Multiple sequence alignment - TraesCS1A01G138100

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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 TraesCS1A01G138100 chr1A 100.000 3926 0 0 1 3926 229172150 229168225 0.000000e+00 7251.0
1 TraesCS1A01G138100 chr1D 95.485 1794 60 11 1 1789 171165332 171163555 0.000000e+00 2844.0
2 TraesCS1A01G138100 chr1D 92.422 1953 104 9 1851 3800 171163245 171161334 0.000000e+00 2747.0
3 TraesCS1A01G138100 chr1D 96.875 128 4 0 3799 3926 171161286 171161159 8.540000e-52 215.0
4 TraesCS1A01G138100 chr1D 83.721 172 18 7 1726 1896 71032759 71032597 1.890000e-33 154.0
5 TraesCS1A01G138100 chr1D 82.486 177 18 8 1722 1896 378705158 378705323 4.090000e-30 143.0
6 TraesCS1A01G138100 chr1B 91.465 1898 152 8 1911 3800 226358258 226356363 0.000000e+00 2599.0
7 TraesCS1A01G138100 chr1B 93.109 1727 95 14 4 1725 226360019 226358312 0.000000e+00 2508.0
8 TraesCS1A01G138100 chr1B 92.188 128 10 0 3799 3926 226356315 226356188 8.670000e-42 182.0
9 TraesCS1A01G138100 chr1B 100.000 31 0 0 1895 1925 226358302 226358272 1.520000e-04 58.4
10 TraesCS1A01G138100 chr6D 83.626 171 18 9 1727 1896 470516676 470516515 6.790000e-33 152.0
11 TraesCS1A01G138100 chr7A 81.461 178 22 8 1720 1896 28048937 28049104 6.840000e-28 135.0
12 TraesCS1A01G138100 chr7A 85.366 123 15 3 3792 3911 370799044 370798922 1.480000e-24 124.0
13 TraesCS1A01G138100 chr7A 86.087 115 14 2 3799 3911 713211863 713211749 5.330000e-24 122.0
14 TraesCS1A01G138100 chr7A 77.193 171 26 10 124 291 383626723 383626883 1.940000e-13 87.9
15 TraesCS1A01G138100 chr7A 90.698 43 2 2 1616 1656 709734258 709734216 5.480000e-04 56.5
16 TraesCS1A01G138100 chr3B 86.957 115 13 2 3799 3911 346393186 346393300 1.150000e-25 128.0
17 TraesCS1A01G138100 chr3A 86.957 115 13 2 3799 3911 293645680 293645566 1.150000e-25 128.0
18 TraesCS1A01G138100 chr2B 86.087 115 14 2 3799 3911 326311826 326311712 5.330000e-24 122.0
19 TraesCS1A01G138100 chr2B 88.333 60 7 0 2442 2501 25673692 25673633 5.440000e-09 73.1
20 TraesCS1A01G138100 chrUn 84.553 123 16 3 3792 3911 337870972 337870850 6.890000e-23 119.0
21 TraesCS1A01G138100 chrUn 88.462 52 6 0 2608 2659 47831500 47831449 3.280000e-06 63.9
22 TraesCS1A01G138100 chr6B 81.579 152 20 5 1746 1896 720662740 720662884 6.890000e-23 119.0
23 TraesCS1A01G138100 chr6B 83.761 117 12 6 1778 1892 578059103 578059214 1.930000e-18 104.0
24 TraesCS1A01G138100 chr6B 77.108 166 34 4 125 288 434143890 434144053 4.180000e-15 93.5
25 TraesCS1A01G138100 chr4D 80.000 165 30 1 2253 2414 116270798 116270962 6.890000e-23 119.0
