Multiple sequence alignment - TraesCS5A01G139100

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 TraesCS5A01G139100 chr5A 100.000 4494 0 0 1 4494 311541909 311546402 0.000000e+00 8299
1 TraesCS5A01G139100 chr5D 93.926 4462 194 46 60 4494 241834151 241838562 0.000000e+00 6667
2 TraesCS5A01G139100 chr5B 96.443 3823 110 15 684 4494 256592562 256596370 0.000000e+00 6283
3 TraesCS5A01G139100 chr7A 75.143 350 74 9 59 401 517582370 517582713 7.790000e-33 152
4 TraesCS5A01G139100 chr6A 86.869 99 12 1 198 295 597317429 597317331 4.750000e-20 110


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 TraesCS5A01G139100 chr5A 311541909 311546402 4493 False 8299 8299 100.000 1 4494 1 chr5A.!!$F1 4493
1 TraesCS5A01G139100 chr5D 241834151 241838562 4411 False 6667 6667 93.926 60 4494 1 chr5D.!!$F1 4434
2 TraesCS5A01G139100 chr5B 256592562 256596370 3808 False 6283 6283 96.443 684 4494 1 chr5B.!!$F1 3810

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
227 231 0.036306 ATCCACCGGAGACAAACACC 59.964 55.0 9.46 0.00 34.05 4.16 F
937 958 0.179205 GGAGACGTAGACGACAACGG 60.179 60.0 9.41 0.00 43.25 4.44 F
2278 2304 0.803768 CTCTCGATGAACTGGCCACG 60.804 60.0 0.00 2.28 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1680 1.246737 CCCAGAAAGCTTCCCACAGC 61.247 60.000 0.0 0.0 40.44 4.40 R
2748 2774 1.444119 GGAGTTCGGCTTGTTGCACA 61.444 55.000 0.0 0.0 45.15 4.57 R
3723 3749 2.200067 GCACTGATCAAGATGACCGAG 58.800 52.381 0.0 0.0 0.00 4.63 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
22 23 4.707105 TGTTCATCTGTTGTCATGACAGT 58.293 39.130 26.48 10.49 43.80 3.55
23 24 5.852827 TGTTCATCTGTTGTCATGACAGTA 58.147 37.500 26.48 18.46 43.80 2.74
24 25 5.696270 TGTTCATCTGTTGTCATGACAGTAC 59.304 40.000 26.48 22.65 43.80 2.73
25 26 5.467035 TCATCTGTTGTCATGACAGTACA 57.533 39.130 26.48 25.50 43.80 2.90
26 27 6.041423 TCATCTGTTGTCATGACAGTACAT 57.959 37.500 25.93 16.32 43.80 2.29
27 28 7.169158 TCATCTGTTGTCATGACAGTACATA 57.831 36.000 25.93 21.13 43.80 2.29
28 29 7.260603 TCATCTGTTGTCATGACAGTACATAG 58.739 38.462 25.93 19.56 43.80 2.23
29 30 6.834168 TCTGTTGTCATGACAGTACATAGA 57.166 37.500 25.93 21.10 43.80 1.98
30 31 7.227049 TCTGTTGTCATGACAGTACATAGAA 57.773 36.000 25.93 13.81 43.80 2.10
31 32 7.840931 TCTGTTGTCATGACAGTACATAGAAT 58.159 34.615 25.93 0.00 43.80 2.40
32 33 8.966868 TCTGTTGTCATGACAGTACATAGAATA 58.033 33.333 25.93 8.66 43.80 1.75
33 34 9.755804 CTGTTGTCATGACAGTACATAGAATAT 57.244 33.333 25.93 0.00 42.94 1.28
76 77 8.177119 ACATGTTGGACAAATATTGTTGTAGT 57.823 30.769 0.00 0.00 45.52 2.73
87 88 9.284594 CAAATATTGTTGTAGTAAACATTCGGG 57.715 33.333 0.00 0.00 39.68 5.14
90 91 5.471556 TGTTGTAGTAAACATTCGGGAGA 57.528 39.130 0.00 0.00 38.10 3.71
92 93 6.469410 TGTTGTAGTAAACATTCGGGAGATT 58.531 36.000 0.00 0.00 38.10 2.40
112 113 4.420143 CGTGCTAAGATCCCACGG 57.580 61.111 14.33 0.00 46.03 4.94
126 127 2.173669 CACGGGACCAGCGCATTAG 61.174 63.158 11.47 0.00 0.00 1.73
128 129 1.153449 CGGGACCAGCGCATTAGAA 60.153 57.895 11.47 0.00 0.00 2.10
129 130 1.429148 CGGGACCAGCGCATTAGAAC 61.429 60.000 11.47 0.00 0.00 3.01
