Multiple sequence alignment - TraesCS2D01G295600

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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 TraesCS2D01G295600 chr2D 100.000 5466 0 0 1 5466 377311405 377316870 0.000000e+00 10094.0
1 TraesCS2D01G295600 chr2A 95.644 5395 163 37 115 5466 511529101 511534466 0.000000e+00 8595.0
2 TraesCS2D01G295600 chr2B 96.863 4048 94 11 261 4297 448915625 448919650 0.000000e+00 6741.0
3 TraesCS2D01G295600 chr2B 86.667 1155 98 27 4345 5466 448920048 448921179 0.000000e+00 1229.0
4 TraesCS2D01G295600 chr2B 90.769 130 7 5 115 239 448915511 448915640 9.420000e-38 169.0
5 TraesCS2D01G295600 chr2B 87.719 57 7 0 21 77 540429479 540429423 3.530000e-07 67.6
6 TraesCS2D01G295600 chr2B 86.792 53 3 4 21 71 723521801 723521851 7.650000e-04 56.5
7 TraesCS2D01G295600 chr2B 86.792 53 3 4 21 71 723545409 723545459 7.650000e-04 56.5
8 TraesCS2D01G295600 chr4B 89.720 107 11 0 1615 1721 648061788 648061894 2.660000e-28 137.0
9 TraesCS2D01G295600 chr4B 88.073 109 13 0 1613 1721 647763006 647762898 4.440000e-26 130.0
10 TraesCS2D01G295600 chr4D 87.826 115 14 0 1607 1721 503140659 503140773 9.550000e-28 135.0
11 TraesCS2D01G295600 chr4D 82.653 98 16 1 4605 4702 479521315 479521219 9.760000e-13 86.1
12 TraesCS2D01G295600 chr5A 88.073 109 13 0 1613 1721 687366215 687366107 4.440000e-26 130.0
13 TraesCS2D01G295600 chr5A 95.556 45 2 0 76 120 104555934 104555978 7.590000e-09 73.1
14 TraesCS2D01G295600 chr5A 95.556 45 2 0 76 120 461883485 461883529 7.590000e-09 73.1
15 TraesCS2D01G295600 chr5A 84.615 65 10 0 1629 1693 390566116 390566052 1.270000e-06 65.8
16 TraesCS2D01G295600 chr5A 86.792 53 3 4 21 71 353650563 353650613 7.650000e-04 56.5
17 TraesCS2D01G295600 chr3D 86.139 101 14 0 1607 1707 530415867 530415967 5.790000e-20 110.0
18 TraesCS2D01G295600 chr3A 87.778 90 11 0 1618 1707 664137502 664137591 7.490000e-19 106.0
19 TraesCS2D01G295600 chr3A 95.556 45 2 0 76 120 343230470 343230426 7.590000e-09 73.1
20 TraesCS2D01G295600 chr3A 93.750 48 1 2 76 122 182639666 182639712 2.730000e-08 71.3
21 TraesCS2D01G295600 chr3A 93.617 47 1 2 76 122 23366670 23366626 9.820000e-08 69.4
22 TraesCS2D01G295600 chr3A 77.876 113 21 3 4605 4716 577631878 577631769 3.530000e-07 67.6
23 TraesCS2D01G295600 chr1A 100.000 42 0 0 76 117 516370706 516370747 1.630000e-10 78.7
24 TraesCS2D01G295600 chr1A 95.556 45 2 0 76 120 75096496 75096452 7.590000e-09 73.1
25 TraesCS2D01G295600 chr7A 93.617 47 3 0 76 122 670345167 670345213 2.730000e-08 71.3
