Multiple sequence alignment - TraesCS5D01G059200

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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 TraesCS5D01G059200 chr5D 100.000 2468 0 0 1 2468 56116694 56119161 0.000000e+00 4558.0
1 TraesCS5D01G059200 chr5D 95.918 49 2 0 37 85 563407918 563407966 2.030000e-11 80.5
2 TraesCS5D01G059200 chr5A 91.937 1786 122 11 693 2468 44940926 44942699 0.000000e+00 2481.0
3 TraesCS5D01G059200 chr5A 85.897 312 17 17 387 692 44940479 44940769 8.570000e-80 307.0
4 TraesCS5D01G059200 chr5A 91.071 56 5 0 37 92 52281209 52281154 2.630000e-10 76.8
5 TraesCS5D01G059200 chr5B 91.823 905 60 8 1443 2337 58888486 58889386 0.000000e+00 1249.0
6 TraesCS5D01G059200 chr5B 90.809 544 27 6 121 652 58885758 58886290 0.000000e+00 706.0
7 TraesCS5D01G059200 chr5B 87.648 591 55 8 810 1389 58887902 58888485 0.000000e+00 671.0
8 TraesCS5D01G059200 chr5B 84.921 126 7 4 699 813 58887256 58887380 1.550000e-22 117.0
9 TraesCS5D01G059200 chr2A 95.918 49 2 0 37 85 203902529 203902481 2.030000e-11 80.5
10 TraesCS5D01G059200 chr2A 90.909 55 4 1 31 85 676450966 676451019 3.400000e-09 73.1
11 TraesCS5D01G059200 chr3A 88.889 63 7 0 37 99 429624842 429624780 7.320000e-11 78.7
12 TraesCS5D01G059200 chr4B 95.745 47 2 0 39 85 347382090 347382044 2.630000e-10 76.8
13 TraesCS5D01G059200 chr6A 90.909 55 5 0 37 91 579055238 579055184 9.470000e-10 75.0
14 TraesCS5D01G059200 chr3D 93.878 49 3 0 37 85 582105005 582105053 9.470000e-10 75.0
15 TraesCS5D01G059200 chr2D 90.909 55 3 2 31 85 74146910 74146858 3.400000e-09 73.1


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 TraesCS5D01G059200 chr5D 56116694 56119161 2467 False 4558.00 4558 100.00000 1 2468 1 chr5D.!!$F1 2467
1 TraesCS5D01G059200 chr5A 44940479 44942699 2220 False 1394.00 2481 88.91700 387 2468 2 chr5A.!!$F1 2081
2 TraesCS5D01G059200 chr5B 58885758 58889386 3628 False 685.75 1249 88.80025 121 2337 4 chr5B.!!$F1 2216

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
82 83 0.037046 GCGGAGTAAAAAGGACCGGA 60.037 55.000 9.46 0.0 43.15 5.14 F
102 103 0.328258 GGCAATACACTGAGTGGGGT 59.672 55.000 17.92 0.0 37.94 4.95 F
901 2391 1.066918 GCAGGGCTATGCACATTGC 59.933 57.895 8.30 8.3 45.77 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1120 2612 0.263765 TACCTCGTCCCAGCCCTATT 59.736 55.0 0.0 0.0 0.00 1.73 R
1394 2892 0.539438 GTGGCCCATGTGGAACTTCA 60.539 55.0 0.0 0.0 38.04 3.02 R
2049 3555 0.871057 GCCTGAACACTGCAAGAGAC 59.129 55.0 0.0 0.0 37.43 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
