Multiple sequence alignment - TraesCS2D01G177400

Loading Multiple Alignment...

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 TraesCS2D01G177400 chr2D 100.000 3390 0 0 1 3390 120996290 120992901 0.000000e+00 6261
1 TraesCS2D01G177400 chr2B 89.157 2776 180 66 654 3381 174386769 174384067 0.000000e+00 3347
2 TraesCS2D01G177400 chr2B 88.755 498 48 4 1 494 174390653 174390160 1.350000e-168 603
3 TraesCS2D01G177400 chr2B 97.761 134 3 0 507 640 174390177 174390044 7.320000e-57 231
4 TraesCS2D01G177400 chr2A 91.456 1744 78 31 509 2224 125200758 125199058 0.000000e+00 2329
5 TraesCS2D01G177400 chr2A 88.266 1159 71 25 2251 3347 125198960 125197805 0.000000e+00 1327
6 TraesCS2D01G177400 chr2A 88.153 498 41 8 1 494 125201226 125200743 8.160000e-161 577


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 TraesCS2D01G177400 chr2D 120992901 120996290 3389 True 6261.000000 6261 100.000000 1 3390 1 chr2D.!!$R1 3389
1 TraesCS2D01G177400 chr2B 174384067 174390653 6586 True 1393.666667 3347 91.891000 1 3381 3 chr2B.!!$R1 3380
2 TraesCS2D01G177400 chr2A 125197805 125201226 3421 True 1411.000000 2329 89.291667 1 3347 3 chr2A.!!$R1 3346

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
452 455 0.392998 ATGCTCCGCTTCCACGAATT 60.393 50.0 0.00 0.00 34.06 2.17 F
1085 4361 0.037882 GAGTAGTGCAGCAGCTGACA 60.038 55.0 27.39 19.51 42.74 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 5153 0.885879 TCAAGATCTGCGTGGTACGT 59.114 50.000 0.00 0.00 44.73 3.57 R
2694 6085 1.071542 TCAAATCTTGGCCTGTCGACA 59.928 47.619 18.88 18.88 0.00 4.35 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
47 48 8.788806 CGAGTTGTGATCCTATATTTCTACTCT 58.211 37.037 0.00 0.00 0.00 3.24
49 50 9.084533 AGTTGTGATCCTATATTTCTACTCTCC 57.915 37.037 0.00 0.00 0.00 3.71
60 61 3.441505 TCTACTCTCCTACTCCCTCCT 57.558 52.381 0.00 0.00 0.00 3.69
118 119 9.452287 AATCCCAGGTCAAAATTTGATAAAATG 57.548 29.630 11.87 6.64 42.47 2.32
170 171 2.679837 TGCTCGATCCAATTCTCTTTGC 59.320 45.455 0.00 0.00 0.00 3.68
176 177 6.690530 TCGATCCAATTCTCTTTGCAAAATT 58.309 32.000 13.84 7.14 0.00 1.82
177 178 7.153985 TCGATCCAATTCTCTTTGCAAAATTT 58.846 30.769 13.84 0.00 0.00 1.82
178 179 7.656948 TCGATCCAATTCTCTTTGCAAAATTTT 59.343 29.630 13.84 0.00 0.00 1.82
196 197 6.853279 AATTTTCACGTGATTTATTGCGAG 57.147 33.333 20.80 0.00 0.00 5.03
199 200 2.670905 TCACGTGATTTATTGCGAGTGG 59.329 45.455 15.76 0.00 0.00 4.00
200 201 1.396996 ACGTGATTTATTGCGAGTGGC 59.603 47.619 0.00 0.00 43.96 5.01
366 368 6.481643 TGTGGGTTTTTGTTAAAAATTCCCA 58.518 32.000 17.38 17.38 46.19 4.37
374 376 6.702716 TTGTTAAAAATTCCCAAGAGTCGT 57.297 33.333 0.00 0.00 0.00 4.34
387 389 5.646360 CCCAAGAGTCGTGGTTTTGTATTAT 59.354 40.000 21.63 0.00 34.01 1.28
406 409 0.961019 TCTCAGCCCAAATGTTGTGC 59.039 50.000 0.00 0.00 34.03 4.57
423 426 0.527113 TGCATTTGTGCGATTCCCTG 59.473 50.000 0.00 0.00 37.69 4.45
438 441 2.695359 TCCCTGTTAACACGAATGCTC 58.305 47.619 3.59 0.00 0.00 4.26
