Multiple sequence alignment - TraesCS7B01G268800

Loading Multiple Alignment...

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 TraesCS7B01G268800 chr7B 100.000 3422 0 0 1 3422 491991416 491994837 0.000000e+00 6320.0
1 TraesCS7B01G268800 chr7B 92.683 2583 166 19 841 3419 73634525 73637088 0.000000e+00 3701.0
2 TraesCS7B01G268800 chr7B 90.538 539 29 3 1 519 274434616 274435152 0.000000e+00 693.0
3 TraesCS7B01G268800 chr7B 89.095 431 44 3 144 573 66707707 66708135 1.810000e-147 532.0
4 TraesCS7B01G268800 chr7B 85.616 438 49 10 144 577 73633812 73634239 6.740000e-122 448.0
5 TraesCS7B01G268800 chr7B 91.892 222 17 1 623 844 242221256 242221476 3.320000e-80 309.0
6 TraesCS7B01G268800 chr7B 91.111 225 18 2 621 844 66708492 66708715 1.540000e-78 303.0
7 TraesCS7B01G268800 chr7B 86.928 153 16 3 1 149 73633423 73633575 5.870000e-38 169.0
8 TraesCS7B01G268800 chr4B 93.848 3446 173 13 1 3421 574023690 574020259 0.000000e+00 5153.0
9 TraesCS7B01G268800 chr4B 91.592 3449 226 27 1 3421 45106381 45102969 0.000000e+00 4704.0
10 TraesCS7B01G268800 chr4B 92.114 2587 182 20 841 3421 555147496 555144926 0.000000e+00 3627.0
11 TraesCS7B01G268800 chr4B 90.278 432 35 6 144 573 555148210 555147784 2.980000e-155 558.0
12 TraesCS7B01G268800 chr4B 88.993 427 45 2 148 573 360930563 360930988 8.410000e-146 527.0
13 TraesCS7B01G268800 chr4B 89.167 240 22 3 608 844 45127873 45127635 2.580000e-76 296.0
14 TraesCS7B01G268800 chr4B 89.496 238 19 4 608 844 203477821 203478053 2.580000e-76 296.0
15 TraesCS7B01G268800 chr4B 97.368 38 1 0 575 612 153741770 153741807 7.930000e-07 65.8
16 TraesCS7B01G268800 chr3B 92.841 2640 144 16 1 2611 418371833 418374456 0.000000e+00 3786.0
17 TraesCS7B01G268800 chr3B 92.667 2591 162 20 841 3421 683820060 683817488 0.000000e+00 3707.0
18 TraesCS7B01G268800 chr3B 92.674 2580 165 21 847 3420 342132589 342130028 0.000000e+00 3696.0
19 TraesCS7B01G268800 chr3B 92.251 271 17 2 575 844 683820417 683820150 6.930000e-102 381.0
20 TraesCS7B01G268800 chr3B 84.956 339 46 4 144 479 503686805 503686469 4.230000e-89 339.0
21 TraesCS7B01G268800 chr3B 85.882 170 20 4 35 200 683820949 683820780 9.760000e-41 178.0
22 TraesCS7B01G268800 chr3B 97.368 38 1 0 575 612 342133318 342133281 7.930000e-07 65.8
23 TraesCS7B01G268800 chr1B 92.689 2585 164 15 841 3421 389282810 389285373 0.000000e+00 3703.0
24 TraesCS7B01G268800 chr1B 86.500 600 52 11 1 573 558711075 558711672 1.730000e-177 632.0
25 TraesCS7B01G268800 chr1B 90.406 271 17 3 575 844 558711733 558711995 7.030000e-92 348.0
26 TraesCS7B01G268800 chr6B 92.492 2584 174 17 841 3421 630263810 630261244 0.000000e+00 3679.0
27 TraesCS7B01G268800 chr6B 93.216 2491 149 9 1 2477 110332305 110329821 0.000000e+00 3646.0
28 TraesCS7B01G268800 chr6B 89.958 239 20 4 608 844 341709728 341709492 4.290000e-79 305.0
29 TraesCS7B01G268800 chr6B 87.248 149 15 3 5 149 355932998 355933146 2.110000e-37 167.0
30 TraesCS7B01G268800 chr6B 86.275 153 17 3 1 149 362211921 362211769 2.730000e-36 163.0
