Multiple sequence alignment - TraesCS1A01G053500

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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 TraesCS1A01G053500 chr1A 100.000 2793 0 0 1 2793 35524794 35527586 0.000000e+00 5158
1 TraesCS1A01G053500 chr1A 89.678 1802 175 7 999 2792 35486138 35487936 0.000000e+00 2287
2 TraesCS1A01G053500 chr1A 88.840 1577 168 4 1000 2570 35578498 35576924 0.000000e+00 1930
3 TraesCS1A01G053500 chr1A 85.832 1574 171 27 999 2553 35536339 35537879 0.000000e+00 1624
4 TraesCS1A01G053500 chr1A 91.855 221 17 1 2574 2793 35576297 35576077 9.720000e-80 307
5 TraesCS1A01G053500 chr1A 89.815 216 15 4 2579 2789 35538510 35538723 1.270000e-68 270
6 TraesCS1A01G053500 chr1D 92.533 1808 123 6 995 2793 36315752 36317556 0.000000e+00 2580
7 TraesCS1A01G053500 chr1D 93.771 899 49 3 1678 2570 36362361 36361464 0.000000e+00 1343
8 TraesCS1A01G053500 chr1D 88.361 653 76 0 995 1647 36363007 36362355 0.000000e+00 785
9 TraesCS1A01G053500 chr1D 76.437 1218 225 42 1136 2330 24145146 24146324 1.110000e-168 603
10 TraesCS1A01G053500 chr1B 90.067 1802 146 18 996 2793 55998453 56000225 0.000000e+00 2305
11 TraesCS1A01G053500 chr1B 89.983 1807 140 19 999 2793 55977189 55978966 0.000000e+00 2296
12 TraesCS1A01G053500 chr1B 89.607 1578 136 15 995 2570 56140810 56139259 0.000000e+00 1980
13 TraesCS1A01G053500 chr1B 86.416 1487 160 25 996 2457 56017105 56018574 0.000000e+00 1589
14 TraesCS1A01G053500 chr1B 90.909 1001 74 12 1 994 191839173 191840163 0.000000e+00 1328
15 TraesCS1A01G053500 chr1B 86.288 722 95 4 995 1715 55964302 55965020 0.000000e+00 782
16 TraesCS1A01G053500 chr1B 93.665 221 13 1 2574 2793 56138633 56138413 2.070000e-86 329
17 TraesCS1A01G053500 chr1B 90.000 220 17 5 2574 2791 56019015 56019231 2.120000e-71 279
18 TraesCS1A01G053500 chr7A 96.991 997 26 4 1 995 682279469 682278475 0.000000e+00 1672
19 TraesCS1A01G053500 chr7A 91.405 989 68 14 1 980 445439075 445438095 0.000000e+00 1339
20 TraesCS1A01G053500 chr7A 98.745 239 2 1 758 995 43534610 43534372 9.250000e-115 424
21 TraesCS1A01G053500 chr5A 96.192 998 33 4 1 997 428218424 428217431 0.000000e+00 1628
22 TraesCS1A01G053500 chr5A 91.726 991 63 15 1 980 571653277 571654259 0.000000e+00 1358
23 TraesCS1A01G053500 chr3B 91.409 1001 73 12 1 994 273186253 273187247 0.000000e+00 1360
24 TraesCS1A01G053500 chr3A 90.838 1026 51 6 1 994 474186585 474185571 0.000000e+00 1334
25 TraesCS1A01G053500 chr5B 90.818 1002 72 14 1 994 268790781 268791770 0.000000e+00 1323
26 TraesCS1A01G053500 chr4B 90.120 1002 84 14 1 994 137803110 137804104 0.000000e+00 1288
27 TraesCS1A01G053500 chr7B 89.703 1010 81 19 1 994 507018488 507019490 0.000000e+00 1267


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 TraesCS1A01G053500 chr1A 35524794 35527586 2792 False 5158.0 5158 100.0000 1 2793 1 chr1A.!!$F2 2792
