Multiple sequence alignment - TraesCS2A01G252000

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 TraesCS2A01G252000 chr2A 100.000 3242 0 0 1 3242 382862258 382859017 0.000000e+00 5987
1 TraesCS2A01G252000 chr2A 95.856 2172 80 7 1074 3242 77797275 77799439 0.000000e+00 3504
2 TraesCS2A01G252000 chr2A 95.291 722 34 0 318 1039 77796263 77796984 0.000000e+00 1146
3 TraesCS2A01G252000 chr2A 93.691 317 18 2 3 317 225651844 225652160 1.050000e-129 473
4 TraesCS2A01G252000 chr1D 93.509 2927 180 4 318 3242 176354849 176357767 0.000000e+00 4344
5 TraesCS2A01G252000 chr1D 93.300 2179 124 4 1068 3242 356876055 356878215 0.000000e+00 3195
6 TraesCS2A01G252000 chr1D 93.906 722 44 0 318 1039 356874944 356875665 0.000000e+00 1090
7 TraesCS2A01G252000 chr2B 95.948 2172 81 3 1077 3242 325632258 325634428 0.000000e+00 3517
8 TraesCS2A01G252000 chr2B 94.652 748 40 0 318 1065 325631288 325632035 0.000000e+00 1160
9 TraesCS2A01G252000 chr2B 94.014 735 43 1 416 1150 484091058 484091791 0.000000e+00 1112
10 TraesCS2A01G252000 chr6B 85.106 2914 405 26 340 3238 583178905 583181804 0.000000e+00 2950
11 TraesCS2A01G252000 chr4B 85.033 2893 410 15 359 3241 460992903 460995782 0.000000e+00 2922
12 TraesCS2A01G252000 chr4B 86.431 2152 279 9 1090 3232 245677509 245675362 0.000000e+00 2344
13 TraesCS2A01G252000 chr6D 94.013 1904 109 4 1344 3242 452076331 452074428 0.000000e+00 2880
14 TraesCS2A01G252000 chr6A 94.869 1793 83 4 1081 2864 359014226 359012434 0.000000e+00 2793
15 TraesCS2A01G252000 chr6A 95.478 575 26 0 453 1027 359015081 359014507 0.000000e+00 918
16 TraesCS2A01G252000 chr6A 93.438 320 18 3 1 317 62536983 62537302 3.790000e-129 472
17 TraesCS2A01G252000 chr7A 94.537 1263 69 0 318 1580 439780237 439781499 0.000000e+00 1951
18 TraesCS2A01G252000 chr4D 94.340 318 16 2 1 317 437804917 437805233 1.350000e-133 486
19 TraesCS2A01G252000 chr4D 93.417 319 19 2 1 317 57748115 57748433 3.790000e-129 472
20 TraesCS2A01G252000 chr7D 94.375 320 11 6 1 317 434050923 434051238 4.860000e-133 484
21 TraesCS2A01G252000 chr5A 94.025 318 17 2 2 317 165432790 165432473 6.290000e-132 481
22 TraesCS2A01G252000 chr1A 94.025 318 16 3 1 317 508762875 508762560 2.260000e-131 479
23 TraesCS2A01G252000 chr3D 93.711 318 18 2 1 317 58269772 58270088 2.930000e-130 475
24 TraesCS2A01G252000 chr2D 93.711 318 19 1 1 317 403280920 403281237 2.930000e-130 475


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 TraesCS2A01G252000 chr2A 382859017 382862258 3241 True 5987.0 5987 100.0000 1 3242 1 chr2A.!!$R1 3241
1 TraesCS2A01G252000 chr2A 77796263 77799439 3176 False 2325.0 3504 95.5735 318 3242 2 chr2A.!!$F2 2924
2 TraesCS2A01G252000 chr1D 176354849 176357767 2918 False 4344.0 4344 93.5090 318 3242 1 chr1D.!!$F1 2924
3 TraesCS2A01G252000 chr1D 356874944 356878215 3271 False 2142.5 3195 93.6030 318 3242 2 chr1D.!!$F2 2924
4 TraesCS2A01G252000 chr2B 325631288 325634428 3140 False 2338.5 3517 95.3000 318 3242 2 chr2B.!!$F2 2924
