Multiple sequence alignment - TraesCS5D01G416500

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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 TraesCS5D01G416500 chr5D 100.000 5123 0 0 1 5123 478743467 478738345 0.000000e+00 9461
1 TraesCS5D01G416500 chr5D 85.909 1909 179 32 1054 2941 478703522 478701683 0.000000e+00 1953
2 TraesCS5D01G416500 chr5D 87.761 670 76 4 3496 4165 478701042 478700379 0.000000e+00 778
3 TraesCS5D01G416500 chr5D 86.799 553 47 8 2942 3493 478701631 478701104 1.230000e-165 593
4 TraesCS5D01G416500 chr5B 91.344 1883 90 23 722 2552 586716059 586714198 0.000000e+00 2507
5 TraesCS5D01G416500 chr5B 89.238 1877 172 12 1072 2939 586462942 586464797 0.000000e+00 2320
6 TraesCS5D01G416500 chr5B 93.216 1312 68 8 2942 4235 586713844 586712536 0.000000e+00 1910
7 TraesCS5D01G416500 chr5B 87.452 1554 156 16 1064 2588 586530538 586532081 0.000000e+00 1753
8 TraesCS5D01G416500 chr5B 92.540 992 55 9 3246 4235 586465112 586466086 0.000000e+00 1404
9 TraesCS5D01G416500 chr5B 88.796 714 55 14 1 697 586716754 586716049 0.000000e+00 852
10 TraesCS5D01G416500 chr5B 81.883 988 114 29 3239 4182 586532096 586533062 0.000000e+00 773
11 TraesCS5D01G416500 chr5B 94.958 238 12 0 2942 3179 586464851 586465088 1.740000e-99 374
12 TraesCS5D01G416500 chr5B 92.202 218 17 0 2726 2943 586714111 586713894 4.980000e-80 309
13 TraesCS5D01G416500 chr5A 91.376 1635 69 16 274 1893 597756125 597754548 0.000000e+00 2172
14 TraesCS5D01G416500 chr5A 91.929 1301 63 12 2942 4235 597753624 597752359 0.000000e+00 1783
15 TraesCS5D01G416500 chr5A 87.427 1551 162 11 1064 2591 597748388 597746848 0.000000e+00 1753
16 TraesCS5D01G416500 chr5A 95.791 879 37 0 2065 2943 597754552 597753674 0.000000e+00 1419
17 TraesCS5D01G416500 chr5A 82.263 981 118 31 3172 4108 597746828 597745860 0.000000e+00 797
18 TraesCS5D01G416500 chr5A 90.604 298 19 6 1 290 597757488 597757192 2.240000e-103 387
19 TraesCS5D01G416500 chr7D 98.879 892 8 2 4234 5123 288474939 288474048 0.000000e+00 1591
20 TraesCS5D01G416500 chr7D 98.305 885 14 1 4237 5120 37515875 37516759 0.000000e+00 1550
21 TraesCS5D01G416500 chr3D 98.878 891 8 2 4235 5123 55082980 55082090 0.000000e+00 1589
22 TraesCS5D01G416500 chr3D 98.985 887 5 2 4235 5120 581078161 581079044 0.000000e+00 1585
23 TraesCS5D01G416500 chr3D 97.982 892 14 4 4230 5120 568853388 568854276 0.000000e+00 1544
24 TraesCS5D01G416500 chr1D 98.878 891 9 1 4234 5123 409587642 409586752 0.000000e+00 1589
