Multiple sequence alignment - TraesCS5D01G360300

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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 TraesCS5D01G360300 chr5D 100.000 4310 0 0 1 4310 440159373 440163682 0.000000e+00 7960.0
1 TraesCS5D01G360300 chr5D 91.910 3906 223 39 424 4310 42016305 42020136 0.000000e+00 5376.0
2 TraesCS5D01G360300 chr5D 89.514 1421 106 20 420 1808 42053935 42052526 0.000000e+00 1759.0
3 TraesCS5D01G360300 chr5D 94.839 620 23 3 1833 2452 42052528 42051918 0.000000e+00 959.0
4 TraesCS5D01G360300 chr5D 89.226 297 32 0 1 297 42054772 42054476 5.260000e-99 372.0
5 TraesCS5D01G360300 chr5B 96.338 3878 131 7 435 4310 535110725 535114593 0.000000e+00 6364.0
6 TraesCS5D01G360300 chr5B 94.357 3509 140 21 811 4310 36720307 36723766 0.000000e+00 5330.0
7 TraesCS5D01G360300 chr5B 93.085 2386 111 17 820 3203 36767815 36765482 0.000000e+00 3443.0
8 TraesCS5D01G360300 chr5B 90.675 311 27 1 1 311 535085045 535085353 3.100000e-111 412.0
9 TraesCS5D01G360300 chr5B 83.553 304 20 15 3781 4084 36765233 36764960 1.540000e-64 257.0
10 TraesCS5D01G360300 chr5B 92.500 80 6 0 4184 4263 36764965 36764886 9.790000e-22 115.0
11 TraesCS5D01G360300 chr5A 96.533 3721 109 12 594 4310 555770318 555774022 0.000000e+00 6139.0
12 TraesCS5D01G360300 chr5A 92.673 3917 229 30 421 4310 30403944 30407829 0.000000e+00 5590.0
13 TraesCS5D01G360300 chr5A 83.280 311 28 6 1 311 555764529 555764815 9.190000e-67 265.0
14 TraesCS5D01G360300 chr3A 94.444 36 2 0 697 732 698563803 698563768 6.020000e-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 TraesCS5D01G360300 chr5D 440159373 440163682 4309 False 7960.000000 7960 100.000000 1 4310 1 chr5D.!!$F2 4309
1 TraesCS5D01G360300 chr5D 42016305 42020136 3831 False 5376.000000 5376 91.910000 424 4310 1 chr5D.!!$F1 3886
2 TraesCS5D01G360300 chr5D 42051918 42054772 2854 True 1030.000000 1759 91.193000 1 2452 3 chr5D.!!$R1 2451
3 TraesCS5D01G360300 chr5B 535110725 535114593 3868 False 6364.000000 6364 96.338000 435 4310 1 chr5B.!!$F3 3875
4 TraesCS5D01G360300 chr5B 36720307 36723766 3459 False 5330.000000 5330 94.357000 811 4310 1 chr5B.!!$F1 3499
5 TraesCS5D01G360300 chr5B 36764886 36767815 2929 True 1271.666667 3443 89.712667 820 4263 3 chr5B.!!$R1 3443
6 TraesCS5D01G360300 chr5A 555770318 555774022 3704 False 6139.000000 6139 96.533000 594 4310 1 chr5A.!!$F3 3716
7 TraesCS5D01G360300 chr5A 30403944 30407829 3885 False 5590.000000 5590 92.673000 421 4310 1 chr5A.!!$F1 3889

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
163 164 0.096281 GCATTTTTCGGCATCGACGA 59.904 50.0 0.0 0.0 45.92 4.20 F
297 298 0.182537 AACTTGTGGCTGCACCTACA 59.817 50.0 0.5 0.0 40.22 2.74 F
301 302 0.322456 TGTGGCTGCACCTACATTCC 60.322 55.0 0.5 0.0 40.22 3.01 F