5 TraesCS2A01G252000 chr2B 484091058 484091791 733 False 1112.0 1112 94.0140 416 1150 1 chr2B.!!$F1 734
6 TraesCS2A01G252000 chr6B 583178905 583181804 2899 False 2950.0 2950 85.1060 340 3238 1 chr6B.!!$F1 2898
7 TraesCS2A01G252000 chr4B 460992903 460995782 2879 False 2922.0 2922 85.0330 359 3241 1 chr4B.!!$F1 2882
8 TraesCS2A01G252000 chr4B 245675362 245677509 2147 True 2344.0 2344 86.4310 1090 3232 1 chr4B.!!$R1 2142
9 TraesCS2A01G252000 chr6D 452074428 452076331 1903 True 2880.0 2880 94.0130 1344 3242 1 chr6D.!!$R1 1898
10 TraesCS2A01G252000 chr6A 359012434 359015081 2647 True 1855.5 2793 95.1735 453 2864 2 chr6A.!!$R1 2411
11 TraesCS2A01G252000 chr7A 439780237 439781499 1262 False 1951.0 1951 94.5370 318 1580 1 chr7A.!!$F1 1262

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
68 69 0.392461 TCATGCCCAAGTTACGCCTC 60.392 55.0 0.00 0.0 0.0 4.70 F
251 252 0.401541 GGGCCCCCTCTGGTAGTTAT 60.402 60.0 12.23 0.0 0.0 1.89 F
1102 1465 0.683504 ATCGACGGGTACTTGCTCCT 60.684 55.0 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2137 0.675633 GAAGTGTGGCCAACAATGCT 59.324 50.000 7.24 0.00 41.57 3.79 R
1978 2347 1.198759 ACGGTAGTGGCCACCTTGAT 61.199 55.000 32.29 16.04 33.62 2.57 R
2329 2708 1.201414 CCCGGTTGGAAAAGAAATCCG 59.799 52.381 0.00 0.00 39.98 4.18 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
23 24 4.024545 GAAGTTCCCCCGGCGGAA 62.025 66.667 30.79 16.85 39.67 4.30
24 25 3.335729 AAGTTCCCCCGGCGGAAT 61.336 61.111 30.79 6.01 43.72 3.01
25 26 3.339738 AAGTTCCCCCGGCGGAATC 62.340 63.158 30.79 15.97 43.72 2.52
37 38 2.279784 GGAATCGCTCCGCCAGAG 60.280 66.667 0.00 0.00 46.29 3.35
38 39 2.279784 GAATCGCTCCGCCAGAGG 60.280 66.667 0.94 0.00 43.46 3.69
59 60 2.074547 CAAAAGTGCTCATGCCCAAG 57.925 50.000 0.00 0.00 38.71 3.61
60 61 1.342174 CAAAAGTGCTCATGCCCAAGT 59.658 47.619 0.00 0.00 38.71 3.16
61 62 1.708341 AAAGTGCTCATGCCCAAGTT 58.292 45.000 0.00 0.00 38.71 2.66
62 63 2.584835 AAGTGCTCATGCCCAAGTTA 57.415 45.000 0.00 0.00 38.71 2.24
63 64 1.826385 AGTGCTCATGCCCAAGTTAC 58.174 50.000 0.00 0.00 38.71 2.50
64 65 0.447801 GTGCTCATGCCCAAGTTACG 59.552 55.000 0.00 0.00 38.71 3.18
65 66 1.305219 TGCTCATGCCCAAGTTACGC 61.305 55.000 0.00 0.00 38.71 4.42
66 67 1.993369 GCTCATGCCCAAGTTACGCC 61.993 60.000 0.00 0.00 0.00 5.68
67 68 0.392998 CTCATGCCCAAGTTACGCCT 60.393 55.000 0.00 0.00 0.00 5.52
68 69 0.392461 TCATGCCCAAGTTACGCCTC 60.392 55.000 0.00 0.00 0.00 4.70
69 70 1.449601 ATGCCCAAGTTACGCCTCG 60.450 57.895 0.00 0.00 0.00 4.63
70 71 1.895020 ATGCCCAAGTTACGCCTCGA 61.895 55.000 0.00 0.00 0.00 4.04
71 72 1.810030 GCCCAAGTTACGCCTCGAG 60.810 63.158 5.13 5.13 0.00 4.04
72 73 1.888018 CCCAAGTTACGCCTCGAGA 59.112 57.895 15.71 0.00 0.00 4.04
73 74 0.458025 CCCAAGTTACGCCTCGAGAC 60.458 60.000 15.71 0.00 0.00 3.36
74 75 0.797249 CCAAGTTACGCCTCGAGACG 60.797 60.000 19.98 19.98 0.00 4.18
75 76 0.797249 CAAGTTACGCCTCGAGACGG 60.797 60.000 24.88 10.54 0.00 4.79
76 77 2.539263 AAGTTACGCCTCGAGACGGC 62.539 60.000 24.88 14.79 44.11 5.68