67 68 9.645059 TGATTTGACAAAAATTTAATATGCGGA 57.355 25.926 4.41 0.00 0.00 5.54
69 70 9.651913 ATTTGACAAAAATTTAATATGCGGAGT 57.348 25.926 4.41 0.00 0.00 3.85
78 79 9.797556 AAATTTAATATGCGGAGTAAAAAGGAC 57.202 29.630 0.00 0.00 0.00 3.85
79 80 6.930667 TTAATATGCGGAGTAAAAAGGACC 57.069 37.500 0.00 0.00 0.00 4.46
80 81 1.734163 ATGCGGAGTAAAAAGGACCG 58.266 50.000 0.00 0.00 45.26 4.79
81 82 0.320946 TGCGGAGTAAAAAGGACCGG 60.321 55.000 0.00 0.00 43.15 5.28
82 83 0.037046 GCGGAGTAAAAAGGACCGGA 60.037 55.000 9.46 0.00 43.15 5.14
83 84 2.005560 GCGGAGTAAAAAGGACCGGAG 61.006 57.143 9.46 0.00 43.15 4.63
96 97 3.369381 CCGGAGGCAATACACTGAG 57.631 57.895 0.00 0.00 46.14 3.35
97 98 0.537188 CCGGAGGCAATACACTGAGT 59.463 55.000 0.00 0.00 46.14 3.41
98 99 1.645034 CGGAGGCAATACACTGAGTG 58.355 55.000 11.70 11.70 39.75 3.51
99 100 1.740380 CGGAGGCAATACACTGAGTGG 60.740 57.143 17.92 0.00 37.94 4.00
100 101 1.407437 GGAGGCAATACACTGAGTGGG 60.407 57.143 17.92 4.63 37.94 4.61
101 102 0.620556 AGGCAATACACTGAGTGGGG 59.379 55.000 17.92 4.27 37.94 4.96
102 103 0.328258 GGCAATACACTGAGTGGGGT 59.672 55.000 17.92 0.00 37.94 4.95
103 104 1.557832 GGCAATACACTGAGTGGGGTA 59.442 52.381 17.92 0.45 37.94 3.69
104 105 2.172717 GGCAATACACTGAGTGGGGTAT 59.827 50.000 17.92 3.02 37.94 2.73
105 106 3.389983 GGCAATACACTGAGTGGGGTATA 59.610 47.826 17.92 0.00 37.94 1.47
106 107 4.377897 GCAATACACTGAGTGGGGTATAC 58.622 47.826 17.92 0.00 37.94 1.47
107 108 4.141801 GCAATACACTGAGTGGGGTATACA 60.142 45.833 17.92 0.00 37.94 2.29
108 109 5.357257 CAATACACTGAGTGGGGTATACAC 58.643 45.833 17.92 0.00 37.94 2.90
109 110 2.897350 ACACTGAGTGGGGTATACACA 58.103 47.619 17.92 1.28 41.21 3.72
110 111 3.450904 ACACTGAGTGGGGTATACACAT 58.549 45.455 17.92 0.00 41.21 3.21
111 112 3.844211 ACACTGAGTGGGGTATACACATT 59.156 43.478 17.92 1.06 41.21 2.71
112 113 4.191544 CACTGAGTGGGGTATACACATTG 58.808 47.826 7.57 0.00 41.21 2.82
113 114 3.844211 ACTGAGTGGGGTATACACATTGT 59.156 43.478 7.57 0.00 41.21 2.71
114 115 4.288626 ACTGAGTGGGGTATACACATTGTT 59.711 41.667 7.57 0.00 41.21 2.83
115 116 4.839121 TGAGTGGGGTATACACATTGTTC 58.161 43.478 7.57 0.00 41.21 3.18
116 117 4.287326 TGAGTGGGGTATACACATTGTTCA 59.713 41.667 7.57 0.69 41.21 3.18
117 118 5.221945 TGAGTGGGGTATACACATTGTTCAA 60.222 40.000 7.57 0.00 41.21 2.69
118 119 5.636123 AGTGGGGTATACACATTGTTCAAA 58.364 37.500 7.57 0.00 41.21 2.69
119 120 6.071984 AGTGGGGTATACACATTGTTCAAAA 58.928 36.000 7.57 0.00 41.21 2.44
156 157 4.460034 AGAGTTTAGACCGTCCTCTTTCTC 59.540 45.833 0.00 0.00 0.00 2.87
