Multiple sequence alignment - TraesCS7D01G483300

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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 TraesCS7D01G483300 chr7D 100.000 2870 0 0 1 2870 593267635 593270504 0.000000e+00 5301
1 TraesCS7D01G483300 chr7D 84.395 314 35 5 1 313 246518018 246517718 2.160000e-76 296
2 TraesCS7D01G483300 chr7D 81.703 317 39 13 1 315 550597702 550598001 2.210000e-61 246
3 TraesCS7D01G483300 chr7A 94.814 1774 69 11 599 2353 686104978 686106747 0.000000e+00 2745
4 TraesCS7D01G483300 chr7A 84.400 891 93 24 2006 2867 686107204 686108077 0.000000e+00 833
5 TraesCS7D01G483300 chr7A 94.545 165 9 0 370 534 593795596 593795432 3.670000e-64 255
6 TraesCS7D01G483300 chr7A 91.111 180 14 1 355 534 547220182 547220005 2.860000e-60 243
7 TraesCS7D01G483300 chr7B 93.522 1590 49 25 555 2114 667634154 667632589 0.000000e+00 2316
8 TraesCS7D01G483300 chr7B 85.231 887 82 25 2028 2870 667631882 667631001 0.000000e+00 867
9 TraesCS7D01G483300 chr7B 89.247 372 30 7 1 371 667634720 667634358 9.370000e-125 457
10 TraesCS7D01G483300 chr7B 86.649 382 31 11 2132 2498 667632601 667632225 3.440000e-109 405
11 TraesCS7D01G483300 chr2D 85.032 314 37 5 1 313 141189278 141189582 7.720000e-81 311
12 TraesCS7D01G483300 chr2D 92.265 181 13 1 370 550 396613963 396613784 3.670000e-64 255
13 TraesCS7D01G483300 chr2D 92.614 176 12 1 359 534 446317817 446317643 4.750000e-63 252
14 TraesCS7D01G483300 chr2D 92.045 176 12 2 359 534 620615636 620615809 2.210000e-61 246
15 TraesCS7D01G483300 chr6B 85.570 298 28 11 21 314 632189671 632189957 6.010000e-77 298
16 TraesCS7D01G483300 chr3D 85.985 264 23 10 6 267 28851151 28850900 1.310000e-68 270
17 TraesCS7D01G483300 chr3D 82.315 311 34 14 11 315 143001751 143002046 1.710000e-62 250
18 TraesCS7D01G483300 chr3D 89.947 189 16 3 347 534 547434407 547434593 1.030000e-59 241
19 TraesCS7D01G483300 chrUn 92.818 181 11 2 370 550 25754365 25754543 7.890000e-66 261
20 TraesCS7D01G483300 chrUn 94.611 167 9 0 370 536 74119615 74119449 2.840000e-65 259
21 TraesCS7D01G483300 chrUn 92.265 181 12 2 370 550 223282634 223282812 3.670000e-64 255
22 TraesCS7D01G483300 chr6D 92.818 181 12 1 370 550 406391359 406391538 7.890000e-66 261
23 TraesCS7D01G483300 chr6D 92.265 181 11 3 364 542 361051316 361051137 1.320000e-63 254
24 TraesCS7D01G483300 chr3B 94.643 168 8 1 369 536 64540049 64540215 2.840000e-65 259
25 TraesCS7D01G483300 chr1D 82.410 307 38 10 6 310 254622209 254621917 1.320000e-63 254
26 TraesCS7D01G483300 chr1D 92.179 179 13 1 356 534 71286519 71286342 4.750000e-63 252
27 TraesCS7D01G483300 chr4B 82.143 308 41 11 15 316 605946670 605946969 4.750000e-63 252
28 TraesCS7D01G483300 chr4A 91.667 180 15 0 355 534 440085903 440086082 1.710000e-62 250
29 TraesCS7D01G483300 chr3A 91.111 180 14 1 355 534 224473395 224473572 2.860000e-60 243
