Multiple sequence alignment - TraesCS3B01G608000

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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 TraesCS3B01G608000 chr3B 100.000 1601 0 0 931 2531 826363862 826362262 0.000000e+00 2957.0
1 TraesCS3B01G608000 chr3B 100.000 665 0 0 1 665 826364792 826364128 0.000000e+00 1229.0
2 TraesCS3B01G608000 chr3B 95.036 685 12 8 1 663 521691150 521690466 0.000000e+00 1057.0
3 TraesCS3B01G608000 chr3D 87.980 990 60 23 931 1867 612530728 612529745 0.000000e+00 1114.0
4 TraesCS3B01G608000 chr3D 88.225 569 40 16 36 582 95951891 95951328 0.000000e+00 654.0
5 TraesCS3B01G608000 chr3D 95.195 333 16 0 1864 2196 612529704 612529372 6.200000e-146 527.0
6 TraesCS3B01G608000 chr3D 93.571 140 7 2 2058 2196 461592027 461592165 9.180000e-50 207.0
7 TraesCS3B01G608000 chr3D 92.308 143 9 2 2055 2196 51106878 51106737 4.270000e-48 202.0
8 TraesCS3B01G608000 chr3D 92.806 139 9 1 2059 2196 313719247 313719109 1.540000e-47 200.0
9 TraesCS3B01G608000 chr3D 93.333 135 8 1 2059 2192 346865475 346865341 5.520000e-47 198.0
10 TraesCS3B01G608000 chr1B 87.353 680 53 19 13 663 572206357 572207032 0.000000e+00 749.0
11 TraesCS3B01G608000 chr1B 96.830 347 9 2 2187 2531 235514843 235514497 1.690000e-161 579.0
12 TraesCS3B01G608000 chr6B 88.443 623 48 12 62 663 127367447 127368066 0.000000e+00 730.0
13 TraesCS3B01G608000 chr6B 84.300 414 55 5 176 582 538158029 538158439 1.820000e-106 396.0
14 TraesCS3B01G608000 chr6B 92.638 163 11 1 1 163 538072226 538072387 1.510000e-57 233.0
15 TraesCS3B01G608000 chr6B 100.000 28 0 0 583 610 127367958 127367985 5.000000e-03 52.8
16 TraesCS3B01G608000 chrUn 87.227 642 58 13 36 656 8821013 8821651 0.000000e+00 710.0
17 TraesCS3B01G608000 chrUn 96.418 335 11 1 2196 2529 387538635 387538301 3.680000e-153 551.0
18 TraesCS3B01G608000 chrUn 96.131 336 11 2 2196 2529 407200618 407200953 4.760000e-152 547.0
19 TraesCS3B01G608000 chrUn 100.000 28 0 0 583 610 8821550 8821577 5.000000e-03 52.8
20 TraesCS3B01G608000 chr7D 88.752 569 37 16 36 582 51453895 51454458 0.000000e+00 671.0
21 TraesCS3B01G608000 chr7D 96.386 83 3 0 583 665 51454431 51454513 1.220000e-28 137.0
22 TraesCS3B01G608000 chr2A 85.618 591 51 19 5 574 733402012 733401435 7.800000e-165 590.0
23 TraesCS3B01G608000 chr2A 87.619 105 11 2 560 663 733399384 733399281 1.230000e-23 121.0
24 TraesCS3B01G608000 chr5B 97.612 335 7 1 2196 2529 430202247 430202581 7.850000e-160 573.0
25 TraesCS3B01G608000 chr5B 97.313 335 8 1 2196 2529 430108897 430109231 3.650000e-158 568.0
26 TraesCS3B01G608000 chr5B 97.015 335 9 1 2196 2529 430214977 430215311 1.700000e-156 562.0
27 TraesCS3B01G608000 chr5B 96.716 335 10 1 2196 2529 430205185 430205519 7.910000e-155 556.0
28 TraesCS3B01G608000 chr5B 96.716 335 10 1 2196 2529 430217915 430218249 7.910000e-155 556.0
