Multiple sequence alignment - TraesCS6D01G328100

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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 TraesCS6D01G328100 chr6D 100.000 3113 0 0 1 3113 432932430 432929318 0.000000e+00 5749.0
1 TraesCS6D01G328100 chr6D 93.145 2626 163 10 114 2735 433156119 433153507 0.000000e+00 3836.0
2 TraesCS6D01G328100 chr6D 93.849 2276 129 6 114 2383 433281466 433279196 0.000000e+00 3417.0
3 TraesCS6D01G328100 chr6D 88.624 1890 193 9 704 2585 433259320 433257445 0.000000e+00 2279.0
4 TraesCS6D01G328100 chr6D 89.966 1774 160 6 812 2578 432914545 432912783 0.000000e+00 2274.0
5 TraesCS6D01G328100 chr6D 86.240 516 61 4 2071 2586 433037324 433036819 4.540000e-153 551.0
6 TraesCS6D01G328100 chr6D 88.579 359 40 1 2382 2740 433279035 433278678 4.770000e-118 435.0
7 TraesCS6D01G328100 chr6D 80.752 452 77 10 114 562 433259886 433259442 8.270000e-91 344.0
8 TraesCS6D01G328100 chr6D 78.465 469 79 15 114 578 432915195 432914745 1.410000e-73 287.0
9 TraesCS6D01G328100 chr6D 81.375 349 53 10 2773 3113 394209984 394209640 1.100000e-69 274.0
10 TraesCS6D01G328100 chr6D 80.051 396 45 14 2745 3113 433278635 433278247 2.380000e-66 263.0
11 TraesCS6D01G328100 chr6D 73.410 346 69 18 2786 3113 89699198 89698858 1.180000e-19 108.0
12 TraesCS6D01G328100 chr6D 82.353 102 15 3 2994 3094 33338232 33338331 5.530000e-13 86.1
13 TraesCS6D01G328100 chr6D 89.474 57 6 0 2770 2826 305268792 305268736 4.310000e-09 73.1
14 TraesCS6D01G328100 chr6D 87.931 58 5 1 590 645 432914759 432914702 2.000000e-07 67.6
15 TraesCS6D01G328100 chr6B 93.536 2274 130 10 114 2380 653873435 653871172 0.000000e+00 3369.0
16 TraesCS6D01G328100 chr6B 87.719 1881 192 12 704 2575 653715842 653713992 0.000000e+00 2158.0
17 TraesCS6D01G328100 chr6B 92.412 1331 85 7 1416 2741 653698578 653697259 0.000000e+00 1884.0
18 TraesCS6D01G328100 chr6B 89.191 1286 103 12 114 1395 653699824 653698571 0.000000e+00 1572.0
19 TraesCS6D01G328100 chr6B 91.667 48 3 1 599 645 653195128 653195081 7.210000e-07 65.8
20 TraesCS6D01G328100 chr6A 93.333 2280 131 13 116 2380 579143933 579141660 0.000000e+00 3349.0
21 TraesCS6D01G328100 chr6A 89.089 1668 166 4 812 2473 579125017 579123360 0.000000e+00 2058.0
22 TraesCS6D01G328100 chr6A 87.193 367 46 1 2375 2741 579141502 579141137 1.730000e-112 416.0
23 TraesCS6D01G328100 chr6A 82.997 347 49 5 2773 3112 438026551 438026208 3.900000e-79 305.0
24 TraesCS6D01G328100 chr6A 79.104 469 79 12 114 578 579125669 579125216 3.900000e-79 305.0
25 TraesCS6D01G328100 chr6A 92.647 136 6 3 1 134 527097540 527097407 3.170000e-45 193.0
