Multiple sequence alignment - TraesCS5D01G318400

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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 TraesCS5D01G318400 chr5D 100.000 2720 0 0 1 2720 411195748 411198467 0.000000e+00 5024.0
1 TraesCS5D01G318400 chr5D 80.216 925 136 29 804 1718 411627439 411628326 0.000000e+00 651.0
2 TraesCS5D01G318400 chr5D 85.429 350 48 3 1066 1414 410444225 410444572 7.160000e-96 361.0
3 TraesCS5D01G318400 chr5D 84.241 349 53 2 1067 1414 411785487 411785140 3.350000e-89 339.0
4 TraesCS5D01G318400 chr5D 79.577 142 29 0 1544 1685 411699521 411699380 4.790000e-18 102.0
5 TraesCS5D01G318400 chr5D 89.062 64 5 2 268 329 446741151 446741214 8.070000e-11 78.7
6 TraesCS5D01G318400 chr5B 92.660 2643 126 22 46 2644 493673112 493675730 0.000000e+00 3744.0
7 TraesCS5D01G318400 chr5B 79.807 931 139 24 798 1718 493931210 493932101 1.370000e-177 632.0
8 TraesCS5D01G318400 chr5B 84.857 350 51 2 1066 1414 492619520 492619868 4.310000e-93 351.0
9 TraesCS5D01G318400 chr5B 97.959 49 0 1 2672 2720 493675732 493675779 1.740000e-12 84.2
10 TraesCS5D01G318400 chr5A 90.692 2471 165 30 74 2493 523135780 523138236 0.000000e+00 3229.0
11 TraesCS5D01G318400 chr5A 81.102 926 126 33 804 1718 523449896 523450783 0.000000e+00 695.0
12 TraesCS5D01G318400 chr5A 84.551 356 47 7 1066 1414 522066673 522067027 2.000000e-91 346.0
13 TraesCS5D01G318400 chr5A 85.556 90 10 1 1568 1654 522067295 522067384 1.040000e-14 91.6
14 TraesCS5D01G318400 chr5A 81.319 91 16 1 1568 1657 522074389 522074479 3.760000e-09 73.1
15 TraesCS5D01G318400 chr7D 100.000 51 0 0 1 51 173494147 173494197 8.020000e-16 95.3
16 TraesCS5D01G318400 chr7D 100.000 51 0 0 1 51 187885925 187885975 8.020000e-16 95.3
17 TraesCS5D01G318400 chr7D 98.113 53 1 0 1 53 365152468 365152416 2.880000e-15 93.5
18 TraesCS5D01G318400 chr3D 100.000 51 0 0 1 51 201210865 201210815 8.020000e-16 95.3
19 TraesCS5D01G318400 chr3D 100.000 51 0 0 1 51 570357889 570357839 8.020000e-16 95.3
20 TraesCS5D01G318400 chr3D 97.959 49 1 0 1 49 500419362 500419410 4.830000e-13 86.1
21 TraesCS5D01G318400 chr2D 100.000 51 0 0 1 51 180222249 180222199 8.020000e-16 95.3
22 TraesCS5D01G318400 chr2D 100.000 51 0 0 1 51 634082798 634082748 8.020000e-16 95.3
23 TraesCS5D01G318400 chr2D 93.443 61 3 1 270 329 2724957 2725017 3.730000e-14 89.8
24 TraesCS5D01G318400 chrUn 100.000 50 0 0 1 50 11502329 11502280 2.880000e-15 93.5
25 TraesCS5D01G318400 chr7A 87.500 64 6 1 268 329 40531657 40531594 3.760000e-09 73.1
