Multiple sequence alignment - TraesCS5D01G516300

Loading Multiple Alignment...

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 TraesCS5D01G516300 chr5D 100.000 3035 0 0 1 3035 539013332 539016366 0.000000e+00 5605
1 TraesCS5D01G516300 chr5D 84.062 320 45 4 1184 1500 410241859 410241543 1.370000e-78 303
2 TraesCS5D01G516300 chr4A 92.986 2937 101 36 154 3035 629488188 629485302 0.000000e+00 4185
3 TraesCS5D01G516300 chr5B 91.212 2401 74 30 138 2472 680579479 680581808 0.000000e+00 3138
4 TraesCS5D01G516300 chr5B 88.660 485 35 12 2558 3035 680581826 680582297 9.440000e-160 573
5 TraesCS5D01G516300 chr5B 80.682 440 67 13 1184 1611 491994863 491994430 2.920000e-85 326
6 TraesCS5D01G516300 chr2D 97.991 448 8 1 995 1441 520537211 520536764 0.000000e+00 776
7 TraesCS5D01G516300 chr4B 88.028 284 17 5 2758 3035 584072879 584073151 1.360000e-83 320
8 TraesCS5D01G516300 chr5A 81.726 394 58 9 1184 1567 521744636 521744247 1.760000e-82 316
9 TraesCS5D01G516300 chr3B 89.773 176 16 2 1198 1372 718850349 718850523 1.100000e-54 224
10 TraesCS5D01G516300 chr3A 89.071 183 17 3 1198 1379 679695088 679695268 1.100000e-54 224
11 TraesCS5D01G516300 chr1B 87.302 189 23 1 1436 1623 460487613 460487425 6.590000e-52 215
12 TraesCS5D01G516300 chr4D 82.439 205 32 4 1198 1400 65577833 65577631 3.110000e-40 176


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 TraesCS5D01G516300 chr5D 539013332 539016366 3034 False 5605.0 5605 100.000 1 3035 1 chr5D.!!$F1 3034
1 TraesCS5D01G516300 chr4A 629485302 629488188 2886 True 4185.0 4185 92.986 154 3035 1 chr4A.!!$R1 2881
2 TraesCS5D01G516300 chr5B 680579479 680582297 2818 False 1855.5 3138 89.936 138 3035 2 chr5B.!!$F1 2897

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
152 153 0.748729 AAAAACTGACGTTCGCCCCA 60.749 50.000 0.0 0.0 31.66 4.96 F
640 682 1.508088 GGCCAGCGGTTTCTCAATG 59.492 57.895 0.0 0.0 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 1984 0.034380 ATGATGGCTGAACTGCTGCT 60.034 50.0 0.00 0.0 40.85 4.24 R
2070 2147 0.106769 TGACTTTTGGCTGCAGTGGA 60.107 50.0 16.64 0.0 0.00 4.02 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 7.551035 AAAGTTGTCTTGATGCTCATCTATC 57.449 36.000 10.76 2.08 38.60 2.08
25 26 6.231258 AGTTGTCTTGATGCTCATCTATCA 57.769 37.500 10.76 4.18 38.60 2.15
26 27 6.828788 AGTTGTCTTGATGCTCATCTATCAT 58.171 36.000 10.76 0.00 38.60 2.45
27 28 7.960262 AGTTGTCTTGATGCTCATCTATCATA 58.040 34.615 10.76 0.00 38.60 2.15
28 29 8.595421 AGTTGTCTTGATGCTCATCTATCATAT 58.405 33.333 10.76 0.00 38.60 1.78
29 30 8.871862 GTTGTCTTGATGCTCATCTATCATATC 58.128 37.037 10.76 0.00 38.60 1.63
30 31 8.363761 TGTCTTGATGCTCATCTATCATATCT 57.636 34.615 10.76 0.00 38.60 1.98
31 32 8.468399 TGTCTTGATGCTCATCTATCATATCTC 58.532 37.037 10.76 0.00 38.60 2.75
32 33 7.644945 GTCTTGATGCTCATCTATCATATCTCG 59.355 40.741 10.76 0.00 38.60 4.04
33 34 7.338957 TCTTGATGCTCATCTATCATATCTCGT 59.661 37.037 10.76 0.00 38.60 4.18
