Multiple sequence alignment - TraesCS1D01G123200

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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 TraesCS1D01G123200 chr1D 100.000 4293 0 0 1 4293 124559387 124563679 0.000000e+00 7928
1 TraesCS1D01G123200 chr1D 100.000 247 0 0 4743 4989 124564129 124564375 1.640000e-124 457
2 TraesCS1D01G123200 chr1D 93.117 247 17 0 4743 4989 19480936 19481182 3.670000e-96 363
3 TraesCS1D01G123200 chr1D 93.117 247 17 0 4743 4989 19491315 19491561 3.670000e-96 363
4 TraesCS1D01G123200 chr1A 96.183 4270 94 22 30 4275 137230990 137235214 0.000000e+00 6918
5 TraesCS1D01G123200 chr1B 94.965 2304 60 9 1990 4275 188791945 188794210 0.000000e+00 3561
6 TraesCS1D01G123200 chr1B 95.473 1988 63 9 11 1991 188789896 188791863 0.000000e+00 3147
7 TraesCS1D01G123200 chr2D 94.737 247 10 3 4743 4989 81454644 81454887 1.010000e-101 381
8 TraesCS1D01G123200 chr6B 93.522 247 16 0 4743 4989 168071036 168071282 7.890000e-98 368
9 TraesCS1D01G123200 chr2A 93.522 247 15 1 4743 4989 30069283 30069038 2.840000e-97 366
10 TraesCS1D01G123200 chr4A 93.117 247 17 0 4743 4989 541171240 541170994 3.670000e-96 363
11 TraesCS1D01G123200 chr3D 92.713 247 18 0 4743 4989 538576063 538575817 1.710000e-94 357
12 TraesCS1D01G123200 chr6D 92.713 247 15 3 4743 4989 168299517 168299274 2.210000e-93 353
13 TraesCS1D01G123200 chr7B 91.935 248 19 1 4743 4989 495040097 495039850 3.700000e-91 346


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 TraesCS1D01G123200 chr1D 124559387 124564375 4988 False 4192.5 7928 100.000 1 4989 2 chr1D.!!$F3 4988
1 TraesCS1D01G123200 chr1A 137230990 137235214 4224 False 6918.0 6918 96.183 30 4275 1 chr1A.!!$F1 4245
2 TraesCS1D01G123200 chr1B 188789896 188794210 4314 False 3354.0 3561 95.219 11 4275 2 chr1B.!!$F1 4264

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
991 1008 0.404040 TTGGCAAGGTAGGTCAAGGG 59.596 55.0 0.0 0.0 0.00 3.95 F
1789 1815 0.108186 GCATTAGGCAAGGCAAACCC 60.108 55.0 0.0 0.0 41.09 4.11 F
2745 2861 0.680061 GGAGAAGTTGACGGTGAGGT 59.320 55.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 2762 0.883833 CTTTGCTTGTTCCGCATCCT 59.116 50.000 0.0 0.0 37.22 3.24 R
3363 3480 1.881973 TCAATTGCTTGGCTGTCTGTC 59.118 47.619 0.0 0.0 32.95 3.51 R
4182 4308 1.708341 AGAAGCACAAACCAGCCAAT 58.292 45.000 0.0 0.0 0.00 3.16 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
