Multiple sequence alignment - TraesCS3D01G532600

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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 TraesCS3D01G532600 chr3D 100.000 2605 0 0 1438 4042 608455447 608452843 0.000000e+00 4811.0
1 TraesCS3D01G532600 chr3D 100.000 1117 0 0 1 1117 608456884 608455768 0.000000e+00 2063.0
2 TraesCS3D01G532600 chr3D 88.406 69 5 2 4 70 523568894 523568961 3.350000e-11 80.5
3 TraesCS3D01G532600 chr3A 95.310 2516 74 17 1552 4042 740747381 740749877 0.000000e+00 3952.0
4 TraesCS3D01G532600 chr3A 95.109 2515 81 16 1552 4042 740716629 740719125 0.000000e+00 3925.0
5 TraesCS3D01G532600 chr3A 96.171 1097 37 3 1 1095 740678482 740679575 0.000000e+00 1788.0
6 TraesCS3D01G532600 chr3A 96.686 875 19 4 1552 2421 740684881 740685750 0.000000e+00 1447.0
7 TraesCS3D01G532600 chr3A 96.721 122 3 1 1438 1558 740679701 740679822 6.850000e-48 202.0
8 TraesCS3D01G532600 chr3A 95.902 122 4 1 1438 1558 740712024 740712145 3.190000e-46 196.0
9 TraesCS3D01G532600 chr3A 95.902 122 4 1 1438 1558 740742776 740742897 3.190000e-46 196.0
10 TraesCS3D01G532600 chrUn 94.538 2087 84 16 1979 4042 43254204 43252125 0.000000e+00 3195.0
11 TraesCS3D01G532600 chrUn 93.866 1728 72 10 1736 3432 43163278 43161554 0.000000e+00 2573.0
12 TraesCS3D01G532600 chrUn 95.574 1333 44 3 1736 3056 43167025 43165696 0.000000e+00 2121.0
13 TraesCS3D01G532600 chrUn 95.403 1327 48 5 1979 3295 278815840 278814517 0.000000e+00 2100.0
14 TraesCS3D01G532600 chrUn 95.403 1327 48 5 1979 3295 278823055 278821732 0.000000e+00 2100.0
15 TraesCS3D01G532600 chrUn 94.812 1118 48 6 1 1117 43169411 43168303 0.000000e+00 1735.0
16 TraesCS3D01G532600 chrUn 95.174 1036 40 6 1 1035 351706062 351707088 0.000000e+00 1628.0
17 TraesCS3D01G532600 chrUn 95.174 1036 40 6 1 1035 364458673 364459699 0.000000e+00 1628.0
18 TraesCS3D01G532600 chrUn 91.975 810 46 6 2876 3666 43098015 43097206 0.000000e+00 1118.0
19 TraesCS3D01G532600 chrUn 89.103 780 73 7 2108 2878 43264523 43263747 0.000000e+00 959.0
20 TraesCS3D01G532600 chrUn 94.355 620 30 3 3423 4042 335931595 335930981 0.000000e+00 946.0
21 TraesCS3D01G532600 chrUn 94.194 620 31 3 3423 4042 43160361 43159747 0.000000e+00 941.0
22 TraesCS3D01G532600 chrUn 94.975 597 27 2 521 1117 43165150 43164557 0.000000e+00 933.0
23 TraesCS3D01G532600 chrUn 94.472 597 30 2 521 1117 371066316 371065723 0.000000e+00 917.0
24 TraesCS3D01G532600 chrUn 90.778 694 39 13 2871 3540 364772375 364773067 0.000000e+00 904.0
25 TraesCS3D01G532600 chrUn 90.778 694 39 13 2871 3540 364774381 364775073 0.000000e+00 904.0
