Multiple sequence alignment - TraesCS6D01G132100

Loading Multiple Alignment...

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 TraesCS6D01G132100 chr6D 100.000 3834 0 0 1 3834 98131114 98127281 0.000000e+00 7081
1 TraesCS6D01G132100 chr6D 93.964 613 28 5 1 612 184475211 184474607 0.000000e+00 918
2 TraesCS6D01G132100 chr6D 100.000 105 0 0 4189 4293 98126926 98126822 1.220000e-45 195
3 TraesCS6D01G132100 chr6A 96.154 3250 82 19 614 3834 117415088 117411853 0.000000e+00 5269
4 TraesCS6D01G132100 chr6B 95.995 3196 86 19 611 3787 183335005 183331833 0.000000e+00 5155
5 TraesCS6D01G132100 chr6B 93.069 101 3 1 4193 4293 183331811 183331715 1.240000e-30 145
6 TraesCS6D01G132100 chrUn 89.414 1502 116 18 2354 3834 308088296 308089775 0.000000e+00 1853
7 TraesCS6D01G132100 chrUn 86.988 1637 137 39 755 2360 308086280 308087871 0.000000e+00 1773
8 TraesCS6D01G132100 chrUn 94.108 611 28 7 1 609 94077247 94077851 0.000000e+00 922
9 TraesCS6D01G132100 chrUn 83.275 574 41 32 755 1305 432033607 432034148 1.080000e-130 477
10 TraesCS6D01G132100 chr4A 89.414 1502 116 18 2354 3834 592546139 592547618 0.000000e+00 1853
11 TraesCS6D01G132100 chr4A 87.455 1666 133 37 726 2360 591499467 591497847 0.000000e+00 1849
12 TraesCS6D01G132100 chr4A 87.262 1680 138 38 712 2360 593112889 593114523 0.000000e+00 1847
13 TraesCS6D01G132100 chr4A 89.281 1502 119 17 2354 3834 593114948 593116428 0.000000e+00 1844
14 TraesCS6D01G132100 chr4A 87.294 1637 132 39 755 2360 592830050 592831641 0.000000e+00 1801
15 TraesCS6D01G132100 chr4A 86.988 1637 137 39 755 2360 592544123 592545714 0.000000e+00 1773
16 TraesCS6D01G132100 chr4A 92.173 626 45 3 2354 2977 591497425 591496802 0.000000e+00 881
17 TraesCS6D01G132100 chr4B 89.855 1449 112 16 2405 3834 20279712 20278280 0.000000e+00 1829
18 TraesCS6D01G132100 chr4B 90.606 1171 95 10 1118 2277 20280908 20279742 0.000000e+00 1539
19 TraesCS6D01G132100 chr4B 85.249 461 46 11 622 1079 20281346 20280905 5.060000e-124 455
20 TraesCS6D01G132100 chr4D 90.549 1365 107 11 2405 3752 10766286 10764927 0.000000e+00 1786
21 TraesCS6D01G132100 chr4D 90.386 1217 92 14 1081 2277 10767527 10766316 0.000000e+00 1576
22 TraesCS6D01G132100 chr4D 86.784 454 21 23 622 1063 10768003 10767577 1.810000e-128 470
23 TraesCS6D01G132100 chr7D 94.754 610 25 6 1 609 612262576 612263179 0.000000e+00 942
24 TraesCS6D01G132100 chr7D 94.156 616 28 5 1 615 584453444 584452836 0.000000e+00 931
25 TraesCS6D01G132100 chr7D 93.791 612 26 7 1 611 245260305 245259705 0.000000e+00 909
26 TraesCS6D01G132100 chr7B 94.728 607 25 5 7 612 482298822 482298222 0.000000e+00 937
27 TraesCS6D01G132100 chr7B 79.326 890 176 8 2442 3327 517625125 517626010 6.100000e-173 617
28 TraesCS6D01G132100 chr3A 94.463 614 25 8 1 612 459819615 459819009 0.000000e+00 937
29 TraesCS6D01G132100 chr3D 93.994 616 30 5 1 615 598110805 598110196 0.000000e+00 926
