Multiple sequence alignment - TraesCS7B01G171400

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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 TraesCS7B01G171400 chr7B 100.000 2872 0 0 1 2872 244284481 244281610 0.000000e+00 5304.0
1 TraesCS7B01G171400 chr1B 97.474 2415 49 4 468 2872 66949858 66952270 0.000000e+00 4111.0
2 TraesCS7B01G171400 chr1B 95.579 475 21 0 1 475 66948929 66949403 0.000000e+00 761.0
3 TraesCS7B01G171400 chr2B 95.566 1060 30 8 1 1053 44908723 44909772 0.000000e+00 1681.0
4 TraesCS7B01G171400 chr2B 97.792 951 19 1 1924 2872 44915082 44916032 0.000000e+00 1639.0
5 TraesCS7B01G171400 chr2B 96.517 890 17 1 1038 1927 44910155 44911030 0.000000e+00 1459.0
6 TraesCS7B01G171400 chr2B 92.192 666 52 0 869 1534 379103810 379103145 0.000000e+00 942.0
7 TraesCS7B01G171400 chr4A 90.971 886 42 21 2004 2872 37903178 37904042 0.000000e+00 1158.0
8 TraesCS7B01G171400 chr4A 94.850 466 23 1 1479 1944 37901923 37902387 0.000000e+00 726.0
9 TraesCS7B01G171400 chr4A 96.491 57 2 0 1953 2009 37903089 37903145 8.470000e-16 95.3
10 TraesCS7B01G171400 chr3B 89.581 883 55 12 2004 2872 244787242 244786383 0.000000e+00 1086.0
11 TraesCS7B01G171400 chr3B 93.648 551 33 2 1170 1719 244793047 244792498 0.000000e+00 822.0
12 TraesCS7B01G171400 chr3B 93.770 305 18 1 1705 2009 244787578 244787275 9.380000e-125 457.0
13 TraesCS7B01G171400 chr2A 92.342 666 51 0 869 1534 227834779 227834114 0.000000e+00 948.0
14 TraesCS7B01G171400 chr2A 80.702 228 19 14 252 473 281678871 281678663 1.380000e-33 154.0
15 TraesCS7B01G171400 chr2A 77.206 272 19 18 212 473 281673288 281673050 5.030000e-23 119.0
16 TraesCS7B01G171400 chr2D 91.904 667 52 2 869 1534 202086882 202086217 0.000000e+00 931.0
17 TraesCS7B01G171400 chr6D 93.041 388 26 1 1623 2009 394590576 394590189 1.490000e-157 566.0
18 TraesCS7B01G171400 chr6D 87.805 246 22 7 2004 2243 394590156 394589913 6.060000e-72 281.0
19 TraesCS7B01G171400 chr6D 90.000 190 19 0 2306 2495 394589918 394589729 2.210000e-61 246.0
20 TraesCS7B01G171400 chr6A 92.268 388 29 1 1623 2009 540608215 540607828 1.500000e-152 549.0
21 TraesCS7B01G171400 chr6A 91.935 186 14 1 2310 2495 540607589 540607405 2.840000e-65 259.0
22 TraesCS7B01G171400 chr6A 92.308 143 11 0 2004 2146 540607795 540607653 1.350000e-48 204.0
23 TraesCS7B01G171400 chr6A 93.976 83 5 0 1529 1611 48656337 48656255 3.000000e-25 126.0
24 TraesCS7B01G171400 chr6A 78.605 215 26 12 88 294 445682388 445682590 1.080000e-24 124.0
25 TraesCS7B01G171400 chr6A 86.486 74 5 4 2174 2243 540607660 540607588 3.070000e-10 76.8
26 TraesCS7B01G171400 chr6B 91.795 390 29 2 1623 2009 590565721 590565332 9.050000e-150 540.0
27 TraesCS7B01G171400 chr6B 91.053 190 17 0 2306 2495 590564945 590564756 1.020000e-64 257.0
28 TraesCS7B01G171400 chr1D 92.079 202 16 0 1782 1983 7200245 7200446 4.680000e-73 285.0
29 TraesCS7B01G171400 chr1D 95.706 163 7 0 1623 1785 7198183 7198345 2.190000e-66 263.0
30 TraesCS7B01G171400 chr1D 95.349 86 4 0 1526 1611 1851446 1851531 1.390000e-28 137.0


