Multiple sequence alignment - TraesCS2D01G035800

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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 TraesCS2D01G035800 chr2D 100.000 4957 0 0 1 4957 13604077 13609033 0.000000e+00 9154.0
1 TraesCS2D01G035800 chr2D 81.773 1218 180 19 3044 4253 13617013 13618196 0.000000e+00 981.0
2 TraesCS2D01G035800 chr2D 80.944 1207 204 20 3052 4250 13541022 13539834 0.000000e+00 931.0
3 TraesCS2D01G035800 chr2D 81.704 1033 149 23 877 1899 13543088 13542086 0.000000e+00 824.0
4 TraesCS2D01G035800 chr2D 93.478 92 5 1 2954 3044 13616950 13617041 8.660000e-28 135.0
5 TraesCS2D01G035800 chr2B 90.431 3083 244 29 1 3046 24816137 24819205 0.000000e+00 4012.0
6 TraesCS2D01G035800 chr2B 93.118 2296 136 11 767 3046 24704489 24706778 0.000000e+00 3345.0
7 TraesCS2D01G035800 chr2B 94.236 1492 83 3 3044 4533 24819175 24820665 0.000000e+00 2276.0
8 TraesCS2D01G035800 chr2B 94.211 1451 76 4 3041 4485 24706745 24708193 0.000000e+00 2207.0
9 TraesCS2D01G035800 chr2B 92.098 772 37 5 1 771 24702208 24702956 0.000000e+00 1066.0
10 TraesCS2D01G035800 chr2B 79.764 1270 196 36 877 2121 24509237 24508004 0.000000e+00 865.0
11 TraesCS2D01G035800 chr2B 82.085 681 105 11 1156 1833 24835930 24836596 2.590000e-157 566.0
12 TraesCS2D01G035800 chr2B 87.387 444 38 5 4522 4957 24822508 24822941 1.240000e-135 494.0
13 TraesCS2D01G035800 chr2B 77.358 477 76 19 2586 3044 24837910 24838372 2.290000e-63 254.0
14 TraesCS2D01G035800 chr2A 93.342 2298 129 12 767 3046 15633314 15635605 0.000000e+00 3374.0
15 TraesCS2D01G035800 chr2A 91.978 1471 78 26 3044 4477 15635575 15637042 0.000000e+00 2026.0
16 TraesCS2D01G035800 chr2A 94.057 774 41 3 1 770 15630999 15631771 0.000000e+00 1170.0
17 TraesCS2D01G035800 chr5B 92.576 229 15 2 4731 4957 567249437 567249209 1.330000e-85 327.0
18 TraesCS2D01G035800 chr5B 72.740 708 173 18 3240 3937 31142911 31143608 2.320000e-53 220.0
19 TraesCS2D01G035800 chr5B 84.848 66 10 0 507 572 394977856 394977791 3.200000e-07 67.6
20 TraesCS2D01G035800 chrUn 77.372 274 60 2 3665 3937 110473794 110474066 1.430000e-35 161.0
21 TraesCS2D01G035800 chrUn 88.889 81 7 2 4834 4912 10132241 10132161 1.140000e-16 99.0
22 TraesCS2D01G035800 chr5A 77.559 254 55 2 3665 3917 700176111 700175859 8.590000e-33 152.0
23 TraesCS2D01G035800 chr5A 72.211 511 126 14 3247 3749 3615715 3615213 5.170000e-30 143.0
24 TraesCS2D01G035800 chr5D 78.431 102 20 2 507 607 336772277 336772177 1.150000e-06 65.8
25 TraesCS2D01G035800 chr3D 88.679 53 6 0 2121 2173 178528789 178528841 1.150000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G035800 chr2D 13604077 13609033 4956 False 9154.000000 9154 100.000000 1 4957 1 chr2D.!!$F1 4956
1 TraesCS2D01G035800 chr2D 13539834 13543088 3254 True 877.500000 931 81.324000 877 4250 2 chr2D.!!$R1 3373
