Multiple sequence alignment - TraesCS1A01G035200

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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 TraesCS1A01G035200 chr1A 100.000 3371 0 0 1 3371 18463267 18459897 0.000000e+00 6226.0
1 TraesCS1A01G035200 chr1D 93.026 3169 142 44 247 3371 17170369 17167236 0.000000e+00 4554.0
2 TraesCS1A01G035200 chr1D 90.780 141 10 2 1 140 17170764 17170626 5.740000e-43 185.0
3 TraesCS1A01G035200 chr1B 92.163 3190 134 39 247 3371 24934355 24931217 0.000000e+00 4399.0
4 TraesCS1A01G035200 chr1B 87.379 103 9 2 43 143 24934709 24934609 7.640000e-22 115.0
5 TraesCS1A01G035200 chr3B 92.593 243 15 3 1499 1738 828111441 828111683 2.490000e-91 346.0
6 TraesCS1A01G035200 chr3B 86.920 237 27 4 1505 1738 823129941 823129706 2.580000e-66 263.0
7 TraesCS1A01G035200 chr3D 92.181 243 16 3 1499 1738 610544041 610544283 1.160000e-89 340.0
8 TraesCS1A01G035200 chr3D 87.705 244 25 5 1505 1744 613806091 613805849 2.560000e-71 279.0
9 TraesCS1A01G035200 chr3A 91.358 243 18 3 1499 1738 744879511 744879753 2.510000e-86 329.0
10 TraesCS1A01G035200 chr3A 86.831 243 29 3 1505 1744 750298755 750298513 5.540000e-68 268.0
11 TraesCS1A01G035200 chr5B 87.719 228 25 2 1506 1730 112194758 112194531 2.580000e-66 263.0
12 TraesCS1A01G035200 chr5D 97.059 34 1 0 169 202 293541583 293541550 1.310000e-04 58.4


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 TraesCS1A01G035200 chr1A 18459897 18463267 3370 True 6226.0 6226 100.000 1 3371 1 chr1A.!!$R1 3370
1 TraesCS1A01G035200 chr1D 17167236 17170764 3528 True 2369.5 4554 91.903 1 3371 2 chr1D.!!$R1 3370
2 TraesCS1A01G035200 chr1B 24931217 24934709 3492 True 2257.0 4399 89.771 43 3371 2 chr1B.!!$R1 3328

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
161 164 0.036952 AGGCACTGATGAAGTCACCG 60.037 55.0 0.00 0.0 36.83 4.94 F
196 199 0.179108 GACGGAAATGTCTCCTCCCG 60.179 60.0 0.00 0.0 42.30 5.14 F
503 673 0.389166 CTCGAGCGGCTCATATTCCC 60.389 60.0 27.83 0.9 0.00 3.97 F
990 1172 0.402504 TAACATCACCACCCACCCAC 59.597 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1617 0.554305 TCCCCTGCTGCATGATTGAT 59.446 50.000 1.31 0.0 0.0 2.57 R
1993 2191 2.797278 CCAGGTAGTAGCCCGCTGG 61.797 68.421 0.00 0.0 0.0 4.85 R
2198 2396 0.323087 TCCTCCGTCGTCTTCATGGA 60.323 55.000 0.00 0.0 0.0 3.41 R
2755 2964 1.003262 CCGCACGCAAACAGAAATGG 61.003 55.000 0.00 0.0 0.0 3.16 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
32 33 1.343681 TGGGTTAAGCGAGGGGAGTAT 60.344 52.381 0.00 0.00 0.00 2.12
