Multiple sequence alignment - TraesCS7B01G184700

Loading Multiple Alignment...

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 TraesCS7B01G184700 chr7B 100.000 2231 0 0 1 2231 298615389 298613159 0.000000e+00 4120
1 TraesCS7B01G184700 chr7B 94.702 1642 77 6 597 2231 357295839 357294201 0.000000e+00 2542
2 TraesCS7B01G184700 chr7B 94.585 1145 54 2 594 1730 341856898 341858042 0.000000e+00 1764
3 TraesCS7B01G184700 chr7B 94.439 935 40 4 597 1520 527364450 527363517 0.000000e+00 1428
4 TraesCS7B01G184700 chr7B 96.389 720 25 1 594 1313 393401862 393402580 0.000000e+00 1184
5 TraesCS7B01G184700 chr7B 95.730 726 30 1 594 1319 565089749 565090473 0.000000e+00 1168
6 TraesCS7B01G184700 chr7B 95.051 687 32 1 1545 2231 115634816 115635500 0.000000e+00 1079
7 TraesCS7B01G184700 chr7B 96.672 601 19 1 1 601 527365104 527364505 0.000000e+00 998
8 TraesCS7B01G184700 chr7B 96.506 601 20 1 1 601 341856237 341856836 0.000000e+00 992
9 TraesCS7B01G184700 chr7B 96.007 601 23 1 1 601 357296503 357295904 0.000000e+00 976
10 TraesCS7B01G184700 chr7B 99.020 204 2 0 1317 1520 149015942 149015739 1.260000e-97 366
11 TraesCS7B01G184700 chr7B 97.076 171 5 0 431 601 393401630 393401800 2.800000e-74 289
12 TraesCS7B01G184700 chr7B 97.076 171 5 0 431 601 423562954 423562784 2.800000e-74 289
13 TraesCS7B01G184700 chr7B 97.076 171 5 0 431 601 565089517 565089687 2.800000e-74 289
14 TraesCS7B01G184700 chr2B 95.323 727 28 3 594 1319 359310132 359310853 0.000000e+00 1149
15 TraesCS7B01G184700 chr2B 95.055 728 31 3 597 1319 197240460 197239733 0.000000e+00 1140
16 TraesCS7B01G184700 chr2B 99.020 204 2 0 1317 1520 251443303 251443506 1.260000e-97 366
17 TraesCS7B01G184700 chr6B 95.062 729 33 1 594 1319 366629698 366630426 0.000000e+00 1144
18 TraesCS7B01G184700 chr6B 94.469 687 37 1 1545 2231 649089349 649090034 0.000000e+00 1057
19 TraesCS7B01G184700 chr6B 98.246 171 3 0 431 601 366629466 366629636 1.290000e-77 300
20 TraesCS7B01G184700 chr6B 97.076 171 5 0 431 601 512245095 512244925 2.800000e-74 289
21 TraesCS7B01G184700 chr6A 94.744 723 38 0 597 1319 249295157 249294435 0.000000e+00 1125
22 TraesCS7B01G184700 chrUn 95.488 687 29 2 1545 2231 267256791 267256107 0.000000e+00 1096
23 TraesCS7B01G184700 chr5B 95.197 687 33 0 1545 2231 362783757 362783071 0.000000e+00 1086
24 TraesCS7B01G184700 chr5B 94.485 689 35 3 1545 2231 389349601 389348914 0.000000e+00 1059
25 TraesCS7B01G184700 chr5B 98.605 430 5 1 1 430 412623053 412623481 0.000000e+00 760
