Multiple sequence alignment - TraesCS5D01G234300

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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 TraesCS5D01G234300 chr5D 100.000 4513 0 0 1 4513 341569018 341564506 0 8335
1 TraesCS5D01G234300 chr5B 95.794 4470 141 24 74 4513 401012615 401008163 0 7169
2 TraesCS5D01G234300 chr5A 93.774 4481 189 52 68 4511 442703781 442699354 0 6647


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 TraesCS5D01G234300 chr5D 341564506 341569018 4512 True 8335 8335 100.000 1 4513 1 chr5D.!!$R1 4512
1 TraesCS5D01G234300 chr5B 401008163 401012615 4452 True 7169 7169 95.794 74 4513 1 chr5B.!!$R1 4439
2 TraesCS5D01G234300 chr5A 442699354 442703781 4427 True 6647 6647 93.774 68 4511 1 chr5A.!!$R1 4443

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
722 742 0.397941 TTCACTCCTTCTGCTGGGTG 59.602 55.000 0.00 0.0 0.00 4.61 F
1203 1235 0.517316 GCTTCGACACACACCATTCC 59.483 55.000 0.00 0.0 0.00 3.01 F
1449 1481 1.404986 CGGGACTATGTTCCTTTCGCA 60.405 52.381 0.00 0.0 35.76 5.10 F
2703 2735 0.609131 ATCCAAGTGAAGTTGCCGGG 60.609 55.000 2.18 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2165 0.179100 CTGACAGCACCCAGTATCCG 60.179 60.000 0.00 0.0 0.00 4.18 R
2703 2735 1.039785 GGAAGGGCTTGATTGCTCCC 61.040 60.000 0.00 0.0 39.05 4.30 R
3205 3237 0.036952 AGGTGACAGAACTGATGCCG 60.037 55.000 8.87 0.0 0.00 5.69 R
4424 4482 1.210478 TGTCAGGAAGCTTGGCTATCC 59.790 52.381 2.10 0.0 38.25 2.59 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
23 24 5.811588 AGTGTATGCGAGTATATATGAGCG 58.188 41.667 0.00 0.00 0.00 5.03
24 25 4.438145 GTGTATGCGAGTATATATGAGCGC 59.562 45.833 16.15 16.15 44.15 5.92
25 26 2.561733 TGCGAGTATATATGAGCGCC 57.438 50.000 18.63 0.00 43.35 6.53
26 27 2.092323 TGCGAGTATATATGAGCGCCT 58.908 47.619 18.63 0.00 43.35 5.52
27 28 2.159379 TGCGAGTATATATGAGCGCCTG 60.159 50.000 18.63 0.00 43.35 4.85
28 29 2.455032 CGAGTATATATGAGCGCCTGC 58.545 52.381 2.29 0.00 43.24 4.85
38 39 3.181967 GCGCCTGCGTCTGTACTG 61.182 66.667 13.57 0.00 42.09 2.74
39 40 3.181967 CGCCTGCGTCTGTACTGC 61.182 66.667 2.83 0.00 34.35 4.40
40 41 2.048222 GCCTGCGTCTGTACTGCA 60.048 61.111 0.00 0.00 35.13 4.41
41 42 1.448540 GCCTGCGTCTGTACTGCAT 60.449 57.895 0.00 0.00 35.60 3.96
42 43 1.021390 GCCTGCGTCTGTACTGCATT 61.021 55.000 0.00 0.00 35.60 3.56
