Multiple sequence alignment - TraesCS5A01G503100

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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 TraesCS5A01G503100 chr5A 100.000 2210 0 0 1 2210 667941002 667943211 0.000000e+00 4082.0
1 TraesCS5A01G503100 chr4D 91.230 1927 100 28 4 1887 487044742 487046642 0.000000e+00 2558.0
2 TraesCS5A01G503100 chr4B 88.350 1957 121 38 1 1919 621984485 621986372 0.000000e+00 2252.0
3 TraesCS5A01G503100 chr4B 80.000 215 38 5 1001 1212 558753852 558753640 1.060000e-33 154.0
4 TraesCS5A01G503100 chr4B 83.621 116 12 2 2100 2208 621986653 621986768 3.880000e-18 102.0
5 TraesCS5A01G503100 chr2A 89.671 213 22 0 1001 1213 679982444 679982232 2.800000e-69 272.0
6 TraesCS5A01G503100 chr2A 87.442 215 27 0 1000 1214 679985807 679985593 4.710000e-62 248.0
7 TraesCS5A01G503100 chr2B 88.940 217 24 0 1001 1217 640085921 640085705 3.620000e-68 268.0
8 TraesCS5A01G503100 chr2B 88.152 211 25 0 1000 1210 640101848 640101638 3.640000e-63 252.0
9 TraesCS5A01G503100 chr2D 88.837 215 24 0 1000 1214 537448405 537448191 4.680000e-67 265.0
10 TraesCS5A01G503100 chr2D 87.963 216 25 1 1000 1215 537456949 537456735 1.010000e-63 254.0
11 TraesCS5A01G503100 chr1B 94.595 37 2 0 2067 2103 364205262 364205226 8.520000e-05 58.4
12 TraesCS5A01G503100 chr6D 96.875 32 1 0 2066 2097 338696157 338696126 1.000000e-03 54.7
13 TraesCS5A01G503100 chr5D 100.000 29 0 0 2066 2094 481269119 481269147 1.000000e-03 54.7
14 TraesCS5A01G503100 chr3B 94.286 35 0 2 2068 2102 521692347 521692315 4.000000e-03 52.8
15 TraesCS5A01G503100 chr3B 94.286 35 0 2 2068 2102 826365988 826365956 4.000000e-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 TraesCS5A01G503100 chr5A 667941002 667943211 2209 False 4082 4082 100.0000 1 2210 1 chr5A.!!$F1 2209
1 TraesCS5A01G503100 chr4D 487044742 487046642 1900 False 2558 2558 91.2300 4 1887 1 chr4D.!!$F1 1883
2 TraesCS5A01G503100 chr4B 621984485 621986768 2283 False 1177 2252 85.9855 1 2208 2 chr4B.!!$F1 2207
3 TraesCS5A01G503100 chr2A 679982232 679985807 3575 True 260 272 88.5565 1000 1214 2 chr2A.!!$R1 214

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
888 919 0.035458 CACACTCCTTCCACTGTCCC 59.965 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 5505 0.179081 GATTAGCGACACCCCCACTC 60.179 60.0 0.0 0.0 0.0 3.51 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
53 65 6.717997 TCCCTTCCACTTTTAACCACTTTATC 59.282 38.462 0.00 0.00 0.00 1.75
108 122 2.924922 ATACGACGGCGCACCTAACG 62.925 60.000 12.58 4.56 42.48 3.18