26 TraesCS6D01G328100 chr7D 84.463 354 45 9 2767 3113 557077370 557077020 1.070000e-89 340.0
27 TraesCS6D01G328100 chr7D 80.682 352 57 9 2770 3113 165884497 165884149 2.380000e-66 263.0
28 TraesCS6D01G328100 chr7D 95.312 128 3 3 1 127 113506480 113506605 1.890000e-47 200.0
29 TraesCS6D01G328100 chr1A 84.150 347 49 4 2772 3113 561586427 561586772 6.430000e-87 331.0
30 TraesCS6D01G328100 chr1A 81.897 348 56 5 2772 3113 561591560 561591906 1.410000e-73 287.0
31 TraesCS6D01G328100 chr1A 98.230 113 2 0 1 113 511836683 511836795 6.810000e-47 198.0
32 TraesCS6D01G328100 chr2B 83.095 349 53 4 2770 3113 5475317 5474970 2.330000e-81 313.0
33 TraesCS6D01G328100 chr7A 83.478 345 46 7 2772 3108 30870578 30870919 8.380000e-81 311.0
34 TraesCS6D01G328100 chr7B 82.704 318 49 4 2786 3098 374772927 374772611 8.500000e-71 278.0
35 TraesCS6D01G328100 chr7B 80.912 351 58 7 2770 3113 402819388 402819736 5.120000e-68 268.0
36 TraesCS6D01G328100 chr5A 81.089 349 61 5 2770 3113 690018950 690018602 1.100000e-69 274.0
37 TraesCS6D01G328100 chr5A 95.238 126 4 2 1 126 22644988 22644865 6.810000e-47 198.0
38 TraesCS6D01G328100 chr5A 80.714 140 27 0 2602 2741 567688812 567688951 3.280000e-20 110.0
39 TraesCS6D01G328100 chr2D 81.341 343 57 3 2773 3113 18189618 18189281 3.960000e-69 272.0
40 TraesCS6D01G328100 chr2D 98.305 118 1 1 1 118 192333383 192333267 4.070000e-49 206.0
41 TraesCS6D01G328100 chr4D 82.595 316 45 7 2771 3079 92078036 92077724 1.420000e-68 270.0
42 TraesCS6D01G328100 chr4D 77.215 237 43 7 2830 3065 54337595 54337369 9.060000e-26 128.0
43 TraesCS6D01G328100 chr5D 81.361 338 51 8 2770 3098 412152840 412153174 6.620000e-67 265.0
44 TraesCS6D01G328100 chr5D 95.238 126 4 2 1 126 331754993 331755116 6.810000e-47 198.0
45 TraesCS6D01G328100 chr5B 80.347 346 62 4 2773 3113 72078121 72077777 1.110000e-64 257.0
46 TraesCS6D01G328100 chr5B 79.710 345 59 9 2770 3108 315942392 315942731 4.010000e-59 239.0
47 TraesCS6D01G328100 chr5B 78.917 351 60 8 2770 3112 617598882 617598538 3.120000e-55 226.0
48 TraesCS6D01G328100 chr4B 79.221 308 59 3 2770 3072 65645992 65645685 3.150000e-50 209.0
49 TraesCS6D01G328100 chr4B 79.592 245 43 5 2770 3009 666069462 666069220 5.340000e-38 169.0
50 TraesCS6D01G328100 chr3D 99.138 116 1 0 1 116 81175982 81175867 3.150000e-50 209.0
51 TraesCS6D01G328100 chr3D 96.694 121 4 0 1 121 385371734 385371614 5.260000e-48 202.0
52 TraesCS6D01G328100 chr1D 96.800 125 2 2 1 125 405584008 405583886 1.130000e-49 207.0
53 TraesCS6D01G328100 chr1D 76.945 347 71 6 2770 3111 447319631 447319289 4.100000e-44 189.0
