Multiple sequence alignment - TraesCS1D01G063600

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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 TraesCS1D01G063600 chr1D 100.000 2740 0 0 1 2740 43822389 43825128 0.000000e+00 5060.0
1 TraesCS1D01G063600 chr1D 94.062 2762 102 29 1 2740 44274306 44277027 0.000000e+00 4135.0
2 TraesCS1D01G063600 chr1D 95.667 1477 56 4 1 1476 44309506 44310975 0.000000e+00 2366.0
3 TraesCS1D01G063600 chr1D 94.815 1408 63 6 777 2182 44628962 44630361 0.000000e+00 2187.0
4 TraesCS1D01G063600 chr1D 92.937 1246 58 10 1516 2740 44370324 44371560 0.000000e+00 1786.0
5 TraesCS1D01G063600 chr1D 89.488 1094 93 10 717 1796 43305828 43306913 0.000000e+00 1363.0
6 TraesCS1D01G063600 chr1D 93.316 748 30 9 2011 2740 44160031 44160776 0.000000e+00 1086.0
7 TraesCS1D01G063600 chr1D 96.379 580 14 3 713 1291 44159096 44159669 0.000000e+00 948.0
8 TraesCS1D01G063600 chr1D 94.931 434 15 4 1 428 44158664 44159096 0.000000e+00 673.0
9 TraesCS1D01G063600 chr1D 80.562 427 71 6 1979 2395 31316909 31316485 4.400000e-83 318.0
10 TraesCS1D01G063600 chr1D 100.000 85 0 0 1283 1367 44159946 44160030 1.020000e-34 158.0
11 TraesCS1D01G063600 chr1B 90.657 2055 149 23 706 2738 63479635 63481668 0.000000e+00 2691.0
12 TraesCS1D01G063600 chr1B 90.112 2053 155 26 706 2738 63468403 63470427 0.000000e+00 2623.0
13 TraesCS1D01G063600 chr1B 89.584 2045 161 25 706 2729 63808647 63810660 0.000000e+00 2549.0
14 TraesCS1D01G063600 chr1B 90.514 1908 135 25 712 2597 63759037 63760920 0.000000e+00 2479.0
15 TraesCS1D01G063600 chr1B 91.980 1409 96 11 706 2112 63614045 63615438 0.000000e+00 1960.0
16 TraesCS1D01G063600 chr1B 86.196 623 55 16 2109 2709 63624149 63624762 0.000000e+00 645.0
17 TraesCS1D01G063600 chr1B 90.780 282 23 3 26 306 63808360 63808639 9.270000e-100 374.0
18 TraesCS1D01G063600 chr1B 90.391 281 25 2 26 306 63468117 63468395 4.310000e-98 368.0
19 TraesCS1D01G063600 chr1B 89.680 281 27 2 26 306 63479349 63479627 9.330000e-95 357.0
20 TraesCS1D01G063600 chr1B 89.324 281 28 2 26 306 63613759 63614037 4.340000e-93 351.0
21 TraesCS1D01G063600 chr1A 90.274 2046 147 26 717 2738 43271785 43269768 0.000000e+00 2628.0
22 TraesCS1D01G063600 chr1A 89.538 2036 158 33 717 2738 43392401 43390407 0.000000e+00 2529.0
23 TraesCS1D01G063600 chr1A 89.354 1099 94 12 713 1796 42670374 42671464 0.000000e+00 1360.0
24 TraesCS1D01G063600 chr1A 91.912 272 19 3 36 306 43392690 43392421 7.160000e-101 377.0
25 TraesCS1D01G063600 chr1A 82.826 460 39 15 2297 2738 43952523 43952960 2.580000e-100 375.0
