Multiple sequence alignment - TraesCS4A01G067100

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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 TraesCS4A01G067100 chr4A 100.000 3176 0 0 1 3176 64568912 64572087 0.000000e+00 5866.0
1 TraesCS4A01G067100 chr4B 93.769 2295 92 24 1 2279 506324040 506326299 0.000000e+00 3398.0
2 TraesCS4A01G067100 chr4B 84.477 947 78 33 2285 3173 506326509 506327444 0.000000e+00 870.0
3 TraesCS4A01G067100 chr4D 92.194 2434 109 33 1 2403 409479579 409477196 0.000000e+00 3367.0
4 TraesCS4A01G067100 chr4D 88.994 318 22 8 2864 3173 409445341 409445029 6.430000e-102 381.0
5 TraesCS4A01G067100 chr4D 85.602 382 34 8 2502 2864 409462671 409462292 6.430000e-102 381.0
6 TraesCS4A01G067100 chr3D 82.955 88 11 4 1257 1342 517809464 517809549 3.400000e-10 76.8


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 TraesCS4A01G067100 chr4A 64568912 64572087 3175 False 5866 5866 100.000 1 3176 1 chr4A.!!$F1 3175
1 TraesCS4A01G067100 chr4B 506324040 506327444 3404 False 2134 3398 89.123 1 3173 2 chr4B.!!$F1 3172
2 TraesCS4A01G067100 chr4D 409477196 409479579 2383 True 3367 3367 92.194 1 2403 1 chr4D.!!$R3 2402

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
971 986 0.108615 CCGAAGTGCCAGAGTAGGTG 60.109 60.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2827 3109 0.731514 CTTTGGCGATGCAACAGCAG 60.732 55.0 12.33 0.0 42.36 4.24 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
40 41 1.083209 CGTCTTCGTCGTCGTCACA 60.083 57.895 1.33 0.00 38.33 3.58
42 43 1.043224 GTCTTCGTCGTCGTCACAAG 58.957 55.000 1.33 0.00 38.33 3.16
248 249 2.328099 GGCCACTTCACCTTCGCAG 61.328 63.158 0.00 0.00 0.00 5.18
273 274 1.131771 CAGCAGGTACGCATACATCG 58.868 55.000 0.00 0.00 32.40 3.84
594 600 2.275748 TCAGGAGGAGATCGCCGT 59.724 61.111 10.07 0.00 40.51 5.68
664 670 7.595130 CGCAGCAACTCTATAAATCATACTACA 59.405 37.037 0.00 0.00 0.00 2.74
685 691 6.743575 ACATGTACTACTCATCTTTTTGGC 57.256 37.500 0.00 0.00 0.00 4.52
686 692 5.351465 ACATGTACTACTCATCTTTTTGGCG 59.649 40.000 0.00 0.00 0.00 5.69
687 693 5.142061 TGTACTACTCATCTTTTTGGCGA 57.858 39.130 0.00 0.00 0.00 5.54
688 694 4.927425 TGTACTACTCATCTTTTTGGCGAC 59.073 41.667 0.00 0.00 0.00 5.19
689 695 4.273148 ACTACTCATCTTTTTGGCGACT 57.727 40.909 0.00 0.00 0.00 4.18
792 806 5.632959 CAGTTCAGTTTTTACGTGTGGAAA 58.367 37.500 0.00 0.00 0.00 3.13
