Multiple sequence alignment - TraesCS5D01G442800

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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 TraesCS5D01G442800 chr5D 100.000 3059 0 0 1 3059 494683800 494686858 0.000000e+00 5650.0
1 TraesCS5D01G442800 chr5D 83.757 1299 187 12 781 2064 494761573 494762862 0.000000e+00 1208.0
2 TraesCS5D01G442800 chr5D 85.041 1103 141 12 984 2068 494654379 494655475 0.000000e+00 1101.0
3 TraesCS5D01G442800 chr5D 98.371 491 4 3 2569 3059 494674129 494674615 0.000000e+00 859.0
4 TraesCS5D01G442800 chr5D 97.963 491 6 3 2569 3059 494672364 494672850 0.000000e+00 848.0
5 TraesCS5D01G442800 chr5B 91.707 1640 117 13 729 2359 610922711 610924340 0.000000e+00 2257.0
6 TraesCS5D01G442800 chr5B 82.196 1539 216 35 557 2076 611322703 611324202 0.000000e+00 1271.0
7 TraesCS5D01G442800 chr5B 81.056 1383 215 32 698 2061 611045111 611046465 0.000000e+00 1059.0
8 TraesCS5D01G442800 chr5B 83.247 1158 178 13 984 2132 611077259 611078409 0.000000e+00 1050.0
9 TraesCS5D01G442800 chr5B 80.085 1406 244 26 786 2173 610873883 610875270 0.000000e+00 1013.0
10 TraesCS5D01G442800 chr5B 93.314 673 30 5 1746 2404 610964172 610964843 0.000000e+00 979.0
11 TraesCS5D01G442800 chr5B 83.647 1009 141 17 755 1748 610958116 610959115 0.000000e+00 928.0
12 TraesCS5D01G442800 chr5B 91.317 668 28 7 1 667 610921994 610922632 0.000000e+00 885.0
13 TraesCS5D01G442800 chr5B 79.920 752 130 17 986 1728 610880427 610881166 1.610000e-147 532.0
14 TraesCS5D01G442800 chr5B 82.836 268 34 7 2394 2654 610924536 610924798 2.370000e-56 230.0
15 TraesCS5D01G442800 chr5B 85.000 160 19 3 2676 2834 610964863 610965018 1.140000e-34 158.0
16 TraesCS5D01G442800 chr5A 90.421 1545 108 16 848 2357 618270419 618271958 0.000000e+00 1997.0
17 TraesCS5D01G442800 chr5A 82.349 1507 206 34 584 2071 618602355 618603820 0.000000e+00 1254.0
18 TraesCS5D01G442800 chr5A 80.577 1421 247 19 698 2102 618158488 618159895 0.000000e+00 1068.0
19 TraesCS5D01G442800 chr5A 89.963 538 34 8 155 688 618269875 618270396 0.000000e+00 676.0
20 TraesCS5D01G442800 chr5A 83.929 392 43 12 2396 2778 618272078 618272458 1.040000e-94 357.0
21 TraesCS5D01G442800 chr5A 95.092 163 7 1 1 163 618268025 618268186 3.910000e-64 255.0
22 TraesCS5D01G442800 chr5A 83.607 122 14 5 2839 2954 618272465 618272586 3.220000e-20 110.0
23 TraesCS5D01G442800 chr5A 100.000 34 0 0 695 728 618270389 618270422 2.550000e-06 63.9
24 TraesCS5D01G442800 chr6D 98.673 603 8 0 2094 2696 26850319 26850921 0.000000e+00 1070.0
25 TraesCS5D01G442800 chr6D 98.673 603 8 0 2094 2696 26886986 26887588 0.000000e+00 1070.0
