Multiple sequence alignment - TraesCS2D01G193000

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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 TraesCS2D01G193000 chr2D 100.000 4181 0 0 1 4181 137028121 137032301 0.000000e+00 7721
1 TraesCS2D01G193000 chr7A 95.235 1784 71 9 1 1773 616934259 616932479 0.000000e+00 2811
2 TraesCS2D01G193000 chr7A 94.565 1803 78 5 1775 3573 616930149 616928363 0.000000e+00 2769
3 TraesCS2D01G193000 chr7A 92.327 404 29 2 3779 4181 616866040 616865638 1.300000e-159 573
4 TraesCS2D01G193000 chr7A 93.966 116 7 0 3569 3684 616866169 616866054 4.300000e-40 176
5 TraesCS2D01G193000 chr6B 81.467 1813 275 44 1 1771 2044749 2046542 0.000000e+00 1430
6 TraesCS2D01G193000 chr7D 79.384 1722 295 41 1 1675 236781288 236779580 0.000000e+00 1158
7 TraesCS2D01G193000 chr7D 82.707 266 46 0 3304 3569 236773977 236773712 1.940000e-58 237
8 TraesCS2D01G193000 chr6A 76.963 1732 314 61 1873 3570 270460069 270461749 0.000000e+00 909
9 TraesCS2D01G193000 chr6A 79.930 573 99 12 1118 1675 270456733 270457304 1.400000e-109 407
10 TraesCS2D01G193000 chr1B 82.677 381 66 0 486 866 639070630 639071010 5.180000e-89 339
11 TraesCS2D01G193000 chr3B 82.906 117 20 0 142 258 104326711 104326827 5.720000e-19 106
12 TraesCS2D01G193000 chr2B 82.906 117 20 0 142 258 794922548 794922664 5.720000e-19 106
13 TraesCS2D01G193000 chr2B 82.906 117 20 0 142 258 794928525 794928641 5.720000e-19 106
14 TraesCS2D01G193000 chr2B 82.051 117 21 0 142 258 794916570 794916686 2.660000e-17 100


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 TraesCS2D01G193000 chr2D 137028121 137032301 4180 False 7721.0 7721 100.0000 1 4181 1 chr2D.!!$F1 4180
1 TraesCS2D01G193000 chr7A 616928363 616934259 5896 True 2790.0 2811 94.9000 1 3573 2 chr7A.!!$R2 3572
2 TraesCS2D01G193000 chr7A 616865638 616866169 531 True 374.5 573 93.1465 3569 4181 2 chr7A.!!$R1 612
3 TraesCS2D01G193000 chr6B 2044749 2046542 1793 False 1430.0 1430 81.4670 1 1771 1 chr6B.!!$F1 1770
4 TraesCS2D01G193000 chr7D 236779580 236781288 1708 True 1158.0 1158 79.3840 1 1675 1 chr7D.!!$R2 1674
5 TraesCS2D01G193000 chr6A 270456733 270461749 5016 False 658.0 909 78.4465 1118 3570 2 chr6A.!!$F1 2452

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
216 221 1.026718 AGAGTGTGCTTTATGCCGGC 61.027 55.0 22.73 22.73 42.00 6.13 F
1869 4609 0.034896 CACTAGCACCAAACGGTCCT 59.965 55.0 0.00 0.00 33.11 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 4720 1.347707 CTCTCACCCCACTTTGCTACA 59.652 52.381 0.0 0.0 0.0 2.74 R
3684 6439 0.443869 CACTCTTGGAATCAACGGCG 59.556 55.000 4.8 4.8 0.0 6.46 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
62 63 5.507637 AGACACCGAGAGTAGGATAAGAAA 58.492 41.667 0.00 0.00 0.00 2.52
216 221 1.026718 AGAGTGTGCTTTATGCCGGC 61.027 55.000 22.73 22.73 42.00 6.13
261 266 7.898014 AGTAGAGAGTTTTGAATGGGTTTTT 57.102 32.000 0.00 0.00 0.00 1.94
285 290 5.192927 AGCGAATTTGTAAAGATGATGGGA 58.807 37.500 0.00 0.00 0.00 4.37
329 334 7.605410 TTTTAATAGGTAACACTACAGCAGC 57.395 36.000 0.00 0.00 41.41 5.25
