Multiple sequence alignment - TraesCS2B01G056100

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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 TraesCS2B01G056100 chr2B 100.000 3725 0 0 1 3725 27405879 27409603 0.000000e+00 6879
1 TraesCS2B01G056100 chr2B 98.550 3103 36 4 632 3725 27355461 27358563 0.000000e+00 5472
2 TraesCS2B01G056100 chr2B 98.324 3103 43 4 632 3725 27249560 27252662 0.000000e+00 5433
3 TraesCS2B01G056100 chr2B 98.324 3103 43 4 632 3725 27287154 27290256 0.000000e+00 5433
4 TraesCS2B01G056100 chr2B 92.105 608 23 4 1 607 27286589 27287172 0.000000e+00 833
5 TraesCS2B01G056100 chr2B 92.910 536 25 1 1 536 788303352 788302830 0.000000e+00 767
6 TraesCS2B01G056100 chr2B 92.724 536 26 2 1 536 788359638 788360160 0.000000e+00 761
7 TraesCS2B01G056100 chr2B 92.724 536 26 2 1 536 788413016 788413538 0.000000e+00 761
8 TraesCS2B01G056100 chr2B 92.351 536 28 2 1 536 788382658 788383180 0.000000e+00 750
9 TraesCS2B01G056100 chr2B 90.299 536 39 3 1 535 141202180 141202703 0.000000e+00 689
10 TraesCS2B01G056100 chr2D 93.948 1834 85 14 1165 2983 15264558 15266380 0.000000e+00 2748
11 TraesCS2B01G056100 chr2D 93.893 1834 86 14 1165 2983 15228847 15230669 0.000000e+00 2743
12 TraesCS2B01G056100 chr2D 94.143 1366 59 9 1165 2519 15249650 15251005 0.000000e+00 2060
13 TraesCS2B01G056100 chr2D 90.955 398 25 7 773 1164 15228512 15228904 3.300000e-145 525
14 TraesCS2B01G056100 chr2D 90.704 398 26 7 773 1164 15249315 15249707 1.530000e-143 520
15 TraesCS2B01G056100 chr2D 90.704 398 26 7 773 1164 15264223 15264615 1.530000e-143 520
16 TraesCS2B01G056100 chr2D 95.588 272 12 0 3238 3509 15334800 15335071 1.590000e-118 436
17 TraesCS2B01G056100 chr2D 88.934 244 18 5 537 771 19849740 19849497 3.640000e-75 292
18 TraesCS2B01G056100 chr2D 95.370 108 5 0 535 642 15228249 15228356 4.950000e-39 172
19 TraesCS2B01G056100 chr2D 95.370 108 5 0 535 642 15249052 15249159 4.950000e-39 172
20 TraesCS2B01G056100 chr2D 95.370 108 5 0 535 642 15263960 15264067 4.950000e-39 172
21 TraesCS2B01G056100 chrUn 93.774 1831 88 14 1168 2983 266171078 266169259 0.000000e+00 2726
22 TraesCS2B01G056100 chrUn 93.826 1393 72 10 1595 2983 379234394 379233012 0.000000e+00 2084
23 TraesCS2B01G056100 chrUn 91.760 534 32 3 1 534 272921279 272920758 0.000000e+00 732
24 TraesCS2B01G056100 chrUn 90.955 398 25 7 773 1164 266171416 266171024 3.300000e-145 525
25 TraesCS2B01G056100 chrUn 93.808 323 15 4 773 1090 375769996 375769674 7.240000e-132 481
26 TraesCS2B01G056100 chrUn 85.484 248 20 5 535 771 16444744 16444502 1.030000e-60 244
27 TraesCS2B01G056100 chrUn 85.484 248 20 5 535 771 366814496 366814254 1.030000e-60 244
