Multiple sequence alignment - TraesCS5D01G193400

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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 TraesCS5D01G193400 chr5D 100.000 2875 0 0 1 2875 297735900 297738774 0.000000e+00 5310.0
1 TraesCS5D01G193400 chr5A 95.348 2472 65 14 1 2446 401318629 401316182 0.000000e+00 3882.0
2 TraesCS5D01G193400 chr5A 96.011 351 10 1 2525 2875 401316186 401315840 4.160000e-158 568.0
3 TraesCS5D01G193400 chr5B 96.770 1424 34 5 139 1562 338480436 338481847 0.000000e+00 2364.0
4 TraesCS5D01G193400 chr5B 96.710 851 19 2 1605 2446 338481845 338482695 0.000000e+00 1408.0
5 TraesCS5D01G193400 chr5B 98.174 219 4 0 2525 2743 338482691 338482909 1.620000e-102 383.0
6 TraesCS5D01G193400 chr5B 97.842 139 3 0 1 139 338475903 338476041 1.030000e-59 241.0
7 TraesCS5D01G193400 chr5B 96.296 135 5 0 2741 2875 338483021 338483155 3.730000e-54 222.0
8 TraesCS5D01G193400 chrUn 81.053 1557 242 27 927 2449 250030275 250031812 0.000000e+00 1192.0
9 TraesCS5D01G193400 chrUn 82.920 1130 162 15 1340 2440 282477066 282475939 0.000000e+00 989.0
10 TraesCS5D01G193400 chrUn 82.489 1125 166 15 1340 2435 267761120 267762242 0.000000e+00 957.0
11 TraesCS5D01G193400 chrUn 82.447 1128 167 15 1340 2438 334501261 334500136 0.000000e+00 957.0
12 TraesCS5D01G193400 chrUn 83.368 962 131 8 1245 2178 337451567 337452527 0.000000e+00 863.0
13 TraesCS5D01G193400 chrUn 83.160 962 133 8 1245 2178 313921520 313920560 0.000000e+00 852.0
14 TraesCS5D01G193400 chrUn 77.277 1043 200 22 1336 2361 287225064 287226086 1.920000e-161 579.0
15 TraesCS5D01G193400 chrUn 77.277 1043 200 22 1336 2361 287476962 287477984 1.920000e-161 579.0
16 TraesCS5D01G193400 chrUn 77.277 1043 200 22 1339 2364 323542288 323541266 1.920000e-161 579.0
17 TraesCS5D01G193400 chrUn 79.545 660 120 12 1173 1824 311734908 311735560 9.390000e-125 457.0
18 TraesCS5D01G193400 chrUn 79.545 660 120 12 1173 1824 311738782 311739434 9.390000e-125 457.0
19 TraesCS5D01G193400 chrUn 92.523 107 4 4 2442 2545 17148598 17148703 1.780000e-32 150.0
20 TraesCS5D01G193400 chrUn 95.918 49 2 0 1003 1051 40974170 40974122 2.370000e-11 80.5
21 TraesCS5D01G193400 chrUn 87.879 66 8 0 1000 1065 45471425 45471490 8.540000e-11 78.7
22 TraesCS5D01G193400 chr3D 78.168 1539 260 50 938 2444 570146641 570145147 0.000000e+00 911.0
23 TraesCS5D01G193400 chr3D 77.718 1481 267 34 964 2404 520319268 520317811 0.000000e+00 848.0
24 TraesCS5D01G193400 chr3D 73.128 1496 327 51 964 2434 497867575 497869020 1.560000e-127 466.0
25 TraesCS5D01G193400 chr3D 83.668 398 46 11 948 1327 520153028 520153424 9.800000e-95 357.0
26 TraesCS5D01G193400 chr3D 96.774 93 3 0 2443 2535 509255197 509255105 3.840000e-34 156.0
27 TraesCS5D01G193400 chr3D 89.394 66 7 0 1000 1065 567190484 567190549 1.840000e-12 84.2
