Multiple sequence alignment - TraesCS7D01G233600

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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 TraesCS7D01G233600 chr7D 100.000 2243 0 0 1 2243 195394797 195397039 0.000000e+00 4143.0
1 TraesCS7D01G233600 chr7D 95.466 1610 46 10 644 2243 354527233 354528825 0.000000e+00 2543.0
2 TraesCS7D01G233600 chr7D 95.038 786 25 2 765 1549 346185045 346184273 0.000000e+00 1223.0
3 TraesCS7D01G233600 chr7D 95.952 667 17 3 1587 2243 346184266 346183600 0.000000e+00 1074.0
4 TraesCS7D01G233600 chr7D 97.152 632 15 2 1 631 558133308 558132679 0.000000e+00 1064.0
5 TraesCS7D01G233600 chr7D 89.944 716 43 16 841 1535 588678986 588678279 0.000000e+00 896.0
6 TraesCS7D01G233600 chr7D 88.550 131 6 3 1414 1535 588841162 588841292 1.390000e-32 150.0
7 TraesCS7D01G233600 chr7D 80.292 137 22 4 1667 1799 291556139 291556004 5.100000e-17 99.0
8 TraesCS7D01G233600 chr7B 92.642 965 65 4 707 1668 253264641 253263680 0.000000e+00 1384.0
9 TraesCS7D01G233600 chr7B 89.959 727 43 13 838 1535 663107679 663108404 0.000000e+00 911.0
10 TraesCS7D01G233600 chr7B 94.983 578 24 4 1668 2243 253263640 253263066 0.000000e+00 902.0
11 TraesCS7D01G233600 chr7B 94.393 107 4 2 1562 1668 248341021 248340917 1.780000e-36 163.0
12 TraesCS7D01G233600 chr4B 92.097 911 66 4 760 1668 141079988 141080894 0.000000e+00 1279.0
13 TraesCS7D01G233600 chr4B 93.772 578 30 4 1668 2243 141080934 141081507 0.000000e+00 863.0
14 TraesCS7D01G233600 chr4B 94.684 395 18 2 1852 2243 621660522 621660916 5.300000e-171 610.0
15 TraesCS7D01G233600 chr4B 92.677 396 25 3 1852 2243 315214466 315214861 3.230000e-158 568.0
16 TraesCS7D01G233600 chr4B 81.022 137 21 5 1667 1800 298693573 298693439 1.100000e-18 104.0
17 TraesCS7D01G233600 chr2B 90.948 928 78 4 744 1668 311334421 311335345 0.000000e+00 1243.0
18 TraesCS7D01G233600 chr2B 92.361 576 36 4 1670 2243 311335387 311335956 0.000000e+00 813.0
19 TraesCS7D01G233600 chr2B 93.687 396 20 4 1852 2243 519069650 519070044 2.480000e-164 588.0
20 TraesCS7D01G233600 chr2B 100.000 41 0 0 802 842 220962970 220963010 2.390000e-10 76.8
21 TraesCS7D01G233600 chr4D 97.468 632 15 1 1 631 447376010 447375379 0.000000e+00 1077.0
22 TraesCS7D01G233600 chr4D 96.419 391 10 3 1856 2243 35719764 35720153 1.880000e-180 641.0
23 TraesCS7D01G233600 chr4D 93.536 263 7 6 1628 1880 35659421 35659159 1.260000e-102 383.0
24 TraesCS7D01G233600 chr4D 93.130 262 8 6 1628 1880 35645040 35644780 2.100000e-100 375.0
25 TraesCS7D01G233600 chr4D 95.455 154 6 1 644 797 384432259 384432411 6.190000e-61 244.0
26 TraesCS7D01G233600 chr4D 94.805 154 8 0 644 797 310939795 310939642 8.000000e-60 241.0
