Multiple sequence alignment - TraesCS5B01G050000

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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 TraesCS5B01G050000 chr5B 100.000 2464 0 0 1 2464 55363409 55365872 0.000000e+00 4551
1 TraesCS5B01G050000 chr5B 100.000 554 0 0 2764 3317 55366172 55366725 0.000000e+00 1024
2 TraesCS5B01G050000 chr5D 95.267 2303 97 7 162 2459 52274674 52276969 0.000000e+00 3639
3 TraesCS5B01G050000 chr5D 95.668 554 22 1 2764 3315 52276983 52277536 0.000000e+00 889
4 TraesCS5B01G050000 chr5D 94.400 125 6 1 1 125 52274553 52274676 1.210000e-44 191
5 TraesCS5B01G050000 chrUn 76.980 1477 258 49 977 2402 28321326 28322771 0.000000e+00 769
6 TraesCS5B01G050000 chr5A 77.162 1191 223 35 1232 2402 659360880 659362041 0.000000e+00 647
7 TraesCS5B01G050000 chr5A 90.526 285 20 2 3038 3315 41419244 41419528 1.450000e-98 370
8 TraesCS5B01G050000 chr5A 88.966 290 22 7 2764 3043 41413127 41413416 1.890000e-92 350
9 TraesCS5B01G050000 chr5A 89.855 207 21 0 2199 2405 41412798 41413004 1.960000e-67 267
10 TraesCS5B01G050000 chr5A 88.725 204 22 1 380 582 41410211 41410414 7.110000e-62 248


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 TraesCS5B01G050000 chr5B 55363409 55366725 3316 False 2787.500000 4551 100.000000 1 3317 2 chr5B.!!$F1 3316
1 TraesCS5B01G050000 chr5D 52274553 52277536 2983 False 1573.000000 3639 95.111667 1 3315 3 chr5D.!!$F1 3314
2 TraesCS5B01G050000 chrUn 28321326 28322771 1445 False 769.000000 769 76.980000 977 2402 1 chrUn.!!$F1 1425
3 TraesCS5B01G050000 chr5A 659360880 659362041 1161 False 647.000000 647 77.162000 1232 2402 1 chr5A.!!$F2 1170
4 TraesCS5B01G050000 chr5A 41410211 41413416 3205 False 288.333333 350 89.182000 380 3043 3 chr5A.!!$F3 2663

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
474 476 0.034616 GTCTCAGCAGTGCACTCCTT 59.965 55.0 18.64 2.01 0.0 3.36 F
656 660 0.249398 ATCCGAGTTCTTTCCCACCG 59.751 55.0 0.00 0.00 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 3860 0.036022 GCTCCAGTCTCAGGTGCTTT 59.964 55.0 0.0 0.0 41.24 3.51 R
2795 4446 1.425412 CCCAAAACAGTACGGACTCG 58.575 55.0 0.0 0.0 43.02 4.18 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
33 34 3.006752 AGCGGAATTTGAAAATGCCTTCA 59.993 39.130 10.46 0.00 41.27 3.02
115 116 5.458452 CGTACGTGTTTTAGTGGTACTTCAA 59.542 40.000 7.22 0.00 33.17 2.69
122 123 8.833493 GTGTTTTAGTGGTACTTCAAATGTAGT 58.167 33.333 0.00 0.00 0.00 2.73
