Multiple sequence alignment - TraesCS5B01G173400

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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 TraesCS5B01G173400 chr5B 100.000 2581 0 0 1 2581 318399454 318402034 0.000000e+00 4767.0
1 TraesCS5B01G173400 chr5D 93.857 2507 85 32 121 2578 280782235 280784721 0.000000e+00 3712.0
2 TraesCS5B01G173400 chr5A 96.673 992 17 2 1604 2579 371031146 371030155 0.000000e+00 1635.0
3 TraesCS5B01G173400 chr5A 88.363 1332 108 25 121 1416 371032945 371031625 0.000000e+00 1557.0
4 TraesCS5B01G173400 chr5A 95.455 44 2 0 64 107 558241811 558241854 1.280000e-08 71.3
5 TraesCS5B01G173400 chr3A 96.875 32 1 0 495 526 572528633 572528664 1.000000e-03 54.7
6 TraesCS5B01G173400 chr6D 94.118 34 2 0 64 97 96999589 96999622 5.000000e-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 TraesCS5B01G173400 chr5B 318399454 318402034 2580 False 4767 4767 100.000 1 2581 1 chr5B.!!$F1 2580
1 TraesCS5B01G173400 chr5D 280782235 280784721 2486 False 3712 3712 93.857 121 2578 1 chr5D.!!$F1 2457
2 TraesCS5B01G173400 chr5A 371030155 371032945 2790 True 1596 1635 92.518 121 2579 2 chr5A.!!$R1 2458

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
423 426 0.985549 CGTGTGCTAAGAGAGAACGC 59.014 55.000 0.0 0.0 40.47 4.84 F
457 460 1.406069 CCGAGGGTGTCAGATCCTTTG 60.406 57.143 0.0 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1305 0.037326 TAGCTCTGTTTGGGCACTCG 60.037 55.0 0.00 0.0 0.00 4.18 R
2050 2398 0.886563 GCTGCAGGCTCAGTCAAAAT 59.113 50.0 17.12 0.0 36.49 1.82 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
19 20 2.915738 GGATAGCGTCACCTATACGG 57.084 55.000 0.00 0.00 40.64 4.02
20 21 1.135460 GGATAGCGTCACCTATACGGC 60.135 57.143 0.00 0.00 40.64 5.68
21 22 1.811359 GATAGCGTCACCTATACGGCT 59.189 52.381 0.00 0.00 40.64 5.52
22 23 2.549064 TAGCGTCACCTATACGGCTA 57.451 50.000 0.00 0.00 40.64 3.93
23 24 1.906990 AGCGTCACCTATACGGCTAT 58.093 50.000 0.00 0.00 40.64 2.97
24 25 3.063510 AGCGTCACCTATACGGCTATA 57.936 47.619 0.00 0.00 40.64 1.31
25 26 2.746362 AGCGTCACCTATACGGCTATAC 59.254 50.000 0.00 0.00 40.64 1.47
26 27 2.485426 GCGTCACCTATACGGCTATACA 59.515 50.000 0.00 0.00 40.64 2.29
27 28 3.128242 GCGTCACCTATACGGCTATACAT 59.872 47.826 0.00 0.00 40.64 2.29
28 29 4.333649 GCGTCACCTATACGGCTATACATA 59.666 45.833 0.00 0.00 40.64 2.29
29 30 5.008415 GCGTCACCTATACGGCTATACATAT 59.992 44.000 0.00 0.00 40.64 1.78
30 31 6.203530 GCGTCACCTATACGGCTATACATATA 59.796 42.308 0.00 0.00 40.64 0.86
