Multiple sequence alignment - TraesCS5B01G079100

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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 TraesCS5B01G079100 chr5B 100.000 3563 0 0 1 3563 96491356 96487794 0.000000e+00 6580.0
1 TraesCS5B01G079100 chr5D 93.902 2427 106 20 438 2859 91343322 91340933 0.000000e+00 3624.0
2 TraesCS5B01G079100 chr5D 87.579 475 37 10 2862 3329 91334268 91333809 6.770000e-147 531.0
3 TraesCS5B01G079100 chr5D 91.532 248 18 3 495 740 91345290 91345044 4.410000e-89 339.0
4 TraesCS5B01G079100 chr5D 86.099 223 22 5 616 838 91345001 91344788 7.690000e-57 231.0
5 TraesCS5B01G079100 chr5D 90.909 165 14 1 3354 3518 91333714 91333551 1.670000e-53 220.0
6 TraesCS5B01G079100 chr5D 83.099 71 12 0 10 80 10542916 10542846 8.260000e-07 65.8
7 TraesCS5B01G079100 chr5A 93.858 2426 99 23 415 2825 84896853 84894463 0.000000e+00 3609.0
8 TraesCS5B01G079100 chr5A 88.136 413 41 6 1 410 84897390 84896983 5.350000e-133 484.0
9 TraesCS5B01G079100 chr5A 93.548 217 14 0 3128 3344 84893631 84893415 1.230000e-84 324.0
10 TraesCS5B01G079100 chr5A 86.316 190 17 5 3341 3522 84893368 84893180 7.800000e-47 198.0
11 TraesCS5B01G079100 chr5A 83.432 169 7 4 2827 2994 84893897 84893749 1.730000e-28 137.0


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 TraesCS5B01G079100 chr5B 96487794 96491356 3562 True 6580.0 6580 100.000 1 3563 1 chr5B.!!$R1 3562
1 TraesCS5B01G079100 chr5D 91340933 91345290 4357 True 1398.0 3624 90.511 438 2859 3 chr5D.!!$R3 2421
2 TraesCS5B01G079100 chr5D 91333551 91334268 717 True 375.5 531 89.244 2862 3518 2 chr5D.!!$R2 656
3 TraesCS5B01G079100 chr5A 84893180 84897390 4210 True 950.4 3609 89.058 1 3522 5 chr5A.!!$R1 3521

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
226 227 0.871722 TTGGACTCAACGAAATGGCG 59.128 50.000 0.0 0.0 37.29 5.69 F
893 2436 1.228245 GCAGCTTCCTCCCAACACA 60.228 57.895 0.0 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 3205 1.585006 GAACGTCTTCCTCGGCTCA 59.415 57.895 0.0 0.0 0.0 4.26 R
2710 4267 0.834261 TCACCATGACAACTCGGGGA 60.834 55.000 0.0 0.0 0.0 4.81 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
29 30 5.049198 TGAATGTGTCTTCTGCAATGAGAAC 60.049 40.000 0.00 0.00 0.00 3.01
31 32 2.802816 GTGTCTTCTGCAATGAGAACGT 59.197 45.455 0.00 0.00 0.00 3.99
51 52 4.511826 ACGTTGAAGAAACCTTGAGACATC 59.488 41.667 0.00 0.00 35.13 3.06
53 54 5.237344 CGTTGAAGAAACCTTGAGACATCTT 59.763 40.000 0.00 0.00 35.13 2.40
226 227 0.871722 TTGGACTCAACGAAATGGCG 59.128 50.000 0.00 0.00 37.29 5.69
230 231 2.066262 GACTCAACGAAATGGCGAGAA 58.934 47.619 0.00 0.00 34.83 2.87
234 235 3.820689 TCAACGAAATGGCGAGAAATTG 58.179 40.909 0.00 0.00 34.83 2.32
235 236 2.262572 ACGAAATGGCGAGAAATTGC 57.737 45.000 0.00 0.00 34.83 3.56
244 245 3.552604 GCGAGAAATTGCCAAGTGTAA 57.447 42.857 0.00 0.00 0.00 2.41
248 249 5.511729 GCGAGAAATTGCCAAGTGTAATTAC 59.488 40.000 8.75 8.75 38.17 1.89
