Multiple sequence alignment - TraesCS3A01G077800

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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 TraesCS3A01G077800 chr3A 100.000 4830 0 0 1 4830 50369002 50364173 0.000000e+00 8920
1 TraesCS3A01G077800 chr3D 93.488 3025 136 34 786 3778 39018693 39021688 0.000000e+00 4438
2 TraesCS3A01G077800 chr3D 89.793 725 44 14 3827 4540 39021706 39022411 0.000000e+00 902
3 TraesCS3A01G077800 chr3D 94.118 204 8 2 4627 4830 39022403 39022602 1.690000e-79 307
4 TraesCS3A01G077800 chr3B 91.131 2176 135 29 2659 4815 61882847 61884983 0.000000e+00 2896
5 TraesCS3A01G077800 chr3B 88.360 2397 178 52 1 2323 61879721 61882090 0.000000e+00 2787
6 TraesCS3A01G077800 chr3B 95.808 167 7 0 2371 2537 61882327 61882493 2.220000e-68 270
7 TraesCS3A01G077800 chr3B 97.030 101 3 0 2450 2550 61882491 61882591 2.310000e-38 171
8 TraesCS3A01G077800 chr7A 73.300 397 75 22 282 668 669342184 669341809 3.050000e-22 117
9 TraesCS3A01G077800 chr1D 82.707 133 15 4 4121 4250 196447820 196447693 1.420000e-20 111


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 TraesCS3A01G077800 chr3A 50364173 50369002 4829 True 8920.000000 8920 100.000000 1 4830 1 chr3A.!!$R1 4829
1 TraesCS3A01G077800 chr3D 39018693 39022602 3909 False 1882.333333 4438 92.466333 786 4830 3 chr3D.!!$F1 4044
2 TraesCS3A01G077800 chr3B 61879721 61884983 5262 False 1531.000000 2896 93.082250 1 4815 4 chr3B.!!$F1 4814

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
402 428 1.067565 ACAGACTACGATGTGCCACAG 60.068 52.381 3.0 0.0 0.00 3.66 F
1266 1306 0.322816 TCGTGGACTACTACCCGCTT 60.323 55.000 0.0 0.0 0.00 4.68 F
2592 3064 0.178068 GCTTCCGGCCTGACTAATCA 59.822 55.000 0.0 0.0 34.27 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1955 1.136695 CTCCTAAGCTCTGCAGGTCAG 59.863 57.143 15.13 5.10 44.21 3.51 R
2907 3424 0.035439 CTTGGCAATACTCCGGGTGT 60.035 55.000 0.00 6.98 0.00 4.16 R
4049 4583 0.253327 AGTTCCATTCCCTCGCCTTC 59.747 55.000 0.00 0.00 0.00 3.46 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
30 31 5.661312 TGTGTATAGGGGATGGTATATCTGC 59.339 44.000 0.00 0.00 0.00 4.26
33 34 7.509318 GTGTATAGGGGATGGTATATCTGCATA 59.491 40.741 0.00 0.00 0.00 3.14
95 96 8.135529 GGGTAATTGTAATGCTCCTTTTATCAC 58.864 37.037 0.00 0.00 0.00 3.06
105 106 5.191722 TGCTCCTTTTATCACCTTAGGTCAT 59.808 40.000 0.00 0.00 31.02 3.06
127 128 1.425412 CCCTGTAAGTTTCGTCCGTG 58.575 55.000 0.00 0.00 0.00 4.94
141 142 4.571919 TCGTCCGTGGAAATAAATCTTGT 58.428 39.130 0.00 0.00 0.00 3.16
180 190 4.218417 AGGATTAGTTGCATTGGAACACAC 59.782 41.667 21.04 10.20 39.29 3.82
193 203 4.650734 TGGAACACACATGCTATTCTTCA 58.349 39.130 0.00 0.00 0.00 3.02
239 249 8.623903 GTCATTGTTGTCATGGTATGTGATTAT 58.376 33.333 0.00 0.00 0.00 1.28
242 252 6.657875 TGTTGTCATGGTATGTGATTATGGA 58.342 36.000 0.00 0.00 0.00 3.41
245 255 7.077050 TGTCATGGTATGTGATTATGGATGA 57.923 36.000 0.00 0.00 0.00 2.92
265 275 5.726980 TGAATTAACAAGATGCTTGGCTT 57.273 34.783 11.40 1.24 0.00 4.35
295 321 3.994392 TCATGCTCGTTAAGGTTCAACTC 59.006 43.478 0.00 0.00 0.00 3.01
339 365 5.362556 AAATCATGTTCAACTCTGTTCGG 57.637 39.130 0.00 0.00 0.00 4.30
348 374 4.056050 TCAACTCTGTTCGGTTAAAGCTC 58.944 43.478 0.00 0.00 0.00 4.09
