Multiple sequence alignment - TraesCS5D01G361900

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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 TraesCS5D01G361900 chr5D 100.000 2947 0 0 1 2947 440946809 440949755 0.000000e+00 5443
1 TraesCS5D01G361900 chr5D 86.733 799 56 26 888 1646 440938304 440939092 0.000000e+00 843
2 TraesCS5D01G361900 chr5D 87.016 516 56 9 1066 1576 440965611 440966120 3.300000e-159 571
3 TraesCS5D01G361900 chr5D 87.037 216 18 5 458 673 440937341 440937546 4.910000e-58 235
4 TraesCS5D01G361900 chr5D 86.458 96 7 4 705 794 440937538 440937633 1.870000e-17 100
5 TraesCS5D01G361900 chr5B 90.655 2001 107 22 1005 2947 536476238 536478216 0.000000e+00 2586
6 TraesCS5D01G361900 chr5B 85.396 808 63 30 888 1646 536384090 536384891 0.000000e+00 787
7 TraesCS5D01G361900 chr5B 86.705 519 52 14 1066 1576 536508534 536509043 7.130000e-156 560
8 TraesCS5D01G361900 chr5B 86.346 520 34 18 888 1376 536425551 536426064 1.550000e-147 532
9 TraesCS5D01G361900 chr5B 83.262 466 37 13 7 463 536429976 536430409 9.900000e-105 390
10 TraesCS5D01G361900 chr5B 88.479 217 15 1 458 674 536383113 536383319 1.360000e-63 254
11 TraesCS5D01G361900 chr5B 84.579 214 24 3 1448 1652 536426062 536426275 1.380000e-48 204
12 TraesCS5D01G361900 chr5B 88.957 163 9 4 546 700 536424651 536424812 3.000000e-45 193
13 TraesCS5D01G361900 chr5A 89.060 1170 73 23 799 1937 557081499 557082644 0.000000e+00 1400
14 TraesCS5D01G361900 chr5A 91.425 828 50 11 2135 2947 556739739 556738918 0.000000e+00 1116
15 TraesCS5D01G361900 chr5A 91.425 828 50 11 2135 2947 557087988 557088809 0.000000e+00 1116
16 TraesCS5D01G361900 chr5A 88.535 785 44 20 888 1646 557076582 557077346 0.000000e+00 909
17 TraesCS5D01G361900 chr5A 85.863 672 39 24 9 651 557080097 557080741 0.000000e+00 664
18 TraesCS5D01G361900 chr5A 84.765 617 65 17 1049 1652 557092692 557093292 2.530000e-165 592
19 TraesCS5D01G361900 chr5A 85.577 520 56 15 1066 1576 557098890 557099399 7.230000e-146 527
20 TraesCS5D01G361900 chr5A 87.892 223 19 3 458 673 557071498 557071719 3.770000e-64 255
21 TraesCS5D01G361900 chr5A 90.099 101 9 1 2143 2243 557108574 557108673 2.380000e-26 130


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 TraesCS5D01G361900 chr5D 440946809 440949755 2946 False 5443.000000 5443 100.000000 1 2947 1 chr5D.!!$F1 2946
1 TraesCS5D01G361900 chr5D 440965611 440966120 509 False 571.000000 571 87.016000 1066 1576 1 chr5D.!!$F2 510
2 TraesCS5D01G361900 chr5D 440937341 440939092 1751 False 392.666667 843 86.742667 458 1646 3 chr5D.!!$F3 1188
3 TraesCS5D01G361900 chr5B 536476238 536478216 1978 False 2586.000000 2586 90.655000 1005 2947 1 chr5B.!!$F1 1942
4 TraesCS5D01G361900 chr5B 536508534 536509043 509 False 560.000000 560 86.705000 1066 1576 1 chr5B.!!$F2 510
5 TraesCS5D01G361900 chr5B 536383113 536384891 1778 False 520.500000 787 86.937500 458 1646 2 chr5B.!!$F3 1188
