Multiple sequence alignment - TraesCS7A01G548600

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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 TraesCS7A01G548600 chr7A 100.000 2132 0 0 196 2327 722935833 722937964 0.000000e+00 3938.0
1 TraesCS7A01G548600 chr7A 99.178 1095 9 0 196 1290 723030130 723031224 0.000000e+00 1973.0
2 TraesCS7A01G548600 chr7A 98.244 1025 18 0 266 1290 722897846 722898870 0.000000e+00 1794.0
3 TraesCS7A01G548600 chr7A 96.667 1050 29 5 244 1290 722987335 722988381 0.000000e+00 1740.0
4 TraesCS7A01G548600 chr7A 96.069 1043 34 6 244 1282 723074056 723075095 0.000000e+00 1692.0
5 TraesCS7A01G548600 chr7A 99.626 803 3 0 1291 2093 700033166 700032364 0.000000e+00 1467.0
6 TraesCS7A01G548600 chr7A 93.750 176 10 1 991 1165 722792899 722793074 1.770000e-66 263.0
7 TraesCS7A01G548600 chr7A 100.000 123 0 0 1 123 722935638 722935760 6.470000e-56 228.0
8 TraesCS7A01G548600 chr7A 98.374 123 2 0 1 123 723029980 723030102 1.400000e-52 217.0
9 TraesCS7A01G548600 chr7A 95.122 123 6 0 1 123 722987182 722987304 6.560000e-46 195.0
10 TraesCS7A01G548600 chr7A 95.122 123 6 0 1 123 723073908 723074030 6.560000e-46 195.0
11 TraesCS7A01G548600 chr7A 92.537 67 4 1 256 322 723081262 723081327 6.850000e-16 95.3
12 TraesCS7A01G548600 chr2B 99.518 1038 5 0 1290 2327 296003621 296002584 0.000000e+00 1890.0
13 TraesCS7A01G548600 chr2B 99.538 650 3 0 1678 2327 8431317 8430668 0.000000e+00 1184.0
14 TraesCS7A01G548600 chr2B 99.385 650 4 0 1678 2327 232268240 232268889 0.000000e+00 1179.0
15 TraesCS7A01G548600 chr2B 98.923 650 7 0 1678 2327 49598104 49597455 0.000000e+00 1162.0
16 TraesCS7A01G548600 chr2B 99.169 361 3 0 1291 1651 232267358 232267718 0.000000e+00 651.0
17 TraesCS7A01G548600 chr2A 99.385 650 4 0 1678 2327 59645006 59645655 0.000000e+00 1179.0
18 TraesCS7A01G548600 chrUn 99.231 650 4 1 1678 2327 301369273 301368625 0.000000e+00 1171.0
19 TraesCS7A01G548600 chr6B 99.077 650 6 0 1678 2327 708465654 708465005 0.000000e+00 1168.0
20 TraesCS7A01G548600 chr6B 98.061 361 7 0 1291 1651 708469705 708469345 1.520000e-176 628.0
21 TraesCS7A01G548600 chr5B 98.923 650 5 1 1678 2327 13749841 13750488 0.000000e+00 1160.0
22 TraesCS7A01G548600 chr7B 87.201 586 68 7 255 836 728012050 728012632 0.000000e+00 660.0
23 TraesCS7A01G548600 chr7B 93.352 361 10 1 922 1282 728012766 728013112 2.650000e-144 521.0
24 TraesCS7A01G548600 chr7B 82.664 548 86 7 251 794 728029317 728029859 5.820000e-131 477.0
25 TraesCS7A01G548600 chr7B 82.065 552 82 9 243 779 728052945 728053494 2.730000e-124 455.0
26 TraesCS7A01G548600 chr7B 91.284 218 12 5 949 1165 728005673 728005884 8.130000e-75 291.0
27 TraesCS7A01G548600 chr7B 91.791 134 11 0 1148 1281 728005896 728006029 1.100000e-43 187.0
28 TraesCS7A01G548600 chr4A 98.892 361 4 0 1291 1651 731009369 731009729 0.000000e+00 645.0
29 TraesCS7A01G548600 chr6A 93.352 361 24 0 1291 1651 90310881 90310521 3.400000e-148 534.0
30 TraesCS7A01G548600 chr7D 95.294 340 9 4 922 1261 627305107 627305439 1.220000e-147 532.0
31 TraesCS7A01G548600 chr7D 95.862 290 12 0 1291 1580 19180769 19180480 9.730000e-129 470.0
32 TraesCS7A01G548600 chr7D 87.821 312 37 1 528 838 627304664 627304975 4.730000e-97 364.0
33 TraesCS7A01G548600 chr7D 96.023 176 6 1 991 1165 627298350 627298525 3.780000e-73 285.0
34 TraesCS7A01G548600 chr3D 88.618 369 36 6 1288 1651 14953505 14953872 5.900000e-121 444.0
35 TraesCS7A01G548600 chr3D 95.849 265 10 1 1388 1651 519347627 519347363 5.940000e-116 427.0
36 TraesCS7A01G548600 chr3D 95.890 73 3 0 1 73 556989451 556989379 4.060000e-23 119.0
37 TraesCS7A01G548600 chr6D 94.382 178 8 2 1291 1467 472747531 472747355 2.950000e-69 272.0
38 TraesCS7A01G548600 chr6D 94.667 75 3 1 1 75 188421710 188421637 5.250000e-22 115.0
39 TraesCS7A01G548600 chr5D 94.737 76 4 0 1 76 35808549 35808474 4.060000e-23 119.0
40 TraesCS7A01G548600 chr5D 94.667 75 4 0 1 75 351413065 351413139 1.460000e-22 117.0
41 TraesCS7A01G548600 chr2D 94.737 76 4 0 1 76 622224074 622223999 4.060000e-23 119.0
42 TraesCS7A01G548600 chr1D 94.595 74 4 0 1 74 474940385 474940458 5.250000e-22 115.0