368 394 2.231235 TCGTTAAGCTCATGAGTGCTCA 59.769 45.455 23.38 4.23 43.29 4.26
387 413 2.736721 TCATGAGCGCTTGTTAACAGAC 59.263 45.455 13.26 4.26 0.00 3.51
396 422 4.201494 CGCTTGTTAACAGACTACGATGTG 60.201 45.833 8.56 0.00 0.00 3.21
397 423 4.434330 GCTTGTTAACAGACTACGATGTGC 60.434 45.833 8.56 0.00 0.00 4.57
398 424 3.581755 TGTTAACAGACTACGATGTGCC 58.418 45.455 3.59 0.00 0.00 5.01
402 428 1.067565 ACAGACTACGATGTGCCACAG 60.068 52.381 3.00 0.00 0.00 3.66
413 439 4.669965 CGATGTGCCACAGTCTACAAAATG 60.670 45.833 3.00 0.00 0.00 2.32
416 442 3.815401 GTGCCACAGTCTACAAAATGAGT 59.185 43.478 0.00 0.00 0.00 3.41
419 445 4.994852 GCCACAGTCTACAAAATGAGTGTA 59.005 41.667 0.00 0.00 42.77 2.90
423 449 6.092670 CACAGTCTACAAAATGAGTGTATGGG 59.907 42.308 0.00 0.00 42.77 4.00
425 451 6.092670 CAGTCTACAAAATGAGTGTATGGGTG 59.907 42.308 0.00 0.00 31.27 4.61
430 456 9.607988 CTACAAAATGAGTGTATGGGTGTAATA 57.392 33.333 0.00 0.00 31.27 0.98
440 466 9.793259 AGTGTATGGGTGTAATATTTATGAAGG 57.207 33.333 0.00 0.00 0.00 3.46
444 471 7.214460 TGGGTGTAATATTTATGAAGGACCA 57.786 36.000 0.00 0.00 0.00 4.02
462 489 4.841246 GGACCATGGTGACTATAGAAGGAT 59.159 45.833 25.52 0.00 0.00 3.24
464 491 4.040952 ACCATGGTGACTATAGAAGGATGC 59.959 45.833 18.99 0.00 0.00 3.91
467 494 3.958147 TGGTGACTATAGAAGGATGCGAA 59.042 43.478 6.78 0.00 0.00 4.70
472 499 6.309251 GTGACTATAGAAGGATGCGAATTAGC 59.691 42.308 6.78 3.27 37.71 3.09
475 502 8.123639 ACTATAGAAGGATGCGAATTAGCTTA 57.876 34.615 11.95 0.00 38.13 3.09
478 505 2.755650 AGGATGCGAATTAGCTTACCG 58.244 47.619 11.95 0.00 38.13 4.02
482 509 1.409790 TGCGAATTAGCTTACCGCCTA 59.590 47.619 11.95 0.00 44.55 3.93
497 524 2.878406 CCGCCTACTATTGGTTGGAATG 59.122 50.000 4.89 0.00 42.13 2.67
517 544 6.015350 GGAATGGGTCGATTAGATTGACTAGA 60.015 42.308 0.00 0.00 42.23 2.43
520 547 5.833667 TGGGTCGATTAGATTGACTAGATGT 59.166 40.000 0.00 0.00 42.23 3.06
532 559 4.412843 TGACTAGATGTGTCAAGGTACCA 58.587 43.478 15.94 0.00 40.89 3.25
534 561 6.192044 TGACTAGATGTGTCAAGGTACCATA 58.808 40.000 15.94 0.00 40.89 2.74
543 570 8.871629 TGTGTCAAGGTACCATAAAAATATGT 57.128 30.769 15.94 0.00 0.00 2.29
545 572 8.120465 GTGTCAAGGTACCATAAAAATATGTCG 58.880 37.037 15.94 0.00 0.00 4.35
547 574 8.120465 GTCAAGGTACCATAAAAATATGTCGTG 58.880 37.037 15.94 0.00 0.00 4.35
548 575 7.825270 TCAAGGTACCATAAAAATATGTCGTGT 59.175 33.333 15.94 0.00 0.00 4.49
549 576 9.100554 CAAGGTACCATAAAAATATGTCGTGTA 57.899 33.333 15.94 0.00 0.00 2.90
551 578 9.321562 AGGTACCATAAAAATATGTCGTGTAAG 57.678 33.333 15.94 0.00 0.00 2.34
552 579 9.316730 GGTACCATAAAAATATGTCGTGTAAGA 57.683 33.333 7.15 0.00 0.00 2.10
582 610 2.031769 TGTGACGTGGTGTACTAACGAG 60.032 50.000 18.08 0.00 39.64 4.18
583 611 1.069022 TGACGTGGTGTACTAACGAGC 60.069 52.381 18.08 11.62 39.64 5.03
592 620 4.378874 GGTGTACTAACGAGCTTAACGAGT 60.379 45.833 0.00 0.00 34.70 4.18
605 633 4.083802 GCTTAACGAGTTGCTCATGAAACT 60.084 41.667 11.71 11.71 44.42 2.66
635 663 6.347563 CGTTATGCCCGTTAAGTTTAACAAGA 60.348 38.462 13.44 0.00 42.34 3.02
642 670 7.597369 GCCCGTTAAGTTTAACAAGATGAAATT 59.403 33.333 13.44 0.00 42.34 1.82
657 685 9.903682 CAAGATGAAATTAGTGATTGACTTTGT 57.096 29.630 0.00 0.00 35.96 2.83
678 706 8.514136 TTTGTTCATTAAAAATTGAGCTACGG 57.486 30.769 0.00 0.00 0.00 4.02
702 730 2.552599 AGCAGTCCGAGATATCGAGA 57.447 50.000 12.11 4.06 34.64 4.04
