Multiple sequence alignment - TraesCS2D01G325900

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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 TraesCS2D01G325900 chr2D 100.000 4485 0 0 1 4485 419367622 419363138 0.000000e+00 8283.0
1 TraesCS2D01G325900 chr2A 92.516 3995 175 52 375 4274 570606190 570610155 0.000000e+00 5607.0
2 TraesCS2D01G325900 chr2A 91.768 328 27 0 1 328 570605880 570606207 1.470000e-124 457.0
3 TraesCS2D01G325900 chr2B 93.900 3295 123 32 375 3608 491714465 491711188 0.000000e+00 4900.0
4 TraesCS2D01G325900 chr2B 87.321 907 78 18 3608 4485 491711156 491710258 0.000000e+00 1003.0
5 TraesCS2D01G325900 chr2B 87.316 339 32 3 1 328 491714786 491714448 1.180000e-100 377.0
6 TraesCS2D01G325900 chr7D 76.832 505 83 24 2581 3063 176166385 176166877 2.070000e-63 254.0
7 TraesCS2D01G325900 chr3D 81.356 118 21 1 4368 4485 25347115 25347231 1.330000e-15 95.3
8 TraesCS2D01G325900 chr7A 81.731 104 19 0 4382 4485 117604834 117604731 2.220000e-13 87.9
9 TraesCS2D01G325900 chr1B 92.308 52 4 0 2807 2858 364918813 364918762 1.730000e-09 75.0
10 TraesCS2D01G325900 chr1A 91.837 49 4 0 2807 2855 319320881 319320929 8.050000e-08 69.4
11 TraesCS2D01G325900 chr1D 95.122 41 2 0 2807 2847 249560898 249560938 1.040000e-06 65.8


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 TraesCS2D01G325900 chr2D 419363138 419367622 4484 True 8283.000000 8283 100.000000 1 4485 1 chr2D.!!$R1 4484
1 TraesCS2D01G325900 chr2A 570605880 570610155 4275 False 3032.000000 5607 92.142000 1 4274 2 chr2A.!!$F1 4273
2 TraesCS2D01G325900 chr2B 491710258 491714786 4528 True 2093.333333 4900 89.512333 1 4485 3 chr2B.!!$R1 4484

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
892 936 0.024111 CGTTTTATCGAACGGCCGAC 59.976 55.000 35.90 23.34 46.29 4.79 F
2536 2605 0.460987 CCGGTGAGATTCTCAGGCAC 60.461 60.000 16.62 5.72 41.46 5.01 F
2660 2729 1.210155 GCACGGCAACATCAAGTCC 59.790 57.895 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 2729 0.105039 GGCCGAGGAGTATGTTGGAG 59.895 60.0 0.0 0.0 0.0 3.86 R
3396 3480 0.037512 CTATCGCCAGCATCCCTCAG 60.038 60.0 0.0 0.0 0.0 3.35 R
3942 4147 0.478072 ATGACAGACAAGGGGTGCAA 59.522 50.0 0.0 0.0 0.0 4.08 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
69 70 6.058833 TCGCCAGATATAACCATGCTTTAAA 58.941 36.000 0.00 0.00 0.00 1.52
82 83 5.394553 CCATGCTTTAAAGAATTGACTCCCC 60.395 44.000 19.48 0.00 0.00 4.81
174 185 7.581213 TTGCTCTTAAATTATGTACCCCATG 57.419 36.000 0.00 0.00 34.86 3.66
231 243 2.037641 TGACTGACTCTGACCACCATTG 59.962 50.000 0.00 0.00 0.00 2.82
252 264 2.029739 GGCTCTCGGCTATTCCTAGTTC 60.030 54.545 0.00 0.00 41.46 3.01
320 332 1.741732 CGTTCCTAGCTCAGCATTGCT 60.742 52.381 5.03 5.03 40.77 3.91
321 333 1.939255 GTTCCTAGCTCAGCATTGCTC 59.061 52.381 8.54 0.00 36.40 4.26
322 334 1.197812 TCCTAGCTCAGCATTGCTCA 58.802 50.000 8.54 0.00 36.40 4.26
323 335 1.138464 TCCTAGCTCAGCATTGCTCAG 59.862 52.381 8.54 6.70 36.40 3.35
324 336 1.138464 CCTAGCTCAGCATTGCTCAGA 59.862 52.381 14.28 6.14 36.40 3.27
325 337 2.419713 CCTAGCTCAGCATTGCTCAGAA 60.420 50.000 14.28 0.00 36.40 3.02
