Multiple sequence alignment - TraesCS2D01G448600

Loading Multiple Alignment...

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 TraesCS2D01G448600 chr2D 100.000 2546 0 0 1 2546 558242683 558240138 0.000000e+00 4702.0
1 TraesCS2D01G448600 chr2D 91.026 312 18 4 157 458 473137637 473137326 1.820000e-111 412.0
2 TraesCS2D01G448600 chr2A 94.482 2048 76 20 508 2546 698828976 698826957 0.000000e+00 3121.0
3 TraesCS2D01G448600 chr2B 92.726 2117 90 16 457 2546 666655297 666653218 0.000000e+00 2998.0
4 TraesCS2D01G448600 chr2B 88.312 154 8 4 1 154 666655434 666655291 2.600000e-40 176.0
5 TraesCS2D01G448600 chr5A 92.508 307 17 3 157 457 558336320 558336626 3.890000e-118 435.0
6 TraesCS2D01G448600 chr5A 78.571 98 14 6 374 467 469903066 469902972 9.840000e-05 58.4
7 TraesCS2D01G448600 chr1A 90.997 311 24 3 156 463 592349090 592348781 1.410000e-112 416.0
8 TraesCS2D01G448600 chr6D 91.531 307 15 4 157 457 423083044 423083345 1.820000e-111 412.0
9 TraesCS2D01G448600 chr5D 91.083 314 15 4 157 457 192957003 192956690 1.820000e-111 412.0
10 TraesCS2D01G448600 chr5D 92.759 290 14 4 156 439 565937862 565937574 1.820000e-111 412.0
11 TraesCS2D01G448600 chr7D 93.214 280 17 2 179 457 272093512 272093234 6.560000e-111 411.0
12 TraesCS2D01G448600 chr7D 90.759 303 21 3 156 457 135334779 135334483 5.100000e-107 398.0
13 TraesCS2D01G448600 chr1D 93.262 282 12 3 156 436 188464206 188464481 2.360000e-110 409.0
14 TraesCS2D01G448600 chr3B 90.476 168 15 1 179 345 498661797 498661630 1.190000e-53 220.0
15 TraesCS2D01G448600 chr3B 81.132 106 4 8 385 476 54403589 54403692 1.260000e-08 71.3
16 TraesCS2D01G448600 chr4D 98.077 52 1 0 1229 1280 478668240 478668189 9.700000e-15 91.6
17 TraesCS2D01G448600 chr4A 98.077 52 1 0 1229 1280 685301975 685301924 9.700000e-15 91.6
18 TraesCS2D01G448600 chr7A 100.000 30 0 0 5 34 636146947 636146918 3.540000e-04 56.5
19 TraesCS2D01G448600 chr7A 100.000 30 0 0 5 34 636208791 636208762 3.540000e-04 56.5


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 TraesCS2D01G448600 chr2D 558240138 558242683 2545 True 4702 4702 100.000 1 2546 1 chr2D.!!$R2 2545
1 TraesCS2D01G448600 chr2A 698826957 698828976 2019 True 3121 3121 94.482 508 2546 1 chr2A.!!$R1 2038
2 TraesCS2D01G448600 chr2B 666653218 666655434 2216 True 1587 2998 90.519 1 2546 2 chr2B.!!$R1 2545

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
283 284 0.106335 TCCGAACACGTAAAAGCCCA 59.894 50.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1591 1.189446 CACACGTCACGAAGCAACTAC 59.811 52.381 2.91 0.0 0.0 2.73 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 4.722700 CCCGTGGGCAAGACCAGG 62.723 72.222 7.67 7.67 42.20 4.45