28 TraesCS2B01G056100 chrUn 85.081 248 21 5 535 771 233477724 233477482 4.810000e-59 239
29 TraesCS2B01G056100 chrUn 92.000 150 12 0 535 684 16657120 16657269 1.050000e-50 211
30 TraesCS2B01G056100 chrUn 90.667 150 14 0 535 684 16611506 16611655 2.270000e-47 200
31 TraesCS2B01G056100 chrUn 94.444 108 6 0 535 642 266171679 266171572 2.300000e-37 167
32 TraesCS2B01G056100 chrUn 94.444 108 6 0 535 642 375770259 375770152 2.300000e-37 167
33 TraesCS2B01G056100 chr2A 93.288 1773 100 11 1222 2983 17300277 17302041 0.000000e+00 2597
34 TraesCS2B01G056100 chr2A 92.000 325 21 5 774 1093 20365241 20365565 5.670000e-123 451
35 TraesCS2B01G056100 chr2A 89.024 246 11 4 535 771 17299609 17299847 1.310000e-74 291
36 TraesCS2B01G056100 chr2A 95.210 167 6 1 2979 3145 17302070 17302234 2.850000e-66 263
37 TraesCS2B01G056100 chr2A 93.567 171 10 1 535 704 20364972 20365142 1.720000e-63 254
38 TraesCS2B01G056100 chr7B 89.589 1777 158 16 1222 2983 70339888 70341652 0.000000e+00 2231
39 TraesCS2B01G056100 chr7B 89.925 536 41 6 1 535 42073869 42074392 0.000000e+00 678
40 TraesCS2B01G056100 chr7B 88.827 537 43 8 1 536 24398189 24398709 0.000000e+00 643
41 TraesCS2B01G056100 chr7B 92.571 175 11 1 2979 3151 69994701 69994875 2.220000e-62 250
42 TraesCS2B01G056100 chr7B 92.000 175 12 1 2979 3151 70071200 70071374 1.030000e-60 244
43 TraesCS2B01G056100 chr6B 91.902 531 31 3 1 531 51944252 51944770 0.000000e+00 732
44 TraesCS2B01G056100 chr6B 90.149 538 35 8 1 536 38019900 38019379 0.000000e+00 684
45 TraesCS2B01G056100 chr6B 92.000 175 12 1 2979 3151 548950596 548950770 1.030000e-60 244
46 TraesCS2B01G056100 chr6B 92.000 175 12 1 2979 3151 549031109 549031283 1.030000e-60 244
47 TraesCS2B01G056100 chr1B 88.476 538 33 7 1 536 271935325 271935835 1.140000e-174 623
48 TraesCS2B01G056100 chr7A 83.012 518 61 15 1264 1779 692056337 692055845 9.490000e-121 444
49 TraesCS2B01G056100 chr7A 93.064 173 10 1 2979 3151 116020789 116020959 6.180000e-63 252


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 TraesCS2B01G056100 chr2B 27405879 27409603 3724 False 6879.000000 6879 100.000000 1 3725 1 chr2B.!!$F3 3724
1 TraesCS2B01G056100 chr2B 27355461 27358563 3102 False 5472.000000 5472 98.550000 632 3725 1 chr2B.!!$F2 3093
2 TraesCS2B01G056100 chr2B 27249560 27252662 3102 False 5433.000000 5433 98.324000 632 3725 1 chr2B.!!$F1 3093
3 TraesCS2B01G056100 chr2B 27286589 27290256 3667 False 3133.000000 5433 95.214500 1 3725 2 chr2B.!!$F8 3724
4 TraesCS2B01G056100 chr2B 788302830 788303352 522 True 767.000000 767 92.910000 1 536 1 chr2B.!!$R1 535
