Multiple sequence alignment - TraesCS3D01G450400

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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 TraesCS3D01G450400 chr3D 100.000 2740 0 0 1 2740 558710013 558707274 0.000000e+00 5060.0
1 TraesCS3D01G450400 chr3D 84.132 605 84 4 987 1579 558662532 558663136 2.370000e-160 575.0
2 TraesCS3D01G450400 chr3D 85.971 278 16 9 717 984 558662199 558662463 2.690000e-70 276.0
3 TraesCS3D01G450400 chr3D 96.721 61 2 0 2680 2740 368292578 368292518 4.830000e-18 102.0
4 TraesCS3D01G450400 chr3A 91.368 2734 162 41 1 2686 695022300 695019593 0.000000e+00 3674.0
5 TraesCS3D01G450400 chr3A 82.206 961 125 25 987 1925 694989797 694988861 0.000000e+00 785.0
6 TraesCS3D01G450400 chr3A 85.357 280 19 9 717 987 694990115 694989849 1.250000e-68 270.0
7 TraesCS3D01G450400 chr3B 92.857 1330 75 8 987 2311 741384615 741383301 0.000000e+00 1912.0
8 TraesCS3D01G450400 chr3B 81.893 972 132 26 987 1932 741352502 741351549 0.000000e+00 780.0
9 TraesCS3D01G450400 chr3B 88.246 536 39 12 463 987 741385182 741384660 1.080000e-173 619.0
10 TraesCS3D01G450400 chr3B 88.448 277 15 6 718 984 741352819 741352550 4.400000e-83 318.0
11 TraesCS3D01G450400 chr3B 83.849 291 42 2 1 286 741397326 741397036 3.480000e-69 272.0
12 TraesCS3D01G450400 chr3B 97.561 41 1 0 526 566 741385096 741385056 1.360000e-08 71.3
13 TraesCS3D01G450400 chr4D 95.588 68 1 2 2675 2740 455762689 455762622 1.040000e-19 108.0
14 TraesCS3D01G450400 chr4D 100.000 56 0 0 2685 2740 381561448 381561503 1.340000e-18 104.0
15 TraesCS3D01G450400 chr4D 100.000 54 0 0 2687 2740 29862266 29862319 1.740000e-17 100.0
16 TraesCS3D01G450400 chrUn 100.000 55 0 0 2686 2740 21561152 21561098 4.830000e-18 102.0
17 TraesCS3D01G450400 chrUn 100.000 55 0 0 2686 2740 29858603 29858549 4.830000e-18 102.0
18 TraesCS3D01G450400 chrUn 82.979 94 10 5 2309 2398 79505243 79505334 2.260000e-11 80.5
19 TraesCS3D01G450400 chr1D 100.000 54 0 0 2687 2740 7591622 7591569 1.740000e-17 100.0
20 TraesCS3D01G450400 chr1D 100.000 54 0 0 2687 2740 370322424 370322371 1.740000e-17 100.0
21 TraesCS3D01G450400 chr1A 92.537 67 3 2 2675 2740 113255467 113255402 8.080000e-16 95.3
22 TraesCS3D01G450400 chr1A 95.652 46 1 1 2317 2362 85909900 85909856 3.780000e-09 73.1
23 TraesCS3D01G450400 chr6B 91.071 56 4 1 2309 2364 554036213 554036159 1.050000e-09 75.0


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 TraesCS3D01G450400 chr3D 558707274 558710013 2739 True 5060.000000 5060 100.0000 1 2740 1 chr3D.!!$R2 2739
1 TraesCS3D01G450400 chr3D 558662199 558663136 937 False 425.500000 575 85.0515 717 1579 2 chr3D.!!$F1 862
2 TraesCS3D01G450400 chr3A 695019593 695022300 2707 True 3674.000000 3674 91.3680 1 2686 1 chr3A.!!$R1 2685
3 TraesCS3D01G450400 chr3A 694988861 694990115 1254 True 527.500000 785 83.7815 717 1925 2 chr3A.!!$R2 1208
