Multiple sequence alignment - TraesCS5A01G228000

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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 TraesCS5A01G228000 chr5A 100.000 4231 0 0 1 4231 444533564 444529334 0.000000e+00 7814.0
1 TraesCS5A01G228000 chr5A 75.976 666 130 21 2158 2800 546770166 546769508 2.460000e-82 316.0
2 TraesCS5A01G228000 chr5D 97.862 3789 74 4 445 4231 347443949 347447732 0.000000e+00 6541.0
3 TraesCS5A01G228000 chr5D 95.585 453 17 2 1 450 347443456 347443908 0.000000e+00 723.0
4 TraesCS5A01G228000 chr5D 77.039 662 124 23 2155 2794 431781542 431782197 5.200000e-94 355.0
5 TraesCS5A01G228000 chr5D 77.074 663 122 22 2155 2794 513308674 513309329 5.200000e-94 355.0
6 TraesCS5A01G228000 chr5D 76.364 660 126 23 2158 2794 433684217 433683565 1.130000e-85 327.0
7 TraesCS5A01G228000 chr5D 91.250 160 12 2 268 426 175300057 175299899 2.560000e-52 217.0
8 TraesCS5A01G228000 chr5D 81.765 170 27 4 1187 1354 431781023 431781190 5.700000e-29 139.0
9 TraesCS5A01G228000 chr5D 80.874 183 29 6 1187 1366 433684738 433684559 5.700000e-29 139.0
10 TraesCS5A01G228000 chr5B 97.654 3496 64 7 746 4231 403708277 403704790 0.000000e+00 5986.0
11 TraesCS5A01G228000 chr5B 96.896 451 13 1 1 450 403708998 403708548 0.000000e+00 754.0
12 TraesCS5A01G228000 chr5B 96.567 233 7 1 445 677 403708507 403708276 6.640000e-103 385.0
13 TraesCS5A01G228000 chr5B 76.818 660 123 22 2158 2794 522861124 522860472 1.130000e-90 344.0
14 TraesCS5A01G228000 chr5B 75.948 686 139 18 2130 2794 522408957 522409637 3.150000e-86 329.0
15 TraesCS5A01G228000 chr5B 81.421 183 28 6 1187 1366 522408463 522408642 1.230000e-30 145.0
16 TraesCS5A01G228000 chr5B 80.874 183 29 6 1187 1366 522861648 522861469 5.700000e-29 139.0
17 TraesCS5A01G228000 chr3A 89.077 650 54 12 3592 4231 431819375 431818733 0.000000e+00 791.0
18 TraesCS5A01G228000 chr3A 95.376 173 8 0 3425 3597 431819683 431819511 4.170000e-70 276.0
19 TraesCS5A01G228000 chr3A 91.824 159 12 1 268 426 251035762 251035919 1.980000e-53 220.0
20 TraesCS5A01G228000 chr3D 90.501 579 39 10 3663 4231 302933678 302934250 0.000000e+00 750.0
21 TraesCS5A01G228000 chr3D 91.632 239 14 4 3425 3661 302933276 302933510 4.080000e-85 326.0
22 TraesCS5A01G228000 chr3D 92.208 154 11 1 268 420 288550458 288550611 2.560000e-52 217.0
23 TraesCS5A01G228000 chr2D 83.891 329 47 6 2154 2479 25348151 25348476 4.110000e-80 309.0
24 TraesCS5A01G228000 chr2D 81.720 186 29 4 1169 1353 25338997 25339178 2.640000e-32 150.0
25 TraesCS5A01G228000 chr6D 92.810 153 11 0 268 420 392273226 392273074 5.510000e-54 222.0
26 TraesCS5A01G228000 chr2B 91.358 162 13 1 267 428 190022890 190023050 1.980000e-53 220.0
27 TraesCS5A01G228000 chr2B 82.222 180 30 2 1175 1353 41132697 41132875 2.040000e-33 154.0
28 TraesCS5A01G228000 chr7D 91.720 157 12 1 264 420 34756863 34757018 2.560000e-52 217.0