28 TraesCS5D01G193400 chr3B 83.263 711 107 7 932 1632 756627779 756628487 0.000000e+00 643.0
29 TraesCS5D01G193400 chr3B 77.332 1147 221 25 1233 2361 756613663 756614788 2.420000e-180 641.0
30 TraesCS5D01G193400 chr3B 77.301 1119 214 22 1276 2369 684770167 684771270 8.750000e-175 623.0
31 TraesCS5D01G193400 chr3B 80.848 778 110 15 1681 2450 756656138 756656884 2.480000e-160 575.0
32 TraesCS5D01G193400 chr3B 72.941 1615 344 61 856 2434 658489808 658491365 2.590000e-130 475.0
33 TraesCS5D01G193400 chr3B 76.395 466 85 15 1937 2382 756682901 756682441 8.010000e-56 228.0
34 TraesCS5D01G193400 chr3B 93.269 104 7 0 2431 2534 620988996 620988893 1.380000e-33 154.0
35 TraesCS5D01G193400 chr3A 73.769 1422 294 55 955 2347 702952843 702951472 1.200000e-133 486.0
36 TraesCS5D01G193400 chr3A 83.417 398 47 11 948 1327 655572389 655572785 4.560000e-93 351.0
37 TraesCS5D01G193400 chr3A 88.793 116 9 1 943 1054 702556043 702556158 3.860000e-29 139.0
38 TraesCS5D01G193400 chr3A 89.000 100 11 0 964 1063 655886632 655886533 1.080000e-24 124.0
39 TraesCS5D01G193400 chr4B 96.809 94 3 0 2434 2527 178078909 178078816 1.070000e-34 158.0
40 TraesCS5D01G193400 chr7D 96.774 93 3 0 2442 2534 49828775 49828867 3.840000e-34 156.0
41 TraesCS5D01G193400 chr7D 95.556 90 4 0 2439 2528 287708654 287708743 8.300000e-31 145.0
42 TraesCS5D01G193400 chr4A 95.000 100 4 1 2428 2527 712733696 712733794 3.840000e-34 156.0
43 TraesCS5D01G193400 chr1B 95.000 100 4 1 2440 2539 164770363 164770461 3.840000e-34 156.0
44 TraesCS5D01G193400 chr1B 94.000 100 6 0 2437 2536 5510598 5510697 4.960000e-33 152.0


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 TraesCS5D01G193400 chr5D 297735900 297738774 2874 False 5310.00 5310 100.0000 1 2875 1 chr5D.!!$F1 2874
1 TraesCS5D01G193400 chr5A 401315840 401318629 2789 True 2225.00 3882 95.6795 1 2875 2 chr5A.!!$R1 2874
2 TraesCS5D01G193400 chr5B 338480436 338483155 2719 False 1094.25 2364 96.9875 139 2875 4 chr5B.!!$F2 2736
3 TraesCS5D01G193400 chrUn 250030275 250031812 1537 False 1192.00 1192 81.0530 927 2449 1 chrUn.!!$F3 1522
4 TraesCS5D01G193400 chrUn 282475939 282477066 1127 True 989.00 989 82.9200 1340 2440 1 chrUn.!!$R2 1100
5 TraesCS5D01G193400 chrUn 267761120 267762242 1122 False 957.00 957 82.4890 1340 2435 1 chrUn.!!$F4 1095
6 TraesCS5D01G193400 chrUn 334500136 334501261 1125 True 957.00 957 82.4470 1340 2438 1 chrUn.!!$R5 1098
7 TraesCS5D01G193400 chrUn 337451567 337452527 960 False 863.00 863 83.3680 1245 2178 1 chrUn.!!$F7 933
8 TraesCS5D01G193400 chrUn 313920560 313921520 960 True 852.00 852 83.1600 1245 2178 1 chrUn.!!$R3 933
9 TraesCS5D01G193400 chrUn 287225064 287226086 1022 False 579.00 579 77.2770 1336 2361 1 chrUn.!!$F5 1025
10 TraesCS5D01G193400 chrUn 287476962 287477984 1022 False 579.00 579 77.2770 1336 2361 1 chrUn.!!$F6 1025
