Multiple sequence alignment - TraesCS6B01G104000

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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 TraesCS6B01G104000 chr6B 100.000 2525 0 0 1 2525 82727283 82724759 0.000000e+00 4663.0
1 TraesCS6B01G104000 chrUn 94.858 2003 70 6 1 1976 26487823 26485827 0.000000e+00 3097.0
2 TraesCS6B01G104000 chrUn 94.855 311 14 2 2022 2330 26485822 26485512 3.780000e-133 484.0
3 TraesCS6B01G104000 chr5A 83.660 1175 163 10 386 1533 608654876 608656048 0.000000e+00 1079.0
4 TraesCS6B01G104000 chr5A 100.000 38 0 0 59 96 608654564 608654601 1.250000e-08 71.3
5 TraesCS6B01G104000 chr5D 82.403 1182 168 21 386 1533 534574060 534572885 0.000000e+00 994.0
6 TraesCS6B01G104000 chr5D 80.900 1178 179 18 386 1533 487951756 487952917 0.000000e+00 887.0
7 TraesCS6B01G104000 chr5D 81.416 226 30 7 2033 2256 310659951 310659736 9.280000e-40 174.0
8 TraesCS6B01G104000 chr5D 97.674 43 1 0 59 101 487951444 487951486 9.690000e-10 75.0
9 TraesCS6B01G104000 chr5D 97.674 43 1 0 59 101 534574372 534574330 9.690000e-10 75.0
10 TraesCS6B01G104000 chr5B 85.169 708 94 4 836 1533 600550375 600551081 0.000000e+00 715.0
11 TraesCS6B01G104000 chr5B 81.992 261 41 5 2045 2304 455987835 455988090 1.520000e-52 217.0
12 TraesCS6B01G104000 chr5B 87.143 70 5 2 59 128 600549851 600549916 2.690000e-10 76.8
13 TraesCS6B01G104000 chr3B 80.372 591 86 20 1897 2481 782829853 782830419 3.000000e-114 422.0
14 TraesCS6B01G104000 chr7B 81.498 454 56 16 2034 2481 234147739 234147308 5.170000e-92 348.0
15 TraesCS6B01G104000 chr4A 85.214 257 32 3 2048 2299 626239873 626240128 2.490000e-65 259.0
16 TraesCS6B01G104000 chr3A 79.028 391 73 5 1924 2308 742454211 742454598 2.490000e-65 259.0
17 TraesCS6B01G104000 chr3A 84.507 213 25 3 2045 2252 549225988 549226197 1.180000e-48 204.0
18 TraesCS6B01G104000 chr3A 77.470 253 49 5 2054 2304 559525925 559525679 7.280000e-31 145.0
19 TraesCS6B01G104000 chr2A 80.000 265 39 4 2045 2304 63022176 63022431 1.540000e-42 183.0
20 TraesCS6B01G104000 chr6A 81.865 193 21 3 659 837 616413823 616413631 1.560000e-32 150.0
21 TraesCS6B01G104000 chr6A 80.690 145 23 4 2054 2197 578568440 578568300 9.550000e-20 108.0
22 TraesCS6B01G104000 chr6A 80.909 110 7 11 1194 1303 616413359 616413264 9.690000e-10 75.0
23 TraesCS6B01G104000 chr2D 88.298 94 10 1 2045 2137 151324310 151324217 7.380000e-21 111.0


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 TraesCS6B01G104000 chr6B 82724759 82727283 2524 True 4663.00 4663 100.0000 1 2525 1 chr6B.!!$R1 2524
1 TraesCS6B01G104000 chrUn 26485512 26487823 2311 True 1790.50 3097 94.8565 1 2330 2 chrUn.!!$R1 2329
