Multiple sequence alignment - TraesCS7B01G281800

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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 TraesCS7B01G281800 chr7B 100.000 3704 0 0 1 3704 516356661 516352958 0.000000e+00 6841.0
1 TraesCS7B01G281800 chr7B 82.033 2282 296 66 1048 3265 516315907 516313676 0.000000e+00 1838.0
2 TraesCS7B01G281800 chr7D 95.555 3532 119 24 1 3519 486631545 486628039 0.000000e+00 5618.0
3 TraesCS7B01G281800 chr7D 81.927 2263 308 69 1048 3265 486576403 486574197 0.000000e+00 1820.0
4 TraesCS7B01G281800 chr7D 94.595 185 6 2 3519 3702 486627935 486627754 2.180000e-72 283.0
5 TraesCS7B01G281800 chr7D 73.522 812 163 30 1105 1893 486242820 486242038 1.020000e-65 261.0
6 TraesCS7B01G281800 chr7A 92.275 2343 117 21 838 3125 555506716 555504383 0.000000e+00 3265.0
7 TraesCS7B01G281800 chr7A 81.762 2259 294 71 1048 3265 555468454 555466273 0.000000e+00 1781.0
8 TraesCS7B01G281800 chr7A 81.478 2273 300 70 1048 3265 555481151 555478945 0.000000e+00 1753.0
9 TraesCS7B01G281800 chr7A 81.122 2246 297 75 1065 3265 555475727 555473564 0.000000e+00 1681.0
10 TraesCS7B01G281800 chr7A 91.492 764 48 6 1 761 555507965 555507216 0.000000e+00 1035.0
11 TraesCS7B01G281800 chr7A 85.714 182 13 6 2896 3066 555461942 555461763 2.940000e-41 180.0
12 TraesCS7B01G281800 chr7A 83.544 158 12 6 3558 3702 555472364 555472208 6.450000e-28 135.0
13 TraesCS7B01G281800 chr7A 97.778 45 1 0 977 1021 555468498 555468454 1.100000e-10 78.7
14 TraesCS7B01G281800 chr1A 86.076 79 10 1 106 184 276807008 276807085 2.370000e-12 84.2
15 TraesCS7B01G281800 chr1D 91.071 56 4 1 129 184 216139132 216139186 1.430000e-09 75.0


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 TraesCS7B01G281800 chr7B 516352958 516356661 3703 True 6841.00 6841 100.0000 1 3704 1 chr7B.!!$R2 3703
1 TraesCS7B01G281800 chr7B 516313676 516315907 2231 True 1838.00 1838 82.0330 1048 3265 1 chr7B.!!$R1 2217
2 TraesCS7B01G281800 chr7D 486627754 486631545 3791 True 2950.50 5618 95.0750 1 3702 2 chr7D.!!$R3 3701
3 TraesCS7B01G281800 chr7D 486574197 486576403 2206 True 1820.00 1820 81.9270 1048 3265 1 chr7D.!!$R2 2217
4 TraesCS7B01G281800 chr7D 486242038 486242820 782 True 261.00 261 73.5220 1105 1893 1 chr7D.!!$R1 788
5 TraesCS7B01G281800 chr7A 555504383 555507965 3582 True 2150.00 3265 91.8835 1 3125 2 chr7A.!!$R3 3124
6 TraesCS7B01G281800 chr7A 555466273 555481151 14878 True 1085.74 1781 85.1368 977 3702 5 chr7A.!!$R2 2725

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
111 113 0.460459 GCAGTTCGACCCCTCTTAGC 60.460 60.0 0.00 0.00 0.00 3.09 F
1205 1642 0.606673 GAGGATAAAGGCATCCCCGC 60.607 60.0 0.00 0.00 44.93 6.13 F
