Multiple sequence alignment - TraesCS1D01G396300

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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 TraesCS1D01G396300 chr1D 100.000 6526 0 0 1 6526 464598725 464592200 0.000000e+00 12052.0
1 TraesCS1D01G396300 chr1D 90.845 142 13 0 4586 4727 464404888 464404747 2.400000e-44 191.0
2 TraesCS1D01G396300 chr1D 84.375 192 24 6 5640 5829 464631048 464631235 4.020000e-42 183.0
3 TraesCS1D01G396300 chr1A 96.815 3516 70 7 1 3489 556943769 556940269 0.000000e+00 5834.0
4 TraesCS1D01G396300 chr1A 95.496 2065 67 14 3522 5569 556940276 556938221 0.000000e+00 3275.0
5 TraesCS1D01G396300 chr1A 92.308 559 27 4 5643 6186 556938105 556937548 0.000000e+00 780.0
6 TraesCS1D01G396300 chr1A 89.674 184 13 3 4544 4727 556830464 556830287 5.090000e-56 230.0
7 TraesCS1D01G396300 chr1A 78.235 170 32 4 6361 6525 556988756 556988925 3.220000e-18 104.0
8 TraesCS1D01G396300 chr1B 92.152 3568 153 57 1 3502 640850722 640847216 0.000000e+00 4920.0
9 TraesCS1D01G396300 chr1B 94.410 2075 63 18 3514 5569 640847234 640845194 0.000000e+00 3140.0
10 TraesCS1D01G396300 chr1B 90.750 400 16 6 5643 6035 640845075 640844690 1.250000e-141 514.0
11 TraesCS1D01G396300 chr1B 90.256 390 22 3 5807 6182 599175857 599175470 4.550000e-136 496.0
12 TraesCS1D01G396300 chr1B 90.145 345 18 5 6033 6362 640844427 640844084 1.000000e-117 435.0
13 TraesCS1D01G396300 chr1B 90.661 257 12 4 449 694 640850348 640850093 1.360000e-86 331.0
14 TraesCS1D01G396300 chr1B 93.567 171 6 3 6361 6526 640844056 640843886 3.910000e-62 250.0
15 TraesCS1D01G396300 chr1B 88.889 171 13 4 6361 6525 599175326 599175156 8.580000e-49 206.0
16 TraesCS1D01G396300 chr1B 94.309 123 7 0 6240 6362 599175476 599175354 8.640000e-44 189.0
17 TraesCS1D01G396300 chr2D 86.355 513 52 12 7 516 627820490 627820987 1.600000e-150 544.0
18 TraesCS1D01G396300 chr2D 84.980 253 32 5 451 700 627820866 627821115 1.090000e-62 252.0
19 TraesCS1D01G396300 chr5A 90.217 184 15 1 4544 4727 412229902 412230082 3.040000e-58 237.0
20 TraesCS1D01G396300 chr4A 87.363 182 14 4 4544 4722 538724706 538724881 3.990000e-47 200.0
21 TraesCS1D01G396300 chr4A 84.404 109 15 2 6373 6480 389141527 389141420 8.950000e-19 106.0
22 TraesCS1D01G396300 chr2B 76.821 151 22 11 5999 6138 568022532 568022384 9.080000e-09 73.1


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 TraesCS1D01G396300 chr1D 464592200 464598725 6525 True 12052.000000 12052 100.000000 1 6526 1 chr1D.!!$R2 6525
1 TraesCS1D01G396300 chr1A 556937548 556943769 6221 True 3296.333333 5834 94.873000 1 6186 3 chr1A.!!$R2 6185
2 TraesCS1D01G396300 chr1B 640843886 640850722 6836 True 1598.333333 4920 91.947500 1 6526 6 chr1B.!!$R2 6525
