Multiple sequence alignment - TraesCS6D01G351000

Loading Multiple Alignment...

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 TraesCS6D01G351000 chr6D 100.000 3074 0 0 1 3074 448428067 448431140 0.000000e+00 5677
1 TraesCS6D01G351000 chr6D 86.406 1177 134 13 963 2132 448485497 448486654 0.000000e+00 1264
2 TraesCS6D01G351000 chr6D 85.579 1165 142 12 963 2120 448059474 448058329 0.000000e+00 1197
3 TraesCS6D01G351000 chr6D 78.430 1108 208 17 962 2062 448365341 448366424 0.000000e+00 693
4 TraesCS6D01G351000 chr6D 92.373 472 30 3 5 471 448141746 448141276 0.000000e+00 667
5 TraesCS6D01G351000 chr6D 76.367 622 134 12 1056 1672 448034339 448033726 3.820000e-84 322
6 TraesCS6D01G351000 chr6D 80.000 260 33 14 2488 2746 448058004 448057763 1.130000e-39 174
7 TraesCS6D01G351000 chr6D 82.840 169 23 5 2213 2377 448486659 448486825 2.470000e-31 147
8 TraesCS6D01G351000 chr6D 83.088 136 21 2 2612 2746 448503612 448503746 4.160000e-24 122
9 TraesCS6D01G351000 chr6B 91.908 2830 152 33 166 2924 679284163 679286986 0.000000e+00 3886
10 TraesCS6D01G351000 chr6B 95.070 2150 73 11 798 2924 679330555 679328416 0.000000e+00 3352
11 TraesCS6D01G351000 chr6B 83.062 1104 168 15 983 2072 679244098 679245196 0.000000e+00 985
12 TraesCS6D01G351000 chr6B 79.927 1091 190 19 984 2066 679278129 679279198 0.000000e+00 774
13 TraesCS6D01G351000 chr6B 83.843 687 103 6 1382 2061 679256080 679256765 0.000000e+00 647
14 TraesCS6D01G351000 chr6B 84.863 621 87 4 1524 2138 678930963 678930344 1.210000e-173 619
15 TraesCS6D01G351000 chr6B 81.967 610 73 19 172 749 679337366 679336762 1.660000e-132 483
16 TraesCS6D01G351000 chr6B 80.935 535 66 13 963 1468 678931515 678930988 1.030000e-104 390
17 TraesCS6D01G351000 chr6B 83.459 133 19 3 2615 2746 678929914 678929784 1.500000e-23 121
18 TraesCS6D01G351000 chr6B 93.151 73 0 1 3002 3074 679287004 679287071 5.420000e-18 102
19 TraesCS6D01G351000 chr6B 93.151 73 0 1 3002 3074 679328398 679328331 5.420000e-18 102
20 TraesCS6D01G351000 chr6A 89.200 1787 150 25 515 2289 594516849 594515094 0.000000e+00 2191
21 TraesCS6D01G351000 chr6A 80.678 1092 181 20 984 2066 594520666 594519596 0.000000e+00 821
22 TraesCS6D01G351000 chr6A 93.587 499 31 1 11 509 594517385 594516888 0.000000e+00 743
23 TraesCS6D01G351000 chr6A 77.247 1068 184 27 1036 2083 594498908 594497880 3.440000e-159 571


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 TraesCS6D01G351000 chr6D 448428067 448431140 3073 False 5677.000000 5677 100.000000 1 3074 1 chr6D.!!$F2 3073
