Multiple sequence alignment - TraesCS4D01G081000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G081000 chr4D 100.000 3858 0 0 1 3858 54811818 54807961 0.000000e+00 7125.0
1 TraesCS4D01G081000 chr4A 96.520 1983 48 6 913 2877 542261493 542263472 0.000000e+00 3260.0
2 TraesCS4D01G081000 chr4A 88.974 916 65 17 1 904 542260621 542261512 0.000000e+00 1099.0
3 TraesCS4D01G081000 chr4A 85.580 638 60 9 3170 3801 542263879 542264490 1.170000e-179 640.0
4 TraesCS4D01G081000 chr4A 89.130 322 24 6 2876 3186 542263541 542263862 1.300000e-104 390.0
5 TraesCS4D01G081000 chr4A 100.000 38 0 0 3821 3858 542264489 542264526 1.920000e-08 71.3
6 TraesCS4D01G081000 chr4B 95.880 1966 32 7 913 2877 81360086 81362003 0.000000e+00 3136.0
7 TraesCS4D01G081000 chr4B 93.107 914 49 11 1 904 81359196 81360105 0.000000e+00 1327.0
8 TraesCS4D01G081000 chr4B 83.150 546 52 17 3329 3858 81363462 81363983 2.720000e-126 462.0
9 TraesCS4D01G081000 chr4B 91.011 267 15 3 2876 3136 81362072 81362335 6.130000e-93 351.0
10 TraesCS4D01G081000 chr4B 83.544 237 37 2 3221 3457 519813573 519813339 1.800000e-53 220.0
11 TraesCS4D01G081000 chr1D 85.833 240 30 4 3220 3457 451388337 451388574 6.400000e-63 252.0
12 TraesCS4D01G081000 chr1D 83.193 238 39 1 3221 3457 111100842 111100605 2.330000e-52 217.0
13 TraesCS4D01G081000 chr1D 98.039 51 0 1 267 316 48391457 48391407 1.910000e-13 87.9
14 TraesCS4D01G081000 chr1B 85.294 238 33 2 3220 3457 620417417 620417182 1.070000e-60 244.0
15 TraesCS4D01G081000 chr5D 85.398 226 32 1 3221 3445 132475385 132475160 2.320000e-57 233.0
16 TraesCS4D01G081000 chr5D 98.039 51 0 1 267 316 241947600 241947550 1.910000e-13 87.9
17 TraesCS4D01G081000 chr5D 98.039 51 0 1 267 316 294634482 294634432 1.910000e-13 87.9
18 TraesCS4D01G081000 chr7B 84.681 235 32 4 3225 3457 40342665 40342897 8.340000e-57 231.0
19 TraesCS4D01G081000 chr7B 80.000 270 48 4 3193 3457 592039184 592038916 1.090000e-45 195.0
20 TraesCS4D01G081000 chr2B 93.333 150 7 1 3531 3680 206749320 206749174 6.490000e-53 219.0
21 TraesCS4D01G081000 chr2B 92.667 150 8 1 3531 3680 361639490 361639636 3.020000e-51 213.0
22 TraesCS4D01G081000 chr6D 82.427 239 38 4 3220 3457 200818482 200818717 5.050000e-49 206.0
23 TraesCS4D01G081000 chr6D 100.000 28 0 0 3460 3487 28413886 28413913 7.000000e-03 52.8
24 TraesCS4D01G081000 chr6D 100.000 28 0 0 3460 3487 57999693 57999666 7.000000e-03 52.8
25 TraesCS4D01G081000 chr6B 80.150 267 49 4 3193 3457 413162846 413162582 3.040000e-46 196.0
26 TraesCS4D01G081000 chr5A 98.039 51 0 1 267 316 311937131 311937081 1.910000e-13 87.9
