Multiple sequence alignment - TraesCS6B01G032900

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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 TraesCS6B01G032900 chr6B 100.000 2822 0 0 1 2822 19239076 19241897 0.000000e+00 5212
1 TraesCS6B01G032900 chr6B 90.041 2179 197 11 656 2822 19232567 19234737 0.000000e+00 2804
2 TraesCS6B01G032900 chr6B 95.616 365 16 0 3 367 445269943 445269579 1.130000e-163 586
3 TraesCS6B01G032900 chr6B 89.902 307 13 4 370 660 445269416 445269112 2.050000e-101 379
4 TraesCS6B01G032900 chr6A 85.891 1857 236 13 986 2822 12055269 12057119 0.000000e+00 1954
5 TraesCS6B01G032900 chr6A 81.416 1921 328 20 912 2821 12076664 12078566 0.000000e+00 1543
6 TraesCS6B01G032900 chr6A 85.714 210 12 7 677 886 12076475 12076666 3.680000e-49 206
7 TraesCS6B01G032900 chr6D 83.484 1986 302 14 854 2821 10451932 10453909 0.000000e+00 1827
8 TraesCS6B01G032900 chr6D 95.775 71 3 0 656 726 10451859 10451929 6.390000e-22 115
9 TraesCS6B01G032900 chr1B 83.053 1723 266 15 1095 2797 297056979 297058695 0.000000e+00 1541
10 TraesCS6B01G032900 chr1D 82.278 1721 283 13 1095 2797 203268383 203270099 0.000000e+00 1469
11 TraesCS6B01G032900 chr1A 82.220 1721 284 12 1095 2797 257415478 257417194 0.000000e+00 1463
12 TraesCS6B01G032900 chr5D 79.631 1841 345 20 998 2822 33679558 33677732 0.000000e+00 1295
13 TraesCS6B01G032900 chr2B 99.697 660 2 0 1 660 365957627 365956968 0.000000e+00 1208
14 TraesCS6B01G032900 chr2B 95.394 673 16 1 3 660 56818224 56818896 0.000000e+00 1057
15 TraesCS6B01G032900 chr2B 95.033 604 15 1 4 592 244290455 244291058 0.000000e+00 935
16 TraesCS6B01G032900 chr2B 97.281 331 9 0 3 333 159985787 159986117 1.900000e-156 562
17 TraesCS6B01G032900 chr2B 88.773 383 27 2 292 658 159986035 159986417 3.310000e-124 455
18 TraesCS6B01G032900 chr4B 79.202 1755 344 13 1087 2822 657255594 657253842 0.000000e+00 1199
19 TraesCS6B01G032900 chr4D 79.749 1511 285 14 1098 2590 509510790 509512297 0.000000e+00 1075
20 TraesCS6B01G032900 chr4D 96.677 331 11 0 3 333 234183444 234183114 4.110000e-153 551
21 TraesCS6B01G032900 chr4D 89.385 358 29 8 304 660 234183184 234182835 2.580000e-120 442
22 TraesCS6B01G032900 chr5B 95.691 673 14 1 3 660 331680761 331680089 0.000000e+00 1068
23 TraesCS6B01G032900 chr2A 93.393 333 17 3 3 332 255904996 255905326 3.270000e-134 488
24 TraesCS6B01G032900 chr2A 88.037 326 20 3 292 598 255905242 255905567 4.440000e-98 368
25 TraesCS6B01G032900 chr2D 92.814 334 20 2 3 333 245298491 245298159 5.470000e-132 481
