Multiple sequence alignment - TraesCS6B01G334300

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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 TraesCS6B01G334300 chr6B 100.000 3278 0 0 1 3278 586655550 586658827 0.000000e+00 6054
1 TraesCS6B01G334300 chr6A 92.942 3287 154 30 38 3270 539648385 539651647 0.000000e+00 4713
2 TraesCS6B01G334300 chr6D 92.980 3077 138 24 38 3072 392882229 392885269 0.000000e+00 4414
3 TraesCS6B01G334300 chr6D 97.115 208 6 0 3071 3278 392886584 392886791 5.200000e-93 351


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 TraesCS6B01G334300 chr6B 586655550 586658827 3277 False 6054.0 6054 100.0000 1 3278 1 chr6B.!!$F1 3277
1 TraesCS6B01G334300 chr6A 539648385 539651647 3262 False 4713.0 4713 92.9420 38 3270 1 chr6A.!!$F1 3232
2 TraesCS6B01G334300 chr6D 392882229 392886791 4562 False 2382.5 4414 95.0475 38 3278 2 chr6D.!!$F1 3240

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
932 952 0.248377 GTTGCAGATTGAGGATGCGC 60.248 55.0 0.0 0.0 42.92 6.09 F
1305 1325 0.037590 TCAATTGCCTAGCCCGTTGT 59.962 50.0 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2180 0.181350 GGAGTTCAATCATCCCGCCT 59.819 55.0 0.00 0.0 0.00 5.52 R
2530 2565 0.260816 AGTATACGGGCCAGACCAGA 59.739 55.0 10.86 0.0 42.05 3.86 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
23 24 6.857777 AGAAGCTGTGCATATCTGTTTATC 57.142 37.500 0.00 0.00 0.00 1.75
24 25 6.590068 AGAAGCTGTGCATATCTGTTTATCT 58.410 36.000 0.00 0.00 0.00 1.98
25 26 7.730084 AGAAGCTGTGCATATCTGTTTATCTA 58.270 34.615 0.00 0.00 0.00 1.98
26 27 7.655328 AGAAGCTGTGCATATCTGTTTATCTAC 59.345 37.037 0.00 0.00 0.00 2.59
27 28 7.060383 AGCTGTGCATATCTGTTTATCTACT 57.940 36.000 0.00 0.00 0.00 2.57
28 29 7.151308 AGCTGTGCATATCTGTTTATCTACTC 58.849 38.462 0.00 0.00 0.00 2.59
29 30 6.367422 GCTGTGCATATCTGTTTATCTACTCC 59.633 42.308 0.00 0.00 0.00 3.85
30 31 6.447162 TGTGCATATCTGTTTATCTACTCCG 58.553 40.000 0.00 0.00 0.00 4.63
31 32 6.264518 TGTGCATATCTGTTTATCTACTCCGA 59.735 38.462 0.00 0.00 0.00 4.55
32 33 6.804295 GTGCATATCTGTTTATCTACTCCGAG 59.196 42.308 0.00 0.00 0.00 4.63
33 34 6.715264 TGCATATCTGTTTATCTACTCCGAGA 59.285 38.462 1.33 0.00 0.00 4.04
34 35 7.024768 GCATATCTGTTTATCTACTCCGAGAC 58.975 42.308 1.33 0.00 0.00 3.36
35 36 7.531716 CATATCTGTTTATCTACTCCGAGACC 58.468 42.308 1.33 0.00 0.00 3.85
36 37 4.851843 TCTGTTTATCTACTCCGAGACCA 58.148 43.478 1.33 0.00 0.00 4.02
46 47 3.159298 CCGAGACCAACTTGGGATG 57.841 57.895 12.62 0.00 44.40 3.51
58 59 5.104817 CCAACTTGGGATGCCATTTCTTATT 60.105 40.000 6.84 0.00 32.67 1.40
59 60 6.408869 CAACTTGGGATGCCATTTCTTATTT 58.591 36.000 6.84 0.00 0.00 1.40
61 62 6.643388 ACTTGGGATGCCATTTCTTATTTTC 58.357 36.000 6.84 0.00 0.00 2.29
62 63 6.213195 ACTTGGGATGCCATTTCTTATTTTCA 59.787 34.615 6.84 0.00 0.00 2.69
63 64 6.224665 TGGGATGCCATTTCTTATTTTCAG 57.775 37.500 0.00 0.00 0.00 3.02
