Multiple sequence alignment - TraesCS7B01G069900

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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 TraesCS7B01G069900 chr7B 100.000 2552 0 0 1 2552 75357407 75354856 0.000000e+00 4713
1 TraesCS7B01G069900 chr7B 89.505 1839 151 22 600 2413 648202537 648204358 0.000000e+00 2289
2 TraesCS7B01G069900 chr3D 92.828 1966 111 13 604 2552 573731197 573733149 0.000000e+00 2822
3 TraesCS7B01G069900 chr3D 90.729 1974 120 28 597 2552 447973577 447971649 0.000000e+00 2573
4 TraesCS7B01G069900 chr5D 92.476 1967 113 17 604 2552 357075966 357074017 0.000000e+00 2780
5 TraesCS7B01G069900 chr5D 92.157 1989 108 18 604 2552 45518953 45516973 0.000000e+00 2765
6 TraesCS7B01G069900 chr5D 91.910 1990 110 28 592 2552 6910290 6908323 0.000000e+00 2736
7 TraesCS7B01G069900 chrUn 92.399 1934 105 13 645 2552 43407879 43409796 0.000000e+00 2719
8 TraesCS7B01G069900 chr4D 91.797 1975 117 15 604 2552 78732767 78730812 0.000000e+00 2708
9 TraesCS7B01G069900 chr2D 91.612 1967 127 21 605 2552 84780830 84782777 0.000000e+00 2684
10 TraesCS7B01G069900 chr2D 91.105 1720 115 13 592 2299 16065477 16067170 0.000000e+00 2294
11 TraesCS7B01G069900 chr2D 90.718 1239 92 10 591 1825 435209590 435210809 0.000000e+00 1629
12 TraesCS7B01G069900 chr2D 95.318 598 28 0 4 601 200457076 200457673 0.000000e+00 950
13 TraesCS7B01G069900 chr2D 95.318 598 28 0 4 601 542916530 542915933 0.000000e+00 950
14 TraesCS7B01G069900 chr3B 91.254 1978 122 14 604 2552 370213883 370215838 0.000000e+00 2647
15 TraesCS7B01G069900 chr7A 91.097 1988 126 20 597 2552 12744489 12742521 0.000000e+00 2643
16 TraesCS7B01G069900 chr7D 90.859 1991 128 23 604 2552 372082800 372084778 0.000000e+00 2619
17 TraesCS7B01G069900 chr7D 88.734 1722 147 24 604 2298 565949616 565947915 0.000000e+00 2061
18 TraesCS7B01G069900 chr7D 93.628 1334 65 11 1233 2552 487833527 487832200 0.000000e+00 1975
19 TraesCS7B01G069900 chr7D 95.318 598 28 0 4 601 144525984 144525387 0.000000e+00 950
20 TraesCS7B01G069900 chr7D 95.167 600 29 0 2 601 119934140 119933541 0.000000e+00 948
21 TraesCS7B01G069900 chr7D 95.318 598 27 1 4 601 428005661 428006257 0.000000e+00 948
22 TraesCS7B01G069900 chr2B 90.669 2004 129 31 597 2552 173503424 173501431 0.000000e+00 2612
23 TraesCS7B01G069900 chr2B 89.951 1851 138 20 606 2413 19091951 19093796 0.000000e+00 2344
24 TraesCS7B01G069900 chr6D 90.010 1982 127 23 604 2552 312544300 312542357 0.000000e+00 2497
25 TraesCS7B01G069900 chr6D 89.154 839 59 17 1484 2298 459068893 459069723 0.000000e+00 1016
