Multiple sequence alignment - TraesCS7D01G465700

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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 TraesCS7D01G465700 chr7D 100.000 3710 0 0 1 3710 579761925 579758216 0.000000e+00 6852.0
1 TraesCS7D01G465700 chr7D 84.460 2471 350 24 116 2572 621260938 621263388 0.000000e+00 2405.0
2 TraesCS7D01G465700 chr7D 82.410 2365 380 28 236 2583 632020435 632022780 0.000000e+00 2030.0
3 TraesCS7D01G465700 chr7D 81.235 2462 402 34 92 2532 632080941 632083363 0.000000e+00 1932.0
4 TraesCS7D01G465700 chr7D 95.918 49 2 0 3063 3111 598614010 598614058 3.070000e-11 80.5
5 TraesCS7D01G465700 chr7D 97.561 41 1 0 3071 3111 219834542 219834502 1.850000e-08 71.3
6 TraesCS7D01G465700 chr7A 95.048 2807 129 7 60 2860 671425474 671422672 0.000000e+00 4405.0
7 TraesCS7D01G465700 chr7A 81.913 2499 410 32 111 2589 736006743 736004267 0.000000e+00 2073.0
8 TraesCS7D01G465700 chr7A 79.234 2480 457 43 92 2543 735822479 735820030 0.000000e+00 1674.0
9 TraesCS7D01G465700 chr7A 83.859 539 56 18 3132 3662 671422554 671422039 5.570000e-133 484.0
10 TraesCS7D01G465700 chr1B 83.276 2314 366 20 280 2582 577925984 577923681 0.000000e+00 2109.0
11 TraesCS7D01G465700 chr1B 82.014 139 14 5 2848 2976 683292125 683292262 1.410000e-19 108.0
12 TraesCS7D01G465700 chr1B 82.014 139 14 5 2848 2976 683308355 683308492 1.410000e-19 108.0
13 TraesCS7D01G465700 chr1B 100.000 40 0 0 3071 3110 667833971 667833932 1.430000e-09 75.0
14 TraesCS7D01G465700 chr7B 97.366 1177 30 1 498 1673 645397381 645396205 0.000000e+00 2001.0
15 TraesCS7D01G465700 chr7B 81.121 2516 433 28 92 2589 744249609 744252100 0.000000e+00 1977.0
16 TraesCS7D01G465700 chr7B 92.085 1415 64 16 1668 3070 645395991 645394613 0.000000e+00 1949.0
17 TraesCS7D01G465700 chr7B 80.905 2519 418 47 92 2582 747526250 747523767 0.000000e+00 1929.0
18 TraesCS7D01G465700 chr7B 91.343 566 20 9 3169 3708 645394412 645393850 0.000000e+00 747.0
19 TraesCS7D01G465700 chr7B 90.854 164 12 2 127 287 645401169 645401006 2.240000e-52 217.0
20 TraesCS7D01G465700 chr7B 90.909 66 5 1 61 125 645401347 645401282 1.840000e-13 87.9
21 TraesCS7D01G465700 chr7B 97.222 36 1 0 3132 3167 645394614 645394579 1.110000e-05 62.1
22 TraesCS7D01G465700 chr1D 81.295 139 15 4 2848 2976 490546418 490546555 6.560000e-18 102.0
23 TraesCS7D01G465700 chr6B 86.567 67 5 4 3071 3133 7555430 7555364 1.850000e-08 71.3
24 TraesCS7D01G465700 chr4D 97.561 41 1 0 3071 3111 380252190 380252230 1.850000e-08 71.3
25 TraesCS7D01G465700 chr4D 97.561 41 1 0 3071 3111 451169212 451169252 1.850000e-08 71.3
26 TraesCS7D01G465700 chr3D 93.478 46 2 1 3066 3111 33864761 33864805 2.390000e-07 67.6
27 TraesCS7D01G465700 chr1A 91.837 49 2 2 3063 3111 58276420 58276374 2.390000e-07 67.6
28 TraesCS7D01G465700 chr1A 93.478 46 2 1 3066 3111 517330197 517330153 2.390000e-07 67.6
29 TraesCS7D01G465700 chr2A 100.000 29 0 0 3112 3140 112748104 112748076 2.000000e-03 54.7