326 338 1.740297 AGCTCAGCATTGCTCAGAAG 58.260 50.000 14.28 7.92 36.40 2.85
327 339 1.003349 AGCTCAGCATTGCTCAGAAGT 59.997 47.619 14.28 0.00 36.40 3.01
328 340 1.397692 GCTCAGCATTGCTCAGAAGTC 59.602 52.381 14.28 0.00 36.40 3.01
329 341 2.936114 GCTCAGCATTGCTCAGAAGTCT 60.936 50.000 14.28 0.00 36.40 3.24
330 342 3.336468 CTCAGCATTGCTCAGAAGTCTT 58.664 45.455 8.54 0.00 36.40 3.01
331 343 3.748083 TCAGCATTGCTCAGAAGTCTTT 58.252 40.909 8.54 0.00 36.40 2.52
332 344 4.139786 TCAGCATTGCTCAGAAGTCTTTT 58.860 39.130 8.54 0.00 36.40 2.27
333 345 4.581824 TCAGCATTGCTCAGAAGTCTTTTT 59.418 37.500 8.54 0.00 36.40 1.94
360 372 9.860898 TTTTTCCTTTTGAAGAAGAAGAAGAAG 57.139 29.630 0.00 0.00 33.63 2.85
361 373 8.807948 TTTCCTTTTGAAGAAGAAGAAGAAGA 57.192 30.769 0.00 0.00 33.63 2.87
362 374 8.807948 TTCCTTTTGAAGAAGAAGAAGAAGAA 57.192 30.769 0.00 0.00 0.00 2.52
363 375 8.443953 TCCTTTTGAAGAAGAAGAAGAAGAAG 57.556 34.615 0.00 0.00 0.00 2.85
364 376 8.267894 TCCTTTTGAAGAAGAAGAAGAAGAAGA 58.732 33.333 0.00 0.00 0.00 2.87
365 377 8.897752 CCTTTTGAAGAAGAAGAAGAAGAAGAA 58.102 33.333 0.00 0.00 0.00 2.52
366 378 9.715123 CTTTTGAAGAAGAAGAAGAAGAAGAAC 57.285 33.333 0.00 0.00 0.00 3.01
367 379 7.793927 TTGAAGAAGAAGAAGAAGAAGAACC 57.206 36.000 0.00 0.00 0.00 3.62
368 380 6.889198 TGAAGAAGAAGAAGAAGAAGAACCA 58.111 36.000 0.00 0.00 0.00 3.67
369 381 7.512992 TGAAGAAGAAGAAGAAGAAGAACCAT 58.487 34.615 0.00 0.00 0.00 3.55
370 382 7.443575 TGAAGAAGAAGAAGAAGAAGAACCATG 59.556 37.037 0.00 0.00 0.00 3.66
371 383 6.836242 AGAAGAAGAAGAAGAAGAACCATGT 58.164 36.000 0.00 0.00 0.00 3.21
372 384 7.967908 AGAAGAAGAAGAAGAAGAACCATGTA 58.032 34.615 0.00 0.00 0.00 2.29
373 385 8.601546 AGAAGAAGAAGAAGAAGAACCATGTAT 58.398 33.333 0.00 0.00 0.00 2.29
374 386 9.225436 GAAGAAGAAGAAGAAGAACCATGTATT 57.775 33.333 0.00 0.00 0.00 1.89
375 387 8.785329 AGAAGAAGAAGAAGAACCATGTATTC 57.215 34.615 0.00 0.00 0.00 1.75
376 388 8.378565 AGAAGAAGAAGAAGAACCATGTATTCA 58.621 33.333 9.05 0.00 0.00 2.57
377 389 8.558973 AAGAAGAAGAAGAACCATGTATTCAG 57.441 34.615 9.05 0.00 0.00 3.02
378 390 6.597280 AGAAGAAGAAGAACCATGTATTCAGC 59.403 38.462 9.05 1.97 0.00 4.26
379 391 5.809001 AGAAGAAGAACCATGTATTCAGCA 58.191 37.500 9.05 0.00 0.00 4.41
380 392 6.421485 AGAAGAAGAACCATGTATTCAGCAT 58.579 36.000 9.05 0.00 0.00 3.79
381 393 6.888632 AGAAGAAGAACCATGTATTCAGCATT 59.111 34.615 9.05 0.41 0.00 3.56
382 394 6.446781 AGAAGAACCATGTATTCAGCATTG 57.553 37.500 9.05 0.00 0.00 2.82
383 395 4.644103 AGAACCATGTATTCAGCATTGC 57.356 40.909 0.00 0.00 0.00 3.56
384 396 4.275810 AGAACCATGTATTCAGCATTGCT 58.724 39.130 5.03 5.03 40.77 3.91
385 397 4.337555 AGAACCATGTATTCAGCATTGCTC 59.662 41.667 8.54 0.00 36.40 4.26
398 410 2.996621 GCATTGCTCAGAAGTTACTCGT 59.003 45.455 0.16 0.00 0.00 4.18
428 440 3.181499 ACGGTAACTGACAGACGATCATC 60.181 47.826 10.08 0.00 0.00 2.92
429 441 3.181500 CGGTAACTGACAGACGATCATCA 60.181 47.826 10.08 0.00 0.00 3.07
441 455 1.565305 GATCATCACACACTCGCTCC 58.435 55.000 0.00 0.00 0.00 4.70
457 471 2.163613 CGCTCCAATTTTTCCTACACCC 59.836 50.000 0.00 0.00 0.00 4.61