6 TraesCS5D01G361900 chr5B 536424651 536430409 5758 False 329.750000 532 85.786000 7 1652 4 chr5B.!!$F4 1645
7 TraesCS5D01G361900 chr5A 556738918 556739739 821 True 1116.000000 1116 91.425000 2135 2947 1 chr5A.!!$R1 812
8 TraesCS5D01G361900 chr5A 557076582 557082644 6062 False 991.000000 1400 87.819333 9 1937 3 chr5A.!!$F4 1928
9 TraesCS5D01G361900 chr5A 557087988 557093292 5304 False 854.000000 1116 88.095000 1049 2947 2 chr5A.!!$F5 1898
10 TraesCS5D01G361900 chr5A 557098890 557099399 509 False 527.000000 527 85.577000 1066 1576 1 chr5A.!!$F2 510

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
134 3643 0.033228 CAGAGGATGATCTGGGCGAC 59.967 60.0 0.00 0.00 42.52 5.19 F
209 3718 0.179018 ACAATCTTATCCTGCGCCCC 60.179 55.0 4.18 0.00 0.00 5.80 F
829 5110 0.250252 GCAGAGAGAATGGGGCTAGC 60.250 60.0 6.04 6.04 0.00 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1040 5360 0.035176 GATGAGATGAGAGCAGGGGC 59.965 60.0 0.00 0.0 41.61 5.80 R
1775 6135 0.179034 CTACCTGCTGGCCAAGATCC 60.179 60.0 7.01 0.0 36.63 3.36 R
2615 9940 0.722676 ACCCTCCCTCCTGATTGGTA 59.277 55.0 0.00 0.0 37.07 3.25 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
20 21 3.994931 AACCTGCCCGAAGTACTATTT 57.005 42.857 0.00 0.00 0.00 1.40
22 23 3.105283 ACCTGCCCGAAGTACTATTTCT 58.895 45.455 0.00 0.00 0.00 2.52
31 3540 2.317973 AGTACTATTTCTCTCCGGCCC 58.682 52.381 0.00 0.00 0.00 5.80
91 3600 3.005684 TCGTCCGGTAAACTAAAGAGCAA 59.994 43.478 0.00 0.00 0.00 3.91
92 3601 3.742369 CGTCCGGTAAACTAAAGAGCAAA 59.258 43.478 0.00 0.00 0.00 3.68
119 3628 0.610174 TGGCTAACCAGTCAGCAGAG 59.390 55.000 0.00 0.00 42.67 3.35
120 3629 0.107945 GGCTAACCAGTCAGCAGAGG 60.108 60.000 0.00 0.00 39.63 3.69
121 3630 0.898320 GCTAACCAGTCAGCAGAGGA 59.102 55.000 0.00 0.00 37.73 3.71
122 3631 1.484240 GCTAACCAGTCAGCAGAGGAT 59.516 52.381 0.00 0.00 37.73 3.24
123 3632 2.741228 GCTAACCAGTCAGCAGAGGATG 60.741 54.545 0.00 0.00 37.73 3.51
124 3633 1.649321 AACCAGTCAGCAGAGGATGA 58.351 50.000 0.00 0.00 37.03 2.92
125 3634 1.876849 ACCAGTCAGCAGAGGATGAT 58.123 50.000 0.00 0.00 42.17 2.45
126 3635 1.761784 ACCAGTCAGCAGAGGATGATC 59.238 52.381 0.00 0.00 42.17 2.92
127 3636 2.040939 CCAGTCAGCAGAGGATGATCT 58.959 52.381 0.00 0.00 42.17 2.75
129 3638 2.040939 AGTCAGCAGAGGATGATCTGG 58.959 52.381 5.92 0.00 45.66 3.86
130 3639 1.070445 GTCAGCAGAGGATGATCTGGG 59.930 57.143 5.92 0.00 45.66 4.45
131 3640 0.250381 CAGCAGAGGATGATCTGGGC 60.250 60.000 5.92 0.00 45.66 5.36
133 3642 1.752358 GCAGAGGATGATCTGGGCGA 61.752 60.000 5.92 0.00 45.66 5.54
134 3643 0.033228 CAGAGGATGATCTGGGCGAC 59.967 60.000 0.00 0.00 42.52 5.19
140 3649 0.249120 ATGATCTGGGCGACGAACAA 59.751 50.000 0.00 0.00 0.00 2.83
145 3654 2.070783 TCTGGGCGACGAACAAATTAC 58.929 47.619 0.00 0.00 0.00 1.89
163 3672 3.825611 GCCAATCATGCCGGCGTT 61.826 61.111 21.21 7.26 35.79 4.84
