Multiple sequence alignment - TraesCS1D01G231200

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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 TraesCS1D01G231200 chr1D 100.000 2603 0 0 1 2603 319613538 319616140 0.000000e+00 4807.0
1 TraesCS1D01G231200 chr1D 88.848 807 71 13 182 972 398483954 398483151 0.000000e+00 974.0
2 TraesCS1D01G231200 chr1D 94.253 87 4 1 2517 2603 362607869 362607784 5.850000e-27 132.0
3 TraesCS1D01G231200 chr1A 93.738 1565 59 25 968 2514 403635075 403633532 0.000000e+00 2311.0
4 TraesCS1D01G231200 chr1A 88.136 177 15 4 13 185 403635244 403635070 3.400000e-49 206.0
5 TraesCS1D01G231200 chr1B 91.645 1544 66 22 968 2474 432376518 432378035 0.000000e+00 2078.0
6 TraesCS1D01G231200 chr1B 86.533 698 83 9 276 968 512974329 512973638 0.000000e+00 758.0
7 TraesCS1D01G231200 chr1B 100.000 35 0 0 2518 2552 485693894 485693860 6.010000e-07 65.8
8 TraesCS1D01G231200 chr4D 89.962 797 66 11 184 971 8143149 8142358 0.000000e+00 1016.0
9 TraesCS1D01G231200 chr5B 88.406 828 62 14 179 974 403157222 403156397 0.000000e+00 966.0
10 TraesCS1D01G231200 chr5A 91.040 692 54 4 184 867 826878 827569 0.000000e+00 928.0
11 TraesCS1D01G231200 chr5A 87.277 786 89 10 182 961 472107090 472107870 0.000000e+00 887.0
12 TraesCS1D01G231200 chr6D 87.961 814 58 13 181 972 402360235 402361030 0.000000e+00 924.0
13 TraesCS1D01G231200 chr6A 86.859 799 80 14 181 972 85578146 85578926 0.000000e+00 870.0
14 TraesCS1D01G231200 chr3D 86.981 699 79 11 277 968 90118797 90118104 0.000000e+00 776.0
15 TraesCS1D01G231200 chr7D 88.408 647 62 10 327 968 102943008 102943646 0.000000e+00 767.0
16 TraesCS1D01G231200 chr7D 93.537 294 19 0 182 475 97624359 97624652 3.080000e-119 438.0
17 TraesCS1D01G231200 chr7D 86.350 337 23 7 2075 2392 470227464 470227796 1.920000e-91 346.0


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 TraesCS1D01G231200 chr1D 319613538 319616140 2602 False 4807.0 4807 100.000 1 2603 1 chr1D.!!$F1 2602
1 TraesCS1D01G231200 chr1D 398483151 398483954 803 True 974.0 974 88.848 182 972 1 chr1D.!!$R2 790
2 TraesCS1D01G231200 chr1A 403633532 403635244 1712 True 1258.5 2311 90.937 13 2514 2 chr1A.!!$R1 2501
3 TraesCS1D01G231200 chr1B 432376518 432378035 1517 False 2078.0 2078 91.645 968 2474 1 chr1B.!!$F1 1506
4 TraesCS1D01G231200 chr1B 512973638 512974329 691 True 758.0 758 86.533 276 968 1 chr1B.!!$R2 692
5 TraesCS1D01G231200 chr4D 8142358 8143149 791 True 1016.0 1016 89.962 184 971 1 chr4D.!!$R1 787
