Multiple sequence alignment - TraesCS1D01G216100

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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 TraesCS1D01G216100 chr1D 100.000 3283 0 0 1 3283 301639034 301642316 0.000000e+00 6063.0
1 TraesCS1D01G216100 chr1B 97.624 2525 41 11 160 2666 407304191 407306714 0.000000e+00 4313.0
2 TraesCS1D01G216100 chr1B 98.732 631 7 1 2654 3283 407308808 407309438 0.000000e+00 1120.0
3 TraesCS1D01G216100 chr1B 91.139 79 7 0 2559 2637 407306679 407306601 1.250000e-19 108.0
4 TraesCS1D01G216100 chr1A 93.134 2447 90 39 160 2556 376512226 376514644 0.000000e+00 3517.0
5 TraesCS1D01G216100 chr1A 90.551 635 28 11 2663 3283 376514643 376515259 0.000000e+00 811.0
6 TraesCS1D01G216100 chr1A 90.123 81 5 3 2559 2636 415638127 415638047 5.800000e-18 102.0
7 TraesCS1D01G216100 chr1A 87.778 90 8 3 2550 2636 568391198 568391287 5.800000e-18 102.0
8 TraesCS1D01G216100 chr7B 88.506 87 7 3 2553 2636 482485037 482484951 5.800000e-18 102.0
9 TraesCS1D01G216100 chr7A 88.372 86 7 3 2554 2636 190472980 190473065 2.080000e-17 100.0
10 TraesCS1D01G216100 chr2A 89.873 79 7 1 2554 2631 632593127 632593205 2.080000e-17 100.0
11 TraesCS1D01G216100 chr2A 80.583 103 19 1 2828 2929 116166138 116166036 9.770000e-11 78.7
12 TraesCS1D01G216100 chr5D 87.500 88 8 3 2554 2638 482103358 482103271 7.500000e-17 99.0
13 TraesCS1D01G216100 chr5D 81.720 93 15 1 2852 2944 499874211 499874121 3.510000e-10 76.8
14 TraesCS1D01G216100 chr2D 83.673 98 16 0 2553 2650 567483585 567483488 3.490000e-15 93.5
15 TraesCS1D01G216100 chr5B 81.720 93 15 1 2852 2944 621265390 621265300 3.510000e-10 76.8


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 TraesCS1D01G216100 chr1D 301639034 301642316 3282 False 6063.0 6063 100.0000 1 3283 1 chr1D.!!$F1 3282
1 TraesCS1D01G216100 chr1B 407304191 407309438 5247 False 2716.5 4313 98.1780 160 3283 2 chr1B.!!$F1 3123
2 TraesCS1D01G216100 chr1A 376512226 376515259 3033 False 2164.0 3517 91.8425 160 3283 2 chr1A.!!$F2 3123

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
98 99 0.036671 CAGTCTCACTGCATCTGCCA 60.037 55.000 0.0 0.0 39.62 4.92 F
100 101 0.248565 GTCTCACTGCATCTGCCAGA 59.751 55.000 0.0 0.0 41.18 3.86 F
101 102 0.978907 TCTCACTGCATCTGCCAGAA 59.021 50.000 0.0 0.0 41.18 3.02 F
