Multiple sequence alignment - TraesCS2D01G474100

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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 TraesCS2D01G474100 chr2D 100.000 6300 0 0 1 6300 577346824 577340525 0.000000e+00 11635.0
1 TraesCS2D01G474100 chr2D 78.335 1634 239 69 1171 2731 551704597 551703006 0.000000e+00 950.0
2 TraesCS2D01G474100 chr2D 87.066 317 31 7 3337 3649 577342721 577342411 3.610000e-92 350.0
3 TraesCS2D01G474100 chr2D 87.066 317 31 7 4104 4414 577343488 577343176 3.610000e-92 350.0
4 TraesCS2D01G474100 chr2D 72.303 686 106 48 693 1309 551823103 551822433 3.060000e-28 137.0
5 TraesCS2D01G474100 chr2A 96.081 4287 106 19 2039 6300 715425078 715420829 0.000000e+00 6929.0
6 TraesCS2D01G474100 chr2A 96.128 1627 42 5 428 2038 715426868 715425247 0.000000e+00 2636.0
7 TraesCS2D01G474100 chr2A 91.403 442 17 13 1 426 715427372 715426936 2.530000e-163 586.0
8 TraesCS2D01G474100 chr2A 86.120 317 34 7 4104 4414 715423773 715423461 3.640000e-87 333.0
9 TraesCS2D01G474100 chr2A 85.127 316 35 8 3338 3649 715423032 715422725 4.740000e-81 313.0
10 TraesCS2D01G474100 chr2A 78.065 465 87 9 2313 2768 692327975 692327517 4.810000e-71 279.0
11 TraesCS2D01G474100 chr2A 72.566 678 106 43 696 1305 692272948 692272283 1.420000e-31 148.0
12 TraesCS2D01G474100 chr2B 95.133 2856 102 16 3461 6300 694474118 694471284 0.000000e+00 4470.0
13 TraesCS2D01G474100 chr2B 89.890 3551 245 47 1 3476 694477648 694474137 0.000000e+00 4464.0
14 TraesCS2D01G474100 chr2B 91.444 3144 194 27 622 3724 694445735 694442626 0.000000e+00 4246.0
15 TraesCS2D01G474100 chr2B 91.386 3146 196 20 622 3724 694424958 694421845 0.000000e+00 4239.0
16 TraesCS2D01G474100 chr2B 95.013 2627 98 17 3697 6300 694421836 694419220 0.000000e+00 4095.0
17 TraesCS2D01G474100 chr2B 95.826 2180 79 9 3704 5878 694442608 694440436 0.000000e+00 3511.0
18 TraesCS2D01G474100 chr2B 87.456 574 44 18 1 554 694425988 694425423 2.480000e-178 636.0
19 TraesCS2D01G474100 chr2B 87.456 574 44 18 1 554 694446765 694446200 2.480000e-178 636.0
20 TraesCS2D01G474100 chr2B 93.915 378 20 3 5925 6300 694440435 694440059 9.170000e-158 568.0
21 TraesCS2D01G474100 chr2B 86.709 316 31 6 3337 3649 694442209 694441902 2.180000e-89 340.0
22 TraesCS2D01G474100 chr2B 86.520 319 31 7 3337 3651 694473486 694473176 2.180000e-89 340.0
23 TraesCS2D01G474100 chr2B 86.076 316 34 5 3337 3649 694421430 694421122 1.310000e-86 331.0
