Multiple sequence alignment - TraesCS6B01G416200

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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 TraesCS6B01G416200 chr6B 100.000 4653 0 0 1 4653 688580935 688576283 0.000000e+00 8593
1 TraesCS6B01G416200 chr6B 93.751 4497 142 53 1 4433 688888964 688893385 0.000000e+00 6619
2 TraesCS6B01G416200 chr6B 89.106 1175 83 22 2471 3628 688943521 688944667 0.000000e+00 1419
3 TraesCS6B01G416200 chr6B 88.270 1202 87 21 2446 3619 688520770 688519595 0.000000e+00 1389
4 TraesCS6B01G416200 chr6B 82.603 1414 131 59 1058 2420 688522117 688520768 0.000000e+00 1142
5 TraesCS6B01G416200 chr6B 81.899 1464 122 71 662 2057 688936146 688937534 0.000000e+00 1103
6 TraesCS6B01G416200 chr6B 94.301 579 24 7 1 574 688882062 688882636 0.000000e+00 878
7 TraesCS6B01G416200 chr6B 92.758 359 22 2 2063 2417 688941493 688941851 2.480000e-142 516
8 TraesCS6B01G416200 chr6B 83.294 419 55 9 3018 3433 688382597 688383003 5.690000e-99 372
9 TraesCS6B01G416200 chr6B 82.558 430 61 9 3029 3456 689060762 689060345 2.650000e-97 366
10 TraesCS6B01G416200 chr6B 80.813 443 71 11 3029 3471 689163643 689163215 7.460000e-88 335
11 TraesCS6B01G416200 chr6B 95.000 180 6 2 557 735 688883720 688883897 3.550000e-71 279
12 TraesCS6B01G416200 chr6B 92.308 91 6 1 2946 3036 688381923 688382012 1.360000e-25 128
13 TraesCS6B01G416200 chr6B 94.872 78 4 0 4576 4653 688893600 688893677 6.320000e-24 122
14 TraesCS6B01G416200 chr6B 78.947 171 22 7 2803 2963 689061501 689061335 2.290000e-18 104
15 TraesCS6B01G416200 chr6D 92.802 1681 66 21 2039 3705 453491380 453493019 0.000000e+00 2383
16 TraesCS6B01G416200 chr6D 90.683 923 43 15 1101 1998 453489630 453490534 0.000000e+00 1188
17 TraesCS6B01G416200 chr6D 90.212 848 68 7 2790 3628 453499219 453500060 0.000000e+00 1092
18 TraesCS6B01G416200 chr6D 91.753 776 49 9 2044 2811 453498439 453499207 0.000000e+00 1064
19 TraesCS6B01G416200 chr6D 79.058 1805 181 93 307 2029 453495090 453496779 0.000000e+00 1057
20 TraesCS6B01G416200 chr6D 92.971 313 7 5 1785 2094 453491079 453491379 4.270000e-120 442
21 TraesCS6B01G416200 chr6D 84.935 385 36 12 484 850 453489121 453489501 2.050000e-98 370
22 TraesCS6B01G416200 chr6D 87.826 115 11 1 998 1112 453489497 453489608 1.050000e-26 132
23 TraesCS6B01G416200 chr6A 86.861 1408 97 29 2027 3416 599809024 599810361 0.000000e+00 1495
24 TraesCS6B01G416200 chr6A 81.678 846 112 29 105 925 599807118 599807945 0.000000e+00 664
25 TraesCS6B01G416200 chr6A 82.485 668 51 28 1363 2028 599808328 599808931 4.120000e-145 525
26 TraesCS6B01G416200 chr6A 95.597 159 7 0 1101 1259 599808012 599808170 5.970000e-64 255
27 TraesCS6B01G416200 chr6A 82.061 262 22 13 3453 3705 599810368 599810613 2.840000e-47 200