253 254 1.142870 CAACCACAGGACCCTTCAGAA 59.857 52.381 0.0 0.0 0.00 3.02 F
255 256 2.065799 ACCACAGGACCCTTCAGAAAT 58.934 47.619 0.0 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1109 0.765510 GAAGGTTGGAGGTGGACTGT 59.234 55.000 0.00 0.00 0.00 3.55 R
1480 1545 1.003928 TGCTGCATCTGAACACTCCAT 59.996 47.619 0.00 0.00 0.00 3.41 R
1551 1616 2.325484 TCTGACTGGTTAAGCTCCACA 58.675 47.619 6.19 1.14 0.00 4.17 R
1604 1669 6.007703 ACTTCGATATTTTTGGGGACAGAAA 58.992 36.000 0.00 0.00 46.84 2.52 R
2624 2690 5.413309 ACTGAATGAACTACTTCCTCTGG 57.587 43.478 0.00 0.00 0.00 3.86 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 2.698855 GCTCTATCCCTTCACTTGCA 57.301 50.000 0.00 0.00 0.00 4.08
20 21 2.991250 GCTCTATCCCTTCACTTGCAA 58.009 47.619 0.00 0.00 0.00 4.08
21 22 2.941720 GCTCTATCCCTTCACTTGCAAG 59.058 50.000 24.84 24.84 0.00 4.01
22 23 2.941720 CTCTATCCCTTCACTTGCAAGC 59.058 50.000 26.27 0.00 0.00 4.01
23 24 2.305635 TCTATCCCTTCACTTGCAAGCA 59.694 45.455 26.27 10.53 0.00 3.91
24 25 1.999648 ATCCCTTCACTTGCAAGCAA 58.000 45.000 26.27 17.31 0.00 3.91
25 26 1.999648 TCCCTTCACTTGCAAGCAAT 58.000 45.000 26.27 4.09 35.20 3.56
26 27 3.153369 TCCCTTCACTTGCAAGCAATA 57.847 42.857 26.27 8.49 35.20 1.90
27 28 3.495331 TCCCTTCACTTGCAAGCAATAA 58.505 40.909 26.27 13.52 35.20 1.40
28 29 3.894427 TCCCTTCACTTGCAAGCAATAAA 59.106 39.130 26.27 11.87 35.20 1.40
29 30 4.343526 TCCCTTCACTTGCAAGCAATAAAA 59.656 37.500 26.27 10.25 35.20 1.52
30 31 5.011943 TCCCTTCACTTGCAAGCAATAAAAT 59.988 36.000 26.27 0.83 35.20 1.82
31 32 5.121142 CCCTTCACTTGCAAGCAATAAAATG 59.879 40.000 26.27 13.96 35.20 2.32
32 33 5.927689 CCTTCACTTGCAAGCAATAAAATGA 59.072 36.000 26.27 16.02 35.20 2.57
33 34 6.090358 CCTTCACTTGCAAGCAATAAAATGAG 59.910 38.462 26.27 12.17 35.20 2.90
34 35 6.088016 TCACTTGCAAGCAATAAAATGAGT 57.912 33.333 26.27 0.00 35.20 3.41
35 36 6.514947 TCACTTGCAAGCAATAAAATGAGTT 58.485 32.000 26.27 0.00 35.20 3.01
36 37 7.656412 TCACTTGCAAGCAATAAAATGAGTTA 58.344 30.769 26.27 0.00 35.20 2.24
37 38 8.140628 TCACTTGCAAGCAATAAAATGAGTTAA 58.859 29.630 26.27 0.00 35.20 2.01
38 39 8.216453 CACTTGCAAGCAATAAAATGAGTTAAC 58.784 33.333 26.27 0.00 35.20 2.01
39 40 8.143835 ACTTGCAAGCAATAAAATGAGTTAACT 58.856 29.630 26.27 8.13 35.20 2.24
40 41 9.624697 CTTGCAAGCAATAAAATGAGTTAACTA 57.375 29.630 14.65 0.00 35.20 2.24