31 TraesCS7B01G268800 chr2B 92.168 2579 180 19 847 3421 344007227 344009787 0.000000e+00 3624.0
32 TraesCS7B01G268800 chr2B 89.538 411 43 0 163 573 345616470 345616060 3.910000e-144 521.0
33 TraesCS7B01G268800 chr1D 84.553 246 35 2 295 540 215672089 215672331 1.230000e-59 241.0
34 TraesCS7B01G268800 chr6D 82.716 243 35 4 315 556 223796451 223796687 3.460000e-50 209.0
35 TraesCS7B01G268800 chr4D 85.430 151 19 2 608 757 329355096 329355244 1.640000e-33 154.0
36 TraesCS7B01G268800 chr5D 97.368 38 1 0 575 612 372677522 372677559 7.930000e-07 65.8


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 TraesCS7B01G268800 chr7B 491991416 491994837 3421 False 6320.000000 6320 100.000000 1 3422 1 chr7B.!!$F3 3421
1 TraesCS7B01G268800 chr7B 73633423 73637088 3665 False 1439.333333 3701 88.409000 1 3419 3 chr7B.!!$F5 3418
2 TraesCS7B01G268800 chr7B 274434616 274435152 536 False 693.000000 693 90.538000 1 519 1 chr7B.!!$F2 518
3 TraesCS7B01G268800 chr7B 66707707 66708715 1008 False 417.500000 532 90.103000 144 844 2 chr7B.!!$F4 700
4 TraesCS7B01G268800 chr4B 574020259 574023690 3431 True 5153.000000 5153 93.848000 1 3421 1 chr4B.!!$R3 3420
5 TraesCS7B01G268800 chr4B 45102969 45106381 3412 True 4704.000000 4704 91.592000 1 3421 1 chr4B.!!$R1 3420
6 TraesCS7B01G268800 chr4B 555144926 555148210 3284 True 2092.500000 3627 91.196000 144 3421 2 chr4B.!!$R4 3277
7 TraesCS7B01G268800 chr3B 418371833 418374456 2623 False 3786.000000 3786 92.841000 1 2611 1 chr3B.!!$F1 2610
8 TraesCS7B01G268800 chr3B 342130028 342133318 3290 True 1880.900000 3696 95.021000 575 3420 2 chr3B.!!$R2 2845
9 TraesCS7B01G268800 chr3B 683817488 683820949 3461 True 1422.000000 3707 90.266667 35 3421 3 chr3B.!!$R3 3386
10 TraesCS7B01G268800 chr1B 389282810 389285373 2563 False 3703.000000 3703 92.689000 841 3421 1 chr1B.!!$F1 2580
11 TraesCS7B01G268800 chr1B 558711075 558711995 920 False 490.000000 632 88.453000 1 844 2 chr1B.!!$F2 843
12 TraesCS7B01G268800 chr6B 630261244 630263810 2566 True 3679.000000 3679 92.492000 841 3421 1 chr6B.!!$R4 2580
13 TraesCS7B01G268800 chr6B 110329821 110332305 2484 True 3646.000000 3646 93.216000 1 2477 1 chr6B.!!$R1 2476
14 TraesCS7B01G268800 chr2B 344007227 344009787 2560 False 3624.000000 3624 92.168000 847 3421 1 chr2B.!!$F1 2574

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
578 834 0.381801 CACCCAAATGATACGCAGGC 59.618 55.0 0.0 0.0 0.0 4.85 F
1093 1528 0.035036 TGCCAAACCAACCGACGATA 59.965 50.0 0.0 0.0 0.0 2.92 F
1272 1707 0.610232 AAAGCACCAAGCCCTGCTAG 60.610 55.0 0.0 0.0 43.1 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 2204 0.599060 TGTGCTTGTCGTCGGTGATA 59.401 50.000 0.00 0.00 0.00 2.15 R
1894 2332 0.877071 CATCTTTGCACAGCGAAGGT 59.123 50.000 16.58 8.76 46.66 3.50 R
2522 2969 1.768275 TCCGAATGTATGGGAGTGCAT 59.232 47.619 0.00 0.00 0.00 3.96 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
208 463 6.075762 TGTTATGCGATGTAGTACGGTAAT 57.924 37.500 0.00 0.00 0.00 1.89
