Multiple sequence alignment - TraesCS4D01G235500

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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 TraesCS4D01G235500 chr4D 100.000 3006 0 0 1 3006 396673540 396670535 0.000000e+00 5552
1 TraesCS4D01G235500 chr4A 91.136 1681 75 18 463 2097 78182320 78180668 0.000000e+00 2211
2 TraesCS4D01G235500 chr4A 88.251 732 60 11 2263 2989 78180586 78179876 0.000000e+00 852
3 TraesCS4D01G235500 chr4A 91.142 429 25 5 1 425 78182738 78182319 1.210000e-158 569
4 TraesCS4D01G235500 chr4B 90.688 1686 74 25 493 2128 488680668 488679016 0.000000e+00 2167
5 TraesCS4D01G235500 chr4B 93.750 512 22 5 7 517 488681185 488680683 0.000000e+00 760
6 TraesCS4D01G235500 chr4B 88.959 317 28 6 2645 2956 488646281 488645967 4.700000e-103 385
7 TraesCS4D01G235500 chr4B 92.821 195 12 1 2249 2443 488678149 488677957 6.340000e-72 281


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 TraesCS4D01G235500 chr4D 396670535 396673540 3005 True 5552.000000 5552 100.000000 1 3006 1 chr4D.!!$R1 3005
1 TraesCS4D01G235500 chr4A 78179876 78182738 2862 True 1210.666667 2211 90.176333 1 2989 3 chr4A.!!$R1 2988
2 TraesCS4D01G235500 chr4B 488677957 488681185 3228 True 1069.333333 2167 92.419667 7 2443 3 chr4B.!!$R2 2436

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
927 1026 0.108585 ACACTCTGAAACGCCCACAT 59.891 50.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 3440 0.034476 GCATCGCCATCTCCATCTCA 59.966 55.0 0.0 0.0 0.0 3.27 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
57 58 1.226542 CATGCATGAGGAGGTGGCT 59.773 57.895 22.59 0.00 0.00 4.75
81 82 2.032834 ACGTTGGCGCCCATTGTA 59.967 55.556 26.77 0.00 42.83 2.41
187 188 4.889995 TCCTCCACGCTCATATATATCCTG 59.110 45.833 0.00 0.00 0.00 3.86
248 249 1.076705 GGGAGAGGCAATTGGGTCC 60.077 63.158 7.72 0.00 0.00 4.46
249 250 1.076705 GGAGAGGCAATTGGGTCCC 60.077 63.158 7.72 0.00 0.00 4.46
250 251 1.691219 GAGAGGCAATTGGGTCCCA 59.309 57.895 6.47 6.47 0.00 4.37
251 252 0.394899 GAGAGGCAATTGGGTCCCAG 60.395 60.000 11.40 0.38 33.81 4.45
252 253 1.380380 GAGGCAATTGGGTCCCAGG 60.380 63.158 11.40 6.33 33.81 4.45
253 254 1.856873 AGGCAATTGGGTCCCAGGA 60.857 57.895 11.40 0.00 33.81 3.86
294 296 2.966516 CCTACCCTCTCCATGTAAGTCC 59.033 54.545 0.00 0.00 0.00 3.85
309 311 4.893524 TGTAAGTCCACTCTGAGTTCTTCA 59.106 41.667 7.77 9.96 0.00 3.02
377 379 5.095691 TCAAATTTTGCGAGAGTTGAGTC 57.904 39.130 3.42 0.00 0.00 3.36
428 430 1.434188 TCTCCAAAAGCTGGTCCTCA 58.566 50.000 0.00 0.00 46.51 3.86
491 493 7.027874 TGAGTATGGGAGTAGGAAAATTTGT 57.972 36.000 0.00 0.00 0.00 2.83
496 498 5.560724 TGGGAGTAGGAAAATTTGTCTGAG 58.439 41.667 0.00 0.00 0.00 3.35
506 545 3.667497 ATTTGTCTGAGCTCGTCTTCA 57.333 42.857 9.64 1.22 0.00 3.02
