Multiple sequence alignment - TraesCS5A01G349000

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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 TraesCS5A01G349000 chr5A 100.000 4297 0 0 1 4297 552313394 552317690 0.000000e+00 7936.0
1 TraesCS5A01G349000 chr5A 94.663 1068 49 4 3037 4097 552355155 552356221 0.000000e+00 1650.0
2 TraesCS5A01G349000 chr5A 82.882 1735 223 45 2089 3785 552375665 552377363 0.000000e+00 1491.0
3 TraesCS5A01G349000 chr5A 81.638 1416 171 51 2089 3491 315334514 315335853 0.000000e+00 1092.0
4 TraesCS5A01G349000 chr5A 88.833 797 66 15 1178 1973 552374815 552375589 0.000000e+00 957.0
5 TraesCS5A01G349000 chr5A 87.343 798 84 9 1190 1973 315333685 315334479 0.000000e+00 898.0
6 TraesCS5A01G349000 chr5A 94.937 158 7 1 4141 4297 552356219 552356376 3.320000e-61 246.0
7 TraesCS5A01G349000 chr5A 81.529 314 22 7 848 1131 552372215 552372522 4.320000e-55 226.0
8 TraesCS5A01G349000 chr5A 92.424 132 9 1 955 1085 315332828 315332959 2.040000e-43 187.0
9 TraesCS5A01G349000 chr5A 100.000 28 0 0 4051 4078 475382735 475382708 8.000000e-03 52.8
10 TraesCS5A01G349000 chr5B 94.752 2363 102 8 775 3117 531219814 531222174 0.000000e+00 3657.0
11 TraesCS5A01G349000 chr5B 84.527 1732 197 36 2080 3781 531299097 531300787 0.000000e+00 1648.0
12 TraesCS5A01G349000 chr5B 90.159 945 74 8 3101 4034 531222190 531223126 0.000000e+00 1212.0
13 TraesCS5A01G349000 chr5B 87.089 790 77 14 1178 1965 531298248 531299014 0.000000e+00 870.0
14 TraesCS5A01G349000 chr5B 84.592 331 23 11 3 329 531218645 531218951 1.940000e-78 303.0
15 TraesCS5A01G349000 chr5B 89.503 181 18 1 4081 4260 531223305 531223485 1.200000e-55 228.0
16 TraesCS5A01G349000 chr5B 87.079 178 10 6 955 1131 531295026 531295191 5.670000e-44 189.0
17 TraesCS5A01G349000 chr5D 92.934 2038 112 18 775 2784 437038781 437040814 0.000000e+00 2937.0
18 TraesCS5A01G349000 chr5D 84.739 1304 149 31 2089 3369 437065937 437067213 0.000000e+00 1260.0
19 TraesCS5A01G349000 chr5D 81.907 1426 167 57 2082 3491 238779508 238778158 0.000000e+00 1120.0
20 TraesCS5A01G349000 chr5D 88.348 781 67 17 1197 1973 437065101 437065861 0.000000e+00 917.0
21 TraesCS5A01G349000 chr5D 87.037 810 81 16 1200 1990 238780318 238779514 0.000000e+00 893.0
22 TraesCS5A01G349000 chr5D 92.542 590 38 5 3713 4297 437046444 437047032 0.000000e+00 841.0
23 TraesCS5A01G349000 chr5D 91.593 452 34 4 3846 4294 437041844 437042294 4.720000e-174 621.0
24 TraesCS5A01G349000 chr5D 93.411 258 11 3 3483 3739 437046175 437046427 1.130000e-100 377.0
25 TraesCS5A01G349000 chr5D 86.014 286 33 7 44 329 437038009 437038287 2.510000e-77 300.0
