Multiple sequence alignment - TraesCS2D01G194800

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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 TraesCS2D01G194800 chr2D 100.000 3791 0 0 1 3791 140552033 140548243 0.000000e+00 7001.0
1 TraesCS2D01G194800 chr2A 95.761 3326 90 23 130 3427 160685774 160689076 0.000000e+00 5313.0
2 TraesCS2D01G194800 chr2A 92.500 360 22 3 3434 3791 160689110 160689466 9.390000e-141 510.0
3 TraesCS2D01G194800 chr2B 94.698 3093 87 30 375 3427 199529792 199532847 0.000000e+00 4732.0
4 TraesCS2D01G194800 chr2B 84.135 208 19 10 3596 3791 199532963 199533168 5.000000e-44 189.0
5 TraesCS2D01G194800 chr3A 86.466 133 18 0 5 137 464597773 464597641 3.050000e-31 147.0
6 TraesCS2D01G194800 chr3D 87.302 126 13 2 3 127 613444386 613444263 1.420000e-29 141.0
7 TraesCS2D01G194800 chr3D 94.595 37 2 0 98 134 563840160 563840124 1.470000e-04 58.4


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 TraesCS2D01G194800 chr2D 140548243 140552033 3790 True 7001.0 7001 100.0000 1 3791 1 chr2D.!!$R1 3790
1 TraesCS2D01G194800 chr2A 160685774 160689466 3692 False 2911.5 5313 94.1305 130 3791 2 chr2A.!!$F1 3661
2 TraesCS2D01G194800 chr2B 199529792 199533168 3376 False 2460.5 4732 89.4165 375 3791 2 chr2B.!!$F1 3416

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
63 64 0.097674 GCCACACGCACAATCTCATC 59.902 55.0 0.0 0.0 37.47 2.92 F
1204 1254 0.248949 GTACTACTACAGCCAGCCGC 60.249 60.0 0.0 0.0 37.98 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1742 1.524482 CTGCAGGAAGTAGGAGGCC 59.476 63.158 5.57 0.00 0.00 5.19 R
2878 2935 0.315301 CTACATGCGCGTACGACGTA 60.315 55.000 21.65 20.68 44.73 3.57 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
17 18 4.039042 GCCGGAAGTGGGTAGGTA 57.961 61.111 5.05 0.00 0.00 3.08
18 19 2.524611 GCCGGAAGTGGGTAGGTAT 58.475 57.895 5.05 0.00 0.00 2.73
19 20 1.708341 GCCGGAAGTGGGTAGGTATA 58.292 55.000 5.05 0.00 0.00 1.47
20 21 1.342496 GCCGGAAGTGGGTAGGTATAC 59.658 57.143 5.05 0.00 0.00 1.47
21 22 2.954792 CCGGAAGTGGGTAGGTATACT 58.045 52.381 0.00 0.00 32.12 2.12
22 23 3.751893 GCCGGAAGTGGGTAGGTATACTA 60.752 52.174 5.05 0.00 32.12 1.82
35 36 7.593875 GTAGGTATACTACGAGTATGAGGTG 57.406 44.000 14.14 0.00 41.23 4.00
36 37 6.430962 AGGTATACTACGAGTATGAGGTGA 57.569 41.667 14.14 0.00 41.23 4.02
37 38 6.229733 AGGTATACTACGAGTATGAGGTGAC 58.770 44.000 14.14 6.41 41.23 3.67
38 39 5.994054 GGTATACTACGAGTATGAGGTGACA 59.006 44.000 14.14 0.00 41.23 3.58
39 40 6.147492 GGTATACTACGAGTATGAGGTGACAG 59.853 46.154 14.14 0.00 41.23 3.51
40 41 3.280295 ACTACGAGTATGAGGTGACAGG 58.720 50.000 0.00 0.00 0.00 4.00
41 42 1.475403 ACGAGTATGAGGTGACAGGG 58.525 55.000 0.00 0.00 0.00 4.45
