Multiple sequence alignment - TraesCS6D01G347400

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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 TraesCS6D01G347400 chr6D 100.000 3287 0 0 1 3287 446097509 446100795 0.000000e+00 6071.0
1 TraesCS6D01G347400 chr6D 84.777 1524 167 40 383 1874 446150541 446149051 0.000000e+00 1469.0
2 TraesCS6D01G347400 chr6D 91.755 473 36 2 1875 2344 446149089 446148617 0.000000e+00 654.0
3 TraesCS6D01G347400 chr6D 97.500 40 1 0 1874 1913 446099343 446099382 5.890000e-08 69.4
4 TraesCS6D01G347400 chr6D 97.500 40 1 0 1835 1874 446099382 446099421 5.890000e-08 69.4
5 TraesCS6D01G347400 chr6A 95.721 1145 36 5 2146 3284 592796977 592798114 0.000000e+00 1831.0
6 TraesCS6D01G347400 chr6A 92.052 931 74 0 1219 2149 592716411 592717341 0.000000e+00 1310.0
7 TraesCS6D01G347400 chr6A 87.411 842 90 8 1882 2707 592856659 592855818 0.000000e+00 953.0
8 TraesCS6D01G347400 chr6A 92.654 422 21 5 359 777 592710149 592710563 1.690000e-167 599.0
9 TraesCS6D01G347400 chr6A 91.736 363 26 3 857 1215 592710584 592710946 4.900000e-138 501.0
10 TraesCS6D01G347400 chr6A 87.705 366 37 8 27 389 592709376 592709736 1.410000e-113 420.0
11 TraesCS6D01G347400 chr6A 88.696 345 23 7 2459 2800 165815244 165815575 1.100000e-109 407.0
12 TraesCS6D01G347400 chr6A 90.583 223 20 1 962 1184 592866651 592866430 8.920000e-76 294.0
13 TraesCS6D01G347400 chr6A 79.095 464 58 22 392 847 592867097 592866665 1.930000e-72 283.0
14 TraesCS6D01G347400 chr6A 91.667 168 12 2 3121 3287 165815978 165816144 7.090000e-57 231.0
15 TraesCS6D01G347400 chr6A 100.000 39 0 0 1875 1913 592717028 592717066 4.550000e-09 73.1
16 TraesCS6D01G347400 chr6B 89.869 1066 93 9 816 1874 674195912 674196969 0.000000e+00 1356.0
17 TraesCS6D01G347400 chr6B 87.359 1155 115 14 741 1874 674378580 674377436 0.000000e+00 1295.0
18 TraesCS6D01G347400 chr6B 87.805 861 79 14 1875 2710 674377474 674376615 0.000000e+00 985.0
19 TraesCS6D01G347400 chr6B 94.128 579 31 1 1874 2452 674196930 674197505 0.000000e+00 878.0
20 TraesCS6D01G347400 chr6B 92.934 467 28 3 364 828 674195402 674195865 0.000000e+00 675.0
21 TraesCS6D01G347400 chr6B 91.117 349 23 7 27 371 674194635 674194979 1.790000e-127 466.0
22 TraesCS6D01G347400 chr6B 94.007 267 16 0 2450 2716 674214440 674214706 3.950000e-109 405.0
23 TraesCS6D01G347400 chr6B 85.590 229 22 2 2696 2914 674376464 674376237 2.550000e-56 230.0
24 TraesCS6D01G347400 chr6B 85.946 185 17 6 27 203 674378936 674378753 4.330000e-44 189.0
25 TraesCS6D01G347400 chr6B 88.889 72 7 1 133 203 674378701 674378630 1.620000e-13 87.9
