Multiple sequence alignment - TraesCS3B01G363600

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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 TraesCS3B01G363600 chr3B 100.000 2405 0 0 1 2405 575448925 575446521 0.000000e+00 4442.0
1 TraesCS3B01G363600 chr5B 93.939 1254 59 8 1168 2405 16283939 16285191 0.000000e+00 1879.0
2 TraesCS3B01G363600 chr1B 93.871 930 48 5 1483 2405 286759173 286760100 0.000000e+00 1393.0
3 TraesCS3B01G363600 chr1B 90.549 984 76 8 859 1830 38110864 38111842 0.000000e+00 1286.0
4 TraesCS3B01G363600 chr1B 92.061 781 48 6 681 1451 286758402 286759178 0.000000e+00 1086.0
5 TraesCS3B01G363600 chr1B 95.331 514 22 2 1894 2405 38111954 38112467 0.000000e+00 815.0
6 TraesCS3B01G363600 chr1B 95.122 123 6 0 680 802 38110732 38110854 6.780000e-46 195.0
7 TraesCS3B01G363600 chr1B 85.256 156 19 3 1958 2111 661148030 661148183 8.900000e-35 158.0
8 TraesCS3B01G363600 chr1B 85.714 91 13 0 1264 1354 661137071 661137161 1.970000e-16 97.1
9 TraesCS3B01G363600 chr1D 95.876 679 27 1 3 681 409609827 409609150 0.000000e+00 1098.0
10 TraesCS3B01G363600 chr1D 95.294 680 28 2 3 681 96986993 96986317 0.000000e+00 1075.0
11 TraesCS3B01G363600 chr1D 82.390 318 39 5 2010 2325 475249464 475249766 6.590000e-66 261.0
12 TraesCS3B01G363600 chr1D 89.116 147 11 4 2168 2309 318391136 318391282 6.830000e-41 178.0
13 TraesCS3B01G363600 chr1D 85.714 91 13 0 1264 1354 475239258 475239348 1.970000e-16 97.1
14 TraesCS3B01G363600 chr7D 95.723 678 27 2 3 678 310912338 310913015 0.000000e+00 1090.0
15 TraesCS3B01G363600 chr7D 95.322 684 27 3 3 681 134279777 134279094 0.000000e+00 1081.0
16 TraesCS3B01G363600 chr7D 76.471 187 41 3 679 865 159085470 159085287 5.470000e-17 99.0
17 TraesCS3B01G363600 chr7D 88.000 75 9 0 681 755 159083369 159083295 3.290000e-14 89.8
18 TraesCS3B01G363600 chr7D 93.478 46 3 0 688 733 582058459 582058504 4.290000e-08 69.4
19 TraesCS3B01G363600 chr3D 95.441 680 27 2 3 681 178476468 178475792 0.000000e+00 1081.0
20 TraesCS3B01G363600 chr3D 95.294 680 28 2 3 681 518395818 518395142 0.000000e+00 1075.0
21 TraesCS3B01G363600 chrUn 95.315 683 26 3 1 681 20068932 20068254 0.000000e+00 1079.0
22 TraesCS3B01G363600 chr5D 95.441 680 26 2 3 681 505291259 505290584 0.000000e+00 1079.0
23 TraesCS3B01G363600 chr6D 95.294 680 28 3 3 681 369888439 369887763 0.000000e+00 1075.0
24 TraesCS3B01G363600 chr4B 89.853 749 69 4 1663 2405 120577255 120578002 0.000000e+00 955.0
25 TraesCS3B01G363600 chr4B 85.524 677 71 14 680 1349 120511566 120512222 0.000000e+00 682.0
26 TraesCS3B01G363600 chr4B 86.232 138 11 1 1504 1641 120577144 120577273 2.490000e-30 143.0
27 TraesCS3B01G363600 chr6A 85.589 569 74 7 1782 2345 147978714 147978149 7.410000e-165 590.0
28 TraesCS3B01G363600 chr7B 81.270 630 75 24 1721 2342 611603965 611604559 1.010000e-128 470.0
29 TraesCS3B01G363600 chr4A 89.385 179 18 1 2168 2345 607632595 607632417 8.650000e-55 224.0
30 TraesCS3B01G363600 chr7A 88.742 151 11 5 2165 2309 46133235 46133385 1.900000e-41 180.0