42 43 0.103208 CGAGTATGAGGTGACAGGGC 59.897 60.000 0.00 0.00 0.00 5.19
43 44 1.490574 GAGTATGAGGTGACAGGGCT 58.509 55.000 0.00 0.00 0.00 5.19
44 45 1.137872 GAGTATGAGGTGACAGGGCTG 59.862 57.143 0.00 0.00 0.00 4.85
45 46 0.462759 GTATGAGGTGACAGGGCTGC 60.463 60.000 0.00 0.00 0.00 5.25
46 47 1.626356 TATGAGGTGACAGGGCTGCC 61.626 60.000 11.05 11.05 0.00 4.85
47 48 3.640407 GAGGTGACAGGGCTGCCA 61.640 66.667 22.05 0.00 0.00 4.92
48 49 3.909086 GAGGTGACAGGGCTGCCAC 62.909 68.421 22.05 9.34 42.18 5.01
49 50 4.269523 GGTGACAGGGCTGCCACA 62.270 66.667 22.05 11.55 44.24 4.17
50 51 2.980233 GTGACAGGGCTGCCACAC 60.980 66.667 22.05 18.74 42.41 3.82
51 52 4.624364 TGACAGGGCTGCCACACG 62.624 66.667 22.05 7.64 0.00 4.49
57 58 3.673484 GGCTGCCACACGCACAAT 61.673 61.111 15.17 0.00 44.64 2.71
58 59 2.126734 GCTGCCACACGCACAATC 60.127 61.111 0.00 0.00 44.64 2.67
59 60 2.620112 GCTGCCACACGCACAATCT 61.620 57.895 0.00 0.00 44.64 2.40
60 61 1.499056 CTGCCACACGCACAATCTC 59.501 57.895 0.00 0.00 44.64 2.75
61 62 1.227793 TGCCACACGCACAATCTCA 60.228 52.632 0.00 0.00 44.64 3.27
62 63 0.606130 TGCCACACGCACAATCTCAT 60.606 50.000 0.00 0.00 44.64 2.90
63 64 0.097674 GCCACACGCACAATCTCATC 59.902 55.000 0.00 0.00 37.47 2.92
64 65 1.730501 CCACACGCACAATCTCATCT 58.269 50.000 0.00 0.00 0.00 2.90
65 66 2.892374 CCACACGCACAATCTCATCTA 58.108 47.619 0.00 0.00 0.00 1.98
66 67 2.604914 CCACACGCACAATCTCATCTAC 59.395 50.000 0.00 0.00 0.00 2.59
67 68 3.253230 CACACGCACAATCTCATCTACA 58.747 45.455 0.00 0.00 0.00 2.74
68 69 3.061295 CACACGCACAATCTCATCTACAC 59.939 47.826 0.00 0.00 0.00 2.90
69 70 3.253230 CACGCACAATCTCATCTACACA 58.747 45.455 0.00 0.00 0.00 3.72
70 71 3.679502 CACGCACAATCTCATCTACACAA 59.320 43.478 0.00 0.00 0.00 3.33
71 72 3.679980 ACGCACAATCTCATCTACACAAC 59.320 43.478 0.00 0.00 0.00 3.32
72 73 3.679502 CGCACAATCTCATCTACACAACA 59.320 43.478 0.00 0.00 0.00 3.33
73 74 4.330894 CGCACAATCTCATCTACACAACAT 59.669 41.667 0.00 0.00 0.00 2.71
74 75 5.566623 GCACAATCTCATCTACACAACATG 58.433 41.667 0.00 0.00 0.00 3.21
75 76 5.122869 GCACAATCTCATCTACACAACATGT 59.877 40.000 0.00 0.00 46.06 3.21
76 77 6.313658 GCACAATCTCATCTACACAACATGTA 59.686 38.462 0.00 0.00 43.19 2.29
77 78 7.011763 GCACAATCTCATCTACACAACATGTAT 59.988 37.037 0.00 0.00 43.01 2.29
78 79 9.533253 CACAATCTCATCTACACAACATGTATA 57.467 33.333 0.00 0.00 43.01 1.47
81 82 9.716531 AATCTCATCTACACAACATGTATATGG 57.283 33.333 0.00 0.00 43.59 2.74
82 83 8.477419 TCTCATCTACACAACATGTATATGGA 57.523 34.615 0.00 0.00 43.59 3.41
83 84 8.579863 TCTCATCTACACAACATGTATATGGAG 58.420 37.037 0.00 4.26 43.59 3.86
84 85 7.154656 TCATCTACACAACATGTATATGGAGC 58.845 38.462 0.00 0.00 43.59 4.70
85 86 6.731292 TCTACACAACATGTATATGGAGCT 57.269 37.500 0.00 0.00 43.01 4.09