27 TraesCS4D01G081000 chr5A 100.000 28 0 0 3460 3487 413419534 413419507 7.000000e-03 52.8
28 TraesCS4D01G081000 chr5A 100.000 28 0 0 3460 3487 621020666 621020693 7.000000e-03 52.8
29 TraesCS4D01G081000 chr3D 96.296 54 1 1 264 316 71517681 71517734 1.910000e-13 87.9
30 TraesCS4D01G081000 chr3D 96.296 54 1 1 264 316 426451862 426451915 1.910000e-13 87.9
31 TraesCS4D01G081000 chr3D 93.182 44 2 1 3195 3238 472881850 472881892 3.220000e-06 63.9
32 TraesCS4D01G081000 chr3D 100.000 28 0 0 3460 3487 424015367 424015340 7.000000e-03 52.8
33 TraesCS4D01G081000 chr3A 96.296 54 1 1 264 316 34532452 34532505 1.910000e-13 87.9
34 TraesCS4D01G081000 chr3A 95.122 41 2 0 3193 3233 514270902 514270942 8.950000e-07 65.8
35 TraesCS4D01G081000 chr7D 97.561 41 1 0 3193 3233 178613922 178613962 1.920000e-08 71.3
36 TraesCS4D01G081000 chr7D 95.238 42 2 0 3193 3234 409808302 409808261 2.490000e-07 67.6
37 TraesCS4D01G081000 chr7D 93.182 44 2 1 3193 3235 433467096 433467053 3.220000e-06 63.9
38 TraesCS4D01G081000 chr3B 82.895 76 6 4 3147 3222 408630858 408630926 1.160000e-05 62.1
39 TraesCS4D01G081000 chr1A 86.792 53 4 3 3171 3222 72674395 72674345 5.380000e-04 56.5
40 TraesCS4D01G081000 chr1A 94.444 36 1 1 3453 3487 497270012 497270047 2.000000e-03 54.7
41 TraesCS4D01G081000 chrUn 100.000 28 0 0 3460 3487 80232784 80232811 7.000000e-03 52.8
42 TraesCS4D01G081000 chrUn 100.000 28 0 0 3460 3487 81477751 81477778 7.000000e-03 52.8


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 TraesCS4D01G081000 chr4D 54807961 54811818 3857 True 7125.00 7125 100.0000 1 3858 1 chr4D.!!$R1 3857
1 TraesCS4D01G081000 chr4A 542260621 542264526 3905 False 1092.06 3260 92.0408 1 3858 5 chr4A.!!$F1 3857
2 TraesCS4D01G081000 chr4B 81359196 81363983 4787 False 1319.00 3136 90.7870 1 3858 4 chr4B.!!$F1 3857

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
115 119 0.391793 GTCTAGTTGCTCACCTGGCC 60.392 60.000 0.00 0.0 0.00 5.36 F
265 270 1.134367 CAATCAGTGAGCTGCATTGGG 59.866 52.381 1.02 0.0 42.29 4.12 F
293 298 0.391793 GTGCTAGAAGCTCCCACACC 60.392 60.000 0.00 0.0 42.97 4.16 F
2058 2081 0.397941 AGCAGCAGTGGCAACTTCTA 59.602 50.000 0.00 0.0 44.61 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2064 1.882912 TGTAGAAGTTGCCACTGCTG 58.117 50.0 8.74 0.00 39.58 4.41 R
2058 2081 2.010582 AAAACACGGGCACGCATTGT 62.011 50.0 9.12 1.65 46.04 2.71 R
2132 2155 2.357009 GAGGTCATGTGATCCATTGTGC 59.643 50.0 0.00 0.00 0.00 4.57 R
3028 3150 0.176219 TGGCCGTGTAAAGATACCCG 59.824 55.0 0.00 0.00 33.41 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
