Multiple sequence alignment - TraesCS5D01G274900

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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 TraesCS5D01G274900 chr5D 100.000 4530 0 0 1 4530 377538955 377534426 0.000000e+00 8366
1 TraesCS5D01G274900 chr5B 91.964 3024 131 36 1 2920 450846584 450843569 0.000000e+00 4135
2 TraesCS5D01G274900 chr5B 90.015 1372 63 33 3201 4530 450843290 450841951 0.000000e+00 1707
3 TraesCS5D01G274900 chr5B 90.726 248 15 5 4283 4530 516605678 516605439 1.570000e-84 324
4 TraesCS5D01G274900 chr5A 92.013 2191 87 25 1 2107 478326724 478324538 0.000000e+00 2996
5 TraesCS5D01G274900 chr5A 90.158 1077 57 10 2154 3184 478324545 478323472 0.000000e+00 1356
6 TraesCS5D01G274900 chr5A 91.429 700 30 16 3189 3874 478323400 478322717 0.000000e+00 933
7 TraesCS5D01G274900 chr5A 87.322 702 47 25 3855 4530 478322685 478322000 0.000000e+00 765
8 TraesCS5D01G274900 chr7A 94.048 168 10 0 4363 4530 229143261 229143094 5.820000e-64 255
9 TraesCS5D01G274900 chr7D 93.023 172 12 0 4359 4530 216082336 216082165 7.520000e-63 252
10 TraesCS5D01G274900 chr7B 92.179 179 12 2 4354 4530 184299349 184299527 7.520000e-63 252
11 TraesCS5D01G274900 chr4A 91.358 162 10 3 4371 4530 707060512 707060671 7.630000e-53 219
12 TraesCS5D01G274900 chr3A 91.195 159 12 2 4371 4529 17533080 17532924 9.870000e-52 215
13 TraesCS5D01G274900 chr3B 88.889 162 15 2 4371 4530 772957667 772957507 3.580000e-46 196


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 TraesCS5D01G274900 chr5D 377534426 377538955 4529 True 8366.0 8366 100.0000 1 4530 1 chr5D.!!$R1 4529
1 TraesCS5D01G274900 chr5B 450841951 450846584 4633 True 2921.0 4135 90.9895 1 4530 2 chr5B.!!$R2 4529
2 TraesCS5D01G274900 chr5A 478322000 478326724 4724 True 1512.5 2996 90.2305 1 4530 4 chr5A.!!$R1 4529

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
528 555 0.762418 TTGCTCCCGTTTTCTCCTCA 59.238 50.000 0.0 0.0 0.00 3.86 F
576 618 1.471676 CCACTCGTCCCAAGATACTGC 60.472 57.143 0.0 0.0 0.00 4.40 F
2361 2482 1.377202 TGGCGGAATTGCTGGACTC 60.377 57.895 0.0 0.0 34.52 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2482 0.035152 TAGGTGTGCAGGCAATCAGG 60.035 55.000 0.00 0.00 0.00 3.86 R
2523 2654 1.459592 CTAACACGCTGGGACGAAAAG 59.540 52.381 0.00 0.00 36.70 2.27 R
4100 4489 0.038166 GAAGATGTGGGACCCAGCAA 59.962 55.000 15.52 2.77 32.34 3.91 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
30 36 4.566697 CCCCGGCAAATTTAATCCCTTTTT 60.567 41.667 0.00 0.00 0.00 1.94