1 TraesCS6D01G351000 chr6D 448485497 448486825 1328 False 705.500000 1264 84.623000 963 2377 2 chr6D.!!$F4 1414
2 TraesCS6D01G351000 chr6D 448365341 448366424 1083 False 693.000000 693 78.430000 962 2062 1 chr6D.!!$F1 1100
3 TraesCS6D01G351000 chr6D 448057763 448059474 1711 True 685.500000 1197 82.789500 963 2746 2 chr6D.!!$R3 1783
4 TraesCS6D01G351000 chr6D 448033726 448034339 613 True 322.000000 322 76.367000 1056 1672 1 chr6D.!!$R1 616
5 TraesCS6D01G351000 chr6B 679284163 679287071 2908 False 1994.000000 3886 92.529500 166 3074 2 chr6B.!!$F4 2908
6 TraesCS6D01G351000 chr6B 679328331 679330555 2224 True 1727.000000 3352 94.110500 798 3074 2 chr6B.!!$R3 2276
7 TraesCS6D01G351000 chr6B 679244098 679245196 1098 False 985.000000 985 83.062000 983 2072 1 chr6B.!!$F1 1089
8 TraesCS6D01G351000 chr6B 679278129 679279198 1069 False 774.000000 774 79.927000 984 2066 1 chr6B.!!$F3 1082
9 TraesCS6D01G351000 chr6B 679256080 679256765 685 False 647.000000 647 83.843000 1382 2061 1 chr6B.!!$F2 679
10 TraesCS6D01G351000 chr6B 679336762 679337366 604 True 483.000000 483 81.967000 172 749 1 chr6B.!!$R1 577
11 TraesCS6D01G351000 chr6B 678929784 678931515 1731 True 376.666667 619 83.085667 963 2746 3 chr6B.!!$R2 1783
12 TraesCS6D01G351000 chr6A 594515094 594520666 5572 True 1251.666667 2191 87.821667 11 2289 3 chr6A.!!$R2 2278
13 TraesCS6D01G351000 chr6A 594497880 594498908 1028 True 571.000000 571 77.247000 1036 2083 1 chr6A.!!$R1 1047

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
241 3513 0.107848 GCCACCACCGCACTACTATT 60.108 55.0 0.00 0.00 0.00 1.73 F
495 3770 0.531200 GAACGGACTCGAGGTGGATT 59.469 55.0 18.41 4.16 40.11 3.01 F
590 3899 1.156736 TTCGCTAGCTTGGCAAGAAC 58.843 50.0 30.45 13.73 0.00 3.01 F
843 4174 1.182667 TACAGAGGATGACGTGTGGG 58.817 55.0 0.00 0.00 31.09 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1541 4943 0.541998 TTTCTCGGTCTGGAGGAGCA 60.542 55.000 0.00 0.00 42.06 4.26 R
1890 5304 0.661780 GTAGCAGGATAGTCGCTGCG 60.662 60.000 17.25 17.25 41.96 5.18 R
1912 5326 1.227527 CACAGTGGTGTTGCTCGGA 60.228 57.895 0.00 0.00 40.24 4.55 R
2810 6331 1.024271 CATCAAGGGCGTGGGTATTG 58.976 55.000 0.00 0.00 0.00 1.90 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
24 3296 6.273825 GCGAGGTATTCTCTAATTCTCAACA 58.726 40.000 0.00 0.00 40.30 3.33
84 3356 8.511604 TGGTTTTAATTTTCTGCAATCCAAAA 57.488 26.923 0.00 0.00 0.00 2.44