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 TraesCS3B01G363600 chr3B 575446521 575448925 2404 True 4442.000000 4442 100.000000 1 2405 1 chr3B.!!$R1 2404
1 TraesCS3B01G363600 chr5B 16283939 16285191 1252 False 1879.000000 1879 93.939000 1168 2405 1 chr5B.!!$F1 1237
2 TraesCS3B01G363600 chr1B 286758402 286760100 1698 False 1239.500000 1393 92.966000 681 2405 2 chr1B.!!$F4 1724
3 TraesCS3B01G363600 chr1B 38110732 38112467 1735 False 765.333333 1286 93.667333 680 2405 3 chr1B.!!$F3 1725
4 TraesCS3B01G363600 chr1D 409609150 409609827 677 True 1098.000000 1098 95.876000 3 681 1 chr1D.!!$R2 678
5 TraesCS3B01G363600 chr1D 96986317 96986993 676 True 1075.000000 1075 95.294000 3 681 1 chr1D.!!$R1 678
6 TraesCS3B01G363600 chr7D 310912338 310913015 677 False 1090.000000 1090 95.723000 3 678 1 chr7D.!!$F1 675
7 TraesCS3B01G363600 chr7D 134279094 134279777 683 True 1081.000000 1081 95.322000 3 681 1 chr7D.!!$R1 678
8 TraesCS3B01G363600 chr3D 178475792 178476468 676 True 1081.000000 1081 95.441000 3 681 1 chr3D.!!$R1 678
9 TraesCS3B01G363600 chr3D 518395142 518395818 676 True 1075.000000 1075 95.294000 3 681 1 chr3D.!!$R2 678
10 TraesCS3B01G363600 chrUn 20068254 20068932 678 True 1079.000000 1079 95.315000 1 681 1 chrUn.!!$R1 680
11 TraesCS3B01G363600 chr5D 505290584 505291259 675 True 1079.000000 1079 95.441000 3 681 1 chr5D.!!$R1 678
12 TraesCS3B01G363600 chr6D 369887763 369888439 676 True 1075.000000 1075 95.294000 3 681 1 chr6D.!!$R1 678
13 TraesCS3B01G363600 chr4B 120511566 120512222 656 False 682.000000 682 85.524000 680 1349 1 chr4B.!!$F1 669
14 TraesCS3B01G363600 chr4B 120577144 120578002 858 False 549.000000 955 88.042500 1504 2405 2 chr4B.!!$F2 901
15 TraesCS3B01G363600 chr6A 147978149 147978714 565 True 590.000000 590 85.589000 1782 2345 1 chr6A.!!$R1 563
16 TraesCS3B01G363600 chr7B 611603965 611604559 594 False 470.000000 470 81.270000 1721 2342 1 chr7B.!!$F1 621


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
748 760 0.396811 GCCTCGGCTACCCATAACAT 59.603 55.0 0.0 0.0 38.26 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1805 1.311859 CAAGTGAGCAGCCAGTTCAA 58.688 50.0 0.0 0.0 39.28 2.69 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
94 96 7.606839 AGTTAGAGCTAGTTTGGGTTGAAATAC 59.393 37.037 0.00 0.00 0.00 1.89
199 202 8.050930 GGTTCTAATTGGGTTAGTTATCCTTGA 58.949 37.037 0.00 0.00 40.58 3.02
416 428 2.028876 CACCGGTTGTTTTTCTCCCTT 58.971 47.619 2.97 0.00 0.00 3.95
430 442 3.276091 CCTTTGTCGTGCGTGGCA 61.276 61.111 0.00 0.00 35.60 4.92
432 444 2.202946 TTTGTCGTGCGTGGCAGA 60.203 55.556 0.00 0.00 40.08 4.26
495 507 1.887198 GTTCCTTCTCTGTCTCACGGA 59.113 52.381 0.00 0.00 31.67 4.69
514 526 3.496130 CGGACATATCATTGGTCTTGCTC 59.504 47.826 0.00 0.00 0.00 4.26
540 552 6.128688 GCTCTAGCGCTAATTCTAATTTGGAG 60.129 42.308 19.37 16.24 0.00 3.86
645 657 5.441718 TTCTAGATGCCCAAAGATTCAGT 57.558 39.130 0.00 0.00 0.00 3.41
