Multiple sequence alignment - TraesCS3D01G318600

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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 TraesCS3D01G318600 chr3D 100.000 2988 0 0 1 2988 432512160 432515147 0.000000e+00 5518
1 TraesCS3D01G318600 chr3D 98.966 870 8 1 1 869 575934941 575934072 0.000000e+00 1555
2 TraesCS3D01G318600 chr3B 94.102 1136 45 10 869 1988 564759013 564760142 0.000000e+00 1707
3 TraesCS3D01G318600 chr3B 81.353 665 90 22 2334 2987 173248870 173249511 7.390000e-141 510
4 TraesCS3D01G318600 chr3B 87.129 303 17 13 2038 2330 564760152 564760442 1.030000e-84 324
5 TraesCS3D01G318600 chr4D 98.970 874 6 2 1 871 481897824 481898697 0.000000e+00 1561
6 TraesCS3D01G318600 chr4D 98.851 870 9 1 1 869 88085451 88086320 0.000000e+00 1550
7 TraesCS3D01G318600 chr4D 98.737 871 6 3 1 869 494279917 494279050 0.000000e+00 1543
8 TraesCS3D01G318600 chr4D 90.239 461 32 8 938 1386 465352078 465351619 9.230000e-165 590
9 TraesCS3D01G318600 chr4D 90.955 398 34 1 996 1393 465161970 465161575 4.380000e-148 534
10 TraesCS3D01G318600 chr4D 90.404 396 36 1 998 1393 465185727 465185334 1.230000e-143 520
11 TraesCS3D01G318600 chr4D 90.625 288 27 0 1698 1985 465157641 465157354 1.680000e-102 383
12 TraesCS3D01G318600 chr4D 89.726 292 30 0 1698 1989 465183710 465183419 1.010000e-99 374
13 TraesCS3D01G318600 chr4D 93.750 144 9 0 1482 1625 465351554 465351411 1.800000e-52 217
14 TraesCS3D01G318600 chr4D 94.118 119 7 0 1507 1625 465161437 465161319 6.580000e-42 182
15 TraesCS3D01G318600 chr7D 99.300 857 6 0 1 857 602729558 602730414 0.000000e+00 1550
16 TraesCS3D01G318600 chr7D 98.736 870 10 1 1 869 626894825 626895694 0.000000e+00 1544
17 TraesCS3D01G318600 chr7D 99.067 857 8 0 1 857 453303366 453302510 0.000000e+00 1539
18 TraesCS3D01G318600 chr7D 98.511 873 9 1 1 869 140812574 140811702 0.000000e+00 1537
19 TraesCS3D01G318600 chr5D 98.400 875 9 2 1 870 486283291 486284165 0.000000e+00 1533
20 TraesCS3D01G318600 chr3A 92.174 805 41 17 869 1664 569890715 569891506 0.000000e+00 1118
21 TraesCS3D01G318600 chr3A 90.798 652 41 11 2340 2987 578929784 578930420 0.000000e+00 854
22 TraesCS3D01G318600 chr3A 94.476 525 23 4 869 1393 570113918 570114436 0.000000e+00 804
23 TraesCS3D01G318600 chr3A 94.878 410 18 1 1665 2074 570114814 570115220 3.250000e-179 638
24 TraesCS3D01G318600 chr3A 92.923 325 18 2 1665 1988 569891549 569891869 4.510000e-128 468
25 TraesCS3D01G318600 chr3A 95.545 202 8 1 2130 2330 570115210 570115411 3.720000e-84 322
26 TraesCS3D01G318600 chr3A 91.441 222 14 4 1437 1656 570114543 570114761 1.740000e-77 300