29 TraesCS5A01G228000 chr6A 92.157 153 12 0 268 420 411770405 411770253 2.560000e-52 217.0
30 TraesCS5A01G228000 chr2A 81.720 186 29 4 1169 1353 27952442 27952623 2.640000e-32 150.0
31 TraesCS5A01G228000 chr1A 100.000 32 0 0 1963 1994 49259280 49259311 4.570000e-05 60.2
32 TraesCS5A01G228000 chr3B 100.000 31 0 0 1966 1996 134272189 134272219 1.640000e-04 58.4
33 TraesCS5A01G228000 chrUn 96.970 33 0 1 1965 1997 1419322 1419291 2.000000e-03 54.7
34 TraesCS5A01G228000 chrUn 96.970 33 0 1 1965 1997 1431954 1431923 2.000000e-03 54.7
35 TraesCS5A01G228000 chrUn 96.970 33 0 1 1965 1997 328990405 328990436 2.000000e-03 54.7
36 TraesCS5A01G228000 chrUn 96.970 33 0 1 1965 1997 334654361 334654392 2.000000e-03 54.7
37 TraesCS5A01G228000 chrUn 96.970 33 0 1 1965 1997 348428590 348428559 2.000000e-03 54.7


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 TraesCS5A01G228000 chr5A 444529334 444533564 4230 True 7814.0 7814 100.0000 1 4231 1 chr5A.!!$R1 4230
1 TraesCS5A01G228000 chr5A 546769508 546770166 658 True 316.0 316 75.9760 2158 2800 1 chr5A.!!$R2 642
2 TraesCS5A01G228000 chr5D 347443456 347447732 4276 False 3632.0 6541 96.7235 1 4231 2 chr5D.!!$F2 4230
3 TraesCS5A01G228000 chr5D 513308674 513309329 655 False 355.0 355 77.0740 2155 2794 1 chr5D.!!$F1 639
4 TraesCS5A01G228000 chr5D 431781023 431782197 1174 False 247.0 355 79.4020 1187 2794 2 chr5D.!!$F3 1607
5 TraesCS5A01G228000 chr5D 433683565 433684738 1173 True 233.0 327 78.6190 1187 2794 2 chr5D.!!$R2 1607
6 TraesCS5A01G228000 chr5B 403704790 403708998 4208 True 2375.0 5986 97.0390 1 4231 3 chr5B.!!$R1 4230
7 TraesCS5A01G228000 chr5B 522860472 522861648 1176 True 241.5 344 78.8460 1187 2794 2 chr5B.!!$R2 1607
8 TraesCS5A01G228000 chr5B 522408463 522409637 1174 False 237.0 329 78.6845 1187 2794 2 chr5B.!!$F1 1607
9 TraesCS5A01G228000 chr3A 431818733 431819683 950 True 533.5 791 92.2265 3425 4231 2 chr3A.!!$R1 806
10 TraesCS5A01G228000 chr3D 302933276 302934250 974 False 538.0 750 91.0665 3425 4231 2 chr3D.!!$F2 806

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
282 285 1.139095 GCGTACTCCCTCCGTTCAG 59.861 63.158 0.00 0.0 0.00 3.02 F
1166 1217 1.351017 TCAGGCTTCACCCTTGTTAGG 59.649 52.381 0.00 0.0 40.58 2.69 F
1344 1395 5.408079 ACAAATATGACCCATGGGATCTT 57.592 39.130 38.07 26.1 38.96 2.40 F
2993 3322 0.865769 CTGAACAGTGCAACGGGTAC 59.134 55.000 0.00 0.0 45.86 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1395 3.173965 AGAAGGTAGCAGCTTACTTGGA 58.826 45.455 14.13 0.0 35.86 3.53 R
2993 3322 4.034048 GTGTCTATAACCCAATCAACTGCG 59.966 45.833 0.00 0.0 0.00 5.18 R
3202 3531 3.036819 AGCAGCTATTGGACATCTCTCA 58.963 45.455 0.00 0.0 0.00 3.27 R
4030 4678 2.370189 AGTATGCCTATGAAGCCTGACC 59.630 50.000 0.00 0.0 0.00 4.02 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
282 285 1.139095 GCGTACTCCCTCCGTTCAG 59.861 63.158 0.00 0.00 0.00 3.02
292 295 5.070580 ACTCCCTCCGTTCAGAAATATAAGG 59.929 44.000 0.00 0.00 0.00 2.69
