Multiple sequence alignment - TraesCS6D01G090900

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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 TraesCS6D01G090900 chr6D 100.000 5715 0 0 1 5715 56845131 56850845 0.000000e+00 10554
1 TraesCS6D01G090900 chr6A 94.686 5702 251 33 29 5715 71446270 71451934 0.000000e+00 8804
2 TraesCS6D01G090900 chr6B 93.342 2959 174 17 2764 5715 127323879 127326821 0.000000e+00 4351
3 TraesCS6D01G090900 chr6B 90.562 2384 158 36 16 2369 127321137 127323483 0.000000e+00 3094
4 TraesCS6D01G090900 chr6B 93.684 380 21 3 2403 2780 127323486 127323864 2.990000e-157 566


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 TraesCS6D01G090900 chr6D 56845131 56850845 5714 False 10554.000000 10554 100.000000 1 5715 1 chr6D.!!$F1 5714
1 TraesCS6D01G090900 chr6A 71446270 71451934 5664 False 8804.000000 8804 94.686000 29 5715 1 chr6A.!!$F1 5686
2 TraesCS6D01G090900 chr6B 127321137 127326821 5684 False 2670.333333 4351 92.529333 16 5715 3 chr6B.!!$F1 5699

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
491 505 0.397816 CCACTCCGATTCCTCCTCCT 60.398 60.0 0.00 0.00 0.00 3.69 F
1183 1209 0.474184 CAAGGAATGCGGGTAGGGAT 59.526 55.0 0.00 0.00 0.00 3.85 F
1442 1468 0.898320 TGAGCAGCTTACCTCAGACC 59.102 55.0 0.00 0.00 33.44 3.85 F
2633 2673 0.984230 AGATGTTGTCCGGTGGTCAT 59.016 50.0 0.00 2.95 0.00 3.06 F
4015 4089 0.392336 TGCCAGGCCAACAAATGTTC 59.608 50.0 9.64 0.00 35.83 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 1332 1.077265 AACAACTGGGCTGATGGGG 59.923 57.895 0.00 0.0 0.00 4.96 R
2633 2673 2.420687 GGGCCAAAACAATTGGAACACA 60.421 45.455 10.83 0.0 42.06 3.72 R
2921 2991 4.035017 CGCACAAAGTTTTCCAGTACAAG 58.965 43.478 0.00 0.0 0.00 3.16 R
4226 4301 0.114954 ATGCCAACCCAATGGACAGT 59.885 50.000 0.00 0.0 43.54 3.55 R
5183 5259 0.620556 CTAATGGTGCAGGAGGTGGT 59.379 55.000 0.00 0.0 0.00 4.16 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
25 26 3.441500 AAAAGGGGGAGACTTGATCAC 57.558 47.619 0.00 0.00 0.00 3.06
32 33 3.706594 GGGGAGACTTGATCACACATAGA 59.293 47.826 0.00 0.00 0.00 1.98
49 50 6.987992 ACACATAGAGTAGTTCGGAACAAAAA 59.012 34.615 21.86 2.84 0.00 1.94
79 80 9.513727 GAATTTCAGATAATTTGAGAAAGGAGC 57.486 33.333 0.00 0.00 32.45 4.70
84 85 5.582665 AGATAATTTGAGAAAGGAGCGTGTC 59.417 40.000 0.00 0.00 0.00 3.67
