Multiple sequence alignment - TraesCS7B01G311500

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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 TraesCS7B01G311500 chr7B 100.000 3512 0 0 1 3512 556739114 556735603 0.000000e+00 6486
1 TraesCS7B01G311500 chr7D 92.571 3540 161 32 1 3512 522919534 522916069 0.000000e+00 4987
2 TraesCS7B01G311500 chr7D 82.812 256 39 5 120 372 31567254 31567001 1.270000e-54 224
3 TraesCS7B01G311500 chr7A 93.899 2721 124 22 1 2704 603099625 603096930 0.000000e+00 4067
4 TraesCS7B01G311500 chr7A 90.171 234 17 5 2694 2923 603090018 603089787 2.050000e-77 300
5 TraesCS7B01G311500 chr3D 82.528 269 38 6 120 384 523338521 523338258 9.810000e-56 228
6 TraesCS7B01G311500 chr5D 82.143 252 44 1 119 369 485912321 485912572 7.640000e-52 215
7 TraesCS7B01G311500 chr5D 79.134 254 52 1 120 372 28665156 28664903 1.300000e-39 174
8 TraesCS7B01G311500 chrUn 82.072 251 44 1 120 369 92970871 92971121 2.750000e-51 213
9 TraesCS7B01G311500 chr3A 79.851 268 45 8 114 377 56733190 56733452 1.660000e-43 187
10 TraesCS7B01G311500 chr5B 79.600 250 50 1 124 372 43348756 43348507 1.000000e-40 178


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 TraesCS7B01G311500 chr7B 556735603 556739114 3511 True 6486 6486 100.000 1 3512 1 chr7B.!!$R1 3511
1 TraesCS7B01G311500 chr7D 522916069 522919534 3465 True 4987 4987 92.571 1 3512 1 chr7D.!!$R2 3511
2 TraesCS7B01G311500 chr7A 603096930 603099625 2695 True 4067 4067 93.899 1 2704 1 chr7A.!!$R2 2703

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
613 636 0.625849 GTTGATCCACCCTGACCCAT 59.374 55.0 0.0 0.0 0.00 4.00 F
1035 1074 1.099689 CTGTGATGATGTGCATGGCA 58.900 50.0 0.0 0.0 37.34 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2206 0.397254 AGGTAGCAGTAGCCCGTCAT 60.397 55.0 0.00 0.0 43.56 3.06 R
2769 2808 0.249699 AGACGCATGACAACCGTTGA 60.250 50.0 18.19 0.0 35.06 3.18 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
32 33 4.525996 CCAATGTGTCATTGGGTCATAGA 58.474 43.478 25.14 0.00 43.58 1.98
110 112 8.696374 CATCTTAAAATGTACTCCCTCTGTCTA 58.304 37.037 0.00 0.00 0.00 2.59
111 113 8.294954 TCTTAAAATGTACTCCCTCTGTCTAG 57.705 38.462 0.00 0.00 0.00 2.43
129 131 6.261435 TGTCTAGAAAGAAATACTCCCTCCA 58.739 40.000 0.00 0.00 32.16 3.86
152 154 7.922278 TCCATTCCACAATGTAGTACGTATAAC 59.078 37.037 0.00 0.71 38.22 1.89