26 TraesCS7B01G184700 chr5B 99.507 203 1 0 1318 1520 112486596 112486798 9.730000e-99 370
27 TraesCS7B01G184700 chr5B 99.020 204 2 0 1317 1520 157227869 157227666 1.260000e-97 366
28 TraesCS7B01G184700 chr5B 98.246 171 3 0 431 601 558899337 558899507 1.290000e-77 300
29 TraesCS7B01G184700 chr4B 95.058 688 32 2 1545 2231 633588540 633587854 0.000000e+00 1081
30 TraesCS7B01G184700 chr1B 94.760 687 35 1 1545 2231 486126677 486125992 0.000000e+00 1068
31 TraesCS7B01G184700 chr1B 99.020 204 2 0 1317 1520 533704882 533704679 1.260000e-97 366
32 TraesCS7B01G184700 chr3B 94.469 687 37 1 1545 2231 532704940 532705625 0.000000e+00 1057
33 TraesCS7B01G184700 chr3B 98.608 431 4 2 1 430 429648707 429648278 0.000000e+00 761
34 TraesCS7B01G184700 chr3B 99.020 204 2 0 1317 1520 321618062 321618265 1.260000e-97 366
35 TraesCS7B01G184700 chr3B 99.020 204 2 0 1317 1520 665181799 665181596 1.260000e-97 366
36 TraesCS7B01G184700 chr6D 98.605 430 5 1 1 430 131054891 131055319 0.000000e+00 760
37 TraesCS7B01G184700 chr5D 98.605 430 5 1 1 430 243979014 243979442 0.000000e+00 760
38 TraesCS7B01G184700 chr1D 98.605 430 5 1 1 430 86545802 86546230 0.000000e+00 760
39 TraesCS7B01G184700 chr1D 98.605 430 5 1 1 430 402983057 402982629 0.000000e+00 760


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 TraesCS7B01G184700 chr7B 298613159 298615389 2230 True 4120.0 4120 100.0000 1 2231 1 chr7B.!!$R2 2230
1 TraesCS7B01G184700 chr7B 357294201 357296503 2302 True 1759.0 2542 95.3545 1 2231 2 chr7B.!!$R4 2230
2 TraesCS7B01G184700 chr7B 341856237 341858042 1805 False 1378.0 1764 95.5455 1 1730 2 chr7B.!!$F2 1729
3 TraesCS7B01G184700 chr7B 527363517 527365104 1587 True 1213.0 1428 95.5555 1 1520 2 chr7B.!!$R5 1519
4 TraesCS7B01G184700 chr7B 115634816 115635500 684 False 1079.0 1079 95.0510 1545 2231 1 chr7B.!!$F1 686
5 TraesCS7B01G184700 chr7B 393401630 393402580 950 False 736.5 1184 96.7325 431 1313 2 chr7B.!!$F3 882
6 TraesCS7B01G184700 chr7B 565089517 565090473 956 False 728.5 1168 96.4030 431 1319 2 chr7B.!!$F4 888
7 TraesCS7B01G184700 chr2B 359310132 359310853 721 False 1149.0 1149 95.3230 594 1319 1 chr2B.!!$F2 725
8 TraesCS7B01G184700 chr2B 197239733 197240460 727 True 1140.0 1140 95.0550 597 1319 1 chr2B.!!$R1 722
9 TraesCS7B01G184700 chr6B 649089349 649090034 685 False 1057.0 1057 94.4690 1545 2231 1 chr6B.!!$F1 686
10 TraesCS7B01G184700 chr6B 366629466 366630426 960 False 722.0 1144 96.6540 431 1319 2 chr6B.!!$F2 888
11 TraesCS7B01G184700 chr6A 249294435 249295157 722 True 1125.0 1125 94.7440 597 1319 1 chr6A.!!$R1 722