510 533 1.868251 CGCTCTCGACAGTTACGGC 60.868 63.158 0.00 0.00 38.10 5.68
581 610 2.421314 CACGTCCACAGCTCCACA 59.579 61.111 0.00 0.00 0.00 4.17
589 618 1.004595 CACAGCTCCACACATCATCG 58.995 55.000 0.00 0.00 0.00 3.84
598 627 1.655597 CACACATCATCGAGTGAACCG 59.344 52.381 9.28 1.71 40.97 4.44
655 691 1.684869 GGAAAATGGCCAGGGATTCGA 60.685 52.381 13.05 0.00 0.00 3.71
728 771 4.213564 ACAACTGCCCAAAATTCAAACA 57.786 36.364 0.00 0.00 0.00 2.83
729 772 4.779696 ACAACTGCCCAAAATTCAAACAT 58.220 34.783 0.00 0.00 0.00 2.71
736 779 4.754114 GCCCAAAATTCAAACATGCAACTA 59.246 37.500 0.00 0.00 0.00 2.24
740 783 8.351461 CCCAAAATTCAAACATGCAACTATTTT 58.649 29.630 0.00 0.00 0.00 1.82
749 792 4.201950 ACATGCAACTATTTTCGCTGATCC 60.202 41.667 0.00 0.00 0.00 3.36
777 820 2.863740 CGCACTGTTGAGTTGAGTTGTA 59.136 45.455 0.00 0.00 0.00 2.41
791 834 4.270008 TGAGTTGTACTCCAGATCATCGA 58.730 43.478 4.52 0.00 44.44 3.59
792 835 4.705023 TGAGTTGTACTCCAGATCATCGAA 59.295 41.667 4.52 0.00 44.44 3.71
793 836 5.000012 AGTTGTACTCCAGATCATCGAAC 58.000 43.478 0.00 0.00 0.00 3.95
794 837 4.707448 AGTTGTACTCCAGATCATCGAACT 59.293 41.667 0.00 0.00 0.00 3.01
795 838 5.886474 AGTTGTACTCCAGATCATCGAACTA 59.114 40.000 0.00 0.00 0.00 2.24
796 839 6.547880 AGTTGTACTCCAGATCATCGAACTAT 59.452 38.462 0.00 0.00 0.00 2.12
842 885 1.528776 AGGAGTAGGATCGGCGACC 60.529 63.158 13.76 15.96 0.00 4.79
878 922 2.203042 TCGGCCGTCCAACGTTTT 60.203 55.556 27.15 0.00 40.58 2.43
883 927 1.070038 GCCGTCCAACGTTTTATCGA 58.930 50.000 0.00 0.00 40.58 3.59
892 936 0.024111 CGTTTTATCGAACGGCCGAC 59.976 55.000 35.90 23.34 46.29 4.79
1022 1070 5.734720 TGTGAAGCTTCTTTCCGATATTCT 58.265 37.500 26.09 0.00 0.00 2.40
1023 1071 5.582269 TGTGAAGCTTCTTTCCGATATTCTG 59.418 40.000 26.09 0.00 0.00 3.02
1084 1139 1.078426 GGTGTGATCGACCAAGGGG 60.078 63.158 8.52 0.00 41.29 4.79
1380 1440 4.008933 AGGCTCACCGTGCTGTCC 62.009 66.667 0.00 0.00 42.76 4.02
1641 1701 1.515519 GCTGCCGAACGTCGACATA 60.516 57.895 17.16 0.00 43.74 2.29
1911 1971 3.994853 GGCTGCGCTTTGGGCTTT 61.995 61.111 9.73 0.00 42.10 3.51
1944 2004 2.328099 CGTTCTGGTCCTTGCCTGC 61.328 63.158 0.00 0.00 0.00 4.85
2169 2229 0.466739 TGCCGAGGCCTTACGATCTA 60.467 55.000 15.05 0.00 41.09 1.98
2349 2409 0.462047 GGCTGGACCATCCTAACGTG 60.462 60.000 7.14 0.00 37.46 4.49
2443 2503 0.803768 CTCCTCGATGCTTCACGGTG 60.804 60.000 0.56 0.56 0.00 4.94
2455 2524 3.542676 ACGGTGCGTGTTCCTGGA 61.543 61.111 0.00 0.00 39.18 3.86
2456 2525 2.047274 CGGTGCGTGTTCCTGGAT 60.047 61.111 0.00 0.00 0.00 3.41
2457 2526 2.100631 CGGTGCGTGTTCCTGGATC 61.101 63.158 0.00 0.00 0.00 3.36
2459 2528 0.605319 GGTGCGTGTTCCTGGATCAA 60.605 55.000 8.97 0.00 0.00 2.57
2460 2529 1.234821 GTGCGTGTTCCTGGATCAAA 58.765 50.000 8.97 0.00 0.00 2.69
2461 2530 1.812571 GTGCGTGTTCCTGGATCAAAT 59.187 47.619 8.97 0.00 0.00 2.32
2499 2568 2.704572 CTCCAAACTCTGCTCCGAATT 58.295 47.619 0.00 0.00 0.00 2.17
2518 2587 6.311200 CCGAATTGGATCAAAATTTCTGAACC 59.689 38.462 16.01 16.01 42.00 3.62
2526 2595 5.070001 TCAAAATTTCTGAACCGGTGAGAT 58.930 37.500 8.52 0.00 0.00 2.75
