Multiple sequence alignment - TraesCS2B01G028700

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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 TraesCS2B01G028700 chr2B 100.000 3835 0 0 722 4556 13337662 13341496 0.000000e+00 7083.0
1 TraesCS2B01G028700 chr2B 96.714 3348 79 5 1239 4556 13388844 13392190 0.000000e+00 5544.0
2 TraesCS2B01G028700 chr2B 93.580 2944 155 18 976 3897 13201680 13204611 0.000000e+00 4359.0
3 TraesCS2B01G028700 chr2B 94.891 2192 88 6 932 3099 13357925 13360116 0.000000e+00 3406.0
4 TraesCS2B01G028700 chr2B 93.799 1145 66 3 2750 3893 13144774 13145914 0.000000e+00 1716.0
5 TraesCS2B01G028700 chr2B 100.000 270 0 0 1 270 13336941 13337210 2.450000e-137 499.0
6 TraesCS2B01G028700 chr2B 97.770 269 6 0 1 269 765538535 765538803 8.930000e-127 464.0
7 TraesCS2B01G028700 chr2B 91.640 311 21 2 932 1237 13379241 13379551 4.210000e-115 425.0
8 TraesCS2B01G028700 chr2B 95.283 212 10 0 722 933 663821804 663822015 2.030000e-88 337.0
9 TraesCS2B01G028700 chr2B 95.238 210 10 0 722 931 779906756 779906965 2.630000e-87 333.0
10 TraesCS2B01G028700 chr2B 94.762 210 11 0 722 931 726486600 726486391 1.220000e-85 327.0
11 TraesCS2B01G028700 chr2B 97.656 128 3 0 4429 4556 13207507 13207634 2.130000e-53 220.0
12 TraesCS2B01G028700 chr2B 93.750 128 8 0 4429 4556 13154044 13154171 4.650000e-45 193.0
13 TraesCS2B01G028700 chr2B 93.077 130 9 0 4236 4365 13152614 13152743 1.670000e-44 191.0
14 TraesCS2B01G028700 chr2B 95.506 89 3 1 4089 4176 798809089 798809001 1.710000e-29 141.0
15 TraesCS2B01G028700 chr2B 100.000 44 0 0 3892 3935 13146043 13146086 1.050000e-11 82.4
16 TraesCS2B01G028700 chr2B 90.000 60 6 0 4493 4552 16773615 16773556 1.360000e-10 78.7
17 TraesCS2B01G028700 chr2D 92.331 2986 203 14 932 3897 9856488 9859467 0.000000e+00 4222.0
18 TraesCS2B01G028700 chr2D 97.398 269 7 0 1 269 640757199 640757467 4.150000e-125 459.0
19 TraesCS2B01G028700 chr2D 95.312 128 6 0 4429 4556 9873263 9873390 2.150000e-48 204.0
20 TraesCS2B01G028700 chr2D 90.769 130 12 0 4236 4365 9872719 9872848 1.680000e-39 174.0
21 TraesCS2B01G028700 chr2A 91.890 2984 214 15 934 3897 9939476 9936501 0.000000e+00 4145.0
22 TraesCS2B01G028700 chr2A 87.786 131 13 1 4429 4556 9904925 9904795 2.840000e-32 150.0
23 TraesCS2B01G028700 chrUn 96.226 424 2 1 2537 2946 476519408 476519831 0.000000e+00 682.0
24 TraesCS2B01G028700 chrUn 93.955 397 24 0 1317 1713 479131598 479131994 6.520000e-168 601.0
25 TraesCS2B01G028700 chrUn 100.000 321 0 0 4236 4556 477356242 477355922 1.090000e-165 593.0
26 TraesCS2B01G028700 chr4A 98.148 270 5 0 1 270 723571487 723571756 5.340000e-129 472.0
27 TraesCS2B01G028700 chr4A 97.070 273 5 2 1 270 737861016 737860744 1.490000e-124 457.0
28 TraesCS2B01G028700 chr7B 97.407 270 7 0 1 270 106591116 106591385 1.150000e-125 460.0
29 TraesCS2B01G028700 chr7B 97.059 272 6 1 1 270 633022336 633022607 1.490000e-124 457.0