23 24 3.046460 GCGCTTTGCAACAATCGCG 62.046 57.895 16.76 16.76 45.45 5.87
108 112 3.306780 GGTAGCTTTGGTCTAGTTGCTCA 60.307 47.826 0.00 0.00 32.72 4.26
111 115 2.551071 GCTTTGGTCTAGTTGCTCACCT 60.551 50.000 0.00 0.00 0.00 4.00
115 119 0.391793 GTCTAGTTGCTCACCTGGCC 60.392 60.000 0.00 0.00 0.00 5.36
131 135 3.042481 GCCCCCAGCCAATCTATTC 57.958 57.895 0.00 0.00 34.35 1.75
147 151 1.410004 ATTCGCCAGGAGAACCGATA 58.590 50.000 7.94 0.00 41.83 2.92
206 211 6.600388 TGAGTAATTATGATAGCAGGGCAAA 58.400 36.000 0.00 0.00 0.00 3.68
235 240 6.757897 TCATTACTAATGCTTTGTTCCCTG 57.242 37.500 4.13 0.00 38.77 4.45
265 270 1.134367 CAATCAGTGAGCTGCATTGGG 59.866 52.381 1.02 0.00 42.29 4.12
293 298 0.391793 GTGCTAGAAGCTCCCACACC 60.392 60.000 0.00 0.00 42.97 4.16
320 330 2.310647 GGGTTGGGGAAGGATTAGTGAA 59.689 50.000 0.00 0.00 0.00 3.18
324 334 3.256704 TGGGGAAGGATTAGTGAACTGT 58.743 45.455 0.00 0.00 0.00 3.55
465 480 3.790126 AGCCATAAAGGAAATTGTGGGT 58.210 40.909 2.28 2.28 44.30 4.51
475 490 6.438186 AGGAAATTGTGGGTCATTGATTTT 57.562 33.333 0.00 0.00 0.00 1.82
592 608 8.839343 TGTGCAACATAGATATTTTGGTGATAG 58.161 33.333 0.00 0.00 45.67 2.08
593 609 9.056005 GTGCAACATAGATATTTTGGTGATAGA 57.944 33.333 0.00 0.00 36.32 1.98
614 630 1.623811 AGTGGCGGTGATAACAGAGTT 59.376 47.619 0.00 0.00 0.00 3.01
753 769 1.216427 TGCTCCAGAGAGATAGAGGCA 59.784 52.381 0.00 0.00 43.39 4.75
762 778 2.038689 AGAGATAGAGGCACATGCATGG 59.961 50.000 29.41 19.00 44.36 3.66
817 833 9.812347 TTGTGGCATTATTTGAGGATATATCTT 57.188 29.630 12.42 4.77 0.00 2.40
896 918 8.682936 ATCTCCTTATGTTAGGTGCTTAATTG 57.317 34.615 0.00 0.00 36.63 2.32
897 919 7.630082 TCTCCTTATGTTAGGTGCTTAATTGT 58.370 34.615 0.00 0.00 36.63 2.71
898 920 8.107095 TCTCCTTATGTTAGGTGCTTAATTGTT 58.893 33.333 0.00 0.00 36.63 2.83
899 921 8.050778 TCCTTATGTTAGGTGCTTAATTGTTG 57.949 34.615 0.00 0.00 36.63 3.33
900 922 7.668052 TCCTTATGTTAGGTGCTTAATTGTTGT 59.332 33.333 0.00 0.00 36.63 3.32
901 923 8.303876 CCTTATGTTAGGTGCTTAATTGTTGTT 58.696 33.333 0.00 0.00 0.00 2.83
902 924 9.691362 CTTATGTTAGGTGCTTAATTGTTGTTT 57.309 29.630 0.00 0.00 0.00 2.83
906 928 9.871238 TGTTAGGTGCTTAATTGTTGTTTTAAA 57.129 25.926 0.00 0.00 0.00 1.52
955 977 2.229062 GCTCTGTTTTCAGTTTAGCCCC 59.771 50.000 0.00 0.00 46.98 5.80
997 1019 7.439356 CAGACTCTTCAACTTGTTCAGTTCATA 59.561 37.037 0.00 0.00 44.60 2.15
1210 1232 6.509656 CAGCCTCCGTTTTATACTGTATGTA 58.490 40.000 10.51 0.00 35.37 2.29
1481 1504 2.228822 GACGTTTGCCACTTCATTCCAT 59.771 45.455 0.00 0.00 0.00 3.41
1587 1610 1.928868 CCCTTTGGATTGGCAAGAGT 58.071 50.000 5.96 0.00 0.00 3.24