71 72 1.438651 TGCTTGGCTCGTAATGACAC 58.561 50.000 0.00 0.00 0.00 3.67
119 122 6.400579 GCAGATGCTCACATACATACATAC 57.599 41.667 0.00 0.00 36.35 2.39
120 123 5.928264 GCAGATGCTCACATACATACATACA 59.072 40.000 0.00 0.00 36.35 2.29
121 124 6.128715 GCAGATGCTCACATACATACATACAC 60.129 42.308 0.00 0.00 36.35 2.90
140 143 4.774124 ACACACACTCATCCCTATGAATG 58.226 43.478 0.00 0.00 43.41 2.67
141 144 3.562973 CACACACTCATCCCTATGAATGC 59.437 47.826 0.00 0.00 41.91 3.56
142 145 3.200605 ACACACTCATCCCTATGAATGCA 59.799 43.478 0.00 0.00 41.91 3.96
143 146 3.813724 CACACTCATCCCTATGAATGCAG 59.186 47.826 0.00 0.00 41.91 4.41
144 147 3.181447 ACACTCATCCCTATGAATGCAGG 60.181 47.826 0.00 0.00 41.91 4.85
145 148 2.224719 ACTCATCCCTATGAATGCAGGC 60.225 50.000 0.00 0.00 41.57 4.85
146 149 1.776063 TCATCCCTATGAATGCAGGCA 59.224 47.619 0.00 0.00 39.20 4.75
147 150 1.884579 CATCCCTATGAATGCAGGCAC 59.115 52.381 0.00 0.00 34.84 5.01
148 151 1.216064 TCCCTATGAATGCAGGCACT 58.784 50.000 0.00 0.00 43.88 4.40
161 164 0.036952 AGGCACTGATGAAGTCACCG 60.037 55.000 0.00 0.00 36.83 4.94
196 199 0.179108 GACGGAAATGTCTCCTCCCG 60.179 60.000 0.00 0.00 42.30 5.14
201 204 0.984230 AAATGTCTCCTCCCGCTGAA 59.016 50.000 0.00 0.00 0.00 3.02
202 205 1.207791 AATGTCTCCTCCCGCTGAAT 58.792 50.000 0.00 0.00 0.00 2.57
203 206 0.467384 ATGTCTCCTCCCGCTGAATG 59.533 55.000 0.00 0.00 0.00 2.67
204 207 0.614697 TGTCTCCTCCCGCTGAATGA 60.615 55.000 0.00 0.00 0.00 2.57
205 208 0.537188 GTCTCCTCCCGCTGAATGAA 59.463 55.000 0.00 0.00 0.00 2.57
206 209 1.139853 GTCTCCTCCCGCTGAATGAAT 59.860 52.381 0.00 0.00 0.00 2.57
209 212 3.648067 TCTCCTCCCGCTGAATGAATATT 59.352 43.478 0.00 0.00 0.00 1.28
211 214 3.136443 TCCTCCCGCTGAATGAATATTGT 59.864 43.478 0.00 0.00 0.00 2.71
212 215 3.499918 CCTCCCGCTGAATGAATATTGTC 59.500 47.826 0.00 0.00 0.00 3.18
213 216 3.130633 TCCCGCTGAATGAATATTGTCG 58.869 45.455 0.00 0.00 0.00 4.35
214 217 2.224079 CCCGCTGAATGAATATTGTCGG 59.776 50.000 0.00 0.00 32.97 4.79
216 219 3.559655 CCGCTGAATGAATATTGTCGGAA 59.440 43.478 0.00 0.00 34.04 4.30
218 221 5.448496 CCGCTGAATGAATATTGTCGGAAAA 60.448 40.000 0.00 0.00 34.04 2.29
219 222 5.452302 CGCTGAATGAATATTGTCGGAAAAC 59.548 40.000 0.00 0.00 0.00 2.43
220 223 5.743872 GCTGAATGAATATTGTCGGAAAACC 59.256 40.000 0.00 0.00 0.00 3.27
221 224 6.404734 GCTGAATGAATATTGTCGGAAAACCT 60.405 38.462 0.00 0.00 0.00 3.50
222 225 7.201696 GCTGAATGAATATTGTCGGAAAACCTA 60.202 37.037 0.00 0.00 0.00 3.08
224 227 9.015367 TGAATGAATATTGTCGGAAAACCTAAA 57.985 29.630 0.00 0.00 0.00 1.85
