Multiple sequence alignment - TraesCS6B01G156500

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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 TraesCS6B01G156500 chr6B 100.000 2111 0 0 1 2111 159175491 159177601 0.000000e+00 3899
1 TraesCS6B01G156500 chr6B 98.943 757 7 1 1 756 669044830 669044074 0.000000e+00 1352
2 TraesCS6B01G156500 chr6B 99.070 753 7 0 1 753 712302390 712303142 0.000000e+00 1352
3 TraesCS6B01G156500 chr6B 87.387 444 41 9 866 1306 159133386 159133817 1.450000e-136 496
4 TraesCS6B01G156500 chr6B 85.941 441 50 8 866 1306 159061258 159060830 5.310000e-126 460
5 TraesCS6B01G156500 chr6B 84.528 265 35 4 1359 1619 159060723 159060461 7.470000e-65 257
6 TraesCS6B01G156500 chr6B 85.517 145 10 6 754 889 158276559 158276417 7.850000e-30 141
7 TraesCS6B01G156500 chr5B 99.602 753 3 0 1 753 139344583 139343831 0.000000e+00 1375
8 TraesCS6B01G156500 chr4A 99.469 753 4 0 1 753 585668443 585667691 0.000000e+00 1369
9 TraesCS6B01G156500 chr4A 99.337 754 5 0 1 754 609815076 609815829 0.000000e+00 1365
10 TraesCS6B01G156500 chr4B 99.074 756 7 0 1 756 420205346 420204591 0.000000e+00 1358
11 TraesCS6B01G156500 chr2B 98.280 756 10 1 1 753 10801675 10802430 0.000000e+00 1321
12 TraesCS6B01G156500 chr2B 90.969 753 66 2 1 753 682794034 682793284 0.000000e+00 1013
13 TraesCS6B01G156500 chr3A 97.344 753 20 0 1 753 654384875 654384123 0.000000e+00 1280
14 TraesCS6B01G156500 chr6A 91.398 930 57 16 754 1667 100669780 100670702 0.000000e+00 1253
15 TraesCS6B01G156500 chr6A 85.132 417 39 8 866 1279 100648263 100647867 2.520000e-109 405
16 TraesCS6B01G156500 chr6A 82.530 332 28 8 1659 1961 100671280 100671610 4.470000e-67 265
17 TraesCS6B01G156500 chr6A 78.089 429 42 17 1719 2111 100643796 100643384 7.580000e-55 224
18 TraesCS6B01G156500 chr6D 91.152 825 49 15 755 1563 83441401 83442217 0.000000e+00 1098
19 TraesCS6B01G156500 chr6D 86.918 558 35 14 1592 2111 83442214 83442771 1.800000e-165 592
20 TraesCS6B01G156500 chr6D 87.385 436 43 8 871 1306 83397223 83396800 6.770000e-135 490
21 TraesCS6B01G156500 chr6D 86.091 417 35 11 866 1279 83429704 83430100 5.380000e-116 427
22 TraesCS6B01G156500 chr6D 95.238 84 3 1 1444 1527 83388412 83388330 4.730000e-27 132
23 TraesCS6B01G156500 chr7A 81.552 992 118 33 868 1835 486175730 486176680 0.000000e+00 758
24 TraesCS6B01G156500 chr7B 80.161 993 129 43 865 1835 453125463 453124517 0.000000e+00 680


