Multiple sequence alignment - TraesCS3A01G024900

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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 TraesCS3A01G024900 chr3A 100.000 2783 0 0 1 2783 13355972 13353190 0.000000e+00 5140
1 TraesCS3A01G024900 chr3D 92.780 1953 104 13 320 2247 7027450 7029390 0.000000e+00 2791
2 TraesCS3A01G024900 chr3D 90.000 310 20 3 2 302 7026885 7027192 9.350000e-105 390
3 TraesCS3A01G024900 chr3D 89.655 261 24 3 2524 2783 7031081 7031339 2.070000e-86 329
4 TraesCS3A01G024900 chr3B 91.616 1813 106 18 321 2094 8527760 8529565 0.000000e+00 2464
5 TraesCS3A01G024900 chr3B 87.164 483 37 7 2316 2782 8538661 8539134 2.460000e-145 525
6 TraesCS3A01G024900 chr3B 91.946 298 22 1 2 299 8527197 8527492 1.540000e-112 416
7 TraesCS3A01G024900 chr6B 90.217 368 24 8 24 381 645339560 645339195 1.170000e-128 470
8 TraesCS3A01G024900 chr6B 89.296 355 23 8 2 343 336892223 336891871 5.510000e-117 431
9 TraesCS3A01G024900 chr1B 89.014 355 22 11 2 343 179580864 179580514 9.210000e-115 424
10 TraesCS3A01G024900 chr7D 88.968 281 27 2 193 471 109922377 109922655 7.380000e-91 344
11 TraesCS3A01G024900 chr7D 91.053 190 13 2 193 380 60105333 60105146 1.280000e-63 254


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 TraesCS3A01G024900 chr3A 13353190 13355972 2782 True 5140 5140 100.000000 1 2783 1 chr3A.!!$R1 2782
1 TraesCS3A01G024900 chr3D 7026885 7031339 4454 False 1170 2791 90.811667 2 2783 3 chr3D.!!$F1 2781
2 TraesCS3A01G024900 chr3B 8527197 8529565 2368 False 1440 2464 91.781000 2 2094 2 chr3B.!!$F2 2092

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
283 293 0.104671 TTGAACTGCTGGCAAAAGCC 59.895 50.000 0.0 0.0 42.83 4.35 F
1203 1492 1.139734 TGAATCCGAGAGCGACAGC 59.860 57.895 0.0 0.0 45.58 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1524 0.244721 GCCATGTTTCCTGTGCCTTC 59.755 55.0 0.0 0.0 0.0 3.46 R
2734 4446 0.108774 TGGACCGTGTGTTATTGCCA 59.891 50.0 0.0 0.0 0.0 4.92 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
26 27 1.165270 CCTGACCGGAATTGTGGTTC 58.835 55.000 9.46 0.00 38.99 3.62
47 48 3.068729 GCAGGCGAATTTGGGGCTC 62.069 63.158 0.00 0.00 36.88 4.70
148 154 2.424601 ACCGCAATCATTGGATCTGTTG 59.575 45.455 0.00 0.00 31.88 3.33
219 229 1.098050 CCAGCTGCAGTTGTATTCCC 58.902 55.000 26.22 2.06 0.00 3.97
220 230 1.340405 CCAGCTGCAGTTGTATTCCCT 60.340 52.381 26.22 4.44 0.00 4.20
226 236 3.107601 TGCAGTTGTATTCCCTCTAGCT 58.892 45.455 0.00 0.00 0.00 3.32
237 247 1.220206 CTCTAGCTGCCTGGTGGTG 59.780 63.158 0.00 0.00 35.27 4.17
283 293 0.104671 TTGAACTGCTGGCAAAAGCC 59.895 50.000 0.00 0.00 42.83 4.35
302 312 2.622942 GCCTGGATTGTTGTTCTGTTGA 59.377 45.455 0.00 0.00 0.00 3.18
303 313 3.256631 GCCTGGATTGTTGTTCTGTTGAT 59.743 43.478 0.00 0.00 0.00 2.57
