Multiple sequence alignment - TraesCS2B01G037200

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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 TraesCS2B01G037200 chr2B 100.000 3446 0 0 1 3446 17458482 17461927 0.000000e+00 6364.0
1 TraesCS2B01G037200 chr2B 97.420 2984 56 6 248 3213 17161943 17164923 0.000000e+00 5064.0
2 TraesCS2B01G037200 chr2B 91.168 1721 86 22 300 1989 17492186 17490501 0.000000e+00 2276.0
3 TraesCS2B01G037200 chr2B 93.588 1388 60 12 1165 2552 17033325 17031967 0.000000e+00 2043.0
4 TraesCS2B01G037200 chr2B 93.633 911 45 8 2536 3446 17031925 17031028 0.000000e+00 1349.0
5 TraesCS2B01G037200 chr2B 94.415 573 31 1 1980 2552 17485952 17485381 0.000000e+00 880.0
6 TraesCS2B01G037200 chr2B 93.793 145 5 4 2536 2680 17485339 17485199 7.490000e-52 215.0
7 TraesCS2B01G037200 chr2B 84.884 172 26 0 1357 1528 17528966 17529137 1.270000e-39 174.0
8 TraesCS2B01G037200 chr2D 90.460 2327 160 31 248 2552 11314876 11312590 0.000000e+00 3011.0
9 TraesCS2B01G037200 chr2D 85.836 939 89 25 2536 3441 11312548 11311621 0.000000e+00 957.0
10 TraesCS2B01G037200 chr2D 87.549 763 79 12 394 1148 11389544 11390298 0.000000e+00 869.0
11 TraesCS2B01G037200 chr2D 85.141 747 99 11 410 1148 11169409 11168667 0.000000e+00 754.0
12 TraesCS2B01G037200 chr2D 84.786 723 101 9 410 1127 11309285 11308567 0.000000e+00 717.0
13 TraesCS2B01G037200 chr2D 85.065 308 44 2 2132 2439 26380924 26380619 2.580000e-81 313.0
14 TraesCS2B01G037200 chr2D 93.909 197 7 3 1 193 117188526 117188331 3.360000e-75 292.0
15 TraesCS2B01G037200 chr2D 92.271 207 10 5 1 203 102661042 102661246 4.350000e-74 289.0
16 TraesCS2B01G037200 chrUn 88.577 1462 122 22 248 1675 345395874 345397324 0.000000e+00 1733.0
17 TraesCS2B01G037200 chrUn 90.063 956 65 14 248 1181 409964665 409963718 0.000000e+00 1212.0
18 TraesCS2B01G037200 chrUn 91.284 631 51 3 1917 2547 463210718 463211344 0.000000e+00 857.0
19 TraesCS2B01G037200 chrUn 90.650 631 55 3 1917 2547 403133617 403132991 0.000000e+00 835.0
20 TraesCS2B01G037200 chrUn 90.774 607 52 3 1917 2523 472465365 472465967 0.000000e+00 808.0
21 TraesCS2B01G037200 chrUn 100.000 398 0 0 2289 2686 478980869 478981266 0.000000e+00 736.0
22 TraesCS2B01G037200 chrUn 91.195 477 37 3 1700 2176 449633131 449632660 0.000000e+00 643.0
23 TraesCS2B01G037200 chrUn 86.250 560 62 8 1128 1675 449633681 449633125 8.230000e-166 593.0
24 TraesCS2B01G037200 chrUn 92.120 368 28 1 2180 2547 433865566 433865932 5.100000e-143 518.0
25 TraesCS2B01G037200 chrUn 82.072 251 39 2 1357 1607 313025838 313026082 3.480000e-50 209.0
26 TraesCS2B01G037200 chrUn 80.952 252 42 3 1357 1608 12511253 12511008 9.760000e-46 195.0
27 TraesCS2B01G037200 chrUn 78.333 120 14 6 2536 2652 403132944 403132834 2.220000e-07 67.6
28 TraesCS2B01G037200 chrUn 78.333 120 14 6 2536 2652 433865979 433866089 2.220000e-07 67.6
29 TraesCS2B01G037200 chrUn 90.909 44 2 2 2536 2579 463211391 463211432 1.340000e-04 58.4
30 TraesCS2B01G037200 chrUn 100.000 29 0 0 1700 1728 345397318 345397346 2.000000e-03 54.7
31 TraesCS2B01G037200 chr3D 84.485 767 106 12 388 1149 478540043 478539285 0.000000e+00 745.0
32 TraesCS2B01G037200 chr3D 94.416 197 7 2 1 193 568485001 568484805 2.010000e-77 300.0