26 TraesCS2D01G295600 chr1B 93.750 48 1 2 76 122 688707795 688707841 2.730000e-08 71.3
27 TraesCS2D01G295600 chr1B 86.792 53 3 4 21 71 514713153 514713203 7.650000e-04 56.5
28 TraesCS2D01G295600 chr7B 86.792 53 3 4 21 71 17917699 17917649 7.650000e-04 56.5
29 TraesCS2D01G295600 chr3B 86.792 53 3 4 21 71 200331767 200331817 7.650000e-04 56.5
30 TraesCS2D01G295600 chr1D 86.792 53 3 4 21 71 90518856 90518806 7.650000e-04 56.5
31 TraesCS2D01G295600 chr7D 88.889 45 2 3 29 71 141559741 141559784 1.000000e-02 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 TraesCS2D01G295600 chr2D 377311405 377316870 5465 False 10094 10094 100.000 1 5466 1 chr2D.!!$F1 5465
1 TraesCS2D01G295600 chr2A 511529101 511534466 5365 False 8595 8595 95.644 115 5466 1 chr2A.!!$F1 5351
2 TraesCS2D01G295600 chr2B 448915511 448921179 5668 False 2713 6741 91.433 115 5466 3 chr2B.!!$F3 5351

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
335 341 0.796312 ATTGTGACGCCAACGCTAAG 59.204 50.000 0.00 0.0 45.53 2.18 F
527 534 1.879575 ATCCTTCCAGATCGGGTGAA 58.120 50.000 11.92 0.0 34.36 3.18 F
1796 1825 1.327690 CCCTAACCCTAGCAGCACGA 61.328 60.000 0.00 0.0 0.00 4.35 F
2439 2468 0.744874 CCGTCCCGATCTAAAGCTGA 59.255 55.000 0.00 0.0 0.00 4.26 F
3348 3400 1.078656 GCCTCCTCCATCTCCTCCTAT 59.921 57.143 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1825 0.467844 TGATGCTTGCTTGTGGTGGT 60.468 50.000 0.00 0.0 0.00 4.16 R
2436 2465 0.810031 CGCCCTGGGAAACGTATCAG 60.810 60.000 19.27 0.0 0.00 2.90 R
3339 3391 0.324285 GGCCATGCTCATAGGAGGAG 59.676 60.000 6.52 0.0 45.19 3.69 R
4208 4260 0.461516 CGTGAGCAGGCAGACATCAT 60.462 55.000 0.00 0.0 0.00 2.45 R
5323 5757 1.620259 GGGGGCATGGATCAAAGGA 59.380 57.895 0.00 0.0 0.00 3.36 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
21 22 4.351131 CGTCCCTTTGCTAAATACAACC 57.649 45.455 0.00 0.00 0.00 3.77
22 23 4.007659 CGTCCCTTTGCTAAATACAACCT 58.992 43.478 0.00 0.00 0.00 3.50
23 24 4.094442 CGTCCCTTTGCTAAATACAACCTC 59.906 45.833 0.00 0.00 0.00 3.85
24 25 4.398358 GTCCCTTTGCTAAATACAACCTCC 59.602 45.833 0.00 0.00 0.00 4.30
25 26 4.043561 TCCCTTTGCTAAATACAACCTCCA 59.956 41.667 0.00 0.00 0.00 3.86
26 27 4.956075 CCCTTTGCTAAATACAACCTCCAT 59.044 41.667 0.00 0.00 0.00 3.41
27 28 5.067805 CCCTTTGCTAAATACAACCTCCATC 59.932 44.000 0.00 0.00 0.00 3.51
28 29 5.067805 CCTTTGCTAAATACAACCTCCATCC 59.932 44.000 0.00 0.00 0.00 3.51
29 30 4.164843 TGCTAAATACAACCTCCATCCC 57.835 45.455 0.00 0.00 0.00 3.85