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 TraesCS7A01G548600 chr7A 722935638 722937964 2326 False 2083.0 3938 100.0000 1 2327 2 chr7A.!!$F4 2326
1 TraesCS7A01G548600 chr7A 722897846 722898870 1024 False 1794.0 1794 98.2440 266 1290 1 chr7A.!!$F2 1024
2 TraesCS7A01G548600 chr7A 700032364 700033166 802 True 1467.0 1467 99.6260 1291 2093 1 chr7A.!!$R1 802
3 TraesCS7A01G548600 chr7A 723029980 723031224 1244 False 1095.0 1973 98.7760 1 1290 2 chr7A.!!$F6 1289
4 TraesCS7A01G548600 chr7A 722987182 722988381 1199 False 967.5 1740 95.8945 1 1290 2 chr7A.!!$F5 1289
5 TraesCS7A01G548600 chr7A 723073908 723075095 1187 False 943.5 1692 95.5955 1 1282 2 chr7A.!!$F7 1281
6 TraesCS7A01G548600 chr2B 296002584 296003621 1037 True 1890.0 1890 99.5180 1290 2327 1 chr2B.!!$R3 1037
7 TraesCS7A01G548600 chr2B 8430668 8431317 649 True 1184.0 1184 99.5380 1678 2327 1 chr2B.!!$R1 649
8 TraesCS7A01G548600 chr2B 49597455 49598104 649 True 1162.0 1162 98.9230 1678 2327 1 chr2B.!!$R2 649
9 TraesCS7A01G548600 chr2B 232267358 232268889 1531 False 915.0 1179 99.2770 1291 2327 2 chr2B.!!$F1 1036
10 TraesCS7A01G548600 chr2A 59645006 59645655 649 False 1179.0 1179 99.3850 1678 2327 1 chr2A.!!$F1 649
11 TraesCS7A01G548600 chrUn 301368625 301369273 648 True 1171.0 1171 99.2310 1678 2327 1 chrUn.!!$R1 649
12 TraesCS7A01G548600 chr6B 708465005 708469705 4700 True 898.0 1168 98.5690 1291 2327 2 chr6B.!!$R1 1036
13 TraesCS7A01G548600 chr5B 13749841 13750488 647 False 1160.0 1160 98.9230 1678 2327 1 chr5B.!!$F1 649
14 TraesCS7A01G548600 chr7B 728012050 728013112 1062 False 590.5 660 90.2765 255 1282 2 chr7B.!!$F4 1027
15 TraesCS7A01G548600 chr7B 728029317 728029859 542 False 477.0 477 82.6640 251 794 1 chr7B.!!$F1 543
16 TraesCS7A01G548600 chr7B 728052945 728053494 549 False 455.0 455 82.0650 243 779 1 chr7B.!!$F2 536
17 TraesCS7A01G548600 chr7D 627304664 627305439 775 False 448.0 532 91.5575 528 1261 2 chr7D.!!$F2 733

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
988 1055 1.03703 CAGCCACAACACACAACCCT 61.037 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 6004 0.321653 AGCGCCACGAAGAGGAAAAT 60.322 50.0 2.29 0.0 42.26 1.82 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
536 540 1.310904 CCCGAAAAACTTCCGTCCAA 58.689 50.000 0.00 0.0 0.00 3.53
616 621 4.326548 GCATATTAGAACCCTTCGCGATAC 59.673 45.833 10.88 0.0 34.02 2.24
815 830 2.481952 GCAAAGCTTACACTCTCCACAG 59.518 50.000 0.00 0.0 0.00 3.66
988 1055 1.037030 CAGCCACAACACACAACCCT 61.037 55.000 0.00 0.0 0.00 4.34
1186 1253 4.715130 TAGGGCCTGACGGGTGCT 62.715 66.667 18.53 0.0 37.43 4.40
1705 5436 3.245766 CCTTTCCCTTCTCATTCCCCTTT 60.246 47.826 0.00 0.0 0.00 3.11
2273 6004 2.243478 ACAGAGATCTCAGGAGGCTACA 59.757 50.000 24.39 0.0 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.619074 GGGTTTTGAGGCTATCAGCAGT 60.619 50.000 0.00 0.0 44.75 4.40
69 70 2.781431 ATTTTCCACTCGGCCCCACC 62.781 60.000 0.00 0.0 0.00 4.61
616 621 1.743394 GGCCGGACTTTGTAATCTTGG 59.257 52.381 5.05 0.0 0.00 3.61
815 830 3.057019 TCATTCATATTAGTGTCGCCGC 58.943 45.455 0.00 0.0 0.00 6.53
988 1055 2.513753 GGTCATCATGTTGTGGGTTCA 58.486 47.619 3.76 0.0 0.00 3.18
1239 1306 4.063967 CTGCGGTCCGTGTGGCTA 62.064 66.667 13.94 0.0 34.14 3.93
1386 1453 2.159142 CGGTCCTATAAAACAGGCTCGT 60.159 50.000 0.00 0.0 32.82 4.18
2273 6004 0.321653 AGCGCCACGAAGAGGAAAAT 60.322 50.000 2.29 0.0 42.26 1.82


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

AutoCloner maintained by Alex Coulton.