360 363 7.375053 AGTGAACAAACACACTAAAACATGTT 58.625 30.769 4.92 4.92 44.06 2.71
436 439 6.760291 AGGGAGTACTAAAGAAACTGTTCAG 58.240 40.000 0.00 0.00 36.09 3.02
447 450 4.348168 AGAAACTGTTCAGACCATACCTGT 59.652 41.667 6.83 0.00 36.09 4.00
456 506 7.336679 TGTTCAGACCATACCTGTTTATGAATG 59.663 37.037 0.00 0.00 31.96 2.67
500 550 7.235812 AGGGTGTCCTAGATCATAATTTAGGTC 59.764 40.741 0.00 0.00 42.75 3.85
542 592 4.747265 ATCCCCATATATGTTGCCAAGT 57.253 40.909 11.73 0.00 0.00 3.16
604 654 6.418101 TCCAATAGATTCAAAAGGAGACTGG 58.582 40.000 0.00 0.00 42.68 4.00
678 728 5.613358 AGTCATGTTTAAGCAGCTGTAAC 57.387 39.130 16.64 14.29 0.00 2.50
731 781 2.691526 TGCCGACTATCGTTTATGACCT 59.308 45.455 0.00 0.00 38.40 3.85
767 817 7.930865 GGCATATAATAGGAGCCTAGAAATCTG 59.069 40.741 2.33 1.18 42.01 2.90
867 917 8.696374 TGATACCTTCGTCTTCTATTCATTCTT 58.304 33.333 0.00 0.00 0.00 2.52
868 918 9.187455 GATACCTTCGTCTTCTATTCATTCTTC 57.813 37.037 0.00 0.00 0.00 2.87
869 919 7.176589 ACCTTCGTCTTCTATTCATTCTTCT 57.823 36.000 0.00 0.00 0.00 2.85
950 1001 9.726438 AATTCCTGTACCATATTAGATAACTGC 57.274 33.333 0.00 0.00 0.00 4.40
1166 1217 1.351017 TCAGGCTTCACCCTTGTTAGG 59.649 52.381 0.00 0.00 40.58 2.69
1344 1395 5.408079 ACAAATATGACCCATGGGATCTT 57.592 39.130 38.07 26.10 38.96 2.40
1384 1435 8.567285 ACCTTCTCTGTATTGTTCTTATTTGG 57.433 34.615 0.00 0.00 0.00 3.28
1739 1798 6.826231 AGAGAGAGAACTCGTGATTTCTGATA 59.174 38.462 7.14 0.00 46.64 2.15
1802 1862 6.640092 GCAATCTTCTAGCAATATTTCAAGCC 59.360 38.462 0.00 0.00 0.00 4.35
1806 1866 7.056006 TCTTCTAGCAATATTTCAAGCCATGA 58.944 34.615 0.00 0.00 35.85 3.07
1833 1893 9.880157 GTAAACTAGTGGTCATGGTAAATAAGA 57.120 33.333 0.00 0.00 0.00 2.10
1901 1961 7.540299 CATATCCATTATGTATGCATGCAACA 58.460 34.615 26.68 26.63 36.58 3.33
1903 1963 7.706100 ATCCATTATGTATGCATGCAACATA 57.294 32.000 30.58 30.58 35.54 2.29
1913 1973 9.247126 TGTATGCATGCAACATATTCAAAATAC 57.753 29.630 26.68 16.96 32.87 1.89
1957 2017 6.033341 GCAAAAGTCACACAAAACATAGACA 58.967 36.000 0.00 0.00 0.00 3.41
2099 2161 8.792830 TGGATTATTCACCTTTACTTTCTCTG 57.207 34.615 0.00 0.00 0.00 3.35
2993 3322 0.865769 CTGAACAGTGCAACGGGTAC 59.134 55.000 0.00 0.00 45.86 3.34
3202 3531 0.551131 AATTGTCCCCCTGCCTCTCT 60.551 55.000 0.00 0.00 0.00 3.10
3232 3561 2.236146 TCCAATAGCTGCTCGAAGGAAA 59.764 45.455 4.91 0.00 0.00 3.13
3233 3562 3.009723 CCAATAGCTGCTCGAAGGAAAA 58.990 45.455 4.91 0.00 0.00 2.29
3296 3625 5.105997 ACCTTCATTTGCTAGCATTTCTGTC 60.106 40.000 20.13 0.00 0.00 3.51
3656 4128 5.433526 ACAGTGTAAAAAGGCTCAACAGTA 58.566 37.500 0.00 0.00 0.00 2.74
3736 4374 0.749649 CTCAGAACTCCCCGAGATGG 59.250 60.000 0.00 0.00 33.32 3.51
3778 4416 2.488937 CAATGTACTGTGCTGCATTCCA 59.511 45.455 5.27 0.00 30.17 3.53
3842 4490 4.379302 ACTCAATCCAGGCTCTTTCTTT 57.621 40.909 0.00 0.00 0.00 2.52
3843 4491 4.734266 ACTCAATCCAGGCTCTTTCTTTT 58.266 39.130 0.00 0.00 0.00 2.27
