Multiple sequence alignment - TraesCS5D01G338400

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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 TraesCS5D01G338400 chr5D 100.000 2345 0 0 1 2345 426778840 426781184 0.000000e+00 4331
1 TraesCS5D01G338400 chr5D 91.333 150 12 1 1479 1627 427152407 427152556 1.100000e-48 204
2 TraesCS5D01G338400 chr5B 92.492 919 58 7 1435 2345 516554593 516555508 0.000000e+00 1304
3 TraesCS5D01G338400 chr5B 89.747 868 54 17 1490 2345 516709078 516709922 0.000000e+00 1077
4 TraesCS5D01G338400 chr5B 89.747 868 54 17 1490 2345 516723443 516724287 0.000000e+00 1077
5 TraesCS5D01G338400 chr5B 85.618 744 65 22 1643 2345 516674020 516674762 0.000000e+00 743
6 TraesCS5D01G338400 chr5B 85.618 744 65 22 1643 2345 516677882 516678624 0.000000e+00 743
7 TraesCS5D01G338400 chr5B 85.618 744 65 22 1643 2345 516681256 516681998 0.000000e+00 743
8 TraesCS5D01G338400 chr5B 88.078 562 35 14 1490 2043 516583989 516584526 2.540000e-179 638
9 TraesCS5D01G338400 chr5B 87.958 191 12 2 1479 1658 516676455 516676645 5.080000e-52 215
10 TraesCS5D01G338400 chr3D 92.926 721 42 6 1 714 585932181 585931463 0.000000e+00 1040
11 TraesCS5D01G338400 chr7A 92.500 720 47 6 1 714 71975918 71975200 0.000000e+00 1024
12 TraesCS5D01G338400 chr2B 92.479 718 42 6 1 715 717581255 717580547 0.000000e+00 1016
13 TraesCS5D01G338400 chr5A 85.133 1056 74 20 715 1705 540884382 540885419 0.000000e+00 1003
14 TraesCS5D01G338400 chr5A 85.449 646 62 15 1708 2344 541608821 541608199 0.000000e+00 643
15 TraesCS5D01G338400 chr5A 80.569 422 45 12 744 1133 541231067 541231483 8.200000e-75 291
16 TraesCS5D01G338400 chr7B 93.056 648 40 4 1 643 623569461 623568814 0.000000e+00 942
17 TraesCS5D01G338400 chrUn 88.078 562 35 14 1490 2043 67076384 67076921 2.540000e-179 638
18 TraesCS5D01G338400 chrUn 88.193 559 34 14 1493 2043 284184928 284184394 2.540000e-179 638
19 TraesCS5D01G338400 chrUn 92.568 148 7 2 2201 2345 474571948 474571802 2.360000e-50 209
20 TraesCS5D01G338400 chr2D 83.777 413 50 11 309 715 429278079 429277678 2.200000e-100 375
21 TraesCS5D01G338400 chr3B 94.301 193 9 2 524 714 805556329 805556521 6.340000e-76 294
22 TraesCS5D01G338400 chr3B 93.299 194 11 2 524 715 752135251 752135058 3.810000e-73 285
23 TraesCS5D01G338400 chr3B 92.000 200 13 3 524 720 727480392 727480591 6.380000e-71 278
24 TraesCS5D01G338400 chr6A 93.264 193 11 2 525 715 595892643 595892835 1.370000e-72 283


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 TraesCS5D01G338400 chr5D 426778840 426781184 2344 False 4331 4331 100.000 1 2345 1 chr5D.!!$F1 2344
