Multiple sequence alignment - TraesCS6D01G169200

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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 TraesCS6D01G169200 chr6D 100.000 4092 0 0 1 4092 155540771 155544862 0.000000e+00 7557
1 TraesCS6D01G169200 chr6D 90.335 269 24 2 3826 4092 3832125 3831857 6.510000e-93 351
2 TraesCS6D01G169200 chr6D 90.335 269 24 2 3826 4092 430311400 430311668 6.510000e-93 351
3 TraesCS6D01G169200 chr6B 96.479 3777 87 21 256 4018 278538862 278542606 0.000000e+00 6196
4 TraesCS6D01G169200 chr6B 90.335 269 23 3 3826 4092 704702375 704702642 2.340000e-92 350
5 TraesCS6D01G169200 chr6A 97.294 3178 71 9 924 4092 209266658 209269829 0.000000e+00 5378
6 TraesCS6D01G169200 chr6A 97.516 322 4 1 495 816 209265996 209266313 7.730000e-152 547
7 TraesCS6D01G169200 chr6A 84.279 229 23 7 270 490 209265459 209265682 1.150000e-50 211
8 TraesCS6D01G169200 chr7B 77.032 1772 358 35 1334 3082 511062677 511064422 0.000000e+00 972
9 TraesCS6D01G169200 chr7D 76.763 1773 367 34 1334 3082 484361992 484363743 0.000000e+00 950
10 TraesCS6D01G169200 chr7A 76.543 1799 367 42 1310 3082 552679371 552681140 0.000000e+00 933
11 TraesCS6D01G169200 chr3D 91.078 269 22 2 3826 4092 144777734 144777466 3.010000e-96 363
12 TraesCS6D01G169200 chr1A 90.335 269 24 2 3826 4092 531692674 531692942 6.510000e-93 351
13 TraesCS6D01G169200 chr5B 89.591 269 26 2 3826 4092 426623177 426622909 1.410000e-89 340
14 TraesCS6D01G169200 chr4A 89.591 269 25 3 3826 4092 630904005 630903738 5.070000e-89 339


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 TraesCS6D01G169200 chr6D 155540771 155544862 4091 False 7557.000000 7557 100.000000 1 4092 1 chr6D.!!$F1 4091
1 TraesCS6D01G169200 chr6B 278538862 278542606 3744 False 6196.000000 6196 96.479000 256 4018 1 chr6B.!!$F1 3762
2 TraesCS6D01G169200 chr6A 209265459 209269829 4370 False 2045.333333 5378 93.029667 270 4092 3 chr6A.!!$F1 3822
3 TraesCS6D01G169200 chr7B 511062677 511064422 1745 False 972.000000 972 77.032000 1334 3082 1 chr7B.!!$F1 1748
4 TraesCS6D01G169200 chr7D 484361992 484363743 1751 False 950.000000 950 76.763000 1334 3082 1 chr7D.!!$F1 1748
5 TraesCS6D01G169200 chr7A 552679371 552681140 1769 False 933.000000 933 76.543000 1310 3082 1 chr7A.!!$F1 1772

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
72 73 0.039798 CTCGAGGACCGTCGTTTTCA 60.040 55.0 3.91 0.0 40.93 2.69 F
1745 2326 0.033991 TCCTAACCTCTGCTCGCTCT 60.034 55.0 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2586 0.815615 GGCTAGAAATGCCCTGGTCG 60.816 60.000 0.0 0.0 44.32 4.79 R
3597 4184 1.063912 CATGACACCACACACACACAC 59.936 52.381 0.0 0.0 0.00 3.82 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
22 23 4.919793 GGAACCTTTATATCCTAAGGGCC 58.080 47.826 0.00 0.00 44.21 5.80
23 24 4.263816 GGAACCTTTATATCCTAAGGGCCC 60.264 50.000 16.46 16.46 44.21 5.80
24 25 4.244624 ACCTTTATATCCTAAGGGCCCT 57.755 45.455 22.28 22.28 44.21 5.19
25 26 4.176753 ACCTTTATATCCTAAGGGCCCTC 58.823 47.826 28.84 0.00 44.21 4.30
26 27 3.523972 CCTTTATATCCTAAGGGCCCTCC 59.476 52.174 28.84 0.00 37.78 4.30
36 37 4.995594 GGCCCTCCCAAGAGAATG 57.004 61.111 0.00 0.00 43.39 2.67
37 38 2.002625 GGCCCTCCCAAGAGAATGT 58.997 57.895 0.00 0.00 43.39 2.71
38 39 0.106967 GGCCCTCCCAAGAGAATGTC 60.107 60.000 0.00 0.00 43.39 3.06