65 66 5.163374 GGGATGCCATTTCTTATTTTCAGCT 60.163 40.000 0.00 0.00 0.00 4.24
66 67 5.751990 GGATGCCATTTCTTATTTTCAGCTG 59.248 40.000 7.63 7.63 0.00 4.24
67 68 4.497300 TGCCATTTCTTATTTTCAGCTGC 58.503 39.130 9.47 0.00 0.00 5.25
68 69 4.021280 TGCCATTTCTTATTTTCAGCTGCA 60.021 37.500 9.47 0.00 0.00 4.41
72 76 7.520292 GCCATTTCTTATTTTCAGCTGCAAAAA 60.520 33.333 15.43 14.51 0.00 1.94
122 126 6.897413 AGCCCAGATTTAATTTATGTTCCAGT 59.103 34.615 0.00 0.00 0.00 4.00
124 128 8.135529 GCCCAGATTTAATTTATGTTCCAGTAC 58.864 37.037 0.00 0.00 0.00 2.73
145 149 7.647715 CAGTACGATTTTCTGGATTTGTTTTGT 59.352 33.333 0.00 0.00 0.00 2.83
146 150 6.826893 ACGATTTTCTGGATTTGTTTTGTG 57.173 33.333 0.00 0.00 0.00 3.33
152 156 8.614469 TTTTCTGGATTTGTTTTGTGTTTCTT 57.386 26.923 0.00 0.00 0.00 2.52
154 158 7.593875 TCTGGATTTGTTTTGTGTTTCTTTG 57.406 32.000 0.00 0.00 0.00 2.77
175 179 3.078837 GTGTTGGTATCGTGGAATGGTT 58.921 45.455 0.00 0.00 0.00 3.67
187 191 3.056607 GTGGAATGGTTTCAGGGTGAATG 60.057 47.826 0.00 0.00 36.11 2.67
194 198 1.381867 TTCAGGGTGAATGGATGGGT 58.618 50.000 0.00 0.00 30.26 4.51
200 204 1.408822 GGTGAATGGATGGGTCCTGTC 60.409 57.143 0.00 0.00 45.32 3.51
201 205 1.561542 GTGAATGGATGGGTCCTGTCT 59.438 52.381 0.00 0.00 45.32 3.41
206 210 1.780309 TGGATGGGTCCTGTCTTGTTT 59.220 47.619 0.00 0.00 45.32 2.83
208 212 2.224769 GGATGGGTCCTGTCTTGTTTGA 60.225 50.000 0.00 0.00 41.60 2.69
215 219 3.730715 GTCCTGTCTTGTTTGATTTTGCG 59.269 43.478 0.00 0.00 0.00 4.85
218 222 4.442073 CCTGTCTTGTTTGATTTTGCGAAG 59.558 41.667 0.00 0.00 0.00 3.79
220 224 4.797868 TGTCTTGTTTGATTTTGCGAAGTG 59.202 37.500 0.00 0.00 0.00 3.16
230 234 0.534203 TTGCGAAGTGTTGGAGGACC 60.534 55.000 0.00 0.00 0.00 4.46
248 252 3.118884 GGACCGATGCTTTACTAGTTCCA 60.119 47.826 0.00 0.00 0.00 3.53
251 255 3.132289 CCGATGCTTTACTAGTTCCAGGA 59.868 47.826 0.00 0.00 0.00 3.86
253 257 5.010719 CCGATGCTTTACTAGTTCCAGGATA 59.989 44.000 0.00 0.00 0.00 2.59
257 261 9.998106 GATGCTTTACTAGTTCCAGGATAATAA 57.002 33.333 0.00 0.00 0.00 1.40
350 354 2.289565 CGGGTTATGAGCCTTTTCTCC 58.710 52.381 4.03 0.00 41.38 3.71
415 419 1.578897 TGGGTCGAATCCATTCTCCA 58.421 50.000 4.79 7.04 34.69 3.86
433 437 5.875224 TCTCCAATGACAAGGTACAATGAA 58.125 37.500 4.35 0.00 0.00 2.57
452 456 9.113838 ACAATGAAATGTTACTGATACATCCTC 57.886 33.333 0.00 0.00 35.26 3.71
462 466 2.236146 TGATACATCCTCGCAGGTTGTT 59.764 45.455 18.09 10.18 43.77 2.83
472 477 1.334960 CGCAGGTTGTTGCCTTAGTTG 60.335 52.381 0.00 0.00 41.01 3.16
474 479 2.543653 GCAGGTTGTTGCCTTAGTTGTG 60.544 50.000 0.00 0.00 38.13 3.33
481 486 6.806739 GGTTGTTGCCTTAGTTGTGAATAATC 59.193 38.462 0.00 0.00 0.00 1.75
564 570 8.786826 ACTCGTCTGATGTTAAATTTGGATTA 57.213 30.769 0.00 0.00 0.00 1.75
678 684 6.223120 ACCATTTTGCCAAACTTCTAATGTC 58.777 36.000 0.00 0.00 0.00 3.06
679 685 6.041979 ACCATTTTGCCAAACTTCTAATGTCT 59.958 34.615 0.00 0.00 0.00 3.41
