Multiple sequence alignment - TraesCS7D01G296600

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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 TraesCS7D01G296600 chr7D 100.000 2402 0 0 1 2402 373581970 373579569 0.000000e+00 4436
1 TraesCS7D01G296600 chr7A 92.093 2188 153 10 1 2173 419561000 419558818 0.000000e+00 3064
2 TraesCS7D01G296600 chr7A 93.878 196 12 0 2124 2319 419558818 419558623 1.810000e-76 296
3 TraesCS7D01G296600 chr7A 94.444 90 5 0 2313 2402 419503127 419503038 3.220000e-29 139
4 TraesCS7D01G296600 chr1B 87.169 1434 171 10 1 1427 356448774 356450201 0.000000e+00 1616
5 TraesCS7D01G296600 chr1A 86.234 1402 180 10 1 1394 330147789 330146393 0.000000e+00 1507
6 TraesCS7D01G296600 chr1A 85.724 1429 188 11 1 1419 63809307 63810729 0.000000e+00 1495
7 TraesCS7D01G296600 chr4D 88.687 1158 120 9 279 1428 190443514 190442360 0.000000e+00 1402
8 TraesCS7D01G296600 chr4D 81.250 1264 223 12 155 1414 132965635 132964382 0.000000e+00 1009
9 TraesCS7D01G296600 chr5D 83.043 1433 225 18 1 1426 300710525 300711946 0.000000e+00 1284
10 TraesCS7D01G296600 chr2B 81.507 1433 252 12 1 1428 259369920 259371344 0.000000e+00 1166
11 TraesCS7D01G296600 chr4B 78.297 1433 294 16 1 1427 232153566 232154987 0.000000e+00 907
12 TraesCS7D01G296600 chr6B 78.884 251 44 6 1695 1939 578747242 578746995 6.870000e-36 161


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 TraesCS7D01G296600 chr7D 373579569 373581970 2401 True 4436 4436 100.0000 1 2402 1 chr7D.!!$R1 2401
1 TraesCS7D01G296600 chr7A 419558623 419561000 2377 True 1680 3064 92.9855 1 2319 2 chr7A.!!$R2 2318
2 TraesCS7D01G296600 chr1B 356448774 356450201 1427 False 1616 1616 87.1690 1 1427 1 chr1B.!!$F1 1426
3 TraesCS7D01G296600 chr1A 330146393 330147789 1396 True 1507 1507 86.2340 1 1394 1 chr1A.!!$R1 1393
4 TraesCS7D01G296600 chr1A 63809307 63810729 1422 False 1495 1495 85.7240 1 1419 1 chr1A.!!$F1 1418
5 TraesCS7D01G296600 chr4D 190442360 190443514 1154 True 1402 1402 88.6870 279 1428 1 chr4D.!!$R2 1149
6 TraesCS7D01G296600 chr4D 132964382 132965635 1253 True 1009 1009 81.2500 155 1414 1 chr4D.!!$R1 1259
7 TraesCS7D01G296600 chr5D 300710525 300711946 1421 False 1284 1284 83.0430 1 1426 1 chr5D.!!$F1 1425
8 TraesCS7D01G296600 chr2B 259369920 259371344 1424 False 1166 1166 81.5070 1 1428 1 chr2B.!!$F1 1427
9 TraesCS7D01G296600 chr4B 232153566 232154987 1421 False 907 907 78.2970 1 1427 1 chr4B.!!$F1 1426

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
25 27 0.682532 TGGCAAAGCATTATGGCGGA 60.683 50.000 0.0 0.0 44.38 5.54 F
988 1011 1.207329 GCTTAGAGACACAACGGGGAT 59.793 52.381 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1203 0.108138 CCCACTGAATGTCCTCCGTC 60.108 60.0 0.0 0.0 0.00 4.79 R
