Multiple sequence alignment - TraesCS2B01G548500

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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 TraesCS2B01G548500 chr2B 100.000 3519 0 0 1 3519 744387569 744391087 0.000000e+00 6499.0
1 TraesCS2B01G548500 chr2B 91.366 1471 31 18 456 1880 774716549 774715129 0.000000e+00 1925.0
2 TraesCS2B01G548500 chr2B 93.960 1043 26 5 2514 3519 774693764 774692722 0.000000e+00 1543.0
3 TraesCS2B01G548500 chr2B 98.107 317 6 0 2201 2517 774694110 774693794 1.430000e-153 553.0
4 TraesCS2B01G548500 chr2B 82.278 632 42 28 401 968 774944801 774944176 1.900000e-132 483.0
5 TraesCS2B01G548500 chr2B 95.848 289 11 1 1920 2207 774715129 774714841 1.910000e-127 466.0
6 TraesCS2B01G548500 chr2B 80.882 204 28 8 9 204 774945219 774945019 2.190000e-32 150.0
7 TraesCS2B01G548500 chr2B 87.805 123 5 5 1 123 774717028 774716916 6.130000e-28 135.0
8 TraesCS2B01G548500 chr2B 91.549 71 6 0 401 471 774716636 774716566 8.040000e-17 99.0
9 TraesCS2B01G548500 chr2D 92.191 2241 72 31 698 2866 631239708 631237499 0.000000e+00 3073.0
10 TraesCS2B01G548500 chr2D 94.887 665 25 7 9 667 631240461 631239800 0.000000e+00 1031.0
11 TraesCS2B01G548500 chr2D 86.899 603 39 14 2936 3519 631237278 631236697 1.070000e-179 640.0
12 TraesCS2B01G548500 chr2D 80.507 631 54 24 401 968 631480493 631479869 1.510000e-113 420.0
13 TraesCS2B01G548500 chr2D 80.995 442 26 20 579 968 631805415 631805850 7.380000e-77 298.0
14 TraesCS2B01G548500 chr2D 90.863 197 13 4 401 593 631805204 631805399 3.480000e-65 259.0
15 TraesCS2B01G548500 chr2D 92.174 115 7 2 9 123 631804786 631804898 1.010000e-35 161.0
16 TraesCS2B01G548500 chr2D 81.373 204 27 8 9 204 631480911 631480711 4.700000e-34 156.0
17 TraesCS2B01G548500 chr2D 95.890 73 3 0 2864 2936 631237386 631237314 6.170000e-23 119.0
18 TraesCS2B01G548500 chr2D 81.000 100 17 2 3245 3342 435228698 435228599 1.050000e-10 78.7
19 TraesCS2B01G548500 chr2A 92.254 2156 67 26 832 2933 760118694 760120803 0.000000e+00 2964.0
20 TraesCS2B01G548500 chr2A 96.055 583 23 0 2937 3519 760120843 760121425 0.000000e+00 950.0
21 TraesCS2B01G548500 chr2A 96.405 306 10 1 179 484 760118396 760118700 1.460000e-138 503.0
22 TraesCS2B01G548500 chr2A 96.992 133 2 2 9 141 760118260 760118390 4.570000e-54 222.0
23 TraesCS2B01G548500 chr2A 77.866 253 37 9 1806 2051 25586781 25586541 4.740000e-29 139.0
24 TraesCS2B01G548500 chr5D 86.165 1236 104 32 873 2064 518872610 518873822 0.000000e+00 1273.0
