Multiple sequence alignment - TraesCS7D01G480800

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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 TraesCS7D01G480800 chr7D 100.000 2510 0 0 1 2510 591294716 591297225 0 4636
1 TraesCS7D01G480800 chr7B 91.882 2365 119 32 1 2317 672396417 672394078 0 3236
2 TraesCS7D01G480800 chr7A 92.002 1688 66 21 687 2314 681818248 681819926 0 2305
3 TraesCS7D01G480800 chr7A 91.963 647 48 3 1 646 681817605 681818248 0 904


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 TraesCS7D01G480800 chr7D 591294716 591297225 2509 False 4636.0 4636 100.0000 1 2510 1 chr7D.!!$F1 2509
1 TraesCS7D01G480800 chr7B 672394078 672396417 2339 True 3236.0 3236 91.8820 1 2317 1 chr7B.!!$R1 2316
2 TraesCS7D01G480800 chr7A 681817605 681819926 2321 False 1604.5 2305 91.9825 1 2314 2 chr7A.!!$F1 2313

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
302 308 0.040058 TAACCAGTCCCGACCTAGCA 59.96 55.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1836 0.035152 TCGCCAGCAACCATCTCATT 60.035 50.0 0.0 0.0 0.0 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
28 29 0.313672 TTTGCGTGTTCAATCTGCCC 59.686 50.000 0.00 0.00 0.00 5.36
86 87 5.324409 ACTAGAGATTTGGCATTCAAACCA 58.676 37.500 0.00 0.00 46.72 3.67
87 88 4.525912 AGAGATTTGGCATTCAAACCAC 57.474 40.909 0.00 0.00 46.72 4.16
97 98 3.060339 GCATTCAAACCACGCTGAAAAAG 60.060 43.478 0.00 0.00 35.31 2.27
98 99 4.358851 CATTCAAACCACGCTGAAAAAGA 58.641 39.130 0.00 0.00 35.31 2.52
107 108 6.665465 ACCACGCTGAAAAAGAAATACTTAC 58.335 36.000 0.00 0.00 37.93 2.34
133 136 1.183549 GTCCGGCTCCTTTCTAGTCA 58.816 55.000 0.00 0.00 0.00 3.41
134 137 1.135053 GTCCGGCTCCTTTCTAGTCAC 60.135 57.143 0.00 0.00 0.00 3.67
135 138 0.175989 CCGGCTCCTTTCTAGTCACC 59.824 60.000 0.00 0.00 0.00 4.02
136 139 1.187087 CGGCTCCTTTCTAGTCACCT 58.813 55.000 0.00 0.00 0.00 4.00
137 140 1.134965 CGGCTCCTTTCTAGTCACCTG 60.135 57.143 0.00 0.00 0.00 4.00
138 141 1.903183 GGCTCCTTTCTAGTCACCTGT 59.097 52.381 0.00 0.00 0.00 4.00
139 142 3.097614 GGCTCCTTTCTAGTCACCTGTA 58.902 50.000 0.00 0.00 0.00 2.74
140 143 3.514309 GGCTCCTTTCTAGTCACCTGTAA 59.486 47.826 0.00 0.00 0.00 2.41
141 144 4.496360 GCTCCTTTCTAGTCACCTGTAAC 58.504 47.826 0.00 0.00 0.00 2.50
157 160 7.125053 TCACCTGTAACTGTAATGGATCATACA 59.875 37.037 0.00 0.23 0.00 2.29
182 185 2.351726 GAGAATCGTTTCACCGAATGGG 59.648 50.000 8.83 0.00 40.73 4.00
200 203 7.915397 CCGAATGGGTTATAATTCTGTCAAAAG 59.085 37.037 0.00 0.00 31.83 2.27
201 204 7.432252 CGAATGGGTTATAATTCTGTCAAAAGC 59.568 37.037 0.00 0.00 31.83 3.51
203 206 7.775053 TGGGTTATAATTCTGTCAAAAGCTT 57.225 32.000 0.00 0.00 0.00 3.74
297 303 1.447314 CGCTTAACCAGTCCCGACC 60.447 63.158 0.00 0.00 0.00 4.79
302 308 0.040058 TAACCAGTCCCGACCTAGCA 59.960 55.000 0.00 0.00 0.00 3.49
321 327 4.469657 AGCAACACCTACTTTTGATCCAA 58.530 39.130 0.00 0.00 0.00 3.53
