Multiple sequence alignment - TraesCS5D01G093800

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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 TraesCS5D01G093800 chr5D 100.000 3305 0 0 1 3305 103177547 103174243 0.000000e+00 6104.0
1 TraesCS5D01G093800 chr5B 91.918 2747 98 41 1 2708 112196245 112193584 0.000000e+00 3729.0
2 TraesCS5D01G093800 chr5B 92.167 383 17 6 2931 3305 112193173 112192796 2.260000e-146 529.0
3 TraesCS5D01G093800 chr5B 85.388 219 29 2 1545 1763 660589477 660589692 1.190000e-54 224.0
4 TraesCS5D01G093800 chr5B 95.200 125 6 0 2764 2888 112193284 112193160 7.230000e-47 198.0
5 TraesCS5D01G093800 chr5B 100.000 45 0 0 2888 2932 64270267 64270311 2.110000e-12 84.2
6 TraesCS5D01G093800 chr5A 92.785 2564 88 29 1 2548 95867686 95870168 0.000000e+00 3620.0
7 TraesCS5D01G093800 chr5A 88.215 297 28 6 3004 3298 95870579 95870870 6.790000e-92 348.0
8 TraesCS5D01G093800 chr1B 87.281 228 26 2 1548 1775 24933086 24932862 1.180000e-64 257.0
9 TraesCS5D01G093800 chr1A 87.281 228 26 2 1548 1775 18461762 18461538 1.180000e-64 257.0
10 TraesCS5D01G093800 chr1A 100.000 45 0 0 2888 2932 481671032 481671076 2.110000e-12 84.2
11 TraesCS5D01G093800 chr1D 85.965 228 29 2 1548 1775 17169108 17168884 1.190000e-59 241.0
12 TraesCS5D01G093800 chr1D 92.593 54 4 0 2888 2941 207834897 207834844 9.830000e-11 78.7
13 TraesCS5D01G093800 chr3B 85.714 224 29 2 1548 1771 828111448 828111668 1.980000e-57 233.0
14 TraesCS5D01G093800 chr3D 85.268 224 30 2 1548 1771 610544048 610544268 9.230000e-56 228.0
15 TraesCS5D01G093800 chr3A 84.821 224 31 2 1548 1771 744879518 744879738 4.290000e-54 222.0
16 TraesCS5D01G093800 chr7B 98.000 50 0 1 2889 2938 125009658 125009706 5.880000e-13 86.1
17 TraesCS5D01G093800 chr7A 100.000 45 0 0 2888 2932 530506467 530506423 2.110000e-12 84.2
18 TraesCS5D01G093800 chr4A 100.000 45 0 0 2888 2932 656836004 656836048 2.110000e-12 84.2
19 TraesCS5D01G093800 chr2D 100.000 45 0 0 2888 2932 123988215 123988171 2.110000e-12 84.2
20 TraesCS5D01G093800 chr2D 100.000 45 0 0 2888 2932 586497962 586498006 2.110000e-12 84.2
21 TraesCS5D01G093800 chr2D 100.000 45 0 0 2888 2932 644537733 644537689 2.110000e-12 84.2


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 TraesCS5D01G093800 chr5D 103174243 103177547 3304 True 6104.000000 6104 100.000 1 3305 1 chr5D.!!$R1 3304
1 TraesCS5D01G093800 chr5B 112192796 112196245 3449 True 1485.333333 3729 93.095 1 3305 3 chr5B.!!$R1 3304