4 TraesCS3D01G450400 chr3B 741383301 741385182 1881 True 867.433333 1912 92.8880 463 2311 3 chr3B.!!$R3 1848
5 TraesCS3D01G450400 chr3B 741351549 741352819 1270 True 549.000000 780 85.1705 718 1932 2 chr3B.!!$R2 1214

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
154 160 0.044244 TCCTTGGAGGAGGGGTTAGG 59.956 60.0 0.0 0.0 40.06 2.69 F
222 228 0.108138 CATCGTGTCCTTCCTGGTCC 60.108 60.0 0.0 0.0 37.07 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1400 1.130373 CGCGTGCACCTAATCAATTGT 59.870 47.619 12.15 0.0 0.0 2.71 R
2067 2288 1.732941 AACTTCACGACACACAAGCA 58.267 45.000 0.00 0.0 0.0 3.91 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
30 31 1.315257 ATGGCAACGCAGGGTTCATC 61.315 55.000 0.00 0.00 36.49 2.92
34 35 0.374758 CAACGCAGGGTTCATCATCG 59.625 55.000 0.00 0.00 36.49 3.84
51 52 1.139095 CGCTACGGGTCTTGACTCC 59.861 63.158 0.61 0.40 0.00 3.85
54 55 1.390565 CTACGGGTCTTGACTCCGAT 58.609 55.000 25.63 16.73 45.96 4.18
72 73 4.900635 CGATAGGAGGAATTTTGGGTTG 57.099 45.455 0.00 0.00 0.00 3.77
82 83 5.053811 GGAATTTTGGGTTGTAAGGTGTTG 58.946 41.667 0.00 0.00 0.00 3.33
85 86 4.722361 TTTGGGTTGTAAGGTGTTGTTC 57.278 40.909 0.00 0.00 0.00 3.18
100 101 0.388134 TGTTCCTCGACAACGCTAGC 60.388 55.000 4.06 4.06 39.58 3.42
122 127 4.236527 CCCCCTTAAGTATGTTGAAGCT 57.763 45.455 0.97 0.00 0.00 3.74
153 159 1.560146 GTTCCTTGGAGGAGGGGTTAG 59.440 57.143 0.00 0.00 46.73 2.34
154 160 0.044244 TCCTTGGAGGAGGGGTTAGG 59.956 60.000 0.00 0.00 40.06 2.69
157 163 0.253020 TTGGAGGAGGGGTTAGGGTC 60.253 60.000 0.00 0.00 0.00 4.46
171 177 4.452733 GGTCCGTGCTCCTTCCGG 62.453 72.222 0.00 0.00 43.03 5.14
175 181 2.050350 CCGTGCTCCTTCCGGACTA 61.050 63.158 1.83 0.00 44.41 2.59
200 206 2.609459 CCACCGTGTAGATGCAAGATTC 59.391 50.000 0.00 0.00 0.00 2.52
202 208 2.501723 ACCGTGTAGATGCAAGATTCCT 59.498 45.455 0.00 0.00 0.00 3.36
206 212 4.447054 CGTGTAGATGCAAGATTCCTCATC 59.553 45.833 0.00 0.00 36.49 2.92
212 218 1.936547 GCAAGATTCCTCATCGTGTCC 59.063 52.381 0.76 0.00 41.92 4.02
218 224 1.186200 TCCTCATCGTGTCCTTCCTG 58.814 55.000 0.00 0.00 0.00 3.86
222 228 0.108138 CATCGTGTCCTTCCTGGTCC 60.108 60.000 0.00 0.00 37.07 4.46
242 248 0.895530 GATCAACTCCGAGTCCACCA 59.104 55.000 0.35 0.00 0.00 4.17
243 249 0.608640 ATCAACTCCGAGTCCACCAC 59.391 55.000 0.35 0.00 0.00 4.16
245 251 0.321671 CAACTCCGAGTCCACCACAT 59.678 55.000 0.35 0.00 0.00 3.21
260 267 1.033202 CACATGCATGTAGCCCAGCA 61.033 55.000 30.92 0.00 44.83 4.41
287 294 2.959275 GCCGACGAGGACACAATAG 58.041 57.895 0.00 0.00 45.00 1.73
288 295 0.527817 GCCGACGAGGACACAATAGG 60.528 60.000 0.00 0.00 45.00 2.57
289 296 0.815734 CCGACGAGGACACAATAGGT 59.184 55.000 0.00 0.00 45.00 3.08
290 297 1.202268 CCGACGAGGACACAATAGGTC 60.202 57.143 0.00 0.00 45.00 3.85
308 315 2.066393 CCATCTTCCGCCCAGAGGA 61.066 63.158 0.00 0.00 35.69 3.71
398 424 0.317160 TGTGCGGACCACTTCACTAG 59.683 55.000 4.04 0.00 44.92 2.57
400 426 1.045407 TGCGGACCACTTCACTAGTT 58.955 50.000 0.00 0.00 33.85 2.24