33 TraesCS2B01G037200 chr3D 93.467 199 8 4 1 194 332148897 332149095 1.210000e-74 291.0
34 TraesCS2B01G037200 chr7B 93.909 197 8 2 1 193 745069179 745068983 9.350000e-76 294.0
35 TraesCS2B01G037200 chr1D 92.344 209 10 4 1 205 394338654 394338448 3.360000e-75 292.0
36 TraesCS2B01G037200 chr5D 93.467 199 7 4 1 194 69680384 69680581 1.210000e-74 291.0
37 TraesCS2B01G037200 chr2A 91.905 210 11 5 1 205 26032007 26032215 4.350000e-74 289.0
38 TraesCS2B01G037200 chr3A 93.000 200 8 5 1 196 675302417 675302220 1.570000e-73 287.0


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 TraesCS2B01G037200 chr2B 17458482 17461927 3445 False 6364.000000 6364 100.000000 1 3446 1 chr2B.!!$F2 3445
1 TraesCS2B01G037200 chr2B 17161943 17164923 2980 False 5064.000000 5064 97.420000 248 3213 1 chr2B.!!$F1 2965
2 TraesCS2B01G037200 chr2B 17490501 17492186 1685 True 2276.000000 2276 91.168000 300 1989 1 chr2B.!!$R1 1689
3 TraesCS2B01G037200 chr2B 17031028 17033325 2297 True 1696.000000 2043 93.610500 1165 3446 2 chr2B.!!$R2 2281
4 TraesCS2B01G037200 chr2B 17485199 17485952 753 True 547.500000 880 94.104000 1980 2680 2 chr2B.!!$R3 700
5 TraesCS2B01G037200 chr2D 11308567 11314876 6309 True 1561.666667 3011 87.027333 248 3441 3 chr2D.!!$R4 3193
6 TraesCS2B01G037200 chr2D 11389544 11390298 754 False 869.000000 869 87.549000 394 1148 1 chr2D.!!$F1 754
7 TraesCS2B01G037200 chr2D 11168667 11169409 742 True 754.000000 754 85.141000 410 1148 1 chr2D.!!$R1 738
8 TraesCS2B01G037200 chrUn 409963718 409964665 947 True 1212.000000 1212 90.063000 248 1181 1 chrUn.!!$R2 933
9 TraesCS2B01G037200 chrUn 345395874 345397346 1472 False 893.850000 1733 94.288500 248 1728 2 chrUn.!!$F4 1480
10 TraesCS2B01G037200 chrUn 472465365 472465967 602 False 808.000000 808 90.774000 1917 2523 1 chrUn.!!$F2 606
11 TraesCS2B01G037200 chrUn 449632660 449633681 1021 True 618.000000 643 88.722500 1128 2176 2 chrUn.!!$R4 1048
12 TraesCS2B01G037200 chrUn 463210718 463211432 714 False 457.700000 857 91.096500 1917 2579 2 chrUn.!!$F6 662
13 TraesCS2B01G037200 chrUn 403132834 403133617 783 True 451.300000 835 84.491500 1917 2652 2 chrUn.!!$R3 735
14 TraesCS2B01G037200 chrUn 433865566 433866089 523 False 292.800000 518 85.226500 2180 2652 2 chrUn.!!$F5 472
15 TraesCS2B01G037200 chr3D 478539285 478540043 758 True 745.000000 745 84.485000 388 1149 1 chr3D.!!$R1 761

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
192 193 0.108138 GGCGCAACTGGTCATCTAGT 60.108 55.0 10.83 0.0 36.97 2.57 F
1065 1104 0.389948 GCCCGTCATCGTTCAACTCT 60.390 55.0 0.00 0.0 35.01 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1373 1419 0.320771 GGACTGCATCCGACACTGTT 60.321 55.000 0.00 0.0 37.88 3.16 R
2851 2971 1.334869 CAAGTGAAACCTCTTTGCGCT 59.665 47.619 9.73 0.0 37.80 5.92 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
23 24 6.978674 TCTTGACCTACCGATGATCTAATT 57.021 37.500 0.00 0.00 0.00 1.40
24 25 7.361457 TCTTGACCTACCGATGATCTAATTT 57.639 36.000 0.00 0.00 0.00 1.82
25 26 7.210174 TCTTGACCTACCGATGATCTAATTTG 58.790 38.462 0.00 0.00 0.00 2.32
26 27 6.479972 TGACCTACCGATGATCTAATTTGT 57.520 37.500 0.00 0.00 0.00 2.83