2 TraesCS2D01G035800 chr2D 13616950 13618196 1246 False 558.000000 981 87.625500 2954 4253 2 chr2D.!!$F2 1299
3 TraesCS2D01G035800 chr2B 24816137 24822941 6804 False 2260.666667 4012 90.684667 1 4957 3 chr2B.!!$F2 4956
4 TraesCS2D01G035800 chr2B 24702208 24708193 5985 False 2206.000000 3345 93.142333 1 4485 3 chr2B.!!$F1 4484
5 TraesCS2D01G035800 chr2B 24508004 24509237 1233 True 865.000000 865 79.764000 877 2121 1 chr2B.!!$R1 1244
6 TraesCS2D01G035800 chr2B 24835930 24838372 2442 False 410.000000 566 79.721500 1156 3044 2 chr2B.!!$F3 1888
7 TraesCS2D01G035800 chr2A 15630999 15637042 6043 False 2190.000000 3374 93.125667 1 4477 3 chr2A.!!$F1 4476
8 TraesCS2D01G035800 chr5B 31142911 31143608 697 False 220.000000 220 72.740000 3240 3937 1 chr5B.!!$F1 697

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
544 550 0.322906 GGAGGTCAGGGAGCAAAAGG 60.323 60.000 0.0 0.0 31.89 3.11 F
737 764 1.039785 GGAGCTGGAAGGGGAATTGC 61.040 60.000 0.0 0.0 0.00 3.56 F
1705 3299 1.725164 GTCCAACGTACTGTAGCTTGC 59.275 52.381 0.0 0.0 0.00 4.01 F
3014 5323 1.325640 CTCATGTTGATCGCAAGTCGG 59.674 52.381 0.0 0.0 39.05 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 2986 1.294857 GAAGAAGCGAATCTCCTGGC 58.705 55.000 0.00 0.00 0.00 4.85 R
2298 3931 1.869767 CGGTAGCATCCAGAATTCTGC 59.130 52.381 27.01 17.79 42.47 4.26 R
3164 5473 0.596600 GTGCTTTGTCTCGTCGGTGA 60.597 55.000 0.00 0.00 0.00 4.02 R
4502 6872 0.028770 GAGTCGAGCAGGAGACATCG 59.971 60.000 0.00 0.00 39.67 3.84 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
141 143 0.882927 TAACTCAACCGTGCAGTGGC 60.883 55.000 4.82 0.00 41.68 5.01
404 410 8.458843 GGCAGTCAAATTTAATTAGCTAGTTCA 58.541 33.333 4.56 0.00 0.00 3.18
472 478 4.160626 CCTACTTCTGGTCAACCTTAGAGG 59.839 50.000 0.10 0.00 42.49 3.69
531 537 6.322201 CCATAATAATGGCCAATATGGAGGTC 59.678 42.308 28.87 0.00 46.17 3.85
544 550 0.322906 GGAGGTCAGGGAGCAAAAGG 60.323 60.000 0.00 0.00 31.89 3.11
585 611 1.416243 ATGGGTTGCTATTGCCATGG 58.584 50.000 7.63 7.63 38.71 3.66
630 656 6.354938 TCTAGTCTCTCAGCCTTCGTATTTA 58.645 40.000 0.00 0.00 0.00 1.40
668 694 4.018960 ACTTTTGGAGCTCACTACATCCAT 60.019 41.667 17.19 0.00 41.33 3.41
682 708 8.739039 TCACTACATCCATCAAAATTGTTTAGG 58.261 33.333 0.00 0.00 0.00 2.69
693 719 6.040616 TCAAAATTGTTTAGGGCGTAGGAAAA 59.959 34.615 0.00 0.00 0.00 2.29
732 759 1.229951 ACATGGAGCTGGAAGGGGA 60.230 57.895 0.00 0.00 0.00 4.81
737 764 1.039785 GGAGCTGGAAGGGGAATTGC 61.040 60.000 0.00 0.00 0.00 3.56
774 2349 3.164268 CATTGATGAGTGGGTCCCAAAA 58.836 45.455 13.78 0.94 34.18 2.44
800 2375 2.029666 CGGAGACATGGCGATCCC 59.970 66.667 1.31 0.00 0.00 3.85
811 2386 2.813474 CGATCCCGAGTTTGCGCA 60.813 61.111 5.66 5.66 38.22 6.09
