Multiple sequence alignment - TraesCS1B01G086900

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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 TraesCS1B01G086900 chr1B 100.000 3630 0 0 1 3630 76140520 76136891 0.000000e+00 6704.0
1 TraesCS1B01G086900 chr1B 91.739 2070 78 33 306 2322 76024631 76022602 0.000000e+00 2789.0
2 TraesCS1B01G086900 chr1B 90.534 1965 86 34 440 2341 76108484 76106557 0.000000e+00 2507.0
3 TraesCS1B01G086900 chr1B 93.911 1051 31 6 978 2019 71188982 71190008 0.000000e+00 1555.0
4 TraesCS1B01G086900 chr1B 91.012 968 43 14 1 966 71187768 71188693 0.000000e+00 1266.0
5 TraesCS1B01G086900 chr1B 92.647 340 14 1 2014 2342 71190204 71190543 2.540000e-131 479.0
6 TraesCS1B01G086900 chr1B 93.284 134 5 2 3 132 76024765 76024632 1.030000e-45 195.0
7 TraesCS1B01G086900 chr1B 92.593 135 7 1 1 132 76108727 76108593 1.330000e-44 191.0
8 TraesCS1B01G086900 chr1B 87.500 112 13 1 306 416 76108592 76108481 1.060000e-25 128.0
9 TraesCS1B01G086900 chr5D 87.517 721 73 8 1168 1888 16594131 16593428 0.000000e+00 817.0
10 TraesCS1B01G086900 chr5D 90.722 485 34 7 2500 2974 70164922 70165405 1.420000e-178 636.0
11 TraesCS1B01G086900 chr5D 85.859 396 33 11 1956 2342 16593412 16593031 2.030000e-107 399.0
12 TraesCS1B01G086900 chr5D 94.488 127 7 0 2344 2470 70164807 70164933 2.860000e-46 196.0
13 TraesCS1B01G086900 chrUn 90.253 554 36 14 3042 3591 272053429 272053968 0.000000e+00 708.0
14 TraesCS1B01G086900 chr6B 88.889 585 47 12 3042 3624 647958437 647957869 0.000000e+00 704.0
15 TraesCS1B01G086900 chr7B 88.889 576 49 6 3042 3610 675957321 675956754 0.000000e+00 695.0
16 TraesCS1B01G086900 chr7B 77.515 338 50 14 581 913 626944698 626945014 2.880000e-41 180.0
17 TraesCS1B01G086900 chr7B 79.916 239 37 11 666 897 138729775 138730009 8.060000e-37 165.0
18 TraesCS1B01G086900 chr1A 89.331 553 44 9 3041 3591 91552766 91553305 0.000000e+00 680.0
19 TraesCS1B01G086900 chr5A 88.636 572 46 12 3042 3610 403904856 403904301 0.000000e+00 678.0
20 TraesCS1B01G086900 chr5A 87.659 551 54 10 3044 3591 685057074 685056535 2.380000e-176 628.0
21 TraesCS1B01G086900 chr5A 94.595 37 2 0 2344 2380 547589464 547589428 1.410000e-04 58.4
22 TraesCS1B01G086900 chr3A 88.636 572 43 14 3042 3610 732887065 732886513 0.000000e+00 676.0
23 TraesCS1B01G086900 chr7A 87.633 566 51 13 3042 3605 663761747 663761199 1.100000e-179 640.0
24 TraesCS1B01G086900 chr7A 80.716 363 52 14 2343 2695 238558495 238558141 2.150000e-67 267.0
25 TraesCS1B01G086900 chr7A 84.232 241 30 4 2743 2977 238558128 238557890 1.010000e-55 228.0
26 TraesCS1B01G086900 chr7A 86.500 200 18 7 131 326 161898582 161898388 1.020000e-50 211.0
27 TraesCS1B01G086900 chr7A 97.619 42 1 0 2344 2385 42259801 42259760 5.030000e-09 73.1
28 TraesCS1B01G086900 chr2A 85.639 571 65 9 3042 3610 726083268 726082713 5.220000e-163 584.0
