Multiple sequence alignment - TraesCS4B01G239800

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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 TraesCS4B01G239800 chr4B 100.000 2949 0 0 1 2949 497377980 497375032 0.000000e+00 5446.0
1 TraesCS4B01G239800 chr4B 95.918 49 2 0 23 71 123986941 123986989 2.440000e-11 80.5
2 TraesCS4B01G239800 chr4B 95.918 49 2 0 23 71 330183107 330183155 2.440000e-11 80.5
3 TraesCS4B01G239800 chr6D 97.536 2881 68 3 70 2949 119198854 119201732 0.000000e+00 4924.0
4 TraesCS4B01G239800 chr6D 95.080 2886 103 13 68 2949 386196955 386199805 0.000000e+00 4506.0
5 TraesCS4B01G239800 chr6D 95.918 49 2 0 23 71 298304588 298304636 2.440000e-11 80.5
6 TraesCS4B01G239800 chr4D 97.467 2882 66 7 70 2949 481022267 481025143 0.000000e+00 4911.0
7 TraesCS4B01G239800 chr4D 94.804 2887 141 6 68 2949 476027722 476024840 0.000000e+00 4492.0
8 TraesCS4B01G239800 chr2B 94.069 2883 165 5 70 2949 288127917 288125038 0.000000e+00 4372.0
9 TraesCS4B01G239800 chr3A 96.018 2486 77 8 469 2949 748463358 748460890 0.000000e+00 4023.0
10 TraesCS4B01G239800 chr3A 95.897 2486 80 8 469 2949 748669081 748666613 0.000000e+00 4006.0
11 TraesCS4B01G239800 chr3A 95.858 2487 79 10 469 2949 748747560 748745092 0.000000e+00 4000.0
12 TraesCS4B01G239800 chr3A 95.656 2486 86 8 469 2949 748555565 748553097 0.000000e+00 3973.0
13 TraesCS4B01G239800 chr3B 95.272 1417 41 7 67 1481 679636989 679638381 0.000000e+00 2222.0
14 TraesCS4B01G239800 chr3B 99.429 175 1 0 2775 2949 172178356 172178182 4.740000e-83 318.0
15 TraesCS4B01G239800 chr3B 98.291 117 2 0 2775 2891 679638370 679638486 3.850000e-49 206.0
16 TraesCS4B01G239800 chr3B 75.000 344 44 26 257 585 586865190 586864874 1.440000e-23 121.0
17 TraesCS4B01G239800 chr6A 93.750 80 5 0 70 149 596779038 596778959 1.440000e-23 121.0
18 TraesCS4B01G239800 chr3D 74.212 349 49 25 257 589 447635463 447635140 1.120000e-19 108.0
19 TraesCS4B01G239800 chr7A 97.959 49 1 0 23 71 572071603 572071555 5.240000e-13 86.1
20 TraesCS4B01G239800 chr6B 97.959 49 1 0 23 71 610758709 610758757 5.240000e-13 86.1
21 TraesCS4B01G239800 chr2A 97.959 49 1 0 23 71 67821454 67821502 5.240000e-13 86.1
22 TraesCS4B01G239800 chr1D 95.918 49 2 0 23 71 373206857 373206905 2.440000e-11 80.5
23 TraesCS4B01G239800 chr1B 95.918 49 2 0 23 71 200580616 200580664 2.440000e-11 80.5
