Multiple sequence alignment - TraesCS2D01G472400

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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 TraesCS2D01G472400 chr2D 100.000 3095 0 0 1 3095 576190371 576193465 0.000000e+00 5716.0
1 TraesCS2D01G472400 chr2A 92.962 3055 143 37 89 3095 714206378 714209408 0.000000e+00 4385.0
2 TraesCS2D01G472400 chr2B 92.680 2978 134 41 95 3021 692161365 692164309 0.000000e+00 4215.0
3 TraesCS2D01G472400 chr2B 94.805 77 4 0 3019 3095 692164468 692164544 1.510000e-23 121.0
4 TraesCS2D01G472400 chr2B 80.263 76 15 0 1114 1189 690666757 690666682 1.200000e-04 58.4
5 TraesCS2D01G472400 chr6B 79.588 534 70 22 2215 2728 173816982 173817496 2.280000e-91 346.0
6 TraesCS2D01G472400 chr7B 76.836 531 65 30 2215 2731 171091135 171090649 2.380000e-61 246.0
7 TraesCS2D01G472400 chr1B 80.132 302 43 11 2215 2515 87189660 87189375 3.130000e-50 209.0
8 TraesCS2D01G472400 chr5D 81.712 257 32 7 2215 2471 181607417 181607176 1.880000e-47 200.0
9 TraesCS2D01G472400 chr4A 92.683 82 5 1 2230 2310 20573249 20573330 1.950000e-22 117.0


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 TraesCS2D01G472400 chr2D 576190371 576193465 3094 False 5716 5716 100.0000 1 3095 1 chr2D.!!$F1 3094
1 TraesCS2D01G472400 chr2A 714206378 714209408 3030 False 4385 4385 92.9620 89 3095 1 chr2A.!!$F1 3006
2 TraesCS2D01G472400 chr2B 692161365 692164544 3179 False 2168 4215 93.7425 95 3095 2 chr2B.!!$F1 3000
3 TraesCS2D01G472400 chr6B 173816982 173817496 514 False 346 346 79.5880 2215 2728 1 chr6B.!!$F1 513

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
50 51 0.039074 AGTCTGAAAGGTGTCGAGCG 60.039 55.0 0.00 0.00 0.00 5.03 F
1563 1607 0.107066 TCGGGAACATGCTGCATGAT 60.107 50.0 40.25 32.14 43.81 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1676 0.909610 TGAAGACAGGGGAGCGGAAT 60.910 55.0 0.00 0.0 0.00 3.01 R
2472 2517 1.792757 TTTCAGGGCTGAGGCATGGT 61.793 55.0 20.33 0.0 40.21 3.55 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 9.359653 TGTTACCACTTATATTACTCTCCCTAC 57.640 37.037 0.00 0.00 0.00 3.18
27 28 8.510505 GTTACCACTTATATTACTCTCCCTACG 58.489 40.741 0.00 0.00 0.00 3.51
28 29 6.008960 ACCACTTATATTACTCTCCCTACGG 58.991 44.000 0.00 0.00 0.00 4.02
29 30 5.418209 CCACTTATATTACTCTCCCTACGGG 59.582 48.000 0.00 0.00 46.11 5.28
