Multiple sequence alignment - TraesCS2B01G338100

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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 TraesCS2B01G338100 chr2B 100.000 2993 0 0 1 2993 483136140 483133148 0.000000e+00 5528.0
1 TraesCS2B01G338100 chr2B 90.476 483 30 7 2327 2805 362091618 362092088 9.110000e-175 623.0
2 TraesCS2B01G338100 chr2B 86.207 174 21 3 2785 2956 362092035 362092207 5.090000e-43 185.0
3 TraesCS2B01G338100 chr2D 96.380 1768 57 2 430 2196 407632947 407631186 0.000000e+00 2904.0
4 TraesCS2B01G338100 chr2D 86.253 451 32 8 3 428 407633479 407633034 2.100000e-126 462.0
5 TraesCS2B01G338100 chr2A 95.041 1714 56 5 430 2135 575374440 575372748 0.000000e+00 2667.0
6 TraesCS2B01G338100 chr2A 88.586 403 16 8 47 428 575374923 575374530 2.100000e-126 462.0
7 TraesCS2B01G338100 chr2A 100.000 47 0 0 2163 2209 575372747 575372701 1.480000e-13 87.9
8 TraesCS2B01G338100 chr1B 93.353 662 29 3 2330 2991 162357811 162358457 0.000000e+00 965.0
9 TraesCS2B01G338100 chr6B 97.505 521 12 1 2333 2853 42200177 42199658 0.000000e+00 889.0
10 TraesCS2B01G338100 chr6B 96.250 80 2 1 2915 2993 42199309 42199230 2.420000e-26 130.0
11 TraesCS2B01G338100 chr5A 87.910 488 31 12 2327 2813 616732705 616733165 1.570000e-152 549.0
12 TraesCS2B01G338100 chr5A 87.705 488 32 12 2327 2813 616714662 616715122 7.300000e-151 544.0
13 TraesCS2B01G338100 chr4B 86.885 488 36 12 2327 2813 299702538 299702078 3.420000e-144 521.0
14 TraesCS2B01G338100 chr6A 91.250 320 20 3 2331 2650 592572567 592572878 2.130000e-116 429.0
15 TraesCS2B01G338100 chr6A 77.667 300 21 17 2708 2993 592573234 592573501 1.120000e-29 141.0


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 TraesCS2B01G338100 chr2B 483133148 483136140 2992 True 5528.0 5528 100.000000 1 2993 1 chr2B.!!$R1 2992
1 TraesCS2B01G338100 chr2B 362091618 362092207 589 False 404.0 623 88.341500 2327 2956 2 chr2B.!!$F1 629
2 TraesCS2B01G338100 chr2D 407631186 407633479 2293 True 1683.0 2904 91.316500 3 2196 2 chr2D.!!$R1 2193
3 TraesCS2B01G338100 chr2A 575372701 575374923 2222 True 1072.3 2667 94.542333 47 2209 3 chr2A.!!$R1 2162
4 TraesCS2B01G338100 chr1B 162357811 162358457 646 False 965.0 965 93.353000 2330 2991 1 chr1B.!!$F1 661
5 TraesCS2B01G338100 chr6B 42199230 42200177 947 True 509.5 889 96.877500 2333 2993 2 chr6B.!!$R1 660
6 TraesCS2B01G338100 chr6A 592572567 592573501 934 False 285.0 429 84.458500 2331 2993 2 chr6A.!!$F1 662

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
898 1025 0.391661 CTGACCTCCAATCACACCCG 60.392 60.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2394 0.034896 GCACCGTTGAGGAAGGAAGA 59.965 55.0 0.0 0.0 45.0 2.87 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
24 25 3.687212 GGTTTGGTTGGGTTTCACTTTTG 59.313 43.478 0.00 0.00 0.00 2.44
25 26 4.563786 GGTTTGGTTGGGTTTCACTTTTGA 60.564 41.667 0.00 0.00 0.00 2.69
32 33 2.567985 GGTTTCACTTTTGAGTCCGGA 58.432 47.619 0.00 0.00 31.71 5.14
