Multiple sequence alignment - TraesCS2D01G552000

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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 TraesCS2D01G552000 chr2D 100.000 6660 0 0 1 6660 627257253 627250594 0.000000e+00 12299.0
1 TraesCS2D01G552000 chr2B 89.336 3779 204 80 68 3738 769083165 769079478 0.000000e+00 4562.0
2 TraesCS2D01G552000 chr2B 90.909 1012 53 15 3923 4907 769079379 769078380 0.000000e+00 1323.0
3 TraesCS2D01G552000 chr2B 87.161 958 67 26 5563 6497 769077339 769076415 0.000000e+00 1037.0
4 TraesCS2D01G552000 chr2B 91.639 299 24 1 5202 5499 769077815 769077517 4.810000e-111 412.0
5 TraesCS2D01G552000 chr2B 100.000 42 0 0 6585 6626 769076309 769076268 1.990000e-10 78.7
6 TraesCS2D01G552000 chr2B 95.918 49 1 1 4 51 769083249 769083201 1.990000e-10 78.7
7 TraesCS2D01G552000 chr2B 89.655 58 6 0 6585 6642 769075552 769075495 2.580000e-09 75.0
8 TraesCS2D01G552000 chr2A 97.040 2466 53 11 3745 6208 757950336 757947889 0.000000e+00 4132.0
9 TraesCS2D01G552000 chr2A 90.945 2253 94 30 5 2215 757954093 757951909 0.000000e+00 2929.0
10 TraesCS2D01G552000 chr2A 95.928 1498 33 10 2261 3738 757951908 757950419 0.000000e+00 2403.0
11 TraesCS2D01G552000 chr2A 94.118 187 9 1 6226 6410 757947737 757947551 3.930000e-72 283.0
12 TraesCS2D01G552000 chr2A 94.444 162 8 1 6499 6660 757947474 757947314 1.430000e-61 248.0


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 TraesCS2D01G552000 chr2D 627250594 627257253 6659 True 12299.000000 12299 100.000000 1 6660 1 chr2D.!!$R1 6659
1 TraesCS2D01G552000 chr2B 769075495 769083249 7754 True 1080.914286 4562 92.088286 4 6642 7 chr2B.!!$R1 6638
2 TraesCS2D01G552000 chr2A 757947314 757954093 6779 True 1999.000000 4132 94.495000 5 6660 5 chr2A.!!$R1 6655

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
873 1020 0.168128 CCGGATTGCTTGTTTCGTCC 59.832 55.000 0.00 0.00 0.00 4.79 F
1745 1905 0.654683 GATTGTGCCGATGAGCTCAC 59.345 55.000 20.97 12.13 36.09 3.51 F
2458 2621 1.457643 CGGCCTCTGGGTCCATAGA 60.458 63.158 0.00 0.92 32.63 1.98 F
3185 3371 2.035632 ACCAGCTAGCCTCACTGTATC 58.964 52.381 12.13 0.00 0.00 2.24 F
4758 5050 0.809385 CTCATTGCCAGCCTTCACAG 59.191 55.000 0.00 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 2771 0.387239 GAAACCACGGCATGCAGTTC 60.387 55.000 21.31 12.29 0.00 3.01 R