312 314 5.643379 AACACTTTTCTCTGCAAACTTGA 57.357 34.783 0.00 0.00 0.00 3.02
394 412 7.069331 CAGATGAAGAGTGTTTATAGAGGGAGT 59.931 40.741 0.00 0.00 0.00 3.85
395 413 8.282982 AGATGAAGAGTGTTTATAGAGGGAGTA 58.717 37.037 0.00 0.00 0.00 2.59
396 414 7.642082 TGAAGAGTGTTTATAGAGGGAGTAC 57.358 40.000 0.00 0.00 0.00 2.73
443 461 2.270205 CGGCCTGGCTTCATGACT 59.730 61.111 19.68 0.00 0.00 3.41
463 481 4.718961 ACTGAGCAAGTACATCAACCTTT 58.281 39.130 0.00 0.00 37.36 3.11
494 512 3.735208 CGACTCAGATTACTGCATTCGGT 60.735 47.826 0.00 0.00 43.17 4.69
613 636 0.625849 GTTGATCCACCCTGACCCAT 59.374 55.000 0.00 0.00 0.00 4.00
712 735 1.550072 TGCTCATCTGATCGTTGACCA 59.450 47.619 0.00 0.00 0.00 4.02
781 806 4.201980 CGACATTGCTGATCATGGACATTT 60.202 41.667 0.00 0.00 0.00 2.32
826 851 1.675415 GCTTGTCTTCTCCTGCTCCAG 60.675 57.143 0.00 0.00 0.00 3.86
868 894 4.646572 TGGCTTCTTCTTCTTCTTCTTCC 58.353 43.478 0.00 0.00 0.00 3.46
971 1010 1.382420 CCACTGGAGGGAGCTAGCT 60.382 63.158 19.45 19.45 0.00 3.32
1035 1074 1.099689 CTGTGATGATGTGCATGGCA 58.900 50.000 0.00 0.00 37.34 4.92
1068 1107 1.895231 GGTTTCTTTGACCGGCGGT 60.895 57.895 34.81 34.81 39.44 5.68
1368 1407 4.008933 GTGCTCTGGTCCACCGCT 62.009 66.667 8.63 0.00 39.43 5.52
1409 1448 1.784525 GTTCTCCTCAACACGTCCAG 58.215 55.000 0.00 0.00 0.00 3.86
1427 1466 2.617276 CCAGCCTTCAGATTCAGAGCAA 60.617 50.000 0.00 0.00 0.00 3.91
1429 1468 2.039480 AGCCTTCAGATTCAGAGCAACA 59.961 45.455 0.00 0.00 0.00 3.33
1524 1563 3.414700 GTGGCGCTTCACTCCGTG 61.415 66.667 7.64 0.00 34.98 4.94
1593 1632 4.451150 GAGCCGCCACCGATGTCA 62.451 66.667 0.00 0.00 36.29 3.58
1596 1635 2.186644 CCGCCACCGATGTCATCA 59.813 61.111 13.22 0.00 36.29 3.07
1660 1699 2.825836 CCAAGGCCCAGATCGTGC 60.826 66.667 0.00 0.00 0.00 5.34
1729 1768 1.134371 GCATGTACCAGAAGGAGGGAC 60.134 57.143 0.00 0.00 40.59 4.46
1887 1926 4.724602 GACTCGTGCGAGCTGCCA 62.725 66.667 19.86 0.00 45.54 4.92
2167 2206 3.342627 GCGCGGTGTACAGCAACA 61.343 61.111 23.74 0.00 36.87 3.33
2168 2207 2.677003 GCGCGGTGTACAGCAACAT 61.677 57.895 23.74 0.00 36.87 2.71
2466 2505 4.202409 CCCTACAAGAATCTGGGATCCTTC 60.202 50.000 12.58 7.53 40.23 3.46
2606 2645 3.766691 GGTGCGGGAAGTAGGCGA 61.767 66.667 0.00 0.00 0.00 5.54
2646 2685 4.116238 GGAGAAGAAAGCTAATCCGACAG 58.884 47.826 0.00 0.00 0.00 3.51
2689 2728 4.221482 AGAAAAGAAATGCCAATCTGGTCC 59.779 41.667 0.00 0.00 40.46 4.46