30 31 6.008960 CACTTATATTACTCTCCCTACGGGT 58.991 44.000 0.00 0.00 44.74 5.28
31 32 7.170965 CACTTATATTACTCTCCCTACGGGTA 58.829 42.308 0.00 0.00 44.74 3.69
32 33 7.336427 CACTTATATTACTCTCCCTACGGGTAG 59.664 44.444 0.00 0.00 44.74 3.18
33 34 5.857106 ATATTACTCTCCCTACGGGTAGT 57.143 43.478 12.15 12.15 44.74 2.73
34 35 3.567478 TTACTCTCCCTACGGGTAGTC 57.433 52.381 11.23 0.00 44.74 2.59
35 36 1.594129 ACTCTCCCTACGGGTAGTCT 58.406 55.000 5.23 0.00 44.74 3.24
36 37 1.212441 ACTCTCCCTACGGGTAGTCTG 59.788 57.143 5.23 0.00 44.74 3.51
37 38 1.489649 CTCTCCCTACGGGTAGTCTGA 59.510 57.143 5.23 0.00 44.74 3.27
38 39 1.918262 TCTCCCTACGGGTAGTCTGAA 59.082 52.381 5.23 0.00 44.74 3.02
39 40 2.309755 TCTCCCTACGGGTAGTCTGAAA 59.690 50.000 5.23 0.00 44.74 2.69
40 41 2.688958 CTCCCTACGGGTAGTCTGAAAG 59.311 54.545 5.23 0.00 44.74 2.62
41 42 1.755380 CCCTACGGGTAGTCTGAAAGG 59.245 57.143 5.23 0.00 38.25 3.11
42 43 2.454538 CCTACGGGTAGTCTGAAAGGT 58.545 52.381 5.23 0.00 0.00 3.50
43 44 2.165845 CCTACGGGTAGTCTGAAAGGTG 59.834 54.545 5.23 0.00 0.00 4.00
44 45 1.713297 ACGGGTAGTCTGAAAGGTGT 58.287 50.000 0.00 0.00 0.00 4.16
45 46 1.617357 ACGGGTAGTCTGAAAGGTGTC 59.383 52.381 0.00 0.00 0.00 3.67
46 47 1.402456 CGGGTAGTCTGAAAGGTGTCG 60.402 57.143 0.00 0.00 0.00 4.35
47 48 1.891150 GGGTAGTCTGAAAGGTGTCGA 59.109 52.381 0.00 0.00 0.00 4.20
48 49 2.094649 GGGTAGTCTGAAAGGTGTCGAG 60.095 54.545 0.00 0.00 0.00 4.04
49 50 2.597520 GTAGTCTGAAAGGTGTCGAGC 58.402 52.381 0.00 0.00 0.00 5.03
50 51 0.039074 AGTCTGAAAGGTGTCGAGCG 60.039 55.000 0.00 0.00 0.00 5.03
51 52 0.039437 GTCTGAAAGGTGTCGAGCGA 60.039 55.000 0.00 0.00 0.00 4.93
52 53 0.241213 TCTGAAAGGTGTCGAGCGAG 59.759 55.000 0.00 0.00 0.00 5.03
53 54 0.039074 CTGAAAGGTGTCGAGCGAGT 60.039 55.000 0.00 0.00 0.00 4.18
54 55 0.387929 TGAAAGGTGTCGAGCGAGTT 59.612 50.000 0.00 0.00 0.00 3.01
55 56 1.610038 TGAAAGGTGTCGAGCGAGTTA 59.390 47.619 0.00 0.00 0.00 2.24
56 57 1.984297 GAAAGGTGTCGAGCGAGTTAC 59.016 52.381 0.00 0.00 0.00 2.50
57 58 0.243095 AAGGTGTCGAGCGAGTTACC 59.757 55.000 10.92 10.92 0.00 2.85
58 59 0.892358 AGGTGTCGAGCGAGTTACCA 60.892 55.000 17.44 1.21 0.00 3.25
59 60 0.172803 GGTGTCGAGCGAGTTACCAT 59.827 55.000 12.93 0.00 0.00 3.55
60 61 1.402968 GGTGTCGAGCGAGTTACCATA 59.597 52.381 12.93 0.00 0.00 2.74