2139 2648 0.109532 TTGTTGATGGGTTCTGCCGA 59.890 50.0 0.0 0.0 38.44 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2551 0.255318 CTCCTTTGCCTCAGCCATCT 59.745 55.000 0.00 0.0 38.69 2.90 R
2139 2648 3.364549 TGCTTGATCAATTTCCCCGATT 58.635 40.909 8.96 0.0 0.00 3.34 R
2395 2904 3.510531 AGTGGGAAAGAAACCCTTCTC 57.489 47.619 0.00 0.0 46.82 2.87 R
4218 4839 0.171231 CGAGCCACGAGATGAAGACA 59.829 55.000 0.00 0.0 45.77 3.41 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 2.033602 AGCCAACCGTAACTGGGC 59.966 61.111 0.00 0.00 44.92 5.36
20 21 2.031465 CAACCGTAACTGGGCCGT 59.969 61.111 0.00 0.00 0.00 5.68
33 34 1.363080 GGCCGTACCCGAGAAGATC 59.637 63.158 0.00 0.00 35.63 2.75
34 35 1.363080 GCCGTACCCGAGAAGATCC 59.637 63.158 0.00 0.00 35.63 3.36
36 37 1.099879 CCGTACCCGAGAAGATCCGT 61.100 60.000 0.00 0.00 35.63 4.69
97 98 4.022849 GCAGATATATTGGCTGGTTCAACC 60.023 45.833 0.00 0.00 39.22 3.77
98 99 4.214119 CAGATATATTGGCTGGTTCAACCG 59.786 45.833 1.02 0.00 42.58 4.44
104 105 1.073548 GCTGGTTCAACCGGGGTTA 59.926 57.895 17.63 0.00 44.90 2.85
108 109 1.145325 TGGTTCAACCGGGGTTATGTT 59.855 47.619 6.32 0.00 42.58 2.71
109 110 1.814394 GGTTCAACCGGGGTTATGTTC 59.186 52.381 6.32 0.00 36.46 3.18
118 119 2.353579 CGGGGTTATGTTCGATTTGTCC 59.646 50.000 0.00 0.00 0.00 4.02
129 130 7.701809 TGTTCGATTTGTCCCAAAAATTTAC 57.298 32.000 0.00 0.00 0.00 2.01
134 135 7.928706 TCGATTTGTCCCAAAAATTTACATTGT 59.071 29.630 0.00 0.00 0.00 2.71
135 136 8.220434 CGATTTGTCCCAAAAATTTACATTGTC 58.780 33.333 0.00 0.00 0.00 3.18
139 140 7.730084 TGTCCCAAAAATTTACATTGTCATCA 58.270 30.769 0.00 0.00 0.00 3.07
159 160 1.226945 GGGGCATTTTTCGGCATCG 60.227 57.895 0.00 0.00 37.82 3.84
163 164 0.096281 GCATTTTTCGGCATCGACGA 59.904 50.000 0.00 0.00 45.92 4.20
173 174 1.471676 GGCATCGACGACCTCAAATCT 60.472 52.381 0.00 0.00 0.00 2.40
176 177 3.489398 GCATCGACGACCTCAAATCTAGT 60.489 47.826 0.00 0.00 0.00 2.57
183 184 6.238566 CGACGACCTCAAATCTAGTGGTAATA 60.239 42.308 0.00 0.00 33.36 0.98
216 217 4.630505 GTGCTAGTGTAGAAAACCCTAAGC 59.369 45.833 0.00 0.00 0.00 3.09
235 236 9.057089 CCCTAAGCTAACTTTACCTATTTCATG 57.943 37.037 0.00 0.00 37.33 3.07
238 239 5.828328 AGCTAACTTTACCTATTTCATGGGC 59.172 40.000 0.00 0.00 33.57 5.36
266 267 8.485392 CCCCATGTTGTTGAATTTTAATCCTAT 58.515 33.333 0.00 0.00 0.00 2.57
288 289 4.469657 TCAAGACCAATAAACTTGTGGCT 58.530 39.130 0.00 0.00 40.89 4.75
297 298 0.182537 AACTTGTGGCTGCACCTACA 59.817 50.000 0.50 0.00 40.22 2.74
299 300 1.202927 ACTTGTGGCTGCACCTACATT 60.203 47.619 0.50 0.00 40.22 2.71
300 301 1.470098 CTTGTGGCTGCACCTACATTC 59.530 52.381 0.50 0.00 40.22 2.67
301 302 0.322456 TGTGGCTGCACCTACATTCC 60.322 55.000 0.50 0.00 40.22 3.01
304 305 0.837272 GGCTGCACCTACATTCCCTA 59.163 55.000 0.50 0.00 34.51 3.53
305 306 1.202698 GGCTGCACCTACATTCCCTAG 60.203 57.143 0.50 0.00 34.51 3.02
