Multiple sequence alignment - TraesCS6B01G240300

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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 TraesCS6B01G240300 chr6B 100.000 4874 0 0 1 4874 419939234 419944107 0 9001
1 TraesCS6B01G240300 chr2B 93.961 4885 282 7 1 4874 158021964 158017082 0 7374
2 TraesCS6B01G240300 chr2B 93.741 4889 284 16 1 4874 208176383 208171502 0 7313
3 TraesCS6B01G240300 chrUn 93.614 4886 298 8 1 4874 131727272 131722389 0 7282
4 TraesCS6B01G240300 chrUn 93.594 4886 299 8 1 4874 4433394 4438277 0 7276
5 TraesCS6B01G240300 chr3B 93.616 4887 292 11 1 4874 515072682 515067803 0 7278
6 TraesCS6B01G240300 chr3B 93.428 4884 305 10 1 4874 515755107 515759984 0 7227
7 TraesCS6B01G240300 chr5B 93.449 4885 305 9 1 4874 208670026 208674906 0 7234
8 TraesCS6B01G240300 chr1B 93.391 4887 304 16 1 4874 364442154 364437274 0 7217
9 TraesCS6B01G240300 chr1B 93.370 4887 305 12 1 4874 201396923 201392043 0 7212


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 TraesCS6B01G240300 chr6B 419939234 419944107 4873 False 9001 9001 100.000 1 4874 1 chr6B.!!$F1 4873
1 TraesCS6B01G240300 chr2B 158017082 158021964 4882 True 7374 7374 93.961 1 4874 1 chr2B.!!$R1 4873
2 TraesCS6B01G240300 chr2B 208171502 208176383 4881 True 7313 7313 93.741 1 4874 1 chr2B.!!$R2 4873
3 TraesCS6B01G240300 chrUn 131722389 131727272 4883 True 7282 7282 93.614 1 4874 1 chrUn.!!$R1 4873
4 TraesCS6B01G240300 chrUn 4433394 4438277 4883 False 7276 7276 93.594 1 4874 1 chrUn.!!$F1 4873
5 TraesCS6B01G240300 chr3B 515067803 515072682 4879 True 7278 7278 93.616 1 4874 1 chr3B.!!$R1 4873
6 TraesCS6B01G240300 chr3B 515755107 515759984 4877 False 7227 7227 93.428 1 4874 1 chr3B.!!$F1 4873
7 TraesCS6B01G240300 chr5B 208670026 208674906 4880 False 7234 7234 93.449 1 4874 1 chr5B.!!$F1 4873
8 TraesCS6B01G240300 chr1B 364437274 364442154 4880 True 7217 7217 93.391 1 4874 1 chr1B.!!$R2 4873
9 TraesCS6B01G240300 chr1B 201392043 201396923 4880 True 7212 7212 93.370 1 4874 1 chr1B.!!$R1 4873


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
910 917 0.107654 ATAACGAGACCAAGGCCTGC 60.108 55.0 5.69 0.00 0.00 4.85 F
1376 1383 0.038709 GAGCCGAAGATGATCGAGGG 60.039 60.0 0.00 1.35 45.48 4.30 F
2390 2403 0.399091 AGCTCATCTTCGGGGGATCA 60.399 55.0 0.00 0.00 0.00 2.92 F
3598 3611 0.179032 TGTCGTGGCTCATTTGTGGT 60.179 50.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2072 0.609406 GGAGGTGGCTTTCCTGTTCC 60.609 60.0 1.69 0.00 35.20 3.62 R
