Multiple sequence alignment - TraesCS5D01G191100

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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 TraesCS5D01G191100 chr5D 100.000 2672 0 0 967 3638 293370773 293373444 0.000000e+00 4935.0
1 TraesCS5D01G191100 chr5D 100.000 794 0 0 1 794 293369807 293370600 0.000000e+00 1467.0
2 TraesCS5D01G191100 chr5B 95.976 2684 88 11 967 3638 334871660 334874335 0.000000e+00 4340.0
3 TraesCS5D01G191100 chr5B 94.025 318 12 2 483 794 334871075 334871391 3.290000e-130 475.0
4 TraesCS5D01G191100 chr5B 95.556 45 1 1 412 455 334870986 334871030 1.810000e-08 71.3
5 TraesCS5D01G191100 chr5A 95.995 1523 57 2 967 2486 386178266 386179787 0.000000e+00 2471.0
6 TraesCS5D01G191100 chr5A 87.197 742 45 21 83 794 386177028 386177749 0.000000e+00 798.0
7 TraesCS5D01G191100 chr5A 91.519 507 35 6 2486 2988 487792705 487792203 0.000000e+00 691.0
8 TraesCS5D01G191100 chr5A 83.794 506 51 13 2487 2968 143578559 143578061 5.540000e-123 451.0
9 TraesCS5D01G191100 chr5A 84.956 339 32 8 2989 3310 386179781 386180117 3.500000e-85 326.0
10 TraesCS5D01G191100 chr5A 91.477 176 12 2 3339 3514 386180555 386180727 4.690000e-59 239.0
11 TraesCS5D01G191100 chr5A 92.063 126 6 2 3517 3638 386180859 386180984 1.340000e-39 174.0
12 TraesCS5D01G191100 chr6B 89.662 503 41 10 2488 2986 523190984 523191479 6.630000e-177 630.0
13 TraesCS5D01G191100 chr7B 88.525 488 44 10 2485 2968 516793213 516793692 6.770000e-162 580.0
14 TraesCS5D01G191100 chr7B 91.667 48 4 0 99 146 18508374 18508421 2.340000e-07 67.6
15 TraesCS5D01G191100 chr1B 89.201 463 41 9 2488 2947 568969701 568969245 1.470000e-158 569.0
16 TraesCS5D01G191100 chr1B 85.714 518 58 7 2484 2988 264852702 264853216 1.920000e-147 532.0
17 TraesCS5D01G191100 chr4B 87.885 487 52 5 2506 2988 420447053 420446570 1.900000e-157 566.0
18 TraesCS5D01G191100 chr1A 87.905 463 43 11 2488 2947 517103372 517102920 1.920000e-147 532.0
19 TraesCS5D01G191100 chr7D 84.381 525 55 12 2488 2988 274698003 274698524 1.170000e-134 490.0


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 TraesCS5D01G191100 chr5D 293369807 293373444 3637 False 3201.000000 4935 100.000000 1 3638 2 chr5D.!!$F1 3637
1 TraesCS5D01G191100 chr5B 334870986 334874335 3349 False 1628.766667 4340 95.185667 412 3638 3 chr5B.!!$F1 3226
2 TraesCS5D01G191100 chr5A 386177028 386180984 3956 False 801.600000 2471 90.337600 83 3638 5 chr5A.!!$F1 3555
3 TraesCS5D01G191100 chr5A 487792203 487792705 502 True 691.000000 691 91.519000 2486 2988 1 chr5A.!!$R2 502
4 TraesCS5D01G191100 chr1B 264852702 264853216 514 False 532.000000 532 85.714000 2484 2988 1 chr1B.!!$F1 504
5 TraesCS5D01G191100 chr7D 274698003 274698524 521 False 490.000000 490 84.381000 2488 2988 1 chr7D.!!$F1 500

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
19 20 0.328258 GGCTACCACAACCACTGGAT 59.672 55.000 0.71 0.00 32.55 3.41 F