306 307 1.486726 GCTGCACCTACATTCCCTAGT 59.513 52.381 0.00 0.00 0.00 2.57
307 308 2.483889 GCTGCACCTACATTCCCTAGTC 60.484 54.545 0.00 0.00 0.00 2.59
308 309 2.103263 CTGCACCTACATTCCCTAGTCC 59.897 54.545 0.00 0.00 0.00 3.85
309 310 2.292918 TGCACCTACATTCCCTAGTCCT 60.293 50.000 0.00 0.00 0.00 3.85
310 311 3.052414 TGCACCTACATTCCCTAGTCCTA 60.052 47.826 0.00 0.00 0.00 2.94
311 312 3.321396 GCACCTACATTCCCTAGTCCTAC 59.679 52.174 0.00 0.00 0.00 3.18
312 313 4.805744 CACCTACATTCCCTAGTCCTACT 58.194 47.826 0.00 0.00 0.00 2.57
313 314 4.828387 CACCTACATTCCCTAGTCCTACTC 59.172 50.000 0.00 0.00 0.00 2.59
314 315 4.140971 ACCTACATTCCCTAGTCCTACTCC 60.141 50.000 0.00 0.00 0.00 3.85
315 316 4.140994 CCTACATTCCCTAGTCCTACTCCA 60.141 50.000 0.00 0.00 0.00 3.86
316 317 4.561254 ACATTCCCTAGTCCTACTCCAT 57.439 45.455 0.00 0.00 0.00 3.41
317 318 4.227197 ACATTCCCTAGTCCTACTCCATG 58.773 47.826 0.00 0.00 0.00 3.66
318 319 4.078571 ACATTCCCTAGTCCTACTCCATGA 60.079 45.833 0.00 0.00 0.00 3.07
319 320 4.834406 TTCCCTAGTCCTACTCCATGAT 57.166 45.455 0.00 0.00 0.00 2.45
320 321 4.119556 TCCCTAGTCCTACTCCATGATG 57.880 50.000 0.00 0.00 0.00 3.07
321 322 3.467483 TCCCTAGTCCTACTCCATGATGT 59.533 47.826 0.00 0.00 0.00 3.06
322 323 3.829601 CCCTAGTCCTACTCCATGATGTC 59.170 52.174 0.00 0.00 0.00 3.06
324 325 4.895889 CCTAGTCCTACTCCATGATGTCAA 59.104 45.833 0.00 0.00 0.00 3.18
337 338 4.492494 TGATGTCAATATGAGTGTGCCT 57.508 40.909 0.00 0.00 0.00 4.75
341 342 6.707608 TGATGTCAATATGAGTGTGCCTAATC 59.292 38.462 0.00 0.00 0.00 1.75
342 343 5.988287 TGTCAATATGAGTGTGCCTAATCA 58.012 37.500 0.00 0.00 0.00 2.57
345 346 7.012610 TGTCAATATGAGTGTGCCTAATCAATG 59.987 37.037 0.00 0.00 0.00 2.82
346 347 5.954296 ATATGAGTGTGCCTAATCAATGC 57.046 39.130 0.00 0.00 0.00 3.56
348 349 1.678101 GAGTGTGCCTAATCAATGCCC 59.322 52.381 0.00 0.00 0.00 5.36
350 351 0.334335 TGTGCCTAATCAATGCCCCA 59.666 50.000 0.00 0.00 0.00 4.96
351 352 1.063038 TGTGCCTAATCAATGCCCCAT 60.063 47.619 0.00 0.00 0.00 4.00
352 353 1.342174 GTGCCTAATCAATGCCCCATG 59.658 52.381 0.00 0.00 0.00 3.66
353 354 1.217436 TGCCTAATCAATGCCCCATGA 59.783 47.619 0.00 0.00 0.00 3.07
355 356 1.881973 CCTAATCAATGCCCCATGACG 59.118 52.381 0.00 0.00 0.00 4.35
356 357 2.487086 CCTAATCAATGCCCCATGACGA 60.487 50.000 0.00 0.00 0.00 4.20
357 358 1.392589 AATCAATGCCCCATGACGAC 58.607 50.000 0.00 0.00 0.00 4.34
360 361 1.105457 CAATGCCCCATGACGACAAT 58.895 50.000 0.00 0.00 0.00 2.71
361 362 1.105457 AATGCCCCATGACGACAATG 58.895 50.000 0.00 0.00 0.00 2.82
365 366 2.018644 GCCCCATGACGACAATGACAT 61.019 52.381 0.00 0.00 0.00 3.06
366 367 1.942657 CCCCATGACGACAATGACATC 59.057 52.381 0.00 0.00 0.00 3.06
367 368 2.631267 CCCATGACGACAATGACATCA 58.369 47.619 0.00 0.00 0.00 3.07
368 369 3.208594 CCCATGACGACAATGACATCAT 58.791 45.455 0.00 0.00 38.41 2.45