2326 2421 0.034670 ACCCAAGGAGAGCAAGATGC 60.035 55.0 0.0 0.0 45.46 3.91 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
25 27 0.682532 TGGCAAAGCATTATGGCGGA 60.683 50.000 0.00 0.00 44.38 5.54
180 192 7.221828 TCAAAAGTCGTTGATCTTATCGATG 57.778 36.000 8.54 0.00 32.56 3.84
227 239 6.046593 AGACTTAATGAGACAAACGTTGTGA 58.953 36.000 0.00 0.00 45.52 3.58
237 249 4.059511 ACAAACGTTGTGACCAATCGATA 58.940 39.130 0.00 0.00 43.48 2.92
308 320 6.756542 ACTTCATTGCTTGGAGTTTTACAAAC 59.243 34.615 0.00 0.00 41.80 2.93
312 325 5.392767 TGCTTGGAGTTTTACAAACAACA 57.607 34.783 2.38 0.00 0.00 3.33
380 395 9.545105 AAACAATATGAGAGAAAATTGCAACAA 57.455 25.926 0.00 0.00 33.57 2.83
448 463 3.581332 AGTTGGAAGTTATCTTGTCCGGA 59.419 43.478 0.00 0.00 33.64 5.14
492 507 4.251268 GCGTACTTTACATGGAACTCCTT 58.749 43.478 0.00 0.00 36.82 3.36
535 550 8.801299 TGCAAATAGACATATGAAAGTTTTGGA 58.199 29.630 10.38 10.41 0.00 3.53
759 777 8.456471 AGAATGTATGTGAACTGATTGTCATTG 58.544 33.333 0.00 0.00 0.00 2.82
840 861 3.013921 GCATACCAAGTTTCGATGGGAA 58.986 45.455 7.65 0.00 41.17 3.97
915 937 5.104318 GGTAAAAGAGAGGGATGGACAAGAT 60.104 44.000 0.00 0.00 0.00 2.40
988 1011 1.207329 GCTTAGAGACACAACGGGGAT 59.793 52.381 0.00 0.00 0.00 3.85
1092 1121 1.668419 GTTTGGCTCTGCGATATGGT 58.332 50.000 0.00 0.00 0.00 3.55
1193 1225 0.543749 GGAGGACATTCAGTGGGAGG 59.456 60.000 0.00 0.00 0.00 4.30
1214 1246 1.497278 CGGCGACAGTGTTTGATGG 59.503 57.895 0.00 0.00 0.00 3.51
1334 1368 2.068834 TCCGAGACTAGGGATTGGTC 57.931 55.000 1.35 0.00 37.54 4.02
1454 1491 4.381505 GGAAAGGTGACACTTTGCTTTTCA 60.382 41.667 8.24 0.00 43.03 2.69
1462 1499 6.751888 GTGACACTTTGCTTTTCATAAACACT 59.248 34.615 0.00 0.00 0.00 3.55
1486 1523 4.003648 GGGGTGGATTATTAATCGAGCTG 58.996 47.826 21.89 0.00 41.79 4.24
1541 1578 2.540265 ATCCTGCTCGGCTCTATTTG 57.460 50.000 0.00 0.00 0.00 2.32
1577 1614 1.060191 GCTTGCGAGCGCTTGTTAAC 61.060 55.000 25.20 9.60 39.48 2.01
1622 1659 3.230976 TGAGATGAGTGTGTAGGTGTGT 58.769 45.455 0.00 0.00 0.00 3.72
1650 1687 2.915869 AGAAAGATGGTGGGTACAGGA 58.084 47.619 0.00 0.00 0.00 3.86
1659 1696 1.612442 GGGTACAGGAGGAGGTGCA 60.612 63.158 0.00 0.00 0.00 4.57
1670 1707 1.072331 AGGAGGTGCACTGGTTTACTG 59.928 52.381 17.98 0.00 0.00 2.74
1705 1742 5.047377 GCTAGGTTGGTTTGATTGGATTGAA 60.047 40.000 0.00 0.00 0.00 2.69
1708 1745 7.552050 AGGTTGGTTTGATTGGATTGAATAA 57.448 32.000 0.00 0.00 0.00 1.40
1718 1755 9.656040 TTGATTGGATTGAATAAATGGTTTGAG 57.344 29.630 0.00 0.00 0.00 3.02
1724 1761 7.147915 GGATTGAATAAATGGTTTGAGGTGCTA 60.148 37.037 0.00 0.00 0.00 3.49
1727 1764 6.889177 TGAATAAATGGTTTGAGGTGCTATGA 59.111 34.615 0.00 0.00 0.00 2.15
1743 1780 9.023962 AGGTGCTATGAAATTTTCTCACATAAA 57.976 29.630 10.33 0.00 0.00 1.40
1797 1834 0.389817 ATGAGCTGCGCGTGAAACTA 60.390 50.000 8.43 0.00 31.75 2.24
1810 1847 5.220080 CGCGTGAAACTATTTAGCTCGTTTA 60.220 40.000 0.00 0.00 30.47 2.01
