Multiple sequence alignment - TraesCS4A01G125200

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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 TraesCS4A01G125200 chr4A 100.000 2510 0 0 1 2510 161151432 161153941 0.000000e+00 4636.0
1 TraesCS4A01G125200 chr4A 96.864 1945 59 2 244 2188 161163761 161165703 0.000000e+00 3253.0
2 TraesCS4A01G125200 chr4A 82.782 1028 127 27 1 1014 468300420 468301411 0.000000e+00 872.0
3 TraesCS4A01G125200 chr4A 90.649 385 22 12 6 386 332174403 332174029 1.340000e-137 499.0
4 TraesCS4A01G125200 chr4A 89.351 385 28 12 6 386 332194962 332194587 2.920000e-129 472.0
5 TraesCS4A01G125200 chr4A 86.217 341 33 8 2171 2510 451888351 451888678 8.540000e-95 357.0
6 TraesCS4A01G125200 chr4A 88.811 286 23 4 730 1014 297673891 297673614 2.390000e-90 342.0
7 TraesCS4A01G125200 chr4A 79.457 516 73 26 1 500 302949874 302949376 4.000000e-88 335.0
8 TraesCS4A01G125200 chr4A 86.207 319 31 6 699 1015 297681725 297681418 1.440000e-87 333.0
9 TraesCS4A01G125200 chr4A 85.427 199 21 6 1120 1315 389319689 389319496 1.520000e-47 200.0
10 TraesCS4A01G125200 chr4A 97.436 78 1 1 2433 2510 200908566 200908490 5.630000e-27 132.0
11 TraesCS4A01G125200 chr5A 87.474 1461 127 40 775 2187 495160617 495159165 0.000000e+00 1633.0
12 TraesCS4A01G125200 chr5A 86.792 424 52 4 6 427 453049457 453049036 1.050000e-128 470.0
13 TraesCS4A01G125200 chr5A 85.816 423 58 2 6 427 453041666 453041245 4.930000e-122 448.0
14 TraesCS4A01G125200 chr5A 86.310 336 30 12 2177 2510 266461919 266462240 3.970000e-93 351.0
15 TraesCS4A01G125200 chr5A 85.380 342 37 6 2170 2510 178598420 178598749 2.390000e-90 342.0
16 TraesCS4A01G125200 chr5A 78.698 507 77 27 5 500 357324163 357324649 2.420000e-80 309.0
17 TraesCS4A01G125200 chr3A 85.251 1173 130 36 1364 2510 147542958 147544113 0.000000e+00 1168.0
18 TraesCS4A01G125200 chr3A 88.928 849 84 8 1600 2447 464253991 464254830 0.000000e+00 1038.0
19 TraesCS4A01G125200 chr3A 86.643 846 88 21 1364 2188 147550623 147551464 0.000000e+00 913.0
20 TraesCS4A01G125200 chr3A 93.075 361 23 2 1364 1724 291951636 291951278 6.150000e-146 527.0
21 TraesCS4A01G125200 chr3A 79.144 724 121 22 1 715 508109779 508109077 8.130000e-130 473.0
22 TraesCS4A01G125200 chr3A 80.425 659 95 26 65 711 286803899 286803263 2.920000e-129 472.0
23 TraesCS4A01G125200 chr3A 85.442 419 46 11 1 408 372085470 372085056 2.990000e-114 422.0
24 TraesCS4A01G125200 chr3A 82.915 199 26 6 1120 1315 389665132 389665325 3.320000e-39 172.0
25 TraesCS4A01G125200 chr3A 92.929 99 5 2 1364 1462 390236954 390237050 2.600000e-30 143.0
26 TraesCS4A01G125200 chr7A 94.355 744 36 6 1769 2510 41681611 41680872 0.000000e+00 1136.0