11 TraesCS5D01G193400 chrUn 323541266 323542288 1022 True 579.00 579 77.2770 1339 2364 1 chrUn.!!$R4 1025
12 TraesCS5D01G193400 chrUn 311734908 311739434 4526 False 457.00 457 79.5450 1173 1824 2 chrUn.!!$F8 651
13 TraesCS5D01G193400 chr3D 570145147 570146641 1494 True 911.00 911 78.1680 938 2444 1 chr3D.!!$R3 1506
14 TraesCS5D01G193400 chr3D 520317811 520319268 1457 True 848.00 848 77.7180 964 2404 1 chr3D.!!$R2 1440
15 TraesCS5D01G193400 chr3D 497867575 497869020 1445 False 466.00 466 73.1280 964 2434 1 chr3D.!!$F1 1470
16 TraesCS5D01G193400 chr3B 756627779 756628487 708 False 643.00 643 83.2630 932 1632 1 chr3B.!!$F4 700
17 TraesCS5D01G193400 chr3B 756613663 756614788 1125 False 641.00 641 77.3320 1233 2361 1 chr3B.!!$F3 1128
18 TraesCS5D01G193400 chr3B 684770167 684771270 1103 False 623.00 623 77.3010 1276 2369 1 chr3B.!!$F2 1093
19 TraesCS5D01G193400 chr3B 756656138 756656884 746 False 575.00 575 80.8480 1681 2450 1 chr3B.!!$F5 769
20 TraesCS5D01G193400 chr3B 658489808 658491365 1557 False 475.00 475 72.9410 856 2434 1 chr3B.!!$F1 1578
21 TraesCS5D01G193400 chr3A 702951472 702952843 1371 True 486.00 486 73.7690 955 2347 1 chr3A.!!$R2 1392

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
97 111 0.32586 TGCCTCGGGTACTATTGGGT 60.326 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2363 2.479837 ACTTCGCTTTGTCGATCACAA 58.52 42.857 6.62 6.62 43.68 3.33 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
36 37 5.480073 CAGGAGAAAGTATGAGGATAGAGGG 59.520 48.000 0.00 0.00 0.00 4.30
38 39 4.164204 AGAAAGTATGAGGATAGAGGGCC 58.836 47.826 0.00 0.00 0.00 5.80
40 41 2.896039 AGTATGAGGATAGAGGGCCAC 58.104 52.381 6.18 0.00 0.00 5.01
88 89 2.978824 GCACTCTTGCCTCGGGTA 59.021 61.111 0.00 0.00 43.66 3.69
97 111 0.325860 TGCCTCGGGTACTATTGGGT 60.326 55.000 0.00 0.00 0.00 4.51
344 362 5.163591 TGCATCACTATTTGAAGGCTGAATG 60.164 40.000 0.00 0.00 38.68 2.67
638 657 4.760530 ATAATGCCTCTGCTAGTGACAA 57.239 40.909 0.00 0.00 38.71 3.18
734 753 2.550830 AATCTGCGAGTGACAGGTTT 57.449 45.000 0.00 0.00 34.86 3.27
843 862 4.389374 GCCCTACTATTGCTGCTGATAAA 58.611 43.478 0.00 0.00 0.00 1.40
886 905 3.070159 ACATCCCCGTTGATCATAGACAG 59.930 47.826 0.00 0.00 0.00 3.51
889 908 3.772572 TCCCCGTTGATCATAGACAGAAA 59.227 43.478 0.00 0.00 0.00 2.52
1065 1095 5.598830 ACACAACTCCAGTATCCAGGTATAG 59.401 44.000 0.00 0.00 0.00 1.31
1574 1649 2.939460 ACAAGCTTGTTGTTGTGACC 57.061 45.000 26.36 0.00 38.47 4.02
2093 2363 5.453339 CGATCTTATGGTATGGTTGACAGGT 60.453 44.000 0.00 0.00 0.00 4.00
2173 2810 3.233507 GAAGAGCTGAGGGAGATCATCT 58.766 50.000 0.00 0.00 39.79 2.90
2249 2886 2.730934 ATGGACAGCATGCTCTTCAT 57.269 45.000 19.68 14.65 42.53 2.57
2451 3580 4.323104 GCATGATTATCAGGTACTCCCTCC 60.323 50.000 8.65 0.00 43.86 4.30
2458 3587 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
2460 3589 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
