Multiple sequence alignment - TraesCS6B01G165400

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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 TraesCS6B01G165400 chr6B 100.000 3760 0 0 1 3760 172270137 172266378 0.000000e+00 6944.0
1 TraesCS6B01G165400 chr6B 97.780 1081 24 0 1810 2890 489798392 489799472 0.000000e+00 1864.0
2 TraesCS6B01G165400 chr6B 93.554 1117 65 7 1 1113 559485978 559487091 0.000000e+00 1657.0
3 TraesCS6B01G165400 chr6B 96.396 999 36 0 1423 2421 559487162 559488160 0.000000e+00 1646.0
4 TraesCS6B01G165400 chr6B 98.037 866 17 0 2895 3760 489799802 489800667 0.000000e+00 1506.0
5 TraesCS6B01G165400 chr6B 93.857 407 18 2 3102 3508 275294282 275294681 1.160000e-169 606.0
6 TraesCS6B01G165400 chr6B 93.750 272 14 1 3489 3760 275294721 275294989 4.520000e-109 405.0
7 TraesCS6B01G165400 chr6B 97.468 79 2 0 2895 2973 275294197 275294275 6.550000e-28 135.0
8 TraesCS6B01G165400 chr6B 96.875 64 2 0 2827 2890 275293774 275293837 1.430000e-19 108.0
9 TraesCS6B01G165400 chr4A 95.514 2831 92 8 1 2830 90327132 90329928 0.000000e+00 4492.0
10 TraesCS6B01G165400 chr4A 94.721 2330 86 25 437 2765 95388792 95386499 0.000000e+00 3587.0
11 TraesCS6B01G165400 chr4A 95.759 448 18 1 3030 3476 90343217 90343664 0.000000e+00 721.0
12 TraesCS6B01G165400 chr4A 96.691 272 9 0 3489 3760 90352563 90352834 1.590000e-123 453.0
13 TraesCS6B01G165400 chr4A 96.644 149 5 0 2895 3043 90343053 90343201 8.060000e-62 248.0
14 TraesCS6B01G165400 chr4A 96.875 64 2 0 2827 2890 90342634 90342697 1.430000e-19 108.0
15 TraesCS6B01G165400 chr5A 95.002 2781 111 9 1 2765 616788464 616791232 0.000000e+00 4340.0
16 TraesCS6B01G165400 chr5A 96.063 2489 89 4 1 2488 582939618 582942098 0.000000e+00 4045.0
17 TraesCS6B01G165400 chr5A 93.699 1095 63 6 1 1093 129147818 129148908 0.000000e+00 1635.0
18 TraesCS6B01G165400 chr7B 95.905 1343 55 0 1423 2765 209399821 209401163 0.000000e+00 2176.0
19 TraesCS6B01G165400 chr7B 92.884 1082 68 8 3 1082 648439990 648441064 0.000000e+00 1563.0
20 TraesCS6B01G165400 chr7B 96.875 928 25 3 1846 2773 336598391 336597468 0.000000e+00 1550.0
21 TraesCS6B01G165400 chr7B 95.000 480 22 2 3030 3508 139716074 139715596 0.000000e+00 752.0
22 TraesCS6B01G165400 chr7B 87.821 468 56 1 2304 2770 715228024 715227557 7.100000e-152 547.0
23 TraesCS6B01G165400 chr7B 96.417 307 10 1 3202 3508 336596366 336596061 4.330000e-139 505.0
24 TraesCS6B01G165400 chr7B 95.588 272 12 0 3489 3760 139715556 139715285 1.600000e-118 436.0
25 TraesCS6B01G165400 chr7B 93.407 273 14 2 3489 3760 336596021 336595752 5.850000e-108 401.0
26 TraesCS6B01G165400 chr7B 98.551 69 1 0 2975 3043 139716158 139716090 5.100000e-24 122.0
27 TraesCS6B01G165400 chr7B 98.214 56 1 0 1155 1210 286566581 286566526 8.590000e-17 99.0