110 111 2.603560 GTGTAATAGGAGCAACTGTCGC 59.396 50.000 0.00 0.00 0.00 5.19
111 112 2.232696 TGTAATAGGAGCAACTGTCGCA 59.767 45.455 0.00 0.00 0.00 5.10
116 117 1.267806 AGGAGCAACTGTCGCAAAATG 59.732 47.619 0.00 0.00 0.00 2.32
117 118 1.266718 GGAGCAACTGTCGCAAAATGA 59.733 47.619 0.00 0.00 0.00 2.57
118 119 2.095059 GGAGCAACTGTCGCAAAATGAT 60.095 45.455 0.00 0.00 0.00 2.45
119 120 3.166657 GAGCAACTGTCGCAAAATGATC 58.833 45.455 0.00 0.00 0.00 2.92
120 121 2.553602 AGCAACTGTCGCAAAATGATCA 59.446 40.909 0.00 0.00 0.00 2.92
121 122 3.192001 AGCAACTGTCGCAAAATGATCAT 59.808 39.130 1.18 1.18 0.00 2.45
147 149 6.257849 CCAAAAGATGATCATTTCATGGCTTG 59.742 38.462 10.14 6.58 45.29 4.01
160 162 2.386661 TGGCTTGCCGAAAACAAAAA 57.613 40.000 7.18 0.00 0.00 1.94
161 163 2.003301 TGGCTTGCCGAAAACAAAAAC 58.997 42.857 7.18 0.00 0.00 2.43
162 164 1.005452 GGCTTGCCGAAAACAAAAACG 60.005 47.619 0.00 0.00 0.00 3.60
202 205 2.154854 TTTCTCCGTCTTGCTGACTG 57.845 50.000 8.36 3.12 43.25 3.51
262 267 9.934190 ATTGTAGCACATTGTTTTTCATTTTTC 57.066 25.926 0.00 0.00 0.00 2.29
265 270 9.209297 GTAGCACATTGTTTTTCATTTTTCAAC 57.791 29.630 0.00 0.00 0.00 3.18
285 299 1.062587 CACGATGGCCTGAAAATCGAC 59.937 52.381 24.41 0.00 44.57 4.20
325 339 4.712476 CTGGGACCTCATCTTGAATAAGG 58.288 47.826 0.00 0.00 34.59 2.69
331 345 7.382898 GGACCTCATCTTGAATAAGGTATCTC 58.617 42.308 0.00 0.00 40.39 2.75
335 349 7.877097 CCTCATCTTGAATAAGGTATCTCAAGG 59.123 40.741 9.98 0.00 43.20 3.61
382 396 6.670077 AACCAAAAATAAAGCGCAAAAGAA 57.330 29.167 11.47 0.00 0.00 2.52
491 505 0.397816 CCACTCCGATTCCTCCTCCT 60.398 60.000 0.00 0.00 0.00 3.69
580 599 3.470645 TTCTAGGCCTCCGCTTAATTC 57.529 47.619 9.68 0.00 34.44 2.17
667 686 1.908066 GATTTCCGCGTGCGTTTCCT 61.908 55.000 13.70 0.00 37.81 3.36
760 779 3.741245 ACTACTGAGTCAGCCTAGGAA 57.259 47.619 20.31 0.00 34.37 3.36
761 780 4.258457 ACTACTGAGTCAGCCTAGGAAT 57.742 45.455 20.31 0.00 34.37 3.01
762 781 4.211920 ACTACTGAGTCAGCCTAGGAATC 58.788 47.826 20.31 0.59 34.37 2.52
763 782 3.396685 ACTGAGTCAGCCTAGGAATCT 57.603 47.619 20.31 4.39 34.37 2.40
764 783 3.030291 ACTGAGTCAGCCTAGGAATCTG 58.970 50.000 20.31 10.81 34.37 2.90
765 784 3.295093 CTGAGTCAGCCTAGGAATCTGA 58.705 50.000 14.75 13.17 32.37 3.27
769 788 0.749649 CAGCCTAGGAATCTGACGCT 59.250 55.000 14.75 0.00 0.00 5.07