44 45 3.140814 GCCGGGTTTCTCATGGCC 61.141 66.667 2.18 0.00 39.83 5.36
57 58 2.301296 CTCATGGCCAGGTATAGAGTGG 59.699 54.545 18.43 0.00 0.00 4.00
58 59 2.090775 TCATGGCCAGGTATAGAGTGGA 60.091 50.000 18.43 0.00 32.60 4.02
78 79 2.244651 CGAATTAAGGAGGGCCGCG 61.245 63.158 0.00 0.00 39.96 6.46
115 116 5.638234 AGAGTTATCAGTCCGTAAAAACTGC 59.362 40.000 0.00 0.00 42.10 4.40
118 119 0.515564 CAGTCCGTAAAAACTGCCCG 59.484 55.000 0.00 0.00 36.76 6.13
154 155 2.775384 TCGCCCAAACCCAGACTTATAT 59.225 45.455 0.00 0.00 0.00 0.86
155 156 3.139077 CGCCCAAACCCAGACTTATATC 58.861 50.000 0.00 0.00 0.00 1.63
156 157 3.181454 CGCCCAAACCCAGACTTATATCT 60.181 47.826 0.00 0.00 0.00 1.98
157 158 4.039973 CGCCCAAACCCAGACTTATATCTA 59.960 45.833 0.00 0.00 0.00 1.98
158 159 5.280011 CGCCCAAACCCAGACTTATATCTAT 60.280 44.000 0.00 0.00 0.00 1.98
159 160 6.070995 CGCCCAAACCCAGACTTATATCTATA 60.071 42.308 0.00 0.00 0.00 1.31
160 161 7.104290 GCCCAAACCCAGACTTATATCTATAC 58.896 42.308 0.00 0.00 0.00 1.47
161 162 7.621796 CCCAAACCCAGACTTATATCTATACC 58.378 42.308 0.00 0.00 0.00 2.73
162 163 7.458170 CCCAAACCCAGACTTATATCTATACCT 59.542 40.741 0.00 0.00 0.00 3.08
163 164 8.314751 CCAAACCCAGACTTATATCTATACCTG 58.685 40.741 0.00 0.00 0.00 4.00
164 165 8.314751 CAAACCCAGACTTATATCTATACCTGG 58.685 40.741 0.00 0.00 39.55 4.45
165 166 5.958987 ACCCAGACTTATATCTATACCTGGC 59.041 44.000 0.00 0.00 38.77 4.85
166 167 5.364157 CCCAGACTTATATCTATACCTGGCC 59.636 48.000 0.00 0.00 38.77 5.36
167 168 5.958380 CCAGACTTATATCTATACCTGGCCA 59.042 44.000 4.71 4.71 34.34 5.36
168 169 6.613271 CCAGACTTATATCTATACCTGGCCAT 59.387 42.308 5.51 0.00 34.34 4.40
169 170 7.785028 CCAGACTTATATCTATACCTGGCCATA 59.215 40.741 5.51 0.00 34.34 2.74
170 171 8.634444 CAGACTTATATCTATACCTGGCCATAC 58.366 40.741 5.51 0.00 0.00 2.39
171 172 7.785506 AGACTTATATCTATACCTGGCCATACC 59.214 40.741 5.51 0.00 39.84 2.73
172 173 7.663041 ACTTATATCTATACCTGGCCATACCT 58.337 38.462 5.51 0.00 40.22 3.08
173 174 7.785506 ACTTATATCTATACCTGGCCATACCTC 59.214 40.741 5.51 0.00 40.22 3.85
174 175 2.803956 TCTATACCTGGCCATACCTCG 58.196 52.381 5.51 0.00 40.22 4.63
175 176 1.825474 CTATACCTGGCCATACCTCGG 59.175 57.143 5.51 5.16 40.22 4.63
176 177 0.836400 ATACCTGGCCATACCTCGGG 60.836 60.000 5.51 4.26 40.22 5.14
205 206 4.451150 CTAGCCAAGCCCGACGCA 62.451 66.667 0.00 0.00 41.38 5.24
206 207 3.950794 CTAGCCAAGCCCGACGCAA 62.951 63.158 0.00 0.00 41.38 4.85
207 208 3.538785 TAGCCAAGCCCGACGCAAA 62.539 57.895 0.00 0.00 41.38 3.68
208 209 3.972276 GCCAAGCCCGACGCAAAA 61.972 61.111 0.00 0.00 41.38 2.44
209 210 2.725008 CCAAGCCCGACGCAAAAA 59.275 55.556 0.00 0.00 41.38 1.94
223 224 2.600470 AAAAACCCAGGCCCGAGC 60.600 61.111 0.00 0.00 38.76 5.03