28 TraesCS6B01G165400 chr7B 100.000 34 0 0 1177 1210 15070845 15070878 3.140000e-06 63.9
29 TraesCS6B01G165400 chr3D 95.104 1205 53 5 1 1204 189779053 189780252 0.000000e+00 1893.0
30 TraesCS6B01G165400 chr3D 90.722 97 8 1 1211 1306 20088176 20088080 1.100000e-25 128.0
31 TraesCS6B01G165400 chr1D 93.372 1222 66 8 1 1215 442118599 442117386 0.000000e+00 1794.0
32 TraesCS6B01G165400 chr1D 89.047 493 51 1 2317 2809 442107961 442107472 3.210000e-170 608.0
33 TraesCS6B01G165400 chr2D 97.705 1002 23 0 1384 2385 110057614 110056613 0.000000e+00 1724.0
34 TraesCS6B01G165400 chr2D 93.352 1083 68 3 1 1082 548894951 548896030 0.000000e+00 1598.0
35 TraesCS6B01G165400 chr2D 97.436 468 12 0 2298 2765 110056727 110056260 0.000000e+00 798.0
36 TraesCS6B01G165400 chr2D 87.162 148 16 3 3616 3760 30404630 30404777 8.360000e-37 165.0
37 TraesCS6B01G165400 chr1B 88.464 1387 125 14 1423 2809 439538842 439537491 0.000000e+00 1642.0
38 TraesCS6B01G165400 chr2B 97.884 756 14 2 3006 3760 572102197 572101443 0.000000e+00 1306.0
39 TraesCS6B01G165400 chr4B 94.915 472 23 1 3037 3508 314547655 314548125 0.000000e+00 737.0
40 TraesCS6B01G165400 chr4B 94.167 480 26 2 3030 3508 658790093 658789615 0.000000e+00 730.0
41 TraesCS6B01G165400 chr4B 97.987 149 3 0 2895 3043 314547483 314547631 3.730000e-65 259.0
42 TraesCS6B01G165400 chr4B 97.987 149 3 0 2895 3043 658790257 658790109 3.730000e-65 259.0
43 TraesCS6B01G165400 chr4B 96.667 150 5 0 3489 3638 658789575 658789426 2.240000e-62 250.0
44 TraesCS6B01G165400 chr4B 96.000 150 6 0 3489 3638 314548165 314548314 1.040000e-60 244.0
45 TraesCS6B01G165400 chr4B 96.341 82 3 0 3679 3760 314548319 314548400 6.550000e-28 135.0
46 TraesCS6B01G165400 chr4B 98.438 64 1 0 2827 2890 314547055 314547118 3.070000e-21 113.0
47 TraesCS6B01G165400 chr4B 98.438 64 1 0 2827 2890 658790682 658790619 3.070000e-21 113.0
48 TraesCS6B01G165400 chr2A 98.160 326 6 0 3168 3493 100234052 100234377 1.520000e-158 569.0
49 TraesCS6B01G165400 chr2A 95.588 272 12 0 3489 3760 100234431 100234702 1.600000e-118 436.0
50 TraesCS6B01G165400 chr3A 86.957 92 10 1 1316 1405 27778750 27778659 6.640000e-18 102.0
51 TraesCS6B01G165400 chr7A 96.429 56 2 0 1155 1210 77196744 77196799 4.000000e-15 93.5


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 TraesCS6B01G165400 chr6B 172266378 172270137 3759 True 6944.000000 6944 100.000000 1 3760 1 chr6B.!!$R1 3759
1 TraesCS6B01G165400 chr6B 489798392 489800667 2275 False 1685.000000 1864 97.908500 1810 3760 2 chr6B.!!$F2 1950
2 TraesCS6B01G165400 chr6B 559485978 559488160 2182 False 1651.500000 1657 94.975000 1 2421 2 chr6B.!!$F3 2420
3 TraesCS6B01G165400 chr6B 275293774 275294989 1215 False 313.500000 606 95.487500 2827 3760 4 chr6B.!!$F1 933
4 TraesCS6B01G165400 chr4A 90327132 90329928 2796 False 4492.000000 4492 95.514000 1 2830 1 chr4A.!!$F1 2829