29 TraesCS3B01G608000 chr5B 96.131 336 11 2 2196 2529 430111835 430112170 4.760000e-152 547.0
30 TraesCS3B01G608000 chr5B 82.507 383 49 13 1 379 557288130 557288498 1.130000e-83 320.0
31 TraesCS3B01G608000 chr5B 92.806 139 9 1 2059 2196 650346939 650347077 1.540000e-47 200.0
32 TraesCS3B01G608000 chr2B 85.160 593 50 21 4 574 728761731 728761155 7.850000e-160 573.0
33 TraesCS3B01G608000 chr3A 85.357 560 49 9 1326 1864 747052794 747053341 1.320000e-152 549.0
34 TraesCS3B01G608000 chr3A 85.965 399 41 12 932 1322 747052368 747052759 1.810000e-111 412.0
35 TraesCS3B01G608000 chr3A 93.443 183 12 0 1877 2059 747055078 747055260 3.210000e-69 272.0
36 TraesCS3B01G608000 chr2D 84.305 446 32 15 4 421 599396926 599396491 3.920000e-108 401.0
37 TraesCS3B01G608000 chr4B 80.676 414 59 18 176 583 23841344 23840946 4.090000e-78 302.0
38 TraesCS3B01G608000 chr4D 92.143 140 9 2 2058 2196 497251724 497251862 1.990000e-46 196.0
39 TraesCS3B01G608000 chr4D 92.086 139 10 1 2059 2196 5115416 5115554 7.140000e-46 195.0
40 TraesCS3B01G608000 chr1A 91.429 140 11 1 2057 2195 98291579 98291718 9.240000e-45 191.0


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 TraesCS3B01G608000 chr3B 826362262 826364792 2530 True 2093.0 2957 100.0000 1 2531 2 chr3B.!!$R2 2530
1 TraesCS3B01G608000 chr3B 521690466 521691150 684 True 1057.0 1057 95.0360 1 663 1 chr3B.!!$R1 662
2 TraesCS3B01G608000 chr3D 612529372 612530728 1356 True 820.5 1114 91.5875 931 2196 2 chr3D.!!$R5 1265
3 TraesCS3B01G608000 chr3D 95951328 95951891 563 True 654.0 654 88.2250 36 582 1 chr3D.!!$R2 546
4 TraesCS3B01G608000 chr1B 572206357 572207032 675 False 749.0 749 87.3530 13 663 1 chr1B.!!$F1 650
5 TraesCS3B01G608000 chr6B 127367447 127368066 619 False 391.4 730 94.2215 62 663 2 chr6B.!!$F3 601
6 TraesCS3B01G608000 chrUn 8821013 8821651 638 False 381.4 710 93.6135 36 656 2 chrUn.!!$F2 620
7 TraesCS3B01G608000 chr7D 51453895 51454513 618 False 404.0 671 92.5690 36 665 2 chr7D.!!$F1 629
8 TraesCS3B01G608000 chr2A 733399281 733402012 2731 True 355.5 590 86.6185 5 663 2 chr2A.!!$R1 658
9 TraesCS3B01G608000 chr5B 430202247 430205519 3272 False 564.5 573 97.1640 2196 2529 2 chr5B.!!$F4 333
10 TraesCS3B01G608000 chr5B 430214977 430218249 3272 False 559.0 562 96.8655 2196 2529 2 chr5B.!!$F5 333
11 TraesCS3B01G608000 chr5B 430108897 430112170 3273 False 557.5 568 96.7220 2196 2529 2 chr5B.!!$F3 333
12 TraesCS3B01G608000 chr2B 728761155 728761731 576 True 573.0 573 85.1600 4 574 1 chr2B.!!$R1 570
13 TraesCS3B01G608000 chr3A 747052368 747055260 2892 False 411.0 549 88.2550 932 2059 3 chr3A.!!$F1 1127

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
428 458 1.067706 TCCTCGTTTGATTTACGCCGA 60.068 47.619 0.0 0.0 38.81 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 4044 0.179051 AGAGGCATGCAAGCTAGAGC 60.179 55.0 21.36 0.0 42.49 4.09 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