275 276 4.054825 GCCCGGTCCGAACACGTA 62.055 66.667 14.39 0.00 0.00 3.57
276 277 2.650196 CCCGGTCCGAACACGTAA 59.350 61.111 14.39 0.00 0.00 3.18
277 278 1.006337 CCCGGTCCGAACACGTAAA 60.006 57.895 14.39 0.00 0.00 2.01
278 279 0.599728 CCCGGTCCGAACACGTAAAA 60.600 55.000 14.39 0.00 0.00 1.52
279 280 0.785979 CCGGTCCGAACACGTAAAAG 59.214 55.000 14.39 0.00 0.00 2.27
280 281 0.162294 CGGTCCGAACACGTAAAAGC 59.838 55.000 4.91 0.00 0.00 3.51
281 282 0.514255 GGTCCGAACACGTAAAAGCC 59.486 55.000 0.00 0.00 0.00 4.35
282 283 0.514255 GTCCGAACACGTAAAAGCCC 59.486 55.000 0.00 0.00 0.00 5.19
283 284 0.106335 TCCGAACACGTAAAAGCCCA 59.894 50.000 0.00 0.00 0.00 5.36
284 285 1.161843 CCGAACACGTAAAAGCCCAT 58.838 50.000 0.00 0.00 0.00 4.00
285 286 1.129811 CCGAACACGTAAAAGCCCATC 59.870 52.381 0.00 0.00 0.00 3.51
286 287 1.201877 CGAACACGTAAAAGCCCATCG 60.202 52.381 0.00 0.00 0.00 3.84
287 288 1.129811 GAACACGTAAAAGCCCATCGG 59.870 52.381 0.00 0.00 0.00 4.18
316 317 4.883354 GCCCGGCCCATCCTTCAG 62.883 72.222 0.00 0.00 0.00 3.02
317 318 3.089874 CCCGGCCCATCCTTCAGA 61.090 66.667 0.00 0.00 0.00 3.27
318 319 2.679342 CCCGGCCCATCCTTCAGAA 61.679 63.158 0.00 0.00 0.00 3.02
319 320 1.302949 CCGGCCCATCCTTCAGAAA 59.697 57.895 0.00 0.00 0.00 2.52
320 321 0.323360 CCGGCCCATCCTTCAGAAAA 60.323 55.000 0.00 0.00 0.00 2.29
321 322 1.544724 CGGCCCATCCTTCAGAAAAA 58.455 50.000 0.00 0.00 0.00 1.94
322 323 1.202348 CGGCCCATCCTTCAGAAAAAC 59.798 52.381 0.00 0.00 0.00 2.43
323 324 1.202348 GGCCCATCCTTCAGAAAAACG 59.798 52.381 0.00 0.00 0.00 3.60
324 325 1.402852 GCCCATCCTTCAGAAAAACGC 60.403 52.381 0.00 0.00 0.00 4.84
325 326 1.135689 CCCATCCTTCAGAAAAACGCG 60.136 52.381 3.53 3.53 0.00 6.01
326 327 1.804151 CCATCCTTCAGAAAAACGCGA 59.196 47.619 15.93 0.00 0.00 5.87
327 328 2.225491 CCATCCTTCAGAAAAACGCGAA 59.775 45.455 15.93 0.00 0.00 4.70
328 329 3.304391 CCATCCTTCAGAAAAACGCGAAA 60.304 43.478 15.93 0.00 0.00 3.46
329 330 4.286910 CATCCTTCAGAAAAACGCGAAAA 58.713 39.130 15.93 0.00 0.00 2.29
330 331 3.687200 TCCTTCAGAAAAACGCGAAAAC 58.313 40.909 15.93 0.00 0.00 2.43
331 332 2.462565 CCTTCAGAAAAACGCGAAAACG 59.537 45.455 15.93 0.00 39.50 3.60
332 333 3.347443 CTTCAGAAAAACGCGAAAACGA 58.653 40.909 15.93 0.00 36.70 3.85
333 334 3.595709 TCAGAAAAACGCGAAAACGAT 57.404 38.095 15.93 0.00 36.70 3.73
334 335 3.284914 TCAGAAAAACGCGAAAACGATG 58.715 40.909 15.93 3.16 36.70 3.84
335 336 2.400408 CAGAAAAACGCGAAAACGATGG 59.600 45.455 15.93 0.00 36.70 3.51
336 337 1.711824 GAAAAACGCGAAAACGATGGG 59.288 47.619 15.93 0.00 36.70 4.00
337 338 0.662077 AAAACGCGAAAACGATGGGC 60.662 50.000 15.93 0.00 36.70 5.36
338 339 2.466520 AAACGCGAAAACGATGGGCC 62.467 55.000 15.93 0.00 36.70 5.80
