Multiple sequence alignment - TraesCS1B01G100500

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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 TraesCS1B01G100500 chr1B 100.000 5089 0 0 1 5089 109351738 109346650 0.000000e+00 9398.0
1 TraesCS1B01G100500 chr1B 96.907 582 14 2 4511 5089 364936027 364935447 0.000000e+00 972.0
2 TraesCS1B01G100500 chr2B 96.600 4530 129 11 1 4521 638283838 638288351 0.000000e+00 7489.0
3 TraesCS1B01G100500 chr2B 94.774 861 39 3 2678 3537 39117374 39118229 0.000000e+00 1336.0
4 TraesCS1B01G100500 chr2B 97.079 582 14 1 4511 5089 676066415 676066996 0.000000e+00 977.0
5 TraesCS1B01G100500 chr2B 96.907 582 15 1 4511 5089 499449707 499449126 0.000000e+00 972.0
6 TraesCS1B01G100500 chr2B 96.735 582 16 1 4511 5089 71425994 71426575 0.000000e+00 966.0
7 TraesCS1B01G100500 chr2B 94.724 398 19 2 2281 2677 39117010 39117406 7.240000e-173 617.0
8 TraesCS1B01G100500 chr2B 94.079 152 9 0 1174 1325 184121780 184121629 1.100000e-56 231.0
9 TraesCS1B01G100500 chr3B 95.522 2680 105 10 1 2672 629796463 629799135 0.000000e+00 4270.0
10 TraesCS1B01G100500 chr3B 95.264 1837 84 2 2678 4511 629799108 629800944 0.000000e+00 2907.0
11 TraesCS1B01G100500 chr3B 96.667 810 19 2 1 807 5801298 5800494 0.000000e+00 1339.0
12 TraesCS1B01G100500 chr3B 93.417 881 29 13 804 1681 5800108 5799254 0.000000e+00 1279.0
13 TraesCS1B01G100500 chr3B 95.219 753 30 3 1629 2378 5799270 5798521 0.000000e+00 1186.0
14 TraesCS1B01G100500 chr2D 96.331 2535 74 11 1 2529 344564935 344567456 0.000000e+00 4148.0
15 TraesCS1B01G100500 chr2D 94.568 1841 83 10 2678 4512 344567518 344569347 0.000000e+00 2830.0
16 TraesCS1B01G100500 chr2D 82.272 581 88 9 2184 2759 356536017 356535447 5.920000e-134 488.0
17 TraesCS1B01G100500 chr5B 96.393 2301 80 3 2213 4511 547904249 547906548 0.000000e+00 3786.0
18 TraesCS1B01G100500 chr5B 96.157 2186 58 15 1 2178 547902079 547904246 0.000000e+00 3548.0
19 TraesCS1B01G100500 chr5B 85.400 1000 121 20 19 1007 395330744 395331729 0.000000e+00 1014.0
20 TraesCS1B01G100500 chr5B 96.907 582 15 1 4511 5089 362914081 362914662 0.000000e+00 972.0
21 TraesCS1B01G100500 chr5B 96.907 582 15 1 4511 5089 449144312 449144893 0.000000e+00 972.0
22 TraesCS1B01G100500 chr5B 96.735 582 16 1 4511 5089 498764721 498764140 0.000000e+00 966.0
23 TraesCS1B01G100500 chr5B 96.735 582 16 1 4511 5089 552899568 552898987 0.000000e+00 966.0
24 TraesCS1B01G100500 chr5B 91.803 122 8 1 1204 1325 239392640 239392521 8.760000e-38 169.0
25 TraesCS1B01G100500 chrUn 95.741 2301 87 4 2213 4511 49944449 49946740 0.000000e+00 3696.0
26 TraesCS1B01G100500 chrUn 96.842 2185 57 9 1 2178 49942267 49944446 0.000000e+00 3642.0
27 TraesCS1B01G100500 chrUn 93.478 46 3 0 1429 1474 70167421 70167376 9.140000e-08 69.4