33 34 2.289820 GGTTTCACTTTTGAGTCCGGAC 59.710 50.000 27.67 27.67 31.71 4.79
36 37 1.760613 TCACTTTTGAGTCCGGACAGT 59.239 47.619 35.00 25.24 0.00 3.55
37 38 2.169769 TCACTTTTGAGTCCGGACAGTT 59.830 45.455 35.00 16.29 0.00 3.16
40 41 0.599204 TTTGAGTCCGGACAGTTCGC 60.599 55.000 35.00 16.87 0.00 4.70
43 44 3.998672 GTCCGGACAGTTCGCCCA 61.999 66.667 29.75 0.00 0.00 5.36
44 45 3.691342 TCCGGACAGTTCGCCCAG 61.691 66.667 0.00 0.00 0.00 4.45
45 46 4.760047 CCGGACAGTTCGCCCAGG 62.760 72.222 0.00 0.00 0.00 4.45
62 63 1.154035 GGCGTTTGGAGCGGATTTG 60.154 57.895 0.00 0.00 35.00 2.32
63 64 1.154035 GCGTTTGGAGCGGATTTGG 60.154 57.895 0.00 0.00 0.00 3.28
72 75 2.045340 CGGATTTGGGGGCTCGTT 60.045 61.111 0.00 0.00 0.00 3.85
79 82 0.988832 TTGGGGGCTCGTTGTAGATT 59.011 50.000 0.00 0.00 0.00 2.40
93 96 4.336889 TGTAGATTATTTGAGGGCTCCG 57.663 45.455 0.00 0.00 0.00 4.63
107 110 2.139118 GGCTCCGATTGTAGATGCTTC 58.861 52.381 0.00 0.00 0.00 3.86
108 111 2.483714 GGCTCCGATTGTAGATGCTTCA 60.484 50.000 2.07 0.00 0.00 3.02
149 152 5.800296 TGCAAACAGTAGCCAAAGACTATA 58.200 37.500 0.00 0.00 0.00 1.31
210 213 1.288633 TCCCCATGGAATCATGTTGCT 59.711 47.619 15.22 0.00 46.96 3.91
211 214 1.411246 CCCCATGGAATCATGTTGCTG 59.589 52.381 15.22 0.00 46.96 4.41
249 252 6.207614 TCTCAATAACAGCGCTAGTCAGATAT 59.792 38.462 10.99 0.00 0.00 1.63
386 414 1.355971 ACGTGGCGTATTAGCAACAG 58.644 50.000 0.00 0.00 41.01 3.16
393 421 2.033662 GCGTATTAGCAACAGTAGCTGC 60.034 50.000 0.00 0.00 43.33 5.25
428 457 8.438513 CGACAGGATATGCATCAAAATTACTAG 58.561 37.037 0.19 0.00 32.32 2.57
459 578 6.527023 CAGTGGTTACTATAGTGTCAAAGACG 59.473 42.308 15.90 0.00 34.74 4.18
478 598 4.158025 AGACGCCTTATATTATGAGACGGG 59.842 45.833 8.57 0.27 0.00 5.28
498 618 2.436911 GGGGGAGTATTTCTTAGGCGAA 59.563 50.000 0.00 0.00 0.00 4.70
517 637 4.267690 GCGAATTGTTAGTGTCATCGATCA 59.732 41.667 0.00 0.00 0.00 2.92
557 677 1.214589 GACTGTCATGGGCGTACGT 59.785 57.895 17.90 0.00 0.00 3.57
689 809 3.709633 TGATGGCGCCAGCTCAGT 61.710 61.111 40.84 22.14 44.37 3.41
898 1025 0.391661 CTGACCTCCAATCACACCCG 60.392 60.000 0.00 0.00 0.00 5.28
938 1065 1.655329 GTCGCCATCTACTCCTCCG 59.345 63.158 0.00 0.00 0.00 4.63
946 1073 1.077930 CTACTCCTCCGTCGACCCA 60.078 63.158 10.58 0.00 0.00 4.51
950 1077 2.675423 CCTCCGTCGACCCACTCA 60.675 66.667 10.58 0.00 0.00 3.41
954 1081 2.579787 CGTCGACCCACTCATCGC 60.580 66.667 10.58 0.00 38.24 4.58
1199 1326 4.828925 GGAGCCGCAGCCTGAGTC 62.829 72.222 0.00 0.00 41.25 3.36
1200 1327 3.768922 GAGCCGCAGCCTGAGTCT 61.769 66.667 0.00 0.00 41.25 3.24
1201 1328 3.714871 GAGCCGCAGCCTGAGTCTC 62.715 68.421 0.00 0.00 41.25 3.36
1202 1329 4.074526 GCCGCAGCCTGAGTCTCA 62.075 66.667 1.78 1.78 0.00 3.27
1203 1330 2.183811 CCGCAGCCTGAGTCTCAG 59.816 66.667 21.18 21.18 43.91 3.35
1314 1441 2.044946 AAGGCGATGGTGAAGGCC 60.045 61.111 0.00 0.00 45.91 5.19
1320 1447 1.602237 GATGGTGAAGGCCGGAAGA 59.398 57.895 5.05 0.00 0.00 2.87
