Multiple sequence alignment - TraesCS5D01G024900

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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 TraesCS5D01G024900 chr5D 100.000 3367 0 0 1 3367 22050801 22054167 0.000000e+00 6218
1 TraesCS5D01G024900 chr5D 84.404 2443 265 57 979 3367 21772490 21770110 0.000000e+00 2294
2 TraesCS5D01G024900 chr5D 84.200 2443 269 59 979 3367 21805723 21803344 0.000000e+00 2265
3 TraesCS5D01G024900 chr5D 84.159 2443 271 59 979 3367 21731444 21729064 0.000000e+00 2261
4 TraesCS5D01G024900 chr5D 80.238 420 65 13 2943 3353 21728327 21727917 1.960000e-77 300
5 TraesCS5D01G024900 chr5A 86.343 1955 179 34 1444 3367 15114092 15112195 0.000000e+00 2050
6 TraesCS5D01G024900 chr5A 88.421 475 44 4 979 1449 15115128 15114661 2.270000e-156 562
7 TraesCS5D01G024900 chr7D 99.694 979 3 0 1 979 49955170 49954192 0.000000e+00 1792
8 TraesCS5D01G024900 chr6D 99.693 978 3 0 1 978 291354430 291355407 0.000000e+00 1790
9 TraesCS5D01G024900 chr6D 99.387 979 6 0 1 979 1041946 1042924 0.000000e+00 1775
10 TraesCS5D01G024900 chr6D 99.189 986 6 1 1 984 6053396 6052411 0.000000e+00 1775
11 TraesCS5D01G024900 chr6D 99.387 979 6 0 1 979 20712526 20713504 0.000000e+00 1775
12 TraesCS5D01G024900 chr1D 99.693 978 3 0 1 978 41702335 41703312 0.000000e+00 1790
13 TraesCS5D01G024900 chr3D 99.189 986 6 1 1 984 540009334 540008349 0.000000e+00 1775
14 TraesCS5D01G024900 chr3D 99.387 979 6 0 1 979 588872897 588873875 0.000000e+00 1775
15 TraesCS5D01G024900 chr2D 99.387 979 6 0 1 979 228404460 228405438 0.000000e+00 1775
16 TraesCS5D01G024900 chr5B 85.872 1720 175 23 1686 3367 15521771 15520082 0.000000e+00 1770
17 TraesCS5D01G024900 chr5B 85.434 1222 121 20 1686 2878 15470134 15468941 0.000000e+00 1218
18 TraesCS5D01G024900 chr5B 88.730 488 53 2 2880 3367 15468671 15468186 2.240000e-166 595
19 TraesCS5D01G024900 chr5B 88.730 488 53 2 2880 3367 15513069 15512584 2.240000e-166 595
20 TraesCS5D01G024900 chrUn 88.730 488 53 2 2880 3367 362302238 362301753 2.240000e-166 595


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 TraesCS5D01G024900 chr5D 22050801 22054167 3366 False 6218.0 6218 100.0000 1 3367 1 chr5D.!!$F1 3366
1 TraesCS5D01G024900 chr5D 21770110 21772490 2380 True 2294.0 2294 84.4040 979 3367 1 chr5D.!!$R1 2388
2 TraesCS5D01G024900 chr5D 21803344 21805723 2379 True 2265.0 2265 84.2000 979 3367 1 chr5D.!!$R2 2388