28 TraesCS1B01G100500 chr4D 96.312 2115 69 4 569 2677 451885704 451883593 0.000000e+00 3465.0
29 TraesCS1B01G100500 chr4D 95.640 1835 70 4 2678 4511 451883625 451881800 0.000000e+00 2937.0
30 TraesCS1B01G100500 chr4D 85.814 1001 114 24 19 1007 379509316 379508332 0.000000e+00 1037.0
31 TraesCS1B01G100500 chr6A 95.312 1664 75 2 2848 4511 74542208 74543868 0.000000e+00 2638.0
32 TraesCS1B01G100500 chr6A 94.654 1272 68 0 3241 4512 602833708 602834979 0.000000e+00 1973.0
33 TraesCS1B01G100500 chr7B 94.781 1667 85 1 2848 4514 459588255 459586591 0.000000e+00 2595.0
34 TraesCS1B01G100500 chr3D 85.890 1304 171 8 3223 4520 549726284 549724988 0.000000e+00 1376.0
35 TraesCS1B01G100500 chr3D 82.444 581 87 7 2184 2759 455016787 455016217 1.270000e-135 494.0
36 TraesCS1B01G100500 chr3D 82.131 582 85 12 2184 2755 549727473 549726901 9.910000e-132 481.0
37 TraesCS1B01G100500 chr4B 86.000 1000 115 21 19 1007 575619411 575618426 0.000000e+00 1048.0
38 TraesCS1B01G100500 chr4B 96.735 582 16 1 4511 5089 633494138 633494719 0.000000e+00 966.0
39 TraesCS1B01G100500 chr7A 85.285 999 123 20 19 1007 641404994 641404010 0.000000e+00 1009.0
40 TraesCS1B01G100500 chr5D 93.478 46 3 0 1429 1474 90292737 90292782 9.140000e-08 69.4


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 TraesCS1B01G100500 chr1B 109346650 109351738 5088 True 9398.0 9398 100.0000 1 5089 1 chr1B.!!$R1 5088
1 TraesCS1B01G100500 chr1B 364935447 364936027 580 True 972.0 972 96.9070 4511 5089 1 chr1B.!!$R2 578
2 TraesCS1B01G100500 chr2B 638283838 638288351 4513 False 7489.0 7489 96.6000 1 4521 1 chr2B.!!$F2 4520
3 TraesCS1B01G100500 chr2B 676066415 676066996 581 False 977.0 977 97.0790 4511 5089 1 chr2B.!!$F3 578
4 TraesCS1B01G100500 chr2B 39117010 39118229 1219 False 976.5 1336 94.7490 2281 3537 2 chr2B.!!$F4 1256
5 TraesCS1B01G100500 chr2B 499449126 499449707 581 True 972.0 972 96.9070 4511 5089 1 chr2B.!!$R2 578
6 TraesCS1B01G100500 chr2B 71425994 71426575 581 False 966.0 966 96.7350 4511 5089 1 chr2B.!!$F1 578
7 TraesCS1B01G100500 chr3B 629796463 629800944 4481 False 3588.5 4270 95.3930 1 4511 2 chr3B.!!$F1 4510
8 TraesCS1B01G100500 chr3B 5798521 5801298 2777 True 1268.0 1339 95.1010 1 2378 3 chr3B.!!$R1 2377
9 TraesCS1B01G100500 chr2D 344564935 344569347 4412 False 3489.0 4148 95.4495 1 4512 2 chr2D.!!$F1 4511
10 TraesCS1B01G100500 chr2D 356535447 356536017 570 True 488.0 488 82.2720 2184 2759 1 chr2D.!!$R1 575
11 TraesCS1B01G100500 chr5B 547902079 547906548 4469 False 3667.0 3786 96.2750 1 4511 2 chr5B.!!$F4 4510
12 TraesCS1B01G100500 chr5B 395330744 395331729 985 False 1014.0 1014 85.4000 19 1007 1 chr5B.!!$F2 988
13 TraesCS1B01G100500 chr5B 362914081 362914662 581 False 972.0 972 96.9070 4511 5089 1 chr5B.!!$F1 578