43 44 1.739035 GCCTGCGTCTGTACTGCATTA 60.739 52.381 0.00 0.00 35.60 1.90
44 45 2.616960 CCTGCGTCTGTACTGCATTAA 58.383 47.619 0.00 0.00 35.60 1.40
45 46 3.000041 CCTGCGTCTGTACTGCATTAAA 59.000 45.455 0.00 0.00 35.60 1.52
46 47 3.435327 CCTGCGTCTGTACTGCATTAAAA 59.565 43.478 0.00 0.00 35.60 1.52
47 48 4.083537 CCTGCGTCTGTACTGCATTAAAAA 60.084 41.667 0.00 0.00 35.60 1.94
69 70 7.648039 AAAAAGTGTATGAGTACCCACAAAA 57.352 32.000 0.00 0.00 0.00 2.44
70 71 7.648039 AAAAGTGTATGAGTACCCACAAAAA 57.352 32.000 0.00 0.00 0.00 1.94
71 72 6.877611 AAGTGTATGAGTACCCACAAAAAG 57.122 37.500 0.00 0.00 0.00 2.27
72 73 6.182507 AGTGTATGAGTACCCACAAAAAGA 57.817 37.500 0.00 0.00 0.00 2.52
79 80 6.416415 TGAGTACCCACAAAAAGAAAGTGTA 58.584 36.000 0.00 0.00 0.00 2.90
82 83 7.057894 AGTACCCACAAAAAGAAAGTGTATGA 58.942 34.615 0.00 0.00 0.00 2.15
305 311 0.651031 GCGAAAACATACTCCCTCGC 59.349 55.000 0.00 0.00 43.91 5.03
397 403 0.963856 GGAAAATCGGGGGAAACGCT 60.964 55.000 0.00 0.00 44.03 5.07
508 525 3.854669 CCGGCGAGCCATTCTCCT 61.855 66.667 9.30 0.00 38.62 3.69
637 654 6.756542 GTGAGGTATGAGCTTGTTTTGTTTTT 59.243 34.615 0.00 0.00 0.00 1.94
652 669 5.945466 TTGTTTTTATCCCGTGGTTAGTC 57.055 39.130 0.00 0.00 0.00 2.59
654 671 3.632643 TTTTATCCCGTGGTTAGTCCC 57.367 47.619 0.00 0.00 34.77 4.46
684 704 3.151958 ATCCCGACGCCAAGATCCG 62.152 63.158 0.00 0.00 0.00 4.18
712 732 2.262915 CCTCGCGCTTCACTCCTT 59.737 61.111 5.56 0.00 0.00 3.36
719 739 1.018226 CGCTTCACTCCTTCTGCTGG 61.018 60.000 0.00 0.00 0.00 4.85
720 740 0.676151 GCTTCACTCCTTCTGCTGGG 60.676 60.000 0.00 0.00 0.00 4.45
721 741 0.689623 CTTCACTCCTTCTGCTGGGT 59.310 55.000 0.00 0.00 0.00 4.51
722 742 0.397941 TTCACTCCTTCTGCTGGGTG 59.602 55.000 0.00 0.00 0.00 4.61
724 744 1.845205 ACTCCTTCTGCTGGGTGCT 60.845 57.895 0.00 0.00 43.37 4.40
725 745 1.376942 CTCCTTCTGCTGGGTGCTG 60.377 63.158 0.00 0.00 43.37 4.41
727 747 3.060615 CTTCTGCTGGGTGCTGGC 61.061 66.667 0.00 0.00 43.37 4.85
931 953 4.382362 GGCTGCAGCAGATTTAGGAAAAAT 60.382 41.667 37.63 0.00 44.36 1.82
1043 1075 2.093973 CGGACAACAGGACTAGAAGCAT 60.094 50.000 0.00 0.00 0.00 3.79
1044 1076 3.526534 GGACAACAGGACTAGAAGCATC 58.473 50.000 0.00 0.00 0.00 3.91
1176 1208 1.308998 CCGATTGCACCATCTTACCC 58.691 55.000 0.00 0.00 0.00 3.69
1203 1235 0.517316 GCTTCGACACACACCATTCC 59.483 55.000 0.00 0.00 0.00 3.01