133 134 1.804151 GACCAGCGCATTAGAACAACA 59.196 47.619 11.47 0.00 0.00 3.33
146 150 2.940410 AGAACAACAACCGTCGACAAAT 59.060 40.909 17.16 0.00 0.00 2.32
161 165 7.287950 CGTCGACAAATAGAAGTGAAAATTGA 58.712 34.615 17.16 0.00 0.00 2.57
163 167 9.107367 GTCGACAAATAGAAGTGAAAATTGAAG 57.893 33.333 11.55 0.00 0.00 3.02
173 177 6.101650 AGTGAAAATTGAAGGAATCCAACC 57.898 37.500 0.61 0.00 0.00 3.77
179 183 2.542550 TGAAGGAATCCAACCCGTAGA 58.457 47.619 0.61 0.00 0.00 2.59
183 187 1.276989 GGAATCCAACCCGTAGACACA 59.723 52.381 0.00 0.00 0.00 3.72
184 188 2.093128 GGAATCCAACCCGTAGACACAT 60.093 50.000 0.00 0.00 0.00 3.21
188 192 2.073816 CCAACCCGTAGACACATGAAC 58.926 52.381 0.00 0.00 0.00 3.18
193 197 2.259618 CCGTAGACACATGAACGAAGG 58.740 52.381 0.00 0.00 37.53 3.46
195 199 2.000447 GTAGACACATGAACGAAGGCC 59.000 52.381 0.00 0.00 0.00 5.19
204 208 1.314730 GAACGAAGGCCAGAACCAAA 58.685 50.000 5.01 0.00 0.00 3.28
212 216 1.547675 GGCCAGAACCAAACAGATCCA 60.548 52.381 0.00 0.00 0.00 3.41
227 231 0.036306 ATCCACCGGAGACAAACACC 59.964 55.000 9.46 0.00 34.05 4.16
239 243 0.391927 CAAACACCGGCCGAATCCTA 60.392 55.000 30.73 0.00 0.00 2.94
256 260 3.811083 TCCTACGAGATCCTTCAGAGTC 58.189 50.000 0.00 0.00 0.00 3.36
274 278 0.468226 TCACACCTCAACACACCCTC 59.532 55.000 0.00 0.00 0.00 4.30
276 280 0.986019 ACACCTCAACACACCCTCCA 60.986 55.000 0.00 0.00 0.00 3.86
289 293 2.628178 CACCCTCCAACGATGCTAGATA 59.372 50.000 0.00 0.00 0.00 1.98
290 294 2.628657 ACCCTCCAACGATGCTAGATAC 59.371 50.000 0.00 0.00 0.00 2.24
294 298 3.028130 TCCAACGATGCTAGATACACCA 58.972 45.455 0.00 0.00 0.00 4.17
297 301 1.337071 ACGATGCTAGATACACCACCG 59.663 52.381 0.00 0.00 0.00 4.94
302 306 1.001888 TAGATACACCACCGGGGCA 59.998 57.895 6.32 0.00 42.05 5.36
303 307 1.046472 TAGATACACCACCGGGGCAG 61.046 60.000 6.32 0.00 42.05 4.85
328 332 3.440522 GCCAGGCGAAGAGAACTTTATTT 59.559 43.478 0.00 0.00 36.39 1.40
332 336 6.127897 CCAGGCGAAGAGAACTTTATTTCATT 60.128 38.462 0.00 0.00 36.39 2.57
335 339 8.360390 AGGCGAAGAGAACTTTATTTCATTTTT 58.640 29.630 0.00 0.00 36.39 1.94
348 352 1.064017 TCATTTTTAGGGAGCCGCCAT 60.064 47.619 0.00 0.00 38.95 4.40
349 353 1.338020 CATTTTTAGGGAGCCGCCATC 59.662 52.381 0.00 0.00 38.95 3.51
350 354 0.746563 TTTTTAGGGAGCCGCCATCG 60.747 55.000 0.00 0.00 38.95 3.84
351 355 1.906105 TTTTAGGGAGCCGCCATCGT 61.906 55.000 0.00 0.00 38.95 3.73
352 356 2.306255 TTTAGGGAGCCGCCATCGTC 62.306 60.000 0.00 0.00 38.95 4.20
364 368 4.514577 ATCGTCGCCTCGCCTTGG 62.515 66.667 0.00 0.00 0.00 3.61
368 372 4.069232 TCGCCTCGCCTTGGACAG 62.069 66.667 0.00 0.00 0.00 3.51
371 375 2.035442 GCCTCGCCTTGGACAGAAC 61.035 63.158 0.00 0.00 0.00 3.01
373 377 0.951040 CCTCGCCTTGGACAGAACAC 60.951 60.000 0.00 0.00 0.00 3.32
378 383 2.024414 GCCTTGGACAGAACACAAACT 58.976 47.619 0.00 0.00 0.00 2.66
389 394 5.944007 ACAGAACACAAACTCTAACCAAACT 59.056 36.000 0.00 0.00 0.00 2.66
391 396 7.608761 ACAGAACACAAACTCTAACCAAACTAA 59.391 33.333 0.00 0.00 0.00 2.24
393 398 9.016438 AGAACACAAACTCTAACCAAACTAAAA 57.984 29.630 0.00 0.00 0.00 1.52
395 400 9.634163 AACACAAACTCTAACCAAACTAAAAAG 57.366 29.630 0.00 0.00 0.00 2.27