707 735 2.811431 AGTCCGAGATATCGAGAGCTTG 59.189 50.000 12.11 5.56 34.64 4.01
713 741 4.556912 CGAGATATCGAGAGCTTGTTATGC 59.443 45.833 2.99 0.00 34.64 3.14
721 749 1.325943 GAGCTTGTTATGCTCGTCAGC 59.674 52.381 0.00 0.00 45.73 4.26
836 864 3.984018 CGTATTCCCCAAATATACGCG 57.016 47.619 3.53 3.53 40.14 6.01
841 869 3.096489 TCCCCAAATATACGCGTGTAC 57.904 47.619 24.59 0.00 32.26 2.90
891 920 1.669265 GACGCCCTAAATTACTGCCAC 59.331 52.381 0.00 0.00 0.00 5.01
895 926 4.072131 CGCCCTAAATTACTGCCACATAT 58.928 43.478 0.00 0.00 0.00 1.78
902 933 9.778741 CCTAAATTACTGCCACATATAGAGAAA 57.221 33.333 0.00 0.00 0.00 2.52
906 938 9.851686 AATTACTGCCACATATAGAGAAAATGA 57.148 29.630 0.00 0.00 0.00 2.57
909 941 8.839310 ACTGCCACATATAGAGAAAATGATAC 57.161 34.615 0.00 0.00 0.00 2.24
911 943 6.873605 TGCCACATATAGAGAAAATGATACGG 59.126 38.462 0.00 0.00 0.00 4.02
998 1038 4.527583 GAGCAGAGCAGAGGCCCG 62.528 72.222 0.00 0.00 42.56 6.13
1034 1074 2.300956 AGACCAGCAAGAGAGACAGA 57.699 50.000 0.00 0.00 0.00 3.41
1266 1306 0.322816 TCGTGGACTACTACCCGCTT 60.323 55.000 0.00 0.00 0.00 4.68
1332 1372 2.743752 CGTGGACTGCAATGCCGAG 61.744 63.158 1.53 0.00 0.00 4.63
1510 1550 0.610174 CCAGTTGCCACTCTGCTCTA 59.390 55.000 0.00 0.00 0.00 2.43
1678 1721 6.801539 TTTATCACTGCTTGGTTTCTGTAG 57.198 37.500 0.00 0.00 0.00 2.74
1679 1722 4.623932 ATCACTGCTTGGTTTCTGTAGA 57.376 40.909 0.00 0.00 0.00 2.59
1763 1806 2.286872 GCCTAGTGCTCGAGTACAGTA 58.713 52.381 31.11 18.50 36.87 2.74
1765 1808 3.315749 GCCTAGTGCTCGAGTACAGTAAT 59.684 47.826 31.11 15.43 36.87 1.89
1766 1809 4.555116 GCCTAGTGCTCGAGTACAGTAATC 60.555 50.000 31.11 13.65 36.87 1.75
1767 1810 4.575236 CCTAGTGCTCGAGTACAGTAATCA 59.425 45.833 31.11 7.87 32.87 2.57
1768 1811 5.239744 CCTAGTGCTCGAGTACAGTAATCAT 59.760 44.000 31.11 13.44 32.87 2.45
1846 1893 5.044772 TGAGTAGATCTAACTGAGTGGGAGT 60.045 44.000 3.40 0.00 0.00 3.85
1887 1934 7.983166 AAACTATGTTATGGTCCCAGTAGTA 57.017 36.000 0.00 0.00 0.00 1.82
1893 1940 2.984435 TGGTCCCAGTAGTAGTGTGA 57.016 50.000 4.31 0.00 0.00 3.58
1895 1942 3.786553 TGGTCCCAGTAGTAGTGTGATT 58.213 45.455 4.31 0.00 0.00 2.57
1907 1954 9.360901 AGTAGTAGTGTGATTGATGTATGATCT 57.639 33.333 0.00 0.00 0.00 2.75
1908 1955 9.619316 GTAGTAGTGTGATTGATGTATGATCTC 57.381 37.037 0.00 0.00 0.00 2.75
1978 2038 4.463050 AGATAGGGTTAGGAGAGTCCAG 57.537 50.000 0.00 0.00 39.61 3.86
2101 2164 9.276590 CAAGTTTATCATGATTAGTGGCAGATA 57.723 33.333 14.65 0.00 0.00 1.98
2144 2207 7.950512 TCTCAAAATATGCTTTGTTCCTCAAA 58.049 30.769 0.93 0.00 42.79 2.69
2198 2269 2.485659 TGAGATCTTCAGGGGCAATCT 58.514 47.619 0.00 0.00 0.00 2.40
2273 2349 7.011576 CGAGTAGTATATATGTAGACCTGCAGG 59.988 44.444 31.60 31.60 42.17 4.85
2295 2371 1.775459 AGCATCAGCATCCTTGATCCT 59.225 47.619 0.00 0.00 45.49 3.24
2323 2399 7.581213 TGTGTTGTTCTAGGATTGTTGAAAT 57.419 32.000 0.00 0.00 0.00 2.17
2450 2729 3.948360 TGGGGGTGGCCTGTCCTA 61.948 66.667 3.32 0.00 35.26 2.94
2451 2730 3.090532 GGGGGTGGCCTGTCCTAG 61.091 72.222 3.32 0.00 35.26 3.02
2592 3064 0.178068 GCTTCCGGCCTGACTAATCA 59.822 55.000 0.00 0.00 34.27 2.57
2593 3065 1.202698 GCTTCCGGCCTGACTAATCAT 60.203 52.381 0.00 0.00 33.22 2.45
2594 3066 2.487934 CTTCCGGCCTGACTAATCATG 58.512 52.381 0.00 0.00 33.22 3.07