945 2524 5.515270 TCATGAAGTTTATCGAGCAGTAACG 59.485 40.000 0.00 0.00 0.00 3.18
956 2535 5.224888 TCGAGCAGTAACGAAACATTTAGT 58.775 37.500 0.00 0.00 35.62 2.24
1224 2804 9.811995 GTTACAATGACCTATCTGTATAACACA 57.188 33.333 0.00 0.00 35.30 3.72
1246 2826 6.855914 CACATTTGGTAGTGTGTTCACAATAC 59.144 38.462 25.30 25.30 46.01 1.89
1406 2986 3.184541 CCGTAGATTACAACACCCGAAG 58.815 50.000 0.00 0.00 0.00 3.79
1518 3100 6.859112 ATATATTAGACATCGTGCCTCCTT 57.141 37.500 0.00 0.00 0.00 3.36
1691 3285 1.953559 TGCAGTCTGTTCTGTCCAAC 58.046 50.000 0.93 0.00 37.70 3.77
1701 3295 2.985139 GTTCTGTCCAACGTACTGTAGC 59.015 50.000 0.00 0.00 0.00 3.58
1705 3299 1.725164 GTCCAACGTACTGTAGCTTGC 59.275 52.381 0.00 0.00 0.00 4.01
1723 3317 9.582223 GTAGCTTGCTTAATATAATCAACGAAC 57.418 33.333 0.00 0.00 0.00 3.95
1736 3330 5.862924 ATCAACGAACTCAGTTTGTATGG 57.137 39.130 11.06 4.60 38.99 2.74
1842 3437 6.159988 GCTAAGTCTCAAGAGAGCAACTTTA 58.840 40.000 0.00 0.00 38.84 1.85
2020 3638 7.119846 AGCTTTGATCGCTTGTTTTCTAGTAAT 59.880 33.333 0.00 0.00 32.98 1.89
2090 3715 4.928661 ACTATCACGAAATCTGCACAAC 57.071 40.909 0.00 0.00 0.00 3.32
2095 3720 5.342806 TCACGAAATCTGCACAACTTAAG 57.657 39.130 0.00 0.00 0.00 1.85
2176 3801 5.804692 TTACTCTTTGTCGAAAAAGTGCA 57.195 34.783 24.03 12.40 38.16 4.57
2231 3857 8.748412 TCATCAAATTTGGTTTATAGAAGGGTG 58.252 33.333 17.90 0.00 0.00 4.61
2234 3860 5.914898 ATTTGGTTTATAGAAGGGTGCAC 57.085 39.130 8.80 8.80 0.00 4.57
2252 3885 9.158097 AGGGTGCACATAAATAAATAAATGGAT 57.842 29.630 20.43 0.00 0.00 3.41
2298 3931 9.844790 TGTCCTTATATGTCGGTATATTTTACG 57.155 33.333 0.00 0.00 0.00 3.18
2304 3937 8.997621 ATATGTCGGTATATTTTACGCAGAAT 57.002 30.769 0.00 0.00 0.00 2.40
2814 5118 6.828785 TCATTATTCAAGCCTTCCCTAGAAAC 59.171 38.462 0.00 0.00 0.00 2.78
2853 5157 8.248253 ACGATGTTATATGTGTAGACAAACTCA 58.752 33.333 0.00 0.00 35.11 3.41
3014 5323 1.325640 CTCATGTTGATCGCAAGTCGG 59.674 52.381 0.00 0.00 39.05 4.79
3031 5340 3.071479 GTCGGTGCTTACTTGGAAATGA 58.929 45.455 0.00 0.00 0.00 2.57
3032 5341 3.125316 GTCGGTGCTTACTTGGAAATGAG 59.875 47.826 0.00 0.00 0.00 2.90
3033 5342 3.074412 CGGTGCTTACTTGGAAATGAGT 58.926 45.455 0.00 0.00 0.00 3.41
3034 5343 3.502211 CGGTGCTTACTTGGAAATGAGTT 59.498 43.478 0.00 0.00 0.00 3.01
3035 5344 4.023193 CGGTGCTTACTTGGAAATGAGTTT 60.023 41.667 0.00 0.00 0.00 2.66
3036 5345 5.180492 CGGTGCTTACTTGGAAATGAGTTTA 59.820 40.000 0.00 0.00 0.00 2.01
3037 5346 6.612306 GGTGCTTACTTGGAAATGAGTTTAG 58.388 40.000 0.00 0.00 0.00 1.85
3038 5347 6.430000 GGTGCTTACTTGGAAATGAGTTTAGA 59.570 38.462 0.00 0.00 0.00 2.10
3039 5348 7.361286 GGTGCTTACTTGGAAATGAGTTTAGAG 60.361 40.741 0.00 0.00 0.00 2.43
3040 5349 7.387948 GTGCTTACTTGGAAATGAGTTTAGAGA 59.612 37.037 0.00 0.00 0.00 3.10
3041 5350 7.936847 TGCTTACTTGGAAATGAGTTTAGAGAA 59.063 33.333 0.00 0.00 0.00 2.87