26 TraesCS1D01G063600 chr1A 89.680 281 27 2 26 306 43272083 43271805 9.330000e-95 357.0
27 TraesCS1D01G063600 chr2D 92.734 289 21 0 426 714 371841091 371841379 4.220000e-113 418.0
28 TraesCS1D01G063600 chr2D 89.474 133 12 2 304 436 460725345 460725215 1.690000e-37 167.0
29 TraesCS1D01G063600 chr7D 93.525 278 18 0 435 712 550979995 550979718 5.460000e-112 414.0
30 TraesCS1D01G063600 chr7D 97.222 108 3 0 304 411 478908770 478908877 1.680000e-42 183.0
31 TraesCS1D01G063600 chr5B 92.982 285 19 1 428 712 513963519 513963802 5.460000e-112 414.0
32 TraesCS1D01G063600 chr5B 88.776 196 19 3 303 498 167283425 167283617 1.270000e-58 237.0
33 TraesCS1D01G063600 chr3D 92.361 288 19 1 428 712 111181233 111181520 9.130000e-110 407.0
34 TraesCS1D01G063600 chr3D 90.397 302 27 2 412 712 382108036 382108336 1.980000e-106 396.0
35 TraesCS1D01G063600 chr7A 91.438 292 25 0 423 714 547571418 547571709 4.250000e-108 401.0
36 TraesCS1D01G063600 chr6D 91.468 293 23 2 420 712 24480127 24479837 4.250000e-108 401.0
37 TraesCS1D01G063600 chr6D 76.679 819 127 35 1796 2572 404615812 404615016 1.980000e-106 396.0
38 TraesCS1D01G063600 chr6D 79.158 475 85 8 1866 2338 290905099 290905561 1.580000e-82 316.0
39 TraesCS1D01G063600 chr6D 80.303 198 30 4 1825 2021 132056372 132056561 1.020000e-29 141.0
40 TraesCS1D01G063600 chr4D 80.778 463 75 7 1795 2256 466133866 466133417 1.560000e-92 350.0
41 TraesCS1D01G063600 chr7B 95.041 121 5 1 290 410 420072677 420072796 3.600000e-44 189.0
42 TraesCS1D01G063600 chr7B 91.667 132 9 2 289 418 58655882 58656013 6.030000e-42 182.0
43 TraesCS1D01G063600 chr6A 90.000 130 10 3 292 419 434619513 434619641 6.070000e-37 165.0
44 TraesCS1D01G063600 chrUn 95.000 40 0 2 1796 1835 250540242 250540279 8.190000e-06 62.1


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 TraesCS1D01G063600 chr1D 43822389 43825128 2739 False 5060.00 5060 100.0000 1 2740 1 chr1D.!!$F2 2739
1 TraesCS1D01G063600 chr1D 44274306 44277027 2721 False 4135.00 4135 94.0620 1 2740 1 chr1D.!!$F3 2739
2 TraesCS1D01G063600 chr1D 44309506 44310975 1469 False 2366.00 2366 95.6670 1 1476 1 chr1D.!!$F4 1475
3 TraesCS1D01G063600 chr1D 44628962 44630361 1399 False 2187.00 2187 94.8150 777 2182 1 chr1D.!!$F6 1405
4 TraesCS1D01G063600 chr1D 44370324 44371560 1236 False 1786.00 1786 92.9370 1516 2740 1 chr1D.!!$F5 1224
5 TraesCS1D01G063600 chr1D 43305828 43306913 1085 False 1363.00 1363 89.4880 717 1796 1 chr1D.!!$F1 1079
6 TraesCS1D01G063600 chr1D 44158664 44160776 2112 False 716.25 1086 96.1565 1 2740 4 chr1D.!!$F7 2739
7 TraesCS1D01G063600 chr1B 63759037 63760920 1883 False 2479.00 2479 90.5140 712 2597 1 chr1B.!!$F2 1885