29 TraesCS1B01G086900 chr2A 78.073 301 55 11 620 913 702183483 702183779 2.880000e-41 180.0
30 TraesCS1B01G086900 chr2A 80.795 151 26 3 2527 2675 437678480 437678629 8.240000e-22 115.0
31 TraesCS1B01G086900 chr4D 79.129 551 86 19 2437 2977 196837069 196837600 1.600000e-93 353.0
32 TraesCS1B01G086900 chr4D 89.326 178 13 5 133 305 35722303 35722479 6.100000e-53 219.0
33 TraesCS1B01G086900 chr4D 90.909 77 7 0 2341 2417 196818928 196819004 1.780000e-18 104.0
34 TraesCS1B01G086900 chr3D 90.449 178 12 2 133 305 506177131 506177308 2.820000e-56 230.0
35 TraesCS1B01G086900 chr3D 76.036 338 59 16 581 913 454357688 454358008 4.850000e-34 156.0
36 TraesCS1B01G086900 chr3D 88.991 109 12 0 2003 2111 45686139 45686031 6.320000e-28 135.0
37 TraesCS1B01G086900 chr3B 82.759 261 42 3 657 914 779197194 779196934 2.820000e-56 230.0
38 TraesCS1B01G086900 chr3B 88.710 186 14 7 125 305 766376877 766377060 1.700000e-53 220.0
39 TraesCS1B01G086900 chr3B 90.826 109 10 0 2003 2111 71350488 71350380 2.920000e-31 147.0
40 TraesCS1B01G086900 chr3B 100.000 30 0 0 2344 2373 823449225 823449196 5.060000e-04 56.5
41 TraesCS1B01G086900 chr2B 88.947 190 16 2 120 305 771215329 771215141 2.820000e-56 230.0
42 TraesCS1B01G086900 chr2B 77.219 338 47 13 581 913 646809375 646809687 1.730000e-38 171.0
43 TraesCS1B01G086900 chr2D 87.310 197 21 4 127 322 11484150 11483957 4.720000e-54 222.0
44 TraesCS1B01G086900 chr2D 100.000 29 0 0 2346 2374 602110799 602110827 2.000000e-03 54.7
45 TraesCS1B01G086900 chr2D 100.000 29 0 0 2346 2374 602136997 602137025 2.000000e-03 54.7
46 TraesCS1B01G086900 chr4A 86.667 195 19 6 131 320 712846744 712846552 3.670000e-50 209.0
47 TraesCS1B01G086900 chr7D 84.163 221 22 11 126 337 596067487 596067271 6.150000e-48 202.0
48 TraesCS1B01G086900 chr7D 79.904 209 36 5 707 913 297756772 297756976 8.120000e-32 148.0
49 TraesCS1B01G086900 chr1D 78.731 268 51 6 646 908 208168548 208168282 1.340000e-39 174.0
50 TraesCS1B01G086900 chr1D 82.286 175 22 7 743 914 63605427 63605259 3.780000e-30 143.0
51 TraesCS1B01G086900 chr5B 76.437 348 62 14 584 923 343329527 343329192 1.730000e-38 171.0
52 TraesCS1B01G086900 chr4B 84.416 154 20 3 581 730 35858258 35858105 8.120000e-32 148.0
53 TraesCS1B01G086900 chr6D 100.000 30 0 0 2344 2373 413768725 413768754 5.060000e-04 56.5


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 TraesCS1B01G086900 chr1B 76136891 76140520 3629 True 6704.0 6704 100.000000 1 3630 1 chr1B.!!$R1 3629
1 TraesCS1B01G086900 chr1B 76022602 76024765 2163 True 1492.0 2789 92.511500 3 2322 2 chr1B.!!$R2 2319
2 TraesCS1B01G086900 chr1B 71187768 71190543 2775 False 1100.0 1555 92.523333 1 2342 3 chr1B.!!$F1 2341
3 TraesCS1B01G086900 chr1B 76106557 76108727 2170 True 942.0 2507 90.209000 1 2341 3 chr1B.!!$R3 2340
4 TraesCS1B01G086900 chr5D 16593031 16594131 1100 True 608.0 817 86.688000 1168 2342 2 chr5D.!!$R1 1174