127 3399 9.184523 TGTGGGGAGTGTCAATAAAATTTATAG 57.815 33.333 0.00 0.00 0.00 1.31
158 3430 8.707796 ATTATAATCTCGTCTTCTCACCCTAA 57.292 34.615 0.00 0.00 0.00 2.69
241 3513 0.107848 GCCACCACCGCACTACTATT 60.108 55.000 0.00 0.00 0.00 1.73
281 3553 3.119316 GCCGACCTGATCTTATCGATGAT 60.119 47.826 8.54 2.73 36.70 2.45
288 3560 8.359875 ACCTGATCTTATCGATGATAGTCAAT 57.640 34.615 8.54 0.00 30.84 2.57
297 3569 9.827411 TTATCGATGATAGTCAATAAGTCTTCG 57.173 33.333 8.54 0.00 37.63 3.79
314 3586 2.684001 TCGTACACATGCCCCTAAAG 57.316 50.000 0.00 0.00 0.00 1.85
324 3596 2.205342 TGCCCCTAAAGATTAGTGCCT 58.795 47.619 6.48 0.00 0.00 4.75
333 3605 1.689273 AGATTAGTGCCTCGGATCCAC 59.311 52.381 13.41 1.35 0.00 4.02
387 3662 1.831106 ACTTGACACCAGATATCGCCA 59.169 47.619 0.00 0.00 0.00 5.69
407 3682 4.310672 GCCTATGTGCGACGAGAG 57.689 61.111 0.00 0.00 0.00 3.20
495 3770 0.531200 GAACGGACTCGAGGTGGATT 59.469 55.000 18.41 4.16 40.11 3.01
509 3784 2.369394 GTGGATTGAAGCCCGAAAGAT 58.631 47.619 0.00 0.00 0.00 2.40
510 3785 2.098117 GTGGATTGAAGCCCGAAAGATG 59.902 50.000 0.00 0.00 0.00 2.90
511 3786 2.026356 TGGATTGAAGCCCGAAAGATGA 60.026 45.455 0.00 0.00 0.00 2.92
513 3788 3.065925 GGATTGAAGCCCGAAAGATGAAG 59.934 47.826 0.00 0.00 0.00 3.02
585 3894 1.663643 CGTATTTTCGCTAGCTTGGCA 59.336 47.619 13.93 0.00 0.00 4.92
590 3899 1.156736 TTCGCTAGCTTGGCAAGAAC 58.843 50.000 30.45 13.73 0.00 3.01
597 3906 4.578105 GCTAGCTTGGCAAGAACTCATATT 59.422 41.667 30.45 6.23 0.00 1.28
598 3907 4.978083 AGCTTGGCAAGAACTCATATTG 57.022 40.909 30.45 0.68 0.00 1.90
746 4060 5.473504 TGTGCTACTTCCATTTTTCTCTTCC 59.526 40.000 0.00 0.00 0.00 3.46
843 4174 1.182667 TACAGAGGATGACGTGTGGG 58.817 55.000 0.00 0.00 31.09 4.61
933 4264 1.272769 CGTCTCCTTTCTCCGTTCCTT 59.727 52.381 0.00 0.00 0.00 3.36
1441 4828 3.424300 ACGACTCGTTCACCGTCA 58.576 55.556 0.00 0.00 36.35 4.35
1549 4951 1.452833 GACCTTGGCATGCTCCTCC 60.453 63.158 18.92 0.10 0.00 4.30
1886 5300 4.048241 TGTGTGAGTACATTGACGTCAA 57.952 40.909 31.41 31.41 39.39 3.18
1890 5304 3.183775 GTGAGTACATTGACGTCAACACC 59.816 47.826 31.87 19.22 38.86 4.16
2084 5498 1.544314 GGGGCATTAGCTGAGTGATCC 60.544 57.143 0.00 0.00 41.70 3.36
2148 5566 6.634805 ACATCGCTACATCTATCCTAATTGG 58.365 40.000 0.00 0.00 37.10 3.16
2153 5571 7.124298 TCGCTACATCTATCCTAATTGGCTATT 59.876 37.037 0.00 0.00 35.26 1.73
2384 5816 5.233083 AGGTCTTTGTCATCACTCATCAA 57.767 39.130 0.00 0.00 0.00 2.57
2451 5883 8.862325 ACTTTGTTGACCTATGTTATGATCAA 57.138 30.769 0.00 0.00 0.00 2.57
