Multiple sequence alignment - TraesCS1D01G116400

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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 TraesCS1D01G116400 chr1D 100.000 4641 0 0 1 4641 112218431 112213791 0.000000e+00 8571.0
1 TraesCS1D01G116400 chr1A 95.718 4297 111 27 399 4641 119152390 119148113 0.000000e+00 6848.0
2 TraesCS1D01G116400 chr1A 78.588 425 50 27 3936 4344 23615464 23615065 4.640000e-60 243.0
3 TraesCS1D01G116400 chr1B 95.491 4280 124 29 399 4641 171412274 171408027 0.000000e+00 6770.0
4 TraesCS1D01G116400 chr6B 86.944 337 42 2 1 336 213574073 213573738 1.220000e-100 377.0
5 TraesCS1D01G116400 chr6B 87.500 80 10 0 216 295 636788939 636788860 4.940000e-15 93.5
6 TraesCS1D01G116400 chr2A 80.523 421 41 27 3938 4341 719334631 719334235 7.600000e-73 285.0
7 TraesCS1D01G116400 chr2A 77.982 436 56 26 3924 4341 461165301 461165714 2.160000e-58 237.0
8 TraesCS1D01G116400 chr2A 86.905 84 9 2 214 296 665949486 665949568 4.940000e-15 93.5
9 TraesCS1D01G116400 chr4A 79.215 433 50 27 3925 4341 628853739 628854147 9.900000e-67 265.0
10 TraesCS1D01G116400 chr7A 79.254 429 47 27 3938 4348 612998738 612998334 1.280000e-65 261.0
11 TraesCS1D01G116400 chr5A 83.513 279 32 12 3938 4209 673087446 673087175 9.970000e-62 248.0
12 TraesCS1D01G116400 chr5A 76.879 346 65 10 1 337 239466472 239466133 1.030000e-41 182.0
13 TraesCS1D01G116400 chr5A 87.302 63 6 2 4281 4341 41344787 41344725 2.320000e-08 71.3
14 TraesCS1D01G116400 chr2D 77.674 430 69 23 3921 4340 606714524 606714112 2.160000e-58 237.0
15 TraesCS1D01G116400 chr5D 74.105 363 64 17 3992 4341 52249162 52248817 6.310000e-24 122.0
16 TraesCS1D01G116400 chr4B 91.358 81 7 0 215 295 428974721 428974641 1.370000e-20 111.0


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 TraesCS1D01G116400 chr1D 112213791 112218431 4640 True 8571 8571 100.000 1 4641 1 chr1D.!!$R1 4640
1 TraesCS1D01G116400 chr1A 119148113 119152390 4277 True 6848 6848 95.718 399 4641 1 chr1A.!!$R2 4242
2 TraesCS1D01G116400 chr1B 171408027 171412274 4247 True 6770 6770 95.491 399 4641 1 chr1B.!!$R1 4242

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
361 362 0.112412 GAAGCTTGGGGGACTCCAAA 59.888 55.0 2.1 0.0 45.13 3.28 F
1506 1526 0.175989 GGAGGAGAGGTTTGCGGTAG 59.824 60.0 0.0 0.0 0.00 3.18 F
2626 2672 0.318120 CAATGCACCACTTCCCAACC 59.682 55.0 0.0 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2008 0.750249 TTGAGACCAGCAAGACGACA 59.250 50.0 0.0 0.0 0.00 4.35 R
3473 3520 5.676079 GCTTAACTTTTCATATGCCGCAAGA 60.676 40.0 0.0 0.0 43.02 3.02 R
4111 4167 0.179097 TTGTTTGTTGCTTTCGGGCC 60.179 50.0 0.0 0.0 0.00 5.80 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
18 19 2.125310 CCACATGGCCTTACGCGA 60.125 61.111 15.93 0.00 38.94 5.87
19 20 1.523711 CCACATGGCCTTACGCGAT 60.524 57.895 15.93 0.00 38.94 4.58
21 22 3.333414 CATGGCCTTACGCGATGG 58.667 61.111 15.93 12.87 46.70 3.51
22 23 1.227527 CATGGCCTTACGCGATGGA 60.228 57.895 15.93 0.00 46.70 3.41
23 24 1.227556 ATGGCCTTACGCGATGGAC 60.228 57.895 15.93 14.59 38.94 4.02
24 25 2.588034 GGCCTTACGCGATGGACC 60.588 66.667 15.93 12.75 38.94 4.46
25 26 2.185867 GCCTTACGCGATGGACCA 59.814 61.111 15.93 0.00 0.00 4.02
26 27 1.883084 GCCTTACGCGATGGACCAG 60.883 63.158 15.93 0.00 0.00 4.00