25 TraesCS2B01G548500 chr5D 87.089 395 35 4 2118 2510 518873934 518874314 1.940000e-117 433.0
26 TraesCS2B01G548500 chr5B 87.803 1074 99 9 1009 2064 652520521 652521580 0.000000e+00 1229.0
27 TraesCS2B01G548500 chr5B 82.878 403 37 10 2118 2510 652521684 652522064 2.020000e-87 333.0
28 TraesCS2B01G548500 chr5B 78.235 510 77 23 319 816 652519425 652519912 2.660000e-76 296.0
29 TraesCS2B01G548500 chr3A 77.330 794 136 28 1154 1923 629056630 629057403 2.510000e-116 429.0
30 TraesCS2B01G548500 chr3A 81.100 418 67 8 1434 1848 696344426 696344018 1.220000e-84 324.0
31 TraesCS2B01G548500 chr3A 78.808 151 19 7 2525 2663 629015586 629015437 4.840000e-14 89.8
32 TraesCS2B01G548500 chr3A 78.808 151 19 7 2525 2663 696244834 696244685 4.840000e-14 89.8
33 TraesCS2B01G548500 chr5A 81.228 570 72 23 1958 2510 645423314 645423865 9.030000e-116 427.0
34 TraesCS2B01G548500 chr5A 85.271 129 11 4 1796 1924 645423190 645423310 3.690000e-25 126.0
35 TraesCS2B01G548500 chr3B 77.397 730 127 27 1144 1848 744512785 744512069 1.970000e-107 399.0
36 TraesCS2B01G548500 chr3B 77.361 720 127 25 1154 1849 746846928 746847635 9.160000e-106 394.0
37 TraesCS2B01G548500 chr3B 77.266 717 131 24 1154 1848 747384518 747385224 3.290000e-105 392.0
38 TraesCS2B01G548500 chr3B 77.254 721 125 25 1157 1852 744599113 744598407 1.530000e-103 387.0
39 TraesCS2B01G548500 chr3B 76.190 336 45 25 3133 3433 817039855 817040190 1.020000e-30 145.0
40 TraesCS2B01G548500 chr3D 80.164 489 82 9 1434 1921 560640548 560641022 5.590000e-93 351.0
41 TraesCS2B01G548500 chr3D 81.000 100 17 2 3245 3342 545270089 545270188 1.050000e-10 78.7
42 TraesCS2B01G548500 chr6D 75.455 440 81 18 1154 1571 438456912 438457346 4.640000e-44 189.0
43 TraesCS2B01G548500 chr1B 78.229 271 37 16 3093 3342 531186073 531186342 1.690000e-33 154.0
44 TraesCS2B01G548500 chr4A 74.545 330 41 28 3139 3425 284637783 284637454 1.730000e-18 104.0
45 TraesCS2B01G548500 chr7A 75.479 261 30 22 3139 3365 276918408 276918148 2.890000e-16 97.1
46 TraesCS2B01G548500 chrUn 100.000 29 0 0 3171 3199 62161245 62161217 2.000000e-03 54.7


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 TraesCS2B01G548500 chr2B 744387569 744391087 3518 False 6499.000000 6499 100.000000 1 3519 1 chr2B.!!$F1 3518
1 TraesCS2B01G548500 chr2B 774692722 774694110 1388 True 1048.000000 1543 96.033500 2201 3519 2 chr2B.!!$R1 1318
2 TraesCS2B01G548500 chr2B 774714841 774717028 2187 True 656.250000 1925 91.642000 1 2207 4 chr2B.!!$R2 2206