6 TraesCS1D01G231200 chr5B 403156397 403157222 825 True 966.0 966 88.406 179 974 1 chr5B.!!$R1 795
7 TraesCS1D01G231200 chr5A 826878 827569 691 False 928.0 928 91.040 184 867 1 chr5A.!!$F1 683
8 TraesCS1D01G231200 chr5A 472107090 472107870 780 False 887.0 887 87.277 182 961 1 chr5A.!!$F2 779
9 TraesCS1D01G231200 chr6D 402360235 402361030 795 False 924.0 924 87.961 181 972 1 chr6D.!!$F1 791
10 TraesCS1D01G231200 chr6A 85578146 85578926 780 False 870.0 870 86.859 181 972 1 chr6A.!!$F1 791
11 TraesCS1D01G231200 chr3D 90118104 90118797 693 True 776.0 776 86.981 277 968 1 chr3D.!!$R1 691
12 TraesCS1D01G231200 chr7D 102943008 102943646 638 False 767.0 767 88.408 327 968 1 chr7D.!!$F2 641

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
968 1190 0.392336 GGGGTCTGCTAGAGATGCTG 59.608 60.0 0.0 0.0 31.63 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2252 1.203441 TGGATGCAGAAGCCAGGAGT 61.203 55.0 0.0 0.0 41.13 3.85 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
26 27 7.962441 ACCTAAAAGGCAAGATGTGTATTTTT 58.038 30.769 0.00 0.00 39.63 1.94
27 28 8.088365 ACCTAAAAGGCAAGATGTGTATTTTTC 58.912 33.333 0.00 0.00 39.63 2.29
79 82 4.923871 TGCGTCATAGAAAGAGAAGTGTTC 59.076 41.667 0.00 0.00 0.00 3.18
80 83 4.923871 GCGTCATAGAAAGAGAAGTGTTCA 59.076 41.667 0.00 0.00 0.00 3.18
122 126 9.302345 AGTGTTTTTACACATCGTATCATAGAG 57.698 33.333 10.65 0.00 42.68 2.43
133 137 9.307121 ACATCGTATCATAGAGAAGACAAAAAG 57.693 33.333 0.00 0.00 0.00 2.27
251 257 0.790207 GCAGTTTCACGAAGATCGCA 59.210 50.000 0.00 0.00 45.12 5.10
288 294 3.414700 CGCAGCCGAACAGACACC 61.415 66.667 0.00 0.00 36.29 4.16
443 515 3.957535 CGCGCCTCATTGCCCATC 61.958 66.667 0.00 0.00 0.00 3.51
444 516 3.957535 GCGCCTCATTGCCCATCG 61.958 66.667 0.00 0.00 0.00 3.84
445 517 3.282157 CGCCTCATTGCCCATCGG 61.282 66.667 0.00 0.00 0.00 4.18
446 518 2.124151 GCCTCATTGCCCATCGGT 60.124 61.111 0.00 0.00 0.00 4.69
447 519 2.189499 GCCTCATTGCCCATCGGTC 61.189 63.158 0.00 0.00 0.00 4.79
448 520 1.889105 CCTCATTGCCCATCGGTCG 60.889 63.158 0.00 0.00 0.00 4.79
449 521 2.513666 TCATTGCCCATCGGTCGC 60.514 61.111 0.00 0.00 0.00 5.19
450 522 3.940640 CATTGCCCATCGGTCGCG 61.941 66.667 0.00 0.00 0.00 5.87
558 778 1.445095 CTCTATTGCCAGGCGAGCT 59.555 57.895 7.66 0.00 0.00 4.09
675 895 1.597700 CGATCGATTGCGGCGTCTAC 61.598 60.000 10.26 0.00 38.28 2.59
824 1044 5.076873 CAACCTCCAAAGATAAGGGTTTCA 58.923 41.667 0.00 0.00 35.24 2.69
859 1079 5.130477 TGTGGTGGCCCTTAAAATTTTTACA 59.870 36.000 9.06 0.00 0.00 2.41
877 1097 9.636789 ATTTTTACAGGTTGGACTACTTTTACT 57.363 29.630 0.00 0.00 0.00 2.24