3 TraesCS1D01G396300 chr1B 599175156 599175857 701 True 297.000000 496 91.151333 5807 6525 3 chr1B.!!$R1 718
4 TraesCS1D01G396300 chr2D 627820490 627821115 625 False 398.000000 544 85.667500 7 700 2 chr2D.!!$F1 693

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
544 547 1.032794 TCAGACAGCGACTGTTCTGT 58.967 50.000 22.33 13.88 45.44 3.41 F
1413 1474 0.251341 GGGCATTTGACCTGGTCACT 60.251 55.000 28.35 16.12 42.60 3.41 F
1542 1603 0.438830 GTCAACGCGTGAGGATTGTC 59.561 55.000 14.98 0.00 36.74 3.18 F
1680 1741 1.347378 GTGGCAAATGTTTGGGGTGAT 59.653 47.619 7.51 0.00 38.57 3.06 F
1689 1750 1.867233 GTTTGGGGTGATCGATCATCG 59.133 52.381 29.53 0.00 38.81 3.84 F
2608 2669 1.742268 GAGGCTGAGCAGGAAACAATC 59.258 52.381 6.82 0.00 0.00 2.67 F
4095 4209 2.751259 TCTTTGCTTCCATGCAGATGAC 59.249 45.455 0.00 0.00 44.27 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2398 0.322456 TCACACCACTAGCCCATTGC 60.322 55.000 0.00 0.0 41.71 3.56 R
2488 2549 2.090760 TGCTGCGCCTGAAATTGATAA 58.909 42.857 4.18 0.0 0.00 1.75 R
2560 2621 3.308053 CGACAGAAGTATGCACCTCATTG 59.692 47.826 0.00 0.0 36.63 2.82 R
2608 2669 5.452077 GCTAACCTTAGTACTCTCATGGTGG 60.452 48.000 0.00 0.0 33.32 4.61 R
3299 3360 7.495901 TGAAAGACTTGCAATGGACAATAAAA 58.504 30.769 0.00 0.0 0.00 1.52 R
4206 4320 3.045634 TGGTTCATGAGGATAATCCGGT 58.954 45.455 0.00 0.0 42.75 5.28 R
5615 5826 0.037590 TGCTCGGTACATTTGGGCTT 59.962 50.000 0.00 0.0 0.00 4.35 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
42 43 5.050644 TGCTAGAATGTTGCTCACAAATG 57.949 39.130 0.00 0.00 39.50 2.32
88 89 8.367156 AGTTTCTTTTCAGCATGGCTTTTAATA 58.633 29.630 0.00 0.00 36.40 0.98
90 91 8.761575 TTCTTTTCAGCATGGCTTTTAATAAG 57.238 30.769 0.00 0.00 36.40 1.73
92 93 5.657826 TTCAGCATGGCTTTTAATAAGCA 57.342 34.783 18.00 9.21 44.71 3.91
93 94 4.997565 TCAGCATGGCTTTTAATAAGCAC 58.002 39.130 18.00 11.21 44.71 4.40
96 98 5.870978 CAGCATGGCTTTTAATAAGCACTTT 59.129 36.000 18.00 3.85 44.71 2.66
211 213 9.167311 ACAGTTGGATTAACATTCTTCTGATAC 57.833 33.333 0.00 0.00 41.88 2.24
379 382 3.256383 TCATTTCCTGTGACAAGCCATTG 59.744 43.478 0.00 0.00 42.46 2.82
544 547 1.032794 TCAGACAGCGACTGTTCTGT 58.967 50.000 22.33 13.88 45.44 3.41
680 694 7.181845 AGTTCTTCTGATCTCCTTCCTTACATT 59.818 37.037 0.00 0.00 0.00 2.71
696 738 6.983890 TCCTTACATTTTCTTTTGCTTCCAAC 59.016 34.615 0.00 0.00 0.00 3.77
733 775 3.920231 TTGCTATCTTGGCACATCTCT 57.080 42.857 0.00 0.00 39.30 3.10
734 776 3.189618 TGCTATCTTGGCACATCTCTG 57.810 47.619 0.00 0.00 39.30 3.35
961 1019 7.625828 AAAGGTGGGAACGAATTTAATCTAG 57.374 36.000 0.00 0.00 0.00 2.43
1028 1086 2.521465 TGGTGTTGCAGGGCTTGG 60.521 61.111 0.00 0.00 0.00 3.61
