Multiple sequence alignment - TraesCS3B01G091500

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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 TraesCS3B01G091500 chr3B 100.000 3826 0 0 1 3826 60551361 60547536 0.000000 7066.0
1 TraesCS3B01G091500 chr7B 97.569 3826 90 3 1 3824 724306236 724302412 0.000000 6547.0
2 TraesCS3B01G091500 chr7B 97.103 3693 102 4 1 3691 725464812 725461123 0.000000 6222.0
3 TraesCS3B01G091500 chr7B 96.451 3240 106 6 556 3794 689571962 689575193 0.000000 5337.0
4 TraesCS3B01G091500 chr7B 95.688 3270 102 9 556 3824 640098149 640101380 0.000000 5221.0
5 TraesCS3B01G091500 chr1B 97.100 3827 89 6 1 3826 531293400 531297205 0.000000 6433.0
6 TraesCS3B01G091500 chr1B 96.786 3827 92 7 2 3807 56406784 56410600 0.000000 6357.0
7 TraesCS3B01G091500 chr1B 96.654 3826 107 8 2 3807 644236591 644240415 0.000000 6336.0
8 TraesCS3B01G091500 chr1B 96.605 3829 98 8 2 3807 63659450 63663269 0.000000 6322.0
9 TraesCS3B01G091500 chr1B 95.993 2695 88 15 1145 3826 447997001 447999688 0.000000 4361.0
10 TraesCS3B01G091500 chr5B 96.732 3825 103 9 2 3807 449643746 449647567 0.000000 6351.0
11 TraesCS3B01G091500 chr2B 96.628 3826 95 10 2 3807 67284039 67280228 0.000000 6320.0
12 TraesCS3B01G091500 chr2B 96.790 3240 86 7 556 3794 121622196 121618974 0.000000 5391.0
13 TraesCS3B01G091500 chr2B 100.000 33 0 0 3792 3824 121618962 121618930 0.000012 62.1
14 TraesCS3B01G091500 chr6B 95.928 3831 112 12 2 3807 719840774 719844585 0.000000 6170.0
15 TraesCS3B01G091500 chr6B 95.243 3826 113 7 2 3807 621031597 621035373 0.000000 5993.0
16 TraesCS3B01G091500 chr4B 96.544 3183 96 4 556 3737 366562158 366558989 0.000000 5256.0
17 TraesCS3B01G091500 chr4B 93.981 3273 144 30 556 3807 39581455 39578215 0.000000 4903.0


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 TraesCS3B01G091500 chr3B 60547536 60551361 3825 True 7066.00 7066 100.000 1 3826 1 chr3B.!!$R1 3825
1 TraesCS3B01G091500 chr7B 724302412 724306236 3824 True 6547.00 6547 97.569 1 3824 1 chr7B.!!$R1 3823
2 TraesCS3B01G091500 chr7B 725461123 725464812 3689 True 6222.00 6222 97.103 1 3691 1 chr7B.!!$R2 3690
3 TraesCS3B01G091500 chr7B 689571962 689575193 3231 False 5337.00 5337 96.451 556 3794 1 chr7B.!!$F2 3238
4 TraesCS3B01G091500 chr7B 640098149 640101380 3231 False 5221.00 5221 95.688 556 3824 1 chr7B.!!$F1 3268
5 TraesCS3B01G091500 chr1B 531293400 531297205 3805 False 6433.00 6433 97.100 1 3826 1 chr1B.!!$F4 3825
6 TraesCS3B01G091500 chr1B 56406784 56410600 3816 False 6357.00 6357 96.786 2 3807 1 chr1B.!!$F1 3805