2738 2777 1.373570 GCTCGGGGAACTTCAAGATG 58.626 55.000 0.00 0.00 0.00 2.90
2739 2778 2.014068 GCTCGGGGAACTTCAAGATGG 61.014 57.143 0.00 0.00 0.00 3.51
2760 2799 1.204941 GGACACTCATCTAGCCGTTGT 59.795 52.381 0.00 0.00 0.00 3.32
2769 2808 6.823689 ACTCATCTAGCCGTTGTATTGAAATT 59.176 34.615 0.00 0.00 0.00 1.82
2807 2846 0.478072 TTCCAGCTCAAGCCTTTCCA 59.522 50.000 0.00 0.00 43.38 3.53
2829 2868 6.380274 TCCATCTACAGTTTATTCCTTCTCGT 59.620 38.462 0.00 0.00 0.00 4.18
2837 2876 0.531200 ATTCCTTCTCGTGACCGTCC 59.469 55.000 0.00 0.00 35.01 4.79
2840 2879 1.444553 CTTCTCGTGACCGTCCTGC 60.445 63.158 0.00 0.00 35.01 4.85
2863 2902 2.579201 GCAGCACGGCTCTCCTTA 59.421 61.111 0.00 0.00 36.40 2.69
2864 2903 1.520342 GCAGCACGGCTCTCCTTAG 60.520 63.158 0.00 0.00 36.40 2.18
2865 2904 1.949847 GCAGCACGGCTCTCCTTAGA 61.950 60.000 0.00 0.00 36.40 2.10
2866 2905 0.749649 CAGCACGGCTCTCCTTAGAT 59.250 55.000 0.00 0.00 36.40 1.98
2867 2906 1.957177 CAGCACGGCTCTCCTTAGATA 59.043 52.381 0.00 0.00 36.40 1.98
2874 2913 4.142790 CGGCTCTCCTTAGATAACTACCA 58.857 47.826 0.00 0.00 0.00 3.25
2883 2922 8.642935 TCCTTAGATAACTACCAGATCATCAG 57.357 38.462 0.00 0.00 0.00 2.90
2897 2936 4.699735 AGATCATCAGCATACTCTACCTCG 59.300 45.833 0.00 0.00 0.00 4.63
2918 2957 6.744537 CCTCGATTCATCATTTCAAACTTCAC 59.255 38.462 0.00 0.00 0.00 3.18
2953 2992 8.529424 TTTTCGGTATCAACTCCTTCTATCTA 57.471 34.615 0.00 0.00 0.00 1.98
2961 3000 5.473846 TCAACTCCTTCTATCTATACCGCAG 59.526 44.000 0.00 0.00 0.00 5.18
2963 3002 5.386924 ACTCCTTCTATCTATACCGCAGTT 58.613 41.667 0.00 0.00 0.00 3.16
2968 3007 5.122512 TCTATCTATACCGCAGTTGAAGC 57.877 43.478 0.00 0.00 0.00 3.86
2976 3015 1.442769 CGCAGTTGAAGCACCTACAT 58.557 50.000 0.00 0.00 0.00 2.29
2983 3022 6.546395 CAGTTGAAGCACCTACATGTAAATC 58.454 40.000 7.06 0.64 0.00 2.17
2985 3024 6.942576 AGTTGAAGCACCTACATGTAAATCTT 59.057 34.615 7.06 7.81 0.00 2.40
2990 3029 5.643777 AGCACCTACATGTAAATCTTGTGTC 59.356 40.000 7.06 4.99 36.20 3.67
3000 3039 6.943981 TGTAAATCTTGTGTCTTTCTTGTCG 58.056 36.000 0.00 0.00 0.00 4.35
3009 3048 3.007635 GTCTTTCTTGTCGGTAATGGGG 58.992 50.000 0.00 0.00 0.00 4.96
3017 3056 1.413812 GTCGGTAATGGGGGTAATCGT 59.586 52.381 0.00 0.00 0.00 3.73
3046 3085 7.903995 ACCATTGTAAAATAAAAGCATGTGG 57.096 32.000 0.00 0.00 0.00 4.17
3070 3109 2.832563 TGCACATTCACAAGAACTCGA 58.167 42.857 0.00 0.00 36.39 4.04