24 TraesCS4B01G239800 chr1B 95.918 49 2 0 23 71 298676730 298676778 2.440000e-11 80.5


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 TraesCS4B01G239800 chr4B 497375032 497377980 2948 True 5446 5446 100.0000 1 2949 1 chr4B.!!$R1 2948
1 TraesCS4B01G239800 chr6D 119198854 119201732 2878 False 4924 4924 97.5360 70 2949 1 chr6D.!!$F1 2879
2 TraesCS4B01G239800 chr6D 386196955 386199805 2850 False 4506 4506 95.0800 68 2949 1 chr6D.!!$F3 2881
3 TraesCS4B01G239800 chr4D 481022267 481025143 2876 False 4911 4911 97.4670 70 2949 1 chr4D.!!$F1 2879
4 TraesCS4B01G239800 chr4D 476024840 476027722 2882 True 4492 4492 94.8040 68 2949 1 chr4D.!!$R1 2881
5 TraesCS4B01G239800 chr2B 288125038 288127917 2879 True 4372 4372 94.0690 70 2949 1 chr2B.!!$R1 2879
6 TraesCS4B01G239800 chr3A 748460890 748463358 2468 True 4023 4023 96.0180 469 2949 1 chr3A.!!$R1 2480
7 TraesCS4B01G239800 chr3A 748666613 748669081 2468 True 4006 4006 95.8970 469 2949 1 chr3A.!!$R3 2480
8 TraesCS4B01G239800 chr3A 748745092 748747560 2468 True 4000 4000 95.8580 469 2949 1 chr3A.!!$R4 2480
9 TraesCS4B01G239800 chr3A 748553097 748555565 2468 True 3973 3973 95.6560 469 2949 1 chr3A.!!$R2 2480
10 TraesCS4B01G239800 chr3B 679636989 679638486 1497 False 1214 2222 96.7815 67 2891 2 chr3B.!!$F1 2824

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
51 52 0.036294 GGTACTTTGCTTCGAGGGCT 60.036 55.000 12.40 0.0 0.00 5.19 F
619 622 0.995675 ACCCCTCCCCATCTCCATTG 60.996 60.000 0.00 0.0 0.00 2.82 F
1484 1493 1.140052 ACATCACAAGTGACGGTTCCA 59.860 47.619 4.84 0.0 43.11 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1243 0.105709 TCTATGTCCCATCCCGCTCA 60.106 55.000 0.00 0.0 0.0 4.26 R
1899 1908 1.028905 CTTGAGCCAACCCAAACGAA 58.971 50.000 0.00 0.0 0.0 3.85 R
2668 2686 1.729881 GAATCCTTGGATGCACGGC 59.270 57.895 4.71 0.0 0.0 5.68 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
24 25 7.573968 GGCTTTATAGAAAATGTGAGTCCAT 57.426 36.000 0.00 0.00 0.00 3.41
25 26 7.420800 GGCTTTATAGAAAATGTGAGTCCATG 58.579 38.462 0.00 0.00 0.00 3.66
26 27 7.420800 GCTTTATAGAAAATGTGAGTCCATGG 58.579 38.462 4.97 4.97 0.00 3.66
27 28 7.283127 GCTTTATAGAAAATGTGAGTCCATGGA 59.717 37.037 11.44 11.44 0.00 3.41
28 29 9.347240 CTTTATAGAAAATGTGAGTCCATGGAT 57.653 33.333 19.62 7.07 0.00 3.41
31 32 6.319048 AGAAAATGTGAGTCCATGGATAGT 57.681 37.500 19.62 5.76 0.00 2.12
32 33 6.118170 AGAAAATGTGAGTCCATGGATAGTG 58.882 40.000 19.62 0.00 0.00 2.74
