Multiple sequence alignment - TraesCS5D01G339300

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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 TraesCS5D01G339300 chr5D 100.000 2643 0 0 1 2643 428474508 428471866 0.000000e+00 4881
1 TraesCS5D01G339300 chr5D 82.540 1638 192 33 704 2258 428465577 428463951 0.000000e+00 1354
2 TraesCS5D01G339300 chr5D 90.332 993 67 6 750 1713 428460267 428459275 0.000000e+00 1275
3 TraesCS5D01G339300 chr5D 95.164 517 22 2 1745 2260 428459280 428458766 0.000000e+00 813
4 TraesCS5D01G339300 chr5D 87.728 603 62 8 55 655 428460930 428460338 0.000000e+00 693
5 TraesCS5D01G339300 chr5D 94.444 378 17 4 2267 2643 241110390 241110764 1.760000e-161 579
6 TraesCS5D01G339300 chr5D 93.407 364 24 0 2280 2643 370623646 370623283 8.320000e-150 540
7 TraesCS5D01G339300 chr5B 93.142 1779 79 12 7 1754 517652271 517650505 0.000000e+00 2569
8 TraesCS5D01G339300 chr5B 79.094 1545 252 47 762 2259 687879817 687881337 0.000000e+00 998
9 TraesCS5D01G339300 chr5B 86.014 429 50 6 1834 2258 517648768 517648346 4.010000e-123 451
10 TraesCS5D01G339300 chr5B 83.923 311 46 4 345 652 687879330 687879639 7.150000e-76 294
11 TraesCS5D01G339300 chr5A 89.832 1967 139 18 331 2259 544035493 544033550 0.000000e+00 2468
12 TraesCS5D01G339300 chr7D 96.164 365 13 1 2280 2643 150754853 150755217 1.750000e-166 595
13 TraesCS5D01G339300 chr7D 93.956 364 19 2 2280 2643 420370543 420370183 4.970000e-152 547
14 TraesCS5D01G339300 chr6D 94.766 363 19 0 2281 2643 131933353 131932991 1.370000e-157 566
15 TraesCS5D01G339300 chr3D 94.231 364 18 3 2280 2643 571056800 571056440 1.070000e-153 553
16 TraesCS5D01G339300 chr3A 93.716 366 23 0 2278 2643 7599567 7599932 1.380000e-152 549
17 TraesCS5D01G339300 chr6A 93.699 365 22 1 2280 2643 144246701 144246337 1.790000e-151 545
18 TraesCS5D01G339300 chr6B 93.872 359 22 0 2285 2643 348693901 348693543 2.310000e-150 542


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 TraesCS5D01G339300 chr5D 428471866 428474508 2642 True 4881.00 4881 100.0000 1 2643 1 chr5D.!!$R2 2642
1 TraesCS5D01G339300 chr5D 428458766 428465577 6811 True 1033.75 1354 88.9410 55 2260 4 chr5D.!!$R3 2205
2 TraesCS5D01G339300 chr5B 517648346 517652271 3925 True 1510.00 2569 89.5780 7 2258 2 chr5B.!!$R1 2251
3 TraesCS5D01G339300 chr5B 687879330 687881337 2007 False 646.00 998 81.5085 345 2259 2 chr5B.!!$F1 1914
4 TraesCS5D01G339300 chr5A 544033550 544035493 1943 True 2468.00 2468 89.8320 331 2259 1 chr5A.!!$R1 1928

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
369 4969 1.828595 TGCTGGACGGACTAAATAGCA 59.171 47.619 0.0 0.0 37.36 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 8686 0.251634 GGCACAAGAGAGGGAGAAGG 59.748 60.0 0.0 0.0 0.0 3.46 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
44 45 9.362539 CATTTAATTAAGCCCTCATATGAATGC 57.637 33.333 15.10 15.10 32.76 3.56
47 48 5.970317 TTAAGCCCTCATATGAATGCATG 57.030 39.130 21.64 5.03 35.94 4.06