27 TraesCS3D01G318600 chr2B 93.019 573 32 7 2335 2902 714794372 714794941 0.000000e+00 830
28 TraesCS3D01G318600 chr2B 87.311 662 72 10 2335 2988 771007998 771008655 0.000000e+00 747
29 TraesCS3D01G318600 chr1A 89.394 660 42 12 2335 2988 464126292 464125655 0.000000e+00 806
30 TraesCS3D01G318600 chr7A 87.576 660 65 10 2335 2988 645313047 645313695 0.000000e+00 749
31 TraesCS3D01G318600 chr7A 87.424 660 67 11 2334 2988 729317426 729318074 0.000000e+00 745
32 TraesCS3D01G318600 chr6A 87.367 657 71 9 2335 2988 2591458 2590811 0.000000e+00 743
33 TraesCS3D01G318600 chr6A 86.905 672 72 15 2323 2988 11041074 11040413 0.000000e+00 739
34 TraesCS3D01G318600 chr6A 92.521 361 16 3 1444 1798 166114845 166115200 9.560000e-140 507
35 TraesCS3D01G318600 chr2A 87.160 662 72 10 2335 2988 55475764 55475108 0.000000e+00 739
36 TraesCS3D01G318600 chr4A 90.698 430 34 3 962 1385 5122189 5122618 4.320000e-158 568
37 TraesCS3D01G318600 chr4A 91.960 398 30 1 996 1393 5193111 5193506 9.360000e-155 556
38 TraesCS3D01G318600 chr4A 89.744 312 31 1 1674 1984 5200516 5200827 6.000000e-107 398
39 TraesCS3D01G318600 chr4A 89.274 317 33 1 1674 1989 5122969 5123285 2.160000e-106 396
40 TraesCS3D01G318600 chr4A 90.345 145 14 0 1482 1626 5122699 5122843 1.090000e-44 191
41 TraesCS3D01G318600 chr4B 91.169 419 31 1 973 1385 582023717 582023299 5.590000e-157 564


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 TraesCS3D01G318600 chr3D 432512160 432515147 2987 False 5518.000000 5518 100.000000 1 2988 1 chr3D.!!$F1 2987
1 TraesCS3D01G318600 chr3D 575934072 575934941 869 True 1555.000000 1555 98.966000 1 869 1 chr3D.!!$R1 868
2 TraesCS3D01G318600 chr3B 564759013 564760442 1429 False 1015.500000 1707 90.615500 869 2330 2 chr3B.!!$F2 1461
3 TraesCS3D01G318600 chr3B 173248870 173249511 641 False 510.000000 510 81.353000 2334 2987 1 chr3B.!!$F1 653
4 TraesCS3D01G318600 chr4D 481897824 481898697 873 False 1561.000000 1561 98.970000 1 871 1 chr4D.!!$F2 870
5 TraesCS3D01G318600 chr4D 88085451 88086320 869 False 1550.000000 1550 98.851000 1 869 1 chr4D.!!$F1 868
6 TraesCS3D01G318600 chr4D 494279050 494279917 867 True 1543.000000 1543 98.737000 1 869 1 chr4D.!!$R1 868
7 TraesCS3D01G318600 chr4D 465183419 465185727 2308 True 447.000000 520 90.065000 998 1989 2 chr4D.!!$R3 991
8 TraesCS3D01G318600 chr4D 465351411 465352078 667 True 403.500000 590 91.994500 938 1625 2 chr4D.!!$R4 687
9 TraesCS3D01G318600 chr4D 465157354 465161970 4616 True 366.333333 534 91.899333 996 1985 3 chr4D.!!$R2 989
10 TraesCS3D01G318600 chr7D 602729558 602730414 856 False 1550.000000 1550 99.300000 1 857 1 chr7D.!!$F1 856
