Multiple sequence alignment - TraesCS5D01G101000

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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 TraesCS5D01G101000 chr5D 100.000 3853 0 0 1 3853 114006131 114002279 0.000000e+00 7116.0
1 TraesCS5D01G101000 chr5D 96.330 109 3 1 60 168 560242935 560243042 1.100000e-40 178.0
2 TraesCS5D01G101000 chr5D 94.595 37 2 0 153 189 295307327 295307363 1.500000e-04 58.4
3 TraesCS5D01G101000 chr5A 95.425 3650 90 28 165 3759 119219315 119215688 0.000000e+00 5744.0
4 TraesCS5D01G101000 chr5A 95.161 62 3 0 1 62 119219377 119219316 8.810000e-17 99.0
5 TraesCS5D01G101000 chr5A 93.750 48 1 2 3264 3309 381757741 381757694 1.920000e-08 71.3
6 TraesCS5D01G101000 chr5B 93.696 2776 80 32 229 2982 124767498 124764796 0.000000e+00 4069.0
7 TraesCS5D01G101000 chr5B 96.388 886 18 4 2980 3853 124764675 124763792 0.000000e+00 1447.0
8 TraesCS5D01G101000 chr5B 95.536 112 4 1 57 168 464325577 464325467 1.100000e-40 178.0
9 TraesCS5D01G101000 chr5B 95.536 112 4 1 60 171 669302698 669302588 1.100000e-40 178.0
10 TraesCS5D01G101000 chr5B 95.413 109 4 1 60 168 322861103 322860996 5.120000e-39 172.0
11 TraesCS5D01G101000 chr5B 89.286 56 2 2 3246 3301 602247107 602247056 2.480000e-07 67.6
12 TraesCS5D01G101000 chr5B 100.000 28 0 0 170 197 73344033 73344060 7.000000e-03 52.8
13 TraesCS5D01G101000 chr1D 95.495 111 4 1 59 169 366680640 366680749 3.960000e-40 176.0
14 TraesCS5D01G101000 chr1D 94.643 56 3 0 6 61 110983315 110983370 1.910000e-13 87.9
15 TraesCS5D01G101000 chr1D 92.857 56 4 0 6 61 185726444 185726389 8.870000e-12 82.4
16 TraesCS5D01G101000 chr7B 94.643 112 5 1 60 171 34609755 34609645 5.120000e-39 172.0
17 TraesCS5D01G101000 chr3A 95.413 109 4 1 60 168 642924938 642924831 5.120000e-39 172.0
18 TraesCS5D01G101000 chr3A 95.413 109 4 1 60 168 746352862 746352755 5.120000e-39 172.0
19 TraesCS5D01G101000 chr3A 95.082 61 3 0 1 61 743023147 743023207 3.170000e-16 97.1
20 TraesCS5D01G101000 chr2D 91.667 120 6 4 60 177 75761234 75761117 3.080000e-36 163.0
21 TraesCS5D01G101000 chr2D 92.157 51 1 3 3264 3312 380408321 380408272 6.910000e-08 69.4
22 TraesCS5D01G101000 chr7A 94.643 56 3 0 6 61 86137344 86137289 1.910000e-13 87.9
23 TraesCS5D01G101000 chr7A 94.643 56 3 0 6 61 99996631 99996576 1.910000e-13 87.9
24 TraesCS5D01G101000 chr7A 94.643 56 3 0 6 61 100005831 100005776 1.910000e-13 87.9
25 TraesCS5D01G101000 chr3B 94.643 56 3 0 6 61 41426521 41426576 1.910000e-13 87.9
26 TraesCS5D01G101000 chr3B 91.667 60 4 1 3 61 248252005 248251946 8.870000e-12 82.4
27 TraesCS5D01G101000 chr3D 95.833 48 2 0 3264 3311 362864577 362864624 1.150000e-10 78.7
28 TraesCS5D01G101000 chr3D 100.000 28 0 0 170 197 514669966 514669939 7.000000e-03 52.8
29 TraesCS5D01G101000 chr7D 97.674 43 1 0 3264 3306 34070802 34070844 1.480000e-09 75.0