2536 2605 0.460987 CCGGTGAGATTCTCAGGCAC 60.461 60.000 16.62 5.72 41.46 5.01
2573 2642 3.385384 CCGCTGAGCTGGGAGTCA 61.385 66.667 1.78 0.00 0.00 3.41
2660 2729 1.210155 GCACGGCAACATCAAGTCC 59.790 57.895 0.00 0.00 0.00 3.85
3396 3480 1.464608 TCTTTGATTAGCTGCGTGTGC 59.535 47.619 0.00 0.00 43.20 4.57
3580 3673 1.540267 CCTGCATGGGAACGGTAAAA 58.460 50.000 0.00 0.00 0.00 1.52
3608 3701 7.951530 AAGTGTTCTTAATTTGCCATGAAAG 57.048 32.000 0.00 0.00 31.46 2.62
3616 3741 3.634568 TTTGCCATGAAAGTAACACGG 57.365 42.857 0.00 0.00 0.00 4.94
3635 3760 2.645802 GGATTGGCCACCGTAAATGTA 58.354 47.619 3.88 0.00 36.34 2.29
3636 3761 3.219281 GGATTGGCCACCGTAAATGTAT 58.781 45.455 3.88 0.00 36.34 2.29
3637 3762 3.004315 GGATTGGCCACCGTAAATGTATG 59.996 47.826 3.88 0.00 36.34 2.39
3638 3763 2.791347 TGGCCACCGTAAATGTATGT 57.209 45.000 0.00 0.00 0.00 2.29
3639 3764 2.634600 TGGCCACCGTAAATGTATGTC 58.365 47.619 0.00 0.00 0.00 3.06
3640 3765 2.027100 TGGCCACCGTAAATGTATGTCA 60.027 45.455 0.00 0.00 0.00 3.58
3642 3767 3.181504 GGCCACCGTAAATGTATGTCAAC 60.182 47.826 0.00 0.00 0.00 3.18
3722 3851 1.858458 TCTGTGAAAGCAACGAGAACG 59.142 47.619 0.00 0.00 45.75 3.95
3766 3932 2.677228 CTGTCCCCGGCCAAGATT 59.323 61.111 2.24 0.00 0.00 2.40
3777 3958 1.807886 CCAAGATTCTGGCTGCAGC 59.192 57.895 30.88 30.88 41.14 5.25
3951 4156 0.260816 AGATCATGCATTGCACCCCT 59.739 50.000 14.66 6.19 43.04 4.79
4104 4311 4.647424 TGAACAATTGGTCCTGTGTTTC 57.353 40.909 20.61 6.83 34.44 2.78
4149 4356 1.339631 GGACACGACCATCCAATCCAA 60.340 52.381 0.00 0.00 34.87 3.53
4211 4418 6.458232 ACAGCTGATCTTTACTACTACTGG 57.542 41.667 23.35 0.00 0.00 4.00
4218 4425 7.609056 TGATCTTTACTACTACTGGTTTCCAC 58.391 38.462 0.00 0.00 0.00 4.02
4231 4438 2.032924 GGTTTCCACGGACACTTTCTTG 59.967 50.000 2.57 0.00 0.00 3.02
4241 4448 6.851330 CACGGACACTTTCTTGAGTAATTTTC 59.149 38.462 0.00 0.00 0.00 2.29
4287 4495 4.477302 CATGAAGCGATACATGCATTCA 57.523 40.909 0.00 0.00 37.62 2.57
4327 4536 6.844097 AACATGACCCGGTAAAACAAATAT 57.156 33.333 0.00 0.00 0.00 1.28
4331 4540 7.558444 ACATGACCCGGTAAAACAAATATATGT 59.442 33.333 0.00 0.00 34.24 2.29
4352 4561 6.757897 TGTATCAATCCAAAACCATCTGTC 57.242 37.500 0.00 0.00 0.00 3.51
4354 4563 7.629157 TGTATCAATCCAAAACCATCTGTCTA 58.371 34.615 0.00 0.00 0.00 2.59
4356 4565 9.125026 GTATCAATCCAAAACCATCTGTCTAAT 57.875 33.333 0.00 0.00 0.00 1.73
4358 4567 9.699410 ATCAATCCAAAACCATCTGTCTAATAA 57.301 29.630 0.00 0.00 0.00 1.40
4359 4568 9.177608 TCAATCCAAAACCATCTGTCTAATAAG 57.822 33.333 0.00 0.00 0.00 1.73
4360 4569 8.960591 CAATCCAAAACCATCTGTCTAATAAGT 58.039 33.333 0.00 0.00 0.00 2.24
4376 4585 9.351570 GTCTAATAAGTAAACAGTGTCACTACC 57.648 37.037 4.85 0.00 0.00 3.18
4385 4594 1.900486 AGTGTCACTACCCCTACAAGC 59.100 52.381 2.87 0.00 0.00 4.01
4395 4604 1.952296 CCCCTACAAGCTTGATGATGC 59.048 52.381 32.50 0.00 0.00 3.91
4396 4605 1.600957 CCCTACAAGCTTGATGATGCG 59.399 52.381 32.50 11.46 0.00 4.73
4397 4606 2.283298 CCTACAAGCTTGATGATGCGT 58.717 47.619 32.50 10.21 0.00 5.24
4398 4607 2.031314 CCTACAAGCTTGATGATGCGTG 59.969 50.000 32.50 3.05 42.62 5.34