1 TraesCS1A01G053500 chr1A 35486138 35487936 1798 False 2287.0 2287 89.6780 999 2792 1 chr1A.!!$F1 1793
2 TraesCS1A01G053500 chr1A 35576077 35578498 2421 True 1118.5 1930 90.3475 1000 2793 2 chr1A.!!$R1 1793
3 TraesCS1A01G053500 chr1A 35536339 35538723 2384 False 947.0 1624 87.8235 999 2789 2 chr1A.!!$F3 1790
4 TraesCS1A01G053500 chr1D 36315752 36317556 1804 False 2580.0 2580 92.5330 995 2793 1 chr1D.!!$F2 1798
5 TraesCS1A01G053500 chr1D 36361464 36363007 1543 True 1064.0 1343 91.0660 995 2570 2 chr1D.!!$R1 1575
6 TraesCS1A01G053500 chr1D 24145146 24146324 1178 False 603.0 603 76.4370 1136 2330 1 chr1D.!!$F1 1194
7 TraesCS1A01G053500 chr1B 55998453 56000225 1772 False 2305.0 2305 90.0670 996 2793 1 chr1B.!!$F3 1797
8 TraesCS1A01G053500 chr1B 55977189 55978966 1777 False 2296.0 2296 89.9830 999 2793 1 chr1B.!!$F2 1794
9 TraesCS1A01G053500 chr1B 191839173 191840163 990 False 1328.0 1328 90.9090 1 994 1 chr1B.!!$F4 993
10 TraesCS1A01G053500 chr1B 56138413 56140810 2397 True 1154.5 1980 91.6360 995 2793 2 chr1B.!!$R1 1798
11 TraesCS1A01G053500 chr1B 56017105 56019231 2126 False 934.0 1589 88.2080 996 2791 2 chr1B.!!$F5 1795
12 TraesCS1A01G053500 chr1B 55964302 55965020 718 False 782.0 782 86.2880 995 1715 1 chr1B.!!$F1 720
13 TraesCS1A01G053500 chr7A 682278475 682279469 994 True 1672.0 1672 96.9910 1 995 1 chr7A.!!$R3 994
14 TraesCS1A01G053500 chr7A 445438095 445439075 980 True 1339.0 1339 91.4050 1 980 1 chr7A.!!$R2 979
15 TraesCS1A01G053500 chr5A 428217431 428218424 993 True 1628.0 1628 96.1920 1 997 1 chr5A.!!$R1 996
16 TraesCS1A01G053500 chr5A 571653277 571654259 982 False 1358.0 1358 91.7260 1 980 1 chr5A.!!$F1 979
17 TraesCS1A01G053500 chr3B 273186253 273187247 994 False 1360.0 1360 91.4090 1 994 1 chr3B.!!$F1 993
18 TraesCS1A01G053500 chr3A 474185571 474186585 1014 True 1334.0 1334 90.8380 1 994 1 chr3A.!!$R1 993
19 TraesCS1A01G053500 chr5B 268790781 268791770 989 False 1323.0 1323 90.8180 1 994 1 chr5B.!!$F1 993
20 TraesCS1A01G053500 chr4B 137803110 137804104 994 False 1288.0 1288 90.1200 1 994 1 chr4B.!!$F1 993
21 TraesCS1A01G053500 chr7B 507018488 507019490 1002 False 1267.0 1267 89.7030 1 994 1 chr7B.!!$F1 993

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
479 527 1.840181 CAATCGATCCGCTCTTTCGA 58.160 50.0 0.00 0.0 44.93 3.71 F
1103 1161 0.814010 GCCGCGGAGATGGTTACAAT 60.814 55.0 33.48 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1455 0.106519 GTGGGATGGCATAGCAAGGT 60.107 55.0 0.0 0.0 0.00 3.50 R
2353 2481 0.319297 GACGAACTACGCAACACCCT 60.319 55.0 0.0 0.0 46.94 4.34 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
164 165 2.893424 AGCCTCCACACAAAATCCAAT 58.107 42.857 0.00 0.00 0.00 3.16
308 309 2.517998 TGGTTAGGGTTTGGGCATAC 57.482 50.000 0.00 0.00 0.00 2.39
