Multiple sequence alignment - TraesCS1B01G214100

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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 TraesCS1B01G214100 chr1B 100.000 2585 0 0 1 2585 388871239 388868655 0.000000e+00 4774
1 TraesCS1B01G214100 chr1B 95.702 954 39 2 1633 2585 150324275 150323323 0.000000e+00 1533
2 TraesCS1B01G214100 chr1B 95.593 953 41 1 1633 2585 398421303 398422254 0.000000e+00 1526
3 TraesCS1B01G214100 chr1B 95.488 953 43 0 1633 2585 1586270 1585318 0.000000e+00 1522
4 TraesCS1B01G214100 chr1B 80.895 1162 215 7 428 1585 435755189 435754031 0.000000e+00 909
5 TraesCS1B01G214100 chrUn 93.650 1622 97 4 6 1625 286839151 286837534 0.000000e+00 2420
6 TraesCS1B01G214100 chrUn 93.588 1622 98 4 6 1625 286832941 286831324 0.000000e+00 2414
7 TraesCS1B01G214100 chrUn 93.557 1552 95 3 6 1555 310501468 310503016 0.000000e+00 2307
8 TraesCS1B01G214100 chr1D 90.386 1633 146 8 1 1625 231013977 231012348 0.000000e+00 2135
9 TraesCS1B01G214100 chr1D 85.695 1503 207 8 3 1501 361816958 361815460 0.000000e+00 1578
10 TraesCS1B01G214100 chr1D 85.320 1124 155 9 506 1625 361811357 361810240 0.000000e+00 1153
11 TraesCS1B01G214100 chr1D 84.816 461 69 1 5 465 361811809 361811350 1.810000e-126 462
12 TraesCS1B01G214100 chr5D 89.710 1623 165 2 1 1622 553049735 553048114 0.000000e+00 2071
13 TraesCS1B01G214100 chr2B 96.432 953 33 1 1633 2585 734731591 734730640 0.000000e+00 1570
14 TraesCS1B01G214100 chr2B 95.597 954 40 2 1633 2585 272687593 272686641 0.000000e+00 1528
15 TraesCS1B01G214100 chr7B 96.013 953 37 1 1633 2585 265201429 265202380 0.000000e+00 1548
16 TraesCS1B01G214100 chr7B 95.698 953 40 1 1633 2585 498610126 498611077 0.000000e+00 1531
17 TraesCS1B01G214100 chr7B 90.648 802 72 2 3 803 575437648 575438447 0.000000e+00 1062
18 TraesCS1B01G214100 chr7B 88.487 747 83 2 876 1622 575438446 575439189 0.000000e+00 900
19 TraesCS1B01G214100 chr6B 95.597 954 41 1 1633 2585 514095289 514096242 0.000000e+00 1528
20 TraesCS1B01G214100 chr6B 93.750 800 48 2 823 1622 320607201 320607998 0.000000e+00 1199
21 TraesCS1B01G214100 chr4B 95.593 953 41 1 1633 2585 100888688 100889639 0.000000e+00 1526


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 TraesCS1B01G214100 chr1B 388868655 388871239 2584 True 4774.000000 4774 100.0000 1 2585 1 chr1B.!!$R3 2584
1 TraesCS1B01G214100 chr1B 150323323 150324275 952 True 1533.000000 1533 95.7020 1633 2585 1 chr1B.!!$R2 952
2 TraesCS1B01G214100 chr1B 398421303 398422254 951 False 1526.000000 1526 95.5930 1633 2585 1 chr1B.!!$F1 952
3 TraesCS1B01G214100 chr1B 1585318 1586270 952 True 1522.000000 1522 95.4880 1633 2585 1 chr1B.!!$R1 952
4 TraesCS1B01G214100 chr1B 435754031 435755189 1158 True 909.000000 909 80.8950 428 1585 1 chr1B.!!$R4 1157
5 TraesCS1B01G214100 chrUn 286837534 286839151 1617 True 2420.000000 2420 93.6500 6 1625 1 chrUn.!!$R2 1619
6 TraesCS1B01G214100 chrUn 286831324 286832941 1617 True 2414.000000 2414 93.5880 6 1625 1 chrUn.!!$R1 1619
7 TraesCS1B01G214100 chrUn 310501468 310503016 1548 False 2307.000000 2307 93.5570 6 1555 1 chrUn.!!$F1 1549
