Multiple sequence alignment - TraesCS4A01G025500

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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 TraesCS4A01G025500 chr4A 100.000 3105 0 0 1 3105 17674206 17677310 0.000000e+00 5734
1 TraesCS4A01G025500 chr4D 88.222 3065 171 71 163 3103 449057239 449054241 0.000000e+00 3485
2 TraesCS4A01G025500 chr4D 93.814 97 6 0 71 167 449057361 449057265 2.500000e-31 147
3 TraesCS4A01G025500 chr4B 90.352 2446 132 50 277 2681 561387625 561385243 0.000000e+00 3114
4 TraesCS4A01G025500 chr4B 81.193 218 19 11 85 281 561387870 561387654 4.150000e-34 156
5 TraesCS4A01G025500 chr5A 75.527 237 52 6 1765 1999 620858154 620858386 9.100000e-21 111
6 TraesCS4A01G025500 chr5D 75.785 223 50 4 1779 1999 496847363 496847583 3.270000e-20 110


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 TraesCS4A01G025500 chr4A 17674206 17677310 3104 False 5734 5734 100.0000 1 3105 1 chr4A.!!$F1 3104
1 TraesCS4A01G025500 chr4D 449054241 449057361 3120 True 1816 3485 91.0180 71 3103 2 chr4D.!!$R1 3032
2 TraesCS4A01G025500 chr4B 561385243 561387870 2627 True 1635 3114 85.7725 85 2681 2 chr4B.!!$R1 2596

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
191 222 0.242825 TTCGTGTTCGGTCTAGCCTG 59.757 55.0 2.39 0.0 37.69 4.85 F
496 560 0.525761 CGACGGTGGCAAAAATGGAT 59.474 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1154 1244 1.134250 GCTCCAAGTCATCCTTCTCCC 60.134 57.143 0.0 0.0 0.0 4.30 R
2423 2526 0.178944 TGGTCTCGTTCCCTTCCAGA 60.179 55.000 0.0 0.0 0.0 3.86 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
32 33 2.121786 CACAAAGTCATGTGCAAGTGC 58.878 47.619 0.00 0.00 43.67 4.40
42 43 2.171940 GCAAGTGCAGTCGCTTCG 59.828 61.111 0.00 0.00 40.78 3.79
43 44 2.856032 CAAGTGCAGTCGCTTCGG 59.144 61.111 0.00 0.00 40.78 4.30
44 45 3.044305 AAGTGCAGTCGCTTCGGC 61.044 61.111 0.00 0.00 38.58 5.54
45 46 3.807631 AAGTGCAGTCGCTTCGGCA 62.808 57.895 0.00 0.00 38.58 5.69
63 64 4.657436 GGCACGGATAAGATAGATAGGG 57.343 50.000 0.00 0.00 0.00 3.53
64 65 3.385111 GGCACGGATAAGATAGATAGGGG 59.615 52.174 0.00 0.00 0.00 4.79
65 66 3.181474 GCACGGATAAGATAGATAGGGGC 60.181 52.174 0.00 0.00 0.00 5.80
66 67 4.023980 CACGGATAAGATAGATAGGGGCA 58.976 47.826 0.00 0.00 0.00 5.36
67 68 4.466370 CACGGATAAGATAGATAGGGGCAA 59.534 45.833 0.00 0.00 0.00 4.52
68 69 4.466726 ACGGATAAGATAGATAGGGGCAAC 59.533 45.833 0.00 0.00 0.00 4.17
83 84 1.452108 CAACCGGAATCAGGAGGCC 60.452 63.158 9.46 0.00 0.00 5.19
141 142 2.325082 ACGATCCGTGGCAAGCAAC 61.325 57.895 0.00 0.00 39.18 4.17
181 212 1.554042 CCCCGTCAGTTTCGTGTTCG 61.554 60.000 0.00 0.00 38.55 3.95
191 222 0.242825 TTCGTGTTCGGTCTAGCCTG 59.757 55.000 2.39 0.00 37.69 4.85
265 296 2.555547 AAGCTTTGCACCGCCACTC 61.556 57.895 0.00 0.00 0.00 3.51
309 373 1.899142 ACCGCCATGGCTTGTTAATTT 59.101 42.857 33.07 5.59 43.94 1.82
310 374 2.270047 CCGCCATGGCTTGTTAATTTG 58.730 47.619 33.07 13.97 39.32 2.32
311 375 2.094286 CCGCCATGGCTTGTTAATTTGA 60.094 45.455 33.07 0.00 39.32 2.69
312 376 3.583806 CGCCATGGCTTGTTAATTTGAA 58.416 40.909 33.07 0.00 39.32 2.69
313 377 4.183101 CGCCATGGCTTGTTAATTTGAAT 58.817 39.130 33.07 0.00 39.32 2.57
354 418 1.204941 CTCGTCAAGTCCTTCCCGAAT 59.795 52.381 0.00 0.00 0.00 3.34