401 427 2.029649 GTGCGGACCACTTCACTAGTTA 60.030 50.000 0.00 0.00 41.35 2.24
402 428 2.230508 TGCGGACCACTTCACTAGTTAG 59.769 50.000 0.00 0.00 33.85 2.34
403 429 2.230750 GCGGACCACTTCACTAGTTAGT 59.769 50.000 0.00 0.00 33.85 2.24
448 476 5.857268 AGGACACAAAAATCATGGAAAAGG 58.143 37.500 0.00 0.00 0.00 3.11
454 482 8.090214 ACACAAAAATCATGGAAAAGGTATCAG 58.910 33.333 0.00 0.00 0.00 2.90
486 515 8.210265 TCACAATAATATCAGTATCAAGCCACA 58.790 33.333 0.00 0.00 0.00 4.17
567 651 2.795329 CCACTAATGGCAAACACCTCT 58.205 47.619 0.00 0.00 39.82 3.69
568 652 3.157087 CCACTAATGGCAAACACCTCTT 58.843 45.455 0.00 0.00 39.82 2.85
569 653 3.573967 CCACTAATGGCAAACACCTCTTT 59.426 43.478 0.00 0.00 39.82 2.52
570 654 4.039124 CCACTAATGGCAAACACCTCTTTT 59.961 41.667 0.00 0.00 39.82 2.27
571 655 5.453198 CCACTAATGGCAAACACCTCTTTTT 60.453 40.000 0.00 0.00 39.82 1.94
674 758 2.355756 GCCTGTACGACTGTCCGTAATA 59.644 50.000 11.91 6.19 45.12 0.98
1107 1289 2.656069 GCTGGGGAAGCGGTACAGA 61.656 63.158 11.17 0.00 43.45 3.41
1218 1400 2.947652 CGAGGACTCCATCGGTAAGTAA 59.052 50.000 0.00 0.00 35.33 2.24
1921 2142 7.588143 ACTTGTGTCTCATTCGATTAAGAAG 57.412 36.000 0.00 0.00 33.19 2.85
1990 2211 1.680735 CCACAGTGCTTTTGTGCCTAA 59.319 47.619 9.39 0.00 43.50 2.69
1993 2214 4.180057 CACAGTGCTTTTGTGCCTAAAAA 58.820 39.130 0.00 0.00 39.43 1.94
2063 2284 4.419282 TCATGAAAAAGAGGCAAGGGAAT 58.581 39.130 0.00 0.00 0.00 3.01
2067 2288 5.393866 TGAAAAAGAGGCAAGGGAATAGTT 58.606 37.500 0.00 0.00 0.00 2.24
2127 2350 8.817100 CATGATCATGTGGAATGAAATTTTCTG 58.183 33.333 24.87 0.00 33.25 3.02
2195 2418 5.824904 ATGATCATGGCTTGTGTTACTTC 57.175 39.130 7.59 0.00 0.00 3.01
2196 2419 4.009675 TGATCATGGCTTGTGTTACTTCC 58.990 43.478 0.00 0.00 0.00 3.46
2221 2444 7.537306 CCGTTAATTACAGAGTTTGGTTTCATG 59.463 37.037 0.00 0.00 0.00 3.07
2279 2503 3.713764 CTCATACAAGGGGATCCTCTGTT 59.286 47.826 17.06 7.77 44.07 3.16
2354 2579 3.633986 CCCCAGCTCCATTTCATAGAAAC 59.366 47.826 0.00 0.00 0.00 2.78
2355 2580 3.633986 CCCAGCTCCATTTCATAGAAACC 59.366 47.826 0.00 0.00 0.00 3.27
2375 2600 3.810386 ACCAAACCAAAACACACACAAAC 59.190 39.130 0.00 0.00 0.00 2.93
2386 2611 2.291465 CACACACAAACATCTGGACTGG 59.709 50.000 0.00 0.00 0.00 4.00
2389 2614 1.800586 CACAAACATCTGGACTGGACG 59.199 52.381 0.00 0.00 0.00 4.79
2437 2662 3.784429 AAAAAGGGCAGCCACCATA 57.216 47.368 15.19 0.00 0.00 2.74
2473 2698 3.651803 TTTGCCAAAATTACAGGTCCG 57.348 42.857 0.00 0.00 0.00 4.79
2488 2713 3.002348 CAGGTCCGAAACAGAGAAACAAC 59.998 47.826 0.00 0.00 0.00 3.32
2494 2719 3.363178 GAAACAGAGAAACAACGCCAAG 58.637 45.455 0.00 0.00 0.00 3.61
2561 2786 5.870433 CACATGGATCTCATCTGCTATCTTC 59.130 44.000 0.00 0.00 32.92 2.87
2628 2853 2.726633 ACACCTTGAATCGTTTTTGCG 58.273 42.857 0.00 0.00 0.00 4.85
2643 2868 5.335127 GTTTTTGCGCAAGATAGATGACAT 58.665 37.500 23.68 0.00 43.02 3.06
2658 2883 5.319453 AGATGACATTGTGTTTCCTGACAT 58.681 37.500 0.00 0.00 0.00 3.06
