Multiple sequence alignment - TraesCS4A01G029600

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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 TraesCS4A01G029600 chr4A 100.000 2579 0 0 1 2579 21636926 21634348 0.000000e+00 4763.0
1 TraesCS4A01G029600 chr4D 96.007 2204 80 7 379 2579 445483599 445485797 0.000000e+00 3576.0
2 TraesCS4A01G029600 chr4D 91.144 271 13 6 57 321 445483044 445483309 8.780000e-95 357.0
3 TraesCS4A01G029600 chr4B 93.747 2159 98 14 442 2579 556059439 556061581 0.000000e+00 3205.0
4 TraesCS4A01G029600 chr4B 88.166 338 16 8 98 417 556059013 556059344 5.210000e-102 381.0
5 TraesCS4A01G029600 chr6A 96.078 51 1 1 3 53 606758737 606758688 5.910000e-12 82.4
6 TraesCS4A01G029600 chr7A 92.982 57 1 2 3 59 62177918 62177971 2.130000e-11 80.5
7 TraesCS4A01G029600 chr7A 91.525 59 4 1 3 60 151325215 151325157 2.130000e-11 80.5
8 TraesCS4A01G029600 chr7A 94.118 51 2 1 3 53 293097086 293097037 2.750000e-10 76.8
9 TraesCS4A01G029600 chr3A 95.918 49 2 0 3 51 624860704 624860656 2.130000e-11 80.5
10 TraesCS4A01G029600 chr3A 95.652 46 2 0 3 48 13738486 13738531 9.900000e-10 75.0
11 TraesCS4A01G029600 chr2A 94.231 52 3 0 3 54 142674198 142674147 2.130000e-11 80.5
12 TraesCS4A01G029600 chr1A 97.826 46 1 0 3 48 54017455 54017500 2.130000e-11 80.5
13 TraesCS4A01G029600 chr1A 94.118 51 2 1 3 53 8129723 8129772 2.750000e-10 76.8


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 TraesCS4A01G029600 chr4A 21634348 21636926 2578 True 4763.0 4763 100.0000 1 2579 1 chr4A.!!$R1 2578
1 TraesCS4A01G029600 chr4D 445483044 445485797 2753 False 1966.5 3576 93.5755 57 2579 2 chr4D.!!$F1 2522
2 TraesCS4A01G029600 chr4B 556059013 556061581 2568 False 1793.0 3205 90.9565 98 2579 2 chr4B.!!$F1 2481

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
123 124 0.03601 GTCCATCCACACAGACCCAG 60.036 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2387 0.532573 GAGTGTCAAGATGGCGAGGA 59.467 55.0 0.0 0.0 0.0 3.71 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
23 24 4.760530 AAGCACATGGATAGAGTAAGCA 57.239 40.909 0.00 0.0 0.00 3.91
24 25 4.065321 AGCACATGGATAGAGTAAGCAC 57.935 45.455 0.00 0.0 0.00 4.40
25 26 3.708631 AGCACATGGATAGAGTAAGCACT 59.291 43.478 0.00 0.0 37.87 4.40
26 27 4.895889 AGCACATGGATAGAGTAAGCACTA 59.104 41.667 0.00 0.0 34.21 2.74
27 28 4.985409 GCACATGGATAGAGTAAGCACTAC 59.015 45.833 0.00 0.0 34.21 2.73
28 29 5.451937 GCACATGGATAGAGTAAGCACTACA 60.452 44.000 0.00 0.0 34.21 2.74
29 30 6.739843 GCACATGGATAGAGTAAGCACTACAT 60.740 42.308 0.00 0.0 34.21 2.29
30 31 7.212976 CACATGGATAGAGTAAGCACTACATT 58.787 38.462 0.00 0.0 34.21 2.71
31 32 7.170489 CACATGGATAGAGTAAGCACTACATTG 59.830 40.741 0.00 0.0 34.21 2.82
