Multiple sequence alignment - TraesCS7D01G293000

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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 TraesCS7D01G293000 chr7D 100.000 3970 0 0 1 3970 362367173 362371142 0.000000e+00 7332
1 TraesCS7D01G293000 chr7D 98.309 3845 44 8 139 3970 95100904 95097068 0.000000e+00 6721
2 TraesCS7D01G293000 chr7D 98.576 913 10 1 3061 3970 590589759 590588847 0.000000e+00 1611
3 TraesCS7D01G293000 chr7D 98.206 223 4 0 140 362 590576360 590576582 1.340000e-104 390
4 TraesCS7D01G293000 chr7D 95.575 226 10 0 137 362 95092377 95092602 2.920000e-96 363
5 TraesCS7D01G293000 chr6D 98.393 3858 33 14 140 3970 102252338 102248483 0.000000e+00 6754
6 TraesCS7D01G293000 chr6D 95.292 2719 106 6 140 2839 277340135 277337420 0.000000e+00 4292
7 TraesCS7D01G293000 chr4D 98.434 3831 53 5 140 3970 122726627 122722804 0.000000e+00 6735
8 TraesCS7D01G293000 chr3D 98.053 3698 39 16 300 3970 53788544 53792235 0.000000e+00 6399
9 TraesCS7D01G293000 chr3D 98.441 2823 29 3 140 2959 5493961 5496771 0.000000e+00 4955
10 TraesCS7D01G293000 chr2A 96.403 3864 78 15 137 3970 2356022 2359854 0.000000e+00 6309
11 TraesCS7D01G293000 chr2A 94.737 1520 46 3 140 1650 712854797 712853303 0.000000e+00 2333
12 TraesCS7D01G293000 chr2A 95.516 223 10 0 140 362 2362926 2362704 1.360000e-94 357
13 TraesCS7D01G293000 chr2A 95.111 225 11 0 138 362 712847303 712847527 4.880000e-94 355
14 TraesCS7D01G293000 chr1D 95.251 3832 114 27 140 3970 80650664 80646900 0.000000e+00 6006
15 TraesCS7D01G293000 chr4A 97.396 2381 54 6 1594 3968 84937030 84939408 0.000000e+00 4047
16 TraesCS7D01G293000 chr5A 96.568 1515 44 6 2462 3970 35060153 35061665 0.000000e+00 2503
17 TraesCS7D01G293000 chrUn 98.681 910 12 0 3061 3970 108020454 108021363 0.000000e+00 1615
18 TraesCS7D01G293000 chr7B 96.403 139 5 0 1 139 324390368 324390230 3.090000e-56 230


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 TraesCS7D01G293000 chr7D 362367173 362371142 3969 False 7332 7332 100.000 1 3970 1 chr7D.!!$F2 3969
1 TraesCS7D01G293000 chr7D 95097068 95100904 3836 True 6721 6721 98.309 139 3970 1 chr7D.!!$R1 3831
2 TraesCS7D01G293000 chr7D 590588847 590589759 912 True 1611 1611 98.576 3061 3970 1 chr7D.!!$R2 909
3 TraesCS7D01G293000 chr6D 102248483 102252338 3855 True 6754 6754 98.393 140 3970 1 chr6D.!!$R1 3830
4 TraesCS7D01G293000 chr6D 277337420 277340135 2715 True 4292 4292 95.292 140 2839 1 chr6D.!!$R2 2699
5 TraesCS7D01G293000 chr4D 122722804 122726627 3823 True 6735 6735 98.434 140 3970 1 chr4D.!!$R1 3830
6 TraesCS7D01G293000 chr3D 53788544 53792235 3691 False 6399 6399 98.053 300 3970 1 chr3D.!!$F2 3670
7 TraesCS7D01G293000 chr3D 5493961 5496771 2810 False 4955 4955 98.441 140 2959 1 chr3D.!!$F1 2819
8 TraesCS7D01G293000 chr2A 2356022 2359854 3832 False 6309 6309 96.403 137 3970 1 chr2A.!!$F1 3833
9 TraesCS7D01G293000 chr2A 712853303 712854797 1494 True 2333 2333 94.737 140 1650 1 chr2A.!!$R2 1510