22 23 2.036387 TGAAGACCTCACGTTTGGAGA 58.964 47.619 10.23 0.00 34.24 3.71
23 24 2.223971 TGAAGACCTCACGTTTGGAGAC 60.224 50.000 10.23 1.72 34.24 3.36
25 26 0.666577 GACCTCACGTTTGGAGACGG 60.667 60.000 10.23 0.10 46.77 4.79
27 28 1.300620 CTCACGTTTGGAGACGGCA 60.301 57.895 0.00 0.00 46.77 5.69
102 104 2.498078 ACCAACCGTTCCAACAAACAAT 59.502 40.909 0.00 0.00 0.00 2.71
114 116 4.418392 CAACAAACAATAGAGCATGCCTC 58.582 43.478 15.66 11.38 41.07 4.70
250 263 4.183858 CGGCCGCCCTCCCATTTA 62.184 66.667 14.67 0.00 0.00 1.40
251 264 2.518587 GGCCGCCCTCCCATTTAC 60.519 66.667 0.00 0.00 0.00 2.01
252 265 2.274104 GCCGCCCTCCCATTTACA 59.726 61.111 0.00 0.00 0.00 2.41
253 266 1.152756 GCCGCCCTCCCATTTACAT 60.153 57.895 0.00 0.00 0.00 2.29
550 564 6.266330 AGCTAATTTTGTTGGCTTCTTCTTCT 59.734 34.615 0.00 0.00 0.00 2.85
551 565 6.925718 GCTAATTTTGTTGGCTTCTTCTTCTT 59.074 34.615 0.00 0.00 0.00 2.52
552 566 7.115520 GCTAATTTTGTTGGCTTCTTCTTCTTC 59.884 37.037 0.00 0.00 0.00 2.87
566 580 3.231818 TCTTCTTCCTCCTCAGTCGTTT 58.768 45.455 0.00 0.00 0.00 3.60
794 808 1.154225 GCCGTGTTTCTTGATGCGG 60.154 57.895 0.00 0.00 41.79 5.69
917 933 2.111384 GATCCTAGGACACTTGAGCCA 58.889 52.381 15.42 0.00 0.00 4.75
991 1008 0.404040 TTGGCAAGGTAGGTCAAGGG 59.596 55.000 0.00 0.00 0.00 3.95
1311 1328 9.852091 GCAAGATTGAGAATTTTCTTGTCTATT 57.148 29.630 11.76 0.00 44.34 1.73
1323 1340 5.784750 TCTTGTCTATTGAGCAATCAACG 57.215 39.130 0.00 0.00 31.89 4.10
1789 1815 0.108186 GCATTAGGCAAGGCAAACCC 60.108 55.000 0.00 0.00 41.09 4.11
1832 1858 7.013750 TGGTAAAAACATAGTGTGATGCTTTCA 59.986 33.333 0.00 0.00 27.63 2.69
1835 1861 4.558226 ACATAGTGTGATGCTTTCAGGA 57.442 40.909 0.00 0.00 34.17 3.86
1957 1983 6.875948 TGTTTACTATGAACATGTTGCTGT 57.124 33.333 17.58 11.36 32.44 4.40
2024 2134 9.030452 TCCACAAATTAGTTATTGCCTGTATTT 57.970 29.630 0.00 0.00 0.00 1.40
2173 2283 3.198200 ACACAACCACTACCACTACAACA 59.802 43.478 0.00 0.00 0.00 3.33
2206 2316 2.122769 TCGGTGTCACTTCCCCCA 60.123 61.111 2.35 0.00 0.00 4.96
2577 2693 5.798434 GGTTACAAACACAGTTGTCTGAAAC 59.202 40.000 2.17 0.00 43.76 2.78
2646 2762 5.415701 AGCTGTTGAAAAAGAAGTTGAGACA 59.584 36.000 0.00 0.00 0.00 3.41
2745 2861 0.680061 GGAGAAGTTGACGGTGAGGT 59.320 55.000 0.00 0.00 0.00 3.85
3116 3233 3.625313 TCATTTGTTGCTCTGTCACGAAA 59.375 39.130 0.00 0.00 0.00 3.46
3121 3238 4.627058 TGTTGCTCTGTCACGAAATAAGA 58.373 39.130 0.00 0.00 0.00 2.10
