Multiple sequence alignment - TraesCS1D01G395800

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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 TraesCS1D01G395800 chr1D 100.000 3134 0 0 1 3134 464168632 464165499 0.000000e+00 5788.0
1 TraesCS1D01G395800 chr1B 92.900 2479 111 23 1 2469 640402201 640399778 0.000000e+00 3542.0
2 TraesCS1D01G395800 chr1A 95.179 1784 53 10 691 2461 556450663 556448900 0.000000e+00 2787.0
3 TraesCS1D01G395800 chr1A 92.286 713 44 3 1 705 556451957 556451248 0.000000e+00 1002.0
4 TraesCS1D01G395800 chr1A 82.075 636 60 25 2523 3132 556447402 556446795 7.810000e-136 494.0
5 TraesCS1D01G395800 chr6A 79.733 375 52 9 3 366 431138530 431138891 1.870000e-62 250.0
6 TraesCS1D01G395800 chrUn 74.737 380 58 28 1 372 41020788 41021137 5.450000e-28 135.0
7 TraesCS1D01G395800 chr4A 74.775 333 58 17 18 342 532109810 532109496 3.280000e-25 126.0
8 TraesCS1D01G395800 chr2D 77.686 242 28 14 1 237 95178823 95179043 1.180000e-24 124.0
9 TraesCS1D01G395800 chr2D 87.736 106 10 2 1 106 591300175 591300277 1.530000e-23 121.0
10 TraesCS1D01G395800 chr2D 86.957 69 8 1 2 70 649554457 649554524 3.350000e-10 76.8
11 TraesCS1D01G395800 chr3B 87.368 95 9 1 12 106 10644521 10644430 4.270000e-19 106.0
12 TraesCS1D01G395800 chr5D 94.595 37 2 0 1675 1711 353076414 353076378 1.210000e-04 58.4
13 TraesCS1D01G395800 chr5A 90.698 43 4 0 1669 1711 452687907 452687949 1.210000e-04 58.4


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 TraesCS1D01G395800 chr1D 464165499 464168632 3133 True 5788.000000 5788 100.000000 1 3134 1 chr1D.!!$R1 3133
1 TraesCS1D01G395800 chr1B 640399778 640402201 2423 True 3542.000000 3542 92.900000 1 2469 1 chr1B.!!$R1 2468
2 TraesCS1D01G395800 chr1A 556446795 556451957 5162 True 1427.666667 2787 89.846667 1 3132 3 chr1A.!!$R1 3131

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
961 1579 0.030235 GTTCCAAACACCACTTCGGC 59.97 55.0 0.0 0.0 39.03 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 4545 0.039978 CTATAGCGCTCACAGACCGG 60.04 60.0 16.34 0.0 0.0 5.28 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
113 114 8.834004 AGTAGTTTGTAGTATGGAACTATGGA 57.166 34.615 0.00 0.00 42.63 3.41
129 130 2.006805 TGGATTTGCAATGTCCACCA 57.993 45.000 23.08 13.49 37.12 4.17
156 157 5.461032 ACTCCGATGAACTATGATCCTTC 57.539 43.478 0.00 0.00 0.00 3.46
165 166 0.673985 TATGATCCTTCTGTCCGGCG 59.326 55.000 0.00 0.00 0.00 6.46
