Multiple sequence alignment - TraesCS3B01G541800

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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 TraesCS3B01G541800 chr3B 100.000 2579 0 0 1 2579 779703155 779700577 0.000000e+00 4763
1 TraesCS3B01G541800 chr3B 93.699 1349 60 4 965 2294 779694122 779692780 0.000000e+00 1997
2 TraesCS3B01G541800 chr3B 88.734 1367 123 18 965 2308 780090055 780088697 0.000000e+00 1642
3 TraesCS3B01G541800 chr3B 97.407 964 23 2 1 963 771488785 771487823 0.000000e+00 1640
4 TraesCS3B01G541800 chr3B 97.306 965 25 1 1 964 43881004 43881968 0.000000e+00 1637
5 TraesCS3B01G541800 chr3B 87.801 1410 135 18 965 2347 780061042 780059643 0.000000e+00 1616
6 TraesCS3B01G541800 chr3B 87.775 1366 136 11 965 2307 779714136 779712779 0.000000e+00 1568
7 TraesCS3B01G541800 chr3B 87.116 1366 143 12 965 2307 779989589 779988234 0.000000e+00 1517
8 TraesCS3B01G541800 chr3B 87.080 1339 138 9 963 2281 779646079 779644756 0.000000e+00 1482
9 TraesCS3B01G541800 chr3B 87.656 721 75 9 1591 2307 779975000 779974290 0.000000e+00 826
10 TraesCS3B01G541800 chr3B 88.067 419 43 4 1888 2306 779813246 779812835 8.290000e-135 490
11 TraesCS3B01G541800 chr3B 89.316 234 20 2 2335 2568 779644508 779644280 3.250000e-74 289
12 TraesCS3B01G541800 chr3B 89.447 199 21 0 2377 2575 779818284 779818086 4.260000e-63 252
13 TraesCS3B01G541800 chr3B 88.442 199 23 0 2377 2575 779812802 779812604 9.220000e-60 241
14 TraesCS3B01G541800 chr3D 88.198 1415 126 12 965 2347 583001406 583000001 0.000000e+00 1650
15 TraesCS3B01G541800 chr3D 82.909 1650 199 47 965 2578 582899598 582897996 0.000000e+00 1408
16 TraesCS3B01G541800 chr3D 82.606 1650 196 51 965 2578 582930012 582928418 0.000000e+00 1373
17 TraesCS3B01G541800 chr3D 89.715 982 81 8 965 1926 582909634 582908653 0.000000e+00 1236
18 TraesCS3B01G541800 chr3D 89.308 982 85 8 965 1926 582920781 582919800 0.000000e+00 1214
19 TraesCS3B01G541800 chr3D 90.057 875 68 7 965 1820 582922056 582921182 0.000000e+00 1116
20 TraesCS3B01G541800 chr3D 81.134 1235 156 42 1379 2578 582934964 582933772 0.000000e+00 918
21 TraesCS3B01G541800 chr3D 92.647 204 15 0 2375 2578 583000002 582999799 6.980000e-76 294
22 TraesCS3B01G541800 chr3D 91.111 90 6 2 1936 2024 582908506 582908418 1.250000e-23 121
23 TraesCS3B01G541800 chr3D 91.111 90 6 2 1936 2024 582919653 582919565 1.250000e-23 121
24 TraesCS3B01G541800 chr1B 97.409 965 24 1 1 964 609986799 609987763 0.000000e+00 1642
25 TraesCS3B01G541800 chr5B 97.308 966 25 1 1 965 709667768 709666803 0.000000e+00 1639
26 TraesCS3B01G541800 chr6B 97.308 966 23 2 1 964 578590525 578591489 0.000000e+00 1637
27 TraesCS3B01G541800 chr4B 97.306 965 25 1 1 964 438647568 438646604 0.000000e+00 1637
28 TraesCS3B01G541800 chr4B 97.205 966 25 2 1 965 57586475 57585511 0.000000e+00 1633
29 TraesCS3B01G541800 chr4B 97.205 966 26 1 1 965 163821295 163820330 0.000000e+00 1633