160 161 6.151480 AGTTTAGACCGTCCTCTTTCTCTAAG 59.849 42.308 0.00 0.00 35.04 2.18
176 177 7.834881 TTCTCTAAGAGTGAGTTTAGTCCAA 57.165 36.000 0.00 0.00 33.59 3.53
188 189 7.278868 GTGAGTTTAGTCCAAGTAATGATCCAG 59.721 40.741 0.00 0.00 0.00 3.86
200 201 3.634218 ATGATCCAGTCCTCTCCATCT 57.366 47.619 0.00 0.00 0.00 2.90
201 202 2.675583 TGATCCAGTCCTCTCCATCTG 58.324 52.381 0.00 0.00 0.00 2.90
202 203 2.023598 TGATCCAGTCCTCTCCATCTGT 60.024 50.000 0.00 0.00 0.00 3.41
227 228 9.157104 GTTCTTCTTCTATTCTAAGTGAAAGGG 57.843 37.037 0.00 0.00 38.29 3.95
326 327 2.747460 CCCAGGCACATCACCGTG 60.747 66.667 0.00 0.00 40.00 4.94
350 351 2.609339 CTCCTCCCCGGATCTCCA 59.391 66.667 0.73 0.00 42.12 3.86
365 366 2.048316 CCAATGCACGCCAAACCC 60.048 61.111 0.00 0.00 0.00 4.11
456 462 4.704833 CCCCCTGACCTGCACGTG 62.705 72.222 12.28 12.28 0.00 4.49
476 499 4.841617 TCTCGCCGGCATCCTCCT 62.842 66.667 28.98 0.00 0.00 3.69
547 577 1.453155 CTGCTTACGGTGGAAATGCT 58.547 50.000 0.00 0.00 0.00 3.79
595 625 5.277683 CGTCATTGCTTATGCTAGAATTGCT 60.278 40.000 9.06 0.00 40.48 3.91
599 629 3.628942 TGCTTATGCTAGAATTGCTGTGG 59.371 43.478 9.06 0.00 40.48 4.17
605 635 2.440409 CTAGAATTGCTGTGGGCTGTT 58.560 47.619 0.00 0.00 42.39 3.16
630 660 4.222366 TCATTGCTTATGGTGGAAATGCAA 59.778 37.500 0.00 0.00 41.94 4.08
662 693 3.561310 TGGCGATTAGTCTTGCATGATTC 59.439 43.478 5.49 1.23 0.00 2.52
688 719 7.225538 CCAAACTCCATGATTGCTTACTACTAG 59.774 40.741 0.00 0.00 0.00 2.57
720 1670 2.401583 TGTAGTGTGATGTGATGGGC 57.598 50.000 0.00 0.00 0.00 5.36
756 1714 5.245531 TGATGGATTGTAGAGTTGGAACAC 58.754 41.667 0.00 0.00 39.29 3.32
813 1773 6.840789 GCGCAATGCTTTTTGTAATTATTAGC 59.159 34.615 0.30 0.00 41.73 3.09
844 2329 2.096248 TGGTCCTTGTGTTGGTTCAAC 58.904 47.619 4.04 4.04 43.78 3.18
901 2391 1.066918 GCAGGGCTATGCACATTGC 59.933 57.895 8.30 8.30 45.77 3.56
929 2419 5.630680 GTGTGTTGCTTGATTGTTATCCAAG 59.369 40.000 0.00 0.00 36.25 3.61
941 2431 5.437289 TGTTATCCAAGAACTTTGCACTG 57.563 39.130 0.00 0.00 0.00 3.66
944 2434 1.677576 TCCAAGAACTTTGCACTGCAG 59.322 47.619 13.48 13.48 40.61 4.41
1032 2522 5.504755 CACACGAAGATCTTTTGCGAAATAC 59.495 40.000 18.63 0.00 0.00 1.89
1073 2563 1.587547 GCAATAGCTAGTCTGGGTGC 58.412 55.000 0.00 0.00 37.91 5.01
1079 2569 1.446792 CTAGTCTGGGTGCGTGCTG 60.447 63.158 0.00 0.00 0.00 4.41
1109 2599 1.351350 AGGTTACAAGAACCCTGAGCC 59.649 52.381 2.84 0.00 41.18 4.70
1119 2611 2.808906 ACCCTGAGCCCAAATTCTAC 57.191 50.000 0.00 0.00 0.00 2.59
1120 2612 1.992557 ACCCTGAGCCCAAATTCTACA 59.007 47.619 0.00 0.00 0.00 2.74
