Multiple sequence alignment - TraesCS5A01G144400

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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 TraesCS5A01G144400 chr5A 100.000 3878 0 0 1 3878 320269034 320272911 0.000000e+00 7162.0
1 TraesCS5A01G144400 chr5A 91.176 68 3 3 82 146 567566320 567566387 5.340000e-14 89.8
2 TraesCS5A01G144400 chr5B 99.265 3807 28 0 72 3878 239325710 239321904 0.000000e+00 6876.0
3 TraesCS5A01G144400 chr5B 100.000 52 0 0 1 52 270679168 270679219 3.190000e-16 97.1
4 TraesCS5A01G144400 chr6B 98.977 3811 38 1 68 3878 346416948 346413139 0.000000e+00 6820.0
5 TraesCS5A01G144400 chr4B 98.266 3806 62 3 74 3878 92549626 92553428 0.000000e+00 6660.0
6 TraesCS5A01G144400 chr7B 99.232 2863 22 0 72 2934 516450101 516452963 0.000000e+00 5166.0
7 TraesCS5A01G144400 chr7B 92.809 1349 93 3 2530 3878 27982672 27984016 0.000000e+00 1951.0
8 TraesCS5A01G144400 chr7B 99.789 947 2 0 2932 3878 516455488 516456434 0.000000e+00 1738.0
9 TraesCS5A01G144400 chr7B 88.440 891 74 13 1641 2525 27975970 27976837 0.000000e+00 1048.0
10 TraesCS5A01G144400 chr7D 87.267 3432 366 40 458 3878 580113544 580110173 0.000000e+00 3851.0
11 TraesCS5A01G144400 chr1B 98.012 1811 32 1 2068 3878 269072707 269070901 0.000000e+00 3142.0
12 TraesCS5A01G144400 chr1A 85.829 2992 376 23 900 3878 94244447 94241491 0.000000e+00 3133.0
13 TraesCS5A01G144400 chr1A 87.013 77 6 4 82 155 319318576 319318501 2.480000e-12 84.2
14 TraesCS5A01G144400 chr2A 98.461 1754 27 0 81 1834 608937909 608936156 0.000000e+00 3090.0
15 TraesCS5A01G144400 chr2A 98.151 1136 18 1 1934 3066 608935391 608934256 0.000000e+00 1978.0
16 TraesCS5A01G144400 chr2A 87.013 77 8 2 390 465 79479964 79480039 6.900000e-13 86.1
17 TraesCS5A01G144400 chr3A 87.444 1569 181 12 2318 3878 711443773 711442213 0.000000e+00 1792.0
18 TraesCS5A01G144400 chr3A 83.554 681 97 9 1382 2052 711444846 711444171 1.180000e-174 623.0
19 TraesCS5A01G144400 chr6A 84.724 1702 204 24 906 2599 106071456 106069803 0.000000e+00 1652.0
20 TraesCS5A01G144400 chr6A 89.394 66 6 1 87 151 59822348 59822283 8.930000e-12 82.4
21 TraesCS5A01G144400 chr7A 91.706 844 48 10 1934 2771 143077393 143078220 0.000000e+00 1151.0
22 TraesCS5A01G144400 chr6D 85.185 972 103 27 638 1607 87951475 87950543 0.000000e+00 959.0
23 TraesCS5A01G144400 chr3B 77.361 720 144 16 113 823 478094976 478095685 3.610000e-110 409.0
24 TraesCS5A01G144400 chr5D 97.872 47 1 0 1 47 234054341 234054295 8.930000e-12 82.4