3042 5351 8.784043 GCTTACTTGGAAATGAGTTTAGAGAAA 58.216 33.333 0.00 0.00 0.00 2.52
3044 5353 7.208225 ACTTGGAAATGAGTTTAGAGAAAGC 57.792 36.000 0.00 0.00 0.00 3.51
3045 5354 7.001073 ACTTGGAAATGAGTTTAGAGAAAGCT 58.999 34.615 0.00 0.00 0.00 3.74
3046 5355 7.503902 ACTTGGAAATGAGTTTAGAGAAAGCTT 59.496 33.333 0.00 0.00 0.00 3.74
3047 5356 8.918202 TTGGAAATGAGTTTAGAGAAAGCTTA 57.082 30.769 0.00 0.00 0.00 3.09
3048 5357 8.324163 TGGAAATGAGTTTAGAGAAAGCTTAC 57.676 34.615 0.00 0.00 0.00 2.34
3049 5358 7.936847 TGGAAATGAGTTTAGAGAAAGCTTACA 59.063 33.333 0.00 0.00 0.00 2.41
3050 5359 8.951243 GGAAATGAGTTTAGAGAAAGCTTACAT 58.049 33.333 0.00 0.00 0.00 2.29
3051 5360 9.766277 GAAATGAGTTTAGAGAAAGCTTACATG 57.234 33.333 0.00 0.00 0.00 3.21
3052 5361 7.856145 ATGAGTTTAGAGAAAGCTTACATGG 57.144 36.000 0.00 0.00 0.00 3.66
3053 5362 7.004555 TGAGTTTAGAGAAAGCTTACATGGA 57.995 36.000 0.00 0.00 0.00 3.41
3054 5363 7.450074 TGAGTTTAGAGAAAGCTTACATGGAA 58.550 34.615 0.00 0.00 0.00 3.53
3055 5364 7.936847 TGAGTTTAGAGAAAGCTTACATGGAAA 59.063 33.333 0.00 0.00 0.00 3.13
3056 5365 8.870075 AGTTTAGAGAAAGCTTACATGGAAAT 57.130 30.769 0.00 0.00 0.00 2.17
3057 5366 8.734386 AGTTTAGAGAAAGCTTACATGGAAATG 58.266 33.333 0.00 0.00 0.00 2.32
3073 5382 5.010282 TGGAAATGAGGTTAGAGAAAAGCC 58.990 41.667 0.00 0.00 0.00 4.35
3164 5473 1.937191 ATTTCCCTGTTCCGGCAAAT 58.063 45.000 0.00 0.00 0.00 2.32
3334 5643 2.433145 CGCCGGGATGATCATCGG 60.433 66.667 25.60 24.99 44.70 4.18
3567 5882 1.247567 AGGGTTGATTCGCCAAACAG 58.752 50.000 0.00 0.00 35.53 3.16
3772 6089 2.888834 GCAATATTTGGCGGTGGAAT 57.111 45.000 0.00 0.00 0.00 3.01
4037 6375 6.655848 TGGTAATACATGTTTGGTAGTTGTCC 59.344 38.462 2.30 0.00 0.00 4.02
4054 6392 1.064017 GTCCATGGTTTCTGGGGCATA 60.064 52.381 12.58 0.00 34.36 3.14
4071 6409 7.817440 TGGGGCATAATAAGGTCAAGTTATTA 58.183 34.615 0.00 0.00 36.97 0.98
4433 6803 4.046286 TGCCACCATTAAAATCACCTCT 57.954 40.909 0.00 0.00 0.00 3.69
4453 6823 5.452078 TCTGCTTTGACATAACAAAAGGG 57.548 39.130 0.00 0.00 38.90 3.95
4460 6830 7.065204 GCTTTGACATAACAAAAGGGAAAAACA 59.935 33.333 0.00 0.00 38.90 2.83
4481 6851 0.991920 CCCAGCCCTTACTCTTTCCA 59.008 55.000 0.00 0.00 0.00 3.53
4491 6861 0.179018 ACTCTTTCCAGGTGCCACAC 60.179 55.000 0.00 0.00 0.00 3.82
4502 6872 2.985847 GCCACACAAGCCCTCACC 60.986 66.667 0.00 0.00 0.00 4.02
4508 6878 1.021390 CACAAGCCCTCACCGATGTC 61.021 60.000 0.00 0.00 0.00 3.06
4523 6893 1.380403 ATGTCTCCTGCTCGACTCCG 61.380 60.000 0.00 0.00 37.07 4.63
4554 8778 0.176680 CTTGCCAGCTATCTCACGGT 59.823 55.000 0.00 0.00 0.00 4.83
4575 8799 2.235650 TCTGAGCAACCTCCTCAAGATG 59.764 50.000 0.00 0.00 38.73 2.90
4577 8801 0.990374 AGCAACCTCCTCAAGATGCT 59.010 50.000 0.00 0.00 40.78 3.79
4585 8809 1.699083 TCCTCAAGATGCTGTTCACCA 59.301 47.619 0.00 0.00 0.00 4.17
