Multiple sequence alignment - TraesCS2A01G392800

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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 TraesCS2A01G392800 chr2A 100.000 3215 0 0 1 3215 642727884 642731098 0.000000e+00 5938.0
1 TraesCS2A01G392800 chr2B 94.847 2057 65 15 704 2729 584475290 584477336 0.000000e+00 3173.0
2 TraesCS2A01G392800 chr2B 91.713 724 27 6 1 691 584474519 584475242 0.000000e+00 974.0
3 TraesCS2A01G392800 chr2B 96.744 430 11 3 2755 3183 584477318 584477745 0.000000e+00 713.0
4 TraesCS2A01G392800 chr2B 97.143 35 1 0 3181 3215 584477826 584477860 3.460000e-05 60.2
5 TraesCS2A01G392800 chr2D 94.539 1520 42 5 1230 2729 498101940 498103438 0.000000e+00 2309.0
6 TraesCS2A01G392800 chr2D 90.952 1271 48 26 1 1224 498100420 498101670 0.000000e+00 1648.0
7 TraesCS2A01G392800 chr2D 93.438 381 24 1 64 444 425214346 425213967 6.020000e-157 564.0
8 TraesCS2A01G392800 chr2D 92.268 388 29 1 64 451 627324652 627324266 1.690000e-152 549.0
9 TraesCS2A01G392800 chr2D 85.537 484 35 9 2764 3215 498103437 498103917 1.040000e-129 473.0
10 TraesCS2A01G392800 chr2D 97.368 38 1 0 285 322 620610659 620610696 7.440000e-07 65.8
11 TraesCS2A01G392800 chr1B 89.796 245 25 0 200 444 167949881 167949637 6.700000e-82 315.0
12 TraesCS2A01G392800 chr7D 100.000 35 0 0 288 322 546767729 546767695 7.440000e-07 65.8
13 TraesCS2A01G392800 chr3A 97.143 35 1 0 288 322 56739440 56739406 3.460000e-05 60.2


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 TraesCS2A01G392800 chr2A 642727884 642731098 3214 False 5938.000000 5938 100.000000 1 3215 1 chr2A.!!$F1 3214
1 TraesCS2A01G392800 chr2B 584474519 584477860 3341 False 1230.050000 3173 95.111750 1 3215 4 chr2B.!!$F1 3214
2 TraesCS2A01G392800 chr2D 498100420 498103917 3497 False 1476.666667 2309 90.342667 1 3215 3 chr2D.!!$F2 3214

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
626 636 0.095935 CGTTTGATTCTGGCTCTGCG 59.904 55.0 0.00 0.00 0.00 5.18 F
701 736 0.103208 CGGACTTTCTCCATCGAGGG 59.897 60.0 10.57 10.57 39.39 4.30 F
1920 2264 0.595053 AGTGCAAGACGACGACACTG 60.595 55.0 0.00 0.00 39.97 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 2264 0.462047 CATACCCCTCACGAAGCACC 60.462 60.000 0.00 0.0 0.0 5.01 R
2067 2411 0.818296 CCAGTGTACCCTCCTCTTCG 59.182 60.000 0.00 0.0 0.0 3.79 R