33 34 4.428294 AATGTGAGTCCATGGATAGTGG 57.572 45.455 19.62 0.00 38.11 4.00
34 35 2.832838 TGTGAGTCCATGGATAGTGGT 58.167 47.619 19.62 0.00 37.96 4.16
35 36 3.989056 TGTGAGTCCATGGATAGTGGTA 58.011 45.455 19.62 0.00 37.96 3.25
36 37 3.704566 TGTGAGTCCATGGATAGTGGTAC 59.295 47.826 19.62 10.79 37.96 3.34
37 38 3.961408 GTGAGTCCATGGATAGTGGTACT 59.039 47.826 19.62 8.03 37.96 2.73
38 39 4.406003 GTGAGTCCATGGATAGTGGTACTT 59.594 45.833 19.62 0.00 37.96 2.24
39 40 5.030147 TGAGTCCATGGATAGTGGTACTTT 58.970 41.667 19.62 0.00 37.96 2.66
40 41 5.104941 TGAGTCCATGGATAGTGGTACTTTG 60.105 44.000 19.62 0.00 37.96 2.77
41 42 3.877508 GTCCATGGATAGTGGTACTTTGC 59.122 47.826 19.62 0.00 37.96 3.68
42 43 3.780294 TCCATGGATAGTGGTACTTTGCT 59.220 43.478 11.44 0.00 37.96 3.91
43 44 4.227300 TCCATGGATAGTGGTACTTTGCTT 59.773 41.667 11.44 0.00 37.96 3.91
44 45 4.576463 CCATGGATAGTGGTACTTTGCTTC 59.424 45.833 5.56 0.00 31.96 3.86
45 46 3.857052 TGGATAGTGGTACTTTGCTTCG 58.143 45.455 0.00 0.00 0.00 3.79
46 47 3.512329 TGGATAGTGGTACTTTGCTTCGA 59.488 43.478 0.00 0.00 0.00 3.71
47 48 4.113354 GGATAGTGGTACTTTGCTTCGAG 58.887 47.826 0.00 0.00 0.00 4.04
48 49 2.457366 AGTGGTACTTTGCTTCGAGG 57.543 50.000 0.00 0.00 0.00 4.63
49 50 1.002087 AGTGGTACTTTGCTTCGAGGG 59.998 52.381 0.00 0.00 0.00 4.30
50 51 0.321298 TGGTACTTTGCTTCGAGGGC 60.321 55.000 0.00 0.86 0.00 5.19
51 52 0.036294 GGTACTTTGCTTCGAGGGCT 60.036 55.000 12.40 0.00 0.00 5.19
52 53 1.206371 GGTACTTTGCTTCGAGGGCTA 59.794 52.381 12.40 3.82 0.00 3.93
53 54 2.354403 GGTACTTTGCTTCGAGGGCTAA 60.354 50.000 12.40 10.28 0.00 3.09
54 55 2.789409 ACTTTGCTTCGAGGGCTAAT 57.211 45.000 12.40 1.95 0.00 1.73
55 56 3.906720 ACTTTGCTTCGAGGGCTAATA 57.093 42.857 12.40 0.00 0.00 0.98
56 57 4.216411 ACTTTGCTTCGAGGGCTAATAA 57.784 40.909 12.40 0.00 0.00 1.40
57 58 4.585879 ACTTTGCTTCGAGGGCTAATAAA 58.414 39.130 12.40 5.28 0.00 1.40
58 59 4.395231 ACTTTGCTTCGAGGGCTAATAAAC 59.605 41.667 12.40 0.00 0.00 2.01
59 60 3.906720 TGCTTCGAGGGCTAATAAACT 57.093 42.857 12.40 0.00 0.00 2.66
60 61 4.216411 TGCTTCGAGGGCTAATAAACTT 57.784 40.909 12.40 0.00 0.00 2.66
61 62 4.585879 TGCTTCGAGGGCTAATAAACTTT 58.414 39.130 12.40 0.00 0.00 2.66
62 63 5.007682 TGCTTCGAGGGCTAATAAACTTTT 58.992 37.500 12.40 0.00 0.00 2.27
63 64 5.106317 TGCTTCGAGGGCTAATAAACTTTTG 60.106 40.000 12.40 0.00 0.00 2.44
64 65 4.957759 TCGAGGGCTAATAAACTTTTGC 57.042 40.909 0.00 0.00 0.00 3.68