2626 6136 2.673368 CAAGGCGATGTCAAAGTAGTCC 59.327 50.000 0.00 0.00 0.00 3.85
2710 6220 6.323203 TCTACACACACTAGTCCTGTAAAC 57.677 41.667 0.00 0.00 0.00 2.01
2736 6246 2.589014 CCTTTCGCATTCTCTTTGTGC 58.411 47.619 0.00 0.00 35.59 4.57
2751 6272 5.985781 TCTTTGTGCGTCAAATTTCTAGTC 58.014 37.500 7.20 0.00 43.78 2.59
2820 6341 9.261180 GATATGGTATAATGATCAATACCCACG 57.739 37.037 24.47 0.00 44.73 4.94
2856 6379 2.027385 GATTTCAGAACAGGGGGCATC 58.973 52.381 0.00 0.00 0.00 3.91
2865 6388 2.391678 ACAGGGGGCATCATGAAAATC 58.608 47.619 0.00 0.00 0.00 2.17
2924 6447 6.183360 GGATAGTGGCTGTAGGTAATGTGTTA 60.183 42.308 0.00 0.00 0.00 2.41
2925 6448 5.492855 AGTGGCTGTAGGTAATGTGTTAA 57.507 39.130 0.00 0.00 0.00 2.01
2926 6449 5.488341 AGTGGCTGTAGGTAATGTGTTAAG 58.512 41.667 0.00 0.00 0.00 1.85
2928 6451 6.211986 AGTGGCTGTAGGTAATGTGTTAAGTA 59.788 38.462 0.00 0.00 0.00 2.24
2929 6452 6.534079 GTGGCTGTAGGTAATGTGTTAAGTAG 59.466 42.308 0.00 0.00 0.00 2.57
2931 6454 7.396907 TGGCTGTAGGTAATGTGTTAAGTAGTA 59.603 37.037 0.00 0.00 0.00 1.82
2932 6455 7.704047 GGCTGTAGGTAATGTGTTAAGTAGTAC 59.296 40.741 0.00 0.00 0.00 2.73
2933 6456 8.246180 GCTGTAGGTAATGTGTTAAGTAGTACA 58.754 37.037 2.52 0.00 0.00 2.90
2950 6473 8.848474 AGTAGTACATAATGTTTTGCTTCTGT 57.152 30.769 2.52 0.00 0.00 3.41
2951 6474 9.284968 AGTAGTACATAATGTTTTGCTTCTGTT 57.715 29.630 2.52 0.00 0.00 3.16
2952 6475 9.893305 GTAGTACATAATGTTTTGCTTCTGTTT 57.107 29.630 0.00 0.00 0.00 2.83
2957 6480 9.630098 ACATAATGTTTTGCTTCTGTTTATCAG 57.370 29.630 0.00 0.00 44.85 2.90
2968 6491 4.416516 TCTGTTTATCAGAGGAGGTGTCA 58.583 43.478 0.00 0.00 46.77 3.58
2969 6492 4.464244 TCTGTTTATCAGAGGAGGTGTCAG 59.536 45.833 0.00 0.00 46.77 3.51
2970 6493 4.160329 TGTTTATCAGAGGAGGTGTCAGT 58.840 43.478 0.00 0.00 0.00 3.41
2971 6494 4.593206 TGTTTATCAGAGGAGGTGTCAGTT 59.407 41.667 0.00 0.00 0.00 3.16
2972 6495 5.778241 TGTTTATCAGAGGAGGTGTCAGTTA 59.222 40.000 0.00 0.00 0.00 2.24
2973 6496 6.440647 TGTTTATCAGAGGAGGTGTCAGTTAT 59.559 38.462 0.00 0.00 0.00 1.89
2974 6497 7.618117 TGTTTATCAGAGGAGGTGTCAGTTATA 59.382 37.037 0.00 0.00 0.00 0.98
2975 6498 7.825331 TTATCAGAGGAGGTGTCAGTTATAG 57.175 40.000 0.00 0.00 0.00 1.31
2976 6499 5.452341 TCAGAGGAGGTGTCAGTTATAGA 57.548 43.478 0.00 0.00 0.00 1.98
2977 6500 5.194432 TCAGAGGAGGTGTCAGTTATAGAC 58.806 45.833 0.00 0.00 36.55 2.59
2978 6501 4.950475 CAGAGGAGGTGTCAGTTATAGACA 59.050 45.833 0.00 0.00 43.23 3.41