2662 2887 5.647658 TGACATTGTGTTTCCTGACATATCC 59.352 40.000 0.00 0.00 0.00 2.59
2664 2889 2.627945 TGTGTTTCCTGACATATCCGC 58.372 47.619 0.00 0.00 0.00 5.54
2670 2895 0.034059 CCTGACATATCCGCCTGGTC 59.966 60.000 0.00 0.00 36.30 4.02
2674 2899 0.986019 ACATATCCGCCTGGTCCCAA 60.986 55.000 0.00 0.00 36.30 4.12
2683 2908 1.557269 CCTGGTCCCAACTCCTGAGG 61.557 65.000 0.00 0.00 0.00 3.86
2695 2920 2.983229 CTCCTGAGGTGGAGTCAATTG 58.017 52.381 0.00 0.00 46.33 2.32
2696 2921 1.003580 TCCTGAGGTGGAGTCAATTGC 59.996 52.381 0.00 0.00 0.00 3.56
2697 2922 1.271543 CCTGAGGTGGAGTCAATTGCA 60.272 52.381 0.00 0.00 0.00 4.08
2698 2923 2.507484 CTGAGGTGGAGTCAATTGCAA 58.493 47.619 0.00 0.00 0.00 4.08
2699 2924 2.486982 CTGAGGTGGAGTCAATTGCAAG 59.513 50.000 4.94 0.00 0.00 4.01
2700 2925 2.106338 TGAGGTGGAGTCAATTGCAAGA 59.894 45.455 4.94 0.00 0.00 3.02
2701 2926 3.149196 GAGGTGGAGTCAATTGCAAGAA 58.851 45.455 4.94 0.00 0.00 2.52
2702 2927 3.565307 AGGTGGAGTCAATTGCAAGAAA 58.435 40.909 4.94 0.00 0.00 2.52
2703 2928 3.319122 AGGTGGAGTCAATTGCAAGAAAC 59.681 43.478 4.94 2.49 0.00 2.78
2704 2929 3.552890 GGTGGAGTCAATTGCAAGAAACC 60.553 47.826 4.94 5.54 0.00 3.27
2705 2930 3.068024 GTGGAGTCAATTGCAAGAAACCA 59.932 43.478 4.94 7.93 0.00 3.67
2706 2931 3.068024 TGGAGTCAATTGCAAGAAACCAC 59.932 43.478 4.94 0.00 0.00 4.16
2707 2932 3.552890 GGAGTCAATTGCAAGAAACCACC 60.553 47.826 4.94 5.79 0.00 4.61
2708 2933 3.030291 AGTCAATTGCAAGAAACCACCA 58.970 40.909 4.94 0.00 0.00 4.17
2709 2934 3.123050 GTCAATTGCAAGAAACCACCAC 58.877 45.455 4.94 0.00 0.00 4.16
2710 2935 2.762887 TCAATTGCAAGAAACCACCACA 59.237 40.909 4.94 0.00 0.00 4.17
2711 2936 3.387374 TCAATTGCAAGAAACCACCACAT 59.613 39.130 4.94 0.00 0.00 3.21
2712 2937 4.128643 CAATTGCAAGAAACCACCACATT 58.871 39.130 4.94 0.00 0.00 2.71
2713 2938 3.902881 TTGCAAGAAACCACCACATTT 57.097 38.095 0.00 0.00 0.00 2.32
2714 2939 3.176552 TGCAAGAAACCACCACATTTG 57.823 42.857 0.00 0.00 0.00 2.32
2715 2940 1.866601 GCAAGAAACCACCACATTTGC 59.133 47.619 0.00 0.00 33.64 3.68
2716 2941 2.126467 CAAGAAACCACCACATTTGCG 58.874 47.619 0.00 0.00 0.00 4.85
2717 2942 0.673437 AGAAACCACCACATTTGCGG 59.327 50.000 0.00 0.00 0.00 5.69
2718 2943 0.943835 GAAACCACCACATTTGCGGC 60.944 55.000 0.00 0.00 0.00 6.53
2719 2944 1.398958 AAACCACCACATTTGCGGCT 61.399 50.000 0.00 0.00 0.00 5.52
2720 2945 0.538516 AACCACCACATTTGCGGCTA 60.539 50.000 0.00 0.00 0.00 3.93
2721 2946 0.960364 ACCACCACATTTGCGGCTAG 60.960 55.000 0.00 0.00 0.00 3.42
2722 2947 1.656818 CCACCACATTTGCGGCTAGG 61.657 60.000 0.00 0.00 0.00 3.02
2723 2948 0.960364 CACCACATTTGCGGCTAGGT 60.960 55.000 0.00 0.00 0.00 3.08
2724 2949 0.251165 ACCACATTTGCGGCTAGGTT 60.251 50.000 0.00 0.00 0.00 3.50
2725 2950 0.887933 CCACATTTGCGGCTAGGTTT 59.112 50.000 0.00 0.00 0.00 3.27
2726 2951 1.402720 CCACATTTGCGGCTAGGTTTG 60.403 52.381 0.00 0.00 0.00 2.93
