Multiple sequence alignment - TraesCS3D01G338100

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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 TraesCS3D01G338100 chr3D 100.000 2615 0 0 1 2615 451163581 451160967 0.000000e+00 4830.0
1 TraesCS3D01G338100 chr3B 90.792 2487 109 46 168 2615 592825870 592823465 0.000000e+00 3214.0
2 TraesCS3D01G338100 chr3A 89.556 1733 53 32 276 1955 594302282 594300625 0.000000e+00 2080.0
3 TraesCS3D01G338100 chr3A 86.100 482 52 14 2145 2615 594298522 594298045 3.000000e-139 505.0
4 TraesCS3D01G338100 chr1A 79.661 413 47 19 1099 1504 495332560 495332942 2.000000e-66 263.0
5 TraesCS3D01G338100 chr1D 77.672 421 61 18 1095 1504 398379933 398380331 2.620000e-55 226.0
6 TraesCS3D01G338100 chr1B 77.647 425 57 20 1120 1531 533815489 533815888 9.420000e-55 224.0
7 TraesCS3D01G338100 chr5A 87.805 164 15 5 1367 1528 520681110 520681270 1.240000e-43 187.0
8 TraesCS3D01G338100 chr5D 90.580 138 13 0 1367 1504 409575934 409576071 1.600000e-42 183.0
9 TraesCS3D01G338100 chr5B 89.855 138 14 0 1367 1504 491280364 491280501 7.440000e-41 178.0
10 TraesCS3D01G338100 chr5B 75.772 421 63 23 1121 1528 491246065 491246459 2.670000e-40 176.0
11 TraesCS3D01G338100 chr7B 94.118 51 2 1 224 273 409725662 409725612 2.790000e-10 76.8


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 TraesCS3D01G338100 chr3D 451160967 451163581 2614 True 4830.0 4830 100.000 1 2615 1 chr3D.!!$R1 2614
1 TraesCS3D01G338100 chr3B 592823465 592825870 2405 True 3214.0 3214 90.792 168 2615 1 chr3B.!!$R1 2447
2 TraesCS3D01G338100 chr3A 594298045 594302282 4237 True 1292.5 2080 87.828 276 2615 2 chr3A.!!$R1 2339

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
814 839 0.027455 CTCTAGCTCGCACTCACTCG 59.973 60.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2044 0.538977 AAGTGCTCAGCAGGTGCATT 60.539 50.0 0.0 2.35 46.52 3.56 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
30 31 9.651913 ATTTGACTCTTTTTAAAAACTTCAGCA 57.348 25.926 9.31 1.73 0.00 4.41
31 32 9.651913 TTTGACTCTTTTTAAAAACTTCAGCAT 57.348 25.926 9.31 0.00 0.00 3.79
43 44 7.883229 AAAACTTCAGCATAAAATAAACCGG 57.117 32.000 0.00 0.00 0.00 5.28
44 45 6.827586 AACTTCAGCATAAAATAAACCGGA 57.172 33.333 9.46 0.00 0.00 5.14
45 46 7.404671 AACTTCAGCATAAAATAAACCGGAT 57.595 32.000 9.46 0.00 0.00 4.18
46 47 7.027778 ACTTCAGCATAAAATAAACCGGATC 57.972 36.000 9.46 0.00 0.00 3.36
47 48 6.828785 ACTTCAGCATAAAATAAACCGGATCT 59.171 34.615 9.46 0.00 0.00 2.75
48 49 7.990886 ACTTCAGCATAAAATAAACCGGATCTA 59.009 33.333 9.46 0.00 0.00 1.98
49 50 8.740123 TTCAGCATAAAATAAACCGGATCTAA 57.260 30.769 9.46 0.00 0.00 2.10
50 51 8.740123 TCAGCATAAAATAAACCGGATCTAAA 57.260 30.769 9.46 0.00 0.00 1.85
51 52 9.179909 TCAGCATAAAATAAACCGGATCTAAAA 57.820 29.630 9.46 0.00 0.00 1.52
52 53 9.796120 CAGCATAAAATAAACCGGATCTAAAAA 57.204 29.630 9.46 0.00 0.00 1.94
81 82 9.912634 TTTCATAAAATGACTCCTTTTGATGAC 57.087 29.630 0.00 0.00 37.18 3.06
82 83 7.751732 TCATAAAATGACTCCTTTTGATGACG 58.248 34.615 3.10 0.00 34.72 4.35
83 84 4.425577 AAATGACTCCTTTTGATGACGC 57.574 40.909 0.00 0.00 0.00 5.19
84 85 1.808411 TGACTCCTTTTGATGACGCC 58.192 50.000 0.00 0.00 0.00 5.68
85 86 1.347707 TGACTCCTTTTGATGACGCCT 59.652 47.619 0.00 0.00 0.00 5.52