26 TraesCS6B01G032900 chr2D 85.122 410 20 11 292 660 245298244 245297835 5.700000e-102 381


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 TraesCS6B01G032900 chr6B 19239076 19241897 2821 False 5212.0 5212 100.0000 1 2822 1 chr6B.!!$F2 2821
1 TraesCS6B01G032900 chr6B 19232567 19234737 2170 False 2804.0 2804 90.0410 656 2822 1 chr6B.!!$F1 2166
2 TraesCS6B01G032900 chr6B 445269112 445269943 831 True 482.5 586 92.7590 3 660 2 chr6B.!!$R1 657
3 TraesCS6B01G032900 chr6A 12055269 12057119 1850 False 1954.0 1954 85.8910 986 2822 1 chr6A.!!$F1 1836
4 TraesCS6B01G032900 chr6A 12076475 12078566 2091 False 874.5 1543 83.5650 677 2821 2 chr6A.!!$F2 2144
5 TraesCS6B01G032900 chr6D 10451859 10453909 2050 False 971.0 1827 89.6295 656 2821 2 chr6D.!!$F1 2165
6 TraesCS6B01G032900 chr1B 297056979 297058695 1716 False 1541.0 1541 83.0530 1095 2797 1 chr1B.!!$F1 1702
7 TraesCS6B01G032900 chr1D 203268383 203270099 1716 False 1469.0 1469 82.2780 1095 2797 1 chr1D.!!$F1 1702
8 TraesCS6B01G032900 chr1A 257415478 257417194 1716 False 1463.0 1463 82.2200 1095 2797 1 chr1A.!!$F1 1702
9 TraesCS6B01G032900 chr5D 33677732 33679558 1826 True 1295.0 1295 79.6310 998 2822 1 chr5D.!!$R1 1824
10 TraesCS6B01G032900 chr2B 365956968 365957627 659 True 1208.0 1208 99.6970 1 660 1 chr2B.!!$R1 659
11 TraesCS6B01G032900 chr2B 56818224 56818896 672 False 1057.0 1057 95.3940 3 660 1 chr2B.!!$F1 657
12 TraesCS6B01G032900 chr2B 244290455 244291058 603 False 935.0 935 95.0330 4 592 1 chr2B.!!$F2 588
13 TraesCS6B01G032900 chr2B 159985787 159986417 630 False 508.5 562 93.0270 3 658 2 chr2B.!!$F3 655
14 TraesCS6B01G032900 chr4B 657253842 657255594 1752 True 1199.0 1199 79.2020 1087 2822 1 chr4B.!!$R1 1735
15 TraesCS6B01G032900 chr4D 509510790 509512297 1507 False 1075.0 1075 79.7490 1098 2590 1 chr4D.!!$F1 1492
16 TraesCS6B01G032900 chr4D 234182835 234183444 609 True 496.5 551 93.0310 3 660 2 chr4D.!!$R1 657
17 TraesCS6B01G032900 chr5B 331680089 331680761 672 True 1068.0 1068 95.6910 3 660 1 chr5B.!!$R1 657
18 TraesCS6B01G032900 chr2A 255904996 255905567 571 False 428.0 488 90.7150 3 598 2 chr2A.!!$F1 595
19 TraesCS6B01G032900 chr2D 245297835 245298491 656 True 431.0 481 88.9680 3 660 2 chr2D.!!$R1 657

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
87 88 0.6112 TAACTCTGCCAAAGCCGCTA 59.389 50.0 0.0 0.0 38.69 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2365 0.31716 TGACACCGGTGAGCTAGTTG 59.683 55.0 40.21 11.7 0.0 3.16 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
87 88 0.611200 TAACTCTGCCAAAGCCGCTA 59.389 50.000 0.00 0.00 38.69 4.26
