Multiple sequence alignment - TraesCS1B01G061300

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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 TraesCS1B01G061300 chr1B 100.000 4379 0 0 1 4379 46059119 46063497 0.000000e+00 8087
1 TraesCS1B01G061300 chr1B 99.500 2599 11 1 1 2599 46000212 46002808 0.000000e+00 4726
2 TraesCS1B01G061300 chr1B 98.661 1792 17 5 2594 4379 46002844 46004634 0.000000e+00 3169
3 TraesCS1B01G061300 chr1B 94.643 392 19 2 3988 4379 4586080 4585691 1.350000e-169 606
4 TraesCS1B01G061300 chr1B 72.881 767 157 38 2256 2995 46549411 46550153 2.650000e-52 217
5 TraesCS1B01G061300 chr4D 87.144 1859 137 46 533 2356 4488333 4490124 0.000000e+00 2015
6 TraesCS1B01G061300 chr4D 92.437 1071 63 11 2594 3656 4490431 4491491 0.000000e+00 1513
7 TraesCS1B01G061300 chr4D 91.954 261 20 1 2340 2599 4490135 4490395 8.950000e-97 364
8 TraesCS1B01G061300 chr4D 72.761 547 96 33 982 1516 4471997 4472502 7.640000e-28 135
9 TraesCS1B01G061300 chr4A 91.607 1406 87 15 2595 3993 598779353 598777972 0.000000e+00 1914
10 TraesCS1B01G061300 chr4A 86.089 1409 131 32 141 1534 598782360 598781002 0.000000e+00 1456
11 TraesCS1B01G061300 chr4A 97.606 376 9 0 3988 4363 700529898 700529523 0.000000e+00 645
12 TraesCS1B01G061300 chr4A 87.523 545 44 14 1555 2090 598780546 598780017 3.740000e-170 608
13 TraesCS1B01G061300 chr4A 94.643 392 20 1 3988 4379 726321305 726320915 1.350000e-169 606
14 TraesCS1B01G061300 chr4A 93.511 262 14 3 2340 2599 598779650 598779390 1.910000e-103 387
15 TraesCS1B01G061300 chr4A 90.661 257 20 3 2103 2356 598779915 598779660 5.420000e-89 339
16 TraesCS1B01G061300 chr4B 88.995 1463 116 25 1161 2599 7463004 7464445 0.000000e+00 1768
17 TraesCS1B01G061300 chr4B 88.995 1463 116 25 1161 2599 7476842 7478283 0.000000e+00 1768
18 TraesCS1B01G061300 chr4B 86.341 1413 151 16 2594 3983 7478319 7479712 0.000000e+00 1502
19 TraesCS1B01G061300 chr4B 86.270 1413 152 16 2594 3983 7464481 7465874 0.000000e+00 1496
20 TraesCS1B01G061300 chr4B 88.816 760 67 15 354 1101 7462246 7462999 0.000000e+00 917
21 TraesCS1B01G061300 chr4B 94.898 392 20 0 3988 4379 649631398 649631789 8.050000e-172 614
22 TraesCS1B01G061300 chr4B 94.430 395 19 2 3988 4379 2697105 2697499 4.840000e-169 604
23 TraesCS1B01G061300 chr4B 89.372 414 36 5 694 1101 7476426 7476837 8.400000e-142 514
24 TraesCS1B01G061300 chr4B 90.057 352 28 6 354 702 7475896 7476243 2.400000e-122 449
25 TraesCS1B01G061300 chr7B 94.643 392 20 1 3988 4379 49614465 49614855 1.350000e-169 606
26 TraesCS1B01G061300 chr6D 94.643 392 20 1 3988 4379 97856984 97857374 1.350000e-169 606
27 TraesCS1B01G061300 chr7D 94.388 392 22 0 3988 4379 18723073 18723464 1.740000e-168 603


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 TraesCS1B01G061300 chr1B 46059119 46063497 4378 False 8087.000000 8087 100.000000 1 4379 1 chr1B.!!$F1 4378
1 TraesCS1B01G061300 chr1B 46000212 46004634 4422 False 3947.500000 4726 99.080500 1 4379 2 chr1B.!!$F3 4378
2 TraesCS1B01G061300 chr1B 46549411 46550153 742 False 217.000000 217 72.881000 2256 2995 1 chr1B.!!$F2 739
3 TraesCS1B01G061300 chr4D 4488333 4491491 3158 False 1297.333333 2015 90.511667 533 3656 3 chr4D.!!$F2 3123
4 TraesCS1B01G061300 chr4A 598777972 598782360 4388 True 940.800000 1914 89.878200 141 3993 5 chr4A.!!$R3 3852
5 TraesCS1B01G061300 chr4B 7462246 7465874 3628 False 1393.666667 1768 88.027000 354 3983 3 chr4B.!!$F3 3629
6 TraesCS1B01G061300 chr4B 7475896 7479712 3816 False 1058.250000 1768 88.691250 354 3983 4 chr4B.!!$F4 3629