1831 1868 8.615585 CGTTTATTAAACTTGTTGAGCTTAACG 58.384 33.333 15.73 5.90 39.23 3.18
1874 1911 2.176045 TGTCCATTGAGAACCGAGCTA 58.824 47.619 0.00 0.00 0.00 3.32
1880 1917 1.064458 GAGAACCGAGCTACGAGCC 59.936 63.158 7.07 0.00 43.77 4.70
1898 1935 3.024547 AGCCTAACGAGTTGAGCTATCA 58.975 45.455 11.22 0.00 32.76 2.15
1899 1936 3.117046 GCCTAACGAGTTGAGCTATCAC 58.883 50.000 0.00 0.00 34.35 3.06
1901 1938 2.279582 AACGAGTTGAGCTATCACCG 57.720 50.000 0.00 0.00 34.35 4.94
1918 1955 5.666969 TCACCGTTCATTAAGTTTGTGAG 57.333 39.130 0.00 0.00 0.00 3.51
1940 1977 3.873952 GCTACGAGCTTTTGATTCATCCT 59.126 43.478 0.00 0.00 38.45 3.24
1948 1985 5.184671 AGCTTTTGATTCATCCTTGACCTTC 59.815 40.000 0.00 0.00 0.00 3.46
1978 2015 9.965902 ATGAATTATTTCAAGTTGTCCTCTAGT 57.034 29.630 2.11 0.00 44.70 2.57
1983 2020 9.793259 TTATTTCAAGTTGTCCTCTAGTTTCAT 57.207 29.630 2.11 0.00 0.00 2.57
1990 2027 6.268847 AGTTGTCCTCTAGTTTCATCTTCAGT 59.731 38.462 0.00 0.00 0.00 3.41
2002 2039 4.959723 TCATCTTCAGTGTGACACATGAA 58.040 39.130 18.95 20.18 36.74 2.57
2036 2073 6.530019 AAGATTAAACCTGGGCAACTTATG 57.470 37.500 0.00 0.00 0.00 1.90
2093 2139 3.653344 ACAATATCATCGATGTCCGTGG 58.347 45.455 24.09 13.13 39.75 4.94
2139 2185 5.535333 AGCGAGCACACTACTAAACTAAAA 58.465 37.500 0.00 0.00 0.00 1.52
2256 2351 6.128391 ACAAATACCGTACACTACTTTGCATG 60.128 38.462 0.00 0.00 0.00 4.06
2259 2354 4.131596 ACCGTACACTACTTTGCATGTTT 58.868 39.130 0.00 0.00 0.00 2.83
2260 2355 4.024387 ACCGTACACTACTTTGCATGTTTG 60.024 41.667 0.00 0.00 0.00 2.93
2281 2376 3.706594 TGGTCTTATTTGTTTGGGTTGCA 59.293 39.130 0.00 0.00 0.00 4.08
2286 2381 2.307934 TTTGTTTGGGTTGCAGCTTC 57.692 45.000 0.00 0.00 0.00 3.86
2319 2414 5.290885 CAGTTGTCTATAGCGTGCAAATACA 59.709 40.000 0.00 0.00 0.00 2.29
2320 2415 6.018751 CAGTTGTCTATAGCGTGCAAATACAT 60.019 38.462 0.00 0.00 0.00 2.29
2321 2416 6.201044 AGTTGTCTATAGCGTGCAAATACATC 59.799 38.462 0.00 0.00 0.00 3.06
2322 2417 5.842907 TGTCTATAGCGTGCAAATACATCT 58.157 37.500 0.00 0.00 0.00 2.90
2323 2418 5.920840 TGTCTATAGCGTGCAAATACATCTC 59.079 40.000 0.00 0.00 0.00 2.75
2324 2419 5.920840 GTCTATAGCGTGCAAATACATCTCA 59.079 40.000 0.00 0.00 0.00 3.27
2325 2420 6.587990 GTCTATAGCGTGCAAATACATCTCAT 59.412 38.462 0.00 0.00 0.00 2.90
2326 2421 3.957671 AGCGTGCAAATACATCTCATG 57.042 42.857 0.00 0.00 0.00 3.07
2327 2422 2.032550 AGCGTGCAAATACATCTCATGC 59.967 45.455 0.00 0.00 39.29 4.06
2328 2423 2.223317 GCGTGCAAATACATCTCATGCA 60.223 45.455 0.00 0.00 44.07 3.96
2333 2428 5.827666 TGCAAATACATCTCATGCATCTTG 58.172 37.500 0.00 0.00 41.67 3.02
2334 2429 4.680110 GCAAATACATCTCATGCATCTTGC 59.320 41.667 0.00 0.00 45.29 4.01
2335 2430 5.507482 GCAAATACATCTCATGCATCTTGCT 60.507 40.000 0.00 0.00 45.31 3.91
2336 2431 5.943706 AATACATCTCATGCATCTTGCTC 57.056 39.130 0.00 0.00 45.31 4.26