78 79 0.388520 CGACGATGACAGACCAAGCA 60.389 55.000 0.00 0.00 0.00 3.91 F
260 263 1.134788 AGGCATCTTTTAGTCGACGGG 60.135 52.381 10.46 0.18 0.00 5.28 F
510 557 1.374125 GTTGCGTGCCCAATTTCCC 60.374 57.895 0.00 0.00 0.00 3.97 F
1546 1943 1.485480 AGATGGACTACGACGAGAGGA 59.515 52.381 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1882 1.769733 CAGCACCAAATCCAACAACG 58.230 50.000 0.0 0.0 0.00 4.10 R
1800 2197 2.669419 GCCAATGCCAAAGCGAATC 58.331 52.632 0.0 0.0 44.31 2.52 R
2235 2636 2.414481 CAGGTTCTCAAAGTGATCTGCG 59.586 50.000 0.0 0.0 0.00 5.18 R
2504 2905 0.109179 TCCGCTTCGCTTACGCTTTA 60.109 50.000 0.0 0.0 39.84 1.85 R
2928 3353 0.242017 GAGCGATGGCAAACTGCTTT 59.758 50.000 1.5 0.0 44.28 3.51 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
17 18 4.397348 GGCTACCACAACCACTGG 57.603 61.111 0.00 0.00 34.62 4.00
18 19 1.758592 GGCTACCACAACCACTGGA 59.241 57.895 0.71 0.00 32.55 3.86
19 20 0.328258 GGCTACCACAACCACTGGAT 59.672 55.000 0.71 0.00 32.55 3.41
20 21 1.453155 GCTACCACAACCACTGGATG 58.547 55.000 0.71 2.47 32.55 3.51
32 33 1.131126 CACTGGATGGACGTTCAATGC 59.869 52.381 0.00 0.00 0.00 3.56
33 34 1.003580 ACTGGATGGACGTTCAATGCT 59.996 47.619 0.00 0.00 0.00 3.79
34 35 2.086869 CTGGATGGACGTTCAATGCTT 58.913 47.619 0.00 0.00 0.00 3.91
35 36 1.811965 TGGATGGACGTTCAATGCTTG 59.188 47.619 0.00 0.00 0.00 4.01
36 37 2.083774 GGATGGACGTTCAATGCTTGA 58.916 47.619 0.00 0.00 38.04 3.02
37 38 2.487762 GGATGGACGTTCAATGCTTGAA 59.512 45.455 0.00 7.09 46.68 2.69
51 52 3.485394 TGCTTGAAGGATAGCAACAACA 58.515 40.909 0.00 0.00 43.88 3.33
52 53 4.081406 TGCTTGAAGGATAGCAACAACAT 58.919 39.130 0.00 0.00 43.88 2.71
53 54 4.156556 TGCTTGAAGGATAGCAACAACATC 59.843 41.667 0.00 0.00 43.88 3.06
54 55 4.156556 GCTTGAAGGATAGCAACAACATCA 59.843 41.667 0.00 0.00 37.35 3.07
55 56 5.675575 GCTTGAAGGATAGCAACAACATCAG 60.676 44.000 0.00 0.00 37.35 2.90
56 57 3.691118 TGAAGGATAGCAACAACATCAGC 59.309 43.478 0.00 0.00 0.00 4.26
57 58 2.283298 AGGATAGCAACAACATCAGCG 58.717 47.619 0.00 0.00 0.00 5.18
58 59 1.331756 GGATAGCAACAACATCAGCGG 59.668 52.381 0.00 0.00 0.00 5.52
59 60 0.734889 ATAGCAACAACATCAGCGGC 59.265 50.000 0.00 0.00 0.00 6.53
60 61 1.634757 TAGCAACAACATCAGCGGCG 61.635 55.000 0.51 0.51 0.00 6.46
61 62 2.965147 GCAACAACATCAGCGGCGA 61.965 57.895 12.98 0.00 0.00 5.54
62 63 1.154413 CAACAACATCAGCGGCGAC 60.154 57.895 12.98 1.23 0.00 5.19
74 75 2.571757 GGCGACGATGACAGACCA 59.428 61.111 0.00 0.00 0.00 4.02
75 76 1.080093 GGCGACGATGACAGACCAA 60.080 57.895 0.00 0.00 0.00 3.67
76 77 1.078759 GGCGACGATGACAGACCAAG 61.079 60.000 0.00 0.00 0.00 3.61
77 78 1.687494 GCGACGATGACAGACCAAGC 61.687 60.000 0.00 0.00 0.00 4.01
78 79 0.388520 CGACGATGACAGACCAAGCA 60.389 55.000 0.00 0.00 0.00 3.91
79 80 1.737029 CGACGATGACAGACCAAGCAT 60.737 52.381 0.00 0.00 0.00 3.79
80 81 1.929836 GACGATGACAGACCAAGCATC 59.070 52.381 0.00 0.00 35.10 3.91