234 235 3.196469 TGTTGCATGGTTTTGAGGTTTCA 59.804 39.130 0.00 0.00 0.00 2.69
235 236 4.187694 GTTGCATGGTTTTGAGGTTTCAA 58.812 39.130 0.00 0.00 41.44 2.69
236 237 4.057406 TGCATGGTTTTGAGGTTTCAAG 57.943 40.909 0.00 0.00 43.76 3.02
254 255 1.214589 GTATGAGGGACGCGTGTGT 59.785 57.895 20.70 0.00 0.00 3.72
255 256 1.076533 GTATGAGGGACGCGTGTGTG 61.077 60.000 20.70 0.00 0.00 3.82
256 257 2.220615 TATGAGGGACGCGTGTGTGG 62.221 60.000 20.70 0.00 0.00 4.17
351 352 6.721318 AGGACTTGGATTTGCTATGTCTTAA 58.279 36.000 0.00 0.00 34.10 1.85
415 416 3.657727 AGGGAAGTTGGAGAAAATGGAGA 59.342 43.478 0.00 0.00 0.00 3.71
473 478 9.638239 GTTTATGTAGGATGAAAATGAAAGCAA 57.362 29.630 0.00 0.00 0.00 3.91
501 506 2.474735 CGCCCAAACACAAACAATTAGC 59.525 45.455 0.00 0.00 0.00 3.09
577 582 4.211374 CGACTCAGTTTGGTTCGATTCTTT 59.789 41.667 0.00 0.00 0.00 2.52
589 594 5.228012 GGTTCGATTCTTTGATTTTCGATGC 59.772 40.000 0.00 0.00 38.47 3.91
634 646 2.171448 AGAGCCCGCAAACTTATCTCAT 59.829 45.455 0.00 0.00 0.00 2.90
882 1499 9.784680 TCTCACTACTTATATTGTTTCTTCGAC 57.215 33.333 0.00 0.00 0.00 4.20
897 1514 6.497785 TTCTTCGACGATCTTTCTTCTACT 57.502 37.500 0.00 0.00 0.00 2.57
898 1515 6.109320 TCTTCGACGATCTTTCTTCTACTC 57.891 41.667 0.00 0.00 0.00 2.59
899 1516 4.879104 TCGACGATCTTTCTTCTACTCC 57.121 45.455 0.00 0.00 0.00 3.85
900 1517 4.515361 TCGACGATCTTTCTTCTACTCCT 58.485 43.478 0.00 0.00 0.00 3.69
901 1518 5.668471 TCGACGATCTTTCTTCTACTCCTA 58.332 41.667 0.00 0.00 0.00 2.94
902 1519 5.523188 TCGACGATCTTTCTTCTACTCCTAC 59.477 44.000 0.00 0.00 0.00 3.18
959 1577 2.223479 CCAAGTTCCAAACACCACTTCG 60.223 50.000 0.00 0.00 0.00 3.79
960 1578 1.675552 AGTTCCAAACACCACTTCGG 58.324 50.000 0.00 0.00 42.50 4.30
961 1579 0.030235 GTTCCAAACACCACTTCGGC 59.970 55.000 0.00 0.00 39.03 5.54
962 1580 0.394488 TTCCAAACACCACTTCGGCA 60.394 50.000 0.00 0.00 39.03 5.69
963 1581 1.098712 TCCAAACACCACTTCGGCAC 61.099 55.000 0.00 0.00 39.03 5.01
964 1582 1.101049 CCAAACACCACTTCGGCACT 61.101 55.000 0.00 0.00 39.03 4.40
965 1583 0.738389 CAAACACCACTTCGGCACTT 59.262 50.000 0.00 0.00 39.03 3.16
967 1585 0.818040 AACACCACTTCGGCACTTCC 60.818 55.000 0.00 0.00 39.03 3.46
968 1586 1.071471 CACCACTTCGGCACTTCCT 59.929 57.895 0.00 0.00 39.03 3.36
969 1587 1.071471 ACCACTTCGGCACTTCCTG 59.929 57.895 0.00 0.00 39.03 3.86
970 1588 2.328099 CCACTTCGGCACTTCCTGC 61.328 63.158 0.00 0.00 46.31 4.85
971 1589 1.302033 CACTTCGGCACTTCCTGCT 60.302 57.895 0.00 0.00 46.25 4.24
972 1590 1.004440 ACTTCGGCACTTCCTGCTC 60.004 57.895 0.00 0.00 46.25 4.26
