Multiple sequence alignment - TraesCS5D01G542000

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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 TraesCS5D01G542000 chr5D 100.000 3557 0 0 1 3557 552699847 552696291 0.000000e+00 6569
1 TraesCS5D01G542000 chr5D 89.941 169 6 4 3113 3274 552696576 552696412 1.290000e-49 207
2 TraesCS5D01G542000 chr5D 89.941 169 6 4 3272 3436 552696735 552696574 1.290000e-49 207
3 TraesCS5D01G542000 chr4A 92.207 3298 200 23 167 3436 615445241 615448509 0.000000e+00 4614
4 TraesCS5D01G542000 chr4A 77.280 1206 206 41 1392 2571 615970089 615971252 0.000000e+00 647
5 TraesCS5D01G542000 chr4A 91.328 369 20 6 3113 3469 615448341 615448709 8.870000e-136 494
6 TraesCS5D01G542000 chr4A 91.124 169 7 2 3113 3273 615448507 615448675 4.620000e-54 222
7 TraesCS5D01G542000 chr4A 83.333 210 26 6 507 712 615960676 615960880 6.060000e-43 185
8 TraesCS5D01G542000 chr4A 84.615 169 15 6 3269 3436 615448185 615448343 1.320000e-34 158
9 TraesCS5D01G542000 chr4A 96.471 85 3 0 3472 3556 615450082 615450166 1.330000e-29 141
10 TraesCS5D01G542000 chr4A 92.553 94 7 0 925 1018 615969222 615969315 6.190000e-28 135
11 TraesCS5D01G542000 chr5B 87.751 1641 148 23 1820 3436 697859925 697861536 0.000000e+00 1868
12 TraesCS5D01G542000 chr5B 90.969 1063 84 9 791 1849 697858855 697859909 0.000000e+00 1421
13 TraesCS5D01G542000 chr5B 93.888 769 39 2 1 761 697858090 697858858 0.000000e+00 1153
14 TraesCS5D01G542000 chr5B 92.123 457 24 4 3113 3557 697861368 697861824 5.010000e-178 634
15 TraesCS5D01G542000 chr5B 91.176 170 7 2 3113 3274 697861534 697861703 1.290000e-54 224
16 TraesCS5D01G542000 chr5B 90.625 160 14 1 3269 3427 697861213 697861372 1.000000e-50 211
17 TraesCS5D01G542000 chr5B 89.655 87 7 2 1078 1163 697859248 697859333 3.750000e-20 110


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 TraesCS5D01G542000 chr5D 552696291 552699847 3556 True 2327.666667 6569 93.294000 1 3557 3 chr5D.!!$R1 3556
1 TraesCS5D01G542000 chr4A 615445241 615450166 4925 False 1125.800000 4614 91.149000 167 3556 5 chr4A.!!$F2 3389
2 TraesCS5D01G542000 chr4A 615969222 615971252 2030 False 391.000000 647 84.916500 925 2571 2 chr4A.!!$F3 1646
3 TraesCS5D01G542000 chr5B 697858090 697861824 3734 False 803.000000 1868 90.883857 1 3557 7 chr5B.!!$F1 3556

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
