Multiple sequence alignment - TraesCS6D01G138400

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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 TraesCS6D01G138400 chr6D 100.000 7016 0 0 1 7016 106964832 106957817 0.000000e+00 12957.0
1 TraesCS6D01G138400 chr6D 86.957 391 34 12 6624 6998 467879604 467879993 2.340000e-114 424.0
2 TraesCS6D01G138400 chr6D 84.878 410 31 17 6613 6998 54386523 54386925 1.100000e-102 385.0
3 TraesCS6D01G138400 chr6D 100.000 42 0 0 19 60 408159188 408159229 2.100000e-10 78.7
4 TraesCS6D01G138400 chr6A 96.042 6745 167 32 315 7016 130443790 130437103 0.000000e+00 10885.0
5 TraesCS6D01G138400 chr6A 89.347 291 8 13 58 333 130444082 130443800 1.870000e-90 344.0
6 TraesCS6D01G138400 chr6A 91.892 111 8 1 2545 2654 278475304 278475194 3.390000e-33 154.0
7 TraesCS6D01G138400 chr6B 96.908 5951 148 17 319 6260 194433007 194427084 0.000000e+00 9937.0
8 TraesCS6D01G138400 chr6B 97.959 49 1 0 278 326 194433074 194433026 1.250000e-12 86.1
9 TraesCS6D01G138400 chr1B 88.308 402 25 13 6624 7008 533819671 533820067 4.960000e-126 462.0
10 TraesCS6D01G138400 chr1B 86.224 392 37 11 6627 7001 434640857 434640466 6.550000e-110 409.0
11 TraesCS6D01G138400 chr1B 100.000 30 0 0 1260 1289 630473316 630473287 1.000000e-03 56.5
12 TraesCS6D01G138400 chr4D 86.750 400 32 18 6624 7008 117655212 117655605 6.500000e-115 425.0
13 TraesCS6D01G138400 chr4D 88.710 62 3 4 6936 6996 495907692 495907634 9.760000e-09 73.1
14 TraesCS6D01G138400 chr3A 86.534 401 27 16 6624 7001 734740922 734740526 3.910000e-112 416.0
15 TraesCS6D01G138400 chr3A 85.752 379 50 4 3811 4187 114168181 114168557 1.420000e-106 398.0
16 TraesCS6D01G138400 chr3A 84.343 396 40 14 6624 6998 703739765 703740159 1.110000e-97 368.0
17 TraesCS6D01G138400 chr3A 90.991 111 9 1 2545 2654 266651886 266651776 1.580000e-31 148.0
18 TraesCS6D01G138400 chr3A 90.179 112 9 1 2545 2654 70020916 70020805 2.040000e-30 145.0
19 TraesCS6D01G138400 chr3A 95.918 49 2 0 4329 4377 114168573 114168621 5.830000e-11 80.5
20 TraesCS6D01G138400 chr2A 86.016 379 50 3 3811 4187 218931902 218932279 3.050000e-108 403.0
21 TraesCS6D01G138400 chr2A 91.837 49 4 0 4329 4377 218932295 218932343 1.260000e-07 69.4
22 TraesCS6D01G138400 chr5B 85.213 399 37 16 6624 7001 528669745 528669348 2.370000e-104 390.0
23 TraesCS6D01G138400 chr2D 88.779 303 24 7 6631 6924 615611113 615610812 5.170000e-96 363.0
24 TraesCS6D01G138400 chr2D 82.558 86 10 5 6922 7005 2898026 2897944 3.510000e-08 71.3
25 TraesCS6D01G138400 chr7B 81.726 394 52 11 6625 6998 610490538 610490931 1.900000e-80 311.0
26 TraesCS6D01G138400 chr7B 81.864 397 45 15 6626 6998 610544714 610545107 6.830000e-80 309.0
27 TraesCS6D01G138400 chr7D 90.991 111 9 1 2545 2654 574467592 574467482 1.580000e-31 148.0
28 TraesCS6D01G138400 chr7A 85.714 112 14 1 2545 2654 103479250 103479139 4.450000e-22 117.0
29 TraesCS6D01G138400 chr1D 100.000 30 0 0 1260 1289 458761174 458761145 1.000000e-03 56.5