2622 3094 3.064408 CACCATCGTGATCTTGGTCATTG 59.936 47.826 7.08 0.00 41.77 2.82
2694 3211 0.889994 TGACAAGCACATGAATGGCC 59.110 50.000 0.00 0.00 0.00 5.36
2925 3442 0.322098 CACACCCGGAGTATTGCCAA 60.322 55.000 0.73 0.00 0.00 4.52
3216 3733 1.474498 CCCAAGGGATACTACGGCAAC 60.474 57.143 0.00 0.00 37.50 4.17
3301 3818 3.068064 TGATCCGGCTCGTGCAGA 61.068 61.111 12.07 7.79 41.91 4.26
3396 3913 4.115199 GGTGGAGCCAAGCCGGAT 62.115 66.667 5.05 0.00 36.56 4.18
3462 3979 4.117661 GACCTCGACTTCGGCGCT 62.118 66.667 7.64 0.00 40.29 5.92
3630 4147 0.765510 AACCCAGTGGAGTGGAAGAC 59.234 55.000 11.95 0.00 40.44 3.01
3808 4342 8.281893 GCATGCTTATGTAAATTTTGTGTTTGT 58.718 29.630 11.37 0.00 0.00 2.83
3836 4370 7.307493 TCAAGACATATTCAATCTTGTTCGG 57.693 36.000 11.75 0.00 46.20 4.30
3908 4442 9.086336 CATCAATCAACAACTTAAAAACACAGT 57.914 29.630 0.00 0.00 0.00 3.55
3925 4459 3.986572 CACAGTCTGCTCGATCCATAATC 59.013 47.826 0.00 0.00 0.00 1.75
3997 4531 9.457436 TTGAACCTAACTATAAATTTCCTCACC 57.543 33.333 0.00 0.00 0.00 4.02
3998 4532 8.050930 TGAACCTAACTATAAATTTCCTCACCC 58.949 37.037 0.00 0.00 0.00 4.61
3999 4533 6.589135 ACCTAACTATAAATTTCCTCACCCG 58.411 40.000 0.00 0.00 0.00 5.28
4000 4534 5.469084 CCTAACTATAAATTTCCTCACCCGC 59.531 44.000 0.00 0.00 0.00 6.13
4001 4535 4.497291 ACTATAAATTTCCTCACCCGCA 57.503 40.909 0.00 0.00 0.00 5.69
4002 4536 4.850680 ACTATAAATTTCCTCACCCGCAA 58.149 39.130 0.00 0.00 0.00 4.85
4003 4537 5.258051 ACTATAAATTTCCTCACCCGCAAA 58.742 37.500 0.00 0.00 0.00 3.68
4004 4538 5.712917 ACTATAAATTTCCTCACCCGCAAAA 59.287 36.000 0.00 0.00 0.00 2.44
4005 4539 3.828875 AAATTTCCTCACCCGCAAAAA 57.171 38.095 0.00 0.00 0.00 1.94
4038 4572 6.983906 AATTTTCCAGGTGAGAATTTCTGT 57.016 33.333 3.03 0.00 34.96 3.41
4048 4582 8.383619 CAGGTGAGAATTTCTGTAACGAATTAG 58.616 37.037 3.03 0.00 0.00 1.73
4049 4583 7.549488 AGGTGAGAATTTCTGTAACGAATTAGG 59.451 37.037 3.03 0.00 0.00 2.69
4064 4613 0.837272 TTAGGAAGGCGAGGGAATGG 59.163 55.000 0.00 0.00 0.00 3.16
4211 4761 0.883833 AGGCAAGTCAAAGCAATCCG 59.116 50.000 0.00 0.00 0.00 4.18
4222 4773 3.782889 AAGCAATCCGTTCTTTATGCC 57.217 42.857 0.00 0.00 34.44 4.40
4290 4841 4.273148 ACTAGTACAAGGTCAAAGCTGG 57.727 45.455 0.00 0.00 0.00 4.85
4345 4896 3.054878 CACGTAGCTTTTTCGTACCACT 58.945 45.455 0.00 0.00 36.05 4.00
4385 4936 0.038618 CAACGAGTGATCCACGTCCA 60.039 55.000 8.80 0.00 39.64 4.02
4430 4982 9.886132 ATGTAACAATCGGTAATCTCTAAACTT 57.114 29.630 0.00 0.00 0.00 2.66
4471 5029 9.801873 GCTGCCTAAAGTTTTATTCATAAATCA 57.198 29.630 0.00 0.00 32.78 2.57
4547 5105 6.864342 TGTTACGAAATTTTGGTCAGGAAAA 58.136 32.000 10.22 0.00 0.00 2.29
4615 5173 7.555087 TGCATTGTATTTTCCATTTTAGGAGG 58.445 34.615 0.00 0.00 39.25 4.30
4649 5208 6.422776 AATGTTGGTGTTCGATCAATACTC 57.577 37.500 0.00 0.00 0.00 2.59
4663 5222 6.201806 CGATCAATACTCATTTTGGTCTCCTC 59.798 42.308 0.00 0.00 32.05 3.71
4723 5282 7.000472 TCTGAGAATGGTTCCATATTGATTCC 59.000 38.462 4.67 0.00 0.00 3.01
4784 5343 1.470098 AGTGCGACATTTTGGCTCATC 59.530 47.619 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.216117 GCATTACAATTACCCTATACTTCGATT 57.784 33.333 0.00 0.00 0.00 3.34
59 60 7.959175 AGCATTACAATTACCCTATACTTCGA 58.041 34.615 0.00 0.00 0.00 3.71
60 61 7.331193 GGAGCATTACAATTACCCTATACTTCG 59.669 40.741 0.00 0.00 0.00 3.79