4587 8811 2.227388 CCTCAAGATGCTGTTCACCAAC 59.773 50.000 0.00 0.00 0.00 3.77
4588 8812 2.880268 CTCAAGATGCTGTTCACCAACA 59.120 45.455 0.00 0.00 40.40 3.33
4605 8829 3.495193 CAACATTTCATGCTTGACTCCG 58.505 45.455 1.02 0.00 0.00 4.63
4606 8830 3.057969 ACATTTCATGCTTGACTCCGA 57.942 42.857 1.02 0.00 0.00 4.55
4636 8860 4.019174 CAACTTATTGCCAACTCTCCCAT 58.981 43.478 0.00 0.00 0.00 4.00
4638 8862 3.266772 ACTTATTGCCAACTCTCCCATGA 59.733 43.478 0.00 0.00 0.00 3.07
4641 8865 1.077429 GCCAACTCTCCCATGACCC 60.077 63.158 0.00 0.00 0.00 4.46
4664 8888 2.103042 AATCTCGTCAAGCCGCTGC 61.103 57.895 0.00 0.00 37.95 5.25
4677 8901 3.512516 GCTGCCCACGCTCCAATC 61.513 66.667 0.00 0.00 35.36 2.67
4697 8921 5.808366 ATCAGTGTGTCAAAGAGGTAGAA 57.192 39.130 0.00 0.00 0.00 2.10
4704 8928 6.809196 GTGTGTCAAAGAGGTAGAATGACTAG 59.191 42.308 5.88 0.00 40.70 2.57
4706 8930 7.030768 GTGTCAAAGAGGTAGAATGACTAGAC 58.969 42.308 0.00 0.00 40.70 2.59
4730 8954 2.046023 TTGATGGTGAGCTGCCCG 60.046 61.111 0.00 0.00 0.00 6.13
4731 8955 2.526450 CTTGATGGTGAGCTGCCCGA 62.526 60.000 0.00 0.00 0.00 5.14
4732 8956 2.202987 GATGGTGAGCTGCCCGAG 60.203 66.667 0.00 0.00 0.00 4.63
4733 8957 3.005539 ATGGTGAGCTGCCCGAGT 61.006 61.111 0.00 0.00 0.00 4.18
4734 8958 2.527951 GATGGTGAGCTGCCCGAGTT 62.528 60.000 0.00 0.00 0.00 3.01
4735 8959 2.743928 GGTGAGCTGCCCGAGTTG 60.744 66.667 0.00 0.00 0.00 3.16
4736 8960 3.426568 GTGAGCTGCCCGAGTTGC 61.427 66.667 0.00 0.00 0.00 4.17
4737 8961 4.704833 TGAGCTGCCCGAGTTGCC 62.705 66.667 0.00 0.00 0.00 4.52
4767 8991 0.606673 GCTTCTCTTCACCCCACACC 60.607 60.000 0.00 0.00 0.00 4.16
4768 8992 0.320771 CTTCTCTTCACCCCACACCG 60.321 60.000 0.00 0.00 0.00 4.94
4769 8993 1.764571 TTCTCTTCACCCCACACCGG 61.765 60.000 0.00 0.00 0.00 5.28
4785 9009 1.012841 CCGGCTGAAGAAGAAGCATC 58.987 55.000 0.00 0.00 41.36 3.91
4787 9011 2.159043 CCGGCTGAAGAAGAAGCATCTA 60.159 50.000 0.00 0.00 41.36 1.98
4799 9023 6.481644 AGAAGAAGCATCTAAAGCCGAAATAG 59.518 38.462 0.00 0.00 33.77 1.73
4808 9032 8.988934 CATCTAAAGCCGAAATAGCAAATACTA 58.011 33.333 0.00 0.00 0.00 1.82
4821 9045 3.751175 GCAAATACTAGAGCAACACCACA 59.249 43.478 0.00 0.00 0.00 4.17
4841 9072 3.197766 ACAAGACACCTCTGAACAGTTGA 59.802 43.478 0.00 0.00 0.00 3.18
4848 9079 4.926238 CACCTCTGAACAGTTGATGTAGTC 59.074 45.833 0.00 0.00 43.00 2.59
4851 9082 5.139435 TCTGAACAGTTGATGTAGTCCAG 57.861 43.478 0.00 0.00 43.00 3.86
4861 9092 6.013379 AGTTGATGTAGTCCAGGAGAATGAAA 60.013 38.462 0.00 0.00 0.00 2.69
4892 9123 3.268034 ACCAGTCTCTCCTCCTTTTCT 57.732 47.619 0.00 0.00 0.00 2.52
4893 9124 4.405756 ACCAGTCTCTCCTCCTTTTCTA 57.594 45.455 0.00 0.00 0.00 2.10
4894 9125 4.090819 ACCAGTCTCTCCTCCTTTTCTAC 58.909 47.826 0.00 0.00 0.00 2.59
4896 9127 3.129638 CAGTCTCTCCTCCTTTTCTACCG 59.870 52.174 0.00 0.00 0.00 4.02