26 TraesCS1A01G138100 chr4D 84.874 119 16 2 3799 3915 230464204 230464086 6.890000e-23 119.0
27 TraesCS1A01G138100 chr4D 100.000 28 0 0 1869 1896 349903756 349903729 7.000000e-03 52.8
28 TraesCS1A01G138100 chr4B 80.120 166 28 3 2253 2414 178071729 178071893 6.890000e-23 119.0
29 TraesCS1A01G138100 chr4A 80.000 165 30 1 2253 2414 460239586 460239422 6.890000e-23 119.0
30 TraesCS1A01G138100 chr7B 77.439 164 35 2 125 287 295117213 295117375 3.230000e-16 97.1
31 TraesCS1A01G138100 chr7B 76.364 165 35 4 125 287 295103275 295103437 6.990000e-13 86.1
32 TraesCS1A01G138100 chr7B 90.698 43 2 2 1616 1656 711062949 711062907 5.480000e-04 56.5
33 TraesCS1A01G138100 chr5B 78.000 150 24 5 1747 1896 2611112 2611252 6.990000e-13 86.1
34 TraesCS1A01G138100 chr2D 90.385 52 5 0 2608 2659 6708248 6708299 7.040000e-08 69.4
35 TraesCS1A01G138100 chr7D 90.698 43 2 2 1616 1656 617019060 617019018 5.480000e-04 56.5


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 TraesCS1A01G138100 chr1A 229168225 229172150 3925 True 7251.000000 7251 100.000000 1 3926 1 chr1A.!!$R1 3925
1 TraesCS1A01G138100 chr1D 171161159 171165332 4173 True 1935.333333 2844 94.927333 1 3926 3 chr1D.!!$R2 3925
2 TraesCS1A01G138100 chr1B 226356188 226360019 3831 True 1336.850000 2599 94.190500 4 3926 4 chr1B.!!$R1 3922

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
685 689 0.479378 GTACCGATCCTCCTCCTCCT 59.521 60.0 0.00 0.0 0.00 3.69 F
1646 1659 0.107459 GGGAATGGCTGGTCAGTCTC 60.107 60.0 4.16 0.0 33.37 3.36 F
1859 2138 0.179150 ACACGCGCACACACAAAATT 60.179 45.0 5.73 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2259 0.107312 CTTGTCAGGCTAGCCATGCT 60.107 55.0 34.7 12.31 43.41 3.79 R
2606 2913 0.456142 GCTGTACACGTCGCTCATCA 60.456 55.0 0.0 0.00 0.00 3.07 R
2970 3277 1.033574 GCTGTAGTAGAGGCGATGGT 58.966 55.0 0.0 0.00 0.00 3.55 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
47 48 2.103432 TGAGGTGTTCTTTTGTCCGCTA 59.897 45.455 0.00 0.00 0.00 4.26
63 64 3.545124 CTACCGTGGTGGCTTGGCA 62.545 63.158 0.72 0.00 43.94 4.92
71 72 1.675641 GTGGCTTGGCATTCGTCCT 60.676 57.895 0.00 0.00 0.00 3.85
80 81 1.338200 GGCATTCGTCCTGAGTGTCTT 60.338 52.381 0.00 0.00 36.13 3.01
129 130 4.100653 CACAGATAGCATTCCCTCTTGAGA 59.899 45.833 0.00 0.00 0.00 3.27
257 259 1.336332 GGGATGATGATGACGAGTCCG 60.336 57.143 0.34 0.00 42.50 4.79
316 318 5.242171 GTGCATGATCCATGGTGAATTGATA 59.758 40.000 12.58 0.00 41.64 2.15
321 323 7.514784 TGATCCATGGTGAATTGATAATGTC 57.485 36.000 12.58 0.00 0.00 3.06
401 403 2.805099 GCAATTCAACCGAAATTGGCAA 59.195 40.909 0.68 0.68 34.01 4.52
