Multiple sequence alignment - TraesCS3A01G462500

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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 TraesCS3A01G462500 chr3A 100.000 2315 0 0 1 2315 697581556 697583870 0.000000e+00 4276.0
1 TraesCS3A01G462500 chr3A 98.944 284 3 0 310 593 177686658 177686375 2.050000e-140 508.0
2 TraesCS3A01G462500 chr3A 80.307 391 63 12 936 1315 697461707 697461320 1.350000e-72 283.0
3 TraesCS3A01G462500 chr3A 90.141 142 5 1 13 145 528603609 528603468 2.360000e-40 176.0
4 TraesCS3A01G462500 chr3A 86.207 145 5 1 13 142 637603405 637603549 2.400000e-30 143.0
5 TraesCS3A01G462500 chr3A 82.014 139 21 2 1593 1730 697626485 697626620 5.230000e-22 115.0
6 TraesCS3A01G462500 chr3A 82.014 139 21 3 1593 1730 697684685 697684820 5.230000e-22 115.0
7 TraesCS3A01G462500 chr3D 92.462 1393 66 13 592 1949 562462615 562464003 0.000000e+00 1954.0
8 TraesCS3A01G462500 chr3D 87.671 657 59 10 680 1315 562357938 562358593 0.000000e+00 745.0
9 TraesCS3A01G462500 chr3D 87.671 657 59 10 680 1315 562439532 562440187 0.000000e+00 745.0
10 TraesCS3A01G462500 chr3D 97.838 370 7 1 1947 2315 562464034 562464403 2.510000e-179 638.0
11 TraesCS3A01G462500 chr3D 80.496 605 75 17 590 1172 562386338 562386921 7.650000e-115 424.0
12 TraesCS3A01G462500 chr3D 79.661 413 65 15 918 1315 561728966 561728558 1.750000e-71 279.0
13 TraesCS3A01G462500 chr3D 78.718 390 73 9 959 1342 562215276 562214891 3.820000e-63 252.0
14 TraesCS3A01G462500 chr3D 89.928 139 5 1 13 142 287047414 287047552 1.100000e-38 171.0
15 TraesCS3A01G462500 chr3D 89.209 139 6 1 13 142 287046688 287046826 5.120000e-37 165.0
16 TraesCS3A01G462500 chr3D 84.138 145 8 3 16 145 45690341 45690197 2.410000e-25 126.0
17 TraesCS3A01G462500 chr3B 87.320 694 71 8 637 1315 749651547 749652238 0.000000e+00 778.0
18 TraesCS3A01G462500 chr3B 94.064 219 11 1 2099 2315 749683596 749683814 4.770000e-87 331.0
19 TraesCS3A01G462500 chr3B 78.923 427 68 17 902 1315 749052377 749051960 1.050000e-68 270.0
20 TraesCS3A01G462500 chr3B 93.388 121 7 1 1946 2066 749683378 749683497 6.570000e-41 178.0
21 TraesCS3A01G462500 chr3B 85.350 157 14 4 1734 1885 749652452 749652604 1.110000e-33 154.0
22 TraesCS3A01G462500 chr3B 94.898 98 5 0 594 691 749683247 749683344 1.110000e-33 154.0
23 TraesCS3A01G462500 chr3B 100.000 37 0 0 2064 2100 749683477 749683513 4.130000e-08 69.4
24 TraesCS3A01G462500 chr1B 96.078 459 10 4 143 593 123429449 123429907 0.000000e+00 741.0
25 TraesCS3A01G462500 chr1B 98.227 282 5 0 312 593 268648978 268649259 5.750000e-136 494.0
26 TraesCS3A01G462500 chr7B 94.989 459 11 3 143 596 731163744 731164195 0.000000e+00 710.0
27 TraesCS3A01G462500 chr7B 89.209 139 6 1 13 142 676247758 676247896 5.120000e-37 165.0
28 TraesCS3A01G462500 chr6A 97.603 292 2 2 310 596 492801716 492801425 1.600000e-136 496.0