440 443 1.393539 CCTGTTAACACGAATGCTCCG 59.606 52.381 3.59 0.00 0.00 4.63
441 444 0.793861 TGTTAACACGAATGCTCCGC 59.206 50.000 3.59 0.00 0.00 5.54
448 451 2.802667 CGAATGCTCCGCTTCCACG 61.803 63.158 0.00 0.00 0.00 4.94
450 453 1.003839 AATGCTCCGCTTCCACGAA 60.004 52.632 0.00 0.00 34.06 3.85
452 455 0.392998 ATGCTCCGCTTCCACGAATT 60.393 50.000 0.00 0.00 34.06 2.17
453 456 0.605319 TGCTCCGCTTCCACGAATTT 60.605 50.000 0.00 0.00 34.06 1.82
461 464 3.678072 CGCTTCCACGAATTTCTTAGTCA 59.322 43.478 0.00 0.00 34.06 3.41
468 471 9.878667 TTCCACGAATTTCTTAGTCAATATACA 57.121 29.630 0.00 0.00 0.00 2.29
487 490 9.938280 AATATACAGTAACAGAAAAGTACAGCA 57.062 29.630 0.00 0.00 0.00 4.41
490 493 7.653767 ACAGTAACAGAAAAGTACAGCATAC 57.346 36.000 0.00 0.00 0.00 2.39
491 494 7.214381 ACAGTAACAGAAAAGTACAGCATACA 58.786 34.615 0.00 0.00 0.00 2.29
492 495 7.170998 ACAGTAACAGAAAAGTACAGCATACAC 59.829 37.037 0.00 0.00 0.00 2.90
493 496 7.385205 CAGTAACAGAAAAGTACAGCATACACT 59.615 37.037 0.00 0.00 0.00 3.55
494 497 6.787085 AACAGAAAAGTACAGCATACACTC 57.213 37.500 0.00 0.00 0.00 3.51
495 498 5.238583 ACAGAAAAGTACAGCATACACTCC 58.761 41.667 0.00 0.00 0.00 3.85
496 499 5.012148 ACAGAAAAGTACAGCATACACTCCT 59.988 40.000 0.00 0.00 0.00 3.69
497 500 5.934625 CAGAAAAGTACAGCATACACTCCTT 59.065 40.000 0.00 0.00 0.00 3.36
498 501 6.428159 CAGAAAAGTACAGCATACACTCCTTT 59.572 38.462 0.00 0.00 0.00 3.11
499 502 6.998673 AGAAAAGTACAGCATACACTCCTTTT 59.001 34.615 0.00 0.00 34.58 2.27
500 503 6.803154 AAAGTACAGCATACACTCCTTTTC 57.197 37.500 0.00 0.00 0.00 2.29
501 504 5.746990 AGTACAGCATACACTCCTTTTCT 57.253 39.130 0.00 0.00 0.00 2.52
502 505 6.852420 AGTACAGCATACACTCCTTTTCTA 57.148 37.500 0.00 0.00 0.00 2.10
503 506 7.241042 AGTACAGCATACACTCCTTTTCTAA 57.759 36.000 0.00 0.00 0.00 2.10
504 507 7.676947 AGTACAGCATACACTCCTTTTCTAAA 58.323 34.615 0.00 0.00 0.00 1.85
505 508 8.154856 AGTACAGCATACACTCCTTTTCTAAAA 58.845 33.333 0.00 0.00 0.00 1.52
685 3949 2.186384 GCCAGCGCTCTCACTCAT 59.814 61.111 7.13 0.00 0.00 2.90
769 4033 2.612200 CTAGACGCGCTAGCTCTCT 58.388 57.895 19.53 11.65 40.15 3.10
770 4034 0.511221 CTAGACGCGCTAGCTCTCTC 59.489 60.000 19.53 2.25 40.15 3.20
783 4047 1.067213 GCTCTCTCAAGCTTTCGTCCT 60.067 52.381 0.00 0.00 39.27 3.85
821 4085 3.322466 CAGGAGAAGCCCCCGTGT 61.322 66.667 0.00 0.00 37.37 4.49
844 4108 2.184322 GTCCTCGCTCATCGCCAA 59.816 61.111 0.00 0.00 38.27 4.52
845 4109 2.167861 GTCCTCGCTCATCGCCAAC 61.168 63.158 0.00 0.00 38.27 3.77
846 4110 2.892425 CCTCGCTCATCGCCAACC 60.892 66.667 0.00 0.00 38.27 3.77
847 4111 2.125552 CTCGCTCATCGCCAACCA 60.126 61.111 0.00 0.00 38.27 3.67
920 4191 3.369147 CCGATCATTCTTGCGGATACATC 59.631 47.826 0.00 0.00 46.29 3.06
929 4200 1.841663 GCGGATACATCGCGCCAATT 61.842 55.000 0.00 0.00 43.71 2.32
994 4265 3.840666 TGTGCTTGAAGAGAGTAGGGATT 59.159 43.478 0.00 0.00 0.00 3.01
995 4266 5.023452 TGTGCTTGAAGAGAGTAGGGATTA 58.977 41.667 0.00 0.00 0.00 1.75
996 4267 5.483937 TGTGCTTGAAGAGAGTAGGGATTAA 59.516 40.000 0.00 0.00 0.00 1.40