27 TraesCS4A01G125200 chr7A 86.934 949 105 19 1507 2447 516898522 516899459 0.000000e+00 1048.0
28 TraesCS4A01G125200 chr7A 84.329 1021 120 23 6 1018 463807788 463806800 0.000000e+00 963.0
29 TraesCS4A01G125200 chr7A 84.344 1022 117 23 6 1018 463799734 463798747 0.000000e+00 961.0
30 TraesCS4A01G125200 chr7A 86.623 770 87 12 1743 2510 536655620 536654865 0.000000e+00 837.0
31 TraesCS4A01G125200 chr7A 93.827 243 14 1 777 1018 541721894 541721652 5.100000e-97 364.0
32 TraesCS4A01G125200 chr7A 93.004 243 16 1 777 1018 541714223 541713981 1.100000e-93 353.0
33 TraesCS4A01G125200 chr7A 84.536 194 21 7 1125 1315 569513746 569513933 1.530000e-42 183.0
34 TraesCS4A01G125200 chr7A 97.468 79 1 1 2432 2510 203648404 203648327 1.570000e-27 134.0
35 TraesCS4A01G125200 chr7A 97.468 79 1 1 2432 2510 511420696 511420773 1.570000e-27 134.0
36 TraesCS4A01G125200 chr1A 84.739 1055 118 26 1472 2510 192482613 192481586 0.000000e+00 1016.0
37 TraesCS4A01G125200 chr1A 87.571 877 96 12 1572 2447 204038480 204037616 0.000000e+00 1003.0
38 TraesCS4A01G125200 chr1A 83.105 438 54 15 2081 2510 353037314 353036889 5.070000e-102 381.0
39 TraesCS4A01G125200 chr1A 87.461 319 26 6 702 1018 286375539 286375845 3.070000e-94 355.0
40 TraesCS4A01G125200 chr1A 93.548 62 4 0 621 682 8110709 8110770 2.660000e-15 93.5
41 TraesCS4A01G125200 chr2A 86.914 917 100 17 1539 2447 437997772 437998676 0.000000e+00 1011.0
42 TraesCS4A01G125200 chr2A 84.532 1015 131 20 1448 2447 513474778 513473775 0.000000e+00 981.0
43 TraesCS4A01G125200 chr2A 82.361 720 107 16 1735 2447 188320967 188321673 2.130000e-170 608.0
44 TraesCS4A01G125200 chr2A 85.116 430 59 5 1 427 98446189 98445762 3.830000e-118 435.0
45 TraesCS4A01G125200 chr2A 83.879 428 64 5 1 425 98438032 98437607 1.080000e-108 403.0
46 TraesCS4A01G125200 chr2A 83.529 425 58 6 6 427 427938687 427938272 1.090000e-103 387.0
47 TraesCS4A01G125200 chr2A 86.520 319 28 6 699 1014 434698075 434698381 1.110000e-88 337.0
48 TraesCS4A01G125200 chr2A 88.652 282 17 8 2167 2447 503150320 503150053 1.860000e-86 329.0
49 TraesCS4A01G125200 chr2A 86.275 255 29 3 466 715 406855920 406856173 3.180000e-69 272.0
50 TraesCS4A01G125200 chr6A 87.802 869 92 10 1580 2447 465053131 465052276 0.000000e+00 1005.0
51 TraesCS4A01G125200 chr6A 82.716 81 10 4 1124 1202 323045803 323045881 4.480000e-08 69.4
52 TraesCS4A01G125200 chr1D 84.772 394 41 16 1 387 174357024 174356643 6.550000e-101 377.0


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 TraesCS4A01G125200 chr4A 161151432 161153941 2509 False 4636 4636 100.000 1 2510 1 chr4A.!!$F1 2509
