Multiple sequence alignment - TraesCS5D01G527600

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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 TraesCS5D01G527600 chr5D 100.000 4478 0 0 1 4478 544698439 544702916 0.000000e+00 8270.0
1 TraesCS5D01G527600 chr5D 94.915 118 4 2 1937 2054 532242495 532242610 2.750000e-42 183.0
2 TraesCS5D01G527600 chr5B 95.339 2446 88 17 2052 4478 687162117 687159679 0.000000e+00 3862.0
3 TraesCS5D01G527600 chr5B 96.854 1939 52 7 16 1949 687164049 687162115 0.000000e+00 3234.0
4 TraesCS5D01G527600 chr5B 98.198 111 2 0 1943 2053 558558586 558558696 1.270000e-45 195.0
5 TraesCS5D01G527600 chr4A 94.813 1870 67 15 2623 4467 624631806 624633670 0.000000e+00 2889.0
6 TraesCS5D01G527600 chr4A 85.682 440 43 11 2099 2525 577046092 577045660 3.180000e-121 446.0
7 TraesCS5D01G527600 chr1D 84.442 1112 166 5 2820 3928 7879223 7880330 0.000000e+00 1088.0
8 TraesCS5D01G527600 chr1D 91.304 46 4 0 1452 1497 7350366 7350321 3.740000e-06 63.9
9 TraesCS5D01G527600 chr1B 84.843 1082 163 1 2848 3928 9594573 9593492 0.000000e+00 1088.0
10 TraesCS5D01G527600 chr1B 84.353 1112 167 5 2820 3928 10074702 10075809 0.000000e+00 1083.0
11 TraesCS5D01G527600 chr1A 84.765 1083 164 1 2847 3928 9362640 9363722 0.000000e+00 1085.0
12 TraesCS5D01G527600 chr1A 88.085 898 47 26 190 1053 569448766 569447895 0.000000e+00 1011.0
13 TraesCS5D01G527600 chr1A 91.667 600 36 7 3877 4467 569447374 569446780 0.000000e+00 819.0
14 TraesCS5D01G527600 chr1A 88.291 316 32 3 157 471 569449810 569449499 1.520000e-99 374.0
15 TraesCS5D01G527600 chr1A 93.035 201 11 1 190 390 569449488 569449291 1.580000e-74 291.0
16 TraesCS5D01G527600 chr1A 80.890 382 57 12 90 469 569447860 569447493 2.040000e-73 287.0
17 TraesCS5D01G527600 chr1A 88.496 113 10 3 60 172 569449966 569449857 2.810000e-27 134.0
18 TraesCS5D01G527600 chrUn 83.800 1142 174 9 2820 3957 238779977 238778843 0.000000e+00 1074.0
19 TraesCS5D01G527600 chrUn 83.800 1142 174 9 2820 3957 240356297 240357431 0.000000e+00 1074.0
20 TraesCS5D01G527600 chr3D 83.656 1138 174 10 2819 3952 27878208 27877079 0.000000e+00 1061.0
21 TraesCS5D01G527600 chr4D 87.514 905 67 24 918 1802 26253077 26253955 0.000000e+00 1003.0
22 TraesCS5D01G527600 chr4D 84.696 477 49 9 2052 2525 26254179 26254634 5.280000e-124 455.0
23 TraesCS5D01G527600 chr4D 86.339 183 22 1 657 839 26252773 26252952 3.530000e-46 196.0
24 TraesCS5D01G527600 chr4D 82.011 189 18 10 201 379 26252647 26252829 3.610000e-31 147.0
25 TraesCS5D01G527600 chr4D 98.305 59 0 1 2585 2643 26254633 26254690 7.920000e-18 102.0
26 TraesCS5D01G527600 chr4B 85.429 1002 89 17 936 1916 38792631 38793596 0.000000e+00 989.0
27 TraesCS5D01G527600 chr4B 87.327 434 41 7 2099 2522 38793625 38794054 6.730000e-133 484.0
28 TraesCS5D01G527600 chr4B 85.340 191 23 3 657 845 38792308 38792495 4.570000e-45 193.0
29 TraesCS5D01G527600 chr2A 100.000 111 0 0 1944 2054 16547048 16546938 5.870000e-49 206.0
30 TraesCS5D01G527600 chr2A 95.161 124 5 1 1947 2070 722814114 722813992 1.270000e-45 195.0
31 TraesCS5D01G527600 chr6B 96.667 120 2 2 1937 2056 20752489 20752606 9.830000e-47 198.0
32 TraesCS5D01G527600 chr6A 97.414 116 3 0 1945 2060 106923444 106923559 9.830000e-47 198.0
33 TraesCS5D01G527600 chr2B 97.414 116 3 0 1947 2062 588684903 588685018 9.830000e-47 198.0