339 340 4.174129 CGCGAAAACGATGGGCCC 62.174 66.667 17.59 17.59 34.06 5.80
340 341 4.174129 GCGAAAACGATGGGCCCG 62.174 66.667 19.37 7.98 0.00 6.13
341 342 3.505184 CGAAAACGATGGGCCCGG 61.505 66.667 19.37 11.81 0.00 5.73
342 343 3.138128 GAAAACGATGGGCCCGGG 61.138 66.667 19.09 19.09 0.00 5.73
378 379 2.565841 CCTTCGGGCTCAAAATCTAGG 58.434 52.381 0.00 0.00 0.00 3.02
379 380 1.943340 CTTCGGGCTCAAAATCTAGGC 59.057 52.381 0.00 0.00 37.55 3.93
382 383 2.707902 GGCTCAAAATCTAGGCCCG 58.292 57.895 0.00 0.00 37.12 6.13
383 384 0.180406 GGCTCAAAATCTAGGCCCGA 59.820 55.000 0.00 0.00 37.12 5.14
384 385 1.587547 GCTCAAAATCTAGGCCCGAG 58.412 55.000 0.00 0.00 0.00 4.63
385 386 1.587547 CTCAAAATCTAGGCCCGAGC 58.412 55.000 0.00 0.00 38.76 5.03
430 431 3.428282 CCGGGTCGGGCTTTTTCG 61.428 66.667 0.00 0.00 44.15 3.46
431 432 3.428282 CGGGTCGGGCTTTTTCGG 61.428 66.667 0.00 0.00 0.00 4.30
432 433 3.060000 GGGTCGGGCTTTTTCGGG 61.060 66.667 0.00 0.00 0.00 5.14
433 434 3.744719 GGTCGGGCTTTTTCGGGC 61.745 66.667 0.00 0.00 0.00 6.13
434 435 3.744719 GTCGGGCTTTTTCGGGCC 61.745 66.667 0.00 0.00 46.89 5.80
440 441 3.747976 CTTTTTCGGGCCGGGCTG 61.748 66.667 30.31 30.31 0.00 4.85
457 458 2.193248 GCCCATGGCCAGGACTAC 59.807 66.667 21.32 0.65 44.06 2.73
458 459 2.378634 GCCCATGGCCAGGACTACT 61.379 63.158 21.32 0.00 44.06 2.57
459 460 1.926426 GCCCATGGCCAGGACTACTT 61.926 60.000 21.32 0.00 44.06 2.24
460 461 1.507140 CCCATGGCCAGGACTACTTA 58.493 55.000 21.32 0.00 0.00 2.24
461 462 2.057922 CCCATGGCCAGGACTACTTAT 58.942 52.381 21.32 0.00 0.00 1.73
462 463 3.248024 CCCATGGCCAGGACTACTTATA 58.752 50.000 21.32 0.00 0.00 0.98
463 464 3.846588 CCCATGGCCAGGACTACTTATAT 59.153 47.826 21.32 0.00 0.00 0.86
570 582 2.870372 GTCCGATTGTGCTGGTGC 59.130 61.111 0.00 0.00 40.20 5.01
883 895 1.892441 AAAACCCCACAACCCCCACT 61.892 55.000 0.00 0.00 0.00 4.00
889 901 3.953775 ACAACCCCCACTGCCTCG 61.954 66.667 0.00 0.00 0.00 4.63
958 970 1.227853 AGTCCACGGGAGCAAACAC 60.228 57.895 0.00 0.00 29.39 3.32
1092 1111 4.335647 CACCGCCTCAAGCCCACT 62.336 66.667 0.00 0.00 38.78 4.00
1626 1646 3.253432 GTCTTCCAGTTCGAGCCATTTTT 59.747 43.478 0.00 0.00 0.00 1.94
1678 1698 0.387565 ACAAAACCGCCATTGGACAC 59.612 50.000 6.95 0.00 0.00 3.67
1711 1731 1.440708 GAGACGACGAGAGGACAAGA 58.559 55.000 0.00 0.00 0.00 3.02
1712 1732 1.805345 GAGACGACGAGAGGACAAGAA 59.195 52.381 0.00 0.00 0.00 2.52
1850 1872 5.878669 CGGCAGGGTTTAGGGTATATATTTC 59.121 44.000 0.00 0.00 0.00 2.17
1851 1873 6.296259 CGGCAGGGTTTAGGGTATATATTTCT 60.296 42.308 0.00 0.00 0.00 2.52
1873 1895 2.598637 CCGACAGTTATGATGTGACACG 59.401 50.000 0.22 0.00 0.00 4.49
1996 2018 3.266636 TCAACGACAAACTTGCAGAGAA 58.733 40.909 0.00 0.00 0.00 2.87
2044 2066 4.277257 TCGCATTTCAGATACAACATGC 57.723 40.909 0.00 0.00 34.85 4.06
