Multiple sequence alignment - TraesCS3D01G422200

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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 TraesCS3D01G422200 chr3D 100.000 3920 0 0 1 3920 534220968 534217049 0.000000e+00 7239.0
1 TraesCS3D01G422200 chr3D 97.484 1272 22 5 1587 2854 52842757 52844022 0.000000e+00 2163.0
2 TraesCS3D01G422200 chr3D 98.500 1067 16 0 2854 3920 52844074 52845140 0.000000e+00 1882.0
3 TraesCS3D01G422200 chr3D 97.200 250 4 1 1344 1590 52842442 52842691 1.680000e-113 420.0
4 TraesCS3D01G422200 chr3D 97.200 250 4 1 1344 1590 52850151 52849902 1.680000e-113 420.0
5 TraesCS3D01G422200 chr3D 89.212 241 23 3 963 1200 43538627 43538387 8.230000e-77 298.0
6 TraesCS3D01G422200 chr3D 92.810 153 10 1 592 743 533943414 533943262 1.830000e-53 220.0
7 TraesCS3D01G422200 chr3D 94.175 103 5 1 862 964 533943258 533943157 5.240000e-34 156.0
8 TraesCS3D01G422200 chr5D 98.345 1269 17 2 1590 2854 52374209 52372941 0.000000e+00 2224.0
9 TraesCS3D01G422200 chr5D 98.109 1269 20 2 1590 2854 356119179 356117911 0.000000e+00 2207.0
10 TraesCS3D01G422200 chr5D 97.877 1272 23 2 1587 2854 282366584 282367855 0.000000e+00 2196.0
11 TraesCS3D01G422200 chr5D 97.799 1272 24 2 1587 2854 422770686 422771957 0.000000e+00 2191.0
12 TraesCS3D01G422200 chr5D 98.782 1067 10 1 2854 3920 422772009 422773072 0.000000e+00 1895.0
13 TraesCS3D01G422200 chr5D 98.844 1038 12 0 2883 3920 356117852 356116815 0.000000e+00 1851.0
14 TraesCS3D01G422200 chr5D 97.211 251 4 1 1343 1590 356119497 356119247 4.680000e-114 422.0
15 TraesCS3D01G422200 chr5D 97.200 250 4 1 1344 1590 52374527 52374278 1.680000e-113 420.0
16 TraesCS3D01G422200 chr5D 96.484 256 6 1 1338 1590 422770362 422770617 1.680000e-113 420.0
17 TraesCS3D01G422200 chr5D 96.457 254 5 2 1340 1590 356111771 356112023 2.180000e-112 416.0
18 TraesCS3D01G422200 chr7D 98.113 1272 20 2 1587 2854 634768160 634769431 0.000000e+00 2213.0
19 TraesCS3D01G422200 chr7D 97.190 1281 23 3 1587 2854 538836360 538837640 0.000000e+00 2154.0
20 TraesCS3D01G422200 chr7D 96.792 1278 28 3 1590 2854 112190987 112189710 0.000000e+00 2121.0
21 TraesCS3D01G422200 chr7D 96.721 1281 29 3 1587 2854 445229244 445230524 0.000000e+00 2121.0
22 TraesCS3D01G422200 chr7D 95.745 1269 24 3 1590 2854 426836918 426835676 0.000000e+00 2017.0
23 TraesCS3D01G422200 chr7D 98.778 1064 13 0 2857 3920 426835621 426834558 0.000000e+00 1893.0
24 TraesCS3D01G422200 chr7D 98.407 1067 17 0 2854 3920 538837692 538838758 0.000000e+00 1877.0
25 TraesCS3D01G422200 chr7D 98.496 1064 15 1 2857 3920 112189655 112188593 0.000000e+00 1875.0
26 TraesCS3D01G422200 chr7D 98.313 1067 12 1 2854 3920 634769483 634770543 0.000000e+00 1866.0
27 TraesCS3D01G422200 chr7D 97.200 250 4 1 1344 1590 426837236 426836987 1.680000e-113 420.0
28 TraesCS3D01G422200 chr7D 85.398 226 32 1 963 1187 584772072 584771847 2.360000e-57 233.0
