Multiple sequence alignment - TraesCS5B01G149700

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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 TraesCS5B01G149700 chr5B 100.000 5795 0 0 1 5795 278004692 278010486 0.000000e+00 10702.0
1 TraesCS5B01G149700 chr5D 95.848 4769 147 20 89 4828 244617031 244621777 0.000000e+00 7662.0
2 TraesCS5B01G149700 chr5D 86.197 1007 86 25 4814 5795 244621790 244622768 0.000000e+00 1040.0
3 TraesCS5B01G149700 chr5A 94.444 5004 186 39 817 5795 328798382 328803318 0.000000e+00 7616.0
4 TraesCS5B01G149700 chr5A 87.432 366 37 9 2952 3311 667026856 667027218 4.180000e-111 412.0
5 TraesCS5B01G149700 chr5A 87.444 223 22 6 3094 3312 531217297 531217077 9.640000e-63 252.0
6 TraesCS5B01G149700 chr5A 90.845 142 11 2 2965 3105 531218778 531218638 7.670000e-44 189.0
7 TraesCS5B01G149700 chr4B 88.701 354 32 8 2964 3312 75737997 75737647 5.370000e-115 425.0
8 TraesCS5B01G149700 chr4B 89.333 150 15 1 8 156 612485592 612485741 2.760000e-43 187.0
9 TraesCS5B01G149700 chr1A 87.571 354 36 8 2964 3312 65759836 65760186 2.510000e-108 403.0
10 TraesCS5B01G149700 chr1A 81.087 460 69 12 153 603 545097873 545097423 9.240000e-93 351.0
11 TraesCS5B01G149700 chr1A 82.126 207 32 4 2957 3159 267262316 267262521 7.720000e-39 172.0
12 TraesCS5B01G149700 chr6A 82.391 460 63 8 157 603 572973827 572974281 9.110000e-103 385.0
13 TraesCS5B01G149700 chr6B 82.009 428 45 19 124 525 644359973 644360394 9.300000e-88 335.0
14 TraesCS5B01G149700 chr1D 83.473 357 47 11 273 624 70451654 70452003 7.240000e-84 322.0
15 TraesCS5B01G149700 chr1D 88.312 154 16 1 2 153 70451414 70451567 3.570000e-42 183.0
16 TraesCS5B01G149700 chrUn 83.429 350 52 6 273 620 312032887 312032542 2.610000e-83 320.0
17 TraesCS5B01G149700 chrUn 83.429 350 52 6 273 620 372881263 372881608 2.610000e-83 320.0
18 TraesCS5B01G149700 chrUn 92.188 128 9 1 2 128 264527740 264527613 4.610000e-41 180.0
19 TraesCS5B01G149700 chr2A 83.429 350 52 6 273 620 760853315 760853660 2.610000e-83 320.0
20 TraesCS5B01G149700 chr7D 83.529 340 51 5 273 610 63019259 63018923 4.360000e-81 313.0
21 TraesCS5B01G149700 chr7D 81.627 332 54 7 273 601 614545942 614545615 9.570000e-68 268.0
22 TraesCS5B01G149700 chr7D 92.969 128 8 1 2 128 147016019 147015892 9.920000e-43 185.0
23 TraesCS5B01G149700 chr7D 87.662 154 17 1 2 153 579367573 579367420 1.660000e-40 178.0
24 TraesCS5B01G149700 chr3B 82.692 312 51 3 3438 3746 216873664 216873353 2.060000e-69 274.0
25 TraesCS5B01G149700 chr3B 79.630 270 42 8 5014 5280 446631185 446630926 1.280000e-41 182.0
26 TraesCS5B01G149700 chr3B 92.188 128 9 1 2 128 428717777 428717650 4.610000e-41 180.0