366 430 5.646360 GTCCTTCCCGAATTGAACTGAATTA 59.354 40.000 0.00 0.00 0.00 1.40
429 493 0.887933 TCCTTTCTTTGCCATTCCGC 59.112 50.000 0.00 0.00 0.00 5.54
442 506 3.347216 CCATTCCGCCCATAATTAGGAG 58.653 50.000 0.00 0.00 32.03 3.69
443 507 3.009033 CCATTCCGCCCATAATTAGGAGA 59.991 47.826 0.00 0.00 32.03 3.71
444 508 4.256920 CATTCCGCCCATAATTAGGAGAG 58.743 47.826 0.00 0.00 32.03 3.20
468 532 2.859165 TGCCTCGGAATTCAGTTTCT 57.141 45.000 7.93 0.00 0.00 2.52
495 559 0.820074 ACGACGGTGGCAAAAATGGA 60.820 50.000 0.00 0.00 0.00 3.41
496 560 0.525761 CGACGGTGGCAAAAATGGAT 59.474 50.000 0.00 0.00 0.00 3.41
497 561 1.732077 CGACGGTGGCAAAAATGGATG 60.732 52.381 0.00 0.00 0.00 3.51
515 582 4.320608 GATGTTTTCCAGCCAGAAACAA 57.679 40.909 5.17 0.00 43.82 2.83
517 584 2.159310 TGTTTTCCAGCCAGAAACAACG 60.159 45.455 0.00 0.00 39.51 4.10
519 586 0.749818 TTCCAGCCAGAAACAACGCA 60.750 50.000 0.00 0.00 0.00 5.24
520 587 1.165907 TCCAGCCAGAAACAACGCAG 61.166 55.000 0.00 0.00 0.00 5.18
521 588 1.283793 CAGCCAGAAACAACGCAGG 59.716 57.895 0.00 0.00 0.00 4.85
589 662 1.228862 AAAATGCCCGAACTGCCCT 60.229 52.632 0.00 0.00 0.00 5.19
593 666 4.344865 GCCCGAACTGCCCTCCAA 62.345 66.667 0.00 0.00 0.00 3.53
595 668 2.747855 CCGAACTGCCCTCCAAGC 60.748 66.667 0.00 0.00 0.00 4.01
646 719 1.171308 TAACTACGAGCCAAGCGAGT 58.829 50.000 0.00 0.00 0.00 4.18
656 729 1.213013 CAAGCGAGTGTAGGCGAGT 59.787 57.895 0.00 0.00 0.00 4.18
663 736 2.186076 GAGTGTAGGCGAGTCATTTCG 58.814 52.381 0.00 0.00 43.23 3.46
725 798 2.025727 GATAGGGACGACCACGCG 59.974 66.667 3.53 3.53 43.89 6.01
749 822 2.469516 CCACGCCTCATTTACGCCC 61.470 63.158 0.00 0.00 0.00 6.13
835 908 1.165270 CCGTGGGATTTCCTTCACAC 58.835 55.000 6.75 0.00 44.85 3.82
851 924 1.037030 ACACCACAGCCAACCAACAG 61.037 55.000 0.00 0.00 0.00 3.16
855 928 1.000060 CCACAGCCAACCAACAGATTG 60.000 52.381 0.00 0.00 35.40 2.67
856 929 1.682854 CACAGCCAACCAACAGATTGT 59.317 47.619 0.00 0.00 33.60 2.71
857 930 2.884012 CACAGCCAACCAACAGATTGTA 59.116 45.455 0.00 0.00 33.60 2.41
859 932 3.317993 ACAGCCAACCAACAGATTGTAAC 59.682 43.478 0.00 0.00 33.60 2.50
860 933 3.569701 CAGCCAACCAACAGATTGTAACT 59.430 43.478 0.00 0.00 33.60 2.24
861 934 3.821033 AGCCAACCAACAGATTGTAACTC 59.179 43.478 0.00 0.00 33.60 3.01
862 935 3.364964 GCCAACCAACAGATTGTAACTCG 60.365 47.826 0.00 0.00 33.60 4.18
863 936 3.364964 CCAACCAACAGATTGTAACTCGC 60.365 47.826 0.00 0.00 33.60 5.03
864 937 3.402628 ACCAACAGATTGTAACTCGCT 57.597 42.857 0.00 0.00 33.60 4.93
865 938 3.326747 ACCAACAGATTGTAACTCGCTC 58.673 45.455 0.00 0.00 33.60 5.03
884 957 0.885879 CCGTAAAACAAAGGGGAGGC 59.114 55.000 0.00 0.00 0.00 4.70
958 1048 2.647875 CAGGATCGCCGCCTCTAG 59.352 66.667 0.00 0.00 39.96 2.43
959 1049 3.299190 AGGATCGCCGCCTCTAGC 61.299 66.667 0.00 0.00 39.96 3.42
960 1050 4.365505 GGATCGCCGCCTCTAGCC 62.366 72.222 0.00 0.00 38.78 3.93
1154 1244 4.760047 CGGCGGGGACAAGGACAG 62.760 72.222 0.00 0.00 0.00 3.51
1483 1574 1.201825 GCGCACGAACTGAACTGAC 59.798 57.895 0.30 0.00 0.00 3.51
1485 1576 1.853319 GCACGAACTGAACTGACCG 59.147 57.895 0.00 0.00 0.00 4.79
1696 1787 2.805353 CGCTGGGACAAGTCGTCG 60.805 66.667 0.00 0.00 46.42 5.12
1810 1901 1.185618 TCAGGTCCCAGTTCGAGGTG 61.186 60.000 0.00 0.00 0.00 4.00