627 689 9.850198 ATGGAAAAATGGAATTCAAAGAAAGAA 57.150 25.926 7.93 0.00 33.67 2.52
628 690 9.678260 TGGAAAAATGGAATTCAAAGAAAGAAA 57.322 25.926 7.93 0.00 33.67 2.52
670 732 3.265995 GGGAGTCTGGGTTAAATTGAGGA 59.734 47.826 0.00 0.00 0.00 3.71
671 733 4.263771 GGGAGTCTGGGTTAAATTGAGGAA 60.264 45.833 0.00 0.00 0.00 3.36
672 734 4.700692 GGAGTCTGGGTTAAATTGAGGAAC 59.299 45.833 0.00 0.00 0.00 3.62
674 736 6.296259 GGAGTCTGGGTTAAATTGAGGAACTA 60.296 42.308 0.00 0.00 41.55 2.24
675 737 6.712276 AGTCTGGGTTAAATTGAGGAACTAG 58.288 40.000 0.00 0.00 41.55 2.57
676 738 6.500751 AGTCTGGGTTAAATTGAGGAACTAGA 59.499 38.462 0.00 0.00 41.55 2.43
677 739 6.594547 GTCTGGGTTAAATTGAGGAACTAGAC 59.405 42.308 0.00 0.00 41.55 2.59
802 871 5.554747 AGATGTTCATCCATCCATTATCCCT 59.445 40.000 8.89 0.00 41.79 4.20
808 877 4.474303 TCCATCCATTATCCCTTTGCAT 57.526 40.909 0.00 0.00 0.00 3.96
927 1026 0.108585 ACACTCTGAAACGCCCACAT 59.891 50.000 0.00 0.00 0.00 3.21
932 1031 1.303236 TGAAACGCCCACATCCTGG 60.303 57.895 0.00 0.00 40.26 4.45
959 1058 6.944290 TGCTCAAAATCCTCCATATAATCCTG 59.056 38.462 0.00 0.00 0.00 3.86
962 1061 8.044574 TCAAAATCCTCCATATAATCCTGACA 57.955 34.615 0.00 0.00 0.00 3.58
983 1082 1.196808 TCGAATTTGAGCAACTTCGGC 59.803 47.619 25.10 0.00 46.50 5.54
994 1093 0.165944 AACTTCGGCGCAAATTCTCG 59.834 50.000 10.83 0.75 0.00 4.04
1063 1162 2.125952 CATCGACGTGGCTCAGCA 60.126 61.111 0.00 0.00 0.00 4.41
1179 1278 1.738099 CCTGGAAGTGAACGGCGAG 60.738 63.158 16.62 0.00 0.00 5.03
1435 1537 4.379243 AGCGGTGCTCAGGGTTCG 62.379 66.667 0.00 0.00 30.62 3.95
1776 1886 1.460504 TCGGAGTACAGGTGCTACAG 58.539 55.000 0.00 0.00 0.00 2.74
2023 2145 2.926200 CTGACTCTGAACGGTAGCATTG 59.074 50.000 0.00 0.00 0.00 2.82
2128 2262 3.902881 AGATCCTCTTGCCTGTTACTG 57.097 47.619 0.00 0.00 0.00 2.74
2129 2263 2.093235 AGATCCTCTTGCCTGTTACTGC 60.093 50.000 0.00 0.00 0.00 4.40
2130 2264 1.352083 TCCTCTTGCCTGTTACTGCT 58.648 50.000 0.00 0.00 0.00 4.24
2131 2265 1.276421 TCCTCTTGCCTGTTACTGCTC 59.724 52.381 0.00 0.00 0.00 4.26
2132 2266 1.277557 CCTCTTGCCTGTTACTGCTCT 59.722 52.381 0.00 0.00 0.00 4.09
2134 2268 2.233431 CTCTTGCCTGTTACTGCTCTCT 59.767 50.000 0.00 0.00 0.00 3.10
2135 2269 2.232452 TCTTGCCTGTTACTGCTCTCTC 59.768 50.000 0.00 0.00 0.00 3.20
2137 2271 0.179124 GCCTGTTACTGCTCTCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
2138 2272 1.178276 CCTGTTACTGCTCTCTCCGT 58.822 55.000 0.00 0.00 0.00 4.69
2139 2273 1.133407 CCTGTTACTGCTCTCTCCGTC 59.867 57.143 0.00 0.00 0.00 4.79
2140 2274 1.133407 CTGTTACTGCTCTCTCCGTCC 59.867 57.143 0.00 0.00 0.00 4.79
2142 2276 0.035725 TTACTGCTCTCTCCGTCCGA 60.036 55.000 0.00 0.00 0.00 4.55
2145 2279 0.243907 CTGCTCTCTCCGTCCGAAAA 59.756 55.000 0.00 0.00 0.00 2.29