27 TraesCS5B01G149700 chr3B 91.538 130 8 2 2 128 729212069 729211940 5.970000e-40 176.0
28 TraesCS5B01G149700 chr2B 86.957 207 23 4 5069 5274 693886515 693886718 4.520000e-56 230.0
29 TraesCS5B01G149700 chr7A 85.854 205 25 3 5077 5280 342763626 342763425 1.260000e-51 215.0
30 TraesCS5B01G149700 chr7A 81.776 214 27 5 5068 5280 558674924 558675126 9.990000e-38 169.0
31 TraesCS5B01G149700 chr3A 81.818 242 35 9 5040 5277 456925837 456926073 1.650000e-45 195.0
32 TraesCS5B01G149700 chr4D 88.235 153 17 1 2 153 490674101 490673949 1.280000e-41 182.0
33 TraesCS5B01G149700 chr4D 81.818 110 20 0 2962 3071 375718315 375718206 6.180000e-15 93.5
34 TraesCS5B01G149700 chr4A 91.538 130 8 2 2 128 655732660 655732531 5.970000e-40 176.0
35 TraesCS5B01G149700 chr4A 81.098 164 18 12 2962 3118 277904942 277905099 1.020000e-22 119.0
36 TraesCS5B01G149700 chr6D 90.411 73 6 1 5155 5227 471489761 471489832 1.720000e-15 95.3
37 TraesCS5B01G149700 chr6D 91.803 61 2 2 2250 2309 417390662 417390604 1.340000e-11 82.4


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 TraesCS5B01G149700 chr5B 278004692 278010486 5794 False 10702.0 10702 100.0000 1 5795 1 chr5B.!!$F1 5794
1 TraesCS5B01G149700 chr5D 244617031 244622768 5737 False 4351.0 7662 91.0225 89 5795 2 chr5D.!!$F1 5706
2 TraesCS5B01G149700 chr5A 328798382 328803318 4936 False 7616.0 7616 94.4440 817 5795 1 chr5A.!!$F1 4978
3 TraesCS5B01G149700 chr5A 531217077 531218778 1701 True 220.5 252 89.1445 2965 3312 2 chr5A.!!$R1 347
4 TraesCS5B01G149700 chr1D 70451414 70452003 589 False 252.5 322 85.8925 2 624 2 chr1D.!!$F1 622

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
738 761 0.261696 AGTTTGGCCCACCTGAACTT 59.738 50.000 0.0 0.0 38.85 2.66 F
739 762 0.389025 GTTTGGCCCACCTGAACTTG 59.611 55.000 0.0 0.0 36.63 3.16 F
1827 1854 2.025605 TGCAATCTTTGATGCTCCCTCT 60.026 45.455 0.0 0.0 42.97 3.69 F
1859 1886 2.554032 ACTATTTGCTTGTCGCTGCTTT 59.446 40.909 0.0 0.0 40.11 3.51 F
3597 4983 1.119684 GGGCAACACTCCCAGTTTTT 58.880 50.000 0.0 0.0 43.37 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2117 3.749226 TGTACATGAACATGCTGGTTGA 58.251 40.909 13.71 0.0 42.39 3.18 R
2394 2422 4.237018 AGGTCAGGGTCAGGTAAAAAGTA 58.763 43.478 0.00 0.0 0.00 2.24 R
3512 4897 0.114168 TGGCAGGTTAAATGGCAGGT 59.886 50.000 12.53 0.0 46.94 4.00 R
3733 5121 1.295423 CCAACGGTGACCCTACCAG 59.705 63.158 0.00 0.0 40.89 4.00 R
5286 6754 0.034477 CTTGGTTCCCGCCAGGTTAT 60.034 55.000 0.00 0.0 40.01 1.89 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
20 21 3.041940 CCGAAGGCACCGTGTGAC 61.042 66.667 8.04 5.12 46.14 3.67