42 43 9.787532 TGCAAGCAATAAAATGAGTTAACTATC 57.212 29.630 8.42 0.00 0.00 2.08
43 44 9.237846 GCAAGCAATAAAATGAGTTAACTATCC 57.762 33.333 8.42 0.00 0.00 2.59
64 65 9.949174 CTATCCTATATCAAGATGATCACTTCG 57.051 37.037 0.00 0.49 38.26 3.79
65 66 8.586879 ATCCTATATCAAGATGATCACTTCGA 57.413 34.615 0.00 5.39 38.26 3.71
66 67 8.409358 TCCTATATCAAGATGATCACTTCGAA 57.591 34.615 0.00 0.00 38.26 3.71
67 68 9.029368 TCCTATATCAAGATGATCACTTCGAAT 57.971 33.333 0.00 1.17 38.26 3.34
68 69 9.299963 CCTATATCAAGATGATCACTTCGAATC 57.700 37.037 0.00 0.00 38.26 2.52
69 70 9.852091 CTATATCAAGATGATCACTTCGAATCA 57.148 33.333 0.00 0.00 38.26 2.57
71 72 7.854557 ATCAAGATGATCACTTCGAATCAAA 57.145 32.000 0.00 0.00 29.59 2.69
72 73 7.671495 TCAAGATGATCACTTCGAATCAAAA 57.329 32.000 0.00 0.00 0.00 2.44
73 74 7.521529 TCAAGATGATCACTTCGAATCAAAAC 58.478 34.615 0.00 0.00 0.00 2.43
74 75 6.428385 AGATGATCACTTCGAATCAAAACC 57.572 37.500 0.00 0.00 0.00 3.27
75 76 6.176183 AGATGATCACTTCGAATCAAAACCT 58.824 36.000 0.00 0.00 0.00 3.50
76 77 5.862924 TGATCACTTCGAATCAAAACCTC 57.137 39.130 0.00 0.00 0.00 3.85
77 78 5.551233 TGATCACTTCGAATCAAAACCTCT 58.449 37.500 0.00 0.00 0.00 3.69
78 79 5.639506 TGATCACTTCGAATCAAAACCTCTC 59.360 40.000 0.00 0.00 0.00 3.20
79 80 4.315803 TCACTTCGAATCAAAACCTCTCC 58.684 43.478 0.00 0.00 0.00 3.71
80 81 4.065088 CACTTCGAATCAAAACCTCTCCA 58.935 43.478 0.00 0.00 0.00 3.86
81 82 4.153117 CACTTCGAATCAAAACCTCTCCAG 59.847 45.833 0.00 0.00 0.00 3.86
82 83 4.202367 ACTTCGAATCAAAACCTCTCCAGT 60.202 41.667 0.00 0.00 0.00 4.00
83 84 3.926616 TCGAATCAAAACCTCTCCAGTC 58.073 45.455 0.00 0.00 0.00 3.51
84 85 3.578716 TCGAATCAAAACCTCTCCAGTCT 59.421 43.478 0.00 0.00 0.00 3.24
85 86 3.929610 CGAATCAAAACCTCTCCAGTCTC 59.070 47.826 0.00 0.00 0.00 3.36
86 87 4.561530 CGAATCAAAACCTCTCCAGTCTCA 60.562 45.833 0.00 0.00 0.00 3.27
87 88 3.753294 TCAAAACCTCTCCAGTCTCAC 57.247 47.619 0.00 0.00 0.00 3.51
88 89 3.309296 TCAAAACCTCTCCAGTCTCACT 58.691 45.455 0.00 0.00 0.00 3.41
89 90 3.070159 TCAAAACCTCTCCAGTCTCACTG 59.930 47.826 0.00 0.00 45.53 3.66
90 91 0.972883 AACCTCTCCAGTCTCACTGC 59.027 55.000 0.00 0.00 44.63 4.40
91 92 0.178950 ACCTCTCCAGTCTCACTGCA 60.179 55.000 0.00 0.00 44.63 4.41
92 93 1.193323 CCTCTCCAGTCTCACTGCAT 58.807 55.000 0.00 0.00 44.63 3.96
93 94 1.136695 CCTCTCCAGTCTCACTGCATC 59.863 57.143 0.00 0.00 44.63 3.91