1948 2039 4.101448 AAGAAGCGCGGCCTCCAT 62.101 61.111 8.83 0.00 0.00 3.41
1952 2043 4.537433 AGCGCGGCCTCCATCTTC 62.537 66.667 8.83 0.00 0.00 2.87
1954 2045 4.161295 CGCGGCCTCCATCTTCCA 62.161 66.667 0.00 0.00 0.00 3.53
2070 2161 2.807045 CAGTGAGCTCGCCGACAC 60.807 66.667 23.37 8.26 0.00 3.67
2132 2223 3.864789 AGGATCGGCCATTAGTTGATT 57.135 42.857 2.24 0.00 40.02 2.57
2133 2224 4.974645 AGGATCGGCCATTAGTTGATTA 57.025 40.909 2.24 0.00 40.02 1.75
2213 2309 9.353999 GATGTTTTTGCTATATTTTCGTCCTTT 57.646 29.630 0.00 0.00 0.00 3.11
2289 2385 1.472480 GTAAGTACGTACCGGGAAGCA 59.528 52.381 21.80 0.00 0.00 3.91
2290 2386 0.968405 AAGTACGTACCGGGAAGCAA 59.032 50.000 21.80 0.00 0.00 3.91
2291 2387 0.529378 AGTACGTACCGGGAAGCAAG 59.471 55.000 21.80 0.00 0.00 4.01
2292 2388 0.459063 GTACGTACCGGGAAGCAAGG 60.459 60.000 15.00 0.00 0.00 3.61
2374 2474 3.828657 TGCTCTTACTCAGCAGCAG 57.171 52.632 0.00 0.00 42.09 4.24
2390 2490 3.822996 CAGCAGAGCAAATTTCTCACAG 58.177 45.455 15.46 8.90 33.15 3.66
2421 2524 3.634397 TCCAGTGGAGAAATGTGATCC 57.366 47.619 8.12 0.00 0.00 3.36
2422 2525 3.184628 TCCAGTGGAGAAATGTGATCCT 58.815 45.455 8.12 0.00 34.04 3.24
2423 2526 3.588842 TCCAGTGGAGAAATGTGATCCTT 59.411 43.478 8.12 0.00 34.04 3.36
2425 2528 4.324099 CCAGTGGAGAAATGTGATCCTTCT 60.324 45.833 1.68 0.00 34.04 2.85
2440 2543 2.371910 CTTCTGGAAGGGAACGAGAC 57.628 55.000 2.66 0.00 34.87 3.36
2442 2545 0.178944 TCTGGAAGGGAACGAGACCA 60.179 55.000 0.00 0.00 0.00 4.02
2443 2546 0.905357 CTGGAAGGGAACGAGACCAT 59.095 55.000 0.00 0.00 0.00 3.55
2463 2580 5.482175 ACCATAAAAATGGGGTGAAATCGAA 59.518 36.000 9.13 0.00 45.84 3.71
2464 2581 5.810074 CCATAAAAATGGGGTGAAATCGAAC 59.190 40.000 0.00 0.00 38.04 3.95
2465 2582 4.946478 AAAAATGGGGTGAAATCGAACA 57.054 36.364 0.00 0.00 0.00 3.18
2477 2598 2.649331 ATCGAACAGTAACCGACCTG 57.351 50.000 0.00 0.00 35.02 4.00
2483 2604 1.148310 CAGTAACCGACCTGTTGCAG 58.852 55.000 0.00 0.00 33.83 4.41
2487 2608 3.451178 AGTAACCGACCTGTTGCAGATAT 59.549 43.478 0.00 0.00 33.83 1.63
2504 2625 2.042686 TATGGAATGCACTGAGTGGC 57.957 50.000 15.24 7.36 33.64 5.01
2529 2650 7.011773 CGAACTGAACTGACATGAGTAATTTG 58.988 38.462 0.00 0.00 0.00 2.32
2573 2694 0.533308 GTATTATTGCCCACGCCGGA 60.533 55.000 5.05 0.00 36.56 5.14
2574 2695 0.250124 TATTATTGCCCACGCCGGAG 60.250 55.000 5.05 3.72 36.56 4.63
2613 2743 3.909086 AACTCGCTGGAGCTTGCCC 62.909 63.158 0.00 0.00 44.48 5.36
2648 2778 0.464452 GATACCCGGGAACTGACTGG 59.536 60.000 32.02 0.00 36.31 4.00
2694 2843 4.767255 CCTGGGCACGGAGACAGC 62.767 72.222 0.00 0.00 0.00 4.40
2705 2854 2.292016 ACGGAGACAGCGATATTCTCTG 59.708 50.000 15.39 15.39 44.96 3.35
2708 2857 3.305950 GGAGACAGCGATATTCTCTGCAT 60.306 47.826 10.36 0.00 32.76 3.96
2709 2858 3.911868 AGACAGCGATATTCTCTGCATC 58.088 45.455 0.00 0.00 32.76 3.91
2711 2860 3.651206 ACAGCGATATTCTCTGCATCAG 58.349 45.455 0.00 0.00 32.76 2.90
2712 2861 3.069300 ACAGCGATATTCTCTGCATCAGT 59.931 43.478 0.00 0.00 32.76 3.41
2717 2866 6.763135 AGCGATATTCTCTGCATCAGTAAAAA 59.237 34.615 0.00 0.00 32.61 1.94
2767 2916 1.901464 GGACTGGAAGCGGCCAAAA 60.901 57.895 2.24 0.00 37.52 2.44
2797 2946 2.124122 CACGCCGATGACGAATTCATA 58.876 47.619 6.22 0.00 45.67 2.15
2799 2948 2.987149 ACGCCGATGACGAATTCATATC 59.013 45.455 6.22 5.10 45.67 1.63