49 50 3.154710 AGCCCTCATATGAATGCATGTG 58.845 45.455 21.64 4.02 42.85 3.21
50 51 2.889045 GCCCTCATATGAATGCATGTGT 59.111 45.455 17.08 0.00 42.31 3.72
51 52 3.305131 GCCCTCATATGAATGCATGTGTG 60.305 47.826 17.08 7.75 42.31 3.82
108 4702 3.200483 GGGACCAACACCGACAATATAC 58.800 50.000 0.00 0.00 0.00 1.47
129 4723 2.356382 CTCTACCGACTTGGAGCTAGTG 59.644 54.545 0.00 0.00 42.00 2.74
168 4762 7.839680 AAACAGGACAGAGTTATTCCAAAAT 57.160 32.000 0.00 0.00 0.00 1.82
259 4853 1.939785 CGGCATCGCAGAGTCGTAC 60.940 63.158 0.00 0.00 43.63 3.67
317 4912 4.053295 GCCTAGACTACAACAAACGAACA 58.947 43.478 0.00 0.00 0.00 3.18
318 4913 4.084693 GCCTAGACTACAACAAACGAACAC 60.085 45.833 0.00 0.00 0.00 3.32
319 4914 4.147653 CCTAGACTACAACAAACGAACACG 59.852 45.833 0.00 0.00 0.00 4.49
324 4919 2.620242 ACAACAAACGAACACGGTACT 58.380 42.857 0.00 0.00 0.00 2.73
328 4923 4.045636 ACAAACGAACACGGTACTAAGT 57.954 40.909 0.00 0.00 0.00 2.24
355 4950 3.620427 TTAGCCGTCTATTTTGCTGGA 57.380 42.857 0.00 0.00 35.34 3.86
369 4969 1.828595 TGCTGGACGGACTAAATAGCA 59.171 47.619 0.00 0.00 37.36 3.49
393 4995 7.068226 GCATACTTTTGGTGGTTTATCCTATGT 59.932 37.037 0.00 0.00 37.07 2.29
596 5199 3.469863 TTTGTCGCGGGCAAGGAGT 62.470 57.895 6.13 0.00 0.00 3.85
851 5529 7.227512 AGCAATATAACACAGCTCATAAAGGAC 59.772 37.037 0.00 0.00 0.00 3.85
920 5598 3.496884 TGCAGGCGTACAAGTTAAAAGAG 59.503 43.478 0.00 0.00 0.00 2.85
940 5618 3.535561 AGGTTGAATCATTGAGCTACGG 58.464 45.455 0.00 0.00 0.00 4.02
962 5646 4.202264 GGTGAGATGATCGGTAAGACCATT 60.202 45.833 0.00 0.00 38.47 3.16
965 5649 6.316390 GTGAGATGATCGGTAAGACCATTTTT 59.684 38.462 0.00 0.00 38.47 1.94
1023 5715 0.833287 TCTTGCTCAGCATCTACCCC 59.167 55.000 0.00 0.00 38.76 4.95
1083 5775 0.322277 GCAGGGATGATGATGGCGAT 60.322 55.000 0.00 0.00 0.00 4.58
1100 5792 2.355716 GCGATGCCCCCTATAGCAATAA 60.356 50.000 0.00 0.00 43.36 1.40
1217 5933 4.298103 AGCATGTTCCTTCTTGAGACAT 57.702 40.909 0.00 0.00 0.00 3.06
1277 5993 1.795872 CCGCGTCTGACACAACATTAA 59.204 47.619 4.92 0.00 0.00 1.40
1393 6109 2.586648 ACCCCATGAGGTTTGAGAAC 57.413 50.000 0.00 0.00 36.44 3.01
1396 6112 1.271379 CCCATGAGGTTTGAGAACGGT 60.271 52.381 0.00 0.00 36.61 4.83
1422 6138 1.599797 GGGCTACCAACAACACGCT 60.600 57.895 0.00 0.00 36.50 5.07
1503 6219 1.134877 CGAGGTGCAGACTGTGATGAT 60.135 52.381 3.99 0.00 0.00 2.45
1727 6447 0.953727 ATGTGTGGTGTGTGATGTGC 59.046 50.000 0.00 0.00 0.00 4.57
1731 6451 1.404748 TGTGGTGTGTGATGTGCTTTG 59.595 47.619 0.00 0.00 0.00 2.77
1736 6456 3.428725 GGTGTGTGATGTGCTTTGTGAAA 60.429 43.478 0.00 0.00 0.00 2.69
1740 6460 2.791004 GTGATGTGCTTTGTGAAACTGC 59.209 45.455 0.00 0.00 38.04 4.40
1741 6461 2.223782 TGATGTGCTTTGTGAAACTGCC 60.224 45.455 0.00 0.00 38.04 4.85
1846 8258 7.036220 CCTCTTCGAGATACTACAACATGTTT 58.964 38.462 8.77 3.54 0.00 2.83
1859 8271 4.449743 ACAACATGTTTTCTCATGCATTGC 59.550 37.500 8.77 0.46 46.15 3.56
1928 8343 4.322057 TCCTATAACCCCCTATACCGTC 57.678 50.000 0.00 0.00 0.00 4.79