94 95 2.101783 CTCTCCAGTCTCACTGCATCT 58.898 52.381 0.00 0.00 44.63 2.90
95 96 1.823610 TCTCCAGTCTCACTGCATCTG 59.176 52.381 0.00 0.00 44.63 2.90
96 97 0.248565 TCCAGTCTCACTGCATCTGC 59.751 55.000 0.00 0.00 44.63 4.26
97 98 0.743701 CCAGTCTCACTGCATCTGCC 60.744 60.000 0.00 0.00 44.63 4.85
98 99 0.036671 CAGTCTCACTGCATCTGCCA 60.037 55.000 0.00 0.00 39.62 4.92
99 100 0.249676 AGTCTCACTGCATCTGCCAG 59.750 55.000 0.00 0.51 41.18 4.85
100 101 0.248565 GTCTCACTGCATCTGCCAGA 59.751 55.000 0.00 0.00 41.18 3.86
101 102 0.978907 TCTCACTGCATCTGCCAGAA 59.021 50.000 0.00 0.00 41.18 3.02
102 103 1.348696 TCTCACTGCATCTGCCAGAAA 59.651 47.619 0.00 0.00 41.18 2.52
103 104 2.156917 CTCACTGCATCTGCCAGAAAA 58.843 47.619 0.00 0.00 41.18 2.29
104 105 2.753452 CTCACTGCATCTGCCAGAAAAT 59.247 45.455 0.00 0.00 41.18 1.82
105 106 2.490509 TCACTGCATCTGCCAGAAAATG 59.509 45.455 0.00 0.00 41.18 2.32
106 107 2.230508 CACTGCATCTGCCAGAAAATGT 59.769 45.455 0.00 0.00 41.18 2.71
107 108 2.490903 ACTGCATCTGCCAGAAAATGTC 59.509 45.455 0.00 0.00 41.18 3.06
108 109 2.490509 CTGCATCTGCCAGAAAATGTCA 59.509 45.455 0.00 0.00 41.18 3.58
109 110 2.229543 TGCATCTGCCAGAAAATGTCAC 59.770 45.455 0.00 0.00 41.18 3.67
110 111 2.490903 GCATCTGCCAGAAAATGTCACT 59.509 45.455 0.00 0.00 34.31 3.41
111 112 3.672511 GCATCTGCCAGAAAATGTCACTG 60.673 47.826 0.00 0.00 34.31 3.66
112 113 3.490439 TCTGCCAGAAAATGTCACTGA 57.510 42.857 0.00 0.00 34.07 3.41
113 114 3.819368 TCTGCCAGAAAATGTCACTGAA 58.181 40.909 0.00 0.00 34.07 3.02
114 115 4.401022 TCTGCCAGAAAATGTCACTGAAT 58.599 39.130 0.00 0.00 34.07 2.57
115 116 4.828939 TCTGCCAGAAAATGTCACTGAATT 59.171 37.500 0.00 0.00 34.07 2.17
116 117 5.302568 TCTGCCAGAAAATGTCACTGAATTT 59.697 36.000 0.00 0.00 34.07 1.82
117 118 5.531634 TGCCAGAAAATGTCACTGAATTTC 58.468 37.500 0.00 5.61 34.07 2.17
118 119 4.618489 GCCAGAAAATGTCACTGAATTTCG 59.382 41.667 0.00 0.00 35.66 3.46
119 120 5.762045 CCAGAAAATGTCACTGAATTTCGT 58.238 37.500 0.00 0.00 35.66 3.85
120 121 5.626543 CCAGAAAATGTCACTGAATTTCGTG 59.373 40.000 12.27 12.27 35.66 4.35
121 122 6.429624 CAGAAAATGTCACTGAATTTCGTGA 58.570 36.000 15.33 15.33 37.79 4.35
122 123 7.080099 CAGAAAATGTCACTGAATTTCGTGAT 58.920 34.615 19.47 9.25 41.63 3.06
123 124 8.229811 CAGAAAATGTCACTGAATTTCGTGATA 58.770 33.333 19.47 17.95 41.63 2.15