2 TraesCS5D01G093800 chr5A 95867686 95870870 3184 False 1984.000000 3620 90.500 1 3298 2 chr5A.!!$F1 3297

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
406 416 0.107508 ACCCACAGGCGAATCTGATG 60.108 55.0 7.65 3.47 38.11 3.07 F
1320 1353 0.510359 GCCTCTAATTCGCGCAGATG 59.490 55.0 8.75 0.03 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1875 0.041386 AGGTAGAGGTGGTGGAGGAC 59.959 60.0 0.0 0.0 0.0 3.85 R
2980 3287 0.107017 CACATCAACCTAGCCCCCAG 60.107 60.0 0.0 0.0 0.0 4.45 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
157 166 1.321474 CCAAGTGGATGTGCTTGTGT 58.679 50.000 0.00 0.00 40.13 3.72
283 293 1.596752 GCACACCATGGTCACGTCA 60.597 57.895 16.53 0.00 0.00 4.35
284 294 1.163420 GCACACCATGGTCACGTCAA 61.163 55.000 16.53 0.00 0.00 3.18
285 295 1.304254 CACACCATGGTCACGTCAAA 58.696 50.000 16.53 0.00 0.00 2.69
286 296 1.002900 CACACCATGGTCACGTCAAAC 60.003 52.381 16.53 0.00 0.00 2.93
287 297 0.591170 CACCATGGTCACGTCAAACC 59.409 55.000 16.53 4.67 36.03 3.27
292 302 1.096416 TGGTCACGTCAAACCAAACC 58.904 50.000 10.69 0.00 42.48 3.27
293 303 1.340211 TGGTCACGTCAAACCAAACCT 60.340 47.619 10.69 0.00 42.48 3.50
294 304 1.064952 GGTCACGTCAAACCAAACCTG 59.935 52.381 6.44 0.00 35.53 4.00
295 305 1.741145 GTCACGTCAAACCAAACCTGT 59.259 47.619 0.00 0.00 0.00 4.00
296 306 2.011222 TCACGTCAAACCAAACCTGTC 58.989 47.619 0.00 0.00 0.00 3.51
297 307 1.064952 CACGTCAAACCAAACCTGTCC 59.935 52.381 0.00 0.00 0.00 4.02
298 308 0.666374 CGTCAAACCAAACCTGTCCC 59.334 55.000 0.00 0.00 0.00 4.46
299 309 1.749286 CGTCAAACCAAACCTGTCCCT 60.749 52.381 0.00 0.00 0.00 4.20
300 310 2.384828 GTCAAACCAAACCTGTCCCTT 58.615 47.619 0.00 0.00 0.00 3.95
301 311 3.558033 GTCAAACCAAACCTGTCCCTTA 58.442 45.455 0.00 0.00 0.00 2.69
302 312 3.955551 GTCAAACCAAACCTGTCCCTTAA 59.044 43.478 0.00 0.00 0.00 1.85
303 313 4.403113 GTCAAACCAAACCTGTCCCTTAAA 59.597 41.667 0.00 0.00 0.00 1.52
304 314 5.024118 TCAAACCAAACCTGTCCCTTAAAA 58.976 37.500 0.00 0.00 0.00 1.52
305 315 5.484290 TCAAACCAAACCTGTCCCTTAAAAA 59.516 36.000 0.00 0.00 0.00 1.94
337 347 1.301479 GTCCCGTCTCACCACCAAC 60.301 63.158 0.00 0.00 0.00 3.77
338 348 1.762858 TCCCGTCTCACCACCAACA 60.763 57.895 0.00 0.00 0.00 3.33
339 349 1.597027 CCCGTCTCACCACCAACAC 60.597 63.158 0.00 0.00 0.00 3.32
406 416 0.107508 ACCCACAGGCGAATCTGATG 60.108 55.000 7.65 3.47 38.11 3.07
628 640 1.153005 CCTCCCTCTCCATTGCTGC 60.153 63.158 0.00 0.00 0.00 5.25