1125 2617 4.823989 CCTGAGCCCAAATTCTACAATAGG 59.176 45.833 0.00 0.00 0.00 2.57
1132 2624 4.386312 CCAAATTCTACAATAGGGCTGGGA 60.386 45.833 0.00 0.00 0.00 4.37
1133 2625 4.439253 AATTCTACAATAGGGCTGGGAC 57.561 45.455 0.00 0.00 0.00 4.46
1194 2686 3.334583 TTAAAGCAGCAGTACAGAGGG 57.665 47.619 0.00 0.00 0.00 4.30
1319 2814 4.881273 CACCAGGATCGTAATTCATTTCCA 59.119 41.667 0.00 0.00 0.00 3.53
1348 2846 3.773418 TCCCTTTTCACGTATGAACCA 57.227 42.857 0.00 0.00 44.66 3.67
1394 2892 0.617413 CAGAGAACCCCAGAGCATGT 59.383 55.000 0.00 0.00 0.00 3.21
1395 2893 0.617413 AGAGAACCCCAGAGCATGTG 59.383 55.000 0.00 0.00 0.00 3.21
1437 2935 2.540931 CCAACTTGACTTTGTTGCATGC 59.459 45.455 11.82 11.82 41.34 4.06
1441 2939 3.243301 ACTTGACTTTGTTGCATGCTCTG 60.243 43.478 20.33 5.78 0.00 3.35
1534 3034 6.042781 GGATGATACTCCAACCAGTATTACCA 59.957 42.308 0.00 0.00 39.31 3.25
1560 3063 2.088763 AGACGACGATGTGCTTGCG 61.089 57.895 0.00 0.00 0.00 4.85
1610 3113 3.316573 CTCCTCCTGCCACGGTTCC 62.317 68.421 0.00 0.00 0.00 3.62
1698 3201 9.865321 AAATTGATTGTCATATCTTTGTTCTGG 57.135 29.630 0.00 0.00 0.00 3.86
1718 3221 7.630242 TCTGGTCCTGAATATTTGAATGAAC 57.370 36.000 0.00 0.00 0.00 3.18
1732 3235 2.631160 ATGAACGGGTGTTGTCAAGA 57.369 45.000 0.00 0.00 38.78 3.02
1773 3276 8.476447 TGTCCAATGTCATACAAATGCATTAAT 58.524 29.630 13.39 6.48 37.55 1.40
1809 3315 2.743636 ATGTACACCGTCAGTTCCAG 57.256 50.000 0.00 0.00 0.00 3.86
1831 3337 6.813152 CCAGGACTTTGTTGGCAAAATATAAG 59.187 38.462 0.00 0.00 43.17 1.73
1832 3338 6.311200 CAGGACTTTGTTGGCAAAATATAAGC 59.689 38.462 0.00 0.00 43.17 3.09
1856 3362 6.443792 CAAATCAAACGCTAGGGTTTACTTT 58.556 36.000 30.49 26.65 38.01 2.66
1917 3423 7.716799 ACAAAGGAATATGCTTGACCATTTA 57.283 32.000 0.00 0.00 0.00 1.40
1922 3428 0.740737 ATGCTTGACCATTTAGGCGC 59.259 50.000 0.00 0.00 43.14 6.53
1965 3471 4.389687 GCCAAACGATTTCGGACTAAGTTA 59.610 41.667 4.84 0.00 44.95 2.24
2014 3520 9.702253 ACAATGATATAGACCGAGTATTATCCT 57.298 33.333 0.00 0.00 0.00 3.24
2034 3540 9.793259 TTATCCTGTAGAAAATGAACTGAAACT 57.207 29.630 0.00 0.00 0.00 2.66
2044 3550 1.166531 AACTGAAACTGGGTCGCTGC 61.167 55.000 0.00 0.00 0.00 5.25
2049 3555 2.058829 AAACTGGGTCGCTGCGTTTG 62.059 55.000 22.48 11.06 0.00 2.93
2225 3731 3.329386 AGACTGATTTGATGGACACACG 58.671 45.455 0.00 0.00 0.00 4.49
2229 3735 3.066380 TGATTTGATGGACACACGTCTG 58.934 45.455 0.00 0.00 42.21 3.51
2349 3857 5.995282 TGTATCAGAATTCAAAAGTCGGTGT 59.005 36.000 8.44 0.00 0.00 4.16
