Multiple sequence alignment - TraesCS6B01G029800

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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 TraesCS6B01G029800 chr6B 100.000 5265 0 0 1 5265 17997497 18002761 0.000000e+00 9723.0
1 TraesCS6B01G029800 chr6B 98.101 3528 61 4 1018 4540 17764714 17761188 0.000000e+00 6139.0
2 TraesCS6B01G029800 chr6B 78.351 3081 582 57 1267 4310 18266455 18269487 0.000000e+00 1916.0
3 TraesCS6B01G029800 chr6B 77.786 2764 519 67 1279 4008 18225435 18228137 0.000000e+00 1615.0
4 TraesCS6B01G029800 chr6B 76.782 3002 548 91 1367 4301 18165120 18168039 0.000000e+00 1544.0
5 TraesCS6B01G029800 chr6B 77.685 2402 428 51 1274 3643 18812735 18815060 0.000000e+00 1367.0
6 TraesCS6B01G029800 chr6B 90.437 983 42 16 118 1090 17765699 17764759 0.000000e+00 1247.0
7 TraesCS6B01G029800 chr6B 96.269 402 15 0 4864 5265 17734662 17734261 0.000000e+00 660.0
8 TraesCS6B01G029800 chr6B 99.701 334 1 0 4533 4866 17735316 17734983 3.490000e-171 612.0
9 TraesCS6B01G029800 chr6B 80.333 661 114 11 3647 4300 18633194 18633845 2.200000e-133 486.0
10 TraesCS6B01G029800 chr6B 76.868 696 82 40 488 1130 18262429 18263098 2.370000e-83 320.0
11 TraesCS6B01G029800 chr6B 90.496 242 13 4 5034 5265 17732284 17732043 1.420000e-80 311.0
12 TraesCS6B01G029800 chr6B 87.786 131 15 1 1 131 17767028 17766899 9.130000e-33 152.0
13 TraesCS6B01G029800 chr6B 94.667 75 1 3 1018 1090 17764773 17764700 4.310000e-21 113.0
14 TraesCS6B01G029800 chr6B 86.538 104 12 2 484 587 18164055 18164156 4.310000e-21 113.0
15 TraesCS6B01G029800 chr6B 84.956 113 12 3 494 601 18216546 18216658 5.570000e-20 110.0
16 TraesCS6B01G029800 chr6D 95.735 3822 152 7 1052 4866 9860742 9856925 0.000000e+00 6144.0
17 TraesCS6B01G029800 chr6D 79.566 2212 358 55 1269 3433 10310543 10308379 0.000000e+00 1495.0
18 TraesCS6B01G029800 chr6D 92.083 960 39 14 83 1023 9861674 9860733 0.000000e+00 1317.0
19 TraesCS6B01G029800 chr6D 79.056 1800 327 33 1265 3028 9913010 9914795 0.000000e+00 1190.0
20 TraesCS6B01G029800 chr6D 76.080 1250 249 29 3156 4394 9914950 9916160 1.620000e-169 606.0
21 TraesCS6B01G029800 chr6D 83.244 561 81 9 3749 4300 10308107 10307551 2.190000e-138 503.0
22 TraesCS6B01G029800 chr6D 89.011 91 8 2 3 93 454259379 454259291 1.550000e-20 111.0
23 TraesCS6B01G029800 chr6A 95.714 3010 122 3 1765 4771 11008532 11005527 0.000000e+00 4837.0
24 TraesCS6B01G029800 chr6A 79.141 1769 314 31 1265 3010 11681280 11679544 0.000000e+00 1171.0
25 TraesCS6B01G029800 chr6A 78.868 1784 319 35 1265 3024 11732791 11731042 0.000000e+00 1153.0
26 TraesCS6B01G029800 chr6A 76.934 2029 342 67 1975 3959 11475832 11477778 0.000000e+00 1038.0
27 TraesCS6B01G029800 chr6A 76.635 2003 365 62 2343 4310 11498308 11500242 0.000000e+00 1011.0
28 TraesCS6B01G029800 chr6A 78.261 1449 260 31 2104 3515 10931946 10930516 0.000000e+00 880.0
29 TraesCS6B01G029800 chr6A 89.986 699 41 12 338 1023 11009978 11009296 0.000000e+00 876.0
