Multiple sequence alignment - TraesCS4A01G231000

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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 TraesCS4A01G231000 chr4A 100.000 3251 0 0 1 3251 540415072 540418322 0.000000e+00 6004.0
1 TraesCS4A01G231000 chr4A 96.378 2595 73 14 668 3251 540059188 540061772 0.000000e+00 4252.0
2 TraesCS4A01G231000 chr4A 87.065 719 38 26 9 672 540058594 540059312 0.000000e+00 761.0
3 TraesCS4A01G231000 chr4A 89.231 130 14 0 668 797 540415619 540415748 2.600000e-36 163.0
4 TraesCS4A01G231000 chr4D 93.237 2765 139 13 14 2764 56745515 56742785 0.000000e+00 4026.0
5 TraesCS4A01G231000 chr4D 86.059 2116 251 22 668 2743 49937915 49935804 0.000000e+00 2233.0
6 TraesCS4A01G231000 chr4D 94.227 485 16 3 2773 3250 56742740 56742261 0.000000e+00 730.0
7 TraesCS4A01G231000 chr4D 85.813 578 74 2 1394 1968 50031868 50031296 9.980000e-170 606.0
8 TraesCS4A01G231000 chr4D 82.421 603 51 20 92 672 49938360 49937791 2.940000e-130 475.0
9 TraesCS4A01G231000 chr4D 83.495 515 48 17 2744 3251 49935772 49935288 2.300000e-121 446.0
10 TraesCS4A01G231000 chr4D 88.060 134 15 1 668 801 56744976 56744844 1.210000e-34 158.0
11 TraesCS4A01G231000 chr3A 83.851 483 63 13 2740 3214 57010850 57010375 2.300000e-121 446.0
12 TraesCS4A01G231000 chr3A 83.376 391 49 15 2828 3211 56962947 56962566 6.680000e-92 348.0
13 TraesCS4A01G231000 chr3A 93.750 48 3 0 2744 2791 56963003 56962956 4.500000e-09 73.1
14 TraesCS4A01G231000 chr4B 84.755 387 48 8 2744 3127 242924247 242923869 8.510000e-101 377.0
15 TraesCS4A01G231000 chr4B 94.286 175 9 1 3077 3251 83312376 83312203 1.920000e-67 267.0
16 TraesCS4A01G231000 chr5B 84.238 387 50 8 2744 3127 115862911 115862533 1.840000e-97 366.0
17 TraesCS4A01G231000 chr5A 83.180 327 46 5 2744 3068 600165348 600165029 1.140000e-74 291.0
18 TraesCS4A01G231000 chr6D 92.437 119 9 0 956 1074 454585291 454585173 1.550000e-38 171.0
19 TraesCS4A01G231000 chr2D 91.597 119 10 0 956 1074 524269699 524269581 7.220000e-37 165.0
20 TraesCS4A01G231000 chr6A 90.756 119 11 0 956 1074 521552226 521552108 3.360000e-35 159.0
21 TraesCS4A01G231000 chr6A 91.150 113 10 0 956 1068 524317493 524317381 1.560000e-33 154.0
22 TraesCS4A01G231000 chr1D 91.379 116 10 0 956 1071 14149004 14149119 3.360000e-35 159.0
23 TraesCS4A01G231000 chr7A 89.916 119 12 0 956 1074 422485336 422485218 1.560000e-33 154.0
24 TraesCS4A01G231000 chr2A 91.525 59 4 1 3057 3115 172527390 172527333 2.690000e-11 80.5


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 TraesCS4A01G231000 chr4A 540415072 540418322 3250 False 3083.500000 6004 94.615500 1 3251 2 chr4A.!!$F2 3250
1 TraesCS4A01G231000 chr4A 540058594 540061772 3178 False 2506.500000 4252 91.721500 9 3251 2 chr4A.!!$F1 3242
2 TraesCS4A01G231000 chr4D 56742261 56745515 3254 True 1638.000000 4026 91.841333 14 3250 3 chr4D.!!$R3 3236
3 TraesCS4A01G231000 chr4D 49935288 49938360 3072 True 1051.333333 2233 83.991667 92 3251 3 chr4D.!!$R2 3159
4 TraesCS4A01G231000 chr4D 50031296 50031868 572 True 606.000000 606 85.813000 1394 1968 1 chr4D.!!$R1 574

