Multiple sequence alignment - TraesCS2D01G520800

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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 TraesCS2D01G520800 chr2D 100.000 3317 0 0 1 3317 609775961 609772645 0.000000e+00 6126
1 TraesCS2D01G520800 chr2B 91.841 3162 179 32 1 3138 744167385 744164279 0.000000e+00 4337
2 TraesCS2D01G520800 chr2B 89.286 112 12 0 3179 3290 744164284 744164173 1.240000e-29 141
3 TraesCS2D01G520800 chr2A 89.068 2479 188 37 840 3310 742720059 742717656 0.000000e+00 3000
4 TraesCS2D01G520800 chr2A 94.363 816 34 6 1 812 742720922 742720115 0.000000e+00 1242
5 TraesCS2D01G520800 chr5B 82.743 226 27 5 970 1189 61352857 61352638 1.210000e-44 191


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 TraesCS2D01G520800 chr2D 609772645 609775961 3316 True 6126 6126 100.0000 1 3317 1 chr2D.!!$R1 3316
1 TraesCS2D01G520800 chr2B 744164173 744167385 3212 True 2239 4337 90.5635 1 3290 2 chr2B.!!$R1 3289
2 TraesCS2D01G520800 chr2A 742717656 742720922 3266 True 2121 3000 91.7155 1 3310 2 chr2A.!!$R1 3309

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
172 173 0.095417 GTGCCGACGAGCTGAAATTC 59.905 55.0 0.0 0.0 0.0 2.17 F
1536 1584 0.468029 CCAAGACCCACAACCTGCTT 60.468 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2148 3.06351 TGCTCTTCCATTGTCTTCCAG 57.936 47.619 0.0 0.0 0.0 3.86 R
2407 2455 0.02930 CAACACAAAGCCTCACCGTG 59.971 55.000 0.0 0.0 0.0 4.94 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
76 77 0.895100 TGCTCACTTGGGCATTGGAC 60.895 55.000 0.00 0.00 33.23 4.02
172 173 0.095417 GTGCCGACGAGCTGAAATTC 59.905 55.000 0.00 0.00 0.00 2.17
360 361 3.128188 CCAGAGCAGCAGCAGCAG 61.128 66.667 12.92 0.00 45.49 4.24
481 482 3.708220 GAGAGTGCCGAAGCCCTCG 62.708 68.421 0.00 0.00 46.92 4.63
522 523 1.862147 CCGACGACGCAGACTAACG 60.862 63.158 0.64 0.00 38.29 3.18
537 541 3.693085 GACTAACGACAGACCATACTGGA 59.307 47.826 0.00 0.00 40.96 3.86
540 544 3.314541 ACGACAGACCATACTGGAAAC 57.685 47.619 0.00 0.00 40.96 2.78
732 736 3.571401 CCTGAAACTTTTGATGCCTCTGT 59.429 43.478 0.00 0.00 0.00 3.41
733 737 4.543692 CTGAAACTTTTGATGCCTCTGTG 58.456 43.478 0.00 0.00 0.00 3.66
734 738 3.953612 TGAAACTTTTGATGCCTCTGTGT 59.046 39.130 0.00 0.00 0.00 3.72
735 739 3.996150 AACTTTTGATGCCTCTGTGTG 57.004 42.857 0.00 0.00 0.00 3.82
758 766 4.655963 ACCTAAAGTTGCACATCACTGAT 58.344 39.130 0.00 0.00 0.00 2.90
760 768 4.940046 CCTAAAGTTGCACATCACTGATCT 59.060 41.667 0.00 0.00 0.00 2.75
762 770 4.761235 AAGTTGCACATCACTGATCTTG 57.239 40.909 0.00 0.00 0.00 3.02
763 771 3.748083 AGTTGCACATCACTGATCTTGT 58.252 40.909 0.00 0.00 0.00 3.16
770 778 7.660112 TGCACATCACTGATCTTGTAAAAATT 58.340 30.769 0.00 0.00 0.00 1.82