2069 2091 5.470368 TGAAGCAACAGTAGCTACAACTAG 58.530 41.667 25.28 11.85 42.53 2.57
2110 2132 9.406828 CATATGCAAATTAGAATCCAACTCATG 57.593 33.333 0.00 0.00 0.00 3.07
2164 2188 1.134491 ACCTACCTAGCATGCCGAAAC 60.134 52.381 15.66 0.00 0.00 2.78
2223 2247 4.408993 TTCAGCATTGTTCTCATTCGTG 57.591 40.909 0.00 0.00 0.00 4.35
2238 2262 3.529634 TTCGTGTCAGGCAATTTTACG 57.470 42.857 0.00 0.00 0.00 3.18
2271 2295 8.218338 CTGGTAGACAGCAAATTCAGATAATT 57.782 34.615 0.00 0.00 40.97 1.40
2290 2314 7.605691 AGATAATTCTATGCCACACAGCTATTC 59.394 37.037 0.00 0.00 0.00 1.75
2291 2315 4.486125 TTCTATGCCACACAGCTATTCA 57.514 40.909 0.00 0.00 0.00 2.57
2448 2477 5.578005 ATGCCATCAGTTGATTTCTTCTG 57.422 39.130 0.00 0.00 31.21 3.02
2470 2499 4.098654 TGGGACAATTTAAACCACACACAG 59.901 41.667 0.00 0.00 31.92 3.66
2471 2500 4.098807 GGGACAATTTAAACCACACACAGT 59.901 41.667 0.00 0.00 0.00 3.55
2472 2501 5.278604 GGACAATTTAAACCACACACAGTC 58.721 41.667 0.00 0.00 0.00 3.51
2473 2502 5.163602 GGACAATTTAAACCACACACAGTCA 60.164 40.000 0.00 0.00 0.00 3.41
2474 2503 5.646606 ACAATTTAAACCACACACAGTCAC 58.353 37.500 0.00 0.00 0.00 3.67
2475 2504 5.184096 ACAATTTAAACCACACACAGTCACA 59.816 36.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.824041 CATGAGAAACCCGGCCCG 60.824 66.667 0.00 0.00 0.00 6.13
27 28 3.140814 GGCCATGAGAAACCCGGC 61.141 66.667 0.00 0.00 42.21 6.13
36 37 2.301296 CCACTCTATACCTGGCCATGAG 59.699 54.545 15.66 13.18 0.00 2.90
37 38 2.090775 TCCACTCTATACCTGGCCATGA 60.091 50.000 15.66 0.00 0.00 3.07
44 45 4.592485 AATTCGCTCCACTCTATACCTG 57.408 45.455 0.00 0.00 0.00 4.00
57 58 0.880718 CGGCCCTCCTTAATTCGCTC 60.881 60.000 0.00 0.00 0.00 5.03
58 59 1.146263 CGGCCCTCCTTAATTCGCT 59.854 57.895 0.00 0.00 0.00 4.93
78 79 2.029838 TAACTCTCCTACGGACGGAC 57.970 55.000 0.00 0.00 0.00 4.79
93 94 4.694037 GGCAGTTTTTACGGACTGATAACT 59.306 41.667 7.61 0.00 44.65 2.24
94 95 4.142752 GGGCAGTTTTTACGGACTGATAAC 60.143 45.833 7.61 0.00 44.65 1.89
95 96 4.004982 GGGCAGTTTTTACGGACTGATAA 58.995 43.478 7.61 0.00 44.65 1.75
96 97 3.602483 GGGCAGTTTTTACGGACTGATA 58.398 45.455 7.61 0.00 44.65 2.15
97 98 2.433436 GGGCAGTTTTTACGGACTGAT 58.567 47.619 7.61 0.00 44.65 2.90
115 116 1.201877 CGAAAATGCTCAACGTACGGG 60.202 52.381 21.06 11.50 0.00 5.28
118 119 1.465187 GGGCGAAAATGCTCAACGTAC 60.465 52.381 0.00 0.00 34.69 3.67
154 155 2.556782 CCGAGGTATGGCCAGGTATAGA 60.557 54.545 13.05 0.00 40.61 1.98
155 156 1.825474 CCGAGGTATGGCCAGGTATAG 59.175 57.143 13.05 0.92 40.61 1.31
156 157 1.551560 CCCGAGGTATGGCCAGGTATA 60.552 57.143 13.05 0.00 40.61 1.47
157 158 0.836400 CCCGAGGTATGGCCAGGTAT 60.836 60.000 13.05 0.00 40.61 2.73
