Multiple sequence alignment - TraesCS1D01G318700

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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 TraesCS1D01G318700 chr1D 100.000 3144 0 0 1 3144 413060694 413063837 0.000000e+00 5806
1 TraesCS1D01G318700 chr1D 86.986 1629 115 42 732 2289 412641928 412643530 0.000000e+00 1744
2 TraesCS1D01G318700 chr1D 86.986 1629 115 42 732 2289 412745906 412747508 0.000000e+00 1744
3 TraesCS1D01G318700 chr1D 86.986 1629 115 42 732 2289 412763069 412764671 0.000000e+00 1744
4 TraesCS1D01G318700 chr1D 89.104 1294 85 25 1018 2281 412897788 412899055 0.000000e+00 1557
5 TraesCS1D01G318700 chr1D 88.889 1296 84 28 1018 2281 412684094 412685361 0.000000e+00 1541
6 TraesCS1D01G318700 chr1D 89.072 1272 86 28 1042 2281 412814479 412815729 0.000000e+00 1530
7 TraesCS1D01G318700 chr1D 85.823 1185 122 28 990 2131 412507211 412508392 0.000000e+00 1216
8 TraesCS1D01G318700 chr1D 91.436 759 48 10 1522 2274 412855325 412856072 0.000000e+00 1026
9 TraesCS1D01G318700 chr1D 90.722 388 29 4 589 972 412897318 412897702 7.780000e-141 510
10 TraesCS1D01G318700 chr1D 91.061 358 28 3 589 942 412683612 412683969 6.100000e-132 481
11 TraesCS1D01G318700 chr1D 91.798 317 21 2 658 972 412814077 412814390 1.340000e-118 436
12 TraesCS1D01G318700 chr1A 96.205 3057 89 14 26 3063 510184195 510187243 0.000000e+00 4977
13 TraesCS1D01G318700 chr1A 95.951 2297 68 17 1 2289 509494617 509492338 0.000000e+00 3703
14 TraesCS1D01G318700 chr1A 87.366 1591 128 49 732 2274 509720185 509718620 0.000000e+00 1757
15 TraesCS1D01G318700 chr1A 87.241 1591 130 48 732 2274 509793565 509792000 0.000000e+00 1746
16 TraesCS1D01G318700 chr1A 88.638 1285 108 25 1018 2281 509914760 509913493 0.000000e+00 1530
17 TraesCS1D01G318700 chr4B 89.744 1443 100 27 732 2144 633465802 633467226 0.000000e+00 1801
18 TraesCS1D01G318700 chr4B 89.320 1442 108 28 732 2144 633398670 633400094 0.000000e+00 1768
19 TraesCS1D01G318700 chr1B 87.810 1575 124 42 738 2269 556064578 556063029 0.000000e+00 1783
20 TraesCS1D01G318700 chr1B 91.468 1008 55 18 618 1612 556965929 556966918 0.000000e+00 1356
21 TraesCS1D01G318700 chr1B 88.054 1105 85 28 1196 2281 556834311 556835387 0.000000e+00 1266
22 TraesCS1D01G318700 chr1B 88.054 1105 85 28 1196 2281 556862732 556863808 0.000000e+00 1266
23 TraesCS1D01G318700 chr1B 91.658 947 26 20 2174 3089 556971236 556972160 0.000000e+00 1262
24 TraesCS1D01G318700 chr1B 93.401 591 35 4 1 589 596471590 596471002 0.000000e+00 872