336 344 4.330074 GGTAACACTACAGCAGCACTAATG 59.670 45.833 0.00 0.00 0.00 1.90
463 471 2.603473 CCCTGGGACGACTCACCA 60.603 66.667 7.01 0.00 0.00 4.17
523 532 7.048512 AGTCACTAGGGAGCAATTATACAAAC 58.951 38.462 0.00 0.00 0.00 2.93
609 618 4.202131 TGAAAACGGGTGGTCCAATTTAAC 60.202 41.667 0.00 0.00 34.36 2.01
847 856 3.013219 GCAGGAGGAAGGATTTCAAGAC 58.987 50.000 0.00 0.00 34.90 3.01
871 946 2.795329 AGGACAAGGCTGGTATGTTTG 58.205 47.619 0.00 0.00 0.00 2.93
872 947 2.375174 AGGACAAGGCTGGTATGTTTGA 59.625 45.455 0.00 0.00 0.00 2.69
884 959 9.726438 GGCTGGTATGTTTGATAGAATTATACT 57.274 33.333 0.00 0.00 0.00 2.12
1036 1111 6.630203 TTGGAAGGGTTCTTTATGTAGCTA 57.370 37.500 0.00 0.00 32.52 3.32
1291 1395 6.780706 TTTAACTGATGGTCTTTTCGTCTC 57.219 37.500 0.00 0.00 0.00 3.36
1312 1416 8.875803 CGTCTCTAGGTAATGATCATACTAGAC 58.124 40.741 25.54 21.42 34.78 2.59
1581 1689 1.739067 AAAGATGGACTAAGCGTGGC 58.261 50.000 0.00 0.00 0.00 5.01
1587 1695 0.179124 GGACTAAGCGTGGCTGAGAG 60.179 60.000 8.95 1.61 39.42 3.20
1657 1765 4.923871 TGCAAAACACTAAAAACAAAGCGA 59.076 33.333 0.00 0.00 0.00 4.93
1725 1833 1.242076 GTGGAACAGAGCTGCAATGT 58.758 50.000 1.02 2.91 41.80 2.71
1798 4511 0.664761 CAACGCTGCTATCCCAATGG 59.335 55.000 0.00 0.00 0.00 3.16
1826 4566 2.497138 TGTGCCTGTTGATGTTGAGAG 58.503 47.619 0.00 0.00 0.00 3.20
1830 4570 4.093998 GTGCCTGTTGATGTTGAGAGTATG 59.906 45.833 0.00 0.00 0.00 2.39
1850 4590 1.198637 GAACTGTGATGCAGAGTTGGC 59.801 52.381 13.66 0.00 45.67 4.52
1866 4606 1.599797 GGCACTAGCACCAAACGGT 60.600 57.895 0.00 0.00 44.61 4.83
1869 4609 0.034896 CACTAGCACCAAACGGTCCT 59.965 55.000 0.00 0.00 33.11 3.85
1980 4720 5.485353 TGCACCTAAGGATATTGCTATAGCT 59.515 40.000 24.61 8.91 42.66 3.32
2090 4830 4.077822 AGCAGGAACCATTCTCTTTTCTG 58.922 43.478 0.00 0.00 0.00 3.02
2097 4837 4.070716 ACCATTCTCTTTTCTGTCTGCAG 58.929 43.478 7.63 7.63 43.87 4.41
2139 4879 6.239600 GGAAAAGGCTTGTTCTAGGGAAAAAT 60.240 38.462 0.00 0.00 32.81 1.82
2140 4880 7.039293 GGAAAAGGCTTGTTCTAGGGAAAAATA 60.039 37.037 0.00 0.00 32.81 1.40
2142 4882 7.849322 AAGGCTTGTTCTAGGGAAAAATAAA 57.151 32.000 0.00 0.00 32.81 1.40
2201 4941 1.978580 AGGTACAAGAGAAGGTGGTGG 59.021 52.381 0.00 0.00 0.00 4.61
2218 4958 4.019858 TGGTGGTGTAGAGATTCAGAGAG 58.980 47.826 0.00 0.00 0.00 3.20
2238 4978 2.040012 AGTCAGAGAAGGTCCTACGACA 59.960 50.000 0.00 0.00 41.13 4.35
2304 5044 3.315191 ACCATCAAGAAGTGAAAACACCG 59.685 43.478 0.00 0.00 40.50 4.94
2361 5101 0.744281 AGTTCACCAAAACAAGGGCG 59.256 50.000 0.00 0.00 0.00 6.13
2367 5107 2.817258 CACCAAAACAAGGGCGATAAGA 59.183 45.455 0.00 0.00 0.00 2.10
2382 5122 4.795278 GCGATAAGATTGAAACTTGCCTTG 59.205 41.667 0.00 0.00 0.00 3.61
2454 5194 5.848286 ATGTCCCAAAGGATGCATATCTA 57.152 39.130 0.00 0.00 46.41 1.98
2476 5216 4.284178 ACTGGCATATGCTCCTGAAAATT 58.716 39.130 26.12 0.00 41.70 1.82
2499 5239 4.601084 TGGACAAGTTAAACTGGACCAAA 58.399 39.130 0.00 0.00 40.22 3.28
2510 5250 1.737793 CTGGACCAAATACGGAGTTGC 59.262 52.381 1.30 0.00 37.78 4.17
