Multiple sequence alignment - TraesCS3D01G226300

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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 TraesCS3D01G226300 chr3D 100.000 4029 0 0 1 4029 308060307 308056279 0.000000e+00 7441.0
1 TraesCS3D01G226300 chr3D 88.281 128 15 0 2435 2562 337974607 337974480 1.940000e-33 154.0
2 TraesCS3D01G226300 chr3B 95.005 3764 107 30 6 3740 413416670 413420381 0.000000e+00 5834.0
3 TraesCS3D01G226300 chr3B 92.537 201 10 3 3828 4028 413421122 413421317 2.370000e-72 283.0
4 TraesCS3D01G226300 chr3B 88.372 129 13 2 2435 2562 435959560 435959433 1.940000e-33 154.0
5 TraesCS3D01G226300 chr3B 95.349 43 2 0 100 142 644679777 644679735 7.230000e-08 69.4
6 TraesCS3D01G226300 chr3A 96.119 3427 93 16 304 3713 427335393 427331990 0.000000e+00 5555.0
7 TraesCS3D01G226300 chr3A 92.754 276 13 5 3745 4019 427331807 427331538 3.770000e-105 392.0
8 TraesCS3D01G226300 chr3A 88.889 324 26 7 1 315 427335844 427335522 1.360000e-104 390.0
9 TraesCS3D01G226300 chr3A 89.062 128 14 0 2435 2562 455803790 455803663 4.170000e-35 159.0
10 TraesCS3D01G226300 chr1B 79.385 325 49 17 2436 2754 654716328 654716640 3.150000e-51 213.0
11 TraesCS3D01G226300 chr1B 90.741 54 3 2 97 149 18211165 18211217 2.010000e-08 71.3
12 TraesCS3D01G226300 chr1A 88.148 135 12 4 2629 2761 565294204 565294336 1.500000e-34 158.0
13 TraesCS3D01G226300 chr1A 85.714 126 18 0 2436 2561 565293976 565294101 2.530000e-27 134.0
14 TraesCS3D01G226300 chr1D 84.127 126 20 0 2436 2561 471001676 471001801 5.470000e-24 122.0
15 TraesCS3D01G226300 chr1D 86.916 107 13 1 2623 2729 481365824 481365719 7.070000e-23 119.0
16 TraesCS3D01G226300 chr7D 100.000 43 0 0 100 142 7080163 7080205 3.340000e-11 80.5
17 TraesCS3D01G226300 chr7D 87.931 58 5 2 86 142 163564176 163564232 2.600000e-07 67.6
18 TraesCS3D01G226300 chr4B 95.349 43 2 0 100 142 139759822 139759780 7.230000e-08 69.4
19 TraesCS3D01G226300 chr6A 89.796 49 5 0 94 142 466097976 466098024 3.360000e-06 63.9
20 TraesCS3D01G226300 chr5A 89.583 48 4 1 92 138 374621114 374621161 4.350000e-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 TraesCS3D01G226300 chr3D 308056279 308060307 4028 True 7441.000000 7441 100.000000 1 4029 1 chr3D.!!$R1 4028
1 TraesCS3D01G226300 chr3B 413416670 413421317 4647 False 3058.500000 5834 93.771000 6 4028 2 chr3B.!!$F1 4022
2 TraesCS3D01G226300 chr3A 427331538 427335844 4306 True 2112.333333 5555 92.587333 1 4019 3 chr3A.!!$R2 4018

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
993 1149 0.756070 ACTTAGCTACCTCCCGCTCC 60.756 60.000 0.0 0.0 37.68 4.70 F
1086 1242 1.445582 CCAACTCACCCGCTACGAC 60.446 63.158 0.0 0.0 0.00 4.34 F