30 TraesCS7D01G465700 chr3B 100.000 28 0 0 3112 3139 561233810 561233783 7.000000e-03 52.8


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 TraesCS7D01G465700 chr7D 579758216 579761925 3709 True 6852.0 6852 100.0000 1 3710 1 chr7D.!!$R2 3709
1 TraesCS7D01G465700 chr7D 621260938 621263388 2450 False 2405.0 2405 84.4600 116 2572 1 chr7D.!!$F2 2456
2 TraesCS7D01G465700 chr7D 632020435 632022780 2345 False 2030.0 2030 82.4100 236 2583 1 chr7D.!!$F3 2347
3 TraesCS7D01G465700 chr7D 632080941 632083363 2422 False 1932.0 1932 81.2350 92 2532 1 chr7D.!!$F4 2440
4 TraesCS7D01G465700 chr7A 671422039 671425474 3435 True 2444.5 4405 89.4535 60 3662 2 chr7A.!!$R3 3602
5 TraesCS7D01G465700 chr7A 736004267 736006743 2476 True 2073.0 2073 81.9130 111 2589 1 chr7A.!!$R2 2478
6 TraesCS7D01G465700 chr7A 735820030 735822479 2449 True 1674.0 1674 79.2340 92 2543 1 chr7A.!!$R1 2451
7 TraesCS7D01G465700 chr1B 577923681 577925984 2303 True 2109.0 2109 83.2760 280 2582 1 chr1B.!!$R1 2302
8 TraesCS7D01G465700 chr7B 744249609 744252100 2491 False 1977.0 1977 81.1210 92 2589 1 chr7B.!!$F1 2497
9 TraesCS7D01G465700 chr7B 747523767 747526250 2483 True 1929.0 1929 80.9050 92 2582 1 chr7B.!!$R1 2490
10 TraesCS7D01G465700 chr7B 645393850 645401347 7497 True 844.0 2001 93.2965 61 3708 6 chr7B.!!$R2 3647

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
332 516 1.695242 TGTCCCTTGTACCATGTTCGT 59.305 47.619 0.0 0.0 0.00 3.85 F
2160 5940 1.332195 GCCCAAAGCTGAAGGTTCTT 58.668 50.000 0.0 0.0 38.99 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 6018 1.296056 GCTGCAAATGCCTTGGCTTG 61.296 55.0 13.18 10.63 41.18 4.01 R
3071 6879 0.042131 TGTTATGGGACGGAGGGAGT 59.958 55.0 0.00 0.00 0.00 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 6.507900 TGAGAGAGCAGTATTAAGTGTATGC 58.492 40.000 0.00 0.00 0.00 3.14
27 28 6.096846 TGAGAGAGCAGTATTAAGTGTATGCA 59.903 38.462 0.00 0.00 36.15 3.96
28 29 7.060383 AGAGAGCAGTATTAAGTGTATGCAT 57.940 36.000 3.79 3.79 36.15 3.96
29 30 6.927936 AGAGAGCAGTATTAAGTGTATGCATG 59.072 38.462 10.16 0.00 36.15 4.06
30 31 5.468072 AGAGCAGTATTAAGTGTATGCATGC 59.532 40.000 11.82 11.82 36.15 4.06
31 32 4.212004 AGCAGTATTAAGTGTATGCATGCG 59.788 41.667 14.09 0.00 36.15 4.73
32 33 4.024893 GCAGTATTAAGTGTATGCATGCGT 60.025 41.667 18.07 18.07 33.92 5.24
33 34 5.434706 CAGTATTAAGTGTATGCATGCGTG 58.565 41.667 22.77 0.09 0.00 5.34
34 35 5.234116 CAGTATTAAGTGTATGCATGCGTGA 59.766 40.000 22.77 6.01 0.00 4.35
35 36 4.536364 ATTAAGTGTATGCATGCGTGAC 57.464 40.909 22.77 17.40 0.00 3.67
36 37 1.807139 AAGTGTATGCATGCGTGACA 58.193 45.000 22.77 17.51 0.00 3.58
37 38 2.028420 AGTGTATGCATGCGTGACAT 57.972 45.000 22.77 14.50 40.66 3.06
38 39 2.358957 AGTGTATGCATGCGTGACATT 58.641 42.857 22.77 14.42 36.64 2.71
39 40 3.530535 AGTGTATGCATGCGTGACATTA 58.469 40.909 22.77 0.00 36.64 1.90
40 41 3.309682 AGTGTATGCATGCGTGACATTAC 59.690 43.478 22.77 11.62 36.64 1.89
