Multiple sequence alignment - TraesCS7A01G502100

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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 TraesCS7A01G502100 chr7A 100.000 3839 0 0 1 3839 691440781 691436943 0.000000e+00 7090.0
1 TraesCS7A01G502100 chr7A 90.123 81 8 0 2365 2445 691438261 691438181 5.250000e-19 106.0
2 TraesCS7A01G502100 chr7A 90.123 81 8 0 2521 2601 691438417 691438337 5.250000e-19 106.0
3 TraesCS7A01G502100 chr7A 100.000 48 0 0 2102 2149 691438584 691438537 5.280000e-14 89.8
4 TraesCS7A01G502100 chr7A 100.000 48 0 0 2198 2245 691438680 691438633 5.280000e-14 89.8
5 TraesCS7A01G502100 chr5D 93.920 3602 140 27 1 3527 445804425 445808022 0.000000e+00 5365.0
6 TraesCS7A01G502100 chr5D 87.669 519 25 17 3328 3839 445808549 445809035 5.570000e-158 568.0
7 TraesCS7A01G502100 chr5D 90.338 207 13 2 3328 3527 445808481 445808687 8.180000e-67 265.0
8 TraesCS7A01G502100 chr5D 89.855 207 14 3 3328 3527 445807884 445808090 3.800000e-65 259.0
9 TraesCS7A01G502100 chr5D 96.774 93 3 0 2151 2243 445806569 445806661 5.140000e-34 156.0
10 TraesCS7A01G502100 chr5D 81.633 147 15 6 2467 2601 445806765 445806911 1.130000e-20 111.0
11 TraesCS7A01G502100 chr5D 97.959 49 1 0 2198 2246 445806568 445806616 6.830000e-13 86.1
12 TraesCS7A01G502100 chr7D 93.130 3610 146 32 1 3527 599187150 599183560 0.000000e+00 5199.0
13 TraesCS7A01G502100 chr7D 86.513 519 28 18 3328 3839 599183494 599183011 2.030000e-147 532.0
14 TraesCS7A01G502100 chr7D 91.304 207 11 3 3328 3527 599183698 599183492 3.780000e-70 276.0
15 TraesCS7A01G502100 chr7D 90.821 207 12 3 3328 3527 599183562 599183356 1.760000e-68 270.0
16 TraesCS7A01G502100 chr7D 82.313 147 14 6 2467 2601 599184819 599184673 2.420000e-22 117.0
17 TraesCS7A01G502100 chr7D 97.872 47 1 0 2200 2246 599185014 599184968 8.840000e-12 82.4
18 TraesCS7A01G502100 chr7B 92.193 3023 134 29 1 2928 678639589 678636574 0.000000e+00 4181.0
19 TraesCS7A01G502100 chr7B 90.497 684 42 6 2978 3654 678636581 678635914 0.000000e+00 881.0
20 TraesCS7A01G502100 chr7B 94.845 97 5 0 2102 2198 678637376 678637280 6.640000e-33 152.0
21 TraesCS7A01G502100 chr7B 81.633 147 15 6 2467 2601 678637227 678637081 1.130000e-20 111.0
22 TraesCS7A01G502100 chr7B 73.487 347 51 28 2962 3304 678635112 678634803 4.080000e-15 93.5
23 TraesCS7A01G502100 chr7B 97.917 48 1 0 2102 2149 678637328 678637281 2.460000e-12 84.2
24 TraesCS7A01G502100 chr7B 100.000 30 0 0 3681 3710 678635833 678635804 5.360000e-04 56.5