124 125 8.950210 AGAAAATGTCACTGAATTTCGTGATAT 58.050 29.630 19.47 18.89 41.67 1.63
125 126 8.900511 AAAATGTCACTGAATTTCGTGATATG 57.099 30.769 21.61 5.37 39.87 1.78
126 127 7.848223 AATGTCACTGAATTTCGTGATATGA 57.152 32.000 21.61 11.75 39.87 2.15
127 128 7.848223 ATGTCACTGAATTTCGTGATATGAA 57.152 32.000 20.91 10.84 41.63 2.57
128 129 7.848223 TGTCACTGAATTTCGTGATATGAAT 57.152 32.000 19.47 0.00 41.63 2.57
129 130 8.267620 TGTCACTGAATTTCGTGATATGAATT 57.732 30.769 19.47 0.00 41.63 2.17
130 131 9.377312 TGTCACTGAATTTCGTGATATGAATTA 57.623 29.630 19.47 1.18 41.63 1.40
176 177 2.016905 AGCAACACTCTCCTGTAGGT 57.983 50.000 0.00 0.00 36.34 3.08
194 195 8.755977 CCTGTAGGTAGTATCTGGTTTTAAGAA 58.244 37.037 0.00 0.00 0.00 2.52
253 254 1.142870 CAACCACAGGACCCTTCAGAA 59.857 52.381 0.00 0.00 0.00 3.02
255 256 2.065799 ACCACAGGACCCTTCAGAAAT 58.934 47.619 0.00 0.00 0.00 2.17
259 260 4.262164 CCACAGGACCCTTCAGAAATTTTG 60.262 45.833 0.00 0.00 0.00 2.44
260 261 3.321968 ACAGGACCCTTCAGAAATTTTGC 59.678 43.478 0.00 0.00 0.00 3.68
426 432 7.542130 GGTCAATCTCATTCCACAAATTTACAC 59.458 37.037 0.00 0.00 0.00 2.90
1068 1109 2.507854 GCAGATAGGGCAGGCGGTA 61.508 63.158 0.00 0.00 0.00 4.02
1480 1545 5.820423 TGAGAAAGTTGCAAAAGTACTGCTA 59.180 36.000 0.00 0.00 40.59 3.49
1551 1616 3.823304 GCTTTCATTCTTGTCCAGACCTT 59.177 43.478 0.00 0.00 0.00 3.50
1604 1669 1.812571 GTCACCCTGATTGCGACAATT 59.187 47.619 6.54 0.00 0.00 2.32
2520 2585 6.398095 TCATCACTTCGTCACTACATTTGAT 58.602 36.000 0.00 0.00 0.00 2.57
2626 2692 5.029807 TCAGCGACAATTAATATGGACCA 57.970 39.130 0.00 0.00 0.00 4.02
2744 4916 2.562912 GCACAACGTCATGCCTGG 59.437 61.111 11.88 0.00 35.73 4.45
2808 4980 8.515414 GCAAAATGTGGAACTAGTAAAGATCTT 58.485 33.333 0.88 0.88 38.04 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.698855 TGCAAGTGAAGGGATAGAGC 57.301 50.000 0.00 0.00 0.00 4.09
1 2 2.941720 GCTTGCAAGTGAAGGGATAGAG 59.058 50.000 26.55 0.00 0.00 2.43
2 3 2.305635 TGCTTGCAAGTGAAGGGATAGA 59.694 45.455 26.55 0.00 0.00 1.98
3 4 2.715046 TGCTTGCAAGTGAAGGGATAG 58.285 47.619 26.55 0.00 0.00 2.08
4 5 2.877097 TGCTTGCAAGTGAAGGGATA 57.123 45.000 26.55 1.22 0.00 2.59
5 6 1.999648 TTGCTTGCAAGTGAAGGGAT 58.000 45.000 26.55 0.00 0.00 3.85
6 7 1.999648 ATTGCTTGCAAGTGAAGGGA 58.000 45.000 26.55 0.00 0.00 4.20
7 8 3.940209 TTATTGCTTGCAAGTGAAGGG 57.060 42.857 26.55 1.60 0.00 3.95
