Multiple sequence alignment - TraesCS7A01G289500

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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 TraesCS7A01G289500 chr7A 100.000 2247 0 0 1 2247 352181685 352183931 0.000000e+00 4150
1 TraesCS7A01G289500 chrUn 94.123 2297 83 16 1 2247 93409465 93411759 0.000000e+00 3446
2 TraesCS7A01G289500 chrUn 93.391 1846 76 13 1 1801 216518436 216520280 0.000000e+00 2691
3 TraesCS7A01G289500 chrUn 96.842 570 15 3 396 963 249999801 250000369 0.000000e+00 950
4 TraesCS7A01G289500 chrUn 88.933 506 16 9 3 469 346596330 346596834 2.490000e-164 588
5 TraesCS7A01G289500 chrUn 90.647 417 18 8 2 398 389445201 389444786 3.280000e-148 534
6 TraesCS7A01G289500 chr5D 93.984 2294 89 14 2 2247 503218383 503216091 0.000000e+00 3426
7 TraesCS7A01G289500 chr5D 95.051 1556 68 7 700 2247 329120677 329122231 0.000000e+00 2438
8 TraesCS7A01G289500 chr5D 92.932 1613 70 12 3 1572 503278062 503279673 0.000000e+00 2307
9 TraesCS7A01G289500 chr2D 93.859 2296 91 16 1 2247 272793727 272796021 0.000000e+00 3413
10 TraesCS7A01G289500 chr6D 93.859 2296 89 17 1 2247 168251704 168249412 0.000000e+00 3411
11 TraesCS7A01G289500 chr6D 93.337 1846 77 13 1 1801 168255092 168253248 0.000000e+00 2686
12 TraesCS7A01G289500 chr3A 93.255 2298 102 19 1 2247 672909841 672912136 0.000000e+00 3336
13 TraesCS7A01G289500 chr3A 88.964 743 30 6 1 704 594899458 594900187 0.000000e+00 870
14 TraesCS7A01G289500 chr3A 93.496 123 6 2 1 122 671091459 671091338 4.930000e-42 182
15 TraesCS7A01G289500 chr6A 93.209 2297 104 17 1 2247 260116114 260118408 0.000000e+00 3330
16 TraesCS7A01G289500 chr3B 93.074 2310 96 16 1 2247 201527190 201524882 0.000000e+00 3321
17 TraesCS7A01G289500 chr5A 92.564 2044 102 14 1 1997 619266537 619264497 0.000000e+00 2887
18 TraesCS7A01G289500 chr3D 92.822 1616 70 9 1 1572 589279376 589280989 0.000000e+00 2300
19 TraesCS7A01G289500 chr1A 92.517 1617 67 14 1 1572 554512414 554510807 0.000000e+00 2266
20 TraesCS7A01G289500 chr4A 92.784 970 27 11 1 929 73812342 73813309 0.000000e+00 1363
21 TraesCS7A01G289500 chr6B 93.496 123 6 2 1 122 503844271 503844150 4.930000e-42 182


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 TraesCS7A01G289500 chr7A 352181685 352183931 2246 False 4150.0 4150 100.000 1 2247 1 chr7A.!!$F1 2246
1 TraesCS7A01G289500 chrUn 93409465 93411759 2294 False 3446.0 3446 94.123 1 2247 1 chrUn.!!$F1 2246
2 TraesCS7A01G289500 chrUn 216518436 216520280 1844 False 2691.0 2691 93.391 1 1801 1 chrUn.!!$F2 1800
3 TraesCS7A01G289500 chrUn 249999801 250000369 568 False 950.0 950 96.842 396 963 1 chrUn.!!$F3 567
4 TraesCS7A01G289500 chrUn 346596330 346596834 504 False 588.0 588 88.933 3 469 1 chrUn.!!$F4 466
