Multiple sequence alignment - TraesCS3A01G277900

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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 TraesCS3A01G277900 chr3A 100.000 5036 0 0 1 5036 507473932 507468897 0.000000e+00 9300.0
1 TraesCS3A01G277900 chr3B 96.035 4262 144 10 9 4254 501395993 501391741 0.000000e+00 6911.0
2 TraesCS3A01G277900 chr3B 91.537 898 63 6 474 1369 8469306 8470192 0.000000e+00 1225.0
3 TraesCS3A01G277900 chr3B 88.510 792 52 21 4256 5025 501391698 501390924 0.000000e+00 922.0
4 TraesCS3A01G277900 chr3B 91.954 87 7 0 1407 1493 8470191 8470277 6.850000e-24 122.0
5 TraesCS3A01G277900 chr3D 94.380 2740 124 17 1493 4231 385430869 385428159 0.000000e+00 4180.0
6 TraesCS3A01G277900 chr3D 92.531 897 56 4 474 1369 6814623 6815509 0.000000e+00 1275.0
7 TraesCS3A01G277900 chr3D 88.501 687 47 16 4360 5036 385428018 385427354 0.000000e+00 802.0
8 TraesCS3A01G277900 chr3D 93.750 480 21 4 1 476 385431333 385430859 0.000000e+00 712.0
9 TraesCS3A01G277900 chr4B 89.165 1006 106 3 480 1484 23693373 23692370 0.000000e+00 1251.0
10 TraesCS3A01G277900 chr6D 87.759 1013 117 5 475 1484 42403836 42404844 0.000000e+00 1177.0
11 TraesCS3A01G277900 chrUn 86.824 1017 134 0 477 1493 88309298 88308282 0.000000e+00 1136.0
12 TraesCS3A01G277900 chrUn 86.739 1018 135 0 476 1493 88263469 88262452 0.000000e+00 1133.0
13 TraesCS3A01G277900 chrUn 97.619 42 1 0 4275 4316 357034052 357034011 6.990000e-09 73.1
14 TraesCS3A01G277900 chrUn 93.478 46 3 0 4275 4320 83668064 83668109 9.050000e-08 69.4
15 TraesCS3A01G277900 chr5A 87.716 985 86 11 474 1450 12187508 12186551 0.000000e+00 1116.0
16 TraesCS3A01G277900 chr5A 93.878 49 3 0 1445 1493 12185427 12185379 1.940000e-09 75.0
17 TraesCS3A01G277900 chr5A 85.484 62 3 6 4275 4333 650273964 650273906 5.440000e-05 60.2
18 TraesCS3A01G277900 chr4A 88.542 576 63 3 910 1484 647268346 647268919 0.000000e+00 695.0
19 TraesCS3A01G277900 chr1B 91.071 56 3 2 4263 4317 512989102 512989048 1.940000e-09 75.0
20 TraesCS3A01G277900 chr7A 95.556 45 2 0 4275 4319 688368171 688368127 6.990000e-09 73.1
21 TraesCS3A01G277900 chr7A 87.302 63 6 2 4263 4323 661638912 661638850 2.520000e-08 71.3
22 TraesCS3A01G277900 chr1D 97.619 42 1 0 4275 4316 411590277 411590236 6.990000e-09 73.1
23 TraesCS3A01G277900 chr2B 93.478 46 3 0 4273 4318 796974866 796974911 9.050000e-08 69.4


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 TraesCS3A01G277900 chr3A 507468897 507473932 5035 True 9300.0 9300 100.000000 1 5036 1 chr3A.!!$R1 5035