764 1047 5.617528 TTAAACACTAGTGGACCTTGACA 57.382 39.130 26.12 0.00 34.19 3.58
771 1054 5.707298 CACTAGTGGACCTTGACATGAAATT 59.293 40.000 15.49 0.00 0.00 1.82
781 1064 6.431234 ACCTTGACATGAAATTTCTGTAGGTC 59.569 38.462 23.04 18.59 30.39 3.85
782 1065 6.430925 CCTTGACATGAAATTTCTGTAGGTCA 59.569 38.462 18.64 17.19 0.00 4.02
783 1066 7.121759 CCTTGACATGAAATTTCTGTAGGTCAT 59.878 37.037 19.02 3.09 0.00 3.06
784 1067 7.615582 TGACATGAAATTTCTGTAGGTCATC 57.384 36.000 18.64 7.67 0.00 2.92
919 1202 3.614092 CACAGACCACATGCTAAATCCT 58.386 45.455 0.00 0.00 0.00 3.24
939 1222 6.642733 TCCTCTCCTGTTGGAAATAATCTT 57.357 37.500 0.00 0.00 42.66 2.40
940 1223 7.032598 TCCTCTCCTGTTGGAAATAATCTTT 57.967 36.000 0.00 0.00 42.66 2.52
941 1224 8.158025 TCCTCTCCTGTTGGAAATAATCTTTA 57.842 34.615 0.00 0.00 42.66 1.85
1045 1331 0.325933 CACAACTGGCATCCTCCTCA 59.674 55.000 0.00 0.00 0.00 3.86
1233 1549 2.226896 CGTCGAATCGCTCAGGCTG 61.227 63.158 8.58 8.58 36.09 4.85
1366 1688 2.218037 CTCGCAGCTGCACTACCTCA 62.218 60.000 36.03 9.52 42.21 3.86
1408 1730 0.627451 TGGCTTCAATGGCTCCATCT 59.373 50.000 1.31 0.00 35.31 2.90
1420 1742 4.519437 CCATCTCGCCGCAGCTCA 62.519 66.667 0.00 0.00 36.60 4.26
1465 1787 3.123804 CTGCGTCTCTACAACAACAACT 58.876 45.455 0.00 0.00 0.00 3.16
1500 1822 1.298014 GTACCAGCTCAGCAGGCTT 59.702 57.895 8.28 0.00 38.85 4.35
1509 1831 1.210204 TCAGCAGGCTTCCCAGGATT 61.210 55.000 0.00 0.00 0.00 3.01
1512 1834 1.034292 GCAGGCTTCCCAGGATTGTC 61.034 60.000 0.00 0.00 0.00 3.18
1549 1874 0.951558 CAACTTTCTCACCAACCCGG 59.048 55.000 0.00 0.00 42.50 5.73
1551 1876 0.841289 ACTTTCTCACCAACCCGGAA 59.159 50.000 0.73 0.00 38.63 4.30
1595 1920 0.955428 CCCACCGTCACCTTCATGTG 60.955 60.000 0.00 0.00 37.59 3.21
1622 1947 0.537188 CTCAACTACCTCACCGGCAT 59.463 55.000 0.00 0.00 35.61 4.40
1630 1955 1.299648 CTCACCGGCATCTTCCCAA 59.700 57.895 0.00 0.00 0.00 4.12
1650 1975 1.514443 GTTCGTTCTCGAGAGCGGG 60.514 63.158 39.10 20.97 46.43 6.13
1729 2054 2.069776 CCAGAGAAGCTCCCCAACA 58.930 57.895 0.00 0.00 0.00 3.33
1785 2110 1.170919 GCCAGATACCGGCGTCTCTA 61.171 60.000 6.01 0.00 40.35 2.43
1924 2255 0.535797 GACGATCCCTCCGGTTCTTT 59.464 55.000 0.00 0.00 0.00 2.52
1936 2267 0.250338 GGTTCTTTGACGGCTCCAGT 60.250 55.000 0.00 0.00 0.00 4.00
2019 2350 0.535335 ACCTCGGCGAGCTCAATTTA 59.465 50.000 30.55 0.00 0.00 1.40
2139 2470 1.270041 GGTCAGATTCCGCCATCTCTC 60.270 57.143 0.00 0.00 30.50 3.20
2238 2569 1.720781 AGGCAACCAAGCTGGAATTT 58.279 45.000 8.91 0.00 40.96 1.82
2252 2583 6.173339 AGCTGGAATTTTTGTATCTCTTCGA 58.827 36.000 0.00 0.00 0.00 3.71