3106 3145 1.181786 CGCCTCTCCTCTTTCTCACT 58.818 55.000 0.00 0.00 0.00 3.41
3118 3157 5.028549 TCTTTCTCACTAGGATTGATGCC 57.971 43.478 0.00 0.00 0.00 4.40
3124 3163 3.973305 TCACTAGGATTGATGCCCACATA 59.027 43.478 0.00 0.00 36.35 2.29
3126 3165 2.965671 AGGATTGATGCCCACATAGG 57.034 50.000 0.00 0.00 36.35 2.57
3148 3187 6.122277 AGGCAATTATCATCTCCTTTTCGAA 58.878 36.000 0.00 0.00 0.00 3.71
3159 3198 1.135972 CCTTTTCGAATGTGTGCCGAG 60.136 52.381 0.00 0.00 33.66 4.63
3161 3200 1.428448 TTTCGAATGTGTGCCGAGAG 58.572 50.000 0.00 0.00 33.66 3.20
3187 3226 5.983540 AGTTTCTACCATGGAAGCTCTTAG 58.016 41.667 21.47 7.88 30.51 2.18
3190 3229 2.409948 ACCATGGAAGCTCTTAGTGC 57.590 50.000 21.47 0.00 0.00 4.40
3231 3273 2.231235 TGTCTCGCTCAACTGCTAATCA 59.769 45.455 0.00 0.00 0.00 2.57
3240 3282 1.755179 ACTGCTAATCATGGCCACAC 58.245 50.000 8.16 0.00 30.79 3.82
3241 3283 1.027357 CTGCTAATCATGGCCACACC 58.973 55.000 8.16 0.00 39.84 4.16
3274 3316 8.282592 GGAAATTGATTCAACCAAAAAGCTAAC 58.717 33.333 0.15 0.00 39.98 2.34
3324 3366 4.788679 TCTGTAGTGATCTATCCCGTTGA 58.211 43.478 0.00 0.00 0.00 3.18
3333 3375 3.934068 TCTATCCCGTTGACCAAAGAAC 58.066 45.455 0.00 0.00 0.00 3.01
3346 3388 4.332828 ACCAAAGAACAAGTACATAGCCC 58.667 43.478 0.00 0.00 0.00 5.19
3350 3392 4.124851 AGAACAAGTACATAGCCCGAAG 57.875 45.455 0.00 0.00 0.00 3.79
3357 3399 5.864418 AGTACATAGCCCGAAGAATACAA 57.136 39.130 0.00 0.00 0.00 2.41
3416 3460 0.036671 GGACAACCCAACGAGGTAGG 60.037 60.000 0.00 0.00 40.05 3.18
3423 3468 1.272807 CCAACGAGGTAGGAGGGAAA 58.727 55.000 0.00 0.00 0.00 3.13
3424 3469 1.207329 CCAACGAGGTAGGAGGGAAAG 59.793 57.143 0.00 0.00 0.00 2.62
3428 3473 1.796017 GAGGTAGGAGGGAAAGGGAG 58.204 60.000 0.00 0.00 0.00 4.30
3438 3483 0.697854 GGAAAGGGAGGGGGCTATGA 60.698 60.000 0.00 0.00 0.00 2.15
3445 3490 0.464554 GAGGGGGCTATGACAAGTGC 60.465 60.000 0.00 0.00 0.00 4.40
3447 3492 0.837272 GGGGGCTATGACAAGTGCTA 59.163 55.000 0.00 0.00 0.00 3.49
3450 3495 2.158755 GGGGCTATGACAAGTGCTATGT 60.159 50.000 0.00 0.00 0.00 2.29
3458 3503 2.480419 GACAAGTGCTATGTGTGTGACC 59.520 50.000 0.00 0.00 0.00 4.02
3460 3505 0.037326 AGTGCTATGTGTGTGACCGG 60.037 55.000 0.00 0.00 0.00 5.28
3461 3506 1.019278 GTGCTATGTGTGTGACCGGG 61.019 60.000 6.32 0.00 0.00 5.73
3462 3507 1.295423 GCTATGTGTGTGACCGGGT 59.705 57.895 6.32 0.00 0.00 5.28
