Multiple sequence alignment - TraesCS3B01G332100

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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 TraesCS3B01G332100 chr3B 100.000 3963 0 0 1 3963 537470271 537466309 0.000000e+00 7319.0
1 TraesCS3B01G332100 chr3D 94.622 3496 123 29 153 3616 411005806 411002344 0.000000e+00 5354.0
2 TraesCS3B01G332100 chr3D 93.352 361 17 4 3603 3963 411000906 411000553 9.750000e-146 527.0
3 TraesCS3B01G332100 chr3A 95.301 3022 102 13 267 3268 540653930 540656931 0.000000e+00 4758.0
4 TraesCS3B01G332100 chr3A 90.117 597 47 7 3269 3865 540656962 540657546 0.000000e+00 765.0
5 TraesCS3B01G332100 chr3A 94.340 53 2 1 153 204 540653539 540653591 3.280000e-11 80.5
6 TraesCS3B01G332100 chr4B 90.435 115 11 0 1 115 9467165 9467279 6.860000e-33 152.0
7 TraesCS3B01G332100 chr4B 87.719 114 14 0 2 115 37925899 37926012 2.480000e-27 134.0
8 TraesCS3B01G332100 chr1B 86.441 118 16 0 1 118 684976556 684976439 3.210000e-26 130.0
9 TraesCS3B01G332100 chr7B 85.593 118 17 0 1 118 112124904 112124787 1.500000e-24 124.0
10 TraesCS3B01G332100 chr7B 81.818 121 22 0 1 121 663972953 663972833 7.010000e-18 102.0
11 TraesCS3B01G332100 chr1A 81.513 119 20 2 1 118 587851904 587851787 3.260000e-16 97.1
12 TraesCS3B01G332100 chrUn 100.000 28 0 0 3173 3200 86615134 86615161 7.000000e-03 52.8


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 TraesCS3B01G332100 chr3B 537466309 537470271 3962 True 7319.000000 7319 100.000000 1 3963 1 chr3B.!!$R1 3962
1 TraesCS3B01G332100 chr3D 411000553 411005806 5253 True 2940.500000 5354 93.987000 153 3963 2 chr3D.!!$R1 3810
2 TraesCS3B01G332100 chr3A 540653539 540657546 4007 False 1867.833333 4758 93.252667 153 3865 3 chr3A.!!$F1 3712

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
114 115 0.035630 GTGCCTGTTGGAGATGCTCT 60.036 55.0 0.00 0.00 34.57 4.09 F
821 1166 0.109272 TGAGCGTTGACGTCATCTCC 60.109 55.0 26.22 17.21 42.22 3.71 F
1149 1501 0.603065 GCCGATTTCCCTTTTGCTGT 59.397 50.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2376 0.106769 TGGAGCCAGCTTTGTTGTGA 60.107 50.0 0.00 0.0 0.00 3.58 R
2533 2889 0.536233 TGTGTACCACCGCATGCTTT 60.536 50.0 17.13 0.0 32.73 3.51 R
3001 3357 0.380378 GCAAGGTCAAACGAGCACAA 59.620 50.0 0.00 0.0 33.19 3.33 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 1.542544 GCATTTTAGCGCTTCTGCTG 58.457 50.000 18.68 8.77 46.70 4.41
20 21 1.796617 GCATTTTAGCGCTTCTGCTGG 60.797 52.381 18.68 0.56 46.70 4.85
21 22 1.739466 CATTTTAGCGCTTCTGCTGGA 59.261 47.619 18.68 0.00 46.70 3.86
22 23 1.442769 TTTTAGCGCTTCTGCTGGAG 58.557 50.000 18.68 0.00 46.70 3.86
23 24 1.021390 TTTAGCGCTTCTGCTGGAGC 61.021 55.000 18.68 13.69 46.70 4.70
51 52 3.849953 CGACGCGCCAAACCTAGC 61.850 66.667 5.73 0.00 0.00 3.42
57 58 3.668386 GCCAAACCTAGCGTTGCT 58.332 55.556 0.00 0.00 43.41 3.91
