Multiple sequence alignment - TraesCS4D01G042800

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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 TraesCS4D01G042800 chr4D 100.000 3367 0 0 1 3367 19900079 19903445 0.000000e+00 6218
1 TraesCS4D01G042800 chr3A 96.341 3252 97 11 129 3367 105557476 105554234 0.000000e+00 5326
2 TraesCS4D01G042800 chrUn 96.218 3252 103 17 129 3367 261569211 261565967 0.000000e+00 5306
3 TraesCS4D01G042800 chr5D 96.218 3252 104 16 129 3367 503338922 503342167 0.000000e+00 5306
4 TraesCS4D01G042800 chr5D 96.213 3248 110 10 129 3367 6253793 6250550 0.000000e+00 5304
5 TraesCS4D01G042800 chr5D 95.999 3249 111 14 129 3367 503312989 503316228 0.000000e+00 5262
6 TraesCS4D01G042800 chr5B 96.160 3255 100 11 129 3367 57515644 57512399 0.000000e+00 5295
7 TraesCS4D01G042800 chr1D 95.876 3249 106 12 129 3367 254458897 254462127 0.000000e+00 5232
8 TraesCS4D01G042800 chr1D 95.414 3249 128 17 129 3367 51832477 51829240 0.000000e+00 5155
9 TraesCS4D01G042800 chr1D 97.761 134 2 1 1 133 427183316 427183183 2.610000e-56 230
10 TraesCS4D01G042800 chr1D 97.727 132 3 0 1 132 1068 937 9.400000e-56 228
11 TraesCS4D01G042800 chr7A 95.190 3098 133 13 279 3367 537841776 537838686 0.000000e+00 4881
12 TraesCS4D01G042800 chr7A 94.424 269 14 1 129 397 710798354 710798087 2.420000e-111 412
13 TraesCS4D01G042800 chr2D 98.462 130 2 0 1 130 343492706 343492577 2.610000e-56 230
14 TraesCS4D01G042800 chr7D 98.450 129 2 0 1 129 15176835 15176963 9.400000e-56 228
15 TraesCS4D01G042800 chr7D 97.059 136 3 1 1 135 524820328 524820193 9.400000e-56 228
16 TraesCS4D01G042800 chr7D 97.015 134 4 0 1 134 322059544 322059411 3.380000e-55 226
17 TraesCS4D01G042800 chr7D 93.878 147 7 2 1 145 181815904 181815758 1.570000e-53 220
18 TraesCS4D01G042800 chr3D 97.727 132 3 0 1 132 2011292 2011161 9.400000e-56 228
19 TraesCS4D01G042800 chr6D 96.377 138 3 1 1 138 247919552 247919687 3.380000e-55 226


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 TraesCS4D01G042800 chr4D 19900079 19903445 3366 False 6218 6218 100.000 1 3367 1 chr4D.!!$F1 3366
1 TraesCS4D01G042800 chr3A 105554234 105557476 3242 True 5326 5326 96.341 129 3367 1 chr3A.!!$R1 3238
2 TraesCS4D01G042800 chrUn 261565967 261569211 3244 True 5306 5306 96.218 129 3367 1 chrUn.!!$R1 3238
3 TraesCS4D01G042800 chr5D 503338922 503342167 3245 False 5306 5306 96.218 129 3367 1 chr5D.!!$F2 3238
4 TraesCS4D01G042800 chr5D 6250550 6253793 3243 True 5304 5304 96.213 129 3367 1 chr5D.!!$R1 3238
5 TraesCS4D01G042800 chr5D 503312989 503316228 3239 False 5262 5262 95.999 129 3367 1 chr5D.!!$F1 3238
6 TraesCS4D01G042800 chr5B 57512399 57515644 3245 True 5295 5295 96.160 129 3367 1 chr5B.!!$R1 3238
7 TraesCS4D01G042800 chr1D 254458897 254462127 3230 False 5232 5232 95.876 129 3367 1 chr1D.!!$F1 3238
8 TraesCS4D01G042800 chr1D 51829240 51832477 3237 True 5155 5155 95.414 129 3367 1 chr1D.!!$R2 3238