31 32 7.254898 GCGTCACCTATACGGCTATACATATAA 60.255 40.741 0.00 0.00 40.64 0.98
32 33 8.781196 CGTCACCTATACGGCTATACATATAAT 58.219 37.037 0.00 0.00 36.71 1.28
54 55 6.832520 ATAATTGCATTAGGTGTGTTGACA 57.167 33.333 0.00 0.00 0.00 3.58
55 56 5.528043 AATTGCATTAGGTGTGTTGACAA 57.472 34.783 0.00 0.00 32.49 3.18
56 57 4.566545 TTGCATTAGGTGTGTTGACAAG 57.433 40.909 0.00 0.00 32.49 3.16
57 58 3.814625 TGCATTAGGTGTGTTGACAAGA 58.185 40.909 0.00 0.00 32.49 3.02
58 59 4.203226 TGCATTAGGTGTGTTGACAAGAA 58.797 39.130 0.00 0.00 32.49 2.52
59 60 4.642437 TGCATTAGGTGTGTTGACAAGAAA 59.358 37.500 0.00 0.00 32.49 2.52
60 61 5.215160 GCATTAGGTGTGTTGACAAGAAAG 58.785 41.667 0.00 0.00 32.49 2.62
61 62 5.221048 GCATTAGGTGTGTTGACAAGAAAGT 60.221 40.000 0.00 0.00 32.49 2.66
62 63 6.017440 GCATTAGGTGTGTTGACAAGAAAGTA 60.017 38.462 0.00 0.00 32.49 2.24
63 64 7.308589 GCATTAGGTGTGTTGACAAGAAAGTAT 60.309 37.037 0.00 0.00 32.49 2.12
64 65 7.490962 TTAGGTGTGTTGACAAGAAAGTATG 57.509 36.000 0.00 0.00 32.49 2.39
65 66 5.437060 AGGTGTGTTGACAAGAAAGTATGT 58.563 37.500 0.00 0.00 32.49 2.29
66 67 6.588204 AGGTGTGTTGACAAGAAAGTATGTA 58.412 36.000 0.00 0.00 32.49 2.29
67 68 7.224297 AGGTGTGTTGACAAGAAAGTATGTAT 58.776 34.615 0.00 0.00 32.49 2.29
68 69 7.387948 AGGTGTGTTGACAAGAAAGTATGTATC 59.612 37.037 0.00 0.00 32.49 2.24
69 70 7.387948 GGTGTGTTGACAAGAAAGTATGTATCT 59.612 37.037 0.00 0.00 32.49 1.98
70 71 8.774586 GTGTGTTGACAAGAAAGTATGTATCTT 58.225 33.333 0.00 0.00 32.49 2.40
90 91 4.935702 CTTGATTGCAAGGTTGTTTGAGA 58.064 39.130 4.94 0.00 46.13 3.27
91 92 4.572985 TGATTGCAAGGTTGTTTGAGAG 57.427 40.909 4.94 0.00 0.00 3.20
92 93 4.206375 TGATTGCAAGGTTGTTTGAGAGA 58.794 39.130 4.94 0.00 0.00 3.10
93 94 4.276678 TGATTGCAAGGTTGTTTGAGAGAG 59.723 41.667 4.94 0.00 0.00 3.20
94 95 3.558931 TGCAAGGTTGTTTGAGAGAGA 57.441 42.857 0.00 0.00 0.00 3.10
95 96 3.884895 TGCAAGGTTGTTTGAGAGAGAA 58.115 40.909 0.00 0.00 0.00 2.87
96 97 4.464008 TGCAAGGTTGTTTGAGAGAGAAT 58.536 39.130 0.00 0.00 0.00 2.40
97 98 5.620206 TGCAAGGTTGTTTGAGAGAGAATA 58.380 37.500 0.00 0.00 0.00 1.75
98 99 6.240894 TGCAAGGTTGTTTGAGAGAGAATAT 58.759 36.000 0.00 0.00 0.00 1.28
99 100 6.716628 TGCAAGGTTGTTTGAGAGAGAATATT 59.283 34.615 0.00 0.00 0.00 1.28
100 101 7.231317 TGCAAGGTTGTTTGAGAGAGAATATTT 59.769 33.333 0.00 0.00 0.00 1.40
101 102 8.084684 GCAAGGTTGTTTGAGAGAGAATATTTT 58.915 33.333 0.00 0.00 0.00 1.82
102 103 9.617975 CAAGGTTGTTTGAGAGAGAATATTTTC 57.382 33.333 0.00 0.00 0.00 2.29
103 104 8.924511 AGGTTGTTTGAGAGAGAATATTTTCA 57.075 30.769 8.56 0.00 34.08 2.69