8 9 5.927689 TCATTTTATTGCTTGCAAGTGAAGG 59.072 36.000 26.55 13.74 0.00 3.46
9 10 6.643770 ACTCATTTTATTGCTTGCAAGTGAAG 59.356 34.615 26.55 14.54 0.00 3.02
10 11 6.514947 ACTCATTTTATTGCTTGCAAGTGAA 58.485 32.000 26.55 19.32 0.00 3.18
11 12 6.088016 ACTCATTTTATTGCTTGCAAGTGA 57.912 33.333 26.55 17.68 0.00 3.41
12 13 6.774354 AACTCATTTTATTGCTTGCAAGTG 57.226 33.333 26.55 14.55 0.00 3.16
13 14 8.143835 AGTTAACTCATTTTATTGCTTGCAAGT 58.856 29.630 26.55 10.62 0.00 3.16
14 15 8.524870 AGTTAACTCATTTTATTGCTTGCAAG 57.475 30.769 22.44 22.44 0.00 4.01
16 17 9.787532 GATAGTTAACTCATTTTATTGCTTGCA 57.212 29.630 12.39 0.00 0.00 4.08
17 18 9.237846 GGATAGTTAACTCATTTTATTGCTTGC 57.762 33.333 12.39 0.00 0.00 4.01
38 39 9.949174 CGAAGTGATCATCTTGATATAGGATAG 57.051 37.037 13.14 0.00 37.20 2.08
39 40 9.686683 TCGAAGTGATCATCTTGATATAGGATA 57.313 33.333 13.14 0.00 37.20 2.59
40 41 8.586879 TCGAAGTGATCATCTTGATATAGGAT 57.413 34.615 13.14 0.00 37.20 3.24
41 42 8.409358 TTCGAAGTGATCATCTTGATATAGGA 57.591 34.615 13.14 0.00 37.20 2.94
42 43 9.299963 GATTCGAAGTGATCATCTTGATATAGG 57.700 37.037 13.14 0.00 37.20 2.57
43 44 9.852091 TGATTCGAAGTGATCATCTTGATATAG 57.148 33.333 13.14 2.05 37.20 1.31
45 46 9.551734 TTTGATTCGAAGTGATCATCTTGATAT 57.448 29.630 13.14 5.66 37.20 1.63
46 47 8.947055 TTTGATTCGAAGTGATCATCTTGATA 57.053 30.769 13.14 2.15 37.20 2.15
47 48 7.854557 TTTGATTCGAAGTGATCATCTTGAT 57.145 32.000 13.14 6.58 40.34 2.57
48 49 7.361201 GGTTTTGATTCGAAGTGATCATCTTGA 60.361 37.037 13.14 4.56 33.16 3.02
49 50 6.744537 GGTTTTGATTCGAAGTGATCATCTTG 59.255 38.462 13.14 2.50 33.16 3.02
50 51 6.656693 AGGTTTTGATTCGAAGTGATCATCTT 59.343 34.615 3.35 4.44 33.16 2.40
51 52 6.176183 AGGTTTTGATTCGAAGTGATCATCT 58.824 36.000 3.35 0.00 33.16 2.90
52 53 6.314896 AGAGGTTTTGATTCGAAGTGATCATC 59.685 38.462 3.35 0.00 33.16 2.92
53 54 6.176183 AGAGGTTTTGATTCGAAGTGATCAT 58.824 36.000 3.35 0.00 33.16 2.45
54 55 5.551233 AGAGGTTTTGATTCGAAGTGATCA 58.449 37.500 3.35 0.00 31.78 2.92
55 56 5.064071 GGAGAGGTTTTGATTCGAAGTGATC 59.936 44.000 3.35 0.00 0.00 2.92
56 57 4.938226 GGAGAGGTTTTGATTCGAAGTGAT 59.062 41.667 3.35 0.00 0.00 3.06
57 58 4.202315 TGGAGAGGTTTTGATTCGAAGTGA 60.202 41.667 3.35 0.00 0.00 3.41
58 59 4.065088 TGGAGAGGTTTTGATTCGAAGTG 58.935 43.478 3.35 0.00 0.00 3.16
59 60 4.202367 ACTGGAGAGGTTTTGATTCGAAGT 60.202 41.667 3.35 0.00 0.00 3.01