3 TraesCS5D01G024900 chr5D 21727917 21731444 3527 True 1280.5 2261 82.1985 979 3367 2 chr5D.!!$R3 2388
4 TraesCS5D01G024900 chr5A 15112195 15115128 2933 True 1306.0 2050 87.3820 979 3367 2 chr5A.!!$R1 2388
5 TraesCS5D01G024900 chr7D 49954192 49955170 978 True 1792.0 1792 99.6940 1 979 1 chr7D.!!$R1 978
6 TraesCS5D01G024900 chr6D 291354430 291355407 977 False 1790.0 1790 99.6930 1 978 1 chr6D.!!$F3 977
7 TraesCS5D01G024900 chr6D 1041946 1042924 978 False 1775.0 1775 99.3870 1 979 1 chr6D.!!$F1 978
8 TraesCS5D01G024900 chr6D 6052411 6053396 985 True 1775.0 1775 99.1890 1 984 1 chr6D.!!$R1 983
9 TraesCS5D01G024900 chr6D 20712526 20713504 978 False 1775.0 1775 99.3870 1 979 1 chr6D.!!$F2 978
10 TraesCS5D01G024900 chr1D 41702335 41703312 977 False 1790.0 1790 99.6930 1 978 1 chr1D.!!$F1 977
11 TraesCS5D01G024900 chr3D 540008349 540009334 985 True 1775.0 1775 99.1890 1 984 1 chr3D.!!$R1 983
12 TraesCS5D01G024900 chr3D 588872897 588873875 978 False 1775.0 1775 99.3870 1 979 1 chr3D.!!$F1 978
13 TraesCS5D01G024900 chr2D 228404460 228405438 978 False 1775.0 1775 99.3870 1 979 1 chr2D.!!$F1 978
14 TraesCS5D01G024900 chr5B 15520082 15521771 1689 True 1770.0 1770 85.8720 1686 3367 1 chr5B.!!$R2 1681
15 TraesCS5D01G024900 chr5B 15468186 15470134 1948 True 906.5 1218 87.0820 1686 3367 2 chr5B.!!$R3 1681

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
996 997 0.818296 AGTCCCAGATACACGCTGAC 59.182 55.0 0.0 0.0 35.39 3.51 F
1941 2572 0.988063 TGGTGCATACTGCCAAGGTA 59.012 50.0 0.0 0.0 44.23 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2707 0.175989 GAGCACCCTCTTTACCCTCG 59.824 60.000 0.0 0.0 35.16 4.63 R
3023 3953 1.132643 CGAGTCACTCCTTTCCGGTAG 59.867 57.143 0.0 0.0 0.00 3.18 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
711 712 8.230486 GTCGATTCAACACAAATGTTCTCTTAT 58.770 33.333 0.00 0.00 46.46 1.73
775 776 4.096231 TCAGGAAAACATAACCATCATGCG 59.904 41.667 0.00 0.00 0.00 4.73
801 802 3.320610 TGAGCTAGTCTTAGAGGCCAT 57.679 47.619 5.01 0.00 0.00 4.40
981 982 2.896039 AGGGCATATCTCCTACAGTCC 58.104 52.381 0.00 0.00 0.00 3.85
992 993 1.067212 CCTACAGTCCCAGATACACGC 59.933 57.143 0.00 0.00 0.00 5.34
996 997 0.818296 AGTCCCAGATACACGCTGAC 59.182 55.000 0.00 0.00 35.39 3.51
1001 1002 1.202302 CCAGATACACGCTGACGACAT 60.202 52.381 0.00 0.00 43.93 3.06