10 TraesCS7D01G293000 chr1D 80646900 80650664 3764 True 6006 6006 95.251 140 3970 1 chr1D.!!$R1 3830
11 TraesCS7D01G293000 chr4A 84937030 84939408 2378 False 4047 4047 97.396 1594 3968 1 chr4A.!!$F1 2374
12 TraesCS7D01G293000 chr5A 35060153 35061665 1512 False 2503 2503 96.568 2462 3970 1 chr5A.!!$F1 1508
13 TraesCS7D01G293000 chrUn 108020454 108021363 909 False 1615 1615 98.681 3061 3970 1 chrUn.!!$F1 909

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
480 505 0.389817 CAGACATGAGTCCGGCGAAA 60.390 55.000 9.3 0.0 46.15 3.46 F
910 970 5.046376 TCAAATGATGTTCTGCTCTGGTCTA 60.046 40.000 0.0 0.0 0.00 2.59 F
2381 2444 2.094675 GCACACATGCCCTTCTATGTT 58.905 47.619 0.0 0.0 46.97 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 2444 7.230913 ACTTAGCAGTGACTTTAGTGTTCTCTA 59.769 37.037 0.00 0.00 0.00 2.43 R
2919 2982 5.287674 TCAACAATTCCAAAAGCAATGGA 57.712 34.783 1.41 1.41 45.09 3.41 R
3762 3852 0.767375 AAAGTCCTCTGGCTGAAGCA 59.233 50.000 4.43 0.00 44.36 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
24 25 7.510675 TCAGTGGGGTAAATATTCTTCTTCT 57.489 36.000 0.00 0.00 0.00 2.85
25 26 8.618240 TCAGTGGGGTAAATATTCTTCTTCTA 57.382 34.615 0.00 0.00 0.00 2.10
26 27 9.225682 TCAGTGGGGTAAATATTCTTCTTCTAT 57.774 33.333 0.00 0.00 0.00 1.98
27 28 9.853177 CAGTGGGGTAAATATTCTTCTTCTATT 57.147 33.333 0.00 0.00 0.00 1.73
28 29 9.853177 AGTGGGGTAAATATTCTTCTTCTATTG 57.147 33.333 0.00 0.00 0.00 1.90
29 30 8.568794 GTGGGGTAAATATTCTTCTTCTATTGC 58.431 37.037 0.00 0.00 0.00 3.56
30 31 7.724061 TGGGGTAAATATTCTTCTTCTATTGCC 59.276 37.037 0.00 0.00 0.00 4.52
31 32 7.176865 GGGGTAAATATTCTTCTTCTATTGCCC 59.823 40.741 0.00 0.00 34.00 5.36
32 33 7.176865 GGGTAAATATTCTTCTTCTATTGCCCC 59.823 40.741 0.00 0.00 31.46 5.80
33 34 7.945109 GGTAAATATTCTTCTTCTATTGCCCCT 59.055 37.037 0.00 0.00 0.00 4.79
34 35 9.004717 GTAAATATTCTTCTTCTATTGCCCCTC 57.995 37.037 0.00 0.00 0.00 4.30
35 36 3.933861 TTCTTCTTCTATTGCCCCTCC 57.066 47.619 0.00 0.00 0.00 4.30
36 37 2.845659 TCTTCTTCTATTGCCCCTCCA 58.154 47.619 0.00 0.00 0.00 3.86
37 38 3.397527 TCTTCTTCTATTGCCCCTCCAT 58.602 45.455 0.00 0.00 0.00 3.41
38 39 3.788142 TCTTCTTCTATTGCCCCTCCATT 59.212 43.478 0.00 0.00 0.00 3.16
39 40 4.230502 TCTTCTTCTATTGCCCCTCCATTT 59.769 41.667 0.00 0.00 0.00 2.32
40 41 5.431731 TCTTCTTCTATTGCCCCTCCATTTA 59.568 40.000 0.00 0.00 0.00 1.40
41 42 5.310409 TCTTCTATTGCCCCTCCATTTAG 57.690 43.478 0.00 0.00 0.00 1.85
42 43 4.975147 TCTTCTATTGCCCCTCCATTTAGA 59.025 41.667 0.00 0.00 0.00 2.10
43 44 4.706842 TCTATTGCCCCTCCATTTAGAC 57.293 45.455 0.00 0.00 0.00 2.59
44 45 4.044308 TCTATTGCCCCTCCATTTAGACA 58.956 43.478 0.00 0.00 0.00 3.41
45 46 3.979501 ATTGCCCCTCCATTTAGACAT 57.020 42.857 0.00 0.00 0.00 3.06
46 47 5.849475 TCTATTGCCCCTCCATTTAGACATA 59.151 40.000 0.00 0.00 0.00 2.29
47 48 4.437682 TTGCCCCTCCATTTAGACATAG 57.562 45.455 0.00 0.00 0.00 2.23