30 TraesCS7D01G483300 chr3A 90.710 183 15 2 352 534 362899862 362899682 2.860000e-60 243
31 TraesCS7D01G483300 chr3A 81.928 249 30 7 68 313 718377604 718377840 2.260000e-46 196
32 TraesCS7D01G483300 chr2A 78.025 314 44 19 12 315 443766418 443766716 1.060000e-39 174


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 TraesCS7D01G483300 chr7D 593267635 593270504 2869 False 5301.00 5301 100.00000 1 2870 1 chr7D.!!$F2 2869
1 TraesCS7D01G483300 chr7A 686104978 686108077 3099 False 1789.00 2745 89.60700 599 2867 2 chr7A.!!$F1 2268
2 TraesCS7D01G483300 chr7B 667631001 667634720 3719 True 1011.25 2316 88.66225 1 2870 4 chr7B.!!$R1 2869

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
905 1110 0.396417 CACGACCATCTCCTCTCCCT 60.396 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2695 4029 0.181587 TTCCCCTTGTTGAGCGTTCA 59.818 50.0 0.0 0.0 0.0 3.18 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
89 90 5.576447 AGTGTTTTGTCGGTGAGAAAAAT 57.424 34.783 3.79 0.00 36.75 1.82
139 141 7.446001 ACATTTGGTGTTCAATTTTGTTTGT 57.554 28.000 0.00 0.00 38.01 2.83
167 169 3.433513 TTTTTGCAAAGGCCAAAATGC 57.566 38.095 12.41 10.38 39.05 3.56
175 177 6.179040 TGCAAAGGCCAAAATGCTTAATATT 58.821 32.000 18.67 0.00 39.49 1.28
179 181 9.344309 CAAAGGCCAAAATGCTTAATATTTTTG 57.656 29.630 5.01 0.00 36.02 2.44
195 197 8.846943 AATATTTTTGCCTAAAACTTTGGAGG 57.153 30.769 0.00 0.12 38.48 4.30
216 218 6.239600 GGAGGTAGCATTTGGATGTGACTATA 60.240 42.308 0.00 0.00 35.63 1.31
218 220 7.573710 AGGTAGCATTTGGATGTGACTATAAA 58.426 34.615 0.00 0.00 35.63 1.40
272 274 6.145858 TCACATTTCAAAAATCATTTCCTGCG 59.854 34.615 0.00 0.00 0.00 5.18
310 312 1.136891 CCGGGAGCCAAATTGGATTTC 59.863 52.381 17.47 9.37 35.51 2.17
311 313 1.136891 CGGGAGCCAAATTGGATTTCC 59.863 52.381 17.47 17.22 35.51 3.13
322 324 6.980397 CCAAATTGGATTTCCGATCTAAAAGG 59.020 38.462 6.04 0.00 40.96 3.11
378 380 6.847421 TTAGTTTACAGAAGTACTCCCTCC 57.153 41.667 0.00 0.00 0.00 4.30
379 381 3.762823 AGTTTACAGAAGTACTCCCTCCG 59.237 47.826 0.00 0.00 0.00 4.63
380 382 3.446442 TTACAGAAGTACTCCCTCCGT 57.554 47.619 0.00 0.00 0.00 4.69
381 383 2.305858 ACAGAAGTACTCCCTCCGTT 57.694 50.000 0.00 0.00 0.00 4.44
382 384 2.169330 ACAGAAGTACTCCCTCCGTTC 58.831 52.381 0.00 0.00 0.00 3.95
383 385 1.477295 CAGAAGTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 0.00 3.62
384 386 1.358445 AGAAGTACTCCCTCCGTTCCT 59.642 52.381 0.00 0.00 0.00 3.36
385 387 2.579860 AGAAGTACTCCCTCCGTTCCTA 59.420 50.000 0.00 0.00 0.00 2.94
386 388 3.011032 AGAAGTACTCCCTCCGTTCCTAA 59.989 47.826 0.00 0.00 0.00 2.69
387 389 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
388 390 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
389 391 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