58 59 1.956802 GCCAAACCTAGCGTTGCTT 59.043 52.632 0.00 0.00 40.44 3.91
59 60 0.387239 GCCAAACCTAGCGTTGCTTG 60.387 55.000 0.00 0.00 40.44 4.01
60 61 0.387239 CCAAACCTAGCGTTGCTTGC 60.387 55.000 0.00 0.00 40.44 4.01
61 62 0.725784 CAAACCTAGCGTTGCTTGCG 60.726 55.000 0.00 0.00 40.44 4.85
74 75 3.762293 TTGCGCTGCAAACCAGAT 58.238 50.000 9.73 0.00 45.96 2.90
75 76 2.040330 TTGCGCTGCAAACCAGATT 58.960 47.368 9.73 0.00 45.96 2.40
76 77 0.388659 TTGCGCTGCAAACCAGATTT 59.611 45.000 9.73 0.00 45.96 2.17
77 78 0.388659 TGCGCTGCAAACCAGATTTT 59.611 45.000 9.73 0.00 44.64 1.82
78 79 1.611006 TGCGCTGCAAACCAGATTTTA 59.389 42.857 9.73 0.00 44.64 1.52
79 80 2.253603 GCGCTGCAAACCAGATTTTAG 58.746 47.619 0.00 0.00 44.64 1.85
80 81 2.253603 CGCTGCAAACCAGATTTTAGC 58.746 47.619 0.00 0.00 44.64 3.09
81 82 2.351641 CGCTGCAAACCAGATTTTAGCA 60.352 45.455 0.00 0.00 44.64 3.49
82 83 2.989166 GCTGCAAACCAGATTTTAGCAC 59.011 45.455 0.00 0.00 44.64 4.40
83 84 3.236816 CTGCAAACCAGATTTTAGCACG 58.763 45.455 0.00 0.00 44.64 5.34
84 85 1.985684 GCAAACCAGATTTTAGCACGC 59.014 47.619 0.00 0.00 0.00 5.34
85 86 2.595386 CAAACCAGATTTTAGCACGCC 58.405 47.619 0.00 0.00 0.00 5.68
86 87 0.802494 AACCAGATTTTAGCACGCCG 59.198 50.000 0.00 0.00 0.00 6.46
87 88 1.062525 CCAGATTTTAGCACGCCGC 59.937 57.895 0.00 0.00 42.91 6.53
103 104 3.216292 GCGTGTTGGGTGCCTGTT 61.216 61.111 0.00 0.00 0.00 3.16
104 105 2.721231 CGTGTTGGGTGCCTGTTG 59.279 61.111 0.00 0.00 0.00 3.33
105 106 2.844451 CGTGTTGGGTGCCTGTTGG 61.844 63.158 0.00 0.00 0.00 3.77
106 107 1.454847 GTGTTGGGTGCCTGTTGGA 60.455 57.895 0.00 0.00 34.57 3.53
107 108 1.152777 TGTTGGGTGCCTGTTGGAG 60.153 57.895 0.00 0.00 34.57 3.86
108 109 1.150536 GTTGGGTGCCTGTTGGAGA 59.849 57.895 0.00 0.00 34.57 3.71
109 110 0.251341 GTTGGGTGCCTGTTGGAGAT 60.251 55.000 0.00 0.00 34.57 2.75
110 111 0.251297 TTGGGTGCCTGTTGGAGATG 60.251 55.000 0.00 0.00 34.57 2.90
111 112 2.048603 GGGTGCCTGTTGGAGATGC 61.049 63.158 0.00 0.00 34.57 3.91
112 113 1.001641 GGTGCCTGTTGGAGATGCT 60.002 57.895 0.00 0.00 34.57 3.79
113 114 1.028868 GGTGCCTGTTGGAGATGCTC 61.029 60.000 0.00 0.00 34.57 4.26
114 115 0.035630 GTGCCTGTTGGAGATGCTCT 60.036 55.000 0.00 0.00 34.57 4.09
115 116 0.694771 TGCCTGTTGGAGATGCTCTT 59.305 50.000 0.00 0.00 34.57 2.85
116 117 1.908619 TGCCTGTTGGAGATGCTCTTA 59.091 47.619 0.00 0.00 34.57 2.10
117 118 2.284190 GCCTGTTGGAGATGCTCTTAC 58.716 52.381 0.00 0.00 34.57 2.34
118 119 2.911484 CCTGTTGGAGATGCTCTTACC 58.089 52.381 0.00 0.00 34.57 2.85
119 120 2.237143 CCTGTTGGAGATGCTCTTACCA 59.763 50.000 0.00 0.00 34.57 3.25
120 121 3.307691 CCTGTTGGAGATGCTCTTACCAA 60.308 47.826 0.00 0.00 38.12 3.67
123 124 3.895232 TGGAGATGCTCTTACCAACTC 57.105 47.619 0.00 0.00 33.05 3.01
124 125 3.445008 TGGAGATGCTCTTACCAACTCT 58.555 45.455 0.00 0.00 33.96 3.24