779 787 4.662468 TCTTGTAAAAATTGCAGTGCCA 57.338 36.364 13.72 0.72 0.00 4.92
806 815 4.676546 TCTGCAAGACTTCATCTACATCG 58.323 43.478 0.00 0.00 38.67 3.84
821 830 3.773860 ACATCGAAATATTGCCGCAAA 57.226 38.095 10.42 0.21 0.00 3.68
830 839 6.019640 CGAAATATTGCCGCAAAGATGAAATT 60.020 34.615 10.42 0.00 0.00 1.82
838 875 5.230726 GCCGCAAAGATGAAATTGTTAGATG 59.769 40.000 0.00 0.00 0.00 2.90
876 913 7.881643 TGGAAATGTGGTTTGAATTTAATCG 57.118 32.000 0.00 0.00 0.00 3.34
877 914 7.661968 TGGAAATGTGGTTTGAATTTAATCGA 58.338 30.769 0.00 0.00 0.00 3.59
890 927 9.992910 TTGAATTTAATCGATTTGACTCAGATG 57.007 29.630 17.19 0.00 0.00 2.90
921 963 1.699634 TGGAGAAGTTTCAGGTCAGGG 59.300 52.381 0.00 0.00 0.00 4.45
924 966 1.202818 AGAAGTTTCAGGTCAGGGCAC 60.203 52.381 0.00 0.00 0.00 5.01
934 977 3.966543 CAGGGCACGGGGGAAAGT 61.967 66.667 0.00 0.00 0.00 2.66
979 1024 2.280119 GCACTCGCACCACACTCA 60.280 61.111 0.00 0.00 38.36 3.41
984 1029 0.529833 CTCGCACCACACTCATCTCT 59.470 55.000 0.00 0.00 0.00 3.10
985 1030 0.528017 TCGCACCACACTCATCTCTC 59.472 55.000 0.00 0.00 0.00 3.20
986 1031 0.529833 CGCACCACACTCATCTCTCT 59.470 55.000 0.00 0.00 0.00 3.10
1423 1471 1.613630 GCCTCCTTCCACCTCCTCA 60.614 63.158 0.00 0.00 0.00 3.86
1536 1584 0.468029 CCAAGACCCACAACCTGCTT 60.468 55.000 0.00 0.00 0.00 3.91
1966 2014 6.820656 CACTTATCATTGCTTCTTCCAGTACT 59.179 38.462 0.00 0.00 0.00 2.73
2100 2148 1.161563 TTCGCCCCGTGTTCTTTGTC 61.162 55.000 0.00 0.00 0.00 3.18
2175 2223 2.688446 ACTCATTGATGCATTGCTGGAG 59.312 45.455 10.49 7.63 0.00 3.86
2187 2235 1.965414 TGCTGGAGAAGGGAATGGTA 58.035 50.000 0.00 0.00 0.00 3.25
2220 2268 1.752683 AGTACGACGAGGAGATGCTT 58.247 50.000 0.00 0.00 0.00 3.91
2253 2301 1.216678 TCACCCAAGCCAAGGAAAGAA 59.783 47.619 0.00 0.00 0.00 2.52
2271 2319 4.124851 AGAACTAGGTACTCAATTGCCG 57.875 45.455 0.00 0.00 41.75 5.69
2298 2346 4.118410 CAGAGTCTGACAGTGATAATGCC 58.882 47.826 15.46 0.00 32.44 4.40
2301 2349 4.511527 AGTCTGACAGTGATAATGCCTTG 58.488 43.478 10.88 0.00 0.00 3.61
2326 2374 3.084039 GGTGTGATCTGAATTCTGGCAA 58.916 45.455 11.89 0.00 0.00 4.52
2328 2376 3.755378 GTGTGATCTGAATTCTGGCAACT 59.245 43.478 11.89 0.00 37.61 3.16
2331 2379 4.574013 GTGATCTGAATTCTGGCAACTAGG 59.426 45.833 11.89 0.00 37.61 3.02
2341 2389 0.673437 GGCAACTAGGCAGCAAAACA 59.327 50.000 0.00 0.00 43.51 2.83
2407 2455 5.468072 AGAGTGTGACTGAAACAATGATGTC 59.532 40.000 0.00 0.00 39.40 3.06
2411 2459 3.498018 TGACTGAAACAATGATGTCACGG 59.502 43.478 0.00 0.00 39.40 4.94
2452 2500 4.033358 GGAGATCTAATGTGAGTTTGTGCG 59.967 45.833 0.00 0.00 0.00 5.34
2457 2505 3.773860 AATGTGAGTTTGTGCGTTTGA 57.226 38.095 0.00 0.00 0.00 2.69
2470 2518 2.096819 TGCGTTTGACACTGAAGGAAAC 59.903 45.455 0.00 0.00 0.00 2.78