1827 2306 0.809385 CTCACAAGCTGCAGATTGGG 59.191 55.0 38.97 37.29 45.43 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 2205 0.106719 CTGACCGCCCCACCATTAAT 60.107 55.000 0.00 0.00 0.00 1.40 R
2640 3176 0.326595 TCAAGCGGTAAGGAATGCCA 59.673 50.000 0.00 0.00 36.29 4.92 R
3145 16381 1.198178 GCCAAAGCAATGTGCCATTTG 59.802 47.619 7.58 7.58 46.52 2.32 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
64 65 7.824289 GGAAAGCATAGGATAGCATGTGTATAA 59.176 37.037 0.00 0.00 0.00 0.98
110 112 1.187087 AGCAGTTCGACCCCTCTTAG 58.813 55.000 0.00 0.00 0.00 2.18
111 113 0.460459 GCAGTTCGACCCCTCTTAGC 60.460 60.000 0.00 0.00 0.00 3.09
121 123 1.906574 CCCCTCTTAGCAGTGTGGTTA 59.093 52.381 0.00 0.00 0.00 2.85
156 158 6.428465 TCAAAAGAAACCAAAACAAAACTCCC 59.572 34.615 0.00 0.00 0.00 4.30
165 167 3.553828 AACAAAACTCCCGAGTCTTCA 57.446 42.857 0.00 0.00 41.58 3.02
200 202 5.469479 CCTTTTCTTTTGAAGTGTGTGTGT 58.531 37.500 0.00 0.00 39.88 3.72
202 204 5.446143 TTTCTTTTGAAGTGTGTGTGTGT 57.554 34.783 0.00 0.00 39.88 3.72
203 205 4.418013 TCTTTTGAAGTGTGTGTGTGTG 57.582 40.909 0.00 0.00 0.00 3.82
204 206 3.818210 TCTTTTGAAGTGTGTGTGTGTGT 59.182 39.130 0.00 0.00 0.00 3.72
267 269 5.477984 AGTGAGCAATGACACACCAAAATAT 59.522 36.000 11.85 0.00 39.18 1.28
307 309 6.384224 TGCACTTTCAGCAAGAATTTGATAG 58.616 36.000 0.00 0.00 39.39 2.08
339 341 2.102578 AGTGAGCTTTTGGTGTGCTTT 58.897 42.857 0.00 0.00 37.16 3.51
352 355 5.181748 TGGTGTGCTTTAAAAATGCTTTGT 58.818 33.333 0.38 0.00 0.00 2.83
503 507 3.185299 ATGGTGGGCCGAAACGTCA 62.185 57.895 0.00 0.00 37.67 4.35
520 524 3.202151 ACGTCACCCAAATAGGATCCAAT 59.798 43.478 15.82 0.00 41.22 3.16
525 529 6.015940 GTCACCCAAATAGGATCCAATCATTC 60.016 42.308 15.82 0.00 41.22 2.67
534 538 1.462616 TCCAATCATTCCACCAAGCG 58.537 50.000 0.00 0.00 0.00 4.68
545 549 2.325082 ACCAAGCGCACCGAATGAC 61.325 57.895 11.47 0.00 0.00 3.06
599 603 3.321497 AGAGATCTTGTTGAGCAACGTC 58.679 45.455 8.63 4.84 43.94 4.34
642 647 9.814899 TTGATTCTTGTGTGTTTATCATGTTTT 57.185 25.926 0.00 0.00 0.00 2.43
679 684 4.394729 ACTTCATTTGGACCGTATGTTGT 58.605 39.130 5.76 4.12 0.00 3.32
789 794 5.360649 AATTTTAGAGGGGTGAGCTAGAC 57.639 43.478 0.00 0.00 0.00 2.59
836 1264 4.270008 ACGAGGAATTAAAAGATGGGTGG 58.730 43.478 0.00 0.00 0.00 4.61
841 1269 7.255139 CGAGGAATTAAAAGATGGGTGGATAAC 60.255 40.741 0.00 0.00 0.00 1.89
864 1292 7.158099 ACTAAATTGGAGCACAAGGAATTAC 57.842 36.000 0.49 0.00 43.48 1.89
865 1293 4.701956 AATTGGAGCACAAGGAATTACG 57.298 40.909 0.49 0.00 43.48 3.18
869 1297 3.007506 TGGAGCACAAGGAATTACGAGAA 59.992 43.478 0.00 0.00 0.00 2.87
873 1301 6.183309 AGCACAAGGAATTACGAGAATTTC 57.817 37.500 0.00 0.00 0.00 2.17
1205 1642 0.606673 GAGGATAAAGGCATCCCCGC 60.607 60.000 0.00 0.00 44.93 6.13