81 82 1.276138 ACGATGACAGACCAAGCATCA 59.724 47.619 0.00 0.00 37.56 3.07
82 83 2.289631 ACGATGACAGACCAAGCATCAA 60.290 45.455 0.00 0.00 37.56 2.57
83 84 2.094894 CGATGACAGACCAAGCATCAAC 59.905 50.000 0.00 0.00 37.56 3.18
84 85 1.896220 TGACAGACCAAGCATCAACC 58.104 50.000 0.00 0.00 0.00 3.77
128 129 1.664321 ATGCCTACGAGGTCACCGTC 61.664 60.000 0.00 0.00 40.95 4.79
129 130 3.061260 GCCTACGAGGTCACCGTCC 62.061 68.421 0.00 0.00 40.95 4.79
209 212 6.803154 AAATTTACAGTCTAGACACAAGCC 57.197 37.500 24.44 0.00 0.00 4.35
214 217 4.344978 ACAGTCTAGACACAAGCCTATCA 58.655 43.478 24.44 0.00 0.00 2.15
219 222 7.013750 CAGTCTAGACACAAGCCTATCATCTTA 59.986 40.741 24.44 0.00 0.00 2.10
227 230 9.247861 ACACAAGCCTATCATCTTAAGATTTTT 57.752 29.630 15.49 6.09 31.21 1.94
228 231 9.727627 CACAAGCCTATCATCTTAAGATTTTTC 57.272 33.333 15.49 3.69 31.21 2.29
242 245 9.737025 CTTAAGATTTTTCGAAGTTAACGTAGG 57.263 33.333 0.00 0.00 0.00 3.18
244 247 5.697633 AGATTTTTCGAAGTTAACGTAGGCA 59.302 36.000 0.00 0.00 0.00 4.75
247 250 4.445452 TTCGAAGTTAACGTAGGCATCT 57.555 40.909 0.00 0.00 0.00 2.90
248 251 4.445452 TCGAAGTTAACGTAGGCATCTT 57.555 40.909 0.00 0.00 0.00 2.40
249 252 4.813027 TCGAAGTTAACGTAGGCATCTTT 58.187 39.130 0.00 0.00 0.00 2.52
254 257 7.462462 CGAAGTTAACGTAGGCATCTTTTAGTC 60.462 40.741 0.00 0.00 0.00 2.59
257 260 3.767278 ACGTAGGCATCTTTTAGTCGAC 58.233 45.455 7.70 7.70 0.00 4.20
259 262 2.295253 AGGCATCTTTTAGTCGACGG 57.705 50.000 10.46 0.00 0.00 4.79
260 263 1.134788 AGGCATCTTTTAGTCGACGGG 60.135 52.381 10.46 0.18 0.00 5.28
263 266 2.347755 GCATCTTTTAGTCGACGGGAAC 59.652 50.000 10.46 0.00 0.00 3.62
278 281 2.972625 GGGAACGTGTGATCATCAGAA 58.027 47.619 0.00 0.00 0.00 3.02
281 284 4.396166 GGGAACGTGTGATCATCAGAATTT 59.604 41.667 0.00 0.00 0.00 1.82
282 285 5.584649 GGGAACGTGTGATCATCAGAATTTA 59.415 40.000 0.00 0.00 0.00 1.40
283 286 6.093495 GGGAACGTGTGATCATCAGAATTTAA 59.907 38.462 0.00 0.00 0.00 1.52
284 287 7.361713 GGGAACGTGTGATCATCAGAATTTAAA 60.362 37.037 0.00 0.00 0.00 1.52
285 288 7.481798 GGAACGTGTGATCATCAGAATTTAAAC 59.518 37.037 0.00 0.00 0.00 2.01
286 289 6.842163 ACGTGTGATCATCAGAATTTAAACC 58.158 36.000 0.00 0.00 0.00 3.27
287 290 6.655003 ACGTGTGATCATCAGAATTTAAACCT 59.345 34.615 0.00 0.00 0.00 3.50
288 291 6.963242 CGTGTGATCATCAGAATTTAAACCTG 59.037 38.462 0.00 11.30 0.00 4.00
289 292 7.148423 CGTGTGATCATCAGAATTTAAACCTGA 60.148 37.037 18.68 18.68 40.68 3.86
294 297 5.859205 ATCAGAATTTAAACCTGATGGGC 57.141 39.130 23.45 0.00 43.62 5.36
295 298 4.934356 TCAGAATTTAAACCTGATGGGCT 58.066 39.130 14.63 0.00 39.10 5.19
297 300 4.706476 CAGAATTTAAACCTGATGGGCTGA 59.294 41.667 11.89 0.00 39.10 4.26
298 301 5.185635 CAGAATTTAAACCTGATGGGCTGAA 59.814 40.000 11.89 0.00 39.10 3.02
299 302 5.420104 AGAATTTAAACCTGATGGGCTGAAG 59.580 40.000 0.00 0.00 39.10 3.02
300 303 4.380843 TTTAAACCTGATGGGCTGAAGA 57.619 40.909 0.00 0.00 39.10 2.87
