Multiple sequence alignment - TraesCS7D01G330800

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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 TraesCS7D01G330800 chr7D 100.000 3317 0 0 1 3317 422209266 422212582 0.000000e+00 6126.0
1 TraesCS7D01G330800 chr7D 89.796 98 9 1 1008 1104 621067871 621067968 1.250000e-24 124.0
2 TraesCS7D01G330800 chr7B 91.975 1919 84 17 436 2329 438881504 438879631 0.000000e+00 2627.0
3 TraesCS7D01G330800 chr7B 88.088 680 40 9 2367 3027 438878274 438877617 0.000000e+00 769.0
4 TraesCS7D01G330800 chr7B 88.557 402 41 5 1 401 438883311 438882914 1.790000e-132 483.0
5 TraesCS7D01G330800 chr7B 92.241 116 8 1 3203 3317 438876796 438876681 2.650000e-36 163.0
6 TraesCS7D01G330800 chr7B 90.991 111 8 1 3045 3155 438877317 438877209 7.410000e-32 148.0
7 TraesCS7D01G330800 chr7B 97.368 38 0 1 409 446 438881570 438881534 2.760000e-06 63.9
8 TraesCS7D01G330800 chr7A 88.694 2114 143 29 275 2333 510908019 510905947 0.000000e+00 2492.0
9 TraesCS7D01G330800 chr7A 86.313 716 48 14 2359 3046 510905880 510905187 0.000000e+00 734.0
10 TraesCS7D01G330800 chr1B 95.165 393 17 2 1296 1687 650473593 650473202 1.310000e-173 619.0
11 TraesCS7D01G330800 chr1B 95.370 108 5 0 1137 1244 650473010 650473117 4.400000e-39 172.0
12 TraesCS7D01G330800 chr1B 95.522 67 3 0 1754 1820 650473206 650473140 1.260000e-19 108.0
13 TraesCS7D01G330800 chr2D 81.745 745 101 15 1008 1728 649879999 649880732 1.020000e-164 590.0
14 TraesCS7D01G330800 chr2A 80.315 762 97 17 1020 1746 734293246 734292503 8.150000e-146 527.0
15 TraesCS7D01G330800 chr3D 83.135 504 65 6 1011 1502 575514726 575514231 3.040000e-120 442.0
16 TraesCS7D01G330800 chr1A 83.410 217 36 0 1181 1397 4159727 4159511 5.610000e-48 202.0


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 TraesCS7D01G330800 chr7D 422209266 422212582 3316 False 6126.000000 6126 100.000000 1 3317 1 chr7D.!!$F1 3316
1 TraesCS7D01G330800 chr7B 438876681 438883311 6630 True 708.983333 2627 91.536667 1 3317 6 chr7B.!!$R1 3316
2 TraesCS7D01G330800 chr7A 510905187 510908019 2832 True 1613.000000 2492 87.503500 275 3046 2 chr7A.!!$R1 2771
3 TraesCS7D01G330800 chr2D 649879999 649880732 733 False 590.000000 590 81.745000 1008 1728 1 chr2D.!!$F1 720
4 TraesCS7D01G330800 chr2A 734292503 734293246 743 True 527.000000 527 80.315000 1020 1746 1 chr2A.!!$R1 726

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
169 170 0.250513 GGTGTCACCACATCCTCCTC 59.749 60.0 17.59 0.0 43.71 3.71 F
875 2267 0.322975 CACCACCAGCAGCTAAGTCT 59.677 55.0 0.00 0.0 0.00 3.24 F
1899 3341 1.043816 CTATCACAGTCGCCCCAGAT 58.956 55.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 3312 0.103208 GGGGCGACTGTGATAGTGAG 59.897 60.0 0.00 0.0 40.53 3.51 R
2163 3613 0.109132 CCGCCAAAATGGAGCAAGAC 60.109 55.0 0.00 0.0 40.96 3.01 R
3188 6310 0.171231 GATTGGGCGGCAAGACTTTC 59.829 55.0 12.47 0.0 0.00 2.62 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
43 44 1.152008 CCCCTCCTATCCCCTCCAC 60.152 68.421 0.00 0.00 0.00 4.02
44 45 1.534235 CCCTCCTATCCCCTCCACG 60.534 68.421 0.00 0.00 0.00 4.94