26 TraesCS7B01G069900 chr6D 95.151 598 29 0 4 601 395001702 395002299 0.000000e+00 944
27 TraesCS7B01G069900 chr1D 91.415 1724 111 18 604 2299 17040734 17039020 0.000000e+00 2329
28 TraesCS7B01G069900 chr1D 95.151 598 29 0 4 601 125623706 125623109 0.000000e+00 944
29 TraesCS7B01G069900 chr3A 88.978 1742 131 30 604 2304 683237671 683235950 0.000000e+00 2097
30 TraesCS7B01G069900 chr1B 95.318 598 26 2 4 601 572790353 572789758 0.000000e+00 948
31 TraesCS7B01G069900 chr1B 93.955 579 24 4 1984 2552 261684065 261683488 0.000000e+00 865
32 TraesCS7B01G069900 chr6B 92.037 653 48 4 2 652 457960442 457959792 0.000000e+00 915
33 TraesCS7B01G069900 chr6B 87.936 373 37 5 597 969 16347756 16348120 1.400000e-117 433
34 TraesCS7B01G069900 chr5B 85.282 496 60 6 606 1097 18695158 18694672 1.360000e-137 499


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 TraesCS7B01G069900 chr7B 75354856 75357407 2551 True 4713 4713 100.000 1 2552 1 chr7B.!!$R1 2551
1 TraesCS7B01G069900 chr7B 648202537 648204358 1821 False 2289 2289 89.505 600 2413 1 chr7B.!!$F1 1813
2 TraesCS7B01G069900 chr3D 573731197 573733149 1952 False 2822 2822 92.828 604 2552 1 chr3D.!!$F1 1948
3 TraesCS7B01G069900 chr3D 447971649 447973577 1928 True 2573 2573 90.729 597 2552 1 chr3D.!!$R1 1955
4 TraesCS7B01G069900 chr5D 357074017 357075966 1949 True 2780 2780 92.476 604 2552 1 chr5D.!!$R3 1948
5 TraesCS7B01G069900 chr5D 45516973 45518953 1980 True 2765 2765 92.157 604 2552 1 chr5D.!!$R2 1948
6 TraesCS7B01G069900 chr5D 6908323 6910290 1967 True 2736 2736 91.910 592 2552 1 chr5D.!!$R1 1960
7 TraesCS7B01G069900 chrUn 43407879 43409796 1917 False 2719 2719 92.399 645 2552 1 chrUn.!!$F1 1907
8 TraesCS7B01G069900 chr4D 78730812 78732767 1955 True 2708 2708 91.797 604 2552 1 chr4D.!!$R1 1948
9 TraesCS7B01G069900 chr2D 84780830 84782777 1947 False 2684 2684 91.612 605 2552 1 chr2D.!!$F2 1947
10 TraesCS7B01G069900 chr2D 16065477 16067170 1693 False 2294 2294 91.105 592 2299 1 chr2D.!!$F1 1707
11 TraesCS7B01G069900 chr2D 435209590 435210809 1219 False 1629 1629 90.718 591 1825 1 chr2D.!!$F4 1234
12 TraesCS7B01G069900 chr2D 200457076 200457673 597 False 950 950 95.318 4 601 1 chr2D.!!$F3 597
13 TraesCS7B01G069900 chr2D 542915933 542916530 597 True 950 950 95.318 4 601 1 chr2D.!!$R1 597
14 TraesCS7B01G069900 chr3B 370213883 370215838 1955 False 2647 2647 91.254 604 2552 1 chr3B.!!$F1 1948
15 TraesCS7B01G069900 chr7A 12742521 12744489 1968 True 2643 2643 91.097 597 2552 1 chr7A.!!$R1 1955
16 TraesCS7B01G069900 chr7D 372082800 372084778 1978 False 2619 2619 90.859 604 2552 1 chr7D.!!$F1 1948