11 TraesCS3D01G318600 chr7D 626894825 626895694 869 False 1544.000000 1544 98.736000 1 869 1 chr7D.!!$F2 868
12 TraesCS3D01G318600 chr7D 453302510 453303366 856 True 1539.000000 1539 99.067000 1 857 1 chr7D.!!$R2 856
13 TraesCS3D01G318600 chr7D 140811702 140812574 872 True 1537.000000 1537 98.511000 1 869 1 chr7D.!!$R1 868
14 TraesCS3D01G318600 chr5D 486283291 486284165 874 False 1533.000000 1533 98.400000 1 870 1 chr5D.!!$F1 869
15 TraesCS3D01G318600 chr3A 578929784 578930420 636 False 854.000000 854 90.798000 2340 2987 1 chr3A.!!$F1 647
16 TraesCS3D01G318600 chr3A 569890715 569891869 1154 False 793.000000 1118 92.548500 869 1988 2 chr3A.!!$F2 1119
17 TraesCS3D01G318600 chr3A 570113918 570115411 1493 False 516.000000 804 94.085000 869 2330 4 chr3A.!!$F3 1461
18 TraesCS3D01G318600 chr2B 714794372 714794941 569 False 830.000000 830 93.019000 2335 2902 1 chr2B.!!$F1 567
19 TraesCS3D01G318600 chr2B 771007998 771008655 657 False 747.000000 747 87.311000 2335 2988 1 chr2B.!!$F2 653
20 TraesCS3D01G318600 chr1A 464125655 464126292 637 True 806.000000 806 89.394000 2335 2988 1 chr1A.!!$R1 653
21 TraesCS3D01G318600 chr7A 645313047 645313695 648 False 749.000000 749 87.576000 2335 2988 1 chr7A.!!$F1 653
22 TraesCS3D01G318600 chr7A 729317426 729318074 648 False 745.000000 745 87.424000 2334 2988 1 chr7A.!!$F2 654
23 TraesCS3D01G318600 chr6A 2590811 2591458 647 True 743.000000 743 87.367000 2335 2988 1 chr6A.!!$R1 653
24 TraesCS3D01G318600 chr6A 11040413 11041074 661 True 739.000000 739 86.905000 2323 2988 1 chr6A.!!$R2 665
25 TraesCS3D01G318600 chr2A 55475108 55475764 656 True 739.000000 739 87.160000 2335 2988 1 chr2A.!!$R1 653
26 TraesCS3D01G318600 chr4A 5122189 5123285 1096 False 385.000000 568 90.105667 962 1989 3 chr4A.!!$F3 1027

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
993 1004 0.333312 ACAGTCACAAAACCCCACCA 59.667 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 7426 0.03309 GTTTCGAGAGTTCGGGGTGT 59.967 55.0 0.0 0.0 46.67 4.16 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
73 74 2.047274 ATCGTCAACACTGGCCCG 60.047 61.111 0.00 0.00 0.00 6.13
324 325 0.460284 CCACGCGCTCCAGAAAGTAT 60.460 55.000 5.73 0.00 0.00 2.12
888 889 0.746063 TGTCAGTTTGCCAAGCCAAG 59.254 50.000 0.00 0.00 0.00 3.61
905 906 1.398739 CAAGTCTTCGAGAGCTAGCGA 59.601 52.381 9.55 6.32 34.32 4.93
911 912 4.448395 GTCTTCGAGAGCTAGCGACTATAA 59.552 45.833 9.55 9.41 36.11 0.98
931 936 2.764637 AAATCCCACAGCGTCCCACC 62.765 60.000 0.00 0.00 0.00 4.61
993 1004 0.333312 ACAGTCACAAAACCCCACCA 59.667 50.000 0.00 0.00 0.00 4.17