52 53 0.325671 ATCCCCTCCACGATGTCAGT 60.326 55.000 0.00 0.00 0.00 3.41
53 54 0.544357 TCCCCTCCACGATGTCAGTT 60.544 55.000 0.00 0.00 0.00 3.16
55 56 0.391661 CCCTCCACGATGTCAGTTGG 60.392 60.000 0.00 0.00 0.00 3.77
58 59 2.040544 CCACGATGTCAGTTGGCCC 61.041 63.158 0.00 0.00 0.00 5.80
62 63 1.077429 GATGTCAGTTGGCCCCTCC 60.077 63.158 0.00 0.00 0.00 4.30
66 67 2.612115 CAGTTGGCCCCTCCTCCT 60.612 66.667 0.00 0.00 35.26 3.69
74 75 1.690985 CCCCTCCTCCTTCCTCCAC 60.691 68.421 0.00 0.00 0.00 4.02
84 85 2.225791 CTTCCTCCACGGCATCGACA 62.226 60.000 0.00 0.00 40.11 4.35
93 94 1.901085 GGCATCGACACTCCTCCTT 59.099 57.895 0.00 0.00 0.00 3.36
105 106 1.275291 CTCCTCCTTTTCACGCCACTA 59.725 52.381 0.00 0.00 0.00 2.74
106 107 1.906574 TCCTCCTTTTCACGCCACTAT 59.093 47.619 0.00 0.00 0.00 2.12
114 115 2.758327 ACGCCACTATCGGAGCCA 60.758 61.111 0.00 0.00 0.00 4.75
117 118 1.004440 GCCACTATCGGAGCCATCC 60.004 63.158 0.00 0.00 42.81 3.51
143 144 4.803908 CCTTGCCGCCTTCCTCCC 62.804 72.222 0.00 0.00 0.00 4.30
156 157 2.273179 CCTCCCTTCGACGGTGTCA 61.273 63.158 7.24 0.00 32.09 3.58
159 160 2.732016 CCTTCGACGGTGTCACCA 59.268 61.111 21.91 0.00 38.47 4.17
169 170 0.250513 GGTGTCACCACATCCTCCTC 59.749 60.000 17.59 0.00 43.71 3.71
171 172 1.205893 GTGTCACCACATCCTCCTCTC 59.794 57.143 0.00 0.00 41.44 3.20
182 183 4.779733 TCCTCTCCCCTCCACGGC 62.780 72.222 0.00 0.00 0.00 5.68
204 205 1.076923 GGTCGGCACCTCCTCTCTA 60.077 63.158 0.00 0.00 40.00 2.43
208 209 2.787567 GGCACCTCCTCTCTACGCC 61.788 68.421 0.00 0.00 0.00 5.68
215 216 1.879380 CTCCTCTCTACGCCATCTCTG 59.121 57.143 0.00 0.00 0.00 3.35
221 222 1.957177 TCTACGCCATCTCTGATGTCC 59.043 52.381 6.78 0.00 0.00 4.02
262 263 3.008813 AGCCTATTGCCTGTGGATAGATG 59.991 47.826 0.00 0.00 42.71 2.90
278 279 3.439857 AGATGCTTGCCCTTTCAACTA 57.560 42.857 0.00 0.00 0.00 2.24
286 287 5.452078 TTGCCCTTTCAACTACTCAATTG 57.548 39.130 0.00 0.00 0.00 2.32
448 1783 4.238761 TGTACCAAAGAGAGAGTTGTCG 57.761 45.455 0.00 0.00 0.00 4.35
462 1837 0.388778 TTGTCGTATTTCGCAGCCGA 60.389 50.000 0.00 0.00 42.66 5.54
483 1858 0.530744 AAACTCGGTGCATCGCTCTA 59.469 50.000 16.22 0.00 0.00 2.43
520 1895 7.921787 TGCGAAACAAAATTACTCACTCTTAA 58.078 30.769 0.00 0.00 0.00 1.85
563 1938 4.899352 AGAGTTGCTCAAATGTAGGAGT 57.101 40.909 0.00 0.00 33.66 3.85
576 1951 7.758076 TCAAATGTAGGAGTACAACTTATCGTG 59.242 37.037 0.00 0.00 42.54 4.35
589 1964 5.470047 ACTTATCGTGTTGAACCTTCTCT 57.530 39.130 0.00 0.00 0.00 3.10
596 1971 4.389374 GTGTTGAACCTTCTCTGGATCAA 58.611 43.478 0.00 2.79 43.46 2.57
605 1980 4.997395 CCTTCTCTGGATCAAGTTTTTCGA 59.003 41.667 0.00 0.00 0.00 3.71
628 2003 4.819105 AAGGATTGTGTCATCGGAGTAA 57.181 40.909 0.00 0.00 0.00 2.24
659 2034 3.495806 GGATAGGCCCTCATCAACAAGAG 60.496 52.174 0.00 0.00 0.00 2.85
781 2167 6.365247 GCTAACACGATTTTCACTAGAACAGA 59.635 38.462 0.00 0.00 32.39 3.41
782 2168 7.095774 GCTAACACGATTTTCACTAGAACAGAA 60.096 37.037 0.00 0.00 32.39 3.02
783 2169 6.771188 ACACGATTTTCACTAGAACAGAAG 57.229 37.500 0.00 0.00 32.39 2.85
784 2170 6.513180 ACACGATTTTCACTAGAACAGAAGA 58.487 36.000 0.00 0.00 32.39 2.87
796 2182 7.333174 CACTAGAACAGAAGAAAGAAAGGGATC 59.667 40.741 0.00 0.00 0.00 3.36
