Multiple sequence alignment - TraesCS4B01G368000

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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 TraesCS4B01G368000 chr4B 100.000 2471 0 0 1 2471 654608062 654605592 0.000000e+00 4564.0
1 TraesCS4B01G368000 chr4B 93.375 2098 93 16 1 2077 654812004 654809932 0.000000e+00 3062.0
2 TraesCS4B01G368000 chr4B 94.000 1600 42 22 3 1579 654735530 654733962 0.000000e+00 2374.0
3 TraesCS4B01G368000 chr4B 93.459 1116 44 15 40 1133 656328818 656329926 0.000000e+00 1629.0
4 TraesCS4B01G368000 chr4B 93.577 794 27 11 40 812 656325608 656326398 0.000000e+00 1162.0
5 TraesCS4B01G368000 chr4B 94.968 616 31 0 1136 1751 656329871 656330486 0.000000e+00 966.0
6 TraesCS4B01G368000 chr4B 97.791 498 11 0 1576 2073 654733860 654733363 0.000000e+00 859.0
7 TraesCS4B01G368000 chr4B 95.374 454 21 0 1136 1589 656326744 656327197 0.000000e+00 723.0
8 TraesCS4B01G368000 chr4B 97.468 395 9 1 2077 2471 654731280 654730887 0.000000e+00 673.0
9 TraesCS4B01G368000 chr4B 95.696 395 14 2 2077 2471 655077308 655076917 1.250000e-177 632.0
10 TraesCS4B01G368000 chr4B 93.970 398 20 2 2077 2471 654805920 654805524 1.260000e-167 599.0
11 TraesCS4B01G368000 chr4B 94.798 346 17 1 2126 2471 655107455 655107111 2.800000e-149 538.0
12 TraesCS4B01G368000 chr4B 87.661 389 23 6 1691 2077 654809168 654808803 1.760000e-116 429.0
13 TraesCS4B01G368000 chr4B 85.405 185 22 2 2077 2261 654746079 654745900 1.170000e-43 187.0
14 TraesCS4B01G368000 chr4B 88.793 116 8 2 2077 2192 654647114 654647004 1.190000e-28 137.0
15 TraesCS4B01G368000 chr4B 88.793 116 8 3 2077 2192 654766614 654766504 1.190000e-28 137.0
16 TraesCS4B01G368000 chr4B 98.592 71 1 0 2401 2471 654834540 654834470 2.580000e-25 126.0
17 TraesCS4B01G368000 chrUn 93.638 1116 42 15 40 1133 60682285 60683393 0.000000e+00 1640.0
18 TraesCS4B01G368000 chrUn 93.459 1116 44 15 40 1133 60740036 60741144 0.000000e+00 1629.0
19 TraesCS4B01G368000 chrUn 93.412 1108 51 16 40 1133 221989415 221988316 0.000000e+00 1622.0
20 TraesCS4B01G368000 chrUn 86.883 1357 110 29 547 1875 154538744 154540060 0.000000e+00 1458.0
21 TraesCS4B01G368000 chrUn 86.735 1357 109 30 547 1875 154530762 154532075 0.000000e+00 1443.0
22 TraesCS4B01G368000 chrUn 87.068 1330 100 28 579 1875 201389512 201390802 0.000000e+00 1437.0
23 TraesCS4B01G368000 chrUn 86.490 1362 111 29 547 1875 201383512 201384833 0.000000e+00 1428.0
24 TraesCS4B01G368000 chrUn 86.441 1357 115 28 547 1875 201365314 201366629 0.000000e+00 1423.0
25 TraesCS4B01G368000 chrUn 95.455 616 28 0 1136 1751 60683338 60683953 0.000000e+00 983.0
26 TraesCS4B01G368000 chrUn 94.814 617 30 2 1136 1751 413760678 413760063 0.000000e+00 961.0
27 TraesCS4B01G368000 chrUn 94.805 616 32 0 1136 1751 413773207 413773822 0.000000e+00 961.0
28 TraesCS4B01G368000 chrUn 94.669 619 30 2 1136 1751 416009668 416010286 0.000000e+00 957.0
29 TraesCS4B01G368000 chrUn 94.481 616 34 0 1136 1751 60741089 60741704 0.000000e+00 950.0
30 TraesCS4B01G368000 chrUn 95.525 581 19 3 40 615 359663738 359663160 0.000000e+00 922.0
31 TraesCS4B01G368000 chrUn 91.756 655 28 7 500 1133 413761272 413760623 0.000000e+00 887.0
32 TraesCS4B01G368000 chrUn 91.756 655 28 7 500 1133 413772613 413773262 0.000000e+00 887.0
33 TraesCS4B01G368000 chrUn 92.105 646 26 6 500 1125 416009074 416009714 0.000000e+00 887.0
34 TraesCS4B01G368000 chrUn 89.205 704 60 5 1188 1875 377065803 377065100 0.000000e+00 865.0
35 TraesCS4B01G368000 chrUn 87.500 768 68 10 1136 1875 201387437 201388204 0.000000e+00 861.0
36 TraesCS4B01G368000 chrUn 88.873 710 62 6 1182 1875 154535968 154536676 0.000000e+00 857.0
37 TraesCS4B01G368000 chrUn 85.213 399 36 11 2089 2471 154568464 154568855 2.980000e-104 388.0
38 TraesCS4B01G368000 chrUn 93.151 219 12 2 335 550 154530508 154530726 3.970000e-83 318.0
39 TraesCS4B01G368000 chrUn 89.474 171 15 2 12 182 154524957 154525124 1.920000e-51 213.0
40 TraesCS4B01G368000 chr6A 93.617 47 2 1 1869 1914 134209469 134209423 4.410000e-08 69.4
41 TraesCS4B01G368000 chr6B 92.857 42 3 0 1872 1913 198405147 198405106 7.380000e-06 62.1
42 TraesCS4B01G368000 chr5D 97.222 36 1 0 1886 1921 354840902 354840867 7.380000e-06 62.1
43 TraesCS4B01G368000 chr3A 97.222 36 1 0 1886 1921 489053034 489052999 7.380000e-06 62.1