26 TraesCS5D01G318400 chr6B 97.222 36 1 0 268 303 624775717 624775752 8.130000e-06 62.1


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 TraesCS5D01G318400 chr5D 411195748 411198467 2719 False 5024.0 5024 100.0000 1 2720 1 chr5D.!!$F2 2719
1 TraesCS5D01G318400 chr5D 411627439 411628326 887 False 651.0 651 80.2160 804 1718 1 chr5D.!!$F3 914
2 TraesCS5D01G318400 chr5B 493673112 493675779 2667 False 1914.1 3744 95.3095 46 2720 2 chr5B.!!$F3 2674
3 TraesCS5D01G318400 chr5B 493931210 493932101 891 False 632.0 632 79.8070 798 1718 1 chr5B.!!$F2 920
4 TraesCS5D01G318400 chr5A 523135780 523138236 2456 False 3229.0 3229 90.6920 74 2493 1 chr5A.!!$F2 2419
5 TraesCS5D01G318400 chr5A 523449896 523450783 887 False 695.0 695 81.1020 804 1718 1 chr5A.!!$F3 914
6 TraesCS5D01G318400 chr5A 522066673 522067384 711 False 218.8 346 85.0535 1066 1654 2 chr5A.!!$F4 588


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
38 39 0.472471 TGGCCGAAACTTGACTTCCT 59.528 50.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1939 0.3199 GCTGACGTGGAAGAGCTTCA 60.32 55.0 11.9 0.0 41.2 3.02 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
17 18 2.433004 ACCCCCGAAACTTTCCCG 59.567 61.111 0.00 0.00 0.00 5.14
18 19 2.360726 CCCCCGAAACTTTCCCGG 60.361 66.667 0.00 0.00 42.64 5.73
19 20 2.433004 CCCCGAAACTTTCCCGGT 59.567 61.111 0.00 0.00 41.53 5.28
20 21 1.969589 CCCCGAAACTTTCCCGGTG 60.970 63.158 0.00 0.00 41.53 4.94
21 22 1.969589 CCCGAAACTTTCCCGGTGG 60.970 63.158 0.00 0.00 41.53 4.61
22 23 2.622962 CCGAAACTTTCCCGGTGGC 61.623 63.158 0.00 0.00 38.55 5.01
23 24 2.622962 CGAAACTTTCCCGGTGGCC 61.623 63.158 0.00 0.00 0.00 5.36
34 35 4.475527 GGTGGCCGAAACTTGACT 57.524 55.556 0.00 0.00 0.00 3.41
35 36 2.715536 GGTGGCCGAAACTTGACTT 58.284 52.632 0.00 0.00 0.00 3.01
36 37 0.591659 GGTGGCCGAAACTTGACTTC 59.408 55.000 0.00 0.00 0.00 3.01
37 38 0.591659 GTGGCCGAAACTTGACTTCC 59.408 55.000 0.00 0.00 0.00 3.46
38 39 0.472471 TGGCCGAAACTTGACTTCCT 59.528 50.000 0.00 0.00 0.00 3.36
39 40 1.695242 TGGCCGAAACTTGACTTCCTA 59.305 47.619 0.00 0.00 0.00 2.94
40 41 2.304761 TGGCCGAAACTTGACTTCCTAT 59.695 45.455 0.00 0.00 0.00 2.57
41 42 3.516300 TGGCCGAAACTTGACTTCCTATA 59.484 43.478 0.00 0.00 0.00 1.31
42 43 4.163458 TGGCCGAAACTTGACTTCCTATAT 59.837 41.667 0.00 0.00 0.00 0.86
43 44 5.364446 TGGCCGAAACTTGACTTCCTATATA 59.636 40.000 0.00 0.00 0.00 0.86
44 45 6.042781 TGGCCGAAACTTGACTTCCTATATAT 59.957 38.462 0.00 0.00 0.00 0.86
