Multiple sequence alignment - TraesCS5A01G099500

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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 TraesCS5A01G099500 chr5A 100.000 4544 0 0 1 4544 142753305 142748762 0.000000e+00 8392.0
1 TraesCS5A01G099500 chr5D 95.421 3975 114 36 1 3932 126959979 126956030 0.000000e+00 6270.0
2 TraesCS5A01G099500 chr5B 95.232 2517 84 11 1 2509 140099215 140101703 0.000000e+00 3951.0
3 TraesCS5A01G099500 chr5B 96.092 1177 37 3 2505 3675 140114557 140115730 0.000000e+00 1910.0
4 TraesCS5A01G099500 chr6D 86.642 539 71 1 3964 4501 296364698 296364160 3.030000e-166 595.0
5 TraesCS5A01G099500 chr4D 74.392 781 176 22 1778 2546 475954163 475953395 3.410000e-81 313.0
6 TraesCS5A01G099500 chr4A 74.069 779 182 19 1778 2546 682991851 682991083 7.390000e-78 302.0
7 TraesCS5A01G099500 chr2D 90.541 74 7 0 1556 1629 89428898 89428825 1.040000e-16 99.0
8 TraesCS5A01G099500 chr2D 100.000 31 0 0 1466 1496 629420423 629420393 1.770000e-04 58.4
9 TraesCS5A01G099500 chr2D 80.519 77 11 4 1466 1540 628639720 628639646 6.350000e-04 56.5
10 TraesCS5A01G099500 chr2B 81.818 77 10 4 1466 1540 771926462 771926536 1.360000e-05 62.1
11 TraesCS5A01G099500 chr2B 88.000 50 5 1 1447 1496 772823716 772823668 1.770000e-04 58.4
12 TraesCS5A01G099500 chr2A 81.818 77 10 4 1466 1540 758715108 758715182 1.360000e-05 62.1


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 TraesCS5A01G099500 chr5A 142748762 142753305 4543 True 8392 8392 100.000 1 4544 1 chr5A.!!$R1 4543
1 TraesCS5A01G099500 chr5D 126956030 126959979 3949 True 6270 6270 95.421 1 3932 1 chr5D.!!$R1 3931
2 TraesCS5A01G099500 chr5B 140099215 140101703 2488 False 3951 3951 95.232 1 2509 1 chr5B.!!$F1 2508
3 TraesCS5A01G099500 chr5B 140114557 140115730 1173 False 1910 1910 96.092 2505 3675 1 chr5B.!!$F2 1170
4 TraesCS5A01G099500 chr6D 296364160 296364698 538 True 595 595 86.642 3964 4501 1 chr6D.!!$R1 537
5 TraesCS5A01G099500 chr4D 475953395 475954163 768 True 313 313 74.392 1778 2546 1 chr4D.!!$R1 768
6 TraesCS5A01G099500 chr4A 682991083 682991851 768 True 302 302 74.069 1778 2546 1 chr4A.!!$R1 768

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
116 117 0.745468 GGTCGCTTCTAAGACCGGAT 59.255 55.000 9.46 0.00 46.08 4.18 F
556 561 1.202663 AGGTAGCTAGCATCGACTCGA 60.203 52.381 24.01 3.06 41.13 4.04 F
1087 1107 0.396435 AGAACAACGCCTCACATCCA 59.604 50.000 0.00 0.00 0.00 3.41 F
1088 1108 0.798776 GAACAACGCCTCACATCCAG 59.201 55.000 0.00 0.00 0.00 3.86 F
2469 2497 0.826062 TCATCATCAAGAGGCTCGCA 59.174 50.000 9.22 0.00 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1079 1099 1.951602 GCAATGCTATGCTGGATGTGA 59.048 47.619 0.00 0.00 43.06 3.58 R
2469 2497 0.107897 TGCAGTTGTCGTGGTCTTGT 60.108 50.000 0.00 0.00 0.00 3.16 R
2775 2803 2.045926 GCGTCCTTGTCCATGGCT 60.046 61.111 6.96 0.00 0.00 4.75 R
2785 2813 2.214181 ATCTTCTCACGCGCGTCCTT 62.214 55.000 35.61 9.14 0.00 3.36 R
3960 4022 0.032615 ACTTGTTTGGGTGAAGGGCA 60.033 50.000 0.00 0.00 0.00 5.36 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