369 370 3.249320 CCCATGACGACAATGACATCATC 59.751 47.826 0.00 0.00 35.10 2.92
371 372 3.502191 TGACGACAATGACATCATCGA 57.498 42.857 21.64 0.00 35.10 3.59
372 373 3.438360 TGACGACAATGACATCATCGAG 58.562 45.455 21.64 2.38 35.10 4.04
373 374 3.128589 TGACGACAATGACATCATCGAGA 59.871 43.478 21.64 9.30 35.10 4.04
375 376 4.494484 ACGACAATGACATCATCGAGAAA 58.506 39.130 21.64 0.00 35.10 2.52
376 377 4.929211 ACGACAATGACATCATCGAGAAAA 59.071 37.500 21.64 0.00 35.10 2.29
377 378 5.408299 ACGACAATGACATCATCGAGAAAAA 59.592 36.000 21.64 0.00 35.10 1.94
398 399 4.942761 AATTACATTGACATGATGGGGC 57.057 40.909 0.00 0.00 34.11 5.80
399 400 3.378861 TTACATTGACATGATGGGGCA 57.621 42.857 0.00 0.00 34.11 5.36
400 401 2.464796 ACATTGACATGATGGGGCAT 57.535 45.000 0.00 0.00 34.11 4.40
402 403 3.109151 ACATTGACATGATGGGGCATTT 58.891 40.909 0.00 0.00 34.11 2.32
403 404 3.520317 ACATTGACATGATGGGGCATTTT 59.480 39.130 0.00 0.00 34.11 1.82
404 405 4.019141 ACATTGACATGATGGGGCATTTTT 60.019 37.500 0.00 0.00 34.11 1.94
407 408 3.055963 TGACATGATGGGGCATTTTTCAC 60.056 43.478 0.00 0.00 0.00 3.18
408 409 2.905085 ACATGATGGGGCATTTTTCACA 59.095 40.909 0.00 0.00 0.00 3.58
409 410 3.520317 ACATGATGGGGCATTTTTCACAT 59.480 39.130 0.00 0.00 0.00 3.21
410 411 4.019141 ACATGATGGGGCATTTTTCACATT 60.019 37.500 0.00 0.00 0.00 2.71
411 412 3.940319 TGATGGGGCATTTTTCACATTG 58.060 40.909 0.00 0.00 0.00 2.82
413 414 3.399440 TGGGGCATTTTTCACATTGAC 57.601 42.857 0.00 0.00 0.00 3.18
414 415 2.702478 TGGGGCATTTTTCACATTGACA 59.298 40.909 0.00 0.00 0.00 3.58
416 417 3.934579 GGGGCATTTTTCACATTGACATC 59.065 43.478 0.00 0.00 0.00 3.06
417 418 4.563168 GGGGCATTTTTCACATTGACATCA 60.563 41.667 0.00 0.00 0.00 3.07
418 419 5.180271 GGGCATTTTTCACATTGACATCAT 58.820 37.500 0.00 0.00 0.00 2.45
636 1078 8.237811 ACCATAATTAAGGAGGCAACAAATAG 57.762 34.615 13.56 0.00 41.41 1.73
663 1105 4.504461 AGACTCTAAGTTTGCGCATTATCG 59.496 41.667 12.75 3.86 0.00 2.92
742 1185 2.813754 TGCTCTTAAAAGACAGCGCAAT 59.186 40.909 11.47 0.00 31.97 3.56
1041 1523 1.589414 ACCCATTTCTCCTCCTCCTG 58.411 55.000 0.00 0.00 0.00 3.86
1416 1898 4.457496 CGCACCAGGCTCCACGAT 62.457 66.667 0.00 0.00 41.67 3.73
1874 2383 2.780414 TGGGAGGATGAGGAATGATGT 58.220 47.619 0.00 0.00 0.00 3.06
1894 2403 4.361783 TGTGGGTCTATTTCCAGATCAGA 58.638 43.478 0.00 0.00 33.13 3.27
1953 2462 0.815213 GGCATGCAGATGAGGCGTTA 60.815 55.000 21.36 0.00 0.00 3.18
2042 2551 3.822735 CACTCTTTCTGCTTGAATGGGAA 59.177 43.478 10.87 0.00 34.87 3.97
2139 2648 0.109532 TTGTTGATGGGTTCTGCCGA 59.890 50.000 0.00 0.00 38.44 5.54
2580 3089 1.063417 CAGGGGGATTTGGAATCAGCT 60.063 52.381 3.39 0.00 0.00 4.24
2710 3219 5.163478 ACAGAGCTTGTGAAGAAAATGCTTT 60.163 36.000 4.14 0.00 38.99 3.51
2775 3284 4.946478 ACATAGATACTGTGAGAAGGGC 57.054 45.455 0.00 0.00 0.00 5.19