3159 3276 4.681483 GCAGGTAAAAACATCAGAACAAGC 59.319 41.667 0.00 0.00 0.00 4.01
3190 3307 6.457799 GGTTGAAGCAAGAAAACGAGAAGTTA 60.458 38.462 0.00 0.00 43.37 2.24
3346 3463 2.304180 AGCACAGGATCTAAGCAACACT 59.696 45.455 0.00 0.00 0.00 3.55
3363 3480 2.025887 ACACTCTAAGCCCCAAATCTGG 60.026 50.000 0.00 0.00 43.10 3.86
3442 3559 7.890655 AGAAGTTTAAGCTCCATAGAATTTGGT 59.109 33.333 0.00 0.00 35.64 3.67
3592 3709 4.082949 CGGAAATTGGTACTGGGAAAAGAC 60.083 45.833 0.00 0.00 0.00 3.01
4005 4125 4.439968 AGCTAACTGATAAAACCCGTAGC 58.560 43.478 0.00 0.00 0.00 3.58
4006 4126 4.161754 AGCTAACTGATAAAACCCGTAGCT 59.838 41.667 0.00 0.00 33.00 3.32
4048 4174 6.762333 TGACCATCTGTCTGGATGTATATTG 58.238 40.000 6.12 0.00 44.75 1.90
4051 4177 8.262601 ACCATCTGTCTGGATGTATATTGTTA 57.737 34.615 6.12 0.00 40.85 2.41
4134 4260 8.453320 TCATTCTGTGTGAAATGTACAATCATC 58.547 33.333 15.30 12.46 38.29 2.92
4226 4365 6.827641 TCACTGTCGTTATTTGCAAAGTATC 58.172 36.000 18.19 7.11 0.00 2.24
4229 4368 7.478667 CACTGTCGTTATTTGCAAAGTATCTTC 59.521 37.037 18.19 6.10 0.00 2.87
4275 4414 6.385033 ACTCAAAGAAAATGTAGCATCAAGC 58.615 36.000 0.00 0.00 46.19 4.01
4284 4423 3.329093 GCATCAAGCTCCCCTCCT 58.671 61.111 0.00 0.00 41.15 3.69
4285 4424 1.148048 GCATCAAGCTCCCCTCCTC 59.852 63.158 0.00 0.00 41.15 3.71
4286 4425 1.344191 GCATCAAGCTCCCCTCCTCT 61.344 60.000 0.00 0.00 41.15 3.69
4287 4426 0.758123 CATCAAGCTCCCCTCCTCTC 59.242 60.000 0.00 0.00 0.00 3.20
4288 4427 0.399806 ATCAAGCTCCCCTCCTCTCC 60.400 60.000 0.00 0.00 0.00 3.71
4289 4428 1.002792 CAAGCTCCCCTCCTCTCCT 59.997 63.158 0.00 0.00 0.00 3.69
4290 4429 1.048160 CAAGCTCCCCTCCTCTCCTC 61.048 65.000 0.00 0.00 0.00 3.71
4291 4430 1.228215 AAGCTCCCCTCCTCTCCTCT 61.228 60.000 0.00 0.00 0.00 3.69
4292 4431 1.152546 GCTCCCCTCCTCTCCTCTC 60.153 68.421 0.00 0.00 0.00 3.20
4760 4899 4.899239 GCACCCAGATCCGCGGAG 62.899 72.222 33.87 21.34 0.00 4.63
4761 4900 4.227134 CACCCAGATCCGCGGAGG 62.227 72.222 33.87 29.04 42.97 4.30
4762 4901 4.779733 ACCCAGATCCGCGGAGGT 62.780 66.667 33.87 29.73 41.99 3.85
4763 4902 4.227134 CCCAGATCCGCGGAGGTG 62.227 72.222 33.87 29.12 41.99 4.00
4764 4903 4.899239 CCAGATCCGCGGAGGTGC 62.899 72.222 33.87 21.10 41.99 5.01
4826 4965 4.109675 GGCTATGGTGGTGCCGGT 62.110 66.667 1.90 0.00 41.21 5.28
4827 4966 2.824041 GCTATGGTGGTGCCGGTG 60.824 66.667 1.90 0.00 41.21 4.94