34 TraesCS5D01G527600 chr7B 96.639 119 3 1 1944 2061 137792623 137792741 3.530000e-46 196.0
35 TraesCS5D01G527600 chr7A 96.639 119 3 1 1943 2061 501070781 501070664 3.530000e-46 196.0


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 TraesCS5D01G527600 chr5D 544698439 544702916 4477 False 8270.000000 8270 100.000000 1 4478 1 chr5D.!!$F2 4477
1 TraesCS5D01G527600 chr5B 687159679 687164049 4370 True 3548.000000 3862 96.096500 16 4478 2 chr5B.!!$R1 4462
2 TraesCS5D01G527600 chr4A 624631806 624633670 1864 False 2889.000000 2889 94.813000 2623 4467 1 chr4A.!!$F1 1844
3 TraesCS5D01G527600 chr1D 7879223 7880330 1107 False 1088.000000 1088 84.442000 2820 3928 1 chr1D.!!$F1 1108
4 TraesCS5D01G527600 chr1B 9593492 9594573 1081 True 1088.000000 1088 84.843000 2848 3928 1 chr1B.!!$R1 1080
5 TraesCS5D01G527600 chr1B 10074702 10075809 1107 False 1083.000000 1083 84.353000 2820 3928 1 chr1B.!!$F1 1108
6 TraesCS5D01G527600 chr1A 9362640 9363722 1082 False 1085.000000 1085 84.765000 2847 3928 1 chr1A.!!$F1 1081
7 TraesCS5D01G527600 chr1A 569446780 569449966 3186 True 486.000000 1011 88.410667 60 4467 6 chr1A.!!$R1 4407
8 TraesCS5D01G527600 chrUn 238778843 238779977 1134 True 1074.000000 1074 83.800000 2820 3957 1 chrUn.!!$R1 1137
9 TraesCS5D01G527600 chrUn 240356297 240357431 1134 False 1074.000000 1074 83.800000 2820 3957 1 chrUn.!!$F1 1137
10 TraesCS5D01G527600 chr3D 27877079 27878208 1129 True 1061.000000 1061 83.656000 2819 3952 1 chr3D.!!$R1 1133
11 TraesCS5D01G527600 chr4D 26252647 26254690 2043 False 380.600000 1003 87.773000 201 2643 5 chr4D.!!$F1 2442
12 TraesCS5D01G527600 chr4B 38792308 38794054 1746 False 555.333333 989 86.032000 657 2522 3 chr4B.!!$F1 1865

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
315 1394 0.330604 AATGTCCACATCTGCCTGCT 59.669 50.0 0.00 0.00 35.10 4.24 F
1962 3217 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.0 13.34 13.34 0.00 4.55 F
1963 3218 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 3292 0.107017 TAGGTACTCCCTCCGTTCGG 60.107 60.000 4.74 4.74 44.81 4.30 R
3351 4638 0.396139 TCCATTCCTCTGCAATGCCC 60.396 55.000 1.53 0.00 30.94 5.36 R
3599 4887 1.340017 ACCAGCATGCCGAAACTGTAT 60.340 47.619 15.66 0.00 31.97 2.29 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
74 75 2.927028 AGCCAGTAAACAGTTTCCGTT 58.073 42.857 0.48 0.00 0.00 4.44
75 76 2.616842 AGCCAGTAAACAGTTTCCGTTG 59.383 45.455 0.48 0.00 0.00 4.10
269 1340 4.084589 GCCGAACATGGATTTGTGTTTTTC 60.085 41.667 0.00 0.00 38.57 2.29
270 1341 4.148000 CCGAACATGGATTTGTGTTTTTCG 59.852 41.667 0.00 0.00 38.57 3.46
315 1394 0.330604 AATGTCCACATCTGCCTGCT 59.669 50.000 0.00 0.00 35.10 4.24
394 1473 5.888724 TCGCCCAATCAGTTATTTATTTCCA 59.111 36.000 0.00 0.00 0.00 3.53
453 1532 3.838120 TCGAGCAAGTCTACAATCACAG 58.162 45.455 0.00 0.00 0.00 3.66
583 1665 4.756642 CAGCAAACCAAGATGAGTAAGTCA 59.243 41.667 0.00 0.00 40.38 3.41
700 1783 7.484035 AGAAATATTTCCACATAGCGACTTC 57.516 36.000 21.86 0.00 37.92 3.01
878 1963 6.487689 AGTAGCTCTGTTAATTTCAGCAAC 57.512 37.500 0.00 0.00 33.48 4.17
881 1966 5.523369 AGCTCTGTTAATTTCAGCAACAAC 58.477 37.500 5.73 0.00 32.16 3.32
898 1984 2.612212 ACAACCGCCGATCATTTACATC 59.388 45.455 0.00 0.00 0.00 3.06
957 2093 8.850156 ACAAAGAGTTGTATTGTCTTGCTATTT 58.150 29.630 0.00 0.00 46.33 1.40
