Multiple sequence alignment - TraesCS3D01G203300

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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 TraesCS3D01G203300 chr3D 100.000 2465 0 0 1 2465 252333959 252336423 0.000000e+00 4553.0
1 TraesCS3D01G203300 chr3D 87.703 553 59 7 1862 2413 365522426 365522970 9.620000e-179 636.0
2 TraesCS3D01G203300 chr3D 96.250 80 3 0 1 80 579163325 579163246 5.530000e-27 132.0
3 TraesCS3D01G203300 chr3D 94.048 84 5 0 2 85 68839797 68839714 7.160000e-26 128.0
4 TraesCS3D01G203300 chr3A 96.719 1646 27 13 241 1861 332220749 332219106 0.000000e+00 2715.0
5 TraesCS3D01G203300 chr3A 95.954 173 6 1 83 255 332227622 332227451 1.870000e-71 279.0
6 TraesCS3D01G203300 chr3B 95.302 1639 49 7 129 1755 313807314 313808936 0.000000e+00 2575.0
7 TraesCS3D01G203300 chr3B 85.179 587 76 8 1862 2442 759931308 759930727 2.110000e-165 592.0
8 TraesCS3D01G203300 chr3B 96.330 109 4 0 1753 1861 313810245 313810353 1.950000e-41 180.0
9 TraesCS3D01G203300 chr5D 86.224 588 75 5 1862 2445 135754571 135755156 1.240000e-177 632.0
10 TraesCS3D01G203300 chr5D 97.436 78 2 0 2 79 320660616 320660539 1.540000e-27 134.0
11 TraesCS3D01G203300 chr5D 96.250 80 3 0 2 81 134489742 134489821 5.530000e-27 132.0
12 TraesCS3D01G203300 chr5D 96.552 58 0 2 835 891 285247432 285247488 7.260000e-16 95.3
13 TraesCS3D01G203300 chr5D 88.235 51 6 0 846 896 113391895 113391845 7.360000e-06 62.1
14 TraesCS3D01G203300 chr7D 85.399 589 78 7 1862 2445 51802759 51803344 2.710000e-169 604.0
15 TraesCS3D01G203300 chr7D 96.250 80 3 0 1 80 604446482 604446403 5.530000e-27 132.0
16 TraesCS3D01G203300 chr6B 87.669 519 60 4 1862 2377 488894132 488894649 3.510000e-168 601.0
17 TraesCS3D01G203300 chr6B 84.812 586 84 5 1861 2445 151420780 151420199 3.530000e-163 584.0
18 TraesCS3D01G203300 chr6B 98.182 55 1 0 841 895 119849607 119849553 2.020000e-16 97.1
19 TraesCS3D01G203300 chrUn 85.445 584 74 8 1862 2439 371794396 371794974 4.540000e-167 597.0
20 TraesCS3D01G203300 chr5B 84.932 584 81 6 1862 2442 314292972 314292393 3.530000e-163 584.0
21 TraesCS3D01G203300 chr5B 96.552 58 0 2 835 891 322858705 322858761 7.260000e-16 95.3
22 TraesCS3D01G203300 chr2B 84.760 584 79 8 1862 2439 680772807 680773386 5.910000e-161 577.0
23 TraesCS3D01G203300 chr2D 96.429 84 3 0 2 85 26447379 26447296 3.310000e-29 139.0
24 TraesCS3D01G203300 chr2D 96.386 83 3 0 1 83 82219974 82220056 1.190000e-28 137.0
25 TraesCS3D01G203300 chr5A 97.468 79 2 0 2 80 673402038 673402116 4.280000e-28 135.0
26 TraesCS3D01G203300 chr5A 96.552 58 0 2 835 891 377119601 377119657 7.260000e-16 95.3
27 TraesCS3D01G203300 chr1D 97.468 79 2 0 2 80 377957659 377957581 4.280000e-28 135.0