5 TraesCS1B01G086900 chr5D 70164807 70165405 598 False 416.0 636 92.605000 2344 2974 2 chr5D.!!$F1 630
6 TraesCS1B01G086900 chrUn 272053429 272053968 539 False 708.0 708 90.253000 3042 3591 1 chrUn.!!$F1 549
7 TraesCS1B01G086900 chr6B 647957869 647958437 568 True 704.0 704 88.889000 3042 3624 1 chr6B.!!$R1 582
8 TraesCS1B01G086900 chr7B 675956754 675957321 567 True 695.0 695 88.889000 3042 3610 1 chr7B.!!$R1 568
9 TraesCS1B01G086900 chr1A 91552766 91553305 539 False 680.0 680 89.331000 3041 3591 1 chr1A.!!$F1 550
10 TraesCS1B01G086900 chr5A 403904301 403904856 555 True 678.0 678 88.636000 3042 3610 1 chr5A.!!$R1 568
11 TraesCS1B01G086900 chr5A 685056535 685057074 539 True 628.0 628 87.659000 3044 3591 1 chr5A.!!$R3 547
12 TraesCS1B01G086900 chr3A 732886513 732887065 552 True 676.0 676 88.636000 3042 3610 1 chr3A.!!$R1 568
13 TraesCS1B01G086900 chr7A 663761199 663761747 548 True 640.0 640 87.633000 3042 3605 1 chr7A.!!$R3 563
14 TraesCS1B01G086900 chr7A 238557890 238558495 605 True 247.5 267 82.474000 2343 2977 2 chr7A.!!$R4 634
15 TraesCS1B01G086900 chr2A 726082713 726083268 555 True 584.0 584 85.639000 3042 3610 1 chr2A.!!$R1 568
16 TraesCS1B01G086900 chr4D 196837069 196837600 531 False 353.0 353 79.129000 2437 2977 1 chr4D.!!$F3 540

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
104 112 0.327924 TTTGTGATCAGGTGGCCGAT 59.672 50.000 0.0 0.0 0.00 4.18 F
201 209 2.639839 AGCTAATGTCCACTCTGTTGGT 59.360 45.455 0.0 0.0 37.93 3.67 F
1418 1743 1.374190 GGAGATGCGGGATGCTGAT 59.626 57.895 0.0 0.0 46.63 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1743 0.609131 GCTGCTCCTTGCCCTTGTAA 60.609 55.000 0.00 0.0 42.00 2.41 R
1675 2032 1.153168 ATGGTGTACGCAGATGCCC 60.153 57.895 8.97 0.0 37.91 5.36 R
3161 3765 0.112412 AAGGGCTCATTTGAACCGGT 59.888 50.000 0.00 0.0 31.18 5.28 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
104 112 0.327924 TTTGTGATCAGGTGGCCGAT 59.672 50.000 0.00 0.00 0.00 4.18
184 192 7.563888 ACATAGTTATGTCACGTCTAAGCTA 57.436 36.000 0.00 0.00 42.96 3.32
196 204 4.142359 ACGTCTAAGCTAATGTCCACTCTG 60.142 45.833 0.00 0.00 0.00 3.35
199 207 5.578727 GTCTAAGCTAATGTCCACTCTGTTG 59.421 44.000 0.00 0.00 0.00 3.33
201 209 2.639839 AGCTAATGTCCACTCTGTTGGT 59.360 45.455 0.00 0.00 37.93 3.67
203 211 3.807209 GCTAATGTCCACTCTGTTGGTGT 60.807 47.826 0.00 0.00 37.93 4.16
209 217 3.694566 GTCCACTCTGTTGGTGTTCTTTT 59.305 43.478 0.00 0.00 37.93 2.27
210 218 4.157840 GTCCACTCTGTTGGTGTTCTTTTT 59.842 41.667 0.00 0.00 37.93 1.94
255 263 6.023357 TGTTGCTGCATTATGTATTTGTGT 57.977 33.333 1.84 0.00 0.00 3.72
256 264 5.862860 TGTTGCTGCATTATGTATTTGTGTG 59.137 36.000 1.84 0.00 0.00 3.82
499 513 8.873830 ACAGTGATTAACTATTGAAGTTCATCG 58.126 33.333 6.36 0.99 45.64 3.84
624 660 6.263168 ACTCAAAAATCTCACCGATCAAAGTT 59.737 34.615 0.00 0.00 0.00 2.66
947 984 4.996758 GCAATTAGCAGGAACCAAACAATT 59.003 37.500 0.00 0.00 44.79 2.32
