Multiple sequence alignment - TraesCS6A01G215200

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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 TraesCS6A01G215200 chr6A 100.000 2303 0 0 1 2303 395871826 395869524 0.000000e+00 4253
1 TraesCS6A01G215200 chr6A 94.340 1961 99 8 1 1955 613365429 613367383 0.000000e+00 2996
2 TraesCS6A01G215200 chr6A 92.166 868 51 9 1 854 162276245 162275381 0.000000e+00 1210
3 TraesCS6A01G215200 chr6B 96.221 1958 71 2 1 1955 171789886 171787929 0.000000e+00 3203
4 TraesCS6A01G215200 chr6B 91.962 423 24 5 1881 2303 171787972 171787560 3.300000e-163 584
5 TraesCS6A01G215200 chr2B 92.632 1968 121 12 1 1951 77332734 77334694 0.000000e+00 2809
6 TraesCS6A01G215200 chr2B 85.421 439 42 13 1881 2303 77334655 77335087 9.770000e-119 436
7 TraesCS6A01G215200 chr4D 91.853 1964 116 11 1 1955 386931235 386933163 0.000000e+00 2700
8 TraesCS6A01G215200 chr4D 85.421 439 42 13 1881 2303 386933120 386933552 9.770000e-119 436
9 TraesCS6A01G215200 chr6D 91.333 1996 122 22 1 1955 15118144 15120129 0.000000e+00 2680
10 TraesCS6A01G215200 chr6D 85.194 439 43 13 1881 2303 15120086 15120518 4.550000e-117 431
11 TraesCS6A01G215200 chr1A 92.691 1724 103 13 1 1710 565153957 565155671 0.000000e+00 2464
12 TraesCS6A01G215200 chr1A 84.580 441 42 15 1881 2303 8732733 8733165 4.580000e-112 414
13 TraesCS6A01G215200 chr1A 84.081 446 34 13 1880 2303 435375387 435375817 1.660000e-106 396
14 TraesCS6A01G215200 chr7B 90.361 1774 130 24 557 2303 499717348 499715589 0.000000e+00 2290
15 TraesCS6A01G215200 chr7B 92.891 1266 76 6 696 1955 228682905 228681648 0.000000e+00 1827
16 TraesCS6A01G215200 chr3A 92.081 1086 78 4 873 1955 55445528 55446608 0.000000e+00 1522
17 TraesCS6A01G215200 chr3A 85.160 438 44 9 1881 2303 55446565 55446996 1.630000e-116 429
18 TraesCS6A01G215200 chr5A 94.145 854 45 3 1 851 225611247 225612098 0.000000e+00 1295
19 TraesCS6A01G215200 chr5A 83.535 911 103 22 1428 2303 190761351 190762249 0.000000e+00 808
20 TraesCS6A01G215200 chr3D 93.140 860 48 5 1 851 61930485 61931342 0.000000e+00 1251
21 TraesCS6A01G215200 chr1B 91.253 423 31 3 1881 2303 564740543 564740127 2.570000e-159 571
22 TraesCS6A01G215200 chr4B 85.194 439 43 10 1881 2303 483772079 483772511 4.550000e-117 431
23 TraesCS6A01G215200 chr4B 84.966 439 44 13 1881 2303 82006070 82006502 2.110000e-115 425
24 TraesCS6A01G215200 chr1D 84.340 447 32 14 1880 2303 337210632 337211063 9.910000e-109 403
25 TraesCS6A01G215200 chr2A 88.983 236 25 1 1636 1870 211904729 211904964 8.050000e-75 291