762 774 1.488393 GACAAGGGCCAGATAAGCTCT 59.512 52.381 6.18 0.0 45.12 4.09 F
1375 1872 0.736325 AGACGGCGACTTTCCATTCG 60.736 55.000 16.62 0.0 38.31 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2580 0.340208 TCTCCCTCTCCCCTTTCCTC 59.660 60.0 0.0 0.0 0.00 3.71 R
2997 3586 0.813184 GGATGTGTGCCTGACAATGG 59.187 55.0 0.0 0.0 35.91 3.16 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
38 39 7.122501 GGAAAATAAATGGGAATGGTGCATTTT 59.877 33.333 0.00 0.00 33.90 1.82
58 59 8.850452 GCATTTTTGTAGCAAAGTTGATACTAC 58.150 33.333 17.54 9.58 46.91 2.73
61 62 8.630054 TTTTGTAGCAAAGTTGATACTACCAT 57.370 30.769 17.54 0.00 46.91 3.55
133 134 7.169813 CACTATAATTTGCTCTTGCTACATCGA 59.830 37.037 0.00 0.00 40.48 3.59
156 157 6.738200 CGACACTAGCTTTACAAAATGTCATG 59.262 38.462 0.00 0.00 35.95 3.07
248 249 4.522722 CCGGAGGCCTAAGTCTTAATAG 57.477 50.000 4.42 0.00 46.14 1.73
260 261 8.865001 CCTAAGTCTTAATAGATATTTCGCAGC 58.135 37.037 0.00 0.00 31.86 5.25
276 279 4.827692 TCGCAGCAAGTCCTAAAAGATTA 58.172 39.130 0.00 0.00 0.00 1.75
281 284 7.041780 CGCAGCAAGTCCTAAAAGATTATATGT 60.042 37.037 0.00 0.00 0.00 2.29
282 285 8.072567 GCAGCAAGTCCTAAAAGATTATATGTG 58.927 37.037 0.00 0.00 0.00 3.21
321 324 5.952526 TGTAGACGAACAAGACTGTCATA 57.047 39.130 10.88 0.00 33.45 2.15
392 400 2.037772 AGCCGTGGAGCTTATGGATTAG 59.962 50.000 12.85 0.00 41.41 1.73
444 452 5.126067 GGCCGATATGTTGCCTATCATTAT 58.874 41.667 0.00 0.00 42.01 1.28
447 455 6.761242 GCCGATATGTTGCCTATCATTATGTA 59.239 38.462 0.00 0.00 0.00 2.29
545 553 3.135994 CTCTTCTCTACCGACTCCTAGC 58.864 54.545 0.00 0.00 0.00 3.42
641 653 2.808543 CTCCTTACTGGCAGTGTTGTTC 59.191 50.000 29.65 0.00 35.26 3.18
665 677 4.407818 CGCGTGATTTGCTTTGGTATTTA 58.592 39.130 0.00 0.00 0.00 1.40
666 678 4.854291 CGCGTGATTTGCTTTGGTATTTAA 59.146 37.500 0.00 0.00 0.00 1.52
669 681 6.183359 GCGTGATTTGCTTTGGTATTTAACTG 60.183 38.462 0.00 0.00 0.00 3.16
762 774 1.488393 GACAAGGGCCAGATAAGCTCT 59.512 52.381 6.18 0.00 45.12 4.09
785 797 4.155826 TGTTTATCATCGTCAAGCAAAGGG 59.844 41.667 0.00 0.00 0.00 3.95
794 806 2.485814 GTCAAGCAAAGGGTAAGAGCTG 59.514 50.000 0.00 0.00 35.42 4.24
866 878 7.991736 TCTTTTATGATTTTCGCTTTTTGTCG 58.008 30.769 0.00 0.00 0.00 4.35
913 926 8.735692 AATGGAGTTTGACAAAATGAAACATT 57.264 26.923 5.47 8.08 32.96 2.71
1025 1038 2.746279 AGCAGCCTAGCTCTCTCTAA 57.254 50.000 0.00 0.00 42.18 2.10