30 TraesCS2B01G028700 chr7B 76.153 759 165 13 2748 3499 586967188 586966439 7.150000e-103 385.0
31 TraesCS2B01G028700 chr5D 97.407 270 7 0 1 270 378839985 378839716 1.150000e-125 460.0
32 TraesCS2B01G028700 chr5D 94.444 90 3 2 4098 4186 367998165 367998077 2.210000e-28 137.0
33 TraesCS2B01G028700 chr6B 97.059 272 6 1 1 270 88927255 88926984 1.490000e-124 457.0
34 TraesCS2B01G028700 chr6B 95.215 209 10 0 723 931 715100486 715100278 9.450000e-87 331.0
35 TraesCS2B01G028700 chr6B 92.727 220 16 0 725 944 612747862 612747643 7.360000e-83 318.0
36 TraesCS2B01G028700 chr6B 87.069 116 11 4 4080 4194 468624564 468624676 1.330000e-25 128.0
37 TraesCS2B01G028700 chr6B 87.069 116 11 4 4080 4194 468652657 468652769 1.330000e-25 128.0
38 TraesCS2B01G028700 chr1B 97.059 272 6 1 1 270 648779341 648779612 1.490000e-124 457.0
39 TraesCS2B01G028700 chr1B 95.238 210 10 0 722 931 648779795 648780004 2.630000e-87 333.0
40 TraesCS2B01G028700 chr3B 95.714 210 9 0 722 931 761832776 761832985 5.650000e-89 339.0
41 TraesCS2B01G028700 chr3B 94.762 210 11 0 722 931 58297303 58297094 1.220000e-85 327.0
42 TraesCS2B01G028700 chr3B 94.318 88 5 0 4089 4176 807080266 807080179 7.950000e-28 135.0
43 TraesCS2B01G028700 chr7A 75.706 708 150 17 2748 3445 617703836 617703141 7.300000e-88 335.0
44 TraesCS2B01G028700 chr7A 75.706 708 150 18 2748 3445 625538121 625537426 7.300000e-88 335.0
45 TraesCS2B01G028700 chr5B 95.169 207 10 0 725 931 666651540 666651334 1.220000e-85 327.0
46 TraesCS2B01G028700 chr4B 96.512 86 3 0 4098 4183 376149795 376149710 4.750000e-30 143.0
47 TraesCS2B01G028700 chr5A 96.471 85 3 0 4098 4182 207681836 207681920 1.710000e-29 141.0
48 TraesCS2B01G028700 chr7D 95.402 87 4 0 4098 4184 401541966 401542052 6.150000e-29 139.0


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 TraesCS2B01G028700 chr2B 13336941 13341496 4555 False 3791.0 7083 100.0000 1 4556 2 chr2B.!!$F10 4555
1 TraesCS2B01G028700 chr2B 13388844 13392190 3346 False 5544.0 5544 96.7140 1239 4556 1 chr2B.!!$F3 3317
2 TraesCS2B01G028700 chr2B 13357925 13360116 2191 False 3406.0 3406 94.8910 932 3099 1 chr2B.!!$F1 2167
3 TraesCS2B01G028700 chr2B 13201680 13207634 5954 False 2289.5 4359 95.6180 976 4556 2 chr2B.!!$F9 3580
4 TraesCS2B01G028700 chr2B 13144774 13146086 1312 False 899.2 1716 96.8995 2750 3935 2 chr2B.!!$F7 1185
5 TraesCS2B01G028700 chr2D 9856488 9859467 2979 False 4222.0 4222 92.3310 932 3897 1 chr2D.!!$F1 2965
6 TraesCS2B01G028700 chr2A 9936501 9939476 2975 True 4145.0 4145 91.8900 934 3897 1 chr2A.!!$R2 2963
7 TraesCS2B01G028700 chr7B 586966439 586967188 749 True 385.0 385 76.1530 2748 3499 1 chr7B.!!$R1 751
8 TraesCS2B01G028700 chr1B 648779341 648780004 663 False 395.0 457 96.1485 1 931 2 chr1B.!!$F1 930
9 TraesCS2B01G028700 chr7A 617703141 617703836 695 True 335.0 335 75.7060 2748 3445 1 chr7A.!!$R1 697