550 554 9.840427 CGTTTAATTAGTGGTTTCTCATGATTT 57.160 29.630 0.00 0.00 0.00 2.17
603 607 3.293311 TCACTTGAACCGTACTACTGC 57.707 47.619 0.00 0.00 0.00 4.40
648 652 4.319839 CGTTTCTTTCCTTTCTCCTCTTGC 60.320 45.833 0.00 0.00 0.00 4.01
685 689 0.479378 GTACCGATCCTCCTCCTCCT 59.521 60.000 0.00 0.00 0.00 3.69
686 690 0.772384 TACCGATCCTCCTCCTCCTC 59.228 60.000 0.00 0.00 0.00 3.71
700 704 3.041211 TCCTCCTCTCTCTCTCTCTCTG 58.959 54.545 0.00 0.00 0.00 3.35
706 710 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
707 711 3.072330 TCTCTCTCTCTCTCTGTGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
708 712 3.145286 TCTCTCTCTCTCTGTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
709 713 2.884012 CTCTCTCTCTCTGTGTGTGTGT 59.116 50.000 0.00 0.00 0.00 3.72
836 844 2.499289 CTCTTGAGCCCCGCATATAGAT 59.501 50.000 0.00 0.00 0.00 1.98
979 990 2.862597 AGGGGAGAGGGCTAGATATAGG 59.137 54.545 0.00 0.00 0.00 2.57
1078 1089 5.442391 AGTCAGGTGAGTAATACTCCTCTC 58.558 45.833 16.89 5.89 44.44 3.20
1112 1123 6.631016 TCTGCTTTCTAAGTGATCGTTATGT 58.369 36.000 0.00 0.00 0.00 2.29
1541 1554 2.890766 CGGCAGGGTGTACAAGGGT 61.891 63.158 0.00 0.00 0.00 4.34
1646 1659 0.107459 GGGAATGGCTGGTCAGTCTC 60.107 60.000 4.16 0.00 33.37 3.36
1647 1660 0.107459 GGAATGGCTGGTCAGTCTCC 60.107 60.000 4.16 0.18 33.37 3.71
1663 1676 2.753452 GTCTCCCTCTAATCGTGACACA 59.247 50.000 6.37 0.00 0.00 3.72
1664 1677 2.753452 TCTCCCTCTAATCGTGACACAC 59.247 50.000 6.37 0.00 0.00 3.82
1701 1714 8.518151 TTTGCACAAATTGACATGTACATTAG 57.482 30.769 5.37 0.00 0.00 1.73
1784 1797 2.309528 TGGCACCGAGTGATACAATC 57.690 50.000 8.04 0.00 35.23 2.67
1796 2075 9.776158 CCGAGTGATACAATCATAAGAGTATAC 57.224 37.037 0.00 0.00 42.04 1.47
1810 2089 9.607988 CATAAGAGTATACATCCGATCTCTACT 57.392 37.037 5.50 0.00 32.92 2.57
1826 2105 7.308891 CGATCTCTACTTAGTTAGGATGCACAT 60.309 40.741 0.00 0.00 0.00 3.21
1828 2107 8.397575 TCTCTACTTAGTTAGGATGCACATAG 57.602 38.462 0.00 0.00 0.00 2.23
1833 2112 4.443978 AGTTAGGATGCACATAGCCAAT 57.556 40.909 0.00 0.00 44.83 3.16
1836 2115 3.862877 AGGATGCACATAGCCAATACA 57.137 42.857 0.00 0.00 44.83 2.29
1837 2116 3.480470 AGGATGCACATAGCCAATACAC 58.520 45.455 0.00 0.00 44.83 2.90
1838 2117 2.224079 GGATGCACATAGCCAATACACG 59.776 50.000 0.00 0.00 44.83 4.49
1839 2118 1.013596 TGCACATAGCCAATACACGC 58.986 50.000 0.00 0.00 44.83 5.34
1840 2119 1.013596 GCACATAGCCAATACACGCA 58.986 50.000 0.00 0.00 37.23 5.24
1841 2120 1.268032 GCACATAGCCAATACACGCAC 60.268 52.381 0.00 0.00 37.23 5.34
1845 2124 1.355796 TAGCCAATACACGCACACGC 61.356 55.000 0.00 0.00 45.53 5.34