1347 1379 2.010145 TGAATTACAGAGAGCGGCAC 57.990 50.000 1.45 0.00 0.00 5.01
1389 1421 2.351276 CACTGCCTGGTACCACCC 59.649 66.667 11.60 5.25 37.50 4.61
1449 1481 1.404986 CGGGACTATGTTCCTTTCGCA 60.405 52.381 0.00 0.00 35.76 5.10
1584 1616 5.523552 TGATAAGTACATTGATCAACTGGCG 59.476 40.000 11.07 0.00 0.00 5.69
1685 1717 5.690409 TGTATATTGCTTACTGCTACTTCGC 59.310 40.000 0.00 0.00 43.37 4.70
1853 1885 1.834263 AGAGGTGTCCCAGCTGTTATC 59.166 52.381 13.81 0.87 42.53 1.75
1963 1995 3.548745 TGGTGAGCCTCTAATCATGTG 57.451 47.619 0.00 0.00 35.27 3.21
2133 2165 3.039011 TGATAGGGTTCTAAGACCTGGC 58.961 50.000 0.00 0.00 39.71 4.85
2214 2246 4.884668 ACGTACAAAGGAGGATCTTGAA 57.115 40.909 0.00 0.00 33.73 2.69
2325 2357 5.580998 AGAGTAAATACTGAGTCCTGTCCA 58.419 41.667 0.00 0.00 36.50 4.02
2508 2540 5.246203 TCCAGCATCAATAGGTATACTGTCC 59.754 44.000 2.25 0.00 0.00 4.02
2526 2558 5.047377 ACTGTCCGGTCAATGCATTATTTTT 60.047 36.000 12.53 0.00 0.00 1.94
2547 2579 3.009723 TGCTTTGCCTACTTAGATGTGC 58.990 45.455 0.00 0.00 0.00 4.57
2548 2580 2.356069 GCTTTGCCTACTTAGATGTGCC 59.644 50.000 0.00 0.00 0.00 5.01
2553 2585 2.408050 CCTACTTAGATGTGCCGATGC 58.592 52.381 0.00 0.00 38.26 3.91
2565 2597 3.485947 TGCCGATGCATTAACAAGTTC 57.514 42.857 0.00 0.00 44.23 3.01
2570 2602 5.730568 GCCGATGCATTAACAAGTTCTTAGG 60.731 44.000 0.00 0.00 37.47 2.69
2680 2712 5.169295 GTGTTACACCTCTTCCTGATGTAC 58.831 45.833 3.79 0.00 0.00 2.90
2703 2735 0.609131 ATCCAAGTGAAGTTGCCGGG 60.609 55.000 2.18 0.00 0.00 5.73
2740 2772 2.559840 CAAGCAGGCTCAACGCAG 59.440 61.111 0.00 0.00 41.67 5.18
2785 2817 4.402474 GGTTAATTCCAGGGGTTTCATCTG 59.598 45.833 0.00 0.00 0.00 2.90
2907 2939 1.296392 GAATGCAGGTTTTGGGGGC 59.704 57.895 0.00 0.00 0.00 5.80
3053 3085 2.939103 GCTTGTTATGCCTGAATCTCGT 59.061 45.455 0.00 0.00 0.00 4.18
3055 3087 3.179443 TGTTATGCCTGAATCTCGTCC 57.821 47.619 0.00 0.00 0.00 4.79
3197 3229 7.055667 TGTATAGCAATAAGTAAGCTGCTCT 57.944 36.000 1.00 0.00 43.85 4.09
3203 3235 5.181748 CAATAAGTAAGCTGCTCTTGTCCT 58.818 41.667 1.00 0.00 36.25 3.85
3205 3237 1.082690 GTAAGCTGCTCTTGTCCTGC 58.917 55.000 1.00 0.00 36.25 4.85
3228 3260 2.225019 GCATCAGTTCTGTCACCTTGTG 59.775 50.000 0.00 0.00 34.45 3.33
3389 3421 5.242838 TGTCTTGACAAAGGTGAACAAACTT 59.757 36.000 0.44 0.00 33.90 2.66
