Multiple sequence alignment - TraesCS5D01G325100

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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 TraesCS5D01G325100 chr5D 100.000 2339 0 0 1 2339 416601785 416599447 0.000000e+00 4320.0
1 TraesCS5D01G325100 chr5B 91.175 1915 117 26 449 2339 503328313 503326427 0.000000e+00 2553.0
2 TraesCS5D01G325100 chr5A 95.458 1475 45 7 872 2339 529369263 529367804 0.000000e+00 2333.0
3 TraesCS5D01G325100 chr5A 82.018 456 42 20 5 448 529370272 529369845 3.700000e-93 351.0
4 TraesCS5D01G325100 chr7B 85.333 75 8 3 700 772 202103046 202102973 8.960000e-10 75.0
5 TraesCS5D01G325100 chr7A 76.056 142 30 4 700 839 569442856 569442717 1.160000e-08 71.3


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 TraesCS5D01G325100 chr5D 416599447 416601785 2338 True 4320 4320 100.000 1 2339 1 chr5D.!!$R1 2338
1 TraesCS5D01G325100 chr5B 503326427 503328313 1886 True 2553 2553 91.175 449 2339 1 chr5B.!!$R1 1890
2 TraesCS5D01G325100 chr5A 529367804 529370272 2468 True 1342 2333 88.738 5 2339 2 chr5A.!!$R1 2334

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
365 373 0.098376 CAGCGATCCTTCAAAGCAGC 59.902 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 2009 0.966875 AGTATGTACCGGTGCCGTCA 60.967 55.0 19.93 8.91 37.81 4.35 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 8.219546 TGAGTCATTCATGTTTGTTTGTAAGA 57.780 30.769 0.00 0.00 0.00 2.10
34 35 8.225603 AGTCATTCATGTTTGTTTGTAAGAGT 57.774 30.769 0.00 0.00 0.00 3.24
48 49 6.947644 TTGTAAGAGTGAAGTTTAAACCCC 57.052 37.500 14.72 7.56 0.00 4.95
59 60 7.229907 GTGAAGTTTAAACCCCTGTTATTCTGA 59.770 37.037 14.72 0.00 33.30 3.27
69 70 3.812053 CCTGTTATTCTGATGCAGCTACC 59.188 47.826 2.53 0.00 0.00 3.18
76 77 0.329261 TGATGCAGCTACCTTTGGCT 59.671 50.000 2.53 0.00 39.60 4.75
77 78 1.272092 TGATGCAGCTACCTTTGGCTT 60.272 47.619 2.53 0.00 36.59 4.35
78 79 1.821136 GATGCAGCTACCTTTGGCTTT 59.179 47.619 0.00 0.00 36.59 3.51
79 80 0.961019 TGCAGCTACCTTTGGCTTTG 59.039 50.000 0.00 0.00 36.59 2.77
80 81 0.389037 GCAGCTACCTTTGGCTTTGC 60.389 55.000 0.00 0.00 36.59 3.68
90 91 2.815647 GGCTTTGCCGAGGTCGAG 60.816 66.667 0.00 0.00 39.62 4.04
91 92 3.491652 GCTTTGCCGAGGTCGAGC 61.492 66.667 6.48 6.48 43.02 5.03
92 93 3.181967 CTTTGCCGAGGTCGAGCG 61.182 66.667 9.28 2.00 43.02 5.03
95 96 4.717629 TGCCGAGGTCGAGCGTTG 62.718 66.667 9.28 2.94 43.02 4.10