27 28 1.227263 CCTTACGCGATGGACCAGG 60.227 63.158 15.93 2.75 0.00 4.45
28 29 1.672854 CCTTACGCGATGGACCAGGA 61.673 60.000 15.93 0.00 0.00 3.86
29 30 0.527817 CTTACGCGATGGACCAGGAC 60.528 60.000 15.93 0.00 0.00 3.85
30 31 2.274232 TTACGCGATGGACCAGGACG 62.274 60.000 15.93 5.80 0.00 4.79
31 32 3.822192 CGCGATGGACCAGGACGA 61.822 66.667 18.23 0.00 0.00 4.20
32 33 2.202756 GCGATGGACCAGGACGAC 60.203 66.667 18.23 8.87 0.00 4.34
33 34 2.102357 CGATGGACCAGGACGACG 59.898 66.667 11.40 0.00 0.00 5.12
34 35 2.202756 GATGGACCAGGACGACGC 60.203 66.667 0.00 0.00 0.00 5.19
35 36 3.718210 GATGGACCAGGACGACGCC 62.718 68.421 0.00 0.00 0.00 5.68
37 38 3.998672 GGACCAGGACGACGCCAA 61.999 66.667 10.28 0.00 0.00 4.52
38 39 2.737376 GACCAGGACGACGCCAAC 60.737 66.667 10.28 0.00 0.00 3.77
39 40 4.309950 ACCAGGACGACGCCAACC 62.310 66.667 10.28 2.70 0.00 3.77
41 42 4.003788 CAGGACGACGCCAACCCT 62.004 66.667 10.28 0.40 0.00 4.34
42 43 3.692406 AGGACGACGCCAACCCTC 61.692 66.667 10.28 0.00 0.00 4.30
52 53 4.738998 CAACCCTCGGCATGCCCA 62.739 66.667 30.79 18.42 0.00 5.36
53 54 4.431131 AACCCTCGGCATGCCCAG 62.431 66.667 30.79 26.91 0.00 4.45
107 108 4.796231 CCGCCGAGGACGAACCAG 62.796 72.222 7.36 0.00 45.00 4.00
110 111 4.796231 CCGAGGACGAACCAGCCG 62.796 72.222 0.00 0.00 42.66 5.52
111 112 3.744719 CGAGGACGAACCAGCCGA 61.745 66.667 0.00 0.00 42.66 5.54
112 113 2.126031 GAGGACGAACCAGCCGAC 60.126 66.667 0.00 0.00 42.04 4.79
113 114 3.644399 GAGGACGAACCAGCCGACC 62.644 68.421 0.00 0.00 42.04 4.79
114 115 4.754667 GGACGAACCAGCCGACCC 62.755 72.222 0.00 0.00 36.22 4.46
115 116 4.754667 GACGAACCAGCCGACCCC 62.755 72.222 0.00 0.00 0.00 4.95
117 118 4.760047 CGAACCAGCCGACCCCTG 62.760 72.222 0.00 0.00 0.00 4.45
122 123 4.101448 CAGCCGACCCCTGGGAAG 62.101 72.222 16.20 4.64 38.96 3.46
127 128 3.787001 GACCCCTGGGAAGCCGAG 61.787 72.222 16.20 0.00 38.96 4.63
128 129 4.332543 ACCCCTGGGAAGCCGAGA 62.333 66.667 16.20 0.00 38.96 4.04
129 130 3.474570 CCCCTGGGAAGCCGAGAG 61.475 72.222 16.20 0.00 37.50 3.20
150 151 4.394712 CAGGCCCGACACCCTGTC 62.395 72.222 0.00 0.00 42.87 3.51
159 160 4.323477 CACCCTGTCCCGCGGAAA 62.323 66.667 30.73 12.10 31.38 3.13
160 161 4.324991 ACCCTGTCCCGCGGAAAC 62.325 66.667 30.73 24.17 31.38 2.78
172 173 3.408851 GGAAACGCCGACGACACC 61.409 66.667 0.00 0.00 43.93 4.16
173 174 3.759828 GAAACGCCGACGACACCG 61.760 66.667 0.00 0.00 43.93 4.94
174 175 4.268939 AAACGCCGACGACACCGA 62.269 61.111 0.00 0.00 43.93 4.69
175 176 3.771568 AAACGCCGACGACACCGAA 62.772 57.895 0.00 0.00 43.93 4.30
176 177 4.695231 ACGCCGACGACACCGAAG 62.695 66.667 0.00 0.00 43.93 3.79
190 191 4.821589 GAAGGGGGACTGCGCGAG 62.822 72.222 12.10 7.21 0.00 5.03
208 209 4.758251 CCCGACGCCATGAGCACA 62.758 66.667 0.00 0.00 44.04 4.57
209 210 3.190849 CCGACGCCATGAGCACAG 61.191 66.667 0.00 0.00 44.04 3.66
210 211 3.190849 CGACGCCATGAGCACAGG 61.191 66.667 0.00 0.00 44.04 4.00
211 212 2.046892 GACGCCATGAGCACAGGT 60.047 61.111 0.00 0.00 44.04 4.00
212 213 2.359107 ACGCCATGAGCACAGGTG 60.359 61.111 0.00 10.13 44.04 4.00
213 214 3.129502 CGCCATGAGCACAGGTGG 61.130 66.667 0.00 0.00 44.04 4.61
214 215 2.753043 GCCATGAGCACAGGTGGG 60.753 66.667 6.00 0.00 42.97 4.61
215 216 2.044650 CCATGAGCACAGGTGGGG 60.045 66.667 0.00 0.00 0.00 4.96