104 105 9.354673 AGGTTGTTTGAGAGAGAATATTTTCAA 57.645 29.630 8.56 3.42 34.08 2.69
105 106 9.399403 GGTTGTTTGAGAGAGAATATTTTCAAC 57.601 33.333 8.56 4.53 34.08 3.18
106 107 9.399403 GTTGTTTGAGAGAGAATATTTTCAACC 57.601 33.333 8.56 0.00 34.08 3.77
107 108 7.806690 TGTTTGAGAGAGAATATTTTCAACCG 58.193 34.615 8.56 0.00 34.08 4.44
108 109 7.659799 TGTTTGAGAGAGAATATTTTCAACCGA 59.340 33.333 8.56 0.00 34.08 4.69
109 110 7.596749 TTGAGAGAGAATATTTTCAACCGAC 57.403 36.000 8.56 0.26 34.08 4.79
110 111 5.805486 TGAGAGAGAATATTTTCAACCGACG 59.195 40.000 8.56 0.00 34.08 5.12
111 112 5.109903 AGAGAGAATATTTTCAACCGACGG 58.890 41.667 13.61 13.61 34.08 4.79
112 113 5.080969 AGAGAATATTTTCAACCGACGGA 57.919 39.130 23.38 0.00 34.08 4.69
113 114 5.671493 AGAGAATATTTTCAACCGACGGAT 58.329 37.500 23.38 5.64 34.08 4.18
114 115 6.113411 AGAGAATATTTTCAACCGACGGATT 58.887 36.000 23.38 6.90 34.08 3.01
115 116 6.037172 AGAGAATATTTTCAACCGACGGATTG 59.963 38.462 23.38 19.81 34.08 2.67
116 117 4.893424 ATATTTTCAACCGACGGATTGG 57.107 40.909 23.38 6.70 35.11 3.16
117 118 1.970092 TTTTCAACCGACGGATTGGT 58.030 45.000 23.38 0.00 45.59 3.67
118 119 2.835580 TTTCAACCGACGGATTGGTA 57.164 45.000 23.38 10.05 42.43 3.25
119 120 2.083167 TTCAACCGACGGATTGGTAC 57.917 50.000 23.38 0.00 42.43 3.34
128 129 1.624813 ACGGATTGGTACGAGGGAAAA 59.375 47.619 0.00 0.00 35.06 2.29
152 153 9.466497 AAATGTTGATGTCCTACAATCTTATGT 57.534 29.630 0.00 0.00 34.42 2.29
158 159 6.048732 TGTCCTACAATCTTATGTGCTTGA 57.951 37.500 0.00 0.00 34.75 3.02
208 209 2.905075 TGTGTGATAGAAATCAGGCGG 58.095 47.619 0.00 0.00 42.80 6.13
328 331 1.768870 GGACATGTGCAGGTAGGGTAT 59.231 52.381 13.07 0.00 0.00 2.73
339 342 2.704065 AGGTAGGGTATGTACATGTGGC 59.296 50.000 18.81 1.72 0.00 5.01
417 420 1.893137 ACATGGACGTGTGCTAAGAGA 59.107 47.619 0.00 0.00 0.00 3.10
423 426 0.985549 CGTGTGCTAAGAGAGAACGC 59.014 55.000 0.00 0.00 40.47 4.84
437 440 3.207547 AACGCTTCTTTTGGGCCGC 62.208 57.895 0.00 0.00 0.00 6.53
457 460 1.406069 CCGAGGGTGTCAGATCCTTTG 60.406 57.143 0.00 0.00 0.00 2.77
466 469 2.041755 GTCAGATCCTTTGAAGGGGGTT 59.958 50.000 9.78 0.00 46.47 4.11
481 494 5.988865 AGGGGGTTTCTAGTTAAATAGGG 57.011 43.478 9.89 0.00 0.00 3.53
486 499 7.351952 GGGGTTTCTAGTTAAATAGGGTTGAT 58.648 38.462 9.89 0.00 0.00 2.57
607 640 6.512177 ACAATTTAGACGCTCGTATTGATC 57.488 37.500 17.30 0.00 0.00 2.92
846 883 3.556004 GCTGTCTACCTTTCAGTCAGCTT 60.556 47.826 12.30 0.00 45.64 3.74
912 950 3.808174 ACACTAACTCGTTCTTTTCTGCC 59.192 43.478 0.00 0.00 0.00 4.85