25 TraesCS5D01G416500 chr1D 97.875 894 17 2 4232 5123 33587779 33586886 0.000000e+00 1544
26 TraesCS5D01G416500 chr1D 85.388 219 22 7 1 210 460919381 460919164 8.640000e-53 219
27 TraesCS5D01G416500 chr1D 85.321 218 22 6 1 210 317596204 317595989 3.110000e-52 217
28 TraesCS5D01G416500 chr6D 98.316 891 13 2 4231 5120 462872304 462873193 0.000000e+00 1561
29 TraesCS5D01G416500 chr6D 97.882 897 16 3 4229 5123 4957413 4956518 0.000000e+00 1548
30 TraesCS5D01G416500 chr6A 77.491 813 159 19 1125 1928 21151161 21150364 2.790000e-127 466
31 TraesCS5D01G416500 chr1B 73.403 1346 304 44 1125 2446 444865332 444864017 2.170000e-123 453
32 TraesCS5D01G416500 chr1B 86.878 221 17 9 1 210 41627363 41627144 2.380000e-58 237
33 TraesCS5D01G416500 chr1A 73.275 1362 303 48 1160 2495 427041026 427039700 4.710000e-120 442
34 TraesCS5D01G416500 chr4B 85.294 272 21 11 1 254 34875119 34875389 3.930000e-66 263
35 TraesCS5D01G416500 chr4D 86.111 216 21 5 1 209 23074994 23075207 1.860000e-54 224
36 TraesCS5D01G416500 chr4D 85.321 218 24 5 1 211 505256326 505256542 8.640000e-53 219
37 TraesCS5D01G416500 chr6B 85.321 218 22 8 1 210 151201420 151201635 3.110000e-52 217


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 TraesCS5D01G416500 chr5D 478738345 478743467 5122 True 9461.000000 9461 100.000000 1 5123 1 chr5D.!!$R1 5122
1 TraesCS5D01G416500 chr5D 478700379 478703522 3143 True 1108.000000 1953 86.823000 1054 4165 3 chr5D.!!$R2 3111
2 TraesCS5D01G416500 chr5B 586712536 586716754 4218 True 1394.500000 2507 91.389500 1 4235 4 chr5B.!!$R1 4234
3 TraesCS5D01G416500 chr5B 586462942 586466086 3144 False 1366.000000 2320 92.245333 1072 4235 3 chr5B.!!$F1 3163
4 TraesCS5D01G416500 chr5B 586530538 586533062 2524 False 1263.000000 1753 84.667500 1064 4182 2 chr5B.!!$F2 3118
5 TraesCS5D01G416500 chr5A 597745860 597757488 11628 True 1385.166667 2172 89.898333 1 4235 6 chr5A.!!$R1 4234
6 TraesCS5D01G416500 chr7D 288474048 288474939 891 True 1591.000000 1591 98.879000 4234 5123 1 chr7D.!!$R1 889
7 TraesCS5D01G416500 chr7D 37515875 37516759 884 False 1550.000000 1550 98.305000 4237 5120 1 chr7D.!!$F1 883
8 TraesCS5D01G416500 chr3D 55082090 55082980 890 True 1589.000000 1589 98.878000 4235 5123 1 chr3D.!!$R1 888
9 TraesCS5D01G416500 chr3D 581078161 581079044 883 False 1585.000000 1585 98.985000 4235 5120 1 chr3D.!!$F2 885