66 67 3.992943 ATTCCATGGACAACGTAGGAA 57.007 42.857 15.91 0.00 39.24 3.36
80 86 6.427547 ACAACGTAGGAATTTCCGAATAAACA 59.572 34.615 9.77 0.00 42.75 2.83
106 112 5.439721 TCCATTTTGTATGTCAGGGATCTG 58.560 41.667 0.00 0.00 42.21 2.90
131 137 3.009253 TGTTTCCTTTTAGGTATCCGCCA 59.991 43.478 0.00 0.00 36.53 5.69
167 173 8.230472 AGTCAGATGAAACACTCTTTGATTTT 57.770 30.769 0.00 0.00 0.00 1.82
169 175 8.348507 GTCAGATGAAACACTCTTTGATTTTCT 58.651 33.333 0.00 0.00 0.00 2.52
255 262 6.490381 ACATCATTCATTTGCATAGAGCTCAT 59.510 34.615 17.77 4.64 45.94 2.90
329 336 0.687354 ACGAGCACCAGGACTTGAAT 59.313 50.000 0.00 0.00 0.00 2.57
330 337 1.072331 ACGAGCACCAGGACTTGAATT 59.928 47.619 0.00 0.00 0.00 2.17
339 346 4.105697 ACCAGGACTTGAATTTTAGTGGGA 59.894 41.667 0.00 0.00 0.00 4.37
353 360 6.645884 TTTAGTGGGATGGGTATAACACTT 57.354 37.500 0.00 0.00 39.59 3.16
364 371 4.628766 GGGTATAACACTTTTCTCGACCAC 59.371 45.833 0.00 0.00 0.00 4.16
416 424 3.864003 GCGGTACTTGTCTTGGATAGAAC 59.136 47.826 0.00 0.00 33.81 3.01
438 446 4.634443 ACTACATAACACGAGGAAAATGCC 59.366 41.667 0.00 0.00 0.00 4.40
488 496 1.681264 GGGCCCCATTTATCAGTTTCG 59.319 52.381 12.23 0.00 0.00 3.46
697 706 2.542595 GGAGAACAACATATAACGCGGG 59.457 50.000 12.47 0.00 0.00 6.13
773 782 1.677217 GCCCCAACTGTCAGTCTCATC 60.677 57.143 5.82 0.00 0.00 2.92
982 994 1.216710 GTAAGCTCGAGCCAGCACT 59.783 57.895 32.94 11.52 42.40 4.40
988 1000 2.236223 CTCGAGCCAGCACTGACCAT 62.236 60.000 0.00 0.00 0.00 3.55
1027 1039 4.598894 CCGGCTCCGATCAGCAGG 62.599 72.222 10.28 9.30 46.48 4.85
1047 1059 3.296737 AGCTCCCCTTCCTCCCCT 61.297 66.667 0.00 0.00 0.00 4.79
1218 1233 4.996434 GGCACGCACCTCACTGCT 62.996 66.667 0.00 0.00 34.77 4.24
1345 1366 0.319900 GCTCTCCGACTTTGCAGACA 60.320 55.000 0.00 0.00 0.00 3.41
1635 1812 4.082523 TTCGCGGAGGGGCTTCTG 62.083 66.667 6.13 0.00 42.39 3.02
1761 1939 6.569226 GCTTTGACTCTATGCATGAACAAACT 60.569 38.462 10.16 0.00 0.00 2.66
1768 1946 3.631145 TGCATGAACAAACTGAAGCTC 57.369 42.857 0.00 0.00 0.00 4.09
1773 1951 3.884895 TGAACAAACTGAAGCTCTTCCA 58.115 40.909 7.12 0.00 38.77 3.53
1774 1952 3.627577 TGAACAAACTGAAGCTCTTCCAC 59.372 43.478 7.12 0.00 38.77 4.02
1818 1996 5.405935 AACTTAAACCCATCAAATCCTGC 57.594 39.130 0.00 0.00 0.00 4.85
1825 2003 3.181440 ACCCATCAAATCCTGCGACATAT 60.181 43.478 0.00 0.00 0.00 1.78
1826 2004 4.041567 ACCCATCAAATCCTGCGACATATA 59.958 41.667 0.00 0.00 0.00 0.86
1827 2005 4.393062 CCCATCAAATCCTGCGACATATAC 59.607 45.833 0.00 0.00 0.00 1.47
1828 2006 4.996758 CCATCAAATCCTGCGACATATACA 59.003 41.667 0.00 0.00 0.00 2.29