3482 3668 0.237761 CTTGTCTTCTGTGCTGCTGC 59.762 55.000 8.89 8.89 40.20 5.25 R
3747 4012 1.422781 CATGGCAGTGGTATGGAGGAT 59.577 52.381 0.00 0.00 0.00 3.24 R
5073 5365 0.607489 CAGGTCCTTTGGCCACTCAG 60.607 60.000 3.88 1.04 0.00 3.35 R
5769 6546 1.144057 AACTATTCCTGGCGCTCCG 59.856 57.895 7.64 0.00 34.14 4.63 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
85 106 2.367512 GGGGCAGGAGGGTCATCT 60.368 66.667 0.00 0.00 0.00 2.90
87 108 1.690633 GGGCAGGAGGGTCATCTCA 60.691 63.158 0.00 0.00 35.58 3.27
97 118 3.147595 TCATCTCACCGGGCGGAG 61.148 66.667 6.32 10.15 38.96 4.63
138 162 2.032860 ATAGGCTAGCGCTGGTGGTG 62.033 60.000 22.90 4.14 36.09 4.17
154 178 0.667453 GGTGTAGAGTAGGGCGCTAC 59.333 60.000 28.41 28.41 46.36 3.58
247 290 2.045045 CTGCCCGCCTGGATCAAA 60.045 61.111 0.00 0.00 37.49 2.69
251 294 2.354729 CCGCCTGGATCAAACCCA 59.645 61.111 0.00 0.00 37.49 4.51
252 295 1.304052 CCGCCTGGATCAAACCCAA 60.304 57.895 0.00 0.00 37.49 4.12
253 296 1.595093 CCGCCTGGATCAAACCCAAC 61.595 60.000 0.00 0.00 37.49 3.77
254 297 1.595093 CGCCTGGATCAAACCCAACC 61.595 60.000 0.00 0.00 32.53 3.77
255 298 1.257750 GCCTGGATCAAACCCAACCC 61.258 60.000 0.00 0.00 32.53 4.11
412 477 3.064324 GAATTGGGCTGCTGCGGT 61.064 61.111 10.62 0.00 40.82 5.68
627 742 1.299089 GCGTGGTTTGTTGCTGGTC 60.299 57.895 0.00 0.00 0.00 4.02
628 743 1.999071 GCGTGGTTTGTTGCTGGTCA 61.999 55.000 0.00 0.00 0.00 4.02
748 873 4.148825 CCTCCGTGGCCTTCCTCG 62.149 72.222 3.32 1.05 45.91 4.63
868 1015 2.154462 CTCTGACCGGATTGCTTGTTT 58.846 47.619 9.46 0.00 0.00 2.83
872 1019 0.872388 ACCGGATTGCTTGTTTCGTC 59.128 50.000 9.46 0.00 0.00 4.20
873 1020 0.168128 CCGGATTGCTTGTTTCGTCC 59.832 55.000 0.00 0.00 0.00 4.79
895 1042 4.959596 GGCGGCGGCTGATCTCTC 62.960 72.222 27.22 0.00 39.81 3.20
1039 1186 2.590092 GGTTCCACCAGGGGATCG 59.410 66.667 0.00 0.00 38.42 3.69
1074 1221 3.350219 GTCTACAACCACCATCACCAT 57.650 47.619 0.00 0.00 0.00 3.55
1082 1229 0.680921 CACCATCACCATCACCACCC 60.681 60.000 0.00 0.00 0.00 4.61
1107 1257 0.908198 ACATGCTCTCCTTCCAGTCC 59.092 55.000 0.00 0.00 0.00 3.85
1112 1262 1.190643 CTCTCCTTCCAGTCCTCCAC 58.809 60.000 0.00 0.00 0.00 4.02
1131 1281 4.760047 AGCGACGTCACCATGGGC 62.760 66.667 18.09 7.79 0.00 5.36