673 685 6.055588 CCTTTCTAGGTGTTTCAGTTTCAGA 58.944 40.000 0.00 0.00 36.74 3.27
678 690 4.589908 AGGTGTTTCAGTTTCAGACTTGT 58.410 39.130 0.00 0.00 36.10 3.16
748 760 0.396811 GCCTCGGCTACCCATAACAT 59.603 55.000 0.00 0.00 38.26 2.71
762 774 9.667107 CTACCCATAACATCACGGATTAATAAT 57.333 33.333 0.00 0.00 0.00 1.28
774 786 6.590292 CACGGATTAATAATAGCCTCACGATT 59.410 38.462 0.00 0.00 0.00 3.34
822 834 8.695456 ACCATTAAAATTATGCTAACCCTCAAG 58.305 33.333 0.00 0.00 0.00 3.02
830 842 2.373836 TGCTAACCCTCAAGCCAAACTA 59.626 45.455 0.00 0.00 37.97 2.24
832 844 3.809324 GCTAACCCTCAAGCCAAACTACA 60.809 47.826 0.00 0.00 32.40 2.74
865 877 2.092882 CGGGCGGACGAAAACTCTC 61.093 63.158 0.00 0.00 35.47 3.20
1044 1066 1.830145 CTTCCAATCCGTCCCCGAT 59.170 57.895 0.00 0.00 35.63 4.18
1063 1085 1.410004 TATCGGCGAGGAGATTGGTT 58.590 50.000 17.22 0.00 0.00 3.67
1142 1164 3.447742 CATCAAGTCGAATGACCGATCA 58.552 45.455 4.44 0.00 46.74 2.92
1172 1194 4.031129 CTGGACTGCAGCCTGGCT 62.031 66.667 17.22 17.22 40.77 4.75
1239 1261 2.202703 GCACGCGGTTACGAGGAT 60.203 61.111 12.47 0.00 44.51 3.24
1319 1343 3.918253 ATGCCGCCGTTGTGGTCAT 62.918 57.895 0.00 0.00 44.42 3.06
1379 1403 2.235016 CGCACCGTGACGTCAAACT 61.235 57.895 21.95 1.70 0.00 2.66
1385 1409 0.852777 CGTGACGTCAAACTGGACAG 59.147 55.000 21.95 0.00 37.66 3.51
1386 1410 0.582005 GTGACGTCAAACTGGACAGC 59.418 55.000 21.95 0.00 37.66 4.40
1455 1482 4.524328 CAGCTCAGTAAAATTTTGGGTCCT 59.476 41.667 13.76 0.71 0.00 3.85
1491 1518 4.278513 CCCGGGGTTTGTGGAGCA 62.279 66.667 14.71 0.00 0.00 4.26
1510 1537 1.067582 CCGGCGTGGTCCTAGATTC 59.932 63.158 6.01 0.00 0.00 2.52
1536 1563 1.130777 TCATGGGATTGGATCGAGCA 58.869 50.000 1.84 0.00 0.00 4.26
1550 1577 1.151777 CGAGCAACCACACGAGTTGT 61.152 55.000 5.62 0.00 45.14 3.32
1603 1630 1.133025 GTGGAATCCAATCACCGCAAG 59.867 52.381 2.31 0.00 34.18 4.01
1667 1694 8.541234 AGAAAGGTAATCTCTTTCCTTAATCGT 58.459 33.333 11.48 0.00 46.65 3.73
1700 1727 0.034670 ATCCACTCCTTCCTTGCTGC 60.035 55.000 0.00 0.00 0.00 5.25
1709 1736 2.092753 CCTTCCTTGCTGCTGAATCCTA 60.093 50.000 0.00 0.00 0.00 2.94
1727 1754 2.092753 CCTACATGTTGTGCTGATCCCT 60.093 50.000 2.30 0.00 0.00 4.20
1729 1756 2.880443 ACATGTTGTGCTGATCCCTTT 58.120 42.857 0.00 0.00 0.00 3.11
1786 1822 0.535780 CCTGTTGAACTGGCTGCTCA 60.536 55.000 8.33 0.00 30.42 4.26
1804 1840 1.150827 CACTTGTTGCTCGATGCTGA 58.849 50.000 8.07 0.00 43.37 4.26
1805 1841 1.532437 CACTTGTTGCTCGATGCTGAA 59.468 47.619 8.07 0.00 43.37 3.02
1867 1984 8.770828 GCTTTGAGTTTCTGTATAGTGTTGTTA 58.229 33.333 0.00 0.00 0.00 2.41
1873 1990 7.172703 AGTTTCTGTATAGTGTTGTTACTTGCC 59.827 37.037 0.00 0.00 32.19 4.52
1911 2028 1.194772 GCTGTTGTTCACGCTAGGAAC 59.805 52.381 4.04 4.04 43.78 3.62
1946 2063 6.021672 ACATGGGATATAGCATCTCTGAGAA 58.978 40.000 12.00 0.00 0.00 2.87
1954 2071 3.027412 AGCATCTCTGAGAACGTACCAT 58.973 45.455 12.00 0.00 0.00 3.55
2256 2385 4.785346 AATGATAGGTCTCCAGCATGTT 57.215 40.909 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 6.124088 CCTCTTGTTTCGATAATTTGAGGG 57.876 41.667 10.90 0.00 36.03 4.30