225 228 9.849166 GAATGAATATTGTCGGAAAACCTAAAA 57.151 29.630 0.00 0.00 0.00 1.52
235 238 8.301002 TGTCGGAAAACCTAAAATAAATTGAGG 58.699 33.333 3.46 3.46 32.62 3.86
236 239 8.517056 GTCGGAAAACCTAAAATAAATTGAGGA 58.483 33.333 9.73 0.00 31.48 3.71
237 240 8.517056 TCGGAAAACCTAAAATAAATTGAGGAC 58.483 33.333 9.73 0.00 31.48 3.85
238 241 7.758076 CGGAAAACCTAAAATAAATTGAGGACC 59.242 37.037 9.73 0.00 31.48 4.46
239 242 8.812972 GGAAAACCTAAAATAAATTGAGGACCT 58.187 33.333 0.00 0.00 31.48 3.85
255 424 7.931015 TGAGGACCTAAGTTCATATGGTATT 57.069 36.000 2.13 0.00 0.00 1.89
256 425 7.963532 TGAGGACCTAAGTTCATATGGTATTC 58.036 38.462 2.13 0.00 0.00 1.75
331 501 9.146984 TCGTACTTTATTTGCATATATGTAGGC 57.853 33.333 14.14 0.00 38.08 3.93
379 549 4.450053 TCGAGCTTAACTAGGGTAGAGAC 58.550 47.826 0.00 0.00 0.00 3.36
398 568 3.929610 AGACTGCGTAGAAGCTCAATTTC 59.070 43.478 7.78 0.00 38.13 2.17
401 571 2.666508 TGCGTAGAAGCTCAATTTCGAC 59.333 45.455 0.00 0.00 38.13 4.20
405 575 1.728971 AGAAGCTCAATTTCGACGCAG 59.271 47.619 0.00 0.00 0.00 5.18
432 602 2.307496 TTTCATCCAAGCACCATGGT 57.693 45.000 13.00 13.00 39.09 3.55
433 603 2.307496 TTCATCCAAGCACCATGGTT 57.693 45.000 16.84 0.00 38.82 3.67
503 673 0.389166 CTCGAGCGGCTCATATTCCC 60.389 60.000 27.83 0.90 0.00 3.97
534 705 1.815421 GCACCCCTATGTCTGCACG 60.815 63.158 0.00 0.00 0.00 5.34
541 712 2.811431 CCCTATGTCTGCACGAAAAACA 59.189 45.455 0.00 0.00 0.00 2.83
700 871 5.593909 CACTAATCCTGTCTCACTCTCTCAT 59.406 44.000 0.00 0.00 0.00 2.90
990 1172 0.402504 TAACATCACCACCCACCCAC 59.597 55.000 0.00 0.00 0.00 4.61
1269 1462 5.964958 TTTAGCCTGAATTCTGGTTCTTG 57.035 39.130 26.61 6.48 37.30 3.02
1319 1514 6.185511 TCTTGATTCTTCTTCTCATGCCATT 58.814 36.000 0.00 0.00 0.00 3.16
1464 1659 3.319198 GCTGAAGGTGGGGACGGA 61.319 66.667 0.00 0.00 0.00 4.69
1932 2130 4.436998 CTCCGCCTCGCCGACTTT 62.437 66.667 0.00 0.00 0.00 2.66
2116 2314 1.227645 GACCAGCAGCACACACTGA 60.228 57.895 0.00 0.00 40.25 3.41
2257 2455 2.544685 CGATGCCGTCAAAGAGAGAAT 58.455 47.619 0.00 0.00 0.00 2.40
2316 2514 1.130054 ATCACCACCTCACTGCTGGT 61.130 55.000 0.00 0.00 38.95 4.00
2413 2611 4.446051 GCGAGCTCAGATTAATCCTACAAC 59.554 45.833 15.40 0.46 0.00 3.32
2440 2638 1.136329 AGCATGGACTTGGAGGGTGT 61.136 55.000 0.00 0.00 0.00 4.16
2457 2655 7.110155 GGAGGGTGTTGTGAGATATAGAAAAA 58.890 38.462 0.00 0.00 0.00 1.94
2484 2683 3.063588 TGCATTTGTTGTGCATTGTGTTG 59.936 39.130 0.00 0.00 46.76 3.33
2517 2717 3.303938 AGACAAGGTCGATCATGGAGAT 58.696 45.455 5.81 0.00 40.48 2.75