635 647 1.822613 CTCCATTGCTGCGCTGGAT 60.823 57.895 19.36 0.98 38.36 3.41
764 776 2.232452 ACATCCATCCGCACTAGCTATC 59.768 50.000 0.00 0.00 39.10 2.08
902 914 1.228862 GCAAGGGGAGGAAAAGGCA 60.229 57.895 0.00 0.00 0.00 4.75
931 943 2.572104 GTTTTGCCCCTCCTCTCTTCTA 59.428 50.000 0.00 0.00 0.00 2.10
961 973 3.733337 TGTCTTCTCAGCTTGAAACTCC 58.267 45.455 0.00 0.00 0.00 3.85
1088 1107 4.227197 ACCCTCTCTCTCTTCTTCAACAA 58.773 43.478 0.00 0.00 0.00 2.83
1129 1162 0.740868 ACACCAGCACAATCGGATCG 60.741 55.000 0.00 0.00 0.00 3.69
1320 1353 0.510359 GCCTCTAATTCGCGCAGATG 59.490 55.000 8.75 0.03 0.00 2.90
1321 1354 0.510359 CCTCTAATTCGCGCAGATGC 59.490 55.000 8.75 0.00 37.78 3.91
1322 1355 1.211743 CTCTAATTCGCGCAGATGCA 58.788 50.000 8.75 0.00 42.21 3.96
1402 1435 2.755876 AGCTGATCCCTGCGTCGA 60.756 61.111 0.00 0.00 41.42 4.20
1857 1890 1.606889 GTCGTCCTCCACCACCTCT 60.607 63.158 0.00 0.00 0.00 3.69
1974 2007 3.869272 GCATTGGAGGCGTCGCTG 61.869 66.667 18.11 7.36 0.00 5.18
2004 2037 4.275508 AGCCACAGCCACCACCAG 62.276 66.667 0.00 0.00 41.25 4.00
2010 2043 4.586235 AGCCACCACCAGCACCAC 62.586 66.667 0.00 0.00 0.00 4.16
2280 2313 0.832135 TCTTGTCCGGGTTCAGCTCT 60.832 55.000 0.00 0.00 0.00 4.09
2281 2314 0.895530 CTTGTCCGGGTTCAGCTCTA 59.104 55.000 0.00 0.00 0.00 2.43
2282 2315 1.275291 CTTGTCCGGGTTCAGCTCTAA 59.725 52.381 0.00 0.00 0.00 2.10
2314 2347 1.227263 GTGATGTGATCGTCGGGGG 60.227 63.158 0.00 0.00 32.69 5.40
2322 2355 0.824182 GATCGTCGGGGGATGAGAGT 60.824 60.000 0.00 0.00 0.00 3.24
2328 2361 0.176680 CGGGGGATGAGAGTTGTGAG 59.823 60.000 0.00 0.00 0.00 3.51
2330 2363 0.615331 GGGGATGAGAGTTGTGAGCA 59.385 55.000 0.00 0.00 0.00 4.26
2360 2393 3.737032 CATTGGGTTATGCATGCATGA 57.263 42.857 37.43 29.35 37.82 3.07
2362 2395 3.523606 TTGGGTTATGCATGCATGAAC 57.476 42.857 37.43 32.47 37.82 3.18
2364 2397 1.405105 GGGTTATGCATGCATGAACGT 59.595 47.619 37.43 18.01 37.82 3.99
2403 2436 2.417719 ATTAGGTCTCCCCGCCTTAT 57.582 50.000 0.00 0.00 38.74 1.73
2404 2437 2.185663 TTAGGTCTCCCCGCCTTATT 57.814 50.000 0.00 0.00 38.74 1.40
2405 2438 2.185663 TAGGTCTCCCCGCCTTATTT 57.814 50.000 0.00 0.00 38.74 1.40
2406 2439 2.185663 AGGTCTCCCCGCCTTATTTA 57.814 50.000 0.00 0.00 38.74 1.40
2407 2440 2.047830 AGGTCTCCCCGCCTTATTTAG 58.952 52.381 0.00 0.00 38.74 1.85
2408 2441 1.767088 GGTCTCCCCGCCTTATTTAGT 59.233 52.381 0.00 0.00 0.00 2.24
2438 2472 3.731431 AGGGTTATGTGGTATGGTCTCA 58.269 45.455 0.00 0.00 0.00 3.27
