Multiple sequence alignment - TraesCS2D01G329300

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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 TraesCS2D01G329300 chr2D 100.000 5523 0 0 1 5523 422330067 422324545 0.000000e+00 10200
1 TraesCS2D01G329300 chr2D 88.618 123 12 2 3020 3141 607675739 607675860 1.240000e-31 148
2 TraesCS2D01G329300 chr2A 91.843 3114 127 46 1 3025 568583883 568580808 0.000000e+00 4226
3 TraesCS2D01G329300 chr2A 92.845 2432 116 25 3138 5523 568580810 568578391 0.000000e+00 3474
4 TraesCS2D01G329300 chr2A 86.154 130 14 4 3016 3143 678423516 678423643 2.680000e-28 137
5 TraesCS2D01G329300 chr2A 85.938 128 16 2 3020 3146 715964211 715964337 9.650000e-28 135
6 TraesCS2D01G329300 chr2B 95.462 1741 66 7 3079 4813 494880012 494878279 0.000000e+00 2765
7 TraesCS2D01G329300 chr2B 92.463 1937 96 18 1132 3063 494881952 494880061 0.000000e+00 2723
8 TraesCS2D01G329300 chr2B 89.414 1143 61 26 1 1127 494883176 494882078 0.000000e+00 1386
9 TraesCS2D01G329300 chr2B 83.972 705 56 27 4849 5523 494878097 494877420 1.690000e-174 623
10 TraesCS2D01G329300 chr2B 90.566 106 9 1 3020 3125 296067364 296067468 7.460000e-29 139
11 TraesCS2D01G329300 chr3A 92.271 207 16 0 2164 2370 723749982 723750188 1.500000e-75 294
12 TraesCS2D01G329300 chr7B 90.517 116 10 1 3020 3135 511462091 511462205 9.580000e-33 152
13 TraesCS2D01G329300 chr1D 93.137 102 6 1 3024 3125 205490291 205490391 1.240000e-31 148
14 TraesCS2D01G329300 chr6D 90.090 111 11 0 3024 3134 410395585 410395475 1.600000e-30 145
15 TraesCS2D01G329300 chr1A 89.474 114 10 2 3024 3135 463825450 463825337 5.770000e-30 143
16 TraesCS2D01G329300 chr3D 88.136 118 14 0 3021 3138 107672337 107672220 2.070000e-29 141


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 TraesCS2D01G329300 chr2D 422324545 422330067 5522 True 10200.00 10200 100.00000 1 5523 1 chr2D.!!$R1 5522
1 TraesCS2D01G329300 chr2A 568578391 568583883 5492 True 3850.00 4226 92.34400 1 5523 2 chr2A.!!$R1 5522
2 TraesCS2D01G329300 chr2B 494877420 494883176 5756 True 1874.25 2765 90.32775 1 5523 4 chr2B.!!$R1 5522

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
257 269 0.036010 CATGTGGTTCCTTCTCGGCT 60.036 55.000 0.00 0.0 0.00 5.52 F
510 523 0.326264 TCCCTTTGCTTCCTCTGCTC 59.674 55.000 0.00 0.0 0.00 4.26 F
511 524 0.327591 CCCTTTGCTTCCTCTGCTCT 59.672 55.000 0.00 0.0 0.00 4.09 F
514 527 0.399454 TTTGCTTCCTCTGCTCTGCT 59.601 50.000 0.00 0.0 0.00 4.24 F
806 830 0.458025 CGTCGGTGGTTAGGAGCTTC 60.458 60.000 0.00 0.0 0.00 3.86 F
807 831 0.896226 GTCGGTGGTTAGGAGCTTCT 59.104 55.000 0.00 0.0 0.00 2.85 F
2243 2462 1.136329 ATGAGCTTGTCCCCAGTGGT 61.136 55.000 8.74 0.0 34.77 4.16 F