30 TraesCS6D01G132100 chr5D 93.791 612 29 8 1 611 216058655 216058052 0.000000e+00 911


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 TraesCS6D01G132100 chr6D 98126822 98131114 4292 True 3638.000000 7081 100.000000 1 4293 2 chr6D.!!$R2 4292
1 TraesCS6D01G132100 chr6D 184474607 184475211 604 True 918.000000 918 93.964000 1 612 1 chr6D.!!$R1 611
2 TraesCS6D01G132100 chr6A 117411853 117415088 3235 True 5269.000000 5269 96.154000 614 3834 1 chr6A.!!$R1 3220
3 TraesCS6D01G132100 chr6B 183331715 183335005 3290 True 2650.000000 5155 94.532000 611 4293 2 chr6B.!!$R1 3682
4 TraesCS6D01G132100 chrUn 308086280 308089775 3495 False 1813.000000 1853 88.201000 755 3834 2 chrUn.!!$F3 3079
5 TraesCS6D01G132100 chrUn 94077247 94077851 604 False 922.000000 922 94.108000 1 609 1 chrUn.!!$F1 608
6 TraesCS6D01G132100 chrUn 432033607 432034148 541 False 477.000000 477 83.275000 755 1305 1 chrUn.!!$F2 550
7 TraesCS6D01G132100 chr4A 593112889 593116428 3539 False 1845.500000 1847 88.271500 712 3834 2 chr4A.!!$F3 3122
8 TraesCS6D01G132100 chr4A 592544123 592547618 3495 False 1813.000000 1853 88.201000 755 3834 2 chr4A.!!$F2 3079
9 TraesCS6D01G132100 chr4A 592830050 592831641 1591 False 1801.000000 1801 87.294000 755 2360 1 chr4A.!!$F1 1605
10 TraesCS6D01G132100 chr4A 591496802 591499467 2665 True 1365.000000 1849 89.814000 726 2977 2 chr4A.!!$R1 2251
11 TraesCS6D01G132100 chr4B 20278280 20281346 3066 True 1274.333333 1829 88.570000 622 3834 3 chr4B.!!$R1 3212
12 TraesCS6D01G132100 chr4D 10764927 10768003 3076 True 1277.333333 1786 89.239667 622 3752 3 chr4D.!!$R1 3130
13 TraesCS6D01G132100 chr7D 612262576 612263179 603 False 942.000000 942 94.754000 1 609 1 chr7D.!!$F1 608
14 TraesCS6D01G132100 chr7D 584452836 584453444 608 True 931.000000 931 94.156000 1 615 1 chr7D.!!$R2 614
15 TraesCS6D01G132100 chr7D 245259705 245260305 600 True 909.000000 909 93.791000 1 611 1 chr7D.!!$R1 610
16 TraesCS6D01G132100 chr7B 482298222 482298822 600 True 937.000000 937 94.728000 7 612 1 chr7B.!!$R1 605
17 TraesCS6D01G132100 chr7B 517625125 517626010 885 False 617.000000 617 79.326000 2442 3327 1 chr7B.!!$F1 885
18 TraesCS6D01G132100 chr3A 459819009 459819615 606 True 937.000000 937 94.463000 1 612 1 chr3A.!!$R1 611
19 TraesCS6D01G132100 chr3D 598110196 598110805 609 True 926.000000 926 93.994000 1 615 1 chr3D.!!$R1 614
20 TraesCS6D01G132100 chr5D 216058052 216058655 603 True 911.000000 911 93.791000 1 611 1 chr5D.!!$R1 610

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
129 131 2.427095 GCCACAGTTGAACCACTTCTTT 59.573 45.455 0.0 0.0 0.00 2.52 F
1716 1832 0.873312 CAGCATCAGTCCCGACATCG 60.873 60.000 0.0 0.0 39.44 3.84 F
2335 2452 3.868077 ACTTGCGAGCTGAACATCTTATC 59.132 43.478 0.0 0.0 0.00 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2213 0.249573 GCAGTTGCACATGCCACTTT 60.250 50.0 7.81 0.0 43.42 2.66 R
2995 3548 0.605319 TGCCGATTCCTGCGAAAACT 60.605 50.0 0.00 0.0 0.00 2.66 R