1257 1274 4.760047 GTGGTGCTCGTCGGCCAT 62.760 66.667 2.24 0.00 33.20 4.40
1377 1394 2.434134 GCCGTCGTACGTGCTTGAG 61.434 63.158 16.05 0.00 40.58 3.02
1423 1477 5.063564 GCGTGGAAGTAGTATTTCCTGAAAG 59.936 44.000 21.28 8.32 43.63 2.62
1429 1483 9.157104 GGAAGTAGTATTTCCTGAAAGAGAAAG 57.843 37.037 15.40 0.00 40.75 2.62
1435 2544 1.352352 TCCTGAAAGAGAAAGCCCCTG 59.648 52.381 0.00 0.00 34.07 4.45
1440 2773 3.330701 TGAAAGAGAAAGCCCCTGTGTAT 59.669 43.478 0.00 0.00 0.00 2.29
1467 2800 5.047188 TGAATGTTTGCTCGCGATCTAATA 58.953 37.500 10.36 7.72 0.00 0.98
1468 2801 5.696270 TGAATGTTTGCTCGCGATCTAATAT 59.304 36.000 10.36 9.93 0.00 1.28
1479 2812 7.210718 TCGCGATCTAATATGTTTTCCTCTA 57.789 36.000 3.71 0.00 0.00 2.43
1480 2813 7.654568 TCGCGATCTAATATGTTTTCCTCTAA 58.345 34.615 3.71 0.00 0.00 2.10
1551 2884 1.445095 CTCAAGATCCCGAGGGCAG 59.555 63.158 2.58 0.00 34.68 4.85
1638 2982 4.091939 GGTACACTCCGCCCACCC 62.092 72.222 0.00 0.00 0.00 4.61
1720 6725 2.266055 GACCTGACGCTGGGAAGG 59.734 66.667 13.66 13.66 35.82 3.46
1904 6909 3.432186 GGATGAGGTGATGGAAATCGACA 60.432 47.826 0.00 0.00 0.00 4.35
1971 6976 4.193334 CCTCGCTGACATCGCCGA 62.193 66.667 0.00 0.00 0.00 5.54
2031 7036 0.605083 AGTCTGCTGCTTGACGATGA 59.395 50.000 16.17 0.00 38.16 2.92
2083 7089 5.064707 CCATCTGTTTACCTTTGATACCGTG 59.935 44.000 0.00 0.00 0.00 4.94
2103 7109 1.212490 CGTTGCCGGCATTTGTGAT 59.788 52.632 33.25 0.00 0.00 3.06
2124 7130 6.536582 GTGATTTGTCACATCTACTGCTGTAT 59.463 38.462 3.72 0.00 40.16 2.29
2129 7135 6.338146 TGTCACATCTACTGCTGTATTTACC 58.662 40.000 3.72 0.00 0.00 2.85
2130 7136 6.154534 TGTCACATCTACTGCTGTATTTACCT 59.845 38.462 3.72 0.00 0.00 3.08
2131 7137 6.477033 GTCACATCTACTGCTGTATTTACCTG 59.523 42.308 3.72 0.00 0.00 4.00
2194 7200 5.236655 TCTACTGCACTCTATTTCAGACG 57.763 43.478 0.00 0.00 0.00 4.18
2208 7218 6.573664 ATTTCAGACGGATGATGTTTCAAA 57.426 33.333 0.00 0.00 34.96 2.69
2271 7286 5.880332 TGAAGATAAATGTTAGTGAGCACCC 59.120 40.000 0.00 0.00 0.00 4.61
2272 7287 4.442706 AGATAAATGTTAGTGAGCACCCG 58.557 43.478 0.00 0.00 0.00 5.28
2330 7345 4.518211 ACTCGTGACCGGGAGTAATATAAG 59.482 45.833 6.32 0.00 41.50 1.73
2331 7346 4.717877 TCGTGACCGGGAGTAATATAAGA 58.282 43.478 6.32 0.00 33.95 2.10
2332 7347 5.319453 TCGTGACCGGGAGTAATATAAGAT 58.681 41.667 6.32 0.00 33.95 2.40
2341 7356 9.857957 CCGGGAGTAATATAAGATAGAGAAAAC 57.142 37.037 0.00 0.00 0.00 2.43
2399 7414 6.803154 AATTTTCGTCCCTCAACTCTAAAG 57.197 37.500 0.00 0.00 0.00 1.85
2407 7422 3.244561 CCCTCAACTCTAAAGCCAGACAA 60.245 47.826 0.00 0.00 0.00 3.18
2411 7426 6.169557 TCAACTCTAAAGCCAGACAAAGTA 57.830 37.500 0.00 0.00 0.00 2.24
2725 7758 1.068083 GGCATCGAAGATGCTCGGA 59.932 57.895 27.25 0.00 45.12 4.55
