Multiple sequence alignment - TraesCS3A01G215800

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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 TraesCS3A01G215800 chr3A 100.000 2321 0 0 1 2321 393239214 393236894 0.000000e+00 4287.0
1 TraesCS3A01G215800 chr3A 95.628 915 20 5 1037 1946 435414845 435413946 0.000000e+00 1450.0
2 TraesCS3A01G215800 chr3B 95.900 1561 41 8 517 2069 201499228 201500773 0.000000e+00 2507.0
3 TraesCS3A01G215800 chr3B 95.719 654 27 1 517 1170 544899592 544900244 0.000000e+00 1051.0
4 TraesCS3A01G215800 chr1D 94.365 1473 74 3 517 1988 244393081 244394545 0.000000e+00 2252.0
5 TraesCS3A01G215800 chr1D 96.283 1076 39 1 517 1592 254482667 254483741 0.000000e+00 1764.0
6 TraesCS3A01G215800 chr1D 93.688 301 9 3 2023 2321 244394546 244394838 2.120000e-120 442.0
7 TraesCS3A01G215800 chr5D 97.014 1105 30 1 517 1618 483802086 483800982 0.000000e+00 1855.0
8 TraesCS3A01G215800 chr5D 96.590 1085 34 3 517 1600 6218511 6217429 0.000000e+00 1796.0
9 TraesCS3A01G215800 chr5D 92.278 518 35 5 1 513 560561962 560561445 0.000000e+00 730.0
10 TraesCS3A01G215800 chr5D 93.443 61 3 1 2114 2174 418985403 418985344 3.180000e-14 89.8
11 TraesCS3A01G215800 chr1A 95.327 1177 35 6 517 1688 554472908 554471747 0.000000e+00 1851.0
12 TraesCS3A01G215800 chr1A 96.172 653 10 4 1412 2063 554471482 554470844 0.000000e+00 1053.0
13 TraesCS3A01G215800 chr2D 96.866 1085 33 1 517 1600 643859031 643860115 0.000000e+00 1814.0
14 TraesCS3A01G215800 chr2D 96.338 983 30 2 517 1494 628290826 628289845 0.000000e+00 1611.0
15 TraesCS3A01G215800 chr6D 92.366 524 34 5 3 521 155124437 155124959 0.000000e+00 741.0
16 TraesCS3A01G215800 chr6D 91.778 523 40 3 1 521 254124692 254125213 0.000000e+00 725.0
17 TraesCS3A01G215800 chr6D 94.872 156 4 4 1980 2131 354356040 354356195 8.290000e-60 241.0
18 TraesCS3A01G215800 chr6D 93.519 108 5 2 2120 2225 100540801 100540908 2.390000e-35 159.0
19 TraesCS3A01G215800 chr4A 92.131 521 38 3 3 521 140892450 140892969 0.000000e+00 732.0
20 TraesCS3A01G215800 chr4A 91.635 526 38 5 1 521 16896409 16895885 0.000000e+00 723.0
21 TraesCS3A01G215800 chr4A 91.603 524 39 5 1 521 241822857 241823378 0.000000e+00 719.0
22 TraesCS3A01G215800 chr4A 98.951 286 3 0 1633 1918 73809852 73809567 1.590000e-141 512.0
23 TraesCS3A01G215800 chr4A 95.161 62 3 0 2260 2321 78568421 78568360 5.280000e-17 99.0
24 TraesCS3A01G215800 chr1B 91.794 524 40 3 1 521 36968374 36967851 0.000000e+00 726.0
25 TraesCS3A01G215800 chr4D 91.619 525 38 3 1 521 7823525 7824047 0.000000e+00 721.0
26 TraesCS3A01G215800 chr2A 91.619 525 38 5 1 521 511527308 511526786 0.000000e+00 721.0
27 TraesCS3A01G215800 chr5B 95.864 411 14 3 1628 2038 559429707 559430114 0.000000e+00 662.0
28 TraesCS3A01G215800 chr7B 98.133 375 5 2 1690 2063 300903252 300902879 0.000000e+00 652.0