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
146 159 0.178961 GAGCCCAAACCTCCAAACCT 60.179 55.0 0.0 0.0 0.0 3.50 F
1495 1610 0.249868 GGTGCTGTATCATGCCGCTA 60.250 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2239 0.037697 CCGGTTCGACTCCATCAACA 60.038 55.000 0.0 0.0 0.0 3.33 R
2541 2657 2.282180 GATGGTGGTGGCGGTGTT 60.282 61.111 0.0 0.0 0.0 3.32 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
51 53 1.732259 GCAACGTGACATAGAACCAGG 59.268 52.381 0.00 0.00 0.00 4.45
66 68 2.406559 ACCAGGCTGATCTTGATAGCT 58.593 47.619 17.94 0.00 37.58 3.32
71 75 3.071312 AGGCTGATCTTGATAGCTTGAGG 59.929 47.826 0.00 0.00 37.58 3.86
129 142 2.771763 AAGGAACAGCTGGCGTCGAG 62.772 60.000 19.93 0.00 0.00 4.04
140 153 2.434359 CGTCGAGCCCAAACCTCC 60.434 66.667 0.00 0.00 0.00 4.30
141 154 2.747686 GTCGAGCCCAAACCTCCA 59.252 61.111 0.00 0.00 0.00 3.86
142 155 1.072505 GTCGAGCCCAAACCTCCAA 59.927 57.895 0.00 0.00 0.00 3.53
143 156 0.536460 GTCGAGCCCAAACCTCCAAA 60.536 55.000 0.00 0.00 0.00 3.28
144 157 0.536460 TCGAGCCCAAACCTCCAAAC 60.536 55.000 0.00 0.00 0.00 2.93
145 158 1.524008 CGAGCCCAAACCTCCAAACC 61.524 60.000 0.00 0.00 0.00 3.27
146 159 0.178961 GAGCCCAAACCTCCAAACCT 60.179 55.000 0.00 0.00 0.00 3.50
147 160 0.264657 AGCCCAAACCTCCAAACCTT 59.735 50.000 0.00 0.00 0.00 3.50
192 228 5.266242 CCTGTACACCGTATACGTAGAAAC 58.734 45.833 22.87 16.53 37.74 2.78
367 404 4.914420 CGCTCCGCTCGAATCGCT 62.914 66.667 0.00 0.00 0.00 4.93
686 774 4.882396 GCCGCCCTTCGCTCTCTC 62.882 72.222 0.00 0.00 36.73 3.20
687 775 4.560856 CCGCCCTTCGCTCTCTCG 62.561 72.222 0.00 0.00 36.73 4.04
689 777 4.882396 GCCCTTCGCTCTCTCGCC 62.882 72.222 0.00 0.00 0.00 5.54
690 778 4.560856 CCCTTCGCTCTCTCGCCG 62.561 72.222 0.00 0.00 0.00 6.46
692 780 4.186433 CTTCGCTCTCTCGCCGCT 62.186 66.667 0.00 0.00 0.00 5.52
693 781 4.482684 TTCGCTCTCTCGCCGCTG 62.483 66.667 0.00 0.00 0.00 5.18
721 809 3.080300 ACCTCGTCTCAGATTCAGAGT 57.920 47.619 6.04 0.00 34.73 3.24
735 823 4.500116 GAGTCCGACGCTGAGCCC 62.500 72.222 0.00 0.00 0.00 5.19
757 845 2.529389 AGCCGGAAACCACCCTCT 60.529 61.111 5.05 0.00 0.00 3.69
825 913 4.475135 GGCTTGGACTCGGAGGCC 62.475 72.222 23.53 23.53 46.38 5.19
1004 1107 1.789078 GCCTACATCTGCCCAATGCG 61.789 60.000 0.00 0.00 45.60 4.73
1005 1108 0.464373 CCTACATCTGCCCAATGCGT 60.464 55.000 0.00 0.00 45.60 5.24
1131 1237 2.597713 CGCGTTCAGCTCTGCAACA 61.598 57.895 0.00 0.00 45.59 3.33
1380 1492 1.471684 ACACTCGTGACTTATCGTCCC 59.528 52.381 3.74 0.00 42.13 4.46
1400 1512 1.294659 CGGCAGAGTGAAAGTGGCTC 61.295 60.000 0.00 0.00 34.70 4.70
1440 1555 0.604578 ACCTGATTTGTGCATGCACC 59.395 50.000 40.01 27.56 45.63 5.01
1495 1610 0.249868 GGTGCTGTATCATGCCGCTA 60.250 55.000 0.00 0.00 0.00 4.26
1572 1687 0.318762 AAGTCGCTCAGTTGAGGTCC 59.681 55.000 10.88 0.00 42.29 4.46
1575 1690 2.659610 GCTCAGTTGAGGTCCGCT 59.340 61.111 10.88 0.00 42.29 5.52
1605 1720 2.925706 TCTACCGTGCCTTGGCCA 60.926 61.111 0.00 0.00 0.00 5.36
1667 1782 2.389020 CGCACCAGAGCTCTTGCAG 61.389 63.158 30.25 21.73 42.74 4.41
1754 1869 3.125146 CCGTCAAAATCGATGCTTGAAGA 59.875 43.478 24.92 7.18 32.43 2.87
1884 1999 2.244695 TGCCGTCTGAAGAGGTTTCTA 58.755 47.619 0.00 0.00 31.96 2.10