219 474 3.793559 AGTACGGTAATGCAATCCAGTC 58.206 45.455 0.00 0.00 0.00 3.51
247 502 7.325097 CGCATTACGTAGATGAACATATACACA 59.675 37.037 16.20 4.16 35.78 3.72
276 531 5.354234 AGAACACAGTGATGAAGAAAAACGT 59.646 36.000 7.81 0.00 0.00 3.99
365 620 9.927668 ATGCAGTACAATTTTAATTTGCTAAGT 57.072 25.926 0.00 0.00 32.45 2.24
573 829 4.981806 AATTGACCACCCAAATGATACG 57.018 40.909 0.00 0.00 0.00 3.06
574 830 1.745232 TGACCACCCAAATGATACGC 58.255 50.000 0.00 0.00 0.00 4.42
578 834 0.381801 CACCCAAATGATACGCAGGC 59.618 55.000 0.00 0.00 0.00 4.85
773 1112 1.727880 GCAGTGTAAAATACGTGGCGA 59.272 47.619 0.00 0.00 0.00 5.54
870 1302 6.591834 GTGCAGTTCTGTATTGTAGAAGATGT 59.408 38.462 0.00 0.00 35.03 3.06
1069 1504 3.499737 GCCACAAGCCCACGATCG 61.500 66.667 14.88 14.88 34.35 3.69
1087 1522 1.080569 GCAGATGCCAAACCAACCG 60.081 57.895 0.00 0.00 34.31 4.44
1093 1528 0.035036 TGCCAAACCAACCGACGATA 59.965 50.000 0.00 0.00 0.00 2.92
1179 1614 4.010349 CTCCCCTTAAATTCAGACCACAC 58.990 47.826 0.00 0.00 0.00 3.82
1209 1644 2.821969 GCCTTCTCATCCACAACAACAT 59.178 45.455 0.00 0.00 0.00 2.71
1272 1707 0.610232 AAAGCACCAAGCCCTGCTAG 60.610 55.000 0.00 0.00 43.10 3.42
1282 1717 2.106938 CCTGCTAGCGGCGATGAA 59.893 61.111 18.67 0.00 45.43 2.57
1298 1733 4.611943 CGATGAAGTTCACCGATGAGTAT 58.388 43.478 14.79 0.00 34.73 2.12
1385 1820 1.449353 GCAGATGGCGATCTCCCTT 59.551 57.895 8.44 0.00 36.75 3.95
1499 1934 0.762082 CCCTCTGCCAGCTCTCCATA 60.762 60.000 0.00 0.00 0.00 2.74
1540 1975 1.457346 CTCTTCCAAATGAGCGCCTT 58.543 50.000 2.29 0.00 0.00 4.35
1751 2186 3.815962 ACATGCTCATCGACGACTACTAT 59.184 43.478 0.00 0.00 0.00 2.12
1873 2311 2.304092 AGCGTACGAGATATGGAACCA 58.696 47.619 21.65 0.00 0.00 3.67
1902 2340 3.382832 CCCAGGACGACCTTCGCT 61.383 66.667 2.87 0.00 45.36 4.93
1911 2349 1.221466 CGACCTTCGCTGTGCAAAGA 61.221 55.000 8.49 0.00 31.14 2.52
2019 2458 3.118482 TGAACCAACAATGCCAACAATGT 60.118 39.130 0.00 0.00 41.76 2.71
2134 2575 5.179929 CCATGCAGAATCGCTTGTAATGATA 59.820 40.000 0.00 0.00 35.78 2.15
2298 2742 0.953727 GCAGTGTGCAAACAGGATGA 59.046 50.000 10.29 0.00 44.26 2.92
2744 3201 2.307768 CCCAGCCAGTCTCGTAATAGA 58.692 52.381 0.00 0.00 0.00 1.98
2749 3206 4.277174 CAGCCAGTCTCGTAATAGATCTGT 59.723 45.833 5.18 0.00 0.00 3.41
2889 3347 1.134670 GGAGTTCGATACAGCAGCCTT 60.135 52.381 0.00 0.00 0.00 4.35
3022 3484 3.379372 CCAATTGCATCTTCACTACCCAG 59.621 47.826 0.00 0.00 0.00 4.45
3365 3952 1.661463 TCCCATCCACAGCTCTTCTT 58.339 50.000 0.00 0.00 0.00 2.52
3421 4008 2.353610 GGTGCTTGGCAAGGATGGG 61.354 63.158 27.25 3.41 41.47 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 413 4.520111 TGCACTGCATTTTTCTAGTGATGT 59.480 37.500 0.00 0.00 42.28 3.06
208 463 0.254462 TAATGCGGGACTGGATTGCA 59.746 50.000 7.97 0.00 40.23 4.08
219 474 2.816689 TGTTCATCTACGTAATGCGGG 58.183 47.619 0.00 0.00 46.52 6.13
247 502 8.450578 TTTTCTTCATCACTGTGTTCTATGTT 57.549 30.769 7.79 0.00 0.00 2.71
276 531 5.240623 AGTGCATTTCTTATTTCCGTGTTCA 59.759 36.000 0.00 0.00 0.00 3.18