397 402 9.849166 CACAAACTCTAACCAAACTAAAAAGAA 57.151 29.630 0.00 0.00 0.00 2.52
402 407 8.186163 ACTCTAACCAAACTAAAAAGAAAACGG 58.814 33.333 0.00 0.00 0.00 4.44
404 409 8.400186 TCTAACCAAACTAAAAAGAAAACGGAG 58.600 33.333 0.00 0.00 0.00 4.63
409 414 8.186163 CCAAACTAAAAAGAAAACGGAGTAGTT 58.814 33.333 0.00 0.00 45.00 2.24
415 426 2.074576 GAAAACGGAGTAGTTGCCCTC 58.925 52.381 0.00 0.00 45.00 4.30
420 431 1.324005 GGAGTAGTTGCCCTCTCGCT 61.324 60.000 0.00 0.00 0.00 4.93
421 432 1.390565 GAGTAGTTGCCCTCTCGCTA 58.609 55.000 0.00 0.00 0.00 4.26
423 434 1.104630 GTAGTTGCCCTCTCGCTAGT 58.895 55.000 0.00 0.00 0.00 2.57
428 439 2.139323 TGCCCTCTCGCTAGTAAAGA 57.861 50.000 0.00 0.00 0.00 2.52
434 445 1.065199 TCTCGCTAGTAAAGACCGGGA 60.065 52.381 6.32 0.00 0.00 5.14
443 454 0.981183 AAAGACCGGGATACACTGCA 59.019 50.000 6.32 0.00 39.74 4.41
448 459 1.144057 CGGGATACACTGCACCTCC 59.856 63.158 0.00 0.00 39.74 4.30
449 460 1.613317 CGGGATACACTGCACCTCCA 61.613 60.000 0.00 0.00 39.74 3.86
450 461 0.839946 GGGATACACTGCACCTCCAT 59.160 55.000 0.00 0.00 39.74 3.41
451 462 2.047061 GGGATACACTGCACCTCCATA 58.953 52.381 0.00 0.00 39.74 2.74
452 463 2.438021 GGGATACACTGCACCTCCATAA 59.562 50.000 0.00 0.00 39.74 1.90
458 469 3.838317 ACACTGCACCTCCATAACTCTAA 59.162 43.478 0.00 0.00 0.00 2.10
468 479 2.224066 CCATAACTCTAAGGCCACCGAG 60.224 54.545 5.01 9.63 0.00 4.63
470 481 1.349067 AACTCTAAGGCCACCGAGTT 58.651 50.000 20.97 20.97 40.71 3.01
471 482 2.226962 ACTCTAAGGCCACCGAGTTA 57.773 50.000 5.01 0.00 33.21 2.24
472 483 2.100989 ACTCTAAGGCCACCGAGTTAG 58.899 52.381 5.01 2.88 33.21 2.34
475 486 2.901839 TCTAAGGCCACCGAGTTAGTTT 59.098 45.455 5.01 0.00 0.00 2.66
476 487 4.088634 TCTAAGGCCACCGAGTTAGTTTA 58.911 43.478 5.01 0.00 0.00 2.01
477 488 2.756840 AGGCCACCGAGTTAGTTTAC 57.243 50.000 5.01 0.00 0.00 2.01
479 490 1.676916 GGCCACCGAGTTAGTTTACCC 60.677 57.143 0.00 0.00 0.00 3.69
480 491 2.000429 CCACCGAGTTAGTTTACCCG 58.000 55.000 0.00 0.00 0.00 5.28
481 492 1.353076 CACCGAGTTAGTTTACCCGC 58.647 55.000 0.00 0.00 0.00 6.13
515 527 7.486551 TCAAGCGGGATAAAAATAAATTTGTCG 59.513 33.333 0.00 0.00 32.92 4.35
518 530 6.197655 GCGGGATAAAAATAAATTTGTCGGTC 59.802 38.462 0.00 0.00 32.92 4.79
520 532 7.548967 GGGATAAAAATAAATTTGTCGGTCCA 58.451 34.615 0.00 0.00 32.92 4.02
521 533 8.035984 GGGATAAAAATAAATTTGTCGGTCCAA 58.964 33.333 0.00 0.00 32.92 3.53
562 577 6.510746 AGTTTAATTTTGAACTTTCAGCGC 57.489 33.333 0.00 0.00 38.61 5.92
569 584 0.386478 GAACTTTCAGCGCTTGCAGG 60.386 55.000 7.50 0.00 42.66 4.85
570 585 2.126580 CTTTCAGCGCTTGCAGGC 60.127 61.111 7.50 11.41 42.66 4.85
605 620 2.871096 ACTCGATTTTGCAGGGGTTA 57.129 45.000 0.00 0.00 0.00 2.85
610 625 2.757868 CGATTTTGCAGGGGTTATGGAA 59.242 45.455 0.00 0.00 0.00 3.53
618 633 4.017958 TGCAGGGGTTATGGAACTCATTTA 60.018 41.667 0.00 0.00 37.84 1.40
623 638 4.035208 GGGTTATGGAACTCATTTACGCAG 59.965 45.833 0.00 0.00 35.94 5.18
675 690 1.393539 CGGAGCAGTAACAATCGGTTG 59.606 52.381 6.92 6.92 40.73 3.77
937 958 0.179205 GGAGACGTAGACGACAACGG 60.179 60.000 9.41 0.00 43.25 4.44
1172 1193 1.679032 CCCGTGATCCACTTCCTTTCC 60.679 57.143 0.00 0.00 31.34 3.13