48 49 3.664320 TGCCCCTCCATTTAGACATAGA 58.336 45.455 0.00 0.00 0.00 1.98
49 50 4.044308 TGCCCCTCCATTTAGACATAGAA 58.956 43.478 0.00 0.00 0.00 2.10
50 51 4.476846 TGCCCCTCCATTTAGACATAGAAA 59.523 41.667 0.00 0.00 0.00 2.52
51 52 5.066593 GCCCCTCCATTTAGACATAGAAAG 58.933 45.833 0.00 0.00 0.00 2.62
52 53 5.625150 CCCCTCCATTTAGACATAGAAAGG 58.375 45.833 0.00 0.00 0.00 3.11
53 54 5.369699 CCCCTCCATTTAGACATAGAAAGGA 59.630 44.000 0.00 0.00 0.00 3.36
54 55 6.044871 CCCCTCCATTTAGACATAGAAAGGAT 59.955 42.308 0.00 0.00 0.00 3.24
55 56 6.939163 CCCTCCATTTAGACATAGAAAGGATG 59.061 42.308 0.00 0.00 0.00 3.51
56 57 7.202130 CCCTCCATTTAGACATAGAAAGGATGA 60.202 40.741 0.00 0.00 0.00 2.92
57 58 8.381636 CCTCCATTTAGACATAGAAAGGATGAT 58.618 37.037 0.00 0.00 0.00 2.45
58 59 9.790344 CTCCATTTAGACATAGAAAGGATGATT 57.210 33.333 0.00 0.00 0.00 2.57
64 65 9.770097 TTAGACATAGAAAGGATGATTAAGCAG 57.230 33.333 0.00 0.00 0.00 4.24
65 66 6.709846 AGACATAGAAAGGATGATTAAGCAGC 59.290 38.462 0.00 0.00 0.00 5.25
66 67 6.599445 ACATAGAAAGGATGATTAAGCAGCT 58.401 36.000 9.05 0.00 0.00 4.24
67 68 6.485984 ACATAGAAAGGATGATTAAGCAGCTG 59.514 38.462 10.11 10.11 0.00 4.24
68 69 5.108187 AGAAAGGATGATTAAGCAGCTGA 57.892 39.130 20.43 0.00 0.00 4.26
69 70 5.503927 AGAAAGGATGATTAAGCAGCTGAA 58.496 37.500 20.43 2.80 0.00 3.02
70 71 5.948162 AGAAAGGATGATTAAGCAGCTGAAA 59.052 36.000 20.43 8.52 0.00 2.69
71 72 6.435277 AGAAAGGATGATTAAGCAGCTGAAAA 59.565 34.615 20.43 8.13 0.00 2.29
72 73 6.786967 AAGGATGATTAAGCAGCTGAAAAT 57.213 33.333 20.43 12.86 0.00 1.82
73 74 6.145338 AGGATGATTAAGCAGCTGAAAATG 57.855 37.500 20.43 0.00 0.00 2.32
74 75 5.889853 AGGATGATTAAGCAGCTGAAAATGA 59.110 36.000 20.43 7.77 0.00 2.57
75 76 6.550108 AGGATGATTAAGCAGCTGAAAATGAT 59.450 34.615 20.43 12.26 0.00 2.45
76 77 6.641314 GGATGATTAAGCAGCTGAAAATGATG 59.359 38.462 20.43 0.00 0.00 3.07
77 78 5.898174 TGATTAAGCAGCTGAAAATGATGG 58.102 37.500 20.43 0.00 0.00 3.51
78 79 2.667473 AAGCAGCTGAAAATGATGGC 57.333 45.000 20.43 0.00 0.00 4.40
79 80 1.848652 AGCAGCTGAAAATGATGGCT 58.151 45.000 20.43 0.00 0.00 4.75
83 84 6.386211 AAGCAGCTGAAAATGATGGCTGATA 61.386 40.000 20.43 0.00 46.52 2.15
84 85 7.643625 AAGCAGCTGAAAATGATGGCTGATAT 61.644 38.462 20.43 0.09 46.52 1.63
85 86 5.707242 AGCTGAAAATGATGGCTGATATG 57.293 39.130 0.00 0.00 31.68 1.78
86 87 5.382616 AGCTGAAAATGATGGCTGATATGA 58.617 37.500 0.00 0.00 31.68 2.15
87 88 6.010850 AGCTGAAAATGATGGCTGATATGAT 58.989 36.000 0.00 0.00 31.68 2.45
88 89 6.071896 AGCTGAAAATGATGGCTGATATGATG 60.072 38.462 0.00 0.00 31.68 3.07
89 90 6.072119 GCTGAAAATGATGGCTGATATGATGA 60.072 38.462 0.00 0.00 0.00 2.92
90 91 7.523216 GCTGAAAATGATGGCTGATATGATGAA 60.523 37.037 0.00 0.00 0.00 2.57
91 92 7.654568 TGAAAATGATGGCTGATATGATGAAC 58.345 34.615 0.00 0.00 0.00 3.18
92 93 7.504574 TGAAAATGATGGCTGATATGATGAACT 59.495 33.333 0.00 0.00 0.00 3.01
93 94 6.819397 AATGATGGCTGATATGATGAACTG 57.181 37.500 0.00 0.00 0.00 3.16