28 TraesCS3D01G203300 chr6D 98.182 55 1 0 841 895 52724695 52724641 2.020000e-16 97.1
29 TraesCS3D01G203300 chr6A 98.182 55 1 0 841 895 63610635 63610581 2.020000e-16 97.1
30 TraesCS3D01G203300 chr2A 100.000 34 0 0 1500 1533 771497965 771497932 2.050000e-06 63.9


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 TraesCS3D01G203300 chr3D 252333959 252336423 2464 False 4553.0 4553 100.000 1 2465 1 chr3D.!!$F1 2464
1 TraesCS3D01G203300 chr3D 365522426 365522970 544 False 636.0 636 87.703 1862 2413 1 chr3D.!!$F2 551
2 TraesCS3D01G203300 chr3A 332219106 332220749 1643 True 2715.0 2715 96.719 241 1861 1 chr3A.!!$R1 1620
3 TraesCS3D01G203300 chr3B 313807314 313810353 3039 False 1377.5 2575 95.816 129 1861 2 chr3B.!!$F1 1732
4 TraesCS3D01G203300 chr3B 759930727 759931308 581 True 592.0 592 85.179 1862 2442 1 chr3B.!!$R1 580
5 TraesCS3D01G203300 chr5D 135754571 135755156 585 False 632.0 632 86.224 1862 2445 1 chr5D.!!$F2 583
6 TraesCS3D01G203300 chr7D 51802759 51803344 585 False 604.0 604 85.399 1862 2445 1 chr7D.!!$F1 583
7 TraesCS3D01G203300 chr6B 488894132 488894649 517 False 601.0 601 87.669 1862 2377 1 chr6B.!!$F1 515
8 TraesCS3D01G203300 chr6B 151420199 151420780 581 True 584.0 584 84.812 1861 2445 1 chr6B.!!$R2 584
9 TraesCS3D01G203300 chrUn 371794396 371794974 578 False 597.0 597 85.445 1862 2439 1 chrUn.!!$F1 577
10 TraesCS3D01G203300 chr5B 314292393 314292972 579 True 584.0 584 84.932 1862 2442 1 chr5B.!!$R1 580
11 TraesCS3D01G203300 chr2B 680772807 680773386 579 False 577.0 577 84.760 1862 2439 1 chr2B.!!$F1 577

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
71 72 0.033781 GCCTCATGCAAGCAACCAAA 59.966 50.0 0.0 0.0 40.77 3.28 F
77 78 0.179150 TGCAAGCAACCAAACACGTC 60.179 50.0 0.0 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1469 1.138337 GATGCGATCTGCTAGCAGTG 58.862 55.000 36.99 28.59 46.63 3.66 R
1485 1498 1.954382 AGACAACACAGAGCTACACGA 59.046 47.619 0.00 0.00 0.00 4.35 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
20 21 2.791383 TGAATGCAGGAAACCAAACG 57.209 45.000 0.00 0.00 0.00 3.60
21 22 1.339610 TGAATGCAGGAAACCAAACGG 59.660 47.619 0.00 0.00 0.00 4.44
22 23 0.678950 AATGCAGGAAACCAAACGGG 59.321 50.000 0.00 0.00 44.81 5.28
23 24 1.815817 ATGCAGGAAACCAAACGGGC 61.816 55.000 0.00 0.00 42.05 6.13
24 25 3.047735 CAGGAAACCAAACGGGCC 58.952 61.111 0.00 0.00 42.05 5.80
25 26 1.830408 CAGGAAACCAAACGGGCCA 60.830 57.895 4.39 0.00 42.05 5.36
26 27 1.075896 AGGAAACCAAACGGGCCAA 60.076 52.632 4.39 0.00 42.05 4.52
27 28 0.688087 AGGAAACCAAACGGGCCAAA 60.688 50.000 4.39 0.00 42.05 3.28
28 29 0.394938 GGAAACCAAACGGGCCAAAT 59.605 50.000 4.39 0.00 42.05 2.32