9 TraesCS4D01G042800 chr7A 537838686 537841776 3090 True 4881 4881 95.190 279 3367 1 chr7A.!!$R1 3088

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
81 82 0.034756 TTCTTTGCCGTCAGCTAGCA 59.965 50.0 18.83 0.0 44.23 3.49 F
1066 1078 0.040067 CGTTGGCAGTTTCAGGCTTC 60.040 55.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 1244 1.112113 GTCGAGATCCTGCACCCTTA 58.888 55.000 0.0 0.0 0.0 2.69 R
2548 2587 1.134098 CCCATCGCCCACTTGAACTAT 60.134 52.381 0.0 0.0 0.0 2.12 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
19 20 0.586802 GACCTGTTTTGTCGTCTGCC 59.413 55.000 0.00 0.00 0.00 4.85
20 21 0.107410 ACCTGTTTTGTCGTCTGCCA 60.107 50.000 0.00 0.00 0.00 4.92
21 22 1.238439 CCTGTTTTGTCGTCTGCCAT 58.762 50.000 0.00 0.00 0.00 4.40
22 23 1.608590 CCTGTTTTGTCGTCTGCCATT 59.391 47.619 0.00 0.00 0.00 3.16
23 24 2.034558 CCTGTTTTGTCGTCTGCCATTT 59.965 45.455 0.00 0.00 0.00 2.32
24 25 3.300009 CTGTTTTGTCGTCTGCCATTTC 58.700 45.455 0.00 0.00 0.00 2.17
25 26 2.948979 TGTTTTGTCGTCTGCCATTTCT 59.051 40.909 0.00 0.00 0.00 2.52
26 27 3.380004 TGTTTTGTCGTCTGCCATTTCTT 59.620 39.130 0.00 0.00 0.00 2.52
27 28 4.142271 TGTTTTGTCGTCTGCCATTTCTTT 60.142 37.500 0.00 0.00 0.00 2.52
28 29 3.624326 TTGTCGTCTGCCATTTCTTTG 57.376 42.857 0.00 0.00 0.00 2.77
29 30 1.266718 TGTCGTCTGCCATTTCTTTGC 59.733 47.619 0.00 0.00 0.00 3.68
30 31 0.881118 TCGTCTGCCATTTCTTTGCC 59.119 50.000 0.00 0.00 0.00 4.52
31 32 0.883833 CGTCTGCCATTTCTTTGCCT 59.116 50.000 0.00 0.00 0.00 4.75
32 33 1.270550 CGTCTGCCATTTCTTTGCCTT 59.729 47.619 0.00 0.00 0.00 4.35
33 34 2.669391 CGTCTGCCATTTCTTTGCCTTC 60.669 50.000 0.00 0.00 0.00 3.46
34 35 2.560105 GTCTGCCATTTCTTTGCCTTCT 59.440 45.455 0.00 0.00 0.00 2.85
35 36 2.559668 TCTGCCATTTCTTTGCCTTCTG 59.440 45.455 0.00 0.00 0.00 3.02
36 37 1.001181 TGCCATTTCTTTGCCTTCTGC 59.999 47.619 0.00 0.00 41.77 4.26
37 38 1.274447 GCCATTTCTTTGCCTTCTGCT 59.726 47.619 0.00 0.00 42.00 4.24
38 39 2.289257 GCCATTTCTTTGCCTTCTGCTT 60.289 45.455 0.00 0.00 42.00 3.91
39 40 3.804759 GCCATTTCTTTGCCTTCTGCTTT 60.805 43.478 0.00 0.00 42.00 3.51
40 41 4.383173 CCATTTCTTTGCCTTCTGCTTTT 58.617 39.130 0.00 0.00 42.00 2.27
41 42 4.212636 CCATTTCTTTGCCTTCTGCTTTTG 59.787 41.667 0.00 0.00 42.00 2.44
42 43 3.457610 TTCTTTGCCTTCTGCTTTTGG 57.542 42.857 0.00 0.00 42.00 3.28
43 44 1.688197 TCTTTGCCTTCTGCTTTTGGG 59.312 47.619 0.00 0.00 42.00 4.12
44 45 1.413812 CTTTGCCTTCTGCTTTTGGGT 59.586 47.619 0.00 0.00 42.00 4.51
45 46 2.373335 TTGCCTTCTGCTTTTGGGTA 57.627 45.000 0.00 0.00 42.00 3.69
46 47 1.909700 TGCCTTCTGCTTTTGGGTAG 58.090 50.000 0.00 0.00 42.00 3.18
47 48 0.528017 GCCTTCTGCTTTTGGGTAGC 59.472 55.000 0.00 0.00 39.10 3.58
48 49 1.888391 GCCTTCTGCTTTTGGGTAGCT 60.888 52.381 0.00 0.00 39.38 3.32
49 50 1.815003 CCTTCTGCTTTTGGGTAGCTG 59.185 52.381 0.00 0.00 39.38 4.24
50 51 2.553028 CCTTCTGCTTTTGGGTAGCTGA 60.553 50.000 0.00 0.00 42.45 4.26
51 52 3.350833 CTTCTGCTTTTGGGTAGCTGAT 58.649 45.455 0.00 0.00 43.23 2.90