1841 2019 5.555552 CGACATATACATGCAAACAAACGA 58.444 37.500 0.00 0.00 35.39 3.85
1858 2036 1.135460 ACGAAGTTCTAGGCTACGCAC 60.135 52.381 0.56 0.00 37.78 5.34
1860 2038 2.531206 GAAGTTCTAGGCTACGCACAG 58.469 52.381 0.00 0.00 0.00 3.66
1863 2041 1.103803 TTCTAGGCTACGCACAGGAG 58.896 55.000 0.00 0.00 0.00 3.69
1872 2062 1.609208 ACGCACAGGAGCAAGAAAAT 58.391 45.000 0.00 0.00 0.00 1.82
1879 2069 4.216902 CACAGGAGCAAGAAAATGACATCA 59.783 41.667 0.00 0.00 0.00 3.07
1885 2075 4.082895 AGCAAGAAAATGACATCACTGCTC 60.083 41.667 0.00 0.00 34.05 4.26
1895 2085 5.604565 TGACATCACTGCTCGATGAATAAT 58.395 37.500 14.75 0.00 42.39 1.28
1897 2087 6.642540 TGACATCACTGCTCGATGAATAATAC 59.357 38.462 14.75 0.00 42.39 1.89
1899 2089 6.865726 ACATCACTGCTCGATGAATAATACTC 59.134 38.462 14.75 0.00 42.39 2.59
1923 2113 2.102252 CAGAAGATCCTAGACTGGTGGC 59.898 54.545 0.00 0.00 0.00 5.01
1926 2116 2.114616 AGATCCTAGACTGGTGGCAAG 58.885 52.381 0.00 0.00 0.00 4.01
1930 2120 0.107945 CTAGACTGGTGGCAAGAGGC 60.108 60.000 0.00 0.00 43.74 4.70
1959 2150 6.759497 AAAAAGGGTACTATCACTTGATGC 57.241 37.500 1.77 0.00 36.05 3.91
1963 2154 3.181479 GGGTACTATCACTTGATGCGTCA 60.181 47.826 3.97 3.97 36.05 4.35
1985 2176 8.300286 CGTCATGACTATAACTGGTAATCAGAT 58.700 37.037 22.95 0.00 46.18 2.90
1999 2190 7.751732 TGGTAATCAGATGAGAAAAATCAACG 58.248 34.615 0.00 0.00 31.76 4.10
2000 2191 7.148255 TGGTAATCAGATGAGAAAAATCAACGG 60.148 37.037 0.00 0.00 31.76 4.44
2014 2205 7.924103 AAAATCAACGGTTTGTTAATCAGAC 57.076 32.000 0.00 0.00 39.29 3.51
2035 2230 2.510691 CGTGGTCCATGTACGCCC 60.511 66.667 2.56 0.00 0.00 6.13
2083 2278 0.321919 CAGGTCAGCTGGCTAAAGCA 60.322 55.000 19.48 0.00 46.08 3.91
2110 2305 4.797912 ATCCCTGGGATCTTTTTCTACC 57.202 45.455 22.79 0.00 38.09 3.18
2238 2433 5.183522 TGTGTCACGTACCTTTTTCCTTTTT 59.816 36.000 0.00 0.00 0.00 1.94
2291 2486 1.063806 GAAGTGACTAGTGTGCTGCG 58.936 55.000 0.00 0.00 0.00 5.18
2399 2618 4.992319 TCGTTACGAGGTTGATGTCAAAAT 59.008 37.500 2.33 0.00 37.63 1.82
2432 2651 9.625747 AAAACAAAACATATTTCATGGGTTTCT 57.374 25.926 0.00 0.00 31.80 2.52
2453 2672 1.417517 TGATGCCTGTGTGAAGACTGT 59.582 47.619 0.00 0.00 0.00 3.55
2526 2749 2.290641 TGTGTGGATATTGGTGGTGGTC 60.291 50.000 0.00 0.00 0.00 4.02
2648 2872 8.512966 TCAACGACAAATTAATATGGATTGGA 57.487 30.769 0.00 0.00 0.00 3.53
2649 2873 8.620416 TCAACGACAAATTAATATGGATTGGAG 58.380 33.333 0.00 0.00 0.00 3.86
2650 2874 7.510549 ACGACAAATTAATATGGATTGGAGG 57.489 36.000 0.00 0.00 0.00 4.30