4828 4967 2.124736 CTATGGTGGTGCCGGTGG 60.125 66.667 1.90 0.00 41.21 4.61
4829 4968 3.697439 CTATGGTGGTGCCGGTGGG 62.697 68.421 1.90 0.00 41.21 4.61
4832 4971 4.360405 GGTGGTGCCGGTGGGAAT 62.360 66.667 1.90 0.00 34.06 3.01
4833 4972 2.750237 GTGGTGCCGGTGGGAATC 60.750 66.667 1.90 0.00 34.06 2.52
4834 4973 4.402528 TGGTGCCGGTGGGAATCG 62.403 66.667 1.90 0.00 34.06 3.34
4841 4980 3.873812 GGTGGGAATCGGCCGGAT 61.874 66.667 27.83 15.00 36.78 4.18
4842 4981 2.591715 GTGGGAATCGGCCGGATG 60.592 66.667 27.83 0.00 34.93 3.51
4843 4982 4.562425 TGGGAATCGGCCGGATGC 62.562 66.667 27.83 19.17 34.93 3.91
4844 4983 4.562425 GGGAATCGGCCGGATGCA 62.562 66.667 27.83 5.39 43.89 3.96
4845 4984 3.279875 GGAATCGGCCGGATGCAC 61.280 66.667 27.83 10.88 43.89 4.57
4846 4985 2.513666 GAATCGGCCGGATGCACA 60.514 61.111 27.83 3.54 43.89 4.57
4847 4986 2.514592 AATCGGCCGGATGCACAG 60.515 61.111 27.83 0.00 43.89 3.66
4848 4987 4.552365 ATCGGCCGGATGCACAGG 62.552 66.667 27.83 0.00 43.89 4.00
4913 5052 3.622826 CCCGTTGGTCCGACTGGT 61.623 66.667 10.90 0.00 36.30 4.00
4914 5053 2.424302 CCGTTGGTCCGACTGGTT 59.576 61.111 7.69 0.00 36.30 3.67
4915 5054 1.666872 CCGTTGGTCCGACTGGTTC 60.667 63.158 7.69 0.00 36.30 3.62
4916 5055 1.666872 CGTTGGTCCGACTGGTTCC 60.667 63.158 7.69 0.00 36.30 3.62
4917 5056 1.666872 GTTGGTCCGACTGGTTCCG 60.667 63.158 1.48 0.00 34.66 4.30
4918 5057 2.874664 TTGGTCCGACTGGTTCCGG 61.875 63.158 0.00 0.00 46.57 5.14
4919 5058 4.754667 GGTCCGACTGGTTCCGGC 62.755 72.222 0.00 0.00 44.96 6.13
4920 5059 3.692406 GTCCGACTGGTTCCGGCT 61.692 66.667 0.00 0.00 44.96 5.52
4921 5060 3.379445 TCCGACTGGTTCCGGCTC 61.379 66.667 0.00 0.00 44.96 4.70
4922 5061 4.796231 CCGACTGGTTCCGGCTCG 62.796 72.222 0.00 12.29 39.22 5.03
4923 5062 4.052229 CGACTGGTTCCGGCTCGT 62.052 66.667 0.00 0.00 0.00 4.18
4924 5063 2.126031 GACTGGTTCCGGCTCGTC 60.126 66.667 0.00 0.00 0.00 4.20
4925 5064 3.644399 GACTGGTTCCGGCTCGTCC 62.644 68.421 0.00 0.00 0.00 4.79
4926 5065 4.452733 CTGGTTCCGGCTCGTCCC 62.453 72.222 0.00 0.00 0.00 4.46
4933 5072 4.271816 CGGCTCGTCCCGGATCTG 62.272 72.222 0.73 0.00 44.46 2.90
4934 5073 3.917760 GGCTCGTCCCGGATCTGG 61.918 72.222 14.26 14.26 0.00 3.86
4935 5074 3.148279 GCTCGTCCCGGATCTGGT 61.148 66.667 19.51 0.00 0.00 4.00
4936 5075 2.808315 CTCGTCCCGGATCTGGTG 59.192 66.667 19.51 10.83 0.00 4.17
4937 5076 1.753078 CTCGTCCCGGATCTGGTGA 60.753 63.158 19.51 12.95 0.00 4.02