96 102 7.487484 AGAAAAGCAAAAGAAGAAGAAGAAGG 58.513 34.615 0.00 0.00 0.00 3.46
345 372 6.423862 TCTTTGTCTTTTGTCCGTATTTTCG 58.576 36.000 0.00 0.00 0.00 3.46
359 386 4.090930 CGTATTTTCGCGGTATTATCCTGG 59.909 45.833 6.13 0.00 0.00 4.45
524 551 2.349532 CGTTTCTTGCTCCCGTTTTCTC 60.350 50.000 0.00 0.00 0.00 2.87
525 552 1.892209 TTCTTGCTCCCGTTTTCTCC 58.108 50.000 0.00 0.00 0.00 3.71
528 555 0.762418 TTGCTCCCGTTTTCTCCTCA 59.238 50.000 0.00 0.00 0.00 3.86
576 618 1.471676 CCACTCGTCCCAAGATACTGC 60.472 57.143 0.00 0.00 0.00 4.40
611 653 2.222685 CGTCAAAGATTTCGAGCTCTGC 60.223 50.000 12.85 0.00 0.00 4.26
853 903 4.203618 GGCAACGCCTACTTCCTC 57.796 61.111 0.00 0.00 46.69 3.71
1250 1316 5.111989 TGCTTTCATCGGTAAATCTCTCTG 58.888 41.667 0.00 0.00 0.00 3.35
1251 1317 5.105351 TGCTTTCATCGGTAAATCTCTCTGA 60.105 40.000 0.00 0.00 0.00 3.27
1488 1560 5.297547 TCAAACTGTAGCCTCTTTACTGTG 58.702 41.667 0.00 0.00 34.66 3.66
1489 1561 4.957684 AACTGTAGCCTCTTTACTGTGT 57.042 40.909 0.00 0.00 34.66 3.72
1494 1566 6.662234 ACTGTAGCCTCTTTACTGTGTATGTA 59.338 38.462 0.00 0.00 33.63 2.29
1518 1590 7.321745 AGTACAGGCAAGCTTAATTGAATAC 57.678 36.000 0.00 0.00 31.55 1.89
1537 1609 8.939201 TGAATACTTGCAGTGATTTTTGAAAA 57.061 26.923 0.00 0.00 0.00 2.29
1592 1671 4.021719 AGTTTCATCACCCAGCTGAAATTG 60.022 41.667 17.39 6.39 42.37 2.32
1600 1679 4.508861 CACCCAGCTGAAATTGAACTTTTG 59.491 41.667 17.39 0.00 0.00 2.44
1668 1747 3.492482 GCCCTGCTTCTTCTGAGATCTAC 60.492 52.174 0.00 0.00 0.00 2.59
1671 1750 4.350346 CTGCTTCTTCTGAGATCTACACG 58.650 47.826 0.00 0.00 0.00 4.49
1672 1751 4.010349 TGCTTCTTCTGAGATCTACACGA 58.990 43.478 0.00 0.00 0.00 4.35
1704 1788 8.461222 TGATCATGTTCTTGGTGAAATTGTATC 58.539 33.333 5.42 0.00 36.30 2.24
1731 1815 1.744741 GACTGCAGGAGCTGGCTTC 60.745 63.158 19.93 0.00 43.74 3.86
1773 1857 5.172205 GTTCAAGCTGGAGAGGTAGTAAAG 58.828 45.833 0.00 0.00 0.00 1.85
1795 1879 6.793518 AGATTCCTCCTCAATCCCATATTT 57.206 37.500 0.00 0.00 31.52 1.40
1803 1887 7.506938 CCTCCTCAATCCCATATTTACATTGTT 59.493 37.037 0.00 0.00 0.00 2.83
1815 1899 4.811555 TTACATTGTTGCAGTGTCTGTC 57.188 40.909 0.00 0.00 35.92 3.51
1843 1927 7.750229 ATATGTATTTTCGCATGTCATCCTT 57.250 32.000 0.00 0.00 0.00 3.36
1860 1944 5.652014 TCATCCTTAGCACATACCAAAAAGG 59.348 40.000 0.00 0.00 45.67 3.11
1890 1989 9.549509 GCATTTTCACATCGTAACTACAAATTA 57.450 29.630 0.00 0.00 0.00 1.40
1897 1996 8.661257 CACATCGTAACTACAAATTATCCACAA 58.339 33.333 0.00 0.00 0.00 3.33