2966 3341 1.206371 GCTTGCTTCATGCCCTGAAAT 59.794 47.619 1.11 0.0 43.2 2.17 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
100 101 2.430244 CGGTCAAGGTCGTGTCCG 60.430 66.667 7.86 7.86 42.28 4.79
557 567 2.158928 AGTGCCCAATTTATACGCGGTA 60.159 45.455 12.47 0.00 0.00 4.02
565 575 4.725556 ATTTATACGCGGTATGTGCAAG 57.274 40.909 12.47 0.00 30.79 4.01
616 626 6.467047 TCGTAGTATTTCGAGTCGTTTGATTC 59.533 38.462 13.12 1.45 0.00 2.52
622 632 1.656095 CGAGTCGTTTGATTCTGGCTC 59.344 52.381 3.82 0.00 0.00 4.70
623 633 2.672478 CGAGTCGTTTGATTCTGGCTCT 60.672 50.000 3.82 0.00 0.00 4.09
626 636 0.095935 CGTTTGATTCTGGCTCTGCG 59.904 55.000 0.00 0.00 0.00 5.18
627 637 1.160137 GTTTGATTCTGGCTCTGCGT 58.840 50.000 0.00 0.00 0.00 5.24
678 713 2.995939 TGCTGTTGAAATCGAGCTAGTG 59.004 45.455 0.00 0.00 32.41 2.74
691 726 3.612004 CGAGCTAGTGTTTCGGACTTTCT 60.612 47.826 0.00 0.00 0.00 2.52
693 728 2.994578 GCTAGTGTTTCGGACTTTCTCC 59.005 50.000 0.00 0.00 35.33 3.71
696 731 3.665190 AGTGTTTCGGACTTTCTCCATC 58.335 45.455 0.00 0.00 39.39 3.51
698 733 2.297880 TGTTTCGGACTTTCTCCATCGA 59.702 45.455 0.00 0.00 39.39 3.59
699 734 2.924290 GTTTCGGACTTTCTCCATCGAG 59.076 50.000 0.00 0.00 39.39 4.04
700 735 1.103803 TCGGACTTTCTCCATCGAGG 58.896 55.000 0.00 0.00 39.39 4.63
701 736 0.103208 CGGACTTTCTCCATCGAGGG 59.897 60.000 10.57 10.57 39.39 4.30
702 737 1.486211 GGACTTTCTCCATCGAGGGA 58.514 55.000 19.23 19.23 39.21 4.20
720 790 3.117888 AGGGAAGTGTCACAAACTGTCAT 60.118 43.478 5.62 0.00 0.00 3.06
722 792 3.627577 GGAAGTGTCACAAACTGTCATGT 59.372 43.478 5.62 0.00 0.00 3.21
723 793 4.096382 GGAAGTGTCACAAACTGTCATGTT 59.904 41.667 5.62 0.00 0.00 2.71
814 885 1.078426 CCCAGTCCAGGCTAAACCG 60.078 63.158 0.00 0.00 46.52 4.44
862 942 2.287668 ACTCGTGTTGTCTCTTCTTCCG 60.288 50.000 0.00 0.00 0.00 4.30
863 943 1.679680 TCGTGTTGTCTCTTCTTCCGT 59.320 47.619 0.00 0.00 0.00 4.69
864 944 2.052157 CGTGTTGTCTCTTCTTCCGTC 58.948 52.381 0.00 0.00 0.00 4.79
893 973 4.521062 CTCGCCGCTCCCTCCTTG 62.521 72.222 0.00 0.00 0.00 3.61
948 1028 2.683933 CACCCTACCTCGCCCACT 60.684 66.667 0.00 0.00 0.00 4.00
1467 1811 1.153823 CGTCTTCGCCGTCTCCAAT 60.154 57.895 0.00 0.00 0.00 3.16
1486 1830 0.738975 TAACCACATCTCGCTCTCCG 59.261 55.000 0.00 0.00 38.61 4.63
1578 1922 4.382320 TACCGCAACCTGTCCCGC 62.382 66.667 0.00 0.00 0.00 6.13
1869 2213 3.307782 ACAAGTTCACGAGGTTGTTTACG 59.692 43.478 0.00 0.00 28.62 3.18
1870 2214 1.862827 AGTTCACGAGGTTGTTTACGC 59.137 47.619 0.00 0.00 0.00 4.42