1650 1777 2.664851 CTGCCGTCGTCTGCCAAA 60.665 61.111 0.00 0.00 0.00 3.28
1719 1846 2.514824 GACCCTGGCGAGCATTCC 60.515 66.667 0.00 0.00 0.00 3.01
1902 2029 0.452184 GAGATGAACTCGACGAGGCA 59.548 55.000 27.39 23.38 35.84 4.75
1980 2107 0.392998 CGGTGGCTATGGAGTGCTTT 60.393 55.000 0.00 0.00 0.00 3.51
2211 2338 3.893720 GGTTATATACCACGTCGTCTGG 58.106 50.000 0.00 0.00 46.92 3.86
2212 2339 3.565482 GGTTATATACCACGTCGTCTGGA 59.435 47.826 8.75 0.00 46.92 3.86
2213 2340 4.531332 GTTATATACCACGTCGTCTGGAC 58.469 47.826 8.75 0.00 42.48 4.02
2214 2341 2.112380 TATACCACGTCGTCTGGACA 57.888 50.000 8.75 0.00 46.42 4.02
2215 2342 1.250328 ATACCACGTCGTCTGGACAA 58.750 50.000 8.75 0.00 46.42 3.18
2216 2343 0.594602 TACCACGTCGTCTGGACAAG 59.405 55.000 8.75 0.00 46.42 3.16
2217 2344 2.022129 CCACGTCGTCTGGACAAGC 61.022 63.158 0.00 0.00 46.42 4.01
2218 2345 2.050351 ACGTCGTCTGGACAAGCG 60.050 61.111 0.00 4.74 46.42 4.68
2219 2346 2.254350 CGTCGTCTGGACAAGCGA 59.746 61.111 1.63 0.00 46.42 4.93
2220 2347 2.081212 CGTCGTCTGGACAAGCGAC 61.081 63.158 13.56 13.56 46.42 5.19
2221 2348 1.007734 GTCGTCTGGACAAGCGACA 60.008 57.895 16.86 0.00 46.04 4.35
2222 2349 1.007734 TCGTCTGGACAAGCGACAC 60.008 57.895 1.63 0.00 32.12 3.67
2223 2350 2.365068 CGTCTGGACAAGCGACACG 61.365 63.158 1.63 0.00 0.00 4.49
2224 2351 2.022129 GTCTGGACAAGCGACACGG 61.022 63.158 0.00 0.00 0.00 4.94
2225 2352 2.738521 CTGGACAAGCGACACGGG 60.739 66.667 0.00 0.00 0.00 5.28
2226 2353 3.220999 CTGGACAAGCGACACGGGA 62.221 63.158 0.00 0.00 0.00 5.14
2227 2354 2.432628 GGACAAGCGACACGGGAG 60.433 66.667 0.00 0.00 0.00 4.30
2228 2355 2.649034 GACAAGCGACACGGGAGA 59.351 61.111 0.00 0.00 0.00 3.71
2229 2356 1.733399 GACAAGCGACACGGGAGAC 60.733 63.158 0.00 0.00 0.00 3.36
2241 2368 3.133437 GGGAGACGATCTGGATCCA 57.867 57.895 15.27 15.27 34.40 3.41
2242 2369 0.965439 GGGAGACGATCTGGATCCAG 59.035 60.000 32.60 32.60 44.86 3.86
2243 2370 1.698506 GGAGACGATCTGGATCCAGT 58.301 55.000 35.34 24.63 43.96 4.00
2244 2371 2.035632 GGAGACGATCTGGATCCAGTT 58.964 52.381 35.34 29.27 43.96 3.16
2245 2372 2.432510 GGAGACGATCTGGATCCAGTTT 59.567 50.000 35.34 25.65 43.96 2.66
2246 2373 3.491792 GGAGACGATCTGGATCCAGTTTC 60.492 52.174 35.34 29.57 43.96 2.78
2247 2374 3.370104 AGACGATCTGGATCCAGTTTCT 58.630 45.455 35.34 27.29 43.96 2.52
2248 2375 3.383185 AGACGATCTGGATCCAGTTTCTC 59.617 47.826 35.34 26.76 43.96 2.87
2249 2376 3.370104 ACGATCTGGATCCAGTTTCTCT 58.630 45.455 35.34 19.40 43.96 3.10
2250 2377 4.537751 ACGATCTGGATCCAGTTTCTCTA 58.462 43.478 35.34 18.81 43.96 2.43
2251 2378 4.339814 ACGATCTGGATCCAGTTTCTCTAC 59.660 45.833 35.34 16.54 43.96 2.59
2252 2379 4.555708 CGATCTGGATCCAGTTTCTCTACG 60.556 50.000 35.34 22.78 43.96 3.51
2253 2380 3.964411 TCTGGATCCAGTTTCTCTACGA 58.036 45.455 35.34 14.31 43.96 3.43
2254 2381 3.695060 TCTGGATCCAGTTTCTCTACGAC 59.305 47.826 35.34 0.00 43.96 4.34
2255 2382 2.758979 TGGATCCAGTTTCTCTACGACC 59.241 50.000 11.44 0.00 0.00 4.79