3318 3331 0.037882 GCAGCAGAAAAGGCTTTCCC 60.038 55.0 13.76 8.46 41.72 3.97 R
3637 3650 0.250901 ACCGCATCAAGGAACTGCTT 60.251 50.0 0.00 0.00 40.86 3.91 R
4640 4662 0.906775 TACACATCCCCCGGTTTCTC 59.093 55.0 0.00 0.00 0.00 2.87 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
71 73 0.981183 AAGACAAGGGGCACGATGTA 59.019 50.000 1.13 0.00 0.00 2.29
155 159 7.290110 TGATGATATGGGTAGTACAAGAGTG 57.710 40.000 2.06 0.00 0.00 3.51
281 287 2.176889 GGCTAGGGTTACACAGAGTCA 58.823 52.381 0.00 0.00 0.00 3.41
351 357 0.322456 CGCCAAGGAAAGTCCCATCA 60.322 55.000 0.00 0.00 37.19 3.07
459 465 2.380590 AGTCCAGAACTCCCTCAGTAGT 59.619 50.000 0.00 0.00 32.30 2.73
471 477 2.557676 CCTCAGTAGTCCCTGAACCAGA 60.558 54.545 0.00 0.00 40.78 3.86
654 661 4.994217 TCAATCTGCTGACGTATTTTGTGA 59.006 37.500 0.00 0.00 0.00 3.58
740 747 2.561373 GAAGCGGTTTCCTTGGCG 59.439 61.111 0.00 0.00 0.00 5.69
910 917 0.107654 ATAACGAGACCAAGGCCTGC 60.108 55.000 5.69 0.00 0.00 4.85
926 933 2.165234 GCCTGCTCCTTTTCTTCAATCC 59.835 50.000 0.00 0.00 0.00 3.01
1005 1012 1.254026 TCGGACCTTCGACAATGTCT 58.746 50.000 11.92 0.00 33.92 3.41
1017 1024 0.742281 CAATGTCTGGCTCCGACCTG 60.742 60.000 7.89 0.00 0.00 4.00
1019 1026 4.803426 GTCTGGCTCCGACCTGCG 62.803 72.222 0.00 0.00 40.47 5.18
1066 1073 5.240891 TCACAGAAGAAGATGTGCTAAAGG 58.759 41.667 0.52 0.00 45.12 3.11
1071 1078 4.213564 AGAAGATGTGCTAAAGGTGAGG 57.786 45.455 0.00 0.00 0.00 3.86
1155 1162 2.681778 CCCGAGCCTGGTGAGAGT 60.682 66.667 0.00 0.00 0.00 3.24
1170 1177 0.104304 AGAGTGTGGTGTTCGTGTCC 59.896 55.000 0.00 0.00 0.00 4.02
1252 1259 5.645056 TTATGGGCTAGAATTCCATGACA 57.355 39.130 0.65 0.00 41.00 3.58
1293 1300 4.578871 TCCACATCTCATCGTTCATTGTT 58.421 39.130 0.00 0.00 0.00 2.83
1317 1324 2.665603 GAAGCCTTCCTCCGCACT 59.334 61.111 0.00 0.00 0.00 4.40
1320 1327 1.900545 AAGCCTTCCTCCGCACTACC 61.901 60.000 0.00 0.00 0.00 3.18
1376 1383 0.038709 GAGCCGAAGATGATCGAGGG 60.039 60.000 0.00 1.35 45.48 4.30
1377 1384 0.468214 AGCCGAAGATGATCGAGGGA 60.468 55.000 0.00 0.00 45.48 4.20
1416 1423 2.173569 AGGGGCAGTTATAAGCAAGAGG 59.826 50.000 0.00 0.00 0.00 3.69
1450 1457 2.859992 CCCGAGGGCTCTTTTCAAG 58.140 57.895 0.00 0.00 0.00 3.02
1497 1505 0.824759 GGTTCTACATCACCGCTCCT 59.175 55.000 0.00 0.00 0.00 3.69
1539 1547 4.394712 CCTGCCTTTCGCTCGGGT 62.395 66.667 0.00 0.00 38.78 5.28