1254 1407 1.137825 CAACAACGGCGGTGTGTTT 59.862 52.632 33.14 13.91 0.00 2.83
1392 1548 3.300857 CGACCGTGAGCTGAATATACTG 58.699 50.000 0.00 0.00 0.00 2.74
1581 1741 4.022849 AGTCTAAAGCAGGATTTGTGCAAC 60.023 41.667 0.00 0.00 43.82 4.17
1713 1873 1.091537 TAAGCATTAACAGCCGCACC 58.908 50.000 0.00 0.00 0.00 5.01
1745 1905 0.654683 GATTGTGCCGATGAGCTCAC 59.345 55.000 20.97 12.13 36.09 3.51
1846 2006 6.672147 TGAGAATTGCTTCTAAGAAACAAGC 58.328 36.000 0.00 0.00 41.87 4.01
2002 2162 2.226674 GTGGGCTGCAGTAAGTTTCTTC 59.773 50.000 16.64 0.00 0.00 2.87
2015 2175 8.017946 CAGTAAGTTTCTTCCAAATGTCTAAGC 58.982 37.037 0.00 0.00 0.00 3.09
2020 2180 8.103305 AGTTTCTTCCAAATGTCTAAGCATCTA 58.897 33.333 0.00 0.00 0.00 1.98
2023 2183 9.466497 TTCTTCCAAATGTCTAAGCATCTATTT 57.534 29.630 0.00 0.00 0.00 1.40
2026 2186 9.466497 TTCCAAATGTCTAAGCATCTATTTTCT 57.534 29.630 0.00 0.00 0.00 2.52
2044 2204 9.208022 CTATTTTCTGTATGTGTTCTGTTCTGA 57.792 33.333 0.00 0.00 0.00 3.27
2058 2218 9.098355 TGTTCTGTTCTGATATTAATGTAGTGC 57.902 33.333 0.00 0.00 0.00 4.40
2227 2387 9.811995 AGCCTTTTTCGTAGTTTATTTTCTTTT 57.188 25.926 0.00 0.00 0.00 2.27
2414 2577 6.837312 TGGATGAAGTTTATAGGGGTGTATG 58.163 40.000 0.00 0.00 0.00 2.39
2458 2621 1.457643 CGGCCTCTGGGTCCATAGA 60.458 63.158 0.00 0.92 32.63 1.98
2608 2771 4.202243 TGGCATTTTGGACTCTTCCTTTTG 60.202 41.667 0.00 0.00 43.31 2.44
2670 2833 2.827322 ACAGCACATGCACATAAACCAT 59.173 40.909 6.64 0.00 45.16 3.55
3114 3280 9.174166 TCCTAACTTTGTCTGATTATTTAAGGC 57.826 33.333 0.00 0.00 0.00 4.35
3184 3370 2.166907 ACCAGCTAGCCTCACTGTAT 57.833 50.000 12.13 0.00 0.00 2.29
3185 3371 2.035632 ACCAGCTAGCCTCACTGTATC 58.964 52.381 12.13 0.00 0.00 2.24
3243 3429 6.151985 ACATCAACTTTGTGGAGTTACAACAA 59.848 34.615 0.00 0.00 40.04 2.83
3327 3513 9.613428 TTGATGATCTCCTAAAATACGAAACAT 57.387 29.630 0.00 0.00 0.00 2.71
3452 3638 6.306837 GTGCGTCTCTATATTTAGACTGCATC 59.693 42.308 23.02 17.54 45.06 3.91
3678 3866 2.158058 CTACGTTGCACACACCTGCG 62.158 60.000 0.00 0.00 40.31 5.18
3742 3930 9.944663 TTAGCCAAAAGTTTAATTAGCATATCG 57.055 29.630 0.00 0.00 0.00 2.92
3747 4012 9.891828 CAAAAGTTTAATTAGCATATCGGCATA 57.108 29.630 0.00 0.00 35.83 3.14
3840 4105 9.265901 CCACTTGGAGATATGTAAATTAGACTG 57.734 37.037 0.00 0.00 37.39 3.51