57 58 2.616330 CCGCATGAACCAACACGCT 61.616 57.895 0.00 0.00 0.00 5.07
81 82 1.647346 GACCAACACACACTTCGACA 58.353 50.000 0.00 0.00 0.00 4.35
87 88 3.319137 ACACACACTTCGACATATGCT 57.681 42.857 1.58 0.00 0.00 3.79
177 196 3.240310 AGTATAGACCCGTGCCTATGT 57.760 47.619 0.00 0.00 0.00 2.29
218 237 1.005156 GAGGATGGAGCGATGCCTC 60.005 63.158 0.00 0.00 38.45 4.70
251 270 1.206578 CCGTGCGTCAAACCATGTC 59.793 57.895 0.00 0.00 0.00 3.06
270 289 3.749088 TGTCTTTTTCTTCGTGTGTGTGT 59.251 39.130 0.00 0.00 0.00 3.72
271 290 4.088648 GTCTTTTTCTTCGTGTGTGTGTG 58.911 43.478 0.00 0.00 0.00 3.82
341 361 1.152483 TAGCCCCGCCCGTAACTAT 60.152 57.895 0.00 0.00 0.00 2.12
362 382 2.441375 TCCCATAAATCTCCATTCGCCA 59.559 45.455 0.00 0.00 0.00 5.69
401 421 3.790089 AAAGGGAAACAGAGAACCGAT 57.210 42.857 0.00 0.00 0.00 4.18
402 422 2.770164 AGGGAAACAGAGAACCGATG 57.230 50.000 0.00 0.00 0.00 3.84
433 453 6.858993 GTCCGTTATTTTTGCTTGTGTTATCA 59.141 34.615 0.00 0.00 0.00 2.15
436 456 6.358558 CGTTATTTTTGCTTGTGTTATCACGT 59.641 34.615 0.00 0.00 46.49 4.49
462 482 9.586732 TGGAAAGGAGAAATCAGAAAATTCTAA 57.413 29.630 0.00 0.00 35.34 2.10
521 541 2.055684 ACCGAAAAGGAAAAACCGGA 57.944 45.000 9.46 0.00 45.00 5.14
571 591 2.103934 GAGCTCTCTGCACGCGAT 59.896 61.111 15.93 0.00 45.94 4.58
572 592 1.943693 GAGCTCTCTGCACGCGATC 60.944 63.158 15.93 3.92 45.94 3.69
573 593 2.103934 GCTCTCTGCACGCGATCT 59.896 61.111 15.93 0.00 42.31 2.75
676 698 1.798813 GAGATGCCGAGTCACGTTTTT 59.201 47.619 0.00 0.00 40.78 1.94
726 749 2.988493 TCGTTATACGTGTGAGTTTGGC 59.012 45.455 0.00 0.00 43.14 4.52
738 761 0.261696 AGTTTGGCCCACCTGAACTT 59.738 50.000 0.00 0.00 38.85 2.66
739 762 0.389025 GTTTGGCCCACCTGAACTTG 59.611 55.000 0.00 0.00 36.63 3.16
801 824 6.961361 ATCTAGGTTTTCTTTCCTCTTCCT 57.039 37.500 0.00 0.00 35.51 3.36
1349 1372 8.447787 TTCTCTTTCGTTTCTTCTTTGTTTTG 57.552 30.769 0.00 0.00 0.00 2.44
1412 1439 2.099098 AGCTGGGTTTCAAGTTTCAACG 59.901 45.455 0.00 0.00 0.00 4.10
1516 1543 5.095490 GTCGATTAGTTCCTGCCAATTTTG 58.905 41.667 0.00 0.00 0.00 2.44
1817 1844 6.094464 CCTGTCATGTCTAATGCAATCTTTGA 59.906 38.462 0.00 0.00 0.00 2.69
1819 1846 7.477494 TGTCATGTCTAATGCAATCTTTGATG 58.523 34.615 0.00 0.00 0.00 3.07
1827 1854 2.025605 TGCAATCTTTGATGCTCCCTCT 60.026 45.455 0.00 0.00 42.97 3.69
1839 1866 5.188555 TGATGCTCCCTCTGATCCATATTAC 59.811 44.000 0.00 0.00 0.00 1.89
1859 1886 2.554032 ACTATTTGCTTGTCGCTGCTTT 59.446 40.909 0.00 0.00 40.11 3.51
2021 2048 3.562141 TCAACATGGGAAAGTACAACACG 59.438 43.478 0.00 0.00 0.00 4.49
2394 2422 5.183904 GTGAGCCATATGGAAAAGTCTTTGT 59.816 40.000 26.47 0.00 37.39 2.83
2624 2652 2.935849 CTGAATGCCTGCACGTTATACA 59.064 45.455 0.00 0.00 0.00 2.29