1555 1563 2.741092 GTCCTCCACAACGGCTGA 59.259 61.111 0.00 0.00 33.14 4.26
1715 1724 4.016706 CAAACGTCGCCCCCTCCT 62.017 66.667 0.00 0.00 0.00 3.69
1776 1785 3.958147 CTTCATGGGTGCGACGCCT 62.958 63.158 18.69 0.00 33.98 5.52
1816 1825 4.456911 TGTTCTTTGGATCACAAGAGATGC 59.543 41.667 0.00 0.00 40.82 3.91
1817 1826 4.290711 TCTTTGGATCACAAGAGATGCA 57.709 40.909 0.00 0.00 43.34 3.96
1858 1867 2.823147 GCCTGAGCTGCAATCGCT 60.823 61.111 1.02 0.00 41.15 4.93
1862 1871 3.267860 GAGCTGCAATCGCTCGGG 61.268 66.667 10.30 0.00 43.69 5.14
1877 1886 3.127548 CGCTCGGGTACTCAAGTAAGTAA 59.872 47.826 0.00 0.00 33.68 2.24
1943 1952 3.555966 CCTTTAACCAGCTATCCCTTGG 58.444 50.000 0.00 0.00 37.98 3.61
1945 1954 4.141158 CCTTTAACCAGCTATCCCTTGGAT 60.141 45.833 0.65 0.65 45.40 3.41
1971 1980 5.183140 GGAGTGGATAGCAAAAGCAAAACTA 59.817 40.000 0.00 0.00 0.00 2.24
2013 2022 4.222847 GAGACCACGCCGGATCCC 62.223 72.222 5.05 0.00 38.63 3.85
2063 2072 3.798511 GGAAGAGGGCGAAGGGGG 61.799 72.222 0.00 0.00 0.00 5.40
2085 2097 4.035102 AGGAAAGCCACCTCCGCC 62.035 66.667 0.00 0.00 36.78 6.13
2129 2142 0.764752 ATCGACAATCCCTCCCTCCC 60.765 60.000 0.00 0.00 0.00 4.30
2155 2168 2.183679 AGAAGAGGACCGCTTCTGAAT 58.816 47.619 32.25 14.15 45.86 2.57
2181 2194 2.672996 GCCAAGGCCTCAAAGCGA 60.673 61.111 5.23 0.00 34.56 4.93
2275 2288 0.454600 CTCCAGCGAGCCGTAAGTAA 59.545 55.000 0.00 0.00 0.00 2.24
2390 2403 0.399091 AGCTCATCTTCGGGGGATCA 60.399 55.000 0.00 0.00 0.00 2.92
2431 2444 1.475034 GCGAAATACCTCCATCTGCCA 60.475 52.381 0.00 0.00 0.00 4.92
2447 2460 1.455849 CCATACCATCATGCGGGGT 59.544 57.895 7.30 7.51 38.70 4.95
2675 2688 2.435410 GGGGTTTGAGGTACGCGG 60.435 66.667 12.47 0.00 0.00 6.46
2734 2747 3.622630 CGCCCTGTATAGATAGTAGCCT 58.377 50.000 0.00 0.00 0.00 4.58
2735 2748 3.378742 CGCCCTGTATAGATAGTAGCCTG 59.621 52.174 0.00 0.00 0.00 4.85
2796 2809 6.865726 CGAGGATCATAATCTCAGTTGTAAGG 59.134 42.308 0.00 0.00 33.17 2.69
2866 2879 2.290260 TGATGGAGTTGCCGAACTGAAT 60.290 45.455 0.00 0.00 42.80 2.57
2913 2926 1.396648 CATCGCGCTGGTCAATAAACA 59.603 47.619 5.56 0.00 0.00 2.83
3082 3095 2.422127 GCCAGAAAAAGTAATGCGGCTA 59.578 45.455 0.00 0.00 35.39 3.93
3150 3163 1.747355 CGAAGCATTGAGGAAATGGCT 59.253 47.619 0.67 0.00 45.05 4.75
3157 3170 4.382254 GCATTGAGGAAATGGCTGAAATGA 60.382 41.667 0.00 0.00 45.05 2.57
3209 3222 6.146184 CGCTATGAGTTTCTTGAAAGAGAACA 59.854 38.462 14.69 7.19 35.50 3.18
3216 3229 5.524971 TTCTTGAAAGAGAACACCGAGTA 57.475 39.130 0.00 0.00 36.22 2.59