997 4268 6.156949 TGTGCTTGAAGAGAGTAGGGATTAAT 59.843 38.462 0.00 0.00 0.00 1.40
998 4269 7.051000 GTGCTTGAAGAGAGTAGGGATTAATT 58.949 38.462 0.00 0.00 0.00 1.40
1014 4285 4.871871 TTAATTGATGGGGGTAAGCTCA 57.128 40.909 0.00 0.00 0.00 4.26
1037 4308 1.400846 GCTGATGATGCTCTTGTGTGG 59.599 52.381 0.00 0.00 0.00 4.17
1055 4326 4.023291 TGTGGCAGTTCTTCTTCCTTTTT 58.977 39.130 0.00 0.00 30.81 1.94
1064 4335 7.276438 CAGTTCTTCTTCCTTTTTGTTTTCTGG 59.724 37.037 0.00 0.00 0.00 3.86
1085 4361 0.037882 GAGTAGTGCAGCAGCTGACA 60.038 55.000 27.39 19.51 42.74 3.58
1089 4365 1.890979 GTGCAGCAGCTGACAGTGT 60.891 57.895 27.39 0.00 42.74 3.55
1099 4375 1.400494 GCTGACAGTGTTGGTTTCGTT 59.600 47.619 3.99 0.00 0.00 3.85
1129 4405 0.955428 TCAACTGGGTGCAGAATCGC 60.955 55.000 0.00 0.00 0.00 4.58
1132 4408 1.817099 CTGGGTGCAGAATCGCCTC 60.817 63.158 0.00 0.00 36.85 4.70
1213 4489 2.033675 TCGCAGTAAGTCACTCGTTTCA 59.966 45.455 0.00 0.00 34.26 2.69
1370 4646 1.301558 GAGCATGCTCTCCATCGGG 60.302 63.158 35.26 0.00 39.80 5.14
1373 4649 2.037620 GCATGCTCTCCATCGGGACT 62.038 60.000 11.37 0.00 38.64 3.85
1463 4748 0.990374 AGGTGAAGAAGCTGCAGGAT 59.010 50.000 17.12 0.00 34.56 3.24
1811 5096 0.107312 CCAGCCTCAAGGATCCAGTG 60.107 60.000 15.82 11.78 37.39 3.66
1833 5118 4.885325 TGGAAACAAAACTGGAGAAGGTAC 59.115 41.667 0.00 0.00 37.44 3.34
1834 5119 4.024302 GGAAACAAAACTGGAGAAGGTACG 60.024 45.833 0.00 0.00 0.00 3.67
1835 5120 3.832615 ACAAAACTGGAGAAGGTACGT 57.167 42.857 0.00 0.00 0.00 3.57
1836 5121 4.942761 ACAAAACTGGAGAAGGTACGTA 57.057 40.909 0.00 0.00 0.00 3.57
1837 5122 5.280654 ACAAAACTGGAGAAGGTACGTAA 57.719 39.130 0.00 0.00 0.00 3.18
1838 5123 5.861727 ACAAAACTGGAGAAGGTACGTAAT 58.138 37.500 0.00 0.00 0.00 1.89
1845 5130 6.830324 ACTGGAGAAGGTACGTAATACACATA 59.170 38.462 0.00 0.00 35.23 2.29
1876 5161 9.778993 ATTCGATGTACATATATTACGTACCAC 57.221 33.333 8.71 0.00 35.67 4.16
1972 5266 8.032451 TGCAAAAGTAATGCTATTTTCCTAACC 58.968 33.333 0.00 0.00 44.14 2.85
2026 5320 3.141398 TGCTTCAAAAGAAGATGAGCGT 58.859 40.909 9.26 0.00 34.26 5.07
2030 5324 2.303022 TCAAAAGAAGATGAGCGTCCCT 59.697 45.455 0.00 0.00 0.00 4.20
2129 5423 1.677966 CCACGACGAGGAGGAGGAA 60.678 63.158 5.25 0.00 0.00 3.36
2132 5426 0.393267 ACGACGAGGAGGAGGAAGAG 60.393 60.000 0.00 0.00 0.00 2.85
2135 5429 0.930726 ACGAGGAGGAGGAAGAGGAT 59.069 55.000 0.00 0.00 0.00 3.24
2138 5432 2.888414 CGAGGAGGAGGAAGAGGATTAC 59.112 54.545 0.00 0.00 0.00 1.89
2139 5433 3.688702 CGAGGAGGAGGAAGAGGATTACA 60.689 52.174 0.00 0.00 0.00 2.41
2140 5434 4.290942 GAGGAGGAGGAAGAGGATTACAA 58.709 47.826 0.00 0.00 0.00 2.41
2141 5435 4.901927 AGGAGGAGGAAGAGGATTACAAT 58.098 43.478 0.00 0.00 0.00 2.71
2144 5438 5.309282 GGAGGAGGAAGAGGATTACAATGAT 59.691 44.000 0.00 0.00 0.00 2.45
2147 5441 6.388100 AGGAGGAAGAGGATTACAATGATGAA 59.612 38.462 0.00 0.00 0.00 2.57
2149 5443 7.419518 GGAGGAAGAGGATTACAATGATGAAGA 60.420 40.741 0.00 0.00 0.00 2.87
2150 5444 8.043429 AGGAAGAGGATTACAATGATGAAGAT 57.957 34.615 0.00 0.00 0.00 2.40
