Multiple sequence alignment - TraesCS5B01G070800

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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 TraesCS5B01G070800 chr5B 100.000 2549 0 0 1 2549 81902098 81904646 0.000000e+00 4708.0
1 TraesCS5B01G070800 chr5B 96.774 1705 49 5 569 2270 682395996 682394295 0.000000e+00 2839.0
2 TraesCS5B01G070800 chr5B 93.403 576 30 4 1 568 367521361 367520786 0.000000e+00 846.0
3 TraesCS5B01G070800 chr1B 96.696 1846 50 10 561 2400 307939696 307941536 0.000000e+00 3061.0
4 TraesCS5B01G070800 chr1B 96.730 1835 53 6 569 2400 616703966 616702136 0.000000e+00 3049.0
5 TraesCS5B01G070800 chr1B 95.439 1754 70 7 561 2309 561526121 561527869 0.000000e+00 2787.0
6 TraesCS5B01G070800 chr1B 95.421 1747 69 7 569 2309 581717561 581715820 0.000000e+00 2772.0
7 TraesCS5B01G070800 chr1B 98.462 130 2 0 2420 2549 307941653 307941782 1.970000e-56 230.0
8 TraesCS5B01G070800 chr1B 98.462 130 2 0 2420 2549 616702017 616701888 1.970000e-56 230.0
9 TraesCS5B01G070800 chr1B 100.000 95 0 0 2306 2400 561527935 561528029 2.610000e-40 176.0
10 TraesCS5B01G070800 chr2B 96.432 1850 56 9 558 2400 776161400 776163246 0.000000e+00 3042.0
11 TraesCS5B01G070800 chr2B 94.077 574 27 6 1 568 228097170 228097742 0.000000e+00 865.0
12 TraesCS5B01G070800 chr2B 98.462 130 0 1 2420 2549 282317512 282317639 7.090000e-56 228.0
13 TraesCS5B01G070800 chr2B 98.462 130 0 1 2420 2549 492638686 492638813 7.090000e-56 228.0
14 TraesCS5B01G070800 chr2B 90.110 91 8 1 437 526 57632639 57632729 1.600000e-22 117.0
15 TraesCS5B01G070800 chr2B 100.000 28 0 0 526 553 57632746 57632773 5.000000e-03 52.8
16 TraesCS5B01G070800 chr7B 95.363 1747 69 9 569 2309 720989190 720987450 0.000000e+00 2767.0
17 TraesCS5B01G070800 chr7B 100.000 95 0 0 2306 2400 734147078 734147172 2.610000e-40 176.0
18 TraesCS5B01G070800 chr3B 95.361 1746 71 6 569 2309 108092312 108090572 0.000000e+00 2767.0
19 TraesCS5B01G070800 chr3B 95.301 1745 74 5 569 2309 46395680 46393940 0.000000e+00 2761.0
20 TraesCS5B01G070800 chr3B 87.432 366 35 9 1 357 552954060 552954423 6.560000e-111 411.0
21 TraesCS5B01G070800 chr3B 98.462 130 0 1 2420 2549 108090294 108090167 7.090000e-56 228.0
22 TraesCS5B01G070800 chr3B 98.462 130 0 1 2420 2549 722336714 722336841 7.090000e-56 228.0
23 TraesCS5B01G070800 chr3B 100.000 95 0 0 2306 2400 19703045 19703139 2.610000e-40 176.0
24 TraesCS5B01G070800 chr3B 97.297 74 2 0 352 425 552954523 552954596 2.660000e-25 126.0
25 TraesCS5B01G070800 chr6B 86.924 543 52 10 1 526 332985821 332986361 2.180000e-165 592.0
26 TraesCS5B01G070800 chr6B 100.000 130 0 0 2420 2549 271093839 271093710 9.110000e-60 241.0
27 TraesCS5B01G070800 chr6B 98.462 130 0 1 2420 2549 658365407 658365280 7.090000e-56 228.0
28 TraesCS5B01G070800 chr2A 86.630 546 51 11 1 526 176310215 176310758 3.650000e-163 584.0
29 TraesCS5B01G070800 chr2A 86.322 541 47 12 1 529 357252180 357251655 4.760000e-157 564.0
30 TraesCS5B01G070800 chr7A 86.364 550 52 12 1 529 424919606 424919059 1.700000e-161 579.0
31 TraesCS5B01G070800 chr2D 86.339 549 54 10 1 529 213494150 213493603 1.700000e-161 579.0
32 TraesCS5B01G070800 chr2D 98.947 95 1 0 2306 2400 610932261 610932355 1.210000e-38 171.0
33 TraesCS5B01G070800 chr6A 98.462 130 0 1 2420 2549 30120029 30119902 7.090000e-56 228.0
34 TraesCS5B01G070800 chr4A 100.000 95 0 0 2306 2400 610780018 610779924 2.610000e-40 176.0
35 TraesCS5B01G070800 chrUn 98.947 95 1 0 2306 2400 60560344 60560438 1.210000e-38 171.0
36 TraesCS5B01G070800 chr6D 91.429 70 6 0 164 233 46228669 46228738 2.090000e-16 97.1