390 392 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
391 393 6.141790 AGTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
392 394 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
393 395 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
394 396 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
395 397 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
396 398 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
397 399 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
398 400 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
399 401 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
400 402 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
401 403 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
402 404 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
403 405 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
418 420 9.996554 TGTCTTTCTAGATATTTCAACAAGTGA 57.003 29.630 0.00 0.00 31.86 3.41
450 452 8.764524 ACAGAGTAAAATGAGTGAATCTACAC 57.235 34.615 0.00 0.00 40.60 2.90
505 507 8.698973 TGGTAGTCCATTTGAAATGTTTAGAA 57.301 30.769 15.93 0.00 39.03 2.10
506 508 9.137459 TGGTAGTCCATTTGAAATGTTTAGAAA 57.863 29.630 15.93 0.00 39.03 2.52
507 509 9.626045 GGTAGTCCATTTGAAATGTTTAGAAAG 57.374 33.333 15.93 0.00 0.00 2.62
510 512 8.912988 AGTCCATTTGAAATGTTTAGAAAGACA 58.087 29.630 15.93 0.00 0.00 3.41
511 513 9.528018 GTCCATTTGAAATGTTTAGAAAGACAA 57.472 29.630 15.93 0.00 0.00 3.18
526 528 9.947433 TTAGAAAGACAAATATTTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
527 529 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
528 530 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
529 531 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
545 547 2.821969 GGAGGGAGTAGTACGTGACAAA 59.178 50.000 0.00 0.00 0.00 2.83
547 549 4.262164 GGAGGGAGTAGTACGTGACAAAAA 60.262 45.833 0.00 0.00 0.00 1.94
549 551 4.099881 AGGGAGTAGTACGTGACAAAAACA 59.900 41.667 0.00 0.00 0.00 2.83
550 552 4.810491 GGGAGTAGTACGTGACAAAAACAA 59.190 41.667 0.00 0.00 0.00 2.83
551 553 5.277011 GGGAGTAGTACGTGACAAAAACAAC 60.277 44.000 0.00 0.00 0.00 3.32
552 554 5.277011 GGAGTAGTACGTGACAAAAACAACC 60.277 44.000 0.00 0.00 0.00 3.77
553 555 3.661758 AGTACGTGACAAAAACAACCG 57.338 42.857 0.00 0.00 0.00 4.44
623 816 2.277084 CATAGCCCACGTACAAGGTTC 58.723 52.381 0.00 0.00 0.00 3.62
627 820 1.880646 GCCCACGTACAAGGTTCACAT 60.881 52.381 0.00 0.00 0.00 3.21
710 909 4.141965 ATGCGCATCGGACGGTCA 62.142 61.111 19.28 0.00 0.00 4.02
820 1024 2.100197 AGATTGAAGACCGGTCGATCA 58.900 47.619 30.37 30.37 38.07 2.92
821 1025 2.099921 AGATTGAAGACCGGTCGATCAG 59.900 50.000 31.28 0.00 38.07 2.90
830 1034 1.544537 CCGGTCGATCAGAGATCTCCT 60.545 57.143 19.30 4.44 0.00 3.69
847 1051 0.895559 CCTCCAACTGCCAAACCCTC 60.896 60.000 0.00 0.00 0.00 4.30
888 1093 2.022240 GATCACTCTCCTCCCGCCAC 62.022 65.000 0.00 0.00 0.00 5.01