24 TraesCS2D01G474100 chr2B 87.645 259 23 4 3087 3339 694421713 694421458 6.180000e-75 292.0
25 TraesCS2D01G474100 chr2B 87.308 260 21 5 3820 4076 694422478 694422228 2.870000e-73 287.0
26 TraesCS2D01G474100 chr2B 87.259 259 24 4 3087 3339 694442492 694442237 2.870000e-73 287.0
27 TraesCS2D01G474100 chr2B 87.259 259 22 5 3820 4076 694443258 694443009 1.030000e-72 285.0
28 TraesCS2D01G474100 chr2B 86.873 259 25 4 3087 3339 694473769 694473514 1.340000e-71 281.0
29 TraesCS2D01G474100 chr2B 86.154 260 24 6 3820 4076 694474524 694474274 2.890000e-68 270.0
30 TraesCS2D01G474100 chr2B 94.340 53 3 0 547 599 694425005 694424953 1.460000e-11 82.4
31 TraesCS2D01G474100 chr2B 92.453 53 4 0 547 599 694445782 694445730 6.770000e-10 76.8
32 TraesCS2D01G474100 chr5B 81.933 869 125 21 4407 5254 57719020 57718163 0.000000e+00 706.0
33 TraesCS2D01G474100 chr5B 84.498 458 60 4 2340 2790 571202518 571202971 5.800000e-120 442.0
34 TraesCS2D01G474100 chr5B 88.182 220 21 5 5250 5467 57716684 57716468 2.250000e-64 257.0
35 TraesCS2D01G474100 chr5B 87.204 211 21 5 5305 5514 57716471 57716266 1.060000e-57 235.0
36 TraesCS2D01G474100 chr5D 88.850 565 58 2 4690 5254 464114963 464115522 0.000000e+00 689.0
37 TraesCS2D01G474100 chr5D 83.514 461 68 4 2334 2790 464106921 464107377 2.100000e-114 424.0
38 TraesCS2D01G474100 chr5D 84.892 417 53 5 1369 1778 464111276 464111689 4.540000e-111 412.0
39 TraesCS2D01G474100 chr5D 82.670 427 64 8 2344 2768 474821391 474820973 2.770000e-98 370.0
40 TraesCS2D01G474100 chr5D 88.182 220 20 6 5250 5467 464116982 464117197 2.250000e-64 257.0
41 TraesCS2D01G474100 chr5D 74.009 681 101 38 691 1302 464105580 464106253 2.300000e-49 207.0
42 TraesCS2D01G474100 chr5A 87.633 566 63 5 4690 5254 43656383 43655824 0.000000e+00 651.0
43 TraesCS2D01G474100 chr5A 87.456 566 64 5 4690 5254 43742283 43741724 0.000000e+00 645.0
44 TraesCS2D01G474100 chr5A 87.279 566 65 5 4690 5254 43694752 43694193 1.920000e-179 640.0
45 TraesCS2D01G474100 chr5A 85.024 414 52 5 1372 1778 43699836 43699426 4.540000e-111 412.0
46 TraesCS2D01G474100 chr5A 84.578 415 52 7 1372 1778 43659923 43659513 9.840000e-108 401.0
47 TraesCS2D01G474100 chr5A 84.541 414 54 5 1372 1778 43745979 43745569 9.840000e-108 401.0
48 TraesCS2D01G474100 chr5A 80.688 523 76 18 1274 1778 584554218 584554733 3.560000e-102 383.0
49 TraesCS2D01G474100 chr5A 89.671 213 19 3 5250 5461 43612676 43612466 1.040000e-67 268.0