301 304 4.591321 TTAAACCTGATGGGCTGAAGAT 57.409 40.909 0.00 0.00 39.10 2.40
302 305 5.708736 TTAAACCTGATGGGCTGAAGATA 57.291 39.130 0.00 0.00 39.10 1.98
303 306 4.803329 AAACCTGATGGGCTGAAGATAT 57.197 40.909 0.00 0.00 39.10 1.63
304 307 4.363991 AACCTGATGGGCTGAAGATATC 57.636 45.455 0.00 0.00 39.10 1.63
305 308 3.321039 ACCTGATGGGCTGAAGATATCA 58.679 45.455 5.32 0.00 39.10 2.15
306 309 3.327172 ACCTGATGGGCTGAAGATATCAG 59.673 47.826 5.32 0.00 46.38 2.90
307 310 5.189475 ACCTGATGGGCTGAAGATATCAGT 61.189 45.833 5.32 0.00 45.88 3.41
322 325 6.815089 AGATATCAGTGTCTTTCTGACCATC 58.185 40.000 5.32 0.00 44.75 3.51
325 328 3.070018 CAGTGTCTTTCTGACCATCCAC 58.930 50.000 0.00 0.00 44.75 4.02
326 329 2.975489 AGTGTCTTTCTGACCATCCACT 59.025 45.455 0.00 0.00 44.75 4.00
327 330 4.021104 CAGTGTCTTTCTGACCATCCACTA 60.021 45.833 0.00 0.00 44.75 2.74
328 331 4.021016 AGTGTCTTTCTGACCATCCACTAC 60.021 45.833 0.00 0.00 44.75 2.73
329 332 3.901222 TGTCTTTCTGACCATCCACTACA 59.099 43.478 0.00 0.00 44.75 2.74
330 333 4.021104 TGTCTTTCTGACCATCCACTACAG 60.021 45.833 0.00 0.00 44.75 2.74
332 335 4.220821 TCTTTCTGACCATCCACTACAGAC 59.779 45.833 0.00 0.00 37.34 3.51
333 336 3.458044 TCTGACCATCCACTACAGACT 57.542 47.619 0.00 0.00 33.57 3.24
334 337 3.092301 TCTGACCATCCACTACAGACTG 58.908 50.000 0.00 0.00 33.57 3.51
336 339 3.239449 TGACCATCCACTACAGACTGTT 58.761 45.455 14.50 0.00 0.00 3.16
337 340 3.646162 TGACCATCCACTACAGACTGTTT 59.354 43.478 14.50 0.00 0.00 2.83
338 341 3.997021 GACCATCCACTACAGACTGTTTG 59.003 47.826 14.50 11.21 0.00 2.93
343 367 5.607939 TCCACTACAGACTGTTTGAAAGA 57.392 39.130 14.50 1.35 0.00 2.52
352 376 5.628193 CAGACTGTTTGAAAGATTGATGCAC 59.372 40.000 0.00 0.00 0.00 4.57
446 473 2.050442 CCGCAACGAAAACCTGGC 60.050 61.111 0.00 0.00 0.00 4.85
510 557 1.374125 GTTGCGTGCCCAATTTCCC 60.374 57.895 0.00 0.00 0.00 3.97
1287 1684 3.865929 CTTCCACACAGACGCGGCT 62.866 63.158 9.84 9.84 0.00 5.52
1546 1943 1.485480 AGATGGACTACGACGAGAGGA 59.515 52.381 0.00 0.00 0.00 3.71
2099 2500 4.868268 ACTATACCTGCTAGTGGAAGTGA 58.132 43.478 10.24 0.00 0.00 3.41
2235 2636 8.860128 GCAGTTTGCTTTCTATGTAAAATTACC 58.140 33.333 1.13 0.00 40.96 2.85
2242 2643 7.798982 GCTTTCTATGTAAAATTACCGCAGATC 59.201 37.037 1.13 0.00 32.72 2.75
2331 2732 5.280945 CAGAACATGAAATCGTTGGTTGTT 58.719 37.500 0.00 0.00 0.00 2.83
2576 2998 3.668656 GCGTGTTTTGAAATTGGCTAGAC 59.331 43.478 0.00 0.00 0.00 2.59
2780 3204 5.521372 GCCAGAATTTTGCCAGAATATGAAC 59.479 40.000 0.00 0.00 0.00 3.18
2784 3208 7.219535 CAGAATTTTGCCAGAATATGAACGAAG 59.780 37.037 0.00 0.00 0.00 3.79
2806 3230 1.275573 AGTTCCCGAACAGAGCCTAAC 59.724 52.381 10.07 0.00 43.47 2.34
2856 3280 1.105457 TGCAAGCAGACAAGCAAACT 58.895 45.000 0.00 0.00 36.85 2.66
2863 3287 6.672147 CAAGCAGACAAGCAAACTTAGTTAT 58.328 36.000 0.00 0.00 33.74 1.89
3178 3625 9.575868 TCACATGGTTTTCTGTTTTTATAGGTA 57.424 29.630 0.00 0.00 0.00 3.08