1 TraesCS3A01G277900 chr3B 501390924 501395993 5069 True 3916.5 6911 92.272500 9 5025 2 chr3B.!!$R1 5016
2 TraesCS3A01G277900 chr3B 8469306 8470277 971 False 673.5 1225 91.745500 474 1493 2 chr3B.!!$F1 1019
3 TraesCS3A01G277900 chr3D 385427354 385431333 3979 True 1898.0 4180 92.210333 1 5036 3 chr3D.!!$R1 5035
4 TraesCS3A01G277900 chr3D 6814623 6815509 886 False 1275.0 1275 92.531000 474 1369 1 chr3D.!!$F1 895
5 TraesCS3A01G277900 chr4B 23692370 23693373 1003 True 1251.0 1251 89.165000 480 1484 1 chr4B.!!$R1 1004
6 TraesCS3A01G277900 chr6D 42403836 42404844 1008 False 1177.0 1177 87.759000 475 1484 1 chr6D.!!$F1 1009
7 TraesCS3A01G277900 chrUn 88308282 88309298 1016 True 1136.0 1136 86.824000 477 1493 1 chrUn.!!$R2 1016
8 TraesCS3A01G277900 chrUn 88262452 88263469 1017 True 1133.0 1133 86.739000 476 1493 1 chrUn.!!$R1 1017
9 TraesCS3A01G277900 chr5A 12185379 12187508 2129 True 595.5 1116 90.797000 474 1493 2 chr5A.!!$R2 1019
10 TraesCS3A01G277900 chr4A 647268346 647268919 573 False 695.0 695 88.542000 910 1484 1 chr4A.!!$F1 574

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
959 976 1.268743 GGACAAATAAGCCGCATCAGC 60.269 52.381 0.0 0.00 37.42 4.26 F
2154 3302 0.744874 CTCTTCCTATTGACGGCCGA 59.255 55.000 35.9 10.61 0.00 5.54 F
3162 4310 0.179018 CCCCACCCGATGATTCTTCC 60.179 60.000 0.0 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2600 3748 0.174389 CTGTGGGATGTCTGTCTCCG 59.826 60.0 0.00 0.0 31.95 4.63 R
3832 4980 0.179129 CCATGTTCCATTTCGGCAGC 60.179 55.0 0.00 0.0 33.14 5.25 R
4960 6190 0.672401 TTTCTTCCTTGCTACGGCGG 60.672 55.0 13.24 0.0 42.25 6.13 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
54 55 7.358770 TCAATGAAAATCCCTTTTGTCTGAA 57.641 32.000 0.00 0.00 34.73 3.02
55 56 7.965718 TCAATGAAAATCCCTTTTGTCTGAAT 58.034 30.769 0.00 0.00 34.73 2.57
56 57 9.087871 TCAATGAAAATCCCTTTTGTCTGAATA 57.912 29.630 0.00 0.00 34.73 1.75
57 58 9.362539 CAATGAAAATCCCTTTTGTCTGAATAG 57.637 33.333 0.00 0.00 34.73 1.73
112 113 5.830912 TGTAAAATGCTGGTTTCTTGTCTG 58.169 37.500 0.00 0.00 0.00 3.51
144 145 8.485976 AAGAAAATTGCTCAGTCAGACTATAC 57.514 34.615 1.67 0.00 0.00 1.47
154 157 7.433719 GCTCAGTCAGACTATACACATGTTTAG 59.566 40.741 1.67 7.66 36.22 1.85
248 252 1.606668 GTTCCGTGGAGCAACATTTGA 59.393 47.619 0.00 0.00 0.00 2.69
367 372 7.504922 TTGTATATGCTTCGTTTCATTTTGC 57.495 32.000 0.00 0.00 0.00 3.68
448 453 2.817258 TCACACCGTCCATTGGATTTTC 59.183 45.455 9.01 0.00 32.73 2.29
702 711 2.106338 ACGAATATCCATCATGGTGCCA 59.894 45.455 2.79 0.00 39.03 4.92
941 951 2.092861 TGGAACTTTCACCTGTTTCGGA 60.093 45.455 0.00 0.00 0.00 4.55
