Multiple sequence alignment - TraesCS1D01G039700

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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 TraesCS1D01G039700 chr1D 100.000 2207 0 0 1 2207 19138068 19135862 0.000000e+00 4076.0
1 TraesCS1D01G039700 chr1D 95.652 46 2 0 1218 1263 361153773 361153728 8.450000e-10 75.0
2 TraesCS1D01G039700 chr1D 90.909 55 4 1 1210 1263 367401656 367401602 3.040000e-09 73.1
3 TraesCS1D01G039700 chr1D 95.349 43 1 1 1218 1259 467535518 467535560 1.410000e-07 67.6
4 TraesCS1D01G039700 chr1B 96.751 831 26 1 1377 2207 28586028 28585199 0.000000e+00 1384.0
5 TraesCS1D01G039700 chr1B 88.723 736 31 12 503 1208 28586921 28586208 0.000000e+00 852.0
6 TraesCS1D01G039700 chr1B 91.485 505 28 6 2 505 28589690 28589200 0.000000e+00 680.0
7 TraesCS1D01G039700 chr1B 90.179 112 7 3 1267 1378 28586186 28586079 2.280000e-30 143.0
8 TraesCS1D01G039700 chr1B 87.500 56 3 2 1211 1263 15143694 15143640 6.580000e-06 62.1
9 TraesCS1D01G039700 chr1A 92.381 945 49 4 1262 2206 20984712 20983791 0.000000e+00 1325.0
10 TraesCS1D01G039700 chr1A 91.346 520 30 6 337 855 20985699 20985194 0.000000e+00 697.0
11 TraesCS1D01G039700 chr1A 91.774 389 16 6 825 1209 20985186 20984810 5.400000e-146 527.0
12 TraesCS1D01G039700 chr1A 87.474 479 27 14 2 470 20986275 20985820 2.510000e-144 521.0
13 TraesCS1D01G039700 chr1A 87.500 56 3 2 1210 1263 186994645 186994592 6.580000e-06 62.1
14 TraesCS1D01G039700 chr2A 82.434 797 136 4 1412 2206 12073186 12072392 0.000000e+00 693.0
15 TraesCS1D01G039700 chr2A 80.812 813 152 4 1396 2206 12048311 12047501 3.090000e-178 634.0
16 TraesCS1D01G039700 chr2A 80.443 813 155 4 1396 2206 12103019 12102209 3.110000e-173 617.0
17 TraesCS1D01G039700 chr2A 85.027 187 28 0 1020 1206 684392318 684392504 8.040000e-45 191.0
18 TraesCS1D01G039700 chr2D 80.812 813 152 4 1396 2206 11509627 11508817 3.090000e-178 634.0
19 TraesCS1D01G039700 chr2D 80.713 814 151 4 1396 2206 11477720 11476910 1.440000e-176 628.0
20 TraesCS1D01G039700 chr2D 84.343 198 31 0 1008 1205 13421442 13421639 6.220000e-46 195.0
21 TraesCS1D01G039700 chr2B 80.196 818 154 7 1393 2206 792486599 792487412 6.740000e-170 606.0
22 TraesCS1D01G039700 chr2B 80.074 813 158 4 1396 2206 17873742 17872932 3.140000e-168 601.0
23 TraesCS1D01G039700 chr2B 84.574 188 29 0 1017 1204 24089541 24089728 1.040000e-43 187.0
24 TraesCS1D01G039700 chr2B 84.492 187 29 0 1020 1206 646591999 646592185 3.740000e-43 185.0
25 TraesCS1D01G039700 chr7B 86.957 161 21 0 1045 1205 719122399 719122239 4.840000e-42 182.0
26 TraesCS1D01G039700 chr5D 83.854 192 28 3 1020 1210 523939958 523939769 1.740000e-41 180.0
27 TraesCS1D01G039700 chr5D 83.854 192 28 3 1020 1210 523993795 523993606 1.740000e-41 180.0
28 TraesCS1D01G039700 chr6B 93.333 45 2 1 1223 1267 706325451 706325408 5.090000e-07 65.8
29 TraesCS1D01G039700 chr5B 90.196 51 4 1 1218 1267 311079328 311079278 5.090000e-07 65.8
30 TraesCS1D01G039700 chrUn 88.462 52 6 0 1216 1267 307259635 307259686 1.830000e-06 63.9