94 95 4.648651 TGATGGCTGATATGATGAACTGG 58.351 43.478 0.00 0.00 0.00 4.00
95 96 4.348754 TGATGGCTGATATGATGAACTGGA 59.651 41.667 0.00 0.00 0.00 3.86
96 97 4.077300 TGGCTGATATGATGAACTGGAC 57.923 45.455 0.00 0.00 0.00 4.02
97 98 3.181451 TGGCTGATATGATGAACTGGACC 60.181 47.826 0.00 0.00 0.00 4.46
98 99 3.181451 GGCTGATATGATGAACTGGACCA 60.181 47.826 0.00 0.00 0.00 4.02
99 100 4.063689 GCTGATATGATGAACTGGACCAG 58.936 47.826 20.45 20.45 37.52 4.00
100 101 4.639334 CTGATATGATGAACTGGACCAGG 58.361 47.826 25.34 7.84 35.51 4.45
101 102 3.181451 TGATATGATGAACTGGACCAGGC 60.181 47.826 25.34 16.62 35.51 4.85
102 103 0.994247 ATGATGAACTGGACCAGGCA 59.006 50.000 25.34 21.36 35.51 4.75
103 104 0.994247 TGATGAACTGGACCAGGCAT 59.006 50.000 25.34 24.62 35.51 4.40
104 105 1.355381 TGATGAACTGGACCAGGCATT 59.645 47.619 25.34 10.87 35.51 3.56
105 106 2.575735 TGATGAACTGGACCAGGCATTA 59.424 45.455 25.34 19.62 35.51 1.90
106 107 2.489938 TGAACTGGACCAGGCATTAC 57.510 50.000 25.34 9.92 35.51 1.89
107 108 1.702401 TGAACTGGACCAGGCATTACA 59.298 47.619 25.34 12.13 35.51 2.41
108 109 2.308570 TGAACTGGACCAGGCATTACAT 59.691 45.455 25.34 0.00 35.51 2.29
109 110 2.717639 ACTGGACCAGGCATTACATC 57.282 50.000 25.34 0.00 35.51 3.06
110 111 1.915489 ACTGGACCAGGCATTACATCA 59.085 47.619 25.34 0.00 35.51 3.07
111 112 2.292267 CTGGACCAGGCATTACATCAC 58.708 52.381 14.26 0.00 0.00 3.06
112 113 1.632920 TGGACCAGGCATTACATCACA 59.367 47.619 0.00 0.00 0.00 3.58
113 114 2.241941 TGGACCAGGCATTACATCACAT 59.758 45.455 0.00 0.00 0.00 3.21
114 115 2.620115 GGACCAGGCATTACATCACATG 59.380 50.000 0.00 0.00 0.00 3.21
115 116 2.026641 ACCAGGCATTACATCACATGC 58.973 47.619 0.00 0.00 44.39 4.06
121 122 3.961182 GCATTACATCACATGCCTCAAG 58.039 45.455 0.00 0.00 40.04 3.02
122 123 3.379372 GCATTACATCACATGCCTCAAGT 59.621 43.478 0.00 0.00 40.04 3.16
123 124 4.497006 GCATTACATCACATGCCTCAAGTC 60.497 45.833 0.00 0.00 40.04 3.01
124 125 2.119801 ACATCACATGCCTCAAGTCC 57.880 50.000 0.00 0.00 0.00 3.85
125 126 1.632409 ACATCACATGCCTCAAGTCCT 59.368 47.619 0.00 0.00 0.00 3.85
126 127 2.040813 ACATCACATGCCTCAAGTCCTT 59.959 45.455 0.00 0.00 0.00 3.36
127 128 3.264193 ACATCACATGCCTCAAGTCCTTA 59.736 43.478 0.00 0.00 0.00 2.69
128 129 4.263462 ACATCACATGCCTCAAGTCCTTAA 60.263 41.667 0.00 0.00 0.00 1.85
129 130 3.674997 TCACATGCCTCAAGTCCTTAAC 58.325 45.455 0.00 0.00 0.00 2.01
130 131 2.749621 CACATGCCTCAAGTCCTTAACC 59.250 50.000 0.00 0.00 0.00 2.85
131 132 2.375174 ACATGCCTCAAGTCCTTAACCA 59.625 45.455 0.00 0.00 0.00 3.67
132 133 2.561478 TGCCTCAAGTCCTTAACCAC 57.439 50.000 0.00 0.00 0.00 4.16
133 134 1.771854 TGCCTCAAGTCCTTAACCACA 59.228 47.619 0.00 0.00 0.00 4.17
134 135 2.152016 GCCTCAAGTCCTTAACCACAC 58.848 52.381 0.00 0.00 0.00 3.82
135 136 2.486548 GCCTCAAGTCCTTAACCACACA 60.487 50.000 0.00 0.00 0.00 3.72
136 137 3.403038 CCTCAAGTCCTTAACCACACAG 58.597 50.000 0.00 0.00 0.00 3.66
137 138 3.071023 CCTCAAGTCCTTAACCACACAGA 59.929 47.826 0.00 0.00 0.00 3.41
