Multiple sequence alignment - TraesCS7A01G040000

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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 TraesCS7A01G040000 chr7A 100.000 1741 0 0 910 2650 18055312 18053572 0.000000e+00 3216.0
1 TraesCS7A01G040000 chr7A 83.463 1669 231 26 990 2650 17888405 17886774 0.000000e+00 1511.0
2 TraesCS7A01G040000 chr7A 82.387 1709 253 30 966 2650 17812710 17811026 0.000000e+00 1445.0
3 TraesCS7A01G040000 chr7A 83.521 1244 195 9 1411 2650 17774686 17773449 0.000000e+00 1153.0
4 TraesCS7A01G040000 chr7A 100.000 616 0 0 1 616 18056221 18055606 0.000000e+00 1138.0
5 TraesCS7A01G040000 chr7A 76.954 1766 301 60 925 2650 17686877 17685178 0.000000e+00 909.0
6 TraesCS7A01G040000 chr7A 92.920 226 9 4 188 412 17687681 17687462 3.290000e-84 322.0
7 TraesCS7A01G040000 chr7A 96.875 192 6 0 1 192 17688710 17688519 3.290000e-84 322.0
8 TraesCS7A01G040000 chr7A 94.030 201 11 1 415 615 17687144 17686945 1.190000e-78 303.0
9 TraesCS7A01G040000 chr7A 89.916 119 12 0 1001 1119 17913018 17912900 1.270000e-33 154.0
10 TraesCS7A01G040000 chr7A 92.857 84 6 0 10 93 17366159 17366076 3.580000e-24 122.0
11 TraesCS7A01G040000 chr4A 95.552 1731 68 5 924 2650 714729536 714731261 0.000000e+00 2761.0
12 TraesCS7A01G040000 chr4A 83.017 1737 244 35 923 2650 714418254 714419948 0.000000e+00 1526.0
13 TraesCS7A01G040000 chr4A 92.246 619 33 6 1 616 714728861 714729467 0.000000e+00 863.0
14 TraesCS7A01G040000 chr4A 89.076 119 13 0 1001 1119 714943640 714943758 5.910000e-32 148.0
15 TraesCS7A01G040000 chr4A 100.000 42 0 0 13 54 715711199 715711240 7.860000e-11 78.7
16 TraesCS7A01G040000 chr4A 100.000 39 0 0 16 54 715883886 715883848 3.660000e-09 73.1
17 TraesCS7A01G040000 chrUn 83.064 1671 230 29 990 2650 294163018 294164645 0.000000e+00 1469.0
18 TraesCS7A01G040000 chrUn 86.047 1247 160 13 1411 2650 278339811 278341050 0.000000e+00 1327.0
19 TraesCS7A01G040000 chrUn 86.047 1247 160 13 1411 2650 278347088 278348327 0.000000e+00 1327.0
20 TraesCS7A01G040000 chrUn 79.755 326 49 13 966 1282 467580092 467580409 1.230000e-53 220.0
21 TraesCS7A01G040000 chr6B 82.038 1698 273 23 966 2650 208175453 208177131 0.000000e+00 1417.0
22 TraesCS7A01G040000 chr7D 85.106 141 5 7 13 146 17871770 17871639 2.140000e-26 130.0


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 TraesCS7A01G040000 chr7A 18053572 18056221 2649 True 2177 3216 100.00000 1 2650 2 chr7A.!!$R7 2649
1 TraesCS7A01G040000 chr7A 17886774 17888405 1631 True 1511 1511 83.46300 990 2650 1 chr7A.!!$R4 1660
2 TraesCS7A01G040000 chr7A 17811026 17812710 1684 True 1445 1445 82.38700 966 2650 1 chr7A.!!$R3 1684
3 TraesCS7A01G040000 chr7A 17773449 17774686 1237 True 1153 1153 83.52100 1411 2650 1 chr7A.!!$R2 1239
4 TraesCS7A01G040000 chr7A 17685178 17688710 3532 True 464 909 90.19475 1 2650 4 chr7A.!!$R6 2649
5 TraesCS7A01G040000 chr4A 714728861 714731261 2400 False 1812 2761 93.89900 1 2650 2 chr4A.!!$F4 2649
6 TraesCS7A01G040000 chr4A 714418254 714419948 1694 False 1526 1526 83.01700 923 2650 1 chr4A.!!$F1 1727
7 TraesCS7A01G040000 chrUn 294163018 294164645 1627 False 1469 1469 83.06400 990 2650 1 chrUn.!!$F3 1660
8 TraesCS7A01G040000 chrUn 278339811 278341050 1239 False 1327 1327 86.04700 1411 2650 1 chrUn.!!$F1 1239
9 TraesCS7A01G040000 chrUn 278347088 278348327 1239 False 1327 1327 86.04700 1411 2650 1 chrUn.!!$F2 1239