2958 3177 1.067060 GTGAAACCCACAAGCCACTTC 59.933 52.381 0.00 0.0 45.03 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2462 0.899720 CACCGTCTACTTTAGGGCCA 59.100 55.000 6.18 0.0 0.00 5.36 R
2578 2797 6.808008 TGTCTTCTTTCAGATCACCATTTC 57.192 37.500 0.00 0.0 0.00 2.17 R
2594 2813 4.707448 ACAGGATCAACTCGTATGTCTTCT 59.293 41.667 0.00 0.0 0.00 2.85 R
2604 2823 3.364366 GCAGTTTTCACAGGATCAACTCG 60.364 47.826 0.00 0.0 29.04 4.18 R
2840 3059 7.447374 TGATTTCTCATCGTTTACATTGGTT 57.553 32.000 0.00 0.0 0.00 3.67 R
2945 3164 2.034879 ATCGCGAAGTGGCTTGTGG 61.035 57.895 15.24 0.0 39.32 4.17 R
3239 3495 0.180406 AACAACAGGTGGCGAGACTT 59.820 50.000 0.00 0.0 0.00 3.01 R
4635 4922 0.254462 GAGAAGAGCAAGGAAGGGGG 59.746 60.000 0.00 0.0 0.00 5.40 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
64 68 1.003718 CCCTGTTTCCACCCGTCTC 60.004 63.158 0.00 0.00 0.00 3.36
99 103 6.238484 CGAATTTTGATCTGGATTGGTAGGAC 60.238 42.308 0.00 0.00 0.00 3.85
212 216 2.776913 CGACTCCCCTTCCTCTCGC 61.777 68.421 0.00 0.00 0.00 5.03
214 218 2.042435 CTCCCCTTCCTCTCGCCT 60.042 66.667 0.00 0.00 0.00 5.52
229 233 1.269723 TCGCCTGCTACTATTCATCGG 59.730 52.381 0.00 0.00 0.00 4.18
255 267 3.198068 CATACATGTGGTTCCTTCTCGG 58.802 50.000 9.11 0.00 0.00 4.63
257 269 0.036010 CATGTGGTTCCTTCTCGGCT 60.036 55.000 0.00 0.00 0.00 5.52
325 337 4.974888 GCTGTCCTGCGTATTTACTACTAC 59.025 45.833 0.00 0.00 0.00 2.73
328 340 6.118170 TGTCCTGCGTATTTACTACTACTCT 58.882 40.000 0.00 0.00 0.00 3.24
329 341 6.600822 TGTCCTGCGTATTTACTACTACTCTT 59.399 38.462 0.00 0.00 0.00 2.85
330 342 6.911511 GTCCTGCGTATTTACTACTACTCTTG 59.088 42.308 0.00 0.00 0.00 3.02
331 343 6.039047 TCCTGCGTATTTACTACTACTCTTGG 59.961 42.308 0.00 0.00 0.00 3.61
332 344 6.039047 CCTGCGTATTTACTACTACTCTTGGA 59.961 42.308 0.00 0.00 0.00 3.53
333 345 6.789262 TGCGTATTTACTACTACTCTTGGAC 58.211 40.000 0.00 0.00 0.00 4.02
334 346 6.375174 TGCGTATTTACTACTACTCTTGGACA 59.625 38.462 0.00 0.00 0.00 4.02
336 348 7.192232 CGTATTTACTACTACTCTTGGACACC 58.808 42.308 0.00 0.00 0.00 4.16
337 349 5.633830 TTTACTACTACTCTTGGACACCG 57.366 43.478 0.00 0.00 0.00 4.94
339 351 1.134560 CTACTACTCTTGGACACCGCC 59.865 57.143 0.00 0.00 0.00 6.13
340 352 1.218316 CTACTCTTGGACACCGCCC 59.782 63.158 0.00 0.00 0.00 6.13
341 353 2.558554 CTACTCTTGGACACCGCCCG 62.559 65.000 0.00 0.00 0.00 6.13
343 355 3.649277 CTCTTGGACACCGCCCGAG 62.649 68.421 0.00 0.00 36.68 4.63
358 371 3.896133 GAGGCCCGACGACGCATA 61.896 66.667 0.00 0.00 38.29 3.14
359 372 3.825833 GAGGCCCGACGACGCATAG 62.826 68.421 0.00 0.00 38.29 2.23
443 456 1.079057 GTGAGAGGGAGGGAAACGC 60.079 63.158 0.00 0.00 0.00 4.84
510 523 0.326264 TCCCTTTGCTTCCTCTGCTC 59.674 55.000 0.00 0.00 0.00 4.26