1032 1090 1.073722 TGTTGCAGGGCTTGGAGAG 59.926 57.895 0.00 0.00 0.00 3.20
1413 1474 0.251341 GGGCATTTGACCTGGTCACT 60.251 55.000 28.35 16.12 42.60 3.41
1479 1540 3.300388 CTCTGAGGTACTGAAGCCCATA 58.700 50.000 0.00 0.00 41.55 2.74
1515 1576 9.860898 ATCTTTGAAGATGCACCTTATTTTTAC 57.139 29.630 0.00 0.00 43.81 2.01
1542 1603 0.438830 GTCAACGCGTGAGGATTGTC 59.561 55.000 14.98 0.00 36.74 3.18
1659 1720 2.945668 GCATGTGAACTGGATAACCTCC 59.054 50.000 0.00 0.00 45.19 4.30
1680 1741 1.347378 GTGGCAAATGTTTGGGGTGAT 59.653 47.619 7.51 0.00 38.57 3.06
1689 1750 1.867233 GTTTGGGGTGATCGATCATCG 59.133 52.381 29.53 0.00 38.81 3.84
1719 1780 4.441495 CCAAACTTTCAGGACCCAAAGAAC 60.441 45.833 16.92 0.00 34.30 3.01
1854 1915 7.429340 CGATATTCTCAAACTTATGTTGTTGCC 59.571 37.037 0.00 0.00 36.39 4.52
1987 2048 2.833943 GGGCAATTTGTCCTGGAGAAAT 59.166 45.455 22.17 22.17 39.55 2.17
2001 2062 3.198635 TGGAGAAATTGGCAGTAGAGGAG 59.801 47.826 0.00 0.00 0.00 3.69
2064 2125 2.076863 GCACTTGAGCGGACTGTAAAT 58.923 47.619 0.00 0.00 0.00 1.40
2169 2230 2.769095 AGTAGAGCACCCAGATTTCTCC 59.231 50.000 0.00 0.00 0.00 3.71
2337 2398 7.175641 GGGTATAAGGATGATGGAATTGAAGTG 59.824 40.741 0.00 0.00 0.00 3.16
2608 2669 1.742268 GAGGCTGAGCAGGAAACAATC 59.258 52.381 6.82 0.00 0.00 2.67
3121 3182 5.329493 GTGGCCACGAAAATGTAATACTTC 58.671 41.667 22.49 0.00 0.00 3.01
3299 3360 3.793797 CCAGGTCGGTTTTTCTTGTTT 57.206 42.857 0.00 0.00 0.00 2.83
3365 3426 6.206048 TCACTGGCTCATTGCATATAGAATTG 59.794 38.462 0.00 0.00 45.15 2.32
3460 3555 5.828328 AGATGTGAATCTGTCATGATGCAAT 59.172 36.000 0.00 0.00 38.90 3.56
3474 3569 9.512435 GTCATGATGCAATCTTATATAATTGGC 57.488 33.333 0.00 5.04 45.81 4.52
3492 3587 7.539034 AATTGGCTTGTGGTTAGAAATAAGT 57.461 32.000 0.00 0.00 0.00 2.24
3493 3588 6.969993 TTGGCTTGTGGTTAGAAATAAGTT 57.030 33.333 0.00 0.00 0.00 2.66
3494 3589 8.644374 ATTGGCTTGTGGTTAGAAATAAGTTA 57.356 30.769 0.00 0.00 0.00 2.24
3495 3590 8.466617 TTGGCTTGTGGTTAGAAATAAGTTAA 57.533 30.769 0.00 0.00 0.00 2.01
3496 3591 8.466617 TGGCTTGTGGTTAGAAATAAGTTAAA 57.533 30.769 0.00 0.00 0.00 1.52
3497 3592 8.915036 TGGCTTGTGGTTAGAAATAAGTTAAAA 58.085 29.630 0.00 0.00 0.00 1.52
3498 3593 9.923143 GGCTTGTGGTTAGAAATAAGTTAAAAT 57.077 29.630 0.00 0.00 0.00 1.82
3623 3719 9.691362 TTACAAGATGATTGAAGTTAAAAAGGC 57.309 29.630 0.00 0.00 0.00 4.35
3652 3748 9.618890 AGCTTATCATGTGTATGTTATCTTGTT 57.381 29.630 0.00 0.00 35.73 2.83
4095 4209 2.751259 TCTTTGCTTCCATGCAGATGAC 59.249 45.455 0.00 0.00 44.27 3.06
4727 4841 5.016831 AGGGCTTAACTGAATTTTGGTAGG 58.983 41.667 0.00 0.00 0.00 3.18
4760 4874 9.545105 TTTTGAGTAGAACGTAAACCAAGATTA 57.455 29.630 0.00 0.00 0.00 1.75
4839 4953 1.024271 TCTGCTGCACCTTTCAACAC 58.976 50.000 0.00 0.00 0.00 3.32