2881 3390 9.057089 AGAAGCTATGTGCATTAGGTAAAATAC 57.943 33.333 10.58 0.00 45.94 1.89
3241 3848 7.463544 TGATTGTTAGAAACAGATGCATTACG 58.536 34.615 0.00 0.00 43.27 3.18
3341 3951 0.107066 CATGCTCATACCCCTGCACA 60.107 55.000 0.00 0.00 38.29 4.57
3356 3966 3.127548 CCTGCACATGTCACCAACTTATC 59.872 47.826 0.00 0.00 0.00 1.75
3631 4251 3.869272 CTGTCGCGGCTGGCATTC 61.869 66.667 13.81 0.00 43.84 2.67
3731 4351 1.514678 GCAGATGTTCGTTGGCCACA 61.515 55.000 3.88 0.00 0.00 4.17
3826 4447 1.416813 CTAGCTGCGCTCGTTCTTGG 61.417 60.000 9.73 0.00 40.44 3.61
3882 4503 3.252701 ACGACGTCTTCTCACTTGTATGT 59.747 43.478 14.70 0.00 0.00 2.29
3956 4577 1.982938 GTGCGAGGAGGTACAGGGT 60.983 63.158 0.00 0.00 0.00 4.34
4218 4839 0.035317 TTGCTGTGCTCGTCTTCCAT 59.965 50.000 0.00 0.00 0.00 3.41
4219 4840 0.671472 TGCTGTGCTCGTCTTCCATG 60.671 55.000 0.00 0.00 0.00 3.66
4245 4866 1.956170 CTCGTGGCTCGCTGTGTTT 60.956 57.895 3.73 0.00 39.67 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.293179 GTACGGCCCAGTTACGGTT 59.707 57.895 0.00 0.00 0.00 4.44
17 18 1.099879 ACGGATCTTCTCGGGTACGG 61.100 60.000 0.00 0.00 41.39 4.02
20 21 1.064906 ACAGACGGATCTTCTCGGGTA 60.065 52.381 0.00 0.00 30.42 3.69
33 34 5.154932 CGATTATTCTAGGCTAACAGACGG 58.845 45.833 0.00 0.00 0.00 4.79
34 35 5.154932 CCGATTATTCTAGGCTAACAGACG 58.845 45.833 0.00 0.00 0.00 4.18
36 37 4.021368 GCCCGATTATTCTAGGCTAACAGA 60.021 45.833 0.00 0.00 36.51 3.41
66 67 3.056250 AGCCAATATATCTGCCACTCTCG 60.056 47.826 3.50 0.00 0.00 4.04
76 77 4.389374 CGGTTGAACCAGCCAATATATCT 58.611 43.478 15.58 0.00 38.47 1.98
97 98 2.353579 GGACAAATCGAACATAACCCCG 59.646 50.000 0.00 0.00 0.00 5.73
98 99 2.686405 GGGACAAATCGAACATAACCCC 59.314 50.000 0.00 0.00 0.00 4.95
99 100 3.349022 TGGGACAAATCGAACATAACCC 58.651 45.455 0.00 0.00 31.92 4.11
118 119 7.066043 CCCCATGATGACAATGTAAATTTTTGG 59.934 37.037 0.00 0.00 0.00 3.28
129 130 3.830744 AAATGCCCCATGATGACAATG 57.169 42.857 0.00 0.00 0.00 2.82
134 135 1.755959 CCGAAAAATGCCCCATGATGA 59.244 47.619 0.00 0.00 0.00 2.92
135 136 1.807377 GCCGAAAAATGCCCCATGATG 60.807 52.381 0.00 0.00 0.00 3.07
139 140 0.465287 GATGCCGAAAAATGCCCCAT 59.535 50.000 0.00 0.00 0.00 4.00
159 160 3.870633 ACCACTAGATTTGAGGTCGTC 57.129 47.619 0.00 0.00 0.00 4.20
163 164 7.993183 CACCAATATTACCACTAGATTTGAGGT 59.007 37.037 0.00 0.00 36.40 3.85
173 174 7.131907 AGCACATACACCAATATTACCACTA 57.868 36.000 0.00 0.00 0.00 2.74
176 177 6.989759 CACTAGCACATACACCAATATTACCA 59.010 38.462 0.00 0.00 0.00 3.25
183 184 5.932619 TCTACACTAGCACATACACCAAT 57.067 39.130 0.00 0.00 0.00 3.16
193 194 4.630505 GCTTAGGGTTTTCTACACTAGCAC 59.369 45.833 0.00 0.00 43.47 4.40
216 217 5.277828 GCGCCCATGAAATAGGTAAAGTTAG 60.278 44.000 0.00 0.00 0.00 2.34
235 236 4.067913 CAACAACATGGGGCGCCC 62.068 66.667 38.57 38.57 45.71 6.13