1014 1015 3.023832 TGACGACATGGCTTCAGATCTA 58.976 45.455 3.08 0.00 0.00 1.98
1021 1022 4.223700 ACATGGCTTCAGATCTAGTGAACA 59.776 41.667 0.00 0.00 30.69 3.18
1023 1024 5.426689 TGGCTTCAGATCTAGTGAACATT 57.573 39.130 0.00 0.00 30.69 2.71
1035 1036 6.971602 TCTAGTGAACATTAAGGCTATCGAG 58.028 40.000 0.00 0.00 0.00 4.04
1047 1048 2.159085 GGCTATCGAGTGCCTTAGTTGT 60.159 50.000 20.15 0.00 45.26 3.32
1048 1049 3.522553 GCTATCGAGTGCCTTAGTTGTT 58.477 45.455 0.00 0.00 0.00 2.83
1049 1050 3.307242 GCTATCGAGTGCCTTAGTTGTTG 59.693 47.826 0.00 0.00 0.00 3.33
1050 1051 2.902705 TCGAGTGCCTTAGTTGTTGT 57.097 45.000 0.00 0.00 0.00 3.32
1051 1052 2.479837 TCGAGTGCCTTAGTTGTTGTG 58.520 47.619 0.00 0.00 0.00 3.33
1052 1053 2.101750 TCGAGTGCCTTAGTTGTTGTGA 59.898 45.455 0.00 0.00 0.00 3.58
1053 1054 2.221055 CGAGTGCCTTAGTTGTTGTGAC 59.779 50.000 0.00 0.00 0.00 3.67
1088 1089 6.415573 AGCGGTAATCTTCTCCTTTTACAAT 58.584 36.000 0.00 0.00 0.00 2.71
1114 1116 8.919018 TCAGATCTAGATGATACTACTCCCTA 57.081 38.462 10.74 0.00 35.14 3.53
1122 1124 8.155620 AGATGATACTACTCCCTACGGTTATA 57.844 38.462 0.00 0.00 0.00 0.98
1255 1257 2.830321 AGTACCAGGGTCTTACCTTTCG 59.170 50.000 0.00 0.00 39.34 3.46
1258 1260 1.338769 CCAGGGTCTTACCTTTCGGTG 60.339 57.143 0.00 0.00 45.18 4.94
1271 1273 3.451178 CCTTTCGGTGAAGATTCCCTAGA 59.549 47.826 0.00 0.00 0.00 2.43
1275 1277 5.063017 TCGGTGAAGATTCCCTAGATAGT 57.937 43.478 0.00 0.00 0.00 2.12
1397 1404 4.822026 TCCTTCGAAAAGATGAAGAGGAC 58.178 43.478 0.00 0.00 43.34 3.85
1465 2049 4.508124 GTGGCTTCTTCAATGGATACTACG 59.492 45.833 0.00 0.00 37.61 3.51
1550 2134 7.015289 TCGAATCAATTTGAAGAGCTTTTACG 58.985 34.615 2.68 0.00 0.00 3.18
1572 2156 6.411376 ACGAAACCATGGAGAAATGTATACA 58.589 36.000 21.47 8.27 0.00 2.29
1574 2158 7.556275 ACGAAACCATGGAGAAATGTATACAAT 59.444 33.333 21.47 0.00 0.00 2.71
1618 2202 1.618343 CCAACCCGAATTTTGGCTTCT 59.382 47.619 0.00 0.00 36.10 2.85
1651 2235 5.009010 TCAACTTTCCTTACTAACGACGTCT 59.991 40.000 14.70 0.00 0.00 4.18
1652 2236 4.791974 ACTTTCCTTACTAACGACGTCTG 58.208 43.478 14.70 9.79 0.00 3.51
1703 2288 7.148641 ACATAGCATACGGTATTTCAGAAGAG 58.851 38.462 0.00 0.00 33.52 2.85
1788 2375 9.447157 AGATAGATAAGTGTACGACTATAACCC 57.553 37.037 0.00 0.00 33.09 4.11
1797 2404 7.039082 AGTGTACGACTATAACCCTGGTAAAAA 60.039 37.037 0.00 0.00 30.86 1.94
1811 2418 5.163693 CCTGGTAAAAAGTAATAAGTGGCCG 60.164 44.000 0.00 0.00 0.00 6.13