86 87 1.734465 GACTCCTTTTGATGACGCCTG 59.266 52.381 0.00 0.00 0.00 4.85
87 88 1.347707 ACTCCTTTTGATGACGCCTGA 59.652 47.619 0.00 0.00 0.00 3.86
88 89 2.026822 ACTCCTTTTGATGACGCCTGAT 60.027 45.455 0.00 0.00 0.00 2.90
89 90 2.353889 CTCCTTTTGATGACGCCTGATG 59.646 50.000 0.00 0.00 0.00 3.07
90 91 1.202222 CCTTTTGATGACGCCTGATGC 60.202 52.381 0.00 0.00 0.00 3.91
91 92 1.741706 CTTTTGATGACGCCTGATGCT 59.258 47.619 0.00 0.00 38.05 3.79
92 93 2.689553 TTTGATGACGCCTGATGCTA 57.310 45.000 0.00 0.00 38.05 3.49
93 94 2.689553 TTGATGACGCCTGATGCTAA 57.310 45.000 0.00 0.00 38.05 3.09
94 95 2.229675 TGATGACGCCTGATGCTAAG 57.770 50.000 0.00 0.00 38.05 2.18
95 96 1.756538 TGATGACGCCTGATGCTAAGA 59.243 47.619 0.00 0.00 38.05 2.10
96 97 2.131183 GATGACGCCTGATGCTAAGAC 58.869 52.381 0.00 0.00 38.05 3.01
97 98 0.179137 TGACGCCTGATGCTAAGACG 60.179 55.000 0.00 0.00 38.05 4.18
98 99 1.483424 GACGCCTGATGCTAAGACGC 61.483 60.000 0.00 0.00 38.05 5.19
99 100 2.240500 CGCCTGATGCTAAGACGCC 61.241 63.158 0.00 0.00 38.05 5.68
100 101 1.153369 GCCTGATGCTAAGACGCCA 60.153 57.895 0.00 0.00 36.87 5.69
101 102 0.533755 GCCTGATGCTAAGACGCCAT 60.534 55.000 0.00 0.00 36.87 4.40
102 103 1.959042 CCTGATGCTAAGACGCCATT 58.041 50.000 0.00 0.00 0.00 3.16
103 104 1.600957 CCTGATGCTAAGACGCCATTG 59.399 52.381 0.00 0.00 0.00 2.82
104 105 2.283298 CTGATGCTAAGACGCCATTGT 58.717 47.619 0.00 0.00 0.00 2.71
105 106 3.457234 CTGATGCTAAGACGCCATTGTA 58.543 45.455 0.00 0.00 0.00 2.41
106 107 3.457234 TGATGCTAAGACGCCATTGTAG 58.543 45.455 0.00 0.00 0.00 2.74
107 108 3.132111 TGATGCTAAGACGCCATTGTAGA 59.868 43.478 0.00 0.00 0.00 2.59
108 109 3.819564 TGCTAAGACGCCATTGTAGAT 57.180 42.857 0.00 0.00 0.00 1.98
109 110 4.929819 TGCTAAGACGCCATTGTAGATA 57.070 40.909 0.00 0.00 0.00 1.98
110 111 4.617959 TGCTAAGACGCCATTGTAGATAC 58.382 43.478 0.00 0.00 0.00 2.24
111 112 3.988517 GCTAAGACGCCATTGTAGATACC 59.011 47.826 0.00 0.00 0.00 2.73
112 113 4.500887 GCTAAGACGCCATTGTAGATACCA 60.501 45.833 0.00 0.00 0.00 3.25
113 114 4.689612 AAGACGCCATTGTAGATACCAT 57.310 40.909 0.00 0.00 0.00 3.55
114 115 3.995199 AGACGCCATTGTAGATACCATG 58.005 45.455 0.00 0.00 0.00 3.66
115 116 3.067106 GACGCCATTGTAGATACCATGG 58.933 50.000 11.19 11.19 46.62 3.66
118 119 1.806542 CCATTGTAGATACCATGGCGC 59.193 52.381 13.04 0.00 40.97 6.53
119 120 1.806542 CATTGTAGATACCATGGCGCC 59.193 52.381 22.73 22.73 0.00 6.53
120 121 1.128200 TTGTAGATACCATGGCGCCT 58.872 50.000 29.70 9.99 0.00 5.52
121 122 1.128200 TGTAGATACCATGGCGCCTT 58.872 50.000 29.70 19.97 0.00 4.35
122 123 1.202639 TGTAGATACCATGGCGCCTTG 60.203 52.381 30.20 30.20 0.00 3.61
123 124 0.396435 TAGATACCATGGCGCCTTGG 59.604 55.000 43.81 43.81 44.08 3.61
124 125 2.519302 ATACCATGGCGCCTTGGC 60.519 61.111 44.80 16.70 42.80 4.52
134 135 4.643387 GCCTTGGCACGACACCCT 62.643 66.667 6.79 0.00 0.00 4.34
135 136 2.358737 CCTTGGCACGACACCCTC 60.359 66.667 0.00 0.00 0.00 4.30
136 137 2.425592 CTTGGCACGACACCCTCA 59.574 61.111 0.00 0.00 0.00 3.86
137 138 1.961277 CTTGGCACGACACCCTCAC 60.961 63.158 0.00 0.00 0.00 3.51
138 139 2.383245 CTTGGCACGACACCCTCACT 62.383 60.000 0.00 0.00 0.00 3.41
139 140 2.357517 GGCACGACACCCTCACTG 60.358 66.667 0.00 0.00 0.00 3.66
140 141 2.357517 GCACGACACCCTCACTGG 60.358 66.667 0.00 0.00 0.00 4.00