2151 5445 9.163894 AGGAAGAGGATTACAATGATGAAGATA 57.836 33.333 0.00 0.00 0.00 1.98
2191 5485 7.516198 AAACAGATTCAGATTGTAAGTTGCT 57.484 32.000 0.00 0.00 0.00 3.91
2195 5489 7.547370 ACAGATTCAGATTGTAAGTTGCTAGAC 59.453 37.037 0.00 0.00 0.00 2.59
2196 5490 7.010923 CAGATTCAGATTGTAAGTTGCTAGACC 59.989 40.741 0.00 0.00 0.00 3.85
2197 5491 5.086104 TCAGATTGTAAGTTGCTAGACCC 57.914 43.478 0.00 0.00 0.00 4.46
2198 5492 4.530553 TCAGATTGTAAGTTGCTAGACCCA 59.469 41.667 0.00 0.00 0.00 4.51
2200 5494 5.122396 CAGATTGTAAGTTGCTAGACCCAAC 59.878 44.000 0.00 0.00 42.11 3.77
2219 5513 6.263168 ACCCAACTAATTTCACTTCAGACTTG 59.737 38.462 0.00 0.00 0.00 3.16
2239 5533 6.893583 ACTTGACTAATTAGCATGGAGTGAT 58.106 36.000 12.54 0.00 0.00 3.06
2305 5672 1.475280 GCATGCAGGAAGATTGAAGCA 59.525 47.619 14.21 0.00 36.34 3.91
2326 5693 9.716507 GAAGCATTTCTTCGCATAGTAATTAAA 57.283 29.630 0.00 0.00 41.48 1.52
2351 5720 6.659745 ATGCATGCATGGACTTATTTGTAT 57.340 33.333 31.74 2.65 35.03 2.29
2393 5767 5.932303 GTCATTGTTCTAGAGGTGTAAAGCA 59.068 40.000 0.00 0.00 0.00 3.91
2425 5799 6.240894 ACACACAAGGTCAAGATCATTATGT 58.759 36.000 0.00 0.00 0.00 2.29
2464 5838 8.908903 AGCTCTATAACTGATATGCATAGTACC 58.091 37.037 12.79 2.39 0.00 3.34
2532 5908 9.256228 TCCAAGTATCAACAGTTAGAGTTATCT 57.744 33.333 0.00 0.00 39.75 1.98
2593 5973 6.216569 CAGATTACACGGATGTTATAGTGCT 58.783 40.000 0.00 0.00 40.48 4.40
2678 6058 3.265791 GCGGAGGACATATGATGGAATC 58.734 50.000 10.38 0.00 45.83 2.52
2694 6085 2.430382 AATCGGCACTGAACGGACGT 62.430 55.000 0.00 0.00 0.00 4.34
2775 6167 5.018374 AGTCTTACTCCCTCTTTCCTTCT 57.982 43.478 0.00 0.00 0.00 2.85
2814 6206 7.328493 GGATTACTCCCTTTGATTTTTGTTTCG 59.672 37.037 0.00 0.00 35.28 3.46
2849 6241 9.735362 ATATATCCATGTTCCATGTATACTCCT 57.265 33.333 4.17 0.00 0.00 3.69
2903 6296 7.065803 TGGAAACTAGATGTTGCAGTAATTAGC 59.934 37.037 0.00 0.00 39.13 3.09
2946 6349 6.476378 ACCTCATGTGCACTTTATCTTAGTT 58.524 36.000 19.41 0.00 0.00 2.24
2950 6353 9.760660 CTCATGTGCACTTTATCTTAGTTTAAC 57.239 33.333 19.41 0.00 0.00 2.01
2982 6399 4.022935 TCAATCTCAAGAACATGGTGCAAC 60.023 41.667 0.00 0.00 0.00 4.17
2984 6401 0.950836 TCAAGAACATGGTGCAACGG 59.049 50.000 0.00 0.00 38.12 4.44
3032 6449 2.305052 GGGTACAGCAACTAGGGTTCTT 59.695 50.000 0.00 0.00 32.73 2.52
3242 6659 3.648339 GCCGATGTGCCAATTGAATAT 57.352 42.857 7.12 0.00 0.00 1.28
3247 6664 5.221106 CCGATGTGCCAATTGAATATGAGTT 60.221 40.000 7.12 0.00 0.00 3.01
3255 6672 6.200286 GCCAATTGAATATGAGTTCATTGCAG 59.800 38.462 7.12 0.00 37.88 4.41
3262 6679 7.989170 TGAATATGAGTTCATTGCAGAGTACAT 59.011 33.333 0.00 0.00 37.76 2.29
3263 6680 7.725818 ATATGAGTTCATTGCAGAGTACATG 57.274 36.000 0.00 0.00 37.76 3.21
3264 6681 4.256110 TGAGTTCATTGCAGAGTACATGG 58.744 43.478 0.00 0.00 0.00 3.66
3265 6682 4.256920 GAGTTCATTGCAGAGTACATGGT 58.743 43.478 0.00 0.00 0.00 3.55
3266 6683 4.005650 AGTTCATTGCAGAGTACATGGTG 58.994 43.478 0.00 0.00 0.00 4.17
3267 6684 3.701205 TCATTGCAGAGTACATGGTGT 57.299 42.857 0.00 0.00 0.00 4.16