26 TraesCS5A01G349000 chr5D 88.085 235 16 6 554 787 437038502 437038725 7.080000e-68 268.0
27 TraesCS5A01G349000 chr5D 92.486 173 9 2 329 501 437038322 437038490 1.190000e-60 244.0
28 TraesCS5A01G349000 chr5D 93.130 131 8 1 955 1084 437063328 437063458 1.580000e-44 191.0
29 TraesCS5A01G349000 chr5D 92.424 132 9 1 955 1085 238783264 238783133 2.040000e-43 187.0
30 TraesCS5A01G349000 chr5D 98.462 65 1 0 2797 2861 437040892 437040828 9.760000e-22 115.0
31 TraesCS5A01G349000 chr4B 78.403 551 115 4 1200 1748 168160230 168160778 5.280000e-94 355.0
32 TraesCS5A01G349000 chr4B 80.827 266 45 4 2312 2574 168184825 168185087 2.030000e-48 204.0
33 TraesCS5A01G349000 chr4B 100.000 28 0 0 4051 4078 641256481 641256508 8.000000e-03 52.8
34 TraesCS5A01G349000 chr4D 78.285 548 111 7 1205 1748 108218488 108217945 3.180000e-91 346.0
35 TraesCS5A01G349000 chr3B 100.000 28 0 0 4051 4078 202513033 202513006 8.000000e-03 52.8
36 TraesCS5A01G349000 chr1A 100.000 28 0 0 4051 4078 62256055 62256028 8.000000e-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 TraesCS5A01G349000 chr5A 552313394 552317690 4296 False 7936.000000 7936 100.000000 1 4297 1 chr5A.!!$F1 4296
1 TraesCS5A01G349000 chr5A 552355155 552356376 1221 False 948.000000 1650 94.800000 3037 4297 2 chr5A.!!$F3 1260
2 TraesCS5A01G349000 chr5A 552372215 552377363 5148 False 891.333333 1491 84.414667 848 3785 3 chr5A.!!$F4 2937
3 TraesCS5A01G349000 chr5A 315332828 315335853 3025 False 725.666667 1092 87.135000 955 3491 3 chr5A.!!$F2 2536
4 TraesCS5A01G349000 chr5B 531218645 531223485 4840 False 1350.000000 3657 89.751500 3 4260 4 chr5B.!!$F1 4257
5 TraesCS5A01G349000 chr5B 531295026 531300787 5761 False 902.333333 1648 86.231667 955 3781 3 chr5B.!!$F2 2826
6 TraesCS5A01G349000 chr5D 437038009 437047032 9023 False 798.285714 2937 91.009286 44 4297 7 chr5D.!!$F1 4253
7 TraesCS5A01G349000 chr5D 437063328 437067213 3885 False 789.333333 1260 88.739000 955 3369 3 chr5D.!!$F2 2414
8 TraesCS5A01G349000 chr5D 238778158 238783264 5106 True 733.333333 1120 87.122667 955 3491 3 chr5D.!!$R2 2536
9 TraesCS5A01G349000 chr4B 168160230 168160778 548 False 355.000000 355 78.403000 1200 1748 1 chr4B.!!$F1 548
10 TraesCS5A01G349000 chr4D 108217945 108218488 543 True 346.000000 346 78.285000 1205 1748 1 chr4D.!!$R1 543

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
231 247 0.399949 TTCCTGTGGACTGGTGGAGT 60.400 55.000 2.95 0.0 37.76 3.85 F
359 410 1.004394 GCCCCCAGTAGTTAGCTGTTT 59.996 52.381 0.00 0.0 32.41 2.83 F
523 882 1.066587 GAGCTCGGTCGGATTGGAG 59.933 63.158 0.00 0.0 0.00 3.86 F