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 TraesCS6D01G138400 chr6D 106957817 106964832 7015 True 12957.00 12957 100.0000 1 7016 1 chr6D.!!$R1 7015
1 TraesCS6D01G138400 chr6A 130437103 130444082 6979 True 5614.50 10885 92.6945 58 7016 2 chr6A.!!$R2 6958
2 TraesCS6D01G138400 chr6B 194427084 194433074 5990 True 5011.55 9937 97.4335 278 6260 2 chr6B.!!$R1 5982

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
521 567 0.682209 CACTGCCCAATCCTTCCCAG 60.682 60.000 0.0 0.0 0.00 4.45 F
851 902 0.749454 GAGATTGGGTGCCTGCGATT 60.749 55.000 0.0 0.0 0.00 3.34 F
1703 1771 0.105593 CTCAGCAGCACCGTGGATAT 59.894 55.000 0.0 0.0 0.00 1.63 F
2088 2156 4.580167 TGTTGCTTTTCTGTGCATACTTCT 59.420 37.500 0.0 0.0 39.07 2.85 F
2720 2789 4.818534 TGCTTACAAACTTGCTTCAGAG 57.181 40.909 0.0 0.0 0.00 3.35 F
3813 3882 4.321230 CCATCTAAACAAACAGAAGGTGGC 60.321 45.833 0.0 0.0 0.00 5.01 F
5063 5143 0.407528 TGCTGGCCCCTTTGTAATGA 59.592 50.000 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 1771 3.454375 GAAGGTTGACAGAACTTCGACA 58.546 45.455 0.00 0.00 31.25 4.35 R
2720 2789 4.223320 TCGTTTTTCTTGGTCTTGCATC 57.777 40.909 0.00 0.00 0.00 3.91 R
3505 3574 2.048222 CGCGGAAAGTGCCTGAGA 60.048 61.111 0.00 0.00 0.00 3.27 R
3813 3882 5.743872 TGAAACGTCAGTCATATTCTCATCG 59.256 40.000 0.00 0.00 0.00 3.84 R
4143 4212 3.071479 GTTAACTTCGCCCATCACAGAA 58.929 45.455 0.00 0.00 0.00 3.02 R
5723 5803 2.685380 CGAGGAAGGTGGGGCTCT 60.685 66.667 0.00 0.00 0.00 4.09 R
6640 6731 0.737715 AAAGATCGGTGCAGACGAGC 60.738 55.000 18.07 18.07 46.05 5.03 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
35 36 7.925043 AATGATCATATTCTCAATCCTCTGC 57.075 36.000 9.04 0.00 0.00 4.26
36 37 6.683312 TGATCATATTCTCAATCCTCTGCT 57.317 37.500 0.00 0.00 0.00 4.24
37 38 7.787623 TGATCATATTCTCAATCCTCTGCTA 57.212 36.000 0.00 0.00 0.00 3.49
38 39 8.376803 TGATCATATTCTCAATCCTCTGCTAT 57.623 34.615 0.00 0.00 0.00 2.97
39 40 8.823794 TGATCATATTCTCAATCCTCTGCTATT 58.176 33.333 0.00 0.00 0.00 1.73
40 41 9.669887 GATCATATTCTCAATCCTCTGCTATTT 57.330 33.333 0.00 0.00 0.00 1.40
42 43 9.281371 TCATATTCTCAATCCTCTGCTATTTTG 57.719 33.333 0.00 0.00 0.00 2.44
43 44 9.064706 CATATTCTCAATCCTCTGCTATTTTGT 57.935 33.333 0.00 0.00 0.00 2.83
46 47 9.638176 ATTCTCAATCCTCTGCTATTTTGTATT 57.362 29.630 0.00 0.00 0.00 1.89
47 48 8.442632 TCTCAATCCTCTGCTATTTTGTATTG 57.557 34.615 0.00 0.00 0.00 1.90
48 49 7.012704 TCTCAATCCTCTGCTATTTTGTATTGC 59.987 37.037 0.00 0.00 0.00 3.56
49 50 6.602803 TCAATCCTCTGCTATTTTGTATTGCA 59.397 34.615 0.00 0.00 0.00 4.08
53 54 4.644103 CTGCTATTTTGTATTGCAGGCT 57.356 40.909 11.60 0.00 44.95 4.58
54 55 4.357142 CTGCTATTTTGTATTGCAGGCTG 58.643 43.478 10.94 10.94 44.95 4.85
55 56 3.763360 TGCTATTTTGTATTGCAGGCTGT 59.237 39.130 17.16 0.00 0.00 4.40
56 57 4.142403 TGCTATTTTGTATTGCAGGCTGTC 60.142 41.667 17.16 9.10 0.00 3.51
237 245 6.586463 ACAGATACATCTAGACACGTTTGTTG 59.414 38.462 0.00 0.00 33.40 3.33
239 247 7.116376 CAGATACATCTAGACACGTTTGTTGTT 59.884 37.037 0.00 0.00 33.40 2.83