216 217 2.605607 CCATGAGCACAGGTGGGGA 61.606 63.158 0.00 0.00 0.00 4.81
217 218 1.077930 CATGAGCACAGGTGGGGAG 60.078 63.158 1.10 0.00 0.00 4.30
218 219 2.304056 ATGAGCACAGGTGGGGAGG 61.304 63.158 1.10 0.00 0.00 4.30
219 220 2.930562 GAGCACAGGTGGGGAGGT 60.931 66.667 1.10 0.00 0.00 3.85
220 221 3.252284 AGCACAGGTGGGGAGGTG 61.252 66.667 1.10 0.00 0.00 4.00
221 222 4.351054 GCACAGGTGGGGAGGTGG 62.351 72.222 1.10 0.00 0.00 4.61
222 223 2.529136 CACAGGTGGGGAGGTGGA 60.529 66.667 0.00 0.00 0.00 4.02
223 224 2.529389 ACAGGTGGGGAGGTGGAC 60.529 66.667 0.00 0.00 0.00 4.02
224 225 3.706373 CAGGTGGGGAGGTGGACG 61.706 72.222 0.00 0.00 0.00 4.79
304 305 3.866582 GGGGGAGGAGTGCGATGG 61.867 72.222 0.00 0.00 0.00 3.51
305 306 4.554036 GGGGAGGAGTGCGATGGC 62.554 72.222 0.00 0.00 40.52 4.40
306 307 4.899239 GGGAGGAGTGCGATGGCG 62.899 72.222 0.00 0.00 44.10 5.69
339 340 2.197324 CGAGAGGGAGAGGGGGAG 59.803 72.222 0.00 0.00 0.00 4.30
340 341 2.612251 GAGAGGGAGAGGGGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
341 342 2.015726 GAGAGGGAGAGGGGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
342 343 2.018086 AGAGGGAGAGGGGGAGGAG 61.018 68.421 0.00 0.00 0.00 3.69
343 344 2.015726 GAGGGAGAGGGGGAGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
344 345 1.550374 AGGGAGAGGGGGAGGAGAA 60.550 63.158 0.00 0.00 0.00 2.87
345 346 1.074850 GGGAGAGGGGGAGGAGAAG 60.075 68.421 0.00 0.00 0.00 2.85
346 347 1.764454 GGAGAGGGGGAGGAGAAGC 60.764 68.421 0.00 0.00 0.00 3.86
347 348 1.313129 GAGAGGGGGAGGAGAAGCT 59.687 63.158 0.00 0.00 0.00 3.74
348 349 0.326143 GAGAGGGGGAGGAGAAGCTT 60.326 60.000 0.00 0.00 0.00 3.74
349 350 0.620121 AGAGGGGGAGGAGAAGCTTG 60.620 60.000 2.10 0.00 0.00 4.01
350 351 1.617839 AGGGGGAGGAGAAGCTTGG 60.618 63.158 2.10 0.00 0.00 3.61
351 352 2.684499 GGGGGAGGAGAAGCTTGGG 61.684 68.421 2.10 0.00 0.00 4.12
352 353 2.684499 GGGGAGGAGAAGCTTGGGG 61.684 68.421 2.10 0.00 0.00 4.96
353 354 2.684499 GGGAGGAGAAGCTTGGGGG 61.684 68.421 2.10 0.00 0.00 5.40
354 355 1.616628 GGAGGAGAAGCTTGGGGGA 60.617 63.158 2.10 0.00 0.00 4.81
355 356 1.604915 GAGGAGAAGCTTGGGGGAC 59.395 63.158 2.10 0.00 0.00 4.46
356 357 0.912006 GAGGAGAAGCTTGGGGGACT 60.912 60.000 2.10 0.00 0.00 3.85
357 358 0.912006 AGGAGAAGCTTGGGGGACTC 60.912 60.000 2.10 2.50 0.00 3.36
358 359 1.604915 GAGAAGCTTGGGGGACTCC 59.395 63.158 2.10 0.00 0.00 3.85
359 360 1.151810 AGAAGCTTGGGGGACTCCA 60.152 57.895 2.10 0.00 37.22 3.86
360 361 0.772124 AGAAGCTTGGGGGACTCCAA 60.772 55.000 2.10 3.24 43.82 3.53
361 362 0.112412 GAAGCTTGGGGGACTCCAAA 59.888 55.000 2.10 0.00 45.13 3.28
363 364 1.068352 AGCTTGGGGGACTCCAAAGT 61.068 55.000 10.39 0.00 46.30 2.66
364 365 0.178961 GCTTGGGGGACTCCAAAGTT 60.179 55.000 10.39 0.00 46.30 2.66
365 366 1.757764 GCTTGGGGGACTCCAAAGTTT 60.758 52.381 10.39 0.00 46.30 2.66
366 367 2.677914 CTTGGGGGACTCCAAAGTTTT 58.322 47.619 5.01 0.00 45.13 2.43
367 368 3.839778 CTTGGGGGACTCCAAAGTTTTA 58.160 45.455 5.01 0.00 45.13 1.52
368 369 3.232720 TGGGGGACTCCAAAGTTTTAC 57.767 47.619 0.00 0.00 35.28 2.01
369 370 2.158430 TGGGGGACTCCAAAGTTTTACC 60.158 50.000 0.00 0.00 35.28 2.85
370 371 2.522185 GGGGACTCCAAAGTTTTACCC 58.478 52.381 0.00 0.00 35.83 3.69
371 372 2.109480 GGGGACTCCAAAGTTTTACCCT 59.891 50.000 0.00 0.00 36.50 4.34