95 96 4.736896 GCGCTCCGTCCCGAAAGT 62.737 66.667 0.00 0.00 0.00 2.66
96 97 2.506438 CGCTCCGTCCCGAAAGTC 60.506 66.667 0.00 0.00 0.00 3.01
97 98 2.125633 GCTCCGTCCCGAAAGTCC 60.126 66.667 0.00 0.00 0.00 3.85
98 99 2.647158 GCTCCGTCCCGAAAGTCCT 61.647 63.158 0.00 0.00 0.00 3.85
99 100 1.511768 CTCCGTCCCGAAAGTCCTC 59.488 63.158 0.00 0.00 0.00 3.71
100 101 1.946475 CTCCGTCCCGAAAGTCCTCC 61.946 65.000 0.00 0.00 0.00 4.30
101 102 2.577593 CGTCCCGAAAGTCCTCCC 59.422 66.667 0.00 0.00 0.00 4.30
102 103 2.987962 GTCCCGAAAGTCCTCCCC 59.012 66.667 0.00 0.00 0.00 4.81
103 104 1.612739 GTCCCGAAAGTCCTCCCCT 60.613 63.158 0.00 0.00 0.00 4.79
104 105 1.160145 TCCCGAAAGTCCTCCCCTT 59.840 57.895 0.00 0.00 0.00 3.95
105 106 0.414629 TCCCGAAAGTCCTCCCCTTA 59.585 55.000 0.00 0.00 0.00 2.69
106 107 0.540454 CCCGAAAGTCCTCCCCTTAC 59.460 60.000 0.00 0.00 0.00 2.34
107 108 1.569653 CCGAAAGTCCTCCCCTTACT 58.430 55.000 0.00 0.00 0.00 2.24
108 109 1.907255 CCGAAAGTCCTCCCCTTACTT 59.093 52.381 0.00 0.00 35.01 2.24
109 110 2.305052 CCGAAAGTCCTCCCCTTACTTT 59.695 50.000 0.00 0.00 44.05 2.66
110 111 3.244805 CCGAAAGTCCTCCCCTTACTTTT 60.245 47.826 0.00 0.00 42.06 2.27
111 112 4.395625 CGAAAGTCCTCCCCTTACTTTTT 58.604 43.478 0.00 0.00 42.06 1.94
206 207 4.517934 CCTGGGCTCCCTGGCATG 62.518 72.222 16.54 0.00 45.84 4.06
232 233 2.912025 GGTTGTGCCCACCTGGTG 60.912 66.667 20.01 20.01 36.04 4.17
246 247 4.752594 GGTGGGCCCCCTCTGGTA 62.753 72.222 22.27 0.00 36.94 3.25
247 248 3.090532 GTGGGCCCCCTCTGGTAG 61.091 72.222 22.27 0.00 36.94 3.18
248 249 3.622263 TGGGCCCCCTCTGGTAGT 61.622 66.667 22.27 0.00 36.94 2.73
249 250 2.286197 GGGCCCCCTCTGGTAGTT 60.286 66.667 12.23 0.00 0.00 2.24
250 251 1.003835 GGGCCCCCTCTGGTAGTTA 59.996 63.158 12.23 0.00 0.00 2.24
251 252 0.401541 GGGCCCCCTCTGGTAGTTAT 60.402 60.000 12.23 0.00 0.00 1.89
252 253 1.519498 GGCCCCCTCTGGTAGTTATT 58.481 55.000 0.00 0.00 0.00 1.40
253 254 1.850998 GGCCCCCTCTGGTAGTTATTT 59.149 52.381 0.00 0.00 0.00 1.40
254 255 2.422945 GGCCCCCTCTGGTAGTTATTTG 60.423 54.545 0.00 0.00 0.00 2.32
255 256 2.932261 CCCCCTCTGGTAGTTATTTGC 58.068 52.381 0.00 0.00 0.00 3.68
256 257 2.509964 CCCCCTCTGGTAGTTATTTGCT 59.490 50.000 0.00 0.00 0.00 3.91
257 258 3.433740 CCCCCTCTGGTAGTTATTTGCTC 60.434 52.174 0.00 0.00 0.00 4.26
258 259 3.433740 CCCCTCTGGTAGTTATTTGCTCC 60.434 52.174 0.00 0.00 0.00 4.70
259 260 3.199946 CCCTCTGGTAGTTATTTGCTCCA 59.800 47.826 0.00 0.00 0.00 3.86
260 261 4.324254 CCCTCTGGTAGTTATTTGCTCCAA 60.324 45.833 0.00 0.00 0.00 3.53
261 262 5.440610 CCTCTGGTAGTTATTTGCTCCAAT 58.559 41.667 0.00 0.00 0.00 3.16
262 263 5.297776 CCTCTGGTAGTTATTTGCTCCAATG 59.702 44.000 0.00 0.00 0.00 2.82
263 264 6.061022 TCTGGTAGTTATTTGCTCCAATGA 57.939 37.500 0.00 0.00 0.00 2.57
264 265 5.880332 TCTGGTAGTTATTTGCTCCAATGAC 59.120 40.000 0.00 0.00 0.00 3.06
265 266 5.815581 TGGTAGTTATTTGCTCCAATGACT 58.184 37.500 6.54 6.54 0.00 3.41
266 267 5.880332 TGGTAGTTATTTGCTCCAATGACTC 59.120 40.000 5.09 0.53 0.00 3.36