164 167 8.342270 ACTAACCCAATTAGAACCTCTCTACTA 58.658 37.037 0.81 0.00 42.75 1.82
168 171 6.954352 AACTAACCCAATTAGAACCTCTCT 57.046 37.500 0.81 0.00 42.75 3.10
400 412 3.129813 ACGACAAAGGGAGAAAAACAACC 59.870 43.478 0.00 0.00 0.00 3.77
416 428 2.661537 CTCTGCCACGCACGACAA 60.662 61.111 0.00 0.00 33.79 3.18
430 442 2.136878 CCCTGGTAGATGCGCCTCT 61.137 63.158 19.26 19.26 0.00 3.69
432 444 2.041922 TCCCTGGTAGATGCGCCT 60.042 61.111 4.18 0.00 0.00 5.52
495 507 2.874701 GCGAGCAAGACCAATGATATGT 59.125 45.455 0.00 0.00 0.00 2.29
540 552 6.410540 ACCAAGTTTGATCAGGATCTACTTC 58.589 40.000 18.68 5.28 39.25 3.01
630 642 2.158475 AGGTGAACTGAATCTTTGGGCA 60.158 45.455 0.00 0.00 0.00 5.36
660 672 7.954788 AGAGATACAAGTCTGAAACTGAAAC 57.045 36.000 0.00 0.00 38.58 2.78
701 713 6.316140 GGTGCACTTAGTGATGAATATGTTCA 59.684 38.462 17.40 7.39 40.07 3.18
748 760 5.242171 TCGTGAGGCTATTATTAATCCGTGA 59.758 40.000 0.00 0.00 0.00 4.35
762 774 3.527507 AGGATCCTAATCGTGAGGCTA 57.472 47.619 14.27 0.00 33.73 3.93
830 842 3.584834 GCCCGTCAAAATTGCTAAATGT 58.415 40.909 0.00 0.00 0.00 2.71
832 844 2.416701 CCGCCCGTCAAAATTGCTAAAT 60.417 45.455 0.00 0.00 0.00 1.40
865 877 2.037772 GTGGGATATGCACTACTCTGGG 59.962 54.545 0.00 0.00 0.00 4.45
876 888 4.927782 TGCGGGCGTGGGATATGC 62.928 66.667 0.00 0.00 40.71 3.14
1044 1066 1.068588 CAACCAATCTCCTCGCCGATA 59.931 52.381 0.00 0.00 0.00 2.92
1119 1141 1.548719 TCGGTCATTCGACTTGATGGT 59.451 47.619 0.93 0.00 42.21 3.55
1207 1229 1.598130 GTGCACCTGGAAGACGCTT 60.598 57.895 5.22 0.00 34.07 4.68
1239 1261 1.746239 CATGTGCGTCCATGCCTCA 60.746 57.895 3.97 0.00 36.15 3.86
1379 1403 4.056125 CGAGGAGCACGCTGTCCA 62.056 66.667 0.00 0.00 35.02 4.02
1386 1410 3.456431 CTAGGCGTCGAGGAGCACG 62.456 68.421 9.75 0.00 39.09 5.34
1427 1451 2.200373 AATTTTACTGAGCTGGGCGT 57.800 45.000 0.00 0.00 0.00 5.68
1481 1508 4.555709 ACGCCGGTGCTCCACAAA 62.556 61.111 16.69 0.00 35.86 2.83
1510 1537 3.004002 CGATCCAATCCCATGACATGTTG 59.996 47.826 14.26 11.46 0.00 3.33
1536 1563 0.868602 CGTCGACAACTCGTGTGGTT 60.869 55.000 17.16 0.00 41.96 3.67
1700 1727 4.256110 TCAGCACAACATGTAGGATTCAG 58.744 43.478 0.00 0.00 0.00 3.02
1709 1736 2.559668 CAAAGGGATCAGCACAACATGT 59.440 45.455 0.00 0.00 0.00 3.21
1727 1754 3.215568 CAGCGCCCACCACACAAA 61.216 61.111 2.29 0.00 0.00 2.83
1771 1805 1.311859 CAAGTGAGCAGCCAGTTCAA 58.688 50.000 0.00 0.00 39.28 2.69
1805 1841 2.596631 CACCAAGCCAGCACAGCT 60.597 61.111 0.00 0.00 44.19 4.24
1839 1956 7.282224 ACAACACTATACAGAAACTCAAAGCAA 59.718 33.333 0.00 0.00 0.00 3.91
1911 2028 5.877012 GCTATATCCCATGTTGGTATGTCAG 59.123 44.000 0.00 0.00 35.17 3.51
1946 2063 6.105397 TCTTTTCAAGTCCTTATGGTACGT 57.895 37.500 0.00 0.00 34.23 3.57
1954 2071 4.042809 TCCATGGCTCTTTTCAAGTCCTTA 59.957 41.667 6.96 0.00 0.00 2.69
2245 2374 2.089980 CTCCTTTCCAACATGCTGGAG 58.910 52.381 17.04 7.56 46.20 3.86
2256 2385 5.779241 ATTCAACTCCATACTCCTTTCCA 57.221 39.130 0.00 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.