25 TraesCS7A01G502100 chr4B 90.549 656 50 6 1253 1897 12867536 12868190 0.000000e+00 857.0
26 TraesCS7A01G502100 chr4B 83.223 602 84 11 3 591 12852047 12852644 1.570000e-148 536.0
27 TraesCS7A01G502100 chr4B 83.085 603 83 13 3 591 12873949 12874546 7.300000e-147 531.0
28 TraesCS7A01G502100 chr4B 88.288 222 16 4 1003 1215 12867318 12867538 1.370000e-64 257.0
29 TraesCS7A01G502100 chr1B 78.855 454 73 15 1 444 630678089 630677649 6.280000e-73 285.0
30 TraesCS7A01G502100 chr1A 78.525 461 76 20 1 449 30337042 30337491 8.120000e-72 281.0
31 TraesCS7A01G502100 chr1A 76.739 460 86 18 1 449 369270402 369269953 1.780000e-58 237.0
32 TraesCS7A01G502100 chr2A 77.523 436 82 16 16 444 639697674 639698100 8.240000e-62 248.0
33 TraesCS7A01G502100 chr3B 80.511 313 52 9 16 325 31217706 31217400 8.290000e-57 231.0
34 TraesCS7A01G502100 chr3B 74.328 409 83 14 11 410 755120630 755121025 1.850000e-33 154.0


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 TraesCS7A01G502100 chr7A 691436943 691440781 3838 True 1496.320000 7090 96.049200 1 3839 5 chr7A.!!$R1 3838
1 TraesCS7A01G502100 chr5D 445804425 445809035 4610 False 972.871429 5365 91.164000 1 3839 7 chr5D.!!$F1 3838
2 TraesCS7A01G502100 chr7D 599183011 599187150 4139 True 1079.400000 5199 90.325500 1 3839 6 chr7D.!!$R1 3838
3 TraesCS7A01G502100 chr7B 678634803 678639589 4786 True 794.171429 4181 90.081714 1 3710 7 chr7B.!!$R1 3709
4 TraesCS7A01G502100 chr4B 12867318 12868190 872 False 557.000000 857 89.418500 1003 1897 2 chr4B.!!$F3 894
5 TraesCS7A01G502100 chr4B 12852047 12852644 597 False 536.000000 536 83.223000 3 591 1 chr4B.!!$F1 588
6 TraesCS7A01G502100 chr4B 12873949 12874546 597 False 531.000000 531 83.085000 3 591 1 chr4B.!!$F2 588

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
372 378 0.172352 CTCCCTCTGCGTCAAGTCTC 59.828 60.0 0.0 0.0 0.00 3.36 F
452 460 2.224305 CCGAAGACCTTTCAGTGACCTT 60.224 50.0 0.0 0.0 0.00 3.50 F
848 880 2.231235 GACTGGGGTAATTGCTGTTTGG 59.769 50.0 0.0 0.0 0.00 3.28 F
2346 2466 1.043116 AGCCTAGGCACGCTGATACA 61.043 55.0 34.7 0.0 44.88 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2452 0.034756 TTGTGTGTATCAGCGTGCCT 59.965 50.000 0.0 0.0 0.00 4.75 R
2346 2466 1.242076 GCTTCACTCCATGCTTGTGT 58.758 50.000 9.6 0.0 33.82 3.72 R
2565 2721 0.454600 TACGCTTGCTCCTCTTACGG 59.545 55.000 0.0 0.0 0.00 4.02 R
3182 3341 3.119280 TCCGAAATGACATGCTCTACGAA 60.119 43.478 0.0 0.0 0.00 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
50 52 2.490115 ACGAAGTTTTCCAACAGCAACA 59.510 40.909 0.00 0.00 37.78 3.33
