Multiple sequence alignment - TraesCS3B01G235900

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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 TraesCS3B01G235900 chr3B 100.000 2222 0 0 1 2222 368742273 368744494 0.000000e+00 4104
1 TraesCS3B01G235900 chr3B 92.694 2231 128 23 2 2222 368873655 368871450 0.000000e+00 3184
2 TraesCS3B01G235900 chr6D 96.235 2231 75 8 1 2222 124529703 124531933 0.000000e+00 3646
3 TraesCS3B01G235900 chr7B 96.147 2232 76 9 1 2222 644461024 644463255 0.000000e+00 3637
4 TraesCS3B01G235900 chr6B 96.188 2230 74 10 1 2222 307002399 307000173 0.000000e+00 3637
5 TraesCS3B01G235900 chr7D 96.102 2232 77 9 1 2222 626685655 626683424 0.000000e+00 3631
6 TraesCS3B01G235900 chr7D 96.138 2227 77 8 5 2222 381961576 381959350 0.000000e+00 3627
7 TraesCS3B01G235900 chr7D 96.056 2231 79 8 1 2222 382062259 382064489 0.000000e+00 3624
8 TraesCS3B01G235900 chr3A 96.099 2230 79 8 1 2222 633104838 633107067 0.000000e+00 3629
9 TraesCS3B01G235900 chr2B 95.518 2231 90 9 1 2222 391119250 391117021 0.000000e+00 3557
10 TraesCS3B01G235900 chr2B 94.987 399 16 3 1155 1550 357271040 357270643 6.740000e-175 623


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 TraesCS3B01G235900 chr3B 368742273 368744494 2221 False 4104 4104 100.000 1 2222 1 chr3B.!!$F1 2221
1 TraesCS3B01G235900 chr3B 368871450 368873655 2205 True 3184 3184 92.694 2 2222 1 chr3B.!!$R1 2220
2 TraesCS3B01G235900 chr6D 124529703 124531933 2230 False 3646 3646 96.235 1 2222 1 chr6D.!!$F1 2221
3 TraesCS3B01G235900 chr7B 644461024 644463255 2231 False 3637 3637 96.147 1 2222 1 chr7B.!!$F1 2221
4 TraesCS3B01G235900 chr6B 307000173 307002399 2226 True 3637 3637 96.188 1 2222 1 chr6B.!!$R1 2221
5 TraesCS3B01G235900 chr7D 626683424 626685655 2231 True 3631 3631 96.102 1 2222 1 chr7D.!!$R2 2221
6 TraesCS3B01G235900 chr7D 381959350 381961576 2226 True 3627 3627 96.138 5 2222 1 chr7D.!!$R1 2217
7 TraesCS3B01G235900 chr7D 382062259 382064489 2230 False 3624 3624 96.056 1 2222 1 chr7D.!!$F1 2221
8 TraesCS3B01G235900 chr3A 633104838 633107067 2229 False 3629 3629 96.099 1 2222 1 chr3A.!!$F1 2221
9 TraesCS3B01G235900 chr2B 391117021 391119250 2229 True 3557 3557 95.518 1 2222 1 chr2B.!!$R2 2221

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
237 238 0.324943 TTCCAACCTCTGCTAGTGGC 59.675 55.0 0.0 0.0 42.22 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2150 0.107703 CCATTAGCGCTCCTGTCCAA 60.108 55.0 16.34 0.0 0.0 3.53 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
20 21 2.666026 GCCGCTTTTCTTCCTTTTCTG 58.334 47.619 0.00 0.00 0.00 3.02
55 56 2.106684 AGTTCTCACCCTCCCAGAAAAC 59.893 50.000 0.00 0.00 0.00 2.43
148 149 8.458573 ACCTATTTGTCACAAAGTTCAATACA 57.541 30.769 9.27 0.00 0.00 2.29
166 167 8.239038 TCAATACACTCTAGAGGAGGTAAATG 57.761 38.462 23.50 20.39 45.83 2.32