96 97 4.719369 GCCGAGGTCGAGCGTTGT 62.719 66.667 9.28 0.00 43.02 3.32
97 98 2.872557 CCGAGGTCGAGCGTTGTA 59.127 61.111 9.28 0.00 43.02 2.41
98 99 1.210931 CCGAGGTCGAGCGTTGTAA 59.789 57.895 9.28 0.00 43.02 2.41
99 100 0.387622 CCGAGGTCGAGCGTTGTAAA 60.388 55.000 9.28 0.00 43.02 2.01
100 101 1.411394 CGAGGTCGAGCGTTGTAAAA 58.589 50.000 9.28 0.00 43.02 1.52
101 102 1.123756 CGAGGTCGAGCGTTGTAAAAC 59.876 52.381 9.28 0.00 43.02 2.43
106 107 2.217167 GTCGAGCGTTGTAAAACGTCTT 59.783 45.455 18.96 5.94 46.91 3.01
121 122 4.207891 ACGTCTTATGATGGTTTCTGCT 57.792 40.909 3.16 0.00 33.67 4.24
125 126 5.122239 CGTCTTATGATGGTTTCTGCTTTGA 59.878 40.000 0.00 0.00 0.00 2.69
143 144 7.787028 TGCTTTGACTTAATAAAAGTTTGGGT 58.213 30.769 0.00 0.00 34.18 4.51
188 196 6.923199 AAACATCAAGTTGATTGGAGGATT 57.077 33.333 15.85 3.15 41.19 3.01
198 206 2.879103 TTGGAGGATTTGGTGTCTCC 57.121 50.000 0.00 0.00 44.39 3.71
200 208 0.744771 GGAGGATTTGGTGTCTCCGC 60.745 60.000 0.00 0.00 36.78 5.54
204 212 1.133025 GGATTTGGTGTCTCCGCAATG 59.867 52.381 0.00 0.00 39.52 2.82
214 222 3.133691 GTCTCCGCAATGATATGCTTCA 58.866 45.455 0.00 0.00 44.21 3.02
217 225 2.815503 TCCGCAATGATATGCTTCATGG 59.184 45.455 0.00 0.00 44.21 3.66
222 230 5.447624 CAATGATATGCTTCATGGCAAGA 57.552 39.130 0.58 0.00 45.68 3.02
224 232 6.455647 CAATGATATGCTTCATGGCAAGAAT 58.544 36.000 5.53 0.00 45.68 2.40
226 234 7.014615 AATGATATGCTTCATGGCAAGAATGC 61.015 38.462 5.53 11.61 45.68 3.56
227 235 9.095058 AATGATATGCTTCATGGCAAGAATGCT 62.095 37.037 19.65 12.12 45.68 3.79
237 245 1.522668 CAAGAATGCTCCACCGTTGA 58.477 50.000 0.00 0.00 0.00 3.18
238 246 1.466167 CAAGAATGCTCCACCGTTGAG 59.534 52.381 0.00 0.00 0.00 3.02
249 257 3.217242 CCGTTGAGGTGTCAAGAGG 57.783 57.895 0.00 0.00 43.55 3.69
256 264 2.632996 TGAGGTGTCAAGAGGTTACCTG 59.367 50.000 9.39 0.00 41.58 4.00
261 269 2.171659 TGTCAAGAGGTTACCTGTGCAA 59.828 45.455 9.39 0.00 31.76 4.08
273 281 3.898482 ACCTGTGCAACTACTTTTCCTT 58.102 40.909 0.00 0.00 38.04 3.36
274 282 3.632145 ACCTGTGCAACTACTTTTCCTTG 59.368 43.478 0.00 0.00 38.04 3.61
278 286 2.875933 TGCAACTACTTTTCCTTGTCGG 59.124 45.455 0.00 0.00 0.00 4.79
281 289 3.487120 ACTACTTTTCCTTGTCGGCTT 57.513 42.857 0.00 0.00 0.00 4.35
283 291 4.566987 ACTACTTTTCCTTGTCGGCTTAG 58.433 43.478 0.00 0.00 0.00 2.18
284 292 2.779506 ACTTTTCCTTGTCGGCTTAGG 58.220 47.619 2.76 2.76 0.00 2.69