901 1106 2.418910 CGCCACGACCATCTCCTCT 61.419 63.158 0.00 0.00 0.00 3.69
905 1110 0.396417 CACGACCATCTCCTCTCCCT 60.396 60.000 0.00 0.00 0.00 4.20
907 1112 0.825840 CGACCATCTCCTCTCCCTCC 60.826 65.000 0.00 0.00 0.00 4.30
1047 1260 2.124693 GCTCCTCGTCCTCCTCCTG 61.125 68.421 0.00 0.00 0.00 3.86
1153 1372 4.344865 TGGCCAAGTTCCCGGAGC 62.345 66.667 0.61 0.00 0.00 4.70
1161 1380 3.003173 TTCCCGGAGCTCACCCTG 61.003 66.667 17.19 0.00 0.00 4.45
1605 1824 2.760477 CCCGGGGTCATCACCAAA 59.240 61.111 14.71 0.00 45.94 3.28
1823 2042 4.489771 GATGGGCTGGTGGTCCGG 62.490 72.222 0.00 0.00 44.07 5.14
1895 2115 4.201763 CGCAGATTAGATGAGATCGATCGA 60.202 45.833 21.86 21.86 34.26 3.59
1902 2122 2.225068 TGAGATCGATCGAAAAGCCC 57.775 50.000 23.50 8.84 0.00 5.19
1952 2173 3.684788 CACTCATTCGGAACTCGGATTTT 59.315 43.478 0.00 0.00 34.23 1.82
2028 2251 2.677968 AATGCCTGCCCTGTGGGTTT 62.678 55.000 4.42 0.00 46.51 3.27
2029 2252 2.991540 GCCTGCCCTGTGGGTTTC 60.992 66.667 4.42 0.00 46.51 2.78
2091 2314 4.628333 CCTTATTGCACTTCAAAATGGCTG 59.372 41.667 0.00 0.00 38.34 4.85
2122 2345 3.686726 GCCTCTAGTTCTCAACACCATTG 59.313 47.826 0.00 0.00 0.00 2.82
2130 2353 4.097551 TCTCAACACCATTGAATGTCCA 57.902 40.909 4.27 0.00 0.00 4.02
2141 2364 4.715534 TTGAATGTCCACCTCCAGTTTA 57.284 40.909 0.00 0.00 0.00 2.01
2174 2397 1.811266 CAACGCCATCTCGGGTCAG 60.811 63.158 0.00 0.00 34.06 3.51
2213 2436 3.004734 ACTGGCCAATTTTTGAGAGTTCG 59.995 43.478 7.01 0.00 0.00 3.95
2254 2477 5.819825 AACTTGACCAAAAGAACAGAGTC 57.180 39.130 0.00 0.00 0.00 3.36
2316 2539 4.679373 AGGATATGCGAGATCTTGTTGT 57.321 40.909 11.71 0.00 0.00 3.32
2326 2549 5.622460 GCGAGATCTTGTTGTCTTTCCTAGA 60.622 44.000 11.71 0.00 0.00 2.43
2356 2579 8.746922 TGATCAAATTTGACACTAGCAAAATC 57.253 30.769 22.71 12.00 40.49 2.17
2370 2593 8.956426 CACTAGCAAAATCCCTACATAAAAAGA 58.044 33.333 0.00 0.00 0.00 2.52
2395 3690 4.271816 CTGATAGCCGCCGCGACT 62.272 66.667 15.93 11.21 41.18 4.18
2396 3691 4.569023 TGATAGCCGCCGCGACTG 62.569 66.667 15.93 0.00 41.18 3.51
2405 3700 3.842923 CCGCGACTGCCTCCATCT 61.843 66.667 8.23 0.00 38.08 2.90
2407 3702 1.448540 CGCGACTGCCTCCATCTTT 60.449 57.895 0.00 0.00 38.08 2.52
2410 3713 1.137086 GCGACTGCCTCCATCTTTCTA 59.863 52.381 0.00 0.00 33.98 2.10
2414 3717 4.098044 CGACTGCCTCCATCTTTCTACTTA 59.902 45.833 0.00 0.00 0.00 2.24
2503 3811 1.524621 CGCAATACCTGGGCCTCAG 60.525 63.158 4.53 12.83 43.00 3.35
2504 3812 1.609783 GCAATACCTGGGCCTCAGT 59.390 57.895 16.96 8.49 41.83 3.41
2540 3849 3.681897 GTCCACAAACAACATTGCACAAA 59.318 39.130 0.00 0.00 33.52 2.83
2541 3850 4.153117 GTCCACAAACAACATTGCACAAAA 59.847 37.500 0.00 0.00 33.52 2.44
2542 3851 4.756642 TCCACAAACAACATTGCACAAAAA 59.243 33.333 0.00 0.00 33.52 1.94
2578 3892 5.600908 AGTAACGACGTTGCATTACAATT 57.399 34.783 26.80 4.60 41.27 2.32