3 TraesCS2B01G548500 chr2B 774944176 774945219 1043 True 316.500000 483 81.580000 9 968 2 chr2B.!!$R3 959
4 TraesCS2B01G548500 chr2D 631236697 631240461 3764 True 1215.750000 3073 92.466750 9 3519 4 chr2D.!!$R2 3510
5 TraesCS2B01G548500 chr2D 631479869 631480911 1042 True 288.000000 420 80.940000 9 968 2 chr2D.!!$R3 959
6 TraesCS2B01G548500 chr2D 631804786 631805850 1064 False 239.333333 298 88.010667 9 968 3 chr2D.!!$F1 959
7 TraesCS2B01G548500 chr2A 760118260 760121425 3165 False 1159.750000 2964 95.426500 9 3519 4 chr2A.!!$F1 3510
8 TraesCS2B01G548500 chr5D 518872610 518874314 1704 False 853.000000 1273 86.627000 873 2510 2 chr5D.!!$F1 1637
9 TraesCS2B01G548500 chr5B 652519425 652522064 2639 False 619.333333 1229 82.972000 319 2510 3 chr5B.!!$F1 2191
10 TraesCS2B01G548500 chr3A 629056630 629057403 773 False 429.000000 429 77.330000 1154 1923 1 chr3A.!!$F1 769
11 TraesCS2B01G548500 chr5A 645423190 645423865 675 False 276.500000 427 83.249500 1796 2510 2 chr5A.!!$F1 714
12 TraesCS2B01G548500 chr3B 744512069 744512785 716 True 399.000000 399 77.397000 1144 1848 1 chr3B.!!$R1 704
13 TraesCS2B01G548500 chr3B 746846928 746847635 707 False 394.000000 394 77.361000 1154 1849 1 chr3B.!!$F1 695
14 TraesCS2B01G548500 chr3B 747384518 747385224 706 False 392.000000 392 77.266000 1154 1848 1 chr3B.!!$F2 694
15 TraesCS2B01G548500 chr3B 744598407 744599113 706 True 387.000000 387 77.254000 1157 1852 1 chr3B.!!$R2 695

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
269 309 0.036952 ACTCCCTGAACATGCACGAG 60.037 55.000 0.0 0.0 0.0 4.18 F
789 1059 1.606668 GCGAAGGTTGATGTGTTTCCA 59.393 47.619 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2765 0.976073 CACCTCCGGGACATACTGGT 60.976 60.0 0.0 0.0 38.12 4.00 R
2701 3679 0.676466 CAGCCTGACGCCATAAACCA 60.676 55.0 0.0 0.0 38.78 3.67 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
34 35 5.221581 TGGTGGTACCTAACTTGAAAGTCTC 60.222 44.000 14.36 0.00 39.58 3.36
113 114 4.037923 GCTGAGAGGATTTGGTGTGAAAAA 59.962 41.667 0.00 0.00 0.00 1.94
169 176 3.270027 TCGTTGGATCTAGCACAAATGG 58.730 45.455 0.00 0.00 0.00 3.16
174 183 3.142174 GGATCTAGCACAAATGGCCTAC 58.858 50.000 3.32 0.00 0.00 3.18
254 294 0.608640 ACGGGTCATTCAGTCACTCC 59.391 55.000 0.00 0.00 0.00 3.85
266 306 1.160137 GTCACTCCCTGAACATGCAC 58.840 55.000 0.00 0.00 0.00 4.57
269 309 0.036952 ACTCCCTGAACATGCACGAG 60.037 55.000 0.00 0.00 0.00 4.18
361 451 4.933505 TCATTTGCCTTGTGTTTGATCA 57.066 36.364 0.00 0.00 0.00 2.92