285 293 2.105993 ACTTTTCCTTGTCGGCTTAGGT 59.894 45.455 8.31 0.00 0.00 3.08
332 340 9.989869 GTACAGTAAAAGAAAAAGCATCTATCC 57.010 33.333 0.00 0.00 0.00 2.59
343 351 7.573968 AAAAGCATCTATCCAAGTATTCACC 57.426 36.000 0.00 0.00 0.00 4.02
349 357 2.113860 TCCAAGTATTCACCTGCAGC 57.886 50.000 8.66 0.00 0.00 5.25
358 366 1.078918 CACCTGCAGCGATCCTTCA 60.079 57.895 8.66 0.00 0.00 3.02
365 373 0.098376 CAGCGATCCTTCAAAGCAGC 59.902 55.000 0.00 0.00 0.00 5.25
422 430 1.284198 ACTAGGTGGCTCTCTCGGTTA 59.716 52.381 0.00 0.00 0.00 2.85
440 448 4.831698 ACGGGTCGTTCGTGAAAA 57.168 50.000 0.00 0.00 36.35 2.29
518 572 5.359009 AGCCAAAATTAGTGTGATGATGGAG 59.641 40.000 0.00 0.00 0.00 3.86
533 587 3.776969 TGATGGAGAGGATTGCACTAACT 59.223 43.478 0.00 0.00 0.00 2.24
540 594 6.407525 GGAGAGGATTGCACTAACTCTACAAT 60.408 42.308 12.81 0.00 38.67 2.71
542 596 7.721402 AGAGGATTGCACTAACTCTACAATAG 58.279 38.462 8.45 0.00 36.80 1.73
551 605 8.784994 GCACTAACTCTACAATAGTCATAGCTA 58.215 37.037 0.00 0.00 0.00 3.32
556 610 8.754991 ACTCTACAATAGTCATAGCTACTTGT 57.245 34.615 0.00 0.00 32.73 3.16
557 611 8.625651 ACTCTACAATAGTCATAGCTACTTGTG 58.374 37.037 0.00 0.00 31.65 3.33
558 612 7.941919 TCTACAATAGTCATAGCTACTTGTGG 58.058 38.462 0.00 0.00 31.65 4.17
577 631 7.174946 ACTTGTGGTGATCTAATCGAACAATTT 59.825 33.333 0.00 0.00 32.10 1.82
578 632 7.072177 TGTGGTGATCTAATCGAACAATTTC 57.928 36.000 0.00 0.00 0.00 2.17
586 640 4.336532 AATCGAACAATTTCACTACCGC 57.663 40.909 0.00 0.00 0.00 5.68
588 642 2.073816 CGAACAATTTCACTACCGCCT 58.926 47.619 0.00 0.00 0.00 5.52
591 645 4.501071 GAACAATTTCACTACCGCCTCTA 58.499 43.478 0.00 0.00 0.00 2.43
603 657 1.549170 CCGCCTCTACACTAACCAACT 59.451 52.381 0.00 0.00 0.00 3.16
615 669 4.281182 CACTAACCAACTAGTCACTGGAGT 59.719 45.833 17.24 9.18 34.16 3.85
648 702 2.169832 ACACTTGGTGTTGGAGATCG 57.830 50.000 0.00 0.00 45.08 3.69
652 706 3.058914 CACTTGGTGTTGGAGATCGAAAC 60.059 47.826 0.00 0.00 0.00 2.78
660 714 4.253685 GTTGGAGATCGAAACCATCTTGA 58.746 43.478 8.88 0.00 33.56 3.02
670 724 4.379813 CGAAACCATCTTGAAGAACCATGG 60.380 45.833 11.19 11.19 40.05 3.66
681 735 4.082463 TGAAGAACCATGGGTTTATTTCGC 60.082 41.667 18.09 7.85 46.95 4.70
698 752 0.159345 CGCTGAAAATTGCACGCAAC 59.841 50.000 6.60 0.00 38.88 4.17
712 766 3.425193 GCACGCAACCAAAATAGAGTTTG 59.575 43.478 0.00 0.00 38.07 2.93
716 770 4.675114 CGCAACCAAAATAGAGTTTGTCAC 59.325 41.667 2.21 0.00 36.87 3.67