1855 2134 4.528740 GCACACGCGCACACACAA 62.529 61.111 5.73 0.00 0.00 3.33
1856 2135 2.099254 CACACGCGCACACACAAA 59.901 55.556 5.73 0.00 0.00 2.83
1857 2136 1.512947 CACACGCGCACACACAAAA 60.513 52.632 5.73 0.00 0.00 2.44
1858 2137 0.865218 CACACGCGCACACACAAAAT 60.865 50.000 5.73 0.00 0.00 1.82
1859 2138 0.179150 ACACGCGCACACACAAAATT 60.179 45.000 5.73 0.00 0.00 1.82
1860 2139 1.064208 ACACGCGCACACACAAAATTA 59.936 42.857 5.73 0.00 0.00 1.40
1861 2140 1.446465 CACGCGCACACACAAAATTAC 59.554 47.619 5.73 0.00 0.00 1.89
1862 2141 1.049251 CGCGCACACACAAAATTACC 58.951 50.000 8.75 0.00 0.00 2.85
1863 2142 1.414378 GCGCACACACAAAATTACCC 58.586 50.000 0.30 0.00 0.00 3.69
1864 2143 1.933052 GCGCACACACAAAATTACCCC 60.933 52.381 0.30 0.00 0.00 4.95
1868 2147 3.723260 CACACACAAAATTACCCCCAAC 58.277 45.455 0.00 0.00 0.00 3.77
1875 2154 5.641636 CACAAAATTACCCCCAACAAATAGC 59.358 40.000 0.00 0.00 0.00 2.97
1949 2256 1.539827 GCGTGGTAGGTGCAGATTTTT 59.460 47.619 0.00 0.00 0.00 1.94
1952 2259 3.749088 CGTGGTAGGTGCAGATTTTTGTA 59.251 43.478 0.00 0.00 0.00 2.41
1954 2261 3.756434 TGGTAGGTGCAGATTTTTGTAGC 59.244 43.478 0.00 0.00 0.00 3.58
1956 2263 4.399303 GGTAGGTGCAGATTTTTGTAGCAT 59.601 41.667 0.00 0.00 37.56 3.79
1958 2265 3.194116 AGGTGCAGATTTTTGTAGCATGG 59.806 43.478 0.00 0.00 37.56 3.66
2038 2345 1.559682 GTGATCTTCTTGGGCCACCTA 59.440 52.381 5.23 0.00 37.76 3.08
2050 2357 0.180406 GCCACCTATCACACCCGAAT 59.820 55.000 0.00 0.00 0.00 3.34
2140 2447 1.665916 CAGCGTGGAGTCACACCTG 60.666 63.158 0.00 9.46 43.79 4.00
2189 2496 5.423886 TCCATTTTCCACACTTTTGGTTTC 58.576 37.500 0.00 0.00 37.93 2.78
2198 2505 1.200484 ACTTTTGGTTTCGTGCGTGTT 59.800 42.857 0.00 0.00 0.00 3.32
2284 2591 1.001240 CGAGGATGAAGATCGCGCTC 61.001 60.000 5.56 0.00 0.00 5.03
2287 2594 1.299468 GATGAAGATCGCGCTCGGT 60.299 57.895 5.56 0.00 36.13 4.69
2383 2690 2.169352 CCTCCTCGACCATGACTTCAAT 59.831 50.000 0.00 0.00 0.00 2.57
2578 2885 4.222810 GGGTCTGGTGGCTAAATTGATTTT 59.777 41.667 0.00 0.00 0.00 1.82
2583 2890 6.719370 TCTGGTGGCTAAATTGATTTTACTGT 59.281 34.615 0.00 0.00 0.00 3.55
2628 2935 1.092348 TGAGCGACGTGTACAGCTAT 58.908 50.000 7.27 0.00 40.39 2.97
2647 2954 3.958860 GGGTGGTGCTGCTGGAGT 61.959 66.667 0.00 0.00 0.00 3.85
2652 2959 2.263741 GGTGCTGCTGGAGTTGGTG 61.264 63.158 0.00 0.00 0.00 4.17
2655 2962 1.227943 GCTGCTGGAGTTGGTGACA 60.228 57.895 0.00 0.00 39.83 3.58
2682 2989 3.973516 TCGCTGGACAAGTCGCGT 61.974 61.111 17.52 0.00 45.25 6.01
2760 3067 2.897823 AGGTGTTGGGGATCCTAGAT 57.102 50.000 12.58 0.00 0.00 1.98
2771 3078 2.520069 GATCCTAGATCCAAGGCTCGA 58.480 52.381 6.81 0.00 33.84 4.04