2571 2774 9.797642 TGCTTAATGATCATGGACAACTATTAT 57.202 29.630 9.46 0.00 0.00 1.28
2608 2811 1.260825 CAGCTAGCATGATCACTTGCG 59.739 52.381 18.83 4.26 46.91 4.85
2639 2842 9.668497 TTCTTCTACTTCTTCTTATTTTAGGGC 57.332 33.333 0.00 0.00 0.00 5.19
2640 2843 9.047947 TCTTCTACTTCTTCTTATTTTAGGGCT 57.952 33.333 0.00 0.00 0.00 5.19
2641 2844 9.320352 CTTCTACTTCTTCTTATTTTAGGGCTC 57.680 37.037 0.00 0.00 0.00 4.70
2668 2877 3.410631 TCGCATTCAGGGTGAAGTTAA 57.589 42.857 0.00 0.00 40.05 2.01
2669 2878 3.950397 TCGCATTCAGGGTGAAGTTAAT 58.050 40.909 0.00 0.00 40.05 1.40
2675 2884 5.766150 TTCAGGGTGAAGTTAATTGTGTG 57.234 39.130 0.00 0.00 31.83 3.82
2676 2885 4.787551 TCAGGGTGAAGTTAATTGTGTGT 58.212 39.130 0.00 0.00 0.00 3.72
2677 2886 4.578516 TCAGGGTGAAGTTAATTGTGTGTG 59.421 41.667 0.00 0.00 0.00 3.82
2678 2887 4.338118 CAGGGTGAAGTTAATTGTGTGTGT 59.662 41.667 0.00 0.00 0.00 3.72
2692 2901 6.761099 TTGTGTGTGTATTGTACCACTTTT 57.239 33.333 0.00 0.00 33.71 2.27
2708 2917 6.507023 ACCACTTTTGTTCATGACAATCTTC 58.493 36.000 0.00 0.00 46.99 2.87
2740 2949 6.645306 TGTCCAAATTATATTGTCTGGTCGA 58.355 36.000 0.00 0.00 0.00 4.20
2741 2950 7.279615 TGTCCAAATTATATTGTCTGGTCGAT 58.720 34.615 0.00 0.00 0.00 3.59
2770 2979 2.270352 TCTCCCATTTCTGTTTGCGT 57.730 45.000 0.00 0.00 0.00 5.24
2771 2980 1.879380 TCTCCCATTTCTGTTTGCGTG 59.121 47.619 0.00 0.00 0.00 5.34
2772 2981 0.313672 TCCCATTTCTGTTTGCGTGC 59.686 50.000 0.00 0.00 0.00 5.34
2773 2982 1.003262 CCCATTTCTGTTTGCGTGCG 61.003 55.000 0.00 0.00 0.00 5.34
2774 2983 1.003262 CCATTTCTGTTTGCGTGCGG 61.003 55.000 0.00 0.00 0.00 5.69
2775 2984 1.371635 ATTTCTGTTTGCGTGCGGC 60.372 52.632 0.00 0.00 43.96 6.53
2776 2985 2.747507 ATTTCTGTTTGCGTGCGGCC 62.748 55.000 0.00 0.00 42.61 6.13
2800 3015 9.182214 GCCAATTATATACATGTGATCCAAGAT 57.818 33.333 9.11 0.00 0.00 2.40
2808 3023 6.203808 ACATGTGATCCAAGATTGTGAATG 57.796 37.500 0.00 0.00 0.00 2.67
2811 3026 4.707934 TGTGATCCAAGATTGTGAATGCAT 59.292 37.500 0.00 0.00 0.00 3.96
2860 3075 4.478203 TCCACCAAAATTGTGATCCAAGA 58.522 39.130 0.00 0.00 36.25 3.02
2862 3077 5.543405 TCCACCAAAATTGTGATCCAAGATT 59.457 36.000 0.00 0.00 36.25 2.40
2863 3078 5.640357 CCACCAAAATTGTGATCCAAGATTG 59.360 40.000 0.00 12.48 36.25 2.67
2864 3079 6.225318 CACCAAAATTGTGATCCAAGATTGT 58.775 36.000 0.00 7.68 36.25 2.71
2865 3080 6.146510 CACCAAAATTGTGATCCAAGATTGTG 59.853 38.462 0.00 12.11 36.25 3.33
2866 3081 6.041865 ACCAAAATTGTGATCCAAGATTGTGA 59.958 34.615 0.00 0.00 36.25 3.58