797 811 4.973663 CAGTTTTTACGTGTGGAAATGGAC 59.026 41.667 0.00 0.00 0.00 4.02
854 868 8.840833 TTGTGCAAATTGTCTACTGAGTAATA 57.159 30.769 0.00 0.00 0.00 0.98
855 869 8.251750 TGTGCAAATTGTCTACTGAGTAATAC 57.748 34.615 0.00 0.00 0.00 1.89
856 870 7.875554 TGTGCAAATTGTCTACTGAGTAATACA 59.124 33.333 3.99 3.99 0.00 2.29
857 871 8.383619 GTGCAAATTGTCTACTGAGTAATACAG 58.616 37.037 7.31 0.00 40.68 2.74
938 953 3.004944 TCCCATGGACAAAAGCGTTTAAC 59.995 43.478 15.22 0.00 0.00 2.01
971 986 0.108615 CCGAAGTGCCAGAGTAGGTG 60.109 60.000 0.00 0.00 0.00 4.00
981 996 1.741770 GAGTAGGTGGTTGGCGCTG 60.742 63.158 7.64 0.00 0.00 5.18
1402 1417 3.640000 CGATGTTCCGGGCGATGC 61.640 66.667 0.00 0.00 0.00 3.91
1404 1419 2.203070 ATGTTCCGGGCGATGCTC 60.203 61.111 0.00 0.00 0.00 4.26
1699 1723 2.884685 CGCTGCAGCTCTTCTCCG 60.885 66.667 34.22 14.00 39.32 4.63
1974 1998 1.376424 CTCCCATGCAAGTGCGAGT 60.376 57.895 0.00 0.00 45.83 4.18
1977 2001 1.164411 CCCATGCAAGTGCGAGTAAA 58.836 50.000 0.00 0.00 45.83 2.01
1982 2006 1.002900 TGCAAGTGCGAGTAAAGCAAC 60.003 47.619 0.00 0.00 46.97 4.17
2043 2070 4.785453 GGAGAAGTGGCTGCCGGG 62.785 72.222 14.98 0.00 0.00 5.73
2135 2162 1.152694 AGAGGGCTGCTGCAACAAA 60.153 52.632 17.89 0.00 41.91 2.83
2146 2173 1.391485 CTGCAACAAAGATCGACGAGG 59.609 52.381 3.01 0.00 0.00 4.63
2184 2211 4.202441 GGATCCAAGTGTAGCATCATTGT 58.798 43.478 6.95 0.00 0.00 2.71
2195 2222 3.423749 AGCATCATTGTTCACATCACCA 58.576 40.909 0.00 0.00 0.00 4.17
2206 2234 2.557924 TCACATCACCATTCAACAAGGC 59.442 45.455 0.00 0.00 0.00 4.35
2218 2246 4.067972 TCAACAAGGCGAAAGTTCTACT 57.932 40.909 0.00 0.00 0.00 2.57
2219 2247 5.204409 TCAACAAGGCGAAAGTTCTACTA 57.796 39.130 0.00 0.00 0.00 1.82
2220 2248 4.986659 TCAACAAGGCGAAAGTTCTACTAC 59.013 41.667 0.00 0.00 0.00 2.73
2221 2249 3.922910 ACAAGGCGAAAGTTCTACTACC 58.077 45.455 0.00 0.00 0.00 3.18
2222 2250 3.577415 ACAAGGCGAAAGTTCTACTACCT 59.423 43.478 0.00 0.00 0.00 3.08
2223 2251 4.040095 ACAAGGCGAAAGTTCTACTACCTT 59.960 41.667 0.00 0.00 36.73 3.50
2224 2252 4.189639 AGGCGAAAGTTCTACTACCTTG 57.810 45.455 0.00 0.00 0.00 3.61
2225 2253 2.671888 GGCGAAAGTTCTACTACCTTGC 59.328 50.000 0.00 0.00 0.00 4.01
2226 2254 3.323243 GCGAAAGTTCTACTACCTTGCA 58.677 45.455 0.00 0.00 0.00 4.08
2294 2526 5.733676 TCAGATAACAGTGCAAAGCTATCA 58.266 37.500 10.77 0.00 0.00 2.15