717 771 5.587289 GCAACCAAAATAGAGTTTGTCACA 58.413 37.500 2.21 0.00 36.87 3.58
732 786 4.760530 TGTCACAGCCTTGCTAATCTAT 57.239 40.909 0.00 0.00 36.40 1.98
735 789 3.455910 TCACAGCCTTGCTAATCTATGGT 59.544 43.478 0.00 0.00 36.40 3.55
804 927 4.083003 TGTTTCTTTGGCCGTATTTAGCAG 60.083 41.667 0.00 0.00 0.00 4.24
808 931 5.676552 TCTTTGGCCGTATTTAGCAGATTA 58.323 37.500 0.00 0.00 0.00 1.75
810 933 7.446769 TCTTTGGCCGTATTTAGCAGATTATA 58.553 34.615 0.00 0.00 0.00 0.98
811 934 7.934665 TCTTTGGCCGTATTTAGCAGATTATAA 59.065 33.333 0.00 0.00 0.00 0.98
812 935 7.429636 TTGGCCGTATTTAGCAGATTATAAC 57.570 36.000 0.00 0.00 0.00 1.89
857 1011 8.197988 ACTTACTACTATTCCTTCGCAATTTG 57.802 34.615 0.00 0.00 0.00 2.32
868 1022 4.450419 CCTTCGCAATTTGTTTTTGCCATA 59.550 37.500 3.08 0.00 45.19 2.74
920 1099 3.188100 CTCGATCGCTTGCGCCAA 61.188 61.111 11.09 0.00 0.00 4.52
1083 1262 0.980231 GCCCACTCATCCACCTCTCT 60.980 60.000 0.00 0.00 0.00 3.10
1234 1413 2.093288 TGGGACATCTACTACGACGAGT 60.093 50.000 0.00 3.47 0.00 4.18
1377 1559 3.055385 ACCCGTATGTGTATGCTTTGACT 60.055 43.478 0.00 0.00 0.00 3.41
1380 1562 4.034048 CCGTATGTGTATGCTTTGACTTCC 59.966 45.833 0.00 0.00 0.00 3.46
1388 1570 1.494721 TGCTTTGACTTCCCCTGTTCT 59.505 47.619 0.00 0.00 0.00 3.01
1391 1573 3.406764 CTTTGACTTCCCCTGTTCTCAG 58.593 50.000 0.00 0.00 41.01 3.35
1443 1625 4.633126 CAGCATTACTCACAGCATTACAGT 59.367 41.667 0.00 0.00 0.00 3.55
1506 1689 5.557891 ACTTACTGCTCATCATTCTTTGC 57.442 39.130 0.00 0.00 0.00 3.68
1544 1727 5.505780 CCCTGGTTATGAATACAAGTTCCA 58.494 41.667 0.00 0.00 0.00 3.53
1545 1728 6.129179 CCCTGGTTATGAATACAAGTTCCAT 58.871 40.000 0.00 0.00 0.00 3.41
1546 1729 6.607198 CCCTGGTTATGAATACAAGTTCCATT 59.393 38.462 0.00 0.00 0.00 3.16
1588 1773 1.680207 TGTTTGCACATACTTGCTGCA 59.320 42.857 0.00 0.00 43.41 4.41
1600 1785 3.460103 ACTTGCTGCAAAAATTGGTCAG 58.540 40.909 16.74 2.89 0.00 3.51
1610 1795 5.523188 GCAAAAATTGGTCAGATTTGTGTCA 59.477 36.000 0.00 0.00 35.23 3.58
1627 1812 1.003580 GTCACCAAAGATGCTCCTGGA 59.996 52.381 0.00 0.00 32.97 3.86
1820 2009 3.313012 TCGTTTGTTCTCATGACCGAT 57.687 42.857 0.00 0.00 0.00 4.18
1947 2136 2.934932 TCCCATGTCAGGCTGCCA 60.935 61.111 22.65 4.75 0.00 4.92
2160 2349 2.196595 CCCCTCAGTTCAGGAATGGTA 58.803 52.381 0.00 0.00 35.20 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.750229 ACAAACATGAATGACTCAACACTAT 57.250 32.000 0.00 0.00 37.67 2.12