34 35 8.511604 TTGATGCTCATCTATCATATCTCGTA 57.488 34.615 10.76 0.00 38.60 3.43
35 36 8.511604 TGATGCTCATCTATCATATCTCGTAA 57.488 34.615 10.76 0.00 38.60 3.18
36 37 9.129532 TGATGCTCATCTATCATATCTCGTAAT 57.870 33.333 10.76 0.00 38.60 1.89
37 38 9.611284 GATGCTCATCTATCATATCTCGTAATC 57.389 37.037 2.77 0.00 35.04 1.75
38 39 7.634522 TGCTCATCTATCATATCTCGTAATCG 58.365 38.462 0.00 0.00 38.55 3.34
39 40 7.495934 TGCTCATCTATCATATCTCGTAATCGA 59.504 37.037 0.00 0.00 44.12 3.59
40 41 8.338986 GCTCATCTATCATATCTCGTAATCGAA 58.661 37.037 0.00 0.00 45.61 3.71
48 49 8.675040 TCATATCTCGTAATCGAAATAAGCAG 57.325 34.615 0.00 0.00 45.61 4.24
49 50 5.830900 ATCTCGTAATCGAAATAAGCAGC 57.169 39.130 0.00 0.00 45.61 5.25
50 51 4.678622 TCTCGTAATCGAAATAAGCAGCA 58.321 39.130 0.00 0.00 45.61 4.41
51 52 5.106442 TCTCGTAATCGAAATAAGCAGCAA 58.894 37.500 0.00 0.00 45.61 3.91
52 53 5.753438 TCTCGTAATCGAAATAAGCAGCAAT 59.247 36.000 0.00 0.00 45.61 3.56
53 54 6.257849 TCTCGTAATCGAAATAAGCAGCAATT 59.742 34.615 0.00 0.00 45.61 2.32
54 55 6.191661 TCGTAATCGAAATAAGCAGCAATTG 58.808 36.000 0.00 0.00 43.34 2.32
55 56 5.108630 CGTAATCGAAATAAGCAGCAATTGC 60.109 40.000 23.05 23.05 45.83 3.56
56 57 7.958125 CGTAATCGAAATAAGCAGCAATTGCC 61.958 42.308 26.45 12.52 46.28 4.52
67 68 3.571571 CAGCAATTGCCATCATAATCCG 58.428 45.455 26.45 0.00 43.38 4.18
68 69 2.029649 AGCAATTGCCATCATAATCCGC 60.030 45.455 26.45 0.00 43.38 5.54
69 70 2.288334 GCAATTGCCATCATAATCCGCA 60.288 45.455 20.06 0.00 34.31 5.69
70 71 3.615592 GCAATTGCCATCATAATCCGCAT 60.616 43.478 20.06 0.00 34.31 4.73
71 72 4.380761 GCAATTGCCATCATAATCCGCATA 60.381 41.667 20.06 0.00 34.31 3.14
72 73 5.337554 CAATTGCCATCATAATCCGCATAG 58.662 41.667 0.00 0.00 0.00 2.23
73 74 3.979101 TGCCATCATAATCCGCATAGA 57.021 42.857 0.00 0.00 0.00 1.98
74 75 3.599343 TGCCATCATAATCCGCATAGAC 58.401 45.455 0.00 0.00 0.00 2.59
75 76 3.261643 TGCCATCATAATCCGCATAGACT 59.738 43.478 0.00 0.00 0.00 3.24
76 77 4.256920 GCCATCATAATCCGCATAGACTT 58.743 43.478 0.00 0.00 0.00 3.01
77 78 5.046663 TGCCATCATAATCCGCATAGACTTA 60.047 40.000 0.00 0.00 0.00 2.24
78 79 5.874810 GCCATCATAATCCGCATAGACTTAA 59.125 40.000 0.00 0.00 0.00 1.85
79 80 6.036517 GCCATCATAATCCGCATAGACTTAAG 59.963 42.308 0.00 0.00 0.00 1.85
80 81 6.036517 CCATCATAATCCGCATAGACTTAAGC 59.963 42.308 1.29 0.00 0.00 3.09
81 82 6.096673 TCATAATCCGCATAGACTTAAGCA 57.903 37.500 1.29 0.00 0.00 3.91
82 83 6.701340 TCATAATCCGCATAGACTTAAGCAT 58.299 36.000 1.29 0.00 0.00 3.79
83 84 7.161404 TCATAATCCGCATAGACTTAAGCATT 58.839 34.615 1.29 0.00 0.00 3.56
84 85 5.679734 AATCCGCATAGACTTAAGCATTG 57.320 39.130 1.29 0.00 0.00 2.82
85 86 4.137116 TCCGCATAGACTTAAGCATTGT 57.863 40.909 1.29 0.00 0.00 2.71
86 87 5.270893 TCCGCATAGACTTAAGCATTGTA 57.729 39.130 1.29 0.00 0.00 2.41
87 88 5.853936 TCCGCATAGACTTAAGCATTGTAT 58.146 37.500 1.29 0.00 0.00 2.29
