Multiple sequence alignment - TraesCS1A01G339200

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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 TraesCS1A01G339200 chr1A 100.000 2615 0 0 1 2615 529244257 529241643 0.000000e+00 4830
1 TraesCS1A01G339200 chr1D 90.116 2074 133 37 1 2032 430976888 430974845 0.000000e+00 2628
2 TraesCS1A01G339200 chr1D 94.256 383 12 6 2227 2609 430974744 430974372 6.280000e-161 577
3 TraesCS1A01G339200 chr1D 91.892 74 2 1 2160 2229 430974838 430974765 1.660000e-17 100
4 TraesCS1A01G339200 chr1B 88.862 2056 129 41 56 2041 582092664 582090639 0.000000e+00 2436
5 TraesCS1A01G339200 chr1B 96.610 59 2 0 1 59 582092744 582092686 5.960000e-17 99


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 TraesCS1A01G339200 chr1A 529241643 529244257 2614 True 4830.000000 4830 100.000 1 2615 1 chr1A.!!$R1 2614
1 TraesCS1A01G339200 chr1D 430974372 430976888 2516 True 1101.666667 2628 92.088 1 2609 3 chr1D.!!$R1 2608
2 TraesCS1A01G339200 chr1B 582090639 582092744 2105 True 1267.500000 2436 92.736 1 2041 2 chr1B.!!$R1 2040

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
430 519 0.178981 AAACTGCCTGCACACTCCAT 60.179 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2285 0.322546 GGCGGTTTCCAAGTGGATCT 60.323 55.0 0.0 0.0 44.98 2.75 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
148 182 9.209175 GTTATTATGTGATGTGAGGACTAATCC 57.791 37.037 0.00 0.00 46.69 3.01
165 199 0.535335 TCCCAGCATTGACGGTCTAC 59.465 55.000 9.88 0.00 0.00 2.59
215 250 4.806330 TGCTCTTAGACTTTTCGTTCGAT 58.194 39.130 0.00 0.00 0.00 3.59
242 283 3.040147 TGGATTCTGTCGTTTCTCACC 57.960 47.619 0.00 0.00 0.00 4.02
258 301 6.834168 TTCTCACCCTAATTTTGGTTCATC 57.166 37.500 0.00 0.00 30.70 2.92
263 306 4.644685 ACCCTAATTTTGGTTCATCATCCG 59.355 41.667 0.00 0.00 0.00 4.18
289 332 2.032071 GTGGCCACGCAGGTAAGT 59.968 61.111 22.49 0.00 40.61 2.24
311 354 3.540314 TGGCAACTTGAAACTGCATTT 57.460 38.095 0.00 0.00 37.83 2.32
333 376 6.484818 TTTGCGTAGTTATTTGACCCTAAC 57.515 37.500 0.00 0.00 0.00 2.34
337 380 4.162888 CGTAGTTATTTGACCCTAACCCCT 59.837 45.833 0.00 0.00 0.00 4.79
342 385 2.563039 TTGACCCTAACCCCTCCTAG 57.437 55.000 0.00 0.00 0.00 3.02
355 398 9.382307 CTAACCCCTCCTAGAAATCTAAACTAT 57.618 37.037 0.00 0.00 0.00 2.12
374 439 1.153147 GGGTTAGGTGCAGCTAGCC 60.153 63.158 36.93 36.93 44.83 3.93
386 475 1.069935 GCTAGCCCCTGACGGAATC 59.930 63.158 2.29 0.00 0.00 2.52
387 476 1.403687 GCTAGCCCCTGACGGAATCT 61.404 60.000 2.29 0.00 0.00 2.40
390 479 1.807814 AGCCCCTGACGGAATCTAAT 58.192 50.000 0.00 0.00 0.00 1.73
392 481 2.158755 AGCCCCTGACGGAATCTAATTG 60.159 50.000 0.00 0.00 0.00 2.32
394 483 2.421388 CCCCTGACGGAATCTAATTGCA 60.421 50.000 0.00 0.00 0.00 4.08
395 484 3.480470 CCCTGACGGAATCTAATTGCAT 58.520 45.455 0.00 0.00 0.00 3.96
396 485 4.504864 CCCCTGACGGAATCTAATTGCATA 60.505 45.833 0.00 0.00 0.00 3.14
397 486 5.248640 CCCTGACGGAATCTAATTGCATAT 58.751 41.667 0.00 0.00 0.00 1.78