30 TraesCS5D01G101000 chr7D 94.000 50 1 2 3264 3313 108173793 108173840 1.480000e-09 75.0
31 TraesCS5D01G101000 chr4B 92.157 51 2 2 3264 3312 564781383 564781333 1.920000e-08 71.3
32 TraesCS5D01G101000 chr6D 89.130 46 1 1 168 209 342786875 342786920 2.000000e-03 54.7
33 TraesCS5D01G101000 chr6B 89.130 46 1 1 168 209 509850704 509850749 2.000000e-03 54.7
34 TraesCS5D01G101000 chr6B 89.130 46 1 1 168 209 531108856 531108901 2.000000e-03 54.7
35 TraesCS5D01G101000 chr6B 100.000 28 0 0 168 195 174251262 174251289 7.000000e-03 52.8
36 TraesCS5D01G101000 chr2B 89.130 46 1 1 168 209 596455622 596455667 2.000000e-03 54.7


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 TraesCS5D01G101000 chr5D 114002279 114006131 3852 True 7116.0 7116 100.000 1 3853 1 chr5D.!!$R1 3852
1 TraesCS5D01G101000 chr5A 119215688 119219377 3689 True 2921.5 5744 95.293 1 3759 2 chr5A.!!$R2 3758
2 TraesCS5D01G101000 chr5B 124763792 124767498 3706 True 2758.0 4069 95.042 229 3853 2 chr5B.!!$R5 3624

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
380 381 0.665835 CGCGATCTGTCTAGAGCCTT 59.334 55.000 0.00 0.0 35.96 4.35 F
1232 1267 1.144708 TGGTTGCTGATGGGAAAGTGA 59.855 47.619 0.00 0.0 0.00 3.41 F
1394 1430 0.390860 CACTGCCTAGCGCCTATCTT 59.609 55.000 2.29 0.0 36.24 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1418 1.066858 GCTATGGCAAGATAGGCGCTA 60.067 52.381 7.64 0.00 38.54 4.26 R
2225 2262 1.069513 TGTGCTTAAGTGTGCCTACGT 59.930 47.619 4.02 0.00 0.00 3.57 R
3053 3217 2.436173 CCCTCTAAGGCTCTAAAGTGGG 59.564 54.545 10.13 10.13 36.67 4.61 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
55 56 7.824289 CCACACATATGTTATTCCCCACTATAG 59.176 40.741 5.37 0.00 36.72 1.31
75 76 2.233305 AGGTACTCCATCCGTTCACT 57.767 50.000 0.00 0.00 35.89 3.41
76 77 2.537143 AGGTACTCCATCCGTTCACTT 58.463 47.619 0.00 0.00 35.89 3.16
77 78 2.904434 AGGTACTCCATCCGTTCACTTT 59.096 45.455 0.00 0.00 35.89 2.66
78 79 3.326880 AGGTACTCCATCCGTTCACTTTT 59.673 43.478 0.00 0.00 35.89 2.27
79 80 3.435671 GGTACTCCATCCGTTCACTTTTG 59.564 47.826 0.00 0.00 0.00 2.44
80 81 3.208747 ACTCCATCCGTTCACTTTTGT 57.791 42.857 0.00 0.00 0.00 2.83
81 82 4.345859 ACTCCATCCGTTCACTTTTGTA 57.654 40.909 0.00 0.00 0.00 2.41
82 83 4.710324 ACTCCATCCGTTCACTTTTGTAA 58.290 39.130 0.00 0.00 0.00 2.41
83 84 4.755123 ACTCCATCCGTTCACTTTTGTAAG 59.245 41.667 0.00 0.00 37.40 2.34
84 85 4.710324 TCCATCCGTTCACTTTTGTAAGT 58.290 39.130 0.00 0.00 45.40 2.24
85 86 4.753107 TCCATCCGTTCACTTTTGTAAGTC 59.247 41.667 0.00 0.00 42.67 3.01
86 87 4.377022 CCATCCGTTCACTTTTGTAAGTCG 60.377 45.833 0.00 0.00 42.67 4.18
87 88 3.784338 TCCGTTCACTTTTGTAAGTCGT 58.216 40.909 0.00 0.00 42.67 4.34
88 89 4.183101 TCCGTTCACTTTTGTAAGTCGTT 58.817 39.130 0.00 0.00 42.67 3.85
89 90 4.630940 TCCGTTCACTTTTGTAAGTCGTTT 59.369 37.500 0.00 0.00 42.67 3.60