65 66 4.328536 TCGAGGGCTAATAAACTTTTGCA 58.671 39.130 0.00 0.00 0.00 4.08
66 67 4.762765 TCGAGGGCTAATAAACTTTTGCAA 59.237 37.500 0.00 0.00 0.00 4.08
74 75 6.816140 GCTAATAAACTTTTGCAATAAGGGCA 59.184 34.615 18.96 0.00 40.00 5.36
90 91 2.816958 CATGTTCGGCAGCTCGCT 60.817 61.111 7.85 0.00 41.91 4.93
153 154 1.553690 GGTGTGGCTCCAGGAAGCTA 61.554 60.000 9.85 2.69 42.13 3.32
254 257 4.393990 GGAGTTCGGGGTATTTACACAAAG 59.606 45.833 0.00 0.00 0.00 2.77
489 492 2.202676 CGCGAGTCCTTCCTCTGC 60.203 66.667 0.00 0.00 0.00 4.26
492 495 1.893919 GCGAGTCCTTCCTCTGCCTT 61.894 60.000 0.00 0.00 0.00 4.35
619 622 0.995675 ACCCCTCCCCATCTCCATTG 60.996 60.000 0.00 0.00 0.00 2.82
629 632 3.881688 CCCATCTCCATTGAGTTCATGTC 59.118 47.826 0.00 0.00 39.75 3.06
688 691 1.551883 GCAGATGAGGCCATTTGGTTT 59.448 47.619 5.01 0.00 35.94 3.27
692 696 4.706476 CAGATGAGGCCATTTGGTTTAGAA 59.294 41.667 5.01 0.00 37.57 2.10
698 702 6.951198 TGAGGCCATTTGGTTTAGAATTTAGA 59.049 34.615 5.01 0.00 37.57 2.10
765 769 8.528643 CCCTGTACCGATTTCTATATGACATAA 58.471 37.037 0.00 0.00 0.00 1.90
1234 1243 7.993183 TCAAGAAACTTAAGTTGAAGGAGACAT 59.007 33.333 21.22 1.65 38.44 3.06
1427 1436 2.787994 ACAAGTTCAGGAAGCATGGAG 58.212 47.619 0.00 0.00 0.00 3.86
1448 1457 4.732285 GTTCGCAATGAAGAGAACTTGA 57.268 40.909 0.00 0.00 42.59 3.02
1484 1493 1.140052 ACATCACAAGTGACGGTTCCA 59.860 47.619 4.84 0.00 43.11 3.53
1672 1681 4.086457 ACACAAACAAGAAACCCAAGACT 58.914 39.130 0.00 0.00 0.00 3.24
1733 1742 6.375455 GGACATTTGTAAGGAATCACACTCAT 59.625 38.462 0.00 0.00 0.00 2.90
1756 1765 6.801539 TCATTTCAGTCGTTCTTTAAGCAT 57.198 33.333 0.00 0.00 0.00 3.79
1794 1803 6.712095 TCTGTTGCATCTGTTATGAAAGAAGT 59.288 34.615 0.00 0.00 0.00 3.01
1899 1908 7.275888 TGTTTCTAAGCATGAGTGTTGAAAT 57.724 32.000 0.00 0.00 0.00 2.17
1952 1961 4.510038 GTCAAGTACGGGAACTAGTTGA 57.490 45.455 14.14 0.00 34.21 3.18
2046 2055 8.448615 GTGTGAGGTTGAACAATATTAAGTACC 58.551 37.037 0.00 0.00 0.00 3.34
2047 2056 8.158132 TGTGAGGTTGAACAATATTAAGTACCA 58.842 33.333 0.00 0.00 0.00 3.25
2048 2057 8.448615 GTGAGGTTGAACAATATTAAGTACCAC 58.551 37.037 0.00 0.00 0.00 4.16
2529 2542 1.217916 TGTTCTTGTGGACCTTGGGA 58.782 50.000 0.00 0.00 0.00 4.37
2666 2684 6.260663 TCAAGCCTAAGGACCCAAATTTTAT 58.739 36.000 0.00 0.00 0.00 1.40
2668 2686 4.962362 AGCCTAAGGACCCAAATTTTATGG 59.038 41.667 0.00 0.00 37.71 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.420800 CATGGACTCACATTTTCTATAAAGCC 58.579 38.462 0.00 0.00 0.00 4.35
