Multiple sequence alignment - TraesCS7A01G513700

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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 TraesCS7A01G513700 chr7A 100.000 3560 0 0 1 3560 700299311 700302870 0.000000e+00 6575.0
1 TraesCS7A01G513700 chr7A 99.271 3565 21 2 1 3560 700337124 700340688 0.000000e+00 6434.0
2 TraesCS7A01G513700 chr7A 87.500 152 19 0 1205 1356 700387290 700387441 3.650000e-40 176.0
3 TraesCS7A01G513700 chr7A 89.189 111 11 1 1475 1584 700377539 700377649 1.720000e-28 137.0
4 TraesCS7A01G513700 chr7D 94.227 2373 96 15 636 2994 610421864 610419519 0.000000e+00 3585.0
5 TraesCS7A01G513700 chr7D 92.737 2382 117 18 635 2994 608272528 608274875 0.000000e+00 3389.0
6 TraesCS7A01G513700 chr7D 90.593 2158 121 27 635 2784 608222218 608224301 0.000000e+00 2785.0
7 TraesCS7A01G513700 chr7D 92.335 1396 97 6 1601 2994 514918648 514920035 0.000000e+00 1977.0
8 TraesCS7A01G513700 chr7D 92.637 584 30 9 1 571 514907648 514908231 0.000000e+00 828.0
9 TraesCS7A01G513700 chr7D 87.129 404 18 13 2970 3360 610419591 610419209 9.130000e-116 427.0
10 TraesCS7A01G513700 chr7D 86.253 371 24 13 3192 3560 608274970 608275315 9.330000e-101 377.0
11 TraesCS7A01G513700 chr7D 90.661 257 20 4 319 571 608221448 608221704 4.400000e-89 339.0
12 TraesCS7A01G513700 chr7D 96.203 158 6 0 2970 3127 608274803 608274960 3.530000e-65 259.0
13 TraesCS7A01G513700 chr7D 90.244 82 8 0 1 82 610425138 610425057 1.350000e-19 108.0
14 TraesCS7A01G513700 chr7D 100.000 28 0 0 610 637 610421928 610421901 6.000000e-03 52.8
15 TraesCS7A01G513700 chr7B 91.938 2369 148 14 656 2994 696238503 696240858 0.000000e+00 3277.0
16 TraesCS7A01G513700 chr7B 94.287 2118 110 6 878 2994 698682699 698684806 0.000000e+00 3230.0
17 TraesCS7A01G513700 chr7B 94.681 1711 88 3 1286 2994 693664476 693666185 0.000000e+00 2652.0
18 TraesCS7A01G513700 chr7B 90.283 1626 117 11 636 2241 693681605 693683209 0.000000e+00 2089.0
19 TraesCS7A01G513700 chr7B 95.407 762 25 3 2233 2994 693684866 693685617 0.000000e+00 1205.0
20 TraesCS7A01G513700 chr7B 95.144 762 27 3 2233 2994 693698819 693699570 0.000000e+00 1194.0
21 TraesCS7A01G513700 chr7B 91.978 536 32 6 1 525 693662376 693662911 0.000000e+00 741.0
22 TraesCS7A01G513700 chr7B 89.109 606 22 13 2970 3560 696240786 696241362 0.000000e+00 713.0
23 TraesCS7A01G513700 chr7B 88.614 606 25 13 2970 3560 698684734 698685310 0.000000e+00 697.0
24 TraesCS7A01G513700 chr7B 86.645 614 31 15 2970 3560 693699498 693700083 1.800000e-177 632.0
25 TraesCS7A01G513700 chr7B 86.567 603 34 20 2970 3560 694749363 694749930 3.900000e-174 621.0
26 TraesCS7A01G513700 chr7B 77.399 938 132 39 638 1561 696297608 696298479 5.340000e-133 484.0
27 TraesCS7A01G513700 chr7B 89.203 389 30 9 1 379 696229656 696230042 3.220000e-130 475.0
28 TraesCS7A01G513700 chr7B 87.376 404 17 9 2970 3360 693685545 693685927 1.960000e-117 433.0
29 TraesCS7A01G513700 chr7B 86.667 390 23 14 1 380 694745984 694746354 4.280000e-109 405.0
30 TraesCS7A01G513700 chr7B 90.728 302 7 7 2971 3272 693716444 693716724 2.010000e-102 383.0
31 TraesCS7A01G513700 chr7B 89.189 296 28 3 2702 2994 693716221 693716515 2.020000e-97 366.0
32 TraesCS7A01G513700 chr7B 89.964 279 12 5 635 899 693663757 693664033 2.630000e-91 346.0
33 TraesCS7A01G513700 chr7B 91.469 211 8 3 3352 3560 693716743 693716945 7.520000e-72 281.0
34 TraesCS7A01G513700 chr7B 94.475 181 7 2 635 814 698682486 698682664 3.500000e-70 276.0
35 TraesCS7A01G513700 chr7B 95.070 142 6 1 933 1073 693664325 693664466 4.630000e-54 222.0
36 TraesCS7A01G513700 chr7B 95.745 94 3 1 393 486 694746337 694746429 2.210000e-32 150.0
37 TraesCS7A01G513700 chr7B 94.286 35 1 1 603 637 693714095 693714128 6.000000e-03 52.8
38 TraesCS7A01G513700 chr7B 100.000 28 0 0 610 637 696238411 696238438 6.000000e-03 52.8
39 TraesCS7A01G513700 chrUn 93.422 2189 114 8 812 2994 77521232 77523396 0.000000e+00 3217.0
40 TraesCS7A01G513700 chrUn 90.239 1629 118 11 636 2244 364810900 364809293 0.000000e+00 2089.0
41 TraesCS7A01G513700 chrUn 95.144 762 27 3 2233 2994 349917742 349916991 0.000000e+00 1194.0
42 TraesCS7A01G513700 chrUn 87.240 674 54 10 636 1289 344773387 344772726 0.000000e+00 739.0
43 TraesCS7A01G513700 chrUn 88.449 606 28 11 2970 3560 77523324 77523902 0.000000e+00 693.0
44 TraesCS7A01G513700 chrUn 89.109 303 12 7 2970 3272 349917063 349916782 1.220000e-94 357.0
45 TraesCS7A01G513700 chrUn 87.109 256 19 8 319 571 77514669 77514913 9.730000e-71 278.0
46 TraesCS7A01G513700 chrUn 89.450 218 10 1 3156 3360 254016968 254017185 2.730000e-66 263.0
47 TraesCS7A01G513700 chrUn 89.450 218 10 1 3156 3360 254027857 254028074 2.730000e-66 263.0
48 TraesCS7A01G513700 chr4A 91.264 538 36 8 1 527 662054456 662053919 0.000000e+00 723.0
49 TraesCS7A01G513700 chr4A 86.701 391 28 6 635 1011 662053132 662052752 2.560000e-111 412.0
50 TraesCS7A01G513700 chr4A 90.722 291 19 3 3272 3560 735216070 735215786 7.210000e-102 381.0
51 TraesCS7A01G513700 chr4A 91.270 252 16 6 322 570 735185010 735184762 4.400000e-89 339.0