2350 3858 6.485313 TGTATCAGAATTCAAAAGTCGGTGTT 59.515 34.615 8.44 0.00 0.00 3.32
2353 3864 5.007626 TCAGAATTCAAAAGTCGGTGTTGAG 59.992 40.000 8.44 0.00 33.10 3.02
2382 3893 3.813443 AGTTACCATGATGATCACAGCC 58.187 45.455 0.00 0.00 0.00 4.85
2407 3918 0.383590 TGTTGACCAACGGTGCAATG 59.616 50.000 0.00 0.00 43.94 2.82
2421 3932 5.753438 ACGGTGCAATGATATGTACTACTTG 59.247 40.000 0.00 0.00 36.34 3.16
2437 3948 8.996271 TGTACTACTTGACCTGTACATATATCG 58.004 37.037 0.00 0.00 39.85 2.92
2442 3953 7.208080 ACTTGACCTGTACATATATCGGAAAC 58.792 38.462 0.00 0.00 0.00 2.78
2456 3967 9.886132 ATATATCGGAAACAAACTTACTGAACT 57.114 29.630 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.645059 TCCGCATATTAAATTTTTGTCAAATCA 57.355 25.926 0.00 0.00 0.00 2.57
43 44 9.651913 ACTCCGCATATTAAATTTTTGTCAAAT 57.348 25.926 0.00 0.00 0.00 2.32
52 53 9.797556 GTCCTTTTTACTCCGCATATTAAATTT 57.202 29.630 0.00 0.00 0.00 1.82
53 54 8.410912 GGTCCTTTTTACTCCGCATATTAAATT 58.589 33.333 0.00 0.00 0.00 1.82
54 55 7.255001 CGGTCCTTTTTACTCCGCATATTAAAT 60.255 37.037 0.00 0.00 35.01 1.40
55 56 6.037391 CGGTCCTTTTTACTCCGCATATTAAA 59.963 38.462 0.00 0.00 35.01 1.52
56 57 5.524646 CGGTCCTTTTTACTCCGCATATTAA 59.475 40.000 0.00 0.00 35.01 1.40
57 58 5.051816 CGGTCCTTTTTACTCCGCATATTA 58.948 41.667 0.00 0.00 35.01 0.98
58 59 3.875134 CGGTCCTTTTTACTCCGCATATT 59.125 43.478 0.00 0.00 35.01 1.28
59 60 3.463944 CGGTCCTTTTTACTCCGCATAT 58.536 45.455 0.00 0.00 35.01 1.78
60 61 2.419021 CCGGTCCTTTTTACTCCGCATA 60.419 50.000 0.00 0.00 39.87 3.14
61 62 1.677820 CCGGTCCTTTTTACTCCGCAT 60.678 52.381 0.00 0.00 39.87 4.73
62 63 0.320946 CCGGTCCTTTTTACTCCGCA 60.321 55.000 0.00 0.00 39.87 5.69
63 64 0.037046 TCCGGTCCTTTTTACTCCGC 60.037 55.000 0.00 0.00 39.87 5.54
64 65 1.405121 CCTCCGGTCCTTTTTACTCCG 60.405 57.143 0.00 0.00 40.72 4.63
65 66 1.678123 GCCTCCGGTCCTTTTTACTCC 60.678 57.143 0.00 0.00 0.00 3.85
66 67 1.002773 TGCCTCCGGTCCTTTTTACTC 59.997 52.381 0.00 0.00 0.00 2.59
67 68 1.061546 TGCCTCCGGTCCTTTTTACT 58.938 50.000 0.00 0.00 0.00 2.24
68 69 1.900245 TTGCCTCCGGTCCTTTTTAC 58.100 50.000 0.00 0.00 0.00 2.01
69 70 2.891191 ATTGCCTCCGGTCCTTTTTA 57.109 45.000 0.00 0.00 0.00 1.52
70 71 2.224917 TGTATTGCCTCCGGTCCTTTTT 60.225 45.455 0.00 0.00 0.00 1.94
71 72 1.353022 TGTATTGCCTCCGGTCCTTTT 59.647 47.619 0.00 0.00 0.00 2.27
72 73 0.988832 TGTATTGCCTCCGGTCCTTT 59.011 50.000 0.00 0.00 0.00 3.11
73 74 0.252197 GTGTATTGCCTCCGGTCCTT 59.748 55.000 0.00 0.00 0.00 3.36
74 75 0.617820 AGTGTATTGCCTCCGGTCCT 60.618 55.000 0.00 0.00 0.00 3.85