7 TraesCS3B01G091500 chr1B 644236591 644240415 3824 False 6336.00 6336 96.654 2 3807 1 chr1B.!!$F5 3805
8 TraesCS3B01G091500 chr1B 63659450 63663269 3819 False 6322.00 6322 96.605 2 3807 1 chr1B.!!$F2 3805
9 TraesCS3B01G091500 chr1B 447997001 447999688 2687 False 4361.00 4361 95.993 1145 3826 1 chr1B.!!$F3 2681
10 TraesCS3B01G091500 chr5B 449643746 449647567 3821 False 6351.00 6351 96.732 2 3807 1 chr5B.!!$F1 3805
11 TraesCS3B01G091500 chr2B 67280228 67284039 3811 True 6320.00 6320 96.628 2 3807 1 chr2B.!!$R1 3805
12 TraesCS3B01G091500 chr2B 121618930 121622196 3266 True 2726.55 5391 98.395 556 3824 2 chr2B.!!$R2 3268
13 TraesCS3B01G091500 chr6B 719840774 719844585 3811 False 6170.00 6170 95.928 2 3807 1 chr6B.!!$F2 3805
14 TraesCS3B01G091500 chr6B 621031597 621035373 3776 False 5993.00 5993 95.243 2 3807 1 chr6B.!!$F1 3805
15 TraesCS3B01G091500 chr4B 366558989 366562158 3169 True 5256.00 5256 96.544 556 3737 1 chr4B.!!$R2 3181
16 TraesCS3B01G091500 chr4B 39578215 39581455 3240 True 4903.00 4903 93.981 556 3807 1 chr4B.!!$R1 3251

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
153 157 3.243367 TGCAAGTACTGTTGTTTCATGCC 60.243 43.478 0.00 0.00 0.0 4.40 F
1527 1542 1.080093 GACTGCGACGGACCATCAA 60.080 57.895 0.00 0.00 0.0 2.57 F
1634 1651 1.555075 GGATGGAAGTGGCACTGTCTA 59.445 52.381 22.83 17.63 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2014 1.675552 AGAGGCTTCTCTAGACGCTC 58.324 55.0 8.18 4.72 37.5 5.03 R
2392 2428 1.176527 CTTGCCATTCACCATCCGTT 58.823 50.0 0.00 0.00 0.0 4.44 R
3564 3673 0.615331 AGCTTCAGATTCTTCCGCCA 59.385 50.0 0.00 0.00 0.0 5.69 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
153 157 3.243367 TGCAAGTACTGTTGTTTCATGCC 60.243 43.478 0.00 0.00 0.00 4.40
183 187 7.823745 AGTGGAAACATCTAGTTGTTTTGAT 57.176 32.000 25.35 13.73 46.84 2.57
240 244 5.518128 CAGACTGTCTAAGCATGTGTACATC 59.482 44.000 10.47 0.00 33.61 3.06
1054 1066 1.821241 CGGTGCAATAGCGTCGATGG 61.821 60.000 6.79 0.00 46.23 3.51
1075 1087 8.240682 CGATGGTTAGGAAAACAAATGATGTAA 58.759 33.333 0.00 0.00 42.99 2.41
1321 1334 2.201732 CGTGCTGTTTATACGAGGCAT 58.798 47.619 0.00 0.00 40.01 4.40
1433 1446 3.415087 GGTGATGGCCCCAGCTCT 61.415 66.667 14.81 0.00 39.73 4.09
1527 1542 1.080093 GACTGCGACGGACCATCAA 60.080 57.895 0.00 0.00 0.00 2.57
1634 1651 1.555075 GGATGGAAGTGGCACTGTCTA 59.445 52.381 22.83 17.63 0.00 2.59
1747 1767 6.543465 TGTTGTCATCAATGAAGAAGAACAGT 59.457 34.615 9.07 0.00 38.75 3.55
1830 1850 6.904463 TCCAAATGGAATGATCATGTATGG 57.096 37.500 9.46 11.85 42.18 2.74
2001 2021 3.764466 CGAAGGGCTGGAGCGTCT 61.764 66.667 0.00 0.00 43.26 4.18