39 40 0.620556 GCCCTCCCAAGAGAATGTCA 59.379 55.000 0.00 0.00 43.39 3.58
40 41 1.407989 GCCCTCCCAAGAGAATGTCAG 60.408 57.143 0.00 0.00 43.39 3.51
41 42 1.407989 CCCTCCCAAGAGAATGTCAGC 60.408 57.143 0.00 0.00 43.39 4.26
42 43 1.649664 CTCCCAAGAGAATGTCAGCG 58.350 55.000 0.00 0.00 43.39 5.18
43 44 0.250234 TCCCAAGAGAATGTCAGCGG 59.750 55.000 0.00 0.00 0.00 5.52
44 45 1.372087 CCCAAGAGAATGTCAGCGGC 61.372 60.000 0.00 0.00 0.00 6.53
45 46 1.372087 CCAAGAGAATGTCAGCGGCC 61.372 60.000 0.00 0.00 0.00 6.13
46 47 1.078143 AAGAGAATGTCAGCGGCCC 60.078 57.895 0.00 0.00 0.00 5.80
47 48 2.514824 GAGAATGTCAGCGGCCCC 60.515 66.667 0.00 0.00 0.00 5.80
48 49 3.011517 AGAATGTCAGCGGCCCCT 61.012 61.111 0.00 0.00 0.00 4.79
49 50 2.514824 GAATGTCAGCGGCCCCTC 60.515 66.667 0.00 0.00 0.00 4.30
50 51 4.473520 AATGTCAGCGGCCCCTCG 62.474 66.667 0.00 0.00 0.00 4.63
68 69 3.745803 GGCTCGAGGACCGTCGTT 61.746 66.667 15.58 0.00 40.93 3.85
69 70 2.257676 GCTCGAGGACCGTCGTTT 59.742 61.111 15.58 0.00 40.93 3.60
70 71 1.372623 GCTCGAGGACCGTCGTTTT 60.373 57.895 15.58 0.00 40.93 2.43
71 72 1.342796 GCTCGAGGACCGTCGTTTTC 61.343 60.000 15.58 0.00 40.93 2.29
72 73 0.039798 CTCGAGGACCGTCGTTTTCA 60.040 55.000 3.91 0.00 40.93 2.69
73 74 0.385029 TCGAGGACCGTCGTTTTCAA 59.615 50.000 11.12 0.00 40.93 2.69
74 75 0.782384 CGAGGACCGTCGTTTTCAAG 59.218 55.000 4.20 0.00 35.14 3.02
75 76 1.145803 GAGGACCGTCGTTTTCAAGG 58.854 55.000 0.00 0.00 0.00 3.61
76 77 0.754472 AGGACCGTCGTTTTCAAGGA 59.246 50.000 0.00 0.00 0.00 3.36
77 78 1.145803 GGACCGTCGTTTTCAAGGAG 58.854 55.000 0.00 0.00 0.00 3.69
78 79 1.145803 GACCGTCGTTTTCAAGGAGG 58.854 55.000 0.00 0.00 0.00 4.30
79 80 0.754472 ACCGTCGTTTTCAAGGAGGA 59.246 50.000 0.00 0.00 34.20 3.71
80 81 1.270147 ACCGTCGTTTTCAAGGAGGAG 60.270 52.381 0.00 0.00 34.20 3.69
81 82 0.790814 CGTCGTTTTCAAGGAGGAGC 59.209 55.000 0.00 0.00 34.20 4.70
82 83 0.790814 GTCGTTTTCAAGGAGGAGCG 59.209 55.000 0.00 0.00 0.00 5.03
83 84 0.677288 TCGTTTTCAAGGAGGAGCGA 59.323 50.000 0.00 0.00 0.00 4.93
84 85 1.071605 CGTTTTCAAGGAGGAGCGAG 58.928 55.000 0.00 0.00 0.00 5.03
85 86 0.799393 GTTTTCAAGGAGGAGCGAGC 59.201 55.000 0.00 0.00 0.00 5.03
86 87 0.670546 TTTTCAAGGAGGAGCGAGCG 60.671 55.000 0.00 0.00 0.00 5.03
87 88 2.507110 TTTCAAGGAGGAGCGAGCGG 62.507 60.000 0.00 0.00 0.00 5.52
120 121 4.762825 GGTACGACTGGTGCAACA 57.237 55.556 3.40 3.40 39.98 3.33
121 122 2.231820 GGTACGACTGGTGCAACAC 58.768 57.895 0.00 0.00 39.98 3.32
145 146 2.355363 CCGCTCCGTGTTCGTGAA 60.355 61.111 0.00 0.00 35.01 3.18
146 147 2.372690 CCGCTCCGTGTTCGTGAAG 61.373 63.158 0.00 0.00 35.01 3.02
147 148 1.660575 CGCTCCGTGTTCGTGAAGT 60.661 57.895 0.00 0.00 35.01 3.01
148 149 1.606350 CGCTCCGTGTTCGTGAAGTC 61.606 60.000 0.00 0.00 35.01 3.01
149 150 1.282930 GCTCCGTGTTCGTGAAGTCC 61.283 60.000 0.00 0.00 35.01 3.85
150 151 1.002250 CTCCGTGTTCGTGAAGTCCG 61.002 60.000 0.00 0.00 35.01 4.79
151 152 1.008194 CCGTGTTCGTGAAGTCCGA 60.008 57.895 0.00 0.00 35.01 4.55
152 153 1.273455 CCGTGTTCGTGAAGTCCGAC 61.273 60.000 0.00 0.00 33.41 4.79
153 154 1.594269 CGTGTTCGTGAAGTCCGACG 61.594 60.000 0.00 0.00 33.41 5.12
154 155 1.659335 TGTTCGTGAAGTCCGACGC 60.659 57.895 0.00 0.00 35.53 5.19
155 156 1.659335 GTTCGTGAAGTCCGACGCA 60.659 57.895 0.00 0.00 35.53 5.24
156 157 1.066093 TTCGTGAAGTCCGACGCAA 59.934 52.632 0.00 0.00 35.53 4.85