890 1110 8.657729 GGACTACTTTTACTGTTTCTATTCTGC 58.342 37.037 0.00 0.00 0.00 4.26
927 1149 9.865484 GCCTAAAATTGTAAAACGCAAAAATTA 57.135 25.926 0.00 0.00 0.00 1.40
968 1190 0.392336 GGGGTCTGCTAGAGATGCTG 59.608 60.000 0.00 0.00 31.63 4.41
972 1194 3.133003 GGGTCTGCTAGAGATGCTGTTAA 59.867 47.826 0.00 0.00 31.63 2.01
973 1195 4.367450 GGTCTGCTAGAGATGCTGTTAAG 58.633 47.826 0.00 0.00 31.63 1.85
1017 1239 1.003355 CATGTGGACCCGCTGTCTT 60.003 57.895 1.01 0.00 43.89 3.01
1094 1324 2.328099 GCCACCGCTCAAGACCAAG 61.328 63.158 0.00 0.00 0.00 3.61
1096 1326 1.371183 CACCGCTCAAGACCAAGGA 59.629 57.895 0.00 0.00 0.00 3.36
1097 1327 0.250295 CACCGCTCAAGACCAAGGAA 60.250 55.000 0.00 0.00 0.00 3.36
1131 1361 2.947938 AATCCGCGATGCTTCCCCTG 62.948 60.000 8.23 0.00 0.00 4.45
1149 1388 4.504916 CTCCTCCTGCTCGCCGTG 62.505 72.222 0.00 0.00 0.00 4.94
1332 1571 3.597728 GGCTCCTACTCGCTCCGG 61.598 72.222 0.00 0.00 0.00 5.14
1634 1882 3.056304 GAGCTCTCTCACAAGTCACAAC 58.944 50.000 6.43 0.00 39.16 3.32
1635 1883 1.789464 GCTCTCTCACAAGTCACAACG 59.211 52.381 0.00 0.00 0.00 4.10
1660 1908 4.142600 CCCCTTCAAAATTCAGCTAGTTCG 60.143 45.833 0.00 0.00 0.00 3.95
1781 2029 1.202325 CGATTTCGATGGGTCCGTGTA 60.202 52.381 0.00 0.00 43.02 2.90
1788 2036 0.830648 ATGGGTCCGTGTATGAGTGG 59.169 55.000 0.00 0.00 0.00 4.00
1805 2053 3.997021 GAGTGGTGTACTGTTTCATCAGG 59.003 47.826 0.00 0.00 40.53 3.86
1846 2094 9.903682 ACACTTGAGATCAATAAAAGTTTCATG 57.096 29.630 0.00 0.00 35.02 3.07
1882 2133 5.094812 TGTGATCTATTTCATGTTTTGCGC 58.905 37.500 0.00 0.00 0.00 6.09
1907 2158 3.117794 CCATTTTGCGGCATACTGATTG 58.882 45.455 2.28 0.00 0.00 2.67
1973 2225 5.648178 TTGCAAACATATCAAGCTGATGT 57.352 34.783 0.00 4.08 37.70 3.06
1993 2252 4.274147 TGTGCCCAACAAAGAAGTTCTAA 58.726 39.130 5.65 0.00 35.24 2.10
2122 2391 4.436584 CCTCTTACTGAATCTTTGCAAGCG 60.437 45.833 0.00 0.00 0.00 4.68
2135 2405 1.667212 TGCAAGCGTATCAAGCTGATG 59.333 47.619 8.40 0.00 45.31 3.07
2174 2444 2.280389 CTCCCCATCCACGATGCG 60.280 66.667 0.00 0.00 38.59 4.73
2187 2457 3.615056 CCACGATGCGTACAGAATTACAA 59.385 43.478 0.00 0.00 38.32 2.41
2327 2597 4.012374 CCAACATGCTGATACCAAAGAGT 58.988 43.478 0.00 0.00 0.00 3.24
2329 2599 5.647658 CCAACATGCTGATACCAAAGAGTTA 59.352 40.000 0.00 0.00 0.00 2.24
2330 2600 6.319658 CCAACATGCTGATACCAAAGAGTTAT 59.680 38.462 0.00 0.00 0.00 1.89
2331 2601 7.148018 CCAACATGCTGATACCAAAGAGTTATT 60.148 37.037 0.00 0.00 0.00 1.40
2376 2649 9.468532 AAAGTGCTAACAGAAAGATGAAAAATC 57.531 29.630 0.00 0.00 0.00 2.17
2415 2688 3.054213 TCACTCAGGATGCCATGAATCAA 60.054 43.478 0.00 0.00 34.76 2.57