123 124 8.832521 TGTTTTAGTGGTACTTCAAATGTAGTG 58.167 33.333 3.29 0.00 0.00 2.74
124 125 7.972832 TTTAGTGGTACTTCAAATGTAGTGG 57.027 36.000 3.29 0.00 0.00 4.00
125 126 4.324267 AGTGGTACTTCAAATGTAGTGGC 58.676 43.478 3.29 0.00 0.00 5.01
126 127 4.069304 GTGGTACTTCAAATGTAGTGGCA 58.931 43.478 3.29 0.00 0.00 4.92
127 128 4.154195 GTGGTACTTCAAATGTAGTGGCAG 59.846 45.833 3.29 0.00 0.00 4.85
128 129 4.202419 TGGTACTTCAAATGTAGTGGCAGT 60.202 41.667 0.00 0.00 0.00 4.40
129 130 4.154195 GGTACTTCAAATGTAGTGGCAGTG 59.846 45.833 4.76 0.00 0.00 3.66
130 131 3.149196 ACTTCAAATGTAGTGGCAGTGG 58.851 45.455 4.76 0.00 0.00 4.00
131 132 2.949177 TCAAATGTAGTGGCAGTGGT 57.051 45.000 4.76 0.00 0.00 4.16
132 133 2.503331 TCAAATGTAGTGGCAGTGGTG 58.497 47.619 4.76 0.00 0.00 4.17
133 134 2.105649 TCAAATGTAGTGGCAGTGGTGA 59.894 45.455 4.76 0.00 0.00 4.02
134 135 3.084039 CAAATGTAGTGGCAGTGGTGAT 58.916 45.455 4.76 0.00 0.00 3.06
135 136 2.408271 ATGTAGTGGCAGTGGTGATG 57.592 50.000 4.76 0.00 0.00 3.07
136 137 1.347062 TGTAGTGGCAGTGGTGATGA 58.653 50.000 4.76 0.00 0.00 2.92
137 138 1.276138 TGTAGTGGCAGTGGTGATGAG 59.724 52.381 4.76 0.00 0.00 2.90
138 139 1.276421 GTAGTGGCAGTGGTGATGAGT 59.724 52.381 4.76 0.00 0.00 3.41
139 140 0.035881 AGTGGCAGTGGTGATGAGTG 59.964 55.000 0.00 0.00 0.00 3.51
140 141 0.035317 GTGGCAGTGGTGATGAGTGA 59.965 55.000 0.00 0.00 0.00 3.41
141 142 0.764271 TGGCAGTGGTGATGAGTGAA 59.236 50.000 0.00 0.00 0.00 3.18
142 143 1.271001 TGGCAGTGGTGATGAGTGAAG 60.271 52.381 0.00 0.00 0.00 3.02
143 144 1.271054 GGCAGTGGTGATGAGTGAAGT 60.271 52.381 0.00 0.00 0.00 3.01
144 145 1.802960 GCAGTGGTGATGAGTGAAGTG 59.197 52.381 0.00 0.00 0.00 3.16
145 146 2.548707 GCAGTGGTGATGAGTGAAGTGA 60.549 50.000 0.00 0.00 0.00 3.41
146 147 3.732212 CAGTGGTGATGAGTGAAGTGAA 58.268 45.455 0.00 0.00 0.00 3.18
147 148 3.744942 CAGTGGTGATGAGTGAAGTGAAG 59.255 47.826 0.00 0.00 0.00 3.02
148 149 3.643320 AGTGGTGATGAGTGAAGTGAAGA 59.357 43.478 0.00 0.00 0.00 2.87
149 150 3.993081 GTGGTGATGAGTGAAGTGAAGAG 59.007 47.826 0.00 0.00 0.00 2.85
150 151 3.897505 TGGTGATGAGTGAAGTGAAGAGA 59.102 43.478 0.00 0.00 0.00 3.10
151 152 4.529769 TGGTGATGAGTGAAGTGAAGAGAT 59.470 41.667 0.00 0.00 0.00 2.75
152 153 5.012458 TGGTGATGAGTGAAGTGAAGAGATT 59.988 40.000 0.00 0.00 0.00 2.40
153 154 5.350914 GGTGATGAGTGAAGTGAAGAGATTG 59.649 44.000 0.00 0.00 0.00 2.67
154 155 4.934001 TGATGAGTGAAGTGAAGAGATTGC 59.066 41.667 0.00 0.00 0.00 3.56