398 487 6.406370 CCCTGACGGAATCTAATTGCATATA 58.594 40.000 0.00 0.00 0.00 0.86
399 488 6.878923 CCCTGACGGAATCTAATTGCATATAA 59.121 38.462 0.00 0.00 0.00 0.98
401 490 8.950210 CCTGACGGAATCTAATTGCATATAAAT 58.050 33.333 0.00 0.00 0.00 1.40
405 494 8.893727 ACGGAATCTAATTGCATATAAATAGGC 58.106 33.333 0.00 0.00 40.21 3.93
406 495 8.892723 CGGAATCTAATTGCATATAAATAGGCA 58.107 33.333 5.28 5.28 46.71 4.75
417 506 9.474920 TGCATATAAATAGGCAAATAAAACTGC 57.525 29.630 6.84 0.00 45.61 4.40
424 513 2.753296 GCAAATAAAACTGCCTGCACA 58.247 42.857 0.00 0.00 32.18 4.57
425 514 2.476241 GCAAATAAAACTGCCTGCACAC 59.524 45.455 0.00 0.00 32.18 3.82
426 515 3.799917 GCAAATAAAACTGCCTGCACACT 60.800 43.478 0.00 0.00 32.18 3.55
427 516 3.923017 AATAAAACTGCCTGCACACTC 57.077 42.857 0.00 0.00 0.00 3.51
428 517 1.604604 TAAAACTGCCTGCACACTCC 58.395 50.000 0.00 0.00 0.00 3.85
429 518 0.395586 AAAACTGCCTGCACACTCCA 60.396 50.000 0.00 0.00 0.00 3.86
430 519 0.178981 AAACTGCCTGCACACTCCAT 60.179 50.000 0.00 0.00 0.00 3.41
431 520 0.178981 AACTGCCTGCACACTCCATT 60.179 50.000 0.00 0.00 0.00 3.16
432 521 0.607489 ACTGCCTGCACACTCCATTC 60.607 55.000 0.00 0.00 0.00 2.67
545 638 0.652592 CAGGTCGCGAATGATTGGTC 59.347 55.000 12.06 0.00 0.00 4.02
578 671 1.755179 ACCCGATCTGCCATTTCTTG 58.245 50.000 0.00 0.00 0.00 3.02
603 696 0.396435 TTGCAACCGTCACTCCATCT 59.604 50.000 0.00 0.00 0.00 2.90
678 775 6.490381 TGTCCTAGAAGCAGATAACGATGTAT 59.510 38.462 0.00 0.00 0.00 2.29
713 810 4.292977 TCGCTGTCACTGACATATAGTG 57.707 45.455 12.34 7.67 41.94 2.74
720 817 7.639113 TGTCACTGACATATAGTGTGATGTA 57.361 36.000 7.84 0.00 44.49 2.29
756 853 4.896562 TTCACAAGTATCGCGTAGTTTG 57.103 40.909 5.77 10.02 0.00 2.93
757 854 3.247442 TCACAAGTATCGCGTAGTTTGG 58.753 45.455 5.77 2.57 0.00 3.28
771 868 5.798434 GCGTAGTTTGGTTTTGAATATGACC 59.202 40.000 0.00 0.00 0.00 4.02
772 869 6.349033 GCGTAGTTTGGTTTTGAATATGACCT 60.349 38.462 0.00 0.00 33.33 3.85
806 903 1.127397 CAACACAGAGCAGCACGTATG 59.873 52.381 0.00 0.00 0.00 2.39
824 922 5.803967 ACGTATGAGTCGATTGTTAAAGTCC 59.196 40.000 0.00 0.00 0.00 3.85
936 1038 2.570181 CCCCCTACGTCACGTCAC 59.430 66.667 5.85 0.00 41.54 3.67
1018 1120 2.503846 AATGGCTTGCCTGGCTGCTA 62.504 55.000 26.73 23.68 0.00 3.49
1024 1126 2.030262 GCCTGGCTGCTATCGGAG 59.970 66.667 12.43 0.00 0.00 4.63
1039 1141 0.106894 CGGAGATAGTTTCCTGGCCC 59.893 60.000 0.00 0.00 32.34 5.80
1134 1245 1.364171 GCCGGATCAGCTGTACGAT 59.636 57.895 22.17 7.11 0.00 3.73
1238 1349 4.808238 GGCGTCCTCGTCGTCGAC 62.808 72.222 15.51 15.51 41.35 4.20
1288 1399 0.032017 TGGCTTCCTCTCCTACCCTC 60.032 60.000 0.00 0.00 0.00 4.30
1295 1406 2.522193 CTCCTACCCTCCCGCCTC 60.522 72.222 0.00 0.00 0.00 4.70
1434 1548 4.766088 CTTTGCTGCGGCTTCGGC 62.766 66.667 20.27 1.36 39.59 5.54
1529 1643 4.641094 GTCGTCTCCGATTGATATCCCTAT 59.359 45.833 0.00 0.00 46.30 2.57
1539 1653 3.779444 TGATATCCCTATCGGACTTGCT 58.221 45.455 0.00 0.00 46.09 3.91
1540 1654 3.511540 TGATATCCCTATCGGACTTGCTG 59.488 47.826 0.00 0.00 46.09 4.41