2867 3082 6.930164 CCAAAATTGTGATCCAAGATTGTGAA 59.070 34.615 0.00 0.00 36.25 3.18
2868 3083 7.604927 CCAAAATTGTGATCCAAGATTGTGAAT 59.395 33.333 0.00 0.00 36.25 2.57
2869 3084 9.642327 CAAAATTGTGATCCAAGATTGTGAATA 57.358 29.630 0.00 0.00 36.25 1.75
2870 3085 9.643693 AAAATTGTGATCCAAGATTGTGAATAC 57.356 29.630 0.00 0.00 36.25 1.89
2871 3086 8.585471 AATTGTGATCCAAGATTGTGAATACT 57.415 30.769 0.00 0.00 36.25 2.12
2872 3087 9.685276 AATTGTGATCCAAGATTGTGAATACTA 57.315 29.630 0.00 0.00 36.25 1.82
2951 3180 5.182001 ACACATGAGCTTGGTCATTAACTTC 59.818 40.000 11.96 0.00 34.81 3.01
2959 3188 5.122396 GCTTGGTCATTAACTTCAATCGACT 59.878 40.000 0.00 0.00 0.00 4.18
2967 3196 2.146342 ACTTCAATCGACTGGTGCAAG 58.854 47.619 0.00 0.00 0.00 4.01
2971 3200 3.734463 TCAATCGACTGGTGCAAGTAAA 58.266 40.909 0.00 0.00 0.00 2.01
2977 3206 4.024387 TCGACTGGTGCAAGTAAACAAATC 60.024 41.667 0.00 0.00 0.00 2.17
2984 3213 9.906660 CTGGTGCAAGTAAACAAATCTATTTAA 57.093 29.630 0.00 0.00 0.00 1.52
3054 3286 4.379302 AAATCATAGGAGCCAGGAATCC 57.621 45.455 3.32 3.32 35.71 3.01
3140 3388 1.525535 GTAGCCTGCATGCCTCCAG 60.526 63.158 16.68 5.42 0.00 3.86
3160 3408 4.261741 CCAGATTAACATGCAATACCAGCC 60.262 45.833 0.00 0.00 0.00 4.85
3194 3442 6.641176 TTATGTGCAGTTTAGTGTATGTCG 57.359 37.500 0.00 0.00 0.00 4.35
3211 3459 4.822036 TGTCGATCTCTCTAAGCTAAGC 57.178 45.455 0.00 0.00 0.00 3.09
3235 3483 6.514048 GCCAGGCAATTAATTAGCTAGAGTTG 60.514 42.308 6.55 0.00 0.00 3.16
3274 3522 0.035176 GGCTGCATGCAAAAAGGGAA 59.965 50.000 22.88 0.00 45.15 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.265454 ACTCCCCTCGCTTAACCCAG 61.265 60.000 0.00 0.00 0.00 4.45
15 16 2.546162 GCTCATACTCCCCTCGCTTAAC 60.546 54.545 0.00 0.00 0.00 2.01
113 116 6.133356 TCATAGGGATGAGTGTGTGTATGTA 58.867 40.000 0.00 0.00 37.15 2.29
119 122 3.562973 GCATTCATAGGGATGAGTGTGTG 59.437 47.826 0.00 0.00 46.40 3.82
120 123 3.200605 TGCATTCATAGGGATGAGTGTGT 59.799 43.478 0.00 0.00 46.40 3.72
121 124 3.812262 TGCATTCATAGGGATGAGTGTG 58.188 45.455 0.00 3.66 46.40 3.82
140 143 0.801251 GTGACTTCATCAGTGCCTGC 59.199 55.000 0.00 0.00 38.28 4.85
141 144 1.446907 GGTGACTTCATCAGTGCCTG 58.553 55.000 0.00 0.00 38.28 4.85
142 145 0.036952 CGGTGACTTCATCAGTGCCT 60.037 55.000 0.00 0.00 38.28 4.75
143 146 1.021390 CCGGTGACTTCATCAGTGCC 61.021 60.000 0.00 0.00 38.28 5.01
144 147 0.037326 TCCGGTGACTTCATCAGTGC 60.037 55.000 0.00 0.00 38.28 4.40
145 148 2.274437 CATCCGGTGACTTCATCAGTG 58.726 52.381 0.00 0.00 38.28 3.66
146 149 1.406069 GCATCCGGTGACTTCATCAGT 60.406 52.381 0.00 0.00 38.28 3.41
