Multiple sequence alignment - TraesCS5D01G287600

Loading Multiple Alignment...

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 TraesCS5D01G287600 chr5D 100.000 2576 0 0 1 2576 387241779 387244354 0.000000e+00 4758.0
1 TraesCS5D01G287600 chr5D 94.783 115 6 0 2327 2441 387244047 387244161 2.040000e-41 180.0
2 TraesCS5D01G287600 chr5D 94.783 115 6 0 2269 2383 387244105 387244219 2.040000e-41 180.0
3 TraesCS5D01G287600 chr3D 91.185 2303 142 28 1 2258 558679303 558681589 0.000000e+00 3072.0
4 TraesCS5D01G287600 chr3D 90.058 171 13 4 2403 2571 558681733 558681901 4.320000e-53 219.0
5 TraesCS5D01G287600 chr2B 91.219 2289 142 21 1 2258 664330484 664328224 0.000000e+00 3059.0
6 TraesCS5D01G287600 chr2B 84.615 312 18 14 2265 2576 664328186 664327905 1.510000e-72 283.0
7 TraesCS5D01G287600 chr2B 90.230 174 17 0 2403 2576 225323397 225323224 7.170000e-56 228.0
8 TraesCS5D01G287600 chr2B 94.488 127 7 0 2327 2453 664328182 664328056 2.020000e-46 196.0
9 TraesCS5D01G287600 chr2B 80.909 110 13 6 2269 2375 664328124 664328020 2.120000e-11 80.5
10 TraesCS5D01G287600 chr5B 91.084 2288 149 15 1 2258 529280456 529282718 0.000000e+00 3044.0
11 TraesCS5D01G287600 chr5B 94.858 1731 78 5 1 1725 659536140 659537865 0.000000e+00 2693.0
12 TraesCS5D01G287600 chr5B 90.968 2004 132 19 268 2256 575037465 575035496 0.000000e+00 2652.0
13 TraesCS5D01G287600 chr5B 79.286 840 102 30 1753 2576 649895068 649895851 2.940000e-144 521.0
14 TraesCS5D01G287600 chr5B 82.844 443 50 16 1780 2210 659546526 659546954 8.700000e-100 374.0
15 TraesCS5D01G287600 chr5B 83.333 312 22 14 2265 2576 575025496 575025215 7.070000e-66 261.0
16 TraesCS5D01G287600 chr5B 95.276 127 6 0 2327 2453 575025492 575025366 4.350000e-48 202.0
17 TraesCS5D01G287600 chr5B 95.276 127 6 0 2327 2453 649895574 649895700 4.350000e-48 202.0
18 TraesCS5D01G287600 chr4B 90.356 2302 160 35 1 2256 622503280 622500995 0.000000e+00 2964.0
19 TraesCS5D01G287600 chr4B 91.379 174 15 0 2403 2576 622500849 622500676 3.310000e-59 239.0
20 TraesCS5D01G287600 chr4D 95.813 1815 52 13 1 1807 473971221 473969423 0.000000e+00 2909.0
21 TraesCS5D01G287600 chr4D 89.394 462 36 5 1805 2258 473876316 473875860 1.030000e-158 569.0
22 TraesCS5D01G287600 chr4D 87.179 312 10 14 2265 2576 473875821 473875540 6.870000e-86 327.0
23 TraesCS5D01G287600 chr4D 96.063 127 5 0 2327 2453 473875817 473875691 9.340000e-50 207.0
24 TraesCS5D01G287600 chr6B 92.885 2024 106 16 1 1989 147950687 147948667 0.000000e+00 2905.0