86 87 7.833285 TCTACACAACATGTATATGGAGCTA 57.167 36.000 0.00 0.00 43.01 3.32
87 88 7.886338 TCTACACAACATGTATATGGAGCTAG 58.114 38.462 0.00 0.00 43.01 3.42
88 89 6.485830 ACACAACATGTATATGGAGCTAGT 57.514 37.500 0.00 0.00 40.88 2.57
89 90 6.889198 ACACAACATGTATATGGAGCTAGTT 58.111 36.000 0.00 0.00 40.88 2.24
90 91 8.018537 ACACAACATGTATATGGAGCTAGTTA 57.981 34.615 0.00 0.00 40.88 2.24
91 92 8.651389 ACACAACATGTATATGGAGCTAGTTAT 58.349 33.333 0.00 0.00 40.88 1.89
92 93 9.494271 CACAACATGTATATGGAGCTAGTTATT 57.506 33.333 0.00 0.00 38.66 1.40
95 96 9.507329 AACATGTATATGGAGCTAGTTATTTGG 57.493 33.333 0.00 0.00 38.66 3.28
96 97 8.660435 ACATGTATATGGAGCTAGTTATTTGGT 58.340 33.333 0.00 0.00 38.66 3.67
97 98 9.507329 CATGTATATGGAGCTAGTTATTTGGTT 57.493 33.333 0.00 0.00 0.00 3.67
99 100 9.914834 TGTATATGGAGCTAGTTATTTGGTTTT 57.085 29.630 0.00 0.00 0.00 2.43
114 115 4.403976 TTTTTCCGGTTGCAACGC 57.596 50.000 22.67 14.53 0.00 4.84
115 116 1.511305 TTTTTCCGGTTGCAACGCA 59.489 47.368 22.67 6.57 36.47 5.24
116 117 0.802607 TTTTTCCGGTTGCAACGCAC 60.803 50.000 22.67 8.75 38.71 5.34
117 118 2.921538 TTTTCCGGTTGCAACGCACG 62.922 55.000 22.67 19.36 38.71 5.34
122 123 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
123 124 4.340019 TTGCAACGCACGGGCATG 62.340 61.111 11.77 9.58 38.71 4.06
125 126 4.341502 GCAACGCACGGGCATGTT 62.342 61.111 11.77 3.22 41.24 2.71
126 127 2.334653 CAACGCACGGGCATGTTT 59.665 55.556 11.77 0.00 41.24 2.83
127 128 1.729131 CAACGCACGGGCATGTTTC 60.729 57.895 11.77 0.00 41.24 2.78
128 129 2.914908 AACGCACGGGCATGTTTCC 61.915 57.895 11.77 0.00 41.24 3.13
129 130 3.055719 CGCACGGGCATGTTTCCT 61.056 61.111 11.77 0.00 41.24 3.36
130 131 1.743623 CGCACGGGCATGTTTCCTA 60.744 57.895 11.77 0.00 41.24 2.94
131 132 1.800681 GCACGGGCATGTTTCCTAC 59.199 57.895 3.77 0.00 40.72 3.18
132 133 0.676782 GCACGGGCATGTTTCCTACT 60.677 55.000 3.77 0.00 40.72 2.57
133 134 1.406341 GCACGGGCATGTTTCCTACTA 60.406 52.381 3.77 0.00 40.72 1.82
153 154 9.495572 CCTACTATTTCCAATTGATCTTCCTAC 57.504 37.037 7.12 0.00 0.00 3.18
154 155 9.197694 CTACTATTTCCAATTGATCTTCCTACG 57.802 37.037 7.12 0.00 0.00 3.51
161 162 5.925397 CCAATTGATCTTCCTACGATCTCTG 59.075 44.000 7.12 0.00 38.43 3.35
162 163 6.239148 CCAATTGATCTTCCTACGATCTCTGA 60.239 42.308 7.12 0.00 38.43 3.27
168 169 7.497579 TGATCTTCCTACGATCTCTGATATAGC 59.502 40.741 0.00 0.00 38.43 2.97
200 201 3.775316 AGAGATGTGGTAGGGTTAGTTGG 59.225 47.826 0.00 0.00 0.00 3.77
204 205 2.224670 TGTGGTAGGGTTAGTTGGCTTG 60.225 50.000 0.00 0.00 0.00 4.01
206 207 2.444010 TGGTAGGGTTAGTTGGCTTGTT 59.556 45.455 0.00 0.00 0.00 2.83
208 209 4.104420 TGGTAGGGTTAGTTGGCTTGTTAA 59.896 41.667 0.00 0.00 0.00 2.01