240 248 8.301720 AGATACATCTAGACACGTTTGTTGTTA 58.698 33.333 0.00 0.00 33.40 2.41
241 249 8.821147 ATACATCTAGACACGTTTGTTGTTAA 57.179 30.769 0.00 0.00 35.47 2.01
242 250 7.724305 ACATCTAGACACGTTTGTTGTTAAT 57.276 32.000 0.00 0.00 35.47 1.40
243 251 8.149973 ACATCTAGACACGTTTGTTGTTAATT 57.850 30.769 0.00 0.00 35.47 1.40
244 252 9.263538 ACATCTAGACACGTTTGTTGTTAATTA 57.736 29.630 0.00 0.00 35.47 1.40
252 260 9.667989 ACACGTTTGTTGTTAATTAAATACTCC 57.332 29.630 0.00 0.00 28.43 3.85
272 288 9.972106 ATACTCCTATACAATGTAGTACTACCC 57.028 37.037 26.41 7.03 35.26 3.69
273 289 8.054931 ACTCCTATACAATGTAGTACTACCCT 57.945 38.462 26.41 13.57 35.26 4.34
274 290 8.509441 ACTCCTATACAATGTAGTACTACCCTT 58.491 37.037 26.41 17.96 35.26 3.95
275 291 8.701908 TCCTATACAATGTAGTACTACCCTTG 57.298 38.462 27.44 27.44 35.55 3.61
276 292 7.232127 TCCTATACAATGTAGTACTACCCTTGC 59.768 40.741 28.24 10.60 34.12 4.01
292 308 4.886121 GCTACTACCGGCCACCGC 62.886 72.222 0.00 0.00 46.86 5.68
521 567 0.682209 CACTGCCCAATCCTTCCCAG 60.682 60.000 0.00 0.00 0.00 4.45
707 753 1.555533 CCCGAAAGCTATCTATCCCCC 59.444 57.143 0.00 0.00 0.00 5.40
844 895 2.124695 GGTCGGAGATTGGGTGCC 60.125 66.667 0.00 0.00 40.67 5.01
845 896 2.670148 GGTCGGAGATTGGGTGCCT 61.670 63.158 0.00 0.00 40.67 4.75
851 902 0.749454 GAGATTGGGTGCCTGCGATT 60.749 55.000 0.00 0.00 0.00 3.34
922 973 2.353610 GGATTTGGTGCCTGGGCTG 61.354 63.158 13.05 0.00 42.51 4.85
938 989 4.595538 TGCGACTCCGTGCCGTTT 62.596 61.111 0.00 0.00 38.24 3.60
939 990 4.072088 GCGACTCCGTGCCGTTTG 62.072 66.667 0.00 0.00 38.24 2.93
940 991 3.411351 CGACTCCGTGCCGTTTGG 61.411 66.667 0.00 0.00 38.77 3.28
941 992 2.280592 GACTCCGTGCCGTTTGGT 60.281 61.111 0.00 0.00 37.67 3.67
942 993 2.590575 ACTCCGTGCCGTTTGGTG 60.591 61.111 0.00 0.00 37.67 4.17
943 994 3.353836 CTCCGTGCCGTTTGGTGG 61.354 66.667 0.00 0.00 37.67 4.61
944 995 4.178169 TCCGTGCCGTTTGGTGGT 62.178 61.111 0.00 0.00 37.67 4.16
945 996 3.213402 CCGTGCCGTTTGGTGGTT 61.213 61.111 0.00 0.00 37.67 3.67
946 997 2.025441 CGTGCCGTTTGGTGGTTG 59.975 61.111 0.00 0.00 37.67 3.77
947 998 2.279186 GTGCCGTTTGGTGGTTGC 60.279 61.111 0.00 0.00 37.67 4.17
948 999 3.532155 TGCCGTTTGGTGGTTGCC 61.532 61.111 0.00 0.00 37.67 4.52
949 1000 3.223589 GCCGTTTGGTGGTTGCCT 61.224 61.111 0.00 0.00 37.67 4.75
950 1001 2.791868 GCCGTTTGGTGGTTGCCTT 61.792 57.895 0.00 0.00 37.67 4.35
1373 1441 3.842923 CTCCATGCCGACTCGCCT 61.843 66.667 0.00 0.00 0.00 5.52
1643 1711 1.377725 CCTGGAGCAAGCATTCCGT 60.378 57.895 0.00 0.00 36.22 4.69
1703 1771 0.105593 CTCAGCAGCACCGTGGATAT 59.894 55.000 0.00 0.00 0.00 1.63
2055 2123 7.715249 GGTTAGACTGAAGCAATGACCATATAA 59.285 37.037 0.00 0.00 0.00 0.98
2088 2156 4.580167 TGTTGCTTTTCTGTGCATACTTCT 59.420 37.500 0.00 0.00 39.07 2.85
2251 2320 9.941325 TGAATTGCCATTTTATTGTGTAGAAAT 57.059 25.926 0.00 0.00 0.00 2.17
2496 2565 5.341872 TCCATCTTTTGTGCCATAATTGG 57.658 39.130 0.00 0.00 46.66 3.16
2720 2789 4.818534 TGCTTACAAACTTGCTTCAGAG 57.181 40.909 0.00 0.00 0.00 3.35
2750 2819 8.865001 CAAGACCAAGAAAAACGAAACAAATAA 58.135 29.630 0.00 0.00 0.00 1.40
