Multiple sequence alignment - TraesCS2B01G218900

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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 TraesCS2B01G218900 chr2B 100.000 3113 0 0 1 3113 208627988 208624876 0.000000e+00 5749
1 TraesCS2B01G218900 chr2B 100.000 1860 0 0 3407 5266 208624582 208622723 0.000000e+00 3435
2 TraesCS2B01G218900 chr2B 90.233 215 20 1 2854 3068 208625089 208624876 4.020000e-71 279
3 TraesCS2B01G218900 chr2B 89.634 164 17 0 3407 3570 208625048 208624885 5.340000e-50 209
4 TraesCS2B01G218900 chr2B 91.406 128 11 0 3407 3534 208625003 208624876 5.420000e-40 176
5 TraesCS2B01G218900 chr2B 93.976 83 5 0 3031 3113 208624582 208624500 5.540000e-25 126
6 TraesCS2B01G218900 chr2A 96.893 2800 61 11 335 3113 152007649 152010443 0.000000e+00 4665
7 TraesCS2B01G218900 chr2A 93.866 1891 70 21 3407 5266 152010406 152012281 0.000000e+00 2808
8 TraesCS2B01G218900 chr2A 90.741 270 25 0 2844 3113 152010219 152010488 1.390000e-95 361
9 TraesCS2B01G218900 chr2A 81.728 405 67 7 1182 1584 657813645 657813246 1.090000e-86 331
10 TraesCS2B01G218900 chr2A 88.390 267 31 0 2844 3110 152010264 152010530 6.580000e-84 322
11 TraesCS2B01G218900 chr2A 86.973 261 31 1 2844 3104 152010309 152010566 1.860000e-74 291
12 TraesCS2B01G218900 chr2A 88.646 229 8 7 1 215 152007107 152007331 4.040000e-66 263
13 TraesCS2B01G218900 chr2A 79.634 383 62 11 3409 3783 152010363 152010737 1.450000e-65 261
14 TraesCS2B01G218900 chr2A 78.238 386 69 10 3407 3783 152010316 152010695 3.170000e-57 233
15 TraesCS2B01G218900 chr2D 96.319 2798 57 17 344 3113 149684735 149681956 0.000000e+00 4554
16 TraesCS2B01G218900 chr2D 94.514 1349 37 9 3407 4753 149681948 149680635 0.000000e+00 2047
17 TraesCS2B01G218900 chr2D 94.831 503 23 3 4765 5266 149680597 149680097 0.000000e+00 782
18 TraesCS2B01G218900 chr2D 89.139 267 29 0 2844 3110 149682090 149681824 3.040000e-87 333
19 TraesCS2B01G218900 chr2D 88.889 270 30 0 2844 3113 149682135 149681866 3.040000e-87 333
20 TraesCS2B01G218900 chr2D 91.057 246 22 0 2868 3113 149682156 149681911 3.040000e-87 333
21 TraesCS2B01G218900 chr2D 81.481 405 68 7 1182 1584 513765038 513764639 5.090000e-85 326
22 TraesCS2B01G218900 chr2D 80.000 380 60 12 3412 3783 149681988 149681617 3.130000e-67 267
23 TraesCS2B01G218900 chr2D 87.879 231 8 5 1 218 149685083 149684860 2.430000e-63 254