1037 2179 3.056536 TCCATAGCCATCGTCATAGCTTC 60.057 47.826 0.00 0.00 36.79 3.86
1283 2425 4.177026 GTCACTGCCATAGATTATAGCCG 58.823 47.826 0.00 0.00 0.00 5.52
1338 2480 4.466828 CGTGCCATAAAGTTCAGAAGTTG 58.533 43.478 3.87 0.00 0.00 3.16
1946 3201 9.561069 AACAGAATCACACAAATTAGACTAACT 57.439 29.630 0.00 0.00 0.00 2.24
1951 3206 9.654663 AATCACACAAATTAGACTAACTACTCC 57.345 33.333 0.00 0.00 0.00 3.85
1952 3207 7.609056 TCACACAAATTAGACTAACTACTCCC 58.391 38.462 0.00 0.00 0.00 4.30
1953 3208 7.453752 TCACACAAATTAGACTAACTACTCCCT 59.546 37.037 0.00 0.00 0.00 4.20
1954 3209 7.760340 CACACAAATTAGACTAACTACTCCCTC 59.240 40.741 0.00 0.00 0.00 4.30
1955 3210 7.093421 ACACAAATTAGACTAACTACTCCCTCC 60.093 40.741 0.00 0.00 0.00 4.30
1956 3211 6.096564 ACAAATTAGACTAACTACTCCCTCCG 59.903 42.308 0.00 0.00 0.00 4.63
1957 3212 4.851639 TTAGACTAACTACTCCCTCCGT 57.148 45.455 0.00 0.00 0.00 4.69
1958 3213 3.735720 AGACTAACTACTCCCTCCGTT 57.264 47.619 0.00 0.00 0.00 4.44
1959 3214 3.619419 AGACTAACTACTCCCTCCGTTC 58.381 50.000 0.00 0.00 0.00 3.95
1960 3215 2.354199 GACTAACTACTCCCTCCGTTCG 59.646 54.545 0.00 0.00 0.00 3.95
1962 3217 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
1963 3218 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
1964 3219 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
1965 3220 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
1966 3221 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1967 3222 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1968 3223 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1969 3224 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1970 3225 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1972 3227 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1973 3228 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
1974 3229 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
1976 3231 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
1979 3234 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
1981 3236 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
1982 3237 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
1985 3240 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
1986 3241 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
1987 3242 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
1988 3243 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
1989 3244 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
1992 3247 7.923344 ACTTGTCTCGAAAATGGATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
1993 3248 7.582667 TGTCTCGAAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
1994 3249 8.007405 TGTCTCGAAAATGGATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
1995 3250 7.921214 TGTCTCGAAAATGGATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
1996 3251 8.138712 GTCTCGAAAATGGATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
1998 3253 9.967346 CTCGAAAATGGATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
2025 3280 9.664332 AATACATCTAGATACATCCATTTCTGC 57.336 33.333 4.54 0.00 0.00 4.26
2026 3281 6.162079 ACATCTAGATACATCCATTTCTGCG 58.838 40.000 4.54 0.00 0.00 5.18
2027 3282 6.015095 ACATCTAGATACATCCATTTCTGCGA 60.015 38.462 4.54 0.00 0.00 5.10
2028 3283 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2029 3284 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