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 TraesCS5B01G070800 chr5B 81902098 81904646 2548 False 4708.0 4708 100.0000 1 2549 1 chr5B.!!$F1 2548
1 TraesCS5B01G070800 chr5B 682394295 682395996 1701 True 2839.0 2839 96.7740 569 2270 1 chr5B.!!$R2 1701
2 TraesCS5B01G070800 chr5B 367520786 367521361 575 True 846.0 846 93.4030 1 568 1 chr5B.!!$R1 567
3 TraesCS5B01G070800 chr1B 581715820 581717561 1741 True 2772.0 2772 95.4210 569 2309 1 chr1B.!!$R1 1740
4 TraesCS5B01G070800 chr1B 307939696 307941782 2086 False 1645.5 3061 97.5790 561 2549 2 chr1B.!!$F1 1988
5 TraesCS5B01G070800 chr1B 616701888 616703966 2078 True 1639.5 3049 97.5960 569 2549 2 chr1B.!!$R2 1980
6 TraesCS5B01G070800 chr1B 561526121 561528029 1908 False 1481.5 2787 97.7195 561 2400 2 chr1B.!!$F2 1839
7 TraesCS5B01G070800 chr2B 776161400 776163246 1846 False 3042.0 3042 96.4320 558 2400 1 chr2B.!!$F4 1842
8 TraesCS5B01G070800 chr2B 228097170 228097742 572 False 865.0 865 94.0770 1 568 1 chr2B.!!$F1 567
9 TraesCS5B01G070800 chr7B 720987450 720989190 1740 True 2767.0 2767 95.3630 569 2309 1 chr7B.!!$R1 1740
10 TraesCS5B01G070800 chr3B 46393940 46395680 1740 True 2761.0 2761 95.3010 569 2309 1 chr3B.!!$R1 1740
11 TraesCS5B01G070800 chr3B 108090167 108092312 2145 True 1497.5 2767 96.9115 569 2549 2 chr3B.!!$R2 1980
12 TraesCS5B01G070800 chr3B 552954060 552954596 536 False 268.5 411 92.3645 1 425 2 chr3B.!!$F3 424
13 TraesCS5B01G070800 chr6B 332985821 332986361 540 False 592.0 592 86.9240 1 526 1 chr6B.!!$F1 525
14 TraesCS5B01G070800 chr2A 176310215 176310758 543 False 584.0 584 86.6300 1 526 1 chr2A.!!$F1 525
15 TraesCS5B01G070800 chr2A 357251655 357252180 525 True 564.0 564 86.3220 1 529 1 chr2A.!!$R1 528
16 TraesCS5B01G070800 chr7A 424919059 424919606 547 True 579.0 579 86.3640 1 529 1 chr7A.!!$R1 528
17 TraesCS5B01G070800 chr2D 213493603 213494150 547 True 579.0 579 86.3390 1 529 1 chr2D.!!$R1 528