32 33 6.791867 TGGATAGAGTAAGCACTACATTGT 57.208 37.500 0.00 0.0 34.21 2.71
33 34 6.573434 TGGATAGAGTAAGCACTACATTGTG 58.427 40.000 0.00 0.0 40.62 3.33
34 35 5.986135 GGATAGAGTAAGCACTACATTGTGG 59.014 44.000 0.00 0.0 38.31 4.17
35 36 6.183360 GGATAGAGTAAGCACTACATTGTGGA 60.183 42.308 7.20 0.0 38.31 4.02
36 37 5.483685 AGAGTAAGCACTACATTGTGGAA 57.516 39.130 7.20 0.0 38.31 3.53
37 38 6.054860 AGAGTAAGCACTACATTGTGGAAT 57.945 37.500 7.20 0.0 38.31 3.01
38 39 5.877012 AGAGTAAGCACTACATTGTGGAATG 59.123 40.000 7.20 0.0 39.13 2.67
39 40 4.943705 AGTAAGCACTACATTGTGGAATGG 59.056 41.667 7.20 0.0 43.00 3.16
40 41 3.719268 AGCACTACATTGTGGAATGGA 57.281 42.857 7.20 0.0 43.00 3.41
44 45 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.0 44.23 4.20
45 46 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.0 43.00 4.30
46 47 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.0 43.00 3.85
47 48 3.189606 ACATTGTGGAATGGAGGGAGTA 58.810 45.455 0.00 0.0 43.00 2.59
48 49 3.591527 ACATTGTGGAATGGAGGGAGTAA 59.408 43.478 0.00 0.0 43.00 2.24
49 50 3.713826 TTGTGGAATGGAGGGAGTAAC 57.286 47.619 0.00 0.0 0.00 2.50
50 51 2.626785 TGTGGAATGGAGGGAGTAACA 58.373 47.619 0.00 0.0 0.00 2.41
51 52 2.983192 TGTGGAATGGAGGGAGTAACAA 59.017 45.455 0.00 0.0 0.00 2.83
52 53 3.396276 TGTGGAATGGAGGGAGTAACAAA 59.604 43.478 0.00 0.0 0.00 2.83
53 54 4.044065 TGTGGAATGGAGGGAGTAACAAAT 59.956 41.667 0.00 0.0 0.00 2.32
54 55 5.016831 GTGGAATGGAGGGAGTAACAAATT 58.983 41.667 0.00 0.0 0.00 1.82
55 56 5.125578 GTGGAATGGAGGGAGTAACAAATTC 59.874 44.000 0.00 0.0 0.00 2.17
56 57 5.015178 TGGAATGGAGGGAGTAACAAATTCT 59.985 40.000 0.00 0.0 0.00 2.40
57 58 5.952347 GGAATGGAGGGAGTAACAAATTCTT 59.048 40.000 0.00 0.0 0.00 2.52
58 59 6.437477 GGAATGGAGGGAGTAACAAATTCTTT 59.563 38.462 0.00 0.0 0.00 2.52
59 60 7.039011 GGAATGGAGGGAGTAACAAATTCTTTT 60.039 37.037 0.00 0.0 0.00 2.27
60 61 6.648879 TGGAGGGAGTAACAAATTCTTTTG 57.351 37.500 0.00 0.0 46.27 2.44
86 87 3.717294 GCCACGACCCCTCACCAT 61.717 66.667 0.00 0.0 0.00 3.55
123 124 0.036010 GTCCATCCACACAGACCCAG 60.036 60.000 0.00 0.0 0.00 4.45
170 176 1.214589 CCCCAGTACACGTCGAAGG 59.785 63.158 0.00 0.0 0.00 3.46
184 190 1.804151 TCGAAGGGCTTTCAATTCACG 59.196 47.619 10.14 0.0 35.43 4.35
193 199 3.131478 CAATTCACGGGGGCGGAC 61.131 66.667 0.00 0.0 0.00 4.79
323 329 1.075659 AGTTGCTGGCTTCCCTTCC 59.924 57.895 0.00 0.0 0.00 3.46
476 784 1.146263 GAGGTTCCATCCGCCGATT 59.854 57.895 0.00 0.0 0.00 3.34
481 789 4.988598 CCATCCGCCGATTCCCCG 62.989 72.222 0.00 0.0 0.00 5.73
485 793 4.308458 CCGCCGATTCCCCGCATA 62.308 66.667 0.00 0.0 0.00 3.14
487 795 3.041940 GCCGATTCCCCGCATACG 61.042 66.667 0.00 0.0 39.67 3.06
488 796 3.041940 CCGATTCCCCGCATACGC 61.042 66.667 0.00 0.0 38.22 4.42