141 142 2.867855 GCACGACACCCTCACTGGA 61.868 63.158 0.00 0.00 38.35 3.86
142 143 1.006102 CACGACACCCTCACTGGAC 60.006 63.158 0.00 0.00 38.35 4.02
143 144 1.456892 ACGACACCCTCACTGGACA 60.457 57.895 0.00 0.00 38.35 4.02
144 145 0.832135 ACGACACCCTCACTGGACAT 60.832 55.000 0.00 0.00 38.35 3.06
145 146 1.182667 CGACACCCTCACTGGACATA 58.817 55.000 0.00 0.00 38.35 2.29
146 147 1.135139 CGACACCCTCACTGGACATAG 59.865 57.143 0.00 0.00 38.35 2.23
147 148 0.905357 ACACCCTCACTGGACATAGC 59.095 55.000 0.00 0.00 38.35 2.97
148 149 1.198713 CACCCTCACTGGACATAGCT 58.801 55.000 0.00 0.00 38.35 3.32
149 150 2.292257 ACACCCTCACTGGACATAGCTA 60.292 50.000 0.00 0.00 38.35 3.32
150 151 2.968574 CACCCTCACTGGACATAGCTAT 59.031 50.000 0.00 0.00 38.35 2.97
151 152 3.006323 CACCCTCACTGGACATAGCTATC 59.994 52.174 2.34 0.00 38.35 2.08
152 153 3.234353 CCCTCACTGGACATAGCTATCA 58.766 50.000 2.34 0.00 38.35 2.15
153 154 3.006323 CCCTCACTGGACATAGCTATCAC 59.994 52.174 2.34 0.74 38.35 3.06
154 155 3.638627 CCTCACTGGACATAGCTATCACA 59.361 47.826 2.34 2.51 38.35 3.58
155 156 4.261952 CCTCACTGGACATAGCTATCACAG 60.262 50.000 19.63 19.63 38.35 3.66
156 157 7.740861 CCTCACTGGACATAGCTATCACAGC 62.741 52.000 20.54 4.74 44.55 4.40
171 172 3.958860 AGCAACAAGAGGGCGCCT 61.959 61.111 28.56 12.77 36.03 5.52
189 190 0.673644 CTTAGCCCAGACCGTTGTGG 60.674 60.000 0.00 0.00 46.41 4.17
197 198 0.822121 AGACCGTTGTGGAAAAGGGC 60.822 55.000 0.00 0.00 42.00 5.19
199 200 2.642700 CGTTGTGGAAAAGGGCCG 59.357 61.111 0.00 0.00 0.00 6.13
202 203 1.830408 TTGTGGAAAAGGGCCGGTG 60.830 57.895 1.90 0.00 0.00 4.94
206 207 1.365999 GGAAAAGGGCCGGTGTTTG 59.634 57.895 1.90 0.00 0.00 2.93
221 222 5.507149 CCGGTGTTTGAATTGTTTCAGATCA 60.507 40.000 0.00 0.00 42.60 2.92
247 249 8.078596 AGCTTTATTTTGTGCTGAGTTTTAGAG 58.921 33.333 0.00 0.00 34.19 2.43
254 256 5.533482 TGTGCTGAGTTTTAGAGAAGAGTC 58.467 41.667 0.00 0.00 0.00 3.36
269 271 8.688747 AGAGAAGAGTCAAATCTGTTCATTTT 57.311 30.769 6.41 0.00 39.26 1.82
273 275 6.974965 AGAGTCAAATCTGTTCATTTTCACC 58.025 36.000 0.00 0.00 0.00 4.02
368 377 3.703052 AGATCCAACAAAATCCATGGAGC 59.297 43.478 21.33 0.86 46.14 4.70
369 378 2.178580 TCCAACAAAATCCATGGAGCC 58.821 47.619 21.33 0.00 37.05 4.70
370 379 1.207811 CCAACAAAATCCATGGAGCCC 59.792 52.381 21.33 0.00 34.82 5.19
371 380 1.901159 CAACAAAATCCATGGAGCCCA 59.099 47.619 21.33 0.00 38.19 5.36
372 381 2.302445 CAACAAAATCCATGGAGCCCAA 59.698 45.455 21.33 0.00 36.95 4.12
406 415 4.173036 GCTGCTGGCTACTCTATTCTAG 57.827 50.000 0.00 0.00 38.06 2.43
573 588 2.309764 AAGGCGTGCGCGATCATTTC 62.310 55.000 26.19 2.89 43.06 2.17
628 643 4.410400 CGAACCACCTCCCTGCCC 62.410 72.222 0.00 0.00 0.00 5.36
767 790 4.731000 CAGCGATATCTATCCGATCGAAAC 59.269 45.833 18.66 0.00 44.04 2.78
814 839 0.027455 CTCTAGCTCGCACTCACTCG 59.973 60.000 0.00 0.00 0.00 4.18
826 851 0.375454 CTCACTCGTACGAGCCTCAG 59.625 60.000 38.10 25.47 45.54 3.35
936 961 0.606604 TCCACGTCCTTCTACAAGCC 59.393 55.000 0.00 0.00 0.00 4.35
990 1015 2.186826 GGCGCATAATTGCCGAGGT 61.187 57.895 10.83 0.00 46.57 3.85
991 1016 1.009675 GCGCATAATTGCCGAGGTG 60.010 57.895 0.30 0.00 46.57 4.00
992 1017 1.009675 CGCATAATTGCCGAGGTGC 60.010 57.895 0.00 0.00 46.57 5.01
1194 1220 2.507992 CTCGGGCTCAACTCGCTG 60.508 66.667 0.00 0.00 0.00 5.18