511 524 0.327591 CCCTTTGCTTCCTCTGCTCT 59.672 55.000 0.00 0.00 0.00 4.09
512 525 1.451067 CCTTTGCTTCCTCTGCTCTG 58.549 55.000 0.00 0.00 0.00 3.35
513 526 0.803740 CTTTGCTTCCTCTGCTCTGC 59.196 55.000 0.00 0.00 0.00 4.26
514 527 0.399454 TTTGCTTCCTCTGCTCTGCT 59.601 50.000 0.00 0.00 0.00 4.24
605 618 6.930722 AGATCCTTTTTAAGCATGGTGTTTTG 59.069 34.615 0.00 0.00 0.00 2.44
634 647 7.357951 GTTCAACTGAACCTATCTTCTTCTG 57.642 40.000 10.87 0.00 46.42 3.02
655 668 5.368523 TCTGTTTTCTGTCCCTCCTCTTTTA 59.631 40.000 0.00 0.00 0.00 1.52
665 678 5.774184 GTCCCTCCTCTTTTATCCGTAGTAT 59.226 44.000 0.00 0.00 0.00 2.12
777 795 3.134623 TCTGTCTGCGGATAAATGGACAT 59.865 43.478 0.00 0.00 34.05 3.06
805 829 1.590147 CGTCGGTGGTTAGGAGCTT 59.410 57.895 0.00 0.00 0.00 3.74
806 830 0.458025 CGTCGGTGGTTAGGAGCTTC 60.458 60.000 0.00 0.00 0.00 3.86
807 831 0.896226 GTCGGTGGTTAGGAGCTTCT 59.104 55.000 0.00 0.00 0.00 2.85
808 832 1.275573 GTCGGTGGTTAGGAGCTTCTT 59.724 52.381 0.00 0.00 0.00 2.52
809 833 1.975680 TCGGTGGTTAGGAGCTTCTTT 59.024 47.619 0.00 0.00 0.00 2.52
811 835 3.146847 CGGTGGTTAGGAGCTTCTTTTT 58.853 45.455 0.00 0.00 0.00 1.94
812 836 3.058224 CGGTGGTTAGGAGCTTCTTTTTG 60.058 47.826 0.00 0.00 0.00 2.44
824 848 7.661437 AGGAGCTTCTTTTTGTTTTGTTTTCTT 59.339 29.630 0.00 0.00 0.00 2.52
853 877 3.834799 GCAGGAAGCAGGCATGGC 61.835 66.667 12.14 12.14 44.79 4.40
854 878 2.044252 CAGGAAGCAGGCATGGCT 60.044 61.111 17.44 17.44 45.15 4.75
859 883 4.333417 AGCAGGCATGGCTTCTTC 57.667 55.556 20.85 9.09 38.81 2.87
902 931 5.128919 GGAGCATTGACTTGTGGATCTTAT 58.871 41.667 0.00 0.00 0.00 1.73
970 1000 1.890979 CATCTCCTCACGCATGGCC 60.891 63.158 0.00 0.00 0.00 5.36
1061 1093 7.125792 TCCTCTTCCATAATCTTCTTGTACC 57.874 40.000 0.00 0.00 0.00 3.34
1256 1430 1.918262 TGGCAGGGAAGTGAAGATCAT 59.082 47.619 0.00 0.00 0.00 2.45
1366 1572 6.243148 AGATTGATGGCATATACTGATTGCA 58.757 36.000 0.00 0.00 38.12 4.08
1434 1640 4.625972 TCATAGCTTGTGTGCATCATTG 57.374 40.909 0.00 0.00 34.99 2.82
1465 1671 4.988540 TCTCACTTTGTTACTCCATGAACG 59.011 41.667 0.00 0.00 0.00 3.95
1543 1751 6.539826 TGTCTCTTATCATTTGCCATACTGTG 59.460 38.462 0.00 0.00 0.00 3.66
1767 1977 5.413499 CAAAAGGCAGTCATTTATTCCCTG 58.587 41.667 0.00 0.00 0.00 4.45
1814 2024 7.701924 TGTCAAGTGTCAATTCTCATTTCAAAC 59.298 33.333 0.00 0.00 0.00 2.93
1923 2133 5.751680 CACAGAGACGTTGTGAATGAAAAT 58.248 37.500 12.49 0.00 46.85 1.82
1989 2199 2.433436 GGAACCAACGGCAGAACTTAT 58.567 47.619 0.00 0.00 0.00 1.73
1995 2205 3.502211 CCAACGGCAGAACTTATGACTTT 59.498 43.478 0.00 0.00 0.00 2.66
1996 2206 4.466828 CAACGGCAGAACTTATGACTTTG 58.533 43.478 0.00 0.00 29.84 2.77
2025 2235 5.182001 AGGTTCTCTTTTGTTCATTCCATCG 59.818 40.000 0.00 0.00 0.00 3.84