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 TraesCS6B01G156500 chr6B 159175491 159177601 2110 False 3899.0 3899 100.0000 1 2111 1 chr6B.!!$F2 2110
1 TraesCS6B01G156500 chr6B 669044074 669044830 756 True 1352.0 1352 98.9430 1 756 1 chr6B.!!$R2 755
2 TraesCS6B01G156500 chr6B 712302390 712303142 752 False 1352.0 1352 99.0700 1 753 1 chr6B.!!$F3 752
3 TraesCS6B01G156500 chr6B 159060461 159061258 797 True 358.5 460 85.2345 866 1619 2 chr6B.!!$R3 753
4 TraesCS6B01G156500 chr5B 139343831 139344583 752 True 1375.0 1375 99.6020 1 753 1 chr5B.!!$R1 752
5 TraesCS6B01G156500 chr4A 585667691 585668443 752 True 1369.0 1369 99.4690 1 753 1 chr4A.!!$R1 752
6 TraesCS6B01G156500 chr4A 609815076 609815829 753 False 1365.0 1365 99.3370 1 754 1 chr4A.!!$F1 753
7 TraesCS6B01G156500 chr4B 420204591 420205346 755 True 1358.0 1358 99.0740 1 756 1 chr4B.!!$R1 755
8 TraesCS6B01G156500 chr2B 10801675 10802430 755 False 1321.0 1321 98.2800 1 753 1 chr2B.!!$F1 752
9 TraesCS6B01G156500 chr2B 682793284 682794034 750 True 1013.0 1013 90.9690 1 753 1 chr2B.!!$R1 752
10 TraesCS6B01G156500 chr3A 654384123 654384875 752 True 1280.0 1280 97.3440 1 753 1 chr3A.!!$R1 752
11 TraesCS6B01G156500 chr6A 100669780 100671610 1830 False 759.0 1253 86.9640 754 1961 2 chr6A.!!$F1 1207
12 TraesCS6B01G156500 chr6D 83441401 83442771 1370 False 845.0 1098 89.0350 755 2111 2 chr6D.!!$F2 1356
13 TraesCS6B01G156500 chr7A 486175730 486176680 950 False 758.0 758 81.5520 868 1835 1 chr7A.!!$F1 967
14 TraesCS6B01G156500 chr7B 453124517 453125463 946 True 680.0 680 80.1610 865 1835 1 chr7B.!!$R1 970

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
960 972 0.035458 GCAAGCTAGTGTGGTGGACT 59.965 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2459 0.599991 AAGATGCTGTGTTGACGCGA 60.6 50.0 15.93 0.0 0.0 5.87 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
27 28 1.611673 CCCATCGTTGCAAACCTCTCT 60.612 52.381 0.00 0.00 46.28 3.10
191 192 0.816018 CAACACCACGCAACCACCTA 60.816 55.000 0.00 0.00 0.00 3.08
757 761 5.120830 GCAACTAACTCCTCACAACACTATG 59.879 44.000 0.00 0.00 0.00 2.23
765 769 3.758023 CCTCACAACACTATGAAATGGCA 59.242 43.478 0.00 0.00 0.00 4.92
778 782 3.752222 TGAAATGGCAATTGGAATGCAAC 59.248 39.130 7.72 0.00 45.60 4.17
786 790 4.751098 GCAATTGGAATGCAACTGAAGAAA 59.249 37.500 7.72 0.00 43.29 2.52
823 835 9.624373 ACAAAGAGCTATTCTGTTATCATCAAT 57.376 29.630 0.00 0.00 35.91 2.57