26 TraesCS3D01G532600 chrUn 90.778 694 39 13 2871 3540 364778393 364779085 0.000000e+00 904.0
27 TraesCS3D01G532600 chrUn 90.778 694 39 13 2871 3540 465410766 465410074 0.000000e+00 904.0
28 TraesCS3D01G532600 chrUn 95.230 566 15 2 1736 2289 471539951 471540516 0.000000e+00 885.0
29 TraesCS3D01G532600 chrUn 94.779 498 22 3 3545 4042 458607001 458606508 0.000000e+00 773.0
30 TraesCS3D01G532600 chrUn 93.939 297 13 2 1449 1745 43168190 43167899 1.030000e-120 444.0
31 TraesCS3D01G532600 chrUn 93.939 297 13 2 1449 1745 371065610 371065319 1.030000e-120 444.0
32 TraesCS3D01G532600 chrUn 89.773 352 27 6 3090 3432 335933139 335932788 3.710000e-120 442.0
33 TraesCS3D01G532600 chrUn 93.603 297 14 2 1449 1745 43164444 43164153 4.800000e-119 438.0
34 TraesCS3D01G532600 chr4A 80.435 138 25 1 981 1116 615946865 615947002 1.990000e-18 104.0
35 TraesCS3D01G532600 chr4A 100.000 29 0 0 886 914 52607208 52607180 2.000000e-03 54.7
36 TraesCS3D01G532600 chr4D 88.889 72 6 1 1 70 487018440 487018511 2.000000e-13 87.9
37 TraesCS3D01G532600 chr2A 89.706 68 5 1 5 70 4895206 4895139 7.200000e-13 86.1
38 TraesCS3D01G532600 chr1D 92.453 53 3 1 3983 4035 300671456 300671507 1.560000e-09 75.0
39 TraesCS3D01G532600 chr5D 86.567 67 7 1 6 70 79136346 79136412 5.600000e-09 73.1
40 TraesCS3D01G532600 chr5D 100.000 36 0 0 977 1012 97074132 97074167 2.610000e-07 67.6
41 TraesCS3D01G532600 chr5A 95.556 45 2 0 5 49 431997698 431997742 5.600000e-09 73.1
42 TraesCS3D01G532600 chr6B 90.566 53 5 0 3990 4042 80047500 80047448 2.020000e-08 71.3
43 TraesCS3D01G532600 chr7D 86.207 58 5 2 3984 4039 587260402 587260458 4.360000e-05 60.2
44 TraesCS3D01G532600 chr4B 92.857 42 1 2 974 1014 161603707 161603667 4.360000e-05 60.2


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 TraesCS3D01G532600 chr3D 608452843 608456884 4041 True 3437.000000 4811 100.000000 1 4042 2 chr3D.!!$R1 4041
1 TraesCS3D01G532600 chr3A 740747381 740749877 2496 False 3952.000000 3952 95.310000 1552 4042 1 chr3A.!!$F5 2490
2 TraesCS3D01G532600 chr3A 740716629 740719125 2496 False 3925.000000 3925 95.109000 1552 4042 1 chr3A.!!$F3 2490
3 TraesCS3D01G532600 chr3A 740684881 740685750 869 False 1447.000000 1447 96.686000 1552 2421 1 chr3A.!!$F1 869
4 TraesCS3D01G532600 chr3A 740678482 740679822 1340 False 995.000000 1788 96.446000 1 1558 2 chr3A.!!$F6 1557
5 TraesCS3D01G532600 chrUn 43252125 43254204 2079 True 3195.000000 3195 94.538000 1979 4042 1 chrUn.!!$R2 2063
6 TraesCS3D01G532600 chrUn 278814517 278815840 1323 True 2100.000000 2100 95.403000 1979 3295 1 chrUn.!!$R4 1316
