Multiple sequence alignment - TraesCS7A01G300500

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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 TraesCS7A01G300500 chr7A 100.000 4140 0 0 1 4140 417151292 417147153 0.000000e+00 7646.0
1 TraesCS7A01G300500 chr7B 95.124 1128 44 3 720 1846 367497233 367496116 0.000000e+00 1768.0
2 TraesCS7A01G300500 chr7B 93.162 1170 46 12 2359 3525 367495168 367494030 0.000000e+00 1687.0
3 TraesCS7A01G300500 chr7B 94.584 517 18 2 1846 2362 367495729 367495223 0.000000e+00 791.0
4 TraesCS7A01G300500 chr7B 83.165 297 37 10 3586 3878 367493888 367493601 4.110000e-65 259.0
5 TraesCS7A01G300500 chr7B 88.000 75 9 0 3900 3974 367493278 367493204 5.700000e-14 89.8
6 TraesCS7A01G300500 chr7B 90.698 43 3 1 3539 3581 367494029 367493988 5.780000e-04 56.5
7 TraesCS7A01G300500 chr7D 95.592 1089 43 1 763 1846 372271163 372270075 0.000000e+00 1740.0
8 TraesCS7A01G300500 chr7D 95.527 1073 39 5 2383 3454 372269295 372268231 0.000000e+00 1707.0
9 TraesCS7A01G300500 chr7D 95.568 519 19 3 1846 2362 372269871 372269355 0.000000e+00 828.0
10 TraesCS7A01G300500 chr7D 85.931 462 24 14 3457 3899 372268185 372267746 4.880000e-124 455.0
11 TraesCS7A01G300500 chr7D 93.724 239 11 4 3902 4140 372267470 372267236 5.090000e-94 355.0
12 TraesCS7A01G300500 chr2A 93.499 723 43 4 1 720 540765863 540765142 0.000000e+00 1072.0
13 TraesCS7A01G300500 chr3B 89.737 419 34 8 306 718 658495531 658495116 1.020000e-145 527.0
14 TraesCS7A01G300500 chr6D 84.428 533 59 12 1 529 464008807 464009319 1.720000e-138 503.0
15 TraesCS7A01G300500 chr1B 85.325 477 57 13 43 513 600922330 600921861 8.050000e-132 481.0
16 TraesCS7A01G300500 chr1B 89.197 361 32 5 361 717 672364287 672364644 1.060000e-120 444.0
17 TraesCS7A01G300500 chr1B 97.248 218 6 0 1 218 672364069 672364286 1.820000e-98 370.0
18 TraesCS7A01G300500 chrUn 90.160 376 25 9 361 727 289037826 289038198 2.900000e-131 479.0
19 TraesCS7A01G300500 chrUn 94.954 218 11 0 1 218 289037608 289037825 3.960000e-90 342.0
20 TraesCS7A01G300500 chr3D 90.160 376 25 9 361 727 586536509 586536137 2.900000e-131 479.0
21 TraesCS7A01G300500 chr3D 94.954 218 11 0 1 218 586536727 586536510 3.960000e-90 342.0
22 TraesCS7A01G300500 chr2D 89.286 364 35 4 361 720 635077004 635077367 1.750000e-123 453.0
23 TraesCS7A01G300500 chr2D 90.826 218 8 1 1 218 635076798 635077003 8.760000e-72 281.0