2506 2554 4.431809 TGTTGCATTTCCTGTCAACTTTG 58.568 39.130 0.00 0.00 40.00 2.77
2508 2556 4.998671 TGCATTTCCTGTCAACTTTGAA 57.001 36.364 0.00 0.00 39.21 2.69
2548 2596 1.299648 CATGCGGAAGTGGAGGGAA 59.700 57.895 0.00 0.00 0.00 3.97
2549 2597 0.107017 CATGCGGAAGTGGAGGGAAT 60.107 55.000 0.00 0.00 0.00 3.01
2551 2599 0.322456 TGCGGAAGTGGAGGGAATTG 60.322 55.000 0.00 0.00 0.00 2.32
2552 2600 1.032114 GCGGAAGTGGAGGGAATTGG 61.032 60.000 0.00 0.00 0.00 3.16
2553 2601 0.394352 CGGAAGTGGAGGGAATTGGG 60.394 60.000 0.00 0.00 0.00 4.12
2554 2602 0.704664 GGAAGTGGAGGGAATTGGGT 59.295 55.000 0.00 0.00 0.00 4.51
2557 2605 0.995024 AGTGGAGGGAATTGGGTCAG 59.005 55.000 0.00 0.00 0.00 3.51
2558 2606 0.991920 GTGGAGGGAATTGGGTCAGA 59.008 55.000 0.00 0.00 0.00 3.27
2559 2607 1.065126 GTGGAGGGAATTGGGTCAGAG 60.065 57.143 0.00 0.00 0.00 3.35
2560 2608 0.548510 GGAGGGAATTGGGTCAGAGG 59.451 60.000 0.00 0.00 0.00 3.69
2561 2609 1.290134 GAGGGAATTGGGTCAGAGGT 58.710 55.000 0.00 0.00 0.00 3.85
2563 2611 1.636003 AGGGAATTGGGTCAGAGGTTC 59.364 52.381 0.00 0.00 0.00 3.62
2564 2612 1.636003 GGGAATTGGGTCAGAGGTTCT 59.364 52.381 0.00 0.00 0.00 3.01
2583 2631 3.188773 CACACAATGTGCTTGCTGG 57.811 52.632 14.01 0.00 41.89 4.85
2616 2664 2.133641 GCCTGTTGGGTTGTTGCCT 61.134 57.895 0.00 0.00 37.43 4.75
2637 2685 2.777832 AGTTGATGAAGGACCTGAGC 57.222 50.000 0.00 0.00 0.00 4.26
2647 2695 2.358003 ACCTGAGCGCTGAGTTGC 60.358 61.111 22.54 3.70 0.00 4.17
2666 2714 1.089920 CGCTGTTAGCCTGCTTCAAT 58.910 50.000 0.00 0.00 38.18 2.57
2671 2719 4.232221 CTGTTAGCCTGCTTCAATGTTTG 58.768 43.478 0.00 0.00 0.00 2.93
2672 2720 3.005684 TGTTAGCCTGCTTCAATGTTTGG 59.994 43.478 0.00 0.00 0.00 3.28
2673 2721 1.708341 AGCCTGCTTCAATGTTTGGT 58.292 45.000 0.00 0.00 0.00 3.67
2674 2722 2.875296 AGCCTGCTTCAATGTTTGGTA 58.125 42.857 0.00 0.00 0.00 3.25
2675 2723 2.558359 AGCCTGCTTCAATGTTTGGTAC 59.442 45.455 0.00 0.00 0.00 3.34
2676 2724 2.558359 GCCTGCTTCAATGTTTGGTACT 59.442 45.455 0.00 0.00 0.00 2.73
2677 2725 3.366374 GCCTGCTTCAATGTTTGGTACTC 60.366 47.826 0.00 0.00 0.00 2.59
2678 2726 4.074970 CCTGCTTCAATGTTTGGTACTCT 58.925 43.478 0.00 0.00 0.00 3.24
2679 2727 4.083110 CCTGCTTCAATGTTTGGTACTCTG 60.083 45.833 0.00 0.00 0.00 3.35
2680 2728 4.460263 TGCTTCAATGTTTGGTACTCTGT 58.540 39.130 0.00 0.00 0.00 3.41
2681 2729 5.616270 TGCTTCAATGTTTGGTACTCTGTA 58.384 37.500 0.00 0.00 0.00 2.74
2682 2730 6.237901 TGCTTCAATGTTTGGTACTCTGTAT 58.762 36.000 0.00 0.00 0.00 2.29
2684 2732 6.403636 GCTTCAATGTTTGGTACTCTGTATGG 60.404 42.308 0.00 0.00 0.00 2.74
2685 2733 6.121776 TCAATGTTTGGTACTCTGTATGGT 57.878 37.500 0.00 0.00 0.00 3.55
2686 2734 5.937540 TCAATGTTTGGTACTCTGTATGGTG 59.062 40.000 0.00 0.00 0.00 4.17
