAATACTCCCTG 58.260 33.333 0.00 0.00 0.00 4.45
781 849 1.978580 GAGGAACTGAGGAACAAGGGA 59.021 52.381 0.00 0.00 41.55 4.20
812 880 6.013984 AGACTTATCCTCAAACCTACGGAAAA 60.014 38.462 0.00 0.00 0.00 2.29
1082 1158 1.138859 TGAGATTCTGCATACCCCACG 59.861 52.381 0.00 0.00 0.00 4.94
1107 1183 7.725844 ACAGATTGTTCTTGAGGGATTAAAAGT 59.274 33.333 0.00 0.00 0.00 2.66
1186 1262 3.807622 ACATTATTTATGCCGTGTCGAGG 59.192 43.478 0.00 0.00 37.81 4.63
1200 1276 5.047802 CACCCACTCTTGCTTGACATTATTT 60.048 40.000 0.00 0.00 0.00 1.40
1557 1657 3.194968 CAGAAATGGCCTTCAGATGCTTT 59.805 43.478 3.32 0.00 0.00 3.51
1854 1982 6.722301 AGCAACAATGTCATCATAGATTTCG 58.278 36.000 0.00 0.00 33.49 3.46
2025 2154 1.445582 GCGTACTTCCAGGTCCACG 60.446 63.158 0.00 0.00 0.00 4.94
2121 2274 9.541143 TTCAACGATGAACTGATTAGCATATAA 57.459 29.630 3.72 0.00 40.59 0.98
2150 2320 5.514274 GACCTTGTTGATTGGTCTTGAAA 57.486 39.130 0.00 0.00 44.84 2.69
2259 2434 6.867519 TCCATCATCCAAACTAGACTACAA 57.132 37.500 0.00 0.00 0.00 2.41
2349 2524 4.389077 CGATGTGTCTGAGTTTAGGGAAAC 59.611 45.833 0.00 0.00 44.56 2.78
2530 2916 3.972133 ACATGAATGCTCTTTCCCATCA 58.028 40.909 0.00 0.00 0.00 3.07
2624 3027 3.960571 AGATTTCTACAGCACCTGCATT 58.039 40.909 0.00 0.00 45.16 3.56
2634 3078 1.017387 GGGCGGCAAGATTTCTACAG 58.983 55.000 12.47 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.