3463 3508 1.019278 GCTATGTGTGTGACCGGGTG 61.019 60.000 3.30 0.00 0.00 4.61
3464 3509 0.606096 CTATGTGTGTGACCGGGTGA 59.394 55.000 3.30 0.00 0.00 4.02
3465 3510 0.319083 TATGTGTGTGACCGGGTGAC 59.681 55.000 10.04 10.04 0.00 3.67
3466 3511 1.691195 ATGTGTGTGACCGGGTGACA 61.691 55.000 15.74 15.74 0.00 3.58
3467 3512 1.594293 GTGTGTGACCGGGTGACAG 60.594 63.158 20.02 0.00 29.26 3.51
3468 3513 2.665185 GTGTGACCGGGTGACAGC 60.665 66.667 20.02 11.00 29.26 4.40
3469 3514 3.157949 TGTGACCGGGTGACAGCA 61.158 61.111 15.74 0.00 0.00 4.41
3470 3515 2.110213 GTGACCGGGTGACAGCAA 59.890 61.111 12.12 0.00 0.00 3.91
3471 3516 2.110213 TGACCGGGTGACAGCAAC 59.890 61.111 3.30 0.00 0.00 4.17
3483 3528 2.375174 TGACAGCAACTTAGGAACCCAT 59.625 45.455 0.00 0.00 0.00 4.00
3488 3533 3.010584 AGCAACTTAGGAACCCATGACAT 59.989 43.478 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.666678 AGAATCTATGACCCAATGACACATT 58.333 36.000 0.00 0.00 0.00 2.71
32 33 6.946009 TGAACCTTCGATTTTAAGGGAAGAAT 59.054 34.615 5.14 0.00 46.56 2.40
110 112 5.492524 TGGAATGGAGGGAGTATTTCTTTCT 59.507 40.000 0.00 0.00 0.00 2.52
111 113 5.590663 GTGGAATGGAGGGAGTATTTCTTTC 59.409 44.000 0.00 0.00 0.00 2.62
129 131 9.880157 AAAGTTATACGTACTACATTGTGGAAT 57.120 29.630 7.20 0.00 0.00 3.01
312 314 9.788960 GAGAAGTCAAACTTTACAAACTTTGAT 57.211 29.630 8.55 0.00 38.80 2.57
385 403 4.900706 TCCAGGTACTAGTACTCCCTCTA 58.099 47.826 27.71 8.36 36.02 2.43
394 412 7.844493 TTTTCTTTCACTCCAGGTACTAGTA 57.156 36.000 0.00 0.00 36.02 1.82
395 413 6.742559 TTTTCTTTCACTCCAGGTACTAGT 57.257 37.500 0.00 0.00 36.02 2.57
396 414 6.595716 CCATTTTCTTTCACTCCAGGTACTAG 59.404 42.308 0.00 0.00 36.02 2.57
443 461 4.887071 ACAAAAGGTTGATGTACTTGCTCA 59.113 37.500 0.00 0.00 38.20 4.26
463 481 0.038251 AATCTGAGTCGCGAGCACAA 60.038 50.000 10.24 0.27 0.00 3.33
494 512 7.124147 TGAACAGATCTGGTATCACTTGTGATA 59.876 37.037 26.08 16.69 34.19 2.15
613 636 2.708216 TGCTGTTGGAAAGTGTGAGA 57.292 45.000 0.00 0.00 0.00 3.27
712 735 1.296002 GGTGGGTGGGATAGAGGTTT 58.704 55.000 0.00 0.00 0.00 3.27
781 806 5.568825 GCCGGGAATATTTATCTGCTAGTGA 60.569 44.000 2.18 0.00 0.00 3.41
826 851 4.690122 CCAATGAGAATTTGAGATTGGGC 58.310 43.478 0.00 0.00 39.53 5.36
953 992 0.105964 TAGCTAGCTCCCTCCAGTGG 60.106 60.000 23.26 1.40 0.00 4.00
1131 1170 0.179124 GCTGGAAGTGCGAGTAGGAG 60.179 60.000 0.00 0.00 35.30 3.69