770 789 0.749649 AGCCTAGGAATCTGACGCTG 59.250 55.000 14.75 0.00 0.00 5.18
771 790 0.878086 GCCTAGGAATCTGACGCTGC 60.878 60.000 14.75 0.00 0.00 5.25
772 791 0.749649 CCTAGGAATCTGACGCTGCT 59.250 55.000 1.05 0.00 0.00 4.24
778 797 1.800586 GAATCTGACGCTGCTGTTCAA 59.199 47.619 0.00 0.00 0.00 2.69
830 849 3.692406 GGAGCGTCGGTCCCTTGT 61.692 66.667 29.10 0.00 43.62 3.16
849 868 5.368256 TTGTAGTTTCGTCAGTCTAGGAC 57.632 43.478 0.00 0.00 0.00 3.85
1046 1071 1.140589 CGAGGTAGGCTCTGCTGTG 59.859 63.158 0.00 0.00 0.00 3.66
1070 1095 3.063670 TGTGCACACATCTTTTGTTCG 57.936 42.857 17.42 0.00 36.00 3.95
1074 1099 3.236816 GCACACATCTTTTGTTCGGATG 58.763 45.455 0.00 0.00 41.56 3.51
1094 1119 5.814188 GGATGCTGAATTCAAAAGGGAAATC 59.186 40.000 9.88 4.85 0.00 2.17
1144 1169 7.388776 TGTCTCTCTTGAGTTAATTTGACATGG 59.611 37.037 0.00 0.00 40.98 3.66
1183 1209 0.474184 CAAGGAATGCGGGTAGGGAT 59.526 55.000 0.00 0.00 0.00 3.85
1198 1224 6.071728 CGGGTAGGGATTATAACTTCGTATGT 60.072 42.308 0.00 0.00 0.00 2.29
1214 1240 4.867599 GTCCGAGTAAGCCCGCGG 62.868 72.222 21.04 21.04 44.83 6.46
1306 1332 1.602605 GGTTGCCACTGGGGTGTAC 60.603 63.158 0.00 0.00 41.53 2.90
1372 1398 5.034554 TCGCAGCAAGTTTGAATTTAGAG 57.965 39.130 0.00 0.00 0.00 2.43
1440 1466 1.930251 AGTGAGCAGCTTACCTCAGA 58.070 50.000 13.57 0.00 38.65 3.27
1442 1468 0.898320 TGAGCAGCTTACCTCAGACC 59.102 55.000 0.00 0.00 33.44 3.85
1460 1486 5.103000 CAGACCAGGTATTAGTCAAACTCG 58.897 45.833 0.00 0.00 32.82 4.18
1507 1533 7.823799 TGAAGTTAATCATTCTGAGCACATGTA 59.176 33.333 0.00 0.00 0.00 2.29
1525 1558 7.362056 GCACATGTACCACTTACTCATGAAATT 60.362 37.037 0.00 0.00 39.07 1.82
1534 1567 7.414540 CCACTTACTCATGAAATTAGCTGTTCC 60.415 40.741 0.00 0.00 0.00 3.62
1586 1621 7.426929 GACACACTCTGTCTAAATGAAATGT 57.573 36.000 0.00 0.00 45.38 2.71
1742 1777 2.352960 CGGATCTGTTAAAAGAGGCAGC 59.647 50.000 1.06 0.00 0.00 5.25
1915 1954 9.603298 CCATACATCGAATTTACTTGATTCATG 57.397 33.333 0.00 0.00 34.02 3.07
2633 2673 0.984230 AGATGTTGTCCGGTGGTCAT 59.016 50.000 0.00 2.95 0.00 3.06
2807 2877 4.052608 TGCTGATTTCACTTTGCACAATG 58.947 39.130 0.00 0.00 0.00 2.82
2910 2980 6.204882 GTCTTTTGCTCATGTAAGTAACCACT 59.795 38.462 0.00 0.00 36.19 4.00
2921 2991 5.935789 TGTAAGTAACCACTACCTTTGATGC 59.064 40.000 0.00 0.00 33.48 3.91
