Multiple sequence alignment - TraesCS2B01G149800

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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 TraesCS2B01G149800 chr2B 100.000 2288 0 0 1 2288 116318256 116320543 0.000000e+00 4226
1 TraesCS2B01G149800 chr2B 85.920 1740 185 25 10 1720 54775218 54776926 0.000000e+00 1801
2 TraesCS2B01G149800 chr2B 84.481 1031 113 22 715 1723 783932662 783931657 0.000000e+00 974
3 TraesCS2B01G149800 chr2B 95.288 573 19 5 1722 2288 150945125 150945695 0.000000e+00 902
4 TraesCS2B01G149800 chr2B 87.873 503 41 7 1727 2228 737850397 737850880 7.090000e-160 573
5 TraesCS2B01G149800 chr2B 89.722 360 30 5 1727 2084 737765385 737765739 9.640000e-124 453
6 TraesCS2B01G149800 chr2B 89.722 360 30 5 1727 2084 737787284 737787638 9.640000e-124 453
7 TraesCS2B01G149800 chr2B 80.126 317 50 11 1738 2054 29129751 29129448 8.230000e-55 224
8 TraesCS2B01G149800 chr2B 89.809 157 7 2 2072 2228 737788837 737788984 2.320000e-45 193
9 TraesCS2B01G149800 chr2B 93.750 80 4 1 2072 2151 737766938 737767016 3.990000e-23 119
10 TraesCS2B01G149800 chr2B 100.000 56 0 0 2233 2288 737789169 737789224 1.120000e-18 104
11 TraesCS2B01G149800 chr2B 100.000 56 0 0 2233 2288 737851041 737851096 1.120000e-18 104
12 TraesCS2B01G149800 chr2B 98.214 56 1 0 2233 2288 737767222 737767277 5.200000e-17 99
13 TraesCS2B01G149800 chr3D 92.812 1739 100 11 1 1722 81833366 81835096 0.000000e+00 2495
14 TraesCS2B01G149800 chr3D 91.757 1759 99 20 2 1729 41618552 41616809 0.000000e+00 2403
15 TraesCS2B01G149800 chr3D 92.070 1261 66 12 491 1722 6288084 6289339 0.000000e+00 1744
16 TraesCS2B01G149800 chr7A 91.949 1739 116 13 1 1722 221704924 221706655 0.000000e+00 2414
17 TraesCS2B01G149800 chr7B 91.638 1734 118 13 1 1724 43687271 43688987 0.000000e+00 2374
18 TraesCS2B01G149800 chr6B 91.422 1737 116 15 1 1723 457228445 457230162 0.000000e+00 2351
19 TraesCS2B01G149800 chr6B 95.296 574 16 7 1722 2288 211962775 211963344 0.000000e+00 900
20 TraesCS2B01G149800 chr6B 82.955 176 26 4 1727 1899 56016785 56016611 3.040000e-34 156
21 TraesCS2B01G149800 chr3A 90.951 1746 118 16 1 1723 71154417 71156145 0.000000e+00 2313
22 TraesCS2B01G149800 chr6D 90.126 1742 132 18 1 1722 446604650 446602929 0.000000e+00 2228
23 TraesCS2B01G149800 chr1D 90.063 1741 130 21 1 1722 369900538 369902254 0.000000e+00 2217
24 TraesCS2B01G149800 chr1B 92.502 1547 85 16 2 1538 155744900 155746425 0.000000e+00 2185
25 TraesCS2B01G149800 chr4A 89.347 1746 153 20 1 1723 743365753 743364018 0.000000e+00 2163