973 1591 1.743252 CTTCGGCACTTCCTGCTCC 60.743 63.158 0.00 0.00 46.25 4.70
974 1592 3.254024 TTCGGCACTTCCTGCTCCC 62.254 63.158 0.00 0.00 46.25 4.30
975 1593 4.785453 CGGCACTTCCTGCTCCCC 62.785 72.222 0.00 0.00 46.25 4.81
976 1594 4.785453 GGCACTTCCTGCTCCCCG 62.785 72.222 0.00 0.00 46.25 5.73
1896 2517 4.814294 GGCGAGGCGAACGTGGAT 62.814 66.667 0.00 0.00 0.00 3.41
1906 2527 1.164411 GAACGTGGATGTGGCATTGA 58.836 50.000 0.00 0.00 0.00 2.57
2199 2820 2.668550 GTCTGTGCCCGTGTTCCC 60.669 66.667 0.00 0.00 0.00 3.97
2200 2821 2.847234 TCTGTGCCCGTGTTCCCT 60.847 61.111 0.00 0.00 0.00 4.20
2201 2822 2.358737 CTGTGCCCGTGTTCCCTC 60.359 66.667 0.00 0.00 0.00 4.30
2202 2823 4.308458 TGTGCCCGTGTTCCCTCG 62.308 66.667 0.00 0.00 0.00 4.63
2223 2844 1.272490 CTCGCTCCCAGTGTTTGAGTA 59.728 52.381 0.00 0.00 0.00 2.59
2474 4507 0.259938 GGGTAACGGAGAGGAGGGTA 59.740 60.000 0.00 0.00 37.60 3.69
2482 4515 1.481615 GGAGAGGAGGGTATGGGTCTC 60.482 61.905 0.00 0.00 0.00 3.36
2484 4517 3.872431 GGAGGGTATGGGTCTCCG 58.128 66.667 0.00 0.00 37.85 4.63
2491 4524 1.677820 GGTATGGGTCTCCGTTGTTGG 60.678 57.143 0.00 0.00 35.24 3.77
2492 4525 1.276989 GTATGGGTCTCCGTTGTTGGA 59.723 52.381 0.00 0.00 36.37 3.53
2499 4532 4.025401 CCGTTGTTGGAGCGGCAC 62.025 66.667 1.45 0.00 38.99 5.01
2501 4534 2.946762 GTTGTTGGAGCGGCACTC 59.053 61.111 1.45 0.00 45.45 3.51
2509 4542 3.477224 GAGCGGCACTCGGAGCTAG 62.477 68.421 4.58 0.00 40.39 3.42
2512 4545 4.228567 GGCACTCGGAGCTAGGGC 62.229 72.222 4.58 0.20 42.90 5.19
2513 4546 4.228567 GCACTCGGAGCTAGGGCC 62.229 72.222 4.58 0.00 37.41 5.80
2519 4552 3.541713 GGAGCTAGGGCCGGTCTG 61.542 72.222 5.77 0.00 39.73 3.51
2520 4553 2.760385 GAGCTAGGGCCGGTCTGT 60.760 66.667 5.77 0.00 39.73 3.41
2522 4555 3.075005 GCTAGGGCCGGTCTGTGA 61.075 66.667 5.77 0.00 0.00 3.58
2523 4556 3.082579 GCTAGGGCCGGTCTGTGAG 62.083 68.421 5.77 0.00 0.00 3.51
2524 4557 3.075005 TAGGGCCGGTCTGTGAGC 61.075 66.667 5.77 0.00 0.00 4.26
2531 4564 3.463574 CGGTCTGTGAGCGCTATAG 57.536 57.895 11.50 9.46 45.89 1.31
2556 4622 2.210116 GGATACAGGCACATGTAACCG 58.790 52.381 0.00 3.04 38.39 4.44
2563 4629 2.027192 AGGCACATGTAACCGTCAGATT 60.027 45.455 0.00 0.00 0.00 2.40
2569 4635 3.868757 TGTAACCGTCAGATTCAGAGG 57.131 47.619 0.00 0.00 0.00 3.69
2570 4636 3.427573 TGTAACCGTCAGATTCAGAGGA 58.572 45.455 0.86 0.00 0.00 3.71
2572 4638 4.282449 TGTAACCGTCAGATTCAGAGGAAA 59.718 41.667 0.86 0.00 36.43 3.13