61 62 8.376270 AGGAGCATTACAATTACCCTATACTTC 58.624 37.037 0.00 0.00 0.00 3.01
63 64 7.873699 AGGAGCATTACAATTACCCTATACT 57.126 36.000 0.00 0.00 0.00 2.12
64 65 8.919777 AAAGGAGCATTACAATTACCCTATAC 57.080 34.615 0.00 0.00 0.00 1.47
80 81 5.191722 TGACCTAAGGTGATAAAAGGAGCAT 59.808 40.000 0.00 0.00 35.25 3.79
95 96 1.410004 TACAGGGCGATGACCTAAGG 58.590 55.000 0.00 0.00 40.42 2.69
105 106 0.037975 GGACGAAACTTACAGGGCGA 60.038 55.000 0.00 0.00 0.00 5.54
154 155 4.640201 TGTTCCAATGCAACTAATCCTAGC 59.360 41.667 0.00 0.00 0.00 3.42
157 158 4.218417 GTGTGTTCCAATGCAACTAATCCT 59.782 41.667 0.00 0.00 0.00 3.24
158 159 4.022416 TGTGTGTTCCAATGCAACTAATCC 60.022 41.667 0.00 0.00 0.00 3.01
160 161 5.472148 CATGTGTGTTCCAATGCAACTAAT 58.528 37.500 0.00 0.00 0.00 1.73
167 177 3.788333 ATAGCATGTGTGTTCCAATGC 57.212 42.857 0.00 0.00 35.47 3.56
204 214 5.351458 CATGACAACAATGACTAGATCCGA 58.649 41.667 0.00 0.00 0.00 4.55
206 216 5.431765 ACCATGACAACAATGACTAGATCC 58.568 41.667 0.00 0.00 0.00 3.36
207 217 7.712639 ACATACCATGACAACAATGACTAGATC 59.287 37.037 0.00 0.00 0.00 2.75
239 249 5.394443 GCCAAGCATCTTGTTAATTCATCCA 60.394 40.000 5.92 0.00 0.00 3.41
242 252 5.927281 AGCCAAGCATCTTGTTAATTCAT 57.073 34.783 5.92 0.00 0.00 2.57
272 282 3.997021 AGTTGAACCTTAACGAGCATGAG 59.003 43.478 0.00 0.00 33.39 2.90
273 283 3.994392 GAGTTGAACCTTAACGAGCATGA 59.006 43.478 0.00 0.00 33.39 3.07
274 284 3.181530 CGAGTTGAACCTTAACGAGCATG 60.182 47.826 0.00 0.00 33.39 4.06
275 285 2.993899 CGAGTTGAACCTTAACGAGCAT 59.006 45.455 0.00 0.00 33.39 3.79
278 304 5.388164 GCTTAACGAGTTGAACCTTAACGAG 60.388 44.000 0.00 0.00 33.39 4.18
280 306 4.446719 AGCTTAACGAGTTGAACCTTAACG 59.553 41.667 0.00 0.00 33.39 3.18
316 342 5.299279 ACCGAACAGAGTTGAACATGATTTT 59.701 36.000 0.00 0.00 0.00 1.82
317 343 4.821805 ACCGAACAGAGTTGAACATGATTT 59.178 37.500 0.00 0.00 0.00 2.17
318 344 4.389374 ACCGAACAGAGTTGAACATGATT 58.611 39.130 0.00 0.00 0.00 2.57
319 345 4.008074 ACCGAACAGAGTTGAACATGAT 57.992 40.909 0.00 0.00 0.00 2.45
320 346 3.469008 ACCGAACAGAGTTGAACATGA 57.531 42.857 0.00 0.00 0.00 3.07
328 354 3.057734 CGAGCTTTAACCGAACAGAGTT 58.942 45.455 0.00 0.00 0.00 3.01
332 358 4.942765 CTTAACGAGCTTTAACCGAACAG 58.057 43.478 0.00 0.00 0.00 3.16
348 374 2.610433 TGAGCACTCATGAGCTTAACG 58.390 47.619 22.83 5.67 40.10 3.18
368 394 3.045601 AGTCTGTTAACAAGCGCTCAT 57.954 42.857 12.06 1.99 0.00 2.90
369 395 2.526304 AGTCTGTTAACAAGCGCTCA 57.474 45.000 12.06 1.37 0.00 4.26
370 396 2.341760 CGTAGTCTGTTAACAAGCGCTC 59.658 50.000 12.06 0.00 0.00 5.03
371 397 2.030540 TCGTAGTCTGTTAACAAGCGCT 60.031 45.455 2.64 2.64 0.00 5.92
374 400 4.434330 GCACATCGTAGTCTGTTAACAAGC 60.434 45.833 10.03 5.44 0.00 4.01
377 403 3.006003 TGGCACATCGTAGTCTGTTAACA 59.994 43.478 8.28 8.28 0.00 2.41
387 413 2.163613 TGTAGACTGTGGCACATCGTAG 59.836 50.000 22.35 11.56 44.52 3.51
396 422 3.815401 ACACTCATTTTGTAGACTGTGGC 59.185 43.478 0.00 0.00 0.00 5.01
397 423 6.092670 CCATACACTCATTTTGTAGACTGTGG 59.907 42.308 0.00 0.00 33.01 4.17
398 424 6.092670 CCCATACACTCATTTTGTAGACTGTG 59.907 42.308 0.00 0.00 33.01 3.66
402 428 5.938125 ACACCCATACACTCATTTTGTAGAC 59.062 40.000 0.00 0.00 33.01 2.59
416 442 9.787435 GTCCTTCATAAATATTACACCCATACA 57.213 33.333 0.00 0.00 0.00 2.29