24 TraesCS2B01G218900 chr2D 89.937 159 16 0 3407 3565 149682083 149681925 6.910000e-49 206
25 TraesCS2B01G218900 chr2D 89.024 164 18 0 3407 3570 149682128 149681965 2.490000e-48 204
26 TraesCS2B01G218900 chrUn 84.819 415 56 6 1182 1591 295855479 295855067 1.360000e-110 411
27 TraesCS2B01G218900 chr3D 84.819 415 52 9 1184 1591 557925524 557925114 1.770000e-109 407
28 TraesCS2B01G218900 chr3B 84.173 417 55 9 1182 1591 740545090 740544678 1.370000e-105 394
29 TraesCS2B01G218900 chr3B 81.465 437 67 12 1158 1590 222318432 222318858 3.900000e-91 346
30 TraesCS2B01G218900 chr5B 82.448 433 64 9 1163 1592 538542385 538542808 8.330000e-98 368
31 TraesCS2B01G218900 chr5D 82.494 417 62 8 1179 1592 442331793 442332201 6.490000e-94 355
32 TraesCS2B01G218900 chr3A 82.143 420 66 8 1172 1590 178987299 178986888 8.390000e-93 351
33 TraesCS2B01G218900 chr6D 81.455 426 68 11 1182 1602 332499020 332499439 6.530000e-89 339
34 TraesCS2B01G218900 chr6A 79.551 445 60 18 1183 1596 99424049 99424493 6.670000e-74 289


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 TraesCS2B01G218900 chr2B 208622723 208627988 5265 True 1662.333333 5749 94.208167 1 5266 6 chr2B.!!$R1 5265
1 TraesCS2B01G218900 chr2A 152007107 152012281 5174 False 1150.500000 4665 87.922625 1 5266 8 chr2A.!!$F1 5265
2 TraesCS2B01G218900 chr2D 149680097 149685083 4986 True 931.300000 4554 90.158900 1 5266 10 chr2D.!!$R2 5265

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
323 337 0.108662 CCCAGCAATTTTTCCGAGGC 60.109 55.0 0.0 0.0 0.0 4.70 F
1705 2041 0.034767 TGCTGGCTTGATTCAGGAGG 60.035 55.0 0.0 0.0 0.0 4.30 F
2602 2938 0.669619 CATCAGCCACAACAAGCACA 59.330 50.0 0.0 0.0 0.0 4.57 F
2991 3327 0.111061 AGCAGCTCAACACAATCCCA 59.889 50.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2288 0.537143 TCCATTGCTGCCTCAACGTT 60.537 50.0 0.0 0.0 0.00 3.99 R
2905 3241 0.328258 CGATGAACCTTCCTTGGGGT 59.672 55.0 0.0 0.0 37.44 4.95 R
3928 4264 1.394266 CCTTTGGTGCCACTGCTGTT 61.394 55.0 0.0 0.0 38.71 3.16 R
4951 5321 0.602562 ACCAACCATTTGTCGGCATG 59.397 50.0 0.0 0.0 0.00 4.06 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
84 90 0.468226 ATCGCTTTCCGCCCTTATCA 59.532 50.000 0.00 0.00 36.73 2.15
101 111 0.687757 TCAACTCCGGGGAGATCCAG 60.688 60.000 21.16 0.00 44.53 3.86
108 118 4.925861 GGGAGATCCAGCCGCTGC 62.926 72.222 15.36 1.50 37.91 5.25
146 156 2.651361 CCTTCGCTGGACACGACT 59.349 61.111 0.00 0.00 39.67 4.18