54 TraesCS6D01G328100 chr1D 79.134 254 45 5 2770 3016 365062975 365063227 5.340000e-38 169.0
55 TraesCS6D01G328100 chr1D 78.333 180 27 8 2915 3086 11743515 11743340 4.250000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G328100 chr6D 432929318 432932430 3112 True 5749.000000 5749 100.0000 1 3113 1 chr6D.!!$R4 3112
1 TraesCS6D01G328100 chr6D 433153507 433156119 2612 True 3836.000000 3836 93.1450 114 2735 1 chr6D.!!$R6 2621
2 TraesCS6D01G328100 chr6D 433278247 433281466 3219 True 1371.666667 3417 87.4930 114 3113 3 chr6D.!!$R9 2999
3 TraesCS6D01G328100 chr6D 433257445 433259886 2441 True 1311.500000 2279 84.6880 114 2585 2 chr6D.!!$R8 2471
4 TraesCS6D01G328100 chr6D 432912783 432915195 2412 True 876.200000 2274 85.4540 114 2578 3 chr6D.!!$R7 2464
5 TraesCS6D01G328100 chr6D 433036819 433037324 505 True 551.000000 551 86.2400 2071 2586 1 chr6D.!!$R5 515
6 TraesCS6D01G328100 chr6B 653871172 653873435 2263 True 3369.000000 3369 93.5360 114 2380 1 chr6B.!!$R3 2266
7 TraesCS6D01G328100 chr6B 653713992 653715842 1850 True 2158.000000 2158 87.7190 704 2575 1 chr6B.!!$R2 1871
8 TraesCS6D01G328100 chr6B 653697259 653699824 2565 True 1728.000000 1884 90.8015 114 2741 2 chr6B.!!$R4 2627
9 TraesCS6D01G328100 chr6A 579141137 579143933 2796 True 1882.500000 3349 90.2630 116 2741 2 chr6A.!!$R4 2625
10 TraesCS6D01G328100 chr6A 579123360 579125669 2309 True 1181.500000 2058 84.0965 114 2473 2 chr6A.!!$R3 2359

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
864 899 1.093159 CGCCCACTAGACGTACTTCT 58.907 55.0 7.11 7.11 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2670 2922 0.329596 GGTGGAGGTGAGGCAAATCT 59.67 55.0 0.0 0.0 0.0 2.4 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
124 125 8.566260 GTTGGAGACGTATCATTACATACTACT 58.434 37.037 12.92 0.00 0.00 2.57
125 126 9.783081 TTGGAGACGTATCATTACATACTACTA 57.217 33.333 12.92 0.00 0.00 1.82
159 160 1.292860 CAATGCCGCACAACCCAAT 59.707 52.632 0.00 0.00 0.00 3.16
456 468 5.230182 TGCGATGATATGGTTAGCTAAGTG 58.770 41.667 6.38 0.00 0.00 3.16
607 621 3.183793 GGTAGGTACCCACAAATACGG 57.816 52.381 12.74 0.00 40.53 4.02
693 726 7.488322 GGCAGCAAACTTATATATTTTGTCCA 58.512 34.615 14.38 0.00 33.57 4.02
778 813 2.260869 ACCGTGCAAGCACATCCAC 61.261 57.895 23.23 0.00 46.47 4.02
785 820 1.470098 GCAAGCACATCCACCTAAGTG 59.530 52.381 0.00 0.00 44.12 3.16
821 856 3.717294 ATCCCCACACCAGACGGC 61.717 66.667 0.00 0.00 34.57 5.68
864 899 1.093159 CGCCCACTAGACGTACTTCT 58.907 55.000 7.11 7.11 0.00 2.85
867 906 3.314635 CGCCCACTAGACGTACTTCTTAT 59.685 47.826 7.24 0.00 0.00 1.73
868 907 4.512944 CGCCCACTAGACGTACTTCTTATA 59.487 45.833 7.24 0.00 0.00 0.98