948 985 5.469760 GCAATTAGCAGGAACCAAACAATTT 59.530 36.000 0.00 0.00 44.79 1.82
1074 1389 8.902806 TGGATGCGTCAAGAATTTAATATTCTT 58.097 29.630 8.47 14.60 45.99 2.52
1418 1743 1.374190 GGAGATGCGGGATGCTGAT 59.626 57.895 0.00 0.00 46.63 2.90
1534 1882 1.416401 CACCCACTTCTACACCTGTGT 59.584 52.381 8.17 8.17 46.87 3.72
1544 1892 8.709646 CACTTCTACACCTGTGTAAATAAGAAC 58.290 37.037 21.46 0.00 44.47 3.01
1626 1983 6.732896 AAGGTAGAATGTTCGATCCTATGT 57.267 37.500 0.00 0.00 0.00 2.29
1853 2210 3.540617 TGTGCTGTGCTTCAGTTTCTTA 58.459 40.909 10.20 0.00 45.23 2.10
1868 2225 5.357314 CAGTTTCTTAGATCGTCTACTCCCA 59.643 44.000 0.00 0.00 0.00 4.37
1898 2255 1.682087 GGTGGTGCCTACCCTTGATTC 60.682 57.143 0.00 0.00 46.96 2.52
1907 2264 6.879458 GTGCCTACCCTTGATTCGAATATTAT 59.121 38.462 11.38 0.00 0.00 1.28
1908 2265 7.390718 GTGCCTACCCTTGATTCGAATATTATT 59.609 37.037 11.38 0.00 0.00 1.40
1909 2266 7.606456 TGCCTACCCTTGATTCGAATATTATTC 59.394 37.037 11.38 6.37 0.00 1.75
1910 2267 7.606456 GCCTACCCTTGATTCGAATATTATTCA 59.394 37.037 11.38 1.29 0.00 2.57
1911 2268 8.936864 CCTACCCTTGATTCGAATATTATTCAC 58.063 37.037 11.38 0.00 0.00 3.18
1912 2269 9.712305 CTACCCTTGATTCGAATATTATTCACT 57.288 33.333 11.38 0.97 0.00 3.41
1958 2315 0.892358 ATTCAGTGGTGCAGCTGGTG 60.892 55.000 17.12 11.39 33.81 4.17
1959 2316 2.963928 TTCAGTGGTGCAGCTGGTGG 62.964 60.000 17.12 2.60 33.81 4.61
1960 2317 3.492353 AGTGGTGCAGCTGGTGGT 61.492 61.111 17.12 0.00 0.00 4.16
1961 2318 3.289834 GTGGTGCAGCTGGTGGTG 61.290 66.667 17.12 0.00 43.87 4.17
1969 2326 4.962836 GCTGGTGGTGCAGCTGGT 62.963 66.667 17.12 0.00 40.95 4.00
2019 2586 1.697982 GGATAGGCGTTGGGGATACTT 59.302 52.381 0.00 0.00 0.00 2.24
2042 2609 0.676151 GCTGCCCTCAAGTCCAAGAG 60.676 60.000 0.00 0.00 0.00 2.85
2052 2619 0.540830 AGTCCAAGAGCGTCCTCACT 60.541 55.000 0.00 0.00 40.68 3.41
2359 2941 5.163343 GGATTATGCTAGATAATACCCCGCA 60.163 44.000 0.00 0.00 0.00 5.69
2455 3037 8.672823 TCATTGAAAGTCCATCAGATTATGAG 57.327 34.615 0.00 0.00 42.53 2.90
2459 3041 9.605275 TTGAAAGTCCATCAGATTATGAGTAAG 57.395 33.333 0.00 0.00 42.53 2.34
2482 3065 8.807667 AAGAAACAATCTTGCTTCTAAACATG 57.192 30.769 8.54 0.00 46.71 3.21
2494 3077 7.420002 TGCTTCTAAACATGCATGATTGATAC 58.580 34.615 32.75 18.42 0.00 2.24
2536 3119 9.367444 TCGCCAACTTTAAAAAGAATTGTTTTA 57.633 25.926 13.14 6.64 39.31 1.52
2645 3229 8.403236 ACTACAATAAAGTCAACCACAAAGTTC 58.597 33.333 0.00 0.00 0.00 3.01
2669 3254 8.185003 TCTCATAATTTGTGAGTGTTACATCG 57.815 34.615 18.93 0.00 42.82 3.84
2706 3303 4.344359 TGGCACACATACTTACAGTCAA 57.656 40.909 0.00 0.00 0.00 3.18
2813 3416 8.644318 GACAATACTATTTTGTCTACGGATGT 57.356 34.615 8.82 0.00 46.03 3.06
2875 3478 6.712241 TTCTTTGATCGTGTCAAGATCTTC 57.288 37.500 23.59 5.80 46.85 2.87
2924 3527 5.859648 TCAATAAACTTTTTCGCGGATTTCC 59.140 36.000 6.13 0.00 0.00 3.13
2925 3528 2.717580 AACTTTTTCGCGGATTTCCC 57.282 45.000 6.13 0.00 0.00 3.97