29 30 1.202710 GGAAACCAAACGGGCCAAATT 60.203 47.619 4.39 0.00 42.05 1.82
30 31 2.139917 GAAACCAAACGGGCCAAATTC 58.860 47.619 4.39 0.00 42.05 2.17
31 32 1.419381 AACCAAACGGGCCAAATTCT 58.581 45.000 4.39 0.00 42.05 2.40
32 33 1.419381 ACCAAACGGGCCAAATTCTT 58.581 45.000 4.39 0.00 42.05 2.52
33 34 1.343142 ACCAAACGGGCCAAATTCTTC 59.657 47.619 4.39 0.00 42.05 2.87
34 35 1.337728 CCAAACGGGCCAAATTCTTCC 60.338 52.381 4.39 0.00 0.00 3.46
35 36 0.973632 AAACGGGCCAAATTCTTCCC 59.026 50.000 4.39 0.00 35.42 3.97
37 38 2.892640 GGGCCAAATTCTTCCCGC 59.107 61.111 4.39 0.00 0.00 6.13
38 39 2.721167 GGGCCAAATTCTTCCCGCC 61.721 63.158 4.39 0.00 35.60 6.13
39 40 2.721167 GGCCAAATTCTTCCCGCCC 61.721 63.158 0.00 0.00 0.00 6.13
40 41 3.063743 GCCAAATTCTTCCCGCCCG 62.064 63.158 0.00 0.00 0.00 6.13
41 42 2.414785 CCAAATTCTTCCCGCCCGG 61.415 63.158 0.00 0.00 0.00 5.73
63 64 3.145551 GGCTGGGCCTCATGCAAG 61.146 66.667 4.53 0.00 46.69 4.01
64 65 3.834799 GCTGGGCCTCATGCAAGC 61.835 66.667 4.53 0.00 43.89 4.01
65 66 2.361992 CTGGGCCTCATGCAAGCA 60.362 61.111 4.53 0.00 43.89 3.91
66 67 1.980232 CTGGGCCTCATGCAAGCAA 60.980 57.895 4.53 0.00 43.89 3.91
67 68 2.221906 CTGGGCCTCATGCAAGCAAC 62.222 60.000 4.53 0.00 43.89 4.17
68 69 2.575461 GGCCTCATGCAAGCAACC 59.425 61.111 0.00 0.00 43.89 3.77
69 70 2.277591 GGCCTCATGCAAGCAACCA 61.278 57.895 0.00 0.00 43.89 3.67
70 71 1.667151 GCCTCATGCAAGCAACCAA 59.333 52.632 0.00 0.00 40.77 3.67
71 72 0.033781 GCCTCATGCAAGCAACCAAA 59.966 50.000 0.00 0.00 40.77 3.28
72 73 1.787012 CCTCATGCAAGCAACCAAAC 58.213 50.000 0.00 0.00 0.00 2.93
73 74 1.068895 CCTCATGCAAGCAACCAAACA 59.931 47.619 0.00 0.00 0.00 2.83
74 75 2.129607 CTCATGCAAGCAACCAAACAC 58.870 47.619 0.00 0.00 0.00 3.32
75 76 0.854062 CATGCAAGCAACCAAACACG 59.146 50.000 0.00 0.00 0.00 4.49
76 77 0.459489 ATGCAAGCAACCAAACACGT 59.541 45.000 0.00 0.00 0.00 4.49
77 78 0.179150 TGCAAGCAACCAAACACGTC 60.179 50.000 0.00 0.00 0.00 4.34
78 79 0.869880 GCAAGCAACCAAACACGTCC 60.870 55.000 0.00 0.00 0.00 4.79
79 80 0.738389 CAAGCAACCAAACACGTCCT 59.262 50.000 0.00 0.00 0.00 3.85
80 81 1.134175 CAAGCAACCAAACACGTCCTT 59.866 47.619 0.00 0.00 0.00 3.36
81 82 1.470051 AGCAACCAAACACGTCCTTT 58.530 45.000 0.00 0.00 0.00 3.11
82 83 1.134175 AGCAACCAAACACGTCCTTTG 59.866 47.619 7.87 7.87 0.00 2.77
83 84 1.133407 GCAACCAAACACGTCCTTTGA 59.867 47.619 14.25 0.00 31.32 2.69
84 85 2.794631 GCAACCAAACACGTCCTTTGAG 60.795 50.000 14.25 8.55 31.32 3.02
85 86 2.680841 CAACCAAACACGTCCTTTGAGA 59.319 45.455 14.25 0.00 31.32 3.27
86 87 3.208747 ACCAAACACGTCCTTTGAGAT 57.791 42.857 14.25 0.90 31.32 2.75
87 88 2.878406 ACCAAACACGTCCTTTGAGATG 59.122 45.455 14.25 3.44 31.32 2.90
88 89 2.350772 CCAAACACGTCCTTTGAGATGC 60.351 50.000 14.25 0.00 31.32 3.91