25 TraesCS5D01G287600 chr6B 91.333 2100 142 20 1 2065 567118187 567116093 0.000000e+00 2833.0
26 TraesCS5D01G287600 chr6B 89.380 1902 136 38 404 2256 717730829 717732713 0.000000e+00 2333.0
27 TraesCS5D01G287600 chr6B 90.805 174 16 0 2403 2576 717732859 717733032 1.540000e-57 233.0
28 TraesCS5D01G287600 chr6B 92.000 150 11 1 2322 2471 223250019 223250167 2.600000e-50 209.0
29 TraesCS5D01G287600 chr6B 86.301 73 8 1 2255 2325 717732797 717732869 7.640000e-11 78.7
30 TraesCS5D01G287600 chr2D 91.651 2120 120 21 1 2079 12316059 12313956 0.000000e+00 2881.0
31 TraesCS5D01G287600 chr2D 92.195 205 14 2 2373 2576 12313653 12313450 3.240000e-74 289.0
32 TraesCS5D01G287600 chr7B 92.100 2038 124 22 1 2027 36428066 36426055 0.000000e+00 2837.0
33 TraesCS5D01G287600 chr7B 81.409 511 51 22 2078 2576 36426054 36425576 6.730000e-101 377.0
34 TraesCS5D01G287600 chr7B 78.138 494 73 16 1780 2258 316357569 316357096 5.430000e-72 281.0
35 TraesCS5D01G287600 chr3B 87.782 2259 210 45 1 2208 718831357 718829114 0.000000e+00 2582.0
36 TraesCS5D01G287600 chr3B 86.269 721 62 18 1377 2063 10032856 10032139 0.000000e+00 749.0
37 TraesCS5D01G287600 chr3B 84.661 339 24 16 2265 2576 10032037 10031700 1.920000e-81 313.0
38 TraesCS5D01G287600 chr3B 89.333 150 15 1 2322 2471 718828921 718828773 1.220000e-43 187.0
39 TraesCS5D01G287600 chr3B 85.556 180 18 5 2084 2256 10032254 10032076 5.660000e-42 182.0
40 TraesCS5D01G287600 chr1D 86.735 2141 174 52 505 2571 491071255 491069151 0.000000e+00 2279.0
41 TraesCS5D01G287600 chr1B 85.903 1816 165 54 812 2576 359219908 359218133 0.000000e+00 1851.0
42 TraesCS5D01G287600 chr7D 82.734 139 17 4 2126 2258 536967148 536967285 1.620000e-22 117.0


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 TraesCS5D01G287600 chr5D 387241779 387244354 2575 False 1706.000000 4758 96.522000 1 2576 3 chr5D.!!$F1 2575
1 TraesCS5D01G287600 chr3D 558679303 558681901 2598 False 1645.500000 3072 90.621500 1 2571 2 chr3D.!!$F1 2570
2 TraesCS5D01G287600 chr2B 664327905 664330484 2579 True 904.625000 3059 87.807750 1 2576 4 chr2B.!!$R2 2575
3 TraesCS5D01G287600 chr5B 529280456 529282718 2262 False 3044.000000 3044 91.084000 1 2258 1 chr5B.!!$F1 2257
4 TraesCS5D01G287600 chr5B 659536140 659537865 1725 False 2693.000000 2693 94.858000 1 1725 1 chr5B.!!$F2 1724
5 TraesCS5D01G287600 chr5B 575035496 575037465 1969 True 2652.000000 2652 90.968000 268 2256 1 chr5B.!!$R1 1988