29 TraesCS3A01G462500 chr5B 97.561 287 7 0 310 596 658143432 658143146 2.070000e-135 492.0
30 TraesCS3A01G462500 chr4A 97.909 287 1 1 310 596 715305559 715305278 2.070000e-135 492.0
31 TraesCS3A01G462500 chr4A 90.141 142 5 1 13 145 715300582 715300441 2.360000e-40 176.0
32 TraesCS3A01G462500 chr1D 91.496 341 18 5 259 593 458416899 458417234 2.100000e-125 459.0
33 TraesCS3A01G462500 chr1D 79.577 142 8 7 22 142 477414172 477414313 5.300000e-12 82.4
34 TraesCS3A01G462500 chr1D 78.667 150 11 4 17 145 361241953 361241804 1.910000e-11 80.5
35 TraesCS3A01G462500 chr1D 85.366 82 6 3 67 142 477320823 477320904 1.910000e-11 80.5
36 TraesCS3A01G462500 chr2D 84.768 453 57 8 143 590 644707421 644707866 5.870000e-121 444.0
37 TraesCS3A01G462500 chr1A 99.405 168 1 0 143 310 35501275 35501442 2.890000e-79 305.0
38 TraesCS3A01G462500 chrUn 98.810 168 2 0 143 310 64721616 64721783 1.340000e-77 300.0
39 TraesCS3A01G462500 chrUn 98.810 168 2 0 143 310 64724046 64724213 1.340000e-77 300.0
40 TraesCS3A01G462500 chrUn 98.810 168 2 0 143 310 64726476 64726643 1.340000e-77 300.0
41 TraesCS3A01G462500 chrUn 98.246 171 3 0 143 313 83553365 83553195 1.340000e-77 300.0
42 TraesCS3A01G462500 chrUn 98.810 168 2 0 143 310 207829650 207829817 1.340000e-77 300.0
43 TraesCS3A01G462500 chr5A 89.928 139 5 4 13 142 689516272 689516410 1.100000e-38 171.0
44 TraesCS3A01G462500 chr4D 89.437 142 6 1 13 145 28852399 28852258 1.100000e-38 171.0
45 TraesCS3A01G462500 chr4D 80.272 147 8 9 17 142 32407338 32407484 8.810000e-15 91.6
46 TraesCS3A01G462500 chr2A 88.028 142 6 4 13 145 715773046 715772907 8.560000e-35 158.0
47 TraesCS3A01G462500 chr2A 84.106 151 3 2 13 142 90430762 90430912 2.410000e-25 126.0
48 TraesCS3A01G462500 chr2A 82.237 152 6 2 12 142 90456436 90456587 6.760000e-21 111.0
49 TraesCS3A01G462500 chr7D 87.218 133 9 6 17 142 305153030 305153161 6.670000e-31 145.0


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 TraesCS3A01G462500 chr3A 697581556 697583870 2314 False 4276 4276 100.000 1 2315 1 chr3A.!!$F2 2314
1 TraesCS3A01G462500 chr3D 562462615 562464403 1788 False 1296 1954 95.150 592 2315 2 chr3D.!!$F5 1723
2 TraesCS3A01G462500 chr3D 562357938 562358593 655 False 745 745 87.671 680 1315 1 chr3D.!!$F1 635
3 TraesCS3A01G462500 chr3D 562439532 562440187 655 False 745 745 87.671 680 1315 1 chr3D.!!$F3 635
4 TraesCS3A01G462500 chr3D 562386338 562386921 583 False 424 424 80.496 590 1172 1 chr3D.!!$F2 582
5 TraesCS3A01G462500 chr3B 749651547 749652604 1057 False 466 778 86.335 637 1885 2 chr3B.!!$F1 1248
6 TraesCS3A01G462500 chrUn 64721616 64726643 5027 False 300 300 98.810 143 310 3 chrUn.!!$F2 167

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
121 122 0.042361 CGGACGTAGACGATCGGAAG 60.042 60.0 20.98 8.99 43.02 3.46 F
