Multiple sequence alignment - TraesCS3A01G284900

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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 TraesCS3A01G284900 chr3A 100.000 4354 0 0 1 4354 513896023 513891670 0.000000e+00 8041.0
1 TraesCS3A01G284900 chr3D 92.619 3902 175 49 1 3851 394063624 394059785 0.000000e+00 5505.0
2 TraesCS3A01G284900 chr3D 85.714 413 28 18 3952 4354 394059746 394059355 1.460000e-109 407.0
3 TraesCS3A01G284900 chr3B 94.804 2598 104 20 400 2979 513671940 513669356 0.000000e+00 4021.0
4 TraesCS3A01G284900 chr3B 87.827 1224 82 26 950 2148 511383871 511385052 0.000000e+00 1373.0
5 TraesCS3A01G284900 chr3B 86.735 784 58 28 3589 4354 513668539 513667784 0.000000e+00 830.0
6 TraesCS3A01G284900 chr3B 91.162 611 34 8 336 927 511383265 511383874 0.000000e+00 811.0
7 TraesCS3A01G284900 chr3B 92.918 353 24 1 3014 3366 513669359 513669008 3.000000e-141 512.0
8 TraesCS3A01G284900 chr3B 90.253 277 21 2 1 271 513672615 513672339 1.490000e-94 357.0
9 TraesCS3A01G284900 chr3B 92.793 111 7 1 3411 3520 513668893 513668783 4.510000e-35 159.0
10 TraesCS3A01G284900 chr1A 82.258 124 18 4 147 269 579109336 579109216 2.140000e-18 104.0
11 TraesCS3A01G284900 chr2D 81.148 122 17 4 151 271 618308449 618308333 4.640000e-15 93.5


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 TraesCS3A01G284900 chr3A 513891670 513896023 4353 True 8041.0 8041 100.0000 1 4354 1 chr3A.!!$R1 4353
1 TraesCS3A01G284900 chr3D 394059355 394063624 4269 True 2956.0 5505 89.1665 1 4354 2 chr3D.!!$R1 4353
2 TraesCS3A01G284900 chr3B 513667784 513672615 4831 True 1175.8 4021 91.5006 1 4354 5 chr3B.!!$R1 4353
3 TraesCS3A01G284900 chr3B 511383265 511385052 1787 False 1092.0 1373 89.4945 336 2148 2 chr3B.!!$F1 1812

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
644 931 0.860533 CCCACGCAATTGCTTTGTTG 59.139 50.0 26.86 13.31 37.65 3.33 F
1005 1302 0.038744 CAGGAGCAACAGGAATGGGT 59.961 55.0 0.00 0.00 0.00 4.51 F
2548 2881 0.250338 GTTTCTTCAGTGGCCCTCGT 60.250 55.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2254 1.028905 TTGTTGTTCTCTTTGCGGGG 58.971 50.0 0.0 0.0 0.00 5.73 R
2908 3242 0.853530 GGGCTTCCCATTGATAGGGT 59.146 55.0 0.0 0.0 46.82 4.34 R
3409 3855 0.036732 CTAAAGGCACAGCACCCTGA 59.963 55.0 0.0 0.0 41.77 3.86 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
254 261 6.530120 TGGTCTTGTATGACTTTGCTCTTTA 58.470 36.000 0.00 0.00 37.16 1.85
255 262 7.168219 TGGTCTTGTATGACTTTGCTCTTTAT 58.832 34.615 0.00 0.00 37.16 1.40
425 707 1.883275 CCATTAAAACTGACGCCCACA 59.117 47.619 0.00 0.00 0.00 4.17
