Multiple sequence alignment - TraesCS4B01G168800

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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 TraesCS4B01G168800 chr4B 100.000 2828 0 0 1 2828 369146952 369149779 0.000000e+00 5223
1 TraesCS4B01G168800 chr4D 89.138 1740 91 41 826 2497 297832823 297834532 0.000000e+00 2076
2 TraesCS4B01G168800 chr4D 87.832 452 18 16 404 830 297832349 297832788 1.960000e-136 496
3 TraesCS4B01G168800 chr4D 87.179 234 10 9 1 214 297831705 297831938 6.050000e-62 248
4 TraesCS4B01G168800 chr4D 93.458 107 6 1 283 389 297831963 297832068 1.050000e-34 158
5 TraesCS4B01G168800 chr4D 85.156 128 14 4 2698 2822 297840859 297840984 2.960000e-25 126
6 TraesCS4B01G168800 chr4A 92.984 1012 41 13 829 1816 189670968 189669963 0.000000e+00 1448
7 TraesCS4B01G168800 chr4A 86.117 886 68 22 1954 2827 189669827 189668985 0.000000e+00 904
8 TraesCS4B01G168800 chr4A 89.220 436 22 14 404 830 189671425 189671006 3.230000e-144 521
9 TraesCS4B01G168800 chr4A 87.755 98 5 4 1872 1962 189669950 189669853 1.070000e-19 108


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 TraesCS4B01G168800 chr4B 369146952 369149779 2827 False 5223.00 5223 100.00000 1 2828 1 chr4B.!!$F1 2827
1 TraesCS4B01G168800 chr4D 297831705 297834532 2827 False 744.50 2076 89.40175 1 2497 4 chr4D.!!$F2 2496
2 TraesCS4B01G168800 chr4A 189668985 189671425 2440 True 745.25 1448 89.01900 404 2827 4 chr4A.!!$R1 2423

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
948 1320 0.03213 CACGCCACTACACACACTCT 59.968 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2776 3252 0.752743 ATAGGCCGGTAGTGCGTGTA 60.753 55.0 1.9 0.0 0.0 2.9 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
38 39 1.531739 TTCACCGCAAAAGCCATCCC 61.532 55.000 0.00 0.00 0.00 3.85
45 46 1.872952 GCAAAAGCCATCCCACAAAAC 59.127 47.619 0.00 0.00 0.00 2.43
50 51 1.826340 GCCATCCCACAAAACCCCAC 61.826 60.000 0.00 0.00 0.00 4.61
195 216 2.985847 GGCTGTCACCTTGCCCAC 60.986 66.667 0.00 0.00 40.71 4.61
203 224 2.468868 ACCTTGCCCACCATGGTGA 61.469 57.895 40.60 22.17 46.81 4.02
224 253 6.198966 GGTGACACTTTTCATTGATGTTTGAC 59.801 38.462 5.39 0.00 0.00 3.18
228 257 6.980397 ACACTTTTCATTGATGTTTGACCTTC 59.020 34.615 0.00 0.00 0.00 3.46
230 259 6.324770 ACTTTTCATTGATGTTTGACCTTCCT 59.675 34.615 0.00 0.00 0.00 3.36
231 260 5.964958 TTCATTGATGTTTGACCTTCCTC 57.035 39.130 0.00 0.00 0.00 3.71
232 261 4.984295 TCATTGATGTTTGACCTTCCTCA 58.016 39.130 0.00 0.00 0.00 3.86
233 262 4.761739 TCATTGATGTTTGACCTTCCTCAC 59.238 41.667 0.00 0.00 0.00 3.51
234 263 3.855255 TGATGTTTGACCTTCCTCACA 57.145 42.857 0.00 0.00 0.00 3.58
235 264 4.371624 TGATGTTTGACCTTCCTCACAT 57.628 40.909 0.00 0.00 0.00 3.21
236 265 4.728772 TGATGTTTGACCTTCCTCACATT 58.271 39.130 0.00 0.00 0.00 2.71
237 266 5.139727 TGATGTTTGACCTTCCTCACATTT 58.860 37.500 0.00 0.00 0.00 2.32
238 267 5.598005 TGATGTTTGACCTTCCTCACATTTT 59.402 36.000 0.00 0.00 0.00 1.82
239 268 5.930837 TGTTTGACCTTCCTCACATTTTT 57.069 34.783 0.00 0.00 0.00 1.94
264 293 7.576750 TTTAGAGTACTCAAATTGCGTACTG 57.423 36.000 27.06 0.35 45.59 2.74
265 294 5.135508 AGAGTACTCAAATTGCGTACTGT 57.864 39.130 27.06 21.90 45.59 3.55
266 295 6.263516 AGAGTACTCAAATTGCGTACTGTA 57.736 37.500 27.06 4.70 45.59 2.74