238 239 2.453983 AAATTCAACAACATGGGGCG 57.546 45.000 0.00 0.00 0.00 6.13
266 267 4.278170 CAGCCACAAGTTTATTGGTCTTGA 59.722 41.667 10.41 0.00 40.35 3.02
268 269 3.005791 GCAGCCACAAGTTTATTGGTCTT 59.994 43.478 0.00 0.00 32.50 3.01
277 278 1.318576 GTAGGTGCAGCCACAAGTTT 58.681 50.000 13.29 0.00 43.88 2.66
288 289 2.116238 GGACTAGGGAATGTAGGTGCA 58.884 52.381 0.00 0.00 0.00 4.57
297 298 4.834406 TCATGGAGTAGGACTAGGGAAT 57.166 45.455 0.00 0.00 0.00 3.01
299 300 3.467483 ACATCATGGAGTAGGACTAGGGA 59.533 47.826 0.00 0.00 0.00 4.20
300 301 3.829601 GACATCATGGAGTAGGACTAGGG 59.170 52.174 0.00 0.00 0.00 3.53
301 302 4.474394 TGACATCATGGAGTAGGACTAGG 58.526 47.826 0.00 0.00 0.00 3.02
304 305 6.784473 TCATATTGACATCATGGAGTAGGACT 59.216 38.462 0.00 0.00 0.00 3.85
305 306 6.997655 TCATATTGACATCATGGAGTAGGAC 58.002 40.000 0.00 0.00 0.00 3.85
306 307 6.784473 ACTCATATTGACATCATGGAGTAGGA 59.216 38.462 0.00 0.00 0.00 2.94
307 308 6.872547 CACTCATATTGACATCATGGAGTAGG 59.127 42.308 0.00 0.00 0.00 3.18
308 309 7.384387 CACACTCATATTGACATCATGGAGTAG 59.616 40.741 0.00 0.00 0.00 2.57
309 310 7.212274 CACACTCATATTGACATCATGGAGTA 58.788 38.462 0.00 0.00 0.00 2.59
310 311 6.053650 CACACTCATATTGACATCATGGAGT 58.946 40.000 0.00 0.00 0.00 3.85
311 312 5.049612 GCACACTCATATTGACATCATGGAG 60.050 44.000 0.00 0.00 0.00 3.86
312 313 4.818005 GCACACTCATATTGACATCATGGA 59.182 41.667 0.00 0.00 0.00 3.41
313 314 4.023450 GGCACACTCATATTGACATCATGG 60.023 45.833 0.00 0.00 0.00 3.66
314 315 4.820173 AGGCACACTCATATTGACATCATG 59.180 41.667 0.00 0.00 0.00 3.07
315 316 5.045012 AGGCACACTCATATTGACATCAT 57.955 39.130 0.00 0.00 0.00 2.45
316 317 4.492494 AGGCACACTCATATTGACATCA 57.508 40.909 0.00 0.00 0.00 3.07
317 318 6.707608 TGATTAGGCACACTCATATTGACATC 59.292 38.462 0.00 0.00 0.00 3.06
318 319 6.594744 TGATTAGGCACACTCATATTGACAT 58.405 36.000 0.00 0.00 0.00 3.06
319 320 5.988287 TGATTAGGCACACTCATATTGACA 58.012 37.500 0.00 0.00 0.00 3.58
320 321 6.925610 TTGATTAGGCACACTCATATTGAC 57.074 37.500 0.00 0.00 0.00 3.18
321 322 6.016860 GCATTGATTAGGCACACTCATATTGA 60.017 38.462 0.00 0.00 0.00 2.57
322 323 6.147581 GCATTGATTAGGCACACTCATATTG 58.852 40.000 0.00 0.00 0.00 1.90
324 325 4.763793 GGCATTGATTAGGCACACTCATAT 59.236 41.667 0.00 0.00 0.00 1.78
337 338 2.092699 TGTCGTCATGGGGCATTGATTA 60.093 45.455 0.00 0.00 0.00 1.75
341 342 1.105457 ATTGTCGTCATGGGGCATTG 58.895 50.000 0.00 0.00 0.00 2.82
342 343 1.105457 CATTGTCGTCATGGGGCATT 58.895 50.000 0.00 0.00 0.00 3.56
345 346 0.676466 TGTCATTGTCGTCATGGGGC 60.676 55.000 0.00 0.00 0.00 5.80
346 347 1.942657 GATGTCATTGTCGTCATGGGG 59.057 52.381 0.00 0.00 0.00 4.96
348 349 3.060070 CGATGATGTCATTGTCGTCATGG 60.060 47.826 19.01 15.07 40.30 3.66
350 351 4.045636 TCGATGATGTCATTGTCGTCAT 57.954 40.909 15.49 15.49 42.09 3.06