4938 5077 2.005960 CTCGTCCCGGATCTGGTGAC 62.006 65.000 22.75 22.75 0.00 3.67
4939 5078 2.052690 CGTCCCGGATCTGGTGACT 61.053 63.158 26.53 0.00 31.13 3.41
4940 5079 0.750546 CGTCCCGGATCTGGTGACTA 60.751 60.000 26.53 6.66 31.13 2.59
4941 5080 0.745468 GTCCCGGATCTGGTGACTAC 59.255 60.000 24.24 11.19 0.00 2.73
4950 5089 4.487412 GGTGACTACCGGACGGCG 62.487 72.222 9.46 4.80 37.19 6.46
4987 5126 3.578456 GGTGTGGCCAACGATCTG 58.422 61.111 7.24 0.00 37.17 2.90
4988 5127 2.040544 GGTGTGGCCAACGATCTGG 61.041 63.158 7.24 0.00 39.71 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.544267 CTCCAAACGTGAGGTCTTCAAC 59.456 50.000 6.45 0.00 37.61 3.18
1 2 2.432874 TCTCCAAACGTGAGGTCTTCAA 59.567 45.455 6.45 0.00 37.61 2.69
2 3 2.036387 TCTCCAAACGTGAGGTCTTCA 58.964 47.619 6.45 0.00 0.00 3.02
3 4 2.405172 GTCTCCAAACGTGAGGTCTTC 58.595 52.381 6.45 0.00 0.00 2.87
4 5 1.269621 CGTCTCCAAACGTGAGGTCTT 60.270 52.381 6.45 0.00 37.86 3.01
5 6 0.314302 CGTCTCCAAACGTGAGGTCT 59.686 55.000 6.45 0.00 37.86 3.85
6 7 0.666577 CCGTCTCCAAACGTGAGGTC 60.667 60.000 6.45 0.00 41.01 3.85
7 8 1.366366 CCGTCTCCAAACGTGAGGT 59.634 57.895 6.45 0.00 41.01 3.85
8 9 2.027625 GCCGTCTCCAAACGTGAGG 61.028 63.158 0.00 0.00 41.01 3.86
9 10 0.878523 TTGCCGTCTCCAAACGTGAG 60.879 55.000 0.00 0.00 41.01 3.51
14 15 0.586802 GTGACTTGCCGTCTCCAAAC 59.413 55.000 5.07 0.00 43.25 2.93
22 23 1.594293 CTCCAACGTGACTTGCCGT 60.594 57.895 0.00 0.00 39.32 5.68
23 24 0.670546 ATCTCCAACGTGACTTGCCG 60.671 55.000 0.00 0.00 0.00 5.69
25 26 1.512926 ACATCTCCAACGTGACTTGC 58.487 50.000 0.00 0.00 0.00 4.01
27 28 3.194005 ACAACATCTCCAACGTGACTT 57.806 42.857 0.00 0.00 0.00 3.01
114 116 4.081030 CTCGTGCTGCTGCCAACG 62.081 66.667 18.36 18.36 39.12 4.10
162 164 2.496470 GTGGTGGTCTCTTACGGATCTT 59.504 50.000 0.00 0.00 0.00 2.40
163 165 2.100989 GTGGTGGTCTCTTACGGATCT 58.899 52.381 0.00 0.00 0.00 2.75
164 166 1.202268 CGTGGTGGTCTCTTACGGATC 60.202 57.143 0.00 0.00 0.00 3.36
165 167 0.815734 CGTGGTGGTCTCTTACGGAT 59.184 55.000 0.00 0.00 0.00 4.18
166 168 1.870055 GCGTGGTGGTCTCTTACGGA 61.870 60.000 0.00 0.00 35.49 4.69
167 169 1.445582 GCGTGGTGGTCTCTTACGG 60.446 63.158 0.00 0.00 35.49 4.02
168 170 0.456312 GAGCGTGGTGGTCTCTTACG 60.456 60.000 0.00 0.00 41.93 3.18
169 171 0.108756 GGAGCGTGGTGGTCTCTTAC 60.109 60.000 0.00 0.00 44.62 2.34
170 172 0.541063 TGGAGCGTGGTGGTCTCTTA 60.541 55.000 0.00 0.00 44.62 2.10