1541 1655 0.394565 ATCCCTATCGGACTTGCTGC 59.605 55.000 0.00 0.00 46.09 5.25
1542 1656 1.227674 CCCTATCGGACTTGCTGCC 60.228 63.158 0.00 0.00 0.00 4.85
1544 1658 2.202878 TATCGGACTTGCTGCCGC 60.203 61.111 0.00 0.00 46.79 6.53
1545 1659 3.733344 TATCGGACTTGCTGCCGCC 62.733 63.158 0.00 0.00 46.79 6.13
1605 1719 1.081376 GCACCGTCGATCGATAGGG 60.081 63.158 31.93 27.73 42.86 3.53
1610 1728 1.874562 GTCGATCGATAGGGACGGG 59.125 63.158 22.50 0.00 0.00 5.28
1619 1737 2.037144 GATAGGGACGGGTTAAGCTCA 58.963 52.381 4.41 0.00 0.00 4.26
1624 1742 1.206371 GGACGGGTTAAGCTCAGCTAA 59.794 52.381 0.00 0.00 38.25 3.09
1626 1744 3.124560 GACGGGTTAAGCTCAGCTAATC 58.875 50.000 0.00 0.00 38.25 1.75
1787 1906 8.164070 AGTAGTGAGGAAAAGATATTGTTGGTT 58.836 33.333 0.00 0.00 0.00 3.67
1858 2003 1.205179 TGGCAATGTGATTGTGATGGC 59.795 47.619 0.00 0.00 42.20 4.40
1885 2030 1.337167 GGAATGTGGTCTTTTGCTGCC 60.337 52.381 0.00 0.00 0.00 4.85
1919 2064 1.933853 ACTGTGCACGAACTCTCAAAC 59.066 47.619 13.13 0.00 0.00 2.93
1922 2067 0.878523 TGCACGAACTCTCAAACCGG 60.879 55.000 0.00 0.00 0.00 5.28
1925 2070 1.038280 ACGAACTCTCAAACCGGACT 58.962 50.000 9.46 0.00 0.00 3.85
1946 2091 5.727434 ACTAAATCCGTGGATACTTTTCGT 58.273 37.500 0.96 0.00 33.97 3.85
1963 2108 1.739196 GTAGGGTTTGGCGGTCGAC 60.739 63.158 7.13 7.13 0.00 4.20
2056 2207 2.407268 CAGACTTGCAGTGCCAACA 58.593 52.632 13.72 0.00 0.00 3.33
2057 2208 0.956633 CAGACTTGCAGTGCCAACAT 59.043 50.000 13.72 0.00 0.00 2.71
2058 2209 2.153645 CAGACTTGCAGTGCCAACATA 58.846 47.619 13.72 0.00 0.00 2.29
2059 2210 2.095567 CAGACTTGCAGTGCCAACATAC 60.096 50.000 13.72 0.00 0.00 2.39
2060 2211 2.154462 GACTTGCAGTGCCAACATACT 58.846 47.619 13.72 0.00 0.00 2.12
2061 2212 1.881973 ACTTGCAGTGCCAACATACTG 59.118 47.619 13.72 0.00 45.40 2.74
2064 2215 2.945510 CAGTGCCAACATACTGCCA 58.054 52.632 0.00 0.00 38.01 4.92
2065 2216 0.806868 CAGTGCCAACATACTGCCAG 59.193 55.000 0.00 0.00 38.01 4.85
2066 2217 0.322816 AGTGCCAACATACTGCCAGG 60.323 55.000 0.00 0.00 0.00 4.45
2067 2218 1.001020 TGCCAACATACTGCCAGGG 60.001 57.895 0.00 0.00 0.00 4.45
2068 2219 2.418083 GCCAACATACTGCCAGGGC 61.418 63.158 2.62 2.62 42.35 5.19
2078 2229 4.764143 GCCAGGGCACAAACCTAT 57.236 55.556 5.20 0.00 41.49 2.57
2079 2230 3.894742 GCCAGGGCACAAACCTATA 57.105 52.632 5.20 0.00 41.49 1.31
2080 2231 2.364972 GCCAGGGCACAAACCTATAT 57.635 50.000 5.20 0.00 41.49 0.86
2081 2232 1.956477 GCCAGGGCACAAACCTATATG 59.044 52.381 5.20 0.00 41.49 1.78
2082 2233 1.956477 CCAGGGCACAAACCTATATGC 59.044 52.381 0.00 0.00 36.32 3.14
2085 2236 3.845625 GCACAAACCTATATGCCGC 57.154 52.632 0.00 0.00 31.71 6.53
2086 2237 1.308998 GCACAAACCTATATGCCGCT 58.691 50.000 0.00 0.00 31.71 5.52
2087 2238 1.002468 GCACAAACCTATATGCCGCTG 60.002 52.381 0.00 0.00 31.71 5.18
2088 2239 2.288666 CACAAACCTATATGCCGCTGT 58.711 47.619 0.00 0.00 0.00 4.40
2089 2240 2.287915 CACAAACCTATATGCCGCTGTC 59.712 50.000 0.00 0.00 0.00 3.51
2090 2241 2.093181 ACAAACCTATATGCCGCTGTCA 60.093 45.455 0.00 0.00 0.00 3.58