869 2261 2.111878 GTGACACCACCAGCAGCT 59.888 61.111 0.00 0.00 37.33 4.24
875 2267 0.322975 CACCACCAGCAGCTAAGTCT 59.677 55.000 0.00 0.00 0.00 3.24
926 2318 1.279271 AGCTAGCGACCCAACTGAAAT 59.721 47.619 9.55 0.00 0.00 2.17
931 2323 4.222124 AGCGACCCAACTGAAATCTATT 57.778 40.909 0.00 0.00 0.00 1.73
932 2324 5.353394 AGCGACCCAACTGAAATCTATTA 57.647 39.130 0.00 0.00 0.00 0.98
933 2325 5.360591 AGCGACCCAACTGAAATCTATTAG 58.639 41.667 0.00 0.00 0.00 1.73
1568 2998 2.046892 GCTGCATCGACACCTGGT 60.047 61.111 0.00 0.00 0.00 4.00
1792 3228 2.680352 ATGTCCAGGTCGCCGTCT 60.680 61.111 0.00 0.00 0.00 4.18
1816 3252 3.636043 CCAACGGCGCGCGATTAT 61.636 61.111 37.18 13.82 0.00 1.28
1820 3256 3.475774 CGGCGCGCGATTATACCC 61.476 66.667 37.18 21.98 0.00 3.69
1876 3312 1.079681 TATGGTGGACGAACGGTGC 60.080 57.895 0.00 0.00 37.52 5.01
1879 3315 2.028484 GTGGACGAACGGTGCTCA 59.972 61.111 0.00 0.00 37.93 4.26
1882 3318 1.174078 TGGACGAACGGTGCTCACTA 61.174 55.000 0.00 0.00 37.93 2.74
1899 3341 1.043816 CTATCACAGTCGCCCCAGAT 58.956 55.000 0.00 0.00 0.00 2.90
1924 3366 2.258726 GGTTGTGGTGGTTCGCTCC 61.259 63.158 0.00 0.00 0.00 4.70
2198 3648 1.817099 CGGCTGCCATCCAACTCTC 60.817 63.158 20.29 0.00 0.00 3.20
2227 3702 3.737266 GGTGATGCATTTTGTGTCACTTG 59.263 43.478 12.64 0.00 39.22 3.16
2263 3739 7.757097 ATATTCAGTGTCGAGTATGTTTGAC 57.243 36.000 0.00 0.00 32.99 3.18
2264 3740 4.577834 TCAGTGTCGAGTATGTTTGACA 57.422 40.909 0.00 0.00 38.77 3.58
2265 3741 4.546570 TCAGTGTCGAGTATGTTTGACAG 58.453 43.478 0.00 0.00 41.06 3.51
2266 3742 3.121944 CAGTGTCGAGTATGTTTGACAGC 59.878 47.826 0.00 0.00 41.06 4.40
2267 3743 3.057019 GTGTCGAGTATGTTTGACAGCA 58.943 45.455 0.00 0.00 41.06 4.41
2269 3745 4.025229 GTGTCGAGTATGTTTGACAGCAAA 60.025 41.667 0.00 0.00 41.06 3.68
2305 3781 1.935799 AAGTGCATGCCCATAAACCA 58.064 45.000 16.68 0.00 0.00 3.67
2317 3793 3.130340 CCCATAAACCATTCTTTGTCCCG 59.870 47.826 0.00 0.00 0.00 5.14
2324 3800 2.159627 CCATTCTTTGTCCCGAGTTTCG 59.840 50.000 0.00 0.00 40.07 3.46
2329 3805 1.860676 TTGTCCCGAGTTTCGTCTTG 58.139 50.000 0.00 0.00 38.40 3.02
2344 3852 4.215908 TCGTCTTGGCTAGATATTGAGGT 58.784 43.478 1.20 0.00 34.79 3.85
2350 3858 6.611642 TCTTGGCTAGATATTGAGGTGTACTT 59.388 38.462 0.00 0.00 0.00 2.24
2351 3859 6.406692 TGGCTAGATATTGAGGTGTACTTC 57.593 41.667 0.00 0.00 0.00 3.01
2352 3860 5.304614 TGGCTAGATATTGAGGTGTACTTCC 59.695 44.000 0.00 0.00 0.00 3.46
2353 3861 5.304614 GGCTAGATATTGAGGTGTACTTCCA 59.695 44.000 0.00 0.00 0.00 3.53
2360 3868 3.804036 TGAGGTGTACTTCCAACAACAG 58.196 45.455 9.58 0.00 37.00 3.16
2364 3872 2.548480 GTGTACTTCCAACAACAGGAGC 59.452 50.000 0.00 0.00 36.33 4.70
2374 5175 2.762745 ACAACAGGAGCGTAAACGATT 58.237 42.857 6.71 0.00 43.02 3.34
2377 5178 4.933400 ACAACAGGAGCGTAAACGATTATT 59.067 37.500 6.71 0.00 43.02 1.40
2378 5179 5.163893 ACAACAGGAGCGTAAACGATTATTG 60.164 40.000 6.71 6.26 43.02 1.90
2415 5216 1.336131 TGTTGCATTAGCTTTGCCCA 58.664 45.000 16.13 11.07 42.74 5.36
2516 5337 7.761249 GCTTTGCACCTGTATTTATGAGATTTT 59.239 33.333 0.00 0.00 0.00 1.82
2517 5338 8.984891 TTTGCACCTGTATTTATGAGATTTTG 57.015 30.769 0.00 0.00 0.00 2.44