3225 3238 2.891580 AGAACACCGAGTAGAGCAAGAA 59.108 45.455 0.00 0.00 0.00 2.52
3247 3260 1.455849 CTGAAGAAGGCCACCACCA 59.544 57.895 5.01 0.00 0.00 4.17
3264 3277 1.978617 CAAAGCCAAGGATGCCCGT 60.979 57.895 0.00 0.00 37.58 5.28
3304 3317 4.704103 AGGAGCTCCGTCAGGCCA 62.704 66.667 26.95 0.00 42.08 5.36
3318 3331 3.357079 GCCAGGGATATTGCGGCG 61.357 66.667 0.51 0.51 32.14 6.46
3359 3372 4.045104 CGTAGGAAATTCACGGATCTGAG 58.955 47.826 9.00 0.00 32.19 3.35
3598 3611 0.179032 TGTCGTGGCTCATTTGTGGT 60.179 50.000 0.00 0.00 0.00 4.16
3637 3650 4.215399 CGAAGAGTTATTTTGGCTTGGTGA 59.785 41.667 0.00 0.00 0.00 4.02
3838 3851 1.011333 GCAGGGCGCTCGTTTAATAA 58.989 50.000 7.64 0.00 37.77 1.40
3846 3859 3.722665 GCGCTCGTTTAATAAAGACGCAA 60.723 43.478 0.00 0.00 39.44 4.85
3940 3958 2.823196 CTTGTGCGTTCAAGTGTTGA 57.177 45.000 11.57 0.00 39.66 3.18
3955 3973 5.048846 AGTGTTGAAAATACCTCCTGTGT 57.951 39.130 0.00 0.00 38.90 3.72
4003 4022 2.354103 CCTGAAAGATGGCAGTCTTCGA 60.354 50.000 11.01 0.00 37.46 3.71
4177 4198 2.522185 TCGATGGTGGGGCTACTATAC 58.478 52.381 0.00 0.00 0.00 1.47
4238 4259 2.063015 ATGTGCCTGACCGGGAAACA 62.063 55.000 6.32 1.48 33.53 2.83
4262 4284 3.756434 TCCTTGTTAAAGCGGAGGAATTG 59.244 43.478 0.00 0.00 33.77 2.32
4272 4294 4.589908 AGCGGAGGAATTGTAAACATTCT 58.410 39.130 0.00 0.00 0.00 2.40
4279 4301 5.838521 AGGAATTGTAAACATTCTGGTGGTT 59.161 36.000 0.00 0.00 32.84 3.67
4292 4314 1.972075 TGGTGGTTGATCGAGTGGTTA 59.028 47.619 0.00 0.00 0.00 2.85
4352 4374 2.586648 TCTCTACTGAGGTGCTCACA 57.413 50.000 2.21 0.00 40.58 3.58
4357 4379 1.130054 ACTGAGGTGCTCACATGGGT 61.130 55.000 0.00 0.00 35.39 4.51
4506 4528 4.218852 GCATATAAGGCCTAACTCGAGACT 59.781 45.833 21.68 8.26 0.00 3.24
4521 4543 2.657143 GAGACTCCGAACACTCCCTAT 58.343 52.381 0.00 0.00 0.00 2.57
4542 4564 7.387948 CCCTATGGTATTCGGTCTTTATGAAAG 59.612 40.741 0.00 0.00 39.88 2.62
4581 4603 0.642710 AGCCCCTAGTGTCCAGGTAT 59.357 55.000 0.00 0.00 0.00 2.73
4585 4607 0.389391 CCTAGTGTCCAGGTATGCGG 59.611 60.000 0.00 0.00 0.00 5.69
4637 4659 1.202580 CCAGCTTCCTCCTCGGTTATG 60.203 57.143 0.00 0.00 0.00 1.90
4639 4661 0.831307 GCTTCCTCCTCGGTTATGGT 59.169 55.000 0.00 0.00 0.00 3.55
4640 4662 1.473434 GCTTCCTCCTCGGTTATGGTG 60.473 57.143 0.00 0.00 0.00 4.17
4642 4666 1.776662 TCCTCCTCGGTTATGGTGAG 58.223 55.000 0.00 0.00 0.00 3.51