75 76 0.462047 CAGTGTATTGCCTCCGGTCC 60.462 60.000 0.00 0.00 0.00 4.46
76 77 0.535335 TCAGTGTATTGCCTCCGGTC 59.465 55.000 0.00 0.00 0.00 4.79
77 78 0.537188 CTCAGTGTATTGCCTCCGGT 59.463 55.000 0.00 0.00 0.00 5.28
78 79 0.537188 ACTCAGTGTATTGCCTCCGG 59.463 55.000 0.00 0.00 0.00 5.14
79 80 1.645034 CACTCAGTGTATTGCCTCCG 58.355 55.000 0.00 0.00 0.00 4.63
80 81 1.407437 CCCACTCAGTGTATTGCCTCC 60.407 57.143 3.56 0.00 0.00 4.30
81 82 1.407437 CCCCACTCAGTGTATTGCCTC 60.407 57.143 3.56 0.00 0.00 4.70
82 83 0.620556 CCCCACTCAGTGTATTGCCT 59.379 55.000 3.56 0.00 0.00 4.75
83 84 0.328258 ACCCCACTCAGTGTATTGCC 59.672 55.000 3.56 0.00 0.00 4.52
84 85 3.560636 ATACCCCACTCAGTGTATTGC 57.439 47.619 3.56 0.00 0.00 3.56
85 86 5.105106 TGTGTATACCCCACTCAGTGTATTG 60.105 44.000 3.56 0.00 33.92 1.90
86 87 5.027460 TGTGTATACCCCACTCAGTGTATT 58.973 41.667 3.56 0.00 33.92 1.89
87 88 4.616553 TGTGTATACCCCACTCAGTGTAT 58.383 43.478 3.56 0.00 33.92 2.29
88 89 4.050315 TGTGTATACCCCACTCAGTGTA 57.950 45.455 3.56 0.00 33.92 2.90
89 90 2.897350 TGTGTATACCCCACTCAGTGT 58.103 47.619 3.56 0.00 33.92 3.55
90 91 4.191544 CAATGTGTATACCCCACTCAGTG 58.808 47.826 0.00 0.00 33.92 3.66
91 92 3.844211 ACAATGTGTATACCCCACTCAGT 59.156 43.478 0.00 0.00 33.92 3.41
92 93 4.487714 ACAATGTGTATACCCCACTCAG 57.512 45.455 0.00 0.00 33.92 3.35
93 94 4.287326 TGAACAATGTGTATACCCCACTCA 59.713 41.667 0.00 0.00 33.92 3.41
94 95 4.839121 TGAACAATGTGTATACCCCACTC 58.161 43.478 0.00 0.00 33.92 3.51
95 96 4.919774 TGAACAATGTGTATACCCCACT 57.080 40.909 0.00 0.00 33.92 4.00
96 97 5.968528 TTTGAACAATGTGTATACCCCAC 57.031 39.130 0.00 0.00 0.00 4.61
97 98 6.978674 TTTTTGAACAATGTGTATACCCCA 57.021 33.333 0.00 0.00 0.00 4.96
98 99 8.745590 ACTATTTTTGAACAATGTGTATACCCC 58.254 33.333 0.00 0.00 0.00 4.95
105 106 9.665719 AAAGGAAACTATTTTTGAACAATGTGT 57.334 25.926 0.00 0.00 42.68 3.72
119 120 9.433153 CGGTCTAAACTCTAAAAGGAAACTATT 57.567 33.333 0.00 0.00 42.68 1.73
129 130 6.661304 AAGAGGACGGTCTAAACTCTAAAA 57.339 37.500 12.89 0.00 37.53 1.52
156 157 9.360093 CATTACTTGGACTAAACTCACTCTTAG 57.640 37.037 0.00 0.00 0.00 2.18
160 161 7.492994 GGATCATTACTTGGACTAAACTCACTC 59.507 40.741 0.00 0.00 0.00 3.51
176 177 4.271807 TGGAGAGGACTGGATCATTACT 57.728 45.455 0.00 0.00 0.00 2.24
188 189 4.466015 AGAAGAAGAACAGATGGAGAGGAC 59.534 45.833 0.00 0.00 0.00 3.85
200 201 9.712305 CCTTTCACTTAGAATAGAAGAAGAACA 57.288 33.333 0.00 0.00 35.83 3.18
201 202 9.157104 CCCTTTCACTTAGAATAGAAGAAGAAC 57.843 37.037 0.00 0.00 35.83 3.01
202 203 8.881262 ACCCTTTCACTTAGAATAGAAGAAGAA 58.119 33.333 0.00 0.00 35.83 2.52