1380 1419 3.411418 GAGGAGAACGGCGCGATCA 62.411 63.158 12.10 0.00 31.23 2.92
1383 1422 3.676605 TTGAGGAGAACGGCGCGA 61.677 61.111 12.10 0.00 0.00 5.87
1409 1448 2.419324 CTGTTGCTCTGAATCTGAAGGC 59.581 50.000 0.00 0.00 0.00 4.35
1427 1466 2.281070 CGGCAACAGGTGAGCTGT 60.281 61.111 12.08 12.08 36.49 4.40
1429 1468 2.281070 CACGGCAACAGGTGAGCT 60.281 61.111 0.00 0.00 36.25 4.09
1588 1627 2.202932 GACGCCGCCTGATGACAT 60.203 61.111 0.00 0.00 0.00 3.06
1749 1788 1.292061 CGTGGTTGAAGGTGTCGAAA 58.708 50.000 0.00 0.00 0.00 3.46
2167 2206 0.397254 AGGTAGCAGTAGCCCGTCAT 60.397 55.000 0.00 0.00 43.56 3.06
2168 2207 1.000019 AGGTAGCAGTAGCCCGTCA 60.000 57.895 0.00 0.00 43.56 4.35
2626 2665 3.769844 TCCTGTCGGATTAGCTTTCTTCT 59.230 43.478 0.00 0.00 33.30 2.85
2646 2685 1.749258 GCCCAGAAACCACCGATCC 60.749 63.158 0.00 0.00 0.00 3.36
2648 2687 2.046314 CGCCCAGAAACCACCGAT 60.046 61.111 0.00 0.00 0.00 4.18
2657 2696 2.228822 GCATTTCTTTTCTCGCCCAGAA 59.771 45.455 0.00 0.00 39.56 3.02
2705 2744 4.570663 GAGCCGTCGATGGTCCGG 62.571 72.222 24.33 15.73 44.46 5.14
2726 2765 3.244561 TGAGTGTCCCCATCTTGAAGTTC 60.245 47.826 0.00 0.00 0.00 3.01
2738 2777 1.043673 ACGGCTAGATGAGTGTCCCC 61.044 60.000 0.00 0.00 0.00 4.81
2739 2778 0.824759 AACGGCTAGATGAGTGTCCC 59.175 55.000 0.00 0.00 0.00 4.46
2760 2799 5.861251 GCATGACAACCGTTGAATTTCAATA 59.139 36.000 18.19 0.00 38.79 1.90
2769 2808 0.249699 AGACGCATGACAACCGTTGA 60.250 50.000 18.19 0.00 35.06 3.18
2778 2817 0.390340 TGAGCTGGAAGACGCATGAC 60.390 55.000 0.00 0.00 34.07 3.06
2779 2818 0.321346 TTGAGCTGGAAGACGCATGA 59.679 50.000 0.00 0.00 34.07 3.07
2807 2846 7.259161 GTCACGAGAAGGAATAAACTGTAGAT 58.741 38.462 0.00 0.00 0.00 1.98
2854 2893 6.717540 TGATCTGGTAGTTATCTAAGGAGAGC 59.282 42.308 0.00 0.00 34.35 4.09
2856 2895 8.448816 TGATGATCTGGTAGTTATCTAAGGAGA 58.551 37.037 0.00 0.00 35.71 3.71
2858 2897 7.177568 GCTGATGATCTGGTAGTTATCTAAGGA 59.822 40.741 1.50 0.00 0.00 3.36
2859 2898 7.039434 TGCTGATGATCTGGTAGTTATCTAAGG 60.039 40.741 1.50 0.00 0.00 2.69
2863 2902 6.931790 ATGCTGATGATCTGGTAGTTATCT 57.068 37.500 1.50 0.00 0.00 1.98
2864 2903 7.835822 AGTATGCTGATGATCTGGTAGTTATC 58.164 38.462 1.50 0.00 0.00 1.75
2865 2904 7.673504 AGAGTATGCTGATGATCTGGTAGTTAT 59.326 37.037 1.50 0.00 0.00 1.89
2866 2905 7.007116 AGAGTATGCTGATGATCTGGTAGTTA 58.993 38.462 1.50 0.00 0.00 2.24