2088 2187 8.651588 GGTATGCACTTCTTATTCGAGATAATG 58.348 37.037 0.00 0.00 0.00 1.90
2110 2209 3.065786 GCATCTCTTTCGATGAAATGGCA 59.934 43.478 5.07 0.00 42.63 4.92
2146 2265 7.977789 ACAAAAGTTCAAAAACTGAAATGGT 57.022 28.000 0.00 0.00 45.67 3.55
2157 2276 5.514274 AACTGAAATGGTAGTTGTGTTGG 57.486 39.130 0.00 0.00 35.91 3.77
2195 2315 4.084693 GCTTGTCTACGACAGGTTTGTAAC 60.085 45.833 7.74 0.00 43.69 2.50
2207 2327 5.531287 ACAGGTTTGTAACTGATGGTTCTTC 59.469 40.000 0.00 0.00 39.17 2.87
2208 2328 5.765182 CAGGTTTGTAACTGATGGTTCTTCT 59.235 40.000 0.00 0.00 39.17 2.85
2209 2329 6.263168 CAGGTTTGTAACTGATGGTTCTTCTT 59.737 38.462 0.00 0.00 39.17 2.52
2244 2365 2.128035 GGCCGATTTGAGATACTGTCG 58.872 52.381 0.00 0.00 0.00 4.35
2250 2371 2.941453 TTGAGATACTGTCGCTGTCC 57.059 50.000 0.00 0.00 0.00 4.02
2361 2482 1.377202 TGGCGGAATTGCTGGACTC 60.377 57.895 0.00 0.00 34.52 3.36
2523 2654 7.041848 ACAGCCAAAAGTAAAATTCTTTGCATC 60.042 33.333 0.00 0.00 35.65 3.91
2658 2802 7.740519 AAGTAAAATTCTGTGCATAATTCGC 57.259 32.000 0.00 0.00 0.00 4.70
2665 2809 3.374988 TCTGTGCATAATTCGCTTTCAGG 59.625 43.478 0.00 0.00 0.00 3.86
2666 2810 3.342719 TGTGCATAATTCGCTTTCAGGA 58.657 40.909 0.00 0.00 0.00 3.86
2670 2814 6.082338 GTGCATAATTCGCTTTCAGGATATG 58.918 40.000 0.00 0.00 0.00 1.78
2700 2844 1.202580 GCACAACTGTCTGTCTCCTGT 60.203 52.381 0.00 0.00 0.00 4.00
2744 2890 1.949799 AAGTCCATGCCTCTCTGACT 58.050 50.000 0.00 0.00 37.88 3.41
2790 2936 8.035984 TGAAAATTGAATGCTGCTTCATGATTA 58.964 29.630 12.85 2.22 35.20 1.75
2870 3017 2.028567 GGCATCCACCTACTAGATCAGC 60.029 54.545 0.00 0.00 0.00 4.26
2937 3111 3.241322 GCATTAGCAATCGTTTGATGCAC 59.759 43.478 18.91 1.31 39.02 4.57
2965 3139 3.148412 ACATGTGTAGCTTGTGCATCAA 58.852 40.909 0.00 0.00 42.74 2.57
2973 3147 3.735591 AGCTTGTGCATCAAAATTGCTT 58.264 36.364 0.00 0.00 42.74 3.91
2974 3148 3.496884 AGCTTGTGCATCAAAATTGCTTG 59.503 39.130 0.00 0.00 42.74 4.01
3044 3238 5.428496 TTCAGTTTCTTCACTGCTTCATG 57.572 39.130 0.00 0.00 43.51 3.07
3092 3287 3.440173 TCTCCTGGATTTTCGTTTCATGC 59.560 43.478 0.00 0.00 0.00 4.06
3095 3290 3.057315 CCTGGATTTTCGTTTCATGCTGT 60.057 43.478 0.00 0.00 0.00 4.40
3134 3329 2.573462 CCCTCTGACTGAAATTCTGGGA 59.427 50.000 4.93 0.20 34.34 4.37
3136 3331 4.507335 CCCTCTGACTGAAATTCTGGGAAA 60.507 45.833 4.93 0.00 34.34 3.13
3137 3332 4.457257 CCTCTGACTGAAATTCTGGGAAAC 59.543 45.833 4.93 0.00 0.00 2.78
3138 3333 5.310409 TCTGACTGAAATTCTGGGAAACT 57.690 39.130 4.93 0.00 0.00 2.66
