Multiple sequence alignment - TraesCS7A01G320300

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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 TraesCS7A01G320300 chr7A 100.000 3422 0 0 1 3422 462327811 462331232 0.000000e+00 6320.0
1 TraesCS7A01G320300 chr7D 93.611 3506 122 48 2 3422 403763995 403767483 0.000000e+00 5140.0
2 TraesCS7A01G320300 chr7D 97.143 35 1 0 682 716 24427538 24427504 3.690000e-05 60.2
3 TraesCS7A01G320300 chr7B 95.111 2700 78 18 763 3422 413095171 413097856 0.000000e+00 4205.0
4 TraesCS7A01G320300 chr7B 87.500 608 40 18 102 683 413094298 413094895 0.000000e+00 669.0
5 TraesCS7A01G320300 chr6D 82.278 316 25 14 3112 3422 453770239 453770528 9.490000e-61 244.0
6 TraesCS7A01G320300 chr4B 78.313 332 30 20 1035 1364 562287 561996 3.510000e-40 176.0
7 TraesCS7A01G320300 chr2A 100.000 30 0 0 674 703 606806076 606806047 4.770000e-04 56.5
8 TraesCS7A01G320300 chr2A 100.000 28 0 0 676 703 17251888 17251861 6.000000e-03 52.8
9 TraesCS7A01G320300 chr5A 100.000 28 0 0 675 702 619753452 619753425 6.000000e-03 52.8
10 TraesCS7A01G320300 chr4A 100.000 28 0 0 678 705 683858550 683858577 6.000000e-03 52.8
11 TraesCS7A01G320300 chr2B 100.000 28 0 0 676 703 27088461 27088434 6.000000e-03 52.8
12 TraesCS7A01G320300 chr2B 100.000 28 0 0 676 703 518774861 518774834 6.000000e-03 52.8
13 TraesCS7A01G320300 chr2B 96.774 31 1 0 676 706 518794246 518794216 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 TraesCS7A01G320300 chr7A 462327811 462331232 3421 False 6320 6320 100.0000 1 3422 1 chr7A.!!$F1 3421
1 TraesCS7A01G320300 chr7D 403763995 403767483 3488 False 5140 5140 93.6110 2 3422 1 chr7D.!!$F1 3420
2 TraesCS7A01G320300 chr7B 413094298 413097856 3558 False 2437 4205 91.3055 102 3422 2 chr7B.!!$F1 3320

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
259 298 0.659427 CGAGCAGTACCATGGCAATG 59.341 55.0 13.04 10.31 0.0 2.82 F
1932 2234 0.109723 CCCCCACCAAGTTCTCGAAA 59.890 55.0 0.00 0.00 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2402 1.000145 GGACGGAATCGAAGTCTTGC 59.000 55.0 11.52 0.0 40.11 4.01 R
3133 3467 1.592400 CTGTGTTGCTGATGCTGGGG 61.592 60.0 0.00 0.0 40.48 4.96 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
259 298 0.659427 CGAGCAGTACCATGGCAATG 59.341 55.000 13.04 10.31 0.00 2.82
318 357 6.832520 TTTGAAGCTTGCCATAGTTATTCA 57.167 33.333 2.10 0.00 0.00 2.57
355 394 9.394477 GCAAAGTTGTAGGTTAAAGAATAACAG 57.606 33.333 1.32 0.00 0.00 3.16
539 580 7.891561 ACATGGCAAACTTTATTAACTTAGCA 58.108 30.769 0.00 0.00 0.00 3.49
620 661 8.499967 GGCATATTTTATGTTGAAACGGTTTTT 58.500 29.630 7.65 0.00 0.00 1.94