1812 2419 4.156373 TGGTAAAAAGTAATAAGTGGCCGC 59.844 41.667 8.71 8.71 0.00 6.53
1863 2470 7.585579 TTAATCTGCATTATCTGAAATGGCA 57.414 32.000 0.00 0.00 37.34 4.92
1887 2517 5.024118 CCCCTACTAGTGGGTATTATCCAG 58.976 50.000 22.48 5.16 43.09 3.86
1902 2533 9.681692 GGTATTATCCAGTTTTAACGTTTGTTT 57.318 29.630 5.91 0.00 39.54 2.83
1941 2572 0.988063 TGGTGCATACTGCCAAGGTA 59.012 50.000 0.00 0.00 44.23 3.08
1943 2574 1.209504 GGTGCATACTGCCAAGGTAGA 59.790 52.381 11.30 0.00 44.23 2.59
1949 2580 4.688021 CATACTGCCAAGGTAGACTCTTC 58.312 47.826 11.30 0.00 0.00 2.87
1964 2595 4.841246 AGACTCTTCTAGGAGGCAAGAAAA 59.159 41.667 0.00 0.00 43.43 2.29
1968 2599 4.018960 TCTTCTAGGAGGCAAGAAAATGCT 60.019 41.667 0.00 0.00 45.68 3.79
1984 2615 9.798994 AAGAAAATGCTATCATTGATCTGAAAC 57.201 29.630 1.55 0.00 41.77 2.78
2011 2642 4.479158 ACACAAGGCCCAAGATAAAAAGA 58.521 39.130 0.00 0.00 0.00 2.52
2021 2652 7.417797 GGCCCAAGATAAAAAGAGATTATGCAA 60.418 37.037 0.00 0.00 0.00 4.08
2043 2674 5.919348 ATGATGAAATAGTCAGGGATGGT 57.081 39.130 0.00 0.00 40.43 3.55
2074 2705 7.722949 AAACATAATCCATCACCTGAACATT 57.277 32.000 0.00 0.00 0.00 2.71
2075 2706 6.704289 ACATAATCCATCACCTGAACATTG 57.296 37.500 0.00 0.00 0.00 2.82
2076 2707 5.068198 ACATAATCCATCACCTGAACATTGC 59.932 40.000 0.00 0.00 0.00 3.56
2083 2714 0.981183 ACCTGAACATTGCGAGGGTA 59.019 50.000 0.00 0.00 0.00 3.69
2183 2814 8.629986 CAAAGAATTTCGTCATGTACATTGTTC 58.370 33.333 5.37 3.61 35.03 3.18
2190 2821 5.989168 TCGTCATGTACATTGTTCTCAAGTT 59.011 36.000 5.37 0.00 36.97 2.66
2237 2884 7.286215 ACAGAAGTATGTGTACAGTGTACTT 57.714 36.000 28.78 18.19 38.06 2.24
2238 2885 7.145985 ACAGAAGTATGTGTACAGTGTACTTG 58.854 38.462 28.78 15.87 36.16 3.16
2239 2886 6.089551 CAGAAGTATGTGTACAGTGTACTTGC 59.910 42.308 28.78 20.04 36.16 4.01
2240 2887 5.723672 AGTATGTGTACAGTGTACTTGCT 57.276 39.130 28.78 19.84 33.09 3.91
2241 2888 6.829229 AGTATGTGTACAGTGTACTTGCTA 57.171 37.500 28.78 14.98 33.09 3.49
2242 2889 7.406031 AGTATGTGTACAGTGTACTTGCTAT 57.594 36.000 28.78 18.46 33.09 2.97
2243 2890 7.481642 AGTATGTGTACAGTGTACTTGCTATC 58.518 38.462 28.78 15.36 33.09 2.08
2244 2891 5.715434 TGTGTACAGTGTACTTGCTATCA 57.285 39.130 28.78 15.34 0.00 2.15
2245 2892 6.280855 TGTGTACAGTGTACTTGCTATCAT 57.719 37.500 28.78 0.00 0.00 2.45
2246 2893 6.099341 TGTGTACAGTGTACTTGCTATCATG 58.901 40.000 28.78 0.00 0.00 3.07