308 333 6.680810 TGGATTGTTGTTCTGTTGATTGATC 58.319 36.000 0.00 0.00 0.00 2.92
346 602 8.780249 TGAACCTTTAAGCTACTGTTTTGATAC 58.220 33.333 0.00 0.00 0.00 2.24
360 617 9.436957 ACTGTTTTGATACTAAGTGGATTACAG 57.563 33.333 0.00 0.00 34.51 2.74
381 638 7.923414 ACAGGAATCAGTTTGGTACTATTTC 57.077 36.000 0.00 0.00 34.56 2.17
382 639 7.690256 ACAGGAATCAGTTTGGTACTATTTCT 58.310 34.615 0.00 0.00 34.56 2.52
387 644 9.431887 GAATCAGTTTGGTACTATTTCTGTGTA 57.568 33.333 0.00 0.00 34.56 2.90
395 652 5.984323 GGTACTATTTCTGTGTAGCCTTAGC 59.016 44.000 0.00 0.00 40.32 3.09
417 674 6.049790 AGCTTTAAACGAGTCTCACTTTCTT 58.950 36.000 0.00 0.00 0.00 2.52
491 754 9.620259 AAATATCACTAGTCCCTTGATTTCTTC 57.380 33.333 0.00 0.00 32.24 2.87
581 845 3.181451 ACAGACCTTGTCACATGTGTCAT 60.181 43.478 23.27 11.23 33.87 3.06
592 856 8.028540 TGTCACATGTGTCATGTTAATTAGTC 57.971 34.615 24.63 1.06 0.00 2.59
728 1012 8.462016 GTTAATCTTTTCTTAGACATGCCACAT 58.538 33.333 0.00 0.00 0.00 3.21
881 1170 7.233389 TGATTTACACACTTCTTCTCTAGCT 57.767 36.000 0.00 0.00 0.00 3.32
1203 1492 1.139734 TGAATCCGAGAGCGACAGC 59.860 57.895 0.00 0.00 45.58 4.40
1235 1524 1.219393 GGAAGAGGAAGGACCGCAG 59.781 63.158 0.00 0.00 44.74 5.18
1311 1600 1.203237 AGGTCAAAGAGGAGGAGCTCA 60.203 52.381 17.19 0.00 34.56 4.26
1407 1696 3.077556 AGGAGGAAGCATCGCCGT 61.078 61.111 0.00 0.00 0.00 5.68
1548 1837 1.186200 CCGAGGACAAGATCAGGTCA 58.814 55.000 15.82 0.00 35.74 4.02
1563 1852 1.440145 GGTCAAGGCATAGGAAGCGC 61.440 60.000 0.00 0.00 0.00 5.92
1630 1922 4.828925 GCCACAGGAGCCGCTCTC 62.829 72.222 19.68 10.11 41.15 3.20
1647 1939 3.036819 CTCTCTGTCCTTGGATGATGGA 58.963 50.000 0.00 0.00 0.00 3.41
1653 1945 0.822532 CCTTGGATGATGGAGCTGCC 60.823 60.000 1.53 0.00 37.10 4.85
1699 1991 1.691196 CAAGGGGTCTCACAAAAGCA 58.309 50.000 0.00 0.00 0.00 3.91
1701 1993 1.140312 AGGGGTCTCACAAAAGCAGA 58.860 50.000 0.00 0.00 0.00 4.26
1706 1998 1.604278 GTCTCACAAAAGCAGACACCC 59.396 52.381 0.00 0.00 37.17 4.61
1873 2167 1.250328 TGGCCAGTTGCTGAATGAAG 58.750 50.000 0.00 0.00 40.92 3.02
1958 2253 2.219458 TGTACCGAAACATTTGGCGAA 58.781 42.857 0.00 0.00 0.00 4.70
1991 2286 0.468226 TCCAGCGTTTCCTCTGTTGT 59.532 50.000 0.00 0.00 0.00 3.32
2068 2364 8.756376 CAAGTTCACTATTGCATTTTTGTTTG 57.244 30.769 0.00 0.00 0.00 2.93
2084 2380 3.331150 TGTTTGTTGAGCCATACTACGG 58.669 45.455 0.00 0.00 0.00 4.02
2096 2393 4.433615 CCATACTACGGTGGATCATATGC 58.566 47.826 0.00 0.00 37.72 3.14
2102 2399 2.568956 ACGGTGGATCATATGCTGCTAT 59.431 45.455 0.00 0.00 0.00 2.97
2106 2403 4.323333 GGTGGATCATATGCTGCTATGTCT 60.323 45.833 14.42 7.35 32.13 3.41
2107 2404 5.105187 GGTGGATCATATGCTGCTATGTCTA 60.105 44.000 14.42 9.31 32.13 2.59
2143 2440 3.188048 GGATACTAGCTACGCGTACACAT 59.812 47.826 16.41 4.01 0.00 3.21
2184 2481 4.994471 TGTGGCGGTGCAGCAGAG 62.994 66.667 17.33 0.35 39.27 3.35