3615 3647 3.426292 GCGAACAAAAATGGCCTACTCTC 60.426 47.826 3.32 0.00 0.00 3.20
3626 3658 0.178995 CCTACTCTCCTCCGGGGTAC 60.179 65.000 0.00 0.00 36.25 3.34
3816 3848 9.341899 CTGAATGTTTGCTTTATTACCAGTAAC 57.658 33.333 0.00 0.00 0.00 2.50
3827 3859 2.694616 ACCAGTAACCCCATTGCTTT 57.305 45.000 0.00 0.00 29.51 3.51
3888 3922 2.037251 ACTGTGCTGTTACCTGAACGAT 59.963 45.455 0.00 0.00 41.35 3.73
3894 3928 3.368236 GCTGTTACCTGAACGATCTGAAC 59.632 47.826 1.01 0.26 41.35 3.18
3895 3929 4.556233 CTGTTACCTGAACGATCTGAACA 58.444 43.478 1.01 4.42 41.35 3.18
4096 4137 7.698970 GTGCAGTTCTGAGTAGTATAAAGAGTC 59.301 40.741 3.84 0.00 0.00 3.36
4237 4278 9.686683 AGATTGCAGGTAATATTACTGTCTTTT 57.313 29.630 21.86 5.63 34.16 2.27
4301 4357 2.012673 CATAGCTTCAGACAACAGGCC 58.987 52.381 0.00 0.00 0.00 5.19
4353 4409 8.534496 TGGTATGTTCCTACTTACTCCTAAAAC 58.466 37.037 0.00 0.00 35.99 2.43
4424 4482 6.034256 GCTTTACTGCAGTGCATAATTTCTTG 59.966 38.462 29.57 5.94 38.13 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.438145 GCGCTCATATATACTCGCATACAC 59.562 45.833 15.33 0.00 41.84 2.90
2 3 4.497507 GGCGCTCATATATACTCGCATACA 60.498 45.833 19.33 0.00 43.72 2.29
3 4 3.975670 GGCGCTCATATATACTCGCATAC 59.024 47.826 19.33 5.77 43.72 2.39
4 5 3.883489 AGGCGCTCATATATACTCGCATA 59.117 43.478 19.33 0.00 43.72 3.14
5 6 2.690497 AGGCGCTCATATATACTCGCAT 59.310 45.455 19.33 13.29 43.72 4.73
6 7 2.092323 AGGCGCTCATATATACTCGCA 58.908 47.619 19.33 0.00 43.72 5.10
7 8 2.455032 CAGGCGCTCATATATACTCGC 58.545 52.381 7.64 13.11 41.55 5.03
8 9 2.455032 GCAGGCGCTCATATATACTCG 58.545 52.381 7.64 0.00 34.30 4.18
9 10 2.159366 ACGCAGGCGCTCATATATACTC 60.159 50.000 14.32 0.00 44.19 2.59
10 11 1.819288 ACGCAGGCGCTCATATATACT 59.181 47.619 14.32 0.00 44.19 2.12
11 12 2.159366 AGACGCAGGCGCTCATATATAC 60.159 50.000 14.32 0.00 44.19 1.47
12 13 2.092323 AGACGCAGGCGCTCATATATA 58.908 47.619 14.32 0.00 44.19 0.86
13 14 0.891373 AGACGCAGGCGCTCATATAT 59.109 50.000 14.32 0.00 44.19 0.86
14 15 0.039165 CAGACGCAGGCGCTCATATA 60.039 55.000 14.32 0.00 44.19 0.86
15 16 1.300465 CAGACGCAGGCGCTCATAT 60.300 57.895 14.32 0.00 44.19 1.78
16 17 1.381165 TACAGACGCAGGCGCTCATA 61.381 55.000 14.32 4.51 44.19 2.15
17 18 2.710902 TACAGACGCAGGCGCTCAT 61.711 57.895 14.32 5.37 44.19 2.90
18 19 3.370231 TACAGACGCAGGCGCTCA 61.370 61.111 14.32 0.10 44.19 4.26