2256 2383 2.101082 GGATCCAGTTTCTCTACGACCC 59.899 54.545 6.95 0.00 0.00 4.46
2257 2384 1.553706 TCCAGTTTCTCTACGACCCC 58.446 55.000 0.00 0.00 0.00 4.95
2258 2385 0.535797 CCAGTTTCTCTACGACCCCC 59.464 60.000 0.00 0.00 0.00 5.40
2272 2399 3.878358 CCCCCTCTCCGATCTTCC 58.122 66.667 0.00 0.00 0.00 3.46
2273 2400 1.234529 CCCCCTCTCCGATCTTCCT 59.765 63.158 0.00 0.00 0.00 3.36
2274 2401 0.399233 CCCCCTCTCCGATCTTCCTT 60.399 60.000 0.00 0.00 0.00 3.36
2275 2402 1.044611 CCCCTCTCCGATCTTCCTTC 58.955 60.000 0.00 0.00 0.00 3.46
2276 2403 1.044611 CCCTCTCCGATCTTCCTTCC 58.955 60.000 0.00 0.00 0.00 3.46
2277 2404 1.412361 CCCTCTCCGATCTTCCTTCCT 60.412 57.143 0.00 0.00 0.00 3.36
2278 2405 1.960689 CCTCTCCGATCTTCCTTCCTC 59.039 57.143 0.00 0.00 0.00 3.71
2279 2406 2.660572 CTCTCCGATCTTCCTTCCTCA 58.339 52.381 0.00 0.00 0.00 3.86
2280 2407 3.027412 CTCTCCGATCTTCCTTCCTCAA 58.973 50.000 0.00 0.00 0.00 3.02
2281 2408 2.761208 TCTCCGATCTTCCTTCCTCAAC 59.239 50.000 0.00 0.00 0.00 3.18
2282 2409 1.476891 TCCGATCTTCCTTCCTCAACG 59.523 52.381 0.00 0.00 0.00 4.10
2283 2410 1.471676 CCGATCTTCCTTCCTCAACGG 60.472 57.143 0.00 0.00 0.00 4.44
2284 2411 1.204941 CGATCTTCCTTCCTCAACGGT 59.795 52.381 0.00 0.00 0.00 4.83
2285 2412 2.622436 GATCTTCCTTCCTCAACGGTG 58.378 52.381 0.00 0.00 0.00 4.94
2286 2413 0.034896 TCTTCCTTCCTCAACGGTGC 59.965 55.000 0.00 0.00 0.00 5.01
2287 2414 0.955919 CTTCCTTCCTCAACGGTGCC 60.956 60.000 0.00 0.00 0.00 5.01
2288 2415 2.725203 TTCCTTCCTCAACGGTGCCG 62.725 60.000 9.29 9.29 46.03 5.69
2299 2426 1.495951 CGGTGCCGTCAAGTAAAGC 59.504 57.895 1.93 0.00 34.35 3.51
2300 2427 1.873863 GGTGCCGTCAAGTAAAGCC 59.126 57.895 0.00 0.00 0.00 4.35
2301 2428 1.583495 GGTGCCGTCAAGTAAAGCCC 61.583 60.000 0.00 0.00 0.00 5.19
2302 2429 1.669760 TGCCGTCAAGTAAAGCCCG 60.670 57.895 0.00 0.00 0.00 6.13
2303 2430 2.396157 GCCGTCAAGTAAAGCCCGG 61.396 63.158 0.00 0.00 38.45 5.73
2304 2431 1.743995 CCGTCAAGTAAAGCCCGGG 60.744 63.158 19.09 19.09 0.00 5.73
2305 2432 1.004200 CGTCAAGTAAAGCCCGGGT 60.004 57.895 24.63 4.48 0.00 5.28
2306 2433 1.296056 CGTCAAGTAAAGCCCGGGTG 61.296 60.000 24.63 10.81 0.00 4.61
2307 2434 0.958876 GTCAAGTAAAGCCCGGGTGG 60.959 60.000 24.63 0.00 37.09 4.61
2322 2449 3.678692 TGGCCGCGGTTGTACGTA 61.679 61.111 28.70 0.00 35.98 3.57
2323 2450 3.181290 GGCCGCGGTTGTACGTAC 61.181 66.667 28.70 18.90 35.98 3.67
2324 2451 2.126346 GCCGCGGTTGTACGTACT 60.126 61.111 28.70 0.00 35.98 2.73
2325 2452 2.438954 GCCGCGGTTGTACGTACTG 61.439 63.158 28.70 9.25 35.98 2.74
2326 2453 2.438954 CCGCGGTTGTACGTACTGC 61.439 63.158 25.12 17.55 42.99 4.40
2327 2454 1.443194 CGCGGTTGTACGTACTGCT 60.443 57.895 25.12 0.00 43.98 4.24
2328 2455 0.179192 CGCGGTTGTACGTACTGCTA 60.179 55.000 25.12 3.27 43.98 3.49
2471 2598 2.143122 GCGTCAGGTTGAATCTGTTCA 58.857 47.619 5.23 0.00 42.41 3.18
2511 2638 1.899437 GATGAAGGTGTCGGGCTGGA 61.899 60.000 0.00 0.00 0.00 3.86
2512 2639 1.274703 ATGAAGGTGTCGGGCTGGAT 61.275 55.000 0.00 0.00 0.00 3.41