5 TraesCS6B01G165400 chr4A 95386499 95388792 2293 True 3587.000000 3587 94.721000 437 2765 1 chr4A.!!$R1 2328
6 TraesCS6B01G165400 chr4A 90342634 90343664 1030 False 359.000000 721 96.426000 2827 3476 3 chr4A.!!$F3 649
7 TraesCS6B01G165400 chr5A 616788464 616791232 2768 False 4340.000000 4340 95.002000 1 2765 1 chr5A.!!$F3 2764
8 TraesCS6B01G165400 chr5A 582939618 582942098 2480 False 4045.000000 4045 96.063000 1 2488 1 chr5A.!!$F2 2487
9 TraesCS6B01G165400 chr5A 129147818 129148908 1090 False 1635.000000 1635 93.699000 1 1093 1 chr5A.!!$F1 1092
10 TraesCS6B01G165400 chr7B 209399821 209401163 1342 False 2176.000000 2176 95.905000 1423 2765 1 chr7B.!!$F2 1342
11 TraesCS6B01G165400 chr7B 648439990 648441064 1074 False 1563.000000 1563 92.884000 3 1082 1 chr7B.!!$F3 1079
12 TraesCS6B01G165400 chr7B 336595752 336598391 2639 True 818.666667 1550 95.566333 1846 3760 3 chr7B.!!$R4 1914
13 TraesCS6B01G165400 chr7B 139715285 139716158 873 True 436.666667 752 96.379667 2975 3760 3 chr7B.!!$R3 785
14 TraesCS6B01G165400 chr3D 189779053 189780252 1199 False 1893.000000 1893 95.104000 1 1204 1 chr3D.!!$F1 1203
15 TraesCS6B01G165400 chr1D 442117386 442118599 1213 True 1794.000000 1794 93.372000 1 1215 1 chr1D.!!$R2 1214
16 TraesCS6B01G165400 chr2D 548894951 548896030 1079 False 1598.000000 1598 93.352000 1 1082 1 chr2D.!!$F2 1081
17 TraesCS6B01G165400 chr2D 110056260 110057614 1354 True 1261.000000 1724 97.570500 1384 2765 2 chr2D.!!$R1 1381
18 TraesCS6B01G165400 chr1B 439537491 439538842 1351 True 1642.000000 1642 88.464000 1423 2809 1 chr1B.!!$R1 1386
19 TraesCS6B01G165400 chr2B 572101443 572102197 754 True 1306.000000 1306 97.884000 3006 3760 1 chr2B.!!$R1 754
20 TraesCS6B01G165400 chr4B 658789426 658790682 1256 True 338.000000 730 96.814750 2827 3638 4 chr4B.!!$R1 811
21 TraesCS6B01G165400 chr4B 314547055 314548400 1345 False 297.600000 737 96.736200 2827 3760 5 chr4B.!!$F1 933
22 TraesCS6B01G165400 chr2A 100234052 100234702 650 False 502.500000 569 96.874000 3168 3760 2 chr2A.!!$F1 592

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
626 633 1.453155 ATTCTTCATGTCGGCACACC 58.547 50.0 0.0 0.0 34.48 4.16 F
1362 1380 2.628657 AGGTCACACAACTCACTCTACC 59.371 50.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1775 2.540383 TGATAGTTCCAGCTGACACCT 58.460 47.619 17.39 7.79 0.00 4.00 R
2890 2982 2.686118 GCAAGGAGCAAGATCAAGGGAT 60.686 50.000 0.00 0.00 44.79 3.85 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
37 38 5.477291 CCCCATCTTAGCTAGTCGATTTCTA 59.523 44.000 0.00 0.00 0.00 2.10
40 41 8.091449 CCCATCTTAGCTAGTCGATTTCTAAAT 58.909 37.037 0.00 0.00 0.00 1.40
120 121 7.450323 TCCTTACTTCCAGGTTTCCATTTTTAG 59.550 37.037 0.00 0.00 32.59 1.85
461 462 2.681706 ACACTCAGTCATTTCTCGCAG 58.318 47.619 0.00 0.00 0.00 5.18