61 62 2.448219 GTGTCGAGCGAGTTACCATAC 58.552 52.381 0.00 0.00 0.00 2.39
62 63 1.402968 TGTCGAGCGAGTTACCATACC 59.597 52.381 0.00 0.00 0.00 2.73
63 64 1.402968 GTCGAGCGAGTTACCATACCA 59.597 52.381 0.00 0.00 0.00 3.25
64 65 2.034305 GTCGAGCGAGTTACCATACCAT 59.966 50.000 0.00 0.00 0.00 3.55
65 66 3.251729 GTCGAGCGAGTTACCATACCATA 59.748 47.826 0.00 0.00 0.00 2.74
66 67 3.501062 TCGAGCGAGTTACCATACCATAG 59.499 47.826 0.00 0.00 0.00 2.23
67 68 3.501062 CGAGCGAGTTACCATACCATAGA 59.499 47.826 0.00 0.00 0.00 1.98
68 69 4.156190 CGAGCGAGTTACCATACCATAGAT 59.844 45.833 0.00 0.00 0.00 1.98
69 70 5.353400 CGAGCGAGTTACCATACCATAGATA 59.647 44.000 0.00 0.00 0.00 1.98
70 71 6.038382 CGAGCGAGTTACCATACCATAGATAT 59.962 42.308 0.00 0.00 0.00 1.63
71 72 7.101652 AGCGAGTTACCATACCATAGATATG 57.898 40.000 0.00 0.00 0.00 1.78
84 85 5.941788 CCATAGATATGGCCCTTATTACCC 58.058 45.833 0.00 0.00 45.92 3.69
85 86 5.672194 CCATAGATATGGCCCTTATTACCCT 59.328 44.000 0.00 0.00 45.92 4.34
86 87 6.160459 CCATAGATATGGCCCTTATTACCCTT 59.840 42.308 0.00 0.00 45.92 3.95
87 88 5.780958 AGATATGGCCCTTATTACCCTTC 57.219 43.478 0.00 0.00 0.00 3.46
88 89 5.170198 AGATATGGCCCTTATTACCCTTCA 58.830 41.667 0.00 0.00 0.00 3.02
89 90 5.615261 AGATATGGCCCTTATTACCCTTCAA 59.385 40.000 0.00 0.00 0.00 2.69
90 91 4.618378 ATGGCCCTTATTACCCTTCAAA 57.382 40.909 0.00 0.00 0.00 2.69
91 92 4.405756 TGGCCCTTATTACCCTTCAAAA 57.594 40.909 0.00 0.00 0.00 2.44
92 93 4.753186 TGGCCCTTATTACCCTTCAAAAA 58.247 39.130 0.00 0.00 0.00 1.94
93 94 4.775253 TGGCCCTTATTACCCTTCAAAAAG 59.225 41.667 0.00 0.00 0.00 2.27
94 95 4.382685 GGCCCTTATTACCCTTCAAAAAGC 60.383 45.833 0.00 0.00 0.00 3.51
95 96 4.382685 GCCCTTATTACCCTTCAAAAAGCC 60.383 45.833 0.00 0.00 0.00 4.35
182 183 9.044150 AGACTAATACTATAGACGTCACTGAAC 57.956 37.037 19.50 0.00 0.00 3.18
221 232 4.422057 TGCGGGGAAAGACATATCCTATA 58.578 43.478 0.00 0.00 35.95 1.31
223 234 5.128827 TGCGGGGAAAGACATATCCTATATC 59.871 44.000 0.00 0.00 35.95 1.63
224 235 5.364157 GCGGGGAAAGACATATCCTATATCT 59.636 44.000 0.00 0.00 35.95 1.98
226 237 7.255660 GCGGGGAAAGACATATCCTATATCTAG 60.256 44.444 0.00 0.00 35.95 2.43
227 238 7.999545 CGGGGAAAGACATATCCTATATCTAGA 59.000 40.741 0.00 0.00 35.95 2.43
228 239 9.362151 GGGGAAAGACATATCCTATATCTAGAG 57.638 40.741 0.00 0.00 35.95 2.43