267 268 6.116126 GGTAGTTATTTGCTCCAATGACTCT 58.884 40.000 5.09 0.00 0.00 3.24
268 269 6.599638 GGTAGTTATTTGCTCCAATGACTCTT 59.400 38.462 5.09 0.00 0.00 2.85
269 270 7.769044 GGTAGTTATTTGCTCCAATGACTCTTA 59.231 37.037 5.09 0.00 0.00 2.10
270 271 9.162764 GTAGTTATTTGCTCCAATGACTCTTAA 57.837 33.333 5.09 0.00 0.00 1.85
271 272 8.635765 AGTTATTTGCTCCAATGACTCTTAAA 57.364 30.769 0.00 0.00 0.00 1.52
272 273 9.247861 AGTTATTTGCTCCAATGACTCTTAAAT 57.752 29.630 0.00 0.00 0.00 1.40
277 278 7.807977 TGCTCCAATGACTCTTAAATAATCC 57.192 36.000 0.00 0.00 0.00 3.01
278 279 7.345691 TGCTCCAATGACTCTTAAATAATCCA 58.654 34.615 0.00 0.00 0.00 3.41
279 280 8.000709 TGCTCCAATGACTCTTAAATAATCCAT 58.999 33.333 0.00 0.00 0.00 3.41
280 281 9.507329 GCTCCAATGACTCTTAAATAATCCATA 57.493 33.333 0.00 0.00 0.00 2.74
296 297 9.872684 AATAATCCATACAAATCTCCATGAAGT 57.127 29.630 0.00 0.00 0.00 3.01
297 298 9.872684 ATAATCCATACAAATCTCCATGAAGTT 57.127 29.630 0.00 0.00 0.00 2.66
298 299 8.599624 AATCCATACAAATCTCCATGAAGTTT 57.400 30.769 0.00 0.00 0.00 2.66
299 300 8.599624 ATCCATACAAATCTCCATGAAGTTTT 57.400 30.769 0.00 0.00 0.00 2.43
300 301 9.699410 ATCCATACAAATCTCCATGAAGTTTTA 57.301 29.630 0.00 0.00 0.00 1.52
301 302 9.177608 TCCATACAAATCTCCATGAAGTTTTAG 57.822 33.333 0.00 0.00 0.00 1.85
302 303 7.917505 CCATACAAATCTCCATGAAGTTTTAGC 59.082 37.037 0.00 0.00 0.00 3.09
303 304 8.680903 CATACAAATCTCCATGAAGTTTTAGCT 58.319 33.333 0.00 0.00 0.00 3.32
304 305 7.530426 ACAAATCTCCATGAAGTTTTAGCTT 57.470 32.000 0.00 0.00 0.00 3.74
305 306 7.373493 ACAAATCTCCATGAAGTTTTAGCTTG 58.627 34.615 0.00 0.00 0.00 4.01
306 307 7.014615 ACAAATCTCCATGAAGTTTTAGCTTGT 59.985 33.333 0.00 0.00 0.00 3.16
307 308 7.530426 AATCTCCATGAAGTTTTAGCTTGTT 57.470 32.000 0.00 0.00 0.00 2.83
308 309 6.959639 TCTCCATGAAGTTTTAGCTTGTTT 57.040 33.333 0.00 0.00 0.00 2.83
309 310 6.738114 TCTCCATGAAGTTTTAGCTTGTTTG 58.262 36.000 0.00 0.00 0.00 2.93
310 311 5.841810 TCCATGAAGTTTTAGCTTGTTTGG 58.158 37.500 0.00 0.00 0.00 3.28
311 312 5.596361 TCCATGAAGTTTTAGCTTGTTTGGA 59.404 36.000 0.00 0.00 31.05 3.53
312 313 5.922544 CCATGAAGTTTTAGCTTGTTTGGAG 59.077 40.000 0.00 0.00 0.00 3.86
313 314 6.461509 CCATGAAGTTTTAGCTTGTTTGGAGT 60.462 38.462 0.00 0.00 0.00 3.85
314 315 6.524101 TGAAGTTTTAGCTTGTTTGGAGTT 57.476 33.333 0.00 0.00 0.00 3.01
315 316 6.329496 TGAAGTTTTAGCTTGTTTGGAGTTG 58.671 36.000 0.00 0.00 0.00 3.16
316 317 5.914898 AGTTTTAGCTTGTTTGGAGTTGT 57.085 34.783 0.00 0.00 0.00 3.32
322 323 2.360801 GCTTGTTTGGAGTTGTAAGGCA 59.639 45.455 0.00 0.00 0.00 4.75
330 331 2.436417 GAGTTGTAAGGCAATCTGGCA 58.564 47.619 2.87 0.00 46.46 4.92
331 332 2.819608 GAGTTGTAAGGCAATCTGGCAA 59.180 45.455 2.87 0.00 46.46 4.52
338 339 1.027357 GGCAATCTGGCAACGATGAT 58.973 50.000 0.00 0.00 43.14 2.45
346 347 1.718757 GGCAACGATGATGGGTGAGC 61.719 60.000 0.00 0.00 0.00 4.26
463 464 3.941483 GCAAATCAAGGAAAGATCGAGGA 59.059 43.478 0.00 0.00 0.00 3.71
464 465 4.396166 GCAAATCAAGGAAAGATCGAGGAA 59.604 41.667 0.00 0.00 0.00 3.36