2867 2906 5.837979 AGAGTATGCTGATGATCTGGTAGTT 59.162 40.000 1.50 0.00 0.00 2.24
2874 2913 4.699735 CGAGGTAGAGTATGCTGATGATCT 59.300 45.833 0.00 0.00 0.00 2.75
2883 2922 5.378292 TGATGAATCGAGGTAGAGTATGC 57.622 43.478 0.00 0.00 0.00 3.14
2897 2936 9.414295 TCAATGTGAAGTTTGAAATGATGAATC 57.586 29.630 0.00 0.00 0.00 2.52
2918 2957 6.677913 AGTTGATACCGAAAAACCTTCAATG 58.322 36.000 0.00 0.00 0.00 2.82
2927 2966 7.848128 AGATAGAAGGAGTTGATACCGAAAAA 58.152 34.615 0.00 0.00 0.00 1.94
2932 2971 7.987649 GGTATAGATAGAAGGAGTTGATACCG 58.012 42.308 0.00 0.00 30.18 4.02
2933 2972 7.415429 GCGGTATAGATAGAAGGAGTTGATACC 60.415 44.444 0.00 0.00 35.14 2.73
2953 2992 0.324943 AGGTGCTTCAACTGCGGTAT 59.675 50.000 0.00 0.00 26.22 2.73
2961 3000 6.743575 AGATTTACATGTAGGTGCTTCAAC 57.256 37.500 5.56 0.00 0.00 3.18
2963 3002 6.149308 CACAAGATTTACATGTAGGTGCTTCA 59.851 38.462 5.56 0.00 0.00 3.02
2968 3007 7.672983 AAGACACAAGATTTACATGTAGGTG 57.327 36.000 5.56 10.73 0.00 4.00
2976 3015 6.018262 CCGACAAGAAAGACACAAGATTTACA 60.018 38.462 0.00 0.00 0.00 2.41
2983 3022 5.334105 CCATTACCGACAAGAAAGACACAAG 60.334 44.000 0.00 0.00 0.00 3.16
2985 3024 4.062293 CCATTACCGACAAGAAAGACACA 58.938 43.478 0.00 0.00 0.00 3.72
2990 3029 2.290705 ACCCCCATTACCGACAAGAAAG 60.291 50.000 0.00 0.00 0.00 2.62
3000 3039 2.052468 AGGACGATTACCCCCATTACC 58.948 52.381 0.00 0.00 0.00 2.85
3017 3056 9.868277 CATGCTTTTATTTTACAATGGTAAGGA 57.132 29.630 0.00 0.00 40.40 3.36
3046 3085 3.709987 AGTTCTTGTGAATGTGCAAAGC 58.290 40.909 0.00 0.00 34.40 3.51
3053 3092 5.990408 GAACAATCGAGTTCTTGTGAATGT 58.010 37.500 9.62 0.00 43.46 2.71
3070 3109 2.501723 AGGCGACAGATACCAGAACAAT 59.498 45.455 0.00 0.00 0.00 2.71
3118 3157 5.813383 AGGAGATGATAATTGCCTATGTGG 58.187 41.667 0.00 0.00 39.35 4.17
3124 3163 5.684704 TCGAAAAGGAGATGATAATTGCCT 58.315 37.500 0.00 0.00 0.00 4.75
3126 3165 7.377928 CACATTCGAAAAGGAGATGATAATTGC 59.622 37.037 0.00 0.00 0.00 3.56
3148 3187 0.681733 AACTCACTCTCGGCACACAT 59.318 50.000 0.00 0.00 0.00 3.21
3159 3198 3.935828 GCTTCCATGGTAGAAACTCACTC 59.064 47.826 21.61 0.00 0.00 3.51
3161 3200 3.935828 GAGCTTCCATGGTAGAAACTCAC 59.064 47.826 21.61 2.52 36.75 3.51
3187 3226 2.706636 ACATCAGTGTGGTGTGCAC 58.293 52.632 10.75 10.75 40.78 4.57
3241 3283 5.979993 TGGTTGAATCAATTTCCATGGATG 58.020 37.500 17.06 11.57 33.04 3.51
3242 3284 6.623979 TTGGTTGAATCAATTTCCATGGAT 57.376 33.333 17.06 0.00 33.04 3.41