4850 4964 6.037830 TGCACCTTTCAACACTAAGAAGTAAC 59.962 38.462 0.00 0.00 33.48 2.50
4912 5026 5.395682 TCTCCATCCAGCATTTTGAAAAG 57.604 39.130 0.00 0.00 0.00 2.27
4988 5102 2.362503 ACCTCGGCGGTGATCTCA 60.363 61.111 7.21 0.00 46.80 3.27
4990 5104 1.330655 ACCTCGGCGGTGATCTCATT 61.331 55.000 7.21 0.00 46.80 2.57
5000 5114 2.877168 GGTGATCTCATTGGTCATGCTC 59.123 50.000 0.00 0.00 32.13 4.26
5035 5149 4.466827 ACATATCAGATGATGGCTGCAAA 58.533 39.130 5.58 0.00 36.05 3.68
5036 5150 4.519350 ACATATCAGATGATGGCTGCAAAG 59.481 41.667 5.58 0.00 36.05 2.77
5148 5265 3.240134 TTCAGAGCGGGCACACCTC 62.240 63.158 0.00 0.00 36.97 3.85
5149 5266 4.767255 CAGAGCGGGCACACCTCC 62.767 72.222 0.30 0.00 36.97 4.30
5239 5356 0.918258 TGCCTGGCACATGATCCTTA 59.082 50.000 19.30 0.00 38.20 2.69
5310 5427 1.177401 GATGAACTGAAAGGGTGCCC 58.823 55.000 0.00 0.00 39.30 5.36
5361 5478 2.215907 TGGTTTGTGAAATTGTGCCG 57.784 45.000 0.00 0.00 0.00 5.69
5409 5531 2.498644 TTGTGTGTGGGTGTTGAGAA 57.501 45.000 0.00 0.00 0.00 2.87
5412 5534 2.290641 TGTGTGTGGGTGTTGAGAAAGT 60.291 45.455 0.00 0.00 0.00 2.66
5610 5821 9.649167 AAAAACAGATTTCATTTGGATGATCTC 57.351 29.630 0.00 0.00 41.71 2.75
5611 5822 6.615264 ACAGATTTCATTTGGATGATCTCG 57.385 37.500 0.00 0.00 41.71 4.04
5612 5823 6.118170 ACAGATTTCATTTGGATGATCTCGT 58.882 36.000 0.00 0.00 41.71 4.18
5613 5824 6.259608 ACAGATTTCATTTGGATGATCTCGTC 59.740 38.462 0.00 0.00 41.71 4.20
5614 5825 5.464722 AGATTTCATTTGGATGATCTCGTCG 59.535 40.000 0.00 0.00 41.71 5.12
5615 5826 4.385358 TTCATTTGGATGATCTCGTCGA 57.615 40.909 0.00 0.00 41.71 4.20
5616 5827 4.385358 TCATTTGGATGATCTCGTCGAA 57.615 40.909 0.00 0.00 37.37 3.71
5617 5828 4.363138 TCATTTGGATGATCTCGTCGAAG 58.637 43.478 0.00 0.00 37.37 3.79
5618 5829 2.209838 TTGGATGATCTCGTCGAAGC 57.790 50.000 0.00 0.00 32.78 3.86
5619 5830 0.385751 TGGATGATCTCGTCGAAGCC 59.614 55.000 0.00 0.00 32.78 4.35
5620 5831 0.319125 GGATGATCTCGTCGAAGCCC 60.319 60.000 0.00 0.00 32.78 5.19
5621 5832 0.385751 GATGATCTCGTCGAAGCCCA 59.614 55.000 0.00 0.00 0.00 5.36
5622 5833 0.824109 ATGATCTCGTCGAAGCCCAA 59.176 50.000 0.00 0.00 0.00 4.12
5623 5834 0.606096 TGATCTCGTCGAAGCCCAAA 59.394 50.000 0.00 0.00 0.00 3.28
5624 5835 1.207089 TGATCTCGTCGAAGCCCAAAT 59.793 47.619 0.00 0.00 0.00 2.32
5625 5836 1.594862 GATCTCGTCGAAGCCCAAATG 59.405 52.381 0.00 0.00 0.00 2.32
5626 5837 0.320374 TCTCGTCGAAGCCCAAATGT 59.680 50.000 0.00 0.00 0.00 2.71
5627 5838 1.546923 TCTCGTCGAAGCCCAAATGTA 59.453 47.619 0.00 0.00 0.00 2.29
5628 5839 1.659098 CTCGTCGAAGCCCAAATGTAC 59.341 52.381 0.00 0.00 0.00 2.90
5629 5840 0.725117 CGTCGAAGCCCAAATGTACC 59.275 55.000 0.00 0.00 0.00 3.34
5630 5841 0.725117 GTCGAAGCCCAAATGTACCG 59.275 55.000 0.00 0.00 0.00 4.02