267 296 6.864342 AGAGTACTCAAATTGCGTACTGTAT 58.136 36.000 27.06 13.70 45.59 2.29
268 297 7.321153 AGAGTACTCAAATTGCGTACTGTATT 58.679 34.615 27.06 8.63 45.59 1.89
269 298 7.817962 AGAGTACTCAAATTGCGTACTGTATTT 59.182 33.333 27.06 8.01 45.59 1.40
270 299 8.319143 AGTACTCAAATTGCGTACTGTATTTT 57.681 30.769 23.03 2.86 44.40 1.82
271 300 8.780249 AGTACTCAAATTGCGTACTGTATTTTT 58.220 29.630 23.03 2.24 44.40 1.94
272 301 7.851822 ACTCAAATTGCGTACTGTATTTTTG 57.148 32.000 0.00 0.00 0.00 2.44
273 302 7.422399 ACTCAAATTGCGTACTGTATTTTTGT 58.578 30.769 0.00 0.00 0.00 2.83
274 303 8.561212 ACTCAAATTGCGTACTGTATTTTTGTA 58.439 29.630 0.00 0.00 0.00 2.41
275 304 9.388346 CTCAAATTGCGTACTGTATTTTTGTAA 57.612 29.630 0.00 0.00 0.00 2.41
276 305 9.171701 TCAAATTGCGTACTGTATTTTTGTAAC 57.828 29.630 0.00 0.00 0.00 2.50
277 306 8.421701 CAAATTGCGTACTGTATTTTTGTAACC 58.578 33.333 0.00 0.00 0.00 2.85
278 307 6.864360 TTGCGTACTGTATTTTTGTAACCT 57.136 33.333 0.00 0.00 0.00 3.50
279 308 6.864360 TGCGTACTGTATTTTTGTAACCTT 57.136 33.333 0.00 0.00 0.00 3.50
280 309 6.890558 TGCGTACTGTATTTTTGTAACCTTC 58.109 36.000 0.00 0.00 0.00 3.46
281 310 6.011277 GCGTACTGTATTTTTGTAACCTTCG 58.989 40.000 0.00 0.00 0.00 3.79
291 320 5.666969 TTTGTAACCTTCGTCACATTGAG 57.333 39.130 0.00 0.00 0.00 3.02
292 321 3.659786 TGTAACCTTCGTCACATTGAGG 58.340 45.455 0.00 0.00 33.88 3.86
294 323 2.457366 ACCTTCGTCACATTGAGGAC 57.543 50.000 0.00 0.00 40.47 3.85
366 395 3.185797 GTCCTGTGTTAATTCACGTGGAC 59.814 47.826 17.00 17.89 46.08 4.02
381 410 0.679505 TGGACGGAACTTGGTCTCAG 59.320 55.000 0.00 0.00 33.70 3.35
389 418 4.502962 GGAACTTGGTCTCAGATTCTCAG 58.497 47.826 0.00 0.00 0.00 3.35
390 419 4.221703 GGAACTTGGTCTCAGATTCTCAGA 59.778 45.833 0.00 0.00 0.00 3.27
391 420 5.104982 GGAACTTGGTCTCAGATTCTCAGAT 60.105 44.000 0.00 0.00 0.00 2.90
395 424 4.347607 TGGTCTCAGATTCTCAGATCACA 58.652 43.478 0.00 0.00 0.00 3.58
396 425 4.159321 TGGTCTCAGATTCTCAGATCACAC 59.841 45.833 0.00 0.00 0.00 3.82
397 426 4.159321 GGTCTCAGATTCTCAGATCACACA 59.841 45.833 0.00 0.00 0.00 3.72
398 427 5.337089 GGTCTCAGATTCTCAGATCACACAA 60.337 44.000 0.00 0.00 0.00 3.33
399 428 6.339730 GTCTCAGATTCTCAGATCACACAAT 58.660 40.000 0.00 0.00 0.00 2.71
400 429 6.817641 GTCTCAGATTCTCAGATCACACAATT 59.182 38.462 0.00 0.00 0.00 2.32
514 809 4.114794 TCGATCGACTGTTATCGTCACTA 58.885 43.478 15.15 4.49 44.11 2.74
543 838 7.147373 ACAGTATAATTACTTAGGTGCACCCAT 60.147 37.037 32.29 17.64 36.50 4.00
664 987 4.609947 TGCGATCAAATAAATGATGCACC 58.390 39.130 0.00 0.00 40.08 5.01
666 989 3.665409 CGATCAAATAAATGATGCACCGC 59.335 43.478 0.00 0.00 40.08 5.68
669 992 4.500205 ATCAAATAAATGATGCACCGCAGG 60.500 41.667 0.00 0.00 46.38 4.85
719 1042 1.268992 TTCCCATACCACGGACAGGG 61.269 60.000 0.00 0.00 37.65 4.45
808 1135 2.742053 CAAATACCAGGACCAGTTCACG 59.258 50.000 0.00 0.00 0.00 4.35
823 1150 3.880490 AGTTCACGCTCCACAACAAATTA 59.120 39.130 0.00 0.00 0.00 1.40
830 1157 4.213270 CGCTCCACAACAAATTACTCTGAA 59.787 41.667 0.00 0.00 0.00 3.02
832 1159 6.568462 CGCTCCACAACAAATTACTCTGAAAT 60.568 38.462 0.00 0.00 0.00 2.17
843 1209 3.791973 ACTCTGAAATCTAGCAGACGG 57.208 47.619 0.00 0.00 36.31 4.79
874 1240 6.034591 GCCACATTCGCGATATATAACTACT 58.965 40.000 10.88 0.00 0.00 2.57
875 1241 6.196724 GCCACATTCGCGATATATAACTACTC 59.803 42.308 10.88 0.00 0.00 2.59