52 53 2.715046 TCTGCTTTTGGGTAGCTGATG 58.285 47.619 0.00 0.00 40.30 3.07
53 54 1.747355 CTGCTTTTGGGTAGCTGATGG 59.253 52.381 0.00 0.00 39.18 3.51
54 55 0.457443 GCTTTTGGGTAGCTGATGGC 59.543 55.000 0.00 0.00 42.19 4.40
55 56 1.838112 CTTTTGGGTAGCTGATGGCA 58.162 50.000 0.00 0.00 44.79 4.92
56 57 2.170166 CTTTTGGGTAGCTGATGGCAA 58.830 47.619 0.00 0.00 44.79 4.52
57 58 2.300956 TTTGGGTAGCTGATGGCAAA 57.699 45.000 0.00 0.00 44.79 3.68
58 59 1.838112 TTGGGTAGCTGATGGCAAAG 58.162 50.000 0.00 0.00 44.79 2.77
59 60 0.991146 TGGGTAGCTGATGGCAAAGA 59.009 50.000 0.00 0.00 44.79 2.52
60 61 1.065199 TGGGTAGCTGATGGCAAAGAG 60.065 52.381 0.00 0.00 44.79 2.85
61 62 1.065126 GGGTAGCTGATGGCAAAGAGT 60.065 52.381 0.00 0.00 44.79 3.24
62 63 2.619074 GGGTAGCTGATGGCAAAGAGTT 60.619 50.000 0.00 0.00 44.79 3.01
63 64 3.084786 GGTAGCTGATGGCAAAGAGTTT 58.915 45.455 0.00 0.00 44.79 2.66
64 65 3.127721 GGTAGCTGATGGCAAAGAGTTTC 59.872 47.826 0.00 0.00 44.79 2.78
65 66 3.151912 AGCTGATGGCAAAGAGTTTCT 57.848 42.857 4.85 0.00 44.79 2.52
66 67 3.494332 AGCTGATGGCAAAGAGTTTCTT 58.506 40.909 4.85 0.00 44.79 2.52
67 68 3.893813 AGCTGATGGCAAAGAGTTTCTTT 59.106 39.130 4.85 0.00 46.75 2.52
75 76 3.971032 AAAGAGTTTCTTTGCCGTCAG 57.029 42.857 3.43 0.00 44.34 3.51
76 77 1.230324 AGAGTTTCTTTGCCGTCAGC 58.770 50.000 0.00 0.00 44.14 4.26
77 78 1.202698 AGAGTTTCTTTGCCGTCAGCT 60.203 47.619 0.00 0.00 44.23 4.24
78 79 2.037251 AGAGTTTCTTTGCCGTCAGCTA 59.963 45.455 0.00 0.00 44.23 3.32
79 80 2.413453 GAGTTTCTTTGCCGTCAGCTAG 59.587 50.000 0.00 0.00 44.23 3.42
80 81 1.135944 GTTTCTTTGCCGTCAGCTAGC 60.136 52.381 6.62 6.62 44.23 3.42
81 82 0.034756 TTCTTTGCCGTCAGCTAGCA 59.965 50.000 18.83 0.00 44.23 3.49
82 83 0.390340 TCTTTGCCGTCAGCTAGCAG 60.390 55.000 18.83 9.54 44.23 4.24
83 84 0.390340 CTTTGCCGTCAGCTAGCAGA 60.390 55.000 18.83 12.26 44.23 4.26
84 85 0.670546 TTTGCCGTCAGCTAGCAGAC 60.671 55.000 25.73 25.73 44.23 3.51
87 88 2.580867 CGTCAGCTAGCAGACGGC 60.581 66.667 39.52 18.28 46.97 5.68
88 89 3.342370 CGTCAGCTAGCAGACGGCA 62.342 63.158 39.52 7.94 46.97 5.69
89 90 2.819117 CGTCAGCTAGCAGACGGCAA 62.819 60.000 39.52 7.24 46.97 4.52
101 102 2.359107 CGGCAAAGAGCTGGCAGA 60.359 61.111 20.86 0.00 46.20 4.26
102 103 1.748122 CGGCAAAGAGCTGGCAGAT 60.748 57.895 20.86 13.42 46.20 2.90
103 104 1.807886 GGCAAAGAGCTGGCAGATG 59.192 57.895 20.86 9.26 44.79 2.90
104 105 1.664321 GGCAAAGAGCTGGCAGATGG 61.664 60.000 20.86 2.18 44.79 3.51
105 106 1.807886 CAAAGAGCTGGCAGATGGC 59.192 57.895 20.86 2.95 43.74 4.40
118 119 4.317671 GCAGATGGCAAATTAGCTGATT 57.682 40.909 0.00 0.00 43.97 2.57
119 120 4.296690 GCAGATGGCAAATTAGCTGATTC 58.703 43.478 3.93 0.00 43.97 2.52
120 121 4.795308 GCAGATGGCAAATTAGCTGATTCC 60.795 45.833 3.93 3.31 43.97 3.01
121 122 4.340097 CAGATGGCAAATTAGCTGATTCCA 59.660 41.667 12.34 12.34 32.32 3.53
122 123 4.583489 AGATGGCAAATTAGCTGATTCCAG 59.417 41.667 14.48 6.05 43.22 3.86
123 124 3.700538 TGGCAAATTAGCTGATTCCAGT 58.299 40.909 3.93 0.00 42.35 4.00