3272 3342 6.420638 TGCCATATCTCCATAGGATTGAATG 58.579 40.000 0.00 0.00 0.00 2.67
3422 3492 2.288025 GGTGTCTTAGGCCGGTGGA 61.288 63.158 1.90 0.00 0.00 4.02
3941 4013 5.308237 AGTCTTTAGTGTGTTCTCATCCCTT 59.692 40.000 0.00 0.00 0.00 3.95
3945 4017 6.877611 TTAGTGTGTTCTCATCCCTTTTTC 57.122 37.500 0.00 0.00 0.00 2.29
3949 4021 3.564225 GTGTTCTCATCCCTTTTTCGTGT 59.436 43.478 0.00 0.00 0.00 4.49
3953 4025 4.575885 TCTCATCCCTTTTTCGTGTAAGG 58.424 43.478 0.00 0.00 40.50 2.69
4001 4073 1.171308 AATGTGCTAAGCAGTGCCAG 58.829 50.000 12.58 10.74 40.08 4.85
4004 4078 3.136791 GCTAAGCAGTGCCAGGCC 61.137 66.667 12.58 0.00 0.00 5.19
4013 4087 0.760189 AGTGCCAGGCCAACAAATGT 60.760 50.000 9.64 0.00 0.00 2.71
4015 4089 0.392336 TGCCAGGCCAACAAATGTTC 59.608 50.000 9.64 0.00 35.83 3.18
4016 4090 0.392336 GCCAGGCCAACAAATGTTCA 59.608 50.000 5.01 0.00 35.83 3.18
4022 4096 6.042143 CCAGGCCAACAAATGTTCATAATAC 58.958 40.000 5.01 0.00 35.83 1.89
4057 4131 8.024285 GTGTCATCTAGTAGCATAACAGTATCC 58.976 40.741 0.00 0.00 0.00 2.59
4066 4140 4.895889 AGCATAACAGTATCCAGAGCTGTA 59.104 41.667 0.00 0.00 41.94 2.74
4185 4260 2.684881 CTGTCCATGACAAGGTTATGGC 59.315 50.000 13.57 10.06 45.50 4.40
4226 4301 6.591750 AGTCTTTAAGACCTCGAGAAATCA 57.408 37.500 20.05 0.00 46.18 2.57
4267 4342 5.606348 TGGCTGAGGTAAACAAATGTTTT 57.394 34.783 15.92 0.00 45.07 2.43
4328 4404 7.592938 TGCTATATTTGTCCTTTCAGTTTGTG 58.407 34.615 0.00 0.00 0.00 3.33
4379 4455 4.393062 TCCTCATTCTCATTTTGCTTCGTC 59.607 41.667 0.00 0.00 0.00 4.20
4383 4459 4.488126 TTCTCATTTTGCTTCGTCCTTG 57.512 40.909 0.00 0.00 0.00 3.61
4468 4544 0.904649 ATGGTGAGGCAATGTCGAGA 59.095 50.000 0.00 0.00 0.00 4.04
4657 4733 1.676014 GGGGAGTGGAAACTGTCATCG 60.676 57.143 0.00 0.00 0.00 3.84
4709 4785 3.183775 ACAGAACAATAAACTCGTCGTGC 59.816 43.478 0.00 0.00 0.00 5.34
4749 4825 5.224441 TGCCCCTTAGAACTGTATTAGGAT 58.776 41.667 0.00 0.00 0.00 3.24
4780 4856 2.344093 ACTACCATGGGTGTTCTCCT 57.656 50.000 18.09 0.00 36.19 3.69
4795 4871 2.066262 TCTCCTGCGAAATTCGTGTTC 58.934 47.619 17.05 0.57 42.81 3.18
4831 4907 1.207811 CCCATTTGCTTGATTGGGTCC 59.792 52.381 0.00 0.00 43.25 4.46
5021 5097 6.474819 TTCAAACAATGTACCGTGAGTATG 57.525 37.500 0.21 0.00 32.28 2.39
5077 5153 0.393944 TCTACCTGACTCCGACGCAT 60.394 55.000 0.00 0.00 0.00 4.73