8 TraesCS1B01G214100 chr1D 231012348 231013977 1629 True 2135.000000 2135 90.3860 1 1625 1 chr1D.!!$R1 1624
9 TraesCS1B01G214100 chr1D 361810240 361816958 6718 True 1064.333333 1578 85.2770 3 1625 3 chr1D.!!$R2 1622
10 TraesCS1B01G214100 chr5D 553048114 553049735 1621 True 2071.000000 2071 89.7100 1 1622 1 chr5D.!!$R1 1621
11 TraesCS1B01G214100 chr2B 734730640 734731591 951 True 1570.000000 1570 96.4320 1633 2585 1 chr2B.!!$R2 952
12 TraesCS1B01G214100 chr2B 272686641 272687593 952 True 1528.000000 1528 95.5970 1633 2585 1 chr2B.!!$R1 952
13 TraesCS1B01G214100 chr7B 265201429 265202380 951 False 1548.000000 1548 96.0130 1633 2585 1 chr7B.!!$F1 952
14 TraesCS1B01G214100 chr7B 498610126 498611077 951 False 1531.000000 1531 95.6980 1633 2585 1 chr7B.!!$F2 952
15 TraesCS1B01G214100 chr7B 575437648 575439189 1541 False 981.000000 1062 89.5675 3 1622 2 chr7B.!!$F3 1619
16 TraesCS1B01G214100 chr6B 514095289 514096242 953 False 1528.000000 1528 95.5970 1633 2585 1 chr6B.!!$F2 952
17 TraesCS1B01G214100 chr6B 320607201 320607998 797 False 1199.000000 1199 93.7500 823 1622 1 chr6B.!!$F1 799
18 TraesCS1B01G214100 chr4B 100888688 100889639 951 False 1526.000000 1526 95.5930 1633 2585 1 chr4B.!!$F1 952

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
787 790 0.920763 TCATCCCTCACAATGGGCCT 60.921 55.0 4.53 0.0 44.23 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 6738 4.080638 TGTGTCCACATGATTATGCTACCA 60.081 41.667 0.0 0.0 37.85 3.25 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
134 135 3.006967 TCCTACTTCTGACAGCAAGTTCC 59.993 47.826 18.92 0.00 34.60 3.62
139 140 1.620819 TCTGACAGCAAGTTCCCTCTC 59.379 52.381 0.00 0.00 0.00 3.20
302 303 4.956075 AGTTGTTCAAGTGGAAAGGAATGT 59.044 37.500 0.00 0.00 37.23 2.71
382 383 7.147549 CCAGAGTGTATTCCTTATCCAGGTTTA 60.148 40.741 0.00 0.00 44.37 2.01
559 560 1.923316 GCTGAAACAGTTGCTGAAGCG 60.923 52.381 2.26 0.00 37.58 4.68
572 573 3.314913 TGCTGAAGCGTTTCTGAATTCAA 59.685 39.130 20.21 0.00 45.83 2.69
648 649 7.214467 TCTTTACTAGCAAATTTTGGACTGG 57.786 36.000 10.96 5.22 0.00 4.00
656 657 6.600388 AGCAAATTTTGGACTGGGTTATTTT 58.400 32.000 10.96 0.00 0.00 1.82
712 713 1.209019 AGACATCCACAGTCAGATGGC 59.791 52.381 12.71 10.33 46.99 4.40
787 790 0.920763 TCATCCCTCACAATGGGCCT 60.921 55.000 4.53 0.00 44.23 5.19
920 6022 7.946219 TGCAATTGATGATACTATTCAATCCCT 59.054 33.333 10.34 0.00 38.73 4.20
949 6051 1.160137 GCAGTGGCTTTCAGATCGTT 58.840 50.000 0.00 0.00 36.96 3.85
1308 6416 2.632996 AGATCAGTTTCGGTGTCCTGAA 59.367 45.455 0.00 0.00 37.48 3.02
1333 6441 1.004080 ATGCAGCAGCGAGTTGTCT 60.004 52.632 0.00 0.00 46.23 3.41
1442 6550 3.275143 TGCAACAAAACTTTCCGAGAGA 58.725 40.909 0.00 0.00 0.00 3.10
1487 6595 2.059756 AAGGGAGGAGGGATTGTCAA 57.940 50.000 0.00 0.00 0.00 3.18
1622 6730 2.125912 CCAGAACGACAGCGAGGG 60.126 66.667 0.00 0.00 41.64 4.30
1625 6733 0.242825 CAGAACGACAGCGAGGGTAA 59.757 55.000 0.00 0.00 41.64 2.85
1626 6734 0.963962 AGAACGACAGCGAGGGTAAA 59.036 50.000 0.00 0.00 41.64 2.01
1627 6735 1.549170 AGAACGACAGCGAGGGTAAAT 59.451 47.619 0.00 0.00 41.64 1.40
1628 6736 2.756760 AGAACGACAGCGAGGGTAAATA 59.243 45.455 0.00 0.00 41.64 1.40
