Multiple sequence alignment - TraesCS7D01G154100

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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 TraesCS7D01G154100 chr7D 100.000 3302 0 0 1 3302 101784160 101780859 0.000000e+00 6098.0
1 TraesCS7D01G154100 chr7B 96.298 2215 73 6 514 2725 59101364 59099156 0.000000e+00 3627.0
2 TraesCS7D01G154100 chr7B 92.022 539 25 3 2761 3299 59078581 59079101 0.000000e+00 741.0
3 TraesCS7D01G154100 chr7B 91.186 295 23 2 1 293 59101946 59101653 6.640000e-107 398.0
4 TraesCS7D01G154100 chr7B 89.381 226 11 7 292 510 59101492 59101273 4.200000e-69 272.0
5 TraesCS7D01G154100 chr7A 96.660 1976 45 6 402 2364 105642250 105640283 0.000000e+00 3264.0
6 TraesCS7D01G154100 chr7A 85.375 253 30 6 2 248 105642499 105642248 4.230000e-64 255.0
7 TraesCS7D01G154100 chr6D 87.209 1290 162 2 991 2277 436832413 436833702 0.000000e+00 1465.0
8 TraesCS7D01G154100 chr6A 87.054 1290 164 3 991 2277 585108592 585109881 0.000000e+00 1454.0
9 TraesCS7D01G154100 chr6B 86.977 1290 165 2 991 2277 660564376 660563087 0.000000e+00 1448.0
10 TraesCS7D01G154100 chr5B 78.059 989 170 36 1253 2220 466333670 466332708 6.140000e-162 580.0
11 TraesCS7D01G154100 chr5A 78.014 987 164 40 1258 2220 490816306 490815349 3.700000e-159 571.0
12 TraesCS7D01G154100 chr5D 77.586 986 170 39 1258 2220 387728920 387727963 1.730000e-152 549.0
13 TraesCS7D01G154100 chr2D 85.542 166 17 6 1 165 394241113 394240954 2.040000e-37 167.0
14 TraesCS7D01G154100 chr2D 84.756 164 23 2 7 169 93650268 93650430 2.640000e-36 163.0
15 TraesCS7D01G154100 chr2D 83.832 167 24 3 1 165 592117521 592117356 4.410000e-34 156.0
16 TraesCS7D01G154100 chr1B 85.443 158 21 2 7 163 161987926 161988082 2.640000e-36 163.0
17 TraesCS7D01G154100 chr4B 82.857 175 30 0 2551 2725 63120194 63120368 1.230000e-34 158.0
18 TraesCS7D01G154100 chr4D 83.832 167 24 3 1 165 484745350 484745515 4.410000e-34 156.0
19 TraesCS7D01G154100 chr3D 82.320 181 25 7 1 176 86970895 86970717 2.050000e-32 150.0
20 TraesCS7D01G154100 chr3D 86.232 138 17 2 2549 2685 23855852 23855716 7.380000e-32 148.0
21 TraesCS7D01G154100 chr3B 82.840 169 26 3 1 167 152908461 152908628 7.380000e-32 148.0
22 TraesCS7D01G154100 chr3B 81.395 86 16 0 2574 2659 541513359 541513444 1.640000e-08 71.3
23 TraesCS7D01G154100 chr1A 83.217 143 22 2 2577 2718 29044402 29044543 2.670000e-26 130.0
24 TraesCS7D01G154100 chrUn 87.500 88 10 1 2571 2658 23529378 23529292 2.100000e-17 100.0
25 TraesCS7D01G154100 chrUn 80.000 110 13 8 2621 2725 23529291 23529186 4.570000e-09 73.1