30 TraesCS3B01G541800 chr2B 96.923 975 26 4 1 971 110662241 110661267 0.000000e+00 1631
31 TraesCS3B01G541800 chrUn 89.620 684 51 10 1263 1926 384980110 384980793 0.000000e+00 852
32 TraesCS3B01G541800 chrUn 86.870 655 67 3 1025 1660 471057466 471058120 0.000000e+00 715
33 TraesCS3B01G541800 chrUn 88.780 410 42 1 1691 2096 475746719 475746310 1.380000e-137 499
34 TraesCS3B01G541800 chrUn 87.678 422 45 4 1885 2306 341036639 341037053 3.860000e-133 484
35 TraesCS3B01G541800 chrUn 86.301 438 41 10 2142 2578 370989216 370988797 2.340000e-125 459
36 TraesCS3B01G541800 chrUn 86.429 420 49 5 1888 2307 388576771 388576360 1.090000e-123 453
37 TraesCS3B01G541800 chrUn 86.190 420 50 5 1888 2307 41606262 41605851 5.060000e-122 448
38 TraesCS3B01G541800 chrUn 86.341 410 48 5 1888 2297 349985928 349985527 8.470000e-120 440
39 TraesCS3B01G541800 chrUn 86.150 361 32 9 2142 2502 475804843 475804501 8.710000e-100 374
40 TraesCS3B01G541800 chrUn 89.447 199 21 0 2377 2575 41609688 41609490 4.260000e-63 252
41 TraesCS3B01G541800 chrUn 87.864 206 23 2 2372 2575 341037079 341037284 9.220000e-60 241
42 TraesCS3B01G541800 chrUn 90.608 181 17 0 2395 2575 388576310 388576130 9.220000e-60 241
43 TraesCS3B01G541800 chrUn 89.503 181 19 0 2395 2575 41605801 41605621 2.000000e-56 230
44 TraesCS3B01G541800 chrUn 91.111 90 6 2 1936 2024 370990103 370990015 1.250000e-23 121
45 TraesCS3B01G541800 chr6A 80.308 909 132 29 1001 1866 932282 933186 0.000000e+00 643
46 TraesCS3B01G541800 chr6A 81.905 210 36 2 1661 1869 982395 982187 2.640000e-40 176
47 TraesCS3B01G541800 chr6D 79.538 909 137 29 1001 1865 1760655 1761558 1.020000e-168 603
48 TraesCS3B01G541800 chr6D 79.515 908 139 30 1001 1865 1903389 1902486 1.020000e-168 603
49 TraesCS3B01G541800 chr6D 76.432 908 158 33 1001 1865 1849984 1849090 8.470000e-120 440
50 TraesCS3B01G541800 chr6D 84.259 216 31 3 1656 1869 1645292 1645506 9.350000e-50 207
51 TraesCS3B01G541800 chr6D 81.944 216 36 3 1656 1869 1649001 1649215 2.040000e-41 180
52 TraesCS3B01G541800 chr6D 83.444 151 24 1 1719 1869 1811756 1811607 3.460000e-29 139


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 TraesCS3B01G541800 chr3B 779700577 779703155 2578 True 4763.0 4763 100.000000 1 2579 1 chr3B.!!$R3 2578
1 TraesCS3B01G541800 chr3B 779692780 779694122 1342 True 1997.0 1997 93.699000 965 2294 1 chr3B.!!$R2 1329
2 TraesCS3B01G541800 chr3B 780088697 780090055 1358 True 1642.0 1642 88.734000 965 2308 1 chr3B.!!$R9 1343
3 TraesCS3B01G541800 chr3B 771487823 771488785 962 True 1640.0 1640 97.407000 1 963 1 chr3B.!!$R1 962
4 TraesCS3B01G541800 chr3B 43881004 43881968 964 False 1637.0 1637 97.306000 1 964 1 chr3B.!!$F1 963
5 TraesCS3B01G541800 chr3B 780059643 780061042 1399 True 1616.0 1616 87.801000 965 2347 1 chr3B.!!$R8 1382
6 TraesCS3B01G541800 chr3B 779712779 779714136 1357 True 1568.0 1568 87.775000 965 2307 1 chr3B.!!$R4 1342
