Multiple sequence alignment - TraesCS2D01G343000

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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 TraesCS2D01G343000 chr2D 100.000 3928 0 0 535 4462 439443607 439439680 0.000000e+00 7254
1 TraesCS2D01G343000 chr2D 100.000 256 0 0 1 256 439444141 439443886 1.450000e-129 473
2 TraesCS2D01G343000 chr2D 93.141 277 18 1 1549 1825 439442500 439442225 5.370000e-109 405
3 TraesCS2D01G343000 chr2D 93.141 277 18 1 1642 1917 439442593 439442317 5.370000e-109 405
4 TraesCS2D01G343000 chr2D 91.848 184 15 0 1549 1732 439442407 439442224 1.590000e-64 257
5 TraesCS2D01G343000 chr2D 91.848 184 15 0 1735 1918 439442593 439442410 1.590000e-64 257
6 TraesCS2D01G343000 chr2A 95.933 3787 94 25 535 4297 549677246 549680996 0.000000e+00 6085
7 TraesCS2D01G343000 chr2A 96.283 269 10 0 1549 1817 549678359 549678627 4.100000e-120 442
8 TraesCS2D01G343000 chr2A 93.863 277 17 0 1642 1918 549678266 549678542 6.900000e-113 418
9 TraesCS2D01G343000 chr2A 93.939 264 3 6 1 256 549676866 549677124 1.950000e-103 387
10 TraesCS2D01G343000 chr2A 94.022 184 11 0 1549 1732 549678452 549678635 3.400000e-71 279
11 TraesCS2D01G343000 chr2A 90.710 183 15 2 1735 1916 549678266 549678447 4.460000e-60 243
12 TraesCS2D01G343000 chr2A 97.500 80 2 0 4383 4462 549680991 549681070 2.160000e-28 137
13 TraesCS2D01G343000 chr2A 92.771 83 6 0 1549 1631 549678545 549678627 2.180000e-23 121
14 TraesCS2D01G343000 chr2B 93.761 2741 128 21 1733 4462 517383871 517381163 0.000000e+00 4074
15 TraesCS2D01G343000 chr2B 91.077 1244 50 19 538 1732 517384917 517383686 0.000000e+00 1626
16 TraesCS2D01G343000 chr2B 92.760 221 6 3 46 256 517385489 517385269 1.210000e-80 311
17 TraesCS2D01G343000 chr2B 93.011 186 12 1 1640 1825 517383871 517383687 2.050000e-68 270
18 TraesCS2D01G343000 chrUn 86.184 152 12 2 4141 4283 388893916 388893765 5.980000e-34 156
19 TraesCS2D01G343000 chrUn 85.526 152 13 2 4141 4283 53260721 53260872 2.780000e-32 150
20 TraesCS2D01G343000 chr1A 86.184 152 12 2 4141 4283 554479057 554478906 5.980000e-34 156
21 TraesCS2D01G343000 chr6D 86.806 144 10 2 4141 4275 210720021 210719878 7.730000e-33 152
22 TraesCS2D01G343000 chr6D 84.868 152 14 2 4141 4283 114267569 114267418 1.290000e-30 145
23 TraesCS2D01G343000 chr7D 85.526 152 13 2 4141 4283 628576716 628576867 2.780000e-32 150