10 TraesCS5D01G416500 chr3D 568853388 568854276 888 False 1544.000000 1544 97.982000 4230 5120 1 chr3D.!!$F1 890
11 TraesCS5D01G416500 chr1D 409586752 409587642 890 True 1589.000000 1589 98.878000 4234 5123 1 chr1D.!!$R3 889
12 TraesCS5D01G416500 chr1D 33586886 33587779 893 True 1544.000000 1544 97.875000 4232 5123 1 chr1D.!!$R1 891
13 TraesCS5D01G416500 chr6D 462872304 462873193 889 False 1561.000000 1561 98.316000 4231 5120 1 chr6D.!!$F1 889
14 TraesCS5D01G416500 chr6D 4956518 4957413 895 True 1548.000000 1548 97.882000 4229 5123 1 chr6D.!!$R1 894
15 TraesCS5D01G416500 chr6A 21150364 21151161 797 True 466.000000 466 77.491000 1125 1928 1 chr6A.!!$R1 803
16 TraesCS5D01G416500 chr1B 444864017 444865332 1315 True 453.000000 453 73.403000 1125 2446 1 chr1B.!!$R2 1321
17 TraesCS5D01G416500 chr1A 427039700 427041026 1326 True 442.000000 442 73.275000 1160 2495 1 chr1A.!!$R1 1335

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
726 1833 0.033781 TCACTGCCCAAAAATGCTGC 59.966 50.0 0.00 0.00 0.00 5.25 F
962 2094 0.036875 AAAGTACTGACTGGCCAGGC 59.963 55.0 35.42 34.37 38.44 4.85 F
2284 3515 1.092921 TGCGACCTTGCGAACTTGTT 61.093 50.0 0.00 0.00 37.81 2.83 F
3212 4519 0.813184 GTCGAAGGATACCACGGTGA 59.187 55.0 10.28 0.00 36.52 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2715 3957 0.031314 ATGCGTCTCTGTATCCAGCG 59.969 55.000 0.00 0.0 38.66 5.18 R
2959 4260 2.656947 TGCCTTTGTTGCTTCTAGGT 57.343 45.000 0.00 0.0 0.00 3.08 R
3798 5190 1.003839 CCCGCAACTGCACCTCTAA 60.004 57.895 2.12 0.0 42.21 2.10 R
5077 12360 2.101582 GCGTAGACTGATGGAGGTTCAT 59.898 50.000 0.00 0.0 0.00 2.57 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
27 28 9.524106 TGAAATACGTTGAAATACGATCTGTAT 57.476 29.630 0.00 4.91 45.81 2.29
70 72 6.410540 GCCTAGGAGGATTATCATGGTTAAG 58.589 44.000 14.75 0.00 37.67 1.85
79 81 6.944862 GGATTATCATGGTTAAGAAGCCTCAT 59.055 38.462 0.00 0.00 0.00 2.90
122 125 4.097741 CCCTCATTTCAATGTATTTCGCCA 59.902 41.667 0.00 0.00 37.65 5.69
223 234 3.723260 TGAATTTTTCAAAAGACGGCCC 58.277 40.909 0.00 0.00 36.59 5.80
235 246 4.113815 CGGCCCCATTGGAGCTCA 62.114 66.667 17.19 0.00 35.39 4.26
299 1393 5.119931 TCACTTTGTATTTGCGAGCAATT 57.880 34.783 11.53 10.46 35.70 2.32
320 1414 9.585099 GCAATTTCAAAATGTTGGAGTATATCA 57.415 29.630 0.00 0.00 35.29 2.15
442 1538 1.904287 TGGGTGGAAATACTGTGTGC 58.096 50.000 0.00 0.00 0.00 4.57
462 1558 9.008965 TGTGTGCTGTTTGTCATAAAATATAGT 57.991 29.630 0.00 0.00 0.00 2.12
463 1559 9.277565 GTGTGCTGTTTGTCATAAAATATAGTG 57.722 33.333 0.00 0.00 0.00 2.74
