Multiple sequence alignment - TraesCS7D01G271400

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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 TraesCS7D01G271400 chr7D 100.000 3492 0 0 1 3492 259842392 259838901 0.000000e+00 6449
1 TraesCS7D01G271400 chr7D 88.453 433 44 6 1 430 596066420 596066849 5.170000e-143 518
2 TraesCS7D01G271400 chr7A 94.248 3077 78 34 469 3492 282370329 282367299 0.000000e+00 4610
3 TraesCS7D01G271400 chr7B 93.629 2637 100 28 1 2615 239361448 239364038 0.000000e+00 3877
4 TraesCS7D01G271400 chr7B 97.479 357 8 1 2678 3034 239364323 239364678 2.980000e-170 608
5 TraesCS7D01G271400 chr7B 89.613 491 19 14 3030 3492 239364715 239365201 2.320000e-166 595
6 TraesCS7D01G271400 chr7B 89.655 435 41 4 1 433 484274003 484273571 5.090000e-153 551
7 TraesCS7D01G271400 chr1D 88.736 435 45 4 1 433 136948629 136948197 2.390000e-146 529
8 TraesCS7D01G271400 chrUn 88.657 432 45 4 1 430 95231438 95231867 1.110000e-144 523
9 TraesCS7D01G271400 chr3A 88.276 435 47 4 1 433 562894286 562893854 5.170000e-143 518
10 TraesCS7D01G271400 chr3A 84.259 324 42 6 1 321 550459961 550460278 1.220000e-79 307
11 TraesCS7D01G271400 chr3A 90.385 156 15 0 1539 1694 718836827 718836672 4.570000e-49 206
12 TraesCS7D01G271400 chr5B 87.529 433 48 6 1 430 70694438 70694009 2.420000e-136 496
13 TraesCS7D01G271400 chr5B 87.248 149 19 0 1549 1697 504307100 504306952 1.670000e-38 171
14 TraesCS7D01G271400 chr6D 88.020 409 46 3 1 407 468582480 468582887 6.780000e-132 481
15 TraesCS7D01G271400 chr6B 86.806 432 51 6 1 430 10691309 10691736 8.770000e-131 477
16 TraesCS7D01G271400 chr3B 91.558 154 13 0 1541 1694 786970552 786970399 2.730000e-51 213
17 TraesCS7D01G271400 chr3D 90.909 154 14 0 1541 1694 588489280 588489127 1.270000e-49 207
18 TraesCS7D01G271400 chr5A 87.248 149 19 0 1549 1697 530302400 530302252 1.670000e-38 171
19 TraesCS7D01G271400 chr5D 86.577 149 20 0 1549 1697 417040861 417040713 7.750000e-37 165


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 TraesCS7D01G271400 chr7D 259838901 259842392 3491 True 6449.000000 6449 100.000000 1 3492 1 chr7D.!!$R1 3491
1 TraesCS7D01G271400 chr7A 282367299 282370329 3030 True 4610.000000 4610 94.248000 469 3492 1 chr7A.!!$R1 3023
2 TraesCS7D01G271400 chr7B 239361448 239365201 3753 False 1693.333333 3877 93.573667 1 3492 3 chr7B.!!$F1 3491


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
51 52 0.389391 CACCGATGCCCTACCTAGTG 59.611 60.0 0.0 0.0 0.0 2.74 F
1055 1072 0.034380 ACGAGCCAGCTACCACTAGA 60.034 55.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1223 0.244994 ATCCATAGATCGCGGCTGTC 59.755 55.0 6.13 0.0 0.0 3.51 R
2673 2963 0.530650 AGAGAGAGAGAGAGAGCGCG 60.531 60.0 0.00 0.0 0.0 6.86 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
48 49 2.138179 GCCACCGATGCCCTACCTA 61.138 63.158 0.00 0.00 0.00 3.08
51 52 0.389391 CACCGATGCCCTACCTAGTG 59.611 60.000 0.00 0.00 0.00 2.74