50 TraesCS2D01G474100 chr5A 86.730 211 24 4 5305 5514 43612464 43612257 1.370000e-56 231.0
51 TraesCS2D01G474100 chr7B 84.112 428 65 3 2340 2767 626565863 626565439 1.630000e-110 411.0
52 TraesCS2D01G474100 chr7A 85.890 163 20 2 4522 4681 660082361 660082523 3.020000e-38 171.0


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 TraesCS2D01G474100 chr2D 577340525 577346824 6299 True 11635.000000 11635 100.000000 1 6300 1 chr2D.!!$R3 6299
1 TraesCS2D01G474100 chr2D 551703006 551704597 1591 True 950.000000 950 78.335000 1171 2731 1 chr2D.!!$R1 1560
2 TraesCS2D01G474100 chr2D 577342411 577343488 1077 True 350.000000 350 87.066000 3337 4414 2 chr2D.!!$R4 1077
3 TraesCS2D01G474100 chr2A 715420829 715427372 6543 True 2159.400000 6929 90.971800 1 6300 5 chr2A.!!$R3 6299
4 TraesCS2D01G474100 chr2B 694471284 694477648 6364 True 1965.000000 4470 88.914000 1 6300 5 chr2B.!!$R3 6299
5 TraesCS2D01G474100 chr2B 694419220 694425988 6768 True 1423.200000 4239 89.889143 1 6300 7 chr2B.!!$R1 6299
6 TraesCS2D01G474100 chr2B 694440059 694446765 6706 True 1243.725000 4246 90.290125 1 6300 8 chr2B.!!$R2 6299
7 TraesCS2D01G474100 chr5B 57716266 57719020 2754 True 399.333333 706 85.773000 4407 5514 3 chr5B.!!$R1 1107
8 TraesCS2D01G474100 chr5D 464105580 464117197 11617 False 397.800000 689 83.889400 691 5467 5 chr5D.!!$F1 4776
9 TraesCS2D01G474100 chr5A 43694193 43694752 559 True 640.000000 640 87.279000 4690 5254 1 chr5A.!!$R1 564
10 TraesCS2D01G474100 chr5A 43655824 43659923 4099 True 526.000000 651 86.105500 1372 5254 2 chr5A.!!$R4 3882
11 TraesCS2D01G474100 chr5A 43741724 43745979 4255 True 523.000000 645 85.998500 1372 5254 2 chr5A.!!$R5 3882
12 TraesCS2D01G474100 chr5A 584554218 584554733 515 False 383.000000 383 80.688000 1274 1778 1 chr5A.!!$F1 504

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
455 544 0.453793 CAAAAGTGTGTCGTTGCCCA 59.546 50.000 0.0 0.0 0.00 5.36 F
491 581 1.200760 TACACCCAGCACAGCCTCAT 61.201 55.000 0.0 0.0 0.00 2.90 F
1277 6774 3.181329 TGAGGGCACATAAGGAAAGAGA 58.819 45.455 0.0 0.0 0.00 3.10 F
1278 6775 3.198635 TGAGGGCACATAAGGAAAGAGAG 59.801 47.826 0.0 0.0 0.00 3.20 F
2521 8370 0.250513 GGAGTTCCTCTGCGACCATT 59.749 55.000 0.0 0.0 0.00 3.16 F
2741 8590 0.801251 GACTCTCACATTGGCACAGC 59.199 55.000 0.0 0.0 42.39 4.40 F
4556 12126 1.571919 GTGTATTCGCGCCAGAATCT 58.428 50.000 12.9 0.0 40.83 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 7589 3.176411 TGGATGAGTCTCCACTGACAAT 58.824 45.455 7.10 0.0 40.43 2.71 R