829 841 9.412460 AGCTATTCTGTTATCATCAATCCAAAA 57.588 29.630 0.00 0.00 0.00 2.44
840 852 7.727331 TCATCAATCCAAAAATTGTTTGACC 57.273 32.000 0.64 0.00 37.77 4.02
841 853 7.507829 TCATCAATCCAAAAATTGTTTGACCT 58.492 30.769 0.64 0.00 37.77 3.85
842 854 7.656948 TCATCAATCCAAAAATTGTTTGACCTC 59.343 33.333 0.64 0.00 37.77 3.85
843 855 6.882656 TCAATCCAAAAATTGTTTGACCTCA 58.117 32.000 0.64 0.00 37.77 3.86
844 856 6.985645 TCAATCCAAAAATTGTTTGACCTCAG 59.014 34.615 0.64 0.00 37.77 3.35
845 857 5.275067 TCCAAAAATTGTTTGACCTCAGG 57.725 39.130 0.64 0.00 0.00 3.86
847 859 5.602145 TCCAAAAATTGTTTGACCTCAGGAT 59.398 36.000 0.00 0.00 0.00 3.24
848 860 6.780031 TCCAAAAATTGTTTGACCTCAGGATA 59.220 34.615 0.00 0.00 0.00 2.59
849 861 7.454380 TCCAAAAATTGTTTGACCTCAGGATAT 59.546 33.333 0.00 0.00 0.00 1.63
960 972 0.035458 GCAAGCTAGTGTGGTGGACT 59.965 55.000 0.00 0.00 0.00 3.85
1005 1017 2.769652 ATCGTTGTGGGCACATGGCT 62.770 55.000 0.00 0.00 44.01 4.75
1086 1098 3.947834 CCGAGAAAGGTATGCTTTGGAAT 59.052 43.478 0.00 0.00 0.00 3.01
1124 1136 2.965831 TCTTATAGCTCGGTTGGCTCAT 59.034 45.455 0.00 0.00 40.74 2.90
1134 1146 2.436417 GGTTGGCTCATTGTGCTTCTA 58.564 47.619 10.26 0.00 0.00 2.10
1164 1177 4.243270 CGAGGTGGGACTAAACAAGTTAG 58.757 47.826 0.00 0.00 44.29 2.34
1165 1178 4.021719 CGAGGTGGGACTAAACAAGTTAGA 60.022 45.833 0.28 0.00 41.70 2.10
1166 1179 5.480205 GAGGTGGGACTAAACAAGTTAGAG 58.520 45.833 0.28 0.00 41.70 2.43
1167 1180 4.906060 AGGTGGGACTAAACAAGTTAGAGT 59.094 41.667 0.28 1.38 41.70 3.24
1169 1182 5.699915 GGTGGGACTAAACAAGTTAGAGTTC 59.300 44.000 0.28 1.44 41.70 3.01
1202 1222 0.685097 TAGACCTGCCTCTGCGTTTT 59.315 50.000 0.00 0.00 41.78 2.43
1227 1247 2.640826 ACCGGTTCTCCTGTTTTGGATA 59.359 45.455 0.00 0.00 35.30 2.59
1317 1374 1.496060 TGGCCTGACCATGGTAGTAG 58.504 55.000 19.80 15.95 46.36 2.57
1353 1410 3.496884 TCAAGTAGCCAAAACGACATGAC 59.503 43.478 0.00 0.00 0.00 3.06
1373 1430 5.985911 TGACTAACTAACTAATGCTTCCCC 58.014 41.667 0.00 0.00 0.00 4.81
1431 1523 7.040478 CCGAATGATTCATATTTTAGCCTGGAA 60.040 37.037 5.95 0.00 0.00 3.53
1440 1532 1.663695 TTAGCCTGGAATAGCAACGC 58.336 50.000 0.00 0.00 0.00 4.84
1448 1540 4.130118 CTGGAATAGCAACGCTTCCTAAT 58.870 43.478 7.91 0.00 40.44 1.73
1550 1648 5.139727 TGAACCTGTGAAGACCATTGAAAT 58.860 37.500 0.00 0.00 0.00 2.17
1575 1674 6.382859 TGACATCTAATCTACCCAGTTAGCAA 59.617 38.462 0.00 0.00 0.00 3.91