3268 6685 4.817318 TCATTGCAGAGTACATGGTGTA 57.183 40.909 0.00 0.00 0.00 2.90
3302 6733 2.957402 TGCCCACTCTCTTCATTTGT 57.043 45.000 0.00 0.00 0.00 2.83
3304 6735 3.149196 TGCCCACTCTCTTCATTTGTTC 58.851 45.455 0.00 0.00 0.00 3.18
3327 6758 4.261825 CGTCCCAAAACAAGCTGGATTTTA 60.262 41.667 0.00 0.00 34.35 1.52
3329 6760 6.230472 GTCCCAAAACAAGCTGGATTTTAAT 58.770 36.000 0.00 0.00 34.35 1.40
3330 6761 7.382898 GTCCCAAAACAAGCTGGATTTTAATA 58.617 34.615 0.00 0.00 34.35 0.98
3331 6762 7.330946 GTCCCAAAACAAGCTGGATTTTAATAC 59.669 37.037 0.00 0.00 34.35 1.89
3332 6763 7.234577 TCCCAAAACAAGCTGGATTTTAATACT 59.765 33.333 0.00 0.00 34.35 2.12
3333 6764 7.877612 CCCAAAACAAGCTGGATTTTAATACTT 59.122 33.333 0.00 0.00 34.35 2.24
3377 6813 4.098196 TGATGGACCATGCATGTATTTGTG 59.902 41.667 24.58 10.29 0.00 3.33
3381 6817 5.478332 TGGACCATGCATGTATTTGTGTAAA 59.522 36.000 24.58 3.54 0.00 2.01
3382 6818 6.015095 TGGACCATGCATGTATTTGTGTAAAA 60.015 34.615 24.58 1.32 0.00 1.52
3383 6819 7.041107 GGACCATGCATGTATTTGTGTAAAAT 58.959 34.615 24.58 0.00 0.00 1.82
3384 6820 7.010367 GGACCATGCATGTATTTGTGTAAAATG 59.990 37.037 24.58 6.44 0.00 2.32
3385 6821 7.609960 ACCATGCATGTATTTGTGTAAAATGA 58.390 30.769 24.58 0.00 0.00 2.57
3386 6822 8.093307 ACCATGCATGTATTTGTGTAAAATGAA 58.907 29.630 24.58 0.00 0.00 2.57
3387 6823 9.100554 CCATGCATGTATTTGTGTAAAATGAAT 57.899 29.630 24.58 0.00 0.00 2.57
3388 6824 9.909043 CATGCATGTATTTGTGTAAAATGAATG 57.091 29.630 18.91 0.00 0.00 2.67
3389 6825 7.961855 TGCATGTATTTGTGTAAAATGAATGC 58.038 30.769 17.09 17.09 35.39 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.976073 CCGCAAAGGAGGGAGTAGGA 60.976 60.000 0.00 0.00 45.00 2.94
48 49 1.265454 ACCGCAAAGGAGGGAGTAGG 61.265 60.000 0.00 0.00 45.00 3.18
49 50 0.613777 AACCGCAAAGGAGGGAGTAG 59.386 55.000 0.00 0.00 45.00 2.57
81 82 7.546250 TTTGACCTGGGATTTAAATAGCAAA 57.454 32.000 0.00 0.67 0.00 3.68
95 96 8.313292 TCTCATTTTATCAAATTTTGACCTGGG 58.687 33.333 13.80 7.59 43.48 4.45
118 119 5.929415 CCCTCTCTTCTTGTTTGTAACTCTC 59.071 44.000 0.00 0.00 0.00 3.20
170 171 7.497404 TCGCAATAAATCACGTGAAAATTTTG 58.503 30.769 24.13 20.82 0.00 2.44
176 177 4.377943 CCACTCGCAATAAATCACGTGAAA 60.378 41.667 24.13 11.64 0.00 2.69
177 178 3.124466 CCACTCGCAATAAATCACGTGAA 59.876 43.478 24.13 6.61 0.00 3.18
178 179 2.670905 CCACTCGCAATAAATCACGTGA 59.329 45.455 22.48 22.48 0.00 4.35
196 197 0.179045 ATATTGAGGTGCTCCGCCAC 60.179 55.000 6.08 0.00 36.32 5.01
199 200 3.304057 GCTTAAATATTGAGGTGCTCCGC 60.304 47.826 1.11 1.11 39.05 5.54
200 201 4.130118 AGCTTAAATATTGAGGTGCTCCG 58.870 43.478 0.00 0.00 39.05 4.63
211 212 9.877178 CTATCTTATCGTGGGAGCTTAAATATT 57.123 33.333 0.00 0.00 0.00 1.28
330 332 5.301805 ACAAAAACCCACAATTCTAGGACTG 59.698 40.000 0.00 0.00 0.00 3.51
361 363 2.294074 CAAAACCACGACTCTTGGGAA 58.706 47.619 6.52 0.00 38.59 3.97
362 364 1.210967 ACAAAACCACGACTCTTGGGA 59.789 47.619 6.52 0.00 38.59 4.37
366 368 7.383687 TGAGATAATACAAAACCACGACTCTT 58.616 34.615 0.00 0.00 0.00 2.85