2317 8159 5.324784 TGACTAAGTATGTCGAGCACAAT 57.675 39.130 0.00 0.0 38.97 2.71 R
2521 8370 1.119684 AGGTAGCCATACACGATGCA 58.880 50.000 0.00 0.0 33.79 3.96 R
3238 9144 3.499918 GTGCACAGAGTCACAATTAGCTT 59.500 43.478 13.17 0.0 33.63 3.74 R
4520 12086 8.027189 GCGAATACACCTGTATGAACTATATGA 58.973 37.037 0.00 0.0 40.78 2.15 R
4607 12177 0.250234 TCGGGAACTGAGCCTTCATG 59.750 55.000 0.00 0.0 39.80 3.07 R
5847 15123 1.893801 CGGAAACTCTCTAGGTGTGGT 59.106 52.381 0.00 0.0 0.00 4.16 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
215 216 4.854399 TCTTGGTTTACTGAATTTGCACG 58.146 39.130 0.00 0.00 0.00 5.34
250 251 9.535270 GTCGAATTTGTAAATCTCTTCAAGAAG 57.465 33.333 3.43 3.43 37.61 2.85
301 320 2.706190 GGGGAGCACTGTTAGTGGATAT 59.294 50.000 10.62 0.00 46.01 1.63
455 544 0.453793 CAAAAGTGTGTCGTTGCCCA 59.546 50.000 0.00 0.00 0.00 5.36
491 581 1.200760 TACACCCAGCACAGCCTCAT 61.201 55.000 0.00 0.00 0.00 2.90
506 596 4.598894 CATCTCGCCCCGCTCAGG 62.599 72.222 0.00 0.00 40.63 3.86
679 1203 4.705023 GCCACCATGTATTTCCTTTGTAGT 59.295 41.667 0.00 0.00 0.00 2.73
888 6316 7.275779 GTGTTTTATGTAGATTCAGCTCTCGAA 59.724 37.037 0.00 0.00 0.00 3.71
1028 6472 4.220382 ACACCAGCAAAAGCAATATAGCAA 59.780 37.500 0.00 0.00 36.85 3.91
1276 6773 3.634397 TGAGGGCACATAAGGAAAGAG 57.366 47.619 0.00 0.00 0.00 2.85
1277 6774 3.181329 TGAGGGCACATAAGGAAAGAGA 58.819 45.455 0.00 0.00 0.00 3.10
1278 6775 3.198635 TGAGGGCACATAAGGAAAGAGAG 59.801 47.826 0.00 0.00 0.00 3.20
1537 7136 7.777095 TGGTGCTTACTAATTTGACAAAGTTT 58.223 30.769 6.15 0.00 0.00 2.66
1655 7260 9.950496 AATAAAAGAGAGATAACATATCCGCAT 57.050 29.630 0.00 0.00 0.00 4.73
1926 7535 7.148573 CCAACACTACTATCAAACATGTCACTC 60.149 40.741 0.00 0.00 0.00 3.51
1980 7589 3.308401 TGCCAGGATCAGCACTAATCTA 58.692 45.455 0.00 0.00 33.08 1.98
2521 8370 0.250513 GGAGTTCCTCTGCGACCATT 59.749 55.000 0.00 0.00 0.00 3.16
2591 8440 4.082679 ACAGTTCTCAGTCACGGTATTCTC 60.083 45.833 0.00 0.00 0.00 2.87
2741 8590 0.801251 GACTCTCACATTGGCACAGC 59.199 55.000 0.00 0.00 42.39 4.40
4520 12086 1.734465 GTCATTGAGCTAACTTGCGCT 59.266 47.619 9.73 0.00 39.61 5.92
4556 12126 1.571919 GTGTATTCGCGCCAGAATCT 58.428 50.000 12.90 0.00 40.83 2.40
4681 12251 6.839657 CCTGGTAGAGGTAAATCTTCTTCCTA 59.160 42.308 0.00 0.00 39.33 2.94
4682 12252 7.344871 CCTGGTAGAGGTAAATCTTCTTCCTAA 59.655 40.741 0.00 0.00 39.33 2.69
4781 12390 3.198872 GTTCAGAGAAGGCCGGAATTAG 58.801 50.000 5.05 0.00 0.00 1.73