3139 3334 5.065914 TCTGACTGAAATTCTGGGAAACTG 58.934 41.667 4.93 0.00 0.00 3.16
3140 3335 4.792068 TGACTGAAATTCTGGGAAACTGT 58.208 39.130 4.93 0.00 0.00 3.55
3141 3336 4.821805 TGACTGAAATTCTGGGAAACTGTC 59.178 41.667 4.93 0.00 0.00 3.51
3157 3353 2.958355 ACTGTCCAAACCTGAATGTTGG 59.042 45.455 0.00 0.00 0.00 3.77
3313 3602 2.959372 GCTGCTGCTGCACATGAA 59.041 55.556 23.99 0.00 45.31 2.57
3316 3605 2.177531 GCTGCTGCACATGAACCG 59.822 61.111 11.11 0.00 39.41 4.44
3540 3829 1.342496 CTGGAAGTGAGCTCAGTGTCA 59.658 52.381 24.53 21.54 0.00 3.58
3552 3841 1.375140 AGTGTCAGTCTGCATGCCG 60.375 57.895 16.68 9.39 0.00 5.69
3642 3934 1.648504 ACCGTTGCCTTAGCGTAATC 58.351 50.000 0.00 0.00 44.31 1.75
3678 3970 2.766970 TTGTTTAGGCGTTGAACTGC 57.233 45.000 4.08 4.08 0.00 4.40
3776 4078 3.614176 GTCGAGTTTAACCGGTGGTTATC 59.386 47.826 8.52 3.34 45.95 1.75
3817 4119 3.290710 ACATTTGGTTGTTCTCTGCTGT 58.709 40.909 0.00 0.00 0.00 4.40
3822 4124 2.169561 TGGTTGTTCTCTGCTGTGTGTA 59.830 45.455 0.00 0.00 0.00 2.90
3825 4127 3.751479 TGTTCTCTGCTGTGTGTATGT 57.249 42.857 0.00 0.00 0.00 2.29
3843 4145 3.144657 TGTCTGTGATGCTGATGGTTT 57.855 42.857 0.00 0.00 0.00 3.27
3847 4149 3.507233 TCTGTGATGCTGATGGTTTTTCC 59.493 43.478 0.00 0.00 0.00 3.13
3973 4349 1.277557 CCTGTGCTGCTCCTAGTCTTT 59.722 52.381 0.00 0.00 0.00 2.52
3978 4354 3.697045 GTGCTGCTCCTAGTCTTTCTCTA 59.303 47.826 0.00 0.00 0.00 2.43
3979 4355 3.951037 TGCTGCTCCTAGTCTTTCTCTAG 59.049 47.826 0.00 0.00 35.86 2.43
3980 4356 3.951680 GCTGCTCCTAGTCTTTCTCTAGT 59.048 47.826 0.00 0.00 34.72 2.57
3981 4357 4.202010 GCTGCTCCTAGTCTTTCTCTAGTG 60.202 50.000 0.00 0.00 34.72 2.74
3992 4381 3.806949 TTCTCTAGTGGGTTTTGCCAT 57.193 42.857 0.00 0.00 39.65 4.40
4008 4397 0.171231 CCATCGAGTGCGTCTTCAGA 59.829 55.000 0.00 0.00 38.98 3.27
4026 4415 5.988310 TCAGATCAGGTTTACGGTCTTTA 57.012 39.130 0.00 0.00 0.00 1.85
4044 4433 5.744819 GTCTTTAGAGAATACGTCTTCAGGC 59.255 44.000 15.13 2.33 36.41 4.85
4134 4523 2.827800 TCTTCTCTTCCACACAGCAG 57.172 50.000 0.00 0.00 0.00 4.24
4135 4524 1.155042 CTTCTCTTCCACACAGCAGC 58.845 55.000 0.00 0.00 0.00 5.25
4136 4525 0.469494 TTCTCTTCCACACAGCAGCA 59.531 50.000 0.00 0.00 0.00 4.41
4283 4678 1.001760 GGAGGGAGGCACCAGTAGA 59.998 63.158 2.69 0.00 41.20 2.59
4287 4682 2.736826 GGAGGCACCAGTAGAGGGC 61.737 68.421 0.00 0.00 38.79 5.19
4289 4684 4.162690 GGCACCAGTAGAGGGCGG 62.163 72.222 0.00 0.00 0.00 6.13
4291 4686 3.390521 CACCAGTAGAGGGCGGCA 61.391 66.667 12.47 0.00 0.00 5.69