91 92 2.156917 TGAATGCTTTGTCTGGCTCAG 58.843 47.619 0.00 0.00 0.00 3.35
115 116 2.187073 GGTCGCTTCTAAGACCGGA 58.813 57.895 9.46 0.00 46.08 5.14
116 117 0.745468 GGTCGCTTCTAAGACCGGAT 59.255 55.000 9.46 0.00 46.08 4.18
117 118 1.952296 GGTCGCTTCTAAGACCGGATA 59.048 52.381 9.46 0.00 46.08 2.59
118 119 2.030981 GGTCGCTTCTAAGACCGGATAG 60.031 54.545 9.46 7.94 46.08 2.08
259 264 6.910191 ACATAGACCCACCATTCATTTATCA 58.090 36.000 0.00 0.00 0.00 2.15
279 284 3.563808 TCAATTTGGACTGAAGAACACCG 59.436 43.478 0.00 0.00 0.00 4.94
281 286 3.823281 TTTGGACTGAAGAACACCGTA 57.177 42.857 0.00 0.00 0.00 4.02
422 427 6.262944 TGACTTTGCCTAATCGCATGATTAAT 59.737 34.615 0.00 0.00 44.35 1.40
464 469 2.647529 TACGCATGATGAACGACACT 57.352 45.000 0.00 0.00 0.00 3.55
483 488 3.288809 CTTGCAAGCCAAGGTTTAGTC 57.711 47.619 14.65 0.00 45.78 2.59
484 489 2.656947 TGCAAGCCAAGGTTTAGTCT 57.343 45.000 0.00 0.00 0.00 3.24
525 530 6.106003 TCTCGATCTAGTCTCTAGATCATGC 58.894 44.000 29.64 15.05 46.25 4.06
555 560 1.231221 AGGTAGCTAGCATCGACTCG 58.769 55.000 24.01 0.00 0.00 4.18
556 561 1.202663 AGGTAGCTAGCATCGACTCGA 60.203 52.381 24.01 3.06 41.13 4.04
647 659 4.377021 AGGAAATTAATAGCGCGTCATGA 58.623 39.130 8.43 0.00 0.00 3.07
714 726 2.352229 CGCACAACGCTTGGTGTG 60.352 61.111 9.01 9.01 38.91 3.82
834 852 2.794028 GGAGAACCGATCCCGTCCC 61.794 68.421 0.00 0.00 0.00 4.46
1078 1098 2.612212 TCAAGAACTCAAGAACAACGCC 59.388 45.455 0.00 0.00 0.00 5.68
1079 1099 2.614057 CAAGAACTCAAGAACAACGCCT 59.386 45.455 0.00 0.00 0.00 5.52
1087 1107 0.396435 AGAACAACGCCTCACATCCA 59.604 50.000 0.00 0.00 0.00 3.41
1088 1108 0.798776 GAACAACGCCTCACATCCAG 59.201 55.000 0.00 0.00 0.00 3.86
1089 1109 1.237285 AACAACGCCTCACATCCAGC 61.237 55.000 0.00 0.00 0.00 4.85
1090 1110 1.672030 CAACGCCTCACATCCAGCA 60.672 57.895 0.00 0.00 0.00 4.41
1091 1111 1.028330 CAACGCCTCACATCCAGCAT 61.028 55.000 0.00 0.00 0.00 3.79
1097 1125 2.860009 CCTCACATCCAGCATAGCATT 58.140 47.619 0.00 0.00 0.00 3.56
1124 1152 4.334552 TGCATTGATCCAGTGTGTTGTAT 58.665 39.130 0.00 0.00 0.00 2.29
1152 1180 1.519455 GCTCGATCTTGGACACCGG 60.519 63.158 0.00 0.00 0.00 5.28
1724 1752 1.399714 ATGGATGCCTCGTCGTCTAA 58.600 50.000 0.00 0.00 0.00 2.10
1746 1774 2.544721 TGGAGCTGGAGATTGAAGAGT 58.455 47.619 0.00 0.00 0.00 3.24
2263 2291 4.457496 CGGCAGTCATGGAGCGGT 62.457 66.667 0.00 0.00 0.00 5.68
2415 2443 1.062685 CGTGTCGTCGCTGCTCTAT 59.937 57.895 0.00 0.00 0.00 1.98
2469 2497 0.826062 TCATCATCAAGAGGCTCGCA 59.174 50.000 9.22 0.00 0.00 5.10
2493 2521 1.029408 ACCACGACAACTGCAGCAAA 61.029 50.000 15.27 0.00 0.00 3.68
2649 2677 3.986006 GACACGACCGGGAGCACA 61.986 66.667 6.32 0.00 0.00 4.57
2654 2682 3.775654 GACCGGGAGCACAGGGAG 61.776 72.222 6.32 0.00 0.00 4.30
2785 2813 3.479203 CCCGGCTAGCCATGGACA 61.479 66.667 32.47 0.00 35.37 4.02
3562 3590 0.598158 GCCGAACTCCACGTGTGTTA 60.598 55.000 19.42 1.51 31.12 2.41
3563 3591 1.938016 GCCGAACTCCACGTGTGTTAT 60.938 52.381 19.42 4.11 31.12 1.89
3606 3634 2.670414 GAGCTGAAGACCAAGATTGTCG 59.330 50.000 0.00 0.00 0.00 4.35
