Multiple sequence alignment - TraesCS3B01G176300

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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 TraesCS3B01G176300 chr3B 100.000 2264 0 0 1 2264 179362670 179360407 0.000000e+00 4181
1 TraesCS3B01G176300 chr3B 95.291 1720 62 10 1 1702 112909769 112911487 0.000000e+00 2710
2 TraesCS3B01G176300 chr2B 98.129 1710 26 2 1 1704 798600940 798602649 0.000000e+00 2976
3 TraesCS3B01G176300 chr2B 96.263 562 18 2 1705 2264 154583496 154582936 0.000000e+00 918
4 TraesCS3B01G176300 chr2B 94.858 564 13 4 1705 2264 798602994 798603545 0.000000e+00 867
5 TraesCS3B01G176300 chr2B 87.461 319 16 10 1704 2022 798602875 798603169 1.660000e-91 346
6 TraesCS3B01G176300 chr7B 97.661 1710 34 2 1 1704 707572962 707571253 0.000000e+00 2931
7 TraesCS3B01G176300 chr7B 92.953 1717 107 5 1 1705 34282317 34280603 0.000000e+00 2488
8 TraesCS3B01G176300 chr7B 96.435 561 19 1 1704 2264 577213250 577213809 0.000000e+00 924
9 TraesCS3B01G176300 chr7B 90.764 563 26 3 1704 2264 102654578 102655116 0.000000e+00 728
10 TraesCS3B01G176300 chr7B 90.893 560 26 5 1705 2264 707570917 707570383 0.000000e+00 728
11 TraesCS3B01G176300 chr3A 96.558 1714 47 6 1 1702 44774235 44772522 0.000000e+00 2828
12 TraesCS3B01G176300 chr2A 92.940 1714 107 4 1 1702 372742753 372744464 0.000000e+00 2483
13 TraesCS3B01G176300 chr5D 92.696 1725 102 14 1 1705 387840692 387838972 0.000000e+00 2466
14 TraesCS3B01G176300 chr5B 92.321 1719 113 12 1 1705 578837561 578835848 0.000000e+00 2425
15 TraesCS3B01G176300 chr5B 90.043 462 20 3 1805 2264 436478702 436479139 1.950000e-160 575
16 TraesCS3B01G176300 chr5B 94.502 291 16 0 1705 1995 454662923 454663213 1.230000e-122 449
17 TraesCS3B01G176300 chr4A 91.473 1724 124 11 1 1702 737660720 737662442 0.000000e+00 2348
18 TraesCS3B01G176300 chr4A 94.211 570 23 1 1705 2264 698021605 698021036 0.000000e+00 861
19 TraesCS3B01G176300 chrUn 90.764 563 26 3 1704 2264 361055822 361055284 0.000000e+00 728
20 TraesCS3B01G176300 chr7A 90.764 563 26 3 1704 2264 497717483 497716945 0.000000e+00 728
21 TraesCS3B01G176300 chr6B 90.351 570 31 8 1705 2264 661053644 661054199 0.000000e+00 726
22 TraesCS3B01G176300 chr5A 90.747 562 27 3 1704 2264 591475655 591476192 0.000000e+00 726
23 TraesCS3B01G176300 chr1B 90.442 565 26 9 1704 2264 302770392 302769852 0.000000e+00 719
24 TraesCS3B01G176300 chr1B 88.434 562 23 12 1704 2264 649299273 649298753 6.820000e-180 640


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 TraesCS3B01G176300 chr3B 179360407 179362670 2263 True 4181.000000 4181 100.000000 1 2264 1 chr3B.!!$R1 2263
1 TraesCS3B01G176300 chr3B 112909769 112911487 1718 False 2710.000000 2710 95.291000 1 1702 1 chr3B.!!$F1 1701
2 TraesCS3B01G176300 chr2B 798600940 798603545 2605 False 1396.333333 2976 93.482667 1 2264 3 chr2B.!!$F1 2263
3 TraesCS3B01G176300 chr2B 154582936 154583496 560 True 918.000000 918 96.263000 1705 2264 1 chr2B.!!$R1 559
4 TraesCS3B01G176300 chr7B 34280603 34282317 1714 True 2488.000000 2488 92.953000 1 1705 1 chr7B.!!$R1 1704
5 TraesCS3B01G176300 chr7B 707570383 707572962 2579 True 1829.500000 2931 94.277000 1 2264 2 chr7B.!!$R2 2263
6 TraesCS3B01G176300 chr7B 577213250 577213809 559 False 924.000000 924 96.435000 1704 2264 1 chr7B.!!$F2 560
7 TraesCS3B01G176300 chr7B 102654578 102655116 538 False 728.000000 728 90.764000 1704 2264 1 chr7B.!!$F1 560
8 TraesCS3B01G176300 chr3A 44772522 44774235 1713 True 2828.000000 2828 96.558000 1 1702 1 chr3A.!!$R1 1701
9 TraesCS3B01G176300 chr2A 372742753 372744464 1711 False 2483.000000 2483 92.940000 1 1702 1 chr2A.!!$F1 1701
10 TraesCS3B01G176300 chr5D 387838972 387840692 1720 True 2466.000000 2466 92.696000 1 1705 1 chr5D.!!$R1 1704
11 TraesCS3B01G176300 chr5B 578835848 578837561 1713 True 2425.000000 2425 92.321000 1 1705 1 chr5B.!!$R1 1704
12 TraesCS3B01G176300 chr4A 737660720 737662442 1722 False 2348.000000 2348 91.473000 1 1702 1 chr4A.!!$F1 1701
13 TraesCS3B01G176300 chr4A 698021036 698021605 569 True 861.000000 861 94.211000 1705 2264 1 chr4A.!!$R1 559
14 TraesCS3B01G176300 chrUn 361055284 361055822 538 True 728.000000 728 90.764000 1704 2264 1 chrUn.!!$R1 560
15 TraesCS3B01G176300 chr7A 497716945 497717483 538 True 728.000000 728 90.764000 1704 2264 1 chr7A.!!$R1 560
16 TraesCS3B01G176300 chr6B 661053644 661054199 555 False 726.000000 726 90.351000 1705 2264 1 chr6B.!!$F1 559
17 TraesCS3B01G176300 chr5A 591475655 591476192 537 False 726.000000 726 90.747000 1704 2264 1 chr5A.!!$F1 560
18 TraesCS3B01G176300 chr1B 302769852 302770392 540 True 719.000000 719 90.442000 1704 2264 1 chr1B.!!$R1 560
19 TraesCS3B01G176300 chr1B 649298753 649299273 520 True 640.000000 640 88.434000 1704 2264 1 chr1B.!!$R2 560