158 159 1.458777 CCCGAGGTATGGCCAGGTA 60.459 63.158 13.05 0.00 40.61 3.08
159 160 2.768344 CCCGAGGTATGGCCAGGT 60.768 66.667 13.05 0.00 40.61 4.00
160 161 4.256180 GCCCGAGGTATGGCCAGG 62.256 72.222 13.05 6.01 41.97 4.45
188 189 3.950794 TTGCGTCGGGCTTGGCTAG 62.951 63.158 0.00 0.00 44.05 3.42
189 190 3.538785 TTTGCGTCGGGCTTGGCTA 62.539 57.895 0.00 0.00 44.05 3.93
190 191 4.947147 TTTGCGTCGGGCTTGGCT 62.947 61.111 0.00 0.00 44.05 4.75
191 192 3.492311 TTTTTGCGTCGGGCTTGGC 62.492 57.895 0.00 0.00 44.05 4.52
192 193 2.725008 TTTTTGCGTCGGGCTTGG 59.275 55.556 0.00 0.00 44.05 3.61
206 207 2.600470 GCTCGGGCCTGGGTTTTT 60.600 61.111 14.54 0.00 0.00 1.94
258 259 3.572196 TTACGTGTTCGGACCGGGC 62.572 63.158 15.25 0.21 41.85 6.13
259 260 0.599728 TTTTACGTGTTCGGACCGGG 60.600 55.000 15.25 0.00 41.85 5.73
260 261 0.785979 CTTTTACGTGTTCGGACCGG 59.214 55.000 15.25 0.00 41.85 5.28
261 262 0.162294 GCTTTTACGTGTTCGGACCG 59.838 55.000 7.84 7.84 41.85 4.79
262 263 0.514255 GGCTTTTACGTGTTCGGACC 59.486 55.000 0.00 0.00 41.85 4.46
263 264 0.514255 GGGCTTTTACGTGTTCGGAC 59.486 55.000 0.00 0.00 41.85 4.79
264 265 0.106335 TGGGCTTTTACGTGTTCGGA 59.894 50.000 0.00 0.00 41.85 4.55
265 266 1.129811 GATGGGCTTTTACGTGTTCGG 59.870 52.381 0.00 0.00 41.85 4.30
266 267 1.201877 CGATGGGCTTTTACGTGTTCG 60.202 52.381 0.00 0.00 43.34 3.95
267 268 1.129811 CCGATGGGCTTTTACGTGTTC 59.870 52.381 0.00 0.00 0.00 3.18
268 269 1.161843 CCGATGGGCTTTTACGTGTT 58.838 50.000 0.00 0.00 0.00 3.32
269 270 0.675522 CCCGATGGGCTTTTACGTGT 60.676 55.000 0.00 0.00 35.35 4.49
270 271 2.094904 CCCGATGGGCTTTTACGTG 58.905 57.895 0.00 0.00 35.35 4.49
271 272 4.629779 CCCGATGGGCTTTTACGT 57.370 55.556 0.00 0.00 35.35 3.57
299 300 4.883354 CTGAAGGATGGGCCGGGC 62.883 72.222 22.00 22.00 43.43 6.13
300 301 2.210144 TTTCTGAAGGATGGGCCGGG 62.210 60.000 2.18 0.00 43.43 5.73
301 302 0.323360 TTTTCTGAAGGATGGGCCGG 60.323 55.000 0.00 0.00 43.43 6.13
302 303 1.202348 GTTTTTCTGAAGGATGGGCCG 59.798 52.381 0.00 0.00 43.43 6.13
303 304 1.202348 CGTTTTTCTGAAGGATGGGCC 59.798 52.381 0.00 0.00 0.00 5.80
304 305 1.402852 GCGTTTTTCTGAAGGATGGGC 60.403 52.381 0.00 0.00 0.00 5.36
305 306 1.135689 CGCGTTTTTCTGAAGGATGGG 60.136 52.381 0.00 0.00 0.00 4.00
306 307 1.804151 TCGCGTTTTTCTGAAGGATGG 59.196 47.619 5.77 0.00 0.00 3.51
307 308 3.536158 TTCGCGTTTTTCTGAAGGATG 57.464 42.857 5.77 0.00 0.00 3.51
308 309 4.287720 GTTTTCGCGTTTTTCTGAAGGAT 58.712 39.130 5.77 0.00 0.00 3.24
309 310 3.687200 GTTTTCGCGTTTTTCTGAAGGA 58.313 40.909 5.77 0.00 0.00 3.36
310 311 2.462565 CGTTTTCGCGTTTTTCTGAAGG 59.537 45.455 5.77 0.00 36.22 3.46
311 312 3.347443 TCGTTTTCGCGTTTTTCTGAAG 58.653 40.909 5.77 0.00 43.73 3.02
312 313 3.386613 TCGTTTTCGCGTTTTTCTGAA 57.613 38.095 5.77 0.00 43.73 3.02
