Multiple sequence alignment - TraesCS7D01G523300

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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 TraesCS7D01G523300 chr7D 100.000 3295 0 0 1 3295 619896178 619892884 0.000000e+00 6085.0
1 TraesCS7D01G523300 chr7D 83.175 630 67 25 1944 2561 619999370 619998768 1.040000e-149 540.0
2 TraesCS7D01G523300 chr7D 91.554 296 25 0 1526 1821 619999736 619999441 3.060000e-110 409.0
3 TraesCS7D01G523300 chr7A 92.881 2360 114 26 525 2843 715224075 715226421 0.000000e+00 3378.0
4 TraesCS7D01G523300 chr7A 93.470 536 26 6 1 531 715222368 715222899 0.000000e+00 787.0
5 TraesCS7D01G523300 chr7B 92.924 1597 82 15 227 1816 716566087 716567659 0.000000e+00 2294.0
6 TraesCS7D01G523300 chr7B 88.271 1330 103 35 505 1816 716650067 716651361 0.000000e+00 1543.0
7 TraesCS7D01G523300 chr7B 92.393 631 29 6 2671 3287 716678447 716679072 0.000000e+00 881.0
8 TraesCS7D01G523300 chr7B 89.162 692 55 11 1983 2673 716661980 716662652 0.000000e+00 845.0
9 TraesCS7D01G523300 chr7B 88.468 607 46 12 1930 2526 716651619 716652211 0.000000e+00 712.0
10 TraesCS7D01G523300 chr7B 88.303 607 47 12 1930 2526 716567917 716568509 0.000000e+00 706.0
11 TraesCS7D01G523300 chr7B 88.138 607 48 12 1930 2526 716581566 716582158 0.000000e+00 701.0
12 TraesCS7D01G523300 chr7B 94.318 176 10 0 1641 1816 716581133 716581308 1.510000e-68 270.0
13 TraesCS7D01G523300 chr4B 85.628 828 109 6 995 1813 70999392 70998566 0.000000e+00 861.0
14 TraesCS7D01G523300 chr4D 85.145 828 114 5 995 1813 48121587 48120760 0.000000e+00 839.0
15 TraesCS7D01G523300 chr4D 81.829 820 145 4 995 1813 48116899 48116083 0.000000e+00 686.0
16 TraesCS7D01G523300 chrUn 88.138 607 48 12 1930 2526 370758524 370759116 0.000000e+00 701.0
17 TraesCS7D01G523300 chrUn 87.644 607 51 12 1930 2526 224998981 224998389 0.000000e+00 684.0
18 TraesCS7D01G523300 chrUn 87.654 243 16 10 1641 1869 224999414 224999172 1.510000e-68 270.0
19 TraesCS7D01G523300 chr3D 74.515 361 92 0 1453 1813 507534972 507534612 1.220000e-34 158.0
20 TraesCS7D01G523300 chr4A 81.343 134 19 3 254 382 549920412 549920544 1.620000e-18 104.0
21 TraesCS7D01G523300 chr5D 90.909 66 5 1 268 332 485938212 485938147 1.630000e-13 87.9
22 TraesCS7D01G523300 chr2D 80.488 123 14 8 259 374 5765644 5765763 5.860000e-13 86.1