7 TraesCS3B01G541800 chr3B 779988234 779989589 1355 True 1517.0 1517 87.116000 965 2307 1 chr3B.!!$R7 1342
8 TraesCS3B01G541800 chr3B 779644280 779646079 1799 True 885.5 1482 88.198000 963 2568 2 chr3B.!!$R10 1605
9 TraesCS3B01G541800 chr3B 779974290 779975000 710 True 826.0 826 87.656000 1591 2307 1 chr3B.!!$R6 716
10 TraesCS3B01G541800 chr3B 779812604 779813246 642 True 365.5 490 88.254500 1888 2575 2 chr3B.!!$R11 687
11 TraesCS3B01G541800 chr3D 582897996 582899598 1602 True 1408.0 1408 82.909000 965 2578 1 chr3D.!!$R1 1613
12 TraesCS3B01G541800 chr3D 582928418 582934964 6546 True 1145.5 1373 81.870000 965 2578 2 chr3D.!!$R4 1613
13 TraesCS3B01G541800 chr3D 582999799 583001406 1607 True 972.0 1650 90.422500 965 2578 2 chr3D.!!$R5 1613
14 TraesCS3B01G541800 chr3D 582919565 582922056 2491 True 817.0 1214 90.158667 965 2024 3 chr3D.!!$R3 1059
15 TraesCS3B01G541800 chr3D 582908418 582909634 1216 True 678.5 1236 90.413000 965 2024 2 chr3D.!!$R2 1059
16 TraesCS3B01G541800 chr1B 609986799 609987763 964 False 1642.0 1642 97.409000 1 964 1 chr1B.!!$F1 963
17 TraesCS3B01G541800 chr5B 709666803 709667768 965 True 1639.0 1639 97.308000 1 965 1 chr5B.!!$R1 964
18 TraesCS3B01G541800 chr6B 578590525 578591489 964 False 1637.0 1637 97.308000 1 964 1 chr6B.!!$F1 963
19 TraesCS3B01G541800 chr4B 438646604 438647568 964 True 1637.0 1637 97.306000 1 964 1 chr4B.!!$R3 963
20 TraesCS3B01G541800 chr4B 57585511 57586475 964 True 1633.0 1633 97.205000 1 965 1 chr4B.!!$R1 964
21 TraesCS3B01G541800 chr4B 163820330 163821295 965 True 1633.0 1633 97.205000 1 965 1 chr4B.!!$R2 964
22 TraesCS3B01G541800 chr2B 110661267 110662241 974 True 1631.0 1631 96.923000 1 971 1 chr2B.!!$R1 970
23 TraesCS3B01G541800 chrUn 384980110 384980793 683 False 852.0 852 89.620000 1263 1926 1 chrUn.!!$F1 663
24 TraesCS3B01G541800 chrUn 471057466 471058120 654 False 715.0 715 86.870000 1025 1660 1 chrUn.!!$F2 635
25 TraesCS3B01G541800 chrUn 341036639 341037284 645 False 362.5 484 87.771000 1885 2575 2 chrUn.!!$F3 690
26 TraesCS3B01G541800 chrUn 388576130 388576771 641 True 347.0 453 88.518500 1888 2575 2 chrUn.!!$R6 687
27 TraesCS3B01G541800 chrUn 41605621 41609688 4067 True 310.0 448 88.380000 1888 2575 3 chrUn.!!$R4 687
28 TraesCS3B01G541800 chrUn 370988797 370990103 1306 True 290.0 459 88.706000 1936 2578 2 chrUn.!!$R5 642
29 TraesCS3B01G541800 chr6A 932282 933186 904 False 643.0 643 80.308000 1001 1866 1 chr6A.!!$F1 865
30 TraesCS3B01G541800 chr6D 1760655 1761558 903 False 603.0 603 79.538000 1001 1865 1 chr6D.!!$F1 864
31 TraesCS3B01G541800 chr6D 1902486 1903389 903 True 603.0 603 79.515000 1001 1865 1 chr6D.!!$R3 864
32 TraesCS3B01G541800 chr6D 1849090 1849984 894 True 440.0 440 76.432000 1001 1865 1 chr6D.!!$R2 864

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