27 28 6.280643 TGACCTACCGATGATCTAATTTGTG 58.719 40.000 0.00 0.00 0.00 3.33
28 29 5.611374 ACCTACCGATGATCTAATTTGTGG 58.389 41.667 0.00 0.00 0.00 4.17
29 30 4.452455 CCTACCGATGATCTAATTTGTGGC 59.548 45.833 0.00 0.00 0.00 5.01
30 31 3.884895 ACCGATGATCTAATTTGTGGCA 58.115 40.909 0.00 0.00 0.00 4.92
31 32 4.464008 ACCGATGATCTAATTTGTGGCAT 58.536 39.130 0.00 0.00 0.00 4.40
32 33 4.889409 ACCGATGATCTAATTTGTGGCATT 59.111 37.500 0.00 0.00 0.00 3.56
33 34 6.061441 ACCGATGATCTAATTTGTGGCATTA 58.939 36.000 0.00 0.00 0.00 1.90
34 35 6.716628 ACCGATGATCTAATTTGTGGCATTAT 59.283 34.615 0.00 0.00 0.00 1.28
35 36 7.231317 ACCGATGATCTAATTTGTGGCATTATT 59.769 33.333 0.00 0.00 0.00 1.40
36 37 8.729756 CCGATGATCTAATTTGTGGCATTATTA 58.270 33.333 0.00 0.00 0.00 0.98
37 38 9.546909 CGATGATCTAATTTGTGGCATTATTAC 57.453 33.333 0.00 0.00 0.00 1.89
40 41 9.625747 TGATCTAATTTGTGGCATTATTACTCA 57.374 29.630 0.00 0.00 0.00 3.41
43 44 9.625747 TCTAATTTGTGGCATTATTACTCATGA 57.374 29.630 0.00 0.00 0.00 3.07
46 47 9.941325 AATTTGTGGCATTATTACTCATGAAAA 57.059 25.926 0.00 0.00 0.00 2.29
94 95 7.948034 TTGGGGTATAAGTTCTTACCAAATG 57.052 36.000 13.95 0.00 39.75 2.32
95 96 7.034967 TGGGGTATAAGTTCTTACCAAATGT 57.965 36.000 13.95 0.00 39.75 2.71
96 97 8.160434 TGGGGTATAAGTTCTTACCAAATGTA 57.840 34.615 13.95 0.00 39.75 2.29
97 98 8.048514 TGGGGTATAAGTTCTTACCAAATGTAC 58.951 37.037 13.95 0.00 39.75 2.90
98 99 8.270030 GGGGTATAAGTTCTTACCAAATGTACT 58.730 37.037 13.95 0.00 39.75 2.73
99 100 9.322773 GGGTATAAGTTCTTACCAAATGTACTC 57.677 37.037 13.95 0.00 39.75 2.59
100 101 9.880157 GGTATAAGTTCTTACCAAATGTACTCA 57.120 33.333 9.15 0.00 38.20 3.41
148 149 8.641499 ACAAATATTTTCAACACGAACATTGT 57.359 26.923 0.00 0.00 31.73 2.71
149 150 9.092876 ACAAATATTTTCAACACGAACATTGTT 57.907 25.926 0.63 0.63 37.69 2.83
150 151 9.913451 CAAATATTTTCAACACGAACATTGTTT 57.087 25.926 3.08 0.00 34.91 2.83
155 156 9.748100 ATTTTCAACACGAACATTGTTTTAAAC 57.252 25.926 3.08 0.20 34.91 2.01
156 157 6.541754 TCAACACGAACATTGTTTTAAACG 57.458 33.333 3.08 4.90 34.91 3.60
157 158 5.512082 TCAACACGAACATTGTTTTAAACGG 59.488 36.000 3.08 0.00 34.91 4.44
158 159 4.352887 ACACGAACATTGTTTTAAACGGG 58.647 39.130 3.08 5.94 0.00 5.28
159 160 4.142425 ACACGAACATTGTTTTAAACGGGT 60.142 37.500 9.00 9.00 0.00 5.28
160 161 4.438471 CACGAACATTGTTTTAAACGGGTC 59.562 41.667 3.08 3.20 0.00 4.46
161 162 4.336153 ACGAACATTGTTTTAAACGGGTCT 59.664 37.500 3.08 0.00 0.00 3.85
162 163 5.163632 ACGAACATTGTTTTAAACGGGTCTT 60.164 36.000 3.08 0.00 0.00 3.01
163 164 5.744819 CGAACATTGTTTTAAACGGGTCTTT 59.255 36.000 3.08 0.00 0.00 2.52
164 165 6.291374 CGAACATTGTTTTAAACGGGTCTTTG 60.291 38.462 3.08 0.00 0.00 2.77
165 166 4.806775 ACATTGTTTTAAACGGGTCTTTGC 59.193 37.500 3.28 0.00 0.00 3.68
166 167 3.067721 TGTTTTAAACGGGTCTTTGCG 57.932 42.857 3.28 0.00 0.00 4.85
167 168 1.782569 GTTTTAAACGGGTCTTTGCGC 59.217 47.619 0.00 0.00 0.00 6.09
168 169 0.311477 TTTAAACGGGTCTTTGCGCC 59.689 50.000 4.18 0.00 0.00 6.53
169 170 0.818445 TTAAACGGGTCTTTGCGCCA 60.818 50.000 4.18 0.00 0.00 5.69
170 171 0.606944 TAAACGGGTCTTTGCGCCAT 60.607 50.000 4.18 0.00 0.00 4.40
171 172 1.460273 AAACGGGTCTTTGCGCCATT 61.460 50.000 4.18 0.00 0.00 3.16