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 TraesCS7B01G171400 chr7B 244281610 244284481 2871 True 5304.000000 5304 100.00000 1 2872 1 chr7B.!!$R1 2871
1 TraesCS7B01G171400 chr1B 66948929 66952270 3341 False 2436.000000 4111 96.52650 1 2872 2 chr1B.!!$F1 2871
2 TraesCS7B01G171400 chr2B 44915082 44916032 950 False 1639.000000 1639 97.79200 1924 2872 1 chr2B.!!$F1 948
3 TraesCS7B01G171400 chr2B 44908723 44911030 2307 False 1570.000000 1681 96.04150 1 1927 2 chr2B.!!$F2 1926
4 TraesCS7B01G171400 chr2B 379103145 379103810 665 True 942.000000 942 92.19200 869 1534 1 chr2B.!!$R1 665
5 TraesCS7B01G171400 chr4A 37901923 37904042 2119 False 659.766667 1158 94.10400 1479 2872 3 chr4A.!!$F1 1393
6 TraesCS7B01G171400 chr3B 244792498 244793047 549 True 822.000000 822 93.64800 1170 1719 1 chr3B.!!$R1 549
7 TraesCS7B01G171400 chr3B 244786383 244787578 1195 True 771.500000 1086 91.67550 1705 2872 2 chr3B.!!$R2 1167
8 TraesCS7B01G171400 chr2A 227834114 227834779 665 True 948.000000 948 92.34200 869 1534 1 chr2A.!!$R1 665
9 TraesCS7B01G171400 chr2D 202086217 202086882 665 True 931.000000 931 91.90400 869 1534 1 chr2D.!!$R1 665
10 TraesCS7B01G171400 chr6D 394589729 394590576 847 True 364.333333 566 90.28200 1623 2495 3 chr6D.!!$R1 872
11 TraesCS7B01G171400 chr6A 540607405 540608215 810 True 272.200000 549 90.74925 1623 2495 4 chr6A.!!$R2 872
12 TraesCS7B01G171400 chr6B 590564756 590565721 965 True 398.500000 540 91.42400 1623 2495 2 chr6B.!!$R1 872
13 TraesCS7B01G171400 chr1D 7198183 7200446 2263 False 274.000000 285 93.89250 1623 1983 2 chr1D.!!$F2 360