2030 3285 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
2031 3286 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
2032 3287 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
2033 3288 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
2034 3289 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
2035 3290 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
2036 3291 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
2037 3292 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
2038 3293 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
2039 3294 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
2040 3295 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
2041 3296 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
2042 3297 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
2043 3298 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2044 3299 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2045 3300 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2046 3301 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2047 3302 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2048 3303 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2049 3304 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2050 3305 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2229 3491 8.523915 AAATTATGCATGTTCAAGATGTCCTA 57.476 30.769 10.16 0.00 0.00 2.94
2375 3643 2.432146 GTCACCAGAGATAGCACCATGA 59.568 50.000 0.00 0.00 0.00 3.07
2376 3644 3.106827 TCACCAGAGATAGCACCATGAA 58.893 45.455 0.00 0.00 0.00 2.57
2651 3921 8.542926 TCAATGAGATCTTATTGTCCTCTTTCA 58.457 33.333 29.21 12.13 37.67 2.69
2720 3990 6.959639 TTCAAATTTTCCTTCTGCTACACT 57.040 33.333 0.00 0.00 0.00 3.55
2992 4278 9.695526 TTCTCAATACACATGGAAAATCAAAAG 57.304 29.630 0.00 0.00 0.00 2.27
3253 4539 6.177610 ACAAGACGGGCTCTTATTTATGAAA 58.822 36.000 0.00 0.00 37.08 2.69
3261 4547 6.015180 GGGCTCTTATTTATGAAATCATGCCA 60.015 38.462 14.96 0.00 37.15 4.92
3584 4872 1.133792 CGGAACTTTGGGGGCATATCT 60.134 52.381 0.00 0.00 0.00 1.98
3599 4887 4.202020 GGCATATCTCACAAGTCAGACGTA 60.202 45.833 0.00 0.00 0.00 3.57
3940 5229 4.846779 TGCCTTAAAACACATGGAGAAC 57.153 40.909 0.00 0.00 0.00 3.01
3962 5251 6.182039 ACAACATCACCATGATTTTAGTCG 57.818 37.500 0.00 0.00 34.28 4.18
3967 5256 7.272244 ACATCACCATGATTTTAGTCGACATA 58.728 34.615 19.50 4.50 34.28 2.29
3971 5260 7.984617 TCACCATGATTTTAGTCGACATATTGA 59.015 33.333 19.50 3.88 0.00 2.57
3977 5266 8.611757 TGATTTTAGTCGACATATTGATTGGTG 58.388 33.333 19.50 0.00 0.00 4.17
3983 5272 5.296780 GTCGACATATTGATTGGTGTTGGAT 59.703 40.000 11.55 0.00 0.00 3.41
4051 5340 7.809546 TGTTGTACCAATAATCAGTTGTGAA 57.190 32.000 0.00 0.00 35.88 3.18
4073 5362 9.244799 GTGAACATGTCATAGTCGAAACATATA 57.755 33.333 0.00 0.00 38.90 0.86
4109 5398 8.740123 TGAACTTATTTCAGTAGTTTGGTTGA 57.260 30.769 0.00 0.00 39.45 3.18
4162 5451 5.227569 TCCTGACAGCTGAGATACAAAAA 57.772 39.130 23.35 0.00 0.00 1.94
4236 5525 4.220382 CCCACATCCAATTTTTCTGCAGTA 59.780 41.667 14.67 0.00 0.00 2.74
4249 5538 0.904649 TGCAGTACAGTCATCCCCAG 59.095 55.000 0.00 0.00 0.00 4.45
4369 5661 0.246635 CACACCTTCCGTCCCTACAG 59.753 60.000 0.00 0.00 0.00 2.74
4410 5708 2.155924 GCGACACTGCAGTTTTCTAGAC 59.844 50.000 18.94 4.30 34.15 2.59