240 253 7.920682 GCACTAATTGTAAATGTAAATGGGAGG 59.079 37.037 0.00 0.00 0.00 4.30
249 262 7.208225 TGCTTGTGCACTAATTGTAAATGTA 57.792 32.000 19.41 0.00 45.31 2.29
250 263 6.083098 TGCTTGTGCACTAATTGTAAATGT 57.917 33.333 19.41 0.00 45.31 2.71
313 326 1.066605 TCGCCAATTCCTCGCTAGTAC 59.933 52.381 0.00 0.00 0.00 2.73
318 331 1.133025 CAAATTCGCCAATTCCTCGCT 59.867 47.619 0.00 0.00 30.37 4.93
320 333 1.548986 GCAAATTCGCCAATTCCTCG 58.451 50.000 0.00 0.00 30.37 4.63
323 336 2.119457 GATCGCAAATTCGCCAATTCC 58.881 47.619 0.00 0.00 30.37 3.01
550 564 0.038526 GCGAAACGACTGAGGAGGAA 60.039 55.000 0.00 0.00 0.00 3.36
551 565 0.894184 AGCGAAACGACTGAGGAGGA 60.894 55.000 0.00 0.00 0.00 3.71
552 566 0.038159 AAGCGAAACGACTGAGGAGG 60.038 55.000 0.00 0.00 0.00 4.30
650 664 1.518774 GATTCGCCCTCCGGTAACA 59.481 57.895 0.00 0.00 37.59 2.41
688 702 1.228429 GTGTAGCCAAACCCAGCCA 60.228 57.895 0.00 0.00 0.00 4.75
794 808 1.269778 GGGGCTGAAACTTGCAGAAAC 60.270 52.381 0.29 0.00 35.39 2.78
1243 1260 5.103982 TGAGGCATAATCAATCTTGGAAGGA 60.104 40.000 0.00 0.00 0.00 3.36
1245 1262 5.826737 ACTGAGGCATAATCAATCTTGGAAG 59.173 40.000 0.00 0.00 0.00 3.46
1249 1266 8.162878 ACATAACTGAGGCATAATCAATCTTG 57.837 34.615 0.00 0.00 0.00 3.02
1311 1328 1.432514 GAGCTGTCGTTGATTGCTCA 58.567 50.000 14.60 0.00 46.41 4.26
1323 1340 2.399916 AATGAAGAGGCAGAGCTGTC 57.600 50.000 0.00 0.00 34.93 3.51
1789 1815 1.815421 CATCTTCCAACGAGCCCGG 60.815 63.158 0.00 0.00 40.78 5.73
1832 1858 9.700831 ATTAAAAAGAATGTGTAGCCTAATCCT 57.299 29.630 0.00 0.00 0.00 3.24
1957 1983 2.559668 ACGGTCGTGGAAGATGAACTAA 59.440 45.455 0.00 0.00 0.00 2.24
2173 2283 2.515901 GAGGCAGTGGTGGTGGTT 59.484 61.111 0.00 0.00 0.00 3.67
2206 2316 5.722263 TCATCATCAATGTTTCGGCATTTT 58.278 33.333 0.00 0.00 37.00 1.82
2360 2476 5.444663 ACCAAATCTCTGAGCTTGAAAAC 57.555 39.130 16.31 0.00 0.00 2.43
2577 2693 3.756117 AGCTGGGAAGTTAACTTTGAGG 58.244 45.455 21.40 13.18 36.11 3.86
2646 2762 0.883833 CTTTGCTTGTTCCGCATCCT 59.116 50.000 0.00 0.00 37.22 3.24
2745 2861 8.043710 CCTCTAGCCTCTTTAATTTCTTCTCAA 58.956 37.037 0.00 0.00 0.00 3.02
3159 3276 4.301628 GTTTTCTTGCTTCAACCCATCAG 58.698 43.478 0.00 0.00 0.00 2.90
3190 3307 4.498009 CGCAGTTGTTCAACCTCTTTTGAT 60.498 41.667 11.38 0.00 35.42 2.57
3346 3463 2.239654 CTGTCCAGATTTGGGGCTTAGA 59.760 50.000 1.81 0.00 45.10 2.10
3363 3480 1.881973 TCAATTGCTTGGCTGTCTGTC 59.118 47.619 0.00 0.00 32.95 3.51