759 3309 0.193321 ATTTTGCCCCTCCCAAAGGT 59.807 50.0 0.00 0.00 44.56 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1038 3995 1.002134 CGCCCCAAAGATCACCACT 60.002 57.895 0.00 0.00 0.0 4.00 R
2227 5569 2.840038 AGTGAACTAGTGATGATGGCCA 59.160 45.455 8.56 8.56 0.0 5.36 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
22 23 1.235724 AACGAGTTAGCTTTGGTGGC 58.764 50.000 0.00 0.00 0.00 5.01
23 24 0.107831 ACGAGTTAGCTTTGGTGGCA 59.892 50.000 0.00 0.00 0.00 4.92
24 25 0.798776 CGAGTTAGCTTTGGTGGCAG 59.201 55.000 0.00 0.00 0.00 4.85
25 26 0.523519 GAGTTAGCTTTGGTGGCAGC 59.476 55.000 10.30 10.30 36.16 5.25
26 27 0.178992 AGTTAGCTTTGGTGGCAGCA 60.179 50.000 16.56 16.56 38.61 4.41
27 28 0.242017 GTTAGCTTTGGTGGCAGCAG 59.758 55.000 19.65 10.41 38.61 4.24
28 29 1.526575 TTAGCTTTGGTGGCAGCAGC 61.527 55.000 19.65 19.58 38.61 5.25
29 30 4.712425 GCTTTGGTGGCAGCAGCG 62.712 66.667 19.65 14.94 43.41 5.18
30 31 4.047059 CTTTGGTGGCAGCAGCGG 62.047 66.667 19.65 9.91 43.41 5.52
49 50 4.083862 GTCCTCGGCGGCCTTCTT 62.084 66.667 18.34 0.00 0.00 2.52
50 51 4.082523 TCCTCGGCGGCCTTCTTG 62.083 66.667 18.34 0.39 0.00 3.02
51 52 4.394712 CCTCGGCGGCCTTCTTGT 62.395 66.667 18.34 0.00 0.00 3.16
52 53 2.815647 CTCGGCGGCCTTCTTGTC 60.816 66.667 18.34 0.00 0.00 3.18
53 54 4.735132 TCGGCGGCCTTCTTGTCG 62.735 66.667 18.34 0.00 0.00 4.35
57 58 2.358737 CGGCCTTCTTGTCGGCTT 60.359 61.111 0.00 0.00 45.57 4.35
58 59 2.391389 CGGCCTTCTTGTCGGCTTC 61.391 63.158 0.00 0.00 45.57 3.86
59 60 1.302511 GGCCTTCTTGTCGGCTTCA 60.303 57.895 0.00 0.00 45.57 3.02
60 61 1.301677 GGCCTTCTTGTCGGCTTCAG 61.302 60.000 0.00 0.00 45.57 3.02
61 62 1.916697 GCCTTCTTGTCGGCTTCAGC 61.917 60.000 0.00 0.00 42.98 4.26
62 63 0.321122 CCTTCTTGTCGGCTTCAGCT 60.321 55.000 0.00 0.00 41.70 4.24
63 64 1.517242 CTTCTTGTCGGCTTCAGCTT 58.483 50.000 0.00 0.00 41.70 3.74
64 65 1.876156 CTTCTTGTCGGCTTCAGCTTT 59.124 47.619 0.00 0.00 41.70 3.51
65 66 1.512926 TCTTGTCGGCTTCAGCTTTC 58.487 50.000 0.00 0.00 41.70 2.62
66 67 1.070758 TCTTGTCGGCTTCAGCTTTCT 59.929 47.619 0.00 0.00 41.70 2.52
67 68 1.462670 CTTGTCGGCTTCAGCTTTCTC 59.537 52.381 0.00 0.00 41.70 2.87
68 69 0.667487 TGTCGGCTTCAGCTTTCTCG 60.667 55.000 0.00 0.00 41.70 4.04
69 70 1.079819 TCGGCTTCAGCTTTCTCGG 60.080 57.895 0.00 0.00 41.70 4.63
70 71 2.744768 CGGCTTCAGCTTTCTCGGC 61.745 63.158 0.00 0.00 41.70 5.54
71 72 2.744768 GGCTTCAGCTTTCTCGGCG 61.745 63.158 0.00 0.00 41.70 6.46
72 73 2.029844 GCTTCAGCTTTCTCGGCGT 61.030 57.895 6.85 0.00 38.21 5.68
73 74 1.960994 GCTTCAGCTTTCTCGGCGTC 61.961 60.000 6.85 0.00 38.21 5.19
74 75 1.678269 CTTCAGCTTTCTCGGCGTCG 61.678 60.000 1.15 1.15 37.82 5.12
75 76 3.181967 CAGCTTTCTCGGCGTCGG 61.182 66.667 10.62 0.00 36.95 4.79
76 77 3.681835 AGCTTTCTCGGCGTCGGT 61.682 61.111 10.62 0.00 36.95 4.69
77 78 3.479269 GCTTTCTCGGCGTCGGTG 61.479 66.667 10.62 2.85 36.95 4.94
78 79 2.809601 CTTTCTCGGCGTCGGTGG 60.810 66.667 10.62 0.00 36.95 4.61