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 TraesCS7A01G513700 chr7A 700299311 700302870 3559 False 6575.000000 6575 100.000000 1 3560 1 chr7A.!!$F1 3559
1 TraesCS7A01G513700 chr7A 700337124 700340688 3564 False 6434.000000 6434 99.271000 1 3560 1 chr7A.!!$F2 3559
2 TraesCS7A01G513700 chr7D 514918648 514920035 1387 False 1977.000000 1977 92.335000 1601 2994 1 chr7D.!!$F2 1393
3 TraesCS7A01G513700 chr7D 608221448 608224301 2853 False 1562.000000 2785 90.627000 319 2784 2 chr7D.!!$F3 2465
4 TraesCS7A01G513700 chr7D 608272528 608275315 2787 False 1341.666667 3389 91.731000 635 3560 3 chr7D.!!$F4 2925
5 TraesCS7A01G513700 chr7D 610419209 610425138 5929 True 1043.200000 3585 92.900000 1 3360 4 chr7D.!!$R1 3359
6 TraesCS7A01G513700 chr7D 514907648 514908231 583 False 828.000000 828 92.637000 1 571 1 chr7D.!!$F1 570
7 TraesCS7A01G513700 chr7B 698682486 698685310 2824 False 1401.000000 3230 92.458667 635 3560 3 chr7B.!!$F9 2925
8 TraesCS7A01G513700 chr7B 696238411 696241362 2951 False 1347.600000 3277 93.682333 610 3560 3 chr7B.!!$F8 2950
9 TraesCS7A01G513700 chr7B 693681605 693685927 4322 False 1242.333333 2089 91.022000 636 3360 3 chr7B.!!$F4 2724
10 TraesCS7A01G513700 chr7B 693662376 693666185 3809 False 990.250000 2652 92.923250 1 2994 4 chr7B.!!$F3 2993
11 TraesCS7A01G513700 chr7B 693698819 693700083 1264 False 913.000000 1194 90.894500 2233 3560 2 chr7B.!!$F5 1327
12 TraesCS7A01G513700 chr7B 696297608 696298479 871 False 484.000000 484 77.399000 638 1561 1 chr7B.!!$F2 923
13 TraesCS7A01G513700 chr7B 694745984 694749930 3946 False 392.000000 621 89.659667 1 3560 3 chr7B.!!$F7 3559
14 TraesCS7A01G513700 chr7B 693714095 693716945 2850 False 270.700000 383 91.418000 603 3560 4 chr7B.!!$F6 2957
15 TraesCS7A01G513700 chrUn 364809293 364810900 1607 True 2089.000000 2089 90.239000 636 2244 1 chrUn.!!$R2 1608
16 TraesCS7A01G513700 chrUn 77521232 77523902 2670 False 1955.000000 3217 90.935500 812 3560 2 chrUn.!!$F4 2748
17 TraesCS7A01G513700 chrUn 349916782 349917742 960 True 775.500000 1194 92.126500 2233 3272 2 chrUn.!!$R3 1039
18 TraesCS7A01G513700 chrUn 344772726 344773387 661 True 739.000000 739 87.240000 636 1289 1 chrUn.!!$R1 653
19 TraesCS7A01G513700 chr4A 662052752 662054456 1704 True 567.500000 723 88.982500 1 1011 2 chr4A.!!$R3 1010