30 31 3.139077 GCTAAATACAACCTCCATCCCG 58.861 50.000 0.00 0.00 0.00 5.14
31 32 3.181458 GCTAAATACAACCTCCATCCCGA 60.181 47.826 0.00 0.00 0.00 5.14
32 33 4.685030 GCTAAATACAACCTCCATCCCGAA 60.685 45.833 0.00 0.00 0.00 4.30
33 34 4.519906 AAATACAACCTCCATCCCGAAT 57.480 40.909 0.00 0.00 0.00 3.34
34 35 4.519906 AATACAACCTCCATCCCGAATT 57.480 40.909 0.00 0.00 0.00 2.17
35 36 5.640158 AATACAACCTCCATCCCGAATTA 57.360 39.130 0.00 0.00 0.00 1.40
36 37 5.843019 ATACAACCTCCATCCCGAATTAT 57.157 39.130 0.00 0.00 0.00 1.28
37 38 4.519906 ACAACCTCCATCCCGAATTATT 57.480 40.909 0.00 0.00 0.00 1.40
38 39 4.867086 ACAACCTCCATCCCGAATTATTT 58.133 39.130 0.00 0.00 0.00 1.40
39 40 5.269189 ACAACCTCCATCCCGAATTATTTT 58.731 37.500 0.00 0.00 0.00 1.82
40 41 5.719563 ACAACCTCCATCCCGAATTATTTTT 59.280 36.000 0.00 0.00 0.00 1.94
102 103 9.793259 AGACAAATCTAAGACAAGTAATTTGGA 57.207 29.630 9.60 0.00 38.04 3.53
105 106 9.329913 CAAATCTAAGACAAGTAATTTGGAACG 57.670 33.333 0.00 0.00 41.25 3.95
106 107 8.842358 AATCTAAGACAAGTAATTTGGAACGA 57.158 30.769 0.00 0.00 41.25 3.85
107 108 8.842358 ATCTAAGACAAGTAATTTGGAACGAA 57.158 30.769 0.00 0.00 41.25 3.85
108 109 8.306680 TCTAAGACAAGTAATTTGGAACGAAG 57.693 34.615 0.00 0.00 41.25 3.79
109 110 5.941948 AGACAAGTAATTTGGAACGAAGG 57.058 39.130 0.00 0.00 41.25 3.46
110 111 4.760204 AGACAAGTAATTTGGAACGAAGGG 59.240 41.667 0.00 0.00 41.25 3.95
111 112 4.721132 ACAAGTAATTTGGAACGAAGGGA 58.279 39.130 0.00 0.00 41.25 4.20
112 113 4.760204 ACAAGTAATTTGGAACGAAGGGAG 59.240 41.667 0.00 0.00 41.25 4.30
113 114 4.635699 AGTAATTTGGAACGAAGGGAGT 57.364 40.909 0.00 0.00 0.00 3.85
118 119 7.931948 AGTAATTTGGAACGAAGGGAGTATATG 59.068 37.037 0.00 0.00 0.00 1.78
183 186 5.638234 ACTCGCTAGTTGTACAAAAGATTCC 59.362 40.000 18.74 3.32 29.00 3.01
188 191 3.502211 AGTTGTACAAAAGATTCCTGGCG 59.498 43.478 10.51 0.00 0.00 5.69
201 204 1.000843 TCCTGGCGATGATGATTACCG 59.999 52.381 0.00 0.00 0.00 4.02
228 234 9.283768 TCACAACTCACAAACATATGTATTCTT 57.716 29.630 9.21 0.00 30.84 2.52
249 255 5.934625 TCTTAGCTTTCTCTTTCTCGCAAAT 59.065 36.000 0.00 0.00 0.00 2.32
251 257 7.602644 TCTTAGCTTTCTCTTTCTCGCAAATAA 59.397 33.333 0.00 0.00 0.00 1.40
253 259 7.150783 AGCTTTCTCTTTCTCGCAAATAAAT 57.849 32.000 0.00 0.00 0.00 1.40
335 341 0.796312 ATTGTGACGCCAACGCTAAG 59.204 50.000 0.00 0.00 45.53 2.18
340 347 2.414138 GTGACGCCAACGCTAAGTATTT 59.586 45.455 0.00 0.00 45.53 1.40
446 453 7.487829 TCACAAAGTTGATGTTTAAACTCTTGC 59.512 33.333 18.72 7.16 35.60 4.01