2187 2484 3.426568 GGCGGTGCAGCAGAGAAC 61.427 66.667 17.33 0.00 39.27 3.01
2190 2487 0.460987 GCGGTGCAGCAGAGAACTAT 60.461 55.000 17.33 0.00 37.05 2.12
2198 2495 3.999663 GCAGCAGAGAACTATGAAACACT 59.000 43.478 0.46 0.00 0.00 3.55
2199 2496 5.171476 GCAGCAGAGAACTATGAAACACTA 58.829 41.667 0.46 0.00 0.00 2.74
2233 2530 4.013050 GGGCTAGAGCTTTTCTGTTTGAT 58.987 43.478 0.81 0.00 41.70 2.57
2236 2533 5.048434 GGCTAGAGCTTTTCTGTTTGATTGT 60.048 40.000 0.81 0.00 41.70 2.71
2240 2537 6.866480 AGAGCTTTTCTGTTTGATTGTTTGA 58.134 32.000 0.00 0.00 33.93 2.69
2241 2538 7.322664 AGAGCTTTTCTGTTTGATTGTTTGAA 58.677 30.769 0.00 0.00 33.93 2.69
2242 2539 7.983484 AGAGCTTTTCTGTTTGATTGTTTGAAT 59.017 29.630 0.00 0.00 33.93 2.57
2243 2540 7.912383 AGCTTTTCTGTTTGATTGTTTGAATG 58.088 30.769 0.00 0.00 0.00 2.67
2244 2541 6.630045 GCTTTTCTGTTTGATTGTTTGAATGC 59.370 34.615 0.00 0.00 0.00 3.56
2245 2542 7.466320 GCTTTTCTGTTTGATTGTTTGAATGCT 60.466 33.333 0.00 0.00 0.00 3.79
2247 2544 6.831727 TCTGTTTGATTGTTTGAATGCTTG 57.168 33.333 0.00 0.00 0.00 4.01
2249 2546 6.476380 TCTGTTTGATTGTTTGAATGCTTGTC 59.524 34.615 0.00 0.00 0.00 3.18
2250 2547 6.104665 TGTTTGATTGTTTGAATGCTTGTCA 58.895 32.000 0.00 0.00 0.00 3.58
2252 2549 7.924947 TGTTTGATTGTTTGAATGCTTGTCATA 59.075 29.630 0.00 0.00 34.33 2.15
2253 2550 7.872163 TTGATTGTTTGAATGCTTGTCATAC 57.128 32.000 0.00 0.00 34.33 2.39
2254 2551 7.218228 TGATTGTTTGAATGCTTGTCATACT 57.782 32.000 6.86 0.00 34.33 2.12
2255 2552 7.307694 TGATTGTTTGAATGCTTGTCATACTC 58.692 34.615 6.86 0.74 34.33 2.59
2257 2554 5.069318 TGTTTGAATGCTTGTCATACTCCA 58.931 37.500 6.86 0.00 34.33 3.86
2259 2556 5.885230 TTGAATGCTTGTCATACTCCAAG 57.115 39.130 0.00 0.00 40.77 3.61
2260 2557 5.164620 TGAATGCTTGTCATACTCCAAGA 57.835 39.130 3.72 0.00 40.36 3.02
2262 2559 5.645067 TGAATGCTTGTCATACTCCAAGAAG 59.355 40.000 3.72 0.00 40.36 2.85
2263 2560 4.890158 TGCTTGTCATACTCCAAGAAGA 57.110 40.909 3.72 0.00 40.36 2.87
2264 2561 5.227569 TGCTTGTCATACTCCAAGAAGAA 57.772 39.130 3.72 0.00 40.36 2.52
2265 2562 4.997395 TGCTTGTCATACTCCAAGAAGAAC 59.003 41.667 3.72 0.00 40.36 3.01
2266 2563 4.092091 GCTTGTCATACTCCAAGAAGAACG 59.908 45.833 3.72 0.00 40.36 3.95
2267 2564 3.585862 TGTCATACTCCAAGAAGAACGC 58.414 45.455 0.00 0.00 0.00 4.84
2277 2877 2.067365 AGAAGAACGCCCAAAAACCT 57.933 45.000 0.00 0.00 0.00 3.50
2282 2882 2.235155 AGAACGCCCAAAAACCTTTTGT 59.765 40.909 10.15 0.00 0.00 2.83
2289 2889 2.421775 CCAAAAACCTTTTGTTGTGGCC 59.578 45.455 0.00 0.00 36.61 5.36
2291 2891 4.508662 CAAAAACCTTTTGTTGTGGCCTA 58.491 39.130 3.32 0.00 37.23 3.93
2296 2896 3.075432 ACCTTTTGTTGTGGCCTACCTAT 59.925 43.478 3.32 0.00 36.63 2.57
2311 2911 7.092891 TGGCCTACCTATATCACCTTCATATTG 60.093 40.741 3.32 0.00 36.63 1.90
