Multiple sequence alignment - TraesCS5A01G022900

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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 TraesCS5A01G022900 chr5A 100.000 4214 0 0 1 4214 18668662 18672875 0.000000e+00 7782.0
1 TraesCS5A01G022900 chr5D 93.404 4275 166 51 1 4214 27007793 27012012 0.000000e+00 6226.0
2 TraesCS5A01G022900 chr5D 91.379 58 4 1 4107 4164 443636601 443636545 1.260000e-10 78.7
3 TraesCS5A01G022900 chr5B 93.805 3164 140 21 404 3517 19548705 19551862 0.000000e+00 4706.0
4 TraesCS5A01G022900 chr5B 87.562 402 27 11 1 385 19548361 19548756 1.080000e-120 444.0
5 TraesCS5A01G022900 chr7B 91.031 223 16 4 3215 3433 595536901 595537123 8.860000e-77 298.0
6 TraesCS5A01G022900 chr7B 86.634 202 26 1 2968 3168 595536703 595536904 5.480000e-54 222.0
7 TraesCS5A01G022900 chr7B 95.918 49 2 0 4107 4155 434839255 434839303 3.490000e-11 80.5
8 TraesCS5A01G022900 chr2D 97.143 175 5 0 3242 3416 382456326 382456500 3.190000e-76 296.0
9 TraesCS5A01G022900 chr2D 91.379 58 4 1 4107 4164 619562343 619562399 1.260000e-10 78.7
10 TraesCS5A01G022900 chr2A 94.643 56 3 0 4105 4160 559118408 559118463 2.090000e-13 87.9
11 TraesCS5A01G022900 chr2A 91.228 57 5 0 4104 4160 170470388 170470444 1.260000e-10 78.7
12 TraesCS5A01G022900 chr2B 92.982 57 4 0 4104 4160 216462805 216462861 2.700000e-12 84.2
13 TraesCS5A01G022900 chr1B 91.379 58 4 1 4107 4164 508392351 508392295 1.260000e-10 78.7
14 TraesCS5A01G022900 chr1A 94.118 51 3 0 4107 4157 106228075 106228125 1.260000e-10 78.7


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 TraesCS5A01G022900 chr5A 18668662 18672875 4213 False 7782 7782 100.0000 1 4214 1 chr5A.!!$F1 4213
1 TraesCS5A01G022900 chr5D 27007793 27012012 4219 False 6226 6226 93.4040 1 4214 1 chr5D.!!$F1 4213
2 TraesCS5A01G022900 chr5B 19548361 19551862 3501 False 2575 4706 90.6835 1 3517 2 chr5B.!!$F1 3516

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
398 415 0.390735 GGATTTGCTTTGCTGGGCAG 60.391 55.0 0.00 0.0 40.61 4.85 F
826 860 0.695924 TGGTAGAATGTGGGTGGTGG 59.304 55.0 0.00 0.0 0.00 4.61 F
1553 1588 1.290134 AAAGTCTCAGGGGCCTTAGG 58.710 55.0 0.84 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2317 1.073444 ACATAGGGCATGGATCAGCAG 59.927 52.381 0.0 0.0 39.13 4.24 R
2647 2705 2.887152 AGGCTTCTGCAATTTCGTTCTT 59.113 40.909 0.0 0.0 41.91 2.52 R
3395 3462 0.670546 TGTGCTACGCTTCAGCTTCC 60.671 55.000 0.0 0.0 39.83 3.46 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
130 131 1.000233 TAGTTTCCGCCGGTAGGGA 60.000 57.895 16.32 11.78 38.47 4.20
133 134 1.382146 TTTCCGCCGGTAGGGATCT 60.382 57.895 16.32 0.00 38.47 2.75
134 135 1.397390 TTTCCGCCGGTAGGGATCTC 61.397 60.000 16.32 0.00 38.47 2.75