307 322 7.274904 GCCATTAGAATTGTATAGCATGCATTG 59.725 37.037 21.98 1.19 0.00 2.82
347 363 5.014755 AGGAACACAATTAATGGTACCCTCA 59.985 40.000 10.07 0.00 0.00 3.86
352 368 9.569122 AACACAATTAATGGTACCCTCATATAC 57.431 33.333 10.07 0.00 0.00 1.47
418 443 3.011517 GCAGCCTCCTCCCTCCAA 61.012 66.667 0.00 0.00 0.00 3.53
431 456 4.319177 CTCCCTCCAAGCTATAAAATCCG 58.681 47.826 0.00 0.00 0.00 4.18
432 457 2.814336 CCCTCCAAGCTATAAAATCCGC 59.186 50.000 0.00 0.00 0.00 5.54
433 458 2.814336 CCTCCAAGCTATAAAATCCGCC 59.186 50.000 0.00 0.00 0.00 6.13
434 459 2.814336 CTCCAAGCTATAAAATCCGCCC 59.186 50.000 0.00 0.00 0.00 6.13
435 460 1.535462 CCAAGCTATAAAATCCGCCCG 59.465 52.381 0.00 0.00 0.00 6.13
436 461 2.489971 CAAGCTATAAAATCCGCCCGA 58.510 47.619 0.00 0.00 0.00 5.14
437 462 2.457366 AGCTATAAAATCCGCCCGAG 57.543 50.000 0.00 0.00 0.00 4.63
438 463 0.796927 GCTATAAAATCCGCCCGAGC 59.203 55.000 0.00 0.00 0.00 5.03
439 464 1.876416 GCTATAAAATCCGCCCGAGCA 60.876 52.381 0.00 0.00 39.83 4.26
440 465 2.489971 CTATAAAATCCGCCCGAGCAA 58.510 47.619 0.00 0.00 39.83 3.91
441 466 1.981256 ATAAAATCCGCCCGAGCAAT 58.019 45.000 0.00 0.00 39.83 3.56
558 592 4.675029 CACCGGCGTTCCCTCGTT 62.675 66.667 6.01 0.00 0.00 3.85
859 894 3.849951 CCCATGGTCGTCTCCCCG 61.850 72.222 11.73 0.00 0.00 5.73
937 972 2.362120 GCCTGCAATGCCCTCAGT 60.362 61.111 1.53 0.00 0.00 3.41
963 998 2.677848 GCTCCAGAAACCCCTCCC 59.322 66.667 0.00 0.00 0.00 4.30
969 1004 0.548510 CAGAAACCCCTCCCCTGATC 59.451 60.000 0.00 0.00 0.00 2.92
973 1008 1.056700 AACCCCTCCCCTGATCATCG 61.057 60.000 0.00 0.00 0.00 3.84
974 1009 2.219875 CCCCTCCCCTGATCATCGG 61.220 68.421 0.00 0.00 0.00 4.18
976 1011 2.746359 CTCCCCTGATCATCGGCC 59.254 66.667 0.00 0.00 0.00 6.13
977 1012 2.849162 TCCCCTGATCATCGGCCC 60.849 66.667 0.00 0.00 0.00 5.80
978 1013 4.320456 CCCCTGATCATCGGCCCG 62.320 72.222 0.00 0.00 0.00 6.13
1086 1130 2.614446 CGTGACGGACTCGGTCACT 61.614 63.158 31.33 2.42 41.07 3.41
1563 1607 0.107066 TCGGGAACATGCTGCATGAT 60.107 50.000 40.25 32.14 43.81 2.45
1566 1610 1.395635 GGAACATGCTGCATGATGGA 58.604 50.000 40.25 2.55 43.81 3.41
1581 1625 2.586357 GGAGAAGGCGCGGATGTC 60.586 66.667 8.83 0.00 0.00 3.06
1587 1631 3.419759 GGCGCGGATGTCACGTTT 61.420 61.111 8.83 0.00 0.00 3.60
1590 1634 1.705727 CGCGGATGTCACGTTTACC 59.294 57.895 0.00 0.00 0.00 2.85