88 89 5.926542 TCCGCATAGACTTAAGCATTGTATC 59.073 40.000 1.29 0.00 0.00 2.24
89 90 5.696270 CCGCATAGACTTAAGCATTGTATCA 59.304 40.000 1.29 0.00 0.00 2.15
90 91 6.202762 CCGCATAGACTTAAGCATTGTATCAA 59.797 38.462 1.29 0.00 0.00 2.57
91 92 7.065894 CGCATAGACTTAAGCATTGTATCAAC 58.934 38.462 1.29 0.00 0.00 3.18
92 93 7.355778 GCATAGACTTAAGCATTGTATCAACC 58.644 38.462 1.29 0.00 0.00 3.77
93 94 7.227512 GCATAGACTTAAGCATTGTATCAACCT 59.772 37.037 1.29 0.00 0.00 3.50
94 95 9.764363 CATAGACTTAAGCATTGTATCAACCTA 57.236 33.333 1.29 0.00 0.00 3.08
96 97 8.668510 AGACTTAAGCATTGTATCAACCTATG 57.331 34.615 1.29 0.00 0.00 2.23
97 98 8.486210 AGACTTAAGCATTGTATCAACCTATGA 58.514 33.333 1.29 0.00 43.67 2.15
98 99 9.109393 GACTTAAGCATTGTATCAACCTATGAA 57.891 33.333 1.29 0.00 42.54 2.57
99 100 9.632638 ACTTAAGCATTGTATCAACCTATGAAT 57.367 29.630 1.29 0.00 42.54 2.57
103 104 8.297470 AGCATTGTATCAACCTATGAATTTGT 57.703 30.769 0.00 0.00 42.54 2.83
104 105 8.408601 AGCATTGTATCAACCTATGAATTTGTC 58.591 33.333 0.00 0.00 42.54 3.18
105 106 8.190122 GCATTGTATCAACCTATGAATTTGTCA 58.810 33.333 0.00 0.00 42.54 3.58
110 111 9.076596 GTATCAACCTATGAATTTGTCAAAAGC 57.923 33.333 1.31 0.00 42.54 3.51
111 112 6.454795 TCAACCTATGAATTTGTCAAAAGCC 58.545 36.000 1.31 0.00 40.50 4.35
112 113 5.405935 ACCTATGAATTTGTCAAAAGCCC 57.594 39.130 1.31 0.00 40.50 5.19
113 114 5.086621 ACCTATGAATTTGTCAAAAGCCCT 58.913 37.500 1.31 0.00 40.50 5.19
114 115 5.543790 ACCTATGAATTTGTCAAAAGCCCTT 59.456 36.000 1.31 0.00 40.50 3.95
115 116 6.101997 CCTATGAATTTGTCAAAAGCCCTTC 58.898 40.000 1.31 2.25 40.50 3.46
116 117 3.976169 TGAATTTGTCAAAAGCCCTTCG 58.024 40.909 1.31 0.00 31.51 3.79
117 118 3.383185 TGAATTTGTCAAAAGCCCTTCGT 59.617 39.130 1.31 0.00 31.51 3.85
118 119 2.861462 TTTGTCAAAAGCCCTTCGTG 57.139 45.000 0.00 0.00 0.00 4.35
119 120 2.045561 TTGTCAAAAGCCCTTCGTGA 57.954 45.000 0.00 0.00 0.00 4.35
120 121 1.305201 TGTCAAAAGCCCTTCGTGAC 58.695 50.000 13.65 13.65 37.71 3.67
121 122 1.305201 GTCAAAAGCCCTTCGTGACA 58.695 50.000 14.83 0.00 37.42 3.58
122 123 1.673920 GTCAAAAGCCCTTCGTGACAA 59.326 47.619 14.83 0.00 37.42 3.18
123 124 1.946768 TCAAAAGCCCTTCGTGACAAG 59.053 47.619 0.00 0.00 0.00 3.16
124 125 1.676006 CAAAAGCCCTTCGTGACAAGT 59.324 47.619 0.00 0.00 0.00 3.16
125 126 2.052782 AAAGCCCTTCGTGACAAGTT 57.947 45.000 0.00 0.00 0.00 2.66
126 127 2.922740 AAGCCCTTCGTGACAAGTTA 57.077 45.000 0.00 0.00 0.00 2.24
127 128 2.922740 AGCCCTTCGTGACAAGTTAA 57.077 45.000 0.00 0.00 0.00 2.01
128 129 2.767505 AGCCCTTCGTGACAAGTTAAG 58.232 47.619 0.00 0.00 0.00 1.85
129 130 1.197036 GCCCTTCGTGACAAGTTAAGC 59.803 52.381 0.00 0.00 0.00 3.09
130 131 1.804748 CCCTTCGTGACAAGTTAAGCC 59.195 52.381 0.00 0.00 0.00 4.35
131 132 2.489971 CCTTCGTGACAAGTTAAGCCA 58.510 47.619 0.00 0.00 0.00 4.75
132 133 2.875933 CCTTCGTGACAAGTTAAGCCAA 59.124 45.455 0.00 0.00 0.00 4.52
133 134 3.314080 CCTTCGTGACAAGTTAAGCCAAA 59.686 43.478 0.00 0.00 0.00 3.28
