Multiple sequence alignment - TraesCS6A01G201300

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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 TraesCS6A01G201300 chr6A 100.000 2384 0 0 1 2384 328975411 328977794 0.000000e+00 4403
1 TraesCS6A01G201300 chr6A 94.176 1820 91 3 1 1805 328989369 328991188 0.000000e+00 2760
2 TraesCS6A01G201300 chr6A 89.479 922 70 12 9 910 252796440 252795526 0.000000e+00 1140
3 TraesCS6A01G201300 chr6A 88.516 923 76 13 9 908 252779699 252778784 0.000000e+00 1090
4 TraesCS6A01G201300 chr6A 82.303 469 55 18 1 450 150995826 150995367 4.810000e-102 381
5 TraesCS6A01G201300 chr6A 90.769 195 15 3 1511 1703 273121208 273121015 8.460000e-65 257
6 TraesCS6A01G201300 chr6A 90.000 190 17 2 1515 1703 273129227 273129039 6.580000e-61 244
7 TraesCS6A01G201300 chr6A 93.701 127 7 1 1568 1694 144635049 144635174 3.130000e-44 189
8 TraesCS6A01G201300 chr6A 90.977 133 7 4 1674 1805 240068505 240068377 8.760000e-40 174
9 TraesCS6A01G201300 chr6A 89.623 106 6 4 1674 1779 140739964 140740064 1.920000e-26 130
10 TraesCS6A01G201300 chr7A 94.393 1819 76 6 1 1805 378456059 378457865 0.000000e+00 2771
11 TraesCS6A01G201300 chr7A 99.487 585 3 0 1800 2384 639765239 639765823 0.000000e+00 1064
12 TraesCS6A01G201300 chr7A 85.730 932 100 23 1 910 493103222 493104142 0.000000e+00 953
13 TraesCS6A01G201300 chr7A 84.081 446 55 13 17 450 632503632 632504073 1.320000e-112 416
14 TraesCS6A01G201300 chr7A 94.737 76 3 1 1469 1543 222125905 222125830 1.500000e-22 117
15 TraesCS6A01G201300 chr2A 92.126 1016 63 9 534 1546 654611196 654612197 0.000000e+00 1417
16 TraesCS6A01G201300 chr2A 92.119 774 56 5 612 1382 300946909 300947680 0.000000e+00 1086
17 TraesCS6A01G201300 chr2A 92.057 768 56 5 618 1382 301198832 301199597 0.000000e+00 1075
18 TraesCS6A01G201300 chr2A 93.023 731 47 4 819 1546 654603390 654604119 0.000000e+00 1064
19 TraesCS6A01G201300 chr2A 91.085 774 64 5 612 1382 300954856 300955627 0.000000e+00 1042
20 TraesCS6A01G201300 chr2A 86.493 422 37 14 1 410 115068632 115068219 1.680000e-121 446
21 TraesCS6A01G201300 chr2A 87.760 384 35 7 9 383 507812495 507812115 2.810000e-119 438
22 TraesCS6A01G201300 chr3A 91.675 1009 80 4 537 1543 667920689 667919683 0.000000e+00 1395
23 TraesCS6A01G201300 chr3A 90.981 1009 77 6 537 1543 667908792 667907796 0.000000e+00 1347
24 TraesCS6A01G201300 chr3A 99.145 585 5 0 1800 2384 517103531 517102947 0.000000e+00 1053
25 TraesCS6A01G201300 chr3A 90.550 709 55 2 17 714 22103225 22103932 0.000000e+00 928
26 TraesCS6A01G201300 chr3A 90.510 706 54 3 43 736 243917024 243916320 0.000000e+00 920
27 TraesCS6A01G201300 chr3A 84.397 423 47 13 1 410 571126907 571126491 4.770000e-107 398
28 TraesCS6A01G201300 chr3A 84.397 423 46 14 1 410 571134385 571133970 4.770000e-107 398
29 TraesCS6A01G201300 chr3A 86.598 194 18 8 1515 1703 734275967 734276157 8.640000e-50 207