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 TraesCS7D01G154100 chr7D 101780859 101784160 3301 True 6098.000000 6098 100.000000 1 3302 1 chr7D.!!$R1 3301
1 TraesCS7D01G154100 chr7B 59099156 59101946 2790 True 1432.333333 3627 92.288333 1 2725 3 chr7B.!!$R1 2724
2 TraesCS7D01G154100 chr7B 59078581 59079101 520 False 741.000000 741 92.022000 2761 3299 1 chr7B.!!$F1 538
3 TraesCS7D01G154100 chr7A 105640283 105642499 2216 True 1759.500000 3264 91.017500 2 2364 2 chr7A.!!$R1 2362
4 TraesCS7D01G154100 chr6D 436832413 436833702 1289 False 1465.000000 1465 87.209000 991 2277 1 chr6D.!!$F1 1286
5 TraesCS7D01G154100 chr6A 585108592 585109881 1289 False 1454.000000 1454 87.054000 991 2277 1 chr6A.!!$F1 1286
6 TraesCS7D01G154100 chr6B 660563087 660564376 1289 True 1448.000000 1448 86.977000 991 2277 1 chr6B.!!$R1 1286
7 TraesCS7D01G154100 chr5B 466332708 466333670 962 True 580.000000 580 78.059000 1253 2220 1 chr5B.!!$R1 967
8 TraesCS7D01G154100 chr5A 490815349 490816306 957 True 571.000000 571 78.014000 1258 2220 1 chr5A.!!$R1 962
9 TraesCS7D01G154100 chr5D 387727963 387728920 957 True 549.000000 549 77.586000 1258 2220 1 chr5D.!!$R1 962

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
940 1123 0.036294 CCCGTTGGTCTCCTCTTTCC 60.036 60.0 0.0 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2740 2935 0.041312 CGCGTTGGAACTCTTTGGTG 60.041 55.0 0.0 0.0 0.0 4.17 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
84 85 4.070552 GAGGCGCCCGTCTGAGTT 62.071 66.667 26.15 0.00 0.00 3.01
88 89 2.811317 CGCCCGTCTGAGTTGCTC 60.811 66.667 0.00 0.00 0.00 4.26
98 100 4.024556 CGTCTGAGTTGCTCTTTTGTGATT 60.025 41.667 0.00 0.00 0.00 2.57
99 101 5.504665 CGTCTGAGTTGCTCTTTTGTGATTT 60.505 40.000 0.00 0.00 0.00 2.17
133 136 2.520020 TCCGTCCGGGCGTATGAT 60.520 61.111 28.93 0.00 34.94 2.45
180 183 5.069119 AGACGCTCTGAATTATGATGGTGTA 59.931 40.000 0.00 0.00 0.00 2.90
204 207 1.733402 TTTTGCGACAGTTGCCCCAG 61.733 55.000 10.50 0.00 0.00 4.45
213 216 4.523083 GACAGTTGCCCCAGTTATGATAA 58.477 43.478 0.00 0.00 0.00 1.75
243 247 8.518430 TGGTTATTTACTCACATGCACATATT 57.482 30.769 0.00 0.00 0.00 1.28
245 249 7.798516 GGTTATTTACTCACATGCACATATTCG 59.201 37.037 0.00 0.00 0.00 3.34
246 250 8.547894 GTTATTTACTCACATGCACATATTCGA 58.452 33.333 0.00 0.00 0.00 3.71
256 262 3.141398 GCACATATTCGATGGATGTGGT 58.859 45.455 24.57 1.73 46.85 4.16
264 270 5.873179 TTCGATGGATGTGGTTAAGTTTC 57.127 39.130 0.00 0.00 0.00 2.78
272 278 3.460103 TGTGGTTAAGTTTCAGTCGACC 58.540 45.455 13.01 0.00 0.00 4.79
360 530 6.545508 TGTACGAATCTTCATGCAAAATCAG 58.454 36.000 0.00 0.00 0.00 2.90
361 531 5.633830 ACGAATCTTCATGCAAAATCAGT 57.366 34.783 0.00 0.00 0.00 3.41