5 TraesCS2B01G056100 chr2B 788359638 788360160 522 False 761.000000 761 92.724000 1 536 1 chr2B.!!$F5 535
6 TraesCS2B01G056100 chr2B 788413016 788413538 522 False 761.000000 761 92.724000 1 536 1 chr2B.!!$F7 535
7 TraesCS2B01G056100 chr2B 788382658 788383180 522 False 750.000000 750 92.351000 1 536 1 chr2B.!!$F6 535
8 TraesCS2B01G056100 chr2B 141202180 141202703 523 False 689.000000 689 90.299000 1 535 1 chr2B.!!$F4 534
9 TraesCS2B01G056100 chr2D 15228249 15230669 2420 False 1146.666667 2743 93.406000 535 2983 3 chr2D.!!$F2 2448
10 TraesCS2B01G056100 chr2D 15263960 15266380 2420 False 1146.666667 2748 93.340667 535 2983 3 chr2D.!!$F4 2448
11 TraesCS2B01G056100 chr2D 15249052 15251005 1953 False 917.333333 2060 93.405667 535 2519 3 chr2D.!!$F3 1984
12 TraesCS2B01G056100 chrUn 379233012 379234394 1382 True 2084.000000 2084 93.826000 1595 2983 1 chrUn.!!$R5 1388
13 TraesCS2B01G056100 chrUn 266169259 266171679 2420 True 1139.333333 2726 93.057667 535 2983 3 chrUn.!!$R6 2448
14 TraesCS2B01G056100 chrUn 272920758 272921279 521 True 732.000000 732 91.760000 1 534 1 chrUn.!!$R3 533
15 TraesCS2B01G056100 chrUn 375769674 375770259 585 True 324.000000 481 94.126000 535 1090 2 chrUn.!!$R7 555
16 TraesCS2B01G056100 chr2A 17299609 17302234 2625 False 1050.333333 2597 92.507333 535 3145 3 chr2A.!!$F1 2610
17 TraesCS2B01G056100 chr2A 20364972 20365565 593 False 352.500000 451 92.783500 535 1093 2 chr2A.!!$F2 558
18 TraesCS2B01G056100 chr7B 70339888 70341652 1764 False 2231.000000 2231 89.589000 1222 2983 1 chr7B.!!$F5 1761
19 TraesCS2B01G056100 chr7B 42073869 42074392 523 False 678.000000 678 89.925000 1 535 1 chr7B.!!$F2 534
20 TraesCS2B01G056100 chr7B 24398189 24398709 520 False 643.000000 643 88.827000 1 536 1 chr7B.!!$F1 535
21 TraesCS2B01G056100 chr6B 51944252 51944770 518 False 732.000000 732 91.902000 1 531 1 chr6B.!!$F1 530
22 TraesCS2B01G056100 chr6B 38019379 38019900 521 True 684.000000 684 90.149000 1 536 1 chr6B.!!$R1 535
23 TraesCS2B01G056100 chr1B 271935325 271935835 510 False 623.000000 623 88.476000 1 536 1 chr1B.!!$F1 535

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
266 267 0.034616 CCATCTCCGCCTTCATCTCC 59.965 60.000 0.00 0.0 0.0 3.71 F
274 275 0.179034 GCCTTCATCTCCGCCTTCAT 60.179 55.000 0.00 0.0 0.0 2.57 F
1618 1758 0.320050 TGTGCGTGCAGTGGAAGATA 59.680 50.000 0.94 0.0 0.0 1.98 F
1622 1762 1.404181 GCGTGCAGTGGAAGATACTCA 60.404 52.381 0.94 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1395 3.726517 CAGAACGTTGGCCTGCGG 61.727 66.667 20.17 3.71 0.0 5.69 R
2192 2339 7.195374 TGAGCTAGTAATTCACCCTGTAAAT 57.805 36.000 0.00 0.00 0.0 1.40 R
2670 2819 0.308376 TAACGGCGTTTTTGGTGAGC 59.692 50.000 31.53 0.00 0.0 4.26 R