157 158 1.210545 TTCGTGAAGTCCGACGCAAC 61.211 55.000 0.00 0.00 35.53 4.17
158 159 2.844146 GTGAAGTCCGACGCAACG 59.156 61.111 0.00 0.00 0.00 4.10
159 160 3.033764 TGAAGTCCGACGCAACGC 61.034 61.111 0.00 0.00 0.00 4.84
160 161 3.774702 GAAGTCCGACGCAACGCC 61.775 66.667 0.00 0.00 0.00 5.68
164 165 4.946266 TCCGACGCAACGCCGAAA 62.946 61.111 0.00 0.00 0.00 3.46
165 166 3.784412 CCGACGCAACGCCGAAAT 61.784 61.111 0.00 0.00 0.00 2.17
166 167 2.570581 CGACGCAACGCCGAAATG 60.571 61.111 0.00 0.00 0.00 2.32
167 168 2.202298 GACGCAACGCCGAAATGG 60.202 61.111 0.00 0.00 42.50 3.16
168 169 3.661025 GACGCAACGCCGAAATGGG 62.661 63.158 0.00 0.00 38.63 4.00
176 177 3.564027 CCGAAATGGGCTCGCGAC 61.564 66.667 3.71 1.87 34.95 5.19
177 178 3.913573 CGAAATGGGCTCGCGACG 61.914 66.667 3.71 0.00 0.00 5.12
178 179 2.508439 GAAATGGGCTCGCGACGA 60.508 61.111 3.71 0.00 0.00 4.20
179 180 2.799540 GAAATGGGCTCGCGACGAC 61.800 63.158 3.71 3.37 0.00 4.34
180 181 4.814294 AATGGGCTCGCGACGACC 62.814 66.667 19.76 19.76 0.00 4.79
185 186 3.774702 GCTCGCGACGACCCAAAC 61.775 66.667 3.71 0.00 0.00 2.93
186 187 3.110178 CTCGCGACGACCCAAACC 61.110 66.667 3.71 0.00 0.00 3.27
187 188 3.569049 CTCGCGACGACCCAAACCT 62.569 63.158 3.71 0.00 0.00 3.50
188 189 3.110178 CGCGACGACCCAAACCTC 61.110 66.667 0.00 0.00 0.00 3.85
189 190 3.110178 GCGACGACCCAAACCTCG 61.110 66.667 0.00 0.00 35.96 4.63
190 191 3.110178 CGACGACCCAAACCTCGC 61.110 66.667 0.00 0.00 32.98 5.03
191 192 2.741211 GACGACCCAAACCTCGCC 60.741 66.667 0.00 0.00 32.98 5.54
192 193 3.524648 GACGACCCAAACCTCGCCA 62.525 63.158 0.00 0.00 32.98 5.69
193 194 2.046314 CGACCCAAACCTCGCCAT 60.046 61.111 0.00 0.00 0.00 4.40
194 195 2.398554 CGACCCAAACCTCGCCATG 61.399 63.158 0.00 0.00 0.00 3.66
195 196 1.002624 GACCCAAACCTCGCCATGA 60.003 57.895 0.00 0.00 0.00 3.07
196 197 1.303317 ACCCAAACCTCGCCATGAC 60.303 57.895 0.00 0.00 0.00 3.06
197 198 2.398554 CCCAAACCTCGCCATGACG 61.399 63.158 0.00 0.00 0.00 4.35
198 199 1.671054 CCAAACCTCGCCATGACGT 60.671 57.895 0.16 0.00 0.00 4.34
199 200 1.497278 CAAACCTCGCCATGACGTG 59.503 57.895 0.16 0.00 0.00 4.49
207 208 3.716195 CCATGACGTGGGCCCTCA 61.716 66.667 25.70 19.40 44.79 3.86
208 209 2.350895 CATGACGTGGGCCCTCAA 59.649 61.111 25.70 8.39 0.00 3.02
209 210 2.040544 CATGACGTGGGCCCTCAAC 61.041 63.158 25.70 12.48 0.00 3.18
210 211 3.268103 ATGACGTGGGCCCTCAACC 62.268 63.158 25.70 11.45 0.00 3.77
217 218 4.115199 GGCCCTCAACCGCTCCAT 62.115 66.667 0.00 0.00 0.00 3.41
218 219 2.514824 GCCCTCAACCGCTCCATC 60.515 66.667 0.00 0.00 0.00 3.51
219 220 2.989639 CCCTCAACCGCTCCATCA 59.010 61.111 0.00 0.00 0.00 3.07
220 221 1.528824 CCCTCAACCGCTCCATCAT 59.471 57.895 0.00 0.00 0.00 2.45
221 222 0.533755 CCCTCAACCGCTCCATCATC 60.534 60.000 0.00 0.00 0.00 2.92
222 223 0.877649 CCTCAACCGCTCCATCATCG 60.878 60.000 0.00 0.00 0.00 3.84
223 224 1.493950 CTCAACCGCTCCATCATCGC 61.494 60.000 0.00 0.00 0.00 4.58
224 225 2.203070 AACCGCTCCATCATCGCC 60.203 61.111 0.00 0.00 0.00 5.54
225 226 3.030168 AACCGCTCCATCATCGCCA 62.030 57.895 0.00 0.00 0.00 5.69
226 227 2.969238 CCGCTCCATCATCGCCAC 60.969 66.667 0.00 0.00 0.00 5.01
227 228 2.202919 CGCTCCATCATCGCCACA 60.203 61.111 0.00 0.00 0.00 4.17
228 229 2.242572 CGCTCCATCATCGCCACAG 61.243 63.158 0.00 0.00 0.00 3.66
229 230 1.144716 GCTCCATCATCGCCACAGA 59.855 57.895 0.00 0.00 0.00 3.41