1026 1039 3.243359 AGCAGCCTAGCTCTCTCTAAT 57.757 47.619 0.00 0.00 42.18 1.73
1034 1047 7.779798 CAGCCTAGCTCTCTCTAATTATATCCT 59.220 40.741 0.00 0.00 36.40 3.24
1185 1675 8.725148 AGTTACATGTCAATTTCTCTGATGAAC 58.275 33.333 0.00 0.00 0.00 3.18
1193 1683 7.857885 GTCAATTTCTCTGATGAACGAAACTTT 59.142 33.333 0.00 0.00 0.00 2.66
1201 1691 9.746711 CTCTGATGAACGAAACTTTATTAAGTG 57.253 33.333 0.00 0.00 43.74 3.16
1221 1711 6.293004 AGTGTCCAGTTTTGAAAATCCAAA 57.707 33.333 0.00 0.00 34.56 3.28
1297 1794 7.716799 AATTTGTCTGCTGGGTGATTATAAA 57.283 32.000 0.00 0.00 0.00 1.40
1304 1801 7.816995 GTCTGCTGGGTGATTATAAATCTCTAG 59.183 40.741 1.70 0.00 0.00 2.43
1307 1804 6.037786 TGGGTGATTATAAATCTCTAGGCG 57.962 41.667 1.70 0.00 0.00 5.52
1323 1820 3.757745 AGGCGTACATAATTGCACAAC 57.242 42.857 0.00 0.00 0.00 3.32
1335 1832 8.476447 ACATAATTGCACAACCATTGATCATTA 58.524 29.630 0.00 0.00 0.00 1.90
1339 1836 9.887629 AATTGCACAACCATTGATCATTATTTA 57.112 25.926 0.00 0.00 0.00 1.40
1341 1838 9.887629 TTGCACAACCATTGATCATTATTTATT 57.112 25.926 0.00 0.00 0.00 1.40
1342 1839 9.887629 TGCACAACCATTGATCATTATTTATTT 57.112 25.926 0.00 0.00 0.00 1.40
1375 1872 0.736325 AGACGGCGACTTTCCATTCG 60.736 55.000 16.62 0.00 38.31 3.34
1388 1903 5.409826 ACTTTCCATTCGATGTTCTGACTTC 59.590 40.000 0.00 0.00 0.00 3.01
1389 1904 3.861840 TCCATTCGATGTTCTGACTTCC 58.138 45.455 0.00 0.00 0.00 3.46
1390 1905 2.939103 CCATTCGATGTTCTGACTTCCC 59.061 50.000 0.00 0.00 0.00 3.97
1569 2084 5.054477 GCAGGTATCACTTTAATAAGCGGA 58.946 41.667 0.00 0.00 34.60 5.54
1629 2144 2.623535 CCGAACATGGGTAACATCGAA 58.376 47.619 0.00 0.00 37.84 3.71
1814 2329 3.606687 GAAATGGTGACCCGTATTCACT 58.393 45.455 0.00 0.00 42.63 3.41
1816 2331 1.344065 TGGTGACCCGTATTCACTGT 58.656 50.000 0.00 0.00 42.63 3.55
1873 2433 2.264480 CGGGCGTCACTGGAATCA 59.736 61.111 0.00 0.00 0.00 2.57
1971 2531 1.807139 TCAGCTTCATAGTTTGCGCA 58.193 45.000 5.66 5.66 0.00 6.09
2148 2708 0.255318 CTCCAGCCCTGATGCTCTTT 59.745 55.000 0.00 0.00 40.32 2.52
2151 2711 0.680280 CAGCCCTGATGCTCTTTGCT 60.680 55.000 0.00 0.00 40.32 3.91
2311 2889 3.394674 TCTTGGCTGTGTCGATAACAA 57.605 42.857 5.54 0.00 40.31 2.83
2329 2907 0.534203 AACCATCCGCAACACTTCGT 60.534 50.000 0.00 0.00 0.00 3.85
2364 2942 5.381757 ACCAGTTGTTTCCTACTATTTGCA 58.618 37.500 0.00 0.00 0.00 4.08