1200 1223 1.512735 AGAGTCCTCCTATTTGCCCC 58.487 55.000 0.00 0.00 0.00 5.80
1243 1269 8.175716 GCACTTAATACTGGTAACTTGAATCAC 58.824 37.037 0.00 0.00 37.61 3.06
1306 1332 1.472878 TGCCGTGCAAACTTTACACAA 59.527 42.857 5.84 0.00 34.76 3.33
1366 1392 3.554692 GACCGGCGCAGTTCATCG 61.555 66.667 10.83 0.43 0.00 3.84
1504 1530 2.665519 CGATGTTCCTTTTGACCTTGCG 60.666 50.000 0.00 0.00 0.00 4.85
1529 1555 4.461781 AGCTGCAGAATTTTGACTATGCTT 59.538 37.500 20.43 0.00 34.80 3.91
1582 1608 2.334946 GCCCAACGCTCTTCATGCA 61.335 57.895 0.00 0.00 0.00 3.96
1609 1635 4.156008 ACATCGGATGTTTTTGAAGCTACC 59.844 41.667 17.62 0.00 41.63 3.18
1615 1641 0.878416 TTTTTGAAGCTACCGCGCAT 59.122 45.000 8.75 0.00 42.32 4.73
1654 1680 3.136123 CACGCTGGCATCAAGGGG 61.136 66.667 0.00 0.00 0.00 4.79
1903 1929 0.901124 AGAGTGACCAGCATCTGTCC 59.099 55.000 0.00 0.00 0.00 4.02
2278 2304 0.803768 CTCTCGATGAACTGGCCACG 60.804 60.000 0.00 2.28 0.00 4.94
2294 2320 1.684734 ACGGAGCATAGTTCCCGGT 60.685 57.895 0.00 0.00 45.63 5.28
2854 2880 7.056635 AGACCATTTCAAATCTGATACGGAAT 58.943 34.615 0.00 0.00 0.00 3.01
3206 3232 2.354259 GTGCACTTCAATGGAGAGAGG 58.646 52.381 10.32 0.00 0.00 3.69
3436 3462 6.766944 ACAAAATTGCAACATGGAAGATGAAA 59.233 30.769 0.00 0.00 29.36 2.69
3535 3561 1.538419 GCTCATAGTACCCTTGTCGGC 60.538 57.143 0.00 0.00 0.00 5.54
3555 3581 3.294214 GCCTTGATCCATTTCACCTGAT 58.706 45.455 0.00 0.00 0.00 2.90
3649 3675 4.502950 CCCAAGAATGCAGTAGAGATCCTC 60.503 50.000 0.00 0.00 0.00 3.71
3696 3722 3.015327 CTGGAAATGCTCTTCTCCAAGG 58.985 50.000 0.00 0.00 37.51 3.61
3720 3746 2.101770 GCTGCGCTTTGGCTGATC 59.898 61.111 9.73 0.00 36.09 2.92
3723 3749 1.712977 CTGCGCTTTGGCTGATCTCC 61.713 60.000 9.73 0.00 36.09 3.71
3730 3756 0.614697 TTGGCTGATCTCCTCGGTCA 60.615 55.000 0.00 0.00 43.16 4.02
3746 3772 2.679059 CGGTCATCTTGATCAGTGCCTT 60.679 50.000 0.00 0.00 0.00 4.35
3747 3773 2.681848 GGTCATCTTGATCAGTGCCTTG 59.318 50.000 0.00 0.00 0.00 3.61
3750 3776 4.456911 GTCATCTTGATCAGTGCCTTGAAA 59.543 41.667 0.00 0.00 0.00 2.69
3751 3777 5.125097 GTCATCTTGATCAGTGCCTTGAAAT 59.875 40.000 0.00 0.00 0.00 2.17
3752 3778 5.124936 TCATCTTGATCAGTGCCTTGAAATG 59.875 40.000 0.00 0.00 0.00 2.32
3753 3779 4.401022 TCTTGATCAGTGCCTTGAAATGT 58.599 39.130 0.00 0.00 0.00 2.71
3754 3780 4.828939 TCTTGATCAGTGCCTTGAAATGTT 59.171 37.500 0.00 0.00 0.00 2.71
3755 3781 4.508461 TGATCAGTGCCTTGAAATGTTG 57.492 40.909 0.00 0.00 0.00 3.33
3756 3782 4.143543 TGATCAGTGCCTTGAAATGTTGA 58.856 39.130 0.00 0.00 0.00 3.18
3757 3783 4.583907 TGATCAGTGCCTTGAAATGTTGAA 59.416 37.500 0.00 0.00 0.00 2.69
4029 4061 3.243267 GGGTGTTGATTTGTGCGTTAACT 60.243 43.478 3.71 0.00 0.00 2.24
4104 4137 5.737860 TGTCTCTTTGCACTATGATGATGT 58.262 37.500 0.00 0.00 0.00 3.06
4106 4139 6.656270 TGTCTCTTTGCACTATGATGATGTTT 59.344 34.615 0.00 0.00 0.00 2.83
4133 4166 5.564048 TTTTGCTACTACGTTTTGGTGTT 57.436 34.783 0.00 0.00 0.00 3.32
4135 4168 4.799419 TGCTACTACGTTTTGGTGTTTC 57.201 40.909 0.00 0.00 0.00 2.78
4152 4185 8.117813 TGGTGTTTCTTTTCTTTTACTTCTGT 57.882 30.769 0.00 0.00 0.00 3.41