30 TraesCS6A01G201300 chr3A 85.938 192 21 6 1515 1703 371177883 371178071 1.450000e-47 200
31 TraesCS6A01G201300 chr5A 88.423 907 84 13 17 907 484422087 484422988 0.000000e+00 1074
32 TraesCS6A01G201300 chr5A 98.480 592 8 1 1793 2384 2081448 2080858 0.000000e+00 1042
33 TraesCS6A01G201300 chr5A 90.323 744 57 8 1 730 168463948 168464690 0.000000e+00 961
34 TraesCS6A01G201300 chr5A 89.034 611 61 5 537 1145 136738961 136738355 0.000000e+00 752
35 TraesCS6A01G201300 chr5A 86.580 231 25 4 1511 1736 239967617 239967388 1.410000e-62 250
36 TraesCS6A01G201300 chr5A 85.646 209 25 3 1532 1736 239986986 239986779 5.160000e-52 215
37 TraesCS6A01G201300 chr5A 89.764 127 8 4 1674 1799 438828496 438828618 8.820000e-35 158
38 TraesCS6A01G201300 chr5B 99.316 585 4 0 1800 2384 580378864 580379448 0.000000e+00 1059
39 TraesCS6A01G201300 chr5B 98.803 585 7 0 1800 2384 473816843 473816259 0.000000e+00 1042
40 TraesCS6A01G201300 chr5B 98.803 585 7 0 1800 2384 641826617 641827201 0.000000e+00 1042
41 TraesCS6A01G201300 chr3B 99.145 585 5 0 1800 2384 54309586 54310170 0.000000e+00 1053
42 TraesCS6A01G201300 chr2B 98.974 585 6 0 1800 2384 384098883 384099467 0.000000e+00 1048
43 TraesCS6A01G201300 chr2B 98.803 585 7 0 1800 2384 626241022 626240438 0.000000e+00 1042
44 TraesCS6A01G201300 chr1A 91.071 504 42 3 537 1038 243992591 243992089 0.000000e+00 678
45 TraesCS6A01G201300 chr1A 88.722 133 7 7 1674 1805 259987855 259987730 3.170000e-34 156
46 TraesCS6A01G201300 chr4A 86.019 422 39 14 1 410 393013865 393013452 3.640000e-118 435
47 TraesCS6A01G201300 chr4A 84.762 420 44 14 3 410 152303874 152303463 1.030000e-108 403
48 TraesCS6A01G201300 chr4A 82.571 459 67 9 1 449 498249979 498250434 2.220000e-105 392
49 TraesCS6A01G201300 chr4A 93.204 103 6 1 1703 1805 108260641 108260742 1.480000e-32 150
50 TraesCS6A01G201300 chr7D 95.455 66 3 0 1473 1538 141957744 141957679 3.240000e-19 106


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 TraesCS6A01G201300 chr6A 328975411 328977794 2383 False 4403 4403 100.000 1 2384 1 chr6A.!!$F3 2383
1 TraesCS6A01G201300 chr6A 328989369 328991188 1819 False 2760 2760 94.176 1 1805 1 chr6A.!!$F4 1804
2 TraesCS6A01G201300 chr6A 252795526 252796440 914 True 1140 1140 89.479 9 910 1 chr6A.!!$R4 901
3 TraesCS6A01G201300 chr6A 252778784 252779699 915 True 1090 1090 88.516 9 908 1 chr6A.!!$R3 899
4 TraesCS6A01G201300 chr7A 378456059 378457865 1806 False 2771 2771 94.393 1 1805 1 chr7A.!!$F1 1804
5 TraesCS6A01G201300 chr7A 639765239 639765823 584 False 1064 1064 99.487 1800 2384 1 chr7A.!!$F4 584
6 TraesCS6A01G201300 chr7A 493103222 493104142 920 False 953 953 85.730 1 910 1 chr7A.!!$F2 909
7 TraesCS6A01G201300 chr2A 654611196 654612197 1001 False 1417 1417 92.126 534 1546 1 chr2A.!!$F5 1012
8 TraesCS6A01G201300 chr2A 300946909 300947680 771 False 1086 1086 92.119 612 1382 1 chr2A.!!$F1 770