2979 6502 5.596361 CAGAGGAGGTGTCAGTTATAGACAT 59.404 44.000 0.00 0.00 46.52 3.06
2980 6503 5.830991 AGAGGAGGTGTCAGTTATAGACATC 59.169 44.000 0.00 0.00 46.52 3.06
2981 6504 5.519808 AGGAGGTGTCAGTTATAGACATCA 58.480 41.667 9.01 0.00 46.88 3.07
2982 6505 5.596361 AGGAGGTGTCAGTTATAGACATCAG 59.404 44.000 9.01 0.00 46.88 2.90
2983 6506 5.221342 GGAGGTGTCAGTTATAGACATCAGG 60.221 48.000 9.01 0.00 46.88 3.86
2984 6507 4.100189 AGGTGTCAGTTATAGACATCAGGC 59.900 45.833 9.01 0.00 46.88 4.85
2985 6508 4.100189 GGTGTCAGTTATAGACATCAGGCT 59.900 45.833 1.98 0.00 46.52 4.58
2986 6509 5.046529 GTGTCAGTTATAGACATCAGGCTG 58.953 45.833 8.58 8.58 46.52 4.85
2987 6510 4.100035 TGTCAGTTATAGACATCAGGCTGG 59.900 45.833 15.73 1.44 40.80 4.85
2988 6511 4.100189 GTCAGTTATAGACATCAGGCTGGT 59.900 45.833 15.73 3.88 36.06 4.00
2989 6512 4.716784 TCAGTTATAGACATCAGGCTGGTT 59.283 41.667 15.73 0.00 0.00 3.67
2990 6513 5.189736 TCAGTTATAGACATCAGGCTGGTTT 59.810 40.000 15.73 0.00 0.00 3.27
2991 6514 5.882557 CAGTTATAGACATCAGGCTGGTTTT 59.117 40.000 15.73 0.00 0.00 2.43
2992 6515 7.047891 CAGTTATAGACATCAGGCTGGTTTTA 58.952 38.462 15.73 0.00 0.00 1.52
2993 6516 7.716998 CAGTTATAGACATCAGGCTGGTTTTAT 59.283 37.037 15.73 7.55 0.00 1.40
2994 6517 7.934120 AGTTATAGACATCAGGCTGGTTTTATC 59.066 37.037 15.73 2.38 0.00 1.75
2995 6518 4.851639 AGACATCAGGCTGGTTTTATCT 57.148 40.909 15.73 4.78 0.00 1.98
2996 6519 5.184892 AGACATCAGGCTGGTTTTATCTT 57.815 39.130 15.73 0.00 0.00 2.40
2997 6520 5.574188 AGACATCAGGCTGGTTTTATCTTT 58.426 37.500 15.73 0.00 0.00 2.52
2998 6521 5.649831 AGACATCAGGCTGGTTTTATCTTTC 59.350 40.000 15.73 0.00 0.00 2.62
2999 6522 5.324409 ACATCAGGCTGGTTTTATCTTTCA 58.676 37.500 15.73 0.00 0.00 2.69
3000 6523 5.954150 ACATCAGGCTGGTTTTATCTTTCAT 59.046 36.000 15.73 0.00 0.00 2.57
3029 6552 4.825422 TCTTTCTCACAGAGGTTGCTATG 58.175 43.478 0.00 0.00 0.00 2.23
3030 6553 2.680312 TCTCACAGAGGTTGCTATGC 57.320 50.000 0.00 0.00 0.00 3.14
3031 6554 1.901833 TCTCACAGAGGTTGCTATGCA 59.098 47.619 0.00 0.00 36.47 3.96
3032 6555 2.302733 TCTCACAGAGGTTGCTATGCAA 59.697 45.455 0.45 0.45 46.80 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.273825 TGTTGAGAATTAGAGAATACCTCGC 58.726 40.000 0.00 0.00 46.49 5.03
1 2 7.923344 ACATGTTGAGAATTAGAGAATACCTCG 59.077 37.037 0.00 0.00 46.49 4.63
2 3 9.039870 CACATGTTGAGAATTAGAGAATACCTC 57.960 37.037 0.00 0.00 42.28 3.85
3 4 7.989741 CCACATGTTGAGAATTAGAGAATACCT 59.010 37.037 0.00 0.00 0.00 3.08
5 6 7.280876 TGCCACATGTTGAGAATTAGAGAATAC 59.719 37.037 0.14 0.00 0.00 1.89