2471 2505 4.085733 TCAATTAGGATGGTGTTGTTGGG 58.914 43.478 0.00 0.00 0.00 4.12
2557 2591 4.018490 TGCCTACTTGTTAGATCGGTGTA 58.982 43.478 0.00 0.00 0.00 2.90
2561 2623 6.513066 GCCTACTTGTTAGATCGGTGTAGTAG 60.513 46.154 14.90 14.90 35.68 2.57
2564 2626 4.895224 TGTTAGATCGGTGTAGTAGCTG 57.105 45.455 0.00 0.00 0.00 4.24
2584 2646 1.884579 GCATGCAAGGAGGGTGATATG 59.115 52.381 14.21 0.00 0.00 1.78
2594 2656 8.049117 GCAAGGAGGGTGATATGATATATTGAA 58.951 37.037 0.00 0.00 0.00 2.69
2701 2763 5.514204 GCACCATCTTCTTCGAATTCAATTG 59.486 40.000 6.22 0.00 0.00 2.32
2708 2770 1.586042 CGAATTCAATTGCGGGCCG 60.586 57.895 24.35 24.35 0.00 6.13
2709 2771 1.806568 GAATTCAATTGCGGGCCGA 59.193 52.632 33.44 10.70 0.00 5.54
2710 2772 0.385390 GAATTCAATTGCGGGCCGAT 59.615 50.000 33.44 13.02 0.00 4.18
2711 2773 0.385390 AATTCAATTGCGGGCCGATC 59.615 50.000 33.44 14.10 0.00 3.69
2712 2774 0.751277 ATTCAATTGCGGGCCGATCA 60.751 50.000 33.44 17.05 0.00 2.92
2713 2775 0.962855 TTCAATTGCGGGCCGATCAA 60.963 50.000 33.44 25.01 0.00 2.57
2714 2776 0.751277 TCAATTGCGGGCCGATCAAT 60.751 50.000 33.44 26.11 32.36 2.57
2715 2777 0.102844 CAATTGCGGGCCGATCAATT 59.897 50.000 33.44 29.86 40.00 2.32
2716 2778 0.385390 AATTGCGGGCCGATCAATTC 59.615 50.000 33.44 10.67 36.10 2.17
2717 2779 1.455383 ATTGCGGGCCGATCAATTCC 61.455 55.000 33.44 9.82 0.00 3.01
2718 2780 3.287520 GCGGGCCGATCAATTCCC 61.288 66.667 33.44 4.02 35.42 3.97
2720 2782 2.192175 GGGCCGATCAATTCCCGT 59.808 61.111 0.00 0.00 0.00 5.28
2721 2783 1.453197 GGGCCGATCAATTCCCGTT 60.453 57.895 0.00 0.00 0.00 4.44
2722 2784 1.035385 GGGCCGATCAATTCCCGTTT 61.035 55.000 0.00 0.00 0.00 3.60
2723 2785 0.380733 GGCCGATCAATTCCCGTTTC 59.619 55.000 0.00 0.00 0.00 2.78
2724 2786 0.380733 GCCGATCAATTCCCGTTTCC 59.619 55.000 0.00 0.00 0.00 3.13
2725 2787 1.021968 CCGATCAATTCCCGTTTCCC 58.978 55.000 0.00 0.00 0.00 3.97
2726 2788 1.021968 CGATCAATTCCCGTTTCCCC 58.978 55.000 0.00 0.00 0.00 4.81
2727 2789 1.399714 GATCAATTCCCGTTTCCCCC 58.600 55.000 0.00 0.00 0.00 5.40
2831 3138 4.282957 TGCTTCCATGTTTAGGCATGAAAA 59.717 37.500 0.00 0.00 46.65 2.29
2832 3139 5.221601 TGCTTCCATGTTTAGGCATGAAAAA 60.222 36.000 0.00 0.00 46.65 1.94
2833 3140 5.876460 GCTTCCATGTTTAGGCATGAAAAAT 59.124 36.000 0.00 0.00 46.65 1.82
2842 3149 7.117523 TGTTTAGGCATGAAAAATGCAATACAC 59.882 33.333 12.01 7.91 46.21 2.90
2871 3178 7.750903 GTGGTTATTGATTAAGACTGCTTGTTC 59.249 37.037 0.00 0.00 35.56 3.18