184 198 2.785269 TCAGCATGTTAATCCCCTGGAT 59.215 45.455 0.00 0.00 40.21 3.41
191 205 6.461509 GCATGTTAATCCCCTGGATACTTTTG 60.462 42.308 0.00 0.00 42.27 2.44
200 218 5.583457 CCCCTGGATACTTTTGTTAACGTAG 59.417 44.000 0.26 0.87 37.61 3.51
225 243 9.803507 AGCCCATACCTTAAAGTAAAATATACC 57.196 33.333 0.00 0.00 0.00 2.73
226 244 9.577222 GCCCATACCTTAAAGTAAAATATACCA 57.423 33.333 0.00 0.00 0.00 3.25
246 264 0.598158 GTGAGTACAAACGACGCCCA 60.598 55.000 0.00 0.00 0.00 5.36
269 287 5.994668 CAGAAAAAGAGAGCTCTAACCAAGT 59.005 40.000 18.25 0.00 39.39 3.16
274 292 3.513515 AGAGAGCTCTAACCAAGTTCCAG 59.486 47.826 18.25 0.00 38.35 3.86
285 303 2.606826 GTTCCAGGTCCGGTCCCT 60.607 66.667 14.60 11.72 0.00 4.20
405 432 1.603802 CACCACGATGTTCTGTTTGCT 59.396 47.619 0.00 0.00 0.00 3.91
467 494 9.656323 TTTGTCCAATACTCCTACATATCTACT 57.344 33.333 0.00 0.00 0.00 2.57
471 498 8.334734 TCCAATACTCCTACATATCTACTACCC 58.665 40.741 0.00 0.00 0.00 3.69
489 516 1.213013 CCGAGACGACCACAAGGAG 59.787 63.158 0.00 0.00 38.69 3.69
490 517 1.444553 CGAGACGACCACAAGGAGC 60.445 63.158 0.00 0.00 38.69 4.70
492 519 0.247736 GAGACGACCACAAGGAGCAT 59.752 55.000 0.00 0.00 38.69 3.79
550 577 1.380380 GGGACAGGGCAATCAAGGG 60.380 63.158 0.00 0.00 0.00 3.95
585 612 3.123621 GTGTCGTCTAGCTTCACCAAATG 59.876 47.826 0.00 0.00 0.00 2.32
648 678 3.299977 CCACCACCGTCGACTCCA 61.300 66.667 14.70 0.00 0.00 3.86
788 818 2.267961 GCGTCGGTTTGGGATCCT 59.732 61.111 12.58 0.00 0.00 3.24
792 822 0.036306 GTCGGTTTGGGATCCTGTGT 59.964 55.000 12.58 0.00 0.00 3.72
888 919 0.035458 CACACTCCTTCCACTGTCCC 59.965 60.000 0.00 0.00 0.00 4.46
917 951 0.445436 CAATCACAGAGCAGGCGAAC 59.555 55.000 0.00 0.00 0.00 3.95
966 1001 2.206536 GGGGGCGAGGAGAGATCAG 61.207 68.421 0.00 0.00 0.00 2.90
967 1002 1.152652 GGGGCGAGGAGAGATCAGA 60.153 63.158 0.00 0.00 0.00 3.27
968 1003 1.460273 GGGGCGAGGAGAGATCAGAC 61.460 65.000 0.00 0.00 0.00 3.51
969 1004 1.460273 GGGCGAGGAGAGATCAGACC 61.460 65.000 0.00 0.00 0.00 3.85
970 1005 1.652012 GCGAGGAGAGATCAGACCG 59.348 63.158 0.00 0.00 0.00 4.79
1131 4529 0.760567 AGACCAGCGGCATCTCCATA 60.761 55.000 1.45 0.00 34.01 2.74
1213 4611 1.216710 GTCTTCCTCGGCTGACCAG 59.783 63.158 0.00 0.00 34.57 4.00
1214 4612 1.984570 TCTTCCTCGGCTGACCAGG 60.985 63.158 0.00 0.00 36.25 4.45
1215 4613 1.984570 CTTCCTCGGCTGACCAGGA 60.985 63.158 0.00 0.00 39.84 3.86
1226 4624 3.412879 GACCAGGAGACGCCGCTAC 62.413 68.421 0.00 0.00 43.43 3.58
1232 4630 2.439701 AGACGCCGCTACCTGCTA 60.440 61.111 0.00 0.00 40.11 3.49
