Multiple sequence alignment - TraesCS2D01G051400

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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 TraesCS2D01G051400 chr2D 100.000 4551 0 0 1 4551 19554640 19559190 0.000000e+00 8405.0
1 TraesCS2D01G051400 chr2D 84.541 1766 174 51 1080 2803 10220610 10218902 0.000000e+00 1657.0
2 TraesCS2D01G051400 chr2D 86.264 364 27 9 965 1328 19255642 19255982 1.550000e-99 374.0
3 TraesCS2D01G051400 chr2D 83.191 351 39 11 2539 2884 19520803 19521138 2.060000e-78 303.0
4 TraesCS2D01G051400 chr2D 84.774 243 27 5 2295 2528 19520588 19520829 7.610000e-58 235.0
5 TraesCS2D01G051400 chr3D 96.861 4555 94 11 3 4551 589674279 589669768 0.000000e+00 7574.0
6 TraesCS2D01G051400 chr1B 91.599 2202 129 18 346 2528 44798949 44801113 0.000000e+00 2990.0
7 TraesCS2D01G051400 chr1B 91.716 169 11 2 1 169 44798681 44798846 9.850000e-57 231.0
8 TraesCS2D01G051400 chr1B 84.135 208 28 4 2883 3087 588446897 588446692 3.590000e-46 196.0
9 TraesCS2D01G051400 chr1B 95.238 42 2 0 2624 2665 44801148 44801189 2.940000e-07 67.6
10 TraesCS2D01G051400 chrUn 90.000 1230 81 24 1 1220 3514518 3513321 0.000000e+00 1552.0
11 TraesCS2D01G051400 chrUn 89.919 1230 82 24 1 1220 324103218 324102021 0.000000e+00 1546.0
12 TraesCS2D01G051400 chrUn 83.193 1785 193 52 1075 2803 12288510 12286777 0.000000e+00 1535.0
13 TraesCS2D01G051400 chrUn 90.559 805 49 6 1730 2528 3510691 3509908 0.000000e+00 1040.0
14 TraesCS2D01G051400 chrUn 91.493 670 35 10 559 1220 244467129 244466474 0.000000e+00 902.0
15 TraesCS2D01G051400 chrUn 81.620 963 158 12 1153 2113 8821 9766 0.000000e+00 780.0
16 TraesCS2D01G051400 chrUn 92.149 484 35 1 1222 1705 3511167 3510687 0.000000e+00 680.0
17 TraesCS2D01G051400 chrUn 76.440 955 185 26 1177 2126 359563179 359564098 8.850000e-132 481.0
18 TraesCS2D01G051400 chrUn 75.970 928 165 41 3402 4311 12286172 12285285 4.210000e-115 425.0
19 TraesCS2D01G051400 chrUn 86.410 390 26 9 2145 2528 366506591 366506223 7.090000e-108 401.0
20 TraesCS2D01G051400 chrUn 91.716 169 11 2 1 169 320429489 320429654 9.850000e-57 231.0
21 TraesCS2D01G051400 chrUn 91.716 169 11 2 1 169 320432845 320433010 9.850000e-57 231.0
22 TraesCS2D01G051400 chrUn 91.716 169 11 2 1 169 351823795 351823960 9.850000e-57 231.0
23 TraesCS2D01G051400 chrUn 91.716 169 11 2 1 169 412405112 412405277 9.850000e-57 231.0
24 TraesCS2D01G051400 chrUn 91.837 49 4 0 2624 2672 3509864 3509816 8.170000e-08 69.4
25 TraesCS2D01G051400 chrUn 91.837 49 4 0 2624 2672 366506179 366506131 8.170000e-08 69.4
26 TraesCS2D01G051400 chr2A 82.221 1558 220 30 935 2469 10486961 10485438 0.000000e+00 1290.0
27 TraesCS2D01G051400 chr2A 87.805 205 25 0 2883 3087 26933183 26932979 1.640000e-59 241.0
28 TraesCS2D01G051400 chr2A 83.854 192 29 2 4163 4352 20383343 20383534 1.010000e-41 182.0