27 TraesCS7D01G233600 chr4D 96.528 144 5 0 644 787 153518857 153518714 2.880000e-59 239.0
28 TraesCS7D01G233600 chr4D 81.022 137 21 4 1667 1799 305471157 305471022 1.100000e-18 104.0
29 TraesCS7D01G233600 chr1D 97.314 633 15 2 1 631 241568553 241569185 0.000000e+00 1074.0
30 TraesCS7D01G233600 chr1D 96.989 631 17 1 1 631 74603328 74603956 0.000000e+00 1059.0
31 TraesCS7D01G233600 chr3D 97.310 632 16 1 1 631 364160378 364161009 0.000000e+00 1072.0
32 TraesCS7D01G233600 chr3D 97.310 632 14 2 1 631 53722344 53721715 0.000000e+00 1070.0
33 TraesCS7D01G233600 chr3D 93.548 155 9 1 644 797 368369469 368369315 1.730000e-56 230.0
34 TraesCS7D01G233600 chr6D 97.013 636 14 4 1 633 365243313 365242680 0.000000e+00 1064.0
35 TraesCS7D01G233600 chr6D 83.824 68 11 0 1667 1734 167227074 167227141 5.170000e-07 65.8
36 TraesCS7D01G233600 chr5D 97.152 632 15 2 1 631 368199996 368199367 0.000000e+00 1064.0
37 TraesCS7D01G233600 chr5D 95.808 167 4 2 1852 2015 427199018 427198852 1.320000e-67 267.0
38 TraesCS7D01G233600 chr2D 96.845 634 17 2 1 633 525621371 525620740 0.000000e+00 1057.0
39 TraesCS7D01G233600 chr2D 94.805 154 8 0 644 797 295070431 295070278 8.000000e-60 241.0
40 TraesCS7D01G233600 chr2D 91.667 108 8 1 1562 1668 3575706 3575599 4.990000e-32 148.0
41 TraesCS7D01G233600 chr7A 86.742 709 52 20 851 1524 680406665 680407366 0.000000e+00 750.0
42 TraesCS7D01G233600 chr7A 90.683 161 9 5 1667 1824 238547042 238547199 2.260000e-50 209.0
43 TraesCS7D01G233600 chr3B 94.684 395 18 2 1852 2243 658959599 658959993 5.300000e-171 610.0
44 TraesCS7D01G233600 chr3B 93.451 397 20 4 1852 2243 383919956 383920351 3.210000e-163 584.0
45 TraesCS7D01G233600 chr3B 95.122 41 2 0 802 842 556457111 556457151 5.170000e-07 65.8
46 TraesCS7D01G233600 chr1B 93.434 396 21 4 1852 2243 30060643 30061037 1.150000e-162 582.0
47 TraesCS7D01G233600 chr1B 87.578 161 15 3 1668 1824 280436043 280436202 4.920000e-42 182.0
48 TraesCS7D01G233600 chr1B 86.875 160 17 3 1668 1824 560819451 560819609 2.290000e-40 176.0
49 TraesCS7D01G233600 chr1A 94.375 160 7 1 644 803 273196585 273196428 6.190000e-61 244.0
50 TraesCS7D01G233600 chr1A 93.750 160 10 0 644 803 230722851 230722692 8.000000e-60 241.0
51 TraesCS7D01G233600 chr2A 93.750 160 9 1 644 803 235806342 235806500 2.880000e-59 239.0
52 TraesCS7D01G233600 chr2A 89.062 64 5 2 1545 1606 412388447 412388510 6.640000e-11 78.7
53 TraesCS7D01G233600 chr5B 87.817 197 15 4 1668 1855 308024013 308023817 2.900000e-54 222.0
54 TraesCS7D01G233600 chr5B 88.125 160 15 3 1668 1824 570010608 570010766 1.060000e-43 187.0
55 TraesCS7D01G233600 chr5B 91.589 107 7 2 1562 1668 308024157 308024053 1.800000e-31 147.0