378 548 1.374758 GTGAAGCCTCAGTCGGGTG 60.375 63.158 0.00 0.00 34.45 4.61
409 579 7.325660 AGCAAAACTGATAGTTGATACCATG 57.674 36.000 0.00 0.00 38.66 3.66
473 643 1.361668 CGCCATGAGCACAGGTACAC 61.362 60.000 0.00 0.00 44.04 2.90
591 774 4.768583 AGCATCCATTCTTCTCTTGTCTC 58.231 43.478 0.00 0.00 0.00 3.36
802 985 1.298859 GAGGCACACATTCGGTCCAC 61.299 60.000 0.00 0.00 0.00 4.02
810 993 1.671054 ATTCGGTCCACTGTTGCGG 60.671 57.895 0.00 0.00 0.00 5.69
940 1123 0.036294 CCCGTTGGTCTCCTCTTTCC 60.036 60.000 0.00 0.00 0.00 3.13
1779 1968 2.232941 CACCTACAACCACATCTACGGT 59.767 50.000 0.00 0.00 36.98 4.83
2412 2607 3.013219 CCACTCTCTGATCGAAGACTGA 58.987 50.000 0.00 0.00 42.51 3.41
2464 2659 8.731605 GGAAATACGAGGAAGAATTCTTTTCTT 58.268 33.333 21.33 16.52 46.56 2.52
2466 2661 5.948992 ACGAGGAAGAATTCTTTTCTTGG 57.051 39.130 26.41 20.68 46.56 3.61
2506 2701 6.659776 AGCGTTTTTCTCACTATGTTTTCTC 58.340 36.000 0.00 0.00 0.00 2.87
2595 2790 0.593128 AGCACATGCCAACTTCGAAC 59.407 50.000 0.00 0.00 43.38 3.95
2597 2792 0.586319 CACATGCCAACTTCGAACGT 59.414 50.000 0.00 0.00 0.00 3.99
2623 2818 4.090930 TCGATGACAAGTTTAGTTAAGCGC 59.909 41.667 0.00 0.00 0.00 5.92
2662 2857 3.382865 TGACAAGCATGGCAACTTTTGTA 59.617 39.130 0.00 0.00 43.21 2.41
2663 2858 4.039004 TGACAAGCATGGCAACTTTTGTAT 59.961 37.500 0.00 0.00 43.21 2.29
2665 2860 5.367302 ACAAGCATGGCAACTTTTGTATTT 58.633 33.333 3.61 0.00 37.61 1.40
2666 2861 5.466393 ACAAGCATGGCAACTTTTGTATTTC 59.534 36.000 3.61 0.00 37.61 2.17
2700 2895 0.249489 AGAAGCCTGTCGTGTGTCAC 60.249 55.000 0.00 0.00 0.00 3.67
2703 2898 1.067416 GCCTGTCGTGTGTCACTGA 59.933 57.895 4.27 0.00 31.34 3.41
2718 2913 8.946085 GTGTGTCACTGAAATTTATCATCCTTA 58.054 33.333 4.27 0.00 0.00 2.69
2725 2920 7.010183 ACTGAAATTTATCATCCTTACGTGACG 59.990 37.037 2.24 2.24 0.00 4.35
2726 2921 6.256975 TGAAATTTATCATCCTTACGTGACGG 59.743 38.462 10.66 0.00 0.00 4.79
2727 2922 4.724074 TTTATCATCCTTACGTGACGGT 57.276 40.909 10.66 0.00 0.00 4.83
2728 2923 2.579207 ATCATCCTTACGTGACGGTG 57.421 50.000 10.66 0.00 0.00 4.94
2729 2924 0.108992 TCATCCTTACGTGACGGTGC 60.109 55.000 10.66 0.00 0.00 5.01
2730 2925 1.082117 CATCCTTACGTGACGGTGCC 61.082 60.000 10.66 0.00 0.00 5.01
2731 2926 2.552585 ATCCTTACGTGACGGTGCCG 62.553 60.000 10.66 9.29 46.03 5.69
2743 2938 4.030452 GTGCCGTTGCTCTGCACC 62.030 66.667 14.18 0.00 46.52 5.01
2744 2939 4.560743 TGCCGTTGCTCTGCACCA 62.561 61.111 0.00 0.00 38.71 4.17
2745 2940 3.286751 GCCGTTGCTCTGCACCAA 61.287 61.111 0.00 0.00 38.71 3.67
2746 2941 2.844451 GCCGTTGCTCTGCACCAAA 61.844 57.895 0.00 0.00 38.71 3.28