26 TraesCS5D01G442800 chr1D 79.568 1204 192 26 981 2136 491604286 491603089 0.000000e+00 811.0


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 TraesCS5D01G442800 chr5D 494683800 494686858 3058 False 5650.000000 5650 100.000 1 3059 1 chr5D.!!$F2 3058
1 TraesCS5D01G442800 chr5D 494761573 494762862 1289 False 1208.000000 1208 83.757 781 2064 1 chr5D.!!$F3 1283
2 TraesCS5D01G442800 chr5D 494654379 494655475 1096 False 1101.000000 1101 85.041 984 2068 1 chr5D.!!$F1 1084
3 TraesCS5D01G442800 chr5D 494672364 494674615 2251 False 853.500000 859 98.167 2569 3059 2 chr5D.!!$F4 490
4 TraesCS5D01G442800 chr5B 611322703 611324202 1499 False 1271.000000 1271 82.196 557 2076 1 chr5B.!!$F6 1519
5 TraesCS5D01G442800 chr5B 610921994 610924798 2804 False 1124.000000 2257 88.620 1 2654 3 chr5B.!!$F7 2653
6 TraesCS5D01G442800 chr5B 611045111 611046465 1354 False 1059.000000 1059 81.056 698 2061 1 chr5B.!!$F4 1363
7 TraesCS5D01G442800 chr5B 611077259 611078409 1150 False 1050.000000 1050 83.247 984 2132 1 chr5B.!!$F5 1148
8 TraesCS5D01G442800 chr5B 610873883 610875270 1387 False 1013.000000 1013 80.085 786 2173 1 chr5B.!!$F1 1387
9 TraesCS5D01G442800 chr5B 610958116 610959115 999 False 928.000000 928 83.647 755 1748 1 chr5B.!!$F3 993
10 TraesCS5D01G442800 chr5B 610964172 610965018 846 False 568.500000 979 89.157 1746 2834 2 chr5B.!!$F8 1088
11 TraesCS5D01G442800 chr5B 610880427 610881166 739 False 532.000000 532 79.920 986 1728 1 chr5B.!!$F2 742
12 TraesCS5D01G442800 chr5A 618602355 618603820 1465 False 1254.000000 1254 82.349 584 2071 1 chr5A.!!$F2 1487
13 TraesCS5D01G442800 chr5A 618158488 618159895 1407 False 1068.000000 1068 80.577 698 2102 1 chr5A.!!$F1 1404
14 TraesCS5D01G442800 chr5A 618268025 618272586 4561 False 576.483333 1997 90.502 1 2954 6 chr5A.!!$F3 2953
15 TraesCS5D01G442800 chr6D 26850319 26850921 602 False 1070.000000 1070 98.673 2094 2696 1 chr6D.!!$F1 602
16 TraesCS5D01G442800 chr6D 26886986 26887588 602 False 1070.000000 1070 98.673 2094 2696 1 chr6D.!!$F2 602
17 TraesCS5D01G442800 chr1D 491603089 491604286 1197 True 811.000000 811 79.568 981 2136 1 chr1D.!!$R1 1155

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
667 2381 0.442699 GCAGAAAACCTAACTCGCCG 59.557 55.0 0.00 0.0 0.00 6.46 F
1294 3083 0.246635 CGAGAATGGAGAACCGGTGT 59.753 55.0 8.52 0.0 39.42 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 3562 0.957395 ATCTGTCAGCCGCAACAAGG 60.957 55.0 0.0 0.0 0.0 3.61 R
3039 5119 2.134789 AGCCTTTTCATCTGCCGATT 57.865 45.0 0.0 0.0 0.0 3.34 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
139 140 6.292923 TCGATTTTAGAGGGAAAACAAGTCA 58.707 36.000 0.00 0.00 31.35 3.41