90 91 4.959757 CCGTTCACTTTTGTAAGTCGTTTC 59.040 41.667 0.00 0.00 42.67 2.78
91 92 5.446206 CCGTTCACTTTTGTAAGTCGTTTCA 60.446 40.000 0.00 0.00 42.67 2.69
92 93 5.671140 CGTTCACTTTTGTAAGTCGTTTCAG 59.329 40.000 0.00 0.00 42.67 3.02
93 94 6.454583 CGTTCACTTTTGTAAGTCGTTTCAGA 60.455 38.462 0.00 0.00 42.67 3.27
94 95 6.340537 TCACTTTTGTAAGTCGTTTCAGAC 57.659 37.500 0.00 0.00 42.67 3.51
95 96 5.870433 TCACTTTTGTAAGTCGTTTCAGACA 59.130 36.000 0.00 0.00 42.67 3.41
96 97 6.369340 TCACTTTTGTAAGTCGTTTCAGACAA 59.631 34.615 0.00 0.00 42.67 3.18
97 98 6.682863 CACTTTTGTAAGTCGTTTCAGACAAG 59.317 38.462 0.00 0.00 42.67 3.16
98 99 6.370718 ACTTTTGTAAGTCGTTTCAGACAAGT 59.629 34.615 0.00 0.00 40.60 3.16
99 100 5.712217 TTGTAAGTCGTTTCAGACAAGTG 57.288 39.130 0.00 0.00 43.24 3.16
100 101 5.001237 TGTAAGTCGTTTCAGACAAGTGA 57.999 39.130 0.00 0.00 43.24 3.41
101 102 5.412640 TGTAAGTCGTTTCAGACAAGTGAA 58.587 37.500 0.00 0.00 43.24 3.18
102 103 5.870433 TGTAAGTCGTTTCAGACAAGTGAAA 59.130 36.000 0.00 0.00 42.79 2.69
103 104 6.537301 TGTAAGTCGTTTCAGACAAGTGAAAT 59.463 34.615 2.59 0.00 45.71 2.17
104 105 6.436843 AAGTCGTTTCAGACAAGTGAAATT 57.563 33.333 2.59 0.00 45.71 1.82
105 106 5.810525 AGTCGTTTCAGACAAGTGAAATTG 58.189 37.500 2.59 0.24 45.71 2.32
106 107 5.584649 AGTCGTTTCAGACAAGTGAAATTGA 59.415 36.000 2.59 2.32 45.71 2.57
107 108 5.904080 GTCGTTTCAGACAAGTGAAATTGAG 59.096 40.000 2.59 0.00 45.71 3.02
108 109 4.672413 CGTTTCAGACAAGTGAAATTGAGC 59.328 41.667 2.59 0.00 45.71 4.26
109 110 5.504665 CGTTTCAGACAAGTGAAATTGAGCT 60.505 40.000 2.59 0.00 45.71 4.09
110 111 5.428496 TTCAGACAAGTGAAATTGAGCTG 57.572 39.130 0.00 5.01 37.41 4.24
111 112 4.454678 TCAGACAAGTGAAATTGAGCTGT 58.545 39.130 0.00 0.00 37.38 4.40
112 113 4.883585 TCAGACAAGTGAAATTGAGCTGTT 59.116 37.500 0.00 0.00 37.38 3.16
113 114 5.357878 TCAGACAAGTGAAATTGAGCTGTTT 59.642 36.000 0.00 0.00 37.38 2.83
114 115 6.038356 CAGACAAGTGAAATTGAGCTGTTTT 58.962 36.000 0.00 0.00 34.50 2.43
115 116 6.020121 CAGACAAGTGAAATTGAGCTGTTTTG 60.020 38.462 0.00 0.00 34.50 2.44
116 117 4.567959 ACAAGTGAAATTGAGCTGTTTTGC 59.432 37.500 0.00 0.00 34.20 3.68
117 118 4.389890 AGTGAAATTGAGCTGTTTTGCA 57.610 36.364 0.00 0.00 34.99 4.08
118 119 4.114794 AGTGAAATTGAGCTGTTTTGCAC 58.885 39.130 0.00 0.00 34.99 4.57
119 120 3.864583 GTGAAATTGAGCTGTTTTGCACA 59.135 39.130 0.00 0.00 34.99 4.57
120 121 4.329528 GTGAAATTGAGCTGTTTTGCACAA 59.670 37.500 0.00 0.00 44.68 3.33
123 124 3.523606 TTGAGCTGTTTTGCACAATGT 57.476 38.095 0.00 0.00 38.28 2.71
124 125 3.082698 TGAGCTGTTTTGCACAATGTC 57.917 42.857 0.00 0.00 33.87 3.06
125 126 2.689471 TGAGCTGTTTTGCACAATGTCT 59.311 40.909 0.00 0.00 33.87 3.41
126 127 3.047796 GAGCTGTTTTGCACAATGTCTG 58.952 45.455 0.00 0.00 33.87 3.51
127 128 2.689471 AGCTGTTTTGCACAATGTCTGA 59.311 40.909 0.00 0.00 33.87 3.27
128 129 3.130869 AGCTGTTTTGCACAATGTCTGAA 59.869 39.130 0.00 0.00 33.87 3.02