3631 3665 4.210120 GTGTGCATATTTCGTTTGCCAAAA 59.790 37.500 0.00 0.00 35.51 2.44
3718 3765 8.715191 AAACTGAAAAATAAGAATGTGCACAA 57.285 26.923 25.72 7.20 0.00 3.33
3723 3770 7.387397 TGAAAAATAAGAATGTGCACAAATCCC 59.613 33.333 25.72 10.99 0.00 3.85
3775 3837 3.121738 ACAAGTCGACTGGGTTTTAGG 57.878 47.619 23.70 6.03 0.00 2.69
3782 3844 3.006537 TCGACTGGGTTTTAGGAAGACTG 59.993 47.826 0.00 0.00 0.00 3.51
3798 3860 8.056407 AGGAAGACTGCTATAAATTTGAAACC 57.944 34.615 0.00 0.00 0.00 3.27
3800 3862 6.436843 AGACTGCTATAAATTTGAAACCGG 57.563 37.500 0.00 0.00 0.00 5.28
3801 3863 4.993905 ACTGCTATAAATTTGAAACCGGC 58.006 39.130 0.00 0.00 0.00 6.13
3802 3864 4.705023 ACTGCTATAAATTTGAAACCGGCT 59.295 37.500 0.00 0.00 0.00 5.52
3803 3865 5.883673 ACTGCTATAAATTTGAAACCGGCTA 59.116 36.000 0.00 0.00 0.00 3.93
3804 3866 6.546034 ACTGCTATAAATTTGAAACCGGCTAT 59.454 34.615 0.00 0.00 0.00 2.97
3811 3873 2.672961 TGAAACCGGCTATGTCTCAG 57.327 50.000 0.00 0.00 0.00 3.35
3859 3921 1.547372 TCTTTACTCCACCGTGTAGCC 59.453 52.381 0.00 0.00 0.00 3.93
3874 3936 5.009710 CCGTGTAGCCTCATATTCTGTCTTA 59.990 44.000 0.00 0.00 0.00 2.10
3875 3937 6.294787 CCGTGTAGCCTCATATTCTGTCTTAT 60.295 42.308 0.00 0.00 0.00 1.73
3935 3997 4.976864 GGTTAAGACCCCAGAGTTAAACA 58.023 43.478 0.00 0.00 40.25 2.83
3936 3998 5.001874 GGTTAAGACCCCAGAGTTAAACAG 58.998 45.833 0.00 0.00 40.25 3.16
3937 3999 5.455755 GGTTAAGACCCCAGAGTTAAACAGT 60.456 44.000 0.00 0.00 40.25 3.55
3938 4000 3.771577 AGACCCCAGAGTTAAACAGTG 57.228 47.619 0.00 0.00 0.00 3.66
3939 4001 2.152016 GACCCCAGAGTTAAACAGTGC 58.848 52.381 0.00 0.00 0.00 4.40
3940 4002 1.202891 ACCCCAGAGTTAAACAGTGCC 60.203 52.381 0.00 0.00 0.00 5.01
3941 4003 1.534729 CCCAGAGTTAAACAGTGCCC 58.465 55.000 0.00 0.00 0.00 5.36
3942 4004 1.534729 CCAGAGTTAAACAGTGCCCC 58.465 55.000 0.00 0.00 0.00 5.80
3943 4005 1.534729 CAGAGTTAAACAGTGCCCCC 58.465 55.000 0.00 0.00 0.00 5.40
3944 4006 1.145571 AGAGTTAAACAGTGCCCCCA 58.854 50.000 0.00 0.00 0.00 4.96
3945 4007 1.497286 AGAGTTAAACAGTGCCCCCAA 59.503 47.619 0.00 0.00 0.00 4.12
3946 4008 1.886542 GAGTTAAACAGTGCCCCCAAG 59.113 52.381 0.00 0.00 0.00 3.61
3947 4009 0.317160 GTTAAACAGTGCCCCCAAGC 59.683 55.000 0.00 0.00 0.00 4.01
3948 4010 0.105964 TTAAACAGTGCCCCCAAGCA 60.106 50.000 0.00 0.00 41.46 3.91
3949 4011 0.105964 TAAACAGTGCCCCCAAGCAA 60.106 50.000 0.00 0.00 46.19 3.91
3950 4012 0.763986 AAACAGTGCCCCCAAGCAAT 60.764 50.000 0.00 0.00 46.19 3.56
3952 4014 2.999063 AGTGCCCCCAAGCAATGC 60.999 61.111 0.00 0.00 46.19 3.56
3953 4015 4.086547 GTGCCCCCAAGCAATGCC 62.087 66.667 0.00 0.00 46.19 4.40
3954 4016 4.319949 TGCCCCCAAGCAATGCCT 62.320 61.111 0.00 0.00 40.56 4.75
3955 4017 2.043046 GCCCCCAAGCAATGCCTA 60.043 61.111 0.00 0.00 0.00 3.93
3956 4018 1.458209 GCCCCCAAGCAATGCCTAT 60.458 57.895 0.00 0.00 0.00 2.57
3957 4019 1.050421 GCCCCCAAGCAATGCCTATT 61.050 55.000 0.00 0.00 0.00 1.73
3958 4020 1.499368 CCCCCAAGCAATGCCTATTT 58.501 50.000 0.00 0.00 0.00 1.40
3959 4021 1.413812 CCCCCAAGCAATGCCTATTTC 59.586 52.381 0.00 0.00 0.00 2.17
3960 4022 2.391678 CCCCAAGCAATGCCTATTTCT 58.608 47.619 0.00 0.00 0.00 2.52
