Multiple sequence alignment - TraesCS7A01G287300

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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 TraesCS7A01G287300 chr7A 100.000 1646 0 0 806 2451 342306033 342304388 0.000000e+00 3040.0
1 TraesCS7A01G287300 chr7A 95.107 981 46 2 806 1785 533368333 533367354 0.000000e+00 1544.0
2 TraesCS7A01G287300 chr7A 96.106 565 17 4 1778 2337 533341279 533340715 0.000000e+00 917.0
3 TraesCS7A01G287300 chr7A 100.000 359 0 0 1 359 342306838 342306480 0.000000e+00 664.0
4 TraesCS7A01G287300 chr7A 94.937 237 11 1 124 359 533368618 533368382 1.070000e-98 370.0
5 TraesCS7A01G287300 chr7A 94.495 109 4 2 1 109 533368704 533368598 1.510000e-37 167.0
6 TraesCS7A01G287300 chr2D 95.901 1659 54 7 806 2451 397963349 397961692 0.000000e+00 2675.0
7 TraesCS7A01G287300 chr2D 94.841 1570 70 5 892 2451 54392198 54393766 0.000000e+00 2440.0
8 TraesCS7A01G287300 chr2D 95.501 978 35 6 1480 2449 250920887 250919911 0.000000e+00 1554.0
9 TraesCS7A01G287300 chr2D 82.890 789 68 31 1255 1996 100318539 100317771 0.000000e+00 647.0
10 TraesCS7A01G287300 chr2D 94.958 238 10 2 1 238 54391445 54391680 2.980000e-99 372.0
11 TraesCS7A01G287300 chr1D 95.048 1656 70 7 806 2450 465259862 465261516 0.000000e+00 2593.0
12 TraesCS7A01G287300 chr1D 83.547 468 44 19 1993 2449 403280267 403279822 8.160000e-110 407.0
13 TraesCS7A01G287300 chr1D 87.739 261 26 6 1 260 82790421 82790166 1.420000e-77 300.0
14 TraesCS7A01G287300 chr6D 96.103 975 31 5 1477 2449 288070267 288071236 0.000000e+00 1583.0
15 TraesCS7A01G287300 chr6D 93.380 287 13 5 2164 2449 452251262 452251543 1.050000e-113 420.0
16 TraesCS7A01G287300 chr6D 76.978 417 56 19 806 1217 2175900 2175519 4.130000e-48 202.0
17 TraesCS7A01G287300 chr6D 76.978 417 56 19 806 1217 2182059 2181678 4.130000e-48 202.0
18 TraesCS7A01G287300 chr6D 93.617 47 2 1 2120 2165 452251299 452251345 4.370000e-08 69.4
19 TraesCS7A01G287300 chr7D 93.458 642 39 3 1484 2122 157759016 157759657 0.000000e+00 950.0
20 TraesCS7A01G287300 chr7D 89.456 294 19 6 1310 1603 157758736 157759017 6.440000e-96 361.0
21 TraesCS7A01G287300 chr7D 93.617 47 2 1 2120 2165 556661077 556661031 4.370000e-08 69.4
22 TraesCS7A01G287300 chr7B 86.755 755 62 12 815 1564 359363786 359364507 0.000000e+00 806.0
23 TraesCS7A01G287300 chr7B 89.011 364 27 9 4 359 675595331 675594973 2.890000e-119 438.0
24 TraesCS7A01G287300 chr7B 90.391 281 25 2 1 281 359363221 359363499 3.850000e-98 368.0
25 TraesCS7A01G287300 chr7B 81.765 340 35 12 806 1139 675594911 675594593 2.420000e-65 259.0
26 TraesCS7A01G287300 chr3B 84.876 767 62 17 806 1564 762576242 762576962 0.000000e+00 725.0
27 TraesCS7A01G287300 chr3B 83.706 761 72 26 1258 1999 245922964 245922237 0.000000e+00 671.0
28 TraesCS7A01G287300 chr3B 93.380 287 14 5 2164 2449 739237567 739237285 1.050000e-113 420.0
29 TraesCS7A01G287300 chr3B 93.357 286 15 4 2164 2449 740382202 740382483 1.050000e-113 420.0
30 TraesCS7A01G287300 chr3B 93.478 46 3 0 2120 2165 198376226 198376271 4.370000e-08 69.4
31 TraesCS7A01G287300 chr1B 87.160 662 51 5 908 1564 126506643 126507275 0.000000e+00 721.0
32 TraesCS7A01G287300 chr1B 90.526 285 24 3 4 288 126505946 126506227 8.280000e-100 374.0
33 TraesCS7A01G287300 chr5A 86.212 689 59 16 806 1489 675835758 675836415 0.000000e+00 713.0
34 TraesCS7A01G287300 chr5A 92.193 269 19 2 1 269 675835191 675835457 1.780000e-101 379.0
35 TraesCS7A01G287300 chr5A 82.353 272 30 9 1 260 183030518 183030253 1.140000e-53 220.0
36 TraesCS7A01G287300 chr2B 90.850 306 23 5 1 306 49635551 49635851 2.930000e-109 405.0
37 TraesCS7A01G287300 chr2B 86.555 238 24 4 908 1139 49636142 49636377 3.130000e-64 255.0
38 TraesCS7A01G287300 chr6A 88.031 259 27 2 101 359 69498793 69498539 1.100000e-78 303.0
39 TraesCS7A01G287300 chr4D 84.564 298 22 9 806 1098 295253335 295253057 8.630000e-70 274.0
40 TraesCS7A01G287300 chr4A 90.306 196 14 1 908 1098 536096 535901 4.050000e-63 252.0
41 TraesCS7A01G287300 chr3D 82.986 288 25 11 1255 1530 284206241 284205966 3.150000e-59 239.0
42 TraesCS7A01G287300 chr6B 86.014 143 17 3 1115 1256 699124120 699124260 1.520000e-32 150.0
43 TraesCS7A01G287300 chr6B 95.000 40 0 2 1300 1337 608039267 608039306 7.320000e-06 62.1
44 TraesCS7A01G287300 chr2A 75.953 341 54 14 806 1146 549138167 549137855 1.520000e-32 150.0
45 TraesCS7A01G287300 chr2A 91.579 95 8 0 265 359 303639468 303639374 5.500000e-27 132.0
46 TraesCS7A01G287300 chr1A 74.608 319 53 14 806 1124 379190302 379190012 5.540000e-22 115.0
47 TraesCS7A01G287300 chr1A 91.026 78 7 0 1343 1420 65759542 65759465 3.330000e-19 106.0