2247 2894 6.071616 TGTGTACAGTGTACTTGCTATCATGA 60.072 38.462 28.78 0.00 0.00 3.07
2248 2895 6.811665 GTGTACAGTGTACTTGCTATCATGAA 59.188 38.462 28.78 6.15 0.00 2.57
2249 2896 7.492669 GTGTACAGTGTACTTGCTATCATGAAT 59.507 37.037 28.78 0.00 0.00 2.57
2250 2897 7.706607 TGTACAGTGTACTTGCTATCATGAATC 59.293 37.037 28.78 2.47 0.00 2.52
2251 2898 6.882656 ACAGTGTACTTGCTATCATGAATCT 58.117 36.000 0.00 0.00 0.00 2.40
2252 2899 7.334090 ACAGTGTACTTGCTATCATGAATCTT 58.666 34.615 0.00 0.00 0.00 2.40
2253 2900 8.478066 ACAGTGTACTTGCTATCATGAATCTTA 58.522 33.333 0.00 0.00 0.00 2.10
2254 2901 9.486497 CAGTGTACTTGCTATCATGAATCTTAT 57.514 33.333 0.00 0.00 0.00 1.73
2315 2962 3.657625 CAGTGCACGACGAAACATTTTAC 59.342 43.478 12.01 0.00 0.00 2.01
2322 2969 5.842327 CACGACGAAACATTTTACCTAACAC 59.158 40.000 0.00 0.00 0.00 3.32
2327 2974 7.190871 ACGAAACATTTTACCTAACACAACAG 58.809 34.615 0.00 0.00 0.00 3.16
2332 2979 4.886247 TTTACCTAACACAACAGCACAC 57.114 40.909 0.00 0.00 0.00 3.82
2351 2998 5.560953 GCACACGAGAAAGCTTAAAGTTGAT 60.561 40.000 0.00 0.00 0.00 2.57
2382 3029 2.954316 TGTAGTACCTGCACAATCACG 58.046 47.619 0.00 0.00 0.00 4.35
2402 3051 6.827641 TCACGCAATATGTAAGAAGTTTCAC 58.172 36.000 0.00 0.00 0.00 3.18
2458 3113 3.981071 TGGTAATGAGGTTCAGGAGTG 57.019 47.619 0.00 0.00 0.00 3.51
2534 3189 5.048991 GGTTGTCCACATCAAGTACGAAATT 60.049 40.000 0.00 0.00 0.00 1.82
2689 3344 2.039879 TGCTCTAGACTTTGTTTCCCCC 59.960 50.000 0.00 0.00 0.00 5.40
2695 3350 1.878088 GACTTTGTTTCCCCCGAGAAC 59.122 52.381 0.00 0.00 0.00 3.01
2713 3368 7.136772 CCGAGAACGTTAGACAATGTATGATA 58.863 38.462 0.00 0.00 32.57 2.15
2726 3381 8.581057 ACAATGTATGATACTGAACGAAGATC 57.419 34.615 4.03 0.00 0.00 2.75
2766 3421 3.672808 AGCACAGATCAAAGGAAGACAG 58.327 45.455 0.00 0.00 0.00 3.51
2805 3460 7.966204 CCTTTTTACACGAATATGTTAACCCTG 59.034 37.037 2.48 0.00 33.85 4.45
2832 3487 9.817809 TGTTTTGGTGCAAACATAGTTTAATTA 57.182 25.926 0.00 0.00 32.79 1.40
2870 3532 6.272822 ACAAAAATTATTGGGCTCTCTGAC 57.727 37.500 0.00 0.00 34.56 3.51
2882 3812 3.131223 GGCTCTCTGACTACATGCTTGTA 59.869 47.826 11.56 11.56 37.28 2.41
2908 3838 5.756195 TCCATATTTCTACTTGCATGTGC 57.244 39.130 15.08 0.00 42.50 4.57
3023 3953 7.324616 CCTTGAAAGACGATCTGAAACATTTTC 59.675 37.037 0.00 0.00 0.00 2.29
3025 3955 8.601845 TGAAAGACGATCTGAAACATTTTCTA 57.398 30.769 0.00 0.00 0.00 2.10