41 42 3.309682 GTGTATGCATGCGTGACATTACT 59.690 43.478 22.77 0.00 36.64 2.24
42 43 3.938334 TGTATGCATGCGTGACATTACTT 59.062 39.130 22.77 0.00 36.64 2.24
43 44 4.394610 TGTATGCATGCGTGACATTACTTT 59.605 37.500 22.77 0.00 36.64 2.66
44 45 3.469899 TGCATGCGTGACATTACTTTC 57.530 42.857 14.09 0.00 36.64 2.62
45 46 2.161410 TGCATGCGTGACATTACTTTCC 59.839 45.455 14.09 0.00 36.64 3.13
46 47 2.161410 GCATGCGTGACATTACTTTCCA 59.839 45.455 10.93 0.00 36.64 3.53
47 48 3.181497 GCATGCGTGACATTACTTTCCAT 60.181 43.478 10.93 0.00 36.64 3.41
48 49 4.035091 GCATGCGTGACATTACTTTCCATA 59.965 41.667 10.93 0.00 36.64 2.74
49 50 5.448496 GCATGCGTGACATTACTTTCCATAA 60.448 40.000 10.93 0.00 36.64 1.90
50 51 6.728200 CATGCGTGACATTACTTTCCATAAT 58.272 36.000 0.00 0.00 36.64 1.28
51 52 6.751514 TGCGTGACATTACTTTCCATAATT 57.248 33.333 0.00 0.00 0.00 1.40
52 53 7.151999 TGCGTGACATTACTTTCCATAATTT 57.848 32.000 0.00 0.00 0.00 1.82
53 54 7.026562 TGCGTGACATTACTTTCCATAATTTG 58.973 34.615 0.00 0.00 0.00 2.32
54 55 7.094592 TGCGTGACATTACTTTCCATAATTTGA 60.095 33.333 0.00 0.00 0.00 2.69
55 56 7.753132 GCGTGACATTACTTTCCATAATTTGAA 59.247 33.333 0.00 0.00 0.00 2.69
56 57 9.787532 CGTGACATTACTTTCCATAATTTGAAT 57.212 29.630 0.00 0.00 0.00 2.57
58 59 9.585099 TGACATTACTTTCCATAATTTGAATGC 57.415 29.630 0.00 0.00 0.00 3.56
69 70 9.806203 TCCATAATTTGAATGCATTTCTGTAAG 57.194 29.630 14.33 1.28 35.23 2.34
332 516 1.695242 TGTCCCTTGTACCATGTTCGT 59.305 47.619 0.00 0.00 0.00 3.85
781 4334 3.627123 TGTATGTTGCTCCATGGATTTCG 59.373 43.478 16.63 4.42 0.00 3.46
1161 4719 2.714250 TGTACTTCCAGGGAACATTGGT 59.286 45.455 0.00 0.00 36.26 3.67
1535 5093 7.651027 ATGATGGGTTGATAAAAGAGAAAGG 57.349 36.000 0.00 0.00 0.00 3.11
1641 5199 2.687370 GGTGGTTATTTTGGCAAGCAG 58.313 47.619 0.00 0.00 33.19 4.24
2043 5823 3.650942 TCCAACACCTCAACTACCTTGAT 59.349 43.478 0.00 0.00 38.26 2.57
2053 5833 4.534500 TCAACTACCTTGATGGCTTTCCTA 59.466 41.667 0.00 0.00 40.22 2.94
2157 5937 1.620323 GATTGCCCAAAGCTGAAGGTT 59.380 47.619 0.00 0.00 44.23 3.50
2160 5940 1.332195 GCCCAAAGCTGAAGGTTCTT 58.668 50.000 0.00 0.00 38.99 2.52
2174 5954 3.690460 AGGTTCTTGAAAGTATGCCTGG 58.310 45.455 0.00 0.00 0.00 4.45
2238 6018 3.197766 TCCCAGAATACATGCGGGATATC 59.802 47.826 0.00 0.00 41.08 1.63
2325 6106 4.030913 CTGGTCCTGAGTGGGATAAGTTA 58.969 47.826 0.00 0.00 37.73 2.24
2424 6205 2.157738 GACAACTGCAAGCTGGATTCT 58.842 47.619 0.00 0.00 37.60 2.40
2555 6346 3.967332 ATTTCCTGCCTTTTGTCCATG 57.033 42.857 0.00 0.00 0.00 3.66
2557 6348 1.619654 TCCTGCCTTTTGTCCATGTG 58.380 50.000 0.00 0.00 0.00 3.21
2562 6353 3.561143 TGCCTTTTGTCCATGTGTACTT 58.439 40.909 0.00 0.00 0.00 2.24
2821 6625 6.293407 GCTGTTATTAACTGTGCTTCAAGTCA 60.293 38.462 13.05 0.00 33.43 3.41
2920 6724 4.771114 TGCCTATTAAAGCTGGCTCTTA 57.229 40.909 11.38 0.00 45.11 2.10
2945 6753 0.538057 TTCCCTTTCTGTGCAGGCAG 60.538 55.000 0.00 0.00 37.81 4.85