2280 2611 2.040178 CTAACCGGCTCTATCCCAGTT 58.960 52.381 0.00 0.00 0.00 3.16
2322 2653 2.366916 CCTGACTCAGTTGGACTTGTCT 59.633 50.000 5.32 0.00 33.22 3.41
2336 2667 3.609853 ACTTGTCTGTGAACTTGCTCAA 58.390 40.909 0.00 0.00 0.00 3.02
2355 2686 2.367202 GGGTCCGATTCCCAGCTCA 61.367 63.158 4.98 0.00 44.05 4.26
2423 2754 1.065199 GCTCACTGGAATGATCCCACA 60.065 52.381 0.00 0.00 45.95 4.17
2444 2775 1.552337 AGAGATCGGCAACATGACTGT 59.448 47.619 0.00 0.00 37.12 3.55
2488 2819 1.613437 CCAACCATTTTGAAGGCGAGT 59.387 47.619 0.00 0.00 0.00 4.18
2526 2857 5.699915 CACATCGCTCAGGAATCTTCAATAT 59.300 40.000 0.00 0.00 0.00 1.28
2558 2889 5.105554 TGTTTGACAACAACTTTAGTGGCAT 60.106 36.000 0.00 0.00 40.10 4.40
2655 2986 1.541147 CCGCAAAGATTGTGTGATGGT 59.459 47.619 3.31 0.00 39.46 3.55
2656 2987 2.746904 CCGCAAAGATTGTGTGATGGTA 59.253 45.455 3.31 0.00 39.46 3.25
2657 2988 3.190327 CCGCAAAGATTGTGTGATGGTAA 59.810 43.478 3.31 0.00 39.46 2.85
2658 2989 4.320861 CCGCAAAGATTGTGTGATGGTAAA 60.321 41.667 3.31 0.00 39.46 2.01
2720 3053 1.671742 CTGCCACCGTACCTCAAGT 59.328 57.895 0.00 0.00 0.00 3.16
2799 3132 2.586425 CAAGGTGTTTGGTGTCCATCT 58.414 47.619 0.00 0.00 31.53 2.90
2812 3145 4.952335 GGTGTCCATCTCATCTTGGATTTT 59.048 41.667 0.00 0.00 43.61 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
764 1047 6.774656 GGATGGATGACCTACAGAAATTTCAT 59.225 38.462 19.99 10.13 37.04 2.57
771 1054 3.452264 CACTGGATGGATGACCTACAGAA 59.548 47.826 0.00 0.00 36.50 3.02
795 1078 3.058983 CCTTTGGAAAATTTCTTTGCCGC 60.059 43.478 5.65 0.00 42.42 6.53
829 1112 3.677648 CAGCTGCTTGTGGGGTGC 61.678 66.667 0.00 0.00 0.00 5.01
919 1202 9.449719 GACTTAAAGATTATTTCCAACAGGAGA 57.550 33.333 0.00 0.00 31.86 3.71
965 1248 2.502130 TGGTGTGTGAGTGACTACCAAA 59.498 45.455 1.83 0.00 38.65 3.28
1045 1331 2.122768 AGAAATCAAGAGGGCGAGGAT 58.877 47.619 0.00 0.00 0.00 3.24
1296 1618 2.785713 TGTCGTTGAGATCGAACACA 57.214 45.000 10.22 9.87 39.01 3.72
1300 1622 3.713288 AGTTGTTGTCGTTGAGATCGAA 58.287 40.909 0.00 0.00 39.01 3.71
1420 1742 2.600729 CCAGGCCAGAGAGGTTGCT 61.601 63.158 5.01 0.00 40.61 3.91
1423 1745 0.768221 TCAACCAGGCCAGAGAGGTT 60.768 55.000 5.01 8.15 44.74 3.50
1483 1805 1.599047 GAAGCCTGCTGAGCTGGTA 59.401 57.895 27.56 0.00 46.96 3.25
1500 1822 1.912731 TCGAAATGGACAATCCTGGGA 59.087 47.619 0.00 0.00 37.46 4.37
1509 1831 1.002624 GCCCAGGTCGAAATGGACA 60.003 57.895 16.77 0.00 39.02 4.02
1512 1834 1.452108 GGAGCCCAGGTCGAAATGG 60.452 63.158 9.69 9.69 36.27 3.16
1549 1874 0.460459 GAGAACCTGCGGTAGCCTTC 60.460 60.000 0.62 0.00 44.33 3.46
1551 1876 1.609501 TGAGAACCTGCGGTAGCCT 60.610 57.895 0.62 0.15 44.33 4.58