4736 4760 1.839747 AACGGGTCCCTACTGCACA 60.840 57.895 6.29 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 0.981183 TACATCGTGCCCCTTGTCTT 59.019 50.000 0.00 0.00 0.00 3.01
62 64 2.914059 ACCTGGGTAAATACATCGTGC 58.086 47.619 0.00 0.00 0.00 5.34
177 181 3.996957 AGGCTAGCTTCTAGGGTTTAGT 58.003 45.455 15.72 0.00 0.00 2.24
281 287 9.830186 ATATGTAGATCTCCTACCATTGTAACT 57.170 33.333 0.00 0.00 45.60 2.24
351 357 0.826672 AAGACTTCGTCCCGTGTCCT 60.827 55.000 0.00 0.00 34.39 3.85
445 451 1.717077 TCAGGGACTACTGAGGGAGTT 59.283 52.381 0.00 0.00 42.26 3.01
459 465 2.978978 TCATTGAAGTCTGGTTCAGGGA 59.021 45.455 0.00 0.00 37.72 4.20
471 477 2.417379 CCGGACTCGTCATCATTGAAGT 60.417 50.000 0.00 0.00 33.63 3.01
654 661 0.459585 GCCGTGGTGTGACGTCATAT 60.460 55.000 23.12 0.00 37.66 1.78
740 747 0.319040 TCTCTGCTGTGACAAGACGC 60.319 55.000 0.00 0.00 0.00 5.19
910 917 5.877012 TCGATTGAGGATTGAAGAAAAGGAG 59.123 40.000 0.00 0.00 0.00 3.69
926 933 1.539065 CGAGGGGTGGATTCGATTGAG 60.539 57.143 0.00 0.00 36.49 3.02
1027 1034 1.064463 TGTGATGGAAGAAGGCATCCC 60.064 52.381 0.00 0.00 34.68 3.85
1066 1073 1.043673 AGATACCTGGCGTCCCTCAC 61.044 60.000 0.00 0.00 0.00 3.51
1071 1078 0.031721 CGGTTAGATACCTGGCGTCC 59.968 60.000 0.00 0.00 45.40 4.79
1117 1124 1.147817 AGTGGGAATGACTTGCCCTTT 59.852 47.619 5.97 0.00 41.96 3.11
1155 1162 3.310652 TGGGACACGAACACCACA 58.689 55.556 0.00 0.00 0.00 4.17
1252 1259 2.143419 GGATGGACTCCGGAGCCAT 61.143 63.158 38.57 38.57 43.22 4.40
1293 1300 0.178068 GGAGGAAGGCTTCGCATACA 59.822 55.000 20.26 0.00 0.00 2.29
1313 1320 1.218316 CCGAAGTGAGGGGTAGTGC 59.782 63.158 0.00 0.00 0.00 4.40
1317 1324 1.553248 CACAATCCGAAGTGAGGGGTA 59.447 52.381 0.00 0.00 37.97 3.69
1320 1327 1.026718 GCCACAATCCGAAGTGAGGG 61.027 60.000 6.04 0.00 37.97 4.30
1448 1455 1.986882 CCACAAACCAAGCTCCTCTT 58.013 50.000 0.00 0.00 34.78 2.85
1450 1457 0.823356 TGCCACAAACCAAGCTCCTC 60.823 55.000 0.00 0.00 0.00 3.71
1458 1466 0.033601 ACTCCTGTTGCCACAAACCA 60.034 50.000 0.00 0.00 30.36 3.67
1539 1547 2.741092 GTCAGCCGTTGTGGAGGA 59.259 61.111 0.00 0.00 42.00 3.71
1555 1563 1.604604 CCTTTGTTGACCCATGACGT 58.395 50.000 0.00 0.00 0.00 4.34
1644 1653 2.034179 CGCCACTACGACCAGATTGATA 59.966 50.000 0.00 0.00 34.06 2.15
1715 1724 1.064758 CCGGATTGAATTCCCACAGGA 60.065 52.381 0.00 0.00 41.88 3.86
1776 1785 7.390440 CCAAAGAACAGTTTATACATCTCCACA 59.610 37.037 0.00 0.00 0.00 4.17
1858 1867 5.359009 CAGGATTACTTACTTGAGTACCCGA 59.641 44.000 0.00 0.00 33.60 5.14