2518 5339 6.563422 TGCACCTGTATTTATGAGATTTTGC 58.437 36.000 0.00 0.00 0.00 3.68
2519 5340 6.377996 TGCACCTGTATTTATGAGATTTTGCT 59.622 34.615 0.00 0.00 0.00 3.91
2520 5341 6.694411 GCACCTGTATTTATGAGATTTTGCTG 59.306 38.462 0.00 0.00 0.00 4.41
2521 5342 6.694411 CACCTGTATTTATGAGATTTTGCTGC 59.306 38.462 0.00 0.00 0.00 5.25
2522 5343 6.604795 ACCTGTATTTATGAGATTTTGCTGCT 59.395 34.615 0.00 0.00 0.00 4.24
2523 5344 7.123247 ACCTGTATTTATGAGATTTTGCTGCTT 59.877 33.333 0.00 0.00 0.00 3.91
2524 5345 7.977853 CCTGTATTTATGAGATTTTGCTGCTTT 59.022 33.333 0.00 0.00 0.00 3.51
2663 5491 7.172361 TGTTCAAATAAACTTTAGCCCATTTGC 59.828 33.333 0.00 0.00 34.77 3.68
2694 5522 1.000506 TCCGGTTCGTCTTTTGAGAGG 59.999 52.381 0.00 0.00 0.00 3.69
2849 5687 0.034863 GGCCAACTGGTTTATCCCGA 60.035 55.000 0.00 0.00 37.57 5.14
2877 5716 0.536724 TCCATGTGAGTATGCGTGCT 59.463 50.000 0.00 0.00 0.00 4.40
2921 5760 0.038599 AGCACATCCAACTCCATGCA 59.961 50.000 0.00 0.00 35.51 3.96
2922 5761 0.889994 GCACATCCAACTCCATGCAA 59.110 50.000 0.00 0.00 33.27 4.08
2923 5762 1.273048 GCACATCCAACTCCATGCAAA 59.727 47.619 0.00 0.00 33.27 3.68
2924 5763 2.288948 GCACATCCAACTCCATGCAAAA 60.289 45.455 0.00 0.00 33.27 2.44
2925 5764 3.581755 CACATCCAACTCCATGCAAAAG 58.418 45.455 0.00 0.00 0.00 2.27
2926 5765 2.028748 ACATCCAACTCCATGCAAAAGC 60.029 45.455 0.00 0.00 0.00 3.51
2927 5766 0.968405 TCCAACTCCATGCAAAAGCC 59.032 50.000 0.00 0.00 0.00 4.35
2928 5767 0.037046 CCAACTCCATGCAAAAGCCC 60.037 55.000 0.00 0.00 0.00 5.19
2929 5768 0.680618 CAACTCCATGCAAAAGCCCA 59.319 50.000 0.00 0.00 0.00 5.36
2930 5769 1.276989 CAACTCCATGCAAAAGCCCAT 59.723 47.619 0.00 0.00 0.00 4.00
2931 5770 0.899720 ACTCCATGCAAAAGCCCATG 59.100 50.000 0.00 0.00 38.78 3.66
2932 5771 0.461339 CTCCATGCAAAAGCCCATGC 60.461 55.000 0.00 0.00 42.86 4.06
3027 6140 2.954318 CAATTAGGTGCCAGGATCCTTG 59.046 50.000 13.00 10.50 33.34 3.61
3030 6143 1.076485 GGTGCCAGGATCCTTGCAT 60.076 57.895 35.49 4.08 44.57 3.96
3064 6186 0.036765 AGGGAAGCGTGCAATAACGA 60.037 50.000 0.17 0.00 46.49 3.85
3065 6187 0.373716 GGGAAGCGTGCAATAACGAG 59.626 55.000 0.17 0.00 46.49 4.18
3086 6208 2.675348 GGGACTGATTCTTCTGCTTTCG 59.325 50.000 0.00 0.00 0.00 3.46
3120 6242 0.944311 ACGTGTCTAGCTGGCAAACG 60.944 55.000 14.27 14.27 28.98 3.60
3124 6246 0.166814 GTCTAGCTGGCAAACGCTTG 59.833 55.000 4.98 3.88 37.68 4.01
3128 6250 2.844451 GCTGGCAAACGCTTGACCA 61.844 57.895 1.13 8.03 40.19 4.02
3132 6254 1.444119 GGCAAACGCTTGACCACTGA 61.444 55.000 1.98 0.00 34.08 3.41
3140 6262 1.821061 CTTGACCACTGACGCTCCCT 61.821 60.000 0.00 0.00 0.00 4.20
3151 6273 2.124529 GCTCCCTGGCAGCTTACC 60.125 66.667 9.56 0.00 33.75 2.85
3155 6277 2.616458 CCCTGGCAGCTTACCCCTT 61.616 63.158 9.56 0.00 0.00 3.95
3156 6278 1.384191 CCTGGCAGCTTACCCCTTT 59.616 57.895 9.56 0.00 0.00 3.11
3157 6279 0.251787 CCTGGCAGCTTACCCCTTTT 60.252 55.000 9.56 0.00 0.00 2.27
3158 6280 0.890683 CTGGCAGCTTACCCCTTTTG 59.109 55.000 0.00 0.00 0.00 2.44
3159 6281 0.541764 TGGCAGCTTACCCCTTTTGG 60.542 55.000 0.03 0.00 39.97 3.28
3160 6282 0.251608 GGCAGCTTACCCCTTTTGGA 60.252 55.000 0.00 0.00 44.07 3.53
3161 6283 1.627864 GCAGCTTACCCCTTTTGGAA 58.372 50.000 0.00 0.00 44.07 3.53
