Multiple sequence alignment - TraesCS5A01G283500

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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 TraesCS5A01G283500 chr5A 100.000 3298 0 0 1 3298 491708629 491711926 0.000000e+00 6091.0
1 TraesCS5A01G283500 chr5A 94.383 1620 85 3 1683 3298 493018147 493019764 0.000000e+00 2483.0
2 TraesCS5A01G283500 chr5A 99.766 428 1 0 934 1361 493016338 493016765 0.000000e+00 785.0
3 TraesCS5A01G283500 chr5A 91.979 187 12 3 1359 1543 493017086 493017271 3.260000e-65 259.0
4 TraesCS5A01G283500 chr5A 90.164 122 8 3 1572 1689 493017269 493017390 4.410000e-34 156.0
5 TraesCS5A01G283500 chr5A 86.747 83 9 1 553 635 490049860 490049940 1.260000e-14 91.6
6 TraesCS5A01G283500 chr5D 94.425 1955 86 12 1359 3298 389696388 389698334 0.000000e+00 2985.0
7 TraesCS5A01G283500 chr5D 93.561 1755 84 8 1359 3103 388814160 388812425 0.000000e+00 2588.0
8 TraesCS5A01G283500 chr5D 88.788 883 38 10 526 1364 388815358 388814493 0.000000e+00 1026.0
9 TraesCS5A01G283500 chr5D 91.456 316 20 3 999 1314 389679443 389679751 8.460000e-116 427.0
10 TraesCS5A01G283500 chr5D 92.529 174 10 2 3125 3298 388812431 388812261 2.540000e-61 246.0
11 TraesCS5A01G283500 chr5D 98.000 50 1 0 1312 1361 389696006 389696055 1.630000e-13 87.9
12 TraesCS5A01G283500 chr5B 94.976 1891 79 7 1359 3238 469972665 469974550 0.000000e+00 2952.0
13 TraesCS5A01G283500 chr5B 93.338 1591 80 10 1359 2941 467166717 467165145 0.000000e+00 2327.0
14 TraesCS5A01G283500 chr5B 88.851 888 43 22 525 1364 467167938 467167059 0.000000e+00 1040.0
15 TraesCS5A01G283500 chr5B 97.289 332 9 0 2967 3298 467165147 467164816 6.180000e-157 564.0
16 TraesCS5A01G283500 chr5B 91.736 363 20 3 999 1361 469967852 469968204 2.290000e-136 496.0
17 TraesCS5A01G283500 chr5B 80.451 133 18 4 573 705 465867407 465867531 9.740000e-16 95.3
18 TraesCS5A01G283500 chr6A 94.052 538 21 2 1 534 581126407 581125877 0.000000e+00 806.0
19 TraesCS5A01G283500 chr3A 93.585 530 21 5 1 526 203954302 203954822 0.000000e+00 778.0
20 TraesCS5A01G283500 chr7A 92.435 542 30 2 1 538 70299558 70299024 0.000000e+00 763.0
21 TraesCS5A01G283500 chr4A 93.006 529 25 5 1 525 567852327 567852847 0.000000e+00 761.0
22 TraesCS5A01G283500 chr2A 94.366 355 16 1 176 526 88978749 88978395 2.890000e-150 542.0
23 TraesCS5A01G283500 chr2A 92.045 176 7 3 1 176 88980136 88979968 1.180000e-59 241.0
24 TraesCS5A01G283500 chr3D 74.497 298 70 5 2673 2967 513621303 513621009 1.240000e-24 124.0


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 TraesCS5A01G283500 chr5A 491708629 491711926 3297 False 6091.000000 6091 100.000000 1 3298 1 chr5A.!!$F2 3297