350 351 4.356442 GCGGGTTTGGCGTGCATT 62.356 61.111 0.00 0.00 0.00 3.56
404 405 2.043248 GGACGGTGGCTAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
456 462 4.615815 AGGATGCCGGCGAGATGC 62.616 66.667 23.90 15.41 45.38 3.91
476 499 2.665008 GATGGCTGCATACCGCTGGA 62.665 60.000 0.50 0.00 43.06 3.86
547 577 0.751277 CCCGCAGCAATCCACCATAA 60.751 55.000 0.00 0.00 0.00 1.90
595 625 0.467844 AGCAATGACAACAGCCCACA 60.468 50.000 0.00 0.00 0.00 4.17
599 629 2.493278 ACCATAAGCAATGACAACAGCC 59.507 45.455 0.89 0.00 37.86 4.85
605 635 4.381825 GCATTTCCACCATAAGCAATGACA 60.382 41.667 0.89 0.00 37.86 3.58
630 660 3.054361 AGACTAATCGCCAACCTCCAAAT 60.054 43.478 0.00 0.00 0.00 2.32
662 693 5.882557 AGTAGTAAGCAATCATGGAGTTTGG 59.117 40.000 0.00 0.00 0.00 3.28
700 1650 2.421952 GGCCCATCACATCACACTACAT 60.422 50.000 0.00 0.00 0.00 2.29
720 1670 2.584835 TCCATCAACCAAGACAAGGG 57.415 50.000 0.00 0.00 0.00 3.95
756 1714 8.938906 CCAAATCAAATTTTAACATGGAAGAGG 58.061 33.333 0.00 0.00 0.00 3.69
813 1773 2.677836 CACAAGGACCAACCATATCACG 59.322 50.000 0.00 0.00 42.04 4.35
898 2388 1.172175 TCAAGCAACACACTGTGCAA 58.828 45.000 9.20 0.00 36.98 4.08
899 2389 1.391577 ATCAAGCAACACACTGTGCA 58.608 45.000 9.20 0.00 36.98 4.57
900 2390 2.121786 CAATCAAGCAACACACTGTGC 58.878 47.619 9.20 0.00 36.98 4.57
901 2391 3.425577 ACAATCAAGCAACACACTGTG 57.574 42.857 7.68 7.68 39.75 3.66
902 2392 5.278463 GGATAACAATCAAGCAACACACTGT 60.278 40.000 0.00 0.00 0.00 3.55
903 2393 5.156355 GGATAACAATCAAGCAACACACTG 58.844 41.667 0.00 0.00 0.00 3.66
904 2394 4.826733 TGGATAACAATCAAGCAACACACT 59.173 37.500 0.00 0.00 0.00 3.55
929 2419 0.102844 TTGCCTGCAGTGCAAAGTTC 59.897 50.000 28.91 6.98 45.11 3.01
1032 2522 1.067199 GCAGCCGTTTCATCTTTGCG 61.067 55.000 0.00 0.00 0.00 4.85
1073 2563 3.114616 CTTCGGCACTCCAGCACG 61.115 66.667 0.00 0.00 35.83 5.34
1079 2569 1.001633 TCTTGTAACCTTCGGCACTCC 59.998 52.381 0.00 0.00 0.00 3.85
1109 2599 3.891366 CCCAGCCCTATTGTAGAATTTGG 59.109 47.826 0.00 0.00 0.00 3.28
1119 2611 1.338136 ACCTCGTCCCAGCCCTATTG 61.338 60.000 0.00 0.00 0.00 1.90
1120 2612 0.263765 TACCTCGTCCCAGCCCTATT 59.736 55.000 0.00 0.00 0.00 1.73
1125 2617 1.144057 CACATACCTCGTCCCAGCC 59.856 63.158 0.00 0.00 0.00 4.85
1132 2624 1.135083 CCGCTTCTTCACATACCTCGT 60.135 52.381 0.00 0.00 0.00 4.18
1133 2625 1.135083 ACCGCTTCTTCACATACCTCG 60.135 52.381 0.00 0.00 0.00 4.63
1194 2686 3.831911 TCAAAGATTTGGGTTCCATCCAC 59.168 43.478 5.52 0.00 38.66 4.02
1331 2826 5.666969 TGAGTTGGTTCATACGTGAAAAG 57.333 39.130 0.00 0.00 45.38 2.27