876 1242 6.691818 CCACATTCGCGATATATAACTACTCC 59.308 42.308 10.88 0.00 0.00 3.85
877 1243 7.415318 CCACATTCGCGATATATAACTACTCCT 60.415 40.741 10.88 0.00 0.00 3.69
878 1244 7.640630 CACATTCGCGATATATAACTACTCCTC 59.359 40.741 10.88 0.00 0.00 3.71
879 1245 7.553402 ACATTCGCGATATATAACTACTCCTCT 59.447 37.037 10.88 0.00 0.00 3.69
902 1268 2.404995 GCTAGCTGGGCACTGCAAG 61.405 63.158 20.71 1.03 43.24 4.01
946 1318 1.069090 CCACGCCACTACACACACT 59.931 57.895 0.00 0.00 0.00 3.55
948 1320 0.032130 CACGCCACTACACACACTCT 59.968 55.000 0.00 0.00 0.00 3.24
958 1330 5.470437 CACTACACACACTCTCTCTGTCTTA 59.530 44.000 0.00 0.00 0.00 2.10
965 1337 1.064946 CTCTCTGTCTTAGGCCGCG 59.935 63.158 0.00 0.00 0.00 6.46
1052 1430 1.377856 GGAGGAGCACAAGGAAGGC 60.378 63.158 0.00 0.00 0.00 4.35
1144 1540 1.285023 CAACAGACAAGCCAGCAGC 59.715 57.895 0.00 0.00 44.25 5.25
1309 1720 0.379316 CCGTGTCGACGTCATCCATA 59.621 55.000 17.16 0.00 44.54 2.74
1414 1825 3.584868 AAGAACGACCCCGCGGAAG 62.585 63.158 30.73 20.57 39.95 3.46
1865 2287 1.381928 CCGCAGGCGAACTACTCCTA 61.382 60.000 16.21 0.00 46.14 2.94
1866 2288 0.454600 CGCAGGCGAACTACTCCTAA 59.545 55.000 8.15 0.00 42.83 2.69
1867 2289 1.067212 CGCAGGCGAACTACTCCTAAT 59.933 52.381 8.15 0.00 42.83 1.73
1891 2313 8.753497 ATAATTCCTAAACACCTCTGAATTCC 57.247 34.615 2.27 0.00 35.01 3.01
1892 2314 5.843019 TTCCTAAACACCTCTGAATTCCT 57.157 39.130 2.27 0.00 0.00 3.36
1895 2317 6.708285 TCCTAAACACCTCTGAATTCCTTAC 58.292 40.000 2.27 0.00 0.00 2.34
1962 2389 1.735198 GCATGCATGGTGTGTGTGC 60.735 57.895 27.34 8.13 39.26 4.57
1963 2390 1.961378 CATGCATGGTGTGTGTGCT 59.039 52.632 19.40 0.00 39.52 4.40
1964 2391 0.109458 CATGCATGGTGTGTGTGCTC 60.109 55.000 19.40 0.00 39.52 4.26
1987 2449 7.254692 GCTCATCATAATCATATCATTGACCGG 60.255 40.741 0.00 0.00 0.00 5.28
1995 2457 2.979814 ATCATTGACCGGTTGATCGA 57.020 45.000 9.42 2.50 0.00 3.59
2008 2470 2.868583 GTTGATCGACTCATGGTCATGG 59.131 50.000 5.79 4.91 44.70 3.66
2017 2479 3.198635 ACTCATGGTCATGGTCCAAGTAG 59.801 47.826 12.94 12.21 39.24 2.57
2018 2480 2.505407 TCATGGTCATGGTCCAAGTAGG 59.495 50.000 12.94 0.00 39.24 3.18
2019 2481 2.335681 TGGTCATGGTCCAAGTAGGA 57.664 50.000 0.00 0.00 46.75 2.94
2020 2482 5.666138 TCATGGTCATGGTCCAAGTAGGAG 61.666 50.000 12.94 0.00 41.47 3.69
2022 2484 8.748779 TCATGGTCATGGTCCAAGTAGGAGTA 62.749 46.154 12.94 0.00 41.47 2.59
2023 2485 9.953596 TCATGGTCATGGTCCAAGTAGGAGTAT 62.954 44.444 12.94 0.00 41.47 2.12
2032 2494 6.085555 TCCAAGTAGGAGTATATTCTTGCG 57.914 41.667 0.00 0.00 43.07 4.85
2033 2495 5.831525 TCCAAGTAGGAGTATATTCTTGCGA 59.168 40.000 0.00 0.00 43.07 5.10
2034 2496 6.322969 TCCAAGTAGGAGTATATTCTTGCGAA 59.677 38.462 0.00 0.00 43.07 4.70
2035 2497 6.984474 CCAAGTAGGAGTATATTCTTGCGAAA 59.016 38.462 0.00 0.00 41.22 3.46
2038 2500 7.085116 AGTAGGAGTATATTCTTGCGAAATCG 58.915 38.462 0.00 0.00 43.27 3.34
2048 2510 0.383737 TGCGAAATCGTGTTGCGTTC 60.384 50.000 4.59 0.00 42.22 3.95
2051 2513 2.743172 CGAAATCGTGTTGCGTTCTAC 58.257 47.619 0.00 0.00 42.13 2.59
2053 2515 3.605056 CGAAATCGTGTTGCGTTCTACTA 59.395 43.478 0.00 0.00 42.13 1.82
2054 2516 4.258899 CGAAATCGTGTTGCGTTCTACTAG 60.259 45.833 0.00 0.00 42.13 2.57
2055 2517 4.430137 AATCGTGTTGCGTTCTACTAGA 57.570 40.909 0.00 0.00 42.13 2.43
2056 2518 3.193157 TCGTGTTGCGTTCTACTAGAC 57.807 47.619 0.00 0.00 42.13 2.59