79 80 3.277211 CTTTCTCGGCGTCGGTGGA 62.277 63.158 10.62 2.77 36.95 4.02
80 81 3.562779 TTTCTCGGCGTCGGTGGAC 62.563 63.158 10.62 0.00 39.89 4.02
82 83 4.129737 CTCGGCGTCGGTGGACAT 62.130 66.667 10.62 0.00 43.61 3.06
83 84 4.429212 TCGGCGTCGGTGGACATG 62.429 66.667 10.62 0.00 43.61 3.21
85 86 4.388499 GGCGTCGGTGGACATGGT 62.388 66.667 0.00 0.00 43.61 3.55
86 87 3.118454 GCGTCGGTGGACATGGTG 61.118 66.667 0.00 0.00 43.61 4.17
87 88 2.654289 CGTCGGTGGACATGGTGA 59.346 61.111 0.00 0.00 43.61 4.02
88 89 1.218047 CGTCGGTGGACATGGTGAT 59.782 57.895 0.00 0.00 43.61 3.06
89 90 1.083806 CGTCGGTGGACATGGTGATG 61.084 60.000 0.00 0.00 43.61 3.07
90 91 0.249120 GTCGGTGGACATGGTGATGA 59.751 55.000 0.00 0.00 42.91 2.92
91 92 1.134401 GTCGGTGGACATGGTGATGAT 60.134 52.381 0.00 0.00 42.91 2.45
92 93 1.134431 TCGGTGGACATGGTGATGATG 60.134 52.381 0.00 0.00 33.36 3.07
93 94 1.134431 CGGTGGACATGGTGATGATGA 60.134 52.381 0.00 0.00 33.36 2.92
94 95 2.680513 CGGTGGACATGGTGATGATGAA 60.681 50.000 0.00 0.00 33.36 2.57
95 96 2.947652 GGTGGACATGGTGATGATGAAG 59.052 50.000 0.00 0.00 33.36 3.02
96 97 2.947652 GTGGACATGGTGATGATGAAGG 59.052 50.000 0.00 0.00 33.36 3.46
97 98 1.952296 GGACATGGTGATGATGAAGGC 59.048 52.381 0.00 0.00 33.36 4.35
98 99 1.600957 GACATGGTGATGATGAAGGCG 59.399 52.381 0.00 0.00 33.36 5.52
99 100 1.210234 ACATGGTGATGATGAAGGCGA 59.790 47.619 0.00 0.00 33.36 5.54
100 101 2.158711 ACATGGTGATGATGAAGGCGAT 60.159 45.455 0.00 0.00 33.36 4.58
101 102 1.957668 TGGTGATGATGAAGGCGATG 58.042 50.000 0.00 0.00 0.00 3.84
102 103 0.590195 GGTGATGATGAAGGCGATGC 59.410 55.000 0.00 0.00 0.00 3.91
103 104 0.234106 GTGATGATGAAGGCGATGCG 59.766 55.000 0.00 0.00 0.00 4.73
104 105 0.881600 TGATGATGAAGGCGATGCGG 60.882 55.000 0.00 0.00 0.00 5.69
105 106 0.601046 GATGATGAAGGCGATGCGGA 60.601 55.000 0.00 0.00 0.00 5.54
106 107 0.882042 ATGATGAAGGCGATGCGGAC 60.882 55.000 0.00 0.00 0.00 4.79
107 108 2.586079 ATGAAGGCGATGCGGACG 60.586 61.111 0.00 0.00 0.00 4.79
108 109 3.371097 ATGAAGGCGATGCGGACGT 62.371 57.895 0.00 0.00 0.00 4.34
109 110 2.011741 ATGAAGGCGATGCGGACGTA 62.012 55.000 0.00 0.00 0.00 3.57
110 111 1.944676 GAAGGCGATGCGGACGTAG 60.945 63.158 0.00 0.00 0.00 3.51
111 112 2.332362 GAAGGCGATGCGGACGTAGA 62.332 60.000 0.00 0.00 0.00 2.59
112 113 2.609183 AAGGCGATGCGGACGTAGAC 62.609 60.000 0.00 0.00 0.00 2.59
113 114 3.017314 GCGATGCGGACGTAGACG 61.017 66.667 0.00 0.00 46.33 4.18
114 115 2.705220 CGATGCGGACGTAGACGA 59.295 61.111 9.41 0.00 43.02 4.20
115 116 1.278937 CGATGCGGACGTAGACGAT 59.721 57.895 9.41 0.00 43.02 3.73
116 117 0.721811 CGATGCGGACGTAGACGATC 60.722 60.000 9.41 2.90 43.02 3.69
117 118 0.721811 GATGCGGACGTAGACGATCG 60.722 60.000 14.88 14.88 43.02 3.69
118 119 2.052414 GCGGACGTAGACGATCGG 60.052 66.667 20.98 3.20 43.02 4.18
119 120 2.528743 GCGGACGTAGACGATCGGA 61.529 63.158 20.98 0.81 43.02 4.55
120 121 2.009108 CGGACGTAGACGATCGGAA 58.991 57.895 20.98 0.69 43.02 4.30