2326 2558 9.535170 TTCCTTGTAAATCAAAATATGTACCCA 57.465 29.630 0.00 0.00 35.48 4.51
2371 2604 8.394877 CGAAATATGTTACAAGCAAGTAATGGA 58.605 33.333 4.61 0.00 36.47 3.41
2384 2623 8.177119 AGCAAGTAATGGAATAGTGTGAAAAA 57.823 30.769 0.00 0.00 0.00 1.94
2411 2650 5.039920 TGCTCATCTGGCATAAGTACAAT 57.960 39.130 0.00 0.00 34.56 2.71
2412 2651 6.173427 TGCTCATCTGGCATAAGTACAATA 57.827 37.500 0.00 0.00 34.56 1.90
2413 2652 6.591001 TGCTCATCTGGCATAAGTACAATAA 58.409 36.000 0.00 0.00 34.56 1.40
2420 2659 7.620880 TCTGGCATAAGTACAATAACTGAACT 58.379 34.615 0.00 0.00 0.00 3.01
2437 2676 5.241949 ACTGAACTGTTTAGACTCGTGAGAT 59.758 40.000 17.86 0.00 40.84 2.75
2445 2684 6.183360 TGTTTAGACTCGTGAGATCCATACAG 60.183 42.308 3.44 0.00 40.84 2.74
2457 2718 2.905075 TCCATACAGTGCCGATTTCAG 58.095 47.619 0.00 0.00 0.00 3.02
2463 2724 6.038161 CCATACAGTGCCGATTTCAGAAATAA 59.962 38.462 8.45 0.00 0.00 1.40
2466 2727 5.240623 ACAGTGCCGATTTCAGAAATAACAA 59.759 36.000 8.45 0.00 0.00 2.83
2470 2731 4.562789 GCCGATTTCAGAAATAACAAAGGC 59.437 41.667 8.45 12.00 0.00 4.35
2494 2757 8.136057 GCAATATACTCTGATGCCACATATAC 57.864 38.462 0.00 0.00 0.00 1.47
2509 2772 8.094548 TGCCACATATACCTATGAAGTATGAAC 58.905 37.037 0.00 0.00 38.49 3.18
2583 2851 7.272951 CGTTTGTATGTAATTTGTGCACTTTG 58.727 34.615 19.41 0.00 0.00 2.77
2584 2852 7.563270 GTTTGTATGTAATTTGTGCACTTTGG 58.437 34.615 19.41 0.00 0.00 3.28
2618 2886 8.962679 GTTTCCACCATCCATTTATACAACTTA 58.037 33.333 0.00 0.00 0.00 2.24
2628 2896 6.038271 CCATTTATACAACTTAGAGTGGTGGC 59.962 42.308 0.00 0.00 32.42 5.01
2644 2912 0.037326 TGGCGAGAGGAACATGTGTC 60.037 55.000 0.00 0.00 0.00 3.67
2645 2913 0.247736 GGCGAGAGGAACATGTGTCT 59.752 55.000 0.00 1.82 0.00 3.41
2647 2915 2.480416 GGCGAGAGGAACATGTGTCTAG 60.480 54.545 0.00 4.13 0.00 2.43
2649 2917 3.017442 CGAGAGGAACATGTGTCTAGGA 58.983 50.000 0.00 0.00 0.00 2.94
2653 2921 6.380079 AGAGGAACATGTGTCTAGGAAAAT 57.620 37.500 0.00 0.00 0.00 1.82
2654 2922 6.176183 AGAGGAACATGTGTCTAGGAAAATG 58.824 40.000 0.00 0.00 0.00 2.32
2703 2972 3.119319 TGTTTCTACCATAGCCATCCCA 58.881 45.455 0.00 0.00 0.00 4.37
2713 2982 4.895297 CCATAGCCATCCCAGTAAAATTGT 59.105 41.667 0.00 0.00 0.00 2.71
2752 3021 4.039852 TGCCATCGACTAATATACAAGCCA 59.960 41.667 0.00 0.00 0.00 4.75
2778 3047 1.335964 ACCAACACATCGACTGACTCG 60.336 52.381 0.00 0.00 44.44 4.18
2787 3056 2.424557 TCGACTGACTCGACTTAAGCT 58.575 47.619 1.29 0.00 46.75 3.74