5631 5842 0.609151 TCGAAGCCCAAATGTACCGA 59.391 50.000 0.00 0.00 0.00 4.69
5632 5843 1.006832 CGAAGCCCAAATGTACCGAG 58.993 55.000 0.00 0.00 0.00 4.63
5633 5844 0.733150 GAAGCCCAAATGTACCGAGC 59.267 55.000 0.00 0.00 0.00 5.03
5634 5845 0.037590 AAGCCCAAATGTACCGAGCA 59.962 50.000 0.00 0.00 0.00 4.26
5635 5846 0.392998 AGCCCAAATGTACCGAGCAG 60.393 55.000 0.00 0.00 0.00 4.24
5636 5847 0.392461 GCCCAAATGTACCGAGCAGA 60.392 55.000 0.00 0.00 0.00 4.26
5637 5848 1.369625 CCCAAATGTACCGAGCAGAC 58.630 55.000 0.00 0.00 0.00 3.51
5638 5849 0.999406 CCAAATGTACCGAGCAGACG 59.001 55.000 0.00 0.00 0.00 4.18
5639 5850 1.671850 CCAAATGTACCGAGCAGACGT 60.672 52.381 0.00 0.00 0.00 4.34
5640 5851 2.066262 CAAATGTACCGAGCAGACGTT 58.934 47.619 0.00 0.00 0.00 3.99
5641 5852 1.710013 AATGTACCGAGCAGACGTTG 58.290 50.000 0.00 0.00 0.00 4.10
5674 5885 5.769484 AAATCATGCTCAGCTAATCCAAG 57.231 39.130 0.00 0.00 0.00 3.61
5802 6013 9.680315 TTTCTTTTGTCGTTTTCAAAGTAGAAA 57.320 25.926 11.07 11.07 38.20 2.52
5883 6097 6.528537 AGCAAATTAAGCAACATATGGACA 57.471 33.333 7.80 0.00 0.00 4.02
5929 6143 1.444836 TGTAGAAAAATGCGGGTCGG 58.555 50.000 0.00 0.00 0.00 4.79
5945 6159 0.830648 TCGGGAACAAGATGGCTAGG 59.169 55.000 0.00 0.00 0.00 3.02
6053 6537 7.268586 AGTATCAAAGTGCGAATAACATCTCT 58.731 34.615 0.00 0.00 0.00 3.10
6144 6639 4.812403 ATTATTGGACCACATGGGATGA 57.188 40.909 0.00 0.00 41.15 2.92
6201 6696 2.022238 GCTTGCAAGTACCCATACCCC 61.022 57.143 26.55 2.58 30.88 4.95
6216 6715 0.621862 ACCCCAGGAGAAGATGGTCC 60.622 60.000 0.00 0.00 34.58 4.46
6219 6718 1.617018 CCAGGAGAAGATGGTCCGCA 61.617 60.000 0.00 0.00 37.97 5.69
6288 6787 6.006275 TGGGATGATCCTAAGAAAGAAAGG 57.994 41.667 11.87 0.00 36.57 3.11
6292 6791 6.548993 GGATGATCCTAAGAAAGAAAGGCAAT 59.451 38.462 3.71 0.00 32.53 3.56
6330 6829 9.013229 TGACTAGCATGTTAAATCAAGTGAAAT 57.987 29.630 0.00 0.00 0.00 2.17
6405 6934 4.213059 GTGCATTGCTAAGATCTCTAAGGC 59.787 45.833 10.49 3.52 0.00 4.35
6411 6940 3.305064 GCTAAGATCTCTAAGGCTGGACG 60.305 52.174 0.00 0.00 0.00 4.79
6431 6960 3.709653 ACGCTTAGATCCATTTCACCCTA 59.290 43.478 0.00 0.00 0.00 3.53
6470 6999 1.204146 ACACCTGTGTTGAGGTCACT 58.796 50.000 0.00 0.00 45.15 3.41
6518 7052 0.602905 ACAGTGTTTAGGCGCACCTC 60.603 55.000 10.83 0.00 46.34 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.744771 GCAGGGATCAGGGTCGTTTC 60.745 60.000 0.00 0.00 0.00 2.78
211 213 1.737838 TTAGCTGATCCTGCAAACCG 58.262 50.000 0.00 0.00 0.00 4.44
379 382 4.527944 AGGAGATTTGCCCTAAAACTAGC 58.472 43.478 0.00 0.00 32.28 3.42
544 547 3.454858 AGGAGATTTGCCCAGAGAACTA 58.545 45.455 0.00 0.00 0.00 2.24
680 694 5.852282 AAGCTAGTTGGAAGCAAAAGAAA 57.148 34.783 0.00 0.00 42.62 2.52