24 TraesCS2D01G343000 chr1B 85.430 151 11 4 4131 4271 427664555 427664704 3.600000e-31 147
25 TraesCS2D01G343000 chr4D 84.868 152 14 2 4141 4283 206972802 206972953 1.290000e-30 145


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 TraesCS2D01G343000 chr2D 439439680 439444141 4461 True 1508.50 7254 94.996333 1 4462 6 chr2D.!!$R1 4461
1 TraesCS2D01G343000 chr2A 549676866 549681070 4204 False 1014.00 6085 94.377625 1 4462 8 chr2A.!!$F1 4461
2 TraesCS2D01G343000 chr2B 517381163 517385489 4326 True 1570.25 4074 92.652250 46 4462 4 chr2B.!!$R1 4416

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
705 825 2.947938 ATTGCTCTGATTCGGGCCCG 62.948 60.0 39.13 39.13 41.35 6.13 F
1272 1411 1.056700 ACCCTGCGGATCTATTGCCT 61.057 55.0 0.00 0.00 0.00 4.75 F
1708 1865 0.031585 CAGTGCTGCATTGTTGTGCT 59.968 50.0 16.02 0.00 45.27 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1777 0.256752 CTCCCATGGCATCAACTCCA 59.743 55.000 6.09 0.0 36.7 3.86 R
2642 2804 2.504367 ACTTCGCTTTGTTGGTGCTAT 58.496 42.857 0.00 0.0 0.0 2.97 R
3683 3847 3.673956 TAATGCGCCACCCACCTCG 62.674 63.158 4.18 0.0 0.0 4.63 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
224 242 4.733725 CCCGTTCCCTCCCCCTCA 62.734 72.222 0.00 0.00 0.00 3.86
705 825 2.947938 ATTGCTCTGATTCGGGCCCG 62.948 60.000 39.13 39.13 41.35 6.13
823 952 5.858475 AGATTGTCGTCTTTTTATTGAGCG 58.142 37.500 0.00 0.00 0.00 5.03
1094 1233 2.272146 GATTGGAGCGCAGGGGAA 59.728 61.111 11.47 0.00 0.00 3.97
1168 1307 1.903294 GAGTGCTCTGCCCTGATGA 59.097 57.895 0.00 0.00 0.00 2.92
1272 1411 1.056700 ACCCTGCGGATCTATTGCCT 61.057 55.000 0.00 0.00 0.00 4.75
1337 1476 4.379243 CGCCAGTTGCCTCGACCT 62.379 66.667 0.00 0.00 36.24 3.85
1384 1526 2.280797 GAAGCAGTGACGGTGGCA 60.281 61.111 0.00 0.00 0.00 4.92
1441 1598 4.514594 TCTCCCGGGGGCCATCAT 62.515 66.667 23.50 0.00 34.68 2.45
1442 1599 3.958860 CTCCCGGGGGCCATCATC 61.959 72.222 23.50 0.00 34.68 2.92
1445 1602 2.153401 CCCGGGGGCCATCATCTTA 61.153 63.158 14.71 0.00 0.00 2.10
1620 1777 0.241749 CTGCATTGTTGTGCCGTGAT 59.758 50.000 0.00 0.00 44.43 3.06
1632 1789 1.718757 GCCGTGATGGAGTTGATGCC 61.719 60.000 0.00 0.00 42.00 4.40
1633 1790 0.392863 CCGTGATGGAGTTGATGCCA 60.393 55.000 0.00 0.00 42.00 4.92
1708 1865 0.031585 CAGTGCTGCATTGTTGTGCT 59.968 50.000 16.02 0.00 45.27 4.40
1730 1887 1.002134 AAGGAGTTGATGCCGTGGG 60.002 57.895 0.00 0.00 0.00 4.61