4401 4610 2.247637 CAAGCTTGATGATGCGTGTTG 58.752 47.619 22.31 0.00 34.81 3.33
4406 4615 2.183478 TGATGATGCGTGTTGACCTT 57.817 45.000 0.00 0.00 0.00 3.50
4408 4617 1.806542 GATGATGCGTGTTGACCTTGT 59.193 47.619 0.00 0.00 0.00 3.16
4410 4619 2.139917 TGATGCGTGTTGACCTTGTAC 58.860 47.619 0.00 0.00 0.00 2.90
4413 4622 1.301423 GCGTGTTGACCTTGTACCAA 58.699 50.000 0.00 0.00 0.00 3.67
4421 4630 1.944709 GACCTTGTACCAACACACACC 59.055 52.381 0.00 0.00 34.61 4.16
4430 4639 3.686016 ACCAACACACACCATCTAATCC 58.314 45.455 0.00 0.00 0.00 3.01
4431 4640 3.073798 ACCAACACACACCATCTAATCCA 59.926 43.478 0.00 0.00 0.00 3.41
4435 4644 3.273434 CACACACCATCTAATCCAGTGG 58.727 50.000 1.40 1.40 37.74 4.00
4441 4650 2.486191 CCATCTAATCCAGTGGCCTCAC 60.486 54.545 3.51 0.00 43.93 3.51
4442 4651 1.951209 TCTAATCCAGTGGCCTCACA 58.049 50.000 3.51 0.00 45.91 3.58
4468 4677 3.184683 CAACAGCGAGCCGAGAGC 61.185 66.667 0.00 0.00 44.25 4.09
4482 4691 2.223688 CCGAGAGCATCAACCAGTCTAG 60.224 54.545 0.00 0.00 37.82 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.124151 GGCGAGTGGGCAATGGAT 60.124 61.111 0.00 0.00 41.77 3.41
40 41 1.691976 TGGTTATATCTGGCGAGTGGG 59.308 52.381 0.00 0.00 0.00 4.61
82 83 9.533253 CTCTTTTAATTGGCAAAGTATTATGGG 57.467 33.333 3.01 0.00 32.67 4.00
174 185 4.087930 CGTTTGTCGACATATTTTGCAACC 59.912 41.667 20.80 0.00 42.86 3.77
231 243 1.623163 ACTAGGAATAGCCGAGAGCC 58.377 55.000 0.00 0.00 45.47 4.70
274 286 5.563842 CATTTCCTTCGTAAGTGCAGAATC 58.436 41.667 0.00 0.00 39.48 2.52
334 346 9.860898 CTTCTTCTTCTTCTTCAAAAGGAAAAA 57.139 29.630 0.00 0.00 34.44 1.94
335 347 9.243105 TCTTCTTCTTCTTCTTCAAAAGGAAAA 57.757 29.630 0.00 0.00 34.44 2.29
336 348 8.807948 TCTTCTTCTTCTTCTTCAAAAGGAAA 57.192 30.769 0.00 0.00 34.44 3.13
337 349 8.807948 TTCTTCTTCTTCTTCTTCAAAAGGAA 57.192 30.769 0.00 0.00 0.00 3.36
338 350 8.267894 TCTTCTTCTTCTTCTTCTTCAAAAGGA 58.732 33.333 0.00 0.00 0.00 3.36
339 351 8.443953 TCTTCTTCTTCTTCTTCTTCAAAAGG 57.556 34.615 0.00 0.00 0.00 3.11
340 352 9.715123 GTTCTTCTTCTTCTTCTTCTTCAAAAG 57.285 33.333 0.00 0.00 0.00 2.27
341 353 8.678199 GGTTCTTCTTCTTCTTCTTCTTCAAAA 58.322 33.333 0.00 0.00 0.00 2.44
342 354 7.829211 TGGTTCTTCTTCTTCTTCTTCTTCAAA 59.171 33.333 0.00 0.00 0.00 2.69
343 355 7.338710 TGGTTCTTCTTCTTCTTCTTCTTCAA 58.661 34.615 0.00 0.00 0.00 2.69
344 356 6.889198 TGGTTCTTCTTCTTCTTCTTCTTCA 58.111 36.000 0.00 0.00 0.00 3.02
345 357 7.443879 ACATGGTTCTTCTTCTTCTTCTTCTTC 59.556 37.037 0.00 0.00 0.00 2.87
346 358 7.286313 ACATGGTTCTTCTTCTTCTTCTTCTT 58.714 34.615 0.00 0.00 0.00 2.52
347 359 6.836242 ACATGGTTCTTCTTCTTCTTCTTCT 58.164 36.000 0.00 0.00 0.00 2.85
348 360 8.785329 ATACATGGTTCTTCTTCTTCTTCTTC 57.215 34.615 0.00 0.00 0.00 2.87
349 361 9.225436 GAATACATGGTTCTTCTTCTTCTTCTT 57.775 33.333 0.00 0.00 0.00 2.52
350 362 8.378565 TGAATACATGGTTCTTCTTCTTCTTCT 58.621 33.333 12.47 0.00 0.00 2.85
351 363 8.553459 TGAATACATGGTTCTTCTTCTTCTTC 57.447 34.615 12.47 0.00 0.00 2.87
352 364 7.120432 GCTGAATACATGGTTCTTCTTCTTCTT 59.880 37.037 12.47 0.00 0.00 2.52
353 365 6.597280 GCTGAATACATGGTTCTTCTTCTTCT 59.403 38.462 12.47 0.00 0.00 2.85