125 126 3.449018 TGGAGATGCTCTTACCAACTCTC 59.551 47.826 0.00 0.00 33.96 3.20
126 127 3.490078 GGAGATGCTCTTACCAACTCTCG 60.490 52.174 0.00 0.00 33.96 4.04
127 128 2.159170 AGATGCTCTTACCAACTCTCGC 60.159 50.000 0.00 0.00 0.00 5.03
128 129 1.257743 TGCTCTTACCAACTCTCGCT 58.742 50.000 0.00 0.00 0.00 4.93
129 130 1.618837 TGCTCTTACCAACTCTCGCTT 59.381 47.619 0.00 0.00 0.00 4.68
130 131 2.823747 TGCTCTTACCAACTCTCGCTTA 59.176 45.455 0.00 0.00 0.00 3.09
131 132 3.180613 GCTCTTACCAACTCTCGCTTAC 58.819 50.000 0.00 0.00 0.00 2.34
132 133 3.427243 CTCTTACCAACTCTCGCTTACG 58.573 50.000 0.00 0.00 42.01 3.18
133 134 2.816087 TCTTACCAACTCTCGCTTACGT 59.184 45.455 0.00 0.00 41.18 3.57
134 135 2.907910 TACCAACTCTCGCTTACGTC 57.092 50.000 0.00 0.00 41.18 4.34
135 136 1.245732 ACCAACTCTCGCTTACGTCT 58.754 50.000 0.00 0.00 41.18 4.18
136 137 1.068472 ACCAACTCTCGCTTACGTCTG 60.068 52.381 0.00 0.00 41.18 3.51
137 138 1.068472 CCAACTCTCGCTTACGTCTGT 60.068 52.381 0.00 0.00 41.18 3.41
138 139 2.161012 CCAACTCTCGCTTACGTCTGTA 59.839 50.000 0.00 0.00 41.18 2.74
139 140 3.162068 CAACTCTCGCTTACGTCTGTAC 58.838 50.000 0.00 0.00 41.18 2.90
140 141 2.697654 ACTCTCGCTTACGTCTGTACT 58.302 47.619 0.00 0.00 41.18 2.73
141 142 2.415857 ACTCTCGCTTACGTCTGTACTG 59.584 50.000 0.00 0.00 41.18 2.74
142 143 1.129998 TCTCGCTTACGTCTGTACTGC 59.870 52.381 0.00 0.00 41.18 4.40
143 144 0.179207 TCGCTTACGTCTGTACTGCG 60.179 55.000 12.64 12.64 46.31 5.18
144 145 0.453950 CGCTTACGTCTGTACTGCGT 60.454 55.000 19.61 19.61 43.12 5.24
145 146 1.694639 GCTTACGTCTGTACTGCGTT 58.305 50.000 20.42 10.09 39.64 4.84
146 147 2.725759 CGCTTACGTCTGTACTGCGTTA 60.726 50.000 20.42 13.91 43.12 3.18
147 148 3.236816 GCTTACGTCTGTACTGCGTTAA 58.763 45.455 20.42 13.87 39.64 2.01
148 149 3.670055 GCTTACGTCTGTACTGCGTTAAA 59.330 43.478 20.42 12.53 39.64 1.52
149 150 4.148696 GCTTACGTCTGTACTGCGTTAAAA 59.851 41.667 20.42 12.05 39.64 1.52
150 151 5.332506 GCTTACGTCTGTACTGCGTTAAAAA 60.333 40.000 20.42 11.81 39.64 1.94
256 583 6.993786 TTTTTGAAGTCAGTATGTGTGTGA 57.006 33.333 0.00 0.00 37.40 3.58
373 700 7.253817 CGAGAAATCTTGAAAACGTAGATCCTC 60.254 40.741 12.76 12.76 31.63 3.71
535 865 0.534877 GGATACGCATGCACATCCCA 60.535 55.000 26.52 3.49 32.38 4.37
584 918 2.175236 GCTTCTCTCAAAAGCCCCG 58.825 57.895 0.00 0.00 42.63 5.73
691 1036 0.179134 GCCCGCACACTACTAGACTG 60.179 60.000 0.00 0.00 0.00 3.51
714 1059 1.201647 GTACGGAGTGCTGAGCTACAA 59.798 52.381 5.83 0.00 45.73 2.41
726 1071 3.982475 TGAGCTACAACACTTGTCTCTG 58.018 45.455 0.00 0.00 44.12 3.35
812 1157 2.838386 TATCTACGGTGAGCGTTGAC 57.162 50.000 21.65 0.00 0.00 3.18
819 1164 0.388649 GGTGAGCGTTGACGTCATCT 60.389 55.000 20.80 16.23 42.22 2.90
821 1166 0.109272 TGAGCGTTGACGTCATCTCC 60.109 55.000 26.22 17.21 42.22 3.71