2727 2952 0.243636 ACATTTGCGGCTAGGTTTGC 59.756 50.000 0.00 0.00 0.00 3.68
2728 2953 0.243365 CATTTGCGGCTAGGTTTGCA 59.757 50.000 0.00 0.00 35.15 4.08
2729 2954 0.527565 ATTTGCGGCTAGGTTTGCAG 59.472 50.000 0.00 0.00 38.75 4.41
2730 2955 1.523154 TTTGCGGCTAGGTTTGCAGG 61.523 55.000 0.00 0.00 38.75 4.85
2731 2956 2.046314 GCGGCTAGGTTTGCAGGA 60.046 61.111 0.00 0.00 0.00 3.86
2732 2957 1.674322 GCGGCTAGGTTTGCAGGAA 60.674 57.895 0.00 0.00 0.00 3.36
2733 2958 1.241315 GCGGCTAGGTTTGCAGGAAA 61.241 55.000 0.00 0.00 0.00 3.13
2734 2959 0.521735 CGGCTAGGTTTGCAGGAAAC 59.478 55.000 8.99 8.99 42.97 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.815421 GCGATGATGAACCCTGCGT 60.815 57.895 0.00 0.00 0.00 5.24
18 19 0.249447 TAGCGATGATGAACCCTGCG 60.249 55.000 0.00 0.00 0.00 5.18
30 31 0.456221 AGTCAAGACCCGTAGCGATG 59.544 55.000 0.00 0.00 0.00 3.84
34 35 1.139095 CGGAGTCAAGACCCGTAGC 59.861 63.158 16.75 0.00 39.02 3.58
51 52 4.270008 ACAACCCAAAATTCCTCCTATCG 58.730 43.478 0.00 0.00 0.00 2.92
52 53 6.321435 CCTTACAACCCAAAATTCCTCCTATC 59.679 42.308 0.00 0.00 0.00 2.08
54 55 5.075344 ACCTTACAACCCAAAATTCCTCCTA 59.925 40.000 0.00 0.00 0.00 2.94
58 59 4.552674 ACACCTTACAACCCAAAATTCCT 58.447 39.130 0.00 0.00 0.00 3.36
64 65 3.447944 GGAACAACACCTTACAACCCAAA 59.552 43.478 0.00 0.00 0.00 3.28
66 67 2.242708 AGGAACAACACCTTACAACCCA 59.757 45.455 0.00 0.00 33.55 4.51
70 71 3.118702 TGTCGAGGAACAACACCTTACAA 60.119 43.478 0.00 0.00 37.93 2.41
72 73 3.102052 TGTCGAGGAACAACACCTTAC 57.898 47.619 0.00 0.00 37.93 2.34
82 83 1.077089 GGCTAGCGTTGTCGAGGAAC 61.077 60.000 9.00 0.00 39.71 3.62
85 86 2.202756 GGGCTAGCGTTGTCGAGG 60.203 66.667 9.00 0.00 39.71 4.63
115 116 2.959484 CGGGAGGCCTCAGCTTCAA 61.959 63.158 33.29 0.00 46.55 2.69
122 127 2.203938 AAGGAACGGGAGGCCTCA 60.204 61.111 33.29 0.00 37.71 3.86
153 159 4.452733 CGGAAGGAGCACGGACCC 62.453 72.222 0.00 0.00 0.00 4.46
171 177 3.734293 GCATCTACACGGTGGAAGTAGTC 60.734 52.174 13.48 0.00 37.20 2.59
175 181 0.973632 TGCATCTACACGGTGGAAGT 59.026 50.000 13.48 0.00 0.00 3.01
200 206 0.176680 CCAGGAAGGACACGATGAGG 59.823 60.000 0.00 0.00 41.22 3.86
202 208 0.895530 GACCAGGAAGGACACGATGA 59.104 55.000 0.00 0.00 41.22 2.92
206 212 1.605058 ATCGGACCAGGAAGGACACG 61.605 60.000 0.00 0.00 41.22 4.49
212 218 1.134670 GGAGTTGATCGGACCAGGAAG 60.135 57.143 0.00 0.00 0.00 3.46
218 224 0.100861 GACTCGGAGTTGATCGGACC 59.899 60.000 12.67 0.00 33.96 4.46
222 228 0.179134 GGTGGACTCGGAGTTGATCG 60.179 60.000 12.67 0.00 0.00 3.69
242 248 0.750546 CTGCTGGGCTACATGCATGT 60.751 55.000 33.20 33.20 45.15 3.21
243 249 0.464916 TCTGCTGGGCTACATGCATG 60.465 55.000 25.09 25.09 45.15 4.06
245 251 1.222661 CTCTGCTGGGCTACATGCA 59.777 57.895 0.00 0.00 45.15 3.96
260 267 1.751162 CCTCGTCGGCCTCTTCTCT 60.751 63.158 0.00 0.00 0.00 3.10
286 293 2.285368 TGGGCGGAAGATGGACCT 60.285 61.111 0.00 0.00 0.00 3.85
287 294 2.190578 CTGGGCGGAAGATGGACC 59.809 66.667 0.00 0.00 0.00 4.46