26 TraesCS6D01G347400 chr3A 87.826 345 26 4 2459 2800 591694517 591694186 1.110000e-104 390.0
27 TraesCS6D01G347400 chr3A 93.865 163 9 1 2946 3108 591694191 591694030 9.110000e-61 244.0
28 TraesCS6D01G347400 chr3A 92.727 165 9 2 3124 3287 591693786 591693624 5.480000e-58 235.0
29 TraesCS6D01G347400 chr2B 76.159 151 26 7 2066 2210 112203552 112203406 1.640000e-08 71.3
30 TraesCS6D01G347400 chr2B 100.000 29 0 0 1921 1949 112203685 112203657 2.000000e-03 54.7
31 TraesCS6D01G347400 chr2D 71.812 298 63 17 1999 2284 73864287 73863999 7.610000e-07 65.8


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 TraesCS6D01G347400 chr6D 446097509 446100795 3286 False 2069.933333 6071 98.333333 1 3287 3 chr6D.!!$F1 3286
1 TraesCS6D01G347400 chr6D 446148617 446150541 1924 True 1061.500000 1469 88.266000 383 2344 2 chr6D.!!$R1 1961
2 TraesCS6D01G347400 chr6A 592796977 592798114 1137 False 1831.000000 1831 95.721000 2146 3284 1 chr6A.!!$F1 1138
3 TraesCS6D01G347400 chr6A 592855818 592856659 841 True 953.000000 953 87.411000 1882 2707 1 chr6A.!!$R1 825
4 TraesCS6D01G347400 chr6A 592716411 592717341 930 False 691.550000 1310 96.026000 1219 2149 2 chr6A.!!$F4 930
5 TraesCS6D01G347400 chr6A 592709376 592710946 1570 False 506.666667 599 90.698333 27 1215 3 chr6A.!!$F3 1188
6 TraesCS6D01G347400 chr6A 165815244 165816144 900 False 319.000000 407 90.181500 2459 3287 2 chr6A.!!$F2 828
7 TraesCS6D01G347400 chr6A 592866430 592867097 667 True 288.500000 294 84.839000 392 1184 2 chr6A.!!$R2 792
8 TraesCS6D01G347400 chr6B 674194635 674197505 2870 False 843.750000 1356 92.012000 27 2452 4 chr6B.!!$F2 2425
9 TraesCS6D01G347400 chr6B 674376237 674378936 2699 True 557.380000 1295 87.117800 27 2914 5 chr6B.!!$R1 2887
10 TraesCS6D01G347400 chr3A 591693624 591694517 893 True 289.666667 390 91.472667 2459 3287 3 chr3A.!!$R1 828

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
996 1553 0.179004 TGCATTTCCACCGTTCCACT 60.179 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2587 3174 0.40404 CTTGGTGACTTTGCCCCCTA 59.596 55.0 0.0 0.0 0.0 3.53 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
231 240 4.545823 TCAAAGGCGTGAACACTTTTAG 57.454 40.909 3.51 0.00 32.52 1.85
652 1119 3.369921 GGCCAAGCCCTTGAACTG 58.630 61.111 9.50 0.00 44.06 3.16
676 1148 2.098117 GCATGCTTTGCGAGGTTCTTAT 59.902 45.455 11.37 0.00 42.54 1.73
680 1152 4.827692 TGCTTTGCGAGGTTCTTATCTTA 58.172 39.130 0.00 0.00 0.00 2.10
681 1153 5.428253 TGCTTTGCGAGGTTCTTATCTTAT 58.572 37.500 0.00 0.00 0.00 1.73
682 1154 5.523916 TGCTTTGCGAGGTTCTTATCTTATC 59.476 40.000 0.00 0.00 0.00 1.75