2513 2640 1.450312 GAAGGTGTCGGGCTGGATG 60.450 63.158 0.00 0.00 0.00 3.51
2564 2691 2.551270 ACCCTGCAGATCTTGTTCCTA 58.449 47.619 17.39 0.00 0.00 2.94
2810 3297 4.862092 CGAGCTCACGCCATCGCT 62.862 66.667 15.40 0.00 39.84 4.93
2811 3298 3.260483 GAGCTCACGCCATCGCTG 61.260 66.667 9.40 0.00 39.84 5.18
2814 3301 3.260483 CTCACGCCATCGCTGCTC 61.260 66.667 0.00 0.00 39.84 4.26
2815 3302 4.819761 TCACGCCATCGCTGCTCC 62.820 66.667 0.00 0.00 39.84 4.70
2946 3720 2.640302 GCTGTCGCTGTCCCTCTGA 61.640 63.158 0.00 0.00 0.00 3.27
2991 3777 2.606751 TCGAAAGAGGAAGAGAGGGT 57.393 50.000 0.00 0.00 34.84 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.541466 AGTGAAACCCAACCAAACCAA 58.459 42.857 0.00 0.00 37.80 3.67
10 11 2.294074 CGGACTCAAAAGTGAAACCCA 58.706 47.619 0.00 0.00 37.80 4.51
16 17 1.760613 ACTGTCCGGACTCAAAAGTGA 59.239 47.619 33.39 10.58 35.28 3.41
19 20 1.792949 CGAACTGTCCGGACTCAAAAG 59.207 52.381 33.39 23.91 0.00 2.27
24 25 2.126031 GGCGAACTGTCCGGACTC 60.126 66.667 33.39 21.99 0.00 3.36
25 26 3.692406 GGGCGAACTGTCCGGACT 61.692 66.667 33.39 15.57 28.45 3.85
43 44 1.303317 AAATCCGCTCCAAACGCCT 60.303 52.632 0.00 0.00 0.00 5.52
44 45 1.154035 CAAATCCGCTCCAAACGCC 60.154 57.895 0.00 0.00 0.00 5.68
45 46 1.154035 CCAAATCCGCTCCAAACGC 60.154 57.895 0.00 0.00 0.00 4.84
53 54 4.489771 CGAGCCCCCAAATCCGCT 62.490 66.667 0.00 0.00 0.00 5.52
55 56 2.045340 AACGAGCCCCCAAATCCG 60.045 61.111 0.00 0.00 0.00 4.18
62 63 3.487120 AATAATCTACAACGAGCCCCC 57.513 47.619 0.00 0.00 0.00 5.40
63 64 4.448210 TCAAATAATCTACAACGAGCCCC 58.552 43.478 0.00 0.00 0.00 5.80
72 75 3.964688 TCGGAGCCCTCAAATAATCTACA 59.035 43.478 0.00 0.00 0.00 2.74
79 82 3.964688 TCTACAATCGGAGCCCTCAAATA 59.035 43.478 0.00 0.00 0.00 1.40
93 96 4.184629 ACGGACTTGAAGCATCTACAATC 58.815 43.478 0.00 0.00 0.00 2.67
107 110 2.159627 GCAGTACATCCAAACGGACTTG 59.840 50.000 0.00 0.00 34.62 3.16
108 111 2.224426 TGCAGTACATCCAAACGGACTT 60.224 45.455 0.00 0.00 34.62 3.01
142 145 8.915057 TTAACTCGCTACCAATACTATAGTCT 57.085 34.615 9.12 0.00 0.00 3.24
149 152 4.049186 CGCATTAACTCGCTACCAATACT 58.951 43.478 0.00 0.00 0.00 2.12
210 213 7.239763 TGTTATTGAGACAAGGTAGATCACA 57.760 36.000 0.00 0.00 0.00 3.58
211 214 6.256757 GCTGTTATTGAGACAAGGTAGATCAC 59.743 42.308 0.00 0.00 0.00 3.06
249 252 1.008403 ACTGGTCCTCTAGCCTGGTA 58.992 55.000 0.00 0.00 0.00 3.25
386 414 3.802685 CCTGTCGTTAATTAGGCAGCTAC 59.197 47.826 1.71 0.00 0.00 3.58
393 421 6.873605 TGATGCATATCCTGTCGTTAATTAGG 59.126 38.462 0.00 0.00 32.09 2.69
428 457 8.048534 TGACACTATAGTAACCACTGAAGTAC 57.951 38.462 4.74 0.00 36.14 2.73
433 552 7.574404 CGTCTTTGACACTATAGTAACCACTGA 60.574 40.741 4.74 2.75 32.76 3.41
441 560 5.909621 AAGGCGTCTTTGACACTATAGTA 57.090 39.130 4.74 0.00 32.09 1.82
459 578 4.138487 CCCCCGTCTCATAATATAAGGC 57.862 50.000 0.00 0.00 0.00 4.35
478 598 3.832615 TTCGCCTAAGAAATACTCCCC 57.167 47.619 0.00 0.00 0.00 4.81