429 711 1.981256 AAAACTGACGCCCACATCTT 58.019 45.000 0.00 0.00 0.00 2.40
644 931 0.860533 CCCACGCAATTGCTTTGTTG 59.139 50.000 26.86 13.31 37.65 3.33
663 950 6.189677 TGTTGTTGCAATAACTATAGCACC 57.810 37.500 30.92 9.70 36.62 5.01
687 974 5.458041 AGCACTGTTCTTAATGCACAAAT 57.542 34.783 0.00 0.00 40.63 2.32
699 986 3.574284 TGCACAAATTACACATCCTGC 57.426 42.857 0.00 0.00 0.00 4.85
836 1124 4.275936 GGTGACAGCAAGTACAGAAAACAT 59.724 41.667 0.00 0.00 0.00 2.71
882 1179 7.392673 GCATATAACATGGATTCTCAACCAGAT 59.607 37.037 0.00 0.00 39.62 2.90
908 1205 7.339482 ACATCTTTTTACTAGAATCCTCCACC 58.661 38.462 0.00 0.00 0.00 4.61
947 1244 6.710692 CATCACCATGCTAAAAGGAAAAAC 57.289 37.500 0.00 0.00 0.00 2.43
948 1245 5.860941 TCACCATGCTAAAAGGAAAAACA 57.139 34.783 0.00 0.00 0.00 2.83
974 1271 3.665173 GCCAAAAGCTTCTACGATCAG 57.335 47.619 0.00 0.00 38.99 2.90
1005 1302 0.038744 CAGGAGCAACAGGAATGGGT 59.961 55.000 0.00 0.00 0.00 4.51
1102 1399 2.625737 CTCCCACAACATCTGTAGCAG 58.374 52.381 0.00 0.00 36.10 4.24
1328 1626 7.497595 TGTAAATATCTCCGTGCAGAATACTT 58.502 34.615 0.00 0.00 0.00 2.24
1371 1669 1.272147 ACTTCAGATCCTTGGTTGGGC 60.272 52.381 0.00 0.00 0.00 5.36
1421 1719 1.722751 GCACAACTTCTGTCGATTGCG 60.723 52.381 0.00 0.00 35.47 4.85
1504 1802 4.960938 GCTGGTGATCAGGTATGTTATGA 58.039 43.478 0.00 0.00 43.54 2.15
1558 1856 7.704899 GGTAATTACCATTGTTATTTGTGCTCC 59.295 37.037 26.65 0.00 45.73 4.70
1561 1859 3.190535 ACCATTGTTATTTGTGCTCCGAC 59.809 43.478 0.00 0.00 0.00 4.79
1760 2059 4.841422 AGAAATCTCATGCTAGCAACTGT 58.159 39.130 23.54 1.20 0.00 3.55
1773 2072 6.100004 GCTAGCAACTGTCATCTTAGTACAA 58.900 40.000 10.63 0.00 0.00 2.41
1981 2293 6.564328 ACAACAAACTAGCAAAAGAAGGAAG 58.436 36.000 0.00 0.00 0.00 3.46
2037 2359 3.146066 TGGAATGTTTGTCACTAGCCAC 58.854 45.455 0.00 0.00 0.00 5.01
2111 2435 3.865011 TTTTGTGTGCATGTGAGTGTT 57.135 38.095 0.00 0.00 0.00 3.32
2228 2561 7.759489 TTTTGTCACCTAGTCTTATGCATTT 57.241 32.000 3.54 0.00 0.00 2.32
2232 2565 5.525378 GTCACCTAGTCTTATGCATTTGAGG 59.475 44.000 3.54 6.38 0.00 3.86
2431 2764 3.821033 AGAATTAAACTCCACAGTGGCAC 59.179 43.478 15.64 10.29 37.47 5.01
2538 2871 3.074412 AGTTGGTATGGCGTTTCTTCAG 58.926 45.455 0.00 0.00 0.00 3.02
2548 2881 0.250338 GTTTCTTCAGTGGCCCTCGT 60.250 55.000 0.00 0.00 0.00 4.18
2551 2884 1.153549 CTTCAGTGGCCCTCGTAGC 60.154 63.158 0.00 0.00 0.00 3.58
2648 2982 9.716531 TGTTTTCTCATGCTATCTATAAGATGG 57.283 33.333 0.00 0.00 35.37 3.51
2699 3033 7.653767 AAATCTCAGTAAACGAACTACCAAG 57.346 36.000 0.00 0.00 0.00 3.61
2714 3048 7.437267 CGAACTACCAAGTAATTCATTACCGAT 59.563 37.037 6.14 0.00 42.71 4.18