959 976 1.268743 GGACAAATAAGCCGCATCAGC 60.269 52.381 0.00 0.00 37.42 4.26
1061 1078 1.694696 GACACAGGTGTTCTTCCCTCT 59.305 52.381 6.51 0.00 45.05 3.69
1132 1149 4.514066 GTGTTAGGAAATGAACAGACCGTT 59.486 41.667 0.00 0.00 41.86 4.44
1133 1150 5.008316 GTGTTAGGAAATGAACAGACCGTTT 59.992 40.000 0.00 0.00 38.19 3.60
1369 1387 3.044156 ACTGCATGGTACTCATCCTCAT 58.956 45.455 0.00 0.00 32.92 2.90
1489 2636 5.595952 CCAAAATTTCTGATCTTCCTAGGGG 59.404 44.000 9.46 2.49 0.00 4.79
1498 2645 3.993658 TCTTCCTAGGGGCTTCTATGA 57.006 47.619 9.46 0.00 0.00 2.15
1729 2876 2.417651 CCATGTTGCTTGTTATGCAGGG 60.418 50.000 0.00 0.00 41.71 4.45
1815 2962 6.677781 TTTTGGCGATCAGGTTAATCTAAG 57.322 37.500 0.00 0.00 0.00 2.18
1821 2968 5.815740 GCGATCAGGTTAATCTAAGGACAAA 59.184 40.000 0.00 0.00 0.00 2.83
1848 2995 9.878599 AAACTTTGTCATATTTCGTAGTTGAAG 57.121 29.630 0.00 0.00 0.00 3.02
1852 2999 5.810587 TGTCATATTTCGTAGTTGAAGGAGC 59.189 40.000 0.00 0.00 0.00 4.70
2109 3257 2.100197 TCTGGGGAGATGACAGTTACG 58.900 52.381 0.00 0.00 34.02 3.18
2124 3272 2.484264 AGTTACGCTTCAAGATGTTGCC 59.516 45.455 0.00 0.00 33.23 4.52
2154 3302 0.744874 CTCTTCCTATTGACGGCCGA 59.255 55.000 35.90 10.61 0.00 5.54
2172 3320 2.229784 CCGACCGGTTTGTTCTAGTACT 59.770 50.000 9.42 0.00 0.00 2.73
2225 3373 4.614475 TGTCTAGGTCATGATCCAAGAGT 58.386 43.478 1.24 0.00 0.00 3.24
2448 3596 1.072266 TTGGAACATACAGCTGGGGT 58.928 50.000 19.93 10.00 39.30 4.95
2514 3662 3.308688 CCTCCTCCCACAACATGAAGAAT 60.309 47.826 0.00 0.00 0.00 2.40
2600 3748 0.593773 GCTCGATCTTCCTCAGTCGC 60.594 60.000 0.00 0.00 34.33 5.19
2898 4046 0.248215 GGCTTCGTCAATGCATTCCG 60.248 55.000 9.53 14.65 0.00 4.30
2940 4088 6.807230 CCCTACAGACATTACATCGTATTAGC 59.193 42.308 0.00 0.00 0.00 3.09
2976 4124 2.552315 GCGTGAAAATTGGGAAGAGACA 59.448 45.455 0.00 0.00 0.00 3.41
3031 4179 0.464036 ACAGCGCATATTTCGGGAGA 59.536 50.000 11.47 0.00 0.00 3.71
3041 4189 4.521559 TCGGGAGACTGAGCAGTT 57.478 55.556 4.42 0.00 42.04 3.16
3096 4244 2.360726 TCTGGAGCTACACGGCGA 60.361 61.111 16.62 0.00 37.29 5.54
3159 4307 2.415983 TATCCCCACCCGATGATTCT 57.584 50.000 0.00 0.00 0.00 2.40
3162 4310 0.179018 CCCCACCCGATGATTCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
3321 4469 6.109156 TGAAGCTTGTCCAAGTAGTTCATA 57.891 37.500 2.10 0.00 40.45 2.15
3334 4482 9.770097 CCAAGTAGTTCATACATACTGAATCAT 57.230 33.333 0.00 0.00 36.79 2.45
3533 4681 2.519013 GGCTCCACCTTTTGATTCAGT 58.481 47.619 0.00 0.00 34.51 3.41
3534 4682 2.489722 GGCTCCACCTTTTGATTCAGTC 59.510 50.000 0.00 0.00 34.51 3.51
3537 4685 3.486383 TCCACCTTTTGATTCAGTCACC 58.514 45.455 0.00 0.00 36.32 4.02