2389 2967 2.037902 TCGGCTATTGTGTTTGGTCTCA 59.962 45.455 0.00 0.00 0.00 3.27
2423 3001 3.099905 TGTCACAGACCCAGATAAGGAG 58.900 50.000 0.00 0.00 0.00 3.69
2448 3029 0.254462 TGGCCCATCGTGCTTTATCA 59.746 50.000 0.00 0.00 0.00 2.15
2490 3071 2.620112 CCTGGCTTCCTTGTGCACG 61.620 63.158 13.13 0.00 0.00 5.34
2542 3123 1.077787 CTAGCAATGGCCGGGACAA 60.078 57.895 6.69 0.00 42.56 3.18
2546 3127 2.282887 AATGGCCGGGACAACCAC 60.283 61.111 6.69 0.00 40.22 4.16
2549 3130 3.948719 GGCCGGGACAACCACAGA 61.949 66.667 2.18 0.00 40.22 3.41
2577 3158 3.981071 TGCCAAGTAGTGAAGCACTAT 57.019 42.857 10.15 0.00 46.56 2.12
2594 3175 7.181862 AAGCACTATGTGTGATATTTCCTCCG 61.182 42.308 5.08 0.00 45.46 4.63
2626 3207 3.740397 TTGCACCTGCGCTCATGC 61.740 61.111 19.17 19.17 45.83 4.06
2707 3295 6.025896 GCATACGATCAATTGGCTATCATTG 58.974 40.000 5.42 0.00 0.00 2.82
2744 3332 3.381045 TGTCACATTCGTGTCTGACTTC 58.619 45.455 9.51 1.84 44.02 3.01
2748 3336 2.102420 ACATTCGTGTCTGACTTCCACA 59.898 45.455 9.51 0.00 0.00 4.17
2756 3344 3.584406 TGTCTGACTTCCACATCTCCAAT 59.416 43.478 9.51 0.00 0.00 3.16
2781 3369 6.417191 TTTTACATGCTTCTTCGTACATCC 57.583 37.500 0.00 0.00 0.00 3.51
2783 3371 3.262420 ACATGCTTCTTCGTACATCCAC 58.738 45.455 0.00 0.00 0.00 4.02
2788 3376 3.323243 CTTCTTCGTACATCCACGGTTT 58.677 45.455 0.00 0.00 42.19 3.27
2795 3383 4.082081 TCGTACATCCACGGTTTCTATGTT 60.082 41.667 0.00 0.00 42.19 2.71
2855 3444 4.866486 GTCTTATTTGGATTGCTTGCAAGG 59.134 41.667 27.10 9.80 36.96 3.61
2899 3488 6.494952 TCAGGCCCCAATACAATTTACTTAA 58.505 36.000 0.00 0.00 0.00 1.85
2958 3547 6.074195 CCATGGCGCTAATAATGAATTTTGTG 60.074 38.462 7.64 0.00 0.00 3.33
2961 3550 6.529829 TGGCGCTAATAATGAATTTTGTGTTC 59.470 34.615 7.64 0.00 0.00 3.18
2962 3551 6.751888 GGCGCTAATAATGAATTTTGTGTTCT 59.248 34.615 7.64 0.00 0.00 3.01
2997 3586 1.623811 TGAAACTCCAGGCCTCTACAC 59.376 52.381 0.00 0.00 0.00 2.90
3027 3616 6.919662 GTCAGGCACACATCCATATTTTATTG 59.080 38.462 0.00 0.00 0.00 1.90
3066 3655 3.791245 TGAGGCCAAAAACATCAACAAC 58.209 40.909 5.01 0.00 0.00 3.32
3078 3667 8.458573 AAAACATCAACAACCAGAGTACATAA 57.541 30.769 0.00 0.00 0.00 1.90
3079 3668 7.435068 AACATCAACAACCAGAGTACATAAC 57.565 36.000 0.00 0.00 0.00 1.89
3080 3669 6.530120 ACATCAACAACCAGAGTACATAACA 58.470 36.000 0.00 0.00 0.00 2.41
3081 3670 6.995686 ACATCAACAACCAGAGTACATAACAA 59.004 34.615 0.00 0.00 0.00 2.83