12 TraesCS7B01G184700 chrUn 267256107 267256791 684 True 1096.0 1096 95.4880 1545 2231 1 chrUn.!!$R1 686
13 TraesCS7B01G184700 chr5B 362783071 362783757 686 True 1086.0 1086 95.1970 1545 2231 1 chr5B.!!$R2 686
14 TraesCS7B01G184700 chr5B 389348914 389349601 687 True 1059.0 1059 94.4850 1545 2231 1 chr5B.!!$R3 686
15 TraesCS7B01G184700 chr4B 633587854 633588540 686 True 1081.0 1081 95.0580 1545 2231 1 chr4B.!!$R1 686
16 TraesCS7B01G184700 chr1B 486125992 486126677 685 True 1068.0 1068 94.7600 1545 2231 1 chr1B.!!$R1 686
17 TraesCS7B01G184700 chr3B 532704940 532705625 685 False 1057.0 1057 94.4690 1545 2231 1 chr3B.!!$F2 686

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
838 930 1.00444 GCAGACCGGCTTCAGAAGT 60.004 57.895 11.94 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1749 0.24746 CCTCTTGATCGTGAGCACCA 59.753 55.0 8.7 0.0 0.0 4.17 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
26 27 3.956199 ACGGGTATCGATAGGTTTCTTCA 59.044 43.478 5.09 0.00 42.43 3.02
77 78 7.559897 ACAAACATCCGGGTGAAATAGATAAAT 59.440 33.333 24.73 0.00 0.00 1.40
388 389 9.268268 TCTTTCACCAGTACTGTAGTAAAAATG 57.732 33.333 21.18 4.68 31.52 2.32
417 418 7.331791 ACATGGAAGATTCTAGACTAAACCAC 58.668 38.462 0.00 0.00 0.00 4.16
468 469 1.164041 CGGCCTCCACAAAAGTCGTT 61.164 55.000 0.00 0.00 0.00 3.85
545 546 1.269012 CCCAAGGACATTGCACCAAT 58.731 50.000 0.00 0.00 37.60 3.16
595 675 2.815647 CGGTCCAGAAAGCGCTCC 60.816 66.667 12.06 4.35 32.99 4.70
696 776 2.224499 TGGTCACTATTCTGCAGCAACA 60.224 45.455 9.47 0.00 0.00 3.33
811 903 5.007136 GCTTGGCTAGTCATCAACAATAGAC 59.993 44.000 0.00 0.00 0.00 2.59
838 930 1.004440 GCAGACCGGCTTCAGAAGT 60.004 57.895 11.94 0.00 0.00 3.01
988 1080 1.073284 ACATTTACCCGCAGAACTGGT 59.927 47.619 3.99 0.00 39.53 4.00
1001 1093 2.376518 AGAACTGGTCCATGGTTGACAT 59.623 45.455 12.58 0.00 41.57 3.06
1041 1133 0.817634 CCAACGCTTCCAACAGGACA 60.818 55.000 0.00 0.00 0.00 4.02
1054 1146 1.819288 ACAGGACACAATCTCGACGAT 59.181 47.619 0.00 0.00 0.00 3.73
1109 1201 4.321974 GGAAATTTGGAAAGAGCGGAATGT 60.322 41.667 0.00 0.00 0.00 2.71
1120 1212 5.112129 AGAGCGGAATGTTAGGGTATTTT 57.888 39.130 0.00 0.00 0.00 1.82
1149 1241 0.104671 CAGTGCCTGTTGGGGTTTTG 59.895 55.000 0.00 0.00 35.12 2.44
1157 1249 3.492337 CTGTTGGGGTTTTGGTAGCTAA 58.508 45.455 0.00 0.00 0.00 3.09
1252 1346 5.719085 TGATACATTGTATTTGGCCTTTGGT 59.281 36.000 10.55 0.00 0.00 3.67
1313 1410 5.504392 GCAAATCTTTTGCCTTGTTTCAAG 58.496 37.500 12.74 2.90 39.38 3.02
1408 1513 5.592054 CTTAGACAGCGGATTACATTGAGA 58.408 41.667 0.00 0.00 0.00 3.27