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 TraesCS7A01G300500 chr7A 417147153 417151292 4139 True 7646.000000 7646 100.000000 1 4140 1 chr7A.!!$R1 4139
1 TraesCS7A01G300500 chr7B 367493204 367497233 4029 True 775.216667 1768 90.788833 720 3974 6 chr7B.!!$R1 3254
2 TraesCS7A01G300500 chr7D 372267236 372271163 3927 True 1017.000000 1740 93.268400 763 4140 5 chr7D.!!$R1 3377
3 TraesCS7A01G300500 chr2A 540765142 540765863 721 True 1072.000000 1072 93.499000 1 720 1 chr2A.!!$R1 719
4 TraesCS7A01G300500 chr6D 464008807 464009319 512 False 503.000000 503 84.428000 1 529 1 chr6D.!!$F1 528
5 TraesCS7A01G300500 chr1B 672364069 672364644 575 False 407.000000 444 93.222500 1 717 2 chr1B.!!$F1 716
6 TraesCS7A01G300500 chrUn 289037608 289038198 590 False 410.500000 479 92.557000 1 727 2 chrUn.!!$F1 726
7 TraesCS7A01G300500 chr3D 586536137 586536727 590 True 410.500000 479 92.557000 1 727 2 chr3D.!!$R1 726
8 TraesCS7A01G300500 chr2D 635076798 635077367 569 False 367.000000 453 90.056000 1 720 2 chr2D.!!$F1 719

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
689 701 0.795735 TCGTTCGACGGAAGATTCGC 60.796 55.0 0.0 0.0 42.81 4.70 F
1220 1237 0.606604 TACCGCTCCCTTGACAGTTC 59.393 55.0 0.0 0.0 0.00 3.01 F
2763 3279 0.036732 AGCAAGTTCCCGCTGAATCA 59.963 50.0 0.0 0.0 37.02 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2648 3164 2.480037 CAGCAGCAGTTCACGATTACAA 59.520 45.455 0.00 0.0 0.00 2.41 R
3042 3558 0.179048 CGCCCTAATGATCCTGCACA 60.179 55.000 0.00 0.0 0.00 4.57 R
3956 4947 0.179078 CAGGTTGGCTTGCTTGCAAA 60.179 50.000 9.39 0.0 34.04 3.68 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
63 64 2.490903 CAGGATCTGGTTCCAGCAAAAG 59.509 50.000 13.44 1.08 38.32 2.27
83 84 2.043252 AGAACTCCCTGGTAGTAGCACT 59.957 50.000 0.00 0.00 0.00 4.40
123 125 1.452651 CGGTGGCTGCTGATTCCAT 60.453 57.895 0.00 0.00 31.83 3.41
224 226 1.483415 GGTTCCGGCACCTCTTGTATA 59.517 52.381 16.83 0.00 33.50 1.47
227 229 3.746045 TCCGGCACCTCTTGTATATTC 57.254 47.619 0.00 0.00 0.00 1.75
237 239 2.101750 TCTTGTATATTCGCCTTGCCGA 59.898 45.455 0.00 0.00 35.09 5.54
244 246 1.231958 TTCGCCTTGCCGATTTTCGT 61.232 50.000 0.00 0.00 38.40 3.85
280 282 3.190849 CAGCATCGCCACCGTCAG 61.191 66.667 0.00 0.00 35.54 3.51
420 422 1.898574 CAAGGTTGCTTGGAGCGGT 60.899 57.895 0.00 0.00 46.26 5.68
495 501 2.578480 GGGAAGAAGAAAGGGGATGAGT 59.422 50.000 0.00 0.00 0.00 3.41
541 548 1.727511 AAACACGACACGACGAGGGA 61.728 55.000 0.00 0.00 37.03 4.20