10 TraesCS2B01G028700 chr7A 625537426 625538121 695 True 335.0 335 75.7060 2748 3445 1 chr7A.!!$R2 697

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
809 812 0.842030 TGTTGAGGCCCATCTGTCCT 60.842 55.0 0.00 0.00 0.00 3.85 F
1112 1119 0.179048 CTTCGGGCATGCCATGTCTA 60.179 55.0 36.56 14.79 37.98 2.59 F
1630 1638 0.404040 AAGGATTGGCCGGAACAAGA 59.596 50.0 5.05 0.00 43.43 3.02 F
1899 1913 0.466543 CCCCGACGGATCCAACAATA 59.533 55.0 17.49 0.00 0.00 1.90 F
2014 2028 0.810648 GGCTCCATGCGATGTTTTCA 59.189 50.0 0.00 0.00 44.05 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2535 2549 0.930726 AACACCACTTCCTTTCCCCA 59.069 50.000 0.00 0.0 0.00 4.96 R
3077 3106 4.129380 CCTCTCATTGTTGTCAGAACACA 58.871 43.478 0.00 0.0 34.35 3.72 R
3341 3370 2.234143 GCAAGCTCTTTCAACCTCCTT 58.766 47.619 0.00 0.0 0.00 3.36 R
3389 3418 6.280643 CCATTGTAGGACGATCAAAGTCATA 58.719 40.000 0.00 0.0 40.20 2.15 R
4084 6595 6.003859 ATGGGACGGAGTACTATATAGGAG 57.996 45.833 14.25 0.0 42.21 3.69 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
54 55 3.937814 TGACCACGTCATCAATAAAGCT 58.062 40.909 0.00 0.00 37.67 3.74
56 57 3.932710 GACCACGTCATCAATAAAGCTGA 59.067 43.478 0.00 0.00 32.09 4.26
77 78 5.875224 TGAAGAATACCATGTGGAAGTTGA 58.125 37.500 5.96 0.00 38.94 3.18
94 95 4.026052 AGTTGATTTCAAATGCTAGGGGG 58.974 43.478 0.00 0.00 37.63 5.40
96 97 4.059773 TGATTTCAAATGCTAGGGGGTT 57.940 40.909 0.00 0.00 0.00 4.11
180 183 4.058817 ACTTGTTGTTCGACCAATCTCTC 58.941 43.478 0.00 0.00 0.00 3.20
809 812 0.842030 TGTTGAGGCCCATCTGTCCT 60.842 55.000 0.00 0.00 0.00 3.85
810 813 1.204146 GTTGAGGCCCATCTGTCCTA 58.796 55.000 0.00 0.00 0.00 2.94
868 871 3.166560 AGTACCGACACTTTAGTCCCT 57.833 47.619 0.00 0.00 35.07 4.20
916 919 1.064463 ACGAACCGGGACTATAGGTCA 60.064 52.381 6.32 0.00 46.16 4.02
944 947 3.107642 ACTAGTGGTCCGTCAAAACTG 57.892 47.619 0.00 0.00 0.00 3.16
961 964 6.379703 TCAAAACTGGTTGAAGAGATGGAAAA 59.620 34.615 0.00 0.00 34.59 2.29
1108 1115 1.314534 TTGTCTTCGGGCATGCCATG 61.315 55.000 36.56 27.48 37.98 3.66
1112 1119 0.179048 CTTCGGGCATGCCATGTCTA 60.179 55.000 36.56 14.79 37.98 2.59
1156 1164 3.052954 CAAATGGCAGCAGCACCA 58.947 55.556 9.47 9.47 44.61 4.17
1166 1174 0.689055 AGCAGCACCATGACAGAAGA 59.311 50.000 0.00 0.00 0.00 2.87
1213 1221 3.181489 GCTCATCTCAAAGAATGGCAAGG 60.181 47.826 0.00 0.00 0.00 3.61
1237 1245 1.505425 GTTGGGGTTCTACACGTCAC 58.495 55.000 0.00 0.00 0.00 3.67
1276 1284 0.697854 AGACAACACCACCTTCCCCT 60.698 55.000 0.00 0.00 0.00 4.79
1335 1343 3.264193 AGTTCACTCCTGTATGGATTGCA 59.736 43.478 0.00 0.00 45.16 4.08
1374 1382 3.714798 TCAGTGACCCCAAGTTTAGACTT 59.285 43.478 0.00 0.00 46.85 3.01
1399 1407 4.102210 CCAAGCTCAGAATCTCAAGGGATA 59.898 45.833 0.00 0.00 0.00 2.59
1471 1479 5.126061 AGTCAAATAATAGCAGCCAAAGGTG 59.874 40.000 0.00 0.00 44.57 4.00
1558 1566 4.143333 ACGCCTCGAACCCATCCG 62.143 66.667 0.00 0.00 0.00 4.18