1567 1672 0.821517 TGCACCCGTACATCTACCTG 59.178 55.000 0.00 0.00 0.00 4.00
1685 1790 4.220413 CGCTGTCGTCCTCCTCTA 57.780 61.111 0.00 0.00 0.00 2.43
1945 2051 2.817258 GCGCCAGTCTCTATCTCTACAT 59.183 50.000 0.00 0.00 0.00 2.29
1986 2093 4.735132 GTAGTGCTGCGCCGTCCA 62.735 66.667 9.97 0.00 0.00 4.02
2035 2142 2.020694 GCCTCCATCATCACCAACTGG 61.021 57.143 0.00 0.00 42.17 4.00
2092 2200 2.764314 GGTGATGATGGTGTGCCGC 61.764 63.158 0.00 0.00 37.67 6.53
2116 2225 1.650912 GCACGGGCATCTTGCTATG 59.349 57.895 3.77 0.00 44.28 2.23
2143 2252 6.656632 TTTGCATATAAGTCCAAACACCAA 57.343 33.333 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.618890 GTGAGCTCTAGAGATGAGATAATATCT 57.381 37.037 24.24 1.83 43.70 1.98
388 389 8.983724 GTTTAGTCTAGAATCTTCCATGTATGC 58.016 37.037 0.00 0.00 0.00 3.14
417 418 6.183361 TGTCTCTATCCTGGTGTATCCATTTG 60.183 42.308 0.00 0.00 46.12 2.32
468 469 1.980232 ACGAGTACCATCGCCCACA 60.980 57.895 4.57 0.00 46.60 4.17
595 675 4.837860 AGATAGCTTCTCCCATAGGTTGAG 59.162 45.833 0.00 0.00 0.00 3.02
696 776 0.868406 GAAACTGCGCACTGTAAGCT 59.132 50.000 5.66 0.00 37.60 3.74
838 930 0.407528 TTGCAATTAGGCCACCCTCA 59.592 50.000 5.01 0.00 41.75 3.86
1001 1093 1.881925 CGCTCCACCAATTCTTCACCA 60.882 52.381 0.00 0.00 0.00 4.17
1041 1133 2.541178 GGTAAGCGATCGTCGAGATTGT 60.541 50.000 17.81 0.00 43.74 2.71
1054 1146 3.379650 GCATAAGGCAGGTAAGCGA 57.620 52.632 0.00 0.00 43.97 4.93
1109 1201 6.092944 CACTGCGACATTACAAAATACCCTAA 59.907 38.462 0.00 0.00 0.00 2.69
1149 1241 6.018669 CCATCTCGTCTTTGATTTTAGCTACC 60.019 42.308 0.00 0.00 0.00 3.18
1157 1249 1.398390 GCGCCATCTCGTCTTTGATTT 59.602 47.619 0.00 0.00 0.00 2.17
1252 1346 5.222278 AGAAGGAGTATTAGGGGTCTTGA 57.778 43.478 0.00 0.00 0.00 3.02
1313 1410 8.583765 GCATGAATAAAAGTGTATCCGTTTTTC 58.416 33.333 0.00 0.00 0.00 2.29
1543 1648 0.690762 AGATGTACGGGTGCAAGGTT 59.309 50.000 0.00 0.00 0.00 3.50
1567 1672 0.941463 CTGACGCTGACACTGACACC 60.941 60.000 0.00 0.00 0.00 4.16
1589 1694 2.124570 GTGCGTCAGGGGCATCAT 60.125 61.111 0.00 0.00 43.19 2.45
1644 1749 0.247460 CCTCTTGATCGTGAGCACCA 59.753 55.000 8.70 0.00 0.00 4.17
1685 1790 4.148825 CCGCCGCCTGCTAGTCTT 62.149 66.667 0.00 0.00 38.05 3.01
1986 2093 3.923864 TTCAGTCGGGCGTGCAGT 61.924 61.111 0.00 0.00 0.00 4.40
2035 2142 8.439172 TCTCTACTCCTACTCCTATAAAAGACC 58.561 40.741 0.00 0.00 0.00 3.85
2143 2252 1.961394 TGCTCAAAGACCGTGTCTACT 59.039 47.619 6.93 0.00 42.59 2.57


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

AutoCloner maintained by Alex Coulton.