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 TraesCS4B01G368000 chr4B 654605592 654608062 2470 True 4564.000000 4564 100.000000 1 2471 1 chr4B.!!$R1 2470
1 TraesCS4B01G368000 chr4B 654805524 654812004 6480 True 1363.333333 3062 91.668667 1 2471 3 chr4B.!!$R9 2470
2 TraesCS4B01G368000 chr4B 654730887 654735530 4643 True 1302.000000 2374 96.419667 3 2471 3 chr4B.!!$R8 2468
3 TraesCS4B01G368000 chr4B 656325608 656330486 4878 False 1120.000000 1629 94.344500 40 1751 4 chr4B.!!$F1 1711
4 TraesCS4B01G368000 chrUn 221988316 221989415 1099 True 1622.000000 1622 93.412000 40 1133 1 chrUn.!!$R1 1093
5 TraesCS4B01G368000 chrUn 201365314 201366629 1315 False 1423.000000 1423 86.441000 547 1875 1 chrUn.!!$F3 1328
6 TraesCS4B01G368000 chrUn 60682285 60683953 1668 False 1311.500000 1640 94.546500 40 1751 2 chrUn.!!$F4 1711
7 TraesCS4B01G368000 chrUn 60740036 60741704 1668 False 1289.500000 1629 93.970000 40 1751 2 chrUn.!!$F5 1711
8 TraesCS4B01G368000 chrUn 201383512 201390802 7290 False 1242.000000 1437 87.019333 547 1875 3 chrUn.!!$F7 1328
9 TraesCS4B01G368000 chrUn 154530508 154540060 9552 False 1019.000000 1458 88.910500 335 1875 4 chrUn.!!$F6 1540
10 TraesCS4B01G368000 chrUn 413760063 413761272 1209 True 924.000000 961 93.285000 500 1751 2 chrUn.!!$R4 1251
11 TraesCS4B01G368000 chrUn 413772613 413773822 1209 False 924.000000 961 93.280500 500 1751 2 chrUn.!!$F8 1251
12 TraesCS4B01G368000 chrUn 359663160 359663738 578 True 922.000000 922 95.525000 40 615 1 chrUn.!!$R2 575
13 TraesCS4B01G368000 chrUn 416009074 416010286 1212 False 922.000000 957 93.387000 500 1751 2 chrUn.!!$F9 1251
14 TraesCS4B01G368000 chrUn 377065100 377065803 703 True 865.000000 865 89.205000 1188 1875 1 chrUn.!!$R3 687