149 150 7.177744 AGAGGGAAAACAAGTCACTTTACAAAA 59.822 33.333 0.00 0.00 0.00 2.44
150 151 7.094631 AGGGAAAACAAGTCACTTTACAAAAC 58.905 34.615 0.00 0.00 0.00 2.43
153 154 8.432359 GGAAAACAAGTCACTTTACAAAACAAG 58.568 33.333 0.00 0.00 0.00 3.16
265 1962 4.844655 TGATGACAGATCCCATCATCTCAT 59.155 41.667 22.37 6.10 45.92 2.90
277 1974 6.383436 TCCCATCATCTCATCTATGATCCTTC 59.617 42.308 0.00 0.00 41.13 3.46
278 1975 6.156429 CCCATCATCTCATCTATGATCCTTCA 59.844 42.308 0.00 0.00 41.13 3.02
279 1976 7.147461 CCCATCATCTCATCTATGATCCTTCAT 60.147 40.741 0.00 0.00 41.13 2.57
280 1977 7.929245 CCATCATCTCATCTATGATCCTTCATC 59.071 40.741 0.00 0.00 41.13 2.92
281 1978 8.478877 CATCATCTCATCTATGATCCTTCATCA 58.521 37.037 0.00 0.00 46.01 3.07
282 1979 8.431910 TCATCTCATCTATGATCCTTCATCAA 57.568 34.615 0.00 0.00 45.06 2.57
283 1980 8.532819 TCATCTCATCTATGATCCTTCATCAAG 58.467 37.037 0.00 0.00 45.06 3.02
284 1981 7.852550 TCTCATCTATGATCCTTCATCAAGT 57.147 36.000 0.00 0.00 45.06 3.16
285 1982 7.668492 TCTCATCTATGATCCTTCATCAAGTG 58.332 38.462 0.00 0.00 45.06 3.16
286 1983 6.228995 TCATCTATGATCCTTCATCAAGTGC 58.771 40.000 0.00 0.00 45.06 4.40
287 1984 5.883685 TCTATGATCCTTCATCAAGTGCT 57.116 39.130 0.00 0.00 45.06 4.40
288 1985 5.851720 TCTATGATCCTTCATCAAGTGCTC 58.148 41.667 0.00 0.00 45.06 4.26
333 2030 1.522355 CTCCATGATCAGCGGCGTT 60.522 57.895 9.37 0.00 0.00 4.84
362 2059 2.058057 CGGCCCAAAAAGTTTGATTCG 58.942 47.619 0.00 0.25 0.00 3.34
411 2108 2.168521 CTCCAACTCCAAAGGCGATCTA 59.831 50.000 0.00 0.00 0.00 1.98
458 2155 7.389330 TGTTAAGATGTTAAACGTGACCATGAT 59.611 33.333 0.00 0.00 29.74 2.45
493 2191 2.365582 ACTGCTTTCGTTGGTGTTCTT 58.634 42.857 0.00 0.00 0.00 2.52
519 2217 0.955919 CTCTTGCCCGTTCTTCCCAC 60.956 60.000 0.00 0.00 0.00 4.61
626 2330 2.087009 GCCGTCCGTCTTTCTCACG 61.087 63.158 0.00 0.00 36.99 4.35
667 2381 0.442699 GCAGAAAACCTAACTCGCCG 59.557 55.000 0.00 0.00 0.00 6.46
669 2383 0.683412 AGAAAACCTAACTCGCCGGT 59.317 50.000 1.90 0.00 0.00 5.28
690 2441 0.747644 CTCTCTCTGCTCTCCGCTCA 60.748 60.000 0.00 0.00 40.11 4.26
739 2497 1.104577 GCGTCTCTCCTTCCCGATCT 61.105 60.000 0.00 0.00 0.00 2.75
973 2737 1.133915 TCGTTCCTCTGGCCAAACTTT 60.134 47.619 7.01 0.00 0.00 2.66
976 2740 1.981256 TCCTCTGGCCAAACTTTCAC 58.019 50.000 7.01 0.00 0.00 3.18
1230 3019 5.957842 TTGTAAGTTTTGAATCTGCCGAT 57.042 34.783 0.00 0.00 0.00 4.18
1231 3020 5.295431 TGTAAGTTTTGAATCTGCCGATG 57.705 39.130 0.00 0.00 0.00 3.84
1232 3021 2.927553 AGTTTTGAATCTGCCGATGC 57.072 45.000 0.00 0.00 38.26 3.91
1242 3031 1.703438 CTGCCGATGCTGCTGAAGAC 61.703 60.000 0.00 0.00 38.71 3.01
1258 3047 1.068474 AGACGTGAAGGCGAAATTCG 58.932 50.000 11.47 11.47 43.89 3.34