2788 3057 3.593096 TCGACTGACTCGACTTAAGCTA 58.407 45.455 1.29 0.00 46.75 3.32
2789 3058 3.999001 TCGACTGACTCGACTTAAGCTAA 59.001 43.478 1.29 0.00 46.75 3.09
2790 3059 4.090034 CGACTGACTCGACTTAAGCTAAC 58.910 47.826 1.29 0.00 46.14 2.34
2791 3060 4.413969 GACTGACTCGACTTAAGCTAACC 58.586 47.826 1.29 0.00 0.00 2.85
2794 3063 5.709164 ACTGACTCGACTTAAGCTAACCTAA 59.291 40.000 1.29 0.00 0.00 2.69
2796 3065 7.093858 ACTGACTCGACTTAAGCTAACCTAAAT 60.094 37.037 1.29 0.00 0.00 1.40
2810 3092 7.893833 AGCTAACCTAAATAACCAGGAAAATGT 59.106 33.333 0.00 0.00 35.76 2.71
2813 3095 6.697395 ACCTAAATAACCAGGAAAATGTTGC 58.303 36.000 0.00 0.00 35.76 4.17
2817 3099 0.314935 ACCAGGAAAATGTTGCAGCG 59.685 50.000 0.00 0.00 0.00 5.18
2827 3109 0.871722 TGTTGCAGCGTCACCATAAC 59.128 50.000 0.00 0.00 0.00 1.89
2847 3129 1.444895 GCTGTTGCATCGCCAAAGG 60.445 57.895 0.00 0.00 39.41 3.11
2864 3146 2.887151 AGGAGCCAACTGTGCTATTT 57.113 45.000 0.00 0.00 39.69 1.40
2865 3147 4.301072 AAGGAGCCAACTGTGCTATTTA 57.699 40.909 0.00 0.00 39.69 1.40
2878 3160 9.923143 AACTGTGCTATTTAACCCTAAAAATTC 57.077 29.630 0.00 0.00 30.87 2.17
2879 3161 9.084533 ACTGTGCTATTTAACCCTAAAAATTCA 57.915 29.630 0.00 0.00 30.87 2.57
2888 3170 4.821940 ACCCTAAAAATTCAAACAGGGGA 58.178 39.130 9.20 0.00 45.92 4.81
2889 3171 5.220521 ACCCTAAAAATTCAAACAGGGGAA 58.779 37.500 9.20 0.00 45.92 3.97
2901 3183 9.762381 ATTCAAACAGGGGAAATAACATTAGTA 57.238 29.630 0.00 0.00 0.00 1.82
2902 3184 8.570068 TCAAACAGGGGAAATAACATTAGTAC 57.430 34.615 0.00 0.00 0.00 2.73
2949 3234 7.907389 AGAGGACTAGAAACACATTATTGTCA 58.093 34.615 0.00 0.00 36.93 3.58
2953 3238 7.698130 GGACTAGAAACACATTATTGTCATTGC 59.302 37.037 0.00 0.00 36.93 3.56
2962 3247 7.134815 CACATTATTGTCATTGCTAACTAGGC 58.865 38.462 0.00 0.00 32.34 3.93
2976 3261 7.210174 TGCTAACTAGGCATTATCACTTACTG 58.790 38.462 0.00 0.00 34.56 2.74
2996 3281 4.079253 CTGCCCACTACCACTAATTGTTT 58.921 43.478 0.00 0.00 0.00 2.83
2998 3283 3.824443 GCCCACTACCACTAATTGTTTGT 59.176 43.478 0.00 0.00 0.00 2.83
3032 3317 3.339141 GAGAAACCAACACCTCAGGATC 58.661 50.000 0.00 0.00 0.00 3.36
3035 3320 0.608640 ACCAACACCTCAGGATCGTC 59.391 55.000 0.00 0.00 0.00 4.20
3052 3337 5.049405 GGATCGTCGCATTTTCCATAGAAAT 60.049 40.000 0.00 0.00 41.55 2.17
3058 3345 8.471457 CGTCGCATTTTCCATAGAAATAAATTG 58.529 33.333 0.00 0.00 41.55 2.32