680 686 6.366877 CCATTTTGCCAAACTTCTAATGTCTG 59.633 38.462 0.00 0.00 0.00 3.51
682 688 5.437289 TTGCCAAACTTCTAATGTCTGTG 57.563 39.130 0.00 0.00 0.00 3.66
684 690 4.887071 TGCCAAACTTCTAATGTCTGTGTT 59.113 37.500 0.00 0.00 0.00 3.32
685 691 5.215160 GCCAAACTTCTAATGTCTGTGTTG 58.785 41.667 0.00 0.00 0.00 3.33
688 694 6.485313 CCAAACTTCTAATGTCTGTGTTGGTA 59.515 38.462 0.00 0.00 0.00 3.25
689 695 7.012894 CCAAACTTCTAATGTCTGTGTTGGTAA 59.987 37.037 0.00 0.00 0.00 2.85
692 698 7.280356 ACTTCTAATGTCTGTGTTGGTAAGTT 58.720 34.615 0.00 0.00 0.00 2.66
775 792 7.223584 TGATTGATGTTTGTGGAGTTCTCTTA 58.776 34.615 0.00 0.00 0.00 2.10
784 801 5.984725 TGTGGAGTTCTCTTACAAGTTTGA 58.015 37.500 0.00 0.00 0.00 2.69
844 864 4.832248 TGCCACTTTCAGTTATACCTGAG 58.168 43.478 0.00 0.00 42.16 3.35
847 867 5.351740 GCCACTTTCAGTTATACCTGAGTTC 59.648 44.000 0.00 0.00 42.16 3.01
848 868 5.577164 CCACTTTCAGTTATACCTGAGTTCG 59.423 44.000 0.00 0.00 42.16 3.95
852 872 6.459670 TTCAGTTATACCTGAGTTCGCATA 57.540 37.500 0.00 0.00 42.16 3.14
861 881 5.777802 ACCTGAGTTCGCATATCTAGAATG 58.222 41.667 0.00 3.69 0.00 2.67
864 884 6.161855 TGAGTTCGCATATCTAGAATGGTT 57.838 37.500 0.00 0.00 0.00 3.67
868 888 5.048153 TCGCATATCTAGAATGGTTCTCG 57.952 43.478 0.00 1.99 41.14 4.04
869 889 4.519350 TCGCATATCTAGAATGGTTCTCGT 59.481 41.667 0.00 0.00 41.14 4.18
870 890 5.704053 TCGCATATCTAGAATGGTTCTCGTA 59.296 40.000 0.00 0.00 41.14 3.43
871 891 5.795939 CGCATATCTAGAATGGTTCTCGTAC 59.204 44.000 0.00 0.00 41.14 3.67
872 892 6.348622 CGCATATCTAGAATGGTTCTCGTACT 60.349 42.308 0.00 0.00 41.14 2.73
873 893 7.024768 GCATATCTAGAATGGTTCTCGTACTC 58.975 42.308 0.00 0.00 41.14 2.59
874 894 7.094549 GCATATCTAGAATGGTTCTCGTACTCT 60.095 40.741 0.00 0.00 41.14 3.24
882 902 6.777213 ATGGTTCTCGTACTCTTTATCTGT 57.223 37.500 0.00 0.00 0.00 3.41
890 910 8.828644 TCTCGTACTCTTTATCTGTGTAGAATC 58.171 37.037 0.00 0.00 36.32 2.52
932 952 0.248377 GTTGCAGATTGAGGATGCGC 60.248 55.000 0.00 0.00 42.92 6.09
941 961 3.005539 AGGATGCGCACAGAGGGT 61.006 61.111 14.90 0.00 0.00 4.34
947 967 2.617274 GCGCACAGAGGGTTTGGAC 61.617 63.158 0.30 0.00 0.00 4.02
955 975 2.127708 AGAGGGTTTGGACTCTTGTGT 58.872 47.619 0.00 0.00 41.05 3.72
961 981 3.939592 GGTTTGGACTCTTGTGTATAGGC 59.060 47.826 0.00 0.00 0.00 3.93
968 988 2.294791 CTCTTGTGTATAGGCTCCCTCG 59.705 54.545 0.00 0.00 34.61 4.63
1101 1121 0.898320 ACCACCTCCTTGAGATCACG 59.102 55.000 0.00 0.00 0.00 4.35
1137 1157 0.471617 CTGGGGTCCTGGCTATTGAG 59.528 60.000 0.00 0.00 0.00 3.02
1193 1213 1.687123 GCGGGCTAAGTCTGAGGATAA 59.313 52.381 0.00 0.00 0.00 1.75
1293 1313 6.509656 TGGCAGAGATAATTCAATCAATTGC 58.490 36.000 0.00 0.00 35.34 3.56
1305 1325 0.037590 TCAATTGCCTAGCCCGTTGT 59.962 50.000 0.00 0.00 0.00 3.32
1413 1433 3.372025 GGAGGTTAGGGATTGCAGAACAT 60.372 47.826 0.00 0.00 0.00 2.71
1419 1439 2.311542 AGGGATTGCAGAACATTGGGTA 59.688 45.455 0.00 0.00 0.00 3.69