1821 1978 1.470805 CGTGATGGAGTTGATGCCGTA 60.471 52.381 0.00 0.00 0.00 4.02
1944 2101 2.158957 ACCACATGACGGGATGATGTAC 60.159 50.000 0.00 0.00 0.00 2.90
2516 2678 5.945784 AGCATACCATGTTTTTCTTGCTCTA 59.054 36.000 0.00 0.00 34.27 2.43
2658 2820 5.478233 TTACATATAGCACCAACAAAGCG 57.522 39.130 0.00 0.00 0.00 4.68
2942 3106 6.540551 TCTTGTTACAACAGTTGAGTATTGCA 59.459 34.615 20.56 5.96 40.50 4.08
3266 3430 3.405831 CAGTGACAAGAGATCTGGCAAA 58.594 45.455 0.00 0.00 0.00 3.68
3526 3690 7.851228 TCTTTCTTAGCATTACTGATGAAGGA 58.149 34.615 0.00 0.00 38.03 3.36
3683 3847 2.031163 AGCCTCACCAGCGACAAC 59.969 61.111 0.00 0.00 34.64 3.32
3820 3984 5.044328 TCAAGAGTGTATAGGTAGAGGGTGT 60.044 44.000 0.00 0.00 0.00 4.16
3822 3986 3.890147 GAGTGTATAGGTAGAGGGTGTGG 59.110 52.174 0.00 0.00 0.00 4.17
3952 4117 5.934402 AATAGTTTGTCCTGGATACGTCT 57.066 39.130 0.00 0.00 42.51 4.18
3956 4121 4.062991 GTTTGTCCTGGATACGTCTTGTT 58.937 43.478 0.00 0.00 42.51 2.83
4070 4238 6.292488 GCATCCTTTTTCATCTGTTGTGTTTG 60.292 38.462 0.00 0.00 0.00 2.93
4106 4274 4.588528 TGTGAATCTGTGATGATATCCCGA 59.411 41.667 0.00 0.00 0.00 5.14
4117 4285 9.599866 TGTGATGATATCCCGATATGATAAAAC 57.400 33.333 0.00 1.28 34.36 2.43
4136 4304 3.249189 TGCTCCTTGGCCGTCCTT 61.249 61.111 0.00 0.00 0.00 3.36
4178 4346 4.273318 ACCTGAGCAGTTTCTTGAAAACT 58.727 39.130 0.00 0.00 40.80 2.66
4206 4374 8.084684 GCTTCAGATATGAAATTTTGGGTATCC 58.915 37.037 4.06 0.00 0.00 2.59
4207 4375 9.135189 CTTCAGATATGAAATTTTGGGTATCCA 57.865 33.333 4.06 0.00 42.25 3.41
4208 4376 8.696043 TCAGATATGAAATTTTGGGTATCCAG 57.304 34.615 0.00 0.00 45.04 3.86
4211 4379 4.683766 TGAAATTTTGGGTATCCAGGGA 57.316 40.909 0.00 0.00 45.04 4.20
4213 4381 3.688049 AATTTTGGGTATCCAGGGAGG 57.312 47.619 0.00 0.00 45.04 4.30
4214 4382 2.068831 TTTTGGGTATCCAGGGAGGT 57.931 50.000 0.00 0.00 45.04 3.85
4231 4401 1.177401 GGTCCTTGTCAAGATTGCCC 58.823 55.000 14.42 2.77 0.00 5.36
4243 4413 6.166279 GTCAAGATTGCCCGATAATAGATCA 58.834 40.000 0.00 0.00 0.00 2.92
4275 4445 3.741476 CGCCCTGCTTGTTCTGCC 61.741 66.667 0.00 0.00 0.00 4.85
4292 4462 0.958822 GCCCCCAATAATGTAAGCGG 59.041 55.000 0.00 0.00 0.00 5.52
4294 4464 2.661718 CCCCCAATAATGTAAGCGGTT 58.338 47.619 4.76 4.76 0.00 4.44
4295 4465 3.028130 CCCCCAATAATGTAAGCGGTTT 58.972 45.455 4.64 0.00 0.00 3.27