1339 4737 4.620723 TCCTGATGGTTTAGCTTCTAGGA 58.379 43.478 0.00 0.00 34.23 2.94
1423 4821 5.957771 TCAGGAATGTATAGCTCCAACTT 57.042 39.130 0.00 0.00 0.00 2.66
1424 4822 5.918608 TCAGGAATGTATAGCTCCAACTTC 58.081 41.667 0.00 0.00 0.00 3.01
1445 4843 0.599991 ATGTGCGCTGTTTCGTCTGA 60.600 50.000 9.73 0.00 0.00 3.27
1482 4880 7.878477 ATCAATTGCAAACTGAACTATGTTG 57.122 32.000 16.02 6.66 0.00 3.33
1509 4907 7.125507 AGGAATCTCATCTTTAGAGAGAAAGCA 59.874 37.037 10.71 0.00 44.60 3.91
1537 4935 4.768448 TGAGCATTCCACATGATGAACTTT 59.232 37.500 0.00 0.00 0.00 2.66
1539 4937 6.094464 TGAGCATTCCACATGATGAACTTTAG 59.906 38.462 0.00 0.00 0.00 1.85
1542 4940 6.481134 CATTCCACATGATGAACTTTAGTCG 58.519 40.000 0.00 0.00 0.00 4.18
1589 4987 8.868916 CCGTCTTTCCCATTTTTACAATTATTG 58.131 33.333 3.07 3.07 0.00 1.90
1735 5143 1.066430 ACACGCCGGATGAAGTACAAT 60.066 47.619 5.05 0.00 0.00 2.71
1754 5164 3.985019 ATGCCCAAAAATGCAGAATGA 57.015 38.095 0.00 0.00 41.46 2.57
1778 5205 9.444600 TGAGTAATTGAGTTTAGGGATGTAAAC 57.555 33.333 0.00 0.00 41.39 2.01
1784 5211 5.716228 TGAGTTTAGGGATGTAAACCGAGTA 59.284 40.000 3.46 0.00 41.83 2.59
1785 5212 6.127535 TGAGTTTAGGGATGTAAACCGAGTAG 60.128 42.308 3.46 0.00 41.83 2.57
1786 5213 4.660789 TTAGGGATGTAAACCGAGTAGC 57.339 45.455 0.00 0.00 0.00 3.58
1795 5222 6.913873 TGTAAACCGAGTAGCATTTAATCC 57.086 37.500 0.00 0.00 0.00 3.01
1800 5227 3.493503 CCGAGTAGCATTTAATCCCGTTC 59.506 47.826 0.00 0.00 0.00 3.95
1824 5251 4.820894 ACCCACTTATGGTCTAACAGTC 57.179 45.455 0.00 0.00 45.66 3.51
1832 5259 9.226606 CACTTATGGTCTAACAGTCCAATAAAA 57.773 33.333 0.00 0.00 37.01 1.52
1833 5260 9.802039 ACTTATGGTCTAACAGTCCAATAAAAA 57.198 29.630 0.00 0.00 37.01 1.94
1889 5322 4.304939 ACTTACTAAACGGACTTGCAGAC 58.695 43.478 0.00 0.00 0.00 3.51
1896 5329 1.606350 CGGACTTGCAGACGTCGTTC 61.606 60.000 10.46 3.89 0.00 3.95
1910 5343 2.837878 CGTCGTTCATTTGCCATTTACG 59.162 45.455 0.00 0.00 0.00 3.18
1912 5345 3.844099 GTCGTTCATTTGCCATTTACGTC 59.156 43.478 0.00 0.00 0.00 4.34
1919 5380 5.298276 TCATTTGCCATTTACGTCCCTAATC 59.702 40.000 0.00 0.00 0.00 1.75
1945 5406 6.410540 AGTTACTTGTCCAAGGAGATCAATC 58.589 40.000 11.45 0.00 42.53 2.67
1948 5409 4.229123 ACTTGTCCAAGGAGATCAATCCAT 59.771 41.667 11.45 0.00 42.26 3.41
1950 5411 4.529897 TGTCCAAGGAGATCAATCCATTG 58.470 43.478 3.98 5.42 42.26 2.82
1957 5418 4.482025 AGGAGATCAATCCATTGGGGTTTA 59.518 41.667 2.09 0.00 42.26 2.01
1967 5428 2.209690 TTGGGGTTTAGGCTGCTAAC 57.790 50.000 0.00 0.00 0.00 2.34