263 264 7.672983 ATTTCGATGAATACAGTTGAGTTGT 57.327 32.000 0.00 0.00 0.00 3.32
283 284 9.685828 GAGTTGTATTCTATAGCTTTCTACAGG 57.314 37.037 0.00 0.00 0.00 4.00
332 333 0.960861 TGACAACACAACCACGCCAA 60.961 50.000 0.00 0.00 0.00 4.52
490 508 2.029918 GCCAACAGAAAGCCCTAACAAG 60.030 50.000 0.00 0.00 0.00 3.16
683 703 0.264359 CATCACCTCTCTCCCTCCCT 59.736 60.000 0.00 0.00 0.00 4.20
712 732 4.536687 CGATCCGGCCAAAAGCGC 62.537 66.667 2.24 0.00 45.17 5.92
842 863 3.422303 CATCGCCACACCACACCG 61.422 66.667 0.00 0.00 0.00 4.94
856 877 3.151710 ACCGCACCGCATAGCCTA 61.152 61.111 0.00 0.00 0.00 3.93
1044 1079 2.186384 CTCCAAGCCTCCGAGCAG 59.814 66.667 0.00 0.00 34.23 4.24
1045 1080 4.087892 TCCAAGCCTCCGAGCAGC 62.088 66.667 0.00 0.00 34.23 5.25
1046 1081 4.399395 CCAAGCCTCCGAGCAGCA 62.399 66.667 0.00 0.00 34.23 4.41
1047 1082 2.818714 CAAGCCTCCGAGCAGCAG 60.819 66.667 0.00 0.00 34.23 4.24
1048 1083 4.774503 AAGCCTCCGAGCAGCAGC 62.775 66.667 0.00 0.00 42.56 5.25
1202 1252 1.202428 GCAGTACTACTACAGCCAGCC 60.202 57.143 0.00 0.00 30.89 4.85
1203 1253 1.065701 CAGTACTACTACAGCCAGCCG 59.934 57.143 0.00 0.00 0.00 5.52
1204 1254 0.248949 GTACTACTACAGCCAGCCGC 60.249 60.000 0.00 0.00 37.98 6.53
1205 1255 0.681887 TACTACTACAGCCAGCCGCA 60.682 55.000 0.00 0.00 41.38 5.69
1206 1256 1.227089 CTACTACAGCCAGCCGCAG 60.227 63.158 0.00 0.00 41.38 5.18
1207 1257 3.371097 TACTACAGCCAGCCGCAGC 62.371 63.158 0.00 0.00 41.38 5.25
1208 1258 4.765449 CTACAGCCAGCCGCAGCA 62.765 66.667 8.00 0.00 43.56 4.41
1209 1259 4.765449 TACAGCCAGCCGCAGCAG 62.765 66.667 8.00 2.73 43.56 4.24
1640 1693 1.625759 CGCGTGCAACAGCTGATGTA 61.626 55.000 23.35 16.45 43.00 2.29
2241 2294 0.673333 TCGCCGTCAACTGCATGAAT 60.673 50.000 0.00 0.00 0.00 2.57
2517 2570 0.984961 CATTGGAGAGGGGAGCAGGA 60.985 60.000 0.00 0.00 0.00 3.86
2878 2935 0.544357 TGGGTCCTCAGATCAACGGT 60.544 55.000 0.00 0.00 0.00 4.83
2880 2937 1.136500 GGGTCCTCAGATCAACGGTAC 59.864 57.143 0.00 0.00 0.00 3.34
3143 3205 8.319143 TGTAAGGTTAAGAAATTCTTCTTCCG 57.681 34.615 11.97 0.00 46.88 4.30
3183 3245 1.328680 CGTGCATGCTTCTGTCATACC 59.671 52.381 20.33 0.00 0.00 2.73
3225 3303 5.220340 GCATGCTTGCTTACTTTTGCATTAG 60.220 40.000 16.80 0.00 45.77 1.73
3352 3436 6.072112 TCAAACATGAACCACTAAAGCTTC 57.928 37.500 0.00 0.00 0.00 3.86
3405 3489 7.504924 TCGTTTCTATTTGTTTCAGGAATGT 57.495 32.000 0.00 0.00 0.00 2.71
3427 3512 5.011329 TGTTCTCGTTAAGCCTTTCCTTCTA 59.989 40.000 0.00 0.00 0.00 2.10
3429 3514 7.093640 TGTTCTCGTTAAGCCTTTCCTTCTATA 60.094 37.037 0.00 0.00 0.00 1.31
3431 3516 7.434492 TCTCGTTAAGCCTTTCCTTCTATATG 58.566 38.462 0.00 0.00 0.00 1.78
3432 3517 7.069578 TCTCGTTAAGCCTTTCCTTCTATATGT 59.930 37.037 0.00 0.00 0.00 2.29
3456 3568 9.047371 TGTCAACACGAAAGAAAACTATATTGA 57.953 29.630 0.00 0.00 0.00 2.57