129 130 3.864583 GCTGTTTTGCACAATGTCTGAAA 59.135 39.130 0.00 0.00 33.87 2.69
130 131 4.259930 GCTGTTTTGCACAATGTCTGAAAC 60.260 41.667 0.00 7.59 33.87 2.78
131 132 4.814147 TGTTTTGCACAATGTCTGAAACA 58.186 34.783 11.27 11.27 43.51 2.83
132 133 9.926214 AGCTGTTTTGCACAATGTCTGAAACAT 62.926 37.037 14.04 3.38 42.06 2.71
142 143 5.886960 ATGTCTGAAACATCTACAAAGCC 57.113 39.130 0.00 0.00 45.78 4.35
143 144 4.973168 TGTCTGAAACATCTACAAAGCCT 58.027 39.130 0.00 0.00 31.20 4.58
144 145 5.376625 TGTCTGAAACATCTACAAAGCCTT 58.623 37.500 0.00 0.00 31.20 4.35
145 146 6.530120 TGTCTGAAACATCTACAAAGCCTTA 58.470 36.000 0.00 0.00 31.20 2.69
146 147 7.168219 TGTCTGAAACATCTACAAAGCCTTAT 58.832 34.615 0.00 0.00 31.20 1.73
147 148 8.318412 TGTCTGAAACATCTACAAAGCCTTATA 58.682 33.333 0.00 0.00 31.20 0.98
148 149 9.162764 GTCTGAAACATCTACAAAGCCTTATAA 57.837 33.333 0.00 0.00 0.00 0.98
149 150 9.733556 TCTGAAACATCTACAAAGCCTTATAAA 57.266 29.630 0.00 0.00 0.00 1.40
154 155 9.515226 AACATCTACAAAGCCTTATAAAAGTGA 57.485 29.630 0.00 0.00 0.00 3.41
155 156 9.515226 ACATCTACAAAGCCTTATAAAAGTGAA 57.485 29.630 0.00 0.00 0.00 3.18
158 159 9.344772 TCTACAAAGCCTTATAAAAGTGAAACA 57.655 29.630 0.00 0.00 41.43 2.83
159 160 9.612620 CTACAAAGCCTTATAAAAGTGAAACAG 57.387 33.333 0.00 0.00 41.43 3.16
160 161 8.232913 ACAAAGCCTTATAAAAGTGAAACAGA 57.767 30.769 0.00 0.00 41.43 3.41
161 162 8.352942 ACAAAGCCTTATAAAAGTGAAACAGAG 58.647 33.333 0.00 0.00 41.43 3.35
162 163 7.454260 AAGCCTTATAAAAGTGAAACAGAGG 57.546 36.000 0.00 0.00 41.43 3.69
163 164 5.946377 AGCCTTATAAAAGTGAAACAGAGGG 59.054 40.000 0.00 0.00 41.43 4.30
216 217 6.867293 GCATTACTAGTCTAAGTTAATCCCCG 59.133 42.308 0.00 0.00 0.00 5.73
339 340 2.598439 CGCGAGCATCTGAGTATTTTGC 60.598 50.000 0.00 0.00 0.00 3.68
378 379 1.371145 GCGCGATCTGTCTAGAGCC 60.371 63.158 12.10 0.00 35.96 4.70
379 380 1.791103 GCGCGATCTGTCTAGAGCCT 61.791 60.000 12.10 0.00 35.96 4.58
380 381 0.665835 CGCGATCTGTCTAGAGCCTT 59.334 55.000 0.00 0.00 35.96 4.35
383 384 3.120041 GCGATCTGTCTAGAGCCTTTTC 58.880 50.000 0.00 0.00 35.96 2.29
643 649 2.659610 GTCCTGGACGCTTGCTCT 59.340 61.111 11.71 0.00 0.00 4.09
785 791 4.575236 GGAGACCGATTCCAATTAAAGACC 59.425 45.833 0.00 0.00 34.74 3.85
962 977 1.597461 CGTTGAGGGGAAGGAGGTC 59.403 63.158 0.00 0.00 0.00 3.85
963 978 1.597461 GTTGAGGGGAAGGAGGTCG 59.403 63.158 0.00 0.00 0.00 4.79
968 983 2.663196 GGGAAGGAGGTCGTGGTG 59.337 66.667 0.00 0.00 0.00 4.17
971 986 2.122547 AAGGAGGTCGTGGTGGGT 60.123 61.111 0.00 0.00 0.00 4.51
1117 1133 1.153647 CTCAAGGCCGACGTATGCA 60.154 57.895 10.54 0.00 0.00 3.96
1166 1182 3.777522 TCCTCTTTCCAATCCTCTTCTCC 59.222 47.826 0.00 0.00 0.00 3.71
1232 1267 1.144708 TGGTTGCTGATGGGAAAGTGA 59.855 47.619 0.00 0.00 0.00 3.41
1373 1409 2.754946 ATTCTGCATTTTGCCACTGG 57.245 45.000 0.00 0.00 44.23 4.00