2737 2935 2.033194 GTACGAAGGGCAGCACACC 61.033 63.158 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2565 2759 1.201414 TGAGCTTCATGCATGCAACTG 59.799 47.619 26.68 19.56 45.94 3.16 R
2966 3164 2.933495 AGCGCGTAGTCAGTGAAATA 57.067 45.000 8.43 0.00 0.00 1.40 R
3760 4242 0.933796 GCAGCCTCGTGAGCTTATTC 59.066 55.000 0.00 0.00 38.95 1.75 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
47 52 7.555582 CGTATGTACGTACTATACTTTCGTCA 58.444 38.462 27.00 9.92 44.13 4.35
60 66 4.741342 ACTTTCGTCAGGGTTATTAGTCG 58.259 43.478 0.00 0.00 0.00 4.18
74 80 2.017138 TAGTCGCATCGCATTTTGGA 57.983 45.000 0.00 0.00 0.00 3.53
81 87 3.367327 CGCATCGCATTTTGGATCAAAAA 59.633 39.130 10.43 10.43 44.68 1.94
119 125 9.804758 TTTAATTTTGAACTAAAACCACGACAT 57.195 25.926 0.00 0.00 40.80 3.06
155 161 8.888836 TCGGAGGGAGTATATTTATATGTGAA 57.111 34.615 0.00 0.00 0.00 3.18
290 301 5.970317 AAAAACTAATAAACCCGGACAGG 57.030 39.130 0.73 0.00 40.63 4.00
355 506 4.422840 TGCATGCGACCATTAATTCAAAG 58.577 39.130 14.09 0.00 0.00 2.77
416 568 3.615834 GCGTTGTACTACTGGGTAAAGCT 60.616 47.826 5.91 0.00 0.00 3.74
426 578 3.321682 ACTGGGTAAAGCTACACGTTGTA 59.678 43.478 0.00 0.00 33.75 2.41
450 602 3.245990 GTCAAAATTCTTGGCTGCAACAC 59.754 43.478 0.50 0.00 0.00 3.32
618 770 3.815401 CAGTAACCTGCAGTAATATGCCC 59.185 47.826 13.81 0.00 45.91 5.36
619 771 2.364972 AACCTGCAGTAATATGCCCC 57.635 50.000 13.81 0.00 45.91 5.80
676 828 4.304110 GACAGTTTGTTCTGACGGATACA 58.696 43.478 0.65 0.00 38.63 2.29
683 835 1.471119 TCTGACGGATACACCCAGAC 58.529 55.000 0.00 0.00 33.94 3.51
777 931 8.129211 TGATTCTACACATCACACTAGAATACG 58.871 37.037 0.00 0.00 36.50 3.06
778 932 6.997239 TCTACACATCACACTAGAATACGT 57.003 37.500 0.00 0.00 0.00 3.57
779 933 8.496707 TTCTACACATCACACTAGAATACGTA 57.503 34.615 0.00 0.00 0.00 3.57
780 934 7.913423 TCTACACATCACACTAGAATACGTAC 58.087 38.462 0.00 0.00 0.00 3.67
781 935 5.566623 ACACATCACACTAGAATACGTACG 58.433 41.667 15.01 15.01 0.00 3.67
782 936 5.122869 ACACATCACACTAGAATACGTACGT 59.877 40.000 25.98 25.98 0.00 3.57
783 937 6.313658 ACACATCACACTAGAATACGTACGTA 59.686 38.462 28.62 28.62 34.87 3.57
989 1145 1.183549 ACACACTTAGCTACCTCCCG 58.816 55.000 0.00 0.00 0.00 5.14
993 1149 0.756070 ACTTAGCTACCTCCCGCTCC 60.756 60.000 0.00 0.00 37.68 4.70
997 1153 2.907917 CTACCTCCCGCTCCCTCG 60.908 72.222 0.00 0.00 0.00 4.63
1086 1242 1.445582 CCAACTCACCCGCTACGAC 60.446 63.158 0.00 0.00 0.00 4.34
1404 1563 3.163503 GGGGACGGTGAGGGAAAA 58.836 61.111 0.00 0.00 0.00 2.29
1594 1753 3.809832 AGCTTATGCGATGTGTTCATACC 59.190 43.478 0.00 0.00 45.42 2.73
1736 1896 9.832445 TTCATTAGGGTTCTTATAGTTCATCAC 57.168 33.333 0.00 0.00 0.00 3.06
2178 2352 9.571816 ACTACACTCCCTATCTGTTATACTTAC 57.428 37.037 0.00 0.00 0.00 2.34
2179 2353 7.507733 ACACTCCCTATCTGTTATACTTACG 57.492 40.000 0.00 0.00 0.00 3.18
2201 2375 7.517614 ACGATAGATCTACAACACTGATCAT 57.482 36.000 4.10 0.00 39.07 2.45