31 TraesCS1D01G039700 chr4A 91.304 46 4 0 1218 1263 586504186 586504231 1.830000e-06 63.9


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 TraesCS1D01G039700 chr1D 19135862 19138068 2206 True 4076.00 4076 100.00000 1 2207 1 chr1D.!!$R1 2206
1 TraesCS1D01G039700 chr1B 28585199 28589690 4491 True 764.75 1384 91.78450 2 2207 4 chr1B.!!$R2 2205
2 TraesCS1D01G039700 chr1A 20983791 20986275 2484 True 767.50 1325 90.74375 2 2206 4 chr1A.!!$R2 2204
3 TraesCS1D01G039700 chr2A 12072392 12073186 794 True 693.00 693 82.43400 1412 2206 1 chr2A.!!$R2 794
4 TraesCS1D01G039700 chr2A 12047501 12048311 810 True 634.00 634 80.81200 1396 2206 1 chr2A.!!$R1 810
5 TraesCS1D01G039700 chr2A 12102209 12103019 810 True 617.00 617 80.44300 1396 2206 1 chr2A.!!$R3 810
6 TraesCS1D01G039700 chr2D 11508817 11509627 810 True 634.00 634 80.81200 1396 2206 1 chr2D.!!$R2 810
7 TraesCS1D01G039700 chr2D 11476910 11477720 810 True 628.00 628 80.71300 1396 2206 1 chr2D.!!$R1 810
8 TraesCS1D01G039700 chr2B 792486599 792487412 813 False 606.00 606 80.19600 1393 2206 1 chr2B.!!$F3 813
9 TraesCS1D01G039700 chr2B 17872932 17873742 810 True 601.00 601 80.07400 1396 2206 1 chr2B.!!$R1 810

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
172 174 2.839975 TGCGGTTATTGAACTGTGTCA 58.16 42.857 0.0 0.0 42.98 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 4107 0.389817 TATCGCCTGCACACACTCAC 60.39 55.0 0.0 0.0 0.0 3.51 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
133 135 6.124340 ACCACAAAGATCTCATGATTGCATA 58.876 36.000 13.72 0.00 32.27 3.14
171 173 3.889196 TTGCGGTTATTGAACTGTGTC 57.111 42.857 0.00 0.00 42.98 3.67
172 174 2.839975 TGCGGTTATTGAACTGTGTCA 58.160 42.857 0.00 0.00 42.98 3.58
342 352 9.703892 AAGCATAAAACAAAGCATGTATTACAA 57.296 25.926 0.00 0.00 42.99 2.41
343 353 9.139174 AGCATAAAACAAAGCATGTATTACAAC 57.861 29.630 0.00 0.00 42.99 3.32
365 375 5.548406 ACCATACTCTACCAACAGTTGAAC 58.452 41.667 15.36 0.00 29.54 3.18
374 384 3.632145 ACCAACAGTTGAACTAAAGCCAG 59.368 43.478 15.36 0.00 0.00 4.85
375 385 3.882888 CCAACAGTTGAACTAAAGCCAGA 59.117 43.478 15.36 0.00 0.00 3.86
505 3050 4.267536 TGCTTCAAGAGAGCTATTTGCAT 58.732 39.130 0.00 0.00 45.94 3.96
685 3230 5.438761 TTTAAGTTGAGAAGCTTTCCTGC 57.561 39.130 0.00 0.00 0.00 4.85
710 3257 5.426689 ACACATAGAGAAAAGCATCCTGA 57.573 39.130 0.00 0.00 0.00 3.86
790 3356 6.598457 CAGATGAATTGTCCTCTTGATCAAGT 59.402 38.462 29.80 12.21 39.38 3.16
883 3485 5.163364 CCGCTAGCTCATATGGAATATCCTT 60.163 44.000 13.93 0.00 37.44 3.36
899 3501 4.785346 ATCCTTCTCGTACCTGGTACTA 57.215 45.455 28.89 20.12 36.93 1.82
900 3502 3.878778 TCCTTCTCGTACCTGGTACTAC 58.121 50.000 28.89 11.22 36.93 2.73
901 3503 3.521126 TCCTTCTCGTACCTGGTACTACT 59.479 47.826 28.89 0.00 36.93 2.57
902 3504 3.626670 CCTTCTCGTACCTGGTACTACTG 59.373 52.174 28.89 16.63 36.93 2.74
903 3505 3.988976 TCTCGTACCTGGTACTACTGT 57.011 47.619 28.89 0.00 36.93 3.55