2687 2735 4.967084 TGTTTGGTACTCTGTATGGTGT 57.033 40.909 0.00 0.00 0.00 4.16
2688 2736 6.614694 ATGTTTGGTACTCTGTATGGTGTA 57.385 37.500 0.00 0.00 0.00 2.90
2689 2737 5.786311 TGTTTGGTACTCTGTATGGTGTAC 58.214 41.667 0.00 0.00 35.77 2.90
2713 2764 5.678583 TCTGAGAGCTGGGAAAGATTAATG 58.321 41.667 0.00 0.00 0.00 1.90
2714 2765 4.785301 TGAGAGCTGGGAAAGATTAATGG 58.215 43.478 0.00 0.00 0.00 3.16
2745 2796 0.250513 ATGAGTCCCTTTGCTCCGTC 59.749 55.000 0.00 0.00 0.00 4.79
2752 2803 2.081462 CCCTTTGCTCCGTCGTTTTAT 58.919 47.619 0.00 0.00 0.00 1.40
2759 2810 3.493129 TGCTCCGTCGTTTTATCATATGC 59.507 43.478 0.00 0.00 0.00 3.14
2765 2816 6.481976 TCCGTCGTTTTATCATATGCTCATTT 59.518 34.615 0.00 0.00 0.00 2.32
2810 2861 4.260743 GCCTTTCAAGTTTCAATGCAAACC 60.261 41.667 0.00 0.00 37.01 3.27
2813 2864 4.462508 TCAAGTTTCAATGCAAACCACA 57.537 36.364 0.00 0.00 37.01 4.17
2825 2876 3.457610 CAAACCACATTGCCTTGAGTT 57.542 42.857 0.00 0.00 0.00 3.01
2826 2877 3.383761 CAAACCACATTGCCTTGAGTTC 58.616 45.455 0.00 0.00 0.00 3.01
2827 2878 1.238439 ACCACATTGCCTTGAGTTCG 58.762 50.000 0.00 0.00 0.00 3.95
2834 2885 1.603456 TGCCTTGAGTTCGCATTCAA 58.397 45.000 0.00 0.00 32.75 2.69
2836 2887 2.162208 TGCCTTGAGTTCGCATTCAATC 59.838 45.455 0.00 0.00 33.25 2.67
2839 2890 4.348656 CCTTGAGTTCGCATTCAATCATG 58.651 43.478 0.00 0.00 33.25 3.07
2840 2891 3.409851 TGAGTTCGCATTCAATCATGC 57.590 42.857 0.00 0.00 45.34 4.06
2870 2921 7.775397 AAATTGAAGTGAAATGAAACCAGTG 57.225 32.000 0.00 0.00 0.00 3.66
2899 2950 4.813697 GGTCTTTCTCATATTCTCACTGGC 59.186 45.833 0.00 0.00 0.00 4.85
2921 2979 3.423539 TGTTCTCTGAGGAAACCATGG 57.576 47.619 11.19 11.19 0.00 3.66
2936 2994 0.940126 CATGGAAGTATGCGCAGGAC 59.060 55.000 18.32 16.68 0.00 3.85
2995 3053 4.870636 ACCATGCCTGGAAGATTTATGAA 58.129 39.130 15.66 0.00 46.37 2.57
2996 3054 5.461327 ACCATGCCTGGAAGATTTATGAAT 58.539 37.500 15.66 0.00 46.37 2.57
3055 3113 3.745975 TCTGGTATTGCAGTGAAGTTTCG 59.254 43.478 0.00 0.00 0.00 3.46
3063 3121 3.498397 TGCAGTGAAGTTTCGATTCCTTC 59.502 43.478 10.61 10.61 36.09 3.46
3064 3122 3.498397 GCAGTGAAGTTTCGATTCCTTCA 59.502 43.478 14.38 14.38 41.55 3.02
3068 3126 6.798959 CAGTGAAGTTTCGATTCCTTCAAATC 59.201 38.462 18.01 10.00 44.32 2.17
3071 3129 8.504005 GTGAAGTTTCGATTCCTTCAAATCTTA 58.496 33.333 18.01 0.00 44.32 2.10
3080 3138 7.912250 CGATTCCTTCAAATCTTAATTCCAGTG 59.088 37.037 0.00 0.00 34.19 3.66
3094 3152 4.687901 TTCCAGTGCTATGCTATGCTTA 57.312 40.909 0.00 0.00 0.00 3.09
3097 3155 6.550938 TCCAGTGCTATGCTATGCTTATAT 57.449 37.500 0.00 0.00 0.00 0.86
3098 3156 6.950842 TCCAGTGCTATGCTATGCTTATATT 58.049 36.000 0.00 0.00 0.00 1.28
3099 3157 6.820152 TCCAGTGCTATGCTATGCTTATATTG 59.180 38.462 0.00 0.00 0.00 1.90