770 1149 1.286570 TTGCATTCACCAGCAAGCG 59.713 52.632 0.00 0.0 44.98 4.68 F
2403 8992 0.596577 TCGTCACCACTTCCTTCTCG 59.403 55.000 0.00 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 8324 1.372838 CGCACACTTGGTCCACAACA 61.373 55.0 0.00 0.0 34.76 3.33 R
2354 8943 0.758734 GGCAAACTTGGCCCTTCTTT 59.241 50.0 0.00 0.0 46.85 2.52 R
2403 8992 2.159627 CACGAACAACACAAGGCCTATC 59.840 50.0 5.16 0.0 0.00 2.08 R
2593 9182 5.885912 ACAGGACCCAATGATTGTAATGTAC 59.114 40.0 4.27 0.0 0.00 2.90 R
4028 15456 0.103208 GCAGTCCTAGGTGATCCGTG 59.897 60.0 9.08 0.0 39.05 4.94 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
40 41 1.756430 TGACGGGATCTCTGACTCTG 58.244 55.000 0.00 0.00 0.00 3.35
81 82 3.959991 GAGGCCTGGGCTTGTCGTC 62.960 68.421 24.77 6.70 38.98 4.20
83 84 4.373116 GCCTGGGCTTGTCGTCGA 62.373 66.667 4.12 0.00 38.26 4.20
84 85 2.579201 CCTGGGCTTGTCGTCGAT 59.421 61.111 0.00 0.00 0.00 3.59
85 86 1.811266 CCTGGGCTTGTCGTCGATG 60.811 63.158 0.00 0.00 0.00 3.84
86 87 2.434185 TGGGCTTGTCGTCGATGC 60.434 61.111 0.00 3.80 0.00 3.91
87 88 3.195698 GGGCTTGTCGTCGATGCC 61.196 66.667 21.06 21.06 42.56 4.40
88 89 2.434185 GGCTTGTCGTCGATGCCA 60.434 61.111 22.98 6.07 42.79 4.92
89 90 2.740714 GGCTTGTCGTCGATGCCAC 61.741 63.158 22.98 3.61 42.79 5.01
90 91 2.740714 GCTTGTCGTCGATGCCACC 61.741 63.158 0.00 0.00 0.00 4.61
91 92 2.431771 TTGTCGTCGATGCCACCG 60.432 61.111 0.00 0.00 0.00 4.94
92 93 3.215597 TTGTCGTCGATGCCACCGT 62.216 57.895 0.00 0.00 0.00 4.83
118 131 1.813513 ACTCCAGCATACACAAGCAC 58.186 50.000 0.00 0.00 0.00 4.40
125 138 1.896220 CATACACAAGCACCCACTGT 58.104 50.000 0.00 0.00 0.00 3.55
172 185 3.807622 TGTACTAAAACTGCAGAGCACAC 59.192 43.478 23.35 9.39 33.79 3.82
173 186 1.867233 ACTAAAACTGCAGAGCACACG 59.133 47.619 23.35 4.77 33.79 4.49
174 187 2.135139 CTAAAACTGCAGAGCACACGA 58.865 47.619 23.35 0.00 33.79 4.35
183 196 0.613292 AGAGCACACGAGAGACCCAT 60.613 55.000 0.00 0.00 0.00 4.00
204 220 2.351276 GTGATCCGGGGCACAAGT 59.649 61.111 18.68 0.00 35.19 3.16
222 238 1.168714 GTGAGCCATTTCCTGTGGAC 58.831 55.000 0.00 0.00 39.12 4.02
229 245 1.073763 CATTTCCTGTGGACTGGTGGA 59.926 52.381 2.95 0.00 36.48 4.02
230 246 0.764890 TTTCCTGTGGACTGGTGGAG 59.235 55.000 2.95 0.00 36.48 3.86
231 247 0.399949 TTCCTGTGGACTGGTGGAGT 60.400 55.000 2.95 0.00 37.76 3.85
232 248 1.121407 TCCTGTGGACTGGTGGAGTG 61.121 60.000 2.95 0.00 33.83 3.51
233 249 1.372683 CTGTGGACTGGTGGAGTGG 59.627 63.158 0.00 0.00 33.83 4.00
234 250 1.383943 TGTGGACTGGTGGAGTGGT 60.384 57.895 0.00 0.00 33.83 4.16
235 251 1.071471 GTGGACTGGTGGAGTGGTG 59.929 63.158 0.00 0.00 33.83 4.17
236 252 1.383943 TGGACTGGTGGAGTGGTGT 60.384 57.895 0.00 0.00 33.83 4.16