3905 4170 0.984230 TCAGTACAGCCCTTTGGAGG 59.016 55.000 0.00 0.00 43.15 4.30
3941 4207 6.072112 TGTCTCTCCTTTAATTTGTTGTGC 57.928 37.500 0.00 0.00 0.00 4.57
4272 4547 2.824041 CACATGGTGCCCGCCTAC 60.824 66.667 0.00 0.00 0.00 3.18
4297 4572 7.226720 ACTGGTTTTACATCTTACACAGTGAAG 59.773 37.037 7.81 6.95 35.56 3.02
4547 4836 1.317613 TGGGTGCACTGTCAATGTTC 58.682 50.000 17.98 0.00 0.00 3.18
4704 4996 7.340999 TGTCATCTGCCACTAAGTACTAATACA 59.659 37.037 0.00 0.00 33.30 2.29
4758 5050 0.809385 CTCATTGCCAGCCTTCACAG 59.191 55.000 0.00 0.00 0.00 3.66
4838 5130 7.308770 CCTGAAGTTCTGATTTATTTGCAGACA 60.309 37.037 11.06 0.00 38.30 3.41
5029 5321 4.149396 GCTTCACTTCAACATGTTCAATGC 59.851 41.667 8.48 2.11 0.00 3.56
5123 5415 3.259876 TCGTGAAATAAGTAGTGGTGGCT 59.740 43.478 0.00 0.00 0.00 4.75
5124 5416 4.000988 CGTGAAATAAGTAGTGGTGGCTT 58.999 43.478 0.00 0.00 0.00 4.35
5126 5418 5.616866 CGTGAAATAAGTAGTGGTGGCTTTG 60.617 44.000 0.00 0.00 0.00 2.77
5128 5420 4.650972 AATAAGTAGTGGTGGCTTTGGA 57.349 40.909 0.00 0.00 0.00 3.53
5130 5422 3.525800 AAGTAGTGGTGGCTTTGGAAT 57.474 42.857 0.00 0.00 0.00 3.01
5131 5423 3.073274 AGTAGTGGTGGCTTTGGAATC 57.927 47.619 0.00 0.00 0.00 2.52
5132 5424 2.644798 AGTAGTGGTGGCTTTGGAATCT 59.355 45.455 0.00 0.00 0.00 2.40
5133 5425 2.683211 AGTGGTGGCTTTGGAATCTT 57.317 45.000 0.00 0.00 0.00 2.40
5174 5466 2.902486 TCAGTTGCTGTCCTGAGATCTT 59.098 45.455 0.00 0.00 32.93 2.40
5408 6027 3.338249 TCCTCTGCAAGAATTAGCACAC 58.662 45.455 0.00 0.00 46.34 3.82
5474 6093 1.153628 ACACGGCCTAGCAATCGTC 60.154 57.895 0.00 0.00 33.31 4.20
5477 6096 1.518572 CGGCCTAGCAATCGTCGTT 60.519 57.895 0.00 0.00 0.00 3.85
5540 6317 6.136071 GGTGCTAAAAATATGTATGCACTCG 58.864 40.000 13.52 0.00 45.63 4.18
5543 6320 6.074005 GCTAAAAATATGTATGCACTCGAGC 58.926 40.000 13.61 0.00 0.00 5.03
5552 6329 0.942410 TGCACTCGAGCGGTAACAAC 60.942 55.000 13.61 0.00 37.31 3.32
5582 6359 4.393062 CGATGTCTCAACTAAGCAATTGGT 59.607 41.667 3.82 3.82 0.00 3.67
5766 6543 3.961408 CCCTACAGGCTGTTATACTGACT 59.039 47.826 27.24 0.00 35.65 3.41
5814 6591 4.434545 ACATCCTTGAGATCATTCCCTG 57.565 45.455 0.00 0.00 30.59 4.45
5918 6695 1.075374 CCTTCCTCCCATCAACCACAA 59.925 52.381 0.00 0.00 0.00 3.33