5 TraesCS7A01G289500 chr5D 503216091 503218383 2292 True 3426.0 3426 93.984 2 2247 1 chr5D.!!$R1 2245
6 TraesCS7A01G289500 chr5D 329120677 329122231 1554 False 2438.0 2438 95.051 700 2247 1 chr5D.!!$F1 1547
7 TraesCS7A01G289500 chr5D 503278062 503279673 1611 False 2307.0 2307 92.932 3 1572 1 chr5D.!!$F2 1569
8 TraesCS7A01G289500 chr2D 272793727 272796021 2294 False 3413.0 3413 93.859 1 2247 1 chr2D.!!$F1 2246
9 TraesCS7A01G289500 chr6D 168249412 168255092 5680 True 3048.5 3411 93.598 1 2247 2 chr6D.!!$R1 2246
10 TraesCS7A01G289500 chr3A 672909841 672912136 2295 False 3336.0 3336 93.255 1 2247 1 chr3A.!!$F2 2246
11 TraesCS7A01G289500 chr3A 594899458 594900187 729 False 870.0 870 88.964 1 704 1 chr3A.!!$F1 703
12 TraesCS7A01G289500 chr6A 260116114 260118408 2294 False 3330.0 3330 93.209 1 2247 1 chr6A.!!$F1 2246
13 TraesCS7A01G289500 chr3B 201524882 201527190 2308 True 3321.0 3321 93.074 1 2247 1 chr3B.!!$R1 2246
14 TraesCS7A01G289500 chr5A 619264497 619266537 2040 True 2887.0 2887 92.564 1 1997 1 chr5A.!!$R1 1996
15 TraesCS7A01G289500 chr3D 589279376 589280989 1613 False 2300.0 2300 92.822 1 1572 1 chr3D.!!$F1 1571
16 TraesCS7A01G289500 chr1A 554510807 554512414 1607 True 2266.0 2266 92.517 1 1572 1 chr1A.!!$R1 1571
17 TraesCS7A01G289500 chr4A 73812342 73813309 967 False 1363.0 1363 92.784 1 929 1 chr4A.!!$F1 928

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
673 712 1.749063 CAAAAGAGGGTAAATCGGCCC 59.251 52.381 0.0 0.0 45.16 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 5092 0.672401 TTGCGAGTTTCCTTAGCCCG 60.672 55.0 0.0 0.0 0.0 6.13 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
42 43 2.548904 CTCTACGGGATAGACCTCAACG 59.451 54.545 0.00 0.00 34.80 4.10
60 61 6.649557 CCTCAACGGAAAACTATTGAGTAACT 59.350 38.462 10.89 0.00 44.28 2.24
61 62 7.816031 CCTCAACGGAAAACTATTGAGTAACTA 59.184 37.037 10.89 0.00 44.28 2.24
63 64 7.326789 TCAACGGAAAACTATTGAGTAACTACG 59.673 37.037 0.00 0.00 33.58 3.51
64 65 5.574443 ACGGAAAACTATTGAGTAACTACGC 59.426 40.000 0.00 0.00 33.58 4.42
65 66 5.574055 CGGAAAACTATTGAGTAACTACGCA 59.426 40.000 0.00 0.00 33.58 5.24
113 114 9.956640 CCTCATAGAAAATTATTGGCTCTAGAT 57.043 33.333 0.00 0.00 0.00 1.98
269 287 4.439860 GGGGAAATAGGGATGTCTCCTAT 58.560 47.826 0.00 0.00 46.39 2.57
271 289 4.323868 GGGAAATAGGGATGTCTCCTATGC 60.324 50.000 3.71 0.69 44.38 3.14
287 305 6.959954 TCTCCTATGCTACCCATAATATGTGT 59.040 38.462 0.00 0.00 36.04 3.72
320 340 9.762933 TGACATAATTTCATAGTCATTCGATCA 57.237 29.630 0.00 0.00 34.59 2.92
473 512 7.768582 CCATCTGTCTAGAGATCGTCATATACT 59.231 40.741 0.00 0.00 36.14 2.12
484 523 8.630054 AGATCGTCATATACTTCTAGAAAGCT 57.370 34.615 6.63 0.00 0.00 3.74
557 596 9.267084 GAGAAAAGAAGAATCTACTTCAACTGT 57.733 33.333 0.00 0.00 45.83 3.55