2019 2134 4.510340 GTGAACCATTATAAGTACCAGGCG 59.490 45.833 0.00 0.00 0.00 5.52
2154 2269 1.674322 CGAACCGGTTGATTGGGCT 60.674 57.895 27.87 0.00 0.00 5.19
2217 2332 2.930682 GAGCTCAAGATGGTTCGGTAAC 59.069 50.000 9.40 0.00 34.66 2.50
2314 2429 3.137533 GAGGCATTAGAGATGGAACTGC 58.862 50.000 0.00 0.00 0.00 4.40
2541 2657 3.538591 CTCCAGCTGTAGCATTTCATCA 58.461 45.455 13.81 0.00 45.16 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 4.333913 TCCTCAAGCTATCAAGATCAGC 57.666 45.455 0.00 0.00 35.49 4.26
129 142 0.392706 CAAGGTTTGGAGGTTTGGGC 59.607 55.000 0.00 0.00 0.00 5.36
140 153 1.856265 GACCGAGGCAGCAAGGTTTG 61.856 60.000 7.06 0.00 37.07 2.93
141 154 1.600916 GACCGAGGCAGCAAGGTTT 60.601 57.895 7.06 0.00 37.07 3.27
142 155 2.032681 GACCGAGGCAGCAAGGTT 59.967 61.111 7.06 0.00 37.07 3.50
143 156 4.379243 CGACCGAGGCAGCAAGGT 62.379 66.667 5.48 5.48 40.11 3.50
145 158 4.379243 ACCGACCGAGGCAGCAAG 62.379 66.667 0.00 0.00 33.69 4.01
146 159 4.373116 GACCGACCGAGGCAGCAA 62.373 66.667 0.00 0.00 33.69 3.91
672 760 4.882396 GGCGAGAGAGCGAAGGGC 62.882 72.222 0.00 0.00 44.05 5.19
673 761 4.560856 CGGCGAGAGAGCGAAGGG 62.561 72.222 0.00 0.00 38.18 3.95
676 764 4.482684 CAGCGGCGAGAGAGCGAA 62.483 66.667 12.98 0.00 40.39 4.70
691 779 4.208686 GACGAGGTAGGGCCGCAG 62.209 72.222 0.00 0.00 43.70 5.18
692 780 4.753662 AGACGAGGTAGGGCCGCA 62.754 66.667 0.00 0.00 43.70 5.69
693 781 3.902086 GAGACGAGGTAGGGCCGC 61.902 72.222 0.00 0.00 43.70 6.53
694 782 2.439701 TGAGACGAGGTAGGGCCG 60.440 66.667 0.00 0.00 43.70 6.13
695 783 0.468400 ATCTGAGACGAGGTAGGGCC 60.468 60.000 0.00 0.00 37.58 5.80
706 794 2.223157 CGTCGGACTCTGAATCTGAGAC 60.223 54.545 21.37 15.54 32.05 3.36
801 889 1.078848 CGAGTCCAAGCCCAGGAAG 60.079 63.158 0.00 0.00 36.80 3.46
825 913 4.863539 TCGTCGTGCGAGCGATCG 62.864 66.667 20.40 20.40 45.68 3.69
852 940 2.286523 CCAGTCCGGGAGCAAGACT 61.287 63.158 0.00 0.00 41.49 3.24
1131 1237 0.388649 GAACATCGCCACTGTCGAGT 60.389 55.000 0.00 0.00 39.47 4.18
1380 1492 2.328099 GCCACTTTCACTCTGCCGG 61.328 63.158 0.00 0.00 0.00 6.13
1440 1555 3.748048 ACTTTGAGACGTTGTGGATCATG 59.252 43.478 0.00 0.00 0.00 3.07
1495 1610 0.914417 ATGAAGTGGTCCACCCCGAT 60.914 55.000 18.80 3.19 34.49 4.18
1572 1687 3.246226 CGGTAGAGATTTTGATTCCAGCG 59.754 47.826 0.00 0.00 0.00 5.18
1575 1690 3.938963 GCACGGTAGAGATTTTGATTCCA 59.061 43.478 0.00 0.00 0.00 3.53
1605 1720 2.433239 GGCTTCCTGCATTTTGATCCAT 59.567 45.455 0.00 0.00 45.15 3.41
1667 1782 1.676006 CGTCAATAAAGGCCATCCACC 59.324 52.381 5.01 0.00 33.74 4.61
1754 1869 4.916041 TCTGGATCAACCTGAACAATCT 57.084 40.909 0.00 0.00 42.27 2.40
1884 1999 1.852067 GAACCAGCGATTTGTGCCGT 61.852 55.000 0.00 0.00 0.00 5.68
2019 2134 2.380084 TATGCTTGAACTCGGTCCAC 57.620 50.000 0.00 0.00 0.00 4.02
2124 2239 0.037697 CCGGTTCGACTCCATCAACA 60.038 55.000 0.00 0.00 0.00 3.33
2154 2269 3.689161 CCTTGATGTCGCAATACCTTTGA 59.311 43.478 0.00 0.00 0.00 2.69
2314 2429 7.361286 GCAAGGAGACAGGTTTAAACTAGATTG 60.361 40.741 17.50 12.05 0.00 2.67
2541 2657 2.282180 GATGGTGGTGGCGGTGTT 60.282 61.111 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.