155 156 3.320626 TGAGTGAAGTGAAGAGATTGCG 58.679 45.455 0.00 0.00 0.00 4.85
156 157 2.072298 AGTGAAGTGAAGAGATTGCGC 58.928 47.619 0.00 0.00 0.00 6.09
157 158 1.129437 GTGAAGTGAAGAGATTGCGCC 59.871 52.381 4.18 0.00 0.00 6.53
158 159 0.729690 GAAGTGAAGAGATTGCGCCC 59.270 55.000 4.18 0.00 0.00 6.13
159 160 0.036732 AAGTGAAGAGATTGCGCCCA 59.963 50.000 4.18 0.00 0.00 5.36
160 161 0.036732 AGTGAAGAGATTGCGCCCAA 59.963 50.000 4.18 0.00 35.01 4.12
185 186 6.409704 TGGAATTGTGTTCAGAGAGATTAGG 58.590 40.000 0.00 0.00 0.00 2.69
187 188 6.536941 GGAATTGTGTTCAGAGAGATTAGGTC 59.463 42.308 0.00 0.00 0.00 3.85
189 190 3.119459 TGTGTTCAGAGAGATTAGGTCGC 60.119 47.826 0.00 0.00 0.00 5.19
199 200 6.266558 AGAGAGATTAGGTCGCTGATTATGTT 59.733 38.462 0.00 0.00 37.09 2.71
200 201 6.219473 AGAGATTAGGTCGCTGATTATGTTG 58.781 40.000 0.00 0.00 35.50 3.33
206 207 5.730550 AGGTCGCTGATTATGTTGAACTTA 58.269 37.500 0.00 0.00 0.00 2.24
209 210 5.904080 GTCGCTGATTATGTTGAACTTATGC 59.096 40.000 0.00 0.00 0.00 3.14
211 212 5.207768 GCTGATTATGTTGAACTTATGCCG 58.792 41.667 0.00 0.00 0.00 5.69
237 238 4.527509 TCTTTTGTGTTTTGCCAGTGAA 57.472 36.364 0.00 0.00 0.00 3.18
238 239 4.493547 TCTTTTGTGTTTTGCCAGTGAAG 58.506 39.130 0.00 0.00 0.00 3.02
239 240 3.951775 TTTGTGTTTTGCCAGTGAAGT 57.048 38.095 0.00 0.00 0.00 3.01
240 241 3.951775 TTGTGTTTTGCCAGTGAAGTT 57.048 38.095 0.00 0.00 0.00 2.66
249 250 1.027357 CCAGTGAAGTTGCTGTGCTT 58.973 50.000 0.00 0.00 0.00 3.91
250 251 1.406539 CCAGTGAAGTTGCTGTGCTTT 59.593 47.619 0.00 0.00 0.00 3.51
254 255 2.098614 TGAAGTTGCTGTGCTTTCCAA 58.901 42.857 0.00 0.00 0.00 3.53
301 302 1.287730 CTGTGCAGAGAGGTGAACGC 61.288 60.000 4.50 0.00 0.00 4.84
302 303 1.300931 GTGCAGAGAGGTGAACGCA 60.301 57.895 0.00 0.00 0.00 5.24
304 305 0.035317 TGCAGAGAGGTGAACGCATT 59.965 50.000 0.00 0.00 0.00 3.56
333 334 1.695893 CGTCGCAATGCACTACAGGG 61.696 60.000 5.91 0.00 0.00 4.45
357 358 1.526887 GAGAATCCCGTGGATGCCA 59.473 57.895 6.24 0.00 42.27 4.92
391 393 0.752376 CTACGGACCACTCTCCTCCC 60.752 65.000 0.00 0.00 0.00 4.30
392 394 2.220786 TACGGACCACTCTCCTCCCC 62.221 65.000 0.00 0.00 0.00 4.81
403 405 2.285668 CCTCCCCTGGCTCCTTGA 60.286 66.667 0.00 0.00 0.00 3.02
418 420 2.024273 TCCTTGATACGGGACTCCTTCT 60.024 50.000 0.00 0.00 0.00 2.85
425 427 1.908483 GGGACTCCTTCTGGCGATT 59.092 57.895 0.00 0.00 0.00 3.34
457 459 1.671379 GGACCCGTCTGCCTTTGTC 60.671 63.158 0.00 0.00 0.00 3.18
463 465 0.601046 CGTCTGCCTTTGTCTCAGCA 60.601 55.000 0.00 0.00 0.00 4.41