230 231 0.879400 GCTCCATCATCGCCACAGAG 60.879 60.000 0.00 0.00 0.00 3.35
231 232 0.749049 CTCCATCATCGCCACAGAGA 59.251 55.000 0.00 0.00 0.00 3.10
232 233 0.461548 TCCATCATCGCCACAGAGAC 59.538 55.000 0.00 0.00 0.00 3.36
233 234 0.873312 CCATCATCGCCACAGAGACG 60.873 60.000 0.00 0.00 0.00 4.18
234 235 0.101219 CATCATCGCCACAGAGACGA 59.899 55.000 0.00 0.00 40.53 4.20
235 236 0.101399 ATCATCGCCACAGAGACGAC 59.899 55.000 0.00 0.00 38.85 4.34
236 237 0.960861 TCATCGCCACAGAGACGACT 60.961 55.000 0.00 0.00 38.85 4.18
237 238 0.799917 CATCGCCACAGAGACGACTG 60.800 60.000 0.00 0.00 42.78 3.51
238 239 2.549611 ATCGCCACAGAGACGACTGC 62.550 60.000 0.00 0.00 41.06 4.40
239 240 2.653702 GCCACAGAGACGACTGCT 59.346 61.111 0.00 0.00 41.06 4.24
240 241 1.883732 GCCACAGAGACGACTGCTA 59.116 57.895 0.00 0.00 41.06 3.49
241 242 0.179150 GCCACAGAGACGACTGCTAG 60.179 60.000 0.00 0.00 41.06 3.42
242 243 0.453793 CCACAGAGACGACTGCTAGG 59.546 60.000 0.00 0.00 41.06 3.02
243 244 0.179150 CACAGAGACGACTGCTAGGC 60.179 60.000 0.00 0.00 41.06 3.93
250 251 4.498520 GACTGCTAGGCGCTGCGA 62.499 66.667 28.07 3.63 40.84 5.10
251 252 3.781770 GACTGCTAGGCGCTGCGAT 62.782 63.158 28.07 15.68 40.84 4.58
252 253 2.587194 CTGCTAGGCGCTGCGATT 60.587 61.111 28.07 14.85 40.11 3.34
253 254 2.879070 CTGCTAGGCGCTGCGATTG 61.879 63.158 28.07 14.72 40.11 2.67
254 255 4.305036 GCTAGGCGCTGCGATTGC 62.305 66.667 28.07 20.33 43.20 3.56
267 268 6.088085 GCGCTGCGATTGCTTTTAAAATATAT 59.912 34.615 28.07 0.00 43.34 0.86
268 269 7.431628 CGCTGCGATTGCTTTTAAAATATATG 58.568 34.615 18.66 0.00 43.34 1.78
290 291 1.068127 GTATAGCGTTGGATGACCGGT 59.932 52.381 6.92 6.92 39.42 5.28
296 297 1.435577 GTTGGATGACCGGTACACAC 58.564 55.000 7.34 5.09 39.42 3.82
316 317 3.429543 CACATGTGGAAGAAAATTTGCGG 59.570 43.478 18.51 0.00 0.00 5.69
321 322 2.295909 TGGAAGAAAATTTGCGGGTGAG 59.704 45.455 0.00 0.00 0.00 3.51
325 326 1.343142 GAAAATTTGCGGGTGAGGGTT 59.657 47.619 0.00 0.00 0.00 4.11
327 328 0.178975 AATTTGCGGGTGAGGGTTGA 60.179 50.000 0.00 0.00 0.00 3.18
341 342 4.202567 TGAGGGTTGAAGATGCCTTAAAGT 60.203 41.667 0.00 0.00 31.62 2.66
418 427 2.667348 GAACAGGAGTTCCCCTCGA 58.333 57.895 0.00 0.00 46.68 4.04
424 433 0.178301 GGAGTTCCCCTCGAATCCAC 59.822 60.000 0.00 0.00 41.46 4.02
439 448 2.328099 CCACTCTCCAAGCGCAACC 61.328 63.158 11.47 0.00 0.00 3.77
490 499 2.632028 AGAATCGCAGCTCCATGATAGT 59.368 45.455 0.00 0.00 0.00 2.12
866 1188 2.682494 TTCCGTCTCCTTCCCCCG 60.682 66.667 0.00 0.00 0.00 5.73
994 1556 1.139947 CTCTTCCTTCTCCGGCGAC 59.860 63.158 9.30 0.00 0.00 5.19
1048 1610 1.707989 AGCGATAGAGAGAGATCCCCA 59.292 52.381 0.00 0.00 39.76 4.96
1051 1613 3.287222 CGATAGAGAGAGATCCCCATCC 58.713 54.545 0.00 0.00 39.76 3.51
1058 1620 3.457749 AGAGAGATCCCCATCCTGTTTTC 59.542 47.826 0.00 0.00 0.00 2.29
1145 1711 0.684535 TTCTTGCGTGTCCCTGATGA 59.315 50.000 0.00 0.00 0.00 2.92
1460 2026 3.074369 TCCTCGCCAGCATTCGGA 61.074 61.111 0.00 0.00 0.00 4.55
1745 2326 0.033991 TCCTAACCTCTGCTCGCTCT 60.034 55.000 0.00 0.00 0.00 4.09
2005 2586 1.298339 GAACTGTGTGCACGTTGGC 60.298 57.895 13.13 0.44 31.78 4.52
2658 3239 2.373169 TCACTGACAATGGGCTTCTTCT 59.627 45.455 0.00 0.00 0.00 2.85
2966 3547 1.338200 GCTCTAAGGTCACACAGGTGG 60.338 57.143 4.24 0.00 45.32 4.61
3123 3707 1.155859 TTCATTGCTGGTGGGGCTT 59.844 52.632 0.00 0.00 0.00 4.35
3129 3713 1.207488 TGCTGGTGGGGCTTGTCTAT 61.207 55.000 0.00 0.00 0.00 1.98