3048 3978 0.033504 GAAAGGAGTGACTCGGCACA 59.966 55.000 6.50 0.00 41.19 4.57
3123 4053 5.612725 TTCTCCTTGAGGCAACAAAATTT 57.387 34.783 0.00 0.00 41.41 1.82
3240 4170 3.679502 GCATTTATTTGTGGCACTTGGAC 59.320 43.478 19.83 0.00 0.00 4.02
3247 4177 2.303175 TGTGGCACTTGGACCTAAAAC 58.697 47.619 19.83 0.00 0.00 2.43
3326 4256 0.527565 AATTGCTTCGTGGACCATGC 59.472 50.000 9.00 6.78 0.00 4.06
3331 4261 3.266686 TTCGTGGACCATGCCAGGG 62.267 63.158 9.00 0.00 42.53 4.45
3345 4275 3.397527 TGCCAGGGAAGATTCCTAGAAT 58.602 45.455 11.28 0.00 46.72 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
711 712 2.025037 AGCAACCTTGAGGGCATAATGA 60.025 45.455 1.54 0.00 40.27 2.57
775 776 4.439563 GCCTCTAAGACTAGCTCAAGTGTC 60.440 50.000 0.00 0.00 0.00 3.67
981 982 0.170339 TGTCGTCAGCGTGTATCTGG 59.830 55.000 0.00 0.00 39.49 3.86
992 993 2.159128 AGATCTGAAGCCATGTCGTCAG 60.159 50.000 12.66 12.66 41.71 3.51
996 997 3.067320 TCACTAGATCTGAAGCCATGTCG 59.933 47.826 5.18 0.00 0.00 4.35
1001 1002 5.426689 AATGTTCACTAGATCTGAAGCCA 57.573 39.130 5.18 0.00 0.00 4.75
1014 1015 5.352284 CACTCGATAGCCTTAATGTTCACT 58.648 41.667 0.00 0.00 0.00 3.41
1035 1036 3.377172 ACAAGTCACAACAACTAAGGCAC 59.623 43.478 0.00 0.00 0.00 5.01
1047 1048 1.806247 CGCTCACCTCACAAGTCACAA 60.806 52.381 0.00 0.00 0.00 3.33
1048 1049 0.249447 CGCTCACCTCACAAGTCACA 60.249 55.000 0.00 0.00 0.00 3.58
1049 1050 0.946221 CCGCTCACCTCACAAGTCAC 60.946 60.000 0.00 0.00 0.00 3.67
1050 1051 1.367471 CCGCTCACCTCACAAGTCA 59.633 57.895 0.00 0.00 0.00 3.41
1051 1052 0.601558 TACCGCTCACCTCACAAGTC 59.398 55.000 0.00 0.00 0.00 3.01
1052 1053 1.045407 TTACCGCTCACCTCACAAGT 58.955 50.000 0.00 0.00 0.00 3.16
1053 1054 2.093973 AGATTACCGCTCACCTCACAAG 60.094 50.000 0.00 0.00 0.00 3.16
1088 1089 8.225863 AGGGAGTAGTATCATCTAGATCTGAA 57.774 38.462 5.18 0.00 38.19 3.02
1197 1199 4.323553 ACTGTGAACTAGTGTTGGAGAC 57.676 45.455 0.00 0.00 36.39 3.36
1255 1257 6.551601 TCTCAACTATCTAGGGAATCTTCACC 59.448 42.308 0.00 0.00 0.00 4.02
1258 1260 7.151976 GCTTCTCAACTATCTAGGGAATCTTC 58.848 42.308 0.00 0.00 0.00 2.87
1275 1277 9.230122 TCATATGTTAATTCTGTTGCTTCTCAA 57.770 29.630 1.90 0.00 0.00 3.02
1290 1294 8.297470 AGGCACTGAACATTTCATATGTTAAT 57.703 30.769 1.90 1.71 41.76 1.40
1380 1386 5.931441 AACTTGTCCTCTTCATCTTTTCG 57.069 39.130 0.00 0.00 0.00 3.46
1465 2049 7.307989 CCAACCATTATCATAATGTCGACCTTC 60.308 40.741 14.12 0.00 0.00 3.46