124 125 4.854173 TGGCAAATTAGCTGATTCCAGTA 58.146 39.130 3.93 0.00 42.35 2.74
125 126 4.883585 TGGCAAATTAGCTGATTCCAGTAG 59.116 41.667 3.93 0.00 42.35 2.57
126 127 4.884164 GGCAAATTAGCTGATTCCAGTAGT 59.116 41.667 3.93 0.00 42.35 2.73
127 128 5.220931 GGCAAATTAGCTGATTCCAGTAGTG 60.221 44.000 3.93 0.00 42.35 2.74
159 160 5.424252 TGGAATTCCCTTCTATGTAGTTCGT 59.576 40.000 21.90 0.00 34.08 3.85
175 176 9.817809 ATGTAGTTCGTACAATTCACATTATCT 57.182 29.630 0.00 0.00 45.00 1.98
277 278 7.093771 GGTTGATTGTATCCTTCACCATTTCTT 60.094 37.037 0.00 0.00 0.00 2.52
324 325 4.400251 CACCATGAATCCACTAATTGCTGT 59.600 41.667 0.00 0.00 0.00 4.40
428 429 3.067461 AGCTGTAGAAGGTATTGCGAGAG 59.933 47.826 0.00 0.00 33.90 3.20
455 456 5.642063 CCAGAAGCAGAAGGTAAAATACGAA 59.358 40.000 0.00 0.00 0.00 3.85
734 740 3.054802 AGGAAGGGCTGAGTTGAGTATTG 60.055 47.826 0.00 0.00 0.00 1.90
770 776 4.591321 ATGCTCACCTTCTTATTTCCCA 57.409 40.909 0.00 0.00 0.00 4.37
772 778 4.272489 TGCTCACCTTCTTATTTCCCATG 58.728 43.478 0.00 0.00 0.00 3.66
837 844 8.670521 AGGAATTTTGGGAACAGAATATTTCT 57.329 30.769 0.00 0.00 43.71 2.52
1066 1078 0.040067 CGTTGGCAGTTTCAGGCTTC 60.040 55.000 0.00 0.00 0.00 3.86
1162 1177 4.127171 AGTGTGTGCGAGTTGTCTATTTT 58.873 39.130 0.00 0.00 0.00 1.82
1239 1254 6.464222 TCGGATAAATAAGATAAGGGTGCAG 58.536 40.000 0.00 0.00 0.00 4.41
1362 1377 5.147330 AGAATGTGAGACCATTAACACGA 57.853 39.130 0.00 0.00 35.24 4.35
1742 1768 9.817809 GACCATGATATATTTTTATCTAGGCGA 57.182 33.333 0.00 0.00 31.79 5.54
1998 2034 7.989826 AGATAATCGAAAACAAAGGATCTTGG 58.010 34.615 0.00 0.00 0.00 3.61
2014 2050 7.574607 AGGATCTTGGGTACTATTCGAAATTT 58.425 34.615 0.00 0.00 0.00 1.82
2055 2091 4.321230 GGACCATTGAGCAACTCGAAAAAT 60.321 41.667 0.00 0.00 32.35 1.82
2072 2108 6.700081 TCGAAAAATCTCGGATTCGATTACAT 59.300 34.615 8.77 0.00 45.94 2.29
2196 2232 8.628882 ACAATTGGAAAAGTCTAAAAACGAAG 57.371 30.769 10.83 0.00 0.00 3.79
2269 2305 0.673644 CAACAGGCCGTACAAGGAGG 60.674 60.000 0.00 0.00 0.00 4.30
2323 2359 4.794762 CGAGTTACATTTCCGTACGATTCA 59.205 41.667 18.76 0.00 0.00 2.57
2351 2387 0.619255 TTGGCATTCTCGGGTCCCTA 60.619 55.000 6.29 0.00 0.00 3.53
2499 2535 7.749126 GTCAACGAAATTCATAAAATTCTCCGT 59.251 33.333 0.00 0.00 0.00 4.69
2548 2587 4.160329 AGGGATTGAGAATATAGGTCGCA 58.840 43.478 0.00 0.00 0.00 5.10
2562 2601 0.727398 GTCGCATAGTTCAAGTGGGC 59.273 55.000 0.00 0.00 0.00 5.36
2644 2683 4.368067 TGCAGAAGGTACTAGGGGTATTT 58.632 43.478 0.00 0.00 38.49 1.40
2647 2686 5.130643 GCAGAAGGTACTAGGGGTATTTCTT 59.869 44.000 0.00 0.00 38.49 2.52
2760 2799 1.476891 GCTCAGATACCCGTGAGTGAA 59.523 52.381 1.61 0.00 41.99 3.18
2805 2844 3.873910 TGCTCTGGCTAAACCTATTGAC 58.126 45.455 0.00 0.00 40.22 3.18
2807 2846 3.679083 GCTCTGGCTAAACCTATTGACGT 60.679 47.826 0.00 0.00 40.22 4.34
2835 2874 4.434330 GGCGAAATTATAGCTTCCGAATCG 60.434 45.833 0.00 0.00 0.00 3.34
2837 2876 4.386049 CGAAATTATAGCTTCCGAATCGCT 59.614 41.667 0.00 1.02 37.77 4.93
2846 2885 3.309954 GCTTCCGAATCGCTCTTAATTGT 59.690 43.478 0.00 0.00 0.00 2.71