481 601 8.328864 CACTAACAATTCGCCTAAGAAATACTC 58.671 37.037 0.00 0.00 33.43 2.59
495 615 5.949233 TGATCGATGACACTAACAATTCG 57.051 39.130 0.54 0.00 0.00 3.34
498 618 5.755375 GGTGATGATCGATGACACTAACAAT 59.245 40.000 0.54 0.00 0.00 2.71
517 637 0.744874 ATCGACGAATGGACGGTGAT 59.255 50.000 0.00 0.00 37.61 3.06
557 677 1.346395 ACTACACTTGAACCGGATGCA 59.654 47.619 9.46 0.00 0.00 3.96
689 809 1.271856 TAACTCGGGTCAATCTGCCA 58.728 50.000 0.00 0.00 0.00 4.92
938 1065 2.579787 CGCGATGAGTGGGTCGAC 60.580 66.667 7.13 7.13 40.11 4.20
946 1073 1.006220 TGTGCTTGACGCGATGAGT 60.006 52.632 15.93 0.00 43.27 3.41
950 1077 3.121030 GCCTGTGCTTGACGCGAT 61.121 61.111 15.93 0.00 43.27 4.58
994 1121 4.175337 GCAGCTACCCATGCCGGA 62.175 66.667 5.05 0.00 36.41 5.14
1202 1329 4.079850 CGTGCTCAGGCTCAGGCT 62.080 66.667 0.00 0.00 39.66 4.58
1203 1330 4.074526 TCGTGCTCAGGCTCAGGC 62.075 66.667 0.00 0.00 39.59 4.85
1314 1441 0.108424 CCACTTCCTGCTCTCTTCCG 60.108 60.000 0.00 0.00 0.00 4.30
1320 1447 2.178580 CTCTTCTCCACTTCCTGCTCT 58.821 52.381 0.00 0.00 0.00 4.09
1650 1777 0.107410 TGTTTGTGTTGAGGGAGCGT 60.107 50.000 0.00 0.00 0.00 5.07
1719 1846 1.144936 GGAATCTGACCTCCTGCCG 59.855 63.158 1.28 0.00 0.00 5.69
1779 1906 0.666274 CGCTCGATTGCCGGCTAATA 60.666 55.000 29.70 10.85 39.14 0.98
1833 1960 2.322161 CATTGCTGCTTGGTTTTCTCG 58.678 47.619 0.00 0.00 0.00 4.04
1902 2029 1.260544 GCTCTTTTCCTGCCAATGGT 58.739 50.000 0.00 0.00 0.00 3.55
1980 2107 8.705594 CCATGGAAAGAGTACTAAAGGAAGATA 58.294 37.037 5.56 0.00 0.00 1.98
2209 2336 3.220999 CTCCCGTGTCGCTTGTCCA 62.221 63.158 0.00 0.00 0.00 4.02
2210 2337 2.432628 CTCCCGTGTCGCTTGTCC 60.433 66.667 0.00 0.00 0.00 4.02
2211 2338 1.733399 GTCTCCCGTGTCGCTTGTC 60.733 63.158 0.00 0.00 0.00 3.18
2212 2339 2.338984 GTCTCCCGTGTCGCTTGT 59.661 61.111 0.00 0.00 0.00 3.16
2213 2340 2.543687 ATCGTCTCCCGTGTCGCTTG 62.544 60.000 0.00 0.00 37.94 4.01
2214 2341 2.267681 GATCGTCTCCCGTGTCGCTT 62.268 60.000 0.00 0.00 37.94 4.68
2215 2342 2.750637 ATCGTCTCCCGTGTCGCT 60.751 61.111 0.00 0.00 37.94 4.93
2216 2343 2.278013 GATCGTCTCCCGTGTCGC 60.278 66.667 0.00 0.00 37.94 5.19
2217 2344 1.062685 CAGATCGTCTCCCGTGTCG 59.937 63.158 0.00 0.00 37.94 4.35
2218 2345 1.030488 TCCAGATCGTCTCCCGTGTC 61.030 60.000 0.00 0.00 37.94 3.67
2219 2346 0.395862 ATCCAGATCGTCTCCCGTGT 60.396 55.000 0.00 0.00 37.94 4.49
2220 2347 0.312416 GATCCAGATCGTCTCCCGTG 59.688 60.000 0.00 0.00 37.94 4.94
2221 2348 0.824182 GGATCCAGATCGTCTCCCGT 60.824 60.000 6.95 0.00 38.69 5.28
2222 2349 0.823769 TGGATCCAGATCGTCTCCCG 60.824 60.000 11.44 0.00 38.69 5.14
2223 2350 0.965439 CTGGATCCAGATCGTCTCCC 59.035 60.000 34.54 0.00 46.30 4.30
2224 2351 1.698506 ACTGGATCCAGATCGTCTCC 58.301 55.000 41.91 0.52 46.30 3.71
2225 2352 3.383185 AGAAACTGGATCCAGATCGTCTC 59.617 47.826 41.91 25.86 46.30 3.36
2226 2353 3.370104 AGAAACTGGATCCAGATCGTCT 58.630 45.455 41.91 31.09 46.30 4.18
2227 2354 3.383185 AGAGAAACTGGATCCAGATCGTC 59.617 47.826 41.91 30.37 46.30 4.20
