Multiple sequence alignment - TraesCS3A01G128000

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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 TraesCS3A01G128000 chr3A 100.000 2950 0 0 336 3285 104559602 104556653 0.000000e+00 5448.0
1 TraesCS3A01G128000 chr3A 100.000 31 0 0 1 31 104559937 104559907 1.270000e-04 58.4
2 TraesCS3A01G128000 chr3B 95.988 2293 67 12 740 3014 137604694 137602409 0.000000e+00 3701.0
3 TraesCS3A01G128000 chr3B 92.840 419 17 5 336 742 137605345 137604928 2.180000e-166 595.0
4 TraesCS3A01G128000 chr3B 83.902 205 19 9 3074 3278 137602404 137602214 2.010000e-42 183.0
5 TraesCS3A01G128000 chr3B 84.375 64 6 4 3003 3064 665251075 665251136 3.540000e-05 60.2
6 TraesCS3A01G128000 chr3D 96.800 2000 54 4 740 2733 88094083 88092088 0.000000e+00 3330.0
7 TraesCS3A01G128000 chr3D 90.132 304 18 6 2721 3014 88092068 88091767 5.140000e-103 385.0
8 TraesCS3A01G128000 chr3D 93.927 247 13 2 496 742 88094690 88094446 4.000000e-99 372.0
9 TraesCS3A01G128000 chr3D 83.568 213 19 13 3074 3285 88091762 88091565 5.600000e-43 185.0
10 TraesCS3A01G128000 chr3D 93.548 124 8 0 336 459 88094906 88094783 5.600000e-43 185.0
11 TraesCS3A01G128000 chr4A 94.737 38 2 0 3012 3049 681656169 681656206 3.540000e-05 60.2
12 TraesCS3A01G128000 chr4A 84.211 57 5 3 3007 3060 626642942 626642887 6.000000e-03 52.8


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 TraesCS3A01G128000 chr3A 104556653 104559937 3284 True 2753.2 5448 100.000 1 3285 2 chr3A.!!$R1 3284
1 TraesCS3A01G128000 chr3B 137602214 137605345 3131 True 1493.0 3701 90.910 336 3278 3 chr3B.!!$R1 2942
2 TraesCS3A01G128000 chr3D 88091565 88094906 3341 True 891.4 3330 91.595 336 3285 5 chr3D.!!$R1 2949

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
450 451 0.035317 TGATTCAAGGTGCGAGCTGT 59.965 50.0 0.00 0.00 0.00 4.40 F
866 1431 0.396695 ATCGGATCCGGGTAGTGTGT 60.397 55.0 32.79 6.26 40.25 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2651 1.202580 GCTGTGTGAGTCTCCACTTGT 60.203 52.381 17.20 0.0 37.89 3.16 R
2684 3257 0.042708 CAAGCTCGCGGATCAAATCG 60.043 55.000 6.13 0.0 0.00 3.34 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
431 432 0.329261 TGCTTGGCATACCTCTTGCT 59.671 50.000 0.00 0.00 40.03 3.91
450 451 0.035317 TGATTCAAGGTGCGAGCTGT 59.965 50.000 0.00 0.00 0.00 4.40