3588 4175 1.597742 ATGTTGAGGTGCTGTGTGTC 58.402 50.000 0.00 0.00 0.00 3.67
3597 4184 2.320367 GTGCTGTGTGTCGTTCTCTAG 58.680 52.381 0.00 0.00 0.00 2.43
3598 4185 1.954382 TGCTGTGTGTCGTTCTCTAGT 59.046 47.619 0.00 0.00 0.00 2.57
3750 4340 2.983192 TGACAGGTCCCTGATTTTACCA 59.017 45.455 19.95 3.63 46.30 3.25
3878 4470 5.627499 TGTTTATCAAGGATGTCAAGTGC 57.373 39.130 0.00 0.00 0.00 4.40
3931 4523 1.660560 GGCTGCTCGATGTGCCAAAT 61.661 55.000 15.00 0.00 44.34 2.32
4033 4625 3.061322 TCTTGTACAATTCCGGTTCGTG 58.939 45.455 9.13 0.00 0.00 4.35
4043 4635 0.600255 CCGGTTCGTGCTTCTCTTGT 60.600 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.263816 GGGCCCTTAGGATATAAAGGTTCC 60.264 50.000 17.04 9.11 40.64 3.62
1 2 4.602294 AGGGCCCTTAGGATATAAAGGTTC 59.398 45.833 22.28 0.00 40.64 3.62
2 3 4.588520 AGGGCCCTTAGGATATAAAGGTT 58.411 43.478 22.28 0.00 40.64 3.50
3 4 4.176753 GAGGGCCCTTAGGATATAAAGGT 58.823 47.826 29.39 0.00 40.64 3.50
4 5 3.523972 GGAGGGCCCTTAGGATATAAAGG 59.476 52.174 29.39 4.63 41.69 3.11
5 6 4.846168 GGAGGGCCCTTAGGATATAAAG 57.154 50.000 29.39 0.00 33.47 1.85
19 20 0.106967 GACATTCTCTTGGGAGGGCC 60.107 60.000 0.00 0.00 39.86 5.80
20 21 0.620556 TGACATTCTCTTGGGAGGGC 59.379 55.000 0.00 0.00 39.86 5.19
21 22 1.407989 GCTGACATTCTCTTGGGAGGG 60.408 57.143 0.00 0.00 39.86 4.30
22 23 1.741732 CGCTGACATTCTCTTGGGAGG 60.742 57.143 0.00 0.00 39.86 4.30
23 24 1.649664 CGCTGACATTCTCTTGGGAG 58.350 55.000 0.00 0.00 40.73 4.30
24 25 0.250234 CCGCTGACATTCTCTTGGGA 59.750 55.000 0.00 0.00 0.00 4.37
25 26 1.372087 GCCGCTGACATTCTCTTGGG 61.372 60.000 0.00 0.00 0.00 4.12
26 27 1.372087 GGCCGCTGACATTCTCTTGG 61.372 60.000 0.00 0.00 0.00 3.61
27 28 1.372087 GGGCCGCTGACATTCTCTTG 61.372 60.000 0.00 0.00 0.00 3.02
28 29 1.078143 GGGCCGCTGACATTCTCTT 60.078 57.895 0.00 0.00 0.00 2.85
29 30 2.586792 GGGCCGCTGACATTCTCT 59.413 61.111 0.00 0.00 0.00 3.10
30 31 2.514824 GGGGCCGCTGACATTCTC 60.515 66.667 13.57 0.00 0.00 2.87
31 32 3.011517 AGGGGCCGCTGACATTCT 61.012 61.111 23.51 0.00 0.00 2.40
32 33 2.514824 GAGGGGCCGCTGACATTC 60.515 66.667 29.42 7.99 0.00 2.67
33 34 4.473520 CGAGGGGCCGCTGACATT 62.474 66.667 29.42 0.76 0.00 2.71
51 52 2.760387 AAAACGACGGTCCTCGAGCC 62.760 60.000 6.99 2.59 42.43 4.70
52 53 1.342796 GAAAACGACGGTCCTCGAGC 61.343 60.000 6.99 0.00 42.43 5.03
53 54 0.039798 TGAAAACGACGGTCCTCGAG 60.040 55.000 5.13 5.13 42.43 4.04
54 55 0.385029 TTGAAAACGACGGTCCTCGA 59.615 50.000 15.00 0.00 42.43 4.04
55 56 0.782384 CTTGAAAACGACGGTCCTCG 59.218 55.000 1.91 8.60 45.88 4.63
56 57 1.145803 CCTTGAAAACGACGGTCCTC 58.854 55.000 1.91 0.00 0.00 3.71
57 58 0.754472 TCCTTGAAAACGACGGTCCT 59.246 50.000 1.91 0.00 0.00 3.85
58 59 1.145803 CTCCTTGAAAACGACGGTCC 58.854 55.000 1.91 0.00 0.00 4.46
59 60 1.145803 CCTCCTTGAAAACGACGGTC 58.854 55.000 0.00 0.00 0.00 4.79
60 61 0.754472 TCCTCCTTGAAAACGACGGT 59.246 50.000 0.00 0.00 0.00 4.83
61 62 1.429463 CTCCTCCTTGAAAACGACGG 58.571 55.000 0.00 0.00 0.00 4.79
62 63 0.790814 GCTCCTCCTTGAAAACGACG 59.209 55.000 0.00 0.00 0.00 5.12
63 64 0.790814 CGCTCCTCCTTGAAAACGAC 59.209 55.000 0.00 0.00 0.00 4.34
64 65 0.677288 TCGCTCCTCCTTGAAAACGA 59.323 50.000 0.00 0.00 0.00 3.85
65 66 1.071605 CTCGCTCCTCCTTGAAAACG 58.928 55.000 0.00 0.00 0.00 3.60
66 67 0.799393 GCTCGCTCCTCCTTGAAAAC 59.201 55.000 0.00 0.00 0.00 2.43