2948 3551 8.106462 TCCCTTGTCATGTTAAGATATTCAACA 58.894 33.333 11.53 0.00 36.66 3.33
2977 3580 9.875675 GTGTAGCTGATCAATTCTTCAATAATC 57.124 33.333 0.00 0.00 0.00 1.75
2978 3581 9.842775 TGTAGCTGATCAATTCTTCAATAATCT 57.157 29.630 0.00 0.00 0.00 2.40
2980 3583 8.749026 AGCTGATCAATTCTTCAATAATCTGT 57.251 30.769 0.00 0.00 0.00 3.41
2981 3584 9.186837 AGCTGATCAATTCTTCAATAATCTGTT 57.813 29.630 0.00 0.00 0.00 3.16
2982 3585 9.448294 GCTGATCAATTCTTCAATAATCTGTTC 57.552 33.333 0.00 0.00 0.00 3.18
3028 3631 9.639601 TCATCATAATGATAGACGAATGGTTAC 57.360 33.333 0.00 0.00 36.98 2.50
3029 3632 8.587111 CATCATAATGATAGACGAATGGTTACG 58.413 37.037 0.00 0.00 34.28 3.18
3030 3633 6.584942 TCATAATGATAGACGAATGGTTACGC 59.415 38.462 0.00 0.00 0.00 4.42
3031 3634 3.786516 TGATAGACGAATGGTTACGCA 57.213 42.857 0.00 0.00 0.00 5.24
3032 3635 3.702330 TGATAGACGAATGGTTACGCAG 58.298 45.455 0.00 0.00 0.00 5.18
3034 3637 2.450609 AGACGAATGGTTACGCAGTT 57.549 45.000 0.00 0.00 37.78 3.16
3035 3638 2.066262 AGACGAATGGTTACGCAGTTG 58.934 47.619 0.00 0.00 37.78 3.16
3036 3639 2.063266 GACGAATGGTTACGCAGTTGA 58.937 47.619 0.00 0.00 37.78 3.18
3037 3640 1.796459 ACGAATGGTTACGCAGTTGAC 59.204 47.619 0.00 0.00 37.78 3.18
3038 3641 1.127951 CGAATGGTTACGCAGTTGACC 59.872 52.381 0.00 0.00 37.78 4.02
3054 3657 6.595716 GCAGTTGACCATCACTAGTAGAAAAT 59.404 38.462 3.59 0.00 0.00 1.82
3064 3667 7.490657 TCACTAGTAGAAAATAGGGCTTTCA 57.509 36.000 3.59 0.00 35.62 2.69
3077 3680 0.665298 GCTTTCATTCGGGCCAGATC 59.335 55.000 6.36 0.00 0.00 2.75
3078 3681 0.940126 CTTTCATTCGGGCCAGATCG 59.060 55.000 6.36 0.00 0.00 3.69
3079 3682 0.463654 TTTCATTCGGGCCAGATCGG 60.464 55.000 6.36 0.00 38.11 4.18
3080 3683 1.622607 TTCATTCGGGCCAGATCGGT 61.623 55.000 6.36 0.00 36.97 4.69
3081 3684 0.757561 TCATTCGGGCCAGATCGGTA 60.758 55.000 6.36 0.00 36.97 4.02
3082 3685 0.600255 CATTCGGGCCAGATCGGTAC 60.600 60.000 6.36 0.00 36.97 3.34
3114 3717 3.593834 GGTTTAGTCACGAACCGGT 57.406 52.632 0.00 0.00 36.31 5.28
3144 3748 1.460255 CATGGGTCCCAGGTTGTGT 59.540 57.895 17.70 0.00 36.75 3.72
3152 3756 1.215673 TCCCAGGTTGTGTGGCTAAAA 59.784 47.619 0.00 0.00 33.24 1.52
3161 3765 5.182380 GGTTGTGTGGCTAAAAGCATTAGTA 59.818 40.000 10.02 0.05 44.75 1.82
3287 3892 4.635699 AGACCTTTAGTTCCGGTTTGAT 57.364 40.909 0.00 0.00 0.00 2.57
3343 3948 2.296471 AGTCTCGGTTCGTGTCTCAAAT 59.704 45.455 0.00 0.00 0.00 2.32
3371 3976 7.754851 GACTAAAGGTCCCATTTTCAAACTA 57.245 36.000 0.00 0.00 38.93 2.24
3382 3992 5.269189 CATTTTCAAACTATACCACCCCCT 58.731 41.667 0.00 0.00 0.00 4.79
3386 3996 0.029371 AACTATACCACCCCCTCCCC 60.029 60.000 0.00 0.00 0.00 4.81
3387 3997 0.939961 ACTATACCACCCCCTCCCCT 60.940 60.000 0.00 0.00 0.00 4.79
3413 4023 1.803289 GGTGGATCGCCTTTTCAGC 59.197 57.895 0.00 0.00 34.31 4.26
3580 4197 3.363970 CGGCCATATCTTTTGCATACGAC 60.364 47.826 2.24 0.00 0.00 4.34