26 TraesCS2B01G149800 chr7D 89.202 1741 133 28 1 1723 568007505 568005802 0.000000e+00 2122
27 TraesCS2B01G149800 chr7D 87.069 580 57 12 1157 1727 121215538 121214968 6.890000e-180 640
28 TraesCS2B01G149800 chr2D 94.674 582 14 8 1722 2288 110862106 110862685 0.000000e+00 887
29 TraesCS2B01G149800 chr1A 96.401 389 9 4 1903 2288 524403202 524402816 8.920000e-179 636
30 TraesCS2B01G149800 chr2A 88.435 294 18 8 1998 2276 763479318 763479610 7.830000e-90 340
31 TraesCS2B01G149800 chr3B 80.000 230 37 8 1835 2060 13441336 13441112 6.540000e-36 161


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 TraesCS2B01G149800 chr2B 116318256 116320543 2287 False 4226.000000 4226 100.000000 1 2288 1 chr2B.!!$F2 2287
1 TraesCS2B01G149800 chr2B 54775218 54776926 1708 False 1801.000000 1801 85.920000 10 1720 1 chr2B.!!$F1 1710
2 TraesCS2B01G149800 chr2B 783931657 783932662 1005 True 974.000000 974 84.481000 715 1723 1 chr2B.!!$R2 1008
3 TraesCS2B01G149800 chr2B 150945125 150945695 570 False 902.000000 902 95.288000 1722 2288 1 chr2B.!!$F3 566
4 TraesCS2B01G149800 chr2B 737850397 737851096 699 False 338.500000 573 93.936500 1727 2288 2 chr2B.!!$F6 561
5 TraesCS2B01G149800 chr2B 737787284 737789224 1940 False 250.000000 453 93.177000 1727 2288 3 chr2B.!!$F5 561
6 TraesCS2B01G149800 chr2B 737765385 737767277 1892 False 223.666667 453 93.895333 1727 2288 3 chr2B.!!$F4 561
7 TraesCS2B01G149800 chr3D 81833366 81835096 1730 False 2495.000000 2495 92.812000 1 1722 1 chr3D.!!$F2 1721
8 TraesCS2B01G149800 chr3D 41616809 41618552 1743 True 2403.000000 2403 91.757000 2 1729 1 chr3D.!!$R1 1727
9 TraesCS2B01G149800 chr3D 6288084 6289339 1255 False 1744.000000 1744 92.070000 491 1722 1 chr3D.!!$F1 1231
10 TraesCS2B01G149800 chr7A 221704924 221706655 1731 False 2414.000000 2414 91.949000 1 1722 1 chr7A.!!$F1 1721
11 TraesCS2B01G149800 chr7B 43687271 43688987 1716 False 2374.000000 2374 91.638000 1 1724 1 chr7B.!!$F1 1723
12 TraesCS2B01G149800 chr6B 457228445 457230162 1717 False 2351.000000 2351 91.422000 1 1723 1 chr6B.!!$F2 1722
13 TraesCS2B01G149800 chr6B 211962775 211963344 569 False 900.000000 900 95.296000 1722 2288 1 chr6B.!!$F1 566
14 TraesCS2B01G149800 chr3A 71154417 71156145 1728 False 2313.000000 2313 90.951000 1 1723 1 chr3A.!!$F1 1722
15 TraesCS2B01G149800 chr6D 446602929 446604650 1721 True 2228.000000 2228 90.126000 1 1722 1 chr6D.!!$R1 1721
16 TraesCS2B01G149800 chr1D 369900538 369902254 1716 False 2217.000000 2217 90.063000 1 1722 1 chr1D.!!$F1 1721
17 TraesCS2B01G149800 chr1B 155744900 155746425 1525 False 2185.000000 2185 92.502000 2 1538 1 chr1B.!!$F1 1536