3162 6284 1.967779 GCAGCTTACCCCTTTTGGAAA 59.032 47.619 0.00 0.00 44.07 3.13
3163 6285 2.029020 GCAGCTTACCCCTTTTGGAAAG 60.029 50.000 0.00 0.00 44.07 2.62
3164 6286 3.496331 CAGCTTACCCCTTTTGGAAAGA 58.504 45.455 2.15 0.00 44.07 2.52
3165 6287 3.255888 CAGCTTACCCCTTTTGGAAAGAC 59.744 47.826 2.15 0.00 44.07 3.01
3166 6288 3.117284 AGCTTACCCCTTTTGGAAAGACA 60.117 43.478 2.15 0.00 44.07 3.41
3167 6289 3.005472 GCTTACCCCTTTTGGAAAGACAC 59.995 47.826 2.15 0.00 44.07 3.67
3168 6290 2.082140 ACCCCTTTTGGAAAGACACC 57.918 50.000 2.15 0.00 44.07 4.16
3169 6291 1.338107 CCCCTTTTGGAAAGACACCC 58.662 55.000 2.15 0.00 44.07 4.61
3170 6292 1.338107 CCCTTTTGGAAAGACACCCC 58.662 55.000 2.15 0.00 44.07 4.95
3171 6293 1.338107 CCTTTTGGAAAGACACCCCC 58.662 55.000 2.15 0.00 44.07 5.40
3188 6310 0.687354 CCCCCTCATGTCCGATTAGG 59.313 60.000 0.00 0.00 42.97 2.69
3200 6322 1.933853 CCGATTAGGAAAGTCTTGCCG 59.066 52.381 3.75 0.00 45.00 5.69
3201 6323 1.327764 CGATTAGGAAAGTCTTGCCGC 59.672 52.381 3.75 0.00 0.00 6.53
3251 6738 1.112916 CCCCAACGAGCAAAAAGGGT 61.113 55.000 0.00 0.00 34.44 4.34
3263 6750 2.335316 AAAAGGGTAGCACACGTTCA 57.665 45.000 0.00 0.00 0.00 3.18
3265 6752 0.466543 AAGGGTAGCACACGTTCACA 59.533 50.000 0.00 0.00 0.00 3.58
3298 6785 0.464036 TGACACGCCCTGGTCATATC 59.536 55.000 0.00 0.00 39.00 1.63
3300 6787 1.956170 CACGCCCTGGTCATATCGC 60.956 63.158 0.00 0.00 0.00 4.58
3301 6788 2.134287 ACGCCCTGGTCATATCGCT 61.134 57.895 0.00 0.00 0.00 4.93
3302 6789 1.069765 CGCCCTGGTCATATCGCTT 59.930 57.895 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.203803 GGGATAGGAGGGGTCGGG 60.204 72.222 0.00 0.00 0.00 5.14
43 44 1.450312 GAGGGGCCAACTGACATCG 60.450 63.158 4.39 0.00 0.00 3.84
44 45 1.077429 GGAGGGGCCAACTGACATC 60.077 63.158 4.39 0.00 36.34 3.06
52 53 2.614013 GGAAGGAGGAGGGGCCAA 60.614 66.667 4.39 0.00 40.02 4.52
53 54 3.626596 AGGAAGGAGGAGGGGCCA 61.627 66.667 4.39 0.00 40.02 5.36
55 56 2.770475 GGAGGAAGGAGGAGGGGC 60.770 72.222 0.00 0.00 0.00 5.80
58 59 2.060980 CCGTGGAGGAAGGAGGAGG 61.061 68.421 0.00 0.00 45.00 4.30
62 63 1.144936 GATGCCGTGGAGGAAGGAG 59.855 63.158 0.00 0.00 45.00 3.69
66 67 2.279810 TGTCGATGCCGTGGAGGAA 61.280 57.895 0.00 0.00 45.00 3.36
74 75 1.949847 AAGGAGGAGTGTCGATGCCG 61.950 60.000 0.00 0.00 37.07 5.69
84 85 0.250338 GTGGCGTGAAAAGGAGGAGT 60.250 55.000 0.00 0.00 0.00 3.85
93 94 0.459585 GCTCCGATAGTGGCGTGAAA 60.460 55.000 0.00 0.00 0.00 2.69
105 106 0.467384 CAGAAGTGGATGGCTCCGAT 59.533 55.000 0.00 0.00 45.37 4.18
106 107 0.904865 ACAGAAGTGGATGGCTCCGA 60.905 55.000 0.00 0.00 45.37 4.55
114 115 0.036010 CGGCAAGGACAGAAGTGGAT 60.036 55.000 0.00 0.00 0.00 3.41
117 118 2.328099 GGCGGCAAGGACAGAAGTG 61.328 63.158 3.07 0.00 0.00 3.16
118 119 2.032681 GGCGGCAAGGACAGAAGT 59.967 61.111 3.07 0.00 0.00 3.01
124 125 2.436824 GAGGAAGGCGGCAAGGAC 60.437 66.667 13.08 0.00 0.00 3.85
156 157 1.003573 GGGGAGAGGAGGATGTGGT 59.996 63.158 0.00 0.00 0.00 4.16
159 160 1.231751 TGGAGGGGAGAGGAGGATGT 61.232 60.000 0.00 0.00 0.00 3.06
182 183 3.934391 GAGGAGGTGCCGACCAACG 62.934 68.421 9.30 0.00 45.98 4.10