3466 3578 7.667043 AGAAAACTATATTGAACAGCGTCAA 57.333 32.000 3.49 3.49 41.59 3.18
3468 3580 8.177663 AGAAAACTATATTGAACAGCGTCAATG 58.822 33.333 18.09 8.43 45.62 2.82
3490 3602 5.948588 TGCGCAAACAAAGATTATGTATGT 58.051 33.333 8.16 0.00 0.00 2.29
3496 3608 9.065871 GCAAACAAAGATTATGTATGTCACTTC 57.934 33.333 0.00 0.00 0.00 3.01
3500 3612 9.167311 ACAAAGATTATGTATGTCACTTCCTTC 57.833 33.333 0.00 0.00 0.00 3.46
3522 3635 3.686726 CACCTGATCCAAAAGAGTAGCAC 59.313 47.826 0.00 0.00 0.00 4.40
3542 3655 2.840651 ACTAGGTCAATGTTCAGAGGGG 59.159 50.000 0.00 0.00 0.00 4.79
3549 3662 2.821969 CAATGTTCAGAGGGGTCTTTGG 59.178 50.000 0.00 0.00 0.00 3.28
3572 3685 1.464997 GATCTCCGGCTGACACAAAAC 59.535 52.381 0.00 0.00 0.00 2.43
3621 3734 6.801718 TTAAGCTAGTGCCAAATACCTCTA 57.198 37.500 0.00 0.00 40.80 2.43
3701 3822 2.846206 TGAGAGTGACAAATGGCCCTAT 59.154 45.455 0.00 0.00 0.00 2.57
3702 3823 4.037222 TGAGAGTGACAAATGGCCCTATA 58.963 43.478 0.00 0.00 0.00 1.31
3744 3866 2.482721 GACAATACCTGGTGAAACGGTG 59.517 50.000 10.23 0.00 38.12 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.342496 GTATACCTACCCACTTCCGGC 59.658 57.143 0.00 0.00 0.00 6.13
1 2 2.954792 AGTATACCTACCCACTTCCGG 58.045 52.381 0.00 0.00 0.00 5.14
3 4 4.718961 TCGTAGTATACCTACCCACTTCC 58.281 47.826 0.00 0.00 42.69 3.46
4 5 5.372373 ACTCGTAGTATACCTACCCACTTC 58.628 45.833 0.00 0.00 42.69 3.01
6 7 6.270927 TCATACTCGTAGTATACCTACCCACT 59.729 42.308 0.00 0.00 42.69 4.00
7 8 6.467677 TCATACTCGTAGTATACCTACCCAC 58.532 44.000 0.00 0.00 42.69 4.61
8 9 6.296087 CCTCATACTCGTAGTATACCTACCCA 60.296 46.154 0.00 0.00 42.69 4.51
9 10 6.112058 CCTCATACTCGTAGTATACCTACCC 58.888 48.000 0.00 0.00 42.69 3.69
10 11 6.593382 CACCTCATACTCGTAGTATACCTACC 59.407 46.154 0.00 0.00 42.69 3.18
11 12 7.330700 GTCACCTCATACTCGTAGTATACCTAC 59.669 44.444 0.00 1.41 39.26 3.18
12 13 7.015584 TGTCACCTCATACTCGTAGTATACCTA 59.984 40.741 0.00 0.00 39.26 3.08
13 14 6.183361 TGTCACCTCATACTCGTAGTATACCT 60.183 42.308 0.00 0.00 39.26 3.08
14 15 5.994054 TGTCACCTCATACTCGTAGTATACC 59.006 44.000 0.00 0.00 39.26 2.73
15 16 6.147492 CCTGTCACCTCATACTCGTAGTATAC 59.853 46.154 0.00 0.00 39.26 1.47
16 17 6.228995 CCTGTCACCTCATACTCGTAGTATA 58.771 44.000 7.06 0.00 39.26 1.47
17 18 5.064558 CCTGTCACCTCATACTCGTAGTAT 58.935 45.833 2.79 2.79 41.82 2.12
18 19 4.449131 CCTGTCACCTCATACTCGTAGTA 58.551 47.826 0.00 0.00 34.82 1.82
19 20 3.280295 CCTGTCACCTCATACTCGTAGT 58.720 50.000 0.00 0.00 0.00 2.73
20 21 2.619177 CCCTGTCACCTCATACTCGTAG 59.381 54.545 0.00 0.00 0.00 3.51
21 22 2.651455 CCCTGTCACCTCATACTCGTA 58.349 52.381 0.00 0.00 0.00 3.43
22 23 1.475403 CCCTGTCACCTCATACTCGT 58.525 55.000 0.00 0.00 0.00 4.18