172 173 1.460273 AACGGGTCTTTGCGCCATTT 61.460 50.000 4.18 0.00 0.00 2.32
173 174 1.444212 CGGGTCTTTGCGCCATTTG 60.444 57.895 4.18 0.00 0.00 2.32
174 175 1.079888 GGGTCTTTGCGCCATTTGG 60.080 57.895 4.18 0.00 38.53 3.28
184 185 3.050339 CCATTTGGCGCAACTGGT 58.950 55.556 10.83 0.00 38.71 4.00
185 186 1.080569 CCATTTGGCGCAACTGGTC 60.081 57.895 10.83 0.00 38.71 4.02
186 187 1.659233 CATTTGGCGCAACTGGTCA 59.341 52.632 10.83 0.00 0.00 4.02
187 188 0.244450 CATTTGGCGCAACTGGTCAT 59.756 50.000 10.83 0.00 0.00 3.06
188 189 0.527565 ATTTGGCGCAACTGGTCATC 59.472 50.000 10.83 0.00 0.00 2.92
189 190 0.537143 TTTGGCGCAACTGGTCATCT 60.537 50.000 10.83 0.00 0.00 2.90
190 191 0.323302 TTGGCGCAACTGGTCATCTA 59.677 50.000 10.83 0.00 0.00 1.98
191 192 0.108186 TGGCGCAACTGGTCATCTAG 60.108 55.000 10.83 0.00 0.00 2.43
192 193 0.108138 GGCGCAACTGGTCATCTAGT 60.108 55.000 10.83 0.00 36.97 2.57
193 194 1.136305 GGCGCAACTGGTCATCTAGTA 59.864 52.381 10.83 0.00 34.34 1.82
194 195 2.224066 GGCGCAACTGGTCATCTAGTAT 60.224 50.000 10.83 0.00 34.34 2.12
195 196 2.797156 GCGCAACTGGTCATCTAGTATG 59.203 50.000 0.30 0.00 34.34 2.39
196 197 3.490933 GCGCAACTGGTCATCTAGTATGA 60.491 47.826 0.30 0.00 34.34 2.15
197 198 4.682787 CGCAACTGGTCATCTAGTATGAA 58.317 43.478 6.48 0.00 34.34 2.57
198 199 5.292765 CGCAACTGGTCATCTAGTATGAAT 58.707 41.667 6.48 0.00 34.34 2.57
199 200 5.176406 CGCAACTGGTCATCTAGTATGAATG 59.824 44.000 6.48 0.00 34.34 2.67
200 201 6.283694 GCAACTGGTCATCTAGTATGAATGA 58.716 40.000 6.48 0.00 34.34 2.57
201 202 6.763135 GCAACTGGTCATCTAGTATGAATGAA 59.237 38.462 6.48 0.00 34.34 2.57
202 203 7.280876 GCAACTGGTCATCTAGTATGAATGAAA 59.719 37.037 6.48 0.00 34.34 2.69
203 204 8.824781 CAACTGGTCATCTAGTATGAATGAAAG 58.175 37.037 6.48 4.53 34.34 2.62
204 205 7.504403 ACTGGTCATCTAGTATGAATGAAAGG 58.496 38.462 6.48 0.00 33.69 3.11
205 206 7.126421 ACTGGTCATCTAGTATGAATGAAAGGT 59.874 37.037 6.48 0.00 33.69 3.50
206 207 7.275183 TGGTCATCTAGTATGAATGAAAGGTG 58.725 38.462 6.48 0.00 0.00 4.00
207 208 6.203723 GGTCATCTAGTATGAATGAAAGGTGC 59.796 42.308 6.48 0.00 0.00 5.01
208 209 6.989169 GTCATCTAGTATGAATGAAAGGTGCT 59.011 38.462 6.48 0.00 0.00 4.40
209 210 8.144478 GTCATCTAGTATGAATGAAAGGTGCTA 58.856 37.037 6.48 0.00 0.00 3.49
210 211 8.704668 TCATCTAGTATGAATGAAAGGTGCTAA 58.295 33.333 3.32 0.00 0.00 3.09
211 212 9.330063 CATCTAGTATGAATGAAAGGTGCTAAA 57.670 33.333 0.00 0.00 0.00 1.85
212 213 9.905713 ATCTAGTATGAATGAAAGGTGCTAAAA 57.094 29.630 0.00 0.00 0.00 1.52
213 214 9.733556 TCTAGTATGAATGAAAGGTGCTAAAAA 57.266 29.630 0.00 0.00 0.00 1.94
236 237 5.774498 AACAAAAAGAACTGAGTGGATCC 57.226 39.130 4.20 4.20 0.00 3.36
237 238 4.792068 ACAAAAAGAACTGAGTGGATCCA 58.208 39.130 11.44 11.44 0.00 3.41
238 239 5.200483 ACAAAAAGAACTGAGTGGATCCAA 58.800 37.500 18.20 0.00 0.00 3.53
239 240 5.067805 ACAAAAAGAACTGAGTGGATCCAAC 59.932 40.000 18.20 14.28 0.00 3.77
240 241 4.437682 AAAGAACTGAGTGGATCCAACA 57.562 40.909 18.20 18.09 0.00 3.33
241 242 3.692257 AGAACTGAGTGGATCCAACAG 57.308 47.619 31.52 31.52 38.02 3.16
242 243 3.242867 AGAACTGAGTGGATCCAACAGA 58.757 45.455 36.00 16.53 36.69 3.41
243 244 3.260380 AGAACTGAGTGGATCCAACAGAG 59.740 47.826 36.00 24.05 36.69 3.35
244 245 2.614259 ACTGAGTGGATCCAACAGAGT 58.386 47.619 36.00 24.54 36.69 3.24