2747 2942 1.283793 CCGTTGCTCTGCACCAAAG 59.716 57.895 0.00 0.00 38.71 2.77
2748 2943 1.165907 CCGTTGCTCTGCACCAAAGA 61.166 55.000 0.00 0.00 38.71 2.52
2749 2944 0.236711 CGTTGCTCTGCACCAAAGAG 59.763 55.000 0.00 0.00 43.42 2.85
2750 2945 1.312815 GTTGCTCTGCACCAAAGAGT 58.687 50.000 2.31 0.00 42.68 3.24
2751 2946 1.678101 GTTGCTCTGCACCAAAGAGTT 59.322 47.619 2.31 0.00 42.68 3.01
2752 2947 1.597742 TGCTCTGCACCAAAGAGTTC 58.402 50.000 2.31 0.00 42.68 3.01
2753 2948 0.877743 GCTCTGCACCAAAGAGTTCC 59.122 55.000 2.31 0.00 42.68 3.62
2754 2949 1.815408 GCTCTGCACCAAAGAGTTCCA 60.815 52.381 2.31 0.00 42.68 3.53
2755 2950 2.575532 CTCTGCACCAAAGAGTTCCAA 58.424 47.619 0.00 0.00 37.08 3.53
2756 2951 2.291741 CTCTGCACCAAAGAGTTCCAAC 59.708 50.000 0.00 0.00 37.08 3.77
2757 2952 1.002468 CTGCACCAAAGAGTTCCAACG 60.002 52.381 0.00 0.00 0.00 4.10
2758 2953 0.317854 GCACCAAAGAGTTCCAACGC 60.318 55.000 0.00 0.00 0.00 4.84
2759 2954 0.041312 CACCAAAGAGTTCCAACGCG 60.041 55.000 3.53 3.53 33.71 6.01
2760 2955 1.164041 ACCAAAGAGTTCCAACGCGG 61.164 55.000 12.47 0.00 33.71 6.46
2761 2956 1.574428 CAAAGAGTTCCAACGCGGG 59.426 57.895 12.47 2.26 33.71 6.13
2762 2957 0.882927 CAAAGAGTTCCAACGCGGGA 60.883 55.000 12.47 5.32 33.71 5.14
2763 2958 0.179040 AAAGAGTTCCAACGCGGGAA 60.179 50.000 12.47 12.28 44.50 3.97
2779 2974 2.124320 AAGCACAACCACCGCACT 60.124 55.556 0.00 0.00 0.00 4.40
2788 2983 0.393808 ACCACCGCACTGAACTTTGT 60.394 50.000 0.00 0.00 0.00 2.83
2857 3052 2.665000 CTCCGGTGCCAGTGACAT 59.335 61.111 0.00 0.00 0.00 3.06
2869 3064 0.607489 AGTGACATTGCTGGTGAGGC 60.607 55.000 0.00 0.00 0.00 4.70
2870 3065 0.890542 GTGACATTGCTGGTGAGGCA 60.891 55.000 0.00 0.00 37.97 4.75
2871 3066 0.038599 TGACATTGCTGGTGAGGCAT 59.961 50.000 0.00 0.00 39.54 4.40
2872 3067 0.737219 GACATTGCTGGTGAGGCATC 59.263 55.000 0.00 0.00 39.54 3.91
2873 3068 0.682209 ACATTGCTGGTGAGGCATCC 60.682 55.000 0.00 0.00 39.54 3.51
2874 3069 0.681887 CATTGCTGGTGAGGCATCCA 60.682 55.000 0.00 0.00 39.54 3.41
2875 3070 0.260816 ATTGCTGGTGAGGCATCCAT 59.739 50.000 0.00 0.00 39.54 3.41
2876 3071 0.394762 TTGCTGGTGAGGCATCCATC 60.395 55.000 0.00 0.00 39.54 3.51
2877 3072 1.225426 GCTGGTGAGGCATCCATCA 59.775 57.895 0.00 0.00 33.01 3.07
2878 3073 1.099879 GCTGGTGAGGCATCCATCAC 61.100 60.000 0.00 0.00 44.10 3.06
2879 3074 0.253894 CTGGTGAGGCATCCATCACA 59.746 55.000 3.52 0.00 46.14 3.58
2891 3086 4.774124 CATCCATCACACATCAGTAACCT 58.226 43.478 0.00 0.00 0.00 3.50
2927 3122 2.494918 CGGTGTCCACGATCTCCC 59.505 66.667 0.00 0.00 0.00 4.30
3228 3423 0.610174 CCACTACTTGCTCTGCTCCA 59.390 55.000 0.00 0.00 0.00 3.86
3259 3454 1.067060 CCATGCCGTGATCTTCGACTA 59.933 52.381 11.24 0.49 0.00 2.59