3547 4695 0.396435 TTCAGTCACCGGCTCACATT 59.604 50.000 0.00 0.00 0.00 2.71
3555 4703 1.376424 CGGCTCACATTGTGGCTCT 60.376 57.895 21.56 0.00 34.78 4.09
3562 4710 0.959372 ACATTGTGGCTCTGCTGCTC 60.959 55.000 0.00 0.00 0.00 4.26
3563 4711 1.378250 ATTGTGGCTCTGCTGCTCC 60.378 57.895 0.00 0.00 0.00 4.70
3570 4718 1.837789 CTCTGCTGCTCCCCATCAT 59.162 57.895 0.00 0.00 0.00 2.45
3574 4722 1.276859 TGCTGCTCCCCATCATGAGT 61.277 55.000 0.09 0.00 0.00 3.41
3635 4783 4.536090 TGACAATCAAGAGGGTGAATACCT 59.464 41.667 0.00 0.00 46.66 3.08
3657 4805 2.611518 GAAGATGAGGACCTTCACACG 58.388 52.381 0.00 0.00 38.80 4.49
3679 4827 3.316573 GAGCAGGCTACGTTGGGCT 62.317 63.158 10.58 10.58 40.24 5.19
3681 4829 1.971695 GCAGGCTACGTTGGGCTTT 60.972 57.895 13.05 0.00 37.49 3.51
3692 4840 1.824852 GTTGGGCTTTGAACCTATGGG 59.175 52.381 0.00 0.00 38.88 4.00
3695 4843 1.474330 GGCTTTGAACCTATGGGTGG 58.526 55.000 0.00 0.00 46.67 4.61
3698 4846 1.638589 CTTTGAACCTATGGGTGGGGA 59.361 52.381 0.00 0.00 46.67 4.81
3704 4852 0.707616 CCTATGGGTGGGGAAAACCA 59.292 55.000 0.00 0.00 42.91 3.67
3720 4868 2.544359 CACCGCGTCGACAGTTTG 59.456 61.111 17.16 3.11 0.00 2.93
3733 4881 2.914379 AGTTTGCTACTGGACGTGC 58.086 52.632 0.00 0.00 35.19 5.34
3750 4898 0.927537 TGCACGAAAACTGTGACTCG 59.072 50.000 0.00 5.28 39.73 4.18
3831 4979 3.053842 AGGATGTTGATCAAGCTGGACAT 60.054 43.478 8.80 8.29 0.00 3.06
3832 4980 3.066342 GGATGTTGATCAAGCTGGACATG 59.934 47.826 8.80 0.00 0.00 3.21
3917 5065 2.852495 TTCGATGTTGCGCCCTCTCC 62.852 60.000 4.18 0.00 0.00 3.71
3918 5066 2.586792 GATGTTGCGCCCTCTCCT 59.413 61.111 4.18 0.00 0.00 3.69
3919 5067 1.522580 GATGTTGCGCCCTCTCCTC 60.523 63.158 4.18 0.00 0.00 3.71
3994 5145 1.139947 GAAGACGCGGAGGAGGAAG 59.860 63.158 12.47 0.00 0.00 3.46
3997 5148 3.398353 GACGCGGAGGAGGAAGACG 62.398 68.421 12.47 0.00 0.00 4.18
4014 5165 2.813179 CGACAGCGGCTGTAATGGC 61.813 63.158 33.45 20.02 45.44 4.40
4038 5189 2.356125 CCCTTCCTCACACCCATAGTTG 60.356 54.545 0.00 0.00 0.00 3.16
4049 5200 4.532126 ACACCCATAGTTGATCTGTCTCAA 59.468 41.667 0.00 0.00 32.84 3.02
4092 5243 1.601430 GATGCCGATTCCAGCTTCTTC 59.399 52.381 0.00 0.00 32.15 2.87
4137 5288 1.075542 TGTAGTTGATGCCGCTTTCG 58.924 50.000 0.00 0.00 0.00 3.46
4180 5331 6.733280 GCGTTTCATTTTTGCTGACATTATTG 59.267 34.615 0.00 0.00 0.00 1.90
4183 5334 5.177326 TCATTTTTGCTGACATTATTGGGC 58.823 37.500 0.00 0.00 0.00 5.36
4196 5347 1.559368 ATTGGGCTTGTTATGCAGCA 58.441 45.000 0.00 0.00 0.00 4.41
4202 5353 3.431207 GGGCTTGTTATGCAGCATGATTT 60.431 43.478 18.81 0.00 39.69 2.17