2835 3142 2.657237 GCGTACCACTGCCTCAGT 59.343 61.111 0.00 0.00 46.51 3.41
2970 3277 0.535780 CCTTGCAGGTGCTGTCAGAA 60.536 55.000 3.32 0.00 42.66 3.02
2985 3292 2.950309 GTCAGAACCATCGCCTCTACTA 59.050 50.000 0.00 0.00 0.00 1.82
3004 3311 2.932194 AGCTCCTGGAAGCAGGCA 60.932 61.111 16.74 0.00 45.00 4.75
3068 3375 1.237285 GGCAGGCAGGTGTAGTGTTG 61.237 60.000 0.00 0.00 0.00 3.33
3069 3376 1.856265 GCAGGCAGGTGTAGTGTTGC 61.856 60.000 0.00 0.00 35.87 4.17
3075 3382 2.771089 CAGGTGTAGTGTTGCTGATGT 58.229 47.619 0.00 0.00 0.00 3.06
3128 3435 1.617947 CCCTAGAGGTGAGTGGGTGC 61.618 65.000 0.00 0.00 33.49 5.01
3140 3447 1.301716 TGGGTGCAAACGAGCTCTC 60.302 57.895 12.85 0.00 34.99 3.20
3185 3493 2.663826 TTCTTGGGCACACAACAAAC 57.336 45.000 0.00 0.00 0.00 2.93
3238 3547 9.856488 ATTACTAGTAGGTGCGTATATCAATTG 57.144 33.333 2.23 0.00 0.00 2.32
3281 3590 0.948623 CACCAACACGAAGCCGATCA 60.949 55.000 0.00 0.00 39.50 2.92
3331 3640 6.305693 AGCTACAGTGCTCTTTTGTAAAAG 57.694 37.500 10.14 10.14 45.17 2.27
3332 3641 5.239525 AGCTACAGTGCTCTTTTGTAAAAGG 59.760 40.000 14.99 8.52 44.22 3.11
3334 3643 3.636764 ACAGTGCTCTTTTGTAAAAGGGG 59.363 43.478 16.36 10.96 44.73 4.79
3537 3851 1.602323 GATCCGGCACCCACAAACA 60.602 57.895 0.00 0.00 0.00 2.83
3540 3854 1.228003 CCGGCACCCACAAACACTA 60.228 57.895 0.00 0.00 0.00 2.74
3582 3896 2.823747 CCATGAAGGCCATCATACATGG 59.176 50.000 22.42 17.12 45.10 3.66
3660 3974 6.897413 ACAATCTGAAGGGGCATAACTAAAAT 59.103 34.615 0.00 0.00 0.00 1.82
3686 4000 3.202906 AGAAGTAAAGTTCGTTGCAGCA 58.797 40.909 0.24 0.00 0.00 4.41
3695 4009 2.920490 GTTCGTTGCAGCAAAAAGACAA 59.080 40.909 10.11 0.00 0.00 3.18
3708 4022 9.252962 CAGCAAAAAGACAAATTTTGATAGAGT 57.747 29.630 15.81 0.00 45.96 3.24
3709 4023 9.252962 AGCAAAAAGACAAATTTTGATAGAGTG 57.747 29.630 15.81 7.82 45.96 3.51
3769 4083 3.880047 TGGTGGAGTATACTTTCACGG 57.120 47.619 22.62 0.00 33.96 4.94
3772 4086 3.446516 GGTGGAGTATACTTTCACGGTCT 59.553 47.826 22.62 0.00 33.96 3.85
3777 4091 5.312120 AGTATACTTTCACGGTCTGACTG 57.688 43.478 14.91 14.91 0.00 3.51
3779 4093 0.753262 ACTTTCACGGTCTGACTGCT 59.247 50.000 16.33 1.58 0.00 4.24
3821 4184 4.499526 GCATGATCAACTTGACCACAAACA 60.500 41.667 0.00 0.00 35.49 2.83
3871 4234 9.334693 GAACAAGAAAGTACTAAGATTGCAATG 57.665 33.333 18.59 4.68 0.00 2.82
3917 4280 9.900710 TGAAAGCTTTATTAATAAAGTTTGCGA 57.099 25.926 32.82 23.68 46.20 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.056107 CCTCAAGTGGAGTCACCGAAATA 60.056 47.826 0.00 0.00 44.64 1.40
47 48 3.808218 AATGCCAAGCCACCACGGT 62.808 57.895 0.00 0.00 36.97 4.83
63 64 2.160205 TCGAAGACACTCAGGACGAAT 58.840 47.619 0.00 0.00 0.00 3.34