23 24 0.103208 GCCCTGTCACCTCATACTCG 59.897 60.000 0.00 0.00 0.00 4.18
24 25 1.137872 CAGCCCTGTCACCTCATACTC 59.862 57.143 0.00 0.00 0.00 2.59
25 26 1.198713 CAGCCCTGTCACCTCATACT 58.801 55.000 0.00 0.00 0.00 2.12
26 27 0.462759 GCAGCCCTGTCACCTCATAC 60.463 60.000 0.00 0.00 0.00 2.39
27 28 1.626356 GGCAGCCCTGTCACCTCATA 61.626 60.000 0.00 0.00 34.82 2.15
28 29 2.673523 GCAGCCCTGTCACCTCAT 59.326 61.111 0.00 0.00 0.00 2.90
29 30 3.640407 GGCAGCCCTGTCACCTCA 61.640 66.667 0.00 0.00 34.82 3.86
30 31 3.640407 TGGCAGCCCTGTCACCTC 61.640 66.667 9.64 0.00 40.71 3.85
34 35 4.624364 CGTGTGGCAGCCCTGTCA 62.624 66.667 9.64 0.00 43.73 3.58
44 45 0.097674 GATGAGATTGTGCGTGTGGC 59.902 55.000 0.00 0.00 43.96 5.01
45 46 1.730501 AGATGAGATTGTGCGTGTGG 58.269 50.000 0.00 0.00 0.00 4.17
46 47 3.061295 GTGTAGATGAGATTGTGCGTGTG 59.939 47.826 0.00 0.00 0.00 3.82
47 48 3.254060 GTGTAGATGAGATTGTGCGTGT 58.746 45.455 0.00 0.00 0.00 4.49
48 49 3.253230 TGTGTAGATGAGATTGTGCGTG 58.747 45.455 0.00 0.00 0.00 5.34
49 50 3.592898 TGTGTAGATGAGATTGTGCGT 57.407 42.857 0.00 0.00 0.00 5.24
50 51 3.679502 TGTTGTGTAGATGAGATTGTGCG 59.320 43.478 0.00 0.00 0.00 5.34
51 52 5.122869 ACATGTTGTGTAGATGAGATTGTGC 59.877 40.000 0.00 0.00 39.91 4.57
52 53 6.732531 ACATGTTGTGTAGATGAGATTGTG 57.267 37.500 0.00 0.00 39.91 3.33
61 62 7.308450 AGCTCCATATACATGTTGTGTAGAT 57.692 36.000 2.30 0.00 45.94 1.98
62 63 6.731292 AGCTCCATATACATGTTGTGTAGA 57.269 37.500 2.30 0.00 45.94 2.59
63 64 7.661968 ACTAGCTCCATATACATGTTGTGTAG 58.338 38.462 2.30 0.00 45.94 2.74
64 65 7.597288 ACTAGCTCCATATACATGTTGTGTA 57.403 36.000 2.30 0.00 46.73 2.90
65 66 6.485830 ACTAGCTCCATATACATGTTGTGT 57.514 37.500 2.30 0.00 44.95 3.72
66 67 9.494271 AATAACTAGCTCCATATACATGTTGTG 57.506 33.333 2.30 0.52 0.00 3.33
69 70 9.507329 CCAAATAACTAGCTCCATATACATGTT 57.493 33.333 2.30 0.00 0.00 2.71
70 71 8.660435 ACCAAATAACTAGCTCCATATACATGT 58.340 33.333 2.69 2.69 0.00 3.21
71 72 9.507329 AACCAAATAACTAGCTCCATATACATG 57.493 33.333 0.00 0.00 0.00 3.21
73 74 9.914834 AAAACCAAATAACTAGCTCCATATACA 57.085 29.630 0.00 0.00 0.00 2.29
97 98 0.802607 GTGCGTTGCAACCGGAAAAA 60.803 50.000 23.42 0.00 41.47 1.94
98 99 1.226717 GTGCGTTGCAACCGGAAAA 60.227 52.632 23.42 0.53 41.47 2.29
99 100 2.409651 GTGCGTTGCAACCGGAAA 59.590 55.556 23.42 2.31 41.47 3.13
100 101 3.943034 CGTGCGTTGCAACCGGAA 61.943 61.111 23.42 2.27 41.47 4.30
105 106 4.341502 ATGCCCGTGCGTTGCAAC 62.342 61.111 19.89 19.89 41.47 4.17
106 107 4.340019 CATGCCCGTGCGTTGCAA 62.340 61.111 0.00 0.00 41.47 4.08
108 109 3.839642 AAACATGCCCGTGCGTTGC 62.840 57.895 0.00 0.00 41.78 4.17
109 110 1.729131 GAAACATGCCCGTGCGTTG 60.729 57.895 0.00 0.00 41.78 4.10
110 111 2.642700 GAAACATGCCCGTGCGTT 59.357 55.556 0.00 0.00 41.78 4.84