7 TraesCS3D01G532600 chrUn 278821732 278823055 1323 True 2100.000000 2100 95.403000 1979 3295 1 chrUn.!!$R5 1316
8 TraesCS3D01G532600 chrUn 351706062 351707088 1026 False 1628.000000 1628 95.174000 1 1035 1 chrUn.!!$F1 1034
9 TraesCS3D01G532600 chrUn 364458673 364459699 1026 False 1628.000000 1628 95.174000 1 1035 1 chrUn.!!$F2 1034
10 TraesCS3D01G532600 chrUn 43159747 43169411 9664 True 1312.142857 2573 94.423286 1 4042 7 chrUn.!!$R8 4041
11 TraesCS3D01G532600 chrUn 43097206 43098015 809 True 1118.000000 1118 91.975000 2876 3666 1 chrUn.!!$R1 790
12 TraesCS3D01G532600 chrUn 43263747 43264523 776 True 959.000000 959 89.103000 2108 2878 1 chrUn.!!$R3 770
13 TraesCS3D01G532600 chrUn 364772375 364779085 6710 False 904.000000 904 90.778000 2871 3540 3 chrUn.!!$F4 669
14 TraesCS3D01G532600 chrUn 465410074 465410766 692 True 904.000000 904 90.778000 2871 3540 1 chrUn.!!$R7 669
15 TraesCS3D01G532600 chrUn 471539951 471540516 565 False 885.000000 885 95.230000 1736 2289 1 chrUn.!!$F3 553
16 TraesCS3D01G532600 chrUn 335930981 335933139 2158 True 694.000000 946 92.064000 3090 4042 2 chrUn.!!$R9 952
17 TraesCS3D01G532600 chrUn 371065319 371066316 997 True 680.500000 917 94.205500 521 1745 2 chrUn.!!$R10 1224

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
63 64 2.814280 TTCACCTCACTCCGAGAAAC 57.186 50.0 1.33 0.0 45.45 2.78 F
838 4588 5.460646 AGGACTGCAATGAATTAACAAACG 58.539 37.5 0.00 0.0 0.00 3.60 F
1110 4860 5.448225 CGGTATACACAGAACATACGTGACT 60.448 44.0 5.01 0.0 34.69 3.41 F
1942 6615 0.250513 ATCACTTCTCCGGTTCAGGC 59.749 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 4764 1.130561 GCCGTGTACCTCTTTGATTGC 59.869 52.381 0.00 0.00 0.00 3.56 R
1749 6398 1.544825 TATAGATCCAGCCTGGCCGC 61.545 60.000 16.57 0.00 37.47 6.53 R
2502 7184 1.550524 TCAACGGTCCAGATCAAGGAG 59.449 52.381 7.13 0.60 35.42 3.69 R
3186 13897 0.657840 GCTTAATGGGTGCAGCGTAG 59.342 55.000 10.24 3.69 0.00 3.51 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 64 2.814280 TTCACCTCACTCCGAGAAAC 57.186 50.000 1.33 0.00 45.45 2.78
86 87 7.713764 ACAATTTTGATTTTGTTGGTAGCTC 57.286 32.000 0.00 0.00 32.28 4.09
476 478 9.906660 TTCAGATATTTTGACGCAACTTAAATT 57.093 25.926 0.00 0.00 0.00 1.82
558 4306 6.172630 TGCAATGAGTGACACTTGTGTATAT 58.827 36.000 10.01 0.00 0.00 0.86
838 4588 5.460646 AGGACTGCAATGAATTAACAAACG 58.539 37.500 0.00 0.00 0.00 3.60
1110 4860 5.448225 CGGTATACACAGAACATACGTGACT 60.448 44.000 5.01 0.00 34.69 3.41
1517 5282 6.773638 ACATAGAGAGAAGAACCACAACAAT 58.226 36.000 0.00 0.00 0.00 2.71
1638 5403 7.527084 GCCAGAAGAAGCGTTTATATATAGG 57.473 40.000 0.00 0.00 0.00 2.57