4431 5729 4.151883 ACCCGTACCAAACTAAGACACTA 58.848 43.478 0.00 0.00 0.00 2.74
4447 5745 5.710984 AGACACTATCTTGGTCTGTAAACG 58.289 41.667 0.00 0.00 40.21 3.60
4458 5756 5.180271 TGGTCTGTAAACGTGGGATTTATC 58.820 41.667 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.602905 ACGTCTGGGTTAGCAACAGC 60.603 55.000 0.00 0.00 32.42 4.40
1 2 1.148310 CACGTCTGGGTTAGCAACAG 58.852 55.000 0.00 0.00 0.00 3.16
2 3 0.466543 ACACGTCTGGGTTAGCAACA 59.533 50.000 0.00 0.00 0.00 3.33
3 4 2.443887 TACACGTCTGGGTTAGCAAC 57.556 50.000 0.00 0.00 0.00 4.17
4 5 3.259876 AGAATACACGTCTGGGTTAGCAA 59.740 43.478 0.00 0.00 0.00 3.91
5 6 2.829720 AGAATACACGTCTGGGTTAGCA 59.170 45.455 0.00 0.00 0.00 3.49
6 7 3.521947 AGAATACACGTCTGGGTTAGC 57.478 47.619 0.00 0.00 0.00 3.09
7 8 5.721232 AGAAAGAATACACGTCTGGGTTAG 58.279 41.667 0.00 0.00 0.00 2.34
8 9 5.337009 GGAGAAAGAATACACGTCTGGGTTA 60.337 44.000 0.00 0.00 0.00 2.85
9 10 4.562963 GGAGAAAGAATACACGTCTGGGTT 60.563 45.833 0.00 0.00 0.00 4.11
10 11 3.056035 GGAGAAAGAATACACGTCTGGGT 60.056 47.826 0.00 0.00 0.00 4.51
11 12 3.056107 TGGAGAAAGAATACACGTCTGGG 60.056 47.826 0.00 0.00 0.00 4.45
12 13 4.188247 TGGAGAAAGAATACACGTCTGG 57.812 45.455 0.00 0.00 0.00 3.86
13 14 4.092091 GCTTGGAGAAAGAATACACGTCTG 59.908 45.833 0.00 0.00 38.24 3.51
14 15 4.246458 GCTTGGAGAAAGAATACACGTCT 58.754 43.478 0.00 0.00 38.24 4.18
90 91 5.769662 ACCTTATGAGATGACAGCACAAAAA 59.230 36.000 0.00 0.00 0.00 1.94
91 92 5.181811 CACCTTATGAGATGACAGCACAAAA 59.818 40.000 0.00 0.00 0.00 2.44
269 1340 7.168219 TCAAAAGATAAATCTATCATCCCCCG 58.832 38.462 0.00 0.00 37.05 5.73
270 1341 8.940397 TTCAAAAGATAAATCTATCATCCCCC 57.060 34.615 0.00 0.00 37.05 5.40
315 1394 1.177895 AATGTTCATGTGGCCGCACA 61.178 50.000 23.94 15.73 39.62 4.57
394 1473 1.561542 CTTATCTGCCAGAGGGGTTGT 59.438 52.381 0.00 0.00 39.65 3.32
453 1532 2.194271 GCCGTGTTATAGCTGTCTGAC 58.806 52.381 0.00 0.00 0.00 3.51
700 1783 1.915141 ACAAGCAATTGGGTGAGGAG 58.085 50.000 7.72 0.00 0.00 3.69
878 1963 2.872245 AGATGTAAATGATCGGCGGTTG 59.128 45.455 7.21 0.00 0.00 3.77
881 1966 2.480419 GGAAGATGTAAATGATCGGCGG 59.520 50.000 7.21 0.00 0.00 6.13
957 2093 0.696501 GGTAAAGGTGAAGGCAGGGA 59.303 55.000 0.00 0.00 0.00 4.20
1037 2179 2.102084 TCGATTCCATGGCTGAGAAGAG 59.898 50.000 6.96 0.00 0.00 2.85
1283 2425 1.425428 GCGATGCTAAGTGTGGCAC 59.575 57.895 11.55 11.55 44.88 5.01
1338 2480 1.661112 GCTGGTACACTTTGCGAGATC 59.339 52.381 0.00 0.00 0.00 2.75
1946 3201 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
1947 3202 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1948 3203 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1949 3204 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1950 3205 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1951 3206 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1952 3207 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
1953 3208 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
1954 3209 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
1955 3210 3.495193 TCGAGACAAGTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
1956 3211 5.834239 TTTCGAGACAAGTAATTCCGAAC 57.166 39.130 0.00 0.00 34.86 3.95
1957 3212 6.128391 CCATTTTCGAGACAAGTAATTCCGAA 60.128 38.462 0.00 0.00 33.57 4.30