4188 4781 0.250727 TCTTTTGAGGGAACGCAGGG 60.251 55.0 0.00 0.0 42.58 4.45 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
129 131 2.427095 GCCACAGTTGAACCACTTCTTT 59.573 45.455 0.00 0.00 0.00 2.52
171 174 9.731819 GACGTCAAGAACTAAGATATGATGTTA 57.268 33.333 11.55 0.00 37.21 2.41
496 504 9.494479 CATATTATGTTGTTTCTCATGTGACAC 57.506 33.333 7.04 7.04 0.00 3.67
567 575 5.123820 GTGAGCCATTGCATTAGTAAAGTGA 59.876 40.000 0.00 0.00 41.13 3.41
569 577 5.256474 AGCCATTGCATTAGTAAAGTGAGT 58.744 37.500 0.00 0.00 41.13 3.41
620 629 5.068723 GGGCATTGTGCTAGTACTAGTTCTA 59.931 44.000 26.76 17.72 44.28 2.10
659 669 6.910259 AAAAATTACCTCCTAGTCTCCCAT 57.090 37.500 0.00 0.00 0.00 4.00
790 802 7.931275 AGCTAAAATCGAACCCTTTAATCATC 58.069 34.615 0.00 0.00 0.00 2.92
1716 1832 0.873312 CAGCATCAGTCCCGACATCG 60.873 60.000 0.00 0.00 39.44 3.84
2097 2213 4.717629 CTCGTTGCGGCCGTCAGA 62.718 66.667 28.70 19.10 0.00 3.27
2318 2434 6.908825 TGGTGTAAGACAATAATTCACTTGC 58.091 36.000 0.00 0.00 0.00 4.01
2325 2441 4.002982 ACAATAATTCACTTGCGAGCTGA 58.997 39.130 0.00 1.55 0.00 4.26
2335 2452 3.868077 ACTTGCGAGCTGAACATCTTATC 59.132 43.478 0.00 0.00 0.00 1.75
2644 3197 4.783621 GCTGGGCAGACCGCATCA 62.784 66.667 4.42 0.00 45.17 3.07
3252 3805 1.203052 ACTGAATCTGGCGCAATTTGG 59.797 47.619 10.83 5.56 0.00 3.28
3284 3837 6.303054 TCCATGAGGTATAGAGAGAAGACAG 58.697 44.000 0.00 0.00 35.89 3.51
3330 3883 3.198853 ACTGGGCAGAGGATTAAAGACTC 59.801 47.826 0.00 0.00 0.00 3.36
3334 3887 2.483889 GCAGAGGATTAAAGACTCCCCG 60.484 54.545 0.00 0.00 31.49 5.73
3483 4043 4.404073 ACCTCTGCCTATTCTCTGTACTTG 59.596 45.833 0.00 0.00 0.00 3.16
3583 4154 7.167468 ACGACTTCAAAAGTTTATTTGATGCAC 59.833 33.333 12.69 8.37 45.77 4.57
3584 4155 7.167302 CGACTTCAAAAGTTTATTTGATGCACA 59.833 33.333 12.69 0.00 45.77 4.57
3695 4279 0.623723 TGATCCAGTTAGGGGGTTGC 59.376 55.000 0.00 0.00 38.24 4.17
4206 4799 2.257353 CCCTGCGTTCCCTCAAAAG 58.743 57.895 0.00 0.00 0.00 2.27
4236 4829 3.433314 GGTCAGTTGCATCATCCTGAGAT 60.433 47.826 0.00 0.00 34.80 2.75
4259 4852 4.022676 TGCGATCGATGTTACTATGCCTAA 60.023 41.667 21.57 0.00 0.00 2.69
4260 4853 4.921515 GCGATCGATGTTACTATGCCTAAA 59.078 41.667 21.57 0.00 0.00 1.85
4261 4854 5.577164 GCGATCGATGTTACTATGCCTAAAT 59.423 40.000 21.57 0.00 0.00 1.40
4262 4855 6.454318 GCGATCGATGTTACTATGCCTAAATG 60.454 42.308 21.57 0.00 0.00 2.32
4266 4859 6.419710 TCGATGTTACTATGCCTAAATGTTCG 59.580 38.462 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 131 8.996024 TCTTGACGTCAACAATTCTGATATAA 57.004 30.769 26.53 1.00 0.00 0.98
440 448 9.378551 AGCGTTTTACAAAGATCACATATCTAA 57.621 29.630 0.00 0.00 0.00 2.10
441 449 8.942338 AGCGTTTTACAAAGATCACATATCTA 57.058 30.769 0.00 0.00 0.00 1.98
496 504 3.244700 ACACTCCTTGAAATCCTCCACAG 60.245 47.826 0.00 0.00 0.00 3.66
657 667 7.752239 CAGCAGTGTTATTCTCCAACTTTTATG 59.248 37.037 0.00 0.00 0.00 1.90