1028 1086 8.674263 ATCAATTACAAACAGATCCATCTCTC 57.326 34.615 0.00 0.00 34.22 3.20
1032 1090 8.896744 TCTGAATCAATTACAAACAGATCCATC 58.103 33.333 0.00 0.00 0.00 3.51
1413 1474 1.979855 CCCCATCACTGAACACAACA 58.020 50.000 0.00 0.00 0.00 3.33
1515 1576 1.920574 CTCACGCGTTGACTTGGATAG 59.079 52.381 10.22 0.00 0.00 2.08
1542 1603 1.221840 CTTGGACACGGAGGGATGG 59.778 63.158 0.00 0.00 0.00 3.51
1596 1657 2.628178 AGACACAACACCTTCATCTCGA 59.372 45.455 0.00 0.00 0.00 4.04
1659 1720 0.599728 CACCCCAAACATTTGCCACG 60.600 55.000 0.00 0.00 36.86 4.94
1689 1750 3.771577 TCCTGAAAGTTTGGAGGACTC 57.228 47.619 8.36 0.00 29.25 3.36
1695 1756 3.053245 TCTTTGGGTCCTGAAAGTTTGGA 60.053 43.478 11.47 0.00 32.11 3.53
1719 1780 1.531423 AGCATGACAGCAAAGTGAGG 58.469 50.000 0.00 0.00 36.85 3.86
1854 1915 4.031028 CGTCAAAAGTGCTCTTTGTCTTG 58.969 43.478 14.11 8.97 42.26 3.02
1987 2048 2.290847 CAGCCTCCTCTACTGCCAA 58.709 57.895 0.00 0.00 0.00 4.52
2169 2230 0.593128 CGACTTCCCCAGTGCAAAAG 59.407 55.000 0.00 0.00 35.01 2.27
2337 2398 0.322456 TCACACCACTAGCCCATTGC 60.322 55.000 0.00 0.00 41.71 3.56
2488 2549 2.090760 TGCTGCGCCTGAAATTGATAA 58.909 42.857 4.18 0.00 0.00 1.75
2560 2621 3.308053 CGACAGAAGTATGCACCTCATTG 59.692 47.826 0.00 0.00 36.63 2.82
2608 2669 5.452077 GCTAACCTTAGTACTCTCATGGTGG 60.452 48.000 0.00 0.00 33.32 4.61
3121 3182 8.567285 AGAGGAATAAAGTTGAATTAGGTGTG 57.433 34.615 0.00 0.00 0.00 3.82
3299 3360 7.495901 TGAAAGACTTGCAATGGACAATAAAA 58.504 30.769 0.00 0.00 0.00 1.52
3320 3381 7.922278 CCAGTGAAAAGATTCAGTTTCATGAAA 59.078 33.333 16.91 16.91 44.93 2.69
3441 3536 9.734984 ATATAAGATTGCATCATGACAGATTCA 57.265 29.630 0.00 0.00 39.11 2.57
3601 3697 7.544804 AGGCCTTTTTAACTTCAATCATCTT 57.455 32.000 0.00 0.00 0.00 2.40
3623 3719 9.935241 AAGATAACATACACATGATAAGCTAGG 57.065 33.333 0.00 0.00 35.96 3.02
3676 3773 7.658179 TTGACAGTTTAACTAGCTTGATCAG 57.342 36.000 1.04 0.00 0.00 2.90
3754 3852 6.477253 AGTTTTATCAGAGAAGGGAAGAACC 58.523 40.000 0.00 0.00 38.08 3.62
3959 4065 9.430399 AATGGTTTTCTGATCATCATTCCTTAT 57.570 29.630 0.00 0.00 0.00 1.73
3960 4066 8.827832 AATGGTTTTCTGATCATCATTCCTTA 57.172 30.769 0.00 0.00 0.00 2.69
3961 4067 7.618512 AGAATGGTTTTCTGATCATCATTCCTT 59.381 33.333 14.45 2.32 39.54 3.36
4056 4170 6.153340 AGCAAAGAACACCATGTAAGCAATAT 59.847 34.615 0.00 0.00 0.00 1.28
4057 4171 5.476599 AGCAAAGAACACCATGTAAGCAATA 59.523 36.000 0.00 0.00 0.00 1.90
4060 4174 3.221771 AGCAAAGAACACCATGTAAGCA 58.778 40.909 0.00 0.00 0.00 3.91
4095 4209 8.737168 TTTCCTCATAAACTCTAACATGGATG 57.263 34.615 0.00 0.00 0.00 3.51
4206 4320 3.045634 TGGTTCATGAGGATAATCCGGT 58.954 45.455 0.00 0.00 42.75 5.28
4727 4841 8.430828 GGTTTACGTTCTACTCAAAACTCATAC 58.569 37.037 0.00 0.00 0.00 2.39
