Multiple sequence alignment - TraesCS4A01G190700

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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 TraesCS4A01G190700 chr4A 100.000 2591 0 0 1 2591 469243809 469246399 0.000000e+00 4785.0
1 TraesCS4A01G190700 chr4A 100.000 625 0 0 2938 3562 469246746 469247370 0.000000e+00 1155.0
2 TraesCS4A01G190700 chr4A 80.903 576 98 10 1927 2500 742789473 742788908 9.070000e-121 444.0
3 TraesCS4A01G190700 chr4A 90.196 51 5 0 783 833 469244495 469244545 2.290000e-07 67.6
4 TraesCS4A01G190700 chr4A 90.196 51 5 0 687 737 469244591 469244641 2.290000e-07 67.6
5 TraesCS4A01G190700 chr4D 96.702 1334 34 2 1261 2591 106680011 106678685 0.000000e+00 2211.0
6 TraesCS4A01G190700 chr4D 96.592 939 31 1 329 1267 106680981 106680044 0.000000e+00 1555.0
7 TraesCS4A01G190700 chr4D 92.834 628 39 5 2938 3562 106678538 106677914 0.000000e+00 905.0
8 TraesCS4A01G190700 chr4D 90.000 290 20 2 48 328 106681330 106681041 2.020000e-97 366.0
9 TraesCS4A01G190700 chr4D 86.328 256 22 2 2342 2591 106677063 106676815 2.110000e-67 267.0
10 TraesCS4A01G190700 chr4D 94.624 93 5 0 2938 3030 106676710 106676618 1.030000e-30 145.0
11 TraesCS4A01G190700 chr4D 98.113 53 1 0 1 53 106681428 106681376 3.790000e-15 93.5
12 TraesCS4A01G190700 chr4D 88.889 54 6 0 783 836 106680624 106680571 2.290000e-07 67.6
13 TraesCS4A01G190700 chr4B 95.940 1330 43 3 1262 2588 169936636 169937957 0.000000e+00 2146.0
14 TraesCS4A01G190700 chr4B 93.661 631 32 6 2938 3561 169938109 169938738 0.000000e+00 937.0
15 TraesCS4A01G190700 chr4B 93.956 364 19 2 329 690 169931164 169931526 6.720000e-152 547.0
16 TraesCS4A01G190700 chr4B 96.341 328 10 2 702 1028 169931648 169931974 4.050000e-149 538.0
17 TraesCS4A01G190700 chr4B 96.386 249 7 1 1021 1267 169936354 169936602 3.310000e-110 409.0
18 TraesCS4A01G190700 chr4B 92.334 287 14 2 50 328 169930818 169931104 5.540000e-108 401.0
19 TraesCS4A01G190700 chr4B 94.118 51 3 0 687 737 169931728 169931778 1.060000e-10 78.7
20 TraesCS4A01G190700 chr7D 81.424 576 96 9 1927 2500 1186587 1186021 9.010000e-126 460.0
21 TraesCS4A01G190700 chr7D 79.646 226 37 4 1576 1792 1186902 1186677 1.710000e-33 154.0
22 TraesCS4A01G190700 chrUn 81.547 569 93 9 1935 2500 51486736 51487295 3.240000e-125 459.0
23 TraesCS4A01G190700 chrUn 81.625 566 92 10 1938 2500 316653649 316653093 3.240000e-125 459.0
24 TraesCS4A01G190700 chrUn 80.776 567 99 8 1935 2500 245964275 245964832 5.460000e-118 435.0
25 TraesCS4A01G190700 chrUn 79.965 569 101 7 1935 2500 269323189 269323747 1.190000e-109 407.0
26 TraesCS4A01G190700 chrUn 80.788 203 30 4 1576 1769 245963954 245964156 2.220000e-32 150.0
27 TraesCS4A01G190700 chrUn 78.319 226 40 5 1576 1792 269322868 269323093 1.720000e-28 137.0