517 574 1.388065 TTGGGTTTTGGGTCTGCACG 61.388 55.000 0.00 0.00 0.00 5.34
627 684 5.633655 TGAAACTTTTCTAGGGGTGTGTA 57.366 39.130 3.48 0.00 38.02 2.90
629 686 5.131475 TGAAACTTTTCTAGGGGTGTGTACT 59.869 40.000 3.48 0.00 38.02 2.73
654 711 8.389779 TGAAGCACATTCAACATCTAAGTTTA 57.610 30.769 0.00 0.00 45.00 2.01
747 1312 2.698797 TCTTCCTCTTCGGTTCTGTTGT 59.301 45.455 0.00 0.00 0.00 3.32
791 1356 1.202758 ACGCAGAGTTCATGTTTCCCA 60.203 47.619 0.00 0.00 0.00 4.37
805 1370 4.735369 TGTTTCCCATTGGTGTGAAGTAT 58.265 39.130 1.20 0.00 0.00 2.12
866 1431 0.396695 ATCGGATCCGGGTAGTGTGT 60.397 55.000 32.79 6.26 40.25 3.72
972 1537 9.350357 TGTCGTATTTGTCTTTAAGACTATCAC 57.650 33.333 23.27 15.27 45.27 3.06
1046 1611 7.058525 TGATCTGTTGCTCATGGAATATCTTT 58.941 34.615 0.00 0.00 0.00 2.52
1195 1762 1.908299 CCCTTGCACCCCAGGTTTC 60.908 63.158 1.58 0.00 31.02 2.78
1197 1764 1.181098 CCTTGCACCCCAGGTTTCAG 61.181 60.000 0.00 0.00 31.02 3.02
1519 2086 1.571955 AATTGGCCCTTGGTGATTCC 58.428 50.000 0.00 0.00 0.00 3.01
1714 2281 2.930040 CTGCTCGTTCGTTGGTTCATAT 59.070 45.455 0.00 0.00 0.00 1.78
2376 2949 4.421365 GGCAATGCCTGGTTCTCA 57.579 55.556 18.47 0.00 46.69 3.27
2470 3043 2.461695 TGGACTGGGATCTCTCTGTTC 58.538 52.381 0.00 0.00 0.00 3.18
2631 3204 4.402056 ACTATGGACGGGTTGTTATCTG 57.598 45.455 0.00 0.00 0.00 2.90
2650 3223 0.301687 GGCGATTGCTACATGTGTCG 59.698 55.000 9.11 11.08 42.25 4.35
2658 3231 5.933187 TTGCTACATGTGTCGTTTGTATT 57.067 34.783 9.11 0.00 0.00 1.89
2684 3257 1.461127 GACGAACTGGATTGTGCAGTC 59.539 52.381 4.59 0.00 46.32 3.51
2719 3292 4.154015 CGAGCTTGTTATTCATGTGTGGAA 59.846 41.667 0.00 0.00 0.00 3.53
2834 3441 5.707298 AGATGTGTACCTGGATTGTTGAAAG 59.293 40.000 0.00 0.00 0.00 2.62
2839 3446 7.084486 GTGTACCTGGATTGTTGAAAGAATTC 58.916 38.462 0.00 0.00 36.04 2.17
2845 3452 7.977853 CCTGGATTGTTGAAAGAATTCCATTAG 59.022 37.037 0.65 0.00 34.49 1.73
2865 3472 3.191078 GCATATGCTTCTCTGGACACT 57.809 47.619 20.64 0.00 38.21 3.55
2866 3473 2.871022 GCATATGCTTCTCTGGACACTG 59.129 50.000 20.64 0.00 38.21 3.66
2895 3502 2.114616 CTCCCTACATCCTCAGTTGCT 58.885 52.381 0.00 0.00 0.00 3.91
2934 3545 3.441572 CCTGTTCTTGGCAGAAATAGGTG 59.558 47.826 14.57 0.00 40.90 4.00
2943 3554 3.826729 GGCAGAAATAGGTGTTTTGGACT 59.173 43.478 0.00 0.00 0.00 3.85