1738 2205 1.276421 GGCTCTACTTGTTCCAGCAGA 59.724 52.381 0.00 0.00 0.00 4.26
1827 2306 0.809385 CTCACAAGCTGCAGATTGGG 59.191 55.000 38.97 37.29 45.43 4.12
2055 2572 7.168219 ACTTCATGAGTAATGTTGTGTACCAT 58.832 34.615 0.00 0.00 36.65 3.55
2056 2573 6.983474 TCATGAGTAATGTTGTGTACCATG 57.017 37.500 0.00 0.00 37.56 3.66
2057 2574 5.353956 TCATGAGTAATGTTGTGTACCATGC 59.646 40.000 0.00 0.00 37.56 4.06
2058 2575 4.646572 TGAGTAATGTTGTGTACCATGCA 58.353 39.130 0.00 0.00 0.00 3.96
2142 2659 0.861837 CGAGATATTGGCGTTGGCTC 59.138 55.000 0.00 0.00 39.81 4.70
2161 2678 3.181465 GCTCTGAATTTGGGTATCTCCGA 60.181 47.826 0.00 0.00 37.00 4.55
2269 2786 6.205464 AGCCAGTCGATCATTTTATAATGGTG 59.795 38.462 6.12 0.00 41.23 4.17
2640 3176 3.834231 TGTTACGGGAGTTACCTAAAGCT 59.166 43.478 0.00 0.00 43.33 3.74
2648 3184 3.621558 AGTTACCTAAAGCTGGCATTCC 58.378 45.455 0.00 0.00 0.00 3.01
2780 3317 6.041423 TCATTGACTGTTCTCTGCAAGATA 57.959 37.500 0.00 0.00 45.62 1.98
2887 3428 6.968263 AGTTAGCAGAAGTATATGAGAGCA 57.032 37.500 0.00 0.00 0.00 4.26
3068 16301 0.329261 CTTGGTTGGCCAGGATCAGA 59.671 55.000 5.11 0.00 46.91 3.27
3073 16306 1.002069 TTGGCCAGGATCAGAATGGT 58.998 50.000 5.11 0.00 36.43 3.55
3081 16314 2.579860 AGGATCAGAATGGTGAAGGCTT 59.420 45.455 0.00 0.00 36.16 4.35
3107 16342 1.702401 TGTTCTGCTTGTGTCCCCATA 59.298 47.619 0.00 0.00 0.00 2.74
3145 16381 8.502387 TGTTTGTTTATTTGCAAGAAATATGGC 58.498 29.630 10.66 0.00 0.00 4.40
3187 16423 5.183904 GGCTGGTAAAAGCATATGGGATAAG 59.816 44.000 4.56 0.00 45.43 1.73
3207 16445 7.600752 GGATAAGTAGCTTATGACAGTGGATTC 59.399 40.741 6.17 0.00 36.87 2.52
3210 16448 6.578023 AGTAGCTTATGACAGTGGATTCTTC 58.422 40.000 0.00 0.00 0.00 2.87
3317 16557 2.627515 ACTCTATGTCGGTACCGCTA 57.372 50.000 29.64 19.91 39.59 4.26
3349 16589 2.568623 ATTGGTCAGTTGGAGTGGAC 57.431 50.000 0.00 0.00 0.00 4.02
3361 16601 1.550976 GGAGTGGACGAAATCTGGTCT 59.449 52.381 0.00 0.00 33.70 3.85
3457 16697 4.932799 CAGCTTGATTTTGATTTGGCATGA 59.067 37.500 0.00 0.00 0.00 3.07
3474 16715 3.126858 GCATGATCTGTCACGCCTTTTTA 59.873 43.478 0.00 0.00 37.58 1.52
3488 16729 6.631636 CACGCCTTTTTAGTTACTTCAGTTTC 59.368 38.462 0.00 0.00 0.00 2.78
3491 16732 7.466860 CGCCTTTTTAGTTACTTCAGTTTCTGT 60.467 37.037 0.00 0.00 32.61 3.41
3504 16745 7.285858 ACTTCAGTTTCTGTAACAGTAGACTCT 59.714 37.037 0.04 0.00 39.30 3.24
3506 16747 8.687292 TCAGTTTCTGTAACAGTAGACTCTAA 57.313 34.615 0.04 0.00 39.30 2.10
3508 16749 9.182933 CAGTTTCTGTAACAGTAGACTCTAAAC 57.817 37.037 0.04 0.00 39.30 2.01
3509 16750 8.910944 AGTTTCTGTAACAGTAGACTCTAAACA 58.089 33.333 0.04 0.00 39.30 2.83
3511 16752 8.461249 TTCTGTAACAGTAGACTCTAAACAGT 57.539 34.615 0.00 0.00 34.77 3.55