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 TraesCS6A01G215200 chr6A 395869524 395871826 2302 True 4253.0 4253 100.0000 1 2303 1 chr6A.!!$R2 2302
1 TraesCS6A01G215200 chr6A 613365429 613367383 1954 False 2996.0 2996 94.3400 1 1955 1 chr6A.!!$F1 1954
2 TraesCS6A01G215200 chr6A 162275381 162276245 864 True 1210.0 1210 92.1660 1 854 1 chr6A.!!$R1 853
3 TraesCS6A01G215200 chr6B 171787560 171789886 2326 True 1893.5 3203 94.0915 1 2303 2 chr6B.!!$R1 2302
4 TraesCS6A01G215200 chr2B 77332734 77335087 2353 False 1622.5 2809 89.0265 1 2303 2 chr2B.!!$F1 2302
5 TraesCS6A01G215200 chr4D 386931235 386933552 2317 False 1568.0 2700 88.6370 1 2303 2 chr4D.!!$F1 2302
6 TraesCS6A01G215200 chr6D 15118144 15120518 2374 False 1555.5 2680 88.2635 1 2303 2 chr6D.!!$F1 2302
7 TraesCS6A01G215200 chr1A 565153957 565155671 1714 False 2464.0 2464 92.6910 1 1710 1 chr1A.!!$F3 1709
8 TraesCS6A01G215200 chr7B 499715589 499717348 1759 True 2290.0 2290 90.3610 557 2303 1 chr7B.!!$R2 1746
9 TraesCS6A01G215200 chr7B 228681648 228682905 1257 True 1827.0 1827 92.8910 696 1955 1 chr7B.!!$R1 1259
10 TraesCS6A01G215200 chr3A 55445528 55446996 1468 False 975.5 1522 88.6205 873 2303 2 chr3A.!!$F1 1430
11 TraesCS6A01G215200 chr5A 225611247 225612098 851 False 1295.0 1295 94.1450 1 851 1 chr5A.!!$F2 850
12 TraesCS6A01G215200 chr5A 190761351 190762249 898 False 808.0 808 83.5350 1428 2303 1 chr5A.!!$F1 875
13 TraesCS6A01G215200 chr3D 61930485 61931342 857 False 1251.0 1251 93.1400 1 851 1 chr3D.!!$F1 850