6253 7164 6.042143 CAGCTAAAGAGAGAAGGATGAGAAC 58.958 44.000 0.00 0.00 0.00 3.01
6271 7182 6.223852 TGAGAACAGAAAATGTAGGAGTGAC 58.776 40.000 0.00 0.00 43.00 3.67
6447 7370 0.674895 GGATGAAGCAACTGACGGCT 60.675 55.000 0.00 0.00 43.46 5.52
6497 7424 8.934023 TCTTCCAACCTATACTTGTGAATTTT 57.066 30.769 0.00 0.00 0.00 1.82
6540 7531 0.950836 TTCACACAAGATGTTGGCCG 59.049 50.000 7.59 0.00 40.64 6.13
6546 7537 2.325082 AAGATGTTGGCCGACGCAC 61.325 57.895 18.54 11.56 36.38 5.34
6562 7553 8.612903 GCCGACGCACAAATTCAAAAATTGAA 62.613 38.462 7.87 7.87 43.54 2.69
6628 8331 1.774856 AGCACTCCTAACCCAAACACT 59.225 47.619 0.00 0.00 0.00 3.55
6642 8345 2.409948 AACACTGGAGGCTTATCAGC 57.590 50.000 11.57 0.00 46.52 4.26
6655 8358 4.127907 GCTTATCAGCCCTACTTTGGTAC 58.872 47.826 0.00 0.00 40.61 3.34
6656 8359 2.981859 ATCAGCCCTACTTTGGTACG 57.018 50.000 0.00 0.00 0.00 3.67
6657 8360 1.636148 TCAGCCCTACTTTGGTACGT 58.364 50.000 0.00 0.00 0.00 3.57
6659 8362 3.164268 TCAGCCCTACTTTGGTACGTAA 58.836 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 178 2.742589 GTTCCTTCTTAAACAGAGGGCG 59.257 50.000 0.00 0.00 46.60 6.13
247 290 1.383386 GGTTTGGGTTGGGTTGGGT 60.383 57.895 0.00 0.00 0.00 4.51
251 294 0.105709 CTCTGGGTTTGGGTTGGGTT 60.106 55.000 0.00 0.00 0.00 4.11
252 295 1.541672 CTCTGGGTTTGGGTTGGGT 59.458 57.895 0.00 0.00 0.00 4.51
253 296 1.228862 CCTCTGGGTTTGGGTTGGG 60.229 63.158 0.00 0.00 0.00 4.12
254 297 1.228862 CCCTCTGGGTTTGGGTTGG 60.229 63.158 0.00 0.00 38.25 3.77
255 298 0.409484 ATCCCTCTGGGTTTGGGTTG 59.591 55.000 2.25 0.00 44.74 3.77
438 512 4.925576 CCTCCGCGAATCCCGACG 62.926 72.222 8.23 0.00 41.76 5.12
439 513 3.769875 GACCTCCGCGAATCCCGAC 62.770 68.421 8.23 0.00 41.76 4.79
440 514 3.524606 GACCTCCGCGAATCCCGA 61.525 66.667 8.23 0.00 41.76 5.14
542 616 3.695606 GCGACTCACCTGCCTCCA 61.696 66.667 0.00 0.00 0.00 3.86
627 742 1.101049 AGCAACCGACCAACCAACTG 61.101 55.000 0.00 0.00 0.00 3.16
628 743 1.101049 CAGCAACCGACCAACCAACT 61.101 55.000 0.00 0.00 0.00 3.16
750 875 2.524306 AGATAGGATCTCCAGCGGAAG 58.476 52.381 0.00 0.00 38.89 3.46
751 876 2.685106 AGATAGGATCTCCAGCGGAA 57.315 50.000 0.00 0.00 38.89 4.30
816 963 0.912486 CCCGGAAGAGAAATGGAGGT 59.088 55.000 0.73 0.00 0.00 3.85
821 968 1.139853 CTCCTCCCCGGAAGAGAAATG 59.860 57.143 19.69 6.19 42.53 2.32