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 TraesCS5A01G144400 chr5A 320269034 320272911 3877 False 7162.0 7162 100.0000 1 3878 1 chr5A.!!$F1 3877
1 TraesCS5A01G144400 chr5B 239321904 239325710 3806 True 6876.0 6876 99.2650 72 3878 1 chr5B.!!$R1 3806
2 TraesCS5A01G144400 chr6B 346413139 346416948 3809 True 6820.0 6820 98.9770 68 3878 1 chr6B.!!$R1 3810
3 TraesCS5A01G144400 chr4B 92549626 92553428 3802 False 6660.0 6660 98.2660 74 3878 1 chr4B.!!$F1 3804
4 TraesCS5A01G144400 chr7B 516450101 516456434 6333 False 3452.0 5166 99.5105 72 3878 2 chr7B.!!$F3 3806
5 TraesCS5A01G144400 chr7B 27982672 27984016 1344 False 1951.0 1951 92.8090 2530 3878 1 chr7B.!!$F2 1348
6 TraesCS5A01G144400 chr7B 27975970 27976837 867 False 1048.0 1048 88.4400 1641 2525 1 chr7B.!!$F1 884
7 TraesCS5A01G144400 chr7D 580110173 580113544 3371 True 3851.0 3851 87.2670 458 3878 1 chr7D.!!$R1 3420
8 TraesCS5A01G144400 chr1B 269070901 269072707 1806 True 3142.0 3142 98.0120 2068 3878 1 chr1B.!!$R1 1810
9 TraesCS5A01G144400 chr1A 94241491 94244447 2956 True 3133.0 3133 85.8290 900 3878 1 chr1A.!!$R1 2978
10 TraesCS5A01G144400 chr2A 608934256 608937909 3653 True 2534.0 3090 98.3060 81 3066 2 chr2A.!!$R1 2985
11 TraesCS5A01G144400 chr3A 711442213 711444846 2633 True 1207.5 1792 85.4990 1382 3878 2 chr3A.!!$R1 2496
12 TraesCS5A01G144400 chr6A 106069803 106071456 1653 True 1652.0 1652 84.7240 906 2599 1 chr6A.!!$R2 1693
13 TraesCS5A01G144400 chr7A 143077393 143078220 827 False 1151.0 1151 91.7060 1934 2771 1 chr7A.!!$F1 837
14 TraesCS5A01G144400 chr6D 87950543 87951475 932 True 959.0 959 85.1850 638 1607 1 chr6D.!!$R1 969
15 TraesCS5A01G144400 chr3B 478094976 478095685 709 False 409.0 409 77.3610 113 823 1 chr3B.!!$F1 710

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
63 64 0.250467 CATCCGGGGACATGGATCAC 60.250 60.0 0.00 0.0 42.08 3.06 F
64 65 0.400525 ATCCGGGGACATGGATCACT 60.401 55.0 0.00 0.0 40.39 3.41 F
735 739 0.827507 AGGTCGGCCACTGCAAAATT 60.828 50.0 9.71 0.0 40.13 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 3087 2.186826 GCCTGTCGTTGCTTGGTGT 61.187 57.895 0.00 0.0 0.00 4.16 R
2685 3590 4.378774 CCACAAATTTGTCAATGGCTTCA 58.621 39.130 20.85 0.0 39.91 3.02 R
3326 6765 0.828022 CCCGTGTACCATTAGCAGGA 59.172 55.000 0.00 0.0 0.00 3.86 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
21 22 4.981806 TGCTATATTTGGCCTCACAAAC 57.018 40.909 3.32 0.00 42.51 2.93