2822 2988 4.036852 CGGGATGAAGGGATTAAAAGAAGC 59.963 45.833 0.00 0.00 0.00 3.86
2823 2989 4.036852 GGGATGAAGGGATTAAAAGAAGCG 59.963 45.833 0.00 0.00 0.00 4.68
2838 3004 7.829378 AAAAGAAGCGTCTCGAATAGTTTAT 57.171 32.000 1.62 0.00 30.70 1.40
2844 3010 6.087522 AGCGTCTCGAATAGTTTATGATAGC 58.912 40.000 0.00 0.00 0.00 2.97
2887 3062 2.125753 GCTCTGCTCAGGTGACGG 60.126 66.667 0.00 0.00 0.00 4.79
2889 3064 1.214062 CTCTGCTCAGGTGACGGAC 59.786 63.158 0.00 0.00 0.00 4.79
2890 3065 2.126307 CTGCTCAGGTGACGGACG 60.126 66.667 0.00 0.00 0.00 4.79
2891 3066 4.357947 TGCTCAGGTGACGGACGC 62.358 66.667 0.00 0.00 32.50 5.19
2916 3091 0.102481 CAAGTGGATAGGACCGTCCG 59.898 60.000 12.04 0.00 42.75 4.79
2918 3093 0.750911 AGTGGATAGGACCGTCCGTC 60.751 60.000 12.04 13.40 42.75 4.79
2925 3100 3.126528 GACCGTCCGTCCATAGGG 58.873 66.667 0.00 0.00 35.23 3.53
2926 3101 1.454479 GACCGTCCGTCCATAGGGA 60.454 63.158 0.00 0.00 42.29 4.20
2927 3102 1.453762 GACCGTCCGTCCATAGGGAG 61.454 65.000 0.00 0.00 46.12 4.30
2934 3109 3.232279 GTCCATAGGGAGGAGCAGT 57.768 57.895 0.00 0.00 46.12 4.40
2935 3110 2.383442 GTCCATAGGGAGGAGCAGTA 57.617 55.000 0.00 0.00 46.12 2.74
2936 3111 2.896039 GTCCATAGGGAGGAGCAGTAT 58.104 52.381 0.00 0.00 46.12 2.12
2937 3112 3.243724 GTCCATAGGGAGGAGCAGTATT 58.756 50.000 0.00 0.00 46.12 1.89
2938 3113 3.259625 GTCCATAGGGAGGAGCAGTATTC 59.740 52.174 0.00 0.00 46.12 1.75
2949 3124 7.014808 GGGAGGAGCAGTATTCTACATATATCC 59.985 44.444 0.00 0.00 0.00 2.59
2979 3154 1.700029 CGCGCTCGTTCACGTATTT 59.300 52.632 5.56 0.00 40.80 1.40
2989 3164 6.023564 GCTCGTTCACGTATTTGTTTAATTCG 60.024 38.462 0.00 0.00 41.21 3.34
3003 3178 2.559998 AATTCGGCGCCATAAACAAG 57.440 45.000 28.98 7.38 0.00 3.16
3013 3188 3.239254 GCCATAAACAAGTGCCGTAAAC 58.761 45.455 0.00 0.00 0.00 2.01
3025 3200 0.730840 CCGTAAACCCGAATCTTGGC 59.269 55.000 0.00 0.00 0.00 4.52
3036 3211 5.178797 CCCGAATCTTGGCGATAAGATAAT 58.821 41.667 12.94 1.87 44.43 1.28
3038 3213 5.292101 CCGAATCTTGGCGATAAGATAATCC 59.708 44.000 12.94 5.12 44.43 3.01
3088 3263 0.459934 AGATCTGTTCAGCTCAGCGC 60.460 55.000 0.00 0.00 39.57 5.92
3104 3279 3.984749 GCTCGCCTCCGGATCCTC 61.985 72.222 3.57 0.00 34.56 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.827089 TGCACATGACTTTGTGGGGG 60.827 55.000 0.00 0.00 45.69 5.40
9 10 1.000060 CTTGCACATGACTTTGTGGGG 60.000 52.381 0.00 0.00 45.69 4.96
10 11 1.682854 ACTTGCACATGACTTTGTGGG 59.317 47.619 0.00 0.00 45.69 4.61
11 12 2.734670 CACTTGCACATGACTTTGTGG 58.265 47.619 0.00 0.00 45.69 4.17
13 14 2.497107 GCACTTGCACATGACTTTGT 57.503 45.000 0.00 0.00 41.59 2.83
25 26 2.171940 CGAAGCGACTGCACTTGC 59.828 61.111 0.00 0.00 46.23 4.01
26 27 2.856032 CCGAAGCGACTGCACTTG 59.144 61.111 0.00 0.00 46.23 3.16
27 28 3.044305 GCCGAAGCGACTGCACTT 61.044 61.111 0.00 0.00 46.23 3.16
28 29 4.299547 TGCCGAAGCGACTGCACT 62.300 61.111 0.00 0.00 46.23 4.40
29 30 4.077188 GTGCCGAAGCGACTGCAC 62.077 66.667 13.95 13.95 46.09 4.57
32 33 2.607668 TATCCGTGCCGAAGCGACTG 62.608 60.000 0.00 0.00 44.31 3.51
33 34 1.940883 TTATCCGTGCCGAAGCGACT 61.941 55.000 0.00 0.00 44.31 4.18
34 35 1.480219 CTTATCCGTGCCGAAGCGAC 61.480 60.000 0.00 0.00 44.31 5.19
35 36 1.226859 CTTATCCGTGCCGAAGCGA 60.227 57.895 0.00 0.00 44.31 4.93