67 68 0.670546 CGCTCGCTCCTCCTTGAAAA 60.671 55.000 0.00 0.00 0.00 2.29
68 69 1.079819 CGCTCGCTCCTCCTTGAAA 60.080 57.895 0.00 0.00 0.00 2.69
69 70 2.573869 CGCTCGCTCCTCCTTGAA 59.426 61.111 0.00 0.00 0.00 2.69
70 71 3.452786 CCGCTCGCTCCTCCTTGA 61.453 66.667 0.00 0.00 0.00 3.02
93 94 1.139734 AGTCGTACCGCATCTGCTG 59.860 57.895 0.09 0.00 39.32 4.41
94 95 1.139734 CAGTCGTACCGCATCTGCT 59.860 57.895 0.09 0.00 39.32 4.24
95 96 1.878522 CCAGTCGTACCGCATCTGC 60.879 63.158 0.00 0.00 37.78 4.26
96 97 0.802222 CACCAGTCGTACCGCATCTG 60.802 60.000 0.00 0.00 0.00 2.90
97 98 1.511305 CACCAGTCGTACCGCATCT 59.489 57.895 0.00 0.00 0.00 2.90
98 99 2.165301 GCACCAGTCGTACCGCATC 61.165 63.158 0.00 0.00 0.00 3.91
99 100 2.125673 GCACCAGTCGTACCGCAT 60.126 61.111 0.00 0.00 0.00 4.73
100 101 3.153270 TTGCACCAGTCGTACCGCA 62.153 57.895 0.00 0.00 0.00 5.69
101 102 2.356553 TTGCACCAGTCGTACCGC 60.357 61.111 0.00 0.00 0.00 5.68
102 103 1.300311 TGTTGCACCAGTCGTACCG 60.300 57.895 0.00 0.00 0.00 4.02
103 104 2.231820 GTGTTGCACCAGTCGTACC 58.768 57.895 0.00 0.00 0.00 3.34
128 129 2.355363 TTCACGAACACGGAGCGG 60.355 61.111 0.00 0.00 0.00 5.52
129 130 1.606350 GACTTCACGAACACGGAGCG 61.606 60.000 0.00 0.00 0.00 5.03
130 131 1.282930 GGACTTCACGAACACGGAGC 61.283 60.000 0.00 0.00 0.00 4.70
131 132 1.002250 CGGACTTCACGAACACGGAG 61.002 60.000 0.00 0.00 0.00 4.63
132 133 1.008194 CGGACTTCACGAACACGGA 60.008 57.895 0.00 0.00 0.00 4.69
133 134 1.008194 TCGGACTTCACGAACACGG 60.008 57.895 0.00 0.00 37.42 4.94
134 135 1.594269 CGTCGGACTTCACGAACACG 61.594 60.000 6.57 0.00 42.55 4.49
135 136 1.873355 GCGTCGGACTTCACGAACAC 61.873 60.000 6.57 0.00 42.55 3.32
136 137 1.659335 GCGTCGGACTTCACGAACA 60.659 57.895 6.57 0.00 42.55 3.18
137 138 1.210545 TTGCGTCGGACTTCACGAAC 61.211 55.000 6.57 0.00 42.55 3.95
138 139 1.066093 TTGCGTCGGACTTCACGAA 59.934 52.632 6.57 0.00 42.55 3.85
139 140 1.659335 GTTGCGTCGGACTTCACGA 60.659 57.895 6.57 0.00 38.32 4.35
140 141 2.844146 GTTGCGTCGGACTTCACG 59.156 61.111 6.57 0.00 39.09 4.35
141 142 2.844146 CGTTGCGTCGGACTTCAC 59.156 61.111 6.57 0.00 0.00 3.18
142 143 3.033764 GCGTTGCGTCGGACTTCA 61.034 61.111 6.57 1.40 0.00 3.02
143 144 3.774702 GGCGTTGCGTCGGACTTC 61.775 66.667 6.57 0.00 0.00 3.01
150 151 2.202298 CCATTTCGGCGTTGCGTC 60.202 61.111 6.85 0.00 0.00 5.19
151 152 3.732892 CCCATTTCGGCGTTGCGT 61.733 61.111 6.85 0.00 0.00 5.24
159 160 3.564027 GTCGCGAGCCCATTTCGG 61.564 66.667 10.24 0.00 38.45 4.30
160 161 3.913573 CGTCGCGAGCCCATTTCG 61.914 66.667 10.24 2.39 40.85 3.46
161 162 2.508439 TCGTCGCGAGCCCATTTC 60.508 61.111 10.24 0.00 0.00 2.17
162 163 2.813908 GTCGTCGCGAGCCCATTT 60.814 61.111 10.24 0.00 36.23 2.32
163 164 4.814294 GGTCGTCGCGAGCCCATT 62.814 66.667 10.24 0.00 46.63 3.16
169 170 3.110178 GGTTTGGGTCGTCGCGAG 61.110 66.667 10.24 3.82 36.23 5.03
170 171 3.562779 GAGGTTTGGGTCGTCGCGA 62.563 63.158 3.71 3.71 0.00 5.87
171 172 3.110178 GAGGTTTGGGTCGTCGCG 61.110 66.667 0.00 0.00 0.00 5.87
172 173 3.110178 CGAGGTTTGGGTCGTCGC 61.110 66.667 0.00 0.00 36.66 5.19
173 174 3.110178 GCGAGGTTTGGGTCGTCG 61.110 66.667 0.00 0.00 43.09 5.12
174 175 2.741211 GGCGAGGTTTGGGTCGTC 60.741 66.667 0.00 0.00 38.48 4.20
175 176 2.890766 ATGGCGAGGTTTGGGTCGT 61.891 57.895 0.00 0.00 38.48 4.34
176 177 2.046314 ATGGCGAGGTTTGGGTCG 60.046 61.111 0.00 0.00 39.25 4.79