2613 4680 1.079819 CGCACGACTCCATGACCTT 60.080 57.895 0.00 0.00 0.00 3.50
2625 4692 4.097361 GACCTTCCACCGCCTCCC 62.097 72.222 0.00 0.00 0.00 4.30
2698 4765 4.373116 GCTCACTGGTTCGCCCGA 62.373 66.667 0.00 0.00 36.08 5.14
2731 4798 1.007387 GTGCCGGTTCCAGCAAAAG 60.007 57.895 1.90 0.00 41.48 2.27
2753 4821 1.968540 AGCCTTCGGTTTGCAGCTC 60.969 57.895 0.00 0.00 0.00 4.09
2758 4826 0.586319 TTCGGTTTGCAGCTCTTTCG 59.414 50.000 0.00 0.00 0.00 3.46
2759 4827 1.441016 CGGTTTGCAGCTCTTTCGC 60.441 57.895 0.00 0.00 0.00 4.70
2772 4840 0.179272 CTTTCGCTGAAAGTCGTCGC 60.179 55.000 17.42 0.00 42.61 5.19
2774 4842 1.002250 TTCGCTGAAAGTCGTCGCTC 61.002 55.000 0.00 0.00 35.52 5.03
2790 4858 0.670546 GCTCTAGCCGTTTGCAGACA 60.671 55.000 8.25 0.00 44.83 3.41
2801 4869 0.472044 TTGCAGACAAGGTGGTAGCA 59.528 50.000 0.00 0.00 32.28 3.49
2810 4878 3.004315 ACAAGGTGGTAGCAACAAATTCG 59.996 43.478 13.33 0.00 0.00 3.34
2811 4879 2.858745 AGGTGGTAGCAACAAATTCGT 58.141 42.857 13.33 0.00 0.00 3.85
2820 4888 2.050691 CAACAAATTCGTTGCTTCCGG 58.949 47.619 0.00 0.00 41.31 5.14
2821 4889 0.596082 ACAAATTCGTTGCTTCCGGG 59.404 50.000 0.00 0.00 41.31 5.73
2863 4933 1.616159 AATCAAAAGACGGGGTGGTG 58.384 50.000 0.00 0.00 0.00 4.17
2864 4934 0.768622 ATCAAAAGACGGGGTGGTGA 59.231 50.000 0.00 0.00 0.00 4.02
2865 4935 0.547075 TCAAAAGACGGGGTGGTGAA 59.453 50.000 0.00 0.00 0.00 3.18
2866 4936 1.064611 TCAAAAGACGGGGTGGTGAAA 60.065 47.619 0.00 0.00 0.00 2.69
2867 4937 1.751924 CAAAAGACGGGGTGGTGAAAA 59.248 47.619 0.00 0.00 0.00 2.29
2868 4938 2.146920 AAAGACGGGGTGGTGAAAAA 57.853 45.000 0.00 0.00 0.00 1.94
2925 5016 4.873817 CAGTGGTTGCAAATTCTGAATGA 58.126 39.130 16.08 0.00 0.00 2.57
2938 5029 5.703978 TTCTGAATGATTCCGAGCAAAAA 57.296 34.783 2.26 0.00 0.00 1.94
2975 5066 3.986996 AAAAATCAAAGGCTGGGATGG 57.013 42.857 2.34 0.00 0.00 3.51
2976 5067 2.629017 AAATCAAAGGCTGGGATGGT 57.371 45.000 2.34 0.00 0.00 3.55
2977 5068 3.756082 AAATCAAAGGCTGGGATGGTA 57.244 42.857 2.34 0.00 0.00 3.25
2978 5069 3.303351 AATCAAAGGCTGGGATGGTAG 57.697 47.619 2.34 0.00 0.00 3.18
2979 5070 0.255890 TCAAAGGCTGGGATGGTAGC 59.744 55.000 0.00 0.00 39.17 3.58
2980 5071 0.034186 CAAAGGCTGGGATGGTAGCA 60.034 55.000 0.00 0.00 41.63 3.49
2981 5072 0.704076 AAAGGCTGGGATGGTAGCAA 59.296 50.000 0.00 0.00 41.63 3.91
2982 5073 0.257039 AAGGCTGGGATGGTAGCAAG 59.743 55.000 0.00 0.00 41.63 4.01
2983 5074 0.621571 AGGCTGGGATGGTAGCAAGA 60.622 55.000 0.00 0.00 41.63 3.02