23 TraesCS7D01G523300 chr2D 82.243 107 12 5 265 365 602496617 602496722 5.860000e-13 86.1
24 TraesCS7D01G523300 chr2D 94.545 55 3 0 265 319 624184924 624184978 5.860000e-13 86.1
25 TraesCS7D01G523300 chr2D 94.118 51 3 0 264 314 624194764 624194814 9.800000e-11 78.7
26 TraesCS7D01G523300 chr1D 85.714 70 10 0 264 333 306669092 306669023 1.270000e-09 75.0


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 TraesCS7D01G523300 chr7D 619892884 619896178 3294 True 6085.0 6085 100.0000 1 3295 1 chr7D.!!$R1 3294
1 TraesCS7D01G523300 chr7D 619998768 619999736 968 True 474.5 540 87.3645 1526 2561 2 chr7D.!!$R2 1035
2 TraesCS7D01G523300 chr7A 715222368 715226421 4053 False 2082.5 3378 93.1755 1 2843 2 chr7A.!!$F1 2842
3 TraesCS7D01G523300 chr7B 716566087 716568509 2422 False 1500.0 2294 90.6135 227 2526 2 chr7B.!!$F3 2299
4 TraesCS7D01G523300 chr7B 716650067 716652211 2144 False 1127.5 1543 88.3695 505 2526 2 chr7B.!!$F5 2021
5 TraesCS7D01G523300 chr7B 716678447 716679072 625 False 881.0 881 92.3930 2671 3287 1 chr7B.!!$F2 616
6 TraesCS7D01G523300 chr7B 716661980 716662652 672 False 845.0 845 89.1620 1983 2673 1 chr7B.!!$F1 690
7 TraesCS7D01G523300 chr7B 716581133 716582158 1025 False 485.5 701 91.2280 1641 2526 2 chr7B.!!$F4 885
8 TraesCS7D01G523300 chr4B 70998566 70999392 826 True 861.0 861 85.6280 995 1813 1 chr4B.!!$R1 818
9 TraesCS7D01G523300 chr4D 48116083 48121587 5504 True 762.5 839 83.4870 995 1813 2 chr4D.!!$R1 818
10 TraesCS7D01G523300 chrUn 370758524 370759116 592 False 701.0 701 88.1380 1930 2526 1 chrUn.!!$F1 596
11 TraesCS7D01G523300 chrUn 224998389 224999414 1025 True 477.0 684 87.6490 1641 2526 2 chrUn.!!$R1 885

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
992 2210 1.300233 GTGATCGATCCGAGGCACC 60.3 63.158 22.31 0.0 39.91 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2937 8228 0.462759 GGTCCTGGCAGAGCATACAC 60.463 60.0 17.94 0.1 34.37 2.9 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
25 26 4.693566 CCCGCACAACTTTTTCTATAGTCA 59.306 41.667 0.00 0.00 0.00 3.41
31 32 8.958043 GCACAACTTTTTCTATAGTCAGTTTTG 58.042 33.333 0.00 8.21 0.00 2.44
37 38 9.827411 CTTTTTCTATAGTCAGTTTTGTAAGCC 57.173 33.333 0.00 0.00 0.00 4.35
87 88 5.455525 GCCATTGGTTCGATTTAGATTTTCG 59.544 40.000 4.26 0.00 0.00 3.46
169 170 7.087639 CAGAACTAGCTAAGCATATGAGTACC 58.912 42.308 6.97 0.00 0.00 3.34