1 TraesCS5A01G283500 chr5A 493016338 493019764 3426 False 920.750000 2483 94.073000 934 3298 4 chr5A.!!$F3 2364
2 TraesCS5A01G283500 chr5D 389696006 389698334 2328 False 1536.450000 2985 96.212500 1312 3298 2 chr5D.!!$F2 1986
3 TraesCS5A01G283500 chr5D 388812261 388815358 3097 True 1286.666667 2588 91.626000 526 3298 3 chr5D.!!$R1 2772
4 TraesCS5A01G283500 chr5B 469972665 469974550 1885 False 2952.000000 2952 94.976000 1359 3238 1 chr5B.!!$F3 1879
5 TraesCS5A01G283500 chr5B 467164816 467167938 3122 True 1310.333333 2327 93.159333 525 3298 3 chr5B.!!$R1 2773
6 TraesCS5A01G283500 chr6A 581125877 581126407 530 True 806.000000 806 94.052000 1 534 1 chr6A.!!$R1 533
7 TraesCS5A01G283500 chr3A 203954302 203954822 520 False 778.000000 778 93.585000 1 526 1 chr3A.!!$F1 525
8 TraesCS5A01G283500 chr7A 70299024 70299558 534 True 763.000000 763 92.435000 1 538 1 chr7A.!!$R1 537
9 TraesCS5A01G283500 chr4A 567852327 567852847 520 False 761.000000 761 93.006000 1 525 1 chr4A.!!$F1 524
10 TraesCS5A01G283500 chr2A 88978395 88980136 1741 True 391.500000 542 93.205500 1 526 2 chr2A.!!$R1 525

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
256 1485 0.251165 CCTTGACCGGGACAATGGTT 60.251 55.0 12.15 0.0 38.99 3.67 F
1553 3250 0.174845 CAAGGCATCGTCGGTTCCTA 59.825 55.0 0.00 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 4524 1.342174 TCCACAACACGAGGGTAAGAC 59.658 52.381 0.0 0.0 0.0 3.01 R
3068 5555 2.553028 CCAAGTGGGACAGCTACAACAT 60.553 50.000 0.0 0.0 41.8 2.71 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
25 26 2.347114 CAGTGCCCATCACCGACA 59.653 61.111 0.00 0.00 46.81 4.35
35 36 0.603569 ATCACCGACACACTCCACTC 59.396 55.000 0.00 0.00 0.00 3.51
140 141 5.736486 GGTGTTTCCGATAAGAAATCCTC 57.264 43.478 0.00 0.00 38.01 3.71
153 161 9.183368 GATAAGAAATCCTCAATCCTCACTTTT 57.817 33.333 0.00 0.00 0.00 2.27
248 1477 2.250921 TAATGGTACCTTGACCGGGA 57.749 50.000 14.36 0.00 42.99 5.14
256 1485 0.251165 CCTTGACCGGGACAATGGTT 60.251 55.000 12.15 0.00 38.99 3.67
268 1497 5.064707 CGGGACAATGGTTGTTCATAGTAAG 59.935 44.000 3.74 0.00 45.52 2.34
328 1558 8.212312 TCTACAAAATTACAAGTTGGTGTAGGA 58.788 33.333 7.96 3.72 38.36 2.94
375 1605 7.201565 GCTAGACTGTGTTTATCAAACTCATCC 60.202 40.741 0.00 3.62 42.05 3.51
656 1896 3.872431 GGGCGCTAGTAGACCCAT 58.128 61.111 19.14 0.00 42.33 4.00
723 1964 1.066587 GCCTCTCCGTCCGATTCTG 59.933 63.158 0.00 0.00 0.00 3.02
823 2086 1.680314 GCCTTTCCCCCTTGCAGAG 60.680 63.158 0.00 0.00 0.00 3.35