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 TraesCS7A01G287300 chr7A 342304388 342306838 2450 True 1852.000000 3040 100.000000 1 2451 2 chr7A.!!$R2 2450
1 TraesCS7A01G287300 chr7A 533340715 533341279 564 True 917.000000 917 96.106000 1778 2337 1 chr7A.!!$R1 559
2 TraesCS7A01G287300 chr7A 533367354 533368704 1350 True 693.666667 1544 94.846333 1 1785 3 chr7A.!!$R3 1784
3 TraesCS7A01G287300 chr2D 397961692 397963349 1657 True 2675.000000 2675 95.901000 806 2451 1 chr2D.!!$R3 1645
4 TraesCS7A01G287300 chr2D 250919911 250920887 976 True 1554.000000 1554 95.501000 1480 2449 1 chr2D.!!$R2 969
5 TraesCS7A01G287300 chr2D 54391445 54393766 2321 False 1406.000000 2440 94.899500 1 2451 2 chr2D.!!$F1 2450
6 TraesCS7A01G287300 chr2D 100317771 100318539 768 True 647.000000 647 82.890000 1255 1996 1 chr2D.!!$R1 741
7 TraesCS7A01G287300 chr1D 465259862 465261516 1654 False 2593.000000 2593 95.048000 806 2450 1 chr1D.!!$F1 1644
8 TraesCS7A01G287300 chr6D 288070267 288071236 969 False 1583.000000 1583 96.103000 1477 2449 1 chr6D.!!$F1 972
9 TraesCS7A01G287300 chr7D 157758736 157759657 921 False 655.500000 950 91.457000 1310 2122 2 chr7D.!!$F1 812
10 TraesCS7A01G287300 chr7B 359363221 359364507 1286 False 587.000000 806 88.573000 1 1564 2 chr7B.!!$F1 1563
11 TraesCS7A01G287300 chr7B 675594593 675595331 738 True 348.500000 438 85.388000 4 1139 2 chr7B.!!$R1 1135
12 TraesCS7A01G287300 chr3B 762576242 762576962 720 False 725.000000 725 84.876000 806 1564 1 chr3B.!!$F3 758
13 TraesCS7A01G287300 chr3B 245922237 245922964 727 True 671.000000 671 83.706000 1258 1999 1 chr3B.!!$R1 741
14 TraesCS7A01G287300 chr1B 126505946 126507275 1329 False 547.500000 721 88.843000 4 1564 2 chr1B.!!$F1 1560
15 TraesCS7A01G287300 chr5A 675835191 675836415 1224 False 546.000000 713 89.202500 1 1489 2 chr5A.!!$F1 1488
16 TraesCS7A01G287300 chr2B 49635551 49636377 826 False 330.000000 405 88.702500 1 1139 2 chr2B.!!$F1 1138