2515 2791 4.689612 CACTACAGGGTGCAAGGTATAT 57.310 45.455 0.00 0.00 0.00 0.86
2516 2792 5.036117 CACTACAGGGTGCAAGGTATATT 57.964 43.478 0.00 0.00 0.00 1.28
2517 2793 5.437060 CACTACAGGGTGCAAGGTATATTT 58.563 41.667 0.00 0.00 0.00 1.40
2518 2794 5.296780 CACTACAGGGTGCAAGGTATATTTG 59.703 44.000 0.00 0.00 0.00 2.32
2519 2795 4.316025 ACAGGGTGCAAGGTATATTTGT 57.684 40.909 0.00 0.00 0.00 2.83
2520 2796 4.672899 ACAGGGTGCAAGGTATATTTGTT 58.327 39.130 0.00 0.00 0.00 2.83
2521 2797 4.462483 ACAGGGTGCAAGGTATATTTGTTG 59.538 41.667 0.00 0.00 0.00 3.33
2522 2798 4.023291 AGGGTGCAAGGTATATTTGTTGG 58.977 43.478 0.00 0.00 0.00 3.77
2523 2799 4.020543 GGGTGCAAGGTATATTTGTTGGA 58.979 43.478 0.00 0.00 0.00 3.53
2524 2800 4.464597 GGGTGCAAGGTATATTTGTTGGAA 59.535 41.667 0.00 0.00 0.00 3.53
2525 2801 5.407502 GGTGCAAGGTATATTTGTTGGAAC 58.592 41.667 0.00 0.00 0.00 3.62
2526 2802 5.185056 GGTGCAAGGTATATTTGTTGGAACT 59.815 40.000 0.00 0.00 0.00 3.01
2527 2803 6.376018 GGTGCAAGGTATATTTGTTGGAACTA 59.624 38.462 0.00 0.00 0.00 2.24
2528 2804 7.094118 GGTGCAAGGTATATTTGTTGGAACTAA 60.094 37.037 0.00 0.00 0.00 2.24
2529 2805 8.466798 GTGCAAGGTATATTTGTTGGAACTAAT 58.533 33.333 0.00 4.90 37.87 1.73
2530 2806 8.465999 TGCAAGGTATATTTGTTGGAACTAATG 58.534 33.333 8.78 0.00 35.65 1.90
2531 2807 7.435192 GCAAGGTATATTTGTTGGAACTAATGC 59.565 37.037 8.78 1.66 35.65 3.56
2532 2808 8.465999 CAAGGTATATTTGTTGGAACTAATGCA 58.534 33.333 8.78 0.00 35.65 3.96
2533 2809 8.766994 AGGTATATTTGTTGGAACTAATGCAT 57.233 30.769 0.00 0.00 35.65 3.96
2534 2810 8.850156 AGGTATATTTGTTGGAACTAATGCATC 58.150 33.333 0.00 0.00 35.65 3.91
2535 2811 8.629158 GGTATATTTGTTGGAACTAATGCATCA 58.371 33.333 0.00 0.00 35.65 3.07
2536 2812 9.450807 GTATATTTGTTGGAACTAATGCATCAC 57.549 33.333 0.00 0.00 35.65 3.06
2537 2813 6.594788 ATTTGTTGGAACTAATGCATCACT 57.405 33.333 0.00 0.00 34.06 3.41
2538 2814 7.701539 ATTTGTTGGAACTAATGCATCACTA 57.298 32.000 0.00 0.00 34.06 2.74
2539 2815 6.741992 TTGTTGGAACTAATGCATCACTAG 57.258 37.500 0.00 0.42 29.97 2.57
2540 2816 5.185454 TGTTGGAACTAATGCATCACTAGG 58.815 41.667 0.00 0.00 0.00 3.02
2541 2817 5.045942 TGTTGGAACTAATGCATCACTAGGA 60.046 40.000 0.00 0.00 0.00 2.94
2542 2818 5.894298 TGGAACTAATGCATCACTAGGAT 57.106 39.130 0.00 0.00 36.39 3.24
2557 2833 9.716531 CATCACTAGGATGTCATACACATAATT 57.283 33.333 11.14 0.00 46.53 1.40
2559 2835 9.546428 TCACTAGGATGTCATACACATAATTTG 57.454 33.333 0.00 0.00 46.53 2.32
2560 2836 9.546428 CACTAGGATGTCATACACATAATTTGA 57.454 33.333 0.00 0.00 46.53 2.69