1602 1610 5.130145 TGATCACCCAACAAATGTTTTCCTT 59.870 36.000 0.00 0.00 35.83 3.36
1630 1638 0.404040 AAGGATTGGCCGGAACAAGA 59.596 50.000 5.05 0.00 43.43 3.02
1655 1663 3.005791 ACTGGCCAAAAATACAGTCTTGC 59.994 43.478 7.01 0.00 39.84 4.01
1659 1667 4.261994 GGCCAAAAATACAGTCTTGCTTCA 60.262 41.667 0.00 0.00 0.00 3.02
1738 1746 3.067106 AGTGATCCGCAGTACTTTGTTG 58.933 45.455 0.00 0.00 0.00 3.33
1820 1834 1.191489 TTGGTGCCGGAGATGTCAGA 61.191 55.000 5.05 0.00 0.00 3.27
1849 1863 5.139727 ACTTTCTCCACACCAAATTCATCA 58.860 37.500 0.00 0.00 0.00 3.07
1899 1913 0.466543 CCCCGACGGATCCAACAATA 59.533 55.000 17.49 0.00 0.00 1.90
2014 2028 0.810648 GGCTCCATGCGATGTTTTCA 59.189 50.000 0.00 0.00 44.05 2.69
2126 2140 2.968574 GGGTGCTGGATGATAGAAGAGA 59.031 50.000 0.00 0.00 0.00 3.10
2197 2211 6.588204 AGTAACACAACAGGATTAACTGACA 58.412 36.000 0.00 0.00 40.97 3.58
2232 2246 9.871238 CCCATACATAGTGTTAGATTACCATAC 57.129 37.037 0.00 0.00 0.00 2.39
2337 2351 4.481195 GGCAAGAGTGGCTGTTCA 57.519 55.556 0.00 0.00 46.62 3.18
2504 2518 1.138069 TCTCACTGTTGGTGCTTTCGA 59.862 47.619 0.00 0.00 44.98 3.71
2535 2549 5.533903 GGTGATGCTATTGATGATTTGGAGT 59.466 40.000 0.00 0.00 0.00 3.85
3389 3418 3.592059 GCATGTTGGTGCATTCAAGATT 58.408 40.909 11.01 0.00 44.43 2.40
4170 6681 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
4176 6687 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
4207 6718 4.190772 CCAAACTTTGCACCATTTGACTT 58.809 39.130 14.37 0.00 34.62 3.01
4208 6719 5.355596 CCAAACTTTGCACCATTTGACTTA 58.644 37.500 14.37 0.00 34.62 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.875224 TCAACTTCCACATGGTATTCTTCA 58.125 37.500 0.00 0.00 36.34 3.02
56 57 7.451255 TGAAATCAACTTCCACATGGTATTCTT 59.549 33.333 0.00 0.00 36.34 2.52
77 78 3.790126 ACAACCCCCTAGCATTTGAAAT 58.210 40.909 0.00 0.00 0.00 2.17
180 183 0.948678 GATCGACCTCTCCTTCTCCG 59.051 60.000 0.00 0.00 0.00 4.63
779 782 3.803082 CTCAACATGGCCGGTGCG 61.803 66.667 1.90 0.57 38.85 5.34
790 793 0.842030 AGGACAGATGGGCCTCAACA 60.842 55.000 4.53 0.00 0.00 3.33
793 796 0.339859 ACTAGGACAGATGGGCCTCA 59.660 55.000 4.53 0.00 33.28 3.86
799 802 5.674525 TCTTGCATAAACTAGGACAGATGG 58.325 41.667 0.00 0.00 0.00 3.51
809 812 3.262405 AGTCCCGGTTCTTGCATAAACTA 59.738 43.478 0.00 0.00 0.00 2.24
810 813 2.039879 AGTCCCGGTTCTTGCATAAACT 59.960 45.455 0.00 0.00 0.00 2.66
868 871 3.570550 CCATTAGTCCCGGTTTTTGAACA 59.429 43.478 0.00 0.00 0.00 3.18
916 919 5.733620 TGACGGACCACTAGTAGAAAAAT 57.266 39.130 3.59 0.00 0.00 1.82
944 947 5.711976 TGGAGAATTTTCCATCTCTTCAACC 59.288 40.000 13.54 0.00 42.24 3.77
961 964 6.719829 TCGTGGTACATATGATAGTGGAGAAT 59.280 38.462 10.38 0.00 44.52 2.40
1041 1044 9.829507 TGGAATTTGTTTTGATGTATCTTTGTT 57.170 25.926 0.00 0.00 0.00 2.83
1098 1105 2.225019 CGAAGAATAGACATGGCATGCC 59.775 50.000 30.54 30.54 0.00 4.40
1101 1108 3.470709 CACCGAAGAATAGACATGGCAT 58.529 45.455 0.00 0.00 0.00 4.40