354 366 6.372659 TGCTGAATACATGGTTCTTCTTCTTC 59.627 38.462 12.47 0.00 0.00 2.87
355 367 6.240894 TGCTGAATACATGGTTCTTCTTCTT 58.759 36.000 12.47 0.00 0.00 2.52
356 368 5.809001 TGCTGAATACATGGTTCTTCTTCT 58.191 37.500 12.47 0.00 0.00 2.85
357 369 6.690194 ATGCTGAATACATGGTTCTTCTTC 57.310 37.500 12.47 0.10 0.00 2.87
358 370 6.626623 GCAATGCTGAATACATGGTTCTTCTT 60.627 38.462 0.00 3.05 0.00 2.52
359 371 5.163581 GCAATGCTGAATACATGGTTCTTCT 60.164 40.000 0.00 0.00 0.00 2.85
360 372 5.039333 GCAATGCTGAATACATGGTTCTTC 58.961 41.667 0.00 4.07 0.00 2.87
361 373 4.708421 AGCAATGCTGAATACATGGTTCTT 59.292 37.500 7.07 0.00 37.57 2.52
362 374 4.275810 AGCAATGCTGAATACATGGTTCT 58.724 39.130 7.07 0.00 37.57 3.01
363 375 4.096833 TGAGCAATGCTGAATACATGGTTC 59.903 41.667 14.48 1.79 39.88 3.62
364 376 4.018490 TGAGCAATGCTGAATACATGGTT 58.982 39.130 14.48 0.00 39.88 3.67
365 377 3.623703 TGAGCAATGCTGAATACATGGT 58.376 40.909 14.48 0.00 39.88 3.55
366 378 3.881089 TCTGAGCAATGCTGAATACATGG 59.119 43.478 14.48 0.00 39.88 3.66
367 379 5.066117 ACTTCTGAGCAATGCTGAATACATG 59.934 40.000 14.48 1.48 39.88 3.21
368 380 5.191426 ACTTCTGAGCAATGCTGAATACAT 58.809 37.500 14.48 0.00 39.88 2.29
369 381 4.582869 ACTTCTGAGCAATGCTGAATACA 58.417 39.130 14.48 2.51 39.88 2.29
370 382 5.557891 AACTTCTGAGCAATGCTGAATAC 57.442 39.130 14.48 0.00 39.88 1.89
371 383 6.409704 AGTAACTTCTGAGCAATGCTGAATA 58.590 36.000 14.48 0.00 39.88 1.75
372 384 5.251764 AGTAACTTCTGAGCAATGCTGAAT 58.748 37.500 14.48 0.00 39.88 2.57
373 385 4.645535 AGTAACTTCTGAGCAATGCTGAA 58.354 39.130 14.48 10.21 39.88 3.02
374 386 4.248859 GAGTAACTTCTGAGCAATGCTGA 58.751 43.478 14.48 2.26 39.88 4.26
375 387 3.061831 CGAGTAACTTCTGAGCAATGCTG 59.938 47.826 14.48 0.00 39.88 4.41
376 388 3.257393 CGAGTAACTTCTGAGCAATGCT 58.743 45.455 7.79 7.79 43.88 3.79
377 389 2.996621 ACGAGTAACTTCTGAGCAATGC 59.003 45.455 0.00 0.00 0.00 3.56
378 390 4.686091 TGAACGAGTAACTTCTGAGCAATG 59.314 41.667 0.00 0.00 0.00 2.82
379 391 4.883083 TGAACGAGTAACTTCTGAGCAAT 58.117 39.130 0.00 0.00 0.00 3.56
380 392 4.316205 TGAACGAGTAACTTCTGAGCAA 57.684 40.909 0.00 0.00 0.00 3.91
381 393 4.049186 GTTGAACGAGTAACTTCTGAGCA 58.951 43.478 0.00 0.00 0.00 4.26
382 394 3.119792 CGTTGAACGAGTAACTTCTGAGC 59.880 47.826 13.13 0.00 46.05 4.26
383 395 3.669122 CCGTTGAACGAGTAACTTCTGAG 59.331 47.826 20.47 0.00 46.05 3.35
384 396 3.316029 TCCGTTGAACGAGTAACTTCTGA 59.684 43.478 20.47 0.43 46.05 3.27
385 397 3.424529 GTCCGTTGAACGAGTAACTTCTG 59.575 47.826 20.47 0.00 46.05 3.02
398 410 1.408340 TGTCAGTTACCGTCCGTTGAA 59.592 47.619 0.00 0.00 0.00 2.69
428 440 3.300009 GAAAAATTGGAGCGAGTGTGTG 58.700 45.455 0.00 0.00 0.00 3.82
429 441 2.293399 GGAAAAATTGGAGCGAGTGTGT 59.707 45.455 0.00 0.00 0.00 3.72
441 455 2.413634 GCGTCGGGTGTAGGAAAAATTG 60.414 50.000 0.00 0.00 0.00 2.32
457 471 2.607180 TGTAAATGTCATGATGGCGTCG 59.393 45.455 0.00 0.00 0.00 5.12
519 542 0.390735 CGAAGTAAACCGGTCCCTGG 60.391 60.000 8.04 0.00 0.00 4.45
581 610 0.895530 ACCGGTTCACTCGATGATGT 59.104 50.000 0.00 0.00 37.11 3.06