2565 5305 2.307496 ATGTCAATGCAAACCCAGGA 57.693 45.000 0.00 0.00 0.00 3.86
2788 5533 5.590530 TGCTCCAAAACTTTTTGCTCTTA 57.409 34.783 8.65 0.00 44.62 2.10
2810 5555 5.715439 ATTGAGAGGGACACCATGAATTA 57.285 39.130 0.00 0.00 40.13 1.40
2816 5561 8.762645 TGAGAGGGACACCATGAATTATATATC 58.237 37.037 0.00 0.00 40.13 1.63
2900 5645 5.130292 TGTAAGTCAGTGGTAGTGCTAAC 57.870 43.478 0.00 0.00 0.00 2.34
2946 5697 0.038744 AGGAACAGGTGGCCAATCTG 59.961 55.000 26.67 26.67 34.91 2.90
2979 5730 4.555709 ACGGCAAGCGGGTCACAA 62.556 61.111 4.64 0.00 0.00 3.33
3006 5757 1.699656 CCGTTCTCAATGAGCAGGCG 61.700 60.000 5.18 6.94 0.00 5.52
3027 5781 3.935203 CGGCTGTCATTCTAACTCATGTT 59.065 43.478 0.00 0.00 39.98 2.71
3040 5794 9.725019 TTCTAACTCATGTTGATGAAGTAATGT 57.275 29.630 0.00 0.00 38.17 2.71
3054 5808 3.522553 AGTAATGTTAGCGCTTCCAGAC 58.477 45.455 18.68 14.25 0.00 3.51
3134 5888 1.402968 CGGTGGATTTCATGGCTCAAG 59.597 52.381 0.00 0.00 0.00 3.02
3253 6008 2.044769 TGGTCTTACTACTTGCCCCCTA 59.955 50.000 0.00 0.00 0.00 3.53
3254 6009 3.311103 TGGTCTTACTACTTGCCCCCTAT 60.311 47.826 0.00 0.00 0.00 2.57
3258 6013 6.901857 GGTCTTACTACTTGCCCCCTATATAT 59.098 42.308 0.00 0.00 0.00 0.86
3260 6015 9.484806 GTCTTACTACTTGCCCCCTATATATAA 57.515 37.037 0.00 0.00 0.00 0.98
3263 6018 9.848238 TTACTACTTGCCCCCTATATATAAACT 57.152 33.333 0.00 0.00 0.00 2.66
3367 6122 4.122143 AGCTAGCTGATGACAAGTTCTC 57.878 45.455 18.57 0.00 0.00 2.87
3372 6127 4.567971 AGCTGATGACAAGTTCTCAGAAG 58.432 43.478 13.72 0.00 37.85 2.85
3384 6139 5.789521 AGTTCTCAGAAGAAGTAAAGAGGC 58.210 41.667 0.00 0.00 42.24 4.70
3386 6141 4.079970 TCTCAGAAGAAGTAAAGAGGCGA 58.920 43.478 0.00 0.00 0.00 5.54
3390 6145 4.750098 CAGAAGAAGTAAAGAGGCGAACAA 59.250 41.667 0.00 0.00 0.00 2.83
3484 6239 3.500680 ACCTTGCAATACTTACACAACCG 59.499 43.478 0.00 0.00 0.00 4.44
3489 6244 3.331150 CAATACTTACACAACCGCCTCA 58.669 45.455 0.00 0.00 0.00 3.86
3536 6291 2.229062 GCCAGGCTTAGAAAAACACCTC 59.771 50.000 3.29 0.00 0.00 3.85
3573 6328 4.943705 TCCTACTTTCAGGTTTGCATCATC 59.056 41.667 0.00 0.00 36.99 2.92
3582 6337 8.750515 TTCAGGTTTGCATCATCATCTTTATA 57.249 30.769 0.00 0.00 0.00 0.98
3668 6423 3.399181 TAGGTGGAGCGCAAGGGG 61.399 66.667 11.47 0.00 38.28 4.79
3684 6439 1.003696 AGGGGCTAGTTCAAGTTCAGC 59.996 52.381 0.00 0.00 0.00 4.26
3686 6441 0.444260 GGCTAGTTCAAGTTCAGCGC 59.556 55.000 0.00 0.00 32.97 5.92
3688 6443 0.716108 CTAGTTCAAGTTCAGCGCCG 59.284 55.000 2.29 0.00 0.00 6.46
3689 6444 0.032952 TAGTTCAAGTTCAGCGCCGT 59.967 50.000 2.29 0.00 0.00 5.68
3691 6446 0.657368 GTTCAAGTTCAGCGCCGTTG 60.657 55.000 2.29 0.00 0.00 4.10
3692 6447 0.812014 TTCAAGTTCAGCGCCGTTGA 60.812 50.000 2.29 0.00 0.00 3.18
3696 6451 1.134694 GTTCAGCGCCGTTGATTCC 59.865 57.895 4.04 0.00 0.00 3.01
3697 6452 1.302112 TTCAGCGCCGTTGATTCCA 60.302 52.632 4.04 0.00 0.00 3.53
3698 6453 0.886938 TTCAGCGCCGTTGATTCCAA 60.887 50.000 4.04 0.00 0.00 3.53
3699 6454 1.135315 CAGCGCCGTTGATTCCAAG 59.865 57.895 2.29 0.00 32.06 3.61
3700 6455 1.003839 AGCGCCGTTGATTCCAAGA 60.004 52.632 2.29 0.00 32.06 3.02