2058 8482 8.258007 ACGGAATTGTACTCTCAAATAGATCAA 58.742 33.333 0.00 0.00 32.41 2.57
2069 8494 8.498054 TCTCAAATAGATCAATTGAAGTGGAC 57.502 34.615 13.09 0.80 33.08 4.02
2192 8617 8.353423 ACTGCTAAGAACATAATTTCCATTGT 57.647 30.769 0.00 0.00 0.00 2.71
2223 8648 1.069636 CAAAGAGCCGACTTGAGTTGC 60.070 52.381 0.00 0.00 0.00 4.17
2260 8685 8.503428 AAATGGGAGATACATCTATGTCTTCT 57.497 34.615 0.00 3.85 41.97 2.85
2261 8686 7.716799 ATGGGAGATACATCTATGTCTTCTC 57.283 40.000 18.66 18.66 42.94 2.87
2266 8691 8.635765 GAGATACATCTATGTCTTCTCCTTCT 57.364 38.462 17.27 4.39 40.57 2.85
2267 8692 8.635765 AGATACATCTATGTCTTCTCCTTCTC 57.364 38.462 0.00 0.00 41.97 2.87
2268 8693 7.669722 AGATACATCTATGTCTTCTCCTTCTCC 59.330 40.741 0.00 0.00 41.97 3.71
2269 8694 4.898861 ACATCTATGTCTTCTCCTTCTCCC 59.101 45.833 0.00 0.00 35.87 4.30
2270 8695 4.890499 TCTATGTCTTCTCCTTCTCCCT 57.110 45.455 0.00 0.00 0.00 4.20
2271 8696 4.798882 TCTATGTCTTCTCCTTCTCCCTC 58.201 47.826 0.00 0.00 0.00 4.30
2272 8697 3.774842 ATGTCTTCTCCTTCTCCCTCT 57.225 47.619 0.00 0.00 0.00 3.69
2273 8698 3.094484 TGTCTTCTCCTTCTCCCTCTC 57.906 52.381 0.00 0.00 0.00 3.20
2274 8699 2.652348 TGTCTTCTCCTTCTCCCTCTCT 59.348 50.000 0.00 0.00 0.00 3.10
2275 8700 3.076785 TGTCTTCTCCTTCTCCCTCTCTT 59.923 47.826 0.00 0.00 0.00 2.85
2276 8701 3.447229 GTCTTCTCCTTCTCCCTCTCTTG 59.553 52.174 0.00 0.00 0.00 3.02
2277 8702 3.076785 TCTTCTCCTTCTCCCTCTCTTGT 59.923 47.826 0.00 0.00 0.00 3.16
2278 8703 2.813907 TCTCCTTCTCCCTCTCTTGTG 58.186 52.381 0.00 0.00 0.00 3.33
2279 8704 1.206849 CTCCTTCTCCCTCTCTTGTGC 59.793 57.143 0.00 0.00 0.00 4.57
2280 8705 0.251634 CCTTCTCCCTCTCTTGTGCC 59.748 60.000 0.00 0.00 0.00 5.01
2281 8706 0.251634 CTTCTCCCTCTCTTGTGCCC 59.748 60.000 0.00 0.00 0.00 5.36
2282 8707 1.544825 TTCTCCCTCTCTTGTGCCCG 61.545 60.000 0.00 0.00 0.00 6.13
2283 8708 3.672295 CTCCCTCTCTTGTGCCCGC 62.672 68.421 0.00 0.00 0.00 6.13
2285 8710 4.379243 CCTCTCTTGTGCCCGCGT 62.379 66.667 4.92 0.00 0.00 6.01
2286 8711 2.811317 CTCTCTTGTGCCCGCGTC 60.811 66.667 4.92 0.00 0.00 5.19
2287 8712 4.717629 TCTCTTGTGCCCGCGTCG 62.718 66.667 4.92 0.00 0.00 5.12
2325 8750 2.612746 GGTGGCTCCCCAACCCTA 60.613 66.667 0.00 0.00 43.39 3.53
2326 8751 2.680370 GGTGGCTCCCCAACCCTAG 61.680 68.421 0.00 0.00 43.39 3.02
2327 8752 3.015145 TGGCTCCCCAACCCTAGC 61.015 66.667 0.00 0.00 38.46 3.42
2329 8754 4.176752 GCTCCCCAACCCTAGCCG 62.177 72.222 0.00 0.00 0.00 5.52
2330 8755 2.687566 CTCCCCAACCCTAGCCGT 60.688 66.667 0.00 0.00 0.00 5.68
2331 8756 2.686106 TCCCCAACCCTAGCCGTC 60.686 66.667 0.00 0.00 0.00 4.79
2332 8757 4.157120 CCCCAACCCTAGCCGTCG 62.157 72.222 0.00 0.00 0.00 5.12
2333 8758 4.832608 CCCAACCCTAGCCGTCGC 62.833 72.222 0.00 0.00 0.00 5.19
2334 8759 4.832608 CCAACCCTAGCCGTCGCC 62.833 72.222 0.00 0.00 34.57 5.54
2357 8782 1.626321 GGCCTAGCCTATCTTCCTTCC 59.374 57.143 0.00 0.00 46.69 3.46
2358 8783 2.615391 GCCTAGCCTATCTTCCTTCCT 58.385 52.381 0.00 0.00 0.00 3.36