2313 2913 7.125811 GCCTACCTATATCACCTTCATATTGGA 59.874 40.741 7.04 0.00 34.50 3.53
2317 2930 8.164070 ACCTATATCACCTTCATATTGGAAACC 58.836 37.037 7.04 0.00 34.50 3.27
2333 2948 6.620877 TGGAAACCTCTACTCAATGTGTAT 57.379 37.500 0.00 0.00 0.00 2.29
2338 2953 6.458232 ACCTCTACTCAATGTGTATCTGTC 57.542 41.667 0.00 0.00 0.00 3.51
2347 2962 9.973450 ACTCAATGTGTATCTGTCATAATCTAC 57.027 33.333 0.00 0.00 0.00 2.59
2364 2979 8.880750 CATAATCTACCATATGAGCAAGTGATG 58.119 37.037 3.65 0.00 32.43 3.07
2368 2983 7.966812 TCTACCATATGAGCAAGTGATGTAAT 58.033 34.615 3.65 0.00 0.00 1.89
2369 2984 8.090831 TCTACCATATGAGCAAGTGATGTAATC 58.909 37.037 3.65 0.00 45.83 1.75
2388 3003 4.585955 ATCGTGACATATCCACACCTAC 57.414 45.455 0.00 0.00 34.36 3.18
2400 3015 5.113446 TCCACACCTACAAACAACCTTTA 57.887 39.130 0.00 0.00 0.00 1.85
2401 3016 4.883006 TCCACACCTACAAACAACCTTTAC 59.117 41.667 0.00 0.00 0.00 2.01
2402 3017 4.641094 CCACACCTACAAACAACCTTTACA 59.359 41.667 0.00 0.00 0.00 2.41
2404 3019 6.350277 CCACACCTACAAACAACCTTTACAAA 60.350 38.462 0.00 0.00 0.00 2.83
2405 3020 6.750039 CACACCTACAAACAACCTTTACAAAG 59.250 38.462 0.00 0.00 35.79 2.77
2406 3021 6.660094 ACACCTACAAACAACCTTTACAAAGA 59.340 34.615 3.25 0.00 38.28 2.52
2407 3022 7.148137 ACACCTACAAACAACCTTTACAAAGAG 60.148 37.037 3.25 0.00 38.28 2.85
2409 3024 7.612633 ACCTACAAACAACCTTTACAAAGAGAA 59.387 33.333 3.25 0.00 38.28 2.87
2410 3025 7.913821 CCTACAAACAACCTTTACAAAGAGAAC 59.086 37.037 3.25 0.00 38.28 3.01
2411 3026 6.319399 ACAAACAACCTTTACAAAGAGAACG 58.681 36.000 3.25 0.00 38.28 3.95
2413 3028 6.746745 AACAACCTTTACAAAGAGAACGAA 57.253 33.333 3.25 0.00 38.28 3.85
2414 3029 6.359480 ACAACCTTTACAAAGAGAACGAAG 57.641 37.500 3.25 0.00 38.28 3.79
2416 3031 6.258068 ACAACCTTTACAAAGAGAACGAAGAG 59.742 38.462 3.25 0.00 38.28 2.85
2419 3034 6.183360 ACCTTTACAAAGAGAACGAAGAGAGT 60.183 38.462 3.25 0.00 38.28 3.24
2420 3035 6.144724 CCTTTACAAAGAGAACGAAGAGAGTG 59.855 42.308 3.25 0.00 38.28 3.51
2437 3054 1.682854 AGTGCAAACAACACATCCTGG 59.317 47.619 0.00 0.00 40.59 4.45
2448 3065 4.537135 ACACATCCTGGTAGTACACAAG 57.463 45.455 2.06 0.00 0.00 3.16
2461 3078 4.319177 AGTACACAAGAGATGCCTTCAAC 58.681 43.478 0.00 0.00 0.00 3.18
2472 3089 8.148437 AGAGATGCCTTCAACTGATATCATAT 57.852 34.615 5.72 0.00 0.00 1.78
2496 3113 1.462616 TCAACAGTGCAGCAAAGTGT 58.537 45.000 0.00 0.00 32.52 3.55
2498 3115 2.354510 TCAACAGTGCAGCAAAGTGTAC 59.645 45.455 0.00 0.00 33.57 2.90
2520 3137 1.469423 GGTAGTTGCTACACGCTCTCC 60.469 57.143 0.13 0.00 38.58 3.71
2531 3148 2.094494 ACACGCTCTCCACATAACTCAG 60.094 50.000 0.00 0.00 0.00 3.35
2533 3150 1.135915 CGCTCTCCACATAACTCAGCT 59.864 52.381 0.00 0.00 0.00 4.24
2536 3153 4.367450 GCTCTCCACATAACTCAGCTTAG 58.633 47.826 0.00 0.00 0.00 2.18
2537 3154 4.367450 CTCTCCACATAACTCAGCTTAGC 58.633 47.826 0.00 0.00 0.00 3.09