1629 1649 2.867109 CCAACTCATGGTCAAGAGGT 57.133 50.000 7.89 0.00 44.85 3.85
1776 1796 8.528044 AAACTAAAAGTTGGATTACACTTCCA 57.472 30.769 0.00 0.00 38.66 3.53
1792 1812 0.874390 TCCAAGCATGAACAAGCGTC 59.126 50.000 0.00 0.00 35.48 5.19
1878 1898 2.046892 GAGGTGCTGACATGCGGT 60.047 61.111 0.00 0.00 35.36 5.68
1902 1922 6.704050 GTGAAGAGTATGATTTAGAGAAGGGC 59.296 42.308 0.00 0.00 0.00 5.19
1929 1949 4.162320 TGGAGGTTGATAGAGAACATGTCC 59.838 45.833 0.00 0.00 0.00 4.02
2118 2138 1.027357 GCATTGCATTCCGAGGATGT 58.973 50.000 3.15 0.00 0.00 3.06
2160 2180 1.461268 TGGACCAAGAGTGCTGGGA 60.461 57.895 0.00 0.00 37.41 4.37
2282 2302 0.734889 GTCATGGGGTGCTGATTTCG 59.265 55.000 0.00 0.00 0.00 3.46
2429 2455 6.036517 CCTCTGGACATTTCAGATTTTACTCG 59.963 42.308 0.00 0.00 40.07 4.18
2436 2463 8.322906 ACATTTCAGATTTTACTCGATGTTCA 57.677 30.769 0.00 0.00 0.00 3.18
2460 2487 6.707440 ATAGAGTAGTCAGTCACATCCTTG 57.293 41.667 0.00 0.00 0.00 3.61
2528 2563 3.761897 TCCAGTTGGGAATTTGTACCTG 58.238 45.455 0.00 0.00 44.80 4.00
2529 2564 2.825532 CCAGTTGGGAATTTGTACCTGG 59.174 50.000 0.00 0.00 40.01 4.45
2530 2565 3.496331 CAGTTGGGAATTTGTACCTGGT 58.504 45.455 4.05 4.05 0.00 4.00
2540 2575 1.192146 TGTACCTGGTCTGGTCTGGC 61.192 60.000 0.63 0.00 41.22 4.85
2560 2595 2.286891 GCCCGTATACTCTGTCGAACTC 60.287 54.545 0.56 0.00 0.00 3.01
2567 2602 6.629649 CGTATACTCTGTCGAACTCAGAATTC 59.370 42.308 5.80 0.00 40.68 2.17
2644 2684 5.048083 TGGACAAAATTGTATTGGACTCTGC 60.048 40.000 0.00 0.00 42.43 4.26
2668 2708 1.208052 GTCCCAGCTTCATAGTGCTCA 59.792 52.381 0.00 0.00 37.44 4.26
2682 2723 0.528924 TGCTCATGTGCAAATGCCTC 59.471 50.000 19.51 4.21 40.29 4.70
2741 2782 4.526650 ACATGGTTTACATTTCCTTGGACC 59.473 41.667 0.00 0.00 37.84 4.46
2756 2797 1.209128 GGACCGCTCGTTGACATATG 58.791 55.000 0.00 0.00 0.00 1.78
2757 2798 0.577269 GACCGCTCGTTGACATATGC 59.423 55.000 1.58 0.00 0.00 3.14
2758 2799 0.175760 ACCGCTCGTTGACATATGCT 59.824 50.000 1.58 0.00 0.00 3.79
2759 2800 0.578683 CCGCTCGTTGACATATGCTG 59.421 55.000 1.58 0.00 0.00 4.41
2760 2801 1.280982 CGCTCGTTGACATATGCTGT 58.719 50.000 1.58 0.00 42.15 4.40
2761 2802 2.459934 CGCTCGTTGACATATGCTGTA 58.540 47.619 1.58 0.00 38.54 2.74
2762 2803 3.052745 CGCTCGTTGACATATGCTGTAT 58.947 45.455 1.58 0.00 38.54 2.29
2780 2825 6.037062 TGCTGTATTCAAGAACCAATCATACG 59.963 38.462 0.00 0.00 0.00 3.06
2790 2835 6.454795 AGAACCAATCATACGTTTGCAAAAT 58.545 32.000 14.67 7.94 0.00 1.82
2882 2927 1.663161 GCACTACTGGTTGCGCTTTTC 60.663 52.381 9.73 0.00 0.00 2.29
2893 2938 0.463116 GCGCTTTTCCCCGAATCCTA 60.463 55.000 0.00 0.00 0.00 2.94
2895 2940 1.309950 GCTTTTCCCCGAATCCTAGC 58.690 55.000 0.00 0.00 0.00 3.42
2897 2942 0.463116 TTTTCCCCGAATCCTAGCGC 60.463 55.000 0.00 0.00 0.00 5.92
2898 2943 1.335132 TTTCCCCGAATCCTAGCGCT 61.335 55.000 17.26 17.26 0.00 5.92