2721 3055 8.557029 CCAAGTAATTCATTACCGATTCCTTAC 58.443 37.037 6.14 0.00 42.71 2.34
2751 3085 6.437928 TCTTGCATATGATTATTTTCGCACC 58.562 36.000 6.97 0.00 0.00 5.01
2767 3101 1.482182 GCACCCCTCCCAATCAAAATC 59.518 52.381 0.00 0.00 0.00 2.17
2908 3242 5.160607 AGTCACCGAATCATTCCAGTAAA 57.839 39.130 0.00 0.00 0.00 2.01
2943 3278 1.492993 GCCCAGGAGACCAGGACTTT 61.493 60.000 0.00 0.00 0.00 2.66
2944 3279 1.068121 CCCAGGAGACCAGGACTTTT 58.932 55.000 0.00 0.00 0.00 2.27
2975 3311 6.401153 GCTTTCTGTACGATGTTTGTCCTTAG 60.401 42.308 0.00 0.00 0.00 2.18
2978 3314 1.722011 ACGATGTTTGTCCTTAGGCG 58.278 50.000 0.00 0.00 0.00 5.52
3009 3345 3.108847 TCCAAACTTTGTTTCCCAGGT 57.891 42.857 0.88 0.00 0.00 4.00
3011 3347 4.611367 TCCAAACTTTGTTTCCCAGGTAA 58.389 39.130 0.88 0.00 0.00 2.85
3012 3348 5.212745 TCCAAACTTTGTTTCCCAGGTAAT 58.787 37.500 0.88 0.00 0.00 1.89
3013 3349 6.374588 TCCAAACTTTGTTTCCCAGGTAATA 58.625 36.000 0.88 0.00 0.00 0.98
3070 3427 8.694394 GCTTTGACAAATAACATCTGAACTTTC 58.306 33.333 0.05 0.00 0.00 2.62
3097 3454 4.180057 CTCTGCTAGTGTCTGACATTTCC 58.820 47.826 14.37 0.73 0.00 3.13
3113 3470 6.494491 TGACATTTCCATGGAACTGAAGAATT 59.506 34.615 37.61 21.84 37.93 2.17
3130 3487 2.185004 ATTATACGGCTGGTGCATCC 57.815 50.000 0.00 0.00 41.91 3.51
3131 3488 1.128200 TTATACGGCTGGTGCATCCT 58.872 50.000 0.00 0.00 41.91 3.24
3163 3520 1.559814 CGTATGCGATGTTGAGCGG 59.440 57.895 0.00 0.00 41.33 5.52
3320 3677 4.408821 TTCCTTGCCGCATCCGCT 62.409 61.111 0.00 0.00 35.30 5.52
3358 3715 3.754850 TGGCTGTCAAATCTGTGAGAATG 59.245 43.478 0.00 0.00 0.00 2.67
3392 3835 2.224670 TGGCAAACTAGTACACCCCTTG 60.225 50.000 0.00 0.00 0.00 3.61
3406 3849 2.646121 CCTTGGCAGGGAGTTCAAC 58.354 57.895 10.68 0.00 36.36 3.18
3409 3855 2.310538 CTTGGCAGGGAGTTCAACTTT 58.689 47.619 0.00 0.00 0.00 2.66
3469 3916 3.071167 ACCTGTAAAGTGTCCTGAAGTCC 59.929 47.826 0.00 0.00 0.00 3.85
3488 3935 1.543208 CCTGTGAGTTGGCTGCTTGTA 60.543 52.381 0.00 0.00 0.00 2.41
3505 3952 1.431243 TGTACAAATTGGAGCCCCCTT 59.569 47.619 0.00 0.00 35.38 3.95
3530 3977 0.928505 AATGGATGGCATCACCTGGA 59.071 50.000 27.39 5.56 40.22 3.86
3531 3978 1.155323 ATGGATGGCATCACCTGGAT 58.845 50.000 27.39 7.50 40.22 3.41
3627 4266 7.598189 CTCTGATCATATATGCAGAGTTTGG 57.402 40.000 26.56 12.99 45.69 3.28
3628 4267 7.071069 TCTGATCATATATGCAGAGTTTGGT 57.929 36.000 15.23 0.00 32.85 3.67
3643 4282 2.050442 GGTTTGGTTGCCGCTTCG 60.050 61.111 0.00 0.00 0.00 3.79
3675 4314 0.109827 CATTGACAATTCCACGCGCA 60.110 50.000 5.73 0.00 0.00 6.09
3716 4356 3.181455 ACACTGCCACTTGTCTACATTGA 60.181 43.478 0.00 0.00 0.00 2.57
3717 4357 4.005650 CACTGCCACTTGTCTACATTGAT 58.994 43.478 0.00 0.00 0.00 2.57