36 37 0.597637 ATCTTATCCGTGCCGAAGCG 60.598 55.000 0.00 0.00 44.31 4.68
37 38 2.030185 TCTATCTTATCCGTGCCGAAGC 60.030 50.000 0.00 0.00 40.48 3.86
38 39 3.917329 TCTATCTTATCCGTGCCGAAG 57.083 47.619 0.00 0.00 0.00 3.79
39 40 4.398358 CCTATCTATCTTATCCGTGCCGAA 59.602 45.833 0.00 0.00 0.00 4.30
40 41 3.945921 CCTATCTATCTTATCCGTGCCGA 59.054 47.826 0.00 0.00 0.00 5.54
41 42 3.066900 CCCTATCTATCTTATCCGTGCCG 59.933 52.174 0.00 0.00 0.00 5.69
42 43 3.385111 CCCCTATCTATCTTATCCGTGCC 59.615 52.174 0.00 0.00 0.00 5.01
43 44 3.181474 GCCCCTATCTATCTTATCCGTGC 60.181 52.174 0.00 0.00 0.00 5.34
44 45 4.023980 TGCCCCTATCTATCTTATCCGTG 58.976 47.826 0.00 0.00 0.00 4.94
45 46 4.332683 TGCCCCTATCTATCTTATCCGT 57.667 45.455 0.00 0.00 0.00 4.69
46 47 4.141914 GGTTGCCCCTATCTATCTTATCCG 60.142 50.000 0.00 0.00 0.00 4.18
47 48 4.141914 CGGTTGCCCCTATCTATCTTATCC 60.142 50.000 0.00 0.00 0.00 2.59
48 49 4.141914 CCGGTTGCCCCTATCTATCTTATC 60.142 50.000 0.00 0.00 0.00 1.75
49 50 3.775316 CCGGTTGCCCCTATCTATCTTAT 59.225 47.826 0.00 0.00 0.00 1.73
50 51 3.170717 CCGGTTGCCCCTATCTATCTTA 58.829 50.000 0.00 0.00 0.00 2.10
51 52 1.978580 CCGGTTGCCCCTATCTATCTT 59.021 52.381 0.00 0.00 0.00 2.40
52 53 1.149288 TCCGGTTGCCCCTATCTATCT 59.851 52.381 0.00 0.00 0.00 1.98
53 54 1.640917 TCCGGTTGCCCCTATCTATC 58.359 55.000 0.00 0.00 0.00 2.08
54 55 2.112279 TTCCGGTTGCCCCTATCTAT 57.888 50.000 0.00 0.00 0.00 1.98
55 56 1.975680 GATTCCGGTTGCCCCTATCTA 59.024 52.381 0.00 0.00 0.00 1.98
56 57 0.765510 GATTCCGGTTGCCCCTATCT 59.234 55.000 0.00 0.00 0.00 1.98
57 58 0.472471 TGATTCCGGTTGCCCCTATC 59.528 55.000 0.00 0.00 0.00 2.08
58 59 0.474184 CTGATTCCGGTTGCCCCTAT 59.526 55.000 0.00 0.00 0.00 2.57
59 60 1.632018 CCTGATTCCGGTTGCCCCTA 61.632 60.000 0.00 0.00 0.00 3.53
60 61 2.677228 CTGATTCCGGTTGCCCCT 59.323 61.111 0.00 0.00 0.00 4.79
61 62 2.440247 CCTGATTCCGGTTGCCCC 60.440 66.667 0.00 0.00 0.00 5.80
62 63 1.452108 CTCCTGATTCCGGTTGCCC 60.452 63.158 0.00 0.00 0.00 5.36
63 64 1.452108 CCTCCTGATTCCGGTTGCC 60.452 63.158 0.00 0.00 0.00 4.52
64 65 2.115291 GCCTCCTGATTCCGGTTGC 61.115 63.158 0.00 0.00 0.00 4.17
65 66 1.452108 GGCCTCCTGATTCCGGTTG 60.452 63.158 0.00 0.00 0.00 3.77
66 67 2.998949 GGCCTCCTGATTCCGGTT 59.001 61.111 0.00 0.00 0.00 4.44
67 68 3.470888 CGGCCTCCTGATTCCGGT 61.471 66.667 0.00 0.00 38.35 5.28
69 70 4.918201 GCCGGCCTCCTGATTCCG 62.918 72.222 18.11 0.00 41.41 4.30
83 84 4.688419 CGCACACAAGCCAAGCCG 62.688 66.667 0.00 0.00 0.00 5.52
207 238 4.547905 CCATCGGTCGGTCGGTCG 62.548 72.222 0.00 0.00 0.00 4.79
250 281 2.972505 ACGAGTGGCGGTGCAAAG 60.973 61.111 0.00 0.00 46.49 2.77
272 303 1.275657 GTTCCATCAATACGCCGCG 59.724 57.895 12.14 12.14 0.00 6.46
299 363 7.377397 TCGGTTCGTTCAATTCAAATTAACAAG 59.623 33.333 0.00 0.00 0.00 3.16
309 373 2.482336 CCATGTCGGTTCGTTCAATTCA 59.518 45.455 0.00 0.00 0.00 2.57
310 374 2.727916 GCCATGTCGGTTCGTTCAATTC 60.728 50.000 0.00 0.00 36.97 2.17
311 375 1.199097 GCCATGTCGGTTCGTTCAATT 59.801 47.619 0.00 0.00 36.97 2.32
312 376 0.802494 GCCATGTCGGTTCGTTCAAT 59.198 50.000 0.00 0.00 36.97 2.57
313 377 1.231958 GGCCATGTCGGTTCGTTCAA 61.232 55.000 0.00 0.00 36.97 2.69
429 493 4.219288 GGCATTTGCTCTCCTAATTATGGG 59.781 45.833 2.12 0.00 41.70 4.00