2946 6754 1.975407 CCCTTTCTGTGCAGGCAGG 60.975 63.158 4.64 9.35 37.12 4.85
2947 6755 2.633509 CCTTTCTGTGCAGGCAGGC 61.634 63.158 4.64 0.00 37.12 4.85
2948 6756 1.900016 CTTTCTGTGCAGGCAGGCA 60.900 57.895 4.64 0.00 42.53 4.75
2951 6759 1.246056 TTCTGTGCAGGCAGGCAATC 61.246 55.000 5.40 0.00 46.93 2.67
2980 6788 1.208052 GTAATGGAGCCAGAGTCTGCA 59.792 52.381 15.10 7.59 36.37 4.41
2982 6790 0.908656 ATGGAGCCAGAGTCTGCACT 60.909 55.000 15.10 13.53 34.78 4.40
2984 6792 0.459489 GGAGCCAGAGTCTGCACTAG 59.541 60.000 15.10 1.79 30.63 2.57
3006 6814 5.907421 AGTGCATCCCCATATTCCAAATAT 58.093 37.500 0.00 0.00 0.00 1.28
3009 6817 5.716228 TGCATCCCCATATTCCAAATATGTC 59.284 40.000 15.09 2.83 31.77 3.06
3010 6818 5.716228 GCATCCCCATATTCCAAATATGTCA 59.284 40.000 15.09 3.37 31.77 3.58
3017 6825 8.517878 CCCATATTCCAAATATGTCAGTTGATC 58.482 37.037 15.09 0.00 34.06 2.92
3023 6831 6.313658 TCCAAATATGTCAGTTGATCGTGAAG 59.686 38.462 0.00 0.00 34.06 3.02
3028 6836 3.131396 GTCAGTTGATCGTGAAGGTGTT 58.869 45.455 0.00 0.00 0.00 3.32
3029 6837 3.560068 GTCAGTTGATCGTGAAGGTGTTT 59.440 43.478 0.00 0.00 0.00 2.83
3030 6838 4.035208 GTCAGTTGATCGTGAAGGTGTTTT 59.965 41.667 0.00 0.00 0.00 2.43
3031 6839 4.638421 TCAGTTGATCGTGAAGGTGTTTTT 59.362 37.500 0.00 0.00 0.00 1.94
3075 6883 7.941795 ACTTTGTATGCGTGTTATATACTCC 57.058 36.000 0.00 0.00 0.00 3.85
3076 6884 6.927381 ACTTTGTATGCGTGTTATATACTCCC 59.073 38.462 0.00 0.00 0.00 4.30
3077 6885 6.659745 TTGTATGCGTGTTATATACTCCCT 57.340 37.500 0.00 0.00 0.00 4.20
3078 6886 6.263516 TGTATGCGTGTTATATACTCCCTC 57.736 41.667 0.00 0.00 0.00 4.30
3079 6887 4.803098 ATGCGTGTTATATACTCCCTCC 57.197 45.455 0.00 0.00 0.00 4.30
3080 6888 2.555325 TGCGTGTTATATACTCCCTCCG 59.445 50.000 0.00 0.00 0.00 4.63
3081 6889 2.555757 GCGTGTTATATACTCCCTCCGT 59.444 50.000 0.00 0.00 0.00 4.69
3082 6890 3.365767 GCGTGTTATATACTCCCTCCGTC 60.366 52.174 0.00 0.00 0.00 4.79
3083 6891 3.190118 CGTGTTATATACTCCCTCCGTCC 59.810 52.174 0.00 0.00 0.00 4.79
3084 6892 3.509184 GTGTTATATACTCCCTCCGTCCC 59.491 52.174 0.00 0.00 0.00 4.46
3085 6893 3.140707 TGTTATATACTCCCTCCGTCCCA 59.859 47.826 0.00 0.00 0.00 4.37
3086 6894 4.202749 TGTTATATACTCCCTCCGTCCCAT 60.203 45.833 0.00 0.00 0.00 4.00
3087 6895 5.015497 TGTTATATACTCCCTCCGTCCCATA 59.985 44.000 0.00 0.00 0.00 2.74
3088 6896 4.687262 ATATACTCCCTCCGTCCCATAA 57.313 45.455 0.00 0.00 0.00 1.90
3089 6897 2.077687 TACTCCCTCCGTCCCATAAC 57.922 55.000 0.00 0.00 0.00 1.89
3090 6898 0.042131 ACTCCCTCCGTCCCATAACA 59.958 55.000 0.00 0.00 0.00 2.41
3091 6899 1.344087 ACTCCCTCCGTCCCATAACAT 60.344 52.381 0.00 0.00 0.00 2.71
3092 6900 2.090943 ACTCCCTCCGTCCCATAACATA 60.091 50.000 0.00 0.00 0.00 2.29
3093 6901 2.969950 CTCCCTCCGTCCCATAACATAA 59.030 50.000 0.00 0.00 0.00 1.90
3094 6902 2.969950 TCCCTCCGTCCCATAACATAAG 59.030 50.000 0.00 0.00 0.00 1.73
3095 6903 2.969950 CCCTCCGTCCCATAACATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3096 6904 3.006967 CCCTCCGTCCCATAACATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