3110 3699 6.115446 ACATAGTCAATCACATTCGAACCAT 58.885 36.000 0.00 0.00 0.00 3.55
3123 3712 6.255020 ACATTCGAACCATTACAAGATACGAC 59.745 38.462 0.00 0.00 0.00 4.34
3128 3717 3.191669 CCATTACAAGATACGACGCCAA 58.808 45.455 0.00 0.00 0.00 4.52
3149 3738 6.675728 GCCAACGATTAAGTCTGATTTCTTCC 60.676 42.308 0.00 0.00 0.00 3.46
3152 3741 4.317418 CGATTAAGTCTGATTTCTTCCGCG 60.317 45.833 0.00 0.00 0.00 6.46
3196 3955 2.511600 CCCTCGCCATCCACGTTC 60.512 66.667 0.00 0.00 0.00 3.95
3253 4012 2.073816 CGATACCAACCAGTGAACACC 58.926 52.381 1.11 0.00 0.00 4.16
3284 4043 5.106436 ACATGTAGACAACAAGATACGACGA 60.106 40.000 0.00 0.00 42.70 4.20
3289 4048 2.722629 ACAACAAGATACGACGACAACG 59.277 45.455 0.00 0.00 45.75 4.10
3340 4102 4.017591 TCCAAGAAGGAATAAATGCCCTCA 60.018 41.667 0.00 0.00 45.65 3.86
3356 4118 1.182667 CTCACCTCACCGTATCCACA 58.817 55.000 0.00 0.00 0.00 4.17
3409 4173 4.400251 CCTAGTTGTCGATACCAACCAGTA 59.600 45.833 12.31 0.99 42.46 2.74
3469 4233 7.348080 AGGAGATGATACAAGTTCGTCATTA 57.652 36.000 0.00 0.00 31.86 1.90
3470 4234 7.203910 AGGAGATGATACAAGTTCGTCATTAC 58.796 38.462 0.00 0.00 31.86 1.89
3473 4237 9.900710 GAGATGATACAAGTTCGTCATTACTAT 57.099 33.333 0.00 0.00 31.86 2.12
3521 5655 3.496331 AGTTTTCACCCGGACATGAAAT 58.504 40.909 21.61 10.75 42.72 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.673514 CACCATTCCCATTTATTTTCCAGG 58.326 41.667 0.00 0.00 0.00 4.45
11 12 4.533707 TGCACCATTCCCATTTATTTTCCA 59.466 37.500 0.00 0.00 0.00 3.53
13 14 7.628769 AAATGCACCATTCCCATTTATTTTC 57.371 32.000 0.00 0.00 37.40 2.29
38 39 7.880713 TCAATGGTAGTATCAACTTTGCTACAA 59.119 33.333 5.92 0.00 37.15 2.41
133 134 7.510549 ACATGACATTTTGTAAAGCTAGTGT 57.489 32.000 0.00 0.00 0.00 3.55
185 186 5.825593 AAGAGTAACTTGGGACATCTTGA 57.174 39.130 0.00 0.00 39.30 3.02
239 240 8.077836 ACTTGCTGCGAAATATCTATTAAGAC 57.922 34.615 0.00 0.00 33.57 3.01
241 242 7.386299 AGGACTTGCTGCGAAATATCTATTAAG 59.614 37.037 0.00 0.00 0.00 1.85
248 249 5.734855 TTTAGGACTTGCTGCGAAATATC 57.265 39.130 0.00 0.00 0.00 1.63
281 284 4.832823 TCTACAAGAGATGGAGACAACACA 59.167 41.667 0.00 0.00 44.42 3.72
282 285 5.392767 TCTACAAGAGATGGAGACAACAC 57.607 43.478 0.00 0.00 44.42 3.32
321 324 0.228742 CGCGCGCGTGAATAAAGTAT 59.771 50.000 42.49 0.00 34.35 2.12
479 487 8.976353 TCATTTTATTTTTGCTTAGCCAGGATA 58.024 29.630 0.29 0.00 0.00 2.59
545 553 0.382515 GTAGAGCGCACTGACCCTAG 59.617 60.000 18.10 0.00 0.00 3.02