4831 12440 4.288105 AGGGACAAGGAATATGCTATGGAG 59.712 45.833 0.00 0.00 0.00 3.86
4888 12497 5.334802 CGTGATCAAGGAAATAAAGCACACA 60.335 40.000 0.00 0.00 0.00 3.72
4889 12498 6.446318 GTGATCAAGGAAATAAAGCACACAA 58.554 36.000 0.00 0.00 0.00 3.33
5107 12716 2.046411 TACGAGTACACCGGCGGA 60.046 61.111 35.78 7.50 0.00 5.54
5327 14422 9.968743 CCTTTGTTTTTGTTCTAGTATATCGTC 57.031 33.333 0.00 0.00 0.00 4.20
5575 14831 5.170748 GGTCCAATTAAGGCACATTTCTTG 58.829 41.667 0.00 0.00 0.00 3.02
5615 14883 2.213499 CGGGATGCCACATCTCTTAAC 58.787 52.381 3.39 0.00 0.00 2.01
5691 14967 9.804977 AAGATATATCATTTTCTAAGGCAGCTT 57.195 29.630 15.08 0.00 0.00 3.74
5692 14968 9.228949 AGATATATCATTTTCTAAGGCAGCTTG 57.771 33.333 15.08 0.00 0.00 4.01
5847 15123 6.721668 AGTACACTCTTCATATATAGCAGCCA 59.278 38.462 0.00 0.00 0.00 4.75
5952 15235 2.807967 CAGCAAGAATCAAACCGTCTCA 59.192 45.455 0.00 0.00 0.00 3.27
6028 15311 1.453197 GGGGGTGCCAACCTTATCG 60.453 63.158 0.00 0.00 46.70 2.92
6272 15557 2.369633 TGCATGTCCATCCCGAGCT 61.370 57.895 0.00 0.00 0.00 4.09
6281 15566 1.115467 CATCCCGAGCTAGTGTCCTT 58.885 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 216 7.752695 AGATTTACAAATTCGACCATTCTGTC 58.247 34.615 0.00 0.00 0.00 3.51
279 296 0.472925 TCCACTAACAGTGCTCCCCA 60.473 55.000 0.64 0.00 44.63 4.96
284 301 6.551227 TGTCTGATATATCCACTAACAGTGCT 59.449 38.462 10.25 0.00 44.63 4.40
285 302 6.749139 TGTCTGATATATCCACTAACAGTGC 58.251 40.000 10.25 0.00 44.63 4.40
294 313 7.482169 TTGATACCCTGTCTGATATATCCAC 57.518 40.000 10.25 7.48 0.00 4.02
301 320 4.682320 GCGGTTTTGATACCCTGTCTGATA 60.682 45.833 0.00 0.00 34.56 2.15
411 434 7.025963 GCCCTAACGAGTATACATACATACAC 58.974 42.308 5.50 0.00 34.42 2.90
455 544 3.197983 GGTGTATGTAGAAAGGCTGAGGT 59.802 47.826 0.00 0.00 0.00 3.85
506 596 3.787001 CCTCCGCCCCACCTCTTC 61.787 72.222 0.00 0.00 0.00 2.87
1028 6472 9.666191 TCTGCTTATCATCTATCATACCCATAT 57.334 33.333 0.00 0.00 0.00 1.78
1276 6773 8.017418 TCTTTATCATTCTCCTTCTTCTCCTC 57.983 38.462 0.00 0.00 0.00 3.71
1277 6774 7.071071 CCTCTTTATCATTCTCCTTCTTCTCCT 59.929 40.741 0.00 0.00 0.00 3.69
1278 6775 7.070571 TCCTCTTTATCATTCTCCTTCTTCTCC 59.929 40.741 0.00 0.00 0.00 3.71
1471 7070 3.881220 ACGGAAAGAGAACCTTCACAAA 58.119 40.909 0.00 0.00 33.02 2.83
1561 7165 8.864069 AATATCAGTGACTAATCGAACAAGAG 57.136 34.615 0.00 0.00 0.00 2.85
1870 7479 8.918202 TGATTTCAAGAGTTTGGTAATAGTGT 57.082 30.769 0.00 0.00 34.97 3.55