89 90 2.549754 CAAACACGTCCTTTGAGATGCT 59.450 45.455 8.87 0.00 31.32 3.79
90 91 2.086054 ACACGTCCTTTGAGATGCTC 57.914 50.000 0.00 0.00 0.00 4.26
91 92 1.620819 ACACGTCCTTTGAGATGCTCT 59.379 47.619 0.00 0.00 0.00 4.09
92 93 2.826128 ACACGTCCTTTGAGATGCTCTA 59.174 45.455 0.00 0.00 0.00 2.43
93 94 3.258372 ACACGTCCTTTGAGATGCTCTAA 59.742 43.478 0.00 0.00 0.00 2.10
94 95 4.081420 ACACGTCCTTTGAGATGCTCTAAT 60.081 41.667 0.00 0.00 0.00 1.73
95 96 4.872691 CACGTCCTTTGAGATGCTCTAATT 59.127 41.667 0.00 0.00 0.00 1.40
96 97 5.352569 CACGTCCTTTGAGATGCTCTAATTT 59.647 40.000 0.00 0.00 0.00 1.82
97 98 6.535150 CACGTCCTTTGAGATGCTCTAATTTA 59.465 38.462 0.00 0.00 0.00 1.40
98 99 6.535508 ACGTCCTTTGAGATGCTCTAATTTAC 59.464 38.462 0.00 0.00 0.00 2.01
99 100 6.758886 CGTCCTTTGAGATGCTCTAATTTACT 59.241 38.462 0.00 0.00 0.00 2.24
100 101 7.043059 CGTCCTTTGAGATGCTCTAATTTACTC 60.043 40.741 0.00 0.00 0.00 2.59
101 102 7.984617 GTCCTTTGAGATGCTCTAATTTACTCT 59.015 37.037 0.00 0.00 0.00 3.24
102 103 8.543774 TCCTTTGAGATGCTCTAATTTACTCTT 58.456 33.333 0.00 0.00 0.00 2.85
103 104 9.171877 CCTTTGAGATGCTCTAATTTACTCTTT 57.828 33.333 0.00 0.00 0.00 2.52
104 105 9.985318 CTTTGAGATGCTCTAATTTACTCTTTG 57.015 33.333 0.00 0.00 0.00 2.77
105 106 9.725019 TTTGAGATGCTCTAATTTACTCTTTGA 57.275 29.630 0.00 0.00 0.00 2.69
106 107 9.896645 TTGAGATGCTCTAATTTACTCTTTGAT 57.103 29.630 0.00 0.00 0.00 2.57
107 108 9.896645 TGAGATGCTCTAATTTACTCTTTGATT 57.103 29.630 0.00 0.00 0.00 2.57
109 110 8.619546 AGATGCTCTAATTTACTCTTTGATTGC 58.380 33.333 0.00 0.00 0.00 3.56
110 111 7.088589 TGCTCTAATTTACTCTTTGATTGCC 57.911 36.000 0.00 0.00 0.00 4.52
111 112 6.886459 TGCTCTAATTTACTCTTTGATTGCCT 59.114 34.615 0.00 0.00 0.00 4.75
112 113 7.394359 TGCTCTAATTTACTCTTTGATTGCCTT 59.606 33.333 0.00 0.00 0.00 4.35
113 114 8.246871 GCTCTAATTTACTCTTTGATTGCCTTT 58.753 33.333 0.00 0.00 0.00 3.11
114 115 9.565213 CTCTAATTTACTCTTTGATTGCCTTTG 57.435 33.333 0.00 0.00 0.00 2.77
115 116 8.522830 TCTAATTTACTCTTTGATTGCCTTTGG 58.477 33.333 0.00 0.00 0.00 3.28
116 117 5.467035 TTTACTCTTTGATTGCCTTTGGG 57.533 39.130 0.00 0.00 0.00 4.12
117 118 2.962859 ACTCTTTGATTGCCTTTGGGT 58.037 42.857 0.00 0.00 34.45 4.51
118 119 3.308401 ACTCTTTGATTGCCTTTGGGTT 58.692 40.909 0.00 0.00 34.45 4.11
119 120 3.711190 ACTCTTTGATTGCCTTTGGGTTT 59.289 39.130 0.00 0.00 34.45 3.27
120 121 4.164030 ACTCTTTGATTGCCTTTGGGTTTT 59.836 37.500 0.00 0.00 34.45 2.43
121 122 4.702831 TCTTTGATTGCCTTTGGGTTTTC 58.297 39.130 0.00 0.00 34.45 2.29
122 123 4.163078 TCTTTGATTGCCTTTGGGTTTTCA 59.837 37.500 0.00 0.00 34.45 2.69
123 124 3.749665 TGATTGCCTTTGGGTTTTCAG 57.250 42.857 0.00 0.00 34.45 3.02