29 TraesCS3D01G422200 chr4D 97.340 1278 20 4 1590 2854 392724525 392723249 0.000000e+00 2159.0
30 TraesCS3D01G422200 chr4D 99.060 1064 9 1 2857 3920 392723194 392722132 0.000000e+00 1908.0
31 TraesCS3D01G422200 chr4D 93.313 329 21 1 2516 2843 428642002 428642330 5.890000e-133 484.0
32 TraesCS3D01G422200 chr4D 97.200 250 4 1 1344 1590 392724846 392724597 1.680000e-113 420.0
33 TraesCS3D01G422200 chr3B 95.270 1353 52 7 1 1347 706323923 706322577 0.000000e+00 2134.0
34 TraesCS3D01G422200 chr3B 86.325 234 30 2 960 1192 751242674 751242906 1.810000e-63 254.0
35 TraesCS3D01G422200 chr3B 86.036 222 29 1 963 1184 29793543 29793324 1.820000e-58 237.0
36 TraesCS3D01G422200 chr1A 97.095 1067 27 2 2857 3920 20824820 20823755 0.000000e+00 1796.0
37 TraesCS3D01G422200 chr1A 96.443 253 5 2 1341 1590 13807264 13807515 7.840000e-112 414.0
38 TraesCS3D01G422200 chr3A 95.724 304 10 3 23 325 669949782 669949481 1.640000e-133 486.0
39 TraesCS3D01G422200 chr3A 93.644 236 15 0 729 964 669933688 669933453 1.730000e-93 353.0
40 TraesCS3D01G422200 chr3A 95.545 202 7 2 535 734 669948871 669948670 4.890000e-84 322.0
41 TraesCS3D01G422200 chr4A 88.696 230 25 1 963 1192 690247277 690247049 2.980000e-71 279.0
42 TraesCS3D01G422200 chr6D 92.670 191 8 2 354 543 35494766 35494581 1.800000e-68 270.0
43 TraesCS3D01G422200 chr7B 92.935 184 10 1 353 536 154162469 154162649 8.350000e-67 265.0
44 TraesCS3D01G422200 chr2D 86.475 244 30 3 956 1197 349605737 349605495 8.350000e-67 265.0
45 TraesCS3D01G422200 chr2D 94.083 169 9 1 963 1131 36665137 36664970 5.030000e-64 255.0
46 TraesCS3D01G422200 chr6B 92.896 183 10 1 354 536 6878310 6878489 3.000000e-66 263.0
47 TraesCS3D01G422200 chr6B 91.489 188 12 1 349 536 684219227 684219410 5.030000e-64 255.0
48 TraesCS3D01G422200 chr4B 92.778 180 11 1 357 536 88849223 88849046 3.890000e-65 259.0
49 TraesCS3D01G422200 chr4B 91.848 184 12 1 353 536 617203606 617203786 1.810000e-63 254.0
50 TraesCS3D01G422200 chr2A 91.935 186 12 1 352 537 31697315 31697497 1.400000e-64 257.0
51 TraesCS3D01G422200 chr7A 91.892 185 12 1 352 536 714589235 714589416 5.030000e-64 255.0
52 TraesCS3D01G422200 chr7A 87.097 62 5 2 242 300 32532910 32532971 2.530000e-07 67.6
53 TraesCS3D01G422200 chr7A 84.615 52 8 0 249 300 108452392 108452341 7.000000e-03 52.8
54 TraesCS3D01G422200 chr1D 85.654 237 31 3 963 1197 236890293 236890528 3.030000e-61 246.0
55 TraesCS3D01G422200 chr2B 94.118 34 2 0 243 276 8774629 8774662 7.000000e-03 52.8


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 TraesCS3D01G422200 chr3D 534217049 534220968 3919 True 7239.000000 7239 100.000000 1 3920 1 chr3D.!!$R3 3919
1 TraesCS3D01G422200 chr3D 52842442 52845140 2698 False 1488.333333 2163 97.728000 1344 3920 3 chr3D.!!$F1 2576