2651 2875 6.016276 ACGACAAATTAATATGGATTGGAGGC 60.016 38.462 0.00 0.00 0.00 4.70
2652 2876 6.016360 CGACAAATTAATATGGATTGGAGGCA 60.016 38.462 0.00 0.00 0.00 4.75
2653 2877 7.294017 ACAAATTAATATGGATTGGAGGCAG 57.706 36.000 0.00 0.00 0.00 4.85
2654 2878 6.840705 ACAAATTAATATGGATTGGAGGCAGT 59.159 34.615 0.00 0.00 0.00 4.40
2655 2879 8.004215 ACAAATTAATATGGATTGGAGGCAGTA 58.996 33.333 0.00 0.00 0.00 2.74
2656 2880 8.517878 CAAATTAATATGGATTGGAGGCAGTAG 58.482 37.037 0.00 0.00 0.00 2.57
2657 2881 6.763715 TTAATATGGATTGGAGGCAGTAGT 57.236 37.500 0.00 0.00 0.00 2.73
2658 2882 5.653255 AATATGGATTGGAGGCAGTAGTT 57.347 39.130 0.00 0.00 0.00 2.24
2659 2883 5.653255 ATATGGATTGGAGGCAGTAGTTT 57.347 39.130 0.00 0.00 0.00 2.66
2660 2884 3.806949 TGGATTGGAGGCAGTAGTTTT 57.193 42.857 0.00 0.00 0.00 2.43
2661 2885 4.112634 TGGATTGGAGGCAGTAGTTTTT 57.887 40.909 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.433004 CGGGAAAGTTTCGGGGGT 59.567 61.111 9.46 0.00 0.00 4.95
1 2 2.360726 CCGGGAAAGTTTCGGGGG 60.361 66.667 9.46 6.66 40.07 5.40
5 6 2.622962 GGCCACCGGGAAAGTTTCG 61.623 63.158 6.32 0.00 35.59 3.46
6 7 2.622962 CGGCCACCGGGAAAGTTTC 61.623 63.158 6.32 7.09 44.15 2.78
7 8 2.596338 CGGCCACCGGGAAAGTTT 60.596 61.111 6.32 0.00 44.15 2.66
17 18 0.591659 GAAGTCAAGTTTCGGCCACC 59.408 55.000 2.24 0.00 0.00 4.61
18 19 0.591659 GGAAGTCAAGTTTCGGCCAC 59.408 55.000 2.24 0.00 0.00 5.01
19 20 0.472471 AGGAAGTCAAGTTTCGGCCA 59.528 50.000 2.24 0.00 0.00 5.36
20 21 2.467566 TAGGAAGTCAAGTTTCGGCC 57.532 50.000 0.00 0.00 0.00 6.13
21 22 9.654663 ATTATATATAGGAAGTCAAGTTTCGGC 57.345 33.333 0.00 0.00 0.00 5.54
34 35 9.884636 CGTTGTCCATGGAATTATATATAGGAA 57.115 33.333 18.20 0.00 0.00 3.36
35 36 9.042450 ACGTTGTCCATGGAATTATATATAGGA 57.958 33.333 18.20 0.00 0.00 2.94
39 40 9.042450 TCCTACGTTGTCCATGGAATTATATAT 57.958 33.333 18.20 0.11 0.00 0.86
40 41 8.425237 TCCTACGTTGTCCATGGAATTATATA 57.575 34.615 18.20 4.47 0.00 0.86
41 42 7.311092 TCCTACGTTGTCCATGGAATTATAT 57.689 36.000 18.20 3.42 0.00 0.86
42 43 6.734502 TCCTACGTTGTCCATGGAATTATA 57.265 37.500 18.20 5.00 0.00 0.98
43 44 5.623956 TCCTACGTTGTCCATGGAATTAT 57.376 39.130 18.20 3.98 0.00 1.28
44 45 5.423704 TTCCTACGTTGTCCATGGAATTA 57.576 39.130 18.20 2.96 0.00 1.40
48 49 3.992943 AATTCCTACGTTGTCCATGGA 57.007 42.857 11.44 11.44 0.00 3.41
59 60 5.583457 AGGTGTTTATTCGGAAATTCCTACG 59.417 40.000 10.64 0.00 33.30 3.51
66 67 6.850752 AAATGGAGGTGTTTATTCGGAAAT 57.149 33.333 0.00 0.00 0.00 2.17
80 86 3.591527 TCCCTGACATACAAAATGGAGGT 59.408 43.478 0.00 0.00 0.00 3.85