2564 2840 8.355169 AGGATGTCATACACATAATTTGATTGC 58.645 33.333 0.00 0.00 46.53 3.56
2565 2841 8.136800 GGATGTCATACACATAATTTGATTGCA 58.863 33.333 0.00 0.00 46.53 4.08
2566 2842 9.687210 GATGTCATACACATAATTTGATTGCAT 57.313 29.630 0.00 0.00 46.53 3.96
2567 2843 9.687210 ATGTCATACACATAATTTGATTGCATC 57.313 29.630 0.00 0.00 44.56 3.91
2568 2844 8.905850 TGTCATACACATAATTTGATTGCATCT 58.094 29.630 0.00 0.00 0.00 2.90
2574 2850 9.346005 ACACATAATTTGATTGCATCTAGATCA 57.654 29.630 1.03 1.64 0.00 2.92
2575 2851 9.608617 CACATAATTTGATTGCATCTAGATCAC 57.391 33.333 1.03 0.00 30.10 3.06
2576 2852 8.790718 ACATAATTTGATTGCATCTAGATCACC 58.209 33.333 1.03 0.00 30.10 4.02
2577 2853 6.645790 AATTTGATTGCATCTAGATCACCC 57.354 37.500 1.03 0.54 30.10 4.61
2578 2854 4.776435 TTGATTGCATCTAGATCACCCA 57.224 40.909 1.03 2.83 30.10 4.51
2579 2855 4.776435 TGATTGCATCTAGATCACCCAA 57.224 40.909 1.03 4.89 0.00 4.12
2580 2856 5.314718 TGATTGCATCTAGATCACCCAAT 57.685 39.130 1.03 9.22 0.00 3.16
2581 2857 6.438186 TGATTGCATCTAGATCACCCAATA 57.562 37.500 1.03 0.00 0.00 1.90
2582 2858 7.024345 TGATTGCATCTAGATCACCCAATAT 57.976 36.000 1.03 0.00 0.00 1.28
2583 2859 8.149631 TGATTGCATCTAGATCACCCAATATA 57.850 34.615 1.03 1.32 0.00 0.86
2584 2860 8.605065 TGATTGCATCTAGATCACCCAATATAA 58.395 33.333 1.03 0.00 0.00 0.98
2585 2861 8.798859 ATTGCATCTAGATCACCCAATATAAC 57.201 34.615 1.03 0.00 0.00 1.89
2586 2862 7.315066 TGCATCTAGATCACCCAATATAACA 57.685 36.000 1.03 0.00 0.00 2.41
2587 2863 7.921304 TGCATCTAGATCACCCAATATAACAT 58.079 34.615 1.03 0.00 0.00 2.71
2588 2864 7.825761 TGCATCTAGATCACCCAATATAACATG 59.174 37.037 1.03 0.00 0.00 3.21
2589 2865 8.043113 GCATCTAGATCACCCAATATAACATGA 58.957 37.037 1.03 0.00 0.00 3.07
2590 2866 9.948964 CATCTAGATCACCCAATATAACATGAA 57.051 33.333 1.03 0.00 0.00 2.57
2591 2867 9.950496 ATCTAGATCACCCAATATAACATGAAC 57.050 33.333 0.00 0.00 0.00 3.18
2592 2868 8.933653 TCTAGATCACCCAATATAACATGAACA 58.066 33.333 0.00 0.00 0.00 3.18
2593 2869 9.212641 CTAGATCACCCAATATAACATGAACAG 57.787 37.037 0.00 0.00 0.00 3.16
2594 2870 7.805163 AGATCACCCAATATAACATGAACAGA 58.195 34.615 0.00 0.00 0.00 3.41
2595 2871 7.935755 AGATCACCCAATATAACATGAACAGAG 59.064 37.037 0.00 0.00 0.00 3.35
2596 2872 7.194112 TCACCCAATATAACATGAACAGAGA 57.806 36.000 0.00 0.00 0.00 3.10
2597 2873 7.275183 TCACCCAATATAACATGAACAGAGAG 58.725 38.462 0.00 0.00 0.00 3.20
2598 2874 6.484643 CACCCAATATAACATGAACAGAGAGG 59.515 42.308 0.00 0.00 0.00 3.69
2599 2875 6.000219 CCCAATATAACATGAACAGAGAGGG 59.000 44.000 0.00 0.00 0.00 4.30