2 TraesCS6B01G104000 chr5A 608654564 608656048 1484 False 575.15 1079 91.8300 59 1533 2 chr5A.!!$F1 1474
3 TraesCS6B01G104000 chr5D 534572885 534574372 1487 True 534.50 994 90.0385 59 1533 2 chr5D.!!$R2 1474
4 TraesCS6B01G104000 chr5D 487951444 487952917 1473 False 481.00 887 89.2870 59 1533 2 chr5D.!!$F1 1474
5 TraesCS6B01G104000 chr5B 600549851 600551081 1230 False 395.90 715 86.1560 59 1533 2 chr5B.!!$F2 1474
6 TraesCS6B01G104000 chr3B 782829853 782830419 566 False 422.00 422 80.3720 1897 2481 1 chr3B.!!$F1 584

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
252 262 0.035317 CTAGGTGACCTGCAACTGCA 59.965 55.0 15.83 4.01 46.23 4.41 F
284 294 0.452585 GAGGAAGAAGGAGACGACGG 59.547 60.0 0.00 0.00 0.00 4.79 F
1398 1460 0.106819 GGATGCAGACCTTGGCAGAT 60.107 55.0 5.59 0.00 44.24 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1418 0.040058 TGCATGACCAAAGGAGCCAT 59.960 50.0 0.0 0.0 0.00 4.40 R
1452 1514 0.181114 TGGATGGAGAAGCCCAATCG 59.819 55.0 0.0 0.0 40.04 3.34 R
2382 2463 0.032615 TTGGAGGTGGTGTTGGCTTT 60.033 50.0 0.0 0.0 0.00 3.51 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 2.418334 GCGGGAATAAGGAAGAAGACGT 60.418 50.000 0.00 0.00 0.00 4.34
148 158 1.630369 ACAGTGAAGGATAAGGCAGCA 59.370 47.619 0.00 0.00 0.00 4.41
156 166 1.666189 GGATAAGGCAGCAACGAGAAC 59.334 52.381 0.00 0.00 0.00 3.01
246 256 2.283604 TCGGCTAGGTGACCTGCA 60.284 61.111 15.83 0.00 34.61 4.41
247 257 1.911269 TCGGCTAGGTGACCTGCAA 60.911 57.895 15.83 5.48 34.61 4.08
248 258 1.741770 CGGCTAGGTGACCTGCAAC 60.742 63.158 15.83 0.21 34.61 4.17
250 260 0.674895 GGCTAGGTGACCTGCAACTG 60.675 60.000 15.83 0.00 46.23 3.16
251 261 1.301677 GCTAGGTGACCTGCAACTGC 61.302 60.000 15.83 5.22 46.23 4.40
252 262 0.035317 CTAGGTGACCTGCAACTGCA 59.965 55.000 15.83 4.01 46.23 4.41
284 294 0.452585 GAGGAAGAAGGAGACGACGG 59.547 60.000 0.00 0.00 0.00 4.79
354 364 9.950496 ATTCTATCTCTTGTACACAAAAGTCAT 57.050 29.630 0.00 0.00 35.15 3.06
362 396 1.956477 ACACAAAAGTCATGGCACTCC 59.044 47.619 0.00 0.00 0.00 3.85
397 431 1.007387 GTTGGTGCTTTGGCTTCCG 60.007 57.895 0.00 0.00 39.59 4.30
401 435 1.172812 GGTGCTTTGGCTTCCGTTCT 61.173 55.000 0.00 0.00 39.59 3.01
492 526 5.723887 AGGTGACATACATCCTCTTCTCTTT 59.276 40.000 0.00 0.00 0.00 2.52
606 640 3.196039 TGGCATTTCATGATTTCCCAGTG 59.804 43.478 0.00 0.00 0.00 3.66
780 823 5.605534 AGATGGATGGAAGACGTTCATAAG 58.394 41.667 0.00 0.00 34.33 1.73
790 833 3.449018 AGACGTTCATAAGTGATGCCTCT 59.551 43.478 0.00 0.00 35.29 3.69
803 846 0.622136 TGCCTCTACGTACAGGAGGA 59.378 55.000 25.68 12.69 46.82 3.71
805 848 2.308690 GCCTCTACGTACAGGAGGATT 58.691 52.381 25.68 0.00 46.82 3.01
920 982 0.668535 TATCCTCACATCGCCACGAG 59.331 55.000 0.00 0.00 39.91 4.18
