Multiple sequence alignment - TraesCS7B01G112600

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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 TraesCS7B01G112600 chr7B 100.000 2549 0 0 1 2549 129570001 129567453 0.000000e+00 4708.0
1 TraesCS7B01G112600 chr7B 94.548 1981 96 9 569 2549 81247811 81249779 0.000000e+00 3049.0
2 TraesCS7B01G112600 chr2B 95.661 1982 75 7 569 2549 62450928 62452899 0.000000e+00 3173.0
3 TraesCS7B01G112600 chr2B 94.675 1953 90 7 569 2519 565228142 565226202 0.000000e+00 3018.0
4 TraesCS7B01G112600 chr2B 85.311 531 61 13 44 568 418933652 418934171 1.340000e-147 532.0
5 TraesCS7B01G112600 chr1B 95.516 1985 82 6 566 2549 639164488 639162510 0.000000e+00 3166.0
6 TraesCS7B01G112600 chr1B 89.205 528 53 4 44 568 327827535 327828061 0.000000e+00 656.0
7 TraesCS7B01G112600 chr1B 86.142 534 61 9 44 568 689374642 689374113 4.760000e-157 564.0
8 TraesCS7B01G112600 chr4B 95.411 1983 85 4 567 2549 648881435 648879459 0.000000e+00 3153.0
9 TraesCS7B01G112600 chr4B 95.626 1966 77 7 566 2528 657233509 657231550 0.000000e+00 3145.0
10 TraesCS7B01G112600 chr4B 95.264 1985 74 9 567 2549 89561741 89563707 0.000000e+00 3127.0
11 TraesCS7B01G112600 chr4B 95.182 1951 82 6 569 2512 80653674 80651729 0.000000e+00 3072.0
12 TraesCS7B01G112600 chr2D 94.475 1991 89 15 566 2549 64508695 64510671 0.000000e+00 3048.0
13 TraesCS7B01G112600 chr6B 94.355 1984 97 10 567 2549 44370163 44368194 0.000000e+00 3029.0
14 TraesCS7B01G112600 chr3B 91.579 570 43 4 4 568 504705188 504705757 0.000000e+00 782.0
15 TraesCS7B01G112600 chr1A 91.009 545 38 9 32 568 423643035 423643576 0.000000e+00 725.0
16 TraesCS7B01G112600 chr1D 90.702 527 46 3 44 568 208065199 208064674 0.000000e+00 699.0
17 TraesCS7B01G112600 chr1D 89.943 527 49 4 44 568 228082107 228082631 0.000000e+00 676.0
18 TraesCS7B01G112600 chr1D 88.994 527 52 6 44 568 228281284 228281806 0.000000e+00 647.0
19 TraesCS7B01G112600 chr1D 94.872 39 2 0 4 42 208065263 208065225 7.610000e-06 62.1
20 TraesCS7B01G112600 chr1D 92.857 42 3 0 1 42 228281217 228281258 7.610000e-06 62.1
21 TraesCS7B01G112600 chr4A 88.750 560 52 8 12 563 122741117 122740561 0.000000e+00 675.0


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 TraesCS7B01G112600 chr7B 129567453 129570001 2548 True 4708.00 4708 100.0000 1 2549 1 chr7B.!!$R1 2548
1 TraesCS7B01G112600 chr7B 81247811 81249779 1968 False 3049.00 3049 94.5480 569 2549 1 chr7B.!!$F1 1980
2 TraesCS7B01G112600 chr2B 62450928 62452899 1971 False 3173.00 3173 95.6610 569 2549 1 chr2B.!!$F1 1980
3 TraesCS7B01G112600 chr2B 565226202 565228142 1940 True 3018.00 3018 94.6750 569 2519 1 chr2B.!!$R1 1950
4 TraesCS7B01G112600 chr2B 418933652 418934171 519 False 532.00 532 85.3110 44 568 1 chr2B.!!$F2 524
5 TraesCS7B01G112600 chr1B 639162510 639164488 1978 True 3166.00 3166 95.5160 566 2549 1 chr1B.!!$R1 1983
6 TraesCS7B01G112600 chr1B 327827535 327828061 526 False 656.00 656 89.2050 44 568 1 chr1B.!!$F1 524
7 TraesCS7B01G112600 chr1B 689374113 689374642 529 True 564.00 564 86.1420 44 568 1 chr1B.!!$R2 524
8 TraesCS7B01G112600 chr4B 648879459 648881435 1976 True 3153.00 3153 95.4110 567 2549 1 chr4B.!!$R2 1982