479 527 1.840181 CAATCGATCCGCTCTTTCGA 58.160 50.000 0.00 0.00 44.93 3.71
507 555 4.823442 ACCGAAAAGTTACGAAAGGGAAAT 59.177 37.500 0.00 0.00 0.00 2.17
580 630 2.029470 CGATTTGCTTAGGGTTTGGCAA 60.029 45.455 0.00 0.00 41.90 4.52
661 712 5.782677 TGGCTTAGGGTTTAGGTCATTTA 57.217 39.130 0.00 0.00 0.00 1.40
1103 1161 0.814010 GCCGCGGAGATGGTTACAAT 60.814 55.000 33.48 0.00 0.00 2.71
1165 1226 1.803453 AATGCTCAAGCCCTGGGGAA 61.803 55.000 16.03 0.00 41.18 3.97
1171 1232 2.561053 AAGCCCTGGGGAAGCCAAT 61.561 57.895 16.03 0.00 37.50 3.16
1174 1235 2.772924 CCTGGGGAAGCCAATGGT 59.227 61.111 0.00 0.00 0.00 3.55
1279 1340 1.424493 CGAGAGGCTAAAGCTTGGCG 61.424 60.000 15.40 2.82 41.70 5.69
1287 1348 1.167155 TAAAGCTTGGCGTCGGCAAA 61.167 50.000 30.56 15.89 46.84 3.68
1292 1353 3.758973 TTGGCGTCGGCAAAGTGGA 62.759 57.895 29.40 8.14 44.79 4.02
1319 1380 4.932105 GGGCACTGGCAACCCCAA 62.932 66.667 8.39 0.00 44.81 4.12
1326 1387 0.821711 CTGGCAACCCCAAAGTCGAA 60.822 55.000 0.00 0.00 44.81 3.71
1349 1410 1.503401 TACCCTGAGGTCACCGAGGA 61.503 60.000 15.12 0.00 46.45 3.71
1445 1506 3.890705 CGTGAGTGCATCGTCGCG 61.891 66.667 13.06 13.06 40.00 5.87
1553 1614 1.689273 GGAAGACATCTACGGCCTCAT 59.311 52.381 0.00 0.00 0.00 2.90
1566 1627 4.147449 CTCATCGGCGCACTCCCA 62.147 66.667 10.83 0.00 0.00 4.37
1567 1628 3.451556 CTCATCGGCGCACTCCCAT 62.452 63.158 10.83 0.00 0.00 4.00
1572 1633 2.584608 GGCGCACTCCCATGTAGT 59.415 61.111 10.83 0.00 0.00 2.73
1636 1706 0.683504 GAGTTCCCGTGCCTCCTCTA 60.684 60.000 0.00 0.00 0.00 2.43
1637 1707 0.252103 AGTTCCCGTGCCTCCTCTAA 60.252 55.000 0.00 0.00 0.00 2.10
1674 1744 2.223464 TTACATTCCAGCCCCTGCCC 62.223 60.000 0.00 0.00 38.69 5.36
1685 1755 2.150051 CCCTGCCCCTCCTCCATAC 61.150 68.421 0.00 0.00 0.00 2.39
1817 1891 1.205064 CAACTCAACAAGCGCCTCG 59.795 57.895 2.29 0.00 0.00 4.63
1842 1916 3.374745 CAACAGTAAGCAAGCAAAGTGG 58.625 45.455 0.00 0.00 0.00 4.00
1863 1937 3.242870 GGATTCGCAGATCACAATTCACC 60.243 47.826 0.00 0.00 35.04 4.02
1871 1948 5.575606 GCAGATCACAATTCACCTTCAATTG 59.424 40.000 0.00 0.00 43.89 2.32
2170 2292 4.956085 TCGTTCACATACATCCCTATTGG 58.044 43.478 0.00 0.00 0.00 3.16
2249 2377 6.502136 AGAAGATGTTTTTGCTAGCTAACC 57.498 37.500 17.23 8.35 0.00 2.85
2332 2460 4.279982 ACCAAAAGGTTTCGAAAACCCTA 58.720 39.130 21.98 0.00 41.18 3.53
2540 2669 1.918293 CTGGGTGTGAGTGGGGCTA 60.918 63.158 0.00 0.00 0.00 3.93
2554 2683 0.396974 GGGCTAATGGATGGGCACAA 60.397 55.000 0.00 0.00 0.00 3.33
2611 3526 7.166167 GGGTTATTTCTTTGTTCTACCAGAGA 58.834 38.462 0.00 0.00 0.00 3.10
2780 3699 2.198827 ATTTCCATGCAACTCGACCA 57.801 45.000 0.00 0.00 0.00 4.02
2784 3703 1.879380 TCCATGCAACTCGACCAAAAG 59.121 47.619 0.00 0.00 0.00 2.27
2785 3704 1.879380 CCATGCAACTCGACCAAAAGA 59.121 47.619 0.00 0.00 0.00 2.52