3083 3370 8.296713 TGAATAAAAGGAACACTAACAATGAGC 58.703 33.333 0.00 0.00 0.00 4.26
3122 3409 6.372103 GGAAATCATCACATTTGGCAAATCAA 59.628 34.615 22.02 11.02 0.00 2.57
3123 3410 7.094720 GGAAATCATCACATTTGGCAAATCAAA 60.095 33.333 22.02 10.68 40.37 2.69
3173 3460 6.759497 AGAGCACCAATTTTATCCAACTAC 57.241 37.500 0.00 0.00 0.00 2.73
3174 3461 6.485171 AGAGCACCAATTTTATCCAACTACT 58.515 36.000 0.00 0.00 0.00 2.57
3175 3462 6.599638 AGAGCACCAATTTTATCCAACTACTC 59.400 38.462 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 209 3.558411 GACATGTCGAGCAGCGGC 61.558 66.667 10.69 0.00 46.88 6.53
248 249 2.815647 GCGTACCTGCTGTGAGGC 60.816 66.667 0.00 0.00 36.46 4.70
273 274 0.798009 GCAATGCACGTGTACATGGC 60.798 55.000 18.38 17.29 36.14 4.40
302 308 3.603671 GACTACTAGGCGGGCCGG 61.604 72.222 29.48 13.56 41.95 6.13
303 309 2.518825 AGACTACTAGGCGGGCCG 60.519 66.667 24.35 24.35 41.95 6.13
304 310 3.130227 CAGACTACTAGGCGGGCC 58.870 66.667 0.18 0.18 0.00 5.80
305 311 1.677637 AAGCAGACTACTAGGCGGGC 61.678 60.000 0.00 0.00 0.00 6.13
380 386 4.849329 CTCACCGTCGTAGCGCCC 62.849 72.222 2.29 0.00 0.00 6.13
531 537 2.890371 GTACGTGAGCCGGACCAT 59.110 61.111 5.05 0.00 45.06 3.55
664 670 5.581085 GTCGCCAAAAAGATGAGTAGTACAT 59.419 40.000 2.52 0.00 0.00 2.29
668 674 4.273148 AGTCGCCAAAAAGATGAGTAGT 57.727 40.909 0.00 0.00 0.00 2.73
670 676 5.298276 ACAAAAGTCGCCAAAAAGATGAGTA 59.702 36.000 0.00 0.00 0.00 2.59
671 677 4.097892 ACAAAAGTCGCCAAAAAGATGAGT 59.902 37.500 0.00 0.00 0.00 3.41
672 678 4.610945 ACAAAAGTCGCCAAAAAGATGAG 58.389 39.130 0.00 0.00 0.00 2.90
674 680 5.399301 CAGTACAAAAGTCGCCAAAAAGATG 59.601 40.000 0.00 0.00 0.00 2.90
675 681 5.067283 ACAGTACAAAAGTCGCCAAAAAGAT 59.933 36.000 0.00 0.00 0.00 2.40
676 682 4.396790 ACAGTACAAAAGTCGCCAAAAAGA 59.603 37.500 0.00 0.00 0.00 2.52
679 685 4.877251 ACTACAGTACAAAAGTCGCCAAAA 59.123 37.500 0.00 0.00 0.00 2.44
680 686 4.444536 ACTACAGTACAAAAGTCGCCAAA 58.555 39.130 0.00 0.00 0.00 3.28
681 687 4.062677 ACTACAGTACAAAAGTCGCCAA 57.937 40.909 0.00 0.00 0.00 4.52
682 688 3.738830 ACTACAGTACAAAAGTCGCCA 57.261 42.857 0.00 0.00 0.00 5.69
705 711 7.765819 TGAGAATTCGAGATGTACATGAACAAT 59.234 33.333 14.43 3.70 32.02 2.71
706 712 7.096551 TGAGAATTCGAGATGTACATGAACAA 58.903 34.615 14.43 1.33 32.02 2.83
707 713 6.630071 TGAGAATTCGAGATGTACATGAACA 58.370 36.000 14.43 2.72 0.00 3.18