1 2 7.566760 AACAAACATGAATGACTCAACACTA 57.433 32.000 0.00 0.00 37.67 2.74
2 3 6.455360 AACAAACATGAATGACTCAACACT 57.545 33.333 0.00 0.00 37.67 3.55
3 4 6.531240 ACAAACAAACATGAATGACTCAACAC 59.469 34.615 0.00 0.00 37.67 3.32
4 5 6.629128 ACAAACAAACATGAATGACTCAACA 58.371 32.000 0.00 0.00 37.67 3.33
5 6 8.627487 TTACAAACAAACATGAATGACTCAAC 57.373 30.769 0.00 0.00 37.67 3.18
6 7 8.681806 TCTTACAAACAAACATGAATGACTCAA 58.318 29.630 0.00 0.00 37.67 3.02
9 10 8.131100 CACTCTTACAAACAAACATGAATGACT 58.869 33.333 0.00 0.00 0.00 3.41
10 11 8.128582 TCACTCTTACAAACAAACATGAATGAC 58.871 33.333 0.00 0.00 0.00 3.06
11 12 8.219546 TCACTCTTACAAACAAACATGAATGA 57.780 30.769 0.00 0.00 0.00 2.57
12 13 8.854979 TTCACTCTTACAAACAAACATGAATG 57.145 30.769 0.00 0.00 0.00 2.67
13 14 8.686334 ACTTCACTCTTACAAACAAACATGAAT 58.314 29.630 0.00 0.00 0.00 2.57
32 33 7.230712 CAGAATAACAGGGGTTTAAACTTCACT 59.769 37.037 17.50 5.96 38.45 3.41
34 35 7.291566 TCAGAATAACAGGGGTTTAAACTTCA 58.708 34.615 17.50 0.00 38.45 3.02
45 46 1.952296 GCTGCATCAGAATAACAGGGG 59.048 52.381 0.00 0.00 32.44 4.79
48 49 4.701765 AGGTAGCTGCATCAGAATAACAG 58.298 43.478 3.61 0.00 32.44 3.16
59 60 1.547372 CAAAGCCAAAGGTAGCTGCAT 59.453 47.619 3.61 0.00 39.87 3.96
76 77 3.509137 AACGCTCGACCTCGGCAAA 62.509 57.895 0.00 0.00 40.29 3.68
77 78 3.986006 AACGCTCGACCTCGGCAA 61.986 61.111 0.00 0.00 40.29 4.52
78 79 4.717629 CAACGCTCGACCTCGGCA 62.718 66.667 0.00 0.00 40.29 5.69
79 80 2.807631 TTACAACGCTCGACCTCGGC 62.808 60.000 0.00 0.00 40.29 5.54
80 81 0.387622 TTTACAACGCTCGACCTCGG 60.388 55.000 0.00 0.00 40.29 4.63
82 83 2.850441 GTTTTACAACGCTCGACCTC 57.150 50.000 0.00 0.00 0.00 3.85
92 93 8.287503 AGAAACCATCATAAGACGTTTTACAAC 58.712 33.333 0.00 0.00 32.61 3.32
95 96 6.741358 GCAGAAACCATCATAAGACGTTTTAC 59.259 38.462 0.00 0.00 32.61 2.01
96 97 6.653320 AGCAGAAACCATCATAAGACGTTTTA 59.347 34.615 0.52 0.52 32.61 1.52
97 98 5.473504 AGCAGAAACCATCATAAGACGTTTT 59.526 36.000 0.00 0.00 32.61 2.43
98 99 5.003804 AGCAGAAACCATCATAAGACGTTT 58.996 37.500 0.00 0.00 34.20 3.60
99 100 4.579869 AGCAGAAACCATCATAAGACGTT 58.420 39.130 0.00 0.00 0.00 3.99
100 101 4.207891 AGCAGAAACCATCATAAGACGT 57.792 40.909 0.00 0.00 0.00 4.34
101 102 5.122239 TCAAAGCAGAAACCATCATAAGACG 59.878 40.000 0.00 0.00 0.00 4.18
106 107 7.994425 TTAAGTCAAAGCAGAAACCATCATA 57.006 32.000 0.00 0.00 0.00 2.15