111 112 2.457743 TAGGAAACATGCCCGTGCGT 62.458 55.000 0.00 0.00 41.78 5.24
112 113 1.743623 TAGGAAACATGCCCGTGCG 60.744 57.895 0.00 0.00 41.78 5.34
113 114 0.676782 AGTAGGAAACATGCCCGTGC 60.677 55.000 0.00 0.00 38.26 5.34
114 115 2.684001 TAGTAGGAAACATGCCCGTG 57.316 50.000 0.00 0.00 0.00 4.94
115 116 3.926058 AATAGTAGGAAACATGCCCGT 57.074 42.857 0.00 0.00 0.00 5.28
116 117 3.564225 GGAAATAGTAGGAAACATGCCCG 59.436 47.826 0.00 0.00 0.00 6.13
117 118 4.532834 TGGAAATAGTAGGAAACATGCCC 58.467 43.478 0.00 0.00 0.00 5.36
118 119 6.715347 ATTGGAAATAGTAGGAAACATGCC 57.285 37.500 0.00 0.00 0.00 4.40
119 120 7.771183 TCAATTGGAAATAGTAGGAAACATGC 58.229 34.615 5.42 0.00 0.00 4.06
120 121 9.956720 GATCAATTGGAAATAGTAGGAAACATG 57.043 33.333 5.42 0.00 0.00 3.21
121 122 9.927081 AGATCAATTGGAAATAGTAGGAAACAT 57.073 29.630 5.42 0.00 0.00 2.71
122 123 9.753674 AAGATCAATTGGAAATAGTAGGAAACA 57.246 29.630 5.42 0.00 0.00 2.83
124 125 9.408648 GGAAGATCAATTGGAAATAGTAGGAAA 57.591 33.333 5.42 0.00 0.00 3.13
125 126 8.781951 AGGAAGATCAATTGGAAATAGTAGGAA 58.218 33.333 5.42 0.00 0.00 3.36
126 127 8.337118 AGGAAGATCAATTGGAAATAGTAGGA 57.663 34.615 5.42 0.00 0.00 2.94
127 128 9.495572 GTAGGAAGATCAATTGGAAATAGTAGG 57.504 37.037 5.42 0.00 0.00 3.18
128 129 9.197694 CGTAGGAAGATCAATTGGAAATAGTAG 57.802 37.037 5.42 0.00 0.00 2.57
129 130 8.920174 TCGTAGGAAGATCAATTGGAAATAGTA 58.080 33.333 5.42 0.00 0.00 1.82
130 131 7.792032 TCGTAGGAAGATCAATTGGAAATAGT 58.208 34.615 5.42 0.00 0.00 2.12
131 132 8.839310 ATCGTAGGAAGATCAATTGGAAATAG 57.161 34.615 5.42 0.00 0.00 1.73
132 133 8.651389 AGATCGTAGGAAGATCAATTGGAAATA 58.349 33.333 5.42 0.00 45.05 1.40
133 134 7.512992 AGATCGTAGGAAGATCAATTGGAAAT 58.487 34.615 5.42 0.00 45.05 2.17
149 150 8.458573 AATTAGGCTATATCAGAGATCGTAGG 57.541 38.462 0.00 0.00 0.00 3.18
168 169 8.437274 ACCCTACCACATCTCTAATAATTAGG 57.563 38.462 0.00 0.00 34.00 2.69
176 177 5.424252 CCAACTAACCCTACCACATCTCTAA 59.576 44.000 0.00 0.00 0.00 2.10
184 185 2.224695 ACAAGCCAACTAACCCTACCAC 60.225 50.000 0.00 0.00 0.00 4.16
187 188 5.874895 CTTAACAAGCCAACTAACCCTAC 57.125 43.478 0.00 0.00 0.00 3.18
232 233 9.093970 TCAACTGTATTCATCGAAATTCGTTAT 57.906 29.630 15.34 0.00 41.35 1.89
240 241 8.771920 ATACAACTCAACTGTATTCATCGAAA 57.228 30.769 0.00 0.00 36.76 3.46
282 283 1.173913 AAACCACGCCAGCTATTTCC 58.826 50.000 0.00 0.00 0.00 3.13
283 284 3.687698 TCTAAAACCACGCCAGCTATTTC 59.312 43.478 0.00 0.00 0.00 2.17
440 458 1.167851 CGAACCCTGCATCAACACAT 58.832 50.000 0.00 0.00 0.00 3.21
683 703 0.609406 CCGGATCGATGAGGAGGCTA 60.609 60.000 0.54 0.00 0.00 3.93
712 732 0.243907 AGATCGATGGTATTCCGCCG 59.756 55.000 0.54 0.00 36.30 6.46
842 863 0.389166 CTAGCTAGGCTATGCGGTGC 60.389 60.000 13.32 0.00 40.54 5.01
