Multiple sequence alignment - TraesCS4A01G198300

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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 TraesCS4A01G198300 chr4A 100.000 3076 0 0 1 3076 483952403 483949328 0.000000e+00 5681.0
1 TraesCS4A01G198300 chr4A 90.476 231 13 4 847 1077 373804806 373805027 2.320000e-76 296.0
2 TraesCS4A01G198300 chr4A 90.476 231 13 4 847 1077 606355196 606355417 2.320000e-76 296.0
3 TraesCS4A01G198300 chr4A 95.833 168 7 0 492 659 624286536 624286703 3.910000e-69 272.0
4 TraesCS4A01G198300 chr4A 89.535 86 7 2 752 837 738713424 738713507 1.170000e-19 108.0
5 TraesCS4A01G198300 chr4A 100.000 30 0 0 2221 2250 108193047 108193018 4.280000e-04 56.5
6 TraesCS4A01G198300 chr4D 96.153 3093 57 16 1 3076 95780104 95783151 0.000000e+00 4996.0
7 TraesCS4A01G198300 chr4B 96.078 2805 75 12 274 3075 135210689 135213461 0.000000e+00 4538.0
8 TraesCS4A01G198300 chr4B 98.305 236 4 0 1 236 135210458 135210693 6.140000e-112 414.0
9 TraesCS4A01G198300 chr4B 94.118 170 8 1 492 659 211593425 211593256 1.090000e-64 257.0
10 TraesCS4A01G198300 chr4B 94.118 170 8 1 492 659 286753629 286753460 1.090000e-64 257.0
11 TraesCS4A01G198300 chr2A 79.192 817 102 41 842 1637 706995025 706995794 3.540000e-139 505.0
12 TraesCS4A01G198300 chr2A 79.412 340 62 7 1093 1428 645311418 645311753 1.840000e-57 233.0
13 TraesCS4A01G198300 chr5D 82.616 604 72 20 841 1428 214919830 214919244 1.270000e-138 503.0
14 TraesCS4A01G198300 chr5A 82.529 601 73 21 841 1428 282588085 282587504 1.650000e-137 499.0
15 TraesCS4A01G198300 chr5A 90.476 231 13 3 847 1077 598933355 598933576 2.320000e-76 296.0
16 TraesCS4A01G198300 chr5A 87.591 137 10 4 455 590 282588399 282588269 5.310000e-33 152.0
17 TraesCS4A01G198300 chr5B 87.558 434 45 4 1001 1428 230248524 230248094 7.660000e-136 494.0
18 TraesCS4A01G198300 chr5B 94.118 170 8 1 492 659 36727182 36727351 1.090000e-64 257.0
19 TraesCS4A01G198300 chr2D 81.653 605 80 23 842 1428 567477118 567477709 9.980000e-130 473.0
20 TraesCS4A01G198300 chr2B 86.437 435 48 7 1001 1428 680193945 680194375 1.670000e-127 466.0
21 TraesCS4A01G198300 chr2B 93.023 86 4 2 752 837 141003017 141003100 1.160000e-24 124.0
22 TraesCS4A01G198300 chr1D 95.000 220 10 1 525 744 12646754 12646536 8.170000e-91 344.0
23 TraesCS4A01G198300 chr1D 91.860 86 5 2 752 837 185107795 185107878 5.390000e-23 119.0
24 TraesCS4A01G198300 chr7D 90.948 232 12 2 847 1078 548559393 548559615 1.390000e-78 303.0
25 TraesCS4A01G198300 chr6B 90.948 232 11 4 847 1077 60485158 60484936 1.390000e-78 303.0
26 TraesCS4A01G198300 chr1B 90.476 231 13 4 847 1077 258836430 258836651 2.320000e-76 296.0