339 345 4.761975 TCCAAGTTTTGTATAGCTACCCG 58.238 43.478 0.00 0.00 0.00 5.28
408 414 5.248640 TCCAGTTGGAAGATCAACAAGATC 58.751 41.667 9.85 0.00 46.74 2.75
620 629 6.369065 GCCTGTCATAGTTATTACTACCATGC 59.631 42.308 0.00 0.00 39.59 4.06
685 694 5.854338 TGGAAAGAAAAATATTGTTCGTCGC 59.146 36.000 11.85 5.88 0.00 5.19
934 943 2.694109 CCAACCTTACCCAAAACCGAAA 59.306 45.455 0.00 0.00 0.00 3.46
1455 1467 2.125512 ATCAAGCTCACGCCGGTC 60.126 61.111 1.90 0.00 36.60 4.79
1523 1535 3.819337 CTGGGCTGATCTCATTACATTGG 59.181 47.826 0.00 0.00 0.00 3.16
1633 1667 8.143193 CAGAAGCTGTACTATCATTGAGAAGAT 58.857 37.037 5.96 0.00 0.00 2.40
1634 1668 9.360901 AGAAGCTGTACTATCATTGAGAAGATA 57.639 33.333 5.96 0.00 0.00 1.98
1667 1707 3.594603 TTCTGAACTGAAGTCGGATCC 57.405 47.619 0.00 0.00 0.00 3.36
1852 1896 2.281345 CCCATCTGCCGCTCATCC 60.281 66.667 0.00 0.00 0.00 3.51
1873 1917 4.221422 TACGGGAGCGCCTCATGC 62.221 66.667 2.29 0.00 31.08 4.06
1923 1967 1.982073 GCCGGCGATGTCAAAGAAGG 61.982 60.000 12.58 0.00 0.00 3.46
1962 2018 1.678635 CCCCCGCATCTTGCTTCAA 60.679 57.895 0.00 0.00 42.25 2.69
1997 2053 7.936950 GACTGATTCGATTCATCTGATACAA 57.063 36.000 10.23 0.00 0.00 2.41
2014 2085 3.369381 AAGATCGATCTTGTGGCCG 57.631 52.632 34.07 0.00 44.91 6.13
2015 2086 0.537188 AAGATCGATCTTGTGGCCGT 59.463 50.000 34.07 12.45 44.91 5.68
2016 2087 0.537188 AGATCGATCTTGTGGCCGTT 59.463 50.000 22.32 0.00 31.97 4.44
2017 2088 0.652592 GATCGATCTTGTGGCCGTTG 59.347 55.000 18.29 0.00 0.00 4.10
2018 2089 1.369091 ATCGATCTTGTGGCCGTTGC 61.369 55.000 0.00 0.00 0.00 4.17
2019 2090 2.480555 GATCTTGTGGCCGTTGCG 59.519 61.111 0.00 0.00 38.85 4.85
2020 2091 2.031919 ATCTTGTGGCCGTTGCGA 59.968 55.556 0.00 0.00 38.85 5.10
2021 2092 2.240612 GATCTTGTGGCCGTTGCGAC 62.241 60.000 0.00 0.00 45.43 5.19
2050 2124 3.849953 GGCGACGCCGTCACAATC 61.850 66.667 25.24 0.00 39.62 2.67
2056 2130 2.202171 GCCGTCACAATCGCAACG 60.202 61.111 0.00 0.00 35.01 4.10
2074 2148 0.638746 CGTGAACGTAGCCGCTTAAG 59.361 55.000 0.00 0.00 37.70 1.85
2314 2395 2.755103 GGCTTGAAGAATGGTTAGGGTG 59.245 50.000 0.00 0.00 0.00 4.61
2317 2398 3.328382 TGAAGAATGGTTAGGGTGTCG 57.672 47.619 0.00 0.00 0.00 4.35
2318 2399 2.901192 TGAAGAATGGTTAGGGTGTCGA 59.099 45.455 0.00 0.00 0.00 4.20
2319 2400 3.325425 TGAAGAATGGTTAGGGTGTCGAA 59.675 43.478 0.00 0.00 0.00 3.71
2320 2401 3.611766 AGAATGGTTAGGGTGTCGAAG 57.388 47.619 0.00 0.00 0.00 3.79
2321 2402 2.236395 AGAATGGTTAGGGTGTCGAAGG 59.764 50.000 0.00 0.00 0.00 3.46
2322 2403 1.652947 ATGGTTAGGGTGTCGAAGGT 58.347 50.000 0.00 0.00 0.00 3.50
2323 2404 0.682852 TGGTTAGGGTGTCGAAGGTG 59.317 55.000 0.00 0.00 0.00 4.00
2324 2405 0.683412 GGTTAGGGTGTCGAAGGTGT 59.317 55.000 0.00 0.00 0.00 4.16
2325 2406 1.895131 GGTTAGGGTGTCGAAGGTGTA 59.105 52.381 0.00 0.00 0.00 2.90
2326 2407 2.299867 GGTTAGGGTGTCGAAGGTGTAA 59.700 50.000 0.00 0.00 0.00 2.41