4294 4689 2.359169 CCAGTAGAGGGCGGCAAGA 61.359 63.158 12.47 0.00 0.00 3.02
4295 4690 1.142748 CAGTAGAGGGCGGCAAGAG 59.857 63.158 12.47 0.00 0.00 2.85
4296 4691 1.000486 AGTAGAGGGCGGCAAGAGA 60.000 57.895 12.47 0.00 0.00 3.10
4314 4709 0.759060 GAAGGAGGAGGAGGAGGAGC 60.759 65.000 0.00 0.00 0.00 4.70
4348 4747 1.517913 GCGCGGTGTAGGTTAGGAC 60.518 63.158 8.83 0.00 0.00 3.85
4349 4748 1.941999 GCGCGGTGTAGGTTAGGACT 61.942 60.000 8.83 0.00 0.00 3.85
4350 4749 0.529378 CGCGGTGTAGGTTAGGACTT 59.471 55.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 102 5.838529 TCCTCCCAATTTCGTTTCTTTTTC 58.161 37.500 0.00 0.00 0.00 2.29
345 372 1.263217 CGCAAACCAGGATAATACCGC 59.737 52.381 0.00 0.00 34.73 5.68
359 386 0.872388 ACCGAGAAATCACCGCAAAC 59.128 50.000 0.00 0.00 0.00 2.93
554 592 0.464452 GTATCTTGGGACGAGTGGGG 59.536 60.000 0.00 0.00 0.00 4.96
576 618 0.385598 TTGACGACGAACAGAGCTCG 60.386 55.000 8.37 6.04 42.06 5.03
1146 1212 1.991230 CTTCTTCATCCCCACCGGT 59.009 57.895 0.00 0.00 0.00 5.28
1250 1316 9.543018 CGTAATAACAGAAAAATGGAGAAGTTC 57.457 33.333 0.00 0.00 0.00 3.01
1251 1317 8.512138 CCGTAATAACAGAAAAATGGAGAAGTT 58.488 33.333 0.00 0.00 0.00 2.66
1488 1560 7.494625 TCAATTAAGCTTGCCTGTACTACATAC 59.505 37.037 9.86 0.00 0.00 2.39
1489 1561 7.561251 TCAATTAAGCTTGCCTGTACTACATA 58.439 34.615 9.86 0.00 0.00 2.29
1494 1566 7.112779 AGTATTCAATTAAGCTTGCCTGTACT 58.887 34.615 9.86 6.15 0.00 2.73
1537 1609 7.177392 GCAATAGGGATCCTTAACTATGCATTT 59.823 37.037 19.98 0.00 34.61 2.32
1550 1629 2.053244 CTGTCAGGCAATAGGGATCCT 58.947 52.381 12.58 0.00 37.71 3.24
1592 1671 6.131544 TGTAAGGCTTCAGTTCAAAAGTTC 57.868 37.500 1.30 0.00 0.00 3.01
1600 1679 4.319177 ACAGACATGTAAGGCTTCAGTTC 58.681 43.478 1.30 3.16 38.09 3.01
1668 1747 4.997905 AGAACATGATCAAACACTCGTG 57.002 40.909 0.00 0.00 35.09 4.35
1671 1750 5.239306 TCACCAAGAACATGATCAAACACTC 59.761 40.000 0.00 0.00 0.00 3.51
1672 1751 5.132502 TCACCAAGAACATGATCAAACACT 58.867 37.500 0.00 0.00 0.00 3.55
1731 1815 2.156917 ACAGCAATGACATGTGGAGTG 58.843 47.619 1.15 0.00 0.00 3.51
1773 1857 7.461749 TGTAAATATGGGATTGAGGAGGAATC 58.538 38.462 0.00 0.00 0.00 2.52
1795 1879 3.802866 TGACAGACACTGCAACAATGTA 58.197 40.909 0.00 0.00 34.37 2.29
1803 1887 8.962884 AAATACATATTATGACAGACACTGCA 57.037 30.769 10.62 0.00 34.37 4.41
1815 1899 9.494479 GGATGACATGCGAAAATACATATTATG 57.506 33.333 2.03 2.03 0.00 1.90
1876 1968 8.025243 AGTGTTGTGGATAATTTGTAGTTACG 57.975 34.615 0.00 0.00 0.00 3.18