3097 6905 3.555168 CCTCCGTCCCATAACATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
3098 6906 2.035449 TCCGTCCCATAACATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
3099 6907 2.223971 CCGTCCCATAACATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
3100 6908 3.454375 CGTCCCATAACATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
3101 6909 3.869246 CGTCCCATAACATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
3102 6910 4.331717 CGTCCCATAACATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
3103 6911 5.163794 CGTCCCATAACATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
3137 6945 1.149288 TGGGACAGAGGGAGTACTTGT 59.851 52.381 0.00 0.00 0.00 3.16
3205 7178 2.936919 TTCACAGCATGACTTCCAGT 57.063 45.000 0.00 0.00 39.69 4.00
3227 7200 4.925646 GTGAATTTTCCACATGCCTCTTTC 59.074 41.667 0.00 0.00 34.81 2.62
3243 7216 5.888161 GCCTCTTTCAAGATTCCCTGAAATA 59.112 40.000 10.38 5.09 33.93 1.40
3294 7267 7.114811 CGGTATTCTTTGGAAAAATGAACACAG 59.885 37.037 0.00 0.00 34.90 3.66
3368 7346 0.179059 TGGCCGCATGATCACGTATT 60.179 50.000 0.00 0.00 0.00 1.89
3374 7352 2.728318 CGCATGATCACGTATTGGAGAG 59.272 50.000 0.00 0.00 0.00 3.20
3402 7380 9.981460 AATTTTAATAGACAGAAGTGGGAGAAT 57.019 29.630 0.00 0.00 0.00 2.40
3508 7486 8.500773 TGGAGAACAATGAAAAATACGACTAAC 58.499 33.333 0.00 0.00 0.00 2.34
3545 7530 9.391006 CACTTACCACAACATTGTTACCTATAT 57.609 33.333 0.86 0.00 39.91 0.86
3617 7626 2.462456 TCCTGTGCAAGTGCTCTTAG 57.538 50.000 4.69 0.00 42.66 2.18
3635 7644 4.216257 TCTTAGCATGTCAAGTTGCTTTCC 59.784 41.667 4.80 0.00 46.71 3.13
3652 7661 5.128827 TGCTTTCCTCCTTTACATCGTAGAT 59.871 40.000 0.00 0.00 45.12 1.98
3672 7681 6.236558 AGATAGTTTAGTTTCCCTGTAGCC 57.763 41.667 0.00 0.00 0.00 3.93
3683 7692 1.378514 CTGTAGCCGCCCACCATTT 60.379 57.895 0.00 0.00 0.00 2.32
3692 7701 3.368531 GCCGCCCACCATTTTATTTACAA 60.369 43.478 0.00 0.00 0.00 2.41
3696 7705 6.350277 CCGCCCACCATTTTATTTACAAGTAA 60.350 38.462 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.655328 GCATACACTTAATACTGCTCTCTCATT 59.345 37.037 0.00 0.00 0.00 2.57
2 3 6.096846 TGCATACACTTAATACTGCTCTCTCA 59.903 38.462 0.00 0.00 0.00 3.27
3 4 6.507900 TGCATACACTTAATACTGCTCTCTC 58.492 40.000 0.00 0.00 0.00 3.20
4 5 6.471233 TGCATACACTTAATACTGCTCTCT 57.529 37.500 0.00 0.00 0.00 3.10
5 6 6.347240 GCATGCATACACTTAATACTGCTCTC 60.347 42.308 14.21 0.00 0.00 3.20
6 7 5.468072 GCATGCATACACTTAATACTGCTCT 59.532 40.000 14.21 0.00 0.00 4.09
7 8 5.613360 CGCATGCATACACTTAATACTGCTC 60.613 44.000 19.57 0.00 0.00 4.26
8 9 4.212004 CGCATGCATACACTTAATACTGCT 59.788 41.667 19.57 0.00 0.00 4.24
9 10 4.024893 ACGCATGCATACACTTAATACTGC 60.025 41.667 19.57 0.00 0.00 4.40
10 11 5.234116 TCACGCATGCATACACTTAATACTG 59.766 40.000 19.57 0.00 0.00 2.74
11 12 5.234329 GTCACGCATGCATACACTTAATACT 59.766 40.000 19.57 0.00 0.00 2.12
12 13 5.006261 TGTCACGCATGCATACACTTAATAC 59.994 40.000 19.57 0.16 0.00 1.89