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
19 20 0.032217 CCTCTCCTGCTTCTCCTCCT 60.032 60.0 0.00 0.0 0.00 3.69 F
984 1462 0.455802 TGCGCCAAATACACAATGCG 60.456 50.0 4.18 0.0 44.38 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 2207 2.019249 AGATGCACATTTCATCCCACG 58.981 47.619 0.00 0.0 40.79 4.94 R
2565 6201 2.282958 TGGGTTCTCGAGCCTCGT 60.283 61.111 14.64 0.0 46.39 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
19 20 0.032217 CCTCTCCTGCTTCTCCTCCT 60.032 60.000 0.00 0.00 0.00 3.69
22 23 0.032217 CTCCTGCTTCTCCTCCTCCT 60.032 60.000 0.00 0.00 0.00 3.69
50 51 1.748879 CCACGGATGAAATGGGCGT 60.749 57.895 0.00 0.00 0.00 5.68
188 189 1.282157 CTCTTTCCCCCACGAAGGAAT 59.718 52.381 0.00 0.00 41.69 3.01
210 211 4.351938 CCGCGTCCGACCTCAACA 62.352 66.667 4.92 0.00 36.29 3.33
243 244 3.993865 TAGCGAGCCCCACCCATGA 62.994 63.158 0.00 0.00 0.00 3.07
386 387 5.249622 TCTCTCTCTTCACTTCTCTGTAGGA 59.750 44.000 0.00 0.00 0.00 2.94
428 429 1.640670 AGAGCAGAGGAGAGAAGAGGT 59.359 52.381 0.00 0.00 0.00 3.85
525 988 4.872664 TCAGTTTTGGTTCAACACGTTTT 58.127 34.783 0.00 0.00 30.47 2.43
685 1158 7.360269 GCCATGAAAATAAAATGTTGTGGTCTG 60.360 37.037 0.00 0.00 0.00 3.51
852 1326 6.530567 TGTGTTATTACGCTTGATTTCTTCG 58.469 36.000 0.00 0.00 35.77 3.79
876 1350 2.079925 AGAGAAAGAACATTGAGGCGC 58.920 47.619 0.00 0.00 0.00 6.53
960 1438 4.455877 GCAAACATACTGCAAGAACTACCT 59.544 41.667 0.00 0.00 39.69 3.08
984 1462 0.455802 TGCGCCAAATACACAATGCG 60.456 50.000 4.18 0.00 44.38 4.73
992 1470 4.438200 CCAAATACACAATGCGGAAGGTAC 60.438 45.833 0.00 0.00 0.00 3.34
1331 2207 0.819259 TCAACACAGCTGCAGGTTCC 60.819 55.000 17.45 0.00 0.00 3.62
1334 2210 2.281070 ACAGCTGCAGGTTCCGTG 60.281 61.111 17.45 7.19 0.00 4.94
1494 2370 6.492007 CCTAAGATTGTGCATATGCTTAGG 57.508 41.667 27.13 25.86 44.70 2.69
1593 2469 2.290071 GCAAGCTCCTAACCCACTGTAA 60.290 50.000 0.00 0.00 0.00 2.41
1668 2544 4.770795 ACCTGTTATGTACTTCATCTGGC 58.229 43.478 0.00 0.00 37.91 4.85
1836 4615 3.592898 ACAATCACACTGCTATCGACA 57.407 42.857 0.00 0.00 0.00 4.35
1839 4618 1.834188 TCACACTGCTATCGACAGGA 58.166 50.000 6.49 0.00 39.55 3.86
1868 4648 4.362677 ACTTTTATCAGTCTGAGGGCCTA 58.637 43.478 5.73 0.00 0.00 3.93
1991 5466 8.450180 CAAGTGTATAACAATTGTGCAGATGTA 58.550 33.333 12.82 0.00 45.72 2.29
2047 5560 1.011333 CAACCGTTTCACCTCACGTT 58.989 50.000 0.00 0.00 34.47 3.99
2051 5564 3.578688 ACCGTTTCACCTCACGTTATAC 58.421 45.455 0.00 0.00 34.47 1.47
2094 5607 4.948004 TGCTTGAAGCTCATGAGAATGAAT 59.052 37.500 27.04 4.60 42.97 2.57
2383 6018 1.416401 AGGACCGTGAAAGAAGAGCAA 59.584 47.619 0.00 0.00 0.00 3.91
2565 6201 3.897122 GTGGTGGGGGTGGAGCAA 61.897 66.667 0.00 0.00 0.00 3.91
2765 6415 3.378512 TCTCTCTCTCTCTCTCTCTGCT 58.621 50.000 0.00 0.00 0.00 4.24
2818 6468 6.224584 TCATTCTCAATGTTGTTACCGTGTA 58.775 36.000 0.00 0.00 39.87 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.032615 GAGGAGGAGGAGAAGCAGGA 60.033 60.000 0.00 0.0 0.00 3.86
42 43 4.612279 TGCCCACCAACGCCCATT 62.612 61.111 0.00 0.0 0.00 3.16
210 211 3.015312 GCTAGGGTTTCGGTCGGCT 62.015 63.158 0.00 0.0 0.00 5.52
428 429 3.005539 GGCTGCTCCACCTCCTCA 61.006 66.667 0.00 0.0 34.01 3.86
525 988 2.230025 CCAAAAGGTCACACACACACAA 59.770 45.455 0.00 0.0 0.00 3.33
616 1089 5.769662 AGTCCAGTTAGAAAAATGTGATGCA 59.230 36.000 0.00 0.0 0.00 3.96
685 1158 5.048434 ACTTGAGCAGCTAAGAAATGAAACC 60.048 40.000 14.83 0.0 0.00 3.27
852 1326 4.377841 CGCCTCAATGTTCTTTCTCTGAAC 60.378 45.833 0.00 0.0 42.77 3.18
876 1350 5.652452 AGAAATTTGGGAATAGACCTTTCCG 59.348 40.000 0.00 0.0 43.01 4.30
960 1438 0.880718 TGTGTATTTGGCGCACGACA 60.881 50.000 10.83 0.0 36.04 4.35
984 1462 1.146263 CATCCCAGCGGTACCTTCC 59.854 63.158 10.90 0.0 0.00 3.46
992 1470 2.108566 CAGCTCTCATCCCAGCGG 59.891 66.667 0.00 0.0 40.84 5.52
1028 1506 3.876914 TGTTCCTGCAAAGTTCAGTACAG 59.123 43.478 0.00 0.0 0.00 2.74
1113 1989 8.596380 GTTATTAAGTGTACAATGCAGAGTCTC 58.404 37.037 0.00 0.0 0.00 3.36
1331 2207 2.019249 AGATGCACATTTCATCCCACG 58.981 47.619 0.00 0.0 40.79 4.94
1334 2210 3.294214 AGGAAGATGCACATTTCATCCC 58.706 45.455 5.83 0.0 40.79 3.85
1494 2370 3.555956 CGACTCTATGCCAAACATACCAC 59.444 47.826 0.00 0.0 40.38 4.16
1593 2469 4.576463 GTCATCTCCACAACAGACAACTTT 59.424 41.667 0.00 0.0 0.00 2.66
1839 4618 8.523658 GCCCTCAGACTGATAAAAGTAAAATTT 58.476 33.333 5.42 0.0 0.00 1.82
2047 5560 9.027129 GCAAGTGTATGTAAAACTCGATGTATA 57.973 33.333 0.00 0.0 0.00 1.47
2051 5564 6.408858 AGCAAGTGTATGTAAAACTCGATG 57.591 37.500 0.00 0.0 0.00 3.84
2094 5607 9.866655 ATATTTAGGTGAAAATATCTTCCAGCA 57.133 29.630 0.00 0.0 37.43 4.41
2346 5981 9.064706 TCACGGTCCTGTTTTAACAATAAAATA 57.935 29.630 0.00 0.0 41.63 1.40
2368 6003 6.369065 AGTTTAGGTATTGCTCTTCTTTCACG 59.631 38.462 0.00 0.0 0.00 4.35
2565 6201 2.282958 TGGGTTCTCGAGCCTCGT 60.283 61.111 14.64 0.0 46.39 4.18
2765 6415 4.202253 ACAGAGCGGTCTTTGCATATATGA 60.202 41.667 15.83 0.0 33.85 2.15


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

AutoCloner maintained by Alex Coulton.