489 797 2.029073 CGATTCCCCGCATACGCT 59.971 61.111 0.00 0.0 38.22 5.07
490 798 1.594293 CGATTCCCCGCATACGCTT 60.594 57.895 0.00 0.0 38.22 4.68
491 799 1.557443 CGATTCCCCGCATACGCTTC 61.557 60.000 0.00 0.0 38.22 3.86
492 800 1.227853 ATTCCCCGCATACGCTTCC 60.228 57.895 0.00 0.0 38.22 3.46
587 898 1.557651 GTTTTTGCCGTGCGGTTTTA 58.442 45.000 12.46 0.0 37.65 1.52
601 912 3.243068 GCGGTTTTATTTGATCGATGGCT 60.243 43.478 0.54 0.0 0.00 4.75
771 1084 2.530701 AGGTATCGATCCATCTGTCCC 58.469 52.381 0.00 0.0 0.00 4.46
802 1115 4.220821 TCCACGATTCTGCTAATATCTCCC 59.779 45.833 0.00 0.0 0.00 4.30
822 1135 2.594321 CATGTATGTTGTGGTTTGCGG 58.406 47.619 0.00 0.0 0.00 5.69
823 1136 1.968704 TGTATGTTGTGGTTTGCGGA 58.031 45.000 0.00 0.0 0.00 5.54
828 1141 1.478510 TGTTGTGGTTTGCGGATTTGT 59.521 42.857 0.00 0.0 0.00 2.83
839 1152 3.472652 TGCGGATTTGTACAGTGAAAGT 58.527 40.909 0.00 0.0 0.00 2.66
840 1153 3.880490 TGCGGATTTGTACAGTGAAAGTT 59.120 39.130 0.00 0.0 0.00 2.66
843 1156 5.849604 GCGGATTTGTACAGTGAAAGTTTAC 59.150 40.000 0.00 0.0 0.00 2.01
920 1248 3.848019 CGCTAGTGTTGTGATCAAAATGC 59.152 43.478 0.61 0.0 35.20 3.56
934 1262 6.377712 TGATCAAAATGCCATGTTCAGATGTA 59.622 34.615 0.00 0.0 0.00 2.29
992 1320 0.535335 TGGATCTGCCACTTACGACC 59.465 55.000 0.00 0.0 43.33 4.79
1053 1387 2.751731 CCACCACCACCACCACTCA 61.752 63.158 0.00 0.0 0.00 3.41
1152 1486 3.643320 CCTTCCACTCCAGTATCAGCATA 59.357 47.826 0.00 0.0 0.00 3.14
1595 1930 0.630134 TGAATGATGGGGGCATCACA 59.370 50.000 0.00 0.0 43.42 3.58
1706 2041 5.243283 CAGGAGTACTGTTAGGTGTGTTAGT 59.757 44.000 0.00 0.0 42.42 2.24
1750 2085 0.606401 CTGCCGTGAAGGATGTGGTT 60.606 55.000 0.00 0.0 45.00 3.67
1791 2126 2.157738 GGATGAGAGCACAGCAGTTTT 58.842 47.619 0.00 0.0 0.00 2.43
2227 2562 9.092876 CCTCATCTGTCAACTAACTTTTATCTC 57.907 37.037 0.00 0.0 0.00 2.75
2300 2635 0.820891 CCCCTGCCATCCAATCTTCG 60.821 60.000 0.00 0.0 0.00 3.79
2349 2684 0.843984 AGTGGCACCCTGTGTAGTTT 59.156 50.000 15.27 0.0 35.75 2.66
2353 2688 1.202770 GGCACCCTGTGTAGTTTCTGT 60.203 52.381 0.00 0.0 35.75 3.41
2355 2690 3.495453 GGCACCCTGTGTAGTTTCTGTTA 60.495 47.826 0.00 0.0 35.75 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.163078 AGTGCTTACTCTATCCATGTGCTT 59.837 41.667 0.00 0.00 0.00 3.91
3 4 3.708631 AGTGCTTACTCTATCCATGTGCT 59.291 43.478 0.00 0.00 0.00 4.40
4 5 4.065321 AGTGCTTACTCTATCCATGTGC 57.935 45.455 0.00 0.00 0.00 4.57
5 6 6.149129 TGTAGTGCTTACTCTATCCATGTG 57.851 41.667 0.00 0.00 33.23 3.21
6 7 6.985653 ATGTAGTGCTTACTCTATCCATGT 57.014 37.500 0.00 0.00 33.23 3.21
7 8 7.170489 CACAATGTAGTGCTTACTCTATCCATG 59.830 40.741 0.00 0.00 33.23 3.66
8 9 7.212976 CACAATGTAGTGCTTACTCTATCCAT 58.787 38.462 0.00 0.00 33.23 3.41
9 10 6.406961 CCACAATGTAGTGCTTACTCTATCCA 60.407 42.308 0.00 0.00 38.18 3.41