148 158 1.444553 CTTCGCTGGACACGACTCC 60.445 63.158 0.00 0.00 39.67 3.85
149 159 1.867919 CTTCGCTGGACACGACTCCT 61.868 60.000 0.00 0.00 39.67 3.69
152 162 1.979693 GCTGGACACGACTCCTCCT 60.980 63.158 0.00 0.00 0.00 3.69
155 165 1.000646 GGACACGACTCCTCCTCCT 60.001 63.158 0.00 0.00 0.00 3.69
167 181 1.066071 CCTCCTCCTTTTTCCGTCCTC 60.066 57.143 0.00 0.00 0.00 3.71
180 194 2.755876 TCCTCGCCGCAGACATCT 60.756 61.111 0.00 0.00 0.00 2.90
218 232 4.270325 CCTGACGATTAAATCCGTTCTTCC 59.730 45.833 0.00 0.00 39.30 3.46
219 233 5.080969 TGACGATTAAATCCGTTCTTCCT 57.919 39.130 0.00 0.00 39.30 3.36
220 234 5.107133 TGACGATTAAATCCGTTCTTCCTC 58.893 41.667 0.00 0.00 39.30 3.71
221 235 4.439968 ACGATTAAATCCGTTCTTCCTCC 58.560 43.478 0.00 0.00 35.21 4.30
222 236 3.808174 CGATTAAATCCGTTCTTCCTCCC 59.192 47.826 0.00 0.00 0.00 4.30
223 237 4.443034 CGATTAAATCCGTTCTTCCTCCCT 60.443 45.833 0.00 0.00 0.00 4.20
224 238 2.789409 AAATCCGTTCTTCCTCCCTG 57.211 50.000 0.00 0.00 0.00 4.45
225 239 0.253327 AATCCGTTCTTCCTCCCTGC 59.747 55.000 0.00 0.00 0.00 4.85
226 240 0.909610 ATCCGTTCTTCCTCCCTGCA 60.910 55.000 0.00 0.00 0.00 4.41
227 241 1.125093 TCCGTTCTTCCTCCCTGCAA 61.125 55.000 0.00 0.00 0.00 4.08
228 242 0.250727 CCGTTCTTCCTCCCTGCAAA 60.251 55.000 0.00 0.00 0.00 3.68
229 243 1.604604 CGTTCTTCCTCCCTGCAAAA 58.395 50.000 0.00 0.00 0.00 2.44
230 244 1.953686 CGTTCTTCCTCCCTGCAAAAA 59.046 47.619 0.00 0.00 0.00 1.94
273 287 1.180029 CTTCCCACAAAGCATCCCAG 58.820 55.000 0.00 0.00 0.00 4.45
274 288 0.899717 TTCCCACAAAGCATCCCAGC 60.900 55.000 0.00 0.00 0.00 4.85
275 289 2.353610 CCCACAAAGCATCCCAGCC 61.354 63.158 0.00 0.00 34.23 4.85
276 290 1.607178 CCACAAAGCATCCCAGCCA 60.607 57.895 0.00 0.00 34.23 4.75
305 319 2.280457 GGCCGAGCAGTAGCATCC 60.280 66.667 0.00 0.00 45.49 3.51
310 324 1.524002 GAGCAGTAGCATCCCAGCA 59.476 57.895 0.00 0.00 45.49 4.41
318 332 3.448660 AGTAGCATCCCAGCAATTTTTCC 59.551 43.478 0.00 0.00 36.85 3.13
319 333 1.205417 AGCATCCCAGCAATTTTTCCG 59.795 47.619 0.00 0.00 36.85 4.30
320 334 1.204467 GCATCCCAGCAATTTTTCCGA 59.796 47.619 0.00 0.00 0.00 4.55
321 335 2.736400 GCATCCCAGCAATTTTTCCGAG 60.736 50.000 0.00 0.00 0.00 4.63
322 336 1.544724 TCCCAGCAATTTTTCCGAGG 58.455 50.000 0.00 0.00 0.00 4.63
323 337 0.108662 CCCAGCAATTTTTCCGAGGC 60.109 55.000 0.00 0.00 0.00 4.70
324 338 0.602562 CCAGCAATTTTTCCGAGGCA 59.397 50.000 0.00 0.00 0.00 4.75