2984 5075 0.255890 GGCTGGGATGGTAGCAAGAA 59.744 55.000 0.00 0.00 41.63 2.52
2985 5076 1.133668 GGCTGGGATGGTAGCAAGAAT 60.134 52.381 0.00 0.00 41.63 2.40
2986 5077 2.225467 GCTGGGATGGTAGCAAGAATC 58.775 52.381 0.00 0.00 39.67 2.52
2987 5078 2.421952 GCTGGGATGGTAGCAAGAATCA 60.422 50.000 0.00 0.00 39.67 2.57
2988 5079 3.889815 CTGGGATGGTAGCAAGAATCAA 58.110 45.455 0.00 0.00 0.00 2.57
2989 5080 4.272489 CTGGGATGGTAGCAAGAATCAAA 58.728 43.478 0.00 0.00 0.00 2.69
2990 5081 4.671831 TGGGATGGTAGCAAGAATCAAAA 58.328 39.130 0.00 0.00 0.00 2.44
2991 5082 5.083122 TGGGATGGTAGCAAGAATCAAAAA 58.917 37.500 0.00 0.00 0.00 1.94
2992 5083 5.047377 TGGGATGGTAGCAAGAATCAAAAAC 60.047 40.000 0.00 0.00 0.00 2.43
3015 5106 3.064207 GTGGTAGCACAAATCGAAGACA 58.936 45.455 19.87 0.00 42.51 3.41
3017 5108 3.244078 TGGTAGCACAAATCGAAGACAGT 60.244 43.478 0.00 0.00 42.51 3.55
3048 5140 6.824305 AAAAAGTTGGAGTGGTCTCATATG 57.176 37.500 0.00 0.00 42.05 1.78
3055 5147 3.556633 GGAGTGGTCTCATATGCATCCAG 60.557 52.174 0.19 0.00 42.05 3.86
3078 5170 0.879090 AAAAATCGAAGACGGGGTGC 59.121 50.000 0.00 0.00 42.51 5.01
3089 5181 2.432510 AGACGGGGTGCAAAAATCAAAA 59.567 40.909 0.00 0.00 0.00 2.44
3090 5182 2.542178 GACGGGGTGCAAAAATCAAAAC 59.458 45.455 0.00 0.00 0.00 2.43
3091 5183 2.093447 ACGGGGTGCAAAAATCAAAACA 60.093 40.909 0.00 0.00 0.00 2.83
3092 5184 2.939103 CGGGGTGCAAAAATCAAAACAA 59.061 40.909 0.00 0.00 0.00 2.83
3099 5191 4.690748 TGCAAAAATCAAAACAAACGGTGA 59.309 33.333 0.00 0.00 0.00 4.02
3102 5194 7.062848 GCAAAAATCAAAACAAACGGTGATAG 58.937 34.615 0.00 0.00 30.60 2.08
3104 5196 5.446143 AATCAAAACAAACGGTGATAGCA 57.554 34.783 0.00 0.00 30.60 3.49
3105 5197 4.902443 TCAAAACAAACGGTGATAGCAA 57.098 36.364 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 6.042552 AGGATCATAGTTCATCGGAGTTCAAT 59.957 38.462 0.00 0.00 0.00 2.57
156 157 3.130633 TCAATATTTCATCGCCGGACAG 58.869 45.455 5.05 0.00 0.00 3.51
165 166 6.662616 CAGTTCACCCGATCAATATTTCATC 58.337 40.000 0.00 0.00 0.00 2.92
234 235 0.108804 CACACGCGTCCCTCATACTT 60.109 55.000 9.86 0.00 0.00 2.24
235 236 1.248785 ACACACGCGTCCCTCATACT 61.249 55.000 9.86 0.00 0.00 2.12
236 237 1.076533 CACACACGCGTCCCTCATAC 61.077 60.000 9.86 0.00 0.00 2.39
254 255 2.513753 CTTGTATGTTGGCTTCCACCA 58.486 47.619 0.00 0.00 38.16 4.17
255 256 1.818674 CCTTGTATGTTGGCTTCCACC 59.181 52.381 0.00 0.00 30.78 4.61
256 257 1.202348 GCCTTGTATGTTGGCTTCCAC 59.798 52.381 0.00 0.00 43.05 4.02
310 311 1.006102 CTCAAACTCCCGCAGACGT 60.006 57.895 0.00 0.00 37.70 4.34