1897 1996 5.590259 AGCACTCAAAGTTATTCACAAGTGT 59.410 36.000 0.00 0.00 36.22 3.55
2144 2263 4.024048 CACAGTGATTCCAACACAACTACC 60.024 45.833 0.00 0.00 40.25 3.18
2146 2265 4.133820 CCACAGTGATTCCAACACAACTA 58.866 43.478 0.62 0.00 40.25 2.24
2157 2276 0.798776 CAAGCCGTCCACAGTGATTC 59.201 55.000 0.62 0.00 0.00 2.52
2195 2315 5.218139 GCAGAAAACAAGAAGAACCATCAG 58.782 41.667 0.00 0.00 0.00 2.90
2244 2365 1.810030 GGTGAACGATCCGGACAGC 60.810 63.158 6.12 5.77 0.00 4.40
2361 2482 0.035152 TAGGTGTGCAGGCAATCAGG 60.035 55.000 0.00 0.00 0.00 3.86
2523 2654 1.459592 CTAACACGCTGGGACGAAAAG 59.540 52.381 0.00 0.00 36.70 2.27
2658 2802 6.147492 GTGCTAGAATGCTCATATCCTGAAAG 59.853 42.308 0.00 0.00 32.14 2.62
2665 2809 5.757320 ACAGTTGTGCTAGAATGCTCATATC 59.243 40.000 0.00 0.00 36.53 1.63
2666 2810 5.678583 ACAGTTGTGCTAGAATGCTCATAT 58.321 37.500 0.00 0.00 36.53 1.78
2670 2814 3.370366 CAGACAGTTGTGCTAGAATGCTC 59.630 47.826 0.00 0.00 0.00 4.26
2728 2872 2.171568 ATCAGTCAGAGAGGCATGGA 57.828 50.000 0.00 0.00 0.00 3.41
2790 2936 4.596643 AGCAGTCTGGCTATTGAGGAATAT 59.403 41.667 1.14 0.00 43.70 1.28
2937 3111 3.124128 CACAAGCTACACATGTACAGCTG 59.876 47.826 25.80 21.53 38.59 4.24
2965 3139 3.511540 GGGCTAGGAAAGACAAGCAATTT 59.488 43.478 0.00 0.00 33.25 1.82
2973 3147 2.708861 TCACTTTGGGCTAGGAAAGACA 59.291 45.455 0.00 0.00 33.25 3.41
2974 3148 3.418684 TCACTTTGGGCTAGGAAAGAC 57.581 47.619 0.00 0.00 34.02 3.01
3044 3238 2.754552 TCATTGTGCTAACATCCTTGGC 59.245 45.455 0.00 0.00 35.83 4.52
3092 3287 2.549329 GGCATGCCCTTTTCAAAAACAG 59.451 45.455 27.24 0.00 0.00 3.16
3114 3309 3.988976 TCCCAGAATTTCAGTCAGAGG 57.011 47.619 0.00 0.00 0.00 3.69
3134 3329 4.141959 CCAACATTCAGGTTTGGACAGTTT 60.142 41.667 0.00 0.00 0.00 2.66
3136 3331 2.958355 CCAACATTCAGGTTTGGACAGT 59.042 45.455 0.00 0.00 0.00 3.55
3137 3332 2.958355 ACCAACATTCAGGTTTGGACAG 59.042 45.455 6.59 0.00 33.39 3.51
3138 3333 3.025322 ACCAACATTCAGGTTTGGACA 57.975 42.857 6.59 0.00 33.39 4.02
3186 3467 7.755822 CACTGGTTAGTCATTTCTCTAGTGTAC 59.244 40.741 0.00 0.00 34.07 2.90
3376 3665 3.797225 GATGGGAGCATGCGCGAGA 62.797 63.158 12.10 1.78 45.49 4.04
3384 3673 2.107750 CGACGCTGATGGGAGCAT 59.892 61.111 0.00 0.00 39.07 3.79
3385 3674 4.147449 CCGACGCTGATGGGAGCA 62.147 66.667 0.00 0.00 39.07 4.26
3540 3829 2.125912 GACGACGGCATGCAGACT 60.126 61.111 24.99 2.29 0.00 3.24
3552 3841 1.729838 GCTGGTCACTGACGACGAC 60.730 63.158 0.00 0.00 36.73 4.34
3678 3970 3.678072 ACAATCCACGACGACACATTAAG 59.322 43.478 0.00 0.00 0.00 1.85