1958 3213 5.350365 CCATTTTCGAGACAAGTAATTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
1959 3214 5.350365 TCCATTTTCGAGACAAGTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
1960 3215 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
1962 3217 7.687941 ACATCCATTTTCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
1963 3218 8.964476 ATACATCCATTTTCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
1964 3219 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
1965 3220 7.782049 AGATACATCCATTTTCGAGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
1966 3221 6.644347 AGATACATCCATTTTCGAGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
1967 3222 8.138074 TCTAGATACATCCATTTTCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
1968 3223 8.007405 TCTAGATACATCCATTTTCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
1969 3224 7.582667 TCTAGATACATCCATTTTCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
1970 3225 8.138712 AGTTCTAGATACATCCATTTTCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
1972 3227 9.967346 TTAGTTCTAGATACATCCATTTTCGAG 57.033 33.333 0.00 0.00 0.00 4.04
2001 3256 7.176690 TCGCAGAAATGGATGTATCTAGATGTA 59.823 37.037 15.79 4.44 0.00 2.29
2002 3257 6.015095 TCGCAGAAATGGATGTATCTAGATGT 60.015 38.462 15.79 1.25 0.00 3.06
2003 3258 6.309980 GTCGCAGAAATGGATGTATCTAGATG 59.690 42.308 15.79 0.00 39.69 2.90
2004 3259 6.015095 TGTCGCAGAAATGGATGTATCTAGAT 60.015 38.462 10.73 10.73 39.69 1.98
2005 3260 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
2006 3261 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
2007 3262 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
2008 3263 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
2009 3264 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
2010 3265 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
2011 3266 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
2012 3267 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
2013 3268 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
2014 3269 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
2015 3270 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
2016 3271 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
2017 3272 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
2018 3273 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2019 3274 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2020 3275 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2021 3276 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2022 3277 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2023 3278 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2024 3279 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2025 3280 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2026 3281 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2027 3282 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2028 3283 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2029 3284 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2030 3285 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2031 3286 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2032 3287 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2033 3288 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2034 3289 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2035 3290 0.967380 GGTACTCCCTCCGTTCGGAA 60.967 60.000 14.79 0.04 33.41 4.30