6 TraesCS5D01G287600 chr5B 649895068 649895851 783 False 361.500000 521 87.281000 1753 2576 2 chr5B.!!$F4 823
7 TraesCS5D01G287600 chr4B 622500676 622503280 2604 True 1601.500000 2964 90.867500 1 2576 2 chr4B.!!$R1 2575
8 TraesCS5D01G287600 chr4D 473969423 473971221 1798 True 2909.000000 2909 95.813000 1 1807 1 chr4D.!!$R1 1806
9 TraesCS5D01G287600 chr4D 473875540 473876316 776 True 367.666667 569 90.878667 1805 2576 3 chr4D.!!$R2 771
10 TraesCS5D01G287600 chr6B 147948667 147950687 2020 True 2905.000000 2905 92.885000 1 1989 1 chr6B.!!$R1 1988
11 TraesCS5D01G287600 chr6B 567116093 567118187 2094 True 2833.000000 2833 91.333000 1 2065 1 chr6B.!!$R2 2064
12 TraesCS5D01G287600 chr6B 717730829 717733032 2203 False 881.566667 2333 88.828667 404 2576 3 chr6B.!!$F2 2172
13 TraesCS5D01G287600 chr2D 12313450 12316059 2609 True 1585.000000 2881 91.923000 1 2576 2 chr2D.!!$R1 2575
14 TraesCS5D01G287600 chr7B 36425576 36428066 2490 True 1607.000000 2837 86.754500 1 2576 2 chr7B.!!$R2 2575
15 TraesCS5D01G287600 chr3B 718828773 718831357 2584 True 1384.500000 2582 88.557500 1 2471 2 chr3B.!!$R2 2470
16 TraesCS5D01G287600 chr3B 10031700 10032856 1156 True 414.666667 749 85.495333 1377 2576 3 chr3B.!!$R1 1199
17 TraesCS5D01G287600 chr1D 491069151 491071255 2104 True 2279.000000 2279 86.735000 505 2571 1 chr1D.!!$R1 2066
18 TraesCS5D01G287600 chr1B 359218133 359219908 1775 True 1851.000000 1851 85.903000 812 2576 1 chr1B.!!$R1 1764

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
331 334 0.544357 TTCTGATGGGAGGACCGTGT 60.544 55.0 0.0 0.0 44.64 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2290 0.251922 TACCTGGGTGCGAGTACCTT 60.252 55.0 10.06 0.0 40.66 3.5 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
100 102 0.884514 GAGGTTTCAAGCAGGGAAGC 59.115 55.000 0.00 0.00 0.00 3.86
132 134 9.218359 CATCAACAAATCATTAGATTCAACGAG 57.782 33.333 0.00 0.00 43.52 4.18
203 205 3.428282 GGCTTACGGCGGTGTTGG 61.428 66.667 13.24 0.00 42.94 3.77
215 217 1.555992 CGGTGTTGGGTATAAGGTGGA 59.444 52.381 0.00 0.00 0.00 4.02
331 334 0.544357 TTCTGATGGGAGGACCGTGT 60.544 55.000 0.00 0.00 44.64 4.49
359 362 2.042162 AGGAGTTCACATTGGAAGCCAT 59.958 45.455 0.00 0.00 31.53 4.40
459 462 1.352352 CCTGACCCTGAACTCATGGTT 59.648 52.381 7.93 0.00 43.45 3.67
491 497 4.323180 GGGAAGAAGAAGGAAGAAGAGGTC 60.323 50.000 0.00 0.00 0.00 3.85
580 586 1.862602 GCCACCGGACATCAACAACC 61.863 60.000 9.46 0.00 0.00 3.77
763 769 0.965866 TAGTGCACGAGGAGGGACTG 60.966 60.000 12.01 0.00 41.55 3.51