2959 2987 9.086336 CACAACAACTATCATTTTTCTGTGTTT 57.914 29.630 0.00 0.00 0.00 2.83
3346 4731 2.850647 GACAAAGTCGTCGCCATAGTAC 59.149 50.000 0.00 0.00 0.00 2.73
3351 4736 2.871022 AGTCGTCGCCATAGTACAGTAG 59.129 50.000 0.00 0.00 0.00 2.57
3373 4758 5.127491 AGTTTGATCCACGGTCTTTTGTTA 58.873 37.500 0.00 0.00 0.00 2.41
3500 4885 3.753272 GAGGTCTGGTAGTACAACGTACA 59.247 47.826 2.06 0.00 0.00 2.90
3512 4897 4.994220 ACAACGTACATGCGTGATTTTA 57.006 36.364 14.17 0.00 45.00 1.52
3515 4900 3.592059 ACGTACATGCGTGATTTTACCT 58.408 40.909 14.17 0.00 43.99 3.08
3597 4983 1.119684 GGGCAACACTCCCAGTTTTT 58.880 50.000 0.00 0.00 43.37 1.94
3832 5220 4.395854 TCATTCATGGTATGCACTTCACAC 59.604 41.667 0.00 0.00 0.00 3.82
4011 5403 3.834231 CCATCTTCCACCCATTTCAGTTT 59.166 43.478 0.00 0.00 0.00 2.66
4295 5687 0.585357 CTGATCAGCCGCTGCAATAC 59.415 55.000 15.98 5.53 41.13 1.89
4414 5806 1.520342 GCCACCATCAGAGTCGAGC 60.520 63.158 0.00 0.00 0.00 5.03
4526 5918 2.567049 CGAGAAAGAGGCCGTCGT 59.433 61.111 0.00 0.00 0.00 4.34
4527 5919 1.514443 CGAGAAAGAGGCCGTCGTC 60.514 63.158 0.00 0.00 0.00 4.20
4650 6042 0.039180 TGGAGGCTGAGACGTCCTTA 59.961 55.000 13.01 0.00 43.52 2.69
4665 6057 0.753111 CCTTAGCACCATTGGAGGCC 60.753 60.000 10.37 0.00 0.00 5.19
4801 6193 2.290071 GCTGTTGTTAGCTAGTGGGGAA 60.290 50.000 0.00 0.00 40.52 3.97
4901 6329 9.809395 AACTCTAGTAGATGCTGTATATTACCA 57.191 33.333 0.00 0.00 0.00 3.25
4906 6334 6.959954 AGTAGATGCTGTATATTACCATCCCA 59.040 38.462 0.00 0.00 34.35 4.37
4928 6356 0.465460 AAACCAGTTTGCGGCTCTCA 60.465 50.000 0.00 0.00 0.00 3.27
4936 6364 2.543777 TTGCGGCTCTCACTAAAACT 57.456 45.000 0.00 0.00 0.00 2.66
4970 6398 0.319555 CGAGACTTCAGGCGGAACAA 60.320 55.000 0.00 0.00 0.00 2.83
4999 6427 5.460419 CGCAAACCTGTACTGCAAATTTTTA 59.540 36.000 5.08 0.00 35.78 1.52
5047 6475 2.665185 GATCCCGCATGGTACCGC 60.665 66.667 7.57 4.44 34.77 5.68
5053 6481 0.949105 CCGCATGGTACCGCTAATCC 60.949 60.000 7.57 0.00 0.00 3.01
5296 6764 2.223377 GGAAGCGATTTATAACCTGGCG 59.777 50.000 0.00 0.00 0.00 5.69
5299 6767 1.541670 GCGATTTATAACCTGGCGGGA 60.542 52.381 21.81 0.00 38.76 5.14
5301 6769 2.546789 CGATTTATAACCTGGCGGGAAC 59.453 50.000 21.81 0.00 38.76 3.62
5320 6788 0.846693 CCAAGGTCCCCATTCCCTAG 59.153 60.000 0.00 0.00 0.00 3.02
5327 6795 1.431633 TCCCCATTCCCTAGAGCGATA 59.568 52.381 0.00 0.00 0.00 2.92
5371 6839 5.051816 TCGCTAAACCGATATAAACCCTTG 58.948 41.667 0.00 0.00 31.36 3.61
5372 6840 4.812626 CGCTAAACCGATATAAACCCTTGT 59.187 41.667 0.00 0.00 0.00 3.16
5373 6841 5.984926 CGCTAAACCGATATAAACCCTTGTA 59.015 40.000 0.00 0.00 0.00 2.41
5374 6842 6.145048 CGCTAAACCGATATAAACCCTTGTAG 59.855 42.308 0.00 0.00 0.00 2.74