134 135 4.201970 CCTTCGTGACAAGTTAAGCCAAAA 60.202 41.667 0.00 0.00 0.00 2.44
135 136 4.966965 TCGTGACAAGTTAAGCCAAAAA 57.033 36.364 0.00 0.00 0.00 1.94
152 153 0.748729 AAAAACTGACGTTCGCCCCA 60.749 50.000 0.00 0.00 31.66 4.96
444 484 2.549633 GCGAGTGCTACATTTGCATT 57.450 45.000 0.00 0.00 42.69 3.56
445 485 2.867429 GCGAGTGCTACATTTGCATTT 58.133 42.857 0.00 0.00 42.69 2.32
446 486 3.244976 GCGAGTGCTACATTTGCATTTT 58.755 40.909 0.00 0.00 42.69 1.82
507 547 1.810031 CGCGGATCTTAAGGCCATCAA 60.810 52.381 5.01 0.00 0.00 2.57
527 567 4.295238 TCAACCCCCATTAAACCCTAATCA 59.705 41.667 0.00 0.00 0.00 2.57
529 569 3.206639 ACCCCCATTAAACCCTAATCAGG 59.793 47.826 0.00 0.00 42.22 3.86
575 617 5.297527 CGTTAATTACCCCTTTTATTCGCCT 59.702 40.000 0.00 0.00 0.00 5.52
636 678 4.344865 TGGGGCCAGCGGTTTCTC 62.345 66.667 4.39 0.00 0.00 2.87
637 679 4.344865 GGGGCCAGCGGTTTCTCA 62.345 66.667 4.39 0.00 0.00 3.27
638 680 2.282180 GGGCCAGCGGTTTCTCAA 60.282 61.111 4.39 0.00 0.00 3.02
639 681 1.678970 GGGCCAGCGGTTTCTCAAT 60.679 57.895 4.39 0.00 0.00 2.57
640 682 1.508088 GGCCAGCGGTTTCTCAATG 59.492 57.895 0.00 0.00 0.00 2.82
641 683 1.508088 GCCAGCGGTTTCTCAATGG 59.492 57.895 0.00 0.00 0.00 3.16
642 684 1.937546 GCCAGCGGTTTCTCAATGGG 61.938 60.000 0.00 0.00 0.00 4.00
643 685 1.508088 CAGCGGTTTCTCAATGGGC 59.492 57.895 0.00 0.00 0.00 5.36
644 686 2.040544 AGCGGTTTCTCAATGGGCG 61.041 57.895 0.00 0.00 0.00 6.13
645 687 2.332654 GCGGTTTCTCAATGGGCGT 61.333 57.895 0.00 0.00 0.00 5.68
1650 1727 4.790861 GTCCCCGTCTTCGCCGTC 62.791 72.222 0.00 0.00 35.54 4.79
1905 1982 1.597027 CACCAACTCGGACCACCAC 60.597 63.158 0.00 0.00 38.63 4.16
1906 1983 2.032071 CCAACTCGGACCACCACC 59.968 66.667 0.00 0.00 36.56 4.61
1907 1984 2.813726 CCAACTCGGACCACCACCA 61.814 63.158 0.00 0.00 36.56 4.17
1908 1985 1.301716 CAACTCGGACCACCACCAG 60.302 63.158 0.00 0.00 35.59 4.00
1909 1986 3.178540 AACTCGGACCACCACCAGC 62.179 63.158 0.00 0.00 35.59 4.85
1910 1987 3.625897 CTCGGACCACCACCAGCA 61.626 66.667 0.00 0.00 35.59 4.41
1923 2000 1.677966 CCAGCAGCAGTTCAGCCAT 60.678 57.895 0.00 0.00 34.23 4.40
1995 2072 2.722487 GAGGACGACGCCGATGAT 59.278 61.111 0.00 0.00 39.50 2.45
2191 2269 1.162698 GCCCCTACGGAGTGTTTTTC 58.837 55.000 0.00 0.00 45.73 2.29
2209 2287 6.072175 TGTTTTTCTGGTACCATGACTATTGC 60.072 38.462 16.75 1.65 0.00 3.56
2369 2448 7.847096 TGGAATGAAGCACTATACTGAACTAA 58.153 34.615 0.00 0.00 0.00 2.24
2370 2449 8.486210 TGGAATGAAGCACTATACTGAACTAAT 58.514 33.333 0.00 0.00 0.00 1.73
2371 2450 9.982651 GGAATGAAGCACTATACTGAACTAATA 57.017 33.333 0.00 0.00 0.00 0.98
2374 2453 9.973450 ATGAAGCACTATACTGAACTAATACTG 57.027 33.333 0.00 0.00 0.00 2.74
2375 2454 9.185680 TGAAGCACTATACTGAACTAATACTGA 57.814 33.333 0.00 0.00 0.00 3.41
2377 2456 9.804758 AAGCACTATACTGAACTAATACTGAAC 57.195 33.333 0.00 0.00 0.00 3.18
2378 2457 9.191479 AGCACTATACTGAACTAATACTGAACT 57.809 33.333 0.00 0.00 0.00 3.01