106 112 5.220989 GGCGGATACCTAAAAGGAAACATTC 60.221 44.000 0.00 0.00 37.67 2.67
131 137 8.209584 AGTGTTTCATCTGACTATCATTAGCAT 58.790 33.333 0.00 0.00 0.00 3.79
167 173 5.355071 TCGCGTGACTAGTTAAGGAATAAGA 59.645 40.000 5.77 0.00 0.00 2.10
169 175 5.565592 TCGCGTGACTAGTTAAGGAATAA 57.434 39.130 5.77 0.00 0.00 1.40
176 182 6.366604 TCATTTTCATTCGCGTGACTAGTTAA 59.633 34.615 5.77 0.00 0.00 2.01
182 188 4.024048 ACTTTCATTTTCATTCGCGTGACT 60.024 37.500 5.77 0.00 0.00 3.41
255 262 0.671796 TGCGTTCACTTCCGAGAGAA 59.328 50.000 0.00 0.00 31.32 2.87
310 317 0.687354 ATTCAAGTCCTGGTGCTCGT 59.313 50.000 0.00 0.00 0.00 4.18
329 336 6.645884 AGTGTTATACCCATCCCACTAAAA 57.354 37.500 0.00 0.00 31.80 1.52
330 337 6.645884 AAGTGTTATACCCATCCCACTAAA 57.354 37.500 0.00 0.00 33.14 1.85
339 346 5.046159 TGGTCGAGAAAAGTGTTATACCCAT 60.046 40.000 0.00 0.00 0.00 4.00
395 402 5.326200 AGTTCTATCCAAGACAAGTACCG 57.674 43.478 0.00 0.00 32.51 4.02
408 415 6.630444 TCCTCGTGTTATGTAGTTCTATCC 57.370 41.667 0.00 0.00 0.00 2.59
416 424 4.876107 AGGCATTTTCCTCGTGTTATGTAG 59.124 41.667 0.00 0.00 0.00 2.74
488 496 1.394917 CAGCGTGATAAGGTGTTGCTC 59.605 52.381 0.00 0.00 32.96 4.26
697 706 2.721090 GCACAAGTGACGCATTTTTCTC 59.279 45.455 4.04 0.00 0.00 2.87
1044 1056 3.068691 TGCGAGGAGGACGAAGGG 61.069 66.667 0.00 0.00 0.00 3.95
1047 1059 2.282958 AGGTGCGAGGAGGACGAA 60.283 61.111 0.00 0.00 42.62 3.85
1761 1939 0.319900 GCTGACGTGGAAGAGCTTCA 60.320 55.000 11.90 0.00 41.20 3.02
1768 1946 7.218773 CACAATTTTATTATGCTGACGTGGAAG 59.781 37.037 0.00 0.00 0.00 3.46
1773 1951 6.751514 TCCACAATTTTATTATGCTGACGT 57.248 33.333 0.00 0.00 0.00 4.34
1774 1952 7.250569 AGTTCCACAATTTTATTATGCTGACG 58.749 34.615 0.00 0.00 0.00 4.35
1818 1996 5.555552 TCGTTTGTTTGCATGTATATGTCG 58.444 37.500 1.14 0.00 36.65 4.35
1825 2003 5.493133 AGAACTTCGTTTGTTTGCATGTA 57.507 34.783 0.00 0.00 0.00 2.29
1826 2004 4.370364 AGAACTTCGTTTGTTTGCATGT 57.630 36.364 0.00 0.00 0.00 3.21
1827 2005 4.911610 CCTAGAACTTCGTTTGTTTGCATG 59.088 41.667 0.00 0.00 0.00 4.06
1828 2006 4.556699 GCCTAGAACTTCGTTTGTTTGCAT 60.557 41.667 0.00 0.00 0.00 3.96
1853 2031 1.267806 CATTTTCTTGCTCCTGTGCGT 59.732 47.619 0.00 0.00 35.36 5.24
1858 2036 4.458295 AGTGATGTCATTTTCTTGCTCCTG 59.542 41.667 0.00 0.00 0.00 3.86
1860 2038 4.730657 CAGTGATGTCATTTTCTTGCTCC 58.269 43.478 0.00 0.00 0.00 4.70
1863 2041 4.164294 GAGCAGTGATGTCATTTTCTTGC 58.836 43.478 0.00 0.00 0.00 4.01
1867 2045 4.330894 TCATCGAGCAGTGATGTCATTTTC 59.669 41.667 11.16 0.00 42.96 2.29