904 3506 5.420725 TTCTCGTACCTGGTACTACTGTA 57.579 43.478 28.89 11.00 36.93 2.74
905 3507 5.620738 TCTCGTACCTGGTACTACTGTAT 57.379 43.478 28.89 0.00 36.93 2.29
906 3508 6.731292 TCTCGTACCTGGTACTACTGTATA 57.269 41.667 28.89 8.04 36.93 1.47
907 3509 7.308450 TCTCGTACCTGGTACTACTGTATAT 57.692 40.000 28.89 0.00 36.93 0.86
908 3510 8.422577 TCTCGTACCTGGTACTACTGTATATA 57.577 38.462 28.89 5.50 36.93 0.86
909 3511 9.040259 TCTCGTACCTGGTACTACTGTATATAT 57.960 37.037 28.89 0.00 36.93 0.86
1040 3666 4.083862 GGTGACGGTGGAGGAGGC 62.084 72.222 0.00 0.00 0.00 4.70
1050 3676 3.157252 GAGGAGGCGATGAGGGCA 61.157 66.667 0.00 0.00 34.40 5.36
1178 3804 2.179517 GCACCTCGTCGACCTCAG 59.820 66.667 10.58 3.41 0.00 3.35
1213 3839 7.546316 TCAAGCGCATGTGTAAGTAGTATTTTA 59.454 33.333 11.47 0.00 0.00 1.52
1216 3842 9.537192 AGCGCATGTGTAAGTAGTATTTTATTA 57.463 29.630 11.47 0.00 0.00 0.98
1255 3909 7.941795 AAACGTTCTTATATTATGAGACGGG 57.058 36.000 0.00 6.68 0.00 5.28
1257 3911 5.047519 ACGTTCTTATATTATGAGACGGGGG 60.048 44.000 16.71 3.92 0.00 5.40
1258 3912 5.184479 CGTTCTTATATTATGAGACGGGGGA 59.816 44.000 0.00 0.00 0.00 4.81
1260 3914 6.852420 TCTTATATTATGAGACGGGGGAAG 57.148 41.667 0.00 0.00 0.00 3.46
1264 3935 8.495160 TTATATTATGAGACGGGGGAAGTAAA 57.505 34.615 0.00 0.00 0.00 2.01
1348 4019 3.129852 CATGCAATGCAATGCTTTTGG 57.870 42.857 26.10 6.23 46.54 3.28
1349 4020 2.257691 TGCAATGCAATGCTTTTGGT 57.742 40.000 26.10 0.00 46.54 3.67
1350 4021 2.573369 TGCAATGCAATGCTTTTGGTT 58.427 38.095 26.10 0.00 46.54 3.67
1351 4022 2.548904 TGCAATGCAATGCTTTTGGTTC 59.451 40.909 26.10 0.00 46.54 3.62
1352 4023 2.095617 GCAATGCAATGCTTTTGGTTCC 60.096 45.455 19.55 3.61 43.06 3.62
1353 4024 2.083167 ATGCAATGCTTTTGGTTCCG 57.917 45.000 6.82 0.00 0.00 4.30
1354 4025 0.599728 TGCAATGCTTTTGGTTCCGC 60.600 50.000 6.82 0.00 0.00 5.54
1355 4026 0.599728 GCAATGCTTTTGGTTCCGCA 60.600 50.000 0.00 0.00 36.75 5.69
1379 4102 7.464977 GCAAAATGGATGCTTTTGACATGTATC 60.465 37.037 18.77 0.00 43.18 2.24
1384 4107 4.418013 TGCTTTTGACATGTATCAACGG 57.582 40.909 0.00 0.00 38.31 4.44
1390 4113 3.584834 TGACATGTATCAACGGTGAGTG 58.415 45.455 9.97 7.78 37.14 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.804748 GCTTTTCCGGTTGGTGACTAG 59.195 52.381 0.00 0.00 36.30 2.57
133 135 7.996098 ACCGCAAATTAAGCCTAATATATGT 57.004 32.000 0.00 0.00 0.00 2.29
171 173 9.128107 GGCGAATTATAAAATAATCACACCATG 57.872 33.333 0.00 0.00 0.00 3.66
172 174 8.020819 CGGCGAATTATAAAATAATCACACCAT 58.979 33.333 0.00 0.00 0.00 3.55
342 352 5.307196 AGTTCAACTGTTGGTAGAGTATGGT 59.693 40.000 19.55 0.00 0.00 3.55
343 353 5.794894 AGTTCAACTGTTGGTAGAGTATGG 58.205 41.667 19.55 0.00 0.00 2.74
347 357 5.758784 GCTTTAGTTCAACTGTTGGTAGAGT 59.241 40.000 19.55 9.34 0.00 3.24
505 3050 5.838521 TGACACTATGGATTGGCTATGAGTA 59.161 40.000 0.00 0.00 0.00 2.59
678 3223 6.149474 GCTTTTCTCTATGTGTAAGCAGGAAA 59.851 38.462 0.00 0.00 38.23 3.13
685 3230 7.044181 TCAGGATGCTTTTCTCTATGTGTAAG 58.956 38.462 0.00 0.00 34.76 2.34
710 3257 2.679837 CAGCGTTCACCAAATCAGCTAT 59.320 45.455 0.00 0.00 31.75 2.97