2877 3184 8.677148 TTGATTAAGACTGCTTGTTCTTAACT 57.323 30.769 6.05 0.00 37.45 2.24
2878 3185 8.677148 TGATTAAGACTGCTTGTTCTTAACTT 57.323 30.769 6.05 0.00 37.45 2.66
2879 3186 8.559536 TGATTAAGACTGCTTGTTCTTAACTTG 58.440 33.333 6.05 0.00 37.45 3.16
2880 3187 7.859325 TTAAGACTGCTTGTTCTTAACTTGT 57.141 32.000 0.00 0.00 35.56 3.16
2881 3188 6.759497 AAGACTGCTTGTTCTTAACTTGTT 57.241 33.333 0.00 0.00 31.83 2.83
2882 3189 6.124088 AGACTGCTTGTTCTTAACTTGTTG 57.876 37.500 0.00 0.00 0.00 3.33
2883 3190 4.672409 ACTGCTTGTTCTTAACTTGTTGC 58.328 39.130 0.00 0.00 0.00 4.17
2884 3191 4.399303 ACTGCTTGTTCTTAACTTGTTGCT 59.601 37.500 0.00 0.00 0.00 3.91
2885 3192 4.671377 TGCTTGTTCTTAACTTGTTGCTG 58.329 39.130 0.00 0.00 0.00 4.41
2886 3193 3.487207 GCTTGTTCTTAACTTGTTGCTGC 59.513 43.478 0.00 0.00 0.00 5.25
2887 3194 4.734695 GCTTGTTCTTAACTTGTTGCTGCT 60.735 41.667 0.00 0.00 0.00 4.24
2888 3195 4.552166 TGTTCTTAACTTGTTGCTGCTC 57.448 40.909 0.00 0.00 0.00 4.26
2889 3196 4.199310 TGTTCTTAACTTGTTGCTGCTCT 58.801 39.130 0.00 0.00 0.00 4.09
2890 3197 4.640201 TGTTCTTAACTTGTTGCTGCTCTT 59.360 37.500 0.00 0.00 0.00 2.85
2891 3198 5.125417 TGTTCTTAACTTGTTGCTGCTCTTT 59.875 36.000 0.00 0.00 0.00 2.52
2892 3199 6.317642 TGTTCTTAACTTGTTGCTGCTCTTTA 59.682 34.615 0.00 0.00 0.00 1.85
2893 3200 6.935741 TCTTAACTTGTTGCTGCTCTTTAA 57.064 33.333 0.00 0.00 0.00 1.52
2894 3201 7.510549 TCTTAACTTGTTGCTGCTCTTTAAT 57.489 32.000 0.00 0.00 0.00 1.40
2895 3202 8.615878 TCTTAACTTGTTGCTGCTCTTTAATA 57.384 30.769 0.00 0.00 0.00 0.98
2896 3203 9.231297 TCTTAACTTGTTGCTGCTCTTTAATAT 57.769 29.630 0.00 0.00 0.00 1.28
2900 3207 8.737168 ACTTGTTGCTGCTCTTTAATATATGA 57.263 30.769 0.00 0.00 0.00 2.15
2901 3208 9.347240 ACTTGTTGCTGCTCTTTAATATATGAT 57.653 29.630 0.00 0.00 0.00 2.45
2904 3211 8.925700 TGTTGCTGCTCTTTAATATATGATACG 58.074 33.333 0.00 0.00 0.00 3.06
2905 3212 7.525688 TGCTGCTCTTTAATATATGATACGC 57.474 36.000 0.00 0.00 0.00 4.42
2906 3213 7.096551 TGCTGCTCTTTAATATATGATACGCA 58.903 34.615 0.00 0.00 0.00 5.24
2907 3214 7.063426 TGCTGCTCTTTAATATATGATACGCAC 59.937 37.037 0.00 0.00 0.00 5.34
2908 3215 7.063426 GCTGCTCTTTAATATATGATACGCACA 59.937 37.037 0.00 0.00 0.00 4.57
2909 3216 8.239681 TGCTCTTTAATATATGATACGCACAC 57.760 34.615 0.00 0.00 0.00 3.82
2910 3217 8.088365 TGCTCTTTAATATATGATACGCACACT 58.912 33.333 0.00 0.00 0.00 3.55
2911 3218 8.587950 GCTCTTTAATATATGATACGCACACTC 58.412 37.037 0.00 0.00 0.00 3.51