1023 1061 1.573829 GGAAACAACGCTCATCGCCA 61.574 55.000 0.00 0.00 43.23 5.69
1054 1092 4.394610 GGAAGAAAGTTCAGAGGAAGCATC 59.605 45.833 0.00 0.00 32.62 3.91
1175 1213 7.539022 CGAATACGATACAGATACTCAAATGCT 59.461 37.037 0.00 0.00 42.66 3.79
1211 1249 3.491447 GCAGATTGCACCTTCACTTTTGT 60.491 43.478 0.00 0.00 44.26 2.83
1267 1305 8.289618 TGTAACTTGATACATTTTCTGTGCTTC 58.710 33.333 0.00 0.00 38.92 3.86
1426 1544 7.093465 CCCACCTTCAGTACTTCATAGTCTTAA 60.093 40.741 0.00 0.00 35.78 1.85
1501 1619 9.242580 GTTCAGTCATATGAACGCATGTAACGT 62.243 40.741 7.07 0.00 46.81 3.99
1588 1710 6.428385 GACACAATCCAGGTGAAATAGAAG 57.572 41.667 0.00 0.00 39.53 2.85
1642 1974 3.824443 AGGCTTGTAACCTTTTTATGCGT 59.176 39.130 0.00 0.00 31.87 5.24
1813 2159 4.335315 ACATCGGTTAATACAATGCACCAG 59.665 41.667 0.00 0.00 0.00 4.00
1864 2210 0.543277 AGCAATGAGAAGGATCGCCA 59.457 50.000 0.00 0.00 36.29 5.69
2042 2390 0.819259 AGCCGCAACAGAGCTTCAAA 60.819 50.000 0.00 0.00 31.27 2.69
2050 2398 1.964223 ACAGAGCTTCAAACCTCTCGA 59.036 47.619 0.00 0.00 36.33 4.04
2140 2488 3.378512 TCAGCCATGAGAATGTAGTCCT 58.621 45.455 0.00 0.00 0.00 3.85
2283 2631 1.069049 GCCATATGGTGTGAAATGGGC 59.931 52.381 22.79 0.00 39.45 5.36
2523 2871 5.239087 GTGTAATCGGGAAAACTGGTAAACA 59.761 40.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135460 GCCGTATAGGTGACGCTATCC 60.135 57.143 0.00 0.00 43.70 2.59
1 2 1.811359 AGCCGTATAGGTGACGCTATC 59.189 52.381 0.00 0.00 43.70 2.08
2 3 1.906990 AGCCGTATAGGTGACGCTAT 58.093 50.000 0.00 0.00 43.70 2.97
3 4 2.549064 TAGCCGTATAGGTGACGCTA 57.451 50.000 0.00 0.00 43.70 4.26
4 5 1.906990 ATAGCCGTATAGGTGACGCT 58.093 50.000 0.00 0.00 43.70 5.07
5 6 2.485426 TGTATAGCCGTATAGGTGACGC 59.515 50.000 0.00 0.00 43.70 5.19
6 7 4.959596 ATGTATAGCCGTATAGGTGACG 57.040 45.455 0.00 0.00 43.70 4.35
28 29 8.965819 TGTCAACACACCTAATGCAATTATTAT 58.034 29.630 0.00 0.00 38.29 1.28
29 30 8.341892 TGTCAACACACCTAATGCAATTATTA 57.658 30.769 0.00 0.00 38.29 0.98
30 31 7.225784 TGTCAACACACCTAATGCAATTATT 57.774 32.000 0.00 0.00 38.29 1.40
31 32 6.832520 TGTCAACACACCTAATGCAATTAT 57.167 33.333 0.00 0.00 38.29 1.28
32 33 6.488344 TCTTGTCAACACACCTAATGCAATTA 59.512 34.615 0.00 0.00 32.32 1.40
33 34 5.301551 TCTTGTCAACACACCTAATGCAATT 59.698 36.000 0.00 0.00 34.08 2.32
34 35 4.826733 TCTTGTCAACACACCTAATGCAAT 59.173 37.500 0.00 0.00 29.76 3.56
35 36 4.203226 TCTTGTCAACACACCTAATGCAA 58.797 39.130 0.00 0.00 29.76 4.08
36 37 3.814625 TCTTGTCAACACACCTAATGCA 58.185 40.909 0.00 0.00 29.76 3.96