948 1010 2.203280 CACCGCCCTGTGGACAAA 60.203 61.111 0.00 0.00 36.58 2.83
1112 1174 6.707440 TGATCTAGAGGACATCTTGAAGAC 57.293 41.667 5.41 2.32 42.02 3.01
1322 1384 2.617274 GGTTCCTGCACGCCAAGAC 61.617 63.158 0.00 0.00 0.00 3.01
1356 1418 3.816842 GCGGGGAATACCTCTCCTATGTA 60.817 52.174 0.00 0.00 43.57 2.29
1398 1460 0.106819 GGATGCAGACCTTGGCAGAT 60.107 55.000 5.59 0.00 44.24 2.90
1452 1514 1.810030 GATCCTTGTCACGGCCGAC 60.810 63.158 35.90 21.82 36.40 4.79
1475 1537 1.198094 TGGGCTTCTCCATCCAACGA 61.198 55.000 0.00 0.00 36.21 3.85
1500 1562 5.235186 CAGACTCAATCACGAAACTTCAACT 59.765 40.000 0.00 0.00 0.00 3.16
1543 1605 4.332543 TGTGATTTCATTCTGCCGTGATAC 59.667 41.667 0.00 0.00 0.00 2.24
1544 1606 4.332543 GTGATTTCATTCTGCCGTGATACA 59.667 41.667 0.00 0.00 0.00 2.29
1560 1622 6.128553 CCGTGATACACCTATGAATATTGTGC 60.129 42.308 0.00 0.00 0.00 4.57
1582 1644 6.094881 GTGCTATGTTGTGTTGTATTGGGTAT 59.905 38.462 0.00 0.00 0.00 2.73
1584 1646 5.811399 ATGTTGTGTTGTATTGGGTATCG 57.189 39.130 0.00 0.00 0.00 2.92
1589 1651 6.724694 TGTGTTGTATTGGGTATCGTTAAC 57.275 37.500 0.00 0.00 0.00 2.01
1591 1653 4.869297 TGTTGTATTGGGTATCGTTAACCG 59.131 41.667 3.19 0.00 38.10 4.44
1660 1735 3.259123 GGCCTCCATGTTTCATTTTCTGT 59.741 43.478 0.00 0.00 0.00 3.41
1669 1744 1.438651 TCATTTTCTGTCTTCGCCGG 58.561 50.000 0.00 0.00 0.00 6.13
1705 1780 6.250711 TCCCTATGAATATCATGCTGCAATT 58.749 36.000 6.36 1.06 37.70 2.32
1774 1849 7.882791 TGTTGAGAGTGAATTTGATTAGCCTAA 59.117 33.333 0.00 0.00 0.00 2.69
1824 1899 0.107703 TCCATTGGCTCATCGACCAC 60.108 55.000 0.00 0.00 35.10 4.16
1826 1901 1.012086 CATTGGCTCATCGACCACAG 58.988 55.000 0.00 0.00 35.10 3.66
1862 1937 0.250081 CAGATCCTCTAAAGCCCCGC 60.250 60.000 0.00 0.00 0.00 6.13
1884 1959 6.425417 CCGCCCCGCAAATAAATTTATTTTAT 59.575 34.615 26.37 9.83 40.37 1.40
1939 2015 2.691409 TTGCGGGATGAGTTTAGAGG 57.309 50.000 0.00 0.00 0.00 3.69
1971 2047 2.747855 GGAGGCCTTGCGGTTCTG 60.748 66.667 6.77 0.00 0.00 3.02
1985 2061 3.181487 GCGGTTCTGCAAACCAATCATAT 60.181 43.478 22.34 0.00 40.28 1.78
2008 2084 7.701539 ATGGTAAATATTGACAACTGCTTGA 57.298 32.000 5.29 0.00 0.00 3.02
2014 2090 8.524870 AAATATTGACAACTGCTTGAATTCAC 57.475 30.769 7.89 0.00 0.00 3.18
2026 2102 1.866601 TGAATTCACATAGATGCGCGG 59.133 47.619 8.83 0.00 0.00 6.46
2146 2226 1.512926 AAATATGATCGACCAGCGGC 58.487 50.000 0.00 0.00 41.33 6.53
2187 2267 4.036027 ACATCATCATTGTTGCGAAGATCC 59.964 41.667 0.00 0.00 0.00 3.36
2269 2350 1.267806 CACCACCATCTGCAACAACTC 59.732 52.381 0.00 0.00 0.00 3.01
2314 2395 2.478514 TCATCATGAACACCGTTTGTCG 59.521 45.455 0.00 0.00 37.51 4.35
2330 2411 2.203139 CGAAGCACCACCACCACA 60.203 61.111 0.00 0.00 0.00 4.17