1108 1115 1.278238 CACGCCACCGAAGAATAGAC 58.722 55.000 0.00 0.00 38.29 2.59
1112 1119 3.118454 CGCACGCCACCGAAGAAT 61.118 61.111 0.00 0.00 38.29 2.40
1156 1164 2.902486 TGAGCTCTTGGTCTTCTGTCAT 59.098 45.455 16.19 0.00 40.98 3.06
1166 1174 4.749310 CGCCGCTGAGCTCTTGGT 62.749 66.667 16.19 0.00 0.00 3.67
1213 1221 1.005867 TGTAGAACCCCAACGCGAC 60.006 57.895 15.93 0.00 0.00 5.19
1224 1232 0.937699 TGCTGCGTGACGTGTAGAAC 60.938 55.000 6.91 0.00 0.00 3.01
1237 1245 1.067565 TGAGGAAGACTTACTGCTGCG 60.068 52.381 4.13 0.00 0.00 5.18
1276 1284 8.863086 GTTGAACCATATACCTACATACCAGTA 58.137 37.037 0.00 0.00 0.00 2.74
1335 1343 5.529060 GTCACTGATTGGTTTCTCTCTGTTT 59.471 40.000 0.00 0.00 0.00 2.83
1374 1382 3.307975 CCCTTGAGATTCTGAGCTTGGAA 60.308 47.826 0.00 5.08 0.00 3.53
1399 1407 6.626623 GCATGGTTTAAGATGACAAGATTGCT 60.627 38.462 0.00 0.00 0.00 3.91
1478 1486 8.875803 CCGTGATTGTAGTATTTTTGTTAGCTA 58.124 33.333 0.00 0.00 0.00 3.32
1513 1521 3.811083 TGACAAGGTTACCATCGTTTGT 58.189 40.909 3.51 4.86 0.00 2.83
1516 1524 6.045072 TCTTATGACAAGGTTACCATCGTT 57.955 37.500 3.51 0.00 0.00 3.85
1558 1566 2.996168 AAGCTCTGCCACCACACGAC 62.996 60.000 0.00 0.00 0.00 4.34
1602 1610 2.354729 CCAATCCTTGCACCGGGA 59.645 61.111 6.32 4.95 35.96 5.14
1630 1638 6.572314 GCAAGACTGTATTTTTGGCCAGTAAT 60.572 38.462 5.11 12.29 38.23 1.89
1655 1663 9.263538 CTGGATCTATCAGATTCTTCTTTGAAG 57.736 37.037 1.23 1.23 34.53 3.02
1659 1667 7.377696 AGCTGGATCTATCAGATTCTTCTTT 57.622 36.000 2.03 0.00 34.53 2.52
1738 1746 4.514441 CACCATGGATGAATTACAGAGCTC 59.486 45.833 21.47 5.27 0.00 4.09
1820 1834 4.497291 TTGGTGTGGAGAAAGTTACTGT 57.503 40.909 0.00 0.00 0.00 3.55
1849 1863 7.009179 TGAAGTACTCCTCTTCATCATTGTT 57.991 36.000 0.00 0.00 43.88 2.83
1899 1913 5.003804 ACGTCAAGGAAGCAGATTGTTATT 58.996 37.500 0.00 0.00 0.00 1.40
1987 2001 2.514824 GCATGGAGCCCTCGGTTC 60.515 66.667 0.00 0.00 37.23 3.62
2126 2140 5.068636 GTGGAGTATTTCTCATGCATCCAT 58.931 41.667 0.00 0.00 44.40 3.41
2197 2211 8.822805 TCTAACACTATGTATGGGAAAGAACTT 58.177 33.333 0.00 0.00 0.00 2.66
2504 2518 6.778834 TCATCAATAGCATCACCAACAAAT 57.221 33.333 0.00 0.00 0.00 2.32
2535 2549 0.930726 AACACCACTTCCTTTCCCCA 59.069 50.000 0.00 0.00 0.00 4.96
3077 3106 4.129380 CCTCTCATTGTTGTCAGAACACA 58.871 43.478 0.00 0.00 34.35 3.72
3079 3108 4.687901 TCCTCTCATTGTTGTCAGAACA 57.312 40.909 0.00 0.00 0.00 3.18
3341 3370 2.234143 GCAAGCTCTTTCAACCTCCTT 58.766 47.619 0.00 0.00 0.00 3.36
3389 3418 6.280643 CCATTGTAGGACGATCAAAGTCATA 58.719 40.000 0.00 0.00 40.20 2.15
4084 6595 6.003859 ATGGGACGGAGTACTATATAGGAG 57.996 45.833 14.25 0.00 42.21 3.69
4170 6681 6.145534 GCAAAGTTTGGCTAAATTTGTACTCC 59.854 38.462 26.25 12.34 32.75 3.85
4176 6687 4.574013 TGGTGCAAAGTTTGGCTAAATTTG 59.426 37.500 23.38 23.38 33.00 2.32


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

AutoCloner maintained by Alex Coulton.