1632 1676 1.102154 CTCACAGGTGTGTTTTGGCA 58.898 50.000 9.87 0.00 45.76 4.92
1867 1911 1.312815 GCTGCTGTGTGAAAGGAAGT 58.687 50.000 0.00 0.00 0.00 3.01
1896 1940 5.391843 CGATGCAATTGATGTGGAAACAGTA 60.392 40.000 10.34 0.00 44.46 2.74
2019 2063 0.933097 CCGACGGATTCAAGCATCTG 59.067 55.000 8.64 0.00 35.85 2.90
2177 2221 8.535592 GTTCAGAAATCTTACATCTGTATGTCG 58.464 37.037 0.00 0.00 42.92 4.35
2364 2408 8.093307 TGCAATTTATTTGTATGCTTTCCTGAA 58.907 29.630 0.00 0.00 37.65 3.02
2375 2419 5.801350 TGCTTTCCTGAATCTTGATTACG 57.199 39.130 0.00 0.00 0.00 3.18
2431 2476 0.537188 ACACCCTGGCTGATCTAACG 59.463 55.000 0.00 0.00 0.00 3.18
2503 2552 0.527565 CCCTGAAACATCTTTGCCCG 59.472 55.000 0.00 0.00 0.00 6.13
2510 2559 3.369546 AACATCTTTGCCCGTTTTCAG 57.630 42.857 0.00 0.00 0.00 3.02
2518 2584 0.668535 GCCCGTTTTCAGAAGCAGTT 59.331 50.000 0.00 0.00 0.00 3.16
2523 2589 4.058817 CCGTTTTCAGAAGCAGTTAGACT 58.941 43.478 0.00 0.00 0.00 3.24
2585 2652 2.014857 CATTGTCAGGAGCATCACTGG 58.985 52.381 0.00 0.00 35.16 4.00
2789 2862 0.897621 GGCCCAAGGATTCAAACTGG 59.102 55.000 0.00 0.00 0.00 4.00
2871 2944 4.338964 TGTTGTATGGTCATCATTGGCATC 59.661 41.667 0.00 0.00 37.30 3.91
2888 2961 3.997021 GGCATCCATATACCTCTTGAACG 59.003 47.826 0.00 0.00 0.00 3.95
3079 3314 3.063997 CCAGTGTCATAAACATCGAAGCC 59.936 47.826 0.00 0.00 40.80 4.35
3080 3315 2.930040 AGTGTCATAAACATCGAAGCCG 59.070 45.455 0.00 0.00 40.80 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.510505 CGTAGGGAGAGTAATATAAGTGGTAAC 58.489 40.741 0.00 0.00 0.00 2.50
2 3 8.627208 CGTAGGGAGAGTAATATAAGTGGTAA 57.373 38.462 0.00 0.00 0.00 2.85
23 24 2.824341 ACACCTTTCAGACTACCCGTAG 59.176 50.000 0.22 0.22 39.04 3.51
24 25 2.821969 GACACCTTTCAGACTACCCGTA 59.178 50.000 0.00 0.00 0.00 4.02
25 26 1.617357 GACACCTTTCAGACTACCCGT 59.383 52.381 0.00 0.00 0.00 5.28
26 27 1.402456 CGACACCTTTCAGACTACCCG 60.402 57.143 0.00 0.00 0.00 5.28
27 28 1.891150 TCGACACCTTTCAGACTACCC 59.109 52.381 0.00 0.00 0.00 3.69
28 29 2.671632 GCTCGACACCTTTCAGACTACC 60.672 54.545 0.00 0.00 0.00 3.18
29 30 2.597520 GCTCGACACCTTTCAGACTAC 58.402 52.381 0.00 0.00 0.00 2.73
30 31 1.199327 CGCTCGACACCTTTCAGACTA 59.801 52.381 0.00 0.00 0.00 2.59
31 32 0.039074 CGCTCGACACCTTTCAGACT 60.039 55.000 0.00 0.00 0.00 3.24