548 555 2.106683 CACGACGAGGGAAATGGCC 61.107 63.158 0.00 0.00 0.00 5.36
625 636 3.492137 GGTCCACCAGAATACATACGTCC 60.492 52.174 0.00 0.00 35.64 4.79
648 660 4.424711 GGGGTGGCTTCGCATGGA 62.425 66.667 0.00 0.00 0.00 3.41
649 661 2.124151 GGGTGGCTTCGCATGGAT 60.124 61.111 0.00 0.00 0.00 3.41
689 701 0.795735 TCGTTCGACGGAAGATTCGC 60.796 55.000 0.00 0.00 42.81 4.70
691 703 1.278238 GTTCGACGGAAGATTCGCAT 58.722 50.000 0.00 0.00 35.15 4.73
721 733 5.277586 GCCATTTTTAAACGTTTCCCTTTGG 60.278 40.000 18.42 19.29 0.00 3.28
722 734 6.049790 CCATTTTTAAACGTTTCCCTTTGGA 58.950 36.000 18.42 0.00 39.54 3.53
743 755 2.061509 AAAGGGGTGCTAACAACGTT 57.938 45.000 0.00 0.00 32.66 3.99
775 787 6.310224 CGAACATGGTTCAATTGGGTATTTTC 59.690 38.462 5.42 4.28 0.00 2.29
779 791 6.293004 TGGTTCAATTGGGTATTTTCCATC 57.707 37.500 5.42 0.00 33.82 3.51
790 802 5.126545 GGGTATTTTCCATCTAAAAGCGGTT 59.873 40.000 0.00 0.00 32.20 4.44
913 925 3.431673 AAAGCTCTTCTTTCTCCCCAG 57.568 47.619 0.00 0.00 40.89 4.45
972 984 3.374087 GAGCGAAAGAGCAAGCGGC 62.374 63.158 0.00 0.00 45.30 6.53
1053 1065 0.739813 GCTACGCCACCAAGTCGAAT 60.740 55.000 0.00 0.00 0.00 3.34
1081 1093 1.752833 GTCGTCAAGACCCCAGGTT 59.247 57.895 0.00 0.00 43.95 3.50
1220 1237 0.606604 TACCGCTCCCTTGACAGTTC 59.393 55.000 0.00 0.00 0.00 3.01
1304 1322 7.260387 TGTGTTACTGATTATTAGGTGGGAA 57.740 36.000 0.00 0.00 0.00 3.97
1311 1329 5.437060 TGATTATTAGGTGGGAAGCTTGTC 58.563 41.667 2.10 0.00 0.00 3.18
1454 1472 2.713770 GCACCATGCGCTCAGATG 59.286 61.111 9.73 3.35 31.71 2.90
1457 1475 1.818363 ACCATGCGCTCAGATGCAG 60.818 57.895 9.73 0.00 45.52 4.41
1551 1569 0.971959 TCTTGCCCCATGGAATGTGC 60.972 55.000 15.22 8.20 44.81 4.57
1618 1636 5.193679 AGTGGGGATTACTATTGTTGAAGC 58.806 41.667 0.00 0.00 0.00 3.86
1634 1652 3.415212 TGAAGCAGTGCTAATTCTTGCT 58.585 40.909 20.09 0.00 38.25 3.91
1842 1909 3.554934 TCGCATTGCTATTTCTTCCCAT 58.445 40.909 7.12 0.00 0.00 4.00
1906 2360 3.813166 TGGAAACCAATTCTTCTCGTGAC 59.187 43.478 0.00 0.00 38.18 3.67
1917 2371 3.006859 TCTTCTCGTGACATGAACATGGT 59.993 43.478 17.25 0.00 42.91 3.55
1932 2386 6.226787 TGAACATGGTTTTTGACTGTTTGTT 58.773 32.000 0.00 0.00 29.69 2.83
2154 2608 4.221924 GGCCTAATCTTCTCTATGAGGTCC 59.778 50.000 0.00 0.00 28.58 4.46
2276 2732 6.366332 CACAAAGTTGTACTACTCAGATGGTC 59.634 42.308 10.44 0.00 39.91 4.02
2413 2929 3.825014 GTGGAAGGGTCCCTTTACTTTTC 59.175 47.826 24.58 9.70 44.82 2.29
2492 3008 7.946655 TTATGTTCATACTTTGCGGAGATAG 57.053 36.000 0.00 0.00 0.00 2.08