2462 3591 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2463 3592 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2464 3593 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2465 3594 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2470 3599 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2471 3600 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2472 3601 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2535 3672 3.255395 GGACGGAGGGAGTACTTTATAGC 59.745 52.174 0.00 0.00 0.00 2.97
2836 5361 4.667519 GGTAGATCAAAGTACCGATGGT 57.332 45.455 0.00 0.00 40.16 3.55
2853 5378 5.455899 CCGATGGTCCCTACTAGTACTACTT 60.456 48.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.132805 TCTATCCTCATACTTTCTCCTGGAAA 58.867 38.462 0.00 0.00 41.11 3.13
36 37 2.556287 CTTTCGCCTTGACGTGGC 59.444 61.111 5.33 5.33 46.42 5.01
38 39 2.170985 CGCTTTCGCCTTGACGTG 59.829 61.111 0.00 0.00 0.00 4.49
82 83 1.477700 CGTTCACCCAATAGTACCCGA 59.522 52.381 0.00 0.00 0.00 5.14
83 84 1.205417 ACGTTCACCCAATAGTACCCG 59.795 52.381 0.00 0.00 0.00 5.28
85 86 4.067192 ACAAACGTTCACCCAATAGTACC 58.933 43.478 0.00 0.00 0.00 3.34
87 88 4.515944 CCAACAAACGTTCACCCAATAGTA 59.484 41.667 0.00 0.00 0.00 1.82
88 89 3.316868 CCAACAAACGTTCACCCAATAGT 59.683 43.478 0.00 0.00 0.00 2.12
97 111 2.115911 AGCGCCCAACAAACGTTCA 61.116 52.632 2.29 0.00 0.00 3.18
151 166 6.369065 GGACAAAGAATATTTCAGTCGACACT 59.631 38.462 19.50 0.00 32.56 3.55
344 362 5.586243 TCAAGCAGCAAGATAATGAACTACC 59.414 40.000 0.00 0.00 0.00 3.18
843 862 0.538287 GTTTCTGGGCTTCTGGCTGT 60.538 55.000 0.00 0.00 41.46 4.40
886 905 7.430992 AGTACCGGAAGTTCAATACTTTTTC 57.569 36.000 9.46 0.00 47.00 2.29
889 908 7.812690 AAAAGTACCGGAAGTTCAATACTTT 57.187 32.000 21.21 21.21 47.00 2.66
1065 1095 3.025262 AGTGAACTAATCGAGAGGGGAC 58.975 50.000 0.00 0.00 0.00 4.46
2093 2363 2.479837 ACTTCGCTTTGTCGATCACAA 58.520 42.857 6.62 6.62 43.68 3.33
2173 2810 1.553704 GGAAAAGGAGCCCTCGTCTTA 59.446 52.381 0.00 0.00 30.89 2.10
2249 2886 2.270352 ATTCACAAACGAGCTTGGGA 57.730 45.000 5.79 0.00 36.94 4.37
2496 3625 5.996644 TCCGTCCCATAATGTAAGATGTTT 58.003 37.500 0.00 0.00 0.00 2.83
2497 3626 5.454755 CCTCCGTCCCATAATGTAAGATGTT 60.455 44.000 0.00 0.00 0.00 2.71
2501 3630 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2502 3631 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2503 3632 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2505 3634 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2506 3635 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2510 3647 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2514 3651 3.887716 TGCTATAAAGTACTCCCTCCGTC 59.112 47.826 0.00 0.00 0.00 4.79
2836 5361 3.200825 ACGGCAAGTAGTACTAGTAGGGA 59.799 47.826 10.68 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.