641 653 1.444212 CCAAAGCAAATCACGCGGG 60.444 57.895 12.47 6.51 0.00 6.13
665 677 2.936202 ACACAGGTGCATTCTTCAGTT 58.064 42.857 0.00 0.00 0.00 3.16
666 678 2.645838 ACACAGGTGCATTCTTCAGT 57.354 45.000 0.00 0.00 0.00 3.41
669 681 3.854784 GCTTGAACACAGGTGCATTCTTC 60.855 47.826 0.00 0.00 30.89 2.87
762 774 4.155826 CCCTTTGCTTGACGATGATAAACA 59.844 41.667 0.00 0.00 0.00 2.83
766 778 3.627395 ACCCTTTGCTTGACGATGATA 57.373 42.857 0.00 0.00 0.00 2.15
768 780 3.007506 TCTTACCCTTTGCTTGACGATGA 59.992 43.478 0.00 0.00 0.00 2.92
785 797 4.349501 AGATAAACGTACGCAGCTCTTAC 58.650 43.478 16.72 0.00 0.00 2.34
794 806 1.591619 GAGGCCAAGATAAACGTACGC 59.408 52.381 16.72 0.00 0.00 4.42
911 924 7.713073 GCTTAAGTTCCTGTAGAAGCAGATAAT 59.287 37.037 4.02 0.00 39.24 1.28
913 926 6.154534 TGCTTAAGTTCCTGTAGAAGCAGATA 59.845 38.462 4.02 0.00 43.08 1.98
1025 1038 3.821033 GCCGCCTGTTCAAAGGATATAAT 59.179 43.478 0.00 0.00 40.02 1.28
1026 1039 3.211045 GCCGCCTGTTCAAAGGATATAA 58.789 45.455 0.00 0.00 40.02 0.98
1034 1047 3.275617 AGTATATGCCGCCTGTTCAAA 57.724 42.857 0.00 0.00 0.00 2.69
1185 1675 8.953990 CAAAACTGGACACTTAATAAAGTTTCG 58.046 33.333 0.00 0.00 43.60 3.46
1193 1683 9.137459 TGGATTTTCAAAACTGGACACTTAATA 57.863 29.630 0.00 0.00 0.00 0.98
1201 1691 7.609760 AAAGTTTGGATTTTCAAAACTGGAC 57.390 32.000 10.06 0.00 38.21 4.02
1297 1794 5.221441 TGTGCAATTATGTACGCCTAGAGAT 60.221 40.000 0.00 0.00 44.20 2.75
1304 1801 2.162608 TGGTTGTGCAATTATGTACGCC 59.837 45.455 0.00 0.00 44.20 5.68
1307 1804 7.257003 TGATCAATGGTTGTGCAATTATGTAC 58.743 34.615 0.00 0.00 41.92 2.90
1343 1840 9.712359 GAAAGTCGCCGTCTAAATTATTATTTT 57.288 29.630 0.00 0.00 35.61 1.82
1347 1844 6.339730 TGGAAAGTCGCCGTCTAAATTATTA 58.660 36.000 0.00 0.00 0.00 0.98
1350 1847 4.191033 TGGAAAGTCGCCGTCTAAATTA 57.809 40.909 0.00 0.00 0.00 1.40
1354 1851 2.613691 GAATGGAAAGTCGCCGTCTAA 58.386 47.619 0.00 0.00 0.00 2.10
1359 1856 0.301687 CATCGAATGGAAAGTCGCCG 59.698 55.000 0.00 0.00 37.19 6.46
1388 1903 5.300792 TCAGCGGCCTAAATAAAATAAAGGG 59.699 40.000 0.00 0.00 0.00 3.95
1389 1904 6.385649 TCAGCGGCCTAAATAAAATAAAGG 57.614 37.500 0.00 0.00 0.00 3.11
1390 1905 7.432252 CAGTTCAGCGGCCTAAATAAAATAAAG 59.568 37.037 0.00 0.00 0.00 1.85
1480 1995 0.318441 TCGACCTTGTCAAGAGCCAG 59.682 55.000 14.42 0.00 32.09 4.85
1814 2329 3.169908 TCCAGTACCTTGTGCAGATACA 58.830 45.455 0.00 0.00 0.00 2.29