3617 4234 9.515226 ACCCGCATAATATATAAAAGAACACAT 57.485 29.630 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 190 4.008074 ACACCAACAGAGTGGACATTAG 57.992 45.455 0.00 0.00 41.65 1.73
184 192 3.117888 AGAACACCAACAGAGTGGACATT 60.118 43.478 0.00 0.00 41.65 2.71
239 247 7.028962 TCAAAGCTCACACAAATACATAATGC 58.971 34.615 0.00 0.00 0.00 3.56
255 263 3.708403 AGGATGTCACATCAAAGCTCA 57.292 42.857 19.61 0.00 0.00 4.26
256 264 6.500684 TTTAAGGATGTCACATCAAAGCTC 57.499 37.500 19.61 0.83 0.00 4.09
334 342 6.408035 CAAAGCCATCTAGATATGAGCAGAT 58.592 40.000 4.54 0.00 0.00 2.90
438 451 9.170584 GAACCTTCAAAATACTTCGAGAAAAAG 57.829 33.333 0.00 0.00 0.00 2.27
499 513 9.654663 GATAGATAGAGAGAGAGAGTTAAGTCC 57.345 40.741 6.68 0.00 0.00 3.85
560 596 9.442062 ACCGGAAGAGATAGATAGATAGATAGA 57.558 37.037 9.46 0.00 0.00 1.98
569 605 8.138712 GCCATATAAACCGGAAGAGATAGATAG 58.861 40.741 9.46 0.00 0.00 2.08
573 609 6.071334 TGAGCCATATAAACCGGAAGAGATAG 60.071 42.308 9.46 0.00 0.00 2.08
577 613 4.336889 TGAGCCATATAAACCGGAAGAG 57.663 45.455 9.46 0.00 0.00 2.85
793 829 9.221775 GATTTTAAGGTGTATTAAATCACTGCG 57.778 33.333 11.33 0.00 35.24 5.18
878 914 7.217906 CCTTCCGGTTTATAGAGCTTATCTTT 58.782 38.462 0.00 0.00 39.64 2.52
879 915 6.239629 CCCTTCCGGTTTATAGAGCTTATCTT 60.240 42.308 0.00 0.00 39.64 2.40
947 984 3.380393 TCCCTCTTCATTGATCCGGTAA 58.620 45.455 0.00 0.00 0.00 2.85
948 985 3.040655 TCCCTCTTCATTGATCCGGTA 57.959 47.619 0.00 0.00 0.00 4.02
981 1296 2.004589 CTAGGACCTAGGCCCTATCCT 58.995 57.143 22.93 20.79 42.52 3.24
1418 1743 0.609131 GCTGCTCCTTGCCCTTGTAA 60.609 55.000 0.00 0.00 42.00 2.41
1534 1882 3.687698 GCTTCTGCCGGTGTTCTTATTTA 59.312 43.478 1.90 0.00 0.00 1.40
1544 1892 2.809861 ATCCACAGCTTCTGCCGGTG 62.810 60.000 1.90 0.00 41.61 4.94
1675 2032 1.153168 ATGGTGTACGCAGATGCCC 60.153 57.895 8.97 0.00 37.91 5.36
1853 2210 7.394923 CCTAATCTAATTGGGAGTAGACGATCT 59.605 40.741 14.76 0.00 42.95 2.75
1907 2264 8.698210 ACACCATCGTACCTAAATAATAGTGAA 58.302 33.333 0.00 0.00 0.00 3.18
1908 2265 8.241497 ACACCATCGTACCTAAATAATAGTGA 57.759 34.615 0.00 0.00 0.00 3.41
1909 2266 8.358148 AGACACCATCGTACCTAAATAATAGTG 58.642 37.037 0.00 0.00 0.00 2.74
1910 2267 8.474710 AGACACCATCGTACCTAAATAATAGT 57.525 34.615 0.00 0.00 0.00 2.12
1911 2268 9.760077 AAAGACACCATCGTACCTAAATAATAG 57.240 33.333 0.00 0.00 0.00 1.73
1912 2269 9.537192 CAAAGACACCATCGTACCTAAATAATA 57.463 33.333 0.00 0.00 0.00 0.98
1913 2270 8.262227 TCAAAGACACCATCGTACCTAAATAAT 58.738 33.333 0.00 0.00 0.00 1.28
1914 2271 7.613585 TCAAAGACACCATCGTACCTAAATAA 58.386 34.615 0.00 0.00 0.00 1.40
1915 2272 7.172868 TCAAAGACACCATCGTACCTAAATA 57.827 36.000 0.00 0.00 0.00 1.40
1916 2273 6.045072 TCAAAGACACCATCGTACCTAAAT 57.955 37.500 0.00 0.00 0.00 1.40
1917 2274 5.471556 TCAAAGACACCATCGTACCTAAA 57.528 39.130 0.00 0.00 0.00 1.85
1958 2315 1.180029 AATCAATCACCAGCTGCACC 58.820 50.000 8.66 0.00 0.00 5.01