4156 4189 8.303876 TGTTTCTTTTCTTTTACTTCTGTTGCT 58.696 29.630 0.00 0.00 0.00 3.91
4208 4242 2.095213 GCGTGAATGCCGTATTTTCTCA 59.905 45.455 0.00 0.00 0.00 3.27
4263 4297 6.182039 TCTTGATGAAAATAAGGCTGTTCG 57.818 37.500 0.00 0.00 0.00 3.95
4270 4304 4.499037 AAATAAGGCTGTTCGTGGTTTC 57.501 40.909 0.00 0.00 0.00 2.78
4369 4403 4.136796 TCATGTTCTCCAGTCCAAGTTTG 58.863 43.478 0.00 0.00 0.00 2.93
4417 4451 1.301423 TTGTTCTTCCCCGAAACACG 58.699 50.000 0.00 0.00 42.18 4.49
4436 4470 1.001815 CGTGTTAAACTGGTGCCAAGG 60.002 52.381 0.00 0.00 0.00 3.61
4464 4498 7.951591 ACTTGTTATCCATGTTTGCTAAAACT 58.048 30.769 3.29 0.00 45.01 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.707105 ACTGTCATGACAACAGATGAACA 58.293 39.130 27.63 2.81 45.64 3.18
1 2 5.696270 TGTACTGTCATGACAACAGATGAAC 59.304 40.000 27.63 16.19 45.64 3.18
2 3 5.852827 TGTACTGTCATGACAACAGATGAA 58.147 37.500 27.63 6.09 45.64 2.57
3 4 5.467035 TGTACTGTCATGACAACAGATGA 57.533 39.130 27.63 6.75 45.64 2.92
4 5 7.260603 TCTATGTACTGTCATGACAACAGATG 58.739 38.462 28.11 21.61 45.64 2.90
5 6 7.410120 TCTATGTACTGTCATGACAACAGAT 57.590 36.000 28.11 22.83 45.64 2.90
6 7 6.834168 TCTATGTACTGTCATGACAACAGA 57.166 37.500 28.11 24.56 45.64 3.41
50 51 9.290988 ACTACAACAATATTTGTCCAACATGTA 57.709 29.630 0.00 0.00 44.59 2.29
51 52 8.177119 ACTACAACAATATTTGTCCAACATGT 57.823 30.769 0.00 0.00 44.59 3.21
54 55 9.953697 GTTTACTACAACAATATTTGTCCAACA 57.046 29.630 0.00 0.00 44.59 3.33
55 56 9.953697 TGTTTACTACAACAATATTTGTCCAAC 57.046 29.630 0.00 0.00 44.59 3.77
66 67 6.469410 TCTCCCGAATGTTTACTACAACAAT 58.531 36.000 0.00 0.00 40.07 2.71
69 70 6.370718 ACAATCTCCCGAATGTTTACTACAAC 59.629 38.462 0.00 0.00 40.89 3.32
76 77 3.930229 CACGACAATCTCCCGAATGTTTA 59.070 43.478 0.00 0.00 33.55 2.01
87 88 3.181475 TGGGATCTTAGCACGACAATCTC 60.181 47.826 0.00 0.00 0.00 2.75
90 91 2.738643 CGTGGGATCTTAGCACGACAAT 60.739 50.000 0.00 0.00 41.16 2.71
92 93 0.172578 CGTGGGATCTTAGCACGACA 59.827 55.000 0.00 0.00 41.16 4.35
96 97 2.208527 TCCCGTGGGATCTTAGCAC 58.791 57.895 2.72 0.00 39.76 4.40
111 112 0.392461 TGTTCTAATGCGCTGGTCCC 60.392 55.000 9.73 0.00 0.00 4.46
112 113 1.130561 GTTGTTCTAATGCGCTGGTCC 59.869 52.381 9.73 0.00 0.00 4.46
124 125 2.867287 TGTCGACGGTTGTTGTTCTA 57.133 45.000 11.62 0.00 0.00 2.10
126 127 2.810028 TTTGTCGACGGTTGTTGTTC 57.190 45.000 11.62 0.00 0.00 3.18
128 129 3.719924 TCTATTTGTCGACGGTTGTTGT 58.280 40.909 11.62 0.00 0.00 3.32
129 130 4.210537 ACTTCTATTTGTCGACGGTTGTTG 59.789 41.667 11.62 0.46 0.00 3.33
133 134 4.247267 TCACTTCTATTTGTCGACGGTT 57.753 40.909 11.62 0.00 0.00 4.44
146 150 8.576442 GTTGGATTCCTTCAATTTTCACTTCTA 58.424 33.333 3.95 0.00 0.00 2.10
161 165 2.027469 GTGTCTACGGGTTGGATTCCTT 60.027 50.000 3.95 0.00 0.00 3.36
163 167 1.276989 TGTGTCTACGGGTTGGATTCC 59.723 52.381 0.00 0.00 0.00 3.01
173 177 2.259618 CCTTCGTTCATGTGTCTACGG 58.740 52.381 0.00 0.00 34.93 4.02
179 183 0.396435 TCTGGCCTTCGTTCATGTGT 59.604 50.000 3.32 0.00 0.00 3.72
183 187 0.400213 TGGTTCTGGCCTTCGTTCAT 59.600 50.000 3.32 0.00 0.00 2.57
184 188 0.181587 TTGGTTCTGGCCTTCGTTCA 59.818 50.000 3.32 0.00 0.00 3.18