3961 4023 2.101917 CCCCAAGCAATGCCTATTTCTG 59.898 50.000 0.00 0.00 0.00 3.02
3962 4024 2.482490 CCCAAGCAATGCCTATTTCTGC 60.482 50.000 0.00 0.00 0.00 4.26
3966 4028 1.758862 GCAATGCCTATTTCTGCCCTT 59.241 47.619 0.00 0.00 0.00 3.95
3971 4033 2.024306 GCCTATTTCTGCCCTTCACCC 61.024 57.143 0.00 0.00 0.00 4.61
3972 4034 1.284785 CCTATTTCTGCCCTTCACCCA 59.715 52.381 0.00 0.00 0.00 4.51
3977 4039 0.260230 TCTGCCCTTCACCCAAACAA 59.740 50.000 0.00 0.00 0.00 2.83
3983 4045 2.159114 CCCTTCACCCAAACAAGTTGTG 60.159 50.000 9.79 0.00 35.23 3.33
4005 4067 1.369209 CAACGACAAGCTGCAACGG 60.369 57.895 1.02 0.00 0.00 4.44
4020 4082 4.809496 CGGCAGGGCTGGAGCAAT 62.809 66.667 0.20 0.00 44.36 3.56
4045 4107 1.475403 TTTCTACCCTCTCTGCCTCG 58.525 55.000 0.00 0.00 0.00 4.63
4053 4115 0.753479 CTCTCTGCCTCGGGAGCTTA 60.753 60.000 0.00 0.00 33.42 3.09
4190 4252 1.873591 GGCAACTGACATCGTTGAAGT 59.126 47.619 10.80 1.08 43.28 3.01
4199 4261 3.390135 ACATCGTTGAAGTGATCGTTGT 58.610 40.909 0.00 0.00 33.47 3.32
4211 4273 0.667993 ATCGTTGTTGCAACACCTGG 59.332 50.000 31.17 19.23 38.92 4.45
4214 4276 1.388547 GTTGTTGCAACACCTGGAGA 58.611 50.000 31.17 12.70 38.92 3.71
4217 4279 1.142667 TGTTGCAACACCTGGAGATGA 59.857 47.619 27.96 0.63 33.17 2.92
4240 4302 4.030913 ACGGAAGGGAATCAAGTCTATCA 58.969 43.478 0.00 0.00 0.00 2.15
4246 4308 8.378565 GGAAGGGAATCAAGTCTATCATTATGA 58.621 37.037 0.00 0.00 0.00 2.15
4254 4316 8.969260 TCAAGTCTATCATTATGATTGTGCTT 57.031 30.769 13.25 14.91 38.26 3.91
4260 4322 5.979993 ATCATTATGATTGTGCTTTGGCAA 58.020 33.333 1.25 0.00 41.46 4.52
4261 4323 5.813672 ATCATTATGATTGTGCTTTGGCAAC 59.186 36.000 0.00 0.00 41.46 4.17
4302 4364 1.824230 TGCATTTTTCGGGCTAAGCAT 59.176 42.857 0.00 0.00 0.00 3.79
4318 4380 2.163390 CATGCGCTGGTCAGAGACG 61.163 63.158 9.73 0.00 32.65 4.18
4324 4386 1.290324 CTGGTCAGAGACGTGGTGG 59.710 63.158 0.00 0.00 32.65 4.61
4326 4388 2.048127 GTCAGAGACGTGGTGGCC 60.048 66.667 0.00 0.00 0.00 5.36
4327 4389 2.203640 TCAGAGACGTGGTGGCCT 60.204 61.111 3.32 0.00 0.00 5.19
4344 4406 1.377725 CTCAAGCCACCGAGCCATT 60.378 57.895 0.00 0.00 0.00 3.16
4350 4412 1.522092 CCACCGAGCCATTGAGCTA 59.478 57.895 0.00 0.00 45.15 3.32
4361 4423 4.552365 TGAGCTATGGCGCCAGGC 62.552 66.667 35.17 35.17 44.37 4.85
4377 4439 4.457496 GCAGGAGCACGCTGCCTA 62.457 66.667 6.95 0.00 46.52 3.93
4378 4440 2.503061 CAGGAGCACGCTGCCTAT 59.497 61.111 6.95 0.00 46.52 2.57
4383 4445 0.943359 GAGCACGCTGCCTATAGCTG 60.943 60.000 0.00 0.00 46.52 4.24
4398 4460 1.042229 AGCTGCATTTTGCTGAACCA 58.958 45.000 10.10 0.00 45.31 3.67
4402 4464 1.483827 TGCATTTTGCTGAACCACCAA 59.516 42.857 0.75 0.00 45.31 3.67
4410 4472 1.826385 CTGAACCACCAACAGGGATC 58.174 55.000 0.00 0.00 41.15 3.36
4432 4495 9.797556 GGATCGGCTAATGTAATTTTTAGTTTT 57.202 29.630 0.00 0.00 37.87 2.43
4444 4507 9.110617 GTAATTTTTAGTTTTTCTGGACTACGC 57.889 33.333 0.00 0.00 0.00 4.42
4449 4512 3.056749 AGTTTTTCTGGACTACGCGATCT 60.057 43.478 15.93 0.00 0.00 2.75
4458 4521 4.252073 GGACTACGCGATCTTAGGATCTA 58.748 47.826 15.93 0.00 44.42 1.98