59 60 2.487532 CCTACCTAGTGGCGACCGG 61.488 68.421 0.00 0.00 36.63 5.28
369 371 2.861974 AGGAAGGGGCGGGGAAAA 60.862 61.111 0.00 0.00 0.00 2.29
376 378 1.074248 GGGCGGGGAAAAGAGTTGA 59.926 57.895 0.00 0.00 0.00 3.18
380 382 1.574702 CGGGGAAAAGAGTTGACGGC 61.575 60.000 0.00 0.00 0.00 5.68
456 458 3.871594 AGACCTTTTGTGTCTTCTTGTCG 59.128 43.478 0.00 0.00 40.06 4.35
532 534 1.604604 AACCGTGGAAGGAACATGTG 58.395 50.000 0.00 0.00 34.73 3.21
655 657 5.828299 TTCATTTTCTGAAACGGTCTTGT 57.172 34.783 1.58 0.00 40.92 3.16
672 689 1.999048 TGTTTACGTACCGCTCCATG 58.001 50.000 0.00 0.00 0.00 3.66
759 776 4.090786 GTGTGTTTTGTTTTCCGAAGTTGG 59.909 41.667 0.00 0.00 0.00 3.77
900 917 4.557705 CCTCCTTCCCCTATCTTAACTCA 58.442 47.826 0.00 0.00 0.00 3.41
901 918 4.345547 CCTCCTTCCCCTATCTTAACTCAC 59.654 50.000 0.00 0.00 0.00 3.51
902 919 5.212745 CTCCTTCCCCTATCTTAACTCACT 58.787 45.833 0.00 0.00 0.00 3.41
903 920 5.209659 TCCTTCCCCTATCTTAACTCACTC 58.790 45.833 0.00 0.00 0.00 3.51
907 924 4.015541 TCCCCTATCTTAACTCACTCCCTT 60.016 45.833 0.00 0.00 0.00 3.95
1051 1068 1.738099 CACACGAGCCAGCTACCAC 60.738 63.158 0.00 0.00 0.00 4.16
1055 1072 0.034380 ACGAGCCAGCTACCACTAGA 60.034 55.000 0.00 0.00 0.00 2.43
1063 1080 0.526524 GCTACCACTAGACGCAGCAG 60.527 60.000 0.00 0.00 0.00 4.24
1122 1139 4.441695 CGGAGAAGAGCAGGCGCA 62.442 66.667 10.83 0.00 42.27 6.09
1124 1141 2.178890 GGAGAAGAGCAGGCGCATG 61.179 63.158 19.36 19.36 42.27 4.06
1155 1172 2.176889 AGGAGTAGTTAAGGCGCAGAA 58.823 47.619 10.83 0.00 0.00 3.02
1196 1213 1.209019 ACTCGGGCGTAGAGAGTAGAA 59.791 52.381 9.65 0.00 42.71 2.10
1206 1223 2.065906 GAGAGTAGAAGCCGGGCGAG 62.066 65.000 14.39 0.00 0.00 5.03
1653 1670 2.668550 GCCACCCACGTCAAGTCC 60.669 66.667 0.00 0.00 0.00 3.85
1843 1862 2.518349 CCCACACCACACCACACC 60.518 66.667 0.00 0.00 0.00 4.16
1950 1969 2.952310 GGTTGATGATTTAGGGGAGCAC 59.048 50.000 0.00 0.00 0.00 4.40
2459 2484 4.149571 CGACATGATGACTTCGATTGATCC 59.850 45.833 0.00 0.00 33.20 3.36
2527 2552 4.162320 TCAGGTCAGGTCAGCTAATAAAGG 59.838 45.833 0.00 0.00 0.00 3.11
2653 2943 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2654 2944 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2655 2945 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2656 2946 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2657 2947 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2658 2948 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2659 2949 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2660 2950 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2661 2951 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2662 2952 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
2663 2953 2.362397 TCTCTCTCTCTCTCTCTCTCGC 59.638 54.545 0.00 0.00 0.00 5.03
2664 2954 1.067060 TCTCTCTCTCTCTCTCTCGCG 59.933 57.143 0.00 0.00 0.00 5.87
2665 2955 0.529773 TCTCTCTCTCTCTCTCGCGC 60.530 60.000 0.00 0.00 0.00 6.86