428 458 1.067706 TCCTCGTTTGATTTACGCCGA 60.068 47.619 0.00 0.00 38.81 5.54
530 563 3.777087 TGCCAAAGGAAAGATTGATCCA 58.223 40.909 0.00 0.00 38.23 3.41
955 3054 2.428491 TCTAGCGAGATCGATCCTTCC 58.572 52.381 21.66 8.14 43.02 3.46
967 3066 2.498167 GATCCTTCCACCCAATCGATG 58.502 52.381 0.00 0.00 0.00 3.84
981 3081 4.024893 CCAATCGATGAATACCGGAAACTG 60.025 45.833 9.46 0.00 0.00 3.16
1018 3118 1.789576 AATGGCCGACAAGGAGGGTT 61.790 55.000 0.00 0.00 45.00 4.11
1069 3187 4.467084 GGGCGGTTGAGGCGATCA 62.467 66.667 0.00 0.00 37.59 2.92
1096 3214 4.617520 TCCAGTGCGCCGCTGAAA 62.618 61.111 24.62 12.96 43.78 2.69
1098 3216 3.648982 CAGTGCGCCGCTGAAACA 61.649 61.111 20.15 0.00 43.78 2.83
1103 3221 3.016474 GCGCCGCTGAAACAGAGAC 62.016 63.158 0.00 0.00 33.20 3.36
1105 3223 1.221466 CGCCGCTGAAACAGAGACAA 61.221 55.000 2.81 0.00 33.20 3.18
1111 3229 2.682856 GCTGAAACAGAGACAACAACCA 59.317 45.455 2.81 0.00 32.44 3.67
1173 3291 1.294780 GGCCATGCCGATAGAGGAG 59.705 63.158 0.00 0.00 39.62 3.69
1175 3293 0.394565 GCCATGCCGATAGAGGAGTT 59.605 55.000 0.00 0.00 39.76 3.01
1182 3300 1.334243 CCGATAGAGGAGTTCCACGAC 59.666 57.143 0.28 0.00 38.89 4.34
1353 3502 2.654912 CCGCGACGAGTGGTTTGAC 61.655 63.158 8.23 0.00 45.30 3.18
1363 3512 0.872388 GTGGTTTGACAAGGGCTACG 59.128 55.000 0.00 0.00 0.00 3.51
1365 3514 0.872388 GGTTTGACAAGGGCTACGTG 59.128 55.000 0.00 0.00 34.52 4.49
1393 3542 1.000938 ACGACAACTACTTCACCGACC 60.001 52.381 0.00 0.00 0.00 4.79
1509 3700 0.461961 ATGACTACGAGAAGCAGGCC 59.538 55.000 0.00 0.00 0.00 5.19
1733 3955 6.292168 CGGCTATTTACTACGTTTGATTCAGG 60.292 42.308 0.00 0.00 0.00 3.86
1778 4000 5.297547 TCGCTGATTCTGTATTGGGATAAC 58.702 41.667 0.00 0.00 0.00 1.89
1780 4002 5.297547 GCTGATTCTGTATTGGGATAACGA 58.702 41.667 0.00 0.00 0.00 3.85
1822 4044 9.027129 CAATGCAAATGATCCATACTTACTTTG 57.973 33.333 0.00 0.00 0.00 2.77
1833 4055 5.007136 CCATACTTACTTTGCTCTAGCTTGC 59.993 44.000 3.26 0.00 42.66 4.01
1978 5924 6.114221 TGTTGATTTGGCTATTTACTACGC 57.886 37.500 0.00 0.00 0.00 4.42
1993 5939 4.244425 ACTACGCTGGATACACATCATC 57.756 45.455 0.00 0.00 46.17 2.92
2034 5980 0.178068 GATTCTGCCCGAGCCTAACA 59.822 55.000 0.00 0.00 38.69 2.41
2068 6014 7.620880 TCATAATTAATTCCATACTCCCTCCG 58.379 38.462 3.39 0.00 0.00 4.63
2084 6030 1.064505 CTCCGTCCGCGAATAAGTGTA 59.935 52.381 8.23 0.00 41.33 2.90
2134 6080 8.556194 AGTTTTGAAACTTTGACCAACTTTTTC 58.444 29.630 3.37 0.00 46.52 2.29
2136 6082 6.015027 TGAAACTTTGACCAACTTTTTCGA 57.985 33.333 0.00 0.00 0.00 3.71
2213 6159 9.906660 GAAATGTATCTCTACTCCTAATGTCTG 57.093 37.037 0.00 0.00 0.00 3.51
2301 6247 0.252558 GTACTTCCTCCCACCTCCCA 60.253 60.000 0.00 0.00 0.00 4.37