708 714 7.525688 TTGAGAATTCGAGATGTACATGAAC 57.474 36.000 14.43 0.00 0.00 3.18
709 715 7.168135 CGATTGAGAATTCGAGATGTACATGAA 59.832 37.037 14.43 11.11 0.00 2.57
710 716 6.638468 CGATTGAGAATTCGAGATGTACATGA 59.362 38.462 14.43 1.24 0.00 3.07
711 717 6.638468 TCGATTGAGAATTCGAGATGTACATG 59.362 38.462 14.43 0.00 0.00 3.21
792 806 9.421399 TCTATATATAATCACATCCGTGTCCAT 57.579 33.333 0.00 0.00 44.02 3.41
1779 1803 2.919856 AGGTGCAGCGTCTGGTCT 60.920 61.111 10.78 0.00 31.21 3.85
2037 2064 1.377987 GTACATTTCCTGCCCGGCA 60.378 57.895 12.67 12.67 36.92 5.69
2043 2070 1.438651 TGAGCACGTACATTTCCTGC 58.561 50.000 0.00 0.00 0.00 4.85
2045 2072 3.262420 GACATGAGCACGTACATTTCCT 58.738 45.455 0.00 0.00 0.00 3.36
2049 2076 2.760634 TGGACATGAGCACGTACATT 57.239 45.000 0.00 0.00 0.00 2.71
2051 2078 1.343142 ACTTGGACATGAGCACGTACA 59.657 47.619 0.00 0.00 0.00 2.90
2135 2162 2.804167 CAGCAGCCTCGTCGATCT 59.196 61.111 0.00 0.00 0.00 2.75
2166 2193 4.216042 TGTGAACAATGATGCTACACTTGG 59.784 41.667 0.00 0.00 32.39 3.61
2184 2211 3.005684 GCCTTGTTGAATGGTGATGTGAA 59.994 43.478 0.00 0.00 0.00 3.18
2195 2222 5.063880 AGTAGAACTTTCGCCTTGTTGAAT 58.936 37.500 0.00 0.00 0.00 2.57
2206 2234 4.201724 GCATGCAAGGTAGTAGAACTTTCG 60.202 45.833 14.21 0.00 0.00 3.46
2218 2246 3.851458 AGATCTCATGCATGCAAGGTA 57.149 42.857 26.68 12.27 0.00 3.08
2219 2247 2.730934 AGATCTCATGCATGCAAGGT 57.269 45.000 26.68 15.27 0.00 3.50
2220 2248 5.354513 CCTATAAGATCTCATGCATGCAAGG 59.645 44.000 26.68 19.73 0.00 3.61
2221 2249 5.163744 GCCTATAAGATCTCATGCATGCAAG 60.164 44.000 26.68 21.38 0.00 4.01
2222 2250 4.698780 GCCTATAAGATCTCATGCATGCAA 59.301 41.667 26.68 8.62 0.00 4.08
2223 2251 4.259356 GCCTATAAGATCTCATGCATGCA 58.741 43.478 25.04 25.04 0.00 3.96
2224 2252 4.094590 GTGCCTATAAGATCTCATGCATGC 59.905 45.833 22.25 11.82 0.00 4.06
2225 2253 4.329256 CGTGCCTATAAGATCTCATGCATG 59.671 45.833 21.07 21.07 0.00 4.06
2226 2254 4.221482 TCGTGCCTATAAGATCTCATGCAT 59.779 41.667 0.00 0.00 0.00 3.96
2270 2298 6.351711 TGATAGCTTTGCACTGTTATCTGAT 58.648 36.000 16.89 0.00 30.94 2.90
2336 2569 7.148323 TGCTTGTAACATATTTCGTGCAGTTAT 60.148 33.333 0.00 0.00 0.00 1.89
2337 2570 6.147985 TGCTTGTAACATATTTCGTGCAGTTA 59.852 34.615 0.00 0.00 0.00 2.24
2339 2572 4.454161 TGCTTGTAACATATTTCGTGCAGT 59.546 37.500 0.00 0.00 0.00 4.40
2341 2574 5.049060 ACTTGCTTGTAACATATTTCGTGCA 60.049 36.000 0.00 0.00 0.00 4.57