830 848 3.998672 TGGTCGTGCTTCCGGTCC 61.999 66.667 0.00 0.00 0.00 4.46
1128 1149 1.272092 ACTCCATCATGTTGGTGTGGG 60.272 52.381 23.31 12.37 40.88 4.61
1299 1320 7.555087 TCAAATTTTGTCCAACTTCAACTCAT 58.445 30.769 8.89 0.00 0.00 2.90
1375 1400 7.254590 GCAAGTACTTCACATGGATAGATCAAC 60.255 40.741 4.77 0.00 0.00 3.18
1438 1464 2.180159 TAGGAGGCAACGGCTGTTCC 62.180 60.000 8.28 12.74 46.39 3.62
1578 1609 1.436600 CTTGCAAGAGCTCGTGATGT 58.563 50.000 30.34 0.00 42.74 3.06
1579 1610 1.802960 CTTGCAAGAGCTCGTGATGTT 59.197 47.619 30.34 5.82 42.74 2.71
1596 1627 5.026121 TGATGTTACAAGAGGAGGATGAGT 58.974 41.667 0.00 0.00 0.00 3.41
1598 1629 3.444034 TGTTACAAGAGGAGGATGAGTCG 59.556 47.826 0.00 0.00 0.00 4.18
1651 1682 5.532557 TCCGTAGTGATCTTTAGATGCATG 58.467 41.667 2.46 0.00 34.37 4.06
1734 1766 4.604843 TTGCGATGCTTGAGACTATTTG 57.395 40.909 0.00 0.00 0.00 2.32
1895 1995 4.858850 TCAACCCTACCGACATAGTCTAA 58.141 43.478 0.00 0.00 0.00 2.10
1911 2135 0.974010 CTAAGGCGGTAGGGTGTGGA 60.974 60.000 0.00 0.00 0.00 4.02
1984 2209 1.696314 ACACTTGTCTGGTGGGGGT 60.696 57.895 0.00 0.00 38.83 4.95
1989 2214 2.017668 TTGTCTGGTGGGGGTGCAAT 62.018 55.000 0.00 0.00 0.00 3.56
1992 2217 0.548926 TCTGGTGGGGGTGCAATAGA 60.549 55.000 0.00 0.00 0.00 1.98
2010 2235 1.618447 AAAGGGACCCTACCGCCAT 60.618 57.895 15.29 0.00 31.13 4.40
2050 2275 2.283604 TGTCCTACCGCCAGAGCA 60.284 61.111 0.00 0.00 39.83 4.26
2072 2297 3.306379 GCGGTAGGCCAAGGTACT 58.694 61.111 5.01 0.00 35.95 2.73
2073 2298 1.143401 GCGGTAGGCCAAGGTACTC 59.857 63.158 5.01 0.00 33.28 2.59
2074 2299 1.436336 CGGTAGGCCAAGGTACTCG 59.564 63.158 5.01 1.15 38.49 4.18
2075 2300 1.143401 GGTAGGCCAAGGTACTCGC 59.857 63.158 5.01 0.00 38.49 5.03
2076 2301 1.610554 GGTAGGCCAAGGTACTCGCA 61.611 60.000 5.01 0.00 38.49 5.10
2077 2302 0.459759 GTAGGCCAAGGTACTCGCAC 60.460 60.000 5.01 0.00 38.49 5.34
2078 2303 1.610554 TAGGCCAAGGTACTCGCACC 61.611 60.000 5.01 0.00 38.49 5.01
2079 2304 2.436115 GCCAAGGTACTCGCACCC 60.436 66.667 0.00 0.00 38.49 4.61
2250 2696 4.273969 TGGGAGTCGAAAAACAATGTGTAC 59.726 41.667 0.00 0.00 0.00 2.90
2260 2706 7.746916 CGAAAAACAATGTGTACAATTCCGATA 59.253 33.333 0.00 0.00 0.00 2.92
2383 2955 8.558700 CACATGTCATGTCCGATAATTCAAATA 58.441 33.333 15.73 0.00 42.70 1.40
2384 2956 9.119418 ACATGTCATGTCCGATAATTCAAATAA 57.881 29.630 12.87 0.00 39.92 1.40
2385 2957 9.603298 CATGTCATGTCCGATAATTCAAATAAG 57.397 33.333 4.53 0.00 0.00 1.73
2386 2958 8.956533 TGTCATGTCCGATAATTCAAATAAGA 57.043 30.769 0.00 0.00 0.00 2.10
