Multiple sequence alignment - TraesCS2B01G146100

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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 TraesCS2B01G146100 chr2B 100.000 3092 0 0 1 3092 111925876 111928967 0.000000e+00 5710.0
1 TraesCS2B01G146100 chr2B 95.329 1413 63 2 278 1689 113404494 113403084 0.000000e+00 2241.0
2 TraesCS2B01G146100 chr2B 94.872 1404 63 5 1696 3092 113479372 113477971 0.000000e+00 2185.0
3 TraesCS2B01G146100 chr2B 94.352 1381 52 6 1696 3068 113470175 113468813 0.000000e+00 2095.0
4 TraesCS2B01G146100 chr2B 95.120 1209 54 1 481 1689 113471424 113470221 0.000000e+00 1901.0
5 TraesCS2B01G146100 chr2B 91.450 1345 111 3 1 1342 111946812 111948155 0.000000e+00 1844.0
6 TraesCS2B01G146100 chr2B 95.050 1091 48 5 612 1698 113480294 113479206 0.000000e+00 1711.0
7 TraesCS2B01G146100 chr2B 94.629 931 41 4 2170 3092 113413151 113412222 0.000000e+00 1434.0
8 TraesCS2B01G146100 chr2B 93.255 934 61 2 1 933 113380556 113379624 0.000000e+00 1375.0
9 TraesCS2B01G146100 chr2B 93.293 835 56 0 860 1694 113416048 113415214 0.000000e+00 1232.0
10 TraesCS2B01G146100 chr2B 94.830 735 25 5 2366 3092 113402414 113401685 0.000000e+00 1134.0
11 TraesCS2B01G146100 chr2B 96.302 622 23 0 1 622 113482886 113482265 0.000000e+00 1022.0
12 TraesCS2B01G146100 chr2B 95.215 627 30 0 1696 2322 113403038 113402412 0.000000e+00 992.0
13 TraesCS2B01G146100 chr2B 88.845 762 81 4 933 1694 113377794 113377037 0.000000e+00 933.0
14 TraesCS2B01G146100 chr2B 94.898 588 28 2 278 864 113424996 113424410 0.000000e+00 918.0
15 TraesCS2B01G146100 chr2B 91.023 479 43 0 1696 2174 113415173 113414695 0.000000e+00 647.0
16 TraesCS2B01G146100 chr2B 87.063 572 62 5 1696 2267 113376894 113376335 1.210000e-178 636.0
17 TraesCS2B01G146100 chr2B 97.573 206 5 0 278 483 113471886 113471681 1.360000e-93 353.0
18 TraesCS2B01G146100 chr2B 95.215 209 7 2 612 817 113480801 113480593 8.270000e-86 327.0
19 TraesCS2B01G146100 chr2B 82.427 239 39 3 1696 1931 113403242 113403004 4.040000e-49 206.0
20 TraesCS2B01G146100 chr2B 82.427 239 39 3 1696 1931 113470379 113470141 4.040000e-49 206.0
21 TraesCS2B01G146100 chr2D 89.332 1706 170 7 1 1696 74775826 74774123 0.000000e+00 2132.0
22 TraesCS2B01G146100 chr2D 89.541 1415 121 14 1696 3092 74773772 74772367 0.000000e+00 1768.0
23 TraesCS2B01G146100 chr2D 86.122 245 25 2 1696 1931 74774186 74773942 3.960000e-64 255.0
24 TraesCS2B01G146100 chr2D 95.556 45 2 0 2163 2207 74764468 74764424 4.280000e-09 73.1
25 TraesCS2B01G146100 chr2A 90.320 1529 140 4 173 1694 73923914 73922387 0.000000e+00 1997.0
26 TraesCS2B01G146100 chr2A 88.102 1412 142 14 1696 3092 73921735 73920335 0.000000e+00 1653.0
27 TraesCS2B01G146100 chr2A 80.515 621 115 5 974 1594 90768613 90769227 3.610000e-129 472.0
28 TraesCS2B01G146100 chr2A 91.160 181 16 0 1696 1876 73922448 73922268 2.380000e-61 246.0
29 TraesCS2B01G146100 chr2A 92.035 113 8 1 1 112 73924027 73923915 1.150000e-34 158.0
30 TraesCS2B01G146100 chr2A 81.290 155 21 6 821 969 90768376 90768528 5.420000e-23 119.0