447 454 6.472163 ACAAAGTTGATGTTTAAACTCTTGCG 59.528 34.615 18.72 11.56 35.60 4.85
448 455 5.751243 AGTTGATGTTTAAACTCTTGCGT 57.249 34.783 18.72 0.00 30.87 5.24
449 456 6.854496 AGTTGATGTTTAAACTCTTGCGTA 57.146 33.333 18.72 0.00 30.87 4.42
527 534 1.879575 ATCCTTCCAGATCGGGTGAA 58.120 50.000 11.92 0.00 34.36 3.18
774 783 3.129871 GCACATGCATTCTCCTCTACTC 58.870 50.000 0.00 0.00 41.59 2.59
801 810 4.503910 AGCCAACAACACCTTTTTCTTTC 58.496 39.130 0.00 0.00 0.00 2.62
861 870 3.980698 TCCCCCAAAGAGAAAGAGAAAGA 59.019 43.478 0.00 0.00 0.00 2.52
1069 1090 5.480205 TCGTCTATATCTACACATCTCGCT 58.520 41.667 0.00 0.00 0.00 4.93
1070 1091 5.577554 TCGTCTATATCTACACATCTCGCTC 59.422 44.000 0.00 0.00 0.00 5.03
1071 1092 5.499493 CGTCTATATCTACACATCTCGCTCG 60.499 48.000 0.00 0.00 0.00 5.03
1072 1093 2.971430 TATCTACACATCTCGCTCGC 57.029 50.000 0.00 0.00 0.00 5.03
1276 1305 2.116125 GGGGTTGTGAAGCAGGCT 59.884 61.111 0.00 0.00 0.00 4.58
1444 1473 3.608662 AACGTCGCCCTCAACCGA 61.609 61.111 0.00 0.00 0.00 4.69
1796 1825 1.327690 CCCTAACCCTAGCAGCACGA 61.328 60.000 0.00 0.00 0.00 4.35
2072 2101 2.277072 CGAGGGAGGAGGCAGAGA 59.723 66.667 0.00 0.00 0.00 3.10
2110 2139 1.817099 GTGCCTCATCAAGAGCCGG 60.817 63.158 0.00 0.00 43.31 6.13
2436 2465 1.594564 GGCCGTCCCGATCTAAAGC 60.595 63.158 0.00 0.00 0.00 3.51
2439 2468 0.744874 CCGTCCCGATCTAAAGCTGA 59.255 55.000 0.00 0.00 0.00 4.26
2500 2531 2.304180 CACTTCAGGTGGAGGAATCAGT 59.696 50.000 0.00 0.00 41.90 3.41
2514 2546 2.065993 ATCAGTCCGAACAAGACGTG 57.934 50.000 0.00 0.00 39.31 4.49
2688 2720 2.069273 CGACCGATCAGTGAAAGCTTT 58.931 47.619 12.53 12.53 0.00 3.51
2755 2791 1.808945 CGCCTCTCAACAGCAATCTTT 59.191 47.619 0.00 0.00 0.00 2.52
3147 3191 7.219322 TCGAGTGTCCAATCATCATCATAAAT 58.781 34.615 0.00 0.00 0.00 1.40
3339 3391 2.123251 TCTCCGGCCTCCTCCATC 60.123 66.667 0.00 0.00 0.00 3.51
3348 3400 1.078656 GCCTCCTCCATCTCCTCCTAT 59.921 57.143 0.00 0.00 0.00 2.57
3375 3427 4.007644 CACCAGCCTCGCCAGTCA 62.008 66.667 0.00 0.00 0.00 3.41
3603 3655 3.701604 GATCGCGAGCACCGTCCTT 62.702 63.158 21.13 0.00 41.15 3.36
3783 3835 1.741401 CATCAAACTCGGCGCCTCA 60.741 57.895 26.68 10.09 0.00 3.86
3921 3973 2.274437 CACCGTGTCATTCTCATGGAG 58.726 52.381 10.55 0.06 42.63 3.86
3924 3976 2.103771 CCGTGTCATTCTCATGGAGGAT 59.896 50.000 0.00 0.00 42.63 3.24
4329 4381 1.165782 AGGGGGTTTCTGATGGGGA 59.834 57.895 0.00 0.00 0.00 4.81
4658 5061 5.650266 TGTTGCTGATATGTCGGGTTATTTT 59.350 36.000 0.00 0.00 0.00 1.82