3475 3544 6.002082 TCTATTGATGAAGGGCAGAATGATG 58.998 40.000 0.00 0.00 39.69 3.07
3505 3574 6.889301 TGAGAAATGCAAGAGAGAAAACAT 57.111 33.333 0.00 0.00 0.00 2.71
3813 3882 4.321230 CCATCTAAACAAACAGAAGGTGGC 60.321 45.833 0.00 0.00 0.00 5.01
4143 4212 6.174049 GGATGAGGCAGAAAGTAAACTTAGT 58.826 40.000 0.00 0.00 34.61 2.24
4228 4297 7.478322 TGACGAGTCTCAGGTAAAATATACAC 58.522 38.462 4.78 0.00 0.00 2.90
4700 4779 9.956720 GAACTAATGAATAATCCAACTGAATGG 57.043 33.333 0.00 0.00 42.12 3.16
4727 4806 9.546428 AATGTAAATAATTTATTGGAAGCAGGC 57.454 29.630 2.48 0.00 0.00 4.85
4755 4834 9.988350 CAGATTGTTGTATTTTATCTTAGCGTT 57.012 29.630 0.00 0.00 0.00 4.84
4792 4871 4.090761 AGAGACATTTGCTGTTCTTGGA 57.909 40.909 0.00 0.00 38.54 3.53
4923 5002 2.136298 TAGTCAGTGCCTCCAGAGAG 57.864 55.000 0.00 0.00 40.09 3.20
4927 5006 2.563179 GTCAGTGCCTCCAGAGAGTTAA 59.437 50.000 0.00 0.00 38.58 2.01
5063 5143 0.407528 TGCTGGCCCCTTTGTAATGA 59.592 50.000 0.00 0.00 0.00 2.57
5066 5146 2.369394 CTGGCCCCTTTGTAATGACTC 58.631 52.381 0.00 0.00 0.00 3.36
5217 5297 1.604593 GGTGGAAGCAGCACATGGT 60.605 57.895 0.00 0.00 42.89 3.55
5459 5539 2.512692 TAACAGGCATGCTGTGGATT 57.487 45.000 18.92 9.18 34.97 3.01
5460 5540 1.636148 AACAGGCATGCTGTGGATTT 58.364 45.000 18.92 3.69 34.97 2.17
5461 5541 0.892755 ACAGGCATGCTGTGGATTTG 59.107 50.000 18.92 6.13 33.29 2.32
5462 5542 1.179152 CAGGCATGCTGTGGATTTGA 58.821 50.000 18.92 0.00 0.00 2.69
5723 5803 3.164977 TCGGTGGCCCTGTTCACA 61.165 61.111 0.00 0.00 35.74 3.58
5747 5827 3.710722 CACCTTCCTCGGCAGCCT 61.711 66.667 10.54 0.00 0.00 4.58
6010 6090 5.515106 TGAAGGGAGAAAGAAAACCTCAAA 58.485 37.500 0.00 0.00 0.00 2.69
6178 6260 8.515695 TCGTTCAAGGAGACTGAATAATAGTA 57.484 34.615 0.00 0.00 42.68 1.82
6204 6286 7.145323 ACATTCTTCCACTTTTGTTTTATCCG 58.855 34.615 0.00 0.00 0.00 4.18
6207 6289 4.231718 TCCACTTTTGTTTTATCCGTGC 57.768 40.909 0.00 0.00 0.00 5.34
6252 6334 3.051940 TCCTCTTGAGCATGGTATCCT 57.948 47.619 0.00 0.00 0.00 3.24
6254 6336 4.756564 TCCTCTTGAGCATGGTATCCTAT 58.243 43.478 0.00 0.00 0.00 2.57
6300 6382 6.591935 TCAAAAGAGGTTGCTTAGAAGAGAA 58.408 36.000 0.00 0.00 0.00 2.87
6325 6407 4.897509 TGTATCCCATCCTCTATTGCTG 57.102 45.455 0.00 0.00 0.00 4.41
6345 6427 4.326548 GCTGTCGCGTAAAGACTTTTATCT 59.673 41.667 5.77 0.00 39.24 1.98
6352 6434 7.170320 TCGCGTAAAGACTTTTATCTTTTCACT 59.830 33.333 5.77 0.00 44.74 3.41
6424 6506 7.069331 TGTTTGTGAATCCCTGTTTGTATTCTT 59.931 33.333 0.00 0.00 31.16 2.52
6452 6534 4.142752 CGCATGCCCATAATGAGTGATAAG 60.143 45.833 13.15 0.00 0.00 1.73
6494 6576 1.826720 ACCATGCTAGCCCAAATTGTG 59.173 47.619 13.29 0.00 0.00 3.33
6643 6734 2.892425 CGATTCGGTGCCAGGCTC 60.892 66.667 14.15 9.31 0.00 4.70
6644 6735 2.892425 GATTCGGTGCCAGGCTCG 60.892 66.667 14.15 16.44 0.00 5.03
6645 6736 3.665675 GATTCGGTGCCAGGCTCGT 62.666 63.158 21.42 8.52 0.00 4.18
6646 6737 3.665675 ATTCGGTGCCAGGCTCGTC 62.666 63.158 21.42 7.53 0.00 4.20
6650 6741 4.687215 GTGCCAGGCTCGTCTGCA 62.687 66.667 14.15 0.00 33.64 4.41