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 TraesCS4A01G190700 chr4A 469243809 469247370 3561 False 1518.8000 4785 95.09800 1 3562 4 chr4A.!!$F1 3561
1 TraesCS4A01G190700 chr4A 742788908 742789473 565 True 444.0000 444 80.90300 1927 2500 1 chr4A.!!$R1 573
2 TraesCS4A01G190700 chr4D 106676618 106681428 4810 True 701.2625 2211 93.01025 1 3562 8 chr4D.!!$R1 3561
3 TraesCS4A01G190700 chr4B 169936354 169938738 2384 False 1164.0000 2146 95.32900 1021 3561 3 chr4B.!!$F2 2540
4 TraesCS4A01G190700 chr4B 169930818 169931974 1156 False 391.1750 547 94.18725 50 1028 4 chr4B.!!$F1 978
5 TraesCS4A01G190700 chr7D 1186021 1186902 881 True 307.0000 460 80.53500 1576 2500 2 chr7D.!!$R1 924
6 TraesCS4A01G190700 chrUn 51486736 51487295 559 False 459.0000 459 81.54700 1935 2500 1 chrUn.!!$F1 565
7 TraesCS4A01G190700 chrUn 316653093 316653649 556 True 459.0000 459 81.62500 1938 2500 1 chrUn.!!$R1 562
8 TraesCS4A01G190700 chrUn 245963954 245964832 878 False 292.5000 435 80.78200 1576 2500 2 chrUn.!!$F2 924
9 TraesCS4A01G190700 chrUn 269322868 269323747 879 False 272.0000 407 79.14200 1576 2500 2 chrUn.!!$F3 924

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
60 61 0.032130 TTATCGCGAGTGCTCCCATC 59.968 55.0 16.66 0.0 39.65 3.51 F
64 116 0.249447 CGCGAGTGCTCCCATCATTA 60.249 55.0 0.00 0.0 39.65 1.90 F
1102 1336 0.536006 GCCTGCTACTGGGCCTAATG 60.536 60.0 4.53 0.0 42.30 1.90 F
1923 2209 0.249868 CTTGCTCAAGGACACCACGA 60.250 55.0 1.79 0.0 34.87 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1351 0.036010 TCTTGGCTAACAGGAGCTGC 60.036 55.000 0.00 0.00 42.43 5.25 R
1186 1420 1.072173 AGCATTTGGTTTTCCTTGGGC 59.928 47.619 0.00 0.00 41.38 5.36 R
2446 2732 0.459585 GAGCGCCTCCACGTATTTCA 60.460 55.000 2.29 0.00 34.88 2.69 R
3163 3451 0.752743 CCCATATGTGCACACTGGGG 60.753 60.000 38.79 33.56 43.38 4.96 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
53 54 4.376413 CCATTTGTCTATTATCGCGAGTGC 60.376 45.833 16.66 0.86 37.91 4.40
55 56 3.269486 TGTCTATTATCGCGAGTGCTC 57.731 47.619 16.66 2.37 39.65 4.26
56 57 2.031069 TGTCTATTATCGCGAGTGCTCC 60.031 50.000 16.66 0.00 39.65 4.70
58 59 1.269723 CTATTATCGCGAGTGCTCCCA 59.730 52.381 16.66 0.00 39.65 4.37
60 61 0.032130 TTATCGCGAGTGCTCCCATC 59.968 55.000 16.66 0.00 39.65 3.51
61 62 1.106944 TATCGCGAGTGCTCCCATCA 61.107 55.000 16.66 0.00 39.65 3.07
64 116 0.249447 CGCGAGTGCTCCCATCATTA 60.249 55.000 0.00 0.00 39.65 1.90
77 129 7.619302 TGCTCCCATCATTAATTAGGTTTTCTT 59.381 33.333 0.00 0.00 0.00 2.52
142 194 7.485418 ACAACAAAACTATACGTGATTCACA 57.515 32.000 16.61 0.00 33.40 3.58
159 211 0.887933 ACAAATGCACGGGATTCCAC 59.112 50.000 4.80 0.00 0.00 4.02
391 511 2.421424 ACACCGTGTATCTAGACGAACC 59.579 50.000 1.18 0.00 44.54 3.62
431 551 3.185188 CCTGATATGAAAGCGATGAACGG 59.815 47.826 0.00 0.00 42.83 4.44