6 7 7.337938 TGCCACATGTTGAGAATTAGAGAATA 58.662 34.615 0.14 0.00 0.00 1.75
7 8 6.182627 TGCCACATGTTGAGAATTAGAGAAT 58.817 36.000 0.14 0.00 0.00 2.40
8 9 5.559770 TGCCACATGTTGAGAATTAGAGAA 58.440 37.500 0.14 0.00 0.00 2.87
9 10 5.164620 TGCCACATGTTGAGAATTAGAGA 57.835 39.130 0.14 0.00 0.00 3.10
10 11 5.008415 GGATGCCACATGTTGAGAATTAGAG 59.992 44.000 0.14 0.00 0.00 2.43
12 13 4.885907 AGGATGCCACATGTTGAGAATTAG 59.114 41.667 0.14 0.00 0.00 1.73
13 14 4.858850 AGGATGCCACATGTTGAGAATTA 58.141 39.130 0.14 0.00 0.00 1.40
14 15 3.705051 AGGATGCCACATGTTGAGAATT 58.295 40.909 0.14 0.00 0.00 2.17
24 3296 5.589367 AAACATAGGATAGGATGCCACAT 57.411 39.130 0.00 0.00 0.00 3.21
84 3356 3.506398 CCACAACCCATTTTAGGTCCTT 58.494 45.455 0.00 0.00 36.27 3.36
93 3365 0.560688 ACACTCCCCACAACCCATTT 59.439 50.000 0.00 0.00 0.00 2.32
97 3369 0.112412 ATTGACACTCCCCACAACCC 59.888 55.000 0.00 0.00 0.00 4.11
158 3430 7.280205 GGACCTCGATGTAAACTTTTATCATGT 59.720 37.037 0.00 0.00 0.00 3.21
214 3486 2.282816 CGGTGGTGGCCCATTCAA 60.283 61.111 0.00 0.00 44.35 2.69
228 3500 1.895238 ACGGCAATAGTAGTGCGGT 59.105 52.632 24.53 24.53 46.82 5.68
229 3501 1.856597 GTAACGGCAATAGTAGTGCGG 59.143 52.381 23.38 23.38 45.07 5.69
281 3553 6.750501 GCATGTGTACGAAGACTTATTGACTA 59.249 38.462 0.00 0.00 0.00 2.59
288 3560 2.093869 GGGGCATGTGTACGAAGACTTA 60.094 50.000 0.00 0.00 0.00 2.24
297 3569 5.527582 CACTAATCTTTAGGGGCATGTGTAC 59.472 44.000 0.00 0.00 0.00 2.90
314 3586 1.603172 CGTGGATCCGAGGCACTAATC 60.603 57.143 7.39 0.00 41.55 1.75
324 3596 3.116463 CGATGACCGTGGATCCGA 58.884 61.111 7.39 0.00 0.00 4.55
333 3605 0.982673 GAGTTCAACGACGATGACCG 59.017 55.000 7.37 0.00 45.44 4.79
407 3682 3.293311 TGCTACGACAAGGTTAGTGTC 57.707 47.619 0.00 0.00 41.66 3.67
495 3770 1.453155 GCTTCATCTTTCGGGCTTCA 58.547 50.000 0.00 0.00 0.00 3.02
585 3894 9.466497 TTCTTCTAATTGCCAATATGAGTTCTT 57.534 29.630 0.00 0.00 0.00 2.52
1269 4622 1.681666 CCCAGAGAGGCAGAAGCAA 59.318 57.895 0.00 0.00 44.61 3.91
1395 4760 4.843516 AGATTCTTGGACTTCTGAAGGTCT 59.156 41.667 20.61 0.53 33.46 3.85
1401 4766 6.868864 CGTTCTTTAGATTCTTGGACTTCTGA 59.131 38.462 0.00 0.00 0.00 3.27
1441 4828 1.948145 GACGACGAGGATATCACACCT 59.052 52.381 0.00 0.00 39.41 4.00
1541 4943 0.541998 TTTCTCGGTCTGGAGGAGCA 60.542 55.000 0.00 0.00 42.06 4.26
1549 4951 1.738099 CGGCACCTTTCTCGGTCTG 60.738 63.158 0.00 0.00 34.29 3.51
1886 5300 2.052690 AGGATAGTCGCTGCGGTGT 61.053 57.895 23.03 8.23 0.00 4.16