2600 2876 6.000219 CCAATATAACATGAACAGAGAGGGG 59.000 44.000 0.00 0.00 0.00 4.79
2601 2877 6.409695 CCAATATAACATGAACAGAGAGGGGT 60.410 42.308 0.00 0.00 0.00 4.95
2602 2878 6.831664 ATATAACATGAACAGAGAGGGGTT 57.168 37.500 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.539034 AAAATACACATCTTGCCTTTTAGGT 57.461 32.000 0.00 0.00 37.80 3.08
2 3 7.273381 CGAAAAATACACATCTTGCCTTTTAGG 59.727 37.037 0.00 0.00 38.80 2.69
3 4 7.807907 ACGAAAAATACACATCTTGCCTTTTAG 59.192 33.333 0.00 0.00 0.00 1.85
4 5 7.593273 CACGAAAAATACACATCTTGCCTTTTA 59.407 33.333 0.00 0.00 0.00 1.52
5 6 6.420604 CACGAAAAATACACATCTTGCCTTTT 59.579 34.615 0.00 0.00 0.00 2.27
6 7 5.920273 CACGAAAAATACACATCTTGCCTTT 59.080 36.000 0.00 0.00 0.00 3.11
7 8 5.009610 ACACGAAAAATACACATCTTGCCTT 59.990 36.000 0.00 0.00 0.00 4.35
8 9 4.518970 ACACGAAAAATACACATCTTGCCT 59.481 37.500 0.00 0.00 0.00 4.75
9 10 4.616802 CACACGAAAAATACACATCTTGCC 59.383 41.667 0.00 0.00 0.00 4.52
10 11 5.212194 ACACACGAAAAATACACATCTTGC 58.788 37.500 0.00 0.00 0.00 4.01
11 12 8.775220 TTTACACACGAAAAATACACATCTTG 57.225 30.769 0.00 0.00 0.00 3.02
26 27 5.404366 GCTCACACTTCTATTTTACACACGA 59.596 40.000 0.00 0.00 0.00 4.35
27 28 5.176774 TGCTCACACTTCTATTTTACACACG 59.823 40.000 0.00 0.00 0.00 4.49
94 97 9.901724 CTATGATACGATGTGTAAAAACACTTC 57.098 33.333 9.79 11.12 40.97 3.01
95 98 9.647797 TCTATGATACGATGTGTAAAAACACTT 57.352 29.630 9.79 3.78 40.97 3.16
138 142 9.900264 CGAAAGAAAATTTTGTCTTTGGTTAAG 57.100 29.630 18.26 4.19 42.67 1.85
139 143 9.640963 TCGAAAGAAAATTTTGTCTTTGGTTAA 57.359 25.926 18.26 3.97 42.67 2.01
175 180 5.696724 TCTGCTAGAGTTGCTCTAACAAAAC 59.303 40.000 9.59 0.00 41.74 2.43
251 257 1.467342 GCTAGTTTTCGACCCGCAAAT 59.533 47.619 0.00 0.00 0.00 2.32
288 294 8.623310 ATTCCAGTTTTACAGTTTGTTTTACG 57.377 30.769 0.00 0.00 0.00 3.18
427 499 3.957535 CGATGGGCAATGAGGCGC 61.958 66.667 0.00 0.00 45.36 6.53
428 500 3.282157 CCGATGGGCAATGAGGCG 61.282 66.667 0.00 0.00 45.36 5.52
429 501 2.124151 ACCGATGGGCAATGAGGC 60.124 61.111 0.00 0.00 43.27 4.70
430 502 1.889105 CGACCGATGGGCAATGAGG 60.889 63.158 0.00 0.00 36.48 3.86
431 503 2.537560 GCGACCGATGGGCAATGAG 61.538 63.158 0.00 0.00 36.48 2.90
432 504 2.513666 GCGACCGATGGGCAATGA 60.514 61.111 0.00 0.00 36.48 2.57
433 505 3.940640 CGCGACCGATGGGCAATG 61.941 66.667 0.00 0.00 36.48 2.82
692 912 1.813753 CGCCGGAATTCATCACCGT 60.814 57.895 5.05 0.00 44.34 4.83
824 1044 1.747325 GCCACCACAAATGCACACCT 61.747 55.000 0.00 0.00 0.00 4.00
859 1079 6.896883 AGAAACAGTAAAAGTAGTCCAACCT 58.103 36.000 0.00 0.00 0.00 3.50