2392 2428 3.201487 TCAAGTCTCCGGTACCTGATCTA 59.799 47.826 10.90 0.00 0.00 1.98
2425 2461 0.463474 GGCAAGCTCTGGTGGAGATC 60.463 60.000 0.00 0.00 44.45 2.75
2811 2872 1.674322 CACGGGTTTTCGGAGCCAT 60.674 57.895 0.00 0.00 37.01 4.40
3312 3421 3.906218 TCCATATGCTAGCTTGAGATGGT 59.094 43.478 20.52 0.00 35.05 3.55
3551 3660 0.881118 GGTGCAAGAAGAATTGGCGA 59.119 50.000 0.00 0.00 0.00 5.54
3590 3699 0.321034 AGAATCTGAAGCTGCACGCA 60.321 50.000 1.02 0.00 42.61 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 64 2.294791 CCCGGTCTTTGCAACAACAATA 59.705 45.455 0.00 0.00 0.00 1.90
61 65 1.068434 CCCGGTCTTTGCAACAACAAT 59.932 47.619 0.00 0.00 0.00 2.71
183 187 4.986783 AGACGAGTATATCATGAGGACCA 58.013 43.478 0.09 0.00 0.00 4.02
240 244 6.582295 GCAACATGAACTAGTTAATTGGTGTG 59.418 38.462 21.57 14.22 0.00 3.82
250 254 4.794003 GCAAGCAAGCAACATGAACTAGTT 60.794 41.667 8.13 8.13 0.00 2.24
900 912 4.040095 TGAATGTTTGGAATGCATGGACAA 59.960 37.500 0.00 3.27 0.00 3.18
1075 1087 4.941713 ACCTCATCACTTCTACCTTCTCT 58.058 43.478 0.00 0.00 0.00 3.10
1321 1334 4.402793 CCTCTTCGTCCTAGATTCCTTCAA 59.597 45.833 0.00 0.00 0.00 2.69
1634 1651 3.491766 TGGTTCCTCCTTCATCTAGGT 57.508 47.619 0.00 0.00 36.63 3.08
1830 1850 5.788531 CGACAAATGTAGGAATCGACAAAAC 59.211 40.000 0.00 0.00 32.52 2.43
1994 2014 1.675552 AGAGGCTTCTCTAGACGCTC 58.324 55.000 8.18 4.72 37.50 5.03
2001 2021 3.283751 GCTGACTGTAGAGGCTTCTCTA 58.716 50.000 0.00 0.00 45.38 2.43
2206 2232 7.238710 ACCAAGATAACAAACAAGGTAGGAAT 58.761 34.615 0.00 0.00 0.00 3.01
2224 2250 6.664816 TCATCTCAAAATTTGCCTACCAAGAT 59.335 34.615 0.00 0.00 34.34 2.40
2392 2428 1.176527 CTTGCCATTCACCATCCGTT 58.823 50.000 0.00 0.00 0.00 4.44
2425 2461 1.348064 TGTGTCTTGGGGTAGACCAG 58.652 55.000 0.21 0.00 43.11 4.00
2811 2872 7.148052 GGAGTGACTTACTATAGCAGTCTTGAA 60.148 40.741 23.61 9.08 40.53 2.69
3278 3387 7.870027 AGCTAGCATATGGAGGAAAATGATAT 58.130 34.615 18.83 0.00 0.00 1.63
3312 3421 1.404986 CCGGCGTGTCCTTCATTTCTA 60.405 52.381 6.01 0.00 0.00 2.10
3349 3458 5.445964 ACAATTTGAACAGTAGACCTTGGT 58.554 37.500 2.79 0.00 0.00 3.67
3354 3463 5.694910 TCTTCGACAATTTGAACAGTAGACC 59.305 40.000 2.79 0.00 0.00 3.85
3477 3586 2.289631 TGCTCAAGGTCACGAACATGAT 60.290 45.455 0.00 0.00 0.00 2.45
3551 3660 2.715749 TCCGCCATCATCTTGATTGT 57.284 45.000 0.00 0.00 34.28 2.71
3564 3673 0.615331 AGCTTCAGATTCTTCCGCCA 59.385 50.000 0.00 0.00 0.00 5.69
3590 3699 2.355010 AGCAGCTCAAGTTCCTTGTT 57.645 45.000 4.08 0.00 41.66 2.83
3610 3719 4.162320 TCCTGTTCTTGAGACTTCTTGTGT 59.838 41.667 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.