1 2 7.283127 TCCATGGACTCACATTTTCTATAAAGC 59.717 37.037 11.44 0.00 0.00 3.51
2 3 8.737168 TCCATGGACTCACATTTTCTATAAAG 57.263 34.615 11.44 0.00 0.00 1.85
5 6 9.159254 ACTATCCATGGACTCACATTTTCTATA 57.841 33.333 18.99 0.00 0.00 1.31
6 7 7.935755 CACTATCCATGGACTCACATTTTCTAT 59.064 37.037 18.99 0.00 0.00 1.98
7 8 7.275183 CACTATCCATGGACTCACATTTTCTA 58.725 38.462 18.99 0.00 0.00 2.10
8 9 6.118170 CACTATCCATGGACTCACATTTTCT 58.882 40.000 18.99 0.00 0.00 2.52
9 10 5.297776 CCACTATCCATGGACTCACATTTTC 59.702 44.000 18.99 0.00 39.87 2.29
10 11 5.195940 CCACTATCCATGGACTCACATTTT 58.804 41.667 18.99 0.00 39.87 1.82
11 12 4.228210 ACCACTATCCATGGACTCACATTT 59.772 41.667 18.99 0.21 39.87 2.32
12 13 3.782523 ACCACTATCCATGGACTCACATT 59.217 43.478 18.99 1.07 39.87 2.71
13 14 3.387962 ACCACTATCCATGGACTCACAT 58.612 45.455 18.99 1.93 39.87 3.21
14 15 2.832838 ACCACTATCCATGGACTCACA 58.167 47.619 18.99 0.00 39.87 3.58
15 16 3.961408 AGTACCACTATCCATGGACTCAC 59.039 47.826 18.99 8.32 39.87 3.51
16 17 4.265856 AGTACCACTATCCATGGACTCA 57.734 45.455 18.99 4.35 39.87 3.41
17 18 5.360591 CAAAGTACCACTATCCATGGACTC 58.639 45.833 18.99 1.70 39.87 3.36
18 19 4.384208 GCAAAGTACCACTATCCATGGACT 60.384 45.833 18.99 9.21 39.87 3.85
19 20 3.877508 GCAAAGTACCACTATCCATGGAC 59.122 47.826 18.99 1.67 39.87 4.02
20 21 3.780294 AGCAAAGTACCACTATCCATGGA 59.220 43.478 18.88 18.88 39.87 3.41
21 22 4.156455 AGCAAAGTACCACTATCCATGG 57.844 45.455 4.97 4.97 43.43 3.66
22 23 4.271049 CGAAGCAAAGTACCACTATCCATG 59.729 45.833 0.00 0.00 0.00 3.66
23 24 4.161565 TCGAAGCAAAGTACCACTATCCAT 59.838 41.667 0.00 0.00 0.00 3.41
24 25 3.512329 TCGAAGCAAAGTACCACTATCCA 59.488 43.478 0.00 0.00 0.00 3.41
25 26 4.113354 CTCGAAGCAAAGTACCACTATCC 58.887 47.826 0.00 0.00 0.00 2.59
26 27 4.113354 CCTCGAAGCAAAGTACCACTATC 58.887 47.826 0.00 0.00 0.00 2.08
27 28 3.118738 CCCTCGAAGCAAAGTACCACTAT 60.119 47.826 0.00 0.00 0.00 2.12
28 29 2.232941 CCCTCGAAGCAAAGTACCACTA 59.767 50.000 0.00 0.00 0.00 2.74
29 30 1.002087 CCCTCGAAGCAAAGTACCACT 59.998 52.381 0.00 0.00 0.00 4.00
30 31 1.439679 CCCTCGAAGCAAAGTACCAC 58.560 55.000 0.00 0.00 0.00 4.16
31 32 0.321298 GCCCTCGAAGCAAAGTACCA 60.321 55.000 2.34 0.00 0.00 3.25
32 33 0.036294 AGCCCTCGAAGCAAAGTACC 60.036 55.000 9.54 0.00 0.00 3.34
33 34 2.667473 TAGCCCTCGAAGCAAAGTAC 57.333 50.000 9.54 0.00 0.00 2.73