3718 4358 4.005650 ACTGCCACTTGTCTACATTGATG 58.994 43.478 0.00 0.00 0.00 3.07
3748 4388 3.244078 TGAGTACACATGAACACCTGTCC 60.244 47.826 0.00 0.00 0.00 4.02
3775 4423 0.773644 ACTCCCAATCAGCACACCTT 59.226 50.000 0.00 0.00 0.00 3.50
3841 4497 0.796927 CAGCCATATCTGCATCTGCG 59.203 55.000 0.00 0.00 45.83 5.18
3886 4542 1.689352 GACACGCCCAAACCGATACG 61.689 60.000 0.00 0.00 0.00 3.06
3887 4543 1.738830 CACGCCCAAACCGATACGT 60.739 57.895 0.00 0.00 0.00 3.57
3890 4546 1.134226 CGCCCAAACCGATACGTATC 58.866 55.000 23.03 23.03 0.00 2.24
3925 4581 2.155924 GGAGAAAAAGCGAAGACGACAG 59.844 50.000 0.00 0.00 42.66 3.51
3927 4583 0.232303 AAAAAGCGAAGACGACAGCG 59.768 50.000 0.00 0.00 42.66 5.18
3965 4621 4.130281 GGTACGCTCGCACGCAAC 62.130 66.667 0.00 0.00 36.19 4.17
3966 4622 3.103911 GTACGCTCGCACGCAACT 61.104 61.111 0.00 0.00 36.19 3.16
3967 4623 2.803670 TACGCTCGCACGCAACTC 60.804 61.111 0.00 0.00 36.19 3.01
3968 4624 3.263503 TACGCTCGCACGCAACTCT 62.264 57.895 0.00 0.00 36.19 3.24
3969 4625 3.832171 CGCTCGCACGCAACTCTC 61.832 66.667 0.00 0.00 0.00 3.20
3970 4626 2.734723 GCTCGCACGCAACTCTCA 60.735 61.111 0.00 0.00 0.00 3.27
3971 4627 3.004734 GCTCGCACGCAACTCTCAC 62.005 63.158 0.00 0.00 0.00 3.51
3975 4631 1.566563 GCACGCAACTCTCACACTG 59.433 57.895 0.00 0.00 0.00 3.66
4030 4686 3.377798 GTCGACTCCTTTATCGTCTTCCT 59.622 47.826 8.70 0.00 39.38 3.36
4037 4693 4.079672 TCCTTTATCGTCTTCCTCTCCTCT 60.080 45.833 0.00 0.00 0.00 3.69
4038 4694 4.277423 CCTTTATCGTCTTCCTCTCCTCTC 59.723 50.000 0.00 0.00 0.00 3.20
4039 4695 2.358322 ATCGTCTTCCTCTCCTCTCC 57.642 55.000 0.00 0.00 0.00 3.71
4067 4723 0.313987 CTTCCTTTTCAACCGCCACC 59.686 55.000 0.00 0.00 0.00 4.61
4080 4736 4.821589 CCACCTTCCTCTCGCGGC 62.822 72.222 6.13 0.00 0.00 6.53
4081 4737 4.821589 CACCTTCCTCTCGCGGCC 62.822 72.222 6.13 0.00 0.00 6.13
4099 4758 2.161609 GGCCAATTCTTCCACTTGTACG 59.838 50.000 0.00 0.00 0.00 3.67
4100 4759 2.161609 GCCAATTCTTCCACTTGTACGG 59.838 50.000 0.00 0.00 0.00 4.02
4102 4761 3.818773 CCAATTCTTCCACTTGTACGGTT 59.181 43.478 0.00 0.00 0.00 4.44
4103 4762 4.320202 CCAATTCTTCCACTTGTACGGTTG 60.320 45.833 0.00 0.00 0.00 3.77
4104 4763 3.547054 TTCTTCCACTTGTACGGTTGT 57.453 42.857 0.00 0.00 0.00 3.32
4105 4764 4.669206 TTCTTCCACTTGTACGGTTGTA 57.331 40.909 0.00 0.00 0.00 2.41
4126 4794 2.716017 CCTGCCGTCTCCTCCACTC 61.716 68.421 0.00 0.00 0.00 3.51
4127 4795 2.680352 TGCCGTCTCCTCCACTCC 60.680 66.667 0.00 0.00 0.00 3.85
4128 4796 2.680352 GCCGTCTCCTCCACTCCA 60.680 66.667 0.00 0.00 0.00 3.86
4129 4797 3.007973 GCCGTCTCCTCCACTCCAC 62.008 68.421 0.00 0.00 0.00 4.02