2337 2432 3.562343 ACATCTCATGCATCTTGCTCT 57.438 42.857 0.00 0.00 45.31 4.09
2338 2433 3.468770 ACATCTCATGCATCTTGCTCTC 58.531 45.455 0.00 0.00 45.31 3.20
2339 2434 2.616634 TCTCATGCATCTTGCTCTCC 57.383 50.000 0.00 0.00 45.31 3.71
2340 2435 2.117051 TCTCATGCATCTTGCTCTCCT 58.883 47.619 0.00 0.00 45.31 3.69
2341 2436 2.504585 TCTCATGCATCTTGCTCTCCTT 59.495 45.455 0.00 0.00 45.31 3.36
2342 2437 2.614520 CTCATGCATCTTGCTCTCCTTG 59.385 50.000 0.00 0.00 45.31 3.61
2343 2438 1.676529 CATGCATCTTGCTCTCCTTGG 59.323 52.381 0.00 0.00 45.31 3.61
2344 2439 0.034767 TGCATCTTGCTCTCCTTGGG 60.035 55.000 0.75 0.00 45.31 4.12
2345 2440 0.034670 GCATCTTGCTCTCCTTGGGT 60.035 55.000 0.00 0.00 40.96 4.51
2346 2441 1.615384 GCATCTTGCTCTCCTTGGGTT 60.615 52.381 0.00 0.00 40.96 4.11
2347 2442 2.089980 CATCTTGCTCTCCTTGGGTTG 58.910 52.381 0.00 0.00 0.00 3.77
2348 2443 1.434188 TCTTGCTCTCCTTGGGTTGA 58.566 50.000 0.00 0.00 0.00 3.18
2349 2444 1.349026 TCTTGCTCTCCTTGGGTTGAG 59.651 52.381 0.00 0.00 0.00 3.02
2350 2445 0.250901 TTGCTCTCCTTGGGTTGAGC 60.251 55.000 18.80 18.80 43.94 4.26
2351 2446 1.130054 TGCTCTCCTTGGGTTGAGCT 61.130 55.000 22.60 0.00 43.98 4.09
2352 2447 0.037447 GCTCTCCTTGGGTTGAGCTT 59.963 55.000 18.55 0.00 42.19 3.74
2353 2448 1.948144 GCTCTCCTTGGGTTGAGCTTC 60.948 57.143 18.55 0.00 42.19 3.86
2354 2449 0.693049 TCTCCTTGGGTTGAGCTTCC 59.307 55.000 0.00 0.00 0.00 3.46
2355 2450 0.401738 CTCCTTGGGTTGAGCTTCCA 59.598 55.000 0.00 0.00 0.00 3.53
2356 2451 0.110486 TCCTTGGGTTGAGCTTCCAC 59.890 55.000 0.00 0.00 0.00 4.02
2357 2452 0.895559 CCTTGGGTTGAGCTTCCACC 60.896 60.000 0.00 0.00 0.00 4.61
2358 2453 0.178992 CTTGGGTTGAGCTTCCACCA 60.179 55.000 10.99 4.96 0.00 4.17
2359 2454 0.482446 TTGGGTTGAGCTTCCACCAT 59.518 50.000 10.99 0.00 0.00 3.55
2360 2455 0.251297 TGGGTTGAGCTTCCACCATG 60.251 55.000 10.99 0.00 0.00 3.66
2361 2456 1.598701 GGGTTGAGCTTCCACCATGC 61.599 60.000 10.99 0.00 0.00 4.06
2362 2457 0.895100 GGTTGAGCTTCCACCATGCA 60.895 55.000 0.00 0.00 0.00 3.96
2363 2458 1.180029 GTTGAGCTTCCACCATGCAT 58.820 50.000 0.00 0.00 0.00 3.96
2364 2459 1.133790 GTTGAGCTTCCACCATGCATC 59.866 52.381 0.00 0.00 0.00 3.91
2365 2460 0.328926 TGAGCTTCCACCATGCATCA 59.671 50.000 0.00 0.00 0.00 3.07
2366 2461 1.064240 TGAGCTTCCACCATGCATCAT 60.064 47.619 0.00 0.00 0.00 2.45
2367 2462 2.029623 GAGCTTCCACCATGCATCATT 58.970 47.619 0.00 0.00 0.00 2.57
2368 2463 2.429610 GAGCTTCCACCATGCATCATTT 59.570 45.455 0.00 0.00 0.00 2.32
2369 2464 2.167693 AGCTTCCACCATGCATCATTTG 59.832 45.455 0.00 0.00 0.00 2.32
2370 2465 2.740580 GCTTCCACCATGCATCATTTGG 60.741 50.000 0.00 0.00 36.56 3.28
2371 2466 2.528673 TCCACCATGCATCATTTGGA 57.471 45.000 10.25 10.05 33.51 3.53
2372 2467 2.817665 TCCACCATGCATCATTTGGAA 58.182 42.857 10.25 0.00 33.19 3.53