2146 2280 0.677288 TGCTCTCTCCGTCCGAAAAA 59.323 50.000 0.00 0.00 0.00 1.94
2166 2300 6.743575 AAAAACTTCTCCTTCGTATGGATG 57.256 37.500 0.00 0.00 32.56 3.51
2167 2301 5.422214 AAACTTCTCCTTCGTATGGATGT 57.578 39.130 0.00 0.00 32.56 3.06
2170 2304 6.334102 ACTTCTCCTTCGTATGGATGTATC 57.666 41.667 0.00 0.00 32.56 2.24
2171 2305 6.071984 ACTTCTCCTTCGTATGGATGTATCT 58.928 40.000 0.00 0.00 32.56 1.98
2172 2306 7.232188 ACTTCTCCTTCGTATGGATGTATCTA 58.768 38.462 0.00 0.00 32.56 1.98
2173 2307 7.392113 ACTTCTCCTTCGTATGGATGTATCTAG 59.608 40.741 0.00 0.00 32.56 2.43
2176 2310 4.156190 CCTTCGTATGGATGTATCTAGCGT 59.844 45.833 0.00 0.00 0.00 5.07
2177 2311 4.941325 TCGTATGGATGTATCTAGCGTC 57.059 45.455 0.00 0.00 0.00 5.19
2178 2312 4.320870 TCGTATGGATGTATCTAGCGTCA 58.679 43.478 0.00 0.00 0.00 4.35
2179 2313 4.392138 TCGTATGGATGTATCTAGCGTCAG 59.608 45.833 0.00 0.00 0.00 3.51
2181 2315 3.990318 TGGATGTATCTAGCGTCAGTG 57.010 47.619 0.00 0.00 0.00 3.66
2182 2316 2.034685 TGGATGTATCTAGCGTCAGTGC 59.965 50.000 0.00 0.00 0.00 4.40
2184 2318 3.502595 GGATGTATCTAGCGTCAGTGCTA 59.497 47.826 0.00 0.00 45.14 3.49
2192 2326 3.634568 AGCGTCAGTGCTAGATACATC 57.365 47.619 0.00 0.00 45.14 3.06
2193 2327 3.218453 AGCGTCAGTGCTAGATACATCT 58.782 45.455 0.00 0.00 45.14 2.90
2197 2331 6.015856 AGCGTCAGTGCTAGATACATCTATTT 60.016 38.462 0.00 0.00 45.14 1.40
2198 2332 7.175119 AGCGTCAGTGCTAGATACATCTATTTA 59.825 37.037 0.00 0.00 45.14 1.40
2199 2333 7.808381 GCGTCAGTGCTAGATACATCTATTTAA 59.192 37.037 0.00 0.00 38.60 1.52
2200 2334 9.678941 CGTCAGTGCTAGATACATCTATTTAAA 57.321 33.333 0.00 0.00 38.60 1.52
2224 2358 8.648557 AAAAACAAGATTAGGACAAGCTTTTC 57.351 30.769 3.91 3.91 0.00 2.29
2225 2359 5.966742 ACAAGATTAGGACAAGCTTTTCC 57.033 39.130 21.84 21.84 0.00 3.13
2226 2360 4.455877 ACAAGATTAGGACAAGCTTTTCCG 59.544 41.667 22.77 11.32 36.95 4.30
2227 2361 3.010420 AGATTAGGACAAGCTTTTCCGC 58.990 45.455 22.77 14.65 36.95 5.54
2229 2363 1.519408 TAGGACAAGCTTTTCCGCAC 58.481 50.000 22.77 2.69 36.95 5.34
2230 2364 1.082104 GGACAAGCTTTTCCGCACG 60.082 57.895 15.65 0.00 0.00 5.34
2231 2365 1.082104 GACAAGCTTTTCCGCACGG 60.082 57.895 1.73 1.73 0.00 4.94
2232 2366 1.503818 GACAAGCTTTTCCGCACGGA 61.504 55.000 7.89 7.89 43.52 4.69
2235 2369 2.358247 GCTTTTCCGCACGGAGGA 60.358 61.111 12.15 2.60 46.06 3.71
2236 2370 1.964373 GCTTTTCCGCACGGAGGAA 60.964 57.895 12.15 10.21 46.06 3.36
2239 2373 4.100479 TTCCGCACGGAGGAAGTA 57.900 55.556 12.15 0.00 46.06 2.24
2240 2374 1.588082 TTCCGCACGGAGGAAGTAC 59.412 57.895 12.15 0.00 46.06 2.73
2242 2376 0.035152 TCCGCACGGAGGAAGTACTA 60.035 55.000 7.89 0.00 39.76 1.82
2244 2378 2.158769 TCCGCACGGAGGAAGTACTATA 60.159 50.000 7.89 0.00 39.76 1.31
2245 2379 2.818432 CCGCACGGAGGAAGTACTATAT 59.182 50.000 2.01 0.00 37.50 0.86