28 TraesCS6B01G416200 chr6A 87.273 110 14 0 996 1105 599807877 599807986 4.890000e-25 126
29 TraesCS6B01G416200 chrUn 83.848 712 103 6 3948 4648 217713607 217714317 0.000000e+00 667
30 TraesCS6B01G416200 chrUn 78.947 171 22 7 2803 2963 347177638 347177472 2.290000e-18 104
31 TraesCS6B01G416200 chrUn 78.947 171 22 7 2803 2963 460319372 460319206 2.290000e-18 104
32 TraesCS6B01G416200 chr7B 83.848 712 103 6 3948 4648 204056142 204055432 0.000000e+00 667
33 TraesCS6B01G416200 chr1B 83.029 713 104 12 3948 4647 12836249 12836957 8.500000e-177 630
34 TraesCS6B01G416200 chr5A 79.416 719 131 11 3947 4653 107289979 107289266 4.180000e-135 492
35 TraesCS6B01G416200 chr4A 79.219 717 134 11 3948 4651 700970958 700971672 7.000000e-133 484
36 TraesCS6B01G416200 chr5D 88.737 293 32 1 4359 4650 559597396 559597688 1.590000e-94 357
37 TraesCS6B01G416200 chr5D 82.381 420 60 6 3948 4356 559510937 559511353 2.060000e-93 353


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 TraesCS6B01G416200 chr6B 688576283 688580935 4652 True 8593.000000 8593 100.0000 1 4653 1 chr6B.!!$R1 4652
1 TraesCS6B01G416200 chr6B 688888964 688893677 4713 False 3370.500000 6619 94.3115 1 4653 2 chr6B.!!$F3 4652
2 TraesCS6B01G416200 chr6B 688519595 688522117 2522 True 1265.500000 1389 85.4365 1058 3619 2 chr6B.!!$R3 2561
3 TraesCS6B01G416200 chr6B 688936146 688944667 8521 False 1012.666667 1419 87.9210 662 3628 3 chr6B.!!$F4 2966
4 TraesCS6B01G416200 chr6B 688882062 688883897 1835 False 578.500000 878 94.6505 1 735 2 chr6B.!!$F2 734
5 TraesCS6B01G416200 chr6B 688381923 688383003 1080 False 250.000000 372 87.8010 2946 3433 2 chr6B.!!$F1 487
6 TraesCS6B01G416200 chr6B 689060345 689061501 1156 True 235.000000 366 80.7525 2803 3456 2 chr6B.!!$R4 653
7 TraesCS6B01G416200 chr6D 453489121 453500060 10939 False 966.000000 2383 88.7800 307 3705 8 chr6D.!!$F1 3398
8 TraesCS6B01G416200 chr6A 599807118 599810613 3495 False 544.166667 1495 85.9925 105 3705 6 chr6A.!!$F1 3600
9 TraesCS6B01G416200 chrUn 217713607 217714317 710 False 667.000000 667 83.8480 3948 4648 1 chrUn.!!$F1 700
10 TraesCS6B01G416200 chr7B 204055432 204056142 710 True 667.000000 667 83.8480 3948 4648 1 chr7B.!!$R1 700
11 TraesCS6B01G416200 chr1B 12836249 12836957 708 False 630.000000 630 83.0290 3948 4647 1 chr1B.!!$F1 699
12 TraesCS6B01G416200 chr5A 107289266 107289979 713 True 492.000000 492 79.4160 3947 4653 1 chr5A.!!$R1 706
13 TraesCS6B01G416200 chr4A 700970958 700971672 714 False 484.000000 484 79.2190 3948 4651 1 chr4A.!!$F1 703

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
431 440 5.705609 AACATTGTTTCGAAAGCTACCAT 57.294 34.783 11.66 0.0 0.0 3.55 F