313 314 3.284914 CATCGTTTTCGCGTTTTTCTGA 58.715 40.909 5.77 0.00 43.73 3.27
314 315 2.400408 CCATCGTTTTCGCGTTTTTCTG 59.600 45.455 5.77 0.00 43.73 3.02
315 316 2.603652 CCCATCGTTTTCGCGTTTTTCT 60.604 45.455 5.77 0.00 43.73 2.52
316 317 1.711824 CCCATCGTTTTCGCGTTTTTC 59.288 47.619 5.77 0.00 43.73 2.29
317 318 1.761206 CCCATCGTTTTCGCGTTTTT 58.239 45.000 5.77 0.00 43.73 1.94
318 319 0.662077 GCCCATCGTTTTCGCGTTTT 60.662 50.000 5.77 0.00 43.73 2.43
319 320 1.081708 GCCCATCGTTTTCGCGTTT 60.082 52.632 5.77 0.00 43.73 3.60
320 321 2.559330 GCCCATCGTTTTCGCGTT 59.441 55.556 5.77 0.00 43.73 4.84
321 322 3.428282 GGCCCATCGTTTTCGCGT 61.428 61.111 5.77 0.00 43.73 6.01
322 323 4.174129 GGGCCCATCGTTTTCGCG 62.174 66.667 19.95 0.00 43.73 5.87
323 324 4.174129 CGGGCCCATCGTTTTCGC 62.174 66.667 24.92 0.00 43.73 4.70
324 325 3.505184 CCGGGCCCATCGTTTTCG 61.505 66.667 24.92 3.62 45.64 3.46
325 326 3.138128 CCCGGGCCCATCGTTTTC 61.138 66.667 24.92 0.00 0.00 2.29
359 360 1.943340 GCCTAGATTTTGAGCCCGAAG 59.057 52.381 0.00 0.00 0.00 3.79
360 361 1.408266 GGCCTAGATTTTGAGCCCGAA 60.408 52.381 0.00 0.00 37.66 4.30
361 362 0.180406 GGCCTAGATTTTGAGCCCGA 59.820 55.000 0.00 0.00 37.66 5.14
362 363 2.707902 GGCCTAGATTTTGAGCCCG 58.292 57.895 0.00 0.00 37.66 6.13
364 365 0.180406 TCGGGCCTAGATTTTGAGCC 59.820 55.000 0.84 0.00 43.09 4.70
365 366 1.587547 CTCGGGCCTAGATTTTGAGC 58.412 55.000 0.84 0.00 0.00 4.26
366 367 1.587547 GCTCGGGCCTAGATTTTGAG 58.412 55.000 9.63 2.79 0.00 3.02
367 368 3.780624 GCTCGGGCCTAGATTTTGA 57.219 52.632 9.63 0.00 0.00 2.69
414 415 3.428282 CCGAAAAAGCCCGACCCG 61.428 66.667 0.00 0.00 0.00 5.28
415 416 3.060000 CCCGAAAAAGCCCGACCC 61.060 66.667 0.00 0.00 0.00 4.46
416 417 3.744719 GCCCGAAAAAGCCCGACC 61.745 66.667 0.00 0.00 0.00 4.79
417 418 3.744719 GGCCCGAAAAAGCCCGAC 61.745 66.667 0.00 0.00 43.76 4.79
423 424 3.747976 CAGCCCGGCCCGAAAAAG 61.748 66.667 3.71 0.00 0.00 2.27
441 442 1.507140 TAAGTAGTCCTGGCCATGGG 58.493 55.000 15.13 4.96 0.00 4.00
442 443 4.532126 TGATATAAGTAGTCCTGGCCATGG 59.468 45.833 5.51 7.63 0.00 3.66
443 444 5.247110 ACTGATATAAGTAGTCCTGGCCATG 59.753 44.000 5.51 2.84 0.00 3.66
444 445 5.407049 ACTGATATAAGTAGTCCTGGCCAT 58.593 41.667 5.51 0.00 0.00 4.40
445 446 4.816126 ACTGATATAAGTAGTCCTGGCCA 58.184 43.478 4.71 4.71 0.00 5.36
446 447 5.773680 TGTACTGATATAAGTAGTCCTGGCC 59.226 44.000 0.00 0.00 33.35 5.36
447 448 6.264744 TGTGTACTGATATAAGTAGTCCTGGC 59.735 42.308 0.00 0.00 33.35 4.85
448 449 7.818997 TGTGTACTGATATAAGTAGTCCTGG 57.181 40.000 0.00 0.00 33.35 4.45
463 464 8.714179 CGTAAGAATACCATTTTTGTGTACTGA 58.286 33.333 0.00 0.00 43.02 3.41
570 582 6.676995 CGTAACACATCTACAAAAAGCATACG 59.323 38.462 0.00 0.00 0.00 3.06