10 11 5.986135 CCACAATGTAGTGCTTACTCTATCC 59.014 44.000 0.00 0.00 38.18 2.59
11 12 6.806751 TCCACAATGTAGTGCTTACTCTATC 58.193 40.000 0.00 0.00 38.18 2.08
12 13 6.791867 TCCACAATGTAGTGCTTACTCTAT 57.208 37.500 0.00 0.00 38.18 1.98
13 14 6.599356 TTCCACAATGTAGTGCTTACTCTA 57.401 37.500 0.00 0.00 38.18 2.43
14 15 5.483685 TTCCACAATGTAGTGCTTACTCT 57.516 39.130 0.00 0.00 38.18 3.24
15 16 5.065218 CCATTCCACAATGTAGTGCTTACTC 59.935 44.000 0.00 0.00 38.22 2.59
16 17 4.943705 CCATTCCACAATGTAGTGCTTACT 59.056 41.667 0.00 0.00 38.22 2.24
17 18 4.941263 TCCATTCCACAATGTAGTGCTTAC 59.059 41.667 0.00 0.00 38.22 2.34
18 19 5.172687 TCCATTCCACAATGTAGTGCTTA 57.827 39.130 0.00 0.00 38.22 3.09
19 20 4.012374 CTCCATTCCACAATGTAGTGCTT 58.988 43.478 0.00 0.00 38.22 3.91
20 21 3.614092 CTCCATTCCACAATGTAGTGCT 58.386 45.455 0.00 0.00 38.22 4.40
21 22 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
22 23 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
23 24 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
24 25 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
25 26 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
26 27 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
27 28 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
28 29 3.591527 TGTTACTCCCTCCATTCCACAAT 59.408 43.478 0.00 0.00 0.00 2.71
29 30 2.983192 TGTTACTCCCTCCATTCCACAA 59.017 45.455 0.00 0.00 0.00 3.33
30 31 2.626785 TGTTACTCCCTCCATTCCACA 58.373 47.619 0.00 0.00 0.00 4.17
31 32 3.713826 TTGTTACTCCCTCCATTCCAC 57.286 47.619 0.00 0.00 0.00 4.02
32 33 4.946160 ATTTGTTACTCCCTCCATTCCA 57.054 40.909 0.00 0.00 0.00 3.53
33 34 5.510430 AGAATTTGTTACTCCCTCCATTCC 58.490 41.667 0.00 0.00 0.00 3.01
34 35 7.468141 AAAGAATTTGTTACTCCCTCCATTC 57.532 36.000 0.00 0.00 36.60 2.67
35 36 7.670364 CAAAAGAATTTGTTACTCCCTCCATT 58.330 34.615 0.00 0.00 39.02 3.16
36 37 7.232118 CAAAAGAATTTGTTACTCCCTCCAT 57.768 36.000 0.00 0.00 39.02 3.41
37 38 6.648879 CAAAAGAATTTGTTACTCCCTCCA 57.351 37.500 0.00 0.00 39.02 3.86
50 51 1.601914 GCCGGCGTGACAAAAGAATTT 60.602 47.619 12.58 0.00 42.41 1.82
51 52 0.039527 GCCGGCGTGACAAAAGAATT 60.040 50.000 12.58 0.00 0.00 2.17
52 53 1.579429 GCCGGCGTGACAAAAGAAT 59.421 52.632 12.58 0.00 0.00 2.40
53 54 2.548295 GGCCGGCGTGACAAAAGAA 61.548 57.895 22.54 0.00 0.00 2.52
54 55 2.975799 GGCCGGCGTGACAAAAGA 60.976 61.111 22.54 0.00 0.00 2.52
55 56 3.283684 TGGCCGGCGTGACAAAAG 61.284 61.111 22.54 0.00 0.00 2.27
56 57 3.587933 GTGGCCGGCGTGACAAAA 61.588 61.111 22.54 0.00 0.00 2.44
99 100 3.295304 CTGTGTGGATGGACGGCGA 62.295 63.158 16.62 0.00 0.00 5.54
101 102 1.741770 GTCTGTGTGGATGGACGGC 60.742 63.158 0.00 0.00 0.00 5.68