1872 2062 3.531934 ATTCATCGAGCAGTGATGTCA 57.468 42.857 11.16 2.83 42.96 3.58
1879 2069 5.069119 TGTGGAGTATTATTCATCGAGCAGT 59.931 40.000 0.00 0.00 0.00 4.40
1885 2075 7.543868 GGATCTTCTGTGGAGTATTATTCATCG 59.456 40.741 0.00 0.00 0.00 3.84
1895 2085 5.441500 CAGTCTAGGATCTTCTGTGGAGTA 58.558 45.833 0.00 0.00 0.00 2.59
1897 2087 3.636300 CCAGTCTAGGATCTTCTGTGGAG 59.364 52.174 0.00 0.00 0.00 3.86
1899 2089 3.131933 CACCAGTCTAGGATCTTCTGTGG 59.868 52.174 0.00 0.00 0.00 4.17
1951 2142 5.750547 CAGTTATAGTCATGACGCATCAAGT 59.249 40.000 19.85 10.67 38.69 3.16
1959 2150 7.649057 TCTGATTACCAGTTATAGTCATGACG 58.351 38.462 19.85 5.93 43.38 4.35
1963 2154 9.593565 TCTCATCTGATTACCAGTTATAGTCAT 57.406 33.333 0.00 0.00 43.38 3.06
1983 2174 8.568732 TTAACAAACCGTTGATTTTTCTCATC 57.431 30.769 0.00 0.00 38.63 2.92
1985 2176 8.191446 TGATTAACAAACCGTTGATTTTTCTCA 58.809 29.630 0.00 0.00 38.63 3.27
1999 2190 4.084013 CCACGTCTGTCTGATTAACAAACC 60.084 45.833 0.00 0.00 0.00 3.27
2000 2191 4.510340 ACCACGTCTGTCTGATTAACAAAC 59.490 41.667 0.00 0.00 0.00 2.93
2014 2205 1.076533 GCGTACATGGACCACGTCTG 61.077 60.000 1.43 0.00 37.95 3.51
2035 2230 2.487934 CTAGGCCACATCTTCCGAATG 58.512 52.381 5.01 0.00 0.00 2.67
2076 2271 1.476471 CCAGGGATCCAGCTGCTTTAG 60.476 57.143 15.23 0.00 0.00 1.85
2164 2359 1.095807 GCGATTCGGAAAGGAAGGGG 61.096 60.000 8.34 0.00 0.00 4.79
2261 2456 2.898729 AGTCACTTCCACAGTCACAG 57.101 50.000 0.00 0.00 25.81 3.66
2410 2629 8.830201 TCAAGAAACCCATGAAATATGTTTTG 57.170 30.769 0.00 0.00 31.78 2.44
2412 2631 7.550196 GCATCAAGAAACCCATGAAATATGTTT 59.450 33.333 0.00 0.00 33.55 2.83
2413 2632 7.043565 GCATCAAGAAACCCATGAAATATGTT 58.956 34.615 0.00 0.00 0.00 2.71
2414 2633 6.407299 GGCATCAAGAAACCCATGAAATATGT 60.407 38.462 0.00 0.00 0.00 2.29
2417 2636 5.127519 CAGGCATCAAGAAACCCATGAAATA 59.872 40.000 0.00 0.00 0.00 1.40
2432 2651 2.158769 ACAGTCTTCACACAGGCATCAA 60.159 45.455 0.00 0.00 0.00 2.57
2453 2672 4.100479 CCATGAAGGTGCCTGCAA 57.900 55.556 2.54 0.00 34.86 4.08
2526 2749 9.974980 GGATAGGAGAGAGTAAGTATTTTTCAG 57.025 37.037 0.00 0.00 0.00 3.02
2606 2830 8.094798 TGTCGTTGATTTAGCATACTTTTTCT 57.905 30.769 0.00 0.00 0.00 2.52
2662 2886 9.328845 ACTAGGAATTGTTAACTAAACGTCAAA 57.671 29.630 7.22 0.00 41.30 2.69
2663 2887 8.891671 ACTAGGAATTGTTAACTAAACGTCAA 57.108 30.769 7.22 0.00 41.30 3.18
2664 2888 8.891671 AACTAGGAATTGTTAACTAAACGTCA 57.108 30.769 7.22 0.00 41.30 4.35



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

AutoCloner maintained by Alex Coulton.