10 TraesCS7A01G040000 chr6B 208175453 208177131 1678 False 1417 1417 82.03800 966 2650 1 chr6B.!!$F1 1684

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
939 2099 0.447406 CACACACACACACACACAGG 59.553 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2519 3743 0.673985 TAACCATCCTCCTCATCGCG 59.326 55.0 0.0 0.0 0.0 5.87 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
41 42 2.796483 ATCGTTTGCTACCTGCCGCA 62.796 55.000 0.00 0.00 42.00 5.69
126 127 3.825585 TGCATTTGAACAGCCAGAATGTA 59.174 39.130 0.00 0.00 31.96 2.29
174 175 0.911769 TGGCCCATTGGAGTGTCTAG 59.088 55.000 3.62 0.00 0.00 2.43
267 1110 0.902531 GTCCTTGGCTGCTACCTACA 59.097 55.000 0.00 0.00 0.00 2.74
287 1130 8.482943 ACCTACAGCCTTGTTTTAATTTTTCTT 58.517 29.630 0.00 0.00 38.76 2.52
293 1136 8.817100 AGCCTTGTTTTAATTTTTCTTTCTTCG 58.183 29.630 0.00 0.00 0.00 3.79
537 1695 4.158949 GGGTGGGTGATAAACAACATTACC 59.841 45.833 0.00 0.00 38.06 2.85
538 1696 5.014202 GGTGGGTGATAAACAACATTACCT 58.986 41.667 0.00 0.00 38.06 3.08
539 1697 5.479027 GGTGGGTGATAAACAACATTACCTT 59.521 40.000 0.00 0.00 38.06 3.50
540 1698 6.014925 GGTGGGTGATAAACAACATTACCTTT 60.015 38.462 0.00 0.00 38.06 3.11
577 1737 1.000496 ACCGTGACGAGAGAAAGGAAC 60.000 52.381 6.54 0.00 0.00 3.62
927 2087 3.314083 ACACACACACACACACACA 57.686 47.368 0.00 0.00 0.00 3.72
928 2088 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
929 2089 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
939 2099 0.447406 CACACACACACACACACAGG 59.553 55.000 0.00 0.00 0.00 4.00
1157 2319 5.288232 TCTTTTGTTTTTGTCATGCACTTCG 59.712 36.000 0.00 0.00 0.00 3.79
1167 2329 3.426568 GCACTTCGCACTGCCTCC 61.427 66.667 0.00 0.00 41.79 4.30
1285 2462 8.540507 ACTCTTGTATATAGAATGACACCAGT 57.459 34.615 0.00 0.00 0.00 4.00
1332 2511 5.755375 TCTTCGTGGAGATGCATATTTCTTC 59.245 40.000 0.00 0.00 0.00 2.87
1334 2513 5.674525 TCGTGGAGATGCATATTTCTTCTT 58.325 37.500 0.00 0.00 0.00 2.52
1605 2796 5.049680 TCACGGAAACTTATGAAGCTCAAAC 60.050 40.000 0.00 0.00 0.00 2.93
1609 2800 5.009610 GGAAACTTATGAAGCTCAAACACCA 59.990 40.000 0.00 0.00 0.00 4.17
1647 2838 3.304257 GCAAATCCGCGATCTCAAATCAT 60.304 43.478 8.23 0.00 0.00 2.45
1762 2953 4.816385 GGAAGATATTCGCAACCATTCAGA 59.184 41.667 0.00 0.00 0.00 3.27
2007 3217 6.545298 GGAGCTTCTCAAGGTTATGATCAAAT 59.455 38.462 0.00 0.00 39.77 2.32
2009 3219 8.358582 AGCTTCTCAAGGTTATGATCAAATTT 57.641 30.769 0.00 0.00 35.27 1.82
2066 3285 5.047590 TGAAGGTAATGTAGTGCGAGAAGAA 60.048 40.000 0.00 0.00 0.00 2.52
2246 3465 4.617253 TGGTTTAGCTAAGAAGTGCTCA 57.383 40.909 6.24 0.00 40.35 4.26
2250 3469 5.643777 GGTTTAGCTAAGAAGTGCTCATTGA 59.356 40.000 6.24 0.00 40.35 2.57
2259 3478 6.497785 AGAAGTGCTCATTGAAATCTTCTG 57.502 37.500 17.88 0.00 38.69 3.02
2294 3513 2.620627 CCACCATCAACCCCTAGAAACC 60.621 54.545 0.00 0.00 0.00 3.27
2307 3526 4.520492 CCCTAGAAACCAATGATGCCATAC 59.480 45.833 0.00 0.00 31.59 2.39
2456 3680 0.898320 TGCTTGCCACTAGAGAGGTC 59.102 55.000 0.00 0.00 0.00 3.85
2506 3730 1.957877 CCCCTTAGAACTAGAGAGCGG 59.042 57.143 0.00 0.00 0.00 5.52
2519 3743 2.048127 AGCGGCCGAAGTCTTGAC 60.048 61.111 33.48 7.54 0.00 3.18
2522 3746 3.479269 GGCCGAAGTCTTGACGCG 61.479 66.667 3.53 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 5.823045 ACGAATCAAGTCAAGTCCTTCTTTT 59.177 36.000 0.00 0.00 33.63 2.27
174 175 5.894807 AGCATGTTAGGTGATTTGTAATGC 58.105 37.500 0.00 0.00 38.48 3.56
267 1110 8.817100 CGAAGAAAGAAAAATTAAAACAAGGCT 58.183 29.630 0.00 0.00 0.00 4.58