2246 2380 4.005650 CCGCACGGAGGAAGTACTATATA 58.994 47.826 2.01 0.00 37.50 0.86
2247 2381 4.094590 CCGCACGGAGGAAGTACTATATAG 59.905 50.000 2.01 8.27 37.50 1.31
2297 3184 3.305177 TTCCGGCAACTACGAGGCC 62.305 63.158 0.00 0.00 44.27 5.19
2314 3201 1.676006 GGCCGCTGCTTTGTTACATAT 59.324 47.619 0.00 0.00 37.74 1.78
2368 3257 3.314635 GCCCGCGTATACTGCTATATACT 59.685 47.826 4.92 0.00 36.34 2.12
2371 3260 5.263948 CCGCGTATACTGCTATATACTGTG 58.736 45.833 4.92 12.18 36.34 3.66
2403 3292 1.872952 CGATGGTGCTGTCAAGAACAA 59.127 47.619 0.00 0.00 37.45 2.83
2421 3310 9.752961 CAAGAACAAATGCAATATCATCCATTA 57.247 29.630 0.00 0.00 0.00 1.90
2451 3340 3.413166 CATCATGGCGATGCACGT 58.587 55.556 3.45 0.00 44.95 4.49
2452 3341 1.277739 CATCATGGCGATGCACGTC 59.722 57.895 3.45 6.38 44.95 4.34
2468 3357 1.077357 GTCGAGGAGGAGGAGAGCA 60.077 63.158 0.00 0.00 0.00 4.26
2476 3365 3.394836 GAGGAGAGCACGCCCCTT 61.395 66.667 0.00 0.00 36.64 3.95
2498 3387 4.360405 GGGCCATCACAACGGGGT 62.360 66.667 4.39 0.00 0.00 4.95
2499 3388 2.750237 GGCCATCACAACGGGGTC 60.750 66.667 0.00 0.00 0.00 4.46
2500 3389 3.124921 GCCATCACAACGGGGTCG 61.125 66.667 0.00 0.00 43.02 4.79
2501 3390 2.660206 CCATCACAACGGGGTCGA 59.340 61.111 0.00 0.00 40.11 4.20
2502 3391 1.220749 CCATCACAACGGGGTCGAT 59.779 57.895 0.00 0.00 40.11 3.59
2503 3392 1.089481 CCATCACAACGGGGTCGATG 61.089 60.000 0.00 0.00 43.42 3.84
2505 3394 0.108329 ATCACAACGGGGTCGATGTC 60.108 55.000 0.00 0.00 46.83 3.06
2527 3416 1.740296 GTCGCCGTATGTGTTGGCT 60.740 57.895 0.60 0.00 46.67 4.75
2532 3421 2.032634 CGTATGTGTTGGCTGCCGT 61.033 57.895 14.98 0.00 0.00 5.68
2565 3454 0.534652 GCCAGTGAGATGGAGATGGC 60.535 60.000 0.00 0.00 45.61 4.40
2582 3471 4.280494 CGATGCTCCCCGGGTACG 62.280 72.222 21.85 11.38 40.55 3.67
2638 3527 2.408022 GACGACAGCGGCGACTAT 59.592 61.111 12.98 0.00 43.17 2.12
2696 3585 1.494721 GGATGCTTTGGGGGATACTCA 59.505 52.381 0.00 0.00 41.13 3.41
2707 3596 0.100146 GGATACTCACCCGTGTCGTC 59.900 60.000 0.00 0.00 0.00 4.20
2721 3610 3.775654 CGTCTGGAGGTGGAGGGC 61.776 72.222 0.00 0.00 0.00 5.19
2727 3616 4.779733 GAGGTGGAGGGCCGAGGA 62.780 72.222 0.00 0.00 36.79 3.71
2746 3635 3.564027 GAAGAATCGGTGCCGGCG 61.564 66.667 23.90 7.87 40.25 6.46
2769 3658 1.375396 CACCGGCGTTGAGGAATGA 60.375 57.895 6.01 0.00 0.00 2.57
2785 3674 3.878519 GAGAGGAGGCGGTCGTCG 61.879 72.222 2.75 0.00 43.63 5.12
2846 3736 1.137513 GTGCTAGCTGACGTCGTTTT 58.862 50.000 17.23 0.00 0.00 2.43
2876 3766 5.070981 TCTGGCTGATTAAGGTATTGGAGAG 59.929 44.000 0.00 0.00 0.00 3.20
2881 3771 6.648725 GCTGATTAAGGTATTGGAGAGACATC 59.351 42.308 0.00 0.00 0.00 3.06
2882 3772 7.472663 GCTGATTAAGGTATTGGAGAGACATCT 60.473 40.741 0.00 0.00 38.98 2.90