1920 2264 0.595053 AGTGCAAGACGACGACACTG 60.595 55.000 0.00 0.00 39.97 3.66
1929 2273 1.299926 GACGACACTGGTGCTTCGT 60.300 57.895 15.60 15.60 42.40 3.85
1938 2282 0.907704 TGGTGCTTCGTGAGGGGTAT 60.908 55.000 0.00 0.00 0.00 2.73
2067 2411 3.177487 GGTTTTAGACGAGGATGACGAC 58.823 50.000 0.00 0.00 34.70 4.34
2148 2492 1.610522 GCTGATGTTGAGTGCTTTGGT 59.389 47.619 0.00 0.00 0.00 3.67
2235 2579 1.399440 CACTGGATGGTGATTTCTGCG 59.601 52.381 0.00 0.00 39.34 5.18
2260 2604 3.119884 CCGCATGTTGCTGTTTTGAGATA 60.120 43.478 0.00 0.00 42.25 1.98
2266 2610 4.832266 TGTTGCTGTTTTGAGATAATGGGT 59.168 37.500 0.00 0.00 0.00 4.51
2277 2621 4.192317 GAGATAATGGGTGGTGACTTCAC 58.808 47.826 0.34 0.34 45.72 3.18
2414 2776 7.759489 TTGTGAATTGCTAGTTCCACTAAAT 57.241 32.000 0.00 0.00 29.00 1.40
2680 3052 5.119931 TGTTGATTGTTGTAATGAGTGGC 57.880 39.130 0.00 0.00 0.00 5.01
2719 3091 8.017251 AGGGGGTATTACTGTAGAAGATGTTAT 58.983 37.037 0.00 0.00 0.00 1.89
2739 3111 8.924511 TGTTATCACATCTTCCTTTCTTTTCT 57.075 30.769 0.00 0.00 0.00 2.52
2740 3112 9.003658 TGTTATCACATCTTCCTTTCTTTTCTC 57.996 33.333 0.00 0.00 0.00 2.87
2741 3113 9.225436 GTTATCACATCTTCCTTTCTTTTCTCT 57.775 33.333 0.00 0.00 0.00 3.10
2742 3114 9.799106 TTATCACATCTTCCTTTCTTTTCTCTT 57.201 29.630 0.00 0.00 0.00 2.85
2743 3115 8.703378 ATCACATCTTCCTTTCTTTTCTCTTT 57.297 30.769 0.00 0.00 0.00 2.52
2744 3116 8.525290 TCACATCTTCCTTTCTTTTCTCTTTT 57.475 30.769 0.00 0.00 0.00 2.27
2745 3117 8.971073 TCACATCTTCCTTTCTTTTCTCTTTTT 58.029 29.630 0.00 0.00 0.00 1.94
2746 3118 9.028185 CACATCTTCCTTTCTTTTCTCTTTTTG 57.972 33.333 0.00 0.00 0.00 2.44
2747 3119 8.971073 ACATCTTCCTTTCTTTTCTCTTTTTGA 58.029 29.630 0.00 0.00 0.00 2.69
2748 3120 9.460906 CATCTTCCTTTCTTTTCTCTTTTTGAG 57.539 33.333 0.00 0.00 43.96 3.02
2749 3121 8.000780 TCTTCCTTTCTTTTCTCTTTTTGAGG 57.999 34.615 0.00 0.00 42.86 3.86
2750 3122 6.715347 TCCTTTCTTTTCTCTTTTTGAGGG 57.285 37.500 0.00 0.00 42.86 4.30
2751 3123 6.431722 TCCTTTCTTTTCTCTTTTTGAGGGA 58.568 36.000 0.00 0.00 42.86 4.20
2752 3124 6.895204 TCCTTTCTTTTCTCTTTTTGAGGGAA 59.105 34.615 0.00 0.00 43.16 3.97
2819 3191 6.953101 TGGTATATTAGAAACTGTCAAGCCA 58.047 36.000 0.00 0.00 0.00 4.75
2954 3327 3.731717 CCTAGCTTCGAGACGCTTAATTC 59.268 47.826 9.33 0.00 37.68 2.17
2955 3328 3.512033 AGCTTCGAGACGCTTAATTCT 57.488 42.857 0.00 0.00 31.17 2.40