3701 6456 1.021390 AGCGCCGTTGATTCCAAGAG 61.021 55.000 2.29 0.00 32.06 2.85
3702 6457 1.298859 GCGCCGTTGATTCCAAGAGT 61.299 55.000 0.00 0.00 32.06 3.24
3703 6458 0.443869 CGCCGTTGATTCCAAGAGTG 59.556 55.000 0.00 0.00 32.06 3.51
3704 6459 0.169009 GCCGTTGATTCCAAGAGTGC 59.831 55.000 0.00 0.00 32.06 4.40
3705 6460 1.813513 CCGTTGATTCCAAGAGTGCT 58.186 50.000 0.00 0.00 32.06 4.40
3706 6461 2.154462 CCGTTGATTCCAAGAGTGCTT 58.846 47.619 0.00 0.00 32.06 3.91
3718 6473 3.238108 AGAGTGCTTGATGGTAAGTCG 57.762 47.619 0.00 0.00 0.00 4.18
3719 6474 2.826128 AGAGTGCTTGATGGTAAGTCGA 59.174 45.455 0.00 0.00 0.00 4.20
3720 6475 3.119316 AGAGTGCTTGATGGTAAGTCGAG 60.119 47.826 0.00 0.00 0.00 4.04
3729 6484 2.695359 TGGTAAGTCGAGCATCAAACC 58.305 47.619 0.00 0.00 33.17 3.27
3730 6485 2.301870 TGGTAAGTCGAGCATCAAACCT 59.698 45.455 0.00 0.00 33.17 3.50
3731 6486 3.512329 TGGTAAGTCGAGCATCAAACCTA 59.488 43.478 0.00 0.00 33.17 3.08
3732 6487 4.113354 GGTAAGTCGAGCATCAAACCTAG 58.887 47.826 0.00 0.00 33.17 3.02
3733 6488 3.963428 AAGTCGAGCATCAAACCTAGT 57.037 42.857 0.00 0.00 33.17 2.57
3734 6489 3.963428 AGTCGAGCATCAAACCTAGTT 57.037 42.857 0.00 0.00 33.17 2.24
3735 6490 4.273148 AGTCGAGCATCAAACCTAGTTT 57.727 40.909 0.00 0.00 36.05 2.66
3736 6491 5.401531 AGTCGAGCATCAAACCTAGTTTA 57.598 39.130 0.00 0.00 33.70 2.01
3737 6492 5.411781 AGTCGAGCATCAAACCTAGTTTAG 58.588 41.667 0.00 0.00 33.70 1.85
3738 6493 5.047235 AGTCGAGCATCAAACCTAGTTTAGT 60.047 40.000 0.00 0.00 33.70 2.24
3739 6494 5.638234 GTCGAGCATCAAACCTAGTTTAGTT 59.362 40.000 0.00 0.00 33.70 2.24
3740 6495 6.147328 GTCGAGCATCAAACCTAGTTTAGTTT 59.853 38.462 0.00 0.00 33.70 2.66
3741 6496 7.330208 GTCGAGCATCAAACCTAGTTTAGTTTA 59.670 37.037 0.00 0.00 33.70 2.01
3742 6497 7.874016 TCGAGCATCAAACCTAGTTTAGTTTAA 59.126 33.333 0.00 0.00 33.70 1.52
3743 6498 8.665685 CGAGCATCAAACCTAGTTTAGTTTAAT 58.334 33.333 0.00 0.00 33.70 1.40
3749 6504 9.796180 TCAAACCTAGTTTAGTTTAATAAGCCA 57.204 29.630 0.00 0.00 33.70 4.75
3752 6507 8.747538 ACCTAGTTTAGTTTAATAAGCCATGG 57.252 34.615 7.63 7.63 0.00 3.66
3753 6508 8.554011 ACCTAGTTTAGTTTAATAAGCCATGGA 58.446 33.333 18.40 0.00 0.00 3.41
3754 6509 9.403583 CCTAGTTTAGTTTAATAAGCCATGGAA 57.596 33.333 18.40 0.00 0.00 3.53
3775 6530 8.970859 TGGAACAATTGTAAATCAAATGGTTT 57.029 26.923 12.39 0.00 37.04 3.27
3776 6531 8.834465 TGGAACAATTGTAAATCAAATGGTTTG 58.166 29.630 12.39 0.00 37.04 2.93
3777 6532 7.802720 GGAACAATTGTAAATCAAATGGTTTGC 59.197 33.333 12.39 1.41 37.04 3.68
3819 6574 6.528537 TGGAACTAAATCATCATTTGGTGG 57.471 37.500 0.00 0.00 41.50 4.61
3823 6578 2.555732 AATCATCATTTGGTGGCCCT 57.444 45.000 0.00 0.00 0.00 5.19
3845 6600 1.831106 ACTGGAATGGTGTCGAGCATA 59.169 47.619 0.00 0.00 39.45 3.14
3859 6614 5.920840 TGTCGAGCATAATATTAGAGCACAC 59.079 40.000 19.12 13.82 0.00 3.82
3863 6618 6.369890 CGAGCATAATATTAGAGCACACCATT 59.630 38.462 19.12 3.14 0.00 3.16
3896 6651 2.162408 GTGCTCAATCCAGTGCCTTTAC 59.838 50.000 0.00 0.00 0.00 2.01
3914 6669 0.756903 ACGGTCAGCACCAGTTAACT 59.243 50.000 1.12 1.12 44.02 2.24