2538 3155 3.769300 TCTCCACATAACTCAGCTTAGCA 59.231 43.478 7.07 0.00 0.00 3.49
2539 3156 4.406972 TCTCCACATAACTCAGCTTAGCAT 59.593 41.667 7.07 0.00 0.00 3.79
2540 3157 5.598417 TCTCCACATAACTCAGCTTAGCATA 59.402 40.000 7.07 0.00 0.00 3.14
2541 3158 6.268617 TCTCCACATAACTCAGCTTAGCATAT 59.731 38.462 7.07 0.00 0.00 1.78
2543 3160 6.268617 TCCACATAACTCAGCTTAGCATATCT 59.731 38.462 7.07 0.00 0.00 1.98
2544 3161 7.451566 TCCACATAACTCAGCTTAGCATATCTA 59.548 37.037 7.07 0.00 0.00 1.98
2545 3162 8.256605 CCACATAACTCAGCTTAGCATATCTAT 58.743 37.037 7.07 0.00 0.00 1.98
2596 4307 0.797542 TTACGCGTATGTTGCAACCC 59.202 50.000 26.14 13.13 0.00 4.11
2597 4308 1.352882 TACGCGTATGTTGCAACCCG 61.353 55.000 26.14 23.58 0.00 5.28
2604 4315 0.538516 ATGTTGCAACCCGTGGCTTA 60.539 50.000 26.14 5.01 0.00 3.09
2611 4323 3.083386 CCCGTGGCTTAAAGGGGA 58.917 61.111 0.00 0.00 44.09 4.81
2650 4362 1.208706 TGGTGACAAGGTCCTTCACA 58.791 50.000 20.53 12.66 37.44 3.58
2722 4434 2.084546 GACCTTGCTATGTTCACCACC 58.915 52.381 0.00 0.00 0.00 4.61
2755 4467 1.400494 GGCAATAACACACGGTCCATC 59.600 52.381 0.00 0.00 0.00 3.51
2756 4468 1.062002 GCAATAACACACGGTCCATCG 59.938 52.381 0.00 0.00 0.00 3.84
2764 4476 3.576356 CGGTCCATCGCCATGCAC 61.576 66.667 0.00 0.00 0.00 4.57
2776 4488 1.430632 CATGCACGCCTGGTTCATC 59.569 57.895 0.00 0.00 29.62 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.377172 CACAATTCCGGTCAGGGTAAATC 59.623 47.826 0.00 0.00 41.52 2.17
26 27 1.216178 CCCCAAATTCGCCTGCAAG 59.784 57.895 0.00 0.00 0.00 4.01
47 48 0.174617 GTCGCTCCTCCTCTTTCCTG 59.825 60.000 0.00 0.00 0.00 3.86
148 154 1.709147 CTCAGCCACGCATAAGCACC 61.709 60.000 0.00 0.00 42.27 5.01
211 221 2.042464 CAGGCAGCTAGAGGGAATACA 58.958 52.381 0.00 0.00 0.00 2.29
212 222 1.346068 CCAGGCAGCTAGAGGGAATAC 59.654 57.143 0.00 0.00 0.00 1.89
219 229 1.220206 CACCACCAGGCAGCTAGAG 59.780 63.158 0.00 0.00 39.06 2.43
220 230 2.293318 CCACCACCAGGCAGCTAGA 61.293 63.158 0.00 0.00 39.06 2.43
226 236 4.269523 GCTGACCACCACCAGGCA 62.270 66.667 0.00 0.00 39.06 4.75
257 267 1.824230 TGCCAGCAGTTCAAACAAACT 59.176 42.857 0.00 0.00 40.08 2.66
283 293 6.075762 TCAATCAACAGAACAACAATCCAG 57.924 37.500 0.00 0.00 0.00 3.86
302 312 2.715046 TCAAGCTTTCGCCAGATCAAT 58.285 42.857 0.00 0.00 36.60 2.57
303 313 2.183478 TCAAGCTTTCGCCAGATCAA 57.817 45.000 0.00 0.00 36.60 2.57
308 333 0.954452 AAGGTTCAAGCTTTCGCCAG 59.046 50.000 0.00 0.00 30.79 4.85
318 343 7.703328 TCAAAACAGTAGCTTAAAGGTTCAAG 58.297 34.615 0.00 0.00 0.00 3.02
346 602 7.066284 CCAAACTGATTCCTGTAATCCACTTAG 59.934 40.741 0.00 0.00 42.97 2.18
360 617 7.390718 ACACAGAAATAGTACCAAACTGATTCC 59.609 37.037 0.00 0.00 39.39 3.01
395 652 8.436200 CCATAAGAAAGTGAGACTCGTTTAAAG 58.564 37.037 0.00 0.00 0.00 1.85