6657 6748 2.492090 GCTCGTCTGCACCGATCT 59.508 61.111 4.36 0.00 33.27 2.75
6658 6749 1.153745 GCTCGTCTGCACCGATCTT 60.154 57.895 4.36 0.00 33.27 2.40
6664 6760 4.059511 TCGTCTGCACCGATCTTTAAAAA 58.940 39.130 0.00 0.00 0.00 1.94
6749 6848 5.084055 CGTAAGGTTCGCTCCAAAAATTAC 58.916 41.667 0.00 0.00 0.00 1.89
6752 6851 3.756963 AGGTTCGCTCCAAAAATTACCTC 59.243 43.478 0.00 0.00 29.01 3.85
6875 6975 3.817647 AGAGTTGCTCAGTTGTCCAAATC 59.182 43.478 0.00 0.00 33.83 2.17
6886 6986 9.695526 CTCAGTTGTCCAAATCATTTGAAAATA 57.304 29.630 11.98 0.00 43.26 1.40
6890 6990 7.552050 TGTCCAAATCATTTGAAAATAGGGT 57.448 32.000 11.98 0.00 43.26 4.34
6892 6992 6.751888 GTCCAAATCATTTGAAAATAGGGTCG 59.248 38.462 11.98 0.00 43.26 4.79
6896 6996 4.266714 TCATTTGAAAATAGGGTCGGACC 58.733 43.478 19.06 19.06 37.60 4.46
6909 7009 2.604174 CGGACCTCACGCACCAAAC 61.604 63.158 0.00 0.00 0.00 2.93
6916 7016 2.612972 CCTCACGCACCAAACTGTCTAT 60.613 50.000 0.00 0.00 0.00 1.98
6917 7017 2.668457 CTCACGCACCAAACTGTCTATC 59.332 50.000 0.00 0.00 0.00 2.08
6921 7021 2.352651 CGCACCAAACTGTCTATCATGG 59.647 50.000 0.00 0.00 31.94 3.66
6924 7024 4.785301 CACCAAACTGTCTATCATGGGAT 58.215 43.478 0.00 0.00 37.55 3.85
6925 7025 5.195940 CACCAAACTGTCTATCATGGGATT 58.804 41.667 0.00 0.00 34.89 3.01
6978 7089 2.779755 TATTCAACACGGGTGCAGAT 57.220 45.000 0.00 0.00 0.00 2.90
6982 7093 1.672356 AACACGGGTGCAGATGAGC 60.672 57.895 0.00 0.00 0.00 4.26
6986 7097 3.785859 GGGTGCAGATGAGCCCGA 61.786 66.667 0.00 0.00 0.00 5.14
6987 7098 2.202987 GGTGCAGATGAGCCCGAG 60.203 66.667 0.00 0.00 0.00 4.63
7005 7116 4.397417 CCCGAGCTCAGAAAAGAATGATTT 59.603 41.667 15.40 0.00 0.00 2.17
7008 7119 6.536582 CCGAGCTCAGAAAAGAATGATTTCTA 59.463 38.462 15.40 0.00 43.41 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.794553 GCAGAGGATTGAGAATATGATCATTTT 58.205 33.333 14.65 12.44 0.00 1.82
10 11 8.164733 AGCAGAGGATTGAGAATATGATCATTT 58.835 33.333 14.65 2.68 0.00 2.32
11 12 7.691213 AGCAGAGGATTGAGAATATGATCATT 58.309 34.615 14.65 0.00 0.00 2.57
12 13 7.260387 AGCAGAGGATTGAGAATATGATCAT 57.740 36.000 13.81 13.81 0.00 2.45
13 14 6.683312 AGCAGAGGATTGAGAATATGATCA 57.317 37.500 0.00 0.00 0.00 2.92
14 15 9.669887 AAATAGCAGAGGATTGAGAATATGATC 57.330 33.333 0.00 0.00 0.00 2.92
16 17 9.281371 CAAAATAGCAGAGGATTGAGAATATGA 57.719 33.333 0.00 0.00 0.00 2.15
17 18 9.064706 ACAAAATAGCAGAGGATTGAGAATATG 57.935 33.333 0.00 0.00 0.00 1.78
20 21 9.638176 AATACAAAATAGCAGAGGATTGAGAAT 57.362 29.630 0.00 0.00 0.00 2.40
21 22 8.896744 CAATACAAAATAGCAGAGGATTGAGAA 58.103 33.333 0.00 0.00 0.00 2.87
22 23 7.012704 GCAATACAAAATAGCAGAGGATTGAGA 59.987 37.037 0.00 0.00 0.00 3.27
23 24 7.137426 GCAATACAAAATAGCAGAGGATTGAG 58.863 38.462 0.00 0.00 0.00 3.02
24 25 6.602803 TGCAATACAAAATAGCAGAGGATTGA 59.397 34.615 0.00 0.00 0.00 2.57
25 26 6.798482 TGCAATACAAAATAGCAGAGGATTG 58.202 36.000 0.00 0.00 0.00 2.67
33 34 3.763360 ACAGCCTGCAATACAAAATAGCA 59.237 39.130 0.00 0.00 0.00 3.49
34 35 4.142403 TGACAGCCTGCAATACAAAATAGC 60.142 41.667 0.00 0.00 0.00 2.97