3100 3158 6.596888 CCAGTGCTATGCTATGCTTATATTGT 59.403 38.462 0.00 0.00 0.00 2.71
3101 3159 7.120285 CCAGTGCTATGCTATGCTTATATTGTT 59.880 37.037 0.00 0.00 0.00 2.83
3135 3193 3.845781 ACAGACAACACATCCAGTTCT 57.154 42.857 0.00 0.00 0.00 3.01
3137 3195 4.526970 ACAGACAACACATCCAGTTCTTT 58.473 39.130 0.00 0.00 0.00 2.52
3147 3205 7.820648 ACACATCCAGTTCTTTATTCATTCAC 58.179 34.615 0.00 0.00 0.00 3.18
3149 3207 7.966753 CACATCCAGTTCTTTATTCATTCACTG 59.033 37.037 0.00 0.00 0.00 3.66
3159 3217 9.436957 TCTTTATTCATTCACTGTCCTTTCTAC 57.563 33.333 0.00 0.00 0.00 2.59
3161 3219 8.777865 TTATTCATTCACTGTCCTTTCTACTG 57.222 34.615 0.00 0.00 0.00 2.74
3162 3220 6.419484 TTCATTCACTGTCCTTTCTACTGA 57.581 37.500 0.00 0.00 0.00 3.41
3179 3237 3.705051 ACTGATCCTTGATGTGGCAATT 58.295 40.909 0.00 0.00 0.00 2.32
3188 3246 7.098477 TCCTTGATGTGGCAATTATTTTCAAG 58.902 34.615 0.00 0.00 38.86 3.02
3193 3251 8.095792 TGATGTGGCAATTATTTTCAAGTTGAT 58.904 29.630 6.36 0.00 0.00 2.57
3208 3266 4.640771 AGTTGATTTCTCACCCAGCTTA 57.359 40.909 0.00 0.00 0.00 3.09
3214 3272 6.115446 TGATTTCTCACCCAGCTTAATACAG 58.885 40.000 0.00 0.00 0.00 2.74
3292 3351 8.123639 TGCACTTTATCTAGAGTTCTTGTACT 57.876 34.615 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.576615 AGCTGGACCTTGTTGAAGAAC 58.423 47.619 0.00 0.00 0.00 3.01
172 173 1.669115 CCTGAACTGACTGGCCACG 60.669 63.158 0.00 0.00 0.00 4.94
343 344 3.128188 CTGCTGCTGCTGCTCTGG 61.128 66.667 27.67 13.92 40.48 3.86
514 515 4.966965 CAGTATGGTCTGTCGTTAGTCT 57.033 45.455 0.00 0.00 0.00 3.24
537 541 9.462606 AGCTTAATTAATTAGCACAGGTAGTTT 57.537 29.630 21.34 4.06 0.00 2.66
540 544 8.662781 TCAGCTTAATTAATTAGCACAGGTAG 57.337 34.615 21.34 11.20 0.00 3.18
732 736 3.563808 GTGATGTGCAACTTTAGGTCACA 59.436 43.478 0.00 0.00 37.17 3.58
733 737 3.815401 AGTGATGTGCAACTTTAGGTCAC 59.185 43.478 0.00 0.00 38.04 3.67
734 738 3.814842 CAGTGATGTGCAACTTTAGGTCA 59.185 43.478 0.00 0.00 38.04 4.02
735 739 4.065088 TCAGTGATGTGCAACTTTAGGTC 58.935 43.478 0.00 0.00 38.04 3.85
758 766 4.662468 TGGCACTGCAATTTTTACAAGA 57.338 36.364 2.82 0.00 0.00 3.02
760 768 6.500684 TTTTTGGCACTGCAATTTTTACAA 57.499 29.167 2.82 0.00 0.00 2.41
762 770 6.852345 CAGATTTTTGGCACTGCAATTTTTAC 59.148 34.615 2.82 0.00 0.00 2.01
763 771 6.957150 CAGATTTTTGGCACTGCAATTTTTA 58.043 32.000 2.82 0.00 0.00 1.52
779 787 7.750229 TGTAGATGAAGTCTTGCAGATTTTT 57.250 32.000 0.00 0.00 38.42 1.94
795 804 4.388773 GCGGCAATATTTCGATGTAGATGA 59.611 41.667 10.95 0.00 0.00 2.92
797 806 4.314961 TGCGGCAATATTTCGATGTAGAT 58.685 39.130 0.00 0.00 0.00 1.98
798 807 3.723260 TGCGGCAATATTTCGATGTAGA 58.277 40.909 0.00 0.00 0.00 2.59
806 815 6.833342 ATTTCATCTTTGCGGCAATATTTC 57.167 33.333 17.19 0.00 0.00 2.17