351 352 3.128589 TCTCGATGATGTCATTGTCGTCA 59.871 43.478 15.83 8.00 38.57 4.35
352 353 3.695816 TCTCGATGATGTCATTGTCGTC 58.304 45.455 15.83 3.37 38.57 4.20
353 354 3.782889 TCTCGATGATGTCATTGTCGT 57.217 42.857 15.83 0.00 38.57 4.34
375 376 5.189342 TGCCCCATCATGTCAATGTAATTTT 59.811 36.000 0.00 0.00 31.22 1.82
376 377 4.715792 TGCCCCATCATGTCAATGTAATTT 59.284 37.500 0.00 0.00 31.22 1.82
377 378 4.288398 TGCCCCATCATGTCAATGTAATT 58.712 39.130 0.00 0.00 36.63 1.40
380 381 3.598693 ATGCCCCATCATGTCAATGTA 57.401 42.857 0.00 0.00 35.15 2.29
381 382 2.464796 ATGCCCCATCATGTCAATGT 57.535 45.000 0.00 0.00 35.15 2.71
382 383 3.830744 AAATGCCCCATCATGTCAATG 57.169 42.857 0.00 0.00 34.88 2.82
383 384 4.225492 TGAAAAATGCCCCATCATGTCAAT 59.775 37.500 0.00 0.00 0.00 2.57
384 385 3.581770 TGAAAAATGCCCCATCATGTCAA 59.418 39.130 0.00 0.00 0.00 3.18
386 387 3.055963 TGTGAAAAATGCCCCATCATGTC 60.056 43.478 0.00 0.00 0.00 3.06
388 389 3.613494 TGTGAAAAATGCCCCATCATG 57.387 42.857 0.00 0.00 0.00 3.07
389 390 4.225492 TCAATGTGAAAAATGCCCCATCAT 59.775 37.500 0.00 0.00 0.00 2.45
390 391 3.581770 TCAATGTGAAAAATGCCCCATCA 59.418 39.130 0.00 0.00 0.00 3.07
391 392 3.934579 GTCAATGTGAAAAATGCCCCATC 59.065 43.478 0.00 0.00 0.00 3.51
392 393 3.327172 TGTCAATGTGAAAAATGCCCCAT 59.673 39.130 0.00 0.00 0.00 4.00
393 394 2.702478 TGTCAATGTGAAAAATGCCCCA 59.298 40.909 0.00 0.00 0.00 4.96
394 395 3.399440 TGTCAATGTGAAAAATGCCCC 57.601 42.857 0.00 0.00 0.00 5.80
395 396 4.567971 TGATGTCAATGTGAAAAATGCCC 58.432 39.130 0.00 0.00 0.00 5.36
396 397 5.064198 CCATGATGTCAATGTGAAAAATGCC 59.936 40.000 0.00 0.00 0.00 4.40
398 399 5.583061 CCCCATGATGTCAATGTGAAAAATG 59.417 40.000 0.00 0.00 0.00 2.32
399 400 5.338544 CCCCCATGATGTCAATGTGAAAAAT 60.339 40.000 0.00 0.00 0.00 1.82
400 401 4.020396 CCCCCATGATGTCAATGTGAAAAA 60.020 41.667 0.00 0.00 0.00 1.94
402 403 3.098377 CCCCCATGATGTCAATGTGAAA 58.902 45.455 0.00 0.00 0.00 2.69
403 404 2.042842 ACCCCCATGATGTCAATGTGAA 59.957 45.455 0.00 0.00 0.00 3.18
404 405 1.640149 ACCCCCATGATGTCAATGTGA 59.360 47.619 0.00 0.00 0.00 3.58
407 408 2.428171 GACAACCCCCATGATGTCAATG 59.572 50.000 0.00 0.00 41.35 2.82
408 409 2.624029 GGACAACCCCCATGATGTCAAT 60.624 50.000 0.00 0.00 43.02 2.57
409 410 1.272425 GGACAACCCCCATGATGTCAA 60.272 52.381 0.00 0.00 43.02 3.18
410 411 0.331278 GGACAACCCCCATGATGTCA 59.669 55.000 0.00 0.00 43.02 3.58
411 412 0.625849 AGGACAACCCCCATGATGTC 59.374 55.000 0.00 0.90 41.06 3.06
413 414 0.464373 CGAGGACAACCCCCATGATG 60.464 60.000 0.00 0.00 36.73 3.07
414 415 0.914417 ACGAGGACAACCCCCATGAT 60.914 55.000 0.00 0.00 36.73 2.45
416 417 1.377202 CACGAGGACAACCCCCATG 60.377 63.158 0.00 0.00 36.73 3.66
417 418 3.077907 CACGAGGACAACCCCCAT 58.922 61.111 0.00 0.00 36.73 4.00
418 419 3.948719 GCACGAGGACAACCCCCA 61.949 66.667 0.00 0.00 36.73 4.96