326 340 0.603065 AGCAATTTTTCCGAGGCACC 59.397 50.000 0.00 0.00 0.00 5.01
739 1048 3.055719 CCAACGCCAACGCCTCAT 61.056 61.111 0.00 0.00 45.53 2.90
1629 1963 0.106519 CCCCCAATTTCGATGCTCCT 60.107 55.000 0.00 0.00 0.00 3.69
1632 1966 2.099756 CCCCAATTTCGATGCTCCTTTC 59.900 50.000 0.00 0.00 0.00 2.62
1705 2041 0.034767 TGCTGGCTTGATTCAGGAGG 60.035 55.000 0.00 0.00 0.00 4.30
1708 2044 1.493871 CTGGCTTGATTCAGGAGGGAT 59.506 52.381 0.00 0.00 0.00 3.85
1768 2104 2.659610 GAGACCGGCAGAGTGCTT 59.340 61.111 0.00 0.00 44.28 3.91
1808 2144 2.409870 CCTCGGCCACCTGATTTGC 61.410 63.158 2.24 0.00 0.00 3.68
1890 2226 3.009473 CACAAGGAAAAGGAGGATGAGGA 59.991 47.826 0.00 0.00 0.00 3.71
2018 2354 4.812476 CGCCATCTCCAACGCCGA 62.812 66.667 0.00 0.00 0.00 5.54
2264 2600 8.623903 TCTTATGATCATTTAGGCAACAATGAC 58.376 33.333 14.65 4.57 41.41 3.06
2403 2739 2.358267 AGGAAGCTGATAAGTACGACGG 59.642 50.000 0.00 0.00 0.00 4.79
2533 2869 3.228499 CACAGTCAGCAGTGCATCT 57.772 52.632 19.20 9.28 0.00 2.90
2602 2938 0.669619 CATCAGCCACAACAAGCACA 59.330 50.000 0.00 0.00 0.00 4.57
2752 3088 1.524621 AGCACCGCACATATCTGCC 60.525 57.895 0.00 0.00 33.18 4.85
2848 3184 2.373169 TGCAAGTTCCTCCTCATCAACT 59.627 45.455 0.00 0.00 0.00 3.16
2892 3228 2.548875 GTTCATCGAGAGCAGCTCAAT 58.451 47.619 24.64 11.60 44.15 2.57
2905 3241 0.533491 GCTCAATGCAATCCCAGCAA 59.467 50.000 0.00 0.00 46.27 3.91
2991 3327 0.111061 AGCAGCTCAACACAATCCCA 59.889 50.000 0.00 0.00 0.00 4.37
2999 3335 4.564821 GCTCAACACAATCCCAGTTACCTA 60.565 45.833 0.00 0.00 0.00 3.08
3046 3382 1.913419 ACACAATCCCGGTTACCTCAT 59.087 47.619 0.00 0.00 0.00 2.90
3432 3768 2.685100 GGTTACCTCAAGACAGGTTCG 58.315 52.381 0.00 0.00 45.24 3.95
3463 3799 2.874457 GCTCAACACAATCCCGGTTACT 60.874 50.000 0.00 0.00 0.00 2.24
3479 3815 4.755123 CGGTTACTTCAAGACAGGTTCATT 59.245 41.667 0.00 0.00 0.00 2.57
3500 3836 2.420642 GAGAGCAGCTCAACACAATCA 58.579 47.619 24.64 0.00 43.38 2.57
3501 3837 2.810274 GAGAGCAGCTCAACACAATCAA 59.190 45.455 24.64 0.00 43.38 2.57
3527 3863 2.232452 ACCTCAAGACAGGTTCATCGAG 59.768 50.000 0.00 0.00 45.24 4.04
3528 3864 2.493675 CCTCAAGACAGGTTCATCGAGA 59.506 50.000 0.00 0.00 0.00 4.04
3529 3865 3.428725 CCTCAAGACAGGTTCATCGAGAG 60.429 52.174 0.00 0.00 0.00 3.20
3560 3896 7.390440 TCAACACAATTTCGATTACCTCAAGAT 59.610 33.333 0.00 0.00 0.00 2.40
3726 4062 0.734889 CTCGCAACCATCCAATCCAC 59.265 55.000 0.00 0.00 0.00 4.02
