Multiple sequence alignment - TraesCS7A01G213800

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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 TraesCS7A01G213800 chr7A 100.000 3109 0 0 1 3109 177999940 178003048 0.000000e+00 5742
1 TraesCS7A01G213800 chr7A 93.085 564 26 6 28 580 177955191 177955752 0.000000e+00 813
2 TraesCS7A01G213800 chr7B 94.708 2891 102 18 243 3107 141578887 141581752 0.000000e+00 4444
3 TraesCS7A01G213800 chr7B 89.222 167 18 0 1 167 141578303 141578469 3.140000e-50 209
4 TraesCS7A01G213800 chr7D 94.885 1994 68 14 243 2231 175887971 175889935 0.000000e+00 3086
5 TraesCS7A01G213800 chr7D 85.144 727 62 12 2394 3109 175916022 175916713 0.000000e+00 702
6 TraesCS7A01G213800 chr7D 92.814 167 12 0 1 167 175887649 175887815 3.100000e-60 243
7 TraesCS7A01G213800 chr7D 87.671 146 13 5 2248 2389 175889917 175890061 6.900000e-37 165
8 TraesCS7A01G213800 chr1B 80.000 140 22 6 2497 2632 580442322 580442185 7.100000e-17 99
9 TraesCS7A01G213800 chr1A 85.000 100 11 4 2532 2630 526743994 526743898 7.100000e-17 99


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 TraesCS7A01G213800 chr7A 177999940 178003048 3108 False 5742.000000 5742 100.000 1 3109 1 chr7A.!!$F2 3108
1 TraesCS7A01G213800 chr7A 177955191 177955752 561 False 813.000000 813 93.085 28 580 1 chr7A.!!$F1 552
2 TraesCS7A01G213800 chr7B 141578303 141581752 3449 False 2326.500000 4444 91.965 1 3107 2 chr7B.!!$F1 3106
3 TraesCS7A01G213800 chr7D 175887649 175890061 2412 False 1164.666667 3086 91.790 1 2389 3 chr7D.!!$F2 2388
4 TraesCS7A01G213800 chr7D 175916022 175916713 691 False 702.000000 702 85.144 2394 3109 1 chr7D.!!$F1 715

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
716 1073 0.029834 CAGCGCACAAATAGCATCCC 59.97 55.0 11.47 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 2824 0.176449 GATTTGTGGCTGGGATTGGC 59.824 55.0 0.0 0.0 0.0 4.52 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
50 51 2.269241 GGAGAGGGACAAAGGGCG 59.731 66.667 0.00 0.00 0.00 6.13
106 107 4.477975 GAGAGCGACGTGGACCCG 62.478 72.222 0.11 0.00 0.00 5.28
153 154 0.821711 GTGTGGTGGGTGCTTAGCAA 60.822 55.000 9.05 0.00 41.47 3.91
279 623 0.889186 GTTTCCAGGAAAGAGCCGCA 60.889 55.000 15.49 0.00 31.87 5.69
361 709 2.755655 TCTTGTGACACTCTAGCTAGGC 59.244 50.000 20.58 0.00 0.00 3.93
432 780 1.677217 GCGTGAAAGCATTCCTCTCCT 60.677 52.381 0.00 0.00 34.49 3.69
466 814 1.380403 CCACGCACACCTTTGGAACA 61.380 55.000 0.00 0.00 0.00 3.18
582 937 0.447801 CAAGGCTCATTACCACGCAC 59.552 55.000 0.00 0.00 0.00 5.34
603 958 4.820716 CACCTCTCATCATCTCCCATTTTC 59.179 45.833 0.00 0.00 0.00 2.29
631 986 1.523046 GCCATTGATGCATGCCCAA 59.477 52.632 16.68 18.83 0.00 4.12
646 1003 1.533625 CCCAATCAAGCTTTCGTCCA 58.466 50.000 0.00 0.00 0.00 4.02
670 1027 2.048222 TCCGCTGTCAAAGAGGCG 60.048 61.111 0.00 0.00 45.11 5.52
716 1073 0.029834 CAGCGCACAAATAGCATCCC 59.970 55.000 11.47 0.00 0.00 3.85
747 1107 1.472026 GCATGCATTGATTCACCCCAC 60.472 52.381 14.21 0.00 0.00 4.61