926 1274 8.127327 GCGTCTACAAAGTATCTGTGTCTATAA 58.873 37.037 0.00 0.00 33.52 0.98
927 1275 9.435802 CGTCTACAAAGTATCTGTGTCTATAAC 57.564 37.037 0.00 0.00 33.52 1.89
950 1298 5.588648 ACTCTATATATCTTGCTCTCTCCGC 59.411 44.000 0.00 0.00 0.00 5.54
1032 1384 3.717294 ATGGAGGAAGCCGCCGTT 61.717 61.111 1.82 0.00 46.74 4.44
1133 1485 2.309528 TCATGCACCTTAGTTAGCCG 57.690 50.000 0.00 0.00 0.00 5.52
1144 1496 4.948004 CCTTAGTTAGCCGATTTCCCTTTT 59.052 41.667 0.00 0.00 0.00 2.27
1145 1497 5.163652 CCTTAGTTAGCCGATTTCCCTTTTG 60.164 44.000 0.00 0.00 0.00 2.44
1146 1498 2.492088 AGTTAGCCGATTTCCCTTTTGC 59.508 45.455 0.00 0.00 0.00 3.68
1147 1499 2.492088 GTTAGCCGATTTCCCTTTTGCT 59.508 45.455 0.00 0.00 0.00 3.91
1148 1500 0.890683 AGCCGATTTCCCTTTTGCTG 59.109 50.000 0.00 0.00 0.00 4.41
1149 1501 0.603065 GCCGATTTCCCTTTTGCTGT 59.397 50.000 0.00 0.00 0.00 4.40
1150 1502 1.816224 GCCGATTTCCCTTTTGCTGTA 59.184 47.619 0.00 0.00 0.00 2.74
1151 1503 2.415491 GCCGATTTCCCTTTTGCTGTAC 60.415 50.000 0.00 0.00 0.00 2.90
1383 1735 2.674084 GGACGTTTTCTTCGGCCGG 61.674 63.158 27.83 10.69 46.56 6.13
1470 1826 2.427506 GTTCCTCTTGCACCGATCTTT 58.572 47.619 0.00 0.00 0.00 2.52
1492 1848 3.696051 TCAGCCTAATTGATCTTGTTGGC 59.304 43.478 10.22 10.22 39.40 4.52
1560 1916 1.272769 GCCGGTGTACAAGAAGACTCT 59.727 52.381 1.90 0.00 0.00 3.24
1634 1990 1.762419 GCTACTGTTCACGTCGTTCA 58.238 50.000 0.00 0.00 0.00 3.18
1792 2148 2.182030 CTCTCCCTCGTCGTTGCC 59.818 66.667 0.00 0.00 0.00 4.52
2263 2619 1.971167 GATGTTCCCCGTGCTGCAA 60.971 57.895 2.77 0.00 0.00 4.08
2533 2889 2.231380 GGAGGGCTTCCAGGACCAA 61.231 63.158 11.31 0.00 46.01 3.67
2539 2895 1.260544 GCTTCCAGGACCAAAAGCAT 58.739 50.000 16.35 0.00 42.80 3.79
2548 2904 0.538516 ACCAAAAGCATGCGGTGGTA 60.539 50.000 29.91 0.00 40.80 3.25
2900 3256 0.826715 CGAGGAAGGGCAGATCAGAA 59.173 55.000 0.00 0.00 0.00 3.02
2902 3258 2.158842 CGAGGAAGGGCAGATCAGAATT 60.159 50.000 0.00 0.00 0.00 2.17
3156 3515 8.023128 GTCATGTTACATGTTTCTAGTTGCATT 58.977 33.333 22.58 0.00 0.00 3.56
3157 3516 9.225436 TCATGTTACATGTTTCTAGTTGCATTA 57.775 29.630 22.58 0.00 0.00 1.90
3169 3528 7.377766 TCTAGTTGCATTATCCTTTGTGTTC 57.622 36.000 0.00 0.00 0.00 3.18
3317 3706 0.608640 ACTAGGCCAGGACAAAGTCG 59.391 55.000 5.01 0.00 32.65 4.18
3321 3710 2.030562 CCAGGACAAAGTCGCGGT 59.969 61.111 6.13 0.00 32.65 5.68
3370 3759 4.462132 TGCTTATTGGCAGCTTCATTGTTA 59.538 37.500 0.00 0.00 38.19 2.41
3393 3782 3.813724 TCATCAATAGCAATGCAGAGAGC 59.186 43.478 8.35 0.00 45.96 4.09
3408 3798 2.171659 AGAGAGCTCGAGGATGTAGTCA 59.828 50.000 15.58 0.00 34.09 3.41
3539 3929 2.278531 GCGGTGCGTTGTGCTTTT 60.279 55.556 0.00 0.00 46.63 2.27
3601 3991 8.167605 CAATGATGCTGAGAAAATCCTCTATT 57.832 34.615 0.00 0.00 34.38 1.73
3669 5509 5.445964 TGCTTCTCAAAACCCTAAGAGTTT 58.554 37.500 0.00 0.00 39.07 2.66