3442 3559 3.306088 CCCTTGAAGAAGCGTACTCTGAA 60.306 47.826 0.00 0.00 0.00 3.02
3998 4118 2.032620 ACATGACTCCTAAGCTACGGG 58.967 52.381 0.00 0.00 0.00 5.28
3999 4119 2.688446 TCACATGACTCCTAAGCTACGG 59.312 50.000 0.00 0.00 0.00 4.02
4001 4121 4.054671 GCATCACATGACTCCTAAGCTAC 58.945 47.826 0.00 0.00 0.00 3.58
4002 4122 3.963374 AGCATCACATGACTCCTAAGCTA 59.037 43.478 0.00 0.00 0.00 3.32
4003 4123 2.770802 AGCATCACATGACTCCTAAGCT 59.229 45.455 0.00 0.00 0.00 3.74
4004 4124 2.871022 CAGCATCACATGACTCCTAAGC 59.129 50.000 0.00 0.00 0.00 3.09
4005 4125 4.118410 GTCAGCATCACATGACTCCTAAG 58.882 47.826 0.00 0.00 42.06 2.18
4006 4126 3.118629 GGTCAGCATCACATGACTCCTAA 60.119 47.826 0.00 0.00 44.23 2.69
4048 4174 4.080863 ACTTCACCATCAGGATCTGGTAAC 60.081 45.833 4.18 0.00 43.91 2.50
4051 4177 2.238144 CACTTCACCATCAGGATCTGGT 59.762 50.000 0.00 0.00 46.68 4.00
4152 4278 8.690203 TGTCAAAGATTGAGATTAAAGGTCAA 57.310 30.769 0.00 1.35 41.01 3.18
4175 4301 3.731089 CACAAACCAGCCAATTGAATGT 58.269 40.909 7.12 0.00 0.00 2.71
4182 4308 1.708341 AGAAGCACAAACCAGCCAAT 58.292 45.000 0.00 0.00 0.00 3.16
4229 4368 9.796120 TGAGTTAATAAAAATGCCCTTTTATCG 57.204 29.630 11.29 0.00 39.46 2.92
4743 4882 4.899239 CTCCGCGGATCTGGGTGC 62.899 72.222 31.19 1.80 0.00 5.01
4744 4883 4.227134 CCTCCGCGGATCTGGGTG 62.227 72.222 31.19 15.13 33.16 4.61
4745 4884 4.779733 ACCTCCGCGGATCTGGGT 62.780 66.667 31.19 28.38 36.31 4.51
4746 4885 4.227134 CACCTCCGCGGATCTGGG 62.227 72.222 31.19 27.65 36.31 4.45
4747 4886 4.899239 GCACCTCCGCGGATCTGG 62.899 72.222 31.19 28.04 36.31 3.86
4809 4948 4.109675 ACCGGCACCACCATAGCC 62.110 66.667 0.00 0.00 44.89 3.93
4810 4949 2.824041 CACCGGCACCACCATAGC 60.824 66.667 0.00 0.00 39.03 2.97
4811 4950 2.124736 CCACCGGCACCACCATAG 60.125 66.667 0.00 0.00 39.03 2.23
4812 4951 3.722813 CCCACCGGCACCACCATA 61.723 66.667 0.00 0.00 39.03 2.74
4815 4954 4.360405 ATTCCCACCGGCACCACC 62.360 66.667 0.00 0.00 0.00 4.61
4816 4955 2.750237 GATTCCCACCGGCACCAC 60.750 66.667 0.00 0.00 0.00 4.16
4817 4956 4.402528 CGATTCCCACCGGCACCA 62.403 66.667 0.00 0.00 0.00 4.17
4824 4963 3.873812 ATCCGGCCGATTCCCACC 61.874 66.667 30.73 0.00 0.00 4.61
4825 4964 2.591715 CATCCGGCCGATTCCCAC 60.592 66.667 30.73 0.00 0.00 4.61
4826 4965 4.562425 GCATCCGGCCGATTCCCA 62.562 66.667 30.73 2.70 36.11 4.37
4827 4966 4.562425 TGCATCCGGCCGATTCCC 62.562 66.667 30.73 11.28 43.89 3.97