3263 3458 1.862008 GCCGTGATCTTCGACTAGCTG 60.862 57.143 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 100 4.308458 CGGCCCGGTCAGTGACAA 62.308 66.667 24.20 0.00 33.68 3.18
194 197 7.330262 CAAAAATTATCATAACTGGGGCAACT 58.670 34.615 0.00 0.00 0.00 3.16
213 216 8.147058 TGTGCATGTGAGTAAATAACCAAAAAT 58.853 29.630 0.00 0.00 0.00 1.82
243 247 4.900684 TGAAACTTAACCACATCCATCGA 58.099 39.130 0.00 0.00 0.00 3.59
245 249 5.163854 CGACTGAAACTTAACCACATCCATC 60.164 44.000 0.00 0.00 0.00 3.51
246 250 4.695455 CGACTGAAACTTAACCACATCCAT 59.305 41.667 0.00 0.00 0.00 3.41
256 262 3.567164 AGTCTCGGTCGACTGAAACTTAA 59.433 43.478 24.55 3.71 42.39 1.85
264 270 1.538512 TGGTTAAGTCTCGGTCGACTG 59.461 52.381 18.66 18.66 43.14 3.51
341 511 6.034683 GCTTCACTGATTTTGCATGAAGATTC 59.965 38.462 22.08 6.33 45.96 2.52
360 530 1.374758 CACCCGACTGAGGCTTCAC 60.375 63.158 0.00 0.00 0.00 3.18
361 531 1.533033 TCACCCGACTGAGGCTTCA 60.533 57.895 0.00 0.00 0.00 3.02
378 548 7.891183 TCAACTATCAGTTTTGCTAAGTCTC 57.109 36.000 0.00 0.00 36.03 3.36
388 558 6.828785 GGGACATGGTATCAACTATCAGTTTT 59.171 38.462 0.00 0.00 36.03 2.43
409 579 4.762251 AGCTCATTTGTAGAAGTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
447 617 4.112433 TGCTCATGGCGGCATGGA 62.112 61.111 40.81 28.82 45.43 3.41
469 639 3.838244 AGAGTGCTCTTGTTTGGTGTA 57.162 42.857 0.00 0.00 36.31 2.90
591 774 1.694150 TCCTGTGTGAAGACAAGAGGG 59.306 52.381 0.00 0.00 35.75 4.30
816 999 1.791103 GCTCGACCGATCAGCTAGCT 61.791 60.000 12.68 12.68 0.00 3.32
817 1000 1.371145 GCTCGACCGATCAGCTAGC 60.371 63.158 6.62 6.62 0.00 3.42
818 1001 1.082431 CGCTCGACCGATCAGCTAG 60.082 63.158 0.00 0.00 30.96 3.42
819 1002 3.023118 CGCTCGACCGATCAGCTA 58.977 61.111 0.00 0.00 30.96 3.32
940 1123 5.389516 GCTCATGCAAGCAAATGAAGAAAAG 60.390 40.000 5.50 0.00 42.05 2.27
979 1162 1.529713 CCTCCTCCTCCTCGGCTAC 60.530 68.421 0.00 0.00 0.00 3.58
2116 2311 2.100631 GCATCTCCACCACGTTCCG 61.101 63.158 0.00 0.00 0.00 4.30
2434 2629 7.130681 AGAATTCTTCCTCGTATTTCCTCAT 57.869 36.000 0.88 0.00 0.00 2.90
2464 2659 0.317160 CTAGCCCGATATCGTTGCCA 59.683 55.000 24.69 15.51 36.35 4.92
2466 2661 1.344942 CGCTAGCCCGATATCGTTGC 61.345 60.000 22.81 22.53 37.74 4.17
2506 2701 9.573133 GGGTGATATGTAATCAGTTTCAAAAAG 57.427 33.333 0.00 0.00 0.00 2.27
2543 2738 0.528924 CGACACGTATCAGGGTCCAA 59.471 55.000 0.00 0.00 41.30 3.53
2544 2739 0.322726 TCGACACGTATCAGGGTCCA 60.323 55.000 0.00 0.00 41.30 4.02
2595 2790 7.058016 GCTTAACTAAACTTGTCATCGAAAACG 59.942 37.037 0.00 0.00 0.00 3.60
2597 2792 7.067116 CGCTTAACTAAACTTGTCATCGAAAA 58.933 34.615 0.00 0.00 0.00 2.29