181 182 8.629821 AGCATATGAGTACCCATATATTTCCT 57.370 34.615 9.32 0.55 37.57 3.36
205 206 7.546667 CCTCAACTTTTGACATATTTTCCATGG 59.453 37.037 4.97 4.97 35.46 3.66
334 336 9.935241 TCTTAGGATTTATGCTACATTGATCTC 57.065 33.333 0.00 0.00 30.09 2.75
387 393 9.460019 TTTTTCCAAAGGAATCATTTGTCTTTT 57.540 25.926 17.39 0.00 41.71 2.27
422 428 5.931532 ACATCAAACTATGTTCTCGCAAAG 58.068 37.500 0.00 0.00 36.71 2.77
559 1752 7.563888 TTGAAAATTCAAAAATGTGCATGGA 57.436 28.000 6.13 0.00 43.62 3.41
849 2067 2.014128 CGAGGGTGACGCCAAATTATT 58.986 47.619 7.48 0.00 39.65 1.40
851 2069 3.813166 CGAGGGTGACGCCAAATTATTAT 59.187 43.478 7.48 0.00 39.65 1.28
853 2071 5.642063 CGAGGGTGACGCCAAATTATTATAT 59.358 40.000 7.48 0.00 39.65 0.86
856 2074 8.561738 AGGGTGACGCCAAATTATTATATAAG 57.438 34.615 7.48 0.00 39.65 1.73
992 2210 1.300233 GTGATCGATCCGAGGCACC 60.300 63.158 22.31 0.00 39.91 5.01
1311 2547 0.832135 AGCTCTTCCGTCTCAACCCA 60.832 55.000 0.00 0.00 0.00 4.51
1335 2571 2.592993 CCGTGTCCTGGTGGATGGT 61.593 63.158 0.00 0.00 45.29 3.55
1338 2574 0.321653 GTGTCCTGGTGGATGGTGTC 60.322 60.000 0.00 0.00 45.29 3.67
1340 2576 1.229051 TCCTGGTGGATGGTGTCGA 60.229 57.895 0.00 0.00 37.46 4.20
1341 2577 0.617535 TCCTGGTGGATGGTGTCGAT 60.618 55.000 0.00 0.00 37.46 3.59
1350 2586 2.126228 GGTGTCGATGCGGACGAA 60.126 61.111 3.54 0.00 41.31 3.85
1871 3124 6.836242 TGGAAAGGGCACATTAATTTTTCTT 58.164 32.000 0.00 0.00 0.00 2.52
1911 3225 2.094286 CACCACTGCAGTCAAACCAAAA 60.094 45.455 18.64 0.00 0.00 2.44
1953 3341 9.134055 AGGTAGTACAGTATGATTTAAGACTCC 57.866 37.037 2.06 0.00 39.69 3.85
2069 3463 0.753111 AGAATGCCATTCCTTCCCGC 60.753 55.000 13.69 0.00 40.13 6.13
2103 3497 5.765182 GGGAAGGTGATCGTCATTGATATTT 59.235 40.000 0.00 0.00 0.00 1.40
2254 3648 6.456988 GGCTTCACCGACTACAAAATTATCAG 60.457 42.308 0.00 0.00 0.00 2.90
2302 3696 4.553323 GAGGTCTACAAGTGAAGCGTTTA 58.447 43.478 0.00 0.00 0.00 2.01
2327 3731 6.674066 TCAAAAGTTTATCCAAAAGGCGTAG 58.326 36.000 0.00 0.00 0.00 3.51
2355 3773 7.737972 TGTAGTGTGCTTTGTTTATGTATGT 57.262 32.000 0.00 0.00 0.00 2.29
2377 3795 1.741770 GGTGGTGTGCTCCGATGAC 60.742 63.158 0.00 0.00 0.00 3.06
2378 3796 1.005037 GTGGTGTGCTCCGATGACA 60.005 57.895 0.00 0.00 0.00 3.58
2588 7878 9.524496 TGCTAATTATGCTTCCAAATATGAGAT 57.476 29.630 7.94 0.00 0.00 2.75
2617 7907 3.575256 ACGGAATAAGTATGACCGGCATA 59.425 43.478 0.00 7.99 46.45 3.14