551 552 0.890683 GCTAATTTGCTGGCAGGTGT 59.109 50.000 17.64 0.00 0.00 4.16
603 604 3.782443 GGATCGACCGTGCCCCTT 61.782 66.667 0.00 0.00 0.00 3.95
964 965 3.107402 AGCACACCCATCTTCTCTCTA 57.893 47.619 0.00 0.00 0.00 2.43
1102 1465 0.683504 ATCGACGGGTACTTGCTCCT 60.684 55.000 0.00 0.00 0.00 3.69
1108 1471 2.572284 GTACTTGCTCCTCGCCGT 59.428 61.111 0.00 0.00 38.05 5.68
1175 1538 1.212616 CCGAGTTCGATGATTCTGGC 58.787 55.000 2.59 0.00 43.02 4.85
1286 1649 1.918957 CTCCCCTTTCCAGGTCAATCT 59.081 52.381 0.00 0.00 38.79 2.40
1300 1663 3.307691 GGTCAATCTGAGGGTCATTGTCA 60.308 47.826 0.00 0.00 0.00 3.58
1533 1896 0.685097 CCATATGGGTCCAGGTACGG 59.315 60.000 14.52 0.00 0.00 4.02
1547 1910 1.270147 GGTACGGGATCTTCCATTCGG 60.270 57.143 0.00 0.00 38.64 4.30
1650 2013 3.958018 TGTTGATAAATACCTGCGGGTT 58.042 40.909 25.37 7.71 44.73 4.11
1774 2137 2.691526 CCCCTATACTGCGAGTGTTGTA 59.308 50.000 0.00 0.00 0.00 2.41
1978 2347 2.350895 CCAAGCCCATGGACGTCA 59.649 61.111 18.91 3.91 43.54 4.35
1993 2362 0.249120 CGTCATCAAGGTGGCCACTA 59.751 55.000 33.91 17.95 0.00 2.74
2329 2708 4.021719 CCAAATCATGGGGCTAATGATGAC 60.022 45.833 13.64 0.00 46.27 3.06
2344 2723 6.588719 AATGATGACGGATTTCTTTTCCAA 57.411 33.333 0.00 0.00 32.45 3.53
2736 3120 6.419413 CGTTACAAAGGAGATAGATGAGAAGC 59.581 42.308 0.00 0.00 0.00 3.86
2887 3271 1.300620 CTCCAACACGGCAGTTCGA 60.301 57.895 0.00 0.00 33.14 3.71
3163 3552 3.222603 GGGCTTTTATGGTCATCCGAAT 58.777 45.455 0.00 0.00 36.30 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.024545 TTCCGCCGGGGGAACTTC 62.025 66.667 40.65 5.07 41.08 3.01
46 47 1.305219 GCGTAACTTGGGCATGAGCA 61.305 55.000 0.00 0.00 44.61 4.26
47 48 1.429423 GCGTAACTTGGGCATGAGC 59.571 57.895 0.00 0.00 41.10 4.26
48 49 0.392998 AGGCGTAACTTGGGCATGAG 60.393 55.000 0.00 0.00 0.00 2.90
49 50 0.392461 GAGGCGTAACTTGGGCATGA 60.392 55.000 0.00 0.00 0.00 3.07
50 51 1.705337 CGAGGCGTAACTTGGGCATG 61.705 60.000 0.00 0.00 0.00 4.06
51 52 1.449601 CGAGGCGTAACTTGGGCAT 60.450 57.895 0.00 0.00 0.00 4.40
52 53 2.047655 CGAGGCGTAACTTGGGCA 60.048 61.111 0.00 0.00 0.00 5.36
53 54 1.810030 CTCGAGGCGTAACTTGGGC 60.810 63.158 3.91 0.00 0.00 5.36
54 55 0.458025 GTCTCGAGGCGTAACTTGGG 60.458 60.000 13.56 0.00 0.00 4.12
55 56 0.797249 CGTCTCGAGGCGTAACTTGG 60.797 60.000 30.28 0.09 0.00 3.61
56 57 0.797249 CCGTCTCGAGGCGTAACTTG 60.797 60.000 34.54 16.79 0.00 3.16
57 58 1.505353 CCGTCTCGAGGCGTAACTT 59.495 57.895 34.54 0.00 0.00 2.66
58 59 3.048941 GCCGTCTCGAGGCGTAACT 62.049 63.158 34.54 0.00 45.58 2.24
59 60 2.578981 GCCGTCTCGAGGCGTAAC 60.579 66.667 34.54 21.25 45.58 2.50
85 86 1.199425 AAGGGGAGGACTTTCGGGAC 61.199 60.000 0.00 0.00 0.00 4.46
86 87 0.414629 TAAGGGGAGGACTTTCGGGA 59.585 55.000 0.00 0.00 0.00 5.14
87 88 0.540454 GTAAGGGGAGGACTTTCGGG 59.460 60.000 0.00 0.00 0.00 5.14
88 89 1.569653 AGTAAGGGGAGGACTTTCGG 58.430 55.000 0.00 0.00 0.00 4.30
89 90 3.697619 AAAGTAAGGGGAGGACTTTCG 57.302 47.619 0.00 0.00 38.70 3.46