4283 5487 9.952030 TCTACTACTCCTCTGTATAATGATCTG 57.048 37.037 0.00 0.00 0.00 2.90
4290 5494 5.053140 TCTGTATAATGATCTGAGCGCTC 57.947 43.478 30.42 30.42 0.00 5.03
4299 5503 7.593875 AATGATCTGAGCGCTCTTATATTTC 57.406 36.000 35.27 21.40 0.00 2.17
4340 5544 9.646522 ACTTATATAGGCAAAATTGGAGATTGT 57.353 29.630 0.00 0.00 0.00 2.71
4395 5602 1.228533 TTACACCTTTTTCCGCGTCC 58.771 50.000 4.92 0.00 0.00 4.79
4412 5619 2.034685 CGTCCGAATATCAGCTTCAGGA 59.965 50.000 0.00 0.00 0.00 3.86
4416 5623 4.405680 TCCGAATATCAGCTTCAGGAGAAA 59.594 41.667 0.00 0.00 32.35 2.52
4421 5628 7.439356 CGAATATCAGCTTCAGGAGAAAATGTA 59.561 37.037 0.00 0.00 32.35 2.29
4423 5630 4.579869 TCAGCTTCAGGAGAAAATGTACC 58.420 43.478 0.00 0.00 32.35 3.34
4498 5713 1.662044 CCAGCAGTTGGGCTTTCAC 59.338 57.895 0.00 0.00 42.71 3.18
4559 5774 1.153489 CAGAGTCCAGTGCGATGGG 60.153 63.158 7.13 0.00 41.01 4.00
4570 5785 2.393768 GCGATGGGCACACAGACAG 61.394 63.158 0.00 0.00 42.87 3.51
4571 5786 1.004560 CGATGGGCACACAGACAGT 60.005 57.895 0.00 0.00 0.00 3.55
4736 5952 2.168496 CATGGATGGGATCATGAAGGC 58.832 52.381 0.00 0.00 42.25 4.35
4787 6009 3.058432 GGCCCTACTTTTGTTTTCTCGTC 60.058 47.826 0.00 0.00 0.00 4.20
4807 6029 3.624861 GTCTTGATTTGATGATCGTGCCT 59.375 43.478 0.00 0.00 0.00 4.75
4817 6039 3.612247 ATCGTGCCTGGCGCTCTTT 62.612 57.895 27.76 8.68 36.86 2.52
4818 6040 3.357079 CGTGCCTGGCGCTCTTTT 61.357 61.111 27.76 0.00 36.86 2.27
4819 6041 2.563427 GTGCCTGGCGCTCTTTTC 59.437 61.111 24.33 0.00 38.78 2.29
4923 6145 1.066908 CCAGAGATCGAGCAGAAGGTC 59.933 57.143 2.38 0.00 38.87 3.85
4951 6181 1.466950 TCGTGTTTCATTCATTCGCCC 59.533 47.619 0.00 0.00 0.00 6.13
4960 6190 3.311322 TCATTCATTCGCCCGTGTAATTC 59.689 43.478 0.00 0.00 0.00 2.17
4961 6191 1.658994 TCATTCGCCCGTGTAATTCC 58.341 50.000 0.00 0.00 0.00 3.01
4965 6195 3.569690 GCCCGTGTAATTCCGCCG 61.570 66.667 0.00 0.00 0.00 6.46
4966 6196 2.125431 CCCGTGTAATTCCGCCGT 60.125 61.111 0.00 0.00 0.00 5.68
4967 6197 1.141449 CCCGTGTAATTCCGCCGTA 59.859 57.895 0.00 0.00 0.00 4.02
4969 6199 1.485032 CCGTGTAATTCCGCCGTAGC 61.485 60.000 0.00 0.00 0.00 3.58
4999 6229 2.401583 TGTCCATGGTGTATCTGTGC 57.598 50.000 12.58 0.00 0.00 4.57
5010 6240 4.700213 GGTGTATCTGTGCTGTTTTACCAT 59.300 41.667 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 6.969043 TGACCAGTGTCCCATTTTTATCTAT 58.031 36.000 0.00 0.00 41.01 1.98
55 56 6.381498 TGACCAGTGTCCCATTTTTATCTA 57.619 37.500 0.00 0.00 41.01 1.98
56 57 5.255397 TGACCAGTGTCCCATTTTTATCT 57.745 39.130 0.00 0.00 41.01 1.98
57 58 4.142381 GCTGACCAGTGTCCCATTTTTATC 60.142 45.833 0.00 0.00 41.01 1.75