18 TraesCS2B01G149800 chr4A 743364018 743365753 1735 True 2163.000000 2163 89.347000 1 1723 1 chr4A.!!$R1 1722
19 TraesCS2B01G149800 chr7D 568005802 568007505 1703 True 2122.000000 2122 89.202000 1 1723 1 chr7D.!!$R2 1722
20 TraesCS2B01G149800 chr7D 121214968 121215538 570 True 640.000000 640 87.069000 1157 1727 1 chr7D.!!$R1 570
21 TraesCS2B01G149800 chr2D 110862106 110862685 579 False 887.000000 887 94.674000 1722 2288 1 chr2D.!!$F1 566

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
123 130 0.324368 AGGTCGATCTGCCAGGTACA 60.324 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1618 0.963962 AGTGGACAAATGCAAGGCAG 59.036 50.0 0.0 0.0 43.65 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
123 130 0.324368 AGGTCGATCTGCCAGGTACA 60.324 55.000 0.00 0.00 0.00 2.90
161 168 1.002990 CTCACTGGCATCTGCACCA 60.003 57.895 4.33 0.00 44.36 4.17
254 270 0.683504 ACGACGGTCATTAGGAGCCT 60.684 55.000 9.10 0.00 40.99 4.58
429 445 4.860907 CACTGCATTAGATTCCTTTTGCAC 59.139 41.667 0.00 0.00 35.52 4.57
683 710 1.476488 GAGGAGGAGAAGAGTGACAGC 59.524 57.143 0.00 0.00 0.00 4.40
689 716 0.982704 AGAAGAGTGACAGCCATGCT 59.017 50.000 0.00 0.00 40.77 3.79
720 754 6.421485 ACTCATGAATAAGCCATGAACTCTT 58.579 36.000 0.00 0.00 46.56 2.85
1070 1132 0.535102 CTCAGGAACAACACCGGCTT 60.535 55.000 0.00 0.00 0.00 4.35
1099 1161 1.064906 AGGTGATGGTGAAGCTGATGG 60.065 52.381 0.00 0.00 0.00 3.51
1137 1199 0.627469 ATCAGGGTTGGGCCACCTAT 60.627 55.000 14.86 7.19 39.65 2.57
1200 1262 1.979693 GCTCCTCACTCCCGACACT 60.980 63.158 0.00 0.00 0.00 3.55
1341 1408 5.615544 CGAGTCTGCTTTGAACTGTTTATGG 60.616 44.000 0.00 0.00 0.00 2.74
1348 1422 6.015519 TGCTTTGAACTGTTTATGGTTATGCT 60.016 34.615 0.00 0.00 0.00 3.79
1351 1425 8.810652 TTTGAACTGTTTATGGTTATGCTTTC 57.189 30.769 0.00 0.00 0.00 2.62
1422 1511 9.127277 AGTAGTTGATCCTCTGTTTATACTCTC 57.873 37.037 0.00 0.00 0.00 3.20
1439 1529 3.260740 CTCTCCTCTGCTTTGATGTGTC 58.739 50.000 0.00 0.00 0.00 3.67
1571 1661 5.314923 ACATGCAGACAACCAAATATCAC 57.685 39.130 0.00 0.00 0.00 3.06
1629 1719 1.209019 AGGCAACCAAACAACATGCAA 59.791 42.857 0.00 0.00 38.73 4.08
1632 1722 3.066481 GGCAACCAAACAACATGCAAATT 59.934 39.130 0.00 0.00 38.73 1.82
1671 1761 5.163561 GCATTTGCATAGCCAGGTTAAGTTA 60.164 40.000 0.00 0.00 41.59 2.24
1811 1903 3.588955 GCGCTCCAAAAGGATTCAAAAT 58.411 40.909 0.00 0.00 0.00 1.82
1837 1929 0.037790 TATACGTGCACAGTGCTGCA 60.038 50.000 25.83 13.98 45.31 4.41
1948 2050 3.133691 GTGAGTGTGTGATTCTCAGCAA 58.866 45.455 0.00 0.00 38.60 3.91
1952 2054 5.157940 AGTGTGTGATTCTCAGCAATACT 57.842 39.130 0.00 0.00 0.00 2.12