3756 4092 2.026822 AGGTTCTTCATCAACTCGCCAT 60.027 45.455 0.00 0.00 0.00 4.40
3767 4103 2.947652 CAACTCGCCATCATCCAATCTT 59.052 45.455 0.00 0.00 0.00 2.40
3869 4205 3.270877 GCTACCACAAGGAAGGTACATG 58.729 50.000 0.00 0.00 39.31 3.21
3883 4219 2.423577 GTACATGGACAACTCACCACC 58.576 52.381 2.19 0.00 39.06 4.61
3893 4229 2.925706 TCACCACCGGCCAAGCTA 60.926 61.111 0.00 0.00 0.00 3.32
3894 4230 2.746277 CACCACCGGCCAAGCTAC 60.746 66.667 0.00 0.00 0.00 3.58
3895 4231 4.029809 ACCACCGGCCAAGCTACC 62.030 66.667 0.00 0.00 0.00 3.18
3928 4264 3.938963 GGAAGGTTCGTTGATAGCAATCA 59.061 43.478 0.00 0.00 40.43 2.57
4079 4415 0.827089 TGGGGCAATCACCACTGTTG 60.827 55.000 0.00 0.00 32.68 3.33
4482 4818 0.550914 TCCTTGTGACCTTTGTGGCT 59.449 50.000 0.00 0.00 40.22 4.75
4507 4843 1.416813 CTGTCGAGATGCAACGAGGC 61.417 60.000 12.74 2.46 39.16 4.70
4520 4856 1.246056 ACGAGGCGGTAACAGCAGTA 61.246 55.000 0.00 0.00 37.75 2.74
4521 4857 0.525668 CGAGGCGGTAACAGCAGTAG 60.526 60.000 0.00 0.00 37.75 2.57
4522 4858 0.531200 GAGGCGGTAACAGCAGTAGT 59.469 55.000 0.00 0.00 37.75 2.73
4523 4859 1.747355 GAGGCGGTAACAGCAGTAGTA 59.253 52.381 0.00 0.00 37.75 1.82
4524 4860 1.749634 AGGCGGTAACAGCAGTAGTAG 59.250 52.381 0.00 0.00 37.75 2.57
4525 4861 1.475682 GGCGGTAACAGCAGTAGTAGT 59.524 52.381 0.00 0.00 37.75 2.73
4572 4908 5.291128 CGGTTAGTTGCCTTTACTAGTGATG 59.709 44.000 5.39 0.00 30.36 3.07
4723 5062 2.428890 CAAACTATCCTCAGGCGAGTCT 59.571 50.000 0.00 0.00 37.59 3.24
4767 5132 2.158959 CGCGCCGGTCTTCTACTTG 61.159 63.158 1.90 0.00 0.00 3.16
4784 5149 3.063485 ACTTGTTTGCTTTGCGTTTTGT 58.937 36.364 0.00 0.00 0.00 2.83
4791 5156 0.929615 CTTTGCGTTTTGTTGGCCAG 59.070 50.000 5.11 0.00 0.00 4.85
4908 5273 1.021202 CACAACAGAAACGGCCTGAA 58.979 50.000 0.00 0.00 35.69 3.02
5019 5389 1.319614 TTCCATTTAGGGCCGCAAGC 61.320 55.000 0.00 0.00 42.60 4.01
5182 5565 6.989759 TGTTTAGTAGATTGACAGCACTGAAA 59.010 34.615 4.31 0.00 0.00 2.69
5186 5569 7.138692 AGTAGATTGACAGCACTGAAATTTC 57.861 36.000 11.41 11.41 0.00 2.17
5189 5572 1.879380 TGACAGCACTGAAATTTCGGG 59.121 47.619 26.73 16.98 37.89 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 90 2.066999 GCTGGATCTCCCCGGAGTT 61.067 63.158 0.73 2.28 42.49 3.01
146 156 0.981943 GGACGGAAAAAGGAGGAGGA 59.018 55.000 0.00 0.00 0.00 3.71
148 158 1.404315 CGAGGACGGAAAAAGGAGGAG 60.404 57.143 0.00 0.00 35.72 3.69
149 159 0.606604 CGAGGACGGAAAAAGGAGGA 59.393 55.000 0.00 0.00 35.72 3.71