372 373 3.418995 GGGACTCCAAAGTTTTACCCTC 58.581 50.000 0.00 0.00 34.43 4.30
373 374 3.072211 GGACTCCAAAGTTTTACCCTCG 58.928 50.000 0.00 0.00 35.28 4.63
374 375 3.495629 GGACTCCAAAGTTTTACCCTCGT 60.496 47.826 0.00 0.00 35.28 4.18
375 376 4.132336 GACTCCAAAGTTTTACCCTCGTT 58.868 43.478 0.00 0.00 35.28 3.85
376 377 3.881089 ACTCCAAAGTTTTACCCTCGTTG 59.119 43.478 0.00 0.00 28.74 4.10
377 378 3.215975 TCCAAAGTTTTACCCTCGTTGG 58.784 45.455 0.00 0.00 40.28 3.77
378 379 2.287970 CCAAAGTTTTACCCTCGTTGGC 60.288 50.000 0.00 0.00 35.03 4.52
379 380 2.621526 CAAAGTTTTACCCTCGTTGGCT 59.378 45.455 0.00 0.00 0.00 4.75
380 381 2.180432 AGTTTTACCCTCGTTGGCTC 57.820 50.000 0.00 0.00 0.00 4.70
381 382 1.697982 AGTTTTACCCTCGTTGGCTCT 59.302 47.619 0.00 0.00 0.00 4.09
382 383 2.105993 AGTTTTACCCTCGTTGGCTCTT 59.894 45.455 0.00 0.00 0.00 2.85
383 384 2.882761 GTTTTACCCTCGTTGGCTCTTT 59.117 45.455 0.00 0.00 0.00 2.52
384 385 2.943036 TTACCCTCGTTGGCTCTTTT 57.057 45.000 0.00 0.00 0.00 2.27
385 386 2.467566 TACCCTCGTTGGCTCTTTTC 57.532 50.000 0.00 0.00 0.00 2.29
386 387 0.472471 ACCCTCGTTGGCTCTTTTCA 59.528 50.000 0.00 0.00 0.00 2.69
387 388 0.875059 CCCTCGTTGGCTCTTTTCAC 59.125 55.000 0.00 0.00 0.00 3.18
388 389 1.593196 CCTCGTTGGCTCTTTTCACA 58.407 50.000 0.00 0.00 0.00 3.58
389 390 1.946768 CCTCGTTGGCTCTTTTCACAA 59.053 47.619 0.00 0.00 0.00 3.33
390 391 2.357637 CCTCGTTGGCTCTTTTCACAAA 59.642 45.455 0.00 0.00 0.00 2.83
391 392 3.004734 CCTCGTTGGCTCTTTTCACAAAT 59.995 43.478 0.00 0.00 0.00 2.32
392 393 3.963665 TCGTTGGCTCTTTTCACAAATG 58.036 40.909 0.00 0.00 0.00 2.32
393 394 3.629855 TCGTTGGCTCTTTTCACAAATGA 59.370 39.130 0.00 0.00 0.00 2.57
394 395 3.730715 CGTTGGCTCTTTTCACAAATGAC 59.269 43.478 0.00 0.00 33.38 3.06
395 396 4.681744 GTTGGCTCTTTTCACAAATGACA 58.318 39.130 0.00 0.00 33.38 3.58
396 397 4.572985 TGGCTCTTTTCACAAATGACAG 57.427 40.909 0.00 0.00 33.38 3.51
397 398 4.206375 TGGCTCTTTTCACAAATGACAGA 58.794 39.130 0.00 0.00 33.38 3.41
410 411 9.898152 TCACAAATGACAGATATAATACCACAA 57.102 29.630 0.00 0.00 0.00 3.33
443 444 5.231991 CGTGGAGTTTTGAACTTTTTCATGG 59.768 40.000 0.00 0.00 43.03 3.66
1506 1526 0.175989 GGAGGAGAGGTTTGCGGTAG 59.824 60.000 0.00 0.00 0.00 3.18
1514 1534 1.491563 GTTTGCGGTAGTGCACTCG 59.508 57.895 25.56 22.42 46.25 4.18
1886 1922 4.227864 TGGTTGGAAATTGTGCCTTTTT 57.772 36.364 0.00 0.00 0.00 1.94
1972 2008 9.148879 TCACTCTTATAGGCTTAGAGCTATTTT 57.851 33.333 16.29 0.00 41.99 1.82
2037 2073 9.499479 CTCTTAGCATTCTATGGTGTTCATAAT 57.501 33.333 1.88 0.00 41.73 1.28
2190 2226 6.172630 TCTCTGATGCTGCAACTTTGTTATA 58.827 36.000 6.36 0.00 0.00 0.98
2278 2314 3.003275 TCATTCGGCTGTTTGAACTTCAC 59.997 43.478 0.00 0.00 0.00 3.18
2475 2519 1.351707 CACGCTTTGTGCACGACTT 59.648 52.632 13.13 0.00 42.70 3.01
2626 2672 0.318120 CAATGCACCACTTCCCAACC 59.682 55.000 0.00 0.00 0.00 3.77
2644 2690 6.210584 TCCCAACCCTGTTAATTCTTTGATTC 59.789 38.462 0.00 0.00 0.00 2.52
3104 3151 4.695928 GGACAGAGAATGTTTGGTTAGTCC 59.304 45.833 0.00 0.00 44.17 3.85
3109 3156 6.934645 CAGAGAATGTTTGGTTAGTCCTTGTA 59.065 38.462 0.00 0.00 37.07 2.41
3367 3414 4.178956 ACTGGTCAACTTTTACCCACAT 57.821 40.909 0.00 0.00 34.69 3.21
3473 3520 4.576216 TGTTGCATTTGGATGTTTACGT 57.424 36.364 0.00 0.00 35.63 3.57
3737 3788 7.010552 CACTTGTTAGCGAAGTATTTAGAGCAT 59.989 37.037 0.00 0.00 32.27 3.79