17 TraesCS7B01G069900 chr7D 565947915 565949616 1701 True 2061 2061 88.734 604 2298 1 chr7D.!!$R4 1694
18 TraesCS7B01G069900 chr7D 487832200 487833527 1327 True 1975 1975 93.628 1233 2552 1 chr7D.!!$R3 1319
19 TraesCS7B01G069900 chr7D 144525387 144525984 597 True 950 950 95.318 4 601 1 chr7D.!!$R2 597
20 TraesCS7B01G069900 chr7D 119933541 119934140 599 True 948 948 95.167 2 601 1 chr7D.!!$R1 599
21 TraesCS7B01G069900 chr7D 428005661 428006257 596 False 948 948 95.318 4 601 1 chr7D.!!$F2 597
22 TraesCS7B01G069900 chr2B 173501431 173503424 1993 True 2612 2612 90.669 597 2552 1 chr2B.!!$R1 1955
23 TraesCS7B01G069900 chr2B 19091951 19093796 1845 False 2344 2344 89.951 606 2413 1 chr2B.!!$F1 1807
24 TraesCS7B01G069900 chr6D 312542357 312544300 1943 True 2497 2497 90.010 604 2552 1 chr6D.!!$R1 1948
25 TraesCS7B01G069900 chr6D 459068893 459069723 830 False 1016 1016 89.154 1484 2298 1 chr6D.!!$F2 814
26 TraesCS7B01G069900 chr6D 395001702 395002299 597 False 944 944 95.151 4 601 1 chr6D.!!$F1 597
27 TraesCS7B01G069900 chr1D 17039020 17040734 1714 True 2329 2329 91.415 604 2299 1 chr1D.!!$R1 1695
28 TraesCS7B01G069900 chr1D 125623109 125623706 597 True 944 944 95.151 4 601 1 chr1D.!!$R2 597
29 TraesCS7B01G069900 chr3A 683235950 683237671 1721 True 2097 2097 88.978 604 2304 1 chr3A.!!$R1 1700
30 TraesCS7B01G069900 chr1B 572789758 572790353 595 True 948 948 95.318 4 601 1 chr1B.!!$R2 597
31 TraesCS7B01G069900 chr1B 261683488 261684065 577 True 865 865 93.955 1984 2552 1 chr1B.!!$R1 568
32 TraesCS7B01G069900 chr6B 457959792 457960442 650 True 915 915 92.037 2 652 1 chr6B.!!$R1 650

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
52 54 0.694771 TGAAGATGAACTGCAGGCCT 59.305 50.0 19.93 0.0 29.51 5.19 F
1010 1196 0.905357 CCGAGGTCCATGTCTTCCTT 59.095 55.0 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 1552 0.107459 GCTTCGCCCTCCATCTCTTT 60.107 55.000 0.0 0.0 0.00 2.52 R
2455 2761 4.067972 ACCAAGTCATGAACTAACGTGT 57.932 40.909 0.0 0.0 37.17 4.49 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
52 54 0.694771 TGAAGATGAACTGCAGGCCT 59.305 50.000 19.93 0.00 29.51 5.19
106 108 1.531149 CCATTGCGTTCAGTTTCGACT 59.469 47.619 0.00 0.00 0.00 4.18
123 125 4.755411 TCGACTGTAACATTCAGATTCCC 58.245 43.478 0.00 0.00 36.81 3.97
169 171 9.013490 CAGTTAAGTTCAGAGTCAACAATTTTG 57.987 33.333 0.00 0.00 0.00 2.44
376 378 3.537874 GCCCTGGACGCCGTCTAT 61.538 66.667 17.76 0.00 32.47 1.98
387 389 3.220110 ACGCCGTCTATAGATTCCTCAA 58.780 45.455 5.57 0.00 0.00 3.02
418 420 2.352805 CCTCCAACAGCCACCTCC 59.647 66.667 0.00 0.00 0.00 4.30