3286 3328 9.911788 ATCACTACAGATGACCTTAATTTGAAT 57.088 29.630 0.00 0.00 0.00 2.57
3300 3342 5.241728 TCAACGGGATAGATCACTACAGATG 59.758 44.000 0.00 0.00 0.00 2.90
3301 3343 5.241949 GTCAACGGGATAGATCACTACAGAT 59.758 44.000 0.00 0.00 0.00 2.90
3302 3344 4.579340 GTCAACGGGATAGATCACTACAGA 59.421 45.833 0.00 0.00 0.00 3.41
3308 3350 3.536956 TTGGTCAACGGGATAGATCAC 57.463 47.619 0.00 0.00 0.00 3.06
3324 3366 4.332828 GGGCTATGTACTTGTTCTTTGGT 58.667 43.478 0.00 0.00 0.00 3.67
3333 3375 5.597806 TGTATTCTTCGGGCTATGTACTTG 58.402 41.667 0.00 0.00 0.00 3.16
3416 3460 2.562973 TAGCCCCCTCCCTTTCCCTC 62.563 65.000 0.00 0.00 0.00 4.30
3423 3468 0.695803 CTTGTCATAGCCCCCTCCCT 60.696 60.000 0.00 0.00 0.00 4.20
3424 3469 0.988678 ACTTGTCATAGCCCCCTCCC 60.989 60.000 0.00 0.00 0.00 4.30
3428 3473 0.837272 TAGCACTTGTCATAGCCCCC 59.163 55.000 0.00 0.00 0.00 5.40
3438 3483 2.494059 GGTCACACACATAGCACTTGT 58.506 47.619 0.00 0.00 0.00 3.16
3445 3490 0.606096 TCACCCGGTCACACACATAG 59.394 55.000 0.00 0.00 0.00 2.23
3447 3492 1.070786 GTCACCCGGTCACACACAT 59.929 57.895 0.00 0.00 0.00 3.21
3450 3495 2.818841 CTGTCACCCGGTCACACA 59.181 61.111 0.00 0.00 0.00 3.72
3458 3503 0.320374 TCCTAAGTTGCTGTCACCCG 59.680 55.000 0.00 0.00 0.00 5.28
3460 3505 2.152016 GGTTCCTAAGTTGCTGTCACC 58.848 52.381 0.00 0.00 0.00 4.02
3461 3506 2.152016 GGGTTCCTAAGTTGCTGTCAC 58.848 52.381 0.00 0.00 0.00 3.67
3462 3507 1.771854 TGGGTTCCTAAGTTGCTGTCA 59.228 47.619 0.00 0.00 0.00 3.58
3463 3508 2.561478 TGGGTTCCTAAGTTGCTGTC 57.439 50.000 0.00 0.00 0.00 3.51
3464 3509 2.375174 TCATGGGTTCCTAAGTTGCTGT 59.625 45.455 0.00 0.00 0.00 4.40
3465 3510 2.749621 GTCATGGGTTCCTAAGTTGCTG 59.250 50.000 0.00 0.00 0.00 4.41
3466 3511 2.375174 TGTCATGGGTTCCTAAGTTGCT 59.625 45.455 0.00 0.00 0.00 3.91
3467 3512 2.790433 TGTCATGGGTTCCTAAGTTGC 58.210 47.619 0.00 0.00 0.00 4.17
3468 3513 4.396166 GTCATGTCATGGGTTCCTAAGTTG 59.604 45.833 12.90 0.00 0.00 3.16
3469 3514 4.589908 GTCATGTCATGGGTTCCTAAGTT 58.410 43.478 12.90 0.00 0.00 2.66
3470 3515 3.369471 CGTCATGTCATGGGTTCCTAAGT 60.369 47.826 12.90 0.00 0.00 2.24
3471 3516 3.118775 TCGTCATGTCATGGGTTCCTAAG 60.119 47.826 12.90 0.00 0.00 2.18
3488 3533 1.227793 TGGCACAAGCATGTCGTCA 60.228 52.632 0.00 0.00 44.61 4.35


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

AutoCloner maintained by Alex Coulton.