2956 3329 3.440228 AGCTTCGAGACGCTTAATTCTC 58.560 45.455 0.00 0.00 35.80 2.87
2959 3332 4.732355 GCTTCGAGACGCTTAATTCTCTCT 60.732 45.833 7.10 0.00 36.82 3.10
2966 3341 6.116806 AGACGCTTAATTCTCTCTGTCTCTA 58.883 40.000 0.00 0.00 30.06 2.43
2970 3345 7.918562 ACGCTTAATTCTCTCTGTCTCTATTTC 59.081 37.037 0.00 0.00 0.00 2.17
2994 3369 1.402456 GCATGAAGCAAGCCTCACAAG 60.402 52.381 0.00 0.00 44.79 3.16
3106 3508 2.995283 TGATCAGATTTGGGCAGACAG 58.005 47.619 0.00 0.00 0.00 3.51
3164 3567 8.630278 CAGAAGATCTGCTTGGAATTTTATTG 57.370 34.615 0.00 0.00 37.72 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
485 486 3.944871 GCAATATTTGGCAGGGTCG 57.055 52.632 0.00 0.00 0.00 4.79
557 567 1.313772 TGGCACGTAAACTTGCACAT 58.686 45.000 12.82 0.00 42.15 3.21
565 575 1.793714 CGATGGCAATGGCACGTAAAC 60.794 52.381 12.83 0.00 41.84 2.01
616 626 1.005748 TCAACAGACGCAGAGCCAG 60.006 57.895 0.00 0.00 0.00 4.85
622 632 1.278172 CGTGACCTCAACAGACGCAG 61.278 60.000 0.00 0.00 0.00 5.18
623 633 1.299850 CGTGACCTCAACAGACGCA 60.300 57.895 0.00 0.00 0.00 5.24
626 636 2.658707 GCGCGTGACCTCAACAGAC 61.659 63.158 8.43 0.00 0.00 3.51
627 637 2.355837 GCGCGTGACCTCAACAGA 60.356 61.111 8.43 0.00 0.00 3.41
691 726 0.895530 GTGACACTTCCCTCGATGGA 59.104 55.000 5.19 5.19 38.35 3.41
693 728 2.455674 TTGTGACACTTCCCTCGATG 57.544 50.000 7.20 0.00 0.00 3.84
696 731 1.867233 CAGTTTGTGACACTTCCCTCG 59.133 52.381 7.20 0.00 0.00 4.63
698 733 2.238646 TGACAGTTTGTGACACTTCCCT 59.761 45.455 7.20 0.00 0.00 4.20
699 734 2.639065 TGACAGTTTGTGACACTTCCC 58.361 47.619 7.20 0.00 0.00 3.97
700 735 3.627577 ACATGACAGTTTGTGACACTTCC 59.372 43.478 7.20 0.00 33.49 3.46
701 736 4.882671 ACATGACAGTTTGTGACACTTC 57.117 40.909 7.20 0.00 33.49 3.01
702 737 5.643379 AAACATGACAGTTTGTGACACTT 57.357 34.783 7.20 0.00 40.03 3.16
862 942 2.795297 CGAGGCGGACAGAGAGAC 59.205 66.667 0.00 0.00 0.00 3.36
863 943 3.134792 GCGAGGCGGACAGAGAGA 61.135 66.667 0.00 0.00 0.00 3.10
864 944 4.200283 GGCGAGGCGGACAGAGAG 62.200 72.222 0.00 0.00 0.00 3.20
888 968 2.650196 GGCAAATGCGCACAAGGA 59.350 55.556 14.90 0.00 43.26 3.36
948 1028 2.117423 TGAGTGGAGGAGACGGCA 59.883 61.111 0.00 0.00 0.00 5.69
995 1075 3.058160 GCACCTTCTGCATGGCGT 61.058 61.111 0.00 0.00 46.29 5.68
1311 1655 3.966930 GAGGCGGAGGTGGGAGTCT 62.967 68.421 0.00 0.00 0.00 3.24
1450 1794 1.925185 GTTATTGGAGACGGCGAAGAC 59.075 52.381 16.62 1.19 0.00 3.01