2899 2944 0.468585 TTCCCCGAATCCTAGCGCTA 60.469 55.000 17.75 17.75 0.00 4.26
2900 2945 0.894184 TCCCCGAATCCTAGCGCTAG 60.894 60.000 33.03 33.03 0.00 3.42
2984 3032 1.013596 TCAAAACACACGGAGCACTG 58.986 50.000 0.00 0.00 0.00 3.66
2985 3033 0.732571 CAAAACACACGGAGCACTGT 59.267 50.000 0.00 0.00 35.84 3.55
3024 3072 1.577328 ATTTTGCACCGAGCTGTCCG 61.577 55.000 0.00 0.00 45.94 4.79
3109 4483 2.361865 AGCTCCTCCGAAGTCGCT 60.362 61.111 0.00 0.00 38.18 4.93
3124 4498 1.154093 CGCTCCGCTTTACGTCTCA 60.154 57.895 0.00 0.00 41.42 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.590068 AGATAAACAGATATGCACAGCTTCT 58.410 36.000 0.00 0.00 0.00 2.85
1 2 6.857777 AGATAAACAGATATGCACAGCTTC 57.142 37.500 0.00 0.00 0.00 3.86
2 3 7.504403 AGTAGATAAACAGATATGCACAGCTT 58.496 34.615 0.00 0.00 0.00 3.74
3 4 7.060383 AGTAGATAAACAGATATGCACAGCT 57.940 36.000 0.00 0.00 0.00 4.24
4 5 6.367422 GGAGTAGATAAACAGATATGCACAGC 59.633 42.308 0.00 0.00 0.00 4.40
5 6 6.584184 CGGAGTAGATAAACAGATATGCACAG 59.416 42.308 0.00 0.00 0.00 3.66
6 7 6.264518 TCGGAGTAGATAAACAGATATGCACA 59.735 38.462 0.00 0.00 0.00 4.57
7 8 6.678878 TCGGAGTAGATAAACAGATATGCAC 58.321 40.000 0.00 0.00 0.00 4.57
8 9 6.715264 TCTCGGAGTAGATAAACAGATATGCA 59.285 38.462 4.69 0.00 0.00 3.96
9 10 7.024768 GTCTCGGAGTAGATAAACAGATATGC 58.975 42.308 4.69 0.00 0.00 3.14
10 11 7.175119 TGGTCTCGGAGTAGATAAACAGATATG 59.825 40.741 4.69 0.00 0.00 1.78
11 12 7.232188 TGGTCTCGGAGTAGATAAACAGATAT 58.768 38.462 4.69 0.00 0.00 1.63
12 13 6.598503 TGGTCTCGGAGTAGATAAACAGATA 58.401 40.000 4.69 0.00 0.00 1.98
13 14 5.446860 TGGTCTCGGAGTAGATAAACAGAT 58.553 41.667 4.69 0.00 0.00 2.90
14 15 4.851843 TGGTCTCGGAGTAGATAAACAGA 58.148 43.478 4.69 0.00 0.00 3.41
15 16 5.125739 AGTTGGTCTCGGAGTAGATAAACAG 59.874 44.000 4.69 0.00 31.28 3.16
16 17 5.014858 AGTTGGTCTCGGAGTAGATAAACA 58.985 41.667 4.69 0.00 31.28 2.83
17 18 5.579564 AGTTGGTCTCGGAGTAGATAAAC 57.420 43.478 4.69 3.47 0.00 2.01
18 19 5.105473 CCAAGTTGGTCTCGGAGTAGATAAA 60.105 44.000 14.21 0.00 31.35 1.40
19 20 4.401519 CCAAGTTGGTCTCGGAGTAGATAA 59.598 45.833 14.21 0.00 31.35 1.75
20 21 3.952323 CCAAGTTGGTCTCGGAGTAGATA 59.048 47.826 14.21 0.00 31.35 1.98
21 22 2.761208 CCAAGTTGGTCTCGGAGTAGAT 59.239 50.000 14.21 0.00 31.35 1.98
22 23 2.168496 CCAAGTTGGTCTCGGAGTAGA 58.832 52.381 14.21 0.00 31.35 2.59
23 24 1.204941 CCCAAGTTGGTCTCGGAGTAG 59.795 57.143 20.54 0.00 35.17 2.57
24 25 1.203087 TCCCAAGTTGGTCTCGGAGTA 60.203 52.381 20.54 0.00 35.17 2.59
25 26 0.471211 TCCCAAGTTGGTCTCGGAGT 60.471 55.000 20.54 0.00 35.17 3.85
26 27 0.905357 ATCCCAAGTTGGTCTCGGAG 59.095 55.000 20.54 0.00 35.17 4.63
27 28 0.613260 CATCCCAAGTTGGTCTCGGA 59.387 55.000 20.54 10.39 35.17 4.55
28 29 1.026718 GCATCCCAAGTTGGTCTCGG 61.027 60.000 20.54 5.01 35.17 4.63
29 30 1.026718 GGCATCCCAAGTTGGTCTCG 61.027 60.000 20.54 5.39 35.17 4.04
30 31 0.038166 TGGCATCCCAAGTTGGTCTC 59.962 55.000 20.54 6.64 38.46 3.36