1667 1743 1.080434 GCCCGCAGATAGGATCGTC 60.080 63.158 0.00 0.00 0.00 4.20
1859 1946 4.503007 GCTGTTCCGTGTGTGTATATACAG 59.497 45.833 15.93 4.15 36.78 2.74
1918 2005 3.689347 TGTGCTCTGTATTTGCATCCTT 58.311 40.909 0.00 0.00 39.00 3.36
1920 2007 4.523943 TGTGCTCTGTATTTGCATCCTTTT 59.476 37.500 0.00 0.00 39.00 2.27
1955 2044 3.215975 CGGGTTCTTCCACCAAGTTTTA 58.784 45.455 0.00 0.00 38.79 1.52
1956 2045 3.633065 CGGGTTCTTCCACCAAGTTTTAA 59.367 43.478 0.00 0.00 38.79 1.52
1961 2050 5.195001 TCTTCCACCAAGTTTTAATGCAC 57.805 39.130 0.00 0.00 33.27 4.57
1964 2053 3.320541 TCCACCAAGTTTTAATGCACCTG 59.679 43.478 0.00 0.00 0.00 4.00
1975 2064 0.538977 ATGCACCTGCTGAGCACTTT 60.539 50.000 1.40 0.00 41.60 2.66
1979 2068 1.537202 CACCTGCTGAGCACTTTTACC 59.463 52.381 1.40 0.00 33.79 2.85
1993 2082 5.858581 GCACTTTTACCTGCACTTTGATAAG 59.141 40.000 0.00 0.00 37.40 1.73
2004 2093 7.036996 TGCACTTTGATAAGTTGATGAACAA 57.963 32.000 0.00 0.00 41.85 2.83
2009 2098 9.903682 ACTTTGATAAGTTGATGAACAAATCAG 57.096 29.630 10.56 5.49 41.85 2.90
2017 2106 8.862550 AGTTGATGAACAAATCAGAAGTTTTC 57.137 30.769 0.00 0.00 42.53 2.29
2018 2107 7.922811 AGTTGATGAACAAATCAGAAGTTTTCC 59.077 33.333 0.00 0.00 42.53 3.13
2020 2109 5.529581 TGAACAAATCAGAAGTTTTCCCC 57.470 39.130 0.00 0.00 33.04 4.81
2021 2110 4.037446 TGAACAAATCAGAAGTTTTCCCCG 59.963 41.667 0.00 0.00 33.04 5.73
2026 2115 1.679153 TCAGAAGTTTTCCCCGCAAAC 59.321 47.619 0.00 0.00 34.80 2.93
2028 2117 1.681264 AGAAGTTTTCCCCGCAAACAG 59.319 47.619 0.19 0.00 36.71 3.16
2041 2130 2.735444 CGCAAACAGAAGAGAGCCGATA 60.735 50.000 0.00 0.00 0.00 2.92
2098 2187 9.539825 TGCACATTGTATGAACAGTAAAATTTT 57.460 25.926 8.75 8.75 36.83 1.82
2172 2263 8.371699 AGAAACTTTGCTTAGTTCTCTATCTGT 58.628 33.333 4.81 0.00 37.37 3.41
2246 4322 9.696917 AATCAGTACTCCAAAATGCTTTTAAAG 57.303 29.630 0.00 0.00 0.00 1.85
2270 4348 4.704057 GGAGTCTTTCTGGAGCATTGATTT 59.296 41.667 0.00 0.00 0.00 2.17
2321 4401 5.168647 ACCATTCCATCACAATTTTGCAT 57.831 34.783 0.00 0.00 0.00 3.96
2325 4405 4.004196 TCCATCACAATTTTGCATGCAA 57.996 36.364 28.80 28.80 0.00 4.08
2329 4409 2.544686 TCACAATTTTGCATGCAAGTGC 59.455 40.909 30.85 5.31 45.25 4.40
2350 4430 7.604549 AGTGCAACAATCATCAATGTTTATCA 58.395 30.769 0.00 0.00 41.43 2.15
2508 4617 3.297736 CCGAAATGGTCTCTACTAGGGT 58.702 50.000 0.00 0.00 0.00 4.34
2509 4618 3.068307 CCGAAATGGTCTCTACTAGGGTG 59.932 52.174 0.00 0.00 0.00 4.61
2510 4619 3.952323 CGAAATGGTCTCTACTAGGGTGA 59.048 47.826 0.00 0.00 0.00 4.02
2511 4620 4.585162 CGAAATGGTCTCTACTAGGGTGAT 59.415 45.833 0.00 0.00 0.00 3.06
2512 4621 5.069251 CGAAATGGTCTCTACTAGGGTGATT 59.931 44.000 0.00 0.00 0.00 2.57
2513 4622 5.878406 AATGGTCTCTACTAGGGTGATTG 57.122 43.478 0.00 0.00 0.00 2.67
2514 4623 4.603094 TGGTCTCTACTAGGGTGATTGA 57.397 45.455 0.00 0.00 0.00 2.57
2515 4624 4.537751 TGGTCTCTACTAGGGTGATTGAG 58.462 47.826 0.00 0.00 0.00 3.02
2516 4625 3.319689 GGTCTCTACTAGGGTGATTGAGC 59.680 52.174 0.00 0.00 0.00 4.26
2517 4626 3.319689 GTCTCTACTAGGGTGATTGAGCC 59.680 52.174 0.00 0.00 43.30 4.70
2526 4635 4.376340 GGGTGATTGAGCCTATGTTTTG 57.624 45.455 0.00 0.00 39.39 2.44
2527 4636 3.763897 GGGTGATTGAGCCTATGTTTTGT 59.236 43.478 0.00 0.00 39.39 2.83