29 TraesCS3A01G215800 chr7B 95.455 176 5 3 1950 2122 149444836 149445011 6.320000e-71 278.0
30 TraesCS3A01G215800 chr4B 98.397 312 5 0 1669 1980 421404471 421404160 1.210000e-152 549.0
31 TraesCS3A01G215800 chr6A 97.749 311 7 0 1632 1942 495543357 495543047 9.440000e-149 536.0
32 TraesCS3A01G215800 chr6A 97.183 71 2 0 2251 2321 192822596 192822666 1.130000e-23 121.0
33 TraesCS3A01G215800 chr6A 96.296 54 2 0 2268 2321 1715158 1715211 3.180000e-14 89.8
34 TraesCS3A01G215800 chr5A 89.460 389 29 9 1852 2229 11090770 11091157 4.490000e-132 481.0
35 TraesCS3A01G215800 chr5A 96.000 125 5 0 2130 2254 570914791 570914667 1.090000e-48 204.0
36 TraesCS3A01G215800 chr5A 94.624 93 5 0 2229 2321 696746663 696746571 6.680000e-31 145.0
37 TraesCS3A01G215800 chr5A 87.611 113 14 0 2145 2257 644316133 644316021 5.200000e-27 132.0
38 TraesCS3A01G215800 chr6B 89.925 268 19 6 1937 2197 184717871 184718137 2.860000e-89 339.0
39 TraesCS3A01G215800 chr6B 98.182 55 1 0 2135 2189 562109713 562109767 1.900000e-16 97.1
40 TraesCS3A01G215800 chr7D 98.026 152 3 0 2170 2321 509197223 509197374 4.920000e-67 265.0
41 TraesCS3A01G215800 chr7D 98.148 54 1 0 2268 2321 566651351 566651298 6.830000e-16 95.3
42 TraesCS3A01G215800 chr7A 88.688 221 8 6 1977 2194 647448387 647448181 1.060000e-63 254.0


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 TraesCS3A01G215800 chr3A 393236894 393239214 2320 True 4287 4287 100.0000 1 2321 1 chr3A.!!$R1 2320
1 TraesCS3A01G215800 chr3A 435413946 435414845 899 True 1450 1450 95.6280 1037 1946 1 chr3A.!!$R2 909
2 TraesCS3A01G215800 chr3B 201499228 201500773 1545 False 2507 2507 95.9000 517 2069 1 chr3B.!!$F1 1552
3 TraesCS3A01G215800 chr3B 544899592 544900244 652 False 1051 1051 95.7190 517 1170 1 chr3B.!!$F2 653
4 TraesCS3A01G215800 chr1D 254482667 254483741 1074 False 1764 1764 96.2830 517 1592 1 chr1D.!!$F1 1075
5 TraesCS3A01G215800 chr1D 244393081 244394838 1757 False 1347 2252 94.0265 517 2321 2 chr1D.!!$F2 1804
6 TraesCS3A01G215800 chr5D 483800982 483802086 1104 True 1855 1855 97.0140 517 1618 1 chr5D.!!$R3 1101
7 TraesCS3A01G215800 chr5D 6217429 6218511 1082 True 1796 1796 96.5900 517 1600 1 chr5D.!!$R1 1083
8 TraesCS3A01G215800 chr5D 560561445 560561962 517 True 730 730 92.2780 1 513 1 chr5D.!!$R4 512
9 TraesCS3A01G215800 chr1A 554470844 554472908 2064 True 1452 1851 95.7495 517 2063 2 chr1A.!!$R1 1546
10 TraesCS3A01G215800 chr2D 643859031 643860115 1084 False 1814 1814 96.8660 517 1600 1 chr2D.!!$F1 1083
11 TraesCS3A01G215800 chr2D 628289845 628290826 981 True 1611 1611 96.3380 517 1494 1 chr2D.!!$R1 977
12 TraesCS3A01G215800 chr6D 155124437 155124959 522 False 741 741 92.3660 3 521 1 chr6D.!!$F2 518
13 TraesCS3A01G215800 chr6D 254124692 254125213 521 False 725 725 91.7780 1 521 1 chr6D.!!$F3 520