2620 3937 3.601277 CTCAAGCAGAGCACACAGA 57.399 52.632 0.00 0.00 37.59 3.41
2621 3938 1.146637 CTCAAGCAGAGCACACAGAC 58.853 55.000 0.00 0.00 37.59 3.51
2633 3956 2.159393 GCACACAGACACACAACAACAT 60.159 45.455 0.00 0.00 0.00 2.71
2695 4029 3.260380 GGGATCTCGACATCAAGGATCAT 59.740 47.826 3.00 0.00 35.76 2.45
2699 4033 4.686972 TCTCGACATCAAGGATCATGAAC 58.313 43.478 0.00 0.00 0.00 3.18
2739 4074 4.706035 AGATCTTCTGCTTCCATCATCAC 58.294 43.478 0.00 0.00 0.00 3.06
2863 4198 5.533903 ACATTCAACATGGCATAATCCTCTC 59.466 40.000 0.00 0.00 0.00 3.20
2867 4202 0.969149 ATGGCATAATCCTCTCGCGA 59.031 50.000 9.26 9.26 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.211389 GCACTAACACGAACATCAACAAG 58.789 43.478 0.00 0.00 0.00 3.16
9 10 1.424403 CGGCACTAACACGAACATCA 58.576 50.000 0.00 0.00 0.00 3.07
14 15 1.837538 GCTTGCGGCACTAACACGAA 61.838 55.000 0.05 0.00 41.35 3.85
37 38 5.233902 TCCGTTTTGCATGAAAATTGTCAAG 59.766 36.000 1.55 0.00 35.96 3.02
39 40 4.686972 TCCGTTTTGCATGAAAATTGTCA 58.313 34.783 0.00 0.00 35.96 3.58
40 41 4.376311 GCTCCGTTTTGCATGAAAATTGTC 60.376 41.667 0.00 0.00 35.96 3.18
41 42 3.494251 GCTCCGTTTTGCATGAAAATTGT 59.506 39.130 0.00 0.00 35.96 2.71
42 43 3.493877 TGCTCCGTTTTGCATGAAAATTG 59.506 39.130 0.00 0.00 35.96 2.32
43 44 3.726607 TGCTCCGTTTTGCATGAAAATT 58.273 36.364 0.00 0.00 35.96 1.82
44 45 3.243839 ACTGCTCCGTTTTGCATGAAAAT 60.244 39.130 0.00 0.00 38.59 1.82
45 46 2.100584 ACTGCTCCGTTTTGCATGAAAA 59.899 40.909 0.00 0.00 38.59 2.29
46 47 1.680735 ACTGCTCCGTTTTGCATGAAA 59.319 42.857 0.00 0.00 38.59 2.69
47 48 1.317613 ACTGCTCCGTTTTGCATGAA 58.682 45.000 0.00 0.00 38.59 2.57
48 49 2.076100 CTACTGCTCCGTTTTGCATGA 58.924 47.619 0.00 0.00 38.59 3.07
49 50 1.806542 ACTACTGCTCCGTTTTGCATG 59.193 47.619 0.00 0.00 38.59 4.06
58 59 1.455786 CGACAAAACACTACTGCTCCG 59.544 52.381 0.00 0.00 0.00 4.63
175 177 5.221362 GCTACCTCCAAAGTTTTAGGCAAAA 60.221 40.000 11.98 0.00 31.98 2.44
179 181 3.418047 TGCTACCTCCAAAGTTTTAGGC 58.582 45.455 11.98 2.20 31.98 3.93
192 194 3.878778 AGTCACATCCAAATGCTACCTC 58.121 45.455 0.00 0.00 36.26 3.85
292 294 1.136891 CGGAAATCCAATTTGGCTCCC 59.863 52.381 10.76 7.94 37.47 4.30
357 359 3.762823 CGGAGGGAGTACTTCTGTAAACT 59.237 47.826 0.01 0.00 0.00 2.66
367 369 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
368 370 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
369 371 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
370 372 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
371 373 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
372 374 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
373 375 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
374 376 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
375 377 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
376 378 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