199 200 3.741476 GCCTGGTTGAAGCAGCCG 61.741 66.667 18.25 7.48 42.05 5.52
223 224 4.447138 ACACTTCTATGGGTTGTTCCAA 57.553 40.909 0.00 0.00 40.62 3.53
237 238 0.324943 TTCCAACCTCTGCTAGTGGC 59.675 55.000 0.00 0.00 42.22 5.01
262 263 7.469456 GCTGGTTTTTCATTTCTACAACAGGTA 60.469 37.037 0.00 0.00 0.00 3.08
342 343 6.370994 CAGCATTCTCAGATTACTTGACTTGT 59.629 38.462 0.00 0.00 0.00 3.16
360 361 4.714308 ACTTGTTGCTAGCTTAGAGGAGAT 59.286 41.667 17.23 0.00 0.00 2.75
401 405 8.871125 TCATTTACCTTTAAGTCTGAGAGAAGT 58.129 33.333 0.00 0.00 0.00 3.01
403 407 5.379732 ACCTTTAAGTCTGAGAGAAGTCG 57.620 43.478 0.00 0.00 0.00 4.18
526 531 2.092212 CCTCCACTAGCATTGGACCAAT 60.092 50.000 14.28 14.28 38.28 3.16
528 533 4.385199 CCTCCACTAGCATTGGACCAATAA 60.385 45.833 19.41 7.52 38.28 1.40
550 555 3.199677 TCAGTCTAGCTCTCGCTCTTAC 58.800 50.000 0.00 0.00 45.15 2.34
567 572 5.765677 GCTCTTACCCAATTTCCTTATCCTC 59.234 44.000 0.00 0.00 0.00 3.71
598 604 6.462628 GCAAGGTCGGAGTAGTAGGAAAATAT 60.463 42.308 0.00 0.00 0.00 1.28
600 606 7.999450 AGGTCGGAGTAGTAGGAAAATATAG 57.001 40.000 0.00 0.00 0.00 1.31
655 661 9.071276 TCAGACTGAAGAAATTGAAGCTAAATT 57.929 29.630 1.64 2.25 0.00 1.82
746 752 7.757624 AGCTTGAGTTATCTTTTAGTTCTCTCG 59.242 37.037 0.00 0.00 0.00 4.04
752 758 3.079578 TCTTTTAGTTCTCTCGCCTCGA 58.920 45.455 0.00 0.00 0.00 4.04
839 845 7.162082 TCTCTTTTGAACCTCTTAAGATGACC 58.838 38.462 13.92 6.12 0.00 4.02
840 846 6.238648 TCTTTTGAACCTCTTAAGATGACCC 58.761 40.000 13.92 4.07 0.00 4.46
847 855 5.001874 ACCTCTTAAGATGACCCGAAAAAC 58.998 41.667 13.92 0.00 0.00 2.43
1097 1109 1.950909 TCCGGTCTTTTCGTTGCATTT 59.049 42.857 0.00 0.00 0.00 2.32
1100 1112 3.304123 CCGGTCTTTTCGTTGCATTTACA 60.304 43.478 0.00 0.00 0.00 2.41
1202 1214 7.334921 TCGTTCCGTCATATTCCAAATAACTTT 59.665 33.333 0.00 0.00 0.00 2.66
1291 1305 8.798859 ATCATGAGGGTAGTATTTTATCATGC 57.201 34.615 0.09 0.00 41.32 4.06
1372 1386 5.643777 CCATAATGTCTCAAAACGAAGAGGT 59.356 40.000 0.00 0.00 32.76 3.85
1374 1388 5.424121 AATGTCTCAAAACGAAGAGGTTG 57.576 39.130 0.00 0.00 32.76 3.77
1481 1496 5.280521 CCCTAGTTGTACACTCCCTTCATTT 60.281 44.000 0.00 0.00 36.88 2.32
1508 1523 6.601332 AGAACCCTTGTTGATTCTGAACTTA 58.399 36.000 0.00 0.00 33.97 2.24
1535 1550 4.851010 GCAAAGTAAGCGTCCTTTTAACA 58.149 39.130 0.00 0.00 32.47 2.41
1554 1569 1.901833 CAGGCCAGCCCTTTTTAATGT 59.098 47.619 5.01 0.00 43.06 2.71
1577 1592 2.543653 CCGCTTGACCCTGTTTTGAAAG 60.544 50.000 0.00 0.00 0.00 2.62
1706 1721 3.317603 TCGATGAACAGCAGATTGACA 57.682 42.857 0.00 0.00 0.00 3.58
1776 1792 7.272244 AGTTCCGATCCTTTTGTTTGAATTTT 58.728 30.769 0.00 0.00 0.00 1.82
1945 1962 4.695993 TCACTCGCCGCCAATGCA 62.696 61.111 0.00 0.00 37.32 3.96
1976 1993 1.735571 GCCGAAAAGAATGGAACGCTA 59.264 47.619 0.00 0.00 0.00 4.26
2001 2018 2.125552 CTGCTGGATGCGTCGGAA 60.126 61.111 0.00 0.00 46.63 4.30