8 TraesCS1D01G063600 chr1B 63479349 63481668 2319 False 1524.00 2691 90.1685 26 2738 2 chr1B.!!$F4 2712
9 TraesCS1D01G063600 chr1B 63468117 63470427 2310 False 1495.50 2623 90.2515 26 2738 2 chr1B.!!$F3 2712
10 TraesCS1D01G063600 chr1B 63808360 63810660 2300 False 1461.50 2549 90.1820 26 2729 2 chr1B.!!$F6 2703
11 TraesCS1D01G063600 chr1B 63613759 63615438 1679 False 1155.50 1960 90.6520 26 2112 2 chr1B.!!$F5 2086
12 TraesCS1D01G063600 chr1B 63624149 63624762 613 False 645.00 645 86.1960 2109 2709 1 chr1B.!!$F1 600
13 TraesCS1D01G063600 chr1A 43269768 43272083 2315 True 1492.50 2628 89.9770 26 2738 2 chr1A.!!$R1 2712
14 TraesCS1D01G063600 chr1A 43390407 43392690 2283 True 1453.00 2529 90.7250 36 2738 2 chr1A.!!$R2 2702
15 TraesCS1D01G063600 chr1A 42670374 42671464 1090 False 1360.00 1360 89.3540 713 1796 1 chr1A.!!$F1 1083
16 TraesCS1D01G063600 chr6D 404615016 404615812 796 True 396.00 396 76.6790 1796 2572 1 chr6D.!!$R2 776

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
949 959 0.461135 CAACTAATGCATGCCCCCAC 59.539 55.0 16.68 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2221 2.203082 TCCCGATCTCATCCTGGCG 61.203 63.158 0.0 0.0 0.0 5.69 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
179 183 2.002586 ACGTTCATTCTTCGATGCAGG 58.997 47.619 0.00 0.00 0.00 4.85
182 186 1.926561 TCATTCTTCGATGCAGGACG 58.073 50.000 0.00 0.00 0.00 4.79
347 353 6.281405 ACTTGTCGTAGAAATGGATGTATCC 58.719 40.000 3.91 3.91 43.31 2.59
399 408 7.362056 CCATTTCAGTGACAAGTAATTCGGAAT 60.362 37.037 0.00 0.00 0.00 3.01
452 461 3.513517 TGGCCACAGTAGGTAGTAACTT 58.486 45.455 0.00 0.00 0.00 2.66
514 523 4.409247 ACCTCTACAATGGGGAGTAACATC 59.591 45.833 0.00 0.00 0.00 3.06
525 534 3.067106 GGAGTAACATCTGTGTGGTGTG 58.933 50.000 0.00 0.00 38.92 3.82
527 536 3.990469 GAGTAACATCTGTGTGGTGTGAG 59.010 47.826 0.00 0.00 38.92 3.51
571 580 8.880244 AGGTTATATACTCATCTTGCATTGGTA 58.120 33.333 0.00 0.00 0.00 3.25
590 599 9.276590 CATTGGTATGTGTGATGTTACTCATAT 57.723 33.333 0.00 0.00 38.51 1.78
647 656 9.801873 TCTATTTCTTTATTAATTGCTTGCCAC 57.198 29.630 0.00 0.00 0.00 5.01
653 662 8.911965 TCTTTATTAATTGCTTGCCACATCATA 58.088 29.630 0.00 0.00 0.00 2.15
753 762 7.715249 AGTTACTGTACACACTCATTGTTTGAT 59.285 33.333 0.00 0.00 35.67 2.57
754 763 6.304356 ACTGTACACACTCATTGTTTGATG 57.696 37.500 0.00 0.00 35.67 3.07
755 764 5.107109 TGTACACACTCATTGTTTGATGC 57.893 39.130 0.00 0.00 35.67 3.91
756 765 4.578105 TGTACACACTCATTGTTTGATGCA 59.422 37.500 0.00 0.00 35.67 3.96
935 945 9.929180 GTGCCATATCTTCAAGATATACAACTA 57.071 33.333 17.93 1.99 43.95 2.24