2503 3019 5.449107 TTGCGGAGATAGTCATTAGTACC 57.551 43.478 0.00 0.00 0.00 3.34
2528 3044 2.168521 TGTCTACTCTTATGTGCTGGGC 59.831 50.000 0.00 0.00 0.00 5.36
2534 3050 1.140852 TCTTATGTGCTGGGCGCTTAT 59.859 47.619 7.64 0.00 40.03 1.73
2590 3106 3.311596 GGTGCTTAGCTATTTTACACCCG 59.688 47.826 5.60 0.00 40.12 5.28
2614 3130 6.429151 GTTCCAAACAACCCCTAATAGGTAT 58.571 40.000 5.49 0.00 36.27 2.73
2642 3158 6.855836 TGAGCCATTTACAAGTGAAATCATC 58.144 36.000 0.00 0.00 0.00 2.92
2648 3164 8.627403 CCATTTACAAGTGAAATCATCTATGCT 58.373 33.333 0.00 0.00 0.00 3.79
2732 3248 5.011738 TGCTAGATAGTGGTGGCTAAATACC 59.988 44.000 0.00 0.00 37.48 2.73
2754 3270 3.743396 CGCAGATAGAATAGCAAGTTCCC 59.257 47.826 0.00 0.00 0.00 3.97
2763 3279 0.036732 AGCAAGTTCCCGCTGAATCA 59.963 50.000 0.00 0.00 37.02 2.57
2780 3296 4.515191 TGAATCATAAGTTTATGCCTCGCC 59.485 41.667 6.94 0.00 40.19 5.54
3055 3571 0.036105 TCGTGCTGTGCAGGATCATT 60.036 50.000 10.31 0.00 46.20 2.57
3100 3616 4.518211 CAGAAGATTGTGAAGAAGGTGCTT 59.482 41.667 0.00 0.00 0.00 3.91
3183 3699 3.042887 GCGGTGATGTTTTGTGTTTCTC 58.957 45.455 0.00 0.00 0.00 2.87
3220 3736 9.903682 TTAAGCAATCAAGAATTTTCTCTCTTG 57.096 29.630 5.63 5.63 46.56 3.02
3322 3839 2.230750 AGCCTTTGATGCAAGAGCTTTC 59.769 45.455 0.00 0.00 42.74 2.62
3325 3842 1.167851 TTGATGCAAGAGCTTTCGGG 58.832 50.000 0.00 0.00 42.74 5.14
3377 3894 3.575630 CTTAGCTCAGTTAACGCTGTCA 58.424 45.455 14.48 1.32 37.70 3.58
3411 3928 0.383491 CACGAGAACAGTTTGCTGCG 60.383 55.000 0.00 0.00 46.30 5.18
3428 3945 1.312815 GCGCCCTATTCTGCTTTCAT 58.687 50.000 0.00 0.00 0.00 2.57
3456 3973 0.803117 GACGCTTAAGTCCCAAAGGC 59.197 55.000 4.02 0.00 35.22 4.35
3457 3974 0.608308 ACGCTTAAGTCCCAAAGGCC 60.608 55.000 4.02 0.00 0.00 5.19
3458 3975 1.313091 CGCTTAAGTCCCAAAGGCCC 61.313 60.000 0.00 0.00 0.00 5.80
3459 3976 0.970937 GCTTAAGTCCCAAAGGCCCC 60.971 60.000 0.00 0.00 0.00 5.80
3460 3977 0.679960 CTTAAGTCCCAAAGGCCCCG 60.680 60.000 0.00 0.00 0.00 5.73
3566 4125 2.421424 GAGCAAGATTACAGTGCCAAGG 59.579 50.000 0.00 0.00 39.13 3.61
3608 4261 2.095978 AACCGCTTGTGCTACCGTCT 62.096 55.000 0.00 0.00 36.97 4.18
3615 4268 2.154567 TGTGCTACCGTCTAGGGAAT 57.845 50.000 0.00 0.00 46.96 3.01
3630 4283 4.664688 AGGGAATCAAACACATCCTTCT 57.335 40.909 0.00 0.00 32.41 2.85
3664 4317 0.467290 ACAACAATGGCAACTCGGGT 60.467 50.000 0.00 0.00 37.61 5.28
3666 4319 1.468520 CAACAATGGCAACTCGGGTAG 59.531 52.381 0.00 0.00 37.61 3.18