9 TraesCS6A01G201300 chr2A 301198832 301199597 765 False 1075 1075 92.057 618 1382 1 chr2A.!!$F3 764
10 TraesCS6A01G201300 chr2A 654603390 654604119 729 False 1064 1064 93.023 819 1546 1 chr2A.!!$F4 727
11 TraesCS6A01G201300 chr2A 300954856 300955627 771 False 1042 1042 91.085 612 1382 1 chr2A.!!$F2 770
12 TraesCS6A01G201300 chr3A 667919683 667920689 1006 True 1395 1395 91.675 537 1543 1 chr3A.!!$R6 1006
13 TraesCS6A01G201300 chr3A 667907796 667908792 996 True 1347 1347 90.981 537 1543 1 chr3A.!!$R5 1006
14 TraesCS6A01G201300 chr3A 517102947 517103531 584 True 1053 1053 99.145 1800 2384 1 chr3A.!!$R2 584
15 TraesCS6A01G201300 chr3A 22103225 22103932 707 False 928 928 90.550 17 714 1 chr3A.!!$F1 697
16 TraesCS6A01G201300 chr3A 243916320 243917024 704 True 920 920 90.510 43 736 1 chr3A.!!$R1 693
17 TraesCS6A01G201300 chr5A 484422087 484422988 901 False 1074 1074 88.423 17 907 1 chr5A.!!$F3 890
18 TraesCS6A01G201300 chr5A 2080858 2081448 590 True 1042 1042 98.480 1793 2384 1 chr5A.!!$R1 591
19 TraesCS6A01G201300 chr5A 168463948 168464690 742 False 961 961 90.323 1 730 1 chr5A.!!$F1 729
20 TraesCS6A01G201300 chr5A 136738355 136738961 606 True 752 752 89.034 537 1145 1 chr5A.!!$R2 608
21 TraesCS6A01G201300 chr5B 580378864 580379448 584 False 1059 1059 99.316 1800 2384 1 chr5B.!!$F1 584
22 TraesCS6A01G201300 chr5B 473816259 473816843 584 True 1042 1042 98.803 1800 2384 1 chr5B.!!$R1 584
23 TraesCS6A01G201300 chr5B 641826617 641827201 584 False 1042 1042 98.803 1800 2384 1 chr5B.!!$F2 584
24 TraesCS6A01G201300 chr3B 54309586 54310170 584 False 1053 1053 99.145 1800 2384 1 chr3B.!!$F1 584
25 TraesCS6A01G201300 chr2B 384098883 384099467 584 False 1048 1048 98.974 1800 2384 1 chr2B.!!$F1 584
26 TraesCS6A01G201300 chr2B 626240438 626241022 584 True 1042 1042 98.803 1800 2384 1 chr2B.!!$R1 584
27 TraesCS6A01G201300 chr1A 243992089 243992591 502 True 678 678 91.071 537 1038 1 chr1A.!!$R1 501

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
739 784 0.813184 GTGGTACTTGTCGATCCGGA 59.187 55.0 6.61 6.61 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2027 0.110678 ACCCTAGATCGATCTGCCGA 59.889 55.0 33.22 15.64 43.16 5.54 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
333 369 6.734871 GCATCTCATACATCACACATGCATTT 60.735 38.462 0.00 0.00 36.29 2.32
390 434 1.213094 CGTGCGTTATCGGATGGGTC 61.213 60.000 0.00 0.00 39.95 4.46
453 497 6.349611 GGACGTTTGTAGTGGAAGTAGTCATA 60.350 42.308 0.00 0.00 0.00 2.15
657 702 1.883926 TGATGACTCCAACGTCTTCGA 59.116 47.619 0.00 0.00 39.56 3.71
659 704 1.601166 TGACTCCAACGTCTTCGAGA 58.399 50.000 7.80 0.00 40.62 4.04
739 784 0.813184 GTGGTACTTGTCGATCCGGA 59.187 55.000 6.61 6.61 0.00 5.14
1112 1159 0.608640 GAGAAACGGGAGGAGAAGCA 59.391 55.000 0.00 0.00 0.00 3.91
1128 1175 1.598130 GCACACGGGACAAGAGCTT 60.598 57.895 0.00 0.00 0.00 3.74