2105 2315 6.713762 TCAAATCAGAAACCATCAGTGTTT 57.286 33.333 0.00 0.00 38.57 2.83
2117 2327 6.245408 ACCATCAGTGTTTATTGTGGTACAT 58.755 36.000 0.00 0.00 44.52 2.29
2234 2453 3.924686 CCAATGCTTTTCATGAGCTTGTC 59.075 43.478 6.93 0.00 40.75 3.18
2243 2462 1.136329 ATGAGCTTGTCCCCAGTGGT 61.136 55.000 8.74 0.00 34.77 4.16
2578 2797 2.300433 TGATTCTTCAATGGCCGATGG 58.700 47.619 7.65 0.00 0.00 3.51
2594 2813 3.947196 CCGATGGAAATGGTGATCTGAAA 59.053 43.478 0.00 0.00 0.00 2.69
2840 3059 6.711277 AGGCAACAAGACTACAGATGAATTA 58.289 36.000 0.00 0.00 41.41 1.40
2935 3154 4.265073 GTGGGCACAGTAATTTCTGAGAT 58.735 43.478 17.85 0.00 38.63 2.75
2945 3164 7.389053 ACAGTAATTTCTGAGATCTGTGAAACC 59.611 37.037 17.85 10.81 38.63 3.27
2958 3177 1.067060 GTGAAACCCACAAGCCACTTC 59.933 52.381 0.00 0.00 45.03 3.01
2985 3204 4.517285 TGGAGAAGCAATTGATGAGGTAC 58.483 43.478 10.34 0.00 0.00 3.34
2999 3218 6.678878 TGATGAGGTACGATAGATTTACAGC 58.321 40.000 0.00 0.00 41.38 4.40
3016 3235 3.960571 ACAGCATTACCAATCTGCTCTT 58.039 40.909 0.00 0.00 44.09 2.85
3022 3241 8.288208 CAGCATTACCAATCTGCTCTTATAAAG 58.712 37.037 0.00 0.00 44.09 1.85
3033 3252 5.525484 TGCTCTTATAAAGTACTCCCTCCA 58.475 41.667 0.00 0.00 0.00 3.86
3037 3256 6.082707 TCTTATAAAGTACTCCCTCCATCCC 58.917 44.000 0.00 0.00 0.00 3.85
3050 3269 3.123804 CTCCATCCCGAATTACTTGTCG 58.876 50.000 0.00 0.00 37.01 4.35
3063 3282 2.086869 ACTTGTCGCAGAAATGGATGG 58.913 47.619 0.00 0.00 39.69 3.51
3065 3284 2.488204 TGTCGCAGAAATGGATGGAA 57.512 45.000 0.00 0.00 39.69 3.53
3066 3285 2.789213 TGTCGCAGAAATGGATGGAAA 58.211 42.857 0.00 0.00 39.69 3.13
3068 3287 3.129113 TGTCGCAGAAATGGATGGAAATG 59.871 43.478 0.00 0.00 39.69 2.32
3069 3288 2.689471 TCGCAGAAATGGATGGAAATGG 59.311 45.455 0.00 0.00 0.00 3.16
3070 3289 2.689471 CGCAGAAATGGATGGAAATGGA 59.311 45.455 0.00 0.00 0.00 3.41
3072 3291 4.628074 GCAGAAATGGATGGAAATGGATG 58.372 43.478 0.00 0.00 0.00 3.51
3073 3292 4.628074 CAGAAATGGATGGAAATGGATGC 58.372 43.478 0.00 0.00 0.00 3.91
3075 3294 4.905456 AGAAATGGATGGAAATGGATGCAT 59.095 37.500 0.00 0.00 32.53 3.96
3076 3295 5.368523 AGAAATGGATGGAAATGGATGCATT 59.631 36.000 6.63 6.63 40.96 3.56
3077 3296 5.640158 AATGGATGGAAATGGATGCATTT 57.360 34.783 23.31 23.31 37.33 2.32
3082 3334 5.279156 GGATGGAAATGGATGCATTTAGGAC 60.279 44.000 23.16 14.58 35.18 3.85
3086 3338 6.321181 TGGAAATGGATGCATTTAGGACTAAC 59.679 38.462 23.16 9.58 35.18 2.34
3092 3344 7.342581 TGGATGCATTTAGGACTAACAATACA 58.657 34.615 0.00 0.00 0.00 2.29
3155 3409 6.253727 CGGAGAGATATATGATTGCCGTAAAC 59.746 42.308 0.00 0.00 0.00 2.01
3156 3410 7.097192 GGAGAGATATATGATTGCCGTAAACA 58.903 38.462 0.00 0.00 0.00 2.83