2836 7926 4.339814 TGTTTTTATTGGCACGACCTTCTT 59.660 37.500 0.00 0.00 40.22 2.52
2871 7961 2.031191 CCACGAAAATATGTACGCACCC 59.969 50.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 2.746362 CAGCAGTGAAAAGATCCACTCC 59.254 50.000 0.00 0.00 41.26 3.85
888 889 1.011333 AGTCGCTAGCTCTCGAAGAC 58.989 55.000 13.93 10.58 36.41 3.01
905 906 4.196971 GGACGCTGTGGGATTTTTATAGT 58.803 43.478 0.00 0.00 0.00 2.12
911 912 0.893727 GTGGGACGCTGTGGGATTTT 60.894 55.000 0.00 0.00 35.02 1.82
931 936 2.887568 GGCTCCGATGTCTGCACG 60.888 66.667 0.00 0.00 0.00 5.34
935 940 2.202797 CCGTGGCTCCGATGTCTG 60.203 66.667 0.00 0.00 0.00 3.51
993 1004 0.892358 CACAAGCCTCCATGTGCACT 60.892 55.000 19.41 0.15 40.32 4.40
1377 1394 2.231964 TCATGGTGGTGTACGTACCTTC 59.768 50.000 22.43 12.54 41.43 3.46
1423 1477 2.239907 AGGAATACACAGGGGCTTTCTC 59.760 50.000 0.00 0.00 0.00 2.87
1429 1483 2.301346 CATTCAGGAATACACAGGGGC 58.699 52.381 0.00 0.00 0.00 5.80
1435 2544 4.651994 CGAGCAAACATTCAGGAATACAC 58.348 43.478 0.00 0.00 0.00 2.90
1440 2773 0.516877 CGCGAGCAAACATTCAGGAA 59.483 50.000 0.00 0.00 0.00 3.36
1551 2884 1.099879 CAGCATGGAAGTAGGCAGCC 61.100 60.000 1.84 1.84 0.00 4.85
1638 2982 2.154198 TCACGTAATGAACAAAGCGACG 59.846 45.455 0.00 0.00 33.02 5.12
1971 6976 3.077359 GGAAGTCAAGCAGCATACTTGT 58.923 45.455 10.73 0.00 43.97 3.16
2103 7109 7.333423 GGTAAATACAGCAGTAGATGTGACAAA 59.667 37.037 0.00 0.00 45.37 2.83
2194 7200 6.628856 CACGATACGATTTTGAAACATCATCC 59.371 38.462 0.00 0.00 0.00 3.51
2208 7218 2.309528 ACATGCACCACGATACGATT 57.690 45.000 0.00 0.00 0.00 3.34
2261 7276 2.359107 CACATGCGGGTGCTCACT 60.359 61.111 0.00 0.00 43.34 3.41
2271 7286 2.194800 AGTATCTGTCGACACATGCG 57.805 50.000 15.76 4.62 0.00 4.73
2272 7287 4.380087 CGATTAGTATCTGTCGACACATGC 59.620 45.833 15.76 13.98 36.25 4.06
2341 7356 7.427030 CGAAGAGTTGAGAGACGAAAAGTATAG 59.573 40.741 0.00 0.00 0.00 1.31
2377 7392 4.695928 GCTTTAGAGTTGAGGGACGAAAAT 59.304 41.667 0.00 0.00 0.00 1.82
2399 7414 0.953960 CGGGGTGTACTTTGTCTGGC 60.954 60.000 0.00 0.00 0.00 4.85
2407 7422 0.886563 CGAGAGTTCGGGGTGTACTT 59.113 55.000 0.00 0.00 43.05 2.24
2411 7426 0.033090 GTTTCGAGAGTTCGGGGTGT 59.967 55.000 0.00 0.00 46.67 4.16
2569 7589 0.959867 TTGCACGCATGTGGCATACT 60.960 50.000 18.81 0.00 46.51 2.12
2725 7758 4.972733 TGCACGCACCTTGCCCAT 62.973 61.111 0.00 0.00 41.12 4.00
2836 7926 2.849294 TCGTGGTCAAATGACATCCA 57.151 45.000 14.93 1.86 46.47 3.41
2871 7961 1.364626 GAAGATGCTCGGGTGTGCAG 61.365 60.000 0.00 0.00 46.58 4.41


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

AutoCloner maintained by Alex Coulton.