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
145 154 1.144936 CAACCATCTCCCTCGCTCC 59.855 63.158 0.0 0.0 0.0 4.70 F
245 254 1.198094 TGACCCAAGATCGAGCCCAA 61.198 55.000 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1453 0.036010 CCACAGGCGAACTTGAGGAT 60.036 55.000 0.00 0.0 0.00 3.24 R
1853 2048 2.046892 TGCAGGGCGCTTCTCTTC 60.047 61.111 7.64 0.0 43.06 2.87 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
48 49 3.984732 GGCTGCCTTCACCCCCTT 61.985 66.667 12.43 0.00 0.00 3.95
89 90 2.032071 CACAACCCGTCTCACCCC 59.968 66.667 0.00 0.00 0.00 4.95
145 154 1.144936 CAACCATCTCCCTCGCTCC 59.855 63.158 0.00 0.00 0.00 4.70
214 223 1.703438 CGACGACCCTCACCGTAGAG 61.703 65.000 0.00 0.00 39.30 2.43
245 254 1.198094 TGACCCAAGATCGAGCCCAA 61.198 55.000 0.00 0.00 0.00 4.12
326 335 2.324541 CCCGATTCCTCTCCAATCTCT 58.675 52.381 0.00 0.00 0.00 3.10
348 357 3.000819 TCGCCGTTGATCCCCACT 61.001 61.111 0.00 0.00 0.00 4.00
352 361 2.186903 CGTTGATCCCCACTCCCG 59.813 66.667 0.00 0.00 0.00 5.14
930 939 3.210012 ATGGGGCGCACCAGTTCTT 62.210 57.895 37.68 17.88 45.20 2.52
984 1019 2.315781 GATGGAGGTCAGCCGCATCA 62.316 60.000 0.00 0.00 40.50 3.07
985 1020 1.913951 ATGGAGGTCAGCCGCATCAA 61.914 55.000 0.00 0.00 40.50 2.57
1049 1089 2.425592 CACCACACCGGAGCTTGA 59.574 61.111 9.46 0.00 38.63 3.02
1158 1198 2.047750 TCATGCGTGGCTTGCGTA 60.048 55.556 5.98 0.00 34.38 4.42
1348 1407 2.757124 GGACGAGGGGATGGCCAAT 61.757 63.158 10.96 0.00 35.15 3.16
1633 1824 2.766828 GGGTCATCACTAAGTAGGTGCT 59.233 50.000 0.00 0.00 34.97 4.40
1710 1902 2.876581 GGGAACTTGTCATGTTTCCCT 58.123 47.619 15.32 0.00 37.15 4.20
1853 2048 9.090692 CCAAGAAAAGTAATTTTGCATATCCAG 57.909 33.333 5.49 0.00 0.00 3.86
1961 2167 5.373812 GGAAATTCCTGAACTGATCCCTA 57.626 43.478 4.46 0.00 32.53 3.53
2101 2308 6.494491 TGTTTTGGATGATGAACTTGATCCTT 59.506 34.615 0.00 0.00 36.17 3.36
2108 2315 8.782144 GGATGATGAACTTGATCCTTCTTAATC 58.218 37.037 0.00 0.00 32.95 1.75
2156 2363 2.362077 GCTGTAAATGTGCCCCCTTATG 59.638 50.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.876342 GATCCTGGACAATCGGACGC 60.876 60.000 0.00 0.00 0.00 5.19
48 49 1.895131 GGGTTAAGTGGGTGAGACGTA 59.105 52.381 0.00 0.00 0.00 3.57
89 90 1.104577 GCGTAGGAGAGAGGGTGAGG 61.105 65.000 0.00 0.00 0.00 3.86
245 254 0.827925 TTCACTCGTGAGTCTGGGCT 60.828 55.000 0.00 0.00 40.20 5.19
984 1019 1.522355 CATCGCGCAGGTGGATCTT 60.522 57.895 8.75 0.00 0.00 2.40
985 1020 2.107750 CATCGCGCAGGTGGATCT 59.892 61.111 8.75 0.00 0.00 2.75
1049 1089 2.433145 CGACGACCAGCACAGCAT 60.433 61.111 0.00 0.00 0.00 3.79
1158 1198 3.732938 GGGGGTCAGATCTGCAGT 58.267 61.111 18.36 0.42 0.00 4.40
1348 1407 1.856802 CGAGGATGATGTCGATGCAA 58.143 50.000 0.00 0.00 38.50 4.08
1394 1453 0.036010 CCACAGGCGAACTTGAGGAT 60.036 55.000 0.00 0.00 0.00 3.24
1422 1481 3.702048 CCGGGACAAAGCTCGGGA 61.702 66.667 0.00 0.00 38.93 5.14
1521 1589 2.600731 CAAAAGCACGTTCAACACCAA 58.399 42.857 0.00 0.00 0.00 3.67
1853 2048 2.046892 TGCAGGGCGCTTCTCTTC 60.047 61.111 7.64 0.00 43.06 2.87
1873 2069 5.763204 GGAACAGAGATGGAAGTAACAACAA 59.237 40.000 0.00 0.00 0.00 2.83
1961 2167 3.443681 CACAAACAACAACCAGAGGAAGT 59.556 43.478 0.00 0.00 0.00 3.01
2270 2486 7.393551 ACAAGATGACAAAGTTAATTTTGCG 57.606 32.000 19.86 2.09 40.80 4.85


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

AutoCloner maintained by Alex Coulton.