Multiple sequence alignment - TraesCS7B01G023500

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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 TraesCS7B01G023500 chr7B 100.000 3084 0 0 1 3084 22667115 22670198 0 5696
1 TraesCS7B01G023500 chr7B 97.930 3092 56 5 1 3084 22708844 22711935 0 5349
2 TraesCS7B01G023500 chr7B 98.451 2389 26 6 1 2379 22962839 22965226 0 4196
3 TraesCS7B01G023500 chr7B 97.912 2203 40 2 888 3084 22833418 22835620 0 3808
4 TraesCS7B01G023500 chr7B 97.163 1586 36 4 1507 3084 22772235 22773819 0 2671
5 TraesCS7B01G023500 chr7B 96.717 1584 39 5 1507 3084 22893360 22894936 0 2625
6 TraesCS7B01G023500 chr7B 98.433 1468 19 3 1 1465 22891898 22893364 0 2580
7 TraesCS7B01G023500 chr7B 97.819 1467 30 2 1 1465 22770773 22772239 0 2531
8 TraesCS7B01G023500 chr7B 98.335 901 12 2 1 898 22832114 22833014 0 1578
9 TraesCS7B01G023500 chr7B 96.506 830 25 4 1 829 23008063 23008889 0 1369
10 TraesCS7B01G023500 chr7B 84.257 1010 136 14 764 1767 23410815 23411807 0 963
11 TraesCS7B01G023500 chr7B 94.554 606 32 1 2479 3084 22714383 22714987 0 935
12 TraesCS7B01G023500 chr7B 94.389 606 34 0 2479 3084 22897395 22898000 0 931
13 TraesCS7B01G023500 chr7D 94.988 2973 115 21 2 2971 76502330 76505271 0 4634
14 TraesCS7B01G023500 chr7D 94.960 2143 72 4 948 3084 76521420 76523532 0 3326
15 TraesCS7B01G023500 chr7D 97.534 811 18 2 129 938 76520390 76521199 0 1386
16 TraesCS7B01G023500 chr7D 93.548 713 35 5 1925 2632 76482578 76483284 0 1051
17 TraesCS7B01G023500 chr7D 82.270 1207 183 26 751 1949 76725783 76726966 0 1014
18 TraesCS7B01G023500 chr7D 84.864 958 121 13 821 1763 76628809 76629757 0 944
19 TraesCS7B01G023500 chr7A 94.704 2889 123 16 1 2875 80538366 80541238 0 4460


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 TraesCS7B01G023500 chr7B 22667115 22670198 3083 False 5696.000000 5696 100.0000 1 3084 1 chr7B.!!$F1 3083
1 TraesCS7B01G023500 chr7B 22962839 22965226 2387 False 4196.000000 4196 98.4510 1 2379 1 chr7B.!!$F2 2378
2 TraesCS7B01G023500 chr7B 22708844 22714987 6143 False 3142.000000 5349 96.2420 1 3084 2 chr7B.!!$F5 3083
3 TraesCS7B01G023500 chr7B 22832114 22835620 3506 False 2693.000000 3808 98.1235 1 3084 2 chr7B.!!$F7 3083
4 TraesCS7B01G023500 chr7B 22770773 22773819 3046 False 2601.000000 2671 97.4910 1 3084 2 chr7B.!!$F6 3083
5 TraesCS7B01G023500 chr7B 22891898 22898000 6102 False 2045.333333 2625 96.5130 1 3084 3 chr7B.!!$F8 3083
6 TraesCS7B01G023500 chr7B 23008063 23008889 826 False 1369.000000 1369 96.5060 1 829 1 chr7B.!!$F3 828
7 TraesCS7B01G023500 chr7B 23410815 23411807 992 False 963.000000 963 84.2570 764 1767 1 chr7B.!!$F4 1003
8 TraesCS7B01G023500 chr7D 76502330 76505271 2941 False 4634.000000 4634 94.9880 2 2971 1 chr7D.!!$F2 2969
9 TraesCS7B01G023500 chr7D 76520390 76523532 3142 False 2356.000000 3326 96.2470 129 3084 2 chr7D.!!$F5 2955
10 TraesCS7B01G023500 chr7D 76482578 76483284 706 False 1051.000000 1051 93.5480 1925 2632 1 chr7D.!!$F1 707
11 TraesCS7B01G023500 chr7D 76725783 76726966 1183 False 1014.000000 1014 82.2700 751 1949 1 chr7D.!!$F4 1198
12 TraesCS7B01G023500 chr7D 76628809 76629757 948 False 944.000000 944 84.8640 821 1763 1 chr7D.!!$F3 942
13 TraesCS7B01G023500 chr7A 80538366 80541238 2872 False 4460.000000 4460 94.7040 1 2875 1 chr7A.!!$F1 2874