37 38 4.829064 TTCTTGTCAACACACCTAATGC 57.171 40.909 0.00 0.00 29.76 3.56
38 39 6.377327 ACTTTCTTGTCAACACACCTAATG 57.623 37.500 0.00 0.00 29.76 1.90
39 40 7.719633 ACATACTTTCTTGTCAACACACCTAAT 59.280 33.333 0.00 0.00 29.76 1.73
40 41 7.051623 ACATACTTTCTTGTCAACACACCTAA 58.948 34.615 0.00 0.00 29.76 2.69
41 42 6.588204 ACATACTTTCTTGTCAACACACCTA 58.412 36.000 0.00 0.00 29.76 3.08
42 43 5.437060 ACATACTTTCTTGTCAACACACCT 58.563 37.500 0.00 0.00 29.76 4.00
43 44 5.751243 ACATACTTTCTTGTCAACACACC 57.249 39.130 0.00 0.00 29.76 4.16
44 45 8.311650 AGATACATACTTTCTTGTCAACACAC 57.688 34.615 0.00 0.00 29.76 3.82
45 46 8.773645 CAAGATACATACTTTCTTGTCAACACA 58.226 33.333 4.20 0.00 40.80 3.72
46 47 8.988934 TCAAGATACATACTTTCTTGTCAACAC 58.011 33.333 10.63 0.00 44.23 3.32
47 48 9.725019 ATCAAGATACATACTTTCTTGTCAACA 57.275 29.630 10.63 0.00 44.23 3.33
50 51 8.668353 GCAATCAAGATACATACTTTCTTGTCA 58.332 33.333 10.63 0.00 44.23 3.58
51 52 8.668353 TGCAATCAAGATACATACTTTCTTGTC 58.332 33.333 10.63 2.44 44.23 3.18
52 53 8.565896 TGCAATCAAGATACATACTTTCTTGT 57.434 30.769 10.63 0.00 44.23 3.16
69 70 4.644234 TCTCTCAAACAACCTTGCAATCAA 59.356 37.500 0.00 0.00 0.00 2.57
70 71 4.206375 TCTCTCAAACAACCTTGCAATCA 58.794 39.130 0.00 0.00 0.00 2.57
71 72 4.516698 TCTCTCTCAAACAACCTTGCAATC 59.483 41.667 0.00 0.00 0.00 2.67
72 73 4.464008 TCTCTCTCAAACAACCTTGCAAT 58.536 39.130 0.00 0.00 0.00 3.56
73 74 3.884895 TCTCTCTCAAACAACCTTGCAA 58.115 40.909 0.00 0.00 0.00 4.08
74 75 3.558931 TCTCTCTCAAACAACCTTGCA 57.441 42.857 0.00 0.00 0.00 4.08
75 76 6.749923 ATATTCTCTCTCAAACAACCTTGC 57.250 37.500 0.00 0.00 0.00 4.01
76 77 9.617975 GAAAATATTCTCTCTCAAACAACCTTG 57.382 33.333 0.00 0.00 32.57 3.61
77 78 9.354673 TGAAAATATTCTCTCTCAAACAACCTT 57.645 29.630 0.00 0.00 36.48 3.50
78 79 8.924511 TGAAAATATTCTCTCTCAAACAACCT 57.075 30.769 0.00 0.00 36.48 3.50
79 80 9.399403 GTTGAAAATATTCTCTCTCAAACAACC 57.601 33.333 0.00 0.00 36.48 3.77
80 81 9.399403 GGTTGAAAATATTCTCTCTCAAACAAC 57.601 33.333 0.00 0.00 36.48 3.32
81 82 8.289618 CGGTTGAAAATATTCTCTCTCAAACAA 58.710 33.333 10.35 0.00 36.48 2.83
82 83 7.659799 TCGGTTGAAAATATTCTCTCTCAAACA 59.340 33.333 10.35 0.00 36.48 2.83
83 84 7.958025 GTCGGTTGAAAATATTCTCTCTCAAAC 59.042 37.037 0.00 0.00 36.48 2.93
84 85 7.148639 CGTCGGTTGAAAATATTCTCTCTCAAA 60.149 37.037 0.00 0.00 36.48 2.69
85 86 6.310467 CGTCGGTTGAAAATATTCTCTCTCAA 59.690 38.462 0.00 0.00 36.48 3.02
86 87 5.805486 CGTCGGTTGAAAATATTCTCTCTCA 59.195 40.000 0.00 0.00 36.48 3.27
87 88 5.232414 CCGTCGGTTGAAAATATTCTCTCTC 59.768 44.000 2.08 0.00 36.48 3.20