2679 7969 6.692849 ATTATCAAGTGGGAGCATGAGATA 57.307 37.500 0.00 0.00 0.00 1.98
2688 7978 3.582208 GGGAGCATGAGATATCTTCCAGT 59.418 47.826 18.08 1.28 0.00 4.00
2694 7984 7.613585 AGCATGAGATATCTTCCAGTTCTATG 58.386 38.462 6.70 0.00 0.00 2.23
2697 7987 9.421806 CATGAGATATCTTCCAGTTCTATGAAC 57.578 37.037 6.70 2.54 0.00 3.18
2853 8144 8.058847 TCCCAGGGTTATTATCATATAATTGCC 58.941 37.037 5.01 2.06 0.00 4.52
2937 8228 4.513198 AATTGGTGGGTTTGTGTTATCG 57.487 40.909 0.00 0.00 0.00 2.92
2945 8236 3.687698 GGGTTTGTGTTATCGTGTATGCT 59.312 43.478 0.00 0.00 0.00 3.79
2948 8239 5.445939 GGTTTGTGTTATCGTGTATGCTCTG 60.446 44.000 0.00 0.00 0.00 3.35
2957 8248 0.618680 TGTATGCTCTGCCAGGACCT 60.619 55.000 0.00 0.00 0.00 3.85
2959 8250 1.974236 GTATGCTCTGCCAGGACCTAT 59.026 52.381 0.00 0.00 0.00 2.57
2960 8251 2.405618 ATGCTCTGCCAGGACCTATA 57.594 50.000 0.00 0.00 0.00 1.31
2961 8252 2.405618 TGCTCTGCCAGGACCTATAT 57.594 50.000 0.00 0.00 0.00 0.86
2967 8258 5.130145 GCTCTGCCAGGACCTATATATTGAT 59.870 44.000 0.00 0.00 0.00 2.57
2991 8282 8.757982 ATGTTTGATATAAGAGCAAGTCCAAT 57.242 30.769 0.00 0.00 34.26 3.16
3020 8311 7.246311 CACATGCTCTCGAAAGACAAAAATAT 58.754 34.615 0.00 0.00 35.39 1.28
3025 8316 7.114811 TGCTCTCGAAAGACAAAAATATTTTGC 59.885 33.333 14.04 8.68 35.39 3.68
3026 8317 7.410835 GCTCTCGAAAGACAAAAATATTTTGCC 60.411 37.037 14.04 6.75 35.39 4.52
3082 8373 6.349300 GGAGAAGGCTACTCATATCACAAAA 58.651 40.000 0.00 0.00 36.26 2.44
3153 8497 1.427368 ACCAGTAACATGGGAAGGCAA 59.573 47.619 0.00 0.00 45.25 4.52
3289 8644 5.649782 CCTTTTCAGGTGCATTAGAACAT 57.350 39.130 0.00 0.00 35.06 2.71
3290 8645 6.757897 CCTTTTCAGGTGCATTAGAACATA 57.242 37.500 0.00 0.00 35.06 2.29
3291 8646 7.338800 CCTTTTCAGGTGCATTAGAACATAT 57.661 36.000 0.00 0.00 35.06 1.78
3292 8647 7.198390 CCTTTTCAGGTGCATTAGAACATATG 58.802 38.462 0.00 0.00 35.06 1.78
3293 8648 7.148018 CCTTTTCAGGTGCATTAGAACATATGT 60.148 37.037 1.41 1.41 35.06 2.29
3294 8649 6.682423 TTCAGGTGCATTAGAACATATGTG 57.318 37.500 9.63 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.467723 ACTGACTATAGAAAAAGTTGTGCG 57.532 37.500 6.78 0.00 0.00 5.34
37 38 1.698506 AGAGAGGAACCGGAGCATAG 58.301 55.000 9.46 0.00 0.00 2.23
45 46 3.343617 TGGCAAAAATAGAGAGGAACCG 58.656 45.455 0.00 0.00 0.00 4.44
47 48 5.185828 ACCAATGGCAAAAATAGAGAGGAAC 59.814 40.000 0.00 0.00 0.00 3.62