250 266 2.093341 AGTGGTGTTAGTTGTTGGTCGT 60.093 45.455 0.00 0.00 0.00 4.34
254 270 3.243839 GGTGTTAGTTGTTGGTCGTCCTA 60.244 47.826 0.00 0.00 34.23 2.94
263 279 3.087781 GTTGGTCGTCCTAGAGGTAGTT 58.912 50.000 0.00 0.00 36.34 2.24
270 286 3.678252 CGTCCTAGAGGTAGTTGTCTCGA 60.678 52.174 0.00 0.00 35.34 4.04
280 296 4.700365 TGTCTCGACGGTGCGCTG 62.700 66.667 9.73 4.06 0.00 5.18
340 391 3.003480 GTGATCTGGTTGTTCCTACTGC 58.997 50.000 0.00 0.00 37.07 4.40
359 410 1.004394 GCCCCCAGTAGTTAGCTGTTT 59.996 52.381 0.00 0.00 32.41 2.83
384 729 2.621338 TCTTTATGAAGCACGGCAGAG 58.379 47.619 0.00 0.00 32.75 3.35
433 778 2.702270 TGCATAGAGGATAGAGCCCA 57.298 50.000 0.00 0.00 0.00 5.36
451 796 3.507622 GCCCAGTGAAGCTAAAGAAACAT 59.492 43.478 0.00 0.00 0.00 2.71
452 797 4.700213 GCCCAGTGAAGCTAAAGAAACATA 59.300 41.667 0.00 0.00 0.00 2.29
453 798 5.392057 GCCCAGTGAAGCTAAAGAAACATAC 60.392 44.000 0.00 0.00 0.00 2.39
464 809 7.648510 AGCTAAAGAAACATACTAGATGCGTAC 59.351 37.037 0.00 0.00 0.00 3.67
523 882 1.066587 GAGCTCGGTCGGATTGGAG 59.933 63.158 0.00 0.00 0.00 3.86
548 916 6.688073 ATACATTATACTCTGTTCCCTGGG 57.312 41.667 6.33 6.33 0.00 4.45
559 927 2.314852 TGTTCCCTGGGTCTCTGATCTA 59.685 50.000 13.56 0.00 0.00 1.98
567 935 5.221422 CCTGGGTCTCTGATCTAAAGCTAAG 60.221 48.000 0.00 0.00 0.00 2.18
575 943 7.507277 TCTCTGATCTAAAGCTAAGGCAAGATA 59.493 37.037 0.00 0.00 41.70 1.98
577 945 7.069950 TCTGATCTAAAGCTAAGGCAAGATACA 59.930 37.037 0.00 0.00 41.70 2.29
589 957 3.489785 GGCAAGATACATACACGTGCTAC 59.510 47.826 17.22 0.51 38.58 3.58
590 958 3.489785 GCAAGATACATACACGTGCTACC 59.510 47.826 17.22 0.00 36.46 3.18
599 967 2.602878 ACACGTGCTACCGATTAACTG 58.397 47.619 17.22 0.00 0.00 3.16
654 1023 8.694540 CCAATTAATAAATGTTGGGACTGATCA 58.305 33.333 0.00 0.00 37.92 2.92
662 1031 1.588239 TGGGACTGATCAGCCAATCT 58.412 50.000 26.93 9.21 0.00 2.40
711 1083 3.504520 CCTTGTTTAACCGGTGTGCTTAT 59.495 43.478 8.52 0.00 0.00 1.73
712 1084 4.696402 CCTTGTTTAACCGGTGTGCTTATA 59.304 41.667 8.52 0.00 0.00 0.98
730 1102 7.330946 GTGCTTATACTGACTAATGACACACAA 59.669 37.037 0.00 0.00 0.00 3.33
753 1125 4.960938 TGACAGTGACAAAGCTACTCATT 58.039 39.130 0.00 0.00 0.00 2.57
770 1149 1.286570 TTGCATTCACCAGCAAGCG 59.713 52.632 0.00 0.00 44.98 4.68
834 1281 2.290260 ACGACCTGCCTTCAATCAATGA 60.290 45.455 0.00 0.00 35.85 2.57
1035 1502 3.411517 ACCCAGCTTGCCGCCTAT 61.412 61.111 0.00 0.00 40.39 2.57
1044 1511 3.612681 GCCGCCTATGCCCTCGTA 61.613 66.667 0.00 0.00 0.00 3.43
1054 1521 2.420568 GCCCTCGTATCCACCGTCA 61.421 63.158 0.00 0.00 0.00 4.35
1131 1617 2.704464 TCCATCAATCTGTCTGCCAG 57.296 50.000 0.00 0.00 42.97 4.85