3931 6686 3.678056 AACTTGAATGGAGCACGAGTA 57.322 42.857 0.00 0.00 0.00 2.59
3936 6691 2.094182 TGAATGGAGCACGAGTAGAACC 60.094 50.000 0.00 0.00 0.00 3.62
3968 6723 4.588278 GCAAGTTTGCGGATCAACTATAC 58.412 43.478 0.53 0.00 45.11 1.47
4069 6824 9.968870 GTATAGACTAATGAAGGGTTGTCTTAG 57.031 37.037 0.00 0.00 36.39 2.18
4080 6835 5.805728 AGGGTTGTCTTAGTTGTTAGATGG 58.194 41.667 0.00 0.00 0.00 3.51
4087 6842 5.880332 GTCTTAGTTGTTAGATGGGCATGAA 59.120 40.000 0.00 0.00 0.00 2.57
4093 6848 4.870636 TGTTAGATGGGCATGAAAATCCT 58.129 39.130 0.00 0.00 0.00 3.24
4094 6849 6.012337 TGTTAGATGGGCATGAAAATCCTA 57.988 37.500 0.00 0.00 0.00 2.94
4108 6864 1.115467 ATCCTAAGAGGGCGACACTG 58.885 55.000 0.00 0.00 35.59 3.66
4130 6886 0.951040 AGTCTAAGCGCTGTTGTGGC 60.951 55.000 12.58 0.77 0.00 5.01
4132 6888 2.671619 TAAGCGCTGTTGTGGCCC 60.672 61.111 12.58 0.00 0.00 5.80
4176 6932 2.364632 TCTGCGGAACATGTTTATGGG 58.635 47.619 13.36 4.25 38.66 4.00
4179 6935 3.157881 TGCGGAACATGTTTATGGGAAA 58.842 40.909 13.36 0.00 38.66 3.13
4180 6936 3.192422 TGCGGAACATGTTTATGGGAAAG 59.808 43.478 13.36 0.00 38.66 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 6.349033 GCTACGTCCATTAGTCCACAAAATTT 60.349 38.462 0.00 0.00 0.00 1.82
216 221 1.913317 TCTCATCACGCATCAAGACG 58.087 50.000 0.00 0.00 0.00 4.18
261 266 6.353323 TCCCATCATCTTTACAAATTCGCTA 58.647 36.000 0.00 0.00 0.00 4.26
285 290 8.541899 TTAAAATTGTAACTGGTTTCTTCCCT 57.458 30.769 0.00 0.00 0.00 4.20
493 502 3.468071 TTGCTCCCTAGTGACTCCTTA 57.532 47.619 0.00 0.00 0.00 2.69
523 532 3.320541 ACTCTGTCCTGAAGTCTGACTTG 59.679 47.826 26.47 13.39 38.80 3.16
592 601 2.227865 CACAGTTAAATTGGACCACCCG 59.772 50.000 0.00 0.00 37.93 5.28
609 618 1.289109 CGCCAACCCGTACTTCACAG 61.289 60.000 0.00 0.00 0.00 3.66
694 703 8.816144 GTTCTTGTCATTTTTGCACAGAATTTA 58.184 29.630 0.00 0.00 0.00 1.40
847 856 3.157087 ACATACCAGCCTTGTCCTTTTG 58.843 45.455 0.00 0.00 0.00 2.44
894 969 8.732746 AAAAGTGTCAGTTCAAGTTACATACT 57.267 30.769 0.00 0.00 39.32 2.12
900 975 7.681939 AAGTGAAAAGTGTCAGTTCAAGTTA 57.318 32.000 0.00 0.00 36.63 2.24
912 987 5.394115 CCCTGCAGTTTAAAGTGAAAAGTGT 60.394 40.000 24.16 0.00 38.79 3.55
1279 1380 7.481642 TGATCATTACCTAGAGACGAAAAGAC 58.518 38.462 0.00 0.00 0.00 3.01
1312 1416 4.156182 GTGCTTTCGGGATTTTCTTAACG 58.844 43.478 0.00 0.00 0.00 3.18
1417 1521 2.730382 TGCCTGAATGTCATTGCATCT 58.270 42.857 1.88 0.00 31.79 2.90
1485 1593 4.878397 CAGACTCGAAAGCCTTTGGATTAT 59.122 41.667 2.22 0.00 28.17 1.28
1493 1601 4.021016 ACTCATAACAGACTCGAAAGCCTT 60.021 41.667 0.00 0.00 0.00 4.35
1581 1689 3.255642 GCTAGATGCCTTAGACCTCTCAG 59.744 52.174 0.00 0.00 35.15 3.35
1587 1695 3.556004 GGTCATGCTAGATGCCTTAGACC 60.556 52.174 0.00 0.00 42.00 3.85
1725 1833 7.303182 TCTCTTGAAGAGACCTCAACATTAA 57.697 36.000 20.27 0.00 45.77 1.40
1866 4606 5.777449 TCAGGAATATCAGGTTCAGTAGGA 58.223 41.667 0.00 0.00 0.00 2.94
1869 4609 8.328758 ACAAATTCAGGAATATCAGGTTCAGTA 58.671 33.333 0.00 0.00 0.00 2.74
1980 4720 1.347707 CTCTCACCCCACTTTGCTACA 59.652 52.381 0.00 0.00 0.00 2.74