13 14 5.112686 TGTCACGCATGCATACACTTAATA 58.887 37.500 19.57 0.00 0.00 0.98
14 15 3.938334 TGTCACGCATGCATACACTTAAT 59.062 39.130 19.57 0.00 0.00 1.40
15 16 3.330267 TGTCACGCATGCATACACTTAA 58.670 40.909 19.57 0.00 0.00 1.85
16 17 2.966050 TGTCACGCATGCATACACTTA 58.034 42.857 19.57 0.00 0.00 2.24
17 18 1.807139 TGTCACGCATGCATACACTT 58.193 45.000 19.57 0.00 0.00 3.16
18 19 2.028420 ATGTCACGCATGCATACACT 57.972 45.000 19.57 5.98 36.26 3.55
19 20 2.830772 AATGTCACGCATGCATACAC 57.169 45.000 19.57 8.69 37.96 2.90
20 21 3.530535 AGTAATGTCACGCATGCATACA 58.469 40.909 19.57 17.64 37.96 2.29
21 22 4.536364 AAGTAATGTCACGCATGCATAC 57.464 40.909 19.57 12.42 37.96 2.39
22 23 4.035091 GGAAAGTAATGTCACGCATGCATA 59.965 41.667 19.57 0.00 37.96 3.14
23 24 3.181497 GGAAAGTAATGTCACGCATGCAT 60.181 43.478 19.57 0.00 37.96 3.96
24 25 2.161410 GGAAAGTAATGTCACGCATGCA 59.839 45.455 19.57 0.00 37.96 3.96
25 26 2.161410 TGGAAAGTAATGTCACGCATGC 59.839 45.455 7.91 7.91 37.96 4.06
26 27 4.621068 ATGGAAAGTAATGTCACGCATG 57.379 40.909 0.00 0.00 37.96 4.06
27 28 6.942532 ATTATGGAAAGTAATGTCACGCAT 57.057 33.333 0.00 0.00 40.03 4.73
28 29 6.751514 AATTATGGAAAGTAATGTCACGCA 57.248 33.333 0.00 0.00 0.00 5.24
29 30 7.247728 TCAAATTATGGAAAGTAATGTCACGC 58.752 34.615 0.00 0.00 0.00 5.34
30 31 9.787532 ATTCAAATTATGGAAAGTAATGTCACG 57.212 29.630 0.00 0.00 0.00 4.35
32 33 9.585099 GCATTCAAATTATGGAAAGTAATGTCA 57.415 29.630 0.00 0.00 0.00 3.58
33 34 9.585099 TGCATTCAAATTATGGAAAGTAATGTC 57.415 29.630 0.00 0.00 0.00 3.06
39 40 9.158233 CAGAAATGCATTCAAATTATGGAAAGT 57.842 29.630 13.38 0.00 40.72 2.66
40 41 9.158233 ACAGAAATGCATTCAAATTATGGAAAG 57.842 29.630 13.38 0.00 40.72 2.62
43 44 9.806203 CTTACAGAAATGCATTCAAATTATGGA 57.194 29.630 13.38 0.00 40.72 3.41
44 45 9.590451 ACTTACAGAAATGCATTCAAATTATGG 57.410 29.630 13.38 1.87 40.72 2.74
48 49 9.545105 TTCAACTTACAGAAATGCATTCAAATT 57.455 25.926 13.38 0.00 40.72 1.82
49 50 9.715121 ATTCAACTTACAGAAATGCATTCAAAT 57.285 25.926 13.38 0.00 40.72 2.32
361 545 7.303261 CGATATCCTTTAGCGTATCTGTGTAA 58.697 38.462 0.00 0.00 0.00 2.41
362 546 6.128090 CCGATATCCTTTAGCGTATCTGTGTA 60.128 42.308 0.00 0.00 0.00 2.90
781 4334 3.058432 AGCGAACAATATCATGCATGCTC 60.058 43.478 22.25 2.63 0.00 4.26
987 4542 4.579340 CCAGGTTTCATCTTGATCTGGATG 59.421 45.833 16.77 16.77 39.53 3.51
1132 4690 9.615660 AATGTTCCCTGGAAGTACAGATATATA 57.384 33.333 0.00 0.00 40.97 0.86
1161 4719 9.241919 TCAAGGAATTGCAATAGTTTCATCTTA 57.758 29.630 13.39 0.00 0.00 2.10
1295 4853 6.790319 AGTTTCCTCATATTTGTTAGGGTGT 58.210 36.000 0.00 0.00 0.00 4.16
1535 5093 2.968574 TGCTCTTCCTCAGGGATACATC 59.031 50.000 0.00 0.00 41.87 3.06
1641 5199 2.019984 GACATCATCCAAGTTGGGAGC 58.980 52.381 21.85 3.06 41.08 4.70
2043 5823 3.476552 CTCAACAACAGTAGGAAAGCCA 58.523 45.455 0.00 0.00 36.29 4.75
2053 5833 3.885297 AGCATTGTAAGCTCAACAACAGT 59.115 39.130 14.77 0.09 39.51 3.55