814 823 4.732784 TCTAACAATTTCATCTTTGCGGC 58.267 39.130 0.00 0.00 0.00 6.53
830 839 9.658799 TTCCAAATTTTCAACAAACATCTAACA 57.341 25.926 0.00 0.00 0.00 2.41
838 875 7.534282 ACCACATTTCCAAATTTTCAACAAAC 58.466 30.769 0.00 0.00 0.00 2.93
876 913 3.272574 TCAGCCCATCTGAGTCAAATC 57.727 47.619 0.00 0.00 46.34 2.17
890 927 2.797177 ACTTCTCCAAATCTCAGCCC 57.203 50.000 0.00 0.00 0.00 5.19
921 963 1.802337 GAAACCACTTTCCCCCGTGC 61.802 60.000 0.00 0.00 31.03 5.34
924 966 0.893727 CCTGAAACCACTTTCCCCCG 60.894 60.000 0.00 0.00 35.75 5.73
934 977 0.960364 GCGCCTGAATCCTGAAACCA 60.960 55.000 0.00 0.00 0.00 3.67
979 1024 0.031857 CCGCAATCGAGCAGAGAGAT 59.968 55.000 0.00 0.00 38.10 2.75
984 1029 1.227350 CATCCCGCAATCGAGCAGA 60.227 57.895 0.00 0.00 38.10 4.26
985 1030 2.890109 GCATCCCGCAATCGAGCAG 61.890 63.158 0.00 0.00 41.79 4.24
986 1031 2.896854 GCATCCCGCAATCGAGCA 60.897 61.111 0.00 0.00 41.79 4.26
1458 1506 4.990910 AGGCAGAGGTGGTGGGCT 62.991 66.667 0.00 0.00 0.00 5.19
2088 2136 3.861569 GTCTTCCAGACAAAGAACACG 57.138 47.619 0.00 0.00 44.45 4.49
2100 2148 3.063510 TGCTCTTCCATTGTCTTCCAG 57.936 47.619 0.00 0.00 0.00 3.86
2175 2223 3.903467 AGCCAAATCTACCATTCCCTTC 58.097 45.455 0.00 0.00 0.00 3.46
2187 2235 3.181489 CGTCGTACTTCCTAGCCAAATCT 60.181 47.826 0.00 0.00 0.00 2.40
2220 2268 3.706373 GGTGAGAGGCCCTTCGCA 61.706 66.667 16.73 7.09 40.31 5.10
2253 2301 1.485066 CCCGGCAATTGAGTACCTAGT 59.515 52.381 10.34 0.00 0.00 2.57
2271 2319 0.246086 CACTGTCAGACTCTGCTCCC 59.754 60.000 6.91 0.00 0.00 4.30
2298 2346 5.121925 CAGAATTCAGATCACACCACTCAAG 59.878 44.000 8.44 0.00 0.00 3.02
2301 2349 3.937706 CCAGAATTCAGATCACACCACTC 59.062 47.826 8.44 0.00 0.00 3.51
2326 2374 6.889198 TCTAATATCTGTTTTGCTGCCTAGT 58.111 36.000 0.00 0.00 0.00 2.57
2328 2376 7.775093 ACATTCTAATATCTGTTTTGCTGCCTA 59.225 33.333 0.00 0.00 0.00 3.93
2331 2379 7.970061 TGAACATTCTAATATCTGTTTTGCTGC 59.030 33.333 0.00 0.00 32.28 5.25
2407 2455 0.029300 CAACACAAAGCCTCACCGTG 59.971 55.000 0.00 0.00 0.00 4.94
2409 2457 1.069022 CATCAACACAAAGCCTCACCG 60.069 52.381 0.00 0.00 0.00 4.94
2411 2459 2.227388 CTCCATCAACACAAAGCCTCAC 59.773 50.000 0.00 0.00 0.00 3.51
2452 2500 6.861065 TCTATGTTTCCTTCAGTGTCAAAC 57.139 37.500 0.00 0.00 0.00 2.93
2457 2505 5.222130 ACCCATTCTATGTTTCCTTCAGTGT 60.222 40.000 0.00 0.00 0.00 3.55
2470 2518 6.925165 GGAAATGCAACATTACCCATTCTATG 59.075 38.462 0.00 0.00 0.00 2.23
2506 2554 0.250901 TTCCAGGGAACAGCTGCTTC 60.251 55.000 15.27 15.85 0.00 3.86
2508 2556 3.580084 TTCCAGGGAACAGCTGCT 58.420 55.556 15.27 0.00 0.00 4.24
2526 2574 0.523072 CCTCCACTTCCGCATGTTTG 59.477 55.000 0.00 0.00 0.00 2.93
