Multiple sequence alignment - TraesCS4A01G155600

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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 TraesCS4A01G155600 chr4A 100.000 1843 0 0 1595 3437 310766007 310767849 0.000000e+00 3404.0
1 TraesCS4A01G155600 chr4A 94.808 1849 87 8 1595 3437 219306660 219304815 0.000000e+00 2874.0
2 TraesCS4A01G155600 chr4A 100.000 1318 0 0 1 1318 310764413 310765730 0.000000e+00 2435.0
3 TraesCS4A01G155600 chr4A 93.404 1319 82 4 1 1318 219307987 219306673 0.000000e+00 1949.0
4 TraesCS4A01G155600 chr5A 96.916 1848 50 6 1595 3437 482026023 482024178 0.000000e+00 3090.0
5 TraesCS4A01G155600 chr5A 96.445 1294 42 3 29 1318 482027333 482026040 0.000000e+00 2132.0
6 TraesCS4A01G155600 chr3B 96.916 1848 45 8 1595 3437 201557429 201555589 0.000000e+00 3086.0
7 TraesCS4A01G155600 chr3B 95.544 1324 52 5 1 1318 201558765 201557443 0.000000e+00 2111.0
8 TraesCS4A01G155600 chr3B 93.277 1294 82 4 29 1318 703007085 703005793 0.000000e+00 1903.0
9 TraesCS4A01G155600 chr3B 89.894 1326 80 36 1 1318 260377253 260378532 0.000000e+00 1657.0
10 TraesCS4A01G155600 chr5B 96.276 1826 57 8 1595 3415 413610801 413612620 0.000000e+00 2985.0
11 TraesCS4A01G155600 chr5B 95.558 1846 66 9 1595 3437 429039996 429041828 0.000000e+00 2940.0
12 TraesCS4A01G155600 chr5B 95.518 1294 53 5 29 1318 413609491 413610783 0.000000e+00 2063.0
13 TraesCS4A01G155600 chr5B 95.183 1204 49 6 117 1318 429038778 429039974 0.000000e+00 1893.0
14 TraesCS4A01G155600 chr6D 94.827 1759 75 10 1595 3349 322235780 322237526 0.000000e+00 2730.0
15 TraesCS4A01G155600 chr2D 97.118 1492 34 3 1595 3083 33937198 33938683 0.000000e+00 2508.0
16 TraesCS4A01G155600 chr2D 95.133 1315 39 4 29 1318 630272340 630273654 0.000000e+00 2050.0
17 TraesCS4A01G155600 chr2D 94.985 1316 40 3 29 1318 33935864 33937179 0.000000e+00 2041.0
18 TraesCS4A01G155600 chr7B 94.419 1505 72 10 1938 3437 105209190 105210687 0.000000e+00 2303.0
19 TraesCS4A01G155600 chr7B 100.000 43 0 0 1 43 41574194 41574236 2.840000e-11 80.5
20 TraesCS4A01G155600 chr1D 96.910 1327 36 4 1595 2918 254420113 254421437 0.000000e+00 2218.0
21 TraesCS4A01G155600 chr1D 100.000 42 0 0 1 42 217272432 217272473 1.020000e-10 78.7
22 TraesCS4A01G155600 chr5D 96.454 1241 39 4 1596 2833 432422076 432420838 0.000000e+00 2043.0
23 TraesCS4A01G155600 chr4D 94.630 1136 59 2 29 1163 245650734 245651868 0.000000e+00 1759.0
24 TraesCS4A01G155600 chr3D 96.429 1008 30 4 2433 3437 76787017 76788021 0.000000e+00 1657.0