185 186 1.859841 TAGAGAGGAGGTGCCGACCA 61.860 60.000 9.30 0.00 45.98 4.02
204 205 1.690219 GGGGACATCAGAGATGGCGT 61.690 60.000 11.29 0.00 0.00 5.68
208 209 3.453717 TGAGAAAGGGGACATCAGAGATG 59.546 47.826 5.50 5.50 0.00 2.90
215 216 3.549794 CCTTGATGAGAAAGGGGACATC 58.450 50.000 0.00 0.00 40.54 3.06
262 263 2.504367 TGAGTAGTTGAAAGGGCAAGC 58.496 47.619 0.00 0.00 0.00 4.01
356 357 6.573664 TGATTGTTGTAAGAATGGAAGGTG 57.426 37.500 0.00 0.00 0.00 4.00
402 403 9.565213 CATGAGTCTTCTGGTTGATTATTTTTC 57.435 33.333 0.00 0.00 0.00 2.29
407 408 7.092891 TGGTACATGAGTCTTCTGGTTGATTAT 60.093 37.037 0.00 0.00 0.00 1.28
408 409 6.212589 TGGTACATGAGTCTTCTGGTTGATTA 59.787 38.462 0.00 0.00 0.00 1.75
448 1783 3.161306 GAGTTTTTCGGCTGCGAAATAC 58.839 45.455 20.62 20.62 38.85 1.89
462 1837 0.517316 GAGCGATGCACCGAGTTTTT 59.483 50.000 3.51 0.00 0.00 1.94
483 1858 0.593128 GTTTCGCAGGCACAAGATGT 59.407 50.000 0.00 0.00 0.00 3.06
520 1895 4.261578 TCGGTCTAAAACGGAACTTCAT 57.738 40.909 0.00 0.00 34.59 2.57
563 1938 6.518493 AGAAGGTTCAACACGATAAGTTGTA 58.482 36.000 6.03 0.00 44.97 2.41
576 1951 4.646572 ACTTGATCCAGAGAAGGTTCAAC 58.353 43.478 0.00 0.00 40.59 3.18
589 1964 6.648879 ATCCTTTTCGAAAAACTTGATCCA 57.351 33.333 22.67 0.00 0.00 3.41
596 1971 6.202516 TGACACAATCCTTTTCGAAAAACT 57.797 33.333 22.67 8.73 0.00 2.66
605 1980 4.021102 ACTCCGATGACACAATCCTTTT 57.979 40.909 0.00 0.00 0.00 2.27
628 2003 4.419984 TGAGGGCCTATCCATAGTACAT 57.580 45.455 5.73 0.00 36.21 2.29
659 2034 3.823304 GAGGGCTTATCCATTGTGAATCC 59.177 47.826 0.00 0.00 36.21 3.01
781 2167 5.397360 ACATTGTGGATCCCTTTCTTTCTT 58.603 37.500 9.90 0.00 0.00 2.52
782 2168 5.003096 ACATTGTGGATCCCTTTCTTTCT 57.997 39.130 9.90 0.00 0.00 2.52
783 2169 5.243730 TGAACATTGTGGATCCCTTTCTTTC 59.756 40.000 9.90 6.30 0.00 2.62
784 2170 5.011023 GTGAACATTGTGGATCCCTTTCTTT 59.989 40.000 9.90 0.00 0.00 2.52
796 2182 0.030101 AAACGGCGTGAACATTGTGG 59.970 50.000 15.70 0.00 0.00 4.17
869 2261 9.899661 TGAGGCTGCTAAATAATTTTAGACTTA 57.100 29.630 9.14 1.42 44.75 2.24
875 2267 8.965819 TGTGATTGAGGCTGCTAAATAATTTTA 58.034 29.630 0.00 0.00 0.00 1.52
931 2323 6.379386 GCACTCATGCGTACTTCATATACTA 58.621 40.000 0.00 0.00 43.33 1.82
932 2324 5.223382 GCACTCATGCGTACTTCATATACT 58.777 41.667 0.00 0.00 43.33 2.12
933 2325 5.502214 GCACTCATGCGTACTTCATATAC 57.498 43.478 0.00 0.00 43.33 1.47
968 2364 4.591321 AGGAAGGAAACTGGCATGAATA 57.409 40.909 0.00 0.00 42.68 1.75
1760 3196 1.342819 GGACATGATCCTCTCCTTCGG 59.657 57.143 0.00 0.00 45.22 4.30
1777 3213 4.131088 GGAGACGGCGACCTGGAC 62.131 72.222 16.62 0.00 0.00 4.02
1810 3246 5.620205 CGGAGATCTTGACAGGGTATAATCG 60.620 48.000 0.00 0.00 0.00 3.34
1816 3252 2.376109 GACGGAGATCTTGACAGGGTA 58.624 52.381 0.00 0.00 0.00 3.69
1820 3256 0.863538 CGCGACGGAGATCTTGACAG 60.864 60.000 0.00 0.00 0.00 3.51
1876 3312 0.103208 GGGGCGACTGTGATAGTGAG 59.897 60.000 0.00 0.00 40.53 3.51
1879 3315 0.324368 TCTGGGGCGACTGTGATAGT 60.324 55.000 0.00 0.00 44.02 2.12
1882 3318 1.524002 CATCTGGGGCGACTGTGAT 59.476 57.895 0.00 0.00 0.00 3.06
1899 3341 1.932156 AACCACCACAACCTCCAGCA 61.932 55.000 0.00 0.00 0.00 4.41
2082 3524 0.740737 ACTTTGTTCCTGCACTGCAC 59.259 50.000 0.00 0.00 33.79 4.57