499 1601 0.612229 AGTGAGATGTGGGCTCTGTG 59.388 55.000 0.00 0.00 33.57 3.66
586 1689 2.154462 AGCCTCCAAAAATCTGACGTG 58.846 47.619 0.00 0.00 0.00 4.49
658 1765 5.095490 GCACGGGTTTTATTTCTGAGAATG 58.905 41.667 0.00 0.00 0.00 2.67
720 1827 4.098044 TGACGTATTTTCACTGCCCAAAAA 59.902 37.500 0.00 0.00 0.00 1.94
721 1828 5.208463 ACGTATTTTCACTGCCCAAAAAT 57.792 34.783 0.00 0.00 36.73 1.82
722 1829 4.987912 ACGTATTTTCACTGCCCAAAAATG 59.012 37.500 0.00 0.00 35.07 2.32
723 1830 4.143137 CGTATTTTCACTGCCCAAAAATGC 60.143 41.667 0.00 0.00 35.07 3.56
724 1831 3.557228 TTTTCACTGCCCAAAAATGCT 57.443 38.095 0.00 0.00 0.00 3.79
725 1832 2.529780 TTCACTGCCCAAAAATGCTG 57.470 45.000 0.00 0.00 0.00 4.41
726 1833 0.033781 TCACTGCCCAAAAATGCTGC 59.966 50.000 0.00 0.00 0.00 5.25
727 1834 0.249953 CACTGCCCAAAAATGCTGCA 60.250 50.000 4.13 4.13 0.00 4.41
728 1835 0.469070 ACTGCCCAAAAATGCTGCAA 59.531 45.000 6.36 0.00 0.00 4.08
729 1836 1.153353 CTGCCCAAAAATGCTGCAAG 58.847 50.000 6.36 0.00 0.00 4.01
811 1918 0.822164 ATCAAGCTTTGCATCAGCCC 59.178 50.000 13.47 0.00 41.13 5.19
814 1927 0.251474 AAGCTTTGCATCAGCCCAGA 60.251 50.000 13.47 0.00 41.13 3.86
839 1952 1.210234 CTGCCACCCATCACATCAGTA 59.790 52.381 0.00 0.00 0.00 2.74
861 1974 1.002011 GCCTCCTTGTCCTTGTCCC 60.002 63.158 0.00 0.00 0.00 4.46
924 2056 1.287730 CTGTCCTGTGCAAGCTCGTC 61.288 60.000 0.00 0.00 0.00 4.20
925 2057 2.029844 GTCCTGTGCAAGCTCGTCC 61.030 63.158 0.00 0.00 0.00 4.79
926 2058 2.210013 TCCTGTGCAAGCTCGTCCT 61.210 57.895 0.00 0.00 0.00 3.85
927 2059 1.739562 CCTGTGCAAGCTCGTCCTC 60.740 63.158 0.00 0.00 0.00 3.71
928 2060 1.739562 CTGTGCAAGCTCGTCCTCC 60.740 63.158 0.00 0.00 0.00 4.30
929 2061 2.811317 GTGCAAGCTCGTCCTCCG 60.811 66.667 0.00 0.00 38.13 4.63
960 2092 1.339151 GGGAAAGTACTGACTGGCCAG 60.339 57.143 31.60 31.60 35.52 4.85
961 2093 1.339151 GGAAAGTACTGACTGGCCAGG 60.339 57.143 35.42 20.74 38.44 4.45
962 2094 0.036875 AAAGTACTGACTGGCCAGGC 59.963 55.000 35.42 34.37 38.44 4.85
1012 2144 2.435586 CCTGCGGAGAAGCACCAG 60.436 66.667 5.10 0.00 42.92 4.00
1114 2273 1.443872 AATGTCCAGCGACGACGAC 60.444 57.895 12.29 2.46 42.37 4.34
1119 2278 4.477975 CAGCGACGACGACCTCCC 62.478 72.222 12.29 0.00 42.66 4.30
1399 2573 3.352648 GAAAATTGGGATCTTGGACGGA 58.647 45.455 0.00 0.00 0.00 4.69
1537 2711 2.821366 GAGGACATGGCCGTGCTG 60.821 66.667 25.30 8.82 37.74 4.41
1572 2746 4.603535 GGGCAGGCCAGTGTGGTT 62.604 66.667 13.10 0.00 40.46 3.67