5183 5259 5.004361 AGAGCTCCTATGGTTATCAGCTA 57.996 43.478 10.93 0.00 0.00 3.32
5184 5260 4.770010 AGAGCTCCTATGGTTATCAGCTAC 59.230 45.833 10.93 0.00 0.00 3.58
5185 5261 3.835395 AGCTCCTATGGTTATCAGCTACC 59.165 47.826 0.00 0.00 34.93 3.18
5215 5291 1.004745 ACCATTAGCCTGACAACTGGG 59.995 52.381 0.00 0.00 35.96 4.45
5251 5327 1.526917 GCCAGCCATAGTTGCGGAT 60.527 57.895 0.00 0.00 0.00 4.18
5392 5468 1.201429 TCTTGGCCACCTCCTCCTTC 61.201 60.000 3.88 0.00 0.00 3.46
5395 5471 2.671682 GCCACCTCCTCCTTCACC 59.328 66.667 0.00 0.00 0.00 4.02
5634 5710 1.448717 GGCGAGAGGTGGAAGAAGC 60.449 63.158 0.00 0.00 0.00 3.86
5663 5739 2.464459 GGCTTCGGTGAGCAATCCG 61.464 63.158 7.05 7.05 44.49 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.716424 TGTGATCAAGTCTCCCCCTTTT 59.284 45.455 0.00 0.00 0.00 2.27
9 10 0.984230 TGTGTGATCAAGTCTCCCCC 59.016 55.000 0.00 0.00 0.00 5.40
10 11 3.706594 TCTATGTGTGATCAAGTCTCCCC 59.293 47.826 0.00 0.00 0.00 4.81
11 12 4.404073 ACTCTATGTGTGATCAAGTCTCCC 59.596 45.833 0.00 0.00 0.00 4.30
12 13 5.590530 ACTCTATGTGTGATCAAGTCTCC 57.409 43.478 0.00 0.00 0.00 3.71
13 14 7.328277 ACTACTCTATGTGTGATCAAGTCTC 57.672 40.000 0.00 0.00 0.00 3.36
14 15 7.414651 CGAACTACTCTATGTGTGATCAAGTCT 60.415 40.741 0.00 0.00 0.00 3.24
15 16 6.689241 CGAACTACTCTATGTGTGATCAAGTC 59.311 42.308 0.00 0.00 0.00 3.01
16 17 6.404844 CCGAACTACTCTATGTGTGATCAAGT 60.405 42.308 0.00 0.00 0.00 3.16
17 18 5.974158 CCGAACTACTCTATGTGTGATCAAG 59.026 44.000 0.00 0.00 0.00 3.02
18 19 5.650703 TCCGAACTACTCTATGTGTGATCAA 59.349 40.000 0.00 0.00 0.00 2.57
19 20 5.190677 TCCGAACTACTCTATGTGTGATCA 58.809 41.667 0.00 0.00 0.00 2.92
20 21 5.752892 TCCGAACTACTCTATGTGTGATC 57.247 43.478 0.00 0.00 0.00 2.92
21 22 5.417894 TGTTCCGAACTACTCTATGTGTGAT 59.582 40.000 12.43 0.00 0.00 3.06
22 23 4.763279 TGTTCCGAACTACTCTATGTGTGA 59.237 41.667 12.43 0.00 0.00 3.58
23 24 5.055642 TGTTCCGAACTACTCTATGTGTG 57.944 43.478 12.43 0.00 0.00 3.82
24 25 5.717078 TTGTTCCGAACTACTCTATGTGT 57.283 39.130 12.43 0.00 0.00 3.72
25 26 7.170998 AGTTTTTGTTCCGAACTACTCTATGTG 59.829 37.037 12.43 0.00 32.22 3.21
32 33 8.672823 AATTCTAGTTTTTGTTCCGAACTACT 57.327 30.769 12.43 11.63 35.43 2.57
71 72 1.261619 CACTTGTGACACGCTCCTTTC 59.738 52.381 0.22 0.00 0.00 2.62
79 80 3.612860 GCTCCTATTACACTTGTGACACG 59.387 47.826 7.83 0.00 0.00 4.49