58 60 1.211703 TCCAACAGCAACACCTTCAGA 59.788 47.619 0.00 0.00 0.00 3.27
66 68 4.096984 CAGCAACACCTTCAGAAAGAAAGT 59.903 41.667 0.00 0.00 35.40 2.66
143 145 1.547372 CACCCTGAAAAATCAGCCTGG 59.453 52.381 0.28 0.00 36.46 4.45
228 233 1.616187 CCAACTCGGGTCAGACCTAGA 60.616 57.143 19.57 16.75 38.64 2.43
299 304 1.082821 CACATGTGTTGTCGCCACG 60.083 57.895 18.03 0.00 36.00 4.94
372 378 0.172352 CTCCCTCTGCGTCAAGTCTC 59.828 60.000 0.00 0.00 0.00 3.36
452 460 2.224305 CCGAAGACCTTTCAGTGACCTT 60.224 50.000 0.00 0.00 0.00 3.50
562 580 4.689612 TCTGAATCAGGGCAACTATACC 57.310 45.455 10.71 0.00 31.51 2.73
592 611 4.415332 GACGACGCCGAAGCTCCA 62.415 66.667 0.00 0.00 39.50 3.86
834 866 5.982890 AAGTGTTTGAAATATGACTGGGG 57.017 39.130 0.00 0.00 0.00 4.96
848 880 2.231235 GACTGGGGTAATTGCTGTTTGG 59.769 50.000 0.00 0.00 0.00 3.28
1884 2004 6.670695 AATTCTTACTTTGGGTTGCATCTT 57.329 33.333 0.00 0.00 0.00 2.40
1905 2025 6.231211 TCTTCTGAGACTCATTTGGGTAAAC 58.769 40.000 5.42 0.00 0.00 2.01
1959 2079 2.377628 AAAGACTCGCTCGGGTGCAA 62.378 55.000 0.00 0.00 0.00 4.08
2184 2304 2.754552 AGCAGCTGTTCAAGTTCAACAA 59.245 40.909 16.64 0.00 33.36 2.83
2346 2466 1.043116 AGCCTAGGCACGCTGATACA 61.043 55.000 34.70 0.00 44.88 2.29
2546 2702 1.177256 AAGCAGCAGTTTCAGCAGGG 61.177 55.000 0.00 0.00 0.00 4.45
2565 2721 1.079503 GCAATCGACAGAAGTGGACC 58.920 55.000 0.00 0.00 35.23 4.46
2586 2742 1.132643 CGTAAGAGGAGCAAGCGTAGT 59.867 52.381 0.00 0.00 43.02 2.73
2603 2759 3.428999 CGTAGTGTACCCAGTGGATCAAG 60.429 52.174 11.95 0.00 34.81 3.02
2609 2765 3.641434 ACCCAGTGGATCAAGAATCTG 57.359 47.619 11.95 0.00 34.56 2.90
2610 2766 2.295885 CCCAGTGGATCAAGAATCTGC 58.704 52.381 11.95 0.00 34.56 4.26
2626 2782 3.334583 TCTGCTCCGCAAATAGTTCTT 57.665 42.857 0.00 0.00 38.41 2.52
2632 2788 2.734606 TCCGCAAATAGTTCTTGTGACG 59.265 45.455 0.00 0.00 36.59 4.35
2653 2809 8.189460 GTGACGTTATAGGAATAAAGAGTGAGT 58.811 37.037 0.00 0.00 33.05 3.41
2781 2939 4.207955 TCGTACATATCTTGCAGGACTCT 58.792 43.478 0.00 0.00 0.00 3.24
2782 2940 4.276183 TCGTACATATCTTGCAGGACTCTC 59.724 45.833 0.00 0.00 0.00 3.20
2804 2962 3.706373 GTCTGGCTCCCCGCTGAA 61.706 66.667 0.00 0.00 39.13 3.02
2941 3099 0.602562 TTTTGGAGCTCGGCATTTGG 59.397 50.000 7.83 0.00 0.00 3.28
2953 3111 1.533625 GCATTTGGTGGTCTGTAGCA 58.466 50.000 0.00 0.00 0.00 3.49
2996 3154 1.981495 AGCTCTTGGTTGGCTAGTCTT 59.019 47.619 0.00 0.00 34.31 3.01
3213 3372 4.287720 CATGTCATTTCGGATGATGCTTG 58.712 43.478 5.83 1.08 0.00 4.01