2057 2519 2.810274 TCGTGTTGCGTTCTACTAGACT 59.190 45.455 0.00 0.00 42.13 3.24
2119 2583 4.857037 ACACAACTTTCTTTCTTTTGCGTC 59.143 37.500 0.00 0.00 0.00 5.19
2358 2822 6.183360 CCCAATAATGATAGATAGTTGCGCTG 60.183 42.308 9.73 0.00 0.00 5.18
2391 2855 1.974236 GCTATACCATCAGCACCCTCT 59.026 52.381 0.00 0.00 37.73 3.69
2398 2862 0.268869 ATCAGCACCCTCTATCCCCA 59.731 55.000 0.00 0.00 0.00 4.96
2403 2867 2.711547 AGCACCCTCTATCCCCAATTAC 59.288 50.000 0.00 0.00 0.00 1.89
2406 2870 4.747009 GCACCCTCTATCCCCAATTACTTC 60.747 50.000 0.00 0.00 0.00 3.01
2466 2942 9.727627 TGCCATTTTACAGCAAAAATTAAAAAG 57.272 25.926 2.71 0.00 39.51 2.27
2484 2960 5.886960 AAAAGGTCATATGCTTCACTCAC 57.113 39.130 0.00 0.00 0.00 3.51
2513 2989 5.691508 ACTATTCGAAAATTACACCGTCG 57.308 39.130 0.00 0.00 0.00 5.12
2514 2990 5.163513 ACTATTCGAAAATTACACCGTCGT 58.836 37.500 0.00 0.00 33.55 4.34
2515 2991 4.572950 ATTCGAAAATTACACCGTCGTC 57.427 40.909 0.00 0.00 33.55 4.20
2523 2999 5.509716 AATTACACCGTCGTCTATGATGA 57.490 39.130 0.00 0.00 0.00 2.92
2541 3017 5.491982 TGATGAGAGAAAACCTTTCTAGCC 58.508 41.667 1.73 0.00 0.00 3.93
2549 3025 1.588139 CCTTTCTAGCCGTACGCCG 60.588 63.158 10.49 0.00 38.78 6.46
2559 3035 1.267186 GCCGTACGCCGTCATAAAAAG 60.267 52.381 10.49 0.00 33.66 2.27
2572 3048 4.332819 GTCATAAAAAGGTCATGTCCTCCG 59.667 45.833 12.12 0.00 36.74 4.63
2580 3056 0.970937 TCATGTCCTCCGACCTCCAC 60.971 60.000 0.00 0.00 38.32 4.02
2582 3058 3.075641 GTCCTCCGACCTCCACCC 61.076 72.222 0.00 0.00 32.40 4.61
2595 3071 0.928505 TCCACCCGGTACAGGATAGA 59.071 55.000 14.25 3.86 0.00 1.98
2597 3073 1.038280 CACCCGGTACAGGATAGACC 58.962 60.000 14.25 0.00 39.35 3.85
2603 3079 3.317430 CCGGTACAGGATAGACCAAGTAC 59.683 52.174 6.11 0.00 44.30 2.73
2604 3080 3.949754 CGGTACAGGATAGACCAAGTACA 59.050 47.826 16.81 0.00 45.52 2.90
2606 3082 5.068723 CGGTACAGGATAGACCAAGTACAAT 59.931 44.000 16.81 0.00 45.52 2.71
2639 3115 4.776349 ACATGCATCAATAACCTACCGAA 58.224 39.130 0.00 0.00 0.00 4.30
2645 3121 6.266786 TGCATCAATAACCTACCGAAGAGATA 59.733 38.462 0.00 0.00 0.00 1.98
2652 3128 5.082251 ACCTACCGAAGAGATAAAACACC 57.918 43.478 0.00 0.00 0.00 4.16
2677 3153 7.796197 CCTTTTTAAAACATAAACCGCAACATG 59.204 33.333 0.00 0.00 0.00 3.21
2681 3157 5.950758 AAACATAAACCGCAACATGACTA 57.049 34.783 0.00 0.00 0.00 2.59
2690 3166 2.029728 CGCAACATGACTAGCAAGCTAC 59.970 50.000 0.00 0.00 0.00 3.58
2767 3243 8.830201 TTGTAAATTTGTTGCAATCAATAGCT 57.170 26.923 0.59 0.00 34.29 3.32
2769 3245 6.730960 AAATTTGTTGCAATCAATAGCTGG 57.269 33.333 0.59 0.00 34.29 4.85
2772 3248 6.772360 TTTGTTGCAATCAATAGCTGGATA 57.228 33.333 0.59 0.00 34.29 2.59
2776 3252 8.640063 TGTTGCAATCAATAGCTGGATATATT 57.360 30.769 0.59 0.00 34.29 1.28
2779 3255 9.737844 TTGCAATCAATAGCTGGATATATTACA 57.262 29.630 0.00 0.00 0.00 2.41
2788 3264 4.863131 GCTGGATATATTACACGCACTACC 59.137 45.833 0.00 0.00 0.00 3.18
2790 3266 4.082625 TGGATATATTACACGCACTACCGG 60.083 45.833 0.00 0.00 0.00 5.28
2794 3270 0.964860 TTACACGCACTACCGGCCTA 60.965 55.000 0.00 0.00 0.00 3.93
2804 3280 3.875134 CACTACCGGCCTATAAAGGTTTG 59.125 47.826 0.00 0.00 45.64 2.93
2807 3283 4.245251 ACCGGCCTATAAAGGTTTGAAT 57.755 40.909 0.00 0.00 45.64 2.57
2822 3298 8.567285 AAGGTTTGAATCTACTTGAACTATGG 57.433 34.615 0.00 0.00 0.00 2.74