1883 1906 9.809096 TCATGAAGTCTTGACTATAGTTTCATC 57.191 33.333 18.77 4.07 33.22 2.92
2041 2064 7.736447 AAGGTGACTATTTATCTGCATTAGC 57.264 36.000 0.00 0.00 42.68 3.09
2058 2081 0.397941 AGCAGCAGTGGCAACTTCTA 59.602 50.000 0.00 0.00 44.61 2.10
2330 2369 6.264832 CAGTGCAATTTCACTTCAGTGTTTA 58.735 36.000 8.09 0.00 44.26 2.01
2428 2467 1.929836 GCGACTACTGCTTGGAATGAG 59.070 52.381 0.00 0.00 0.00 2.90
2911 3020 7.276953 AGTTGTTGATTTGACGAAAAAGTTG 57.723 32.000 0.00 0.00 0.00 3.16
2912 3021 7.087639 AGTTGTTGATTTGACGAAAAAGTTGA 58.912 30.769 0.00 0.00 0.00 3.18
2914 3023 8.379902 GTTGTTGATTTGACGAAAAAGTTGATT 58.620 29.630 0.00 0.00 0.00 2.57
2915 3024 7.893824 TGTTGATTTGACGAAAAAGTTGATTG 58.106 30.769 0.00 0.00 0.00 2.67
2916 3025 7.543868 TGTTGATTTGACGAAAAAGTTGATTGT 59.456 29.630 0.00 0.00 0.00 2.71
2917 3026 7.448588 TGATTTGACGAAAAAGTTGATTGTG 57.551 32.000 0.00 0.00 0.00 3.33
2918 3027 5.694674 TTTGACGAAAAAGTTGATTGTGC 57.305 34.783 0.00 0.00 0.00 4.57
2921 3030 6.125327 TGACGAAAAAGTTGATTGTGCTTA 57.875 33.333 0.00 0.00 0.00 3.09
2923 3032 6.690957 TGACGAAAAAGTTGATTGTGCTTAAG 59.309 34.615 0.00 0.00 0.00 1.85
2924 3033 6.560711 ACGAAAAAGTTGATTGTGCTTAAGT 58.439 32.000 4.02 0.00 0.00 2.24
2925 3034 7.033185 ACGAAAAAGTTGATTGTGCTTAAGTT 58.967 30.769 4.02 0.00 0.00 2.66
2927 3036 9.180678 CGAAAAAGTTGATTGTGCTTAAGTTAT 57.819 29.630 4.02 0.00 0.00 1.89
3000 3115 1.729586 AAGCTACCCTGAGTTGTGGA 58.270 50.000 0.00 0.00 0.00 4.02
3003 3118 2.026822 AGCTACCCTGAGTTGTGGATTG 60.027 50.000 0.00 0.00 0.00 2.67
3004 3119 2.027192 GCTACCCTGAGTTGTGGATTGA 60.027 50.000 0.00 0.00 0.00 2.57
3005 3120 3.559171 GCTACCCTGAGTTGTGGATTGAA 60.559 47.826 0.00 0.00 0.00 2.69
3006 3121 3.146104 ACCCTGAGTTGTGGATTGAAG 57.854 47.619 0.00 0.00 0.00 3.02
3113 3235 0.179032 GGGGTGGTTTTGCCCTTTTG 60.179 55.000 0.00 0.00 44.25 2.44
3119 3241 2.212652 GGTTTTGCCCTTTTGCTGAAG 58.787 47.619 0.00 0.00 0.00 3.02
3155 4184 5.298527 GGTTTGGGGCAACTATAATGTACTC 59.701 44.000 0.00 0.00 0.00 2.59
3156 4185 5.702065 TTGGGGCAACTATAATGTACTCA 57.298 39.130 0.00 0.00 0.00 3.41
3166 4195 8.755941 CAACTATAATGTACTCACTCCATTTCG 58.244 37.037 0.00 0.00 31.63 3.46
3218 4282 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
3260 4386 1.124477 TTGGCCCCCTTCGCATTTTT 61.124 50.000 0.00 0.00 0.00 1.94
3345 4472 9.529325 TCTCATTGGAAGATATGTTTAACTACG 57.471 33.333 0.00 0.00 0.00 3.51
3448 4595 2.891191 GGGACCAATAAACCAGGACA 57.109 50.000 0.00 0.00 0.00 4.02
3452 4599 3.263425 GGACCAATAAACCAGGACAGAGA 59.737 47.826 0.00 0.00 0.00 3.10
3464 4611 4.148079 CAGGACAGAGATAGTGCTCCATA 58.852 47.826 0.00 0.00 35.35 2.74