474 476 0.034616 GTCTCAGCAGTGCACTCCTT 59.965 55.000 18.64 2.01 0.00 3.36
508 511 1.003718 GCCTCGCCACTAGGTTTGT 60.004 57.895 0.00 0.00 36.43 2.83
509 512 1.019805 GCCTCGCCACTAGGTTTGTC 61.020 60.000 0.00 0.00 36.43 3.18
547 551 8.555840 AGGATACACTTGTTGGAACAACCAGT 62.556 42.308 11.62 11.62 45.67 4.00
554 558 1.227853 GGAACAACCAGTCAGCGGT 60.228 57.895 0.00 0.00 38.85 5.68
595 599 2.637872 GGTCCTTATACATAGCCTGGCA 59.362 50.000 22.65 7.39 0.00 4.92
599 603 3.055530 CCTTATACATAGCCTGGCAGAGG 60.056 52.174 22.65 12.45 46.13 3.69
614 618 2.556286 GAGGGCCTTGTTTTCCTCG 58.444 57.895 7.89 0.00 36.78 4.63
627 631 5.130350 TGTTTTCCTCGTGATTCCTTTCTT 58.870 37.500 0.00 0.00 0.00 2.52
656 660 0.249398 ATCCGAGTTCTTTCCCACCG 59.751 55.000 0.00 0.00 0.00 4.94
674 678 3.376234 CACCGGTCTAGTTTATCGTCAGA 59.624 47.826 2.59 0.00 0.00 3.27
677 681 4.515944 CCGGTCTAGTTTATCGTCAGATCT 59.484 45.833 0.00 0.00 38.26 2.75
711 715 2.410060 CGCGCCTATACGACACCA 59.590 61.111 0.00 0.00 34.06 4.17
735 739 2.147958 CCTCTCTTCCTCCGTATCTCG 58.852 57.143 0.00 0.00 39.52 4.04
745 749 4.033684 CCTCCGTATCTCGAACGTTTTAG 58.966 47.826 0.46 3.22 42.86 1.85
763 767 7.607991 ACGTTTTAGAGGTTTCATTCATCATCT 59.392 33.333 0.00 0.00 0.00 2.90
1540 2478 8.727149 TGACCAAAGGGATCAGATAAATAGATT 58.273 33.333 0.00 0.00 38.05 2.40
1970 2917 1.134401 AGTGGCCCATCGATACTGTTG 60.134 52.381 0.00 0.00 0.00 3.33
1974 2921 2.205074 GCCCATCGATACTGTTGTCAG 58.795 52.381 0.00 0.00 46.18 3.51
2109 3063 1.998315 CTCTTCATTGCACCGAGTCAG 59.002 52.381 0.00 0.00 0.00 3.51
2122 3076 1.656095 CGAGTCAGAAGGTTTGCGATC 59.344 52.381 0.00 0.00 0.00 3.69
2225 3822 9.739276 ATTTATTTATCTGTGTGTTTCAGAGGA 57.261 29.630 0.00 0.00 43.66 3.71
2230 3827 2.797156 CTGTGTGTTTCAGAGGACTTCG 59.203 50.000 0.00 0.00 34.34 3.79
2263 3860 8.028938 GGAAAGCTGCACAAATTTTCTTATCTA 58.971 33.333 1.02 0.00 0.00 1.98
2282 3879 0.036022 AAAGCACCTGAGACTGGAGC 59.964 55.000 8.44 8.44 38.75 4.70
2382 3979 5.067936 TGGAAAAGCTGGAATTTCACGTAAA 59.932 36.000 10.06 0.00 37.29 2.01
2459 4110 6.010850 GGAAATAAAGGGGAAACAGTCTTCT 58.989 40.000 0.00 0.00 0.00 2.85
2460 4111 6.493802 GGAAATAAAGGGGAAACAGTCTTCTT 59.506 38.462 0.00 0.00 0.00 2.52
2461 4112 7.309255 GGAAATAAAGGGGAAACAGTCTTCTTC 60.309 40.741 0.00 0.00 0.00 2.87
2462 4113 4.797912 AAAGGGGAAACAGTCTTCTTCT 57.202 40.909 0.00 0.00 0.00 2.85
2795 4446 7.989826 AGTCATGAACTAACCATTAGCAAATC 58.010 34.615 0.00 0.00 36.07 2.17