2157 5937 4.041567 TCAAGTCCAGGCATACTTTCAAGA 59.958 41.667 0.00 0.00 33.72 3.02
2160 5940 3.072330 TGTCAAGTCCAGGCATACTTTCA 59.928 43.478 0.00 0.00 33.72 2.69
2238 6018 1.296056 GCTGCAAATGCCTTGGCTTG 61.296 55.000 13.18 10.63 41.18 4.01
2424 6205 8.799367 TCAAATACGGTAGAGCTGCTAATATTA 58.201 33.333 0.15 0.00 0.00 0.98
2555 6346 3.520290 TCCGGTCATCATGAAGTACAC 57.480 47.619 0.00 0.00 0.00 2.90
2557 6348 9.436957 AAAATATATCCGGTCATCATGAAGTAC 57.563 33.333 0.00 0.00 0.00 2.73
2562 6353 8.146053 AGGTAAAATATATCCGGTCATCATGA 57.854 34.615 0.00 0.00 0.00 3.07
2799 6603 6.954944 TGTGACTTGAAGCACAGTTAATAAC 58.045 36.000 15.11 0.00 39.86 1.89
2821 6625 2.158871 TGGCAACTAAGAACGGAACTGT 60.159 45.455 0.00 0.00 37.61 3.55
2920 6724 2.624838 CTGCACAGAAAGGGAAATGTGT 59.375 45.455 6.10 0.00 43.84 3.72
2945 6753 0.106015 ATTACCAGCCAGGGATTGCC 60.106 55.000 0.00 0.00 43.89 4.52
2946 6754 1.035139 CATTACCAGCCAGGGATTGC 58.965 55.000 0.00 0.00 43.89 3.56
2947 6755 1.215173 TCCATTACCAGCCAGGGATTG 59.785 52.381 0.00 0.00 43.89 2.67
2948 6756 1.496429 CTCCATTACCAGCCAGGGATT 59.504 52.381 0.00 0.00 43.89 3.01
2951 6759 1.152881 GCTCCATTACCAGCCAGGG 60.153 63.158 0.00 0.00 43.89 4.45
2961 6769 1.208052 GTGCAGACTCTGGCTCCATTA 59.792 52.381 8.17 0.00 31.21 1.90
2980 6788 3.326521 TGGAATATGGGGATGCACTAGT 58.673 45.455 0.00 0.00 0.00 2.57
2982 6790 4.805140 TTTGGAATATGGGGATGCACTA 57.195 40.909 0.00 0.00 0.00 2.74
2984 6792 5.481473 ACATATTTGGAATATGGGGATGCAC 59.519 40.000 19.30 0.00 36.56 4.57
2992 6800 8.232513 CGATCAACTGACATATTTGGAATATGG 58.767 37.037 19.30 8.70 36.56 2.74
3006 6814 2.102420 ACACCTTCACGATCAACTGACA 59.898 45.455 0.00 0.00 0.00 3.58
3009 6817 4.552166 AAAACACCTTCACGATCAACTG 57.448 40.909 0.00 0.00 0.00 3.16
3062 6870 3.509184 GGGACGGAGGGAGTATATAACAC 59.491 52.174 0.00 0.00 0.00 3.32
3070 6878 1.288633 TGTTATGGGACGGAGGGAGTA 59.711 52.381 0.00 0.00 0.00 2.59
3071 6879 0.042131 TGTTATGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
3072 6880 1.424638 ATGTTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3073 6881 2.779429 TATGTTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3074 6882 2.969950 TCTTATGTTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3075 6883 3.555168 GCTCTTATGTTATGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
3076 6884 3.654414 GCTCTTATGTTATGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
3077 6885 2.035449 CGCTCTTATGTTATGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
3078 6886 2.223971 ACGCTCTTATGTTATGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
3079 6887 3.093717 ACGCTCTTATGTTATGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
3080 6888 5.813080 AAAACGCTCTTATGTTATGGGAC 57.187 39.130 0.00 0.00 0.00 4.46
3102 6910 8.656806 CCCTCTGTCCCATAATATTAGTGTAAA 58.343 37.037 1.02 0.00 0.00 2.01
3103 6911 8.014263 TCCCTCTGTCCCATAATATTAGTGTAA 58.986 37.037 1.02 0.00 0.00 2.41