1042 2345 4.647564 AAGGAGAAGATGGTGATGTTGT 57.352 40.909 0.00 0.00 0.00 3.32
1400 3093 9.051679 TCGTGAGAATTCTAAACTTTTGATTCA 57.948 29.630 8.25 0.00 37.03 2.57
1474 3170 8.055279 TGGATTTCAATCTGGTGTTAAAGATC 57.945 34.615 0.00 0.00 35.73 2.75
1501 3197 0.623723 GATTTGCTACACCCTCCCCA 59.376 55.000 0.00 0.00 0.00 4.96
1553 3250 0.174845 CAAGGCATCGTCGGTTCCTA 59.825 55.000 0.00 0.00 0.00 2.94
1568 3265 1.756950 CCTAGCTCCGCCACTGGTA 60.757 63.158 0.00 0.00 0.00 3.25
1607 3304 4.097741 GTCATGCCCATATAGCAACAAACA 59.902 41.667 3.90 0.00 44.83 2.83
1664 3363 5.860716 GCTCAATCAACTCCTTAGCAAAAAG 59.139 40.000 0.00 0.00 0.00 2.27
1677 3378 3.609853 AGCAAAAAGACGCCATATCTCA 58.390 40.909 0.00 0.00 0.00 3.27
1753 4218 3.396685 AGAGGACTGATTGACCTAGCT 57.603 47.619 0.00 0.00 40.76 3.32
1885 4350 2.095059 GCGATTGCAAGATTCCACAACT 60.095 45.455 4.94 0.00 42.15 3.16
1929 4394 6.207417 TGTTCCTTGATTGATCCACTCTTTTC 59.793 38.462 0.00 0.00 0.00 2.29
1933 4398 4.641396 TGATTGATCCACTCTTTTCACGT 58.359 39.130 0.00 0.00 0.00 4.49
1941 4406 4.024387 TCCACTCTTTTCACGTAATGCAAC 60.024 41.667 0.00 0.00 0.00 4.17
1942 4407 4.219033 CACTCTTTTCACGTAATGCAACC 58.781 43.478 0.00 0.00 0.00 3.77
2057 4524 3.670627 GCTCTGGCGGATTAACAACAAAG 60.671 47.826 0.00 0.00 0.00 2.77
2107 4577 2.066700 TTGCCATGCAGTGAGACCCA 62.067 55.000 0.00 0.00 40.61 4.51
2280 4751 9.554395 TTGACAAAGAGTGTGAGTATTTTCATA 57.446 29.630 0.00 0.00 41.96 2.15
2402 4875 1.014352 GTCCGCGGCTTAACATGATT 58.986 50.000 23.51 0.00 0.00 2.57
2418 4891 5.984725 ACATGATTCCTTCACCAATACGTA 58.015 37.500 0.00 0.00 37.11 3.57
2587 5060 1.553690 CCCCAACTCATCACCTCGGT 61.554 60.000 0.00 0.00 0.00 4.69
2634 5115 7.290061 TCTTTTCCTATGCTTATGTATGGCTT 58.710 34.615 0.00 0.00 0.00 4.35
2805 5286 5.302568 TGAAGATTTCAGCAAAGGTGTGATT 59.697 36.000 0.00 0.00 34.08 2.57
2865 5346 4.783227 ACCATGGGTGTGAGTCTAAATAGT 59.217 41.667 18.09 0.00 32.98 2.12
3068 5555 2.342279 CGTTCCCTTGAGTCGGCA 59.658 61.111 0.00 0.00 0.00 5.69
3173 5660 3.355378 TCGTACCTTTAGGACGATCCAA 58.645 45.455 14.94 0.13 40.27 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.465705 TCTTCCTAGCGATGCCCAAG 59.534 55.000 0.00 0.00 0.00 3.61
134 135 5.527026 AGGAAAAGTGAGGATTGAGGATT 57.473 39.130 0.00 0.00 0.00 3.01
135 136 6.838401 ATAGGAAAAGTGAGGATTGAGGAT 57.162 37.500 0.00 0.00 0.00 3.24
136 137 7.749377 TTATAGGAAAAGTGAGGATTGAGGA 57.251 36.000 0.00 0.00 0.00 3.71
153 161 9.144298 CCTTATCCTTCGGCTAATATTATAGGA 57.856 37.037 0.00 4.73 35.24 2.94
256 1485 9.767684 CGAAATAAATGTTGCTTACTATGAACA 57.232 29.630 0.00 0.00 33.09 3.18
268 1497 5.344665 TGCTTTGCTACGAAATAAATGTTGC 59.655 36.000 0.00 0.00 35.42 4.17