22 23 4.599041 TGCTATATTTGGCCTCACAAACT 58.401 39.130 3.32 0.00 42.51 2.66
23 24 5.750524 TGCTATATTTGGCCTCACAAACTA 58.249 37.500 3.32 0.00 42.51 2.24
24 25 6.184068 TGCTATATTTGGCCTCACAAACTAA 58.816 36.000 3.32 0.00 42.51 2.24
25 26 6.318648 TGCTATATTTGGCCTCACAAACTAAG 59.681 38.462 3.32 0.00 42.51 2.18
26 27 6.542370 GCTATATTTGGCCTCACAAACTAAGA 59.458 38.462 3.32 0.00 42.51 2.10
27 28 7.229506 GCTATATTTGGCCTCACAAACTAAGAT 59.770 37.037 3.32 0.00 42.51 2.40
28 29 7.961326 ATATTTGGCCTCACAAACTAAGATT 57.039 32.000 3.32 0.00 42.51 2.40
29 30 6.670695 ATTTGGCCTCACAAACTAAGATTT 57.329 33.333 3.32 0.00 42.51 2.17
30 31 5.452078 TTGGCCTCACAAACTAAGATTTG 57.548 39.130 3.32 0.00 43.81 2.32
39 40 5.437289 CAAACTAAGATTTGTGCACCTCA 57.563 39.130 15.69 0.00 35.28 3.86
40 41 6.017400 CAAACTAAGATTTGTGCACCTCAT 57.983 37.500 15.69 3.07 35.28 2.90
41 42 6.449698 CAAACTAAGATTTGTGCACCTCATT 58.550 36.000 15.69 5.57 35.28 2.57
42 43 6.655078 AACTAAGATTTGTGCACCTCATTT 57.345 33.333 15.69 6.33 0.00 2.32
43 44 6.017400 ACTAAGATTTGTGCACCTCATTTG 57.983 37.500 15.69 6.60 0.00 2.32
44 45 3.308438 AGATTTGTGCACCTCATTTGC 57.692 42.857 15.69 0.00 40.63 3.68
49 50 2.182496 TGCACCTCATTTGCATCCG 58.818 52.632 0.00 0.00 45.06 4.18
50 51 1.314534 TGCACCTCATTTGCATCCGG 61.315 55.000 0.00 0.00 45.06 5.14
51 52 2.008268 GCACCTCATTTGCATCCGGG 62.008 60.000 0.00 0.00 39.93 5.73
52 53 1.076777 ACCTCATTTGCATCCGGGG 60.077 57.895 0.00 0.00 0.00 5.73
53 54 1.227102 CCTCATTTGCATCCGGGGA 59.773 57.895 0.00 0.00 0.00 4.81
54 55 1.103398 CCTCATTTGCATCCGGGGAC 61.103 60.000 0.00 0.00 0.00 4.46
55 56 0.394216 CTCATTTGCATCCGGGGACA 60.394 55.000 0.00 0.00 0.00 4.02
56 57 0.258484 TCATTTGCATCCGGGGACAT 59.742 50.000 0.00 0.00 0.00 3.06
57 58 0.386476 CATTTGCATCCGGGGACATG 59.614 55.000 0.00 0.00 0.00 3.21
58 59 0.756442 ATTTGCATCCGGGGACATGG 60.756 55.000 0.00 0.00 0.00 3.66
59 60 1.857638 TTTGCATCCGGGGACATGGA 61.858 55.000 0.00 0.00 38.73 3.41
60 61 1.644437 TTGCATCCGGGGACATGGAT 61.644 55.000 0.00 0.00 44.28 3.41
61 62 1.302832 GCATCCGGGGACATGGATC 60.303 63.158 0.00 0.00 42.08 3.36
62 63 2.055689 GCATCCGGGGACATGGATCA 62.056 60.000 0.00 0.00 42.08 2.92
63 64 0.250467 CATCCGGGGACATGGATCAC 60.250 60.000 0.00 0.00 42.08 3.06
64 65 0.400525 ATCCGGGGACATGGATCACT 60.401 55.000 0.00 0.00 40.39 3.41
65 66 1.048724 TCCGGGGACATGGATCACTC 61.049 60.000 0.00 0.00 29.32 3.51
66 67 1.050988 CCGGGGACATGGATCACTCT 61.051 60.000 0.00 0.00 0.00 3.24
735 739 0.827507 AGGTCGGCCACTGCAAAATT 60.828 50.000 9.71 0.00 40.13 1.82