872 911 6.862090 CCCACTAGACGTACTTCTTATATTGC 59.138 42.308 7.24 0.00 0.00 3.56
875 914 7.591795 CACTAGACGTACTTCTTATATTGCAGG 59.408 40.741 7.24 0.00 0.00 4.85
1092 1133 1.920574 CGCGAGATCAACGATGACTTT 59.079 47.619 0.00 0.00 38.69 2.66
1194 1235 2.642311 TGAGGTCTTCAAGGCCAATGTA 59.358 45.455 11.62 0.00 44.17 2.29
1309 1350 4.397919 AAGGCTAACAAGGGGTACAAAT 57.602 40.909 0.00 0.00 0.00 2.32
1371 1412 6.378564 AGAATCTAAGTCTCGATTCACTTCCA 59.621 38.462 19.18 0.00 44.90 3.53
1375 1416 2.094286 AGTCTCGATTCACTTCCAGCAG 60.094 50.000 0.00 0.00 0.00 4.24
1422 1463 1.351017 GTCACTCCCATCAAGGACCAA 59.649 52.381 0.00 0.00 41.22 3.67
1725 1767 1.825474 CTCACCACCGAGTCCAACTAT 59.175 52.381 0.00 0.00 0.00 2.12
1732 1774 4.560128 CACCGAGTCCAACTATCCATATG 58.440 47.826 0.00 0.00 0.00 1.78
1737 1779 1.003118 TCCAACTATCCATATGCCGCC 59.997 52.381 0.00 0.00 0.00 6.13
1773 1815 2.821378 CAAGAGTGGAACCAATGATGCA 59.179 45.455 0.00 0.00 37.80 3.96
2004 2046 7.339466 ACAAAGTATTGGTTGTTGAAGAACTCT 59.661 33.333 5.17 0.00 41.01 3.24
2010 2052 2.623416 GTTGTTGAAGAACTCTTGGGGG 59.377 50.000 0.00 0.00 36.11 5.40
2016 2058 1.821088 AGAACTCTTGGGGGACAACT 58.179 50.000 0.00 0.00 34.76 3.16
2127 2169 4.840680 ACTGCATAGAAGGAGTGCCATATA 59.159 41.667 0.00 0.00 38.84 0.86
2144 2186 5.012148 GCCATATACCGCATATCCTCCTATT 59.988 44.000 0.00 0.00 0.00 1.73
2170 2212 9.526713 TCACAAAAATATTACATAATTGCGCAT 57.473 25.926 12.75 0.00 0.00 4.73
2336 2396 8.572185 TGTTAGCTATATCATTCAGAGACTGTC 58.428 37.037 0.00 0.00 32.61 3.51
2380 2610 7.173735 TGCCTTCATGCATACATAATGAACTAG 59.826 37.037 0.00 0.00 37.86 2.57
2496 2744 4.824289 AGGTGGAACAAAATGATGAATGC 58.176 39.130 0.00 0.00 44.16 3.56
2502 2750 6.715718 TGGAACAAAATGATGAATGCCAATTT 59.284 30.769 0.00 0.00 31.92 1.82
2526 2774 9.912634 TTTGTGAATCTTGAGGAAATGAATTAC 57.087 29.630 0.00 0.00 0.00 1.89
2562 2811 3.297134 TCCCCAATTGCTATTGTCCTC 57.703 47.619 17.66 0.00 39.62 3.71
2600 2849 1.484240 GCCAGCTAGACCAGAGATTGT 59.516 52.381 0.00 0.00 0.00 2.71
2620 2869 2.185004 TTTTCTTTCCCCTCTCGCAG 57.815 50.000 0.00 0.00 0.00 5.18
2637 2889 0.329596 CAGGGCAACTAGGGAAAGCT 59.670 55.000 0.00 0.00 0.00 3.74
2667 2919 1.153549 GATCTCCGCCAGCGAGTTT 60.154 57.895 14.67 2.31 42.83 2.66
2670 2922 1.080093 CTCCGCCAGCGAGTTTGTA 60.080 57.895 14.67 0.00 42.83 2.41
2681 2933 2.742053 GCGAGTTTGTAGATTTGCCTCA 59.258 45.455 0.00 0.00 0.00 3.86
2693 2945 4.767255 GCCTCACCTCCACCTGCG 62.767 72.222 0.00 0.00 0.00 5.18
2762 3054 2.038426 AGTGTTTGGATGGATGACGACA 59.962 45.455 0.00 0.00 0.00 4.35
2772 3064 3.914312 TGGATGACGACACTTCTTCTTC 58.086 45.455 0.00 0.00 0.00 2.87