4130 4798 2.352032 CCGTCTCCTCCACTCCACC 61.352 68.421 0.00 0.00 0.00 4.61
4131 4799 2.701780 CGTCTCCTCCACTCCACCG 61.702 68.421 0.00 0.00 0.00 4.94
4132 4800 2.680352 TCTCCTCCACTCCACCGC 60.680 66.667 0.00 0.00 0.00 5.68
4133 4801 2.681778 CTCCTCCACTCCACCGCT 60.682 66.667 0.00 0.00 0.00 5.52
4134 4802 2.997315 TCCTCCACTCCACCGCTG 60.997 66.667 0.00 0.00 0.00 5.18
4135 4803 4.767255 CCTCCACTCCACCGCTGC 62.767 72.222 0.00 0.00 0.00 5.25
4136 4804 4.767255 CTCCACTCCACCGCTGCC 62.767 72.222 0.00 0.00 0.00 4.85
4209 4877 1.153549 CTCGCCCTCACCAGTAAGC 60.154 63.158 0.00 0.00 0.00 3.09
4211 4883 1.741770 CGCCCTCACCAGTAAGCAC 60.742 63.158 0.00 0.00 0.00 4.40
4214 4886 1.299976 CCTCACCAGTAAGCACCCC 59.700 63.158 0.00 0.00 0.00 4.95
4215 4887 1.299976 CTCACCAGTAAGCACCCCC 59.700 63.158 0.00 0.00 0.00 5.40
4216 4888 2.046314 CACCAGTAAGCACCCCCG 60.046 66.667 0.00 0.00 0.00 5.73
4217 4889 2.203877 ACCAGTAAGCACCCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
4218 4890 2.267961 CCAGTAAGCACCCCCGAC 59.732 66.667 0.00 0.00 0.00 4.79
4219 4891 2.267961 CAGTAAGCACCCCCGACC 59.732 66.667 0.00 0.00 0.00 4.79
4220 4892 3.007323 AGTAAGCACCCCCGACCC 61.007 66.667 0.00 0.00 0.00 4.46
4221 4893 4.105553 GTAAGCACCCCCGACCCC 62.106 72.222 0.00 0.00 0.00 4.95
4241 4913 2.520741 CCCCACGTGGCCACTTTT 60.521 61.111 32.28 14.62 0.00 2.27
4253 4930 0.591170 CCACTTTTGTCACGCGGATT 59.409 50.000 12.47 0.00 0.00 3.01
4296 4973 2.447443 GGGATCTGAAGGGTGGTTTTC 58.553 52.381 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.073722 CTGCAGCCTGGGAACTTCA 59.926 57.895 0.00 0.00 0.00 3.02
254 261 1.579429 GCCAAAGAAACACGCCGAT 59.421 52.632 0.00 0.00 0.00 4.18
255 262 2.887889 CGCCAAAGAAACACGCCGA 61.888 57.895 0.00 0.00 0.00 5.54
425 707 7.510675 TGGAGTATGGTTCTTTAAGGAAGAT 57.489 36.000 0.00 0.00 43.65 2.40
429 711 7.695055 TGATTTGGAGTATGGTTCTTTAAGGA 58.305 34.615 0.00 0.00 0.00 3.36
482 764 3.109151 TGGGATACAATACGGTTGTCCT 58.891 45.455 11.08 2.21 39.74 3.85
663 950 5.611796 TTGTGCATTAAGAACAGTGCTAG 57.388 39.130 0.00 0.00 37.02 3.42
671 958 8.028938 AGGATGTGTAATTTGTGCATTAAGAAC 58.971 33.333 0.00 0.00 0.00 3.01
687 974 3.402110 CAAGTGTCAGCAGGATGTGTAA 58.598 45.455 0.00 0.00 39.31 2.41
699 986 1.394917 GCAGTTATCGCCAAGTGTCAG 59.605 52.381 5.80 0.00 32.45 3.51
829 1116 2.030363 TGATGCACCCGTGAATGTTTTC 60.030 45.455 0.00 0.00 0.00 2.29
836 1124 3.073678 GCATATATGATGCACCCGTGAA 58.926 45.455 17.10 0.00 44.00 3.18
869 1159 9.965902 AGTAAAAAGATGTATCTGGTTGAGAAT 57.034 29.630 0.00 0.00 37.19 2.40
882 1179 8.483758 GGTGGAGGATTCTAGTAAAAAGATGTA 58.516 37.037 0.00 0.00 0.00 2.29