4912 5026 1.527311 GTGAAGTGCTCCTTGACGAAC 59.473 52.381 0.00 0.00 32.03 3.95
4981 5095 2.830104 CGAGCATGACCAATGAGATCA 58.170 47.619 0.00 0.00 38.72 2.92
4988 5102 1.079197 TGTCGCGAGCATGACCAAT 60.079 52.632 10.24 0.00 34.18 3.16
4990 5104 2.125952 CTGTCGCGAGCATGACCA 60.126 61.111 10.24 0.07 34.18 4.02
5035 5149 3.077556 AATCCGGTCGAGCAGCCT 61.078 61.111 15.89 0.00 0.00 4.58
5036 5150 2.586357 GAATCCGGTCGAGCAGCC 60.586 66.667 15.89 0.00 0.00 4.85
5239 5356 6.658816 TCTTACAAGATGCCATTACACAACAT 59.341 34.615 0.00 0.00 0.00 2.71
5310 5427 1.134753 AGCTGCTTCTGTCTCTCATCG 59.865 52.381 0.00 0.00 0.00 3.84
5361 5478 3.601443 ACTTCCATCACACTCTACAGC 57.399 47.619 0.00 0.00 0.00 4.40
5409 5531 7.123847 CCAACTATACAGACAGGGTACTTACTT 59.876 40.741 0.00 0.00 0.00 2.24
5412 5534 5.361857 GCCAACTATACAGACAGGGTACTTA 59.638 44.000 0.00 0.00 0.00 2.24
5584 5795 9.649167 GAGATCATCCAAATGAAATCTGTTTTT 57.351 29.630 0.00 0.00 44.85 1.94
5601 5812 0.319125 GGGCTTCGACGAGATCATCC 60.319 60.000 0.00 0.00 0.00 3.51
5602 5813 0.385751 TGGGCTTCGACGAGATCATC 59.614 55.000 0.00 0.00 0.00 2.92
5603 5814 0.824109 TTGGGCTTCGACGAGATCAT 59.176 50.000 0.00 0.00 0.00 2.45
5604 5815 0.606096 TTTGGGCTTCGACGAGATCA 59.394 50.000 0.00 0.00 0.00 2.92
5605 5816 1.594862 CATTTGGGCTTCGACGAGATC 59.405 52.381 0.00 0.00 0.00 2.75
5606 5817 1.066143 ACATTTGGGCTTCGACGAGAT 60.066 47.619 0.00 0.00 0.00 2.75
5607 5818 0.320374 ACATTTGGGCTTCGACGAGA 59.680 50.000 0.00 0.00 0.00 4.04
5608 5819 1.659098 GTACATTTGGGCTTCGACGAG 59.341 52.381 0.00 0.00 0.00 4.18
5609 5820 1.673626 GGTACATTTGGGCTTCGACGA 60.674 52.381 0.00 0.00 0.00 4.20
5610 5821 0.725117 GGTACATTTGGGCTTCGACG 59.275 55.000 0.00 0.00 0.00 5.12
5611 5822 0.725117 CGGTACATTTGGGCTTCGAC 59.275 55.000 0.00 0.00 0.00 4.20
5612 5823 0.609151 TCGGTACATTTGGGCTTCGA 59.391 50.000 0.00 0.00 0.00 3.71
5613 5824 1.006832 CTCGGTACATTTGGGCTTCG 58.993 55.000 0.00 0.00 0.00 3.79
5614 5825 0.733150 GCTCGGTACATTTGGGCTTC 59.267 55.000 0.00 0.00 0.00 3.86
5615 5826 0.037590 TGCTCGGTACATTTGGGCTT 59.962 50.000 0.00 0.00 0.00 4.35
5616 5827 0.392998 CTGCTCGGTACATTTGGGCT 60.393 55.000 0.00 0.00 0.00 5.19
5617 5828 0.392461 TCTGCTCGGTACATTTGGGC 60.392 55.000 0.00 0.00 0.00 5.36
5618 5829 1.369625 GTCTGCTCGGTACATTTGGG 58.630 55.000 0.00 0.00 0.00 4.12
5619 5830 0.999406 CGTCTGCTCGGTACATTTGG 59.001 55.000 0.00 0.00 0.00 3.28
5620 5831 1.710013 ACGTCTGCTCGGTACATTTG 58.290 50.000 0.00 0.00 34.94 2.32
5621 5832 2.066262 CAACGTCTGCTCGGTACATTT 58.934 47.619 0.00 0.00 34.94 2.32
5622 5833 1.000506 ACAACGTCTGCTCGGTACATT 59.999 47.619 0.00 0.00 34.94 2.71
5623 5834 0.601558 ACAACGTCTGCTCGGTACAT 59.398 50.000 0.00 0.00 34.94 2.29