1467 1811 0.738975 CGGAGAGCGAGATGTGGTTA 59.261 55.000 0.00 0.00 0.00 2.85
1506 1850 1.361197 TGGAGGGAGGATATGGCGATA 59.639 52.381 0.00 0.00 0.00 2.92
1869 2213 0.824759 AGAACACTCCAGGATACCGC 59.175 55.000 0.00 0.00 37.17 5.68
1870 2214 2.361438 GGTAGAACACTCCAGGATACCG 59.639 54.545 0.00 0.00 37.17 4.02
1920 2264 0.462047 CATACCCCTCACGAAGCACC 60.462 60.000 0.00 0.00 0.00 5.01
1929 2273 0.934302 TCCCCCTCTCATACCCCTCA 60.934 60.000 0.00 0.00 0.00 3.86
1938 2282 1.492133 CCACAAGCTTCCCCCTCTCA 61.492 60.000 0.00 0.00 0.00 3.27
2067 2411 0.818296 CCAGTGTACCCTCCTCTTCG 59.182 60.000 0.00 0.00 0.00 3.79
2148 2492 3.243401 CGTCGTCATCCACAATCTCCATA 60.243 47.826 0.00 0.00 0.00 2.74
2277 2621 2.746362 GTTGCTGAAATCCTCACCTGAG 59.254 50.000 0.00 0.00 41.71 3.35
2430 2792 6.536582 GCTTTCTACATCTCAAGCAGACAATA 59.463 38.462 0.00 0.00 41.16 1.90
2435 2797 4.815533 AGCTTTCTACATCTCAAGCAGA 57.184 40.909 5.60 0.00 43.48 4.26
2680 3052 1.937191 ACCCCCTTTGGCAAATACAG 58.063 50.000 13.89 1.02 0.00 2.74
2692 3064 6.210522 ACATCTTCTACAGTAATACCCCCTT 58.789 40.000 0.00 0.00 0.00 3.95
2719 3091 8.525290 AAAAGAGAAAAGAAAGGAAGATGTGA 57.475 30.769 0.00 0.00 0.00 3.58
2741 3113 8.700051 TGTGATAACATCTTTTTCCCTCAAAAA 58.300 29.630 0.00 0.00 40.93 1.94
2742 3114 8.243961 TGTGATAACATCTTTTTCCCTCAAAA 57.756 30.769 0.00 0.00 31.73 2.44
2743 3115 7.831691 TGTGATAACATCTTTTTCCCTCAAA 57.168 32.000 0.00 0.00 0.00 2.69
2744 3116 8.055279 GATGTGATAACATCTTTTTCCCTCAA 57.945 34.615 15.12 0.00 42.25 3.02
2745 3117 7.630242 GATGTGATAACATCTTTTTCCCTCA 57.370 36.000 15.12 0.00 42.25 3.86
2756 3128 5.684704 TCCCCAAGAAGATGTGATAACATC 58.315 41.667 14.65 14.65 44.97 3.06
2819 3191 7.291566 ACCTCTAGCACTAGACACTACATTAT 58.708 38.462 3.22 0.00 37.28 1.28
2954 3327 3.703556 TGCCCTGAAATAGAGACAGAGAG 59.296 47.826 0.00 0.00 34.07 3.20
2955 3328 3.713003 TGCCCTGAAATAGAGACAGAGA 58.287 45.455 0.00 0.00 34.07 3.10
2956 3329 4.100653 TCATGCCCTGAAATAGAGACAGAG 59.899 45.833 0.00 0.00 34.07 3.35
2959 3332 4.774124 CTTCATGCCCTGAAATAGAGACA 58.226 43.478 1.11 0.00 43.20 3.41
2966 3341 1.206371 GCTTGCTTCATGCCCTGAAAT 59.794 47.619 1.11 0.00 43.20 2.17
2970 3345 2.890371 GGCTTGCTTCATGCCCTG 59.110 61.111 11.35 0.00 45.27 4.45
3106 3508 6.311200 GGAAATCATAGTTTGCATTTGGTCAC 59.689 38.462 0.00 0.00 30.79 3.67


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

AutoCloner maintained by Alex Coulton.