2800 4451 6.312918 TGAACTAACCATTAGCAAATCGAGTC 59.687 38.462 0.00 0.00 36.71 3.36
2816 4467 0.763035 AGTCCGTACTGTTTTGGGCT 59.237 50.000 0.00 0.00 33.57 5.19
2918 4571 3.809905 AGTTCTTCACTTCACCAAGTCC 58.190 45.455 0.00 0.00 41.24 3.85
2985 4648 4.986659 ACTGACGATGCGTAAAAAGTAGTT 59.013 37.500 0.00 0.00 41.37 2.24
3074 4737 1.381327 CCTACGGAGCCTTCCCTCA 60.381 63.158 0.00 0.00 40.67 3.86
3110 4773 0.684535 TCAGGCTGGTCGAAATCACA 59.315 50.000 15.73 0.00 0.00 3.58
3113 4776 1.026718 GGCTGGTCGAAATCACAGGG 61.027 60.000 0.00 0.00 0.00 4.45
3131 4794 0.242825 GGTTTTACGGCTGGAAAGGC 59.757 55.000 2.51 0.94 0.00 4.35
3156 4819 2.816958 AGCTGGCGCTTCACATCG 60.817 61.111 7.64 0.00 46.47 3.84
3224 4887 0.322546 CCCCTGCAGTAGTTGGTTCC 60.323 60.000 13.81 0.00 0.00 3.62
3239 4902 2.237643 TGGTTCCGATTTTAGGCTGCTA 59.762 45.455 0.00 0.00 0.00 3.49
3245 4908 2.481952 CGATTTTAGGCTGCTAGGATGC 59.518 50.000 0.00 0.00 0.00 3.91
3246 4909 2.348411 TTTTAGGCTGCTAGGATGCC 57.652 50.000 14.15 14.15 46.42 4.40
3250 4913 3.550431 GCTGCTAGGATGCCCGGA 61.550 66.667 0.73 0.00 37.58 5.14
3254 4917 1.069935 GCTAGGATGCCCGGAGTTC 59.930 63.158 0.73 0.00 37.58 3.01
3255 4918 1.686325 GCTAGGATGCCCGGAGTTCA 61.686 60.000 0.73 0.00 37.58 3.18
3280 4943 0.461339 TTTTCGGATGGCTACGAGGC 60.461 55.000 0.00 0.00 40.51 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.308830 GGCATTTTCAAATTCCGCTAGAGATAT 60.309 37.037 0.00 0.00 0.00 1.63
33 34 7.177392 GCCTATAAAATGATGGCCTAGACATTT 59.823 37.037 17.33 17.33 42.25 2.32
67 68 5.100259 CTGTTAGCAGGCATTTCTCAAATG 58.900 41.667 0.00 4.84 41.16 2.32
68 69 4.381292 GCTGTTAGCAGGCATTTCTCAAAT 60.381 41.667 8.78 0.00 41.89 2.32
75 76 1.737793 GTACGCTGTTAGCAGGCATTT 59.262 47.619 8.78 0.00 42.58 2.32
115 116 2.305635 TCATCACCACTGCCACTACATT 59.694 45.455 0.00 0.00 0.00 2.71
122 123 0.764271 TTCACTCATCACCACTGCCA 59.236 50.000 0.00 0.00 0.00 4.92
123 124 1.271054 ACTTCACTCATCACCACTGCC 60.271 52.381 0.00 0.00 0.00 4.85
124 125 1.802960 CACTTCACTCATCACCACTGC 59.197 52.381 0.00 0.00 0.00 4.40
125 126 3.391506 TCACTTCACTCATCACCACTG 57.608 47.619 0.00 0.00 0.00 3.66
126 127 3.643320 TCTTCACTTCACTCATCACCACT 59.357 43.478 0.00 0.00 0.00 4.00
127 128 3.993081 CTCTTCACTTCACTCATCACCAC 59.007 47.826 0.00 0.00 0.00 4.16
128 129 3.897505 TCTCTTCACTTCACTCATCACCA 59.102 43.478 0.00 0.00 0.00 4.17
129 130 4.527509 TCTCTTCACTTCACTCATCACC 57.472 45.455 0.00 0.00 0.00 4.02
130 131 5.163874 GCAATCTCTTCACTTCACTCATCAC 60.164 44.000 0.00 0.00 0.00 3.06