29 TraesCS2D01G051400 chr2B 80.882 1428 200 42 1065 2461 4493275 4494660 0.000000e+00 1057.0
30 TraesCS2D01G051400 chr2B 86.294 197 21 5 1977 2170 38731794 38731601 4.610000e-50 209.0
31 TraesCS2D01G051400 chr2B 83.744 203 33 0 2885 3087 134508970 134508768 4.650000e-45 193.0
32 TraesCS2D01G051400 chr4D 85.854 205 29 0 2883 3087 6262746 6262542 7.670000e-53 219.0
33 TraesCS2D01G051400 chr1A 85.437 206 29 1 2883 3087 329187784 329187989 3.570000e-51 213.0
34 TraesCS2D01G051400 chr1D 83.105 219 31 5 2874 3087 110976202 110975985 1.290000e-45 195.0
35 TraesCS2D01G051400 chr1D 83.654 208 31 1 2883 3087 404971982 404971775 4.650000e-45 193.0
36 TraesCS2D01G051400 chr7B 83.412 211 30 4 2884 3090 83026719 83026928 1.670000e-44 191.0


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 TraesCS2D01G051400 chr2D 19554640 19559190 4550 False 8405.00 8405 100.00000 1 4551 1 chr2D.!!$F2 4550
1 TraesCS2D01G051400 chr2D 10218902 10220610 1708 True 1657.00 1657 84.54100 1080 2803 1 chr2D.!!$R1 1723
2 TraesCS2D01G051400 chr2D 19520588 19521138 550 False 269.00 303 83.98250 2295 2884 2 chr2D.!!$F3 589
3 TraesCS2D01G051400 chr3D 589669768 589674279 4511 True 7574.00 7574 96.86100 3 4551 1 chr3D.!!$R1 4548
4 TraesCS2D01G051400 chr1B 44798681 44801189 2508 False 1096.20 2990 92.85100 1 2665 3 chr1B.!!$F1 2664
5 TraesCS2D01G051400 chrUn 324102021 324103218 1197 True 1546.00 1546 89.91900 1 1220 1 chrUn.!!$R2 1219
6 TraesCS2D01G051400 chrUn 12285285 12288510 3225 True 980.00 1535 79.58150 1075 4311 2 chrUn.!!$R4 3236
7 TraesCS2D01G051400 chrUn 244466474 244467129 655 True 902.00 902 91.49300 559 1220 1 chrUn.!!$R1 661
8 TraesCS2D01G051400 chrUn 3509816 3514518 4702 True 835.35 1552 91.13625 1 2672 4 chrUn.!!$R3 2671
9 TraesCS2D01G051400 chrUn 8821 9766 945 False 780.00 780 81.62000 1153 2113 1 chrUn.!!$F1 960
10 TraesCS2D01G051400 chrUn 359563179 359564098 919 False 481.00 481 76.44000 1177 2126 1 chrUn.!!$F3 949
11 TraesCS2D01G051400 chrUn 320429489 320433010 3521 False 231.00 231 91.71600 1 169 2 chrUn.!!$F5 168
12 TraesCS2D01G051400 chr2A 10485438 10486961 1523 True 1290.00 1290 82.22100 935 2469 1 chr2A.!!$R1 1534
13 TraesCS2D01G051400 chr2B 4493275 4494660 1385 False 1057.00 1057 80.88200 1065 2461 1 chr2B.!!$F1 1396

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
254 255 1.079405 TCCCGAGTGGCAAATCGAC 60.079 57.895 13.47 0.00 41.40 4.20 F
1240 5604 0.898320 AGCAGCTCATACGTGGAAGT 59.102 50.000 0.00 0.00 0.00 3.01 F
1682 6064 2.343387 GGTGGTGGCAATGGCAAC 59.657 61.111 18.48 18.48 46.35 4.17 F
3339 8089 3.653122 TTCTACCTCCCCCTGCCCC 62.653 68.421 0.00 0.00 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 6062 0.031043 TCGACGTCGATGTGGTTGTT 59.969 50.0 34.97 0.00 44.22 2.83 R
2969 7718 0.524862 GTCGTCGCTAGGTTCTCCAA 59.475 55.0 0.00 0.00 35.89 3.53 R
3384 8134 0.465287 TCAGGATCGCAGCTGCATTA 59.535 50.0 36.03 21.95 42.21 1.90 R