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
127 130 2.753055 TCTAAAGGCGTACATGTGCA 57.247 45.000 14.55 0.00 0.00 4.57 F
1166 1800 1.740296 AATTCGTCGACGGGCCAAG 60.740 57.895 35.05 8.08 40.29 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2718 1.065401 CCTGCAGCGAAAAGTGAAACA 59.935 47.619 8.66 0.00 41.43 2.83 R
2875 3539 0.172803 GAGCTGGACGTACGACCAAT 59.827 55.000 32.86 25.75 39.22 3.16 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
127 130 2.753055 TCTAAAGGCGTACATGTGCA 57.247 45.000 14.55 0.00 0.00 4.57
242 245 3.125146 TGCTTGCATTAGTTGATGTCGAC 59.875 43.478 9.11 9.11 0.00 4.20
459 462 2.919666 ATCGGTATGTTGCACAAAGC 57.080 45.000 0.00 0.00 45.96 3.51
1054 1687 5.420725 ACTCATAGTGCTACCACAAATCA 57.579 39.130 0.00 0.00 44.53 2.57
1097 1731 4.688021 GACGAGATTGCACCTCTTAAGAT 58.312 43.478 5.44 0.00 0.00 2.40
1166 1800 1.740296 AATTCGTCGACGGGCCAAG 60.740 57.895 35.05 8.08 40.29 3.61
1891 2546 8.391106 CCTACTGAAACTGCATTACATTAAGAC 58.609 37.037 0.00 0.00 0.00 3.01
2058 2718 3.012518 GCTTGACATGACACTAGCCATT 58.987 45.455 9.77 0.00 0.00 3.16
2178 2838 3.321396 TGTAGTGTGATGGGTCGTTGTTA 59.679 43.478 0.00 0.00 0.00 2.41
2187 2847 1.609580 GGGTCGTTGTTATGGTCTGCA 60.610 52.381 0.00 0.00 0.00 4.41
2557 3218 5.483811 TCCACAACGTCTAGAATAATTGCA 58.516 37.500 0.00 0.00 0.00 4.08
2635 3296 4.319766 GCCATGTTATTTGGTAGCATCGAG 60.320 45.833 0.00 0.00 32.62 4.04
2840 3504 0.533032 AGAGTGTTTAGGGAGAGCGC 59.467 55.000 0.00 0.00 0.00 5.92
2875 3539 3.138304 GGCGGCATCTGAACATGTTATA 58.862 45.455 11.95 2.90 0.00 0.98
2940 3604 1.614850 GGCAGGAAATACGGGTGGAAA 60.615 52.381 0.00 0.00 0.00 3.13
2997 3661 4.175337 ATGTATGCCAGCGCCCGT 62.175 61.111 2.29 0.00 0.00 5.28
3077 5283 1.279271 CGAGAACCTGACCCAAGGATT 59.721 52.381 0.00 0.00 40.02 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 130 6.014584 TGTGTCAAGTCAGATAGTTGGTGTAT 60.015 38.462 0.00 0.00 38.79 2.29
242 245 6.449698 ACAATTACAGAAAGTGCAAGATTGG 58.550 36.000 0.00 0.00 36.63 3.16
328 331 9.646427 ACTTAGCAACTTTCAATTGTAACAAAA 57.354 25.926 5.13 0.00 0.00 2.44
429 432 8.462811 TGTGCAACATACCGATAAAAATTGTAT 58.537 29.630 0.00 0.00 45.67 2.29
452 455 5.880332 ACAAGGTATATACACCAGCTTTGTG 59.120 40.000 14.70 10.82 41.40 3.33
459 462 8.879759 CACTTAAACACAAGGTATATACACCAG 58.120 37.037 14.70 0.00 41.40 4.00
1054 1687 3.327757 TCGATGGGGCTAGAAATAGCAAT 59.672 43.478 9.30 0.46 44.51 3.56
1097 1731 4.142026 CGGTCATACAAGGGAACTGACATA 60.142 45.833 0.00 0.00 42.68 2.29
1166 1800 1.632422 CTCATTGCGATTTGGGTTGC 58.368 50.000 0.00 0.00 0.00 4.17
1891 2546 3.979948 TGCACTTGAATGTCCACAAATG 58.020 40.909 0.00 0.00 0.00 2.32
2058 2718 1.065401 CCTGCAGCGAAAAGTGAAACA 59.935 47.619 8.66 0.00 41.43 2.83
2178 2838 4.080695 ACTCTAATGACACATGCAGACCAT 60.081 41.667 0.00 0.00 33.39 3.55
2187 2847 5.692204 GCTAACGCATACTCTAATGACACAT 59.308 40.000 0.00 0.00 35.78 3.21
2557 3218 3.016736 CGCCTGGGTGATATCTTTGTTT 58.983 45.455 3.98 0.00 0.00 2.83
2635 3296 8.303156 AGAGTACAAGACATGTATATGCATCTC 58.697 37.037 0.19 2.21 45.87 2.75
2675 3336 8.871862 GCAATACATCAATGCACAAATCTTTTA 58.128 29.630 0.00 0.00 39.81 1.52
2840 3504 1.202758 TGCCGCCCATCTTAGTAATGG 60.203 52.381 0.00 0.00 42.84 3.16
2875 3539 0.172803 GAGCTGGACGTACGACCAAT 59.827 55.000 32.86 25.75 39.22 3.16
2940 3604 0.511221 CGCCAGTCGACGTCAATTTT 59.489 50.000 17.16 0.00 41.67 1.82
2997 3661 3.371168 GTGCATTTCAAAAAGACGAGCA 58.629 40.909 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.