30 TraesCS6B01G029800 chr6A 82.986 623 94 9 1367 1983 11473633 11474249 2.140000e-153 553.0
31 TraesCS6B01G029800 chr6A 75.422 1245 250 32 3087 4319 11679437 11678237 2.140000e-153 553.0
32 TraesCS6B01G029800 chr6A 75.481 1248 244 33 3087 4319 11730948 11729748 2.140000e-153 553.0
33 TraesCS6B01G029800 chr6A 93.750 320 15 4 1052 1368 11009305 11008988 4.770000e-130 475.0
34 TraesCS6B01G029800 chr6A 89.200 250 14 7 5028 5265 106681221 106681469 3.080000e-77 300.0
35 TraesCS6B01G029800 chr6A 85.455 110 14 2 465 574 11467515 11467622 4.310000e-21 113.0
36 TraesCS6B01G029800 chr6A 98.113 53 1 0 108 160 11010033 11009981 5.610000e-15 93.5
37 TraesCS6B01G029800 chrUn 79.070 989 187 12 1265 2251 240891857 240892827 0.000000e+00 662.0
38 TraesCS6B01G029800 chrUn 79.070 989 187 12 1265 2251 268932043 268931073 0.000000e+00 662.0
39 TraesCS6B01G029800 chrUn 88.043 92 10 1 483 574 240889730 240889820 2.000000e-19 108.0
40 TraesCS6B01G029800 chrUn 87.368 95 11 1 483 577 268934170 268934077 2.000000e-19 108.0
41 TraesCS6B01G029800 chrUn 89.286 56 5 1 465 520 71251742 71251688 9.460000e-08 69.4
42 TraesCS6B01G029800 chr2B 90.244 246 14 5 5029 5265 45564905 45565149 3.960000e-81 313.0
43 TraesCS6B01G029800 chr2B 88.672 256 17 6 5021 5265 11355907 11356161 8.570000e-78 302.0
44 TraesCS6B01G029800 chr2A 89.919 248 13 6 5029 5265 759091497 759091251 5.120000e-80 309.0
45 TraesCS6B01G029800 chr2A 90.496 242 12 3 5034 5265 759093900 759093660 5.120000e-80 309.0
46 TraesCS6B01G029800 chr4A 87.938 257 19 7 5021 5265 729228260 729228516 5.160000e-75 292.0
47 TraesCS6B01G029800 chr4A 92.683 82 5 1 1 82 450788352 450788272 3.330000e-22 117.0
48 TraesCS6B01G029800 chr1B 88.306 248 17 7 5029 5265 76722127 76721881 2.400000e-73 287.0
49 TraesCS6B01G029800 chr1B 83.333 252 32 8 5023 5265 653523308 653523558 1.910000e-54 224.0
50 TraesCS6B01G029800 chr2D 95.181 83 1 3 1 82 541069687 541069607 1.540000e-25 128.0
51 TraesCS6B01G029800 chr3D 91.954 87 5 2 1 86 588123628 588123543 2.580000e-23 121.0
52 TraesCS6B01G029800 chr1D 91.954 87 3 4 1 86 457875379 457875462 9.260000e-23 119.0
53 TraesCS6B01G029800 chr4B 91.566 83 4 3 1 82 574446675 574446755 1.550000e-20 111.0
54 TraesCS6B01G029800 chr5D 88.043 92 10 1 1 92 264370860 264370770 2.000000e-19 108.0
55 TraesCS6B01G029800 chr5B 88.043 92 9 2 1 92 375719490 375719401 2.000000e-19 108.0


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 TraesCS6B01G029800 chr6B 17997497 18002761 5264 False 9723.000000 9723 100.000000 1 5265 1 chr6B.!!$F1 5264
1 TraesCS6B01G029800 chr6B 17761188 17767028 5840 True 1912.750000 6139 92.747750 1 4540 4 chr6B.!!$R2 4539
2 TraesCS6B01G029800 chr6B 18225435 18228137 2702 False 1615.000000 1615 77.786000 1279 4008 1 chr6B.!!$F3 2729
3 TraesCS6B01G029800 chr6B 18812735 18815060 2325 False 1367.000000 1367 77.685000 1274 3643 1 chr6B.!!$F5 2369