549 551 7.358263 TCCATTAGGGCTATTTTGGTTCAATA 58.642 34.615 0.00 0.00 36.21 1.90
562 564 8.514136 TTTTGGTTCAATAGAAAAACATAGCG 57.486 30.769 0.00 0.00 35.08 4.26
578 580 5.308825 ACATAGCGATAGGGAATTTTCCTG 58.691 41.667 6.49 0.00 46.72 3.86
580 582 3.809905 AGCGATAGGGAATTTTCCTGTC 58.190 45.455 9.86 9.86 46.72 3.51
602 604 5.235186 GTCGCACTCTGCTATTCAATTATGT 59.765 40.000 0.00 0.00 42.25 2.29
608 610 9.926751 CACTCTGCTATTCAATTATGTGTTAAG 57.073 33.333 0.00 0.00 0.00 1.85
636 638 1.380302 GCCCTCAGTGGTGTCCATT 59.620 57.895 0.00 0.00 35.28 3.16
655 657 1.999648 TTGCTCAGTTTTGCCCTCAT 58.000 45.000 0.00 0.00 0.00 2.90
801 803 3.938963 GCCAATTCTATTCAGACCGTTGA 59.061 43.478 0.00 0.00 0.00 3.18
809 811 1.947146 CAGACCGTTGAACGCGTGA 60.947 57.895 14.98 0.00 40.91 4.35
920 965 3.122480 ACCATGGAGAGAGAGAGAGAGA 58.878 50.000 21.47 0.00 0.00 3.10
944 1099 4.057428 GAGAGAGCACGGCGGTGT 62.057 66.667 23.39 11.77 46.13 4.16
1010 1196 0.905357 CCGAGGTCCATGTCTTCCTT 59.095 55.000 0.00 0.00 0.00 3.36
1011 1197 1.406069 CCGAGGTCCATGTCTTCCTTG 60.406 57.143 0.00 0.00 0.00 3.61
1042 1228 0.957395 CACCTCGTGGATGCAAAGCT 60.957 55.000 11.17 0.00 37.04 3.74
1126 1312 1.116308 TTCTCACACACCGAGGAACA 58.884 50.000 0.00 0.00 0.00 3.18
1189 1375 5.250313 AGAATTGGGGAAATTGCACCATTTA 59.750 36.000 8.70 0.00 38.64 1.40
1307 1493 3.748083 TGAATGAACTGCAAGAAGAGCT 58.252 40.909 0.00 0.00 37.43 4.09
1320 1506 5.956068 AAGAAGAGCTTGAAGAATGGTTC 57.044 39.130 0.00 0.00 34.93 3.62
1721 1933 7.929785 AGAAACTTTTGATCAATGAAATGCAGT 59.070 29.630 9.40 0.00 0.00 4.40
1727 1939 6.432607 TGATCAATGAAATGCAGTTCTCTC 57.567 37.500 25.47 15.03 0.00 3.20
1738 1950 2.697654 CAGTTCTCTCCTCTGCCTTTG 58.302 52.381 0.00 0.00 0.00 2.77
1777 1994 1.180029 CTGTGGGCCAAATTCAGAGG 58.820 55.000 8.40 0.00 0.00 3.69
1789 2006 3.922171 ATTCAGAGGGTAGAGCAAAGG 57.078 47.619 0.00 0.00 0.00 3.11
2347 2636 8.994429 TTTCTCTTTGTTTTGCACTGAAATTA 57.006 26.923 0.00 0.00 0.00 1.40
2376 2681 5.047660 GGGTTGGAAATGTATGTTTGCACTA 60.048 40.000 0.00 0.00 38.81 2.74
2520 2831 0.618458 TCTCACCCCCTCCGATTTTG 59.382 55.000 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 5.001232 GCACTTGACATGTAGTTTAGGGAA 58.999 41.667 0.00 0.00 0.00 3.97
106 108 4.927267 ACTGGGGAATCTGAATGTTACA 57.073 40.909 0.00 0.00 0.00 2.41
169 171 5.221342 CCACCTGACTACAATAGATGAGGTC 60.221 48.000 0.00 0.00 33.23 3.85
237 239 6.556495 TCAAGTGGGATTCTAATAGCATCTCT 59.444 38.462 1.78 0.00 0.00 3.10
387 389 2.040412 GTTGGAGGTGTGGAGGAAGATT 59.960 50.000 0.00 0.00 0.00 2.40
418 420 2.866028 GCTGAAGCAGTTGAGGCG 59.134 61.111 0.00 0.00 41.59 5.52