249 250 6.642950 CCTCGTAAACAATTTGCAAATACCAA 59.357 34.615 24.35 7.45 0.00 3.67
316 318 3.112842 GGTTTTTGCCGACGTGGT 58.887 55.556 0.00 0.00 41.21 4.16
480 505 0.389817 CAGACATGAGTCCGGCGAAA 60.390 55.000 9.30 0.00 46.15 3.46
910 970 5.046376 TCAAATGATGTTCTGCTCTGGTCTA 60.046 40.000 0.00 0.00 0.00 2.59
2381 2444 2.094675 GCACACATGCCCTTCTATGTT 58.905 47.619 0.00 0.00 46.97 2.71
2906 2969 2.108075 TGCAACTGGAAGAGATGGGAAA 59.892 45.455 0.00 0.00 37.43 3.13
2969 3032 2.526432 GACACTAACTCCTGGACCTGA 58.474 52.381 0.00 0.00 0.00 3.86
2979 3042 5.671493 ACTCCTGGACCTGATTTTTATACG 58.329 41.667 0.00 0.00 0.00 3.06
3825 3919 2.571653 AGATGTACCTGGCAGCTTACAA 59.428 45.455 23.11 12.16 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.510675 AGAAGAAGAATATTTACCCCACTGA 57.489 36.000 0.00 0.00 0.00 3.41
1 2 9.853177 AATAGAAGAAGAATATTTACCCCACTG 57.147 33.333 0.00 0.00 0.00 3.66
3 4 8.568794 GCAATAGAAGAAGAATATTTACCCCAC 58.431 37.037 0.00 0.00 0.00 4.61
4 5 7.724061 GGCAATAGAAGAAGAATATTTACCCCA 59.276 37.037 0.00 0.00 0.00 4.96
5 6 7.176865 GGGCAATAGAAGAAGAATATTTACCCC 59.823 40.741 0.00 0.00 31.87 4.95
6 7 7.176865 GGGGCAATAGAAGAAGAATATTTACCC 59.823 40.741 0.00 0.00 34.63 3.69
7 8 7.945109 AGGGGCAATAGAAGAAGAATATTTACC 59.055 37.037 0.00 0.00 0.00 2.85
8 9 8.926092 AGGGGCAATAGAAGAAGAATATTTAC 57.074 34.615 0.00 0.00 0.00 2.01
9 10 8.164070 GGAGGGGCAATAGAAGAAGAATATTTA 58.836 37.037 0.00 0.00 0.00 1.40
10 11 7.007116 GGAGGGGCAATAGAAGAAGAATATTT 58.993 38.462 0.00 0.00 0.00 1.40
11 12 6.103205 TGGAGGGGCAATAGAAGAAGAATATT 59.897 38.462 0.00 0.00 0.00 1.28
12 13 5.612688 TGGAGGGGCAATAGAAGAAGAATAT 59.387 40.000 0.00 0.00 0.00 1.28
13 14 4.975147 TGGAGGGGCAATAGAAGAAGAATA 59.025 41.667 0.00 0.00 0.00 1.75
14 15 3.788142 TGGAGGGGCAATAGAAGAAGAAT 59.212 43.478 0.00 0.00 0.00 2.40
15 16 3.189606 TGGAGGGGCAATAGAAGAAGAA 58.810 45.455 0.00 0.00 0.00 2.52
16 17 2.845659 TGGAGGGGCAATAGAAGAAGA 58.154 47.619 0.00 0.00 0.00 2.87
17 18 3.872459 ATGGAGGGGCAATAGAAGAAG 57.128 47.619 0.00 0.00 0.00 2.85
18 19 4.608170 AAATGGAGGGGCAATAGAAGAA 57.392 40.909 0.00 0.00 0.00 2.52
19 20 4.975147 TCTAAATGGAGGGGCAATAGAAGA 59.025 41.667 0.00 0.00 0.00 2.87
20 21 5.066593 GTCTAAATGGAGGGGCAATAGAAG 58.933 45.833 0.00 0.00 0.00 2.85
21 22 4.476846 TGTCTAAATGGAGGGGCAATAGAA 59.523 41.667 0.00 0.00 0.00 2.10
22 23 4.044308 TGTCTAAATGGAGGGGCAATAGA 58.956 43.478 0.00 0.00 0.00 1.98
23 24 4.437682 TGTCTAAATGGAGGGGCAATAG 57.562 45.455 0.00 0.00 0.00 1.73
24 25 5.849475 TCTATGTCTAAATGGAGGGGCAATA 59.151 40.000 0.00 0.00 0.00 1.90
25 26 3.979501 ATGTCTAAATGGAGGGGCAAT 57.020 42.857 0.00 0.00 0.00 3.56
26 27 4.044308 TCTATGTCTAAATGGAGGGGCAA 58.956 43.478 0.00 0.00 0.00 4.52
27 28 3.664320 TCTATGTCTAAATGGAGGGGCA 58.336 45.455 0.00 0.00 0.00 5.36
28 29 4.706842 TTCTATGTCTAAATGGAGGGGC 57.293 45.455 0.00 0.00 0.00 5.80
29 30 5.369699 TCCTTTCTATGTCTAAATGGAGGGG 59.630 44.000 0.00 0.00 0.00 4.79