2912 3219 8.669394 TCTTTAATATATGATACGCACACTCG 57.331 34.615 0.00 0.00 0.00 4.18
2913 3220 8.294577 TCTTTAATATATGATACGCACACTCGT 58.705 33.333 0.00 0.00 45.49 4.18
2914 3221 7.790861 TTAATATATGATACGCACACTCGTG 57.209 36.000 0.00 0.00 46.56 4.35
2923 3230 3.010088 CACACTCGTGCGTATTCGA 57.990 52.632 0.00 0.00 36.06 3.71
2980 3287 6.554334 TGCTTGTTTACCTTTGATAGTCAC 57.446 37.500 0.00 0.00 0.00 3.67
3015 3323 6.449698 GTTGATGTGTTCTGTTTGGAATGAT 58.550 36.000 0.00 0.00 0.00 2.45
3095 3408 7.390027 ACTATATATGCTTGATCCTGTTGGAC 58.610 38.462 0.00 0.00 46.51 4.02
3187 3504 2.240279 CGCCTCCTAAGCTAGGTATGT 58.760 52.381 0.00 0.00 46.32 2.29
3190 3507 2.965831 CCTCCTAAGCTAGGTATGTGCA 59.034 50.000 0.00 0.00 46.32 4.57
3273 3590 9.608617 CACATATGCTTATTTCAGCTGATAAAG 57.391 33.333 19.04 20.07 40.79 1.85
3287 3604 7.669722 TCAGCTGATAAAGTTCCCTGTAAAAAT 59.330 33.333 13.74 0.00 0.00 1.82
3298 3615 8.971073 AGTTCCCTGTAAAAATAATTGATCCAG 58.029 33.333 0.00 0.00 0.00 3.86
3300 3617 9.983024 TTCCCTGTAAAAATAATTGATCCAGTA 57.017 29.630 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 166 7.402054 AGAGGGTGTATCACAAATTCACAATA 58.598 34.615 2.41 0.00 35.86 1.90
306 316 1.752498 GACGGGACAGGTTTGGTTTTT 59.248 47.619 0.00 0.00 0.00 1.94
307 317 1.064240 AGACGGGACAGGTTTGGTTTT 60.064 47.619 0.00 0.00 0.00 2.43
339 349 9.045223 GCACATGGGTATATGTATATGTGTATG 57.955 37.037 18.09 0.00 44.26 2.39
406 416 0.389391 TATTCCGAGCTGCTGGTAGC 59.611 55.000 7.01 2.54 44.01 3.58
526 537 2.774687 GCCCTGTATTTATACACCCCG 58.225 52.381 0.00 0.00 38.28 5.73
628 640 1.737838 TGCTAAGGAAACATCCAGCG 58.262 50.000 0.00 0.00 33.12 5.18
635 647 1.904287 AACGCCATGCTAAGGAAACA 58.096 45.000 0.00 0.00 0.00 2.83
902 914 1.055849 GAGGGGCAAAACCAAACCAT 58.944 50.000 0.00 0.00 42.05 3.55
931 943 4.414337 AGCTGAGAAGACAAGTGAAAGT 57.586 40.909 0.00 0.00 0.00 2.66
961 973 4.081917 GGAGTTCTCCTCTCTACTTTGTGG 60.082 50.000 11.20 0.00 40.30 4.17
1088 1107 5.529430 TGTGTGTCGGTATGTTGAAAGAAAT 59.471 36.000 0.00 0.00 0.00 2.17
1129 1162 5.842907 AGAAAAATAACCAGCCAGTGAAAC 58.157 37.500 0.00 0.00 0.00 2.78
1321 1354 2.360100 AAGAGGCTGCTGCTGCTG 60.360 61.111 26.79 16.73 40.48 4.41
1322 1355 2.046120 GAAGAGGCTGCTGCTGCT 60.046 61.111 26.79 15.21 40.48 4.24
1842 1875 0.041386 AGGTAGAGGTGGTGGAGGAC 59.959 60.000 0.00 0.00 0.00 3.85
1920 1953 3.706373 CCTAGGTGGTGCGGCAGT 61.706 66.667 1.18 0.00 0.00 4.40
1960 1993 4.069232 CTCCAGCGACGCCTCCAA 62.069 66.667 17.79 0.00 0.00 3.53