1971 5432 2.633488 GGGTTTAGGCTGCTAACTCAG 58.367 52.381 0.00 0.00 37.15 3.35
1975 5436 2.534042 TAGGCTGCTAACTCAGACCT 57.466 50.000 0.00 10.10 43.11 3.85
2004 5469 4.141287 AGGTCAAAAATGAATGTCGACCA 58.859 39.130 14.12 4.08 43.12 4.02
2013 5478 3.057019 TGAATGTCGACCAAGAGAAACG 58.943 45.455 14.12 0.00 0.00 3.60
2023 5488 5.277154 CGACCAAGAGAAACGAAGCTTTTAA 60.277 40.000 0.00 0.00 0.00 1.52
2036 5501 1.985684 GCTTTTAAGCGCACATGAACC 59.014 47.619 11.47 0.00 42.88 3.62
2040 5505 1.155889 TAAGCGCACATGAACCACAG 58.844 50.000 11.47 0.00 0.00 3.66
2052 5517 3.592552 GAACCACAGAGTGGGGGTGTC 62.593 61.905 19.37 5.91 44.18 3.67
2063 5528 0.759346 GGGGGTGTCGCTAATCAGAT 59.241 55.000 0.00 0.00 0.00 2.90
2067 5532 0.772926 GTGTCGCTAATCAGATCGCG 59.227 55.000 16.83 16.83 46.28 5.87
2073 5538 2.464865 GCTAATCAGATCGCGACACTT 58.535 47.619 12.93 0.00 0.00 3.16
2074 5539 3.629058 GCTAATCAGATCGCGACACTTA 58.371 45.455 12.93 6.20 0.00 2.24
2076 5541 4.681942 GCTAATCAGATCGCGACACTTATT 59.318 41.667 12.93 18.15 0.00 1.40
2077 5542 5.175856 GCTAATCAGATCGCGACACTTATTT 59.824 40.000 12.93 9.50 0.00 1.40
2078 5543 6.292381 GCTAATCAGATCGCGACACTTATTTT 60.292 38.462 12.93 7.27 0.00 1.82
2079 5544 4.840401 TCAGATCGCGACACTTATTTTG 57.160 40.909 12.93 0.00 0.00 2.44
2082 5547 4.271049 CAGATCGCGACACTTATTTTGGAT 59.729 41.667 12.93 0.00 0.00 3.41
2083 5548 4.876107 AGATCGCGACACTTATTTTGGATT 59.124 37.500 12.93 0.00 0.00 3.01
2084 5549 4.335082 TCGCGACACTTATTTTGGATTG 57.665 40.909 3.71 0.00 0.00 2.67
2085 5550 3.997681 TCGCGACACTTATTTTGGATTGA 59.002 39.130 3.71 0.00 0.00 2.57
2086 5551 4.452795 TCGCGACACTTATTTTGGATTGAA 59.547 37.500 3.71 0.00 0.00 2.69
2087 5552 4.788100 CGCGACACTTATTTTGGATTGAAG 59.212 41.667 0.00 0.00 0.00 3.02
2090 5555 5.414454 CGACACTTATTTTGGATTGAAGGGA 59.586 40.000 0.00 0.00 0.00 4.20
2091 5556 6.403636 CGACACTTATTTTGGATTGAAGGGAG 60.404 42.308 0.00 0.00 0.00 4.30
2092 5557 6.314917 ACACTTATTTTGGATTGAAGGGAGT 58.685 36.000 0.00 0.00 0.00 3.85
2093 5558 7.466804 ACACTTATTTTGGATTGAAGGGAGTA 58.533 34.615 0.00 0.00 0.00 2.59
2094 5559 7.611855 ACACTTATTTTGGATTGAAGGGAGTAG 59.388 37.037 0.00 0.00 0.00 2.57
2095 5560 7.611855 CACTTATTTTGGATTGAAGGGAGTAGT 59.388 37.037 0.00 0.00 0.00 2.73
2096 5561 8.832735 ACTTATTTTGGATTGAAGGGAGTAGTA 58.167 33.333 0.00 0.00 0.00 1.82
2097 5562 9.331282 CTTATTTTGGATTGAAGGGAGTAGTAG 57.669 37.037 0.00 0.00 0.00 2.57
2098 5563 6.945636 TTTTGGATTGAAGGGAGTAGTAGA 57.054 37.500 0.00 0.00 0.00 2.59