2950 3561 0.808755 GGTGTTTTGGACTATGCGGG 59.191 55.000 0.00 0.00 0.00 6.13
2952 3563 0.402504 TGTTTTGGACTATGCGGGGT 59.597 50.000 0.00 0.00 0.00 4.95
2960 3571 0.836400 ACTATGCGGGGTGGGATAGG 60.836 60.000 6.15 0.00 41.17 2.57
2964 3575 2.366435 CGGGGTGGGATAGGGTGT 60.366 66.667 0.00 0.00 0.00 4.16
2965 3576 2.742116 CGGGGTGGGATAGGGTGTG 61.742 68.421 0.00 0.00 0.00 3.82
2967 3578 1.607612 GGGTGGGATAGGGTGTGTG 59.392 63.158 0.00 0.00 0.00 3.82
2968 3579 1.077716 GGTGGGATAGGGTGTGTGC 60.078 63.158 0.00 0.00 0.00 4.57
2977 3592 1.148273 GGGTGTGTGCTGGAGTTGA 59.852 57.895 0.00 0.00 0.00 3.18
2986 3601 3.195610 TGTGCTGGAGTTGATCTTATCGT 59.804 43.478 0.00 0.00 0.00 3.73
3010 3627 7.488150 CGTGTGTAAATCTCTGCTATTAACTGA 59.512 37.037 0.00 0.00 0.00 3.41
3011 3628 9.319143 GTGTGTAAATCTCTGCTATTAACTGAT 57.681 33.333 0.00 0.00 0.00 2.90
3017 3634 6.902771 TCTCTGCTATTAACTGATACTCCC 57.097 41.667 0.00 0.00 0.00 4.30
3018 3635 6.615617 TCTCTGCTATTAACTGATACTCCCT 58.384 40.000 0.00 0.00 0.00 4.20
3019 3636 6.717540 TCTCTGCTATTAACTGATACTCCCTC 59.282 42.308 0.00 0.00 0.00 4.30
3020 3637 5.775701 TCTGCTATTAACTGATACTCCCTCC 59.224 44.000 0.00 0.00 0.00 4.30
3021 3638 4.523173 TGCTATTAACTGATACTCCCTCCG 59.477 45.833 0.00 0.00 0.00 4.63
3022 3639 4.523558 GCTATTAACTGATACTCCCTCCGT 59.476 45.833 0.00 0.00 0.00 4.69
3023 3640 5.709164 GCTATTAACTGATACTCCCTCCGTA 59.291 44.000 0.00 0.00 0.00 4.02
3024 3641 6.208204 GCTATTAACTGATACTCCCTCCGTAA 59.792 42.308 0.00 0.00 0.00 3.18
3025 3642 7.255730 GCTATTAACTGATACTCCCTCCGTAAA 60.256 40.741 0.00 0.00 0.00 2.01
3026 3643 4.732672 AACTGATACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
3027 3644 3.978610 ACTGATACTCCCTCCGTAAACT 58.021 45.455 0.00 0.00 0.00 2.66
3028 3645 5.121380 ACTGATACTCCCTCCGTAAACTA 57.879 43.478 0.00 0.00 0.00 2.24
3029 3646 5.513233 ACTGATACTCCCTCCGTAAACTAA 58.487 41.667 0.00 0.00 0.00 2.24
3030 3647 6.134754 ACTGATACTCCCTCCGTAAACTAAT 58.865 40.000 0.00 0.00 0.00 1.73
3031 3648 7.293073 ACTGATACTCCCTCCGTAAACTAATA 58.707 38.462 0.00 0.00 0.00 0.98
3032 3649 7.949006 ACTGATACTCCCTCCGTAAACTAATAT 59.051 37.037 0.00 0.00 0.00 1.28
3033 3650 9.458727 CTGATACTCCCTCCGTAAACTAATATA 57.541 37.037 0.00 0.00 0.00 0.86
3034 3651 9.458727 TGATACTCCCTCCGTAAACTAATATAG 57.541 37.037 0.00 0.00 0.00 1.31