873 1020 3.474230 GATCAGCCGCCGCCAATTG 62.474 63.158 0.00 0.00 34.57 2.32
885 1032 2.733945 GAGCCGGGAGAGATCAGC 59.266 66.667 2.18 0.00 0.00 4.26
975 1122 3.424105 GGGGGAGCCAGCTGGAAT 61.424 66.667 37.21 23.51 37.39 3.01
1074 1221 1.112315 GCATGTTGTTGGGGTGGTGA 61.112 55.000 0.00 0.00 0.00 4.02
1082 1229 1.815003 GGAAGGAGAGCATGTTGTTGG 59.185 52.381 0.00 0.00 0.00 3.77
1107 1257 2.430921 GTGACGTCGCTGGTGGAG 60.431 66.667 21.55 0.00 0.00 3.86
1112 1262 2.815211 CCATGGTGACGTCGCTGG 60.815 66.667 26.79 22.76 0.00 4.85
1377 1533 5.451937 CCCTTCGTTCAGTATATTCAGCTCA 60.452 44.000 0.00 0.00 0.00 4.26
1392 1548 1.376037 CCTGGTGAGCCCTTCGTTC 60.376 63.158 0.00 0.00 0.00 3.95
1466 1626 2.036217 TGGCAAACTCCATCAGCAAAAG 59.964 45.455 0.00 0.00 0.00 2.27
1581 1741 8.251026 AGAAACTGAAAAGGTAAAAAGGTTCAG 58.749 33.333 9.13 9.13 44.74 3.02
1713 1873 2.871022 GGCACAATCATAGAGCACTCAG 59.129 50.000 0.00 0.00 0.00 3.35
1846 2006 7.709149 AGAATTAGAACCTCAAAGGAAATGG 57.291 36.000 0.00 0.00 37.67 3.16
2002 2162 8.680903 ACAGAAAATAGATGCTTAGACATTTGG 58.319 33.333 0.00 0.00 0.00 3.28
2015 2175 9.979270 GAACAGAACACATACAGAAAATAGATG 57.021 33.333 0.00 0.00 0.00 2.90
2020 2180 8.627208 ATCAGAACAGAACACATACAGAAAAT 57.373 30.769 0.00 0.00 0.00 1.82
2044 2204 8.202137 ACCAGTAAGAACGCACTACATTAATAT 58.798 33.333 0.00 0.00 0.00 1.28
2052 2212 3.572604 AGACCAGTAAGAACGCACTAC 57.427 47.619 0.00 0.00 0.00 2.73
2053 2213 3.319972 ACAAGACCAGTAAGAACGCACTA 59.680 43.478 0.00 0.00 0.00 2.74
2054 2214 2.102588 ACAAGACCAGTAAGAACGCACT 59.897 45.455 0.00 0.00 0.00 4.40
2058 2218 3.184581 GCAGAACAAGACCAGTAAGAACG 59.815 47.826 0.00 0.00 0.00 3.95
2227 2387 9.396022 GAGAAAATGATAATAGTGTGAGGGAAA 57.604 33.333 0.00 0.00 0.00 3.13
2228 2388 8.772250 AGAGAAAATGATAATAGTGTGAGGGAA 58.228 33.333 0.00 0.00 0.00 3.97
2229 2389 8.324191 AGAGAAAATGATAATAGTGTGAGGGA 57.676 34.615 0.00 0.00 0.00 4.20
2233 2393 9.942850 TCACAAGAGAAAATGATAATAGTGTGA 57.057 29.630 0.00 0.00 38.42 3.58
2235 2395 9.950496 ACTCACAAGAGAAAATGATAATAGTGT 57.050 29.630 0.00 0.00 44.98 3.55
2237 2397 9.950496 ACACTCACAAGAGAAAATGATAATAGT 57.050 29.630 0.00 0.00 44.98 2.12
2414 2577 5.339282 GGGAGGGGCTCTTCCATTATATAAC 60.339 48.000 17.80 0.00 41.06 1.89