417 674 4.209307 TCGGCAAATACAAGTGACCATA 57.791 40.909 0.00 0.00 0.00 2.74
473 731 5.443230 AAGGGAAGAAATCAAGGGACTAG 57.557 43.478 0.00 0.00 38.49 2.57
491 754 5.538433 TCCCAATTCTCAAACTGTAAAAGGG 59.462 40.000 0.00 0.00 0.00 3.95
553 817 5.469760 CACATGTGACAAGGTCTGTTGATTA 59.530 40.000 21.64 0.00 38.84 1.75
592 856 7.716998 AGATCCTACCAAAAACATATACTGCTG 59.283 37.037 0.00 0.00 0.00 4.41
846 1135 8.507249 AGAAGTGTGTAAATCAAATCAGTAAGC 58.493 33.333 0.00 0.00 0.00 3.09
881 1170 8.484214 ACTGAACATCTAGGATTATCTAGCAA 57.516 34.615 0.00 0.00 37.30 3.91
1203 1492 2.263077 CTCTTCCTGTGTTTCCGATCG 58.737 52.381 8.51 8.51 0.00 3.69
1235 1524 0.244721 GCCATGTTTCCTGTGCCTTC 59.755 55.000 0.00 0.00 0.00 3.46
1311 1600 1.202592 TCGCTCTCATCGCTAGAGTCT 60.203 52.381 0.00 0.00 42.11 3.24
1503 1792 1.592669 GTCTGATGATCGGTGGCGG 60.593 63.158 0.54 0.00 0.00 6.13
1530 1819 2.417924 CCTTGACCTGATCTTGTCCTCG 60.418 54.545 11.17 2.47 0.00 4.63
1563 1852 1.546029 TCCTCGTCACTTGATCTGTGG 59.454 52.381 15.69 5.10 36.21 4.17
1630 1922 1.489649 AGCTCCATCATCCAAGGACAG 59.510 52.381 0.00 0.00 0.00 3.51
1653 1945 0.247460 TCATCTTGTCTGGCTCACCG 59.753 55.000 0.00 0.00 39.70 4.94
1716 2008 2.882761 GTGATCATGATGGTGATGGTGG 59.117 50.000 14.30 0.00 38.88 4.61
1742 2034 1.067516 CACTGGGTTCAGCAAAGTTGG 59.932 52.381 0.00 0.00 44.59 3.77
1748 2040 1.227823 CCGTCACTGGGTTCAGCAA 60.228 57.895 0.00 0.00 44.59 3.91
1787 2079 3.881688 CCAATCAGGTTCTGAGGCATTAG 59.118 47.826 3.94 0.00 44.08 1.73
1858 2152 1.159285 TCGCCTTCATTCAGCAACTG 58.841 50.000 0.00 0.00 0.00 3.16
1873 2167 8.223769 CAGTAACATTATGAAAGATACATCGCC 58.776 37.037 0.00 0.00 0.00 5.54
1918 2213 4.523083 ACAACAAGTACAGGCTTCAGAAA 58.477 39.130 0.00 0.00 0.00 2.52
1943 2238 2.126914 TGGTTTCGCCAAATGTTTCG 57.873 45.000 0.00 0.00 45.94 3.46
1958 2253 3.686016 ACGCTGGAAATAACATCTGGTT 58.314 40.909 0.00 0.00 43.62 3.67
1991 2286 5.047164 ACCAAATCAGCAAGCAAACATATGA 60.047 36.000 10.38 0.00 0.00 2.15
2063 2359 3.244284 ACCGTAGTATGGCTCAACAAACA 60.244 43.478 8.42 0.00 0.00 2.83
2068 2364 1.479323 TCCACCGTAGTATGGCTCAAC 59.521 52.381 8.42 0.00 35.81 3.18
2084 2380 4.829968 AGACATAGCAGCATATGATCCAC 58.170 43.478 6.97 0.00 36.76 4.02
2198 2495 3.370527 GCTCTAGCCCCAACTGAAACATA 60.371 47.826 0.00 0.00 34.31 2.29
2199 2496 2.619074 GCTCTAGCCCCAACTGAAACAT 60.619 50.000 0.00 0.00 34.31 2.71
2205 2502 2.087646 GAAAAGCTCTAGCCCCAACTG 58.912 52.381 0.00 0.00 43.38 3.16
2206 2503 1.988846 AGAAAAGCTCTAGCCCCAACT 59.011 47.619 0.00 0.00 43.38 3.16
2233 2530 5.534278 TGGAGTATGACAAGCATTCAAACAA 59.466 36.000 0.00 0.00 38.44 2.83
2236 2533 6.003326 TCTTGGAGTATGACAAGCATTCAAA 58.997 36.000 0.00 0.00 42.82 2.69
2240 2537 5.809001 TCTTCTTGGAGTATGACAAGCATT 58.191 37.500 0.00 0.00 42.82 3.56
2241 2538 5.426689 TCTTCTTGGAGTATGACAAGCAT 57.573 39.130 0.00 0.00 42.82 3.79