250 251 6.401688 CGAGAAATTGCCAAGTGTAATTACGA 60.402 38.462 10.92 0.00 38.17 3.43
253 254 6.509418 AATTGCCAAGTGTAATTACGATGT 57.491 33.333 10.92 0.00 37.48 3.06
254 255 5.950758 TTGCCAAGTGTAATTACGATGTT 57.049 34.783 10.92 0.00 0.00 2.71
255 256 5.289917 TGCCAAGTGTAATTACGATGTTG 57.710 39.130 10.92 10.41 0.00 3.33
326 327 5.772521 AGGCAAAACATTTGATGTGACTAC 58.227 37.500 6.99 0.00 44.07 2.73
340 341 5.755409 TGTGACTACATGAATGGGTTACT 57.245 39.130 0.00 0.00 31.23 2.24
347 348 4.088634 ACATGAATGGGTTACTGCACATT 58.911 39.130 0.00 0.00 44.32 2.71
364 365 1.269174 CATTTGTGATGTTGGTCGGCA 59.731 47.619 0.00 0.00 0.00 5.69
365 366 1.393603 TTTGTGATGTTGGTCGGCAA 58.606 45.000 0.00 0.00 0.00 4.52
367 368 1.614996 TGTGATGTTGGTCGGCAATT 58.385 45.000 0.00 0.00 0.00 2.32
377 380 2.026729 TGGTCGGCAATTAGATCACCAA 60.027 45.455 0.00 0.00 29.39 3.67
385 388 6.912591 CGGCAATTAGATCACCAAATTAGTTC 59.087 38.462 0.00 0.00 0.00 3.01
403 406 2.107950 TCCACCATGTTTCCTAAGCG 57.892 50.000 0.00 0.00 0.00 4.68
410 413 2.024176 TGTTTCCTAAGCGAGGCATC 57.976 50.000 2.94 0.00 46.25 3.91
435 563 5.640147 ACTTAATTGAGGTGGAATTGGTCA 58.360 37.500 1.95 0.00 0.00 4.02
456 1988 8.592809 TGGTCAATTTATAGCAATTCCAAACTT 58.407 29.630 0.00 0.00 0.00 2.66
468 2001 8.370182 AGCAATTCCAAACTTCAAGACATAAAT 58.630 29.630 0.00 0.00 0.00 1.40
470 2003 8.853345 CAATTCCAAACTTCAAGACATAAATCG 58.147 33.333 0.00 0.00 0.00 3.34
491 2024 5.533482 TCGAATGGGTTTAAACATGTTTGG 58.467 37.500 29.72 5.56 34.23 3.28
741 2278 8.475331 AAAACTATACACTGACATTCCGTTAG 57.525 34.615 0.00 0.00 37.26 2.34
742 2279 7.400599 AACTATACACTGACATTCCGTTAGA 57.599 36.000 0.00 0.00 34.86 2.10
743 2280 7.400599 ACTATACACTGACATTCCGTTAGAA 57.599 36.000 0.00 0.00 39.32 2.10
744 2281 8.008513 ACTATACACTGACATTCCGTTAGAAT 57.991 34.615 0.00 0.00 46.54 2.40
745 2282 8.475639 ACTATACACTGACATTCCGTTAGAATT 58.524 33.333 0.00 0.00 42.86 2.17
746 2283 9.961265 CTATACACTGACATTCCGTTAGAATTA 57.039 33.333 0.00 0.00 42.86 1.40
878 2421 1.825474 ACCCGATAATATCTCCCGCAG 59.175 52.381 0.00 0.00 0.00 5.18
884 2427 1.428869 AATATCTCCCGCAGCTTCCT 58.571 50.000 0.00 0.00 0.00 3.36
893 2436 1.228245 GCAGCTTCCTCCCAACACA 60.228 57.895 0.00 0.00 0.00 3.72
1179 2722 1.383248 CCTCATCCTCCCGGTCCTT 60.383 63.158 0.00 0.00 0.00 3.36
1239 2782 4.660938 GCCTTCCCCACCAACGCT 62.661 66.667 0.00 0.00 0.00 5.07
1470 3013 4.135153 CTCCACCTCGTCGGCCTG 62.135 72.222 0.00 0.00 35.61 4.85
1527 3070 4.771356 GTCGCGCTCACCGTGCTA 62.771 66.667 5.56 0.00 46.82 3.49
1884 3427 1.073125 TCAAACATGGGGCTCTTCGAA 59.927 47.619 0.00 0.00 0.00 3.71
1976 3519 2.586258 CGGAGGTGATGAACTCGAAT 57.414 50.000 0.00 0.00 34.58 3.34
1977 3520 2.464865 CGGAGGTGATGAACTCGAATC 58.535 52.381 0.00 0.00 34.58 2.52
1978 3521 2.099921 CGGAGGTGATGAACTCGAATCT 59.900 50.000 0.00 0.00 34.58 2.40
1979 3522 3.452474 GGAGGTGATGAACTCGAATCTG 58.548 50.000 0.00 0.00 34.58 2.90