147 150 1.293924 GCATCCGGTGACTTCATCAG 58.706 55.000 0.00 0.00 38.28 2.90
148 151 0.107703 GGCATCCGGTGACTTCATCA 60.108 55.000 0.00 0.00 31.05 3.07
149 152 0.179000 AGGCATCCGGTGACTTCATC 59.821 55.000 0.00 0.00 46.94 2.92
150 153 2.300996 AGGCATCCGGTGACTTCAT 58.699 52.632 0.00 0.00 46.94 2.57
151 154 3.805928 AGGCATCCGGTGACTTCA 58.194 55.556 0.00 0.00 46.94 3.02
155 158 0.527817 CTACGAAGGCATCCGGTGAC 60.528 60.000 0.00 0.73 35.41 3.67
185 188 0.614697 TCATTCAGCGGGAGGAGACA 60.615 55.000 0.00 0.00 0.00 3.41
190 193 3.480470 ACAATATTCATTCAGCGGGAGG 58.520 45.455 0.00 0.00 0.00 4.30
196 199 5.743872 GGTTTTCCGACAATATTCATTCAGC 59.256 40.000 0.00 0.00 0.00 4.26
209 212 8.301002 CCTCAATTTATTTTAGGTTTTCCGACA 58.699 33.333 0.00 0.00 46.35 4.35
211 214 8.517056 GTCCTCAATTTATTTTAGGTTTTCCGA 58.483 33.333 0.00 0.00 46.35 4.55
212 215 7.758076 GGTCCTCAATTTATTTTAGGTTTTCCG 59.242 37.037 0.00 0.00 46.35 4.30
213 216 8.812972 AGGTCCTCAATTTATTTTAGGTTTTCC 58.187 33.333 0.00 0.00 41.05 3.13
225 228 9.799106 CCATATGAACTTAGGTCCTCAATTTAT 57.201 33.333 3.65 0.00 0.00 1.40
226 229 8.778059 ACCATATGAACTTAGGTCCTCAATTTA 58.222 33.333 3.65 0.00 0.00 1.40
227 230 7.643123 ACCATATGAACTTAGGTCCTCAATTT 58.357 34.615 3.65 0.00 0.00 1.82
228 231 7.213178 ACCATATGAACTTAGGTCCTCAATT 57.787 36.000 3.65 0.00 0.00 2.32
229 232 6.831664 ACCATATGAACTTAGGTCCTCAAT 57.168 37.500 3.65 0.00 0.00 2.57
231 234 7.016268 GGAATACCATATGAACTTAGGTCCTCA 59.984 40.741 3.65 0.00 33.91 3.86
232 235 7.016268 TGGAATACCATATGAACTTAGGTCCTC 59.984 40.741 3.65 0.00 41.77 3.71
233 236 6.849697 TGGAATACCATATGAACTTAGGTCCT 59.150 38.462 3.65 0.00 41.77 3.85
235 238 7.444487 GGTTGGAATACCATATGAACTTAGGTC 59.556 40.741 3.65 0.00 46.34 3.85
236 239 7.128883 AGGTTGGAATACCATATGAACTTAGGT 59.871 37.037 3.65 0.00 46.34 3.08
237 240 7.518188 AGGTTGGAATACCATATGAACTTAGG 58.482 38.462 3.65 0.00 46.34 2.69
238 241 9.712305 CTAGGTTGGAATACCATATGAACTTAG 57.288 37.037 3.65 5.32 46.34 2.18
239 242 9.442062 TCTAGGTTGGAATACCATATGAACTTA 57.558 33.333 3.65 0.00 46.34 2.24
242 411 8.974060 TTTCTAGGTTGGAATACCATATGAAC 57.026 34.615 3.65 0.00 46.34 3.18
245 414 9.745018 ATGATTTCTAGGTTGGAATACCATATG 57.255 33.333 0.00 0.00 46.34 1.78
255 424 5.222442 TGGGGAAAATGATTTCTAGGTTGGA 60.222 40.000 0.00 0.00 43.65 3.53
256 425 5.022787 TGGGGAAAATGATTTCTAGGTTGG 58.977 41.667 0.00 0.00 43.65 3.77
268 437 9.499369 TTCAATCCTAATTTATGGGGAAAATGA 57.501 29.630 0.00 0.00 0.00 2.57
307 477 9.226606 TGGCCTACATATATGCAAATAAAGTAC 57.773 33.333 12.79 0.00 0.00 2.73