14 TraesCS1B01G100500 chr5B 449144312 449144893 581 False 972.0 972 96.9070 4511 5089 1 chr5B.!!$F3 578
15 TraesCS1B01G100500 chr5B 498764140 498764721 581 True 966.0 966 96.7350 4511 5089 1 chr5B.!!$R2 578
16 TraesCS1B01G100500 chr5B 552898987 552899568 581 True 966.0 966 96.7350 4511 5089 1 chr5B.!!$R3 578
17 TraesCS1B01G100500 chrUn 49942267 49946740 4473 False 3669.0 3696 96.2915 1 4511 2 chrUn.!!$F1 4510
18 TraesCS1B01G100500 chr4D 451881800 451885704 3904 True 3201.0 3465 95.9760 569 4511 2 chr4D.!!$R2 3942
19 TraesCS1B01G100500 chr4D 379508332 379509316 984 True 1037.0 1037 85.8140 19 1007 1 chr4D.!!$R1 988
20 TraesCS1B01G100500 chr6A 74542208 74543868 1660 False 2638.0 2638 95.3120 2848 4511 1 chr6A.!!$F1 1663
21 TraesCS1B01G100500 chr6A 602833708 602834979 1271 False 1973.0 1973 94.6540 3241 4512 1 chr6A.!!$F2 1271
22 TraesCS1B01G100500 chr7B 459586591 459588255 1664 True 2595.0 2595 94.7810 2848 4514 1 chr7B.!!$R1 1666
23 TraesCS1B01G100500 chr3D 549724988 549727473 2485 True 928.5 1376 84.0105 2184 4520 2 chr3D.!!$R2 2336
24 TraesCS1B01G100500 chr3D 455016217 455016787 570 True 494.0 494 82.4440 2184 2759 1 chr3D.!!$R1 575
25 TraesCS1B01G100500 chr4B 575618426 575619411 985 True 1048.0 1048 86.0000 19 1007 1 chr4B.!!$R1 988
26 TraesCS1B01G100500 chr4B 633494138 633494719 581 False 966.0 966 96.7350 4511 5089 1 chr4B.!!$F1 578
27 TraesCS1B01G100500 chr7A 641404010 641404994 984 True 1009.0 1009 85.2850 19 1007 1 chr7A.!!$R1 988

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
712 726 3.633525 GGTTGTCCTTTTTCCTTAACCGT 59.366 43.478 0.00 0.00 0.00 4.83 F
2301 2757 1.759445 AGATGCTACGCTGGAAGACAT 59.241 47.619 0.00 0.00 34.07 3.06 F
3222 3840 0.313043 ACATGTGCAAGCACTGCTTC 59.687 50.000 23.82 9.27 46.77 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 2773 0.616371 AGGCTGGGCGTAACATACAA 59.384 50.0 0.00 0.0 0.00 2.41 R
3895 4589 1.234821 TGTGATTGGAAGTTCACCGC 58.765 50.0 5.01 0.0 41.22 5.68 R
4884 5585 0.861837 GGCACACGTTCTTGACTCTG 59.138 55.0 0.00 0.0 0.00 3.35 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
216 217 8.587608 CATTTATGTATTCTTATGCCCCAATGT 58.412 33.333 0.00 0.00 0.00 2.71
482 489 5.123344 GCTTAATCGTGTCCCTGTGTAATTT 59.877 40.000 0.00 0.00 0.00 1.82
573 581 7.506938 AGAAATTCCTGGAAATTCTCTTGTTGA 59.493 33.333 26.62 0.00 37.24 3.18
712 726 3.633525 GGTTGTCCTTTTTCCTTAACCGT 59.366 43.478 0.00 0.00 0.00 4.83
878 1284 8.328864 GTGTTATCTTTACTCTTTAGCCATTCG 58.671 37.037 0.00 0.00 0.00 3.34
1043 1449 7.465353 TTGATGGTGAAAGAATTTATGCTCA 57.535 32.000 0.00 0.00 39.27 4.26
1292 1699 5.862845 AGCCACCATGACTCTAATATCAAG 58.137 41.667 0.00 0.00 0.00 3.02
1346 1753 3.801594 CGTGCAACAAGCCAAAAGTAATT 59.198 39.130 0.00 0.00 44.83 1.40
1598 2010 2.472695 AAATCTCTGTGCAACGCCTA 57.527 45.000 0.00 0.00 42.39 3.93