1294 3083 0.246635 CGAGAATGGAGAACCGGTGT 59.753 55.000 8.52 0.00 39.42 4.16
1317 3109 2.312390 TCATACAGCTATACGCACCCA 58.688 47.619 0.00 0.00 42.61 4.51
1392 3188 1.221523 AGGGCTGATCTGGAGGTATCA 59.778 52.381 1.46 0.00 0.00 2.15
1394 3190 1.622811 GGCTGATCTGGAGGTATCAGG 59.377 57.143 12.75 0.00 46.04 3.86
1471 3276 7.023575 CGATAAAGAAACAATTGTTCCTCCAG 58.976 38.462 23.47 8.36 37.25 3.86
2075 3898 5.358160 GGAAGTAATGCCTGCAGAACTATTT 59.642 40.000 17.39 4.12 0.00 1.40
2086 3913 8.571336 GCCTGCAGAACTATTTTCATATATGTT 58.429 33.333 17.39 0.00 0.00 2.71
2439 4499 9.019656 ACTACTGATATCCTCTGTTAGCTAATG 57.980 37.037 9.88 6.30 37.28 1.90
3026 5106 6.799441 CCGACGTGAAAAATCATTAATGTTGA 59.201 34.615 14.97 0.00 0.00 3.18
3027 5107 7.201232 CCGACGTGAAAAATCATTAATGTTGAC 60.201 37.037 14.97 5.83 0.00 3.18
3028 5108 7.322461 CGACGTGAAAAATCATTAATGTTGACA 59.678 33.333 14.97 6.94 0.00 3.58
3029 5109 9.128107 GACGTGAAAAATCATTAATGTTGACAT 57.872 29.630 14.97 0.00 38.41 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 1962 5.221601 GGAGCACTTGATGAAGGATCATAGA 60.222 44.000 0.00 0.00 46.30 1.98
277 1974 2.159421 GCACTTGATGGAGCACTTGATG 60.159 50.000 0.00 0.00 0.00 3.07
278 1975 2.089980 GCACTTGATGGAGCACTTGAT 58.910 47.619 0.00 0.00 0.00 2.57
279 1976 1.072806 AGCACTTGATGGAGCACTTGA 59.927 47.619 0.00 0.00 0.00 3.02
280 1977 1.467734 GAGCACTTGATGGAGCACTTG 59.532 52.381 0.00 0.00 0.00 3.16
281 1978 1.612726 GGAGCACTTGATGGAGCACTT 60.613 52.381 0.00 0.00 0.00 3.16
282 1979 0.035630 GGAGCACTTGATGGAGCACT 60.036 55.000 0.00 0.00 0.00 4.40
283 1980 0.321919 TGGAGCACTTGATGGAGCAC 60.322 55.000 0.00 0.00 0.00 4.40
284 1981 0.622136 ATGGAGCACTTGATGGAGCA 59.378 50.000 0.00 0.00 0.00 4.26
285 1982 1.307097 GATGGAGCACTTGATGGAGC 58.693 55.000 0.00 0.00 0.00 4.70
286 1983 1.137675 TCGATGGAGCACTTGATGGAG 59.862 52.381 0.00 0.00 0.00 3.86
287 1984 1.194218 TCGATGGAGCACTTGATGGA 58.806 50.000 0.00 0.00 0.00 3.41
288 1985 1.938577 CTTCGATGGAGCACTTGATGG 59.061 52.381 0.00 0.00 0.00 3.51
333 2030 2.114488 TTTTTGGGCCGAGGCTACGA 62.114 55.000 14.33 4.78 41.60 3.43
383 2080 0.110486 TTTGGAGTTGGAGCAGGACC 59.890 55.000 0.00 0.00 0.00 4.46
458 2155 6.704493 ACGAAAGCAGTACAACATCTTTTCTA 59.296 34.615 0.00 0.00 0.00 2.10
493 2191 1.906574 AGAACGGGCAAGAGGAACATA 59.093 47.619 0.00 0.00 0.00 2.29
519 2217 6.270815 CAATTTAGAAGCATCCTGACCATTG 58.729 40.000 0.00 0.00 0.00 2.82
617 2321 0.242825 TACCAGACGCCGTGAGAAAG 59.757 55.000 0.00 0.00 0.00 2.62
626 2330 1.471287 GGATGGTTTTTACCAGACGCC 59.529 52.381 3.19 0.00 43.86 5.68
667 2381 1.101049 CGGAGAGCAGAGAGAGGACC 61.101 65.000 0.00 0.00 0.00 4.46