2666 2956 1.821241 CTCTCTCTCTCTCTCGCGCG 61.821 65.000 26.76 26.76 0.00 6.86
2667 2957 3.506312 CTCTCTCTCTCTCGCGCGC 62.506 68.421 27.95 23.91 0.00 6.86
2668 2958 4.936248 CTCTCTCTCTCGCGCGCG 62.936 72.222 44.84 44.84 41.35 6.86
2688 2978 3.572539 CGCGCGCTCTCTCTCTCT 61.573 66.667 30.48 0.00 0.00 3.10
2689 2979 2.327940 GCGCGCTCTCTCTCTCTC 59.672 66.667 26.67 0.00 0.00 3.20
2690 2980 2.180204 GCGCGCTCTCTCTCTCTCT 61.180 63.158 26.67 0.00 0.00 3.10
2691 2981 1.934463 CGCGCTCTCTCTCTCTCTC 59.066 63.158 5.56 0.00 0.00 3.20
2692 2982 0.530650 CGCGCTCTCTCTCTCTCTCT 60.531 60.000 5.56 0.00 0.00 3.10
2812 3102 5.140106 AGGCCTACTAGGTAGCTTCTAAA 57.860 43.478 1.29 0.00 37.80 1.85
3052 3383 7.875041 ACGGAGAGGATTTAATGTTGAGATATG 59.125 37.037 0.00 0.00 0.00 1.78
3097 3428 7.981142 TCCAGGATCAAATGATGAGATGATTA 58.019 34.615 0.00 0.00 42.53 1.75
3164 3501 8.774586 GTTTTGATTGTTTCTAACTCTGAGCTA 58.225 33.333 4.19 0.00 0.00 3.32
3215 3552 8.789881 AGTAATCTATTCTCTTCATTCGAACG 57.210 34.615 0.00 0.00 0.00 3.95
3224 3561 4.052608 TCTTCATTCGAACGCTGTGTTTA 58.947 39.130 8.14 0.00 42.09 2.01
3320 3657 5.401531 TCGTATATTACCATTCCCAGCTC 57.598 43.478 0.00 0.00 0.00 4.09
3359 3696 4.281435 CCTCATTTATATGTTGCATGCCCA 59.719 41.667 16.68 12.50 33.34 5.36
3361 3698 3.706802 TTTATATGTTGCATGCCCACG 57.293 42.857 16.68 0.00 0.00 4.94
3374 3711 4.785453 CCACGCCTCCCCTTGCTC 62.785 72.222 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.487532 CCGGTCGCCACTAGGTAGG 61.488 68.421 0.00 0.00 37.19 3.18
81 82 2.282462 GGTGGGGCAGTCTTGGTG 60.282 66.667 0.00 0.00 0.00 4.17
82 83 2.776526 TGGTGGGGCAGTCTTGGT 60.777 61.111 0.00 0.00 0.00 3.67
271 273 3.009714 GCCTCCTCGTTCCCCCTT 61.010 66.667 0.00 0.00 0.00 3.95
356 358 2.160853 AACTCTTTTCCCCGCCCCT 61.161 57.895 0.00 0.00 0.00 4.79
420 422 3.468140 GTCTACCACCCTCCCGCC 61.468 72.222 0.00 0.00 0.00 6.13
456 458 1.949257 CGTGAGGGGCTGTGAAAAC 59.051 57.895 0.00 0.00 0.00 2.43
532 534 0.179012 TGTTTCCCTTGGAACGTCCC 60.179 55.000 0.00 0.00 41.87 4.46
642 644 3.801594 GGTACGTAAACAAGACCGTTTCA 59.198 43.478 0.00 0.00 39.70 2.69
672 689 2.793278 ACAAAACAATTGCTCCGACC 57.207 45.000 5.05 0.00 0.00 4.79
759 776 1.941294 CTGATTCTCTGATGGTGCTGC 59.059 52.381 0.00 0.00 0.00 5.25
900 917 1.132036 AGGAAAGGGAAGGAAGGGAGT 60.132 52.381 0.00 0.00 0.00 3.85
901 918 1.562008 GAGGAAAGGGAAGGAAGGGAG 59.438 57.143 0.00 0.00 0.00 4.30
902 919 1.670059 GAGGAAAGGGAAGGAAGGGA 58.330 55.000 0.00 0.00 0.00 4.20
903 920 0.626382 GGAGGAAAGGGAAGGAAGGG 59.374 60.000 0.00 0.00 0.00 3.95
907 924 1.916181 GTGATGGAGGAAAGGGAAGGA 59.084 52.381 0.00 0.00 0.00 3.36
1051 1068 2.889503 GCTGCCTGCTGCGTCTAG 60.890 66.667 5.24 0.00 45.60 2.43
1122 1139 1.207488 TACTCCTTGGCAGCACCCAT 61.207 55.000 0.00 0.00 37.83 4.00
1124 1141 1.078143 CTACTCCTTGGCAGCACCC 60.078 63.158 0.00 0.00 37.83 4.61
1206 1223 0.244994 ATCCATAGATCGCGGCTGTC 59.755 55.000 6.13 0.00 0.00 3.51
1759 1776 0.535797 GTAGTGGTAGGAGTGGTGGC 59.464 60.000 0.00 0.00 0.00 5.01