1394 1430 0.390860 CACTGCCTAGCGCCTATCTT 59.609 55.000 2.29 0.00 36.24 2.40
1403 1439 1.630244 GCGCCTATCTTGCCATAGCG 61.630 60.000 0.00 0.00 44.31 4.26
1457 1493 6.405278 TCATTTCTCACTCGGAAGCATATA 57.595 37.500 0.00 0.00 0.00 0.86
1458 1494 6.450545 TCATTTCTCACTCGGAAGCATATAG 58.549 40.000 0.00 0.00 0.00 1.31
1572 1608 5.824624 ACATGTGTTTCTCATCACAGTTTCT 59.175 36.000 0.00 0.00 45.56 2.52
1589 1625 5.754890 CAGTTTCTTTGCATTGCTTTTACCT 59.245 36.000 10.49 0.00 0.00 3.08
1644 1680 5.222254 TGGCTTATTGGGACTAAACCTTCTT 60.222 40.000 0.00 0.00 0.00 2.52
2170 2207 2.936993 GCCTATATTGCCTATGCGTGCT 60.937 50.000 0.00 0.00 41.78 4.40
2225 2262 1.134995 CAGTTCTGTCATCGCCTAGCA 60.135 52.381 0.00 0.00 0.00 3.49
2249 2286 1.134098 AGGCACACTTAAGCACACACT 60.134 47.619 1.29 0.00 0.00 3.55
2916 2954 3.088532 TGCAGGGTAAATTAGCTGTTGG 58.911 45.455 0.00 0.00 0.00 3.77
3053 3217 1.486726 AGTGGCTGCTATAGGGTGTTC 59.513 52.381 1.04 0.00 0.00 3.18
3450 3621 8.994170 TGTGATGAGATACTCTAGATCTAAACG 58.006 37.037 3.57 0.00 33.71 3.60
3500 3671 7.291411 TGTTACTGCCTCTAGATAGAATTCC 57.709 40.000 0.65 0.00 0.00 3.01
3805 3986 5.385617 CAAGACAAATTAAGCGGAGAGTTG 58.614 41.667 0.00 0.00 0.00 3.16
3817 3998 4.056050 GCGGAGAGTTGTTTCAAAGTAGA 58.944 43.478 0.00 0.00 0.00 2.59
3818 3999 4.510340 GCGGAGAGTTGTTTCAAAGTAGAA 59.490 41.667 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.853872 GTGTCACGCAACACTTCATTTATTAA 59.146 34.615 12.32 0.00 44.90 1.40
23 24 5.065988 GGGAATAACATATGTGTGGTGTCAC 59.934 44.000 9.63 0.00 43.87 3.67
55 56 2.100989 AGTGAACGGATGGAGTACCTC 58.899 52.381 0.00 0.00 37.04 3.85
62 63 4.710324 ACTTACAAAAGTGAACGGATGGA 58.290 39.130 0.00 0.00 44.40 3.41
63 64 4.377022 CGACTTACAAAAGTGAACGGATGG 60.377 45.833 0.00 0.00 46.09 3.51
64 65 4.210537 ACGACTTACAAAAGTGAACGGATG 59.789 41.667 0.00 0.00 46.09 3.51
65 66 4.374399 ACGACTTACAAAAGTGAACGGAT 58.626 39.130 0.00 0.00 46.09 4.18
66 67 3.784338 ACGACTTACAAAAGTGAACGGA 58.216 40.909 0.00 0.00 46.09 4.69
67 68 4.525411 AACGACTTACAAAAGTGAACGG 57.475 40.909 0.00 0.00 46.09 4.44
68 69 5.552807 TGAAACGACTTACAAAAGTGAACG 58.447 37.500 0.00 0.00 46.09 3.95
69 70 6.681599 GTCTGAAACGACTTACAAAAGTGAAC 59.318 38.462 0.00 0.00 46.09 3.18
70 71 6.369340 TGTCTGAAACGACTTACAAAAGTGAA 59.631 34.615 0.00 0.00 46.09 3.18
71 72 5.870433 TGTCTGAAACGACTTACAAAAGTGA 59.130 36.000 0.00 0.00 46.09 3.41
72 73 6.102006 TGTCTGAAACGACTTACAAAAGTG 57.898 37.500 0.00 0.00 46.09 3.16
74 75 6.682863 CACTTGTCTGAAACGACTTACAAAAG 59.317 38.462 0.00 0.00 38.77 2.27
75 76 6.369340 TCACTTGTCTGAAACGACTTACAAAA 59.631 34.615 0.00 0.00 35.00 2.44
76 77 5.870433 TCACTTGTCTGAAACGACTTACAAA 59.130 36.000 0.00 0.00 35.00 2.83
77 78 5.412640 TCACTTGTCTGAAACGACTTACAA 58.587 37.500 0.00 0.00 35.00 2.41
78 79 5.001237 TCACTTGTCTGAAACGACTTACA 57.999 39.130 0.00 0.00 35.00 2.41