712 762 7.170393 TCCGTCCCATAATATTATGAGACAG 57.830 40.000 32.29 26.33 44.36 3.51
719 769 7.147585 CCCATAATATTATGAGACAGAGGGAGG 60.148 44.444 29.23 16.57 42.38 4.30
837 1136 6.148948 CAGCATACTTGATAGTAGTCAGCTC 58.851 44.000 0.00 0.00 40.09 4.09
838 1137 5.830457 AGCATACTTGATAGTAGTCAGCTCA 59.170 40.000 0.00 0.00 40.09 4.26
1137 1439 2.045605 CTCCCCCTCCATCTCCATCTAT 59.954 54.545 0.00 0.00 0.00 1.98
1491 1793 2.036731 TCCGTCACCTCCATCGGT 59.963 61.111 0.00 0.00 42.95 4.69
1656 1958 0.744057 TCATGCCACACTACATGCGG 60.744 55.000 0.00 0.00 42.72 5.69
1869 2171 4.590553 TGGGACAGGTGGGGAGCA 62.591 66.667 0.00 0.00 0.00 4.26
1932 2234 0.109723 CCCCCACCAAGTTCTCGAAA 59.890 55.000 0.00 0.00 0.00 3.46
2013 2315 1.418097 ATGTGTGTGAGGGTGAGGCA 61.418 55.000 0.00 0.00 0.00 4.75
2176 2478 3.520290 TCGAGGATGGTGTTGATGTAC 57.480 47.619 0.00 0.00 0.00 2.90
2499 2801 7.336176 AGTCGTGTATAGACTGTGTCTGAATTA 59.664 37.037 10.14 0.00 46.12 1.40
2544 2846 3.506398 TGATCCAGTCAGTACCACTTCA 58.494 45.455 0.00 0.00 31.80 3.02
2576 2878 1.135689 CGTAACCAGCATTCCAGCAAC 60.136 52.381 0.00 0.00 36.85 4.17
2623 2925 5.160607 ACCTGTTCCGATCAATTAGTTCA 57.839 39.130 0.00 0.00 0.00 3.18
2763 3066 9.971922 TGATAGTTATGAGTAGTCAATGATGTG 57.028 33.333 3.93 0.00 35.88 3.21
2813 3116 6.061022 TGGGCATCTATTCTTTAAGTGACA 57.939 37.500 0.00 0.00 0.00 3.58
2914 3243 4.553330 TCCTTGATTACTTGAGGGTCAC 57.447 45.455 0.00 0.00 0.00 3.67
2958 3289 5.089970 AGACAATCTGTATGTGCTGCTTA 57.910 39.130 0.00 0.00 0.00 3.09
2966 3297 1.619654 ATGTGCTGCTTAACCTGCAA 58.380 45.000 0.00 0.00 40.56 4.08
3158 3492 2.224079 AGCATCAGCAACACAGTTTACG 59.776 45.455 0.00 0.00 45.49 3.18
3199 3534 9.539825 TCTTGCTTTTATTTTGTTCTTTATGCA 57.460 25.926 0.00 0.00 0.00 3.96
3398 3733 9.638300 CTTGCTTGACGAAACAAATATATACTC 57.362 33.333 0.00 0.00 0.00 2.59
3399 3734 8.942338 TGCTTGACGAAACAAATATATACTCT 57.058 30.769 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 6.843069 TTGAAGTAAAATTGCCTTGCTTTC 57.157 33.333 0.00 0.00 30.13 2.62
183 191 9.787435 ACCATGTAAAAAGTAGAATGAACAGTA 57.213 29.630 0.00 0.00 0.00 2.74
239 278 0.253044 ATTGCCATGGTACTGCTCGT 59.747 50.000 14.67 0.00 0.00 4.18
241 280 1.755179 ACATTGCCATGGTACTGCTC 58.245 50.000 18.20 0.00 34.27 4.26
259 298 5.236047 TCATGGTGCAAACAATAAAGCAAAC 59.764 36.000 0.00 0.00 38.91 2.93
318 357 4.949856 CCTACAACTTTGCCATAGTCCAAT 59.050 41.667 0.00 0.00 0.00 3.16
500 541 8.500753 AGTTTGCCATGTTCGAACTATATAAA 57.499 30.769 27.32 18.87 36.64 1.40
508 549 7.593644 AGTTAATAAAGTTTGCCATGTTCGAAC 59.406 33.333 21.42 21.42 0.00 3.95
511 552 7.867445 AAGTTAATAAAGTTTGCCATGTTCG 57.133 32.000 0.00 0.00 0.00 3.95
539 580 4.756135 CCAAAGCATTTAGTTTGCCACATT 59.244 37.500 0.00 0.00 41.06 2.71