2458 2621 1.888512 CCTTAACTGGCTGTGTGCATT 59.111 47.619 0.00 0.00 45.15 3.56
2486 2649 6.719370 TGTCCAGAACAAGCCATTATTACTTT 59.281 34.615 0.00 0.00 34.03 2.66
2608 2771 0.387239 GAAACCACGGCATGCAGTTC 60.387 55.000 21.31 12.29 0.00 3.01
2670 2833 5.181056 ACAAACGCATGTCATCAGAACATAA 59.819 36.000 0.00 0.00 0.00 1.90
2785 2948 9.421806 GAGAGATAGTGATGTAAATGATTGAGG 57.578 37.037 0.00 0.00 0.00 3.86
3114 3280 4.763793 ACAATTCTGGACCACTGATTCAAG 59.236 41.667 0.00 0.00 0.00 3.02
3158 3326 2.226674 GTGAGGCTAGCTGGTTTCAAAC 59.773 50.000 15.72 0.00 0.00 2.93
3184 3370 3.331889 AGCCCAGGAAAATTTCAGAGAGA 59.668 43.478 8.09 0.00 0.00 3.10
3185 3371 3.694926 AGCCCAGGAAAATTTCAGAGAG 58.305 45.455 8.09 0.00 0.00 3.20
3341 3527 5.841957 AACAAGCAGAACATCAAGAACTT 57.158 34.783 0.00 0.00 0.00 2.66
3452 3638 8.657387 TTCAGTTCTATATTGGGATCTAGGAG 57.343 38.462 0.00 0.00 0.00 3.69
3482 3668 0.237761 CTTGTCTTCTGTGCTGCTGC 59.762 55.000 8.89 8.89 40.20 5.25
3483 3669 0.237761 GCTTGTCTTCTGTGCTGCTG 59.762 55.000 0.00 0.00 0.00 4.41
3631 3819 2.787473 TTGCCTCCTACAAGGACATG 57.213 50.000 0.00 0.00 40.06 3.21
3632 3820 2.912956 TCTTTGCCTCCTACAAGGACAT 59.087 45.455 0.00 0.00 40.06 3.06
3634 3822 3.636153 ATCTTTGCCTCCTACAAGGAC 57.364 47.619 0.00 0.00 40.06 3.85
3678 3866 9.262358 AGAAGTAGACTTTTGTTGAGAATGTAC 57.738 33.333 0.00 0.00 36.11 2.90
3734 3922 2.470990 TGGAGGATATGCCGATATGCT 58.529 47.619 0.00 0.00 43.80 3.79
3738 3926 3.704566 GTGGTATGGAGGATATGCCGATA 59.295 47.826 0.00 0.00 43.43 2.92
3739 3927 2.501723 GTGGTATGGAGGATATGCCGAT 59.498 50.000 0.00 0.00 43.43 4.18
3740 3928 1.899814 GTGGTATGGAGGATATGCCGA 59.100 52.381 0.00 0.00 43.43 5.54
3741 3929 1.902508 AGTGGTATGGAGGATATGCCG 59.097 52.381 0.00 0.00 43.43 5.69
3742 3930 2.616510 GCAGTGGTATGGAGGATATGCC 60.617 54.545 0.00 0.00 0.00 4.40
3747 4012 1.422781 CATGGCAGTGGTATGGAGGAT 59.577 52.381 0.00 0.00 0.00 3.24
3866 4131 6.658831 ACTGAATCACAATCAAGTACAAACG 58.341 36.000 0.00 0.00 0.00 3.60
3871 4136 6.183360 GGCTGTACTGAATCACAATCAAGTAC 60.183 42.308 3.61 0.00 34.99 2.73
4272 4547 7.226720 ACTTCACTGTGTAAGATGTAAAACCAG 59.773 37.037 19.63 0.00 0.00 4.00
4297 4572 6.446318 TGTGAAAACAAATAGCCATGAGAAC 58.554 36.000 0.00 0.00 0.00 3.01
4343 4618 9.223099 CTATACCAGCAATATGATCATGTTCAA 57.777 33.333 18.72 0.00 0.00 2.69