2132 2150 3.003793 GCTTTTTCGCCTTCTCTTCACTT 59.996 43.478 0.00 0.00 0.00 3.16
2214 2232 3.662247 AGAAAGACACCACTACTTCGG 57.338 47.619 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.002759 GTGAGAACTTGAAAGACTGGCAC 59.997 47.826 0.00 0.00 0.00 5.01
55 56 6.043854 AGCTAGTAAGAAGACTTTCCCTTG 57.956 41.667 0.00 0.00 37.53 3.61
148 149 6.444704 TCCATTCATTTACCTCCTCTAGAGT 58.555 40.000 18.42 3.36 41.47 3.24
166 167 0.677842 AGGCGTACCCGTATCCATTC 59.322 55.000 0.00 0.00 39.21 2.67
199 200 3.939592 GGAACAACCCATAGAAGTGTAGC 59.060 47.826 0.00 0.00 0.00 3.58
237 238 6.805713 ACCTGTTGTAGAAATGAAAAACCAG 58.194 36.000 0.00 0.00 0.00 4.00
550 555 4.446889 CCCTGAGAGGATAAGGAAATTGGG 60.447 50.000 0.00 0.00 37.67 4.12
567 572 0.970937 TACTCCGACCTTGCCCTGAG 60.971 60.000 0.00 0.00 0.00 3.35
655 661 9.444600 CCTGTAAGCAAGTAGGTTAAGATTTTA 57.555 33.333 0.00 0.00 41.45 1.52
657 663 7.686434 TCCTGTAAGCAAGTAGGTTAAGATTT 58.314 34.615 0.00 0.00 41.45 2.17
746 752 1.480954 TCCTATCCACTTTGTCGAGGC 59.519 52.381 0.00 0.00 0.00 4.70
752 758 6.234177 CAAGACTCTTTCCTATCCACTTTGT 58.766 40.000 0.00 0.00 0.00 2.83
839 845 2.033675 GGGTGTACCACTTGTTTTTCGG 59.966 50.000 3.11 0.00 39.85 4.30
840 846 2.033675 GGGGTGTACCACTTGTTTTTCG 59.966 50.000 3.11 0.00 42.91 3.46
970 981 1.696336 ACAGGATGATCCCATTCTCCG 59.304 52.381 8.08 0.00 36.48 4.63
976 987 2.443255 GGTAACCACAGGATGATCCCAT 59.557 50.000 8.08 0.00 39.69 4.00
1026 1037 2.416547 AGACATTTCGTGCTCATTTCCG 59.583 45.455 0.00 0.00 0.00 4.30
1071 1082 4.216687 TGCAACGAAAAGACCGGAAATAAT 59.783 37.500 9.46 0.00 0.00 1.28
1097 1109 5.886474 TGGTGGTTGTTTCTTGTTGTATGTA 59.114 36.000 0.00 0.00 0.00 2.29
1100 1112 4.202111 GCTGGTGGTTGTTTCTTGTTGTAT 60.202 41.667 0.00 0.00 0.00 2.29
1291 1305 5.480073 TCCATAAAAACTTGGGATCCAACAG 59.520 40.000 15.23 8.27 38.75 3.16
1460 1475 5.308497 TCCAAATGAAGGGAGTGTACAACTA 59.692 40.000 0.00 0.00 40.07 2.24
1481 1496 3.394274 TCAGAATCAACAAGGGTTCTCCA 59.606 43.478 0.00 0.00 38.24 3.86
1535 1550 1.901833 CACATTAAAAAGGGCTGGCCT 59.098 47.619 18.27 18.27 36.10 5.19
1554 1569 1.454847 AAAACAGGGTCAAGCGGCA 60.455 52.632 1.45 0.00 0.00 5.69
1610 1625 1.674359 TTTCCTTCTCGCAAAGCACA 58.326 45.000 0.00 0.00 0.00 4.57
1617 1632 2.930826 AGTCCTTTTTCCTTCTCGCA 57.069 45.000 0.00 0.00 0.00 5.10
1706 1721 1.544691 CAAAGCAATGCCAAGAGCTCT 59.455 47.619 11.45 11.45 44.23 4.09
1776 1792 2.015587 AGCGGTTTGGTACGAACAAAA 58.984 42.857 11.39 0.00 39.29 2.44
1779 1795 0.938713 CAAGCGGTTTGGTACGAACA 59.061 50.000 0.00 0.00 32.95 3.18
1945 1962 1.002624 TTTTCGGCGGCATCCTTCT 60.003 52.632 10.53 0.00 0.00 2.85
1976 1993 1.449246 GCATCCAGCAGAGCGAAGT 60.449 57.895 0.00 0.00 44.79 3.01
2001 2018 3.235200 AGAGCGAGCTTCTTATATGGGT 58.765 45.455 0.00 0.00 0.00 4.51
2132 2150 0.107703 CCATTAGCGCTCCTGTCCAA 60.108 55.000 16.34 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.