1 TraesCS5D01G338400 chr5B 516554593 516555508 915 False 1304 1304 92.492 1435 2345 1 chr5B.!!$F1 910
2 TraesCS5D01G338400 chr5B 516709078 516709922 844 False 1077 1077 89.747 1490 2345 1 chr5B.!!$F3 855
3 TraesCS5D01G338400 chr5B 516723443 516724287 844 False 1077 1077 89.747 1490 2345 1 chr5B.!!$F4 855
4 TraesCS5D01G338400 chr5B 516583989 516584526 537 False 638 638 88.078 1490 2043 1 chr5B.!!$F2 553
5 TraesCS5D01G338400 chr5B 516674020 516681998 7978 False 611 743 86.203 1479 2345 4 chr5B.!!$F5 866
6 TraesCS5D01G338400 chr3D 585931463 585932181 718 True 1040 1040 92.926 1 714 1 chr3D.!!$R1 713
7 TraesCS5D01G338400 chr7A 71975200 71975918 718 True 1024 1024 92.500 1 714 1 chr7A.!!$R1 713
8 TraesCS5D01G338400 chr2B 717580547 717581255 708 True 1016 1016 92.479 1 715 1 chr2B.!!$R1 714
9 TraesCS5D01G338400 chr5A 540884382 540885419 1037 False 1003 1003 85.133 715 1705 1 chr5A.!!$F1 990
10 TraesCS5D01G338400 chr5A 541608199 541608821 622 True 643 643 85.449 1708 2344 1 chr5A.!!$R1 636
11 TraesCS5D01G338400 chr7B 623568814 623569461 647 True 942 942 93.056 1 643 1 chr7B.!!$R1 642
12 TraesCS5D01G338400 chrUn 67076384 67076921 537 False 638 638 88.078 1490 2043 1 chrUn.!!$F1 553
13 TraesCS5D01G338400 chrUn 284184394 284184928 534 True 638 638 88.193 1493 2043 1 chrUn.!!$R1 550

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
943 966 0.178918 ATCCCTTCGATCCCCTCCTC 60.179 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 7883 0.251033 TCGAGGTCAGTTCGGAGGAA 60.251 55.0 0.0 0.0 38.54 3.36 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
122 124 1.375326 GGAACAGAGCGGGAAGGTT 59.625 57.895 0.00 0.00 0.00 3.50
133 135 1.070134 CGGGAAGGTTCAGTGACTCAA 59.930 52.381 0.00 0.00 0.00 3.02
238 240 2.104963 GGTAAGGAGGAAGATGGCGATT 59.895 50.000 0.00 0.00 0.00 3.34
262 264 2.311294 GGAACGAATCAGGCCGATG 58.689 57.895 10.25 0.00 33.40 3.84
291 293 1.341531 GGGGACGTAGATCTCATGGTG 59.658 57.143 0.00 0.00 0.00 4.17
294 296 1.683917 GACGTAGATCTCATGGTGGCT 59.316 52.381 0.00 0.00 0.00 4.75
295 297 1.683917 ACGTAGATCTCATGGTGGCTC 59.316 52.381 0.00 0.00 0.00 4.70
423 427 1.098712 TTTGAGCGAAACGTGCCCTT 61.099 50.000 0.00 0.00 0.00 3.95
477 482 1.762522 CTCAGGTGAGTGGCTGGTGT 61.763 60.000 0.00 0.00 37.40 4.16
554 561 2.184322 GCTGCGATTCTCGGTCCA 59.816 61.111 0.00 0.00 40.84 4.02
612 619 2.939640 GCTTTGTCGGGCCTGATTCTTA 60.940 50.000 19.55 1.18 0.00 2.10
617 624 1.559682 TCGGGCCTGATTCTTAAGCTT 59.440 47.619 11.27 3.48 0.00 3.74