112 113 5.413833 TGACTGAGCAATTTTCTTCATCCTC 59.586 40.000 0.00 0.00 0.00 3.71
144 145 4.573900 AGAGAGCAACTCCTAAACATGTG 58.426 43.478 0.00 0.00 45.96 3.21
248 252 5.535030 GTCAACTGTGAGTTATTTTCCCCTT 59.465 40.000 0.00 0.00 36.03 3.95
309 314 6.976925 GGCATATGCTTAAAAGATATGGCATC 59.023 38.462 26.12 0.16 42.74 3.91
344 349 5.736824 CGCAAAATGAAACGAAGCATATACA 59.263 36.000 0.00 0.00 0.00 2.29
367 372 7.306866 GCTTATATACAAGAAAGGAACTCTGCG 60.307 40.741 0.00 0.00 38.49 5.18
448 453 5.277876 GCCATAGATGATCACAGCAAGAAAG 60.278 44.000 0.00 0.00 34.60 2.62
702 711 3.461773 ACGCGCTGTCCCTGCTAT 61.462 61.111 5.73 0.00 0.00 2.97
959 976 3.788797 GCAAGGAACTGTCAAACTCAACG 60.789 47.826 0.00 0.00 40.86 4.10
1061 1078 5.118990 CAGAAACTTCAGTTGAGTGGAAGA 58.881 41.667 7.54 0.00 40.28 2.87
1132 1149 4.360951 AGGACGGTAAGGAAACAATCAA 57.639 40.909 0.00 0.00 0.00 2.57
1133 1150 4.069304 CAAGGACGGTAAGGAAACAATCA 58.931 43.478 0.00 0.00 0.00 2.57
1369 1387 3.521531 TGTAGCATCTGTGGGAATGGTAA 59.478 43.478 0.00 0.00 0.00 2.85
1489 2636 3.944015 AGTTGCCAGAATGTCATAGAAGC 59.056 43.478 0.00 0.00 0.00 3.86
1498 2645 5.255687 TCATTACATCAGTTGCCAGAATGT 58.744 37.500 0.00 0.00 0.00 2.71
1729 2876 1.823041 GGATGAAGGCTCTGCAGGC 60.823 63.158 15.13 15.77 45.92 4.85
1738 2885 3.447586 TGAGTAGTGTACTGGATGAAGGC 59.552 47.826 0.00 0.00 39.59 4.35
1878 3025 6.995091 GGGCCTGCAATAATAGAGAATATAGG 59.005 42.308 0.84 0.00 0.00 2.57
2124 3272 6.088824 GTCAATAGGAAGAGCAAACAACATG 58.911 40.000 0.00 0.00 0.00 3.21
2154 3302 4.525487 TGATCAGTACTAGAACAAACCGGT 59.475 41.667 0.00 0.00 0.00 5.28
2172 3320 4.043686 ACCATCTGCCCATAATCATGATCA 59.956 41.667 9.06 0.00 33.67 2.92
2225 3373 4.778958 AGGATTTTCCAGGCATTGATTGAA 59.221 37.500 0.00 0.00 39.61 2.69
2448 3596 4.408821 AATGCGAGGGCTGCGGAA 62.409 61.111 0.00 0.00 40.82 4.30
2514 3662 5.957771 AGAGAAGCAATGAACCACCTATA 57.042 39.130 0.00 0.00 0.00 1.31
2600 3748 0.174389 CTGTGGGATGTCTGTCTCCG 59.826 60.000 0.00 0.00 31.95 4.63
2898 4046 0.675837 GGGTAGGTCGAAAAGGTGGC 60.676 60.000 0.00 0.00 0.00 5.01
2940 4088 2.396955 ACGCTCTCTACCACGTCGG 61.397 63.158 0.00 2.92 42.50 4.79
2976 4124 7.238305 TCCCATTCCTGAATATACTCATGATGT 59.762 37.037 0.00 0.00 0.00 3.06
3031 4179 5.068636 AGATGACAAATCAAACTGCTCAGT 58.931 37.500 0.00 0.00 39.04 3.41
3159 4307 3.007506 TGGCTTTGTACTGAAGATCGGAA 59.992 43.478 12.01 0.00 0.00 4.30
3162 4310 3.997021 ACTTGGCTTTGTACTGAAGATCG 59.003 43.478 12.01 0.00 0.00 3.69
3244 4392 7.624360 AAAACATTAGTTCAGTCAACTGTGA 57.376 32.000 9.82 0.00 45.60 3.58