1198 7731 4.154737 TGATGTGCTTAGACTGAATGCAAC 59.845 41.667 0.00 0.00 35.34 4.17
1514 8053 3.758023 TCATCACCTACCTTGCATTTGTG 59.242 43.478 0.00 0.00 0.00 3.33
1785 8324 9.277783 GATGTTCCACTATATTATGCAGTTTCT 57.722 33.333 0.00 0.00 0.00 2.52
1808 8361 3.357079 GGACCAAGTGTGCGCCTG 61.357 66.667 4.18 0.00 0.00 4.85
1825 8378 6.295039 GCGCCTGCATTTTATACTTTACTA 57.705 37.500 0.00 0.00 42.15 1.82
2087 8667 6.639632 AATTAATCACTGGTCCACATATGC 57.360 37.500 1.58 0.00 0.00 3.14
2140 8720 7.042335 GTCACCACATATGAGCTAGTTAAGTT 58.958 38.462 10.38 0.00 0.00 2.66
2245 8829 5.420409 CAGGGTAACTTGTTCATCCTAGAC 58.580 45.833 0.00 0.00 39.20 2.59
2403 8992 0.596577 TCGTCACCACTTCCTTCTCG 59.403 55.000 0.00 0.00 0.00 4.04
2593 9182 6.771076 CATTTGACTGAATTCCAAATGCATG 58.229 36.000 23.65 11.31 45.32 4.06
2897 11303 6.317140 TCAGCCAATCAGTTACTGAAATCATC 59.683 38.462 19.42 6.84 44.04 2.92
2957 11372 2.289694 ACTCGATCTCCTTGGTTGTTGG 60.290 50.000 0.00 0.00 0.00 3.77
3031 11446 7.956420 TGTACTTCTGTTCATAACAATTCGT 57.044 32.000 0.00 0.00 41.61 3.85
3175 12225 4.523558 GTGCTAGACTATAAGGGTGTAGGG 59.476 50.000 0.00 0.00 33.12 3.53
3258 13537 4.927267 TTGAAGAGGTGGTACATGGATT 57.073 40.909 0.00 0.00 44.52 3.01
3360 13641 3.091633 ACTTGTATGCCCTGCTTGATT 57.908 42.857 0.00 0.00 0.00 2.57
3558 14912 1.078918 TTGATCTGCCACTGCCTCG 60.079 57.895 0.00 0.00 36.33 4.63
3627 14985 9.295825 AGTGTTGTTCTGTATTGATGGATTTTA 57.704 29.630 0.00 0.00 0.00 1.52
3684 15059 0.792640 CGTGCGCTTCTTGTCATCTT 59.207 50.000 9.73 0.00 0.00 2.40
3685 15060 1.195448 CGTGCGCTTCTTGTCATCTTT 59.805 47.619 9.73 0.00 0.00 2.52
3686 15061 2.349817 CGTGCGCTTCTTGTCATCTTTT 60.350 45.455 9.73 0.00 0.00 2.27
3687 15062 3.120683 CGTGCGCTTCTTGTCATCTTTTA 60.121 43.478 9.73 0.00 0.00 1.52
3688 15063 4.436050 CGTGCGCTTCTTGTCATCTTTTAT 60.436 41.667 9.73 0.00 0.00 1.40
3689 15064 5.024555 GTGCGCTTCTTGTCATCTTTTATC 58.975 41.667 9.73 0.00 0.00 1.75
3703 15084 6.703165 TCATCTTTTATCTCGGTGTGATCATG 59.297 38.462 0.00 0.00 0.00 3.07
3871 15299 0.521735 GCCACGACATTTCAGGAACC 59.478 55.000 0.00 0.00 0.00 3.62
3873 15301 1.806542 CCACGACATTTCAGGAACCTG 59.193 52.381 14.01 14.01 44.86 4.00
4037 15465 2.993899 CACCAGAACTTACACGGATCAC 59.006 50.000 0.00 0.00 0.00 3.06
4038 15466 2.028385 ACCAGAACTTACACGGATCACC 60.028 50.000 0.00 0.00 0.00 4.02
4039 15467 2.233922 CCAGAACTTACACGGATCACCT 59.766 50.000 0.00 0.00 0.00 4.00
4047 15627 0.103208 CACGGATCACCTAGGACTGC 59.897 60.000 17.98 3.62 0.00 4.40
4049 15629 1.101635 CGGATCACCTAGGACTGCGA 61.102 60.000 17.98 3.97 0.00 5.10
4087 15669 7.201670 GGATGAAATACCTTAAATCGAAACGGT 60.202 37.037 0.00 0.00 0.00 4.83