60 61 4.319177 ACTGGAGAGGTTTTGATTCGAAG 58.681 43.478 3.35 0.00 0.00 3.79
61 62 4.040461 AGACTGGAGAGGTTTTGATTCGAA 59.960 41.667 0.00 0.00 0.00 3.71
62 63 3.578716 AGACTGGAGAGGTTTTGATTCGA 59.421 43.478 0.00 0.00 0.00 3.71
63 64 3.929610 GAGACTGGAGAGGTTTTGATTCG 59.070 47.826 0.00 0.00 0.00 3.34
64 65 4.693095 GTGAGACTGGAGAGGTTTTGATTC 59.307 45.833 0.00 0.00 0.00 2.52
65 66 4.349342 AGTGAGACTGGAGAGGTTTTGATT 59.651 41.667 0.00 0.00 0.00 2.57
66 67 3.906846 AGTGAGACTGGAGAGGTTTTGAT 59.093 43.478 0.00 0.00 0.00 2.57
67 68 3.070159 CAGTGAGACTGGAGAGGTTTTGA 59.930 47.826 0.00 0.00 42.35 2.69
68 69 3.397482 CAGTGAGACTGGAGAGGTTTTG 58.603 50.000 0.00 0.00 42.35 2.44
69 70 2.224402 GCAGTGAGACTGGAGAGGTTTT 60.224 50.000 5.90 0.00 46.01 2.43
70 71 1.346068 GCAGTGAGACTGGAGAGGTTT 59.654 52.381 5.90 0.00 46.01 3.27
71 72 0.972883 GCAGTGAGACTGGAGAGGTT 59.027 55.000 5.90 0.00 46.01 3.50
72 73 0.178950 TGCAGTGAGACTGGAGAGGT 60.179 55.000 5.90 0.00 46.01 3.85
73 74 2.663566 TGCAGTGAGACTGGAGAGG 58.336 57.895 5.90 0.00 46.01 3.69
78 79 0.743701 GGCAGATGCAGTGAGACTGG 60.744 60.000 7.19 0.00 46.01 4.00
80 81 0.249676 CTGGCAGATGCAGTGAGACT 59.750 55.000 9.42 0.00 44.36 3.24
81 82 0.248565 TCTGGCAGATGCAGTGAGAC 59.751 55.000 14.43 0.00 44.36 3.36
82 83 0.978907 TTCTGGCAGATGCAGTGAGA 59.021 50.000 19.50 0.00 44.36 3.27
83 84 1.817357 TTTCTGGCAGATGCAGTGAG 58.183 50.000 19.50 0.00 44.36 3.51
84 85 2.275134 TTTTCTGGCAGATGCAGTGA 57.725 45.000 19.50 0.00 44.36 3.41
85 86 2.230508 ACATTTTCTGGCAGATGCAGTG 59.769 45.455 19.50 14.04 44.36 3.66
86 87 2.490903 GACATTTTCTGGCAGATGCAGT 59.509 45.455 19.50 14.62 44.36 4.40
87 88 2.490509 TGACATTTTCTGGCAGATGCAG 59.509 45.455 19.50 11.51 38.24 4.41
88 89 2.229543 GTGACATTTTCTGGCAGATGCA 59.770 45.455 19.50 12.60 46.02 3.96
89 90 2.490903 AGTGACATTTTCTGGCAGATGC 59.509 45.455 19.50 10.33 46.02 3.91
90 91 3.754850 TCAGTGACATTTTCTGGCAGATG 59.245 43.478 19.50 16.10 46.02 2.90
91 92 4.025040 TCAGTGACATTTTCTGGCAGAT 57.975 40.909 19.50 1.97 46.02 2.90
92 93 3.490439 TCAGTGACATTTTCTGGCAGA 57.510 42.857 14.43 14.43 46.02 4.26
93 94 4.778534 ATTCAGTGACATTTTCTGGCAG 57.221 40.909 8.58 8.58 46.02 4.85
94 95 5.531634 GAAATTCAGTGACATTTTCTGGCA 58.468 37.500 12.11 0.00 42.03 4.92
95 96 4.618489 CGAAATTCAGTGACATTTTCTGGC 59.382 41.667 15.21 4.78 0.00 4.85