1 TraesCS4A01G125200 chr4A 161163761 161165703 1942 False 3253 3253 96.864 244 2188 1 chr4A.!!$F2 1944
2 TraesCS4A01G125200 chr4A 468300420 468301411 991 False 872 872 82.782 1 1014 1 chr4A.!!$F4 1013
3 TraesCS4A01G125200 chr5A 495159165 495160617 1452 True 1633 1633 87.474 775 2187 1 chr5A.!!$R3 1412
4 TraesCS4A01G125200 chr3A 147542958 147544113 1155 False 1168 1168 85.251 1364 2510 1 chr3A.!!$F1 1146
5 TraesCS4A01G125200 chr3A 464253991 464254830 839 False 1038 1038 88.928 1600 2447 1 chr3A.!!$F5 847
6 TraesCS4A01G125200 chr3A 147550623 147551464 841 False 913 913 86.643 1364 2188 1 chr3A.!!$F2 824
7 TraesCS4A01G125200 chr3A 508109077 508109779 702 True 473 473 79.144 1 715 1 chr3A.!!$R4 714
8 TraesCS4A01G125200 chr3A 286803263 286803899 636 True 472 472 80.425 65 711 1 chr3A.!!$R1 646
9 TraesCS4A01G125200 chr7A 41680872 41681611 739 True 1136 1136 94.355 1769 2510 1 chr7A.!!$R1 741
10 TraesCS4A01G125200 chr7A 516898522 516899459 937 False 1048 1048 86.934 1507 2447 1 chr7A.!!$F2 940
11 TraesCS4A01G125200 chr7A 463806800 463807788 988 True 963 963 84.329 6 1018 1 chr7A.!!$R4 1012
12 TraesCS4A01G125200 chr7A 463798747 463799734 987 True 961 961 84.344 6 1018 1 chr7A.!!$R3 1012
13 TraesCS4A01G125200 chr7A 536654865 536655620 755 True 837 837 86.623 1743 2510 1 chr7A.!!$R5 767
14 TraesCS4A01G125200 chr1A 192481586 192482613 1027 True 1016 1016 84.739 1472 2510 1 chr1A.!!$R1 1038
15 TraesCS4A01G125200 chr1A 204037616 204038480 864 True 1003 1003 87.571 1572 2447 1 chr1A.!!$R2 875
16 TraesCS4A01G125200 chr2A 437997772 437998676 904 False 1011 1011 86.914 1539 2447 1 chr2A.!!$F4 908
17 TraesCS4A01G125200 chr2A 513473775 513474778 1003 True 981 981 84.532 1448 2447 1 chr2A.!!$R5 999
18 TraesCS4A01G125200 chr2A 188320967 188321673 706 False 608 608 82.361 1735 2447 1 chr2A.!!$F1 712
19 TraesCS4A01G125200 chr6A 465052276 465053131 855 True 1005 1005 87.802 1580 2447 1 chr6A.!!$R1 867

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
834 853 0.846427 AAGGGCTCATCTGGTTCCCA 60.846 55.0 0.0 0.0 39.42 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2012 1.48631 CGGAATGGGATGAGAGTTGGA 59.514 52.381 0.0 0.0 0.0 3.53 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
63 65 8.958119 TTGGAGCTACAGTTATTTAGTTATGG 57.042 34.615 0.00 0.0 0.00 2.74
142 145 9.643693 AGCATTTTAAACATAGATGAAAGTTGG 57.356 29.630 0.00 0.0 0.00 3.77
211 214 9.723601 AAAGTTTTTACATATGATGCACCATTT 57.276 25.926 10.38 0.0 0.00 2.32
350 355 5.128663 CCCAACAGGAGGAAAAGAAAGAAAA 59.871 40.000 0.00 0.0 38.24 2.29
408 417 2.492090 CAGTCGGAGGAAGAGGCG 59.508 66.667 0.00 0.0 0.00 5.52
508 517 1.402984 GCTCGTCGTCTCCAGACAAAT 60.403 52.381 7.48 0.0 44.99 2.32