909 1130 6.761714 ACCCACATAATTTTTGCGTTTTACAA 59.238 30.769 0.00 0.00 0.00 2.41
968 1190 1.946768 TGACAGTGCACCTTGCTTAAC 59.053 47.619 14.63 0.00 45.31 2.01
972 1194 0.399454 ATCTGACAGTGCACCTTGCT 59.601 50.000 14.63 0.00 45.31 3.91
973 1195 1.242076 AATCTGACAGTGCACCTTGC 58.758 50.000 14.63 1.17 45.29 4.01
974 1196 2.417933 GCTAATCTGACAGTGCACCTTG 59.582 50.000 14.63 9.04 0.00 3.61
975 1197 2.304180 AGCTAATCTGACAGTGCACCTT 59.696 45.455 14.63 0.00 0.00 3.50
1017 1239 1.022451 GGAGATGCGCCGGTGTTAAA 61.022 55.000 17.91 0.32 0.00 1.52
1332 1571 1.421410 CGCTGATGTCGGGCTTGTAC 61.421 60.000 0.00 0.00 0.00 2.90
1634 1882 0.108662 GCTGAATTTTGAAGGGGCCG 60.109 55.000 0.00 0.00 0.00 6.13
1635 1883 1.269958 AGCTGAATTTTGAAGGGGCC 58.730 50.000 0.00 0.00 0.00 5.80
1660 1908 5.533903 ACAAGAGCATGAATAATCCATCCAC 59.466 40.000 0.00 0.00 0.00 4.02
1781 2029 5.227569 TGATGAAACAGTACACCACTCAT 57.772 39.130 0.00 0.00 34.26 2.90
1788 2036 6.619801 AAACTTCCTGATGAAACAGTACAC 57.380 37.500 0.00 0.00 36.30 2.90
1846 2094 9.832445 TGAAATAGATCACAGGTATTTAGGAAC 57.168 33.333 0.00 0.00 0.00 3.62
1877 2128 1.372748 CGCAAAATGGAAGGCGCAA 60.373 52.632 10.83 0.00 43.14 4.85
1882 2133 1.750778 AGTATGCCGCAAAATGGAAGG 59.249 47.619 0.00 0.00 0.00 3.46
1907 2158 4.836125 TTCACAAAAGAACTGCCTGATC 57.164 40.909 0.00 0.00 0.00 2.92
1973 2225 4.532834 AGTTAGAACTTCTTTGTTGGGCA 58.467 39.130 0.00 0.00 35.21 5.36
1993 2252 1.203441 TGGATGCAGAAGCCAGGAGT 61.203 55.000 0.00 0.00 41.13 3.85
2028 2287 4.858850 TGAAGGGCACAGAACATGAATAT 58.141 39.130 0.00 0.00 0.00 1.28
2122 2391 1.672881 GTGGGTGCATCAGCTTGATAC 59.327 52.381 0.00 0.00 42.74 2.24
2135 2405 3.272766 GCACTTCTTTTGTGGGTGC 57.727 52.632 0.00 0.00 44.53 5.01
2187 2457 3.253921 GTGTTGGCCGTACTTTTATGGTT 59.746 43.478 0.00 0.00 36.79 3.67
2201 2471 2.235016 TGTTCCAAGTATGTGTTGGCC 58.765 47.619 0.00 0.00 43.72 5.36
2306 2576 5.633830 AACTCTTTGGTATCAGCATGTTG 57.366 39.130 2.65 2.65 37.40 3.33
2376 2649 6.258230 TGAGTGATTTTGCTATTCCAGTTG 57.742 37.500 0.00 0.00 0.00 3.16
2415 2688 2.177594 CTTCGACCTTCCAGCCTGCT 62.178 60.000 0.00 0.00 0.00 4.24
2452 2725 8.487970 CCAAATAGTTAGCACACTATTCATACG 58.512 37.037 16.71 7.29 45.41 3.06
2508 2784 8.766994 ATGCATTAGTTCCAACAAATATACCT 57.233 30.769 0.00 0.00 0.00 3.08
2514 2790 6.594788 AGTGATGCATTAGTTCCAACAAAT 57.405 33.333 0.00 0.00 0.00 2.32
2515 2791 6.150976 CCTAGTGATGCATTAGTTCCAACAAA 59.849 38.462 0.00 0.00 0.00 2.83
2516 2792 5.647658 CCTAGTGATGCATTAGTTCCAACAA 59.352 40.000 0.00 0.00 0.00 2.83