1527 2111 8.728088 TTCGTAAAAGCTCTTCAAATTGATTC 57.272 30.769 0.00 0.00 0.00 2.52
1545 2129 7.931578 ATACATTTCTCCATGGTTTCGTAAA 57.068 32.000 12.58 5.20 0.00 2.01
1572 2156 7.339466 GTGTATGGTTGGAGAGGTAATGAAATT 59.661 37.037 0.00 0.00 41.28 1.82
1574 2158 6.177610 GTGTATGGTTGGAGAGGTAATGAAA 58.822 40.000 0.00 0.00 0.00 2.69
1639 2223 0.672342 AACCTGCAGACGTCGTTAGT 59.328 50.000 17.39 2.71 0.00 2.24
1651 2235 1.912763 GGGCCCAAATCAACCTGCA 60.913 57.895 19.95 0.00 0.00 4.41
1652 2236 1.479368 TTGGGCCCAAATCAACCTGC 61.479 55.000 35.47 0.00 32.44 4.85
1703 2288 2.966050 ACAGAATCTCCTCGTTCAAGC 58.034 47.619 0.00 0.00 0.00 4.01
1788 2375 5.675323 GCGGCCACTTATTACTTTTTACCAG 60.675 44.000 2.24 0.00 0.00 4.00
1797 2404 2.629051 GAGTTGCGGCCACTTATTACT 58.371 47.619 8.23 0.00 0.00 2.24
1894 2524 8.938047 ACGTTGACCTAATATTAAAACAAACG 57.062 30.769 18.61 18.61 0.00 3.60
1902 2533 7.769507 TGCACCAATACGTTGACCTAATATTAA 59.230 33.333 0.00 0.00 37.53 1.40
1941 2572 3.748645 TCTTGCCTCCTAGAAGAGTCT 57.251 47.619 0.00 0.00 37.95 3.24
1943 2574 5.495640 CATTTTCTTGCCTCCTAGAAGAGT 58.504 41.667 0.00 0.00 34.99 3.24
1949 2580 5.371526 TGATAGCATTTTCTTGCCTCCTAG 58.628 41.667 0.00 0.00 43.83 3.02
1984 2615 5.975693 TTATCTTGGGCCTTGTGTTTTAG 57.024 39.130 4.53 0.00 0.00 1.85
2011 2642 9.011095 CCTGACTATTTCATCATTGCATAATCT 57.989 33.333 0.00 0.00 32.17 2.40
2021 2652 5.919348 ACCATCCCTGACTATTTCATCAT 57.081 39.130 0.00 0.00 32.17 2.45
2033 2664 3.772387 TGTTTTGCATAACCATCCCTGA 58.228 40.909 16.06 0.00 0.00 3.86
2074 2705 1.980052 CACCCTCTTTACCCTCGCA 59.020 57.895 0.00 0.00 0.00 5.10
2075 2706 1.449778 GCACCCTCTTTACCCTCGC 60.450 63.158 0.00 0.00 0.00 5.03
2076 2707 0.175989 GAGCACCCTCTTTACCCTCG 59.824 60.000 0.00 0.00 35.16 4.63
2254 2901 9.691362 GCACCAAAATATCAAAAGAGAAGTAAA 57.309 29.630 0.00 0.00 0.00 2.01
2255 2902 8.855110 TGCACCAAAATATCAAAAGAGAAGTAA 58.145 29.630 0.00 0.00 0.00 2.24
2256 2903 8.402798 TGCACCAAAATATCAAAAGAGAAGTA 57.597 30.769 0.00 0.00 0.00 2.24
2257 2904 7.288810 TGCACCAAAATATCAAAAGAGAAGT 57.711 32.000 0.00 0.00 0.00 3.01
2258 2905 6.810182 CCTGCACCAAAATATCAAAAGAGAAG 59.190 38.462 0.00 0.00 0.00 2.85
2259 2906 6.267471 ACCTGCACCAAAATATCAAAAGAGAA 59.733 34.615 0.00 0.00 0.00 2.87
2264 2911 5.543507 ACACCTGCACCAAAATATCAAAA 57.456 34.783 0.00 0.00 0.00 2.44
2315 2962 1.526887 CTCGTGTGCTGTTGTGTTAGG 59.473 52.381 0.00 0.00 0.00 2.69