2827 3303 5.421056 TGAATCTACTTGAACTATGGTCGGT 59.579 40.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.159517 GCGGTGAATCATTGTCCTTGTC 60.160 50.000 0.00 0.00 0.00 3.18
38 39 2.902846 TCCGCGTGGGGTTTTGTG 60.903 61.111 16.49 0.00 36.01 3.33
45 46 1.140375 GTAAGTACTCCGCGTGGGG 59.860 63.158 14.93 14.93 43.71 4.96
50 51 2.477375 TGCTTTTTGTAAGTACTCCGCG 59.523 45.455 0.00 0.00 0.00 6.46
195 216 4.852134 TCAATGAAAAGTGTCACCATGG 57.148 40.909 11.19 11.19 0.00 3.66
203 224 6.469782 AGGTCAAACATCAATGAAAAGTGT 57.530 33.333 0.00 0.00 0.00 3.55
216 245 6.484364 AAAAATGTGAGGAAGGTCAAACAT 57.516 33.333 0.00 0.00 0.00 2.71
247 276 8.561212 ACAAAAATACAGTACGCAATTTGAGTA 58.439 29.630 8.66 8.66 31.51 2.59
248 277 7.422399 ACAAAAATACAGTACGCAATTTGAGT 58.578 30.769 10.63 10.63 34.10 3.41
249 278 7.851822 ACAAAAATACAGTACGCAATTTGAG 57.148 32.000 14.37 0.00 32.45 3.02
250 279 9.171701 GTTACAAAAATACAGTACGCAATTTGA 57.828 29.630 14.37 2.16 32.45 2.69
251 280 8.421701 GGTTACAAAAATACAGTACGCAATTTG 58.578 33.333 9.02 9.02 33.85 2.32
252 281 8.354426 AGGTTACAAAAATACAGTACGCAATTT 58.646 29.630 0.00 0.00 0.00 1.82
253 282 7.878036 AGGTTACAAAAATACAGTACGCAATT 58.122 30.769 0.00 0.00 0.00 2.32
254 283 7.443259 AGGTTACAAAAATACAGTACGCAAT 57.557 32.000 0.00 0.00 0.00 3.56
255 284 6.864360 AGGTTACAAAAATACAGTACGCAA 57.136 33.333 0.00 0.00 0.00 4.85
256 285 6.346758 CGAAGGTTACAAAAATACAGTACGCA 60.347 38.462 0.00 0.00 0.00 5.24
257 286 6.011277 CGAAGGTTACAAAAATACAGTACGC 58.989 40.000 0.00 0.00 0.00 4.42
258 287 7.096106 TGACGAAGGTTACAAAAATACAGTACG 60.096 37.037 0.00 0.00 0.00 3.67
259 288 8.006027 GTGACGAAGGTTACAAAAATACAGTAC 58.994 37.037 0.00 0.00 33.18 2.73
260 289 7.710044 TGTGACGAAGGTTACAAAAATACAGTA 59.290 33.333 0.00 0.00 39.41 2.74
261 290 6.539464 TGTGACGAAGGTTACAAAAATACAGT 59.461 34.615 0.00 0.00 39.41 3.55
262 291 6.950545 TGTGACGAAGGTTACAAAAATACAG 58.049 36.000 0.00 0.00 39.41 2.74
263 292 6.922247 TGTGACGAAGGTTACAAAAATACA 57.078 33.333 0.00 0.00 39.41 2.29
264 293 8.071368 TCAATGTGACGAAGGTTACAAAAATAC 58.929 33.333 0.00 0.00 44.53 1.89
265 294 8.155821 TCAATGTGACGAAGGTTACAAAAATA 57.844 30.769 0.00 0.00 44.53 1.40
266 295 7.033530 TCAATGTGACGAAGGTTACAAAAAT 57.966 32.000 0.00 0.00 44.53 1.82
267 296 6.438259 TCAATGTGACGAAGGTTACAAAAA 57.562 33.333 0.00 0.00 44.53 1.94
268 297 5.008217 CCTCAATGTGACGAAGGTTACAAAA 59.992 40.000 0.00 0.00 44.53 2.44
269 298 4.513692 CCTCAATGTGACGAAGGTTACAAA 59.486 41.667 0.00 0.00 44.53 2.83
270 299 4.062293 CCTCAATGTGACGAAGGTTACAA 58.938 43.478 0.00 0.00 44.53 2.41
271 300 3.322541 TCCTCAATGTGACGAAGGTTACA 59.677 43.478 0.00 0.00 45.29 2.41
272 301 3.678548 GTCCTCAATGTGACGAAGGTTAC 59.321 47.826 0.00 0.00 33.54 2.50
273 302 3.921677 GTCCTCAATGTGACGAAGGTTA 58.078 45.455 0.00 0.00 0.00 2.85
274 303 2.767505 GTCCTCAATGTGACGAAGGTT 58.232 47.619 0.00 0.00 0.00 3.50
275 304 2.457366 GTCCTCAATGTGACGAAGGT 57.543 50.000 0.00 0.00 0.00 3.50
310 339 1.070786 GTGCCTCCTTTCGGTCACA 59.929 57.895 0.00 0.00 0.00 3.58
318 347 0.693049 ATCCTTGTCGTGCCTCCTTT 59.307 50.000 0.00 0.00 0.00 3.11
366 395 3.056536 TGAGAATCTGAGACCAAGTTCCG 60.057 47.826 0.00 0.00 34.92 4.30
381 410 6.531594 TCGTACAATTGTGTGATCTGAGAATC 59.468 38.462 21.42 0.00 38.82 2.52
389 418 4.258743 CGTACGTCGTACAATTGTGTGATC 60.259 45.833 29.40 11.22 38.77 2.92