4241 15824 4.155826 TGCTTAGATCAAACATTTGGTCCG 59.844 41.667 12.89 4.90 46.83 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.427072 CCTTTCCTGTGGGGTGGTCT 61.427 60.000 0.00 0.00 36.25 3.85
1 2 1.074951 CCTTTCCTGTGGGGTGGTC 59.925 63.158 0.00 0.00 36.25 4.02
11 12 1.279271 AGATCCCGTCAACCTTTCCTG 59.721 52.381 0.00 0.00 0.00 3.86
81 82 2.767445 TAGGTCGACGGTGGCATCG 61.767 63.158 20.23 20.23 39.72 3.84
82 83 1.226888 GTAGGTCGACGGTGGCATC 60.227 63.158 9.92 0.00 0.00 3.91
83 84 1.664321 GAGTAGGTCGACGGTGGCAT 61.664 60.000 9.92 0.00 0.00 4.40
84 85 2.282674 AGTAGGTCGACGGTGGCA 60.283 61.111 9.92 0.00 0.00 4.92
85 86 2.488820 GAGTAGGTCGACGGTGGC 59.511 66.667 9.92 0.00 0.00 5.01
86 87 1.654954 CTGGAGTAGGTCGACGGTGG 61.655 65.000 9.92 0.00 0.00 4.61
87 88 1.801332 CTGGAGTAGGTCGACGGTG 59.199 63.158 9.92 0.00 0.00 4.94
88 89 2.045131 GCTGGAGTAGGTCGACGGT 61.045 63.158 9.92 1.52 0.00 4.83
89 90 1.384989 ATGCTGGAGTAGGTCGACGG 61.385 60.000 9.92 0.00 0.00 4.79
90 91 1.002684 GTATGCTGGAGTAGGTCGACG 60.003 57.143 9.92 0.00 0.00 5.12
91 92 2.022195 TGTATGCTGGAGTAGGTCGAC 58.978 52.381 7.13 7.13 0.00 4.20
92 93 2.022195 GTGTATGCTGGAGTAGGTCGA 58.978 52.381 0.00 0.00 0.00 4.20
135 148 2.041701 AGTACACTTGTTACCGGTGGT 58.958 47.619 19.93 5.27 40.16 4.16
197 210 1.068055 CAGGAAATGGCTCACTTGTGC 60.068 52.381 0.00 0.00 0.00 4.57
198 211 2.030540 CACAGGAAATGGCTCACTTGTG 60.031 50.000 0.00 0.00 0.00 3.33
199 212 2.233271 CACAGGAAATGGCTCACTTGT 58.767 47.619 0.00 0.00 0.00 3.16
200 213 1.542915 CCACAGGAAATGGCTCACTTG 59.457 52.381 0.00 0.00 0.00 3.16
204 220 1.067295 AGTCCACAGGAAATGGCTCA 58.933 50.000 0.00 0.00 37.13 4.26
222 238 2.158813 ACAACTAACACCACTCCACCAG 60.159 50.000 0.00 0.00 0.00 4.00
229 245 2.093341 ACGACCAACAACTAACACCACT 60.093 45.455 0.00 0.00 0.00 4.00
230 246 2.282407 ACGACCAACAACTAACACCAC 58.718 47.619 0.00 0.00 0.00 4.16
231 247 2.553086 GACGACCAACAACTAACACCA 58.447 47.619 0.00 0.00 0.00 4.17
232 248 1.869132 GGACGACCAACAACTAACACC 59.131 52.381 0.00 0.00 35.97 4.16
233 249 2.830104 AGGACGACCAACAACTAACAC 58.170 47.619 6.71 0.00 38.94 3.32
234 250 3.890756 TCTAGGACGACCAACAACTAACA 59.109 43.478 6.71 0.00 38.94 2.41
235 251 4.483311 CTCTAGGACGACCAACAACTAAC 58.517 47.826 6.71 0.00 38.94 2.34
236 252 3.508793 CCTCTAGGACGACCAACAACTAA 59.491 47.826 6.71 0.00 38.94 2.24
250 266 3.678252 CGTCGAGACAACTACCTCTAGGA 60.678 52.174 2.23 0.00 38.94 2.94
254 270 1.271271 ACCGTCGAGACAACTACCTCT 60.271 52.381 4.02 0.00 0.00 3.69
263 279 4.700365 CAGCGCACCGTCGAGACA 62.700 66.667 11.47 0.00 0.00 3.41
270 286 2.203015 AACACTTCAGCGCACCGT 60.203 55.556 11.47 0.00 0.00 4.83