79 80 5.961395 TTCACTTGTCTGAAACGACTTAC 57.039 39.130 0.00 0.00 35.00 2.34
80 81 7.279090 TCAATTTCACTTGTCTGAAACGACTTA 59.721 33.333 0.00 0.00 41.76 2.24
81 82 6.093495 TCAATTTCACTTGTCTGAAACGACTT 59.907 34.615 0.00 0.00 41.76 3.01
82 83 5.584649 TCAATTTCACTTGTCTGAAACGACT 59.415 36.000 0.00 0.00 41.76 4.18
83 84 5.806286 TCAATTTCACTTGTCTGAAACGAC 58.194 37.500 0.00 0.00 41.76 4.34
84 85 5.504010 GCTCAATTTCACTTGTCTGAAACGA 60.504 40.000 0.00 0.00 41.76 3.85
85 86 4.672413 GCTCAATTTCACTTGTCTGAAACG 59.328 41.667 0.00 0.00 41.76 3.60
86 87 5.684626 CAGCTCAATTTCACTTGTCTGAAAC 59.315 40.000 0.00 0.00 41.76 2.78
87 88 5.357878 ACAGCTCAATTTCACTTGTCTGAAA 59.642 36.000 12.20 0.00 42.83 2.69
88 89 4.883585 ACAGCTCAATTTCACTTGTCTGAA 59.116 37.500 12.20 0.00 34.76 3.02
89 90 4.454678 ACAGCTCAATTTCACTTGTCTGA 58.545 39.130 12.20 0.00 34.76 3.27
90 91 4.825546 ACAGCTCAATTTCACTTGTCTG 57.174 40.909 0.00 0.00 35.73 3.51
91 92 5.841957 AAACAGCTCAATTTCACTTGTCT 57.158 34.783 0.00 0.00 0.00 3.41
92 93 5.276536 GCAAAACAGCTCAATTTCACTTGTC 60.277 40.000 0.00 0.00 0.00 3.18
93 94 4.567959 GCAAAACAGCTCAATTTCACTTGT 59.432 37.500 0.00 0.00 0.00 3.16
94 95 4.567558 TGCAAAACAGCTCAATTTCACTTG 59.432 37.500 0.00 0.00 34.99 3.16
95 96 4.567959 GTGCAAAACAGCTCAATTTCACTT 59.432 37.500 0.00 0.00 34.99 3.16
96 97 4.114794 GTGCAAAACAGCTCAATTTCACT 58.885 39.130 0.00 0.00 34.99 3.41
97 98 3.864583 TGTGCAAAACAGCTCAATTTCAC 59.135 39.130 0.00 0.00 35.35 3.18
98 99 4.120792 TGTGCAAAACAGCTCAATTTCA 57.879 36.364 0.00 0.00 35.35 2.69
99 100 5.006941 ACATTGTGCAAAACAGCTCAATTTC 59.993 36.000 11.96 0.00 41.87 2.17
100 101 4.877251 ACATTGTGCAAAACAGCTCAATTT 59.123 33.333 11.96 5.37 41.87 1.82
101 102 4.444536 ACATTGTGCAAAACAGCTCAATT 58.555 34.783 11.96 4.12 41.87 2.32
102 103 4.053295 GACATTGTGCAAAACAGCTCAAT 58.947 39.130 9.58 9.58 41.87 2.57
103 104 3.130869 AGACATTGTGCAAAACAGCTCAA 59.869 39.130 0.00 5.99 41.87 3.02
104 105 2.689471 AGACATTGTGCAAAACAGCTCA 59.311 40.909 0.00 0.00 40.74 4.26
105 106 3.047796 CAGACATTGTGCAAAACAGCTC 58.952 45.455 0.00 0.00 40.74 4.09
106 107 2.689471 TCAGACATTGTGCAAAACAGCT 59.311 40.909 0.00 0.00 40.74 4.24
107 108 3.082698 TCAGACATTGTGCAAAACAGC 57.917 42.857 0.00 0.00 40.74 4.40
108 109 4.863689 TGTTTCAGACATTGTGCAAAACAG 59.136 37.500 12.56 0.00 34.89 3.16
109 110 4.814147 TGTTTCAGACATTGTGCAAAACA 58.186 34.783 12.56 12.56 33.98 2.83
110 111 5.971895 ATGTTTCAGACATTGTGCAAAAC 57.028 34.783 0.00 2.73 46.80 2.43
121 122 4.973168 AGGCTTTGTAGATGTTTCAGACA 58.027 39.130 0.00 0.00 43.71 3.41
122 123 5.948992 AAGGCTTTGTAGATGTTTCAGAC 57.051 39.130 0.00 0.00 0.00 3.51
123 124 9.733556 TTTATAAGGCTTTGTAGATGTTTCAGA 57.266 29.630 4.45 0.00 0.00 3.27
128 129 9.515226 TCACTTTTATAAGGCTTTGTAGATGTT 57.485 29.630 4.45 0.00 35.61 2.71
129 130 9.515226 TTCACTTTTATAAGGCTTTGTAGATGT 57.485 29.630 4.45 1.05 35.61 3.06