379 549 2.923655 TCGAAATTGAGCTTCTACGCAG 59.076 45.455 0.00 0.00 0.00 5.18
398 568 4.092821 TGGATGAAATTAAAGACTGCGTCG 59.907 41.667 3.62 0.00 37.67 5.12
401 571 4.795278 GCTTGGATGAAATTAAAGACTGCG 59.205 41.667 0.00 0.00 0.00 5.18
405 575 6.024552 TGGTGCTTGGATGAAATTAAAGAC 57.975 37.500 0.00 0.00 0.00 3.01
406 576 6.351202 CCATGGTGCTTGGATGAAATTAAAGA 60.351 38.462 2.57 0.00 36.26 2.52
408 578 5.248020 ACCATGGTGCTTGGATGAAATTAAA 59.752 36.000 18.99 0.00 37.69 1.52
409 579 4.776837 ACCATGGTGCTTGGATGAAATTAA 59.223 37.500 18.99 0.00 37.69 1.40
410 580 4.352009 ACCATGGTGCTTGGATGAAATTA 58.648 39.130 18.99 0.00 37.69 1.40
411 581 3.175594 ACCATGGTGCTTGGATGAAATT 58.824 40.909 18.99 0.00 37.69 1.82
412 582 2.823959 ACCATGGTGCTTGGATGAAAT 58.176 42.857 18.99 0.00 37.69 2.17
503 673 3.373565 GGTGCAAGGAAAGCCCGG 61.374 66.667 0.00 0.00 40.87 5.73
534 705 2.509052 GGGACACCTTGCTGTTTTTC 57.491 50.000 0.00 0.00 0.00 2.29
564 735 0.949105 CCTGTGGTGTACGTTGAGGC 60.949 60.000 0.00 0.00 0.00 4.70
700 871 1.686110 GGAAAGGGAGAGCGAGGGA 60.686 63.158 0.00 0.00 0.00 4.20
990 1172 0.106519 GGAAGATCATGGTGTGGGGG 60.107 60.000 0.00 0.00 0.00 5.40
1269 1462 4.884164 CCAAGATAAGATGGAAGTGAACCC 59.116 45.833 0.00 0.00 39.12 4.11
1319 1514 2.610976 GCATGCTGCTCAAAATCCAACA 60.611 45.455 11.37 0.00 40.96 3.33
1422 1617 0.554305 TCCCCTGCTGCATGATTGAT 59.446 50.000 1.31 0.00 0.00 2.57
1993 2191 2.797278 CCAGGTAGTAGCCCGCTGG 61.797 68.421 0.00 0.00 0.00 4.85
2198 2396 0.323087 TCCTCCGTCGTCTTCATGGA 60.323 55.000 0.00 0.00 0.00 3.41
2257 2455 1.381191 TGCCTGATCTCGGGTAGCA 60.381 57.895 6.91 0.00 44.34 3.49
2308 2506 2.348998 GTAGCCAGCACCAGCAGT 59.651 61.111 0.00 0.00 45.49 4.40
2413 2611 1.539065 CCAAGTCCATGCTACCGCTAG 60.539 57.143 0.00 0.00 36.97 3.42
2440 2638 8.109705 TGCAAAGCTTTTTCTATATCTCACAA 57.890 30.769 9.53 0.00 0.00 3.33
2484 2683 4.158025 TCGACCTTGTCTAGTTCTTCCATC 59.842 45.833 0.00 0.00 0.00 3.51
2517 2717 3.289836 CAACACCATGCATCCTTATCCA 58.710 45.455 0.00 0.00 0.00 3.41
2588 2791 1.260825 CGCAAGTGATCATGCTAGCTG 59.739 52.381 17.23 11.65 40.39 4.24
2648 2857 3.410631 TTAACTTCACCCTGAATGCGA 57.589 42.857 0.00 0.00 35.59 5.10
2656 2865 4.532834 ACACACACAATTAACTTCACCCT 58.467 39.130 0.00 0.00 0.00 4.34
2668 2877 6.952773 AAAGTGGTACAATACACACACAAT 57.047 33.333 0.00 0.00 44.16 2.71
2669 2878 6.151312 ACAAAAGTGGTACAATACACACACAA 59.849 34.615 0.00 0.00 44.16 3.33
2675 2884 7.589954 GTCATGAACAAAAGTGGTACAATACAC 59.410 37.037 0.00 0.00 44.16 2.90