482 918 0.180406 GGACGGCATATCTGGTGGTT 59.820 55.000 0.00 0.00 0.00 3.67
543 985 0.994247 ATGATGGTGGAGTTGGCTCA 59.006 50.000 0.00 0.00 43.37 4.26
636 1078 2.800544 TGCGCAAACTTAGAGTCTTCAC 59.199 45.455 8.16 0.00 0.00 3.18
663 1105 3.564511 GCTCATGAAGCGAGTCTATCTC 58.435 50.000 0.00 0.00 42.21 2.75
689 1131 5.490139 AAATCGTCATATTCACAGCCTTG 57.510 39.130 0.00 0.00 0.00 3.61
698 1140 6.848296 GCAACTCTAGCAAAATCGTCATATTC 59.152 38.462 0.00 0.00 0.00 1.75
742 1185 1.153061 ATCGGGCTCCATCCTCGTA 59.847 57.895 0.00 0.00 0.00 3.43
749 1192 1.207791 ACTCTTTCATCGGGCTCCAT 58.792 50.000 0.00 0.00 0.00 3.41
1312 1794 1.497991 CAGCGGAAGAACTCAAACGA 58.502 50.000 0.00 0.00 0.00 3.85
1317 1799 2.347490 GCCCAGCGGAAGAACTCA 59.653 61.111 0.00 0.00 0.00 3.41
1371 1853 1.009829 GGCTCAGCATTTCGTCGAAT 58.990 50.000 8.78 0.00 0.00 3.34
1874 2383 5.070981 GTGATCTGATCTGGAAATAGACCCA 59.929 44.000 17.82 0.00 0.00 4.51
1894 2403 8.953313 CACATGGATAAGCATGTTATATGTGAT 58.047 33.333 21.61 0.00 43.16 3.06
1953 2462 3.430453 CTCTGACTCCCTCAAGAACTCT 58.570 50.000 0.00 0.00 0.00 3.24
2042 2551 0.255318 CTCCTTTGCCTCAGCCATCT 59.745 55.000 0.00 0.00 38.69 2.90
2139 2648 3.364549 TGCTTGATCAATTTCCCCGATT 58.635 40.909 8.96 0.00 0.00 3.34
2395 2904 3.510531 AGTGGGAAAGAAACCCTTCTC 57.489 47.619 0.00 0.00 46.82 2.87
2558 3067 1.009997 TGATTCCAAATCCCCCTGCT 58.990 50.000 0.00 0.00 0.00 4.24
2580 3089 4.780815 ACAAGTCATCCAACAAAGACAGA 58.219 39.130 0.00 0.00 33.56 3.41
2710 3219 6.901300 ACAAGTGTAGGGACAATTCCTCTATA 59.099 38.462 0.00 0.00 41.75 1.31
2775 3284 5.655488 AGATCGAGTAATTCTTCCACTGTG 58.345 41.667 0.00 0.00 0.00 3.66
2881 3390 4.431809 CTGAGGAGACTGTAAGCTTCATG 58.568 47.826 0.00 0.00 44.43 3.07
3241 3848 6.224584 AGAAAGTGAGTAAGCTTTCCAGTAC 58.775 40.000 3.20 0.00 46.92 2.73
3341 3951 4.079253 GGTTGTGGATAAGTTGGTGACAT 58.921 43.478 0.00 0.00 42.32 3.06
3356 3966 2.086869 CAGTCTATTGGCTGGTTGTGG 58.913 52.381 0.35 0.00 0.00 4.17
3396 4006 6.464222 TGTTCAGTAGTTGCAGCTAACTAAT 58.536 36.000 12.24 7.03 42.82 1.73
3449 4069 2.580322 TCATTATGGACCAAGCCCTTGA 59.420 45.455 9.50 0.00 42.93 3.02
3766 4386 1.148273 GCCCTGGATGCCGATGTTA 59.852 57.895 0.00 0.00 0.00 2.41
3826 4447 9.900710 CATCACAAAGGACTATACTACATAGTC 57.099 37.037 13.59 13.59 45.91 2.59
3850 4471 4.167268 GAGAAGACGTCGTTTCTAAGCAT 58.833 43.478 17.24 0.00 33.97 3.79
3956 4577 1.039068 CTGGCAAACAACACCCATCA 58.961 50.000 0.00 0.00 0.00 3.07
4218 4839 0.171231 CGAGCCACGAGATGAAGACA 59.829 55.000 0.00 0.00 45.77 3.41
4219 4840 1.142778 GCGAGCCACGAGATGAAGAC 61.143 60.000 5.11 0.00 45.77 3.01
4245 4866 1.152694 AAGGCCAAAGCTGAGCACA 60.153 52.632 7.39 0.00 39.73 4.57
4275 4896 2.562298 CCAAGAGAAGCTCAGAGTCAGT 59.438 50.000 0.00 0.00 32.06 3.41


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

AutoCloner maintained by Alex Coulton.