442 506 1.745087 TGAATTCCGAGGCATTTGCTC 59.255 47.619 2.27 0.00 41.70 4.26
443 507 1.747355 CTGAATTCCGAGGCATTTGCT 59.253 47.619 2.27 0.00 41.70 3.91
444 508 1.474077 ACTGAATTCCGAGGCATTTGC 59.526 47.619 2.27 0.00 41.14 3.68
468 532 2.355363 CCACCGTCGTTTCGCTCA 60.355 61.111 0.00 0.00 0.00 4.26
472 536 0.248134 TTTTTGCCACCGTCGTTTCG 60.248 50.000 0.00 0.00 0.00 3.46
478 542 1.272212 ACATCCATTTTTGCCACCGTC 59.728 47.619 0.00 0.00 0.00 4.79
495 559 3.490761 CGTTGTTTCTGGCTGGAAAACAT 60.491 43.478 10.64 0.00 37.02 2.71
496 560 2.159310 CGTTGTTTCTGGCTGGAAAACA 60.159 45.455 7.12 7.12 37.02 2.83
497 561 2.459934 CGTTGTTTCTGGCTGGAAAAC 58.540 47.619 7.53 5.19 37.02 2.43
510 577 1.600916 GGAGGAGCCTGCGTTGTTT 60.601 57.895 0.00 0.00 0.00 2.83
512 579 4.021925 GGGAGGAGCCTGCGTTGT 62.022 66.667 1.81 0.00 35.11 3.32
555 628 1.165907 TTTTGCAGGTGACAGGAGCG 61.166 55.000 0.00 0.00 0.00 5.03
592 665 4.073200 GCAAATGCGGCCAGGCTT 62.073 61.111 12.43 0.00 0.00 4.35
595 668 4.440127 GGTGCAAATGCGGCCAGG 62.440 66.667 2.24 0.00 45.83 4.45
602 675 2.580326 CATCGCGGGTGCAAATGC 60.580 61.111 6.13 0.00 42.97 3.56
614 687 0.648958 GTAGTTAACGGGTGCATCGC 59.351 55.000 11.46 3.35 0.00 4.58
635 708 2.266055 GCCTACACTCGCTTGGCT 59.734 61.111 0.00 0.00 40.36 4.75
656 729 0.672401 GGGTCGAGGTTGCGAAATGA 60.672 55.000 0.00 0.00 42.55 2.57
663 736 2.358737 CAGGTGGGTCGAGGTTGC 60.359 66.667 0.00 0.00 0.00 4.17
667 740 1.599606 CTCTGACAGGTGGGTCGAGG 61.600 65.000 1.81 0.00 40.72 4.63
768 841 0.754217 GGACCGGGATTTAAAGGCCC 60.754 60.000 6.32 15.66 38.53 5.80
835 908 1.000060 CAATCTGTTGGTTGGCTGTGG 60.000 52.381 0.00 0.00 0.00 4.17
851 924 4.386652 TGTTTTACGGAGCGAGTTACAATC 59.613 41.667 0.00 0.00 0.00 2.67
855 928 4.376717 CCTTTGTTTTACGGAGCGAGTTAC 60.377 45.833 0.00 0.00 0.00 2.50
856 929 3.742369 CCTTTGTTTTACGGAGCGAGTTA 59.258 43.478 0.00 0.00 0.00 2.24
857 930 2.546789 CCTTTGTTTTACGGAGCGAGTT 59.453 45.455 0.00 0.00 0.00 3.01
859 932 1.463444 CCCTTTGTTTTACGGAGCGAG 59.537 52.381 0.00 0.00 0.00 5.03
860 933 1.515081 CCCTTTGTTTTACGGAGCGA 58.485 50.000 0.00 0.00 0.00 4.93
861 934 0.519961 CCCCTTTGTTTTACGGAGCG 59.480 55.000 0.00 0.00 0.00 5.03
862 935 1.810755 CTCCCCTTTGTTTTACGGAGC 59.189 52.381 0.00 0.00 31.19 4.70
863 936 2.433436 CCTCCCCTTTGTTTTACGGAG 58.567 52.381 0.00 0.00 37.28 4.63
864 937 1.546099 GCCTCCCCTTTGTTTTACGGA 60.546 52.381 0.00 0.00 0.00 4.69
865 938 0.885879 GCCTCCCCTTTGTTTTACGG 59.114 55.000 0.00 0.00 0.00 4.02
884 957 1.533129 GCGCGGCTAGGGTTTATTTTG 60.533 52.381 8.83 0.00 34.93 2.44
1012 1102 4.630785 CGGATCGATCTGCGCCGT 62.631 66.667 23.96 0.00 39.68 5.68
1068 1158 2.573869 TCGAAGAGGCGCTTGAGG 59.426 61.111 8.61 0.00 36.83 3.86
1146 1236 2.093235 GTCATCCTTCTCCCTGTCCTTG 60.093 54.545 0.00 0.00 0.00 3.61
1154 1244 1.134250 GCTCCAAGTCATCCTTCTCCC 60.134 57.143 0.00 0.00 0.00 4.30
1381 1471 2.877691 AAAAATCAGCGCTCGGCC 59.122 55.556 7.13 0.00 45.17 6.13
1404 1495 2.286294 GCGATGAAGCAAAGACGATCAT 59.714 45.455 0.00 0.00 37.05 2.45
1413 1504 2.671276 TGCCGGCGATGAAGCAAA 60.671 55.556 23.90 0.00 39.27 3.68
1483 1574 2.271800 CCGAGAAATGGAAGAGAACGG 58.728 52.381 0.00 0.00 0.00 4.44
1485 1576 3.433615 CACACCGAGAAATGGAAGAGAAC 59.566 47.826 0.00 0.00 0.00 3.01