2036 3291 1.379044 GGTACTCCCTCCGTTCGGA 60.379 63.158 13.34 13.34 0.00 4.55
2037 3292 0.107017 TAGGTACTCCCTCCGTTCGG 60.107 60.000 4.74 4.74 44.81 4.30
2038 3293 1.978454 ATAGGTACTCCCTCCGTTCG 58.022 55.000 0.00 0.00 44.81 3.95
2039 3294 4.280425 CCTTTATAGGTACTCCCTCCGTTC 59.720 50.000 0.00 0.00 44.81 3.95
2040 3295 4.221530 CCTTTATAGGTACTCCCTCCGTT 58.778 47.826 0.00 0.00 44.81 4.44
2041 3296 3.437637 CCCTTTATAGGTACTCCCTCCGT 60.438 52.174 0.00 0.00 44.81 4.69
2042 3297 3.163467 CCCTTTATAGGTACTCCCTCCG 58.837 54.545 0.00 0.00 44.81 4.63
2043 3298 4.482400 TCCCTTTATAGGTACTCCCTCC 57.518 50.000 0.00 0.00 44.81 4.30
2044 3299 8.541234 CATTATTCCCTTTATAGGTACTCCCTC 58.459 40.741 0.00 0.00 44.81 4.30
2046 3301 7.631007 CCATTATTCCCTTTATAGGTACTCCC 58.369 42.308 0.00 0.00 41.75 4.30
2047 3302 7.110810 GCCATTATTCCCTTTATAGGTACTCC 58.889 42.308 0.00 0.00 41.75 3.85
2048 3303 7.686434 TGCCATTATTCCCTTTATAGGTACTC 58.314 38.462 0.00 0.00 41.75 2.59
2049 3304 7.642094 TGCCATTATTCCCTTTATAGGTACT 57.358 36.000 0.00 0.00 46.37 2.73
2050 3305 7.888546 ACATGCCATTATTCCCTTTATAGGTAC 59.111 37.037 0.00 0.00 40.19 3.34
2310 3572 7.508296 GGAGATTGATTAGGGTAAGGTAGTGTA 59.492 40.741 0.00 0.00 0.00 2.90
2621 3891 7.072202 AGAGGACAATAAGATCTCATTGATGGT 59.928 37.037 22.99 2.63 36.00 3.55
2651 3921 5.981088 TTGACATGTGAACCTGCAAATAT 57.019 34.783 1.15 0.00 0.00 1.28
2992 4278 2.808543 CAGAGAAAGTGTACCTTGTGGC 59.191 50.000 0.00 0.00 36.63 5.01
3253 4539 2.424601 CCAATGACTCGTTTGGCATGAT 59.575 45.455 0.00 0.00 36.28 2.45
3261 4547 8.964476 ATATGTATTTCTCCAATGACTCGTTT 57.036 30.769 0.00 0.00 0.00 3.60
3351 4638 0.396139 TCCATTCCTCTGCAATGCCC 60.396 55.000 1.53 0.00 30.94 5.36
3584 4872 5.700722 AACTGTATACGTCTGACTTGTGA 57.299 39.130 6.21 0.00 0.00 3.58
3599 4887 1.340017 ACCAGCATGCCGAAACTGTAT 60.340 47.619 15.66 0.00 31.97 2.29
3940 5229 6.128309 TGTCGACTAAAATCATGGTGATGTTG 60.128 38.462 17.92 0.00 35.25 3.33
3962 5251 6.262944 TGCTATCCAACACCAATCAATATGTC 59.737 38.462 0.00 0.00 0.00 3.06
3967 5256 4.343231 TGTGCTATCCAACACCAATCAAT 58.657 39.130 0.00 0.00 35.90 2.57
3971 5260 3.894427 TGTTTGTGCTATCCAACACCAAT 59.106 39.130 0.00 0.00 35.90 3.16
3977 5266 3.244976 GTGCATGTTTGTGCTATCCAAC 58.755 45.455 0.00 0.00 45.27 3.77
3983 5272 5.476599 AGAAATAAGGTGCATGTTTGTGCTA 59.523 36.000 0.00 0.00 45.27 3.49
4092 5381 6.601613 AGTGACAATCAACCAAACTACTGAAA 59.398 34.615 0.00 0.00 0.00 2.69
4102 5391 2.373224 TGCACAGTGACAATCAACCAA 58.627 42.857 4.15 0.00 0.00 3.67
4204 5493 0.630673 TTGGATGTGGGGGATTCCTG 59.369 55.000 2.01 0.00 35.33 3.86
4205 5494 1.624173 ATTGGATGTGGGGGATTCCT 58.376 50.000 2.01 0.00 35.33 3.36
4236 5525 1.842562 CATCTTCCTGGGGATGACTGT 59.157 52.381 18.81 0.00 41.05 3.55
4369 5661 7.270579 GTGTCGCTTATTTACAGATCCAAAAAC 59.729 37.037 0.00 0.00 0.00 2.43
4389 5681 2.155924 GTCTAGAAAACTGCAGTGTCGC 59.844 50.000 22.49 10.90 0.00 5.19
4410 5708 3.672767 AGTGTCTTAGTTTGGTACGGG 57.327 47.619 0.00 0.00 0.00 5.28
4431 5729 2.635915 TCCCACGTTTACAGACCAAGAT 59.364 45.455 0.00 0.00 0.00 2.40
4447 5745 2.922740 TAGGTGGCGATAAATCCCAC 57.077 50.000 16.28 16.28 42.44 4.61


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

AutoCloner maintained by Alex Coulton.