132 133 9.344772 TGTTTCACTTTTATAAGGCTTTGTAGA 57.655 29.630 4.45 0.00 35.61 2.59
133 134 9.612620 CTGTTTCACTTTTATAAGGCTTTGTAG 57.387 33.333 4.45 0.00 35.61 2.74
134 135 9.344772 TCTGTTTCACTTTTATAAGGCTTTGTA 57.655 29.630 4.45 0.00 35.61 2.41
135 136 8.232913 TCTGTTTCACTTTTATAAGGCTTTGT 57.767 30.769 4.45 0.00 35.61 2.83
136 137 7.809806 CCTCTGTTTCACTTTTATAAGGCTTTG 59.190 37.037 4.45 0.00 35.61 2.77
137 138 7.039714 CCCTCTGTTTCACTTTTATAAGGCTTT 60.040 37.037 4.45 0.00 35.61 3.51
138 139 6.434340 CCCTCTGTTTCACTTTTATAAGGCTT 59.566 38.462 4.58 4.58 35.61 4.35
139 140 5.946377 CCCTCTGTTTCACTTTTATAAGGCT 59.054 40.000 0.00 0.00 35.61 4.58
140 141 5.944007 TCCCTCTGTTTCACTTTTATAAGGC 59.056 40.000 0.00 0.00 35.61 4.35
141 142 7.168905 ACTCCCTCTGTTTCACTTTTATAAGG 58.831 38.462 0.00 0.00 35.61 2.69
142 143 9.152595 GTACTCCCTCTGTTTCACTTTTATAAG 57.847 37.037 0.00 0.00 37.40 1.73
143 144 8.877195 AGTACTCCCTCTGTTTCACTTTTATAA 58.123 33.333 0.00 0.00 0.00 0.98
144 145 8.431910 AGTACTCCCTCTGTTTCACTTTTATA 57.568 34.615 0.00 0.00 0.00 0.98
145 146 7.317722 AGTACTCCCTCTGTTTCACTTTTAT 57.682 36.000 0.00 0.00 0.00 1.40
146 147 6.742559 AGTACTCCCTCTGTTTCACTTTTA 57.257 37.500 0.00 0.00 0.00 1.52
147 148 5.632034 AGTACTCCCTCTGTTTCACTTTT 57.368 39.130 0.00 0.00 0.00 2.27
148 149 5.839606 ACTAGTACTCCCTCTGTTTCACTTT 59.160 40.000 0.00 0.00 0.00 2.66
149 150 5.395611 ACTAGTACTCCCTCTGTTTCACTT 58.604 41.667 0.00 0.00 0.00 3.16
150 151 5.000570 ACTAGTACTCCCTCTGTTTCACT 57.999 43.478 0.00 0.00 0.00 3.41
151 152 6.208204 TGTTACTAGTACTCCCTCTGTTTCAC 59.792 42.308 0.91 0.00 0.00 3.18
152 153 6.309357 TGTTACTAGTACTCCCTCTGTTTCA 58.691 40.000 0.91 0.00 0.00 2.69
153 154 6.830873 TGTTACTAGTACTCCCTCTGTTTC 57.169 41.667 0.91 0.00 0.00 2.78
154 155 8.334734 TCTATGTTACTAGTACTCCCTCTGTTT 58.665 37.037 0.91 0.00 0.00 2.83
155 156 7.774625 GTCTATGTTACTAGTACTCCCTCTGTT 59.225 40.741 0.91 0.00 0.00 3.16
156 157 7.127647 AGTCTATGTTACTAGTACTCCCTCTGT 59.872 40.741 0.91 0.00 0.00 3.41
157 158 7.511268 AGTCTATGTTACTAGTACTCCCTCTG 58.489 42.308 0.91 0.00 0.00 3.35
158 159 7.695074 AGTCTATGTTACTAGTACTCCCTCT 57.305 40.000 0.91 0.00 0.00 3.69
187 188 9.765795 GGATTAACTTAGACTAGTAATGCATGT 57.234 33.333 0.00 0.00 0.00 3.21
188 189 9.209175 GGGATTAACTTAGACTAGTAATGCATG 57.791 37.037 0.00 0.00 0.00 4.06
189 190 8.376270 GGGGATTAACTTAGACTAGTAATGCAT 58.624 37.037 0.00 0.00 0.00 3.96
190 191 7.470981 CGGGGATTAACTTAGACTAGTAATGCA 60.471 40.741 0.00 0.00 0.00 3.96
191 192 6.867293 CGGGGATTAACTTAGACTAGTAATGC 59.133 42.308 0.00 0.00 0.00 3.56
192 193 7.949434 ACGGGGATTAACTTAGACTAGTAATG 58.051 38.462 0.00 0.00 0.00 1.90
193 194 8.544687 AACGGGGATTAACTTAGACTAGTAAT 57.455 34.615 0.00 0.00 0.00 1.89
194 195 7.961326 AACGGGGATTAACTTAGACTAGTAA 57.039 36.000 0.00 0.00 0.00 2.24
195 196 9.071276 CATAACGGGGATTAACTTAGACTAGTA 57.929 37.037 0.00 0.00 0.00 1.82