1639 5404 7.321153 GCCAGAAGAAGCGTTTATATATAGGA 58.679 38.462 0.00 0.00 0.00 2.94
1640 5405 7.982354 GCCAGAAGAAGCGTTTATATATAGGAT 59.018 37.037 0.00 0.00 0.00 3.24
1942 6615 0.250513 ATCACTTCTCCGGTTCAGGC 59.749 55.000 0.00 0.00 0.00 4.85
2086 6759 4.558697 GCAAAAATTTCAACGGTAGCCTCT 60.559 41.667 0.00 0.00 0.00 3.69
2422 7104 1.272781 GACGATTGGAAGCTCAGACG 58.727 55.000 0.00 0.00 0.00 4.18
2423 7105 0.888619 ACGATTGGAAGCTCAGACGA 59.111 50.000 0.00 0.00 0.00 4.20
2424 7106 1.272781 CGATTGGAAGCTCAGACGAC 58.727 55.000 0.00 0.00 0.00 4.34
2502 7184 2.476320 GGCGATCTGCTTCAAGGGC 61.476 63.158 8.94 0.00 45.43 5.19
2932 13632 4.353437 ACAACGTCGACGAGGGCC 62.353 66.667 41.52 0.00 43.02 5.80
3003 13703 0.106149 ACGTCCCAAGCTTCGTCTTT 59.894 50.000 5.20 0.00 30.71 2.52
3064 13764 4.473444 ACAAAGGCTTCCTCTCATTGAAA 58.527 39.130 0.00 0.00 30.89 2.69
3148 13859 4.890088 AGTTTAGAACGTCACAAGGCATA 58.110 39.130 0.00 0.00 36.23 3.14
3186 13897 9.770097 TTTCATTAGTCAGTCTGATAATCATCC 57.230 33.333 5.68 0.00 0.00 3.51
3337 14051 9.625747 ACTTTTGAATAATTTTGGGTTGTGAAT 57.374 25.926 0.00 0.00 0.00 2.57
3452 16582 1.081892 CGTGGCATCTCTTGGTCTTG 58.918 55.000 0.00 0.00 0.00 3.02
3454 16584 1.808945 GTGGCATCTCTTGGTCTTGTG 59.191 52.381 0.00 0.00 0.00 3.33
3468 16598 1.819288 TCTTGTGTTTTGGCGGTCAAA 59.181 42.857 3.18 3.18 42.98 2.69
3636 16766 9.302345 GTAGAGATGACGAATTCAAATAGTTCA 57.698 33.333 6.22 0.00 37.92 3.18
3659 16789 9.616156 TTCATTGTAACTTTGTTTGTACTAGGA 57.384 29.630 0.00 0.00 0.00 2.94
3733 16863 2.429250 GAGGAAGTGAGGGAACTAGAGC 59.571 54.545 0.00 0.00 44.43 4.09
3948 17079 3.210227 CACATCACCACCTACAACAACA 58.790 45.455 0.00 0.00 0.00 3.33
3949 17080 3.629855 CACATCACCACCTACAACAACAA 59.370 43.478 0.00 0.00 0.00 2.83
3950 17081 3.630312 ACATCACCACCTACAACAACAAC 59.370 43.478 0.00 0.00 0.00 3.32
4030 17161 0.040646 TATGGTGGACACTCCCTCGT 59.959 55.000 2.13 0.00 35.03 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 6.640499 TCGAGCTACCAACAAAATCAAAATTG 59.360 34.615 0.00 0.00 0.00 2.32
86 87 8.208718 TCATTCTCCCAACTAAATATGTTTCG 57.791 34.615 0.00 0.00 0.00 3.46
117 118 4.113354 CCGTTATAGCGCTCTTTTCTTCT 58.887 43.478 16.34 0.00 0.00 2.85
152 154 1.175983 TGTTGCAACGGGGATTGGTC 61.176 55.000 23.79 0.00 0.00 4.02
400 402 6.930164 TGTTTGATGCTGATATGCAAAGTTTT 59.070 30.769 0.00 0.00 46.61 2.43
519 4267 9.491675 TCACTCATTGCATGAAACATAATTTTT 57.508 25.926 0.00 0.00 39.11 1.94
523 4271 7.031372 GTGTCACTCATTGCATGAAACATAAT 58.969 34.615 0.00 0.00 39.11 1.28
558 4306 8.092521 TGAATTTGAAAACTTTGCAGTTCAAA 57.907 26.923 18.27 18.27 42.89 2.69
798 4546 8.827832 TGCAGTCCTTAGGTAGTTTATACTAA 57.172 34.615 0.00 0.00 38.55 2.24