152 162 1.004200 GGCGAGGACGGAAAAAGGA 60.004 57.895 0.00 0.00 40.15 3.36
155 165 3.045492 GCGGCGAGGACGGAAAAA 61.045 61.111 12.98 0.00 40.15 1.94
167 181 2.697425 CGAAAGATGTCTGCGGCG 59.303 61.111 0.51 0.51 0.00 6.46
243 257 4.321974 GCTTTGTGGGAAGATCGGATTTTT 60.322 41.667 0.00 0.00 0.00 1.94
244 258 3.193479 GCTTTGTGGGAAGATCGGATTTT 59.807 43.478 0.00 0.00 0.00 1.82
245 259 2.755103 GCTTTGTGGGAAGATCGGATTT 59.245 45.455 0.00 0.00 0.00 2.17
246 260 2.290896 TGCTTTGTGGGAAGATCGGATT 60.291 45.455 0.00 0.00 0.00 3.01
247 261 1.281867 TGCTTTGTGGGAAGATCGGAT 59.718 47.619 0.00 0.00 0.00 4.18
248 262 0.690192 TGCTTTGTGGGAAGATCGGA 59.310 50.000 0.00 0.00 0.00 4.55
249 263 1.672881 GATGCTTTGTGGGAAGATCGG 59.327 52.381 0.00 0.00 0.00 4.18
250 264 1.672881 GGATGCTTTGTGGGAAGATCG 59.327 52.381 0.00 0.00 0.00 3.69
251 265 2.027385 GGGATGCTTTGTGGGAAGATC 58.973 52.381 0.00 0.00 0.00 2.75
252 266 1.358787 TGGGATGCTTTGTGGGAAGAT 59.641 47.619 0.00 0.00 0.00 2.40
253 267 0.776810 TGGGATGCTTTGTGGGAAGA 59.223 50.000 0.00 0.00 0.00 2.87
254 268 1.180029 CTGGGATGCTTTGTGGGAAG 58.820 55.000 0.00 0.00 0.00 3.46
261 275 2.773993 AAAATGGCTGGGATGCTTTG 57.226 45.000 0.00 0.00 0.00 2.77
282 296 2.284331 TACTGCTCGGCCCCTCAA 60.284 61.111 0.00 0.00 0.00 3.02
289 303 2.280457 GGGATGCTACTGCTCGGC 60.280 66.667 0.00 0.00 40.48 5.54
292 306 0.107508 TTGCTGGGATGCTACTGCTC 60.108 55.000 0.00 0.00 40.48 4.26
305 319 0.602562 TGCCTCGGAAAAATTGCTGG 59.397 50.000 0.00 0.00 0.00 4.85
310 324 2.316108 ACTTGGTGCCTCGGAAAAATT 58.684 42.857 0.00 0.00 0.00 1.82
318 332 2.223525 GCTACTACTACTTGGTGCCTCG 60.224 54.545 0.00 0.00 0.00 4.63
319 333 2.758979 TGCTACTACTACTTGGTGCCTC 59.241 50.000 0.00 0.00 0.00 4.70
320 334 2.761208 CTGCTACTACTACTTGGTGCCT 59.239 50.000 0.00 0.00 0.00 4.75
321 335 2.738964 GCTGCTACTACTACTTGGTGCC 60.739 54.545 0.00 0.00 0.00 5.01
322 336 2.094182 TGCTGCTACTACTACTTGGTGC 60.094 50.000 0.00 0.00 0.00 5.01
323 337 3.775202 CTGCTGCTACTACTACTTGGTG 58.225 50.000 0.00 0.00 0.00 4.17
324 338 2.166664 GCTGCTGCTACTACTACTTGGT 59.833 50.000 8.53 0.00 36.03 3.67
326 340 3.443037 CTGCTGCTGCTACTACTACTTG 58.557 50.000 17.00 0.00 40.48 3.16
459 762 2.673523 GCCTCCATCACTGTGCCT 59.326 61.111 2.12 0.00 0.00 4.75
924 1253 4.626081 CCCTTATCGGCGCCCAGG 62.626 72.222 23.46 20.01 0.00 4.45
925 1254 4.626081 CCCCTTATCGGCGCCCAG 62.626 72.222 23.46 11.71 0.00 4.45