1980 3523 3.131223 GGAGGTGATGAACTCGAATCTGA 59.869 47.826 0.00 0.00 34.58 3.27
1981 3524 4.382040 GGAGGTGATGAACTCGAATCTGAA 60.382 45.833 0.00 0.00 34.58 3.02
1982 3525 5.350504 AGGTGATGAACTCGAATCTGAAT 57.649 39.130 0.00 0.00 0.00 2.57
1983 3526 5.355596 AGGTGATGAACTCGAATCTGAATC 58.644 41.667 0.00 0.00 0.00 2.52
1984 3527 4.509600 GGTGATGAACTCGAATCTGAATCC 59.490 45.833 0.00 0.00 0.00 3.01
1985 3528 4.208047 GTGATGAACTCGAATCTGAATCCG 59.792 45.833 0.00 0.00 0.00 4.18
1986 3529 4.097892 TGATGAACTCGAATCTGAATCCGA 59.902 41.667 0.00 0.00 0.00 4.55
1987 3530 4.450082 TGAACTCGAATCTGAATCCGAA 57.550 40.909 0.00 0.00 0.00 4.30
1988 3531 4.424626 TGAACTCGAATCTGAATCCGAAG 58.575 43.478 0.00 0.00 0.00 3.79
1997 3540 4.720649 TCTGAATCCGAAGTCGAAATCT 57.279 40.909 1.43 0.00 43.02 2.40
2009 3552 2.801111 GTCGAAATCTAATCTTCCCGCC 59.199 50.000 0.00 0.00 0.00 6.13
2022 3565 0.404040 TCCCGCCAAGAAGAAACCAT 59.596 50.000 0.00 0.00 0.00 3.55
2053 3596 0.601046 TCATCTTCCCGCGATGCATC 60.601 55.000 17.10 17.10 38.47 3.91
2410 3953 2.717809 GGCGTCGAACGTCTCAAGC 61.718 63.158 0.00 0.00 43.82 4.01
2431 3974 2.048127 GCGGCTTGGTCGAGTTCT 60.048 61.111 0.00 0.00 29.41 3.01
2599 4142 0.096454 GCGGTCGCAATTTGTACCTC 59.904 55.000 10.67 8.54 41.49 3.85
2651 4199 5.578157 ACAGTAGGTTCAGTAAATGGGTT 57.422 39.130 0.00 0.00 0.00 4.11
2670 4218 8.830915 ATGGGTTTATTTGTCATACACCAATA 57.169 30.769 0.00 0.00 0.00 1.90
2671 4219 8.651589 TGGGTTTATTTGTCATACACCAATAA 57.348 30.769 0.80 0.00 33.04 1.40
2672 4220 9.261035 TGGGTTTATTTGTCATACACCAATAAT 57.739 29.630 0.80 0.00 34.28 1.28
2673 4221 9.744468 GGGTTTATTTGTCATACACCAATAATC 57.256 33.333 0.80 0.00 34.28 1.75
2703 4257 7.936847 TCATTCATACCACAGTTAGTTGAGTTT 59.063 33.333 0.00 0.00 0.00 2.66
2705 4259 7.490962 TCATACCACAGTTAGTTGAGTTTTG 57.509 36.000 0.00 0.00 0.00 2.44
2710 4267 8.288689 ACCACAGTTAGTTGAGTTTTGTAAAT 57.711 30.769 0.00 0.00 0.00 1.40
2717 4274 4.760204 AGTTGAGTTTTGTAAATCCCCGAG 59.240 41.667 0.00 0.00 0.00 4.63
2720 4277 4.517453 TGAGTTTTGTAAATCCCCGAGTTG 59.483 41.667 0.00 0.00 0.00 3.16
2724 4281 3.992943 TGTAAATCCCCGAGTTGTCAT 57.007 42.857 0.00 0.00 0.00 3.06
2730 4287 0.036164 CCCCGAGTTGTCATGGTGAA 59.964 55.000 0.00 0.00 0.00 3.18
2733 4290 2.031157 CCCGAGTTGTCATGGTGAAAAC 60.031 50.000 5.12 5.12 43.29 2.43
2767 4324 4.527427 TCATGTTTGGGATTCATTGCAAGA 59.473 37.500 4.94 0.00 0.00 3.02
2768 4325 4.952071 TGTTTGGGATTCATTGCAAGAA 57.048 36.364 4.94 9.33 0.00 2.52
2825 4382 6.947733 TGGGTTGATTGACTGAACTGAAATAT 59.052 34.615 0.00 0.00 0.00 1.28
2853 4974 3.243704 GGTTCCATTTAAAGTGCAGCACA 60.244 43.478 27.35 6.64 36.74 4.57
2896 5017 2.540769 CGACAGCAAACATGTTCCGTTT 60.541 45.455 12.39 0.00 37.04 3.60
2901 5022 2.033832 GCAAACATGTTCCGTTTTGCTG 60.034 45.455 18.83 9.34 34.40 4.41
2902 5023 3.186119 CAAACATGTTCCGTTTTGCTGT 58.814 40.909 12.39 0.00 34.40 4.40
2915 5036 4.479619 GTTTTGCTGTATTTCAGAGCCAG 58.520 43.478 0.00 0.00 46.27 4.85