589 618 0.666577 CTTCGTGGACCGGTTCACTC 60.667 60.000 36.91 17.80 37.11 3.51
598 627 2.668280 GCAGTTCGCTTCGTGGACC 61.668 63.158 0.00 0.00 37.77 4.46
617 646 1.302033 CTGCTGACATATCCCCGGC 60.302 63.158 0.00 0.00 0.00 6.13
655 691 3.719268 TGTAGGCCAATGTGATGAACT 57.281 42.857 5.01 0.00 0.00 3.01
714 757 7.437793 AATAGTTGCATGTTTGAATTTTGGG 57.562 32.000 0.00 0.00 0.00 4.12
728 771 4.202441 AGGATCAGCGAAAATAGTTGCAT 58.798 39.130 0.00 0.00 0.00 3.96
729 772 3.609853 AGGATCAGCGAAAATAGTTGCA 58.390 40.909 0.00 0.00 0.00 4.08
736 779 3.670627 GCGTGAAAAGGATCAGCGAAAAT 60.671 43.478 0.00 0.00 0.00 1.82
740 783 0.320334 TGCGTGAAAAGGATCAGCGA 60.320 50.000 0.00 0.00 0.00 4.93
749 792 3.100817 CAACTCAACAGTGCGTGAAAAG 58.899 45.455 0.00 0.00 31.06 2.27
777 820 5.049060 CGAGAATAGTTCGATGATCTGGAGT 60.049 44.000 0.00 0.00 40.36 3.85
878 922 0.457166 CTGTTGTCGGCCGTTCGATA 60.457 55.000 27.15 15.75 41.40 2.92
892 936 2.224079 CACATTCTTGGTCCGACTGTTG 59.776 50.000 0.00 0.00 0.00 3.33
1022 1070 2.218603 GAGGGACGAAACAAGAAAGCA 58.781 47.619 0.00 0.00 0.00 3.91
1023 1071 1.535896 GGAGGGACGAAACAAGAAAGC 59.464 52.381 0.00 0.00 0.00 3.51
1487 1547 2.128507 GGGAGGGAGAGAATCGCGT 61.129 63.158 5.77 0.00 45.29 6.01
1641 1701 4.202430 ACGTTAAAAGACAAGAGGGATGGT 60.202 41.667 0.00 0.00 0.00 3.55
1695 1755 2.112198 CATGCCGCCGAAGCCTTTA 61.112 57.895 0.00 0.00 34.57 1.85
1953 2013 4.107051 CTTCTTGGCTTGCGGCGG 62.107 66.667 9.78 0.00 42.94 6.13
2160 2220 3.478509 GAGCAGGTCCTCTAGATCGTAA 58.521 50.000 0.00 0.00 0.00 3.18
2199 2259 2.671619 TACGTGCCCTTGCCAAGC 60.672 61.111 0.00 0.00 36.33 4.01
2271 2331 1.153939 CAGCGACGTCTCCTTGAGG 60.154 63.158 14.70 0.00 36.69 3.86
2443 2503 3.191371 AGAAATTTGATCCAGGAACACGC 59.809 43.478 0.00 0.00 0.00 5.34
2451 2520 8.108551 AGAAAACAGAGAGAAATTTGATCCAG 57.891 34.615 0.00 0.00 0.00 3.86
2454 2523 8.081025 AGCAAGAAAACAGAGAGAAATTTGATC 58.919 33.333 0.00 0.00 0.00 2.92
2455 2524 7.949434 AGCAAGAAAACAGAGAGAAATTTGAT 58.051 30.769 0.00 0.00 0.00 2.57
2456 2525 7.338800 AGCAAGAAAACAGAGAGAAATTTGA 57.661 32.000 0.00 0.00 0.00 2.69
2457 2526 6.640092 GGAGCAAGAAAACAGAGAGAAATTTG 59.360 38.462 0.00 0.00 0.00 2.32
2459 2528 5.829924 TGGAGCAAGAAAACAGAGAGAAATT 59.170 36.000 0.00 0.00 0.00 1.82
2460 2529 5.380043 TGGAGCAAGAAAACAGAGAGAAAT 58.620 37.500 0.00 0.00 0.00 2.17
2461 2530 4.780815 TGGAGCAAGAAAACAGAGAGAAA 58.219 39.130 0.00 0.00 0.00 2.52
2499 2568 4.022416 CACCGGTTCAGAAATTTTGATCCA 60.022 41.667 2.97 2.60 35.21 3.41
2518 2587 0.460987 GGTGCCTGAGAATCTCACCG 60.461 60.000 9.18 3.66 39.43 4.94
2526 2595 4.329545 GCCACGGGTGCCTGAGAA 62.330 66.667 3.74 0.00 0.00 2.87
2660 2729 0.105039 GGCCGAGGAGTATGTTGGAG 59.895 60.000 0.00 0.00 0.00 3.86
3152 3221 4.508128 TTGAGCGGCCGATCGTCC 62.508 66.667 35.29 15.87 32.52 4.79
3396 3480 0.037512 CTATCGCCAGCATCCCTCAG 60.038 60.000 0.00 0.00 0.00 3.35
3608 3701 1.641123 CGGTGGCCAATCCGTGTTAC 61.641 60.000 23.24 0.42 41.58 2.50
3616 3741 3.630312 ACATACATTTACGGTGGCCAATC 59.370 43.478 7.24 1.24 0.00 2.67
3642 3767 2.347292 GCGTAACAAACTGACGTGACAG 60.347 50.000 0.00 0.00 42.78 3.51