245 246 2.564947 ACTGAGTGGATCCAACAGAGTC 59.435 50.000 36.00 20.86 36.69 3.36
246 247 1.546029 TGAGTGGATCCAACAGAGTCG 59.454 52.381 18.20 0.00 0.00 4.18
1065 1104 0.389948 GCCCGTCATCGTTCAACTCT 60.390 55.000 0.00 0.00 35.01 3.24
1150 1189 1.338973 GACAAGACAGTGTCGGGTACA 59.661 52.381 17.40 0.00 38.68 2.90
1373 1419 3.233259 TTGCAGACCGATGTGCCGA 62.233 57.895 0.00 0.00 44.49 5.54
1585 1637 2.639839 AGCAGATGAGGGTGTACAAACT 59.360 45.455 0.00 0.00 0.00 2.66
1678 1738 9.619316 TGATATTGCATTGGTTATAAATTACGC 57.381 29.630 0.00 0.00 0.00 4.42
1679 1739 9.840427 GATATTGCATTGGTTATAAATTACGCT 57.160 29.630 0.00 0.00 0.00 5.07
1682 1742 6.491394 TGCATTGGTTATAAATTACGCTGTC 58.509 36.000 0.00 0.00 0.00 3.51
1834 1894 4.530710 TGAGCATAAACGAGTACTTGGT 57.469 40.909 14.75 4.75 0.00 3.67
1915 1975 5.411831 CATCCTATAGAGGCAAGCATACA 57.588 43.478 0.00 0.00 43.40 2.29
2710 2830 0.460284 GTGGGCTATGGATATCCGCG 60.460 60.000 17.04 0.00 39.43 6.46
2809 2929 1.137872 AGGCGGCACAATCTAAGAGAG 59.862 52.381 13.08 0.00 0.00 3.20
2832 2952 5.832060 AGCTACATATAACTTCGTGGGTAGT 59.168 40.000 0.00 0.00 31.89 2.73
2851 2971 4.617253 AGTGGCAATGTAACACTCTACA 57.383 40.909 0.00 0.00 41.27 2.74
2917 3037 7.360269 CCAAAATCAAGTGTATTGCCATGAAAC 60.360 37.037 0.00 0.00 0.00 2.78
3280 3431 0.179124 GAGTAGCCGAACCAGAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
3281 3432 1.153549 GTAGCCGAACCAGAGCAGG 60.154 63.158 0.00 0.00 0.00 4.85
3282 3433 1.304962 TAGCCGAACCAGAGCAGGA 60.305 57.895 0.00 0.00 0.00 3.86
3283 3434 1.323271 TAGCCGAACCAGAGCAGGAG 61.323 60.000 0.00 0.00 0.00 3.69
3292 3443 1.342474 CCAGAGCAGGAGGAAGGACTA 60.342 57.143 0.00 0.00 0.00 2.59
3368 3519 4.630940 CCGCAATGCCTTTTCAAATATGTT 59.369 37.500 0.00 0.00 0.00 2.71
3369 3520 5.809562 CCGCAATGCCTTTTCAAATATGTTA 59.190 36.000 0.00 0.00 0.00 2.41
3382 3533 6.502652 TCAAATATGTTATTTCATGGTGCCG 58.497 36.000 0.00 0.00 0.00 5.69
3442 3593 2.688538 GACGTCCTAGGACCCCCT 59.311 66.667 31.78 14.67 46.62 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.978674 AATTAGATCATCGGTAGGTCAAGA 57.021 37.500 0.00 0.00 0.00 3.02
1 2 6.986817 ACAAATTAGATCATCGGTAGGTCAAG 59.013 38.462 0.00 0.00 0.00 3.02
2 3 6.761242 CACAAATTAGATCATCGGTAGGTCAA 59.239 38.462 0.00 0.00 0.00 3.18
3 4 6.280643 CACAAATTAGATCATCGGTAGGTCA 58.719 40.000 0.00 0.00 0.00 4.02
4 5 5.696724 CCACAAATTAGATCATCGGTAGGTC 59.303 44.000 0.00 0.00 0.00 3.85
5 6 5.611374 CCACAAATTAGATCATCGGTAGGT 58.389 41.667 0.00 0.00 0.00 3.08
6 7 4.452455 GCCACAAATTAGATCATCGGTAGG 59.548 45.833 0.00 0.00 0.00 3.18
7 8 5.056480 TGCCACAAATTAGATCATCGGTAG 58.944 41.667 0.00 0.00 0.00 3.18
8 9 5.029807 TGCCACAAATTAGATCATCGGTA 57.970 39.130 0.00 0.00 0.00 4.02
9 10 3.884895 TGCCACAAATTAGATCATCGGT 58.115 40.909 0.00 0.00 0.00 4.69
10 11 5.443185 AATGCCACAAATTAGATCATCGG 57.557 39.130 0.00 0.00 0.00 4.18
11 12 9.546909 GTAATAATGCCACAAATTAGATCATCG 57.453 33.333 0.00 0.00 0.00 3.84
14 15 9.625747 TGAGTAATAATGCCACAAATTAGATCA 57.374 29.630 0.00 0.00 0.00 2.92
17 18 9.625747 TCATGAGTAATAATGCCACAAATTAGA 57.374 29.630 0.00 0.00 0.00 2.10
20 21 9.941325 TTTTCATGAGTAATAATGCCACAAATT 57.059 25.926 0.00 0.00 0.00 1.82