2091 2242 2.942376 CAAACCTATATGCCGCTGTCAA 59.058 45.455 0.00 0.00 0.00 3.18
2092 2243 3.492102 AACCTATATGCCGCTGTCAAT 57.508 42.857 0.00 0.00 0.00 2.57
2093 2244 3.045601 ACCTATATGCCGCTGTCAATC 57.954 47.619 0.00 0.00 0.00 2.67
2094 2245 1.995484 CCTATATGCCGCTGTCAATCG 59.005 52.381 0.00 0.00 0.00 3.34
2095 2246 2.610479 CCTATATGCCGCTGTCAATCGT 60.610 50.000 0.00 0.00 0.00 3.73
2096 2247 2.812358 ATATGCCGCTGTCAATCGTA 57.188 45.000 0.00 0.00 0.00 3.43
2097 2248 2.812358 TATGCCGCTGTCAATCGTAT 57.188 45.000 0.00 0.00 0.00 3.06
2098 2249 2.812358 ATGCCGCTGTCAATCGTATA 57.188 45.000 0.00 0.00 0.00 1.47
2099 2250 2.812358 TGCCGCTGTCAATCGTATAT 57.188 45.000 0.00 0.00 0.00 0.86
2100 2251 3.926821 TGCCGCTGTCAATCGTATATA 57.073 42.857 0.00 0.00 0.00 0.86
2101 2252 4.450082 TGCCGCTGTCAATCGTATATAT 57.550 40.909 0.00 0.00 0.00 0.86
2102 2253 5.570234 TGCCGCTGTCAATCGTATATATA 57.430 39.130 0.00 0.00 0.00 0.86
2103 2254 6.144078 TGCCGCTGTCAATCGTATATATAT 57.856 37.500 0.00 0.00 0.00 0.86
2104 2255 7.266922 TGCCGCTGTCAATCGTATATATATA 57.733 36.000 0.00 0.00 0.00 0.86
2105 2256 7.882179 TGCCGCTGTCAATCGTATATATATAT 58.118 34.615 10.10 10.10 0.00 0.86
2106 2257 7.807907 TGCCGCTGTCAATCGTATATATATATG 59.192 37.037 14.42 13.73 0.00 1.78
2107 2258 7.201359 GCCGCTGTCAATCGTATATATATATGC 60.201 40.741 14.42 12.13 0.00 3.14
2108 2259 7.273598 CCGCTGTCAATCGTATATATATATGCC 59.726 40.741 14.42 5.18 0.00 4.40
2109 2260 7.273598 CGCTGTCAATCGTATATATATATGCCC 59.726 40.741 14.42 3.06 0.00 5.36
2110 2261 8.088365 GCTGTCAATCGTATATATATATGCCCA 58.912 37.037 14.42 3.24 0.00 5.36
2111 2262 9.981114 CTGTCAATCGTATATATATATGCCCAA 57.019 33.333 14.42 2.56 0.00 4.12
2112 2263 9.981114 TGTCAATCGTATATATATATGCCCAAG 57.019 33.333 14.42 2.26 0.00 3.61
2113 2264 9.982651 GTCAATCGTATATATATATGCCCAAGT 57.017 33.333 14.42 0.00 0.00 3.16
2125 2276 8.948401 ATATATGCCCAAGTAGATAGATCGAT 57.052 34.615 0.00 0.00 0.00 3.59
2126 2277 5.590530 ATGCCCAAGTAGATAGATCGATC 57.409 43.478 17.91 17.91 0.00 3.69
2127 2278 4.667573 TGCCCAAGTAGATAGATCGATCT 58.332 43.478 29.58 29.58 39.54 2.75
2128 2279 5.816682 TGCCCAAGTAGATAGATCGATCTA 58.183 41.667 31.66 31.66 43.00 1.98
2154 2305 2.114411 TCCACTTGGAAACCGCCC 59.886 61.111 0.00 0.00 42.18 6.13
2155 2306 2.989253 CCACTTGGAAACCGCCCC 60.989 66.667 0.00 0.00 37.39 5.80
2156 2307 2.989253 CACTTGGAAACCGCCCCC 60.989 66.667 0.00 0.00 0.00 5.40
2157 2308 3.182996 ACTTGGAAACCGCCCCCT 61.183 61.111 0.00 0.00 0.00 4.79
2158 2309 2.361230 CTTGGAAACCGCCCCCTC 60.361 66.667 0.00 0.00 0.00 4.30
2159 2310 3.938637 CTTGGAAACCGCCCCCTCC 62.939 68.421 0.00 0.00 0.00 4.30
2261 2439 3.406764 GGATGAACAGAGCACTCTTGTT 58.593 45.455 12.33 12.33 37.98 2.83
2262 2440 3.188048 GGATGAACAGAGCACTCTTGTTG 59.812 47.826 15.49 2.76 37.98 3.33
2266 2444 3.819564 ACAGAGCACTCTTGTTGTACA 57.180 42.857 0.00 0.00 37.98 2.90
2327 2505 3.181487 GGCATCACATACATTTGGTGTCC 60.181 47.826 0.00 0.00 42.29 4.02
2339 2517 7.639113 ACATTTGGTGTCCATTTATCGTTAT 57.361 32.000 0.00 0.00 35.77 1.89