3667 4320 0.690762 ACAATGGCAACTCGGGTAGT 59.309 50.000 0.00 0.00 41.49 2.73
3669 4322 2.093658 ACAATGGCAACTCGGGTAGTAG 60.094 50.000 0.00 0.00 37.50 2.57
3670 4323 1.120530 ATGGCAACTCGGGTAGTAGG 58.879 55.000 0.00 0.00 37.50 3.18
3671 4324 0.040058 TGGCAACTCGGGTAGTAGGA 59.960 55.000 0.00 0.00 37.50 2.94
3672 4325 0.459078 GGCAACTCGGGTAGTAGGAC 59.541 60.000 0.00 0.00 37.50 3.85
3673 4326 1.472188 GCAACTCGGGTAGTAGGACT 58.528 55.000 0.00 0.00 37.50 3.85
3674 4327 1.134560 GCAACTCGGGTAGTAGGACTG 59.865 57.143 0.00 0.00 37.50 3.51
3726 4396 8.202745 ACTTATAATGCAACTGCTAGAAGAAC 57.797 34.615 4.16 0.00 42.66 3.01
3734 4404 5.125739 GCAACTGCTAGAAGAACTAGGACTA 59.874 44.000 4.16 0.00 46.14 2.59
3735 4405 6.350277 GCAACTGCTAGAAGAACTAGGACTAA 60.350 42.308 4.16 0.00 46.14 2.24
3788 4458 3.051081 AGTTGCACTCTCCATGAAGAC 57.949 47.619 0.00 0.00 0.00 3.01
3796 4466 3.257873 ACTCTCCATGAAGACAGACACAG 59.742 47.826 0.00 0.00 0.00 3.66
3930 4921 2.358737 CCCAACGCTCACACTCCC 60.359 66.667 0.00 0.00 0.00 4.30
3936 4927 3.311110 GCTCACACTCCCCCGTCA 61.311 66.667 0.00 0.00 0.00 4.35
3941 4932 2.923035 CACTCCCCCGTCACACCT 60.923 66.667 0.00 0.00 0.00 4.00
3942 4933 2.923035 ACTCCCCCGTCACACCTG 60.923 66.667 0.00 0.00 0.00 4.00
3948 4939 3.625897 CCGTCACACCTGGCTCCA 61.626 66.667 0.00 0.00 0.00 3.86
3956 4947 0.540365 CACCTGGCTCCACAAACCAT 60.540 55.000 0.00 0.00 31.79 3.55
3958 4949 1.341080 CCTGGCTCCACAAACCATTT 58.659 50.000 0.00 0.00 31.79 2.32
3971 4962 0.469070 ACCATTTGCAAGCAAGCCAA 59.531 45.000 7.60 0.00 37.24 4.52
3974 4965 0.760572 ATTTGCAAGCAAGCCAACCT 59.239 45.000 7.60 0.00 37.24 3.50
4030 5021 2.519377 TCAACAACGACGTCTCCAAT 57.481 45.000 14.70 0.00 0.00 3.16
4064 5055 9.685828 TGCCAAATTTTGAGTTATTTGTACTAC 57.314 29.630 10.72 0.00 39.14 2.73
4096 5087 8.103305 ACCATCACAAGTTGTTACTATCTTCAT 58.897 33.333 5.57 0.00 33.17 2.57
4098 5089 8.607459 CATCACAAGTTGTTACTATCTTCATCC 58.393 37.037 5.57 0.00 33.17 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.166664 CAGTGCTACTACCAGGGAGTTC 59.833 54.545 10.58 3.08 0.00 3.01
83 84 0.877071 GGTGAAGACGACGAGGTACA 59.123 55.000 0.00 0.00 0.00 2.90
123 125 4.081531 GCTGGAACCATCATCCATTTTTGA 60.082 41.667 0.00 0.00 45.57 2.69
210 212 2.143925 GGCGAATATACAAGAGGTGCC 58.856 52.381 0.00 0.00 0.00 5.01
224 226 0.098728 CGAAAATCGGCAAGGCGAAT 59.901 50.000 22.21 11.85 36.00 3.34
227 229 0.793104 GAACGAAAATCGGCAAGGCG 60.793 55.000 9.95 9.95 45.59 5.52
237 239 3.471495 GTTCCAGCGATGAACGAAAAT 57.529 42.857 0.06 0.00 45.77 1.82