1481 1532 1.688884 GGCAGGGAAGCTCCTCTCT 60.689 63.158 0.00 0.00 36.57 3.10
1525 1576 0.469144 GCGAGGGAGAGGGAGAGATT 60.469 60.000 0.00 0.00 0.00 2.40
1568 1619 2.573915 GGTCAAGGGAAAGAGAGGATGT 59.426 50.000 0.00 0.00 0.00 3.06
1585 1636 2.977456 TGCCTGCGTGCGTGAAAT 60.977 55.556 0.00 0.00 0.00 2.17
1619 1670 3.861797 GGGGATCCGGATGCGTGT 61.862 66.667 27.16 0.46 0.00 4.49
1632 1683 2.981302 CGTGTGAGGGAGATGGCA 59.019 61.111 0.00 0.00 0.00 4.92
1761 1812 2.631012 AAATGGGCTGGATCGAGGGC 62.631 60.000 6.88 1.89 0.00 5.19
1788 1839 3.360867 TGCTGGACTCCTTCTCTCTTAG 58.639 50.000 0.00 0.00 0.00 2.18
1961 2012 1.536907 TGACCTTACCCGGCCTTGA 60.537 57.895 0.00 0.00 0.00 3.02
1976 2027 4.881850 CGGCCTTGATTATAGTGGTTTCTT 59.118 41.667 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 17 1.942657 ACATGTCATCCGCAGCATAAC 59.057 47.619 0.00 0.00 0.00 1.89
15 19 1.585297 CACATGTCATCCGCAGCATA 58.415 50.000 0.00 0.00 0.00 3.14
333 369 4.651008 GACGACCGCCCGTGAACA 62.651 66.667 5.09 0.00 43.49 3.18
453 497 1.729470 CGACCCTAGAGCATGCGAGT 61.729 60.000 13.01 4.56 0.00 4.18
657 702 1.160137 GTGTACCACTACCGTCGTCT 58.840 55.000 0.00 0.00 0.00 4.18
659 704 0.593128 GTGTGTACCACTACCGTCGT 59.407 55.000 7.10 0.00 41.11 4.34
710 755 0.459585 CAAGTACCACGATGTCCGGG 60.460 60.000 0.00 0.00 43.93 5.73
739 784 5.367937 ACCAATGCCTAGTATGTCTCAAGAT 59.632 40.000 0.00 0.00 0.00 2.40
770 816 0.105964 TTGGACACACCGAGTTCCTG 59.894 55.000 0.00 0.00 42.61 3.86
930 976 2.750637 GCTCGACCTCTCCGTGGA 60.751 66.667 0.00 0.00 0.00 4.02
980 1026 3.333219 CCTTGGCCCTCTGCTCCA 61.333 66.667 0.00 0.00 40.92 3.86
1069 1116 1.141881 CGCCACCAAGTATCTCGCT 59.858 57.895 0.00 0.00 0.00 4.93
1112 1159 0.318762 GAGAAGCTCTTGTCCCGTGT 59.681 55.000 0.00 0.00 0.00 4.49
1128 1175 3.071206 GAGCAGTCCCGCCAGAGA 61.071 66.667 0.00 0.00 0.00 3.10
1147 1194 0.394565 GACCTTGCAGACTGGTCACT 59.605 55.000 18.79 0.00 46.79 3.41
1184 1231 3.227276 CTCGACCCCGCCAGCTAT 61.227 66.667 0.00 0.00 35.37 2.97
1453 1504 0.620121 CTTCCCTGCCTTCTCCCTCT 60.620 60.000 0.00 0.00 0.00 3.69
1481 1532 2.347490 GCCACCCGCAGAGAAAGA 59.653 61.111 0.00 0.00 37.47 2.52
1525 1576 2.277072 CGCTCCTCCCTCCTCTCA 59.723 66.667 0.00 0.00 0.00 3.27
1551 1602 1.283321 GGCACATCCTCTCTTTCCCTT 59.717 52.381 0.00 0.00 0.00 3.95
1568 1619 1.634757 CTATTTCACGCACGCAGGCA 61.635 55.000 0.00 0.00 0.00 4.75
1585 1636 1.356059 CCCCATCTCCCTCGATCTCTA 59.644 57.143 0.00 0.00 0.00 2.43
1619 1670 3.473647 CCGCTGCCATCTCCCTCA 61.474 66.667 0.00 0.00 0.00 3.86
1788 1839 1.846541 CCGAGAGAAGAAAGATCGGC 58.153 55.000 0.00 0.00 45.47 5.54
1840 1891 0.457166 CGCCGGAGTATGTCGAAACA 60.457 55.000 5.05 0.00 40.38 2.83
1961 2012 5.353394 TCTGCCGAAGAAACCACTATAAT 57.647 39.130 0.00 0.00 29.54 1.28
1976 2027 0.110678 ACCCTAGATCGATCTGCCGA 59.889 55.000 33.22 15.64 43.16 5.54


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

AutoCloner maintained by Alex Coulton.