2030 3237 2.360475 GCTTCCCGGAGCTTTGCT 60.360 61.111 0.73 0.00 43.88 3.91
2088 3310 1.675641 GGGCTGCCAAGTGGTACAG 60.676 63.158 22.05 0.20 41.80 2.74
2284 3515 1.092921 TGCGACCTTGCGAACTTGTT 61.093 50.000 0.00 0.00 37.81 2.83
2423 3654 3.012518 ACATACAAGATGCAGCCTGAAC 58.987 45.455 7.72 0.00 0.00 3.18
2715 3957 7.829378 ATAGTGTCATTCTAAAGACGGAAAC 57.171 36.000 0.00 0.00 37.58 2.78
2759 4003 6.429791 TTTTGAAAGATGACACGACAAAGA 57.570 33.333 0.00 0.00 0.00 2.52
2924 4174 2.939103 CCGGTCACCAAGAATGAGAATC 59.061 50.000 0.00 0.00 0.00 2.52
2959 4260 3.749064 GTCGAGGGTGCAGCGAGA 61.749 66.667 10.24 6.16 34.41 4.04
2960 4261 3.749064 TCGAGGGTGCAGCGAGAC 61.749 66.667 10.24 0.00 0.00 3.36
3043 4344 2.380084 TCTTGGCGATCAGTGGTAAC 57.620 50.000 0.00 0.00 0.00 2.50
3204 4511 2.164624 ACTGCAGTGAGTCGAAGGATAC 59.835 50.000 20.97 0.00 0.00 2.24
3207 4514 2.735762 GCAGTGAGTCGAAGGATACCAC 60.736 54.545 0.00 0.00 37.17 4.16
3212 4519 0.813184 GTCGAAGGATACCACGGTGA 59.187 55.000 10.28 0.00 36.52 4.02
3215 4522 2.094390 TCGAAGGATACCACGGTGAAAG 60.094 50.000 10.28 0.00 36.52 2.62
3218 4525 3.611766 AGGATACCACGGTGAAAGAAG 57.388 47.619 10.28 0.00 37.17 2.85
3230 4537 7.182761 CACGGTGAAAGAAGATTGTGATTATC 58.817 38.462 0.74 0.00 0.00 1.75
3260 4567 2.371841 ACTGTCCAAAGTGATAGCACCA 59.628 45.455 7.66 0.00 46.32 4.17
3288 4601 5.295152 ACAAGGACCAGTTAAAGTAACTCG 58.705 41.667 0.00 0.00 45.38 4.18
3404 4731 3.809905 AGGTGGACAGAGAAAACTCAAC 58.190 45.455 0.00 0.00 0.00 3.18
3405 4732 3.456277 AGGTGGACAGAGAAAACTCAACT 59.544 43.478 0.00 0.00 0.00 3.16
3406 4733 3.810386 GGTGGACAGAGAAAACTCAACTC 59.190 47.826 0.00 0.00 0.00 3.01
3407 4734 4.443598 GGTGGACAGAGAAAACTCAACTCT 60.444 45.833 0.00 0.00 40.94 3.24
3408 4735 5.119694 GTGGACAGAGAAAACTCAACTCTT 58.880 41.667 0.00 0.00 38.69 2.85
3409 4736 5.235401 GTGGACAGAGAAAACTCAACTCTTC 59.765 44.000 0.00 0.00 38.69 2.87
3410 4737 5.129485 TGGACAGAGAAAACTCAACTCTTCT 59.871 40.000 0.00 0.00 38.69 2.85
3411 4738 5.694458 GGACAGAGAAAACTCAACTCTTCTC 59.306 44.000 0.00 3.07 42.66 2.87
3412 4739 5.285651 ACAGAGAAAACTCAACTCTTCTCG 58.714 41.667 0.00 4.01 45.49 4.04
3522 4908 6.773200 ACTTTTCCTCTTCCTTTTTGTAGGAG 59.227 38.462 0.00 0.00 44.82 3.69
3542 4934 7.976135 AGGAGACAATGATGCATCTTATAAC 57.024 36.000 26.32 13.46 0.00 1.89
3657 5049 1.480137 AGGTCAGAGATTCAAGAGCCG 59.520 52.381 0.00 0.00 0.00 5.52
3798 5190 2.228138 TAAGAAACAAGTCGTGGCGT 57.772 45.000 0.00 0.00 0.00 5.68