549 551 7.881775 AAATTCCCTATCGCTATGTTTTTCT 57.118 32.000 0.00 0.00 0.00 2.52
608 610 2.290960 ACCACTGAGGGCAAAAGGATAC 60.291 50.000 0.00 0.00 43.89 2.24
636 638 1.999648 ATGAGGGCAAAACTGAGCAA 58.000 45.000 0.00 0.00 0.00 3.91
655 657 5.221880 GCAAAACTGAGCACAATTCACATA 58.778 37.500 0.00 0.00 0.00 2.29
742 744 1.745489 CCACCTGTAAAGGCCGAGC 60.745 63.158 0.00 0.00 0.00 5.03
750 752 1.765074 GCCTGGTCCCACCTGTAAA 59.235 57.895 0.00 0.00 39.58 2.01
801 803 1.885850 GTCCCACAAGTCACGCGTT 60.886 57.895 10.22 0.00 0.00 4.84
809 811 1.770110 TCTGCTGGGTCCCACAAGT 60.770 57.895 6.47 0.00 0.00 3.16
856 889 4.796231 GTCACCGCCGATGTCGCT 62.796 66.667 0.00 0.00 38.18 4.93
906 951 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
920 965 0.748005 GCCGTGCTCTCTCTCTCTCT 60.748 60.000 0.00 0.00 0.00 3.10
944 1099 1.903877 GCCCTCCACAGCTAGCTTCA 61.904 60.000 16.46 0.00 0.00 3.02
996 1181 2.626840 GAGCTCAAGGAAGACATGGAC 58.373 52.381 9.40 0.00 0.00 4.02
1030 1216 3.063704 CGCCCAGCTTTGCATCCA 61.064 61.111 5.18 0.00 0.00 3.41
1063 1249 1.651987 CACCGCGGACAGACAAATAT 58.348 50.000 35.90 0.00 0.00 1.28
1065 1251 2.325082 GCACCGCGGACAGACAAAT 61.325 57.895 35.90 1.64 0.00 2.32
1088 1274 2.075355 AACCCTCCGAACAATGCCCA 62.075 55.000 0.00 0.00 0.00 5.36
1189 1375 0.246635 CTCAAAGATCCCGACCACGT 59.753 55.000 0.00 0.00 37.88 4.49
1307 1493 3.057104 CAGCATGCAGAACCATTCTTCAA 60.057 43.478 21.98 0.00 36.55 2.69
1366 1552 0.107459 GCTTCGCCCTCCATCTCTTT 60.107 55.000 0.00 0.00 0.00 2.52
1422 1608 6.133253 AGCTTCCTAACCTTCTTCTTCAAT 57.867 37.500 0.00 0.00 0.00 2.57
1450 1636 5.719085 TGGGTATTGGTATTTGTGCTTGATT 59.281 36.000 0.00 0.00 0.00 2.57
1593 1780 8.983702 ACTTTGACCAACATTTAAACTAGGTA 57.016 30.769 0.00 0.00 0.00 3.08
1721 1933 2.037772 GACACAAAGGCAGAGGAGAGAA 59.962 50.000 0.00 0.00 0.00 2.87
1727 1939 3.799281 TTTTTGACACAAAGGCAGAGG 57.201 42.857 0.00 0.00 35.94 3.69
1777 1994 1.750780 GCCTGCCCTTTGCTCTACC 60.751 63.158 0.00 0.00 42.00 3.18
1789 2006 0.250510 GCCCATTAGTCTAGCCTGCC 60.251 60.000 0.00 0.00 0.00 4.85
1928 2172 6.670695 ACTTAATTGTTTGGCTCTGGAATT 57.329 33.333 0.00 0.00 0.00 2.17
2321 2610 7.903995 ATTTCAGTGCAAAACAAAGAGAAAA 57.096 28.000 0.00 0.00 0.00 2.29
2325 2614 7.652909 TCCATAATTTCAGTGCAAAACAAAGAG 59.347 33.333 0.00 0.00 0.00 2.85
2347 2636 4.608170 ACATACATTTCCAACCCTCCAT 57.392 40.909 0.00 0.00 0.00 3.41
2455 2761 4.067972 ACCAAGTCATGAACTAACGTGT 57.932 40.909 0.00 0.00 37.17 4.49
2520 2831 7.581476 TCGAGAACTTGTGGTTTTCATTAATC 58.419 34.615 0.00 0.00 38.48 1.75


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

AutoCloner maintained by Alex Coulton.