32 33 0.039437 TCGCTCGACACCTTTCAGAC 60.039 55.000 0.00 0.00 0.00 3.51
33 34 0.241213 CTCGCTCGACACCTTTCAGA 59.759 55.000 0.00 0.00 0.00 3.27
34 35 0.039074 ACTCGCTCGACACCTTTCAG 60.039 55.000 0.00 0.00 0.00 3.02
35 36 0.387929 AACTCGCTCGACACCTTTCA 59.612 50.000 0.00 0.00 0.00 2.69
36 37 1.984297 GTAACTCGCTCGACACCTTTC 59.016 52.381 0.00 0.00 0.00 2.62
37 38 1.336609 GGTAACTCGCTCGACACCTTT 60.337 52.381 5.99 0.00 0.00 3.11
38 39 0.243095 GGTAACTCGCTCGACACCTT 59.757 55.000 5.99 0.00 0.00 3.50
39 40 0.892358 TGGTAACTCGCTCGACACCT 60.892 55.000 11.67 0.00 37.61 4.00
40 41 0.172803 ATGGTAACTCGCTCGACACC 59.827 55.000 6.19 6.19 37.61 4.16
41 42 2.448219 GTATGGTAACTCGCTCGACAC 58.552 52.381 0.00 0.00 37.61 3.67
42 43 1.402968 GGTATGGTAACTCGCTCGACA 59.597 52.381 0.00 0.00 37.61 4.35
43 44 1.402968 TGGTATGGTAACTCGCTCGAC 59.597 52.381 0.00 0.00 37.61 4.20
44 45 1.753930 TGGTATGGTAACTCGCTCGA 58.246 50.000 0.00 0.00 37.61 4.04
45 46 2.795175 ATGGTATGGTAACTCGCTCG 57.205 50.000 0.00 0.00 37.61 5.03
46 47 5.646577 ATCTATGGTATGGTAACTCGCTC 57.353 43.478 0.00 0.00 37.61 5.03
47 48 6.096987 CCATATCTATGGTATGGTAACTCGCT 59.903 42.308 7.90 0.00 46.42 4.93
48 49 6.273825 CCATATCTATGGTATGGTAACTCGC 58.726 44.000 7.90 0.00 46.42 5.03
62 63 6.831664 AGGGTAATAAGGGCCATATCTATG 57.168 41.667 6.18 0.00 0.00 2.23
63 64 6.971840 TGAAGGGTAATAAGGGCCATATCTAT 59.028 38.462 6.18 0.00 0.00 1.98
64 65 6.335934 TGAAGGGTAATAAGGGCCATATCTA 58.664 40.000 6.18 0.00 0.00 1.98
65 66 5.170198 TGAAGGGTAATAAGGGCCATATCT 58.830 41.667 6.18 0.00 0.00 1.98
66 67 5.514500 TGAAGGGTAATAAGGGCCATATC 57.486 43.478 6.18 0.00 0.00 1.63
67 68 5.941146 TTGAAGGGTAATAAGGGCCATAT 57.059 39.130 6.18 0.00 0.00 1.78
68 69 5.735733 TTTGAAGGGTAATAAGGGCCATA 57.264 39.130 6.18 0.00 0.00 2.74
69 70 4.618378 TTTGAAGGGTAATAAGGGCCAT 57.382 40.909 6.18 0.00 0.00 4.40
70 71 4.405756 TTTTGAAGGGTAATAAGGGCCA 57.594 40.909 6.18 0.00 0.00 5.36
71 72 4.382685 GCTTTTTGAAGGGTAATAAGGGCC 60.383 45.833 0.00 0.00 0.00 5.80
72 73 4.382685 GGCTTTTTGAAGGGTAATAAGGGC 60.383 45.833 0.00 0.00 0.00 5.19
73 74 4.775253 TGGCTTTTTGAAGGGTAATAAGGG 59.225 41.667 0.00 0.00 0.00 3.95
74 75 5.993748 TGGCTTTTTGAAGGGTAATAAGG 57.006 39.130 0.00 0.00 0.00 2.69
75 76 8.846943 AAAATGGCTTTTTGAAGGGTAATAAG 57.153 30.769 9.97 0.00 36.18 1.73