1345 2558 2.490115 TGCCATTGTCCGTGATTTTACC 59.510 45.455 0.00 0.0 0.0 2.85 F
2573 10416 2.028658 CAGCCTGCAAGTTCTCTAGACA 60.029 50.000 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 2853 2.416638 AGAGAATCCCCTAGCAAGCAT 58.583 47.619 0.00 0.0 33.66 3.79 R
2638 10481 1.275291 CAAGGTCTAACTCGCTGGGAA 59.725 52.381 0.00 0.0 0.00 3.97 R
4540 20264 0.032117 TCCTCCATCATCACCGGAGT 60.032 55.000 9.46 0.0 44.12 3.85 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
377 386 6.791303 TGTGAAAGTTCCATGTACTTGTTTC 58.209 36.000 10.24 10.40 36.06 2.78
431 440 5.705609 AACATTGTTTCGAAAGCTACCAT 57.294 34.783 11.66 0.00 0.00 3.55
1343 2556 3.064682 CGATGCCATTGTCCGTGATTTTA 59.935 43.478 0.00 0.00 0.00 1.52
1345 2558 2.490115 TGCCATTGTCCGTGATTTTACC 59.510 45.455 0.00 0.00 0.00 2.85
1517 2778 7.849804 ATATGCCGGTGATAAATTATGTCTC 57.150 36.000 1.90 0.00 0.00 3.36
1572 2853 5.133941 TGGTTTAGTTGTTTCTGCATACCA 58.866 37.500 0.00 0.00 0.00 3.25
2301 8486 6.484643 CGACATTTAGTTCATCAGATTGGGAT 59.515 38.462 0.00 0.00 0.00 3.85
2408 8606 5.586243 GTGGTCTAGAATGCAATTAAGCTCA 59.414 40.000 0.00 0.00 36.07 4.26
2573 10416 2.028658 CAGCCTGCAAGTTCTCTAGACA 60.029 50.000 0.00 0.00 0.00 3.41
2591 10434 5.148651 AGACACTGGTATCACAAGGTTAC 57.851 43.478 0.00 0.00 0.00 2.50
2599 10442 4.814771 GGTATCACAAGGTTACCATGTAGC 59.185 45.833 12.09 3.44 40.26 3.58
2611 10454 3.944087 ACCATGTAGCCTTCTTGTCTTC 58.056 45.455 0.00 0.00 0.00 2.87
2612 10455 2.932614 CCATGTAGCCTTCTTGTCTTCG 59.067 50.000 0.00 0.00 0.00 3.79
2616 10459 2.156343 AGCCTTCTTGTCTTCGTGTC 57.844 50.000 0.00 0.00 0.00 3.67
2638 10481 3.578282 CCTGTAAAAGTTCCCCAGCAATT 59.422 43.478 0.00 0.00 0.00 2.32
2645 10488 0.904394 TTCCCCAGCAATTTCCCAGC 60.904 55.000 0.00 0.00 0.00 4.85
2651 10494 2.083774 CAGCAATTTCCCAGCGAGTTA 58.916 47.619 0.00 0.00 0.00 2.24
2661 10504 2.159226 CCCAGCGAGTTAGACCTTGTAG 60.159 54.545 0.00 0.00 0.00 2.74
2696 10540 3.316588 TCTTTAATTGCTTCCAACGTGCA 59.683 39.130 0.00 0.00 32.95 4.57
3075 18739 1.318576 CGAAAAGGAGCCACCAACTT 58.681 50.000 0.47 0.00 42.04 2.66
3171 18835 3.072211 GTGTTAAGCTTGACCCAGGTAC 58.928 50.000 17.78 5.37 0.00 3.34
3705 19413 9.225436 GATTGAAACTCCAGAATATAATCCTCC 57.775 37.037 0.00 0.00 0.00 4.30
3774 19482 1.765904 TGTGGCTTACTTGTGACCTCA 59.234 47.619 0.00 0.00 0.00 3.86
3827 19535 4.099727 GGGAAGACCTATACTCAACTGTCC 59.900 50.000 0.00 0.00 35.85 4.02
3828 19536 4.099727 GGAAGACCTATACTCAACTGTCCC 59.900 50.000 0.00 0.00 0.00 4.46
3854 19566 1.144057 GGGAGCACCACTATCACCG 59.856 63.158 1.58 0.00 39.85 4.94
3869 19581 6.923508 CACTATCACCGATGCTTTTCATACTA 59.076 38.462 0.00 0.00 35.05 1.82
3925 19637 1.336795 CGGGGTGCCAAAAACTTGATC 60.337 52.381 0.00 0.00 0.00 2.92
3982 19694 1.096386 CGCTGGCTAGTCTCCTACGT 61.096 60.000 0.00 0.00 0.00 3.57