14 TraesCS3A01G215800 chr4A 140892450 140892969 519 False 732 732 92.1310 3 521 1 chr4A.!!$F1 518
15 TraesCS3A01G215800 chr4A 16895885 16896409 524 True 723 723 91.6350 1 521 1 chr4A.!!$R1 520
16 TraesCS3A01G215800 chr4A 241822857 241823378 521 False 719 719 91.6030 1 521 1 chr4A.!!$F2 520
17 TraesCS3A01G215800 chr1B 36967851 36968374 523 True 726 726 91.7940 1 521 1 chr1B.!!$R1 520
18 TraesCS3A01G215800 chr4D 7823525 7824047 522 False 721 721 91.6190 1 521 1 chr4D.!!$F1 520
19 TraesCS3A01G215800 chr2A 511526786 511527308 522 True 721 721 91.6190 1 521 1 chr2A.!!$R1 520

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
513 533 0.256464 ACTCTCGGTGGGAGTAGGAG 59.744 60.0 0.0 0.0 43.6 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2561 0.457853 TGACTCACGATTACGCCTGC 60.458 55.0 0.0 0.0 43.96 4.85 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
89 90 5.658634 TCTGGCTCATGTCTACATAGTTCTT 59.341 40.000 0.00 0.00 34.26 2.52
144 145 5.505654 GGTGGCAATCGGTATTATGAGTTTG 60.506 44.000 0.00 0.00 0.00 2.93
191 192 4.053009 TCAGAGTCCCGGATATGATCAT 57.947 45.455 13.81 13.81 0.00 2.45
293 296 4.476297 TCTAGGTGAGTTCGGGCATATAA 58.524 43.478 0.00 0.00 0.00 0.98
385 391 3.780275 GGGAGGCCTAGGAGGGGT 61.780 72.222 14.75 0.00 35.37 4.95
386 392 2.446802 GGAGGCCTAGGAGGGGTG 60.447 72.222 14.75 0.00 35.37 4.61
387 393 3.164977 GAGGCCTAGGAGGGGTGC 61.165 72.222 14.75 0.00 35.37 5.01
408 420 2.124151 CCCTCAAGCCCAATCCGG 60.124 66.667 0.00 0.00 0.00 5.14
513 533 0.256464 ACTCTCGGTGGGAGTAGGAG 59.744 60.000 0.00 0.00 43.60 3.69
568 588 5.739161 GTCTTTTGTGCCGAAGCTATTTATG 59.261 40.000 0.00 0.00 40.80 1.90
584 604 5.913137 ATTTATGAATCACAGGCCGAAAA 57.087 34.783 0.00 0.00 0.00 2.29
586 606 1.974265 TGAATCACAGGCCGAAAACA 58.026 45.000 0.00 0.00 0.00 2.83
800 821 5.954296 ATGCATGCAGTTATTGATAGACC 57.046 39.130 26.69 0.00 0.00 3.85
855 876 4.037208 GCTAAAGCATTGCATATGTCTGGT 59.963 41.667 11.91 2.76 41.59 4.00
857 878 1.679680 AGCATTGCATATGTCTGGTGC 59.320 47.619 11.91 8.26 39.26 5.01
970 991 1.507562 TGAAAAAGATCGTGCTCGCA 58.492 45.000 2.69 0.00 36.96 5.10
992 1013 6.398918 GCAGTATCTTTTTCACTCAGGACTA 58.601 40.000 0.00 0.00 0.00 2.59
997 1018 6.591750 TCTTTTTCACTCAGGACTAGGTAG 57.408 41.667 0.00 0.00 0.00 3.18
1046 1067 2.091541 AGGTGGTATTCATGTTTGGCG 58.908 47.619 0.00 0.00 0.00 5.69
1075 1096 2.556622 GCTTTGACCGAAATCTTTGGGA 59.443 45.455 10.25 0.00 38.18 4.37
1085 1106 4.415735 GAAATCTTTGGGAACGATTCTGC 58.584 43.478 0.00 0.00 0.00 4.26
1135 1156 1.377690 TCCTTGGGGAAATGCACCTA 58.622 50.000 0.00 0.00 42.26 3.08
1247 1268 0.599558 GCAGCTTGCAAATGGAGTCA 59.400 50.000 11.99 0.00 44.26 3.41
1787 2345 2.874701 GTGGTAGCTGTGAATAGCCATG 59.125 50.000 0.00 0.00 44.76 3.66
2003 2561 8.683550 AAAAAGAGGACGTTTGAAACTTTTAG 57.316 30.769 6.49 0.00 35.86 1.85
2031 2589 4.443063 CGTAATCGTGAGTCAACAAGTGAA 59.557 41.667 0.00 0.00 38.23 3.18