4661 5064 8.349983 GTTGCTGATATGTCGGGTTATTTTAAT 58.650 33.333 0.00 0.00 0.00 1.40
4717 5120 5.477291 GTGTATCTTAGCTATGTAGAGGCCA 59.523 44.000 5.01 0.00 0.00 5.36
4888 5320 4.147587 ATCCACCCTGCCCATGCC 62.148 66.667 0.00 0.00 36.33 4.40
5012 5444 3.427909 CCATCACCAAAATCACGACATGG 60.428 47.826 0.00 0.00 37.19 3.66
5049 5481 0.319555 TAGCACATAAGATCCGGCGC 60.320 55.000 0.00 0.00 0.00 6.53
5090 5522 4.814234 GTGTGGTGTGAATTTAGAGTGTCA 59.186 41.667 0.00 0.00 0.00 3.58
5093 5525 4.065088 GGTGTGAATTTAGAGTGTCAGCA 58.935 43.478 0.00 0.00 0.00 4.41
5228 5662 4.544683 GTGGTGGACTATCTAGGGTTAGT 58.455 47.826 0.00 0.00 32.52 2.24
5323 5757 2.502947 TCAGCTATGATGTTGTCTGCCT 59.497 45.455 0.00 0.00 0.00 4.75
5411 5845 1.007271 CTGACCGACGACAGTTGCT 60.007 57.895 0.00 0.00 0.00 3.91
5434 5868 2.298163 TGTAACTCTGTCCGGTTCTTCC 59.702 50.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.007659 AGGTTGTATTTAGCAAAGGGACG 58.992 43.478 0.00 0.00 0.00 4.79
1 2 4.398358 GGAGGTTGTATTTAGCAAAGGGAC 59.602 45.833 0.00 0.00 0.00 4.46
2 3 4.043561 TGGAGGTTGTATTTAGCAAAGGGA 59.956 41.667 0.00 0.00 0.00 4.20
3 4 4.340617 TGGAGGTTGTATTTAGCAAAGGG 58.659 43.478 0.00 0.00 0.00 3.95
4 5 5.067805 GGATGGAGGTTGTATTTAGCAAAGG 59.932 44.000 0.00 0.00 0.00 3.11
5 6 5.067805 GGGATGGAGGTTGTATTTAGCAAAG 59.932 44.000 0.00 0.00 0.00 2.77
6 7 4.953579 GGGATGGAGGTTGTATTTAGCAAA 59.046 41.667 0.00 0.00 0.00 3.68
7 8 4.532834 GGGATGGAGGTTGTATTTAGCAA 58.467 43.478 0.00 0.00 0.00 3.91
8 9 3.433031 CGGGATGGAGGTTGTATTTAGCA 60.433 47.826 0.00 0.00 0.00 3.49
9 10 3.139077 CGGGATGGAGGTTGTATTTAGC 58.861 50.000 0.00 0.00 0.00 3.09
10 11 4.682778 TCGGGATGGAGGTTGTATTTAG 57.317 45.455 0.00 0.00 0.00 1.85
11 12 5.640158 ATTCGGGATGGAGGTTGTATTTA 57.360 39.130 0.00 0.00 0.00 1.40
12 13 4.519906 ATTCGGGATGGAGGTTGTATTT 57.480 40.909 0.00 0.00 0.00 1.40
13 14 4.519906 AATTCGGGATGGAGGTTGTATT 57.480 40.909 0.00 0.00 0.00 1.89
14 15 5.843019 ATAATTCGGGATGGAGGTTGTAT 57.157 39.130 0.00 0.00 0.00 2.29
15 16 5.640158 AATAATTCGGGATGGAGGTTGTA 57.360 39.130 0.00 0.00 0.00 2.41
16 17 4.519906 AATAATTCGGGATGGAGGTTGT 57.480 40.909 0.00 0.00 0.00 3.32
17 18 5.852282 AAAATAATTCGGGATGGAGGTTG 57.148 39.130 0.00 0.00 0.00 3.77
76 77 9.793259 TCCAAATTACTTGTCTTAGATTTGTCT 57.207 29.630 0.00 0.00 34.40 3.41
79 80 9.329913 CGTTCCAAATTACTTGTCTTAGATTTG 57.670 33.333 0.00 0.00 35.40 2.32
80 81 9.280174 TCGTTCCAAATTACTTGTCTTAGATTT 57.720 29.630 0.00 0.00 32.65 2.17
81 82 8.842358 TCGTTCCAAATTACTTGTCTTAGATT 57.158 30.769 0.00 0.00 32.65 2.40