2350 2431 1.047002 TCCACCACCATTGCCAAAAG 58.953 50.000 0.00 0.00 0.00 2.27
2354 2435 1.070601 ACCACCATTGCCAAAAGCTTC 59.929 47.619 0.00 0.00 44.23 3.86
2355 2436 1.070445 CCACCATTGCCAAAAGCTTCA 59.930 47.619 0.00 0.00 44.23 3.02
2356 2437 2.137523 CACCATTGCCAAAAGCTTCAC 58.862 47.619 0.00 0.00 44.23 3.18
2381 2462 4.315264 ACCACCACCCCCAATGCC 62.315 66.667 0.00 0.00 0.00 4.40
2382 2463 4.313707 CCACCACCCCCAATGCCA 62.314 66.667 0.00 0.00 0.00 4.92
2390 2478 1.003476 CCCCAATGCCAAAGCCAAC 60.003 57.895 0.00 0.00 38.69 3.77
2391 2479 1.753470 CCCAATGCCAAAGCCAACA 59.247 52.632 0.00 0.00 38.69 3.33
2401 2489 0.032615 AAAGCCAACACCACCTCCAA 60.033 50.000 0.00 0.00 0.00 3.53
2402 2490 0.032615 AAGCCAACACCACCTCCAAA 60.033 50.000 0.00 0.00 0.00 3.28
2403 2491 0.755327 AGCCAACACCACCTCCAAAC 60.755 55.000 0.00 0.00 0.00 2.93
2404 2492 1.744320 GCCAACACCACCTCCAAACC 61.744 60.000 0.00 0.00 0.00 3.27
2405 2493 1.112916 CCAACACCACCTCCAAACCC 61.113 60.000 0.00 0.00 0.00 4.11
2406 2494 0.396417 CAACACCACCTCCAAACCCA 60.396 55.000 0.00 0.00 0.00 4.51
2407 2495 0.396556 AACACCACCTCCAAACCCAC 60.397 55.000 0.00 0.00 0.00 4.61
2408 2496 1.530655 CACCACCTCCAAACCCACC 60.531 63.158 0.00 0.00 0.00 4.61
2409 2497 1.699930 ACCACCTCCAAACCCACCT 60.700 57.895 0.00 0.00 0.00 4.00
2410 2498 1.074951 CCACCTCCAAACCCACCTC 59.925 63.158 0.00 0.00 0.00 3.85
2411 2499 1.074951 CACCTCCAAACCCACCTCC 59.925 63.158 0.00 0.00 0.00 4.30
2417 2505 1.536676 CAAACCCACCTCCACCACT 59.463 57.895 0.00 0.00 0.00 4.00
2420 2508 1.286305 AACCCACCTCCACCACTGTT 61.286 55.000 0.00 0.00 0.00 3.16
2424 2512 2.382770 ACCTCCACCACTGTTGCCA 61.383 57.895 0.00 0.00 0.00 4.92
2428 2516 0.257328 TCCACCACTGTTGCCAAAGA 59.743 50.000 0.00 0.00 0.00 2.52
2432 2520 1.340991 ACCACTGTTGCCAAAGACACT 60.341 47.619 0.00 0.00 0.00 3.55
2433 2521 1.066002 CCACTGTTGCCAAAGACACTG 59.934 52.381 0.00 0.00 0.00 3.66
2438 2526 0.682532 TTGCCAAAGACACTGCCACA 60.683 50.000 0.00 0.00 0.00 4.17
2444 2532 2.361757 CAAAGACACTGCCACATCCAAA 59.638 45.455 0.00 0.00 0.00 3.28
2460 2548 2.009882 AAACCCACCTCCACCACCA 61.010 57.895 0.00 0.00 0.00 4.17
2463 2551 1.368268 ACCCACCTCCACCACCATTT 61.368 55.000 0.00 0.00 0.00 2.32
2470 2558 0.541764 TCCACCACCATTTCCCAAGC 60.542 55.000 0.00 0.00 0.00 4.01
2473 2561 0.542702 ACCACCATTTCCCAAGCCAG 60.543 55.000 0.00 0.00 0.00 4.85
2481 2569 4.601794 CCCAAGCCAGCACCACCA 62.602 66.667 0.00 0.00 0.00 4.17
2482 2570 3.297620 CCAAGCCAGCACCACCAC 61.298 66.667 0.00 0.00 0.00 4.16
2483 2571 2.519063 CAAGCCAGCACCACCACA 60.519 61.111 0.00 0.00 0.00 4.17
2484 2572 1.904865 CAAGCCAGCACCACCACAT 60.905 57.895 0.00 0.00 0.00 3.21