174 3683 3.864944 CGGCGTTTGACCGTGTAT 58.135 55.556 0.00 0.00 45.70 2.29
209 3718 0.179018 ACAATCTTATCCTGCGCCCC 60.179 55.000 4.18 0.00 0.00 5.80
240 3749 0.308376 GGTGCTCGATCGAGTAGACC 59.692 60.000 37.59 33.41 43.70 3.85
241 3750 1.015109 GTGCTCGATCGAGTAGACCA 58.985 55.000 37.59 26.53 43.70 4.02
242 3751 1.604755 GTGCTCGATCGAGTAGACCAT 59.395 52.381 37.59 0.00 43.70 3.55
243 3752 2.033550 GTGCTCGATCGAGTAGACCATT 59.966 50.000 37.59 0.00 43.70 3.16
244 3753 2.290916 TGCTCGATCGAGTAGACCATTC 59.709 50.000 37.59 22.09 43.70 2.67
278 3787 2.223745 CTTTGCTTTGCCAATTTGCCT 58.776 42.857 0.00 0.00 0.00 4.75
286 3795 0.674581 GCCAATTTGCCTGCCTTTCC 60.675 55.000 0.00 0.00 0.00 3.13
328 3837 2.478370 CCACACATGATTGCCGATTGAC 60.478 50.000 0.00 0.00 0.00 3.18
346 3855 4.220693 TGACATCCAGATAACAAGTGGG 57.779 45.455 0.00 0.00 31.70 4.61
347 3856 3.054434 TGACATCCAGATAACAAGTGGGG 60.054 47.826 0.00 0.00 31.70 4.96
348 3857 3.189606 ACATCCAGATAACAAGTGGGGA 58.810 45.455 0.00 0.00 31.70 4.81
349 3858 3.591527 ACATCCAGATAACAAGTGGGGAA 59.408 43.478 0.00 0.00 31.70 3.97
351 3860 4.733077 TCCAGATAACAAGTGGGGAAAA 57.267 40.909 0.00 0.00 31.70 2.29
353 3862 3.763897 CCAGATAACAAGTGGGGAAAAGG 59.236 47.826 0.00 0.00 0.00 3.11
354 3863 3.763897 CAGATAACAAGTGGGGAAAAGGG 59.236 47.826 0.00 0.00 0.00 3.95
357 3866 1.156095 CAAGTGGGGAAAAGGGGCT 59.844 57.895 0.00 0.00 0.00 5.19
360 3869 1.913262 GTGGGGAAAAGGGGCTTGG 60.913 63.158 0.00 0.00 0.00 3.61
394 3911 2.817258 CGGTGATCCAGTTAAAAGCCAA 59.183 45.455 0.00 0.00 0.00 4.52
416 3933 2.993264 CAAAGGTGGCAGCTGGGG 60.993 66.667 21.35 8.95 0.00 4.96
509 4049 4.237207 GGGGCCGCCACTAGCTAC 62.237 72.222 12.58 0.00 40.39 3.58
514 4054 2.183300 CGCCACTAGCTACGGCAA 59.817 61.111 23.07 0.00 46.60 4.52
679 4233 3.149648 GGTGGACATGGCATGGGC 61.150 66.667 29.49 20.46 40.13 5.36
691 4245 2.065899 GCATGGGCCTGTATTTACCA 57.934 50.000 4.53 0.00 35.39 3.25
692 4246 2.383855 GCATGGGCCTGTATTTACCAA 58.616 47.619 4.53 0.00 34.45 3.67
693 4247 2.965147 GCATGGGCCTGTATTTACCAAT 59.035 45.455 4.53 0.00 34.45 3.16
694 4248 3.243839 GCATGGGCCTGTATTTACCAATG 60.244 47.826 4.53 0.00 34.45 2.82
695 4249 4.214310 CATGGGCCTGTATTTACCAATGA 58.786 43.478 4.53 0.00 34.45 2.57
696 4250 4.323569 TGGGCCTGTATTTACCAATGAA 57.676 40.909 4.53 0.00 0.00 2.57
697 4251 4.277476 TGGGCCTGTATTTACCAATGAAG 58.723 43.478 4.53 0.00 0.00 3.02
698 4252 4.264172 TGGGCCTGTATTTACCAATGAAGT 60.264 41.667 4.53 0.00 0.00 3.01
699 4253 4.338400 GGGCCTGTATTTACCAATGAAGTC 59.662 45.833 0.84 0.00 0.00 3.01
700 4254 5.193679 GGCCTGTATTTACCAATGAAGTCT 58.806 41.667 0.00 0.00 0.00 3.24
703 4257 6.543831 GCCTGTATTTACCAATGAAGTCTCAT 59.456 38.462 0.00 0.00 44.54 2.90
783 4349 4.523173 AGACGGTTTCTCTATGTGAACAGA 59.477 41.667 0.00 0.00 0.00 3.41
794 4360 7.499563 TCTCTATGTGAACAGAGTGGACTATAC 59.500 40.741 5.09 0.00 39.48 1.47