31 32 0.706433 ATGGCATCCCAAGTTGGTCT 59.294 50.000 20.54 4.43 46.14 3.85
32 33 1.560505 AATGGCATCCCAAGTTGGTC 58.439 50.000 20.54 6.65 46.14 4.02
33 34 1.901833 GAAATGGCATCCCAAGTTGGT 59.098 47.619 20.54 0.00 46.14 3.67
34 35 2.181975 AGAAATGGCATCCCAAGTTGG 58.818 47.619 15.52 15.52 46.14 3.77
35 36 3.967332 AAGAAATGGCATCCCAAGTTG 57.033 42.857 0.00 0.00 46.14 3.16
36 37 6.625532 AAATAAGAAATGGCATCCCAAGTT 57.374 33.333 0.00 0.00 46.14 2.66
42 43 5.751990 CAGCTGAAAATAAGAAATGGCATCC 59.248 40.000 8.42 0.00 0.00 3.51
46 47 4.497300 TGCAGCTGAAAATAAGAAATGGC 58.503 39.130 20.43 0.00 0.00 4.40
72 76 4.721776 ACACCCCTCATATCTATGTGTGTT 59.278 41.667 0.00 0.00 33.83 3.32
78 82 4.080863 GGGCTAACACCCCTCATATCTATG 60.081 50.000 0.00 0.00 45.00 2.23
122 126 7.484975 ACACAAAACAAATCCAGAAAATCGTA 58.515 30.769 0.00 0.00 0.00 3.43
124 128 6.826893 ACACAAAACAAATCCAGAAAATCG 57.173 33.333 0.00 0.00 0.00 3.34
133 137 7.127917 ACACAAAGAAACACAAAACAAATCC 57.872 32.000 0.00 0.00 0.00 3.01
143 147 4.636648 ACGATACCAACACAAAGAAACACA 59.363 37.500 0.00 0.00 0.00 3.72
145 149 4.035792 CCACGATACCAACACAAAGAAACA 59.964 41.667 0.00 0.00 0.00 2.83
146 150 4.273969 TCCACGATACCAACACAAAGAAAC 59.726 41.667 0.00 0.00 0.00 2.78
152 156 3.078097 CCATTCCACGATACCAACACAA 58.922 45.455 0.00 0.00 0.00 3.33
154 158 2.706890 ACCATTCCACGATACCAACAC 58.293 47.619 0.00 0.00 0.00 3.32
175 179 1.284785 GACCCATCCATTCACCCTGAA 59.715 52.381 0.00 0.00 41.09 3.02
187 191 2.162681 CAAACAAGACAGGACCCATCC 58.837 52.381 0.00 0.00 46.69 3.51
194 198 3.629855 TCGCAAAATCAAACAAGACAGGA 59.370 39.130 0.00 0.00 0.00 3.86
200 204 5.483213 CAACACTTCGCAAAATCAAACAAG 58.517 37.500 0.00 0.00 0.00 3.16
201 205 4.328440 CCAACACTTCGCAAAATCAAACAA 59.672 37.500 0.00 0.00 0.00 2.83
206 210 2.293122 CCTCCAACACTTCGCAAAATCA 59.707 45.455 0.00 0.00 0.00 2.57
208 212 2.293399 GTCCTCCAACACTTCGCAAAAT 59.707 45.455 0.00 0.00 0.00 1.82
215 219 1.726853 CATCGGTCCTCCAACACTTC 58.273 55.000 0.00 0.00 0.00 3.01
218 222 0.321653 AAGCATCGGTCCTCCAACAC 60.322 55.000 0.00 0.00 0.00 3.32
220 224 2.007608 GTAAAGCATCGGTCCTCCAAC 58.992 52.381 0.00 0.00 0.00 3.77
230 234 4.386867 TCCTGGAACTAGTAAAGCATCG 57.613 45.455 0.00 0.00 0.00 3.84
257 261 6.262273 ACGATTCCAGTCTTACACAAAACAAT 59.738 34.615 0.00 0.00 0.00 2.71
286 290 7.231317 CCCTTCAACATACATAGGCAAATATGT 59.769 37.037 11.66 11.66 45.86 2.29
288 292 7.297614 ACCCTTCAACATACATAGGCAAATAT 58.702 34.615 0.00 0.00 0.00 1.28
365 369 4.289672 ACTCAGTCCACCATACCAAAAGAT 59.710 41.667 0.00 0.00 0.00 2.40
415 419 9.077885 AGTAACATTTCATTGTACCTTGTCATT 57.922 29.630 0.00 0.00 0.00 2.57
433 437 5.276461 TGCGAGGATGTATCAGTAACATT 57.724 39.130 0.00 0.00 37.69 2.71
452 456 0.951558 AACTAAGGCAACAACCTGCG 59.048 50.000 0.00 0.00 43.60 5.18
462 466 7.093068 TGACCTAGATTATTCACAACTAAGGCA 60.093 37.037 0.00 0.00 0.00 4.75