752 756 3.795826 GCCGAACTAGTGCACCTATACAG 60.796 52.174 14.63 4.06 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 7190 0.320858 TGGATCAAACGGCAGCGTTA 60.321 50.0 1.11 0.0 0.0 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
49 51 6.047870 CCCTCTACTCTCTTGTGATGAATTG 58.952 44.000 0.00 0.00 0.00 2.32
50 52 6.127225 CCCTCTACTCTCTTGTGATGAATTGA 60.127 42.308 0.00 0.00 0.00 2.57
54 56 8.370940 TCTACTCTCTTGTGATGAATTGACTTT 58.629 33.333 0.00 0.00 0.00 2.66
76 79 8.319146 ACTTTCCCTTTGAAGTTATCTTATCGA 58.681 33.333 0.00 0.00 33.63 3.59
183 187 4.669206 ATGTTTTGGTGATCAACTTGCA 57.331 36.364 12.94 6.34 34.67 4.08
752 756 3.795826 GCCGAACTAGTGCACCTATACAG 60.796 52.174 14.63 4.06 0.00 2.74
809 814 5.049405 AGAGACTCTTTGTTATTTGGTTGCG 60.049 40.000 0.00 0.00 0.00 4.85
811 816 3.886505 ACTCTTTGTTATTTGGTTGCGGA 59.113 39.130 0.00 0.00 0.00 5.54
840 845 4.214310 TGAGAGAGACCATCTTCATCCTC 58.786 47.826 0.00 0.00 38.84 3.71
980 4969 7.288810 AGACATCAAAGAGCAACCAAATAAA 57.711 32.000 0.00 0.00 0.00 1.40
1102 5092 2.548127 GAAAGCCCAGAATGCGGTGC 62.548 60.000 0.00 0.00 31.97 5.01
1200 5190 2.218603 GTCGTTGAAGAAGAGGCCAAA 58.781 47.619 5.01 0.00 0.00 3.28
1268 5267 0.877743 CCGATCATCTCTGCGCTCTA 59.122 55.000 9.73 0.00 0.00 2.43
1368 5367 0.250553 TCGATGGTGCCGGAAAGTTT 60.251 50.000 5.05 0.00 0.00 2.66
1455 5457 2.584064 CTCATGGCGCCCTACACA 59.416 61.111 26.77 3.54 0.00 3.72
1487 5489 2.203640 AGTGTCGGAGGACTGCCA 60.204 61.111 0.00 0.00 43.79 4.92
1551 6828 4.109050 GCGAGGAGATCTTTGAGTACTTG 58.891 47.826 0.00 0.00 0.00 3.16
1565 6870 5.014202 TGAGTACTTGGCATACACTAGTCA 58.986 41.667 0.00 0.00 0.00 3.41
1730 7060 2.034221 GACCAAGGGAGGCCACAC 59.966 66.667 5.01 0.00 0.00 3.82
1820 7150 1.123928 GTCAAGATCCCCATCGGACT 58.876 55.000 0.00 0.00 46.09 3.85
1860 7190 0.617820 AGTATGTCCCGAGGCCAACT 60.618 55.000 5.01 0.00 0.00 3.16
1913 7255 1.062148 CGTCGTCTCGTCTATGCTTGA 59.938 52.381 0.00 0.00 0.00 3.02
1926 7406 1.292992 TGCTTGACTATGCTCATGCG 58.707 50.000 6.95 0.00 41.85 4.73
1960 7440 6.475727 AGATCTACCAATCGATTTGTAACGTG 59.524 38.462 19.23 10.37 33.15 4.49
2239 8475 1.414919 TGTTGCAACGTAGACCCTTCT 59.585 47.619 23.79 0.00 35.66 2.85
2298 8539 0.908656 CATTTGCCATCCCCCAACCA 60.909 55.000 0.00 0.00 0.00 3.67
2342 8776 1.173913 CCCCGTCCATTTCAACTTCC 58.826 55.000 0.00 0.00 0.00 3.46
2353 8787 7.614192 GTCCATTTCAACTTCCCTTTAATCCTA 59.386 37.037 0.00 0.00 0.00 2.94
2355 8789 8.416329 CCATTTCAACTTCCCTTTAATCCTATG 58.584 37.037 0.00 0.00 0.00 2.23
2359 8793 8.618240 TCAACTTCCCTTTAATCCTATGTCTA 57.382 34.615 0.00 0.00 0.00 2.59
2393 8857 2.649531 TTTCTTTCCTTTCCTCGGCA 57.350 45.000 0.00 0.00 0.00 5.69
2429 8893 1.408266 GGAGCCACGTACCATTTCCAT 60.408 52.381 0.00 0.00 0.00 3.41
2505 8969 5.163561 TGGAAGAAACCACTGACATTGTTTC 60.164 40.000 12.93 12.93 44.23 2.78
2546 9012 3.023946 CAAATCGTTGGTGCATGGAAA 57.976 42.857 0.00 0.00 0.00 3.13
2561 9027 6.311200 GTGCATGGAAATTGTAGGTTTTGATC 59.689 38.462 0.00 0.00 0.00 2.92