4 TraesCS6B01G029800 chr6B 18262429 18269487 7058 False 1118.000000 1916 77.609500 488 4310 2 chr6B.!!$F7 3822
5 TraesCS6B01G029800 chr6B 18164055 18168039 3984 False 828.500000 1544 81.660000 484 4301 2 chr6B.!!$F6 3817
6 TraesCS6B01G029800 chr6B 17732043 17735316 3273 True 527.666667 660 95.488667 4533 5265 3 chr6B.!!$R1 732
7 TraesCS6B01G029800 chr6B 18633194 18633845 651 False 486.000000 486 80.333000 3647 4300 1 chr6B.!!$F4 653
8 TraesCS6B01G029800 chr6D 9856925 9861674 4749 True 3730.500000 6144 93.909000 83 4866 2 chr6D.!!$R2 4783
9 TraesCS6B01G029800 chr6D 10307551 10310543 2992 True 999.000000 1495 81.405000 1269 4300 2 chr6D.!!$R3 3031
10 TraesCS6B01G029800 chr6D 9913010 9916160 3150 False 898.000000 1190 77.568000 1265 4394 2 chr6D.!!$F1 3129
11 TraesCS6B01G029800 chr6A 11005527 11010033 4506 True 1570.375000 4837 94.390750 108 4771 4 chr6A.!!$R2 4663
12 TraesCS6B01G029800 chr6A 11498308 11500242 1934 False 1011.000000 1011 76.635000 2343 4310 1 chr6A.!!$F2 1967
13 TraesCS6B01G029800 chr6A 10930516 10931946 1430 True 880.000000 880 78.261000 2104 3515 1 chr6A.!!$R1 1411
14 TraesCS6B01G029800 chr6A 11678237 11681280 3043 True 862.000000 1171 77.281500 1265 4319 2 chr6A.!!$R3 3054
15 TraesCS6B01G029800 chr6A 11729748 11732791 3043 True 853.000000 1153 77.174500 1265 4319 2 chr6A.!!$R4 3054
16 TraesCS6B01G029800 chr6A 11473633 11477778 4145 False 795.500000 1038 79.960000 1367 3959 2 chr6A.!!$F4 2592
17 TraesCS6B01G029800 chrUn 240889730 240892827 3097 False 385.000000 662 83.556500 483 2251 2 chrUn.!!$F1 1768
18 TraesCS6B01G029800 chrUn 268931073 268934170 3097 True 385.000000 662 83.219000 483 2251 2 chrUn.!!$R2 1768
19 TraesCS6B01G029800 chr2A 759091251 759093900 2649 True 309.000000 309 90.207500 5029 5265 2 chr2A.!!$R1 236

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
949 2308 0.734889 CACCGCATCTTAAGCCCAAG 59.265 55.000 0.0 0.0 0.0 3.61 F
1592 6427 1.468520 GGGTGATGGACATGTTTGACG 59.531 52.381 0.0 0.0 0.0 4.35 F
1606 6441 3.243602 TGTTTGACGACGAAGATGAGGAA 60.244 43.478 0.0 0.0 0.0 3.36 F
3322 10182 2.957402 TCCAAGGAACAAGCAGTGAT 57.043 45.000 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2783 9543 3.754965 TGAGGCTATTGTTGCTTTCTGT 58.245 40.909 0.00 0.0 0.00 3.41 R
3043 9812 1.133513 AGCACACCAAACCATCCTTCA 60.134 47.619 0.00 0.0 0.00 3.02 R
3367 10227 6.761714 CGCCCTTCAGTATATCTTTGTACTTT 59.238 38.462 0.00 0.0 28.23 2.66 R
4956 12193 0.102663 TGTTTACTCGCCACGTGTCA 59.897 50.000 15.65 0.0 35.30 3.58 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
45 46 9.295214 CATCTGTATGTAGTCCATATCGAAATC 57.705 37.037 0.00 0.00 38.29 2.17
47 48 8.731605 TCTGTATGTAGTCCATATCGAAATCTC 58.268 37.037 0.00 0.00 38.29 2.75
159 1373 1.553248 AGGTGCGGCAGTTTCAGTATA 59.447 47.619 1.18 0.00 0.00 1.47
160 1374 2.170607 AGGTGCGGCAGTTTCAGTATAT 59.829 45.455 1.18 0.00 0.00 0.86
239 1461 7.094592 TGTGTGAAGCATGTTCCGATTATAAAA 60.095 33.333 0.00 0.00 0.00 1.52