529 655 2.832129 TCTAGGTTCGAAACAGGATGCT 59.168 45.455 16.95 0.00 42.53 3.79
536 666 4.265904 TCGAAACAGGATGCTTAAGTCA 57.734 40.909 4.02 3.28 42.53 3.41
541 671 6.401153 CGAAACAGGATGCTTAAGTCACTTAC 60.401 42.308 4.02 0.00 42.53 2.34
789 1059 1.606668 GCGAAGGTTGATGTGTTTCCA 59.393 47.619 0.00 0.00 0.00 3.53
871 1474 3.567576 TGTGTTGACATATTTTGGGCG 57.432 42.857 0.00 0.00 0.00 6.13
1259 2015 2.105128 CCTCCTCCGCGACATCAC 59.895 66.667 8.23 0.00 0.00 3.06
1641 2452 4.441695 CGCCTCTTCCTCAGCGCA 62.442 66.667 11.47 0.00 42.31 6.09
1874 2701 2.579201 CATCGTGGCGGAGGTCTT 59.421 61.111 0.00 0.00 0.00 3.01
1875 2702 1.811266 CATCGTGGCGGAGGTCTTG 60.811 63.158 0.00 0.00 0.00 3.02
1876 2703 3.019003 ATCGTGGCGGAGGTCTTGG 62.019 63.158 0.00 0.00 0.00 3.61
1877 2704 4.003788 CGTGGCGGAGGTCTTGGT 62.004 66.667 0.00 0.00 0.00 3.67
1878 2705 2.358737 GTGGCGGAGGTCTTGGTG 60.359 66.667 0.00 0.00 0.00 4.17
1879 2706 3.636231 TGGCGGAGGTCTTGGTGG 61.636 66.667 0.00 0.00 0.00 4.61
1880 2707 3.319198 GGCGGAGGTCTTGGTGGA 61.319 66.667 0.00 0.00 0.00 4.02
1881 2708 2.047179 GCGGAGGTCTTGGTGGAC 60.047 66.667 0.00 0.00 35.66 4.02
1969 2806 2.162681 GTGCTGCAGGGTTAAGATTGT 58.837 47.619 17.12 0.00 0.00 2.71
2015 2852 2.119495 GGATACCTTCAGCCAGGAGAA 58.881 52.381 1.20 0.00 37.39 2.87
2683 3657 9.113838 CAAACTCCAAGTATACAAGAGCATATT 57.886 33.333 5.50 0.51 0.00 1.28
2688 3662 6.933521 CCAAGTATACAAGAGCATATTCAGCT 59.066 38.462 5.50 0.00 46.82 4.24
2697 3671 6.608539 AGAGCATATTCAGCTATGAGTCAT 57.391 37.500 11.12 11.12 43.58 3.06
2701 3679 6.014413 AGCATATTCAGCTATGAGTCATGTCT 60.014 38.462 16.15 9.20 41.32 3.41
2885 3978 8.575589 ACTTGTATCTATCTATCTGCAGTTCAG 58.424 37.037 14.67 9.40 44.21 3.02
2933 4026 5.851177 CCGTGATGTTACATCACAAAACTTC 59.149 40.000 39.69 21.87 46.38 3.01
3275 4424 8.613482 TGTTTAGTCATTCGTTGTAATGAACAA 58.387 29.630 1.65 0.00 45.05 2.83
3375 4524 1.471684 CTCTGAAGCAGCCATTGTTCC 59.528 52.381 0.00 0.00 0.00 3.62
3477 4626 7.134163 TGAGCTGCAAATCAATTATGTTATCG 58.866 34.615 1.02 0.00 0.00 2.92
3498 4647 3.125316 CGAGCTATTGGAGTTGGTTTGAC 59.875 47.826 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.161876 TCAAGTTAGGTACCACCAGCTTA 58.838 43.478 15.94 0.00 41.95 3.09
7 8 2.616524 TCAAGTTAGGTACCACCAGCT 58.383 47.619 15.94 3.18 41.95 4.24
34 35 7.753659 TCTAGAAATTCAACGACTCTAGAGTG 58.246 38.462 29.84 21.74 42.66 3.51
113 114 9.953565 TTAGATTTTAAGTTAGGTACAGCACAT 57.046 29.630 0.00 0.00 0.00 3.21
147 149 3.310774 CCATTTGTGCTAGATCCAACGAG 59.689 47.826 0.00 0.00 0.00 4.18