155 172 2.395619 CCCGTAATCCCCTAGTCAACT 58.604 52.381 0.00 0.00 0.00 3.16
156 173 2.102588 CCCGTAATCCCCTAGTCAACTG 59.897 54.545 0.00 0.00 0.00 3.16
157 174 2.764572 CCGTAATCCCCTAGTCAACTGT 59.235 50.000 0.00 0.00 0.00 3.55
166 183 0.883153 TAGTCAACTGTTAGCGCGGA 59.117 50.000 8.83 0.00 0.00 5.54
207 224 0.670546 AGATTTGGTCGCTCCGTGTG 60.671 55.000 0.00 0.00 39.52 3.82
218 235 5.151389 GTCGCTCCGTGTGATTAAAATTTT 58.849 37.500 8.75 8.75 37.53 1.82
236 253 1.117142 TTCCCCTGTTCTCGAACCGT 61.117 55.000 7.28 0.00 40.46 4.83
241 258 0.859232 CTGTTCTCGAACCGTTGGTG 59.141 55.000 7.28 0.00 40.46 4.17
280 297 3.628487 CCGGTGGAGAGTAGTAAGAAGAG 59.372 52.174 0.00 0.00 0.00 2.85
286 303 3.688235 AGAGTAGTAAGAAGAGCACGGT 58.312 45.455 0.00 0.00 0.00 4.83
287 304 3.690628 AGAGTAGTAAGAAGAGCACGGTC 59.309 47.826 0.00 0.00 0.00 4.79
392 409 1.660242 AATGGGGGATTTGCTTTGCT 58.340 45.000 0.00 0.00 0.00 3.91
393 410 0.906775 ATGGGGGATTTGCTTTGCTG 59.093 50.000 0.00 0.00 0.00 4.41
394 411 1.193462 TGGGGGATTTGCTTTGCTGG 61.193 55.000 0.00 0.00 0.00 4.85
395 412 1.598517 GGGGATTTGCTTTGCTGGG 59.401 57.895 0.00 0.00 0.00 4.45
396 413 1.078918 GGGATTTGCTTTGCTGGGC 60.079 57.895 0.00 0.00 0.00 5.36
397 414 1.672898 GGATTTGCTTTGCTGGGCA 59.327 52.632 0.00 0.00 36.47 5.36
398 415 0.390735 GGATTTGCTTTGCTGGGCAG 60.391 55.000 0.00 0.00 40.61 4.85
414 431 1.606224 GGCAGCATGTTCAAAACTGGG 60.606 52.381 0.00 0.00 39.31 4.45
437 454 6.126449 GGGGATTCTCTATTTTGGGAAGTACT 60.126 42.308 0.00 0.00 0.00 2.73
451 468 7.549147 TGGGAAGTACTGTACTAACAAATCT 57.451 36.000 19.97 2.75 38.26 2.40
453 470 7.015877 TGGGAAGTACTGTACTAACAAATCTGT 59.984 37.037 19.97 1.32 38.26 3.41
500 522 2.571653 AGGGTATCAGTAGTTGCTGCAA 59.428 45.455 11.69 11.69 36.49 4.08
543 565 1.202580 AGCACTCACACAGGTGTTCTC 60.203 52.381 1.58 0.00 45.45 2.87
552 574 5.066375 TCACACAGGTGTTCTCTGAATTTTG 59.934 40.000 1.58 0.00 45.45 2.44
613 641 6.735556 TGTATAGGATGCCTCTCATGATCTA 58.264 40.000 0.00 0.00 35.05 1.98
614 642 6.605194 TGTATAGGATGCCTCTCATGATCTAC 59.395 42.308 0.00 0.00 35.05 2.59
662 690 9.701098 TGTTTAGAAATAAAAGAGAGCGTCTTA 57.299 29.630 4.96 0.00 45.44 2.10
687 715 4.804139 CGGTTTATCGCTCTACATTTCTGT 59.196 41.667 0.00 0.00 39.49 3.41
706 734 4.021807 TCTGTGCTACGTCAGGAACATTTA 60.022 41.667 0.00 0.00 33.13 1.40
747 781 5.185249 CCTGTCTTCAGCTTGGTAGTTAGTA 59.815 44.000 0.00 0.00 40.09 1.82
751 785 6.008331 TCTTCAGCTTGGTAGTTAGTAGTGA 58.992 40.000 0.00 0.00 0.00 3.41
792 826 2.358898 GGAGTTTGTGCTCTCTTTTGCA 59.641 45.455 0.00 0.00 35.89 4.08
826 860 0.695924 TGGTAGAATGTGGGTGGTGG 59.304 55.000 0.00 0.00 0.00 4.61
882 917 6.150976 TGCTGTATTTGGTACTTTCAGATTGG 59.849 38.462 0.00 0.00 34.27 3.16
906 941 3.350833 AGACCATCCTTTGTTGATCAGC 58.649 45.455 2.05 2.05 0.00 4.26