273 1495 5.512232 GCATGGAAGCCTTCTAGCTAGTATT 60.512 44.000 20.10 9.02 44.11 1.89
449 1673 2.238521 TCCAATCTGGTGCCTTGAAAC 58.761 47.619 0.00 0.00 39.03 2.78
458 1682 3.244215 TGGTGCCTTGAAACACACAAAAA 60.244 39.130 0.00 0.00 38.57 1.94
589 1815 9.467258 CAAAAGCTAATTCTCTCAATGAAACAA 57.533 29.630 0.00 0.00 0.00 2.83
676 1932 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
677 1933 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
678 1934 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
679 1935 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
762 2058 4.937201 TCTATTTGGCTTCTATCGAGCA 57.063 40.909 0.00 0.00 41.89 4.26
763 2059 5.474578 TCTATTTGGCTTCTATCGAGCAT 57.525 39.130 0.00 0.00 41.89 3.79
764 2060 5.233225 TCTATTTGGCTTCTATCGAGCATG 58.767 41.667 0.00 0.00 41.89 4.06
930 2286 7.225734 GGAAGTTAGGATATTGTTGAAGAGCTC 59.774 40.741 5.27 5.27 0.00 4.09
935 2294 1.160137 ATTGTTGAAGAGCTCACCGC 58.840 50.000 17.77 2.32 32.21 5.68
949 2308 0.734889 CACCGCATCTTAAGCCCAAG 59.265 55.000 0.00 0.00 0.00 3.61
1321 6156 2.499693 TGATGTGGCTGTCGAAAGGATA 59.500 45.455 4.40 0.00 0.00 2.59
1592 6427 1.468520 GGGTGATGGACATGTTTGACG 59.531 52.381 0.00 0.00 0.00 4.35
1606 6441 3.243602 TGTTTGACGACGAAGATGAGGAA 60.244 43.478 0.00 0.00 0.00 3.36
2680 9440 3.390135 CAAGCTCCGAGTAACAAAGTCA 58.610 45.455 0.00 0.00 0.00 3.41
2783 9543 3.718434 AGGCATGACAATCTTATCTGGGA 59.282 43.478 0.00 0.00 0.00 4.37
3042 9811 3.450904 TGTGGCCTCAGAAGGTAGTAAT 58.549 45.455 3.32 0.00 45.34 1.89
3043 9812 3.844211 TGTGGCCTCAGAAGGTAGTAATT 59.156 43.478 3.32 0.00 45.34 1.40
3322 10182 2.957402 TCCAAGGAACAAGCAGTGAT 57.043 45.000 0.00 0.00 0.00 3.06
3367 10227 6.346096 GCATACAAGTACCTTAATGGACTCA 58.654 40.000 0.00 0.00 39.71 3.41
3888 10785 3.170717 TCGTACATGTTCTCCCCTTCTT 58.829 45.455 2.30 0.00 0.00 2.52
4866 11780 7.892778 TTTGTGAAATGAATGATGTTGATGG 57.107 32.000 0.00 0.00 0.00 3.51
4867 11781 5.968254 TGTGAAATGAATGATGTTGATGGG 58.032 37.500 0.00 0.00 0.00 4.00
4868 11782 5.715753 TGTGAAATGAATGATGTTGATGGGA 59.284 36.000 0.00 0.00 0.00 4.37
4869 11783 6.210984 TGTGAAATGAATGATGTTGATGGGAA 59.789 34.615 0.00 0.00 0.00 3.97
4870 11784 7.093245 TGTGAAATGAATGATGTTGATGGGAAT 60.093 33.333 0.00 0.00 0.00 3.01
4871 11785 8.415553 GTGAAATGAATGATGTTGATGGGAATA 58.584 33.333 0.00 0.00 0.00 1.75
4872 11786 9.150028 TGAAATGAATGATGTTGATGGGAATAT 57.850 29.630 0.00 0.00 0.00 1.28
4873 11787 9.419297 GAAATGAATGATGTTGATGGGAATATG 57.581 33.333 0.00 0.00 0.00 1.78
4956 12193 4.593206 TGTGATGTCTCTAAGGAAAGGTGT 59.407 41.667 0.00 0.00 0.00 4.16
4961 12198 4.202223 TGTCTCTAAGGAAAGGTGTGACAC 60.202 45.833 7.29 7.29 0.00 3.67
4989 12226 8.085296 TGGCGAGTAAACAACAATGAATATTTT 58.915 29.630 0.00 0.00 0.00 1.82
5116 12353 4.562082 TGACGACACCGAGATTTGTTAAT 58.438 39.130 0.00 0.00 39.50 1.40
5197 12435 4.263572 CAACACAGGCCACCCGGA 62.264 66.667 5.01 0.00 35.76 5.14
5228 14977 4.805231 CGCCGGTACCGCATGTCA 62.805 66.667 29.15 0.00 38.24 3.58