2327 2408 3.244181 GGTTAGGGTGTCGAAGGTGTAAA 60.244 47.826 0.00 0.00 0.00 2.01
2328 2409 2.538512 AGGGTGTCGAAGGTGTAAAC 57.461 50.000 0.00 0.00 0.00 2.01
2329 2410 1.071228 AGGGTGTCGAAGGTGTAAACC 59.929 52.381 0.00 0.00 0.00 3.27
2330 2411 1.142474 GGTGTCGAAGGTGTAAACCG 58.858 55.000 0.00 0.00 34.28 4.44
2331 2412 0.509929 GTGTCGAAGGTGTAAACCGC 59.490 55.000 0.00 0.00 34.28 5.68
2332 2413 0.104487 TGTCGAAGGTGTAAACCGCA 59.896 50.000 0.00 0.00 34.28 5.69
2333 2414 0.788391 GTCGAAGGTGTAAACCGCAG 59.212 55.000 0.00 0.00 34.28 5.18
2334 2415 0.390124 TCGAAGGTGTAAACCGCAGT 59.610 50.000 0.00 0.00 34.28 4.40
2335 2416 0.511221 CGAAGGTGTAAACCGCAGTG 59.489 55.000 0.00 0.00 34.28 3.66
2336 2417 1.870580 CGAAGGTGTAAACCGCAGTGA 60.871 52.381 0.00 0.00 34.28 3.41
2337 2418 2.423577 GAAGGTGTAAACCGCAGTGAT 58.576 47.619 0.00 0.00 34.28 3.06
2338 2419 2.094762 AGGTGTAAACCGCAGTGATC 57.905 50.000 0.00 0.00 34.28 2.92
2339 2420 1.623811 AGGTGTAAACCGCAGTGATCT 59.376 47.619 0.00 0.00 34.28 2.75
2340 2421 2.038557 AGGTGTAAACCGCAGTGATCTT 59.961 45.455 0.00 0.00 34.28 2.40
2341 2422 3.259876 AGGTGTAAACCGCAGTGATCTTA 59.740 43.478 0.00 0.00 34.28 2.10
2342 2423 4.081087 AGGTGTAAACCGCAGTGATCTTAT 60.081 41.667 0.00 0.00 34.28 1.73
2343 2424 4.634443 GGTGTAAACCGCAGTGATCTTATT 59.366 41.667 0.00 0.00 0.00 1.40
2344 2425 5.123344 GGTGTAAACCGCAGTGATCTTATTT 59.877 40.000 0.00 0.00 0.00 1.40
2345 2426 6.021596 GTGTAAACCGCAGTGATCTTATTTG 58.978 40.000 0.00 0.00 0.00 2.32
2346 2427 3.764885 AACCGCAGTGATCTTATTTGC 57.235 42.857 0.00 0.00 0.00 3.68
2347 2428 2.017049 ACCGCAGTGATCTTATTTGCC 58.983 47.619 0.00 0.00 0.00 4.52
2348 2429 2.016318 CCGCAGTGATCTTATTTGCCA 58.984 47.619 0.00 0.00 0.00 4.92
2349 2430 2.620115 CCGCAGTGATCTTATTTGCCAT 59.380 45.455 0.00 0.00 0.00 4.40
2350 2431 3.549423 CCGCAGTGATCTTATTTGCCATG 60.549 47.826 0.00 0.00 0.00 3.66
2351 2432 3.378339 GCAGTGATCTTATTTGCCATGC 58.622 45.455 0.00 0.00 0.00 4.06
2352 2433 3.181484 GCAGTGATCTTATTTGCCATGCA 60.181 43.478 0.00 0.00 36.47 3.96
2353 2434 4.500887 GCAGTGATCTTATTTGCCATGCAT 60.501 41.667 0.00 0.00 38.76 3.96
2354 2435 5.220381 CAGTGATCTTATTTGCCATGCATC 58.780 41.667 0.00 0.00 38.76 3.91
2355 2436 5.009710 CAGTGATCTTATTTGCCATGCATCT 59.990 40.000 0.00 0.00 38.76 2.90
2356 2437 5.241064 AGTGATCTTATTTGCCATGCATCTC 59.759 40.000 0.00 0.00 38.76 2.75
2357 2438 4.214758 TGATCTTATTTGCCATGCATCTCG 59.785 41.667 0.00 0.00 38.76 4.04
2358 2439 2.291465 TCTTATTTGCCATGCATCTCGC 59.709 45.455 0.00 0.00 38.76 5.03
2359 2440 0.587768 TATTTGCCATGCATCTCGCG 59.412 50.000 0.00 0.00 46.97 5.87
2360 2441 2.067091 ATTTGCCATGCATCTCGCGG 62.067 55.000 6.13 0.00 46.97 6.46
2363 2444 2.029518 CCATGCATCTCGCGGCTA 59.970 61.111 6.13 0.00 46.97 3.93
2364 2445 2.025969 CCATGCATCTCGCGGCTAG 61.026 63.158 6.13 0.00 46.97 3.42