4477 4540 5.450818 TCTACCCCATGTATTTGCTCTTT 57.549 39.130 0.00 0.00 0.00 2.52
4484 4547 3.552604 TGTATTTGCTCTTTCCGTTGC 57.447 42.857 0.00 0.00 0.00 4.17
4501 4564 7.189693 TCCGTTGCTTTCTGCTTAATATATG 57.810 36.000 0.00 0.00 43.37 1.78
4502 4565 6.989759 TCCGTTGCTTTCTGCTTAATATATGA 59.010 34.615 0.00 0.00 43.37 2.15
4503 4566 7.497579 TCCGTTGCTTTCTGCTTAATATATGAA 59.502 33.333 0.00 0.00 43.37 2.57
4504 4567 7.587757 CCGTTGCTTTCTGCTTAATATATGAAC 59.412 37.037 0.00 0.00 43.37 3.18
4505 4568 7.318909 CGTTGCTTTCTGCTTAATATATGAACG 59.681 37.037 0.00 0.00 43.37 3.95
4506 4569 6.658831 TGCTTTCTGCTTAATATATGAACGC 58.341 36.000 0.00 0.00 43.37 4.84
4507 4570 6.080406 GCTTTCTGCTTAATATATGAACGCC 58.920 40.000 0.00 0.00 38.95 5.68
4508 4571 6.293407 GCTTTCTGCTTAATATATGAACGCCA 60.293 38.462 0.00 0.00 38.95 5.69
4509 4572 6.785488 TTCTGCTTAATATATGAACGCCAG 57.215 37.500 0.00 0.00 0.00 4.85
4510 4573 4.690748 TCTGCTTAATATATGAACGCCAGC 59.309 41.667 0.00 0.00 0.00 4.85
4511 4574 4.384940 TGCTTAATATATGAACGCCAGCA 58.615 39.130 0.00 0.00 32.44 4.41
4512 4575 4.452114 TGCTTAATATATGAACGCCAGCAG 59.548 41.667 0.00 0.00 31.30 4.24
4513 4576 4.670221 GCTTAATATATGAACGCCAGCAGC 60.670 45.833 0.00 0.00 38.52 5.25
4525 4588 4.215349 AGCAGCGCTGGATCTTTC 57.785 55.556 36.47 19.04 37.57 2.62
4526 4589 1.297689 AGCAGCGCTGGATCTTTCA 59.702 52.632 36.47 0.00 37.57 2.69
4527 4590 0.321919 AGCAGCGCTGGATCTTTCAA 60.322 50.000 36.47 0.00 37.57 2.69
4528 4591 0.523072 GCAGCGCTGGATCTTTCAAA 59.477 50.000 36.47 0.00 0.00 2.69
4529 4592 1.068333 GCAGCGCTGGATCTTTCAAAA 60.068 47.619 36.47 0.00 0.00 2.44
4530 4593 2.607771 GCAGCGCTGGATCTTTCAAAAA 60.608 45.455 36.47 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 2.937149 GGTCTTAGAAGCGACCAATTCC 59.063 50.000 3.72 0.00 46.98 3.01
115 116 8.898761 CGGTTAGCAGATAAGATCACTATCTAT 58.101 37.037 13.95 10.03 41.81 1.98
116 117 8.101419 TCGGTTAGCAGATAAGATCACTATCTA 58.899 37.037 13.95 1.37 41.81 1.98
117 118 6.943146 TCGGTTAGCAGATAAGATCACTATCT 59.057 38.462 10.20 10.20 44.67 1.98
118 119 7.024768 GTCGGTTAGCAGATAAGATCACTATC 58.975 42.308 0.00 1.15 0.00 2.08
242 247 6.762661 GTCCAAATTGATAAATGAATGGTGGG 59.237 38.462 0.00 0.00 0.00 4.61
259 264 3.551846 ACGGTGTTCTTCAGTCCAAATT 58.448 40.909 0.00 0.00 0.00 1.82
279 284 4.332819 CCCCGAAACAGAGATGAAACATAC 59.667 45.833 0.00 0.00 0.00 2.39
281 286 3.009033 TCCCCGAAACAGAGATGAAACAT 59.991 43.478 0.00 0.00 0.00 2.71
392 397 5.888691 TGCGATTAGGCAAAGTCAATTAA 57.111 34.783 0.00 0.00 40.59 1.40
422 427 4.413760 AGGAGTGCAGTACTAGGTTAACA 58.586 43.478 3.79 0.00 40.53 2.41
464 469 2.944129 AGACTAAACCTTGGCTTGCAA 58.056 42.857 0.00 0.00 0.00 4.08
480 485 2.447443 TGTCCACTCGCAGATTAGACT 58.553 47.619 0.00 0.00 33.89 3.24
481 486 2.941453 TGTCCACTCGCAGATTAGAC 57.059 50.000 0.00 0.00 33.89 2.59
482 487 3.291584 AGATGTCCACTCGCAGATTAGA 58.708 45.455 0.00 0.00 33.89 2.10
483 488 3.637432 GAGATGTCCACTCGCAGATTAG 58.363 50.000 0.00 0.00 33.89 1.73
484 489 3.717400 GAGATGTCCACTCGCAGATTA 57.283 47.619 0.00 0.00 33.89 1.75
546 551 2.279921 TCGTACGTACTTCGAGTCGATG 59.720 50.000 22.55 22.69 42.86 3.84