4828 4967 3.279875 GTGCATCCGGCCGATTCC 61.280 66.667 30.73 12.84 43.89 3.01
4829 4968 2.513666 TGTGCATCCGGCCGATTC 60.514 61.111 30.73 13.23 43.89 2.52
4830 4969 2.514592 CTGTGCATCCGGCCGATT 60.515 61.111 30.73 10.89 43.89 3.34
4831 4970 4.552365 CCTGTGCATCCGGCCGAT 62.552 66.667 30.73 15.71 43.89 4.18
4896 5035 3.173167 AACCAGTCGGACCAACGGG 62.173 63.158 4.14 0.00 37.89 5.28
4897 5036 1.666872 GAACCAGTCGGACCAACGG 60.667 63.158 4.14 3.40 35.59 4.44
4898 5037 1.666872 GGAACCAGTCGGACCAACG 60.667 63.158 4.14 0.00 35.59 4.10
4899 5038 1.666872 CGGAACCAGTCGGACCAAC 60.667 63.158 4.14 0.00 33.90 3.77
4900 5039 2.738480 CGGAACCAGTCGGACCAA 59.262 61.111 4.14 0.00 33.90 3.67
4906 5045 3.966026 GACGAGCCGGAACCAGTCG 62.966 68.421 5.05 5.40 36.71 4.18
4907 5046 2.126031 GACGAGCCGGAACCAGTC 60.126 66.667 5.05 2.65 0.00 3.51
4908 5047 3.692406 GGACGAGCCGGAACCAGT 61.692 66.667 5.05 0.00 0.00 4.00
4909 5048 4.452733 GGGACGAGCCGGAACCAG 62.453 72.222 5.05 0.00 37.63 4.00
4922 5061 0.745468 GTAGTCACCAGATCCGGGAC 59.255 60.000 0.00 6.37 0.00 4.46
4923 5062 0.396695 GGTAGTCACCAGATCCGGGA 60.397 60.000 0.00 0.00 45.04 5.14
4924 5063 1.735376 CGGTAGTCACCAGATCCGGG 61.735 65.000 0.00 0.00 46.14 5.73
4925 5064 1.734137 CGGTAGTCACCAGATCCGG 59.266 63.158 0.00 0.00 46.14 5.14
4926 5065 0.750546 TCCGGTAGTCACCAGATCCG 60.751 60.000 0.00 0.00 46.14 4.18
4927 5066 0.745468 GTCCGGTAGTCACCAGATCC 59.255 60.000 0.00 0.00 46.14 3.36
4928 5067 0.381089 CGTCCGGTAGTCACCAGATC 59.619 60.000 0.00 0.00 46.14 2.75
4929 5068 1.035932 CCGTCCGGTAGTCACCAGAT 61.036 60.000 0.00 0.00 46.14 2.90
4930 5069 1.676635 CCGTCCGGTAGTCACCAGA 60.677 63.158 0.00 0.00 46.14 3.86
4931 5070 2.882876 CCGTCCGGTAGTCACCAG 59.117 66.667 0.00 0.00 46.14 4.00
4932 5071 3.376078 GCCGTCCGGTAGTCACCA 61.376 66.667 7.66 0.00 46.14 4.17
4933 5072 4.487412 CGCCGTCCGGTAGTCACC 62.487 72.222 7.66 0.00 41.93 4.02
4967 5106 4.715523 ATCGTTGGCCACACCGGG 62.716 66.667 3.88 0.00 43.94 5.73
4968 5107 3.124921 GATCGTTGGCCACACCGG 61.125 66.667 3.88 0.00 43.94 5.28
4969 5108 2.047274 AGATCGTTGGCCACACCG 60.047 61.111 3.88 8.85 43.94 4.94
4970 5109 2.040544 CCAGATCGTTGGCCACACC 61.041 63.158 3.88 0.00 39.84 4.16
4971 5110 3.578456 CCAGATCGTTGGCCACAC 58.422 61.111 3.88 6.45 0.00 3.82


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

AutoCloner maintained by Alex Coulton.