419 445 7.821566 TGGTCCTTCATAAATATTACACCCAT 58.178 34.615 0.00 0.00 0.00 4.00
423 449 8.567948 CACCATGGTCCTTCATAAATATTACAC 58.432 37.037 16.53 0.00 0.00 2.90
425 451 8.784043 GTCACCATGGTCCTTCATAAATATTAC 58.216 37.037 16.53 0.00 0.00 1.89
430 456 5.456921 AGTCACCATGGTCCTTCATAAAT 57.543 39.130 16.53 0.00 0.00 1.40
435 461 4.878968 TCTATAGTCACCATGGTCCTTCA 58.121 43.478 16.53 0.07 0.00 3.02
440 466 5.788450 CATCCTTCTATAGTCACCATGGTC 58.212 45.833 16.53 4.69 0.00 4.02
444 471 4.152647 TCGCATCCTTCTATAGTCACCAT 58.847 43.478 0.00 0.00 0.00 3.55
462 489 0.177141 AGGCGGTAAGCTAATTCGCA 59.823 50.000 19.75 0.00 46.95 5.10
472 499 3.133362 TCCAACCAATAGTAGGCGGTAAG 59.867 47.826 0.00 0.00 0.00 2.34
475 502 1.575419 TCCAACCAATAGTAGGCGGT 58.425 50.000 0.00 0.00 0.00 5.68
478 505 3.222603 CCCATTCCAACCAATAGTAGGC 58.777 50.000 0.00 0.00 0.00 3.93
482 509 2.574369 TCGACCCATTCCAACCAATAGT 59.426 45.455 0.00 0.00 0.00 2.12
497 524 6.153067 CACATCTAGTCAATCTAATCGACCC 58.847 44.000 0.00 0.00 0.00 4.46
517 544 9.474313 ACATATTTTTATGGTACCTTGACACAT 57.526 29.630 14.36 0.00 0.00 3.21
520 547 7.825270 ACGACATATTTTTATGGTACCTTGACA 59.175 33.333 14.36 0.00 0.00 3.58
543 570 8.588789 CACGTCACATATTTTTATCTTACACGA 58.411 33.333 0.00 0.00 0.00 4.35
545 572 8.662141 ACCACGTCACATATTTTTATCTTACAC 58.338 33.333 0.00 0.00 0.00 2.90
547 574 8.662141 ACACCACGTCACATATTTTTATCTTAC 58.338 33.333 0.00 0.00 0.00 2.34
548 575 8.780846 ACACCACGTCACATATTTTTATCTTA 57.219 30.769 0.00 0.00 0.00 2.10
549 576 7.681939 ACACCACGTCACATATTTTTATCTT 57.318 32.000 0.00 0.00 0.00 2.40
551 578 8.193250 AGTACACCACGTCACATATTTTTATC 57.807 34.615 0.00 0.00 0.00 1.75
552 579 9.656040 TTAGTACACCACGTCACATATTTTTAT 57.344 29.630 0.00 0.00 0.00 1.40
553 580 8.924691 GTTAGTACACCACGTCACATATTTTTA 58.075 33.333 0.00 0.00 0.00 1.52
557 585 5.097529 CGTTAGTACACCACGTCACATATT 58.902 41.667 0.00 0.00 0.00 1.28
566 594 2.342910 AAGCTCGTTAGTACACCACG 57.657 50.000 0.00 0.09 35.18 4.94
582 610 4.083802 AGTTTCATGAGCAACTCGTTAAGC 60.084 41.667 6.92 0.00 32.35 3.09
583 611 5.597813 AGTTTCATGAGCAACTCGTTAAG 57.402 39.130 6.92 0.00 32.35 1.85
592 620 2.479837 ACGAACGAGTTTCATGAGCAA 58.520 42.857 0.14 0.00 33.24 3.91
605 633 2.261345 CTTAACGGGCATAACGAACGA 58.739 47.619 0.14 0.00 34.93 3.85
608 636 5.468072 TGTTAAACTTAACGGGCATAACGAA 59.532 36.000 7.62 0.00 44.52 3.85
652 680 8.638565 CCGTAGCTCAATTTTTAATGAACAAAG 58.361 33.333 0.00 0.00 0.00 2.77
654 682 7.087639 CCCGTAGCTCAATTTTTAATGAACAA 58.912 34.615 0.00 0.00 0.00 2.83
657 685 5.646606 GCCCGTAGCTCAATTTTTAATGAA 58.353 37.500 0.00 0.00 38.99 2.57
675 703 2.678934 TCGGACTGCTAAGCCCGT 60.679 61.111 6.54 0.00 42.34 5.28
678 706 2.414824 CGATATCTCGGACTGCTAAGCC 60.415 54.545 0.34 0.00 41.27 4.35
684 712 1.135803 GCTCTCGATATCTCGGACTGC 60.136 57.143 0.34 0.00 45.10 4.40
685 713 2.422597 AGCTCTCGATATCTCGGACTG 58.577 52.381 0.34 0.00 45.10 3.51
686 714 2.811431 CAAGCTCTCGATATCTCGGACT 59.189 50.000 0.34 0.00 45.10 3.85
687 715 2.550606 ACAAGCTCTCGATATCTCGGAC 59.449 50.000 0.34 0.00 45.10 4.79
688 716 2.852449 ACAAGCTCTCGATATCTCGGA 58.148 47.619 0.34 0.00 45.10 4.55
691 719 5.708948 AGCATAACAAGCTCTCGATATCTC 58.291 41.667 0.34 0.00 38.01 2.75
702 730 1.363744 GCTGACGAGCATAACAAGCT 58.636 50.000 0.00 0.00 45.46 3.74