2255 2815 9.712305 ATCCTGATGGTAAGAATTATACTTTCG 57.288 33.333 0.00 0.00 30.46 3.46
2258 2818 8.138365 TGATGGTAAGAATTATACTTTCGTGC 57.862 34.615 0.00 0.00 30.46 5.34
2305 2865 3.737774 GCGGTAGAGTAGACGTTTTGTTT 59.262 43.478 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 5.907207 TCAAGAACTATGTAGACATGAGCC 58.093 41.667 0.00 0.00 37.15 4.70
70 71 6.758886 GGGTTCAAGAACTATGTAGACATGAG 59.241 42.308 12.22 2.43 40.94 2.90
124 125 5.965334 CACACAAACTCATAATACCGATTGC 59.035 40.000 0.00 0.00 0.00 3.56
144 145 3.562557 ACCTTCGGTACATCAAAACACAC 59.437 43.478 0.00 0.00 32.11 3.82
191 192 3.175438 TGAGACTCCTCTTCATGTCCA 57.825 47.619 0.00 0.00 40.10 4.02
200 201 3.165875 TCGACCATTTTGAGACTCCTCT 58.834 45.455 0.00 0.00 40.10 3.69
258 260 1.475280 CACCTAGAACCATTCCGACGA 59.525 52.381 0.00 0.00 0.00 4.20
353 356 1.411501 CCTCCCTCTCTTCTCTCCCAG 60.412 61.905 0.00 0.00 0.00 4.45
386 392 3.607084 ATTGGGCTTGAGGGGGTGC 62.607 63.158 0.00 0.00 0.00 5.01
387 393 1.380380 GATTGGGCTTGAGGGGGTG 60.380 63.158 0.00 0.00 0.00 4.61
498 518 0.323178 GTGACTCCTACTCCCACCGA 60.323 60.000 0.00 0.00 0.00 4.69
513 533 1.092921 TCCGGCGCATAAATGGTGAC 61.093 55.000 10.83 0.00 0.00 3.67
568 588 1.880027 ACTGTTTTCGGCCTGTGATTC 59.120 47.619 0.00 0.00 0.00 2.52
584 604 2.610438 ATGCCCCTTGATTTCACTGT 57.390 45.000 0.00 0.00 0.00 3.55
586 606 4.322057 AGTAATGCCCCTTGATTTCACT 57.678 40.909 0.00 0.00 0.00 3.41
616 636 0.391130 TCTTCACATGTACCCGCAGC 60.391 55.000 0.00 0.00 0.00 5.25
680 700 6.767902 CCCAGTTAAGTAGTCATGCATTACAT 59.232 38.462 13.29 2.37 40.66 2.29
800 821 5.173673 CGGAAATGCATACCATGATTTTTCG 59.826 40.000 18.61 6.75 33.49 3.46
855 876 1.620323 CCGGAGTGGATATGATCTGCA 59.380 52.381 0.00 0.00 42.00 4.41
857 878 3.826729 TGTACCGGAGTGGATATGATCTG 59.173 47.826 9.46 0.00 42.00 2.90
970 991 6.726764 ACCTAGTCCTGAGTGAAAAAGATACT 59.273 38.462 0.00 0.00 0.00 2.12
992 1013 1.500783 AACACCTGGCATGGCTACCT 61.501 55.000 21.08 0.00 0.00 3.08
997 1018 1.318576 GGTATAACACCTGGCATGGC 58.681 55.000 13.29 13.29 44.79 4.40
1046 1067 1.448985 TTCGGTCAAAGCTGGCATAC 58.551 50.000 0.00 0.00 0.00 2.39
1057 1078 2.550606 CGTTCCCAAAGATTTCGGTCAA 59.449 45.455 0.00 0.00 0.00 3.18
1075 1096 5.863397 CACCAAATTGTAATGCAGAATCGTT 59.137 36.000 0.00 0.00 0.00 3.85
1085 1106 5.982890 AGTTCCTCCACCAAATTGTAATG 57.017 39.130 0.00 0.00 0.00 1.90
1135 1156 0.534412 ACTCGATTAGCTGCTGCACT 59.466 50.000 18.42 4.09 42.74 4.40
1170 1191 1.909532 CCTTCGTTACGAGCTTGTACG 59.090 52.381 13.64 18.16 37.14 3.67
2003 2561 0.457853 TGACTCACGATTACGCCTGC 60.458 55.000 0.00 0.00 43.96 4.85
2143 2703 4.836825 TCAAGGATTTCTCGCTCTTGATT 58.163 39.130 0.00 0.00 38.88 2.57
2255 2815 5.968387 AGTCTATAGCGTTGTATTTGCAC 57.032 39.130 0.00 0.00 0.00 4.57
2258 2818 7.584123 GCATTGAAGTCTATAGCGTTGTATTTG 59.416 37.037 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.