315 316 0.250295 CAAGTCCTCAAACTCCCGCA 60.250 55.000 0.00 0.00 0.00 5.69
321 322 3.837355 AGCAAATCCAAGTCCTCAAACT 58.163 40.909 0.00 0.00 0.00 2.66
470 475 1.153842 GTTTGGGCGTATGGCTTGC 60.154 57.895 8.58 0.00 42.94 4.01
473 478 0.538516 TTGTGTTTGGGCGTATGGCT 60.539 50.000 8.58 0.00 42.94 4.75
501 506 7.076842 AGTGTTCAGTTTGATATTTCCATCG 57.923 36.000 0.00 0.00 0.00 3.84
589 594 3.476552 TGGTTAGAGGTGAGCACTTTTG 58.523 45.455 0.16 0.00 0.00 2.44
882 1499 6.452494 TTGGTAGGAGTAGAAGAAAGATCG 57.548 41.667 0.00 0.00 0.00 3.69
897 1514 3.283751 CTTTGGTGTGTGTTTGGTAGGA 58.716 45.455 0.00 0.00 0.00 2.94
898 1515 2.223711 GCTTTGGTGTGTGTTTGGTAGG 60.224 50.000 0.00 0.00 0.00 3.18
899 1516 2.223711 GGCTTTGGTGTGTGTTTGGTAG 60.224 50.000 0.00 0.00 0.00 3.18
900 1517 1.751924 GGCTTTGGTGTGTGTTTGGTA 59.248 47.619 0.00 0.00 0.00 3.25
901 1518 0.534873 GGCTTTGGTGTGTGTTTGGT 59.465 50.000 0.00 0.00 0.00 3.67
902 1519 0.527385 CGGCTTTGGTGTGTGTTTGG 60.527 55.000 0.00 0.00 0.00 3.28
1046 1664 2.203015 CGGCGTGGTAAGGATGGG 60.203 66.667 0.00 0.00 0.00 4.00
1857 2478 2.491022 GGGACCCGTCATCTCCTCG 61.491 68.421 0.00 0.00 0.00 4.63
1896 2517 2.316867 CGTCAGCGTCAATGCCACA 61.317 57.895 0.00 0.00 34.65 4.17
2114 2735 2.052104 CAAAATGGCCTCGGGGGTC 61.052 63.158 1.90 0.00 40.85 4.46
2192 2813 2.507324 GAGCGAGCGAGGGAACAC 60.507 66.667 0.00 0.00 0.00 3.32
2199 2820 2.771763 AAACACTGGGAGCGAGCGAG 62.772 60.000 0.00 0.00 0.00 5.03
2200 2821 2.867855 AAACACTGGGAGCGAGCGA 61.868 57.895 0.00 0.00 0.00 4.93
2201 2822 2.357517 AAACACTGGGAGCGAGCG 60.358 61.111 0.00 0.00 0.00 5.03
2202 2823 1.294659 CTCAAACACTGGGAGCGAGC 61.295 60.000 0.00 0.00 0.00 5.03
2320 2949 1.005984 TCGTTCATCGCCCGACAAA 60.006 52.632 0.00 0.00 39.67 2.83
2474 4507 2.458892 TCCAACAACGGAGACCCAT 58.541 52.632 0.00 0.00 0.00 4.00
2484 4517 2.946762 GAGTGCCGCTCCAACAAC 59.053 61.111 0.00 0.00 38.27 3.32
2491 4524 3.477224 CTAGCTCCGAGTGCCGCTC 62.477 68.421 0.00 0.00 40.77 5.03
2492 4525 3.522731 CTAGCTCCGAGTGCCGCT 61.523 66.667 0.00 0.00 36.84 5.52
2493 4526 4.577246 CCTAGCTCCGAGTGCCGC 62.577 72.222 0.00 0.00 36.84 6.53
2494 4527 3.905678 CCCTAGCTCCGAGTGCCG 61.906 72.222 0.00 0.00 38.18 5.69
2495 4528 4.228567 GCCCTAGCTCCGAGTGCC 62.229 72.222 0.00 0.00 35.50 5.01
2496 4529 4.228567 GGCCCTAGCTCCGAGTGC 62.229 72.222 0.00 0.00 39.73 4.40
2502 4535 3.541713 CAGACCGGCCCTAGCTCC 61.542 72.222 0.00 0.00 39.73 4.70
2503 4536 2.760385 ACAGACCGGCCCTAGCTC 60.760 66.667 0.00 0.00 39.73 4.09