188 192 0.593128 CTGTTTGGTTCTGGCCTTCG 59.407 55.000 3.32 0.00 0.00 3.79
193 197 1.541588 GTGGATCTGTTTGGTTCTGGC 59.458 52.381 0.00 0.00 0.00 4.85
195 199 1.806542 CGGTGGATCTGTTTGGTTCTG 59.193 52.381 0.00 0.00 0.00 3.02
204 208 1.002087 GTTTGTCTCCGGTGGATCTGT 59.998 52.381 0.00 0.00 0.00 3.41
227 231 0.109689 GATCTCGTAGGATTCGGCCG 60.110 60.000 22.12 22.12 0.00 6.13
239 243 2.490115 GTGTGACTCTGAAGGATCTCGT 59.510 50.000 0.00 0.00 0.00 4.18
256 260 0.535102 GGAGGGTGTGTTGAGGTGTG 60.535 60.000 0.00 0.00 0.00 3.82
274 278 3.123804 GTGGTGTATCTAGCATCGTTGG 58.876 50.000 0.00 0.00 0.00 3.77
276 280 2.223735 CGGTGGTGTATCTAGCATCGTT 60.224 50.000 2.81 0.00 44.88 3.85
302 306 4.722535 TCTCTTCGCCTGGCCCCT 62.723 66.667 14.12 0.00 0.00 4.79
303 307 3.717294 TTCTCTTCGCCTGGCCCC 61.717 66.667 14.12 0.00 0.00 5.80
307 311 4.695455 TGAAATAAAGTTCTCTTCGCCTGG 59.305 41.667 0.00 0.00 32.90 4.45
308 312 5.862924 TGAAATAAAGTTCTCTTCGCCTG 57.137 39.130 0.00 0.00 32.90 4.85
328 332 0.329931 TGGCGGCTCCCTAAAAATGA 59.670 50.000 11.43 0.00 0.00 2.57
332 336 1.153249 CGATGGCGGCTCCCTAAAA 60.153 57.895 11.43 0.00 0.00 1.52
335 339 3.224324 GACGATGGCGGCTCCCTA 61.224 66.667 11.43 0.00 43.91 3.53
350 354 4.373116 TGTCCAAGGCGAGGCGAC 62.373 66.667 0.00 0.00 33.59 5.19
351 355 4.069232 CTGTCCAAGGCGAGGCGA 62.069 66.667 0.00 0.00 0.00 5.54
352 356 3.589654 TTCTGTCCAAGGCGAGGCG 62.590 63.158 0.00 0.00 0.00 5.52
364 368 6.093633 AGTTTGGTTAGAGTTTGTGTTCTGTC 59.906 38.462 0.00 0.00 0.00 3.51
365 369 5.944007 AGTTTGGTTAGAGTTTGTGTTCTGT 59.056 36.000 0.00 0.00 0.00 3.41
368 372 9.628746 TTTTTAGTTTGGTTAGAGTTTGTGTTC 57.371 29.630 0.00 0.00 0.00 3.18
371 375 9.849166 TTCTTTTTAGTTTGGTTAGAGTTTGTG 57.151 29.630 0.00 0.00 0.00 3.33
378 383 8.278729 TCCGTTTTCTTTTTAGTTTGGTTAGA 57.721 30.769 0.00 0.00 0.00 2.10
389 394 5.008911 GGGCAACTACTCCGTTTTCTTTTTA 59.991 40.000 0.00 0.00 0.00 1.52
391 396 3.317149 GGGCAACTACTCCGTTTTCTTTT 59.683 43.478 0.00 0.00 0.00 2.27
393 398 2.105993 AGGGCAACTACTCCGTTTTCTT 59.894 45.455 0.00 0.00 0.00 2.52
395 400 2.074576 GAGGGCAACTACTCCGTTTTC 58.925 52.381 0.00 0.00 0.00 2.29
397 402 1.275573 GAGAGGGCAACTACTCCGTTT 59.724 52.381 0.00 0.00 34.27 3.60
400 405 1.433879 CGAGAGGGCAACTACTCCG 59.566 63.158 0.00 0.00 36.13 4.63
402 407 1.335496 CTAGCGAGAGGGCAACTACTC 59.665 57.143 0.00 0.00 36.15 2.59
404 409 1.104630 ACTAGCGAGAGGGCAACTAC 58.895 55.000 0.00 0.00 34.64 2.73
405 410 2.723322 TACTAGCGAGAGGGCAACTA 57.277 50.000 0.00 0.00 34.64 2.24
409 414 1.749634 GTCTTTACTAGCGAGAGGGCA 59.250 52.381 0.00 0.00 34.64 5.36
415 426 1.386533 TCCCGGTCTTTACTAGCGAG 58.613 55.000 0.00 0.00 40.11 5.03
420 431 3.382546 GCAGTGTATCCCGGTCTTTACTA 59.617 47.826 0.00 0.00 0.00 1.82
421 432 2.167900 GCAGTGTATCCCGGTCTTTACT 59.832 50.000 0.00 0.00 0.00 2.24
423 434 2.093869 GTGCAGTGTATCCCGGTCTTTA 60.094 50.000 0.00 0.00 0.00 1.85
428 439 1.612442 AGGTGCAGTGTATCCCGGT 60.612 57.895 0.00 0.00 0.00 5.28
434 445 4.033709 AGAGTTATGGAGGTGCAGTGTAT 58.966 43.478 0.00 0.00 0.00 2.29
443 454 2.772515 GTGGCCTTAGAGTTATGGAGGT 59.227 50.000 3.32 0.00 0.00 3.85