25 TraesCS4A01G155600 chr3A 96.057 279 7 1 1044 1318 80222141 80221863 5.230000e-123 451.0
26 TraesCS4A01G155600 chrUn 88.608 237 7 3 1 217 451362453 451362217 1.570000e-68 270.0
27 TraesCS4A01G155600 chrUn 100.000 42 0 0 1 42 8039680 8039639 1.020000e-10 78.7
28 TraesCS4A01G155600 chrUn 100.000 42 0 0 1 42 8042553 8042512 1.020000e-10 78.7
29 TraesCS4A01G155600 chrUn 100.000 42 0 0 1 42 400811815 400811856 1.020000e-10 78.7
30 TraesCS4A01G155600 chrUn 100.000 42 0 0 1 42 448650487 448650528 1.020000e-10 78.7
31 TraesCS4A01G155600 chr2A 97.297 148 2 1 1173 1318 771308534 771308681 2.050000e-62 250.0


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 TraesCS4A01G155600 chr4A 310764413 310767849 3436 False 2919.5 3404 100.0000 1 3437 2 chr4A.!!$F1 3436
1 TraesCS4A01G155600 chr4A 219304815 219307987 3172 True 2411.5 2874 94.1060 1 3437 2 chr4A.!!$R1 3436
2 TraesCS4A01G155600 chr5A 482024178 482027333 3155 True 2611.0 3090 96.6805 29 3437 2 chr5A.!!$R1 3408
3 TraesCS4A01G155600 chr3B 201555589 201558765 3176 True 2598.5 3086 96.2300 1 3437 2 chr3B.!!$R2 3436
4 TraesCS4A01G155600 chr3B 703005793 703007085 1292 True 1903.0 1903 93.2770 29 1318 1 chr3B.!!$R1 1289
5 TraesCS4A01G155600 chr3B 260377253 260378532 1279 False 1657.0 1657 89.8940 1 1318 1 chr3B.!!$F1 1317
6 TraesCS4A01G155600 chr5B 413609491 413612620 3129 False 2524.0 2985 95.8970 29 3415 2 chr5B.!!$F1 3386
7 TraesCS4A01G155600 chr5B 429038778 429041828 3050 False 2416.5 2940 95.3705 117 3437 2 chr5B.!!$F2 3320
8 TraesCS4A01G155600 chr6D 322235780 322237526 1746 False 2730.0 2730 94.8270 1595 3349 1 chr6D.!!$F1 1754
9 TraesCS4A01G155600 chr2D 33935864 33938683 2819 False 2274.5 2508 96.0515 29 3083 2 chr2D.!!$F2 3054
10 TraesCS4A01G155600 chr2D 630272340 630273654 1314 False 2050.0 2050 95.1330 29 1318 1 chr2D.!!$F1 1289
11 TraesCS4A01G155600 chr7B 105209190 105210687 1497 False 2303.0 2303 94.4190 1938 3437 1 chr7B.!!$F2 1499
12 TraesCS4A01G155600 chr1D 254420113 254421437 1324 False 2218.0 2218 96.9100 1595 2918 1 chr1D.!!$F2 1323
13 TraesCS4A01G155600 chr5D 432420838 432422076 1238 True 2043.0 2043 96.4540 1596 2833 1 chr5D.!!$R1 1237
14 TraesCS4A01G155600 chr4D 245650734 245651868 1134 False 1759.0 1759 94.6300 29 1163 1 chr4D.!!$F1 1134
15 TraesCS4A01G155600 chr3D 76787017 76788021 1004 False 1657.0 1657 96.4290 2433 3437 1 chr3D.!!$F1 1004

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
343 369 2.299013 TCTTGGCTCTCTTCACGCTTTA 59.701 45.455 0.0 0.0 0.00 1.85 F
1099 1130 3.254892 GTCTTCGATTTCCACTGGAGAC 58.745 50.000 0.0 0.0 31.21 3.36 F