2860 2899 6.166984 TCTTAATTGTATCTCCTGCTCCAG 57.833 41.667 0.00 0.00 0.00 3.86
2910 2949 3.690460 ACCTCTTCAAACAGGGCTTATG 58.310 45.455 0.00 0.00 33.57 1.90
2927 2966 4.864806 GCTTATGGCTATCGATTCGATGAA 59.135 41.667 27.35 10.92 46.43 2.57
2971 3010 6.525629 CGAGAGTTAATTATTGGGGACAGAT 58.474 40.000 0.00 0.00 44.54 2.90
3033 3072 4.864704 TCAAAAAGGGCAAGGTGTAATC 57.135 40.909 0.00 0.00 0.00 1.75
3070 3109 0.250234 CGGTCAAAGAGCATCCTCCA 59.750 55.000 0.00 0.00 38.96 3.86
3074 3113 3.135530 GGTCAAAGAGCATCCTCCATAGT 59.864 47.826 0.00 0.00 38.96 2.12
3088 3127 7.642082 TCCTCCATAGTTCAAGTAGTAACTC 57.358 40.000 0.00 0.00 37.19 3.01
3146 3185 2.237643 TGGTAGCTGAAAAGGCGGATTA 59.762 45.455 0.00 0.00 34.52 1.75
3177 3216 5.598769 ACATTACAATACCTCGCTCCTTAC 58.401 41.667 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.586802 GGCAGACGACAAAACAGGTC 59.413 55.000 0.00 0.00 0.00 3.85
1 2 0.107410 TGGCAGACGACAAAACAGGT 60.107 50.000 0.00 0.00 0.00 4.00
2 3 1.238439 ATGGCAGACGACAAAACAGG 58.762 50.000 0.00 0.00 30.02 4.00
3 4 3.003689 AGAAATGGCAGACGACAAAACAG 59.996 43.478 0.00 0.00 30.02 3.16
4 5 2.948979 AGAAATGGCAGACGACAAAACA 59.051 40.909 0.00 0.00 30.02 2.83
5 6 3.626028 AGAAATGGCAGACGACAAAAC 57.374 42.857 0.00 0.00 30.02 2.43
6 7 4.358851 CAAAGAAATGGCAGACGACAAAA 58.641 39.130 0.00 0.00 30.02 2.44
7 8 3.795150 GCAAAGAAATGGCAGACGACAAA 60.795 43.478 0.00 0.00 30.02 2.83
8 9 2.287547 GCAAAGAAATGGCAGACGACAA 60.288 45.455 0.00 0.00 30.02 3.18
9 10 1.266718 GCAAAGAAATGGCAGACGACA 59.733 47.619 0.00 0.00 0.00 4.35
10 11 1.401539 GGCAAAGAAATGGCAGACGAC 60.402 52.381 0.00 0.00 44.66 4.34
11 12 0.881118 GGCAAAGAAATGGCAGACGA 59.119 50.000 0.00 0.00 44.66 4.20
12 13 3.406682 GGCAAAGAAATGGCAGACG 57.593 52.632 0.00 0.00 44.66 4.18
17 18 1.718396 GCAGAAGGCAAAGAAATGGC 58.282 50.000 0.00 0.00 45.57 4.40
28 29 0.528017 GCTACCCAAAAGCAGAAGGC 59.472 55.000 0.00 0.00 45.30 4.35
29 30 1.815003 CAGCTACCCAAAAGCAGAAGG 59.185 52.381 0.00 0.00 42.62 3.46
30 31 2.783135 TCAGCTACCCAAAAGCAGAAG 58.217 47.619 0.00 0.00 42.62 2.85
31 32 2.949177 TCAGCTACCCAAAAGCAGAA 57.051 45.000 0.00 0.00 42.62 3.02
32 33 2.618816 CCATCAGCTACCCAAAAGCAGA 60.619 50.000 0.00 0.00 42.62 4.26
33 34 1.747355 CCATCAGCTACCCAAAAGCAG 59.253 52.381 0.00 0.00 42.62 4.24
34 35 1.838112 CCATCAGCTACCCAAAAGCA 58.162 50.000 0.00 0.00 42.62 3.91
35 36 0.457443 GCCATCAGCTACCCAAAAGC 59.543 55.000 0.00 0.00 40.40 3.51
36 37 1.838112 TGCCATCAGCTACCCAAAAG 58.162 50.000 0.00 0.00 44.23 2.27
37 38 2.300956 TTGCCATCAGCTACCCAAAA 57.699 45.000 0.00 0.00 44.23 2.44
38 39 2.170166 CTTTGCCATCAGCTACCCAAA 58.830 47.619 0.00 0.00 44.23 3.28
39 40 1.354031 TCTTTGCCATCAGCTACCCAA 59.646 47.619 0.00 0.00 44.23 4.12
40 41 0.991146 TCTTTGCCATCAGCTACCCA 59.009 50.000 0.00 0.00 44.23 4.51
41 42 1.065126 ACTCTTTGCCATCAGCTACCC 60.065 52.381 0.00 0.00 44.23 3.69
42 43 2.409948 ACTCTTTGCCATCAGCTACC 57.590 50.000 0.00 0.00 44.23 3.18