534 540 9.672086 CCAAATTTAACATCAGACGAGTAAAAA 57.328 29.630 0.00 0.00 0.00 1.94
576 582 9.764363 GACTAGTCATATGAATAACATGACCAA 57.236 33.333 18.20 0.15 38.52 3.67
597 603 9.535878 GGGAATAAACAGAAGATTACTGACTAG 57.464 37.037 0.00 0.00 38.55 2.57
751 768 6.566197 AAGAGAACTCCACAAACATCAATC 57.434 37.500 0.00 0.00 0.00 2.67
753 770 6.353323 TGTAAGAGAACTCCACAAACATCAA 58.647 36.000 0.00 0.00 0.00 2.57
775 792 9.107177 TGCATTTGTCATAAAAATCAAACTTGT 57.893 25.926 0.00 0.00 33.63 3.16
804 824 5.252397 AGTGGCATCCATGTATATCAGGAAT 59.748 40.000 0.00 0.00 35.28 3.01
844 864 5.343593 CGAGAACCATTCTAGATATGCGAAC 59.656 44.000 0.00 0.00 40.87 3.95
847 867 4.799678 ACGAGAACCATTCTAGATATGCG 58.200 43.478 5.80 2.68 40.87 4.73
848 868 6.915349 AGTACGAGAACCATTCTAGATATGC 58.085 40.000 5.80 0.00 40.87 3.14
852 872 7.648039 AAAGAGTACGAGAACCATTCTAGAT 57.352 36.000 5.80 0.00 40.87 1.98
861 881 5.952033 ACACAGATAAAGAGTACGAGAACC 58.048 41.667 0.00 0.00 0.00 3.62
864 884 8.734218 ATTCTACACAGATAAAGAGTACGAGA 57.266 34.615 0.00 0.00 0.00 4.04
868 888 8.138712 CAGGGATTCTACACAGATAAAGAGTAC 58.861 40.741 0.00 0.00 0.00 2.73
869 889 7.201920 GCAGGGATTCTACACAGATAAAGAGTA 60.202 40.741 0.00 0.00 0.00 2.59
870 890 6.407525 GCAGGGATTCTACACAGATAAAGAGT 60.408 42.308 0.00 0.00 0.00 3.24
871 891 5.988561 GCAGGGATTCTACACAGATAAAGAG 59.011 44.000 0.00 0.00 0.00 2.85
872 892 5.663106 AGCAGGGATTCTACACAGATAAAGA 59.337 40.000 0.00 0.00 0.00 2.52
873 893 5.757320 CAGCAGGGATTCTACACAGATAAAG 59.243 44.000 0.00 0.00 0.00 1.85
874 894 5.425217 TCAGCAGGGATTCTACACAGATAAA 59.575 40.000 0.00 0.00 0.00 1.40
882 902 4.716784 AGTTATGTCAGCAGGGATTCTACA 59.283 41.667 0.00 0.00 0.00 2.74
890 910 4.334759 CAGATCAAAGTTATGTCAGCAGGG 59.665 45.833 0.00 0.00 0.00 4.45
932 952 2.158755 ACAAGAGTCCAAACCCTCTGTG 60.159 50.000 0.00 0.00 38.06 3.66
941 961 4.081087 GGAGCCTATACACAAGAGTCCAAA 60.081 45.833 0.00 0.00 0.00 3.28
947 967 2.294791 CGAGGGAGCCTATACACAAGAG 59.705 54.545 0.00 0.00 31.76 2.85
955 975 1.040646 CAACAGCGAGGGAGCCTATA 58.959 55.000 0.00 0.00 38.01 1.31
961 981 3.941483 ACAATATTTCAACAGCGAGGGAG 59.059 43.478 0.00 0.00 0.00 4.30
968 988 9.282247 CAGAATCTACAACAATATTTCAACAGC 57.718 33.333 0.00 0.00 0.00 4.40
1137 1157 1.805120 GCCACAGCAATTCCATCATGC 60.805 52.381 0.00 0.00 39.53 4.06
1177 1197 5.537300 TCATGGTTATCCTCAGACTTAGC 57.463 43.478 0.00 0.00 34.23 3.09
1193 1213 1.909459 TACCGGCACAGCATCATGGT 61.909 55.000 0.00 0.00 0.00 3.55
1293 1313 1.153628 CCGAGAACAACGGGCTAGG 60.154 63.158 0.00 0.00 45.65 3.02
1305 1325 2.365617 GGAGCCATAATCAGACCGAGAA 59.634 50.000 0.00 0.00 0.00 2.87
1413 1433 5.593909 CACATTGCAGGAGAAATATACCCAA 59.406 40.000 0.00 0.00 0.00 4.12
1629 1649 4.314522 TCTAGGGGCATTCATTTCAACA 57.685 40.909 0.00 0.00 0.00 3.33
1776 1796 0.602638 TCCGACGCTTGTTCATGCTT 60.603 50.000 8.57 0.31 0.00 3.91
1792 1812 2.232452 AGACTCCAGAACACATTCTCCG 59.768 50.000 0.00 0.00 43.69 4.63