27 TraesCS4A01G198300 chr7B 90.043 231 14 3 847 1077 178408941 178408720 1.080000e-74 291.0
28 TraesCS4A01G198300 chr7A 94.706 170 7 1 492 659 169392764 169392933 2.350000e-66 263.0
29 TraesCS4A01G198300 chr3B 94.706 170 7 1 492 659 327795860 327795691 2.350000e-66 263.0


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 TraesCS4A01G198300 chr4A 483949328 483952403 3075 True 5681.0 5681 100.0000 1 3076 1 chr4A.!!$R2 3075
1 TraesCS4A01G198300 chr4D 95780104 95783151 3047 False 4996.0 4996 96.1530 1 3076 1 chr4D.!!$F1 3075
2 TraesCS4A01G198300 chr4B 135210458 135213461 3003 False 2476.0 4538 97.1915 1 3075 2 chr4B.!!$F1 3074
3 TraesCS4A01G198300 chr2A 706995025 706995794 769 False 505.0 505 79.1920 842 1637 1 chr2A.!!$F2 795
4 TraesCS4A01G198300 chr5D 214919244 214919830 586 True 503.0 503 82.6160 841 1428 1 chr5D.!!$R1 587
5 TraesCS4A01G198300 chr5A 282587504 282588399 895 True 325.5 499 85.0600 455 1428 2 chr5A.!!$R1 973
6 TraesCS4A01G198300 chr2D 567477118 567477709 591 False 473.0 473 81.6530 842 1428 1 chr2D.!!$F1 586

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
777 789 0.323957 AATGCACTGAGCTGAGCTGA 59.676 50.0 13.71 0.99 45.94 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2470 0.109342 CCCCACTGAAGCACTCACTT 59.891 55.0 0.0 0.0 0.0 3.16 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
207 208 2.669569 CCAAGCGGACCACAGGTG 60.670 66.667 0.00 0.00 35.25 4.00
311 321 4.843147 TGTTATTCAGTTGAAAGTGCACG 58.157 39.130 12.01 0.00 37.61 5.34
325 335 0.535335 TGCACGGTAGAATGGACTCC 59.465 55.000 0.00 0.00 0.00 3.85
367 377 1.619704 GCCAGGTAAAAATGGGAGGCT 60.620 52.381 0.00 0.00 37.89 4.58
591 603 3.139850 CCTGATCATTCCTCATCAGCAC 58.860 50.000 0.00 0.00 43.27 4.40
632 644 6.682746 ACTACATATTCTAACCTCAGCATCG 58.317 40.000 0.00 0.00 0.00 3.84
777 789 0.323957 AATGCACTGAGCTGAGCTGA 59.676 50.000 13.71 0.99 45.94 4.26
916 946 1.482593 ACCATCACCACTGCTAGCTAC 59.517 52.381 17.23 0.00 0.00 3.58
988 1042 1.662044 GTTTTCCACCCAGCAGCAG 59.338 57.895 0.00 0.00 0.00 4.24
989 1043 2.202395 TTTTCCACCCAGCAGCAGC 61.202 57.895 0.00 0.00 42.56 5.25
990 1044 2.925416 TTTTCCACCCAGCAGCAGCA 62.925 55.000 3.17 0.00 45.49 4.41
991 1045 3.855503 TTCCACCCAGCAGCAGCAG 62.856 63.158 3.17 0.00 45.49 4.24
1227 1287 2.907236 GAGAAGGGCCTGCTCCTC 59.093 66.667 28.86 17.69 30.10 3.71
1819 1879 3.470567 CGTGAACCTCGACTGCGC 61.471 66.667 0.00 0.00 37.46 6.09
2117 2177 4.081322 ACAAGTTTACTACCACCACCAG 57.919 45.455 0.00 0.00 0.00 4.00
2236 2296 0.918983 TCTTCCATCCACCCATCCAC 59.081 55.000 0.00 0.00 0.00 4.02
2274 2334 5.527582 GCCCCTTTTCTTTTTCTTCTTTTCC 59.472 40.000 0.00 0.00 0.00 3.13
2390 2450 4.517453 AGACAGAGAGACAGACTTGTGTAC 59.483 45.833 0.00 0.00 37.76 2.90