586 593 1.952621 TGTGGAAAGGTCCCTAGGAG 58.047 55.000 11.48 0.00 44.23 3.69
606 613 3.487372 AGTTCTTAAAAAGCGCTTCCCT 58.513 40.909 25.24 13.15 0.00 4.20
626 633 1.453155 ATTCTTCATGTCGGCACACC 58.547 50.000 0.00 0.00 34.48 4.16
723 730 3.755378 GTGATGAGACTTGGCTTGACAAT 59.245 43.478 0.00 0.00 0.00 2.71
740 747 4.100963 TGACAATCAGCCCGATAACATAGT 59.899 41.667 0.00 0.00 32.51 2.12
870 877 2.889045 CCATCCTGAATAGCCAACATGG 59.111 50.000 0.00 0.00 41.55 3.66
965 976 5.878332 TGTAGTGTGTATTGAAATGCAGG 57.122 39.130 0.00 0.00 31.62 4.85
1362 1380 2.628657 AGGTCACACAACTCACTCTACC 59.371 50.000 0.00 0.00 0.00 3.18
1642 1660 3.718434 ACTGAAGCATGGAATAGGATGGA 59.282 43.478 0.00 0.00 0.00 3.41
1757 1775 1.377202 GGATGCCCGCAAACAGAGA 60.377 57.895 0.00 0.00 0.00 3.10
2343 2366 0.835276 TGATGGTCCCAGAGATGCTG 59.165 55.000 0.00 0.00 44.49 4.41
2344 2367 0.835941 GATGGTCCCAGAGATGCTGT 59.164 55.000 0.00 0.00 43.33 4.40
2788 2880 5.366768 AGCTACCTTGTTCCTATTAGCATCA 59.633 40.000 0.00 0.00 35.44 3.07
2893 2989 3.343617 TGACCGTTTGATTCAAGGATCC 58.656 45.455 2.48 2.48 0.00 3.36
3375 4541 6.821388 TGAAGGCACTCTAATATTCTTCTCC 58.179 40.000 10.43 0.60 38.49 3.71
3536 4818 5.067674 GGGCTATGATGAATTGTTGTTGCTA 59.932 40.000 0.00 0.00 0.00 3.49
3669 4951 3.587923 GCAAAATTATGTTGCTGCTGGA 58.412 40.909 12.47 0.00 46.31 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.527507 TCGACTAGCTAAGATGGGGAT 57.472 47.619 0.00 0.00 0.00 3.85
37 38 3.629398 GCTCATCAATGTTCGGAGGATTT 59.371 43.478 0.00 0.00 0.00 2.17
40 41 1.134401 GGCTCATCAATGTTCGGAGGA 60.134 52.381 0.00 0.00 0.00 3.71
120 121 2.029918 AGAAAAGGAATTGTGGAAGCGC 60.030 45.455 0.00 0.00 0.00 5.92
279 280 7.337689 AGTCGCATGCAACCATAATATTATGAT 59.662 33.333 29.23 15.63 42.38 2.45
461 462 0.677842 ATACCGACACCCCGATAAGC 59.322 55.000 0.00 0.00 0.00 3.09
586 593 3.917329 AGGGAAGCGCTTTTTAAGAAC 57.083 42.857 25.84 8.44 0.00 3.01
606 613 2.627945 GGTGTGCCGACATGAAGAATA 58.372 47.619 0.00 0.00 33.63 1.75
626 633 2.416547 ACTTGGTTCTCGATTGAATGCG 59.583 45.455 0.00 0.00 0.00 4.73
723 730 1.070134 GGCACTATGTTATCGGGCTGA 59.930 52.381 0.00 0.00 0.00 4.26
1249 1267 4.689612 AGTGAGCAGTACTTCTTTTGGA 57.310 40.909 0.00 0.00 0.00 3.53
1453 1471 7.650104 GCTCAACATGATAAGAGGAGTTACTAC 59.350 40.741 0.00 0.00 0.00 2.73
1757 1775 2.540383 TGATAGTTCCAGCTGACACCT 58.460 47.619 17.39 7.79 0.00 4.00
2089 2112 4.582701 TTAAAGGCCACACAACAATGAG 57.417 40.909 5.01 0.00 0.00 2.90
2788 2880 9.877178 CTAAAACTGAAGTGACCAGAATATACT 57.123 33.333 0.00 0.00 35.69 2.12
2890 2982 2.686118 GCAAGGAGCAAGATCAAGGGAT 60.686 50.000 0.00 0.00 44.79 3.85
3175 4341 9.382244 GCTGTATATATTAAAGCAAAGTTTCCG 57.618 33.333 8.37 0.00 34.01 4.30
3375 4541 5.689068 GCTTGAGAACCTGATGAAACAAAAG 59.311 40.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.