177 178 1.002624 TCATGGCGAGGTTTGGGTC 60.003 57.895 0.00 0.00 0.00 4.46
178 179 1.303317 GTCATGGCGAGGTTTGGGT 60.303 57.895 0.00 0.00 0.00 4.51
179 180 2.398554 CGTCATGGCGAGGTTTGGG 61.399 63.158 16.21 0.00 0.00 4.12
180 181 1.671054 ACGTCATGGCGAGGTTTGG 60.671 57.895 28.94 0.00 39.72 3.28
181 182 1.497278 CACGTCATGGCGAGGTTTG 59.503 57.895 28.94 10.03 40.73 2.93
182 183 1.671054 CCACGTCATGGCGAGGTTT 60.671 57.895 28.94 0.00 43.24 3.27
183 184 2.047274 CCACGTCATGGCGAGGTT 60.047 61.111 28.94 0.00 43.24 3.50
191 192 2.040544 GTTGAGGGCCCACGTCATG 61.041 63.158 27.56 0.00 42.91 3.07
192 193 2.351276 GTTGAGGGCCCACGTCAT 59.649 61.111 27.56 0.00 42.91 3.06
193 194 3.948719 GGTTGAGGGCCCACGTCA 61.949 66.667 27.56 17.10 41.83 4.35
200 201 4.115199 ATGGAGCGGTTGAGGGCC 62.115 66.667 0.00 0.00 0.00 5.80
201 202 2.514824 GATGGAGCGGTTGAGGGC 60.515 66.667 0.00 0.00 0.00 5.19
202 203 0.533755 GATGATGGAGCGGTTGAGGG 60.534 60.000 0.00 0.00 0.00 4.30
203 204 0.877649 CGATGATGGAGCGGTTGAGG 60.878 60.000 0.00 0.00 0.00 3.86
204 205 1.493950 GCGATGATGGAGCGGTTGAG 61.494 60.000 0.00 0.00 32.74 3.02
205 206 1.521457 GCGATGATGGAGCGGTTGA 60.521 57.895 0.00 0.00 32.74 3.18
206 207 2.537560 GGCGATGATGGAGCGGTTG 61.538 63.158 0.00 0.00 32.74 3.77
207 208 2.203070 GGCGATGATGGAGCGGTT 60.203 61.111 0.00 0.00 32.74 4.44
208 209 3.469970 TGGCGATGATGGAGCGGT 61.470 61.111 0.00 0.00 32.74 5.68
209 210 2.969238 GTGGCGATGATGGAGCGG 60.969 66.667 0.00 0.00 32.74 5.52
210 211 2.202919 TGTGGCGATGATGGAGCG 60.203 61.111 0.00 0.00 36.22 5.03
211 212 0.879400 CTCTGTGGCGATGATGGAGC 60.879 60.000 0.00 0.00 0.00 4.70
212 213 0.749049 TCTCTGTGGCGATGATGGAG 59.251 55.000 0.00 0.00 0.00 3.86
213 214 0.461548 GTCTCTGTGGCGATGATGGA 59.538 55.000 0.00 0.00 0.00 3.41
214 215 2.983433 GTCTCTGTGGCGATGATGG 58.017 57.895 0.00 0.00 0.00 3.51
221 222 1.923227 TAGCAGTCGTCTCTGTGGCG 61.923 60.000 0.00 0.00 46.47 5.69
222 223 0.179150 CTAGCAGTCGTCTCTGTGGC 60.179 60.000 0.00 0.00 37.70 5.01
223 224 0.453793 CCTAGCAGTCGTCTCTGTGG 59.546 60.000 0.00 0.00 37.70 4.17
224 225 0.179150 GCCTAGCAGTCGTCTCTGTG 60.179 60.000 0.00 0.00 37.70 3.66
225 226 1.649390 CGCCTAGCAGTCGTCTCTGT 61.649 60.000 0.00 0.00 37.70 3.41
226 227 1.063327 CGCCTAGCAGTCGTCTCTG 59.937 63.158 0.00 0.00 38.35 3.35
227 228 3.503749 CGCCTAGCAGTCGTCTCT 58.496 61.111 0.00 0.00 0.00 3.10
238 239 1.709147 AAAGCAATCGCAGCGCCTAG 61.709 55.000 10.87 0.68 42.27 3.02
239 240 1.305219 AAAAGCAATCGCAGCGCCTA 61.305 50.000 10.87 0.00 42.27 3.93
240 241 1.305219 TAAAAGCAATCGCAGCGCCT 61.305 50.000 10.87 0.33 42.27 5.52
241 242 0.455972 TTAAAAGCAATCGCAGCGCC 60.456 50.000 10.87 0.00 42.27 6.53
242 243 1.335935 TTTAAAAGCAATCGCAGCGC 58.664 45.000 10.87 0.00 42.27 5.92
243 244 5.871531 ATATTTTAAAAGCAATCGCAGCG 57.128 34.783 9.06 9.06 42.27 5.18
244 245 8.209869 CACATATATTTTAAAAGCAATCGCAGC 58.790 33.333 6.79 0.00 42.27 5.25
245 246 9.236691 ACACATATATTTTAAAAGCAATCGCAG 57.763 29.630 6.79 0.00 42.27 5.18
267 268 2.480587 CGGTCATCCAACGCTATACACA 60.481 50.000 0.00 0.00 0.00 3.72
268 269 2.124903 CGGTCATCCAACGCTATACAC 58.875 52.381 0.00 0.00 0.00 2.90
290 291 5.982516 GCAAATTTTCTTCCACATGTGTGTA 59.017 36.000 23.79 6.87 44.21 2.90
296 297 2.995258 CCCGCAAATTTTCTTCCACATG 59.005 45.455 0.00 0.00 0.00 3.21
303 304 1.618343 CCCTCACCCGCAAATTTTCTT 59.382 47.619 0.00 0.00 0.00 2.52