121 122 8.307582 TCCACCCAAACTTTTATTAAGTCAAA 57.692 30.769 0.00 0.00 0.00 2.69
125 126 5.778241 CCCTCCACCCAAACTTTTATTAAGT 59.222 40.000 0.00 0.00 0.00 2.24
167 175 5.186409 CCAAATCCTCCAATCAACTTGATGT 59.814 40.000 4.99 0.00 37.15 3.06
188 196 3.205338 CATATCATTGCGGAGACACCAA 58.795 45.455 0.00 0.00 38.90 3.67
198 206 2.030628 TGCCATGAAGCATATCATTGCG 60.031 45.455 14.25 0.00 46.17 4.85
200 208 5.447624 TCTTGCCATGAAGCATATCATTG 57.552 39.130 0.00 0.00 43.64 2.82
204 212 4.235360 GCATTCTTGCCATGAAGCATATC 58.765 43.478 0.00 0.00 43.64 1.63
220 228 0.036010 CCTCAACGGTGGAGCATTCT 60.036 55.000 7.03 0.00 0.00 2.40
221 229 0.321653 ACCTCAACGGTGGAGCATTC 60.322 55.000 7.03 0.00 46.80 2.67
222 230 1.761174 ACCTCAACGGTGGAGCATT 59.239 52.632 7.03 0.00 46.80 3.56
231 239 0.393077 ACCTCTTGACACCTCAACGG 59.607 55.000 0.00 0.00 32.68 4.44
232 240 2.240493 AACCTCTTGACACCTCAACG 57.760 50.000 0.00 0.00 32.68 4.10
233 241 3.071167 AGGTAACCTCTTGACACCTCAAC 59.929 47.826 0.00 0.00 34.49 3.18
234 242 3.071023 CAGGTAACCTCTTGACACCTCAA 59.929 47.826 0.00 0.00 37.52 3.02
235 243 2.632996 CAGGTAACCTCTTGACACCTCA 59.367 50.000 0.00 0.00 37.52 3.86
236 244 2.633481 ACAGGTAACCTCTTGACACCTC 59.367 50.000 0.00 0.00 37.52 3.85
237 245 2.368875 CACAGGTAACCTCTTGACACCT 59.631 50.000 0.00 0.00 40.25 4.00
238 246 2.767505 CACAGGTAACCTCTTGACACC 58.232 52.381 0.00 0.00 37.17 4.16
239 247 2.143925 GCACAGGTAACCTCTTGACAC 58.856 52.381 0.00 0.00 37.17 3.67
240 248 1.765904 TGCACAGGTAACCTCTTGACA 59.234 47.619 0.00 0.00 37.17 3.58
241 249 2.543777 TGCACAGGTAACCTCTTGAC 57.456 50.000 0.00 0.00 37.17 3.18
242 250 2.438021 AGTTGCACAGGTAACCTCTTGA 59.562 45.455 0.00 0.00 40.08 3.02
243 251 2.851195 AGTTGCACAGGTAACCTCTTG 58.149 47.619 0.00 0.00 40.08 3.02
244 252 3.646637 AGTAGTTGCACAGGTAACCTCTT 59.353 43.478 0.00 0.00 40.08 2.85
245 253 3.240302 AGTAGTTGCACAGGTAACCTCT 58.760 45.455 0.00 0.00 40.08 3.69
249 257 4.820173 AGGAAAAGTAGTTGCACAGGTAAC 59.180 41.667 0.00 0.00 39.59 2.50
256 264 3.303791 CCGACAAGGAAAAGTAGTTGCAC 60.304 47.826 0.00 0.00 45.00 4.57
261 269 3.487120 AAGCCGACAAGGAAAAGTAGT 57.513 42.857 0.00 0.00 45.00 2.73
273 281 1.749634 GCTTCTCTACCTAAGCCGACA 59.250 52.381 0.00 0.00 41.80 4.35
274 282 1.749634 TGCTTCTCTACCTAAGCCGAC 59.250 52.381 4.75 0.00 46.01 4.79
278 286 6.399639 AATAGACTGCTTCTCTACCTAAGC 57.600 41.667 0.00 0.00 46.60 3.09