68 69 9.635404 CATTTGGTAAGAACTTATACCCCAATA 57.365 33.333 12.05 6.90 40.74 1.90
69 70 8.119891 ACATTTGGTAAGAACTTATACCCCAAT 58.880 33.333 12.05 5.07 40.74 3.16
70 71 7.471890 ACATTTGGTAAGAACTTATACCCCAA 58.528 34.615 9.02 9.02 40.74 4.12
71 72 7.034967 ACATTTGGTAAGAACTTATACCCCA 57.965 36.000 0.00 2.22 40.74 4.96
72 73 8.270030 AGTACATTTGGTAAGAACTTATACCCC 58.730 37.037 0.00 0.07 40.74 4.95
73 74 9.322773 GAGTACATTTGGTAAGAACTTATACCC 57.677 37.037 0.00 0.35 40.74 3.69
74 75 9.880157 TGAGTACATTTGGTAAGAACTTATACC 57.120 33.333 0.00 0.00 41.62 2.73
122 123 9.737427 ACAATGTTCGTGTTGAAAATATTTGTA 57.263 25.926 0.39 0.00 38.60 2.41
123 124 8.641499 ACAATGTTCGTGTTGAAAATATTTGT 57.359 26.923 0.39 0.00 38.60 2.83
124 125 9.913451 AAACAATGTTCGTGTTGAAAATATTTG 57.087 25.926 0.39 0.00 39.14 2.32
129 130 9.748100 GTTTAAAACAATGTTCGTGTTGAAAAT 57.252 25.926 0.00 0.00 39.14 1.82
130 131 7.945178 CGTTTAAAACAATGTTCGTGTTGAAAA 59.055 29.630 0.00 0.00 39.14 2.29
131 132 7.410513 CCGTTTAAAACAATGTTCGTGTTGAAA 60.411 33.333 0.00 0.00 39.14 2.69
132 133 6.033619 CCGTTTAAAACAATGTTCGTGTTGAA 59.966 34.615 0.00 0.00 39.14 2.69
133 134 5.512082 CCGTTTAAAACAATGTTCGTGTTGA 59.488 36.000 0.00 0.00 39.14 3.18
134 135 5.275974 CCCGTTTAAAACAATGTTCGTGTTG 60.276 40.000 0.00 0.00 39.14 3.33
135 136 4.799428 CCCGTTTAAAACAATGTTCGTGTT 59.201 37.500 0.00 0.00 40.92 3.32
136 137 4.142425 ACCCGTTTAAAACAATGTTCGTGT 60.142 37.500 0.00 0.00 0.00 4.49
137 138 4.352887 ACCCGTTTAAAACAATGTTCGTG 58.647 39.130 0.00 0.00 0.00 4.35
138 139 4.336153 AGACCCGTTTAAAACAATGTTCGT 59.664 37.500 0.00 0.00 0.00 3.85
139 140 4.851010 AGACCCGTTTAAAACAATGTTCG 58.149 39.130 0.00 0.00 0.00 3.95
140 141 6.508880 GCAAAGACCCGTTTAAAACAATGTTC 60.509 38.462 0.00 0.00 0.00 3.18
141 142 5.292345 GCAAAGACCCGTTTAAAACAATGTT 59.708 36.000 0.00 0.00 0.00 2.71
142 143 4.806775 GCAAAGACCCGTTTAAAACAATGT 59.193 37.500 0.00 0.00 0.00 2.71
143 144 4.085312 CGCAAAGACCCGTTTAAAACAATG 60.085 41.667 0.00 0.00 0.00 2.82
144 145 4.045783 CGCAAAGACCCGTTTAAAACAAT 58.954 39.130 0.00 0.00 0.00 2.71
145 146 3.436496 CGCAAAGACCCGTTTAAAACAA 58.564 40.909 0.00 0.00 0.00 2.83
146 147 2.795331 GCGCAAAGACCCGTTTAAAACA 60.795 45.455 0.30 0.00 0.00 2.83
147 148 1.782569 GCGCAAAGACCCGTTTAAAAC 59.217 47.619 0.30 0.00 0.00 2.43
148 149 1.269154 GGCGCAAAGACCCGTTTAAAA 60.269 47.619 10.83 0.00 0.00 1.52
149 150 0.311477 GGCGCAAAGACCCGTTTAAA 59.689 50.000 10.83 0.00 0.00 1.52
150 151 0.818445 TGGCGCAAAGACCCGTTTAA 60.818 50.000 10.83 0.00 0.00 1.52
151 152 0.606944 ATGGCGCAAAGACCCGTTTA 60.607 50.000 10.83 0.00 0.00 2.01
152 153 1.460273 AATGGCGCAAAGACCCGTTT 61.460 50.000 10.83 0.00 0.00 3.60
153 154 1.460273 AAATGGCGCAAAGACCCGTT 61.460 50.000 10.83 0.00 0.00 4.44
154 155 1.901464 AAATGGCGCAAAGACCCGT 60.901 52.632 10.83 0.00 0.00 5.28
155 156 1.444212 CAAATGGCGCAAAGACCCG 60.444 57.895 10.83 0.00 0.00 5.28
156 157 1.079888 CCAAATGGCGCAAAGACCC 60.080 57.895 10.83 0.00 0.00 4.46
157 158 4.576993 CCAAATGGCGCAAAGACC 57.423 55.556 10.83 0.00 0.00 3.85
168 169 0.244450 ATGACCAGTTGCGCCAAATG 59.756 50.000 4.18 8.94 38.85 2.32
169 170 0.527565 GATGACCAGTTGCGCCAAAT 59.472 50.000 4.18 0.00 0.00 2.32
170 171 0.537143 AGATGACCAGTTGCGCCAAA 60.537 50.000 4.18 0.00 0.00 3.28