35 36 5.449588 CCTGACAGCCTGCAATACAAAATAG 60.450 44.000 0.00 0.00 0.00 1.73
36 37 4.398988 CCTGACAGCCTGCAATACAAAATA 59.601 41.667 0.00 0.00 0.00 1.40
37 38 3.194116 CCTGACAGCCTGCAATACAAAAT 59.806 43.478 0.00 0.00 0.00 1.82
38 39 2.557924 CCTGACAGCCTGCAATACAAAA 59.442 45.455 0.00 0.00 0.00 2.44
39 40 2.161855 CCTGACAGCCTGCAATACAAA 58.838 47.619 0.00 0.00 0.00 2.83
40 41 1.350684 TCCTGACAGCCTGCAATACAA 59.649 47.619 0.00 0.00 0.00 2.41
41 42 0.983467 TCCTGACAGCCTGCAATACA 59.017 50.000 0.00 0.00 0.00 2.29
42 43 1.373570 GTCCTGACAGCCTGCAATAC 58.626 55.000 0.00 0.00 0.00 1.89
43 44 0.253044 GGTCCTGACAGCCTGCAATA 59.747 55.000 0.00 0.00 0.00 1.90
44 45 1.001641 GGTCCTGACAGCCTGCAAT 60.002 57.895 0.00 0.00 0.00 3.56
45 46 1.993701 TTGGTCCTGACAGCCTGCAA 61.994 55.000 0.00 0.00 0.00 4.08
46 47 2.451191 TTGGTCCTGACAGCCTGCA 61.451 57.895 0.00 0.00 0.00 4.41
47 48 1.968540 GTTGGTCCTGACAGCCTGC 60.969 63.158 0.00 0.00 0.00 4.85
48 49 0.604780 CAGTTGGTCCTGACAGCCTG 60.605 60.000 0.00 0.00 34.23 4.85
49 50 0.764369 TCAGTTGGTCCTGACAGCCT 60.764 55.000 0.00 0.00 36.57 4.58
50 51 0.321122 CTCAGTTGGTCCTGACAGCC 60.321 60.000 0.00 0.00 36.57 4.85
51 52 0.952984 GCTCAGTTGGTCCTGACAGC 60.953 60.000 0.00 0.00 36.57 4.40
52 53 0.683973 AGCTCAGTTGGTCCTGACAG 59.316 55.000 0.00 0.00 36.57 3.51
53 54 0.394192 CAGCTCAGTTGGTCCTGACA 59.606 55.000 0.00 0.00 36.57 3.58
54 55 0.681733 TCAGCTCAGTTGGTCCTGAC 59.318 55.000 0.00 0.00 36.57 3.51
55 56 0.681733 GTCAGCTCAGTTGGTCCTGA 59.318 55.000 0.00 0.00 39.11 3.86
56 57 0.321122 GGTCAGCTCAGTTGGTCCTG 60.321 60.000 0.00 0.00 0.00 3.86
213 215 6.586463 ACAACAAACGTGTCTAGATGTATCTG 59.414 38.462 4.67 0.00 36.80 2.90
215 217 6.946229 ACAACAAACGTGTCTAGATGTATC 57.054 37.500 0.00 0.00 36.80 2.24
248 256 8.054931 AGGGTAGTACTACATTGTATAGGAGT 57.945 38.462 29.38 0.00 37.78 3.85
249 257 8.794553 CAAGGGTAGTACTACATTGTATAGGAG 58.205 40.741 29.38 9.38 37.78 3.69
251 259 7.232941 AGCAAGGGTAGTACTACATTGTATAGG 59.767 40.741 30.74 17.31 36.99 2.57
252 260 8.179509 AGCAAGGGTAGTACTACATTGTATAG 57.820 38.462 30.74 17.76 36.99 1.31
264 280 2.620585 CCGGTAGTAGCAAGGGTAGTAC 59.379 54.545 10.47 10.47 39.95 2.73
267 283 0.388294 GCCGGTAGTAGCAAGGGTAG 59.612 60.000 1.90 0.00 0.00 3.18
268 284 1.044790 GGCCGGTAGTAGCAAGGGTA 61.045 60.000 1.90 0.00 0.00 3.69
269 285 2.364780 GGCCGGTAGTAGCAAGGGT 61.365 63.158 1.90 0.00 0.00 4.34
270 286 2.363975 TGGCCGGTAGTAGCAAGGG 61.364 63.158 1.90 0.00 0.00 3.95
271 287 1.153429 GTGGCCGGTAGTAGCAAGG 60.153 63.158 1.90 0.00 0.00 3.61
272 288 1.153429 GGTGGCCGGTAGTAGCAAG 60.153 63.158 1.90 0.00 0.00 4.01
273 289 2.983791 GGTGGCCGGTAGTAGCAA 59.016 61.111 1.90 0.00 0.00 3.91
274 290 3.454573 CGGTGGCCGGTAGTAGCA 61.455 66.667 1.90 0.00 44.15 3.49
292 308 2.737039 GCTTCTCTCGCAAGGGTAGAAG 60.737 54.545 18.31 18.31 46.09 2.85
388 434 1.732259 GTGTGGGAGTACAATCTTGCG 59.268 52.381 0.00 0.00 31.36 4.85
393 439 0.036765 TGCCGTGTGGGAGTACAATC 60.037 55.000 0.00 0.00 38.47 2.67