1767 1784 4.399483 ACCTGAAGAAGTAGTGGTAGGA 57.601 45.455 0.00 0.00 0.00 2.94
1843 1862 7.622893 AAAAGGAAAGAGAAATAGCTAGCTG 57.377 36.000 27.68 0.00 0.00 4.24
1899 1918 3.053842 ACACTGGATTCCATCAAGCTCAT 60.054 43.478 5.70 0.00 33.41 2.90
1950 1969 2.543802 CGCCATCATCTGCTGCTGG 61.544 63.158 6.69 2.92 42.89 4.85
2082 2101 2.429930 CCCTTGAAGACGTGGCCA 59.570 61.111 0.00 0.00 0.00 5.36
2446 2471 3.624861 GCATCAACAGGATCAATCGAAGT 59.375 43.478 0.00 0.00 32.57 3.01
2459 2484 7.149031 CGCATCAATTTATGTATGCATCAACAG 60.149 37.037 0.19 0.00 40.01 3.16
2527 2552 3.454812 TGATTGTTCCCTAGCTAGTTCCC 59.545 47.826 19.31 5.54 0.00 3.97
2671 2961 3.506312 GAGAGAGAGAGAGCGCGCG 62.506 68.421 28.44 28.44 0.00 6.86
2672 2962 2.105960 GAGAGAGAGAGAGAGCGCGC 62.106 65.000 26.66 26.66 0.00 6.86
2673 2963 0.530650 AGAGAGAGAGAGAGAGCGCG 60.531 60.000 0.00 0.00 0.00 6.86
2674 2964 1.221414 GAGAGAGAGAGAGAGAGCGC 58.779 60.000 0.00 0.00 0.00 5.92
2675 2965 2.602257 TGAGAGAGAGAGAGAGAGCG 57.398 55.000 0.00 0.00 0.00 5.03
2676 2966 2.551459 GCATGAGAGAGAGAGAGAGAGC 59.449 54.545 0.00 0.00 0.00 4.09
2677 2967 3.813724 CAGCATGAGAGAGAGAGAGAGAG 59.186 52.174 0.00 0.00 39.69 3.20
2678 2968 3.434024 CCAGCATGAGAGAGAGAGAGAGA 60.434 52.174 0.00 0.00 39.69 3.10
2679 2969 2.882761 CCAGCATGAGAGAGAGAGAGAG 59.117 54.545 0.00 0.00 39.69 3.20
2680 2970 2.241941 ACCAGCATGAGAGAGAGAGAGA 59.758 50.000 0.00 0.00 39.69 3.10
2681 2971 2.658285 ACCAGCATGAGAGAGAGAGAG 58.342 52.381 0.00 0.00 39.69 3.20
2682 2972 2.824689 ACCAGCATGAGAGAGAGAGA 57.175 50.000 0.00 0.00 39.69 3.10
2683 2973 3.523547 CAAACCAGCATGAGAGAGAGAG 58.476 50.000 0.00 0.00 39.69 3.20
2684 2974 2.354503 GCAAACCAGCATGAGAGAGAGA 60.355 50.000 0.00 0.00 39.69 3.10
2685 2975 2.008329 GCAAACCAGCATGAGAGAGAG 58.992 52.381 0.00 0.00 39.69 3.20
2686 2976 1.348696 TGCAAACCAGCATGAGAGAGA 59.651 47.619 0.00 0.00 40.11 3.10
2687 2977 1.817357 TGCAAACCAGCATGAGAGAG 58.183 50.000 0.00 0.00 40.11 3.20
2740 3030 4.651778 TGCATCCAAAACTGTAGTAAGCT 58.348 39.130 0.00 0.00 0.00 3.74
2812 3102 2.310779 TGGAAGAGCTAGACACAGGT 57.689 50.000 0.00 0.00 0.00 4.00
3022 3312 5.874810 TCAACATTAAATCCTCTCCGTTCTG 59.125 40.000 0.00 0.00 0.00 3.02
3052 3383 4.202295 TGGAGCATATGATGACTGGAAGAC 60.202 45.833 6.97 0.00 37.43 3.01
3097 3428 4.323104 GGAGAGCACAACTATTTGTCTCCT 60.323 45.833 17.89 7.20 44.57 3.69
3164 3501 4.515191 GCAATGTGACACCGATGGTATTAT 59.485 41.667 2.45 0.00 32.11 1.28
3166 3503 2.682856 GCAATGTGACACCGATGGTATT 59.317 45.455 2.45 0.00 32.11 1.89
3276 3613 5.527214 CGATACCTGATGCTAAACCAATTCA 59.473 40.000 0.00 0.00 0.00 2.57
3320 3657 2.412870 TGAGGTACGTGCAGAACAATG 58.587 47.619 5.86 0.00 0.00 2.82
3361 3698 3.803162 GGAGGAGCAAGGGGAGGC 61.803 72.222 0.00 0.00 0.00 4.70
3374 3711 1.916181 ACCACTGAGGGTAATTGGAGG 59.084 52.381 0.00 0.00 43.89 4.30



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

AutoCloner maintained by Alex Coulton.