2387 2959 9.389755 TGTCATGTCCGATAATTCAAATAAGAA 57.610 29.630 0.00 0.00 0.00 2.52
2388 2960 9.869844 GTCATGTCCGATAATTCAAATAAGAAG 57.130 33.333 0.00 0.00 0.00 2.85
2389 2961 8.559536 TCATGTCCGATAATTCAAATAAGAAGC 58.440 33.333 0.00 0.00 0.00 3.86
2390 2962 7.857734 TGTCCGATAATTCAAATAAGAAGCA 57.142 32.000 0.00 0.00 0.00 3.91
2391 2963 8.275015 TGTCCGATAATTCAAATAAGAAGCAA 57.725 30.769 0.00 0.00 0.00 3.91
2392 2964 8.181573 TGTCCGATAATTCAAATAAGAAGCAAC 58.818 33.333 0.00 0.00 0.00 4.17
2393 2965 8.181573 GTCCGATAATTCAAATAAGAAGCAACA 58.818 33.333 0.00 0.00 0.00 3.33
2394 2966 8.902806 TCCGATAATTCAAATAAGAAGCAACAT 58.097 29.630 0.00 0.00 0.00 2.71
2395 2967 9.173939 CCGATAATTCAAATAAGAAGCAACATC 57.826 33.333 0.00 0.00 0.00 3.06
2396 2968 9.173939 CGATAATTCAAATAAGAAGCAACATCC 57.826 33.333 0.00 0.00 0.00 3.51
2397 2969 9.173939 GATAATTCAAATAAGAAGCAACATCCG 57.826 33.333 0.00 0.00 0.00 4.18
2398 2970 4.963276 TCAAATAAGAAGCAACATCCGG 57.037 40.909 0.00 0.00 0.00 5.14
2399 2971 4.331968 TCAAATAAGAAGCAACATCCGGT 58.668 39.130 0.00 0.00 0.00 5.28
2400 2972 5.492895 TCAAATAAGAAGCAACATCCGGTA 58.507 37.500 0.00 0.00 0.00 4.02
2401 2973 5.353123 TCAAATAAGAAGCAACATCCGGTAC 59.647 40.000 0.00 0.00 0.00 3.34
2402 2974 2.851263 AAGAAGCAACATCCGGTACA 57.149 45.000 0.00 0.00 0.00 2.90
2403 2975 3.350219 AAGAAGCAACATCCGGTACAT 57.650 42.857 0.00 0.00 0.00 2.29
2404 2976 4.481368 AAGAAGCAACATCCGGTACATA 57.519 40.909 0.00 0.00 0.00 2.29
2405 2977 4.060038 AGAAGCAACATCCGGTACATAG 57.940 45.455 0.00 0.00 0.00 2.23
2406 2978 3.451178 AGAAGCAACATCCGGTACATAGT 59.549 43.478 0.00 0.00 0.00 2.12
2407 2979 3.906720 AGCAACATCCGGTACATAGTT 57.093 42.857 0.00 0.00 0.00 2.24
2408 2980 3.793559 AGCAACATCCGGTACATAGTTC 58.206 45.455 0.00 0.00 0.00 3.01
2409 2981 3.196901 AGCAACATCCGGTACATAGTTCA 59.803 43.478 0.00 0.00 0.00 3.18
2410 2982 3.936453 GCAACATCCGGTACATAGTTCAA 59.064 43.478 0.00 0.00 0.00 2.69
2411 2983 4.393680 GCAACATCCGGTACATAGTTCAAA 59.606 41.667 0.00 0.00 0.00 2.69
2412 2984 5.065988 GCAACATCCGGTACATAGTTCAAAT 59.934 40.000 0.00 0.00 0.00 2.32
2419 2991 5.584649 CCGGTACATAGTTCAAATGACACAT 59.415 40.000 0.00 0.00 0.00 3.21
2420 2992 6.456853 CCGGTACATAGTTCAAATGACACATG 60.457 42.308 0.00 0.00 0.00 3.21
2477 3049 2.314246 GGTAGCATCCTAAGTACCCGT 58.686 52.381 0.00 0.00 30.43 5.28
2496 3068 3.390311 CCGTAAAGGAGCCCCTAATAAGT 59.610 47.826 0.00 0.00 43.48 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 4.283337 TCATCAACCTTGTCGGGATACTA 58.717 43.478 0.00 0.00 36.97 1.82