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
49 50 5.536161 AGTGCTTCATACTGTTCCACAAAAT 59.464 36.0 0.0 0.0 0.00 1.82 F
50 51 5.630680 GTGCTTCATACTGTTCCACAAAATG 59.369 40.0 0.0 0.0 0.00 2.32 F
1899 5512 0.452987 CAACGGGCAAGTCCATCATG 59.547 55.0 0.0 0.0 36.21 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 4979 0.401738 CCTTGGACTGCCTCTTGGAA 59.598 55.000 0.0 0.0 34.57 3.53 R
1899 5512 2.287909 GCAGTCGATGTCCTCTATGACC 60.288 54.545 0.0 0.0 34.25 4.02 R
3393 8943 1.072806 TGCCTCTTCTGCACACTCATT 59.927 47.619 0.0 0.0 32.85 2.57 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 50 5.536161 AGTGCTTCATACTGTTCCACAAAAT 59.464 36.0 0.0 0.0 0.00 1.82
50 51 5.630680 GTGCTTCATACTGTTCCACAAAATG 59.369 40.0 0.0 0.0 0.00 2.32
1899 5512 0.452987 CAACGGGCAAGTCCATCATG 59.547 55.0 0.0 0.0 36.21 3.07
2490 7946 2.550180 GACAGAGGTGAAGAAAGGCAAC 59.450 50.0 0.0 0.0 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 3.615597 AGGACGACCTCCATGATCA 57.384 52.632 0.0 0.0 44.13 2.92
1368 4979 0.401738 CCTTGGACTGCCTCTTGGAA 59.598 55.000 0.0 0.0 34.57 3.53
1677 5290 4.128580 TCCTGGAACGCCATGAGA 57.871 55.556 0.0 0.0 44.91 3.27
1899 5512 2.287909 GCAGTCGATGTCCTCTATGACC 60.288 54.545 0.0 0.0 34.25 4.02
2490 7946 3.005897 TGTCCTTCTCTTTGTCTTCCTCG 59.994 47.826 0.0 0.0 0.00 4.63
3393 8943 1.072806 TGCCTCTTCTGCACACTCATT 59.927 47.619 0.0 0.0 32.85 2.57


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

AutoCloner maintained by Alex Coulton.