2528 4637 4.380867 GGGTGATTGAGCCTATGTTTTGTG 60.381 45.833 0.00 0.00 39.39 3.33
2529 4638 4.218417 GGTGATTGAGCCTATGTTTTGTGT 59.782 41.667 0.00 0.00 0.00 3.72
2530 4639 5.414454 GGTGATTGAGCCTATGTTTTGTGTA 59.586 40.000 0.00 0.00 0.00 2.90
2531 4640 6.072175 GGTGATTGAGCCTATGTTTTGTGTAA 60.072 38.462 0.00 0.00 0.00 2.41
2532 4641 7.367285 GTGATTGAGCCTATGTTTTGTGTAAA 58.633 34.615 0.00 0.00 0.00 2.01
2533 4642 7.538678 GTGATTGAGCCTATGTTTTGTGTAAAG 59.461 37.037 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.651913 TGCTGAAGTTTTTAAAAAGAGTCAAAT 57.348 25.926 13.58 0.00 0.00 2.32
5 6 9.651913 ATGCTGAAGTTTTTAAAAAGAGTCAAA 57.348 25.926 13.58 8.77 0.00 2.69
17 18 9.413048 CCGGTTTATTTTATGCTGAAGTTTTTA 57.587 29.630 0.00 0.00 0.00 1.52
18 19 8.145122 TCCGGTTTATTTTATGCTGAAGTTTTT 58.855 29.630 0.00 0.00 0.00 1.94
19 20 7.662897 TCCGGTTTATTTTATGCTGAAGTTTT 58.337 30.769 0.00 0.00 0.00 2.43
20 21 7.222000 TCCGGTTTATTTTATGCTGAAGTTT 57.778 32.000 0.00 0.00 0.00 2.66
21 22 6.827586 TCCGGTTTATTTTATGCTGAAGTT 57.172 33.333 0.00 0.00 0.00 2.66
22 23 6.828785 AGATCCGGTTTATTTTATGCTGAAGT 59.171 34.615 0.00 0.00 0.00 3.01
23 24 7.264373 AGATCCGGTTTATTTTATGCTGAAG 57.736 36.000 0.00 0.00 0.00 3.02
24 25 8.740123 TTAGATCCGGTTTATTTTATGCTGAA 57.260 30.769 0.00 0.00 0.00 3.02
25 26 8.740123 TTTAGATCCGGTTTATTTTATGCTGA 57.260 30.769 0.00 0.00 0.00 4.26
26 27 9.796120 TTTTTAGATCCGGTTTATTTTATGCTG 57.204 29.630 0.00 0.00 0.00 4.41
55 56 9.912634 GTCATCAAAAGGAGTCATTTTATGAAA 57.087 29.630 22.26 9.55 41.69 2.69
56 57 8.236586 CGTCATCAAAAGGAGTCATTTTATGAA 58.763 33.333 22.26 10.45 41.69 2.57
57 58 7.626240 GCGTCATCAAAAGGAGTCATTTTATGA 60.626 37.037 14.61 17.77 36.84 2.15
58 59 6.470235 GCGTCATCAAAAGGAGTCATTTTATG 59.530 38.462 14.61 16.24 0.00 1.90
59 60 6.404734 GGCGTCATCAAAAGGAGTCATTTTAT 60.405 38.462 14.61 7.04 0.00 1.40
60 61 5.106317 GGCGTCATCAAAAGGAGTCATTTTA 60.106 40.000 14.61 5.22 0.00 1.52
61 62 4.321230 GGCGTCATCAAAAGGAGTCATTTT 60.321 41.667 9.62 9.62 0.00 1.82
62 63 3.191371 GGCGTCATCAAAAGGAGTCATTT 59.809 43.478 0.00 0.00 0.00 2.32
63 64 2.749621 GGCGTCATCAAAAGGAGTCATT 59.250 45.455 0.00 0.00 0.00 2.57
64 65 2.026822 AGGCGTCATCAAAAGGAGTCAT 60.027 45.455 0.00 0.00 0.00 3.06
65 66 1.347707 AGGCGTCATCAAAAGGAGTCA 59.652 47.619 0.00 0.00 0.00 3.41
66 67 1.734465 CAGGCGTCATCAAAAGGAGTC 59.266 52.381 0.00 0.00 0.00 3.36
67 68 1.347707 TCAGGCGTCATCAAAAGGAGT 59.652 47.619 0.00 0.00 0.00 3.85
68 69 2.099141 TCAGGCGTCATCAAAAGGAG 57.901 50.000 0.00 0.00 0.00 3.69
69 70 2.358957 CATCAGGCGTCATCAAAAGGA 58.641 47.619 0.00 0.00 0.00 3.36
70 71 1.202222 GCATCAGGCGTCATCAAAAGG 60.202 52.381 0.00 0.00 0.00 3.11
71 72 2.184385 GCATCAGGCGTCATCAAAAG 57.816 50.000 0.00 0.00 0.00 2.27
82 83 0.533755 ATGGCGTCTTAGCATCAGGC 60.534 55.000 0.00 0.00 45.30 4.85
83 84 1.600957 CAATGGCGTCTTAGCATCAGG 59.399 52.381 0.00 0.00 39.27 3.86
84 85 2.283298 ACAATGGCGTCTTAGCATCAG 58.717 47.619 0.00 0.00 39.27 2.90
85 86 2.401583 ACAATGGCGTCTTAGCATCA 57.598 45.000 0.00 0.00 39.27 3.07
86 87 3.717707 TCTACAATGGCGTCTTAGCATC 58.282 45.455 0.00 0.00 39.27 3.91
87 88 3.819564 TCTACAATGGCGTCTTAGCAT 57.180 42.857 0.00 0.00 39.27 3.79
88 89 3.819564 ATCTACAATGGCGTCTTAGCA 57.180 42.857 0.00 0.00 39.27 3.49