171 172 0.323302 TAGATGACCAGTTGCGCCAA 59.677 50.000 4.18 0.00 0.00 4.52
172 173 0.108186 CTAGATGACCAGTTGCGCCA 60.108 55.000 4.18 0.00 0.00 5.69
173 174 0.108138 ACTAGATGACCAGTTGCGCC 60.108 55.000 4.18 0.00 0.00 6.53
174 175 2.579207 TACTAGATGACCAGTTGCGC 57.421 50.000 0.00 0.00 0.00 6.09
175 176 4.307443 TCATACTAGATGACCAGTTGCG 57.693 45.455 0.00 0.00 0.00 4.85
176 177 6.283694 TCATTCATACTAGATGACCAGTTGC 58.716 40.000 0.00 0.00 0.00 4.17
177 178 8.722480 TTTCATTCATACTAGATGACCAGTTG 57.278 34.615 0.00 0.00 0.00 3.16
178 179 7.989741 CCTTTCATTCATACTAGATGACCAGTT 59.010 37.037 0.00 0.00 0.00 3.16
179 180 7.126421 ACCTTTCATTCATACTAGATGACCAGT 59.874 37.037 0.00 0.00 0.00 4.00
180 181 7.440556 CACCTTTCATTCATACTAGATGACCAG 59.559 40.741 0.00 0.00 0.00 4.00
181 182 7.275183 CACCTTTCATTCATACTAGATGACCA 58.725 38.462 0.00 0.00 0.00 4.02
182 183 6.203723 GCACCTTTCATTCATACTAGATGACC 59.796 42.308 0.00 0.00 0.00 4.02
183 184 6.989169 AGCACCTTTCATTCATACTAGATGAC 59.011 38.462 0.00 0.00 0.00 3.06
184 185 7.129457 AGCACCTTTCATTCATACTAGATGA 57.871 36.000 0.00 0.00 0.00 2.92
185 186 8.893219 TTAGCACCTTTCATTCATACTAGATG 57.107 34.615 0.00 0.00 0.00 2.90
186 187 9.905713 TTTTAGCACCTTTCATTCATACTAGAT 57.094 29.630 0.00 0.00 0.00 1.98
187 188 9.733556 TTTTTAGCACCTTTCATTCATACTAGA 57.266 29.630 0.00 0.00 0.00 2.43
211 212 7.041721 GGATCCACTCAGTTCTTTTTGTTTTT 58.958 34.615 6.95 0.00 0.00 1.94
212 213 6.154363 TGGATCCACTCAGTTCTTTTTGTTTT 59.846 34.615 11.44 0.00 0.00 2.43
213 214 5.656416 TGGATCCACTCAGTTCTTTTTGTTT 59.344 36.000 11.44 0.00 0.00 2.83
214 215 5.200483 TGGATCCACTCAGTTCTTTTTGTT 58.800 37.500 11.44 0.00 0.00 2.83
215 216 4.792068 TGGATCCACTCAGTTCTTTTTGT 58.208 39.130 11.44 0.00 0.00 2.83
216 217 5.067674 TGTTGGATCCACTCAGTTCTTTTTG 59.932 40.000 15.91 0.00 0.00 2.44
217 218 5.200483 TGTTGGATCCACTCAGTTCTTTTT 58.800 37.500 15.91 0.00 0.00 1.94
218 219 4.792068 TGTTGGATCCACTCAGTTCTTTT 58.208 39.130 15.91 0.00 0.00 2.27
219 220 4.103153 TCTGTTGGATCCACTCAGTTCTTT 59.897 41.667 29.62 0.00 33.26 2.52
220 221 3.648067 TCTGTTGGATCCACTCAGTTCTT 59.352 43.478 29.62 0.00 33.26 2.52
221 222 3.242867 TCTGTTGGATCCACTCAGTTCT 58.757 45.455 29.62 0.00 33.26 3.01
222 223 3.007398 ACTCTGTTGGATCCACTCAGTTC 59.993 47.826 29.62 12.62 33.26 3.01
223 224 2.975489 ACTCTGTTGGATCCACTCAGTT 59.025 45.455 29.62 21.06 33.26 3.16
224 225 2.564947 GACTCTGTTGGATCCACTCAGT 59.435 50.000 29.62 22.15 33.26 3.41
225 226 2.416566 CGACTCTGTTGGATCCACTCAG 60.417 54.545 27.32 27.32 32.98 3.35
226 227 1.546029 CGACTCTGTTGGATCCACTCA 59.454 52.381 15.91 15.55 0.00 3.41
227 228 1.737363 GCGACTCTGTTGGATCCACTC 60.737 57.143 15.91 11.48 0.00 3.51
228 229 0.247736 GCGACTCTGTTGGATCCACT 59.752 55.000 15.91 0.00 0.00 4.00
229 230 0.037326 TGCGACTCTGTTGGATCCAC 60.037 55.000 15.91 10.58 0.00 4.02
230 231 0.904649 ATGCGACTCTGTTGGATCCA 59.095 50.000 11.44 11.44 0.00 3.41
231 232 2.546795 CCTATGCGACTCTGTTGGATCC 60.547 54.545 4.20 4.20 30.76 3.36
232 233 2.362397 TCCTATGCGACTCTGTTGGATC 59.638 50.000 0.00 0.00 30.76 3.36
233 234 2.388735 TCCTATGCGACTCTGTTGGAT 58.611 47.619 0.00 0.00 32.82 3.41
234 235 1.847328 TCCTATGCGACTCTGTTGGA 58.153 50.000 0.00 0.00 0.00 3.53