2575 9041 7.741027 AGGTTTTGATCTCATAGTGCATATG 57.259 36.000 0.00 0.00 42.40 1.78
2578 9044 9.056005 GGTTTTGATCTCATAGTGCATATGTAA 57.944 33.333 4.29 0.00 41.82 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 51 8.604890 CGATAAGATAACTTCAAAGGGAAAGTC 58.395 37.037 0.00 0.00 37.53 3.01
50 52 8.319146 TCGATAAGATAACTTCAAAGGGAAAGT 58.681 33.333 0.00 0.00 37.53 2.66
54 56 9.109393 CAATTCGATAAGATAACTTCAAAGGGA 57.891 33.333 0.00 0.00 37.53 4.20
76 79 9.903682 CATCAAGTGTTCATAAAAGACTCAATT 57.096 29.630 0.00 0.00 0.00 2.32
183 187 0.834612 TCCCAAGTGTCACGAAACCT 59.165 50.000 0.00 0.00 0.00 3.50
702 706 7.983307 AGAGATGAAGATACAAGTGCAAAATC 58.017 34.615 0.00 0.00 0.00 2.17
752 756 5.715434 ACACACCCAATACAATGGTAAAC 57.285 39.130 0.00 0.00 38.91 2.01
809 814 3.753294 TGGTCTCTCTCAAACAACTCC 57.247 47.619 0.00 0.00 0.00 3.85
811 816 5.070981 TGAAGATGGTCTCTCTCAAACAACT 59.929 40.000 0.00 0.00 31.03 3.16
980 4969 1.526917 GCCGCCATGGTTGCTCTAT 60.527 57.895 14.67 0.00 41.21 1.98
1074 5063 1.136329 TCTGGGCTTTCTCTGGGCTT 61.136 55.000 0.00 0.00 0.00 4.35
1185 5175 1.416401 ACGACTTTGGCCTCTTCTTCA 59.584 47.619 3.32 0.00 0.00 3.02
1187 5177 1.270893 GGACGACTTTGGCCTCTTCTT 60.271 52.381 3.32 0.00 0.00 2.52
1200 5190 2.034376 AGGCACTCGAGGACGACT 59.966 61.111 18.41 9.39 43.81 4.18
1268 5267 2.672996 GGACACCGCCTTGCATGT 60.673 61.111 0.00 0.00 31.56 3.21
1368 5367 1.138036 CAGGCGGTCGTCGAATACA 59.862 57.895 0.00 0.00 42.43 2.29
1455 5457 1.075482 CACTGCCACTGGTTGGGAT 59.925 57.895 0.00 0.00 46.39 3.85
1487 5489 3.054802 GGAGAAGGTGATGAACATGGAGT 60.055 47.826 0.00 0.00 0.00 3.85
1680 7010 1.056660 CCCTTACCACACAGTCACCT 58.943 55.000 0.00 0.00 0.00 4.00
1820 7150 3.733236 CGGAGCCAAATCTCACGTA 57.267 52.632 0.00 0.00 34.84 3.57
1860 7190 0.320858 TGGATCAAACGGCAGCGTTA 60.321 50.000 1.11 0.00 0.00 3.18
1926 7406 3.425625 CGATTGGTAGATCTAGCGAGCTC 60.426 52.174 26.63 18.71 37.12 4.09
1931 7411 5.223382 ACAAATCGATTGGTAGATCTAGCG 58.777 41.667 23.22 10.53 43.66 4.26
1934 7414 7.646526 CACGTTACAAATCGATTGGTAGATCTA 59.353 37.037 21.56 7.52 43.66 1.98
2239 8475 1.140312 ACAGAAAGGGACAGGAAGCA 58.860 50.000 0.00 0.00 0.00 3.91
2367 8801 6.350194 GCCGAGGAAAGGAAAGAAATAACAAT 60.350 38.462 0.00 0.00 0.00 2.71
2368 8802 5.048294 GCCGAGGAAAGGAAAGAAATAACAA 60.048 40.000 0.00 0.00 0.00 2.83
2370 8804 4.457949 TGCCGAGGAAAGGAAAGAAATAAC 59.542 41.667 0.00 0.00 0.00 1.89
2386 8850 1.448540 GAGGTGTCATGTGCCGAGG 60.449 63.158 0.00 0.00 0.00 4.63
2393 8857 1.340405 GCTCCCAATGAGGTGTCATGT 60.340 52.381 0.00 0.00 43.04 3.21
2429 8893 1.487976 GGCATGTCTCTCTCCATGGAA 59.512 52.381 17.00 6.19 39.06 3.53
2474 8938 1.145738 AGTGGTTTCTTCCATGCCAGT 59.854 47.619 0.00 0.00 39.81 4.00
2541 9006 9.177608 CTATGAGATCAAAACCTACAATTTCCA 57.822 33.333 0.00 0.00 0.00 3.53
2546 9012 7.112122 TGCACTATGAGATCAAAACCTACAAT 58.888 34.615 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.