2365 2446 2.356793 ATGCATCTCGCGGCTAGC 60.357 61.111 6.04 6.04 46.97 3.42
2366 2447 3.873026 ATGCATCTCGCGGCTAGCC 62.873 63.158 24.75 24.75 46.97 3.93
2367 2448 4.292178 GCATCTCGCGGCTAGCCT 62.292 66.667 30.55 8.77 44.76 4.58
2368 2449 2.049618 CATCTCGCGGCTAGCCTC 60.050 66.667 30.55 22.76 44.76 4.70
2369 2450 2.203422 ATCTCGCGGCTAGCCTCT 60.203 61.111 30.55 4.70 44.76 3.69
2370 2451 2.265182 ATCTCGCGGCTAGCCTCTC 61.265 63.158 30.55 17.93 44.76 3.20
2371 2452 3.972276 CTCGCGGCTAGCCTCTCC 61.972 72.222 30.55 14.98 44.76 3.71
2372 2453 4.507916 TCGCGGCTAGCCTCTCCT 62.508 66.667 30.55 0.00 44.76 3.69
2373 2454 3.972276 CGCGGCTAGCCTCTCCTC 61.972 72.222 30.55 11.60 44.76 3.71
2374 2455 3.611674 GCGGCTAGCCTCTCCTCC 61.612 72.222 30.55 6.97 40.81 4.30
2375 2456 2.197324 CGGCTAGCCTCTCCTCCT 59.803 66.667 30.55 0.00 0.00 3.69
2376 2457 1.901464 CGGCTAGCCTCTCCTCCTC 60.901 68.421 30.55 1.09 0.00 3.71
2377 2458 1.541672 GGCTAGCCTCTCCTCCTCT 59.458 63.158 27.17 0.00 0.00 3.69
2378 2459 0.105709 GGCTAGCCTCTCCTCCTCTT 60.106 60.000 27.17 0.00 0.00 2.85
2379 2460 1.328279 GCTAGCCTCTCCTCCTCTTC 58.672 60.000 2.29 0.00 0.00 2.87
2380 2461 1.133482 GCTAGCCTCTCCTCCTCTTCT 60.133 57.143 2.29 0.00 0.00 2.85
2381 2462 2.689723 GCTAGCCTCTCCTCCTCTTCTT 60.690 54.545 2.29 0.00 0.00 2.52
2382 2463 2.159179 AGCCTCTCCTCCTCTTCTTC 57.841 55.000 0.00 0.00 0.00 2.87
2383 2464 1.645919 AGCCTCTCCTCCTCTTCTTCT 59.354 52.381 0.00 0.00 0.00 2.85
2384 2465 2.031870 GCCTCTCCTCCTCTTCTTCTC 58.968 57.143 0.00 0.00 0.00 2.87
2385 2466 2.666317 CCTCTCCTCCTCTTCTTCTCC 58.334 57.143 0.00 0.00 0.00 3.71
2386 2467 2.666317 CTCTCCTCCTCTTCTTCTCCC 58.334 57.143 0.00 0.00 0.00 4.30
2387 2468 2.244769 CTCTCCTCCTCTTCTTCTCCCT 59.755 54.545 0.00 0.00 0.00 4.20
2388 2469 2.243736 TCTCCTCCTCTTCTTCTCCCTC 59.756 54.545 0.00 0.00 0.00 4.30
2389 2470 2.003830 TCCTCCTCTTCTTCTCCCTCA 58.996 52.381 0.00 0.00 0.00 3.86
2390 2471 2.024464 TCCTCCTCTTCTTCTCCCTCAG 60.024 54.545 0.00 0.00 0.00 3.35
2391 2472 2.387757 CTCCTCTTCTTCTCCCTCAGG 58.612 57.143 0.00 0.00 0.00 3.86
2392 2473 0.829990 CCTCTTCTTCTCCCTCAGGC 59.170 60.000 0.00 0.00 0.00 4.85
2393 2474 0.459489 CTCTTCTTCTCCCTCAGGCG 59.541 60.000 0.00 0.00 0.00 5.52
2394 2475 0.251832 TCTTCTTCTCCCTCAGGCGT 60.252 55.000 0.00 0.00 0.00 5.68
2395 2476 0.174617 CTTCTTCTCCCTCAGGCGTC 59.825 60.000 0.00 0.00 0.00 5.19
2396 2477 1.595993 TTCTTCTCCCTCAGGCGTCG 61.596 60.000 0.00 0.00 0.00 5.12
2397 2478 3.708220 CTTCTCCCTCAGGCGTCGC 62.708 68.421 9.22 9.22 0.00 5.19
2436 2517 2.692741 CCCCCTCCTCCACCTTCC 60.693 72.222 0.00 0.00 0.00 3.46
2437 2518 3.083997 CCCCTCCTCCACCTTCCG 61.084 72.222 0.00 0.00 0.00 4.30
2438 2519 3.083997 CCCTCCTCCACCTTCCGG 61.084 72.222 0.00 0.00 0.00 5.14
2439 2520 3.787001 CCTCCTCCACCTTCCGGC 61.787 72.222 0.00 0.00 0.00 6.13
2440 2521 3.787001 CTCCTCCACCTTCCGGCC 61.787 72.222 0.00 0.00 0.00 6.13