5375 6843 6.073385 GCTAAACCGATATAAACCCTTGTAGC 60.073 42.308 0.00 0.00 0.00 3.58
5376 6844 5.625568 AACCGATATAAACCCTTGTAGCT 57.374 39.130 0.00 0.00 0.00 3.32
5377 6845 4.957296 ACCGATATAAACCCTTGTAGCTG 58.043 43.478 0.00 0.00 0.00 4.24
5378 6846 4.202326 ACCGATATAAACCCTTGTAGCTGG 60.202 45.833 0.00 0.00 0.00 4.85
5436 6904 1.670674 CGGCATTTTGCTGCAATGAGT 60.671 47.619 16.77 0.00 43.46 3.41
5493 6964 0.824595 TCACGAACTCCCTCGGAACA 60.825 55.000 0.00 0.00 43.22 3.18
5507 6978 1.055849 GGAACAACAGGGCCCAAATT 58.944 50.000 27.56 12.33 0.00 1.82
5509 6980 0.764271 AACAACAGGGCCCAAATTGG 59.236 50.000 27.56 10.68 37.25 3.16
5535 7006 1.566298 AAGCCAGTCCCACATCTCCC 61.566 60.000 0.00 0.00 0.00 4.30
5538 7009 2.365635 AGTCCCACATCTCCCCCG 60.366 66.667 0.00 0.00 0.00 5.73
5756 7236 0.533755 ACCTCCATATCAGCAAGCGC 60.534 55.000 0.00 0.00 38.99 5.92
5774 7254 1.728971 CGCTGCTCGTTCATTTCTCTT 59.271 47.619 0.00 0.00 0.00 2.85
5777 7257 3.061965 GCTGCTCGTTCATTTCTCTTCTC 59.938 47.826 0.00 0.00 0.00 2.87
5779 7259 4.825422 TGCTCGTTCATTTCTCTTCTCAT 58.175 39.130 0.00 0.00 0.00 2.90
5789 7269 3.961480 TCTCTTCTCATTTCGGCTTCA 57.039 42.857 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.203153 GGTGTCACACGGTGCCTT 60.203 61.111 8.30 0.00 34.83 4.35
17 18 1.084935 CGTTGTCCGTTGTGGTGTCA 61.085 55.000 0.00 0.00 39.52 3.58
18 19 1.639534 CGTTGTCCGTTGTGGTGTC 59.360 57.895 0.00 0.00 39.52 3.67
20 21 2.326550 GCGTTGTCCGTTGTGGTG 59.673 61.111 0.00 0.00 39.52 4.17
30 31 4.083600 TTCATGCGGCGCGTTGTC 62.084 61.111 26.01 0.00 0.00 3.18
39 40 2.126888 GCGTGTTGGTTCATGCGG 60.127 61.111 0.00 0.00 39.87 5.69
44 45 2.818487 CGTGCAGCGTGTTGGTTCA 61.818 57.895 0.00 0.00 35.54 3.18
51 52 3.269347 GTTGGTCGTGCAGCGTGT 61.269 61.111 8.22 0.00 42.13 4.49
57 58 0.675208 AAGTGTGTGTTGGTCGTGCA 60.675 50.000 0.00 0.00 0.00 4.57
81 82 7.520798 TCATAAACATCTTGAAGGGAGCATAT 58.479 34.615 0.00 0.00 0.00 1.78
163 182 3.181469 TGAATTCTACATAGGCACGGGTC 60.181 47.826 7.05 0.00 0.00 4.46
167 186 4.180817 TGTGTGAATTCTACATAGGCACG 58.819 43.478 7.05 0.00 0.00 5.34
177 196 7.335171 CCTCTGAATGTCAATGTGTGAATTCTA 59.665 37.037 7.05 0.00 38.23 2.10
218 237 3.772636 CGGTCGTGATGACTGCAG 58.227 61.111 13.48 13.48 46.48 4.41
251 270 4.335082 TCACACACACACGAAGAAAAAG 57.665 40.909 0.00 0.00 0.00 2.27
341 361 2.441375 TGGCGAATGGAGATTTATGGGA 59.559 45.455 0.00 0.00 0.00 4.37
362 382 8.909423 TCCCTTTTTGTTCCCATTATATTTCT 57.091 30.769 0.00 0.00 0.00 2.52
409 429 6.858993 GTGATAACACAAGCAAAAATAACGGA 59.141 34.615 0.00 0.00 45.32 4.69
422 442 4.062293 TCCTTTCCACGTGATAACACAAG 58.938 43.478 19.30 7.57 46.20 3.16
433 453 4.351874 TTCTGATTTCTCCTTTCCACGT 57.648 40.909 0.00 0.00 0.00 4.49