908 1205 0.394899 GATGCAACTGAAGGAGGGGG 60.395 60.000 0.00 0.00 0.00 5.40
913 1210 2.439409 CATGGTGATGCAACTGAAGGA 58.561 47.619 0.00 0.00 0.00 3.36
968 1265 2.226437 CCTGGTTGTGGTTTTCTGATCG 59.774 50.000 0.00 0.00 0.00 3.69
974 1271 1.398692 TGCTCCTGGTTGTGGTTTTC 58.601 50.000 0.00 0.00 0.00 2.29
1005 1302 2.897271 TCTGGCCATTAGCAAAGGAA 57.103 45.000 5.51 0.00 46.50 3.36
1102 1399 2.803155 TCCAGCCGTGGACATCTTGC 62.803 60.000 0.00 0.00 46.77 4.01
1328 1626 4.330944 ACGAACAACACCATCAGAACTA 57.669 40.909 0.00 0.00 0.00 2.24
1421 1719 4.750952 GACTTTCTTCAAGGCCTTGTAC 57.249 45.455 37.97 16.83 41.16 2.90
1532 1830 7.704899 GGAGCACAAATAACAATGGTAATTACC 59.295 37.037 25.22 25.22 46.62 2.85
1540 1838 3.727673 CGTCGGAGCACAAATAACAATGG 60.728 47.826 0.00 0.00 0.00 3.16
1773 2072 8.957466 GCTAGTGACAAGGGACTAAATAAATTT 58.043 33.333 0.00 0.00 38.49 1.82
1787 2086 1.741706 CATGGCAAGCTAGTGACAAGG 59.258 52.381 0.00 0.00 40.79 3.61
1944 2254 1.028905 TTGTTGTTCTCTTTGCGGGG 58.971 50.000 0.00 0.00 0.00 5.73
1945 2255 2.099098 AGTTTGTTGTTCTCTTTGCGGG 59.901 45.455 0.00 0.00 0.00 6.13
2037 2359 9.971922 AAAGGATTCATTTTCTGTAGTCTTTTG 57.028 29.630 0.00 0.00 0.00 2.44
2095 2419 3.243168 ACATTGAACACTCACATGCACAC 60.243 43.478 0.00 0.00 0.00 3.82
2111 2435 5.999205 ATGGGAATACTTTGCAACATTGA 57.001 34.783 0.00 0.00 0.00 2.57
2298 2631 3.126858 TGATACTCAATTTTGCTCGTGCC 59.873 43.478 7.05 0.00 38.71 5.01
2431 2764 1.795768 TTGCTCTTCACCTAGTTGCG 58.204 50.000 0.00 0.00 0.00 4.85
2538 2871 1.741770 CAACTGCTACGAGGGCCAC 60.742 63.158 6.18 0.00 0.00 5.01
2548 2881 6.038161 GTGCATTTACCATGTATCAACTGCTA 59.962 38.462 0.00 0.00 0.00 3.49
2551 2884 6.193514 TGTGCATTTACCATGTATCAACTG 57.806 37.500 0.00 0.00 0.00 3.16
2671 3005 9.715121 TGGTAGTTCGTTTACTGAGATTTAATT 57.285 29.630 0.00 0.00 0.00 1.40
2689 3023 8.658499 ATCGGTAATGAATTACTTGGTAGTTC 57.342 34.615 11.84 6.15 41.71 3.01
2699 3033 8.923683 GCTAGTAAGGAATCGGTAATGAATTAC 58.076 37.037 4.87 4.87 41.38 1.89
2714 3048 7.066307 TCATATGCAAGATGCTAGTAAGGAA 57.934 36.000 7.01 0.00 45.31 3.36
2721 3055 9.486857 CGAAAATAATCATATGCAAGATGCTAG 57.513 33.333 7.01 0.00 45.31 3.42
2751 3085 3.453353 AGCATTGATTTTGATTGGGAGGG 59.547 43.478 0.00 0.00 0.00 4.30
2767 3101 6.774354 AAATGTGTCTTTTAAGCAGCATTG 57.226 33.333 0.00 0.00 0.00 2.82
2820 3154 3.064207 GTGACTTGTCAAACGGCATAGA 58.936 45.455 4.93 0.00 0.00 1.98
2908 3242 0.853530 GGGCTTCCCATTGATAGGGT 59.146 55.000 0.00 0.00 46.82 4.34
2923 3258 2.284995 GTCCTGGTCTCCTGGGCT 60.285 66.667 8.67 0.00 42.77 5.19
2943 3278 3.563808 ACATCGTACAGAAAGCTTGCAAA 59.436 39.130 7.33 0.00 0.00 3.68