553 558 3.120683 ACAAACGATCGTACGTACTTCGA 60.121 43.478 34.60 24.36 45.83 3.71
554 559 3.155998 ACAAACGATCGTACGTACTTCG 58.844 45.455 30.10 30.10 45.83 3.79
555 560 5.576231 GTACAAACGATCGTACGTACTTC 57.424 43.478 32.27 17.11 45.83 3.01
647 659 4.812403 TCATACACATGGGAATGGGATT 57.188 40.909 0.00 0.00 32.61 3.01
714 726 1.828331 GCTTGCTTGCTTGCTTGTGC 61.828 55.000 3.47 0.00 40.20 4.57
834 852 2.872388 CGGATGGGACGGGATGGAG 61.872 68.421 0.00 0.00 0.00 3.86
1078 1098 2.031069 GCAATGCTATGCTGGATGTGAG 60.031 50.000 0.00 0.00 43.06 3.51
1079 1099 1.951602 GCAATGCTATGCTGGATGTGA 59.048 47.619 0.00 0.00 43.06 3.58
1087 1107 3.130633 CAATGCAATGCAATGCTATGCT 58.869 40.909 26.10 15.09 46.54 3.79
1088 1108 3.127589 TCAATGCAATGCAATGCTATGC 58.872 40.909 26.10 22.32 46.54 3.14
1089 1109 4.388773 GGATCAATGCAATGCAATGCTATG 59.611 41.667 26.10 22.51 46.54 2.23
1090 1110 4.039852 TGGATCAATGCAATGCAATGCTAT 59.960 37.500 26.10 15.30 46.54 2.97
1091 1111 3.385111 TGGATCAATGCAATGCAATGCTA 59.615 39.130 26.10 13.77 46.54 3.49
1097 1125 2.094442 CACACTGGATCAATGCAATGCA 60.094 45.455 11.44 11.44 44.86 3.96
1696 1724 2.224621 ACGAGGCATCCATATTCTTGGG 60.225 50.000 0.00 0.00 37.37 4.12
1724 1752 3.522750 ACTCTTCAATCTCCAGCTCCATT 59.477 43.478 0.00 0.00 0.00 3.16
1746 1774 2.592993 CCTCGACAGGAAGCCCCAA 61.593 63.158 0.00 0.00 43.65 4.12
2263 2291 2.268920 GCCGAGCATCTCCACCAA 59.731 61.111 0.00 0.00 0.00 3.67
2469 2497 0.107897 TGCAGTTGTCGTGGTCTTGT 60.108 50.000 0.00 0.00 0.00 3.16
2571 2599 2.077821 TAGCGCGCGATTGGGTGATA 62.078 55.000 37.18 6.34 40.70 2.15
2775 2803 2.045926 GCGTCCTTGTCCATGGCT 60.046 61.111 6.96 0.00 0.00 4.75
2785 2813 2.214181 ATCTTCTCACGCGCGTCCTT 62.214 55.000 35.61 9.14 0.00 3.36
2946 2974 2.588034 GGGGCGGCGTTGAGTATC 60.588 66.667 9.37 0.00 0.00 2.24
3268 3296 1.889530 GAAGGGCTGCTGTACCTCGT 61.890 60.000 0.00 0.00 32.29 4.18
3325 3353 0.755079 CTCAGCATCCCGATCAGGAA 59.245 55.000 0.72 0.00 45.00 3.36
3606 3634 2.661195 GGCAAACGAAATATGCACACAC 59.339 45.455 0.00 0.00 41.80 3.82
3664 3698 6.437477 TCTTCTTTCTTACTCAGACATAGCCA 59.563 38.462 0.00 0.00 0.00 4.75
3718 3765 5.614324 TCGTGAGATCTTACATTGGGATT 57.386 39.130 16.95 0.00 33.31 3.01
3749 3796 6.796705 AAAACCCAGTCGACTTGTATTTAG 57.203 37.500 17.26 1.42 0.00 1.85
3750 3797 6.875195 CCTAAAACCCAGTCGACTTGTATTTA 59.125 38.462 17.26 16.68 0.00 1.40
3751 3798 5.704053 CCTAAAACCCAGTCGACTTGTATTT 59.296 40.000 17.26 16.47 0.00 1.40
3752 3799 5.012354 TCCTAAAACCCAGTCGACTTGTATT 59.988 40.000 17.26 10.10 0.00 1.89
3753 3800 4.529377 TCCTAAAACCCAGTCGACTTGTAT 59.471 41.667 17.26 11.02 0.00 2.29
3755 3802 2.701951 TCCTAAAACCCAGTCGACTTGT 59.298 45.455 17.26 13.49 0.00 3.16
3756 3803 3.396260 TCCTAAAACCCAGTCGACTTG 57.604 47.619 17.26 13.04 0.00 3.16
3767 3829 9.788960 CAAATTTATAGCAGTCTTCCTAAAACC 57.211 33.333 0.00 0.00 0.00 3.27
3775 3837 6.967199 CCGGTTTCAAATTTATAGCAGTCTTC 59.033 38.462 0.00 0.00 0.00 2.87
3782 3844 6.735130 ACATAGCCGGTTTCAAATTTATAGC 58.265 36.000 1.90 0.00 0.00 2.97
3798 3860 1.299468 GTCGCCTGAGACATAGCCG 60.299 63.158 0.00 0.00 40.65 5.52