3159 3413 7.065085 AGAGATATATGATTGCCGTAAACATGC 59.935 37.037 2.80 0.00 34.19 4.06
3239 3495 6.239008 GGTTCAATGATCTGTTCCAAGAAACA 60.239 38.462 0.00 0.00 37.56 2.83
3245 3501 5.760253 TGATCTGTTCCAAGAAACAAGTCTC 59.240 40.000 0.00 0.00 38.60 3.36
3374 3630 9.679661 ATGATTATTGTCATTACAGGTTACACA 57.320 29.630 0.00 0.00 35.34 3.72
3427 3683 1.202582 CACCAGAGTCCAGTTACCTCG 59.797 57.143 0.00 0.00 0.00 4.63
3548 3807 4.007659 CACTACAACCCTTTTATCGCCTT 58.992 43.478 0.00 0.00 0.00 4.35
3648 3907 3.935828 GTCCTGTTGGAAAGACAGATAGC 59.064 47.826 5.87 0.00 45.72 2.97
3705 3964 6.633856 AGGATTTGATTATGTTGAAACAGCC 58.366 36.000 1.94 0.00 43.04 4.85
3742 4001 7.411808 TGGAGACAGTAGTAGGTTAGATTCTT 58.588 38.462 0.00 0.00 35.01 2.52
3743 4002 8.554870 TGGAGACAGTAGTAGGTTAGATTCTTA 58.445 37.037 0.00 0.00 35.01 2.10
3868 4127 4.702131 GTGCACCAGGTAGATTTGATTCTT 59.298 41.667 5.22 0.00 0.00 2.52
4032 4318 0.248215 GCCATCCAAAATGCGAGACG 60.248 55.000 0.00 0.00 0.00 4.18
4296 4582 2.418983 ACACTTCTCTTCGTTCGGAC 57.581 50.000 0.00 0.00 0.00 4.79
4343 4629 2.002586 CGCATTCCCAGTGTAAGTGAG 58.997 52.381 0.00 0.00 40.62 3.51
4375 4661 9.254133 CTGAATAGTATCACCACTACATTCTTG 57.746 37.037 0.00 0.00 33.94 3.02
4406 4693 6.268797 AGTACATAAACGCATATGTGTTCG 57.731 37.500 29.48 22.84 46.75 3.95
4633 4920 8.679288 ATTCATTCAAATGTTGATCGTTTCTC 57.321 30.769 2.85 0.00 39.84 2.87
4634 4921 6.611381 TCATTCAAATGTTGATCGTTTCTCC 58.389 36.000 2.85 0.00 39.84 3.71
4635 4922 5.371115 TTCAAATGTTGATCGTTTCTCCC 57.629 39.130 0.00 0.00 39.84 4.30
4710 4999 0.475906 ATAGCAGGAGGTTGATGGCC 59.524 55.000 0.00 0.00 0.00 5.36
4789 5081 8.200792 AGAGGTATAGCTTTCTTTCATGTACTG 58.799 37.037 5.80 0.00 0.00 2.74
4897 5336 2.223829 ACTCACCAGAACGAGTTCAGTG 60.224 50.000 22.29 22.29 39.45 3.66
4910 5349 2.746412 TTCAGTGTGCCATGACCCGG 62.746 60.000 0.00 0.00 0.00 5.73
4937 5382 8.316640 TGTGAACAAGCAACAAAATAAGTTTT 57.683 26.923 0.00 0.00 38.03 2.43
5020 5465 5.599751 ACATGTAGATATAGCATACCCCCA 58.400 41.667 0.00 0.00 0.00 4.96
5021 5466 5.663106 ACATGTAGATATAGCATACCCCCAG 59.337 44.000 0.00 0.00 0.00 4.45
5044 5490 1.372872 GCACATCCGGCACAAAACC 60.373 57.895 0.00 0.00 0.00 3.27
5160 5617 7.290248 ACCAGCTAATGATATACTGTACCAACT 59.710 37.037 0.00 0.00 0.00 3.16
5169 5626 1.480954 ACTGTACCAACTAGGGCATCG 59.519 52.381 0.00 0.00 43.89 3.84
5230 5706 9.453325 CAAATCTAGCTAACTAGTTGTAGTAGC 57.547 37.037 18.56 17.26 45.32 3.58
5287 5763 8.705048 AAGCTAAGCTTCTTGTAACTATGTAC 57.295 34.615 0.00 0.00 46.77 2.90
5293 5769 7.998580 AGCTTCTTGTAACTATGTACTCTACC 58.001 38.462 0.00 0.00 0.00 3.18
5294 5770 7.835181 AGCTTCTTGTAACTATGTACTCTACCT 59.165 37.037 0.00 0.00 0.00 3.08
5295 5771 9.118300 GCTTCTTGTAACTATGTACTCTACCTA 57.882 37.037 0.00 0.00 0.00 3.08