390 419 3.605056 CGTACGTCGTACAATTGTGTGAT 59.395 43.478 29.40 7.18 38.77 3.06
391 420 2.972569 CGTACGTCGTACAATTGTGTGA 59.027 45.455 29.40 14.87 38.77 3.58
514 809 9.774413 GGTGCACCTAAGTAATTATACTGTAAT 57.226 33.333 29.12 0.00 41.57 1.89
543 838 0.038599 TGTGCGAGGGTAGGTGTAGA 59.961 55.000 0.00 0.00 0.00 2.59
633 928 7.731720 TCATTTATTTGATCGCAAAAGCTTTG 58.268 30.769 13.54 8.26 46.19 2.77
642 937 4.609947 GGTGCATCATTTATTTGATCGCA 58.390 39.130 0.00 0.00 37.58 5.10
643 938 3.665409 CGGTGCATCATTTATTTGATCGC 59.335 43.478 0.00 0.00 34.09 4.58
644 939 3.665409 GCGGTGCATCATTTATTTGATCG 59.335 43.478 0.00 0.00 34.09 3.69
645 940 4.609947 TGCGGTGCATCATTTATTTGATC 58.390 39.130 0.00 0.00 34.09 2.92
646 941 4.500205 CCTGCGGTGCATCATTTATTTGAT 60.500 41.667 0.00 0.00 38.13 2.57
647 942 3.181488 CCTGCGGTGCATCATTTATTTGA 60.181 43.478 0.00 0.00 38.13 2.69
648 943 3.117794 CCTGCGGTGCATCATTTATTTG 58.882 45.455 0.00 0.00 38.13 2.32
649 944 2.481795 GCCTGCGGTGCATCATTTATTT 60.482 45.455 0.00 0.00 38.13 1.40
650 945 1.067516 GCCTGCGGTGCATCATTTATT 59.932 47.619 0.00 0.00 38.13 1.40
651 946 0.670162 GCCTGCGGTGCATCATTTAT 59.330 50.000 0.00 0.00 38.13 1.40
652 947 1.383456 GGCCTGCGGTGCATCATTTA 61.383 55.000 0.00 0.00 38.13 1.40
653 948 2.713967 GGCCTGCGGTGCATCATTT 61.714 57.895 0.00 0.00 38.13 2.32
654 949 3.142838 GGCCTGCGGTGCATCATT 61.143 61.111 0.00 0.00 38.13 2.57
655 950 3.942377 TTGGCCTGCGGTGCATCAT 62.942 57.895 3.32 0.00 38.13 2.45
656 951 4.657408 TTGGCCTGCGGTGCATCA 62.657 61.111 3.32 0.00 38.13 3.07
657 952 2.929903 TTTTGGCCTGCGGTGCATC 61.930 57.895 3.32 0.00 38.13 3.91
658 953 2.916703 TTTTGGCCTGCGGTGCAT 60.917 55.556 3.32 0.00 38.13 3.96
659 954 3.910490 GTTTTGGCCTGCGGTGCA 61.910 61.111 3.32 0.00 36.92 4.57
664 987 0.102120 TGTCAAAGTTTTGGCCTGCG 59.898 50.000 3.32 0.00 41.89 5.18
666 989 4.613622 CGTAGATGTCAAAGTTTTGGCCTG 60.614 45.833 3.32 0.00 41.89 4.85
669 992 4.464112 GTCGTAGATGTCAAAGTTTTGGC 58.536 43.478 2.37 2.37 42.84 4.52
719 1042 2.413502 CGCGAGATAGAGATACTGGTGC 60.414 54.545 0.00 0.00 0.00 5.01
753 1080 9.733556 CTCTACATTCATCTAGGAGTAGTATGT 57.266 37.037 0.00 0.00 32.82 2.29
754 1081 9.733556 ACTCTACATTCATCTAGGAGTAGTATG 57.266 37.037 0.00 0.00 31.93 2.39
756 1083 7.662258 GCACTCTACATTCATCTAGGAGTAGTA 59.338 40.741 0.00 0.00 32.36 1.82
758 1085 6.348132 CGCACTCTACATTCATCTAGGAGTAG 60.348 46.154 0.00 0.00 32.36 2.57
759 1086 5.470437 CGCACTCTACATTCATCTAGGAGTA 59.530 44.000 0.00 0.00 32.36 2.59
760 1087 4.277174 CGCACTCTACATTCATCTAGGAGT 59.723 45.833 0.00 0.00 33.60 3.85
761 1088 4.793071 CGCACTCTACATTCATCTAGGAG 58.207 47.826 0.00 0.00 0.00 3.69
762 1089 3.004839 GCGCACTCTACATTCATCTAGGA 59.995 47.826 0.30 0.00 0.00 2.94
763 1090 3.312828 GCGCACTCTACATTCATCTAGG 58.687 50.000 0.30 0.00 0.00 3.02
764 1091 3.005261 AGGCGCACTCTACATTCATCTAG 59.995 47.826 10.83 0.00 0.00 2.43
777 1104 1.009829 CTGGTATTTGAGGCGCACTC 58.990 55.000 10.83 14.24 46.78 3.51
808 1135 5.689383 TTCAGAGTAATTTGTTGTGGAGC 57.311 39.130 0.00 0.00 0.00 4.70
823 1150 2.159170 GCCGTCTGCTAGATTTCAGAGT 60.159 50.000 0.00 0.00 39.71 3.24
830 1157 0.179134 GACACGCCGTCTGCTAGATT 60.179 55.000 0.00 0.00 41.81 2.40
832 1159 2.875485 GACACGCCGTCTGCTAGA 59.125 61.111 0.00 0.00 41.81 2.43