82 83 8.842358 TTCGTTCCAAATTACTTGTCTTAGAT 57.158 30.769 0.00 0.00 32.65 1.98
83 84 7.386848 CCTTCGTTCCAAATTACTTGTCTTAGA 59.613 37.037 0.00 0.00 32.65 2.10
84 85 7.360946 CCCTTCGTTCCAAATTACTTGTCTTAG 60.361 40.741 0.00 0.00 32.65 2.18
85 86 6.428771 CCCTTCGTTCCAAATTACTTGTCTTA 59.571 38.462 0.00 0.00 32.65 2.10
86 87 5.240844 CCCTTCGTTCCAAATTACTTGTCTT 59.759 40.000 0.00 0.00 32.65 3.01
87 88 4.760204 CCCTTCGTTCCAAATTACTTGTCT 59.240 41.667 0.00 0.00 32.65 3.41
88 89 4.758165 TCCCTTCGTTCCAAATTACTTGTC 59.242 41.667 0.00 0.00 32.65 3.18
89 90 4.721132 TCCCTTCGTTCCAAATTACTTGT 58.279 39.130 0.00 0.00 32.65 3.16
90 91 4.760204 ACTCCCTTCGTTCCAAATTACTTG 59.240 41.667 0.00 0.00 34.52 3.16
91 92 4.981812 ACTCCCTTCGTTCCAAATTACTT 58.018 39.130 0.00 0.00 0.00 2.24
92 93 4.635699 ACTCCCTTCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
93 94 7.713942 ACATATACTCCCTTCGTTCCAAATTAC 59.286 37.037 0.00 0.00 0.00 1.89
94 95 7.798071 ACATATACTCCCTTCGTTCCAAATTA 58.202 34.615 0.00 0.00 0.00 1.40
95 96 6.659824 ACATATACTCCCTTCGTTCCAAATT 58.340 36.000 0.00 0.00 0.00 1.82
96 97 6.126883 TGACATATACTCCCTTCGTTCCAAAT 60.127 38.462 0.00 0.00 0.00 2.32
97 98 5.188163 TGACATATACTCCCTTCGTTCCAAA 59.812 40.000 0.00 0.00 0.00 3.28
98 99 4.712829 TGACATATACTCCCTTCGTTCCAA 59.287 41.667 0.00 0.00 0.00 3.53
99 100 4.283337 TGACATATACTCCCTTCGTTCCA 58.717 43.478 0.00 0.00 0.00 3.53
100 101 4.262079 CCTGACATATACTCCCTTCGTTCC 60.262 50.000 0.00 0.00 0.00 3.62
101 102 4.796618 GCCTGACATATACTCCCTTCGTTC 60.797 50.000 0.00 0.00 0.00 3.95
102 103 3.069729 GCCTGACATATACTCCCTTCGTT 59.930 47.826 0.00 0.00 0.00 3.85
103 104 2.628657 GCCTGACATATACTCCCTTCGT 59.371 50.000 0.00 0.00 0.00 3.85
104 105 2.894126 AGCCTGACATATACTCCCTTCG 59.106 50.000 0.00 0.00 0.00 3.79
105 106 4.221041 GGTAGCCTGACATATACTCCCTTC 59.779 50.000 0.00 0.00 0.00 3.46
106 107 4.161102 GGTAGCCTGACATATACTCCCTT 58.839 47.826 0.00 0.00 0.00 3.95
107 108 3.780626 GGTAGCCTGACATATACTCCCT 58.219 50.000 0.00 0.00 0.00 4.20
108 109 2.492484 CGGTAGCCTGACATATACTCCC 59.508 54.545 0.00 0.00 0.00 4.30
109 110 3.155501 ACGGTAGCCTGACATATACTCC 58.844 50.000 0.00 0.00 0.00 3.85
110 111 4.037684 ACAACGGTAGCCTGACATATACTC 59.962 45.833 0.00 0.00 0.00 2.59
111 112 3.958798 ACAACGGTAGCCTGACATATACT 59.041 43.478 0.00 0.00 0.00 2.12
112 113 4.317671 ACAACGGTAGCCTGACATATAC 57.682 45.455 0.00 0.00 0.00 1.47
113 114 5.047590 CCATACAACGGTAGCCTGACATATA 60.048 44.000 0.00 0.00 31.88 0.86