1102 1434 3.291383 CCCGCAAAACCCGAAGCA 61.291 61.111 0.00 0.00 0.00 3.91
1364 1698 1.452651 CGGGCAGACGTAGACCCTA 60.453 63.158 15.17 0.00 40.45 3.53
1705 2041 2.281762 GCGATGTGTCACGAAACTATCC 59.718 50.000 0.00 0.00 0.00 2.59
1708 2044 1.333115 CGCGATGTGTCACGAAACTA 58.667 50.000 0.00 0.00 31.80 2.24
1808 2144 2.355513 CCACATTCTCCTCAACCTCCTG 60.356 54.545 0.00 0.00 0.00 3.86
1952 2288 0.537143 TCCATTGCTGCCTCAACGTT 60.537 50.000 0.00 0.00 0.00 3.99
1997 2333 2.885644 CGTTGGAGATGGCGACGG 60.886 66.667 0.00 0.00 0.00 4.79
2018 2354 1.003355 CCTGTGGCGTTGGAGATGT 60.003 57.895 0.00 0.00 0.00 3.06
2195 2531 9.136323 AGAAACAAGACTCATGTATTCCTTTTT 57.864 29.630 0.00 0.00 0.00 1.94
2264 2600 2.135664 ACGGAAGAACAAGTCACTCG 57.864 50.000 0.00 0.00 0.00 4.18
2403 2739 1.202582 TGGAGTCTTCTAGTTCAGCGC 59.797 52.381 0.00 0.00 0.00 5.92
2533 2869 2.879372 TGCTGGCGCAATGGAATTA 58.121 47.368 10.83 0.00 44.62 1.40
2668 3004 2.930109 ACAGAGAGGATGGTGTACCT 57.070 50.000 2.32 0.00 39.41 3.08
2848 3184 1.541118 TTGAGGTGGCCTGGATGGA 60.541 57.895 3.32 0.00 38.35 3.41
2892 3228 2.283821 GGGGTTGCTGGGATTGCA 60.284 61.111 0.00 0.00 38.80 4.08
2905 3241 0.328258 CGATGAACCTTCCTTGGGGT 59.672 55.000 0.00 0.00 37.44 4.95
2999 3335 2.224281 TGCTGTCGATGAACCTGTCTTT 60.224 45.455 0.00 0.00 0.00 2.52
3046 3382 1.203287 CTGCTCTCGATGAACCTGTCA 59.797 52.381 0.00 0.00 41.67 3.58
3406 3742 3.195825 CCTGTCTTGAGGTAACCGAGATT 59.804 47.826 0.00 0.00 32.23 2.40
3407 3743 2.761208 CCTGTCTTGAGGTAACCGAGAT 59.239 50.000 0.00 0.00 32.23 2.75
3408 3744 2.168496 CCTGTCTTGAGGTAACCGAGA 58.832 52.381 0.00 0.00 37.17 4.04
3409 3745 1.893801 ACCTGTCTTGAGGTAACCGAG 59.106 52.381 0.00 0.00 45.09 4.63
3410 3746 2.005370 ACCTGTCTTGAGGTAACCGA 57.995 50.000 0.00 0.00 45.09 4.69
3463 3799 4.067896 GCTCTCAATGAACCTGTCTTGAA 58.932 43.478 0.00 0.00 0.00 2.69
3491 3827 5.531287 GTCTTGAGGTAACCTTGATTGTGTT 59.469 40.000 0.00 0.00 31.76 3.32
3500 3836 3.714798 TGAACCTGTCTTGAGGTAACCTT 59.285 43.478 0.00 0.00 46.29 3.50
3501 3837 3.314693 TGAACCTGTCTTGAGGTAACCT 58.685 45.455 0.00 0.00 46.29 3.50
3527 3863 2.224079 TCGAAATTGTGTTGAGCTGCTC 59.776 45.455 22.38 22.38 0.00 4.26
3528 3864 2.221169 TCGAAATTGTGTTGAGCTGCT 58.779 42.857 0.00 0.00 0.00 4.24
3529 3865 2.686558 TCGAAATTGTGTTGAGCTGC 57.313 45.000 0.00 0.00 0.00 5.25
3560 3896 5.303333 TGGCATCGAGTTATTGATGTACCTA 59.697 40.000 7.20 0.00 45.69 3.08