754 761 1.192793 GATCGCTAGCTTCACGTGAC 58.807 55.000 19.90 8.02 0.00 3.67
756 763 0.526211 TCGCTAGCTTCACGTGACAT 59.474 50.000 19.90 9.63 0.00 3.06
857 864 2.102757 TGCCAGTACCACGACTACAAAA 59.897 45.455 0.00 0.00 0.00 2.44
862 869 0.752054 ACCACGACTACAAAACGGGA 59.248 50.000 0.00 0.00 31.82 5.14
868 875 2.215196 GACTACAAAACGGGACTTGCA 58.785 47.619 0.00 0.00 0.00 4.08
905 928 1.880340 GCTCTCTTCCGCATCCACG 60.880 63.158 0.00 0.00 0.00 4.94
918 941 4.077184 CCACGCAGCCGGTAGGAA 62.077 66.667 1.90 0.00 41.02 3.36
943 966 0.178918 ATCCCTTCGATCCCCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
945 968 1.234529 CCTTCGATCCCCTCCTCCT 59.765 63.158 0.00 0.00 0.00 3.69
946 969 1.118356 CCTTCGATCCCCTCCTCCTG 61.118 65.000 0.00 0.00 0.00 3.86
949 972 3.237741 GATCCCCTCCTCCTGCCG 61.238 72.222 0.00 0.00 0.00 5.69
955 978 4.504916 CTCCTCCTGCCGCGACAG 62.505 72.222 16.16 16.16 37.42 3.51
1008 1037 2.230940 GCATCCGTCCATGTCGTCG 61.231 63.158 6.75 0.00 0.00 5.12
1062 1091 3.532155 CTCGGGGGCCTCTTCTCG 61.532 72.222 0.52 0.00 0.00 4.04
1122 1151 4.695560 GGGGACGACAAGAAGGTG 57.304 61.111 0.00 0.00 0.00 4.00
1123 1152 1.671379 GGGGACGACAAGAAGGTGC 60.671 63.158 0.00 0.00 0.00 5.01
1124 1153 1.371558 GGGACGACAAGAAGGTGCT 59.628 57.895 0.00 0.00 0.00 4.40
1175 1204 2.659016 CTCGTGGAGCAAGGCTGA 59.341 61.111 0.00 0.00 39.88 4.26
1178 1207 2.431683 GTGGAGCAAGGCTGACCA 59.568 61.111 0.00 0.00 39.88 4.02
1189 1218 3.680786 CTGACCACACCGCGGAGA 61.681 66.667 35.90 6.42 0.00 3.71
1194 1223 2.029073 CACACCGCGGAGAAGTGT 59.971 61.111 35.90 22.84 44.14 3.55
1230 1259 1.290324 GTCGCTTGAGCTGGACAGA 59.710 57.895 3.00 0.00 39.32 3.41
1241 1270 1.306141 TGGACAGAAGGGCGAGGAT 60.306 57.895 0.00 0.00 0.00 3.24
1273 1302 1.505353 GTGTCCGACCTCTACACCG 59.495 63.158 0.00 0.00 38.02 4.94
1275 1304 2.753043 TCCGACCTCTACACCGCC 60.753 66.667 0.00 0.00 0.00 6.13
1277 1306 2.181021 CGACCTCTACACCGCCAC 59.819 66.667 0.00 0.00 0.00 5.01
1278 1307 2.181021 GACCTCTACACCGCCACG 59.819 66.667 0.00 0.00 0.00 4.94
1279 1308 2.282674 ACCTCTACACCGCCACGA 60.283 61.111 0.00 0.00 0.00 4.35
1280 1309 1.664321 GACCTCTACACCGCCACGAT 61.664 60.000 0.00 0.00 0.00 3.73
1281 1310 1.226974 CCTCTACACCGCCACGATG 60.227 63.158 0.00 0.00 0.00 3.84
1341 1396 0.814812 GCGAGGTACGGAGACTAGCT 60.815 60.000 0.00 0.00 42.83 3.32
1359 1421 3.604582 AGCTTAGACAGAGAATTGCCAC 58.395 45.455 0.00 0.00 0.00 5.01
1376 1438 3.058160 CAGAAGGGCTTGGCGTGG 61.058 66.667 0.00 0.00 0.00 4.94
1426 1496 9.685276 TTCTGATACAAGAAACATAATGGTGAT 57.315 29.630 0.00 0.00 33.25 3.06