2342 2575 5.390613 ACTTGCTTGTAACATATTTCGTGC 58.609 37.500 0.00 0.00 0.00 5.34
2343 2576 8.998989 CATTACTTGCTTGTAACATATTTCGTG 58.001 33.333 4.69 0.00 35.56 4.35
2344 2577 8.181573 CCATTACTTGCTTGTAACATATTTCGT 58.818 33.333 4.69 0.00 35.56 3.85
2352 2585 7.663905 ACACTATTCCATTACTTGCTTGTAACA 59.336 33.333 4.69 0.00 35.56 2.41
2411 2650 6.261603 TCTCACGAGTCTAAACAGTTCAGTTA 59.738 38.462 0.00 0.00 0.00 2.24
2412 2651 5.067413 TCTCACGAGTCTAAACAGTTCAGTT 59.933 40.000 0.00 0.00 0.00 3.16
2413 2652 4.579340 TCTCACGAGTCTAAACAGTTCAGT 59.421 41.667 0.00 0.00 0.00 3.41
2420 2659 5.650703 TGTATGGATCTCACGAGTCTAAACA 59.349 40.000 0.00 0.00 0.00 2.83
2427 2666 2.099921 GCACTGTATGGATCTCACGAGT 59.900 50.000 0.00 0.00 0.00 4.18
2437 2676 2.499693 TCTGAAATCGGCACTGTATGGA 59.500 45.455 0.00 0.00 0.00 3.41
2445 2684 5.572896 CCTTTGTTATTTCTGAAATCGGCAC 59.427 40.000 18.22 11.67 32.38 5.01
2470 2731 8.481314 AGGTATATGTGGCATCAGAGTATATTG 58.519 37.037 0.00 0.00 0.00 1.90
2583 2851 1.474077 GATGGTGGAAACAGTGCATCC 59.526 52.381 7.66 7.66 44.46 3.51
2584 2852 1.474077 GGATGGTGGAAACAGTGCATC 59.526 52.381 0.00 0.00 44.46 3.91
2589 2857 6.489603 TGTATAAATGGATGGTGGAAACAGT 58.510 36.000 0.00 0.00 44.46 3.55
2590 2858 7.122650 AGTTGTATAAATGGATGGTGGAAACAG 59.877 37.037 0.00 0.00 44.46 3.16
2618 2886 1.228894 TTCCTCTCGCCACCACTCT 60.229 57.895 0.00 0.00 0.00 3.24
2628 2896 3.017442 TCCTAGACACATGTTCCTCTCG 58.983 50.000 0.00 0.00 0.00 4.04
2693 2962 5.883673 GTGTACAATTTTACTGGGATGGCTA 59.116 40.000 0.00 0.00 0.00 3.93
2703 2972 7.883311 ACCATCAAGCTAGTGTACAATTTTACT 59.117 33.333 0.00 0.00 0.00 2.24
2713 2982 1.905894 TGGCACCATCAAGCTAGTGTA 59.094 47.619 0.00 0.00 32.75 2.90
2769 3038 4.156373 AGGTTAGCTTAAGTCGAGTCAGTC 59.844 45.833 4.02 0.00 0.00 3.51
2772 3041 6.579666 TTTAGGTTAGCTTAAGTCGAGTCA 57.420 37.500 4.02 0.00 0.00 3.41
2773 3042 9.018716 GTTATTTAGGTTAGCTTAAGTCGAGTC 57.981 37.037 4.02 0.00 0.00 3.36
2778 3047 8.262933 TCCTGGTTATTTAGGTTAGCTTAAGTC 58.737 37.037 4.02 0.00 35.54 3.01
2787 3056 8.308207 GCAACATTTTCCTGGTTATTTAGGTTA 58.692 33.333 0.00 0.00 35.54 2.85
2788 3057 7.158697 GCAACATTTTCCTGGTTATTTAGGTT 58.841 34.615 0.00 0.00 35.54 3.50
2789 3058 6.268847 TGCAACATTTTCCTGGTTATTTAGGT 59.731 34.615 0.00 0.00 35.54 3.08
2790 3059 6.696411 TGCAACATTTTCCTGGTTATTTAGG 58.304 36.000 0.00 0.00 35.34 2.69