131 132 6.368791 TGAGAACTCACATTAATTGTCTTCCG 59.631 38.462 0.00 0.00 36.00 4.30
182 183 3.313526 CCCGCAGAAAAAGATAGGATGTG 59.686 47.826 0.00 0.00 0.00 3.21
221 232 8.554528 CATGCACGATTAATTGTTTCTCTAGAT 58.445 33.333 5.54 0.00 0.00 1.98
223 234 6.630443 GCATGCACGATTAATTGTTTCTCTAG 59.370 38.462 14.21 0.00 0.00 2.43
224 235 6.093357 TGCATGCACGATTAATTGTTTCTCTA 59.907 34.615 18.46 0.00 0.00 2.43
226 237 5.094812 TGCATGCACGATTAATTGTTTCTC 58.905 37.500 18.46 0.00 0.00 2.87
227 238 5.058149 TGCATGCACGATTAATTGTTTCT 57.942 34.783 18.46 0.00 0.00 2.52
228 239 5.954434 ATGCATGCACGATTAATTGTTTC 57.046 34.783 25.37 2.33 0.00 2.78
307 322 8.547967 TTGTGTTCCTAGATAGAAACACAATC 57.452 34.615 24.75 2.96 38.63 2.67
340 355 8.201242 TGCATGTATCTTTGTATATGAGGGTA 57.799 34.615 0.00 0.00 0.00 3.69
352 368 5.469760 TCGTGGGATAATGCATGTATCTTTG 59.530 40.000 19.38 12.04 0.00 2.77
418 443 1.608283 GCTCGGGCGGATTTTATAGCT 60.608 52.381 0.00 0.00 0.00 3.32
431 456 4.918201 CGAGGGGATTGCTCGGGC 62.918 72.222 0.00 0.00 37.02 6.13
432 457 3.154473 TCGAGGGGATTGCTCGGG 61.154 66.667 0.00 0.00 40.53 5.14
433 458 1.676678 TTCTCGAGGGGATTGCTCGG 61.677 60.000 13.56 0.00 40.53 4.63
434 459 0.249238 CTTCTCGAGGGGATTGCTCG 60.249 60.000 13.56 0.00 41.38 5.03
435 460 1.115467 TCTTCTCGAGGGGATTGCTC 58.885 55.000 13.56 0.00 0.00 4.26
436 461 1.208293 GTTCTTCTCGAGGGGATTGCT 59.792 52.381 13.56 0.00 0.00 3.91
437 462 1.066143 TGTTCTTCTCGAGGGGATTGC 60.066 52.381 13.56 5.71 0.00 3.56
438 463 3.265791 CTTGTTCTTCTCGAGGGGATTG 58.734 50.000 13.56 0.00 0.00 2.67
439 464 2.907042 ACTTGTTCTTCTCGAGGGGATT 59.093 45.455 13.56 0.00 0.00 3.01
440 465 2.498078 GACTTGTTCTTCTCGAGGGGAT 59.502 50.000 13.56 0.00 0.00 3.85
441 466 1.893801 GACTTGTTCTTCTCGAGGGGA 59.106 52.381 13.56 8.32 0.00 4.81
484 518 1.427020 GCTGGTGATTTGCTCTCGC 59.573 57.895 0.00 0.00 0.00 5.03
488 522 0.322816 TGGAGGCTGGTGATTTGCTC 60.323 55.000 0.00 0.00 0.00 4.26
844 879 2.758327 TCCGGGGAGACGACCATG 60.758 66.667 0.00 0.00 35.47 3.66
920 955 2.362120 ACTGAGGGCATTGCAGGC 60.362 61.111 11.39 4.00 34.05 4.85
963 998 4.996434 GGCGGGCCGATGATCAGG 62.996 72.222 33.44 0.00 0.00 3.86
977 1012 3.839432 GAGGAAGGGGAGTCGGCG 61.839 72.222 0.00 0.00 0.00 6.46
978 1013 3.471806 GGAGGAAGGGGAGTCGGC 61.472 72.222 0.00 0.00 0.00 5.54