2408 2470 5.181622 TGTGTACGTATGTGTCATGTCTGTA 59.818 40.000 0.00 0.00 0.00 2.74
2488 2550 3.094572 CTGCTCAAGAAACATCCCCATT 58.905 45.455 0.00 0.00 0.00 3.16
2725 2792 7.040409 AGCGAATAAGGGATATTTTTCATGTCC 60.040 37.037 0.00 0.00 34.30 4.02
2726 2793 7.255451 GCGAATAAGGGATATTTTTCATGTCCA 60.255 37.037 0.00 0.00 34.30 4.02
2764 2831 8.447924 ACTGATTCATGTGAATAGATGGAAAG 57.552 34.615 8.14 1.00 44.14 2.62
2815 2882 5.415389 GGAAAATTTAGCAAATGCCCAACAT 59.585 36.000 0.94 0.00 43.38 2.71
2900 2967 1.070289 AGTGGTCGGTCTCAACCTTTC 59.930 52.381 0.00 0.00 44.04 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.190833 AGAGTCCTGCCAGGTCTGTG 61.191 60.000 15.43 0.00 33.90 3.66
207 208 9.830975 ATTTGGCAGAAATTTATGGTTTATACC 57.169 29.630 14.29 5.82 45.26 2.73
311 321 3.391296 TGCCAATAGGAGTCCATTCTACC 59.609 47.826 12.86 0.00 36.89 3.18
345 355 2.379005 CCTCCCATTTTTACCTGGCTC 58.621 52.381 0.00 0.00 0.00 4.70
544 556 1.032014 TGCTTCAAAGTTGGTGCCTC 58.968 50.000 6.69 0.00 0.00 4.70
591 603 3.192001 TGTAGTTTCGGTGTGTAGCTAGG 59.808 47.826 0.00 0.00 0.00 3.02
604 616 6.978659 TGCTGAGGTTAGAATATGTAGTTTCG 59.021 38.462 0.00 0.00 0.00 3.46
632 644 0.603707 TTCAGTGTGTAGCTGCTGCC 60.604 55.000 13.43 5.88 40.80 4.85
988 1042 2.594013 GGCCATCCTAGCTGCTGC 60.594 66.667 13.43 7.62 40.05 5.25
989 1043 0.889638 CATGGCCATCCTAGCTGCTG 60.890 60.000 17.61 0.00 0.00 4.41
990 1044 1.058428 TCATGGCCATCCTAGCTGCT 61.058 55.000 17.61 7.57 0.00 4.24
991 1045 0.179009 TTCATGGCCATCCTAGCTGC 60.179 55.000 17.61 0.00 0.00 5.25
992 1046 2.434428 GATTCATGGCCATCCTAGCTG 58.566 52.381 17.61 4.26 0.00 4.24
1227 1287 2.100603 GCCTCGTCGTCGAAGGAG 59.899 66.667 15.71 15.08 45.61 3.69
1469 1529 2.433145 CAGACGCTGGCACGACAT 60.433 61.111 14.63 0.00 36.70 3.06
1479 1539 1.979693 GGGACTCTGACCAGACGCT 60.980 63.158 0.00 0.00 33.22 5.07
2005 2065 1.133513 ACTGCCCCTGTCATGTCAAAA 60.134 47.619 0.00 0.00 0.00 2.44
2006 2066 0.478072 ACTGCCCCTGTCATGTCAAA 59.522 50.000 0.00 0.00 0.00 2.69
2236 2296 1.604593 GGGGCGATGAATGGATGGG 60.605 63.158 0.00 0.00 0.00 4.00
2274 2334 2.675658 TCTGGAAGACAAAAAGGGGG 57.324 50.000 0.00 0.00 38.67 5.40
2327 2387 4.444611 TCTTTTTCCTGAATCCTCCCCTA 58.555 43.478 0.00 0.00 0.00 3.53
2390 2450 5.399013 TCACTTACAGACATGACACATACG 58.601 41.667 0.00 0.00 0.00 3.06
2408 2470 0.109342 CCCCACTGAAGCACTCACTT 59.891 55.000 0.00 0.00 0.00 3.16
2533 2597 4.261489 CCAATTGATTGCATGAGCTCTACC 60.261 45.833 16.19 3.27 42.74 3.18
2756 2823 5.918608 TGTTAGAGTGGCTATCTTTCCATC 58.081 41.667 0.00 0.00 34.47 3.51
2764 2831 7.792374 TCATGAAATTGTTAGAGTGGCTATC 57.208 36.000 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.