25 TraesCS1D01G318700 chr1B 88.581 578 44 12 585 1151 556833743 556834309 0.000000e+00 682
26 TraesCS1D01G318700 chr1B 88.581 578 44 12 585 1151 556862164 556862730 0.000000e+00 682
27 TraesCS1D01G318700 chr1B 92.308 390 28 1 585 974 556968966 556969353 1.270000e-153 553
28 TraesCS1D01G318700 chr5B 91.201 591 47 5 1 587 377119100 377119689 0.000000e+00 798
29 TraesCS1D01G318700 chr2B 90.579 605 48 7 1 599 229186524 229185923 0.000000e+00 793
30 TraesCS1D01G318700 chr7D 90.345 580 50 4 1 578 520394548 520395123 0.000000e+00 756
31 TraesCS1D01G318700 chr2A 89.696 592 50 10 1 587 84363358 84362773 0.000000e+00 745
32 TraesCS1D01G318700 chr6D 81.058 586 104 5 9 589 458604739 458605322 7.950000e-126 460
33 TraesCS1D01G318700 chrUn 80.844 569 97 11 32 593 111150108 111150671 1.340000e-118 436


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 TraesCS1D01G318700 chr1D 413060694 413063837 3143 False 5806.0 5806 100.000000 1 3144 1 chr1D.!!$F6 3143
1 TraesCS1D01G318700 chr1D 412641928 412643530 1602 False 1744.0 1744 86.986000 732 2289 1 chr1D.!!$F2 1557
2 TraesCS1D01G318700 chr1D 412745906 412747508 1602 False 1744.0 1744 86.986000 732 2289 1 chr1D.!!$F3 1557
3 TraesCS1D01G318700 chr1D 412763069 412764671 1602 False 1744.0 1744 86.986000 732 2289 1 chr1D.!!$F4 1557
4 TraesCS1D01G318700 chr1D 412507211 412508392 1181 False 1216.0 1216 85.823000 990 2131 1 chr1D.!!$F1 1141
5 TraesCS1D01G318700 chr1D 412897318 412899055 1737 False 1033.5 1557 89.913000 589 2281 2 chr1D.!!$F9 1692
6 TraesCS1D01G318700 chr1D 412855325 412856072 747 False 1026.0 1026 91.436000 1522 2274 1 chr1D.!!$F5 752
7 TraesCS1D01G318700 chr1D 412683612 412685361 1749 False 1011.0 1541 89.975000 589 2281 2 chr1D.!!$F7 1692
8 TraesCS1D01G318700 chr1D 412814077 412815729 1652 False 983.0 1530 90.435000 658 2281 2 chr1D.!!$F8 1623
9 TraesCS1D01G318700 chr1A 510184195 510187243 3048 False 4977.0 4977 96.205000 26 3063 1 chr1A.!!$F1 3037
10 TraesCS1D01G318700 chr1A 509492338 509494617 2279 True 3703.0 3703 95.951000 1 2289 1 chr1A.!!$R1 2288
11 TraesCS1D01G318700 chr1A 509718620 509720185 1565 True 1757.0 1757 87.366000 732 2274 1 chr1A.!!$R2 1542
12 TraesCS1D01G318700 chr1A 509792000 509793565 1565 True 1746.0 1746 87.241000 732 2274 1 chr1A.!!$R3 1542
13 TraesCS1D01G318700 chr1A 509913493 509914760 1267 True 1530.0 1530 88.638000 1018 2281 1 chr1A.!!$R4 1263
14 TraesCS1D01G318700 chr4B 633465802 633467226 1424 False 1801.0 1801 89.744000 732 2144 1 chr4B.!!$F2 1412