89 90 3.988517 GGTATCTACAATGGCGTCTTAGC 59.011 47.826 0.00 0.00 0.00 3.09
90 91 5.196341 TGGTATCTACAATGGCGTCTTAG 57.804 43.478 0.00 0.00 0.00 2.18
91 92 5.538118 CATGGTATCTACAATGGCGTCTTA 58.462 41.667 0.00 0.00 34.64 2.10
92 93 4.380531 CATGGTATCTACAATGGCGTCTT 58.619 43.478 0.00 0.00 34.64 3.01
93 94 3.995199 CATGGTATCTACAATGGCGTCT 58.005 45.455 0.00 0.00 34.64 4.18
99 100 1.806542 GGCGCCATGGTATCTACAATG 59.193 52.381 24.80 0.00 37.37 2.82
100 101 1.699634 AGGCGCCATGGTATCTACAAT 59.300 47.619 31.54 0.00 0.00 2.71
101 102 1.128200 AGGCGCCATGGTATCTACAA 58.872 50.000 31.54 0.00 0.00 2.41
102 103 1.128200 AAGGCGCCATGGTATCTACA 58.872 50.000 31.54 0.00 0.00 2.74
103 104 1.512926 CAAGGCGCCATGGTATCTAC 58.487 55.000 31.54 0.00 0.00 2.59
104 105 0.396435 CCAAGGCGCCATGGTATCTA 59.604 55.000 36.75 0.00 30.89 1.98
105 106 1.149174 CCAAGGCGCCATGGTATCT 59.851 57.895 36.75 8.78 30.89 1.98
106 107 2.555547 GCCAAGGCGCCATGGTATC 61.556 63.158 41.67 26.91 37.16 2.24
107 108 2.519302 GCCAAGGCGCCATGGTAT 60.519 61.111 41.67 15.28 37.16 2.73
108 109 4.040426 TGCCAAGGCGCCATGGTA 62.040 61.111 41.67 37.83 45.51 3.25
117 118 4.643387 AGGGTGTCGTGCCAAGGC 62.643 66.667 3.61 3.61 42.35 4.35
118 119 2.358737 GAGGGTGTCGTGCCAAGG 60.359 66.667 0.00 0.00 0.00 3.61
119 120 1.961277 GTGAGGGTGTCGTGCCAAG 60.961 63.158 0.00 0.00 0.00 3.61
120 121 2.110213 GTGAGGGTGTCGTGCCAA 59.890 61.111 0.00 0.00 0.00 4.52
121 122 2.842462 AGTGAGGGTGTCGTGCCA 60.842 61.111 0.00 0.00 0.00 4.92
122 123 2.357517 CAGTGAGGGTGTCGTGCC 60.358 66.667 0.00 0.00 0.00 5.01
123 124 2.357517 CCAGTGAGGGTGTCGTGC 60.358 66.667 0.00 0.00 0.00 5.34
124 125 1.006102 GTCCAGTGAGGGTGTCGTG 60.006 63.158 0.00 0.00 38.24 4.35
125 126 0.832135 ATGTCCAGTGAGGGTGTCGT 60.832 55.000 0.00 0.00 38.24 4.34
126 127 1.135139 CTATGTCCAGTGAGGGTGTCG 59.865 57.143 0.00 0.00 38.24 4.35
127 128 1.134670 GCTATGTCCAGTGAGGGTGTC 60.135 57.143 0.00 0.00 38.24 3.67
128 129 0.905357 GCTATGTCCAGTGAGGGTGT 59.095 55.000 0.00 0.00 38.24 4.16
129 130 1.198713 AGCTATGTCCAGTGAGGGTG 58.801 55.000 0.00 0.00 38.24 4.61
130 131 2.848678 TAGCTATGTCCAGTGAGGGT 57.151 50.000 0.00 0.00 38.24 4.34
131 132 3.006323 GTGATAGCTATGTCCAGTGAGGG 59.994 52.174 11.94 0.00 38.24 4.30
132 133 3.638627 TGTGATAGCTATGTCCAGTGAGG 59.361 47.826 11.94 0.00 39.47 3.86
133 134 4.869215 CTGTGATAGCTATGTCCAGTGAG 58.131 47.826 11.94 0.00 0.00 3.51
134 135 4.926140 CTGTGATAGCTATGTCCAGTGA 57.074 45.455 11.94 0.00 0.00 3.41
147 148 2.012673 GCCCTCTTGTTGCTGTGATAG 58.987 52.381 0.00 0.00 0.00 2.08
148 149 1.675714 CGCCCTCTTGTTGCTGTGATA 60.676 52.381 0.00 0.00 0.00 2.15
149 150 0.957395 CGCCCTCTTGTTGCTGTGAT 60.957 55.000 0.00 0.00 0.00 3.06
150 151 1.597854 CGCCCTCTTGTTGCTGTGA 60.598 57.895 0.00 0.00 0.00 3.58
151 152 2.949106 CGCCCTCTTGTTGCTGTG 59.051 61.111 0.00 0.00 0.00 3.66
152 153 2.980233 GCGCCCTCTTGTTGCTGT 60.980 61.111 0.00 0.00 0.00 4.40
153 154 3.741476 GGCGCCCTCTTGTTGCTG 61.741 66.667 18.11 0.00 0.00 4.41
154 155 2.124507 TAAGGCGCCCTCTTGTTGCT 62.125 55.000 26.15 0.00 30.89 3.91
155 156 1.648467 CTAAGGCGCCCTCTTGTTGC 61.648 60.000 26.15 0.00 30.89 4.17
156 157 1.648467 GCTAAGGCGCCCTCTTGTTG 61.648 60.000 26.15 7.34 30.89 3.33
157 158 1.377333 GCTAAGGCGCCCTCTTGTT 60.377 57.895 26.15 12.63 30.89 2.83