2773 3065 3.574396 TGGATGACGACACTTCTTCTTCT 59.426 43.478 0.00 0.00 29.59 2.85
2774 3066 4.039245 TGGATGACGACACTTCTTCTTCTT 59.961 41.667 0.00 0.00 29.59 2.52
2775 3067 4.623595 GGATGACGACACTTCTTCTTCTTC 59.376 45.833 0.00 0.00 29.59 2.87
2777 3069 5.263968 TGACGACACTTCTTCTTCTTCTT 57.736 39.130 0.00 0.00 0.00 2.52
2778 3070 5.282510 TGACGACACTTCTTCTTCTTCTTC 58.717 41.667 0.00 0.00 0.00 2.87
2779 3071 4.291783 ACGACACTTCTTCTTCTTCTTCG 58.708 43.478 0.00 0.00 0.00 3.79
2780 3072 4.036498 ACGACACTTCTTCTTCTTCTTCGA 59.964 41.667 0.00 0.00 0.00 3.71
2781 3073 4.615121 CGACACTTCTTCTTCTTCTTCGAG 59.385 45.833 0.00 0.00 0.00 4.04
2782 3074 5.523438 ACACTTCTTCTTCTTCTTCGAGT 57.477 39.130 0.00 0.00 0.00 4.18
2783 3075 5.908341 ACACTTCTTCTTCTTCTTCGAGTT 58.092 37.500 0.00 0.00 0.00 3.01
2784 3076 5.751028 ACACTTCTTCTTCTTCTTCGAGTTG 59.249 40.000 0.00 0.00 0.00 3.16
2790 3082 5.277857 TCTTCTTCTTCGAGTTGGTCTTT 57.722 39.130 0.00 0.00 0.00 2.52
2798 3090 0.673956 GAGTTGGTCTTTCGGGCTCC 60.674 60.000 0.00 0.00 0.00 4.70
2817 3109 1.204941 CCGATCCTCCTCAAGTTCGTT 59.795 52.381 0.00 0.00 30.69 3.85
2828 3120 1.871039 CAAGTTCGTTCGTTGGGATGT 59.129 47.619 0.00 0.00 0.00 3.06
2858 3150 1.300233 CTCCGGCGTAGATTCCTGC 60.300 63.158 6.01 0.00 0.00 4.85
2864 3156 0.878086 GCGTAGATTCCTGCCAGCTC 60.878 60.000 0.00 0.00 0.00 4.09
2868 3160 0.177604 AGATTCCTGCCAGCTCTTCG 59.822 55.000 0.00 0.00 0.00 3.79
2893 3185 3.046280 CGAGGTTAGGGTTTCTCGC 57.954 57.895 0.00 0.00 41.69 5.03
2895 3187 0.459759 GAGGTTAGGGTTTCTCGCCG 60.460 60.000 0.00 0.00 0.00 6.46
2911 3203 1.917782 GCCGTGCGTATTCAAAGGCA 61.918 55.000 0.00 0.00 39.94 4.75
2918 3210 6.195868 CGTGCGTATTCAAAGGCAATATTTA 58.804 36.000 0.00 0.00 41.46 1.40
2927 3219 8.810652 TTCAAAGGCAATATTTAGTGTCAAAC 57.189 30.769 0.00 0.00 0.00 2.93
2942 3234 7.763172 AGTGTCAAACTATTCAGATCGATTC 57.237 36.000 0.00 0.00 37.36 2.52
2943 3235 6.473778 AGTGTCAAACTATTCAGATCGATTCG 59.526 38.462 0.00 0.00 37.36 3.34
2947 3239 6.039382 TCAAACTATTCAGATCGATTCGAGGA 59.961 38.462 14.81 8.99 39.91 3.71
2954 3246 4.097892 TCAGATCGATTCGAGGATTCAACA 59.902 41.667 14.81 0.00 39.91 3.33
2955 3247 4.443725 CAGATCGATTCGAGGATTCAACAG 59.556 45.833 14.81 0.00 39.91 3.16
2960 3252 0.108804 TCGAGGATTCAACAGCGACC 60.109 55.000 0.00 0.00 0.00 4.79
2996 3315 0.466922 GCTCCTTAGGGCATGTGCAT 60.467 55.000 7.36 0.00 44.36 3.96
3003 3322 0.330604 AGGGCATGTGCATGAAGACT 59.669 50.000 15.53 4.87 44.36 3.24
3009 3328 0.955428 TGTGCATGAAGACTTCCGGC 60.955 55.000 12.66 15.15 0.00 6.13
3013 3332 1.363744 CATGAAGACTTCCGGCTGTC 58.636 55.000 12.66 15.76 0.00 3.51
3025 3344 0.670546 CGGCTGTCATCGACAAGGTT 60.671 55.000 0.00 0.00 42.26 3.50