2242 2539 4.890158 TCTTCTTGGAGTATGACAAGCA 57.110 40.909 0.00 0.00 42.82 3.91
2243 2540 4.092091 CGTTCTTCTTGGAGTATGACAAGC 59.908 45.833 0.00 0.00 42.82 4.01
2244 2541 4.092091 GCGTTCTTCTTGGAGTATGACAAG 59.908 45.833 0.00 0.00 44.09 3.16
2245 2542 3.994392 GCGTTCTTCTTGGAGTATGACAA 59.006 43.478 0.00 0.00 0.00 3.18
2247 2544 2.930682 GGCGTTCTTCTTGGAGTATGAC 59.069 50.000 0.00 0.00 0.00 3.06
2249 2546 2.280628 GGGCGTTCTTCTTGGAGTATG 58.719 52.381 0.00 0.00 0.00 2.39
2250 2547 1.906574 TGGGCGTTCTTCTTGGAGTAT 59.093 47.619 0.00 0.00 0.00 2.12
2252 2549 0.472471 TTGGGCGTTCTTCTTGGAGT 59.528 50.000 0.00 0.00 0.00 3.85
2253 2550 1.604604 TTTGGGCGTTCTTCTTGGAG 58.395 50.000 0.00 0.00 0.00 3.86
2254 2551 2.060050 TTTTGGGCGTTCTTCTTGGA 57.940 45.000 0.00 0.00 0.00 3.53
2255 2552 2.469826 GTTTTTGGGCGTTCTTCTTGG 58.530 47.619 0.00 0.00 0.00 3.61
2257 2554 2.384828 AGGTTTTTGGGCGTTCTTCTT 58.615 42.857 0.00 0.00 0.00 2.52
2259 2556 2.882927 AAGGTTTTTGGGCGTTCTTC 57.117 45.000 0.00 0.00 0.00 2.87
2260 2557 3.266636 CAAAAGGTTTTTGGGCGTTCTT 58.733 40.909 6.42 0.00 0.00 2.52
2262 2559 2.623535 ACAAAAGGTTTTTGGGCGTTC 58.376 42.857 16.08 0.00 33.92 3.95
2263 2560 2.744741 CAACAAAAGGTTTTTGGGCGTT 59.255 40.909 16.08 2.00 37.72 4.84
2264 2561 2.289756 ACAACAAAAGGTTTTTGGGCGT 60.290 40.909 16.08 8.61 37.72 5.68
2265 2562 2.095053 CACAACAAAAGGTTTTTGGGCG 59.905 45.455 16.08 8.13 37.72 6.13
2266 2563 2.421775 CCACAACAAAAGGTTTTTGGGC 59.578 45.455 16.08 0.00 37.72 5.36
2267 2564 2.421775 GCCACAACAAAAGGTTTTTGGG 59.578 45.455 16.08 11.06 39.20 4.12
2277 2877 5.883673 GTGATATAGGTAGGCCACAACAAAA 59.116 40.000 5.01 0.00 37.19 2.44
2282 2882 3.936461 AGGTGATATAGGTAGGCCACAA 58.064 45.455 5.01 0.00 37.19 3.33
2291 2891 8.164070 GGTTTCCAATATGAAGGTGATATAGGT 58.836 37.037 0.00 0.00 0.00 3.08
2296 2896 7.451731 AGAGGTTTCCAATATGAAGGTGATA 57.548 36.000 0.00 0.00 0.00 2.15
2311 2911 6.758886 CAGATACACATTGAGTAGAGGTTTCC 59.241 42.308 0.65 0.00 0.00 3.13
2313 2913 7.039011 TGACAGATACACATTGAGTAGAGGTTT 60.039 37.037 0.65 0.00 0.00 3.27
2333 2948 7.781324 TGCTCATATGGTAGATTATGACAGA 57.219 36.000 2.13 0.00 32.75 3.41
2338 2953 8.880750 CATCACTTGCTCATATGGTAGATTATG 58.119 37.037 2.13 0.00 0.00 1.90
2345 2960 6.868339 CGATTACATCACTTGCTCATATGGTA 59.132 38.462 2.13 0.00 0.00 3.25
2347 2962 5.698089 ACGATTACATCACTTGCTCATATGG 59.302 40.000 2.13 0.00 0.00 2.74
2364 2979 4.945246 AGGTGTGGATATGTCACGATTAC 58.055 43.478 0.00 0.00 37.91 1.89
2368 2983 3.358118 TGTAGGTGTGGATATGTCACGA 58.642 45.455 0.00 0.00 37.91 4.35
2369 2984 3.793797 TGTAGGTGTGGATATGTCACG 57.206 47.619 0.00 0.00 37.91 4.35
2388 3003 6.548171 TCGTTCTCTTTGTAAAGGTTGTTTG 58.452 36.000 4.67 0.00 36.67 2.93
2400 3015 3.181475 TGCACTCTCTTCGTTCTCTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