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 TraesCS2B01G146100 chr2B 111925876 111928967 3091 False 5710.000000 5710 100.000000 1 3092 1 chr2B.!!$F1 3091
1 TraesCS2B01G146100 chr2B 111946812 111948155 1343 False 1844.000000 1844 91.450000 1 1342 1 chr2B.!!$F2 1341
2 TraesCS2B01G146100 chr2B 113477971 113482886 4915 True 1311.250000 2185 95.359750 1 3092 4 chr2B.!!$R6 3091
3 TraesCS2B01G146100 chr2B 113401685 113404494 2809 True 1143.250000 2241 91.950250 278 3092 4 chr2B.!!$R3 2814
4 TraesCS2B01G146100 chr2B 113468813 113471886 3073 True 1138.750000 2095 92.368000 278 3068 4 chr2B.!!$R5 2790
5 TraesCS2B01G146100 chr2B 113412222 113416048 3826 True 1104.333333 1434 92.981667 860 3092 3 chr2B.!!$R4 2232
6 TraesCS2B01G146100 chr2B 113376335 113380556 4221 True 981.333333 1375 89.721000 1 2267 3 chr2B.!!$R2 2266
7 TraesCS2B01G146100 chr2B 113424410 113424996 586 True 918.000000 918 94.898000 278 864 1 chr2B.!!$R1 586
8 TraesCS2B01G146100 chr2D 74772367 74775826 3459 True 1385.000000 2132 88.331667 1 3092 3 chr2D.!!$R2 3091
9 TraesCS2B01G146100 chr2A 73920335 73924027 3692 True 1013.500000 1997 90.404250 1 3092 4 chr2A.!!$R1 3091
10 TraesCS2B01G146100 chr2A 90768376 90769227 851 False 295.500000 472 80.902500 821 1594 2 chr2A.!!$F1 773