118 119 1.479323 TCCATACAACGGTAGCCTGAC 59.521 52.381 0.00 0.00 31.88 3.51
183 186 2.061773 GACGGTAATCATCATCGCCAG 58.938 52.381 0.00 0.00 0.00 4.85
188 191 5.005779 GTGAGTTGTGACGGTAATCATCATC 59.994 44.000 0.00 0.00 0.00 2.92
201 204 8.721478 AGAATACATATGTTTGTGAGTTGTGAC 58.279 33.333 14.77 0.00 0.00 3.67
228 234 7.667043 TTTATTTGCGAGAAAGAGAAAGCTA 57.333 32.000 0.00 0.00 0.00 3.32
335 341 4.452114 TGATGATATCCAGCACGCAAATAC 59.548 41.667 0.00 0.00 36.07 1.89
340 347 2.845363 ATGATGATATCCAGCACGCA 57.155 45.000 0.00 0.00 44.74 5.24
447 454 0.179179 GGCTCAGTGGACGTACGTAC 60.179 60.000 23.91 23.91 0.00 3.67
448 455 0.606130 TGGCTCAGTGGACGTACGTA 60.606 55.000 22.87 3.32 0.00 3.57
449 456 1.457823 TTGGCTCAGTGGACGTACGT 61.458 55.000 23.04 23.04 0.00 3.57
527 534 6.752168 AGCAAACTGACAAGCATAAGATTTT 58.248 32.000 0.00 0.00 0.00 1.82
774 783 0.823460 AAGGTGTTGTTGGCTTGGTG 59.177 50.000 0.00 0.00 0.00 4.17
801 810 2.224257 CCAAAGTGGATTTTGTGGTGGG 60.224 50.000 0.00 0.00 40.96 4.61
861 870 4.757692 TCTCTCTTCCTCTTTCCCTTTCT 58.242 43.478 0.00 0.00 0.00 2.52
1069 1090 4.287781 TGCGGACAAAGACGGCGA 62.288 61.111 16.62 0.00 36.60 5.54
1070 1091 4.072088 GTGCGGACAAAGACGGCG 62.072 66.667 4.80 4.80 36.60 6.46
1071 1092 2.240612 GATGTGCGGACAAAGACGGC 62.241 60.000 15.51 0.00 35.11 5.68
1072 1093 1.635663 GGATGTGCGGACAAAGACGG 61.636 60.000 15.51 0.00 35.11 4.79
1196 1225 1.360551 CCCTCATGTCGAGCTACCG 59.639 63.158 0.00 0.00 40.78 4.02
1760 1789 0.472925 GGGTTTTGGTGGGGATTGGT 60.473 55.000 0.00 0.00 0.00 3.67
1796 1825 0.467844 TGATGCTTGCTTGTGGTGGT 60.468 50.000 0.00 0.00 0.00 4.16
2436 2465 0.810031 CGCCCTGGGAAACGTATCAG 60.810 60.000 19.27 0.00 0.00 2.90
2439 2468 2.124860 GCGCCCTGGGAAACGTAT 60.125 61.111 19.27 0.00 0.00 3.06
2500 2531 1.001706 CAGAGACACGTCTTGTTCGGA 60.002 52.381 0.38 0.00 39.17 4.55
2506 2537 3.120286 CGAATTGTCAGAGACACGTCTTG 59.880 47.826 0.38 2.72 42.60 3.02
2507 2538 3.243434 ACGAATTGTCAGAGACACGTCTT 60.243 43.478 0.38 0.00 42.60 3.01
2514 2546 2.158449 CCAGCAACGAATTGTCAGAGAC 59.842 50.000 0.00 0.00 38.17 3.36
2559 2591 5.416326 ACAACTGAGAACTACTACTAGCAGG 59.584 44.000 0.00 0.00 0.00 4.85
2755 2791 8.592809 AGATTGATTAGTTGGGCAAACAAATTA 58.407 29.630 7.64 0.00 41.61 1.40
2795 2831 7.093354 TCAGCTAATCCAATCGACTATGAATC 58.907 38.462 0.00 0.00 0.00 2.52
2796 2832 6.997655 TCAGCTAATCCAATCGACTATGAAT 58.002 36.000 0.00 0.00 0.00 2.57
2797 2833 6.405278 TCAGCTAATCCAATCGACTATGAA 57.595 37.500 0.00 0.00 0.00 2.57