436 456 9.586732 TTAGAATTTTCTGATTTCTCCTTTCCA 57.413 29.630 3.07 0.00 38.19 3.53
496 516 4.496360 GGTTTTTCCTTTTCGGTTTGTGA 58.504 39.130 0.00 0.00 0.00 3.58
558 578 0.038251 ACAAAGATCGCGTGCAGAGA 60.038 50.000 5.77 0.00 0.00 3.10
562 582 1.565156 GGTGACAAAGATCGCGTGCA 61.565 55.000 5.77 0.00 0.00 4.57
565 585 1.736645 CGGGTGACAAAGATCGCGT 60.737 57.895 5.77 0.00 0.00 6.01
571 591 2.342279 CTCCGCGGGTGACAAAGA 59.658 61.111 27.83 0.26 0.00 2.52
572 592 3.423154 GCTCCGCGGGTGACAAAG 61.423 66.667 27.83 14.65 0.00 2.77
594 614 1.888512 ACTAGTTAACAGGCGGTTCGA 59.111 47.619 6.22 0.00 40.96 3.71
595 615 2.358939 ACTAGTTAACAGGCGGTTCG 57.641 50.000 6.22 0.00 40.96 3.95
603 625 5.462398 ACAAACGAGAGCAACTAGTTAACAG 59.538 40.000 8.04 6.00 42.03 3.16
604 626 5.353938 ACAAACGAGAGCAACTAGTTAACA 58.646 37.500 8.04 0.00 42.03 2.41
676 698 7.208225 TGTGACATGATTACATTTTTCCGAA 57.792 32.000 0.00 0.00 34.15 4.30
691 713 7.703197 ACACGTATAACGAATTATGTGACATGA 59.297 33.333 8.61 0.00 46.05 3.07
693 715 7.703197 TCACACGTATAACGAATTATGTGACAT 59.297 33.333 14.75 2.65 43.05 3.06
694 716 7.028361 TCACACGTATAACGAATTATGTGACA 58.972 34.615 14.75 0.00 43.05 3.58
738 761 2.472816 GTTCCGTCCGTTAGTTGAACA 58.527 47.619 0.00 0.00 37.99 3.18
739 762 1.794701 GGTTCCGTCCGTTAGTTGAAC 59.205 52.381 0.00 0.00 34.41 3.18
801 824 0.549169 CCCTACTTTCCCCAGGGTGA 60.549 60.000 4.22 0.00 43.58 4.02
880 903 2.490115 GACGCTCTCTCTTTCTTCCAGA 59.510 50.000 0.00 0.00 0.00 3.86
1162 1185 0.748367 AGTCTCTCCGCGTGCATCTA 60.748 55.000 4.92 0.00 0.00 1.98
1361 1388 8.408043 AACTTTGTAGGAACATCAATCAATCA 57.592 30.769 0.00 0.00 34.97 2.57
1362 1389 8.514594 TGAACTTTGTAGGAACATCAATCAATC 58.485 33.333 0.00 0.00 34.97 2.67
1363 1390 8.408043 TGAACTTTGTAGGAACATCAATCAAT 57.592 30.769 0.00 0.00 34.97 2.57
1364 1391 7.815840 TGAACTTTGTAGGAACATCAATCAA 57.184 32.000 0.00 0.00 34.97 2.57
1365 1392 9.513906 TTATGAACTTTGTAGGAACATCAATCA 57.486 29.630 0.00 0.00 34.97 2.57
1453 1480 8.739039 CAATTGTTGTCAGGTTCTAATAATCCA 58.261 33.333 0.00 0.00 0.00 3.41
1516 1543 7.826744 AGGAGATTCAGATTCAGTAAAAGAACC 59.173 37.037 0.00 0.00 0.00 3.62
1817 1844 5.348833 AGTAATATGGATCAGAGGGAGCAT 58.651 41.667 0.00 0.00 32.12 3.79
1819 1846 7.430760 AATAGTAATATGGATCAGAGGGAGC 57.569 40.000 0.00 0.00 0.00 4.70
1827 1854 8.310406 CGACAAGCAAATAGTAATATGGATCA 57.690 34.615 0.00 0.00 0.00 2.92
1859 1886 5.463061 GTGTTCTGCGGTTAACTTTGTACTA 59.537 40.000 5.42 0.00 0.00 1.82
2021 2048 7.781056 TGGATTTTCCTAAACCAAATATCTGC 58.219 34.615 0.00 0.00 37.46 4.26
2087 2115 4.395854 TGTACATGAACATGCTGGTTGATC 59.604 41.667 13.71 0.00 42.39 2.92