2228 2355 3.370104 AGAGAAACTGGATCCAGATCGT 58.630 45.455 41.91 26.90 46.30 3.73
2229 2356 4.555708 CGTAGAGAAACTGGATCCAGATCG 60.556 50.000 41.91 25.99 46.30 3.69
2230 2357 4.580995 TCGTAGAGAAACTGGATCCAGATC 59.419 45.833 41.91 34.62 46.30 2.75
2231 2358 4.339814 GTCGTAGAGAAACTGGATCCAGAT 59.660 45.833 41.91 30.98 41.85 2.90
2232 2359 3.695060 GTCGTAGAGAAACTGGATCCAGA 59.305 47.826 41.91 19.56 41.85 3.86
2233 2360 3.181485 GGTCGTAGAGAAACTGGATCCAG 60.181 52.174 35.55 35.55 43.92 3.86
2234 2361 2.758979 GGTCGTAGAGAAACTGGATCCA 59.241 50.000 15.27 15.27 36.95 3.41
2235 2362 2.101082 GGGTCGTAGAGAAACTGGATCC 59.899 54.545 4.20 4.20 36.95 3.36
2236 2363 2.101082 GGGGTCGTAGAGAAACTGGATC 59.899 54.545 0.00 0.00 36.95 3.36
2237 2364 2.108970 GGGGTCGTAGAGAAACTGGAT 58.891 52.381 0.00 0.00 36.95 3.41
2238 2365 1.553706 GGGGTCGTAGAGAAACTGGA 58.446 55.000 0.00 0.00 36.95 3.86
2239 2366 0.535797 GGGGGTCGTAGAGAAACTGG 59.464 60.000 0.00 0.00 36.95 4.00
2255 2382 0.399233 AAGGAAGATCGGAGAGGGGG 60.399 60.000 0.00 0.00 43.63 5.40
2256 2383 1.044611 GAAGGAAGATCGGAGAGGGG 58.955 60.000 0.00 0.00 43.63 4.79
2257 2384 1.044611 GGAAGGAAGATCGGAGAGGG 58.955 60.000 0.00 0.00 43.63 4.30
2258 2385 1.960689 GAGGAAGGAAGATCGGAGAGG 59.039 57.143 0.00 0.00 43.63 3.69
2259 2386 2.660572 TGAGGAAGGAAGATCGGAGAG 58.339 52.381 0.00 0.00 43.63 3.20
2260 2387 2.761208 GTTGAGGAAGGAAGATCGGAGA 59.239 50.000 0.00 0.00 45.75 3.71
2261 2388 2.480416 CGTTGAGGAAGGAAGATCGGAG 60.480 54.545 0.00 0.00 0.00 4.63
2262 2389 1.476891 CGTTGAGGAAGGAAGATCGGA 59.523 52.381 0.00 0.00 0.00 4.55
2263 2390 1.471676 CCGTTGAGGAAGGAAGATCGG 60.472 57.143 0.00 0.00 45.00 4.18
2264 2391 1.204941 ACCGTTGAGGAAGGAAGATCG 59.795 52.381 0.00 0.00 45.00 3.69
2265 2392 2.622436 CACCGTTGAGGAAGGAAGATC 58.378 52.381 0.00 0.00 45.00 2.75
2266 2393 1.339151 GCACCGTTGAGGAAGGAAGAT 60.339 52.381 0.00 0.00 45.00 2.40
2267 2394 0.034896 GCACCGTTGAGGAAGGAAGA 59.965 55.000 0.00 0.00 45.00 2.87
2268 2395 0.955919 GGCACCGTTGAGGAAGGAAG 60.956 60.000 0.00 0.00 45.00 3.46
2269 2396 1.072505 GGCACCGTTGAGGAAGGAA 59.927 57.895 0.00 0.00 45.00 3.36
2270 2397 2.747686 GGCACCGTTGAGGAAGGA 59.252 61.111 0.00 0.00 45.00 3.36
2271 2398 2.742372 CGGCACCGTTGAGGAAGG 60.742 66.667 0.00 0.00 45.00 3.46
2281 2408 1.495951 GCTTTACTTGACGGCACCG 59.504 57.895 7.71 7.71 46.03 4.94
2282 2409 1.583495 GGGCTTTACTTGACGGCACC 61.583 60.000 0.00 0.00 0.00 5.01
2283 2410 1.873863 GGGCTTTACTTGACGGCAC 59.126 57.895 0.00 0.00 0.00 5.01
2284 2411 1.669760 CGGGCTTTACTTGACGGCA 60.670 57.895 0.00 0.00 0.00 5.69
2285 2412 2.396157 CCGGGCTTTACTTGACGGC 61.396 63.158 0.00 0.00 34.54 5.68
2286 2413 1.743995 CCCGGGCTTTACTTGACGG 60.744 63.158 8.08 0.00 40.89 4.79
2287 2414 1.004200 ACCCGGGCTTTACTTGACG 60.004 57.895 24.08 0.00 0.00 4.35
2288 2415 0.958876 CCACCCGGGCTTTACTTGAC 60.959 60.000 24.08 0.00 0.00 3.18
2289 2416 1.377229 CCACCCGGGCTTTACTTGA 59.623 57.895 24.08 0.00 0.00 3.02