1488 1579 1.734465 GCACACCGAGAAATGGAAGAG 59.266 52.381 0.00 0.00 0.00 2.85
2039 2130 4.962836 ACTGGCACTGGCACTGGC 62.963 66.667 12.65 12.65 43.71 4.85
2040 2131 2.981909 CACTGGCACTGGCACTGG 60.982 66.667 0.07 0.00 43.71 4.00
2041 2132 1.964891 CTCACTGGCACTGGCACTG 60.965 63.158 0.07 3.67 43.71 3.66
2042 2133 2.429058 CTCACTGGCACTGGCACT 59.571 61.111 0.07 0.00 43.71 4.40
2043 2134 3.360340 GCTCACTGGCACTGGCAC 61.360 66.667 0.07 0.00 43.71 5.01
2142 2234 2.580815 GCTGCAAATTCCCCAGGC 59.419 61.111 0.00 0.00 0.00 4.85
2213 2309 6.833416 TCAAAAGGGTCAAAATGAGAGAGAAA 59.167 34.615 0.00 0.00 0.00 2.52
2341 2438 9.502091 TGAGTAAGAGCAACAATTTAACATAGT 57.498 29.630 0.00 0.00 0.00 2.12
2342 2439 9.979270 CTGAGTAAGAGCAACAATTTAACATAG 57.021 33.333 0.00 0.00 0.00 2.23
2360 2458 2.090400 TTGCTCTGCTGCTGAGTAAG 57.910 50.000 27.04 11.21 31.80 2.34
2374 2474 5.557891 ACATAGCTGTGAGAAATTTGCTC 57.442 39.130 18.24 3.21 33.22 4.26
2390 2490 0.181114 TCCACTGGATGCCACATAGC 59.819 55.000 0.00 0.00 0.00 2.97
2401 2504 3.184628 AGGATCACATTTCTCCACTGGA 58.815 45.455 0.00 0.00 0.00 3.86
2421 2524 1.066787 GGTCTCGTTCCCTTCCAGAAG 60.067 57.143 0.15 0.15 38.14 2.85
2422 2525 0.974383 GGTCTCGTTCCCTTCCAGAA 59.026 55.000 0.00 0.00 0.00 3.02
2423 2526 0.178944 TGGTCTCGTTCCCTTCCAGA 60.179 55.000 0.00 0.00 0.00 3.86
2425 2528 2.241281 TATGGTCTCGTTCCCTTCCA 57.759 50.000 0.00 0.00 0.00 3.53
2431 2534 3.380320 CCCCATTTTTATGGTCTCGTTCC 59.620 47.826 3.69 0.00 40.06 3.62
2432 2535 4.014406 ACCCCATTTTTATGGTCTCGTTC 58.986 43.478 3.69 0.00 40.06 3.95
2433 2536 3.761752 CACCCCATTTTTATGGTCTCGTT 59.238 43.478 3.69 0.00 40.06 3.85
2434 2537 3.009695 TCACCCCATTTTTATGGTCTCGT 59.990 43.478 3.69 0.00 40.06 4.18
2435 2538 3.616219 TCACCCCATTTTTATGGTCTCG 58.384 45.455 3.69 0.00 40.06 4.04
2436 2539 5.993748 TTTCACCCCATTTTTATGGTCTC 57.006 39.130 3.69 0.00 40.06 3.36
2437 2540 5.127031 CGATTTCACCCCATTTTTATGGTCT 59.873 40.000 3.69 0.00 40.06 3.85
2438 2541 5.126384 TCGATTTCACCCCATTTTTATGGTC 59.874 40.000 3.69 0.00 40.06 4.02
2439 2542 5.020132 TCGATTTCACCCCATTTTTATGGT 58.980 37.500 3.69 0.00 40.06 3.55
2440 2543 5.590530 TCGATTTCACCCCATTTTTATGG 57.409 39.130 0.00 0.00 41.34 2.74
2442 2545 6.210584 ACTGTTCGATTTCACCCCATTTTTAT 59.789 34.615 0.00 0.00 0.00 1.40
2443 2546 5.536916 ACTGTTCGATTTCACCCCATTTTTA 59.463 36.000 0.00 0.00 0.00 1.52
2464 2581 1.148310 CTGCAACAGGTCGGTTACTG 58.852 55.000 0.00 0.00 40.48 2.74
2465 2582 1.045407 TCTGCAACAGGTCGGTTACT 58.955 50.000 0.00 0.00 31.51 2.24
2477 2598 3.628942 TCAGTGCATTCCATATCTGCAAC 59.371 43.478 0.00 0.00 46.51 4.17
2483 2604 2.551459 GCCACTCAGTGCATTCCATATC 59.449 50.000 0.00 0.00 31.34 1.63
2487 2608 1.672030 CGCCACTCAGTGCATTCCA 60.672 57.895 0.00 0.00 31.34 3.53
2504 2625 6.712241 AATTACTCATGTCAGTTCAGTTCG 57.288 37.500 0.00 0.00 0.00 3.95
2529 2650 0.811281 CCGATCAAGAAAGCAACCCC 59.189 55.000 0.00 0.00 0.00 4.95
2573 2694 4.552365 CGCACGCCATCCATCCCT 62.552 66.667 0.00 0.00 0.00 4.20
2616 2746 1.369625 GGGTATCTTGTTCCGCACAG 58.630 55.000 0.00 0.00 36.48 3.66
2648 2778 3.521796 GGGAATGGAAGGCGCTGC 61.522 66.667 7.64 0.00 0.00 5.25
2717 2866 6.212955 CGGTCAGTTCACAAAATGGTTATTT 58.787 36.000 0.00 0.00 38.11 1.40