377 379 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
392 394 9.996554 TCACTTGTTGAAATATCTAGAAAGACA 57.003 29.630 0.00 0.00 33.57 3.41
424 426 9.856488 GTGTAGATTCACTCATTTTACTCTGTA 57.144 33.333 0.00 0.00 35.68 2.74
425 427 8.589338 AGTGTAGATTCACTCATTTTACTCTGT 58.411 33.333 0.00 0.00 44.07 3.41
426 428 8.994429 AGTGTAGATTCACTCATTTTACTCTG 57.006 34.615 0.00 0.00 44.07 3.35
481 483 9.626045 CTTTCTAAACATTTCAAATGGACTACC 57.374 33.333 14.70 0.00 0.00 3.18
484 486 8.912988 TGTCTTTCTAAACATTTCAAATGGACT 58.087 29.630 14.70 1.17 0.00 3.85
485 487 9.528018 TTGTCTTTCTAAACATTTCAAATGGAC 57.472 29.630 14.70 9.36 0.00 4.02
500 502 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
501 503 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
502 504 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
503 505 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
504 506 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
505 507 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
506 508 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
507 509 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
508 510 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
509 511 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
510 512 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
511 513 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
512 514 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
513 515 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
514 516 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
515 517 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
516 518 3.682718 CGTACTACTCCCTCCGTTCCTAA 60.683 52.174 0.00 0.00 0.00 2.69
517 519 2.158900 CGTACTACTCCCTCCGTTCCTA 60.159 54.545 0.00 0.00 0.00 2.94
518 520 1.407989 CGTACTACTCCCTCCGTTCCT 60.408 57.143 0.00 0.00 0.00 3.36
519 521 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
520 522 1.399791 CACGTACTACTCCCTCCGTTC 59.600 57.143 0.00 0.00 0.00 3.95
521 523 1.003580 TCACGTACTACTCCCTCCGTT 59.996 52.381 0.00 0.00 0.00 4.44
522 524 0.615331 TCACGTACTACTCCCTCCGT 59.385 55.000 0.00 0.00 0.00 4.69
523 525 1.012841 GTCACGTACTACTCCCTCCG 58.987 60.000 0.00 0.00 0.00 4.63
524 526 2.119801 TGTCACGTACTACTCCCTCC 57.880 55.000 0.00 0.00 0.00 4.30
525 527 4.510038 TTTTGTCACGTACTACTCCCTC 57.490 45.455 0.00 0.00 0.00 4.30
526 528 4.099881 TGTTTTTGTCACGTACTACTCCCT 59.900 41.667 0.00 0.00 0.00 4.20
527 529 4.370917 TGTTTTTGTCACGTACTACTCCC 58.629 43.478 0.00 0.00 0.00 4.30
528 530 5.277011 GGTTGTTTTTGTCACGTACTACTCC 60.277 44.000 0.00 0.00 0.00 3.85
529 531 5.555069 CGGTTGTTTTTGTCACGTACTACTC 60.555 44.000 0.00 0.00 0.00 2.59
545 547 1.178276 TGGCTTCAACACGGTTGTTT 58.822 45.000 13.95 0.00 43.89 2.83
547 549 0.951558 GATGGCTTCAACACGGTTGT 59.048 50.000 13.95 0.00 37.67 3.32