280 296 4.944249 GCAAAGGGCGAACACTTC 57.056 55.556 0.00 0.00 0.00 3.01
340 391 2.711542 CAAACAGCTAACTACTGGGGG 58.288 52.381 0.00 0.00 39.55 5.40
359 410 2.095263 GCCGTGCTTCATAAAGAAAGCA 60.095 45.455 5.73 5.73 37.74 3.91
405 750 5.587861 TCTATCCTCTATGCATGTCTCCAT 58.412 41.667 10.16 0.00 0.00 3.41
415 760 2.233431 CACTGGGCTCTATCCTCTATGC 59.767 54.545 0.00 0.00 0.00 3.14
433 778 9.593134 CATCTAGTATGTTTCTTTAGCTTCACT 57.407 33.333 0.00 0.00 0.00 3.41
451 796 1.202734 AGCTCCCGTACGCATCTAGTA 60.203 52.381 10.49 0.00 0.00 1.82
452 797 0.465824 AGCTCCCGTACGCATCTAGT 60.466 55.000 10.49 0.00 0.00 2.57
453 798 1.520494 TAGCTCCCGTACGCATCTAG 58.480 55.000 10.49 3.16 0.00 2.43
464 809 5.246023 ATAATCCAGGCGATTAGCTCCCG 62.246 52.174 0.00 0.00 44.72 5.14
510 869 3.936372 ATGTATACTCCAATCCGACCG 57.064 47.619 4.17 0.00 0.00 4.79
523 882 7.234988 ACCCAGGGAACAGAGTATAATGTATAC 59.765 40.741 14.54 0.00 41.00 1.47
539 907 1.872773 AGATCAGAGACCCAGGGAAC 58.127 55.000 14.54 5.87 0.00 3.62
548 916 5.269505 TGCCTTAGCTTTAGATCAGAGAC 57.730 43.478 0.00 0.00 40.80 3.36
559 927 5.523916 CGTGTATGTATCTTGCCTTAGCTTT 59.476 40.000 0.00 0.00 40.80 3.51
567 935 2.550978 AGCACGTGTATGTATCTTGCC 58.449 47.619 18.38 0.00 0.00 4.52
575 943 2.953466 AATCGGTAGCACGTGTATGT 57.047 45.000 18.38 2.28 34.94 2.29
577 945 4.096833 TCAGTTAATCGGTAGCACGTGTAT 59.903 41.667 18.38 9.02 34.94 2.29
639 1008 0.994247 TGGCTGATCAGTCCCAACAT 59.006 50.000 24.11 0.00 30.48 2.71
654 1023 2.896044 TCGATCTATCTGCAGATTGGCT 59.104 45.455 32.94 20.71 37.14 4.75
711 1083 6.754193 TGTCATTGTGTGTCATTAGTCAGTA 58.246 36.000 0.00 0.00 0.00 2.74
712 1084 5.610398 TGTCATTGTGTGTCATTAGTCAGT 58.390 37.500 0.00 0.00 0.00 3.41
730 1102 4.607293 TGAGTAGCTTTGTCACTGTCAT 57.393 40.909 0.00 0.00 0.00 3.06
753 1125 1.898094 ACGCTTGCTGGTGAATGCA 60.898 52.632 0.00 0.00 37.42 3.96
770 1149 1.744741 GCTGCCTTGGAGAGAGCAC 60.745 63.158 0.00 0.00 31.25 4.40
834 1281 1.925972 GGGCCTCCTCCCACTTCTT 60.926 63.158 0.84 0.00 45.82 2.52
957 1423 2.815647 CGAAGGTGGAGAAGCGCC 60.816 66.667 2.29 0.00 0.00 6.53
1035 1502 2.363276 ACGGTGGATACGAGGGCA 60.363 61.111 0.00 0.00 42.51 5.36
1044 1511 1.889105 GCGCATGATGACGGTGGAT 60.889 57.895 0.30 0.00 0.00 3.41
1054 1521 1.426621 CGTTGCTGAAGCGCATGAT 59.573 52.632 11.47 0.00 45.83 2.45
1514 8053 3.083997 ACATGGAGGCCGAGGGTC 61.084 66.667 0.00 0.00 0.00 4.46
1567 8106 1.692042 ATGACCCCAGAGAGCCCAG 60.692 63.158 0.00 0.00 0.00 4.45
1785 8324 1.372838 CGCACACTTGGTCCACAACA 61.373 55.000 0.00 0.00 34.76 3.33
1841 8395 7.820044 AAAATGCAAACAAGAAAAGACGTTA 57.180 28.000 0.00 0.00 0.00 3.18