123 124 4.547367 CTCCCGGCCGTTGGATCC 62.547 72.222 26.12 4.20 0.00 3.36
145 146 2.589157 CGTGTACTGGGGGCTTGGA 61.589 63.158 0.00 0.00 0.00 3.53
170 176 1.890174 CCCCCGTGAATTGAAAGCC 59.110 57.895 0.00 0.00 0.00 4.35
313 319 2.035783 GGGGTGTGGAAGGGAAGC 59.964 66.667 0.00 0.00 0.00 3.86
316 322 1.846124 GAGTGGGGTGTGGAAGGGA 60.846 63.158 0.00 0.00 0.00 4.20
323 329 3.966543 GGGGTGGAGTGGGGTGTG 61.967 72.222 0.00 0.00 0.00 3.82
343 349 1.613061 GATTAGGTGGGGTGGGGTG 59.387 63.158 0.00 0.00 0.00 4.61
344 350 1.999002 CGATTAGGTGGGGTGGGGT 60.999 63.158 0.00 0.00 0.00 4.95
481 789 2.967615 GGCGAGGGAAGCGTATGC 60.968 66.667 0.00 0.00 43.24 3.14
483 791 4.587189 GCGGCGAGGGAAGCGTAT 62.587 66.667 12.98 0.00 35.00 3.06
543 851 0.933047 CGAACAACTCACGAGCACGA 60.933 55.000 11.40 0.00 42.66 4.35
587 898 1.683943 CCCACAGCCATCGATCAAAT 58.316 50.000 0.00 0.00 0.00 2.32
601 912 2.033448 GCATCCACGAACCCCACA 59.967 61.111 0.00 0.00 0.00 4.17
771 1084 2.363680 AGCAGAATCGTGGATCTACAGG 59.636 50.000 10.08 0.00 0.00 4.00
802 1115 2.227626 TCCGCAAACCACAACATACATG 59.772 45.455 0.00 0.00 0.00 3.21
934 1262 1.967762 CAAATGAAACGCGCATCAGT 58.032 45.000 17.71 13.41 0.00 3.41
974 1302 0.527817 CGGTCGTAAGTGGCAGATCC 60.528 60.000 0.00 0.00 39.48 3.36
992 1320 4.899239 GAGTCTCCATGGCGCCCG 62.899 72.222 26.77 15.56 0.00 6.13
1034 1368 2.694616 AGTGGTGGTGGTGGTGGT 60.695 61.111 0.00 0.00 0.00 4.16
1035 1369 2.113139 GAGTGGTGGTGGTGGTGG 59.887 66.667 0.00 0.00 0.00 4.61
1036 1370 1.227943 CTGAGTGGTGGTGGTGGTG 60.228 63.158 0.00 0.00 0.00 4.17
1037 1371 2.452064 CCTGAGTGGTGGTGGTGGT 61.452 63.158 0.00 0.00 0.00 4.16
1038 1372 2.431683 CCTGAGTGGTGGTGGTGG 59.568 66.667 0.00 0.00 0.00 4.61
1253 1587 3.977244 CCCGGCTGCGCTTTTTGT 61.977 61.111 9.73 0.00 0.00 2.83
1595 1930 4.467795 AGTTGCTGATGACCTATGTACACT 59.532 41.667 0.00 0.00 0.00 3.55
1650 1985 3.612795 TCTAGGTGGAAGGCTGCTATA 57.387 47.619 0.00 0.00 0.00 1.31
1706 2041 1.559831 CGCGAGTCATGATGTGCTTA 58.440 50.000 0.00 0.00 0.00 3.09
1750 2085 1.705002 CCCCAACAGTCTCCACCACA 61.705 60.000 0.00 0.00 0.00 4.17
1791 2126 3.258372 CCACAAGCTACAAGGTGACTCTA 59.742 47.826 0.00 0.00 42.68 2.43
1980 2315 2.777536 TGGGAACAGATGCTGGAGT 58.222 52.632 0.00 0.00 35.51 3.85
2052 2387 0.532573 GAGTGTCAAGATGGCGAGGA 59.467 55.000 0.00 0.00 0.00 3.71
2300 2635 9.066892 TGGAACTTTAGATTATATGCATGGAAC 57.933 33.333 10.16 0.00 0.00 3.62
2349 2684 6.295249 TCCATGAACATGAACAAGTAACAGA 58.705 36.000 15.21 0.00 41.20 3.41
2353 2688 6.951062 TGTTCCATGAACATGAACAAGTAA 57.049 33.333 15.21 1.66 45.88 2.24
2473 2808 3.542712 AGATTAAACAAGCAGCACACG 57.457 42.857 0.00 0.00 0.00 4.49
2509 2844 8.723942 AATCACTTTAGTATTAGCCACAGAAG 57.276 34.615 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.