1655 2103 2.338620 GGTTCTGCCCCGCAAAAC 59.661 61.111 0.00 0.00 38.59 2.43
1669 2120 9.298250 TGCCCCGCAAAACTAATAATAATAATA 57.702 29.630 0.00 0.00 34.76 0.98
1876 2331 4.596643 CCAGATTCCTTATCCAGATCCACT 59.403 45.833 0.00 0.00 33.45 4.00
1960 2415 1.841302 ATGACCAAGAAGCCGCTCCA 61.841 55.000 0.00 0.00 0.00 3.86
1981 2436 3.457263 TAGCGCCGCTGTCCATCA 61.457 61.111 23.97 0.00 40.10 3.07
2289 2745 8.072567 CCATCAAGCACTATTTTTAGATGCTAC 58.927 37.037 0.00 0.00 45.65 3.58
2301 2757 1.759445 AGATGCTACGCTGGAAGACAT 59.241 47.619 0.00 0.00 34.07 3.06
2317 2773 6.267471 TGGAAGACATTGTAGCTCCAAAAATT 59.733 34.615 10.17 0.00 0.00 1.82
2357 2818 8.976353 CAGCCTATAGGAGATGTTGTTATAGAT 58.024 37.037 23.61 0.00 37.39 1.98
2701 3225 3.961480 TGAAAATGAGGCGAGAGAGAA 57.039 42.857 0.00 0.00 0.00 2.87
3067 3635 6.081872 AGAATGTTTCTTCTTCTTTGCTGG 57.918 37.500 0.00 0.00 36.36 4.85
3222 3840 0.313043 ACATGTGCAAGCACTGCTTC 59.687 50.000 23.82 9.27 46.77 3.86
3444 4133 3.749609 GCAAAGCAAGCTCAATCCAAAAT 59.250 39.130 0.00 0.00 0.00 1.82
3489 4178 6.306987 TCTAAAGCCCAGAAAGTTCATTCTT 58.693 36.000 0.00 0.00 37.56 2.52
3614 4308 7.363094 GCACTACTTAGATGAGTTTAGTCACCT 60.363 40.741 0.00 0.00 0.00 4.00
3757 4451 4.853924 ACACAAGGCAAAAGAATGGTAG 57.146 40.909 0.00 0.00 0.00 3.18
3895 4589 2.092374 CACACATGGATGCTGACCG 58.908 57.895 0.00 0.00 0.00 4.79
3931 4625 7.750934 CCAATCACAACTGGAGATGGAACAAT 61.751 42.308 0.00 0.00 36.95 2.71
4087 4781 6.441222 AGGGATTGTACCTGATTGTCTACTA 58.559 40.000 0.00 0.00 36.85 1.82
4128 4822 7.366011 GCAGGAGCCCCTTTCTATATAACATAT 60.366 40.741 0.00 0.00 42.02 1.78
4169 4863 9.838339 CCTACAAAGACATCTATGTTTATCCTT 57.162 33.333 0.00 0.00 41.95 3.36
4192 4886 7.095607 CCTTCTTTTCGATCTTATGTAATCCCG 60.096 40.741 0.00 0.00 0.00 5.14
4389 5087 7.629157 TGACTTGGTGTATCATTTCCAATCTA 58.371 34.615 0.00 0.00 38.90 1.98
4691 5392 6.650427 AACCACCTCAAAGTTATTCTTTCC 57.350 37.500 0.00 0.00 43.57 3.13
4818 5519 6.705825 GTGGGCATGATTATACGATATGCATA 59.294 38.462 9.27 9.27 44.33 3.14
4819 5520 7.388776 GTGGGCATGATTATACGATATGCATAT 59.611 37.037 19.17 19.17 44.33 1.78
4829 5530 4.237724 ACGATATGCATATCACAACCTCG 58.762 43.478 34.65 25.68 39.23 4.63
4884 5585 1.818363 GCCCCAAAGCTACTACCGC 60.818 63.158 0.00 0.00 0.00 5.68
4939 5640 2.227194 GTTCCCAATGTCACGAAACCT 58.773 47.619 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
482 489 0.674581 CATTGGCGAGCTTGGTGAGA 60.675 55.000 2.37 0.00 0.00 3.27
573 581 4.638421 CCGAACACACCCACATTATAACAT 59.362 41.667 0.00 0.00 0.00 2.71
712 726 5.505780 AGCATAACAGCTACCCATTAAACA 58.494 37.500 0.00 0.00 44.50 2.83
958 1364 0.025898 CTGCATTCGCACGACATCTG 59.974 55.000 0.00 0.00 45.36 2.90
1142 1548 0.318120 GTGTTGCCAAATGGGTCCTG 59.682 55.000 0.90 0.00 39.65 3.86
1244 1651 4.521256 GTGTTACAATAAGCAACCAGGGAA 59.479 41.667 0.00 0.00 0.00 3.97