96 97 5.626543 CACGAAATTCAGTGACATTTTCTGG 59.373 40.000 15.21 7.62 40.56 3.86
97 98 6.429624 TCACGAAATTCAGTGACATTTTCTG 58.570 36.000 13.59 12.92 41.81 3.02
98 99 6.618287 TCACGAAATTCAGTGACATTTTCT 57.382 33.333 13.59 5.44 41.81 2.52
138 139 9.751542 GTGTTGCTACTCTTATTCTACATACAT 57.248 33.333 0.00 0.00 0.00 2.29
139 140 8.967918 AGTGTTGCTACTCTTATTCTACATACA 58.032 33.333 0.00 0.00 0.00 2.29
140 141 9.453325 GAGTGTTGCTACTCTTATTCTACATAC 57.547 37.037 4.43 0.00 42.93 2.39
153 154 3.129638 CCTACAGGAGAGTGTTGCTACTC 59.870 52.174 0.00 4.24 45.83 2.59
154 155 3.093057 CCTACAGGAGAGTGTTGCTACT 58.907 50.000 0.00 0.00 37.39 2.57
155 156 2.826725 ACCTACAGGAGAGTGTTGCTAC 59.173 50.000 1.29 0.00 38.94 3.58
156 157 3.170991 ACCTACAGGAGAGTGTTGCTA 57.829 47.619 1.29 0.00 38.94 3.49
157 158 2.016905 ACCTACAGGAGAGTGTTGCT 57.983 50.000 1.29 0.00 38.94 3.91
158 159 2.826725 ACTACCTACAGGAGAGTGTTGC 59.173 50.000 1.29 0.00 38.94 4.17
161 162 5.398126 CCAGATACTACCTACAGGAGAGTGT 60.398 48.000 14.16 9.62 36.68 3.55
214 215 0.036388 GATCAGTGCCCGGAAGTTCA 60.036 55.000 0.73 0.00 0.00 3.18
215 216 0.036388 TGATCAGTGCCCGGAAGTTC 60.036 55.000 0.73 0.00 0.00 3.01
253 254 8.815912 AGTATCTGGAGGTTTAATTGCAAAATT 58.184 29.630 1.71 0.00 0.00 1.82
255 256 7.450014 TCAGTATCTGGAGGTTTAATTGCAAAA 59.550 33.333 1.71 0.00 31.51 2.44
259 260 5.297029 GGTCAGTATCTGGAGGTTTAATTGC 59.703 44.000 0.00 0.00 31.51 3.56
260 261 5.523916 CGGTCAGTATCTGGAGGTTTAATTG 59.476 44.000 0.00 0.00 31.51 2.32
426 432 7.805071 GCCTTCTTCAAAATATATCCGTGAATG 59.195 37.037 6.28 3.23 0.00 2.67
980 1012 3.720193 CCTGGTCGTCGTCGTCGT 61.720 66.667 11.41 0.00 38.33 4.34
1068 1109 0.765510 GAAGGTTGGAGGTGGACTGT 59.234 55.000 0.00 0.00 0.00 3.55
1480 1545 1.003928 TGCTGCATCTGAACACTCCAT 59.996 47.619 0.00 0.00 0.00 3.41
1551 1616 2.325484 TCTGACTGGTTAAGCTCCACA 58.675 47.619 6.19 1.14 0.00 4.17
1604 1669 6.007703 ACTTCGATATTTTTGGGGACAGAAA 58.992 36.000 0.00 0.00 46.84 2.52
2624 2690 5.413309 ACTGAATGAACTACTTCCTCTGG 57.587 43.478 0.00 0.00 0.00 3.86
2626 2692 5.799213 CCAACTGAATGAACTACTTCCTCT 58.201 41.667 0.00 0.00 0.00 3.69
2744 4916 5.385617 CCAAACGATTCTCAGACACAATTC 58.614 41.667 0.00 0.00 0.00 2.17
2808 4980 3.589735 TGGGGAGCAAACAAGTAATCCTA 59.410 43.478 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.