2114 5647 8.411683 GGAGTAGTAGAAATTTAGAACCATCGA 58.588 37.037 0.00 0.00 0.00 3.59
2117 5650 6.860080 AGTAGAAATTTAGAACCATCGACGA 58.140 36.000 0.00 0.00 0.00 4.20
2119 5652 7.980099 AGTAGAAATTTAGAACCATCGACGAAT 59.020 33.333 0.00 0.00 0.00 3.34
2120 5653 9.241317 GTAGAAATTTAGAACCATCGACGAATA 57.759 33.333 0.00 0.00 0.00 1.75
2129 5662 6.477033 AGAACCATCGACGAATATTTGAGAAG 59.523 38.462 9.79 5.68 0.00 2.85
2134 5667 7.383572 CCATCGACGAATATTTGAGAAGATTCT 59.616 37.037 9.79 0.00 39.94 2.40
2142 5682 7.789273 ATATTTGAGAAGATTCTGCAGAGTG 57.211 36.000 17.40 0.00 37.73 3.51
2143 5683 4.879197 TTGAGAAGATTCTGCAGAGTGA 57.121 40.909 17.40 2.20 37.73 3.41
2149 5689 0.622136 ATTCTGCAGAGTGATGGCCA 59.378 50.000 17.43 8.56 0.00 5.36
2164 5704 2.202851 CCACGCTCTAGGCTGCAG 60.203 66.667 10.11 10.11 39.13 4.41
2193 5733 4.753516 TTTCCGATTGAAGGAGCTCATA 57.246 40.909 17.19 0.00 39.22 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.359002 GCTGGGCCACAAGTGAAG 58.641 61.111 0.00 0.00 0.00 3.02
26 27 4.663334 AGTGGTTAAAAGTGGAAGGGATC 58.337 43.478 0.00 0.00 0.00 3.36
53 65 6.146837 CAGGCAGAAAGATAACCATATTCTCG 59.853 42.308 0.00 0.00 0.00 4.04
184 198 5.874261 GGTATGGGCTACGTTAACAAAAGTA 59.126 40.000 6.39 0.00 0.00 2.24
191 205 6.108687 ACTTTAAGGTATGGGCTACGTTAAC 58.891 40.000 0.00 0.00 44.32 2.01
200 218 9.577222 TGGTATATTTTACTTTAAGGTATGGGC 57.423 33.333 0.00 0.00 0.00 5.36
224 242 0.782384 GCGTCGTTTGTACTCACTGG 59.218 55.000 0.00 0.00 0.00 4.00
225 243 0.782384 GGCGTCGTTTGTACTCACTG 59.218 55.000 0.00 0.00 0.00 3.66
226 244 0.319297 GGGCGTCGTTTGTACTCACT 60.319 55.000 0.00 0.00 0.00 3.41
246 264 6.181206 ACTTGGTTAGAGCTCTCTTTTTCT 57.819 37.500 22.17 0.00 40.93 2.52
269 287 1.462627 AAAGGGACCGGACCTGGAA 60.463 57.895 22.36 0.00 38.63 3.53
274 292 2.486727 GGATTATGAAAGGGACCGGACC 60.487 54.545 15.20 15.20 0.00 4.46
285 303 3.482436 GTGCCGTATGGGGATTATGAAA 58.518 45.455 2.41 0.00 38.95 2.69
405 432 2.931107 CTTGGGGTGGGGTGTCAA 59.069 61.111 0.00 0.00 0.00 3.18
467 494 1.228521 TTGTGGTCGTCTCGGGGTA 60.229 57.895 0.00 0.00 0.00 3.69
468 495 2.522436 TTGTGGTCGTCTCGGGGT 60.522 61.111 0.00 0.00 0.00 4.95
471 498 1.213013 CTCCTTGTGGTCGTCTCGG 59.787 63.158 0.00 0.00 34.23 4.63
603 630 0.466372 TGGTTGCCGTGTCCATTTCA 60.466 50.000 0.00 0.00 0.00 2.69
648 678 0.461135 GTTTGCATGGGCGGATCAAT 59.539 50.000 0.00 0.00 45.35 2.57
694 724 1.227380 CACATGCCGTCCTCTAGCC 60.227 63.158 0.00 0.00 0.00 3.93
756 786 4.901123 CGCACACGGTCACCACCA 62.901 66.667 0.00 0.00 44.02 4.17
797 827 2.427245 CGAGGGATCGGAGCCAACT 61.427 63.158 15.10 2.44 0.00 3.16