1959 2316 4.644103 ATAAATCAATCACCAGCTGCAC 57.356 40.909 8.66 0.00 0.00 4.57
1960 2317 4.463539 ACAATAAATCAATCACCAGCTGCA 59.536 37.500 8.66 0.00 0.00 4.41
1961 2318 5.002464 ACAATAAATCAATCACCAGCTGC 57.998 39.130 8.66 0.00 0.00 5.25
1962 2319 7.894376 AAAACAATAAATCAATCACCAGCTG 57.106 32.000 6.78 6.78 0.00 4.24
2019 2586 2.033141 GACTTGAGGGCAGCAGCA 59.967 61.111 2.65 0.00 44.61 4.41
2042 2609 1.634702 GAAGACATCAGTGAGGACGC 58.365 55.000 12.53 0.56 0.00 5.19
2052 2619 3.072915 TCTTCTTTGGCAGGAAGACATCA 59.927 43.478 22.26 8.04 41.72 3.07
2111 2678 6.980978 AGATATATATAGCAATCACACGTGGC 59.019 38.462 21.57 13.03 0.00 5.01
2359 2941 3.276846 GTGTTCCCGCAGCAACGT 61.277 61.111 0.00 0.00 0.00 3.99
2403 2985 6.645790 TCTATAGTTCTCCAACCGATAACC 57.354 41.667 0.00 0.00 32.22 2.85
2459 3041 6.642131 TGCATGTTTAGAAGCAAGATTGTTTC 59.358 34.615 12.58 12.58 45.21 2.78
2466 3049 6.151480 TCAATCATGCATGTTTAGAAGCAAGA 59.849 34.615 25.43 11.53 40.76 3.02
2482 3065 9.552114 GCTTATCTGTATTTGTATCAATCATGC 57.448 33.333 0.00 0.00 0.00 4.06
2587 3170 9.747898 TGTAATATTAGGTTGTTCACAGGAAAT 57.252 29.630 0.00 0.00 34.13 2.17
2875 3478 0.247460 TGATCAGCTCCACTCCGTTG 59.753 55.000 0.00 0.00 0.00 4.10
2924 3527 9.166173 TCTGTTGAATATCTTAACATGACAAGG 57.834 33.333 0.00 0.00 34.22 3.61
2948 3551 6.291648 TGAAGAATTGATCAGCTACACTCT 57.708 37.500 0.00 0.00 0.00 3.24
3002 3605 9.639601 GTAACCATTCGTCTATCATTATGATGA 57.360 33.333 17.09 2.23 45.81 2.92
3003 3606 8.587111 CGTAACCATTCGTCTATCATTATGATG 58.413 37.037 17.09 7.86 37.70 3.07
3004 3607 7.275779 GCGTAACCATTCGTCTATCATTATGAT 59.724 37.037 12.62 12.62 40.72 2.45
3005 3608 6.584942 GCGTAACCATTCGTCTATCATTATGA 59.415 38.462 0.00 0.00 0.00 2.15
3006 3609 6.364976 TGCGTAACCATTCGTCTATCATTATG 59.635 38.462 0.00 0.00 0.00 1.90
3007 3610 6.452242 TGCGTAACCATTCGTCTATCATTAT 58.548 36.000 0.00 0.00 0.00 1.28
3008 3611 5.834169 TGCGTAACCATTCGTCTATCATTA 58.166 37.500 0.00 0.00 0.00 1.90
3009 3612 4.689071 TGCGTAACCATTCGTCTATCATT 58.311 39.130 0.00 0.00 0.00 2.57
3010 3613 4.202121 ACTGCGTAACCATTCGTCTATCAT 60.202 41.667 0.00 0.00 0.00 2.45
3011 3614 3.129813 ACTGCGTAACCATTCGTCTATCA 59.870 43.478 0.00 0.00 0.00 2.15
3012 3615 3.703420 ACTGCGTAACCATTCGTCTATC 58.297 45.455 0.00 0.00 0.00 2.08
3013 3616 3.795623 ACTGCGTAACCATTCGTCTAT 57.204 42.857 0.00 0.00 0.00 1.98
3014 3617 3.057386 TCAACTGCGTAACCATTCGTCTA 60.057 43.478 0.00 0.00 0.00 2.59
3015 3618 2.066262 CAACTGCGTAACCATTCGTCT 58.934 47.619 0.00 0.00 0.00 4.18
3016 3619 2.063266 TCAACTGCGTAACCATTCGTC 58.937 47.619 0.00 0.00 0.00 4.20
3017 3620 1.796459 GTCAACTGCGTAACCATTCGT 59.204 47.619 0.00 0.00 0.00 3.85
3018 3621 1.127951 GGTCAACTGCGTAACCATTCG 59.872 52.381 7.70 0.00 0.00 3.34
3019 3622 2.147958 TGGTCAACTGCGTAACCATTC 58.852 47.619 9.94 0.00 36.88 2.67
3020 3623 2.264005 TGGTCAACTGCGTAACCATT 57.736 45.000 9.94 0.00 36.88 3.16