34 35 3.906720 ATTAGCCCTCGAAGCAAAGTA 57.093 42.857 9.54 0.00 0.00 2.24
35 36 2.789409 ATTAGCCCTCGAAGCAAAGT 57.211 45.000 9.54 0.00 0.00 2.66
36 37 4.636206 AGTTTATTAGCCCTCGAAGCAAAG 59.364 41.667 9.54 0.00 0.00 2.77
37 38 4.585879 AGTTTATTAGCCCTCGAAGCAAA 58.414 39.130 9.54 0.00 0.00 3.68
38 39 4.216411 AGTTTATTAGCCCTCGAAGCAA 57.784 40.909 9.54 3.05 0.00 3.91
39 40 3.906720 AGTTTATTAGCCCTCGAAGCA 57.093 42.857 9.54 0.00 0.00 3.91
40 41 5.332707 CAAAAGTTTATTAGCCCTCGAAGC 58.667 41.667 0.00 0.00 0.00 3.86
41 42 5.106317 TGCAAAAGTTTATTAGCCCTCGAAG 60.106 40.000 0.00 0.00 0.00 3.79
42 43 4.762765 TGCAAAAGTTTATTAGCCCTCGAA 59.237 37.500 0.00 0.00 0.00 3.71
43 44 4.328536 TGCAAAAGTTTATTAGCCCTCGA 58.671 39.130 0.00 0.00 0.00 4.04
44 45 4.695217 TGCAAAAGTTTATTAGCCCTCG 57.305 40.909 0.00 0.00 0.00 4.63
45 46 7.706607 CCTTATTGCAAAAGTTTATTAGCCCTC 59.293 37.037 1.71 0.00 0.00 4.30
46 47 7.364673 CCCTTATTGCAAAAGTTTATTAGCCCT 60.365 37.037 1.71 0.00 0.00 5.19
47 48 6.761242 CCCTTATTGCAAAAGTTTATTAGCCC 59.239 38.462 1.71 0.00 0.00 5.19
48 49 6.257849 GCCCTTATTGCAAAAGTTTATTAGCC 59.742 38.462 1.71 0.00 0.00 3.93
49 50 6.816140 TGCCCTTATTGCAAAAGTTTATTAGC 59.184 34.615 1.71 0.00 35.40 3.09
50 51 8.819974 CATGCCCTTATTGCAAAAGTTTATTAG 58.180 33.333 1.71 0.00 42.92 1.73
51 52 8.317679 ACATGCCCTTATTGCAAAAGTTTATTA 58.682 29.630 1.71 0.00 42.92 0.98
52 53 7.167535 ACATGCCCTTATTGCAAAAGTTTATT 58.832 30.769 1.71 0.00 42.92 1.40
53 54 6.710278 ACATGCCCTTATTGCAAAAGTTTAT 58.290 32.000 1.71 0.75 42.92 1.40
54 55 6.107901 ACATGCCCTTATTGCAAAAGTTTA 57.892 33.333 1.71 0.00 42.92 2.01
55 56 4.971939 ACATGCCCTTATTGCAAAAGTTT 58.028 34.783 1.71 0.00 42.92 2.66
56 57 4.622260 ACATGCCCTTATTGCAAAAGTT 57.378 36.364 1.71 0.00 42.92 2.66
57 58 4.568956 GAACATGCCCTTATTGCAAAAGT 58.431 39.130 1.71 0.00 42.92 2.66
58 59 3.613737 CGAACATGCCCTTATTGCAAAAG 59.386 43.478 1.71 8.65 42.92 2.27
59 60 3.583806 CGAACATGCCCTTATTGCAAAA 58.416 40.909 1.71 0.00 42.92 2.44
60 61 2.094286 CCGAACATGCCCTTATTGCAAA 60.094 45.455 1.71 0.00 42.92 3.68
61 62 1.476085 CCGAACATGCCCTTATTGCAA 59.524 47.619 0.00 0.00 42.92 4.08
62 63 1.102154 CCGAACATGCCCTTATTGCA 58.898 50.000 0.00 0.00 43.97 4.08
63 64 0.249031 GCCGAACATGCCCTTATTGC 60.249 55.000 0.00 0.00 0.00 3.56
64 65 1.066002 CTGCCGAACATGCCCTTATTG 59.934 52.381 0.00 0.00 0.00 1.90