2015 4755 2.450320 CCCAGGCCCATCTCTCTGG 61.450 68.421 0.00 0.00 44.60 3.86
2090 4830 5.369833 TCCTAGTGTCTATAGACTGCAGAC 58.630 45.833 28.53 19.40 44.99 3.51
2097 4837 6.239092 GCCTTTTCCTCCTAGTGTCTATAGAC 60.239 46.154 23.53 23.53 44.97 2.59
2139 4879 6.939622 TCTCTCACTGATCTGAGCAAATTTA 58.060 36.000 6.60 0.00 38.07 1.40
2140 4880 5.802465 TCTCTCACTGATCTGAGCAAATTT 58.198 37.500 6.60 0.00 38.07 1.82
2142 4882 5.603596 GATCTCTCACTGATCTGAGCAAAT 58.396 41.667 6.60 1.06 38.07 2.32
2201 4941 6.112734 TCTCTGACTCTCTGAATCTCTACAC 58.887 44.000 0.00 0.00 0.00 2.90
2218 4958 2.434428 TGTCGTAGGACCTTCTCTGAC 58.566 52.381 12.77 2.00 42.73 3.51
2304 5044 7.759433 TCTTCACACAAAACTTTCAAAAGATCC 59.241 33.333 9.39 0.00 39.31 3.36
2361 5101 5.105063 GCCAAGGCAAGTTTCAATCTTATC 58.895 41.667 6.14 0.00 41.49 1.75
2382 5122 5.438761 AAACTGACAGAACTAACATTGCC 57.561 39.130 10.08 0.00 0.00 4.52
2454 5194 3.370840 TTTTCAGGAGCATATGCCAGT 57.629 42.857 23.96 5.80 43.38 4.00
2476 5216 4.237976 TGGTCCAGTTTAACTTGTCCAA 57.762 40.909 11.38 0.00 29.12 3.53
2499 5239 1.827969 AGAAGCTCAGCAACTCCGTAT 59.172 47.619 0.00 0.00 0.00 3.06
2510 5250 1.398739 CAGCAGCATCAAGAAGCTCAG 59.601 52.381 0.00 0.00 39.50 3.35
2565 5305 3.521727 ACCAAAGATAGTGAGTCCAGGT 58.478 45.455 0.00 0.00 0.00 4.00
2572 5312 3.679389 AGTGGCAACCAAAGATAGTGAG 58.321 45.455 0.00 0.00 34.18 3.51
2621 5361 5.746245 CGAAATAGCAACAACAGAACCAAAA 59.254 36.000 0.00 0.00 0.00 2.44
2641 5381 4.130857 TGTGAGTAAAATGCAGACCGAAA 58.869 39.130 0.00 0.00 0.00 3.46
2700 5445 1.137675 TCTCCAGCATCCACAGAATCG 59.862 52.381 0.00 0.00 0.00 3.34
2788 5533 4.598036 AATTCATGGTGTCCCTCTCAAT 57.402 40.909 0.00 0.00 0.00 2.57
2810 5555 6.121776 TGCCGTAAACCCTCATTGATATAT 57.878 37.500 0.00 0.00 0.00 0.86
2816 5561 1.202290 GCATGCCGTAAACCCTCATTG 60.202 52.381 6.36 0.00 0.00 2.82
2871 5616 6.425721 GCACTACCACTGACTTACAACAATAA 59.574 38.462 0.00 0.00 0.00 1.40
2877 5622 5.069383 TGTTAGCACTACCACTGACTTACAA 59.931 40.000 0.00 0.00 0.00 2.41
2891 5636 8.026607 GCTGGACAAATTTAAATGTTAGCACTA 58.973 33.333 17.91 2.52 38.65 2.74
2893 5638 6.090763 GGCTGGACAAATTTAAATGTTAGCAC 59.909 38.462 21.12 13.32 39.62 4.40
2900 5645 6.311935 CACATCAGGCTGGACAAATTTAAATG 59.688 38.462 15.73 8.59 0.00 2.32
2946 5697 1.355066 CCGTTCGCTTCTGCCTCTTC 61.355 60.000 0.00 0.00 35.36 2.87
2979 5730 4.246458 GCTCATTGAGAACGGTTCTAAGT 58.754 43.478 22.46 10.26 40.87 2.24
3006 5757 4.937620 TCAACATGAGTTAGAATGACAGCC 59.062 41.667 0.00 0.00 35.85 4.85
3027 5781 4.570772 GGAAGCGCTAACATTACTTCATCA 59.429 41.667 12.05 0.00 38.76 3.07
3040 5794 2.248280 TTGTTGTCTGGAAGCGCTAA 57.752 45.000 12.05 0.00 0.00 3.09
3367 6122 4.307432 TGTTCGCCTCTTTACTTCTTCTG 58.693 43.478 0.00 0.00 0.00 3.02
3372 6127 3.135994 TGGTTGTTCGCCTCTTTACTTC 58.864 45.455 0.00 0.00 0.00 3.01
3484 6239 2.100252 CCAACACCATGATCAATGAGGC 59.900 50.000 0.00 0.00 38.72 4.70
3489 6244 3.833650 TGCTTTCCAACACCATGATCAAT 59.166 39.130 0.00 0.00 0.00 2.57