3201 3648 6.017400 AGTCTGTTTATTTGTTCCATGCAG 57.983 37.500 0.00 0.00 0.00 4.41
3251 3698 7.734924 TTCTATCTGATGTTTGCATATCCAC 57.265 36.000 0.00 0.00 35.07 4.02
3386 4246 6.183360 TGGTGTTTTGTTTCTCACATACTTCC 60.183 38.462 0.00 0.00 34.43 3.46
3506 4366 7.064728 GTGTATATGTTGTTCTCCTGTTCCTTC 59.935 40.741 0.00 0.00 0.00 3.46
3514 4374 3.170717 TCTCCTGTTCCTTCGGTTGTAT 58.829 45.455 0.00 0.00 0.00 2.29
3515 4375 4.346730 TCTCCTGTTCCTTCGGTTGTATA 58.653 43.478 0.00 0.00 0.00 1.47
3589 4581 5.931146 GGTGCATTCAGTATCCTTATCTCTG 59.069 44.000 0.00 0.00 0.00 3.35
3592 4584 6.162777 GCATTCAGTATCCTTATCTCTGTCC 58.837 44.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.328258 ATCCAGTGGTTGTGGTAGCC 59.672 55.000 9.54 0.00 36.37 3.93
1 2 1.453155 CATCCAGTGGTTGTGGTAGC 58.547 55.000 9.54 0.00 36.37 3.58
2 3 2.113860 CCATCCAGTGGTTGTGGTAG 57.886 55.000 17.19 0.25 43.44 3.18
12 13 1.131126 GCATTGAACGTCCATCCAGTG 59.869 52.381 0.00 0.00 0.00 3.66
13 14 1.003580 AGCATTGAACGTCCATCCAGT 59.996 47.619 0.00 0.00 0.00 4.00
14 15 1.742761 AGCATTGAACGTCCATCCAG 58.257 50.000 0.00 0.00 0.00 3.86
15 16 2.198827 AAGCATTGAACGTCCATCCA 57.801 45.000 0.00 0.00 0.00 3.41
30 31 3.485394 TGTTGTTGCTATCCTTCAAGCA 58.515 40.909 0.00 0.00 46.59 3.91
31 32 4.156556 TGATGTTGTTGCTATCCTTCAAGC 59.843 41.667 0.00 0.00 39.25 4.01
32 33 5.675575 GCTGATGTTGTTGCTATCCTTCAAG 60.676 44.000 0.00 0.00 0.00 3.02
33 34 4.156556 GCTGATGTTGTTGCTATCCTTCAA 59.843 41.667 0.00 0.00 0.00 2.69
34 35 3.691118 GCTGATGTTGTTGCTATCCTTCA 59.309 43.478 0.00 0.00 0.00 3.02
35 36 3.242543 CGCTGATGTTGTTGCTATCCTTC 60.243 47.826 0.00 0.00 0.00 3.46
36 37 2.679837 CGCTGATGTTGTTGCTATCCTT 59.320 45.455 0.00 0.00 0.00 3.36
37 38 2.283298 CGCTGATGTTGTTGCTATCCT 58.717 47.619 0.00 0.00 0.00 3.24
38 39 1.331756 CCGCTGATGTTGTTGCTATCC 59.668 52.381 0.00 0.00 0.00 2.59
39 40 1.268234 GCCGCTGATGTTGTTGCTATC 60.268 52.381 0.00 0.00 0.00 2.08
40 41 0.734889 GCCGCTGATGTTGTTGCTAT 59.265 50.000 0.00 0.00 0.00 2.97
41 42 1.634757 CGCCGCTGATGTTGTTGCTA 61.635 55.000 0.00 0.00 0.00 3.49
42 43 2.956987 GCCGCTGATGTTGTTGCT 59.043 55.556 0.00 0.00 0.00 3.91
43 44 2.502510 CGCCGCTGATGTTGTTGC 60.503 61.111 0.00 0.00 0.00 4.17
44 45 1.154413 GTCGCCGCTGATGTTGTTG 60.154 57.895 0.00 0.00 0.00 3.33
45 46 2.667318 CGTCGCCGCTGATGTTGTT 61.667 57.895 0.00 0.00 0.00 2.83
46 47 2.835701 ATCGTCGCCGCTGATGTTGT 62.836 55.000 0.00 0.00 0.00 3.32
47 48 2.167219 ATCGTCGCCGCTGATGTTG 61.167 57.895 0.00 0.00 0.00 3.33
48 49 2.167219 CATCGTCGCCGCTGATGTT 61.167 57.895 9.36 0.00 35.81 2.71
49 50 2.583319 CATCGTCGCCGCTGATGT 60.583 61.111 9.36 0.00 35.81 3.06
50 51 2.278792 TCATCGTCGCCGCTGATG 60.279 61.111 10.81 10.81 40.61 3.07
51 52 2.278857 GTCATCGTCGCCGCTGAT 60.279 61.111 0.00 0.00 40.82 2.90
52 53 3.683587 CTGTCATCGTCGCCGCTGA 62.684 63.158 0.00 0.00 36.92 4.26
53 54 3.250323 CTGTCATCGTCGCCGCTG 61.250 66.667 0.00 0.00 0.00 5.18