3676 5516 6.902408 TCAAAACCCTAAGAGTTTCTTACCA 58.098 36.000 0.00 0.00 37.89 3.25
3699 5539 9.905713 ACCAGAAGAATTAGTTGATGCTTTATA 57.094 29.630 0.00 0.00 0.00 0.98
3841 5681 2.033299 CACCCGATGTCATAATTGGTGC 59.967 50.000 8.68 0.00 29.93 5.01
3870 5710 5.104527 TTGGAACATTAGAGGTATGACCTGG 60.105 44.000 2.07 0.00 45.12 4.45
3927 5767 7.815068 TCCAAGAGACTAAAGATTCTTTTCTCG 59.185 37.037 22.96 15.36 0.00 4.04
3929 5769 9.364989 CAAGAGACTAAAGATTCTTTTCTCGAT 57.635 33.333 22.96 17.37 0.00 3.59
3936 5776 7.872113 AAAGATTCTTTTCTCGATGCCTTAT 57.128 32.000 5.82 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.849953 GCTAGGTTTGGCGCGTCG 61.850 66.667 6.09 0.00 0.00 5.12
40 41 0.387239 CAAGCAACGCTAGGTTTGGC 60.387 55.000 0.00 0.00 38.25 4.52
41 42 0.387239 GCAAGCAACGCTAGGTTTGG 60.387 55.000 0.00 0.00 38.25 3.28
42 43 0.725784 CGCAAGCAACGCTAGGTTTG 60.726 55.000 0.00 0.00 38.25 2.93
43 44 1.574428 CGCAAGCAACGCTAGGTTT 59.426 52.632 0.00 0.00 38.25 3.27
44 45 3.253955 CGCAAGCAACGCTAGGTT 58.746 55.556 0.00 0.00 38.25 3.50
58 59 0.388659 AAAATCTGGTTTGCAGCGCA 59.611 45.000 11.47 0.00 36.47 6.09
59 60 2.253603 CTAAAATCTGGTTTGCAGCGC 58.746 47.619 0.00 0.00 0.00 5.92
60 61 2.253603 GCTAAAATCTGGTTTGCAGCG 58.746 47.619 4.97 0.00 32.41 5.18
61 62 2.989166 GTGCTAAAATCTGGTTTGCAGC 59.011 45.455 11.38 11.38 38.35 5.25
62 63 3.236816 CGTGCTAAAATCTGGTTTGCAG 58.763 45.455 0.00 0.00 30.54 4.41
63 64 2.606795 GCGTGCTAAAATCTGGTTTGCA 60.607 45.455 0.00 0.00 0.00 4.08
64 65 1.985684 GCGTGCTAAAATCTGGTTTGC 59.014 47.619 0.00 0.00 0.00 3.68
65 66 2.595386 GGCGTGCTAAAATCTGGTTTG 58.405 47.619 0.00 0.00 0.00 2.93
66 67 1.199097 CGGCGTGCTAAAATCTGGTTT 59.801 47.619 0.00 0.00 0.00 3.27
67 68 0.802494 CGGCGTGCTAAAATCTGGTT 59.198 50.000 0.00 0.00 0.00 3.67
68 69 1.644786 GCGGCGTGCTAAAATCTGGT 61.645 55.000 9.37 0.00 41.73 4.00
69 70 1.062525 GCGGCGTGCTAAAATCTGG 59.937 57.895 9.37 0.00 41.73 3.86
70 71 1.296867 CGCGGCGTGCTAAAATCTG 60.297 57.895 15.36 0.00 43.27 2.90
71 72 1.740296 ACGCGGCGTGCTAAAATCT 60.740 52.632 28.88 0.00 43.27 2.40
72 73 2.782615 ACGCGGCGTGCTAAAATC 59.217 55.556 28.88 0.00 43.27 2.17
86 87 3.216292 AACAGGCACCCAACACGC 61.216 61.111 0.00 0.00 0.00 5.34
87 88 2.721231 CAACAGGCACCCAACACG 59.279 61.111 0.00 0.00 0.00 4.49
88 89 1.454847 TCCAACAGGCACCCAACAC 60.455 57.895 0.00 0.00 0.00 3.32
89 90 1.152777 CTCCAACAGGCACCCAACA 60.153 57.895 0.00 0.00 0.00 3.33
90 91 0.251341 ATCTCCAACAGGCACCCAAC 60.251 55.000 0.00 0.00 0.00 3.77
91 92 0.251297 CATCTCCAACAGGCACCCAA 60.251 55.000 0.00 0.00 0.00 4.12
92 93 1.379916 CATCTCCAACAGGCACCCA 59.620 57.895 0.00 0.00 0.00 4.51
93 94 2.048603 GCATCTCCAACAGGCACCC 61.049 63.158 0.00 0.00 0.00 4.61
94 95 1.001641 AGCATCTCCAACAGGCACC 60.002 57.895 0.00 0.00 0.00 5.01
95 96 2.475666 GAGCATCTCCAACAGGCAC 58.524 57.895 0.00 0.00 0.00 5.01