2340 2518 8.740123 ACATTTGGTGTCCATTTATCGTTATA 57.260 30.769 0.00 0.00 35.77 0.98
2381 2559 8.478877 TGGAACAAGTTAAACACACCATAATTT 58.521 29.630 0.00 0.00 31.92 1.82
2382 2560 9.968870 GGAACAAGTTAAACACACCATAATTTA 57.031 29.630 0.00 0.00 0.00 1.40
2431 2609 9.613428 CTATAGTTTGTTTATCCTGAACCATGA 57.387 33.333 0.00 0.00 0.00 3.07
2503 2681 3.677190 GCTTCAGCATTCTCTCACATG 57.323 47.619 0.00 0.00 41.59 3.21
2504 2682 2.223294 GCTTCAGCATTCTCTCACATGC 60.223 50.000 0.00 0.00 45.30 4.06
2532 2710 1.009078 CACGTGCATGGTCAATCGAT 58.991 50.000 11.36 0.00 0.00 3.59
2541 2719 6.033831 GTGCATGGTCAATCGATTTTTAGTTG 59.966 38.462 8.21 3.92 0.00 3.16
2548 2726 6.636850 GTCAATCGATTTTTAGTTGCACTTGT 59.363 34.615 8.21 0.00 0.00 3.16
2609 2787 5.119125 GCCACAAAATTAATCAACTCAGCAC 59.881 40.000 0.00 0.00 0.00 4.40
2610 2788 6.449698 CCACAAAATTAATCAACTCAGCACT 58.550 36.000 0.00 0.00 0.00 4.40
2611 2789 7.592938 CCACAAAATTAATCAACTCAGCACTA 58.407 34.615 0.00 0.00 0.00 2.74
2612 2790 7.538678 CCACAAAATTAATCAACTCAGCACTAC 59.461 37.037 0.00 0.00 0.00 2.73
2613 2791 7.538678 CACAAAATTAATCAACTCAGCACTACC 59.461 37.037 0.00 0.00 0.00 3.18
2614 2792 7.230510 ACAAAATTAATCAACTCAGCACTACCA 59.769 33.333 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 173 2.213499 CGTCAATGCTGGGATTAGTCC 58.787 52.381 0.00 0.00 44.29 3.85
148 182 3.065575 GGTAGACCGTCAATGCTGG 57.934 57.895 0.40 0.00 0.00 4.85
165 199 1.301677 GAGCTTCCAGAAACCAGCGG 61.302 60.000 0.00 0.00 37.35 5.52
200 234 2.767505 AGCCAATCGAACGAAAAGTCT 58.232 42.857 0.12 0.00 0.00 3.24
215 250 2.270352 ACGACAGAATCCAAAGCCAA 57.730 45.000 0.00 0.00 0.00 4.52
242 283 6.639632 ATCGGATGATGAACCAAAATTAGG 57.360 37.500 0.00 0.00 32.21 2.69
258 301 1.430632 GCCACAGTGCAATCGGATG 59.569 57.895 3.37 0.00 0.00 3.51
263 306 2.562912 CGTGGCCACAGTGCAATC 59.437 61.111 34.16 5.35 0.00 2.67
289 332 4.870123 AATGCAGTTTCAAGTTGCCATA 57.130 36.364 0.00 0.00 37.03 2.74
311 354 4.937015 GGTTAGGGTCAAATAACTACGCAA 59.063 41.667 0.00 0.00 33.36 4.85
333 376 6.013293 CCCATAGTTTAGATTTCTAGGAGGGG 60.013 46.154 0.00 0.00 0.00 4.79
337 380 9.155785 CCTAACCCATAGTTTAGATTTCTAGGA 57.844 37.037 0.00 0.00 40.05 2.94
342 385 6.826741 TGCACCTAACCCATAGTTTAGATTTC 59.173 38.462 0.00 0.00 40.05 2.17
355 398 1.602237 GCTAGCTGCACCTAACCCA 59.398 57.895 7.70 0.00 42.31 4.51
374 439 2.917933 TGCAATTAGATTCCGTCAGGG 58.082 47.619 0.00 0.00 38.33 4.45
404 493 2.476241 GTGTGCAGGCAGTTTTATTTGC 59.524 45.455 0.00 0.00 39.56 3.68
405 494 3.981211 AGTGTGCAGGCAGTTTTATTTG 58.019 40.909 0.00 0.00 0.00 2.32
406 495 3.005791 GGAGTGTGCAGGCAGTTTTATTT 59.994 43.478 0.00 0.00 0.00 1.40
407 496 2.558359 GGAGTGTGCAGGCAGTTTTATT 59.442 45.455 0.00 0.00 0.00 1.40
408 497 2.162681 GGAGTGTGCAGGCAGTTTTAT 58.837 47.619 0.00 0.00 0.00 1.40
409 498 1.133945 TGGAGTGTGCAGGCAGTTTTA 60.134 47.619 0.00 0.00 0.00 1.52
410 499 0.395586 TGGAGTGTGCAGGCAGTTTT 60.396 50.000 0.00 0.00 0.00 2.43
411 500 0.178981 ATGGAGTGTGCAGGCAGTTT 60.179 50.000 0.00 0.00 0.00 2.66