30 31 6.500589 TCCTTTCTATGTCTAAATGGAGGG 57.499 41.667 0.00 0.00 0.00 4.30
31 32 7.739825 TCATCCTTTCTATGTCTAAATGGAGG 58.260 38.462 0.00 0.00 0.00 4.30
32 33 9.790344 AATCATCCTTTCTATGTCTAAATGGAG 57.210 33.333 0.00 0.00 0.00 3.86
38 39 9.770097 CTGCTTAATCATCCTTTCTATGTCTAA 57.230 33.333 0.00 0.00 0.00 2.10
39 40 7.875041 GCTGCTTAATCATCCTTTCTATGTCTA 59.125 37.037 0.00 0.00 0.00 2.59
40 41 6.709846 GCTGCTTAATCATCCTTTCTATGTCT 59.290 38.462 0.00 0.00 0.00 3.41
41 42 6.709846 AGCTGCTTAATCATCCTTTCTATGTC 59.290 38.462 0.00 0.00 0.00 3.06
42 43 6.485984 CAGCTGCTTAATCATCCTTTCTATGT 59.514 38.462 0.00 0.00 0.00 2.29
43 44 6.709397 TCAGCTGCTTAATCATCCTTTCTATG 59.291 38.462 9.47 0.00 0.00 2.23
44 45 6.835174 TCAGCTGCTTAATCATCCTTTCTAT 58.165 36.000 9.47 0.00 0.00 1.98
45 46 6.239217 TCAGCTGCTTAATCATCCTTTCTA 57.761 37.500 9.47 0.00 0.00 2.10
46 47 5.108187 TCAGCTGCTTAATCATCCTTTCT 57.892 39.130 9.47 0.00 0.00 2.52
47 48 5.824904 TTCAGCTGCTTAATCATCCTTTC 57.175 39.130 9.47 0.00 0.00 2.62
48 49 6.594788 TTTTCAGCTGCTTAATCATCCTTT 57.405 33.333 9.47 0.00 0.00 3.11
49 50 6.379133 TCATTTTCAGCTGCTTAATCATCCTT 59.621 34.615 9.47 0.00 0.00 3.36
50 51 5.889853 TCATTTTCAGCTGCTTAATCATCCT 59.110 36.000 9.47 0.00 0.00 3.24
51 52 6.140303 TCATTTTCAGCTGCTTAATCATCC 57.860 37.500 9.47 0.00 0.00 3.51
52 53 6.641314 CCATCATTTTCAGCTGCTTAATCATC 59.359 38.462 9.47 0.00 0.00 2.92
53 54 6.513180 CCATCATTTTCAGCTGCTTAATCAT 58.487 36.000 9.47 0.00 0.00 2.45
54 55 5.680408 GCCATCATTTTCAGCTGCTTAATCA 60.680 40.000 9.47 0.00 0.00 2.57
55 56 4.743644 GCCATCATTTTCAGCTGCTTAATC 59.256 41.667 9.47 0.00 0.00 1.75
56 57 4.404715 AGCCATCATTTTCAGCTGCTTAAT 59.595 37.500 9.47 5.44 31.23 1.40
57 58 3.765511 AGCCATCATTTTCAGCTGCTTAA 59.234 39.130 9.47 3.07 31.23 1.85
58 59 3.129813 CAGCCATCATTTTCAGCTGCTTA 59.870 43.478 9.47 0.00 43.84 3.09
59 60 2.094182 CAGCCATCATTTTCAGCTGCTT 60.094 45.455 9.47 0.00 43.84 3.91
60 61 1.476891 CAGCCATCATTTTCAGCTGCT 59.523 47.619 9.47 0.00 43.84 4.24
61 62 1.922570 CAGCCATCATTTTCAGCTGC 58.077 50.000 9.47 0.00 43.84 5.25
63 64 5.382616 TCATATCAGCCATCATTTTCAGCT 58.617 37.500 0.00 0.00 0.00 4.24
64 65 5.700722 TCATATCAGCCATCATTTTCAGC 57.299 39.130 0.00 0.00 0.00 4.26
65 66 7.448748 TCATCATATCAGCCATCATTTTCAG 57.551 36.000 0.00 0.00 0.00 3.02
66 67 7.504574 AGTTCATCATATCAGCCATCATTTTCA 59.495 33.333 0.00 0.00 0.00 2.69
67 68 7.808381 CAGTTCATCATATCAGCCATCATTTTC 59.192 37.037 0.00 0.00 0.00 2.29
68 69 7.255836 CCAGTTCATCATATCAGCCATCATTTT 60.256 37.037 0.00 0.00 0.00 1.82
69 70 6.208797 CCAGTTCATCATATCAGCCATCATTT 59.791 38.462 0.00 0.00 0.00 2.32
70 71 5.710567 CCAGTTCATCATATCAGCCATCATT 59.289 40.000 0.00 0.00 0.00 2.57
71 72 5.013808 TCCAGTTCATCATATCAGCCATCAT 59.986 40.000 0.00 0.00 0.00 2.45
72 73 4.348754 TCCAGTTCATCATATCAGCCATCA 59.651 41.667 0.00 0.00 0.00 3.07
73 74 4.694509 GTCCAGTTCATCATATCAGCCATC 59.305 45.833 0.00 0.00 0.00 3.51