2944 3279 3.138304 ACATCGTACAGAAAGCTTGCAA 58.862 40.909 7.33 0.00 0.00 4.08
2975 3311 1.326245 GTTTGGAAGCAAACAAACGCC 59.674 47.619 12.26 0.00 44.51 5.68
3009 3345 2.956333 TGAGCTACTGAAGGCGCTATTA 59.044 45.455 7.64 0.00 31.96 0.98
3011 3347 1.403814 TGAGCTACTGAAGGCGCTAT 58.596 50.000 7.64 0.00 31.96 2.97
3012 3348 1.067669 CATGAGCTACTGAAGGCGCTA 59.932 52.381 7.64 0.00 31.96 4.26
3013 3349 0.179089 CATGAGCTACTGAAGGCGCT 60.179 55.000 7.64 0.00 35.03 5.92
3070 3427 3.254411 TGTCAGACACTAGCAGAGTTCAG 59.746 47.826 0.00 0.00 35.64 3.02
3097 3454 5.760253 AGCCGTATAATTCTTCAGTTCCATG 59.240 40.000 0.00 0.00 0.00 3.66
3113 3470 1.128200 AAGGATGCACCAGCCGTATA 58.872 50.000 7.86 0.00 45.56 1.47
3130 3487 1.131126 CATACGCAAAGACCTGCCAAG 59.869 52.381 0.00 0.00 39.26 3.61
3131 3488 1.164411 CATACGCAAAGACCTGCCAA 58.836 50.000 0.00 0.00 39.26 4.52
3320 3677 5.163457 TGACAGCCAGATAACATCGATTACA 60.163 40.000 0.00 0.00 0.00 2.41
3358 3715 3.878778 AGTTTGCCACCATCTATCTCAC 58.121 45.455 0.00 0.00 0.00 3.51
3392 3835 1.882623 CTGAAAGTTGAACTCCCTGCC 59.117 52.381 0.00 0.00 0.00 4.85
3406 3849 0.825010 AAGGCACAGCACCCTGAAAG 60.825 55.000 0.00 0.00 41.77 2.62
3409 3855 0.036732 CTAAAGGCACAGCACCCTGA 59.963 55.000 0.00 0.00 41.77 3.86
3469 3916 1.532868 GTACAAGCAGCCAACTCACAG 59.467 52.381 0.00 0.00 0.00 3.66
3488 3935 0.545071 CCAAGGGGGCTCCAATTTGT 60.545 55.000 5.99 0.00 38.24 2.83
3505 3952 0.324460 TGATGCCATCCATTGCACCA 60.324 50.000 1.49 0.00 40.88 4.17
3530 3977 5.603596 ACACTGCAAATCAACAATCAACAT 58.396 33.333 0.00 0.00 0.00 2.71
3531 3978 5.008619 ACACTGCAAATCAACAATCAACA 57.991 34.783 0.00 0.00 0.00 3.33
3532 3979 5.730269 CAACACTGCAAATCAACAATCAAC 58.270 37.500 0.00 0.00 0.00 3.18
3533 3980 5.970140 CAACACTGCAAATCAACAATCAA 57.030 34.783 0.00 0.00 0.00 2.57
3627 4266 2.050442 CCGAAGCGGCAACCAAAC 60.050 61.111 1.45 0.00 41.17 2.93
3643 4282 7.708752 TGGAATTGTCAATGTTTTTACTGAACC 59.291 33.333 0.00 0.00 0.00 3.62
3700 4340 5.240891 ACTGTCATCAATGTAGACAAGTGG 58.759 41.667 10.48 3.85 41.27 4.00
3716 4356 6.015434 TGTTCATGTGTACTCACTACTGTCAT 60.015 38.462 0.00 0.00 44.14 3.06
3717 4357 5.300792 TGTTCATGTGTACTCACTACTGTCA 59.699 40.000 0.00 0.00 44.14 3.58
3718 4358 5.629849 GTGTTCATGTGTACTCACTACTGTC 59.370 44.000 0.00 0.00 44.14 3.51
3738 4378 0.884704 GTGCGATGTGGACAGGTGTT 60.885 55.000 0.00 0.00 39.04 3.32
3743 4383 1.448540 GGGAGTGCGATGTGGACAG 60.449 63.158 0.00 0.00 42.22 3.51
3748 4388 1.012086 CTGATTGGGAGTGCGATGTG 58.988 55.000 0.00 0.00 0.00 3.21
3775 4423 7.902087 CCATTAAGTGGTTGGAATTTAGGAAA 58.098 34.615 0.00 0.00 43.44 3.13