856 877 4.755411 TGCGAATTGTTAGTTAGCTAGCT 58.245 39.130 23.12 23.12 30.92 3.32
1048 1083 2.100410 CGATTGCTGCTGCTGCTG 59.900 61.111 27.67 16.73 40.48 4.41
1049 1084 3.132139 CCGATTGCTGCTGCTGCT 61.132 61.111 27.67 12.31 40.48 4.24
1689 1742 1.524482 CTGCAGGAAGTAGGAGGCC 59.476 63.158 5.57 0.00 0.00 5.19
1815 1868 2.270527 GGGCTGAGCTCCTGGAAC 59.729 66.667 12.15 0.00 0.00 3.62
2517 2570 1.172180 CCAGGTCAACAATGGCACGT 61.172 55.000 0.00 0.00 30.82 4.49
2878 2935 0.315301 CTACATGCGCGTACGACGTA 60.315 55.000 21.65 20.68 44.73 3.57
2880 2937 2.283757 CCTACATGCGCGTACGACG 61.284 63.158 21.65 21.83 45.88 5.12
2881 2938 1.942712 CCCTACATGCGCGTACGAC 60.943 63.158 21.65 10.76 43.93 4.34
2882 2939 1.936436 AACCCTACATGCGCGTACGA 61.936 55.000 21.65 0.00 43.93 3.43
3091 3153 4.732923 CGATCGAAACACAAAAGCAAAGAA 59.267 37.500 10.26 0.00 0.00 2.52
3141 3203 1.318576 AGTTTGCTCCAAAAGGACGG 58.681 50.000 0.00 0.00 35.03 4.79
3143 3205 3.885358 CGTAAGTTTGCTCCAAAAGGAC 58.115 45.455 0.00 0.00 35.03 3.85
3203 3281 4.866486 GCTAATGCAAAAGTAAGCAAGCAT 59.134 37.500 0.00 0.00 44.88 3.79
3205 3283 3.301642 CGCTAATGCAAAAGTAAGCAAGC 59.698 43.478 0.00 0.00 44.88 4.01
3207 3285 4.757799 TCGCTAATGCAAAAGTAAGCAA 57.242 36.364 0.00 0.00 44.88 3.91
3208 3286 4.661125 CATCGCTAATGCAAAAGTAAGCA 58.339 39.130 0.00 0.00 45.92 3.91
3352 3436 5.503683 GCACCTACGTATATATGGTCTAGCG 60.504 48.000 6.89 0.00 0.00 4.26
3405 3489 4.618920 AGAAGGAAAGGCTTAACGAGAA 57.381 40.909 0.00 0.00 0.00 2.87
3429 3514 9.825972 CAATATAGTTTTCTTTCGTGTTGACAT 57.174 29.630 0.00 0.00 0.00 3.06
3431 3516 9.872757 TTCAATATAGTTTTCTTTCGTGTTGAC 57.127 29.630 0.00 0.00 0.00 3.18
3432 3517 9.872757 GTTCAATATAGTTTTCTTTCGTGTTGA 57.127 29.630 0.00 0.00 0.00 3.18
3466 3578 6.563422 ACATACATAATCTTTGTTTGCGCAT 58.437 32.000 12.75 0.00 31.67 4.73
3468 3580 6.021468 GTGACATACATAATCTTTGTTTGCGC 60.021 38.462 0.00 0.00 31.67 6.09
3471 3583 9.559958 GGAAGTGACATACATAATCTTTGTTTG 57.440 33.333 0.00 0.00 33.80 2.93
3490 3602 2.619931 TGGATCAGGTGAAGGAAGTGA 58.380 47.619 0.00 0.00 0.00 3.41
3496 3608 4.026356 ACTCTTTTGGATCAGGTGAAGG 57.974 45.455 0.00 0.00 0.00 3.46
3500 3612 3.686726 GTGCTACTCTTTTGGATCAGGTG 59.313 47.826 0.00 0.00 0.00 4.00
3522 3635 2.840651 ACCCCTCTGAACATTGACCTAG 59.159 50.000 0.00 0.00 0.00 3.02
3542 3655 0.179070 GCCGGAGATCTCCCAAAGAC 60.179 60.000 31.77 10.20 46.96 3.01
3549 3662 1.323271 TGTGTCAGCCGGAGATCTCC 61.323 60.000 29.15 29.15 46.18 3.71
3565 3678 6.090358 CACTACTCGTAATACCCTGTTTTGTG 59.910 42.308 0.00 0.00 0.00 3.33
3572 3685 3.243434 CCAGCACTACTCGTAATACCCTG 60.243 52.174 0.00 0.00 0.00 4.45
3730 3852 1.227823 TCTGCACCGTTTCACCAGG 60.228 57.895 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.