2 TraesCS3D01G422200 chr5D 282366584 282367855 1271 False 2196.000000 2196 97.877000 1587 2854 1 chr5D.!!$F1 1267
3 TraesCS3D01G422200 chr5D 422770362 422773072 2710 False 1502.000000 2191 97.688333 1338 3920 3 chr5D.!!$F3 2582
4 TraesCS3D01G422200 chr5D 356116815 356119497 2682 True 1493.333333 2207 98.054667 1343 3920 3 chr5D.!!$R2 2577
5 TraesCS3D01G422200 chr5D 52372941 52374527 1586 True 1322.000000 2224 97.772500 1344 2854 2 chr5D.!!$R1 1510
6 TraesCS3D01G422200 chr7D 445229244 445230524 1280 False 2121.000000 2121 96.721000 1587 2854 1 chr7D.!!$F1 1267
7 TraesCS3D01G422200 chr7D 634768160 634770543 2383 False 2039.500000 2213 98.213000 1587 3920 2 chr7D.!!$F3 2333
8 TraesCS3D01G422200 chr7D 538836360 538838758 2398 False 2015.500000 2154 97.798500 1587 3920 2 chr7D.!!$F2 2333
9 TraesCS3D01G422200 chr7D 112188593 112190987 2394 True 1998.000000 2121 97.644000 1590 3920 2 chr7D.!!$R2 2330
10 TraesCS3D01G422200 chr7D 426834558 426837236 2678 True 1443.333333 2017 97.241000 1344 3920 3 chr7D.!!$R3 2576
11 TraesCS3D01G422200 chr4D 392722132 392724846 2714 True 1495.666667 2159 97.866667 1344 3920 3 chr4D.!!$R1 2576
12 TraesCS3D01G422200 chr3B 706322577 706323923 1346 True 2134.000000 2134 95.270000 1 1347 1 chr3B.!!$R2 1346
13 TraesCS3D01G422200 chr1A 20823755 20824820 1065 True 1796.000000 1796 97.095000 2857 3920 1 chr1A.!!$R1 1063
14 TraesCS3D01G422200 chr3A 669948670 669949782 1112 True 404.000000 486 95.634500 23 734 2 chr3A.!!$R2 711

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
65 66 0.107214 GCCTTGCAGCCCACTACATA 60.107 55.000 0.00 0.00 0.00 2.29 F
806 812 0.107508 GCCAGCCATGTCAAGCTCTA 60.108 55.000 0.00 0.00 37.18 2.43 F
1239 1245 0.095762 GCCGCTTTGCATGCATTTTC 59.904 50.000 23.37 10.17 0.00 2.29 F
1243 1249 2.690786 GCTTTGCATGCATTTTCTCCA 58.309 42.857 23.37 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1185 0.741221 GGAGAACGACCACATCAGCC 60.741 60.000 0.0 0.0 0.00 4.85 R
1683 1769 3.954258 ACTCATCCATGTACTCGTCATCA 59.046 43.478 0.0 0.0 0.00 3.07 R
2849 3286 4.478206 TTTGCATCAGACTCCCTCTAAG 57.522 45.455 0.0 0.0 0.00 2.18 R
3357 3846 0.813184 CCGGACGCTTAGTAGGACAA 59.187 55.000 0.0 0.0 33.99 3.18 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
17 18 2.262915 AGGAAAGCCAGAGCGACG 59.737 61.111 0.00 0.00 46.67 5.12
65 66 0.107214 GCCTTGCAGCCCACTACATA 60.107 55.000 0.00 0.00 0.00 2.29
158 162 9.573133 CAGCTAGTAAACAAATAAGGAAAATGG 57.427 33.333 0.00 0.00 0.00 3.16
326 331 2.203126 GGATCCAGGCCTTGAGCG 60.203 66.667 15.25 0.00 45.17 5.03
332 337 2.437359 AGGCCTTGAGCGCATGTC 60.437 61.111 11.47 0.00 45.17 3.06
372 377 7.202526 GGTAGGCAATAATACTACACGTACAA 58.797 38.462 0.00 0.00 38.99 2.41
388 393 8.997621 ACACGTACAAGATATTCATACAAAGT 57.002 30.769 0.00 0.00 0.00 2.66
484 489 7.877097 CCTTAATCAAATTCCAACCAATCACAA 59.123 33.333 0.00 0.00 0.00 3.33
517 522 0.611714 AAATCCTCCGTACAACGCCT 59.388 50.000 0.00 0.00 40.91 5.52