3104 6912 7.541074 TCCCTCTGTCCCATAATATTAGTGTA 58.459 38.462 1.02 0.00 0.00 2.90
3105 6913 6.390504 TCCCTCTGTCCCATAATATTAGTGT 58.609 40.000 1.02 0.00 0.00 3.55
3106 6914 6.498651 ACTCCCTCTGTCCCATAATATTAGTG 59.501 42.308 1.02 0.71 0.00 2.74
3107 6915 6.635021 ACTCCCTCTGTCCCATAATATTAGT 58.365 40.000 1.02 0.00 0.00 2.24
3108 6916 7.896496 AGTACTCCCTCTGTCCCATAATATTAG 59.104 40.741 1.02 0.00 0.00 1.73
3109 6917 7.776745 AGTACTCCCTCTGTCCCATAATATTA 58.223 38.462 0.00 0.00 0.00 0.98
3110 6918 6.635021 AGTACTCCCTCTGTCCCATAATATT 58.365 40.000 0.00 0.00 0.00 1.28
3111 6919 6.234404 AGTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
3112 6920 5.681494 AGTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
3113 6921 4.561254 AGTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
3114 6922 4.030913 CAAGTACTCCCTCTGTCCCATAA 58.969 47.826 0.00 0.00 0.00 1.90
3115 6923 3.012502 ACAAGTACTCCCTCTGTCCCATA 59.987 47.826 0.00 0.00 0.00 2.74
3116 6924 2.225650 ACAAGTACTCCCTCTGTCCCAT 60.226 50.000 0.00 0.00 0.00 4.00
3117 6925 1.149288 ACAAGTACTCCCTCTGTCCCA 59.851 52.381 0.00 0.00 0.00 4.37
3118 6926 1.826096 GACAAGTACTCCCTCTGTCCC 59.174 57.143 11.91 0.00 0.00 4.46
3119 6927 2.526432 TGACAAGTACTCCCTCTGTCC 58.474 52.381 17.77 5.24 0.00 4.02
3120 6928 3.677424 GCATGACAAGTACTCCCTCTGTC 60.677 52.174 14.93 14.93 0.00 3.51
3121 6929 2.234908 GCATGACAAGTACTCCCTCTGT 59.765 50.000 0.00 0.00 0.00 3.41
3122 6930 2.499289 AGCATGACAAGTACTCCCTCTG 59.501 50.000 0.00 0.00 0.00 3.35
3123 6931 2.499289 CAGCATGACAAGTACTCCCTCT 59.501 50.000 0.00 0.00 39.69 3.69
3124 6932 2.234908 ACAGCATGACAAGTACTCCCTC 59.765 50.000 0.00 0.00 39.69 4.30
3125 6933 2.234908 GACAGCATGACAAGTACTCCCT 59.765 50.000 0.00 0.00 39.69 4.20
3126 6934 2.622436 GACAGCATGACAAGTACTCCC 58.378 52.381 0.00 0.00 39.69 4.30
3127 6935 2.234908 AGGACAGCATGACAAGTACTCC 59.765 50.000 0.00 0.00 39.69 3.85
3128 6936 3.056536 TCAGGACAGCATGACAAGTACTC 60.057 47.826 0.00 0.00 39.69 2.59
3129 6937 2.899900 TCAGGACAGCATGACAAGTACT 59.100 45.455 0.00 0.00 39.69 2.73
3130 6938 3.319137 TCAGGACAGCATGACAAGTAC 57.681 47.619 0.00 0.00 39.69 2.73
3205 7178 4.588106 TGAAAGAGGCATGTGGAAAATTCA 59.412 37.500 0.00 0.00 0.00 2.57
3227 7200 7.123247 ACTTCCACATTATTTCAGGGAATCTTG 59.877 37.037 0.00 0.00 34.23 3.02
3243 7216 4.728772 TGGATCAGTCAAACTTCCACATT 58.271 39.130 0.00 0.00 31.91 2.71
3294 7267 8.211629 ACTCCCTGACCTAAAACATATTACATC 58.788 37.037 0.00 0.00 0.00 3.06
3368 7346 8.103305 ACTTCTGTCTATTAAAATTGCTCTCCA 58.897 33.333 0.00 0.00 0.00 3.86
3374 7352 7.336931 TCTCCCACTTCTGTCTATTAAAATTGC 59.663 37.037 0.00 0.00 0.00 3.56
3508 7486 4.471904 TGTGGTAAGTGATGCCTCTTAG 57.528 45.455 0.00 0.00 34.34 2.18
3617 7626 2.352127 GGAGGAAAGCAACTTGACATGC 60.352 50.000 0.00 0.00 42.87 4.06
3652 7661 3.368739 GCGGCTACAGGGAAACTAAACTA 60.369 47.826 0.00 0.00 0.00 2.24
3672 7681 5.066968 ACTTGTAAATAAAATGGTGGGCG 57.933 39.130 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.