84 85 4.997395 ACAGTTGCTCCTATTACACTTGTG 59.003 41.667 0.00 0.00 0.00 3.33
147 149 4.763594 TTGATTCGTTTTTGTTTTCGGC 57.236 36.364 0.00 0.00 0.00 5.54
160 162 9.482627 GAAATAGGACTATCTGATTTGATTCGT 57.517 33.333 0.00 0.00 0.00 3.85
161 163 9.703892 AGAAATAGGACTATCTGATTTGATTCG 57.296 33.333 0.00 0.00 0.00 3.34
261 266 1.974265 TTTTCAGGCCATCGTGTTGA 58.026 45.000 5.01 0.00 0.00 3.18
262 267 2.728846 CGATTTTCAGGCCATCGTGTTG 60.729 50.000 5.01 0.00 36.00 3.33
265 270 1.062587 GTCGATTTTCAGGCCATCGTG 59.937 52.381 18.62 3.00 40.57 4.35
325 339 1.418264 GAGAAGGCCCCCTTGAGATAC 59.582 57.143 0.00 0.00 44.82 2.24
331 345 4.033776 TGCGAGAAGGCCCCCTTG 62.034 66.667 0.00 1.44 44.82 3.61
335 349 3.056328 GTTGTGCGAGAAGGCCCC 61.056 66.667 0.00 0.00 0.00 5.80
382 396 0.107410 TGCGGCCACGGATTTATTCT 60.107 50.000 2.24 0.00 41.36 2.40
468 482 1.066587 GAGGAATCGGAGTGGAGCG 59.933 63.158 0.00 0.00 0.00 5.03
469 483 1.045911 AGGAGGAATCGGAGTGGAGC 61.046 60.000 0.00 0.00 0.00 4.70
667 686 0.254747 CCTATCCCCCAAACAAGCGA 59.745 55.000 0.00 0.00 0.00 4.93
755 774 1.186200 ACAGCAGCGTCAGATTCCTA 58.814 50.000 0.00 0.00 0.00 2.94
757 776 0.723981 GAACAGCAGCGTCAGATTCC 59.276 55.000 0.00 0.00 0.00 3.01
758 777 1.432514 TGAACAGCAGCGTCAGATTC 58.567 50.000 0.00 0.00 0.00 2.52
759 778 1.882912 TTGAACAGCAGCGTCAGATT 58.117 45.000 0.00 0.00 0.00 2.40
760 779 1.882912 TTTGAACAGCAGCGTCAGAT 58.117 45.000 0.00 0.00 0.00 2.90
761 780 1.330521 GTTTTGAACAGCAGCGTCAGA 59.669 47.619 0.00 0.00 0.00 3.27
762 781 1.746760 GTTTTGAACAGCAGCGTCAG 58.253 50.000 0.00 0.00 0.00 3.51
763 782 0.027455 CGTTTTGAACAGCAGCGTCA 59.973 50.000 0.00 0.00 0.00 4.35
764 783 0.303493 TCGTTTTGAACAGCAGCGTC 59.697 50.000 0.00 0.00 0.00 5.19
765 784 0.730265 TTCGTTTTGAACAGCAGCGT 59.270 45.000 0.00 0.00 0.00 5.07
766 785 3.525059 TTCGTTTTGAACAGCAGCG 57.475 47.368 0.00 0.00 0.00 5.18
778 797 3.181504 CGGAAAAACCTCACTGTTCGTTT 60.182 43.478 0.00 0.00 36.31 3.60
824 843 3.662247 AGACTGACGAAACTACAAGGG 57.338 47.619 0.00 0.00 0.00 3.95
830 849 4.936411 CAGAGTCCTAGACTGACGAAACTA 59.064 45.833 1.16 0.00 43.53 2.24
849 868 2.125350 GGAACAGCGGCCTCAGAG 60.125 66.667 0.00 0.00 0.00 3.35
861 880 0.865111 CGCAGAACACATTCGGAACA 59.135 50.000 0.00 0.00 40.04 3.18