3033 3352 1.262640 ATCGACAAGGTTAGGCCGGT 61.263 55.000 1.90 0.00 43.70 5.28
3035 3354 0.604511 CGACAAGGTTAGGCCGGTTT 60.605 55.000 1.90 0.00 43.70 3.27
3055 3374 1.376466 GGTATGGGAGCGATGCCAT 59.624 57.895 29.64 29.64 0.00 4.40
3064 3383 3.993234 CGATGCCATCAGCGCGTC 61.993 66.667 8.43 0.00 45.29 5.19
3081 3400 4.379243 CGGTGGCTCGTTCTGGCT 62.379 66.667 0.00 0.00 0.00 4.75
3083 3402 3.426568 GTGGCTCGTTCTGGCTGC 61.427 66.667 0.00 0.00 0.00 5.25
3084 3403 3.939939 TGGCTCGTTCTGGCTGCA 61.940 61.111 0.50 0.00 0.00 4.41
3093 3412 1.246056 TTCTGGCTGCAGCAATGGTC 61.246 55.000 37.63 20.78 44.36 4.02
3098 3417 1.503542 CTGCAGCAATGGTCGTTCC 59.496 57.895 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 9.027129 CGTCTCCAACGTATCTATAATTTTTGA 57.973 33.333 0.00 0.00 46.42 2.69
98 99 8.566260 AGTAGTATGTAATGATACGTCTCCAAC 58.434 37.037 0.00 0.00 34.50 3.77
99 100 8.687292 AGTAGTATGTAATGATACGTCTCCAA 57.313 34.615 0.00 0.00 34.50 3.53
100 101 9.955102 ATAGTAGTATGTAATGATACGTCTCCA 57.045 33.333 0.00 0.00 34.50 3.86
124 125 3.691118 GCATTGCACCTCAAGACTGAATA 59.309 43.478 3.15 0.00 38.22 1.75
125 126 2.490903 GCATTGCACCTCAAGACTGAAT 59.509 45.455 3.15 0.00 38.22 2.57
131 132 2.334946 GCGGCATTGCACCTCAAGA 61.335 57.895 11.39 0.00 38.22 3.02
159 160 3.463728 AAGCGTGTGGTGCGGGTTA 62.464 57.895 0.00 0.00 37.44 2.85
214 215 7.818997 ATAGAAGTACCGTATCTCACAATCA 57.181 36.000 0.00 0.00 0.00 2.57
243 253 3.927142 CAGACGCTCCTTTCGACTAAATT 59.073 43.478 0.00 0.00 31.53 1.82
244 254 3.512680 CAGACGCTCCTTTCGACTAAAT 58.487 45.455 0.00 0.00 31.53 1.40
360 371 2.228822 GTCCAAACAATGCCTGGTACTG 59.771 50.000 0.00 0.00 0.00 2.74
368 379 0.608035 TCCGGAGTCCAAACAATGCC 60.608 55.000 10.49 0.00 0.00 4.40
434 445 4.627467 CCACTTAGCTAACCATATCATCGC 59.373 45.833 0.86 0.00 0.00 4.58
456 468 9.916397 CACGAACATAATAAGTTGATTAAGACC 57.084 33.333 0.00 0.00 0.00 3.85
655 688 1.096967 TGCTGCCGTCTATGCAATGG 61.097 55.000 0.00 0.00 38.46 3.16
693 726 0.515564 GCGTTTTGGCATGAGTACGT 59.484 50.000 0.00 0.00 0.00 3.57
702 737 6.935741 ATGTATCTTTATAGCGTTTTGGCA 57.064 33.333 0.00 0.00 34.64 4.92
778 813 7.392113 TGGTGGTATAAATCAAACACACTTAGG 59.608 37.037 0.00 0.00 0.00 2.69
785 820 5.068591 GGGGATGGTGGTATAAATCAAACAC 59.931 44.000 0.00 0.00 0.00 3.32
864 899 4.104579 TGATGGAGAAGGCCTGCAATATAA 59.895 41.667 15.05 0.00 46.42 0.98
867 906 1.845791 TGATGGAGAAGGCCTGCAATA 59.154 47.619 15.05 0.00 46.42 1.90
868 907 0.627451 TGATGGAGAAGGCCTGCAAT 59.373 50.000 15.05 3.05 46.42 3.56
872 911 5.874093 ACTATAAATGATGGAGAAGGCCTG 58.126 41.667 5.69 0.00 0.00 4.85