108 109 0.394216 CTCGGGCCACAATTCCATGA 60.394 55.000 4.39 0.00 0.00 3.07
109 110 0.680921 ACTCGGGCCACAATTCCATG 60.681 55.000 4.39 0.00 0.00 3.66
114 115 1.004745 AGATTGACTCGGGCCACAATT 59.995 47.619 4.39 0.00 33.92 2.32
118 119 1.941325 CTAAGATTGACTCGGGCCAC 58.059 55.000 4.39 0.00 0.00 5.01
181 182 6.873076 GCCATGGAAAATATGTCAAAAGTTGA 59.127 34.615 18.40 0.00 37.33 3.18
199 200 1.176182 TCCCTATCCTAGGCCATGGA 58.824 55.000 18.40 17.37 44.86 3.41
387 393 8.339344 ACATAGTTTGATGTCATGACAATTCA 57.661 30.769 31.00 26.22 45.41 2.57
513 519 6.311935 TCAACACGGCTAATTACAGTCATAAC 59.688 38.462 0.00 0.00 0.00 1.89
559 1752 8.160106 TCCTTGGTTGCCACAAAAATAATTAAT 58.840 29.630 0.00 0.00 30.78 1.40
658 1865 6.673154 ACTTAAATATTACTTGGCGTCACC 57.327 37.500 0.00 0.00 39.84 4.02
992 2210 2.216750 CTGGGCCGCCATTGTTCTTG 62.217 60.000 12.58 0.00 0.00 3.02
1188 2406 2.735772 GCTTGCGGGGATGGAGAGA 61.736 63.158 0.00 0.00 0.00 3.10
1191 2409 2.045045 TTGCTTGCGGGGATGGAG 60.045 61.111 0.00 0.00 0.00 3.86
1302 2538 1.458777 ACGGGACAGTGGGTTGAGA 60.459 57.895 0.00 0.00 0.00 3.27
1311 2547 2.122989 ACCAGGACACGGGACAGT 60.123 61.111 0.00 0.00 35.72 3.55
1335 2571 1.731613 GTGTTCGTCCGCATCGACA 60.732 57.895 0.00 0.00 37.05 4.35
1338 2574 2.431771 TGGTGTTCGTCCGCATCG 60.432 61.111 0.00 0.00 0.00 3.84
1340 2576 1.667830 CTGTGGTGTTCGTCCGCAT 60.668 57.895 0.00 0.00 43.19 4.73
1341 2577 2.279851 CTGTGGTGTTCGTCCGCA 60.280 61.111 0.00 0.00 42.18 5.69
1350 2586 2.421739 GACGTCTGGCTGTGGTGT 59.578 61.111 8.70 0.00 0.00 4.16
1488 2724 1.296755 CCGTGGTCTCGTCGAAGAGA 61.297 60.000 24.49 24.49 44.23 3.10
1746 2982 1.082117 CACCGGCGACATAGTTGACC 61.082 60.000 9.30 0.00 0.00 4.02
1928 3245 8.910944 TGGAGTCTTAAATCATACTGTACTACC 58.089 37.037 0.00 0.00 0.00 3.18
1930 3247 9.696572 AGTGGAGTCTTAAATCATACTGTACTA 57.303 33.333 0.00 0.00 0.00 1.82
1931 3248 8.470805 CAGTGGAGTCTTAAATCATACTGTACT 58.529 37.037 0.00 0.00 32.24 2.73
1941 3329 4.479786 AGCCTCAGTGGAGTCTTAAATC 57.520 45.455 0.00 0.00 39.64 2.17
1953 3341 2.028112 TGTAGCCTTGTTAGCCTCAGTG 60.028 50.000 0.00 0.00 0.00 3.66
2069 3463 2.060980 CACCTTCCCTCCCTCCTCG 61.061 68.421 0.00 0.00 0.00 4.63
2302 3696 6.096673 ACGCCTTTTGGATAAACTTTTGAT 57.903 33.333 0.00 0.00 44.07 2.57
2327 3731 3.436700 AAACAAAGCACACTACAAGGC 57.563 42.857 0.00 0.00 0.00 4.35
2355 3773 0.980754 ATCGGAGCACACCACCCATA 60.981 55.000 0.00 0.00 0.00 2.74