19 20 2.881352 GTACAGACGCAGGCGCTC 60.881 66.667 14.32 10.40 44.19 5.03
20 21 3.374402 AGTACAGACGCAGGCGCT 61.374 61.111 14.32 9.05 44.19 5.92
21 22 3.181967 CAGTACAGACGCAGGCGC 61.182 66.667 14.32 0.00 44.19 6.53
22 23 3.181967 GCAGTACAGACGCAGGCG 61.182 66.667 12.71 12.71 46.03 5.52
23 24 1.021390 AATGCAGTACAGACGCAGGC 61.021 55.000 0.00 0.00 38.09 4.85
24 25 2.293677 TAATGCAGTACAGACGCAGG 57.706 50.000 0.00 0.00 38.09 4.85
25 26 4.661993 TTTTAATGCAGTACAGACGCAG 57.338 40.909 0.00 0.00 38.09 5.18
45 46 7.648039 TTTTGTGGGTACTCATACACTTTTT 57.352 32.000 0.00 0.00 35.54 1.94
46 47 7.558444 TCTTTTTGTGGGTACTCATACACTTTT 59.442 33.333 0.00 0.00 35.54 2.27
47 48 7.057894 TCTTTTTGTGGGTACTCATACACTTT 58.942 34.615 0.00 0.00 35.54 2.66
48 49 6.597562 TCTTTTTGTGGGTACTCATACACTT 58.402 36.000 0.00 0.00 35.54 3.16
49 50 6.182507 TCTTTTTGTGGGTACTCATACACT 57.817 37.500 0.00 0.00 35.54 3.55
50 51 6.870971 TTCTTTTTGTGGGTACTCATACAC 57.129 37.500 0.00 0.00 35.02 2.90
51 52 7.012894 CACTTTCTTTTTGTGGGTACTCATACA 59.987 37.037 0.00 0.00 32.40 2.29
52 53 7.012989 ACACTTTCTTTTTGTGGGTACTCATAC 59.987 37.037 0.00 0.00 36.16 2.39
53 54 7.057894 ACACTTTCTTTTTGTGGGTACTCATA 58.942 34.615 0.00 0.00 36.16 2.15
54 55 5.891551 ACACTTTCTTTTTGTGGGTACTCAT 59.108 36.000 0.00 0.00 36.16 2.90
55 56 5.258051 ACACTTTCTTTTTGTGGGTACTCA 58.742 37.500 0.00 0.00 36.16 3.41
56 57 5.830000 ACACTTTCTTTTTGTGGGTACTC 57.170 39.130 0.00 0.00 36.16 2.59
57 58 7.057894 TCATACACTTTCTTTTTGTGGGTACT 58.942 34.615 0.00 0.00 36.16 2.73
58 59 7.227910 TCTCATACACTTTCTTTTTGTGGGTAC 59.772 37.037 0.00 0.00 36.16 3.34
59 60 7.284074 TCTCATACACTTTCTTTTTGTGGGTA 58.716 34.615 0.00 0.00 36.16 3.69
60 61 6.126409 TCTCATACACTTTCTTTTTGTGGGT 58.874 36.000 0.00 0.00 36.16 4.51
61 62 6.633500 TCTCATACACTTTCTTTTTGTGGG 57.367 37.500 0.00 0.00 36.16 4.61
397 403 3.713826 AAATCTCGGGGTTTTAGAGCA 57.286 42.857 0.00 0.00 32.42 4.26
523 540 1.304962 TAGAGGGCTTGAGGCGTGA 60.305 57.895 4.43 0.00 42.94 4.35
525 542 2.711922 CGTAGAGGGCTTGAGGCGT 61.712 63.158 0.00 0.00 42.94 5.68
557 574 2.348888 GGAAGGACGGAGCTCGGAA 61.349 63.158 26.25 0.00 44.45 4.30
586 603 0.029834 ATGGCGAAAGATTGCGATGC 59.970 50.000 0.00 0.00 33.56 3.91
637 654 0.398948 GGGGGACTAACCACGGGATA 60.399 60.000 0.00 0.00 44.45 2.59