874 1240 0.685785 CCCAGCTAGCTCACAGAGGA 60.686 60.000 16.15 0.00 0.00 3.71
875 1241 1.821936 CCCAGCTAGCTCACAGAGG 59.178 63.158 16.15 11.97 0.00 3.69
876 1242 1.143620 GCCCAGCTAGCTCACAGAG 59.856 63.158 16.15 1.93 0.00 3.35
877 1243 1.610379 TGCCCAGCTAGCTCACAGA 60.610 57.895 16.15 0.00 0.00 3.41
878 1244 1.449246 GTGCCCAGCTAGCTCACAG 60.449 63.158 23.26 10.67 0.00 3.66
879 1245 1.915266 AGTGCCCAGCTAGCTCACA 60.915 57.895 27.42 18.30 0.00 3.58
902 1268 1.440353 GTGCGCGTGGTGATCAAAC 60.440 57.895 8.43 0.00 0.00 2.93
927 1299 1.959226 GTGTGTGTAGTGGCGTGGG 60.959 63.158 0.00 0.00 0.00 4.61
937 1309 5.004448 CCTAAGACAGAGAGAGTGTGTGTA 58.996 45.833 0.00 0.00 31.30 2.90
946 1318 1.377366 CGCGGCCTAAGACAGAGAGA 61.377 60.000 0.00 0.00 0.00 3.10
948 1320 1.378119 TCGCGGCCTAAGACAGAGA 60.378 57.895 6.13 0.00 0.00 3.10
958 1330 4.057428 GACACTCTGTCGCGGCCT 62.057 66.667 8.89 0.00 37.67 5.19
1119 1515 1.507141 GGCTTGTCTGTTGGTCCGTG 61.507 60.000 0.00 0.00 0.00 4.94
1176 1572 2.284331 TTGGGAGAGTAGCCGGCA 60.284 61.111 31.54 12.31 0.00 5.69
1779 2193 4.284123 GCGATGTGAAGCCAGACA 57.716 55.556 0.00 0.00 0.00 3.41
1821 2243 0.890996 GCAGCTTGTGGCCTTAGTGT 60.891 55.000 3.32 0.00 43.05 3.55
1824 2246 3.595819 GGCAGCTTGTGGCCTTAG 58.404 61.111 3.32 0.00 46.23 2.18
1865 2287 9.190317 GGAATTCAGAGGTGTTTAGGAATTATT 57.810 33.333 7.93 0.00 35.71 1.40
1866 2288 8.560903 AGGAATTCAGAGGTGTTTAGGAATTAT 58.439 33.333 7.93 0.00 35.71 1.28
1867 2289 7.928873 AGGAATTCAGAGGTGTTTAGGAATTA 58.071 34.615 7.93 0.00 35.71 1.40
1891 2313 4.783036 CGAAAGTGCATTGTGATTCGTAAG 59.217 41.667 5.81 0.00 36.02 2.34
1892 2314 4.707563 CGAAAGTGCATTGTGATTCGTAA 58.292 39.130 5.81 0.00 36.02 3.18
1895 2317 3.187478 ACGAAAGTGCATTGTGATTCG 57.813 42.857 10.94 10.94 46.97 3.34
1952 2379 3.940852 TGATTATGATGAGCACACACACC 59.059 43.478 0.00 0.00 0.00 4.16
1954 2381 7.218614 TGATATGATTATGATGAGCACACACA 58.781 34.615 0.00 0.00 0.00 3.72
1962 2389 7.767659 ACCGGTCAATGATATGATTATGATGAG 59.232 37.037 0.00 0.00 0.00 2.90
1963 2390 7.623630 ACCGGTCAATGATATGATTATGATGA 58.376 34.615 0.00 0.00 0.00 2.92
1964 2391 7.854557 ACCGGTCAATGATATGATTATGATG 57.145 36.000 0.00 0.00 0.00 3.07
1995 2457 1.988107 ACTTGGACCATGACCATGAGT 59.012 47.619 21.83 15.70 41.20 3.41
2008 2470 5.921408 CGCAAGAATATACTCCTACTTGGAC 59.079 44.000 0.00 0.00 39.16 4.02
2038 2500 4.543692 TCAAGTCTAGTAGAACGCAACAC 58.456 43.478 0.17 0.00 0.00 3.32
2051 2513 5.442391 ACTCCTACTAGCCTTCAAGTCTAG 58.558 45.833 0.72 0.72 36.70 2.43
2053 2515 4.325084 ACTCCTACTAGCCTTCAAGTCT 57.675 45.455 0.00 0.00 0.00 3.24
2054 2516 4.037089 GCTACTCCTACTAGCCTTCAAGTC 59.963 50.000 0.00 0.00 31.94 3.01
2055 2517 3.955551 GCTACTCCTACTAGCCTTCAAGT 59.044 47.826 0.00 0.00 31.94 3.16
2056 2518 4.211920 AGCTACTCCTACTAGCCTTCAAG 58.788 47.826 0.00 0.00 37.88 3.02
2057 2519 4.252570 AGCTACTCCTACTAGCCTTCAA 57.747 45.455 0.00 0.00 37.88 2.69
2070 2534 2.977914 TGACAGAATGCAAGCTACTCC 58.022 47.619 0.00 0.00 42.53 3.85
2071 2535 3.999663 ACTTGACAGAATGCAAGCTACTC 59.000 43.478 0.00 0.00 46.68 2.59
2072 2536 4.013267 ACTTGACAGAATGCAAGCTACT 57.987 40.909 0.00 0.00 46.68 2.57
2073 2537 4.214119 TCAACTTGACAGAATGCAAGCTAC 59.786 41.667 0.00 0.00 46.68 3.58
2102 2566 4.209288 TCGAGAGACGCAAAAGAAAGAAAG 59.791 41.667 0.00 0.00 42.26 2.62