3098 3287 0.531974 TCGCTCACACCAGGTTCAAC 60.532 55.000 0.00 0.00 0.0 3.18 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
216 217 1.410153 CTGGTTTCTTGCAGCTTTGGT 59.590 47.619 0.00 0.00 0.00 3.67
264 265 1.449353 GCCATCTCCGCCTTCATCT 59.551 57.895 0.00 0.00 0.00 2.90
265 266 0.602372 GCCATCTCCGCCTTCATCTC 60.602 60.000 0.00 0.00 0.00 2.75
266 267 0.034616 CCATCTCCGCCTTCATCTCC 59.965 60.000 0.00 0.00 0.00 3.71
267 268 0.319383 CATCTCCGCCTTCATCTCCG 60.319 60.000 0.00 0.00 0.00 4.63
268 269 2.093537 ATCTCCGCCTTCATCTCCGC 62.094 60.000 0.00 0.00 0.00 5.54
269 270 3.798954 CTCCGCCTTCATCTCCGCC 62.799 68.421 0.00 0.00 0.00 6.13
270 271 3.854669 CCGCCTTCATCTCCGCCT 61.855 66.667 0.00 0.00 0.00 5.52
271 272 2.187946 CGCCTTCATCTCCGCCTT 59.812 61.111 0.00 0.00 0.00 4.35
272 273 1.884926 CGCCTTCATCTCCGCCTTC 60.885 63.158 0.00 0.00 0.00 3.46
273 274 1.221840 GCCTTCATCTCCGCCTTCA 59.778 57.895 0.00 0.00 0.00 3.02
274 275 0.179034 GCCTTCATCTCCGCCTTCAT 60.179 55.000 0.00 0.00 0.00 2.57
275 276 1.876322 CCTTCATCTCCGCCTTCATC 58.124 55.000 0.00 0.00 0.00 2.92
297 298 2.123251 ACCTCCGATCGATGGCCT 60.123 61.111 18.66 0.29 0.00 5.19
416 430 2.724520 CTTGTTGAGCTGTGCCCTT 58.275 52.632 0.00 0.00 0.00 3.95
561 575 0.676466 TTCATGGCCTGCGGTAACAG 60.676 55.000 3.32 0.00 37.42 3.16
1261 1395 4.531659 ACTTGTTTTCTGCTTGTACGTC 57.468 40.909 0.00 0.00 0.00 4.34
1540 1674 2.159142 CGGCCTACTGTATCTTTTCGGT 60.159 50.000 0.00 0.00 0.00 4.69
1618 1758 0.320050 TGTGCGTGCAGTGGAAGATA 59.680 50.000 0.94 0.00 0.00 1.98
1622 1762 1.404181 GCGTGCAGTGGAAGATACTCA 60.404 52.381 0.94 0.00 0.00 3.41
2133 2280 5.882557 CCCAAGTTCTTGTACAAGATGCTAT 59.117 40.000 33.02 20.88 45.78 2.97
2670 2819 1.095228 ACGTTGAACTGCCCACTGTG 61.095 55.000 0.00 0.00 0.00 3.66
2768 2917 9.343539 GCCCTGAAGATTTTGAGTAGTTAATAT 57.656 33.333 0.00 0.00 0.00 1.28
2856 3006 6.804783 AGATCGCCTTTAATTTTGTTTAACCG 59.195 34.615 0.00 0.00 0.00 4.44
2890 3040 6.096423 TGTCCGAGACTACTAGTGCAAATTAT 59.904 38.462 5.39 0.00 33.15 1.28
2892 3042 7.804129 GTCCGAGACTACTAGTGCAAATTATAG 59.196 40.741 5.39 0.00 0.00 1.31
3098 3287 3.571401 GGGGATCTTATTGGTGATGCAAG 59.429 47.826 0.00 0.00 33.57 4.01
3146 3335 6.757478 GGAGACACAGACTTAACCTAATTAGC 59.243 42.308 6.99 0.00 0.00 3.09
3334 3523 3.650942 TCCAGTCCTACCTCACACATTTT 59.349 43.478 0.00 0.00 0.00 1.82
3455 3644 0.030235 GCCAAGACCGACAACAAACC 59.970 55.000 0.00 0.00 0.00 3.27
3518 3707 1.138266 ACTGGTCAACTGCAACGTACT 59.862 47.619 0.00 0.00 0.00 2.73
3646 3835 4.156922 AGACAACTACTCAGAGATCAACCG 59.843 45.833 3.79 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.774110 AGTTGTTGTGGCACCAATCA 58.226 45.000 16.26 6.14 0.00 2.57