3536 6291 8.400947 CCTGAAAGTAGGACATTTATCATGTTG 58.599 37.037 0.00 0.00 40.42 3.33
3621 6376 8.074455 GCCACCTGCATTTCAGAATACATTCT 62.074 42.308 0.00 0.00 45.72 2.40
3668 6423 0.444260 GGCGCTGAACTTGAACTAGC 59.556 55.000 7.64 0.00 0.00 3.42
3672 6427 0.657368 CAACGGCGCTGAACTTGAAC 60.657 55.000 25.98 0.00 0.00 3.18
3684 6439 0.443869 CACTCTTGGAATCAACGGCG 59.556 55.000 4.80 4.80 0.00 6.46
3686 6441 1.813513 AGCACTCTTGGAATCAACGG 58.186 50.000 0.00 0.00 0.00 4.44
3697 6452 3.258372 TCGACTTACCATCAAGCACTCTT 59.742 43.478 0.00 0.00 0.00 2.85
3698 6453 2.826128 TCGACTTACCATCAAGCACTCT 59.174 45.455 0.00 0.00 0.00 3.24
3699 6454 3.182967 CTCGACTTACCATCAAGCACTC 58.817 50.000 0.00 0.00 0.00 3.51
3700 6455 2.675317 GCTCGACTTACCATCAAGCACT 60.675 50.000 0.00 0.00 0.00 4.40
3701 6456 1.661112 GCTCGACTTACCATCAAGCAC 59.339 52.381 0.00 0.00 0.00 4.40
3702 6457 1.275010 TGCTCGACTTACCATCAAGCA 59.725 47.619 0.00 0.00 36.04 3.91
3703 6458 2.010145 TGCTCGACTTACCATCAAGC 57.990 50.000 0.00 0.00 0.00 4.01
3704 6459 3.785486 TGATGCTCGACTTACCATCAAG 58.215 45.455 0.00 0.00 40.56 3.02
3705 6460 3.885724 TGATGCTCGACTTACCATCAA 57.114 42.857 0.00 0.00 40.56 2.57
3706 6461 3.885724 TTGATGCTCGACTTACCATCA 57.114 42.857 0.00 0.00 41.45 3.07
3707 6462 3.309954 GGTTTGATGCTCGACTTACCATC 59.690 47.826 0.00 0.00 35.74 3.51
3708 6463 3.055094 AGGTTTGATGCTCGACTTACCAT 60.055 43.478 0.00 0.00 0.00 3.55
3709 6464 2.301870 AGGTTTGATGCTCGACTTACCA 59.698 45.455 0.00 0.00 0.00 3.25
3710 6465 2.973945 AGGTTTGATGCTCGACTTACC 58.026 47.619 0.00 0.00 0.00 2.85
3711 6466 4.745649 ACTAGGTTTGATGCTCGACTTAC 58.254 43.478 0.00 0.00 0.00 2.34
3712 6467 5.401531 AACTAGGTTTGATGCTCGACTTA 57.598 39.130 0.00 0.00 0.00 2.24
3713 6468 3.963428 ACTAGGTTTGATGCTCGACTT 57.037 42.857 0.00 0.00 0.00 3.01
3714 6469 3.963428 AACTAGGTTTGATGCTCGACT 57.037 42.857 0.00 0.00 0.00 4.18
3715 6470 5.169295 ACTAAACTAGGTTTGATGCTCGAC 58.831 41.667 9.03 0.00 36.37 4.20
3716 6471 5.401531 ACTAAACTAGGTTTGATGCTCGA 57.598 39.130 9.03 0.00 36.37 4.04
3717 6472 6.481954 AAACTAAACTAGGTTTGATGCTCG 57.518 37.500 9.03 0.00 36.37 5.03
3723 6478 9.796180 TGGCTTATTAAACTAAACTAGGTTTGA 57.204 29.630 9.03 0.00 36.93 2.69
3726 6481 9.185680 CCATGGCTTATTAAACTAAACTAGGTT 57.814 33.333 0.00 0.00 39.46 3.50
3727 6482 8.554011 TCCATGGCTTATTAAACTAAACTAGGT 58.446 33.333 6.96 0.00 0.00 3.08
3728 6483 8.974060 TCCATGGCTTATTAAACTAAACTAGG 57.026 34.615 6.96 0.00 0.00 3.02
3730 6485 9.742144 TGTTCCATGGCTTATTAAACTAAACTA 57.258 29.630 6.96 0.00 0.00 2.24
3731 6486 8.644374 TGTTCCATGGCTTATTAAACTAAACT 57.356 30.769 6.96 0.00 0.00 2.66
3732 6487 9.869757 ATTGTTCCATGGCTTATTAAACTAAAC 57.130 29.630 6.96 1.94 0.00 2.01
3734 6489 9.868277 CAATTGTTCCATGGCTTATTAAACTAA 57.132 29.630 6.96 2.85 0.00 2.24
3735 6490 9.030452 ACAATTGTTCCATGGCTTATTAAACTA 57.970 29.630 6.96 1.82 0.00 2.24
3736 6491 7.906327 ACAATTGTTCCATGGCTTATTAAACT 58.094 30.769 6.96 0.00 0.00 2.66
3737 6492 9.646427 TTACAATTGTTCCATGGCTTATTAAAC 57.354 29.630 17.78 5.03 0.00 2.01
3741 6496 8.538701 TGATTTACAATTGTTCCATGGCTTATT 58.461 29.630 17.78 1.22 0.00 1.40