244 246 2.835605 GAACCGTTCCAGCGATGAA 58.164 52.632 0.06 0.00 0.00 2.57
455 459 0.096976 CTGCAGCAAAATACGACCGG 59.903 55.000 0.00 0.00 0.00 5.28
495 501 1.008327 TGCCTTCCATCTCCTCCACTA 59.992 52.381 0.00 0.00 0.00 2.74
541 548 0.917333 TCCCCTACCTTCGGCCATTT 60.917 55.000 2.24 0.00 0.00 2.32
548 555 1.543429 GCATTCCATCCCCTACCTTCG 60.543 57.143 0.00 0.00 0.00 3.79
565 572 6.779539 CCCTTCCTTATCTTATCCTTTTGCAT 59.220 38.462 0.00 0.00 0.00 3.96
666 678 1.919956 ATCTTCCGTCGAACGAGCGT 61.920 55.000 8.63 0.00 46.05 5.07
670 682 0.795735 GCGAATCTTCCGTCGAACGA 60.796 55.000 8.63 0.00 46.05 3.85
674 686 0.527600 CCATGCGAATCTTCCGTCGA 60.528 55.000 0.00 0.00 39.64 4.20
721 733 3.340928 ACGTTGTTAGCACCCCTTTATC 58.659 45.455 0.00 0.00 0.00 1.75
722 734 3.428413 ACGTTGTTAGCACCCCTTTAT 57.572 42.857 0.00 0.00 0.00 1.40
743 755 1.002624 GAACCATGTTCGGGAGCCA 60.003 57.895 0.00 0.00 0.00 4.75
775 787 4.718940 AATCCAAACCGCTTTTAGATGG 57.281 40.909 0.00 0.00 0.00 3.51
779 791 9.965824 ATGATTATTAATCCAAACCGCTTTTAG 57.034 29.630 12.71 0.00 37.09 1.85
966 978 2.574399 GGAGTTCTCTCGCCGCTT 59.426 61.111 0.00 0.00 41.26 4.68
972 984 1.098712 CCTCTCCCGGAGTTCTCTCG 61.099 65.000 14.36 2.59 41.26 4.04
1081 1093 3.606662 GCGCCGCTGATCTCCCTA 61.607 66.667 0.00 0.00 0.00 3.53
1283 1301 6.592870 AGCTTCCCACCTAATAATCAGTAAC 58.407 40.000 0.00 0.00 0.00 2.50
1304 1322 2.605257 TGGTGTACTGGTAGACAAGCT 58.395 47.619 9.61 0.00 31.67 3.74
1311 1329 2.607187 CGCTTCTTGGTGTACTGGTAG 58.393 52.381 0.00 0.00 0.00 3.18
1454 1472 2.202570 CGCTGAAATGCAGGCTGC 60.203 61.111 31.91 31.91 45.03 5.25
1457 1475 0.455633 CACTTCGCTGAAATGCAGGC 60.456 55.000 0.00 0.00 45.03 4.85
1534 1552 3.710926 GCACATTCCATGGGGCAA 58.289 55.556 13.02 0.00 35.58 4.52
1580 1598 2.489329 CCCCACTTCACACATCAACATC 59.511 50.000 0.00 0.00 0.00 3.06
1618 1636 5.556355 TGATTCAGCAAGAATTAGCACTG 57.444 39.130 5.96 0.00 46.76 3.66
1821 1839 2.997980 TGGGAAGAAATAGCAATGCGA 58.002 42.857 0.00 0.00 0.00 5.10
1824 1891 6.949352 ACAGTATGGGAAGAAATAGCAATG 57.051 37.500 0.00 0.00 43.62 2.82
1842 1909 6.829298 AGAGAGACGAATCAAAGGATACAGTA 59.171 38.462 0.00 0.00 41.41 2.74
1906 2360 6.313411 ACAAACAGTCAAAAACCATGTTCATG 59.687 34.615 5.88 5.88 33.17 3.07
1917 2371 6.432783 TGGAAGAGAGAACAAACAGTCAAAAA 59.567 34.615 0.00 0.00 0.00 1.94
1932 2386 3.326006 ACACTGAAGCATTGGAAGAGAGA 59.674 43.478 0.00 0.00 0.00 3.10
2183 2637 5.008613 TCACAATGAGGCTTCTACAACAAAC 59.991 40.000 0.00 0.00 0.00 2.93