2891 3781 3.986435 TGGAGAGACATCTGATTCAGGA 58.014 45.455 13.59 1.54 35.30 3.86
2917 3807 2.032799 TGTGTGCGTGGATTTTGAAGTC 59.967 45.455 0.00 0.00 0.00 3.01
2968 3858 8.786826 TGGTTTGTATAGTGGTTCTTTCATAG 57.213 34.615 0.00 0.00 0.00 2.23
2986 3876 7.672983 TTCATAGATCTTGTTCAGTTGTTCC 57.327 36.000 0.00 0.00 0.00 3.62
2989 3879 7.884877 TCATAGATCTTGTTCAGTTGTTCCATT 59.115 33.333 0.00 0.00 0.00 3.16
2990 3880 6.966534 AGATCTTGTTCAGTTGTTCCATTT 57.033 33.333 0.00 0.00 0.00 2.32
2991 3881 7.352079 AGATCTTGTTCAGTTGTTCCATTTT 57.648 32.000 0.00 0.00 0.00 1.82
2992 3882 7.428826 AGATCTTGTTCAGTTGTTCCATTTTC 58.571 34.615 0.00 0.00 0.00 2.29
2993 3883 5.901552 TCTTGTTCAGTTGTTCCATTTTCC 58.098 37.500 0.00 0.00 0.00 3.13
2994 3884 5.420421 TCTTGTTCAGTTGTTCCATTTTCCA 59.580 36.000 0.00 0.00 0.00 3.53
2995 3885 5.867903 TGTTCAGTTGTTCCATTTTCCAT 57.132 34.783 0.00 0.00 0.00 3.41
2996 3886 5.841810 TGTTCAGTTGTTCCATTTTCCATC 58.158 37.500 0.00 0.00 0.00 3.51
2997 3887 4.764679 TCAGTTGTTCCATTTTCCATCG 57.235 40.909 0.00 0.00 0.00 3.84
2998 3888 3.057596 TCAGTTGTTCCATTTTCCATCGC 60.058 43.478 0.00 0.00 0.00 4.58
2999 3889 3.057315 CAGTTGTTCCATTTTCCATCGCT 60.057 43.478 0.00 0.00 0.00 4.93
3000 3890 4.155826 CAGTTGTTCCATTTTCCATCGCTA 59.844 41.667 0.00 0.00 0.00 4.26
3001 3891 4.949856 AGTTGTTCCATTTTCCATCGCTAT 59.050 37.500 0.00 0.00 0.00 2.97
3002 3892 5.418840 AGTTGTTCCATTTTCCATCGCTATT 59.581 36.000 0.00 0.00 0.00 1.73
3003 3893 5.913137 TGTTCCATTTTCCATCGCTATTT 57.087 34.783 0.00 0.00 0.00 1.40
3004 3894 5.649557 TGTTCCATTTTCCATCGCTATTTG 58.350 37.500 0.00 0.00 0.00 2.32
3005 3895 5.184864 TGTTCCATTTTCCATCGCTATTTGT 59.815 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.203076 CCGTTCGGCGACCTAGGG 62.203 72.222 10.16 6.77 44.77 3.53
15 16 0.580104 CATAATTCCGTTCGGCGACC 59.420 55.000 10.16 0.00 44.77 4.79
57 58 2.413765 GGCGCCAACGTCCAAAAA 59.586 55.556 24.80 0.00 42.83 1.94
81 82 0.987294 CCCTCCAACTGACACCTCAT 59.013 55.000 0.00 0.00 0.00 2.90
187 188 2.451167 CGAGCTGCACTGTGCTAGC 61.451 63.158 31.49 31.49 45.31 3.42
249 250 3.196469 TCACTTACCAGATTCAGCTCCTG 59.804 47.826 0.00 0.00 0.00 3.86
250 251 3.196685 GTCACTTACCAGATTCAGCTCCT 59.803 47.826 0.00 0.00 0.00 3.69
251 252 3.526534 GTCACTTACCAGATTCAGCTCC 58.473 50.000 0.00 0.00 0.00 4.70
277 279 2.432510 GAGTGGACTTACATGGAGAGGG 59.567 54.545 0.00 0.00 0.00 4.30
294 296 4.384056 ACACCATTGAAGAACTCAGAGTG 58.616 43.478 3.05 0.00 36.74 3.51
309 311 5.255397 TCTGTATTTCCCAGAACACCATT 57.745 39.130 0.00 0.00 36.07 3.16
377 379 5.772521 ACAAGAAATTGATTTGAGGTTCGG 58.227 37.500 0.00 0.00 0.00 4.30
491 493 2.192664 AGACTGAAGACGAGCTCAGA 57.807 50.000 15.40 0.00 34.59 3.27
496 498 3.019933 AGAACAAGACTGAAGACGAGC 57.980 47.619 0.00 0.00 0.00 5.03