1862 1871 5.811100 GGCACAGGATTACTTACTTGAGTAC 59.189 44.000 0.00 0.00 32.12 2.73
1971 1980 3.789290 GGGGCCGGACACCGTATT 61.789 66.667 11.00 0.00 46.80 1.89
2013 2022 2.868583 CTCCAGCATCCTGATTAACACG 59.131 50.000 0.00 0.00 41.77 4.49
2063 2072 0.609406 GGAGGTGGCTTTCCTGTTCC 60.609 60.000 1.69 0.00 35.20 3.62
2085 2097 1.615384 CCTTTCTTGAGGGCCTCCTTG 60.615 57.143 30.03 19.04 45.05 3.61
2115 2128 3.666122 CCAGGGAGGGAGGGATTG 58.334 66.667 0.00 0.00 0.00 2.67
2129 2142 2.726351 GCGGTCCTCTTCTCCCCAG 61.726 68.421 0.00 0.00 0.00 4.45
2155 2168 1.004758 AGGCCTTGGCCTCTGGATA 59.995 57.895 26.23 0.00 34.71 2.59
2275 2288 6.495872 GTCCCTTATTACAAAACTCCCCTTTT 59.504 38.462 0.00 0.00 0.00 2.27
2334 2347 5.578005 TGAGATCCGAACTACAAGGTAAG 57.422 43.478 0.00 0.00 0.00 2.34
2390 2403 1.202940 TCTCCATCATCTCCGGACGAT 60.203 52.381 0.00 5.23 0.00 3.73
2431 2444 1.059584 TCCACCCCGCATGATGGTAT 61.060 55.000 0.00 0.00 33.67 2.73
2447 2460 1.906824 GACACCTCAGGGTCGTCCA 60.907 63.158 0.00 0.00 45.41 4.02
2500 2513 2.925170 AGTTGGCGCCAGACCTCT 60.925 61.111 30.75 19.50 0.00 3.69
2502 2515 4.335647 CCAGTTGGCGCCAGACCT 62.336 66.667 30.75 22.75 0.00 3.85
2511 2524 2.025418 CGACCGTACACCAGTTGGC 61.025 63.158 0.00 0.00 39.32 4.52
2675 2688 9.994432 CAAAACTGTCAGAAGGTATATCATTTC 57.006 33.333 6.91 0.00 0.00 2.17
2734 2747 1.265095 GACAACGTACCGAGTCTCACA 59.735 52.381 0.00 0.00 34.66 3.58
2735 2748 1.724018 CGACAACGTACCGAGTCTCAC 60.724 57.143 0.00 0.00 35.05 3.51
2796 2809 2.510768 CTGTATAGGAAGGGCGACAC 57.489 55.000 0.00 0.00 0.00 3.67
2913 2926 2.981859 ACCTTGTGACTCGTCAAGTT 57.018 45.000 0.64 0.00 41.85 2.66
3055 3068 3.676646 GCATTACTTTTTCTGGCTTGCTG 59.323 43.478 0.00 0.00 0.00 4.41
3082 3095 3.901797 CTTCGGCCGCCTTCAAGGT 62.902 63.158 23.51 0.00 37.80 3.50
3137 3150 3.511146 GGTCATTTCAGCCATTTCCTCAA 59.489 43.478 0.00 0.00 0.00 3.02
3138 3151 3.091545 GGTCATTTCAGCCATTTCCTCA 58.908 45.455 0.00 0.00 0.00 3.86
3150 3163 2.542020 TCAGCTTCACGGTCATTTCA 57.458 45.000 0.00 0.00 0.00 2.69
3157 3170 0.674895 GCATCCTTCAGCTTCACGGT 60.675 55.000 0.00 0.00 0.00 4.83
3209 3222 1.819903 GGTCTTCTTGCTCTACTCGGT 59.180 52.381 0.00 0.00 0.00 4.69
3216 3229 3.007831 CCTTCTTCAGGTCTTCTTGCTCT 59.992 47.826 0.00 0.00 37.99 4.09
3264 3277 1.334160 TTATAGCCCTCATCGCGGAA 58.666 50.000 6.13 0.00 0.00 4.30
3304 3317 1.990160 TTTCCCGCCGCAATATCCCT 61.990 55.000 0.00 0.00 0.00 4.20
3318 3331 0.037882 GCAGCAGAAAAGGCTTTCCC 60.038 55.000 13.76 8.46 41.72 3.97