1842 8396 6.720012 AAAATGCAAACAAGAAAAGACGTT 57.280 29.167 0.00 0.00 0.00 3.99
1844 8398 6.760127 TGAAAAATGCAAACAAGAAAAGACG 58.240 32.000 0.00 0.00 0.00 4.18
2065 8645 5.072741 GGCATATGTGGACCAGTGATTAAT 58.927 41.667 4.29 0.00 0.00 1.40
2087 8667 8.960591 AGGAAATACTATGAAACAGTGAAATGG 58.039 33.333 0.00 0.00 0.00 3.16
2354 8943 0.758734 GGCAAACTTGGCCCTTCTTT 59.241 50.000 0.00 0.00 46.85 2.52
2403 8992 2.159627 CACGAACAACACAAGGCCTATC 59.840 50.000 5.16 0.00 0.00 2.08
2593 9182 5.885912 ACAGGACCCAATGATTGTAATGTAC 59.114 40.000 4.27 0.00 0.00 2.90
2897 11303 2.046892 CCAGGAGGCACAAGGACG 60.047 66.667 0.00 0.00 0.00 4.79
2957 11372 1.686587 GCCAACCCAAATGCCCTATAC 59.313 52.381 0.00 0.00 0.00 1.47
3029 11444 3.194968 ACCTGTTTATCCCAGTCAGTACG 59.805 47.826 0.00 0.00 0.00 3.67
3031 11446 5.105064 GCTAACCTGTTTATCCCAGTCAGTA 60.105 44.000 0.00 0.00 0.00 2.74
3163 12213 4.630382 TGAGTTATCCCCTACACCCTTA 57.370 45.455 0.00 0.00 0.00 2.69
3175 12225 8.951243 GGAATAGAAGCCATATTTGAGTTATCC 58.049 37.037 0.00 0.00 0.00 2.59
3258 13537 0.850100 TCTGGCTTCCCTTTGTTCCA 59.150 50.000 0.00 0.00 0.00 3.53
3360 13641 2.875933 CTCTAAAACGCCACAAACTCCA 59.124 45.455 0.00 0.00 0.00 3.86
3399 13681 9.713684 TCCATCCCTTTAATTCTTGACATATTT 57.286 29.630 0.00 0.00 0.00 1.40
3414 14196 4.953579 GCCAACTAATGTTCCATCCCTTTA 59.046 41.667 0.00 0.00 33.52 1.85
3627 14985 9.195411 CAAATAACATGTTTGCTAATCACAACT 57.805 29.630 17.78 0.00 30.75 3.16
3684 15059 5.290885 CGTTTCATGATCACACCGAGATAAA 59.709 40.000 0.00 0.00 0.00 1.40
3685 15060 4.803613 CGTTTCATGATCACACCGAGATAA 59.196 41.667 0.00 0.00 0.00 1.75
3686 15061 4.097286 TCGTTTCATGATCACACCGAGATA 59.903 41.667 0.00 0.00 0.00 1.98
3687 15062 3.119137 TCGTTTCATGATCACACCGAGAT 60.119 43.478 0.00 0.00 0.00 2.75
3688 15063 2.230266 TCGTTTCATGATCACACCGAGA 59.770 45.455 0.00 0.00 0.00 4.04
3689 15064 2.606108 TCGTTTCATGATCACACCGAG 58.394 47.619 0.00 0.00 0.00 4.63
3703 15084 5.622770 ATCTACACCAAACCAATCGTTTC 57.377 39.130 0.00 0.00 42.98 2.78
3848 15274 0.389817 CCTGAAATGTCGTGGCTCGA 60.390 55.000 7.67 7.67 46.83 4.04
3912 15340 9.522804 GTTCATATTGTGTTTTTGTTTCCTGTA 57.477 29.630 0.00 0.00 0.00 2.74
4028 15456 0.103208 GCAGTCCTAGGTGATCCGTG 59.897 60.000 9.08 0.00 39.05 4.94
4037 15465 5.175859 TGAAATTTTACTCGCAGTCCTAGG 58.824 41.667 0.82 0.82 0.00 3.02
4038 15466 5.292101 CCTGAAATTTTACTCGCAGTCCTAG 59.708 44.000 0.00 0.00 0.00 3.02
4039 15467 5.046878 TCCTGAAATTTTACTCGCAGTCCTA 60.047 40.000 0.00 0.00 0.00 2.94
4087 15669 2.088104 AGGGCTGGATGAATCGTCTA 57.912 50.000 2.19 0.00 0.00 2.59
4241 15824 1.990563 CAGTTCGGATTGTGACGGTAC 59.009 52.381 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.