1689 1723 3.008594 TGGGTATGGGCTTATATGGTTCG 59.991 47.826 0.0 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1694 1.972588 AAGCCCATACCCAGAACTCT 58.027 50.000 0.00 0.0 0.00 3.24 R
2211 2245 3.529319 GCATTGGGATAGATATTCCCCCT 59.471 47.826 8.26 0.0 42.91 4.79 R
3277 3323 2.224305 GCAGGTCCTTATTATCTGCCGT 60.224 50.000 0.00 0.0 43.36 5.68 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
67 69 3.567478 ATCCTCTAAAGAAAGGCGCAT 57.433 42.857 10.83 0.00 32.37 4.73
68 70 2.632377 TCCTCTAAAGAAAGGCGCATG 58.368 47.619 10.83 0.00 32.37 4.06
75 77 7.011828 TCTAAAGAAAGGCGCATGTATTAAC 57.988 36.000 10.83 0.00 0.00 2.01
343 369 2.299013 TCTTGGCTCTCTTCACGCTTTA 59.701 45.455 0.00 0.00 0.00 1.85
421 447 5.459107 GCTTCGTATGGTGTCTACAATACAG 59.541 44.000 5.96 0.00 41.77 2.74
644 671 3.380479 TCGAGAACCGAAGATTGTGTT 57.620 42.857 0.00 0.00 45.43 3.32
655 682 5.440685 CGAAGATTGTGTTGGTTGTAAGAC 58.559 41.667 0.00 0.00 0.00 3.01
692 720 5.064558 TGCCCGACAGAATTTTTAAGTGTA 58.935 37.500 0.00 0.00 0.00 2.90
696 724 5.333492 CCGACAGAATTTTTAAGTGTACGCA 60.333 40.000 9.48 0.00 0.00 5.24
699 728 7.322699 CGACAGAATTTTTAAGTGTACGCATTT 59.677 33.333 9.48 0.00 0.00 2.32
955 986 8.713708 TTTACCTCATAAGGGAAACAAATTCA 57.286 30.769 0.00 0.00 46.72 2.57
1099 1130 3.254892 GTCTTCGATTTCCACTGGAGAC 58.745 50.000 0.00 0.00 31.21 3.36
1255 1287 8.674607 GTGGTCAAATAGGATTATTTTCTTCGT 58.325 33.333 0.00 0.00 37.38 3.85
1689 1723 3.008594 TGGGTATGGGCTTATATGGTTCG 59.991 47.826 0.00 0.00 0.00 3.95
1761 1795 9.301153 CATGCAACCTTGGAAATACTTTTATAC 57.699 33.333 0.00 0.00 30.51 1.47
1881 1915 8.511321 TGTATGCTTTTAGCGGGAATATTATTG 58.489 33.333 0.00 0.00 46.26 1.90
1891 1925 5.123979 GCGGGAATATTATTGAAGATGGGAC 59.876 44.000 0.00 0.00 0.00 4.46
1973 2007 5.245526 CGCCCTGGTTAGTAATAATAGGAGT 59.754 44.000 14.24 0.00 0.00 3.85
2211 2245 5.798934 GCGTCTTGTTTATCTCGAAGAACTA 59.201 40.000 0.00 0.00 34.09 2.24
2308 2342 4.097741 CAGGAATGAGTGGTTTTGTCACAA 59.902 41.667 0.00 0.00 37.58 3.33
2643 2685 7.027778 AGATTTGCTTTGTTTTACTCGTCTT 57.972 32.000 0.00 0.00 0.00 3.01
2816 2859 7.798596 TTAGGTGTTAATGTAAACGAACCAA 57.201 32.000 0.00 0.00 31.17 3.67
2897 2941 8.184304 AGAAATCCTATCGAAGCTATAAGTGT 57.816 34.615 0.00 0.00 0.00 3.55
2918 2962 8.511604 AGTGTAGAATTCATACCTTTCCAATG 57.488 34.615 8.44 0.00 0.00 2.82
3009 3053 5.261040 GATCCCAATTCCAATAGGATCCA 57.739 43.478 15.82 0.00 44.81 3.41
3010 3054 4.729552 TCCCAATTCCAATAGGATCCAG 57.270 45.455 15.82 0.28 45.26 3.86
3294 3340 9.654663 ATTAGAATAACGGCAGATAATAAGGAC 57.345 33.333 0.00 0.00 0.00 3.85