669 2383 4.975132 CGGAGAGCAGAGAGAGGA 57.025 61.111 0.00 0.00 0.00 3.71
794 2552 1.456705 GAGGAGGGTGGAGCTCGAT 60.457 63.158 7.83 0.00 0.00 3.59
849 2607 2.034066 ATTGGAGGTGGTGGCACG 59.966 61.111 12.17 0.00 0.00 5.34
973 2737 0.690762 GTGGGCTTGGAGTAAGGTGA 59.309 55.000 0.00 0.00 36.87 4.02
976 2740 0.253327 GAGGTGGGCTTGGAGTAAGG 59.747 60.000 0.00 0.00 36.87 2.69
1013 2784 1.822990 CCATGGCAGCAGAAATCTTGT 59.177 47.619 0.00 0.00 0.00 3.16
1178 2967 3.763097 TGAAATCGGCACAATCATCAC 57.237 42.857 0.00 0.00 0.00 3.06
1230 3019 0.601046 CCTTCACGTCTTCAGCAGCA 60.601 55.000 0.00 0.00 0.00 4.41
1231 3020 1.905922 GCCTTCACGTCTTCAGCAGC 61.906 60.000 0.00 0.00 0.00 5.25
1232 3021 1.621301 CGCCTTCACGTCTTCAGCAG 61.621 60.000 0.00 0.00 0.00 4.24
1258 3047 1.714460 CTCGTCAAGTACACTGAACGC 59.286 52.381 10.36 0.00 35.78 4.84
1317 3109 5.244626 ACTTTTGCTTGAGAAGGTATGCATT 59.755 36.000 3.54 0.00 0.00 3.56
1362 3158 3.181442 CCAGATCAGCCCTCTTGATGAAT 60.181 47.826 0.00 0.00 0.00 2.57
1392 3188 1.959985 CAGTCGTCTCTCATATGCCCT 59.040 52.381 0.00 0.00 0.00 5.19
1394 3190 3.006659 GACAGTCGTCTCTCATATGCC 57.993 52.381 0.00 0.00 39.22 4.40
1417 3213 1.661341 GTGAGATCACACCTGATGGC 58.339 55.000 11.80 0.00 45.75 4.40
1449 3254 5.010617 GCCTGGAGGAACAATTGTTTCTTTA 59.989 40.000 28.75 20.09 43.59 1.85
1450 3255 4.202253 GCCTGGAGGAACAATTGTTTCTTT 60.202 41.667 28.75 11.78 43.59 2.52
1614 3421 1.141657 GCATAACTCTCCTCCATGGCA 59.858 52.381 6.96 0.00 35.26 4.92
1749 3562 0.957395 ATCTGTCAGCCGCAACAAGG 60.957 55.000 0.00 0.00 0.00 3.61
2086 3913 9.802039 ACAACCACTACTAAGAAAATTTGGATA 57.198 29.630 0.00 0.00 0.00 2.59
2439 4499 4.065789 GCCCCATCACAACTATTAGTAGC 58.934 47.826 0.00 0.00 0.00 3.58
3026 5106 4.264253 TCTGCCGATTTCATTTCTGATGT 58.736 39.130 0.00 0.00 0.00 3.06
3027 5107 4.888038 TCTGCCGATTTCATTTCTGATG 57.112 40.909 0.00 0.00 0.00 3.07
3028 5108 5.128205 TCATCTGCCGATTTCATTTCTGAT 58.872 37.500 0.00 0.00 0.00 2.90
3029 5109 4.516323 TCATCTGCCGATTTCATTTCTGA 58.484 39.130 0.00 0.00 0.00 3.27
3032 5112 5.517770 CCTTTTCATCTGCCGATTTCATTTC 59.482 40.000 0.00 0.00 0.00 2.17
3033 5113 5.413499 CCTTTTCATCTGCCGATTTCATTT 58.587 37.500 0.00 0.00 0.00 2.32
3034 5114 4.678840 GCCTTTTCATCTGCCGATTTCATT 60.679 41.667 0.00 0.00 0.00 2.57
3035 5115 3.181483 GCCTTTTCATCTGCCGATTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
3036 5116 2.164219 GCCTTTTCATCTGCCGATTTCA 59.836 45.455 0.00 0.00 0.00 2.69
3037 5117 2.424956 AGCCTTTTCATCTGCCGATTTC 59.575 45.455 0.00 0.00 0.00 2.17
3038 5118 2.450476 AGCCTTTTCATCTGCCGATTT 58.550 42.857 0.00 0.00 0.00 2.17
3039 5119 2.134789 AGCCTTTTCATCTGCCGATT 57.865 45.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.