5624 5835 0.318360 CACAACGTCTGCTCGGTACA 60.318 55.000 0.00 0.00 34.94 2.90
5625 5836 0.039798 TCACAACGTCTGCTCGGTAC 60.040 55.000 0.00 0.00 34.94 3.34
5626 5837 0.240145 CTCACAACGTCTGCTCGGTA 59.760 55.000 0.00 0.00 34.94 4.02
5627 5838 1.007271 CTCACAACGTCTGCTCGGT 60.007 57.895 0.00 0.00 34.94 4.69
5628 5839 0.109086 ATCTCACAACGTCTGCTCGG 60.109 55.000 0.00 0.00 34.94 4.63
5629 5840 2.544480 TATCTCACAACGTCTGCTCG 57.456 50.000 0.00 0.00 0.00 5.03
5630 5841 6.887376 TTTTATATCTCACAACGTCTGCTC 57.113 37.500 0.00 0.00 0.00 4.26
5631 5842 7.549134 TGATTTTTATATCTCACAACGTCTGCT 59.451 33.333 0.00 0.00 0.00 4.24
5632 5843 7.684670 TGATTTTTATATCTCACAACGTCTGC 58.315 34.615 0.00 0.00 0.00 4.26
5633 5844 9.642312 CATGATTTTTATATCTCACAACGTCTG 57.358 33.333 0.00 0.00 0.00 3.51
5634 5845 8.338259 GCATGATTTTTATATCTCACAACGTCT 58.662 33.333 0.00 0.00 0.00 4.18
5635 5846 8.338259 AGCATGATTTTTATATCTCACAACGTC 58.662 33.333 0.00 0.00 0.00 4.34
5636 5847 8.213518 AGCATGATTTTTATATCTCACAACGT 57.786 30.769 0.00 0.00 0.00 3.99
5637 5848 8.337532 TGAGCATGATTTTTATATCTCACAACG 58.662 33.333 0.00 0.00 0.00 4.10
5638 5849 9.661187 CTGAGCATGATTTTTATATCTCACAAC 57.339 33.333 0.00 0.00 0.00 3.32
5639 5850 8.347771 GCTGAGCATGATTTTTATATCTCACAA 58.652 33.333 0.00 0.00 0.00 3.33
5640 5851 7.718314 AGCTGAGCATGATTTTTATATCTCACA 59.282 33.333 7.39 0.00 0.00 3.58
5641 5852 8.097078 AGCTGAGCATGATTTTTATATCTCAC 57.903 34.615 7.39 0.00 0.00 3.51
5674 5885 6.220930 TCGGCCACAACATATAGAAATACTC 58.779 40.000 2.24 0.00 0.00 2.59
5802 6013 7.736447 GCATATGCAAGGAAGAAAGTAGTAT 57.264 36.000 22.84 0.00 41.59 2.12
5883 6097 9.436957 AAGTCTTAGAAACACGACAATCAATAT 57.563 29.630 0.00 0.00 0.00 1.28
5889 6103 6.920569 ACAAAGTCTTAGAAACACGACAAT 57.079 33.333 0.00 0.00 0.00 2.71
5929 6143 2.487986 CCATCCCTAGCCATCTTGTTCC 60.488 54.545 0.00 0.00 0.00 3.62
6144 6639 0.756070 GGTAGCCTCGTAGCCTCCTT 60.756 60.000 0.00 0.00 0.00 3.36
6192 6687 1.701847 CATCTTCTCCTGGGGTATGGG 59.298 57.143 0.00 0.00 0.00 4.00
6201 6696 0.467384 ATGCGGACCATCTTCTCCTG 59.533 55.000 0.00 0.00 0.00 3.86
6216 6715 5.121925 CCATCCAGAATTATTCTCAGATGCG 59.878 44.000 24.76 18.46 41.67 4.73
6219 6718 5.074102 TGCCCATCCAGAATTATTCTCAGAT 59.926 40.000 4.24 7.67 38.11 2.90
6288 6787 6.205784 TGCTAGTCAAAACTAACAACATTGC 58.794 36.000 0.00 0.00 37.53 3.56
6292 6791 6.935741 ACATGCTAGTCAAAACTAACAACA 57.064 33.333 0.00 0.00 37.55 3.33
6405 6934 3.557595 GTGAAATGGATCTAAGCGTCCAG 59.442 47.826 0.37 0.00 46.87 3.86
6411 6940 4.816925 GTGTAGGGTGAAATGGATCTAAGC 59.183 45.833 0.00 0.00 0.00 3.09
6470 6999 6.849085 AATGATGTTAGGTTTGGCACATAA 57.151 33.333 0.00 0.00 39.30 1.90


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

AutoCloner maintained by Alex Coulton.