2517 2793 5.045942 TCCTAGTGATGCATTAGTTCCAACA 60.046 40.000 0.00 0.00 0.00 3.33
2518 2794 5.428253 TCCTAGTGATGCATTAGTTCCAAC 58.572 41.667 0.00 0.00 0.00 3.77
2519 2795 5.692115 TCCTAGTGATGCATTAGTTCCAA 57.308 39.130 0.00 0.00 0.00 3.53
2520 2796 5.614308 CATCCTAGTGATGCATTAGTTCCA 58.386 41.667 0.00 0.00 44.16 3.53
2533 2809 9.546428 CAAATTATGTGTATGACATCCTAGTGA 57.454 33.333 0.00 0.00 41.91 3.41
2534 2810 9.546428 TCAAATTATGTGTATGACATCCTAGTG 57.454 33.333 0.00 0.00 41.91 2.74
2538 2814 8.355169 GCAATCAAATTATGTGTATGACATCCT 58.645 33.333 0.00 0.00 41.91 3.24
2539 2815 8.136800 TGCAATCAAATTATGTGTATGACATCC 58.863 33.333 0.00 0.00 41.91 3.51
2540 2816 9.687210 ATGCAATCAAATTATGTGTATGACATC 57.313 29.630 0.00 0.00 41.91 3.06
2541 2817 9.687210 GATGCAATCAAATTATGTGTATGACAT 57.313 29.630 0.00 0.00 44.96 3.06
2559 2835 8.887717 GTTATATTGGGTGATCTAGATGCAATC 58.112 37.037 10.74 0.00 46.04 2.67
2560 2836 8.385491 TGTTATATTGGGTGATCTAGATGCAAT 58.615 33.333 10.74 3.05 0.00 3.56
2561 2837 7.744733 TGTTATATTGGGTGATCTAGATGCAA 58.255 34.615 10.74 0.00 0.00 4.08
2562 2838 7.315066 TGTTATATTGGGTGATCTAGATGCA 57.685 36.000 10.74 5.42 0.00 3.96
2563 2839 8.043113 TCATGTTATATTGGGTGATCTAGATGC 58.957 37.037 10.74 2.64 0.00 3.91
2564 2840 9.948964 TTCATGTTATATTGGGTGATCTAGATG 57.051 33.333 10.74 0.00 0.00 2.90
2565 2841 9.950496 GTTCATGTTATATTGGGTGATCTAGAT 57.050 33.333 4.47 4.47 0.00 1.98
2566 2842 8.933653 TGTTCATGTTATATTGGGTGATCTAGA 58.066 33.333 0.00 0.00 0.00 2.43
2567 2843 9.212641 CTGTTCATGTTATATTGGGTGATCTAG 57.787 37.037 0.00 0.00 0.00 2.43
2568 2844 8.933653 TCTGTTCATGTTATATTGGGTGATCTA 58.066 33.333 0.00 0.00 0.00 1.98
2569 2845 7.805163 TCTGTTCATGTTATATTGGGTGATCT 58.195 34.615 0.00 0.00 0.00 2.75
2570 2846 7.933577 TCTCTGTTCATGTTATATTGGGTGATC 59.066 37.037 0.00 0.00 0.00 2.92
2571 2847 7.805163 TCTCTGTTCATGTTATATTGGGTGAT 58.195 34.615 0.00 0.00 0.00 3.06
2572 2848 7.194112 TCTCTGTTCATGTTATATTGGGTGA 57.806 36.000 0.00 0.00 0.00 4.02
2573 2849 6.484643 CCTCTCTGTTCATGTTATATTGGGTG 59.515 42.308 0.00 0.00 0.00 4.61
2574 2850 6.409695 CCCTCTCTGTTCATGTTATATTGGGT 60.410 42.308 0.00 0.00 0.00 4.51
2575 2851 6.000219 CCCTCTCTGTTCATGTTATATTGGG 59.000 44.000 0.00 0.00 0.00 4.12
2576 2852 6.000219 CCCCTCTCTGTTCATGTTATATTGG 59.000 44.000 0.00 0.00 0.00 3.16
2577 2853 6.595682 ACCCCTCTCTGTTCATGTTATATTG 58.404 40.000 0.00 0.00 0.00 1.90
2578 2854 6.831664 ACCCCTCTCTGTTCATGTTATATT 57.168 37.500 0.00 0.00 0.00 1.28
2579 2855 6.831664 AACCCCTCTCTGTTCATGTTATAT 57.168 37.500 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.