2455 2536 4.201122 GCCCCCTCTCCCTGCATG 62.201 72.222 0.00 0.00 0.00 4.06
2456 2537 3.496160 CCCCCTCTCCCTGCATGG 61.496 72.222 0.78 0.78 0.00 3.66
2457 2538 4.201122 CCCCTCTCCCTGCATGGC 62.201 72.222 2.62 0.00 0.00 4.40
2458 2539 4.201122 CCCTCTCCCTGCATGGCC 62.201 72.222 2.62 0.00 0.00 5.36
2459 2540 4.559063 CCTCTCCCTGCATGGCCG 62.559 72.222 2.62 0.00 0.00 6.13
2460 2541 3.473647 CTCTCCCTGCATGGCCGA 61.474 66.667 2.62 1.82 0.00 5.54
2461 2542 3.746949 CTCTCCCTGCATGGCCGAC 62.747 68.421 2.62 0.00 0.00 4.79
2480 2561 4.697756 CCTCCTCAACGCCCGCAA 62.698 66.667 0.00 0.00 0.00 4.85
2481 2562 2.436646 CTCCTCAACGCCCGCAAT 60.437 61.111 0.00 0.00 0.00 3.56
2482 2563 2.745884 TCCTCAACGCCCGCAATG 60.746 61.111 0.00 0.00 0.00 2.82
2483 2564 4.481112 CCTCAACGCCCGCAATGC 62.481 66.667 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.666888 GGGCAGATTGAACACGCAAAG 60.667 52.381 0.00 0.00 0.00 2.77
28 29 4.449068 CACACCAAAAGTAGCTGACAGTAG 59.551 45.833 3.99 0.00 0.00 2.57
86 87 8.094798 TCATGTAAGTATTTCTTTTTCAGCGT 57.905 30.769 0.00 0.00 37.56 5.07
87 88 8.230486 ACTCATGTAAGTATTTCTTTTTCAGCG 58.770 33.333 0.00 0.00 37.56 5.18
97 98 4.270325 GCCGGACACTCATGTAAGTATTTC 59.730 45.833 5.05 0.00 39.95 2.17
98 99 4.081087 AGCCGGACACTCATGTAAGTATTT 60.081 41.667 5.05 0.00 39.95 1.40
107 108 0.036010 AAAGGAGCCGGACACTCATG 60.036 55.000 5.05 0.00 35.79 3.07
133 136 7.432148 TGTATGATCCATTACAGTTACAGGT 57.568 36.000 0.00 0.00 0.00 4.00
134 137 8.731275 TTTGTATGATCCATTACAGTTACAGG 57.269 34.615 0.00 0.00 0.00 4.00
135 138 8.830580 CCTTTGTATGATCCATTACAGTTACAG 58.169 37.037 0.00 0.00 0.00 2.74
136 139 8.544622 TCCTTTGTATGATCCATTACAGTTACA 58.455 33.333 0.00 0.00 0.00 2.41
137 140 8.958119 TCCTTTGTATGATCCATTACAGTTAC 57.042 34.615 0.00 0.00 0.00 2.50
138 141 8.988060 TCTCCTTTGTATGATCCATTACAGTTA 58.012 33.333 0.00 0.00 0.00 2.24
139 142 7.861629 TCTCCTTTGTATGATCCATTACAGTT 58.138 34.615 0.00 0.00 0.00 3.16
140 143 7.437713 TCTCCTTTGTATGATCCATTACAGT 57.562 36.000 0.00 0.00 0.00 3.55
141 144 8.915057 ATTCTCCTTTGTATGATCCATTACAG 57.085 34.615 0.00 0.00 0.00 2.74
157 160 3.396260 TCGGTGAAACGATTCTCCTTT 57.604 42.857 20.00 0.00 43.79 3.11
188 191 9.196552 GCTTTGTATTTAAGCTTTTGACAGAAT 57.803 29.630 3.20 0.00 43.56 2.40
200 203 3.182182 GGCTGCAGCTTTGTATTTAAGC 58.818 45.455 35.82 12.52 46.47 3.09
201 204 4.439305 TGGCTGCAGCTTTGTATTTAAG 57.561 40.909 35.82 0.00 41.70 1.85
203 206 4.280677 ACTTTGGCTGCAGCTTTGTATTTA 59.719 37.500 35.82 11.73 41.70 1.40
206 209 2.029649 CACTTTGGCTGCAGCTTTGTAT 60.030 45.455 35.82 16.14 41.70 2.29
268 274 5.163884 GGACTGGTTAAGCGACTGTTTATTC 60.164 44.000 0.00 0.00 0.00 1.75
297 303 5.245531 TGGATCAAAAGTAGGTGTTGCTAG 58.754 41.667 0.00 0.00 0.00 3.42
302 308 7.093509 ACAAAACTTGGATCAAAAGTAGGTGTT 60.094 33.333 12.05 2.37 36.87 3.32