540 545 2.106938 TCTAGCATTGCTCCGCGG 59.893 61.111 22.12 22.12 40.44 6.46
559 564 1.084370 GTAGGTCGCACATGTCCTGC 61.084 60.000 12.86 8.51 0.00 4.85
752 758 0.387202 TGATGTGTTTTGTTGCCCCG 59.613 50.000 0.00 0.00 0.00 5.73
753 759 0.943835 GATGTGTTTTGTTGCCCCGC 60.944 55.000 0.00 0.00 0.00 6.13
801 807 1.601419 CCCAAGCCAGCCATGTCAAG 61.601 60.000 0.00 0.00 0.00 3.02
806 812 0.107508 GCCAGCCATGTCAAGCTCTA 60.108 55.000 0.00 0.00 37.18 2.43
887 893 4.193826 TCTTACCTCAAGCACATCACTC 57.806 45.455 0.00 0.00 33.94 3.51
987 993 2.613977 CCAAGCCTCTATATCCGGCAAG 60.614 54.545 0.00 0.00 46.14 4.01
1005 1011 5.693104 CGGCAAGGTTTACGCTCTAATATTA 59.307 40.000 0.00 0.00 0.00 0.98
1032 1038 5.539574 ACACTTGGATGAAAATGAACCATGA 59.460 36.000 0.00 0.00 32.58 3.07
1133 1139 3.067461 TCAAATTCTTTGAACGGGTGTGG 59.933 43.478 0.00 0.00 45.94 4.17
1179 1185 0.609151 TTTGATTGCATGTGGGGCAG 59.391 50.000 0.00 0.00 43.05 4.85
1185 1191 2.277737 CATGTGGGGCAGGCTGAT 59.722 61.111 20.86 0.00 0.00 2.90
1204 1210 3.695556 TGATGTGGTCGTTCTCCGTATTA 59.304 43.478 0.00 0.00 37.94 0.98
1239 1245 0.095762 GCCGCTTTGCATGCATTTTC 59.904 50.000 23.37 10.17 0.00 2.29
1243 1249 2.690786 GCTTTGCATGCATTTTCTCCA 58.309 42.857 23.37 0.00 0.00 3.86
1251 1257 4.624452 GCATGCATTTTCTCCAGTTTTCTC 59.376 41.667 14.21 0.00 0.00 2.87
1252 1258 4.488126 TGCATTTTCTCCAGTTTTCTCG 57.512 40.909 0.00 0.00 0.00 4.04
1253 1259 4.133820 TGCATTTTCTCCAGTTTTCTCGA 58.866 39.130 0.00 0.00 0.00 4.04
1256 1262 5.123027 GCATTTTCTCCAGTTTTCTCGATCT 59.877 40.000 0.00 0.00 0.00 2.75
1340 1346 3.868661 GGTGCCGATTTTCTTGTGTTTTT 59.131 39.130 0.00 0.00 0.00 1.94
1683 1769 2.722487 GAGACATCCGACGCCGAT 59.278 61.111 0.00 0.00 38.22 4.18
1762 1848 3.699038 GCTCACTCTGTTCTCTCCTATGT 59.301 47.826 0.00 0.00 0.00 2.29
2073 2495 3.364565 GGTGGTACATAGTGCAAACAACG 60.365 47.826 0.00 0.00 44.52 4.10
2405 2827 4.779489 TGTGGGATATGTATCATGAGGAGG 59.221 45.833 0.09 0.00 34.40 4.30
2491 2919 4.890158 TTCTCTTGCCAATCAGTACAGA 57.110 40.909 0.00 0.00 0.00 3.41
2767 3204 3.517100 AGAAGAAGAAGCTGGAGCATGTA 59.483 43.478 0.65 0.00 45.16 2.29
2849 3286 4.583871 AGTTGTCATGGAGGAGTGATTTC 58.416 43.478 0.00 0.00 0.00 2.17
2854 3291 5.721480 TGTCATGGAGGAGTGATTTCTTAGA 59.279 40.000 0.00 0.00 0.00 2.10
2855 3292 6.127225 TGTCATGGAGGAGTGATTTCTTAGAG 60.127 42.308 0.00 0.00 0.00 2.43
3364 3853 7.732025 TCAGATTCACTTAGTTGTTTGTCCTA 58.268 34.615 0.00 0.00 0.00 2.94
3523 4021 0.304098 GATCTGTAGGTCGTCGTCGG 59.696 60.000 1.55 0.00 37.69 4.79
3734 4232 1.202359 GCTAGTCGCCTTCTTCCTCAG 60.202 57.143 0.00 0.00 0.00 3.35
3797 4295 2.236146 TCATGGCGACCTTCATGTAGTT 59.764 45.455 0.00 0.00 40.94 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.468689 GGGCTGGGTCGTACTGGC 62.469 72.222 0.00 0.00 0.00 4.85
201 205 3.793144 CGTGCTTCCTTGGCGCTC 61.793 66.667 7.64 0.00 37.96 5.03