365 620 3.558931 CCAATGTATGGGACTGCAGTA 57.441 47.619 21.73 4.46 46.27 2.74
427 682 8.784994 CATTCCGTACTACATGTATAGTTCTCT 58.215 37.037 5.91 0.00 36.74 3.10
554 810 2.088423 GCGTATCATTTGGGTGGTCAA 58.912 47.619 0.00 0.00 0.00 3.18
555 811 1.003696 TGCGTATCATTTGGGTGGTCA 59.996 47.619 0.00 0.00 0.00 4.02
556 812 1.670811 CTGCGTATCATTTGGGTGGTC 59.329 52.381 0.00 0.00 0.00 4.02
557 813 1.681780 CCTGCGTATCATTTGGGTGGT 60.682 52.381 0.00 0.00 0.00 4.16
558 814 1.024271 CCTGCGTATCATTTGGGTGG 58.976 55.000 0.00 0.00 0.00 4.61
559 815 0.381801 GCCTGCGTATCATTTGGGTG 59.618 55.000 0.00 0.00 0.00 4.61
641 980 4.792066 CTGGTACGGGAGGGGTAA 57.208 61.111 0.00 0.00 0.00 2.85
773 1112 4.153475 ACGTAACGCACTGCATTTTTCTAT 59.847 37.500 1.11 0.00 0.00 1.98
870 1302 5.427378 TGCATTGCTTATACTTCAGCACTA 58.573 37.500 10.49 0.00 45.77 2.74
1069 1504 1.080569 CGGTTGGTTTGGCATCTGC 60.081 57.895 0.00 0.00 41.14 4.26
1087 1522 2.379054 TGCGGTTGTGCATATCGTC 58.621 52.632 6.36 0.83 40.62 4.20
1110 1545 0.242555 TGAACTGCACGATCACGCTA 59.757 50.000 5.09 0.00 43.96 4.26
1179 1614 1.407979 GGATGAGAAGGCCTTTGCATG 59.592 52.381 28.36 0.00 40.13 4.06
1209 1644 1.765904 TGGGAGCGCAATGGATACTTA 59.234 47.619 11.47 0.00 37.61 2.24
1272 1707 2.785258 GGTGAACTTCATCGCCGC 59.215 61.111 0.00 0.00 39.96 6.53
1282 1717 3.069729 GCCCTTATACTCATCGGTGAACT 59.930 47.826 0.00 0.00 33.05 3.01
1298 1733 3.315949 ACGGCCTTGTCGCCCTTA 61.316 61.111 0.00 0.00 46.98 2.69
1344 1779 2.038426 TCTTGTCGTTGGTGTGGATGAT 59.962 45.455 0.00 0.00 0.00 2.45
1499 1934 1.002134 CACCGGGTGATTCTTGCCT 60.002 57.895 22.77 0.00 35.23 4.75
1540 1975 1.879380 CGAAGATGGTGCACCTTTCAA 59.121 47.619 34.75 16.42 36.82 2.69
1729 2164 2.017782 AGTAGTCGTCGATGAGCATGT 58.982 47.619 7.79 0.00 0.00 3.21
1751 2186 8.038351 TCGGTGATATTCTTCTTCATGTTGTTA 58.962 33.333 0.00 0.00 0.00 2.41
1769 2204 0.599060 TGTGCTTGTCGTCGGTGATA 59.401 50.000 0.00 0.00 0.00 2.15
1873 2311 1.160870 TCCTGGGTGAGGGTGATGT 59.839 57.895 0.00 0.00 43.06 3.06
1894 2332 0.877071 CATCTTTGCACAGCGAAGGT 59.123 50.000 16.58 8.76 46.66 3.50
1902 2340 2.290514 CCTCCTTCTCCATCTTTGCACA 60.291 50.000 0.00 0.00 0.00 4.57
1911 2349 1.385206 GGGCCTCCTCCTTCTCCAT 60.385 63.158 0.84 0.00 0.00 3.41
2019 2458 7.716612 TGATGATAATTCTAAGAGAACGCTGA 58.283 34.615 0.00 0.00 37.00 4.26
2134 2575 8.920509 AAAGCAAACTAACGTAATCAAAGTTT 57.079 26.923 0.00 0.00 40.13 2.66
2296 2740 3.455990 ACACAATTTGCACTGCATTCA 57.544 38.095 4.10 0.00 38.76 2.57
2298 2742 3.004210 TCGTACACAATTTGCACTGCATT 59.996 39.130 4.10 0.00 38.76 3.56
2522 2969 1.768275 TCCGAATGTATGGGAGTGCAT 59.232 47.619 0.00 0.00 0.00 3.96
2889 3347 2.354510 GACATGTTTATAAGCGCTGGCA 59.645 45.455 12.58 4.41 43.41 4.92
2929 3387 5.678955 GACTAATGTTTAGTCCCACCTCT 57.321 43.478 13.89 0.00 38.33 3.69
3247 3834 9.638239 GATAAGTTTTTATGCAACCAATTGAGA 57.362 29.630 7.12 0.00 32.07 3.27
3378 3965 0.402504 TTACAGTCCATGGCGGGTTT 59.597 50.000 6.96 0.00 34.36 3.27


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

AutoCloner maintained by Alex Coulton.