1046 1071 2.159114 ACAAAAGATGTGTGCACAACCC 60.159 45.455 23.59 10.27 45.41 4.11
1070 1095 4.806640 TTCCCTTTTGAATTCAGCATCC 57.193 40.909 8.41 0.00 0.00 3.51
1074 1099 4.082245 TCGGATTTCCCTTTTGAATTCAGC 60.082 41.667 8.41 0.00 0.00 4.26
1094 1119 0.031449 AAACCGCCACATTTTGTCGG 59.969 50.000 6.31 6.31 41.68 4.79
1155 1181 2.295909 CCCGCATTCCTTGTCAAGAAAA 59.704 45.455 14.42 8.27 0.00 2.29
1156 1182 1.885887 CCCGCATTCCTTGTCAAGAAA 59.114 47.619 14.42 0.00 0.00 2.52
1183 1209 7.134815 GCTTACTCGGACATACGAAGTTATAA 58.865 38.462 0.00 0.00 37.78 0.98
1214 1240 1.382522 TGAATCCATTGCTTCTCGCC 58.617 50.000 0.00 0.00 38.05 5.54
1233 1259 4.936685 AAATAGCAGAGAACCCTTCCTT 57.063 40.909 0.00 0.00 0.00 3.36
1306 1332 1.077265 AACAACTGGGCTGATGGGG 59.923 57.895 0.00 0.00 0.00 4.96
1372 1398 2.484062 CGATGGTGCAGGCCCATTC 61.484 63.158 8.60 2.60 42.76 2.67
1440 1466 3.836562 ACCGAGTTTGACTAATACCTGGT 59.163 43.478 4.05 4.05 0.00 4.00
1488 1514 4.637534 GTGGTACATGTGCTCAGAATGATT 59.362 41.667 13.86 0.00 44.54 2.57
1507 1533 6.476378 ACAGCTAATTTCATGAGTAAGTGGT 58.524 36.000 0.00 0.00 0.00 4.16
1525 1558 4.948341 TGTAAACACAGAGGAACAGCTA 57.052 40.909 0.00 0.00 0.00 3.32
1534 1567 5.879237 TGCAGTTCTTTTGTAAACACAGAG 58.121 37.500 0.00 0.00 0.00 3.35
1586 1621 3.767673 AGGTACGAGAACAATTCTAGCCA 59.232 43.478 0.00 0.00 40.87 4.75
1742 1777 7.932120 ACGAGAGAAGATTTATAAATCACCG 57.068 36.000 30.52 24.25 45.59 4.94
1915 1954 5.049680 CAGTCATACAACACCACACTTTACC 60.050 44.000 0.00 0.00 0.00 2.85
2132 2171 3.135414 ACATCGCAATTCACAAATCCG 57.865 42.857 0.00 0.00 0.00 4.18
2633 2673 2.420687 GGGCCAAAACAATTGGAACACA 60.421 45.455 10.83 0.00 42.06 3.72
2807 2877 7.604545 AGGAAGACAAATCTAAGAGCTTACAAC 59.395 37.037 0.00 0.00 33.57 3.32
2910 2980 4.901197 TCCAGTACAAGCATCAAAGGTA 57.099 40.909 0.00 0.00 0.00 3.08
2921 2991 4.035017 CGCACAAAGTTTTCCAGTACAAG 58.965 43.478 0.00 0.00 0.00 3.16
3272 3342 5.800941 CGACTAATCAACTCAAGTACTGTCC 59.199 44.000 0.00 0.00 0.00 4.02
3422 3492 7.979537 GGAGTTCTTTAACAAACTGGAACAATT 59.020 33.333 6.43 0.00 36.35 2.32
3595 3665 3.428045 GCCAGTCAACAATGATGCTAACC 60.428 47.826 0.00 0.00 38.01 2.85
3597 3667 3.419943 TGCCAGTCAACAATGATGCTAA 58.580 40.909 0.00 0.00 38.01 3.09
3831 3901 6.691508 TGTGAGGACAGAAATATATCGATGG 58.308 40.000 8.54 0.00 0.00 3.51