938 973 5.609533 TTACCTACTTCCATAACTGGCTC 57.390 43.478 0.00 0.00 42.80 4.70
939 974 3.725634 ACCTACTTCCATAACTGGCTCT 58.274 45.455 0.00 0.00 42.80 4.09
940 975 3.452627 ACCTACTTCCATAACTGGCTCTG 59.547 47.826 0.00 0.00 42.80 3.35
942 977 2.269940 ACTTCCATAACTGGCTCTGGT 58.730 47.619 0.00 0.00 42.80 4.00
1125 1160 4.124851 AGAACTCAACTCGAACACACTT 57.875 40.909 0.00 0.00 0.00 3.16
1303 1338 2.345760 GCCACAGGGTCCTTGCATG 61.346 63.158 0.00 0.00 36.17 4.06
1553 1588 1.290134 AAAGTCTCAGGGGCCTTAGG 58.710 55.000 0.84 0.00 0.00 2.69
1605 1640 3.878778 AGGCTTAGTGGTTGCTCTATTG 58.121 45.455 0.00 0.00 0.00 1.90
1623 1658 3.980646 TTGGAACAGAATTGGTTGACG 57.019 42.857 0.00 0.00 42.39 4.35
1752 1787 5.005740 CACTCCATCATGAAGACTTTGGAA 58.994 41.667 13.16 0.72 33.15 3.53
1899 1934 1.625315 CAGGAAGAGTGTGGACATGGA 59.375 52.381 0.00 0.00 0.00 3.41
1924 1959 8.744568 AAAAAGAATTAGTCCATTGGCAAAAA 57.255 26.923 3.01 0.00 0.00 1.94
1986 2021 3.836365 TCTGTTATGGATGATGCGGAA 57.164 42.857 0.00 0.00 0.00 4.30
1993 2028 6.770303 TGTTATGGATGATGCGGAAATAAGAA 59.230 34.615 0.00 0.00 0.00 2.52
2019 2054 5.185454 TGCGGTTCAAATGAATCTCTGTAT 58.815 37.500 5.00 0.00 36.33 2.29
2064 2099 3.539604 GTTCAGAGACCATGATTCCCAG 58.460 50.000 0.00 0.00 0.00 4.45
2251 2286 3.769300 TGCTGGTCTGCTAGATAAGTCAA 59.231 43.478 0.00 0.00 0.00 3.18
2282 2317 7.275920 AGGTATTCAGATGTATCAACAAGGAC 58.724 38.462 0.00 0.00 39.58 3.85
2379 2414 7.649533 ATTGATTGATGACTTGATTGCCTTA 57.350 32.000 0.00 0.00 0.00 2.69
2562 2597 5.050091 GCAAAACAGATATCCTCCACGTATG 60.050 44.000 0.00 0.00 0.00 2.39
3013 3073 0.623723 ACCACCAACCAACAGTGAGT 59.376 50.000 0.00 0.00 33.21 3.41
3044 3104 2.105128 AGGCGAATCTCGAAGCGG 59.895 61.111 0.00 0.00 43.74 5.52
3063 3123 2.223688 CGGAGAATGTCGAGCTGAGAAT 60.224 50.000 0.00 0.00 0.00 2.40
3075 3135 4.439837 CGAGCTGAGAATGAGAAGATGACA 60.440 45.833 0.00 0.00 0.00 3.58
3129 3189 4.506095 GGCACCCTACTTTTTCTCCTTGTA 60.506 45.833 0.00 0.00 0.00 2.41
3136 3196 5.948992 ACTTTTTCTCCTTGTATGTGCTC 57.051 39.130 0.00 0.00 0.00 4.26
3151 3211 3.697166 TGTGCTCTAGTGATACTGGTCA 58.303 45.455 0.00 0.00 0.00 4.02
3276 3336 1.164411 TGGCTTTGGTGTAGATTGCG 58.836 50.000 0.00 0.00 0.00 4.85
3294 3354 3.404899 TGCGAGTTAAAGTGGGGTAAAG 58.595 45.455 0.00 0.00 0.00 1.85
3310 3370 4.643334 GGGTAAAGGTTGAGAAGTTGTGTT 59.357 41.667 0.00 0.00 0.00 3.32
3395 3462 5.241506 ACCATGATAGTTTTGTGTTCAGTGG 59.758 40.000 0.00 0.00 0.00 4.00
3440 3511 2.562298 TCCTTGCTGCATTTCCGAATTT 59.438 40.909 1.84 0.00 0.00 1.82
3541 3614 3.374058 GGTCTTGATGGTATTGTTCACCG 59.626 47.826 0.00 0.00 39.04 4.94
3555 3628 9.950680 GTATTGTTCACCGAATTTCATTATCAT 57.049 29.630 0.00 0.00 0.00 2.45
3599 3672 5.017294 AGTAGAAGCTAGATTGACAAGGC 57.983 43.478 0.00 0.00 0.00 4.35