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
93 94 0.679321 TCACAGTGTTTGGTGCTGCA 60.679 50.000 0.00 0.0 35.04 4.41 F
103 104 3.357079 GTGCTGCAGGTGGGTTCG 61.357 66.667 17.12 0.0 0.00 3.95 F
1175 1405 0.179037 GCTGGCTGGCTGATATGACA 60.179 55.000 12.22 0.0 0.00 3.58 F
1222 1452 0.629596 TCTAGGGTCTGGTGGACGAT 59.370 55.000 0.00 0.0 45.35 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 1405 0.817013 CCATGTACGCCAAGGCAAAT 59.183 50.000 12.19 0.0 42.06 2.32 R
1444 1677 2.050350 CACCTCGGGCTCGTTCCTA 61.050 63.158 5.57 0.0 37.69 2.94 R
2872 3728 3.382227 TCGTAGAACTGAAACCTGACACA 59.618 43.478 0.00 0.0 0.00 3.72 R
3682 4560 1.421646 GAGAGAGAGAGAGAGAGGGGG 59.578 61.905 0.00 0.0 0.00 5.40 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
76 77 3.717707 CCGTGAAAAGTGTCTCTTCTCA 58.282 45.455 0.00 0.00 35.02 3.27
93 94 0.679321 TCACAGTGTTTGGTGCTGCA 60.679 50.000 0.00 0.00 35.04 4.41
103 104 3.357079 GTGCTGCAGGTGGGTTCG 61.357 66.667 17.12 0.00 0.00 3.95
729 925 5.178252 CAGAAGAGTACTCCACACACAAATG 59.822 44.000 19.38 3.19 0.00 2.32
1175 1405 0.179037 GCTGGCTGGCTGATATGACA 60.179 55.000 12.22 0.00 0.00 3.58
1222 1452 0.629596 TCTAGGGTCTGGTGGACGAT 59.370 55.000 0.00 0.00 45.35 3.73
1444 1677 2.616634 ATGCTCTGAGATTCGCATGT 57.383 45.000 9.28 0.00 41.17 3.21
2754 3608 5.955355 ACTTTAGTCTGAGATGGCTAGAGTT 59.045 40.000 0.00 0.00 28.55 3.01
2872 3728 0.893447 GTACCTCACGGCACTAGGTT 59.107 55.000 6.93 0.00 40.82 3.50
3669 4541 3.323403 CCTCTCTCTCTCTCTCTCTCTCC 59.677 56.522 0.00 0.00 0.00 3.71
3673 4551 2.370189 CTCTCTCTCTCTCTCTCCCTCC 59.630 59.091 0.00 0.00 0.00 4.30
3674 4552 1.421646 CTCTCTCTCTCTCTCCCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
3675 4553 1.010793 TCTCTCTCTCTCTCCCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
3676 4554 1.421646 CTCTCTCTCTCTCCCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
3677 4555 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
3678 4556 0.996762 TCTCTCTCTCCCTCCCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
3679 4557 0.998945 CTCTCTCTCCCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
3680 4558 0.996762 TCTCTCTCCCTCCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
3681 4559 2.015726 TCTCTCCCTCCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
3682 4560 3.036959 TCTCCCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
3683 4561 4.179599 CTCCCTCCCTCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
3706 4600 3.555795 CCCTCTCTCTCTCTCTCTCATCG 60.556 56.522 0.00 0.00 0.00 3.84
3727 4621 0.460987 GAGAGATGTTGGTGCCTCCG 60.461 60.000 0.00 0.00 39.52 4.63
3969 4881 1.451028 GGAGATCAGTGTGGCAGCC 60.451 63.158 3.66 3.66 0.00 4.85
4018 4930 7.823665 AGTTGTGTCGAATATAGTGTACAAGA 58.176 34.615 0.00 0.00 0.00 3.02
4128 5040 1.696063 TATAGCGGGGGTAGACACAC 58.304 55.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.386525 CCTGCAGCACCAAACACTGT 61.387 55.000 8.66 0.0 33.87 3.55
103 104 9.988350 AAAACATATGATTTTCATCGTGTCTAC 57.012 29.630 10.38 0.0 38.26 2.59
729 925 1.203065 CGCCGTCCCGTAAAGAATAC 58.797 55.000 0.00 0.0 0.00 1.89
1175 1405 0.817013 CCATGTACGCCAAGGCAAAT 59.183 50.000 12.19 0.0 42.06 2.32
1444 1677 2.050350 CACCTCGGGCTCGTTCCTA 61.050 63.158 5.57 0.0 37.69 2.94
2872 3728 3.382227 TCGTAGAACTGAAACCTGACACA 59.618 43.478 0.00 0.0 0.00 3.72
3682 4560 1.421646 GAGAGAGAGAGAGAGAGGGGG 59.578 61.905 0.00 0.0 0.00 5.40
3683 4561 2.126882 TGAGAGAGAGAGAGAGAGGGG 58.873 57.143 0.00 0.0 0.00 4.79
3684 4562 3.555795 CGATGAGAGAGAGAGAGAGAGGG 60.556 56.522 0.00 0.0 0.00 4.30
3685 4563 3.070159 ACGATGAGAGAGAGAGAGAGAGG 59.930 52.174 0.00 0.0 0.00 3.69
3706 4600 1.677217 GGAGGCACCAACATCTCTCAC 60.677 57.143 0.00 0.0 38.79 3.51
3727 4621 7.658261 AGCACTTATTTACCCTTTCTCAAAAC 58.342 34.615 0.00 0.0 0.00 2.43
3969 4881 7.601508 ACTCTAACACCCAGAAACGTTATTTAG 59.398 37.037 0.00 0.0 0.00 1.85
4018 4930 6.930068 ACTACAAGTCCAACTGTAACCTAT 57.070 37.500 0.00 0.0 0.00 2.57
4128 5040 2.238942 TGCTGGCATAGGTTACATCG 57.761 50.000 0.00 0.0 0.00 3.84


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

AutoCloner maintained by Alex Coulton.