3722 3851 3.645975 CCGCCAACACACGTCCAC 61.646 66.667 0.00 0.00 0.00 4.02
3775 3956 2.363406 GATTTGGGGGCAGCAGCT 60.363 61.111 0.00 0.00 41.70 4.24
3777 3958 2.761213 GGGATTTGGGGGCAGCAG 60.761 66.667 0.00 0.00 0.00 4.24
3942 4147 0.478072 ATGACAGACAAGGGGTGCAA 59.522 50.000 0.00 0.00 0.00 4.08
3951 4156 3.253188 GCTTGCCAACTAATGACAGACAA 59.747 43.478 0.00 0.00 0.00 3.18
4104 4311 2.432628 GACCGGACGAGCTGTTGG 60.433 66.667 9.46 0.00 33.78 3.77
4205 4412 1.343465 AGTGTCCGTGGAAACCAGTAG 59.657 52.381 5.57 0.00 32.96 2.57
4211 4418 2.940410 TCAAGAAAGTGTCCGTGGAAAC 59.060 45.455 0.60 0.60 32.70 2.78
4218 4425 7.190920 AGAAAATTACTCAAGAAAGTGTCCG 57.809 36.000 0.00 0.00 0.00 4.79
4241 4448 7.710475 TGCAGGGTAATTCTTCTTTTTCAAAAG 59.290 33.333 5.77 5.77 45.17 2.27
4253 4461 2.684881 CGCTTCATGCAGGGTAATTCTT 59.315 45.455 0.00 0.00 43.06 2.52
4303 4511 7.941431 ATATTTGTTTTACCGGGTCATGTTA 57.059 32.000 6.32 0.00 0.00 2.41
4306 4514 7.936584 ACATATATTTGTTTTACCGGGTCATG 58.063 34.615 6.32 0.00 0.00 3.07
4307 4515 9.802039 ATACATATATTTGTTTTACCGGGTCAT 57.198 29.630 6.32 0.00 0.00 3.06
4308 4516 9.275398 GATACATATATTTGTTTTACCGGGTCA 57.725 33.333 6.32 0.00 0.00 4.02
4327 4536 8.274322 AGACAGATGGTTTTGGATTGATACATA 58.726 33.333 0.00 0.00 0.00 2.29
4347 4556 8.857098 AGTGACACTGTTTACTTATTAGACAGA 58.143 33.333 7.47 0.00 42.92 3.41
4351 4560 8.526147 GGGTAGTGACACTGTTTACTTATTAGA 58.474 37.037 18.58 0.00 0.00 2.10
4352 4561 7.763071 GGGGTAGTGACACTGTTTACTTATTAG 59.237 40.741 18.58 0.00 0.00 1.73
4354 4563 6.271624 AGGGGTAGTGACACTGTTTACTTATT 59.728 38.462 18.58 0.00 0.00 1.40
4356 4565 5.149976 AGGGGTAGTGACACTGTTTACTTA 58.850 41.667 18.58 0.00 0.00 2.24
4357 4566 3.971971 AGGGGTAGTGACACTGTTTACTT 59.028 43.478 18.58 0.00 0.00 2.24
4358 4567 3.584294 AGGGGTAGTGACACTGTTTACT 58.416 45.455 18.58 7.03 0.00 2.24
4359 4568 4.281688 TGTAGGGGTAGTGACACTGTTTAC 59.718 45.833 18.58 7.96 0.00 2.01
4360 4569 4.482030 TGTAGGGGTAGTGACACTGTTTA 58.518 43.478 18.58 0.00 0.00 2.01
4363 4572 2.688902 TGTAGGGGTAGTGACACTGT 57.311 50.000 18.58 0.00 0.00 3.55
4366 4575 1.900486 AGCTTGTAGGGGTAGTGACAC 59.100 52.381 0.00 0.00 0.00 3.67
4376 4585 1.600957 CGCATCATCAAGCTTGTAGGG 59.399 52.381 25.19 15.08 0.00 3.53
4385 4594 2.079158 AGGTCAACACGCATCATCAAG 58.921 47.619 0.00 0.00 0.00 3.02
4406 4615 4.691326 TTAGATGGTGTGTGTTGGTACA 57.309 40.909 0.00 0.00 0.00 2.90
4408 4617 4.287326 TGGATTAGATGGTGTGTGTTGGTA 59.713 41.667 0.00 0.00 0.00 3.25
4410 4619 3.684908 TGGATTAGATGGTGTGTGTTGG 58.315 45.455 0.00 0.00 0.00 3.77
4413 4622 3.307691 CCACTGGATTAGATGGTGTGTGT 60.308 47.826 0.00 0.00 0.00 3.72
4416 4625 2.292267 GCCACTGGATTAGATGGTGTG 58.708 52.381 0.00 0.00 33.06 3.82
4421 4630 2.171237 TGTGAGGCCACTGGATTAGATG 59.829 50.000 5.01 0.00 43.55 2.90
4430 4639 3.359002 GGCTTTGTGAGGCCACTG 58.641 61.111 5.01 0.00 46.84 3.66
4455 4664 2.714991 TTGATGCTCTCGGCTCGCT 61.715 57.895 0.00 0.00 42.39 4.93
4458 4667 0.809241 CTGGTTGATGCTCTCGGCTC 60.809 60.000 0.00 0.00 42.39 4.70
4465 4674 2.680312 TGCTAGACTGGTTGATGCTC 57.320 50.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.