235 236 2.898729 ATCCTATGCGACTCTGTTGG 57.101 50.000 0.00 0.00 0.00 3.77
236 237 3.126831 GGAATCCTATGCGACTCTGTTG 58.873 50.000 0.00 0.00 0.00 3.33
237 238 2.103263 GGGAATCCTATGCGACTCTGTT 59.897 50.000 0.00 0.00 0.00 3.16
238 239 1.689273 GGGAATCCTATGCGACTCTGT 59.311 52.381 0.00 0.00 0.00 3.41
239 240 1.336332 CGGGAATCCTATGCGACTCTG 60.336 57.143 0.00 0.00 0.00 3.35
240 241 0.962489 CGGGAATCCTATGCGACTCT 59.038 55.000 0.00 0.00 0.00 3.24
241 242 0.667792 GCGGGAATCCTATGCGACTC 60.668 60.000 0.00 0.00 0.00 3.36
242 243 1.367840 GCGGGAATCCTATGCGACT 59.632 57.895 0.00 0.00 0.00 4.18
243 244 1.668151 GGCGGGAATCCTATGCGAC 60.668 63.158 0.00 0.00 0.00 5.19
244 245 2.741092 GGCGGGAATCCTATGCGA 59.259 61.111 0.00 0.00 0.00 5.10
245 246 2.738521 CGGCGGGAATCCTATGCG 60.739 66.667 0.00 0.00 0.00 4.73
246 247 3.050275 GCGGCGGGAATCCTATGC 61.050 66.667 9.78 1.05 0.00 3.14
496 534 0.036388 TGGCCTCATGGAACTCGAAC 60.036 55.000 3.32 0.00 34.57 3.95
1150 1189 6.771267 GGGGACAAAACGAATAAATAGGAGAT 59.229 38.462 0.00 0.00 0.00 2.75
1373 1419 0.320771 GGACTGCATCCGACACTGTT 60.321 55.000 0.00 0.00 37.88 3.16
1427 1473 4.758251 CGAGTGGCCGTGGCATCA 62.758 66.667 13.76 0.00 44.11 3.07
1500 1546 0.641601 ATCCTCTTCCCTCTCAGCCT 59.358 55.000 0.00 0.00 0.00 4.58
1533 1579 9.460019 TCCAAATCCTTGAAACAAAAAGAATTT 57.540 25.926 0.00 0.00 35.34 1.82
1655 1715 8.625651 ACAGCGTAATTTATAACCAATGCAATA 58.374 29.630 0.00 0.00 0.00 1.90
1678 1738 3.624326 TTTTCATTTGCGAGGTGACAG 57.376 42.857 0.00 0.00 0.00 3.51
1679 1739 4.582701 ATTTTTCATTTGCGAGGTGACA 57.417 36.364 0.00 0.00 0.00 3.58
1682 1742 9.105206 CAAAATTAATTTTTCATTTGCGAGGTG 57.895 29.630 20.92 4.67 37.86 4.00
2193 2254 1.425066 AGCTTCTCCAACCCATTCACA 59.575 47.619 0.00 0.00 0.00 3.58
2287 2348 1.376683 GCACAACGATGCCAGGGTA 60.377 57.895 0.00 0.00 39.86 3.69
2710 2830 2.206576 AGGCCAGTTTGATCACCTTC 57.793 50.000 5.01 0.00 0.00 3.46
2809 2929 5.919141 CACTACCCACGAAGTTATATGTAGC 59.081 44.000 0.00 0.00 41.61 3.58
2832 2952 3.334691 GCTGTAGAGTGTTACATTGCCA 58.665 45.455 0.00 0.00 33.38 4.92
2851 2971 1.334869 CAAGTGAAACCTCTTTGCGCT 59.665 47.619 9.73 0.00 37.80 5.92
2917 3037 3.726517 CTCCAACTGTTGCGGCGG 61.727 66.667 14.94 1.30 0.00 6.13
3259 3410 0.458716 GCTCTGGTTCGGCTACTCAC 60.459 60.000 0.00 0.00 0.00 3.51
3280 3431 0.542333 GGCCAACTAGTCCTTCCTCC 59.458 60.000 0.00 0.00 0.00 4.30
3281 3432 0.542333 GGGCCAACTAGTCCTTCCTC 59.458 60.000 4.39 0.00 0.00 3.71
3282 3433 1.265454 CGGGCCAACTAGTCCTTCCT 61.265 60.000 4.39 0.00 0.00 3.36
3283 3434 1.221021 CGGGCCAACTAGTCCTTCC 59.779 63.158 4.39 0.00 0.00 3.46
3292 3443 0.250770 GGTTCTTCTTCGGGCCAACT 60.251 55.000 4.39 0.00 0.00 3.16
3336 3487 3.399440 AAGGCATTGCGGATTTTTCAA 57.601 38.095 1.91 0.00 0.00 2.69
3337 3488 3.399440 AAAGGCATTGCGGATTTTTCA 57.601 38.095 1.91 0.00 0.00 2.69
3368 3519 2.477176 GCCGCGGCACCATGAAATA 61.477 57.895 43.55 0.00 41.49 1.40
3369 3520 3.825611 GCCGCGGCACCATGAAAT 61.826 61.111 43.55 0.00 41.49 2.17
3415 3566 0.680061 CTAGGACGTCCTTATGGGCC 59.320 60.000 40.23 9.40 46.09 5.80
3422 3573 1.001376 GGGGTCCTAGGACGTCCTT 59.999 63.158 40.23 24.22 46.09 3.36


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

AutoCloner maintained by Alex Coulton.