2919 5040 2.097142 GCTGTATTTCAGAGCCAGCTTG 59.903 50.000 0.00 0.00 46.27 4.01
2925 5048 2.469274 TCAGAGCCAGCTTGAAGAAG 57.531 50.000 0.00 0.00 0.00 2.85
2931 5054 2.157738 GCCAGCTTGAAGAAGTCATGT 58.842 47.619 0.00 0.00 35.70 3.21
2932 5055 2.161211 GCCAGCTTGAAGAAGTCATGTC 59.839 50.000 0.00 0.00 35.70 3.06
2945 5068 8.964476 AAGAAGTCATGTCAGTCTTTTTCTAA 57.036 30.769 0.00 0.00 0.00 2.10
3035 5159 1.741706 AGCGTTCTGAAATGGATGCTG 59.258 47.619 0.00 0.00 0.00 4.41
3098 5225 2.267426 CGTGACTCGTGCATATGGAAA 58.733 47.619 4.56 0.00 34.52 3.13
3099 5226 2.029244 CGTGACTCGTGCATATGGAAAC 59.971 50.000 4.56 0.00 34.52 2.78
3100 5227 4.464968 CGTGACTCGTGCATATGGAAACA 61.465 47.826 4.56 0.00 38.85 2.83
3101 5228 5.731736 CGTGACTCGTGCATATGGAAACAT 61.732 45.833 4.56 0.00 43.81 2.71
3102 5229 6.466799 CGTGACTCGTGCATATGGAAACATA 61.467 44.000 4.56 0.00 44.84 2.29
3103 5230 8.182279 CGTGACTCGTGCATATGGAAACATAG 62.182 46.154 4.56 0.00 44.40 2.23
3142 5310 6.377080 ACTAACTGGATCAGATGATGGACTA 58.623 40.000 0.00 0.00 34.37 2.59
3249 5417 0.608640 GGACGGGATCAACACTGTCT 59.391 55.000 8.12 0.00 0.00 3.41
3250 5418 1.822990 GGACGGGATCAACACTGTCTA 59.177 52.381 8.12 0.00 0.00 2.59
3282 5450 4.435554 CGCTGAAATGCTGAATCAAATACG 59.564 41.667 0.00 0.00 0.00 3.06
3296 5464 3.100817 CAAATACGGAAGCGATTGCAAG 58.899 45.455 7.90 0.00 46.23 4.01
3301 5469 1.501741 GAAGCGATTGCAAGCGGAA 59.498 52.632 34.76 0.00 46.23 4.30
3335 5503 7.064728 CCTTGCACTTTTGTCTCCTAGTATAAC 59.935 40.741 0.00 0.00 0.00 1.89
3358 5579 2.736995 GTGCAACGCCGAGTAGCA 60.737 61.111 0.00 0.00 0.00 3.49
3364 5606 2.026301 CGCCGAGTAGCAGTAGGC 59.974 66.667 5.46 5.46 44.00 3.93
3386 5628 4.572985 TCAATTTGTTTGAGTGAGCAGG 57.427 40.909 0.00 0.00 39.44 4.85
3443 5685 2.684843 GCGGTCAGCTTGGCTCTTG 61.685 63.158 0.00 0.00 44.04 3.02
3444 5686 1.004560 CGGTCAGCTTGGCTCTTGA 60.005 57.895 0.00 0.00 36.40 3.02
3455 5700 4.390297 GCTTGGCTCTTGAGTAAAGTACTG 59.610 45.833 0.00 0.00 39.59 2.74
3459 5704 5.422331 TGGCTCTTGAGTAAAGTACTGCTAT 59.578 40.000 0.00 0.00 39.59 2.97
3470 5715 8.251721 AGTAAAGTACTGCTATGACGAATCTTT 58.748 33.333 0.00 0.00 37.69 2.52
3483 5733 5.571741 TGACGAATCTTTTGTACGACTGATC 59.428 40.000 0.00 0.00 0.00 2.92
3505 5755 1.070275 CAGACTGCACTGCTCACCA 59.930 57.895 1.98 0.00 0.00 4.17
3518 5768 5.416952 CACTGCTCACCATTCCTATCTTTTT 59.583 40.000 0.00 0.00 0.00 1.94
3540 5790 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.752101 AGATGTCTCAAGGTTTCTTCAACG 59.248 41.667 0.00 0.00 36.05 4.10
31 32 7.645058 AAAAGATGTCTCAAGGTTTCTTCAA 57.355 32.000 0.00 0.00 0.00 2.69
72 73 3.728845 TGTTGTTCCAGTAGTCTTGAGC 58.271 45.455 0.00 0.00 0.00 4.26
99 100 5.424573 TGATATGCCATGTTTTCCAATGGAA 59.575 36.000 11.23 11.23 40.27 3.53
102 103 6.342906 ACTTGATATGCCATGTTTTCCAATG 58.657 36.000 0.00 0.00 0.00 2.82
103 104 6.549433 ACTTGATATGCCATGTTTTCCAAT 57.451 33.333 0.00 0.00 0.00 3.16