2359 8784 2.976185 GCCTAGCCTATCTTCCTTCCTT 59.024 50.000 0.00 0.00 0.00 3.36
2360 8785 3.007506 GCCTAGCCTATCTTCCTTCCTTC 59.992 52.174 0.00 0.00 0.00 3.46
2361 8786 3.580895 CCTAGCCTATCTTCCTTCCTTCC 59.419 52.174 0.00 0.00 0.00 3.46
2362 8787 3.429736 AGCCTATCTTCCTTCCTTCCT 57.570 47.619 0.00 0.00 0.00 3.36
2363 8788 3.313791 AGCCTATCTTCCTTCCTTCCTC 58.686 50.000 0.00 0.00 0.00 3.71
2364 8789 2.370519 GCCTATCTTCCTTCCTTCCTCC 59.629 54.545 0.00 0.00 0.00 4.30
2365 8790 2.976185 CCTATCTTCCTTCCTTCCTCCC 59.024 54.545 0.00 0.00 0.00 4.30
2366 8791 1.501582 ATCTTCCTTCCTTCCTCCCG 58.498 55.000 0.00 0.00 0.00 5.14
2367 8792 1.222113 CTTCCTTCCTTCCTCCCGC 59.778 63.158 0.00 0.00 0.00 6.13
2368 8793 2.258748 CTTCCTTCCTTCCTCCCGCC 62.259 65.000 0.00 0.00 0.00 6.13
2369 8794 4.162690 CCTTCCTTCCTCCCGCCG 62.163 72.222 0.00 0.00 0.00 6.46
2370 8795 4.840005 CTTCCTTCCTCCCGCCGC 62.840 72.222 0.00 0.00 0.00 6.53
2436 8861 2.770475 GGGGCTCTTCCTCCCTCC 60.770 72.222 0.00 0.00 42.25 4.30
2437 8862 2.770475 GGGCTCTTCCTCCCTCCC 60.770 72.222 0.00 0.00 39.46 4.30
2438 8863 3.157949 GGCTCTTCCTCCCTCCCG 61.158 72.222 0.00 0.00 0.00 5.14
2439 8864 3.855853 GCTCTTCCTCCCTCCCGC 61.856 72.222 0.00 0.00 0.00 6.13
2440 8865 3.532155 CTCTTCCTCCCTCCCGCG 61.532 72.222 0.00 0.00 0.00 6.46
2441 8866 4.377760 TCTTCCTCCCTCCCGCGT 62.378 66.667 4.92 0.00 0.00 6.01
2442 8867 3.839432 CTTCCTCCCTCCCGCGTC 61.839 72.222 4.92 0.00 0.00 5.19
2443 8868 4.377760 TTCCTCCCTCCCGCGTCT 62.378 66.667 4.92 0.00 0.00 4.18
2444 8869 4.816984 TCCTCCCTCCCGCGTCTC 62.817 72.222 4.92 0.00 0.00 3.36
2446 8871 3.522731 CTCCCTCCCGCGTCTCAG 61.523 72.222 4.92 0.00 0.00 3.35
2474 8899 3.443045 GCCCCAACATGCGTGGAG 61.443 66.667 15.96 5.50 0.00 3.86
2475 8900 2.751436 CCCCAACATGCGTGGAGG 60.751 66.667 15.96 11.12 0.00 4.30
2476 8901 2.034066 CCCAACATGCGTGGAGGT 59.966 61.111 15.96 0.00 0.00 3.85
2477 8902 2.334946 CCCAACATGCGTGGAGGTG 61.335 63.158 15.96 2.78 0.00 4.00
2478 8903 2.562912 CAACATGCGTGGAGGTGC 59.437 61.111 11.36 0.00 0.00 5.01
2479 8904 3.049674 AACATGCGTGGAGGTGCG 61.050 61.111 11.36 0.00 0.00 5.34
2488 8913 3.224324 GGAGGTGCGGCCGATCTA 61.224 66.667 33.48 8.74 43.70 1.98
2489 8914 2.336809 GAGGTGCGGCCGATCTAG 59.663 66.667 33.48 0.00 43.70 2.43
2490 8915 2.123854 AGGTGCGGCCGATCTAGA 60.124 61.111 33.48 0.64 43.70 2.43
2491 8916 1.735376 GAGGTGCGGCCGATCTAGAA 61.735 60.000 33.48 0.69 43.70 2.10
2492 8917 1.300233 GGTGCGGCCGATCTAGAAG 60.300 63.158 33.48 0.00 0.00 2.85
2493 8918 1.951631 GTGCGGCCGATCTAGAAGC 60.952 63.158 33.48 8.12 0.00 3.86
2494 8919 2.731348 GCGGCCGATCTAGAAGCG 60.731 66.667 33.48 10.43 0.00 4.68
2498 8923 2.049985 CCGATCTAGAAGCGGCGG 60.050 66.667 20.14 13.36 38.46 6.13
2499 8924 2.731348 CGATCTAGAAGCGGCGGC 60.731 66.667 9.78 8.43 40.37 6.53
2500 8925 2.731348 GATCTAGAAGCGGCGGCG 60.731 66.667 28.70 28.70 46.35 6.46
2501 8926 3.195591 GATCTAGAAGCGGCGGCGA 62.196 63.158 36.87 12.93 46.35 5.54