3465 4612 4.771577 CAGGACAGAGATAGTGCTCCATAT 59.228 45.833 0.00 0.00 35.35 1.78
3466 4613 5.245751 CAGGACAGAGATAGTGCTCCATATT 59.754 44.000 0.00 0.00 35.35 1.28
3467 4614 5.245751 AGGACAGAGATAGTGCTCCATATTG 59.754 44.000 0.00 0.00 31.66 1.90
3468 4615 5.477510 GACAGAGATAGTGCTCCATATTGG 58.522 45.833 0.00 0.00 39.43 3.16
3469 4616 5.150715 ACAGAGATAGTGCTCCATATTGGA 58.849 41.667 0.00 0.00 45.98 3.53
3485 4632 8.781951 TCCATATTGGAATCTCTAAAAGGTCTT 58.218 33.333 0.00 0.00 45.00 3.01
3498 4645 9.308318 CTCTAAAAGGTCTTAAGAGTAATCTGC 57.692 37.037 5.12 0.00 32.52 4.26
3502 4649 8.499403 AAAGGTCTTAAGAGTAATCTGCATTC 57.501 34.615 5.12 0.00 0.00 2.67
3506 4653 6.752351 GTCTTAAGAGTAATCTGCATTCGTGA 59.248 38.462 5.12 0.00 0.00 4.35
3650 4797 1.879796 GCACAGTTCAGGGGAGACAAG 60.880 57.143 0.00 0.00 0.00 3.16
3707 4856 8.397906 CAACAAACGATTCAAGTCATATACCAT 58.602 33.333 0.00 0.00 0.00 3.55
3708 4857 9.607988 AACAAACGATTCAAGTCATATACCATA 57.392 29.630 0.00 0.00 0.00 2.74
3720 4869 4.597075 TCATATACCATAGAGGGCAAGCAA 59.403 41.667 0.00 0.00 43.89 3.91
3726 4875 2.408271 TAGAGGGCAAGCAACATCAG 57.592 50.000 0.00 0.00 0.00 2.90
3727 4876 0.694771 AGAGGGCAAGCAACATCAGA 59.305 50.000 0.00 0.00 0.00 3.27
3743 4892 6.076981 ACATCAGAAGGAACAACAATTCAC 57.923 37.500 0.00 0.00 0.00 3.18
3749 4898 3.897239 AGGAACAACAATTCACCAGACA 58.103 40.909 0.00 0.00 0.00 3.41
3758 4908 6.916360 ACAATTCACCAGACAACCATATTT 57.084 33.333 0.00 0.00 0.00 1.40
3768 4918 2.311542 ACAACCATATTTCCTGGCAGGA 59.688 45.455 32.01 32.01 44.10 3.86
3790 4940 5.298276 GGAACTACTAGTCTGATCTCACAGG 59.702 48.000 0.00 0.00 38.31 4.00
3797 4947 1.699083 TCTGATCTCACAGGCCAAACA 59.301 47.619 5.01 0.00 38.31 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.065418 CACATCTAACCACCCCCTGAC 60.065 57.143 0.00 0.00 0.00 3.51
115 119 0.890996 GGCGAATAGATTGGCTGGGG 60.891 60.000 8.81 0.00 40.68 4.96
119 123 1.071385 CTCCTGGCGAATAGATTGGCT 59.929 52.381 8.81 0.00 40.68 4.75
130 134 0.395311 AGTATCGGTTCTCCTGGCGA 60.395 55.000 0.00 0.00 0.00 5.54
131 135 0.030908 GAGTATCGGTTCTCCTGGCG 59.969 60.000 0.00 0.00 0.00 5.69
147 151 6.265196 TCCTTTTTCTGCAAATACATGTGAGT 59.735 34.615 9.11 0.00 0.00 3.41
235 240 1.869767 CTCACTGATTGATTAGCGGCC 59.130 52.381 0.00 0.00 32.17 6.13
265 270 0.742635 GCTTCTAGCACTGGGTCTGC 60.743 60.000 0.00 0.00 41.89 4.26
293 298 2.440599 CTTCCCCAACCCCACCTG 59.559 66.667 0.00 0.00 0.00 4.00
298 308 1.063942 CACTAATCCTTCCCCAACCCC 60.064 57.143 0.00 0.00 0.00 4.95
299 309 1.920351 TCACTAATCCTTCCCCAACCC 59.080 52.381 0.00 0.00 0.00 4.11
300 310 3.010250 AGTTCACTAATCCTTCCCCAACC 59.990 47.826 0.00 0.00 0.00 3.77