412 501 0.178981 AATGGAGTGTGCAGGCAGTT 60.179 50.000 0.00 0.00 0.00 3.16
413 502 0.607489 GAATGGAGTGTGCAGGCAGT 60.607 55.000 0.00 0.00 0.00 4.40
414 503 0.607217 TGAATGGAGTGTGCAGGCAG 60.607 55.000 0.00 0.00 0.00 4.85
415 504 0.607217 CTGAATGGAGTGTGCAGGCA 60.607 55.000 0.00 0.00 0.00 4.75
416 505 1.310933 CCTGAATGGAGTGTGCAGGC 61.311 60.000 0.00 0.00 39.60 4.85
417 506 1.310933 GCCTGAATGGAGTGTGCAGG 61.311 60.000 0.00 0.00 46.82 4.85
418 507 1.642037 CGCCTGAATGGAGTGTGCAG 61.642 60.000 0.00 0.00 38.35 4.41
419 508 1.672030 CGCCTGAATGGAGTGTGCA 60.672 57.895 0.00 0.00 38.35 4.57
420 509 3.181367 CGCCTGAATGGAGTGTGC 58.819 61.111 0.00 0.00 38.35 4.57
425 514 3.805267 GCTCACGCCTGAATGGAG 58.195 61.111 0.00 0.00 41.69 3.86
545 638 2.515290 GGGTTAATCCGGTGGGCG 60.515 66.667 0.00 0.00 37.00 6.13
563 656 1.796617 GCGCACAAGAAATGGCAGATC 60.797 52.381 0.30 0.00 0.00 2.75
616 709 6.763715 TTGCAATAGATGGGGAATACTACT 57.236 37.500 0.00 0.00 0.00 2.57
617 710 7.168219 TGATTGCAATAGATGGGGAATACTAC 58.832 38.462 12.97 0.00 0.00 2.73
678 775 5.048782 AGTGACAGCGATTTTTGCAGAAATA 60.049 36.000 14.61 0.00 33.85 1.40
713 810 8.958043 GTGAAAGAAACAAAACTGATACATCAC 58.042 33.333 0.00 0.00 32.50 3.06
720 817 9.736023 GATACTTGTGAAAGAAACAAAACTGAT 57.264 29.630 0.00 0.00 37.10 2.90
756 853 5.343307 AATGCCAGGTCATATTCAAAACC 57.657 39.130 0.00 0.00 0.00 3.27
757 854 5.516339 CGAAATGCCAGGTCATATTCAAAAC 59.484 40.000 0.00 0.00 0.00 2.43
795 892 1.256376 CAATCGACTCATACGTGCTGC 59.744 52.381 0.00 0.00 0.00 5.25
806 903 2.991190 TGCGGACTTTAACAATCGACTC 59.009 45.455 0.00 0.00 0.00 3.36
824 922 1.063006 CCTCATGCCGTTCAATGCG 59.937 57.895 0.00 0.00 0.00 4.73
855 953 2.840176 CGCAAAATGACAGATTACGCAC 59.160 45.455 0.00 0.00 0.00 5.34
859 961 3.685058 GCTCCGCAAAATGACAGATTAC 58.315 45.455 0.00 0.00 0.00 1.89
893 995 3.197549 TCCTGGCCTTGATTAAATTTGGC 59.802 43.478 3.32 3.64 39.61 4.52
1018 1120 1.694696 GGCCAGGAAACTATCTCCGAT 59.305 52.381 0.00 0.00 40.21 4.18
1024 1126 0.106894 CCTCGGGCCAGGAAACTATC 59.893 60.000 14.67 0.00 40.21 2.08
1158 1269 1.389204 CGAACGACTCGCACGAGAAG 61.389 60.000 25.53 19.07 44.53 2.85
1234 1345 4.595538 AAACGGCAGCACGGTCGA 62.596 61.111 1.02 0.00 38.35 4.20
1238 1349 4.326766 CACCAAACGGCAGCACGG 62.327 66.667 7.98 0.00 38.39 4.94
1317 1428 3.391665 CTCCTCCGCCATGTCACCC 62.392 68.421 0.00 0.00 0.00 4.61
1362 1473 2.575262 GGCTCGTAACCGTCGTCG 60.575 66.667 0.00 0.00 35.01 5.12
1605 1719 2.667473 TTAGCTGAGCTTAACCCGTC 57.333 50.000 14.14 0.00 40.44 4.79
1610 1728 4.054671 AGCATCGATTAGCTGAGCTTAAC 58.945 43.478 14.14 0.51 40.44 2.01
1619 1737 5.627499 TGAAACAAAAGCATCGATTAGCT 57.373 34.783 4.49 4.49 44.31 3.32
1624 1742 7.115378 GTGAAGAAATGAAACAAAAGCATCGAT 59.885 33.333 0.00 0.00 0.00 3.59
1626 1744 6.346040 GGTGAAGAAATGAAACAAAAGCATCG 60.346 38.462 0.00 0.00 0.00 3.84
1705 1824 7.547722 TCGCCCGTAATTCGTAGTTATATAGTA 59.452 37.037 0.00 0.00 37.94 1.82
1706 1825 6.371548 TCGCCCGTAATTCGTAGTTATATAGT 59.628 38.462 0.00 0.00 37.94 2.12