281 289 9.476928 ACTTTTAATAGACTGCTTCTCTACCTA 57.523 33.333 0.00 0.00 35.55 3.08
283 291 9.518906 GTACTTTTAATAGACTGCTTCTCTACC 57.481 37.037 0.00 0.00 35.55 3.18
318 326 7.836183 AGGTGAATACTTGGATAGATGCTTTTT 59.164 33.333 0.00 0.00 0.00 1.94
322 330 5.744300 GCAGGTGAATACTTGGATAGATGCT 60.744 44.000 0.00 0.00 34.71 3.79
332 340 1.725641 TCGCTGCAGGTGAATACTTG 58.274 50.000 17.12 0.00 37.00 3.16
339 347 1.219124 GAAGGATCGCTGCAGGTGA 59.781 57.895 17.12 8.79 38.92 4.02
343 351 0.098376 GCTTTGAAGGATCGCTGCAG 59.902 55.000 10.11 10.11 0.00 4.41
349 357 2.315925 TAGGCTGCTTTGAAGGATCG 57.684 50.000 0.00 0.00 0.00 3.69
358 366 1.210722 GGGCTCTACTTAGGCTGCTTT 59.789 52.381 0.00 0.00 41.59 3.51
365 373 1.417890 CCATGTGGGGCTCTACTTAGG 59.582 57.143 0.37 0.00 0.00 2.69
412 420 0.606401 ACGACCCGTTAACCGAGAGA 60.606 55.000 8.65 0.00 36.35 3.10
440 448 3.385111 TGTAAGCCAAAACGGACCATTTT 59.615 39.130 0.00 0.00 36.56 1.82
444 452 2.054232 TTGTAAGCCAAAACGGACCA 57.946 45.000 0.00 0.00 36.56 4.02
445 453 3.653539 ATTTGTAAGCCAAAACGGACC 57.346 42.857 0.00 0.00 45.72 4.46
447 455 5.766174 ACTAGAATTTGTAAGCCAAAACGGA 59.234 36.000 0.00 0.00 45.72 4.69
483 537 1.106285 ATTTTGGCTTCGAGGGCATC 58.894 50.000 24.22 3.59 41.29 3.91
518 572 7.493367 ACTATTGTAGAGTTAGTGCAATCCTC 58.507 38.462 0.00 0.00 33.08 3.71
533 587 7.560262 ACCACAAGTAGCTATGACTATTGTAGA 59.440 37.037 0.00 0.00 30.09 2.59
540 594 6.129874 AGATCACCACAAGTAGCTATGACTA 58.870 40.000 0.00 0.00 0.00 2.59
542 596 5.269505 AGATCACCACAAGTAGCTATGAC 57.730 43.478 0.00 0.00 0.00 3.06
551 605 5.147330 TGTTCGATTAGATCACCACAAGT 57.853 39.130 0.00 0.00 0.00 3.16
553 607 7.174080 TGAAATTGTTCGATTAGATCACCACAA 59.826 33.333 0.00 0.00 36.46 3.33
555 609 6.961554 GTGAAATTGTTCGATTAGATCACCAC 59.038 38.462 0.00 0.00 36.46 4.16
556 610 6.878923 AGTGAAATTGTTCGATTAGATCACCA 59.121 34.615 11.64 0.00 36.26 4.17
557 611 7.308782 AGTGAAATTGTTCGATTAGATCACC 57.691 36.000 11.64 0.04 36.26 4.02
558 612 8.328864 GGTAGTGAAATTGTTCGATTAGATCAC 58.671 37.037 0.00 8.73 36.46 3.06
577 631 3.012518 GTTAGTGTAGAGGCGGTAGTGA 58.987 50.000 0.00 0.00 0.00 3.41
578 632 2.098770 GGTTAGTGTAGAGGCGGTAGTG 59.901 54.545 0.00 0.00 0.00 2.74
586 640 5.711036 AGTGACTAGTTGGTTAGTGTAGAGG 59.289 44.000 0.00 0.00 34.13 3.69
588 642 5.475909 CCAGTGACTAGTTGGTTAGTGTAGA 59.524 44.000 0.00 0.00 34.13 2.59