107 108 2.159170 AGCGAGAGTTGGTAAGAGCATC 60.159 50.000 0.00 0.00 0.00 3.91
108 109 1.827969 AGCGAGAGTTGGTAAGAGCAT 59.172 47.619 0.00 0.00 0.00 3.79
109 110 1.257743 AGCGAGAGTTGGTAAGAGCA 58.742 50.000 0.00 0.00 0.00 4.26
110 111 2.371910 AAGCGAGAGTTGGTAAGAGC 57.628 50.000 0.00 0.00 0.00 4.09
111 112 3.119919 ACGTAAGCGAGAGTTGGTAAGAG 60.120 47.826 0.00 0.00 45.62 2.85
112 113 2.816087 ACGTAAGCGAGAGTTGGTAAGA 59.184 45.455 0.00 0.00 45.62 2.10
113 114 3.119919 AGACGTAAGCGAGAGTTGGTAAG 60.120 47.826 0.00 0.00 45.62 2.34
114 115 2.816087 AGACGTAAGCGAGAGTTGGTAA 59.184 45.455 0.00 0.00 45.62 2.85
115 116 2.161012 CAGACGTAAGCGAGAGTTGGTA 59.839 50.000 0.00 0.00 45.62 3.25
116 117 1.068472 CAGACGTAAGCGAGAGTTGGT 60.068 52.381 0.00 0.00 45.62 3.67
117 118 1.068472 ACAGACGTAAGCGAGAGTTGG 60.068 52.381 0.00 0.00 45.62 3.77
118 119 2.333389 ACAGACGTAAGCGAGAGTTG 57.667 50.000 0.00 0.00 45.62 3.16
119 120 3.072944 AGTACAGACGTAAGCGAGAGTT 58.927 45.455 0.00 0.00 45.62 3.01
120 121 2.415857 CAGTACAGACGTAAGCGAGAGT 59.584 50.000 0.00 0.00 45.62 3.24
121 122 2.788407 GCAGTACAGACGTAAGCGAGAG 60.788 54.545 0.00 0.00 45.62 3.20
122 123 1.129998 GCAGTACAGACGTAAGCGAGA 59.870 52.381 0.00 0.00 45.62 4.04
123 124 1.536149 GCAGTACAGACGTAAGCGAG 58.464 55.000 0.00 0.00 45.62 5.03
124 125 3.689224 GCAGTACAGACGTAAGCGA 57.311 52.632 0.00 0.00 45.62 4.93
125 126 2.266373 CGCAGTACAGACGTAAGCG 58.734 57.895 0.00 0.00 43.41 4.68
126 127 1.694639 AACGCAGTACAGACGTAAGC 58.305 50.000 8.03 0.00 45.00 3.09
127 128 5.811018 TTTTAACGCAGTACAGACGTAAG 57.189 39.130 8.03 0.00 45.00 2.34
235 562 6.345298 TCTTCACACACATACTGACTTCAAA 58.655 36.000 0.00 0.00 0.00 2.69
236 563 5.912892 TCTTCACACACATACTGACTTCAA 58.087 37.500 0.00 0.00 0.00 2.69
237 564 5.529581 TCTTCACACACATACTGACTTCA 57.470 39.130 0.00 0.00 0.00 3.02
239 566 7.624360 TTTTTCTTCACACACATACTGACTT 57.376 32.000 0.00 0.00 0.00 3.01
240 567 7.283127 ACATTTTTCTTCACACACATACTGACT 59.717 33.333 0.00 0.00 0.00 3.41
241 568 7.417612 ACATTTTTCTTCACACACATACTGAC 58.582 34.615 0.00 0.00 0.00 3.51
243 570 9.897744 ATAACATTTTTCTTCACACACATACTG 57.102 29.630 0.00 0.00 0.00 2.74
245 572 8.638565 GCATAACATTTTTCTTCACACACATAC 58.361 33.333 0.00 0.00 0.00 2.39
246 573 7.812191 GGCATAACATTTTTCTTCACACACATA 59.188 33.333 0.00 0.00 0.00 2.29
247 574 6.646240 GGCATAACATTTTTCTTCACACACAT 59.354 34.615 0.00 0.00 0.00 3.21
248 575 5.982516 GGCATAACATTTTTCTTCACACACA 59.017 36.000 0.00 0.00 0.00 3.72
249 576 5.116983 CGGCATAACATTTTTCTTCACACAC 59.883 40.000 0.00 0.00 0.00 3.82
256 583 5.957842 TCTGACGGCATAACATTTTTCTT 57.042 34.783 0.00 0.00 0.00 2.52
373 700 1.064208 AGATTGATGTCGACGGACTCG 59.936 52.381 11.62 0.00 43.79 4.18
535 865 4.719369 GGACACGTCGCTTCGGCT 62.719 66.667 0.00 0.00 39.13 5.52
