Multiple sequence alignment - TraesCS6B01G041000

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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 TraesCS6B01G041000 chr6B 100.000 3250 0 0 1 3250 25497264 25494015 0 6002
1 TraesCS6B01G041000 chr6B 94.532 2725 135 10 530 3250 360704304 360707018 0 4194
2 TraesCS6B01G041000 chr1B 95.489 3259 125 12 1 3250 252941854 252938609 0 5184
3 TraesCS6B01G041000 chr4B 95.302 3257 136 16 1 3250 396033449 396036695 0 5151
4 TraesCS6B01G041000 chr4B 94.976 2727 122 10 530 3250 470146881 470144164 0 4263
5 TraesCS6B01G041000 chr3B 94.663 3260 158 14 1 3250 247190355 247187102 0 5042
6 TraesCS6B01G041000 chr3B 92.173 3258 192 27 1 3248 151806758 151809962 0 4545
7 TraesCS6B01G041000 chr3B 92.694 876 50 7 85 953 649058937 649059805 0 1251
8 TraesCS6B01G041000 chr3B 92.123 876 56 8 85 953 572132541 572133410 0 1223
9 TraesCS6B01G041000 chr3B 94.205 742 38 5 1 741 246980585 246981322 0 1127
10 TraesCS6B01G041000 chr2B 94.042 3256 182 12 1 3250 780391884 780388635 0 4927
11 TraesCS6B01G041000 chr2B 95.639 2729 107 11 530 3250 599890733 599888009 0 4370
12 TraesCS6B01G041000 chr2B 93.846 2730 152 12 530 3250 352047728 352045006 0 4096
13 TraesCS6B01G041000 chr7B 94.148 2734 141 12 530 3250 316772144 316774871 0 4145
14 TraesCS6B01G041000 chr1A 92.159 1033 65 10 2 1025 70930585 70931610 0 1445


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 TraesCS6B01G041000 chr6B 25494015 25497264 3249 True 6002 6002 100.000 1 3250 1 chr6B.!!$R1 3249
1 TraesCS6B01G041000 chr6B 360704304 360707018 2714 False 4194 4194 94.532 530 3250 1 chr6B.!!$F1 2720
2 TraesCS6B01G041000 chr1B 252938609 252941854 3245 True 5184 5184 95.489 1 3250 1 chr1B.!!$R1 3249
3 TraesCS6B01G041000 chr4B 396033449 396036695 3246 False 5151 5151 95.302 1 3250 1 chr4B.!!$F1 3249
4 TraesCS6B01G041000 chr4B 470144164 470146881 2717 True 4263 4263 94.976 530 3250 1 chr4B.!!$R1 2720
5 TraesCS6B01G041000 chr3B 247187102 247190355 3253 True 5042 5042 94.663 1 3250 1 chr3B.!!$R1 3249
6 TraesCS6B01G041000 chr3B 151806758 151809962 3204 False 4545 4545 92.173 1 3248 1 chr3B.!!$F1 3247
7 TraesCS6B01G041000 chr3B 649058937 649059805 868 False 1251 1251 92.694 85 953 1 chr3B.!!$F4 868
8 TraesCS6B01G041000 chr3B 572132541 572133410 869 False 1223 1223 92.123 85 953 1 chr3B.!!$F3 868
9 TraesCS6B01G041000 chr3B 246980585 246981322 737 False 1127 1127 94.205 1 741 1 chr3B.!!$F2 740
10 TraesCS6B01G041000 chr2B 780388635 780391884 3249 True 4927 4927 94.042 1 3250 1 chr2B.!!$R3 3249
11 TraesCS6B01G041000 chr2B 599888009 599890733 2724 True 4370 4370 95.639 530 3250 1 chr2B.!!$R2 2720
12 TraesCS6B01G041000 chr2B 352045006 352047728 2722 True 4096 4096 93.846 530 3250 1 chr2B.!!$R1 2720
13 TraesCS6B01G041000 chr7B 316772144 316774871 2727 False 4145 4145 94.148 530 3250 1 chr7B.!!$F1 2720
14 TraesCS6B01G041000 chr1A 70930585 70931610 1025 False 1445 1445 92.159 2 1025 1 chr1A.!!$F1 1023