807 811 2.661537 CGTGACTGCAACGCCTCA 60.662 61.111 0.00 0.00 0.00 3.86
994 999 2.377136 GTGGTCATCACCTCCACCT 58.623 57.895 0.00 0.00 44.17 4.00
2225 3087 1.254975 TGGATCGCTCCCTGTTTCGA 61.255 55.000 2.20 0.00 41.29 3.71
2476 3381 3.866379 TTTGTCGCCTGCCAGCCAT 62.866 57.895 0.00 0.00 0.00 4.40
2685 3590 2.158623 TGAAGGCCAACAAGTCACAGAT 60.159 45.455 5.01 0.00 0.00 2.90
3280 6719 1.149148 GAGCTTGTCGACCCTTTCAC 58.851 55.000 14.12 0.00 0.00 3.18
3326 6765 4.220602 AGATTAAAGAATTTTGCCCAGCGT 59.779 37.500 0.00 0.00 40.09 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.599041 AGTTTGTGAGGCCAAATATAGCA 58.401 39.130 5.01 0.00 36.75 3.49
1 2 6.542370 TCTTAGTTTGTGAGGCCAAATATAGC 59.458 38.462 5.01 0.00 36.75 2.97
2 3 8.682936 ATCTTAGTTTGTGAGGCCAAATATAG 57.317 34.615 5.01 0.00 36.75 1.31
3 4 9.474313 AAATCTTAGTTTGTGAGGCCAAATATA 57.526 29.630 5.01 0.00 36.75 0.86
4 5 7.961326 AATCTTAGTTTGTGAGGCCAAATAT 57.039 32.000 5.01 0.00 36.75 1.28
5 6 7.601856 CAAATCTTAGTTTGTGAGGCCAAATA 58.398 34.615 5.01 0.00 36.75 1.40
6 7 6.458210 CAAATCTTAGTTTGTGAGGCCAAAT 58.542 36.000 5.01 0.00 36.75 2.32
7 8 5.841810 CAAATCTTAGTTTGTGAGGCCAAA 58.158 37.500 5.01 0.00 35.02 3.28
8 9 5.452078 CAAATCTTAGTTTGTGAGGCCAA 57.548 39.130 5.01 0.00 35.02 4.52
17 18 5.437289 TGAGGTGCACAAATCTTAGTTTG 57.563 39.130 20.43 5.99 43.11 2.93
18 19 6.655078 AATGAGGTGCACAAATCTTAGTTT 57.345 33.333 20.43 2.17 0.00 2.66
19 20 6.449698 CAAATGAGGTGCACAAATCTTAGTT 58.550 36.000 20.43 5.87 0.00 2.24
20 21 5.565439 GCAAATGAGGTGCACAAATCTTAGT 60.565 40.000 20.43 0.00 41.80 2.24
21 22 4.860907 GCAAATGAGGTGCACAAATCTTAG 59.139 41.667 20.43 8.82 41.80 2.18
22 23 4.280425 TGCAAATGAGGTGCACAAATCTTA 59.720 37.500 20.43 3.36 46.76 2.10
23 24 3.069872 TGCAAATGAGGTGCACAAATCTT 59.930 39.130 20.43 8.64 46.76 2.40
24 25 2.629137 TGCAAATGAGGTGCACAAATCT 59.371 40.909 20.43 6.06 46.76 2.40
25 26 3.029320 TGCAAATGAGGTGCACAAATC 57.971 42.857 20.43 13.57 46.76 2.17
32 33 1.434696 CCGGATGCAAATGAGGTGC 59.565 57.895 0.00 0.00 42.55 5.01
33 34 1.386525 CCCCGGATGCAAATGAGGTG 61.387 60.000 0.73 0.00 0.00 4.00
34 35 1.076777 CCCCGGATGCAAATGAGGT 60.077 57.895 0.73 0.00 0.00 3.85
35 36 1.103398 GTCCCCGGATGCAAATGAGG 61.103 60.000 0.73 0.00 0.00 3.86
36 37 0.394216 TGTCCCCGGATGCAAATGAG 60.394 55.000 0.73 0.00 0.00 2.90
37 38 0.258484 ATGTCCCCGGATGCAAATGA 59.742 50.000 0.73 0.00 0.00 2.57
38 39 0.386476 CATGTCCCCGGATGCAAATG 59.614 55.000 0.73 0.00 0.00 2.32