65 66 1.392589 CTGCCGAACATGCCCTTATT 58.607 50.000 0.00 0.00 0.00 1.40
66 67 1.103398 GCTGCCGAACATGCCCTTAT 61.103 55.000 0.00 0.00 0.00 1.73
90 91 1.485124 TTCGCTGAATCTGGGAGCTA 58.515 50.000 6.94 0.00 0.00 3.32
153 154 0.397816 ACGGGCAGATCCTAGAAGCT 60.398 55.000 0.00 0.00 34.39 3.74
198 201 1.377725 CTGGGATCGGCAAAGCTGT 60.378 57.895 0.00 0.00 36.18 4.40
254 257 4.389576 CAACTTCGCGGTGGCAGC 62.390 66.667 6.13 6.62 39.92 5.25
436 439 2.688794 GCTCGACGAGGAGACCGTT 61.689 63.158 25.31 0.00 40.67 4.44
467 470 2.156051 GAGGAAGGACTCGCGGTGTT 62.156 60.000 6.13 0.00 0.00 3.32
489 492 4.722700 CAGGTCGGGGTGGCAAGG 62.723 72.222 0.00 0.00 0.00 3.61
520 523 2.047560 GCCGACAACCTTAGGCGT 60.048 61.111 0.00 0.00 40.17 5.68
619 622 3.069289 TGACTGCATGTGACATGAACTC 58.931 45.455 28.21 16.37 0.00 3.01
629 632 2.094906 CCAAATGGTCTGACTGCATGTG 60.095 50.000 7.85 8.64 0.00 3.21
688 691 7.141758 ACTCATCTGGCCATTCTAAATTCTA 57.858 36.000 5.51 0.00 0.00 2.10
692 696 4.446889 GGGACTCATCTGGCCATTCTAAAT 60.447 45.833 5.51 0.00 0.00 1.40
698 702 1.302907 AAGGGACTCATCTGGCCATT 58.697 50.000 5.51 0.00 38.49 3.16
1234 1243 0.105709 TCTATGTCCCATCCCGCTCA 60.106 55.000 0.00 0.00 0.00 4.26
1427 1436 4.706527 CTCAAGTTCTCTTCATTGCGAAC 58.293 43.478 0.00 0.00 36.81 3.95
1448 1457 4.763279 TGTGATGTCTTCAAACATGATGCT 59.237 37.500 0.00 0.00 39.93 3.79
1484 1493 3.369892 CCAGAAGTCGGATTCCAGTGATT 60.370 47.826 3.09 0.00 0.00 2.57
1612 1621 5.841783 TCCAAGCCTTTTATTAACCTTTGGT 59.158 36.000 0.00 0.00 37.65 3.67
1733 1742 6.426633 TCATGCTTAAAGAACGACTGAAATGA 59.573 34.615 0.00 0.00 0.00 2.57
1756 1765 1.543208 GCAACAGAGGTGGTGTCATCA 60.543 52.381 0.00 0.00 44.05 3.07
1794 1803 7.172342 ACCTTCTATTGCACCACAAGTAATTA 58.828 34.615 0.00 0.00 42.87 1.40
1899 1908 1.028905 CTTGAGCCAACCCAAACGAA 58.971 50.000 0.00 0.00 0.00 3.85
2009 2018 3.383505 TCAACCTCACACATAGGATACGG 59.616 47.826 0.00 0.00 46.39 4.02
2046 2055 4.420168 AGGAAACAATTGTTCAACACGTG 58.580 39.130 23.47 15.48 37.25 4.49
2047 2056 4.712122 AGGAAACAATTGTTCAACACGT 57.288 36.364 23.47 6.71 37.25 4.49
2048 2057 7.537306 CCTTATAGGAAACAATTGTTCAACACG 59.463 37.037 23.47 8.81 37.67 4.49
2529 2542 5.649831 GGTTCTTCTATTTGATTCACAGCCT 59.350 40.000 0.00 0.00 0.00 4.58
2666 2684 2.497792 AATCCTTGGATGCACGGCCA 62.498 55.000 2.24 0.00 0.00 5.36
2668 2686 1.729881 GAATCCTTGGATGCACGGC 59.270 57.895 4.71 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.