3800 3862 2.301577 AAAGTCGCCTGAGACATAGC 57.698 50.000 3.90 0.00 43.24 2.97
3831 3893 3.881089 ACGGTGGAGTAAAGAAAAAGTGG 59.119 43.478 0.00 0.00 0.00 4.00
3834 3896 5.333875 GCTACACGGTGGAGTAAAGAAAAAG 60.334 44.000 20.95 0.00 28.73 2.27
3839 3901 1.547372 GGCTACACGGTGGAGTAAAGA 59.453 52.381 20.95 0.00 28.73 2.52
3925 3987 1.145571 TGGGGGCACTGTTTAACTCT 58.854 50.000 0.00 0.00 0.00 3.24
3926 3988 1.886542 CTTGGGGGCACTGTTTAACTC 59.113 52.381 0.00 0.00 0.00 3.01
3927 3989 1.995376 CTTGGGGGCACTGTTTAACT 58.005 50.000 0.00 0.00 0.00 2.24
3928 3990 0.317160 GCTTGGGGGCACTGTTTAAC 59.683 55.000 0.00 0.00 0.00 2.01
3929 3991 0.105964 TGCTTGGGGGCACTGTTTAA 60.106 50.000 0.00 0.00 37.29 1.52
3931 3993 0.763986 ATTGCTTGGGGGCACTGTTT 60.764 50.000 0.00 0.00 42.27 2.83
3933 3995 1.909781 CATTGCTTGGGGGCACTGT 60.910 57.895 0.00 0.00 42.27 3.55
3934 3996 2.975536 CATTGCTTGGGGGCACTG 59.024 61.111 0.00 0.00 42.27 3.66
3935 3997 2.999063 GCATTGCTTGGGGGCACT 60.999 61.111 0.16 0.00 42.27 4.40
3936 3998 4.086547 GGCATTGCTTGGGGGCAC 62.087 66.667 8.82 0.00 42.27 5.01
3937 3999 2.241043 ATAGGCATTGCTTGGGGGCA 62.241 55.000 8.82 0.00 40.74 5.36
3938 4000 1.050421 AATAGGCATTGCTTGGGGGC 61.050 55.000 8.82 0.00 0.00 5.80
3939 4001 1.413812 GAAATAGGCATTGCTTGGGGG 59.586 52.381 8.82 0.00 0.00 5.40
3940 4002 2.101917 CAGAAATAGGCATTGCTTGGGG 59.898 50.000 8.82 0.00 26.06 4.96
3941 4003 2.482490 GCAGAAATAGGCATTGCTTGGG 60.482 50.000 8.82 0.00 26.06 4.12
3942 4004 2.482490 GGCAGAAATAGGCATTGCTTGG 60.482 50.000 8.82 0.00 35.23 3.61
3943 4005 2.482490 GGGCAGAAATAGGCATTGCTTG 60.482 50.000 8.82 0.00 35.23 4.01
3944 4006 1.758862 GGGCAGAAATAGGCATTGCTT 59.241 47.619 8.82 3.14 35.23 3.91
3945 4007 1.063417 AGGGCAGAAATAGGCATTGCT 60.063 47.619 8.82 0.00 35.23 3.91
3946 4008 1.406903 AGGGCAGAAATAGGCATTGC 58.593 50.000 0.00 0.00 0.00 3.56
3947 4009 3.025978 TGAAGGGCAGAAATAGGCATTG 58.974 45.455 0.00 0.00 35.66 2.82
3948 4010 3.026694 GTGAAGGGCAGAAATAGGCATT 58.973 45.455 0.00 0.00 38.27 3.56
3949 4011 2.659428 GTGAAGGGCAGAAATAGGCAT 58.341 47.619 0.00 0.00 0.00 4.40
3950 4012 1.340991 GGTGAAGGGCAGAAATAGGCA 60.341 52.381 0.00 0.00 0.00 4.75
3951 4013 1.393603 GGTGAAGGGCAGAAATAGGC 58.606 55.000 0.00 0.00 0.00 3.93
3952 4014 1.284785 TGGGTGAAGGGCAGAAATAGG 59.715 52.381 0.00 0.00 0.00 2.57
3953 4015 2.806945 TGGGTGAAGGGCAGAAATAG 57.193 50.000 0.00 0.00 0.00 1.73
3954 4016 3.161866 GTTTGGGTGAAGGGCAGAAATA 58.838 45.455 0.00 0.00 0.00 1.40
3955 4017 1.970640 GTTTGGGTGAAGGGCAGAAAT 59.029 47.619 0.00 0.00 0.00 2.17
3956 4018 1.342474 TGTTTGGGTGAAGGGCAGAAA 60.342 47.619 0.00 0.00 0.00 2.52
3957 4019 0.260230 TGTTTGGGTGAAGGGCAGAA 59.740 50.000 0.00 0.00 0.00 3.02
3958 4020 0.260230 TTGTTTGGGTGAAGGGCAGA 59.740 50.000 0.00 0.00 0.00 4.26
3959 4021 0.675633 CTTGTTTGGGTGAAGGGCAG 59.324 55.000 0.00 0.00 0.00 4.85
3960 4022 0.032615 ACTTGTTTGGGTGAAGGGCA 60.033 50.000 0.00 0.00 0.00 5.36
3961 4023 1.119684 AACTTGTTTGGGTGAAGGGC 58.880 50.000 0.00 0.00 0.00 5.19
3962 4024 2.107366 ACAACTTGTTTGGGTGAAGGG 58.893 47.619 0.00 0.00 39.84 3.95