2350 2806 7.992754 ATGAAGTAAAAGTCAGAAGATTGCT 57.007 32.000 0.00 0.00 0.00 3.91
2397 2913 3.079578 CCTTCGAAAAGTAAAGGGACCC 58.920 50.000 0.59 0.59 36.68 4.46
2405 2921 8.770828 CAAAGAATGTAGTCCTTCGAAAAGTAA 58.229 33.333 0.00 0.00 0.00 2.24
2413 2929 6.727824 AATCACAAAGAATGTAGTCCTTCG 57.272 37.500 0.00 0.00 41.46 3.79
2503 3019 5.295292 CCCAGCACATAAGAGTAGACAAATG 59.705 44.000 0.00 0.00 0.00 2.32
2534 3050 5.105146 ACAAATTTTACAACCACTCCAAGCA 60.105 36.000 0.00 0.00 0.00 3.91
2590 3106 4.669700 ACCTATTAGGGGTTGTTTGGAAC 58.330 43.478 14.26 0.00 40.58 3.62
2614 3130 6.647334 TTTCACTTGTAAATGGCTCAATGA 57.353 33.333 0.00 0.00 0.00 2.57
2642 3158 4.568359 AGCAGTTCACGATTACAAGCATAG 59.432 41.667 0.00 0.00 0.00 2.23
2648 3164 2.480037 CAGCAGCAGTTCACGATTACAA 59.520 45.455 0.00 0.00 0.00 2.41
2732 3248 3.743396 GGGAACTTGCTATTCTATCTGCG 59.257 47.826 0.00 0.00 0.00 5.18
2754 3270 5.613360 CGAGGCATAAACTTATGATTCAGCG 60.613 44.000 12.61 4.31 42.38 5.18
2763 3279 3.886123 ACAAGGCGAGGCATAAACTTAT 58.114 40.909 0.00 0.00 0.00 1.73
2780 3296 7.769044 ACTAAGGCAGTATAATGTACCAACAAG 59.231 37.037 1.67 0.00 35.76 3.16
2862 3378 1.613630 AGTAGGCCTCAGGTGTGGG 60.614 63.158 9.68 0.00 0.00 4.61
3042 3558 0.179048 CGCCCTAATGATCCTGCACA 60.179 55.000 0.00 0.00 0.00 4.57
3055 3571 0.250989 CCTCCACCAAAAACGCCCTA 60.251 55.000 0.00 0.00 0.00 3.53
3100 3616 4.947883 TCTCCTTGGTCTTCTGGATCTTA 58.052 43.478 0.00 0.00 0.00 2.10
3183 3699 7.636259 TCTTGATTGCTTAAAACAAATTCGG 57.364 32.000 0.00 0.00 31.00 4.30
3220 3736 2.149973 ACCAGGATTCTGCAAATCCC 57.850 50.000 24.80 10.52 45.70 3.85
3322 3839 1.153249 TAAGCCGAATTGGAGCCCG 60.153 57.895 0.00 0.00 42.00 6.13
3325 3842 1.265365 GCATCTAAGCCGAATTGGAGC 59.735 52.381 0.00 0.00 42.00 4.70
3377 3894 4.002906 TCTCGTGTGACAAATAAAGCCT 57.997 40.909 0.00 0.00 0.00 4.58
3411 3928 2.026641 TGCATGAAAGCAGAATAGGGC 58.973 47.619 0.00 0.00 40.11 5.19
3428 3945 3.552604 GACTTAAGCGTCCAAAATGCA 57.447 42.857 1.29 0.00 42.76 3.96
3536 4095 2.304761 TGTAATCTTGCTCCCCGTTCTT 59.695 45.455 0.00 0.00 0.00 2.52
3566 4125 8.708742 GGTTGGTTAATTTACTTCAGATTTTGC 58.291 33.333 0.00 0.00 0.00 3.68
3571 4130 5.944007 AGCGGTTGGTTAATTTACTTCAGAT 59.056 36.000 0.00 0.00 0.00 2.90
3608 4261 5.779241 AGAAGGATGTGTTTGATTCCCTA 57.221 39.130 0.00 0.00 0.00 3.53
3615 4268 6.374333 GGCAGTTATTAGAAGGATGTGTTTGA 59.626 38.462 0.00 0.00 0.00 2.69
3630 4283 6.219473 CCATTGTTGTTTGTGGCAGTTATTA 58.781 36.000 0.00 0.00 0.00 0.98