5308 5784 0.594110 CTACCTACCTAGCTGCGCTC 59.406 60.000 9.73 0.00 40.44 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 68 6.369890 TCCAGATCAAAATTCGTCAAGAGAAG 59.630 38.462 0.00 0.00 0.00 2.85
99 103 0.859232 GCGGCACTATGTTGTATCCG 59.141 55.000 0.00 0.00 37.89 4.18
212 216 1.620819 AGGCCGATGAATAGTAGCAGG 59.379 52.381 0.00 0.00 0.00 4.85
214 218 3.227614 TGTAGGCCGATGAATAGTAGCA 58.772 45.455 0.00 0.00 0.00 3.49
229 233 3.560636 AGGAACCACATGTATGTAGGC 57.439 47.619 0.00 0.00 39.39 3.93
255 267 1.063174 GCAGTAACTACATGCAGCAGC 59.937 52.381 0.00 0.00 39.75 5.25
257 269 1.358877 CGCAGTAACTACATGCAGCA 58.641 50.000 0.00 0.00 39.97 4.41
325 337 3.649277 CTCGGGCGGTGTCCAAGAG 62.649 68.421 0.00 0.00 0.00 2.85
341 353 3.825833 CTATGCGTCGTCGGGCCTC 62.826 68.421 0.84 0.00 37.56 4.70
343 355 4.944372 CCTATGCGTCGTCGGGCC 62.944 72.222 3.90 0.00 37.56 5.80
358 371 2.342648 GACGGCGTGGAAACTCCT 59.657 61.111 21.19 0.00 37.46 3.69
359 372 3.110178 CGACGGCGTGGAAACTCC 61.110 66.667 21.19 0.00 36.96 3.85
443 456 1.153429 GTCGAGAACAATCCCCCGG 60.153 63.158 0.00 0.00 0.00 5.73
510 523 3.755378 AGAACAAAGTAGCATTGGAGCAG 59.245 43.478 0.00 0.00 36.85 4.24
511 524 3.754965 AGAACAAAGTAGCATTGGAGCA 58.245 40.909 0.00 0.00 36.85 4.26
512 525 4.773323 AAGAACAAAGTAGCATTGGAGC 57.227 40.909 0.00 0.00 32.02 4.70
513 526 6.974965 AGAAAAGAACAAAGTAGCATTGGAG 58.025 36.000 0.00 0.00 32.02 3.86
514 527 6.772716 AGAGAAAAGAACAAAGTAGCATTGGA 59.227 34.615 0.00 0.00 32.02 3.53
623 636 6.295916 GGAGGGACAGAAAACAGAAGAAGATA 60.296 42.308 0.00 0.00 0.00 1.98
632 645 3.778954 AAGAGGAGGGACAGAAAACAG 57.221 47.619 0.00 0.00 0.00 3.16
633 646 4.519906 AAAAGAGGAGGGACAGAAAACA 57.480 40.909 0.00 0.00 0.00 2.83
634 647 5.648526 GGATAAAAGAGGAGGGACAGAAAAC 59.351 44.000 0.00 0.00 0.00 2.43
655 668 5.180868 CCGACAAGCTAGTAATACTACGGAT 59.819 44.000 15.49 0.00 35.91 4.18
665 678 1.822990 CACCCTCCGACAAGCTAGTAA 59.177 52.381 0.00 0.00 0.00 2.24
777 795 1.743623 CCACCGACGCTAATGGCAA 60.744 57.895 0.00 0.00 41.91 4.52
805 829 8.859156 CAGATCGAAGAAAACAAAACAAAAAGA 58.141 29.630 0.00 0.00 43.58 2.52
806 830 7.632132 GCAGATCGAAGAAAACAAAACAAAAAG 59.368 33.333 0.00 0.00 43.58 2.27
807 831 7.330700 AGCAGATCGAAGAAAACAAAACAAAAA 59.669 29.630 0.00 0.00 43.58 1.94
808 832 6.811170 AGCAGATCGAAGAAAACAAAACAAAA 59.189 30.769 0.00 0.00 43.58 2.44
809 833 6.329496 AGCAGATCGAAGAAAACAAAACAAA 58.671 32.000 0.00 0.00 43.58 2.83
811 835 5.499139 AGCAGATCGAAGAAAACAAAACA 57.501 34.783 0.00 0.00 43.58 2.83
812 836 4.912187 GGAGCAGATCGAAGAAAACAAAAC 59.088 41.667 0.00 0.00 43.58 2.43
912 942 7.946776 AGCTGATTACTTCCTGCCATTATTAAT 59.053 33.333 0.00 0.00 0.00 1.40