944 954 7.439157 TCAAGATATACAACTAATGCATGCC 57.561 36.000 16.68 0.00 0.00 4.40
949 959 0.461135 CAACTAATGCATGCCCCCAC 59.539 55.000 16.68 0.00 0.00 4.61
1131 1153 4.571984 TGTGCTTATGTTTCATCATCCTCG 59.428 41.667 0.00 0.00 0.00 4.63
1172 1194 1.406069 GCTGACGAATGTGAGGGTGAT 60.406 52.381 0.00 0.00 29.01 3.06
1215 1237 5.560724 AGTGTGCTAAGTATCAACAATGGT 58.439 37.500 0.00 0.00 0.00 3.55
1491 1822 8.977505 CGGATTCACACAATTTTGATTTTAGTT 58.022 29.630 0.00 0.00 0.00 2.24
1496 1827 9.755804 TCACACAATTTTGATTTTAGTTATGCA 57.244 25.926 0.00 0.00 0.00 3.96
1599 1930 4.574013 GGCGTAGTGACTCTAGTTTAGCTA 59.426 45.833 0.00 0.00 0.00 3.32
1609 1940 4.742012 TCTAGTTTAGCTATGGGAGGAGG 58.258 47.826 0.00 0.00 0.00 4.30
1651 1984 0.749454 GTGCCTGGCCTCACAATAGG 60.749 60.000 17.53 0.52 39.87 2.57
1659 1992 3.017442 GGCCTCACAATAGGTTTCCTTC 58.983 50.000 0.00 0.00 39.02 3.46
1864 2201 8.819845 TCAGATTATGCATATGTGGTAGAGATT 58.180 33.333 7.36 0.00 0.00 2.40
1907 2245 1.342819 CAGGATGAGATCGGGACCTTC 59.657 57.143 0.00 0.00 39.69 3.46
2044 2382 5.417580 TCCTAAGGCACCACAACAAAATATC 59.582 40.000 0.00 0.00 0.00 1.63
2103 2445 6.040955 CCTGAGCTAGACTAATGAATGGTGTA 59.959 42.308 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 307 0.038744 TTCCGAACGGAGGGAGTACT 59.961 55.000 15.34 0.00 46.06 2.73
380 389 5.160607 TCCATTCCGAATTACTTGTCACT 57.839 39.130 0.00 0.00 0.00 3.41
382 391 4.513442 CCTCCATTCCGAATTACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
399 408 5.962031 ACATACATTAGTTGTACTCCCTCCA 59.038 40.000 0.00 0.00 43.46 3.86
432 441 4.952335 TCTAAGTTACTACCTACTGTGGCC 59.048 45.833 0.00 0.00 0.00 5.36
441 450 8.901793 GCATGTTACTAGTCTAAGTTACTACCT 58.098 37.037 0.00 0.00 31.82 3.08
514 523 0.747644 TGTTGCCTCACACCACACAG 60.748 55.000 0.00 0.00 0.00 3.66
525 534 6.759497 ACCTAATAAATGAAGTGTTGCCTC 57.241 37.500 0.00 0.00 0.00 4.70
553 562 5.585844 CACACATACCAATGCAAGATGAGTA 59.414 40.000 0.00 0.00 36.50 2.59
565 574 9.851686 AATATGAGTAACATCACACATACCAAT 57.148 29.630 0.00 0.00 40.07 3.16
624 633 9.101655 GATGTGGCAAGCAATTAATAAAGAAAT 57.898 29.630 0.00 0.00 0.00 2.17
753 762 6.597672 ACCTTGAAGATACGAAATAACATGCA 59.402 34.615 0.00 0.00 0.00 3.96
754 763 7.016361 ACCTTGAAGATACGAAATAACATGC 57.984 36.000 0.00 0.00 0.00 4.06
895 905 7.658525 AGATATGGCACCATGTCAAAAATAA 57.341 32.000 23.35 0.00 43.85 1.40
897 907 6.154877 TGAAGATATGGCACCATGTCAAAAAT 59.845 34.615 23.35 4.24 43.85 1.82
898 908 5.479724 TGAAGATATGGCACCATGTCAAAAA 59.520 36.000 23.35 7.71 43.85 1.94
899 909 5.015515 TGAAGATATGGCACCATGTCAAAA 58.984 37.500 23.35 9.15 43.85 2.44