3799 3850 6.713762 AAAAGAGTCAAATGTGAATGGTGA 57.286 33.333 0.00 0.00 34.87 4.02
3803 3854 3.256631 AGTCAAATGTGAATGGTGAAGGC 59.743 43.478 0.00 0.00 34.87 4.35
3933 3984 1.808891 GCGTGTTTAGTGGAGTGTGGT 60.809 52.381 0.00 0.00 0.00 4.16
3934 3985 2.557317 CGTGTTTAGTGGAGTGTGGTT 58.443 47.619 0.00 0.00 0.00 3.67
3945 3996 0.106519 AGTGTGGTTTTGCAGAGGCT 60.107 50.000 0.00 0.00 41.91 4.58
3958 4009 3.412624 GAGGCTGGGCTCCATGGAC 62.413 68.421 11.44 8.06 30.82 4.02
3960 4011 3.415087 GCTGGGCTCCATGGACCT 61.415 66.667 24.06 0.00 30.82 3.85
3969 4021 2.173519 CTCCATGGACCTGTTTTGCAT 58.826 47.619 11.44 0.00 0.00 3.96
4120 4176 6.884280 AAAGATAAATATCTGGCCCGAAAG 57.116 37.500 0.00 0.00 41.96 2.62
4608 4685 2.483014 AACGGTAATGCTAACTGGCA 57.517 45.000 0.00 0.00 46.63 4.92
4612 4689 2.486203 CGGTAATGCTAACTGGCAAACA 59.514 45.455 0.00 0.00 45.68 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.523711 ATCGCGTAAGGCCATGTGG 60.524 57.895 5.01 0.00 38.94 4.17
2 3 1.643292 CATCGCGTAAGGCCATGTG 59.357 57.895 5.01 0.00 35.76 3.21
3 4 1.523711 CCATCGCGTAAGGCCATGT 60.524 57.895 5.01 0.00 38.43 3.21
4 5 1.227527 TCCATCGCGTAAGGCCATG 60.228 57.895 5.01 0.00 39.63 3.66
5 6 1.227556 GTCCATCGCGTAAGGCCAT 60.228 57.895 5.01 0.00 38.94 4.40
6 7 2.185867 GTCCATCGCGTAAGGCCA 59.814 61.111 5.01 0.00 38.94 5.36
7 8 2.588034 GGTCCATCGCGTAAGGCC 60.588 66.667 5.77 2.53 38.94 5.19
8 9 1.883084 CTGGTCCATCGCGTAAGGC 60.883 63.158 5.77 0.00 38.69 4.35
9 10 1.227263 CCTGGTCCATCGCGTAAGG 60.227 63.158 5.77 6.97 38.28 2.69
10 11 0.527817 GTCCTGGTCCATCGCGTAAG 60.528 60.000 5.77 0.00 43.44 2.34
11 12 1.514087 GTCCTGGTCCATCGCGTAA 59.486 57.895 5.77 0.00 0.00 3.18
12 13 2.767445 CGTCCTGGTCCATCGCGTA 61.767 63.158 5.77 0.00 0.00 4.42
13 14 4.129737 CGTCCTGGTCCATCGCGT 62.130 66.667 5.77 0.00 0.00 6.01
14 15 3.822192 TCGTCCTGGTCCATCGCG 61.822 66.667 0.00 0.00 0.00 5.87
15 16 2.202756 GTCGTCCTGGTCCATCGC 60.203 66.667 0.00 0.00 0.00 4.58
16 17 2.102357 CGTCGTCCTGGTCCATCG 59.898 66.667 0.00 0.00 0.00 3.84
17 18 2.202756 GCGTCGTCCTGGTCCATC 60.203 66.667 0.00 0.00 0.00 3.51
18 19 3.771160 GGCGTCGTCCTGGTCCAT 61.771 66.667 0.00 0.00 0.00 3.41
20 21 3.998672 TTGGCGTCGTCCTGGTCC 61.999 66.667 0.00 0.00 0.00 4.46
21 22 2.737376 GTTGGCGTCGTCCTGGTC 60.737 66.667 0.00 0.00 0.00 4.02
22 23 4.309950 GGTTGGCGTCGTCCTGGT 62.310 66.667 0.00 0.00 0.00 4.00
24 25 3.934391 GAGGGTTGGCGTCGTCCTG 62.934 68.421 0.31 0.00 0.00 3.86
25 26 3.692406 GAGGGTTGGCGTCGTCCT 61.692 66.667 0.00 0.00 0.00 3.85
35 36 4.738998 TGGGCATGCCGAGGGTTG 62.739 66.667 29.90 0.00 36.85 3.77
36 37 4.431131 CTGGGCATGCCGAGGGTT 62.431 66.667 34.35 0.00 38.13 4.11
90 91 4.796231 CTGGTTCGTCCTCGGCGG 62.796 72.222 7.21 0.00 37.69 6.13
93 94 4.796231 CGGCTGGTTCGTCCTCGG 62.796 72.222 0.00 0.00 37.69 4.63
94 95 3.744719 TCGGCTGGTTCGTCCTCG 61.745 66.667 0.00 0.00 37.07 4.63
95 96 2.126031 GTCGGCTGGTTCGTCCTC 60.126 66.667 0.00 0.00 37.07 3.71
96 97 3.692406 GGTCGGCTGGTTCGTCCT 61.692 66.667 0.00 0.00 37.07 3.85
97 98 4.754667 GGGTCGGCTGGTTCGTCC 62.755 72.222 0.00 0.00 35.65 4.79
98 99 4.754667 GGGGTCGGCTGGTTCGTC 62.755 72.222 0.00 0.00 0.00 4.20
100 101 4.760047 CAGGGGTCGGCTGGTTCG 62.760 72.222 0.00 0.00 0.00 3.95