3726 4062 4.292186 TGATGAAGAACCTTCCTTGAGG 57.708 45.455 4.48 0.00 42.75 3.86
3767 4103 2.619931 TCAGTGAACCTTCCATGAGGA 58.380 47.619 7.43 0.00 43.93 3.71
3869 4205 2.668550 GCCGGTGGTGAGTTGTCC 60.669 66.667 1.90 0.00 0.00 4.02
3883 4219 2.746277 GTGGTGGTAGCTTGGCCG 60.746 66.667 0.00 0.00 0.00 6.13
3928 4264 1.394266 CCTTTGGTGCCACTGCTGTT 61.394 55.000 0.00 0.00 38.71 3.16
3935 4271 1.544724 TATTGCTCCTTTGGTGCCAC 58.455 50.000 7.97 0.00 40.96 5.01
4455 4791 6.015519 CCACAAAGGTCACAAGGATCAAATTA 60.016 38.462 0.00 0.00 0.00 1.40
4465 4801 1.750778 ACAAGCCACAAAGGTCACAAG 59.249 47.619 0.00 0.00 40.61 3.16
4482 4818 2.143122 GTTGCATCTCGACAGGAACAA 58.857 47.619 0.00 0.00 34.32 2.83
4507 4843 5.236047 CCTACTACTACTACTGCTGTTACCG 59.764 48.000 0.09 0.00 0.00 4.02
4520 4856 6.101005 CCACTCTACTTACCCCTACTACTACT 59.899 46.154 0.00 0.00 0.00 2.57
4521 4857 6.126623 ACCACTCTACTTACCCCTACTACTAC 60.127 46.154 0.00 0.00 0.00 2.73
4522 4858 5.973124 ACCACTCTACTTACCCCTACTACTA 59.027 44.000 0.00 0.00 0.00 1.82
4523 4859 4.792972 ACCACTCTACTTACCCCTACTACT 59.207 45.833 0.00 0.00 0.00 2.57
4524 4860 5.122707 ACCACTCTACTTACCCCTACTAC 57.877 47.826 0.00 0.00 0.00 2.73
4525 4861 5.630069 CGAACCACTCTACTTACCCCTACTA 60.630 48.000 0.00 0.00 0.00 1.82
4723 5062 1.423541 TCTGAAAAGCACAGGGGCTAA 59.576 47.619 0.00 0.00 45.07 3.09
4729 5068 2.095567 CGGTGATTCTGAAAAGCACAGG 60.096 50.000 17.27 9.02 36.22 4.00
4756 5095 3.968724 CGCAAAGCAAACAAGTAGAAGAC 59.031 43.478 0.00 0.00 0.00 3.01
4758 5097 3.952535 ACGCAAAGCAAACAAGTAGAAG 58.047 40.909 0.00 0.00 0.00 2.85
4761 5100 4.326009 ACAAAACGCAAAGCAAACAAGTAG 59.674 37.500 0.00 0.00 0.00 2.57
4763 5102 3.063485 ACAAAACGCAAAGCAAACAAGT 58.937 36.364 0.00 0.00 0.00 3.16
4767 5132 2.768222 CCAACAAAACGCAAAGCAAAC 58.232 42.857 0.00 0.00 0.00 2.93
4822 5187 2.893637 AGCACGATACGCAAAAGAGAT 58.106 42.857 0.00 0.00 0.00 2.75
4951 5321 0.602562 ACCAACCATTTGTCGGCATG 59.397 50.000 0.00 0.00 0.00 4.06
5113 5495 3.924072 AGCTAGTTAGATCTAGGCCCCTA 59.076 47.826 0.00 0.00 38.17 3.53
5182 5565 1.705873 AGGCTAGACGATCCCGAAAT 58.294 50.000 0.00 0.00 39.50 2.17
5186 5569 0.249073 CACAAGGCTAGACGATCCCG 60.249 60.000 0.00 0.00 42.50 5.14
5189 5572 0.105039 CCCCACAAGGCTAGACGATC 59.895 60.000 0.00 0.00 0.00 3.69
5240 5624 3.607661 GGGAGCGACGGGGAGATC 61.608 72.222 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.