15 TraesCS1D01G318700 chr4B 633398670 633400094 1424 False 1768.0 1768 89.320000 732 2144 1 chr4B.!!$F1 1412
16 TraesCS1D01G318700 chr1B 556063029 556064578 1549 True 1783.0 1783 87.810000 738 2269 1 chr1B.!!$R1 1531
17 TraesCS1D01G318700 chr1B 556965929 556972160 6231 False 1057.0 1356 91.811333 585 3089 3 chr1B.!!$F3 2504
18 TraesCS1D01G318700 chr1B 556833743 556835387 1644 False 974.0 1266 88.317500 585 2281 2 chr1B.!!$F1 1696
19 TraesCS1D01G318700 chr1B 556862164 556863808 1644 False 974.0 1266 88.317500 585 2281 2 chr1B.!!$F2 1696
20 TraesCS1D01G318700 chr1B 596471002 596471590 588 True 872.0 872 93.401000 1 589 1 chr1B.!!$R2 588
21 TraesCS1D01G318700 chr5B 377119100 377119689 589 False 798.0 798 91.201000 1 587 1 chr5B.!!$F1 586
22 TraesCS1D01G318700 chr2B 229185923 229186524 601 True 793.0 793 90.579000 1 599 1 chr2B.!!$R1 598
23 TraesCS1D01G318700 chr7D 520394548 520395123 575 False 756.0 756 90.345000 1 578 1 chr7D.!!$F1 577
24 TraesCS1D01G318700 chr2A 84362773 84363358 585 True 745.0 745 89.696000 1 587 1 chr2A.!!$R1 586
25 TraesCS1D01G318700 chr6D 458604739 458605322 583 False 460.0 460 81.058000 9 589 1 chr6D.!!$F1 580
26 TraesCS1D01G318700 chrUn 111150108 111150671 563 False 436.0 436 80.844000 32 593 1 chrUn.!!$F1 561

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
89 90 0.322187 GGAAGCCGCCCAACTCTAAA 60.322 55.0 0.00 0.0 0.00 1.85 F
1191 1271 0.982852 TCCTCCGGATGCACTTCCAT 60.983 55.0 3.57 0.0 35.34 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 1488 3.706373 GCGGCCTTCACCCTCTCA 61.706 66.667 0.00 0.00 0.00 3.27 R
2727 6923 1.062525 GATCGATGGCGCCAACAAC 59.937 57.895 36.33 22.55 37.46 3.32 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
28 29 1.182667 GGTAAACAAGTGATGGGGGC 58.817 55.000 0.00 0.00 0.00 5.80
87 88 1.485294 TTGGAAGCCGCCCAACTCTA 61.485 55.000 0.00 0.00 38.64 2.43
89 90 0.322187 GGAAGCCGCCCAACTCTAAA 60.322 55.000 0.00 0.00 0.00 1.85
113 118 5.991328 TCTTCAAGATTAATGTCGATGCC 57.009 39.130 0.00 0.00 0.00 4.40
273 278 4.157246 TGGCCTGTATATCGGTATCACTT 58.843 43.478 3.32 0.00 0.00 3.16
420 425 6.542821 ACTGGTGAAGTTTCAGATATCCAAA 58.457 36.000 0.00 0.00 37.98 3.28
477 483 5.779806 TTGCTAAGCTCAGTTTCGATAAC 57.220 39.130 0.00 0.00 0.00 1.89
1191 1271 0.982852 TCCTCCGGATGCACTTCCAT 60.983 55.000 3.57 0.00 35.34 3.41
1211 1291 1.899814 TGACTGCTTCGTCAGGGTAAT 59.100 47.619 6.93 0.00 38.89 1.89
1678 2112 2.507992 CTCACCCAGCTCTTCGCG 60.508 66.667 0.00 0.00 45.59 5.87