3603 3676 5.994250 AGAAGCTAGATTGACAAGGCAATA 58.006 37.500 0.00 0.00 38.53 1.90
3605 3678 4.455606 AGCTAGATTGACAAGGCAATACC 58.544 43.478 0.22 0.00 38.53 2.73
3622 3695 5.704888 CAATACCAATGTTTCCGCAAACTA 58.295 37.500 3.22 0.00 42.29 2.24
3642 3715 6.044512 ACTAGTTTTGTTACAACTGCTTCG 57.955 37.500 0.00 0.00 35.95 3.79
3683 3756 7.432252 CCAAACTTCTCACTGTTTTGTTCATAC 59.568 37.037 0.00 0.00 34.60 2.39
3686 3759 6.483640 ACTTCTCACTGTTTTGTTCATACTCC 59.516 38.462 0.00 0.00 0.00 3.85
3722 3798 2.995283 TGTTGCTCCATGAATGAGAGG 58.005 47.619 0.00 0.00 0.00 3.69
3727 3803 5.224821 TGCTCCATGAATGAGAGGATAAG 57.775 43.478 0.00 0.00 0.00 1.73
3757 3833 2.865079 TCTGTGCGGTTATTTTTCCCA 58.135 42.857 0.00 0.00 0.00 4.37
3758 3834 2.817258 TCTGTGCGGTTATTTTTCCCAG 59.183 45.455 0.00 0.00 0.00 4.45
3762 3838 4.023021 TGTGCGGTTATTTTTCCCAGTAAC 60.023 41.667 0.00 0.00 0.00 2.50
3765 3841 4.436451 GCGGTTATTTTTCCCAGTAACTCG 60.436 45.833 0.00 0.00 0.00 4.18
3769 3845 6.875726 GGTTATTTTTCCCAGTAACTCGTAGT 59.124 38.462 0.00 0.00 0.00 2.73
3779 3855 4.124238 AGTAACTCGTAGTTGCTGCAAAA 58.876 39.130 17.80 5.59 46.82 2.44
3806 3882 7.831690 AGGTTCATAAAACCACCATTTTTGTTT 59.168 29.630 9.45 0.00 42.69 2.83
3811 3887 4.559862 AACCACCATTTTTGTTTCACCA 57.440 36.364 0.00 0.00 0.00 4.17
3818 3894 6.423604 CACCATTTTTGTTTCACCAGTAATCC 59.576 38.462 0.00 0.00 0.00 3.01
3821 3897 8.310382 CCATTTTTGTTTCACCAGTAATCCATA 58.690 33.333 0.00 0.00 0.00 2.74
3825 3901 7.389803 TTGTTTCACCAGTAATCCATATGTG 57.610 36.000 1.24 0.00 0.00 3.21
3826 3902 6.480763 TGTTTCACCAGTAATCCATATGTGT 58.519 36.000 1.24 0.00 0.00 3.72
3827 3903 7.625469 TGTTTCACCAGTAATCCATATGTGTA 58.375 34.615 1.24 0.00 0.00 2.90
3828 3904 7.551262 TGTTTCACCAGTAATCCATATGTGTAC 59.449 37.037 1.24 1.31 0.00 2.90
3829 3905 6.800072 TCACCAGTAATCCATATGTGTACA 57.200 37.500 1.24 0.00 0.00 2.90
3830 3906 7.373617 TCACCAGTAATCCATATGTGTACAT 57.626 36.000 0.00 2.75 40.22 2.29
3985 4061 0.396060 AAGCTGCTAGCCCATAGAGC 59.604 55.000 13.29 13.20 43.77 4.09
4031 4107 4.046286 TCCAAGTTGGGTAGATGCATTT 57.954 40.909 21.85 0.00 38.32 2.32
4059 4135 1.203523 TCAGTGGTTTTGTTGCACACC 59.796 47.619 0.00 0.00 32.71 4.16
4072 4148 5.108517 TGTTGCACACCATTCTTTCTTTTC 58.891 37.500 0.00 0.00 0.00 2.29
4073 4149 5.105392 TGTTGCACACCATTCTTTCTTTTCT 60.105 36.000 0.00 0.00 0.00 2.52
4074 4150 5.596836 TGCACACCATTCTTTCTTTTCTT 57.403 34.783 0.00 0.00 0.00 2.52
4075 4151 5.976458 TGCACACCATTCTTTCTTTTCTTT 58.024 33.333 0.00 0.00 0.00 2.52
4076 4152 6.405538 TGCACACCATTCTTTCTTTTCTTTT 58.594 32.000 0.00 0.00 0.00 2.27
4077 4153 6.534793 TGCACACCATTCTTTCTTTTCTTTTC 59.465 34.615 0.00 0.00 0.00 2.29
4078 4154 6.758416 GCACACCATTCTTTCTTTTCTTTTCT 59.242 34.615 0.00 0.00 0.00 2.52