9 TraesCS7B01G112600 chr4B 657231550 657233509 1959 True 3145.00 3145 95.6260 566 2528 1 chr4B.!!$R3 1962
10 TraesCS7B01G112600 chr4B 89561741 89563707 1966 False 3127.00 3127 95.2640 567 2549 1 chr4B.!!$F1 1982
11 TraesCS7B01G112600 chr4B 80651729 80653674 1945 True 3072.00 3072 95.1820 569 2512 1 chr4B.!!$R1 1943
12 TraesCS7B01G112600 chr2D 64508695 64510671 1976 False 3048.00 3048 94.4750 566 2549 1 chr2D.!!$F1 1983
13 TraesCS7B01G112600 chr6B 44368194 44370163 1969 True 3029.00 3029 94.3550 567 2549 1 chr6B.!!$R1 1982
14 TraesCS7B01G112600 chr3B 504705188 504705757 569 False 782.00 782 91.5790 4 568 1 chr3B.!!$F1 564
15 TraesCS7B01G112600 chr1A 423643035 423643576 541 False 725.00 725 91.0090 32 568 1 chr1A.!!$F1 536
16 TraesCS7B01G112600 chr1D 228082107 228082631 524 False 676.00 676 89.9430 44 568 1 chr1D.!!$F1 524
17 TraesCS7B01G112600 chr1D 208064674 208065263 589 True 380.55 699 92.7870 4 568 2 chr1D.!!$R1 564
18 TraesCS7B01G112600 chr1D 228281217 228281806 589 False 354.55 647 90.9255 1 568 2 chr1D.!!$F2 567
19 TraesCS7B01G112600 chr4A 122740561 122741117 556 True 675.00 675 88.7500 12 563 1 chr4A.!!$R1 551

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
738 813 0.113776 TATAGGTGGGACTAGGCGGG 59.886 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2236 0.468226 AGGAAAACCACTCTCACGCA 59.532 50.0 0.0 0.0 0.0 5.24 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
184 244 7.025963 GTGATGTCATTTTCATTGTCTCCTTC 58.974 38.462 0.00 0.00 0.00 3.46
189 249 7.069826 TGTCATTTTCATTGTCTCCTTCCTTTT 59.930 33.333 0.00 0.00 0.00 2.27
239 309 7.106439 TGTTTTTATTTGTGTGTGAGACCAT 57.894 32.000 0.00 0.00 0.00 3.55
251 321 5.112686 GTGTGAGACCATGAGACTTATTCC 58.887 45.833 0.00 0.00 0.00 3.01
284 354 6.148948 GTGTGAGACATATGCTATCACTCTC 58.851 44.000 24.43 17.66 40.67 3.20
285 355 6.016360 GTGTGAGACATATGCTATCACTCTCT 60.016 42.308 24.43 10.35 40.67 3.10
340 411 4.037446 GTGAGTCTATTTGTTTTGTGCCCA 59.963 41.667 0.00 0.00 0.00 5.36
364 436 8.255905 CCATATCTTCATGCTCACATCTATGTA 58.744 37.037 0.00 0.00 39.39 2.29
546 621 8.092521 TGGGTTTGCATTTGTTAAATTACATG 57.907 30.769 0.00 0.00 0.00 3.21
564 639 0.950836 TGTCCTTGTGTGCAAATCCG 59.049 50.000 0.00 0.00 33.73 4.18
605 680 1.866015 CCCTCAGTGGTGTCCATCTA 58.134 55.000 0.00 0.00 35.28 1.98
655 730 1.351017 CTCAGTTTTGCCCCTAGTCCA 59.649 52.381 0.00 0.00 0.00 4.02
731 806 1.294068 TCAGCCCTTATAGGTGGGACT 59.706 52.381 10.57 5.62 46.15 3.85
738 813 0.113776 TATAGGTGGGACTAGGCGGG 59.886 60.000 0.00 0.00 0.00 6.13
767 842 5.418676 CGGCCAATTTTATTCAGACCATTT 58.581 37.500 2.24 0.00 0.00 2.32
866 941 2.279851 CAGTGACCACGGCGACAA 60.280 61.111 16.62 0.00 36.20 3.18
966 1045 3.774528 CTAGCTGTGGAGGGCGCA 61.775 66.667 10.83 0.00 0.00 6.09
1086 1168 3.896133 GTCTATCCGCGGTGCCGA 61.896 66.667 27.15 14.53 42.83 5.54
1170 1252 3.545703 CAGCGAGAATGGGGTAAGAATT 58.454 45.455 0.00 0.00 0.00 2.17
1209 1291 0.530744 CGTGGTCGGGATCTTTGAGA 59.469 55.000 0.00 0.00 0.00 3.27
1558 1640 5.128033 TGGAAAGGCATGAATTATGGAGA 57.872 39.130 0.00 0.00 37.26 3.71
1743 1831 4.963276 TGAATTATTCCAGAGCCAAACG 57.037 40.909 2.22 0.00 0.00 3.60