1337 2832 8.506168 AAATATCAATGAGTTGGTTCATACGT 57.494 30.769 0.00 0.00 36.81 3.57
1338 2833 9.225201 CAAAATATCAATGAGTTGGTTCATACG 57.775 33.333 0.00 0.00 36.81 3.06
1394 2892 0.539438 GTGGCCCATGTGGAACTTCA 60.539 55.000 0.00 0.00 38.04 3.02
1395 2893 1.586154 CGTGGCCCATGTGGAACTTC 61.586 60.000 0.00 0.00 38.04 3.01
1463 2961 4.079038 TCCAGGGACAATGGATGATTCATT 60.079 41.667 0.00 0.00 41.96 2.57
1464 2962 3.464456 TCCAGGGACAATGGATGATTCAT 59.536 43.478 0.00 0.00 41.96 2.57
1534 3034 1.211969 CATCGTCGTCTGACCCGTT 59.788 57.895 12.38 4.11 42.37 4.44
1610 3113 0.737715 CAAGTCTTCCTTCGGGCTCG 60.738 60.000 0.00 0.00 37.82 5.03
1616 3119 6.758416 TCATCATGTAATCAAGTCTTCCTTCG 59.242 38.462 0.00 0.00 0.00 3.79
1698 3201 5.357032 ACCCGTTCATTCAAATATTCAGGAC 59.643 40.000 0.00 0.00 0.00 3.85
1718 3221 1.194547 CGTGATTCTTGACAACACCCG 59.805 52.381 0.00 0.00 0.00 5.28
1732 3235 1.952990 TGGACAAATGTGCACGTGATT 59.047 42.857 22.23 7.49 41.48 2.57
1773 3276 7.814107 CGGTGTACATAAGAACTACTGGTTAAA 59.186 37.037 0.00 0.00 38.41 1.52
1782 3288 6.349611 GGAACTGACGGTGTACATAAGAACTA 60.350 42.308 0.00 0.00 0.00 2.24
1809 3315 6.162777 TGCTTATATTTTGCCAACAAAGTCC 58.837 36.000 0.00 0.00 46.08 3.85
1831 3337 3.297830 AAACCCTAGCGTTTGATTTGC 57.702 42.857 4.72 0.00 34.68 3.68
1832 3338 5.622770 AGTAAACCCTAGCGTTTGATTTG 57.377 39.130 14.44 0.00 36.63 2.32
1856 3362 3.882102 AATCAAGGCCCTATGCATACA 57.118 42.857 1.16 0.00 43.89 2.29
1917 3423 7.298122 CGATACAATTTCTTTATAATGCGCCT 58.702 34.615 4.18 0.00 0.00 5.52
1948 3454 8.837059 CAACAAAAATAACTTAGTCCGAAATCG 58.163 33.333 0.00 0.00 39.44 3.34
1988 3494 9.702253 AGGATAATACTCGGTCTATATCATTGT 57.298 33.333 0.00 0.00 0.00 2.71
2014 3520 6.126409 ACCCAGTTTCAGTTCATTTTCTACA 58.874 36.000 0.00 0.00 0.00 2.74
2034 3540 2.970324 GACAAACGCAGCGACCCA 60.970 61.111 24.65 0.00 0.00 4.51
2044 3550 2.351418 TGAACACTGCAAGAGACAAACG 59.649 45.455 0.00 0.00 37.43 3.60
2049 3555 0.871057 GCCTGAACACTGCAAGAGAC 59.129 55.000 0.00 0.00 37.43 3.36
2117 3623 3.323979 AGAACGGTTCCTCTCAAGCTTTA 59.676 43.478 16.84 0.00 0.00 1.85
2225 3731 7.715265 TCAGATTTCAAAGACAAGTACAGAC 57.285 36.000 0.00 0.00 0.00 3.51
2379 3890 1.039856 GTTGGTCAACATTGTGGGCT 58.960 50.000 8.77 0.00 40.84 5.19
2382 3893 1.028905 ACCGTTGGTCAACATTGTGG 58.971 50.000 13.35 8.41 41.20 4.17
2421 3932 7.709613 AGTTTGTTTCCGATATATGTACAGGTC 59.290 37.037 0.33 0.00 0.00 3.85
2437 3948 6.972901 CCAAGAAGTTCAGTAAGTTTGTTTCC 59.027 38.462 5.50 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.