169 176 4.640201 TCAGCAAATATTCAACAGGTAGGC 59.360 41.667 0.00 0.00 0.00 3.93
174 183 7.201461 CCGAAAAATCAGCAAATATTCAACAGG 60.201 37.037 0.00 0.00 0.00 4.00
236 276 0.108138 GGGAGTGACTGAATGACCCG 60.108 60.000 0.00 0.00 0.00 5.28
254 294 1.081892 CTTCCTCGTGCATGTTCAGG 58.918 55.000 5.68 5.81 0.00 3.86
266 306 4.273480 ACATTGTTGAACAGAACTTCCTCG 59.727 41.667 0.00 0.00 0.00 4.63
269 309 4.504097 GCAACATTGTTGAACAGAACTTCC 59.496 41.667 29.04 6.66 0.00 3.46
536 666 8.422566 GCCCTAAAGAGATGTACAATAGTAAGT 58.577 37.037 0.00 0.00 30.67 2.24
771 1041 8.243289 CATTTATTGGAAACACATCAACCTTC 57.757 34.615 0.00 0.00 42.67 3.46
857 1138 0.028902 GTCGCCGCCCAAAATATGTC 59.971 55.000 0.00 0.00 0.00 3.06
908 1511 0.779997 AGGGTTGGGCATGTTCTTCT 59.220 50.000 0.00 0.00 0.00 2.85
1641 2452 3.083997 GTGTCCGGGAGCCTCCAT 61.084 66.667 13.90 0.00 38.64 3.41
1874 2701 2.040359 TCCACCACCAGTCCACCA 60.040 61.111 0.00 0.00 0.00 4.17
1875 2702 2.430367 GTCCACCACCAGTCCACC 59.570 66.667 0.00 0.00 0.00 4.61
1876 2703 2.030562 CGTCCACCACCAGTCCAC 59.969 66.667 0.00 0.00 0.00 4.02
1877 2704 3.936203 GCGTCCACCACCAGTCCA 61.936 66.667 0.00 0.00 0.00 4.02
1878 2705 4.699522 GGCGTCCACCACCAGTCC 62.700 72.222 0.00 0.00 0.00 3.85
1879 2706 4.699522 GGGCGTCCACCACCAGTC 62.700 72.222 0.00 0.00 0.00 3.51
1932 2765 0.976073 CACCTCCGGGACATACTGGT 60.976 60.000 0.00 0.00 38.12 4.00
1933 2766 1.823295 CACCTCCGGGACATACTGG 59.177 63.158 0.00 0.00 38.29 4.00
2015 2852 2.821969 GTTGCCAATCTCCAAGTCATGT 59.178 45.455 0.00 0.00 0.00 3.21
2279 3210 2.096417 GTCTCGACGTTGGGAAAACATG 60.096 50.000 7.03 0.00 0.00 3.21
2683 3657 3.369175 ACCAGACATGACTCATAGCTGA 58.631 45.455 16.42 0.00 30.79 4.26
2688 3662 5.368145 GCCATAAACCAGACATGACTCATA 58.632 41.667 0.00 0.00 0.00 2.15
2697 3671 1.338674 CCTGACGCCATAAACCAGACA 60.339 52.381 0.00 0.00 0.00 3.41
2701 3679 0.676466 CAGCCTGACGCCATAAACCA 60.676 55.000 0.00 0.00 38.78 3.67
2885 3978 4.348198 GCAACTTGCTAGAGAAATGACC 57.652 45.455 6.50 0.00 40.96 4.02
2933 4026 1.269448 CCAACATTCCAAGGAACACGG 59.731 52.381 3.19 0.00 36.91 4.94
3021 4150 9.450807 CAACAAGTTAAACTCTAACAAGAATGG 57.549 33.333 0.00 0.00 0.00 3.16
3275 4424 9.755804 CCTTTTCTTCTTCTTTTTCAATTAGCT 57.244 29.630 0.00 0.00 0.00 3.32
3375 4524 1.998257 CACACGCACGCAGTTTTCG 60.998 57.895 0.00 0.00 41.61 3.46
3477 4626 4.327680 AGTCAAACCAACTCCAATAGCTC 58.672 43.478 0.00 0.00 0.00 4.09
3498 4647 1.349026 ACAGGACCAGATGACCACAAG 59.651 52.381 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.