1816 2331 4.030216 TCATCCAGTACCTTGTGCAGATA 58.970 43.478 0.00 0.00 0.00 1.98
1873 2433 1.713078 ACCTTCAAGCCCCAGAAAGAT 59.287 47.619 0.00 0.00 0.00 2.40
1971 2531 1.985473 ACATCATGCACACACCAAGT 58.015 45.000 0.00 0.00 0.00 3.16
2020 2580 0.340208 TCTCCCTCTCCCCTTTCCTC 59.660 60.000 0.00 0.00 0.00 3.71
2101 2661 5.278907 CCATGAGCTTAAACATGACAACCAA 60.279 40.000 13.26 0.00 44.28 3.67
2148 2708 4.588951 ACGATTATCAATACTGGAGGAGCA 59.411 41.667 0.00 0.00 0.00 4.26
2151 2711 5.067954 TCGACGATTATCAATACTGGAGGA 58.932 41.667 0.00 0.00 0.00 3.71
2311 2889 1.070786 ACGAAGTGTTGCGGATGGT 59.929 52.632 0.00 0.00 42.51 3.55
2329 2907 1.133823 ACAACTGGTCAACATGCTGGA 60.134 47.619 0.00 0.00 0.00 3.86
2389 2967 0.837691 TGTGACAGGAGCCTCCATGT 60.838 55.000 14.46 13.89 39.61 3.21
2448 3029 2.617532 GGCAGAGGAAGCAACAAGATCT 60.618 50.000 0.00 0.00 0.00 2.75
2490 3071 5.052172 CGTAGCAATTACAATGCAGAAATGC 60.052 40.000 0.00 0.00 46.22 3.56
2542 3123 3.642848 ACTTGGCATCATTTTTCTGTGGT 59.357 39.130 0.00 0.00 0.00 4.16
2546 3127 6.258230 TCACTACTTGGCATCATTTTTCTG 57.742 37.500 0.00 0.00 0.00 3.02
2549 3130 5.010922 TGCTTCACTACTTGGCATCATTTTT 59.989 36.000 0.00 0.00 0.00 1.94
2577 3158 4.545208 TTGTCGGAGGAAATATCACACA 57.455 40.909 0.00 0.00 0.00 3.72
2594 3175 5.276820 GCAGGTGCAACTAACAAATTTTGTC 60.277 40.000 14.80 2.84 41.40 3.18
2626 3207 8.581057 AGATATAGAACAAACATGTTAGAGCG 57.419 34.615 12.39 1.22 31.35 5.03
2673 3261 8.386606 GCCAATTGATCGTATGCATTTTAAAAA 58.613 29.630 3.54 0.00 0.00 1.94
2676 3264 6.804677 AGCCAATTGATCGTATGCATTTTAA 58.195 32.000 3.54 0.00 0.00 1.52
2678 3266 5.266733 AGCCAATTGATCGTATGCATTTT 57.733 34.783 3.54 0.00 0.00 1.82
2683 3271 5.808042 ATGATAGCCAATTGATCGTATGC 57.192 39.130 7.12 0.00 0.00 3.14
2689 3277 6.989659 ACCATTCAATGATAGCCAATTGATC 58.010 36.000 7.12 2.80 33.66 2.92
2692 3280 6.401047 AGACCATTCAATGATAGCCAATTG 57.599 37.500 0.00 0.00 0.00 2.32
2694 3282 5.537674 GGAAGACCATTCAATGATAGCCAAT 59.462 40.000 0.00 0.00 35.97 3.16
2707 3295 4.326826 TGTGACAGATTGGAAGACCATTC 58.673 43.478 0.00 0.00 46.34 2.67
2770 3358 2.955614 AGAAACCGTGGATGTACGAAG 58.044 47.619 0.00 0.00 46.46 3.79
2774 3362 6.423001 GGATAACATAGAAACCGTGGATGTAC 59.577 42.308 0.00 0.00 30.69 2.90
2779 3367 4.678574 CGTGGATAACATAGAAACCGTGGA 60.679 45.833 0.00 0.00 0.00 4.02
2781 3369 4.426416 TCGTGGATAACATAGAAACCGTG 58.574 43.478 0.00 0.00 0.00 4.94