109 110 7.613585 TCATGAAAACTTGATATGCCATGTTT 58.386 30.769 0.00 0.00 42.44 2.83
112 113 9.569167 GATATCATGAAAACTTGATATGCCATG 57.431 33.333 17.15 0.00 35.04 3.66
113 114 9.304335 TGATATCATGAAAACTTGATATGCCAT 57.696 29.630 17.15 0.00 35.04 4.40
114 115 8.694581 TGATATCATGAAAACTTGATATGCCA 57.305 30.769 17.15 10.64 35.04 4.92
190 191 4.697352 AGTCCAAATTCTCGAACATCCTTG 59.303 41.667 0.00 0.00 0.00 3.61
194 195 5.622378 GTTGAGTCCAAATTCTCGAACATC 58.378 41.667 0.00 0.00 33.49 3.06
200 201 4.725556 TTTCGTTGAGTCCAAATTCTCG 57.274 40.909 0.00 0.00 33.49 4.04
226 227 6.837992 TCGTAATTACACTTGGCAATTTCTC 58.162 36.000 15.67 0.00 0.00 2.87
230 231 6.509418 ACATCGTAATTACACTTGGCAATT 57.491 33.333 15.67 0.00 0.00 2.32
234 235 5.539582 TCAACATCGTAATTACACTTGGC 57.460 39.130 15.67 0.00 0.00 4.52
235 236 8.964420 ATTTTCAACATCGTAATTACACTTGG 57.036 30.769 15.67 0.00 0.00 3.61
238 239 9.825972 CTGAATTTTCAACATCGTAATTACACT 57.174 29.630 15.67 0.00 36.64 3.55
239 240 9.061610 CCTGAATTTTCAACATCGTAATTACAC 57.938 33.333 15.67 0.00 36.64 2.90
242 243 9.834628 GAACCTGAATTTTCAACATCGTAATTA 57.165 29.630 0.00 0.00 36.64 1.40
244 245 7.881142 TGAACCTGAATTTTCAACATCGTAAT 58.119 30.769 0.00 0.00 36.64 1.89
248 249 5.630680 CCTTGAACCTGAATTTTCAACATCG 59.369 40.000 0.00 0.00 36.92 3.84
250 251 6.729690 TCCTTGAACCTGAATTTTCAACAT 57.270 33.333 0.00 0.00 36.92 2.71
253 254 7.601705 ATCTTCCTTGAACCTGAATTTTCAA 57.398 32.000 3.65 3.65 38.98 2.69
254 255 7.601705 AATCTTCCTTGAACCTGAATTTTCA 57.398 32.000 0.00 0.00 35.57 2.69
255 256 8.143835 TCAAATCTTCCTTGAACCTGAATTTTC 58.856 33.333 0.00 0.00 29.93 2.29
292 293 8.477984 TCAAATGTTTTGCCTTTATTCTATGC 57.522 30.769 0.00 0.00 0.00 3.14
326 327 4.724074 AATGTGCAGTAACCCATTCATG 57.276 40.909 0.00 0.00 0.00 3.07
335 336 4.681025 CCAACATCACAAATGTGCAGTAAC 59.319 41.667 8.67 0.00 45.25 2.50
340 341 2.287487 CGACCAACATCACAAATGTGCA 60.287 45.455 8.67 0.00 45.25 4.57
347 348 1.614996 ATTGCCGACCAACATCACAA 58.385 45.000 0.00 0.00 35.99 3.33
361 362 7.147915 TGGAACTAATTTGGTGATCTAATTGCC 60.148 37.037 0.00 0.00 0.00 4.52
364 365 7.893302 TGGTGGAACTAATTTGGTGATCTAATT 59.107 33.333 0.00 0.00 36.74 1.40
365 366 7.410174 TGGTGGAACTAATTTGGTGATCTAAT 58.590 34.615 0.00 0.00 36.74 1.73
367 368 6.381498 TGGTGGAACTAATTTGGTGATCTA 57.619 37.500 0.00 0.00 36.74 1.98
377 380 6.152831 GCTTAGGAAACATGGTGGAACTAATT 59.847 38.462 0.00 0.00 36.74 1.40
385 388 2.009774 CTCGCTTAGGAAACATGGTGG 58.990 52.381 0.00 0.00 0.00 4.61
403 406 3.557595 CACCTCAATTAAGTCGATGCCTC 59.442 47.826 0.00 0.00 0.00 4.70
410 413 4.700213 ACCAATTCCACCTCAATTAAGTCG 59.300 41.667 0.00 0.00 0.00 4.18
413 416 6.588719 TTGACCAATTCCACCTCAATTAAG 57.411 37.500 0.00 0.00 0.00 1.85
422 550 6.463995 TGCTATAAATTGACCAATTCCACC 57.536 37.500 8.26 0.00 39.88 4.61
456 1988 8.568676 TTAAACCCATTCGATTTATGTCTTGA 57.431 30.769 0.00 0.00 0.00 3.02