1251 1658 4.679654 GTGGCTTGTGTTACAATAAGCAAC 59.320 41.667 25.76 22.90 45.43 4.17
1292 1699 5.529791 AGTATATCGAACAGGTGTGTATGC 58.470 41.667 0.00 0.00 35.08 3.14
1669 2120 4.278419 GGCTACAAAAGTCAGAACCACATT 59.722 41.667 0.00 0.00 0.00 2.71
1670 2121 3.821033 GGCTACAAAAGTCAGAACCACAT 59.179 43.478 0.00 0.00 0.00 3.21
1671 2122 3.211045 GGCTACAAAAGTCAGAACCACA 58.789 45.455 0.00 0.00 0.00 4.17
1944 2399 0.890996 CTTTGGAGCGGCTTCTTGGT 60.891 55.000 10.15 0.00 0.00 3.67
1960 2415 2.434359 GGACAGCGGCGCTACTTT 60.434 61.111 35.90 18.87 36.40 2.66
1981 2436 1.740296 GTTGGTAGCACGCCGTGAT 60.740 57.895 23.33 18.75 35.23 3.06
2023 2478 2.104111 TGTTCGTTGGTGAGTCCTTGAT 59.896 45.455 0.00 0.00 37.07 2.57
2289 2745 1.929836 GAGCTACAATGTCTTCCAGCG 59.070 52.381 0.00 0.00 34.26 5.18
2301 2757 9.685828 GTAACATACAAATTTTTGGAGCTACAA 57.314 29.630 7.47 7.47 42.34 2.41
2317 2773 0.616371 AGGCTGGGCGTAACATACAA 59.384 50.000 0.00 0.00 0.00 2.41
2357 2818 5.473846 AGATCGAGAAAACTCAGTCACAGTA 59.526 40.000 0.00 0.00 0.00 2.74
2435 2900 7.748691 TGTTAATAAACCGGAAAAAGTAGCT 57.251 32.000 9.46 0.00 34.49 3.32
3222 3840 6.665992 TGTATATGGTAAGCTGGAAGTAGG 57.334 41.667 0.00 0.00 35.30 3.18
3444 4133 6.423776 AGATGGATTTTCTTGCCTTTGAAA 57.576 33.333 0.00 0.00 0.00 2.69
3489 4178 8.475639 GGAAGAGTAATGTAGTTCTTACCATGA 58.524 37.037 0.00 0.00 30.49 3.07
3757 4451 5.122396 ACAGAACAGAATAATTGCGAAGGAC 59.878 40.000 0.00 0.00 0.00 3.85
3895 4589 1.234821 TGTGATTGGAAGTTCACCGC 58.765 50.000 5.01 0.00 41.22 5.68
3931 4625 2.324014 AAAGCGGGCTGTGACAGTGA 62.324 55.000 14.82 0.00 33.43 3.41
4046 4740 3.509442 TCCCTTGGAAGTGCATTTGAAT 58.491 40.909 0.00 0.00 0.00 2.57
4087 4781 5.105351 GGGCTCCTGCAACTTGTTTATATTT 60.105 40.000 0.00 0.00 41.91 1.40
4095 4789 2.011617 AAGGGGCTCCTGCAACTTGT 62.012 55.000 5.46 0.00 44.07 3.16
4134 4828 9.445878 CATAGATGTCTTTGTAGGCATTCATAT 57.554 33.333 0.00 0.00 46.45 1.78
4138 4832 7.559590 AACATAGATGTCTTTGTAGGCATTC 57.440 36.000 6.55 0.00 46.45 2.67
4169 4863 6.812998 ACGGGATTACATAAGATCGAAAAGA 58.187 36.000 0.00 0.00 0.00 2.52
4192 4886 5.049405 AGCTAAATGCACAACACTGTCTTAC 60.049 40.000 0.00 0.00 45.94 2.34
4498 5196 8.091449 CCTTATTTCCTATCACTAGATGACCAC 58.909 40.741 0.00 0.00 41.24 4.16
4499 5197 7.256332 GCCTTATTTCCTATCACTAGATGACCA 60.256 40.741 0.00 0.00 41.24 4.02
4691 5392 9.666626 AGTACGAACTCTTTTATAGATTGATCG 57.333 33.333 0.00 0.00 33.42 3.69
4818 5519 3.199880 GGATGAATCCGAGGTTGTGAT 57.800 47.619 0.00 0.00 37.19 3.06
4819 5520 2.691409 GGATGAATCCGAGGTTGTGA 57.309 50.000 0.00 0.00 37.19 3.58
4884 5585 0.861837 GGCACACGTTCTTGACTCTG 59.138 55.000 0.00 0.00 0.00 3.35
4939 5640 7.809546 TGTATGTTTTGGTGATCAACTTGTA 57.190 32.000 12.94 0.00 34.67 2.41


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

AutoCloner maintained by Alex Coulton.