287 1130 5.847304 TCCTAGCTAGTACGTATCGAAGAA 58.153 41.667 19.31 0.00 43.58 2.52
540 1698 6.415280 CGTCACGGTTATTCATCAAACAAAAA 59.585 34.615 0.00 0.00 0.00 1.94
909 2069 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
910 2070 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
911 2071 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
912 2072 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
913 2073 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
914 2074 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
915 2075 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
916 2076 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
917 2077 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
918 2078 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
919 2079 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
920 2080 0.447406 CCTGTGTGTGTGTGTGTGTG 59.553 55.000 0.00 0.00 0.00 3.82
921 2081 0.036164 ACCTGTGTGTGTGTGTGTGT 59.964 50.000 0.00 0.00 0.00 3.72
922 2082 1.933181 CTACCTGTGTGTGTGTGTGTG 59.067 52.381 0.00 0.00 0.00 3.82
923 2083 1.742411 GCTACCTGTGTGTGTGTGTGT 60.742 52.381 0.00 0.00 0.00 3.72
924 2084 0.937304 GCTACCTGTGTGTGTGTGTG 59.063 55.000 0.00 0.00 0.00 3.82
925 2085 0.830648 AGCTACCTGTGTGTGTGTGT 59.169 50.000 0.00 0.00 0.00 3.72
926 2086 2.035961 AGTAGCTACCTGTGTGTGTGTG 59.964 50.000 20.31 0.00 0.00 3.82
927 2087 2.035961 CAGTAGCTACCTGTGTGTGTGT 59.964 50.000 20.31 0.00 0.00 3.72
928 2088 2.035961 ACAGTAGCTACCTGTGTGTGTG 59.964 50.000 20.31 10.83 0.00 3.82
929 2089 2.035961 CACAGTAGCTACCTGTGTGTGT 59.964 50.000 29.22 20.25 42.28 3.72
939 2099 4.720649 TGATCAACCTCACAGTAGCTAC 57.279 45.455 16.43 16.43 0.00 3.58
953 2113 5.215160 GTCCTCACACAACAATTGATCAAC 58.785 41.667 13.59 0.00 0.00 3.18
1181 2346 9.219603 TCCAACAAGATGTTCTTAATAACAGAG 57.780 33.333 11.49 4.90 42.33 3.35
1285 2462 5.759059 AGATTTCAAGCCTACCATGAATGA 58.241 37.500 0.00 0.00 33.45 2.57
1332 2511 4.923893 TGTGACATGCAACAAAGAAGAAG 58.076 39.130 0.00 0.00 0.00 2.85
1334 2513 3.316029 CCTGTGACATGCAACAAAGAAGA 59.684 43.478 9.63 0.00 0.00 2.87
1605 2796 2.060284 CACCGCAATTTGATGTTGGTG 58.940 47.619 0.00 5.83 40.22 4.17
1609 2800 2.522836 TTGCACCGCAATTTGATGTT 57.477 40.000 0.00 0.00 43.99 2.71
1647 2838 3.872696 TGTTGCTGACTTCTTCAACTCA 58.127 40.909 12.20 0.00 39.44 3.41
1762 2953 5.071519 AGTCCTGCTTCATCTATGTTGCTAT 59.928 40.000 9.78 0.00 0.00 2.97
2066 3285 2.028130 CTCAGATAGTTGGCGAGGTCT 58.972 52.381 0.00 0.00 0.00 3.85
2187 3406 8.842280 TGTTATAATTATCCGGCTACCTTTTTG 58.158 33.333 0.00 0.00 0.00 2.44
2189 3408 8.843262 GTTGTTATAATTATCCGGCTACCTTTT 58.157 33.333 0.00 0.00 0.00 2.27
2250 3469 8.258708 GTGGTAGATAAGTGGTACAGAAGATTT 58.741 37.037 0.00 0.00 41.80 2.17
2259 3478 5.864418 TGATGGTGGTAGATAAGTGGTAC 57.136 43.478 0.00 0.00 0.00 3.34
2294 3513 4.577693 AGTAGCAAGTGTATGGCATCATTG 59.422 41.667 1.65 6.40 34.96 2.82
2307 3526 4.416620 CGAGTCTTCCTTAGTAGCAAGTG 58.583 47.826 0.00 0.00 0.00 3.16
2328 3550 1.135915 CATGTCCTCCTCACTTCTCCG 59.864 57.143 0.00 0.00 0.00 4.63
2456 3680 6.021596 GTCGTAAATACTTTGCCATTCACTG 58.978 40.000 0.00 0.00 0.00 3.66
2506 3730 1.805945 ATCGCGTCAAGACTTCGGC 60.806 57.895 5.77 1.29 0.00 5.54
2519 3743 0.673985 TAACCATCCTCCTCATCGCG 59.326 55.000 0.00 0.00 0.00 5.87
2522 3746 4.219115 TCAGAGTAACCATCCTCCTCATC 58.781 47.826 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.