1890 5304 0.661780 GTAGCAGGATAGTCGCTGCG 60.662 60.000 17.25 17.25 41.96 5.18
1912 5326 1.227527 CACAGTGGTGTTGCTCGGA 60.228 57.895 0.00 0.00 40.24 4.55
2084 5498 4.134379 AGCTCATTACCACTCTGACATG 57.866 45.455 0.00 0.00 0.00 3.21
2148 5566 5.643664 TGTGACATTTTGCATCTCAATAGC 58.356 37.500 0.00 0.00 34.12 2.97
2153 5571 6.772770 CAAAATGTGACATTTTGCATCTCA 57.227 33.333 36.06 0.00 40.60 3.27
2626 6136 6.504398 TGATTAACACGCAGAGTAGATAAGG 58.496 40.000 0.00 0.00 0.00 2.69
2710 6220 1.484240 AGAGAATGCGAAAGGGAGGAG 59.516 52.381 0.00 0.00 0.00 3.69
2736 6246 6.310467 TCTCATTTCCGACTAGAAATTTGACG 59.690 38.462 0.00 0.00 42.46 4.35
2810 6331 1.024271 CATCAAGGGCGTGGGTATTG 58.976 55.000 0.00 0.00 0.00 1.90
2820 6341 5.075858 TGAAATCACAAATCATCAAGGGC 57.924 39.130 0.00 0.00 0.00 5.19
2856 6379 9.594478 TTTCATGATTTGATGAGGATTTTCATG 57.406 29.630 0.00 0.00 37.90 3.07
2924 6447 9.284968 ACAGAAGCAAAACATTATGTACTACTT 57.715 29.630 0.00 1.09 29.59 2.24
2925 6448 8.848474 ACAGAAGCAAAACATTATGTACTACT 57.152 30.769 0.00 0.00 29.59 2.57
2926 6449 9.893305 AAACAGAAGCAAAACATTATGTACTAC 57.107 29.630 0.00 0.00 31.07 2.73
2947 6470 4.221703 ACTGACACCTCCTCTGATAAACAG 59.778 45.833 0.00 0.00 46.97 3.16
2948 6471 4.160329 ACTGACACCTCCTCTGATAAACA 58.840 43.478 0.00 0.00 0.00 2.83
2949 6472 4.810191 ACTGACACCTCCTCTGATAAAC 57.190 45.455 0.00 0.00 0.00 2.01
2950 6473 8.059461 TCTATAACTGACACCTCCTCTGATAAA 58.941 37.037 0.00 0.00 0.00 1.40
2951 6474 7.502895 GTCTATAACTGACACCTCCTCTGATAA 59.497 40.741 0.00 0.00 34.80 1.75
2952 6475 6.999272 GTCTATAACTGACACCTCCTCTGATA 59.001 42.308 0.00 0.00 34.80 2.15
2953 6476 5.830991 GTCTATAACTGACACCTCCTCTGAT 59.169 44.000 0.00 0.00 34.80 2.90
2954 6477 5.194432 GTCTATAACTGACACCTCCTCTGA 58.806 45.833 0.00 0.00 34.80 3.27
2955 6478 4.950475 TGTCTATAACTGACACCTCCTCTG 59.050 45.833 0.00 0.00 39.23 3.35
2956 6479 5.194473 TGTCTATAACTGACACCTCCTCT 57.806 43.478 0.00 0.00 39.23 3.69
2957 6480 5.594725 TGATGTCTATAACTGACACCTCCTC 59.405 44.000 0.00 0.00 45.57 3.71
2958 6481 5.519808 TGATGTCTATAACTGACACCTCCT 58.480 41.667 0.00 0.00 45.57 3.69
2959 6482 5.221342 CCTGATGTCTATAACTGACACCTCC 60.221 48.000 0.00 0.00 45.57 4.30
2960 6483 5.737635 GCCTGATGTCTATAACTGACACCTC 60.738 48.000 0.00 0.00 45.57 3.85
2961 6484 4.100189 GCCTGATGTCTATAACTGACACCT 59.900 45.833 0.00 0.00 45.57 4.00
2962 6485 4.100189 AGCCTGATGTCTATAACTGACACC 59.900 45.833 0.00 0.00 45.57 4.16
2963 6486 5.046529 CAGCCTGATGTCTATAACTGACAC 58.953 45.833 0.00 0.00 45.57 3.67