2485 2573 1.152483 AAGCCAGCACCACCACATT 60.152 52.632 0.00 0.00 0.00 2.71
2486 2574 1.466025 AAGCCAGCACCACCACATTG 61.466 55.000 0.00 0.00 0.00 2.82
2487 2575 2.652530 CCAGCACCACCACATTGC 59.347 61.111 0.00 0.00 36.45 3.56
2488 2576 2.652530 CAGCACCACCACATTGCC 59.347 61.111 0.00 0.00 36.91 4.52
2489 2577 2.601367 AGCACCACCACATTGCCC 60.601 61.111 0.00 0.00 36.91 5.36
2490 2578 2.916703 GCACCACCACATTGCCCA 60.917 61.111 0.00 0.00 0.00 5.36
2491 2579 2.506061 GCACCACCACATTGCCCAA 61.506 57.895 0.00 0.00 0.00 4.12
2492 2580 1.667151 CACCACCACATTGCCCAAG 59.333 57.895 0.00 0.00 0.00 3.61
2493 2581 2.209315 ACCACCACATTGCCCAAGC 61.209 57.895 0.00 0.00 40.48 4.01
2494 2582 2.658422 CACCACATTGCCCAAGCC 59.342 61.111 0.00 0.00 38.69 4.35
2495 2583 2.200930 ACCACATTGCCCAAGCCA 59.799 55.556 0.00 0.00 38.69 4.75
2496 2584 1.459158 ACCACATTGCCCAAGCCAA 60.459 52.632 0.00 0.00 38.69 4.52
2497 2585 1.004679 CCACATTGCCCAAGCCAAC 60.005 57.895 0.00 0.00 38.69 3.77
2498 2586 1.747145 CACATTGCCCAAGCCAACA 59.253 52.632 0.00 0.00 38.69 3.33
2499 2587 0.600782 CACATTGCCCAAGCCAACAC 60.601 55.000 0.00 0.00 38.69 3.32
2500 2588 1.047596 ACATTGCCCAAGCCAACACA 61.048 50.000 0.00 0.00 38.69 3.72
2501 2589 0.106335 CATTGCCCAAGCCAACACAA 59.894 50.000 0.00 0.00 38.69 3.33
2502 2590 0.106521 ATTGCCCAAGCCAACACAAC 59.893 50.000 0.00 0.00 38.69 3.32
2503 2591 0.975040 TTGCCCAAGCCAACACAACT 60.975 50.000 0.00 0.00 38.69 3.16
2504 2592 0.975040 TGCCCAAGCCAACACAACTT 60.975 50.000 0.00 0.00 38.69 2.66
2505 2593 0.249447 GCCCAAGCCAACACAACTTC 60.249 55.000 0.00 0.00 0.00 3.01
2506 2594 0.389025 CCCAAGCCAACACAACTTCC 59.611 55.000 0.00 0.00 0.00 3.46
2507 2595 1.110442 CCAAGCCAACACAACTTCCA 58.890 50.000 0.00 0.00 0.00 3.53
2508 2596 1.480137 CCAAGCCAACACAACTTCCAA 59.520 47.619 0.00 0.00 0.00 3.53
2509 2597 2.093764 CCAAGCCAACACAACTTCCAAA 60.094 45.455 0.00 0.00 0.00 3.28
2510 2598 2.929398 CAAGCCAACACAACTTCCAAAC 59.071 45.455 0.00 0.00 0.00 2.93
2511 2599 1.480545 AGCCAACACAACTTCCAAACC 59.519 47.619 0.00 0.00 0.00 3.27
2512 2600 1.472552 GCCAACACAACTTCCAAACCC 60.473 52.381 0.00 0.00 0.00 4.11
2513 2601 2.107366 CCAACACAACTTCCAAACCCT 58.893 47.619 0.00 0.00 0.00 4.34
2514 2602 2.100749 CCAACACAACTTCCAAACCCTC 59.899 50.000 0.00 0.00 0.00 4.30
2515 2603 2.067365 ACACAACTTCCAAACCCTCC 57.933 50.000 0.00 0.00 0.00 4.30
2516 2604 1.286553 ACACAACTTCCAAACCCTCCA 59.713 47.619 0.00 0.00 0.00 3.86
2517 2605 1.681264 CACAACTTCCAAACCCTCCAC 59.319 52.381 0.00 0.00 0.00 4.02
2518 2606 1.328279 CAACTTCCAAACCCTCCACC 58.672 55.000 0.00 0.00 0.00 4.61
2519 2607 0.930726 AACTTCCAAACCCTCCACCA 59.069 50.000 0.00 0.00 0.00 4.17
2520 2608 0.185175 ACTTCCAAACCCTCCACCAC 59.815 55.000 0.00 0.00 0.00 4.16