659 669 6.293955 GCAGCAGTGTTATTCTCCAACTTTTA 60.294 38.462 0.00 0.00 0.00 1.52
675 685 2.301296 ACTCACTCATTAGCAGCAGTGT 59.699 45.455 9.10 0.00 37.97 3.55
790 802 5.931532 ACTGCATTTTCTAGTGATTGAACG 58.068 37.500 0.00 0.00 0.00 3.95
945 986 2.119495 GGTTAAGGGATGGAGCTCAGA 58.881 52.381 17.19 0.93 0.00 3.27
1137 1215 7.725251 TGGAAATTTGCAACTGTAAATCTCTT 58.275 30.769 10.24 0.00 38.97 2.85
1628 1737 5.048921 AGCTGCAATTGTCATACATATCTGC 60.049 40.000 7.40 2.25 0.00 4.26
1634 1743 4.520179 TCAGAGCTGCAATTGTCATACAT 58.480 39.130 7.40 0.00 0.00 2.29
1716 1832 4.745125 CGATGAACATCACCATGGTAGTAC 59.255 45.833 19.28 7.93 37.69 2.73
1834 1950 3.866582 CTCCATCAGGTCCCCGCC 61.867 72.222 0.00 0.00 35.89 6.13
1847 1963 1.557269 GCCCTTCTTCTCCAGCTCCA 61.557 60.000 0.00 0.00 0.00 3.86
2097 2213 0.249573 GCAGTTGCACATGCCACTTT 60.250 50.000 7.81 0.00 43.42 2.66
2318 2434 3.451526 TGCAGATAAGATGTTCAGCTCG 58.548 45.455 0.00 0.00 0.00 5.03
2325 2441 8.621532 TCTTTTGTACTTGCAGATAAGATGTT 57.378 30.769 0.00 0.00 0.00 2.71
2454 3006 5.707764 GCCTTGTCTAGAAACCTGAAGATTT 59.292 40.000 0.00 0.00 0.00 2.17
2644 3197 0.899720 TCCCCTGCTCGATAAACGTT 59.100 50.000 0.00 0.00 43.13 3.99
2714 3267 1.201965 GCTGAACACGCTGACAATAGC 60.202 52.381 0.00 0.00 40.29 2.97
2995 3548 0.605319 TGCCGATTCCTGCGAAAACT 60.605 50.000 0.00 0.00 0.00 2.66
3252 3805 4.408276 TCTATACCTCATGGAGTAGTGCC 58.592 47.826 0.00 0.00 37.04 5.01
3284 3837 4.799428 GTCTACTATTCGGTGTCAAGAAGC 59.201 45.833 0.00 0.00 0.00 3.86
3330 3883 2.203139 TTGCGGTATGATGCGGGG 60.203 61.111 0.00 0.00 0.00 5.73
3334 3887 3.365832 CATCTTTGTTGCGGTATGATGC 58.634 45.455 0.00 0.00 0.00 3.91
3483 4043 4.199432 TCAGATTCTTCTCTTGGCTGTC 57.801 45.455 0.00 0.00 0.00 3.51
3583 4154 5.947228 TCAGTTAACCAAGCTCTGATTTG 57.053 39.130 0.88 0.00 31.51 2.32
3584 4155 5.416952 CCATCAGTTAACCAAGCTCTGATTT 59.583 40.000 8.64 0.68 41.81 2.17
3593 4164 5.887598 TGAATGATCCCATCAGTTAACCAAG 59.112 40.000 0.88 0.00 43.53 3.61
3695 4279 9.986833 CTAGACGATCAGAATATTCTATCACAG 57.013 37.037 17.53 9.68 35.34 3.66
4188 4781 0.250727 TCTTTTGAGGGAACGCAGGG 60.251 55.000 0.00 0.00 42.58 4.45
4189 4782 1.604604 TTCTTTTGAGGGAACGCAGG 58.395 50.000 0.00 0.00 42.58 4.85
4190 4783 3.708563 TTTTCTTTTGAGGGAACGCAG 57.291 42.857 0.00 0.00 42.58 5.18
4191 4784 5.336372 CCATATTTTCTTTTGAGGGAACGCA 60.336 40.000 0.00 0.00 38.85 5.24
4206 4799 6.040166 AGGATGATGCAACTGACCATATTTTC 59.960 38.462 0.00 0.00 0.00 2.29
4236 4829 2.296190 AGGCATAGTAACATCGATCGCA 59.704 45.455 11.09 0.00 0.00 5.10
4259 4852 8.827677 GCTAGATTATAAGTGGAAACGAACATT 58.172 33.333 0.00 0.00 0.00 2.71
4260 4853 7.985184 TGCTAGATTATAAGTGGAAACGAACAT 59.015 33.333 0.00 0.00 0.00 2.71
4261 4854 7.324935 TGCTAGATTATAAGTGGAAACGAACA 58.675 34.615 0.00 0.00 0.00 3.18
4262 4855 7.516943 GCTGCTAGATTATAAGTGGAAACGAAC 60.517 40.741 0.00 0.00 0.00 3.95
4266 4859 6.538742 TGTGCTGCTAGATTATAAGTGGAAAC 59.461 38.462 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.