2783 3371 5.522460 ACATTCGTGGATAACATAGAAACCG 59.478 40.000 0.00 0.00 34.11 4.44
2795 3383 7.876068 GGATGGATTAGTTTACATTCGTGGATA 59.124 37.037 0.00 0.00 0.00 2.59
2816 3405 8.850156 CCAAATAAGACTTACATTTAGGGATGG 58.150 37.037 0.00 0.00 0.00 3.51
2837 3426 1.348366 TGCCTTGCAAGCAATCCAAAT 59.652 42.857 21.43 0.00 37.28 2.32
2848 3437 5.337578 ACTTAAGAAAGTTTGCCTTGCAA 57.662 34.783 10.09 0.00 43.60 4.08
2914 3503 9.554724 CGCCATGGATGTAAATTATGTTTATAC 57.445 33.333 18.40 0.00 0.00 1.47
2938 3527 7.740519 AGAACACAAAATTCATTATTAGCGC 57.259 32.000 0.00 0.00 0.00 5.92
2979 3568 0.984995 GGTGTAGAGGCCTGGAGTTT 59.015 55.000 12.00 0.00 0.00 2.66
2997 3586 0.813184 GGATGTGTGCCTGACAATGG 59.187 55.000 0.00 0.00 35.91 3.16
3027 3616 4.035675 GCCTCATTGCCTTACATCAACTAC 59.964 45.833 0.00 0.00 0.00 2.73
3045 3634 3.431486 GGTTGTTGATGTTTTTGGCCTCA 60.431 43.478 3.32 0.00 0.00 3.86
3091 3680 6.176975 TGTAATGGTTCGAATGTGATTGAC 57.823 37.500 0.00 0.00 0.00 3.18
3110 3699 2.095314 TCGTTGGCGTCGTATCTTGTAA 60.095 45.455 0.00 0.00 39.49 2.41
3123 3712 4.330074 AGAAATCAGACTTAATCGTTGGCG 59.670 41.667 0.00 0.00 39.92 5.69
3128 3717 4.567159 GCGGAAGAAATCAGACTTAATCGT 59.433 41.667 0.00 0.00 0.00 3.73
3149 3738 0.934496 TTCTTGGAGTTGTTGTCGCG 59.066 50.000 0.00 0.00 0.00 5.87
3196 3955 5.730296 AATCCTTGTCTAGGTCATATCCG 57.270 43.478 0.00 0.00 45.03 4.18
3231 3990 2.735134 GTGTTCACTGGTTGGTATCGAC 59.265 50.000 0.00 0.00 0.00 4.20
3253 4012 4.273235 TCTTGTTGTCTACATGTTGTGCTG 59.727 41.667 2.30 0.00 36.44 4.41
3284 4043 6.934645 TGGAAGAAATCAGACTTAATCGTTGT 59.065 34.615 0.00 0.00 0.00 3.32
3289 4048 8.099364 TGTTGTGGAAGAAATCAGACTTAATC 57.901 34.615 0.00 0.00 0.00 1.75
3340 4102 1.136305 CGAATGTGGATACGGTGAGGT 59.864 52.381 0.00 0.00 42.51 3.85
3356 4118 3.967326 TCCTTGTCTGGTCATATCCGAAT 59.033 43.478 0.00 0.00 0.00 3.34
3409 4173 1.204467 CCACTTGTTGTGCTGGTGTTT 59.796 47.619 0.00 0.00 44.92 2.83
3428 4192 3.882888 TCTCCTTGTTGAATGTGTTGTCC 59.117 43.478 0.00 0.00 0.00 4.02
3469 4233 4.655963 AGCATTTATTGATCGGGCATAGT 58.344 39.130 0.00 0.00 0.00 2.12
3470 4234 5.295292 CCTAGCATTTATTGATCGGGCATAG 59.705 44.000 0.00 0.00 0.00 2.23
3473 4237 3.072330 TCCTAGCATTTATTGATCGGGCA 59.928 43.478 0.00 0.00 27.99 5.36


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

AutoCloner maintained by Alex Coulton.