4079 4155 7.278646 GCACACCATTCTTTCTTTTCTTTTCTT 59.721 33.333 0.00 0.00 0.00 2.52
4080 4156 9.154847 CACACCATTCTTTCTTTTCTTTTCTTT 57.845 29.630 0.00 0.00 0.00 2.52
4081 4157 9.725019 ACACCATTCTTTCTTTTCTTTTCTTTT 57.275 25.926 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 4.091075 GGAAACTAGGTTCGAAATCACGTC 59.909 45.833 14.28 0.00 34.70 4.34
97 98 3.992427 GGAAACTAGGTTCGAAATCACGT 59.008 43.478 14.28 0.00 34.70 4.49
130 131 1.793902 ACTAGGGGATTACGGGGAGAT 59.206 52.381 0.00 0.00 0.00 2.75
133 134 0.935942 TGACTAGGGGATTACGGGGA 59.064 55.000 0.00 0.00 0.00 4.81
134 135 1.415289 GTTGACTAGGGGATTACGGGG 59.585 57.143 0.00 0.00 0.00 5.73
136 137 2.764572 ACAGTTGACTAGGGGATTACGG 59.235 50.000 0.00 0.00 0.00 4.02
138 139 5.358090 GCTAACAGTTGACTAGGGGATTAC 58.642 45.833 0.00 0.00 0.00 1.89
139 140 4.098960 CGCTAACAGTTGACTAGGGGATTA 59.901 45.833 0.00 0.00 0.00 1.75
140 141 3.118738 CGCTAACAGTTGACTAGGGGATT 60.119 47.826 0.00 0.00 0.00 3.01
141 142 2.431057 CGCTAACAGTTGACTAGGGGAT 59.569 50.000 0.00 0.00 0.00 3.85
142 143 1.822990 CGCTAACAGTTGACTAGGGGA 59.177 52.381 0.00 0.00 0.00 4.81
143 144 1.739371 GCGCTAACAGTTGACTAGGGG 60.739 57.143 0.00 0.00 0.00 4.79
144 145 1.641577 GCGCTAACAGTTGACTAGGG 58.358 55.000 0.00 0.00 0.00 3.53
145 146 1.269166 CGCGCTAACAGTTGACTAGG 58.731 55.000 5.56 0.00 0.00 3.02
166 183 1.190643 CCCCCAAAACATACCGCAAT 58.809 50.000 0.00 0.00 0.00 3.56
207 224 7.153217 TCGAGAACAGGGGAAAATTTTAATC 57.847 36.000 2.75 0.00 0.00 1.75
218 235 1.117142 AACGGTTCGAGAACAGGGGA 61.117 55.000 17.56 0.00 42.85 4.81
286 303 2.372172 GGAGGTCTTGGGTCAAAAGAGA 59.628 50.000 0.00 0.00 34.40 3.10
287 304 2.784347 GGAGGTCTTGGGTCAAAAGAG 58.216 52.381 0.00 0.00 34.40 2.85
392 409 1.068895 CAGTTTTGAACATGCTGCCCA 59.931 47.619 0.00 0.00 0.00 5.36
393 410 1.606224 CCAGTTTTGAACATGCTGCCC 60.606 52.381 0.00 0.00 0.00 5.36
394 411 1.606224 CCCAGTTTTGAACATGCTGCC 60.606 52.381 0.00 0.00 0.00 4.85
395 412 1.606224 CCCCAGTTTTGAACATGCTGC 60.606 52.381 0.00 0.00 0.00 5.25
396 413 1.962807 TCCCCAGTTTTGAACATGCTG 59.037 47.619 0.00 0.00 0.00 4.41
397 414 2.380064 TCCCCAGTTTTGAACATGCT 57.620 45.000 0.00 0.00 0.00 3.79
398 415 3.259123 AGAATCCCCAGTTTTGAACATGC 59.741 43.478 0.00 0.00 0.00 4.06
414 431 7.339482 ACAGTACTTCCCAAAATAGAGAATCC 58.661 38.462 0.00 0.00 33.66 3.01
437 454 9.562408 TGGTAAAATCACAGATTTGTTAGTACA 57.438 29.630 5.81 0.00 34.62 2.90
500 522 7.933577 TGCTACTGTAGATTATAGCAGCAAATT 59.066 33.333 18.64 0.00 41.43 1.82
511 533 6.183360 CCTGTGTGAGTGCTACTGTAGATTAT 60.183 42.308 18.64 0.92 0.00 1.28
516 538 2.558795 ACCTGTGTGAGTGCTACTGTAG 59.441 50.000 10.48 10.48 0.00 2.74
519 541 1.069204 ACACCTGTGTGAGTGCTACTG 59.931 52.381 1.39 0.00 45.76 2.74