3514 16755 7.423199 TGTAACAGTAGACTCTAAACAGTGTG 58.577 38.462 0.00 0.00 0.00 3.82
3516 16757 7.578310 AACAGTAGACTCTAAACAGTGTGTA 57.422 36.000 0.00 0.00 0.00 2.90
3599 16942 1.180029 ATGCACAATCTGGGAACTGC 58.820 50.000 0.00 0.00 0.00 4.40
3680 17024 0.859232 TTCGTTCTGTGAGAAAGCGC 59.141 50.000 0.00 0.00 35.75 5.92
3690 17034 1.134877 TGAGAAAGCGCCTGATCTCAG 60.135 52.381 21.05 0.00 42.36 3.35
3702 17046 3.823304 CCTGATCTCAGTATCGATGACCA 59.177 47.826 8.54 0.00 42.27 4.02
3703 17047 4.462132 CCTGATCTCAGTATCGATGACCAT 59.538 45.833 8.54 0.00 42.27 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 5.760484 AAAAGTATGGGGTCATGCAAAAT 57.240 34.783 0.00 0.00 38.26 1.82
95 97 0.896226 ACTGCTAAGAGGGGTCGAAC 59.104 55.000 0.00 0.00 0.00 3.95
96 98 0.895530 CACTGCTAAGAGGGGTCGAA 59.104 55.000 0.00 0.00 0.00 3.71
110 112 2.165845 AGTCGTAGGATAACCACACTGC 59.834 50.000 0.00 0.00 38.94 4.40
111 113 3.442625 TGAGTCGTAGGATAACCACACTG 59.557 47.826 0.00 0.00 38.94 3.66
121 123 5.223449 TGGTTTCTTTTGAGTCGTAGGAT 57.777 39.130 0.00 0.00 0.00 3.24
156 158 3.126831 GGCATGGTTATCTGAAGACTCG 58.873 50.000 0.00 0.00 0.00 4.18
165 167 5.779771 TCAAAAGAAAAGGGCATGGTTATCT 59.220 36.000 0.00 0.00 0.00 1.98
307 309 3.618690 AAGCTCACTACACATCCTTCC 57.381 47.619 0.00 0.00 0.00 3.46
339 341 9.585099 GTCATGGATAATCACAAAGCATTTTTA 57.415 29.630 0.00 0.00 35.03 1.52
352 355 4.909695 ACTCATCAGGGTCATGGATAATCA 59.090 41.667 0.00 0.00 0.00 2.57
503 507 5.103129 TGGAATGATTGGATCCTATTTGGGT 60.103 40.000 14.23 0.00 36.20 4.51
520 524 1.971167 GGTGCGCTTGGTGGAATGA 60.971 57.895 9.73 0.00 0.00 2.57
525 529 3.055719 ATTCGGTGCGCTTGGTGG 61.056 61.111 9.73 0.00 0.00 4.61
534 538 1.359459 GGTTCTCGGTCATTCGGTGC 61.359 60.000 0.00 0.00 0.00 5.01
545 549 1.270305 TGTGAGCTTCTTGGTTCTCGG 60.270 52.381 0.00 0.00 0.00 4.63
654 659 7.279090 CACAACATACGGTCCAAATGAAGTATA 59.721 37.037 7.31 0.00 31.66 1.47
658 663 4.215399 ACACAACATACGGTCCAAATGAAG 59.785 41.667 7.31 2.78 0.00 3.02
679 684 6.827586 AACTTAACCACTGAAACTCAAACA 57.172 33.333 0.00 0.00 0.00 2.83
775 780 0.331954 TCTTCGTCTAGCTCACCCCT 59.668 55.000 0.00 0.00 0.00 4.79
789 794 9.170584 GTTTTTAGGAAATGAAACTCTTCTTCG 57.829 33.333 0.00 0.00 32.33 3.79
836 1264 7.391148 TTCCTTGTGCTCCAATTTAGTTATC 57.609 36.000 0.00 0.00 31.20 1.75
841 1269 6.093495 TCGTAATTCCTTGTGCTCCAATTTAG 59.907 38.462 0.00 0.00 31.20 1.85
881 1309 3.318313 TCTCCTTCAGATCCCATTACCC 58.682 50.000 0.00 0.00 0.00 3.69
906 1334 4.679373 ATGGAGAGATGTCGTGCTAAAT 57.321 40.909 0.00 0.00 0.00 1.40
1156 1593 1.455217 GGTAGGAGCGCCAGAGGTA 60.455 63.158 9.88 0.00 36.29 3.08
1445 1906 1.675801 CAGAAGTCCAGGCTGAGCA 59.324 57.895 17.94 0.00 0.00 4.26