2256 2430 8.818057 GCACCGTTCCATGAAATATATATCTAC 58.182 37.037 0.00 0.00 0.00 2.59
2737 2935 2.033194 GTACGAAGGGCAGCACACC 61.033 63.158 0.00 0.00 0.00 4.16
2966 3164 1.676384 GGAACTCTCCAGCAGCACT 59.324 57.895 0.00 0.00 41.96 4.40
3167 3365 0.250640 GAGCCTGGTCTATGCATGGG 60.251 60.000 10.16 2.09 0.00 4.00
3350 3548 0.522180 AGCTCGTACTGTGGACTTCG 59.478 55.000 0.00 0.00 0.00 3.79
3439 3637 7.538575 GTTGCTGTGAGGAATTATTTACACAT 58.461 34.615 0.00 0.00 37.56 3.21
3633 3831 2.398588 TCTTGTGGGAGTAGGCATAGG 58.601 52.381 0.00 0.00 0.00 2.57
3646 3844 0.104855 GCATAGGATGTGTCGCCTCA 59.895 55.000 0.00 0.00 35.73 3.86
3648 3846 2.808202 GCATAGGATGTGTCGCCTCATT 60.808 50.000 0.00 0.00 35.73 2.57
3659 3857 1.739466 TCGCCTCATTGTGATTTGCTC 59.261 47.619 0.00 0.00 0.00 4.26
3660 3858 1.530441 CGCCTCATTGTGATTTGCTCG 60.530 52.381 0.00 0.00 0.00 5.03
3661 3859 1.470098 GCCTCATTGTGATTTGCTCGT 59.530 47.619 0.00 0.00 0.00 4.18
3662 3860 2.095059 GCCTCATTGTGATTTGCTCGTT 60.095 45.455 0.00 0.00 0.00 3.85
3694 3892 9.886132 GGTAGAAGGAATTTATAACTGAGACAA 57.114 33.333 0.00 0.00 0.00 3.18
3729 4086 7.727634 TGATTCATAGATGTGTCCTATCTCAGT 59.272 37.037 0.00 0.00 36.38 3.41
3741 4223 7.442062 GTGTCCTATCTCAGTTCTACCTACTAC 59.558 44.444 0.00 0.00 0.00 2.73
3742 4224 7.126879 TGTCCTATCTCAGTTCTACCTACTACA 59.873 40.741 0.00 0.00 0.00 2.74
3743 4225 7.658575 GTCCTATCTCAGTTCTACCTACTACAG 59.341 44.444 0.00 0.00 0.00 2.74
3744 4226 7.347748 TCCTATCTCAGTTCTACCTACTACAGT 59.652 40.741 0.00 0.00 0.00 3.55
3745 4227 8.649591 CCTATCTCAGTTCTACCTACTACAGTA 58.350 40.741 0.00 0.00 0.00 2.74
3746 4228 9.480053 CTATCTCAGTTCTACCTACTACAGTAC 57.520 40.741 0.00 0.00 0.00 2.73
3747 4229 7.493499 TCTCAGTTCTACCTACTACAGTACT 57.507 40.000 0.00 0.00 0.00 2.73
3748 4230 8.601047 TCTCAGTTCTACCTACTACAGTACTA 57.399 38.462 0.00 0.00 0.00 1.82
3790 4272 1.712977 CGAGGCTGCTGCTTTGATCC 61.713 60.000 15.64 0.00 39.59 3.36
3822 4304 9.959721 ATATATTTGTGTAGTGTTTCACTTCCT 57.040 29.630 7.70 0.00 42.59 3.36
3824 4306 9.787435 ATATTTGTGTAGTGTTTCACTTCCTTA 57.213 29.630 7.70 0.00 42.59 2.69
3882 4901 1.134280 AGCAGATGCCTCACGCTATTT 60.134 47.619 0.14 0.00 43.38 1.40
3883 4902 2.103094 AGCAGATGCCTCACGCTATTTA 59.897 45.455 0.14 0.00 43.38 1.40
3917 4936 3.547746 AGACGAACTGAGATCTAGGGTC 58.452 50.000 0.00 0.00 0.00 4.46
3918 4937 3.201266 AGACGAACTGAGATCTAGGGTCT 59.799 47.826 0.00 6.22 0.00 3.85
3919 4938 3.547746 ACGAACTGAGATCTAGGGTCTC 58.452 50.000 15.19 15.19 41.91 3.36
3960 4979 2.802247 TCTGTCGCAGTTTCAGATGTTG 59.198 45.455 6.72 0.00 34.00 3.33
4019 5038 9.444600 CTAGTCAATTTTAGTTAGTTGCCCTTA 57.555 33.333 0.00 0.00 0.00 2.69
4020 5039 8.879427 AGTCAATTTTAGTTAGTTGCCCTTAT 57.121 30.769 0.00 0.00 0.00 1.73
4022 5041 7.973944 GTCAATTTTAGTTAGTTGCCCTTATGG 59.026 37.037 0.00 0.00 37.09 2.74