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
284 285 0.329596 AAGTGAAGGATGGGCTGACC 59.67 55.0 0.0 0.0 40.81 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 20545 1.537202 GCTTTGATCTCGGTGCAAGTT 59.463 47.619 0.0 0.0 0.0 2.66 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
284 285 0.329596 AAGTGAAGGATGGGCTGACC 59.670 55.000 0.00 0.00 40.81 4.02
310 311 1.667724 GAACGATGCACAGCAGCTAAT 59.332 47.619 5.68 0.00 43.23 1.73
577 3423 2.076622 ATCCGATCTTGAGGGACGCG 62.077 60.000 3.53 3.53 31.52 6.01
629 3479 5.549619 AGAGGAGCCAATAACCAGCTATATT 59.450 40.000 0.00 0.00 36.87 1.28
696 3567 4.703093 TCATGTCTATAGTGGACGTTCACA 59.297 41.667 28.21 14.73 39.93 3.58
760 3633 5.421277 CAAAAATATCAGCCAATTCCAGCA 58.579 37.500 0.00 0.00 0.00 4.41
963 11679 3.871006 ACATACAGCGGTACAATCACATG 59.129 43.478 0.00 0.00 30.94 3.21
1149 15247 2.675242 CCCGGGATACAACTGCCCA 61.675 63.158 18.48 0.00 42.14 5.36
1233 15358 1.228552 GCCACCACCACCATCAACT 60.229 57.895 0.00 0.00 0.00 3.16
1651 15894 5.595257 ACCAAACATGCATGCATATGTAA 57.405 34.783 31.73 3.08 36.56 2.41
1919 16168 6.239600 GGGTACTATCTTTGTGATGGCATCTA 60.240 42.308 26.49 13.92 37.18 1.98
1920 16169 7.390027 GGTACTATCTTTGTGATGGCATCTAT 58.610 38.462 26.49 13.00 37.18 1.98
1921 16170 7.880195 GGTACTATCTTTGTGATGGCATCTATT 59.120 37.037 26.49 7.26 37.18 1.73
1922 16171 7.976135 ACTATCTTTGTGATGGCATCTATTC 57.024 36.000 26.49 14.87 37.18 1.75
1923 16172 6.939163 ACTATCTTTGTGATGGCATCTATTCC 59.061 38.462 26.49 10.83 37.18 3.01
1984 17361 1.214424 GCCAGAGTTAAGGGCCCATTA 59.786 52.381 27.56 16.56 41.90 1.90
2073 17450 2.404789 CGCAGCGCCCATACTTTG 59.595 61.111 2.29 0.00 0.00 2.77
2074 17451 2.398554 CGCAGCGCCCATACTTTGT 61.399 57.895 2.29 0.00 0.00 2.83
2179 20461 4.684485 GCCTATATGCCCCTAGCTTGTATG 60.684 50.000 0.00 0.00 44.23 2.39
2261 20543 6.106673 CGTCATAGTCCACTCCTAAAACATT 58.893 40.000 0.00 0.00 0.00 2.71
2262 20544 6.036083 CGTCATAGTCCACTCCTAAAACATTG 59.964 42.308 0.00 0.00 0.00 2.82
2263 20545 7.103641 GTCATAGTCCACTCCTAAAACATTGA 58.896 38.462 0.00 0.00 0.00 2.57
2399 20681 1.001641 GGCAAGGGAGCTGTGATGT 60.002 57.895 0.00 0.00 34.17 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
284 285 1.133253 CTGTGCATCGTTCCGCTTG 59.867 57.895 0.00 0.00 0.00 4.01
310 311 8.148351 ACTAATCAGCTAACAAAACTGTCTGTA 58.852 33.333 0.00 0.00 33.12 2.74
577 3423 6.765989 TCATATGTGGCACTAAATTGGTAGTC 59.234 38.462 19.83 0.00 31.78 2.59
629 3479 5.453339 GCCAAGTCAACTATGTGCTCCTATA 60.453 44.000 0.00 0.00 0.00 1.31
687 3557 5.530519 TGCTCTCATTATTTGTGAACGTC 57.469 39.130 0.00 0.00 0.00 4.34
790 11504 1.715862 TTTACAACAAGCCACGCGCA 61.716 50.000 5.73 0.00 41.38 6.09
820 11536 0.687427 TGGATCGATGCTCTGACCCA 60.687 55.000 18.23 6.30 0.00 4.51
963 11679 3.329386 TGAGAAAGCTAGTCACATGTGC 58.671 45.455 21.38 15.51 0.00 4.57
1651 15894 7.281549 ACAACTTCAACGTACTTTTATTCCACT 59.718 33.333 0.00 0.00 0.00 4.00
1919 16168 9.722184 CATGAGTTATTCTGATGAGTATGGAAT 57.278 33.333 0.00 0.00 39.54 3.01
1920 16169 8.152898 CCATGAGTTATTCTGATGAGTATGGAA 58.847 37.037 0.00 0.00 39.54 3.53
1921 16170 7.290948 ACCATGAGTTATTCTGATGAGTATGGA 59.709 37.037 0.00 0.00 39.54 3.41
1922 16171 7.387122 CACCATGAGTTATTCTGATGAGTATGG 59.613 40.741 0.00 0.00 39.54 2.74
1923 16172 7.387122 CCACCATGAGTTATTCTGATGAGTATG 59.613 40.741 0.00 0.00 39.54 2.39
1984 17361 2.829120 GAGAGTGGCTCTAGTCCAAACT 59.171 50.000 7.82 9.56 41.35 2.66
2073 17450 1.816224 ACCACAAACTTGACACACCAC 59.184 47.619 0.00 0.00 0.00 4.16
2074 17451 1.815613 CACCACAAACTTGACACACCA 59.184 47.619 0.00 0.00 0.00 4.17
2179 20461 7.375106 ACACAACTTCATCAGATTTCAGATC 57.625 36.000 0.00 0.00 0.00 2.75
2261 20543 2.542020 TTGATCTCGGTGCAAGTTCA 57.458 45.000 0.00 0.00 0.00 3.18
2262 20544 2.413371 GCTTTGATCTCGGTGCAAGTTC 60.413 50.000 0.00 0.00 0.00 3.01
2263 20545 1.537202 GCTTTGATCTCGGTGCAAGTT 59.463 47.619 0.00 0.00 0.00 2.66
2374 20656 0.035152 CAGCTCCCTTGCCATGTGTA 60.035 55.000 0.00 0.00 0.00 2.90
2399 20681 0.107268 ATCGCTGCTGCATGGTATCA 59.893 50.000 16.29 0.00 39.64 2.15


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

AutoCloner maintained by Alex Coulton.