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
46 47 0.178990 GTGAAAGCTGGTCCCCAACT 60.179 55.000 0.0 0.0 30.39 3.16 F
613 618 0.611896 GTTTGGGCTGGTATGCTGGT 60.612 55.000 0.0 0.0 0.00 4.00 F
1565 1811 1.006102 CGCGTGTTTCCAGAGAGGT 60.006 57.895 0.0 0.0 39.02 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1639 1.210478 TCCTGCTAATGTCAAGCTCCC 59.790 52.381 0.00 0.0 40.73 4.30 R
1854 2107 1.497286 AGCTTCCCAAACACCCAAGTA 59.503 47.619 0.00 0.0 0.00 2.24 R
3022 3292 0.390124 CAACAACAGGGTGCTGCAAT 59.610 50.000 2.77 0.0 0.00 3.56 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
39 40 1.507141 CCCACGTGTGAAAGCTGGTC 61.507 60.000 15.65 0.00 0.00 4.02
46 47 0.178990 GTGAAAGCTGGTCCCCAACT 60.179 55.000 0.00 0.00 30.39 3.16
116 117 1.152567 CAAACTTGGTGGCTCCCCA 60.153 57.895 2.66 0.00 39.32 4.96
120 121 0.770557 ACTTGGTGGCTCCCCAGTTA 60.771 55.000 2.66 0.00 43.18 2.24
123 124 0.770557 TGGTGGCTCCCCAGTTAGTT 60.771 55.000 2.66 0.00 43.18 2.24
139 141 4.529377 AGTTAGTTGGATCCACGAGGTTTA 59.471 41.667 15.91 0.00 35.89 2.01
234 236 2.733956 TCCTGCAAAGGTGAACAAAGT 58.266 42.857 0.00 0.00 0.00 2.66
251 253 4.142093 ACAAAGTTGTGAAGAAGCATGCTT 60.142 37.500 32.41 32.41 40.49 3.91
330 332 6.683974 AGATGAATTTGTAGTGGTATGTGC 57.316 37.500 0.00 0.00 0.00 4.57
392 394 5.871396 TTTAATTGTGTTTGGGCTGGTAA 57.129 34.783 0.00 0.00 0.00 2.85
613 618 0.611896 GTTTGGGCTGGTATGCTGGT 60.612 55.000 0.00 0.00 0.00 4.00
1141 1385 1.508545 CTCGAGAGTCGGCATGTGT 59.491 57.895 6.58 0.00 40.88 3.72
1198 1442 1.893801 AGTGGAGGGTGAAGTCTAACG 59.106 52.381 0.00 0.00 0.00 3.18
1243 1488 8.189119 AGATTTGTACCTGAGGATAGATTCTC 57.811 38.462 4.99 0.00 0.00 2.87
1297 1542 1.205655 AGAAGCTTCGCATCACTAGCA 59.794 47.619 20.43 0.00 36.11 3.49
1312 1557 6.978343 TCACTAGCAATGGTATACAACAAC 57.022 37.500 5.01 0.00 0.00 3.32
1394 1639 5.349817 ACAACGCTCTGATGAAGTTAAGATG 59.650 40.000 0.00 0.00 0.00 2.90
1537 1783 4.037446 TGTTTATGAAGGTTGTGTTGCCTC 59.963 41.667 0.00 0.00 33.24 4.70
1565 1811 1.006102 CGCGTGTTTCCAGAGAGGT 60.006 57.895 0.00 0.00 39.02 3.85
1587 1833 1.197721 GCAATGTTTGAGGGTCTCGTG 59.802 52.381 0.00 0.00 32.35 4.35
1826 2076 4.196971 TCTGATCTGGTTGATGCAGATTG 58.803 43.478 0.00 0.00 35.96 2.67
1907 2160 8.316640 AGTTTTATTTGTTTTGTGTCTTGCAA 57.683 26.923 0.00 0.00 0.00 4.08
1962 2218 3.056821 TGCTGTAGTGGACATGTGTACTC 60.057 47.826 1.15 2.92 37.45 2.59
2075 2331 5.359576 ACTGAATAACTTTGTTCAACTGGCA 59.640 36.000 3.20 0.00 37.74 4.92
2284 2547 0.389948 GATGCCGTCGTCTCAGGTTT 60.390 55.000 0.00 0.00 0.00 3.27
2425 2692 2.320215 CTGTTTCAGCGTTGGAGCA 58.680 52.632 0.00 0.00 40.15 4.26
2519 2786 6.521427 GCTGTATCAATGGTATCCTTCCTGAT 60.521 42.308 0.00 0.00 0.00 2.90
2622 2889 2.616376 GCTGATCTAGTTCAGAGCTCGA 59.384 50.000 27.65 6.12 44.88 4.04
2623 2890 3.548014 GCTGATCTAGTTCAGAGCTCGAC 60.548 52.174 27.65 8.83 44.88 4.20
2763 3031 0.990282 AGCAGGGCTGGTGATGGTAT 60.990 55.000 0.00 0.00 40.15 2.73
2802 3070 6.594937 TCTGATCATGAAACGAATGATGTTGA 59.405 34.615 0.00 0.00 43.25 3.18
2809 3078 5.473162 TGAAACGAATGATGTTGACTTGGAT 59.527 36.000 0.00 0.00 0.00 3.41