903 942 6.220930 GGGTGTCTTATATAGTTCGATGCAA 58.779 40.000 0.00 0.00 0.00 4.08
1092 1133 1.001020 ATGCCTTGCCACCATCGAA 60.001 52.632 0.00 0.00 0.00 3.71
1194 1235 3.582780 GTTAAACGACTCGATGAACCCT 58.417 45.455 5.20 0.00 0.00 4.34
1363 1404 0.898326 TCTACGGCTGCTGGAAGTGA 60.898 55.000 13.87 0.00 35.30 3.41
1371 1412 2.055042 CCTCCAGTCTACGGCTGCT 61.055 63.158 0.00 0.00 32.93 4.24
1375 1416 1.255667 TTGGTCCTCCAGTCTACGGC 61.256 60.000 0.00 0.00 45.22 5.68
1422 1463 4.796110 AATATACTCACCACATTGGCCT 57.204 40.909 3.32 0.00 42.67 5.19
1475 1516 9.823647 ATACTATCAGACGACATTCTCAAAAAT 57.176 29.630 0.00 0.00 0.00 1.82
1551 1593 0.393402 CAATGCCCTCTGTAGCAGCA 60.393 55.000 0.00 0.00 43.38 4.41
1732 1774 3.869272 CTTGTCATCTGCGGCGGC 61.869 66.667 9.78 9.68 40.52 6.53
1737 1779 1.128136 CTCTTGCACTTGTCATCTGCG 59.872 52.381 0.00 0.00 33.35 5.18
1773 1815 3.698040 CCTCATAGCTTTTGATGGTTGCT 59.302 43.478 0.00 0.00 37.72 3.91
2004 2046 2.939298 CCCCAAGTTGTCCCCCAA 59.061 61.111 1.45 0.00 0.00 4.12
2010 2052 1.566018 CGTTCTCGCCCCAAGTTGTC 61.566 60.000 1.45 0.00 0.00 3.18
2016 2058 0.834612 AATATCCGTTCTCGCCCCAA 59.165 50.000 0.00 0.00 35.54 4.12
2127 2169 3.239449 TGTGAATAGGAGGATATGCGGT 58.761 45.455 0.00 0.00 0.00 5.68
2144 2186 8.917415 TGCGCAATTATGTAATATTTTTGTGA 57.083 26.923 8.16 0.00 31.38 3.58
2336 2396 1.933500 GCACAAGAGGCAGCACAATTG 60.934 52.381 3.24 3.24 0.00 2.32
2496 2744 7.380536 TCATTTCCTCAAGATTCACAAATTGG 58.619 34.615 0.00 0.00 0.00 3.16
2502 2750 7.606073 TCGTAATTCATTTCCTCAAGATTCACA 59.394 33.333 0.00 0.00 0.00 3.58
2562 2811 1.274476 CGTTGTGGGTTGAACGACG 59.726 57.895 0.00 2.29 46.19 5.12
2600 2849 2.504367 CTGCGAGAGGGGAAAGAAAAA 58.496 47.619 0.00 0.00 0.00 1.94
2620 2869 1.924731 AAAGCTTTCCCTAGTTGCCC 58.075 50.000 5.69 0.00 0.00 5.36
2624 2873 4.035612 GGGAGAAAAGCTTTCCCTAGTT 57.964 45.455 22.60 2.44 45.84 2.24
2637 2889 1.112113 CGGAGATCGAGGGGAGAAAA 58.888 55.000 0.00 0.00 42.43 2.29
2667 2919 2.027192 GTGGAGGTGAGGCAAATCTACA 60.027 50.000 0.00 0.00 0.00 2.74
2670 2922 0.329596 GGTGGAGGTGAGGCAAATCT 59.670 55.000 0.00 0.00 0.00 2.40
2715 2968 2.081585 GAGGCACCAGAAACCCCCTT 62.082 60.000 0.00 0.00 0.00 3.95
2741 2995 2.038426 TGTCGTCATCCATCCAAACACT 59.962 45.455 0.00 0.00 0.00 3.55
2743 2997 2.038426 AGTGTCGTCATCCATCCAAACA 59.962 45.455 0.00 0.00 0.00 2.83
2751 3043 3.574396 AGAAGAAGAAGTGTCGTCATCCA 59.426 43.478 0.00 0.00 34.97 3.41
2762 3054 5.163395 ACCAACTCGAAGAAGAAGAAGAAGT 60.163 40.000 0.00 0.00 34.09 3.01
2772 3064 2.731976 CCGAAAGACCAACTCGAAGAAG 59.268 50.000 0.00 0.00 34.09 2.85
2773 3065 2.547218 CCCGAAAGACCAACTCGAAGAA 60.547 50.000 0.00 0.00 34.09 2.52