3941 4013 5.263968 TGCCAATTTTCCTTACACGAAAA 57.736 34.783 0.00 0.00 41.91 2.29
3945 4017 2.923020 GCATGCCAATTTTCCTTACACG 59.077 45.455 6.36 0.00 0.00 4.49
3972 4044 8.345565 GCACTGCTTAGCACATTTAACTATTAT 58.654 33.333 1.39 0.00 33.79 1.28
3973 4045 7.201696 GGCACTGCTTAGCACATTTAACTATTA 60.202 37.037 1.39 0.00 33.79 0.98
3979 4051 3.153130 TGGCACTGCTTAGCACATTTAA 58.847 40.909 1.39 0.00 33.79 1.52
3990 4062 2.914097 GTTGGCCTGGCACTGCTT 60.914 61.111 22.05 0.00 0.00 3.91
4001 4073 5.128663 AGGGTATTATGAACATTTGTTGGCC 59.871 40.000 0.00 0.00 38.56 5.36
4034 4108 8.164070 TCTGGATACTGTTATGCTACTAGATGA 58.836 37.037 0.00 0.00 36.78 2.92
4043 4117 3.708631 ACAGCTCTGGATACTGTTATGCT 59.291 43.478 1.66 0.00 41.78 3.79
4095 4169 8.834465 CATAAAGTCTAACTTAGAGCATTGCAT 58.166 33.333 11.91 1.36 37.47 3.96
4185 4260 5.255710 AGACTCGATGTCCTTTATCTGTG 57.744 43.478 10.24 0.00 46.46 3.66
4226 4301 0.114954 ATGCCAACCCAATGGACAGT 59.885 50.000 0.00 0.00 43.54 3.55
4328 4404 6.874288 AGCAGAGGCATAAGAATGTATTTC 57.126 37.500 0.00 0.00 44.61 2.17
4379 4455 3.872696 TGTATACACATGGTGAGCAAGG 58.127 45.455 0.08 0.00 36.96 3.61
4383 4459 6.624352 ATGAATTGTATACACATGGTGAGC 57.376 37.500 4.68 0.00 36.96 4.26
4468 4544 5.485353 TCTCGCATAATCCCCTGAATATTCT 59.515 40.000 16.24 0.00 0.00 2.40
4530 4606 4.672542 GCAGCATCGCAGAACTGATAAAAA 60.673 41.667 5.97 0.00 44.35 1.94
4749 4825 5.034200 ACCCATGGTAGTAATCTGGTACAA 58.966 41.667 11.73 0.00 32.18 2.41
4780 4856 5.599359 TTTCATAGAACACGAATTTCGCA 57.401 34.783 18.24 0.00 45.12 5.10
4795 4871 4.411256 AATGGGGCTTTGCATTTCATAG 57.589 40.909 0.00 0.00 0.00 2.23
4831 4907 4.433283 GCAAAATTACAAAGACAGCATGCG 60.433 41.667 13.01 9.99 42.53 4.73
4970 5046 7.645058 TGATAGAAGGGATGGAATTTTGTTC 57.355 36.000 0.00 0.00 0.00 3.18
5021 5097 5.280945 TGCAGATTCACTTTGTAACTTTGC 58.719 37.500 0.00 0.00 0.00 3.68
5183 5259 0.620556 CTAATGGTGCAGGAGGTGGT 59.379 55.000 0.00 0.00 0.00 4.16
5184 5260 0.749454 GCTAATGGTGCAGGAGGTGG 60.749 60.000 0.00 0.00 0.00 4.61
5185 5261 0.749454 GGCTAATGGTGCAGGAGGTG 60.749 60.000 0.00 0.00 0.00 4.00
5215 5291 2.665603 GGAGCTGGAGTGGTGTCC 59.334 66.667 0.00 0.00 37.10 4.02
5263 5339 1.907807 GTGCCTTGATGTTGCCCCA 60.908 57.895 0.00 0.00 0.00 4.96
5418 5494 1.988107 ACATCATCAGGTTCAGGGTGT 59.012 47.619 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.