2521 2609 0.539669 CTTCCAAACCCTCCACCACC 60.540 60.000 0.00 0.00 0.00 4.61
2522 2610 1.289982 TTCCAAACCCTCCACCACCA 61.290 55.000 0.00 0.00 0.00 4.17
2523 2611 1.231641 CCAAACCCTCCACCACCAA 59.768 57.895 0.00 0.00 0.00 3.67
2524 2612 0.178935 CCAAACCCTCCACCACCAAT 60.179 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 6.122277 GTCACATATTCATCAAGGGAAAGGA 58.878 40.000 0.00 0.00 0.00 3.36
148 158 2.432510 GGGATCTCCATCAGTTCTCGTT 59.567 50.000 0.00 0.00 37.91 3.85
156 166 2.746359 GCCCGGGATCTCCATCAG 59.254 66.667 29.31 0.00 37.91 2.90
246 256 6.859112 TCCTCTTCTAGAAGTATTGCAGTT 57.141 37.500 27.59 0.00 39.38 3.16
247 257 6.665680 TCTTCCTCTTCTAGAAGTATTGCAGT 59.334 38.462 27.59 0.00 40.34 4.40
248 258 7.106439 TCTTCCTCTTCTAGAAGTATTGCAG 57.894 40.000 27.59 17.75 40.34 4.41
249 259 7.364232 CCTTCTTCCTCTTCTAGAAGTATTGCA 60.364 40.741 27.59 10.14 41.99 4.08
250 260 6.983890 CCTTCTTCCTCTTCTAGAAGTATTGC 59.016 42.308 27.59 0.00 41.99 3.56
251 261 8.299990 TCCTTCTTCCTCTTCTAGAAGTATTG 57.700 38.462 27.59 17.14 41.99 1.90
252 262 8.340757 TCTCCTTCTTCCTCTTCTAGAAGTATT 58.659 37.037 27.59 0.00 41.99 1.89
260 270 4.263435 GTCGTCTCCTTCTTCCTCTTCTA 58.737 47.826 0.00 0.00 0.00 2.10
284 294 5.621555 GCAATATCTTGGATGATGCATCACC 60.622 44.000 30.92 28.93 42.13 4.02
362 396 1.089481 AACTGATACGCGGTGGCATG 61.089 55.000 12.47 0.00 39.92 4.06
412 446 1.216710 GGCGAAGAGGACCACAGAG 59.783 63.158 0.00 0.00 0.00 3.35
780 823 2.022195 TCCTGTACGTAGAGGCATCAC 58.978 52.381 29.26 3.15 36.73 3.06
790 833 2.874701 GTCGCTAATCCTCCTGTACGTA 59.125 50.000 0.00 0.00 0.00 3.57
803 846 1.141053 CTGGCCCCTTAAGTCGCTAAT 59.859 52.381 0.00 0.00 0.00 1.73
805 848 1.968050 GCTGGCCCCTTAAGTCGCTA 61.968 60.000 0.00 0.00 0.00 4.26
920 982 1.172812 AGGGCGGTGAAAGCAAAGAC 61.173 55.000 0.00 0.00 36.08 3.01
948 1010 1.418334 CTCGAGGGAAGGATGATGGT 58.582 55.000 3.91 0.00 0.00 3.55
1006 1068 9.463443 GATGAAAAGCAAGTAAAACATGTAGTT 57.537 29.630 0.00 0.00 43.89 2.24
1112 1174 1.468565 CCTCGACATTTGCATTGCTGG 60.469 52.381 10.49 0.00 0.00 4.85
1356 1418 0.040058 TGCATGACCAAAGGAGCCAT 59.960 50.000 0.00 0.00 0.00 4.40
1398 1460 2.771943 AGATTCGGGCTTGTGGATCTTA 59.228 45.455 0.00 0.00 0.00 2.10
1452 1514 0.181114 TGGATGGAGAAGCCCAATCG 59.819 55.000 0.00 0.00 40.04 3.34
1475 1537 4.693283 TGAAGTTTCGTGATTGAGTCTGT 58.307 39.130 0.00 0.00 0.00 3.41
1500 1562 2.691526 CACCAGGCTAAGGATACGTGTA 59.308 50.000 0.00 0.00 46.39 2.90
1543 1605 8.071967 CACAACATAGCACAATATTCATAGGTG 58.928 37.037 0.00 0.00 0.00 4.00
1544 1606 7.775093 ACACAACATAGCACAATATTCATAGGT 59.225 33.333 0.00 0.00 0.00 3.08
1560 1622 6.537301 ACGATACCCAATACAACACAACATAG 59.463 38.462 0.00 0.00 0.00 2.23