71 72 0.873054 GACGACCTCGAAGACACTCA 59.127 55.000 0.78 0.00 43.02 3.41
80 81 3.508793 AGGTATCAAAAAGACGACCTCGA 59.491 43.478 0.78 0.00 40.32 4.04
129 130 4.679373 CCACTTGAGACATGGCTACTAT 57.321 45.455 0.00 0.00 0.00 2.12
179 180 4.545678 AGAGCTATTGAGACTGAGGTGAT 58.454 43.478 0.00 0.00 0.00 3.06
235 237 2.546795 GGACTCGTCATCATCATCCCAC 60.547 54.545 0.00 0.00 0.00 4.61
257 259 1.269831 GCATCCTACGGTCATCTCCAC 60.270 57.143 0.00 0.00 0.00 4.02
261 263 1.338337 CGAAGCATCCTACGGTCATCT 59.662 52.381 0.00 0.00 0.00 2.90
279 281 1.817447 TCATGCACCAAAATGATGCGA 59.183 42.857 0.00 0.00 40.65 5.10
288 290 1.826096 CACCATGGATCATGCACCAAA 59.174 47.619 21.47 0.00 40.20 3.28
297 299 6.491062 GGACATTATCAATTCACCATGGATCA 59.509 38.462 21.47 0.74 27.43 2.92
316 318 0.469917 CGGAGCACCCTATGGACATT 59.530 55.000 0.00 0.00 34.81 2.71
401 403 3.417101 TGGTTCGTACAGGCATTTCATT 58.583 40.909 0.00 0.00 0.00 2.57
550 554 8.842764 ACTTTCTCCCCTTTATCATTACCTTTA 58.157 33.333 0.00 0.00 0.00 1.85
592 596 2.467566 ACAAAAGGGCAGTAGTACGG 57.532 50.000 0.00 0.00 0.00 4.02
603 607 6.893759 ACGAAAAGAAAAACAAACAAAAGGG 58.106 32.000 0.00 0.00 0.00 3.95
685 689 3.072330 ACACACACAGAGAGAGAGAGAGA 59.928 47.826 0.00 0.00 0.00 3.10
686 690 3.189080 CACACACACAGAGAGAGAGAGAG 59.811 52.174 0.00 0.00 0.00 3.20
700 704 4.552767 CGAAAGAGGAATGAACACACACAC 60.553 45.833 0.00 0.00 0.00 3.82
706 710 4.970003 CACAAACGAAAGAGGAATGAACAC 59.030 41.667 0.00 0.00 0.00 3.32
707 711 4.878971 TCACAAACGAAAGAGGAATGAACA 59.121 37.500 0.00 0.00 0.00 3.18
708 712 5.205565 GTCACAAACGAAAGAGGAATGAAC 58.794 41.667 0.00 0.00 0.00 3.18
709 713 4.274950 GGTCACAAACGAAAGAGGAATGAA 59.725 41.667 0.00 0.00 0.00 2.57
836 844 5.477291 AGAAAGGAAGAAGACGATCACTGTA 59.523 40.000 0.00 0.00 0.00 2.74
979 990 6.715264 CCCATAAGACACAGTATTTATTCCCC 59.285 42.308 0.00 0.00 0.00 4.81
1078 1089 0.608582 AGAAAGCAGAGCAGCAAGGG 60.609 55.000 0.00 0.00 36.85 3.95
1112 1123 2.606213 TGAGGGCGGTGGATCACA 60.606 61.111 0.00 0.00 35.86 3.58
1481 1494 2.604079 TCCTGCCGGAACCCGTTA 60.604 61.111 5.05 0.00 46.80 3.18
1646 1659 1.825474 AGGTGTGTCACGATTAGAGGG 59.175 52.381 0.00 0.00 34.83 4.30
1647 1660 3.695060 AGTAGGTGTGTCACGATTAGAGG 59.305 47.826 0.00 0.00 34.83 3.69
1679 1692 9.619316 TTAACTAATGTACATGTCAATTTGTGC 57.381 29.630 9.63 0.00 0.00 4.57
1764 1777 2.170397 TGATTGTATCACTCGGTGCCAT 59.830 45.455 0.00 0.00 33.59 4.40
1784 1797 9.607988 AGTAGAGATCGGATGTATACTCTTATG 57.392 37.037 14.53 0.00 36.39 1.90
1796 2075 7.627513 GCATCCTAACTAAGTAGAGATCGGATG 60.628 44.444 0.00 0.00 44.21 3.51