121 122 8.860088 GCCCATCTTTTGGTATATAAGTCATTT 58.140 33.333 0.00 0.00 44.83 2.32
122 123 8.004215 TGCCCATCTTTTGGTATATAAGTCATT 58.996 33.333 0.00 0.00 44.83 2.57
123 124 7.448469 GTGCCCATCTTTTGGTATATAAGTCAT 59.552 37.037 0.00 0.00 44.83 3.06
124 125 6.770785 GTGCCCATCTTTTGGTATATAAGTCA 59.229 38.462 0.00 0.00 44.83 3.41
125 126 6.206829 GGTGCCCATCTTTTGGTATATAAGTC 59.793 42.308 0.00 0.00 44.83 3.01
126 127 6.068670 GGTGCCCATCTTTTGGTATATAAGT 58.931 40.000 0.00 0.00 44.83 2.24
127 128 5.181245 CGGTGCCCATCTTTTGGTATATAAG 59.819 44.000 0.00 0.00 44.83 1.73
128 129 5.067273 CGGTGCCCATCTTTTGGTATATAA 58.933 41.667 0.00 0.00 44.83 0.98
129 130 4.505918 CCGGTGCCCATCTTTTGGTATATA 60.506 45.833 0.00 0.00 44.83 0.86
130 131 3.486383 CGGTGCCCATCTTTTGGTATAT 58.514 45.455 0.00 0.00 44.83 0.86
131 132 2.422235 CCGGTGCCCATCTTTTGGTATA 60.422 50.000 0.00 0.00 44.83 1.47
132 133 1.684869 CCGGTGCCCATCTTTTGGTAT 60.685 52.381 0.00 0.00 44.83 2.73
133 134 0.322997 CCGGTGCCCATCTTTTGGTA 60.323 55.000 0.00 0.00 44.83 3.25
134 135 1.606313 CCGGTGCCCATCTTTTGGT 60.606 57.895 0.00 0.00 44.83 3.67
135 136 1.304052 TCCGGTGCCCATCTTTTGG 60.304 57.895 0.00 0.00 46.00 3.28
136 137 1.315257 CCTCCGGTGCCCATCTTTTG 61.315 60.000 0.00 0.00 0.00 2.44
137 138 1.000896 CCTCCGGTGCCCATCTTTT 60.001 57.895 0.00 0.00 0.00 2.27
138 139 2.231380 ACCTCCGGTGCCCATCTTT 61.231 57.895 0.00 0.00 32.98 2.52
139 140 2.610859 ACCTCCGGTGCCCATCTT 60.611 61.111 0.00 0.00 32.98 2.40
189 190 4.517934 CATGCCAGGGAGCCCAGG 62.518 72.222 12.39 12.39 44.56 4.45
215 216 2.912025 CACCAGGTGGGCACAACC 60.912 66.667 12.40 0.00 42.05 3.77
229 230 4.752594 TACCAGAGGGGGCCCACC 62.753 72.222 24.36 21.15 42.91 4.61
230 231 3.090532 CTACCAGAGGGGGCCCAC 61.091 72.222 26.86 23.59 42.91 4.61
231 232 1.828602 TAACTACCAGAGGGGGCCCA 61.829 60.000 26.86 0.00 42.91 5.36
232 233 0.401541 ATAACTACCAGAGGGGGCCC 60.402 60.000 15.76 15.76 42.91 5.80
233 234 1.519498 AATAACTACCAGAGGGGGCC 58.481 55.000 0.00 0.00 42.91 5.80
234 235 2.932261 CAAATAACTACCAGAGGGGGC 58.068 52.381 0.00 0.00 42.91 5.80
235 236 2.509964 AGCAAATAACTACCAGAGGGGG 59.490 50.000 0.00 0.00 42.91 5.40
236 237 3.433740 GGAGCAAATAACTACCAGAGGGG 60.434 52.174 0.00 0.00 44.81 4.79
237 238 3.199946 TGGAGCAAATAACTACCAGAGGG 59.800 47.826 0.00 0.00 41.29 4.30
238 239 4.487714 TGGAGCAAATAACTACCAGAGG 57.512 45.455 0.00 0.00 0.00 3.69
239 240 6.037610 GTCATTGGAGCAAATAACTACCAGAG 59.962 42.308 0.00 0.00 0.00 3.35
240 241 5.880332 GTCATTGGAGCAAATAACTACCAGA 59.120 40.000 0.00 0.00 0.00 3.86
241 242 5.882557 AGTCATTGGAGCAAATAACTACCAG 59.117 40.000 0.00 0.00 0.00 4.00
242 243 5.815581 AGTCATTGGAGCAAATAACTACCA 58.184 37.500 0.00 0.00 0.00 3.25
243 244 6.116126 AGAGTCATTGGAGCAAATAACTACC 58.884 40.000 0.00 0.00 0.00 3.18
244 245 7.617041 AAGAGTCATTGGAGCAAATAACTAC 57.383 36.000 0.00 0.00 0.00 2.73
245 246 9.733556 TTTAAGAGTCATTGGAGCAAATAACTA 57.266 29.630 0.00 0.00 0.00 2.24
246 247 8.635765 TTTAAGAGTCATTGGAGCAAATAACT 57.364 30.769 0.00 0.00 0.00 2.24