591 645 4.220724 TCCAGTGACTAGTTGGTTAGTGT 58.779 43.478 11.09 0.00 34.13 3.55
615 669 3.650942 ACCAAGTGTCCATAAGAGGAACA 59.349 43.478 0.00 0.00 39.92 3.18
648 702 4.082026 CCCATGGTTCTTCAAGATGGTTTC 60.082 45.833 11.73 0.00 33.06 2.78
652 706 3.091633 ACCCATGGTTCTTCAAGATGG 57.908 47.619 11.73 0.00 34.47 3.51
660 714 4.082245 CAGCGAAATAAACCCATGGTTCTT 60.082 41.667 11.73 3.26 46.20 2.52
670 724 5.608146 GTGCAATTTTCAGCGAAATAAACC 58.392 37.500 0.00 0.00 31.34 3.27
681 735 1.850377 TGGTTGCGTGCAATTTTCAG 58.150 45.000 10.85 0.00 38.28 3.02
698 752 4.520492 AGGCTGTGACAAACTCTATTTTGG 59.480 41.667 0.00 0.00 40.25 3.28
712 766 3.812053 CCATAGATTAGCAAGGCTGTGAC 59.188 47.826 0.07 0.00 40.10 3.67
716 770 3.813443 ACACCATAGATTAGCAAGGCTG 58.187 45.455 0.07 0.00 40.10 4.85
717 771 4.510167 AACACCATAGATTAGCAAGGCT 57.490 40.909 0.00 0.00 43.41 4.58
735 789 1.213537 GCGGTGCTACCTCGTAACA 59.786 57.895 4.21 0.00 35.66 2.41
1068 1247 1.040339 GGCGAGAGAGGTGGATGAGT 61.040 60.000 0.00 0.00 0.00 3.41
1234 1413 1.276622 GCCTTCTGGTAGTCCTGGAA 58.723 55.000 0.00 0.00 35.27 3.53
1377 1559 2.631384 TCCAATCTGAGAACAGGGGAA 58.369 47.619 0.00 0.00 43.60 3.97
1380 1562 4.500499 AGAATCCAATCTGAGAACAGGG 57.500 45.455 0.00 0.00 43.60 4.45
1388 1570 3.007940 ACACGACCAAGAATCCAATCTGA 59.992 43.478 0.00 0.00 0.00 3.27
1391 1573 5.175859 TCTTACACGACCAAGAATCCAATC 58.824 41.667 0.00 0.00 0.00 2.67
1443 1625 6.882140 ACGGTGAGAATACAATGGATGTTTAA 59.118 34.615 0.00 0.00 43.63 1.52
1506 1689 1.002134 AGGGGCATCTTTGGTCACG 60.002 57.895 0.00 0.00 0.00 4.35
1544 1727 5.117584 TGAATTGAACTGCTGCACAAAAAT 58.882 33.333 8.02 0.37 0.00 1.82
1545 1728 4.502016 TGAATTGAACTGCTGCACAAAAA 58.498 34.783 8.02 0.00 0.00 1.94
1546 1729 4.120792 TGAATTGAACTGCTGCACAAAA 57.879 36.364 8.02 0.00 0.00 2.44
1588 1773 6.048509 GGTGACACAAATCTGACCAATTTTT 58.951 36.000 8.08 0.00 0.00 1.94
1600 1785 4.479619 GAGCATCTTTGGTGACACAAATC 58.520 43.478 8.08 0.00 42.67 2.17
1610 1795 3.718434 TGATATCCAGGAGCATCTTTGGT 59.282 43.478 12.88 0.00 39.63 3.67
1820 2009 0.966875 AGTATGTACCGGTGCCGTCA 60.967 55.000 19.93 8.91 37.81 4.35
1825 2014 3.192466 CCTTTGTAGTATGTACCGGTGC 58.808 50.000 19.93 18.21 0.00 5.01
1977 2166 1.607178 CAAGGTGGCATTCCAGGCA 60.607 57.895 0.00 0.00 44.48 4.75
2160 2349 0.991920 ACCTGAACGTCCCATCCATT 59.008 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.