4923 9155 6.885918 TGAAATATCATCTGAAGGACAAGCAA 59.114 34.615 0.00 0.00 0.00 3.91
4928 9160 4.828939 TCATCTGAAGGACAAGCAACAAAT 59.171 37.500 0.00 0.00 0.00 2.32
4933 9165 3.923017 AGGACAAGCAACAAATGTAGC 57.077 42.857 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 118 4.212425 CACTGCACGGTTGAGTTATTTACA 59.788 41.667 0.00 0.00 0.00 2.41
352 357 8.143193 CAGTATGGCAATATTTAAGGCAATTGA 58.857 33.333 10.34 0.00 41.29 2.57
376 381 7.989826 ACTAGCTAATTAAATTTGACTGCCAG 58.010 34.615 0.00 0.00 0.00 4.85
404 410 4.985538 ACATGAATACAAGTGACCAAGGT 58.014 39.130 0.00 0.00 0.00 3.50
456 462 3.835395 AGAGTTCCTCTAAGGTTGACCAG 59.165 47.826 2.56 0.00 39.28 4.00
531 537 1.228675 AGTGCCCTTTTGCTCCCTG 60.229 57.895 0.00 0.00 0.00 4.45
630 656 3.070015 CCAAAAGTTGGCCTCAAGACAAT 59.930 43.478 3.32 0.00 45.17 2.71
656 682 8.739039 CCTAAACAATTTTGATGGATGTAGTGA 58.261 33.333 0.00 0.00 0.00 3.41
668 694 4.653868 TCCTACGCCCTAAACAATTTTGA 58.346 39.130 0.00 0.00 0.00 2.69
682 708 3.181500 GGTGATGTGAATTTTCCTACGCC 60.181 47.826 0.00 0.00 0.00 5.68
732 759 1.474330 GACATCCTTTCCCCGCAATT 58.526 50.000 0.00 0.00 0.00 2.32
774 2349 0.107017 CCATGTCTCCGCCTCCAAAT 60.107 55.000 0.00 0.00 0.00 2.32
857 2436 8.215050 AGTATAAGAGAAACTCTAGCAGAGCTA 58.785 37.037 11.60 0.00 46.12 3.32
916 2495 4.864806 TGCTCGATAAACTTCATGAGTGTC 59.135 41.667 0.00 0.00 39.00 3.67
1223 2803 6.077197 CGTATTGTGAACACACTACCAAATG 58.923 40.000 21.03 9.63 41.53 2.32
1224 2804 5.761234 ACGTATTGTGAACACACTACCAAAT 59.239 36.000 21.03 9.34 41.53 2.32
1246 2826 7.930513 AGCTTATTCTTTTCCAAAGAAAACG 57.069 32.000 14.08 7.64 44.99 3.60
1406 2986 1.294857 GAAGAAGCGAATCTCCTGGC 58.705 55.000 0.00 0.00 0.00 4.85
1544 3126 8.344831 TGATAGTACTGCATGAATTAATTGCAC 58.655 33.333 5.17 0.00 41.18 4.57
1691 3285 9.406828 TGATTATATTAAGCAAGCTACAGTACG 57.593 33.333 0.00 0.00 0.00 3.67
1701 3295 9.855361 CTGAGTTCGTTGATTATATTAAGCAAG 57.145 33.333 0.00 0.00 0.00 4.01
1806 3401 8.958119 TCTTGAGACTTAGCAAAGTAAGAAAA 57.042 30.769 0.00 0.00 46.09 2.29
1842 3437 6.437162 ACATATTCACAACAACATAAGGGCTT 59.563 34.615 0.00 0.00 0.00 4.35
1995 3598 5.035784 ACTAGAAAACAAGCGATCAAAGC 57.964 39.130 0.00 0.00 0.00 3.51
2090 3715 3.131577 TGGCACGTATGGAGTACCTTAAG 59.868 47.826 0.00 0.00 37.04 1.85
2095 3720 2.889045 TCTATGGCACGTATGGAGTACC 59.111 50.000 0.00 0.00 0.00 3.34
2298 3931 1.869767 CGGTAGCATCCAGAATTCTGC 59.130 52.381 27.01 17.79 42.47 4.26
2642 4928 7.038154 TGTATCCAGGTTTCAAAGTTTCAAG 57.962 36.000 0.00 0.00 0.00 3.02
2723 5022 3.818773 ACTACCACGAAGGAAACCAATTG 59.181 43.478 0.00 0.00 41.22 2.32
3014 5323 7.387948 TCTCTAAACTCATTTCCAAGTAAGCAC 59.612 37.037 0.00 0.00 0.00 4.40
3031 5340 8.734386 CATTTCCATGTAAGCTTTCTCTAAACT 58.266 33.333 3.20 0.00 0.00 2.66
3032 5341 8.730680 TCATTTCCATGTAAGCTTTCTCTAAAC 58.269 33.333 3.20 0.00 0.00 2.01