54 55 3.440415 TCTGTCATCGTCGCCGCT 61.440 61.111 0.00 0.00 0.00 5.52
55 56 3.248171 GTCTGTCATCGTCGCCGC 61.248 66.667 0.00 0.00 0.00 6.53
56 57 2.579787 GGTCTGTCATCGTCGCCG 60.580 66.667 0.00 0.00 0.00 6.46
57 58 1.078759 CTTGGTCTGTCATCGTCGCC 61.079 60.000 0.00 0.00 0.00 5.54
58 59 1.687494 GCTTGGTCTGTCATCGTCGC 61.687 60.000 0.00 0.00 0.00 5.19
59 60 0.388520 TGCTTGGTCTGTCATCGTCG 60.389 55.000 0.00 0.00 0.00 5.12
60 61 1.929836 GATGCTTGGTCTGTCATCGTC 59.070 52.381 0.00 0.00 0.00 4.20
61 62 1.276138 TGATGCTTGGTCTGTCATCGT 59.724 47.619 0.00 0.00 38.43 3.73
62 63 2.014335 TGATGCTTGGTCTGTCATCG 57.986 50.000 0.00 0.00 38.43 3.84
63 64 2.421424 GGTTGATGCTTGGTCTGTCATC 59.579 50.000 0.00 0.00 36.70 2.92
64 65 2.224843 TGGTTGATGCTTGGTCTGTCAT 60.225 45.455 0.00 0.00 0.00 3.06
65 66 1.142667 TGGTTGATGCTTGGTCTGTCA 59.857 47.619 0.00 0.00 0.00 3.58
66 67 1.896220 TGGTTGATGCTTGGTCTGTC 58.104 50.000 0.00 0.00 0.00 3.51
67 68 2.233271 CTTGGTTGATGCTTGGTCTGT 58.767 47.619 0.00 0.00 0.00 3.41
68 69 1.542915 CCTTGGTTGATGCTTGGTCTG 59.457 52.381 0.00 0.00 0.00 3.51
69 70 1.145738 ACCTTGGTTGATGCTTGGTCT 59.854 47.619 0.00 0.00 0.00 3.85
70 71 1.270550 CACCTTGGTTGATGCTTGGTC 59.729 52.381 0.00 0.00 0.00 4.02
71 72 1.331214 CACCTTGGTTGATGCTTGGT 58.669 50.000 0.00 0.00 0.00 3.67
72 73 0.037975 GCACCTTGGTTGATGCTTGG 60.038 55.000 0.00 0.00 35.16 3.61
73 74 0.037975 GGCACCTTGGTTGATGCTTG 60.038 55.000 0.00 0.00 38.18 4.01
74 75 0.469705 TGGCACCTTGGTTGATGCTT 60.470 50.000 0.00 0.00 38.18 3.91
75 76 0.469705 TTGGCACCTTGGTTGATGCT 60.470 50.000 0.00 0.00 38.18 3.79
76 77 0.319813 GTTGGCACCTTGGTTGATGC 60.320 55.000 0.00 0.00 37.35 3.91
77 78 0.039256 CGTTGGCACCTTGGTTGATG 60.039 55.000 0.00 0.00 0.00 3.07
78 79 0.179004 TCGTTGGCACCTTGGTTGAT 60.179 50.000 0.00 0.00 0.00 2.57
79 80 1.098712 GTCGTTGGCACCTTGGTTGA 61.099 55.000 0.00 0.00 0.00 3.18
80 81 1.358759 GTCGTTGGCACCTTGGTTG 59.641 57.895 0.00 0.00 0.00 3.77
81 82 1.826487 GGTCGTTGGCACCTTGGTT 60.826 57.895 0.00 0.00 0.00 3.67
82 83 2.203294 GGTCGTTGGCACCTTGGT 60.203 61.111 0.00 0.00 0.00 3.67
83 84 2.113139 AGGTCGTTGGCACCTTGG 59.887 61.111 0.00 0.00 41.95 3.61
134 135 7.817641 ATTTAAACCTAAACAGCTAAGTGAGC 58.182 34.615 0.00 0.00 39.46 4.26
195 198 5.782893 AGATGATAGGCTTGTGTCTAGAC 57.217 43.478 16.32 16.32 33.49 2.59
196 199 7.780271 TCTTAAGATGATAGGCTTGTGTCTAGA 59.220 37.037 0.00 0.00 33.49 2.43
197 200 7.946207 TCTTAAGATGATAGGCTTGTGTCTAG 58.054 38.462 0.00 0.00 33.49 2.43
198 201 7.898014 TCTTAAGATGATAGGCTTGTGTCTA 57.102 36.000 0.00 0.00 34.60 2.59
199 202 6.798427 TCTTAAGATGATAGGCTTGTGTCT 57.202 37.500 0.00 0.00 0.00 3.41
200 203 8.443953 AAATCTTAAGATGATAGGCTTGTGTC 57.556 34.615 18.61 0.00 34.49 3.67
219 222 6.203338 TGCCTACGTTAACTTCGAAAAATCTT 59.797 34.615 3.71 0.00 0.00 2.40
227 230 4.445452 AAGATGCCTACGTTAACTTCGA 57.555 40.909 3.71 0.00 0.00 3.71