654 671 3.164269 CGGGATCAGTGGAGGGGG 61.164 72.222 0.00 0.00 0.00 5.40
719 739 2.669569 ACACATGTCGCCAGCACC 60.670 61.111 0.00 0.00 0.00 5.01
720 740 2.557805 CACACATGTCGCCAGCAC 59.442 61.111 0.00 0.00 0.00 4.40
721 741 2.669229 CCACACATGTCGCCAGCA 60.669 61.111 0.00 0.00 0.00 4.41
722 742 3.434319 CCCACACATGTCGCCAGC 61.434 66.667 0.00 0.00 0.00 4.85
724 744 0.251121 AAATCCCACACATGTCGCCA 60.251 50.000 0.00 0.00 0.00 5.69
725 745 0.887933 AAAATCCCACACATGTCGCC 59.112 50.000 0.00 0.00 0.00 5.54
727 747 4.503910 TCTCTAAAATCCCACACATGTCG 58.496 43.478 0.00 0.00 0.00 4.35
728 748 6.259608 CAGATCTCTAAAATCCCACACATGTC 59.740 42.308 0.00 0.00 0.00 3.06
729 749 6.118170 CAGATCTCTAAAATCCCACACATGT 58.882 40.000 0.00 0.00 0.00 3.21
730 750 6.118170 ACAGATCTCTAAAATCCCACACATG 58.882 40.000 0.00 0.00 0.00 3.21
731 751 6.319048 ACAGATCTCTAAAATCCCACACAT 57.681 37.500 0.00 0.00 0.00 3.21
732 752 5.762179 ACAGATCTCTAAAATCCCACACA 57.238 39.130 0.00 0.00 0.00 3.72
773 793 5.411669 CAGTGTATCCTAACCACCAAACTTC 59.588 44.000 0.00 0.00 0.00 3.01
1043 1075 6.389906 CCAATCACTATGCATATAGACACGA 58.610 40.000 6.92 0.00 38.88 4.35
1044 1076 5.062683 GCCAATCACTATGCATATAGACACG 59.937 44.000 6.92 0.00 38.88 4.49
1176 1208 0.861837 GTGTGTCGAAGCTGAGGTTG 59.138 55.000 0.00 0.00 0.00 3.77
1203 1235 2.956987 CCGGAGCTGCCTTGTTTG 59.043 61.111 0.00 0.00 0.00 2.93
1389 1421 2.711009 TGGAGCAACATATCCCTTAGGG 59.289 50.000 11.94 11.94 46.11 3.53
1449 1481 4.889995 GTCAAGCTCTTATAGGGGCAATTT 59.110 41.667 9.67 0.00 0.00 1.82
1584 1616 3.000925 CGTTGGCAATCGGTATAACTGAC 59.999 47.826 1.92 0.00 36.13 3.51
1685 1717 3.804325 TGAACAAAGTCAGAAGAAGCTCG 59.196 43.478 0.00 0.00 0.00 5.03
1853 1885 3.634568 TTAATTGTGCCAAGAACACCG 57.365 42.857 0.00 0.00 37.22 4.94
1963 1995 4.672587 TGGATGCACAGTATAGAAGGAC 57.327 45.455 0.00 0.00 0.00 3.85
2133 2165 0.179100 CTGACAGCACCCAGTATCCG 60.179 60.000 0.00 0.00 0.00 4.18
2214 2246 3.132646 CCTCTATCTTGTTCTGCTCTGCT 59.867 47.826 0.00 0.00 0.00 4.24
2325 2357 5.304101 CACAGTGGATTCTTCTAGCCTAGAT 59.696 44.000 1.50 0.00 34.22 1.98
2486 2518 5.164233 CGGACAGTATACCTATTGATGCTG 58.836 45.833 0.00 0.00 40.44 4.41
2508 2540 5.783100 AAGCAAAAATAATGCATTGACCG 57.217 34.783 22.27 6.61 46.22 4.79
2526 2558 3.009723 GCACATCTAAGTAGGCAAAGCA 58.990 45.455 0.00 0.00 0.00 3.91