2249 6440 6.326064 TCATTTCTCCCCAAAATCTTTGTTCA 59.674 34.615 0.00 0.00 0.00 3.18
2331 6523 9.056005 TCATATATAAACACTGTCATTTCAGCC 57.944 33.333 0.00 0.00 38.84 4.85
2439 6631 3.003275 ACAAAGTTGGTACGCACATCAAG 59.997 43.478 0.00 0.00 0.00 3.02
2742 6938 1.442520 CTTGTTGTTGGCGCCATCG 60.443 57.895 33.25 12.39 39.07 3.84
2743 6939 1.851021 CTTGTTGTTGGCGCCATCGA 61.851 55.000 33.25 26.49 38.10 3.59
2954 7176 2.124695 GAGAACATCCCCCGCCAC 60.125 66.667 0.00 0.00 0.00 5.01
2986 7209 2.381961 TGGCCAAAATTCTAGTTCCCCT 59.618 45.455 0.61 0.00 0.00 4.79
3037 7263 8.391075 TGTCTTATTAGGTCTTTTGGAAGTTG 57.609 34.615 0.00 0.00 34.41 3.16
3113 7339 4.855531 GTGAATTCCACTTTTTACGCTGT 58.144 39.130 2.27 0.00 42.44 4.40
3114 7340 5.992729 GTGAATTCCACTTTTTACGCTGTA 58.007 37.500 2.27 0.00 42.44 2.74
3115 7341 6.077838 GTGAATTCCACTTTTTACGCTGTAG 58.922 40.000 2.27 0.00 42.44 2.74
3116 7342 5.761234 TGAATTCCACTTTTTACGCTGTAGT 59.239 36.000 2.27 0.00 0.00 2.73
3117 7343 6.261381 TGAATTCCACTTTTTACGCTGTAGTT 59.739 34.615 2.27 0.00 0.00 2.24
3118 7344 6.628919 ATTCCACTTTTTACGCTGTAGTTT 57.371 33.333 0.00 0.00 0.00 2.66
3119 7345 6.439675 TTCCACTTTTTACGCTGTAGTTTT 57.560 33.333 0.00 0.00 0.00 2.43
3120 7346 7.551035 TTCCACTTTTTACGCTGTAGTTTTA 57.449 32.000 0.00 0.00 0.00 1.52
3121 7347 7.733402 TCCACTTTTTACGCTGTAGTTTTAT 57.267 32.000 0.00 0.00 0.00 1.40
3122 7348 8.830201 TCCACTTTTTACGCTGTAGTTTTATA 57.170 30.769 0.00 0.00 0.00 0.98
3123 7349 9.439500 TCCACTTTTTACGCTGTAGTTTTATAT 57.561 29.630 0.00 0.00 0.00 0.86
3131 7357 7.661127 ACGCTGTAGTTTTATATTTGTGACA 57.339 32.000 0.00 0.00 0.00 3.58
3132 7358 7.515643 ACGCTGTAGTTTTATATTTGTGACAC 58.484 34.615 0.00 0.00 0.00 3.67
3133 7359 7.386848 ACGCTGTAGTTTTATATTTGTGACACT 59.613 33.333 7.20 0.00 0.00 3.55
3134 7360 8.865978 CGCTGTAGTTTTATATTTGTGACACTA 58.134 33.333 7.20 0.00 0.00 2.74
3143 7369 9.976776 TTTATATTTGTGACACTAATTACCCCA 57.023 29.630 18.21 2.60 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.466189 AGTGGTGGTTGGCTGAACTG 60.466 55.000 0.00 0.00 34.66 3.16
87 88 7.917505 GGCATCGACATTAATCTTGAAGAATTT 59.082 33.333 0.00 0.00 0.00 1.82
89 90 6.543465 TGGCATCGACATTAATCTTGAAGAAT 59.457 34.615 0.00 0.00 0.00 2.40
113 118 4.039124 ACTTTAATGGCCTCCACAAAACTG 59.961 41.667 3.32 0.00 35.80 3.16
242 247 3.493350 CGATATACAGGCCAGAAAGTGCT 60.493 47.826 5.01 0.00 0.00 4.40
273 278 4.041321 TCCAAAAATGATGGGCATGTCAAA 59.959 37.500 0.00 0.00 37.28 2.69