101 102 4.410400 CCAGGGGTCGGCTGGTTC 62.410 72.222 0.00 0.00 33.82 3.62
105 106 4.101448 CTTCCCAGGGGTCGGCTG 62.101 72.222 5.33 0.00 36.47 4.85
110 111 3.787001 CTCGGCTTCCCAGGGGTC 61.787 72.222 5.33 0.00 36.47 4.46
111 112 4.332543 TCTCGGCTTCCCAGGGGT 62.333 66.667 5.33 0.00 36.47 4.95
112 113 3.474570 CTCTCGGCTTCCCAGGGG 61.475 72.222 5.33 0.92 0.00 4.79
113 114 3.474570 CCTCTCGGCTTCCCAGGG 61.475 72.222 0.00 0.00 0.00 4.45
133 134 4.394712 GACAGGGTGTCGGGCCTG 62.395 72.222 4.71 4.71 37.67 4.85
142 143 4.323477 TTTCCGCGGGACAGGGTG 62.323 66.667 27.83 0.00 0.00 4.61
143 144 4.324991 GTTTCCGCGGGACAGGGT 62.325 66.667 27.83 0.00 0.00 4.34
155 156 3.408851 GGTGTCGTCGGCGTTTCC 61.409 66.667 10.18 6.54 39.49 3.13
156 157 3.759828 CGGTGTCGTCGGCGTTTC 61.760 66.667 10.18 1.97 39.49 2.78
157 158 3.771568 TTCGGTGTCGTCGGCGTTT 62.772 57.895 10.18 0.00 39.49 3.60
158 159 4.268939 TTCGGTGTCGTCGGCGTT 62.269 61.111 10.18 0.00 39.49 4.84
159 160 4.695231 CTTCGGTGTCGTCGGCGT 62.695 66.667 10.18 0.00 39.49 5.68
162 163 4.430765 CCCCTTCGGTGTCGTCGG 62.431 72.222 0.00 0.00 37.69 4.79
163 164 4.430765 CCCCCTTCGGTGTCGTCG 62.431 72.222 0.00 0.00 37.69 5.12
164 165 2.993264 TCCCCCTTCGGTGTCGTC 60.993 66.667 0.00 0.00 37.69 4.20
165 166 3.308705 GTCCCCCTTCGGTGTCGT 61.309 66.667 0.00 0.00 37.69 4.34
166 167 2.995574 AGTCCCCCTTCGGTGTCG 60.996 66.667 0.00 0.00 37.82 4.35
167 168 2.663196 CAGTCCCCCTTCGGTGTC 59.337 66.667 0.00 0.00 0.00 3.67
168 169 3.637273 GCAGTCCCCCTTCGGTGT 61.637 66.667 0.00 0.00 0.00 4.16
169 170 4.760047 CGCAGTCCCCCTTCGGTG 62.760 72.222 0.00 0.00 0.00 4.94
173 174 4.821589 CTCGCGCAGTCCCCCTTC 62.822 72.222 8.75 0.00 0.00 3.46
191 192 4.758251 TGTGCTCATGGCGTCGGG 62.758 66.667 0.00 0.00 45.43 5.14
192 193 3.190849 CTGTGCTCATGGCGTCGG 61.191 66.667 0.00 0.00 45.43 4.79
193 194 3.190849 CCTGTGCTCATGGCGTCG 61.191 66.667 0.00 0.00 45.43 5.12
194 195 2.046892 ACCTGTGCTCATGGCGTC 60.047 61.111 0.00 0.00 45.43 5.19
195 196 2.359107 CACCTGTGCTCATGGCGT 60.359 61.111 0.00 0.00 45.43 5.68
196 197 3.129502 CCACCTGTGCTCATGGCG 61.130 66.667 0.00 0.00 45.43 5.69
197 198 2.753043 CCCACCTGTGCTCATGGC 60.753 66.667 3.34 0.00 42.22 4.40
198 199 2.044650 CCCCACCTGTGCTCATGG 60.045 66.667 2.06 2.06 0.00 3.66
199 200 1.077930 CTCCCCACCTGTGCTCATG 60.078 63.158 0.00 0.00 0.00 3.07
200 201 2.304056 CCTCCCCACCTGTGCTCAT 61.304 63.158 0.00 0.00 0.00 2.90
201 202 2.930019 CCTCCCCACCTGTGCTCA 60.930 66.667 0.00 0.00 0.00 4.26
202 203 2.930562 ACCTCCCCACCTGTGCTC 60.931 66.667 0.00 0.00 0.00 4.26
203 204 3.252284 CACCTCCCCACCTGTGCT 61.252 66.667 0.00 0.00 0.00 4.40
204 205 4.351054 CCACCTCCCCACCTGTGC 62.351 72.222 0.00 0.00 0.00 4.57
205 206 2.529136 TCCACCTCCCCACCTGTG 60.529 66.667 0.00 0.00 0.00 3.66
206 207 2.529389 GTCCACCTCCCCACCTGT 60.529 66.667 0.00 0.00 0.00 4.00
207 208 3.706373 CGTCCACCTCCCCACCTG 61.706 72.222 0.00 0.00 0.00 4.00
287 288 3.866582 CCATCGCACTCCTCCCCC 61.867 72.222 0.00 0.00 0.00 5.40
288 289 4.554036 GCCATCGCACTCCTCCCC 62.554 72.222 0.00 0.00 34.03 4.81
289 290 4.899239 CGCCATCGCACTCCTCCC 62.899 72.222 0.00 0.00 34.03 4.30
321 322 3.430497 TCCCCCTCTCCCTCTCGG 61.430 72.222 0.00 0.00 0.00 4.63
322 323 2.197324 CTCCCCCTCTCCCTCTCG 59.803 72.222 0.00 0.00 0.00 4.04
323 324 2.015726 TCCTCCCCCTCTCCCTCTC 61.016 68.421 0.00 0.00 0.00 3.20