584 918 0.882474 CCCCGGACGATCTATCTGAC 59.118 60.000 0.73 0.00 0.00 3.51
619 961 2.267642 CGGAGATTGGGAACGGCA 59.732 61.111 0.00 0.00 0.00 5.69
691 1036 2.202623 CTCAGCACTCCGTACGCC 60.203 66.667 10.49 0.00 0.00 5.68
714 1059 0.962489 CGAGGGACAGAGACAAGTGT 59.038 55.000 0.00 0.00 0.00 3.55
760 1105 9.647918 AAAAGGGATTAGAAAAAGAGAAGAAGT 57.352 29.630 0.00 0.00 0.00 3.01
812 1157 1.226802 CAGCTGACCGGAGATGACG 60.227 63.158 9.46 0.00 0.00 4.35
926 1274 5.588648 GCGGAGAGAGCAAGATATATAGAGT 59.411 44.000 0.00 0.00 34.19 3.24
927 1275 5.008613 GGCGGAGAGAGCAAGATATATAGAG 59.991 48.000 0.00 0.00 36.08 2.43
928 1276 4.884744 GGCGGAGAGAGCAAGATATATAGA 59.115 45.833 0.00 0.00 36.08 1.98
929 1277 4.260990 CGGCGGAGAGAGCAAGATATATAG 60.261 50.000 0.00 0.00 36.08 1.31
930 1278 3.628032 CGGCGGAGAGAGCAAGATATATA 59.372 47.826 0.00 0.00 36.08 0.86
931 1279 2.425312 CGGCGGAGAGAGCAAGATATAT 59.575 50.000 0.00 0.00 36.08 0.86
932 1280 1.813178 CGGCGGAGAGAGCAAGATATA 59.187 52.381 0.00 0.00 36.08 0.86
933 1281 0.600557 CGGCGGAGAGAGCAAGATAT 59.399 55.000 0.00 0.00 36.08 1.63
950 1298 1.659233 TGCAATCCAACTGCAACGG 59.341 52.632 0.00 0.00 46.47 4.44
979 1327 0.961019 CTCTCTGCCTGGCTAGCTAG 59.039 60.000 20.50 20.50 0.00 3.42
980 1328 1.112315 GCTCTCTGCCTGGCTAGCTA 61.112 60.000 21.03 7.83 35.15 3.32
981 1329 2.433994 GCTCTCTGCCTGGCTAGCT 61.434 63.158 21.03 0.00 35.15 3.32
988 1336 0.252479 ACTTCCATGCTCTCTGCCTG 59.748 55.000 0.00 0.00 42.00 4.85
1005 1357 1.306141 TTCCTCCATGGCCGAGACT 60.306 57.895 6.96 0.00 35.26 3.24
1032 1384 3.311110 GCAGGGACAGGGACACGA 61.311 66.667 0.00 0.00 0.00 4.35
1133 1485 4.453136 TGTACGTACAGCAAAAGGGAAATC 59.547 41.667 24.10 0.00 0.00 2.17
1144 1496 4.376210 GCGTGTTAATTTGTACGTACAGCA 60.376 41.667 26.04 18.09 37.52 4.41
1145 1497 4.076985 GCGTGTTAATTTGTACGTACAGC 58.923 43.478 26.04 18.89 37.52 4.40
1146 1498 5.117440 TGAGCGTGTTAATTTGTACGTACAG 59.883 40.000 26.04 13.66 37.52 2.74
1147 1499 4.981054 TGAGCGTGTTAATTTGTACGTACA 59.019 37.500 24.10 24.10 38.67 2.90
1148 1500 5.499268 TGAGCGTGTTAATTTGTACGTAC 57.501 39.130 18.90 18.90 38.67 3.67
1149 1501 5.862860 TCATGAGCGTGTTAATTTGTACGTA 59.137 36.000 0.00 0.00 38.67 3.57
1150 1502 4.687018 TCATGAGCGTGTTAATTTGTACGT 59.313 37.500 0.00 0.00 38.67 3.57
1151 1503 5.061684 TCTCATGAGCGTGTTAATTTGTACG 59.938 40.000 18.36 0.00 39.37 3.67
1360 1712 1.210870 CCGAAGAAAACGTCCGACAA 58.789 50.000 0.00 0.00 0.00 3.18
1470 1826 3.696051 GCCAACAAGATCAATTAGGCTGA 59.304 43.478 0.00 0.00 37.89 4.26
1492 1848 4.505191 CACATCCCCTACAATTAACGTACG 59.495 45.833 15.01 15.01 0.00 3.67
1634 1990 2.107750 CCCGAGCGACATGAGCAT 59.892 61.111 17.25 5.52 37.01 3.79
1775 2131 2.182030 GGCAACGACGAGGGAGAG 59.818 66.667 0.00 0.00 0.00 3.20
1792 2148 1.004595 TGTAGACGATGACGAGGACG 58.995 55.000 0.00 0.00 42.66 4.79