506 545 6.931840 GGAAGACAAGAACATAGAACAAGACT 59.068 38.462 0.00 0.00 0.00 3.24
625 687 1.019805 GGGTGCGCTCTACAGGTTTC 61.020 60.000 9.73 0.00 0.00 2.78
626 688 1.003718 GGGTGCGCTCTACAGGTTT 60.004 57.895 9.73 0.00 0.00 3.27
627 689 1.913762 AGGGTGCGCTCTACAGGTT 60.914 57.895 9.73 0.00 0.00 3.50
628 690 2.283966 AGGGTGCGCTCTACAGGT 60.284 61.111 9.73 0.00 0.00 4.00
672 734 9.477484 ACACATAAAACTTCACTAGTTGTCTAG 57.523 33.333 0.00 1.37 46.34 2.43
673 735 9.826574 AACACATAAAACTTCACTAGTTGTCTA 57.173 29.630 0.00 0.00 46.34 2.59
674 736 8.732746 AACACATAAAACTTCACTAGTTGTCT 57.267 30.769 0.00 0.00 46.34 3.41
675 737 8.068380 GGAACACATAAAACTTCACTAGTTGTC 58.932 37.037 0.00 0.00 46.34 3.18
676 738 7.012989 GGGAACACATAAAACTTCACTAGTTGT 59.987 37.037 0.00 0.00 46.34 3.32
677 739 7.228706 AGGGAACACATAAAACTTCACTAGTTG 59.771 37.037 0.00 0.00 46.34 3.16
684 746 6.831353 TCTCAAAGGGAACACATAAAACTTCA 59.169 34.615 0.00 0.00 0.00 3.02
727 789 1.937546 CTTCTCAAACGCATGCCCCC 61.938 60.000 13.15 0.00 0.00 5.40
802 871 6.885918 TCTCAAGACTGATAATTCCATGCAAA 59.114 34.615 0.00 0.00 0.00 3.68
808 877 5.819379 GTGCATCTCAAGACTGATAATTCCA 59.181 40.000 0.00 0.00 0.00 3.53
927 1026 0.700564 AGGATTTTGAGCAGCCAGGA 59.299 50.000 0.00 0.00 0.00 3.86
932 1031 6.127786 GGATTATATGGAGGATTTTGAGCAGC 60.128 42.308 0.00 0.00 0.00 5.25
983 1082 1.328680 CCATGTCTCCGAGAATTTGCG 59.671 52.381 0.00 0.00 0.00 4.85
994 1093 1.025041 GGAATTTCGCCCATGTCTCC 58.975 55.000 0.00 0.00 0.00 3.71
1051 1150 1.217511 CTCTCATGCTGAGCCACGT 59.782 57.895 0.23 0.00 43.95 4.49
1120 1219 2.290287 CGTGGGTGATGGTCAGGGA 61.290 63.158 0.00 0.00 0.00 4.20
1179 1278 2.035442 GTCGGTGCTTCTTGGCCTC 61.035 63.158 3.32 0.00 0.00 4.70
1428 1530 2.032071 CCGCCTTTCACGAACCCT 59.968 61.111 0.00 0.00 0.00 4.34
1470 1572 0.457853 CCACGTACACCTCGACCATG 60.458 60.000 0.00 0.00 0.00 3.66
1987 2109 2.108566 CAGAGCAGGCCGGAGATG 59.891 66.667 5.05 0.06 0.00 2.90
2023 2145 1.645704 CTGGCTCTGTGACATGCTGC 61.646 60.000 9.80 0.00 30.31 5.25
2128 2262 3.509388 TTTTTCGGACGGAGAGAGC 57.491 52.632 0.00 0.00 0.00 4.09
2145 2279 5.422214 ACATCCATACGAAGGAGAAGTTT 57.578 39.130 0.00 0.00 38.83 2.66
2146 2280 6.551601 AGATACATCCATACGAAGGAGAAGTT 59.448 38.462 0.00 0.00 38.83 2.66
2147 2281 6.071984 AGATACATCCATACGAAGGAGAAGT 58.928 40.000 0.00 0.00 38.83 3.01
2148 2282 6.582677 AGATACATCCATACGAAGGAGAAG 57.417 41.667 0.00 0.00 38.83 2.85
2150 2284 5.648526 GCTAGATACATCCATACGAAGGAGA 59.351 44.000 0.00 0.00 38.83 3.71
2151 2285 5.447954 CGCTAGATACATCCATACGAAGGAG 60.448 48.000 0.00 0.00 38.83 3.69
2154 2288 5.106673 TGACGCTAGATACATCCATACGAAG 60.107 44.000 0.00 0.00 0.00 3.79
2155 2289 4.758165 TGACGCTAGATACATCCATACGAA 59.242 41.667 0.00 0.00 0.00 3.85
2156 2290 4.320870 TGACGCTAGATACATCCATACGA 58.679 43.478 0.00 0.00 0.00 3.43