827 1187 4.215737 TGCATGCACACCCACCCA 62.216 61.111 18.46 0.00 0.00 4.51
828 1188 3.683937 GCATGCACACCCACCCAC 61.684 66.667 14.21 0.00 0.00 4.61
829 1189 2.990967 CATGCACACCCACCCACC 60.991 66.667 0.00 0.00 0.00 4.61
830 1190 4.299796 ATGCACACCCACCCACCC 62.300 66.667 0.00 0.00 0.00 4.61
850 1210 3.312504 CGTGCGTGCGTATCTCCG 61.313 66.667 0.00 0.00 0.00 4.63
907 1271 1.280142 CACCTCGTATCGCCTCTCG 59.720 63.158 0.00 0.00 40.15 4.04
918 1282 2.432628 CCTCTCGCACGGTGGTTC 60.433 66.667 10.60 0.00 0.00 3.62
1008 1372 1.319799 CCTTCCTCCCCCTCTCCAT 59.680 63.158 0.00 0.00 0.00 3.41
1545 1909 2.926242 GAGGGGGTGAACGGGACA 60.926 66.667 0.00 0.00 0.00 4.02
1776 2140 3.870606 CGTCCGTCGCCAAAGAAT 58.129 55.556 0.00 0.00 0.00 2.40
2111 2477 5.163488 TGGCAGATTTGAGCAGAATAATTGG 60.163 40.000 0.00 0.00 0.00 3.16
2228 2594 3.379372 CGATGAATCTTGCAAATCCACCT 59.621 43.478 0.00 0.00 0.00 4.00
2233 2599 5.990996 TGAATCTTGCAAATCCACCTTTTTC 59.009 36.000 0.00 0.00 0.00 2.29
2235 2601 5.612725 TCTTGCAAATCCACCTTTTTCTT 57.387 34.783 0.00 0.00 0.00 2.52
2347 2717 1.164411 TGCACGATCACATGGAAACC 58.836 50.000 0.00 0.00 0.00 3.27
2360 2730 1.296727 GGAAACCGATCGATCCAACC 58.703 55.000 18.66 11.77 32.08 3.77
2392 2762 9.520515 AGTTCATCACATAGGAAATGTTTACTT 57.479 29.630 0.00 0.00 32.49 2.24
2444 2824 3.417275 AAGCCGATCTCTCGTGCGG 62.417 63.158 0.00 0.00 43.49 5.69
2545 2932 2.226437 CACACAAACCTTTCGATCCCTG 59.774 50.000 0.00 0.00 0.00 4.45
2547 2934 3.071892 ACACAAACCTTTCGATCCCTGTA 59.928 43.478 0.00 0.00 0.00 2.74
2685 3072 3.006859 TCAATCTCACCACACTACCACAG 59.993 47.826 0.00 0.00 0.00 3.66
2773 3160 9.173021 TCATCATTAACGACAATCAAAACCTAT 57.827 29.630 0.00 0.00 0.00 2.57
2805 3192 4.737855 AAACGGCATCACTAGTATCTGT 57.262 40.909 0.00 0.00 0.00 3.41
2828 3215 1.067295 ACCACATCCTCACACACCAT 58.933 50.000 0.00 0.00 0.00 3.55
2841 3228 4.637091 TCACACACCATCATGAAGCAATAG 59.363 41.667 0.00 0.00 0.00 1.73
2949 3336 3.955101 CGGAGTAGCGAGGCGGAG 61.955 72.222 0.00 0.00 0.00 4.63
2950 3337 2.829458 GGAGTAGCGAGGCGGAGT 60.829 66.667 0.00 0.00 0.00 3.85
2951 3338 2.716864 GAGTAGCGAGGCGGAGTC 59.283 66.667 0.00 0.00 0.00 3.36
2956 3343 4.415332 GCGAGGCGGAGTCGTCAA 62.415 66.667 0.00 0.00 44.51 3.18
2999 3386 1.745087 GAAGAAGAATCGCCATTGCCA 59.255 47.619 0.00 0.00 0.00 4.92
3004 3391 0.461135 GAATCGCCATTGCCAACCAT 59.539 50.000 0.00 0.00 0.00 3.55
3055 3443 5.471257 ACCTACTTGTCGATGAAGAAGAAC 58.529 41.667 12.65 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.148825 CCCTCTCCCTCGTTGCCG 62.149 72.222 0.00 0.00 0.00 5.69
106 107 3.754766 GTGACCACGATACCCCTTC 57.245 57.895 0.00 0.00 0.00 3.46
189 218 1.672881 CCATTTCGGCAACTCCTCATC 59.327 52.381 0.00 0.00 0.00 2.92
279 623 4.407945 AGACAGTGTGGTAAAGTGGTAACT 59.592 41.667 0.00 0.00 38.71 2.24
361 709 2.990514 TGACATTTGTACACACGATCGG 59.009 45.455 20.98 10.92 0.00 4.18
432 780 2.360726 TGGCGAGGCGTCTACTGA 60.361 61.111 4.69 0.00 30.55 3.41
466 814 9.045745 ACATAAATGGTTCCCTTTTATCACATT 57.954 29.630 9.83 0.00 39.91 2.71