3841 5246 5.548056 ACAGGAGAACCTAGGAAATTTGAGA 59.452 40.000 17.98 0.00 45.94 3.27
3972 5385 5.997746 AGCTAATTGTGAGTGCAGAAACTAA 59.002 36.000 0.00 0.00 30.49 2.24
3976 5389 2.878406 TGTGAGTGCAGAAACTAAAGCC 59.122 45.455 0.00 0.00 0.00 4.35
4082 5503 5.935789 TGCTAGTTTGTTTGGTGGTATAGAC 59.064 40.000 0.00 0.00 0.00 2.59
4210 5631 9.331282 GATTACCTCAGTTAGCTGTGATTTAAT 57.669 33.333 9.88 9.02 43.05 1.40
4211 5632 9.686683 ATTACCTCAGTTAGCTGTGATTTAATT 57.313 29.630 9.88 0.00 43.05 1.40
4917 8889 9.226606 TGTTAGAATAACCTGTTTATGGACAAG 57.773 33.333 0.00 0.00 30.21 3.16
5065 12348 0.762418 TCCAACACAACTGATCGGGT 59.238 50.000 6.47 0.00 0.00 5.28
5077 12360 3.513912 ACTGATCGGGTTGATGTTGTAGA 59.486 43.478 6.47 0.00 37.47 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 99 4.202050 GCGAAATACATTGAAATGAGGGCT 60.202 41.667 9.94 0.00 39.67 5.19
98 100 4.044426 GCGAAATACATTGAAATGAGGGC 58.956 43.478 9.94 1.58 39.67 5.19
199 204 6.106003 GGGCCGTCTTTTGAAAAATTCATAT 58.894 36.000 0.00 0.00 39.84 1.78
200 205 5.474825 GGGCCGTCTTTTGAAAAATTCATA 58.525 37.500 0.00 0.00 39.84 2.15
201 206 4.314961 GGGCCGTCTTTTGAAAAATTCAT 58.685 39.130 0.00 0.00 39.84 2.57
223 234 1.153005 GGAGGCTGAGCTCCAATGG 60.153 63.158 12.15 0.00 39.45 3.16
299 1393 9.625747 TGCTATGATATACTCCAACATTTTGAA 57.374 29.630 0.00 0.00 34.24 2.69
320 1414 6.963322 AGGTTACTTTCTTTCCTGATGCTAT 58.037 36.000 0.00 0.00 0.00 2.97
440 1536 8.574251 ACCACTATATTTTATGACAAACAGCA 57.426 30.769 0.00 0.00 0.00 4.41
442 1538 9.787532 CCAACCACTATATTTTATGACAAACAG 57.212 33.333 0.00 0.00 0.00 3.16
462 1558 2.811431 CACTCGCTTGTATTTCCAACCA 59.189 45.455 0.00 0.00 0.00 3.67
463 1559 3.071479 TCACTCGCTTGTATTTCCAACC 58.929 45.455 0.00 0.00 0.00 3.77
478 1580 0.179116 CAGAGCCCACATCTCACTCG 60.179 60.000 0.00 0.00 33.15 4.18
481 1583 0.610174 TCACAGAGCCCACATCTCAC 59.390 55.000 0.00 0.00 33.15 3.51
499 1601 7.437862 TGCAAAACTGAATAATTGGACACTTTC 59.562 33.333 0.00 0.00 0.00 2.62
648 1755 4.389374 GGAAAGGTGACACATTCTCAGAA 58.611 43.478 17.66 0.00 0.00 3.02
700 1807 4.143137 GCATTTTTGGGCAGTGAAAATACG 60.143 41.667 0.00 0.00 33.15 3.06
720 1827 1.306148 CATCGATGGTCTTGCAGCAT 58.694 50.000 17.96 0.00 46.34 3.79
721 1828 1.371337 GCATCGATGGTCTTGCAGCA 61.371 55.000 26.00 0.00 36.77 4.41
722 1829 1.354506 GCATCGATGGTCTTGCAGC 59.645 57.895 26.00 5.19 35.22 5.25
723 1830 0.376152 GTGCATCGATGGTCTTGCAG 59.624 55.000 26.00 0.00 44.99 4.41
724 1831 1.026182 GGTGCATCGATGGTCTTGCA 61.026 55.000 26.00 15.81 42.41 4.08