2373 2468 3.376636 TCCACCATGCATCATTTGGAAT 58.623 40.909 10.25 0.00 33.19 3.01
2374 2469 3.133183 TCCACCATGCATCATTTGGAATG 59.867 43.478 10.25 0.00 33.19 2.67
2375 2470 3.118555 CCACCATGCATCATTTGGAATGT 60.119 43.478 10.25 0.00 34.52 2.71
2376 2471 4.099727 CCACCATGCATCATTTGGAATGTA 59.900 41.667 10.25 0.00 34.52 2.29
2377 2472 5.395435 CCACCATGCATCATTTGGAATGTAA 60.395 40.000 10.25 0.00 34.52 2.41
2378 2473 6.107343 CACCATGCATCATTTGGAATGTAAA 58.893 36.000 10.25 0.00 34.52 2.01
2379 2474 6.256975 CACCATGCATCATTTGGAATGTAAAG 59.743 38.462 10.25 0.00 34.52 1.85
2380 2475 5.235616 CCATGCATCATTTGGAATGTAAAGC 59.764 40.000 0.00 0.00 31.94 3.51
2381 2476 5.402997 TGCATCATTTGGAATGTAAAGCA 57.597 34.783 1.09 0.00 0.00 3.91
2382 2477 5.979993 TGCATCATTTGGAATGTAAAGCAT 58.020 33.333 1.09 0.00 40.03 3.79
2383 2478 5.813157 TGCATCATTTGGAATGTAAAGCATG 59.187 36.000 1.09 0.00 37.96 4.06
2384 2479 5.235616 GCATCATTTGGAATGTAAAGCATGG 59.764 40.000 0.00 0.00 37.96 3.66
2385 2480 6.575267 CATCATTTGGAATGTAAAGCATGGA 58.425 36.000 0.00 0.00 37.96 3.41
2386 2481 6.211587 TCATTTGGAATGTAAAGCATGGAG 57.788 37.500 0.00 0.00 37.96 3.86
2387 2482 4.454728 TTTGGAATGTAAAGCATGGAGC 57.545 40.909 0.00 0.00 46.19 4.70
2396 2491 3.499737 GCATGGAGCAACCCGACG 61.500 66.667 0.00 0.00 44.79 5.12
2397 2492 2.047274 CATGGAGCAACCCGACGT 60.047 61.111 0.00 0.00 38.00 4.34
2398 2493 2.047274 ATGGAGCAACCCGACGTG 60.047 61.111 0.00 0.00 38.00 4.49
2399 2494 2.879233 ATGGAGCAACCCGACGTGT 61.879 57.895 0.00 0.00 38.00 4.49
2400 2495 3.041940 GGAGCAACCCGACGTGTG 61.042 66.667 0.00 0.00 0.00 3.82
2401 2496 3.712881 GAGCAACCCGACGTGTGC 61.713 66.667 0.00 6.55 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 192 6.547141 TCTTCATCCCATAAATTGGTGACATC 59.453 38.462 0.00 0.00 44.83 3.06
227 239 3.873910 CACCCTTTGAGTATCGATTGGT 58.126 45.455 1.71 0.00 38.61 3.67
237 249 2.032681 GGCGAGCACCCTTTGAGT 59.967 61.111 0.00 0.00 0.00 3.41
380 395 3.505386 TGTTCTACCCATGCCATTTGTT 58.495 40.909 0.00 0.00 0.00 2.83
427 442 3.934068 TCCGGACAAGATAACTTCCAAC 58.066 45.455 0.00 0.00 33.70 3.77
448 463 6.989759 ACGCCAAATAAAAATCTTCACCTTTT 59.010 30.769 0.00 0.00 0.00 2.27
535 550 5.713389 CCATTAGAACATGATGGGCATATGT 59.287 40.000 0.00 0.00 40.59 2.29
595 610 1.269723 CCCAAACCTCTTTCGCCTTTC 59.730 52.381 0.00 0.00 0.00 2.62
759 777 2.752903 CCCACCATAAGTACCAAGTTGC 59.247 50.000 0.00 0.00 0.00 4.17
813 834 6.405286 CCCATCGAAACTTGGTATGCATTTTA 60.405 38.462 3.54 0.00 0.00 1.52
816 837 3.381272 CCCATCGAAACTTGGTATGCATT 59.619 43.478 3.54 0.00 0.00 3.56
875 896 4.410400 CCGGTTGCCCTGGGAGAC 62.410 72.222 19.27 13.49 0.00 3.36
891 913 4.225267 TCTTGTCCATCCCTCTCTTTTACC 59.775 45.833 0.00 0.00 0.00 2.85
942 964 4.024048 GTCTTGGTCGAAAGAAGCATCAAA 60.024 41.667 1.16 0.00 45.01 2.69
988 1011 6.724441 TCCTCCTTTGTCATCTCTAAGTACAA 59.276 38.462 0.00 0.00 0.00 2.41