1600 1700 6.233434 TGTTGTCAGAGAAGTATCTGCAATT 58.767 36.000 12.54 0.00 45.25 2.32
1619 1719 3.328382 TTTCCATGTCGGTTACAGAGG 57.672 47.619 0.00 0.00 42.70 3.69
1695 2382 6.400727 GCGTTCAGCGATACTTTCTTTCTTTA 60.401 38.462 0.00 0.00 44.77 1.85
1704 2391 9.151471 CGATACTTTCTTTCTTTACCTTGATCA 57.849 33.333 0.00 0.00 0.00 2.92
1709 2402 6.554334 TCTTTCTTTACCTTGATCAAACCG 57.446 37.500 9.88 2.66 0.00 4.44
1730 2423 1.863454 CTGTACGCTGATGAATGCCTC 59.137 52.381 0.00 0.00 0.00 4.70
1749 2447 3.565902 CCTCTGTTCAACTGGGAAGAAAC 59.434 47.826 0.00 0.00 0.00 2.78
1761 2459 4.532834 TGGGAAGAAACTAAAGTGCAGTT 58.467 39.130 0.00 0.00 37.85 3.16
1774 2472 1.083401 GCAGTTCGCGTCAACACAG 60.083 57.895 5.77 0.00 0.00 3.66
1784 2482 0.798776 GTCAACACAGCATCTTCGGG 59.201 55.000 0.00 0.00 0.00 5.14
1793 2491 4.687948 CACAGCATCTTCGGGATATTACAG 59.312 45.833 0.00 0.00 32.64 2.74
1819 2517 2.254546 TATACCCCGCAGAAATGCAG 57.745 50.000 0.00 0.00 34.41 4.41
1867 2581 0.592637 TGTTCAATGACAAGCAGCCG 59.407 50.000 0.00 0.00 0.00 5.52
1964 2700 2.891580 TCTTGCCGTCAGACTCTTAAGT 59.108 45.455 1.63 0.00 38.88 2.24
1984 2720 6.827586 AAGTCTTCCTTGACTAGTGACTAG 57.172 41.667 17.61 17.61 45.49 2.57
1997 2733 4.527509 AGTGACTAGACCATTGACACAG 57.472 45.455 0.00 0.00 33.37 3.66
2014 2750 3.136443 ACACAGTGGAGATCCTCACAAAA 59.864 43.478 15.53 0.00 36.82 2.44
2021 2757 4.192317 GGAGATCCTCACAAAATAAGCGT 58.808 43.478 0.00 0.00 31.08 5.07
2027 2763 6.176975 TCCTCACAAAATAAGCGTATGTTG 57.823 37.500 17.83 17.83 39.82 3.33
2057 2793 3.058708 CCCACAGTATATGCTGCATTTCG 60.059 47.826 21.56 7.90 39.96 3.46
2081 2817 5.803237 AGCAGTAATATAACGGCCTAAGT 57.197 39.130 0.00 0.00 40.86 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.072806 AGGTCAGAGCAGCACATCAAA 59.927 47.619 1.66 0.00 0.00 2.69
191 192 2.249139 GTGTAGGAGAGTGTTCCCTGT 58.751 52.381 0.00 0.00 38.02 4.00
757 761 4.004982 AGTTGCATTCCAATTGCCATTTC 58.995 39.130 0.00 0.00 35.55 2.17
786 790 8.728833 CAGAATAGCTCTTTGTCTTGATCTTTT 58.271 33.333 0.00 0.00 29.07 2.27
823 835 4.959210 TCCTGAGGTCAAACAATTTTTGGA 59.041 37.500 0.00 0.00 34.12 3.53
1086 1098 4.664267 AGGAGACCCAGGCCAGCA 62.664 66.667 5.01 0.00 33.88 4.41
1124 1136 2.434185 CCCGCGCTAGAAGCACAA 60.434 61.111 5.56 0.00 42.58 3.33
1164 1177 7.757624 CAGGTCTAATGACTCTGTTAAGAACTC 59.242 40.741 0.00 0.00 42.54 3.01
1165 1178 7.607250 CAGGTCTAATGACTCTGTTAAGAACT 58.393 38.462 0.00 0.00 42.54 3.01