131 132 4.934001 GCAATCTCTTCACTTCACTCATCA 59.066 41.667 0.00 0.00 0.00 3.07
132 133 4.032672 CGCAATCTCTTCACTTCACTCATC 59.967 45.833 0.00 0.00 0.00 2.92
133 134 3.931468 CGCAATCTCTTCACTTCACTCAT 59.069 43.478 0.00 0.00 0.00 2.90
134 135 3.320626 CGCAATCTCTTCACTTCACTCA 58.679 45.455 0.00 0.00 0.00 3.41
135 136 2.093467 GCGCAATCTCTTCACTTCACTC 59.907 50.000 0.30 0.00 0.00 3.51
136 137 2.072298 GCGCAATCTCTTCACTTCACT 58.928 47.619 0.30 0.00 0.00 3.41
137 138 1.129437 GGCGCAATCTCTTCACTTCAC 59.871 52.381 10.83 0.00 0.00 3.18
138 139 1.442769 GGCGCAATCTCTTCACTTCA 58.557 50.000 10.83 0.00 0.00 3.02
139 140 0.729690 GGGCGCAATCTCTTCACTTC 59.270 55.000 10.83 0.00 0.00 3.01
140 141 0.036732 TGGGCGCAATCTCTTCACTT 59.963 50.000 10.83 0.00 0.00 3.16
141 142 0.036732 TTGGGCGCAATCTCTTCACT 59.963 50.000 12.81 0.00 0.00 3.41
142 143 1.098050 ATTGGGCGCAATCTCTTCAC 58.902 50.000 22.17 0.00 0.00 3.18
143 144 1.097232 CATTGGGCGCAATCTCTTCA 58.903 50.000 24.66 0.00 0.00 3.02
144 145 0.383231 CCATTGGGCGCAATCTCTTC 59.617 55.000 24.66 0.00 0.00 2.87
145 146 0.034186 TCCATTGGGCGCAATCTCTT 60.034 50.000 24.66 3.28 0.00 2.85
146 147 0.034186 TTCCATTGGGCGCAATCTCT 60.034 50.000 24.66 3.68 0.00 3.10
147 148 1.035139 ATTCCATTGGGCGCAATCTC 58.965 50.000 24.66 0.00 0.00 2.75
148 149 1.137479 CAATTCCATTGGGCGCAATCT 59.863 47.619 24.66 4.84 36.63 2.40
149 150 1.134729 ACAATTCCATTGGGCGCAATC 60.135 47.619 24.66 0.00 44.42 2.67
150 151 0.903942 ACAATTCCATTGGGCGCAAT 59.096 45.000 22.17 22.17 44.42 3.56
151 152 0.037512 CACAATTCCATTGGGCGCAA 60.038 50.000 19.29 19.29 44.42 4.85
152 153 1.590665 CACAATTCCATTGGGCGCA 59.409 52.632 10.83 0.00 44.42 6.09
153 154 4.500396 CACAATTCCATTGGGCGC 57.500 55.556 0.00 0.00 44.42 6.53
157 158 5.005740 TCTCTCTGAACACAATTCCATTGG 58.994 41.667 0.00 0.00 44.42 3.16
158 159 6.754702 ATCTCTCTGAACACAATTCCATTG 57.245 37.500 0.00 0.00 45.59 2.82
159 160 7.555554 CCTAATCTCTCTGAACACAATTCCATT 59.444 37.037 0.00 0.00 0.00 3.16
160 161 7.052873 CCTAATCTCTCTGAACACAATTCCAT 58.947 38.462 0.00 0.00 0.00 3.41
173 174 4.582701 AATCAGCGACCTAATCTCTCTG 57.417 45.455 0.00 0.00 0.00 3.35
185 186 5.904080 GCATAAGTTCAACATAATCAGCGAC 59.096 40.000 0.00 0.00 0.00 5.19
187 188 5.207768 GGCATAAGTTCAACATAATCAGCG 58.792 41.667 0.00 0.00 0.00 5.18
189 190 6.183360 ACACGGCATAAGTTCAACATAATCAG 60.183 38.462 0.00 0.00 0.00 2.90
199 200 5.163602 ACAAAAGAAACACGGCATAAGTTCA 60.164 36.000 0.00 0.00 0.00 3.18