374 376 5.186256 TGGGCTGAGATAATACAAAACCA 57.814 39.130 0.00 0.00 0.00 3.67
406 409 4.165779 GTTAACAGGGAATCGCACAAATG 58.834 43.478 0.00 0.00 0.00 2.32
438 441 3.000727 ACTAAGAAATTCGTGGAAGCGG 58.999 45.455 0.00 0.00 0.00 5.52
440 443 5.607119 TTGACTAAGAAATTCGTGGAAGC 57.393 39.130 0.00 0.00 0.00 3.86
461 464 9.938280 TGCTGTACTTTTCTGTTACTGTATATT 57.062 29.630 0.00 0.00 0.00 1.28
468 471 7.442656 AGTGTATGCTGTACTTTTCTGTTACT 58.557 34.615 0.00 0.00 0.00 2.24
473 476 5.482908 AGGAGTGTATGCTGTACTTTTCTG 58.517 41.667 0.00 0.00 0.00 3.02
475 478 6.803154 AAAGGAGTGTATGCTGTACTTTTC 57.197 37.500 0.00 0.00 0.00 2.29
477 480 6.534634 AGAAAAGGAGTGTATGCTGTACTTT 58.465 36.000 0.00 0.00 0.00 2.66
478 481 6.115448 AGAAAAGGAGTGTATGCTGTACTT 57.885 37.500 0.00 0.00 0.00 2.24
479 482 5.746990 AGAAAAGGAGTGTATGCTGTACT 57.253 39.130 0.00 0.00 0.00 2.73
480 483 7.900782 TTTAGAAAAGGAGTGTATGCTGTAC 57.099 36.000 0.00 0.00 0.00 2.90
481 484 8.911918 TTTTTAGAAAAGGAGTGTATGCTGTA 57.088 30.769 0.00 0.00 0.00 2.74
482 485 7.817418 TTTTTAGAAAAGGAGTGTATGCTGT 57.183 32.000 0.00 0.00 0.00 4.40
685 3949 4.348754 CCTACCCCCACGAATTAAATAGGA 59.651 45.833 0.00 0.00 30.23 2.94
769 4033 3.953712 TGTATCAGGACGAAAGCTTGA 57.046 42.857 0.00 0.00 0.00 3.02
770 4034 3.242543 GCATGTATCAGGACGAAAGCTTG 60.243 47.826 0.00 0.00 0.00 4.01
783 4047 1.202521 CGGCCACTACTGCATGTATCA 60.203 52.381 2.24 0.00 0.00 2.15
821 4085 0.388520 CGATGAGCGAGGACACAACA 60.389 55.000 0.00 0.00 44.57 3.33
844 4108 2.285969 AGATGCCCTCTGCCTGGT 60.286 61.111 0.00 0.00 40.16 4.00
845 4109 2.192443 CAGATGCCCTCTGCCTGG 59.808 66.667 0.92 0.00 44.73 4.45
920 4191 1.302383 TACCCTGTGAAATTGGCGCG 61.302 55.000 0.00 0.00 0.00 6.86
994 4265 3.785887 AGTGAGCTTACCCCCATCAATTA 59.214 43.478 4.79 0.00 0.00 1.40
995 4266 2.582636 AGTGAGCTTACCCCCATCAATT 59.417 45.455 4.79 0.00 0.00 2.32
996 4267 2.092212 CAGTGAGCTTACCCCCATCAAT 60.092 50.000 4.79 0.00 0.00 2.57
997 4268 1.281867 CAGTGAGCTTACCCCCATCAA 59.718 52.381 4.79 0.00 0.00 2.57
998 4269 0.911769 CAGTGAGCTTACCCCCATCA 59.088 55.000 4.79 0.00 0.00 3.07
1014 4285 2.290134 ACACAAGAGCATCATCAGCAGT 60.290 45.455 0.00 0.00 37.82 4.40
1022 4293 0.109153 ACTGCCACACAAGAGCATCA 59.891 50.000 0.00 0.00 37.82 3.07
1027 4298 2.843701 AGAAGAACTGCCACACAAGAG 58.156 47.619 0.00 0.00 0.00 2.85
1037 4308 6.813649 AGAAAACAAAAAGGAAGAAGAACTGC 59.186 34.615 0.00 0.00 0.00 4.40
1055 4326 3.466836 CTGCACTACTCACCAGAAAACA 58.533 45.455 0.00 0.00 0.00 2.83
1064 4335 0.037882 TCAGCTGCTGCACTACTCAC 60.038 55.000 24.38 0.00 42.74 3.51
1085 4361 3.349022 TCTGGAAAACGAAACCAACACT 58.651 40.909 0.00 0.00 33.14 3.55
1089 4365 4.824537 TGATGATCTGGAAAACGAAACCAA 59.175 37.500 0.00 0.00 33.14 3.67
1129 4405 0.397941 TCTCCTGCTTGGTGTTGAGG 59.602 55.000 0.00 0.00 37.07 3.86
1132 4408 2.260844 TCTTCTCCTGCTTGGTGTTG 57.739 50.000 0.00 0.00 37.07 3.33
1213 4489 1.820519 ACGCATGCATGGAAGTGAAAT 59.179 42.857 27.34 0.00 0.00 2.17
1245 4521 4.572795 TGAGCATCTACGTACTCTTCAGAG 59.427 45.833 11.02 2.04 41.52 3.35