124 125 2.224257 TGATTGCCTTTGGGTTTTCAGC 60.224 45.455 0.00 0.00 34.45 4.26
125 126 1.198713 TTGCCTTTGGGTTTTCAGCA 58.801 45.000 0.00 0.00 34.45 4.41
126 127 0.752054 TGCCTTTGGGTTTTCAGCAG 59.248 50.000 0.00 0.00 34.45 4.24
127 128 0.601046 GCCTTTGGGTTTTCAGCAGC 60.601 55.000 0.00 0.00 34.45 5.25
128 129 0.318955 CCTTTGGGTTTTCAGCAGCG 60.319 55.000 0.00 0.00 0.00 5.18
129 130 0.318955 CTTTGGGTTTTCAGCAGCGG 60.319 55.000 0.00 0.00 0.00 5.52
130 131 0.753479 TTTGGGTTTTCAGCAGCGGA 60.753 50.000 0.00 0.00 0.00 5.54
131 132 0.753479 TTGGGTTTTCAGCAGCGGAA 60.753 50.000 3.56 3.56 0.00 4.30
152 153 1.021920 GCTCCTCCGTTCTTTGCCTC 61.022 60.000 0.00 0.00 0.00 4.70
155 156 0.737715 CCTCCGTTCTTTGCCTCTCG 60.738 60.000 0.00 0.00 0.00 4.04
202 203 4.662961 TCTCACCACCAGCGCACG 62.663 66.667 11.47 0.00 0.00 5.34
292 293 0.685660 CCTCCTCCCCGCCTATAAAC 59.314 60.000 0.00 0.00 0.00 2.01
626 639 1.202770 AGTCAGAAACCCCCTTGTTCG 60.203 52.381 0.00 0.00 0.00 3.95
655 668 1.740025 CTCTGCCGAAATTTCCTGTCC 59.260 52.381 12.54 0.00 0.00 4.02
937 950 3.373439 CAGAGAGTTCACCTGCTTATTGC 59.627 47.826 0.00 0.00 43.25 3.56
1485 1498 2.159338 GCAGATCGCATCATGTTGGTTT 60.159 45.455 5.93 0.00 41.79 3.27
1691 1723 0.729116 AGCAACGCTATGTGATGTGC 59.271 50.000 0.00 0.00 36.99 4.57
1737 1769 2.766263 ACATCGCCTATCACTCTCCAAA 59.234 45.455 0.00 0.00 0.00 3.28
1883 3228 8.893727 GGCTTGTTGAGTATTGTGATTATTAGT 58.106 33.333 0.00 0.00 0.00 2.24
1981 3331 2.483877 CACGAGGCTCAAGCAATACAAA 59.516 45.455 15.95 0.00 44.36 2.83
2008 3364 5.660417 ACTATTTCATCAAGCCTCTCTCTCA 59.340 40.000 0.00 0.00 0.00 3.27
2023 3379 6.039270 CCTCTCTCTCACTTCTAACATGGTAG 59.961 46.154 11.84 11.84 0.00 3.18
2024 3380 6.722328 TCTCTCTCACTTCTAACATGGTAGA 58.278 40.000 16.71 16.71 0.00 2.59
2072 3431 4.124351 CGCTTCCGTACCCTCGCA 62.124 66.667 0.00 0.00 0.00 5.10
2073 3432 2.499685 GCTTCCGTACCCTCGCAT 59.500 61.111 0.00 0.00 0.00 4.73
2182 3541 4.657013 CTGCCCTAAAGAGTCTTTTTCCT 58.343 43.478 22.66 1.27 0.00 3.36
2225 3585 1.798735 CTCTCTCGCCGGTCGTTTA 59.201 57.895 16.00 4.64 39.67 2.01
2226 3586 0.169672 CTCTCTCGCCGGTCGTTTAA 59.830 55.000 16.00 0.00 39.67 1.52
2233 3593 2.758497 CCGGTCGTTTAAATCGGCT 58.242 52.632 12.26 0.00 34.17 5.52
2252 3613 4.201871 CGGCTTTTTCTTTTTGGTTTTCCC 60.202 41.667 0.00 0.00 39.73 3.97
2276 3637 4.323417 TCTATGCTTGATCGGTTTGTGTT 58.677 39.130 0.00 0.00 0.00 3.32
2422 3785 3.474570 GCCCTCCCATCGCTCTGT 61.475 66.667 0.00 0.00 0.00 3.41
2443 3806 3.211963 GGCCATCACCGCCATGTC 61.212 66.667 0.00 0.00 46.27 3.06
2446 3809 2.516930 CATCACCGCCATGTCCCC 60.517 66.667 0.00 0.00 0.00 4.81
2447 3810 3.809013 ATCACCGCCATGTCCCCC 61.809 66.667 0.00 0.00 0.00 5.40
2452 3815 4.096003 CGCCATGTCCCCCGAGTT 62.096 66.667 0.00 0.00 0.00 3.01