544 664 3.756117 AGACTGGATTCAGAACAAACCC 58.244 45.455 8.39 0.00 43.49 4.11
721 953 1.329599 GCCAAATAGTAGGCGTTTCCG 59.670 52.381 0.00 0.00 41.70 4.30
722 954 2.624636 CCAAATAGTAGGCGTTTCCGT 58.375 47.619 0.00 0.00 40.77 4.69
865 1097 4.521062 AGCGATGCTGCCCGAGAC 62.521 66.667 14.20 0.00 37.57 3.36
1101 1335 1.839894 GCCTGCTACTGGGCCTAAT 59.160 57.895 4.53 0.00 42.30 1.73
1102 1336 0.536006 GCCTGCTACTGGGCCTAATG 60.536 60.000 4.53 0.00 42.30 1.90
1117 1351 4.279420 GGCCTAATGCTTCCTATTTCCAAG 59.721 45.833 0.00 0.00 40.92 3.61
1186 1420 1.516386 CTGTACGCCTACCAGCACG 60.516 63.158 0.00 0.00 0.00 5.34
1239 1473 2.270434 TAGTGGATCCAAAGCTCCCT 57.730 50.000 18.20 10.04 0.00 4.20
1355 1628 1.753649 CAACATGGTGTTTGTGGACCA 59.246 47.619 1.39 0.00 46.26 4.02
1431 1707 8.717821 TGTGTGTATTAATGAAAGCTGAGTTAC 58.282 33.333 0.00 0.00 0.00 2.50
1821 2107 7.981789 TGTATATGTCCTTGCTCTCTTTTAGTG 59.018 37.037 0.00 0.00 0.00 2.74
1923 2209 0.249868 CTTGCTCAAGGACACCACGA 60.250 55.000 1.79 0.00 34.87 4.35
2005 2291 0.935831 CACGACACCGCAACGTCTAA 60.936 55.000 0.00 0.00 38.18 2.10
2354 2640 2.442413 ACCATTACCACAAATGTCCGG 58.558 47.619 0.00 0.00 35.48 5.14
2445 2731 1.204312 GGTTTCTTCGTGTGCGCTC 59.796 57.895 9.73 5.51 38.14 5.03
2446 2732 1.222115 GGTTTCTTCGTGTGCGCTCT 61.222 55.000 9.73 0.00 38.14 4.09
2540 2826 0.321298 TGCGCCTTCCACCTTTCTAC 60.321 55.000 4.18 0.00 0.00 2.59
2541 2827 0.036294 GCGCCTTCCACCTTTCTACT 60.036 55.000 0.00 0.00 0.00 2.57
2542 2828 1.610886 GCGCCTTCCACCTTTCTACTT 60.611 52.381 0.00 0.00 0.00 2.24
2543 2829 2.779506 CGCCTTCCACCTTTCTACTTT 58.220 47.619 0.00 0.00 0.00 2.66
2544 2830 3.867216 GCGCCTTCCACCTTTCTACTTTA 60.867 47.826 0.00 0.00 0.00 1.85
2545 2831 4.514401 CGCCTTCCACCTTTCTACTTTAT 58.486 43.478 0.00 0.00 0.00 1.40
2546 2832 5.667466 CGCCTTCCACCTTTCTACTTTATA 58.333 41.667 0.00 0.00 0.00 0.98
3027 3313 6.549912 ACAAACAGAGTTTACGGAATTACC 57.450 37.500 0.00 0.00 0.00 2.85
3117 3405 0.035439 ATTCGGGCAAACGTGATCCT 60.035 50.000 0.00 0.00 34.94 3.24
3131 3419 0.716108 GATCCTGCGTCACTTTGTCG 59.284 55.000 0.00 0.00 32.37 4.35
3231 3521 3.756434 TGTATTTGTTTCTACTGGCCTGC 59.244 43.478 9.95 0.00 0.00 4.85
3262 3552 2.526304 TGAAGGGAGAAGTTGTGTCG 57.474 50.000 0.00 0.00 0.00 4.35
3297 3587 6.677187 GCCCCGTAGAAAATGTATCTTGTTTC 60.677 42.308 0.00 0.00 0.00 2.78
3359 3649 5.105716 TGGATACAGAGTAGAGTTGCAGAAC 60.106 44.000 0.00 0.00 46.17 3.01
3380 3670 8.372521 CAGAACTTTTTGTTGTTTGTATGTGTC 58.627 33.333 0.00 0.00 39.30 3.67
3458 3749 4.202264 GGATGTGTAGTTACTGGAGATGGG 60.202 50.000 0.00 0.00 0.00 4.00
3461 3752 2.292918 TGTAGTTACTGGAGATGGGCCT 60.293 50.000 4.53 0.00 0.00 5.19
3548 3843 8.871686 AAACAAGCTAGTTTTTAAAGATGGTG 57.128 30.769 0.00 0.00 38.49 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 129 6.206634 AGCGGAAAGAAAAATGACTCATGTAA 59.793 34.615 0.00 0.00 0.00 2.41