251 252 8.686334 GGATTATTTAAGAGTCATTGGAGCAAA 58.314 33.333 0.00 0.00 0.00 3.68
252 253 7.833682 TGGATTATTTAAGAGTCATTGGAGCAA 59.166 33.333 0.00 0.00 0.00 3.91
253 254 7.345691 TGGATTATTTAAGAGTCATTGGAGCA 58.654 34.615 0.00 0.00 0.00 4.26
254 255 7.807977 TGGATTATTTAAGAGTCATTGGAGC 57.192 36.000 0.00 0.00 0.00 4.70
270 271 9.872684 ACTTCATGGAGATTTGTATGGATTATT 57.127 29.630 8.39 0.00 0.00 1.40
271 272 9.872684 AACTTCATGGAGATTTGTATGGATTAT 57.127 29.630 8.39 0.00 0.00 1.28
272 273 9.699410 AAACTTCATGGAGATTTGTATGGATTA 57.301 29.630 8.39 0.00 0.00 1.75
273 274 8.599624 AAACTTCATGGAGATTTGTATGGATT 57.400 30.769 8.39 0.00 0.00 3.01
274 275 8.599624 AAAACTTCATGGAGATTTGTATGGAT 57.400 30.769 8.39 0.00 0.00 3.41
275 276 9.177608 CTAAAACTTCATGGAGATTTGTATGGA 57.822 33.333 17.24 0.00 0.00 3.41
276 277 7.917505 GCTAAAACTTCATGGAGATTTGTATGG 59.082 37.037 17.24 5.69 0.00 2.74
277 278 8.680903 AGCTAAAACTTCATGGAGATTTGTATG 58.319 33.333 17.24 7.62 0.00 2.39
278 279 8.814038 AGCTAAAACTTCATGGAGATTTGTAT 57.186 30.769 17.24 2.55 0.00 2.29
279 280 8.514594 CAAGCTAAAACTTCATGGAGATTTGTA 58.485 33.333 17.24 0.25 0.00 2.41
280 281 7.014615 ACAAGCTAAAACTTCATGGAGATTTGT 59.985 33.333 17.24 6.09 0.00 2.83
281 282 7.373493 ACAAGCTAAAACTTCATGGAGATTTG 58.627 34.615 17.24 9.60 0.00 2.32
282 283 7.530426 ACAAGCTAAAACTTCATGGAGATTT 57.470 32.000 8.39 11.31 0.00 2.17
283 284 7.530426 AACAAGCTAAAACTTCATGGAGATT 57.470 32.000 8.39 0.00 0.00 2.40
284 285 7.373493 CAAACAAGCTAAAACTTCATGGAGAT 58.627 34.615 8.39 0.00 0.00 2.75
285 286 6.239008 CCAAACAAGCTAAAACTTCATGGAGA 60.239 38.462 8.39 0.00 30.58 3.71
286 287 5.922544 CCAAACAAGCTAAAACTTCATGGAG 59.077 40.000 0.00 0.00 30.58 3.86
287 288 5.596361 TCCAAACAAGCTAAAACTTCATGGA 59.404 36.000 0.00 0.00 33.55 3.41
288 289 5.841810 TCCAAACAAGCTAAAACTTCATGG 58.158 37.500 0.00 0.00 0.00 3.66
289 290 6.507023 ACTCCAAACAAGCTAAAACTTCATG 58.493 36.000 0.00 0.00 0.00 3.07
290 291 6.715347 ACTCCAAACAAGCTAAAACTTCAT 57.285 33.333 0.00 0.00 0.00 2.57
291 292 6.071616 ACAACTCCAAACAAGCTAAAACTTCA 60.072 34.615 0.00 0.00 0.00 3.02
292 293 6.330278 ACAACTCCAAACAAGCTAAAACTTC 58.670 36.000 0.00 0.00 0.00 3.01
293 294 6.280855 ACAACTCCAAACAAGCTAAAACTT 57.719 33.333 0.00 0.00 0.00 2.66
294 295 5.914898 ACAACTCCAAACAAGCTAAAACT 57.085 34.783 0.00 0.00 0.00 2.66
295 296 6.695713 CCTTACAACTCCAAACAAGCTAAAAC 59.304 38.462 0.00 0.00 0.00 2.43
296 297 6.681865 GCCTTACAACTCCAAACAAGCTAAAA 60.682 38.462 0.00 0.00 0.00 1.52
297 298 5.221165 GCCTTACAACTCCAAACAAGCTAAA 60.221 40.000 0.00 0.00 0.00 1.85
298 299 4.277423 GCCTTACAACTCCAAACAAGCTAA 59.723 41.667 0.00 0.00 0.00 3.09
299 300 3.818773 GCCTTACAACTCCAAACAAGCTA 59.181 43.478 0.00 0.00 0.00 3.32
300 301 2.623416 GCCTTACAACTCCAAACAAGCT 59.377 45.455 0.00 0.00 0.00 3.74
301 302 2.360801 TGCCTTACAACTCCAAACAAGC 59.639 45.455 0.00 0.00 0.00 4.01
302 303 4.647424 TTGCCTTACAACTCCAAACAAG 57.353 40.909 0.00 0.00 31.73 3.16
303 304 4.892934 AGATTGCCTTACAACTCCAAACAA 59.107 37.500 0.00 0.00 42.27 2.83