2547 2579 5.584649 TCCTAAGAACTTGTTAATGCATCGG 59.415 40.000 0.00 0.00 0.00 4.18
2548 2580 6.313905 ACTCCTAAGAACTTGTTAATGCATCG 59.686 38.462 0.00 0.00 0.00 3.84
2553 2585 7.661847 ACCAGAACTCCTAAGAACTTGTTAATG 59.338 37.037 0.00 0.00 0.00 1.90
2680 2712 3.052036 CGGCAACTTCACTTGGATTTTG 58.948 45.455 0.00 0.00 0.00 2.44
2703 2735 1.039785 GGAAGGGCTTGATTGCTCCC 61.040 60.000 0.00 0.00 39.05 4.30
2740 2772 5.952347 ACCCATTAGAAATTCTTGGAGGAAC 59.048 40.000 13.74 0.00 28.06 3.62
2785 2817 6.500684 TTTGTTGTCTTTCTGATATGCCTC 57.499 37.500 0.00 0.00 0.00 4.70
2907 2939 3.147889 CTCGATCGCCGCAGCAAAG 62.148 63.158 11.09 0.00 39.83 2.77
3053 3085 5.042463 TCATGACAACAACTTTACTGGGA 57.958 39.130 0.00 0.00 0.00 4.37
3055 3087 6.377327 AGTTCATGACAACAACTTTACTGG 57.623 37.500 0.00 0.00 0.00 4.00
3203 3235 0.950555 GTGACAGAACTGATGCCGCA 60.951 55.000 8.87 0.00 0.00 5.69
3205 3237 0.036952 AGGTGACAGAACTGATGCCG 60.037 55.000 8.87 0.00 0.00 5.69
3228 3260 8.190784 AGCATTGGCAATCTTACTAATTGTTAC 58.809 33.333 10.36 0.00 44.61 2.50
3441 3473 0.601558 AAGACCTTCTCGCGCACTAA 59.398 50.000 8.75 0.00 0.00 2.24
3626 3658 4.524316 TCAACCTTGATTGCTTCATTGG 57.476 40.909 0.00 0.00 35.59 3.16
3638 3670 1.250328 CTGCTGCCAATCAACCTTGA 58.750 50.000 0.00 0.00 42.14 3.02
3649 3681 5.249420 TGTTACAACAATATACTGCTGCCA 58.751 37.500 0.00 0.00 35.67 4.92
3652 3684 9.117145 CAAAACTGTTACAACAATATACTGCTG 57.883 33.333 0.00 0.00 38.66 4.41
3699 3731 4.623932 ACCAGAGTAACTTCATGCTGAA 57.376 40.909 0.00 0.00 34.79 3.02
3702 3734 7.168219 TCAATTAACCAGAGTAACTTCATGCT 58.832 34.615 0.00 0.00 0.00 3.79
3816 3848 3.693578 ACAAAAACAACAAAGCAATGGGG 59.306 39.130 0.00 0.00 0.00 4.96
3827 3859 9.798994 AAATAACCGTACATAACAAAAACAACA 57.201 25.926 0.00 0.00 0.00 3.33
3968 4004 3.631250 TCCATTGTTCCATTAAGCTCCC 58.369 45.455 0.00 0.00 0.00 4.30
4008 4046 3.051581 ACATAGTGGAATGGAGCAGGAT 58.948 45.455 0.00 0.00 0.00 3.24
4096 4137 6.257423 TCTTTGCACTAAAACATATGCATCG 58.743 36.000 0.19 0.00 46.75 3.84
4237 4278 7.541162 CCAGCATAATCTTCAAAAGAATCACA 58.459 34.615 0.00 0.00 41.63 3.58
4424 4482 1.210478 TGTCAGGAAGCTTGGCTATCC 59.790 52.381 2.10 0.00 38.25 2.59
4457 4515 3.107402 TCTCTCTTCCTGCACCTACAT 57.893 47.619 0.00 0.00 0.00 2.29
4462 4520 2.290577 ACCATTTCTCTCTTCCTGCACC 60.291 50.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.