88 89 5.105473 TCCGTCGGTTGAAAATATTCTCTCT 60.105 40.000 11.88 0.00 36.48 3.10
89 90 5.107133 TCCGTCGGTTGAAAATATTCTCTC 58.893 41.667 11.88 0.00 36.48 3.20
90 91 5.080969 TCCGTCGGTTGAAAATATTCTCT 57.919 39.130 11.88 0.00 36.48 3.10
91 92 5.986004 ATCCGTCGGTTGAAAATATTCTC 57.014 39.130 11.88 0.00 36.48 2.87
92 93 5.065988 CCAATCCGTCGGTTGAAAATATTCT 59.934 40.000 21.00 0.00 36.48 2.40
93 94 5.163693 ACCAATCCGTCGGTTGAAAATATTC 60.164 40.000 21.00 0.00 36.04 1.75
94 95 4.703093 ACCAATCCGTCGGTTGAAAATATT 59.297 37.500 21.00 6.49 28.43 1.28
95 96 4.266714 ACCAATCCGTCGGTTGAAAATAT 58.733 39.130 21.00 1.02 28.43 1.28
96 97 3.677190 ACCAATCCGTCGGTTGAAAATA 58.323 40.909 21.00 0.00 28.43 1.40
97 98 2.510613 ACCAATCCGTCGGTTGAAAAT 58.489 42.857 21.00 2.31 28.43 1.82
98 99 1.970092 ACCAATCCGTCGGTTGAAAA 58.030 45.000 21.00 0.04 28.43 2.29
99 100 2.415776 GTACCAATCCGTCGGTTGAAA 58.584 47.619 21.00 10.41 36.69 2.69
100 101 1.669502 CGTACCAATCCGTCGGTTGAA 60.670 52.381 21.00 10.67 36.69 2.69
101 102 0.109179 CGTACCAATCCGTCGGTTGA 60.109 55.000 21.00 1.40 36.69 3.18
102 103 0.109179 TCGTACCAATCCGTCGGTTG 60.109 55.000 11.88 14.15 36.69 3.77
103 104 0.171903 CTCGTACCAATCCGTCGGTT 59.828 55.000 11.88 0.00 36.69 4.44
104 105 1.660560 CCTCGTACCAATCCGTCGGT 61.661 60.000 11.88 0.00 39.41 4.69
105 106 1.065273 CCTCGTACCAATCCGTCGG 59.935 63.158 4.39 4.39 0.00 4.79
106 107 1.065273 CCCTCGTACCAATCCGTCG 59.935 63.158 0.00 0.00 0.00 5.12
107 108 0.819582 TTCCCTCGTACCAATCCGTC 59.180 55.000 0.00 0.00 0.00 4.79
108 109 1.269012 TTTCCCTCGTACCAATCCGT 58.731 50.000 0.00 0.00 0.00 4.69
109 110 2.389962 TTTTCCCTCGTACCAATCCG 57.610 50.000 0.00 0.00 0.00 4.18
110 111 3.617284 ACATTTTCCCTCGTACCAATCC 58.383 45.455 0.00 0.00 0.00 3.01
111 112 4.698304 TCAACATTTTCCCTCGTACCAATC 59.302 41.667 0.00 0.00 0.00 2.67
112 113 4.658063 TCAACATTTTCCCTCGTACCAAT 58.342 39.130 0.00 0.00 0.00 3.16
113 114 4.088056 TCAACATTTTCCCTCGTACCAA 57.912 40.909 0.00 0.00 0.00 3.67
114 115 3.773418 TCAACATTTTCCCTCGTACCA 57.227 42.857 0.00 0.00 0.00 3.25
115 116 4.007659 ACATCAACATTTTCCCTCGTACC 58.992 43.478 0.00 0.00 0.00 3.34
116 117 4.094442 GGACATCAACATTTTCCCTCGTAC 59.906 45.833 0.00 0.00 0.00 3.67
117 118 4.019681 AGGACATCAACATTTTCCCTCGTA 60.020 41.667 0.00 0.00 0.00 3.43
118 119 3.081804 GGACATCAACATTTTCCCTCGT 58.918 45.455 0.00 0.00 0.00 4.18
119 120 3.347216 AGGACATCAACATTTTCCCTCG 58.653 45.455 0.00 0.00 0.00 4.63
128 129 7.012704 GCACATAAGATTGTAGGACATCAACAT 59.987 37.037 0.00 0.00 0.00 2.71