3022 3292 2.231721 TCACCATACGAACGATGTTGGA 59.768 45.455 0.14 0.00 0.00 3.53
3066 3336 3.058639 GTGAGTCAGTCCTCATTGTTTGC 60.059 47.826 0.00 0.00 43.03 3.68
3068 3338 2.880890 AGTCAGTCCTCATTGTTTGCAC 59.119 45.455 0.00 0.00 0.00 4.57
3091 3361 7.569297 CACGTTTTTACTATGTTGTTCTGCTA 58.431 34.615 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.119137 GCTTTGCTATTACCAAGTTGGGG 60.119 47.826 25.59 10.88 43.37 4.96
46 47 3.065233 CGCATCAGCTTTGCTATTACCAA 59.935 43.478 14.65 0.00 36.40 3.67
116 117 2.537143 ACCTCGTGGATCCAACTAACT 58.463 47.619 18.20 0.00 37.04 2.24
120 121 3.071892 TGTTAAACCTCGTGGATCCAACT 59.928 43.478 18.20 0.00 37.04 3.16
123 124 3.773418 TTGTTAAACCTCGTGGATCCA 57.227 42.857 11.44 11.44 37.04 3.41
234 236 2.689471 ACACAAGCATGCTTCTTCACAA 59.311 40.909 29.81 0.00 33.42 3.33
251 253 1.001293 AGCATCTTCAGCTTCGACACA 59.999 47.619 0.00 0.00 39.87 3.72
330 332 3.251729 AGCAAGTCACATGCAGTACAAAG 59.748 43.478 7.91 0.00 46.22 2.77
527 530 4.619973 ACAAAACACATACCACTGCAATG 58.380 39.130 0.00 0.00 0.00 2.82
528 531 4.935352 ACAAAACACATACCACTGCAAT 57.065 36.364 0.00 0.00 0.00 3.56
613 618 0.325933 CAATGACCAGCCTCACCTGA 59.674 55.000 0.00 0.00 34.77 3.86
1141 1385 2.481441 ACCAGATGCATGAACCCTAGA 58.519 47.619 2.46 0.00 0.00 2.43
1198 1442 1.452108 CCATCAGAGGGCGGGAAAC 60.452 63.158 0.00 0.00 0.00 2.78
1220 1465 7.921041 TGAGAATCTATCCTCAGGTACAAAT 57.079 36.000 0.00 0.00 34.78 2.32
1243 1488 5.065602 CACCCATGTCAAGAGTCATTGTATG 59.934 44.000 0.00 4.75 0.00 2.39
1394 1639 1.210478 TCCTGCTAATGTCAAGCTCCC 59.790 52.381 0.00 0.00 40.73 4.30
1565 1811 2.301870 ACGAGACCCTCAAACATTGCTA 59.698 45.455 0.00 0.00 0.00 3.49
1587 1833 4.462483 TCCATTTTAGCCATGTCCTCAAAC 59.538 41.667 0.00 0.00 0.00 2.93
1854 2107 1.497286 AGCTTCCCAAACACCCAAGTA 59.503 47.619 0.00 0.00 0.00 2.24
1940 2196 2.897326 AGTACACATGTCCACTACAGCA 59.103 45.455 7.01 0.00 42.70 4.41
2075 2331 8.589338 TGCCAATTTGTTAGTATTTACCAACAT 58.411 29.630 3.21 0.00 37.58 2.71
2284 2547 2.813754 CGGGCAGAGATGAAAACTTTGA 59.186 45.455 0.00 0.00 0.00 2.69
2425 2692 6.422100 CACATTACTTAAGATATGCTCAGCGT 59.578 38.462 10.09 0.00 0.00 5.07
2519 2786 5.508567 TCCTCAGCATTAAATTGATGACCA 58.491 37.500 1.70 0.00 37.13 4.02
2622 2889 2.912771 TCATGTTGTTCAACAGACGGT 58.087 42.857 20.27 4.22 35.95 4.83
2623 2890 3.312421 ACTTCATGTTGTTCAACAGACGG 59.688 43.478 20.27 13.70 35.95 4.79
2652 2920 2.984471 CAGCGAGAGTTTTGCGTAGTTA 59.016 45.455 0.00 0.00 41.40 2.24
2763 3031 6.417258 TCATGATCAGAAACATTAGCCTCAA 58.583 36.000 0.09 0.00 0.00 3.02
2875 3144 6.773638 AGATGAGGAAGTTCAACTACAACAT 58.226 36.000 5.01 0.00 29.61 2.71
3022 3292 0.390124 CAACAACAGGGTGCTGCAAT 59.610 50.000 2.77 0.00 0.00 3.56
3066 3336 6.427150 AGCAGAACAACATAGTAAAAACGTG 58.573 36.000 0.00 0.00 0.00 4.49
3068 3338 8.440059 TGATAGCAGAACAACATAGTAAAAACG 58.560 33.333 0.00 0.00 0.00 3.60
3091 3361 7.907389 TCAGGAAGTTCAACTACAATACTGAT 58.093 34.615 5.01 0.00 28.22 2.90


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

AutoCloner maintained by Alex Coulton.