1959 2061 8.887717 GTGTGATTCTCAGCAATACTTTCTAAT 58.112 33.333 0.00 0.00 0.00 1.73
2074 2177 3.730215 TTTAAGCAAGGGTATCAGGCA 57.270 42.857 0.00 0.00 0.00 4.75
2137 3451 3.038788 TGCACGATACAAAGCAGAAGA 57.961 42.857 0.00 0.00 32.48 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 270 5.303589 AGTGGTGCAAGTACAAGAACTACTA 59.696 40.000 11.41 0.00 33.82 1.82
445 461 2.435372 TGGAGGTGTGCTTGAACTTT 57.565 45.000 0.00 0.00 0.00 2.66
474 490 4.134623 GTGACCGCACCAAGTTCA 57.865 55.556 0.00 0.00 39.14 3.18
581 604 1.132689 ACTGTCAACCTTCCTCCTCCT 60.133 52.381 0.00 0.00 0.00 3.69
683 710 7.221452 GCTTATTCATGAGTTAAAACAGCATGG 59.779 37.037 19.55 10.42 43.62 3.66
689 716 8.347004 TCATGGCTTATTCATGAGTTAAAACA 57.653 30.769 0.00 2.15 43.98 2.83
699 726 5.747197 GCAAAGAGTTCATGGCTTATTCATG 59.253 40.000 0.00 0.00 42.28 3.07
700 727 5.655532 AGCAAAGAGTTCATGGCTTATTCAT 59.344 36.000 0.00 0.00 0.00 2.57
720 754 0.607217 CATGGAGTCAGGCACAGCAA 60.607 55.000 0.00 0.00 0.00 3.91
784 845 1.442987 GTTGCTTGCCCTTGCTGTT 59.557 52.632 0.00 0.00 38.71 3.16
1041 1103 3.118261 TGTTGTTCCTGAGCTTGAACTCT 60.118 43.478 19.17 0.00 41.10 3.24
1070 1132 1.203300 TCACCATCACCTTCCAGGAGA 60.203 52.381 0.00 0.00 39.29 3.71
1137 1199 2.721425 TGATCTGATGAATGGCTGCA 57.279 45.000 0.50 0.00 0.00 4.41
1341 1408 8.076178 ACACTTCATAACAGTTGAAAGCATAAC 58.924 33.333 0.00 0.00 32.98 1.89
1348 1422 7.011950 CAGTACCACACTTCATAACAGTTGAAA 59.988 37.037 0.00 0.00 34.26 2.69
1351 1425 5.334105 GCAGTACCACACTTCATAACAGTTG 60.334 44.000 0.00 0.00 34.26 3.16
1422 1511 2.486472 AGGACACATCAAAGCAGAGG 57.514 50.000 0.00 0.00 0.00 3.69
1439 1529 1.086696 CTTCGGCACAACCATGTAGG 58.913 55.000 0.00 0.00 45.67 3.18
1528 1618 0.963962 AGTGGACAAATGCAAGGCAG 59.036 50.000 0.00 0.00 43.65 4.85
1594 1684 2.044252 CCTGCATGCCCTCTTGCT 60.044 61.111 16.68 0.00 42.07 3.91
1629 1719 1.345089 TGCAGCCTCAAATGCACAATT 59.655 42.857 0.00 0.00 46.97 2.32
1632 1722 4.177673 TGCAGCCTCAAATGCACA 57.822 50.000 0.00 0.00 46.97 4.57
1666 1756 4.706476 TGCATTGCATAGCCTTCTTAACTT 59.294 37.500 7.38 0.00 31.71 2.66
1671 1761 3.094572 AGTTGCATTGCATAGCCTTCTT 58.905 40.909 12.95 0.00 38.76 2.52
1811 1903 3.185594 GCACTGTGCACGTATAGTTTGAA 59.814 43.478 26.70 0.00 44.26 2.69
1948 2050 8.581253 AAAAGCTGCTAACCATTAGAAAGTAT 57.419 30.769 0.90 0.00 35.20 2.12
2074 2177 6.879400 TGGCCTAAAAATTGTACTGTGTTTT 58.121 32.000 3.32 0.00 0.00 2.43
2137 3451 5.565592 TCGCAAGTGCATCTGAATTTTAT 57.434 34.783 3.87 0.00 42.21 1.40


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

AutoCloner maintained by Alex Coulton.