4573 4865 7.414873 CCCATCATATTTCTTCACTGAACACAG 60.415 40.741 0.00 0.00 37.63 3.66
4704 4996 8.466798 GTTCCAACATACAATAAATGTTAGCCT 58.533 33.333 1.46 0.00 43.84 4.58
4758 5050 4.379793 CACGCTCATTGTGTTCTTTTAAGC 59.620 41.667 0.00 0.00 37.28 3.09
4838 5130 2.885388 AGAGATCCATGTTCTCCCCT 57.115 50.000 15.63 0.31 40.43 4.79
5072 5364 1.062488 AGGTCCTTTGGCCACTCAGT 61.062 55.000 3.88 0.00 0.00 3.41
5073 5365 0.607489 CAGGTCCTTTGGCCACTCAG 60.607 60.000 3.88 1.04 0.00 3.35
5146 5438 4.713553 TCAGGACAGCAACTGATTTGTTA 58.286 39.130 0.78 0.00 38.71 2.41
5277 5896 4.630069 AGTTACTCGGCATTCACACATTAC 59.370 41.667 0.00 0.00 0.00 1.89
5408 6027 6.473397 AGAAGTGAATTAAGCTTGTCTTCG 57.527 37.500 9.86 0.00 36.30 3.79
5474 6093 0.304705 GCATATGGCGAACCTCAACG 59.695 55.000 4.56 0.00 36.63 4.10
5540 6317 3.052036 TCGTTGTTAGTTGTTACCGCTC 58.948 45.455 0.00 0.00 0.00 5.03
5543 6320 4.682860 AGACATCGTTGTTAGTTGTTACCG 59.317 41.667 0.00 0.00 35.79 4.02
5552 6329 5.633601 TGCTTAGTTGAGACATCGTTGTTAG 59.366 40.000 0.00 0.00 35.79 2.34
5582 6359 5.768164 GGACCTTCAGGATAGAAAAACAACA 59.232 40.000 0.00 0.00 38.94 3.33
5766 6543 2.016393 CTATTCCTGGCGCTCCGTCA 62.016 60.000 7.64 0.00 39.83 4.35
5767 6544 1.300233 CTATTCCTGGCGCTCCGTC 60.300 63.158 7.64 0.00 34.14 4.79
5768 6545 1.614241 AACTATTCCTGGCGCTCCGT 61.614 55.000 7.64 0.00 34.14 4.69
5769 6546 1.144057 AACTATTCCTGGCGCTCCG 59.856 57.895 7.64 0.00 34.14 4.63
5918 6695 2.708861 TCAAGTATCTGGTTGGTGGTGT 59.291 45.455 0.00 0.00 0.00 4.16
6190 6967 7.870445 CCAAATAGCTAGAAGCCTAAACTAGAG 59.130 40.741 0.00 0.00 43.77 2.43
6253 7164 4.386049 GTCACGTCACTCCTACATTTTCTG 59.614 45.833 0.00 0.00 0.00 3.02
6271 7182 8.655970 TGTCAATAGTTTGATAATTCAGTCACG 58.344 33.333 0.00 0.00 43.49 4.35
6335 7246 4.037208 CCACTGCCATGGAATAAAGATGAC 59.963 45.833 18.40 0.00 43.02 3.06
6402 7325 4.110482 GGCATACGTTGAGTAAGGTGTAG 58.890 47.826 0.00 0.00 39.04 2.74
6447 7370 4.501071 AGAAAGCTTAAACGCTATCGGAA 58.499 39.130 0.00 0.00 39.86 4.30
6460 7383 9.227777 GTATAGGTTGGAAGAAAAGAAAGCTTA 57.772 33.333 0.00 0.00 32.98 3.09
6497 7424 3.429492 TGTGAAATAGCAGCATTGGGAA 58.571 40.909 0.00 0.00 0.00 3.97
6633 8336 3.283259 ACCAAAGTAGGGCTGATAAGC 57.717 47.619 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.