2502 8927 2.479412 GATCTAGAAGCGGCGGCGAT 62.479 60.000 36.87 28.87 46.35 4.58
2503 8928 2.755542 ATCTAGAAGCGGCGGCGATG 62.756 60.000 36.87 17.37 46.35 3.84
2504 8929 4.585526 TAGAAGCGGCGGCGATGG 62.586 66.667 36.87 6.36 46.35 3.51
2608 9033 4.451150 GTCTCCGGCGGCATGTCA 62.451 66.667 23.83 0.83 0.00 3.58
2609 9034 3.469970 TCTCCGGCGGCATGTCAT 61.470 61.111 23.83 0.00 0.00 3.06
2610 9035 2.969238 CTCCGGCGGCATGTCATC 60.969 66.667 23.83 0.00 0.00 2.92
2611 9036 3.451556 CTCCGGCGGCATGTCATCT 62.452 63.158 23.83 0.00 0.00 2.90
2612 9037 3.274586 CCGGCGGCATGTCATCTG 61.275 66.667 15.42 0.00 0.00 2.90
2613 9038 3.274586 CGGCGGCATGTCATCTGG 61.275 66.667 10.53 0.00 0.00 3.86
2614 9039 3.589881 GGCGGCATGTCATCTGGC 61.590 66.667 3.07 0.00 35.94 4.85
2615 9040 2.515523 GCGGCATGTCATCTGGCT 60.516 61.111 0.00 0.00 37.06 4.75
2616 9041 2.117156 GCGGCATGTCATCTGGCTT 61.117 57.895 0.00 0.00 37.06 4.35
2617 9042 1.660560 GCGGCATGTCATCTGGCTTT 61.661 55.000 0.00 0.00 37.06 3.51
2618 9043 1.667236 CGGCATGTCATCTGGCTTTA 58.333 50.000 0.00 0.00 37.06 1.85
2619 9044 1.600957 CGGCATGTCATCTGGCTTTAG 59.399 52.381 0.00 0.00 37.06 1.85
2620 9045 2.742856 CGGCATGTCATCTGGCTTTAGA 60.743 50.000 0.00 0.00 37.06 2.10
2621 9046 3.484407 GGCATGTCATCTGGCTTTAGAT 58.516 45.455 0.00 0.00 37.90 1.98
2622 9047 3.501445 GGCATGTCATCTGGCTTTAGATC 59.499 47.826 0.00 0.00 35.28 2.75
2623 9048 3.186001 GCATGTCATCTGGCTTTAGATCG 59.814 47.826 0.00 0.00 35.28 3.69
2624 9049 3.459232 TGTCATCTGGCTTTAGATCGG 57.541 47.619 0.00 0.00 35.28 4.18
2625 9050 2.139118 GTCATCTGGCTTTAGATCGGC 58.861 52.381 0.00 0.00 35.28 5.54
2626 9051 1.143305 CATCTGGCTTTAGATCGGCG 58.857 55.000 0.00 0.00 35.28 6.46
2627 9052 1.040646 ATCTGGCTTTAGATCGGCGA 58.959 50.000 13.87 13.87 31.97 5.54
2628 9053 0.102481 TCTGGCTTTAGATCGGCGAC 59.898 55.000 13.76 6.55 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.870075 ATGAGGGCTTAATTAAATGATACTCC 57.130 34.615 0.00 0.00 0.00 3.85
44 45 6.101650 TCCCTAAGTAGATATGCACACATG 57.898 41.667 0.00 0.00 37.04 3.21
47 48 6.821665 TGTTTTCCCTAAGTAGATATGCACAC 59.178 38.462 0.00 0.00 0.00 3.82
49 50 8.451908 AATGTTTTCCCTAAGTAGATATGCAC 57.548 34.615 0.00 0.00 0.00 4.57
50 51 9.120538 GAAATGTTTTCCCTAAGTAGATATGCA 57.879 33.333 0.00 0.00 0.00 3.96
51 52 9.343539 AGAAATGTTTTCCCTAAGTAGATATGC 57.656 33.333 0.00 0.00 0.00 3.14
108 4702 2.356382 CACTAGCTCCAAGTCGGTAGAG 59.644 54.545 0.00 0.00 35.71 2.43
129 4723 4.023963 GTCCTGTTTTCCAGTACTTGCTTC 60.024 45.833 0.00 0.00 39.74 3.86
145 4739 7.004086 TCATTTTGGAATAACTCTGTCCTGTT 58.996 34.615 0.00 0.00 32.28 3.16
159 4753 6.493166 TGGATTCAGGTAGTCATTTTGGAAT 58.507 36.000 0.00 0.00 0.00 3.01
259 4853 0.037697 TCGTGGTTGAAGATCGGGTG 60.038 55.000 0.00 0.00 0.00 4.61
309 4904 7.713764 ATAAAACTTAGTACCGTGTTCGTTT 57.286 32.000 0.00 0.00 35.01 3.60
312 4907 9.731519 CTAAAATAAAACTTAGTACCGTGTTCG 57.268 33.333 0.00 0.00 0.00 3.95