2605 2800 2.733026 TCCGCGCTTAACTAAACTTGTC 59.267 45.455 5.56 0.00 0.00 3.18
2618 2813 1.732259 CTAAAGTTGTCATCCGCGCTT 59.268 47.619 5.56 0.00 0.00 4.68
2643 2838 5.466058 TGAAATACAAAAGTTGCCATGCTTG 59.534 36.000 0.00 0.00 0.00 4.01
2662 2857 8.424133 AGGCTTCTGTCAAAAATAAACTGAAAT 58.576 29.630 0.00 0.00 32.71 2.17
2663 2858 7.706179 CAGGCTTCTGTCAAAAATAAACTGAAA 59.294 33.333 0.00 0.00 32.71 2.69
2665 2860 6.738114 CAGGCTTCTGTCAAAAATAAACTGA 58.262 36.000 0.00 0.00 33.96 3.41
2666 2861 6.998258 CAGGCTTCTGTCAAAAATAAACTG 57.002 37.500 0.00 0.00 33.96 3.16
2685 2880 0.529773 TTCAGTGACACACGACAGGC 60.530 55.000 8.59 0.00 39.64 4.85
2694 2889 8.116753 CGTAAGGATGATAAATTTCAGTGACAC 58.883 37.037 0.00 0.00 0.00 3.67
2700 2895 7.337718 CGTCACGTAAGGATGATAAATTTCAG 58.662 38.462 0.00 0.00 46.39 3.02
2703 2898 6.036735 CACCGTCACGTAAGGATGATAAATTT 59.963 38.462 9.68 0.00 46.39 1.82
2732 2927 1.949525 GAACTCTTTGGTGCAGAGCAA 59.050 47.619 0.10 0.00 41.47 3.91
2733 2928 1.597742 GAACTCTTTGGTGCAGAGCA 58.402 50.000 0.10 0.00 41.49 4.26
2734 2929 0.877743 GGAACTCTTTGGTGCAGAGC 59.122 55.000 0.10 0.00 41.49 4.09
2735 2930 2.260844 TGGAACTCTTTGGTGCAGAG 57.739 50.000 0.00 0.00 43.16 3.35
2736 2931 2.297701 GTTGGAACTCTTTGGTGCAGA 58.702 47.619 0.00 0.00 34.49 4.26
2737 2932 1.002468 CGTTGGAACTCTTTGGTGCAG 60.002 52.381 0.00 0.00 34.49 4.41
2738 2933 1.021202 CGTTGGAACTCTTTGGTGCA 58.979 50.000 0.00 0.00 0.00 4.57
2739 2934 0.317854 GCGTTGGAACTCTTTGGTGC 60.318 55.000 0.00 0.00 0.00 5.01
2740 2935 0.041312 CGCGTTGGAACTCTTTGGTG 60.041 55.000 0.00 0.00 0.00 4.17
2741 2936 1.164041 CCGCGTTGGAACTCTTTGGT 61.164 55.000 4.92 0.00 42.00 3.67
2742 2937 1.574428 CCGCGTTGGAACTCTTTGG 59.426 57.895 4.92 0.00 42.00 3.28
2743 2938 0.882927 TCCCGCGTTGGAACTCTTTG 60.883 55.000 4.92 0.00 42.00 2.77
2744 2939 0.179040 TTCCCGCGTTGGAACTCTTT 60.179 50.000 12.14 0.00 39.48 2.52
2745 2940 0.602905 CTTCCCGCGTTGGAACTCTT 60.603 55.000 12.14 0.00 39.48 2.85
2746 2941 1.004918 CTTCCCGCGTTGGAACTCT 60.005 57.895 12.14 0.00 39.48 3.24
2747 2942 2.677979 GCTTCCCGCGTTGGAACTC 61.678 63.158 12.14 4.77 39.48 3.01
2748 2943 2.668550 GCTTCCCGCGTTGGAACT 60.669 61.111 12.14 0.00 39.48 3.01
2749 2944 2.975799 TGCTTCCCGCGTTGGAAC 60.976 61.111 12.14 10.06 39.48 3.62
2750 2945 2.975799 GTGCTTCCCGCGTTGGAA 60.976 61.111 14.87 14.87 42.09 3.53
2751 2946 3.758973 TTGTGCTTCCCGCGTTGGA 62.759 57.895 4.92 1.85 43.27 3.53
2752 2947 3.283684 TTGTGCTTCCCGCGTTGG 61.284 61.111 4.92 0.00 43.27 3.77
2753 2948 2.051345 GTTGTGCTTCCCGCGTTG 60.051 61.111 4.92 0.00 43.27 4.10