2089 2117 3.749226 TGTACATGAACATGCTGGTTGA 58.251 40.909 13.71 0.00 42.39 3.18
2394 2422 4.237018 AGGTCAGGGTCAGGTAAAAAGTA 58.763 43.478 0.00 0.00 0.00 2.24
2624 2652 9.902684 CATGATTAGGCATCTTTCTATATTCCT 57.097 33.333 0.00 0.00 32.34 3.36
2959 2987 3.697045 CACAAACCAAACACACCCTTAGA 59.303 43.478 0.00 0.00 0.00 2.10
3346 4731 3.594603 AGACCGTGGATCAAACTACTG 57.405 47.619 0.00 0.00 0.00 2.74
3351 4736 3.982576 ACAAAAGACCGTGGATCAAAC 57.017 42.857 0.00 0.00 0.00 2.93
3373 4758 4.479156 TTCCCCAAGTTATCCCAGTTTT 57.521 40.909 0.00 0.00 0.00 2.43
3500 4885 1.832883 TGGCAGGTAAAATCACGCAT 58.167 45.000 0.00 0.00 0.00 4.73
3512 4897 0.114168 TGGCAGGTTAAATGGCAGGT 59.886 50.000 12.53 0.00 46.94 4.00
3597 4983 2.566010 GCCGAAAATGCTCGCCAA 59.434 55.556 0.00 0.00 37.51 4.52
3733 5121 1.295423 CCAACGGTGACCCTACCAG 59.705 63.158 0.00 0.00 40.89 4.00
3793 5181 1.755179 ATGATGTTAGGTGCTGGCAC 58.245 50.000 16.33 16.33 45.49 5.01
3832 5220 7.383572 TCAAAACATCACAAAATGGTTTATCGG 59.616 33.333 0.00 0.00 43.06 4.18
4155 5547 3.191371 CAGGACCTGTAAGAACCAAATGC 59.809 47.826 13.84 0.00 34.07 3.56
4306 5698 0.179129 CCCACAAGCGATTTGGATGC 60.179 55.000 13.77 0.00 41.25 3.91
4405 5797 1.747367 CCTCGACCAGCTCGACTCT 60.747 63.158 0.00 0.00 46.75 3.24
4414 5806 2.903357 CCATGACCCCTCGACCAG 59.097 66.667 0.00 0.00 0.00 4.00
4534 5926 1.078143 AGAGTTCCATCTTGCCGCC 60.078 57.895 0.00 0.00 0.00 6.13
4650 6042 4.431131 CCGGCCTCCAATGGTGCT 62.431 66.667 14.12 0.00 0.00 4.40
4665 6057 0.940126 GCATGTCATGGCTTCTACCG 59.060 55.000 14.64 0.00 0.00 4.02
4787 6179 3.071023 CGGATGAATTCCCCACTAGCTAA 59.929 47.826 2.27 0.00 42.06 3.09
4801 6193 4.102210 ACTGTCAAGATCCATCGGATGAAT 59.898 41.667 19.30 4.18 43.27 2.57
4809 6207 4.701765 ACATAGCACTGTCAAGATCCATC 58.298 43.478 0.00 0.00 0.00 3.51
4883 6311 6.728632 TGTGGGATGGTAATATACAGCATCTA 59.271 38.462 20.30 12.20 45.72 1.98
4898 6326 2.433970 CAAACTGGTTTTGTGGGATGGT 59.566 45.455 0.00 0.00 39.96 3.55
4901 6329 2.908688 GCAAACTGGTTTTGTGGGAT 57.091 45.000 0.00 0.00 45.70 3.85
4906 6334 0.102300 GAGCCGCAAACTGGTTTTGT 59.898 50.000 0.00 0.00 45.70 2.83
4928 6356 5.163893 CGTGATACCGCAAATCAGTTTTAGT 60.164 40.000 0.00 0.00 34.12 2.24
4936 6364 2.165641 AGTCTCGTGATACCGCAAATCA 59.834 45.455 0.00 0.00 0.00 2.57
4970 6398 0.881118 CAGTACAGGTTTGCGGCATT 59.119 50.000 2.28 0.00 0.00 3.56
5009 6437 4.996113 CGGAACATATGCCGCAAC 57.004 55.556 8.56 0.00 41.17 4.17
5029 6457 2.355837 CGGTACCATGCGGGATCG 60.356 66.667 13.54 0.00 41.15 3.69
5274 6742 3.211045 GCCAGGTTATAAATCGCTTCCA 58.789 45.455 0.00 0.00 0.00 3.53
5275 6743 2.223377 CGCCAGGTTATAAATCGCTTCC 59.777 50.000 0.00 0.00 0.00 3.46
5277 6745 2.218603 CCGCCAGGTTATAAATCGCTT 58.781 47.619 0.00 0.00 0.00 4.68