2119 2583 2.668457 CCAACCGATGAAAGTTCGAGAG 59.332 50.000 0.00 0.00 38.88 3.20
2168 2632 3.063510 TCCATTCTTCAGCCTCACAAG 57.936 47.619 0.00 0.00 0.00 3.16
2245 2709 1.134367 CACGGATCGAGCTGTAAAGGA 59.866 52.381 15.92 0.00 0.00 3.36
2391 2855 6.183360 CCGTCTAAGTGAAGTAATTGGGGATA 60.183 42.308 0.00 0.00 0.00 2.59
2398 2862 8.258007 TGATGAATCCGTCTAAGTGAAGTAATT 58.742 33.333 0.00 0.00 0.00 1.40
2403 2867 5.410924 TGTGATGAATCCGTCTAAGTGAAG 58.589 41.667 0.00 0.00 0.00 3.02
2406 2870 5.408299 TGTTTGTGATGAATCCGTCTAAGTG 59.592 40.000 0.00 0.00 0.00 3.16
2466 2942 2.893637 ACGTGAGTGAAGCATATGACC 58.106 47.619 6.97 0.00 46.97 4.02
2484 2960 8.624877 CGGTGTAATTTTCGAATAGTATCTACG 58.375 37.037 0.00 0.00 0.00 3.51
2513 2989 9.528018 CTAGAAAGGTTTTCTCTCATCATAGAC 57.472 37.037 7.29 0.00 0.00 2.59
2514 2990 8.200792 GCTAGAAAGGTTTTCTCTCATCATAGA 58.799 37.037 7.29 0.00 0.00 1.98
2515 2991 7.440856 GGCTAGAAAGGTTTTCTCTCATCATAG 59.559 40.741 7.29 0.00 0.00 2.23
2523 2999 4.617762 CGTACGGCTAGAAAGGTTTTCTCT 60.618 45.833 7.57 0.00 0.00 3.10
2549 3025 4.332819 CGGAGGACATGACCTTTTTATGAC 59.667 45.833 17.97 2.76 40.73 3.06
2572 3048 2.356780 CCTGTACCGGGTGGAGGTC 61.357 68.421 10.66 0.00 42.81 3.85
2580 3056 1.687123 CTTGGTCTATCCTGTACCGGG 59.313 57.143 6.32 0.00 35.98 5.73
2582 3058 3.949754 TGTACTTGGTCTATCCTGTACCG 59.050 47.826 0.00 0.00 41.35 4.02
2606 3082 8.567104 GGTTATTGATGCATGTATACAATGACA 58.433 33.333 25.17 6.33 38.37 3.58
2625 3101 8.601476 GTGTTTTATCTCTTCGGTAGGTTATTG 58.399 37.037 0.00 0.00 0.00 1.90
2645 3121 8.176365 GCGGTTTATGTTTTAAAAAGGTGTTTT 58.824 29.630 1.31 0.00 37.48 2.43
2652 3128 8.543774 TCATGTTGCGGTTTATGTTTTAAAAAG 58.456 29.630 1.31 0.00 0.00 2.27
2669 3145 1.081892 AGCTTGCTAGTCATGTTGCG 58.918 50.000 0.00 0.00 0.00 4.85
2677 3153 3.594603 TGGTTCTGTAGCTTGCTAGTC 57.405 47.619 2.20 0.00 0.00 2.59
2681 3157 2.930950 TGTTTGGTTCTGTAGCTTGCT 58.069 42.857 0.00 0.00 0.00 3.91
2690 3166 5.335661 GCCTGTAACCTTATGTTTGGTTCTG 60.336 44.000 0.34 0.00 44.47 3.02
2746 3222 6.465948 TCCAGCTATTGATTGCAACAAATTT 58.534 32.000 15.21 5.52 36.72 1.82
2748 3224 5.664294 TCCAGCTATTGATTGCAACAAAT 57.336 34.783 15.21 13.56 36.72 2.32
2749 3225 5.664294 ATCCAGCTATTGATTGCAACAAA 57.336 34.783 15.21 8.00 36.72 2.83
2750 3226 6.964807 ATATCCAGCTATTGATTGCAACAA 57.035 33.333 0.00 9.07 36.72 2.83
2751 3227 8.640063 AATATATCCAGCTATTGATTGCAACA 57.360 30.769 0.00 0.00 36.72 3.33
2752 3228 9.994432 GTAATATATCCAGCTATTGATTGCAAC 57.006 33.333 0.00 0.00 36.72 4.17
2753 3229 9.737844 TGTAATATATCCAGCTATTGATTGCAA 57.262 29.630 0.00 0.00 38.60 4.08
2754 3230 9.166173 GTGTAATATATCCAGCTATTGATTGCA 57.834 33.333 0.00 0.00 0.00 4.08
2767 3243 4.082625 CCGGTAGTGCGTGTAATATATCCA 60.083 45.833 0.00 0.00 0.00 3.41
2769 3245 3.855950 GCCGGTAGTGCGTGTAATATATC 59.144 47.826 1.90 0.00 0.00 1.63
2772 3248 1.269936 GGCCGGTAGTGCGTGTAATAT 60.270 52.381 1.90 0.00 0.00 1.28
2776 3252 0.752743 ATAGGCCGGTAGTGCGTGTA 60.753 55.000 1.90 0.00 0.00 2.90
2779 3255 1.068127 CTTTATAGGCCGGTAGTGCGT 59.932 52.381 1.90 0.00 0.00 5.24
2788 3264 6.289064 AGTAGATTCAAACCTTTATAGGCCG 58.711 40.000 0.00 0.00 46.22 6.13
2790 3266 8.732746 TCAAGTAGATTCAAACCTTTATAGGC 57.267 34.615 0.00 0.00 46.22 3.93
2804 3280 5.903810 ACCGACCATAGTTCAAGTAGATTC 58.096 41.667 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.