4312 4482 4.261322 GCGGTTTGCAGACAATCATGATAT 60.261 41.667 9.04 0.00 45.45 1.63
4313 4483 5.734220 GCGGTTTGCAGACAATCATGATATT 60.734 40.000 9.04 0.00 45.45 1.28
4315 4485 6.211515 GGTTTGCAGACAATCATGATATTCC 58.788 40.000 9.04 0.00 35.21 3.01
4323 4493 4.993584 ACAATCATGATATTCCACGAGAGC 59.006 41.667 9.04 0.00 0.00 4.09
4330 4500 4.772100 TGATATTCCACGAGAGCATATGGA 59.228 41.667 4.56 0.00 39.50 3.41
4331 4501 3.674528 ATTCCACGAGAGCATATGGAG 57.325 47.619 4.56 0.00 42.12 3.86
4333 4503 1.957177 TCCACGAGAGCATATGGAGTC 59.043 52.381 4.56 0.00 36.30 3.36
4341 4511 2.294791 GAGCATATGGAGTCACGTAGCT 59.705 50.000 4.56 0.00 0.00 3.32
4342 4512 2.695666 AGCATATGGAGTCACGTAGCTT 59.304 45.455 4.56 0.00 0.00 3.74
4348 4518 2.101750 TGGAGTCACGTAGCTTGTGAAA 59.898 45.455 19.40 6.78 46.99 2.69
4405 4575 1.153349 GGGAAGCATGTCGACTCCC 60.153 63.158 20.42 20.42 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.152138 GGGGTTTTCCTTCGGGTGT 59.848 57.895 0.00 0.00 40.46 4.16
41 42 1.605451 CCGGTGGGGGTTTTCCTTC 60.605 63.158 0.00 0.00 40.46 3.46
1094 1233 3.569701 CAGCGCCATAATAACCTCCAAAT 59.430 43.478 2.29 0.00 0.00 2.32
1168 1307 3.341629 CCAGCATCCACACCCCCT 61.342 66.667 0.00 0.00 0.00 4.79
1200 1339 4.400251 CCTGGGGACGAGAGGGGT 62.400 72.222 0.00 0.00 0.00 4.95
1337 1476 1.005037 GCACCAGACATGACCGTGA 60.005 57.895 14.29 0.00 0.00 4.35
1384 1526 1.869132 GTAAAAACTCAAGTCGGCCGT 59.131 47.619 27.15 2.93 0.00 5.68
1620 1777 0.256752 CTCCCATGGCATCAACTCCA 59.743 55.000 6.09 0.00 36.70 3.86
1708 1865 0.396435 ACGGCATCAACTCCTTCACA 59.604 50.000 0.00 0.00 0.00 3.58
1746 1903 1.559682 TCCTCTCCAGGTACAATTGGC 59.440 52.381 10.83 2.02 41.28 4.52
1821 1978 4.457496 CGTGAGCATGACGCCCCT 62.457 66.667 0.00 0.00 39.88 4.79
1944 2101 2.997899 CCCAAGATAGGCAAGAGCG 58.002 57.895 0.00 0.00 43.41 5.03
2261 2421 3.160269 CAAATATGATCCCAGGCCTTCC 58.840 50.000 0.00 0.00 0.00 3.46
2369 2529 6.630443 CAGTCATATTTAGCTCGAATTTGTGC 59.370 38.462 11.10 11.10 0.00 4.57
2516 2678 5.509840 CGCAGAAAATACTACCCAGATAGCT 60.510 44.000 0.00 0.00 0.00 3.32
2642 2804 2.504367 ACTTCGCTTTGTTGGTGCTAT 58.496 42.857 0.00 0.00 0.00 2.97
3683 3847 3.673956 TAATGCGCCACCCACCTCG 62.674 63.158 4.18 0.00 0.00 4.63
3820 3984 1.027255 CAACACACCGACACCAACCA 61.027 55.000 0.00 0.00 0.00 3.67
3822 3986 1.063488 GCAACACACCGACACCAAC 59.937 57.895 0.00 0.00 0.00 3.77
3952 4117 7.633193 AACAAGTTACCAAGTCATACAACAA 57.367 32.000 0.00 0.00 0.00 2.83