2774 3066 1.000506 CCCGAAAGACCAACTCGAAGA 59.999 52.381 0.00 0.00 34.52 2.87
2775 3067 1.429463 CCCGAAAGACCAACTCGAAG 58.571 55.000 0.00 0.00 34.52 3.79
2777 3069 1.005394 GCCCGAAAGACCAACTCGA 60.005 57.895 0.00 0.00 34.52 4.04
2778 3070 1.004918 AGCCCGAAAGACCAACTCG 60.005 57.895 0.00 0.00 0.00 4.18
2779 3071 0.673956 GGAGCCCGAAAGACCAACTC 60.674 60.000 0.00 0.00 0.00 3.01
2780 3072 1.375326 GGAGCCCGAAAGACCAACT 59.625 57.895 0.00 0.00 0.00 3.16
2781 3073 3.982829 GGAGCCCGAAAGACCAAC 58.017 61.111 0.00 0.00 0.00 3.77
2798 3090 2.531206 GAACGAACTTGAGGAGGATCG 58.469 52.381 0.00 0.00 41.63 3.69
2817 3109 3.289836 TCCGTCTAATACATCCCAACGA 58.710 45.455 0.00 0.00 0.00 3.85
2893 3185 0.519519 TTGCCTTTGAATACGCACGG 59.480 50.000 0.00 0.00 0.00 4.94
2895 3187 7.165812 CACTAAATATTGCCTTTGAATACGCAC 59.834 37.037 0.00 0.00 0.00 5.34
2903 3195 8.177119 AGTTTGACACTAAATATTGCCTTTGA 57.823 30.769 0.00 0.00 31.97 2.69
2907 3199 9.461312 TGAATAGTTTGACACTAAATATTGCCT 57.539 29.630 0.00 0.00 41.56 4.75
2918 3210 6.473778 CGAATCGATCTGAATAGTTTGACACT 59.526 38.462 0.00 0.00 39.87 3.55
2927 3219 6.616017 TGAATCCTCGAATCGATCTGAATAG 58.384 40.000 5.59 0.00 34.61 1.73
2942 3234 0.389817 TGGTCGCTGTTGAATCCTCG 60.390 55.000 0.00 0.00 0.00 4.63
2943 3235 1.079503 GTGGTCGCTGTTGAATCCTC 58.920 55.000 0.00 0.00 0.00 3.71
2947 3239 1.568612 CGCAGTGGTCGCTGTTGAAT 61.569 55.000 12.34 0.00 38.65 2.57
2977 3269 0.466922 ATGCACATGCCCTAAGGAGC 60.467 55.000 0.49 0.00 41.18 4.70
2980 3272 1.679680 CTTCATGCACATGCCCTAAGG 59.320 52.381 5.73 0.00 41.18 2.69
2981 3273 2.357009 GTCTTCATGCACATGCCCTAAG 59.643 50.000 5.73 4.90 41.18 2.18
2983 3275 1.561076 AGTCTTCATGCACATGCCCTA 59.439 47.619 5.73 0.00 41.18 3.53
2996 3315 0.976641 ATGACAGCCGGAAGTCTTCA 59.023 50.000 22.17 9.03 35.81 3.02
3003 3322 0.389817 CTTGTCGATGACAGCCGGAA 60.390 55.000 5.05 0.00 43.69 4.30
3009 3328 2.271800 GCCTAACCTTGTCGATGACAG 58.728 52.381 0.00 0.00 43.69 3.51
3013 3332 0.810031 CCGGCCTAACCTTGTCGATG 60.810 60.000 0.00 0.00 35.61 3.84
3033 3352 0.531974 GCATCGCTCCCATACCGAAA 60.532 55.000 0.00 0.00 34.42 3.46
3035 3354 2.734591 GCATCGCTCCCATACCGA 59.265 61.111 0.00 0.00 35.29 4.69
3062 3381 2.432628 CCAGAACGAGCCACCGAC 60.433 66.667 0.00 0.00 0.00 4.79
3064 3383 4.379243 AGCCAGAACGAGCCACCG 62.379 66.667 0.00 0.00 0.00 4.94
3065 3384 2.743928 CAGCCAGAACGAGCCACC 60.744 66.667 0.00 0.00 0.00 4.61
3067 3386 3.889134 CTGCAGCCAGAACGAGCCA 62.889 63.158 0.00 0.00 41.77 4.75
3081 3400 3.667087 GGAACGACCATTGCTGCA 58.333 55.556 0.00 0.00 38.79 4.41


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

AutoCloner maintained by Alex Coulton.