3359 3372 0.749454 CTGGCCCAACTGAGCATACC 60.749 60.000 0.00 0.00 0.00 2.73
3637 3650 0.250901 ACCGCATCAAGGAACTGCTT 60.251 50.000 0.00 0.00 40.86 3.91
3838 3851 3.236816 CATTTTTCGAGCATTGCGTCTT 58.763 40.909 2.38 0.00 0.00 3.01
3846 3859 8.649841 CATTTGAACATAACATTTTTCGAGCAT 58.350 29.630 0.00 0.00 0.00 3.79
3909 3927 4.276183 TGAACGCACAAGTATAAAAAGCCA 59.724 37.500 0.00 0.00 0.00 4.75
3940 3958 1.613255 CGGCCACACAGGAGGTATTTT 60.613 52.381 2.24 0.00 41.22 1.82
4003 4022 4.643387 GTGCGTGGGGGCTGAAGT 62.643 66.667 0.00 0.00 0.00 3.01
4050 4071 5.587043 AGACGTTGGATTAAGTGTGAAAACA 59.413 36.000 0.00 0.00 0.00 2.83
4051 4072 6.056428 AGACGTTGGATTAAGTGTGAAAAC 57.944 37.500 0.00 0.00 0.00 2.43
4217 4238 0.916086 TTTCCCGGTCAGGCACATAT 59.084 50.000 0.00 0.00 39.21 1.78
4238 4259 1.975680 TCCTCCGCTTTAACAAGGACT 59.024 47.619 0.00 0.00 31.25 3.85
4262 4284 4.693566 TCGATCAACCACCAGAATGTTTAC 59.306 41.667 0.00 0.00 0.00 2.01
4272 4294 0.762418 AACCACTCGATCAACCACCA 59.238 50.000 0.00 0.00 0.00 4.17
4279 4301 3.162666 AGACTGGTTAACCACTCGATCA 58.837 45.455 23.69 0.00 42.01 2.92
4292 4314 6.434340 TGTCATGATATAGCGATAGACTGGTT 59.566 38.462 0.00 0.00 39.76 3.67
4301 4323 5.973899 ACTGACTGTCATGATATAGCGAT 57.026 39.130 11.45 0.00 0.00 4.58
4352 4374 4.360405 GTGCCCCGGTTCACCCAT 62.360 66.667 11.11 0.00 0.00 4.00
4357 4379 2.359354 CGATTGTGCCCCGGTTCA 60.359 61.111 0.00 0.00 0.00 3.18
4454 4476 5.673818 GCTCCGAATCATGTCTTTGGTAAAC 60.674 44.000 13.41 3.30 0.00 2.01
4457 4479 3.197766 AGCTCCGAATCATGTCTTTGGTA 59.802 43.478 13.41 4.34 0.00 3.25
4506 4528 2.832643 TACCATAGGGAGTGTTCGGA 57.167 50.000 0.00 0.00 38.05 4.55
4521 4543 4.569162 CGCTTTCATAAAGACCGAATACCA 59.431 41.667 3.63 0.00 41.02 3.25
4581 4603 2.287308 CCACGTCAGAAATTTTTCCGCA 60.287 45.455 0.00 0.00 37.92 5.69
4585 4607 2.031508 TCGGCCACGTCAGAAATTTTTC 60.032 45.455 2.24 0.00 41.85 2.29
4637 4659 1.077716 CATCCCCCGGTTTCTCACC 60.078 63.158 0.00 0.00 43.16 4.02
4639 4661 1.131303 ACACATCCCCCGGTTTCTCA 61.131 55.000 0.00 0.00 0.00 3.27
4640 4662 0.906775 TACACATCCCCCGGTTTCTC 59.093 55.000 0.00 0.00 0.00 2.87
4642 4666 1.210967 TGATACACATCCCCCGGTTTC 59.789 52.381 0.00 0.00 0.00 2.78
4677 4701 2.180432 AGACCCTGCGTAAACCTTTC 57.820 50.000 0.00 0.00 0.00 2.62
4736 4760 2.581354 GGAGACACAGGCGCAGAT 59.419 61.111 10.83 0.00 0.00 2.90



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

AutoCloner maintained by Alex Coulton.