1758 1846 6.884836 AGAGCCAAACGATTAAGGTTAGAATT 59.115 34.615 0.00 0.00 0.00 2.17
1829 1917 9.787532 ATTCAAATACACCGTGATTTAAATCAG 57.212 29.630 27.26 19.68 45.38 2.90
2049 2137 0.799534 CGTTGGTAACCGCTAGGACG 60.800 60.000 0.00 0.00 41.02 4.79
2101 2189 7.943447 GGAAGGAAGGTATACATAGTGAGACTA 59.057 40.741 5.01 0.00 34.82 2.59
2146 2236 2.226437 GAGACCGTGAATGTTTGCACAT 59.774 45.455 0.00 0.00 46.34 3.21
2287 2377 4.760204 GTGTTAGAGTGGCACTTGGTTTAT 59.240 41.667 22.98 0.00 0.00 1.40
2328 2421 8.891671 AATTTGCATGTTAGTTCATGACTTTT 57.108 26.923 10.28 0.00 45.41 2.27
2364 2463 3.787001 GCTTCTCACCCCCTCCGG 61.787 72.222 0.00 0.00 0.00 5.14
2397 2496 2.325583 AAACCACAAGTTCTCGAGCA 57.674 45.000 7.81 0.00 37.88 4.26
2398 2497 2.325583 AACCACAAGTTCTCGAGCAA 57.674 45.000 7.81 0.05 30.99 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.867662 TGAAAGTTCTTCTTCTTCATCCAC 57.132 37.500 0.00 0.00 35.02 4.02
92 141 0.176910 GGCAGAGAGGTCACCTAAGC 59.823 60.000 0.00 0.00 31.76 3.09
101 150 1.215423 ACACCAAAAAGGCAGAGAGGT 59.785 47.619 0.00 0.00 43.14 3.85
184 244 4.104696 ACAACGAAGGTTCAACAAAAGG 57.895 40.909 0.00 0.00 32.98 3.11
189 249 2.088423 AGCAACAACGAAGGTTCAACA 58.912 42.857 0.00 0.00 32.98 3.33
314 384 5.458779 GGCACAAAACAAATAGACTCACAAC 59.541 40.000 0.00 0.00 0.00 3.32
364 436 3.689347 TGACACTAAGCATGGAAGCAAT 58.311 40.909 0.00 0.00 36.85 3.56
546 621 0.951558 ACGGATTTGCACACAAGGAC 59.048 50.000 0.00 0.00 37.04 3.85
564 639 6.553476 AGGGCAAAAGGATAATTAACCCATAC 59.447 38.462 8.09 0.00 37.28 2.39
605 680 2.787994 CATCTGAGGGCAAAACTGAGT 58.212 47.619 0.00 0.00 0.00 3.41
655 730 2.809601 GAACGAGTCGGTGCGCAT 60.810 61.111 15.91 0.00 0.00 4.73
713 788 2.158143 CCTAGTCCCACCTATAAGGGCT 60.158 54.545 0.00 0.00 45.07 5.19
738 813 2.687935 TGAATAAAATTGGCCGCCTCTC 59.312 45.455 11.61 0.00 0.00 3.20
866 941 1.837051 TGGTCAGGGTCGTGCTCTT 60.837 57.895 0.00 0.00 0.00 2.85
907 986 4.858680 GCTAGCTTCCCACCGCCC 62.859 72.222 7.70 0.00 0.00 6.13
966 1045 2.029073 CGGGATATCAACGCCGCT 59.971 61.111 4.83 0.00 0.00 5.52
977 1056 1.731700 CTCGAAGCCGAACGGGATA 59.268 57.895 15.01 0.00 45.04 2.59
1050 1132 0.803768 CGAAGACAGGCATCTCCACG 60.804 60.000 0.00 0.00 37.29 4.94
1086 1168 0.465097 CCCTCCGATCAATGCTTGCT 60.465 55.000 0.00 0.00 0.00 3.91
1089 1171 2.025887 AGAAACCCTCCGATCAATGCTT 60.026 45.455 0.00 0.00 0.00 3.91
1209 1291 2.819608 CACGGAACAGATCAACCCATTT 59.180 45.455 0.00 0.00 0.00 2.32
1417 1499 4.944317 CCTAACCTTCTTCTTCAACATCCC 59.056 45.833 0.00 0.00 0.00 3.85
1461 1543 5.022282 AGTATTTGCAAATGGGTATTGGC 57.978 39.130 30.43 11.38 42.50 4.52
1829 1917 6.366877 CACATTTTCCATGACATTTTGGTCTC 59.633 38.462 0.00 0.00 38.61 3.36
2049 2137 2.165030 CCATGTCAAACTCTTGCCATCC 59.835 50.000 0.00 0.00 28.75 3.51
2146 2236 0.468226 AGGAAAACCACTCTCACGCA 59.532 50.000 0.00 0.00 0.00 5.24
2287 2377 9.956640 ACATGCAAATTTATTCCCTTTAAATCA 57.043 25.926 0.00 0.00 30.79 2.57
2328 2421 2.962421 AGCCCTCCGTTTCATTCAAAAA 59.038 40.909 0.00 0.00 0.00 1.94
2397 2496 6.552008 TCTTCCCTAAACCAAGTCATGAATT 58.448 36.000 1.80 1.80 0.00 2.17
2398 2497 6.139679 TCTTCCCTAAACCAAGTCATGAAT 57.860 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.