1246 4522 4.514401 TGAGCATCTACGTACTCTTCAGA 58.486 43.478 11.02 0.00 34.92 3.27
1811 5096 4.024302 CGTACCTTCTCCAGTTTTGTTTCC 60.024 45.833 0.00 0.00 0.00 3.13
1857 5142 6.602179 TCTGCGTGGTACGTAATATATGTAC 58.398 40.000 0.00 10.15 45.82 2.90
1860 5145 6.552629 AGATCTGCGTGGTACGTAATATATG 58.447 40.000 0.00 0.00 44.73 1.78
1862 5147 6.205270 TCAAGATCTGCGTGGTACGTAATATA 59.795 38.462 0.00 0.00 44.73 0.86
1867 5152 2.086094 TCAAGATCTGCGTGGTACGTA 58.914 47.619 0.00 0.00 44.73 3.57
1868 5153 0.885879 TCAAGATCTGCGTGGTACGT 59.114 50.000 0.00 0.00 44.73 3.57
1869 5154 2.209838 ATCAAGATCTGCGTGGTACG 57.790 50.000 0.00 0.00 45.88 3.67
1870 5155 3.802685 GGTTATCAAGATCTGCGTGGTAC 59.197 47.826 0.00 0.00 0.00 3.34
1876 5161 3.525537 ACACTGGTTATCAAGATCTGCG 58.474 45.455 0.00 0.00 0.00 5.18
1886 5171 5.986135 CCTAGCTATGTGAACACTGGTTATC 59.014 44.000 6.51 0.00 37.36 1.75
1941 5234 9.101655 GGAAAATAGCATTACTTTTGCATGATT 57.898 29.630 0.00 0.00 42.62 2.57
1953 5246 9.923143 AAACAAAGGTTAGGAAAATAGCATTAC 57.077 29.630 0.00 0.00 35.82 1.89
1972 5266 8.682128 AAACAACTACACATACACAAACAAAG 57.318 30.769 0.00 0.00 0.00 2.77
2054 5348 6.183361 TGTCCTCTAGGTAATACTTCCTCGAT 60.183 42.308 0.00 0.00 35.51 3.59
2147 5441 6.542821 TGTTTTGTCCCACTTGAAGATATCT 58.457 36.000 0.00 0.00 0.00 1.98
2149 5443 6.542821 TCTGTTTTGTCCCACTTGAAGATAT 58.457 36.000 0.00 0.00 0.00 1.63
2150 5444 5.935945 TCTGTTTTGTCCCACTTGAAGATA 58.064 37.500 0.00 0.00 0.00 1.98
2151 5445 4.792068 TCTGTTTTGTCCCACTTGAAGAT 58.208 39.130 0.00 0.00 0.00 2.40
2191 5485 7.016268 AGTCTGAAGTGAAATTAGTTGGGTCTA 59.984 37.037 0.00 0.00 0.00 2.59
2195 5489 6.486657 TCAAGTCTGAAGTGAAATTAGTTGGG 59.513 38.462 0.00 0.00 0.00 4.12
2196 5490 7.227512 AGTCAAGTCTGAAGTGAAATTAGTTGG 59.772 37.037 0.00 0.00 31.88 3.77
2197 5491 8.147642 AGTCAAGTCTGAAGTGAAATTAGTTG 57.852 34.615 0.00 0.00 31.88 3.16
2198 5492 9.832445 TTAGTCAAGTCTGAAGTGAAATTAGTT 57.168 29.630 0.00 0.00 31.88 2.24
2219 5513 6.423302 CAGTCATCACTCCATGCTAATTAGTC 59.577 42.308 13.91 7.08 0.00 2.59
2239 5533 6.570571 GCAAAGTAGTAGTCACTCATCAGTCA 60.571 42.308 0.00 0.00 36.14 3.41
2312 5679 8.739461 CATGCATGCATATTTAATTACTATGCG 58.261 33.333 31.73 10.26 46.82 4.73
2322 5689 9.478768 CAAATAAGTCCATGCATGCATATTTAA 57.521 29.630 31.73 16.31 34.91 1.52
2325 5692 7.058023 ACAAATAAGTCCATGCATGCATATT 57.942 32.000 31.73 22.43 34.91 1.28
2326 5693 6.659745 ACAAATAAGTCCATGCATGCATAT 57.340 33.333 31.73 18.04 34.91 1.78
2329 5696 6.468333 AATACAAATAAGTCCATGCATGCA 57.532 33.333 25.04 25.04 0.00 3.96
2330 5697 7.707893 AGAAAATACAAATAAGTCCATGCATGC 59.292 33.333 21.69 11.82 0.00 4.06
2331 5698 9.590451 AAGAAAATACAAATAAGTCCATGCATG 57.410 29.630 20.19 20.19 0.00 4.06
2366 5735 6.665992 TTACACCTCTAGAACAATGACTGT 57.334 37.500 0.00 0.00 41.27 3.55
2393 5767 4.102524 TCTTGACCTTGTGTGTCAGGTATT 59.897 41.667 0.00 0.00 43.14 1.89
2425 5799 8.318412 TCAGTTATAGAGCTTACCATTTCACAA 58.682 33.333 0.00 0.00 0.00 3.33
2454 5828 3.802866 TGCAATTCGATGGTACTATGCA 58.197 40.909 0.00 0.00 39.95 3.96