152 153 5.643379 AGACTTTGTTTGTCTTTCAAGCA 57.357 34.783 0.00 0.00 43.47 3.91
184 185 5.163622 CCGCCTGATTTCTATCACACATTTT 60.164 40.000 0.00 0.00 35.87 1.82
199 200 1.689273 GTGATCTAGACCCGCCTGATT 59.311 52.381 0.00 0.00 0.00 2.57
208 209 4.342378 TGGCTATCACTTGTGATCTAGACC 59.658 45.833 18.11 15.32 0.00 3.85
232 233 1.409064 CAGGCTAGCGGTCATTACTCA 59.591 52.381 9.00 0.00 0.00 3.41
320 322 2.750948 CGCCACATGTACATACCCTAC 58.249 52.381 8.32 0.00 0.00 3.18
347 350 4.082523 CCTCGATGGGCCACACGT 62.083 66.667 26.08 5.98 0.00 4.49
417 420 1.515521 CGGCCCAAAAGAAGCGTTCT 61.516 55.000 0.00 0.00 43.15 3.01
423 426 2.671619 TCGGCGGCCCAAAAGAAG 60.672 61.111 14.55 0.00 0.00 2.85
437 440 0.905357 AAAGGATCTGACACCCTCGG 59.095 55.000 0.00 0.00 0.00 4.63
457 460 6.069206 ACCCTATTTAACTAGAAACCCCCTTC 60.069 42.308 0.00 0.00 0.00 3.46
607 640 4.739046 AGTTGAATCTTGAAGCACGAAG 57.261 40.909 0.00 0.00 0.00 3.79
1023 1061 5.395103 CCTCTGAACTTTCTTCCTCATCGAT 60.395 44.000 0.00 0.00 0.00 3.59
1054 1092 2.064762 GATACGCAGCAGCTCCATAAG 58.935 52.381 0.00 0.00 39.10 1.73
1175 1213 4.053983 GCAATCTGCATCTCTATGAACGA 58.946 43.478 0.00 0.00 44.26 3.85
1211 1249 2.158623 ACTGCACAATCTTGTTCCTCCA 60.159 45.455 0.00 0.00 39.91 3.86
1267 1305 0.037326 TAGCTCTGTTTGGGCACTCG 60.037 55.000 0.00 0.00 0.00 4.18
1547 1669 5.795972 TGTGTCCGTGGATGTTTAAGATAA 58.204 37.500 0.00 0.00 0.00 1.75
1548 1670 5.408880 TGTGTCCGTGGATGTTTAAGATA 57.591 39.130 0.00 0.00 0.00 1.98
1549 1671 4.280436 TGTGTCCGTGGATGTTTAAGAT 57.720 40.909 0.00 0.00 0.00 2.40
1556 1678 3.551259 GGATTGTGTCCGTGGATGT 57.449 52.632 0.00 0.00 37.23 3.06
1594 1716 5.836347 AGCTGTTCTTCATGAAAAGGTTTC 58.164 37.500 9.88 0.00 45.50 2.78
1619 1951 4.165779 CGCATAAAAAGGTTACAAGCCTG 58.834 43.478 0.00 0.00 36.30 4.85
1620 1952 3.824443 ACGCATAAAAAGGTTACAAGCCT 59.176 39.130 0.00 0.00 38.11 4.58
1690 2036 6.151144 GGAATAGGTGTAGAACAATGTTGCTT 59.849 38.462 2.20 0.00 0.00 3.91
1813 2159 8.240883 ACGTTCTGTATAATCTTTTGACACTC 57.759 34.615 0.00 0.00 0.00 3.51
1864 2210 9.690913 TCTCATTGATTATTCATTTGGAGAAGT 57.309 29.630 0.00 0.00 0.00 3.01
2042 2390 2.354203 GGCTCAGTCAAAATCGAGAGGT 60.354 50.000 0.00 0.00 0.00 3.85
2050 2398 0.886563 GCTGCAGGCTCAGTCAAAAT 59.113 50.000 17.12 0.00 36.49 1.82
2283 2631 1.135024 CATCAATTGGCCAGGAAACCG 60.135 52.381 5.11 0.00 0.00 4.44
2523 2871 5.453198 CCAGTTCCACTGCAATAAAAAGGTT 60.453 40.000 0.00 0.00 44.63 3.50


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

AutoCloner maintained by Alex Coulton.