673 712 1.749063 CAAAAGAGGGTAAATCGGCCC 59.251 52.381 0.00 0.00 45.16 5.80
834 873 7.014038 CACGTAGTAAGAGGGGTAGTTATGAAT 59.986 40.741 0.00 0.00 41.61 2.57
976 1019 4.085210 CGATAGTTTTATTCTTCGTCGCCC 60.085 45.833 0.00 0.00 0.00 6.13
987 1030 5.779529 TCTTCGTCGCCCTAAGTAAATAT 57.220 39.130 0.00 0.00 0.00 1.28
1067 1110 2.631580 GGGAATTGAACCCGCGCAA 61.632 57.895 8.75 0.00 37.85 4.85
1126 1169 0.769873 ATCTGCCCCTTATCCAGCTG 59.230 55.000 6.78 6.78 0.00 4.24
1185 1229 9.729281 TTCTATTTATTCCAACCTTCGTACTTT 57.271 29.630 0.00 0.00 0.00 2.66
1205 1249 9.862371 GTACTTTGATCGAGATATTGGACATAT 57.138 33.333 3.20 0.00 0.00 1.78
1216 1260 7.341805 AGATATTGGACATATAATGCCACTCC 58.658 38.462 0.00 0.00 36.60 3.85
1223 1267 7.502226 TGGACATATAATGCCACTCCTTAAAAG 59.498 37.037 0.00 0.00 33.56 2.27
1319 1372 5.379706 AAAGGTCAATATGAAGGAGGAGG 57.620 43.478 0.00 0.00 0.00 4.30
1342 1395 5.930569 GGAAGAAACAATAGTAACGTGGTCT 59.069 40.000 0.00 0.00 0.00 3.85
1345 1398 4.771590 AACAATAGTAACGTGGTCTCGA 57.228 40.909 0.00 0.00 34.70 4.04
1346 1399 4.771590 ACAATAGTAACGTGGTCTCGAA 57.228 40.909 0.00 0.00 34.70 3.71
1368 1421 4.770795 ACATCTAGCATTCTACCCACAAC 58.229 43.478 0.00 0.00 0.00 3.32
1370 1423 2.829720 TCTAGCATTCTACCCACAACGT 59.170 45.455 0.00 0.00 0.00 3.99
1452 1505 5.376625 TCCTATGGTAGATCACAAATTGGC 58.623 41.667 0.00 0.00 0.00 4.52
1493 1546 7.151308 TCGGCATTTCACAAGTTATGAAAATT 58.849 30.769 13.00 0.00 46.26 1.82
1582 5021 9.807921 AAGATTCAAAATGAAGTAAAGGTAGGA 57.192 29.630 0.00 0.00 40.05 2.94
1653 5092 7.339482 TCCCTAGGATAAAGAAGAAGAAAAGC 58.661 38.462 11.48 0.00 0.00 3.51
1723 5162 5.059833 AGTTCGAGAGAGTTTTCAAAGCAT 58.940 37.500 0.00 0.00 43.69 3.79
1729 5168 8.567948 TCGAGAGAGTTTTCAAAGCATAAAAAT 58.432 29.630 0.00 0.00 34.84 1.82
1765 5204 7.027161 GTCTGTTTTCAAAGCACAAAGAGTTA 58.973 34.615 0.00 0.00 0.00 2.24
1770 5209 9.034544 GTTTTCAAAGCACAAAGAGTTATTGAT 57.965 29.630 0.00 0.00 0.00 2.57
1777 5216 8.345724 AGCACAAAGAGTTATTGATGAGATTT 57.654 30.769 0.00 0.00 0.00 2.17
2172 5635 2.661718 ACACCATTCCTTTTGGTTCGT 58.338 42.857 0.00 0.00 45.19 3.85
2173 5636 2.360801 ACACCATTCCTTTTGGTTCGTG 59.639 45.455 0.00 0.00 45.19 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.956299 TGCGTAGTTACTCAATAGTTTTCC 57.044 37.500 0.00 0.00 37.15 3.13
60 61 7.149973 ACTACTAAACTCAATCACTTTGCGTA 58.850 34.615 0.00 0.00 32.18 4.42
61 62 5.989777 ACTACTAAACTCAATCACTTTGCGT 59.010 36.000 0.00 0.00 34.79 5.24
63 64 7.173390 AGGAACTACTAAACTCAATCACTTTGC 59.827 37.037 0.00 0.00 36.02 3.68
64 65 8.608844 AGGAACTACTAAACTCAATCACTTTG 57.391 34.615 0.00 0.00 36.02 2.77
65 66 8.429641 TGAGGAACTACTAAACTCAATCACTTT 58.570 33.333 0.00 0.00 41.55 2.66
113 114 5.586643 TGCGTGCTTCAAACAATACCATATA 59.413 36.000 0.00 0.00 0.00 0.86