474 822 5.105917 CGCACTACATAAATGGTTCCCTTTT 60.106 40.000 0.00 0.00 35.52 2.27
496 844 4.389576 CGTGCTTCTTGTGGCCGC 62.390 66.667 10.11 10.11 0.00 6.53
582 937 4.820716 GTGAAAATGGGAGATGATGAGAGG 59.179 45.833 0.00 0.00 0.00 3.69
631 986 2.808543 GACAACTGGACGAAAGCTTGAT 59.191 45.455 0.00 0.00 0.00 2.57
646 1003 1.412710 TCTTTGACAGCGGAGACAACT 59.587 47.619 0.00 0.00 0.00 3.16
716 1073 2.987821 TCAATGCATGCAATTTGTGACG 59.012 40.909 26.68 2.31 0.00 4.35
759 1119 7.062956 TGTTACTACGACAATGAGTTAATGCTG 59.937 37.037 0.00 0.00 0.00 4.41
827 1187 3.291101 ATACGCACGCACGAAGGGT 62.291 57.895 4.54 6.16 45.35 4.34
828 1188 2.508439 ATACGCACGCACGAAGGG 60.508 61.111 4.54 0.00 36.70 3.95
829 1189 1.472276 GAGATACGCACGCACGAAGG 61.472 60.000 4.54 0.00 36.70 3.46
830 1190 1.472276 GGAGATACGCACGCACGAAG 61.472 60.000 4.54 0.00 36.70 3.79
850 1210 4.072088 GCGCACGCCACTGTACAC 62.072 66.667 0.30 0.00 34.56 2.90
907 1271 3.050275 GAGCCAGAACCACCGTGC 61.050 66.667 0.00 0.00 0.00 5.34
955 1319 5.299782 GGCCCCTAGATATACTACGATGAAG 59.700 48.000 0.00 0.00 0.00 3.02
1121 1485 4.834453 CGCAGAGGAGCAGCAGGG 62.834 72.222 0.00 0.00 0.00 4.45
1697 2061 4.834453 CCAGAGGAGCAGGCGCAG 62.834 72.222 10.83 1.27 42.27 5.18
1760 2124 0.442699 GTGATTCTTTGGCGACGGAC 59.557 55.000 0.00 0.00 0.00 4.79
2228 2594 6.986231 GCAAGATCCCTCAAAGAAAAGAAAAA 59.014 34.615 0.00 0.00 0.00 1.94
2233 2599 5.458041 TTGCAAGATCCCTCAAAGAAAAG 57.542 39.130 0.00 0.00 0.00 2.27
2235 2601 5.047092 GGATTTGCAAGATCCCTCAAAGAAA 60.047 40.000 20.96 0.00 37.65 2.52
2347 2717 1.721389 CTAATGCGGTTGGATCGATCG 59.279 52.381 18.81 9.36 0.00 3.69
2360 2730 6.603237 TTTCCTATGTGATGAACTAATGCG 57.397 37.500 0.00 0.00 0.00 4.73
2391 2761 9.022915 CGTACACTATACATCATTTCCGTAAAA 57.977 33.333 0.00 0.00 0.00 1.52
2392 2762 8.190122 ACGTACACTATACATCATTTCCGTAAA 58.810 33.333 0.00 0.00 0.00 2.01
2414 2794 1.404391 GATCGGCTTCCAGAGAACGTA 59.596 52.381 0.00 0.00 0.00 3.57
2444 2824 0.176449 GATTTGTGGCTGGGATTGGC 59.824 55.000 0.00 0.00 0.00 4.52
2455 2835 2.032030 GTCACCGTGTTGAGATTTGTGG 60.032 50.000 0.00 0.00 0.00 4.17
2532 2919 2.691409 TTGCTACAGGGATCGAAAGG 57.309 50.000 0.00 0.00 0.00 3.11
2545 2932 2.673368 CGTTGTTCCCTCAGATTGCTAC 59.327 50.000 0.00 0.00 0.00 3.58
2547 2934 1.813513 CGTTGTTCCCTCAGATTGCT 58.186 50.000 0.00 0.00 0.00 3.91
2685 3072 2.558359 AGTTGAATGCTAGTTTGGTGCC 59.442 45.455 0.00 0.00 0.00 5.01
2763 3150 7.334921 CCGTTTTGGTAGTATGATAGGTTTTGA 59.665 37.037 0.00 0.00 0.00 2.69
2773 3160 3.936453 GTGATGCCGTTTTGGTAGTATGA 59.064 43.478 0.00 0.00 41.21 2.15
2805 3192 2.301870 GGTGTGTGAGGATGTGGTAGAA 59.698 50.000 0.00 0.00 0.00 2.10
2828 3215 8.144478 GTGGTAGATTAGACTATTGCTTCATGA 58.856 37.037 0.00 0.00 0.00 3.07
2949 3336 2.400399 TCCGAGTTGTTCATTGACGAC 58.600 47.619 0.00 0.00 34.71 4.34
2950 3337 2.295070 TCTCCGAGTTGTTCATTGACGA 59.705 45.455 0.00 0.00 0.00 4.20
2951 3338 2.672714 TCTCCGAGTTGTTCATTGACG 58.327 47.619 0.00 0.00 0.00 4.35
2956 3343 3.165875 TCCTCTTCTCCGAGTTGTTCAT 58.834 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.