818 848 6.055588 GTGTGACTGTGTATATATGGCCTTT 58.944 40.000 3.32 0.00 0.00 3.11
888 919 2.419297 GCTCTGTGATTGTAGGACCTGG 60.419 54.545 3.53 0.00 0.00 4.45
917 951 2.266055 GGCTCACCCTCTGGTTCG 59.734 66.667 0.00 0.00 44.75 3.95
953 988 1.791103 GCCGGTCTGATCTCTCCTCG 61.791 65.000 1.90 0.00 0.00 4.63
954 989 1.791103 CGCCGGTCTGATCTCTCCTC 61.791 65.000 1.90 0.00 0.00 3.71
955 990 1.826054 CGCCGGTCTGATCTCTCCT 60.826 63.158 1.90 0.00 0.00 3.69
956 991 1.791103 CTCGCCGGTCTGATCTCTCC 61.791 65.000 1.90 0.00 0.00 3.71
958 993 1.077357 ACTCGCCGGTCTGATCTCT 60.077 57.895 1.90 0.00 0.00 3.10
959 994 1.357334 GACTCGCCGGTCTGATCTC 59.643 63.158 1.90 0.00 33.81 2.75
960 995 2.122167 GGACTCGCCGGTCTGATCT 61.122 63.158 1.90 0.00 36.55 2.75
961 996 2.122167 AGGACTCGCCGGTCTGATC 61.122 63.158 1.90 0.00 43.43 2.92
966 1001 2.799371 CTACAGGACTCGCCGGTC 59.201 66.667 1.90 0.00 41.56 4.79
968 1003 3.417275 CTGCTACAGGACTCGCCGG 62.417 68.421 0.00 0.00 43.43 6.13
969 1004 2.103143 CTGCTACAGGACTCGCCG 59.897 66.667 0.00 0.00 43.43 6.46
1029 1065 0.179936 GGAGGATGAAGAGCACCAGG 59.820 60.000 0.00 0.00 0.00 4.45
1131 4529 3.338126 GATGACGGCGTGGACGAGT 62.338 63.158 21.19 1.89 43.02 4.18
1213 4611 4.874977 GCAGGTAGCGGCGTCTCC 62.875 72.222 9.37 8.49 0.00 3.71
1226 4624 1.112315 AGCGATGAGGAGGTAGCAGG 61.112 60.000 0.00 0.00 0.00 4.85
1232 4630 0.534412 CTGTTGAGCGATGAGGAGGT 59.466 55.000 0.00 0.00 0.00 3.85
1354 4752 1.610522 GCCCAATGGACATCATACTGC 59.389 52.381 0.00 0.00 34.44 4.40
1423 4821 1.067846 AGACGAAACAGCGCACATAGA 60.068 47.619 11.47 0.00 33.86 1.98
1424 4822 1.059692 CAGACGAAACAGCGCACATAG 59.940 52.381 11.47 0.00 33.86 2.23
1445 4843 6.839124 TTGCAATTGATTCTCAGTTACCAT 57.161 33.333 10.34 0.00 0.00 3.55
1482 4880 7.653311 GCTTTCTCTCTAAAGATGAGATTCCTC 59.347 40.741 0.69 0.00 39.49 3.71
1497 4895 8.256605 GGAATGCTCATATATGCTTTCTCTCTA 58.743 37.037 7.92 0.00 40.70 2.43
1509 4907 8.107729 AGTTCATCATGTGGAATGCTCATATAT 58.892 33.333 5.38 0.00 0.00 0.86
1537 4935 3.503827 ACGAGCATTGATCAACGACTA 57.496 42.857 19.35 0.00 0.00 2.59
1539 4937 2.281762 GGTACGAGCATTGATCAACGAC 59.718 50.000 19.35 13.31 0.00 4.34
1542 4940 3.181510 GGTTGGTACGAGCATTGATCAAC 60.182 47.826 11.07 0.00 34.35 3.18
1589 4987 1.546029 GTGGCCTCAGTTTGGGAAATC 59.454 52.381 3.32 0.00 0.00 2.17
1701 5109 2.285220 CGGCGTGTAAGGATCAAGAATG 59.715 50.000 0.00 0.00 0.00 2.67
1717 5125 1.651987 CATTGTACTTCATCCGGCGT 58.348 50.000 6.01 0.00 0.00 5.68
1735 5143 2.633967 ACTCATTCTGCATTTTTGGGCA 59.366 40.909 0.00 0.00 38.52 5.36