228 231 5.526010 AAAAGATGCCTACGTTAACTTCG 57.474 39.130 3.71 0.00 0.00 3.79
236 239 3.730061 CGTCGACTAAAAGATGCCTACGT 60.730 47.826 14.70 0.00 0.00 3.57
237 240 2.782192 CGTCGACTAAAAGATGCCTACG 59.218 50.000 14.70 0.00 0.00 3.51
242 245 2.288961 TCCCGTCGACTAAAAGATGC 57.711 50.000 14.70 0.00 0.00 3.91
244 247 2.229784 ACGTTCCCGTCGACTAAAAGAT 59.770 45.455 14.70 0.00 46.28 2.40
247 250 1.066908 ACACGTTCCCGTCGACTAAAA 59.933 47.619 14.70 1.65 46.28 1.52
248 251 0.667993 ACACGTTCCCGTCGACTAAA 59.332 50.000 14.70 2.02 46.28 1.85
249 252 0.040157 CACACGTTCCCGTCGACTAA 60.040 55.000 14.70 2.37 46.28 2.24
254 257 0.457853 ATGATCACACGTTCCCGTCG 60.458 55.000 0.00 0.00 46.28 5.12
257 260 1.135112 TCTGATGATCACACGTTCCCG 60.135 52.381 0.00 0.00 40.83 5.14
259 262 5.551760 AAATTCTGATGATCACACGTTCC 57.448 39.130 0.00 0.00 0.00 3.62
260 263 7.481798 GGTTTAAATTCTGATGATCACACGTTC 59.518 37.037 0.00 0.00 0.00 3.95
263 266 6.963242 CAGGTTTAAATTCTGATGATCACACG 59.037 38.462 13.14 0.00 0.00 4.49
272 275 5.361857 CAGCCCATCAGGTTTAAATTCTGAT 59.638 40.000 21.34 21.34 45.75 2.90
274 277 4.706476 TCAGCCCATCAGGTTTAAATTCTG 59.294 41.667 12.53 12.53 38.26 3.02
278 281 4.934356 TCTTCAGCCCATCAGGTTTAAAT 58.066 39.130 0.00 0.00 38.26 1.40
281 284 5.369404 TGATATCTTCAGCCCATCAGGTTTA 59.631 40.000 3.98 0.00 38.26 2.01
282 285 4.166725 TGATATCTTCAGCCCATCAGGTTT 59.833 41.667 3.98 0.00 38.26 3.27
283 286 3.718434 TGATATCTTCAGCCCATCAGGTT 59.282 43.478 3.98 0.00 38.26 3.50
284 287 3.321039 TGATATCTTCAGCCCATCAGGT 58.679 45.455 3.98 0.00 38.26 4.00
285 288 3.940319 CTGATATCTTCAGCCCATCAGG 58.060 50.000 3.98 0.00 45.16 3.86
292 295 8.581039 GTCAGAAAGACACTGATATCTTCAGCC 61.581 44.444 3.98 0.00 45.45 4.85
293 296 6.255453 GTCAGAAAGACACTGATATCTTCAGC 59.745 42.308 3.98 0.00 45.45 4.26
294 297 7.754069 GTCAGAAAGACACTGATATCTTCAG 57.246 40.000 3.98 1.18 46.20 3.02
316 319 3.963428 AACAGTCTGTAGTGGATGGTC 57.037 47.619 5.77 0.00 0.00 4.02
322 325 6.483307 TCAATCTTTCAAACAGTCTGTAGTGG 59.517 38.462 5.77 0.00 0.00 4.00
325 328 7.020010 GCATCAATCTTTCAAACAGTCTGTAG 58.980 38.462 5.77 2.45 0.00 2.74
326 329 6.486320 TGCATCAATCTTTCAAACAGTCTGTA 59.514 34.615 5.77 0.00 0.00 2.74
327 330 5.300034 TGCATCAATCTTTCAAACAGTCTGT 59.700 36.000 0.00 0.00 0.00 3.41
328 331 5.628193 GTGCATCAATCTTTCAAACAGTCTG 59.372 40.000 0.00 0.00 0.00 3.51
329 332 5.300034 TGTGCATCAATCTTTCAAACAGTCT 59.700 36.000 0.00 0.00 0.00 3.24
330 333 5.522456 TGTGCATCAATCTTTCAAACAGTC 58.478 37.500 0.00 0.00 0.00 3.51
332 335 5.401376 CACTGTGCATCAATCTTTCAAACAG 59.599 40.000 0.00 0.00 38.70 3.16
333 336 5.067544 TCACTGTGCATCAATCTTTCAAACA 59.932 36.000 2.12 0.00 0.00 2.83
334 337 5.522456 TCACTGTGCATCAATCTTTCAAAC 58.478 37.500 2.12 0.00 0.00 2.93
336 339 5.532032 TCTTCACTGTGCATCAATCTTTCAA 59.468 36.000 2.12 0.00 0.00 2.69
337 340 5.065235 TCTTCACTGTGCATCAATCTTTCA 58.935 37.500 2.12 0.00 0.00 2.69