2157 2291 4.154375 ACTGACGCTAGATACATCCATACG 59.846 45.833 0.00 0.00 0.00 3.06
2158 2292 5.394802 CACTGACGCTAGATACATCCATAC 58.605 45.833 0.00 0.00 0.00 2.39
2159 2293 4.082733 GCACTGACGCTAGATACATCCATA 60.083 45.833 0.00 0.00 0.00 2.74
2160 2294 3.305676 GCACTGACGCTAGATACATCCAT 60.306 47.826 0.00 0.00 0.00 3.41
2161 2295 2.034685 GCACTGACGCTAGATACATCCA 59.965 50.000 0.00 0.00 0.00 3.41
2171 2305 4.390264 AGATGTATCTAGCACTGACGCTA 58.610 43.478 0.00 0.00 43.56 4.26
2172 2306 3.218453 AGATGTATCTAGCACTGACGCT 58.782 45.455 0.00 0.00 46.26 5.07
2173 2307 3.634568 AGATGTATCTAGCACTGACGC 57.365 47.619 0.00 0.00 34.85 5.19
2199 2333 7.710907 GGAAAAGCTTGTCCTAATCTTGTTTTT 59.289 33.333 26.11 0.00 0.00 1.94
2200 2334 7.210174 GGAAAAGCTTGTCCTAATCTTGTTTT 58.790 34.615 26.11 0.00 0.00 2.43
2201 2335 6.515035 CGGAAAAGCTTGTCCTAATCTTGTTT 60.515 38.462 29.16 2.13 0.00 2.83
2203 2337 4.455877 CGGAAAAGCTTGTCCTAATCTTGT 59.544 41.667 29.16 0.00 0.00 3.16
2204 2338 4.672801 GCGGAAAAGCTTGTCCTAATCTTG 60.673 45.833 29.16 15.23 0.00 3.02
2205 2339 3.440522 GCGGAAAAGCTTGTCCTAATCTT 59.559 43.478 29.16 4.06 0.00 2.40
2206 2340 3.010420 GCGGAAAAGCTTGTCCTAATCT 58.990 45.455 29.16 0.00 0.00 2.40
2207 2341 2.747446 TGCGGAAAAGCTTGTCCTAATC 59.253 45.455 29.16 17.10 38.13 1.75
2208 2342 2.488153 GTGCGGAAAAGCTTGTCCTAAT 59.512 45.455 29.16 0.00 38.13 1.73
2209 2343 1.877443 GTGCGGAAAAGCTTGTCCTAA 59.123 47.619 29.16 16.61 38.13 2.69
2211 2345 1.507141 CGTGCGGAAAAGCTTGTCCT 61.507 55.000 29.16 0.00 38.13 3.85
2214 2348 1.507141 CTCCGTGCGGAAAAGCTTGT 61.507 55.000 14.53 0.00 44.66 3.16
2216 2350 1.966451 CCTCCGTGCGGAAAAGCTT 60.966 57.895 14.53 0.00 44.66 3.74
2217 2351 2.358737 CCTCCGTGCGGAAAAGCT 60.359 61.111 14.53 0.00 44.66 3.74
2218 2352 1.912371 CTTCCTCCGTGCGGAAAAGC 61.912 60.000 14.53 0.00 44.66 3.51
2219 2353 0.602905 ACTTCCTCCGTGCGGAAAAG 60.603 55.000 22.78 22.78 44.66 2.27
2221 2355 0.037975 GTACTTCCTCCGTGCGGAAA 60.038 55.000 14.53 6.22 44.66 3.13
2224 2358 1.030457 ATAGTACTTCCTCCGTGCGG 58.970 55.000 0.00 3.94 0.00 5.69
2225 2359 4.934001 TCTATATAGTACTTCCTCCGTGCG 59.066 45.833 9.58 0.00 0.00 5.34
2226 2360 6.623331 GCTTCTATATAGTACTTCCTCCGTGC 60.623 46.154 9.58 0.00 0.00 5.34
2227 2361 6.430308 TGCTTCTATATAGTACTTCCTCCGTG 59.570 42.308 9.58 0.00 0.00 4.94
2229 2363 7.476667 CATGCTTCTATATAGTACTTCCTCCG 58.523 42.308 9.58 0.00 0.00 4.63
2230 2364 7.123547 AGCATGCTTCTATATAGTACTTCCTCC 59.876 40.741 16.30 0.00 0.00 4.30
2231 2365 7.973388 CAGCATGCTTCTATATAGTACTTCCTC 59.027 40.741 19.98 0.00 0.00 3.71
2232 2366 7.835822 CAGCATGCTTCTATATAGTACTTCCT 58.164 38.462 19.98 0.00 0.00 3.36
2297 3184 6.830736 TGCATATATATGTAACAAAGCAGCG 58.169 36.000 21.10 0.00 36.11 5.18