1754 5164 7.551617 CGGTTTACATCCCTAAACTCAATTACT 59.448 37.037 0.00 0.00 36.98 2.24
1778 5205 3.107642 ACGGGATTAAATGCTACTCGG 57.892 47.619 0.00 0.00 0.00 4.63
1784 5211 3.194755 GGGTTTGAACGGGATTAAATGCT 59.805 43.478 0.00 0.00 0.00 3.79
1785 5212 3.056465 TGGGTTTGAACGGGATTAAATGC 60.056 43.478 0.00 0.00 0.00 3.56
1786 5213 4.219725 AGTGGGTTTGAACGGGATTAAATG 59.780 41.667 0.00 0.00 0.00 2.32
1832 5259 8.918116 GCTAGATATTTCCTTTTCCCTGATTTT 58.082 33.333 0.00 0.00 0.00 1.82
1833 5260 8.285163 AGCTAGATATTTCCTTTTCCCTGATTT 58.715 33.333 0.00 0.00 0.00 2.17
1834 5261 7.820532 AGCTAGATATTTCCTTTTCCCTGATT 58.179 34.615 0.00 0.00 0.00 2.57
1835 5262 7.399674 AGCTAGATATTTCCTTTTCCCTGAT 57.600 36.000 0.00 0.00 0.00 2.90
1855 5288 7.970614 GTCCGTTTAGTAAGTTTTAGCTAGCTA 59.029 37.037 20.67 20.67 0.00 3.32
1870 5303 2.294233 ACGTCTGCAAGTCCGTTTAGTA 59.706 45.455 0.00 0.00 38.92 1.82
1889 5322 2.837878 CGTAAATGGCAAATGAACGACG 59.162 45.455 0.00 0.00 0.00 5.12
1896 5329 4.974368 TTAGGGACGTAAATGGCAAATG 57.026 40.909 0.00 0.00 0.00 2.32
1910 5343 4.159135 TGGACAAGTAACTCGATTAGGGAC 59.841 45.833 0.00 0.00 0.00 4.46
1912 5345 4.730949 TGGACAAGTAACTCGATTAGGG 57.269 45.455 0.00 0.00 0.00 3.53
1919 5380 3.936372 TCTCCTTGGACAAGTAACTCG 57.064 47.619 10.81 0.00 36.72 4.18
1945 5406 0.324645 AGCAGCCTAAACCCCAATGG 60.325 55.000 0.00 0.00 41.37 3.16
1948 5409 1.708551 AGTTAGCAGCCTAAACCCCAA 59.291 47.619 0.00 0.00 35.43 4.12
1950 5411 1.280998 TGAGTTAGCAGCCTAAACCCC 59.719 52.381 0.00 0.00 35.43 4.95
1957 5418 2.534042 TAGGTCTGAGTTAGCAGCCT 57.466 50.000 0.00 0.00 41.74 4.58
2000 5465 4.553756 AAAAGCTTCGTTTCTCTTGGTC 57.446 40.909 0.00 0.00 0.00 4.02
2023 5488 0.952497 CTCTGTGGTTCATGTGCGCT 60.952 55.000 9.73 0.00 0.00 5.92
2036 5501 2.343758 CGACACCCCCACTCTGTG 59.656 66.667 0.00 0.00 36.11 3.66
2040 5505 0.179081 GATTAGCGACACCCCCACTC 60.179 60.000 0.00 0.00 0.00 3.51
2045 5510 1.603172 CGATCTGATTAGCGACACCCC 60.603 57.143 0.00 0.00 0.00 4.95
2063 5528 3.997681 TCAATCCAAAATAAGTGTCGCGA 59.002 39.130 3.71 3.71 0.00 5.87
2067 5532 6.434340 ACTCCCTTCAATCCAAAATAAGTGTC 59.566 38.462 0.00 0.00 0.00 3.67
2069 5534 6.840780 ACTCCCTTCAATCCAAAATAAGTG 57.159 37.500 0.00 0.00 0.00 3.16
2070 5535 7.699878 ACTACTCCCTTCAATCCAAAATAAGT 58.300 34.615 0.00 0.00 0.00 2.24
2071 5536 9.331282 CTACTACTCCCTTCAATCCAAAATAAG 57.669 37.037 0.00 0.00 0.00 1.73
2073 5538 8.618240 TCTACTACTCCCTTCAATCCAAAATA 57.382 34.615 0.00 0.00 0.00 1.40