3804 4106 4.058124 GACATACACACAGCAGAGAACAA 58.942 43.478 0.00 0.00 0.00 2.83
3817 4119 3.959535 TCAGCATCACAGACATACACA 57.040 42.857 0.00 0.00 0.00 3.72
3822 4124 3.361281 AACCATCAGCATCACAGACAT 57.639 42.857 0.00 0.00 0.00 3.06
3825 4127 3.507233 GGAAAAACCATCAGCATCACAGA 59.493 43.478 0.00 0.00 38.79 3.41
3843 4145 6.805713 TGCAAAAACAAAAACCAAAAGGAAA 58.194 28.000 0.00 0.00 0.00 3.13
3847 4149 7.691430 AACTTGCAAAAACAAAAACCAAAAG 57.309 28.000 0.00 0.00 0.00 2.27
3973 4349 2.354704 CGATGGCAAAACCCACTAGAGA 60.355 50.000 0.00 0.00 37.79 3.10
3978 4354 0.110486 ACTCGATGGCAAAACCCACT 59.890 50.000 0.00 0.00 37.79 4.00
3979 4355 0.240945 CACTCGATGGCAAAACCCAC 59.759 55.000 0.00 0.00 37.79 4.61
3980 4356 1.523154 GCACTCGATGGCAAAACCCA 61.523 55.000 0.00 0.00 39.65 4.51
3981 4357 1.212751 GCACTCGATGGCAAAACCC 59.787 57.895 0.00 0.00 37.83 4.11
3992 4381 1.131315 CTGATCTGAAGACGCACTCGA 59.869 52.381 0.00 0.00 39.41 4.04
4008 4397 6.600882 TTCTCTAAAGACCGTAAACCTGAT 57.399 37.500 0.00 0.00 0.00 2.90
4026 4415 2.366533 TCGCCTGAAGACGTATTCTCT 58.633 47.619 22.26 0.00 31.02 3.10
4044 4433 1.801913 CTCTCAACCGTCGCCTTCG 60.802 63.158 0.00 0.00 0.00 3.79
4058 4447 0.383949 GACGCCTCCTGTGATCTCTC 59.616 60.000 0.00 0.00 0.00 3.20
4100 4489 0.038166 GAAGATGTGGGACCCAGCAA 59.962 55.000 15.52 2.77 32.34 3.91
4244 4639 2.016704 CGATACGCATGGACGGCTC 61.017 63.158 0.00 0.00 37.37 4.70
4256 4651 3.671411 CCTCCCTCCGGCGATACG 61.671 72.222 9.30 0.00 0.00 3.06
4271 4666 3.077556 CGCCCTCTACTGGTGCCT 61.078 66.667 0.00 0.00 0.00 4.75
4275 4670 2.606519 TTGCCGCCCTCTACTGGT 60.607 61.111 0.00 0.00 0.00 4.00
4283 4678 2.607750 TCCTTCTCTTGCCGCCCT 60.608 61.111 0.00 0.00 0.00 5.19
4287 4682 0.972983 TCCTCCTCCTTCTCTTGCCG 60.973 60.000 0.00 0.00 0.00 5.69
4289 4684 0.829990 CCTCCTCCTCCTTCTCTTGC 59.170 60.000 0.00 0.00 0.00 4.01
4291 4686 1.290732 CCTCCTCCTCCTCCTTCTCTT 59.709 57.143 0.00 0.00 0.00 2.85
4294 4689 0.933700 CTCCTCCTCCTCCTCCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
4295 4690 0.759060 GCTCCTCCTCCTCCTCCTTC 60.759 65.000 0.00 0.00 0.00 3.46
4296 4691 1.313129 GCTCCTCCTCCTCCTCCTT 59.687 63.158 0.00 0.00 0.00 3.36
4341 4740 1.129917 GCCCCCTCCTAAGTCCTAAC 58.870 60.000 0.00 0.00 0.00 2.34
4348 4747 0.760945 ACATCTCGCCCCCTCCTAAG 60.761 60.000 0.00 0.00 0.00 2.18
4349 4748 0.759436 GACATCTCGCCCCCTCCTAA 60.759 60.000 0.00 0.00 0.00 2.69
4350 4749 1.152525 GACATCTCGCCCCCTCCTA 60.153 63.158 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.