328 1558 1.308998 CGCCACTTTCACAAGACCTT 58.691 50.000 0.00 0.00 33.72 3.50
375 1605 1.407979 GCATGCTCTCAATTCCAAGGG 59.592 52.381 11.37 0.00 0.00 3.95
519 1753 5.046950 CCCTCTCTGCTTTAGTTTCACTAGT 60.047 44.000 0.00 0.00 31.47 2.57
656 1896 2.451990 CGCGTGGATGCATCGTTCA 61.452 57.895 20.15 10.11 34.15 3.18
738 1979 0.896019 AGGTCGAGAGTCCACACAGG 60.896 60.000 0.00 0.00 42.03 4.00
795 2036 2.815647 GGAAAGGCGGCGTCAGAG 60.816 66.667 16.23 0.00 0.00 3.35
814 2077 4.528920 ACTCCTACTACTACTCTGCAAGG 58.471 47.826 0.00 0.00 0.00 3.61
1400 3093 9.702253 TGACATAAGTTCCTCTCTACTATTCTT 57.298 33.333 0.00 0.00 0.00 2.52
1474 3170 5.049405 GGAGGGTGTAGCAAATCGATTTATG 60.049 44.000 22.33 13.59 0.00 1.90
1568 3265 8.328055 TGGGCATGACTCATATCATAGATAAT 57.672 34.615 0.00 0.00 37.20 1.28
1588 3285 3.696045 ACTGTTTGTTGCTATATGGGCA 58.304 40.909 1.81 1.81 37.97 5.36
1664 3363 6.551385 AAGAAATGAATGAGATATGGCGTC 57.449 37.500 0.00 0.00 0.00 5.19
1677 3378 9.933723 AGTAATGCAAAGCTTAAAGAAATGAAT 57.066 25.926 0.00 0.00 0.00 2.57
1753 4218 5.932619 TCTTACTAGCAATAGTCTGGCAA 57.067 39.130 0.00 0.00 0.00 4.52
1885 4350 2.288579 ACATACCTTGTCGCTCGAACAA 60.289 45.455 1.50 1.50 30.89 2.83
1915 4380 4.391830 GCATTACGTGAAAAGAGTGGATCA 59.608 41.667 0.00 0.00 0.00 2.92
1929 4394 3.071479 AGTGGTAAGGTTGCATTACGTG 58.929 45.455 0.00 0.00 34.58 4.49
1933 4398 7.343574 TGACTCTATAGTGGTAAGGTTGCATTA 59.656 37.037 6.75 0.00 35.56 1.90
1969 4434 6.448207 TTGATGTCACAATGAAACAAGTCA 57.552 33.333 0.00 0.00 0.00 3.41
2057 4524 1.342174 TCCACAACACGAGGGTAAGAC 59.658 52.381 0.00 0.00 0.00 3.01
2107 4577 5.627499 TTCGAGCTCTTGCATTAAACATT 57.373 34.783 12.85 0.00 42.74 2.71
2192 4662 2.028748 GGTGTAAGCGTTGACCTTAGGA 60.029 50.000 4.77 0.00 0.00 2.94
2312 4784 5.653330 ACCAACATGTATGCTCATCAAATGA 59.347 36.000 0.00 0.00 37.76 2.57
2322 4795 6.424509 CACAAATCAAAACCAACATGTATGCT 59.575 34.615 0.00 0.00 0.00 3.79
2402 4875 3.758023 TCGAGTTACGTATTGGTGAAGGA 59.242 43.478 0.00 0.00 43.13 3.36
2418 4891 3.632604 ACACATGATCCTACGATCGAGTT 59.367 43.478 24.34 1.27 46.89 3.01
2587 5060 4.308526 TTGGAGGCACAAATACATACCA 57.691 40.909 0.00 0.00 0.00 3.25
2634 5115 9.270640 CCAAAATAATCTTTCCATGTGTTTTGA 57.729 29.630 11.30 0.00 36.60 2.69
2865 5346 4.942944 TCACTTCCACCCTACTCAGATAA 58.057 43.478 0.00 0.00 0.00 1.75
3068 5555 2.553028 CCAAGTGGGACAGCTACAACAT 60.553 50.000 0.00 0.00 41.80 2.71
3155 5642 5.205821 TCTCATTGGATCGTCCTAAAGGTA 58.794 41.667 5.77 0.00 37.46 3.08


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

AutoCloner maintained by Alex Coulton.