4023 5042 7.672239 TCAATTTTAGTTAGTTGCCCTTATGGT 59.328 33.333 0.00 0.00 36.04 3.55
4024 5043 7.640597 ATTTTAGTTAGTTGCCCTTATGGTC 57.359 36.000 0.00 0.00 36.04 4.02
4025 5044 6.382919 TTTAGTTAGTTGCCCTTATGGTCT 57.617 37.500 0.00 0.00 36.04 3.85
4027 5046 3.200165 AGTTAGTTGCCCTTATGGTCTCC 59.800 47.826 0.00 0.00 36.04 3.71
4028 5047 1.972588 AGTTGCCCTTATGGTCTCCT 58.027 50.000 0.00 0.00 36.04 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 52 1.411246 TGCGATGCGACTAATAACCCT 59.589 47.619 0.00 0.00 0.00 4.34
60 66 4.925061 TTTTTGATCCAAAATGCGATGC 57.075 36.364 0.73 0.00 41.89 3.91
290 301 6.702282 GGAGTTGGAGCTTATGAATGTACTAC 59.298 42.308 0.00 0.00 0.00 2.73
416 568 7.356540 CCAAGAATTTTGACATACAACGTGTA 58.643 34.615 0.00 0.00 38.29 2.90
426 578 4.060205 GTTGCAGCCAAGAATTTTGACAT 58.940 39.130 0.00 0.00 0.00 3.06
450 602 1.134037 AGTCCTCTACGGTCTAGCTGG 60.134 57.143 0.00 0.00 28.84 4.85
481 633 0.112412 TTTTGGGAGGAAGGGCAGAC 59.888 55.000 0.00 0.00 0.00 3.51
627 779 6.363357 GCATATAAAATGAACGGCAGATTTCC 59.637 38.462 0.00 0.00 0.00 3.13
637 789 5.403897 ACTGTCGGCATATAAAATGAACG 57.596 39.130 0.00 0.00 0.00 3.95
676 828 2.752903 GTTTGCATTTATCCGTCTGGGT 59.247 45.455 0.00 0.00 37.00 4.51
683 835 8.798153 GTTTAAGATTCTGTTTGCATTTATCCG 58.202 33.333 0.00 0.00 0.00 4.18
726 878 8.251026 CAGTCAATTCCTAATGTGTCTACTGTA 58.749 37.037 0.00 0.00 0.00 2.74
727 879 7.039011 TCAGTCAATTCCTAATGTGTCTACTGT 60.039 37.037 0.00 0.00 33.11 3.55
728 880 7.323420 TCAGTCAATTCCTAATGTGTCTACTG 58.677 38.462 0.00 0.00 0.00 2.74
729 881 7.482169 TCAGTCAATTCCTAATGTGTCTACT 57.518 36.000 0.00 0.00 0.00 2.57
777 931 6.250527 GCGATCTAGCTAGTACTACTACGTAC 59.749 46.154 20.10 0.00 39.97 3.67
778 932 6.318628 GCGATCTAGCTAGTACTACTACGTA 58.681 44.000 20.10 0.00 0.00 3.57
779 933 5.160641 GCGATCTAGCTAGTACTACTACGT 58.839 45.833 20.10 0.00 0.00 3.57
780 934 4.562394 GGCGATCTAGCTAGTACTACTACG 59.438 50.000 20.10 14.39 37.29 3.51
781 935 5.723295 AGGCGATCTAGCTAGTACTACTAC 58.277 45.833 20.10 5.25 37.29 2.73
782 936 5.999205 AGGCGATCTAGCTAGTACTACTA 57.001 43.478 20.10 5.46 37.29 1.82
783 937 4.895668 AGGCGATCTAGCTAGTACTACT 57.104 45.455 20.10 11.42 37.29 2.57
989 1145 0.179097 GGAAGACATGACGAGGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
993 1149 0.458543 CACCGGAAGACATGACGAGG 60.459 60.000 9.46 0.00 0.00 4.63
997 1153 0.673644 CCACCACCGGAAGACATGAC 60.674 60.000 9.46 0.00 0.00 3.06
1062 1218 4.308458 CGGGTGAGTTGGCCGTGA 62.308 66.667 0.00 0.00 0.00 4.35
1092 1248 3.826754 CTGAGCTCGTAGCCGCCA 61.827 66.667 9.64 0.00 43.77 5.69
1404 1563 1.448540 CTTGTTGCTCCGGCGAGAT 60.449 57.895 9.30 0.00 42.25 2.75
1594 1753 6.623986 GCAATAGTAGGACCAGATCTATCACG 60.624 46.154 0.00 0.00 0.00 4.35