196 197 7.015001 CCATAACGGGGATTAACTTAGACTAGT 59.985 40.741 0.00 0.00 0.00 2.57
197 198 7.376615 CCATAACGGGGATTAACTTAGACTAG 58.623 42.308 0.00 0.00 0.00 2.57
198 199 7.294017 CCATAACGGGGATTAACTTAGACTA 57.706 40.000 0.00 0.00 0.00 2.59
199 200 6.170846 CCATAACGGGGATTAACTTAGACT 57.829 41.667 0.00 0.00 0.00 3.24
216 217 4.652421 TGTACCCATGAGACTACCCATAAC 59.348 45.833 0.00 0.00 0.00 1.89
378 379 3.851098 CCTCCTCAGGTACTTCGAAAAG 58.149 50.000 0.00 0.00 34.60 2.27
379 380 2.028385 GCCTCCTCAGGTACTTCGAAAA 60.028 50.000 0.00 0.00 42.74 2.29
380 381 1.549170 GCCTCCTCAGGTACTTCGAAA 59.451 52.381 0.00 0.00 42.74 3.46
383 384 1.433879 CGCCTCCTCAGGTACTTCG 59.566 63.158 0.00 0.00 42.74 3.79
785 791 0.931005 GCGAAGAAGGCAAGTATCGG 59.069 55.000 0.00 0.00 0.00 4.18
952 967 2.663196 CCACCACGACCTCCTTCC 59.337 66.667 0.00 0.00 0.00 3.46
954 969 2.122547 ACCCACCACGACCTCCTT 60.123 61.111 0.00 0.00 0.00 3.36
962 977 2.465860 TCAGTAAATCACCCACCACG 57.534 50.000 0.00 0.00 0.00 4.94
963 978 4.082245 CCAAATCAGTAAATCACCCACCAC 60.082 45.833 0.00 0.00 0.00 4.16
968 983 3.031013 CCCCCAAATCAGTAAATCACCC 58.969 50.000 0.00 0.00 0.00 4.61
1117 1133 2.439104 GGGGAGAAGCGAGCTGGAT 61.439 63.158 0.00 0.00 0.00 3.41
1166 1182 0.595095 GCAAAGTCACAAGCAGGAGG 59.405 55.000 0.00 0.00 0.00 4.30
1232 1267 1.758440 TTGTTCTCTGCTCCAGCCGT 61.758 55.000 0.00 0.00 41.18 5.68
1382 1418 1.066858 GCTATGGCAAGATAGGCGCTA 60.067 52.381 7.64 0.00 38.54 4.26
1394 1430 1.305219 AAAGAAAGCGCGCTATGGCA 61.305 50.000 36.73 0.00 38.60 4.92
1426 1462 8.778358 GCTTCCGAGTGAGAAATGATTATTTAT 58.222 33.333 0.00 0.00 36.66 1.40
1427 1463 7.768582 TGCTTCCGAGTGAGAAATGATTATTTA 59.231 33.333 0.00 0.00 36.66 1.40
1431 1467 5.084818 TGCTTCCGAGTGAGAAATGATTA 57.915 39.130 0.00 0.00 0.00 1.75
1501 1537 2.917933 TCAGAATTTATCCTGCCACGG 58.082 47.619 0.00 0.00 0.00 4.94
1572 1608 6.397272 CCAATCTAGGTAAAAGCAATGCAAA 58.603 36.000 8.35 0.00 0.00 3.68
1589 1625 5.537295 CCATTCCATTGATCAAGCCAATCTA 59.463 40.000 14.54 0.00 32.40 1.98
1644 1680 9.355916 CATGTCCTCCTATAGAAATCCGATATA 57.644 37.037 0.00 0.00 0.00 0.86
1797 1833 8.601845 TGCTACATTGCGTCAGTAAATTATAT 57.398 30.769 0.00 0.00 35.36 0.86
1819 1855 5.314529 AGCATATCATGTTTGCTCTATGCT 58.685 37.500 12.03 8.60 42.88 3.79
2170 2207 2.394930 TGCGCTCAATTAAGTAGGCA 57.605 45.000 9.73 0.00 0.00 4.75
2225 2262 1.069513 TGTGCTTAAGTGTGCCTACGT 59.930 47.619 4.02 0.00 0.00 3.57
2249 2286 9.027202 GTATATTCCCAAGGTTAAGAAAACCAA 57.973 33.333 9.44 0.00 42.69 3.67
3053 3217 2.436173 CCCTCTAAGGCTCTAAAGTGGG 59.564 54.545 10.13 10.13 36.67 4.61
3292 3463 5.063204 CAGTCTCACAAAATTGTACTCCCA 58.937 41.667 0.00 0.00 39.91 4.37
3450 3621 7.886405 AGAGACCAAGTTACGAAACTAAATC 57.114 36.000 0.00 0.00 45.37 2.17


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

AutoCloner maintained by Alex Coulton.