3533 4681 1.302431 CCACAATGTGAGCCGGTGA 60.302 57.895 15.91 0.00 35.23 4.02
3534 4682 2.981560 GCCACAATGTGAGCCGGTG 61.982 63.158 15.91 0.00 35.23 4.94
3537 4685 1.376424 AGAGCCACAATGTGAGCCG 60.376 57.895 15.91 0.00 35.23 5.52
3547 4695 4.025858 GGGAGCAGCAGAGCCACA 62.026 66.667 0.00 0.00 34.23 4.17
3555 4703 1.276859 ACTCATGATGGGGAGCAGCA 61.277 55.000 0.00 0.00 34.48 4.41
3562 4710 5.121811 CAAAAGTAGAGACTCATGATGGGG 58.878 45.833 5.02 0.00 33.58 4.96
3563 4711 4.574013 GCAAAAGTAGAGACTCATGATGGG 59.426 45.833 5.02 0.00 33.58 4.00
3570 4718 4.752101 GCTTCAAGCAAAAGTAGAGACTCA 59.248 41.667 3.89 0.00 41.89 3.41
3574 4722 4.960938 TCAGCTTCAAGCAAAAGTAGAGA 58.039 39.130 13.10 0.00 45.56 3.10
3635 4783 2.303022 GTGTGAAGGTCCTCATCTTCCA 59.697 50.000 0.00 0.00 38.76 3.53
3657 4805 1.741770 CAACGTAGCCTGCTCCACC 60.742 63.158 0.00 0.00 0.00 4.61
3693 4841 4.192453 ACGCGGTGGTTTTCCCCA 62.192 61.111 12.47 0.00 39.73 4.96
3695 4843 3.719144 CGACGCGGTGGTTTTCCC 61.719 66.667 12.47 0.00 39.73 3.97
3698 4846 2.202905 TGTCGACGCGGTGGTTTT 60.203 55.556 12.47 0.00 0.00 2.43
3704 4852 2.410638 TAGCAAACTGTCGACGCGGT 62.411 55.000 12.47 6.93 0.00 5.68
3706 4854 1.002250 AGTAGCAAACTGTCGACGCG 61.002 55.000 11.62 3.53 36.93 6.01
3720 4868 0.942410 TTTCGTGCACGTCCAGTAGC 60.942 55.000 35.74 0.00 40.80 3.58
3729 4877 0.650512 AGTCACAGTTTTCGTGCACG 59.349 50.000 32.76 32.76 41.45 5.34
3733 4881 0.232303 GCCGAGTCACAGTTTTCGTG 59.768 55.000 0.00 0.00 35.63 4.35
3782 4930 5.182001 GTGTGCTGTGGAATATCAAAGTCTT 59.818 40.000 0.00 0.00 0.00 3.01
3831 4979 0.527113 CATGTTCCATTTCGGCAGCA 59.473 50.000 0.00 0.00 33.14 4.41
3832 4980 0.179129 CCATGTTCCATTTCGGCAGC 60.179 55.000 0.00 0.00 33.14 5.25
3856 5004 0.322546 GACATGGGTTCCACCACCTC 60.323 60.000 0.00 0.00 44.72 3.85
3917 5065 2.290122 ATCGGCGCTCTCTTGTGGAG 62.290 60.000 7.64 0.00 43.12 3.86
3918 5066 2.351244 ATCGGCGCTCTCTTGTGGA 61.351 57.895 7.64 0.00 0.00 4.02
3919 5067 2.169789 CATCGGCGCTCTCTTGTGG 61.170 63.158 7.64 0.00 0.00 4.17
3994 5145 1.421410 CCATTACAGCCGCTGTCGTC 61.421 60.000 28.95 0.00 41.21 4.20
3997 5148 2.813179 CGCCATTACAGCCGCTGTC 61.813 63.158 28.95 13.55 41.21 3.51
4014 5165 4.410400 GGGTGTGAGGAAGGGGCG 62.410 72.222 0.00 0.00 0.00 6.13
4038 5189 4.704540 TCCTCTCTGACTTTGAGACAGATC 59.295 45.833 9.79 0.00 43.73 2.75
4049 5200 5.541868 TCATGTCTCTTTTCCTCTCTGACTT 59.458 40.000 0.00 0.00 0.00 3.01
4092 5243 7.724490 TCTAATCCCTACATATCTGGACATG 57.276 40.000 0.00 0.00 0.00 3.21
4137 5288 1.450312 CCAATCACGGCAGACTCCC 60.450 63.158 0.00 0.00 0.00 4.30
4180 5331 1.105457 TCATGCTGCATAACAAGCCC 58.895 50.000 15.78 0.00 0.00 5.19