1458 1528 7.716123 TCTCCACATTTGCTTTTGAATTTGAAT 59.284 29.630 0.00 0.00 0.00 2.57
1515 2475 4.122776 CCACTACTCATCATTACAGGTGC 58.877 47.826 0.00 0.00 0.00 5.01
1714 3937 4.080356 TGGATTGGATGGACAACCTAAGAG 60.080 45.833 0.27 0.00 37.04 2.85
1717 3940 6.183361 GGATTGGATGGACAACCTAAGAGTAT 60.183 42.308 0.27 0.00 37.04 2.12
1718 3941 5.614324 TGGATGGACAACCTAAGAGTATG 57.386 43.478 0.27 0.00 37.04 2.39
1766 3989 3.695830 AGTAGTTCGCCTTGAATTCCA 57.304 42.857 2.27 0.00 39.21 3.53
1825 4048 0.039527 GGTGGACATTTTGTGCCGAC 60.040 55.000 0.00 0.00 37.97 4.79
1850 4073 7.694784 ACATAGTACGGCAAATAATTTTTCGTG 59.305 33.333 11.62 0.00 35.31 4.35
1953 4176 6.212888 TCCCCGTATGTTAGTTTCTTAGAC 57.787 41.667 0.00 0.00 0.00 2.59
1985 7578 7.611467 CCAACAGCAGCCCAATATATATAGAAA 59.389 37.037 0.00 0.00 0.00 2.52
2023 7645 3.655486 TGCATCAACATTTTTGCTCCAG 58.345 40.909 0.00 0.00 36.10 3.86
2220 7849 1.939980 ACTACTCAGAGGTTGTCCCC 58.060 55.000 1.53 0.00 0.00 4.81
2254 7883 0.889306 CCGACTCCTCGTCCTTCTTT 59.111 55.000 0.00 0.00 39.56 2.52
2256 7885 2.597520 CGACTCCTCGTCCTTCTTTTC 58.402 52.381 0.00 0.00 39.56 2.29
2301 7933 4.410400 GGGGTCAACCTCGCCCTG 62.410 72.222 0.00 0.00 42.01 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 124 3.881089 TCGTGTTCTACTTGAGTCACTGA 59.119 43.478 0.00 0.00 32.99 3.41
291 293 1.153208 CATGTCCAGGAGCTGAGCC 60.153 63.158 0.00 0.00 32.44 4.70
294 296 1.556373 CCACCATGTCCAGGAGCTGA 61.556 60.000 0.00 0.00 32.44 4.26
295 297 1.077930 CCACCATGTCCAGGAGCTG 60.078 63.158 0.00 0.00 0.00 4.24
386 388 1.973137 AAAAACGCACTCACGCACGT 61.973 50.000 0.00 0.00 41.16 4.49
419 423 0.807667 CGTGCCTCGATTCTGAAGGG 60.808 60.000 0.00 0.00 42.86 3.95
423 427 1.667154 CTCCCGTGCCTCGATTCTGA 61.667 60.000 0.02 0.00 42.86 3.27
554 561 1.526575 TTTAACCGAGCCGACCGAGT 61.527 55.000 0.00 0.00 0.00 4.18
612 619 2.568623 AAATCAGTCGGTCCAAGCTT 57.431 45.000 0.00 0.00 0.00 3.74
788 795 4.789075 CGCGTGGTGTCCGGGTAG 62.789 72.222 0.00 0.00 34.06 3.18
912 935 3.946606 TCGAAGGGATTTTGGTTCCTAC 58.053 45.455 0.00 0.00 33.53 3.18
918 941 1.063942 GGGGATCGAAGGGATTTTGGT 60.064 52.381 0.00 0.00 34.82 3.67
921 944 1.495148 GGAGGGGATCGAAGGGATTTT 59.505 52.381 0.00 0.00 34.82 1.82
925 948 1.233369 GAGGAGGGGATCGAAGGGA 59.767 63.158 0.00 0.00 0.00 4.20
928 951 1.753368 GCAGGAGGAGGGGATCGAAG 61.753 65.000 0.00 0.00 0.00 3.79
952 975 4.314440 TTCGCCTTGGCTCGCTGT 62.314 61.111 10.12 0.00 0.00 4.40
954 977 4.767255 CCTTCGCCTTGGCTCGCT 62.767 66.667 10.12 0.00 0.00 4.93