2433 2512 6.091441 GGTGCTACATTCTGTTAACTCTTCTG 59.909 42.308 7.22 1.34 0.00 3.02
2463 2542 9.347240 CAGGATAATGTATCTGAAGGAAATTGT 57.653 33.333 0.00 0.00 35.52 2.71
2587 2666 8.550376 ACAAATTTCTTTTGATTTTCACATCGG 58.450 29.630 5.17 0.00 46.36 4.18
2628 2707 4.925646 GCTGGAATTTCATGAACAAGTTCC 59.074 41.667 22.22 22.22 38.77 3.62
2629 2708 5.467035 TGGAATTTCATGAACAAGTTCCC 57.533 39.130 24.14 14.14 38.77 3.97
2637 2716 4.825085 TCATGAACAAGTTCCCAAGTAACC 59.175 41.667 10.19 0.00 38.77 2.85
2751 2841 5.741388 ACAAAGTCAGTTTTCTGCTACTG 57.259 39.130 0.00 0.00 46.59 2.74
2830 2921 3.355378 TCAGGAATTTACAGTGCCATGG 58.645 45.455 7.63 7.63 0.00 3.66
2848 2939 3.389925 TGGCAAAATCTTTCCAGCTTG 57.610 42.857 0.00 0.00 0.00 4.01
2849 2940 2.071540 GGCAAAATCTTTCCAGCTTGC 58.928 47.619 0.00 0.00 0.00 4.01
2854 2945 5.744490 CAAAATCTTTCCAGCTTGCTTTTG 58.256 37.500 0.00 0.00 0.00 2.44
2868 2959 5.278463 GCTTGCTTTTGGTCTCATCTTGTTA 60.278 40.000 0.00 0.00 0.00 2.41
2933 3030 8.308207 GTTCAAGGTTTCTCTAGACTCTGTAAT 58.692 37.037 0.00 0.00 0.00 1.89
2940 3037 7.873719 TTCTCTAGACTCTGTAATCCAAGAG 57.126 40.000 0.00 0.00 31.38 2.85
2941 3038 6.361433 TCTCTAGACTCTGTAATCCAAGAGG 58.639 44.000 4.83 0.00 31.21 3.69
2942 3039 4.890581 TCTAGACTCTGTAATCCAAGAGGC 59.109 45.833 4.83 1.15 36.72 4.70
2943 3040 2.769095 AGACTCTGTAATCCAAGAGGCC 59.231 50.000 0.00 0.00 37.13 5.19
2944 3041 2.501723 GACTCTGTAATCCAAGAGGCCA 59.498 50.000 5.01 0.00 30.56 5.36
2945 3042 2.912956 ACTCTGTAATCCAAGAGGCCAA 59.087 45.455 5.01 0.00 33.09 4.52
2946 3043 3.054802 ACTCTGTAATCCAAGAGGCCAAG 60.055 47.826 5.01 0.00 33.09 3.61
2947 3044 3.181329 TCTGTAATCCAAGAGGCCAAGA 58.819 45.455 5.01 0.00 33.74 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.611284 GATTACGAGATATGATAGATGAGCATC 57.389 37.037 2.27 2.27 35.30 3.91
12 13 8.288913 CGATTACGAGATATGATAGATGAGCAT 58.711 37.037 0.00 0.00 42.66 3.79
13 14 7.495934 TCGATTACGAGATATGATAGATGAGCA 59.504 37.037 0.00 0.00 43.81 4.26
14 15 7.856556 TCGATTACGAGATATGATAGATGAGC 58.143 38.462 0.00 0.00 43.81 4.26
31 32 6.410931 CAATTGCTGCTTATTTCGATTACG 57.589 37.500 0.00 0.00 41.26 3.18
46 47 3.571571 CGGATTATGATGGCAATTGCTG 58.428 45.455 28.42 0.00 41.70 4.41
47 48 2.029649 GCGGATTATGATGGCAATTGCT 60.030 45.455 28.42 11.27 41.70 3.91
48 49 2.288334 TGCGGATTATGATGGCAATTGC 60.288 45.455 22.47 22.47 41.14 3.56
49 50 3.646611 TGCGGATTATGATGGCAATTG 57.353 42.857 0.00 0.00 0.00 2.32
50 51 5.124457 GTCTATGCGGATTATGATGGCAATT 59.876 40.000 0.00 0.00 37.15 2.32
51 52 4.637534 GTCTATGCGGATTATGATGGCAAT 59.362 41.667 0.00 0.00 37.15 3.56
52 53 4.002982 GTCTATGCGGATTATGATGGCAA 58.997 43.478 0.00 0.00 37.15 4.52
53 54 3.261643 AGTCTATGCGGATTATGATGGCA 59.738 43.478 0.00 0.00 38.09 4.92
54 55 3.866651 AGTCTATGCGGATTATGATGGC 58.133 45.455 0.00 0.00 0.00 4.40
55 56 6.036517 GCTTAAGTCTATGCGGATTATGATGG 59.963 42.308 4.02 0.00 0.00 3.51
56 57 6.591448 TGCTTAAGTCTATGCGGATTATGATG 59.409 38.462 4.02 0.00 32.20 3.07