4183 5334 4.497966 CGACAAATCATGCTGCATAACAAG 59.502 41.667 15.78 8.23 0.00 3.16
4254 5416 9.733556 ATCATTATACAGAGGAGTAGTAGAGTG 57.266 37.037 0.00 0.00 0.00 3.51
4276 5480 6.934056 AGAAATATAAGAGCGCTCAGATCAT 58.066 36.000 36.87 22.66 37.82 2.45
4283 5487 7.863375 TCTCTGTAAAGAAATATAAGAGCGCTC 59.137 37.037 30.01 30.01 0.00 5.03
4355 5559 8.355169 GTGTAAATACAACACCTATCTCCGATA 58.645 37.037 0.00 0.00 41.10 2.92
4370 5577 4.275443 ACGCGGAAAAAGGTGTAAATACAA 59.725 37.500 12.47 0.00 38.04 2.41
4383 5590 2.605818 CTGATATTCGGACGCGGAAAAA 59.394 45.455 12.47 0.00 0.00 1.94
4384 5591 2.198406 CTGATATTCGGACGCGGAAAA 58.802 47.619 12.47 0.00 0.00 2.29
4385 5592 1.847818 CTGATATTCGGACGCGGAAA 58.152 50.000 12.47 0.00 0.00 3.13
4395 5602 6.259608 ACATTTTCTCCTGAAGCTGATATTCG 59.740 38.462 0.00 0.00 33.28 3.34
4433 5640 0.795085 CTTCGCCTGAAGTTGCTCAG 59.205 55.000 0.00 0.00 45.38 3.35
4458 5665 2.369394 GGGCCACATTTTCTACTCCTG 58.631 52.381 4.39 0.00 0.00 3.86
4525 5740 2.360852 TGTCTCGGACCGTCTCCC 60.361 66.667 14.79 0.00 35.21 4.30
4526 5741 1.370587 CTCTGTCTCGGACCGTCTCC 61.371 65.000 14.79 1.36 35.33 3.71
4540 5755 1.593787 CCATCGCACTGGACTCTGT 59.406 57.895 0.00 0.00 38.69 3.41
4736 5952 2.579787 GGACGGTGTGATCGAGCG 60.580 66.667 12.94 12.94 40.12 5.03
4787 6009 3.242969 CCAGGCACGATCATCAAATCAAG 60.243 47.826 0.00 0.00 0.00 3.02
4807 6029 2.293399 GGAAAAGAAGAAAAGAGCGCCA 59.707 45.455 2.29 0.00 0.00 5.69
4817 6039 1.512156 GCGCACGGGGAAAAGAAGAA 61.512 55.000 0.30 0.00 0.00 2.52
4818 6040 1.964373 GCGCACGGGGAAAAGAAGA 60.964 57.895 0.30 0.00 0.00 2.87
4819 6041 2.561373 GCGCACGGGGAAAAGAAG 59.439 61.111 0.30 0.00 0.00 2.85
4850 6072 4.776322 TGCGCAACAGGGGATCGG 62.776 66.667 8.16 0.00 0.00 4.18
4923 6145 5.648033 ATGAATGAAACACGATCGATCAG 57.352 39.130 24.34 17.80 0.00 2.90
4951 6181 0.802994 TGCTACGGCGGAATTACACG 60.803 55.000 13.24 0.58 42.25 4.49
4960 6190 0.672401 TTTCTTCCTTGCTACGGCGG 60.672 55.000 13.24 0.00 42.25 6.13
4961 6191 1.062587 CATTTCTTCCTTGCTACGGCG 59.937 52.381 4.80 4.80 42.25 6.46
4965 6195 4.096984 CCATGGACATTTCTTCCTTGCTAC 59.903 45.833 5.56 0.00 37.10 3.58
4966 6196 4.263905 ACCATGGACATTTCTTCCTTGCTA 60.264 41.667 21.47 0.00 37.10 3.49
4967 6197 3.094572 CCATGGACATTTCTTCCTTGCT 58.905 45.455 5.56 0.00 37.10 3.91
4969 6199 3.828451 ACACCATGGACATTTCTTCCTTG 59.172 43.478 21.47 3.47 37.81 3.61
4999 6229 8.981647 CAAAATTTCAGGAAGATGGTAAAACAG 58.018 33.333 0.00 0.00 0.00 3.16
5010 6240 4.975631 TCGGGTACAAAATTTCAGGAAGA 58.024 39.130 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.