1926 7535 3.561725 GCGATCAATTCTGTCCCTTTAGG 59.438 47.826 0.00 0.00 0.00 2.69
1980 7589 3.176411 TGGATGAGTCTCCACTGACAAT 58.824 45.455 7.10 0.00 40.43 2.71
2317 8159 5.324784 TGACTAAGTATGTCGAGCACAAT 57.675 39.130 0.00 0.00 38.97 2.71
2521 8370 1.119684 AGGTAGCCATACACGATGCA 58.880 50.000 0.00 0.00 33.79 3.96
3238 9144 3.499918 GTGCACAGAGTCACAATTAGCTT 59.500 43.478 13.17 0.00 33.63 3.74
4520 12086 8.027189 GCGAATACACCTGTATGAACTATATGA 58.973 37.037 0.00 0.00 40.78 2.15
4556 12126 6.909550 AATTTGGTTAAGTCCTTGCATACA 57.090 33.333 0.00 0.00 0.00 2.29
4607 12177 0.250234 TCGGGAACTGAGCCTTCATG 59.750 55.000 0.00 0.00 39.80 3.07
4681 12251 8.132362 TCAAATTTTGTTGTAATCAGCGTAGTT 58.868 29.630 8.89 0.00 0.00 2.24
4682 12252 7.644490 TCAAATTTTGTTGTAATCAGCGTAGT 58.356 30.769 8.89 0.00 0.00 2.73
4781 12390 0.171455 ATTGGACGTCTCTGCGACTC 59.829 55.000 16.46 0.00 40.59 3.36
4831 12440 2.198304 ATTGGAACCTCCGTGCCCTC 62.198 60.000 0.00 0.00 40.17 4.30
4888 12497 6.535150 CCATGAAGTACGACACATAGACATTT 59.465 38.462 0.00 0.00 0.00 2.32
4889 12498 6.042777 CCATGAAGTACGACACATAGACATT 58.957 40.000 0.00 0.00 0.00 2.71
5327 14422 1.733912 CAACACACACCTCCATCATCG 59.266 52.381 0.00 0.00 0.00 3.84
5506 14762 7.215789 ACCATTTTTGATCAACAATTGCAGTA 58.784 30.769 15.54 0.00 38.36 2.74
5507 14763 6.056884 ACCATTTTTGATCAACAATTGCAGT 58.943 32.000 15.54 9.21 38.36 4.40
5508 14764 6.548441 ACCATTTTTGATCAACAATTGCAG 57.452 33.333 15.54 8.70 38.36 4.41
5509 14765 6.988580 TGTACCATTTTTGATCAACAATTGCA 59.011 30.769 15.54 10.25 38.36 4.08
5510 14766 7.418840 TGTACCATTTTTGATCAACAATTGC 57.581 32.000 15.54 8.15 38.36 3.56
5511 14767 9.258826 TCTTGTACCATTTTTGATCAACAATTG 57.741 29.630 15.54 14.65 38.36 2.32
5512 14768 9.829507 TTCTTGTACCATTTTTGATCAACAATT 57.170 25.926 15.54 6.86 38.36 2.32
5544 14800 2.711542 CCTTAATTGGACCGAACTGCT 58.288 47.619 0.00 0.00 0.00 4.24
5575 14831 2.160013 CGTACTTAAGCAGTGACGCAAC 60.160 50.000 1.29 0.00 35.97 4.17
5691 14967 5.818887 TGATGATCCTCCTGATTTTGTTCA 58.181 37.500 0.00 0.00 32.41 3.18
5692 14968 6.679884 GCTTGATGATCCTCCTGATTTTGTTC 60.680 42.308 0.00 0.00 32.41 3.18
5847 15123 1.893801 CGGAAACTCTCTAGGTGTGGT 59.106 52.381 0.00 0.00 0.00 4.16
5952 15235 2.174854 ACTGTTGAAGCTACCACCCTTT 59.825 45.455 0.00 0.00 0.00 3.11
6128 15413 3.831911 TCCCCTCCAAAATGCTAAACTTG 59.168 43.478 0.00 0.00 0.00 3.16
6281 15566 1.954146 GTTGACGCTGCCTTCGACA 60.954 57.895 10.13 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.