3035 3652 9.678260 GATACTCCCTCCGTAAACTAATATAGA 57.322 37.037 0.00 0.00 0.00 1.98
3095 3712 5.637006 TTGCGTATTTTAAGCCTGACATT 57.363 34.783 0.00 0.00 31.96 2.71
3111 3728 5.449588 CCTGACATTGAGCATGGTTGATTAC 60.450 44.000 0.00 0.00 37.17 1.89
3143 3760 9.743581 ATATATAATCAACCATGCTCAATGTCA 57.256 29.630 0.00 0.00 34.11 3.58
3169 3786 8.049117 AGGTTATACATTGTTGTCATGTCATCT 58.951 33.333 0.00 0.00 37.28 2.90
3176 3793 4.986622 TGTTGTCATGTCATCTAGAGTCG 58.013 43.478 0.00 0.00 0.00 4.18
3177 3794 3.699779 TGTCATGTCATCTAGAGTCGC 57.300 47.619 0.00 0.00 0.00 5.19
3186 3803 3.254411 TCATCTAGAGTCGCTATTGGCAG 59.746 47.826 0.00 0.00 41.91 4.85
3187 3804 2.656002 TCTAGAGTCGCTATTGGCAGT 58.344 47.619 0.00 0.00 41.91 4.40
3193 3810 0.175760 TCGCTATTGGCAGTCACTCC 59.824 55.000 0.00 0.00 41.91 3.85
3194 3811 0.176680 CGCTATTGGCAGTCACTCCT 59.823 55.000 0.00 0.00 41.91 3.69
3195 3812 1.409064 CGCTATTGGCAGTCACTCCTA 59.591 52.381 0.00 0.00 41.91 2.94
3196 3813 2.799917 CGCTATTGGCAGTCACTCCTAC 60.800 54.545 0.00 0.00 41.91 3.18
3203 3820 4.868268 TGGCAGTCACTCCTACTACTATT 58.132 43.478 0.00 0.00 0.00 1.73
3239 3856 7.718399 AGATTGGATATTAGGATGGCCATAT 57.282 36.000 20.84 13.35 36.29 1.78
3248 3865 6.573664 TTAGGATGGCCATATTTTCAATCG 57.426 37.500 20.84 0.00 36.29 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
340 341 5.756833 TGCTCTCAATGACAAGTGCATATAG 59.243 40.000 0.00 0.00 37.16 1.31
353 354 7.177921 AGGAAAAGATCAAATTGCTCTCAATGA 59.822 33.333 0.00 0.00 41.77 2.57
431 432 0.035317 ACAGCTCGCACCTTGAATCA 59.965 50.000 0.00 0.00 0.00 2.57
450 451 0.984961 CTCATCCTCTCCTGCCCCAA 60.985 60.000 0.00 0.00 0.00 4.12
488 501 5.773176 AGACCCAAAACCCAACTAAATACTG 59.227 40.000 0.00 0.00 0.00 2.74
627 684 6.000219 ACTTAGATGTTGAATGTGCTTCAGT 59.000 36.000 0.00 0.00 44.48 3.41
629 686 6.882610 AACTTAGATGTTGAATGTGCTTCA 57.117 33.333 0.00 0.00 42.15 3.02
669 726 7.565680 TGACTCCTTTACAGAGAACTTCTTTT 58.434 34.615 0.00 0.00 32.41 2.27
791 1356 6.942576 GCCTTATATCCATACTTCACACCAAT 59.057 38.462 0.00 0.00 0.00 3.16
805 1370 6.306987 GGAAAATCTCCAAGCCTTATATCCA 58.693 40.000 0.00 0.00 44.67 3.41
972 1537 7.044181 TCTAGCAACAGATTCAGTAAGGAATG 58.956 38.462 0.00 0.00 37.61 2.67
1195 1762 3.797039 TGGAAATCTCGCCATAACTCTG 58.203 45.455 0.00 0.00 0.00 3.35
1197 1764 4.442706 TCTTGGAAATCTCGCCATAACTC 58.557 43.478 0.00 0.00 33.46 3.01