2798 2834 5.047731 CCTCAGCTAATCCAATCGACTATGA 60.048 44.000 0.00 0.00 0.00 2.15
2799 2835 5.047731 TCCTCAGCTAATCCAATCGACTATG 60.048 44.000 0.00 0.00 0.00 2.23
2800 2836 5.047660 GTCCTCAGCTAATCCAATCGACTAT 60.048 44.000 0.00 0.00 0.00 2.12
2801 2837 4.278669 GTCCTCAGCTAATCCAATCGACTA 59.721 45.833 0.00 0.00 0.00 2.59
2802 2838 3.068873 GTCCTCAGCTAATCCAATCGACT 59.931 47.826 0.00 0.00 0.00 4.18
2989 3025 1.459455 ATCGCCGCAGCATCTAGAGT 61.459 55.000 0.00 0.00 39.83 3.24
2993 3029 2.246739 GCAATCGCCGCAGCATCTA 61.247 57.895 0.00 0.00 39.83 1.98
3147 3191 7.908082 GCAACTAATTAATAACGTGCATCAAGA 59.092 33.333 0.00 0.00 0.00 3.02
3330 3382 3.700538 CTCATAGGAGGAGATGGAGGAG 58.299 54.545 0.00 0.00 37.51 3.69
3339 3391 0.324285 GGCCATGCTCATAGGAGGAG 59.676 60.000 6.52 0.00 45.19 3.69
3603 3655 2.284625 ATCCCTGACCGGCACTGA 60.285 61.111 0.00 0.00 0.00 3.41
3654 3706 2.583441 CCACGTCTCCTCCTTGGCA 61.583 63.158 0.00 0.00 35.26 4.92
3783 3835 2.413351 CAGGATGCGGACGTCGAT 59.587 61.111 9.92 1.00 42.43 3.59
3921 3973 1.224722 GATCGGCCTGCTCGAAATCC 61.225 60.000 0.00 0.00 40.15 3.01
3924 3976 1.153568 CTGATCGGCCTGCTCGAAA 60.154 57.895 0.00 0.08 40.15 3.46
3993 4045 3.562779 GACCTCGTCGCCGGTTTGA 62.563 63.158 1.90 0.00 32.62 2.69
4208 4260 0.461516 CGTGAGCAGGCAGACATCAT 60.462 55.000 0.00 0.00 0.00 2.45
4286 4338 2.812836 TGAACACATGCATGGATCCT 57.187 45.000 29.41 6.27 0.00 3.24
4502 4904 7.833786 ACCGTAGAGTAGATGAAAACACATTA 58.166 34.615 0.00 0.00 0.00 1.90
4673 5076 4.458989 ACACACAGTCAAACATCAACAGTT 59.541 37.500 0.00 0.00 0.00 3.16
4688 5091 7.229707 CCTCTACATAGCTAAGATACACACAGT 59.770 40.741 2.38 0.00 0.00 3.55
4941 5373 9.801873 GTTTGGCATATTCTTGCTATTTTTCTA 57.198 29.630 0.00 0.00 42.38 2.10
4945 5377 6.042143 CCGTTTGGCATATTCTTGCTATTTT 58.958 36.000 0.00 0.00 42.38 1.82
4965 5397 1.910671 TGCCCCTTTATAGTGACCGTT 59.089 47.619 0.00 0.00 0.00 4.44
5012 5444 5.106712 TGTGCTAGTTTGTAAGTATTGCAGC 60.107 40.000 0.00 0.00 42.90 5.25
5049 5481 2.202932 CGCCTCCAAGGGTCATCG 60.203 66.667 0.00 0.00 35.37 3.84
5323 5757 1.620259 GGGGGCATGGATCAAAGGA 59.380 57.895 0.00 0.00 0.00 3.36
5376 5810 2.202756 GCACCGGACATCCTCGAC 60.203 66.667 9.46 0.00 0.00 4.20
5380 5814 2.660064 GGTCAGCACCGGACATCCT 61.660 63.158 9.46 0.00 37.00 3.24
5411 5845 2.872732 AGAACCGGACAGAGTTACAGA 58.127 47.619 9.46 0.00 0.00 3.41
5414 5848 2.561858 AGGAAGAACCGGACAGAGTTAC 59.438 50.000 9.46 0.00 44.74 2.50
5434 5868 0.460987 GATGTCCGAGAACCAGGCAG 60.461 60.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.