883 895 2.911221 TAGAGGCTGCTAGCGAGGCA 62.911 60.000 28.90 14.92 43.62 4.75
889 901 3.006247 GGCATTTATAGAGGCTGCTAGC 58.994 50.000 8.10 8.10 41.46 3.42
919 931 2.264794 GGGACATTCGTGCGGTCT 59.735 61.111 0.00 0.00 33.50 3.85
920 932 3.186047 CGGGACATTCGTGCGGTC 61.186 66.667 0.00 0.00 33.50 4.79
921 933 3.998672 ACGGGACATTCGTGCGGT 61.999 61.111 0.00 0.00 41.24 5.68
958 970 1.079543 CTCCCGTGTCAGCTTGAGG 60.080 63.158 0.00 0.00 0.00 3.86
1359 1378 4.477975 AGCAGCGCGTACTCGGTC 62.478 66.667 7.03 3.23 38.18 4.79
1572 1591 1.189446 CACACGTCACGAAGCAACTAC 59.811 52.381 2.91 0.00 0.00 2.73
1626 1646 6.430616 TCTTATGCCATTATTCATTCGATGCA 59.569 34.615 0.00 0.00 0.00 3.96
1850 1872 3.859961 GTGTCACATCATAACTGTCGGAG 59.140 47.826 0.00 0.00 0.00 4.63
1851 1873 3.672241 CGTGTCACATCATAACTGTCGGA 60.672 47.826 3.42 0.00 0.00 4.55
1873 1895 2.223803 TCCTGAGACAGAACTCCTCC 57.776 55.000 0.00 0.00 36.22 4.30
1943 1965 6.830912 TGTCACTTCATCATAGATTAAGGGG 58.169 40.000 4.02 0.00 0.00 4.79
2019 2041 6.522165 GCATGTTGTATCTGAAATGCGATATG 59.478 38.462 0.00 0.00 32.04 1.78
2023 2045 3.688673 TGCATGTTGTATCTGAAATGCGA 59.311 39.130 0.00 0.00 42.53 5.10
2044 2066 4.692625 AGTTGTAGCTACTGTTGCTTCATG 59.307 41.667 23.84 0.00 41.46 3.07
2056 2078 5.051153 GCAATCCTTCCTAGTTGTAGCTAC 58.949 45.833 17.30 17.30 0.00 3.58
2069 2091 5.204409 TGCATATGATTTGCAATCCTTCC 57.796 39.130 8.09 0.00 46.48 3.46
2094 2116 8.822805 ACCTAACTTACATGAGTTGGATTCTAA 58.177 33.333 10.96 0.00 39.61 2.10
2110 2132 3.937079 CCGGTGAAATGGACCTAACTTAC 59.063 47.826 0.00 0.00 0.00 2.34
2223 2247 1.539827 ACCTGCGTAAAATTGCCTGAC 59.460 47.619 0.00 0.00 0.00 3.51
2238 2262 1.275291 TGCTGTCTACCAGTAACCTGC 59.725 52.381 0.00 0.00 43.55 4.85
2257 2281 8.407832 TGTGTGGCATAGAATTATCTGAATTTG 58.592 33.333 0.00 0.00 37.10 2.32
2271 2295 3.181462 CCTGAATAGCTGTGTGGCATAGA 60.181 47.826 0.00 0.00 34.17 1.98
2290 2314 7.864108 TCAACATATTAGAATTGGTGACCTG 57.136 36.000 2.11 0.00 32.38 4.00
2291 2315 9.125026 GAATCAACATATTAGAATTGGTGACCT 57.875 33.333 2.11 0.00 39.70 3.85
2448 2477 4.098807 ACTGTGTGTGGTTTAAATTGTCCC 59.901 41.667 0.00 0.00 0.00 4.46
2470 2499 4.094887 CACTAATAGGCAATGGTGTGTGAC 59.905 45.833 0.00 0.00 0.00 3.67
2471 2500 4.260985 CACTAATAGGCAATGGTGTGTGA 58.739 43.478 0.00 0.00 0.00 3.58
2472 2501 3.378112 CCACTAATAGGCAATGGTGTGTG 59.622 47.826 0.00 0.00 0.00 3.82
2473 2502 3.010138 ACCACTAATAGGCAATGGTGTGT 59.990 43.478 0.20 0.00 42.12 3.72
2474 2503 3.620488 ACCACTAATAGGCAATGGTGTG 58.380 45.455 0.20 0.00 42.12 3.82
2475 2504 4.473559 AGTACCACTAATAGGCAATGGTGT 59.526 41.667 9.69 0.00 43.51 4.16


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

AutoCloner maintained by Alex Coulton.