552 574 7.458397 TCTCCATCATATTATTAACACCCCAC 58.542 38.462 0.00 0.00 0.00 4.61
581 606 7.520798 TGAGAGGCATCCTATACATGAAAAAT 58.479 34.615 0.00 0.00 31.76 1.82
613 641 6.710744 ACAAACTTCCGAGATAATGTTCAAGT 59.289 34.615 0.00 0.00 0.00 3.16
614 642 7.133891 ACAAACTTCCGAGATAATGTTCAAG 57.866 36.000 0.00 0.00 0.00 3.02
662 690 5.692204 CAGAAATGTAGAGCGATAAACCGAT 59.308 40.000 0.00 0.00 0.00 4.18
687 715 4.633175 TGTTAAATGTTCCTGACGTAGCA 58.367 39.130 0.00 0.00 0.00 3.49
706 734 3.452627 GACAGGATCCCTACATGTCTGTT 59.547 47.826 19.03 1.19 42.93 3.16
747 781 6.209391 CCACAGTCCATAAAAGGAAATTCACT 59.791 38.462 0.00 0.00 39.92 3.41
751 785 6.314917 ACTCCACAGTCCATAAAAGGAAATT 58.685 36.000 0.00 0.00 39.92 1.82
766 800 1.765314 AGAGAGCACAAACTCCACAGT 59.235 47.619 0.00 0.00 37.39 3.55
767 801 2.540265 AGAGAGCACAAACTCCACAG 57.460 50.000 0.00 0.00 37.39 3.66
826 860 5.910637 TGAAAATGCTTCACTTGATTTGC 57.089 34.783 0.00 0.00 0.00 3.68
882 917 5.238214 GCTGATCAACAAAGGATGGTCTATC 59.762 44.000 0.00 0.00 29.01 2.08
929 964 5.889289 ACAAAGTAAAAACCAGAGCCAGTTA 59.111 36.000 0.00 0.00 0.00 2.24
930 965 4.709886 ACAAAGTAAAAACCAGAGCCAGTT 59.290 37.500 0.00 0.00 0.00 3.16
931 966 4.278310 ACAAAGTAAAAACCAGAGCCAGT 58.722 39.130 0.00 0.00 0.00 4.00
938 973 9.927668 AATCCATGAATACAAAGTAAAAACCAG 57.072 29.630 0.00 0.00 0.00 4.00
978 1013 6.039605 CCATTGCATACACTGGATATGTTCAA 59.960 38.462 0.00 0.00 46.87 2.69
983 1018 3.760151 CCCCATTGCATACACTGGATATG 59.240 47.826 3.90 0.00 46.87 1.78
1125 1160 1.002624 GCGGGTGAGAAATGGTGGA 60.003 57.895 0.00 0.00 0.00 4.02
1431 1466 5.420739 AGAACCAGAAGATACACTCTCCTTC 59.579 44.000 0.00 0.00 36.26 3.46
1509 1544 4.413087 AGCAGATGTCGTTAACTAACTCG 58.587 43.478 3.71 0.00 34.12 4.18
1553 1588 3.075005 TCTGGCAGCGTACCTCCC 61.075 66.667 10.34 0.00 0.00 4.30
1605 1640 1.880027 AGCGTCAACCAATTCTGTTCC 59.120 47.619 0.00 0.00 0.00 3.62
1752 1787 8.919777 TGATCTCAGAAAATATGATGCTCAAT 57.080 30.769 0.00 0.00 0.00 2.57
1766 1801 7.365497 TGGATAATGCTACTGATCTCAGAAA 57.635 36.000 13.94 1.29 46.59 2.52
1868 1903 3.062763 CACTCTTCCTGCTTGTACAGTG 58.937 50.000 0.00 0.00 35.83 3.66
1899 1934 8.744568 TTTTTGCCAATGGACTAATTCTTTTT 57.255 26.923 2.05 0.00 0.00 1.94
1924 1959 5.848369 TCCTCCTATGTCTTCCATCATGAAT 59.152 40.000 0.00 0.00 34.86 2.57
1986 2021 6.325919 TCATTTGAACCGCAGTTTCTTATT 57.674 33.333 0.00 0.00 35.94 1.40
1993 2028 4.074970 AGAGATTCATTTGAACCGCAGTT 58.925 39.130 0.00 0.00 39.54 3.16
2019 2054 7.272244 ACCGATTAACAGATTGTGTATCATCA 58.728 34.615 0.00 0.00 39.03 3.07
2251 2286 7.290948 TGTTGATACATCTGAATACCTCCTCAT 59.709 37.037 0.00 0.00 0.00 2.90
2282 2317 1.073444 ACATAGGGCATGGATCAGCAG 59.927 52.381 0.00 0.00 39.13 4.24
2313 2348 3.891324 AGAGCATCGATTAGTAGTTCGC 58.109 45.455 0.00 0.00 42.67 4.70