2964 6487 4.100035 CCAGCCTGATGTCTATAACTGACA 59.900 45.833 0.00 0.00 46.58 3.58
2965 6488 4.100189 ACCAGCCTGATGTCTATAACTGAC 59.900 45.833 0.00 0.00 35.21 3.51
2966 6489 4.290093 ACCAGCCTGATGTCTATAACTGA 58.710 43.478 0.00 0.00 0.00 3.41
2967 6490 4.679373 ACCAGCCTGATGTCTATAACTG 57.321 45.455 0.00 0.00 0.00 3.16
2968 6491 5.700402 AAACCAGCCTGATGTCTATAACT 57.300 39.130 0.00 0.00 0.00 2.24
2969 6492 7.934120 AGATAAAACCAGCCTGATGTCTATAAC 59.066 37.037 0.00 0.00 0.00 1.89
2970 6493 8.034313 AGATAAAACCAGCCTGATGTCTATAA 57.966 34.615 0.00 0.00 0.00 0.98
2971 6494 7.618019 AGATAAAACCAGCCTGATGTCTATA 57.382 36.000 0.00 0.00 0.00 1.31
2972 6495 6.506538 AGATAAAACCAGCCTGATGTCTAT 57.493 37.500 0.00 0.00 0.00 1.98
2973 6496 5.957771 AGATAAAACCAGCCTGATGTCTA 57.042 39.130 0.00 0.00 0.00 2.59
2974 6497 4.851639 AGATAAAACCAGCCTGATGTCT 57.148 40.909 0.00 0.00 0.00 3.41
2975 6498 5.415701 TGAAAGATAAAACCAGCCTGATGTC 59.584 40.000 0.00 0.00 0.00 3.06
2976 6499 5.324409 TGAAAGATAAAACCAGCCTGATGT 58.676 37.500 0.00 0.00 0.00 3.06
2977 6500 5.902613 TGAAAGATAAAACCAGCCTGATG 57.097 39.130 0.00 0.00 0.00 3.07
2978 6501 7.398332 AGAAATGAAAGATAAAACCAGCCTGAT 59.602 33.333 0.00 0.00 0.00 2.90
2979 6502 6.721208 AGAAATGAAAGATAAAACCAGCCTGA 59.279 34.615 0.00 0.00 0.00 3.86
2980 6503 6.810182 CAGAAATGAAAGATAAAACCAGCCTG 59.190 38.462 0.00 0.00 0.00 4.85
2981 6504 6.494835 ACAGAAATGAAAGATAAAACCAGCCT 59.505 34.615 0.00 0.00 0.00 4.58
2982 6505 6.691508 ACAGAAATGAAAGATAAAACCAGCC 58.308 36.000 0.00 0.00 0.00 4.85
2983 6506 8.084684 AGAACAGAAATGAAAGATAAAACCAGC 58.915 33.333 0.00 0.00 0.00 4.85
2984 6507 9.971922 AAGAACAGAAATGAAAGATAAAACCAG 57.028 29.630 0.00 0.00 0.00 4.00
2991 6514 9.559732 TGTGAGAAAGAACAGAAATGAAAGATA 57.440 29.630 0.00 0.00 0.00 1.98
2992 6515 8.455903 TGTGAGAAAGAACAGAAATGAAAGAT 57.544 30.769 0.00 0.00 0.00 2.40
2993 6516 7.864108 TGTGAGAAAGAACAGAAATGAAAGA 57.136 32.000 0.00 0.00 0.00 2.52
3029 6552 5.190992 TCAATCCATCAACTATGCATTGC 57.809 39.130 3.54 0.46 41.65 3.56
3030 6553 6.802608 AGTTCAATCCATCAACTATGCATTG 58.197 36.000 3.54 5.32 42.77 2.82
3031 6554 7.123098 TGAAGTTCAATCCATCAACTATGCATT 59.877 33.333 3.54 0.00 33.92 3.56
3032 6555 6.604396 TGAAGTTCAATCCATCAACTATGCAT 59.396 34.615 3.79 3.79 33.92 3.96
3033 6556 5.945191 TGAAGTTCAATCCATCAACTATGCA 59.055 36.000 2.20 0.00 33.92 3.96


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

AutoCloner maintained by Alex Coulton.