43 44 4.006319 AGAAACTCTTTGCCATCAGCTAC 58.994 43.478 0.00 0.00 44.23 3.58
44 45 4.292186 AGAAACTCTTTGCCATCAGCTA 57.708 40.909 0.00 0.00 44.23 3.32
45 46 3.151912 AGAAACTCTTTGCCATCAGCT 57.848 42.857 0.00 0.00 44.23 4.24
46 47 3.930634 AAGAAACTCTTTGCCATCAGC 57.069 42.857 0.00 0.00 44.14 4.26
55 56 2.033424 GCTGACGGCAAAGAAACTCTTT 59.967 45.455 0.00 0.00 46.75 2.52
56 57 1.604278 GCTGACGGCAAAGAAACTCTT 59.396 47.619 0.00 0.00 38.59 2.85
57 58 1.202698 AGCTGACGGCAAAGAAACTCT 60.203 47.619 9.39 0.00 44.79 3.24
58 59 1.230324 AGCTGACGGCAAAGAAACTC 58.770 50.000 9.39 0.00 44.79 3.01
59 60 2.417719 CTAGCTGACGGCAAAGAAACT 58.582 47.619 9.39 0.00 44.79 2.66
60 61 1.135944 GCTAGCTGACGGCAAAGAAAC 60.136 52.381 7.70 0.00 44.79 2.78
61 62 1.156736 GCTAGCTGACGGCAAAGAAA 58.843 50.000 7.70 0.00 44.79 2.52
62 63 0.034756 TGCTAGCTGACGGCAAAGAA 59.965 50.000 17.23 0.00 44.79 2.52
63 64 0.390340 CTGCTAGCTGACGGCAAAGA 60.390 55.000 17.23 0.00 44.79 2.52
64 65 0.390340 TCTGCTAGCTGACGGCAAAG 60.390 55.000 19.26 6.65 44.79 2.77
65 66 0.670546 GTCTGCTAGCTGACGGCAAA 60.671 55.000 30.98 5.98 44.79 3.68
66 67 1.079819 GTCTGCTAGCTGACGGCAA 60.080 57.895 30.98 6.66 44.79 4.52
67 68 2.573869 GTCTGCTAGCTGACGGCA 59.426 61.111 30.98 7.33 44.79 5.69
71 72 0.670546 TTTGCCGTCTGCTAGCTGAC 60.671 55.000 33.23 33.23 42.00 3.51
72 73 0.390340 CTTTGCCGTCTGCTAGCTGA 60.390 55.000 19.26 19.26 42.00 4.26
73 74 0.390340 TCTTTGCCGTCTGCTAGCTG 60.390 55.000 17.23 16.05 42.00 4.24
74 75 0.108424 CTCTTTGCCGTCTGCTAGCT 60.108 55.000 17.23 0.00 42.00 3.32
75 76 1.700600 GCTCTTTGCCGTCTGCTAGC 61.701 60.000 8.10 8.10 42.00 3.42
76 77 0.108424 AGCTCTTTGCCGTCTGCTAG 60.108 55.000 0.00 0.00 44.23 3.42
77 78 0.390340 CAGCTCTTTGCCGTCTGCTA 60.390 55.000 0.00 0.00 44.23 3.49
78 79 1.670406 CAGCTCTTTGCCGTCTGCT 60.670 57.895 0.00 0.00 44.23 4.24
79 80 2.684843 CCAGCTCTTTGCCGTCTGC 61.685 63.158 0.00 0.00 44.23 4.26
80 81 2.684843 GCCAGCTCTTTGCCGTCTG 61.685 63.158 0.00 0.00 44.23 3.51
81 82 2.359230 GCCAGCTCTTTGCCGTCT 60.359 61.111 0.00 0.00 44.23 4.18
82 83 2.669569 TGCCAGCTCTTTGCCGTC 60.670 61.111 0.00 0.00 44.23 4.79
83 84 2.475371 ATCTGCCAGCTCTTTGCCGT 62.475 55.000 0.00 0.00 44.23 5.68
84 85 1.748122 ATCTGCCAGCTCTTTGCCG 60.748 57.895 0.00 0.00 44.23 5.69
85 86 1.664321 CCATCTGCCAGCTCTTTGCC 61.664 60.000 0.00 0.00 44.23 4.52
86 87 1.807886 CCATCTGCCAGCTCTTTGC 59.192 57.895 0.00 0.00 43.29 3.68
87 88 0.963856 TGCCATCTGCCAGCTCTTTG 60.964 55.000 0.00 0.00 40.16 2.77
88 89 0.251474 TTGCCATCTGCCAGCTCTTT 60.251 50.000 0.00 0.00 40.16 2.52
89 90 0.251474 TTTGCCATCTGCCAGCTCTT 60.251 50.000 0.00 0.00 40.16 2.85
90 91 0.033405 ATTTGCCATCTGCCAGCTCT 60.033 50.000 0.00 0.00 40.16 4.09
91 92 0.822164 AATTTGCCATCTGCCAGCTC 59.178 50.000 0.00 0.00 40.16 4.09
92 93 2.029623 CTAATTTGCCATCTGCCAGCT 58.970 47.619 0.00 0.00 40.16 4.24
93 94 1.537562 GCTAATTTGCCATCTGCCAGC 60.538 52.381 0.00 0.00 40.16 4.85
94 95 2.029623 AGCTAATTTGCCATCTGCCAG 58.970 47.619 8.30 0.00 40.16 4.85