3994 19706 0.324368 TCCTACGTGGCTGACCTCAT 60.324 55.000 0.00 0.00 36.63 2.90
4017 19729 3.711842 CGCGCACGCTTTCCTTCA 61.712 61.111 13.70 0.00 39.32 3.02
4023 19735 1.714794 CACGCTTTCCTTCATCGACT 58.285 50.000 0.00 0.00 0.00 4.18
4083 19796 2.427540 GATCGATGAGAGGGGCGTGG 62.428 65.000 0.54 0.00 0.00 4.94
4130 19843 1.287503 GGAGAGGATCGACATCGGC 59.712 63.158 0.73 0.00 42.67 5.54
4136 19849 3.445518 GATCGACATCGGCCAGGCA 62.446 63.158 15.19 0.00 40.29 4.75
4277 20000 2.386935 GGCTAGGGCATCCTTGGGT 61.387 63.158 0.00 0.00 41.56 4.51
4356 20079 4.113815 TTGCCATGGCGGGGAGAG 62.114 66.667 30.87 0.00 45.51 3.20
4429 20152 0.522076 CCGCTTTCTCGCATTTCTGC 60.522 55.000 0.00 0.00 45.31 4.26
4455 20178 0.249489 CCGCGAAACCCTAGATCCAG 60.249 60.000 8.23 0.00 0.00 3.86
4459 20182 3.394719 GCGAAACCCTAGATCCAGAATC 58.605 50.000 0.00 0.00 34.30 2.52
4517 20241 2.450476 GGATTGCAGATCCTTTGTGGT 58.550 47.619 16.25 0.00 35.36 4.16
4525 20249 0.850100 ATCCTTTGTGGTGGTGGTGA 59.150 50.000 0.00 0.00 37.07 4.02
4540 20264 2.922503 TGACCTCCAAGCCGAGCA 60.923 61.111 0.00 0.00 0.00 4.26
4560 20284 0.390860 CTCCGGTGATGATGGAGGAC 59.609 60.000 0.00 0.00 44.49 3.85
4563 20287 1.227674 GGTGATGATGGAGGACCGC 60.228 63.158 0.00 0.00 39.42 5.68
4566 20290 4.241555 ATGATGGAGGACCGCGGC 62.242 66.667 28.58 18.35 39.42 6.53
4602 20397 1.749258 GAATCGGCGGGAAGGCTTT 60.749 57.895 7.21 0.00 44.22 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 11 9.693739 ATGTAATAAAATGTAGACCATTGTGGA 57.306 29.630 2.45 0.00 43.04 4.02
138 143 9.178758 TGTGTACCAAAAATATGCATGTGTATA 57.821 29.630 10.16 0.00 0.00 1.47
252 258 5.583061 GGAAACATGTGTGATATGTACGGAA 59.417 40.000 0.00 0.00 37.77 4.30
781 1912 4.493747 CTCCGGGGTTCGCTCGTC 62.494 72.222 0.00 0.00 37.59 4.20
784 1915 2.417936 GATCTCCGGGGTTCGCTC 59.582 66.667 0.00 0.00 37.59 5.03
1343 2556 3.282021 GTCATGTGGTCAGCATAATGGT 58.718 45.455 0.00 0.00 0.00 3.55
1345 2558 2.620115 GGGTCATGTGGTCAGCATAATG 59.380 50.000 0.00 0.00 0.00 1.90
1425 2683 6.942576 ACTATATCAACTCCCATTTATGCCAC 59.057 38.462 0.00 0.00 0.00 5.01
1572 2853 2.416638 AGAGAATCCCCTAGCAAGCAT 58.583 47.619 0.00 0.00 33.66 3.79
2301 8486 9.783256 GACAAAGTAAAGAAAGCTGAAAAGTTA 57.217 29.630 0.00 0.00 0.00 2.24
2408 8606 9.342308 CTTTATAATCATACACACCCATGTCTT 57.658 33.333 0.00 0.00 36.72 3.01
2591 10434 2.932614 CGAAGACAAGAAGGCTACATGG 59.067 50.000 0.00 0.00 30.53 3.66
2599 10442 2.224066 ACAGGACACGAAGACAAGAAGG 60.224 50.000 0.00 0.00 0.00 3.46
2611 10454 2.148768 GGGGAACTTTTACAGGACACG 58.851 52.381 0.00 0.00 0.00 4.49
2612 10455 3.146847 CTGGGGAACTTTTACAGGACAC 58.853 50.000 0.00 0.00 0.00 3.67
2616 10459 2.286365 TGCTGGGGAACTTTTACAGG 57.714 50.000 0.00 0.00 0.00 4.00