883 3485 3.988976 ACAGTAGTACCAGGTACGAGA 57.011 47.619 21.96 10.39 43.05 4.04
1178 3804 1.537202 ACATGCGCTTGAACTTCTTCC 59.463 47.619 27.85 0.00 0.00 3.46
1229 3883 8.823818 CCCGTCTCATAATATAAGAACGTTTTT 58.176 33.333 9.22 9.22 0.00 1.94
1230 3884 7.440255 CCCCGTCTCATAATATAAGAACGTTTT 59.560 37.037 0.46 0.00 0.00 2.43
1235 3889 6.600882 TCCCCCGTCTCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
1238 3892 6.607004 ACTTCCCCCGTCTCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
1247 3901 4.035112 ACATATTTACTTCCCCCGTCTCA 58.965 43.478 0.00 0.00 0.00 3.27
1248 3902 4.684484 ACATATTTACTTCCCCCGTCTC 57.316 45.455 0.00 0.00 0.00 3.36
1249 3903 4.720273 AGAACATATTTACTTCCCCCGTCT 59.280 41.667 0.00 0.00 0.00 4.18
1250 3904 5.032327 AGAACATATTTACTTCCCCCGTC 57.968 43.478 0.00 0.00 0.00 4.79
1253 3907 5.593095 GGTGAAGAACATATTTACTTCCCCC 59.407 44.000 0.00 0.00 38.22 5.40
1254 3908 6.184789 TGGTGAAGAACATATTTACTTCCCC 58.815 40.000 0.00 0.00 37.40 4.81
1255 3909 7.696992 TTGGTGAAGAACATATTTACTTCCC 57.303 36.000 0.00 0.00 38.22 3.97
1257 3911 8.243426 TGCATTGGTGAAGAACATATTTACTTC 58.757 33.333 0.00 0.00 39.08 3.01
1258 3912 8.121305 TGCATTGGTGAAGAACATATTTACTT 57.879 30.769 0.00 0.00 0.00 2.24
1260 3914 7.043192 GCATGCATTGGTGAAGAACATATTTAC 60.043 37.037 14.21 0.00 0.00 2.01
1264 3935 4.403113 TGCATGCATTGGTGAAGAACATAT 59.597 37.500 18.46 0.00 0.00 1.78
1338 4009 2.611225 TTTGCGGAACCAAAAGCATT 57.389 40.000 0.00 0.00 39.50 3.56
1342 4013 3.104843 TCCATTTTGCGGAACCAAAAG 57.895 42.857 6.29 0.39 44.89 2.27
1343 4014 3.397482 CATCCATTTTGCGGAACCAAAA 58.603 40.909 0.00 2.98 45.50 2.44
1344 4015 2.869636 GCATCCATTTTGCGGAACCAAA 60.870 45.455 0.00 0.00 35.77 3.28
1347 4018 0.532115 AGCATCCATTTTGCGGAACC 59.468 50.000 0.00 0.00 44.82 3.62
1348 4019 2.368655 AAGCATCCATTTTGCGGAAC 57.631 45.000 0.00 0.00 44.82 3.62
1349 4020 3.065655 CAAAAGCATCCATTTTGCGGAA 58.934 40.909 0.00 0.00 44.82 4.30
1350 4021 2.298446 TCAAAAGCATCCATTTTGCGGA 59.702 40.909 6.33 0.00 43.90 5.54
1351 4022 2.412770 GTCAAAAGCATCCATTTTGCGG 59.587 45.455 6.33 0.00 43.90 5.69
1352 4023 3.058450 TGTCAAAAGCATCCATTTTGCG 58.942 40.909 6.33 0.00 43.90 4.85
1353 4024 4.453136 ACATGTCAAAAGCATCCATTTTGC 59.547 37.500 0.00 0.00 43.90 3.68
1354 4025 7.546316 TGATACATGTCAAAAGCATCCATTTTG 59.454 33.333 0.00 5.09 45.01 2.44
1355 4026 7.613585 TGATACATGTCAAAAGCATCCATTTT 58.386 30.769 0.00 0.00 0.00 1.82
1379 4102 1.643292 CTGCACACACTCACCGTTG 59.357 57.895 0.00 0.00 0.00 4.10
1384 4107 0.389817 TATCGCCTGCACACACTCAC 60.390 55.000 0.00 0.00 0.00 3.51
1390 4113 1.999051 CGAGTTATCGCCTGCACAC 59.001 57.895 0.00 0.00 42.97 3.82
1550 4273 1.472376 CCACTCCTTGATCGCCTTCTC 60.472 57.143 0.00 0.00 0.00 2.87
1675 4398 3.838271 ATGACGCGCCTCACCGAT 61.838 61.111 11.35 0.00 0.00 4.18
1783 4506 0.665298 CGATGATCTCCGAGCAGACA 59.335 55.000 0.00 0.00 29.44 3.41


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

AutoCloner maintained by Alex Coulton.