324 325 2.018086 CTCCTCCCCCTCTCCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
325 326 1.595058 TTCTCCTCCCCCTCTCCCTC 61.595 65.000 0.00 0.00 0.00 4.30
326 327 1.550374 TTCTCCTCCCCCTCTCCCT 60.550 63.158 0.00 0.00 0.00 4.20
327 328 1.074850 CTTCTCCTCCCCCTCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
328 329 1.764454 GCTTCTCCTCCCCCTCTCC 60.764 68.421 0.00 0.00 0.00 3.71
329 330 0.326143 AAGCTTCTCCTCCCCCTCTC 60.326 60.000 0.00 0.00 0.00 3.20
330 331 0.620121 CAAGCTTCTCCTCCCCCTCT 60.620 60.000 0.00 0.00 0.00 3.69
331 332 1.631071 CCAAGCTTCTCCTCCCCCTC 61.631 65.000 0.00 0.00 0.00 4.30
332 333 1.617839 CCAAGCTTCTCCTCCCCCT 60.618 63.158 0.00 0.00 0.00 4.79
333 334 2.684499 CCCAAGCTTCTCCTCCCCC 61.684 68.421 0.00 0.00 0.00 5.40
334 335 2.684499 CCCCAAGCTTCTCCTCCCC 61.684 68.421 0.00 0.00 0.00 4.81
335 336 2.684499 CCCCCAAGCTTCTCCTCCC 61.684 68.421 0.00 0.00 0.00 4.30
336 337 1.616628 TCCCCCAAGCTTCTCCTCC 60.617 63.158 0.00 0.00 0.00 4.30
337 338 0.912006 AGTCCCCCAAGCTTCTCCTC 60.912 60.000 0.00 0.00 0.00 3.71
338 339 0.912006 GAGTCCCCCAAGCTTCTCCT 60.912 60.000 0.00 0.00 0.00 3.69
339 340 1.604915 GAGTCCCCCAAGCTTCTCC 59.395 63.158 0.00 0.00 0.00 3.71
340 341 1.201429 TGGAGTCCCCCAAGCTTCTC 61.201 60.000 6.74 0.00 32.31 2.87
341 342 0.772124 TTGGAGTCCCCCAAGCTTCT 60.772 55.000 6.74 0.00 40.99 2.85
342 343 0.112412 TTTGGAGTCCCCCAAGCTTC 59.888 55.000 6.74 0.00 45.89 3.86
343 344 0.113190 CTTTGGAGTCCCCCAAGCTT 59.887 55.000 6.74 0.00 45.89 3.74
344 345 1.068352 ACTTTGGAGTCCCCCAAGCT 61.068 55.000 6.74 0.00 45.89 3.74
345 346 0.178961 AACTTTGGAGTCCCCCAAGC 60.179 55.000 6.74 0.00 45.89 4.01
346 347 2.381752 AAACTTTGGAGTCCCCCAAG 57.618 50.000 6.74 8.84 45.89 3.61
347 348 2.858787 AAAACTTTGGAGTCCCCCAA 57.141 45.000 6.74 0.00 43.90 4.12
348 349 2.158430 GGTAAAACTTTGGAGTCCCCCA 60.158 50.000 6.74 0.00 34.21 4.96
349 350 2.522185 GGTAAAACTTTGGAGTCCCCC 58.478 52.381 6.74 0.00 34.21 5.40
350 351 2.109480 AGGGTAAAACTTTGGAGTCCCC 59.891 50.000 6.74 0.00 37.06 4.81
351 352 3.418995 GAGGGTAAAACTTTGGAGTCCC 58.581 50.000 6.74 0.00 36.77 4.46
352 353 3.072211 CGAGGGTAAAACTTTGGAGTCC 58.928 50.000 0.73 0.73 34.21 3.85
353 354 3.736720 ACGAGGGTAAAACTTTGGAGTC 58.263 45.455 0.00 0.00 34.21 3.36
354 355 3.851458 ACGAGGGTAAAACTTTGGAGT 57.149 42.857 0.00 0.00 37.87 3.85
355 356 3.252458 CCAACGAGGGTAAAACTTTGGAG 59.748 47.826 0.00 0.00 35.07 3.86
356 357 3.215975 CCAACGAGGGTAAAACTTTGGA 58.784 45.455 0.00 0.00 35.07 3.53
357 358 2.287970 GCCAACGAGGGTAAAACTTTGG 60.288 50.000 0.00 0.00 38.09 3.28
358 359 3.007979 GCCAACGAGGGTAAAACTTTG 57.992 47.619 0.00 0.00 38.09 2.77
368 369 0.875059 GTGAAAAGAGCCAACGAGGG 59.125 55.000 0.00 0.00 38.09 4.30
369 370 1.593196 TGTGAAAAGAGCCAACGAGG 58.407 50.000 0.00 0.00 41.84 4.63
370 371 3.691049 TTTGTGAAAAGAGCCAACGAG 57.309 42.857 0.00 0.00 0.00 4.18
371 372 3.629855 TCATTTGTGAAAAGAGCCAACGA 59.370 39.130 0.00 0.00 0.00 3.85
372 373 3.730715 GTCATTTGTGAAAAGAGCCAACG 59.269 43.478 0.00 0.00 0.00 4.10
373 374 4.681744 TGTCATTTGTGAAAAGAGCCAAC 58.318 39.130 0.00 0.00 0.00 3.77
374 375 4.644234 TCTGTCATTTGTGAAAAGAGCCAA 59.356 37.500 0.00 0.00 0.00 4.52
375 376 4.206375 TCTGTCATTTGTGAAAAGAGCCA 58.794 39.130 0.00 0.00 0.00 4.75