3296 3342 6.270231 AGAATAACGGCAGATAATAAGGACCT 59.730 38.462 0.00 0.00 0.00 3.85
3377 3423 6.766944 TGAGATTGTAGAGCAGGTACTAGTAC 59.233 42.308 22.53 22.53 36.02 2.73
3405 3451 9.294030 GTAGATTGATGCATTTCAGTTAAAAGG 57.706 33.333 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 262 8.471457 CGAATTCGAATTAGCCAATAAATTGTG 58.529 33.333 23.29 0.00 43.02 3.33
237 263 8.188139 ACGAATTCGAATTAGCCAATAAATTGT 58.812 29.630 33.05 7.74 43.02 2.71
404 430 6.381133 TGAGTCATCTGTATTGTAGACACCAT 59.619 38.462 0.00 0.00 0.00 3.55
539 566 4.482386 GACAAGCTCGTACACATTGAGTA 58.518 43.478 0.00 0.00 32.32 2.59
644 671 4.455533 GCAGATTCACATGTCTTACAACCA 59.544 41.667 0.00 0.00 0.00 3.67
655 682 1.721664 CGGGCAGGCAGATTCACATG 61.722 60.000 0.00 0.00 0.00 3.21
699 728 4.400120 ACGTGTTATTTCAGGCCCTAAAA 58.600 39.130 0.00 0.00 0.00 1.52
714 743 3.889538 AGATAGAGCCATGCTACGTGTTA 59.110 43.478 0.00 0.00 39.88 2.41
765 796 5.591472 TCGGTAAAGAGGAATCAGACGATTA 59.409 40.000 0.00 0.00 42.06 1.75
1010 1041 6.303054 TCCAGTTGGAAATGATAACAGAACA 58.697 36.000 0.00 0.00 42.18 3.18
1046 1077 9.600432 TCCATTTATAATCCTCCTTTAATTGGG 57.400 33.333 0.00 0.00 30.11 4.12
1099 1130 3.266510 TGAAAGTCCATCGATTCCCAG 57.733 47.619 0.00 0.00 0.00 4.45
1660 1694 1.972588 AAGCCCATACCCAGAACTCT 58.027 50.000 0.00 0.00 0.00 3.24
1689 1723 7.645058 TTCCAAATCTAATCCTGGTTCATTC 57.355 36.000 0.00 0.00 0.00 2.67
1761 1795 5.045872 GCATAAGCAATAAGGAAGCCAAAG 58.954 41.667 0.00 0.00 41.58 2.77
1881 1915 5.246981 TCAATCCATATGGTCCCATCTTC 57.753 43.478 21.28 0.00 37.82 2.87
1973 2007 6.999871 TGAAGCTGCATAGATTATTTGGATCA 59.000 34.615 1.02 0.00 31.57 2.92
2211 2245 3.529319 GCATTGGGATAGATATTCCCCCT 59.471 47.826 8.26 0.00 42.91 4.79
2621 2657 7.012421 AGAGAAGACGAGTAAAACAAAGCAAAT 59.988 33.333 0.00 0.00 0.00 2.32
2630 2672 9.084164 TGCATTAATAGAGAAGACGAGTAAAAC 57.916 33.333 0.00 0.00 0.00 2.43
2685 2728 5.886960 AGGGTTCTCAAAAATTCGAGATG 57.113 39.130 3.75 0.00 38.06 2.90
2897 2941 7.638444 TCCACATTGGAAAGGTATGAATTCTA 58.362 34.615 7.05 0.00 45.00 2.10
3277 3323 2.224305 GCAGGTCCTTATTATCTGCCGT 60.224 50.000 0.00 0.00 43.36 5.68
3294 3340 2.806608 ATGCAACTCTTTTGTGCAGG 57.193 45.000 3.77 0.00 38.95 4.85
3296 3342 2.886523 AGCTATGCAACTCTTTTGTGCA 59.113 40.909 0.00 0.00 39.91 4.57
3377 3423 5.490139 AACTGAAATGCATCAATCTACGG 57.510 39.130 0.00 0.00 0.00 4.02
3381 3427 6.815142 GCCTTTTAACTGAAATGCATCAATCT 59.185 34.615 0.00 0.00 32.57 2.40


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

AutoCloner maintained by Alex Coulton.