2020 2376 0.106769 TGGAGCCAGCTTTGTTGTGA 60.107 50.000 0.00 0.00 0.00 3.58
2071 2427 4.071875 ACGCACGCCCGGTTCATA 62.072 61.111 0.00 0.00 0.00 2.15
2092 2448 1.078848 CTCCTTGCTCGGGTTCCTG 60.079 63.158 0.00 0.00 0.00 3.86
2311 2667 1.320344 TGCCGAAGACGCTGTAGGAT 61.320 55.000 0.00 0.00 38.29 3.24
2533 2889 0.536233 TGTGTACCACCGCATGCTTT 60.536 50.000 17.13 0.00 32.73 3.51
2539 2895 1.373622 CGACATGTGTACCACCGCA 60.374 57.895 1.15 0.00 32.73 5.69
2548 2904 3.188100 CGCATCGCCGACATGTGT 61.188 61.111 1.15 0.00 0.00 3.72
2900 3256 2.124320 AGCCGCCAACGCCATAAT 60.124 55.556 0.00 0.00 38.22 1.28
2902 3258 4.089239 TCAGCCGCCAACGCCATA 62.089 61.111 0.00 0.00 38.22 2.74
3001 3357 0.380378 GCAAGGTCAAACGAGCACAA 59.620 50.000 0.00 0.00 33.19 3.33
3156 3515 8.856153 TGCTAATTTACTGAACACAAAGGATA 57.144 30.769 0.00 0.00 0.00 2.59
3157 3516 7.759489 TGCTAATTTACTGAACACAAAGGAT 57.241 32.000 0.00 0.00 0.00 3.24
3277 3666 9.597170 CCTAGTGGAAGATATGATATGTTCATG 57.403 37.037 19.81 7.86 39.55 3.07
3299 3688 0.741221 GCGACTTTGTCCTGGCCTAG 60.741 60.000 3.32 0.00 0.00 3.02
3331 3720 2.252260 CAGTCCAGGCAAAACGCG 59.748 61.111 3.53 3.53 43.84 6.01
3366 3755 6.993902 TCTCTGCATTGCTATTGATGATAACA 59.006 34.615 10.49 0.00 0.00 2.41
3370 3759 4.456222 GCTCTCTGCATTGCTATTGATGAT 59.544 41.667 10.49 0.00 42.31 2.45
3387 3776 2.171659 TGACTACATCCTCGAGCTCTCT 59.828 50.000 12.85 0.00 0.00 3.10
3393 3782 5.008217 CCTCTACTTTGACTACATCCTCGAG 59.992 48.000 5.13 5.13 0.00 4.04
3408 3798 3.119424 GCTCGCTACTGTTCCTCTACTTT 60.119 47.826 0.00 0.00 0.00 2.66
3466 3856 1.219393 CTTGGTCTCTTCGCCCTCC 59.781 63.158 0.00 0.00 0.00 4.30
3468 3858 1.768684 TTGCTTGGTCTCTTCGCCCT 61.769 55.000 0.00 0.00 0.00 5.19
3469 3859 1.301677 CTTGCTTGGTCTCTTCGCCC 61.302 60.000 0.00 0.00 0.00 6.13
3470 3860 0.320771 TCTTGCTTGGTCTCTTCGCC 60.321 55.000 0.00 0.00 0.00 5.54
3471 3861 1.195674 GTTCTTGCTTGGTCTCTTCGC 59.804 52.381 0.00 0.00 0.00 4.70
3472 3862 2.478134 CTGTTCTTGCTTGGTCTCTTCG 59.522 50.000 0.00 0.00 0.00 3.79
3528 3918 0.584396 TGCGAGGTAAAAGCACAACG 59.416 50.000 0.00 0.00 35.81 4.10
3539 3929 4.367023 AAAGGCGCGTGCGAGGTA 62.367 61.111 19.66 0.00 44.10 3.08
3601 3991 9.290988 GTCTCACTCCTAATCATGTCTCTAATA 57.709 37.037 0.00 0.00 0.00 0.98
3669 5509 7.624549 AGCATCAACTAATTCTTCTGGTAAGA 58.375 34.615 0.00 0.00 0.00 2.10
3870 5710 7.982224 ACAAAGTCAGGTTTGAACTTACTAAC 58.018 34.615 3.44 0.00 39.40 2.34
3874 5714 6.033966 CCAACAAAGTCAGGTTTGAACTTAC 58.966 40.000 3.44 0.00 39.40 2.34
3927 5767 6.107901 ACTGATAGAACCAGATAAGGCATC 57.892 41.667 0.00 0.00 35.69 3.91
3929 5769 5.957771 AACTGATAGAACCAGATAAGGCA 57.042 39.130 0.00 0.00 35.69 4.75
3936 5776 6.070251 TGCCAAGAATAACTGATAGAACCAGA 60.070 38.462 0.00 0.00 35.69 3.86


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

AutoCloner maintained by Alex Coulton.