158 159 2.269241 GCTAAGGCGCCCTCTTGT 59.731 61.111 26.15 0.00 30.89 3.16
159 160 2.514824 GGCTAAGGCGCCCTCTTG 60.515 66.667 26.15 10.36 44.41 3.02
171 172 1.122632 TCCACAACGGTCTGGGCTAA 61.123 55.000 0.00 0.00 35.57 3.09
189 190 0.747852 TTCAAACACCGGCCCTTTTC 59.252 50.000 0.00 0.00 0.00 2.29
197 198 4.300189 TCTGAAACAATTCAAACACCGG 57.700 40.909 0.00 0.00 44.64 5.28
199 200 5.403466 GCTGATCTGAAACAATTCAAACACC 59.597 40.000 3.42 0.00 44.64 4.16
202 203 7.704789 AAAGCTGATCTGAAACAATTCAAAC 57.295 32.000 3.42 0.00 44.64 2.93
221 222 7.940850 TCTAAAACTCAGCACAAAATAAAGCT 58.059 30.769 0.00 0.00 37.95 3.74
239 241 9.046296 TGAACAGATTTGACTCTTCTCTAAAAC 57.954 33.333 0.00 0.00 0.00 2.43
244 246 8.688747 AAAATGAACAGATTTGACTCTTCTCT 57.311 30.769 0.00 0.00 0.00 3.10
247 249 7.592903 GGTGAAAATGAACAGATTTGACTCTTC 59.407 37.037 0.00 0.00 0.00 2.87
254 256 5.119931 TCCGGTGAAAATGAACAGATTTG 57.880 39.130 0.00 0.00 0.00 2.32
269 271 1.896660 GCTTTGCAGGTTCCGGTGA 60.897 57.895 0.00 0.00 0.00 4.02
273 275 1.007387 GGTTGCTTTGCAGGTTCCG 60.007 57.895 0.00 0.00 40.61 4.30
322 325 0.608035 CACGGCTAAAGGGGAAGCAA 60.608 55.000 0.00 0.00 40.61 3.91
368 377 3.090765 CTGGAAGGAGGGGTTGGG 58.909 66.667 0.00 0.00 0.00 4.12
369 378 2.234296 AGCTGGAAGGAGGGGTTGG 61.234 63.158 0.00 0.00 0.00 3.77
370 379 1.001641 CAGCTGGAAGGAGGGGTTG 60.002 63.158 5.57 0.00 0.00 3.77
371 380 2.911926 GCAGCTGGAAGGAGGGGTT 61.912 63.158 17.12 0.00 0.00 4.11
372 381 3.334054 GCAGCTGGAAGGAGGGGT 61.334 66.667 17.12 0.00 0.00 4.95
404 413 5.929992 CCTTCTTTTGTGTTGGACGATACTA 59.070 40.000 0.00 0.00 0.00 1.82
405 414 4.755123 CCTTCTTTTGTGTTGGACGATACT 59.245 41.667 0.00 0.00 0.00 2.12
406 415 4.612939 GCCTTCTTTTGTGTTGGACGATAC 60.613 45.833 0.00 0.00 0.00 2.24
628 643 4.722700 CCGGCTGTTGGACCAGGG 62.723 72.222 0.00 0.00 32.92 4.45
747 767 4.095932 TGGGTTTCGATCGGATAGATATCG 59.904 45.833 16.41 0.00 42.90 2.92
767 790 0.955919 GGACCGCTTTCTTGTCTGGG 60.956 60.000 0.00 0.00 0.00 4.45
826 851 3.067132 CGTTTCGGTTCGGAAAAGC 57.933 52.632 7.02 0.00 37.63 3.51
955 980 1.146263 CCGGAAGTATGGGTCTGCC 59.854 63.158 0.00 0.00 0.00 4.85
956 981 1.523938 GCCGGAAGTATGGGTCTGC 60.524 63.158 5.05 0.00 0.00 4.26
957 982 1.227263 CGCCGGAAGTATGGGTCTG 60.227 63.158 5.05 0.00 0.00 3.51
958 983 3.090219 GCGCCGGAAGTATGGGTCT 62.090 63.158 5.05 0.00 0.00 3.85
1667 1743 4.082679 ACTTTCTACTGTACTCCAAGCGAG 60.083 45.833 0.00 0.00 44.95 5.03
1859 1946 9.482175 ACTATCCTATTAATACCATCTCCACTC 57.518 37.037 0.00 0.00 0.00 3.51
1938 2027 5.452636 GGTGCATTAAAACTTGGTGGAAGAA 60.453 40.000 0.00 0.00 35.42 2.52
1955 2044 0.538977 AAGTGCTCAGCAGGTGCATT 60.539 50.000 0.00 2.35 46.52 3.56
1956 2045 0.538977 AAAGTGCTCAGCAGGTGCAT 60.539 50.000 0.00 0.00 46.52 3.96
1961 2050 1.808945 CAGGTAAAAGTGCTCAGCAGG 59.191 52.381 0.00 0.00 40.08 4.85
1964 2053 1.068954 GTGCAGGTAAAAGTGCTCAGC 60.069 52.381 0.00 0.00 40.54 4.26
1975 2064 6.939730 TCATCAACTTATCAAAGTGCAGGTAA 59.060 34.615 0.00 0.00 45.37 2.85
1979 2068 6.671190 TGTTCATCAACTTATCAAAGTGCAG 58.329 36.000 0.00 0.00 45.37 4.41
1993 2082 7.169813 GGGAAAACTTCTGATTTGTTCATCAAC 59.830 37.037 0.00 0.00 35.61 3.18
2004 2093 2.286365 TGCGGGGAAAACTTCTGATT 57.714 45.000 0.00 0.00 0.00 2.57
2009 2098 1.679153 TCTGTTTGCGGGGAAAACTTC 59.321 47.619 1.29 0.00 38.17 3.01