2464 5838 2.223618 TGTCCATGCATGCAATTCGATG 60.224 45.455 26.68 16.83 0.00 3.84
2593 5973 2.095415 CGGGATCATTACAGCGTCGATA 60.095 50.000 0.00 0.00 0.00 2.92
2678 6058 3.403057 CACGTCCGTTCAGTGCCG 61.403 66.667 0.00 0.00 0.00 5.69
2679 6059 2.279918 ACACGTCCGTTCAGTGCC 60.280 61.111 0.00 0.00 39.31 5.01
2694 6085 1.071542 TCAAATCTTGGCCTGTCGACA 59.928 47.619 18.88 18.88 0.00 4.35
2775 6167 6.911250 GGGAGTAATCCCTCAAAAAGAAAA 57.089 37.500 21.23 0.00 46.39 2.29
2814 6206 5.485353 TGGAACATGGATATATCAGACCTCC 59.515 44.000 14.60 13.20 0.00 4.30
2876 6268 6.992063 ATTACTGCAACATCTAGTTTCCAG 57.008 37.500 0.00 0.00 38.74 3.86
2880 6272 6.816640 TCGCTAATTACTGCAACATCTAGTTT 59.183 34.615 0.00 0.00 38.74 2.66
2903 6296 7.473027 TGAGGTTTTACTTTACTTCACTTCG 57.527 36.000 0.00 0.00 0.00 3.79
2950 6353 4.520111 TGTTCTTGAGATTGACCACATTGG 59.480 41.667 0.00 0.00 45.02 3.16
3011 6428 1.907255 AGAACCCTAGTTGCTGTACCC 59.093 52.381 0.00 0.00 35.94 3.69
3032 6449 1.667151 GGCTGCTTTGCATGTTCCA 59.333 52.632 0.00 0.00 38.13 3.53
3231 6648 7.485810 TCTGCAATGAACTCATATTCAATTGG 58.514 34.615 5.42 0.00 41.78 3.16
3242 6659 4.256110 CCATGTACTCTGCAATGAACTCA 58.744 43.478 0.00 0.00 0.00 3.41
3247 6664 3.701205 ACACCATGTACTCTGCAATGA 57.299 42.857 0.00 0.00 0.00 2.57
3265 6682 3.088532 GGCATTTTCACCTGATGGTACA 58.911 45.455 0.00 0.00 46.60 2.90
3266 6683 2.427095 GGGCATTTTCACCTGATGGTAC 59.573 50.000 0.00 0.00 46.60 3.34
3267 6684 2.042297 TGGGCATTTTCACCTGATGGTA 59.958 45.455 0.00 0.00 46.60 3.25
3269 6686 1.205417 GTGGGCATTTTCACCTGATGG 59.795 52.381 0.00 0.00 39.83 3.51
3270 6687 2.165030 GAGTGGGCATTTTCACCTGATG 59.835 50.000 0.00 0.00 34.67 3.07
3272 6689 1.425066 AGAGTGGGCATTTTCACCTGA 59.575 47.619 0.00 0.00 34.67 3.86
3273 6690 1.815003 GAGAGTGGGCATTTTCACCTG 59.185 52.381 0.00 0.00 34.67 4.00
3274 6691 1.707427 AGAGAGTGGGCATTTTCACCT 59.293 47.619 0.00 0.00 34.67 4.00
3275 6692 2.206576 AGAGAGTGGGCATTTTCACC 57.793 50.000 0.00 0.00 34.67 4.02
3276 6693 3.149196 TGAAGAGAGTGGGCATTTTCAC 58.851 45.455 0.00 0.00 0.00 3.18
3302 6733 1.028905 CCAGCTTGTTTTGGGACGAA 58.971 50.000 0.00 0.00 0.00 3.85
3304 6735 1.247567 ATCCAGCTTGTTTTGGGACG 58.752 50.000 0.00 0.00 35.13 4.79
3333 6764 9.130661 CCATCATGGAATATAGTACCACAAAAA 57.869 33.333 0.00 0.00 40.96 1.94
3356 6792 4.025360 ACACAAATACATGCATGGTCCAT 58.975 39.130 29.41 14.21 0.00 3.41
3357 6793 3.429492 ACACAAATACATGCATGGTCCA 58.571 40.909 29.41 12.59 0.00 4.02
3358 6794 5.574891 TTACACAAATACATGCATGGTCC 57.425 39.130 29.41 0.00 0.00 4.46
3361 6797 8.476657 TTCATTTTACACAAATACATGCATGG 57.523 30.769 29.41 14.24 0.00 3.66
3362 6798 9.909043 CATTCATTTTACACAAATACATGCATG 57.091 29.630 25.09 25.09 0.00 4.06
3363 6799 8.605746 GCATTCATTTTACACAAATACATGCAT 58.394 29.630 0.00 0.00 35.92 3.96
3364 6800 7.961855 GCATTCATTTTACACAAATACATGCA 58.038 30.769 13.24 0.00 35.92 3.96


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

AutoCloner maintained by Alex Coulton.