100 102 6.211587 TCTAATGATTTGTTGATGCAAGGG 57.788 37.500 0.00 0.00 0.00 3.95
132 134 6.183360 CGTCCACTTGGTAGATCATTTCTTTC 60.183 42.308 0.00 0.00 35.79 2.62
215 217 1.342672 ACACCACCGGTTCTTGAGGT 61.343 55.000 2.97 4.99 39.12 3.85
331 334 3.392947 TCCAATGTGAACTCCTACAACCA 59.607 43.478 0.00 0.00 0.00 3.67
359 362 2.359850 GCGCCCATGTCAACCTCA 60.360 61.111 0.00 0.00 0.00 3.86
459 462 4.499472 TCCTTCTTCTTCCCTTTGTAGGA 58.501 43.478 0.00 0.00 45.05 2.94
491 497 5.105797 GCTAGATCATCCATGTCACTCCTAG 60.106 48.000 0.00 0.00 0.00 3.02
580 586 0.999406 GGATCGTCACATTGTCCACG 59.001 55.000 10.31 10.31 0.00 4.94
763 769 0.394352 CCTCCACACCCACCAATAGC 60.394 60.000 0.00 0.00 0.00 2.97
830 848 2.299582 TCGATCCTCCTCGTCCTAGTAG 59.700 54.545 0.00 0.00 39.62 2.57
1068 1088 1.302832 CTCGTCCAGCTTGGCCTTT 60.303 57.895 3.32 0.00 37.47 3.11
1071 1091 4.021925 ACCTCGTCCAGCTTGGCC 62.022 66.667 0.00 0.00 37.47 5.36
1128 1149 1.963515 ACCTTCACCTTGCAAACATCC 59.036 47.619 0.00 0.00 0.00 3.51
1375 1400 5.336213 CCTTTTTGACATCCTCTGGAACATG 60.336 44.000 0.00 0.00 38.20 3.21
1438 1464 3.410508 AGCCTCTCTGAAAAGCTTCTTG 58.589 45.455 0.00 0.00 32.33 3.02
1578 1609 2.427453 GCGACTCATCCTCCTCTTGTAA 59.573 50.000 0.00 0.00 0.00 2.41
1579 1610 2.025155 GCGACTCATCCTCCTCTTGTA 58.975 52.381 0.00 0.00 0.00 2.41
1596 1627 2.529780 TTTCCCTTCTTGTAACGCGA 57.470 45.000 15.93 0.00 0.00 5.87
1598 1629 2.228103 CCCTTTTCCCTTCTTGTAACGC 59.772 50.000 0.00 0.00 0.00 4.84
1651 1682 9.587772 ACAGTCATAGACATACAACTTCAATAC 57.412 33.333 0.00 0.00 34.60 1.89
1734 1766 8.414003 TCACAGATAGTTCATACATAGTGGAAC 58.586 37.037 0.00 0.00 39.83 3.62
1755 1788 9.817365 CAAATAGTTCAACACTAAAGATCACAG 57.183 33.333 0.00 0.00 41.56 3.66
1895 1995 2.203877 TTCCACACCCTACCGCCT 60.204 61.111 0.00 0.00 0.00 5.52
1984 2209 2.508300 GGTAGGGTCCCTTTCTATTGCA 59.492 50.000 17.94 0.00 34.61 4.08
1989 2214 0.688749 GGCGGTAGGGTCCCTTTCTA 60.689 60.000 17.94 0.00 34.61 2.10
1992 2217 0.326808 TATGGCGGTAGGGTCCCTTT 60.327 55.000 17.94 0.00 34.61 3.11
2065 2290 0.251922 TACCTGGGTGCGAGTACCTT 60.252 55.000 10.06 0.00 40.66 3.50
2066 2291 0.969409 GTACCTGGGTGCGAGTACCT 60.969 60.000 10.06 0.00 40.66 3.08
2068 2293 0.455005 GAGTACCTGGGTGCGAGTAC 59.545 60.000 2.07 0.00 35.88 2.73
2069 2294 1.028330 CGAGTACCTGGGTGCGAGTA 61.028 60.000 2.07 0.00 35.88 2.59
2070 2295 2.341101 CGAGTACCTGGGTGCGAGT 61.341 63.158 2.07 0.00 35.88 4.18