264 265 2.577059 GTCGGTGATGAAGGCGGA 59.423 61.111 0.00 0.00 0.00 5.54
265 266 2.511600 GGTCGGTGATGAAGGCGG 60.512 66.667 0.00 0.00 0.00 6.13
266 267 1.519455 GAGGTCGGTGATGAAGGCG 60.519 63.158 0.00 0.00 0.00 5.52
267 268 1.153349 GGAGGTCGGTGATGAAGGC 60.153 63.158 0.00 0.00 0.00 4.35
268 269 1.141881 CGGAGGTCGGTGATGAAGG 59.858 63.158 0.00 0.00 34.75 3.46
269 270 0.747255 ATCGGAGGTCGGTGATGAAG 59.253 55.000 0.00 0.00 39.77 3.02
270 271 0.744874 GATCGGAGGTCGGTGATGAA 59.255 55.000 0.00 0.00 39.77 2.57
271 272 1.444917 CGATCGGAGGTCGGTGATGA 61.445 60.000 7.38 0.00 39.77 2.92
272 273 1.008424 CGATCGGAGGTCGGTGATG 60.008 63.158 7.38 0.00 39.77 3.07
273 274 0.537600 ATCGATCGGAGGTCGGTGAT 60.538 55.000 16.41 0.00 39.45 3.06
274 275 1.153025 ATCGATCGGAGGTCGGTGA 60.153 57.895 16.41 0.00 39.45 4.02
275 276 1.008424 CATCGATCGGAGGTCGGTG 60.008 63.158 16.41 1.44 42.85 4.94
339 352 0.179081 GGCGACGAAGGAGCCTAATT 60.179 55.000 0.00 0.00 46.83 1.40
416 430 5.163237 ACAAGGAAGTACAAAGGTTCTGCTA 60.163 40.000 0.00 0.00 0.00 3.49
512 526 0.875059 CGAAAAAGGCTTTCGCTCCT 59.125 50.000 13.76 0.00 43.52 3.69
515 529 1.886886 TACCGAAAAAGGCTTTCGCT 58.113 45.000 13.76 3.74 46.89 4.93
607 621 0.825010 CCCAAGGACACTGCAAAGCT 60.825 55.000 0.00 0.00 0.00 3.74
1261 1395 3.726517 CAGAACGTTGGCCTGCGG 61.727 66.667 20.17 3.71 0.00 5.69
1540 1674 7.540474 AGGATCTTCTGTACAGAAACTAACA 57.460 36.000 32.19 13.98 45.75 2.41
2192 2339 7.195374 TGAGCTAGTAATTCACCCTGTAAAT 57.805 36.000 0.00 0.00 0.00 1.40
2670 2819 0.308376 TAACGGCGTTTTTGGTGAGC 59.692 50.000 31.53 0.00 0.00 4.26
2768 2917 5.789521 TCAACTTGTTGAAGTATCATCCGA 58.210 37.500 13.05 0.00 41.87 4.55
2825 2975 5.163854 ACAAAATTAAAGGCGATCTCAGACG 60.164 40.000 0.00 0.00 0.00 4.18
2856 3006 3.089117 GTCTCGGACAGACGACAAC 57.911 57.895 0.00 0.00 42.43 3.32
2890 3040 7.398904 TCAGCTGCATTGGTATATATACACCTA 59.601 37.037 21.56 4.32 35.73 3.08
2892 3042 6.406370 TCAGCTGCATTGGTATATATACACC 58.594 40.000 21.56 10.78 34.98 4.16
3079 3268 6.441093 TCAACTTGCATCACCAATAAGATC 57.559 37.500 0.00 0.00 0.00 2.75
3098 3287 0.531974 TCGCTCACACCAGGTTCAAC 60.532 55.000 0.00 0.00 0.00 3.18
3146 3335 4.438744 GGACTCAAAAGCCATATCAAACCG 60.439 45.833 0.00 0.00 0.00 4.44
3234 3423 4.022068 CACCAGCACCTAATTTGAACACAT 60.022 41.667 0.00 0.00 0.00 3.21
3455 3644 2.035066 GCAGGGGTGCTAGCATATTTTG 59.965 50.000 22.51 16.03 0.00 2.44
3518 3707 1.670674 GGTATGTTGCTTCGGTCGTCA 60.671 52.381 0.00 0.00 0.00 4.35
3528 3717 0.885879 TCAGTCGTCGGTATGTTGCT 59.114 50.000 0.00 0.00 0.00 3.91
3646 3835 8.989653 AGAGACTAACTTAACTAATGCTTGAC 57.010 34.615 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.