996 1025 3.248171 GCGAGCGACGACATGGAC 61.248 66.667 0.00 0.00 45.77 4.02
997 1026 4.829518 CGCGAGCGACGACATGGA 62.830 66.667 12.58 0.00 45.77 3.41
1114 1143 0.249911 GTCGTGGACAGCACCTTCTT 60.250 55.000 0.00 0.00 32.09 2.52
1117 1146 2.029073 CGTCGTGGACAGCACCTT 59.971 61.111 0.00 0.00 32.09 3.50
1118 1147 3.208884 GACGTCGTGGACAGCACCT 62.209 63.158 0.63 0.00 32.09 4.00
1121 1150 2.910479 AGGACGTCGTGGACAGCA 60.910 61.111 10.45 0.00 32.09 4.41
1122 1151 2.126424 GAGGACGTCGTGGACAGC 60.126 66.667 16.63 0.00 32.09 4.40
1123 1152 1.924320 GAGGAGGACGTCGTGGACAG 61.924 65.000 16.63 0.00 32.09 3.51
1124 1153 1.970114 GAGGAGGACGTCGTGGACA 60.970 63.158 16.63 0.00 32.09 4.02
1175 1204 3.231736 ACTTCTCCGCGGTGTGGT 61.232 61.111 27.15 20.81 34.40 4.16
1178 1207 2.029073 CACACTTCTCCGCGGTGT 59.971 61.111 27.15 19.00 43.74 4.16
1189 1218 0.592148 GTCTCCTCGACGACACACTT 59.408 55.000 0.00 0.00 32.04 3.16
1194 1223 2.677979 CGCTGTCTCCTCGACGACA 61.678 63.158 0.00 7.11 45.87 4.35
1230 1259 1.049289 GGTACCTCATCCTCGCCCTT 61.049 60.000 4.06 0.00 0.00 3.95
1275 1304 4.854924 TCCATGGCCGGCATCGTG 62.855 66.667 30.85 22.10 33.95 4.35
1341 1396 4.890158 TCTGTGGCAATTCTCTGTCTAA 57.110 40.909 0.00 0.00 0.00 2.10
1359 1421 3.058160 CCACGCCAAGCCCTTCTG 61.058 66.667 0.00 0.00 0.00 3.02
1393 1463 6.228273 TGTTTCTTGTATCAGAAGAAAGCG 57.772 37.500 10.46 0.00 45.55 4.68
1426 1496 2.472695 AGCAAATGTGGAGACGCTAA 57.527 45.000 0.00 0.00 42.82 3.09
1458 1528 4.506758 CCCGGTATTTTCGAGACCTTTTA 58.493 43.478 0.00 0.00 37.49 1.52
1652 2623 4.798387 CGTCACATCAGTATCGATCAACAA 59.202 41.667 0.00 0.00 0.00 2.83
1664 3887 3.973206 TTAATCCCACGTCACATCAGT 57.027 42.857 0.00 0.00 0.00 3.41
1714 3937 3.940657 ACTGACTACGTACTCGCATAC 57.059 47.619 0.00 0.00 41.18 2.39
1717 3940 2.274437 CCTACTGACTACGTACTCGCA 58.726 52.381 0.00 0.00 41.18 5.10
1718 3941 1.004079 GCCTACTGACTACGTACTCGC 60.004 57.143 0.00 0.00 41.18 5.03
1766 3989 7.687941 AAACACGAATAGAAATGGAGTTCAT 57.312 32.000 0.00 0.00 37.79 2.57
1825 4048 7.305190 GCACGAAAAATTATTTGCCGTACTATG 60.305 37.037 13.97 6.36 36.88 2.23
1881 4104 6.987992 TGTCAAACCGATGAAGTAAACTAGTT 59.012 34.615 1.12 1.12 0.00 2.24
1953 4176 1.751927 GGGCTGCTGTTGGAGATGG 60.752 63.158 0.00 0.00 33.10 3.51
2220 7849 0.527817 GTCGGGCTCCTACATTGACG 60.528 60.000 0.00 0.00 0.00 4.35
2254 7883 0.251033 TCGAGGTCAGTTCGGAGGAA 60.251 55.000 0.00 0.00 38.54 3.36
2256 7885 1.507174 GTCGAGGTCAGTTCGGAGG 59.493 63.158 0.00 0.00 38.54 4.30
2301 7933 2.881352 CGGCGAAGAAGGACGAGC 60.881 66.667 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.