683 1155 5.755861 GCTTTGCGAGGTTCTTATCTTATCT 59.244 40.000 0.00 0.00 0.00 1.98
684 1156 6.258947 GCTTTGCGAGGTTCTTATCTTATCTT 59.741 38.462 0.00 0.00 0.00 2.40
973 1515 1.328279 CCTAAATCCCCAAATCCGCC 58.672 55.000 0.00 0.00 0.00 6.13
989 1531 2.879907 CCTGCTGCATTTCCACCG 59.120 61.111 1.31 0.00 0.00 4.94
996 1553 0.179004 TGCATTTCCACCGTTCCACT 60.179 50.000 0.00 0.00 0.00 4.00
1087 1644 1.147153 GAAATCCTCCTCCGCCTGG 59.853 63.158 0.00 0.00 0.00 4.45
1179 1736 3.764466 CTCCGCCTCTTCCGCACT 61.764 66.667 0.00 0.00 0.00 4.40
1217 1774 2.154462 CCTGGGCATAATTTCCGCTAG 58.846 52.381 0.00 0.00 0.00 3.42
1221 1778 2.623416 GGGCATAATTTCCGCTAGCTTT 59.377 45.455 13.93 1.49 0.00 3.51
1291 1848 2.585247 CCGCGGAGGTCGATTTCC 60.585 66.667 24.07 7.83 42.43 3.13
1492 2052 0.174845 CATTCCCGACGAACTAGCCA 59.825 55.000 0.00 0.00 31.79 4.75
1497 2057 1.148157 CCGACGAACTAGCCATGCTG 61.148 60.000 0.00 0.00 40.10 4.41
1545 2105 3.002371 CCCTTCCTTGCTCCTCCC 58.998 66.667 0.00 0.00 0.00 4.30
1548 2108 2.203938 TTCCTTGCTCCTCCCGGT 60.204 61.111 0.00 0.00 0.00 5.28
1561 2121 0.459899 TCCCGGTGATGATGAAGACG 59.540 55.000 0.00 0.00 0.00 4.18
1564 2124 1.482621 CGGTGATGATGAAGACGCCG 61.483 60.000 0.00 0.00 46.63 6.46
1619 2179 1.078848 CCAAGCTGGTCCTCTTCGG 60.079 63.158 0.00 0.00 31.35 4.30
1693 2253 2.107204 ACTTTGATGACAAGTCCTGGCT 59.893 45.455 0.00 0.00 37.32 4.75
1742 2302 1.005630 CCTCAGGGCGCTACTATGC 60.006 63.158 7.64 0.00 0.00 3.14
1777 2337 0.391927 TTGGGCTGTTTATCCGTCCG 60.392 55.000 0.00 0.00 0.00 4.79
2221 2781 3.253188 TGAGTGGTTCTGTGCAAATAAGC 59.747 43.478 0.00 0.00 0.00 3.09
2256 2816 1.626825 GCCCCTCTATATGCCGGTTTA 59.373 52.381 1.90 0.00 0.00 2.01
2297 2861 3.632145 CCAACTGTTTGAAGTGGTAAGCT 59.368 43.478 0.00 0.00 34.24 3.74
2298 2862 4.097892 CCAACTGTTTGAAGTGGTAAGCTT 59.902 41.667 3.48 3.48 34.24 3.74
2299 2863 4.900635 ACTGTTTGAAGTGGTAAGCTTG 57.099 40.909 9.86 0.00 0.00 4.01
2309 2873 2.034179 GTGGTAAGCTTGTTGTTCCCAC 59.966 50.000 9.86 9.42 34.89 4.61
2333 2899 1.993542 TGCTTGTATTTTGCATGCCG 58.006 45.000 16.68 0.00 36.55 5.69
2481 3063 2.748209 AGGGCTTGTTGGTGTTTAGT 57.252 45.000 0.00 0.00 0.00 2.24
2531 3118 5.581085 ACAATTAGATAGCCGTGAAACTCAC 59.419 40.000 0.00 0.00 43.65 3.51
2587 3174 2.093890 TGCGTGCATTCCATCATTCTT 58.906 42.857 0.00 0.00 0.00 2.52
2899 3680 4.220382 TGACTTAAACATGGGCAATTGAGG 59.780 41.667 10.34 0.00 0.00 3.86
2942 3723 4.018050 ACCATCAAGTCTAAGGGAAAGCAT 60.018 41.667 0.00 0.00 0.00 3.79
3039 3820 2.415893 GCTGCCGCTAATGACATTTTGT 60.416 45.455 5.89 0.00 0.00 2.83
3129 4144 8.964476 ATGTAATGTTGACTAAGGATACCTTG 57.036 34.615 12.56 6.03 44.44 3.61