1645 1805 1.976898 CACAAGCACAATGGGGCAT 59.023 52.632 0.00 0.00 0.00 4.40
1736 1896 2.612221 GGGGCTAACCGGATCTAATTCG 60.612 54.545 9.46 0.00 41.60 3.34
1958 2119 7.724490 AAAGGGGGAGAGATCTTTATTTTTG 57.276 36.000 0.00 0.00 0.00 2.44
2176 2350 8.622948 ATGATCAGTGTTGTAGATCTATCGTA 57.377 34.615 5.57 0.00 39.07 3.43
2177 2351 6.944234 TGATCAGTGTTGTAGATCTATCGT 57.056 37.500 5.57 0.00 39.07 3.73
2178 2352 8.296000 AGAATGATCAGTGTTGTAGATCTATCG 58.704 37.037 5.57 0.00 39.07 2.92
2179 2353 9.624697 GAGAATGATCAGTGTTGTAGATCTATC 57.375 37.037 5.57 0.85 39.07 2.08
2201 2375 6.071896 CCATGTCTATATAGTTCTGCCGAGAA 60.072 42.308 9.58 0.00 35.75 2.87
2256 2430 7.531198 GCACTATATATAGCTAACTATGTCGCG 59.469 40.741 18.00 0.00 39.51 5.87
2565 2759 1.201414 TGAGCTTCATGCATGCAACTG 59.799 47.619 26.68 19.56 45.94 3.16
2966 3164 2.933495 AGCGCGTAGTCAGTGAAATA 57.067 45.000 8.43 0.00 0.00 1.40
3152 3350 1.598962 CGCCCCATGCATAGACCAG 60.599 63.158 0.00 0.00 41.33 4.00
3167 3365 3.487120 AATTAGGATAACAGGACCGCC 57.513 47.619 0.00 0.00 0.00 6.13
3211 3409 3.411446 TGTAGGCACAAGTTCAAGATGG 58.589 45.455 0.00 0.00 0.00 3.51
3350 3548 3.211803 TGCACTCGAGTACATGTACAC 57.788 47.619 32.02 25.93 38.48 2.90
3439 3637 1.817357 CAGAAGTTGAGATGGCAGCA 58.183 50.000 5.19 0.00 0.00 4.41
3633 3831 1.725641 TCACAATGAGGCGACACATC 58.274 50.000 0.29 0.00 41.00 3.06
3646 3844 4.507388 CCAAACAAACGAGCAAATCACAAT 59.493 37.500 0.00 0.00 0.00 2.71
3648 3846 3.119316 ACCAAACAAACGAGCAAATCACA 60.119 39.130 0.00 0.00 0.00 3.58
3713 3911 5.772004 AGGTAGAACTGAGATAGGACACAT 58.228 41.667 0.00 0.00 0.00 3.21
3745 4227 9.757227 GTGAGCTTATTCAGTGAGATAAATAGT 57.243 33.333 0.00 0.00 0.00 2.12
3746 4228 8.910666 CGTGAGCTTATTCAGTGAGATAAATAG 58.089 37.037 0.00 0.00 0.00 1.73
3747 4229 8.630037 TCGTGAGCTTATTCAGTGAGATAAATA 58.370 33.333 0.00 0.00 0.00 1.40
3748 4230 7.492524 TCGTGAGCTTATTCAGTGAGATAAAT 58.507 34.615 0.00 0.00 0.00 1.40
3758 4240 2.200067 CAGCCTCGTGAGCTTATTCAG 58.800 52.381 0.00 0.00 38.95 3.02
3760 4242 0.933796 GCAGCCTCGTGAGCTTATTC 59.066 55.000 0.00 0.00 38.95 1.75
3765 4247 4.756458 GCAGCAGCCTCGTGAGCT 62.756 66.667 0.00 0.00 42.70 4.09
3913 4932 3.933861 AATTCACCATACCAGAGACCC 57.066 47.619 0.00 0.00 0.00 4.46
3914 4933 7.304497 AGTATAATTCACCATACCAGAGACC 57.696 40.000 0.00 0.00 0.00 3.85
3917 4936 8.424918 ACAGAAGTATAATTCACCATACCAGAG 58.575 37.037 14.80 0.00 0.00 3.35
3918 4937 8.319057 ACAGAAGTATAATTCACCATACCAGA 57.681 34.615 14.80 0.00 0.00 3.86
3919 4938 7.382488 CGACAGAAGTATAATTCACCATACCAG 59.618 40.741 14.80 0.00 0.00 4.00
3960 4979 7.701445 ACAATTCTGCAAGCTTATTATCACTC 58.299 34.615 0.00 0.00 0.00 3.51
3997 5016 7.672239 ACCATAAGGGCAACTAACTAAAATTGA 59.328 33.333 0.00 0.00 42.05 2.57


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

AutoCloner maintained by Alex Coulton.