288 295 1.144936 CTCTGGGCGGAAGATGGAC 59.855 63.158 0.00 0.00 0.00 4.02
289 296 2.066393 CCTCTGGGCGGAAGATGGA 61.066 63.158 0.00 0.00 0.00 3.41
290 297 2.066393 TCCTCTGGGCGGAAGATGG 61.066 63.158 0.00 0.00 0.00 3.51
291 298 1.144936 GTCCTCTGGGCGGAAGATG 59.855 63.158 0.00 0.00 31.13 2.90
292 299 2.427245 CGTCCTCTGGGCGGAAGAT 61.427 63.158 2.32 0.00 32.66 2.40
293 300 3.068691 CGTCCTCTGGGCGGAAGA 61.069 66.667 2.32 0.00 32.66 2.87
294 301 4.821589 GCGTCCTCTGGGCGGAAG 62.822 72.222 12.56 0.00 34.44 3.46
308 315 0.881118 GGTGATGTTTCCATGTGCGT 59.119 50.000 0.00 0.00 0.00 5.24
313 320 0.726827 CCGTCGGTGATGTTTCCATG 59.273 55.000 2.08 0.00 0.00 3.66
358 384 4.879545 ACAACAATATGTTAGGGTTAGGCG 59.120 41.667 0.00 0.00 38.77 5.52
361 387 5.220777 CCGCACAACAATATGTTAGGGTTAG 60.221 44.000 0.00 0.00 38.77 2.34
367 393 3.687212 TGGTCCGCACAACAATATGTTAG 59.313 43.478 0.00 0.00 38.77 2.34
369 395 2.227865 GTGGTCCGCACAACAATATGTT 59.772 45.455 0.00 0.00 42.08 2.71
371 397 2.083774 AGTGGTCCGCACAACAATATG 58.916 47.619 4.97 0.00 0.00 1.78
374 400 0.951558 GAAGTGGTCCGCACAACAAT 59.048 50.000 4.97 0.00 0.00 2.71
398 424 6.183360 TGTGTTTCCATTTTTCCCTCACTAAC 60.183 38.462 0.00 0.00 0.00 2.34
400 426 5.450453 TGTGTTTCCATTTTTCCCTCACTA 58.550 37.500 0.00 0.00 0.00 2.74
401 427 4.285863 TGTGTTTCCATTTTTCCCTCACT 58.714 39.130 0.00 0.00 0.00 3.41
402 428 4.664150 TGTGTTTCCATTTTTCCCTCAC 57.336 40.909 0.00 0.00 0.00 3.51
403 429 5.396213 CCTTTGTGTTTCCATTTTTCCCTCA 60.396 40.000 0.00 0.00 0.00 3.86
404 430 5.056480 CCTTTGTGTTTCCATTTTTCCCTC 58.944 41.667 0.00 0.00 0.00 4.30
405 431 4.719273 TCCTTTGTGTTTCCATTTTTCCCT 59.281 37.500 0.00 0.00 0.00 4.20
406 432 4.814234 GTCCTTTGTGTTTCCATTTTTCCC 59.186 41.667 0.00 0.00 0.00 3.97
407 433 5.293324 GTGTCCTTTGTGTTTCCATTTTTCC 59.707 40.000 0.00 0.00 0.00 3.13
408 434 5.872070 TGTGTCCTTTGTGTTTCCATTTTTC 59.128 36.000 0.00 0.00 0.00 2.29
409 435 5.799213 TGTGTCCTTTGTGTTTCCATTTTT 58.201 33.333 0.00 0.00 0.00 1.94
410 436 5.413309 TGTGTCCTTTGTGTTTCCATTTT 57.587 34.783 0.00 0.00 0.00 1.82
414 440 4.873746 TTTTGTGTCCTTTGTGTTTCCA 57.126 36.364 0.00 0.00 0.00 3.53
416 442 6.959671 TGATTTTTGTGTCCTTTGTGTTTC 57.040 33.333 0.00 0.00 0.00 2.78
424 450 6.126796 ACCTTTTCCATGATTTTTGTGTCCTT 60.127 34.615 0.00 0.00 0.00 3.36
502 531 6.283544 TGAATATTTGATGTTGCATGGTGT 57.716 33.333 0.00 0.00 0.00 4.16
570 654 6.015265 GTGTTTGCCATTAGTACCCCTAAAAA 60.015 38.462 0.00 0.00 39.07 1.94
571 655 5.477637 GTGTTTGCCATTAGTACCCCTAAAA 59.522 40.000 0.00 0.00 39.07 1.52
572 656 5.011586 GTGTTTGCCATTAGTACCCCTAAA 58.988 41.667 0.00 0.00 39.07 1.85
573 657 4.568169 GGTGTTTGCCATTAGTACCCCTAA 60.568 45.833 0.00 0.00 39.90 2.69
574 658 3.054213 GGTGTTTGCCATTAGTACCCCTA 60.054 47.826 0.00 0.00 0.00 3.53
575 659 2.291346 GGTGTTTGCCATTAGTACCCCT 60.291 50.000 0.00 0.00 0.00 4.79
576 660 2.097036 GGTGTTTGCCATTAGTACCCC 58.903 52.381 0.00 0.00 0.00 4.95