321 327 5.416947 CAAGACGGGTAGCTATACAAAACT 58.583 41.667 0.00 0.00 33.21 2.66
408 414 7.716560 TCACATAATCACAGGATCTTTGTATGG 59.283 37.037 12.07 5.70 29.46 2.74
934 943 1.824230 TCTTGGTTTTTGCTGCTGTGT 59.176 42.857 0.00 0.00 0.00 3.72
1247 1256 1.080025 CCCCCTTCTTCGTCGTCAC 60.080 63.158 0.00 0.00 0.00 3.67
1316 1328 1.450312 GGGTCCATCTCGCTGTTGG 60.450 63.158 0.00 0.00 36.98 3.77
1324 1336 2.202756 GTCACGCGGGTCCATCTC 60.203 66.667 8.89 0.00 0.00 2.75
1325 1337 2.994995 TGTCACGCGGGTCCATCT 60.995 61.111 8.89 0.00 0.00 2.90
1326 1338 2.813908 GTGTCACGCGGGTCCATC 60.814 66.667 8.89 0.00 0.00 3.51
1327 1339 4.735132 CGTGTCACGCGGGTCCAT 62.735 66.667 13.22 0.00 33.65 3.41
1423 1435 3.788766 GATGACGTGCCACACCGC 61.789 66.667 0.00 0.00 0.00 5.68
1455 1467 4.803426 GTGACCTCGCAGCCCTCG 62.803 72.222 0.00 0.00 0.00 4.63
1523 1535 7.855545 AGTAGACATAATCGCAATCAATTGAC 58.144 34.615 11.07 0.00 40.14 3.18
1636 1670 8.926710 CGACTTCAGTTCAGAATGTAGTAATTT 58.073 33.333 0.00 0.00 37.40 1.82
1638 1672 7.036220 CCGACTTCAGTTCAGAATGTAGTAAT 58.964 38.462 0.00 0.00 37.40 1.89
1639 1673 6.208007 TCCGACTTCAGTTCAGAATGTAGTAA 59.792 38.462 0.00 0.00 37.40 2.24
1640 1674 5.708697 TCCGACTTCAGTTCAGAATGTAGTA 59.291 40.000 0.00 0.00 37.40 1.82
1642 1676 5.060662 TCCGACTTCAGTTCAGAATGTAG 57.939 43.478 0.00 0.00 37.40 2.74
1651 1691 2.099263 TCGATGGATCCGACTTCAGTTC 59.901 50.000 7.39 0.00 0.00 3.01
1743 1787 0.521735 GCCGTCCTTGGATGACAAAC 59.478 55.000 10.25 0.00 38.91 2.93
1792 1836 0.035152 TCGCCAGCAACCATCTCATT 60.035 50.000 0.00 0.00 0.00 2.57
1800 1844 1.522580 GAGGATCTCGCCAGCAACC 60.523 63.158 0.00 0.00 0.00 3.77
1905 1949 1.982073 GCCTTCTTTGACATCGCCGG 61.982 60.000 0.00 0.00 0.00 6.13
1949 2002 4.023878 GGAGATGAGATTGAAGCAAGATGC 60.024 45.833 0.00 0.00 45.46 3.91
1962 2018 3.913548 CGAATCAGTCGGAGATGAGAT 57.086 47.619 0.00 0.00 46.45 2.75
1997 2053 0.537188 AACGGCCACAAGATCGATCT 59.463 50.000 22.32 22.32 39.22 2.75
2019 2090 2.811317 CGCCGGCAGACTTGAGTC 60.811 66.667 28.98 2.93 45.08 3.36
2020 2091 3.303135 TCGCCGGCAGACTTGAGT 61.303 61.111 28.98 0.00 0.00 3.41
2021 2092 2.811317 GTCGCCGGCAGACTTGAG 60.811 66.667 30.94 14.15 35.84 3.02
2043 2117 0.231024 CGTTCACGTTGCGATTGTGA 59.769 50.000 7.66 7.66 40.62 3.58
2056 2130 0.997196 CCTTAAGCGGCTACGTTCAC 59.003 55.000 1.35 0.00 43.45 3.18
2074 2148 2.430244 TTCGTGACGCGCTTCTCC 60.430 61.111 15.44 4.90 41.07 3.71
2151 2225 2.268920 GGAGCCATCGCCTCAACA 59.731 61.111 0.00 0.00 34.57 3.33
2284 2362 3.057736 CCATTCTTCAAGCCAGACACTTG 60.058 47.826 0.00 0.00 44.76 3.16
2288 2366 2.957402 ACCATTCTTCAAGCCAGACA 57.043 45.000 0.00 0.00 0.00 3.41
2289 2367 3.691609 CCTAACCATTCTTCAAGCCAGAC 59.308 47.826 0.00 0.00 0.00 3.51
2314 2395 0.788391 CTGCGGTTTACACCTTCGAC 59.212 55.000 0.00 0.00 41.64 4.20
2317 2398 1.873698 TCACTGCGGTTTACACCTTC 58.126 50.000 0.00 0.00 41.64 3.46