4460 9219 5.000591 TGACTTTCCAAATTCATAGTCGCA 58.999 37.5 0.00 0.00 35.85 5.10 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
99 100 1.402259 CGGACATGACTTAGTCGAGCT 59.598 52.381 7.92 0.00 34.95 4.09
150 151 3.637273 GGCCGGGACTCTGTTGGT 61.637 66.667 2.18 0.00 0.00 3.67
254 255 1.079405 TCCCGAGTGGCAAATCGAC 60.079 57.895 13.47 0.00 41.40 4.20
255 256 2.106683 CCCGAGTGGCAAATCGACC 61.107 63.158 13.47 0.00 41.40 4.79
259 260 1.696832 GAGTGGCAAATCGACCGAGC 61.697 60.000 0.00 0.00 0.00 5.03
265 266 1.258982 GCAAATCGACCGAGCATACTG 59.741 52.381 0.00 0.00 0.00 2.74
267 268 2.493713 AATCGACCGAGCATACTGTC 57.506 50.000 0.00 0.00 0.00 3.51
274 275 1.521681 GAGCATACTGTCCACGCCC 60.522 63.158 0.00 0.00 0.00 6.13
397 432 1.405821 GTGCATGCTACTAGAGGTCGT 59.594 52.381 20.33 0.00 0.00 4.34
669 1485 8.874156 TCTAATGAGTGTGGCTATATCTCAATT 58.126 33.333 0.00 0.00 38.38 2.32
676 1502 6.423302 GTGTGGCTATATCTCAATTGACTGAG 59.577 42.308 3.38 0.00 43.62 3.35
809 2111 9.606631 AACTAAGTCTAAGATTTAGCAATCCAG 57.393 33.333 0.00 0.00 39.95 3.86
822 2124 8.593945 TTTAGCAATCCAGATTTCTAATTGGT 57.406 30.769 11.54 16.86 36.76 3.67
933 2447 4.621886 GTCGTTCCTGAGTAGTTGTTCATC 59.378 45.833 0.00 0.00 0.00 2.92
1049 2602 4.401519 AGCTTCATACTCGGTTAGCACTAA 59.598 41.667 0.00 0.00 0.00 2.24
1123 3193 3.724374 CAAACAAGAGTTCTCCGGTACA 58.276 45.455 0.00 0.00 36.84 2.90
1240 5604 0.898320 AGCAGCTCATACGTGGAAGT 59.102 50.000 0.00 0.00 0.00 3.01
1652 6028 4.651585 GTGTACAACACGGCGGTA 57.348 55.556 13.24 0.00 39.53 4.02
1675 6057 3.636231 AGCTAGCGGTGGTGGCAA 61.636 61.111 9.55 0.00 39.89 4.52
1681 6063 3.301554 CGGTGGTGGCAATGGCAA 61.302 61.111 12.09 0.00 43.71 4.52
1682 6064 2.343387 GGTGGTGGCAATGGCAAC 59.657 61.111 18.48 18.48 46.35 4.17
3124 7873 4.141869 GCATTCACTAAGGGGATTTGCAAT 60.142 41.667 0.00 0.00 0.00 3.56
3249 7998 3.700539 CCATCTCACCCATTTATTGCACA 59.299 43.478 0.00 0.00 0.00 4.57
3339 8089 3.653122 TTCTACCTCCCCCTGCCCC 62.653 68.421 0.00 0.00 0.00 5.80
3400 8150 1.154205 ACGTAATGCAGCTGCGATCC 61.154 55.000 32.11 19.07 45.83 3.36
3416 8166 3.721035 CGATCCTGAGCAACACATCATA 58.279 45.455 0.00 0.00 0.00 2.15
3819 8572 6.773200 TGAGATCGACACTTCTATAGGTCAAT 59.227 38.462 0.00 0.00 0.00 2.57
3821 8574 6.773200 AGATCGACACTTCTATAGGTCAATCA 59.227 38.462 9.22 0.00 28.55 2.57
4126 8882 8.752005 AGACTAAATACACCATGCAAACATAT 57.248 30.769 0.00 0.00 33.67 1.78
4324 9083 5.968254 AGGTAAACATGGTCGTTTGTTTTT 58.032 33.333 6.38 0.00 41.90 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 1.487452 GCGCAAATATCTCGTCCGCA 61.487 55.000 0.30 0.00 39.70 5.69
183 184 1.811266 CTCGAACCCATGTCCTGCG 60.811 63.158 0.00 0.00 0.00 5.18
197 198 4.121669 GCACCAGCTCTCGCTCGA 62.122 66.667 0.00 0.00 45.15 4.04
254 255 1.878522 GCGTGGACAGTATGCTCGG 60.879 63.158 0.00 0.00 42.53 4.63
255 256 1.878522 GGCGTGGACAGTATGCTCG 60.879 63.158 0.00 0.00 42.53 5.03