636 645 2.097825 GTTTCAGCAGCCATTGAGGAT 58.902 47.619 0.00 0.0 41.22 3.24
691 700 1.373748 GGACGAGGCGTTGTTGCTA 60.374 57.895 0.00 0.0 41.37 3.49
701 710 1.399599 CGTTGTTGCTATTCGCTGCAA 60.400 47.619 0.00 0.0 45.40 4.08
834 853 0.846427 AAGGGCTCATCTGGTTCCCA 60.846 55.000 0.00 0.0 39.42 4.37
960 979 2.163509 GAAAACAGAAGGAGGGGAAGC 58.836 52.381 0.00 0.0 0.00 3.86
1252 1272 1.670791 ACGCGTGAAGGGAAGAAAAA 58.329 45.000 12.93 0.0 36.53 1.94
1839 1923 5.121142 CCGACGTTTGACCAACTATAATGTT 59.879 40.000 0.00 0.0 32.53 2.71
1927 2012 5.421374 ACCTACTCTAAAATAAGACCGCACT 59.579 40.000 0.00 0.0 0.00 4.40
2351 2449 9.657419 AATTGAAAGAAAGAAAGAACACAACAT 57.343 25.926 0.00 0.0 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 120 9.638239 TCCAACTTTCATCTATGTTTAAAATGC 57.362 29.630 0.00 0.00 0.00 3.56
188 191 8.382130 CACAAATGGTGCATCATATGTAAAAAC 58.618 33.333 14.07 0.00 41.36 2.43
211 214 6.830324 AGCCTTCATGCTTTTAATATCTCACA 59.170 34.615 0.00 0.00 38.85 3.58
217 220 6.494835 CCCCTTAGCCTTCATGCTTTTAATAT 59.505 38.462 0.00 0.00 42.75 1.28
225 228 1.002857 AACCCCTTAGCCTTCATGCT 58.997 50.000 0.00 0.00 45.38 3.79
234 237 5.393135 GCAGATTTACAGAAAACCCCTTAGC 60.393 44.000 0.00 0.00 0.00 3.09
350 355 2.348998 CCCAGCGCTCCTCTTGTT 59.651 61.111 7.13 0.00 0.00 2.83
508 517 2.108168 CCTTGTCACGATCTTCCCCTA 58.892 52.381 0.00 0.00 0.00 3.53
636 645 2.586914 CGCATCGCCTCTGCATCA 60.587 61.111 0.00 0.00 39.64 3.07
672 681 1.812686 TAGCAACAACGCCTCGTCCT 61.813 55.000 0.00 0.00 39.99 3.85
691 700 1.303561 TGCTTCCCTTGCAGCGAAT 60.304 52.632 0.00 0.00 39.04 3.34
722 731 2.124570 ATTGCTTCGCCATCGCCT 60.125 55.556 0.00 0.00 35.26 5.52
747 756 1.150081 CCTCCATCCCTCATGCACC 59.850 63.158 0.00 0.00 0.00 5.01
753 762 2.735772 GCTTCGCCTCCATCCCTCA 61.736 63.158 0.00 0.00 0.00 3.86
807 825 3.424105 ATGAGCCCTTGCCTCCCC 61.424 66.667 0.00 0.00 38.69 4.81
812 830 1.000396 AACCAGATGAGCCCTTGCC 60.000 57.895 0.00 0.00 38.69 4.52
814 832 3.181526 GGAACCAGATGAGCCCTTG 57.818 57.895 0.00 0.00 0.00 3.61
834 853 2.123251 ATCGACCCGGATCTGGCT 60.123 61.111 15.84 0.49 0.00 4.75
838 857 0.395862 AGTCACATCGACCCGGATCT 60.396 55.000 0.73 0.00 46.69 2.75
960 979 1.042559 GTGCCTCTCCTCCTCCTCAG 61.043 65.000 0.00 0.00 0.00 3.35
1252 1272 2.723530 TCTCCTTCCTCCCTCTGTTT 57.276 50.000 0.00 0.00 0.00 2.83
1839 1923 2.038033 GCCCCAACGGATAACTATAGCA 59.962 50.000 0.00 0.00 0.00 3.49
1927 2012 1.486310 CGGAATGGGATGAGAGTTGGA 59.514 52.381 0.00 0.00 0.00 3.53
2243 2334 3.367910 CCTCTCCTCTTTCTCTTCCGTTG 60.368 52.174 0.00 0.00 0.00 4.10
2351 2449 5.297547 AGTGCTCTCAAATTCGTTCAACTA 58.702 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.