1519 2086 2.126228 TTAAGTGCGGACTCGGCG 60.126 61.111 10.99 0.00 36.79 6.46
2078 2651 1.202580 GCTGTGTGAGTCTCCACTTGT 60.203 52.381 17.20 0.00 37.89 3.16
2172 2745 2.079925 GAGTGTTGACTGGATCTTGCC 58.920 52.381 0.00 0.00 30.16 4.52
2306 2879 2.810274 CGCATGGATAGAATGAACAGGG 59.190 50.000 0.00 0.00 0.00 4.45
2376 2949 2.192263 GGAAGAACCTGATGGACCTCT 58.808 52.381 0.00 0.00 37.04 3.69
2426 2999 2.661566 CGTCCTCTGTTGCTGCGTG 61.662 63.158 0.00 0.00 0.00 5.34
2427 3000 2.356313 CGTCCTCTGTTGCTGCGT 60.356 61.111 0.00 0.00 0.00 5.24
2428 3001 3.782244 GCGTCCTCTGTTGCTGCG 61.782 66.667 0.00 0.00 0.00 5.18
2429 3002 2.666190 TGCGTCCTCTGTTGCTGC 60.666 61.111 0.00 0.00 0.00 5.25
2509 3082 1.610086 CTGCTTTGGCCCCCAATCA 60.610 57.895 0.00 0.00 43.55 2.57
2631 3204 0.301687 CGACACATGTAGCAATCGCC 59.698 55.000 0.00 0.00 39.83 5.54
2650 3223 2.096417 AGTTCGTCGCAGCAATACAAAC 60.096 45.455 0.00 0.00 0.00 2.93
2658 3231 1.005037 AATCCAGTTCGTCGCAGCA 60.005 52.632 0.00 0.00 0.00 4.41
2684 3257 0.042708 CAAGCTCGCGGATCAAATCG 60.043 55.000 6.13 0.00 0.00 3.34
2773 3378 8.602424 AGCAGCCTACAATATTACATACCAATA 58.398 33.333 0.00 0.00 0.00 1.90
2814 3419 6.575162 ATTCTTTCAACAATCCAGGTACAC 57.425 37.500 0.00 0.00 0.00 2.90
2845 3452 2.871022 CAGTGTCCAGAGAAGCATATGC 59.129 50.000 20.36 20.36 42.49 3.14
2849 3456 4.833478 ATTACAGTGTCCAGAGAAGCAT 57.167 40.909 0.00 0.00 0.00 3.79
2857 3464 4.003648 GGGAGTCAAATTACAGTGTCCAG 58.996 47.826 0.00 0.00 0.00 3.86
2865 3472 5.724370 TGAGGATGTAGGGAGTCAAATTACA 59.276 40.000 0.00 0.00 0.00 2.41
2866 3473 6.127026 ACTGAGGATGTAGGGAGTCAAATTAC 60.127 42.308 0.00 0.00 0.00 1.89
2934 3545 0.808755 CACCCCGCATAGTCCAAAAC 59.191 55.000 0.00 0.00 0.00 2.43
2943 3554 1.537889 CCCTATCCCACCCCGCATA 60.538 63.158 0.00 0.00 0.00 3.14
2950 3561 1.077716 GCACACACCCTATCCCACC 60.078 63.158 0.00 0.00 0.00 4.61
2952 3563 1.561769 CCAGCACACACCCTATCCCA 61.562 60.000 0.00 0.00 0.00 4.37
2960 3571 1.160137 GATCAACTCCAGCACACACC 58.840 55.000 0.00 0.00 0.00 4.16
2964 3575 3.195610 ACGATAAGATCAACTCCAGCACA 59.804 43.478 0.00 0.00 0.00 4.57
2965 3576 3.553511 CACGATAAGATCAACTCCAGCAC 59.446 47.826 0.00 0.00 0.00 4.40
2967 3578 3.553511 CACACGATAAGATCAACTCCAGC 59.446 47.826 0.00 0.00 0.00 4.85
2968 3579 4.748892 ACACACGATAAGATCAACTCCAG 58.251 43.478 0.00 0.00 0.00 3.86