2638 10481 1.275291 CAAGGTCTAACTCGCTGGGAA 59.725 52.381 0.00 0.00 0.00 3.97
2645 10488 3.190744 TCACAGCTACAAGGTCTAACTCG 59.809 47.826 0.00 0.00 0.00 4.18
2651 10494 4.959210 AGTATGATCACAGCTACAAGGTCT 59.041 41.667 0.00 0.00 0.00 3.85
2661 10504 7.256756 AGCAATTAAAGAGTATGATCACAGC 57.743 36.000 0.00 0.00 0.00 4.40
2696 10540 3.904339 ACACTGGTTCCATAGTCTTCACT 59.096 43.478 0.00 0.00 36.55 3.41
2900 17871 5.289595 TGAATTAATGAGTAGCTAGGCACG 58.710 41.667 0.00 0.00 0.00 5.34
3075 18739 1.697432 ACTTGGGGACGAGATCAACAA 59.303 47.619 0.00 0.00 45.46 2.83
3171 18835 8.574196 AAAACTGAAACTTGGATTATTGAACG 57.426 30.769 0.00 0.00 0.00 3.95
3690 19398 5.300752 AGCACAACGGAGGATTATATTCTG 58.699 41.667 0.00 0.00 0.00 3.02
3774 19482 7.325725 TCCATTGATCATGATTCTAGTGGAT 57.674 36.000 19.56 0.00 34.31 3.41
3827 19535 2.377810 TGGTGCTCCCTGCCATAGG 61.378 63.158 1.59 0.00 46.88 2.57
3828 19536 1.153086 GTGGTGCTCCCTGCCATAG 60.153 63.158 1.59 0.00 42.00 2.23
3854 19566 7.303998 GCTCCATGATTAGTATGAAAAGCATC 58.696 38.462 0.00 0.00 38.44 3.91
3869 19581 4.758692 CGTAGCGGCTCCATGATT 57.241 55.556 5.39 0.00 0.00 2.57
3902 19614 0.106116 AAGTTTTTGGCACCCCGGTA 60.106 50.000 0.00 0.00 0.00 4.02
3905 19617 0.678950 ATCAAGTTTTTGGCACCCCG 59.321 50.000 0.00 0.00 34.97 5.73
3925 19637 3.227276 CCCCTCCACCTCGATCCG 61.227 72.222 0.00 0.00 0.00 4.18
4017 19729 3.034878 CCGGATCTCGCAGTCGAT 58.965 61.111 0.00 0.00 44.56 3.59
4023 19735 3.138128 TCGAAGCCGGATCTCGCA 61.138 61.111 5.05 0.00 37.59 5.10
4116 19829 2.502492 CCTGGCCGATGTCGATCCT 61.502 63.158 3.62 0.00 43.02 3.24
4130 19843 3.633986 GACAAGGAAAGGATATTGCCTGG 59.366 47.826 0.00 0.00 38.58 4.45
4136 19849 6.064717 GGCTATGTGACAAGGAAAGGATATT 58.935 40.000 0.00 0.00 0.00 1.28
4257 19980 2.081161 CCAAGGATGCCCTAGCCCT 61.081 63.158 0.00 0.00 43.48 5.19
4277 20000 4.124351 GGTCGCGTCCGGATGTGA 62.124 66.667 31.31 31.31 34.76 3.58
4373 20096 1.529713 GAACGGGGTGGGCTTTTGA 60.530 57.895 0.00 0.00 0.00 2.69
4455 20178 5.825151 CACCATAGAAAAGAGGAAGGGATTC 59.175 44.000 0.00 0.00 0.00 2.52
4459 20182 3.372025 CCCACCATAGAAAAGAGGAAGGG 60.372 52.174 0.00 0.00 35.12 3.95
4517 20241 2.829384 GGCTTGGAGGTCACCACCA 61.829 63.158 9.31 9.31 46.68 4.17
4525 20249 2.925170 AGTGCTCGGCTTGGAGGT 60.925 61.111 2.96 0.00 34.56 3.85
4540 20264 0.032117 TCCTCCATCATCACCGGAGT 60.032 55.000 9.46 0.00 44.12 3.85
4563 20287 4.715523 TGGAAGAAAGGGCCGCCG 62.716 66.667 2.55 0.00 0.00 6.46
4566 20290 2.746277 CCGTGGAAGAAAGGGCCG 60.746 66.667 0.00 0.00 0.00 6.13
4571 20295 1.369625 CCGATTCCCGTGGAAGAAAG 58.630 55.000 10.51 3.35 45.48 2.62
4572 20296 0.675522 GCCGATTCCCGTGGAAGAAA 60.676 55.000 10.51 0.00 45.48 2.52


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

AutoCloner maintained by Alex Coulton.