2718 2867 5.278758 CCGGTCAGTTCACAAAATGGTTATT 60.279 40.000 0.00 0.00 31.48 1.40
2719 2868 4.217550 CCGGTCAGTTCACAAAATGGTTAT 59.782 41.667 0.00 0.00 31.48 1.89
2720 2869 3.566322 CCGGTCAGTTCACAAAATGGTTA 59.434 43.478 0.00 0.00 31.48 2.85
2721 2870 2.360801 CCGGTCAGTTCACAAAATGGTT 59.639 45.455 0.00 0.00 31.48 3.67
2722 2871 1.953686 CCGGTCAGTTCACAAAATGGT 59.046 47.619 0.00 0.00 31.48 3.55
2723 2872 1.269448 CCCGGTCAGTTCACAAAATGG 59.731 52.381 0.00 0.00 31.48 3.16
2724 2873 1.269448 CCCCGGTCAGTTCACAAAATG 59.731 52.381 0.00 0.00 0.00 2.32
2780 2929 2.345641 CCGATATGAATTCGTCATCGGC 59.654 50.000 27.73 6.71 46.52 5.54
2797 2946 5.646692 TCTTTTAATCCCTTCATCCCGAT 57.353 39.130 0.00 0.00 0.00 4.18
2799 2948 4.036852 GCTTCTTTTAATCCCTTCATCCCG 59.963 45.833 0.00 0.00 0.00 5.14
2822 2988 6.304882 TCGCTATCATAAACTATTCGAGACG 58.695 40.000 0.00 0.00 0.00 4.18
2823 2989 6.743627 CCTCGCTATCATAAACTATTCGAGAC 59.256 42.308 9.05 0.00 42.14 3.36
2838 3004 1.108776 GTACACCCACCTCGCTATCA 58.891 55.000 0.00 0.00 0.00 2.15
2844 3010 1.374252 GCACAGTACACCCACCTCG 60.374 63.158 0.00 0.00 0.00 4.63
2887 3062 2.186076 CTATCCACTTGTTCTCGCGTC 58.814 52.381 5.77 0.00 0.00 5.19
2889 3064 1.134367 TCCTATCCACTTGTTCTCGCG 59.866 52.381 0.00 0.00 0.00 5.87
2890 3065 2.541556 GTCCTATCCACTTGTTCTCGC 58.458 52.381 0.00 0.00 0.00 5.03
2891 3066 2.479730 CGGTCCTATCCACTTGTTCTCG 60.480 54.545 0.00 0.00 0.00 4.04
2892 3067 2.496470 ACGGTCCTATCCACTTGTTCTC 59.504 50.000 0.00 0.00 0.00 2.87
2916 3091 2.383442 TACTGCTCCTCCCTATGGAC 57.617 55.000 0.00 0.00 35.03 4.02
2918 3093 3.515562 AGAATACTGCTCCTCCCTATGG 58.484 50.000 0.00 0.00 0.00 2.74
2919 3094 5.080337 TGTAGAATACTGCTCCTCCCTATG 58.920 45.833 0.00 0.00 43.54 2.23
2920 3095 5.340891 TGTAGAATACTGCTCCTCCCTAT 57.659 43.478 0.00 0.00 43.54 2.57
2921 3096 4.808767 TGTAGAATACTGCTCCTCCCTA 57.191 45.455 0.00 0.00 43.54 3.53
2923 3098 7.014808 GGATATATGTAGAATACTGCTCCTCCC 59.985 44.444 0.00 0.00 43.54 4.30
2925 3100 7.644490 CGGATATATGTAGAATACTGCTCCTC 58.356 42.308 0.00 0.00 43.54 3.71
2926 3101 6.039941 GCGGATATATGTAGAATACTGCTCCT 59.960 42.308 0.00 0.00 43.54 3.69
2927 3102 6.183360 TGCGGATATATGTAGAATACTGCTCC 60.183 42.308 0.00 0.00 43.54 4.70
2929 3104 6.775594 TGCGGATATATGTAGAATACTGCT 57.224 37.500 0.00 0.00 43.54 4.24
2930 3105 6.360947 CGATGCGGATATATGTAGAATACTGC 59.639 42.308 0.00 0.00 43.54 4.40
2931 3106 7.844070 CGATGCGGATATATGTAGAATACTG 57.156 40.000 0.00 0.00 43.54 2.74
2965 3140 6.460452 CCGAATTAAACAAATACGTGAACGAG 59.540 38.462 10.26 0.00 43.02 4.18
2969 3144 5.080731 CGCCGAATTAAACAAATACGTGAA 58.919 37.500 0.00 0.00 0.00 3.18
2979 3154 3.190744 TGTTTATGGCGCCGAATTAAACA 59.809 39.130 31.38 31.38 34.75 2.83
2989 3164 1.153842 GGCACTTGTTTATGGCGCC 60.154 57.895 22.73 22.73 0.00 6.53
3003 3178 1.129811 CAAGATTCGGGTTTACGGCAC 59.870 52.381 0.00 0.00 0.00 5.01
3013 3188 2.526304 TCTTATCGCCAAGATTCGGG 57.474 50.000 0.00 0.00 40.66 5.14
3057 3232 0.747255 ACAGATCTACGCTTCCGCAT 59.253 50.000 0.00 0.00 38.22 4.73
3060 3235 2.455032 CTGAACAGATCTACGCTTCCG 58.545 52.381 0.00 0.00 41.14 4.30
3066 3241 2.458951 GCTGAGCTGAACAGATCTACG 58.541 52.381 18.41 9.72 43.74 3.51


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

AutoCloner maintained by Alex Coulton.