2318 2399 2.038557 AGATCACTGCGGTTTACACCTT 59.961 45.455 0.00 0.00 41.64 3.50
2319 2400 1.623811 AGATCACTGCGGTTTACACCT 59.376 47.619 0.00 0.00 41.64 4.00
2320 2401 2.094762 AGATCACTGCGGTTTACACC 57.905 50.000 0.00 0.00 40.16 4.16
2321 2402 5.796350 AATAAGATCACTGCGGTTTACAC 57.204 39.130 0.00 0.00 0.00 2.90
2322 2403 5.391523 GCAAATAAGATCACTGCGGTTTACA 60.392 40.000 0.00 0.00 0.00 2.41
2323 2404 5.028375 GCAAATAAGATCACTGCGGTTTAC 58.972 41.667 0.00 0.00 0.00 2.01
2324 2405 4.095782 GGCAAATAAGATCACTGCGGTTTA 59.904 41.667 0.00 0.00 33.76 2.01
2325 2406 3.119495 GGCAAATAAGATCACTGCGGTTT 60.119 43.478 0.00 0.00 33.76 3.27
2326 2407 2.423538 GGCAAATAAGATCACTGCGGTT 59.576 45.455 0.00 0.00 33.76 4.44
2327 2408 2.017049 GGCAAATAAGATCACTGCGGT 58.983 47.619 0.00 0.00 33.76 5.68
2328 2409 2.016318 TGGCAAATAAGATCACTGCGG 58.984 47.619 0.00 0.00 33.76 5.69
2329 2410 3.624900 CATGGCAAATAAGATCACTGCG 58.375 45.455 0.00 0.00 33.76 5.18
2330 2411 3.181484 TGCATGGCAAATAAGATCACTGC 60.181 43.478 0.00 0.00 34.76 4.40
2331 2412 4.642445 TGCATGGCAAATAAGATCACTG 57.358 40.909 0.00 0.00 34.76 3.66
2332 2413 5.138276 AGATGCATGGCAAATAAGATCACT 58.862 37.500 2.46 0.00 43.62 3.41
2333 2414 5.449107 AGATGCATGGCAAATAAGATCAC 57.551 39.130 2.46 0.00 43.62 3.06
2334 2415 4.214758 CGAGATGCATGGCAAATAAGATCA 59.785 41.667 2.46 0.00 43.62 2.92
2335 2416 4.720090 CGAGATGCATGGCAAATAAGATC 58.280 43.478 2.46 0.00 43.62 2.75
2336 2417 3.057736 GCGAGATGCATGGCAAATAAGAT 60.058 43.478 2.46 0.00 43.62 2.40
2337 2418 2.291465 GCGAGATGCATGGCAAATAAGA 59.709 45.455 2.46 0.00 43.62 2.10
2338 2419 2.658285 GCGAGATGCATGGCAAATAAG 58.342 47.619 2.46 0.00 43.62 1.73
2339 2420 1.002576 CGCGAGATGCATGGCAAATAA 60.003 47.619 2.46 0.00 46.97 1.40
2340 2421 0.587768 CGCGAGATGCATGGCAAATA 59.412 50.000 2.46 0.00 46.97 1.40
2341 2422 1.357690 CGCGAGATGCATGGCAAAT 59.642 52.632 2.46 0.00 46.97 2.32
2342 2423 2.763273 CCGCGAGATGCATGGCAAA 61.763 57.895 8.23 0.00 46.97 3.68
2343 2424 3.204119 CCGCGAGATGCATGGCAA 61.204 61.111 8.23 0.00 46.97 4.52
2346 2427 2.025969 CTAGCCGCGAGATGCATGG 61.026 63.158 8.23 0.00 46.97 3.66
2347 2428 2.665395 GCTAGCCGCGAGATGCATG 61.665 63.158 8.23 0.13 46.97 4.06
2348 2429 2.356793 GCTAGCCGCGAGATGCAT 60.357 61.111 8.23 0.00 46.97 3.96
2349 2430 4.592192 GGCTAGCCGCGAGATGCA 62.592 66.667 20.16 0.00 46.97 3.96
2350 2431 4.292178 AGGCTAGCCGCGAGATGC 62.292 66.667 27.83 1.15 41.95 3.91
2351 2432 2.049618 GAGGCTAGCCGCGAGATG 60.050 66.667 27.83 0.00 41.95 2.90
2352 2433 2.203422 AGAGGCTAGCCGCGAGAT 60.203 61.111 28.76 11.30 40.92 2.75
2353 2434 2.902846 GAGAGGCTAGCCGCGAGA 60.903 66.667 28.76 0.00 40.92 4.04
2354 2435 3.972276 GGAGAGGCTAGCCGCGAG 61.972 72.222 28.76 0.00 40.92 5.03
2355 2436 4.507916 AGGAGAGGCTAGCCGCGA 62.508 66.667 28.76 0.00 40.92 5.87
2356 2437 3.972276 GAGGAGAGGCTAGCCGCG 61.972 72.222 28.76 0.00 40.92 6.46