720 748 0.519077 CTGGACCGAAAGCTCAAAGC 59.481 55.000 0.00 0.00 42.84 3.51
721 749 0.519077 GCTGGACCGAAAGCTCAAAG 59.481 55.000 0.00 0.00 36.47 2.77
723 751 1.302511 GGCTGGACCGAAAGCTCAA 60.303 57.895 2.60 0.00 39.46 3.02
724 752 2.347490 GGCTGGACCGAAAGCTCA 59.653 61.111 2.60 0.00 39.46 4.26
727 755 0.756903 TATAGGGCTGGACCGAAAGC 59.243 55.000 0.00 0.00 40.62 3.51
763 791 5.076873 TCTCATTCATTTCGGGGTCTTTTT 58.923 37.500 0.00 0.00 0.00 1.94
776 804 8.324306 TCCTTTTGAGTGTATCTCTCATTCATT 58.676 33.333 3.07 0.00 43.13 2.57
779 807 9.823647 TTATCCTTTTGAGTGTATCTCTCATTC 57.176 33.333 3.07 0.00 43.13 2.67
782 810 8.981659 TGATTATCCTTTTGAGTGTATCTCTCA 58.018 33.333 0.00 0.00 43.13 3.27
803 831 5.991861 TGGGGAATACGCTTACTTTGATTA 58.008 37.500 0.00 0.00 0.00 1.75
841 869 7.962964 TTTCTTCCTTGTCTACATGTGTTAG 57.037 36.000 9.11 0.00 0.00 2.34
853 882 5.391449 GGCGTCTTTAATTTCTTCCTTGTC 58.609 41.667 0.00 0.00 0.00 3.18
951 983 9.996554 TTATATACCATGGAAGATATTATGCCG 57.003 33.333 21.47 0.00 0.00 5.69
956 988 9.429109 TCGGCTTATATACCATGGAAGATATTA 57.571 33.333 21.47 10.77 0.00 0.98
1034 1074 4.033776 CCAGCCCCGTGTCCATGT 62.034 66.667 0.00 0.00 0.00 3.21
1054 1094 4.803426 CTGCACCTCGCCGGAGAC 62.803 72.222 5.05 0.00 43.27 3.36
1124 1164 1.683629 CGAGGTTGGAGAGGTAGAGCT 60.684 57.143 0.00 0.00 0.00 4.09
1510 1550 3.034635 ACTAATTGATCGAGGGCAGAGT 58.965 45.455 0.00 0.00 0.00 3.24
1590 1633 9.398921 AGAATAATTAGTGTAGGGGAGAATCAT 57.601 33.333 0.00 0.00 36.25 2.45
1678 1721 6.705863 AAATCAAGCTTATTCCTGACCATC 57.294 37.500 0.00 0.00 0.00 3.51
1679 1722 8.636213 CATAAAATCAAGCTTATTCCTGACCAT 58.364 33.333 0.00 0.00 0.00 3.55
1875 1922 3.767673 TCAATCACACTACTACTGGGACC 59.232 47.826 0.00 0.00 0.00 4.46
1887 1934 7.208777 GTCAGAGATCATACATCAATCACACT 58.791 38.462 0.00 0.00 0.00 3.55
1893 1940 5.071384 TGCAGGTCAGAGATCATACATCAAT 59.929 40.000 0.00 0.00 0.00 2.57
1895 1942 3.962718 TGCAGGTCAGAGATCATACATCA 59.037 43.478 0.00 0.00 0.00 3.07
1908 1955 1.136695 CTCCTAAGCTCTGCAGGTCAG 59.863 57.143 15.13 5.10 44.21 3.51
2101 2164 4.256110 TGAGAAAATCAGATCGTGCATGT 58.744 39.130 5.68 0.00 32.77 3.21
2144 2207 5.900123 AGCTAAGATATACACACCCAAGTCT 59.100 40.000 0.00 0.00 0.00 3.24
2242 2317 7.920151 AGGTCTACATATATACTACTCGTAGCG 59.080 40.741 4.08 0.00 36.66 4.26
2243 2318 9.033481 CAGGTCTACATATATACTACTCGTAGC 57.967 40.741 4.08 0.00 36.66 3.58
2247 2323 7.011576 CCTGCAGGTCTACATATATACTACTCG 59.988 44.444 25.53 0.00 0.00 4.18
2273 2349 2.152830 GATCAAGGATGCTGATGCTCC 58.847 52.381 4.39 0.00 40.48 4.70
2295 2371 6.826231 TCAACAATCCTAGAACAACACAAAGA 59.174 34.615 0.00 0.00 0.00 2.52
2622 3094 7.418840 AATCAAAGATCTATCTCGCAACATC 57.581 36.000 0.00 0.00 35.76 3.06
2905 3422 2.112815 GGCAATACTCCGGGTGTGC 61.113 63.158 11.83 17.58 38.64 4.57
2907 3424 0.035439 CTTGGCAATACTCCGGGTGT 60.035 55.000 0.00 6.98 0.00 4.16
2994 3511 3.319198 GCCCCCGTGAAGGTGAGA 61.319 66.667 0.00 0.00 38.74 3.27
3138 3655 2.992114 AGGAGCTTCACGCGGAGT 60.992 61.111 12.47 0.00 45.59 3.85
3199 3716 0.462789 CCGTTGCCGTAGTATCCCTT 59.537 55.000 0.00 0.00 0.00 3.95
3216 3733 2.637025 CACCCAAGCACGAAACCG 59.363 61.111 0.00 0.00 0.00 4.44
3228 3745 3.755628 GTAGACTCCGCGCACCCA 61.756 66.667 8.75 0.00 0.00 4.51
3282 3799 3.362399 CTGCACGAGCCGGATCACT 62.362 63.158 21.44 0.00 41.13 3.41