95 96 1.752498 CAGCTAATTTGCCATCTGCCA 59.248 47.619 8.30 0.00 40.16 4.92
96 97 2.026641 TCAGCTAATTTGCCATCTGCC 58.973 47.619 8.30 0.00 40.16 4.85
97 98 4.296690 GAATCAGCTAATTTGCCATCTGC 58.703 43.478 8.30 0.00 41.77 4.26
98 99 4.340097 TGGAATCAGCTAATTTGCCATCTG 59.660 41.667 8.30 0.74 0.00 2.90
99 100 4.539726 TGGAATCAGCTAATTTGCCATCT 58.460 39.130 8.30 0.00 0.00 2.90
100 101 4.340381 ACTGGAATCAGCTAATTTGCCATC 59.660 41.667 8.30 2.47 44.59 3.51
101 102 4.284178 ACTGGAATCAGCTAATTTGCCAT 58.716 39.130 8.30 0.00 44.59 4.40
102 103 3.700538 ACTGGAATCAGCTAATTTGCCA 58.299 40.909 8.30 0.00 44.59 4.92
103 104 4.884164 ACTACTGGAATCAGCTAATTTGCC 59.116 41.667 8.30 0.00 44.59 4.52
104 105 5.586243 TCACTACTGGAATCAGCTAATTTGC 59.414 40.000 3.49 3.49 44.59 3.68
105 106 7.255035 CCATCACTACTGGAATCAGCTAATTTG 60.255 40.741 0.00 0.00 44.59 2.32
106 107 6.769822 CCATCACTACTGGAATCAGCTAATTT 59.230 38.462 0.00 0.00 44.59 1.82
107 108 6.100279 TCCATCACTACTGGAATCAGCTAATT 59.900 38.462 0.00 0.00 44.59 1.40
108 109 5.604231 TCCATCACTACTGGAATCAGCTAAT 59.396 40.000 0.00 0.00 44.59 1.73
109 110 4.962362 TCCATCACTACTGGAATCAGCTAA 59.038 41.667 0.00 0.00 44.59 3.09
110 111 4.546674 TCCATCACTACTGGAATCAGCTA 58.453 43.478 0.00 0.00 44.59 3.32
111 112 3.378512 TCCATCACTACTGGAATCAGCT 58.621 45.455 0.00 0.00 44.59 4.24
112 113 3.827008 TCCATCACTACTGGAATCAGC 57.173 47.619 0.00 0.00 44.59 4.26
113 114 6.212187 TCCATATCCATCACTACTGGAATCAG 59.788 42.308 0.00 0.00 45.57 2.90
114 115 6.084060 TCCATATCCATCACTACTGGAATCA 58.916 40.000 0.00 0.00 45.57 2.57
115 116 6.611613 TCCATATCCATCACTACTGGAATC 57.388 41.667 0.00 0.00 45.57 2.52
116 117 7.579940 ATTCCATATCCATCACTACTGGAAT 57.420 36.000 7.84 7.84 45.57 3.01
117 118 7.392766 AATTCCATATCCATCACTACTGGAA 57.607 36.000 3.81 3.81 45.57 3.53
118 119 6.013379 GGAATTCCATATCCATCACTACTGGA 60.013 42.308 20.04 0.00 40.46 3.86
119 120 6.176183 GGAATTCCATATCCATCACTACTGG 58.824 44.000 20.04 0.00 35.71 4.00
120 121 6.013032 AGGGAATTCCATATCCATCACTACTG 60.013 42.308 25.67 0.00 37.46 2.74
121 122 6.094302 AGGGAATTCCATATCCATCACTACT 58.906 40.000 25.67 5.63 37.46 2.57
122 123 6.380079 AGGGAATTCCATATCCATCACTAC 57.620 41.667 25.67 3.33 37.46 2.73
123 124 6.794493 AGAAGGGAATTCCATATCCATCACTA 59.206 38.462 25.67 0.00 38.84 2.74
124 125 5.614402 AGAAGGGAATTCCATATCCATCACT 59.386 40.000 25.67 6.77 38.84 3.41
125 126 5.885465 AGAAGGGAATTCCATATCCATCAC 58.115 41.667 25.67 4.48 38.84 3.06
126 127 7.240405 ACATAGAAGGGAATTCCATATCCATCA 59.760 37.037 25.67 4.94 38.84 3.07
127 128 7.637511 ACATAGAAGGGAATTCCATATCCATC 58.362 38.462 25.67 12.67 38.84 3.51
289 290 4.407296 GGATTCATGGTGAGTAGTTCCTCT 59.593 45.833 0.00 0.00 32.50 3.69
324 325 2.229543 CCAGCAGCAATAACAGAAGCAA 59.770 45.455 0.00 0.00 0.00 3.91
428 429 2.770164 TTACCTTCTGCTTCTGGCTC 57.230 50.000 0.00 0.00 42.39 4.70
455 456 9.945904 AAAAGCTAGACTAAGCAATAAAGTACT 57.054 29.630 0.00 0.00 45.30 2.73
495 496 6.717289 AGTGCCACAACTAGTCCATAAATTA 58.283 36.000 0.00 0.00 0.00 1.40