2513 2548 6.402226 CGCATGAAGTTAGTAAGTTCCTTTCC 60.402 42.308 22.18 9.43 39.55 3.13
2530 2565 4.036027 AGGATATCTGTTTTGCGCATGAAG 59.964 41.667 12.75 7.27 0.00 3.02
2562 2597 6.488006 ACATATATGTGGAGGATCTGTTTTGC 59.512 38.462 17.60 0.00 40.03 3.68
2647 2705 2.887152 AGGCTTCTGCAATTTCGTTCTT 59.113 40.909 0.00 0.00 41.91 2.52
2696 2755 6.206438 GTCCATGAAAGAAAAGAGAAAGAGCT 59.794 38.462 0.00 0.00 0.00 4.09
3013 3073 0.894835 TCGCCTGCACTATCAGAACA 59.105 50.000 0.00 0.00 36.19 3.18
3021 3081 0.815095 TTCGAGATTCGCCTGCACTA 59.185 50.000 0.00 0.00 40.21 2.74
3044 3104 4.039151 TCATTCTCAGCTCGACATTCTC 57.961 45.455 0.00 0.00 0.00 2.87
3075 3135 1.627834 CTGCTCCCTTTCCTGACTCTT 59.372 52.381 0.00 0.00 0.00 2.85
3129 3189 4.281657 TGACCAGTATCACTAGAGCACAT 58.718 43.478 0.00 0.00 0.00 3.21
3136 3196 2.797156 GCGCAATGACCAGTATCACTAG 59.203 50.000 0.30 0.00 0.00 2.57
3194 3254 4.980434 GCTACTATGTGGGTACAACATACG 59.020 45.833 13.72 12.43 40.84 3.06
3276 3336 5.379187 TCAACCTTTACCCCACTTTAACTC 58.621 41.667 0.00 0.00 0.00 3.01
3294 3354 7.027778 ACTAAATCAACACAACTTCTCAACC 57.972 36.000 0.00 0.00 0.00 3.77
3310 3370 8.151141 ACTATCACTATCGTTCGACTAAATCA 57.849 34.615 0.00 0.00 0.00 2.57
3395 3462 0.670546 TGTGCTACGCTTCAGCTTCC 60.671 55.000 0.00 0.00 39.83 3.46
3419 3486 1.838112 ATTCGGAAATGCAGCAAGGA 58.162 45.000 0.00 0.00 0.00 3.36
3420 3487 2.660189 AATTCGGAAATGCAGCAAGG 57.340 45.000 0.00 0.00 0.00 3.61
3421 3488 3.841643 AGAAATTCGGAAATGCAGCAAG 58.158 40.909 0.00 0.00 0.00 4.01
3482 3553 3.126831 GCCACTCATGTATCTGCTACAC 58.873 50.000 0.00 0.00 43.01 2.90
3486 3557 2.847441 CATGCCACTCATGTATCTGCT 58.153 47.619 0.00 0.00 45.79 4.24
3571 3644 8.932945 TTGTCAATCTAGCTTCTACTACATTG 57.067 34.615 0.00 0.00 32.74 2.82
3576 3649 5.656859 TGCCTTGTCAATCTAGCTTCTACTA 59.343 40.000 0.00 0.00 0.00 1.82
3577 3650 4.467795 TGCCTTGTCAATCTAGCTTCTACT 59.532 41.667 0.00 0.00 0.00 2.57
3578 3651 4.759782 TGCCTTGTCAATCTAGCTTCTAC 58.240 43.478 0.00 0.00 0.00 2.59
3579 3652 5.420725 TTGCCTTGTCAATCTAGCTTCTA 57.579 39.130 0.00 0.00 0.00 2.10
3580 3653 3.988976 TGCCTTGTCAATCTAGCTTCT 57.011 42.857 0.00 0.00 0.00 2.85
3581 3654 5.008118 GGTATTGCCTTGTCAATCTAGCTTC 59.992 44.000 0.00 0.00 37.75 3.86
3599 3672 4.555262 AGTTTGCGGAAACATTGGTATTG 58.445 39.130 30.29 0.00 43.51 1.90
3603 3676 3.219281 ACTAGTTTGCGGAAACATTGGT 58.781 40.909 30.29 17.65 43.51 3.67
3605 3678 5.961810 CAAAACTAGTTTGCGGAAACATTG 58.038 37.500 30.29 21.31 43.51 2.82
3622 3695 3.066203 CCCGAAGCAGTTGTAACAAAACT 59.934 43.478 0.00 0.00 38.40 2.66
3642 3715 7.004555 AGAAGTTTGGACCAAAATTTATCCC 57.995 36.000 27.99 17.31 40.78 3.85
3683 3756 0.591170 AAACCAATGAACACGCGGAG 59.409 50.000 12.47 4.93 0.00 4.63