57 58 6.701340 TGCTTAAGTCTATGCGGATTATGAT 58.299 36.000 4.02 0.00 32.20 2.45
58 59 6.096673 TGCTTAAGTCTATGCGGATTATGA 57.903 37.500 4.02 0.00 32.20 2.15
59 60 6.974932 ATGCTTAAGTCTATGCGGATTATG 57.025 37.500 4.02 0.00 32.20 1.90
60 61 6.936900 ACAATGCTTAAGTCTATGCGGATTAT 59.063 34.615 4.02 0.00 32.20 1.28
61 62 6.288294 ACAATGCTTAAGTCTATGCGGATTA 58.712 36.000 4.02 0.00 32.20 1.75
62 63 5.126067 ACAATGCTTAAGTCTATGCGGATT 58.874 37.500 4.02 0.00 32.20 3.01
63 64 4.708177 ACAATGCTTAAGTCTATGCGGAT 58.292 39.130 4.02 0.00 32.20 4.18
64 65 4.137116 ACAATGCTTAAGTCTATGCGGA 57.863 40.909 4.02 0.00 32.20 5.54
65 66 5.696270 TGATACAATGCTTAAGTCTATGCGG 59.304 40.000 4.02 0.00 32.20 5.69
66 67 6.769608 TGATACAATGCTTAAGTCTATGCG 57.230 37.500 4.02 0.00 32.20 4.73
67 68 7.227512 AGGTTGATACAATGCTTAAGTCTATGC 59.772 37.037 4.02 0.00 0.00 3.14
68 69 8.668510 AGGTTGATACAATGCTTAAGTCTATG 57.331 34.615 4.02 1.75 0.00 2.23
70 71 9.764363 CATAGGTTGATACAATGCTTAAGTCTA 57.236 33.333 4.02 0.00 0.00 2.59
71 72 8.486210 TCATAGGTTGATACAATGCTTAAGTCT 58.514 33.333 4.02 0.00 0.00 3.24
72 73 8.662781 TCATAGGTTGATACAATGCTTAAGTC 57.337 34.615 4.02 0.00 0.00 3.01
73 74 9.632638 ATTCATAGGTTGATACAATGCTTAAGT 57.367 29.630 4.02 0.00 33.34 2.24
77 78 8.752187 ACAAATTCATAGGTTGATACAATGCTT 58.248 29.630 0.00 0.00 33.34 3.91
78 79 8.297470 ACAAATTCATAGGTTGATACAATGCT 57.703 30.769 0.00 0.00 33.34 3.79
79 80 8.190122 TGACAAATTCATAGGTTGATACAATGC 58.810 33.333 0.00 0.00 33.34 3.56
84 85 9.076596 GCTTTTGACAAATTCATAGGTTGATAC 57.923 33.333 0.50 0.00 32.84 2.24
85 86 8.250332 GGCTTTTGACAAATTCATAGGTTGATA 58.750 33.333 0.50 0.00 32.84 2.15
86 87 7.099120 GGCTTTTGACAAATTCATAGGTTGAT 58.901 34.615 0.50 0.00 32.84 2.57
87 88 6.454795 GGCTTTTGACAAATTCATAGGTTGA 58.545 36.000 0.50 0.00 32.84 3.18
88 89 5.639082 GGGCTTTTGACAAATTCATAGGTTG 59.361 40.000 0.50 0.00 32.84 3.77
89 90 5.543790 AGGGCTTTTGACAAATTCATAGGTT 59.456 36.000 0.50 0.00 32.84 3.50
90 91 5.086621 AGGGCTTTTGACAAATTCATAGGT 58.913 37.500 0.50 0.00 32.84 3.08
91 92 5.665916 AGGGCTTTTGACAAATTCATAGG 57.334 39.130 0.50 0.00 32.84 2.57
92 93 5.801947 CGAAGGGCTTTTGACAAATTCATAG 59.198 40.000 0.50 0.00 32.84 2.23
93 94 5.242838 ACGAAGGGCTTTTGACAAATTCATA 59.757 36.000 3.27 0.00 32.84 2.15
94 95 4.039124 ACGAAGGGCTTTTGACAAATTCAT 59.961 37.500 3.27 0.00 32.84 2.57
95 96 3.383185 ACGAAGGGCTTTTGACAAATTCA 59.617 39.130 3.27 0.00 0.00 2.57
96 97 3.735746 CACGAAGGGCTTTTGACAAATTC 59.264 43.478 3.27 1.69 0.00 2.17
97 98 3.383185 TCACGAAGGGCTTTTGACAAATT 59.617 39.130 3.27 0.00 0.00 1.82
98 99 2.955660 TCACGAAGGGCTTTTGACAAAT 59.044 40.909 3.27 0.00 0.00 2.32
99 100 2.098443 GTCACGAAGGGCTTTTGACAAA 59.902 45.455 3.27 0.00 36.60 2.83
100 101 1.673920 GTCACGAAGGGCTTTTGACAA 59.326 47.619 3.27 0.00 36.60 3.18
101 102 1.305201 GTCACGAAGGGCTTTTGACA 58.695 50.000 3.27 0.00 36.60 3.58