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
398 534 0.537188 AGCCGATCGAGTTGGACAAT 59.463 50.0 18.66 0.0 32.46 2.71 F
1079 1227 0.738975 CCTATCTTCGTCTGTCCGCA 59.261 55.0 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1380 1528 1.287730 CTCTGTCAGTGCGTGCTTCC 61.288 60.000 0.00 0.0 0.00 3.46 R
2404 2637 3.781079 GCATATGGCAGTGCAAACTAA 57.219 42.857 18.61 0.0 43.97 2.24 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
262 275 2.902423 TTTGGCCACGTGACCAGCTT 62.902 55.000 23.10 0.0 37.24 3.74
398 534 0.537188 AGCCGATCGAGTTGGACAAT 59.463 50.000 18.66 0.0 32.46 2.71
506 652 1.305930 ACGCTCGCCAGAAAAATCCC 61.306 55.000 0.00 0.0 0.00 3.85
617 763 1.881973 GTCCATCTGCTCAGTTTTGCA 59.118 47.619 0.00 0.0 37.63 4.08
618 764 2.294233 GTCCATCTGCTCAGTTTTGCAA 59.706 45.455 0.00 0.0 38.81 4.08
671 817 3.545481 CATGCGCACCGACTCGTC 61.545 66.667 14.90 0.0 0.00 4.20
684 830 2.798499 CGACTCGTCCTGTGAACTTTGT 60.798 50.000 0.00 0.0 0.00 2.83
935 1083 2.601194 GAAGCTAGCTGTGGAGGGCC 62.601 65.000 20.16 0.0 0.00 5.80
1079 1227 0.738975 CCTATCTTCGTCTGTCCGCA 59.261 55.000 0.00 0.0 0.00 5.69
1100 1248 4.812476 CCGGGCGAGCGTTGATCA 62.812 66.667 0.00 0.0 0.00 2.92
1119 1267 1.140852 CAGAGGGTTTCTCACACACCA 59.859 52.381 0.00 0.0 44.81 4.17
1133 1281 2.305928 CACACCAAGGAACCACAATCA 58.694 47.619 0.00 0.0 0.00 2.57
1149 1297 2.579207 ATCATCCGTTCTACGTGTGG 57.421 50.000 0.00 0.0 40.58 4.17
1174 1322 2.704065 GAGAATGGGGTAAGAATCGGGA 59.296 50.000 0.00 0.0 0.00 5.14
1380 1528 1.767681 CTGGAAGAAGAGATGGAGGGG 59.232 57.143 0.00 0.0 34.07 4.79
1514 1662 3.738830 TGTAGGTATGGTAATCGCACC 57.261 47.619 0.00 0.0 39.20 5.01
1965 2122 4.703379 AAAATGAAGGGTGGAAAATGCA 57.297 36.364 0.00 0.0 0.00 3.96
2024 2183 3.959975 CGCGTGGGTTTGTGGTGG 61.960 66.667 0.00 0.0 0.00 4.61
2107 2266 8.465273 AGCAATGTATACATAGTGAGACTGTA 57.535 34.615 18.56 0.0 35.10 2.74
2259 2422 1.339727 ACATGGGTAGGGAAGAAACGC 60.340 52.381 0.00 0.0 0.00 4.84
2265 2428 2.934553 GGTAGGGAAGAAACGCATACAC 59.065 50.000 0.00 0.0 0.00 2.90
2416 2649 9.567848 AACGGAATAATAAATTAGTTTGCACTG 57.432 29.630 0.00 0.0 34.06 3.66
2417 2650 7.700656 ACGGAATAATAAATTAGTTTGCACTGC 59.299 33.333 0.00 0.0 34.06 4.40
2418 2651 7.167468 CGGAATAATAAATTAGTTTGCACTGCC 59.833 37.037 0.00 0.0 34.06 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 3.322466 CCTCACTCCGGGTTGCCT 61.322 66.667 0.00 0.00 0.00 4.75
238 251 2.112297 TCACGTGGCCAAACCTCC 59.888 61.111 17.00 0.00 40.22 4.30
262 275 0.618458 AATCAGCTACCGGCCAAAGA 59.382 50.000 0.00 0.00 43.05 2.52
438 582 4.748892 AGATCGACAGAATCATCGTTGTT 58.251 39.130 6.79 0.00 39.38 2.83
466 610 3.565764 TCAGAGATTTGAATCGCCCAT 57.434 42.857 4.21 0.00 40.35 4.00
506 652 6.576662 ATGTTCGTATCTACTGGAGGTATG 57.423 41.667 0.00 0.00 0.00 2.39
579 725 2.488347 GGACACCACTAAGGGCAAAAGA 60.488 50.000 0.00 0.00 43.89 2.52
671 817 2.135933 GGAGACGACAAAGTTCACAGG 58.864 52.381 0.00 0.00 0.00 4.00
935 1083 4.530857 CTAGCTTCCCACCGCCGG 62.531 72.222 0.00 0.00 0.00 6.13
1100 1248 1.507140 TGGTGTGTGAGAAACCCTCT 58.493 50.000 0.00 0.00 42.44 3.69
1119 1267 2.879103 ACGGATGATTGTGGTTCCTT 57.121 45.000 0.00 0.00 0.00 3.36
1149 1297 2.981859 TTCTTACCCCATTCTCGCTC 57.018 50.000 0.00 0.00 0.00 5.03
1174 1322 2.753296 CCACGAAAATGGTGCAATTGT 58.247 42.857 7.40 0.00 34.77 2.71
1380 1528 1.287730 CTCTGTCAGTGCGTGCTTCC 61.288 60.000 0.00 0.00 0.00 3.46
1514 1662 7.309177 TCCATACATTTTCAACATTACAACCG 58.691 34.615 0.00 0.00 0.00 4.44
1815 1971 8.977505 CATTTTGGTCTTTGATTTAAATCACGT 58.022 29.630 26.69 4.71 44.54 4.49
2168 2329 3.868985 ACCCACGCGGTCTTGGTT 61.869 61.111 12.47 0.00 43.58 3.67
2400 2633 6.272318 GCATATGGCAGTGCAAACTAATTTA 58.728 36.000 18.61 0.00 43.97 1.40
2401 2634 5.111293 GCATATGGCAGTGCAAACTAATTT 58.889 37.500 18.61 0.00 43.97 1.82
2402 2635 4.685924 GCATATGGCAGTGCAAACTAATT 58.314 39.130 18.61 0.00 43.97 1.40
2403 2636 4.311816 GCATATGGCAGTGCAAACTAAT 57.688 40.909 18.61 2.97 43.97 1.73
2404 2637 3.781079 GCATATGGCAGTGCAAACTAA 57.219 42.857 18.61 0.00 43.97 2.24


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

AutoCloner maintained by Alex Coulton.