1589 1651 6.741109 AGGGAAATTTAACACAAAGTAACGG 58.259 36.000 0.00 0.00 0.00 4.44
1591 1653 9.244799 CTCAAGGGAAATTTAACACAAAGTAAC 57.755 33.333 0.00 0.00 0.00 2.50
1660 1735 2.684001 ACAAATACATCCGGCGAAGA 57.316 45.000 9.30 0.00 0.00 2.87
1824 1899 3.888323 TCTGCTAGAGATGCTCTAACCTG 59.112 47.826 5.75 4.74 41.74 4.00
1826 1901 4.082245 GGATCTGCTAGAGATGCTCTAACC 60.082 50.000 12.96 1.64 44.26 2.85
1848 1923 4.191015 GGGGCGGGGCTTTAGAGG 62.191 72.222 0.00 0.00 0.00 3.69
1862 1937 7.934120 TCCCATAAAATAAATTTATTTGCGGGG 59.066 33.333 33.80 33.02 41.27 5.73
1963 2039 0.313672 TGATTGGTTTGCAGAACCGC 59.686 50.000 19.30 13.94 43.15 5.68
1965 2041 4.685924 CCATATGATTGGTTTGCAGAACC 58.314 43.478 18.38 18.38 40.67 3.62
1985 2061 7.517614 TTCAAGCAGTTGTCAATATTTACCA 57.482 32.000 0.00 0.00 34.98 3.25
1988 2064 9.624697 GTGAATTCAAGCAGTTGTCAATATTTA 57.375 29.630 10.35 0.00 34.98 1.40
2001 2077 4.524749 CGCATCTATGTGAATTCAAGCAG 58.475 43.478 10.35 7.34 40.61 4.24
2008 2084 2.238942 TCCGCGCATCTATGTGAATT 57.761 45.000 8.75 0.00 40.61 2.17
2014 2090 9.191995 TGTATATATAAATTCCGCGCATCTATG 57.808 33.333 8.75 0.00 0.00 2.23
2050 2128 6.292114 CGCATGATTTTGGATGTGATGAATTG 60.292 38.462 0.00 0.00 32.80 2.32
2130 2208 1.471829 ATGGCCGCTGGTCGATCATA 61.472 55.000 0.00 0.00 41.67 2.15
2146 2226 7.815549 TGATGATGTTGTTTGATTTCTTCATGG 59.184 33.333 0.00 0.00 33.34 3.66
2269 2350 1.519455 GTGCTCATTCTCCGGTCCG 60.519 63.158 3.60 3.60 0.00 4.79
2314 2395 1.244019 GGATGTGGTGGTGGTGCTTC 61.244 60.000 0.00 0.00 0.00 3.86
2330 2411 1.624813 CTTTTGGCAATGGTGGTGGAT 59.375 47.619 0.00 0.00 0.00 3.41
2350 2431 2.193536 GTGGTGGTGGTGGTGAAGC 61.194 63.158 0.00 0.00 0.00 3.86
2354 2435 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
2355 2436 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
2356 2437 4.596585 GGGTGGTGGTGGTGGTGG 62.597 72.222 0.00 0.00 0.00 4.61
2381 2462 0.754957 TGGAGGTGGTGTTGGCTTTG 60.755 55.000 0.00 0.00 0.00 2.77
2382 2463 0.032615 TTGGAGGTGGTGTTGGCTTT 60.033 50.000 0.00 0.00 0.00 3.51
2390 2478 1.530655 GGTGGGTTTGGAGGTGGTG 60.531 63.158 0.00 0.00 0.00 4.17
2391 2479 1.699930 AGGTGGGTTTGGAGGTGGT 60.700 57.895 0.00 0.00 0.00 4.16
2401 2489 1.286305 AACAGTGGTGGAGGTGGGTT 61.286 55.000 0.00 0.00 0.00 4.11
2402 2490 1.696314 AACAGTGGTGGAGGTGGGT 60.696 57.895 0.00 0.00 0.00 4.51
2403 2491 1.228245 CAACAGTGGTGGAGGTGGG 60.228 63.158 0.00 0.00 0.00 4.61
2404 2492 1.898574 GCAACAGTGGTGGAGGTGG 60.899 63.158 10.86 0.00 0.00 4.61
2405 2493 1.898574 GGCAACAGTGGTGGAGGTG 60.899 63.158 10.86 0.00 0.00 4.00
2406 2494 2.382770 TGGCAACAGTGGTGGAGGT 61.383 57.895 10.86 0.00 46.17 3.85