725 1832 1.026182 TGGTGCATCGATGGTCTTGC 61.026 55.000 26.00 13.24 35.67 4.01
726 1833 1.012086 CTGGTGCATCGATGGTCTTG 58.988 55.000 26.00 2.01 0.00 3.02
727 1834 0.904649 TCTGGTGCATCGATGGTCTT 59.095 50.000 26.00 0.00 0.00 3.01
728 1835 0.463204 CTCTGGTGCATCGATGGTCT 59.537 55.000 26.00 0.00 0.00 3.85
729 1836 0.461548 TCTCTGGTGCATCGATGGTC 59.538 55.000 26.00 11.45 0.00 4.02
798 1905 0.661552 CGATCTGGGCTGATGCAAAG 59.338 55.000 0.00 0.00 41.91 2.77
811 1918 0.531532 GATGGGTGGCAGACGATCTG 60.532 60.000 9.73 9.73 46.90 2.90
814 1927 1.221840 GTGATGGGTGGCAGACGAT 59.778 57.895 0.00 0.00 0.00 3.73
839 1952 2.529389 AAGGACAAGGAGGCGGGT 60.529 61.111 0.00 0.00 0.00 5.28
861 1974 3.779850 ATGCTATGCTGTGGGCGGG 62.780 63.158 0.00 0.00 45.43 6.13
868 1981 0.826256 CCATGCCCATGCTATGCTGT 60.826 55.000 2.75 0.00 37.49 4.40
929 2061 1.669999 TACTTTCCCTACGCGGAGGC 61.670 60.000 32.97 0.00 35.00 4.70
960 2092 3.430862 TGAATGCGCGTCTTGGCC 61.431 61.111 8.43 0.00 0.00 5.36
961 2093 2.187599 AAGTGAATGCGCGTCTTGGC 62.188 55.000 8.43 0.00 0.00 4.52
962 2094 0.238289 AAAGTGAATGCGCGTCTTGG 59.762 50.000 8.43 0.00 0.00 3.61
963 2095 1.595609 GAAAGTGAATGCGCGTCTTG 58.404 50.000 8.43 0.00 0.00 3.02
964 2096 0.517316 GGAAAGTGAATGCGCGTCTT 59.483 50.000 8.43 0.00 0.00 3.01
1012 2144 1.598130 GGCTGTGTGGAGTGGTCAC 60.598 63.158 0.00 0.00 35.82 3.67
1229 2391 3.564218 GGATGGCAGAGCGGGGAT 61.564 66.667 0.00 0.00 0.00 3.85
1564 2738 4.643387 GGGAGCCGCAACCACACT 62.643 66.667 8.50 0.00 0.00 3.55
2030 3237 1.191489 TCGTGGGAGTTGATGGCAGA 61.191 55.000 0.00 0.00 0.00 4.26
2170 3392 1.623311 TGTGGCAGAGCAAAGCTACTA 59.377 47.619 10.91 0.00 41.99 1.82
2297 3528 1.211969 GCGGACAGTACTGCTCGAA 59.788 57.895 30.09 0.00 38.89 3.71
2715 3957 0.031314 ATGCGTCTCTGTATCCAGCG 59.969 55.000 0.00 0.00 38.66 5.18
2718 3960 5.912892 TCAAAATATGCGTCTCTGTATCCA 58.087 37.500 0.00 0.00 0.00 3.41
2759 4003 5.845391 TCCTTCACGGTTTCTGAATTTTT 57.155 34.783 0.00 0.00 0.00 1.94
2959 4260 2.656947 TGCCTTTGTTGCTTCTAGGT 57.343 45.000 0.00 0.00 0.00 3.08
2960 4261 4.943705 TCTAATGCCTTTGTTGCTTCTAGG 59.056 41.667 0.00 0.00 0.00 3.02
3043 4344 7.280876 TCCTTTCTGAATATTTCATCCAACTCG 59.719 37.037 0.00 0.00 39.30 4.18
3204 4511 3.138304 TCACAATCTTCTTTCACCGTGG 58.862 45.455 0.00 0.00 0.00 4.94
3207 4514 7.307493 TGATAATCACAATCTTCTTTCACCG 57.693 36.000 0.00 0.00 0.00 4.94
3212 4519 7.833183 AGGAAGCTGATAATCACAATCTTCTTT 59.167 33.333 0.00 0.00 32.66 2.52