1543 2004 2.183555 CAGGTCCCGGTCGCTTAC 59.816 66.667 0.00 0.00 0.00 2.34
1738 2205 0.106719 CTGACCGCCCCACCATTAAT 60.107 55.000 0.00 0.00 0.00 1.40
1827 2306 0.179108 GTACCCTGATGACGCTGTCC 60.179 60.000 6.30 0.00 0.00 4.02
2055 2572 1.842714 TGGTCCACCAAGACATGCA 59.157 52.632 0.00 0.00 44.35 3.96
2056 2573 4.819783 TGGTCCACCAAGACATGC 57.180 55.556 0.00 0.00 44.35 4.06
2142 2659 3.388024 TCCTCGGAGATACCCAAATTCAG 59.612 47.826 6.58 0.00 33.89 3.02
2161 2678 3.041946 CTGGCCAGTATCTTAACCTCCT 58.958 50.000 25.53 0.00 0.00 3.69
2269 2786 9.209175 AGACTAATTCGGCTAAATATTGATGAC 57.791 33.333 0.00 0.00 0.00 3.06
2473 3009 3.181493 GCATTCTTGGCGATGAACTTGAT 60.181 43.478 0.00 0.00 0.00 2.57
2640 3176 0.326595 TCAAGCGGTAAGGAATGCCA 59.673 50.000 0.00 0.00 36.29 4.92
2648 3184 2.266554 CTGCTCTCTTCAAGCGGTAAG 58.733 52.381 0.00 0.00 42.83 2.34
2780 3317 5.534654 TGCCTACAAGAAACTAAACAGCAAT 59.465 36.000 0.00 0.00 0.00 3.56
2887 3428 7.686438 TGCAGACACATGAAAATAACACTAT 57.314 32.000 0.00 0.00 0.00 2.12
3068 16301 3.219281 ACAACGTAAAGCCTTCACCATT 58.781 40.909 0.00 0.00 0.00 3.16
3073 16306 2.289547 GCAGAACAACGTAAAGCCTTCA 59.710 45.455 0.00 0.00 0.00 3.02
3081 16314 2.610374 GGACACAAGCAGAACAACGTAA 59.390 45.455 0.00 0.00 0.00 3.18
3107 16342 7.804129 GCAAATAAACAAACATGATGCACAAAT 59.196 29.630 0.00 0.00 0.00 2.32
3140 16376 2.312722 GCAATGTGCCATTTGCCATA 57.687 45.000 4.49 0.00 41.82 2.74
3145 16381 1.198178 GCCAAAGCAATGTGCCATTTG 59.802 47.619 7.58 7.58 46.52 2.32
3162 16398 2.243478 TCCCATATGCTTTTACCAGCCA 59.757 45.455 0.00 0.00 39.25 4.75
3187 16423 6.578023 AGAAGAATCCACTGTCATAAGCTAC 58.422 40.000 0.00 0.00 0.00 3.58
3207 16445 8.950210 TGCTACATCTTTATTGGAAAGAAGAAG 58.050 33.333 8.74 5.77 39.43 2.85
3210 16448 8.498054 TCTGCTACATCTTTATTGGAAAGAAG 57.502 34.615 4.01 2.83 39.43 2.85
3288 16528 4.890088 ACCGACATAGAGTAAGCAAACAA 58.110 39.130 0.00 0.00 0.00 2.83
3317 16557 1.899814 TGACCAATAGCTTCAGTCGGT 59.100 47.619 0.00 0.00 0.00 4.69
3417 16657 3.827722 AGCTGTAAGTGGCCTTTTGTAA 58.172 40.909 3.32 0.00 35.30 2.41
3457 16697 5.548406 AGTAACTAAAAAGGCGTGACAGAT 58.452 37.500 0.00 0.00 0.00 2.90
3474 16715 8.910944 TCTACTGTTACAGAAACTGAAGTAACT 58.089 33.333 20.07 0.00 43.96 2.24
3488 16729 7.591795 CACACTGTTTAGAGTCTACTGTTACAG 59.408 40.741 11.21 11.21 37.06 2.74
3491 16732 7.578310 ACACACTGTTTAGAGTCTACTGTTA 57.422 36.000 0.00 0.00 0.00 2.41
3498 16739 9.244292 TCTATTCATACACACTGTTTAGAGTCT 57.756 33.333 0.00 0.00 0.00 3.24
3562 16905 7.880160 TGTGCATATTTAGGCTGAGTAATTT 57.120 32.000 0.00 0.00 33.54 1.82
3599 16942 6.400091 GGAAGAGCGTATTATTTACAGATGCG 60.400 42.308 0.00 0.00 33.08 4.73


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

AutoCloner maintained by Alex Coulton.