3956 4121 9.214957 CTATGAAACAAGTTACCAAGTCATACA 57.785 33.333 0.00 0.00 0.00 2.29
4070 4238 5.049405 CACAGATTCACAGTAAACTCCAACC 60.049 44.000 0.00 0.00 0.00 3.77
4106 4274 4.829492 GCCAAGGAGCAGGTTTTATCATAT 59.171 41.667 0.00 0.00 0.00 1.78
4117 4285 4.785453 GGACGGCCAAGGAGCAGG 62.785 72.222 0.00 0.00 31.65 4.85
4136 4304 1.407936 TTTACCAAAAGCTGCCTGCA 58.592 45.000 0.00 0.00 45.94 4.41
4178 4346 7.243604 ACCCAAAATTTCATATCTGAAGCAA 57.756 32.000 0.00 0.00 42.19 3.91
4208 4376 2.716217 CAATCTTGACAAGGACCTCCC 58.284 52.381 15.13 0.00 36.42 4.30
4211 4379 1.272147 GGGCAATCTTGACAAGGACCT 60.272 52.381 15.13 0.00 38.18 3.85
4213 4381 0.804989 CGGGCAATCTTGACAAGGAC 59.195 55.000 15.13 1.38 38.18 3.85
4214 4382 0.690192 TCGGGCAATCTTGACAAGGA 59.310 50.000 15.13 2.90 38.18 3.36
4231 4401 8.944029 AGCTTTGGATGAATTGATCTATTATCG 58.056 33.333 4.85 0.00 0.00 2.92
4243 4413 1.106285 GGGCGAGCTTTGGATGAATT 58.894 50.000 0.00 0.00 0.00 2.17
4275 4445 3.736740 GCAAACCGCTTACATTATTGGGG 60.737 47.826 0.00 0.00 37.77 4.96
4292 4462 6.694411 GTGGAATATCATGATTGTCTGCAAAC 59.306 38.462 14.65 0.00 38.21 2.93
4294 4464 5.007921 CGTGGAATATCATGATTGTCTGCAA 59.992 40.000 14.65 0.00 39.16 4.08
4295 4465 4.512571 CGTGGAATATCATGATTGTCTGCA 59.487 41.667 14.65 4.98 0.00 4.41
4300 4470 4.993584 GCTCTCGTGGAATATCATGATTGT 59.006 41.667 14.65 1.70 32.89 2.71
4302 4472 5.219343 TGCTCTCGTGGAATATCATGATT 57.781 39.130 14.65 0.00 32.89 2.57
4312 4482 2.362397 GACTCCATATGCTCTCGTGGAA 59.638 50.000 0.00 0.00 40.03 3.53
4313 4483 1.957177 GACTCCATATGCTCTCGTGGA 59.043 52.381 0.00 0.00 38.37 4.02
4315 4485 2.736978 GTGACTCCATATGCTCTCGTG 58.263 52.381 0.00 0.00 0.00 4.35
4323 4493 3.798878 CACAAGCTACGTGACTCCATATG 59.201 47.826 10.02 0.00 36.43 1.78
4330 4500 3.131396 CCTTTTCACAAGCTACGTGACT 58.869 45.455 16.31 0.00 42.88 3.41
4331 4501 2.870411 ACCTTTTCACAAGCTACGTGAC 59.130 45.455 16.31 0.00 42.88 3.67
4333 4503 2.869801 TGACCTTTTCACAAGCTACGTG 59.130 45.455 9.42 9.42 35.63 4.49
4341 4511 4.462508 TTGTTGCATGACCTTTTCACAA 57.537 36.364 0.00 0.00 36.92 3.33
4342 4512 4.462508 TTTGTTGCATGACCTTTTCACA 57.537 36.364 0.00 0.00 36.92 3.58
4348 4518 3.006110 CCTCACATTTGTTGCATGACCTT 59.994 43.478 0.00 0.00 0.00 3.50
4405 4575 0.741221 GACAAGCAAGCGAGGTAGGG 60.741 60.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.