3215 4522 7.930865 AGTAGGAAGCTGATAATCACAATCTTC 59.069 37.037 0.00 0.00 0.00 2.87
3218 4525 6.989169 ACAGTAGGAAGCTGATAATCACAATC 59.011 38.462 0.00 0.00 37.40 2.67
3230 4537 3.070018 CACTTTGGACAGTAGGAAGCTG 58.930 50.000 0.00 0.00 39.67 4.24
3260 4567 5.568620 ACTTTAACTGGTCCTTGTCTGAT 57.431 39.130 0.00 0.00 0.00 2.90
3288 4601 7.812191 TCACATTAGTTTGAACATTAATGGCAC 59.188 33.333 19.37 10.30 37.66 5.01
3322 4636 6.916387 GTCTGCATTTCATCAATGTATCCTTG 59.084 38.462 0.00 0.00 43.95 3.61
3404 4731 6.980978 TGCTATTTCATTACCTTCGAGAAGAG 59.019 38.462 13.90 7.01 40.79 2.85
3405 4732 6.757010 GTGCTATTTCATTACCTTCGAGAAGA 59.243 38.462 13.90 0.00 40.79 2.87
3406 4733 6.535150 TGTGCTATTTCATTACCTTCGAGAAG 59.465 38.462 5.90 5.90 38.14 2.85
3407 4734 6.403049 TGTGCTATTTCATTACCTTCGAGAA 58.597 36.000 0.00 0.00 0.00 2.87
3408 4735 5.972935 TGTGCTATTTCATTACCTTCGAGA 58.027 37.500 0.00 0.00 0.00 4.04
3409 4736 6.479990 TCATGTGCTATTTCATTACCTTCGAG 59.520 38.462 0.00 0.00 0.00 4.04
3410 4737 6.345298 TCATGTGCTATTTCATTACCTTCGA 58.655 36.000 0.00 0.00 0.00 3.71
3411 4738 6.603237 TCATGTGCTATTTCATTACCTTCG 57.397 37.500 0.00 0.00 0.00 3.79
3412 4739 9.807649 ATTTTCATGTGCTATTTCATTACCTTC 57.192 29.630 0.00 0.00 0.00 3.46
3494 4880 9.734984 CCTACAAAAAGGAAGAGGAAAAGTATA 57.265 33.333 0.00 0.00 39.15 1.47
3522 4908 6.425114 AGACCGTTATAAGATGCATCATTGTC 59.575 38.462 27.81 19.07 0.00 3.18
3542 4934 7.926555 AGTTCATTATTTCCATGTACTAGACCG 59.073 37.037 0.00 0.00 32.29 4.79
3657 5049 3.874392 AATTACTTGACCTGCATTGGC 57.126 42.857 0.00 0.00 41.68 4.52
3766 5158 9.483062 CGACTTGTTTCTTAAGATGATCAATTC 57.517 33.333 5.89 11.08 0.00 2.17
3798 5190 1.003839 CCCGCAACTGCACCTCTAA 60.004 57.895 2.12 0.00 42.21 2.10
3972 5385 5.491439 AGTTTAAGGTAGGATGTAAGGGCTT 59.509 40.000 0.00 0.00 0.00 4.35
3976 5389 7.419711 TCAGAGTTTAAGGTAGGATGTAAGG 57.580 40.000 0.00 0.00 0.00 2.69
4043 5460 4.976540 ACTAGCAGTTATGTATTCCCCC 57.023 45.455 0.00 0.00 0.00 5.40
4082 5503 8.839947 TTAATGTGAAGATTGCATATCGTTTG 57.160 30.769 0.00 0.00 0.00 2.93
4210 5631 3.271729 TCAACTGTGAAGCACCGTTTAA 58.728 40.909 4.91 0.00 39.15 1.52
4211 5632 2.907634 TCAACTGTGAAGCACCGTTTA 58.092 42.857 4.91 0.00 39.15 2.01
4917 8889 7.475771 TTGAAAATCAAAGTGTTTATGTGGC 57.524 32.000 0.00 0.00 32.71 5.01
5065 12348 5.497464 TGGAGGTTCATCTACAACATCAA 57.503 39.130 0.33 0.00 36.49 2.57
5077 12360 2.101582 GCGTAGACTGATGGAGGTTCAT 59.898 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.