121 122 0.042361 CGGACGTAGACGATCGGAAG 60.042 60.000 20.98 8.99 43.02 3.46
122 123 0.316854 GGACGTAGACGATCGGAAGC 60.317 60.000 20.98 5.77 43.02 3.86
123 124 0.653897 GACGTAGACGATCGGAAGCG 60.654 60.000 20.98 19.07 43.02 4.68
124 125 1.086067 ACGTAGACGATCGGAAGCGA 61.086 55.000 20.98 0.00 43.02 4.93
125 126 0.383246 CGTAGACGATCGGAAGCGAG 60.383 60.000 20.98 0.55 43.02 5.03
126 127 0.657951 GTAGACGATCGGAAGCGAGC 60.658 60.000 20.98 0.00 0.00 5.03
127 128 1.093496 TAGACGATCGGAAGCGAGCA 61.093 55.000 20.98 0.00 0.00 4.26
128 129 1.941734 GACGATCGGAAGCGAGCAG 60.942 63.158 20.98 0.00 0.00 4.24
129 130 2.103143 CGATCGGAAGCGAGCAGT 59.897 61.111 7.38 0.00 0.00 4.40
130 131 1.941734 CGATCGGAAGCGAGCAGTC 60.942 63.158 7.38 0.00 0.00 3.51
139 140 3.203246 CGAGCAGTCGCGTAATCG 58.797 61.111 5.77 6.78 45.49 3.34
478 3014 1.912043 CCACTCCAACTCTCCTTCCAT 59.088 52.381 0.00 0.00 0.00 3.41
596 3132 3.250280 CCCATCTCAGATTTCAGCAATCG 59.750 47.826 0.00 0.00 45.53 3.34
759 3309 0.193321 ATTTTGCCCCTCCCAAAGGT 59.807 50.000 0.00 0.00 44.56 3.50
870 3443 5.044558 CCTCGATTAAGCACTTCCTCTTAC 58.955 45.833 0.00 0.00 0.00 2.34
1227 4184 2.916502 TATTCATCCGTGGCGCGCTT 62.917 55.000 32.29 6.22 39.71 4.68
1385 4342 5.634896 GTGTGATCATAACCTCAAAAGCTG 58.365 41.667 0.00 0.00 0.00 4.24
1446 4421 0.516877 TTGAACAATGCTTCTCGCCG 59.483 50.000 0.00 0.00 38.05 6.46
1512 4546 4.406649 TGTCTCACTATGATGATCTGGCAA 59.593 41.667 0.00 0.00 0.00 4.52
1517 4551 6.598503 TCACTATGATGATCTGGCAAGAAAT 58.401 36.000 0.00 0.00 35.59 2.17
1530 4564 7.520798 TCTGGCAAGAAATATAGGACATGATT 58.479 34.615 0.00 0.00 0.00 2.57
1590 4625 6.544928 TCTTCACTGGCTATGTTTCTGATA 57.455 37.500 0.00 0.00 0.00 2.15
1598 4633 6.480763 TGGCTATGTTTCTGATAAGGTTTGA 58.519 36.000 0.00 0.00 0.00 2.69
1636 4671 4.022935 ACCAATGTGTGCTATTTCACTGTG 60.023 41.667 0.17 0.17 37.81 3.66
1708 4743 6.601741 TGTTATTACCTTCGAAACAACGTT 57.398 33.333 0.00 0.00 34.70 3.99
1710 4745 7.470900 TGTTATTACCTTCGAAACAACGTTTT 58.529 30.769 0.00 0.00 34.70 2.43
1745 4780 4.321601 GCAATTTGGCATGTACTGGTTACA 60.322 41.667 0.00 0.00 45.03 2.41
1746 4781 8.450558 TGCAATTTGGCATGTACTGGTTACAG 62.451 42.308 0.00 0.00 44.14 2.74
1828 4867 4.891168 TCACAGTTGTAGAACACTAGGTCA 59.109 41.667 5.45 0.00 34.17 4.02
1851 4890 3.999001 TGCAGTCATGTGAGTTTGATCTC 59.001 43.478 0.00 0.00 35.28 2.75
1885 4924 2.082231 CATGACAACAGAAGAGCCTGG 58.918 52.381 0.00 0.00 38.44 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.439129 GCCACCAAAGCTAACTCGTTTAT 59.561 43.478 0.00 0.00 0.00 1.40
1 2 2.809696 GCCACCAAAGCTAACTCGTTTA 59.190 45.455 0.00 0.00 0.00 2.01
2 3 1.607148 GCCACCAAAGCTAACTCGTTT 59.393 47.619 0.00 0.00 0.00 3.60
3 4 1.235724 GCCACCAAAGCTAACTCGTT 58.764 50.000 0.00 0.00 0.00 3.85
4 5 0.107831 TGCCACCAAAGCTAACTCGT 59.892 50.000 0.00 0.00 0.00 4.18
5 6 0.798776 CTGCCACCAAAGCTAACTCG 59.201 55.000 0.00 0.00 0.00 4.18