3033 5342 8.862325 TCATTTCCATGTAAGCTTTCTCTAAA 57.138 30.769 3.20 0.00 0.00 1.85
3034 5343 7.554118 CCTCATTTCCATGTAAGCTTTCTCTAA 59.446 37.037 3.20 0.00 0.00 2.10
3035 5344 7.050377 CCTCATTTCCATGTAAGCTTTCTCTA 58.950 38.462 3.20 0.00 0.00 2.43
3036 5345 5.884792 CCTCATTTCCATGTAAGCTTTCTCT 59.115 40.000 3.20 0.00 0.00 3.10
3037 5346 5.649831 ACCTCATTTCCATGTAAGCTTTCTC 59.350 40.000 3.20 0.00 0.00 2.87
3038 5347 5.574188 ACCTCATTTCCATGTAAGCTTTCT 58.426 37.500 3.20 0.00 0.00 2.52
3039 5348 5.904362 ACCTCATTTCCATGTAAGCTTTC 57.096 39.130 3.20 0.00 0.00 2.62
3040 5349 7.175104 TCTAACCTCATTTCCATGTAAGCTTT 58.825 34.615 3.20 0.00 0.00 3.51
3041 5350 6.721318 TCTAACCTCATTTCCATGTAAGCTT 58.279 36.000 3.48 3.48 0.00 3.74
3042 5351 6.156949 TCTCTAACCTCATTTCCATGTAAGCT 59.843 38.462 0.00 0.00 0.00 3.74
3043 5352 6.349300 TCTCTAACCTCATTTCCATGTAAGC 58.651 40.000 0.00 0.00 0.00 3.09
3044 5353 8.792830 TTTCTCTAACCTCATTTCCATGTAAG 57.207 34.615 0.00 0.00 0.00 2.34
3045 5354 9.231297 CTTTTCTCTAACCTCATTTCCATGTAA 57.769 33.333 0.00 0.00 0.00 2.41
3046 5355 7.336931 GCTTTTCTCTAACCTCATTTCCATGTA 59.663 37.037 0.00 0.00 0.00 2.29
3047 5356 6.151817 GCTTTTCTCTAACCTCATTTCCATGT 59.848 38.462 0.00 0.00 0.00 3.21
3048 5357 6.405176 GGCTTTTCTCTAACCTCATTTCCATG 60.405 42.308 0.00 0.00 0.00 3.66
3049 5358 5.654209 GGCTTTTCTCTAACCTCATTTCCAT 59.346 40.000 0.00 0.00 0.00 3.41
3050 5359 5.010282 GGCTTTTCTCTAACCTCATTTCCA 58.990 41.667 0.00 0.00 0.00 3.53
3051 5360 5.010282 TGGCTTTTCTCTAACCTCATTTCC 58.990 41.667 0.00 0.00 0.00 3.13
3052 5361 6.765915 ATGGCTTTTCTCTAACCTCATTTC 57.234 37.500 0.00 0.00 0.00 2.17
3053 5362 7.381323 CAAATGGCTTTTCTCTAACCTCATTT 58.619 34.615 0.00 0.00 34.08 2.32
3054 5363 6.071165 CCAAATGGCTTTTCTCTAACCTCATT 60.071 38.462 0.00 0.00 0.00 2.57
3055 5364 5.420104 CCAAATGGCTTTTCTCTAACCTCAT 59.580 40.000 0.00 0.00 0.00 2.90
3056 5365 4.766891 CCAAATGGCTTTTCTCTAACCTCA 59.233 41.667 0.00 0.00 0.00 3.86
3057 5366 4.767409 ACCAAATGGCTTTTCTCTAACCTC 59.233 41.667 0.00 0.00 39.32 3.85
3073 5382 8.592105 AAACAATGTGTAAATCTCACCAAATG 57.408 30.769 0.00 0.00 35.25 2.32
3164 5473 0.596600 GTGCTTTGTCTCGTCGGTGA 60.597 55.000 0.00 0.00 0.00 4.02
3334 5643 6.867816 TGTGTGTTTTCCAGCAAATATCAATC 59.132 34.615 0.00 0.00 0.00 2.67
3567 5882 9.912634 TTTTGTCCTCACATTGATATTCTTTTC 57.087 29.630 0.00 0.00 30.55 2.29
3772 6089 1.847798 CTCCCCGGGACAAACATGGA 61.848 60.000 26.32 6.03 0.00 3.41
3834 6151 6.416161 GTGAGTTTGAGCTCAAAATTTCTCAC 59.584 38.462 39.90 39.90 46.47 3.51
4037 6375 4.281688 CCTTATTATGCCCCAGAAACCATG 59.718 45.833 0.00 0.00 0.00 3.66
4307 6677 7.669722 AGGCTAGATGTTTCTAAATTTTGTGGA 59.330 33.333 0.00 0.00 34.06 4.02
4400 6770 1.528776 GGTGGCAACGGTGGGTAAA 60.529 57.895 0.90 0.00 42.51 2.01