2453 3816 2.124695 GCCATGTCCCCCGAGTTC 60.125 66.667 0.00 0.00 0.00 3.01
2454 3817 2.966732 GCCATGTCCCCCGAGTTCA 61.967 63.158 0.00 0.00 0.00 3.18
2455 3818 1.221840 CCATGTCCCCCGAGTTCAG 59.778 63.158 0.00 0.00 0.00 3.02
2456 3819 1.450312 CATGTCCCCCGAGTTCAGC 60.450 63.158 0.00 0.00 0.00 4.26
2457 3820 3.019003 ATGTCCCCCGAGTTCAGCG 62.019 63.158 0.00 0.00 0.00 5.18
2464 3827 4.680237 CGAGTTCAGCGCACCCCA 62.680 66.667 11.47 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.029110 CCGTTTGGTTTCCTGCATTCAT 60.029 45.455 0.00 0.00 0.00 2.57
1 2 1.339610 CCGTTTGGTTTCCTGCATTCA 59.660 47.619 0.00 0.00 0.00 2.57
2 3 1.336795 CCCGTTTGGTTTCCTGCATTC 60.337 52.381 0.00 0.00 0.00 2.67
3 4 0.678950 CCCGTTTGGTTTCCTGCATT 59.321 50.000 0.00 0.00 0.00 3.56
4 5 1.815817 GCCCGTTTGGTTTCCTGCAT 61.816 55.000 0.00 0.00 36.04 3.96
5 6 2.494530 GCCCGTTTGGTTTCCTGCA 61.495 57.895 0.00 0.00 36.04 4.41
6 7 2.338620 GCCCGTTTGGTTTCCTGC 59.661 61.111 0.00 0.00 36.04 4.85
7 8 1.395826 TTGGCCCGTTTGGTTTCCTG 61.396 55.000 0.00 0.00 36.04 3.86
8 9 0.688087 TTTGGCCCGTTTGGTTTCCT 60.688 50.000 0.00 0.00 36.04 3.36
9 10 0.394938 ATTTGGCCCGTTTGGTTTCC 59.605 50.000 0.00 0.00 36.04 3.13
10 11 2.139917 GAATTTGGCCCGTTTGGTTTC 58.860 47.619 0.00 0.00 36.04 2.78
11 12 1.765904 AGAATTTGGCCCGTTTGGTTT 59.234 42.857 0.00 0.00 36.04 3.27
12 13 1.419381 AGAATTTGGCCCGTTTGGTT 58.581 45.000 0.00 0.00 36.04 3.67
13 14 1.343142 GAAGAATTTGGCCCGTTTGGT 59.657 47.619 0.00 0.00 36.04 3.67
14 15 1.337728 GGAAGAATTTGGCCCGTTTGG 60.338 52.381 0.00 0.00 37.09 3.28
15 16 1.337728 GGGAAGAATTTGGCCCGTTTG 60.338 52.381 0.00 0.00 0.00 2.93
16 17 0.973632 GGGAAGAATTTGGCCCGTTT 59.026 50.000 0.00 0.00 0.00 3.60
17 18 2.666085 GGGAAGAATTTGGCCCGTT 58.334 52.632 0.00 0.00 0.00 4.44
18 19 4.434483 GGGAAGAATTTGGCCCGT 57.566 55.556 0.00 0.00 0.00 5.28
20 21 2.721167 GGCGGGAAGAATTTGGCCC 61.721 63.158 0.00 0.00 33.60 5.80
21 22 2.721167 GGGCGGGAAGAATTTGGCC 61.721 63.158 0.00 0.00 37.28 5.36
22 23 2.892640 GGGCGGGAAGAATTTGGC 59.107 61.111 0.00 0.00 0.00 4.52
23 24 2.414785 CCGGGCGGGAAGAATTTGG 61.415 63.158 4.88 0.00 38.47 3.28
24 25 3.196648 CCGGGCGGGAAGAATTTG 58.803 61.111 4.88 0.00 38.47 2.32
47 48 3.834799 GCTTGCATGAGGCCCAGC 61.835 66.667 0.00 0.00 43.89 4.85
48 49 1.980232 TTGCTTGCATGAGGCCCAG 60.980 57.895 0.00 0.00 43.89 4.45
49 50 2.117858 TTGCTTGCATGAGGCCCA 59.882 55.556 0.00 0.00 43.89 5.36
50 51 2.575461 GTTGCTTGCATGAGGCCC 59.425 61.111 0.00 0.00 43.89 5.80
51 52 1.818959 TTGGTTGCTTGCATGAGGCC 61.819 55.000 3.33 0.00 43.89 5.19
52 53 0.033781 TTTGGTTGCTTGCATGAGGC 59.966 50.000 3.33 0.00 45.13 4.70
53 54 1.068895 TGTTTGGTTGCTTGCATGAGG 59.931 47.619 3.33 0.00 0.00 3.86