6 7 0.523519 GCTGCCACCAAAGCTAACTC 59.476 55.000 0.00 0.00 36.47 3.01
7 8 0.178992 TGCTGCCACCAAAGCTAACT 60.179 50.000 0.00 0.00 40.21 2.24
8 9 0.242017 CTGCTGCCACCAAAGCTAAC 59.758 55.000 0.00 0.00 40.21 2.34
9 10 1.526575 GCTGCTGCCACCAAAGCTAA 61.527 55.000 3.85 0.00 40.21 3.09
10 11 1.973281 GCTGCTGCCACCAAAGCTA 60.973 57.895 3.85 0.00 40.21 3.32
11 12 3.300765 GCTGCTGCCACCAAAGCT 61.301 61.111 3.85 0.00 40.21 3.74
12 13 4.712425 CGCTGCTGCCACCAAAGC 62.712 66.667 10.24 0.00 39.96 3.51
13 14 4.047059 CCGCTGCTGCCACCAAAG 62.047 66.667 10.24 0.00 35.36 2.77
33 34 4.082523 CAAGAAGGCCGCCGAGGA 62.083 66.667 3.05 0.00 45.00 3.71
34 35 4.394712 ACAAGAAGGCCGCCGAGG 62.395 66.667 3.05 0.00 44.97 4.63
35 36 2.815647 GACAAGAAGGCCGCCGAG 60.816 66.667 3.05 0.00 0.00 4.63
36 37 4.735132 CGACAAGAAGGCCGCCGA 62.735 66.667 3.05 0.00 0.00 5.54
43 44 0.321122 AGCTGAAGCCGACAAGAAGG 60.321 55.000 0.00 0.00 43.38 3.46
44 45 1.517242 AAGCTGAAGCCGACAAGAAG 58.483 50.000 0.00 0.00 43.38 2.85
45 46 1.873591 GAAAGCTGAAGCCGACAAGAA 59.126 47.619 0.00 0.00 43.38 2.52
46 47 1.070758 AGAAAGCTGAAGCCGACAAGA 59.929 47.619 0.00 0.00 43.38 3.02
47 48 1.462670 GAGAAAGCTGAAGCCGACAAG 59.537 52.381 0.00 0.00 43.38 3.16
48 49 1.512926 GAGAAAGCTGAAGCCGACAA 58.487 50.000 0.00 0.00 43.38 3.18
49 50 0.667487 CGAGAAAGCTGAAGCCGACA 60.667 55.000 0.00 0.00 43.38 4.35
50 51 1.355066 CCGAGAAAGCTGAAGCCGAC 61.355 60.000 0.00 0.00 43.38 4.79
51 52 1.079819 CCGAGAAAGCTGAAGCCGA 60.080 57.895 0.00 0.00 43.38 5.54
52 53 2.744768 GCCGAGAAAGCTGAAGCCG 61.745 63.158 0.00 0.00 43.38 5.52
53 54 2.744768 CGCCGAGAAAGCTGAAGCC 61.745 63.158 0.00 0.00 43.38 4.35
54 55 1.960994 GACGCCGAGAAAGCTGAAGC 61.961 60.000 0.00 0.00 42.49 3.86
55 56 1.678269 CGACGCCGAGAAAGCTGAAG 61.678 60.000 0.00 0.00 38.22 3.02
56 57 1.733041 CGACGCCGAGAAAGCTGAA 60.733 57.895 0.00 0.00 38.22 3.02
57 58 2.126463 CGACGCCGAGAAAGCTGA 60.126 61.111 0.00 0.00 38.22 4.26
58 59 3.181967 CCGACGCCGAGAAAGCTG 61.182 66.667 0.00 0.00 38.22 4.24
59 60 3.681835 ACCGACGCCGAGAAAGCT 61.682 61.111 0.00 0.00 38.22 3.74
60 61 3.479269 CACCGACGCCGAGAAAGC 61.479 66.667 0.00 0.00 38.22 3.51
61 62 2.809601 CCACCGACGCCGAGAAAG 60.810 66.667 0.00 0.00 38.22 2.62
62 63 3.296836 TCCACCGACGCCGAGAAA 61.297 61.111 0.00 0.00 38.22 2.52
63 64 4.047059 GTCCACCGACGCCGAGAA 62.047 66.667 0.00 0.00 38.22 2.87
65 66 4.129737 ATGTCCACCGACGCCGAG 62.130 66.667 0.00 0.00 42.37 4.63
66 67 4.429212 CATGTCCACCGACGCCGA 62.429 66.667 0.00 0.00 42.37 5.54
68 69 4.388499 ACCATGTCCACCGACGCC 62.388 66.667 0.00 0.00 42.37 5.68
69 70 2.852495 ATCACCATGTCCACCGACGC 62.852 60.000 0.00 0.00 42.37 5.19
70 71 1.083806 CATCACCATGTCCACCGACG 61.084 60.000 0.00 0.00 42.37 5.12
71 72 0.249120 TCATCACCATGTCCACCGAC 59.751 55.000 0.00 0.00 39.66 4.79
72 73 1.134431 CATCATCACCATGTCCACCGA 60.134 52.381 0.00 0.00 0.00 4.69