1040 1069 7.413644 TGTTAATACATATGCACACCAATTCG 58.586 34.615 1.58 0.00 0.00 3.34
1092 1121 4.381612 CCCGTCTTCTGTGCAAGTAATAGA 60.382 45.833 0.00 0.00 0.00 1.98
1171 1203 0.108138 CCCACTGAATGTCCTCCGTC 60.108 60.000 0.00 0.00 0.00 4.79
1173 1205 0.176680 CTCCCACTGAATGTCCTCCG 59.823 60.000 0.00 0.00 0.00 4.63
1193 1225 4.025401 CAAACACTGTCGCCGCCC 62.025 66.667 0.00 0.00 0.00 6.13
1214 1246 3.749404 TCGCACGCCATAAAATAACAAC 58.251 40.909 0.00 0.00 0.00 3.32
1317 1351 2.621055 CTCAGACCAATCCCTAGTCTCG 59.379 54.545 0.00 0.00 38.80 4.04
1334 1368 6.709281 ACAATATCATTCATAGGCTCCTCAG 58.291 40.000 0.00 0.00 0.00 3.35
1429 1466 0.310854 GCAAAGTGTCACCTTTCCCG 59.689 55.000 0.00 0.00 32.42 5.14
1431 1468 3.801114 AAAGCAAAGTGTCACCTTTCC 57.199 42.857 0.00 0.00 32.42 3.13
1462 1499 5.046591 CAGCTCGATTAATAATCCACCCCTA 60.047 44.000 7.36 0.00 34.35 3.53
1541 1578 2.977405 AGCGTTCATGAGCTTCAAAC 57.023 45.000 8.01 0.00 41.52 2.93
1577 1614 7.441157 TCATAGGCCGAAACATAACTTTATCTG 59.559 37.037 0.00 0.00 0.00 2.90
1632 1669 1.916181 CCTCCTGTACCCACCATCTTT 59.084 52.381 0.00 0.00 0.00 2.52
1650 1687 1.072331 CAGTAAACCAGTGCACCTCCT 59.928 52.381 14.63 0.00 0.00 3.69
1659 1696 5.958987 AGCCTATAGAAGACAGTAAACCAGT 59.041 40.000 0.00 0.00 0.00 4.00
1670 1707 5.873146 AACCAACCTAGCCTATAGAAGAC 57.127 43.478 0.00 0.00 0.00 3.01
1705 1742 7.716799 TTTCATAGCACCTCAAACCATTTAT 57.283 32.000 0.00 0.00 0.00 1.40
1708 1745 6.610075 AATTTCATAGCACCTCAAACCATT 57.390 33.333 0.00 0.00 0.00 3.16
1718 1755 9.638239 TTTTATGTGAGAAAATTTCATAGCACC 57.362 29.630 8.55 0.00 0.00 5.01
1755 1792 3.313012 AGCTCGTTAGTACACAATGCA 57.687 42.857 0.00 0.00 0.00 3.96
1831 1868 2.421424 AGCCAATCAACGATTTCAGCTC 59.579 45.455 0.00 0.00 29.88 4.09
1842 1879 4.022068 TCTCAATGGACAAAGCCAATCAAC 60.022 41.667 0.00 0.00 42.16 3.18
1874 1911 0.109226 GCTCAACTCGTTAGGCTCGT 60.109 55.000 0.00 0.00 0.00 4.18
1880 1917 3.181499 ACGGTGATAGCTCAACTCGTTAG 60.181 47.826 0.00 0.00 36.92 2.34
1898 1935 4.134563 AGCTCACAAACTTAATGAACGGT 58.865 39.130 0.00 0.00 0.00 4.83
1899 1936 4.749245 AGCTCACAAACTTAATGAACGG 57.251 40.909 0.00 0.00 0.00 4.44
1901 1938 6.462073 TCGTAGCTCACAAACTTAATGAAC 57.538 37.500 0.00 0.00 0.00 3.18
1918 1955 3.873952 AGGATGAATCAAAAGCTCGTAGC 59.126 43.478 0.00 0.00 42.84 3.58
1932 1969 5.573219 TCATGTTGAAGGTCAAGGATGAAT 58.427 37.500 8.93 0.00 37.00 2.57
1940 1977 9.695526 CTTGAAATAATTCATGTTGAAGGTCAA 57.304 29.630 0.00 0.00 44.70 3.18
1978 2015 5.367302 TCATGTGTCACACTGAAGATGAAA 58.633 37.500 8.08 0.00 35.11 2.69
2002 2039 6.542005 CCCAGGTTTAATCTTTTGCAGTTTTT 59.458 34.615 0.00 0.00 0.00 1.94
2012 2049 6.496911 ACATAAGTTGCCCAGGTTTAATCTTT 59.503 34.615 0.00 0.00 0.00 2.52
2017 2054 6.308566 AGTAACATAAGTTGCCCAGGTTTAA 58.691 36.000 0.00 0.00 40.70 1.52