2504 4537 3.077556 CACAGACCGGCCCTAGCT 61.078 66.667 0.00 0.00 39.73 3.32
2505 4538 3.075005 TCACAGACCGGCCCTAGC 61.075 66.667 0.00 0.00 38.76 3.42
2506 4539 3.082579 GCTCACAGACCGGCCCTAG 62.083 68.421 0.00 0.00 0.00 3.02
2507 4540 3.075005 GCTCACAGACCGGCCCTA 61.075 66.667 0.00 0.00 0.00 3.53
2512 4545 0.039978 CTATAGCGCTCACAGACCGG 60.040 60.000 16.34 0.00 0.00 5.28
2513 4546 0.661780 GCTATAGCGCTCACAGACCG 60.662 60.000 16.34 0.00 0.00 4.79
2514 4547 3.187211 GCTATAGCGCTCACAGACC 57.813 57.895 16.34 0.00 0.00 3.85
2525 4558 2.288825 TGCCTGTATCCAACGCTATAGC 60.289 50.000 15.09 15.09 37.78 2.97
2527 4560 2.696187 TGTGCCTGTATCCAACGCTATA 59.304 45.455 0.00 0.00 0.00 1.31
2528 4561 1.484653 TGTGCCTGTATCCAACGCTAT 59.515 47.619 0.00 0.00 0.00 2.97
2529 4562 0.899019 TGTGCCTGTATCCAACGCTA 59.101 50.000 0.00 0.00 0.00 4.26
2530 4563 0.253044 ATGTGCCTGTATCCAACGCT 59.747 50.000 0.00 0.00 0.00 5.07
2531 4564 0.378257 CATGTGCCTGTATCCAACGC 59.622 55.000 0.00 0.00 0.00 4.84
2698 4765 1.081094 GGCACTACAATTTACCGCGT 58.919 50.000 4.92 0.00 0.00 6.01
2701 4768 1.729284 ACCGGCACTACAATTTACCG 58.271 50.000 0.00 0.00 40.30 4.02
2702 4769 2.421073 GGAACCGGCACTACAATTTACC 59.579 50.000 0.00 0.00 0.00 2.85
2758 4826 1.540407 CTAGAGCGACGACTTTCAGC 58.460 55.000 0.00 0.00 0.00 4.26
2759 4827 1.540407 GCTAGAGCGACGACTTTCAG 58.460 55.000 0.00 0.00 0.00 3.02
2772 4840 1.728971 CTTGTCTGCAAACGGCTAGAG 59.271 52.381 0.00 0.00 45.15 2.43
2774 4842 0.798776 CCTTGTCTGCAAACGGCTAG 59.201 55.000 0.00 0.00 45.15 3.42
2790 4858 3.219281 ACGAATTTGTTGCTACCACCTT 58.781 40.909 0.00 0.00 0.00 3.50
2801 4869 1.000717 CCCGGAAGCAACGAATTTGTT 60.001 47.619 0.73 5.16 37.54 2.83
2904 4995 5.733620 ATCATTCAGAATTTGCAACCACT 57.266 34.783 0.00 0.00 0.00 4.00
2959 5050 1.133668 GCTACCATCCCAGCCTTTGAT 60.134 52.381 0.00 0.00 0.00 2.57
2960 5051 0.255890 GCTACCATCCCAGCCTTTGA 59.744 55.000 0.00 0.00 0.00 2.69
2961 5052 0.034186 TGCTACCATCCCAGCCTTTG 60.034 55.000 0.00 0.00 36.95 2.77
2964 5055 0.621571 TCTTGCTACCATCCCAGCCT 60.622 55.000 0.00 0.00 36.95 4.58
2965 5056 0.255890 TTCTTGCTACCATCCCAGCC 59.744 55.000 0.00 0.00 36.95 4.85
2966 5057 2.225467 GATTCTTGCTACCATCCCAGC 58.775 52.381 0.00 0.00 38.31 4.85
2967 5058 3.565764 TGATTCTTGCTACCATCCCAG 57.434 47.619 0.00 0.00 0.00 4.45
2968 5059 4.314522 TTTGATTCTTGCTACCATCCCA 57.685 40.909 0.00 0.00 0.00 4.37
2969 5060 5.410924 GTTTTTGATTCTTGCTACCATCCC 58.589 41.667 0.00 0.00 0.00 3.85