1629 6737 3.383825 AGAACGACAGCGAGGGTAAATAT 59.616 43.478 0.00 0.00 41.64 1.28
1630 6738 3.814005 ACGACAGCGAGGGTAAATATT 57.186 42.857 0.00 0.00 41.64 1.28
1631 6739 3.454375 ACGACAGCGAGGGTAAATATTG 58.546 45.455 0.00 0.00 41.64 1.90
1710 6818 4.744631 CCAACAAGCGCTTTTCTTTAATGT 59.255 37.500 22.51 10.08 0.00 2.71
2073 7183 7.059156 AGCATAGAAAATTTACTGCTCTCCAT 58.941 34.615 9.58 0.00 35.12 3.41
2477 7588 2.850833 TCTCATCAGAACTTGGGGGAT 58.149 47.619 0.00 0.00 0.00 3.85
2559 7670 9.812347 ATTAGCATCATGGGTATTCAAAGAATA 57.188 29.630 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 2.125773 AGAATGCCAGCTTTGAGAGG 57.874 50.000 0.00 0.00 0.00 3.69
139 140 1.536766 TGTCGAAGAATGCCAGCTTTG 59.463 47.619 0.00 0.00 39.69 2.77
302 303 8.698973 TTGACATAAGTTTTGATAAACCCTCA 57.301 30.769 0.00 0.00 43.77 3.86
382 383 0.543749 GTATTGGCAGAGGCTGGAGT 59.456 55.000 0.00 0.00 40.87 3.85
454 455 2.015736 AGCAATTGTAGCGACCAGAG 57.984 50.000 7.40 0.00 37.01 3.35
572 573 6.668283 AGAGGCATACCGTGGAGTTTATATAT 59.332 38.462 0.00 0.00 42.76 0.86
648 649 9.668497 ACATAACTCCAGACTTCTAAAATAACC 57.332 33.333 0.00 0.00 0.00 2.85
656 657 4.219944 ACGCAACATAACTCCAGACTTCTA 59.780 41.667 0.00 0.00 0.00 2.10
712 713 0.165944 GATTGACACGCTCCGTTTGG 59.834 55.000 0.00 0.00 38.32 3.28
787 790 4.974645 ACTCACACAAGGAAATCCACTA 57.025 40.909 1.67 0.00 38.89 2.74
920 6022 4.701663 GCCACTGCTGCAAGTCTA 57.298 55.556 3.02 0.00 35.30 2.59
949 6051 3.516586 TGACTGAATCCAGGACCACTTA 58.483 45.455 0.00 0.00 44.60 2.24
1098 6201 0.731174 GTTTATGGTTTGCACGCGGG 60.731 55.000 12.47 7.92 0.00 6.13
1308 6416 0.810426 CTCGCTGCTGCATGATCTGT 60.810 55.000 16.29 0.00 39.64 3.41
1333 6441 2.626780 CCGAGTCAGAGCCACGACA 61.627 63.158 0.00 0.00 34.48 4.35
1396 6504 4.441634 CGTCACCTTATCTTCCCAAGTAGG 60.442 50.000 0.00 0.00 37.03 3.18
1442 6550 4.994756 CTTGCCCCCAAGCCGGTT 62.995 66.667 1.90 0.00 41.72 4.44
1487 6595 0.106569 TTGGCGCCCATCTTGATCAT 60.107 50.000 26.77 0.00 31.53 2.45
1625 6733 7.944000 TGTCCACATGATTATGCTACCAATATT 59.056 33.333 0.00 0.00 37.85 1.28
1626 6734 7.391554 GTGTCCACATGATTATGCTACCAATAT 59.608 37.037 0.00 0.00 37.85 1.28
1627 6735 6.710295 GTGTCCACATGATTATGCTACCAATA 59.290 38.462 0.00 0.00 37.85 1.90
1628 6736 5.532406 GTGTCCACATGATTATGCTACCAAT 59.468 40.000 0.00 0.00 37.85 3.16
1629 6737 4.881273 GTGTCCACATGATTATGCTACCAA 59.119 41.667 0.00 0.00 37.85 3.67
1630 6738 4.080638 TGTGTCCACATGATTATGCTACCA 60.081 41.667 0.00 0.00 37.85 3.25
1631 6739 4.273480 GTGTGTCCACATGATTATGCTACC 59.727 45.833 0.00 0.00 43.97 3.18
1661 6769 8.392372 GAGACAATCCAATATTTACCCTTACC 57.608 38.462 0.00 0.00 0.00 2.85
1710 6818 5.541484 TCATCATCATGCCTAGCTAGAAAGA 59.459 40.000 22.70 13.69 0.00 2.52
2015 7125 6.312399 TGAAAAGAATGCTTTACGTGATGT 57.688 33.333 0.00 0.00 43.32 3.06
2065 7175 8.164058 AGAAGAAATTTGCTTATATGGAGAGC 57.836 34.615 0.00 0.00 36.95 4.09
2343 7453 5.269554 TCCCACTATTTTGGAGGATGTTT 57.730 39.130 0.00 0.00 39.24 2.83
2465 7576 7.725844 AGATGATATGTTTAATCCCCCAAGTTC 59.274 37.037 0.00 0.00 0.00 3.01
2559 7670 7.354025 CATGATTGCAATGTTGTTGTTATGT 57.646 32.000 18.59 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.