56 TraesCS7D01G233600 chr5B 92.683 41 3 0 802 842 380598298 380598338 2.410000e-05 60.2
57 TraesCS7D01G233600 chr4A 97.297 74 2 0 769 842 462309050 462309123 2.340000e-25 126.0
58 TraesCS7D01G233600 chr6A 84.615 130 5 7 1545 1666 416958135 416958013 5.060000e-22 115.0
59 TraesCS7D01G233600 chr6A 87.500 64 5 3 1545 1606 416958324 416958262 1.110000e-08 71.3
60 TraesCS7D01G233600 chr6A 85.938 64 7 2 1545 1606 416958511 416958448 1.440000e-07 67.6
61 TraesCS7D01G233600 chrUn 78.519 135 25 3 1669 1800 456120208 456120075 3.970000e-13 86.1


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 TraesCS7D01G233600 chr7D 195394797 195397039 2242 False 4143.0 4143 100.0000 1 2243 1 chr7D.!!$F1 2242
1 TraesCS7D01G233600 chr7D 354527233 354528825 1592 False 2543.0 2543 95.4660 644 2243 1 chr7D.!!$F2 1599
2 TraesCS7D01G233600 chr7D 346183600 346185045 1445 True 1148.5 1223 95.4950 765 2243 2 chr7D.!!$R4 1478
3 TraesCS7D01G233600 chr7D 558132679 558133308 629 True 1064.0 1064 97.1520 1 631 1 chr7D.!!$R2 630
4 TraesCS7D01G233600 chr7D 588678279 588678986 707 True 896.0 896 89.9440 841 1535 1 chr7D.!!$R3 694
5 TraesCS7D01G233600 chr7B 253263066 253264641 1575 True 1143.0 1384 93.8125 707 2243 2 chr7B.!!$R2 1536
6 TraesCS7D01G233600 chr7B 663107679 663108404 725 False 911.0 911 89.9590 838 1535 1 chr7B.!!$F1 697
7 TraesCS7D01G233600 chr4B 141079988 141081507 1519 False 1071.0 1279 92.9345 760 2243 2 chr4B.!!$F3 1483
8 TraesCS7D01G233600 chr2B 311334421 311335956 1535 False 1028.0 1243 91.6545 744 2243 2 chr2B.!!$F3 1499
9 TraesCS7D01G233600 chr4D 447375379 447376010 631 True 1077.0 1077 97.4680 1 631 1 chr4D.!!$R6 630
10 TraesCS7D01G233600 chr1D 241568553 241569185 632 False 1074.0 1074 97.3140 1 631 1 chr1D.!!$F2 630
11 TraesCS7D01G233600 chr1D 74603328 74603956 628 False 1059.0 1059 96.9890 1 631 1 chr1D.!!$F1 630
12 TraesCS7D01G233600 chr3D 364160378 364161009 631 False 1072.0 1072 97.3100 1 631 1 chr3D.!!$F1 630
13 TraesCS7D01G233600 chr3D 53721715 53722344 629 True 1070.0 1070 97.3100 1 631 1 chr3D.!!$R1 630
14 TraesCS7D01G233600 chr6D 365242680 365243313 633 True 1064.0 1064 97.0130 1 633 1 chr6D.!!$R1 632
15 TraesCS7D01G233600 chr5D 368199367 368199996 629 True 1064.0 1064 97.1520 1 631 1 chr5D.!!$R1 630
16 TraesCS7D01G233600 chr2D 525620740 525621371 631 True 1057.0 1057 96.8450 1 633 1 chr2D.!!$R3 632
17 TraesCS7D01G233600 chr7A 680406665 680407366 701 False 750.0 750 86.7420 851 1524 1 chr7A.!!$F2 673

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
168 172 1.533625 AAGGTACACGTGCATTGCAT 58.466 45.0 17.22 0.78 41.91 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1934 1.840635 GCTTCCCCACCTATCACTTCT 59.159 52.381 0.0 0.0 0.0 2.85 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