3954 4602 7.383687 TGGGTCATAATTATCTTCACGTATCC 58.616 38.462 0.00 0.00 0.00 2.59
4030 4678 2.558378 CAGTGTGCTCCATACCATCAG 58.442 52.381 0.00 0.00 0.00 2.90
4224 4872 6.426980 TGCAAGCAGATAAAATACTCACTG 57.573 37.500 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 275 5.671493 ACACCTTATATTTCTGAACGGAGG 58.329 41.667 0.00 0.00 0.00 4.30
319 322 6.275494 TGTTCACTCATTTCAGTCCGTATA 57.725 37.500 0.00 0.00 0.00 1.47
323 326 4.035091 TGTTTGTTCACTCATTTCAGTCCG 59.965 41.667 0.00 0.00 0.00 4.79
402 405 5.422331 TCTTTAGTACTCCCTCCATTCACAG 59.578 44.000 0.00 0.00 0.00 3.66
409 412 5.152934 ACAGTTTCTTTAGTACTCCCTCCA 58.847 41.667 0.00 0.00 0.00 3.86
410 413 5.741962 ACAGTTTCTTTAGTACTCCCTCC 57.258 43.478 0.00 0.00 0.00 4.30
500 550 6.856895 GGATTATTTGTCCCTTTCACTTCAG 58.143 40.000 0.00 0.00 0.00 3.02
628 678 1.763770 CCACAACTCTGAAGCCCCT 59.236 57.895 0.00 0.00 0.00 4.79
731 781 7.338710 GCTCCTATTATATGCCTTGTATTCCA 58.661 38.462 0.00 0.00 0.00 3.53
767 817 9.651718 CTGTGTAAGATTAACTGTTTTTCTGTC 57.348 33.333 0.00 0.70 0.00 3.51
867 917 8.518720 TGATGGACCTAAATATATGGGAAAGA 57.481 34.615 0.00 0.00 0.00 2.52
868 918 9.236006 CTTGATGGACCTAAATATATGGGAAAG 57.764 37.037 0.00 0.00 0.00 2.62
869 919 7.669722 GCTTGATGGACCTAAATATATGGGAAA 59.330 37.037 0.00 0.00 0.00 3.13
950 1001 5.464168 CAAAGATGGCAAAACTCTTACTGG 58.536 41.667 1.76 0.00 0.00 4.00
1088 1139 5.425196 TGTAGTGTATGGTTTTAGGGTCC 57.575 43.478 0.00 0.00 0.00 4.46
1166 1217 4.936411 CCATATCACTTCTCTCATCCATGC 59.064 45.833 0.00 0.00 0.00 4.06
1344 1395 3.173965 AGAAGGTAGCAGCTTACTTGGA 58.826 45.455 14.13 0.00 35.86 3.53
1384 1435 9.959749 TCCATTCAGTAACAAATAAGAACAAAC 57.040 29.630 0.00 0.00 0.00 2.93
1739 1798 8.788325 AAGAGTAAAACTTTGTACTGAAGTGT 57.212 30.769 13.51 7.49 37.41 3.55
1802 1862 5.734720 ACCATGACCACTAGTTTACTCATG 58.265 41.667 15.68 15.68 35.03 3.07
1806 1866 9.886132 CTTATTTACCATGACCACTAGTTTACT 57.114 33.333 0.00 0.00 0.00 2.24
1833 1893 3.508012 GCTCCGTCTGAGTATGATATGGT 59.492 47.826 0.00 0.00 43.48 3.55
1995 2055 7.445402 TGGTTTTCTGATGAGAAGGTTCTTAAG 59.555 37.037 0.00 0.00 39.44 1.85
2498 2813 6.070881 AGGCATCCTGTCATCAGAAGATATAC 60.071 42.308 0.00 0.00 43.76 1.47
2993 3322 4.034048 GTGTCTATAACCCAATCAACTGCG 59.966 45.833 0.00 0.00 0.00 5.18
3135 3464 9.730705 GGATATCCAATCATCTGAAGAATGTAA 57.269 33.333 17.34 0.00 35.64 2.41
3202 3531 3.036819 AGCAGCTATTGGACATCTCTCA 58.963 45.455 0.00 0.00 0.00 3.27
3296 3625 3.598019 AATGTACAAGGGCAATTGCTG 57.402 42.857 28.42 21.07 41.70 4.41
3736 4374 8.671921 ACATTGACTGAGATGAAATAATGACAC 58.328 33.333 0.00 0.00 0.00 3.67
3842 4490 7.233348 AGAGTCAGAAAATCATTAAAGGGCAAA 59.767 33.333 0.00 0.00 0.00 3.68
3843 4491 6.721208 AGAGTCAGAAAATCATTAAAGGGCAA 59.279 34.615 0.00 0.00 0.00 4.52
3954 4602 9.146984 TGTACTTGGACGATTTGTAGAAAATAG 57.853 33.333 0.00 0.00 0.00 1.73
4030 4678 2.370189 AGTATGCCTATGAAGCCTGACC 59.630 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.