2089 2135 6.198216 CCAAATTTGAGAAGTACAAAACCACG 59.802 38.462 19.86 0.00 39.95 4.94
2093 2139 7.305993 CGCTTCCAAATTTGAGAAGTACAAAAC 60.306 37.037 29.68 19.32 39.95 2.43
2144 2190 7.976135 AGGATTTCATTTCTTAGATCGATGG 57.024 36.000 0.54 0.00 0.00 3.51
2147 2193 7.489160 TCGAAGGATTTCATTTCTTAGATCGA 58.511 34.615 0.00 0.00 32.67 3.59
2185 2280 4.415881 TGCAACTAGAACACTCTTTGGA 57.584 40.909 0.00 0.00 32.70 3.53
2236 2331 4.524316 ACATGCAAAGTAGTGTACGGTA 57.476 40.909 0.00 0.00 0.00 4.02
2256 2351 5.007234 GCAACCCAAACAAATAAGACCAAAC 59.993 40.000 0.00 0.00 0.00 2.93
2259 2354 3.706594 TGCAACCCAAACAAATAAGACCA 59.293 39.130 0.00 0.00 0.00 4.02
2260 2355 4.306600 CTGCAACCCAAACAAATAAGACC 58.693 43.478 0.00 0.00 0.00 3.85
2286 2381 2.279582 ATAGACAACTGCTTCGACCG 57.720 50.000 0.00 0.00 0.00 4.79
2297 2392 5.712217 TGTATTTGCACGCTATAGACAAC 57.288 39.130 3.21 0.00 0.00 3.32
2298 2393 6.280643 AGATGTATTTGCACGCTATAGACAA 58.719 36.000 3.21 0.00 0.00 3.18
2326 2421 0.034670 ACCCAAGGAGAGCAAGATGC 60.035 55.000 0.00 0.00 45.46 3.91
2327 2422 2.089980 CAACCCAAGGAGAGCAAGATG 58.910 52.381 0.00 0.00 0.00 2.90
2328 2423 1.988107 TCAACCCAAGGAGAGCAAGAT 59.012 47.619 0.00 0.00 0.00 2.40
2329 2424 1.349026 CTCAACCCAAGGAGAGCAAGA 59.651 52.381 0.00 0.00 32.87 3.02
2330 2425 1.818642 CTCAACCCAAGGAGAGCAAG 58.181 55.000 0.00 0.00 32.87 4.01
2331 2426 0.250901 GCTCAACCCAAGGAGAGCAA 60.251 55.000 20.15 0.00 45.70 3.91
2332 2427 1.376466 GCTCAACCCAAGGAGAGCA 59.624 57.895 20.15 0.00 45.70 4.26
2333 2428 0.037447 AAGCTCAACCCAAGGAGAGC 59.963 55.000 18.51 18.51 46.24 4.09
2334 2429 1.339535 GGAAGCTCAACCCAAGGAGAG 60.340 57.143 0.00 0.00 32.87 3.20
2335 2430 0.693049 GGAAGCTCAACCCAAGGAGA 59.307 55.000 0.00 0.00 32.87 3.71
2336 2431 0.401738 TGGAAGCTCAACCCAAGGAG 59.598 55.000 0.00 0.00 0.00 3.69
2337 2432 0.110486 GTGGAAGCTCAACCCAAGGA 59.890 55.000 0.00 0.00 0.00 3.36
2338 2433 0.895559 GGTGGAAGCTCAACCCAAGG 60.896 60.000 0.00 0.00 0.00 3.61
2339 2434 0.178992 TGGTGGAAGCTCAACCCAAG 60.179 55.000 9.30 0.00 33.76 3.61
2340 2435 0.482446 ATGGTGGAAGCTCAACCCAA 59.518 50.000 9.30 0.00 33.76 4.12
2341 2436 0.251297 CATGGTGGAAGCTCAACCCA 60.251 55.000 9.30 4.21 33.76 4.51
2342 2437 1.598701 GCATGGTGGAAGCTCAACCC 61.599 60.000 9.30 0.00 33.76 4.11
2343 2438 0.895100 TGCATGGTGGAAGCTCAACC 60.895 55.000 5.65 5.65 33.76 3.77
2344 2439 1.133790 GATGCATGGTGGAAGCTCAAC 59.866 52.381 2.46 0.00 33.76 3.18
2345 2440 1.272037 TGATGCATGGTGGAAGCTCAA 60.272 47.619 2.46 0.00 33.76 3.02
2346 2441 0.328926 TGATGCATGGTGGAAGCTCA 59.671 50.000 2.46 0.00 33.76 4.26
2347 2442 1.688772 ATGATGCATGGTGGAAGCTC 58.311 50.000 2.46 0.00 33.76 4.09
2348 2443 2.154567 AATGATGCATGGTGGAAGCT 57.845 45.000 2.46 0.00 33.76 3.74
2349 2444 2.546778 CAAATGATGCATGGTGGAAGC 58.453 47.619 2.46 0.00 0.00 3.86