5250 14999 6.207025 GTCACTATCTAGTCGTCATGGGTTAT 59.793 42.308 0.00 0.00 33.46 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 8.723365 TCCCTCCATTTTCTAAATATAAGCTCA 58.277 33.333 0.00 0.00 0.00 4.26
54 55 8.728098 ACTCCCTCCATTTTCTAAATATAAGCT 58.272 33.333 0.00 0.00 0.00 3.74
70 71 7.390718 GCGTGAATAATTAATTACTCCCTCCAT 59.609 37.037 12.74 0.00 0.00 3.41
72 73 6.148976 GGCGTGAATAATTAATTACTCCCTCC 59.851 42.308 12.74 3.87 0.00 4.30
74 75 5.699458 CGGCGTGAATAATTAATTACTCCCT 59.301 40.000 12.74 0.00 0.00 4.20
159 1373 8.396272 AGAAACTGCTAGAAACATTACACAAT 57.604 30.769 0.00 0.00 0.00 2.71
160 1374 7.801716 AGAAACTGCTAGAAACATTACACAA 57.198 32.000 0.00 0.00 0.00 3.33
183 1405 7.813852 AGAAACATTACGCAGACTACTTAAG 57.186 36.000 0.00 0.00 0.00 1.85
239 1461 2.025510 AGGCTTCCATGCTTAGCTTTCT 60.026 45.455 5.60 0.04 35.30 2.52
273 1495 8.403236 CGTGATACATGGATTCGTATAAGGATA 58.597 37.037 0.00 0.00 0.00 2.59
458 1682 2.821969 GCTGTCCATTCACTGTCCAATT 59.178 45.455 0.00 0.00 0.00 2.32
589 1815 6.449830 AGTAGTGATACCCTTTCCTTTTGT 57.550 37.500 0.00 0.00 0.00 2.83
676 1932 2.620112 GCGTGGCTCATGCTTGTGT 61.620 57.895 10.92 0.00 42.44 3.72
677 1933 2.177531 GCGTGGCTCATGCTTGTG 59.822 61.111 10.92 0.00 42.44 3.33
762 2058 5.764192 GGAACTATCTGGAGAGTACGTACAT 59.236 44.000 26.55 15.12 31.82 2.29
763 2059 5.121811 GGAACTATCTGGAGAGTACGTACA 58.878 45.833 26.55 5.32 31.82 2.90
764 2060 5.121811 TGGAACTATCTGGAGAGTACGTAC 58.878 45.833 18.10 18.10 31.82 3.67
930 2286 0.734889 CTTGGGCTTAAGATGCGGTG 59.265 55.000 6.67 0.00 0.00 4.94
1592 6427 6.045318 TGAAATCATCTTCCTCATCTTCGTC 58.955 40.000 0.00 0.00 0.00 4.20
2680 9440 4.644685 ACATTGTTGTTGAAGTAGCAGGTT 59.355 37.500 0.00 0.00 29.55 3.50
2783 9543 3.754965 TGAGGCTATTGTTGCTTTCTGT 58.245 40.909 0.00 0.00 0.00 3.41
3013 9782 3.285484 CTTCTGAGGCCACAATATTGCT 58.715 45.455 15.48 4.26 0.00 3.91
3042 9811 1.686052 GCACACCAAACCATCCTTCAA 59.314 47.619 0.00 0.00 0.00 2.69
3043 9812 1.133513 AGCACACCAAACCATCCTTCA 60.134 47.619 0.00 0.00 0.00 3.02
3367 10227 6.761714 CGCCCTTCAGTATATCTTTGTACTTT 59.238 38.462 0.00 0.00 28.23 2.66
3888 10785 0.991920 GGTGTCTCCCTCCCATTTGA 59.008 55.000 0.00 0.00 0.00 2.69
4866 11780 5.416952 CCATTACCATGGCTCTTCATATTCC 59.583 44.000 13.04 0.00 43.95 3.01
4867 11781 6.506500 CCATTACCATGGCTCTTCATATTC 57.493 41.667 13.04 0.00 43.95 1.75
4956 12193 0.102663 TGTTTACTCGCCACGTGTCA 59.897 50.000 15.65 0.00 35.30 3.58
4961 12198 2.222213 TCATTGTTGTTTACTCGCCACG 59.778 45.455 0.00 0.00 0.00 4.94
4989 12226 3.055385 GTGCCTTATACCAGAAGACACCA 60.055 47.826 0.00 0.00 32.83 4.17
5012 12249 2.000048 TGGTAAAATGAGCCCCTCCTT 59.000 47.619 0.00 0.00 0.00 3.36
5116 12353 2.257371 CGAGTTCGCCGAACCTCA 59.743 61.111 25.05 0.00 42.85 3.86
5228 14977 7.094890 CGTTATAACCCATGACGACTAGATAGT 60.095 40.741 10.01 0.00 46.52 2.12


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

AutoCloner maintained by Alex Coulton.