2357 2438 3.611674 GGAGGAGAGGCTAGCCGC 61.612 72.222 28.28 28.28 41.95 6.53
2358 2439 1.901464 GAGGAGGAGAGGCTAGCCG 60.901 68.421 27.83 0.00 41.95 5.52
2359 2440 0.105709 AAGAGGAGGAGAGGCTAGCC 60.106 60.000 27.19 27.19 0.00 3.93
2360 2441 1.133482 AGAAGAGGAGGAGAGGCTAGC 60.133 57.143 6.04 6.04 0.00 3.42
2361 2442 3.117512 AGAAGAAGAGGAGGAGAGGCTAG 60.118 52.174 0.00 0.00 0.00 3.42
2362 2443 2.856231 AGAAGAAGAGGAGGAGAGGCTA 59.144 50.000 0.00 0.00 0.00 3.93
2363 2444 1.645919 AGAAGAAGAGGAGGAGAGGCT 59.354 52.381 0.00 0.00 0.00 4.58
2364 2445 2.031870 GAGAAGAAGAGGAGGAGAGGC 58.968 57.143 0.00 0.00 0.00 4.70
2365 2446 2.666317 GGAGAAGAAGAGGAGGAGAGG 58.334 57.143 0.00 0.00 0.00 3.69
2366 2447 2.244769 AGGGAGAAGAAGAGGAGGAGAG 59.755 54.545 0.00 0.00 0.00 3.20
2367 2448 2.243736 GAGGGAGAAGAAGAGGAGGAGA 59.756 54.545 0.00 0.00 0.00 3.71
2368 2449 2.024464 TGAGGGAGAAGAAGAGGAGGAG 60.024 54.545 0.00 0.00 0.00 3.69
2369 2450 2.003830 TGAGGGAGAAGAAGAGGAGGA 58.996 52.381 0.00 0.00 0.00 3.71
2370 2451 2.387757 CTGAGGGAGAAGAAGAGGAGG 58.612 57.143 0.00 0.00 0.00 4.30
2371 2452 2.387757 CCTGAGGGAGAAGAAGAGGAG 58.612 57.143 0.00 0.00 33.58 3.69
2372 2453 1.621072 GCCTGAGGGAGAAGAAGAGGA 60.621 57.143 0.00 0.00 33.58 3.71
2373 2454 0.829990 GCCTGAGGGAGAAGAAGAGG 59.170 60.000 0.00 0.00 33.58 3.69
2374 2455 0.459489 CGCCTGAGGGAGAAGAAGAG 59.541 60.000 0.00 0.00 34.16 2.85
2375 2456 0.251832 ACGCCTGAGGGAGAAGAAGA 60.252 55.000 0.00 0.00 36.25 2.87
2376 2457 0.174617 GACGCCTGAGGGAGAAGAAG 59.825 60.000 0.00 0.00 36.25 2.85
2377 2458 1.595993 CGACGCCTGAGGGAGAAGAA 61.596 60.000 0.00 0.00 36.25 2.52
2378 2459 2.046864 CGACGCCTGAGGGAGAAGA 61.047 63.158 0.00 0.00 36.25 2.87
2379 2460 2.492090 CGACGCCTGAGGGAGAAG 59.508 66.667 0.00 0.00 36.25 2.85
2380 2461 3.760035 GCGACGCCTGAGGGAGAA 61.760 66.667 9.14 0.00 36.25 2.87
2419 2500 2.692741 GGAAGGTGGAGGAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
2420 2501 3.083997 CGGAAGGTGGAGGAGGGG 61.084 72.222 0.00 0.00 0.00 4.79
2438 2519 4.201122 CATGCAGGGAGAGGGGGC 62.201 72.222 0.00 0.00 0.00 5.80
2439 2520 3.496160 CCATGCAGGGAGAGGGGG 61.496 72.222 13.35 0.00 0.00 5.40
2440 2521 4.201122 GCCATGCAGGGAGAGGGG 62.201 72.222 24.18 0.00 38.09 4.79
2441 2522 4.201122 GGCCATGCAGGGAGAGGG 62.201 72.222 24.18 0.18 38.09 4.30
2442 2523 4.559063 CGGCCATGCAGGGAGAGG 62.559 72.222 24.18 2.01 38.09 3.69
2443 2524 3.473647 TCGGCCATGCAGGGAGAG 61.474 66.667 24.18 11.23 38.09 3.20
2444 2525 3.785859 GTCGGCCATGCAGGGAGA 61.786 66.667 24.18 16.67 38.09 3.71
2463 2544 3.976701 ATTGCGGGCGTTGAGGAGG 62.977 63.158 0.00 0.00 0.00 4.30
2464 2545 2.436646 ATTGCGGGCGTTGAGGAG 60.437 61.111 0.00 0.00 0.00 3.69
2465 2546 2.745884 CATTGCGGGCGTTGAGGA 60.746 61.111 0.00 0.00 0.00 3.71
2466 2547 4.481112 GCATTGCGGGCGTTGAGG 62.481 66.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.