54 55 2.129607 GTGTTTGGTTGCTTGCATGAG 58.870 47.619 3.33 0.00 0.00 2.90
55 56 1.535649 CGTGTTTGGTTGCTTGCATGA 60.536 47.619 3.33 0.00 0.00 3.07
56 57 0.854062 CGTGTTTGGTTGCTTGCATG 59.146 50.000 0.00 0.00 0.00 4.06
57 58 0.459489 ACGTGTTTGGTTGCTTGCAT 59.541 45.000 0.00 0.00 0.00 3.96
58 59 0.179150 GACGTGTTTGGTTGCTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
59 60 0.869880 GGACGTGTTTGGTTGCTTGC 60.870 55.000 0.00 0.00 0.00 4.01
60 61 0.738389 AGGACGTGTTTGGTTGCTTG 59.262 50.000 0.00 0.00 0.00 4.01
61 62 1.470051 AAGGACGTGTTTGGTTGCTT 58.530 45.000 0.00 0.00 0.00 3.91
62 63 1.134175 CAAAGGACGTGTTTGGTTGCT 59.866 47.619 10.78 0.00 32.26 3.91
63 64 1.133407 TCAAAGGACGTGTTTGGTTGC 59.867 47.619 16.23 0.00 35.88 4.17
64 65 2.680841 TCTCAAAGGACGTGTTTGGTTG 59.319 45.455 16.23 9.54 35.88 3.77
65 66 2.993937 TCTCAAAGGACGTGTTTGGTT 58.006 42.857 16.23 0.00 35.88 3.67
66 67 2.702592 TCTCAAAGGACGTGTTTGGT 57.297 45.000 16.23 0.00 35.88 3.67
67 68 2.350772 GCATCTCAAAGGACGTGTTTGG 60.351 50.000 16.23 9.62 35.88 3.28
68 69 2.549754 AGCATCTCAAAGGACGTGTTTG 59.450 45.455 11.97 11.97 36.42 2.93
69 70 2.808543 GAGCATCTCAAAGGACGTGTTT 59.191 45.455 0.00 0.00 0.00 2.83
70 71 2.417719 GAGCATCTCAAAGGACGTGTT 58.582 47.619 0.00 0.00 0.00 3.32
71 72 2.086054 GAGCATCTCAAAGGACGTGT 57.914 50.000 0.00 0.00 0.00 4.49
84 85 7.859875 GGCAATCAAAGAGTAAATTAGAGCATC 59.140 37.037 0.00 0.00 0.00 3.91
85 86 7.559170 AGGCAATCAAAGAGTAAATTAGAGCAT 59.441 33.333 0.00 0.00 0.00 3.79
86 87 6.886459 AGGCAATCAAAGAGTAAATTAGAGCA 59.114 34.615 0.00 0.00 0.00 4.26
87 88 7.326968 AGGCAATCAAAGAGTAAATTAGAGC 57.673 36.000 0.00 0.00 0.00 4.09
88 89 9.565213 CAAAGGCAATCAAAGAGTAAATTAGAG 57.435 33.333 0.00 0.00 0.00 2.43
89 90 8.522830 CCAAAGGCAATCAAAGAGTAAATTAGA 58.477 33.333 0.00 0.00 0.00 2.10
90 91 7.761249 CCCAAAGGCAATCAAAGAGTAAATTAG 59.239 37.037 0.00 0.00 0.00 1.73
91 92 7.234577 ACCCAAAGGCAATCAAAGAGTAAATTA 59.765 33.333 0.00 0.00 36.11 1.40
92 93 6.043127 ACCCAAAGGCAATCAAAGAGTAAATT 59.957 34.615 0.00 0.00 36.11 1.82
93 94 5.543790 ACCCAAAGGCAATCAAAGAGTAAAT 59.456 36.000 0.00 0.00 36.11 1.40
94 95 4.898861 ACCCAAAGGCAATCAAAGAGTAAA 59.101 37.500 0.00 0.00 36.11 2.01
95 96 4.479158 ACCCAAAGGCAATCAAAGAGTAA 58.521 39.130 0.00 0.00 36.11 2.24
96 97 4.112634 ACCCAAAGGCAATCAAAGAGTA 57.887 40.909 0.00 0.00 36.11 2.59
97 98 2.962859 ACCCAAAGGCAATCAAAGAGT 58.037 42.857 0.00 0.00 36.11 3.24
98 99 4.341366 AAACCCAAAGGCAATCAAAGAG 57.659 40.909 0.00 0.00 36.11 2.85
99 100 4.163078 TGAAAACCCAAAGGCAATCAAAGA 59.837 37.500 0.00 0.00 36.11 2.52
100 101 4.450053 TGAAAACCCAAAGGCAATCAAAG 58.550 39.130 0.00 0.00 36.11 2.77
101 102 4.450053 CTGAAAACCCAAAGGCAATCAAA 58.550 39.130 0.00 0.00 36.11 2.69