2791 3060 6.311200 GCTGCAACATTTTCCTGGTTATTTAG 59.689 38.462 0.00 0.00 0.00 1.85
2794 3063 4.568956 GCTGCAACATTTTCCTGGTTATT 58.431 39.130 0.00 0.00 0.00 1.40
2796 3065 2.030363 CGCTGCAACATTTTCCTGGTTA 60.030 45.455 0.00 0.00 0.00 2.85
2810 3092 1.155889 CAGTTATGGTGACGCTGCAA 58.844 50.000 0.00 0.00 0.00 4.08
2813 3095 3.143675 AGCAGTTATGGTGACGCTG 57.856 52.632 0.00 0.00 35.34 5.18
2827 3109 0.731514 CTTTGGCGATGCAACAGCAG 60.732 55.000 12.33 0.00 42.36 4.24
2840 3122 1.662044 CACAGTTGGCTCCTTTGGC 59.338 57.895 0.00 0.00 0.00 4.52
2847 3129 3.128764 GGGTTAAATAGCACAGTTGGCTC 59.871 47.826 0.00 0.00 42.62 4.70
2864 3146 6.382925 TCCCCTGTTTGAATTTTTAGGGTTA 58.617 36.000 0.00 0.00 42.64 2.85
2865 3147 5.220521 TCCCCTGTTTGAATTTTTAGGGTT 58.779 37.500 0.00 0.00 42.64 4.11
2878 3160 7.394923 TGGTACTAATGTTATTTCCCCTGTTTG 59.605 37.037 0.00 0.00 0.00 2.93
2879 3161 7.395206 GTGGTACTAATGTTATTTCCCCTGTTT 59.605 37.037 0.00 0.00 0.00 2.83
2882 3164 6.317893 GTGTGGTACTAATGTTATTTCCCCTG 59.682 42.308 0.00 0.00 0.00 4.45
2885 3167 7.933215 AAGTGTGGTACTAATGTTATTTCCC 57.067 36.000 0.00 0.00 39.18 3.97
2949 3234 8.432805 AGTAAGTGATAATGCCTAGTTAGCAAT 58.567 33.333 0.00 0.00 44.83 3.56
2962 3247 5.057149 GGTAGTGGGCAGTAAGTGATAATG 58.943 45.833 0.00 0.00 32.78 1.90
2976 3261 3.824443 ACAAACAATTAGTGGTAGTGGGC 59.176 43.478 0.00 0.00 0.00 5.36
2996 3281 5.013547 TGGTTTCTCCTTTTGTTGAGAACA 58.986 37.500 1.67 0.00 44.84 3.18
2998 3283 5.478679 TGTTGGTTTCTCCTTTTGTTGAGAA 59.521 36.000 0.00 0.00 43.82 2.87
3010 3295 1.420138 TCCTGAGGTGTTGGTTTCTCC 59.580 52.381 0.00 0.00 0.00 3.71
3032 3317 8.471457 CAATTTATTTCTATGGAAAATGCGACG 58.529 33.333 8.42 0.00 43.51 5.12
3058 3345 8.515414 AGCTCATTGTTAGTGTTCCTTTTATTC 58.485 33.333 0.00 0.00 0.00 1.75
3090 3377 6.620678 CCAAATGTGATGATTTCCTTACGTT 58.379 36.000 0.00 0.00 0.00 3.99
3091 3378 5.393027 GCCAAATGTGATGATTTCCTTACGT 60.393 40.000 0.00 0.00 0.00 3.57
3092 3379 5.036737 GCCAAATGTGATGATTTCCTTACG 58.963 41.667 0.00 0.00 0.00 3.18
3093 3380 5.964758 TGCCAAATGTGATGATTTCCTTAC 58.035 37.500 0.00 0.00 0.00 2.34
3122 3409 4.804868 TGTCATTTGGTGCATGCTATTT 57.195 36.364 20.33 0.00 0.00 1.40
3123 3410 5.347620 AATGTCATTTGGTGCATGCTATT 57.652 34.783 20.33 1.74 0.00 1.73


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

AutoCloner maintained by Alex Coulton.