259 260 1.144057 GGAGGGCGTGGACAGTATG 59.856 63.158 0.00 0.00 46.00 2.39
265 266 2.746375 ATCCATGGAGGGCGTGGAC 61.746 63.158 21.33 0.00 44.21 4.02
267 268 2.203252 CATCCATGGAGGGCGTGG 60.203 66.667 21.33 0.00 38.24 4.94
650 1466 6.098838 TCAGTCAATTGAGATATAGCCACACT 59.901 38.462 8.80 0.00 0.00 3.55
676 1502 6.367422 CACTTGATGGAGACTCTGTTTAAGTC 59.633 42.308 1.74 0.00 42.84 3.01
677 1503 6.042093 TCACTTGATGGAGACTCTGTTTAAGT 59.958 38.462 1.74 4.97 0.00 2.24
678 1504 6.459066 TCACTTGATGGAGACTCTGTTTAAG 58.541 40.000 1.74 4.41 0.00 1.85
679 1505 6.419484 TCACTTGATGGAGACTCTGTTTAA 57.581 37.500 1.74 0.00 0.00 1.52
680 1506 6.611613 ATCACTTGATGGAGACTCTGTTTA 57.388 37.500 1.74 0.00 32.68 2.01
681 1507 4.963318 TCACTTGATGGAGACTCTGTTT 57.037 40.909 1.74 0.00 0.00 2.83
682 1508 5.954752 TCTATCACTTGATGGAGACTCTGTT 59.045 40.000 1.74 0.00 37.17 3.16
683 1509 5.514169 TCTATCACTTGATGGAGACTCTGT 58.486 41.667 1.74 0.00 37.17 3.41
684 1510 6.127507 TGTTCTATCACTTGATGGAGACTCTG 60.128 42.308 1.74 0.00 41.87 3.35
685 1511 5.954752 TGTTCTATCACTTGATGGAGACTCT 59.045 40.000 1.74 0.00 41.87 3.24
905 2416 3.919223 ACTACTCAGGAACGACTGAAC 57.081 47.619 9.65 0.00 46.05 3.18
933 2447 5.005740 CCACTCCAATATGGTCATGTATGG 58.994 45.833 0.00 0.54 39.03 2.74
1049 2602 5.221048 GCAGTTGTGTGAGGAAGTGTAAATT 60.221 40.000 0.00 0.00 0.00 1.82
1123 3193 1.270550 CGGCATCCTTCTTGTTGCTTT 59.729 47.619 0.00 0.00 35.46 3.51
1652 6028 4.742201 CCACCGCTAGCTGCACGT 62.742 66.667 13.93 0.00 43.06 4.49
1675 6057 0.881118 GTCGATGTGGTTGTTGCCAT 59.119 50.000 0.00 0.00 41.08 4.40
1680 6062 0.031043 TCGACGTCGATGTGGTTGTT 59.969 50.000 34.97 0.00 44.22 2.83
1681 6063 1.655885 TCGACGTCGATGTGGTTGT 59.344 52.632 34.97 0.00 44.22 3.32
1682 6064 4.544762 TCGACGTCGATGTGGTTG 57.455 55.556 34.97 5.74 44.22 3.77
1832 6214 2.292267 CGGGGATCATTCTTGTTGAGG 58.708 52.381 0.00 0.00 0.00 3.86
2673 7152 3.418684 AGAAGAACATACACCCCACAC 57.581 47.619 0.00 0.00 0.00 3.82
2969 7718 0.524862 GTCGTCGCTAGGTTCTCCAA 59.475 55.000 0.00 0.00 35.89 3.53
2975 7724 1.135460 GCTTGTAGTCGTCGCTAGGTT 60.135 52.381 0.00 0.00 0.00 3.50
3033 7782 1.152440 CCCGGCTCTAGTGAGGGAT 60.152 63.158 16.32 0.00 44.70 3.85
3124 7873 4.276183 TGTGTTCTTAAATACAAGCCGCAA 59.724 37.500 0.00 0.00 34.07 4.85
3339 8089 2.539503 CATACGGACATTCGCGCG 59.460 61.111 26.76 26.76 0.00 6.86
3384 8134 0.465287 TCAGGATCGCAGCTGCATTA 59.535 50.000 36.03 21.95 42.21 1.90
3400 8150 7.878477 AATGTTTTTATGATGTGTTGCTCAG 57.122 32.000 0.00 0.00 0.00 3.35
4126 8882 6.930164 TCAACGTTACTAGAGCAACCATAAAA 59.070 34.615 0.00 0.00 0.00 1.52
4269 9026 8.798975 ATAGTGGTTAGAGGATCCTGATTAAA 57.201 34.615 22.02 2.85 33.66 1.52
4460 9219 5.000591 TGACTTTCCAAATTCATAGTCGCA 58.999 37.500 0.00 0.00 35.85 5.10


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

AutoCloner maintained by Alex Coulton.