2534 2582 0.394352 CCCAATTCCCTCCACTTCCG 60.394 60.000 0.00 0.00 0.00 4.30
2548 2596 2.039084 GTGTGAGAACCTCTGACCCAAT 59.961 50.000 0.00 0.00 29.13 3.16
2549 2597 1.416401 GTGTGAGAACCTCTGACCCAA 59.584 52.381 0.00 0.00 29.13 4.12
2551 2599 1.048601 TGTGTGAGAACCTCTGACCC 58.951 55.000 0.00 0.00 29.13 4.46
2552 2600 2.910688 TTGTGTGAGAACCTCTGACC 57.089 50.000 0.00 0.00 29.13 4.02
2553 2601 3.733337 ACATTGTGTGAGAACCTCTGAC 58.267 45.455 0.00 0.00 31.01 3.51
2583 2631 0.040958 CAGGCTTTCGAGCAACACAC 60.041 55.000 0.47 0.00 36.33 3.82
2602 2650 2.691011 TCAACTTAGGCAACAACCCAAC 59.309 45.455 0.00 0.00 41.41 3.77
2608 2656 4.518970 GTCCTTCATCAACTTAGGCAACAA 59.481 41.667 0.00 0.00 41.41 2.83
2616 2664 3.368427 CGCTCAGGTCCTTCATCAACTTA 60.368 47.826 0.00 0.00 0.00 2.24
2647 2695 1.089920 ATTGAAGCAGGCTAACAGCG 58.910 50.000 0.00 0.00 43.62 5.18
2666 2714 4.967084 ACACCATACAGAGTACCAAACA 57.033 40.909 0.00 0.00 0.00 2.83
2671 2719 5.191426 TCAGAGTACACCATACAGAGTACC 58.809 45.833 0.00 0.00 38.01 3.34
2672 2720 6.114089 TCTCAGAGTACACCATACAGAGTAC 58.886 44.000 0.00 0.00 37.65 2.73
2673 2721 6.309389 TCTCAGAGTACACCATACAGAGTA 57.691 41.667 0.00 0.00 0.00 2.59
2674 2722 5.180810 TCTCAGAGTACACCATACAGAGT 57.819 43.478 0.00 0.00 0.00 3.24
2675 2723 4.036262 GCTCTCAGAGTACACCATACAGAG 59.964 50.000 2.93 0.00 31.39 3.35
2676 2724 3.948473 GCTCTCAGAGTACACCATACAGA 59.052 47.826 2.93 0.00 31.39 3.41
2677 2725 3.951037 AGCTCTCAGAGTACACCATACAG 59.049 47.826 2.93 0.00 31.39 2.74
2678 2726 3.696548 CAGCTCTCAGAGTACACCATACA 59.303 47.826 2.93 0.00 31.39 2.29
2679 2727 3.067461 CCAGCTCTCAGAGTACACCATAC 59.933 52.174 2.93 0.00 31.39 2.39
2680 2728 3.291584 CCAGCTCTCAGAGTACACCATA 58.708 50.000 2.93 0.00 31.39 2.74
2681 2729 2.106566 CCAGCTCTCAGAGTACACCAT 58.893 52.381 2.93 0.00 31.39 3.55
2682 2730 1.550327 CCAGCTCTCAGAGTACACCA 58.450 55.000 2.93 0.00 31.39 4.17
2684 2732 1.840737 TCCCAGCTCTCAGAGTACAC 58.159 55.000 2.93 0.00 31.39 2.90
2685 2733 2.604912 TTCCCAGCTCTCAGAGTACA 57.395 50.000 2.93 0.00 31.39 2.90
2686 2734 3.093057 TCTTTCCCAGCTCTCAGAGTAC 58.907 50.000 2.93 0.00 31.39 2.73
2687 2735 3.458044 TCTTTCCCAGCTCTCAGAGTA 57.542 47.619 2.93 0.00 31.39 2.59
2688 2736 2.317371 TCTTTCCCAGCTCTCAGAGT 57.683 50.000 2.93 0.00 31.39 3.24
2689 2737 3.910568 AATCTTTCCCAGCTCTCAGAG 57.089 47.619 0.00 0.00 0.00 3.35
2713 2764 4.031611 AGGGACTCATCTAAACCTGTACC 58.968 47.826 0.00 0.00 0.00 3.34
2714 2765 5.678955 AAGGGACTCATCTAAACCTGTAC 57.321 43.478 0.00 0.00 38.49 2.90
2752 2803 6.888105 TCAGGTAGTCAAAATGAGCATATGA 58.112 36.000 6.97 0.00 0.00 2.15
2759 2810 5.947228 TGCTTTCAGGTAGTCAAAATGAG 57.053 39.130 0.00 0.00 0.00 2.90
2765 2816 5.885230 CATCAATGCTTTCAGGTAGTCAA 57.115 39.130 0.00 0.00 0.00 3.18