3534 4051 2.842462 AGCACGGTGACACCTCCA 60.842 61.111 22.14 0.00 35.66 3.86
3537 4054 3.208884 GACGAGCACGGTGACACCT 62.209 63.158 22.14 3.23 44.46 4.00
3540 4057 2.643272 GAGACGAGCACGGTGACA 59.357 61.111 13.29 0.00 44.46 3.58
3576 4093 3.013276 CAGTAGTGCTCGAACTTGTCA 57.987 47.619 0.00 0.00 0.00 3.58
3630 4147 4.735132 ATGGCACCGTCGTCCGTG 62.735 66.667 0.00 0.00 33.66 4.94
3814 4348 5.882557 AGCCGAACAAGATTGAATATGTCTT 59.117 36.000 0.00 0.00 32.70 3.01
3815 4349 5.295292 CAGCCGAACAAGATTGAATATGTCT 59.705 40.000 0.00 0.00 0.00 3.41
3816 4350 5.294306 TCAGCCGAACAAGATTGAATATGTC 59.706 40.000 0.00 0.00 0.00 3.06
3817 4351 5.185454 TCAGCCGAACAAGATTGAATATGT 58.815 37.500 0.00 0.00 0.00 2.29
3818 4352 5.739752 TCAGCCGAACAAGATTGAATATG 57.260 39.130 0.00 0.00 0.00 1.78
3819 4353 5.471456 GGATCAGCCGAACAAGATTGAATAT 59.529 40.000 0.00 0.00 0.00 1.28
3820 4354 4.816385 GGATCAGCCGAACAAGATTGAATA 59.184 41.667 0.00 0.00 0.00 1.75
3821 4355 3.629398 GGATCAGCCGAACAAGATTGAAT 59.371 43.478 0.00 0.00 0.00 2.57
3822 4356 3.009723 GGATCAGCCGAACAAGATTGAA 58.990 45.455 0.00 0.00 0.00 2.69
3823 4357 2.027285 TGGATCAGCCGAACAAGATTGA 60.027 45.455 0.00 0.00 40.66 2.57
3824 4358 2.358957 TGGATCAGCCGAACAAGATTG 58.641 47.619 0.00 0.00 40.66 2.67
3825 4359 2.787473 TGGATCAGCCGAACAAGATT 57.213 45.000 0.00 0.00 40.66 2.40
3836 4370 5.401550 TGTTCAAATTTTCGATGGATCAGC 58.598 37.500 0.00 0.00 0.00 4.26
3908 4442 7.995488 TCTAGATATGATTATGGATCGAGCAGA 59.005 37.037 1.84 0.00 37.60 4.26
3925 4459 9.941325 AAATTACAGGAAGATGCTCTAGATATG 57.059 33.333 0.00 0.00 0.00 1.78
3976 4510 5.469084 GCGGGTGAGGAAATTTATAGTTAGG 59.531 44.000 0.00 0.00 0.00 2.69
3984 4518 4.939052 TTTTTGCGGGTGAGGAAATTTA 57.061 36.364 0.00 0.00 31.75 1.40
3985 4519 3.828875 TTTTTGCGGGTGAGGAAATTT 57.171 38.095 0.00 0.00 31.75 1.82
4010 4544 9.981460 AGAAATTCTCACCTGGAAAATTATAGT 57.019 29.630 0.00 0.00 0.00 2.12
4017 4551 6.017440 CGTTACAGAAATTCTCACCTGGAAAA 60.017 38.462 0.00 0.00 31.94 2.29
4026 4560 9.151471 CTTCCTAATTCGTTACAGAAATTCTCA 57.849 33.333 0.00 0.00 33.43 3.27
4028 4562 7.065923 GCCTTCCTAATTCGTTACAGAAATTCT 59.934 37.037 0.00 0.00 33.43 2.40
4038 4572 2.101917 CCCTCGCCTTCCTAATTCGTTA 59.898 50.000 0.00 0.00 0.00 3.18
4048 4582 0.748367 GTTCCATTCCCTCGCCTTCC 60.748 60.000 0.00 0.00 0.00 3.46
4049 4583 0.253327 AGTTCCATTCCCTCGCCTTC 59.747 55.000 0.00 0.00 0.00 3.46
4064 4613 7.657336 TCAAATCCAATCACCAGTAAAAGTTC 58.343 34.615 0.00 0.00 0.00 3.01
4193 4743 0.598065 ACGGATTGCTTTGACTTGCC 59.402 50.000 0.00 0.00 0.00 4.52
4211 4761 3.242248 CAGTAGTACGCGGCATAAAGAAC 59.758 47.826 12.47 0.00 0.00 3.01
4222 4773 0.801067 GTTGGAGCCAGTAGTACGCG 60.801 60.000 3.53 3.53 0.00 6.01
4290 4841 6.615088 TGATTGAAGTATCTGCAAAAGCTTC 58.385 36.000 0.00 11.48 32.19 3.86
4405 4957 9.715121 AAAGTTTAGAGATTACCGATTGTTACA 57.285 29.630 0.00 0.00 0.00 2.41
4434 4992 2.810870 TTAGGCAGCCGGGAATTAAA 57.189 45.000 5.55 0.00 0.00 1.52
4631 5190 6.128035 CCAAAATGAGTATTGATCGAACACCA 60.128 38.462 0.00 0.00 0.00 4.17
4649 5208 6.878317 TGTATCTACAGAGGAGACCAAAATG 58.122 40.000 0.00 0.00 0.00 2.32
4723 5282 5.753921 ACGAGAGTAACCTTTCAAGACTTTG 59.246 40.000 0.00 0.00 46.88 2.77


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

AutoCloner maintained by Alex Coulton.