2676 2885 7.283354 TGTCATGAACAAAAGTGGTACAATACA 59.717 33.333 0.00 0.00 35.36 2.29
2677 2886 7.644490 TGTCATGAACAAAAGTGGTACAATAC 58.356 34.615 0.00 0.00 35.36 1.89
2678 2887 7.809546 TGTCATGAACAAAAGTGGTACAATA 57.190 32.000 0.00 0.00 35.36 1.90
2744 2953 7.285401 ACGCAAACAGAAATGGGAGAATTATAT 59.715 33.333 0.00 0.00 34.03 0.86
2747 2956 4.764823 ACGCAAACAGAAATGGGAGAATTA 59.235 37.500 0.00 0.00 34.03 1.40
2755 2964 1.003262 CCGCACGCAAACAGAAATGG 61.003 55.000 0.00 0.00 0.00 3.16
2770 2979 4.646572 TCACATGTATATAATTGGCCGCA 58.353 39.130 0.00 0.00 0.00 5.69
2771 2980 5.220854 GGATCACATGTATATAATTGGCCGC 60.221 44.000 0.00 0.00 0.00 6.53
2772 2981 5.879777 TGGATCACATGTATATAATTGGCCG 59.120 40.000 0.00 0.00 0.00 6.13
2773 2982 7.611467 TCTTGGATCACATGTATATAATTGGCC 59.389 37.037 0.00 0.00 0.00 5.36
2774 2983 8.565896 TCTTGGATCACATGTATATAATTGGC 57.434 34.615 0.00 0.00 0.00 4.52
2800 3015 8.312564 TGGATTTCTTCAAATATGCATTCACAA 58.687 29.630 3.54 0.00 31.94 3.33
2808 3023 7.929785 ACCATCATTGGATTTCTTCAAATATGC 59.070 33.333 0.00 0.00 46.92 3.14
2838 3053 4.478203 TCTTGGATCACAATTTTGGTGGA 58.522 39.130 0.00 0.00 38.65 4.02
2882 3097 7.663827 CATGGATGTATGCATTTTAGTCCATT 58.336 34.615 20.09 9.88 36.67 3.16
2896 3111 6.259167 CCAAAAGGAAAATGCATGGATGTATG 59.741 38.462 0.00 0.00 33.33 2.39
2897 3112 6.156602 TCCAAAAGGAAAATGCATGGATGTAT 59.843 34.615 0.00 0.00 34.50 2.29
2898 3113 5.483231 TCCAAAAGGAAAATGCATGGATGTA 59.517 36.000 0.00 0.00 30.90 2.29
2899 3114 4.286549 TCCAAAAGGAAAATGCATGGATGT 59.713 37.500 0.00 0.00 30.90 3.06
2900 3115 4.834534 TCCAAAAGGAAAATGCATGGATG 58.165 39.130 0.00 0.00 30.90 3.51
2902 3117 4.158786 TCTCCAAAAGGAAAATGCATGGA 58.841 39.130 0.00 0.00 34.52 3.41
2930 3159 5.885230 TGAAGTTAATGACCAAGCTCATG 57.115 39.130 0.00 0.00 30.92 3.07
2951 3180 3.249799 TGTTTACTTGCACCAGTCGATTG 59.750 43.478 0.04 0.04 0.00 2.67
3054 3286 5.929697 TTCTCTTTCTGCTTACACATGTG 57.070 39.130 24.25 24.25 0.00 3.21
3140 3388 4.916983 TGGCTGGTATTGCATGTTAATC 57.083 40.909 0.00 0.00 0.00 1.75
3160 3408 5.428496 AACTGCACATAAATCGATCCATG 57.572 39.130 14.48 14.48 0.00 3.66
3194 3442 3.306019 GCCTGGCTTAGCTTAGAGAGATC 60.306 52.174 12.43 0.00 0.00 2.75
3211 3459 6.016777 CCAACTCTAGCTAATTAATTGCCTGG 60.017 42.308 11.05 8.51 0.00 4.45
3235 3483 1.730121 CGTGATCAACATTGCAGTGCC 60.730 52.381 13.72 0.00 0.00 5.01
3274 3522 6.096001 GCTTTTGGATGACCATCTTTGACTAT 59.904 38.462 9.56 0.00 46.34 2.12


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

AutoCloner maintained by Alex Coulton.