3966 4028 2.223803 ACCACAACTTGTTTGGGTGA 57.776 45.000 14.39 0.00 36.81 4.02
4005 4067 3.145551 CCATTGCTCCAGCCCTGC 61.146 66.667 0.00 0.00 41.18 4.85
4016 4078 4.068599 GAGAGGGTAGAAATAGCCATTGC 58.931 47.826 6.30 0.00 39.94 3.56
4017 4079 5.303971 CAGAGAGGGTAGAAATAGCCATTG 58.696 45.833 6.30 0.00 39.94 2.82
4020 4082 2.700897 GCAGAGAGGGTAGAAATAGCCA 59.299 50.000 6.30 0.00 39.94 4.75
4031 4093 3.670629 CTCCCGAGGCAGAGAGGGT 62.671 68.421 0.00 0.00 44.13 4.34
4033 4095 3.535962 GCTCCCGAGGCAGAGAGG 61.536 72.222 0.00 0.00 31.43 3.69
4152 4214 3.172106 TTGTCGAGGTGCCCCCAA 61.172 61.111 0.00 0.00 34.66 4.12
4176 4238 3.297830 ACGATCACTTCAACGATGTCA 57.702 42.857 0.00 0.00 0.00 3.58
4182 4244 2.286125 TGCAACAACGATCACTTCAACG 60.286 45.455 0.00 0.00 0.00 4.10
4199 4261 2.229792 GTTCATCTCCAGGTGTTGCAA 58.770 47.619 0.00 0.00 0.00 4.08
4211 4273 3.543680 TGATTCCCTTCCGTTCATCTC 57.456 47.619 0.00 0.00 0.00 2.75
4214 4276 3.264450 AGACTTGATTCCCTTCCGTTCAT 59.736 43.478 0.00 0.00 0.00 2.57
4217 4279 4.469945 TGATAGACTTGATTCCCTTCCGTT 59.530 41.667 0.00 0.00 0.00 4.44
4251 4313 3.671702 GCTCAAGACATAGTTGCCAAAGC 60.672 47.826 0.00 0.00 40.48 3.51
4254 4316 2.076100 CGCTCAAGACATAGTTGCCAA 58.924 47.619 0.00 0.00 0.00 4.52
4260 4322 2.455674 TGTTGCGCTCAAGACATAGT 57.544 45.000 9.73 0.00 31.93 2.12
4261 4323 4.093514 CAATTGTTGCGCTCAAGACATAG 58.906 43.478 19.20 6.33 31.93 2.23
4287 4349 1.800032 CGCATGCTTAGCCCGAAAA 59.200 52.632 17.13 0.00 0.00 2.29
4302 4364 3.295273 ACGTCTCTGACCAGCGCA 61.295 61.111 11.47 0.00 0.00 6.09
4307 4369 2.867855 GCCACCACGTCTCTGACCA 61.868 63.158 0.00 0.00 0.00 4.02
4310 4372 2.203640 AGGCCACCACGTCTCTGA 60.204 61.111 5.01 0.00 0.00 3.27
4326 4388 1.377725 AATGGCTCGGTGGCTTGAG 60.378 57.895 5.23 0.00 42.34 3.02
4327 4389 1.675310 CAATGGCTCGGTGGCTTGA 60.675 57.895 5.23 0.00 42.34 3.02
4333 4395 1.224075 CATAGCTCAATGGCTCGGTG 58.776 55.000 0.00 0.00 42.97 4.94
4344 4406 4.552365 GCCTGGCGCCATAGCTCA 62.552 66.667 33.09 11.74 36.60 4.26
4361 4423 0.319383 CTATAGGCAGCGTGCTCCTG 60.319 60.000 17.58 0.32 44.28 3.86
4383 4445 2.237393 TTGGTGGTTCAGCAAAATGC 57.763 45.000 9.65 0.00 46.52 3.56
4398 4460 1.134098 CATTAGCCGATCCCTGTTGGT 60.134 52.381 0.00 0.00 34.77 3.67
4402 4464 4.706842 AATTACATTAGCCGATCCCTGT 57.293 40.909 0.00 0.00 0.00 4.00
4432 4495 2.617308 CCTAAGATCGCGTAGTCCAGAA 59.383 50.000 5.77 0.00 0.00 3.02
4436 4499 3.474693 GATCCTAAGATCGCGTAGTCC 57.525 52.381 5.77 0.00 39.66 3.85
4449 4512 5.610982 AGCAAATACATGGGGTAGATCCTAA 59.389 40.000 0.00 0.00 34.92 2.69
4458 4521 3.365472 GGAAAGAGCAAATACATGGGGT 58.635 45.455 0.00 0.00 0.00 4.95
4484 4547 7.189693 TGGCGTTCATATATTAAGCAGAAAG 57.810 36.000 5.35 0.00 0.00 2.62
4508 4571 0.321919 TTGAAAGATCCAGCGCTGCT 60.322 50.000 31.96 20.35 40.77 4.24
4509 4572 0.523072 TTTGAAAGATCCAGCGCTGC 59.477 50.000 31.96 18.29 0.00 5.25
4510 4573 2.995466 TTTTGAAAGATCCAGCGCTG 57.005 45.000 30.52 30.52 0.00 5.18


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

AutoCloner maintained by Alex Coulton.