914 944 6.841601 AGCTGATTACTTCCTGCCATTATTA 58.158 36.000 0.00 0.00 0.00 0.98
915 945 5.699143 AGCTGATTACTTCCTGCCATTATT 58.301 37.500 0.00 0.00 0.00 1.40
916 946 5.072872 AGAGCTGATTACTTCCTGCCATTAT 59.927 40.000 0.00 0.00 0.00 1.28
970 1000 2.798499 CGGTGTATCTCGTTAAGGCCTG 60.798 54.545 5.69 0.00 0.00 4.85
1231 1405 3.889815 TCTTCACTTCCCTGCCAATATG 58.110 45.455 0.00 0.00 0.00 1.78
1350 1556 9.480053 AAAAATGTAATGCAATCAGTATATGCC 57.520 29.630 0.00 0.00 39.31 4.40
1364 1570 9.571810 TCAATCAGTGTATCAAAAATGTAATGC 57.428 29.630 0.00 0.00 0.00 3.56
1434 1640 5.755861 GGAGTAACAAAGTGAGATCTATGGC 59.244 44.000 0.00 0.00 0.00 4.40
1465 1671 6.148480 ACTGACTAGATGTTTCATTCACTTGC 59.852 38.462 0.00 0.00 0.00 4.01
1471 1677 8.247562 AGTGACTACTGACTAGATGTTTCATTC 58.752 37.037 0.00 0.00 35.34 2.67
1543 1751 4.755411 TCGATACAAGATGAAACCTGGTC 58.245 43.478 0.00 0.00 0.00 4.02
1923 2133 9.567776 TCACTTTAACCATCAGAAGACATTAAA 57.432 29.630 0.00 0.00 0.00 1.52
1989 2199 1.968493 AGAGAACCTACGCCAAAGTCA 59.032 47.619 0.00 0.00 0.00 3.41
1995 2205 2.922740 ACAAAAGAGAACCTACGCCA 57.077 45.000 0.00 0.00 0.00 5.69
1996 2206 3.135994 TGAACAAAAGAGAACCTACGCC 58.864 45.455 0.00 0.00 0.00 5.68
2025 2235 3.851976 ACGGACAAGAGACACTATCAC 57.148 47.619 0.00 0.00 0.00 3.06
2117 2327 9.790389 AACAAAAACGAACACAAGTCAATAATA 57.210 25.926 0.00 0.00 0.00 0.98
2121 2331 6.088883 GTGAACAAAAACGAACACAAGTCAAT 59.911 34.615 0.00 0.00 0.00 2.57
2234 2453 2.499303 CTTTAGGGCCACCACTGGGG 62.499 65.000 6.18 0.00 44.81 4.96
2243 2462 0.899720 CACCGTCTACTTTAGGGCCA 59.100 55.000 6.18 0.00 0.00 5.36
2578 2797 6.808008 TGTCTTCTTTCAGATCACCATTTC 57.192 37.500 0.00 0.00 0.00 2.17
2594 2813 4.707448 ACAGGATCAACTCGTATGTCTTCT 59.293 41.667 0.00 0.00 0.00 2.85
2604 2823 3.364366 GCAGTTTTCACAGGATCAACTCG 60.364 47.826 0.00 0.00 29.04 4.18
2840 3059 7.447374 TGATTTCTCATCGTTTACATTGGTT 57.553 32.000 0.00 0.00 0.00 3.67
2945 3164 2.034879 ATCGCGAAGTGGCTTGTGG 61.035 57.895 15.24 0.00 39.32 4.17
2958 3177 1.009078 TCAATTGCTTCTCCATCGCG 58.991 50.000 0.00 0.00 0.00 5.87
2985 3204 8.438513 CAGATTGGTAATGCTGTAAATCTATCG 58.561 37.037 0.00 0.00 33.71 2.92
3016 3235 4.106825 TCGGGATGGAGGGAGTACTTTATA 59.893 45.833 0.00 0.00 0.00 0.98
3022 3241 1.718280 ATTCGGGATGGAGGGAGTAC 58.282 55.000 0.00 0.00 0.00 2.73
3033 3252 2.167693 TCTGCGACAAGTAATTCGGGAT 59.832 45.455 0.00 0.00 35.73 3.85
3037 3256 4.092821 TCCATTTCTGCGACAAGTAATTCG 59.907 41.667 0.00 0.00 38.31 3.34
3050 3269 4.628074 CATCCATTTCCATCCATTTCTGC 58.372 43.478 0.00 0.00 0.00 4.26
3063 3282 7.333528 TGTTAGTCCTAAATGCATCCATTTC 57.666 36.000 0.00 0.00 45.99 2.17
3065 3284 7.902920 ATTGTTAGTCCTAAATGCATCCATT 57.097 32.000 0.00 0.00 43.32 3.16