448 459 2.431057 ACTCGGTGGCCTTAGAGTTATG 59.569 50.000 17.64 0.89 40.64 1.90
449 460 2.748388 ACTCGGTGGCCTTAGAGTTAT 58.252 47.619 17.64 1.28 40.64 1.89
450 461 2.226962 ACTCGGTGGCCTTAGAGTTA 57.773 50.000 17.64 0.00 40.64 2.24
451 462 1.349067 AACTCGGTGGCCTTAGAGTT 58.651 50.000 24.41 24.41 45.68 3.01
452 463 2.100989 CTAACTCGGTGGCCTTAGAGT 58.899 52.381 17.64 17.64 44.81 3.24
458 469 1.277273 GGTAAACTAACTCGGTGGCCT 59.723 52.381 3.32 0.00 0.00 5.19
537 549 7.918562 AGCGCTGAAAGTTCAAAATTAAACTTA 59.081 29.630 10.39 1.18 43.14 2.24
538 550 6.756542 AGCGCTGAAAGTTCAAAATTAAACTT 59.243 30.769 10.39 7.39 45.21 2.66
540 552 6.510746 AGCGCTGAAAGTTCAAAATTAAAC 57.489 33.333 10.39 0.00 36.64 2.01
544 559 3.245990 GCAAGCGCTGAAAGTTCAAAATT 59.754 39.130 12.58 0.00 36.64 1.82
559 574 1.713597 AATTAAAAGCCTGCAAGCGC 58.286 45.000 0.00 0.00 38.01 5.92
582 597 1.885887 CCCCTGCAAAATCGAGTTTCA 59.114 47.619 8.06 8.72 0.00 2.69
583 598 1.886542 ACCCCTGCAAAATCGAGTTTC 59.113 47.619 8.06 4.58 0.00 2.78
586 601 2.871096 TAACCCCTGCAAAATCGAGT 57.129 45.000 0.00 0.00 0.00 4.18
587 602 2.358898 CCATAACCCCTGCAAAATCGAG 59.641 50.000 0.00 0.00 0.00 4.04
588 603 2.025793 TCCATAACCCCTGCAAAATCGA 60.026 45.455 0.00 0.00 0.00 3.59
589 604 2.374184 TCCATAACCCCTGCAAAATCG 58.626 47.619 0.00 0.00 0.00 3.34
590 605 3.769300 AGTTCCATAACCCCTGCAAAATC 59.231 43.478 0.00 0.00 36.15 2.17
591 606 3.769300 GAGTTCCATAACCCCTGCAAAAT 59.231 43.478 0.00 0.00 36.15 1.82
598 613 4.777463 CGTAAATGAGTTCCATAACCCCT 58.223 43.478 0.00 0.00 36.15 4.79
605 620 2.026262 ACCCTGCGTAAATGAGTTCCAT 60.026 45.455 0.00 0.00 36.99 3.41
610 625 3.219281 ACAAAACCCTGCGTAAATGAGT 58.781 40.909 0.00 0.00 0.00 3.41
618 633 2.547007 GCCAATTTACAAAACCCTGCGT 60.547 45.455 0.00 0.00 0.00 5.24
623 638 2.065512 CGCTGCCAATTTACAAAACCC 58.934 47.619 0.00 0.00 0.00 4.11
652 667 1.359848 CGATTGTTACTGCTCCGCTT 58.640 50.000 0.00 0.00 0.00 4.68
659 674 2.739913 TGTAGCAACCGATTGTTACTGC 59.260 45.455 16.35 2.03 46.86 4.40
672 687 1.212935 ACTCCCATCCCATGTAGCAAC 59.787 52.381 0.00 0.00 0.00 4.17
675 690 0.839946 ACACTCCCATCCCATGTAGC 59.160 55.000 0.00 0.00 0.00 3.58
1172 1193 1.757682 AGGAGGACTCTAGAAGCACG 58.242 55.000 0.00 0.00 0.00 5.34
1218 1241 8.380644 CGTGATTCAAGTTACCAGTATTAAGTG 58.619 37.037 0.00 0.00 0.00 3.16
1229 1255 5.930569 AGGAAAGTACGTGATTCAAGTTACC 59.069 40.000 10.48 7.57 0.00 2.85
1306 1332 7.233348 AGACACCACAAAATTCTCCAATTACAT 59.767 33.333 0.00 0.00 31.51 2.29
1366 1392 3.312697 GGAAATCTTTACAGGCGGATGAC 59.687 47.826 0.00 0.00 0.00 3.06
1407 1433 1.786582 CTTGCAGTGAGAAGCTCGC 59.213 57.895 0.00 0.00 40.84 5.03
1504 1530 4.732938 GCATAGTCAAAATTCTGCAGCTCC 60.733 45.833 9.47 0.00 0.00 4.70
1529 1555 4.274147 TGCTGAAAAGTAACACCTTCCAA 58.726 39.130 0.00 0.00 0.00 3.53
1615 1641 1.995542 AGAAAATCCTCCAGGGCAAGA 59.004 47.619 0.00 0.00 35.41 3.02
1654 1680 1.246737 CCCAGAAAGCTTCCCACAGC 61.247 60.000 0.00 0.00 40.44 4.40
2278 2304 1.483415 TGTAACCGGGAACTATGCTCC 59.517 52.381 6.32 0.00 0.00 4.70
2294 2320 3.870274 TCTCCGATCTTCGACTCTGTAA 58.130 45.455 0.00 0.00 43.74 2.41