317 4912 6.873605 ACGGCTAAAATAAAACTTAGTACCGT 59.126 34.615 0.00 0.00 38.28 4.83
318 4913 7.276438 AGACGGCTAAAATAAAACTTAGTACCG 59.724 37.037 0.00 0.00 37.08 4.02
319 4914 8.484641 AGACGGCTAAAATAAAACTTAGTACC 57.515 34.615 0.00 0.00 0.00 3.34
328 4923 7.757624 CCAGCAAAATAGACGGCTAAAATAAAA 59.242 33.333 0.00 0.00 34.25 1.52
355 4950 6.315393 CACCAAAAGTATGCTATTTAGTCCGT 59.685 38.462 0.00 0.00 0.00 4.69
369 4969 8.113462 ACACATAGGATAAACCACCAAAAGTAT 58.887 33.333 0.00 0.00 42.04 2.12
538 5141 2.154462 CTGTTTTGGCCGAAGATCACT 58.846 47.619 5.34 0.00 0.00 3.41
596 5199 1.388837 TATACCGCGAGCTTCTGGCA 61.389 55.000 8.23 0.00 44.79 4.92
889 5567 1.021390 GTACGCCTGCAGCATCAACT 61.021 55.000 8.66 0.00 44.04 3.16
920 5598 3.063997 CACCGTAGCTCAATGATTCAACC 59.936 47.826 0.00 0.00 0.00 3.77
940 5618 4.592485 ATGGTCTTACCGATCATCTCAC 57.408 45.455 0.00 0.00 39.24 3.51
1023 5715 1.664659 CTGAGCTTCTCTTGCCATTCG 59.335 52.381 0.00 0.00 0.00 3.34
1083 5775 3.010138 GGATGTTATTGCTATAGGGGGCA 59.990 47.826 1.04 0.00 36.62 5.36
1217 5933 0.251653 ACGGGACTGTAGAGCCTCAA 60.252 55.000 0.00 0.00 0.00 3.02
1277 5993 7.011016 GGTTCCTTTTCGAAATTTGATGTTTGT 59.989 33.333 12.12 0.00 0.00 2.83
1393 6109 2.267961 GTAGCCCCCAAGACACCG 59.732 66.667 0.00 0.00 0.00 4.94
1396 6112 1.063070 TGTTGGTAGCCCCCAAGACA 61.063 55.000 4.98 0.00 44.92 3.41
1422 6138 1.702182 TGAGAAGGCCAACATTGCAA 58.298 45.000 5.01 0.00 0.00 4.08
1727 6447 3.354089 AATCACGGCAGTTTCACAAAG 57.646 42.857 0.00 0.00 0.00 2.77
1731 6451 1.335872 CCCAAATCACGGCAGTTTCAC 60.336 52.381 0.00 0.00 0.00 3.18
1736 6456 0.609131 CCTTCCCAAATCACGGCAGT 60.609 55.000 0.00 0.00 0.00 4.40
1740 6460 1.595093 GCCACCTTCCCAAATCACGG 61.595 60.000 0.00 0.00 0.00 4.94
1741 6461 0.893270 TGCCACCTTCCCAAATCACG 60.893 55.000 0.00 0.00 0.00 4.35
1846 8258 1.825090 AAGGACGCAATGCATGAGAA 58.175 45.000 5.91 0.00 32.52 2.87
1859 8271 5.862924 ACTACACATGAATTCAAAGGACG 57.137 39.130 13.09 3.19 0.00 4.79
1902 8314 5.486419 CGGTATAGGGGGTTATAGGAAACAT 59.514 44.000 0.00 0.00 0.00 2.71
2069 8494 6.626488 CGAAGATCGATTAAATGACTTTGCAG 59.374 38.462 0.00 0.00 43.74 4.41
2192 8617 3.056749 GTCGGCTCTTTGAAGTCCTTCTA 60.057 47.826 8.40 0.00 40.14 2.10
2223 8648 7.210174 TGTATCTCCCATTTAGATGAAACTCG 58.790 38.462 0.00 0.00 35.36 4.18
2260 8685 1.270907 GCACAAGAGAGGGAGAAGGA 58.729 55.000 0.00 0.00 0.00 3.36
2261 8686 0.251634 GGCACAAGAGAGGGAGAAGG 59.748 60.000 0.00 0.00 0.00 3.46
2262 8687 0.251634 GGGCACAAGAGAGGGAGAAG 59.748 60.000 0.00 0.00 0.00 2.85
2263 8688 1.544825 CGGGCACAAGAGAGGGAGAA 61.545 60.000 0.00 0.00 0.00 2.87
2264 8689 1.984570 CGGGCACAAGAGAGGGAGA 60.985 63.158 0.00 0.00 0.00 3.71
2265 8690 2.581354 CGGGCACAAGAGAGGGAG 59.419 66.667 0.00 0.00 0.00 4.30
2266 8691 3.706373 GCGGGCACAAGAGAGGGA 61.706 66.667 0.00 0.00 0.00 4.20
2268 8693 4.379243 ACGCGGGCACAAGAGAGG 62.379 66.667 12.47 0.00 0.00 3.69
2269 8694 2.811317 GACGCGGGCACAAGAGAG 60.811 66.667 12.47 0.00 0.00 3.20