1166 1179 6.311690 GCAGGTCTAATGACTCTGTTAAGAAC 59.688 42.308 12.54 0.00 42.54 3.01
1167 1180 6.398918 GCAGGTCTAATGACTCTGTTAAGAA 58.601 40.000 12.54 0.00 42.54 2.52
1169 1182 5.105146 AGGCAGGTCTAATGACTCTGTTAAG 60.105 44.000 12.54 0.00 42.54 1.85
1202 1222 3.007182 CCAAAACAGGAGAACCGGTAGTA 59.993 47.826 8.00 0.00 43.29 1.82
1227 1247 4.475016 ACTATCACTTAGTTGGGCCAAGAT 59.525 41.667 21.62 18.93 37.96 2.40
1317 1374 7.377766 TGGCTACTTGACAACTTTGATTATC 57.622 36.000 0.00 0.00 0.00 1.75
1353 1410 9.457436 TTTTTAGGGGAAGCATTAGTTAGTTAG 57.543 33.333 0.00 0.00 0.00 2.34
1383 1468 1.139853 GAGCTGCCAGGTGCTAGTAAT 59.860 52.381 0.00 0.00 39.91 1.89
1431 1523 7.625828 AAACTAAATTAGGAAGCGTTGCTAT 57.374 32.000 4.92 0.00 38.25 2.97
1550 1648 5.897250 TGCTAACTGGGTAGATTAGATGTCA 59.103 40.000 0.00 0.00 0.00 3.58
1575 1674 5.411831 TGCAGATACTTCTCTGACAACAT 57.588 39.130 5.31 0.00 44.48 2.71
1600 1700 1.553248 CCCTCTGTAACCGACATGGAA 59.447 52.381 0.00 0.00 42.00 3.53
1695 2382 2.423577 GTACAGCGGTTTGATCAAGGT 58.576 47.619 8.41 0.00 0.00 3.50
1730 2423 6.318900 ACTTTAGTTTCTTCCCAGTTGAACAG 59.681 38.462 0.00 0.00 0.00 3.16
1749 2447 1.136690 TGACGCGAACTGCACTTTAG 58.863 50.000 15.93 0.00 46.97 1.85
1761 2459 0.599991 AAGATGCTGTGTTGACGCGA 60.600 50.000 15.93 0.00 0.00 5.87
1774 2472 3.664107 TGCTGTAATATCCCGAAGATGC 58.336 45.455 0.00 0.00 36.33 3.91
1784 2482 6.258068 GCGGGGTATATTTCTGCTGTAATATC 59.742 42.308 15.47 9.59 31.59 1.63
1793 2491 2.543777 TCTGCGGGGTATATTTCTGC 57.456 50.000 0.00 0.00 0.00 4.26
1867 2581 4.095483 CAGTGACAGAAACATAATCAGGCC 59.905 45.833 0.00 0.00 0.00 5.19
1964 2700 5.222068 TGGTCTAGTCACTAGTCAAGGAAGA 60.222 44.000 11.77 0.00 35.72 2.87
1977 2713 3.990469 CACTGTGTCAATGGTCTAGTCAC 59.010 47.826 0.00 0.00 0.00 3.67
1978 2714 3.006859 CCACTGTGTCAATGGTCTAGTCA 59.993 47.826 7.08 0.00 0.00 3.41
1984 2720 2.839486 TCTCCACTGTGTCAATGGTC 57.161 50.000 7.08 0.00 34.89 4.02
1997 2733 4.034510 CGCTTATTTTGTGAGGATCTCCAC 59.965 45.833 9.92 9.92 38.89 4.02
2014 2750 4.335594 GGGAAAAGAGCAACATACGCTTAT 59.664 41.667 0.00 0.00 40.63 1.73
2021 2757 4.098914 ACTGTGGGAAAAGAGCAACATA 57.901 40.909 0.00 0.00 0.00 2.29
2027 2763 4.274459 CAGCATATACTGTGGGAAAAGAGC 59.726 45.833 0.00 0.00 32.78 4.09
2057 2793 6.685657 ACTTAGGCCGTTATATTACTGCTAC 58.314 40.000 7.95 0.00 0.00 3.58
2070 2806 6.412214 ACTTGAACATAATACTTAGGCCGTT 58.588 36.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.