5279 6747 0.872388 CCCGCCAGGTTATAAATCGC 59.128 55.000 0.00 0.00 35.12 4.58
5280 6748 2.536761 TCCCGCCAGGTTATAAATCG 57.463 50.000 0.00 0.00 36.75 3.34
5281 6749 2.882761 GGTTCCCGCCAGGTTATAAATC 59.117 50.000 0.00 0.00 36.75 2.17
5282 6750 2.242708 TGGTTCCCGCCAGGTTATAAAT 59.757 45.455 0.00 0.00 36.75 1.40
5283 6751 1.634459 TGGTTCCCGCCAGGTTATAAA 59.366 47.619 0.00 0.00 36.75 1.40
5284 6752 1.287217 TGGTTCCCGCCAGGTTATAA 58.713 50.000 0.00 0.00 36.75 0.98
5285 6753 1.210967 CTTGGTTCCCGCCAGGTTATA 59.789 52.381 0.00 0.00 40.01 0.98
5286 6754 0.034477 CTTGGTTCCCGCCAGGTTAT 60.034 55.000 0.00 0.00 40.01 1.89
5287 6755 1.377229 CTTGGTTCCCGCCAGGTTA 59.623 57.895 0.00 0.00 40.01 2.85
5308 6776 1.938585 TATCGCTCTAGGGAATGGGG 58.061 55.000 0.00 0.00 40.44 4.96
5342 6810 7.916977 GGGTTTATATCGGTTTAGCGAATTTTT 59.083 33.333 8.17 0.00 0.00 1.94
5350 6818 6.073385 GCTACAAGGGTTTATATCGGTTTAGC 60.073 42.308 0.00 0.00 0.00 3.09
5375 6843 5.940470 CCCATTTATTAGCTAGCTAACCCAG 59.060 44.000 33.80 22.59 40.76 4.45
5376 6844 5.747842 GCCCATTTATTAGCTAGCTAACCCA 60.748 44.000 33.80 21.91 40.76 4.51
5377 6845 4.700692 GCCCATTTATTAGCTAGCTAACCC 59.299 45.833 33.80 14.95 40.76 4.11
5378 6846 5.412904 CAGCCCATTTATTAGCTAGCTAACC 59.587 44.000 33.80 16.57 40.76 2.85
5379 6847 5.412904 CCAGCCCATTTATTAGCTAGCTAAC 59.587 44.000 33.80 20.41 40.76 2.34
5380 6848 5.560724 CCAGCCCATTTATTAGCTAGCTAA 58.439 41.667 33.35 33.35 41.95 3.09
5381 6849 4.565652 GCCAGCCCATTTATTAGCTAGCTA 60.566 45.833 20.67 20.67 37.08 3.32
5382 6850 3.812167 GCCAGCCCATTTATTAGCTAGCT 60.812 47.826 23.12 23.12 37.08 3.32
5383 6851 2.489722 GCCAGCCCATTTATTAGCTAGC 59.510 50.000 6.62 6.62 33.09 3.42
5384 6852 3.084786 GGCCAGCCCATTTATTAGCTAG 58.915 50.000 0.00 0.00 33.33 3.42
5385 6853 3.154827 GGCCAGCCCATTTATTAGCTA 57.845 47.619 0.00 0.00 33.33 3.32
5386 6854 2.001076 GGCCAGCCCATTTATTAGCT 57.999 50.000 0.00 0.00 35.52 3.32
5436 6904 0.550914 AGGCGATTCCCTATTTGCCA 59.449 50.000 3.68 0.00 39.35 4.92
5493 6964 2.758648 GACCAATTTGGGCCCTGTT 58.241 52.632 25.70 12.22 40.64 3.16
5507 6978 2.224159 GGACTGGCTTGAGGGACCA 61.224 63.158 0.00 0.00 0.00 4.02
5509 6980 2.224159 TGGGACTGGCTTGAGGGAC 61.224 63.158 0.00 0.00 0.00 4.46
5643 7123 4.269523 GCCATGCGGGAGGCCATA 62.270 66.667 5.01 0.00 45.18 2.74
5756 7236 4.240888 TGAGAAGAGAAATGAACGAGCAG 58.759 43.478 0.00 0.00 0.00 4.24
5762 7242 5.123027 AGCCGAAATGAGAAGAGAAATGAAC 59.877 40.000 0.00 0.00 0.00 3.18
5774 7254 2.859165 AAGGTGAAGCCGAAATGAGA 57.141 45.000 0.00 0.00 43.70 3.27


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

AutoCloner maintained by Alex Coulton.