521 567 2.103373 GGATTTTCTTTCTCCCCTGCC 58.897 52.381 0.00 0.00 0.00 4.85
844 895 2.409870 GCCTTCCCACCAATCGCAG 61.410 63.158 0.00 0.00 0.00 5.18
845 896 2.361104 GCCTTCCCACCAATCGCA 60.361 61.111 0.00 0.00 0.00 5.10
935 986 2.006169 CAAACAAGGCAACCACCAAAC 58.994 47.619 0.00 0.00 37.17 2.93
936 987 1.065854 CCAAACAAGGCAACCACCAAA 60.066 47.619 0.00 0.00 37.17 3.28
937 988 0.539051 CCAAACAAGGCAACCACCAA 59.461 50.000 0.00 0.00 37.17 3.67
938 989 0.616111 ACCAAACAAGGCAACCACCA 60.616 50.000 0.00 0.00 37.17 4.17
939 990 0.179086 CACCAAACAAGGCAACCACC 60.179 55.000 0.00 0.00 37.17 4.61
940 991 0.179086 CCACCAAACAAGGCAACCAC 60.179 55.000 0.00 0.00 37.17 4.16
941 992 2.206635 CCACCAAACAAGGCAACCA 58.793 52.632 0.00 0.00 37.17 3.67
946 997 2.027460 CACGCCACCAAACAAGGC 59.973 61.111 0.00 0.00 44.89 4.35
947 998 0.820074 TACCACGCCACCAAACAAGG 60.820 55.000 0.00 0.00 0.00 3.61
948 999 0.591170 CTACCACGCCACCAAACAAG 59.409 55.000 0.00 0.00 0.00 3.16
949 1000 0.180642 TCTACCACGCCACCAAACAA 59.819 50.000 0.00 0.00 0.00 2.83
950 1001 0.180642 TTCTACCACGCCACCAAACA 59.819 50.000 0.00 0.00 0.00 2.83
1053 1121 0.107654 GAACTCATCTTCCCCCACGG 60.108 60.000 0.00 0.00 0.00 4.94
1054 1122 0.107654 GGAACTCATCTTCCCCCACG 60.108 60.000 0.00 0.00 34.59 4.94
1057 1125 1.527370 CCGGAACTCATCTTCCCCC 59.473 63.158 0.00 0.00 37.04 5.40
1703 1771 3.454375 GAAGGTTGACAGAACTTCGACA 58.546 45.455 0.00 0.00 31.25 4.35
2055 2123 6.918022 GCACAGAAAAGCAACAACTAGTTAAT 59.082 34.615 8.04 0.00 38.74 1.40
2088 2156 6.017192 ACTCAAGGTCAGTAATAGTTCTCCA 58.983 40.000 0.00 0.00 0.00 3.86
2264 2333 8.865590 TCATAAGAACTTACAAACTTTTTGGC 57.134 30.769 3.82 0.00 0.00 4.52
2526 2595 7.547370 ACATCTTTACTGCAGAACATAAGAGTC 59.453 37.037 23.35 0.00 0.00 3.36
2720 2789 4.223320 TCGTTTTTCTTGGTCTTGCATC 57.777 40.909 0.00 0.00 0.00 3.91
2750 2819 5.351465 CCTTTCACGCAAACATGTACTAGAT 59.649 40.000 0.00 0.00 0.00 1.98
3180 3249 3.899360 TCGAAAGAGACCCCACTAAAGAA 59.101 43.478 0.00 0.00 34.84 2.52
3475 3544 5.410746 TCTCTCTTGCATTTCTCAACACATC 59.589 40.000 0.00 0.00 0.00 3.06
3505 3574 2.048222 CGCGGAAAGTGCCTGAGA 60.048 61.111 0.00 0.00 0.00 3.27
3813 3882 5.743872 TGAAACGTCAGTCATATTCTCATCG 59.256 40.000 0.00 0.00 0.00 3.84
4143 4212 3.071479 GTTAACTTCGCCCATCACAGAA 58.929 45.455 0.00 0.00 0.00 3.02
4228 4297 4.574013 GCAGGTGAAGATTGTCCTAGATTG 59.426 45.833 0.00 0.00 0.00 2.67
4607 4686 5.301551 TGTGTACCACAATGAGCTTGAAATT 59.698 36.000 0.00 0.00 41.69 1.82
4727 4806 7.318909 CGCTAAGATAAAATACAACAATCTGCG 59.681 37.037 0.00 0.00 34.77 5.18
4755 4834 5.535753 TGTCTCTTCAGTCTCACATCAAA 57.464 39.130 0.00 0.00 0.00 2.69
4990 5069 5.716703 CAGTAGGAAAAGGATCAAACCCAAT 59.283 40.000 0.00 0.00 0.00 3.16
4995 5074 7.661847 TCTCTTTCAGTAGGAAAAGGATCAAAC 59.338 37.037 0.00 0.00 44.52 2.93
5063 5143 3.606687 ACAGAACTGGAACAAAACGAGT 58.393 40.909 6.76 0.00 38.70 4.18
5066 5146 6.114221 TCTTTACAGAACTGGAACAAAACG 57.886 37.500 6.76 0.00 38.70 3.60
5723 5803 2.685380 CGAGGAAGGTGGGGCTCT 60.685 66.667 0.00 0.00 0.00 4.09