73 74 1.134431 TCATCATCACCATGTCCACCG 60.134 52.381 0.00 0.00 0.00 4.94
74 75 2.715749 TCATCATCACCATGTCCACC 57.284 50.000 0.00 0.00 0.00 4.61
75 76 2.947652 CCTTCATCATCACCATGTCCAC 59.052 50.000 0.00 0.00 0.00 4.02
76 77 2.684630 GCCTTCATCATCACCATGTCCA 60.685 50.000 0.00 0.00 0.00 4.02
77 78 1.952296 GCCTTCATCATCACCATGTCC 59.048 52.381 0.00 0.00 0.00 4.02
78 79 1.600957 CGCCTTCATCATCACCATGTC 59.399 52.381 0.00 0.00 0.00 3.06
79 80 1.210234 TCGCCTTCATCATCACCATGT 59.790 47.619 0.00 0.00 0.00 3.21
80 81 1.957668 TCGCCTTCATCATCACCATG 58.042 50.000 0.00 0.00 0.00 3.66
81 82 2.501261 CATCGCCTTCATCATCACCAT 58.499 47.619 0.00 0.00 0.00 3.55
82 83 1.957668 CATCGCCTTCATCATCACCA 58.042 50.000 0.00 0.00 0.00 4.17
83 84 0.590195 GCATCGCCTTCATCATCACC 59.410 55.000 0.00 0.00 0.00 4.02
84 85 0.234106 CGCATCGCCTTCATCATCAC 59.766 55.000 0.00 0.00 0.00 3.06
85 86 0.881600 CCGCATCGCCTTCATCATCA 60.882 55.000 0.00 0.00 0.00 3.07
86 87 0.601046 TCCGCATCGCCTTCATCATC 60.601 55.000 0.00 0.00 0.00 2.92
87 88 0.882042 GTCCGCATCGCCTTCATCAT 60.882 55.000 0.00 0.00 0.00 2.45
88 89 1.521457 GTCCGCATCGCCTTCATCA 60.521 57.895 0.00 0.00 0.00 3.07
89 90 2.589492 CGTCCGCATCGCCTTCATC 61.589 63.158 0.00 0.00 0.00 2.92
90 91 2.011741 TACGTCCGCATCGCCTTCAT 62.012 55.000 0.00 0.00 0.00 2.57
91 92 2.607668 CTACGTCCGCATCGCCTTCA 62.608 60.000 0.00 0.00 0.00 3.02
92 93 1.944676 CTACGTCCGCATCGCCTTC 60.945 63.158 0.00 0.00 0.00 3.46
93 94 2.104331 CTACGTCCGCATCGCCTT 59.896 61.111 0.00 0.00 0.00 4.35
94 95 2.827190 TCTACGTCCGCATCGCCT 60.827 61.111 0.00 0.00 0.00 5.52
95 96 2.654404 GTCTACGTCCGCATCGCC 60.654 66.667 0.00 0.00 0.00 5.54
96 97 2.712743 ATCGTCTACGTCCGCATCGC 62.713 60.000 0.00 0.00 40.80 4.58
97 98 0.721811 GATCGTCTACGTCCGCATCG 60.722 60.000 0.00 0.00 40.80 3.84
98 99 0.721811 CGATCGTCTACGTCCGCATC 60.722 60.000 7.03 0.00 40.80 3.91
99 100 1.278937 CGATCGTCTACGTCCGCAT 59.721 57.895 7.03 0.00 40.80 4.73
100 101 2.705220 CGATCGTCTACGTCCGCA 59.295 61.111 7.03 0.00 40.80 5.69
101 102 2.040213 TTCCGATCGTCTACGTCCGC 62.040 60.000 15.09 0.00 40.80 5.54
102 103 0.042361 CTTCCGATCGTCTACGTCCG 60.042 60.000 15.09 7.24 40.80 4.79
103 104 0.316854 GCTTCCGATCGTCTACGTCC 60.317 60.000 15.09 0.00 40.80 4.79
104 105 0.653897 CGCTTCCGATCGTCTACGTC 60.654 60.000 15.09 0.00 37.35 4.34
105 106 1.086067 TCGCTTCCGATCGTCTACGT 61.086 55.000 15.09 0.00 38.82 3.57
106 107 0.383246 CTCGCTTCCGATCGTCTACG 60.383 60.000 15.09 12.35 43.47 3.51
107 108 0.657951 GCTCGCTTCCGATCGTCTAC 60.658 60.000 15.09 0.00 43.47 2.59
108 109 1.093496 TGCTCGCTTCCGATCGTCTA 61.093 55.000 15.09 0.00 43.47 2.59
109 110 2.329678 CTGCTCGCTTCCGATCGTCT 62.330 60.000 15.09 0.00 43.47 4.18
110 111 1.941734 CTGCTCGCTTCCGATCGTC 60.942 63.158 15.09 0.00 43.47 4.20
111 112 2.103143 CTGCTCGCTTCCGATCGT 59.897 61.111 15.09 0.00 43.47 3.73