1707 1826 6.775088 TCGCCCGTAATTCGTAGTTATATAG 58.225 40.000 0.00 0.00 37.94 1.31
1726 1845 2.093658 TGATTTCTAACACCTCTCGCCC 60.094 50.000 0.00 0.00 0.00 6.13
1858 2003 0.606401 AAGACCACATTCCCTGCGTG 60.606 55.000 0.00 0.00 0.00 5.34
1862 2007 2.029649 CAGCAAAAGACCACATTCCCTG 60.030 50.000 0.00 0.00 0.00 4.45
1922 2067 5.809051 ACGAAAAGTATCCACGGATTTAGTC 59.191 40.000 3.41 0.00 36.17 2.59
1925 2070 6.275335 CCTACGAAAAGTATCCACGGATTTA 58.725 40.000 3.41 0.00 36.17 1.40
1932 2077 4.393990 CCAAACCCTACGAAAAGTATCCAC 59.606 45.833 0.00 0.00 34.34 4.02
1943 2088 2.658422 GACCGCCAAACCCTACGA 59.342 61.111 0.00 0.00 0.00 3.43
1946 2091 2.658422 GTCGACCGCCAAACCCTA 59.342 61.111 3.51 0.00 0.00 3.53
1963 2108 3.788766 CGCGAAAAGGTCAGCGGG 61.789 66.667 0.00 0.00 41.99 6.13
2042 2193 2.624316 CAGTATGTTGGCACTGCAAG 57.376 50.000 2.82 0.00 36.09 4.01
2050 2201 2.418083 GCCCTGGCAGTATGTTGGC 61.418 63.158 14.43 13.76 43.38 4.52
2051 2202 3.924507 GCCCTGGCAGTATGTTGG 58.075 61.111 14.43 7.30 41.49 3.77
2061 2212 1.956477 CATATAGGTTTGTGCCCTGGC 59.044 52.381 0.00 0.00 42.35 4.85
2062 2213 1.956477 GCATATAGGTTTGTGCCCTGG 59.044 52.381 0.00 0.00 33.35 4.45
2067 2218 1.002468 CAGCGGCATATAGGTTTGTGC 60.002 52.381 1.45 0.00 36.88 4.57
2068 2219 2.287915 GACAGCGGCATATAGGTTTGTG 59.712 50.000 1.45 0.00 0.00 3.33
2069 2220 2.093181 TGACAGCGGCATATAGGTTTGT 60.093 45.455 1.45 0.00 0.00 2.83
2070 2221 2.560504 TGACAGCGGCATATAGGTTTG 58.439 47.619 1.45 0.00 0.00 2.93
2071 2222 3.275617 TTGACAGCGGCATATAGGTTT 57.724 42.857 1.45 0.00 0.00 3.27
2072 2223 3.403038 GATTGACAGCGGCATATAGGTT 58.597 45.455 1.45 0.00 0.00 3.50
2073 2224 2.610479 CGATTGACAGCGGCATATAGGT 60.610 50.000 1.45 0.00 0.00 3.08
2074 2225 1.995484 CGATTGACAGCGGCATATAGG 59.005 52.381 1.45 0.00 0.00 2.57
2075 2226 2.677199 ACGATTGACAGCGGCATATAG 58.323 47.619 1.45 0.00 0.00 1.31
2076 2227 2.812358 ACGATTGACAGCGGCATATA 57.188 45.000 1.45 0.00 0.00 0.86
2077 2228 2.812358 TACGATTGACAGCGGCATAT 57.188 45.000 1.45 0.00 0.00 1.78
2078 2229 2.812358 ATACGATTGACAGCGGCATA 57.188 45.000 1.45 0.00 0.00 3.14
2079 2230 2.812358 TATACGATTGACAGCGGCAT 57.188 45.000 1.45 0.00 0.00 4.40
2080 2231 2.812358 ATATACGATTGACAGCGGCA 57.188 45.000 1.45 0.00 0.00 5.69
2081 2232 7.201359 GCATATATATATACGATTGACAGCGGC 60.201 40.741 4.54 0.00 0.00 6.53
2082 2233 7.273598 GGCATATATATATACGATTGACAGCGG 59.726 40.741 4.54 0.00 0.00 5.52
2083 2234 7.273598 GGGCATATATATATACGATTGACAGCG 59.726 40.741 4.54 0.00 0.00 5.18
2084 2235 8.088365 TGGGCATATATATATACGATTGACAGC 58.912 37.037 4.54 1.30 0.00 4.40
2085 2236 9.981114 TTGGGCATATATATATACGATTGACAG 57.019 33.333 4.54 0.00 0.00 3.51
2086 2237 9.981114 CTTGGGCATATATATATACGATTGACA 57.019 33.333 4.54 1.25 0.00 3.58
2087 2238 9.982651 ACTTGGGCATATATATATACGATTGAC 57.017 33.333 4.54 2.01 0.00 3.18
2100 2251 8.948401 ATCGATCTATCTACTTGGGCATATAT 57.052 34.615 0.00 0.00 0.00 0.86
2101 2252 8.221251 AGATCGATCTATCTACTTGGGCATATA 58.779 37.037 26.27 0.00 34.40 0.86