294 312 9.762933 TGATCGAATGACTATGAAATTATGTCA 57.237 29.630 0.00 0.00 41.07 3.58
320 340 6.261826 GGCTTATGTTCTTCATGTAGCATTCT 59.738 38.462 13.97 0.00 42.20 2.40
588 627 1.165270 CCCTTCCACGTGTGATTTCC 58.835 55.000 15.65 0.00 0.00 3.13
693 732 3.104519 TGGGATACTAAACGGACCTCA 57.895 47.619 0.00 0.00 0.00 3.86
809 848 6.006275 TCATAACTACCCCTCTTACTACGT 57.994 41.667 0.00 0.00 0.00 3.57
834 873 4.194497 TGGGGGTGGTCCACAGGA 62.194 66.667 23.48 1.39 45.78 3.86
987 1030 8.815565 TGCAATTTTCCATATTCCTAGTTACA 57.184 30.769 0.00 0.00 0.00 2.41
1171 1215 4.482386 TCTCGATCAAAGTACGAAGGTTG 58.518 43.478 0.00 0.00 35.70 3.77
1172 1216 4.778534 TCTCGATCAAAGTACGAAGGTT 57.221 40.909 0.00 0.00 35.70 3.50
1177 1221 6.038936 TGTCCAATATCTCGATCAAAGTACGA 59.961 38.462 0.00 0.00 34.90 3.43
1185 1229 7.928167 GGCATTATATGTCCAATATCTCGATCA 59.072 37.037 0.00 0.00 0.00 2.92
1216 1260 7.606839 AGTCGATTACTCCTTTTCCCTTTTAAG 59.393 37.037 0.00 0.00 30.33 1.85
1261 1314 7.631377 GCCAATAAATGATGAGCTACAAAAGGT 60.631 37.037 0.00 0.00 39.11 3.50
1319 1372 6.183359 CGAGACCACGTTACTATTGTTTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
1342 1395 3.958147 TGGGTAGAATGCTAGATGTTCGA 59.042 43.478 0.00 0.00 0.00 3.71
1345 1398 5.186198 GTTGTGGGTAGAATGCTAGATGTT 58.814 41.667 0.00 0.00 0.00 2.71
1346 1399 4.680708 CGTTGTGGGTAGAATGCTAGATGT 60.681 45.833 0.00 0.00 0.00 3.06
1368 1421 0.588730 CGCGATTGTATGGCCAAACG 60.589 55.000 10.96 4.74 41.68 3.60
1370 1423 1.674359 ATCGCGATTGTATGGCCAAA 58.326 45.000 17.62 0.00 0.00 3.28
1440 1493 2.491693 ACGAATTCCGCCAATTTGTGAT 59.508 40.909 9.17 0.00 44.49 3.06
1443 1496 1.668628 GCACGAATTCCGCCAATTTGT 60.669 47.619 0.00 5.51 46.36 2.83
1452 1505 0.870307 CCGAGTAGGCACGAATTCCG 60.870 60.000 0.00 0.00 45.44 4.30
1493 1546 8.311836 ACAACGAGATTTAGTATCCTTTCTTGA 58.688 33.333 0.00 0.00 0.00 3.02
1568 5007 6.409005 GGTTATTCCCCTCCTACCTTTACTTC 60.409 46.154 0.00 0.00 0.00 3.01
1582 5021 8.566109 ACTTGTCATAAATAAGGTTATTCCCCT 58.434 33.333 0.00 0.00 36.75 4.79
1653 5092 0.672401 TTGCGAGTTTCCTTAGCCCG 60.672 55.000 0.00 0.00 0.00 6.13
1687 5126 8.113173 ACTCTCTCGAACTTAAGTAGACAATT 57.887 34.615 8.92 0.00 0.00 2.32
1690 5129 7.507733 AAACTCTCTCGAACTTAAGTAGACA 57.492 36.000 8.92 0.00 0.00 3.41
1729 5168 6.374333 GCTTTGAAAACAGACATAGGGATACA 59.626 38.462 0.00 0.00 39.74 2.29
1765 5204 2.372264 ACGCCAGCAAATCTCATCAAT 58.628 42.857 0.00 0.00 0.00 2.57
1770 5209 2.472695 AGTAACGCCAGCAAATCTCA 57.527 45.000 0.00 0.00 0.00 3.27
1801 5240 5.311649 AGGGCATGAGGTTCAGTATCATAAT 59.688 40.000 0.00 0.00 32.51 1.28
2126 5589 5.376756 TGGGTTGTACCAAGTCTAAAACT 57.623 39.130 0.00 0.00 41.02 2.66


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

AutoCloner maintained by Alex Coulton.