2071 2296 2.490217 CGAGTACCTGGGTGCGAG 59.510 66.667 2.07 0.00 35.88 5.03
2072 2297 3.755628 GCGAGTACCTGGGTGCGA 61.756 66.667 2.07 0.00 35.88 5.10
2079 2304 4.476410 TCTGCGCGCGAGTACCTG 62.476 66.667 37.18 18.83 0.00 4.00
2138 2518 2.660064 CCTACCGCCAGAGCCTGTT 61.660 63.158 2.18 0.00 34.57 3.16
2250 2696 8.707938 TTGCATCTCACTATATATCGGAATTG 57.292 34.615 0.00 0.00 0.00 2.32
2260 2706 4.152647 TCGGGTCTTGCATCTCACTATAT 58.847 43.478 0.00 0.00 0.00 0.86
2375 2947 5.418840 ACCGGATGTTGCTTCTTATTTGAAT 59.581 36.000 9.46 0.00 0.00 2.57
2383 2955 2.851263 TGTACCGGATGTTGCTTCTT 57.149 45.000 9.46 0.00 0.00 2.52
2384 2956 3.451178 ACTATGTACCGGATGTTGCTTCT 59.549 43.478 9.46 0.00 0.00 2.85
2385 2957 3.793559 ACTATGTACCGGATGTTGCTTC 58.206 45.455 9.46 0.00 0.00 3.86
2386 2958 3.906720 ACTATGTACCGGATGTTGCTT 57.093 42.857 9.46 0.00 0.00 3.91
2387 2959 3.196901 TGAACTATGTACCGGATGTTGCT 59.803 43.478 9.46 0.00 0.00 3.91
2388 2960 3.527533 TGAACTATGTACCGGATGTTGC 58.472 45.455 9.46 0.00 0.00 4.17
2389 2961 6.315144 TCATTTGAACTATGTACCGGATGTTG 59.685 38.462 9.46 0.00 0.00 3.33
2390 2962 6.315393 GTCATTTGAACTATGTACCGGATGTT 59.685 38.462 9.46 3.27 0.00 2.71
2391 2963 5.815740 GTCATTTGAACTATGTACCGGATGT 59.184 40.000 9.46 0.00 0.00 3.06
2392 2964 5.815222 TGTCATTTGAACTATGTACCGGATG 59.185 40.000 9.46 0.00 0.00 3.51
2393 2965 5.815740 GTGTCATTTGAACTATGTACCGGAT 59.184 40.000 9.46 0.00 0.00 4.18
2394 2966 5.172934 GTGTCATTTGAACTATGTACCGGA 58.827 41.667 9.46 0.00 0.00 5.14
2395 2967 4.932799 TGTGTCATTTGAACTATGTACCGG 59.067 41.667 0.00 0.00 0.00 5.28
2396 2968 6.092122 ACATGTGTCATTTGAACTATGTACCG 59.908 38.462 0.00 0.00 0.00 4.02
2397 2969 7.377766 ACATGTGTCATTTGAACTATGTACC 57.622 36.000 0.00 0.00 0.00 3.34
2419 2991 6.648725 TGTCATTTGAACTATCGAACATGACA 59.351 34.615 9.37 9.37 41.89 3.58
2420 2992 6.955963 GTGTCATTTGAACTATCGAACATGAC 59.044 38.462 0.00 5.32 38.41 3.06
2425 2997 6.223138 TGTGTGTCATTTGAACTATCGAAC 57.777 37.500 0.00 0.00 31.72 3.95
2427 2999 6.162777 TGATGTGTGTCATTTGAACTATCGA 58.837 36.000 0.00 0.00 36.83 3.59
2429 3001 6.690098 GCATGATGTGTGTCATTTGAACTATC 59.310 38.462 0.00 0.00 36.72 2.08
2430 3002 6.405065 GGCATGATGTGTGTCATTTGAACTAT 60.405 38.462 0.00 0.00 36.72 2.12
2431 3003 5.106197 GGCATGATGTGTGTCATTTGAACTA 60.106 40.000 0.00 0.00 36.72 2.24
2477 3049 3.644738 CCGACTTATTAGGGGCTCCTTTA 59.355 47.826 12.52 0.00 41.56 1.85
2496 3068 0.686769 GGTTAGGGCCTCTCTTCCGA 60.687 60.000 10.74 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.