2083 3525 1.024271 GACTTTGTTCCTGCACTGCA 58.976 50.000 3.11 3.11 36.92 4.41
2084 3526 1.024271 TGACTTTGTTCCTGCACTGC 58.976 50.000 0.00 0.00 0.00 4.40
2085 3527 3.316029 TGATTGACTTTGTTCCTGCACTG 59.684 43.478 0.00 0.00 0.00 3.66
2086 3528 3.554934 TGATTGACTTTGTTCCTGCACT 58.445 40.909 0.00 0.00 0.00 4.40
2130 3580 3.065233 CAGCGCCATTGTTGCTTCTATTA 59.935 43.478 2.29 0.00 36.69 0.98
2163 3613 0.109132 CCGCCAAAATGGAGCAAGAC 60.109 55.000 0.00 0.00 40.96 3.01
2227 3702 9.907576 CTCGACACTGAATATTTACATTCTTTC 57.092 33.333 0.00 0.00 36.16 2.62
2280 3756 0.251922 ATGGGCATGCACTTTGGTCT 60.252 50.000 22.81 0.00 0.00 3.85
2305 3781 3.064931 GACGAAACTCGGGACAAAGAAT 58.935 45.455 0.00 0.00 45.59 2.40
2317 3793 6.273825 TCAATATCTAGCCAAGACGAAACTC 58.726 40.000 0.00 0.00 36.93 3.01
2324 3800 5.283457 ACACCTCAATATCTAGCCAAGAC 57.717 43.478 0.00 0.00 36.93 3.01
2329 3805 5.304614 TGGAAGTACACCTCAATATCTAGCC 59.695 44.000 9.82 0.00 0.00 3.93
2344 3852 2.805295 CGCTCCTGTTGTTGGAAGTACA 60.805 50.000 0.00 0.00 32.61 2.90
2350 3858 2.215196 GTTTACGCTCCTGTTGTTGGA 58.785 47.619 0.00 0.00 0.00 3.53
2351 3859 1.070175 CGTTTACGCTCCTGTTGTTGG 60.070 52.381 0.00 0.00 0.00 3.77
2352 3860 1.862201 TCGTTTACGCTCCTGTTGTTG 59.138 47.619 0.00 0.00 39.60 3.33
2353 3861 2.228138 TCGTTTACGCTCCTGTTGTT 57.772 45.000 0.00 0.00 39.60 2.83
2360 3868 3.062909 TGTGCAATAATCGTTTACGCTCC 59.937 43.478 0.00 3.63 39.60 4.70
2392 5193 3.125658 GGGCAAAGCTAATGCAACAAATG 59.874 43.478 21.75 0.00 45.60 2.32
2411 5212 4.237724 GTCAACTAAAATTGCTTCTGGGC 58.762 43.478 0.00 0.00 0.00 5.36
2415 5216 7.173218 TCGAAGATGTCAACTAAAATTGCTTCT 59.827 33.333 0.00 0.00 29.69 2.85
2521 5342 3.218398 CAACTGCGTCTAAAAGCGAAAG 58.782 45.455 0.00 0.00 35.87 2.62
2522 5343 2.601266 GCAACTGCGTCTAAAAGCGAAA 60.601 45.455 0.00 0.00 35.87 3.46
2523 5344 1.070175 GCAACTGCGTCTAAAAGCGAA 60.070 47.619 0.00 0.00 35.87 4.70
2524 5345 0.511221 GCAACTGCGTCTAAAAGCGA 59.489 50.000 0.00 0.00 35.87 4.93
2557 5378 6.294120 CCAAAGAAAATTTCAAAAGGATGGGC 60.294 38.462 8.55 0.00 0.00 5.36
2642 5470 7.003402 TGAGCAAATGGGCTAAAGTTTATTT 57.997 32.000 0.00 0.00 45.99 1.40
2663 5491 1.337823 ACGAACCGGATGACCTTTGAG 60.338 52.381 9.46 0.00 0.00 3.02
2694 5522 2.161609 CAGAAAATGAACTACCGGTGCC 59.838 50.000 19.93 3.79 0.00 5.01
2772 5600 3.042481 AAAGCAGGACTTTGGGAGC 57.958 52.632 0.00 0.00 47.00 4.70
2849 5687 1.967319 ACTCACATGGAACGTGCTTT 58.033 45.000 0.00 0.00 34.27 3.51
2943 5782 1.146263 CCTGATAACGTGAGCCCCC 59.854 63.158 0.00 0.00 0.00 5.40
2989 5828 7.817478 CACCTAATTGTTCACATAGTCACACTA 59.183 37.037 0.00 0.00 34.82 2.74
3027 6140 5.637006 TCCCTAACACAAACAACATATGC 57.363 39.130 1.58 0.00 0.00 3.14
3030 6143 4.214545 CGCTTCCCTAACACAAACAACATA 59.785 41.667 0.00 0.00 0.00 2.29
3064 6186 3.618507 CGAAAGCAGAAGAATCAGTCCCT 60.619 47.826 0.00 0.00 0.00 4.20
3065 6187 2.675348 CGAAAGCAGAAGAATCAGTCCC 59.325 50.000 0.00 0.00 0.00 4.46
3086 6208 6.793680 GCTAGACACGTGGTTTTATTTGTAAC 59.206 38.462 21.57 0.00 0.00 2.50
3120 6242 2.029844 GGAGCGTCAGTGGTCAAGC 61.030 63.158 0.00 0.00 38.10 4.01
3124 6246 2.262915 CAGGGAGCGTCAGTGGTC 59.737 66.667 0.00 0.00 35.66 4.02