577 661 2.752903 CAGGTGTTTGCCATTAGTACCC 59.247 50.000 0.00 0.00 0.00 3.69
578 662 2.752903 CCAGGTGTTTGCCATTAGTACC 59.247 50.000 0.00 0.00 0.00 3.34
579 663 3.439129 GTCCAGGTGTTTGCCATTAGTAC 59.561 47.826 0.00 0.00 0.00 2.73
580 664 3.329520 AGTCCAGGTGTTTGCCATTAGTA 59.670 43.478 0.00 0.00 0.00 1.82
581 665 2.108250 AGTCCAGGTGTTTGCCATTAGT 59.892 45.455 0.00 0.00 0.00 2.24
582 666 2.489329 CAGTCCAGGTGTTTGCCATTAG 59.511 50.000 0.00 0.00 0.00 1.73
583 667 2.513753 CAGTCCAGGTGTTTGCCATTA 58.486 47.619 0.00 0.00 0.00 1.90
584 668 1.331214 CAGTCCAGGTGTTTGCCATT 58.669 50.000 0.00 0.00 0.00 3.16
585 669 1.181098 GCAGTCCAGGTGTTTGCCAT 61.181 55.000 0.00 0.00 0.00 4.40
586 670 1.827789 GCAGTCCAGGTGTTTGCCA 60.828 57.895 0.00 0.00 0.00 4.92
587 671 1.391157 TTGCAGTCCAGGTGTTTGCC 61.391 55.000 0.00 0.00 33.98 4.52
588 672 0.031178 CTTGCAGTCCAGGTGTTTGC 59.969 55.000 0.00 0.00 35.42 3.68
589 673 1.679139 TCTTGCAGTCCAGGTGTTTG 58.321 50.000 0.00 0.00 0.00 2.93
590 674 2.435372 TTCTTGCAGTCCAGGTGTTT 57.565 45.000 0.00 0.00 0.00 2.83
1218 1400 1.130373 CGCGTGCACCTAATCAATTGT 59.870 47.619 12.15 0.00 0.00 2.71
1544 1739 2.554775 GGCGATGATGCTGATGCG 59.445 61.111 0.00 0.00 43.34 4.73
1908 2128 8.725148 CCAGCATTTATAGCTTCTTAATCGAAT 58.275 33.333 0.00 0.00 41.14 3.34
1921 2142 5.906073 ACATTTTCACCCAGCATTTATAGC 58.094 37.500 0.00 0.00 0.00 2.97
2063 2284 2.588027 TCACGACACACAAGCAACTA 57.412 45.000 0.00 0.00 0.00 2.24
2067 2288 1.732941 AACTTCACGACACACAAGCA 58.267 45.000 0.00 0.00 0.00 3.91
2104 2325 6.759827 CCCAGAAAATTTCATTCCACATGATC 59.240 38.462 8.55 0.00 0.00 2.92
2105 2326 6.214005 ACCCAGAAAATTTCATTCCACATGAT 59.786 34.615 8.55 0.00 0.00 2.45
2106 2327 5.543405 ACCCAGAAAATTTCATTCCACATGA 59.457 36.000 8.55 0.00 0.00 3.07
2107 2328 5.640357 CACCCAGAAAATTTCATTCCACATG 59.360 40.000 8.55 0.00 0.00 3.21
2108 2329 5.543405 TCACCCAGAAAATTTCATTCCACAT 59.457 36.000 8.55 0.00 0.00 3.21
2127 2350 6.948309 AGCCCAACTTAATCATTATATCACCC 59.052 38.462 0.00 0.00 0.00 4.61
2195 2418 6.961576 TGAAACCAAACTCTGTAATTAACGG 58.038 36.000 0.00 0.00 35.61 4.44
2196 2419 8.286800 TCATGAAACCAAACTCTGTAATTAACG 58.713 33.333 0.00 0.00 0.00 3.18
2354 2579 3.809832 TGTTTGTGTGTGTTTTGGTTTGG 59.190 39.130 0.00 0.00 0.00 3.28
2355 2580 5.407995 AGATGTTTGTGTGTGTTTTGGTTTG 59.592 36.000 0.00 0.00 0.00 2.93
2375 2600 2.981302 TGGCGTCCAGTCCAGATG 59.019 61.111 0.00 0.00 0.00 2.90
2386 2611 0.667792 GACACTCAGAACCTGGCGTC 60.668 60.000 0.00 0.00 31.51 5.19
2389 2614 0.106708 TGTGACACTCAGAACCTGGC 59.893 55.000 7.20 0.00 31.51 4.85
2395 2620 3.904800 TGTCCTTTGTGACACTCAGAA 57.095 42.857 7.20 0.00 40.22 3.02
2452 2677 3.637229 TCGGACCTGTAATTTTGGCAAAA 59.363 39.130 25.94 25.94 34.41 2.44
2473 2698 3.064820 TCTTGGCGTTGTTTCTCTGTTTC 59.935 43.478 0.00 0.00 0.00 2.78
2488 2713 2.873288 GCCTTGAGCTTCTTGGCG 59.127 61.111 5.47 0.00 38.99 5.69
2600 2825 1.621107 GATTCAAGGTGTTGCGCATG 58.379 50.000 12.75 5.30 33.23 4.06