3294 3453 1.059098 ACTGATTGTCCCTGCTGTCA 58.941 50.000 0.00 0.00 0.00 3.58
3356 3515 7.177498 TGACAGTGTTTATGATGCGATATTC 57.823 36.000 0.00 0.00 0.00 1.75
3358 3517 7.042523 TGACAGTGTTTATGATGCGATATTCAG 60.043 37.037 0.00 0.00 0.00 3.02
3379 3539 7.815840 TCAGTCTTGGTTTGTTGAAATATGA 57.184 32.000 0.00 0.00 0.00 2.15
3392 3552 8.800231 TGTTGAAATATGACATTTCTGTTGTG 57.200 30.769 10.20 0.00 38.47 3.33
3401 3561 5.827267 TGACATTTCTGTTGTGGAAGAATGA 59.173 36.000 0.00 0.00 35.14 2.57
3404 3564 6.096705 ACATTTCTGTTGTGGAAGAATGACAA 59.903 34.615 0.00 0.00 32.65 3.18
3488 4177 4.863152 TGACAGTGTTTATGATGCGATG 57.137 40.909 0.00 0.00 0.00 3.84
3520 4419 9.638239 TTTGTTAGAAATATGGCATTTCTGTTC 57.362 29.630 20.85 13.19 45.02 3.18
3554 4453 9.020731 GGTTAGTTTGGATCTTTTCTTCCATAA 57.979 33.333 0.00 0.00 41.52 1.90
3635 4534 3.491267 GCTAGAAGTTCGTATCATGGTGC 59.509 47.826 0.00 0.00 0.00 5.01
3649 4548 3.871006 TCATGGTGCGATCAGTATTGTTC 59.129 43.478 0.00 0.00 0.00 3.18
3657 4556 6.500910 TGCGATCAGTATTGTTCGTACTAAT 58.499 36.000 16.84 0.00 44.44 1.73
3660 4559 7.166970 GCGATCAGTATTGTTCGTACTAATGAA 59.833 37.037 16.84 0.00 44.44 2.57
3751 4704 7.651808 AGCAATAGTATGACCAATGTAAATGC 58.348 34.615 0.00 0.00 0.00 3.56
3753 4706 7.255590 GCAATAGTATGACCAATGTAAATGCCT 60.256 37.037 0.00 0.00 0.00 4.75
3758 4711 5.833406 TGACCAATGTAAATGCCTATGTG 57.167 39.130 0.00 0.00 0.00 3.21
3764 4717 9.415008 ACCAATGTAAATGCCTATGTGTTTATA 57.585 29.630 0.00 0.00 0.00 0.98
3823 4776 7.202016 TGCCTTCTAGAAAGTTGTGTATTTG 57.798 36.000 6.63 0.00 0.00 2.32
3830 4783 9.337396 TCTAGAAAGTTGTGTATTTGTGAATGT 57.663 29.630 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 4.723309 AGCATCACTTTCTTTCTGAAGGT 58.277 39.130 0.00 0.00 44.32 3.50
228 233 1.078426 CGAGCTCCGGGGTGAAAAT 60.078 57.895 8.47 0.00 33.91 1.82
299 304 0.796312 TGCAAGGATCGCGAAAAGTC 59.204 50.000 15.24 5.77 0.00 3.01
372 378 3.567164 GGTGAGATGCAAACTATGGATGG 59.433 47.826 0.00 0.00 40.61 3.51
452 460 2.993264 GACCTCCCGTGGTTCCGA 60.993 66.667 0.00 0.00 41.00 4.55
500 517 2.029307 GATACAGACCTGGTCGGGCC 62.029 65.000 26.80 13.70 44.54 5.80
592 611 1.480212 TTATCTGATGGCGGGCGGAT 61.480 55.000 0.00 0.00 34.64 4.18
834 866 8.755696 TTCATAAATGTCCAAACAGCAATTAC 57.244 30.769 0.00 0.00 39.20 1.89
1884 2004 4.349636 TGGTTTACCCAAATGAGTCTCAGA 59.650 41.667 8.82 0.00 41.50 3.27
1905 2025 1.221840 CCCGAACACCTCTGGATGG 59.778 63.158 0.00 0.00 29.98 3.51
1959 2079 3.589988 CTGCGGTAAGATTCTGTCAAGT 58.410 45.455 0.00 0.00 0.00 3.16
2149 2269 1.077644 CTGCTGCAGCTTCATCCCT 60.078 57.895 36.61 0.00 42.66 4.20