3800 4456 2.414481 CTGCTACCATGATGATAAGCGC 59.586 50.000 0.00 0.00 32.67 5.92
3891 4547 0.753262 TTTCTCCGGAGCTATCCTGC 59.247 55.000 27.39 0.00 44.22 4.85
3950 4606 2.803670 GAGTTGCGTGCGAGCGTA 60.804 61.111 0.00 0.00 40.67 4.42
3959 4615 0.747255 AGTCAGTGTGAGAGTTGCGT 59.253 50.000 0.00 0.00 0.00 5.24
3964 4620 1.539065 CGGCAAAGTCAGTGTGAGAGT 60.539 52.381 0.00 0.00 0.00 3.24
3965 4621 1.143305 CGGCAAAGTCAGTGTGAGAG 58.857 55.000 0.00 0.00 0.00 3.20
3966 4622 0.464036 ACGGCAAAGTCAGTGTGAGA 59.536 50.000 0.00 0.00 0.00 3.27
3967 4623 1.299541 AACGGCAAAGTCAGTGTGAG 58.700 50.000 0.00 0.00 0.00 3.51
3968 4624 1.668751 GAAACGGCAAAGTCAGTGTGA 59.331 47.619 0.00 0.00 0.00 3.58
3969 4625 1.594518 CGAAACGGCAAAGTCAGTGTG 60.595 52.381 0.00 0.00 0.00 3.82
3970 4626 0.655733 CGAAACGGCAAAGTCAGTGT 59.344 50.000 0.00 0.00 0.00 3.55
3971 4627 0.934496 TCGAAACGGCAAAGTCAGTG 59.066 50.000 0.00 0.00 0.00 3.66
3975 4631 2.961522 TGAATCGAAACGGCAAAGTC 57.038 45.000 0.00 0.00 0.00 3.01
4030 4686 1.077357 GCTCGTGGAGGAGAGGAGA 60.077 63.158 0.52 0.00 36.08 3.71
4037 4693 1.002087 GAAAAGGAAGCTCGTGGAGGA 59.998 52.381 0.00 0.00 0.00 3.71
4038 4694 1.270839 TGAAAAGGAAGCTCGTGGAGG 60.271 52.381 0.00 0.00 0.00 4.30
4039 4695 2.169832 TGAAAAGGAAGCTCGTGGAG 57.830 50.000 0.00 0.00 0.00 3.86
4067 4723 1.432270 GAATTGGCCGCGAGAGGAAG 61.432 60.000 8.23 0.00 0.00 3.46
4080 4736 3.408634 ACCGTACAAGTGGAAGAATTGG 58.591 45.455 0.00 0.00 0.00 3.16
4081 4737 4.274950 ACAACCGTACAAGTGGAAGAATTG 59.725 41.667 0.00 0.00 0.00 2.32
4082 4738 4.457466 ACAACCGTACAAGTGGAAGAATT 58.543 39.130 0.00 0.00 0.00 2.17
4099 4758 2.046604 GACGGCAGGGGTACAACC 60.047 66.667 0.00 0.00 37.60 3.77
4100 4759 1.079336 GAGACGGCAGGGGTACAAC 60.079 63.158 0.00 0.00 0.00 3.32
4102 4761 2.682494 GGAGACGGCAGGGGTACA 60.682 66.667 0.00 0.00 0.00 2.90
4103 4762 2.363925 AGGAGACGGCAGGGGTAC 60.364 66.667 0.00 0.00 0.00 3.34
4104 4763 2.043248 GAGGAGACGGCAGGGGTA 60.043 66.667 0.00 0.00 0.00 3.69
4110 4778 2.680352 GGAGTGGAGGAGACGGCA 60.680 66.667 0.00 0.00 0.00 5.69
4196 4864 1.299976 GGGGTGCTTACTGGTGAGG 59.700 63.158 0.00 0.00 0.00 3.86
4228 4900 1.711060 CGTGACAAAAGTGGCCACGT 61.711 55.000 29.68 24.78 44.12 4.49
4230 4902 1.299089 GCGTGACAAAAGTGGCCAC 60.299 57.895 29.22 29.22 32.41 5.01
4241 4913 4.590487 GGAAGAATCCGCGTGACA 57.410 55.556 4.92 0.00 35.59 3.58
4285 4962 0.816421 CCACGAACGAAAACCACCCT 60.816 55.000 0.14 0.00 0.00 4.34
4286 4963 1.650363 CCACGAACGAAAACCACCC 59.350 57.895 0.14 0.00 0.00 4.61
4296 4973 1.225376 TTACCTGCAAGCCACGAACG 61.225 55.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.