2350 2445 2.761767 TCCAAATGATGCATGGTGGAAG 59.238 45.455 2.46 0.00 36.53 3.46
2351 2446 2.817665 TCCAAATGATGCATGGTGGAA 58.182 42.857 2.46 0.00 36.53 3.53
2352 2447 2.528673 TCCAAATGATGCATGGTGGA 57.471 45.000 2.46 8.52 36.88 4.02
2353 2448 3.118555 ACATTCCAAATGATGCATGGTGG 60.119 43.478 2.46 6.06 35.66 4.61
2354 2449 4.131649 ACATTCCAAATGATGCATGGTG 57.868 40.909 2.46 0.00 35.66 4.17
2355 2450 5.936187 TTACATTCCAAATGATGCATGGT 57.064 34.783 2.46 0.00 35.66 3.55
2356 2451 5.235616 GCTTTACATTCCAAATGATGCATGG 59.764 40.000 2.46 0.00 35.49 3.66
2357 2452 5.813157 TGCTTTACATTCCAAATGATGCATG 59.187 36.000 2.46 0.00 0.00 4.06
2358 2453 5.979993 TGCTTTACATTCCAAATGATGCAT 58.020 33.333 0.00 0.00 0.00 3.96
2359 2454 5.402997 TGCTTTACATTCCAAATGATGCA 57.597 34.783 6.67 0.00 0.00 3.96
2360 2455 5.235616 CCATGCTTTACATTCCAAATGATGC 59.764 40.000 6.67 5.68 36.64 3.91
2361 2456 6.575267 TCCATGCTTTACATTCCAAATGATG 58.425 36.000 6.67 0.00 36.64 3.07
2362 2457 6.684613 GCTCCATGCTTTACATTCCAAATGAT 60.685 38.462 6.67 0.00 36.64 2.45
2363 2458 5.394443 GCTCCATGCTTTACATTCCAAATGA 60.394 40.000 6.67 0.00 36.64 2.57
2364 2459 4.807304 GCTCCATGCTTTACATTCCAAATG 59.193 41.667 0.00 0.00 36.64 2.32
2365 2460 4.467082 TGCTCCATGCTTTACATTCCAAAT 59.533 37.500 0.00 0.00 43.37 2.32
2366 2461 3.831333 TGCTCCATGCTTTACATTCCAAA 59.169 39.130 0.00 0.00 43.37 3.28
2367 2462 3.429492 TGCTCCATGCTTTACATTCCAA 58.571 40.909 0.00 0.00 43.37 3.53
2368 2463 3.084536 TGCTCCATGCTTTACATTCCA 57.915 42.857 0.00 0.00 43.37 3.53
2369 2464 3.429410 GGTTGCTCCATGCTTTACATTCC 60.429 47.826 0.00 0.00 43.37 3.01
2370 2465 3.429410 GGGTTGCTCCATGCTTTACATTC 60.429 47.826 0.00 0.00 43.37 2.67
2371 2466 2.497273 GGGTTGCTCCATGCTTTACATT 59.503 45.455 0.00 0.00 43.37 2.71
2372 2467 2.102578 GGGTTGCTCCATGCTTTACAT 58.897 47.619 0.00 0.00 43.37 2.29
2373 2468 1.544724 GGGTTGCTCCATGCTTTACA 58.455 50.000 0.00 0.00 43.37 2.41
2374 2469 0.451783 CGGGTTGCTCCATGCTTTAC 59.548 55.000 0.00 0.00 43.37 2.01
2375 2470 0.326595 TCGGGTTGCTCCATGCTTTA 59.673 50.000 0.00 0.00 43.37 1.85
2376 2471 1.074775 TCGGGTTGCTCCATGCTTT 59.925 52.632 0.00 0.00 43.37 3.51
2377 2472 1.675641 GTCGGGTTGCTCCATGCTT 60.676 57.895 0.00 0.00 43.37 3.91
2378 2473 2.045926 GTCGGGTTGCTCCATGCT 60.046 61.111 0.00 0.00 43.37 3.79
2379 2474 3.499737 CGTCGGGTTGCTCCATGC 61.500 66.667 0.00 0.00 43.25 4.06
2380 2475 2.047274 ACGTCGGGTTGCTCCATG 60.047 61.111 0.00 0.00 38.11 3.66
2381 2476 2.047274 CACGTCGGGTTGCTCCAT 60.047 61.111 0.00 0.00 38.11 3.41
2382 2477 3.542676 ACACGTCGGGTTGCTCCA 61.543 61.111 0.00 0.00 38.11 3.86
2383 2478 3.041940 CACACGTCGGGTTGCTCC 61.042 66.667 0.00 0.00 0.00 4.70
2384 2479 3.712881 GCACACGTCGGGTTGCTC 61.713 66.667 0.00 0.00 33.05 4.26


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

AutoCloner maintained by Alex Coulton.