1974 2007 2.609610 TGGCTGTGGTACCCCTCC 60.610 66.667 10.07 6.06 0.00 4.30
2004 2037 3.194272 GAACGGCAGGTTGTGGTGC 62.194 63.158 0.00 0.00 39.50 5.01
2185 2218 2.032681 GACAAAGCCGCCTCCAGT 59.967 61.111 0.00 0.00 0.00 4.00
2280 2313 1.548081 TCACATTCCCCGACGAGTTA 58.452 50.000 0.00 0.00 0.00 2.24
2281 2314 0.902531 ATCACATTCCCCGACGAGTT 59.097 50.000 0.00 0.00 0.00 3.01
2282 2315 0.175760 CATCACATTCCCCGACGAGT 59.824 55.000 0.00 0.00 0.00 4.18
2314 2347 3.494048 CCCCTATGCTCACAACTCTCATC 60.494 52.174 0.00 0.00 0.00 2.92
2330 2363 4.051661 CATAACCCAATGCATCCCCTAT 57.948 45.455 0.00 0.00 0.00 2.57
2360 2393 4.272100 GTGGCATCCACGTACGTT 57.728 55.556 20.23 0.72 44.95 3.99
2408 2441 9.771140 ACCATACCACATAACCCTAAATTAAAA 57.229 29.630 0.00 0.00 0.00 1.52
2438 2472 0.719465 CCTAATTGAAGAACGCGCGT 59.281 50.000 32.73 32.73 0.00 6.01
2517 2551 2.625790 GGCAGGAACACACACCATTTAA 59.374 45.455 0.00 0.00 0.00 1.52
2557 2591 0.107312 CCTCCTTGCATGCAGCTACT 60.107 55.000 21.50 0.00 45.94 2.57
2561 2623 2.362120 ACCCTCCTTGCATGCAGC 60.362 61.111 21.50 0.00 45.96 5.25
2564 2626 1.884579 CATATCACCCTCCTTGCATGC 59.115 52.381 11.82 11.82 0.00 4.06
2654 2716 7.433425 GTGCAAAGATACAAAGCTATGGATTTC 59.567 37.037 0.00 0.00 0.00 2.17
2701 2763 3.287520 GGGAATTGATCGGCCCGC 61.288 66.667 0.00 0.00 0.00 6.13
2708 2770 1.399714 GGGGGAAACGGGAATTGATC 58.600 55.000 0.00 0.00 0.00 2.92
2709 2771 3.607871 GGGGGAAACGGGAATTGAT 57.392 52.632 0.00 0.00 0.00 2.57
2725 2787 5.804639 TGATCATATCAATACGAAAGGGGG 58.195 41.667 0.00 0.00 36.11 5.40
2726 2788 8.040727 TGTATGATCATATCAATACGAAAGGGG 58.959 37.037 18.18 0.00 43.50 4.79
2727 2789 9.435688 TTGTATGATCATATCAATACGAAAGGG 57.564 33.333 18.18 0.00 43.50 3.95
2732 2794 9.289303 CGACATTGTATGATCATATCAATACGA 57.711 33.333 29.46 19.42 43.50 3.43
2733 2795 9.076596 ACGACATTGTATGATCATATCAATACG 57.923 33.333 30.13 30.13 43.50 3.06
2741 2803 9.410556 CACTCATAACGACATTGTATGATCATA 57.589 33.333 11.49 11.49 0.00 2.15
2742 2804 7.928167 ACACTCATAACGACATTGTATGATCAT 59.072 33.333 13.81 13.81 0.00 2.45
2743 2805 7.264947 ACACTCATAACGACATTGTATGATCA 58.735 34.615 0.00 0.00 0.00 2.92
2762 3069 7.445096 CCAATCCATATACATTAGCAACACTCA 59.555 37.037 0.00 0.00 0.00 3.41
2786 3093 6.719370 AGCATACAAACAAGTTAATTCCTCCA 59.281 34.615 0.00 0.00 0.00 3.86
2831 3138 5.714333 TCAATAACCACCAGTGTATTGCATT 59.286 36.000 12.76 0.00 33.77 3.56