593 634 6.524101 ACCGTTTCAACATAAAATATGCCT 57.476 33.333 0.00 0.00 0.00 4.75
621 662 4.898861 ACATAGAAGGAACCTTGGCAAAAA 59.101 37.500 11.02 0.00 36.26 1.94
622 663 4.280677 CACATAGAAGGAACCTTGGCAAAA 59.719 41.667 11.02 0.00 36.26 2.44
623 664 3.826157 CACATAGAAGGAACCTTGGCAAA 59.174 43.478 11.02 0.00 36.26 3.68
666 707 8.323567 ACGGAGGGAGTAGTTATGAAAATTAAA 58.676 33.333 0.00 0.00 0.00 1.52
712 762 2.704190 TGGATCCATACTCCTCCCTC 57.296 55.000 11.44 0.00 33.69 4.30
913 1214 2.820037 GGCACGACCAGGCTAAGC 60.820 66.667 0.00 0.00 38.86 3.09
1218 1520 2.419739 GGAGGAGAGGTCGCAGGAC 61.420 68.421 0.00 0.00 42.66 3.85
1491 1793 2.372074 GGGGCCGGAGTGGTAATCA 61.372 63.158 5.05 0.00 41.21 2.57
1656 1958 3.233259 GAGGGCGCATAGGAGGCTC 62.233 68.421 10.83 5.78 39.38 4.70
1932 2234 2.237392 GACAATCAGGGTGTCCTTAGCT 59.763 50.000 0.00 0.00 42.67 3.32
2034 2336 1.586042 CAAACGTATGGCATGGCGC 60.586 57.895 20.60 0.00 41.28 6.53
2100 2402 1.000145 GGACGGAATCGAAGTCTTGC 59.000 55.000 11.52 0.00 40.11 4.01
2176 2478 2.247311 GCAATGTACACTTGCCTTCG 57.753 50.000 22.14 2.53 42.47 3.79
2448 2750 2.250031 TGGAAAAAGCATGCCATGTCT 58.750 42.857 15.66 1.27 0.00 3.41
2449 2751 2.747396 TGGAAAAAGCATGCCATGTC 57.253 45.000 15.66 8.03 0.00 3.06
2453 2755 2.036217 CTCACTTGGAAAAAGCATGCCA 59.964 45.455 15.66 0.19 0.00 4.92
2487 2789 5.620206 ACCTGACAACATAATTCAGACACA 58.380 37.500 0.00 0.00 39.36 3.72
2499 2801 7.347222 TCATCTATACCCTAAACCTGACAACAT 59.653 37.037 0.00 0.00 0.00 2.71
2544 2846 6.575162 ATGCTGGTTACGAAAATTTCTCTT 57.425 33.333 4.09 0.00 0.00 2.85
2576 2878 3.250280 TCTTAGCAGAACGGAGCTATACG 59.750 47.826 3.70 3.70 42.39 3.06
2589 2891 2.753452 CGGAACAGGTACTCTTAGCAGA 59.247 50.000 0.00 0.00 34.60 4.26
2676 2978 9.305925 GAATTCAACTAAATAGCCAAAAGGATG 57.694 33.333 0.00 0.00 0.00 3.51
2763 3066 9.413048 GAACACCTATGTAGATGATAAAGCTAC 57.587 37.037 0.00 0.00 46.09 3.58
2813 3116 5.920193 AGCATGCCATTATACTTTTGTGT 57.080 34.783 15.66 0.00 0.00 3.72
2882 3211 7.044181 TCAAGTAATCAAGGAAGACAGCATAG 58.956 38.462 0.00 0.00 0.00 2.23
2914 3243 7.491372 TGTCTTACAGCTATATTTCAGTTTCCG 59.509 37.037 0.00 0.00 0.00 4.30
2958 3289 1.839424 GCTTACCAGGATTGCAGGTT 58.161 50.000 0.00 0.00 36.87 3.50
2966 3297 4.602340 AATATTCGTCGCTTACCAGGAT 57.398 40.909 0.00 0.00 0.00 3.24
3007 3338 6.378280 AGTTTCAGTCAGACCACAAAAGAAAT 59.622 34.615 0.00 0.00 0.00 2.17
3083 3417 6.209986 ACATGAAAAATGAAGCCTTGATCAGA 59.790 34.615 0.00 0.00 0.00 3.27
3133 3467 1.592400 CTGTGTTGCTGATGCTGGGG 61.592 60.000 0.00 0.00 40.48 4.96


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

AutoCloner maintained by Alex Coulton.