2270 8695 4.717629 CGACGCGGGCACAAGAGA 62.718 66.667 12.47 0.00 0.00 3.10
2312 8737 4.176752 CGGCTAGGGTTGGGGAGC 62.177 72.222 0.00 0.00 0.00 4.70
2313 8738 2.687566 ACGGCTAGGGTTGGGGAG 60.688 66.667 0.00 0.00 0.00 4.30
2314 8739 2.686106 GACGGCTAGGGTTGGGGA 60.686 66.667 0.00 0.00 0.00 4.81
2315 8740 4.157120 CGACGGCTAGGGTTGGGG 62.157 72.222 0.00 0.00 0.00 4.96
2316 8741 4.832608 GCGACGGCTAGGGTTGGG 62.833 72.222 0.00 0.00 35.83 4.12
2317 8742 4.832608 GGCGACGGCTAGGGTTGG 62.833 72.222 15.00 0.00 39.81 3.77
2338 8763 2.615391 AGGAAGGAAGATAGGCTAGGC 58.385 52.381 8.55 8.55 0.00 3.93
2339 8764 3.580895 GGAAGGAAGGAAGATAGGCTAGG 59.419 52.174 0.00 0.00 0.00 3.02
2340 8765 4.488770 AGGAAGGAAGGAAGATAGGCTAG 58.511 47.826 0.00 0.00 0.00 3.42
2341 8766 4.484912 GAGGAAGGAAGGAAGATAGGCTA 58.515 47.826 0.00 0.00 0.00 3.93
2342 8767 3.313791 GAGGAAGGAAGGAAGATAGGCT 58.686 50.000 0.00 0.00 0.00 4.58
2343 8768 2.370519 GGAGGAAGGAAGGAAGATAGGC 59.629 54.545 0.00 0.00 0.00 3.93
2344 8769 2.976185 GGGAGGAAGGAAGGAAGATAGG 59.024 54.545 0.00 0.00 0.00 2.57
2345 8770 2.630580 CGGGAGGAAGGAAGGAAGATAG 59.369 54.545 0.00 0.00 0.00 2.08
2346 8771 2.679082 CGGGAGGAAGGAAGGAAGATA 58.321 52.381 0.00 0.00 0.00 1.98
2347 8772 1.501582 CGGGAGGAAGGAAGGAAGAT 58.498 55.000 0.00 0.00 0.00 2.40
2348 8773 1.265454 GCGGGAGGAAGGAAGGAAGA 61.265 60.000 0.00 0.00 0.00 2.87
2349 8774 1.222113 GCGGGAGGAAGGAAGGAAG 59.778 63.158 0.00 0.00 0.00 3.46
2350 8775 2.298661 GGCGGGAGGAAGGAAGGAA 61.299 63.158 0.00 0.00 0.00 3.36
2351 8776 2.687566 GGCGGGAGGAAGGAAGGA 60.688 66.667 0.00 0.00 0.00 3.36
2352 8777 4.162690 CGGCGGGAGGAAGGAAGG 62.163 72.222 0.00 0.00 0.00 3.46
2353 8778 4.840005 GCGGCGGGAGGAAGGAAG 62.840 72.222 9.78 0.00 0.00 3.46
2417 8842 4.806339 AGGGAGGAAGAGCCCCCG 62.806 72.222 0.00 0.00 46.35 5.73
2418 8843 2.770475 GAGGGAGGAAGAGCCCCC 60.770 72.222 0.00 0.00 45.89 5.40
2419 8844 2.770475 GGAGGGAGGAAGAGCCCC 60.770 72.222 0.00 0.00 45.89 5.80
2420 8845 2.770475 GGGAGGGAGGAAGAGCCC 60.770 72.222 0.00 0.00 45.04 5.19
2421 8846 3.157949 CGGGAGGGAGGAAGAGCC 61.158 72.222 0.00 0.00 0.00 4.70
2422 8847 3.855853 GCGGGAGGGAGGAAGAGC 61.856 72.222 0.00 0.00 0.00 4.09
2457 8882 3.443045 CTCCACGCATGTTGGGGC 61.443 66.667 13.70 0.00 34.28 5.80
2458 8883 2.751436 CCTCCACGCATGTTGGGG 60.751 66.667 13.70 11.01 34.28 4.96
2459 8884 2.034066 ACCTCCACGCATGTTGGG 59.966 61.111 13.70 4.38 36.28 4.12
2460 8885 2.981560 GCACCTCCACGCATGTTGG 61.982 63.158 8.76 8.76 0.00 3.77
2461 8886 2.562912 GCACCTCCACGCATGTTG 59.437 61.111 0.00 0.00 0.00 3.33
2462 8887 3.049674 CGCACCTCCACGCATGTT 61.050 61.111 0.00 0.00 0.00 2.71
2471 8896 3.214250 CTAGATCGGCCGCACCTCC 62.214 68.421 23.51 5.20 35.61 4.30
2472 8897 1.735376 TTCTAGATCGGCCGCACCTC 61.735 60.000 23.51 14.17 35.61 3.85
2473 8898 1.739338 CTTCTAGATCGGCCGCACCT 61.739 60.000 23.51 18.72 35.61 4.00
2474 8899 1.300233 CTTCTAGATCGGCCGCACC 60.300 63.158 23.51 11.86 0.00 5.01