74 75 4.506271 GGTCCAGTTCATCATATCAGCCAT 60.506 45.833 0.00 0.00 0.00 4.40
75 76 3.181451 GGTCCAGTTCATCATATCAGCCA 60.181 47.826 0.00 0.00 0.00 4.75
76 77 3.181451 TGGTCCAGTTCATCATATCAGCC 60.181 47.826 0.00 0.00 0.00 4.85
77 78 4.063689 CTGGTCCAGTTCATCATATCAGC 58.936 47.826 11.09 0.00 0.00 4.26
78 79 4.639334 CCTGGTCCAGTTCATCATATCAG 58.361 47.826 17.85 0.00 0.00 2.90
79 80 3.181451 GCCTGGTCCAGTTCATCATATCA 60.181 47.826 17.85 0.00 0.00 2.15
80 81 3.181451 TGCCTGGTCCAGTTCATCATATC 60.181 47.826 17.85 0.00 0.00 1.63
81 82 2.779430 TGCCTGGTCCAGTTCATCATAT 59.221 45.455 17.85 0.00 0.00 1.78
82 83 2.195727 TGCCTGGTCCAGTTCATCATA 58.804 47.619 17.85 0.00 0.00 2.15
83 84 0.994247 TGCCTGGTCCAGTTCATCAT 59.006 50.000 17.85 0.00 0.00 2.45
84 85 0.994247 ATGCCTGGTCCAGTTCATCA 59.006 50.000 17.85 7.62 0.00 3.07
85 86 2.134789 AATGCCTGGTCCAGTTCATC 57.865 50.000 17.85 2.37 0.00 2.92
86 87 2.308570 TGTAATGCCTGGTCCAGTTCAT 59.691 45.455 17.85 16.05 0.00 2.57
87 88 1.702401 TGTAATGCCTGGTCCAGTTCA 59.298 47.619 17.85 14.57 0.00 3.18
88 89 2.489938 TGTAATGCCTGGTCCAGTTC 57.510 50.000 17.85 9.46 0.00 3.01
89 90 2.308570 TGATGTAATGCCTGGTCCAGTT 59.691 45.455 17.85 8.16 0.00 3.16
90 91 1.915489 TGATGTAATGCCTGGTCCAGT 59.085 47.619 17.85 1.49 0.00 4.00
91 92 2.292267 GTGATGTAATGCCTGGTCCAG 58.708 52.381 12.40 12.40 0.00 3.86
92 93 1.632920 TGTGATGTAATGCCTGGTCCA 59.367 47.619 0.00 0.00 0.00 4.02
93 94 2.418368 TGTGATGTAATGCCTGGTCC 57.582 50.000 0.00 0.00 0.00 4.46
94 95 2.033801 GCATGTGATGTAATGCCTGGTC 59.966 50.000 0.00 0.00 42.73 4.02
95 96 2.026641 GCATGTGATGTAATGCCTGGT 58.973 47.619 0.00 0.00 42.73 4.00
96 97 2.787601 GCATGTGATGTAATGCCTGG 57.212 50.000 0.00 0.00 42.73 4.45
100 101 3.379372 ACTTGAGGCATGTGATGTAATGC 59.621 43.478 0.00 0.00 46.80 3.56
101 102 4.036027 GGACTTGAGGCATGTGATGTAATG 59.964 45.833 0.00 0.00 0.00 1.90
102 103 4.080129 AGGACTTGAGGCATGTGATGTAAT 60.080 41.667 0.00 0.00 0.00 1.89
103 104 3.264193 AGGACTTGAGGCATGTGATGTAA 59.736 43.478 0.00 0.00 0.00 2.41
104 105 2.840038 AGGACTTGAGGCATGTGATGTA 59.160 45.455 0.00 0.00 0.00 2.29
105 106 1.632409 AGGACTTGAGGCATGTGATGT 59.368 47.619 0.00 0.00 0.00 3.06
106 107 2.414994 AGGACTTGAGGCATGTGATG 57.585 50.000 0.00 0.00 0.00 3.07
107 108 4.265073 GTTAAGGACTTGAGGCATGTGAT 58.735 43.478 0.00 0.00 0.00 3.06
108 109 3.559171 GGTTAAGGACTTGAGGCATGTGA 60.559 47.826 0.00 0.00 0.00 3.58
109 110 2.749621 GGTTAAGGACTTGAGGCATGTG 59.250 50.000 0.00 0.00 0.00 3.21
110 111 2.375174 TGGTTAAGGACTTGAGGCATGT 59.625 45.455 0.00 0.00 0.00 3.21
111 112 2.749621 GTGGTTAAGGACTTGAGGCATG 59.250 50.000 0.00 0.00 0.00 4.06
112 113 2.375174 TGTGGTTAAGGACTTGAGGCAT 59.625 45.455 0.00 0.00 0.00 4.40
113 114 1.771854 TGTGGTTAAGGACTTGAGGCA 59.228 47.619 0.00 0.00 0.00 4.75
114 115 2.152016 GTGTGGTTAAGGACTTGAGGC 58.848 52.381 0.00 0.00 0.00 4.70
115 116 3.071023 TCTGTGTGGTTAAGGACTTGAGG 59.929 47.826 0.00 0.00 0.00 3.86
116 117 4.336889 TCTGTGTGGTTAAGGACTTGAG 57.663 45.455 0.00 0.00 0.00 3.02