376 377 4.836125 TCTGTCATTTGTGAAAAGAGCC 57.164 40.909 0.00 0.00 0.00 4.70
383 384 9.898152 TGTGGTATTATATCTGTCATTTGTGAA 57.102 29.630 0.00 0.00 0.00 3.18
384 385 9.898152 TTGTGGTATTATATCTGTCATTTGTGA 57.102 29.630 0.00 0.00 0.00 3.58
407 408 7.033530 TCAAAACTCCACGAATTTACATTGT 57.966 32.000 0.00 0.00 0.00 2.71
410 411 7.272037 AGTTCAAAACTCCACGAATTTACAT 57.728 32.000 0.00 0.00 37.02 2.29
420 421 5.523552 CCCATGAAAAAGTTCAAAACTCCAC 59.476 40.000 0.00 0.00 46.66 4.02
425 426 9.157104 TCTTTAACCCATGAAAAAGTTCAAAAC 57.843 29.630 0.00 0.00 46.66 2.43
443 444 9.952188 GAGCTATATTTGGTTTCATCTTTAACC 57.048 33.333 0.00 0.00 43.28 2.85
877 881 0.967887 GCCTCAGGCTTTTTCCTCCC 60.968 60.000 9.09 0.00 46.69 4.30
1059 1075 1.726791 CATCTCGTTGTTCTTGGACGG 59.273 52.381 0.00 0.00 37.39 4.79
1179 1195 1.451567 CTCCGCCTCCTCGTCACTA 60.452 63.158 0.00 0.00 0.00 2.74
1514 1534 1.404583 GCAGGAACAATGGCAATGGAC 60.405 52.381 7.57 0.40 0.00 4.02
1886 1922 7.800155 TGACAGTTCAAACAATGATAACAGA 57.200 32.000 0.00 0.00 38.03 3.41
1972 2008 0.750249 TTGAGACCAGCAAGACGACA 59.250 50.000 0.00 0.00 0.00 4.35
2053 2089 1.999648 TGGCAGCATCCTGAAAAGTT 58.000 45.000 0.00 0.00 41.77 2.66
2215 2251 5.126061 GCAGATTATGTGTTGTGAAAGGGAT 59.874 40.000 0.00 0.00 0.00 3.85
2670 2716 5.982516 GCACAACCACATCTTTCATGTAAAA 59.017 36.000 0.00 0.00 0.00 1.52
3473 3520 5.676079 GCTTAACTTTTCATATGCCGCAAGA 60.676 40.000 0.00 0.00 43.02 3.02
3737 3788 4.160329 ACATCAGTCTGGACTAAGTTCCA 58.840 43.478 2.75 0.00 43.83 3.53
3784 3835 3.663995 TGCCTTCACCATTCACATTTG 57.336 42.857 0.00 0.00 0.00 2.32
3799 3850 6.564557 AATTTCCATACATTCCAATGCCTT 57.435 33.333 0.00 0.00 40.04 4.35
3803 3854 7.434897 CCGTGTTAATTTCCATACATTCCAATG 59.565 37.037 0.00 0.00 42.10 2.82
3933 3984 1.604593 GAGCCCAGCCTCTGCAAAA 60.605 57.895 0.00 0.00 41.13 2.44
3934 3985 2.034687 GAGCCCAGCCTCTGCAAA 59.965 61.111 0.00 0.00 41.13 3.68
3945 3996 1.434513 AAACAGGTCCATGGAGCCCA 61.435 55.000 34.70 2.81 42.97 5.36
4041 4095 6.097915 TGAAACCTGTACCTACTTGAAGAG 57.902 41.667 0.00 0.00 0.00 2.85
4111 4167 0.179097 TTGTTTGTTGCTTTCGGGCC 60.179 50.000 0.00 0.00 0.00 5.80
4116 4172 3.438434 TGGGCTTTTTGTTTGTTGCTTTC 59.562 39.130 0.00 0.00 0.00 2.62
4120 4176 4.368874 AAATGGGCTTTTTGTTTGTTGC 57.631 36.364 0.00 0.00 0.00 4.17
4214 4270 8.700644 GTGTGTGTGTGTGTAAATTTTGTAAAA 58.299 29.630 0.00 0.00 0.00 1.52
4216 4272 7.326305 GTGTGTGTGTGTGTGTAAATTTTGTAA 59.674 33.333 0.00 0.00 0.00 2.41
4218 4274 5.631512 GTGTGTGTGTGTGTGTAAATTTTGT 59.368 36.000 0.00 0.00 0.00 2.83
4219 4275 5.631096 TGTGTGTGTGTGTGTGTAAATTTTG 59.369 36.000 0.00 0.00 0.00 2.44
4220 4276 5.773575 TGTGTGTGTGTGTGTGTAAATTTT 58.226 33.333 0.00 0.00 0.00 1.82
4232 4293 9.750125 AAGTATATACATAGATGTGTGTGTGTG 57.250 33.333 15.18 0.00 41.89 3.82
4493 4558 7.172875 GCTCTATCATGTGCAGTGATATTTCTT 59.827 37.037 17.49 0.18 37.77 2.52
4494 4559 6.649973 GCTCTATCATGTGCAGTGATATTTCT 59.350 38.462 17.49 0.75 37.77 2.52
4567 4643 9.046296 CCGTTAGGAATTATTATATCCATCTGC 57.954 37.037 0.00 0.00 41.02 4.26
4608 4685 5.359756 GGAGTTTCTTTCCAGCAAATGTTT 58.640 37.500 0.00 0.00 34.74 2.83
4612 4689 2.899900 GGGGAGTTTCTTTCCAGCAAAT 59.100 45.455 0.00 0.00 36.40 2.32


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

AutoCloner maintained by Alex Coulton.