200 201 5.173131 CACAAAAGAAACACGGCATAAGTTC 59.827 40.000 0.00 0.00 0.00 3.01
206 207 3.518634 AACACAAAAGAAACACGGCAT 57.481 38.095 0.00 0.00 0.00 4.40
209 210 3.181525 GGCAAAACACAAAAGAAACACGG 60.182 43.478 0.00 0.00 0.00 4.94
211 212 4.450757 ACTGGCAAAACACAAAAGAAACAC 59.549 37.500 0.00 0.00 0.00 3.32
237 238 4.935352 TTAATTGGAAAGCACAGCAACT 57.065 36.364 0.00 0.00 0.00 3.16
238 239 5.520022 CATTAATTGGAAAGCACAGCAAC 57.480 39.130 0.00 0.00 0.00 4.17
254 255 9.646522 ATTACCAGCTTAATCTGTTCCATTAAT 57.353 29.630 5.64 0.00 32.32 1.40
301 302 2.592796 TGCGACGTTTCACATCAATG 57.407 45.000 0.00 0.00 0.00 2.82
302 303 3.491356 CATTGCGACGTTTCACATCAAT 58.509 40.909 0.00 0.00 0.00 2.57
304 305 1.399599 GCATTGCGACGTTTCACATCA 60.400 47.619 0.00 0.00 0.00 3.07
318 319 2.017049 CTAACCCCTGTAGTGCATTGC 58.983 52.381 0.46 0.46 0.00 3.56
333 334 1.492764 TCCACGGGATTCTCCTAACC 58.507 55.000 0.00 0.00 36.57 2.85
357 358 1.592223 GTAGTTCTGAGCCAGCGGT 59.408 57.895 0.00 0.00 0.00 5.68
361 362 0.173708 GGTCCGTAGTTCTGAGCCAG 59.826 60.000 0.00 0.00 0.00 4.85
362 363 0.541063 TGGTCCGTAGTTCTGAGCCA 60.541 55.000 0.00 0.00 0.00 4.75
368 369 1.355043 AGGAGAGTGGTCCGTAGTTCT 59.645 52.381 0.00 0.00 42.05 3.01
369 370 1.744522 GAGGAGAGTGGTCCGTAGTTC 59.255 57.143 0.00 0.00 42.05 3.01
391 393 1.048724 TCCCGTATCAAGGAGCCAGG 61.049 60.000 0.00 0.00 0.00 4.45
392 394 0.105039 GTCCCGTATCAAGGAGCCAG 59.895 60.000 0.00 0.00 31.17 4.85
403 405 1.392710 CGCCAGAAGGAGTCCCGTAT 61.393 60.000 5.25 0.00 36.89 3.06
418 420 1.227350 CGAGGCTGATCAATCGCCA 60.227 57.895 22.46 0.00 43.77 5.69
425 427 3.838271 GTCCGCCGAGGCTGATCA 61.838 66.667 12.70 0.00 40.77 2.92
457 459 2.541288 CAAGGAGTGCACTGCTGAG 58.459 57.895 37.24 28.33 44.15 3.35
498 501 2.344025 GCGAAATCCGACAAACCTAGT 58.656 47.619 0.00 0.00 41.76 2.57
508 511 1.124780 TATCCTTGGGCGAAATCCGA 58.875 50.000 0.00 0.00 41.76 4.55
509 512 1.226746 GTATCCTTGGGCGAAATCCG 58.773 55.000 0.00 0.00 42.21 4.18
547 551 1.561769 ATCCAATCCACCACCGCTGA 61.562 55.000 0.00 0.00 0.00 4.26
549 553 1.077501 CATCCAATCCACCACCGCT 60.078 57.895 0.00 0.00 0.00 5.52
554 558 1.066215 CGAGACACATCCAATCCACCA 60.066 52.381 0.00 0.00 0.00 4.17
595 599 0.036875 CGAGGAAAACAAGGCCCTCT 59.963 55.000 0.00 0.00 42.20 3.69
599 603 1.534729 ATCACGAGGAAAACAAGGCC 58.465 50.000 0.00 0.00 0.00 5.19
606 610 4.023193 GCAAGAAAGGAATCACGAGGAAAA 60.023 41.667 0.00 0.00 0.00 2.29