935 945 0.399376 ATGATGTGGGGGCATGCATT 60.399 50.000 21.36 0.00 0.00 3.56
944 954 3.623703 TGTTTGAGATGATGATGTGGGG 58.376 45.455 0.00 0.00 0.00 4.96
949 959 6.879276 ATAGCCTTGTTTGAGATGATGATG 57.121 37.500 0.00 0.00 0.00 3.07
1172 1194 0.178767 CCTTGATCATGGCCTGTCGA 59.821 55.000 14.21 0.00 0.00 4.20
1215 1237 0.973632 TCTAGCTTCGGGTTTGCTGA 59.026 50.000 0.00 0.00 37.62 4.26
1504 1835 9.196552 CGTATGATCAGAATAGAACAATAAGCA 57.803 33.333 0.09 0.00 0.00 3.91
1505 1836 9.197694 ACGTATGATCAGAATAGAACAATAAGC 57.802 33.333 0.09 0.00 0.00 3.09
1508 1839 9.476202 CCAACGTATGATCAGAATAGAACAATA 57.524 33.333 0.09 0.00 0.00 1.90
1509 1840 7.442364 CCCAACGTATGATCAGAATAGAACAAT 59.558 37.037 0.09 0.00 0.00 2.71
1510 1841 6.761242 CCCAACGTATGATCAGAATAGAACAA 59.239 38.462 0.09 0.00 0.00 2.83
1511 1842 6.127168 ACCCAACGTATGATCAGAATAGAACA 60.127 38.462 0.09 0.00 0.00 3.18
1512 1843 6.281405 ACCCAACGTATGATCAGAATAGAAC 58.719 40.000 0.09 0.00 0.00 3.01
1513 1844 6.097696 TGACCCAACGTATGATCAGAATAGAA 59.902 38.462 0.09 0.00 0.00 2.10
1514 1845 5.596772 TGACCCAACGTATGATCAGAATAGA 59.403 40.000 0.09 0.00 0.00 1.98
1529 1860 3.255642 AGACCATTCAATTTGACCCAACG 59.744 43.478 0.00 0.00 0.00 4.10
1599 1930 2.370445 CCAACGCTCCTCCTCCCAT 61.370 63.158 0.00 0.00 0.00 4.00
1609 1940 5.199448 CATGGAATGTAAAAGCCAACGCTC 61.199 45.833 0.00 0.00 41.90 5.03
1651 1984 5.875359 ACGAATTACAGATCTGGAAGGAAAC 59.125 40.000 24.31 12.53 36.75 2.78
1659 1992 4.392921 ACCTCACGAATTACAGATCTGG 57.607 45.455 26.08 9.98 34.19 3.86
1872 2209 3.134623 TCATCCTGGCGTATGTTTCAGAT 59.865 43.478 0.00 0.00 0.00 2.90
1884 2221 2.203082 TCCCGATCTCATCCTGGCG 61.203 63.158 0.00 0.00 0.00 5.69
1907 2245 8.380644 AGACGTAGTTTATGAAATCACATTTCG 58.619 33.333 0.00 0.00 46.88 3.46
1976 2314 9.171877 ACCATCACATTTTTAGCTTTTGAAAAA 57.828 25.926 7.19 7.19 38.51 1.94
1977 2315 8.729805 ACCATCACATTTTTAGCTTTTGAAAA 57.270 26.923 0.00 0.00 0.00 2.29
2058 2398 7.504926 TCAGGTAGGGTAAATCAATACAGTT 57.495 36.000 0.00 0.00 0.00 3.16
2070 2410 5.722172 TTAGTCTAGCTCAGGTAGGGTAA 57.278 43.478 11.05 6.45 34.77 2.85
2071 2411 5.371769 TCATTAGTCTAGCTCAGGTAGGGTA 59.628 44.000 11.05 0.64 34.77 3.69
2103 2445 2.427245 CCCTCGGTGAAGGCGAGAT 61.427 63.158 0.00 0.00 34.88 2.75
2264 2613 2.754552 GGTTTCCATATTCTGCACAGCA 59.245 45.455 0.00 0.00 36.92 4.41
2580 2978 8.531622 TTCACATTGTTTTTGCGAAATCATAT 57.468 26.923 10.33 5.58 0.00 1.78
2652 3051 8.826546 AGAAATCATAAAATGTTCGTGAATCG 57.173 30.769 0.00 0.00 41.41 3.34
2653 3052 9.226345 GGAGAAATCATAAAATGTTCGTGAATC 57.774 33.333 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.