770 776 7.004691 ACTTTCCACTTTCCTAAACTAAGCAT 58.995 34.615 0.00 0.00 0.00 3.79
772 778 6.879276 ACTTTCCACTTTCCTAAACTAAGC 57.121 37.500 0.00 0.00 0.00 3.09
831 838 9.151471 CGATGAAAGACTTCCTTTGTAGAAATA 57.849 33.333 0.00 0.00 44.63 1.40
837 844 5.221561 TGACCGATGAAAGACTTCCTTTGTA 60.222 40.000 0.00 0.00 44.63 2.41
855 862 3.067180 AGTCTTACGTCTTGTTTGACCGA 59.933 43.478 0.00 0.00 34.30 4.69
941 951 7.981142 ACAAAGTTTTTCGATCACTTACTTCA 58.019 30.769 5.18 0.00 30.37 3.02
1045 1057 2.919494 GCCTGAAACTGCCAACGGG 61.919 63.158 0.00 0.00 37.18 5.28
1049 1061 1.999648 ATGAAGCCTGAAACTGCCAA 58.000 45.000 0.00 0.00 0.00 4.52
1229 1244 1.112113 GTCGAGATCCTGCACCCTTA 58.888 55.000 0.00 0.00 0.00 2.69
1239 1254 5.171147 TCAGAAGTAATTCGTCGAGATCC 57.829 43.478 0.00 0.00 0.00 3.36
1552 1571 5.929697 TTATACATAGGTCGTCGATTCGT 57.070 39.130 5.89 0.00 0.00 3.85
1988 2024 6.555463 TTTCGAATAGTACCCAAGATCCTT 57.445 37.500 0.00 0.00 0.00 3.36
2014 2050 3.383825 GGTCCCTCTACGCAATTCTTCTA 59.616 47.826 0.00 0.00 0.00 2.10
2072 2108 4.397103 TCATCCGCTTCTAGTTCGACTTTA 59.603 41.667 0.00 0.00 0.00 1.85
2269 2305 8.088981 TCAAACAACTATTCAGAGTTCCTAGAC 58.911 37.037 0.00 0.00 37.57 2.59
2548 2587 1.134098 CCCATCGCCCACTTGAACTAT 60.134 52.381 0.00 0.00 0.00 2.12
2562 2601 5.043903 CCTATAATACGAGCAATCCCATCG 58.956 45.833 0.00 0.00 42.04 3.84
2601 2640 5.647658 TGCAAATTCGACTAATTCACCTGAT 59.352 36.000 0.00 0.00 36.76 2.90
2760 2799 1.140252 ACAACACGACCCAAGTAAGCT 59.860 47.619 0.00 0.00 0.00 3.74
2805 2844 4.795970 AGCTATAATTTCGCCTTTCACG 57.204 40.909 0.00 0.00 0.00 4.35
2807 2846 4.272504 CGGAAGCTATAATTTCGCCTTTCA 59.727 41.667 0.00 0.00 0.00 2.69
2835 2874 4.994217 GGAGCAGGAGATACAATTAAGAGC 59.006 45.833 0.00 0.00 0.00 4.09
2837 2876 6.166984 CTGGAGCAGGAGATACAATTAAGA 57.833 41.667 0.00 0.00 0.00 2.10
2860 2899 4.813296 CAGAACGCCTGGAAATTATACC 57.187 45.455 0.00 0.00 39.23 2.73
2910 2949 2.028930 AGGGTTCATCGAATCGATAGCC 60.029 50.000 22.11 22.11 45.19 3.93
2971 3010 2.638480 ACTGCTGTTTTGCCAGTCTA 57.362 45.000 0.00 0.00 34.84 2.59
3033 3072 5.588240 TGACCGATAGCTACATAAACACAG 58.412 41.667 0.00 0.00 0.00 3.66
3070 3109 8.431910 TGGAAAGGAGTTACTACTTGAACTAT 57.568 34.615 10.99 0.00 34.47 2.12
3074 3113 7.311092 TCATGGAAAGGAGTTACTACTTGAA 57.689 36.000 10.99 0.17 34.47 2.69
3088 3127 1.925888 CCCCCTCCTCATGGAAAGG 59.074 63.158 0.00 0.00 42.66 3.11
3126 3165 1.751437 AATCCGCCTTTTCAGCTACC 58.249 50.000 0.00 0.00 0.00 3.18
3137 3176 1.200519 TGTAGCAGGTTAATCCGCCT 58.799 50.000 0.00 0.00 41.99 5.52
3146 3185 5.357257 CGAGGTATTGTAATGTAGCAGGTT 58.643 41.667 0.00 0.00 0.00 3.50
3302 3341 2.362369 CCTGGATCAGCCTCACGGT 61.362 63.158 0.00 0.00 37.63 4.83
3325 3364 5.783100 AAGGCGTGAATGCAAATAAAATG 57.217 34.783 0.00 0.00 36.28 2.32
3326 3365 6.799926 AAAAGGCGTGAATGCAAATAAAAT 57.200 29.167 0.00 0.00 36.28 1.82


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

AutoCloner maintained by Alex Coulton.