2500 9388 1.374252 GCCCTCGAGCGAGAAACAA 60.374 57.895 20.41 0.00 44.53 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.113517 GGCAGGGGCAGAGATACGTA 61.114 60.000 0.00 0.00 43.71 3.57
284 312 3.988050 TATGTCTTCCCGGGCCCGT 62.988 63.158 40.52 23.18 37.81 5.28
955 3054 2.143122 CCGGTATTCATCGATTGGGTG 58.857 52.381 0.00 0.00 0.00 4.61
967 3066 0.725117 CGGTGCAGTTTCCGGTATTC 59.275 55.000 0.00 0.00 42.61 1.75
981 3081 4.222847 GATCCTCGACCCCGGTGC 62.223 72.222 0.00 0.00 36.24 5.01
1069 3187 2.338984 GCACTGGACGTCCGTCTT 59.661 61.111 28.70 10.48 44.04 3.01
1092 3210 2.682856 GCTGGTTGTTGTCTCTGTTTCA 59.317 45.455 0.00 0.00 0.00 2.69
1096 3214 1.475751 CCTGCTGGTTGTTGTCTCTGT 60.476 52.381 0.51 0.00 0.00 3.41
1098 3216 1.131638 TCCTGCTGGTTGTTGTCTCT 58.868 50.000 9.73 0.00 34.23 3.10
1103 3221 0.746063 TTGCTTCCTGCTGGTTGTTG 59.254 50.000 9.73 0.00 43.37 3.33
1105 3223 1.447317 CGTTGCTTCCTGCTGGTTGT 61.447 55.000 9.73 0.00 43.37 3.32
1122 3240 2.985282 TACACGTCGGGAAGCCGT 60.985 61.111 0.00 0.00 34.71 5.68
1173 3291 1.202428 GGCATCTCTAGGTCGTGGAAC 60.202 57.143 0.00 0.00 0.00 3.62
1175 3293 0.755698 GGGCATCTCTAGGTCGTGGA 60.756 60.000 0.00 0.00 0.00 4.02
1182 3300 1.431243 AGGTAGGAGGGCATCTCTAGG 59.569 57.143 0.00 0.00 42.10 3.02
1283 3401 1.550976 GGATCCTCTTGTGAAGGACGT 59.449 52.381 3.84 0.00 34.19 4.34
1330 3479 4.477975 CCACTCGTCGCGGACCTC 62.478 72.222 6.13 0.00 0.00 3.85
1353 3502 1.218316 GACCTCCACGTAGCCCTTG 59.782 63.158 0.00 0.00 0.00 3.61
1363 3512 0.877071 TAGTTGTCGTCGACCTCCAC 59.123 55.000 22.05 13.07 0.00 4.02
1365 3514 1.163554 AGTAGTTGTCGTCGACCTCC 58.836 55.000 22.05 9.96 0.00 4.30
1393 3542 1.103987 TCTTCCTCGATCTCGGCCAG 61.104 60.000 2.24 0.00 40.29 4.85
1655 3877 8.542497 AATATGTAGCAAACACGACTTCTTTA 57.458 30.769 0.00 0.00 42.09 1.85
1698 3920 6.372381 ACGTAGTAAATAGCCGAACCAAAAAT 59.628 34.615 0.00 0.00 41.94 1.82
1733 3955 4.241590 TGCAATTCCTCACAAACATGAC 57.758 40.909 0.00 0.00 0.00 3.06
1778 4000 7.621832 TGCATTGTAAAGTCAATTCTTTTCG 57.378 32.000 0.00 0.00 38.40 3.46
1822 4044 0.179051 AGAGGCATGCAAGCTAGAGC 60.179 55.000 21.36 0.00 42.49 4.09
1833 4055 2.684881 ACCGAGCAAATTAAGAGGCATG 59.315 45.455 0.00 0.00 0.00 4.06
1978 5924 7.203218 TCTTCGTAAAGATGATGTGTATCCAG 58.797 38.462 0.00 0.00 36.59 3.86
2034 5980 5.690865 TGGAATTAATTATGAGCCGACCTT 58.309 37.500 0.00 0.00 0.00 3.50
2068 6014 3.703420 AGATGTACACTTATTCGCGGAC 58.297 45.455 6.13 0.00 0.00 4.79
2084 6030 8.211629 ACTTTGACTTAGGACAAAACTAGATGT 58.788 33.333 0.00 0.00 36.87 3.06
2210 6156 0.892358 ACGCGACCTACCAACTCAGA 60.892 55.000 15.93 0.00 0.00 3.27
2213 6159 1.066136 GAAACGCGACCTACCAACTC 58.934 55.000 15.93 0.00 0.00 3.01
2301 6247 1.098712 TTGGTTTTTCGCGGCTGAGT 61.099 50.000 6.13 0.00 0.00 3.41
2505 9393 0.249911 GAACGAGGGCACAGAGTTGT 60.250 55.000 0.00 0.00 38.31 3.32


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

AutoCloner maintained by Alex Coulton.