2074 5539 7.510675 TCTACTACTCCCTTCAATCCAAAAT 57.489 36.000 0.00 0.00 0.00 1.82
2076 5541 6.945636 TTCTACTACTCCCTTCAATCCAAA 57.054 37.500 0.00 0.00 0.00 3.28
2077 5542 6.945636 TTTCTACTACTCCCTTCAATCCAA 57.054 37.500 0.00 0.00 0.00 3.53
2078 5543 7.510675 AATTTCTACTACTCCCTTCAATCCA 57.489 36.000 0.00 0.00 0.00 3.41
2079 5544 9.549078 CTAAATTTCTACTACTCCCTTCAATCC 57.451 37.037 0.00 0.00 0.00 3.01
2082 5547 9.939802 GTTCTAAATTTCTACTACTCCCTTCAA 57.060 33.333 0.00 0.00 0.00 2.69
2083 5548 8.537858 GGTTCTAAATTTCTACTACTCCCTTCA 58.462 37.037 0.00 0.00 0.00 3.02
2084 5549 8.537858 TGGTTCTAAATTTCTACTACTCCCTTC 58.462 37.037 0.00 0.00 0.00 3.46
2085 5550 8.445361 TGGTTCTAAATTTCTACTACTCCCTT 57.555 34.615 0.00 0.00 0.00 3.95
2086 5551 8.625467 ATGGTTCTAAATTTCTACTACTCCCT 57.375 34.615 0.00 0.00 0.00 4.20
2087 5552 7.652507 CGATGGTTCTAAATTTCTACTACTCCC 59.347 40.741 0.00 0.00 0.00 4.30
2090 5555 7.914346 CGTCGATGGTTCTAAATTTCTACTACT 59.086 37.037 0.00 0.00 0.00 2.57
2091 5556 7.912250 TCGTCGATGGTTCTAAATTTCTACTAC 59.088 37.037 4.48 0.00 0.00 2.73
2092 5557 7.988737 TCGTCGATGGTTCTAAATTTCTACTA 58.011 34.615 4.48 0.00 0.00 1.82
2093 5558 6.860080 TCGTCGATGGTTCTAAATTTCTACT 58.140 36.000 4.48 0.00 0.00 2.57
2094 5559 7.515957 TTCGTCGATGGTTCTAAATTTCTAC 57.484 36.000 4.48 0.00 0.00 2.59
2095 5560 9.976511 ATATTCGTCGATGGTTCTAAATTTCTA 57.023 29.630 4.48 0.00 0.00 2.10
2096 5561 8.888579 ATATTCGTCGATGGTTCTAAATTTCT 57.111 30.769 4.48 0.00 0.00 2.52
2097 5562 9.931210 AAATATTCGTCGATGGTTCTAAATTTC 57.069 29.630 4.48 0.00 0.00 2.17
2098 5563 9.716507 CAAATATTCGTCGATGGTTCTAAATTT 57.283 29.630 4.48 0.00 0.00 1.82
2114 5647 7.044181 TCTGCAGAATCTTCTCAAATATTCGT 58.956 34.615 15.67 0.00 34.70 3.85
2117 5650 8.045507 TCACTCTGCAGAATCTTCTCAAATATT 58.954 33.333 18.85 0.00 34.74 1.28
2119 5652 6.939622 TCACTCTGCAGAATCTTCTCAAATA 58.060 36.000 18.85 0.00 34.74 1.40
2120 5653 5.802465 TCACTCTGCAGAATCTTCTCAAAT 58.198 37.500 18.85 0.00 34.74 2.32
2129 5662 1.307097 GGCCATCACTCTGCAGAATC 58.693 55.000 18.85 0.00 0.00 2.52
2134 5667 2.046988 CGTGGCCATCACTCTGCA 60.047 61.111 9.72 0.00 43.94 4.41
2142 5682 2.280457 GCCTAGAGCGTGGCCATC 60.280 66.667 9.72 1.70 43.11 3.51
2151 5691 3.467374 AATAAGTCTGCAGCCTAGAGC 57.533 47.619 9.47 0.00 44.25 4.09
2159 5699 6.182039 TCAATCGGAAAAATAAGTCTGCAG 57.818 37.500 7.63 7.63 0.00 4.41
2164 5704 6.094186 AGCTCCTTCAATCGGAAAAATAAGTC 59.906 38.462 0.00 0.00 34.44 3.01


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

AutoCloner maintained by Alex Coulton.