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
623 625 0.112606 AGAGGTGGAAGAGGTGACGA 59.887 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2501 0.107456 CAGCTTGTCTGGTCACCTGT 59.893 55.0 0.0 0.0 39.15 4.0 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
195 196 5.513094 GCCTAGTAAGTATCATTGGCCATGA 60.513 44.000 6.09 13.32 46.41 3.07
302 304 1.819632 CTAGGTTGACATGGGCGCC 60.820 63.158 21.18 21.18 0.00 6.53
539 541 0.681243 GAAGGGGGACACAATGAGCC 60.681 60.000 0.00 0.00 0.00 4.70
623 625 0.112606 AGAGGTGGAAGAGGTGACGA 59.887 55.000 0.00 0.00 0.00 4.20
664 669 2.039480 ACGAGTGTCAGAGGTGGTAGTA 59.961 50.000 0.00 0.00 0.00 1.82
700 711 1.800805 CACAAGTGCTAGAGGTGGTG 58.199 55.000 0.00 0.00 0.00 4.17
703 714 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
707 718 1.810532 CTAGAGGTGGTGGTCGAGC 59.189 63.158 7.89 7.89 0.00 5.03
708 719 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.000 16.64 0.00 33.17 4.09
1188 1211 4.678256 AGTCATGGACAGAAGGTAGAAGA 58.322 43.478 0.00 0.00 34.60 2.87
1201 1224 6.766467 AGAAGGTAGAAGATTTTTCGTGTGTT 59.234 34.615 0.00 0.00 0.00 3.32
1576 1599 0.668535 GAAAACTTGCAAGGGCTCGT 59.331 50.000 29.18 6.16 41.91 4.18
1672 1696 0.875908 CACCGGCGTCGATGATGAAT 60.876 55.000 12.93 0.00 39.00 2.57
1991 2501 2.426522 GTCTGGCTTGTTATGCTCACA 58.573 47.619 0.00 0.00 0.00 3.58
2203 2733 0.621571 TCACCTCTAGCCCTGCCAAT 60.622 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.365582 ACTTGTTGCCGTGAAGACTTT 58.634 42.857 0.00 0.00 0.00 2.66
195 196 0.586319 CCGCCGTTATCAAATGCGAT 59.414 50.000 3.51 0.00 0.00 4.58
302 304 4.021981 GGTCCAAGAAAGGGTGAAATCTTG 60.022 45.833 7.26 7.26 45.22 3.02
539 541 6.761731 TGGTTTTCTTATTTTTGCATGTCG 57.238 33.333 0.00 0.00 0.00 4.35
623 625 1.983224 CTTCCTCGACCACCACCAT 59.017 57.895 0.00 0.00 0.00 3.55
664 669 0.966370 GTGCTCCCTCTACGACCACT 60.966 60.000 0.00 0.00 0.00 4.00
698 703 0.038159 ACTTGTGCTAGCTCGACCAC 60.038 55.000 17.23 4.92 0.00 4.16
700 711 1.355066 GCACTTGTGCTAGCTCGACC 61.355 60.000 17.23 0.00 0.00 4.79
703 714 3.721625 TAGCACTTGTGCTAGCTCG 57.278 52.632 25.81 3.24 44.28 5.03
708 719 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
1188 1211 5.219633 GCATAGTTGGAACACACGAAAAAT 58.780 37.500 0.00 0.00 39.29 1.82
1201 1224 3.457234 GACGATCATGTGCATAGTTGGA 58.543 45.455 0.00 0.00 0.00 3.53
1576 1599 1.657751 CGTCCTCCTCTCGTGCATCA 61.658 60.000 0.00 0.00 0.00 3.07
1672 1696 8.596271 TCATACATTAAACAAAGTCTCGACAA 57.404 30.769 0.00 0.00 0.00 3.18
1793 2043 2.204136 TGGGTGTGGGAGGCAGAT 60.204 61.111 0.00 0.00 0.00 2.90
1991 2501 0.107456 CAGCTTGTCTGGTCACCTGT 59.893 55.000 0.00 0.00 39.15 4.00
2203 2733 2.276116 GCTGGACGAGGGAGTGACA 61.276 63.158 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.