102 103 1.305201 TGTCACGAAGGGCTTTTGAC 58.695 50.000 3.27 5.50 36.87 3.18
103 104 1.946768 CTTGTCACGAAGGGCTTTTGA 59.053 47.619 3.27 0.00 0.00 2.69
104 105 1.676006 ACTTGTCACGAAGGGCTTTTG 59.324 47.619 0.00 0.00 0.00 2.44
105 106 2.052782 ACTTGTCACGAAGGGCTTTT 57.947 45.000 0.00 0.00 0.00 2.27
106 107 2.052782 AACTTGTCACGAAGGGCTTT 57.947 45.000 0.00 0.00 0.00 3.51
107 108 2.922740 TAACTTGTCACGAAGGGCTT 57.077 45.000 0.00 0.00 0.00 4.35
108 109 2.767505 CTTAACTTGTCACGAAGGGCT 58.232 47.619 0.00 0.00 0.00 5.19
109 110 1.197036 GCTTAACTTGTCACGAAGGGC 59.803 52.381 0.00 0.00 0.00 5.19
110 111 1.804748 GGCTTAACTTGTCACGAAGGG 59.195 52.381 0.00 0.00 0.00 3.95
111 112 2.489971 TGGCTTAACTTGTCACGAAGG 58.510 47.619 0.00 0.00 0.00 3.46
112 113 4.545823 TTTGGCTTAACTTGTCACGAAG 57.454 40.909 0.00 0.00 0.00 3.79
113 114 4.966965 TTTTGGCTTAACTTGTCACGAA 57.033 36.364 0.00 0.00 0.00 3.85
114 115 4.966965 TTTTTGGCTTAACTTGTCACGA 57.033 36.364 0.00 0.00 0.00 4.35
133 134 0.748729 TGGGGCGAACGTCAGTTTTT 60.749 50.000 0.61 0.00 41.34 1.94
134 135 0.536460 ATGGGGCGAACGTCAGTTTT 60.536 50.000 0.61 0.00 41.34 2.43
135 136 0.322322 TATGGGGCGAACGTCAGTTT 59.678 50.000 0.61 0.00 41.34 2.66
136 137 0.539986 ATATGGGGCGAACGTCAGTT 59.460 50.000 0.61 0.00 44.47 3.16
142 143 2.158841 CGGAAATTATATGGGGCGAACG 59.841 50.000 0.00 0.00 0.00 3.95
174 175 2.363975 GGCACTGGACGATGGGGTA 61.364 63.158 0.00 0.00 0.00 3.69
400 434 4.482386 GAATAAAAAGGCACCTTTCGGAC 58.518 43.478 14.84 3.56 44.50 4.79
401 435 3.508402 GGAATAAAAAGGCACCTTTCGGA 59.492 43.478 14.84 4.43 44.50 4.55
440 480 1.455408 CGCCTTTCGAAACCAAAATGC 59.545 47.619 6.47 0.94 41.67 3.56
441 481 1.455408 GCGCCTTTCGAAACCAAAATG 59.545 47.619 6.47 0.00 41.67 2.32
442 482 1.778334 GCGCCTTTCGAAACCAAAAT 58.222 45.000 6.47 0.00 41.67 1.82
443 483 0.592754 CGCGCCTTTCGAAACCAAAA 60.593 50.000 6.47 0.00 41.67 2.44
444 484 1.009449 CGCGCCTTTCGAAACCAAA 60.009 52.632 6.47 0.00 41.67 3.28
445 485 2.634777 CGCGCCTTTCGAAACCAA 59.365 55.556 6.47 0.00 41.67 3.67
446 486 3.350612 CCGCGCCTTTCGAAACCA 61.351 61.111 6.47 0.00 41.67 3.67
507 547 3.206639 CCTGATTAGGGTTTAATGGGGGT 59.793 47.826 0.00 0.00 40.63 4.95
529 569 4.171103 ATTACGAGGTGGGCCCGC 62.171 66.667 28.23 28.23 38.74 6.13
575 617 0.671163 GTGCGTACGGGTCAAATCCA 60.671 55.000 18.39 0.00 0.00 3.41
617 659 4.660938 GAAACCGCTGGCCCCACT 62.661 66.667 0.00 0.00 0.00 4.00
1611 1688 4.473520 CCCTGCTGACCGCCGATT 62.474 66.667 0.00 0.00 38.05 3.34
1676 1753 1.378382 TGCGGGATCATGTGGTTGG 60.378 57.895 0.00 0.00 0.00 3.77
1869 1946 1.342174 GTGTTCTGGACCACGGTAGAA 59.658 52.381 0.00 0.00 0.00 2.10
1905 1982 1.654954 GATGGCTGAACTGCTGCTGG 61.655 60.000 11.29 1.84 40.85 4.85
1906 1983 0.958876 TGATGGCTGAACTGCTGCTG 60.959 55.000 4.89 4.89 40.85 4.41
1907 1984 0.034380 ATGATGGCTGAACTGCTGCT 60.034 50.000 0.00 0.00 40.85 4.24
1908 1985 0.381089 GATGATGGCTGAACTGCTGC 59.619 55.000 0.00 0.00 40.38 5.25