4433 6803 5.860941 TTCCCTTTTGTTATGTCAAAGCA 57.139 34.783 0.00 0.00 38.32 3.91
4453 6823 3.431415 AGTAAGGGCTGGGATGTTTTTC 58.569 45.455 0.00 0.00 0.00 2.29
4460 6830 1.847088 GGAAAGAGTAAGGGCTGGGAT 59.153 52.381 0.00 0.00 0.00 3.85
4467 6837 1.340114 GGCACCTGGAAAGAGTAAGGG 60.340 57.143 0.00 0.00 33.87 3.95
4481 6851 3.497884 GAGGGCTTGTGTGGCACCT 62.498 63.158 16.26 2.19 34.66 4.00
4491 6861 0.460987 GAGACATCGGTGAGGGCTTG 60.461 60.000 0.65 0.00 29.20 4.01
4502 6872 0.028770 GAGTCGAGCAGGAGACATCG 59.971 60.000 0.00 0.00 39.67 3.84
4508 6878 4.200283 GCCGGAGTCGAGCAGGAG 62.200 72.222 5.05 0.00 39.00 3.69
4533 6903 1.406069 CCGTGAGATAGCTGGCAAGTT 60.406 52.381 0.00 0.00 0.00 2.66
4554 8778 2.015456 TCTTGAGGAGGTTGCTCAGA 57.985 50.000 0.71 0.00 45.45 3.27
4588 8812 2.002586 CGTCGGAGTCAAGCATGAAAT 58.997 47.619 0.00 0.00 37.30 2.17
4605 8829 3.996825 CAATAAGTTGCAGCCCGTC 57.003 52.632 0.00 0.00 0.00 4.79
4664 8888 1.003355 ACACTGATTGGAGCGTGGG 60.003 57.895 0.00 0.00 0.00 4.61
4677 8901 5.406780 GTCATTCTACCTCTTTGACACACTG 59.593 44.000 0.00 0.00 37.30 3.66
4697 8921 4.959210 ACCATCAAGCTAGTGTCTAGTCAT 59.041 41.667 0.00 0.00 0.00 3.06
4704 8928 2.093764 AGCTCACCATCAAGCTAGTGTC 60.094 50.000 0.00 0.00 46.73 3.67
4706 8930 2.277969 CAGCTCACCATCAAGCTAGTG 58.722 52.381 0.00 0.00 46.87 2.74
4730 8954 2.665185 AGAACGTGCGGGCAACTC 60.665 61.111 0.00 0.00 0.00 3.01
4731 8955 2.972505 CAGAACGTGCGGGCAACT 60.973 61.111 0.00 0.00 0.00 3.16
4732 8956 4.683334 GCAGAACGTGCGGGCAAC 62.683 66.667 8.19 0.00 43.99 4.17
4767 8991 2.021355 AGATGCTTCTTCTTCAGCCG 57.979 50.000 0.00 0.00 34.91 5.52
4768 8992 4.201901 GCTTTAGATGCTTCTTCTTCAGCC 60.202 45.833 7.51 0.00 34.91 4.85
4769 8993 4.201901 GGCTTTAGATGCTTCTTCTTCAGC 60.202 45.833 7.51 8.13 36.49 4.26
4785 9009 8.589335 TCTAGTATTTGCTATTTCGGCTTTAG 57.411 34.615 0.00 0.00 0.00 1.85
4787 9011 6.017852 GCTCTAGTATTTGCTATTTCGGCTTT 60.018 38.462 0.00 0.00 0.00 3.51
4799 9023 3.751175 TGTGGTGTTGCTCTAGTATTTGC 59.249 43.478 0.00 0.00 0.00 3.68
4808 9032 1.668419 GTGTCTTGTGGTGTTGCTCT 58.332 50.000 0.00 0.00 0.00 4.09
4821 9045 4.141620 ACATCAACTGTTCAGAGGTGTCTT 60.142 41.667 6.83 0.00 32.90 3.01
4841 9072 4.785376 ACCTTTCATTCTCCTGGACTACAT 59.215 41.667 0.00 0.00 0.00 2.29
4848 9079 4.006319 GAGTTGACCTTTCATTCTCCTGG 58.994 47.826 0.00 0.00 31.92 4.45
4851 9082 4.216472 GGTTGAGTTGACCTTTCATTCTCC 59.784 45.833 0.00 0.00 34.67 3.71
4861 9092 2.630580 GAGAGACTGGTTGAGTTGACCT 59.369 50.000 0.00 0.00 38.04 3.85
4923 9155 4.898320 TGATGAGAGTGTGCTACATTTGT 58.102 39.130 0.00 0.00 0.00 2.83
4928 9160 4.021192 TCATGTTGATGAGAGTGTGCTACA 60.021 41.667 0.00 0.00 33.40 2.74
4933 9165 3.438087 GGGTTCATGTTGATGAGAGTGTG 59.562 47.826 0.00 0.00 39.81 3.82


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

AutoCloner maintained by Alex Coulton.