5846 5926 2.980233 GGGTTGCTGTTCAGCGCT 60.980 61.111 17.95 2.64 36.24 5.92
6178 6260 7.651704 CGGATAAAACAAAAGTGGAAGAATGTT 59.348 33.333 0.00 0.00 32.78 2.71
6204 6286 3.562635 GGAACCAGCAGTACGCAC 58.437 61.111 11.30 0.00 46.13 5.34
6270 6352 7.440523 TCTAAGCAACCTCTTTTGAATTCTC 57.559 36.000 7.05 0.00 0.00 2.87
6279 6361 6.831976 TCTTTCTCTTCTAAGCAACCTCTTT 58.168 36.000 0.00 0.00 0.00 2.52
6325 6407 7.265705 GTGAAAAGATAAAAGTCTTTACGCGAC 59.734 37.037 15.93 0.00 45.18 5.19
6345 6427 7.807907 GTCACTTTCTTTTCTGTTGAGTGAAAA 59.192 33.333 5.02 0.00 42.28 2.29
6352 6434 7.389803 TCATTGTCACTTTCTTTTCTGTTGA 57.610 32.000 0.00 0.00 0.00 3.18
6405 6487 6.801862 CGTTCAAAGAATACAAACAGGGATTC 59.198 38.462 0.00 0.00 0.00 2.52
6424 6506 2.358582 CTCATTATGGGCATGCGTTCAA 59.641 45.455 12.44 3.74 0.00 2.69
6452 6534 6.990349 TGGTATTAGGACCGATTTTCTTGATC 59.010 38.462 0.00 0.00 42.99 2.92
6494 6576 4.248058 CCAAATTCAAGTTGGCCAAGATC 58.752 43.478 21.21 7.55 39.21 2.75
6640 6731 0.737715 AAAGATCGGTGCAGACGAGC 60.738 55.000 18.07 18.07 46.05 5.03
6641 6732 2.561733 TAAAGATCGGTGCAGACGAG 57.438 50.000 17.03 0.00 44.24 4.18
6642 6733 3.306917 TTTAAAGATCGGTGCAGACGA 57.693 42.857 14.80 14.80 45.19 4.20
6643 6734 4.398549 TTTTTAAAGATCGGTGCAGACG 57.601 40.909 4.45 4.45 0.00 4.18
6692 6788 5.768164 GTCTACCATGGAAAAAGAACTGGAA 59.232 40.000 21.47 0.00 0.00 3.53
6784 6883 4.277423 CGTACTGTTTTGACCCCATTTTCT 59.723 41.667 0.00 0.00 0.00 2.52
6785 6884 4.037089 ACGTACTGTTTTGACCCCATTTTC 59.963 41.667 0.00 0.00 0.00 2.29
6786 6885 3.955551 ACGTACTGTTTTGACCCCATTTT 59.044 39.130 0.00 0.00 0.00 1.82
6790 6889 1.485480 TCACGTACTGTTTTGACCCCA 59.515 47.619 0.00 0.00 0.00 4.96
6791 6890 2.243602 TCACGTACTGTTTTGACCCC 57.756 50.000 0.00 0.00 0.00 4.95
6792 6891 2.937799 TGTTCACGTACTGTTTTGACCC 59.062 45.455 0.00 0.00 0.00 4.46
6794 6893 4.852609 ACTGTTCACGTACTGTTTTGAC 57.147 40.909 0.00 0.00 0.00 3.18
6795 6894 6.591062 AGTTTACTGTTCACGTACTGTTTTGA 59.409 34.615 6.35 0.00 33.15 2.69
6796 6895 6.681178 CAGTTTACTGTTCACGTACTGTTTTG 59.319 38.462 6.35 0.00 39.09 2.44
6797 6896 6.768078 CAGTTTACTGTTCACGTACTGTTTT 58.232 36.000 6.35 0.00 39.09 2.43
6821 6920 6.635030 AGACAAATTCAGGGTCTGTAAAAC 57.365 37.500 0.00 0.00 40.21 2.43
6829 6928 4.058124 GGCAAAAAGACAAATTCAGGGTC 58.942 43.478 0.00 0.00 0.00 4.46
6875 6975 4.270008 AGGTCCGACCCTATTTTCAAATG 58.730 43.478 14.32 0.00 39.75 2.32
6886 6986 4.988716 TGCGTGAGGTCCGACCCT 62.989 66.667 14.32 1.60 39.75 4.34
6890 6990 2.798364 TTTGGTGCGTGAGGTCCGA 61.798 57.895 0.00 0.00 0.00 4.55
6892 6992 1.227853 AGTTTGGTGCGTGAGGTCC 60.228 57.895 0.00 0.00 0.00 4.46
6896 6996 2.148916 TAGACAGTTTGGTGCGTGAG 57.851 50.000 0.00 0.00 0.00 3.51
6982 7093 2.977914 TCATTCTTTTCTGAGCTCGGG 58.022 47.619 22.38 11.19 0.00 5.14
6986 7097 9.165035 CTCTTAGAAATCATTCTTTTCTGAGCT 57.835 33.333 11.11 0.00 43.43 4.09
6987 7098 7.909641 GCTCTTAGAAATCATTCTTTTCTGAGC 59.090 37.037 16.15 16.15 43.43 4.26


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

AutoCloner maintained by Alex Coulton.