2322 2969 0.940126 AGCTTTCTCGTGTGCTGTTG 59.060 50.000 0.00 0.00 34.19 3.33
2327 2974 3.879932 ACTTTAAGCTTTCTCGTGTGC 57.120 42.857 3.20 0.00 0.00 4.57
2332 2979 7.693951 CACCATAATCAACTTTAAGCTTTCTCG 59.306 37.037 3.20 0.00 0.00 4.04
2351 2998 4.528987 TGCAGGTACTACAACTCACCATAA 59.471 41.667 0.00 0.00 36.02 1.90
2382 3029 9.677567 TTTTCTGTGAAACTTCTTACATATTGC 57.322 29.630 0.00 0.00 38.04 3.56
2446 3101 0.474660 AAGGCTCCACTCCTGAACCT 60.475 55.000 0.00 0.00 33.43 3.50
2448 3103 0.322008 CCAAGGCTCCACTCCTGAAC 60.322 60.000 0.00 0.00 33.43 3.18
2458 3113 5.609533 TTTGTACTATAGTCCAAGGCTCC 57.390 43.478 9.12 0.00 0.00 4.70
2565 3220 7.545615 GCCGTCAAATATGATCATGTCTATACA 59.454 37.037 18.72 0.00 38.01 2.29
2689 3344 7.856398 AGTATCATACATTGTCTAACGTTCTCG 59.144 37.037 2.82 0.00 43.34 4.04
2695 3350 7.642586 TCGTTCAGTATCATACATTGTCTAACG 59.357 37.037 0.00 0.00 0.00 3.18
2713 3368 1.178276 AGCGGAGATCTTCGTTCAGT 58.822 50.000 24.02 2.28 0.00 3.41
2726 3381 2.872858 GCTCTTTGGGTAATAAGCGGAG 59.127 50.000 0.00 0.00 0.00 4.63
2843 3498 7.888021 TCAGAGAGCCCAATAATTTTTGTTCTA 59.112 33.333 7.69 0.00 0.00 2.10
2850 3505 6.721318 TGTAGTCAGAGAGCCCAATAATTTT 58.279 36.000 0.00 0.00 0.00 1.82
2854 3509 4.443457 GCATGTAGTCAGAGAGCCCAATAA 60.443 45.833 0.00 0.00 0.00 1.40
2882 3812 7.255381 GCACATGCAAGTAGAAATATGGAATCT 60.255 37.037 0.00 0.00 41.59 2.40
2895 3825 1.542915 AGCAAAGGCACATGCAAGTAG 59.457 47.619 6.15 0.00 44.14 2.57
2908 3838 2.575532 TCACAGTTCCTCAAGCAAAGG 58.424 47.619 0.00 0.00 35.05 3.11
2941 3871 6.660521 TCATCTTCTTGACCTGCATTTTGTAT 59.339 34.615 0.00 0.00 0.00 2.29
3023 3953 1.132643 CGAGTCACTCCTTTCCGGTAG 59.867 57.143 0.00 0.00 0.00 3.18
3025 3955 1.533469 CCGAGTCACTCCTTTCCGGT 61.533 60.000 0.00 0.00 0.00 5.28
3048 3978 7.124750 ACTGCAAATCTGATAATAAAGGGCTTT 59.875 33.333 0.00 0.00 36.63 3.51
3133 4063 7.554959 TTCCTCCTAGTTTACATCTTCAGTT 57.445 36.000 0.00 0.00 0.00 3.16
3135 4065 8.097662 ACTTTTCCTCCTAGTTTACATCTTCAG 58.902 37.037 0.00 0.00 0.00 3.02
3229 4159 2.173782 TCAGTTTTAGGTCCAAGTGCCA 59.826 45.455 0.00 0.00 0.00 4.92
3283 4213 4.796312 GCAACACAGTGTTTACAAAACGAT 59.204 37.500 16.70 0.00 38.77 3.73
3331 4261 7.557719 TGGAAAACATGGATTCTAGGAATCTTC 59.442 37.037 16.49 11.88 0.00 2.87


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

AutoCloner maintained by Alex Coulton.