3128 6250 3.699894 CTGCCAGGGAGCGTCAGT 61.700 66.667 0.00 0.00 34.65 3.41
3132 6254 3.003173 TAAGCTGCCAGGGAGCGT 61.003 61.111 25.99 25.03 41.61 5.07
3140 6262 0.541764 CCAAAAGGGGTAAGCTGCCA 60.542 55.000 9.46 0.00 0.00 4.92
3147 6269 3.568443 GGTGTCTTTCCAAAAGGGGTAA 58.432 45.455 0.00 0.00 37.22 2.85
3151 6273 1.338107 GGGGTGTCTTTCCAAAAGGG 58.662 55.000 0.00 0.00 38.37 3.95
3169 6291 0.687354 CCTAATCGGACATGAGGGGG 59.313 60.000 0.00 0.00 33.16 5.40
3170 6292 1.717032 TCCTAATCGGACATGAGGGG 58.283 55.000 0.00 0.00 36.69 4.79
3171 6293 3.134804 ACTTTCCTAATCGGACATGAGGG 59.865 47.826 0.00 0.00 42.97 4.30
3172 6294 4.100189 AGACTTTCCTAATCGGACATGAGG 59.900 45.833 0.00 0.00 42.97 3.86
3173 6295 5.269505 AGACTTTCCTAATCGGACATGAG 57.730 43.478 0.00 0.00 42.97 2.90
3174 6296 5.419542 CAAGACTTTCCTAATCGGACATGA 58.580 41.667 0.00 0.00 42.97 3.07
3175 6297 4.034510 GCAAGACTTTCCTAATCGGACATG 59.965 45.833 0.00 0.00 42.97 3.21
3176 6298 4.192317 GCAAGACTTTCCTAATCGGACAT 58.808 43.478 0.00 0.00 42.97 3.06
3177 6299 3.596214 GCAAGACTTTCCTAATCGGACA 58.404 45.455 0.00 0.00 42.97 4.02
3178 6300 2.937149 GGCAAGACTTTCCTAATCGGAC 59.063 50.000 0.00 0.00 42.97 4.79
3179 6301 2.418197 CGGCAAGACTTTCCTAATCGGA 60.418 50.000 2.30 0.00 41.06 4.55
3180 6302 1.933853 CGGCAAGACTTTCCTAATCGG 59.066 52.381 2.30 0.00 0.00 4.18
3181 6303 1.327764 GCGGCAAGACTTTCCTAATCG 59.672 52.381 2.30 0.00 0.00 3.34
3182 6304 1.671328 GGCGGCAAGACTTTCCTAATC 59.329 52.381 3.07 0.00 0.00 1.75
3183 6305 1.682087 GGGCGGCAAGACTTTCCTAAT 60.682 52.381 12.47 0.00 0.00 1.73
3184 6306 0.322187 GGGCGGCAAGACTTTCCTAA 60.322 55.000 12.47 0.00 0.00 2.69
3185 6307 1.298667 GGGCGGCAAGACTTTCCTA 59.701 57.895 12.47 0.00 0.00 2.94
3186 6308 2.034221 GGGCGGCAAGACTTTCCT 59.966 61.111 12.47 0.00 0.00 3.36
3187 6309 1.250840 ATTGGGCGGCAAGACTTTCC 61.251 55.000 12.47 0.00 0.00 3.13
3188 6310 0.171231 GATTGGGCGGCAAGACTTTC 59.829 55.000 12.47 0.00 0.00 2.62
3189 6311 1.250840 GGATTGGGCGGCAAGACTTT 61.251 55.000 12.47 0.00 0.00 2.66
3190 6312 1.678970 GGATTGGGCGGCAAGACTT 60.679 57.895 12.47 0.00 0.00 3.01
3191 6313 2.044946 GGATTGGGCGGCAAGACT 60.045 61.111 12.47 0.00 0.00 3.24
3192 6314 3.140814 GGGATTGGGCGGCAAGAC 61.141 66.667 12.47 0.00 0.00 3.01
3193 6315 3.656280 TGGGATTGGGCGGCAAGA 61.656 61.111 12.47 0.00 0.00 3.02
3194 6316 3.451894 GTGGGATTGGGCGGCAAG 61.452 66.667 12.47 0.00 0.00 4.01
3198 6320 4.820744 CCAGGTGGGATTGGGCGG 62.821 72.222 0.00 0.00 40.01 6.13
3199 6321 3.995506 GACCAGGTGGGATTGGGCG 62.996 68.421 0.00 0.00 41.15 6.13
3200 6322 2.043953 GACCAGGTGGGATTGGGC 60.044 66.667 0.00 0.00 41.15 5.36
3201 6323 2.683475 GGACCAGGTGGGATTGGG 59.317 66.667 0.00 0.00 41.15 4.12
3263 6750 0.814010 GTCAGCCAGGTTCACGTTGT 60.814 55.000 0.00 0.00 0.00 3.32
3265 6752 0.814010 GTGTCAGCCAGGTTCACGTT 60.814 55.000 0.00 0.00 0.00 3.99
3287 6774 2.609459 GACAACAAGCGATATGACCAGG 59.391 50.000 0.00 0.00 0.00 4.45
3291 6778 3.521560 TGAGGACAACAAGCGATATGAC 58.478 45.455 0.00 0.00 0.00 3.06
3298 6785 1.302033 AGGCTGAGGACAACAAGCG 60.302 57.895 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.