112 113 1.941734 GACTGCTCGCTTCCGATCG 60.942 63.158 8.51 8.51 43.47 3.69
113 114 1.941734 CGACTGCTCGCTTCCGATC 60.942 63.158 0.00 0.00 43.47 3.69
114 115 2.103143 CGACTGCTCGCTTCCGAT 59.897 61.111 0.00 0.00 43.47 4.18
122 123 3.203246 CGATTACGCGACTGCTCG 58.797 61.111 15.93 9.95 43.28 5.03
139 140 2.809010 GACGGGAGAGCAGGTAGC 59.191 66.667 0.00 0.00 46.19 3.58
140 141 1.451567 TCGACGGGAGAGCAGGTAG 60.452 63.158 0.00 0.00 0.00 3.18
141 142 1.748122 GTCGACGGGAGAGCAGGTA 60.748 63.158 0.00 0.00 0.00 3.08
294 2725 4.700365 CGCACGTCTCTCCACGCA 62.700 66.667 0.00 0.00 43.93 5.24
478 3014 0.401356 GTTTAGTCCCACCCCGGAAA 59.599 55.000 0.73 0.00 36.56 3.13
708 3256 2.679082 AGGTATCGCTAGGAATGTGGT 58.321 47.619 0.00 0.00 0.00 4.16
759 3309 5.811796 TCTAGCACCACTTGTAACCTTTA 57.188 39.130 0.00 0.00 0.00 1.85
1038 3995 1.002134 CGCCCCAAAGATCACCACT 60.002 57.895 0.00 0.00 0.00 4.00
1385 4342 5.910166 CACTGTATTGTCGATCACTAGCTAC 59.090 44.000 0.00 0.00 0.00 3.58
1446 4421 3.077359 CTGAGAGTTGGGTTCAATGTCC 58.923 50.000 0.00 0.00 35.10 4.02
1530 4564 1.488812 CACGGGGGATGATTCCTAACA 59.511 52.381 0.00 0.00 42.20 2.41
1540 4574 2.128771 AAGATCAAACACGGGGGATG 57.871 50.000 0.00 0.00 0.00 3.51
1541 4575 2.225017 ACAAAGATCAAACACGGGGGAT 60.225 45.455 0.00 0.00 0.00 3.85
1542 4576 1.144093 ACAAAGATCAAACACGGGGGA 59.856 47.619 0.00 0.00 0.00 4.81
1543 4577 1.269448 CACAAAGATCAAACACGGGGG 59.731 52.381 0.00 0.00 0.00 5.40
1598 4633 3.053842 ACATTGGTCAGAGGAGATGCAAT 60.054 43.478 0.00 0.00 0.00 3.56
1662 4697 4.335416 AGTACTATGCATGCAAACACCTT 58.665 39.130 26.68 8.86 0.00 3.50
1663 4698 3.955471 AGTACTATGCATGCAAACACCT 58.045 40.909 26.68 14.92 0.00 4.00
1664 4699 4.082787 ACAAGTACTATGCATGCAAACACC 60.083 41.667 26.68 12.82 0.00 4.16
1708 4743 9.047371 CATGCCAAATTGCAGATATAATTGAAA 57.953 29.630 0.00 0.00 45.93 2.69
1710 4745 7.728148 ACATGCCAAATTGCAGATATAATTGA 58.272 30.769 0.00 0.00 45.93 2.57
1760 4795 5.584649 ACATTCGCATTGCTAAGCTTAGTAA 59.415 36.000 30.87 30.87 39.18 2.24
1828 4867 4.586884 AGATCAAACTCACATGACTGCAT 58.413 39.130 0.00 0.00 34.29 3.96
1840 4879 4.183101 CAGAGGCTCTTGAGATCAAACTC 58.817 47.826 15.90 3.29 35.15 3.01
1851 4890 3.049708 TGTCATGAACAGAGGCTCTTG 57.950 47.619 15.90 10.61 32.81 3.02
1885 4924 4.567159 GGCAGTACACTTGTGTATAAGCTC 59.433 45.833 21.85 14.45 0.00 4.09
1996 5068 7.939782 TCAATTTACTTGCTTGTCATCAAAGA 58.060 30.769 0.00 0.00 34.66 2.52
2062 5134 7.724305 TCCTCACAACAAGTAATACTTTCAC 57.276 36.000 2.41 0.00 36.03 3.18
2065 5137 6.942576 AGCATCCTCACAACAAGTAATACTTT 59.057 34.615 2.41 0.00 36.03 2.66
2206 5548 7.038729 TGGCCAGATTAATATTTTTGTGGACAA 60.039 33.333 15.61 4.51 38.94 3.18
2222 5564 5.366477 TGAACTAGTGATGATGGCCAGATTA 59.634 40.000 13.05 0.00 0.00 1.75
2227 5569 2.840038 AGTGAACTAGTGATGATGGCCA 59.160 45.455 8.56 8.56 0.00 5.36


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

AutoCloner maintained by Alex Coulton.