2810 2861 0.592637 TGCGAACTCAAGGCAATGTG 59.407 50.000 0.00 0.00 33.01 3.21
2813 2864 2.161855 TGAATGCGAACTCAAGGCAAT 58.838 42.857 0.00 0.00 40.49 3.56
2817 2868 4.348656 CATGATTGAATGCGAACTCAAGG 58.651 43.478 0.00 0.00 35.14 3.61
2836 2887 9.361315 TCATTTCACTTCAATTTAGAATGCATG 57.639 29.630 0.00 0.00 0.00 4.06
2843 2894 8.912988 ACTGGTTTCATTTCACTTCAATTTAGA 58.087 29.630 0.00 0.00 0.00 2.10
2844 2895 8.971321 CACTGGTTTCATTTCACTTCAATTTAG 58.029 33.333 0.00 0.00 0.00 1.85
2847 2898 7.111247 TCACTGGTTTCATTTCACTTCAATT 57.889 32.000 0.00 0.00 0.00 2.32
2870 2921 8.637986 AGTGAGAATATGAGAAAGACCACTATC 58.362 37.037 0.00 0.00 30.48 2.08
2899 2950 3.755378 CCATGGTTTCCTCAGAGAACAAG 59.245 47.826 2.57 0.00 25.80 3.16
2921 2979 2.231215 AGATGTCCTGCGCATACTTC 57.769 50.000 12.24 18.74 0.00 3.01
2936 2994 9.899226 TCTAAGTATTCATCGTGACATTAGATG 57.101 33.333 10.44 10.44 42.11 2.90
2952 3010 8.877779 CATGGTATGCTGCTATTCTAAGTATTC 58.122 37.037 0.00 0.00 0.00 1.75
3024 3082 4.275689 CACTGCAATACCAGAACTGTTGAA 59.724 41.667 0.00 0.00 36.67 2.69
3055 3113 7.704047 GCACTGGAATTAAGATTTGAAGGAATC 59.296 37.037 0.00 0.00 36.50 2.52
3063 3121 7.035840 AGCATAGCACTGGAATTAAGATTTG 57.964 36.000 0.00 0.00 0.00 2.32
3064 3122 8.790718 CATAGCATAGCACTGGAATTAAGATTT 58.209 33.333 0.00 0.00 0.00 2.17
3068 3126 5.704515 AGCATAGCATAGCACTGGAATTAAG 59.295 40.000 0.00 0.00 0.00 1.85
3071 3129 4.096190 AGCATAGCATAGCACTGGAATT 57.904 40.909 0.00 0.00 0.00 2.17
3111 3169 7.004555 AGAACTGGATGTGTTGTCTGTAATA 57.995 36.000 0.00 0.00 0.00 0.98
3124 3182 7.667219 ACAGTGAATGAATAAAGAACTGGATGT 59.333 33.333 0.00 0.00 38.25 3.06
3135 3193 9.219603 CAGTAGAAAGGACAGTGAATGAATAAA 57.780 33.333 0.00 0.00 0.00 1.40
3137 3195 8.134202 TCAGTAGAAAGGACAGTGAATGAATA 57.866 34.615 0.00 0.00 0.00 1.75
3147 3205 5.667539 TCAAGGATCAGTAGAAAGGACAG 57.332 43.478 0.00 0.00 0.00 3.51
3149 3207 5.814705 CACATCAAGGATCAGTAGAAAGGAC 59.185 44.000 0.00 0.00 0.00 3.85
3159 3217 6.401047 AATAATTGCCACATCAAGGATCAG 57.599 37.500 0.00 0.00 0.00 2.90
3161 3219 7.267128 TGAAAATAATTGCCACATCAAGGATC 58.733 34.615 0.00 0.00 0.00 3.36
3162 3220 7.185318 TGAAAATAATTGCCACATCAAGGAT 57.815 32.000 0.00 0.00 0.00 3.24
3179 3237 7.523709 GCTGGGTGAGAAATCAACTTGAAAATA 60.524 37.037 0.00 0.00 0.00 1.40
3188 3246 5.904362 ATTAAGCTGGGTGAGAAATCAAC 57.096 39.130 0.00 0.00 0.00 3.18
3193 3251 5.755409 TCTGTATTAAGCTGGGTGAGAAA 57.245 39.130 0.00 0.00 0.00 2.52
3235 3293 8.993121 CACTAGAGAAAAGATGTTTAAGAAGCA 58.007 33.333 0.00 0.00 0.00 3.91
3281 3340 8.594550 TGCTTAAGGAAGATAAGTACAAGAACT 58.405 33.333 4.29 0.00 34.25 3.01


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

AutoCloner maintained by Alex Coulton.