55 56 4.304939 GAGAACAAGCTTAACGTGTACCT 58.695 43.478 0.00 0.00 40.33 3.08
168 172 1.533625 AAGGTACACGTGCATTGCAT 58.466 45.000 17.22 0.78 41.91 3.96
385 389 8.428063 ACAAATCATGTAGAAAAACATTTGGGA 58.572 29.630 12.54 0.00 41.63 4.37
437 441 3.427161 AGAAGTGCTTGTGTTTTGAGC 57.573 42.857 0.00 0.00 36.95 4.26
455 459 5.840243 TGAGCTTTGTGCATTATGCTTAT 57.160 34.783 18.44 0.00 45.31 1.73
507 511 2.971330 TGTGGCAAAATCTGGTGGAATT 59.029 40.909 0.00 0.00 0.00 2.17
933 963 2.262774 CTCCTGACCAGCACCCATCC 62.263 65.000 0.00 0.00 0.00 3.51
994 1036 4.170062 GGTCATCGTCGGCGTCGA 62.170 66.667 28.73 28.73 43.86 4.20
1146 1188 2.116125 GAGGCCAAGTGGGTGCTT 59.884 61.111 5.01 0.00 39.65 3.91
1178 1220 1.888215 CTCTGCCTCAAGAACAAGCA 58.112 50.000 0.00 0.00 0.00 3.91
1181 1223 1.884579 CTGCCTCAAGAACAAGCACAT 59.115 47.619 0.00 0.00 0.00 3.21
1549 1618 9.427127 GATGCGATACAGTTCTTCTTAATTTTC 57.573 33.333 0.00 0.00 0.00 2.29
1807 1921 2.751259 TGCTCGAACAGTTACCGTCTAT 59.249 45.455 0.00 0.00 0.00 1.98
1820 1934 2.751259 ACCGTCTATTGTAGCAGTTCGA 59.249 45.455 0.00 0.00 0.00 3.71
1840 1954 1.840635 AGAAGTGATAGGTGGGGAAGC 59.159 52.381 0.00 0.00 0.00 3.86
2166 2284 4.261614 GCTACCCAGAAAAACAGGAAGTTG 60.262 45.833 0.00 0.00 41.19 3.16
2222 2340 9.592196 AAATGTATACTAGTTCGGGGTCTATAA 57.408 33.333 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 172 1.630223 TGGTTGCCAAATCTCATGCA 58.370 45.000 0.00 0.0 0.00 3.96
325 329 3.613910 GCCTTACAACGCACAATTCCATT 60.614 43.478 0.00 0.0 0.00 3.16
455 459 7.962995 ATCTAGAAGACTCTATGGTTGAACA 57.037 36.000 0.00 0.0 33.59 3.18
507 511 3.646162 ACTGGCCGTTGGATATCATCTAA 59.354 43.478 4.83 0.0 0.00 2.10
639 644 3.036091 TCTAAATAGTCCCACCCTTCGG 58.964 50.000 0.00 0.0 0.00 4.30
640 645 4.748277 TTCTAAATAGTCCCACCCTTCG 57.252 45.455 0.00 0.0 0.00 3.79
641 646 5.191426 GGTTTCTAAATAGTCCCACCCTTC 58.809 45.833 0.00 0.0 0.00 3.46
642 647 4.017775 GGGTTTCTAAATAGTCCCACCCTT 60.018 45.833 0.00 0.0 39.75 3.95
734 739 3.119709 CTCGCTCCCTCACTCGCTC 62.120 68.421 0.00 0.0 0.00 5.03
1126 1168 2.765969 CACCCACTTGGCCTCCAT 59.234 61.111 3.32 0.0 37.83 3.41
1178 1220 3.049674 CGGTGCAGGCGAACATGT 61.050 61.111 0.00 0.0 0.00 3.21
1306 1355 6.617782 TCTTCAGTTCTTGGATCAATCTCT 57.382 37.500 0.00 0.0 0.00 3.10
1384 1433 3.680786 GGGCACGGAAAGCAACCC 61.681 66.667 0.00 0.0 0.00 4.11
1807 1921 4.521130 ATCACTTCTCGAACTGCTACAA 57.479 40.909 0.00 0.0 0.00 2.41
1820 1934 1.840635 GCTTCCCCACCTATCACTTCT 59.159 52.381 0.00 0.0 0.00 2.85
2166 2284 7.916552 AGTTAACCGCTGTAAATTATGATGTC 58.083 34.615 0.88 0.0 0.00 3.06


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

AutoCloner maintained by Alex Coulton.