549 551 1.072331 AGAGATGGCTTCAACACGGTT 59.928 47.619 3.03 0.00 0.00 4.44
550 552 0.687354 AGAGATGGCTTCAACACGGT 59.313 50.000 3.03 0.00 0.00 4.83
551 553 1.813513 AAGAGATGGCTTCAACACGG 58.186 50.000 3.03 0.00 0.00 4.94
552 554 3.904136 AAAAGAGATGGCTTCAACACG 57.096 42.857 3.03 0.00 0.00 4.49
581 766 0.391661 ATGAGATGGCTTCAACGCGT 60.392 50.000 5.58 5.58 0.00 6.01
582 767 1.524355 CTATGAGATGGCTTCAACGCG 59.476 52.381 3.53 3.53 0.00 6.01
583 768 1.262683 GCTATGAGATGGCTTCAACGC 59.737 52.381 3.03 0.68 33.53 4.84
584 769 2.554142 TGCTATGAGATGGCTTCAACG 58.446 47.619 3.03 0.00 37.67 4.10
585 770 4.153835 GCTATGCTATGAGATGGCTTCAAC 59.846 45.833 3.03 0.00 37.67 3.18
623 816 2.259204 CTGCCCGTTGCCAATGTG 59.741 61.111 0.00 0.00 40.16 3.21
814 1018 3.117701 AGTTGGAGGAGATCTCTGATCGA 60.118 47.826 21.81 11.97 42.10 3.59
820 1024 1.273495 TGGCAGTTGGAGGAGATCTCT 60.273 52.381 21.81 8.41 42.10 3.10
821 1025 1.198713 TGGCAGTTGGAGGAGATCTC 58.801 55.000 14.75 14.75 41.71 2.75
830 1034 0.110486 GAGAGGGTTTGGCAGTTGGA 59.890 55.000 0.00 0.00 0.00 3.53
847 1051 1.268352 GTGGATCGATCGAGGAAGGAG 59.732 57.143 23.84 0.00 0.00 3.69
888 1093 0.825840 GGAGGGAGAGGAGATGGTCG 60.826 65.000 0.00 0.00 0.00 4.79
893 1098 0.330431 AGGAGGGAGGGAGAGGAGAT 60.330 60.000 0.00 0.00 0.00 2.75
901 1106 6.043251 TCAGTGTATATATAGGAGGGAGGGA 58.957 44.000 0.00 0.00 0.00 4.20
905 1110 7.344599 AGTGTCAGTGTATATATAGGAGGGA 57.655 40.000 0.00 0.00 0.00 4.20
907 1112 7.121463 GTGGAGTGTCAGTGTATATATAGGAGG 59.879 44.444 0.00 0.00 0.00 4.30
1153 1372 2.632996 TGAGGTAGTTGAACAGGGTGAG 59.367 50.000 0.00 0.00 0.00 3.51
1161 1380 4.390297 GTCTTGCTGATGAGGTAGTTGAAC 59.610 45.833 0.00 0.00 0.00 3.18
1200 1419 1.577328 CGGAGTTGCGGCTGTTGATT 61.577 55.000 0.00 0.00 0.00 2.57
1895 2115 4.530553 AGACCAAAATTTATCGGGGCTTTT 59.469 37.500 0.00 0.00 31.28 2.27
1902 2122 7.707104 AGCTAATGAAGACCAAAATTTATCGG 58.293 34.615 0.00 0.00 0.00 4.18
2028 2251 2.169769 CCCTAGATTTTACACAGGCCGA 59.830 50.000 0.00 0.00 0.00 5.54
2029 2252 2.561569 CCCTAGATTTTACACAGGCCG 58.438 52.381 0.00 0.00 0.00 6.13
2091 2314 5.599999 TGAGAACTAGAGGCTGTAAATCC 57.400 43.478 0.00 0.00 0.00 3.01
2122 2345 3.751698 GTGTAAACTGGAGGTGGACATTC 59.248 47.826 0.00 0.00 0.00 2.67
2130 2353 0.756903 ACAGCGTGTAAACTGGAGGT 59.243 50.000 0.00 0.00 38.25 3.85
2174 2397 3.057526 GCCAGTGTTACTTTGATTGGGTC 60.058 47.826 0.00 0.00 0.00 4.46
2213 2436 9.076596 GTCAAGTTATTAATGGATTGCAACTTC 57.923 33.333 0.00 0.00 33.68 3.01
2252 2475 0.526211 GTGCCAATCCCTTTTCCGAC 59.474 55.000 0.00 0.00 0.00 4.79
2254 2477 1.604147 GGGTGCCAATCCCTTTTCCG 61.604 60.000 0.00 0.00 41.58 4.30
2339 2562 5.626142 TGTAGGGATTTTGCTAGTGTCAAA 58.374 37.500 0.00 0.00 0.00 2.69
2356 2579 7.999679 TCAGAAATGCATCTTTTTATGTAGGG 58.000 34.615 0.00 0.00 0.00 3.53