2977 3592 6.810911 AGCAGAGATTTACACACGATAAGAT 58.189 36.000 0.00 0.00 0.00 2.40
3063 3680 9.449719 AGGCTTAAAATACGCAAATAGCTATAT 57.550 29.630 6.68 0.00 42.61 0.86
3064 3681 8.717821 CAGGCTTAAAATACGCAAATAGCTATA 58.282 33.333 6.68 0.00 42.61 1.31
3068 3685 5.681543 GTCAGGCTTAAAATACGCAAATAGC 59.318 40.000 0.00 0.00 40.87 2.97
3069 3686 6.781138 TGTCAGGCTTAAAATACGCAAATAG 58.219 36.000 0.00 0.00 0.00 1.73
3072 3689 5.637006 ATGTCAGGCTTAAAATACGCAAA 57.363 34.783 0.00 0.00 0.00 3.68
3082 3699 3.018856 CCATGCTCAATGTCAGGCTTAA 58.981 45.455 0.00 0.00 34.11 1.85
3083 3700 2.025981 ACCATGCTCAATGTCAGGCTTA 60.026 45.455 0.00 0.00 34.11 3.09
3084 3701 1.272313 ACCATGCTCAATGTCAGGCTT 60.272 47.619 0.00 0.00 34.11 4.35
3086 3703 1.135199 CAACCATGCTCAATGTCAGGC 60.135 52.381 0.00 0.00 34.11 4.85
3124 3741 3.021695 CCTGACATTGAGCATGGTTGAT 58.978 45.455 0.00 0.00 37.17 2.57
3125 3742 2.224843 ACCTGACATTGAGCATGGTTGA 60.225 45.455 0.00 0.00 37.17 3.18
3126 3743 2.165167 ACCTGACATTGAGCATGGTTG 58.835 47.619 0.00 0.00 37.17 3.77
3130 3747 6.872628 ATGTATAACCTGACATTGAGCATG 57.127 37.500 0.00 0.00 39.07 4.06
3137 3754 7.994425 TGACAACAATGTATAACCTGACATT 57.006 32.000 0.00 0.00 45.03 2.71
3138 3755 7.611467 ACATGACAACAATGTATAACCTGACAT 59.389 33.333 0.00 0.00 40.74 3.06
3139 3756 6.939730 ACATGACAACAATGTATAACCTGACA 59.060 34.615 0.00 0.00 40.74 3.58
3140 3757 7.119116 TGACATGACAACAATGTATAACCTGAC 59.881 37.037 0.00 0.00 40.74 3.51
3141 3758 7.164803 TGACATGACAACAATGTATAACCTGA 58.835 34.615 0.00 0.00 40.74 3.86
3142 3759 7.376435 TGACATGACAACAATGTATAACCTG 57.624 36.000 0.00 0.00 40.74 4.00
3143 3760 8.049117 AGATGACATGACAACAATGTATAACCT 58.951 33.333 0.00 0.00 40.74 3.50
3176 3793 2.432510 AGTAGGAGTGACTGCCAATAGC 59.567 50.000 0.00 0.00 44.14 2.97
3177 3794 4.890581 AGTAGTAGGAGTGACTGCCAATAG 59.109 45.833 0.00 0.00 30.54 1.73
3186 3803 6.041069 AGCCAATCAATAGTAGTAGGAGTGAC 59.959 42.308 9.72 1.30 0.00 3.67
3187 3804 6.136857 AGCCAATCAATAGTAGTAGGAGTGA 58.863 40.000 9.72 0.39 0.00 3.41
3195 3812 9.950496 CCAATCTTATAGCCAATCAATAGTAGT 57.050 33.333 0.00 0.00 0.00 2.73
3239 3856 9.893305 GAAGAAAAGGATAAAGACGATTGAAAA 57.107 29.630 0.00 0.00 0.00 2.29
3248 3865 8.992835 AATGCAATGAAGAAAAGGATAAAGAC 57.007 30.769 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.