3066 3285 7.998383 TGTATTGTTAGTCCTAAATGCATCCAT 59.002 33.333 0.00 0.00 0.00 3.41
3068 3287 7.801716 TGTATTGTTAGTCCTAAATGCATCC 57.198 36.000 0.00 0.00 0.00 3.51
3069 3288 9.277783 AGATGTATTGTTAGTCCTAAATGCATC 57.722 33.333 13.86 13.86 36.60 3.91
3072 3291 9.982651 TCTAGATGTATTGTTAGTCCTAAATGC 57.017 33.333 0.00 0.00 0.00 3.56
3092 3344 8.637196 TGTCGTAGAAATGGATGTATCTAGAT 57.363 34.615 10.73 10.73 39.69 1.98
3155 3409 2.891112 ACCAAATAATTGCGGTGCATG 58.109 42.857 0.00 0.00 38.76 4.06
3156 3410 3.608316 AACCAAATAATTGCGGTGCAT 57.392 38.095 0.00 0.00 38.76 3.96
3159 3413 5.092781 GTCAGTAACCAAATAATTGCGGTG 58.907 41.667 0.00 0.00 35.10 4.94
3239 3495 0.180406 AACAACAGGTGGCGAGACTT 59.820 50.000 0.00 0.00 0.00 3.01
3245 3501 1.737793 GGATAGAAACAACAGGTGGCG 59.262 52.381 0.00 0.00 0.00 5.69
3374 3630 3.763360 TCCAGTTTCATGGCAATCGATTT 59.237 39.130 8.21 0.00 40.41 2.17
3427 3683 4.866921 GTTGATTCAACTGGTAAACCACC 58.133 43.478 19.90 0.00 41.12 4.61
3548 3807 4.080356 CCCATGTGTCCTCTAAAGATCCAA 60.080 45.833 0.00 0.00 0.00 3.53
3648 3907 4.093408 CCACCGTTGACAATATCACTGAAG 59.907 45.833 0.00 0.00 36.92 3.02
3742 4001 1.675714 CCTGCTTGAACGTGCTCCATA 60.676 52.381 0.00 0.00 0.00 2.74
3743 4002 0.957395 CCTGCTTGAACGTGCTCCAT 60.957 55.000 0.00 0.00 0.00 3.41
3868 4127 2.585330 TCTGGTTTCATCTGCTGCAAA 58.415 42.857 3.02 0.00 0.00 3.68
3995 4281 1.406614 GGCCCTCACTCTTGACATCAG 60.407 57.143 0.00 0.00 0.00 2.90
4032 4318 1.079503 GTTCATCTTCGACAGCACCC 58.920 55.000 0.00 0.00 0.00 4.61
4296 4582 0.794981 GAGTACTCGTCGTGCTGCTG 60.795 60.000 7.22 0.00 38.78 4.41
4343 4629 6.412362 AGTGGTGATACTATTCAGATGTCC 57.588 41.667 0.00 0.00 0.00 4.02
4375 4661 8.388103 ACATATGCGTTTATGTACTTGAGAAAC 58.612 33.333 1.58 0.00 40.22 2.78
4406 4693 1.203523 CTCTGTCTGTAGCCTGTGGAC 59.796 57.143 0.00 0.00 0.00 4.02
4635 4922 0.254462 GAGAAGAGCAAGGAAGGGGG 59.746 60.000 0.00 0.00 0.00 5.40
4710 4999 0.872021 GCCACTAGCGAATCCGACAG 60.872 60.000 0.00 0.00 38.22 3.51
4789 5081 0.389426 CAAACAGGAATGCTGGCAGC 60.389 55.000 31.91 31.91 42.82 5.25
4805 5097 6.981559 TCGCACTACATGTATGTATAAGCAAA 59.018 34.615 5.91 7.33 41.92 3.68
4897 5336 2.114670 CACATCCGGGTCATGGCAC 61.115 63.158 0.00 0.00 0.00 5.01
4910 5349 7.698836 ACTTATTTTGTTGCTTGTTCACATC 57.301 32.000 0.00 0.00 0.00 3.06
4937 5382 3.592898 ATCAGCGTTCTATGTGTGTCA 57.407 42.857 0.00 0.00 0.00 3.58
5160 5617 9.173021 CAAATATTATGGAATAACGATGCCCTA 57.827 33.333 0.00 0.00 42.43 3.53
5215 5691 5.711036 ACTACTGCTGCTACTACAACTAGTT 59.289 40.000 1.12 1.12 34.79 2.24
5230 5706 3.610242 CGCTCTCTGTTTTACTACTGCTG 59.390 47.826 0.00 0.00 0.00 4.41
5308 5784 2.264794 CCGTCAGACTTTCCCCGG 59.735 66.667 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.