1878 1898 6.384015 TGCCCTTCTCTAAATCATACTCTTCA 59.616 38.462 0.00 0.00 0.00 3.02
1929 1949 2.825836 GCACCATTGAGCCCCTCG 60.826 66.667 0.00 0.00 32.35 4.63
2160 2180 0.181350 GGAGTTCAATCATCCCGCCT 59.819 55.000 0.00 0.00 0.00 5.52
2429 2455 7.539436 TGTGACTGACTACTCTATTGAACATC 58.461 38.462 0.00 0.00 0.00 3.06
2436 2463 6.406400 GCAAGGATGTGACTGACTACTCTATT 60.406 42.308 0.00 0.00 0.00 1.73
2460 2487 4.214758 ACCCAACTGTTAACGAATACAAGC 59.785 41.667 0.26 0.00 0.00 4.01
2526 2561 4.087892 CGGGCCAGACCAGACCAG 62.088 72.222 4.39 0.00 42.05 4.00
2527 2562 2.815684 ATACGGGCCAGACCAGACCA 62.816 60.000 10.86 0.00 42.05 4.02
2528 2563 0.757935 TATACGGGCCAGACCAGACC 60.758 60.000 10.86 0.00 42.05 3.85
2529 2564 0.388294 GTATACGGGCCAGACCAGAC 59.612 60.000 10.86 0.00 42.05 3.51
2530 2565 0.260816 AGTATACGGGCCAGACCAGA 59.739 55.000 10.86 0.00 42.05 3.86
2540 2575 2.941064 TGAGTTCGACAGAGTATACGGG 59.059 50.000 0.00 0.00 0.00 5.28
2560 2595 3.147629 GCATCCATCTCAGGGAATTCTG 58.852 50.000 5.23 0.00 38.09 3.02
2644 2684 2.357009 GCACTATGAAGCTGGGACAATG 59.643 50.000 0.00 0.00 38.70 2.82
2668 2708 4.081406 TCTGTTAAGAGGCATTTGCACAT 58.919 39.130 4.74 0.00 44.36 3.21
2715 2756 6.015918 TCCAAGGAAATGTAAACCATGTCAT 58.984 36.000 0.00 0.00 39.27 3.06
2741 2782 1.280982 ACAGCATATGTCAACGAGCG 58.719 50.000 4.29 0.00 37.75 5.03
2756 2797 6.037172 ACGTATGATTGGTTCTTGAATACAGC 59.963 38.462 0.00 0.00 0.00 4.40
2757 2798 7.539712 ACGTATGATTGGTTCTTGAATACAG 57.460 36.000 0.00 0.00 0.00 2.74
2758 2799 7.915293 AACGTATGATTGGTTCTTGAATACA 57.085 32.000 0.00 0.00 0.00 2.29
2759 2800 7.218204 GCAAACGTATGATTGGTTCTTGAATAC 59.782 37.037 7.02 0.00 0.00 1.89
2760 2801 7.094592 TGCAAACGTATGATTGGTTCTTGAATA 60.095 33.333 7.02 0.00 0.00 1.75
2761 2802 6.092748 GCAAACGTATGATTGGTTCTTGAAT 58.907 36.000 7.02 0.00 0.00 2.57
2762 2803 5.009110 TGCAAACGTATGATTGGTTCTTGAA 59.991 36.000 7.02 0.00 0.00 2.69
2780 2825 4.143137 CGCCAGGTTGAATATTTTGCAAAC 60.143 41.667 12.39 0.08 0.00 2.93
2790 2835 0.322456 AAGCAGCGCCAGGTTGAATA 60.322 50.000 13.20 0.00 0.00 1.75
2833 2878 3.525609 ACATATGGGTGGTTATGGTGTCA 59.474 43.478 7.80 0.00 31.46 3.58
2882 2927 1.587054 CTAGCGCTAGGATTCGGGG 59.413 63.158 32.51 8.27 0.00 5.73
2893 2938 3.347411 GTCGATTTGACCTAGCGCT 57.653 52.632 17.26 17.26 42.04 5.92
2907 2954 6.183360 GGAACTTTAATTATGCCCAATGTCGA 60.183 38.462 0.00 0.00 0.00 4.20
2984 3032 0.658897 TCGACTTTGTTTGCCCGAAC 59.341 50.000 0.00 0.00 0.00 3.95
2985 3033 1.600023 ATCGACTTTGTTTGCCCGAA 58.400 45.000 0.00 0.00 0.00 4.30
3024 3072 1.757118 TGCCCATGCTACTAGAGACAC 59.243 52.381 0.00 0.00 38.71 3.67
3109 4483 4.883026 GCTGAGACGTAAAGCGGA 57.117 55.556 0.00 0.00 46.52 5.54
3171 4545 6.797540 ACCCTAGATGATAACAATATCCCCAA 59.202 38.462 0.00 0.00 37.68 4.12


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

AutoCloner maintained by Alex Coulton.