3021 3624 2.489938 ATGGTCAACTGCGTAACCAT 57.510 45.000 16.01 16.01 45.08 3.55
3022 3625 1.070914 TGATGGTCAACTGCGTAACCA 59.929 47.619 13.88 13.88 45.32 3.67
3023 3626 1.463444 GTGATGGTCAACTGCGTAACC 59.537 52.381 6.36 6.36 0.00 2.85
3024 3627 2.413837 AGTGATGGTCAACTGCGTAAC 58.586 47.619 0.00 0.00 0.00 2.50
3025 3628 2.831685 AGTGATGGTCAACTGCGTAA 57.168 45.000 0.00 0.00 0.00 3.18
3026 3629 2.823747 ACTAGTGATGGTCAACTGCGTA 59.176 45.455 0.00 0.00 0.00 4.42
3027 3630 1.618837 ACTAGTGATGGTCAACTGCGT 59.381 47.619 0.00 0.00 0.00 5.24
3028 3631 2.370281 ACTAGTGATGGTCAACTGCG 57.630 50.000 0.00 0.00 0.00 5.18
3029 3632 4.720649 TCTACTAGTGATGGTCAACTGC 57.279 45.455 5.39 0.00 0.00 4.40
3030 3633 9.307121 CTATTTTCTACTAGTGATGGTCAACTG 57.693 37.037 5.39 0.00 0.00 3.16
3031 3634 8.478877 CCTATTTTCTACTAGTGATGGTCAACT 58.521 37.037 5.39 0.00 0.00 3.16
3032 3635 7.711339 CCCTATTTTCTACTAGTGATGGTCAAC 59.289 40.741 5.39 0.00 0.00 3.18
3033 3636 7.635089 GCCCTATTTTCTACTAGTGATGGTCAA 60.635 40.741 5.39 0.00 0.00 3.18
3034 3637 6.183360 GCCCTATTTTCTACTAGTGATGGTCA 60.183 42.308 5.39 0.00 0.00 4.02
3035 3638 6.042208 AGCCCTATTTTCTACTAGTGATGGTC 59.958 42.308 5.39 0.00 0.00 4.02
3036 3639 5.905913 AGCCCTATTTTCTACTAGTGATGGT 59.094 40.000 5.39 0.00 0.00 3.55
3037 3640 6.426646 AGCCCTATTTTCTACTAGTGATGG 57.573 41.667 5.39 0.00 0.00 3.51
3038 3641 7.987458 TGAAAGCCCTATTTTCTACTAGTGATG 59.013 37.037 5.39 0.00 35.94 3.07
3039 3642 8.090788 TGAAAGCCCTATTTTCTACTAGTGAT 57.909 34.615 5.39 0.00 35.94 3.06
3054 3657 1.226262 GGCCCGAATGAAAGCCCTA 59.774 57.895 0.00 0.00 39.60 3.53
3064 3667 1.046472 TGTACCGATCTGGCCCGAAT 61.046 55.000 0.00 0.00 43.94 3.34
3078 3681 0.466963 CCGGGACTAATGGGTGTACC 59.533 60.000 0.00 0.00 40.81 3.34
3079 3682 1.197812 ACCGGGACTAATGGGTGTAC 58.802 55.000 6.32 0.00 0.00 2.90
3080 3683 1.955451 AACCGGGACTAATGGGTGTA 58.045 50.000 6.32 0.00 31.96 2.90
3081 3684 1.069775 AAACCGGGACTAATGGGTGT 58.930 50.000 6.32 0.00 31.96 4.16
3082 3685 2.237893 ACTAAACCGGGACTAATGGGTG 59.762 50.000 6.32 0.00 31.96 4.61
3125 3729 1.978617 CACAACCTGGGACCCATGC 60.979 63.158 15.39 0.00 30.82 4.06
3129 3733 2.115266 CCACACAACCTGGGACCC 59.885 66.667 2.45 2.45 0.00 4.46
3138 3742 5.121221 ACTAATGCTTTTAGCCACACAAC 57.879 39.130 6.84 0.00 41.51 3.32
3144 3748 3.054948 ACCGGTACTAATGCTTTTAGCCA 60.055 43.478 4.49 0.00 41.51 4.75
3152 3756 4.839121 TCATTTGAACCGGTACTAATGCT 58.161 39.130 21.56 1.31 32.50 3.79
3161 3765 0.112412 AAGGGCTCATTTGAACCGGT 59.888 50.000 0.00 0.00 31.18 5.28
3277 3882 1.231958 GGTTCGTGCATCAAACCGGA 61.232 55.000 9.46 0.00 33.68 5.14
3287 3892 0.320073 CTTTAGTCCCGGTTCGTGCA 60.320 55.000 0.00 0.00 0.00 4.57
3371 3976 2.710064 GAGGGGAGGGGGTGGTAT 59.290 66.667 0.00 0.00 0.00 2.73
3526 4142 9.786105 CTTTTTCATAACACCTTTTTGCAAAAT 57.214 25.926 24.39 11.53 0.00 1.82


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

AutoCloner maintained by Alex Coulton.