468 2001 5.533482 CCAAACATGTTTAAACCCATTCGA 58.467 37.500 22.87 0.00 0.00 3.71
470 2003 4.454161 GGCCAAACATGTTTAAACCCATTC 59.546 41.667 22.87 5.28 0.00 2.67
491 2024 7.945109 AGAACTTGGAAATATCCTATTTAGGGC 59.055 37.037 3.84 0.00 46.70 5.19
595 2128 5.565592 TTGCGCCATATAATTGATGATCC 57.434 39.130 4.18 0.00 0.00 3.36
659 2192 7.122799 GCTTATTTTCTAGGACTTCCAACCATT 59.877 37.037 0.00 0.00 38.89 3.16
741 2278 8.644318 TCTCGGTGTATAGCTTTTTCTAATTC 57.356 34.615 0.00 0.00 0.00 2.17
742 2279 9.046296 CATCTCGGTGTATAGCTTTTTCTAATT 57.954 33.333 0.00 0.00 0.00 1.40
743 2280 7.171678 GCATCTCGGTGTATAGCTTTTTCTAAT 59.828 37.037 0.00 0.00 0.00 1.73
744 2281 6.479001 GCATCTCGGTGTATAGCTTTTTCTAA 59.521 38.462 0.00 0.00 0.00 2.10
745 2282 5.983720 GCATCTCGGTGTATAGCTTTTTCTA 59.016 40.000 0.00 0.00 0.00 2.10
746 2283 4.811557 GCATCTCGGTGTATAGCTTTTTCT 59.188 41.667 0.00 0.00 0.00 2.52
878 2421 0.534203 TCGTTGTGTTGGGAGGAAGC 60.534 55.000 0.00 0.00 0.00 3.86
884 2427 1.950909 GAAATGGTCGTTGTGTTGGGA 59.049 47.619 0.00 0.00 0.00 4.37
893 2436 6.072119 GGAAGTATGGAAAAGAAATGGTCGTT 60.072 38.462 0.00 0.00 0.00 3.85
987 2530 2.264794 GTCATCGGGTCAACGGCT 59.735 61.111 0.00 0.00 0.00 5.52
1179 2722 3.706373 GCCTCAGGGAGCGACCAA 61.706 66.667 0.00 0.00 41.20 3.67
1276 2819 3.745803 GACGAGGAAGGCGACCGT 61.746 66.667 0.00 0.00 36.08 4.83
1389 2932 3.587933 GCGAGAGAGCGGATCGGT 61.588 66.667 1.93 0.00 41.33 4.69
1393 2936 3.893763 CACGGCGAGAGAGCGGAT 61.894 66.667 16.62 0.00 40.14 4.18
1423 2966 3.450115 GAGGTAGGTGAGCGCGGT 61.450 66.667 12.23 12.23 0.00 5.68
1470 3013 2.677979 GGTGAGGAAAAGCGCGGAC 61.678 63.158 8.83 0.00 0.00 4.79
1527 3070 3.125376 GCGGATCTTGGGGATGGCT 62.125 63.158 0.00 0.00 34.33 4.75
1662 3205 1.585006 GAACGTCTTCCTCGGCTCA 59.415 57.895 0.00 0.00 0.00 4.26
1866 3409 1.826385 CTTCGAAGAGCCCCATGTTT 58.174 50.000 20.74 0.00 38.43 2.83
1884 3427 3.143515 TCGCTGCTCATCTCGGCT 61.144 61.111 0.00 0.00 33.82 5.52
1959 3502 4.377839 TCAGATTCGAGTTCATCACCTC 57.622 45.455 0.00 0.00 0.00 3.85
1976 3519 4.720649 AGATTTCGACTTCGGATTCAGA 57.279 40.909 0.00 0.00 40.29 3.27
1977 3520 6.920758 AGATTAGATTTCGACTTCGGATTCAG 59.079 38.462 0.00 0.00 40.29 3.02
1978 3521 6.806751 AGATTAGATTTCGACTTCGGATTCA 58.193 36.000 0.00 0.00 40.29 2.57
1979 3522 7.095982 GGAAGATTAGATTTCGACTTCGGATTC 60.096 40.741 0.00 0.00 40.29 2.52
1980 3523 6.702282 GGAAGATTAGATTTCGACTTCGGATT 59.298 38.462 0.00 0.00 40.29 3.01
1981 3524 6.217294 GGAAGATTAGATTTCGACTTCGGAT 58.783 40.000 0.00 0.00 40.29 4.18
1982 3525 5.451520 GGGAAGATTAGATTTCGACTTCGGA 60.452 44.000 0.00 0.00 40.29 4.55
1983 3526 4.745620 GGGAAGATTAGATTTCGACTTCGG 59.254 45.833 0.00 0.00 40.29 4.30
1984 3527 4.441415 CGGGAAGATTAGATTTCGACTTCG 59.559 45.833 0.00 0.00 41.45 3.79
1985 3528 4.209495 GCGGGAAGATTAGATTTCGACTTC 59.791 45.833 0.00 0.00 34.80 3.01
1986 3529 4.120589 GCGGGAAGATTAGATTTCGACTT 58.879 43.478 0.00 0.00 0.00 3.01