39 40 0.756442 CCATGTCCCCGGATGCAAAT 60.756 55.000 0.73 0.00 0.00 2.32
40 41 1.379710 CCATGTCCCCGGATGCAAA 60.380 57.895 0.73 0.00 0.00 3.68
41 42 1.644437 ATCCATGTCCCCGGATGCAA 61.644 55.000 0.73 0.00 40.60 4.08
42 43 2.055689 GATCCATGTCCCCGGATGCA 62.056 60.000 0.73 0.00 42.21 3.96
43 44 1.302832 GATCCATGTCCCCGGATGC 60.303 63.158 0.73 0.00 42.21 3.91
44 45 0.250467 GTGATCCATGTCCCCGGATG 60.250 60.000 0.73 0.00 42.21 3.51
45 46 0.400525 AGTGATCCATGTCCCCGGAT 60.401 55.000 0.73 0.00 44.89 4.18
46 47 1.002921 AGTGATCCATGTCCCCGGA 59.997 57.895 0.73 0.00 35.27 5.14
47 48 1.050988 AGAGTGATCCATGTCCCCGG 61.051 60.000 0.00 0.00 0.00 5.73
48 49 0.105593 CAGAGTGATCCATGTCCCCG 59.894 60.000 0.00 0.00 0.00 5.73
49 50 0.471617 CCAGAGTGATCCATGTCCCC 59.528 60.000 0.00 0.00 0.00 4.81
50 51 0.471617 CCCAGAGTGATCCATGTCCC 59.528 60.000 0.00 0.00 0.00 4.46
51 52 0.471617 CCCCAGAGTGATCCATGTCC 59.528 60.000 0.00 0.00 0.00 4.02
52 53 1.415659 CTCCCCAGAGTGATCCATGTC 59.584 57.143 0.00 0.00 35.21 3.06
53 54 1.008815 TCTCCCCAGAGTGATCCATGT 59.991 52.381 0.00 0.00 41.26 3.21
54 55 1.693062 CTCTCCCCAGAGTGATCCATG 59.307 57.143 0.00 0.00 41.40 3.66
55 56 1.414245 CCTCTCCCCAGAGTGATCCAT 60.414 57.143 0.00 0.00 44.49 3.41
56 57 0.031716 CCTCTCCCCAGAGTGATCCA 60.032 60.000 0.00 0.00 44.49 3.41
57 58 0.263172 TCCTCTCCCCAGAGTGATCC 59.737 60.000 0.00 0.00 44.49 3.36
58 59 1.969923 CATCCTCTCCCCAGAGTGATC 59.030 57.143 0.00 0.00 44.49 2.92
59 60 1.293458 ACATCCTCTCCCCAGAGTGAT 59.707 52.381 0.00 0.00 44.49 3.06
60 61 0.712979 ACATCCTCTCCCCAGAGTGA 59.287 55.000 0.00 0.00 44.49 3.41
61 62 1.118838 GACATCCTCTCCCCAGAGTG 58.881 60.000 0.00 0.00 44.49 3.51
62 63 0.031616 GGACATCCTCTCCCCAGAGT 60.032 60.000 0.00 0.00 44.49 3.24
63 64 1.112315 CGGACATCCTCTCCCCAGAG 61.112 65.000 0.00 0.00 45.44 3.35
64 65 1.075970 CGGACATCCTCTCCCCAGA 60.076 63.158 0.00 0.00 0.00 3.86
65 66 2.801631 GCGGACATCCTCTCCCCAG 61.802 68.421 0.00 0.00 0.00 4.45
66 67 2.764128 GCGGACATCCTCTCCCCA 60.764 66.667 0.00 0.00 0.00 4.96
735 739 3.244770 ACCTAAAAGGATTTCGGCAGTCA 60.245 43.478 0.00 0.00 37.28 3.41
994 999 1.522092 CGCTGTCTTCCATGGCCTA 59.478 57.895 6.96 0.00 0.00 3.93
2225 3087 2.186826 GCCTGTCGTTGCTTGGTGT 61.187 57.895 0.00 0.00 0.00 4.16
2685 3590 4.378774 CCACAAATTTGTCAATGGCTTCA 58.621 39.130 20.85 0.00 39.91 3.02
3280 6719 1.447643 CCTCCCAGGTATGAAGCGG 59.552 63.158 0.00 0.00 0.00 5.52
3326 6765 0.828022 CCCGTGTACCATTAGCAGGA 59.172 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.