2970 5061 5.095490 CGTTTTTGATTCTTGCTACCATCC 58.905 41.667 0.00 0.00 0.00 3.51
2971 5062 5.095490 CCGTTTTTGATTCTTGCTACCATC 58.905 41.667 0.00 0.00 0.00 3.51
2972 5063 4.522789 ACCGTTTTTGATTCTTGCTACCAT 59.477 37.500 0.00 0.00 0.00 3.55
2973 5064 3.886505 ACCGTTTTTGATTCTTGCTACCA 59.113 39.130 0.00 0.00 0.00 3.25
2974 5065 4.226761 CACCGTTTTTGATTCTTGCTACC 58.773 43.478 0.00 0.00 0.00 3.18
2975 5066 4.226761 CCACCGTTTTTGATTCTTGCTAC 58.773 43.478 0.00 0.00 0.00 3.58
2976 5067 3.886505 ACCACCGTTTTTGATTCTTGCTA 59.113 39.130 0.00 0.00 0.00 3.49
2977 5068 2.693074 ACCACCGTTTTTGATTCTTGCT 59.307 40.909 0.00 0.00 0.00 3.91
2978 5069 3.092334 ACCACCGTTTTTGATTCTTGC 57.908 42.857 0.00 0.00 0.00 4.01
2979 5070 4.226761 GCTACCACCGTTTTTGATTCTTG 58.773 43.478 0.00 0.00 0.00 3.02
2980 5071 3.886505 TGCTACCACCGTTTTTGATTCTT 59.113 39.130 0.00 0.00 0.00 2.52
2981 5072 3.252458 GTGCTACCACCGTTTTTGATTCT 59.748 43.478 0.00 0.00 35.92 2.40
2982 5073 3.003897 TGTGCTACCACCGTTTTTGATTC 59.996 43.478 0.00 0.00 41.35 2.52
2983 5074 2.952978 TGTGCTACCACCGTTTTTGATT 59.047 40.909 0.00 0.00 41.35 2.57
2984 5075 2.577700 TGTGCTACCACCGTTTTTGAT 58.422 42.857 0.00 0.00 41.35 2.57
2985 5076 2.039818 TGTGCTACCACCGTTTTTGA 57.960 45.000 0.00 0.00 41.35 2.69
2986 5077 2.853731 TTGTGCTACCACCGTTTTTG 57.146 45.000 0.00 0.00 41.35 2.44
2987 5078 3.549221 CGATTTGTGCTACCACCGTTTTT 60.549 43.478 0.00 0.00 41.35 1.94
2988 5079 2.031508 CGATTTGTGCTACCACCGTTTT 60.032 45.455 0.00 0.00 41.35 2.43
2989 5080 1.533731 CGATTTGTGCTACCACCGTTT 59.466 47.619 0.00 0.00 41.35 3.60
2990 5081 1.153353 CGATTTGTGCTACCACCGTT 58.847 50.000 0.00 0.00 41.35 4.44
2991 5082 0.319083 TCGATTTGTGCTACCACCGT 59.681 50.000 0.00 0.00 41.35 4.83
2992 5083 1.393539 CTTCGATTTGTGCTACCACCG 59.606 52.381 0.00 0.00 41.35 4.94
3030 5121 3.266510 TGCATATGAGACCACTCCAAC 57.733 47.619 6.97 0.00 41.99 3.77
3061 5153 0.250553 TTGCACCCCGTCTTCGATTT 60.251 50.000 0.00 0.00 39.71 2.17
3066 5158 1.611491 TGATTTTTGCACCCCGTCTTC 59.389 47.619 0.00 0.00 0.00 2.87
3075 5167 4.785561 CACCGTTTGTTTTGATTTTTGCAC 59.214 37.500 0.00 0.00 0.00 4.57
3076 5168 4.690748 TCACCGTTTGTTTTGATTTTTGCA 59.309 33.333 0.00 0.00 0.00 4.08
3077 5169 5.209944 TCACCGTTTGTTTTGATTTTTGC 57.790 34.783 0.00 0.00 0.00 3.68
3078 5170 7.062848 GCTATCACCGTTTGTTTTGATTTTTG 58.937 34.615 0.00 0.00 31.20 2.44


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

AutoCloner maintained by Alex Coulton.