1595 1920 2.427812 GTGAGGTAGTTGAGGTAGAGCC 59.572 54.545 0.00 0.00 37.58 4.70
1622 1947 2.363038 TCGAGAACGAACTTTGGGAAGA 59.637 45.455 0.00 0.00 45.74 2.87
1650 1975 2.100989 AGGTCGAGGTAGGTGATGTTC 58.899 52.381 0.00 0.00 0.00 3.18
1924 2255 2.031012 CAGCAACTGGAGCCGTCA 59.969 61.111 0.00 0.00 0.00 4.35
1936 2267 1.671054 GGTCTAGGCGTTGCAGCAA 60.671 57.895 2.83 2.83 39.27 3.91
2004 2335 1.939934 TCCAATAAATTGAGCTCGCCG 59.060 47.619 9.64 0.00 40.14 6.46
2008 2339 5.884771 GGACAGTTCCAATAAATTGAGCTC 58.115 41.667 6.82 6.82 42.30 4.09
2034 2365 0.317160 TGACACCGGTGAGCTAGTTG 59.683 55.000 40.21 11.70 0.00 3.16
2038 2369 1.218047 GCATGACACCGGTGAGCTA 59.782 57.895 40.21 21.91 0.00 3.32
2110 2441 2.611518 CGGAATCTGACCAGTGAGTTC 58.388 52.381 0.00 0.00 0.00 3.01
2139 2470 1.738099 CTCCGGCCAACTCGTGAAG 60.738 63.158 2.24 0.00 0.00 3.02
2170 2501 2.031191 TGAACGAGTTTCCAAACGCTTC 59.969 45.455 4.69 7.40 43.51 3.86
2238 2569 5.607477 AGGTTGTTGTCGAAGAGATACAAA 58.393 37.500 0.00 0.00 37.71 2.83
2252 2583 0.763035 AGAGCCGGTTAGGTTGTTGT 59.237 50.000 1.90 0.00 43.70 3.32
2280 2611 1.597854 CACCAACTCGCCAAGCTCA 60.598 57.895 0.00 0.00 0.00 4.26
2322 2653 1.476833 GGACCCTTGAGCAAGTTCACA 60.477 52.381 9.18 0.00 36.72 3.58
2336 2667 2.041265 AGCTGGGAATCGGACCCT 59.959 61.111 12.17 0.00 46.82 4.34
2355 2686 1.165270 GCTGCGTGAGTTTACCCAAT 58.835 50.000 0.00 0.00 0.00 3.16
2388 2719 1.048601 TGAGCCGGTTGAAGAAGAGT 58.951 50.000 1.90 0.00 0.00 3.24
2423 2754 2.027745 ACAGTCATGTTGCCGATCTCTT 60.028 45.455 0.00 0.00 35.63 2.85
2444 2775 1.483004 TGACGTCCAAGACTTCCAACA 59.517 47.619 14.12 0.00 31.15 3.33
2488 2819 0.611618 GATGTGATGGTGGTGGGCAA 60.612 55.000 0.00 0.00 0.00 4.52
2526 2857 0.179234 TGTTGTCAAACAGGGCGAGA 59.821 50.000 0.00 0.00 41.41 4.04
2558 2889 1.373435 CCAAGGTCTGCCGGTACAA 59.627 57.895 1.90 0.00 40.50 2.41
2590 2921 2.430921 AAAGCTCGCGTCGGTCAG 60.431 61.111 5.77 0.00 0.00 3.51
2655 2986 4.956085 TGCTGTGAAGTTCTGTAGCTTTA 58.044 39.130 19.71 5.26 32.66 1.85
2656 2987 3.808728 TGCTGTGAAGTTCTGTAGCTTT 58.191 40.909 19.71 0.00 32.66 3.51
2657 2988 3.475566 TGCTGTGAAGTTCTGTAGCTT 57.524 42.857 19.71 0.00 32.66 3.74
2658 2989 3.475566 TTGCTGTGAAGTTCTGTAGCT 57.524 42.857 19.71 0.00 32.66 3.32
2712 3045 1.611673 GGCATGTGCAGTACTTGAGGT 60.612 52.381 7.36 0.00 44.36 3.85
2720 3053 1.484653 ACGGAATAGGCATGTGCAGTA 59.515 47.619 7.36 0.00 44.36 2.74
2799 3132 5.902613 GACATCCACAAAATCCAAGATGA 57.097 39.130 4.91 0.00 36.01 2.92


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

AutoCloner maintained by Alex Coulton.