627 631 1.989966 GAACTCGGATCGGACTCGCA 61.990 60.000 0.00 0.00 36.13 5.10
656 660 6.038382 TGACAGATCTGACGATAAACTAGACC 59.962 42.308 29.27 0.00 0.00 3.85
674 678 2.351276 GGCGGGTGGTTGACAGAT 59.649 61.111 0.00 0.00 0.00 2.90
696 700 1.274596 GTGTTGGTGTCGTATAGGCG 58.725 55.000 0.00 0.00 0.00 5.52
699 703 3.695060 AGAGAGGTGTTGGTGTCGTATAG 59.305 47.826 0.00 0.00 0.00 1.31
706 710 1.694696 GAGGAAGAGAGGTGTTGGTGT 59.305 52.381 0.00 0.00 0.00 4.16
707 711 1.002544 GGAGGAAGAGAGGTGTTGGTG 59.997 57.143 0.00 0.00 0.00 4.17
711 715 2.599408 TACGGAGGAAGAGAGGTGTT 57.401 50.000 0.00 0.00 0.00 3.32
735 739 7.581476 TGATGAATGAAACCTCTAAAACGTTC 58.419 34.615 0.00 0.00 0.00 3.95
745 749 5.649395 TGGAACAGATGATGAATGAAACCTC 59.351 40.000 0.00 0.00 0.00 3.85
763 767 4.472470 AGAGGACATGATGAATCTGGAACA 59.528 41.667 0.00 0.00 0.00 3.18
895 899 6.644592 GCTCAACATCTCACCTGATATTACTC 59.355 42.308 0.00 0.00 0.00 2.59
1112 1360 3.233507 ACAACTTGGCATGAGTCCATTT 58.766 40.909 7.45 0.00 32.92 2.32
1970 2917 0.877743 GCAAAGTTCCAGGAGCTGAC 59.122 55.000 6.58 0.00 32.44 3.51
1974 2921 1.809547 GAGAAGCAAAGTTCCAGGAGC 59.190 52.381 0.00 0.00 0.00 4.70
2109 3063 0.953960 ACGGTGGATCGCAAACCTTC 60.954 55.000 0.00 0.00 0.00 3.46
2122 3076 2.781681 ACTGGAAATAGGAACGGTGG 57.218 50.000 0.00 0.00 0.00 4.61
2225 3822 2.416850 CAGCTTTCCTGGCAACGAAGT 61.417 52.381 0.00 0.00 39.66 3.01
2230 3827 1.006922 GTGCAGCTTTCCTGGCAAC 60.007 57.895 0.00 0.00 42.03 4.17
2263 3860 0.036022 GCTCCAGTCTCAGGTGCTTT 59.964 55.000 0.00 0.00 41.24 3.51
2795 4446 1.425412 CCCAAAACAGTACGGACTCG 58.575 55.000 0.00 0.00 43.02 4.18
2800 4451 3.340034 TGATAAGCCCAAAACAGTACGG 58.660 45.455 0.00 0.00 0.00 4.02
2816 4467 9.952030 TTATTCCACAAGTACAACTGATGATAA 57.048 29.630 0.00 0.00 0.00 1.75
3044 4707 3.510846 CGTAGGTCTCCCTGGTCG 58.489 66.667 0.00 0.00 42.67 4.79
3074 4737 0.616964 TGAGATGCAGGTGAGGCTCT 60.617 55.000 16.72 0.00 0.00 4.09
3110 4773 1.546998 CCTTTCCAGCCGTAAAACCCT 60.547 52.381 0.00 0.00 0.00 4.34
3113 4776 0.242825 GGCCTTTCCAGCCGTAAAAC 59.757 55.000 0.00 0.00 41.41 2.43
3156 4819 2.089349 GCGCGACAGAGTTCCTCAC 61.089 63.158 12.10 0.00 32.06 3.51
3224 4887 2.481952 GCATCCTAGCAGCCTAAAATCG 59.518 50.000 0.00 0.00 0.00 3.34
3239 4902 1.201429 AAGTGAACTCCGGGCATCCT 61.201 55.000 0.00 0.00 0.00 3.24
3245 4908 2.152016 GAAAAGGAAGTGAACTCCGGG 58.848 52.381 0.00 0.00 0.00 5.73
3246 4909 1.798813 CGAAAAGGAAGTGAACTCCGG 59.201 52.381 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.