1798 2077 5.706369 GCATCCTAACTAAGTAGAGATCGGA 59.294 44.000 0.00 0.00 0.00 4.55
1810 2089 5.366482 TTGGCTATGTGCATCCTAACTAA 57.634 39.130 0.00 0.00 45.15 2.24
1817 2096 2.224079 CGTGTATTGGCTATGTGCATCC 59.776 50.000 0.00 0.00 45.15 3.51
1826 2105 1.355796 GCGTGTGCGTGTATTGGCTA 61.356 55.000 0.00 0.00 40.81 3.93
1828 2107 2.202298 GCGTGTGCGTGTATTGGC 60.202 61.111 0.00 0.00 40.81 4.52
1838 2117 4.528740 TTGTGTGTGCGCGTGTGC 62.529 61.111 8.43 0.00 37.91 4.57
1839 2118 0.865218 ATTTTGTGTGTGCGCGTGTG 60.865 50.000 8.43 0.00 0.00 3.82
1840 2119 0.179150 AATTTTGTGTGTGCGCGTGT 60.179 45.000 8.43 0.00 0.00 4.49
1841 2120 1.446465 GTAATTTTGTGTGTGCGCGTG 59.554 47.619 8.43 0.00 0.00 5.34
1844 2123 1.414378 GGGTAATTTTGTGTGTGCGC 58.586 50.000 0.00 0.00 0.00 6.09
1845 2124 1.336424 GGGGGTAATTTTGTGTGTGCG 60.336 52.381 0.00 0.00 0.00 5.34
1846 2125 1.689273 TGGGGGTAATTTTGTGTGTGC 59.311 47.619 0.00 0.00 0.00 4.57
1847 2126 3.133003 TGTTGGGGGTAATTTTGTGTGTG 59.867 43.478 0.00 0.00 0.00 3.82
1848 2127 3.375699 TGTTGGGGGTAATTTTGTGTGT 58.624 40.909 0.00 0.00 0.00 3.72
1849 2128 4.408182 TTGTTGGGGGTAATTTTGTGTG 57.592 40.909 0.00 0.00 0.00 3.82
1850 2129 5.638530 ATTTGTTGGGGGTAATTTTGTGT 57.361 34.783 0.00 0.00 0.00 3.72
1851 2130 5.641636 GCTATTTGTTGGGGGTAATTTTGTG 59.358 40.000 0.00 0.00 0.00 3.33
1852 2131 5.308237 TGCTATTTGTTGGGGGTAATTTTGT 59.692 36.000 0.00 0.00 0.00 2.83
1853 2132 5.799213 TGCTATTTGTTGGGGGTAATTTTG 58.201 37.500 0.00 0.00 0.00 2.44
1854 2133 6.441088 TTGCTATTTGTTGGGGGTAATTTT 57.559 33.333 0.00 0.00 0.00 1.82
1855 2134 6.043822 ACTTTGCTATTTGTTGGGGGTAATTT 59.956 34.615 0.00 0.00 0.00 1.82
1856 2135 5.546110 ACTTTGCTATTTGTTGGGGGTAATT 59.454 36.000 0.00 0.00 0.00 1.40
1857 2136 5.090845 ACTTTGCTATTTGTTGGGGGTAAT 58.909 37.500 0.00 0.00 0.00 1.89
1858 2137 4.484912 ACTTTGCTATTTGTTGGGGGTAA 58.515 39.130 0.00 0.00 0.00 2.85
1859 2138 4.083565 GACTTTGCTATTTGTTGGGGGTA 58.916 43.478 0.00 0.00 0.00 3.69
1860 2139 2.897326 GACTTTGCTATTTGTTGGGGGT 59.103 45.455 0.00 0.00 0.00 4.95
1861 2140 2.896685 TGACTTTGCTATTTGTTGGGGG 59.103 45.455 0.00 0.00 0.00 5.40
1862 2141 4.599047 TTGACTTTGCTATTTGTTGGGG 57.401 40.909 0.00 0.00 0.00 4.96
1863 2142 8.087750 TCTTATTTGACTTTGCTATTTGTTGGG 58.912 33.333 0.00 0.00 0.00 4.12
1864 2143 8.915654 GTCTTATTTGACTTTGCTATTTGTTGG 58.084 33.333 0.00 0.00 34.39 3.77
1868 2147 7.526608 TCGGTCTTATTTGACTTTGCTATTTG 58.473 34.615 0.00 0.00 37.16 2.32
1875 2154 6.300354 ACACTTCGGTCTTATTTGACTTTG 57.700 37.500 0.00 0.00 37.16 2.77
1949 2256 0.465705 GTCAGGCTAGCCATGCTACA 59.534 55.000 34.70 11.47 40.44 2.74