2832 3139 5.260424 TCAATAACCACCAGTGTATTGCAT 58.740 37.500 12.76 0.00 33.77 3.96
2833 3140 4.657013 TCAATAACCACCAGTGTATTGCA 58.343 39.130 12.76 0.00 33.77 4.08
2842 3149 5.882557 AGCAGTCTTAATCAATAACCACCAG 59.117 40.000 0.00 0.00 0.00 4.00
2874 3181 9.177608 TCATATATTAAAGAGCAGCAACAAGTT 57.822 29.630 0.00 0.00 0.00 2.66
2875 3182 8.737168 TCATATATTAAAGAGCAGCAACAAGT 57.263 30.769 0.00 0.00 0.00 3.16
2878 3185 8.925700 CGTATCATATATTAAAGAGCAGCAACA 58.074 33.333 0.00 0.00 0.00 3.33
2879 3186 7.900352 GCGTATCATATATTAAAGAGCAGCAAC 59.100 37.037 0.00 0.00 0.00 4.17
2880 3187 7.602265 TGCGTATCATATATTAAAGAGCAGCAA 59.398 33.333 0.00 0.00 0.00 3.91
2881 3188 7.063426 GTGCGTATCATATATTAAAGAGCAGCA 59.937 37.037 0.00 0.00 0.00 4.41
2882 3189 7.063426 TGTGCGTATCATATATTAAAGAGCAGC 59.937 37.037 0.00 0.00 0.00 5.25
2883 3190 8.376203 GTGTGCGTATCATATATTAAAGAGCAG 58.624 37.037 0.00 0.00 0.00 4.24
2884 3191 8.088365 AGTGTGCGTATCATATATTAAAGAGCA 58.912 33.333 0.00 0.00 0.00 4.26
2885 3192 8.467402 AGTGTGCGTATCATATATTAAAGAGC 57.533 34.615 0.00 0.00 0.00 4.09
2886 3193 8.789743 CGAGTGTGCGTATCATATATTAAAGAG 58.210 37.037 0.00 0.00 0.00 2.85
2887 3194 8.294577 ACGAGTGTGCGTATCATATATTAAAGA 58.705 33.333 0.00 0.00 43.61 2.52
2888 3195 8.365938 CACGAGTGTGCGTATCATATATTAAAG 58.634 37.037 0.00 0.00 43.59 1.85
2889 3196 8.222984 CACGAGTGTGCGTATCATATATTAAA 57.777 34.615 0.00 0.00 43.59 1.52
2890 3197 7.790861 CACGAGTGTGCGTATCATATATTAA 57.209 36.000 0.00 0.00 43.59 1.40
2905 3212 0.907837 CTCGAATACGCACGAGTGTG 59.092 55.000 14.40 14.40 46.90 3.82
2906 3213 3.307829 CTCGAATACGCACGAGTGT 57.692 52.632 4.12 4.12 46.90 3.55
2927 3234 1.830477 TCCCAGCAGCAACAAGTTTTT 59.170 42.857 0.00 0.00 0.00 1.94
2928 3235 1.410153 CTCCCAGCAGCAACAAGTTTT 59.590 47.619 0.00 0.00 0.00 2.43
2929 3236 1.035139 CTCCCAGCAGCAACAAGTTT 58.965 50.000 0.00 0.00 0.00 2.66
2980 3287 0.107017 CACATCAACCTAGCCCCCAG 60.107 60.000 0.00 0.00 0.00 4.45
3153 3470 2.024414 GGAGGCGCAAAATTGAGGTAT 58.976 47.619 10.83 0.00 0.00 2.73
3187 3504 3.719268 ACTACCTCCATTTCACATGCA 57.281 42.857 0.00 0.00 0.00 3.96
3190 3507 6.386927 TCTTCCATACTACCTCCATTTCACAT 59.613 38.462 0.00 0.00 0.00 3.21
3252 3569 7.201857 GGGAACTTTATCAGCTGAAATAAGCAT 60.202 37.037 22.50 15.10 46.08 3.79
3253 3570 6.095440 GGGAACTTTATCAGCTGAAATAAGCA 59.905 38.462 22.50 1.17 46.08 3.91
3273 3590 8.749354 ACTGGATCAATTATTTTTACAGGGAAC 58.251 33.333 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.