1987 3530 3.492829 GGCGGGAAGATTAGATTTCGACT 60.493 47.826 0.00 0.00 0.00 4.18
1988 3531 2.801111 GGCGGGAAGATTAGATTTCGAC 59.199 50.000 0.00 0.00 0.00 4.20
1997 3540 3.992943 TTCTTCTTGGCGGGAAGATTA 57.007 42.857 18.06 6.29 45.43 1.75
2009 3552 9.185192 GAGACATGTTTTTATGGTTTCTTCTTG 57.815 33.333 0.00 0.00 32.32 3.02
2022 3565 4.394920 GCGGGAAGATGAGACATGTTTTTA 59.605 41.667 0.00 0.00 0.00 1.52
2301 3844 2.740714 GACGGTGCCGATGAGCAAC 61.741 63.158 18.16 0.00 46.19 4.17
2420 3963 1.006571 GGCGTCAAGAACTCGACCA 60.007 57.895 0.00 0.00 0.00 4.02
2573 4116 4.514577 ATTGCGACCGCCTCTCCG 62.515 66.667 12.08 0.00 41.09 4.63
2599 4142 4.637534 ACTGTACTAGGTACGTATGTGTGG 59.362 45.833 0.00 0.00 41.41 4.17
2670 4218 9.466497 ACTAACTGTGGTATGAATGAATTGATT 57.534 29.630 0.00 0.00 0.00 2.57
2671 4219 9.466497 AACTAACTGTGGTATGAATGAATTGAT 57.534 29.630 0.00 0.00 0.00 2.57
2672 4220 8.729756 CAACTAACTGTGGTATGAATGAATTGA 58.270 33.333 0.00 0.00 0.00 2.57
2673 4221 8.729756 TCAACTAACTGTGGTATGAATGAATTG 58.270 33.333 0.00 0.00 0.00 2.32
2674 4222 8.862325 TCAACTAACTGTGGTATGAATGAATT 57.138 30.769 0.00 0.00 0.00 2.17
2675 4223 8.103305 ACTCAACTAACTGTGGTATGAATGAAT 58.897 33.333 0.00 0.00 0.00 2.57
2676 4224 7.450074 ACTCAACTAACTGTGGTATGAATGAA 58.550 34.615 0.00 0.00 0.00 2.57
2703 4257 3.773418 TGACAACTCGGGGATTTACAA 57.227 42.857 0.00 0.00 0.00 2.41
2705 4259 2.943033 CCATGACAACTCGGGGATTTAC 59.057 50.000 0.00 0.00 0.00 2.01
2710 4267 0.834261 TCACCATGACAACTCGGGGA 60.834 55.000 0.00 0.00 0.00 4.81
2717 4274 5.751243 ACTACAGTTTTCACCATGACAAC 57.249 39.130 0.00 0.56 37.33 3.32
2720 4277 4.275936 AGCAACTACAGTTTTCACCATGAC 59.724 41.667 0.00 0.00 35.83 3.06
2724 4281 4.265893 TGAAGCAACTACAGTTTTCACCA 58.734 39.130 5.51 0.00 35.83 4.17
2730 4287 5.451798 CCCAAACATGAAGCAACTACAGTTT 60.452 40.000 0.00 0.00 35.83 2.66
2733 4290 3.820467 TCCCAAACATGAAGCAACTACAG 59.180 43.478 0.00 0.00 0.00 2.74
2767 4324 4.462133 CATCCAGATCCAGAGCTCAAATT 58.538 43.478 17.77 0.00 0.00 1.82
2768 4325 3.748027 GCATCCAGATCCAGAGCTCAAAT 60.748 47.826 17.77 5.83 0.00 2.32
2825 4382 5.626142 TGCACTTTAAATGGAACCTGACTA 58.374 37.500 0.00 0.00 0.00 2.59
2853 4974 7.013369 TGTCGTTGAGTCTTGCAGAGTATATAT 59.987 37.037 0.00 0.00 0.00 0.86
2901 5022 4.256920 TCTTCAAGCTGGCTCTGAAATAC 58.743 43.478 15.29 0.00 0.00 1.89
2902 5023 4.558226 TCTTCAAGCTGGCTCTGAAATA 57.442 40.909 15.29 8.46 0.00 1.40
2915 5036 4.314121 AGACTGACATGACTTCTTCAAGC 58.686 43.478 0.00 0.00 37.92 4.01
2919 5040 7.489574 AGAAAAAGACTGACATGACTTCTTC 57.510 36.000 0.00 0.42 0.00 2.87
2925 5048 7.715265 TCAGTTAGAAAAAGACTGACATGAC 57.285 36.000 0.00 0.00 43.38 3.06
2932 5055 7.388776 TGATGTGGATCAGTTAGAAAAAGACTG 59.611 37.037 0.00 0.00 41.57 3.51
2945 5068 2.865119 TTGCTGTGATGTGGATCAGT 57.135 45.000 0.00 0.00 39.36 3.41
2994 5118 9.687210 AACGCTTTCATTCTCGTATGTATATAA 57.313 29.630 0.00 0.00 34.50 0.98