2184 2304 0.262580 CATCCCCCACCATGGATTGT 59.737 55.000 21.47 0.00 40.96 2.71
2332 2452 0.034756 TTGTGTGTATCAGCGTGCCT 59.965 50.000 0.00 0.00 0.00 4.75
2346 2466 1.242076 GCTTCACTCCATGCTTGTGT 58.758 50.000 9.60 0.00 33.82 3.72
2546 2702 1.079503 GGTCCACTTCTGTCGATTGC 58.920 55.000 0.00 0.00 0.00 3.56
2565 2721 0.454600 TACGCTTGCTCCTCTTACGG 59.545 55.000 0.00 0.00 0.00 4.02
2586 2742 4.080919 CAGATTCTTGATCCACTGGGTACA 60.081 45.833 0.00 0.00 35.21 2.90
2610 2766 3.181530 CGTCACAAGAACTATTTGCGGAG 60.182 47.826 0.00 0.00 0.00 4.63
2626 2782 8.058667 TCACTCTTTATTCCTATAACGTCACA 57.941 34.615 0.00 0.00 0.00 3.58
2653 2809 1.463056 CTCCAGTCGCGCATGTTTAAA 59.537 47.619 8.75 0.00 0.00 1.52
2660 2816 2.125512 GGTTCTCCAGTCGCGCAT 60.126 61.111 8.75 0.00 0.00 4.73
2707 2863 5.650543 CACCTTTATTGCCTGGATAAACAC 58.349 41.667 0.00 0.00 0.00 3.32
2804 2962 1.908793 ACTACTGCACCACTCCGCT 60.909 57.895 0.00 0.00 0.00 5.52
2809 2967 0.471971 ACCTCCACTACTGCACCACT 60.472 55.000 0.00 0.00 0.00 4.00
2941 3099 3.618690 ATCCTTCTTGCTACAGACCAC 57.381 47.619 0.00 0.00 0.00 4.16
2953 3111 3.201708 AGCACAGCCAGATAATCCTTCTT 59.798 43.478 0.00 0.00 0.00 2.52
2996 3154 4.202556 TGAACCAATGATTCCAGTTCTCCA 60.203 41.667 11.31 0.00 38.10 3.86
3033 3191 0.681243 GGCTCCAGGTTTTAGGGCAG 60.681 60.000 0.00 0.00 0.00 4.85
3180 3339 4.982295 CCGAAATGACATGCTCTACGAATA 59.018 41.667 0.00 0.00 0.00 1.75
3182 3341 3.119280 TCCGAAATGACATGCTCTACGAA 60.119 43.478 0.00 0.00 0.00 3.85
3356 3515 7.424803 TGTCATATTTCAACAAACCAAGACTG 58.575 34.615 0.00 0.00 0.00 3.51
3358 3517 8.816640 AATGTCATATTTCAACAAACCAAGAC 57.183 30.769 0.00 0.00 0.00 3.01
3379 3539 5.593909 TGTCATTCTTCCACAACAGAAATGT 59.406 36.000 0.00 0.00 32.76 2.71
3392 3552 8.826710 TCGTATCATAAACATTGTCATTCTTCC 58.173 33.333 0.00 0.00 0.00 3.46
3425 3585 6.919721 TGCCATATTTCTAACAAACCAAGAC 58.080 36.000 0.00 0.00 0.00 3.01
3488 4177 5.719173 TGCCATATTTCTAACAAACCAAGC 58.281 37.500 0.00 0.00 0.00 4.01
3520 4419 6.884280 AAGATCCAAACTAACCACTTGAAG 57.116 37.500 0.00 0.00 0.00 3.02
3554 4453 8.887036 TTCTCAGCAACGACATATAAACATAT 57.113 30.769 0.00 0.00 0.00 1.78
3555 4454 7.979537 ACTTCTCAGCAACGACATATAAACATA 59.020 33.333 0.00 0.00 0.00 2.29
3556 4455 6.818644 ACTTCTCAGCAACGACATATAAACAT 59.181 34.615 0.00 0.00 0.00 2.71
3715 4668 8.880244 TGGTCATACTATTGCTAGATTTATGGT 58.120 33.333 0.00 0.00 0.00 3.55
3716 4669 9.725019 TTGGTCATACTATTGCTAGATTTATGG 57.275 33.333 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.