3686 3759 1.516453 CAACAAACCAATGAACACGCG 59.484 47.619 3.53 3.53 0.00 6.01
3722 3798 6.608610 ACCGCACAGAACAAAAATACTTATC 58.391 36.000 0.00 0.00 0.00 1.75
3727 3803 7.631915 AAATAACCGCACAGAACAAAAATAC 57.368 32.000 0.00 0.00 0.00 1.89
3734 3810 3.004944 GGGAAAAATAACCGCACAGAACA 59.995 43.478 0.00 0.00 0.00 3.18
3735 3811 3.004944 TGGGAAAAATAACCGCACAGAAC 59.995 43.478 0.00 0.00 0.00 3.01
3737 3813 2.817258 CTGGGAAAAATAACCGCACAGA 59.183 45.455 0.00 0.00 0.00 3.41
3739 3815 2.588620 ACTGGGAAAAATAACCGCACA 58.411 42.857 0.00 0.00 0.00 4.57
3740 3816 4.216902 AGTTACTGGGAAAAATAACCGCAC 59.783 41.667 0.00 0.00 0.00 5.34
3757 3833 3.380479 TTGCAGCAACTACGAGTTACT 57.620 42.857 2.83 0.00 36.03 2.24
3758 3834 4.461992 TTTTGCAGCAACTACGAGTTAC 57.538 40.909 7.54 0.00 36.03 2.50
3762 3838 2.290641 ACCTTTTTGCAGCAACTACGAG 59.709 45.455 7.54 1.72 0.00 4.18
3765 3841 4.040445 TGAACCTTTTTGCAGCAACTAC 57.960 40.909 7.54 0.00 0.00 2.73
3769 3845 5.295540 GGTTTTATGAACCTTTTTGCAGCAA 59.704 36.000 2.83 2.83 37.34 3.91
3779 3855 7.342581 ACAAAAATGGTGGTTTTATGAACCTT 58.657 30.769 12.38 0.00 40.88 3.50
3806 3882 6.800072 TGTACACATATGGATTACTGGTGA 57.200 37.500 7.80 0.00 0.00 4.02
3871 3947 8.424918 TCCTTGTCAAAATACCAAAAGCAAATA 58.575 29.630 0.00 0.00 0.00 1.40
3920 3996 7.046292 TCTGCAGCTATATAACTTCGGTTAA 57.954 36.000 9.47 0.00 42.71 2.01
3921 3997 6.644248 TCTGCAGCTATATAACTTCGGTTA 57.356 37.500 9.47 0.00 43.46 2.85
3926 4002 7.213678 ACTTCCTTCTGCAGCTATATAACTTC 58.786 38.462 9.47 0.00 0.00 3.01
3928 4004 6.739331 ACTTCCTTCTGCAGCTATATAACT 57.261 37.500 9.47 0.00 0.00 2.24
3929 4005 7.793927 AAACTTCCTTCTGCAGCTATATAAC 57.206 36.000 9.47 0.00 0.00 1.89
3996 4072 5.427378 CCAACTTGGAAAACCACAGAATTT 58.573 37.500 0.92 0.00 40.96 1.82
4013 4089 4.666512 AGTGAAATGCATCTACCCAACTT 58.333 39.130 0.00 0.00 0.00 2.66
4072 4148 8.355913 ACCAAAGATCTAGCAAGAAAAGAAAAG 58.644 33.333 0.00 0.00 34.73 2.27
4073 4149 8.237811 ACCAAAGATCTAGCAAGAAAAGAAAA 57.762 30.769 0.00 0.00 34.73 2.29
4074 4150 7.823745 ACCAAAGATCTAGCAAGAAAAGAAA 57.176 32.000 0.00 0.00 34.73 2.52
4075 4151 7.823745 AACCAAAGATCTAGCAAGAAAAGAA 57.176 32.000 0.00 0.00 34.73 2.52
4076 4152 7.119846 GCTAACCAAAGATCTAGCAAGAAAAGA 59.880 37.037 7.84 0.00 37.35 2.52
4077 4153 7.120432 AGCTAACCAAAGATCTAGCAAGAAAAG 59.880 37.037 13.88 0.00 39.39 2.27
4078 4154 6.942576 AGCTAACCAAAGATCTAGCAAGAAAA 59.057 34.615 13.88 0.00 39.39 2.29
4079 4155 6.476378 AGCTAACCAAAGATCTAGCAAGAAA 58.524 36.000 13.88 0.00 39.39 2.52
4080 4156 6.054860 AGCTAACCAAAGATCTAGCAAGAA 57.945 37.500 13.88 0.00 39.39 2.52
4081 4157 5.683876 AGCTAACCAAAGATCTAGCAAGA 57.316 39.130 13.88 0.00 39.39 3.02


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

AutoCloner maintained by Alex Coulton.