1952 2259 0.107312 CTTGTCAGGCTAGCCATGCT 60.107 55.000 34.70 12.31 43.41 3.79
1954 2261 0.393402 TGCTTGTCAGGCTAGCCATG 60.393 55.000 34.70 26.77 43.63 3.66
1956 2263 0.107508 GATGCTTGTCAGGCTAGCCA 60.108 55.000 34.70 13.55 43.63 4.75
1958 2265 2.898729 TAGATGCTTGTCAGGCTAGC 57.101 50.000 6.04 6.04 44.34 3.42
2050 2357 3.019003 GCCCGCTAGCTTCACCAGA 62.019 63.158 13.93 0.00 0.00 3.86
2140 2447 2.921996 CGCCTACGTACGTGAGAAC 58.078 57.895 30.25 13.71 33.53 3.01
2383 2690 1.293498 GAAGTCGGAGAGCTTGGCA 59.707 57.895 0.00 0.00 36.95 4.92
2578 2885 0.970427 TGCCCTGATCGCTCACAGTA 60.970 55.000 0.00 0.00 32.93 2.74
2583 2890 2.685017 AGGTGCCCTGATCGCTCA 60.685 61.111 0.00 0.00 29.57 4.26
2606 2913 0.456142 GCTGTACACGTCGCTCATCA 60.456 55.000 0.00 0.00 0.00 3.07
2647 2954 2.594303 CTTGCGCCCTGTCACCAA 60.594 61.111 4.18 0.00 0.00 3.67
2760 3067 1.587043 CGTCAGAGTCGAGCCTTGGA 61.587 60.000 0.00 0.00 0.00 3.53
2771 3078 1.377994 ACGGGGTAGTCGTCAGAGT 59.622 57.895 0.00 0.00 35.87 3.24
2970 3277 1.033574 GCTGTAGTAGAGGCGATGGT 58.966 55.000 0.00 0.00 0.00 3.55
3122 3429 1.301716 GAGAGCTCGTTTGCACCCA 60.302 57.895 8.37 0.00 34.99 4.51
3128 3435 4.686091 TGACAAACTATGAGAGCTCGTTTG 59.314 41.667 28.01 28.01 45.84 2.93
3140 3447 8.608844 ACTAAGGAAGTTCTTGACAAACTATG 57.391 34.615 2.25 0.00 35.96 2.23
3185 3493 4.351874 TTCAAGAGGGTTTACAGGTCTG 57.648 45.455 0.00 0.00 0.00 3.51
3218 3527 7.859325 AAAACAATTGATATACGCACCTACT 57.141 32.000 13.59 0.00 0.00 2.57
3303 3612 3.326836 AAAGAGCACTGTAGCTTCCTC 57.673 47.619 0.00 0.00 46.75 3.71
3340 3653 6.619801 TTCAAAAGGACTCTAACTTGCTTC 57.380 37.500 0.00 0.00 0.00 3.86
3376 3689 9.883142 AAAAGACTCATTTTATTTGTCCAACAA 57.117 25.926 0.00 0.00 31.77 2.83
3416 3729 8.556213 AGATCCGTTTTAGCTTTTAACATACA 57.444 30.769 0.00 0.00 0.00 2.29
3431 3744 6.816136 AGTCCAATTTTCAAAGATCCGTTTT 58.184 32.000 0.00 0.00 0.00 2.43
3540 3854 4.123545 GTAATGGGGCGGGTGGCT 62.124 66.667 0.00 0.00 42.94 4.75
3582 3896 1.874231 TCACGTCGAGAGGATATCAGC 59.126 52.381 4.83 0.00 0.00 4.26
3660 3974 6.530534 GCTGCAACGAACTTTACTTCTCTATA 59.469 38.462 0.00 0.00 0.00 1.31
3678 3992 6.313252 TCAAAATTTGTCTTTTTGCTGCAAC 58.687 32.000 15.72 4.39 41.58 4.17
3686 4000 7.657354 GCCCACTCTATCAAAATTTGTCTTTTT 59.343 33.333 5.56 0.00 0.00 1.94
3769 4083 2.417339 TCACACGTTAGCAGTCAGAC 57.583 50.000 0.00 0.00 0.00 3.51
3772 4086 2.739292 GTCTTCACACGTTAGCAGTCA 58.261 47.619 0.00 0.00 0.00 3.41
3821 4184 6.322969 TCTTCATTTGCATGCAGGAATTAGAT 59.677 34.615 21.50 3.68 0.00 1.98
3871 4234 7.324616 GCTTTCATCTTAATTCGCAATATCCAC 59.675 37.037 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.