2786 3705 2.489329 CCATGCAACTCGACCAAAAGAT 59.511 45.455 0.00 0.00 0.00 2.40
2788 3707 3.896648 TGCAACTCGACCAAAAGATTC 57.103 42.857 0.00 0.00 0.00 2.52
2789 3708 2.223144 TGCAACTCGACCAAAAGATTCG 59.777 45.455 0.00 0.00 0.00 3.34
2790 3709 2.223377 GCAACTCGACCAAAAGATTCGT 59.777 45.455 0.00 0.00 34.35 3.85
2791 3710 3.430895 GCAACTCGACCAAAAGATTCGTA 59.569 43.478 0.00 0.00 34.35 3.43
2792 3711 4.434330 GCAACTCGACCAAAAGATTCGTAG 60.434 45.833 0.00 0.00 34.35 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 5.120399 AGATTGGAAAACTGTGTGTAACGA 58.880 37.500 0.00 0.00 42.39 3.85
479 527 4.689345 CCTTTCGTAACTTTTCGGTCTCAT 59.311 41.667 0.00 0.00 0.00 2.90
507 555 4.442052 CGAGATGGGATTGCAAACTCTCTA 60.442 45.833 16.91 0.00 0.00 2.43
580 630 3.935203 CGAGTTTCACTTGTCATAGCCAT 59.065 43.478 0.00 0.00 0.00 4.40
661 712 5.073691 CCCTCAACTACTTTCCCATATCCAT 59.926 44.000 0.00 0.00 0.00 3.41
1038 1096 1.555075 CCTTCCTTGGTGAGATCCGAA 59.445 52.381 0.00 0.00 0.00 4.30
1093 1151 3.250744 CACTCGACGACATTGTAACCAT 58.749 45.455 0.00 0.00 0.00 3.55
1095 1153 1.389106 GCACTCGACGACATTGTAACC 59.611 52.381 0.00 0.00 0.00 2.85
1103 1161 3.986006 GGTGGGCACTCGACGACA 61.986 66.667 0.00 0.00 28.45 4.35
1165 1226 3.376078 CCGCAGCAACCATTGGCT 61.376 61.111 1.54 0.00 42.06 4.75
1171 1232 2.439338 AACACACCGCAGCAACCA 60.439 55.556 0.00 0.00 0.00 3.67
1174 1235 2.904866 GGGAACACACCGCAGCAA 60.905 61.111 0.00 0.00 0.00 3.91
1279 1340 1.578206 GCCTCTTCCACTTTGCCGAC 61.578 60.000 0.00 0.00 0.00 4.79
1319 1380 2.970640 ACCTCAGGGTACTTTTCGACTT 59.029 45.455 0.00 0.00 45.32 3.01
1349 1410 4.566488 CCTTCAATAGCTGTGGAGAAACCT 60.566 45.833 8.72 0.00 39.86 3.50
1394 1455 0.106519 GTGGGATGGCATAGCAAGGT 60.107 55.000 0.00 0.00 0.00 3.50
1553 1614 3.071837 TACATGGGAGTGCGCCGA 61.072 61.111 4.18 0.00 0.00 5.54
1636 1706 1.622752 GGGGGTCAAGGGAGGGATT 60.623 63.158 0.00 0.00 0.00 3.01
1637 1707 2.044620 GGGGGTCAAGGGAGGGAT 59.955 66.667 0.00 0.00 0.00 3.85
1685 1755 5.564048 TTATGGAATTAAAAACGGGTCCG 57.436 39.130 7.97 7.97 46.03 4.79
1752 1826 1.136500 GGTAGGACTCCACGTTGATCC 59.864 57.143 0.00 8.93 0.00 3.36
1817 1891 1.604604 TGCTTGCTTACTGTTGGGTC 58.395 50.000 0.00 0.00 0.00 4.46
1842 1916 3.624861 AGGTGAATTGTGATCTGCGAATC 59.375 43.478 0.00 0.00 0.00 2.52
1863 1937 0.899720 ATGGCAGCACCCAATTGAAG 59.100 50.000 7.12 0.03 38.61 3.02
1871 1948 0.967380 AGCTAACAATGGCAGCACCC 60.967 55.000 10.26 0.00 37.78 4.61
2170 2292 4.954875 AGCTGGTACTAGCATTGAGATTC 58.045 43.478 29.93 0.00 46.07 2.52
2353 2481 0.319297 GACGAACTACGCAACACCCT 60.319 55.000 0.00 0.00 46.94 4.34
2540 2669 1.477700 CACGAATTGTGCCCATCCATT 59.522 47.619 0.00 0.00 42.70 3.16
2584 3499 5.867330 TGGTAGAACAAAGAAATAACCCGA 58.133 37.500 0.00 0.00 0.00 5.14
2611 3526 8.140112 AGACATGAAAACTGTAGGAATAGTCT 57.860 34.615 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.