2452 2478 1.991813 TCCATGAAGACAATGGACCCA 59.008 47.619 0.98 0.00 39.36 4.51
2748 2774 1.444119 GGAGTTCGGCTTGTTGCACA 61.444 55.000 0.00 0.00 45.15 4.57
2854 2880 3.221771 CTCCTCAACACCAAACAATCCA 58.778 45.455 0.00 0.00 0.00 3.41
3206 3232 2.706339 ACTCTCCTTGACCATGATGC 57.294 50.000 0.00 0.00 0.00 3.91
3436 3462 7.719633 ACAATACAAGGTATGAAACACTGTTCT 59.280 33.333 0.00 0.00 0.00 3.01
3535 3561 3.635373 CCATCAGGTGAAATGGATCAAGG 59.365 47.826 0.00 0.00 44.37 3.61
3555 3581 3.278668 TTGGACGTTTTCAAGTACCCA 57.721 42.857 0.00 0.00 0.00 4.51
3649 3675 3.244009 ACATCCTGTTGCAGATATCCTCG 60.244 47.826 0.00 0.00 32.44 4.63
3720 3746 2.692557 ACTGATCAAGATGACCGAGGAG 59.307 50.000 0.00 0.00 0.00 3.69
3723 3749 2.200067 GCACTGATCAAGATGACCGAG 58.800 52.381 0.00 0.00 0.00 4.63
3730 3756 5.014858 ACATTTCAAGGCACTGATCAAGAT 58.985 37.500 0.00 0.00 40.86 2.40
3746 3772 8.682710 GCCTACCACTTATAATTCAACATTTCA 58.317 33.333 0.00 0.00 0.00 2.69
3747 3773 8.682710 TGCCTACCACTTATAATTCAACATTTC 58.317 33.333 0.00 0.00 0.00 2.17
3750 3776 8.588290 TTTGCCTACCACTTATAATTCAACAT 57.412 30.769 0.00 0.00 0.00 2.71
3751 3777 8.465999 CATTTGCCTACCACTTATAATTCAACA 58.534 33.333 0.00 0.00 0.00 3.33
3752 3778 8.466798 ACATTTGCCTACCACTTATAATTCAAC 58.533 33.333 0.00 0.00 0.00 3.18
3753 3779 8.465999 CACATTTGCCTACCACTTATAATTCAA 58.534 33.333 0.00 0.00 0.00 2.69
3754 3780 7.068103 CCACATTTGCCTACCACTTATAATTCA 59.932 37.037 0.00 0.00 0.00 2.57
3755 3781 7.284489 TCCACATTTGCCTACCACTTATAATTC 59.716 37.037 0.00 0.00 0.00 2.17
3756 3782 7.122715 TCCACATTTGCCTACCACTTATAATT 58.877 34.615 0.00 0.00 0.00 1.40
3757 3783 6.668645 TCCACATTTGCCTACCACTTATAAT 58.331 36.000 0.00 0.00 0.00 1.28
3831 3863 5.470777 CACAAATCCATTCTGGTGCAATTTT 59.529 36.000 0.00 0.00 39.03 1.82
3925 3957 2.448542 ACCTGACCACTGCACCCT 60.449 61.111 0.00 0.00 0.00 4.34
3948 3980 6.150976 CCATGACCAGCATTTACAAGAACTTA 59.849 38.462 0.00 0.00 34.15 2.24
4029 4061 4.680237 CGCACGGGCCAAGTCAGA 62.680 66.667 2.82 0.00 36.38 3.27
4104 4137 6.748198 CCAAAACGTAGTAGCAAAAACAGAAA 59.252 34.615 0.00 0.00 45.00 2.52
4106 4139 5.354792 ACCAAAACGTAGTAGCAAAAACAGA 59.645 36.000 0.00 0.00 45.00 3.41
4156 4189 5.416271 ACGGTGAAAGAGAGGCTTTTATA 57.584 39.130 0.00 0.00 46.52 0.98
4164 4197 3.024547 TCATCCTACGGTGAAAGAGAGG 58.975 50.000 0.00 0.00 0.00 3.69
4165 4198 3.067461 CCTCATCCTACGGTGAAAGAGAG 59.933 52.174 0.00 0.00 0.00 3.20
4166 4199 3.024547 CCTCATCCTACGGTGAAAGAGA 58.975 50.000 0.00 0.00 0.00 3.10
4188 4222 4.335082 TTGAGAAAATACGGCATTCACG 57.665 40.909 0.00 0.00 37.36 4.35
4302 4336 5.909610 GGCAAACGTTTCAGATATCATTAGC 59.090 40.000 11.37 6.58 0.00 3.09
4304 4338 6.038161 CCAGGCAAACGTTTCAGATATCATTA 59.962 38.462 11.37 0.00 0.00 1.90
4311 4345 1.981256 ACCAGGCAAACGTTTCAGAT 58.019 45.000 11.37 0.00 0.00 2.90
4384 4418 6.072673 GGGGAAGAACAAACTACTGTACATTG 60.073 42.308 0.00 0.00 0.00 2.82
4417 4451 1.339929 CCCTTGGCACCAGTTTAACAC 59.660 52.381 0.00 0.00 0.00 3.32
4436 4470 5.391312 AGCAAACATGGATAACAAGTTCC 57.609 39.130 0.00 0.00 39.85 3.62


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

AutoCloner maintained by Alex Coulton.