3276 4292 3.808174 ACTGAGAAAAAGACACCGCTTAC 59.192 43.478 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 207 5.655488 TCACGCCTTTGAAGAATTTTTCAA 58.345 33.333 17.59 17.59 43.32 2.69
390 844 3.201290 TCGGGTAAAACTTGCGTGTTTA 58.799 40.909 7.20 0.00 38.98 2.01
521 978 6.205101 AGCAATGCAATTCCTTAGAAAGAG 57.795 37.500 8.35 0.00 31.22 2.85
563 1020 8.729805 TTTCTGGTTGAATAAAGTTTTGCAAT 57.270 26.923 0.00 0.00 34.24 3.56
680 1152 7.886338 AGCTCCGAAACTTCAATTTTAAAGAT 58.114 30.769 0.00 0.00 0.00 2.40
681 1153 7.012894 TGAGCTCCGAAACTTCAATTTTAAAGA 59.987 33.333 12.15 0.00 0.00 2.52
682 1154 7.138736 TGAGCTCCGAAACTTCAATTTTAAAG 58.861 34.615 12.15 0.00 0.00 1.85
683 1155 7.033530 TGAGCTCCGAAACTTCAATTTTAAA 57.966 32.000 12.15 0.00 0.00 1.52
684 1156 6.627395 TGAGCTCCGAAACTTCAATTTTAA 57.373 33.333 12.15 0.00 0.00 1.52
973 1515 0.109597 GAACGGTGGAAATGCAGCAG 60.110 55.000 0.00 0.77 0.00 4.24
989 1531 2.700773 GGCGCCATTGGAGTGGAAC 61.701 63.158 24.80 0.00 42.02 3.62
1200 1757 1.897560 AGCTAGCGGAAATTATGCCC 58.102 50.000 9.55 0.00 0.00 5.36
1291 1848 3.787001 GGGGAGGAAGGAGCACCG 61.787 72.222 0.00 0.00 41.83 4.94
1353 1913 3.069318 GGGACGCCGGAGAAGAGT 61.069 66.667 13.83 0.00 0.00 3.24
1497 2057 5.501929 TCAGGATGTCCGGTTGATGAACC 62.502 52.174 3.64 3.64 42.44 3.62
1545 2105 1.482621 CGGCGTCTTCATCATCACCG 61.483 60.000 0.00 0.00 0.00 4.94
1548 2108 0.108186 AAGCGGCGTCTTCATCATCA 60.108 50.000 9.37 0.00 0.00 3.07
1561 2121 1.329906 CATCACTCTGAATGAAGCGGC 59.670 52.381 0.00 0.00 0.00 6.53
1564 2124 2.097142 GGCACATCACTCTGAATGAAGC 59.903 50.000 0.00 0.00 0.00 3.86
1742 2302 1.411394 CCAACAGAAGCATTTGTGCG 58.589 50.000 0.00 0.00 40.27 5.34
1777 2337 1.198637 GTCAAGCATGAGCAACCTGTC 59.801 52.381 0.00 0.00 45.49 3.51
2152 2712 2.380064 AAACAGTCCAAATCTGGCCA 57.620 45.000 4.71 4.71 43.17 5.36
2256 2816 0.693049 GTGGAGTCAAGGATGGTGGT 59.307 55.000 0.00 0.00 0.00 4.16
2297 2861 2.175202 AGCAAAGTGTGGGAACAACAA 58.825 42.857 0.00 0.00 46.06 2.83
2298 2862 1.846007 AGCAAAGTGTGGGAACAACA 58.154 45.000 0.00 0.00 46.06 3.33
2299 2863 2.094234 ACAAGCAAAGTGTGGGAACAAC 60.094 45.455 0.00 0.00 46.06 3.32
2309 2873 4.377635 GGCATGCAAAATACAAGCAAAGTG 60.378 41.667 21.36 0.00 42.15 3.16
2333 2899 7.065085 GCATCATATCACAATGTCCTACCATAC 59.935 40.741 0.00 0.00 0.00 2.39
2531 3118 2.712057 ACAAATGGCTCTTGCTTTCG 57.288 45.000 0.00 0.00 39.59 3.46
2587 3174 0.404040 CTTGGTGACTTTGCCCCCTA 59.596 55.000 0.00 0.00 0.00 3.53
2899 3680 1.536766 TGTTTCTGCTGTAGTGCATGC 59.463 47.619 11.82 11.82 42.48 4.06
3039 3820 2.153645 CAGCAAGCATAAGACACCACA 58.846 47.619 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.