208 213 1.197721 CAAAATCGAGCGTGCTTCCTT 59.802 47.619 0.00 0.00 0.00 3.36
326 331 1.604278 GCGAAAGGGAATAGGACATGC 59.396 52.381 0.00 0.00 0.00 4.06
388 393 2.550606 GCCACGTTGTCATCCTGTAAAA 59.449 45.455 0.00 0.00 0.00 1.52
399 404 4.495844 GCAATTAGATTAGGCCACGTTGTC 60.496 45.833 5.01 0.00 0.00 3.18
484 489 2.239907 GAGGATTTACAGGCTCCTTGGT 59.760 50.000 0.00 0.00 39.52 3.67
517 522 1.202256 CGGAGCAATGCTAGACGTACA 60.202 52.381 8.12 0.00 39.88 2.90
540 545 1.084370 GCAGGACATGTGCGACCTAC 61.084 60.000 12.02 0.00 0.00 3.18
559 564 0.169672 CCTCGGCTTCTGCAACATTG 59.830 55.000 0.00 0.00 41.91 2.82
731 737 2.547642 CGGGGCAACAAAACACATCATT 60.548 45.455 0.00 0.00 39.74 2.57
735 741 1.068921 GCGGGGCAACAAAACACAT 59.931 52.632 0.00 0.00 39.74 3.21
801 807 2.688958 ACCTCGTCATTACTGGTAGAGC 59.311 50.000 0.00 0.00 31.22 4.09
806 812 2.367567 ACAACACCTCGTCATTACTGGT 59.632 45.455 0.00 0.00 32.55 4.00
887 893 7.602753 TGAATGTTGACTATCTATATCCACCG 58.397 38.462 0.00 0.00 0.00 4.94
1005 1011 7.537596 TGGTTCATTTTCATCCAAGTGTATT 57.462 32.000 0.00 0.00 0.00 1.89
1026 1032 4.383335 GCCACATCCAAAATTCATCATGGT 60.383 41.667 0.00 0.00 34.50 3.55
1032 1038 2.562298 ACGTGCCACATCCAAAATTCAT 59.438 40.909 0.00 0.00 0.00 2.57
1118 1124 1.234615 ATCGCCACACCCGTTCAAAG 61.235 55.000 0.00 0.00 0.00 2.77
1133 1139 4.179579 GCCAACCAAGGCGATCGC 62.180 66.667 31.52 31.52 46.12 4.58
1179 1185 0.741221 GGAGAACGACCACATCAGCC 60.741 60.000 0.00 0.00 0.00 4.85
1204 1210 1.404035 GCGGCACCGATTAAAGGAAAT 59.596 47.619 14.43 0.00 42.83 2.17
1239 1245 2.964740 TGCAGATCGAGAAAACTGGAG 58.035 47.619 0.00 0.00 0.00 3.86
1243 1249 3.055530 AGACCATGCAGATCGAGAAAACT 60.056 43.478 0.00 0.00 0.00 2.66
1251 1257 1.485397 CGAGAAGACCATGCAGATCG 58.515 55.000 0.00 0.00 0.00 3.69
1252 1258 1.137872 ACCGAGAAGACCATGCAGATC 59.862 52.381 0.00 0.00 0.00 2.75
1253 1259 1.134580 CACCGAGAAGACCATGCAGAT 60.135 52.381 0.00 0.00 0.00 2.90
1256 1262 1.375908 GCACCGAGAAGACCATGCA 60.376 57.895 0.00 0.00 33.27 3.96
1423 1429 9.480053 TTTTTGCCACAAAATTTGAAATTTTCA 57.520 22.222 21.85 15.27 38.04 2.69
1683 1769 3.954258 ACTCATCCATGTACTCGTCATCA 59.046 43.478 0.00 0.00 0.00 3.07
1762 1848 4.511304 TCAAACCCTAACCCTAACCCTAA 58.489 43.478 0.00 0.00 0.00 2.69
2665 3102 6.475596 TGAATGATATCAGCTTGACTCTGA 57.524 37.500 11.78 0.00 43.79 3.27
2767 3204 5.006386 CCAACCTTCAGTAGCTCAGAAATT 58.994 41.667 0.00 0.00 0.00 1.82
2849 3286 4.478206 TTTGCATCAGACTCCCTCTAAG 57.522 45.455 0.00 0.00 0.00 2.18
3357 3846 0.813184 CCGGACGCTTAGTAGGACAA 59.187 55.000 0.00 0.00 33.99 3.18
3364 3853 1.726265 GACGATCCGGACGCTTAGT 59.274 57.895 21.23 7.22 0.00 2.24
3734 4232 1.208052 TGGTAGATGCAGCAGAGGAAC 59.792 52.381 4.07 0.00 0.00 3.62
3797 4295 1.000955 GCGACCAAGAACTCTTCCTCA 59.999 52.381 0.00 0.00 33.11 3.86


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

AutoCloner maintained by Alex Coulton.