316 317 0.329596 AGGCATCTTCAACCCTCACC 59.670 55.000 0.00 0.00 0.00 4.02
321 322 4.079253 TCACTTTAAGGCATCTTCAACCC 58.921 43.478 0.00 0.00 34.59 4.11
325 326 3.308402 CCCCTCACTTTAAGGCATCTTCA 60.308 47.826 0.00 0.00 34.59 3.02
327 328 2.919602 TCCCCTCACTTTAAGGCATCTT 59.080 45.455 0.00 0.00 37.03 2.40
408 417 1.137282 GAGAGTGGATTCGAGGGGAAC 59.863 57.143 0.00 0.00 37.50 3.62
417 426 0.391661 TGCGCTTGGAGAGTGGATTC 60.392 55.000 9.73 0.00 36.37 2.52
418 427 0.036732 TTGCGCTTGGAGAGTGGATT 59.963 50.000 9.73 0.00 36.05 3.01
424 433 0.603707 TTCAGGTTGCGCTTGGAGAG 60.604 55.000 9.73 0.00 0.00 3.20
439 448 7.644157 CCTCTACTTTTCGTTTTCCTTTTTCAG 59.356 37.037 0.00 0.00 0.00 3.02
449 458 7.116519 CGATTCTTCTCCTCTACTTTTCGTTTT 59.883 37.037 0.00 0.00 0.00 2.43
490 499 0.451628 CACGCGTCTTCGTCTTCGTA 60.452 55.000 9.86 0.00 41.21 3.43
934 1496 1.569479 GCACGACCAAGAACAGAGCC 61.569 60.000 0.00 0.00 0.00 4.70
935 1497 0.601311 AGCACGACCAAGAACAGAGC 60.601 55.000 0.00 0.00 0.00 4.09
936 1498 1.000283 AGAGCACGACCAAGAACAGAG 60.000 52.381 0.00 0.00 0.00 3.35
1048 1610 6.409234 GGGGAAAAGAAAAAGGAAAACAGGAT 60.409 38.462 0.00 0.00 0.00 3.24
1051 1613 4.808895 CGGGGAAAAGAAAAAGGAAAACAG 59.191 41.667 0.00 0.00 0.00 3.16
1058 1620 4.142038 TCTCTTCGGGGAAAAGAAAAAGG 58.858 43.478 0.00 0.00 32.60 3.11
1121 1687 2.037902 TCAGGGACACGCAAGAACAATA 59.962 45.455 0.00 0.00 43.62 1.90
1122 1688 1.202758 TCAGGGACACGCAAGAACAAT 60.203 47.619 0.00 0.00 43.62 2.71
1145 1711 2.412870 TGACGCAATCGAAGAACACAT 58.587 42.857 0.00 0.00 43.58 3.21
1205 1771 3.706373 ACCGCGGCAGAACATCCT 61.706 61.111 28.58 0.00 0.00 3.24
1718 2299 1.609501 AGAGGTTAGGACTGCCGCA 60.610 57.895 0.00 0.00 39.96 5.69
1745 2326 4.758251 CGGCACATCCCACAGCGA 62.758 66.667 0.00 0.00 0.00 4.93
2005 2586 0.815615 GGCTAGAAATGCCCTGGTCG 60.816 60.000 0.00 0.00 44.32 4.79
2044 2625 1.017387 GACGGATCTTGGCCAATGAC 58.983 55.000 20.85 12.54 0.00 3.06
2048 2629 1.198094 TGGAGACGGATCTTGGCCAA 61.198 55.000 19.25 19.25 34.34 4.52
2658 3239 5.174037 ACCCTCGGAAGATTTTATCAACA 57.826 39.130 0.00 0.00 40.84 3.33
2966 3547 4.043200 GCCCAAGAACTGCACGCC 62.043 66.667 0.00 0.00 0.00 5.68
3123 3707 1.220749 GCGGCTGACCCAATAGACA 59.779 57.895 0.00 0.00 0.00 3.41
3333 3920 1.208776 CAGGATGCCAGTGATGACAGA 59.791 52.381 0.00 0.00 0.00 3.41
3356 3943 2.276740 GGTGCCTGGATGGAAGGG 59.723 66.667 0.00 0.00 38.35 3.95
3588 4175 2.789339 CACACACACACACTAGAGAACG 59.211 50.000 0.00 0.00 0.00 3.95
3597 4184 1.063912 CATGACACCACACACACACAC 59.936 52.381 0.00 0.00 0.00 3.82
3598 4185 1.339535 ACATGACACCACACACACACA 60.340 47.619 0.00 0.00 0.00 3.72
3646 4234 2.667470 TCCCGAAGACCAGATTCCTAG 58.333 52.381 0.00 0.00 0.00 3.02
3750 4340 4.558226 TTACAGTCCTCAACATCATGCT 57.442 40.909 0.00 0.00 0.00 3.79
3878 4470 6.311445 AGAATGCATCTTGTTACTAGACAACG 59.689 38.462 0.00 0.00 33.39 4.10
3931 4523 7.176340 CCAAAATATGCCCCTCAAATTTCAAAA 59.824 33.333 0.00 0.00 0.00 2.44
3989 4581 9.699410 AAGACAACATGGGAAGAAATATAATCA 57.301 29.630 0.00 0.00 0.00 2.57
4026 4618 1.149148 GGACAAGAGAAGCACGAACC 58.851 55.000 0.00 0.00 0.00 3.62
4029 4621 1.402852 CGATGGACAAGAGAAGCACGA 60.403 52.381 0.00 0.00 0.00 4.35
4033 4625 1.731720 AAGCGATGGACAAGAGAAGC 58.268 50.000 0.00 0.00 0.00 3.86
4043 4635 5.049474 GCATATCATGTGTTAAAGCGATGGA 60.049 40.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.