2995 5119 9.338291 GAACGCTTTCATTCTCGTATGTATATA 57.662 33.333 0.00 0.00 34.50 0.86
2996 5120 8.082852 AGAACGCTTTCATTCTCGTATGTATAT 58.917 33.333 5.66 0.00 34.50 0.86
2997 5121 7.378728 CAGAACGCTTTCATTCTCGTATGTATA 59.621 37.037 5.66 0.00 32.77 1.47
2998 5122 6.199154 CAGAACGCTTTCATTCTCGTATGTAT 59.801 38.462 5.66 0.00 32.77 2.29
2999 5123 5.515270 CAGAACGCTTTCATTCTCGTATGTA 59.485 40.000 5.66 0.00 32.77 2.29
3000 5124 4.327357 CAGAACGCTTTCATTCTCGTATGT 59.673 41.667 5.66 0.00 32.77 2.29
3001 5125 4.562789 TCAGAACGCTTTCATTCTCGTATG 59.437 41.667 5.66 0.00 32.77 2.39
3002 5126 4.744570 TCAGAACGCTTTCATTCTCGTAT 58.255 39.130 5.66 0.00 32.77 3.06
3003 5127 4.168922 TCAGAACGCTTTCATTCTCGTA 57.831 40.909 5.66 0.00 32.77 3.43
3004 5128 3.026630 TCAGAACGCTTTCATTCTCGT 57.973 42.857 5.66 0.00 32.77 4.18
3005 5129 4.389664 TTTCAGAACGCTTTCATTCTCG 57.610 40.909 5.66 0.00 32.77 4.04
3015 5139 1.741706 CAGCATCCATTTCAGAACGCT 59.258 47.619 0.00 0.00 0.00 5.07
3018 5142 4.157289 ACATCACAGCATCCATTTCAGAAC 59.843 41.667 0.00 0.00 0.00 3.01
3024 5148 5.680408 GCATTACACATCACAGCATCCATTT 60.680 40.000 0.00 0.00 0.00 2.32
3035 5159 0.718904 TGTCGCGCATTACACATCAC 59.281 50.000 8.75 0.00 0.00 3.06
3098 5225 3.010584 AGTTGGCAGTGGAATTCCTATGT 59.989 43.478 24.73 4.49 36.82 2.29
3099 5226 3.624777 AGTTGGCAGTGGAATTCCTATG 58.375 45.455 24.73 21.71 36.82 2.23
3100 5227 5.044846 AGTTAGTTGGCAGTGGAATTCCTAT 60.045 40.000 24.73 10.82 36.82 2.57
3101 5228 4.288626 AGTTAGTTGGCAGTGGAATTCCTA 59.711 41.667 24.73 9.10 36.82 2.94
3102 5229 3.074538 AGTTAGTTGGCAGTGGAATTCCT 59.925 43.478 24.73 2.99 36.82 3.36
3103 5230 3.191371 CAGTTAGTTGGCAGTGGAATTCC 59.809 47.826 18.17 18.17 0.00 3.01
3249 5417 3.378112 CAGCATTTCAGCGGAAAGGAATA 59.622 43.478 24.60 0.00 45.17 1.75
3250 5418 2.165030 CAGCATTTCAGCGGAAAGGAAT 59.835 45.455 24.60 11.24 45.17 3.01
3282 5450 1.922135 TTCCGCTTGCAATCGCTTCC 61.922 55.000 16.84 0.00 39.64 3.46
3301 5469 1.664956 AAAAGTGCAAGGGGAGGGGT 61.665 55.000 0.00 0.00 0.00 4.95
3335 5503 1.369209 CTCGGCGTTGCACACAAAG 60.369 57.895 6.85 0.00 37.58 2.77
3386 5628 3.181500 ACTTTGCCGAAGAAACACAACTC 60.181 43.478 0.00 0.00 38.77 3.01
3443 5685 7.419204 AGATTCGTCATAGCAGTACTTTACTC 58.581 38.462 0.00 0.00 36.76 2.59
3444 5686 7.336161 AGATTCGTCATAGCAGTACTTTACT 57.664 36.000 0.00 0.00 40.28 2.24
3455 5700 5.515626 AGTCGTACAAAAGATTCGTCATAGC 59.484 40.000 0.00 0.00 0.00 2.97
3459 5704 4.862350 TCAGTCGTACAAAAGATTCGTCA 58.138 39.130 0.00 0.00 0.00 4.35
3483 5733 2.341543 AGCAGTGCAGTCTGGTCG 59.658 61.111 19.20 0.00 41.43 4.79
3486 5736 1.670406 GGTGAGCAGTGCAGTCTGG 60.670 63.158 19.20 0.00 36.12 3.86
3487 5737 0.321387 ATGGTGAGCAGTGCAGTCTG 60.321 55.000 19.20 0.01 38.35 3.51
3518 5768 1.555075 ACGGCTGGAGATGCTCTAAAA 59.445 47.619 0.00 0.00 0.00 1.52
3522 5772 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
3523 5773 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.