2628 2853 6.094603 AGGAAACACAATGTCATCTATCTTGC 59.905 38.462 0.00 0.00 0.00 4.01
2643 2868 3.006940 GCGGATATGTCAGGAAACACAA 58.993 45.455 0.00 0.00 30.55 3.33
2658 2883 1.306654 AGTTGGGACCAGGCGGATA 60.307 57.895 0.00 0.00 35.59 2.59
2662 2887 3.322466 AGGAGTTGGGACCAGGCG 61.322 66.667 0.00 0.00 0.00 5.52
2664 2889 1.557269 CCTCAGGAGTTGGGACCAGG 61.557 65.000 0.00 0.00 0.00 4.45
2670 2895 4.232905 TCCACCTCAGGAGTTGGG 57.767 61.111 12.26 3.06 40.91 4.12
2683 2908 3.068024 TGGTTTCTTGCAATTGACTCCAC 59.932 43.478 10.34 0.00 0.00 4.02
2686 2911 3.068024 TGGTGGTTTCTTGCAATTGACTC 59.932 43.478 10.34 0.00 0.00 3.36
2687 2912 3.030291 TGGTGGTTTCTTGCAATTGACT 58.970 40.909 10.34 0.00 0.00 3.41
2688 2913 3.123050 GTGGTGGTTTCTTGCAATTGAC 58.877 45.455 10.34 1.02 0.00 3.18
2689 2914 2.762887 TGTGGTGGTTTCTTGCAATTGA 59.237 40.909 10.34 0.00 0.00 2.57
2690 2915 3.176552 TGTGGTGGTTTCTTGCAATTG 57.823 42.857 0.00 0.00 0.00 2.32
2691 2916 4.420522 AATGTGGTGGTTTCTTGCAATT 57.579 36.364 0.00 0.00 0.00 2.32
2692 2917 4.128643 CAAATGTGGTGGTTTCTTGCAAT 58.871 39.130 0.00 0.00 0.00 3.56
2693 2918 3.529533 CAAATGTGGTGGTTTCTTGCAA 58.470 40.909 0.00 0.00 0.00 4.08
2694 2919 2.741228 GCAAATGTGGTGGTTTCTTGCA 60.741 45.455 0.00 0.00 38.03 4.08
2695 2920 1.866601 GCAAATGTGGTGGTTTCTTGC 59.133 47.619 0.00 0.00 0.00 4.01
2696 2921 2.126467 CGCAAATGTGGTGGTTTCTTG 58.874 47.619 0.00 0.00 0.00 3.02
2697 2922 1.068434 CCGCAAATGTGGTGGTTTCTT 59.932 47.619 4.82 0.00 40.69 2.52
2698 2923 0.673437 CCGCAAATGTGGTGGTTTCT 59.327 50.000 4.82 0.00 40.69 2.52
2699 2924 0.943835 GCCGCAAATGTGGTGGTTTC 60.944 55.000 14.07 0.00 46.99 2.78
2700 2925 1.068921 GCCGCAAATGTGGTGGTTT 59.931 52.632 14.07 0.00 46.99 3.27
2701 2926 0.538516 TAGCCGCAAATGTGGTGGTT 60.539 50.000 14.07 1.84 46.99 3.67
2702 2927 0.960364 CTAGCCGCAAATGTGGTGGT 60.960 55.000 14.07 3.04 46.99 4.16
2703 2928 1.656818 CCTAGCCGCAAATGTGGTGG 61.657 60.000 14.07 10.16 46.99 4.61
2704 2929 0.960364 ACCTAGCCGCAAATGTGGTG 60.960 55.000 14.07 5.59 46.99 4.17
2705 2930 0.251165 AACCTAGCCGCAAATGTGGT 60.251 50.000 14.07 4.51 46.99 4.16
2707 2932 1.981254 CAAACCTAGCCGCAAATGTG 58.019 50.000 0.00 0.00 0.00 3.21
2708 2933 0.243636 GCAAACCTAGCCGCAAATGT 59.756 50.000 0.00 0.00 0.00 2.71
2709 2934 0.243365 TGCAAACCTAGCCGCAAATG 59.757 50.000 0.00 0.00 0.00 2.32
2710 2935 0.527565 CTGCAAACCTAGCCGCAAAT 59.472 50.000 0.00 0.00 33.21 2.32
2711 2936 1.523154 CCTGCAAACCTAGCCGCAAA 61.523 55.000 0.00 0.00 33.21 3.68
2712 2937 1.971167 CCTGCAAACCTAGCCGCAA 60.971 57.895 0.00 0.00 33.21 4.85
2713 2938 2.359850 CCTGCAAACCTAGCCGCA 60.360 61.111 0.00 0.00 0.00 5.69
2714 2939 1.241315 TTTCCTGCAAACCTAGCCGC 61.241 55.000 0.00 0.00 0.00 6.53
2715 2940 0.521735 GTTTCCTGCAAACCTAGCCG 59.478 55.000 0.00 0.00 38.86 5.52


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

AutoCloner maintained by Alex Coulton.