2370 2593 1.242076 GGCGGCTATCAGAAATGCAT 58.758 50.000 0.00 0.00 0.00 3.96
2395 3690 5.734720 CAACTAAGTAGAAAGATGGAGGCA 58.265 41.667 0.00 0.00 0.00 4.75
2396 3691 4.572795 GCAACTAAGTAGAAAGATGGAGGC 59.427 45.833 0.00 0.00 0.00 4.70
2398 3693 5.582665 GTGGCAACTAAGTAGAAAGATGGAG 59.417 44.000 0.00 0.00 37.61 3.86
2399 3694 5.488341 GTGGCAACTAAGTAGAAAGATGGA 58.512 41.667 0.00 0.00 37.61 3.41
2400 3695 4.636206 GGTGGCAACTAAGTAGAAAGATGG 59.364 45.833 0.00 0.00 37.61 3.51
2401 3696 5.122396 GTGGTGGCAACTAAGTAGAAAGATG 59.878 44.000 3.27 0.00 37.61 2.90
2402 3697 5.246307 GTGGTGGCAACTAAGTAGAAAGAT 58.754 41.667 3.27 0.00 37.61 2.40
2403 3698 4.504340 GGTGGTGGCAACTAAGTAGAAAGA 60.504 45.833 3.27 0.00 37.61 2.52
2404 3699 3.751698 GGTGGTGGCAACTAAGTAGAAAG 59.248 47.826 3.27 0.00 37.61 2.62
2405 3700 3.497227 GGGTGGTGGCAACTAAGTAGAAA 60.497 47.826 3.27 0.00 37.61 2.52
2407 3702 1.626825 GGGTGGTGGCAACTAAGTAGA 59.373 52.381 3.27 0.00 37.61 2.59
2410 3713 1.458927 GGGGTGGTGGCAACTAAGT 59.541 57.895 3.27 0.00 37.61 2.24
2414 3717 1.279025 ATATCGGGGTGGTGGCAACT 61.279 55.000 3.27 0.00 37.61 3.16
2485 3793 1.524621 CTGAGGCCCAGGTATTGCG 60.525 63.158 12.13 0.00 39.23 4.85
2503 3811 0.877071 TGGACGTGAACCTCTACGAC 59.123 55.000 0.00 0.00 42.54 4.34
2504 3812 0.877071 GTGGACGTGAACCTCTACGA 59.123 55.000 0.00 0.00 42.54 3.43
2514 3822 2.478709 GCAATGTTGTTTGTGGACGTGA 60.479 45.455 0.00 0.00 0.00 4.35
2540 3849 6.195060 CGTCGTTACTTTTCGTCCAAATTTTT 59.805 34.615 0.00 0.00 0.00 1.94
2541 3850 5.678047 CGTCGTTACTTTTCGTCCAAATTTT 59.322 36.000 0.00 0.00 0.00 1.82
2542 3851 5.199726 CGTCGTTACTTTTCGTCCAAATTT 58.800 37.500 0.00 0.00 0.00 1.82
2543 3852 4.270808 ACGTCGTTACTTTTCGTCCAAATT 59.729 37.500 0.00 0.00 0.00 1.82
2544 3853 3.803778 ACGTCGTTACTTTTCGTCCAAAT 59.196 39.130 0.00 0.00 0.00 2.32
2561 3875 6.418141 TCATCATAATTGTAATGCAACGTCG 58.582 36.000 0.00 0.00 40.28 5.12
2563 3877 7.984391 TCTTCATCATAATTGTAATGCAACGT 58.016 30.769 0.00 0.00 40.28 3.99
2578 3892 8.510243 AGCATTGTAATGTGTTCTTCATCATA 57.490 30.769 6.48 0.00 38.65 2.15
2619 3936 4.793216 GTCTTTGTGATGTTGTTGTGTGTC 59.207 41.667 0.00 0.00 0.00 3.67
2620 3937 4.217334 TGTCTTTGTGATGTTGTTGTGTGT 59.783 37.500 0.00 0.00 0.00 3.72
2621 3938 4.558470 GTGTCTTTGTGATGTTGTTGTGTG 59.442 41.667 0.00 0.00 0.00 3.82
2633 3956 3.880490 GGTATGTTGTGGTGTCTTTGTGA 59.120 43.478 0.00 0.00 0.00 3.58
2695 4029 0.181587 TTCCCCTTGTTGAGCGTTCA 59.818 50.000 0.00 0.00 0.00 3.18
2699 4033 0.674895 CTCCTTCCCCTTGTTGAGCG 60.675 60.000 0.00 0.00 0.00 5.03
2725 4060 1.065199 GGTCAGGTGATGATGGAAGCA 60.065 52.381 0.00 0.00 40.92 3.91
2739 4074 1.888018 CATGCCTTGCTTGGTCAGG 59.112 57.895 0.00 0.00 31.40 3.86
2779 4114 3.872603 TGCTGTCGGGTGGCAACT 61.873 61.111 0.97 0.00 32.79 3.16


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

AutoCloner maintained by Alex Coulton.