3664 4317 7.235193 CAGTCCTACTATACTCCAGTCCTACTA 59.765 44.444 0.00 0.00 0.00 1.82
3666 4319 6.232692 CAGTCCTACTATACTCCAGTCCTAC 58.767 48.000 0.00 0.00 0.00 3.18
3667 4320 5.310068 CCAGTCCTACTATACTCCAGTCCTA 59.690 48.000 0.00 0.00 0.00 2.94
3669 4322 4.104420 TCCAGTCCTACTATACTCCAGTCC 59.896 50.000 0.00 0.00 0.00 3.85
3670 4323 5.163174 ACTCCAGTCCTACTATACTCCAGTC 60.163 48.000 0.00 0.00 0.00 3.51
3671 4324 4.727841 ACTCCAGTCCTACTATACTCCAGT 59.272 45.833 0.00 0.00 0.00 4.00
3672 4325 5.313280 ACTCCAGTCCTACTATACTCCAG 57.687 47.826 0.00 0.00 0.00 3.86
3673 4326 5.728937 AACTCCAGTCCTACTATACTCCA 57.271 43.478 0.00 0.00 0.00 3.86
3674 4327 6.489700 GGTTAACTCCAGTCCTACTATACTCC 59.510 46.154 5.42 0.00 0.00 3.85
3726 4396 4.192317 GTGAATGGTGGCTTTAGTCCTAG 58.808 47.826 0.00 0.00 0.00 3.02
3734 4404 2.106566 TGTGTTGTGAATGGTGGCTTT 58.893 42.857 0.00 0.00 0.00 3.51
3735 4405 1.408702 GTGTGTTGTGAATGGTGGCTT 59.591 47.619 0.00 0.00 0.00 4.35
3772 4442 2.028658 TGTCTGTCTTCATGGAGAGTGC 60.029 50.000 3.13 0.00 0.00 4.40
3788 4458 6.293955 CCCCACTTTATTTGTTACTGTGTCTG 60.294 42.308 0.00 0.00 0.00 3.51
3796 4466 5.849510 AGCAAACCCCACTTTATTTGTTAC 58.150 37.500 0.00 0.00 35.06 2.50
3837 4507 6.877611 AACCAGTGTAAATAACAACAGAGG 57.122 37.500 0.00 0.00 40.63 3.69
3839 4509 7.988599 AGTGTAACCAGTGTAAATAACAACAGA 59.011 33.333 0.00 0.00 37.43 3.41
3840 4510 8.149973 AGTGTAACCAGTGTAAATAACAACAG 57.850 34.615 0.00 0.00 37.43 3.16
3842 4512 9.480053 TCTAGTGTAACCAGTGTAAATAACAAC 57.520 33.333 0.00 0.00 37.43 3.32
3878 4551 7.147143 TGCCAAAAATATAAGAGCGTTTACA 57.853 32.000 0.00 0.00 0.00 2.41
3893 4566 3.260632 GGGGTACATCACTTGCCAAAAAT 59.739 43.478 0.00 0.00 0.00 1.82
3930 4921 4.394712 GGAGCCAGGTGTGACGGG 62.395 72.222 0.00 0.00 0.00 5.28
3936 4927 1.152756 GGTTTGTGGAGCCAGGTGT 60.153 57.895 0.00 0.00 0.00 4.16
3941 4932 0.392336 GCAAATGGTTTGTGGAGCCA 59.608 50.000 4.56 0.00 43.31 4.75
3942 4933 0.392336 TGCAAATGGTTTGTGGAGCC 59.608 50.000 4.56 0.00 42.56 4.70
3948 4939 1.941975 GCTTGCTTGCAAATGGTTTGT 59.058 42.857 9.39 0.00 42.56 2.83
3956 4947 0.179078 CAGGTTGGCTTGCTTGCAAA 60.179 50.000 9.39 0.00 34.04 3.68
3958 4949 3.131155 CAGGTTGGCTTGCTTGCA 58.869 55.556 4.13 0.00 34.04 4.08
4064 5055 4.654091 AACAACTTGTGATGGTTCCAAG 57.346 40.909 0.00 0.00 41.02 3.61
4106 5097 7.933396 TGTTGCATGGAATTCTGAACATATAG 58.067 34.615 1.94 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.