2403 3292 8.480501 GGGCTAAATAATGGATGATATTGCATT 58.519 33.333 0.00 0.62 40.28 3.56
2421 3310 2.586425 CCATGATGAACCGGGCTAAAT 58.414 47.619 6.32 0.00 0.00 1.40
2451 3340 1.077357 GTGCTCTCCTCCTCCTCGA 60.077 63.158 0.00 0.00 0.00 4.04
2452 3341 2.477176 CGTGCTCTCCTCCTCCTCG 61.477 68.421 0.00 0.00 0.00 4.63
2453 3342 2.781158 GCGTGCTCTCCTCCTCCTC 61.781 68.421 0.00 0.00 0.00 3.71
2454 3343 2.757917 GCGTGCTCTCCTCCTCCT 60.758 66.667 0.00 0.00 0.00 3.69
2455 3344 3.844090 GGCGTGCTCTCCTCCTCC 61.844 72.222 0.00 0.00 0.00 4.30
2539 3428 1.078918 CATCTCACTGGCGCTTCCA 60.079 57.895 7.64 0.00 44.18 3.53
2549 3438 1.343789 CATCGCCATCTCCATCTCACT 59.656 52.381 0.00 0.00 0.00 3.41
2551 3440 0.034476 GCATCGCCATCTCCATCTCA 59.966 55.000 0.00 0.00 0.00 3.27
2565 3454 4.280494 CGTACCCGGGGAGCATCG 62.280 72.222 27.92 12.98 34.37 3.84
2665 3554 1.589716 AAAGCATCCTGACCGCTTGC 61.590 55.000 6.45 0.00 44.93 4.01
2683 3572 1.081462 ACGGGTGAGTATCCCCCAA 59.919 57.895 0.00 0.00 41.07 4.12
2696 3585 2.989824 CCTCCAGACGACACGGGT 60.990 66.667 0.00 0.00 0.00 5.28
2721 3610 4.711980 CCGATTCTTCGTCCTCGG 57.288 61.111 0.00 0.00 43.97 4.63
2725 3614 2.165301 CGGCACCGATTCTTCGTCC 61.165 63.158 2.01 0.00 43.97 4.79
2727 3616 2.125673 CCGGCACCGATTCTTCGT 60.126 61.111 11.42 0.00 43.97 3.85
2759 3648 0.826715 CGCCTCCTCTCATTCCTCAA 59.173 55.000 0.00 0.00 0.00 3.02
2760 3649 1.045350 CCGCCTCCTCTCATTCCTCA 61.045 60.000 0.00 0.00 0.00 3.86
2761 3650 1.045911 ACCGCCTCCTCTCATTCCTC 61.046 60.000 0.00 0.00 0.00 3.71
2762 3651 1.002274 ACCGCCTCCTCTCATTCCT 59.998 57.895 0.00 0.00 0.00 3.36
2769 3658 4.719106 ACGACGACCGCCTCCTCT 62.719 66.667 0.00 0.00 43.32 3.69
2846 3736 7.122650 CCAATACCTTAATCAGCCAGAAAGAAA 59.877 37.037 0.00 0.00 0.00 2.52
2853 3743 5.070981 TCTCTCCAATACCTTAATCAGCCAG 59.929 44.000 0.00 0.00 0.00 4.85
2855 3745 5.163301 TGTCTCTCCAATACCTTAATCAGCC 60.163 44.000 0.00 0.00 0.00 4.85
2862 3752 7.565029 TGAATCAGATGTCTCTCCAATACCTTA 59.435 37.037 0.00 0.00 0.00 2.69
2876 3766 6.202379 CACACACATATCCTGAATCAGATGTC 59.798 42.308 12.53 0.00 32.44 3.06
2881 3771 3.246936 CGCACACACATATCCTGAATCAG 59.753 47.826 2.68 2.68 0.00 2.90
2882 3772 3.197265 CGCACACACATATCCTGAATCA 58.803 45.455 0.00 0.00 0.00 2.57
2891 3781 3.755905 TCAAAATCCACGCACACACATAT 59.244 39.130 0.00 0.00 0.00 1.78
2940 3830 8.472007 TGAAAGAACCACTATACAAACCAAAT 57.528 30.769 0.00 0.00 0.00 2.32
2952 3842 8.593679 TGAACAAGATCTATGAAAGAACCACTA 58.406 33.333 0.00 0.00 37.89 2.74
2953 3843 7.453393 TGAACAAGATCTATGAAAGAACCACT 58.547 34.615 0.00 0.00 37.89 4.00
2956 3846 7.913674 ACTGAACAAGATCTATGAAAGAACC 57.086 36.000 0.00 0.00 37.89 3.62


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

AutoCloner maintained by Alex Coulton.