82 134 3.882888 ACAGCGGAAAGAAAAATGACTCA 59.117 39.130 0.00 0.00 0.00 3.41
142 194 1.176527 CAGTGGAATCCCGTGCATTT 58.823 50.000 0.00 0.00 34.29 2.32
211 271 2.368439 TCACGTACTACTACCGCCAAT 58.632 47.619 0.00 0.00 0.00 3.16
282 343 3.186119 CCTGATGTCTTCTTTCTCGCTC 58.814 50.000 0.00 0.00 0.00 5.03
431 551 1.602771 GTGCTCTAAGGTGGTCCCC 59.397 63.158 0.00 0.00 0.00 4.81
479 599 3.469739 AGCCAAAATGTTTTTGCTCCTG 58.530 40.909 10.06 0.00 43.14 3.86
481 601 6.370433 TTTAAGCCAAAATGTTTTTGCTCC 57.630 33.333 14.65 2.99 45.05 4.70
506 626 7.523293 TCCAGTCTTAAATTGAATTTGAGCA 57.477 32.000 15.21 4.67 36.24 4.26
527 647 1.243902 GCGGGTTTGTTCTGAATCCA 58.756 50.000 0.00 0.00 0.00 3.41
544 664 2.799978 TGTACATGTCTTCTGTTGTGCG 59.200 45.455 0.00 0.00 0.00 5.34
643 763 1.078426 ACACCGCTATGTTGCCCTC 60.078 57.895 0.00 0.00 0.00 4.30
646 766 2.485122 GCACACCGCTATGTTGCC 59.515 61.111 0.00 0.00 37.77 4.52
721 953 4.459606 TGTCGATGATTGCGTTTGTTAAC 58.540 39.130 0.00 0.00 0.00 2.01
722 954 4.733972 TGTCGATGATTGCGTTTGTTAA 57.266 36.364 0.00 0.00 0.00 2.01
881 1113 7.550196 CCTCAAAATCAATTTATCCAACAAGGG 59.450 37.037 0.00 0.00 38.24 3.95
1102 1336 2.357323 GAGCTGCTTGGAAATAGGAAGC 59.643 50.000 2.53 0.00 42.07 3.86
1117 1351 0.036010 TCTTGGCTAACAGGAGCTGC 60.036 55.000 0.00 0.00 42.43 5.25
1186 1420 1.072173 AGCATTTGGTTTTCCTTGGGC 59.928 47.619 0.00 0.00 41.38 5.36
2005 2291 1.302511 GGCGGATGGTCACACACTT 60.303 57.895 0.00 0.00 0.00 3.16
2113 2399 1.024271 CCCACTGTGTCCTTGTTGTG 58.976 55.000 7.08 0.00 0.00 3.33
2354 2640 2.435410 CCAAAGGGCCCGTACGTC 60.435 66.667 18.44 5.37 0.00 4.34
2445 2731 0.460284 AGCGCCTCCACGTATTTCAG 60.460 55.000 2.29 0.00 34.88 3.02
2446 2732 0.459585 GAGCGCCTCCACGTATTTCA 60.460 55.000 2.29 0.00 34.88 2.69
2523 2809 2.474410 AAGTAGAAAGGTGGAAGGCG 57.526 50.000 0.00 0.00 0.00 5.52
3048 3334 7.766278 GTCCACAACTTAGATGAGACATTGTAT 59.234 37.037 10.52 0.00 0.00 2.29
3163 3451 0.752743 CCCATATGTGCACACTGGGG 60.753 60.000 38.79 33.56 43.38 4.96
3167 3455 1.076777 GGGCCCATATGTGCACACT 60.077 57.895 24.37 13.90 0.00 3.55
3176 3464 2.815158 ACAAAAGAAACGGGCCCATAT 58.185 42.857 24.92 6.18 0.00 1.78
3178 3466 1.069978 CAACAAAAGAAACGGGCCCAT 59.930 47.619 24.92 1.91 0.00 4.00
3231 3521 6.164176 ACTTCTCCCTTCAACTAATACAACG 58.836 40.000 0.00 0.00 0.00 4.10
3276 3566 9.694520 CATCAGAAACAAGATACATTTTCTACG 57.305 33.333 0.00 0.00 36.40 3.51
3297 3587 1.331214 AAACAGCACCCAACCATCAG 58.669 50.000 0.00 0.00 0.00 2.90
3342 3632 6.116126 ACAAAAAGTTCTGCAACTCTACTCT 58.884 36.000 0.00 0.00 42.45 3.24
3359 3649 5.551737 CGCGACACATACAAACAACAAAAAG 60.552 40.000 0.00 0.00 0.00 2.27
3535 3830 5.012561 CCAATTCCCCACACCATCTTTAAAA 59.987 40.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.