304 305 4.278170 CAGATTGCCTTACAACTCCAAACA 59.722 41.667 0.00 0.00 42.27 2.83
305 306 4.321230 CCAGATTGCCTTACAACTCCAAAC 60.321 45.833 0.00 0.00 42.27 2.93
306 307 3.826157 CCAGATTGCCTTACAACTCCAAA 59.174 43.478 0.00 0.00 42.27 3.28
307 308 3.420893 CCAGATTGCCTTACAACTCCAA 58.579 45.455 0.00 0.00 42.27 3.53
308 309 2.879756 GCCAGATTGCCTTACAACTCCA 60.880 50.000 0.00 0.00 42.27 3.86
309 310 1.745653 GCCAGATTGCCTTACAACTCC 59.254 52.381 0.00 0.00 42.27 3.85
310 311 2.436417 TGCCAGATTGCCTTACAACTC 58.564 47.619 0.00 0.00 42.27 3.01
311 312 2.558359 GTTGCCAGATTGCCTTACAACT 59.442 45.455 0.00 0.00 42.27 3.16
312 313 2.668279 CGTTGCCAGATTGCCTTACAAC 60.668 50.000 0.00 0.00 42.27 3.32
313 314 1.539388 CGTTGCCAGATTGCCTTACAA 59.461 47.619 0.00 0.00 44.01 2.41
314 315 1.164411 CGTTGCCAGATTGCCTTACA 58.836 50.000 0.00 0.00 0.00 2.41
315 316 1.448985 TCGTTGCCAGATTGCCTTAC 58.551 50.000 0.00 0.00 0.00 2.34
316 317 2.016318 CATCGTTGCCAGATTGCCTTA 58.984 47.619 0.00 0.00 0.00 2.69
322 323 1.064463 ACCCATCATCGTTGCCAGATT 60.064 47.619 0.00 0.00 0.00 2.40
330 331 1.153369 CGGCTCACCCATCATCGTT 60.153 57.895 0.00 0.00 0.00 3.85
331 332 2.501128 CGGCTCACCCATCATCGT 59.499 61.111 0.00 0.00 0.00 3.73
414 415 1.684049 CCTCCCGCTGAAGAGACCT 60.684 63.158 0.00 0.00 31.43 3.85
463 464 1.351017 TGTCGCTCCCCAAAAGATCTT 59.649 47.619 0.88 0.88 0.00 2.40
464 465 0.984230 TGTCGCTCCCCAAAAGATCT 59.016 50.000 0.00 0.00 0.00 2.75
551 552 1.320344 CCCTGACCTCGACGGAATCA 61.320 60.000 7.76 0.00 36.31 2.57
603 604 1.447838 GCACTCTTTCGATCCCGCA 60.448 57.895 0.00 0.00 35.37 5.69
964 965 1.451936 GGCAAGAGGTGGACTGTGT 59.548 57.895 0.00 0.00 0.00 3.72
1286 1649 2.163818 GTCGTTGACAATGACCCTCA 57.836 50.000 24.29 0.00 40.70 3.86
1336 1699 1.056660 ACCTCTTGGATGGTGAACGT 58.943 50.000 0.00 0.00 34.90 3.99
1436 1799 1.214367 GAGACCGTCACGCTTGAAAA 58.786 50.000 0.40 0.00 31.90 2.29
1533 1896 2.930826 TAAGCCCGAATGGAAGATCC 57.069 50.000 0.00 0.00 37.49 3.36
1547 1910 5.386924 TCCCTATACTCTCAGTCTTAAGCC 58.613 45.833 0.00 0.00 0.00 4.35
1650 2013 5.901552 TCATGCAGTAATATCTTGACACGA 58.098 37.500 0.00 0.00 0.00 4.35
1774 2137 0.675633 GAAGTGTGGCCAACAATGCT 59.324 50.000 7.24 0.00 41.57 3.79
1978 2347 1.198759 ACGGTAGTGGCCACCTTGAT 61.199 55.000 32.29 16.04 33.62 2.57
2109 2478 3.775654 GCCTGGTCCTCCCGACTG 61.776 72.222 0.00 0.00 41.64 3.51
2110 2479 4.316823 TGCCTGGTCCTCCCGACT 62.317 66.667 0.00 0.00 41.64 4.18
2329 2708 1.201414 CCCGGTTGGAAAAGAAATCCG 59.799 52.381 0.00 0.00 39.98 4.18
2574 2956 8.425577 TTTCAAAAGAGAACTCTAAGTCACTG 57.574 34.615 4.72 0.00 39.39 3.66
2736 3120 4.039245 TCCTTGCGGAGTATATTCTTCCTG 59.961 45.833 0.00 0.00 33.30 3.86
2768 3152 5.310409 TCTCATCTTTTTCTTCACCCACT 57.690 39.130 0.00 0.00 0.00 4.00
2887 3271 3.951680 GCTCCTGTAGTTCTAGAAGCTCT 59.048 47.826 5.12 2.30 0.00 4.09
3163 3552 5.066375 CCAAGATAAATGACGCTCATTCCAA 59.934 40.000 11.80 4.35 45.57 3.53


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

AutoCloner maintained by Alex Coulton.