2407 2495 2.515398 TGGCAACAGTGGTGGAGG 59.485 61.111 10.86 0.00 46.17 4.30
2417 2505 0.682532 TGGCAGTGTCTTTGGCAACA 60.683 50.000 0.00 0.00 46.43 3.33
2424 2512 2.362077 GTTTGGATGTGGCAGTGTCTTT 59.638 45.455 0.00 0.00 0.00 2.52
2428 2516 0.827507 GGGTTTGGATGTGGCAGTGT 60.828 55.000 0.00 0.00 0.00 3.55
2432 2520 1.532794 GGTGGGTTTGGATGTGGCA 60.533 57.895 0.00 0.00 0.00 4.92
2433 2521 1.228862 AGGTGGGTTTGGATGTGGC 60.229 57.895 0.00 0.00 0.00 5.01
2438 2526 1.071314 TGGTGGAGGTGGGTTTGGAT 61.071 55.000 0.00 0.00 0.00 3.41
2444 2532 1.368268 AAATGGTGGTGGAGGTGGGT 61.368 55.000 0.00 0.00 0.00 4.51
2460 2548 1.155859 TGGTGCTGGCTTGGGAAAT 59.844 52.632 0.00 0.00 0.00 2.17
2463 2551 4.284550 GGTGGTGCTGGCTTGGGA 62.285 66.667 0.00 0.00 0.00 4.37
2470 2558 2.652530 GCAATGTGGTGGTGCTGG 59.347 61.111 0.00 0.00 35.36 4.85
2473 2561 2.438951 CTTGGGCAATGTGGTGGTGC 62.439 60.000 0.00 0.00 37.55 5.01
2484 2572 0.975040 AGTTGTGTTGGCTTGGGCAA 60.975 50.000 2.45 2.45 45.54 4.52
2485 2573 0.975040 AAGTTGTGTTGGCTTGGGCA 60.975 50.000 0.00 0.00 40.87 5.36
2486 2574 0.249447 GAAGTTGTGTTGGCTTGGGC 60.249 55.000 0.00 0.00 37.82 5.36
2487 2575 0.389025 GGAAGTTGTGTTGGCTTGGG 59.611 55.000 0.00 0.00 0.00 4.12
2488 2576 1.110442 TGGAAGTTGTGTTGGCTTGG 58.890 50.000 0.00 0.00 0.00 3.61
2489 2577 2.929398 GTTTGGAAGTTGTGTTGGCTTG 59.071 45.455 0.00 0.00 0.00 4.01
2490 2578 2.093711 GGTTTGGAAGTTGTGTTGGCTT 60.094 45.455 0.00 0.00 0.00 4.35
2491 2579 1.480545 GGTTTGGAAGTTGTGTTGGCT 59.519 47.619 0.00 0.00 0.00 4.75
2492 2580 1.472552 GGGTTTGGAAGTTGTGTTGGC 60.473 52.381 0.00 0.00 0.00 4.52
2493 2581 2.100749 GAGGGTTTGGAAGTTGTGTTGG 59.899 50.000 0.00 0.00 0.00 3.77
2494 2582 2.100749 GGAGGGTTTGGAAGTTGTGTTG 59.899 50.000 0.00 0.00 0.00 3.33
2495 2583 2.291930 TGGAGGGTTTGGAAGTTGTGTT 60.292 45.455 0.00 0.00 0.00 3.32
2496 2584 1.286553 TGGAGGGTTTGGAAGTTGTGT 59.713 47.619 0.00 0.00 0.00 3.72
2497 2585 1.681264 GTGGAGGGTTTGGAAGTTGTG 59.319 52.381 0.00 0.00 0.00 3.33
2498 2586 1.411074 GGTGGAGGGTTTGGAAGTTGT 60.411 52.381 0.00 0.00 0.00 3.32
2499 2587 1.328279 GGTGGAGGGTTTGGAAGTTG 58.672 55.000 0.00 0.00 0.00 3.16
2500 2588 0.930726 TGGTGGAGGGTTTGGAAGTT 59.069 50.000 0.00 0.00 0.00 2.66
2501 2589 0.185175 GTGGTGGAGGGTTTGGAAGT 59.815 55.000 0.00 0.00 0.00 3.01
2502 2590 0.539669 GGTGGTGGAGGGTTTGGAAG 60.540 60.000 0.00 0.00 0.00 3.46
2503 2591 1.289982 TGGTGGTGGAGGGTTTGGAA 61.290 55.000 0.00 0.00 0.00 3.53
2504 2592 1.289982 TTGGTGGTGGAGGGTTTGGA 61.290 55.000 0.00 0.00 0.00 3.53
2505 2593 0.178935 ATTGGTGGTGGAGGGTTTGG 60.179 55.000 0.00 0.00 0.00 3.28
2506 2594 3.455737 ATTGGTGGTGGAGGGTTTG 57.544 52.632 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.