Multiple sequence alignment - TraesCS1B01G016300

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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 TraesCS1B01G016300 chr1B 100.000 3281 0 0 1 3281 7929271 7925991 0.000000e+00 6059
1 TraesCS1B01G016300 chr1B 97.473 2968 67 4 315 3281 6325796 6328756 0.000000e+00 5059
2 TraesCS1B01G016300 chr1B 96.888 2731 67 9 254 2981 7130853 7128138 0.000000e+00 4556
3 TraesCS1B01G016300 chr1B 82.513 1138 170 18 904 2027 6340599 6341721 0.000000e+00 972
4 TraesCS1B01G016300 chr1B 83.474 1065 153 15 904 1960 6693307 6692258 0.000000e+00 970
5 TraesCS1B01G016300 chr1B 82.049 1142 169 25 904 2027 629702643 629703766 0.000000e+00 941
6 TraesCS1B01G016300 chr1B 94.931 217 7 1 28 240 7132169 7131953 1.460000e-88 337
7 TraesCS1B01G016300 chr1B 96.907 194 5 1 1 193 6325609 6325802 1.140000e-84 324
8 TraesCS1B01G016300 chr1D 86.792 2385 245 33 758 3099 3122840 3125197 0.000000e+00 2595
9 TraesCS1B01G016300 chr1D 89.322 1667 106 34 69 1685 3613640 3615284 0.000000e+00 2026
10 TraesCS1B01G016300 chr1D 79.710 2553 369 89 482 2972 3227500 3229965 0.000000e+00 1707
11 TraesCS1B01G016300 chr1D 88.383 835 75 6 1731 2543 3615294 3616128 0.000000e+00 985
12 TraesCS1B01G016300 chr1D 92.000 350 22 4 386 732 3122499 3122845 1.370000e-133 486
13 TraesCS1B01G016300 chr1D 84.937 239 30 6 2535 2770 3616158 3616393 1.520000e-58 237
14 TraesCS1B01G016300 chr1D 90.400 125 9 2 12 136 3122065 3122186 9.420000e-36 161
15 TraesCS1B01G016300 chrUn 91.937 1079 73 7 386 1455 9821158 9820085 0.000000e+00 1498
16 TraesCS1B01G016300 chrUn 91.515 660 46 5 1745 2396 9819760 9819103 0.000000e+00 900
17 TraesCS1B01G016300 chrUn 90.252 318 27 3 1396 1709 9820074 9819757 2.360000e-111 412
18 TraesCS1B01G016300 chrUn 89.706 136 12 2 1 136 9821547 9821414 4.350000e-39 172
19 TraesCS1B01G016300 chr1A 85.355 1393 168 18 1118 2488 6499036 6497658 0.000000e+00 1410
20 TraesCS1B01G016300 chr1A 82.171 645 80 19 904 1542 6439196 6438581 3.750000e-144 521
21 TraesCS1B01G016300 chr1A 87.774 319 31 6 789 1099 6500315 6499997 1.860000e-97 366


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 TraesCS1B01G016300 chr1B 7925991 7929271 3280 True 6059.000000 6059 100.000000 1 3281 1 chr1B.!!$R2 3280
1 TraesCS1B01G016300 chr1B 6325609 6328756 3147 False 2691.500000 5059 97.190000 1 3281 2 chr1B.!!$F3 3280
2 TraesCS1B01G016300 chr1B 7128138 7132169 4031 True 2446.500000 4556 95.909500 28 2981 2 chr1B.!!$R3 2953
3 TraesCS1B01G016300 chr1B 6340599 6341721 1122 False 972.000000 972 82.513000 904 2027 1 chr1B.!!$F1 1123
4 TraesCS1B01G016300 chr1B 6692258 6693307 1049 True 970.000000 970 83.474000 904 1960 1 chr1B.!!$R1 1056
5 TraesCS1B01G016300 chr1B 629702643 629703766 1123 False 941.000000 941 82.049000 904 2027 1 chr1B.!!$F2 1123
6 TraesCS1B01G016300 chr1D 3227500 3229965 2465 False 1707.000000 1707 79.710000 482 2972 1 chr1D.!!$F1 2490
7 TraesCS1B01G016300 chr1D 3613640 3616393 2753 False 1082.666667 2026 87.547333 69 2770 3 chr1D.!!$F3 2701
8 TraesCS1B01G016300 chr1D 3122065 3125197 3132 False 1080.666667 2595 89.730667 12 3099 3 chr1D.!!$F2 3087
9 TraesCS1B01G016300 chrUn 9819103 9821547 2444 True 745.500000 1498 90.852500 1 2396 4 chrUn.!!$R1 2395
10 TraesCS1B01G016300 chr1A 6497658 6500315 2657 True 888.000000 1410 86.564500 789 2488 2 chr1A.!!$R2 1699
11 TraesCS1B01G016300 chr1A 6438581 6439196 615 True 521.000000 521 82.171000 904 1542 1 chr1A.!!$R1 638