2017 2106 1.301677 GCTCTCTTCTGTTTGCGGGG 61.302 60.000 0.00 0.00 0.00 5.73
2018 2107 1.301677 GGCTCTCTTCTGTTTGCGGG 61.302 60.000 0.00 0.00 0.00 6.13
2020 2109 0.667487 TCGGCTCTCTTCTGTTTGCG 60.667 55.000 0.00 0.00 0.00 4.85
2021 2110 1.731720 ATCGGCTCTCTTCTGTTTGC 58.268 50.000 0.00 0.00 0.00 3.68
2026 2115 5.814705 ACTTTTGATTATCGGCTCTCTTCTG 59.185 40.000 0.00 0.00 0.00 3.02
2028 2117 6.670077 AACTTTTGATTATCGGCTCTCTTC 57.330 37.500 0.00 0.00 0.00 2.87
2041 2130 7.452813 AGCTCAGGATTAGGAAAACTTTTGATT 59.547 33.333 0.00 0.00 0.00 2.57
2246 4322 2.026822 TCAATGCTCCAGAAAGACTCCC 60.027 50.000 0.00 0.00 0.00 4.30
2283 4363 5.116180 GGAATGGTATTGATTGACGTCTGA 58.884 41.667 17.92 5.87 0.00 3.27
2285 4365 5.097742 TGGAATGGTATTGATTGACGTCT 57.902 39.130 17.92 0.00 0.00 4.18
2289 4369 6.698008 TGTGATGGAATGGTATTGATTGAC 57.302 37.500 0.00 0.00 0.00 3.18
2325 4405 7.604549 TGATAAACATTGATGATTGTTGCACT 58.395 30.769 0.00 0.00 36.26 4.40
2506 4615 4.218417 ACACAAAACATAGGCTCAATCACC 59.782 41.667 0.00 0.00 0.00 4.02
2507 4616 5.376854 ACACAAAACATAGGCTCAATCAC 57.623 39.130 0.00 0.00 0.00 3.06
2508 4617 7.517614 TTTACACAAAACATAGGCTCAATCA 57.482 32.000 0.00 0.00 0.00 2.57
2509 4618 6.528072 GCTTTACACAAAACATAGGCTCAATC 59.472 38.462 0.00 0.00 0.00 2.67
2510 4619 6.209391 AGCTTTACACAAAACATAGGCTCAAT 59.791 34.615 0.00 0.00 0.00 2.57
2511 4620 5.534654 AGCTTTACACAAAACATAGGCTCAA 59.465 36.000 0.00 0.00 0.00 3.02
2512 4621 5.048782 CAGCTTTACACAAAACATAGGCTCA 60.049 40.000 0.00 0.00 0.00 4.26
2513 4622 5.393962 CAGCTTTACACAAAACATAGGCTC 58.606 41.667 0.00 0.00 0.00 4.70
2514 4623 4.321230 GCAGCTTTACACAAAACATAGGCT 60.321 41.667 0.00 0.00 0.00 4.58
2515 4624 3.920412 GCAGCTTTACACAAAACATAGGC 59.080 43.478 0.00 0.00 0.00 3.93
2516 4625 5.119931 TGCAGCTTTACACAAAACATAGG 57.880 39.130 0.00 0.00 0.00 2.57
2517 4626 6.862608 TCAATGCAGCTTTACACAAAACATAG 59.137 34.615 0.00 0.00 0.00 2.23
2518 4627 6.743110 TCAATGCAGCTTTACACAAAACATA 58.257 32.000 0.00 0.00 0.00 2.29
2519 4628 5.599732 TCAATGCAGCTTTACACAAAACAT 58.400 33.333 0.00 0.00 0.00 2.71
2520 4629 5.003692 TCAATGCAGCTTTACACAAAACA 57.996 34.783 0.00 0.00 0.00 2.83
2521 4630 5.691305 TCATCAATGCAGCTTTACACAAAAC 59.309 36.000 0.00 0.00 0.00 2.43
2522 4631 5.840715 TCATCAATGCAGCTTTACACAAAA 58.159 33.333 0.00 0.00 0.00 2.44
2523 4632 5.450592 TCATCAATGCAGCTTTACACAAA 57.549 34.783 0.00 0.00 0.00 2.83
2524 4633 5.416639 AGATCATCAATGCAGCTTTACACAA 59.583 36.000 0.00 0.00 0.00 3.33
2525 4634 4.945543 AGATCATCAATGCAGCTTTACACA 59.054 37.500 0.00 0.00 0.00 3.72
2526 4635 5.065602 TCAGATCATCAATGCAGCTTTACAC 59.934 40.000 0.00 0.00 0.00 2.90
2527 4636 5.187687 TCAGATCATCAATGCAGCTTTACA 58.812 37.500 0.00 0.00 0.00 2.41
2528 4637 5.746307 TCAGATCATCAATGCAGCTTTAC 57.254 39.130 0.00 0.00 0.00 2.01
2529 4638 6.148976 GCTATCAGATCATCAATGCAGCTTTA 59.851 38.462 0.00 0.00 0.00 1.85
2530 4639 5.048643 GCTATCAGATCATCAATGCAGCTTT 60.049 40.000 0.00 0.00 0.00 3.51
2531 4640 4.456222 GCTATCAGATCATCAATGCAGCTT 59.544 41.667 0.00 0.00 0.00 3.74
2532 4641 4.004314 GCTATCAGATCATCAATGCAGCT 58.996 43.478 0.00 0.00 0.00 4.24
2533 4642 3.181519 CGCTATCAGATCATCAATGCAGC 60.182 47.826 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.