2401 3016 3.384668 TGCACTCTCTTCGTTCTCTTTG 58.615 45.455 0.00 0.00 0.00 2.77
2402 3017 3.735237 TGCACTCTCTTCGTTCTCTTT 57.265 42.857 0.00 0.00 0.00 2.52
2404 3019 3.181475 TGTTTGCACTCTCTTCGTTCTCT 60.181 43.478 0.00 0.00 0.00 3.10
2405 3020 3.123804 TGTTTGCACTCTCTTCGTTCTC 58.876 45.455 0.00 0.00 0.00 2.87
2406 3021 3.179443 TGTTTGCACTCTCTTCGTTCT 57.821 42.857 0.00 0.00 0.00 3.01
2407 3022 3.063452 TGTTGTTTGCACTCTCTTCGTTC 59.937 43.478 0.00 0.00 0.00 3.95
2409 3024 2.351726 GTGTTGTTTGCACTCTCTTCGT 59.648 45.455 0.00 0.00 34.30 3.85
2410 3025 2.351418 TGTGTTGTTTGCACTCTCTTCG 59.649 45.455 0.00 0.00 37.70 3.79
2411 3026 4.531332 GATGTGTTGTTTGCACTCTCTTC 58.469 43.478 0.00 0.00 37.70 2.87
2413 3028 2.880890 GGATGTGTTGTTTGCACTCTCT 59.119 45.455 0.00 0.00 37.70 3.10
2414 3029 2.880890 AGGATGTGTTGTTTGCACTCTC 59.119 45.455 0.00 0.00 37.70 3.20
2416 3031 2.287788 CCAGGATGTGTTGTTTGCACTC 60.288 50.000 0.00 0.00 37.70 3.51
2419 3034 1.774110 ACCAGGATGTGTTGTTTGCA 58.226 45.000 0.00 0.00 0.00 4.08
2420 3035 2.884639 ACTACCAGGATGTGTTGTTTGC 59.115 45.455 0.00 0.00 0.00 3.68
2437 3054 5.073311 TGAAGGCATCTCTTGTGTACTAC 57.927 43.478 0.00 0.00 0.00 2.73
2448 3065 9.881649 TTATATGATATCAGTTGAAGGCATCTC 57.118 33.333 11.78 0.00 0.00 2.75
2461 3078 9.264719 TGCACTGTTGAACTTATATGATATCAG 57.735 33.333 11.78 0.00 0.00 2.90
2472 3089 3.694072 ACTTTGCTGCACTGTTGAACTTA 59.306 39.130 0.00 0.00 0.00 2.24
2484 3101 2.104111 ACTACCAGTACACTTTGCTGCA 59.896 45.455 0.00 0.00 36.64 4.41
2565 4276 6.032722 ACATACGCGTAATCTTGAATTGAC 57.967 37.500 24.55 0.00 0.00 3.18
2567 4278 5.169561 GCAACATACGCGTAATCTTGAATTG 59.830 40.000 24.55 17.05 0.00 2.32
2568 4279 5.163804 TGCAACATACGCGTAATCTTGAATT 60.164 36.000 24.55 5.43 0.00 2.17
2574 4285 2.350498 GGTTGCAACATACGCGTAATCT 59.650 45.455 29.55 3.65 0.00 2.40
2596 4307 1.102978 CCATTCCCCTTTAAGCCACG 58.897 55.000 0.00 0.00 0.00 4.94
2597 4308 1.485124 CCCATTCCCCTTTAAGCCAC 58.515 55.000 0.00 0.00 0.00 5.01
2604 4315 2.944390 TCGCCCCCATTCCCCTTT 60.944 61.111 0.00 0.00 0.00 3.11
2611 4323 1.682344 GCTTTTCCTCGCCCCCATT 60.682 57.895 0.00 0.00 0.00 3.16
2647 4359 1.909700 ACACCTTTGGTAGCCATGTG 58.090 50.000 9.77 9.77 35.48 3.21
2650 4362 2.617021 CGGTTACACCTTTGGTAGCCAT 60.617 50.000 0.00 0.00 40.81 4.40
2734 4446 0.108774 TGGACCGTGTGTTATTGCCA 59.891 50.000 0.00 0.00 0.00 4.92
2740 4452 1.079681 GGCGATGGACCGTGTGTTA 60.080 57.895 0.00 0.00 0.00 2.41
2743 4455 2.125147 ATGGCGATGGACCGTGTG 60.125 61.111 0.00 0.00 0.00 3.82
2744 4456 2.125147 CATGGCGATGGACCGTGT 60.125 61.111 0.00 0.00 39.04 4.49
2746 4458 4.094646 TGCATGGCGATGGACCGT 62.095 61.111 10.93 0.00 0.00 4.83
2764 4476 1.519455 GAGGACGATGAACCAGGCG 60.519 63.158 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.