982 1017 0.423544 ATGGAAGGAGGAAGGGGAGT 59.576 55.000 0.00 0.00 0.00 3.85
984 1019 0.624500 CCATGGAAGGAGGAAGGGGA 60.625 60.000 5.56 0.00 0.00 4.81
989 1024 1.846439 GATCACCCATGGAAGGAGGAA 59.154 52.381 15.22 0.00 0.00 3.36
1563 1607 3.371097 GACATCCGCGCCTTCTCCA 62.371 63.158 0.00 0.00 0.00 3.86
1566 1610 2.125512 GTGACATCCGCGCCTTCT 60.126 61.111 0.00 0.00 0.00 2.85
1590 1634 3.521308 GAACAACTGGCCGCACACG 62.521 63.158 0.00 0.00 39.67 4.49
1632 1676 0.909610 TGAAGACAGGGGAGCGGAAT 60.910 55.000 0.00 0.00 0.00 3.01
1867 1911 2.159352 CCACATCAATTGCATCGCTCAA 60.159 45.455 0.00 0.00 0.00 3.02
1896 1940 1.616994 GCTAAAGCCAGGGTGGTTGAT 60.617 52.381 0.00 0.00 40.46 2.57
1989 2033 3.255725 GAATCCGTCGGTTAACATGACA 58.744 45.455 22.39 10.26 32.91 3.58
2177 2221 6.422400 GGCTTACACAGAAGAGATATAACTGC 59.578 42.308 0.00 0.00 32.67 4.40
2337 2381 7.760794 TCAGGAAAGCATACAAATAAATTGCAG 59.239 33.333 0.00 0.00 43.13 4.41
2389 2433 5.885230 TGATTTGTTGCTTCATACCAGAG 57.115 39.130 0.00 0.00 0.00 3.35
2390 2434 5.534278 TGTTGATTTGTTGCTTCATACCAGA 59.466 36.000 0.00 0.00 0.00 3.86
2394 2438 4.923281 GGGTGTTGATTTGTTGCTTCATAC 59.077 41.667 0.00 0.00 0.00 2.39
2431 2476 5.956642 TGTGGTTTACAGTTTCCTTGTTTC 58.043 37.500 0.00 0.00 33.42 2.78
2472 2517 1.792757 TTTCAGGGCTGAGGCATGGT 61.793 55.000 20.33 0.00 40.21 3.55
2503 2552 6.604735 TTCAGTCTAACTGCTTCTGAAAAC 57.395 37.500 2.18 0.00 45.54 2.43
2510 2559 7.093992 AGAACTACATTCAGTCTAACTGCTTC 58.906 38.462 2.18 0.00 45.54 3.86
2518 2584 7.451877 ACTTTCAGGAGAACTACATTCAGTCTA 59.548 37.037 0.00 0.00 40.09 2.59
2523 2589 6.931281 CAGAACTTTCAGGAGAACTACATTCA 59.069 38.462 0.00 0.00 40.09 2.57
2533 2599 3.578716 CCTGTACCAGAACTTTCAGGAGA 59.421 47.826 7.37 0.00 43.28 3.71
2585 2652 2.094854 CACAATTCCTGCAAGAGAAGCC 60.095 50.000 0.00 0.00 34.07 4.35
2772 2845 3.230134 TGTTCCAGTTTGAATCCTTGGG 58.770 45.455 0.00 0.00 0.00 4.12
2789 2862 5.572896 GCAAGCAGTTGGTATGTATTTGTTC 59.427 40.000 0.00 0.00 33.87 3.18
2871 2944 4.506654 CGTTTCCGTTCAAGAGGTATATGG 59.493 45.833 0.00 0.00 0.00 2.74
2888 2961 3.371285 GCAGAGAAGTCATTACCGTTTCC 59.629 47.826 0.00 0.00 0.00 3.13
2988 3062 6.700081 GCATGATCATAGTTTGCATGTTTCAT 59.300 34.615 8.15 0.00 38.76 2.57


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

AutoCloner maintained by Alex Coulton.