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
161 163 2.910688 AATGGCCATGTACCTACTCG 57.089 50.000 21.63 0.00 0.00 4.18 F
1128 5308 0.403655 TCCTATGCAACACCAAGGCA 59.596 50.000 0.00 0.00 42.43 4.75 F
1640 5929 1.004504 GCCTTCGTCGATGAATCAAGC 60.005 52.381 19.90 15.76 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 5915 0.043822 GCGACGCTTGATTCATCGAC 60.044 55.000 13.73 6.46 34.77 4.20 R
1936 6980 0.323087 TCCTCGTCGGATCTCACCAA 60.323 55.000 0.00 0.00 36.69 3.67 R
3060 9673 3.386932 TTTTTGGGCATCCATAGCTCT 57.613 42.857 0.00 0.00 43.63 4.09 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
151 153 3.953612 ACCAACATAGTGTAATGGCCATG 59.046 43.478 21.63 8.23 32.79 3.66
161 163 2.910688 AATGGCCATGTACCTACTCG 57.089 50.000 21.63 0.00 0.00 4.18
207 209 7.966812 AGTTCATGTCAATGCTCTATATGGTA 58.033 34.615 0.00 0.00 33.47 3.25
218 220 5.010617 TGCTCTATATGGTAATTGTCGAGCA 59.989 40.000 6.08 6.08 46.09 4.26
713 2963 6.206634 ACAATCACATAATGTTTTCGTCACCT 59.793 34.615 0.00 0.00 0.00 4.00
831 3086 6.016943 GCATATCTACGTAGAGAGTGAAAGGT 60.017 42.308 27.81 11.50 35.50 3.50
843 3098 5.941788 AGAGTGAAAGGTTGTAAATGGACT 58.058 37.500 0.00 0.00 0.00 3.85
869 3124 5.674052 AAGTTAGAGATGAGCACAGTGAT 57.326 39.130 4.15 0.00 0.00 3.06
965 5065 4.220602 ACTCACCAAAAACAAGCAACTTCT 59.779 37.500 0.00 0.00 0.00 2.85
1128 5308 0.403655 TCCTATGCAACACCAAGGCA 59.596 50.000 0.00 0.00 42.43 4.75
1377 5557 1.973281 CATGCTCGGTGGCAACCTT 60.973 57.895 9.09 0.00 45.17 3.50
1525 5705 2.933287 TCAACATGGGGCCTCCGT 60.933 61.111 0.00 0.00 38.76 4.69
1543 5723 1.823828 GTCGATGTATCAAGCGTCGT 58.176 50.000 6.78 0.00 43.45 4.34
1626 5915 3.451894 GCCAACATGGGGCCTTCG 61.452 66.667 17.33 0.00 45.87 3.79
1633 5922 2.063979 ATGGGGCCTTCGTCGATGA 61.064 57.895 2.39 2.39 0.00 2.92
1640 5929 1.004504 GCCTTCGTCGATGAATCAAGC 60.005 52.381 19.90 15.76 0.00 4.01
1642 5931 1.920574 CTTCGTCGATGAATCAAGCGT 59.079 47.619 19.90 0.00 0.00 5.07
1647 5936 1.273887 GATGAATCAAGCGTCGCCG 59.726 57.895 14.86 5.68 37.07 6.46
1681 5970 4.056125 GGCAGCCACCGCTTTTCC 62.056 66.667 6.55 0.00 45.55 3.13
1936 6980 2.284699 AGGAGGGCTGGCGTAACT 60.285 61.111 0.00 0.00 0.00 2.24
1952 6996 1.254026 AACTTGGTGAGATCCGACGA 58.746 50.000 0.00 0.00 0.00 4.20
2087 7137 4.030134 ACGATATGGAGTTCGAGTTGTC 57.970 45.455 0.00 0.00 38.67 3.18
2603 9203 4.130857 TGTAGCGAAATCCAAGAACAACA 58.869 39.130 0.00 0.00 0.00 3.33
2749 9352 3.947196 GGTGAATGTGCTGGATGTTCATA 59.053 43.478 3.40 0.00 32.19 2.15
2986 9599 4.169264 AGAAACAAAAGGGGAGAAGGGTTA 59.831 41.667 0.00 0.00 0.00 2.85
3060 9673 1.066454 CGACGTATGGTATCACTGGCA 59.934 52.381 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 153 3.795623 TGCCTCAAATCGAGTAGGTAC 57.204 47.619 3.80 0.00 40.48 3.34
161 163 9.109393 TGAACTAGTACATTTATGCCTCAAATC 57.891 33.333 0.00 0.00 0.00 2.17
207 209 1.597742 AGTGTGCTTGCTCGACAATT 58.402 45.000 1.76 0.00 37.72 2.32
218 220 1.447317 CGCCTCCAACAAGTGTGCTT 61.447 55.000 0.00 0.00 34.82 3.91
276 281 9.630098 TGTAGTCCAAGTAAGTAATAACTTTCG 57.370 33.333 0.00 0.00 43.60 3.46
771 3026 4.229123 AGCTAGCCCATTAATGCATCCTAT 59.771 41.667 12.13 0.00 0.00 2.57
831 3086 7.741785 TCTCTAACTTTGGAGTCCATTTACAA 58.258 34.615 14.00 2.63 37.13 2.41
843 3098 4.284490 ACTGTGCTCATCTCTAACTTTGGA 59.716 41.667 0.00 0.00 0.00 3.53
965 5065 5.309806 AGGGTAAAACTAGCAGAGGAAAAGA 59.690 40.000 0.00 0.00 0.00 2.52
1128 5308 1.203758 TCGTCATACACCAGAACGCAT 59.796 47.619 0.00 0.00 0.00 4.73
1332 5512 2.456364 AGGAGGGCCCTGATGTCA 59.544 61.111 34.59 0.00 45.61 3.58
1377 5557 3.818787 GCGACCTCCTCGGCGTTA 61.819 66.667 6.85 0.00 43.18 3.18
1395 5575 0.599204 CCGACGTACAGCCAACACTT 60.599 55.000 0.00 0.00 0.00 3.16
1525 5705 1.593793 CGACGACGCTTGATACATCGA 60.594 52.381 0.00 0.00 36.64 3.59
1570 5750 2.592993 CCTGGGGCTGGAAGAACGA 61.593 63.158 0.00 0.00 34.07 3.85
1626 5915 0.043822 GCGACGCTTGATTCATCGAC 60.044 55.000 13.73 6.46 34.77 4.20
1726 6054 0.687757 TGGAAGACCGATAGCTGCCT 60.688 55.000 0.00 0.00 39.42 4.75
1792 6527 3.406361 CGGCGCCTGATACATCGC 61.406 66.667 26.68 0.00 45.99 4.58
1936 6980 0.323087 TCCTCGTCGGATCTCACCAA 60.323 55.000 0.00 0.00 36.69 3.67
1952 6996 3.164269 CCAGGGCGCTATGGTCCT 61.164 66.667 19.39 8.81 0.00 3.85
1959 7003 1.899814 CCATTATAGACCAGGGCGCTA 59.100 52.381 7.64 0.00 0.00 4.26
2511 9110 7.603180 TGATAGCATCACTCAGGTAACTATT 57.397 36.000 0.00 0.00 38.90 1.73
2572 9172 5.697473 TGGATTTCGCTACAAATCAAACA 57.303 34.783 12.20 2.51 42.40 2.83
2603 9203 7.045416 TCACAACATACGACCAAAATAGCTAT 58.955 34.615 0.00 0.00 0.00 2.97
2749 9352 8.353423 AGTTACACATCTTTATCTTGGCAAAT 57.647 30.769 0.00 0.94 0.00 2.32
2817 9430 7.201609 GCGACCAAGACAAAATTAGATACATGA 60.202 37.037 0.00 0.00 0.00 3.07
3060 9673 3.386932 TTTTTGGGCATCCATAGCTCT 57.613 42.857 0.00 0.00 43.63 4.09


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

AutoCloner maintained by Alex Coulton.