3742 6497 8.076910 TGATTTACAATTGTTCCATGGCTTAT 57.923 30.769 17.78 0.00 0.00 1.73
3743 6498 7.473735 TGATTTACAATTGTTCCATGGCTTA 57.526 32.000 17.78 0.00 0.00 3.09
3744 6499 6.357579 TGATTTACAATTGTTCCATGGCTT 57.642 33.333 17.78 0.00 0.00 4.35
3745 6500 5.999205 TGATTTACAATTGTTCCATGGCT 57.001 34.783 17.78 0.00 0.00 4.75
3746 6501 7.414319 CCATTTGATTTACAATTGTTCCATGGC 60.414 37.037 17.78 0.00 37.84 4.40
3747 6502 7.607223 ACCATTTGATTTACAATTGTTCCATGG 59.393 33.333 17.78 20.57 40.16 3.66
3748 6503 8.550710 ACCATTTGATTTACAATTGTTCCATG 57.449 30.769 17.78 12.17 37.84 3.66
3749 6504 9.571816 AAACCATTTGATTTACAATTGTTCCAT 57.428 25.926 17.78 6.48 37.84 3.41
3750 6505 8.834465 CAAACCATTTGATTTACAATTGTTCCA 58.166 29.630 17.78 7.05 43.26 3.53
3751 6506 7.802720 GCAAACCATTTGATTTACAATTGTTCC 59.197 33.333 17.78 4.52 43.26 3.62
3752 6507 8.558700 AGCAAACCATTTGATTTACAATTGTTC 58.441 29.630 17.78 9.09 43.26 3.18
3753 6508 8.449251 AGCAAACCATTTGATTTACAATTGTT 57.551 26.923 17.78 0.00 43.26 2.83
3754 6509 8.449251 AAGCAAACCATTTGATTTACAATTGT 57.551 26.923 16.68 16.68 45.99 2.71
3808 6563 2.624029 CCAGTTAGGGCCACCAAATGAT 60.624 50.000 6.18 0.00 40.13 2.45
3819 6574 1.751437 GACACCATTCCAGTTAGGGC 58.249 55.000 0.00 0.00 38.24 5.19
3823 6578 1.621317 TGCTCGACACCATTCCAGTTA 59.379 47.619 0.00 0.00 0.00 2.24
3845 6600 7.339212 TGTGCTTTAATGGTGTGCTCTAATATT 59.661 33.333 0.00 0.00 0.00 1.28
3896 6651 1.531149 CAAGTTAACTGGTGCTGACCG 59.469 52.381 9.34 0.00 46.62 4.79
3914 6669 3.585862 GTTCTACTCGTGCTCCATTCAA 58.414 45.455 0.00 0.00 0.00 2.69
3931 6686 6.076981 CAAACTTGCACTTCTATTGGTTCT 57.923 37.500 0.00 0.00 0.00 3.01
3955 6710 2.221055 GCTTTGCCGTATAGTTGATCCG 59.779 50.000 0.00 0.00 0.00 4.18
3963 6718 3.627577 ACTTCCATTGCTTTGCCGTATAG 59.372 43.478 0.00 0.00 0.00 1.31
3965 6720 2.164219 CACTTCCATTGCTTTGCCGTAT 59.836 45.455 0.00 0.00 0.00 3.06
3968 6723 1.010419 GCACTTCCATTGCTTTGCCG 61.010 55.000 0.00 0.00 37.00 5.69
4043 6798 9.968870 CTAAGACAACCCTTCATTAGTCTATAC 57.031 37.037 0.00 0.00 35.47 1.47
4044 6799 9.710818 ACTAAGACAACCCTTCATTAGTCTATA 57.289 33.333 0.00 0.00 35.47 1.31
4069 6824 5.127682 AGGATTTTCATGCCCATCTAACAAC 59.872 40.000 0.00 0.00 0.00 3.32
4080 6835 2.625314 GCCCTCTTAGGATTTTCATGCC 59.375 50.000 0.00 0.00 37.67 4.40
4087 6842 2.093447 CAGTGTCGCCCTCTTAGGATTT 60.093 50.000 0.00 0.00 37.67 2.17
4093 6848 0.037326 CTTGCAGTGTCGCCCTCTTA 60.037 55.000 0.00 0.00 0.00 2.10
4094 6849 1.302033 CTTGCAGTGTCGCCCTCTT 60.302 57.895 0.00 0.00 0.00 2.85
4108 6864 0.868406 ACAACAGCGCTTAGACTTGC 59.132 50.000 7.50 0.00 0.00 4.01
4122 6878 0.260230 TCTTTTCCTGGGCCACAACA 59.740 50.000 0.00 0.00 0.00 3.33
4130 6886 1.205893 CTCGAGGTCTCTTTTCCTGGG 59.794 57.143 3.91 0.00 33.83 4.45
4132 6888 3.445450 TCATCTCGAGGTCTCTTTTCCTG 59.555 47.826 13.56 0.00 33.83 3.86
4135 6891 5.748152 CAGAATCATCTCGAGGTCTCTTTTC 59.252 44.000 13.56 7.29 32.03 2.29


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

AutoCloner maintained by Alex Coulton.