301 311 4.010349 CAGTTCACTAATCCTTCCCCAAC 58.990 47.826 0.00 0.00 0.00 3.77
302 312 3.655777 ACAGTTCACTAATCCTTCCCCAA 59.344 43.478 0.00 0.00 0.00 4.12
320 330 5.594317 GGATTTAACCATCTGCCAATACAGT 59.406 40.000 0.00 0.00 38.84 3.55
324 334 5.042463 TCGGATTTAACCATCTGCCAATA 57.958 39.130 0.00 0.00 30.48 1.90
436 451 3.712016 TTCCTTTATGGCTACAGCACA 57.288 42.857 3.24 0.00 44.36 4.57
475 490 4.448210 GTTACTTGGAGACACTCACCAAA 58.552 43.478 0.00 0.00 44.41 3.28
592 608 2.271800 CTCTGTTATCACCGCCACTTC 58.728 52.381 0.00 0.00 0.00 3.01
593 609 1.623811 ACTCTGTTATCACCGCCACTT 59.376 47.619 0.00 0.00 0.00 3.16
614 630 2.030363 CGTGCAAAACCAATTCCTGCTA 60.030 45.455 0.00 0.00 34.10 3.49
762 778 4.189231 ACCATATAGAAACAGTGGTTCGC 58.811 43.478 15.12 0.00 40.08 4.70
908 930 8.558700 CACAAAATAGCAATTAAGCACCTTTTT 58.441 29.630 0.00 0.00 36.85 1.94
909 931 7.307930 GCACAAAATAGCAATTAAGCACCTTTT 60.308 33.333 0.00 0.00 36.85 2.27
910 932 6.147656 GCACAAAATAGCAATTAAGCACCTTT 59.852 34.615 0.00 0.00 36.85 3.11
911 933 5.639082 GCACAAAATAGCAATTAAGCACCTT 59.361 36.000 0.00 0.00 36.85 3.50
912 934 5.047092 AGCACAAAATAGCAATTAAGCACCT 60.047 36.000 0.00 0.00 36.85 4.00
913 935 5.170748 AGCACAAAATAGCAATTAAGCACC 58.829 37.500 0.00 0.00 36.85 5.01
914 936 6.034256 CAGAGCACAAAATAGCAATTAAGCAC 59.966 38.462 0.00 0.00 36.85 4.40
915 937 6.094719 CAGAGCACAAAATAGCAATTAAGCA 58.905 36.000 0.00 0.00 36.85 3.91
916 938 6.095377 ACAGAGCACAAAATAGCAATTAAGC 58.905 36.000 0.00 0.00 0.00 3.09
917 939 8.524870 AAACAGAGCACAAAATAGCAATTAAG 57.475 30.769 0.00 0.00 0.00 1.85
918 940 8.885494 AAAACAGAGCACAAAATAGCAATTAA 57.115 26.923 0.00 0.00 0.00 1.40
919 941 8.140628 TGAAAACAGAGCACAAAATAGCAATTA 58.859 29.630 0.00 0.00 0.00 1.40
920 942 6.985645 TGAAAACAGAGCACAAAATAGCAATT 59.014 30.769 0.00 0.00 0.00 2.32
955 977 0.031585 TCTGTTGTCGAGGACCAACG 59.968 55.000 10.81 0.00 31.44 4.10
1210 1232 7.962918 GCATACATCGAAGTAAAACAGTGAAAT 59.037 33.333 4.40 0.00 0.00 2.17
1509 1532 3.831333 TGAGTTTATGCATGGGAAAAGCA 59.169 39.130 10.16 1.43 43.14 3.91
1587 1610 7.654022 ACTTTTTCCCTTCATGTGAAAAGTA 57.346 32.000 9.50 5.25 38.70 2.24
1642 1665 2.945668 GCCATACATCACAAGGGAAGTC 59.054 50.000 0.00 0.00 0.00 3.01
2041 2064 1.882912 TGTAGAAGTTGCCACTGCTG 58.117 50.000 8.74 0.00 39.58 4.41
2058 2081 2.010582 AAAACACGGGCACGCATTGT 62.011 50.000 9.12 1.65 46.04 2.71
2116 2139 5.179182 CCATTGTGCCCATCAACTTTTTAAC 59.821 40.000 0.00 0.00 0.00 2.01
2132 2155 2.357009 GAGGTCATGTGATCCATTGTGC 59.643 50.000 0.00 0.00 0.00 4.57
2428 2467 4.067896 TCCGTCCTTCATCCGTAGTATAC 58.932 47.826 0.00 0.00 38.50 1.47