2290 2417 3.996614 CCACCCGGGCTTTACTTG 58.003 61.111 24.08 9.53 0.00 3.16
2304 2431 3.912820 TACGTACAACCGCGGCCAC 62.913 63.158 28.58 16.59 0.00 5.01
2305 2432 3.678692 TACGTACAACCGCGGCCA 61.679 61.111 28.58 4.48 0.00 5.36
2306 2433 3.181290 GTACGTACAACCGCGGCC 61.181 66.667 28.58 7.20 0.00 6.13
2307 2434 2.126346 AGTACGTACAACCGCGGC 60.126 61.111 28.58 7.46 0.00 6.53
2308 2435 2.438954 GCAGTACGTACAACCGCGG 61.439 63.158 26.86 26.86 0.00 6.46
2309 2436 0.179192 TAGCAGTACGTACAACCGCG 60.179 55.000 26.55 0.00 0.00 6.46
2310 2437 1.916000 CTTAGCAGTACGTACAACCGC 59.084 52.381 26.55 20.98 0.00 5.68
2311 2438 2.523015 CCTTAGCAGTACGTACAACCG 58.477 52.381 26.55 13.10 0.00 4.44
2312 2439 2.094338 AGCCTTAGCAGTACGTACAACC 60.094 50.000 26.55 14.01 43.56 3.77
2313 2440 3.227810 AGCCTTAGCAGTACGTACAAC 57.772 47.619 26.55 17.51 43.56 3.32
2314 2441 3.947910 AAGCCTTAGCAGTACGTACAA 57.052 42.857 26.55 11.64 43.56 2.41
2315 2442 3.006110 ACAAAGCCTTAGCAGTACGTACA 59.994 43.478 26.55 3.86 43.56 2.90
2316 2443 3.582780 ACAAAGCCTTAGCAGTACGTAC 58.417 45.455 18.10 18.10 43.56 3.67
2317 2444 3.947910 ACAAAGCCTTAGCAGTACGTA 57.052 42.857 0.00 0.00 43.56 3.57
2318 2445 2.833631 ACAAAGCCTTAGCAGTACGT 57.166 45.000 0.00 0.00 43.56 3.57
2319 2446 2.092211 CGAACAAAGCCTTAGCAGTACG 59.908 50.000 0.00 0.00 43.56 3.67
2320 2447 2.415512 CCGAACAAAGCCTTAGCAGTAC 59.584 50.000 0.00 0.00 43.56 2.73
2321 2448 2.038033 ACCGAACAAAGCCTTAGCAGTA 59.962 45.455 0.00 0.00 43.56 2.74
2322 2449 1.202770 ACCGAACAAAGCCTTAGCAGT 60.203 47.619 0.00 0.00 43.56 4.40
2323 2450 1.523758 ACCGAACAAAGCCTTAGCAG 58.476 50.000 0.00 0.00 43.56 4.24
2324 2451 1.606668 CAACCGAACAAAGCCTTAGCA 59.393 47.619 0.00 0.00 43.56 3.49
2325 2452 1.607148 ACAACCGAACAAAGCCTTAGC 59.393 47.619 0.00 0.00 40.32 3.09
2326 2453 4.062991 ACTACAACCGAACAAAGCCTTAG 58.937 43.478 0.00 0.00 0.00 2.18
2327 2454 3.810941 CACTACAACCGAACAAAGCCTTA 59.189 43.478 0.00 0.00 0.00 2.69
2328 2455 2.616842 CACTACAACCGAACAAAGCCTT 59.383 45.455 0.00 0.00 0.00 4.35
2471 2598 0.820871 GATTCAGCCTGACGACCTCT 59.179 55.000 0.00 0.00 0.00 3.69
2530 2657 1.270147 GCAGGGTATCGAATACGGCTT 60.270 52.381 0.00 0.00 40.21 4.35
2564 2691 0.326264 AAGGCCGAACTGCTGAATCT 59.674 50.000 0.00 0.00 0.00 2.40
2797 3284 3.260483 GAGCAGCGATGGCGTGAG 61.260 66.667 1.46 0.00 46.35 3.51
2798 3285 4.819761 GGAGCAGCGATGGCGTGA 62.820 66.667 1.46 0.00 46.35 4.35
2801 3288 4.957684 ATCGGAGCAGCGATGGCG 62.958 66.667 1.46 0.00 46.35 5.69
2802 3289 3.040763 GATCGGAGCAGCGATGGC 61.041 66.667 1.46 0.00 40.37 4.40
2803 3290 2.732468 CGATCGGAGCAGCGATGG 60.732 66.667 7.38 0.00 0.00 3.51
2804 3291 3.401411 GCGATCGGAGCAGCGATG 61.401 66.667 18.30 0.00 34.19 3.84
2805 3292 4.654412 GGCGATCGGAGCAGCGAT 62.654 66.667 18.30 0.00 36.08 4.58
2913 3687 2.424474 CAGCGCTACTGGAGGAGAT 58.576 57.895 10.99 0.00 43.19 2.75
2959 3745 1.202758 TCTTTCGATTGTGTGGTGGCT 60.203 47.619 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.