838 4588 8.446273 CAGATGTATATAGGCATGTTTTAGTGC 58.554 37.037 0.00 0.00 40.55 4.40
1014 4764 1.130561 GCCGTGTACCTCTTTGATTGC 59.869 52.381 0.00 0.00 0.00 3.56
1062 4812 7.275779 CCGGATATCTCATAATCGGTTTTGTAG 59.724 40.741 0.00 0.00 33.04 2.74
1517 5282 4.119862 GTGCCGTGCTCTTCTTGAATATA 58.880 43.478 0.00 0.00 0.00 0.86
1635 5400 8.632679 CGGTACCTTGTGTAGTTTAATATCCTA 58.367 37.037 10.90 0.00 0.00 2.94
1637 5402 7.491682 TCGGTACCTTGTGTAGTTTAATATCC 58.508 38.462 10.90 0.00 0.00 2.59
1638 5403 9.189723 GATCGGTACCTTGTGTAGTTTAATATC 57.810 37.037 10.90 0.00 0.00 1.63
1639 5404 8.921205 AGATCGGTACCTTGTGTAGTTTAATAT 58.079 33.333 10.90 0.00 0.00 1.28
1640 5405 8.192774 CAGATCGGTACCTTGTGTAGTTTAATA 58.807 37.037 10.90 0.00 0.00 0.98
1684 5449 2.550830 ATACATCGATGGCTTGTCCC 57.449 50.000 28.09 0.00 0.00 4.46
1749 6398 1.544825 TATAGATCCAGCCTGGCCGC 61.545 60.000 16.57 0.00 37.47 6.53
1960 6633 2.616330 CGTTGCAGATGGTGGCGTT 61.616 57.895 0.00 0.00 0.00 4.84
2086 6759 2.363795 CCACTGGTAGAGGCCGGA 60.364 66.667 5.05 0.00 38.27 5.14
2348 7030 1.593296 GACCTTGTAGGCGTCGGAGT 61.593 60.000 0.00 0.00 39.63 3.85
2502 7184 1.550524 TCAACGGTCCAGATCAAGGAG 59.449 52.381 7.13 0.60 35.42 3.69
2932 13632 3.181497 CGGCTTGGATATTCAACAAGTGG 60.181 47.826 0.00 0.00 42.60 4.00
3064 13764 9.955102 AACCGATCTAAGTAAAGAATAAAAGGT 57.045 29.630 0.00 0.00 0.00 3.50
3186 13897 0.657840 GCTTAATGGGTGCAGCGTAG 59.342 55.000 10.24 3.69 0.00 3.51
3335 14049 3.973206 TGTAGACCGATGACAACCATT 57.027 42.857 0.00 0.00 35.17 3.16
3336 14050 3.596214 GTTGTAGACCGATGACAACCAT 58.404 45.455 5.95 0.00 44.60 3.55
3337 14051 2.608506 CGTTGTAGACCGATGACAACCA 60.609 50.000 10.57 0.00 46.58 3.67
3452 16582 2.190161 GTCTTTTGACCGCCAAAACAC 58.810 47.619 9.05 6.80 46.48 3.32
3454 16584 2.570442 TGTCTTTTGACCGCCAAAAC 57.430 45.000 9.05 4.11 46.48 2.43
3468 16598 1.562575 CGTTACGGCCGCTTTGTCTT 61.563 55.000 28.58 5.26 0.00 3.01
3659 16789 1.137086 ACGAGCACGAGCCATAAAGAT 59.863 47.619 11.40 0.00 43.56 2.40
3733 16863 1.330655 ACACATGCTCCCTACCTCCG 61.331 60.000 0.00 0.00 0.00 4.63
3758 16888 5.561919 CGGTGAATGAACTCAATCGGAAAAA 60.562 40.000 0.00 0.00 0.00 1.94
3763 16894 2.346803 ACGGTGAATGAACTCAATCGG 58.653 47.619 0.00 0.00 32.13 4.18
3948 17079 4.705023 CCCAAAGGAAAGGTATCGATTGTT 59.295 41.667 1.71 0.00 33.47 2.83
3949 17080 4.018779 TCCCAAAGGAAAGGTATCGATTGT 60.019 41.667 1.71 0.00 40.08 2.71
3950 17081 4.523083 TCCCAAAGGAAAGGTATCGATTG 58.477 43.478 1.71 0.00 40.08 2.67
3985 17116 4.155709 ACAACCACTTGAGAGATGAGAGA 58.844 43.478 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.