117 118 4.407621 TCTTCTGTGTGGTTAAGGACTTGA 59.592 41.667 0.00 0.00 0.00 3.02
118 119 4.703897 TCTTCTGTGTGGTTAAGGACTTG 58.296 43.478 0.00 0.00 0.00 3.16
119 120 4.409247 ACTCTTCTGTGTGGTTAAGGACTT 59.591 41.667 0.00 0.00 0.00 3.01
120 121 3.967987 ACTCTTCTGTGTGGTTAAGGACT 59.032 43.478 0.00 0.00 0.00 3.85
121 122 4.338379 ACTCTTCTGTGTGGTTAAGGAC 57.662 45.455 0.00 0.00 0.00 3.85
122 123 6.488769 TTTACTCTTCTGTGTGGTTAAGGA 57.511 37.500 0.00 0.00 0.00 3.36
123 124 7.584987 CAATTTACTCTTCTGTGTGGTTAAGG 58.415 38.462 0.00 0.00 0.00 2.69
124 125 7.078228 GCAATTTACTCTTCTGTGTGGTTAAG 58.922 38.462 0.00 0.00 0.00 1.85
125 126 6.544197 TGCAATTTACTCTTCTGTGTGGTTAA 59.456 34.615 0.00 0.00 0.00 2.01
126 127 6.058833 TGCAATTTACTCTTCTGTGTGGTTA 58.941 36.000 0.00 0.00 0.00 2.85
127 128 4.887071 TGCAATTTACTCTTCTGTGTGGTT 59.113 37.500 0.00 0.00 0.00 3.67
128 129 4.460263 TGCAATTTACTCTTCTGTGTGGT 58.540 39.130 0.00 0.00 0.00 4.16
129 130 4.756642 TCTGCAATTTACTCTTCTGTGTGG 59.243 41.667 0.00 0.00 0.00 4.17
130 131 5.929697 TCTGCAATTTACTCTTCTGTGTG 57.070 39.130 0.00 0.00 0.00 3.82
131 132 6.942532 TTTCTGCAATTTACTCTTCTGTGT 57.057 33.333 0.00 0.00 0.00 3.72
132 133 6.638468 GGTTTTCTGCAATTTACTCTTCTGTG 59.362 38.462 0.00 0.00 0.00 3.66
133 134 6.321181 TGGTTTTCTGCAATTTACTCTTCTGT 59.679 34.615 0.00 0.00 0.00 3.41
134 135 6.638468 GTGGTTTTCTGCAATTTACTCTTCTG 59.362 38.462 0.00 0.00 0.00 3.02
135 136 6.239036 GGTGGTTTTCTGCAATTTACTCTTCT 60.239 38.462 0.00 0.00 0.00 2.85
136 137 5.920840 GGTGGTTTTCTGCAATTTACTCTTC 59.079 40.000 0.00 0.00 0.00 2.87
137 138 5.362430 TGGTGGTTTTCTGCAATTTACTCTT 59.638 36.000 0.00 0.00 0.00 2.85
224 225 6.153067 TGGTATTTGCAAATTGTTTACGAGG 58.847 36.000 28.45 0.00 0.00 4.63
249 250 4.379243 GCCCGATCCGCCGATCAT 62.379 66.667 14.20 0.00 44.55 2.45
316 318 2.917227 TCCGACCAGCTGACAGCA 60.917 61.111 28.43 3.64 45.56 4.41
361 363 5.235516 GGATAAGAGGAAACAGAACGAACA 58.764 41.667 0.00 0.00 0.00 3.18
480 505 4.862092 CGCCAGCATCGCTCGACT 62.862 66.667 0.00 0.00 36.40 4.18
848 908 9.495572 CATATCCTTCTATTTACAGAAACCCTC 57.504 37.037 0.00 0.00 34.22 4.30
910 970 5.810095 AGGAAAACTGAAGCAAGCTAGTAT 58.190 37.500 0.00 0.00 0.00 2.12
2381 2444 7.230913 ACTTAGCAGTGACTTTAGTGTTCTCTA 59.769 37.037 0.00 0.00 0.00 2.43
2919 2982 5.287674 TCAACAATTCCAAAAGCAATGGA 57.712 34.783 1.41 1.41 45.09 3.41
2969 3032 6.072728 TGCTTGTCTCAACTGCGTATAAAAAT 60.073 34.615 0.00 0.00 0.00 1.82
2979 3042 3.077359 ACCTAATGCTTGTCTCAACTGC 58.923 45.455 0.00 0.00 0.00 4.40
3106 3196 9.673454 TGCGTGTGTGATAGTATAATAAGTAAG 57.327 33.333 0.00 0.00 0.00 2.34
3116 3206 1.202533 GCCCTGCGTGTGTGATAGTAT 60.203 52.381 0.00 0.00 0.00 2.12
3762 3852 0.767375 AAAGTCCTCTGGCTGAAGCA 59.233 50.000 4.43 0.00 44.36 3.91
3825 3919 7.671711 TCCAGGTACAGGATATATAATGGGAT 58.328 38.462 2.40 0.00 39.81 3.85


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

AutoCloner maintained by Alex Coulton.