2901 3010 7.449934 AACTTAAGCACAATCAACTTTTTCG 57.550 32.000 1.29 0.00 0.00 3.46
2911 3020 9.999009 GGTACCTTAAATAACTTAAGCACAATC 57.001 33.333 4.06 0.00 43.60 2.67
3028 3150 0.176219 TGGCCGTGTAAAGATACCCG 59.824 55.000 0.00 0.00 33.41 5.28
3057 3179 4.229096 CAGCTCAATAACGTGCAAAACAT 58.771 39.130 0.00 0.00 0.00 2.71
3113 3235 2.450476 ACCAACCCAATGATCTTCAGC 58.550 47.619 0.00 0.00 0.00 4.26
3119 3241 1.554617 CCCCAAACCAACCCAATGATC 59.445 52.381 0.00 0.00 0.00 2.92
3155 4184 8.438676 AAGGTCTTATATTTCGAAATGGAGTG 57.561 34.615 29.20 16.45 0.00 3.51
3156 4185 9.462606 AAAAGGTCTTATATTTCGAAATGGAGT 57.537 29.630 29.20 16.18 0.00 3.85
3218 4282 3.537795 AACCAGGACAGAGGTAGTACA 57.462 47.619 2.06 0.00 37.07 2.90
3324 4451 9.321562 GGATTCGTAGTTAAACATATCTTCCAA 57.678 33.333 0.00 0.00 0.00 3.53
3393 4520 8.144862 TGGGCCAAACTTTAATGATAGATTTT 57.855 30.769 2.13 0.00 0.00 1.82
3421 4549 6.068670 CCTGGTTTATTGGTCCCCTTAATAG 58.931 44.000 0.00 0.00 0.00 1.73
3464 4611 9.898152 CTCTTAAGACCTTTTAGAGATTCCAAT 57.102 33.333 0.00 0.00 34.67 3.16
3465 4612 8.881262 ACTCTTAAGACCTTTTAGAGATTCCAA 58.119 33.333 19.43 0.00 35.51 3.53
3466 4613 8.437274 ACTCTTAAGACCTTTTAGAGATTCCA 57.563 34.615 19.43 0.00 35.51 3.53
3472 4619 9.308318 GCAGATTACTCTTAAGACCTTTTAGAG 57.692 37.037 0.00 14.60 36.78 2.43
3485 4632 9.031360 GTTATTCACGAATGCAGATTACTCTTA 57.969 33.333 2.48 0.00 32.50 2.10
3498 4645 6.489675 CCCTTCTGAATGTTATTCACGAATG 58.510 40.000 2.48 6.26 32.50 2.67
3502 4649 3.689161 TGCCCTTCTGAATGTTATTCACG 59.311 43.478 0.36 0.00 0.00 4.35
3506 4653 4.263905 TGTCCTGCCCTTCTGAATGTTATT 60.264 41.667 0.00 0.00 0.00 1.40
3534 4681 0.830648 CTCCTGATCCGTAAAGGCCA 59.169 55.000 5.01 0.00 40.77 5.36
3560 4707 0.597118 GCGCTACAGCTCTCCTGATG 60.597 60.000 0.00 0.00 44.64 3.07
3650 4797 1.999024 CTGTTTGTGTTTGTTGCCCAC 59.001 47.619 0.00 0.00 0.00 4.61
3707 4856 1.908619 TCTGATGTTGCTTGCCCTCTA 59.091 47.619 0.00 0.00 0.00 2.43
3708 4857 0.694771 TCTGATGTTGCTTGCCCTCT 59.305 50.000 0.00 0.00 0.00 3.69
3720 4869 5.010012 GGTGAATTGTTGTTCCTTCTGATGT 59.990 40.000 0.00 0.00 0.00 3.06
3726 4875 4.338118 TGTCTGGTGAATTGTTGTTCCTTC 59.662 41.667 0.00 0.00 0.00 3.46
3727 4876 4.277476 TGTCTGGTGAATTGTTGTTCCTT 58.723 39.130 0.00 0.00 0.00 3.36
3743 4892 2.689983 GCCAGGAAATATGGTTGTCTGG 59.310 50.000 0.00 0.00 42.13 3.86
3758 4908 2.312140 AGACTAGTAGTTCCTGCCAGGA 59.688 50.000 10.05 10.05 44.10 3.86
3768 4918 4.642885 GCCTGTGAGATCAGACTAGTAGTT 59.357 45.833 3.85 0.00 37.61 2.24
3790 4940 4.755123 ACACTGTACTATGTTCTGTTTGGC 59.245 41.667 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.