2754 2949 3.284449 GGTTGTGCTTCCCGCGTT 61.284 61.111 4.92 0.00 43.27 4.84
2755 2950 4.555709 TGGTTGTGCTTCCCGCGT 62.556 61.111 4.92 0.00 43.27 6.01
2756 2951 4.025401 GTGGTTGTGCTTCCCGCG 62.025 66.667 0.00 0.00 43.27 6.46
2757 2952 3.670377 GGTGGTTGTGCTTCCCGC 61.670 66.667 0.00 0.00 39.77 6.13
2758 2953 3.353836 CGGTGGTTGTGCTTCCCG 61.354 66.667 0.00 0.00 0.00 5.14
2759 2954 3.670377 GCGGTGGTTGTGCTTCCC 61.670 66.667 0.00 0.00 0.00 3.97
2760 2955 2.904866 TGCGGTGGTTGTGCTTCC 60.905 61.111 0.00 0.00 0.00 3.46
2761 2956 2.186826 AGTGCGGTGGTTGTGCTTC 61.187 57.895 0.00 0.00 0.00 3.86
2762 2957 2.124320 AGTGCGGTGGTTGTGCTT 60.124 55.556 0.00 0.00 0.00 3.91
2763 2958 2.884997 TTCAGTGCGGTGGTTGTGCT 62.885 55.000 0.00 0.00 0.00 4.40
2764 2959 2.477176 TTCAGTGCGGTGGTTGTGC 61.477 57.895 0.00 0.00 0.00 4.57
2765 2960 1.095228 AGTTCAGTGCGGTGGTTGTG 61.095 55.000 0.00 0.00 0.00 3.33
2766 2961 0.393808 AAGTTCAGTGCGGTGGTTGT 60.394 50.000 0.00 0.00 0.00 3.32
2767 2962 0.738389 AAAGTTCAGTGCGGTGGTTG 59.262 50.000 0.00 0.00 0.00 3.77
2768 2963 0.738389 CAAAGTTCAGTGCGGTGGTT 59.262 50.000 0.00 0.00 0.00 3.67
2772 2967 1.944709 GGTAACAAAGTTCAGTGCGGT 59.055 47.619 0.00 0.00 0.00 5.68
2779 2974 0.584396 CGCTGCGGTAACAAAGTTCA 59.416 50.000 15.40 0.00 0.00 3.18
2815 3010 2.202610 GGATTTTGAAGCCGCGGC 60.203 61.111 42.34 42.34 42.33 6.53
2818 3013 1.373590 TAGCGGGATTTTGAAGCCGC 61.374 55.000 0.00 0.00 38.00 6.53
2829 3024 4.541648 ACCGGAGCCTAGCGGGAT 62.542 66.667 9.46 0.00 37.23 3.85
2849 3044 1.162698 CCTCACCAGCAATGTCACTG 58.837 55.000 0.00 0.00 0.00 3.66
2850 3045 0.607489 GCCTCACCAGCAATGTCACT 60.607 55.000 0.00 0.00 0.00 3.41
2854 3049 0.682209 GGATGCCTCACCAGCAATGT 60.682 55.000 0.00 0.00 44.83 2.71
2857 3052 0.394762 GATGGATGCCTCACCAGCAA 60.395 55.000 0.00 0.00 44.83 3.91
2869 3064 4.774124 AGGTTACTGATGTGTGATGGATG 58.226 43.478 0.00 0.00 0.00 3.51
2906 3101 3.387947 GATCGTGGACACCGGGGT 61.388 66.667 10.56 10.56 0.00 4.95
2907 3102 3.075005 AGATCGTGGACACCGGGG 61.075 66.667 0.00 0.00 0.00 5.73
2908 3103 2.494918 GAGATCGTGGACACCGGG 59.505 66.667 6.32 0.00 0.00 5.73
2909 3104 2.494918 GGAGATCGTGGACACCGG 59.505 66.667 0.00 0.00 0.00 5.28
2927 3122 1.759445 AGGACGATGGTCTTCTCCATG 59.241 52.381 7.84 0.00 46.72 3.66
3167 3362 2.829458 AGGCGGAGGTACGAGAGC 60.829 66.667 0.00 0.00 35.47 4.09
3206 3401 0.901124 AGCAGAGCAAGTAGTGGAGG 59.099 55.000 0.00 0.00 0.00 4.30
3213 3408 1.888436 CGGGTGGAGCAGAGCAAGTA 61.888 60.000 0.00 0.00 0.00 2.24
3216 3411 4.704833 GCGGGTGGAGCAGAGCAA 62.705 66.667 0.00 0.00 34.19 3.91


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

AutoCloner maintained by Alex Coulton.