420 425 4.844655 ACCGTATTAGCCCTCCTATTGATT 59.155 41.667 0.00 0.00 0.00 2.57
469 475 8.204160 ACATAATTCATCAGACCTGTTATCGAA 58.796 33.333 0.00 0.00 0.00 3.71
502 509 1.063070 TAGCCACACAGGGGGAACAA 61.063 55.000 0.00 0.00 38.09 2.83
587 599 6.537355 ACGTTGGAATCTCATGATCCATATT 58.463 36.000 15.61 3.02 33.33 1.28
1366 1488 3.706373 GCGGCCTTCACCCTCTCA 61.706 66.667 0.00 0.00 0.00 3.27
2226 2926 6.745794 TGAACAAAGATTTTGGGGAGAAAT 57.254 33.333 6.51 0.00 0.00 2.17
2269 6460 3.251487 GCGGAAACTTTACAGGCTGTAAA 59.749 43.478 36.98 36.98 46.84 2.01
2348 6540 9.770503 GCATGATTGATTGCATCTACTTAATAG 57.229 33.333 0.00 0.00 38.72 1.73
2350 6542 8.173542 TGCATGATTGATTGCATCTACTTAAT 57.826 30.769 0.00 0.00 43.54 1.40
2351 6543 7.571080 TGCATGATTGATTGCATCTACTTAA 57.429 32.000 0.00 0.00 43.54 1.85
2439 6631 4.771684 GGCAACGCATGTGATGTC 57.228 55.556 14.43 9.59 0.00 3.06
2727 6923 1.062525 GATCGATGGCGCCAACAAC 59.937 57.895 36.33 22.55 37.46 3.32
2742 6938 3.686016 TGGCTTTAGGTTTGGTGAGATC 58.314 45.455 0.00 0.00 0.00 2.75
2743 6939 3.806949 TGGCTTTAGGTTTGGTGAGAT 57.193 42.857 0.00 0.00 0.00 2.75
2831 7029 6.018262 TCTCTAGGACACGTTTCATTTTTGTG 60.018 38.462 3.80 0.00 36.64 3.33
2965 7187 2.381961 AGGGGAACTAGAATTTTGGCCA 59.618 45.455 0.00 0.00 0.00 5.36
3022 7245 5.276461 ACCATTTCAACTTCCAAAAGACC 57.724 39.130 0.00 0.00 36.30 3.85
3023 7246 6.035975 CACAACCATTTCAACTTCCAAAAGAC 59.964 38.462 0.00 0.00 36.30 3.01
3037 7263 8.050778 TGTTATCAAGATACCACAACCATTTC 57.949 34.615 0.00 0.00 0.00 2.17
3091 7317 4.855531 ACAGCGTAAAAAGTGGAATTCAC 58.144 39.130 7.93 4.02 46.39 3.18
3092 7318 5.761234 ACTACAGCGTAAAAAGTGGAATTCA 59.239 36.000 7.93 0.00 0.00 2.57
3093 7319 6.237313 ACTACAGCGTAAAAAGTGGAATTC 57.763 37.500 0.00 0.00 0.00 2.17
3094 7320 6.628919 AACTACAGCGTAAAAAGTGGAATT 57.371 33.333 0.00 0.00 0.00 2.17
3095 7321 6.628919 AAACTACAGCGTAAAAAGTGGAAT 57.371 33.333 0.00 0.00 0.00 3.01
3096 7322 6.439675 AAAACTACAGCGTAAAAAGTGGAA 57.560 33.333 0.00 0.00 0.00 3.53
3097 7323 7.733402 ATAAAACTACAGCGTAAAAAGTGGA 57.267 32.000 0.00 0.00 0.00 4.02
3105 7331 9.205719 TGTCACAAATATAAAACTACAGCGTAA 57.794 29.630 0.00 0.00 0.00 3.18
3106 7332 8.649841 GTGTCACAAATATAAAACTACAGCGTA 58.350 33.333 0.00 0.00 0.00 4.42
3107 7333 7.386848 AGTGTCACAAATATAAAACTACAGCGT 59.613 33.333 5.62 0.00 0.00 5.07
3108 7334 7.739295 AGTGTCACAAATATAAAACTACAGCG 58.261 34.615 5.62 0.00 0.00 5.18
3117 7343 9.976776 TGGGGTAATTAGTGTCACAAATATAAA 57.023 29.630 5.62 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.