2387 3805 4.953579 TGCAAACATAATAAGGAACTCCCC 59.046 41.667 0.00 0.00 38.49 4.81
2430 3848 3.654414 AGCTTGTCACTGTAGCTGTTAC 58.346 45.455 0.00 0.00 43.25 2.50
2431 3849 4.058124 CAAGCTTGTCACTGTAGCTGTTA 58.942 43.478 18.65 0.00 44.05 2.41
2432 3850 2.874701 CAAGCTTGTCACTGTAGCTGTT 59.125 45.455 18.65 0.00 44.05 3.16
2583 7873 5.661056 ACTTATTCCGTCAACAGATCTCA 57.339 39.130 0.00 0.00 0.00 3.27
2588 7878 5.657474 GGTCATACTTATTCCGTCAACAGA 58.343 41.667 0.00 0.00 0.00 3.41
2617 7907 2.222027 CCCTGTTTTCGTGAAGAGCTT 58.778 47.619 0.00 0.00 0.00 3.74
2679 7969 6.051717 CCATTCGTTCATAGAACTGGAAGAT 58.948 40.000 9.72 0.00 37.43 2.40
2688 7978 6.869315 TTGTGAAACCATTCGTTCATAGAA 57.131 33.333 0.00 0.00 38.46 2.10
2694 7984 6.641176 AAACTTTTGTGAAACCATTCGTTC 57.359 33.333 0.00 0.00 38.46 3.95
2697 7987 7.922505 TCATAAACTTTTGTGAAACCATTCG 57.077 32.000 0.00 0.00 35.73 3.34
2877 8168 5.894298 AGGGAATGATGCACAGATACTAA 57.106 39.130 0.00 0.00 0.00 2.24
2878 8169 5.894298 AAGGGAATGATGCACAGATACTA 57.106 39.130 0.00 0.00 0.00 1.82
2937 8228 0.462759 GGTCCTGGCAGAGCATACAC 60.463 60.000 17.94 0.10 34.37 2.90
2945 8236 6.025539 ACATCAATATATAGGTCCTGGCAGA 58.974 40.000 17.94 0.00 0.00 4.26
2948 8239 7.168219 TCAAACATCAATATATAGGTCCTGGC 58.832 38.462 0.00 0.00 0.00 4.85
2967 8258 7.067372 CCATTGGACTTGCTCTTATATCAAACA 59.933 37.037 0.00 0.00 0.00 2.83
2991 8282 0.674581 CTTTCGAGAGCATGTGGCCA 60.675 55.000 0.00 0.00 46.50 5.36
3020 8311 8.373981 TCATCTTTCCATGAATAAAAGGCAAAA 58.626 29.630 0.00 0.00 32.20 2.44
3025 8316 8.964772 ACTTCTCATCTTTCCATGAATAAAAGG 58.035 33.333 0.00 0.00 32.24 3.11
3026 8317 9.784680 CACTTCTCATCTTTCCATGAATAAAAG 57.215 33.333 0.00 0.00 32.24 2.27
3033 8324 6.825213 CCAATACACTTCTCATCTTTCCATGA 59.175 38.462 0.00 0.00 0.00 3.07
3082 8373 4.526970 AGCCATAATGAACTTCGTGGATT 58.473 39.130 0.00 0.00 0.00 3.01
3180 8524 9.694137 AACAAAACTAGTGTCTCTCTATACAAC 57.306 33.333 0.00 0.00 0.00 3.32
3237 8592 7.096230 CGGAACTCAACCAATTCAATTAAACAC 60.096 37.037 0.00 0.00 0.00 3.32
3238 8593 6.920758 CGGAACTCAACCAATTCAATTAAACA 59.079 34.615 0.00 0.00 0.00 2.83
3248 8603 4.094830 AGGTAACGGAACTCAACCAATT 57.905 40.909 0.00 0.00 46.39 2.32
3250 8605 3.564053 AAGGTAACGGAACTCAACCAA 57.436 42.857 0.00 0.00 46.39 3.67


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

AutoCloner maintained by Alex Coulton.