1909 1986 1.941294 GAGATGATGGCTGAACTGCTG 59.059 52.381 3.97 0.00 0.00 4.41
1910 1987 1.558294 TGAGATGATGGCTGAACTGCT 59.442 47.619 3.97 0.00 0.00 4.24
1995 2072 2.333417 GGAGACTGGCTCGTCGTCA 61.333 63.158 4.08 0.00 44.91 4.35
2070 2147 0.106769 TGACTTTTGGCTGCAGTGGA 60.107 50.000 16.64 0.00 0.00 4.02
2191 2269 3.118261 ACCAGCAATAGTCATGGTACCAG 60.118 47.826 21.41 12.37 44.15 4.00
2209 2287 6.318900 GGTCAAGAATAATTAGGGACAACCAG 59.681 42.308 0.00 0.00 43.89 4.00
2269 2347 6.349243 TGGAAATCATCAACAAAGCTCAAT 57.651 33.333 0.00 0.00 0.00 2.57
2369 2448 3.762288 TCGTCTTGCCTGTAGTTCAGTAT 59.238 43.478 0.00 0.00 42.19 2.12
2370 2449 3.151554 TCGTCTTGCCTGTAGTTCAGTA 58.848 45.455 0.00 0.00 42.19 2.74
2371 2450 1.961394 TCGTCTTGCCTGTAGTTCAGT 59.039 47.619 0.00 0.00 42.19 3.41
2372 2451 2.029828 ACTCGTCTTGCCTGTAGTTCAG 60.030 50.000 0.00 0.00 43.27 3.02
2373 2452 1.961394 ACTCGTCTTGCCTGTAGTTCA 59.039 47.619 0.00 0.00 0.00 3.18
2374 2453 2.726832 ACTCGTCTTGCCTGTAGTTC 57.273 50.000 0.00 0.00 0.00 3.01
2375 2454 3.762288 TGATACTCGTCTTGCCTGTAGTT 59.238 43.478 0.00 0.00 0.00 2.24
2376 2455 3.353557 TGATACTCGTCTTGCCTGTAGT 58.646 45.455 0.00 0.00 0.00 2.73
2377 2456 3.793801 GCTGATACTCGTCTTGCCTGTAG 60.794 52.174 0.00 0.00 0.00 2.74
2378 2457 2.099263 GCTGATACTCGTCTTGCCTGTA 59.901 50.000 0.00 0.00 0.00 2.74
2379 2458 1.134965 GCTGATACTCGTCTTGCCTGT 60.135 52.381 0.00 0.00 0.00 4.00
2433 2512 8.964476 TTCCTTCAGATACATTATCCTGAAAC 57.036 34.615 0.00 0.00 34.77 2.78
2500 2579 5.536161 AGCATGCCTTTTCTTCTCTGTAAAA 59.464 36.000 15.66 0.00 0.00 1.52
2587 2666 1.815003 AGCAATCCAAGCAGCAACTAC 59.185 47.619 0.00 0.00 0.00 2.73
2628 2707 5.529060 GCAGAAATGATAGGAGGTTACTTGG 59.471 44.000 0.00 0.00 0.00 3.61
2629 2708 6.352516 AGCAGAAATGATAGGAGGTTACTTG 58.647 40.000 0.00 0.00 0.00 3.16
2637 2716 8.674263 ATTTACAGAAGCAGAAATGATAGGAG 57.326 34.615 0.00 0.00 0.00 3.69
2830 2921 3.036075 AGCAAGCTGGAAAGATTTTGC 57.964 42.857 0.00 0.00 40.74 3.68
2848 2939 5.948992 AGTAACAAGATGAGACCAAAAGC 57.051 39.130 0.00 0.00 0.00 3.51
2849 2940 7.657761 ACTGTAGTAACAAGATGAGACCAAAAG 59.342 37.037 0.00 0.00 34.49 2.27
2854 2945 5.419471 AGGACTGTAGTAACAAGATGAGACC 59.581 44.000 0.00 0.00 34.49 3.85
2933 3030 0.397941 CACTGTCTTGGCCTCTTGGA 59.602 55.000 3.32 0.00 34.57 3.53
2940 3037 1.379044 CATCCCCACTGTCTTGGCC 60.379 63.158 0.00 0.00 35.00 5.36
2941 3038 0.393537 CTCATCCCCACTGTCTTGGC 60.394 60.000 0.00 0.00 35.00 4.52
2942 3039 0.987294 ACTCATCCCCACTGTCTTGG 59.013 55.000 0.00 0.00 36.26 3.61
2943 3040 2.867109 AACTCATCCCCACTGTCTTG 57.133 50.000 0.00 0.00 0.00 3.02
2944 3041 3.395941 AGAAAACTCATCCCCACTGTCTT 59.604 43.478 0.00 0.00 0.00 3.01
2945 3042 2.982488 AGAAAACTCATCCCCACTGTCT 59.018 45.455 0.00 0.00 0.00 3.41
2946 3043 3.425162 AGAAAACTCATCCCCACTGTC 57.575 47.619 0.00 0.00 0.00 3.51
2947 3044 3.395941 AGAAGAAAACTCATCCCCACTGT 59.604 43.478 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.