2475 8900 1.951631 GCTTCTAGATCGGCCGCAC 60.952 63.158 23.51 16.80 0.00 5.34
2476 8901 2.417516 GCTTCTAGATCGGCCGCA 59.582 61.111 23.51 10.36 0.00 5.69
2477 8902 2.731348 CGCTTCTAGATCGGCCGC 60.731 66.667 23.51 7.63 0.00 6.53
2478 8903 2.049985 CCGCTTCTAGATCGGCCG 60.050 66.667 22.12 22.12 36.53 6.13
2481 8906 2.049985 CCGCCGCTTCTAGATCGG 60.050 66.667 22.48 22.48 45.46 4.18
2482 8907 2.731348 GCCGCCGCTTCTAGATCG 60.731 66.667 0.00 0.31 0.00 3.69
2483 8908 2.479412 ATCGCCGCCGCTTCTAGATC 62.479 60.000 0.00 0.00 0.00 2.75
2484 8909 2.565645 ATCGCCGCCGCTTCTAGAT 61.566 57.895 0.00 0.00 0.00 1.98
2485 8910 3.217017 ATCGCCGCCGCTTCTAGA 61.217 61.111 0.00 0.00 0.00 2.43
2486 8911 3.032609 CATCGCCGCCGCTTCTAG 61.033 66.667 0.00 0.00 0.00 2.43
2487 8912 4.585526 CCATCGCCGCCGCTTCTA 62.586 66.667 0.00 0.00 0.00 2.10
2591 9016 3.740128 ATGACATGCCGCCGGAGAC 62.740 63.158 7.68 0.00 0.00 3.36
2592 9017 3.445518 GATGACATGCCGCCGGAGA 62.446 63.158 7.68 0.00 0.00 3.71
2593 9018 2.969238 GATGACATGCCGCCGGAG 60.969 66.667 7.68 0.00 0.00 4.63
2594 9019 3.469970 AGATGACATGCCGCCGGA 61.470 61.111 7.68 0.00 0.00 5.14
2595 9020 3.274586 CAGATGACATGCCGCCGG 61.275 66.667 0.00 0.00 0.00 6.13
2596 9021 3.274586 CCAGATGACATGCCGCCG 61.275 66.667 0.00 0.00 0.00 6.46
2597 9022 3.589881 GCCAGATGACATGCCGCC 61.590 66.667 0.00 0.00 0.00 6.13
2598 9023 1.660560 AAAGCCAGATGACATGCCGC 61.661 55.000 0.00 0.00 0.00 6.53
2599 9024 1.600957 CTAAAGCCAGATGACATGCCG 59.399 52.381 0.00 0.00 0.00 5.69
2600 9025 2.923121 TCTAAAGCCAGATGACATGCC 58.077 47.619 0.00 0.00 0.00 4.40
2601 9026 3.186001 CGATCTAAAGCCAGATGACATGC 59.814 47.826 0.00 0.00 35.37 4.06
2602 9027 3.744942 CCGATCTAAAGCCAGATGACATG 59.255 47.826 0.00 0.00 35.37 3.21
2603 9028 3.805108 GCCGATCTAAAGCCAGATGACAT 60.805 47.826 0.00 0.00 35.37 3.06
2604 9029 2.483714 GCCGATCTAAAGCCAGATGACA 60.484 50.000 0.00 0.00 35.37 3.58
2605 9030 2.139118 GCCGATCTAAAGCCAGATGAC 58.861 52.381 0.00 0.00 35.37 3.06
2606 9031 1.269778 CGCCGATCTAAAGCCAGATGA 60.270 52.381 0.00 0.00 35.37 2.92
2607 9032 1.143305 CGCCGATCTAAAGCCAGATG 58.857 55.000 0.00 0.00 35.37 2.90
2608 9033 1.040646 TCGCCGATCTAAAGCCAGAT 58.959 50.000 0.00 0.00 37.99 2.90
2609 9034 0.102481 GTCGCCGATCTAAAGCCAGA 59.898 55.000 0.00 0.00 0.00 3.86
2610 9035 1.209275 CGTCGCCGATCTAAAGCCAG 61.209 60.000 0.00 0.00 35.63 4.85
2611 9036 1.226859 CGTCGCCGATCTAAAGCCA 60.227 57.895 0.00 0.00 35.63 4.75
2612 9037 1.949631 CCGTCGCCGATCTAAAGCC 60.950 63.158 0.00 0.00 35.63 4.35
2613 9038 2.586773 GCCGTCGCCGATCTAAAGC 61.587 63.158 0.00 0.00 35.63 3.51
2614 9039 2.293627 CGCCGTCGCCGATCTAAAG 61.294 63.158 0.00 0.00 35.63 1.85
2615 9040 2.278336 CGCCGTCGCCGATCTAAA 60.278 61.111 0.00 0.00 35.63 1.85
2616 9041 3.459378 GACGCCGTCGCCGATCTAA 62.459 63.158 1.33 0.00 39.84 2.10
2617 9042 3.945434 GACGCCGTCGCCGATCTA 61.945 66.667 1.33 0.00 39.84 1.98


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

AutoCloner maintained by Alex Coulton.