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
693 699 0.602638 TTGAGTACCTTGTGGCGCAG 60.603 55.0 10.83 0.0 36.63 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 1587 2.158415 CCCCCTCACCATTAGCATGATT 60.158 50.0 0.0 0.0 31.07 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
248 251 1.708341 AAAGAATGGGCTGCAAGTGT 58.292 45.000 0.50 0.00 35.30 3.55
263 266 3.004734 GCAAGTGTACAACAGCCTCAAAT 59.995 43.478 0.00 0.00 0.00 2.32
492 498 8.390354 CAGATTCGAATTATTAGTGCTTGTTGA 58.610 33.333 12.81 0.00 0.00 3.18
570 576 5.059833 CCTGAAGTGGATAGTGAATTAGCC 58.940 45.833 0.00 0.00 0.00 3.93
693 699 0.602638 TTGAGTACCTTGTGGCGCAG 60.603 55.000 10.83 0.00 36.63 5.18
764 773 5.524281 GTGGTCTTCTTTTGTATAGCTAGCC 59.476 44.000 12.13 0.00 0.00 3.93
794 809 6.070767 TGGTCTTCTTTTGTATAGCTAGCTGT 60.071 38.462 27.68 23.01 0.00 4.40
814 829 5.355350 GCTGTGGTGCTCTTCTTTTGTATAT 59.645 40.000 0.00 0.00 0.00 0.86
821 836 7.713073 GGTGCTCTTCTTTTGTATATCTAGCTT 59.287 37.037 0.00 0.00 0.00 3.74
838 856 1.335051 GCTTCGGTGGTCTTCTTTTGC 60.335 52.381 0.00 0.00 0.00 3.68
840 858 2.045561 TCGGTGGTCTTCTTTTGCAA 57.954 45.000 0.00 0.00 0.00 4.08
939 1013 8.537049 ACATTATGTTTCAATCATGGTGTTTG 57.463 30.769 0.00 0.00 0.00 2.93
944 1018 6.041511 TGTTTCAATCATGGTGTTTGTCAAG 58.958 36.000 0.00 0.00 31.09 3.02
1007 1085 0.035439 CCTTGTAGAACCATGGCCGT 60.035 55.000 13.04 0.00 0.00 5.68
1170 1248 1.143684 AGGCATGTGAAGGACAAGTGT 59.856 47.619 0.00 0.00 38.36 3.55
1292 1370 3.181423 TGGGATTGGACCAATAATAGGCC 60.181 47.826 19.84 14.54 33.90 5.19
1350 1430 3.548770 AGGTAACCATGCATCATGAGTG 58.451 45.455 0.09 1.26 43.81 3.51
1359 1439 2.681344 TGCATCATGAGTGCACATTCTC 59.319 45.455 21.04 8.31 46.76 2.87
1390 1470 8.574251 AGTTTGCATATGTACAATAACAAGGA 57.426 30.769 0.00 0.00 32.02 3.36
1436 1516 0.453390 GTGCAGGCTAACAAGGCATC 59.547 55.000 0.00 0.00 36.79 3.91
1569 1649 2.172082 TGCTGCAGAGCCATTAGAAGAT 59.828 45.455 20.43 0.00 45.57 2.40
1588 1668 5.768980 AGATCCAATTGAAGTCTCTCCAA 57.231 39.130 7.12 0.00 0.00 3.53
1621 1701 1.277557 AGAGGCAGTGAACAGGTGATC 59.722 52.381 0.00 0.00 0.00 2.92
1738 1818 3.763360 TGAAATACTTGATGCACTTGGGG 59.237 43.478 0.00 0.00 0.00 4.96
1791 1872 2.081462 CGGTGTTATGGGAAGTTGGTC 58.919 52.381 0.00 0.00 0.00 4.02
1802 1883 3.308402 GGGAAGTTGGTCCTCAATGATCA 60.308 47.826 0.00 0.00 37.73 2.92
1841 1922 2.309755 AGGAGCTTTCCATCACCATGAA 59.690 45.455 0.00 0.00 30.57 2.57
1870 1951 1.133790 GGCTGCTAATGTTGCCTTGAG 59.866 52.381 0.00 0.00 41.92 3.02
1990 2159 7.970614 GTCAAGCATTTGGACCTATCTTTTAAG 59.029 37.037 0.00 0.00 34.97 1.85
2040 2229 5.589192 ACCATATTTGAGAGTACGTGCTAC 58.411 41.667 6.01 4.78 0.00 3.58
2055 2244 9.211485 AGTACGTGCTACTTGTTTTATGTTATT 57.789 29.630 3.62 0.00 30.80 1.40
2059 2248 9.814507 CGTGCTACTTGTTTTATGTTATTGTAA 57.185 29.630 0.00 0.00 0.00 2.41
2101 2291 3.823873 TGTATGACCATTTGCGTTTCCTT 59.176 39.130 0.00 0.00 0.00 3.36
2210 2400 7.492352 CAAGGTATAACTTGGTAATGTAGCC 57.508 40.000 20.90 0.00 43.14 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 4.107127 TGTACCCTTAGGCACAACAAAT 57.893 40.909 0.00 0.00 36.42 2.32
84 85 6.115448 ACTACATGCCAAGAGTAAGAGTTT 57.885 37.500 0.00 0.00 0.00 2.66
248 251 6.707290 TCTTTAGCTATTTGAGGCTGTTGTA 58.293 36.000 0.00 0.00 39.31 2.41
570 576 2.223852 TGGATCATCATTTGGCGCATTG 60.224 45.455 10.83 0.16 0.00 2.82
693 699 4.585162 TCCTATTCGATCTCTTGTTCTCCC 59.415 45.833 0.00 0.00 0.00 4.30
764 773 1.504359 TACAAAAGAAGACCACCGCG 58.496 50.000 0.00 0.00 0.00 6.46
794 809 6.986817 GCTAGATATACAAAAGAAGAGCACCA 59.013 38.462 0.00 0.00 0.00 4.17
814 829 2.217510 AGAAGACCACCGAAGCTAGA 57.782 50.000 0.00 0.00 0.00 2.43
821 836 2.045561 TTGCAAAAGAAGACCACCGA 57.954 45.000 0.00 0.00 0.00 4.69
1113 1191 3.511146 ACACATGTGGTTTCCATCCATTC 59.489 43.478 28.64 0.00 35.28 2.67
1292 1370 5.010314 CCCAAACATCATCACTATCCATTGG 59.990 44.000 0.00 0.00 34.73 3.16
1507 1587 2.158415 CCCCCTCACCATTAGCATGATT 60.158 50.000 0.00 0.00 31.07 2.57
1569 1649 5.694995 ACTTTTGGAGAGACTTCAATTGGA 58.305 37.500 5.42 0.00 28.16 3.53
1621 1701 3.949754 TCTCCAAGCATGCAAAGAATAGG 59.050 43.478 21.98 9.16 0.00 2.57
1738 1818 3.060602 GCTCGGCTAAATCAGGTATCAC 58.939 50.000 0.00 0.00 0.00 3.06
1791 1872 4.380233 GCTTGAAACAGGTGATCATTGAGG 60.380 45.833 14.81 0.47 0.00 3.86
1802 1883 2.439507 TCCTTCAGAGCTTGAAACAGGT 59.560 45.455 10.97 0.00 44.84 4.00
1828 1909 4.520179 CATGTCTTCTTCATGGTGATGGA 58.480 43.478 0.00 0.00 38.97 3.41
1841 1922 3.641434 ACATTAGCAGCCATGTCTTCT 57.359 42.857 2.43 0.00 0.00 2.85
1870 1951 5.235305 ACAACACATAAAAGCATCGATCC 57.765 39.130 0.00 0.00 0.00 3.36
1990 2159 6.034150 TCGTACATGACATAAATCACAACGAC 59.966 38.462 0.00 0.00 36.35 4.34


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

AutoCloner maintained by Alex Coulton.