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
96 98 1.003696 ACCTAAAGGCTTCCACTGCTC 59.996 52.381 0.0 0.0 39.32 4.26 F
993 2194 1.063070 TAAAGCTCCCCACACACCCA 61.063 55.000 0.0 0.0 0.00 4.51 F
1781 4027 0.972471 CAAAGATGGGACCTTGGGGC 60.972 60.000 0.0 0.0 35.63 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 4027 2.125269 GATGTTCCACCGTCCCCG 60.125 66.667 0.00 0.00 0.00 5.73 R
1992 4243 5.524971 TGAGATGTAAGTTATACCACCGG 57.475 43.478 0.00 0.00 0.00 5.28 R
3230 5583 1.549203 CTACAGCAAGGCCAAATGGT 58.451 50.000 5.01 3.45 37.57 3.55 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
96 98 1.003696 ACCTAAAGGCTTCCACTGCTC 59.996 52.381 0.00 0.00 39.32 4.26
563 1729 1.144057 GGTGTAGTGGCATCCGAGG 59.856 63.158 0.00 0.00 0.00 4.63
761 1935 8.705594 TGTATTATTTGGACCAAAAGGACAAAA 58.294 29.630 23.11 9.49 36.90 2.44
993 2194 1.063070 TAAAGCTCCCCACACACCCA 61.063 55.000 0.00 0.00 0.00 4.51
1781 4027 0.972471 CAAAGATGGGACCTTGGGGC 60.972 60.000 0.00 0.00 35.63 5.80
1992 4243 9.846248 ATTCTACTGTAATTTCTGCATTGTTTC 57.154 29.630 0.00 0.00 0.00 2.78
1994 4245 5.460646 ACTGTAATTTCTGCATTGTTTCCG 58.539 37.500 0.00 0.00 0.00 4.30
2317 4600 8.774586 GTGTTAAGTTGCTTCAGAATCTTCTTA 58.225 33.333 0.00 0.00 34.74 2.10
2691 5037 6.358118 TGGAAAATCATATACGTGAGTTGC 57.642 37.500 0.00 0.00 46.40 4.17
2849 5202 1.928868 ACATTTCAAGGAGGCAAGGG 58.071 50.000 0.00 0.00 0.00 3.95
2874 5227 7.065563 GGCTTGATCATCAATATGGATACAGTC 59.934 40.741 0.00 0.00 43.07 3.51
2990 5343 4.929146 AACAACCTAGGTGAGCCTTAAT 57.071 40.909 17.14 0.00 44.18 1.40
3118 5471 1.538950 CAGTGAAAGAGCTTGAAGCCC 59.461 52.381 14.45 0.94 43.77 5.19
3152 5505 0.667993 CGGCTGGCAAAACAGAAGAA 59.332 50.000 1.08 0.00 40.97 2.52
3198 5551 7.284074 TCGAAGGCCCAAGAATAAATGTATAA 58.716 34.615 0.00 0.00 0.00 0.98
3244 5597 0.108041 CATGGACCATTTGGCCTTGC 60.108 55.000 3.52 0.00 39.32 4.01
3261 5614 1.781786 TGCTGTAGCTCCTCCCTTAG 58.218 55.000 5.38 0.00 42.66 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.912043 AGTCAGAACTAAGGCCAGCAT 59.088 47.619 5.01 0.00 32.59 3.79
289 1419 0.763986 ATGGGCACTGGCACCTTTTT 60.764 50.000 4.78 0.00 45.22 1.94
292 1422 2.283388 CATGGGCACTGGCACCTT 60.283 61.111 4.78 0.00 45.22 3.50
298 1428 2.283388 AACTGGCATGGGCACTGG 60.283 61.111 0.00 0.00 43.71 4.00
299 1429 1.303888 AGAACTGGCATGGGCACTG 60.304 57.895 0.00 0.00 43.71 3.66
300 1430 1.001641 GAGAACTGGCATGGGCACT 60.002 57.895 0.00 0.00 43.71 4.40
470 1634 6.820656 CCAGTTCTAGAATTGTTAGTGCTCAT 59.179 38.462 22.17 0.00 0.00 2.90
563 1729 4.155462 TCGACTACACACCAGAATCTACAC 59.845 45.833 0.00 0.00 0.00 2.90
820 1998 1.408702 TCTCACAAGCCAAAAACAGCC 59.591 47.619 0.00 0.00 0.00 4.85
993 2194 0.182537 TTGTAGCGGCCATGGCTATT 59.817 50.000 34.70 21.71 44.14 1.73
1674 3911 9.614792 GTAAATCCAAGTAATTAGGTGAGATGT 57.385 33.333 0.00 0.00 0.00 3.06
1781 4027 2.125269 GATGTTCCACCGTCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
1992 4243 5.524971 TGAGATGTAAGTTATACCACCGG 57.475 43.478 0.00 0.00 0.00 5.28
1994 4245 7.015877 TGGGTATGAGATGTAAGTTATACCACC 59.984 40.741 11.87 0.00 40.97 4.61
2670 5016 8.667987 TTTTGCAACTCACGTATATGATTTTC 57.332 30.769 0.00 0.00 0.00 2.29
2821 5173 5.647658 TGCCTCCTTGAAATGTAGTAATGTG 59.352 40.000 0.00 0.00 0.00 3.21
2849 5202 7.918536 ACTGTATCCATATTGATGATCAAGC 57.081 36.000 13.79 0.00 40.05 4.01
2874 5227 6.234177 AGAATAACAAGTTGACAGAAGGAGG 58.766 40.000 10.54 0.00 0.00 4.30
3152 5505 4.512944 CGAATACCAGCTCACATGCTATTT 59.487 41.667 0.00 0.00 41.98 1.40
3198 5551 4.023193 CGCCAGACTTTTGGAATTGTAGTT 60.023 41.667 0.00 0.00 40.87 2.24
3230 5583 1.549203 CTACAGCAAGGCCAAATGGT 58.451 50.000 5.01 3.45 37.57 3.55


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

AutoCloner maintained by Alex Coulton.