338 341 5.618056 TCTTCACTGTGCATCAATCTTTC 57.382 39.130 2.12 0.00 0.00 2.62
343 367 2.426024 GGCATCTTCACTGTGCATCAAT 59.574 45.455 2.12 0.00 40.53 2.57
352 376 3.902881 AACTCTAGGGCATCTTCACTG 57.097 47.619 0.00 0.00 0.00 3.66
377 401 4.882671 GCATCTTGCCTCGAAGAAAATA 57.117 40.909 0.00 0.00 37.42 1.40
446 473 2.809601 CTTCGCTGTCGGTTCGGG 60.810 66.667 0.00 0.00 36.13 5.14
510 557 2.592308 GGTGGAGGCTGGGCTAAG 59.408 66.667 0.00 0.00 0.00 2.18
1287 1684 2.814023 GATCTTCCCGAGAGCCTGA 58.186 57.895 0.00 0.00 37.93 3.86
1485 1882 1.769733 CAGCACCAAATCCAACAACG 58.230 50.000 0.00 0.00 0.00 4.10
1800 2197 2.669419 GCCAATGCCAAAGCGAATC 58.331 52.632 0.00 0.00 44.31 2.52
2069 2470 8.349568 TCCACTAGCAGGTATAGTACATATTG 57.650 38.462 0.00 0.00 32.24 1.90
2099 2500 8.043710 CAGATTTAAGGAGTATTCAAGGTCACT 58.956 37.037 0.00 0.00 0.00 3.41
2235 2636 2.414481 CAGGTTCTCAAAGTGATCTGCG 59.586 50.000 0.00 0.00 0.00 5.18
2242 2643 9.219603 TGTTCTATTAATCAGGTTCTCAAAGTG 57.780 33.333 0.00 0.00 0.00 3.16
2331 2732 8.281531 AGAAATAACATGGTAATGAAGGGATCA 58.718 33.333 0.00 0.00 43.67 2.92
2362 2763 2.096318 GCACAAAATTTGCAACATCCCG 60.096 45.455 5.52 0.00 39.93 5.14
2441 2842 4.160439 TCAGACGTTCAGCTTGGAGATATT 59.840 41.667 0.00 0.00 0.00 1.28
2442 2843 3.701542 TCAGACGTTCAGCTTGGAGATAT 59.298 43.478 0.00 0.00 0.00 1.63
2504 2905 0.109179 TCCGCTTCGCTTACGCTTTA 60.109 50.000 0.00 0.00 39.84 1.85
2558 2980 6.978080 TGTCAAAGTCTAGCCAATTTCAAAAC 59.022 34.615 0.00 0.00 0.00 2.43
2744 3168 2.653234 ATTCTGGCCACATGATCTCC 57.347 50.000 0.00 0.00 0.00 3.71
2780 3204 2.864968 CTCTGTTCGGGAACTACTTCG 58.135 52.381 12.33 0.00 41.67 3.79
2784 3208 0.896226 AGGCTCTGTTCGGGAACTAC 59.104 55.000 12.33 0.54 41.67 2.73
2806 3230 9.976511 AATGACAATATGCCATTTATCTTCTTG 57.023 29.630 0.00 0.00 25.34 3.02
2828 3252 4.616604 GCTTGTCTGCTTGCACAATAATGA 60.617 41.667 0.00 0.00 32.13 2.57
2890 3314 8.597662 AGCGGTAGATTAAGCGATTTTATAAA 57.402 30.769 0.00 0.00 42.76 1.40
2891 3315 8.597662 AAGCGGTAGATTAAGCGATTTTATAA 57.402 30.769 0.00 0.00 45.43 0.98
2892 3316 9.350357 CTAAGCGGTAGATTAAGCGATTTTATA 57.650 33.333 4.29 0.00 45.43 0.98
2893 3317 7.331193 CCTAAGCGGTAGATTAAGCGATTTTAT 59.669 37.037 4.29 0.00 45.43 1.40
2894 3318 6.643770 CCTAAGCGGTAGATTAAGCGATTTTA 59.356 38.462 4.29 0.00 45.43 1.52
2899 3324 2.295349 CCCTAAGCGGTAGATTAAGCGA 59.705 50.000 0.00 0.00 42.76 4.93
2928 3353 0.242017 GAGCGATGGCAAACTGCTTT 59.758 50.000 1.50 0.00 44.28 3.51
3201 3648 7.367285 TCATAAACAACATACAGAACAAAGGC 58.633 34.615 0.00 0.00 0.00 4.35
3251 3698 7.713073 AGGAGTTGAGAAGTCAAAGAACTAAAG 59.287 37.037 0.00 0.00 44.44 1.85
3386 4246 9.941664 AGATTAGATTCTTTGATGCAAATAACG 57.058 29.630 0.00 0.00 32.70 3.18
3414 4274 9.610705 ATGAAGCCATGCTCTTATAGTATTATG 57.389 33.333 0.00 0.00 38.25 1.90


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

AutoCloner maintained by Alex Coulton.