102 103 3.743899 GCTGAAAACCCAAAGGCAATCAA 60.744 43.478 0.00 0.00 36.11 2.57
103 104 2.224257 GCTGAAAACCCAAAGGCAATCA 60.224 45.455 0.00 0.00 36.11 2.57
104 105 2.224257 TGCTGAAAACCCAAAGGCAATC 60.224 45.455 0.00 0.00 36.11 2.67
105 106 1.767681 TGCTGAAAACCCAAAGGCAAT 59.232 42.857 0.00 0.00 36.11 3.56
106 107 1.138661 CTGCTGAAAACCCAAAGGCAA 59.861 47.619 0.00 0.00 36.11 4.52
107 108 0.752054 CTGCTGAAAACCCAAAGGCA 59.248 50.000 0.00 0.00 36.11 4.75
108 109 0.601046 GCTGCTGAAAACCCAAAGGC 60.601 55.000 0.00 0.00 36.11 4.35
109 110 0.318955 CGCTGCTGAAAACCCAAAGG 60.319 55.000 0.00 0.00 40.04 3.11
110 111 0.318955 CCGCTGCTGAAAACCCAAAG 60.319 55.000 0.00 0.00 0.00 2.77
111 112 0.753479 TCCGCTGCTGAAAACCCAAA 60.753 50.000 0.00 0.00 0.00 3.28
112 113 0.753479 TTCCGCTGCTGAAAACCCAA 60.753 50.000 3.93 0.00 0.00 4.12
113 114 1.152860 TTCCGCTGCTGAAAACCCA 60.153 52.632 3.93 0.00 0.00 4.51
114 115 1.581447 CTTCCGCTGCTGAAAACCC 59.419 57.895 7.87 0.00 0.00 4.11
115 116 1.581447 CCTTCCGCTGCTGAAAACC 59.419 57.895 7.87 0.00 0.00 3.27
116 117 1.081175 GCCTTCCGCTGCTGAAAAC 60.081 57.895 7.87 0.00 0.00 2.43
117 118 3.354678 GCCTTCCGCTGCTGAAAA 58.645 55.556 7.87 0.00 0.00 2.29
128 129 0.325272 AAAGAACGGAGGAGCCTTCC 59.675 55.000 0.00 0.00 44.39 3.46
129 130 1.443802 CAAAGAACGGAGGAGCCTTC 58.556 55.000 0.00 0.00 0.00 3.46
130 131 0.606673 GCAAAGAACGGAGGAGCCTT 60.607 55.000 0.00 0.00 0.00 4.35
131 132 1.003233 GCAAAGAACGGAGGAGCCT 60.003 57.895 0.00 0.00 0.00 4.58
152 153 1.603236 AAGCAGAGGGAGACAGCGAG 61.603 60.000 0.00 0.00 0.00 5.03
155 156 1.163554 CAAAAGCAGAGGGAGACAGC 58.836 55.000 0.00 0.00 0.00 4.40
292 293 2.125912 CTTGGACGAGGGACGCAG 60.126 66.667 0.00 0.00 46.94 5.18
1442 1455 2.890814 AGCAGTGGTAGGAGTAGTTGT 58.109 47.619 0.00 0.00 0.00 3.32
1456 1469 1.138337 GATGCGATCTGCTAGCAGTG 58.862 55.000 36.99 28.59 46.63 3.66
1485 1498 1.954382 AGACAACACAGAGCTACACGA 59.046 47.619 0.00 0.00 0.00 4.35
1746 1778 4.895668 TTCCCACGGTCAGTTATTACTT 57.104 40.909 0.00 0.00 30.26 2.24
1947 3293 7.630728 GCTTGAGCCTCGTGGACATATATATAA 60.631 40.741 7.92 0.00 34.57 0.98
1981 3331 7.401246 AGAGAGAGGCTTGATGAAATAGTTTT 58.599 34.615 0.00 0.00 0.00 2.43
1997 3351 4.441356 CCATGTTAGAAGTGAGAGAGAGGC 60.441 50.000 0.00 0.00 0.00 4.70
2225 3585 6.751514 AAACCAAAAAGAAAAAGCCGATTT 57.248 29.167 0.00 0.00 0.00 2.17
2226 3586 6.183360 GGAAAACCAAAAAGAAAAAGCCGATT 60.183 34.615 0.00 0.00 0.00 3.34
2252 3613 4.333649 ACACAAACCGATCAAGCATAGATG 59.666 41.667 0.00 0.00 0.00 2.90
2439 3802 2.990479 GCTGAACTCGGGGGACAT 59.010 61.111 0.00 0.00 0.00 3.06
2447 3810 4.680237 TGGGGTGCGCTGAACTCG 62.680 66.667 9.73 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.