2102 2253 7.066142 AGATCGATCTATCTACTTGGGCATAT 58.934 38.462 26.27 0.00 34.40 1.78
2103 2254 6.427441 AGATCGATCTATCTACTTGGGCATA 58.573 40.000 26.27 0.00 34.40 3.14
2104 2255 5.268387 AGATCGATCTATCTACTTGGGCAT 58.732 41.667 26.27 0.00 34.40 4.40
2105 2256 4.667573 AGATCGATCTATCTACTTGGGCA 58.332 43.478 26.27 0.00 34.40 5.36
2106 2257 6.952773 ATAGATCGATCTATCTACTTGGGC 57.047 41.667 32.89 2.82 44.58 5.36
2125 2276 7.176865 CGGTTTCCAAGTGGATCTATAGATAGA 59.823 40.741 15.31 2.37 44.98 1.98
2126 2277 7.316640 CGGTTTCCAAGTGGATCTATAGATAG 58.683 42.308 15.31 2.37 44.98 2.08
2127 2278 6.295123 GCGGTTTCCAAGTGGATCTATAGATA 60.295 42.308 15.31 0.00 44.98 1.98
2128 2279 5.511545 GCGGTTTCCAAGTGGATCTATAGAT 60.512 44.000 15.26 15.26 44.98 1.98
2129 2280 4.202223 GCGGTTTCCAAGTGGATCTATAGA 60.202 45.833 4.57 4.57 44.98 1.98
2130 2281 4.058817 GCGGTTTCCAAGTGGATCTATAG 58.941 47.826 0.00 0.00 44.98 1.31
2131 2282 3.181458 GGCGGTTTCCAAGTGGATCTATA 60.181 47.826 0.00 0.00 44.98 1.31
2132 2283 2.421529 GGCGGTTTCCAAGTGGATCTAT 60.422 50.000 0.00 0.00 44.98 1.98
2133 2284 1.065709 GGCGGTTTCCAAGTGGATCTA 60.066 52.381 0.00 0.00 44.98 1.98
2134 2285 0.322546 GGCGGTTTCCAAGTGGATCT 60.323 55.000 0.00 0.00 44.98 2.75
2135 2286 1.313091 GGGCGGTTTCCAAGTGGATC 61.313 60.000 0.00 0.00 44.98 3.36
2136 2287 1.304134 GGGCGGTTTCCAAGTGGAT 60.304 57.895 0.00 0.00 44.98 3.41
2137 2288 2.114411 GGGCGGTTTCCAAGTGGA 59.886 61.111 0.00 0.00 43.73 4.02
2138 2289 2.989253 GGGGCGGTTTCCAAGTGG 60.989 66.667 0.00 0.00 0.00 4.00
2139 2290 2.989253 GGGGGCGGTTTCCAAGTG 60.989 66.667 0.00 0.00 0.00 3.16
2140 2291 3.182996 AGGGGGCGGTTTCCAAGT 61.183 61.111 0.00 0.00 0.00 3.16
2141 2292 2.361230 GAGGGGGCGGTTTCCAAG 60.361 66.667 0.00 0.00 0.00 3.61
2142 2293 3.974293 GGAGGGGGCGGTTTCCAA 61.974 66.667 0.00 0.00 0.00 3.53
2158 2309 3.744749 TTACTCACGATCGCGCGGG 62.745 63.158 31.69 21.28 42.48 6.13
2159 2310 1.870458 TTTACTCACGATCGCGCGG 60.870 57.895 31.69 16.94 42.48 6.46
2160 2311 1.266089 GTTTACTCACGATCGCGCG 59.734 57.895 26.76 26.76 42.48 6.86
2161 2312 0.711670 TTGTTTACTCACGATCGCGC 59.288 50.000 16.60 0.00 42.48 6.86
2162 2313 3.634730 AATTGTTTACTCACGATCGCG 57.365 42.857 16.60 5.75 44.79 5.87
2163 2314 6.268797 TCATAATTGTTTACTCACGATCGC 57.731 37.500 16.60 0.00 0.00 4.58
2164 2315 7.010183 AGGTTCATAATTGTTTACTCACGATCG 59.990 37.037 14.88 14.88 0.00 3.69
2165 2316 8.197988 AGGTTCATAATTGTTTACTCACGATC 57.802 34.615 0.00 0.00 0.00 3.69
2177 2328 9.238368 TCGAAAGGATTTAAGGTTCATAATTGT 57.762 29.630 0.00 0.00 39.27 2.71
2287 2465 0.671251 CCCTCAGATGTCGGCTCTAC 59.329 60.000 0.00 0.00 0.00 2.59
2351 2529 5.886474 TGGTGTGTTTAACTTGTTCCATACA 59.114 36.000 0.00 0.00 34.12 2.29
2352 2530 6.380095 TGGTGTGTTTAACTTGTTCCATAC 57.620 37.500 0.00 0.00 0.00 2.39
2431 2609 2.974698 GCTCCACTGTTGCAGCGT 60.975 61.111 0.00 0.00 34.37 5.07
2514 2692 1.737838 AATCGATTGACCATGCACGT 58.262 45.000 10.50 0.00 0.00 4.49
2553 2731 2.066262 GCGAACAAGATGGAACGAAGA 58.934 47.619 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.