808 5089 6.099845 AGTGGACTATACTCGGGAATGAAAAT 59.900 38.462 0.00 0.00 0.00 1.82
827 5108 0.326522 TGGCAGAGAGAATGGGGCTA 60.327 55.000 0.00 0.00 0.00 3.93
828 5109 0.396060 GGCAGAGAGAATGGGGCTAG 59.604 60.000 0.00 0.00 0.00 3.42
829 5110 0.250252 GCAGAGAGAATGGGGCTAGC 60.250 60.000 6.04 6.04 0.00 3.42
830 5111 0.396060 CAGAGAGAATGGGGCTAGCC 59.604 60.000 26.55 26.55 0.00 3.93
851 5132 2.734606 CAGCAATGAAAACATGCCACAG 59.265 45.455 0.00 0.00 40.93 3.66
852 5133 2.070783 GCAATGAAAACATGCCACAGG 58.929 47.619 0.00 0.00 34.03 4.00
854 5135 3.803021 GCAATGAAAACATGCCACAGGAA 60.803 43.478 0.00 0.00 34.03 3.36
855 5136 4.571919 CAATGAAAACATGCCACAGGAAT 58.428 39.130 0.00 0.00 0.00 3.01
865 5150 2.224257 TGCCACAGGAATTTTTCAAGGC 60.224 45.455 0.00 0.00 39.95 4.35
870 5155 3.321968 ACAGGAATTTTTCAAGGCAGGAC 59.678 43.478 0.00 0.00 0.00 3.85
933 5218 7.499563 GCATGAGCTTCATTATGGATCATATCT 59.500 37.037 0.00 0.00 34.28 1.98
945 5231 5.409712 TGGATCATATCTCTCCACCTGATT 58.590 41.667 0.00 0.00 34.17 2.57
1013 5333 1.962570 TTCCCTCCTCCCTCCCTAGC 61.963 65.000 0.00 0.00 0.00 3.42
1034 5354 1.121407 CCCACTCCACACAGAGACCA 61.121 60.000 0.00 0.00 37.33 4.02
1035 5355 0.319728 CCACTCCACACAGAGACCAG 59.680 60.000 0.00 0.00 37.33 4.00
1036 5356 1.332195 CACTCCACACAGAGACCAGA 58.668 55.000 0.00 0.00 37.33 3.86
1037 5357 1.271934 CACTCCACACAGAGACCAGAG 59.728 57.143 0.00 0.00 37.33 3.35
1038 5358 0.894141 CTCCACACAGAGACCAGAGG 59.106 60.000 0.00 0.00 35.82 3.69
1039 5359 1.188219 TCCACACAGAGACCAGAGGC 61.188 60.000 0.00 0.00 0.00 4.70
1040 5360 1.080230 CACACAGAGACCAGAGGCG 60.080 63.158 0.00 0.00 0.00 5.52
1041 5361 2.125753 CACAGAGACCAGAGGCGC 60.126 66.667 0.00 0.00 0.00 6.53
1043 5363 4.154347 CAGAGACCAGAGGCGCCC 62.154 72.222 26.15 15.34 0.00 6.13
1060 5380 1.719529 CCCCTGCTCTCATCTCATCT 58.280 55.000 0.00 0.00 0.00 2.90
1775 6135 5.164051 CGTATATAGCCGCTCTTTGTCAATG 60.164 44.000 0.00 0.00 0.00 2.82
1867 6229 2.869801 CTCGCTTGACTTGTGTTGGTAA 59.130 45.455 0.00 0.00 0.00 2.85
1890 6252 7.979444 AACATTATCACCCATCGGTAAATAG 57.021 36.000 0.00 0.00 42.04 1.73
1943 6306 9.696917 GGTACTTTCAAATCAATTTCATCAGTT 57.303 29.630 0.00 0.00 0.00 3.16
1956 6319 9.734620 CAATTTCATCAGTTCACAAAAAGAGTA 57.265 29.630 0.00 0.00 0.00 2.59
1958 6321 7.496529 TTCATCAGTTCACAAAAAGAGTAGG 57.503 36.000 0.00 0.00 0.00 3.18
1961 6324 6.920569 TCAGTTCACAAAAAGAGTAGGAAC 57.079 37.500 0.00 0.00 34.82 3.62
1983 6346 8.630037 GGAACTCAGAAAAGTGAAAAAGGAATA 58.370 33.333 0.00 0.00 0.00 1.75
1999 6362 2.480845 GAATATACAGACGTGGGTGCC 58.519 52.381 0.00 0.00 0.00 5.01
2100 6465 1.740296 GTTCATGTGGACCGACCGG 60.740 63.158 6.94 6.94 42.61 5.28
2288 6710 1.870055 CGGTGGGCACAGTACGTACT 61.870 60.000 22.45 22.45 36.90 2.73
2639 9994 3.435601 CCAATCAGGAGGGAGGGTTTATG 60.436 52.174 0.00 0.00 41.22 1.90
2769 10142 5.007724 CCCTTTTCGATGCCATTAGTTCTAC 59.992 44.000 0.00 0.00 0.00 2.59
2770 10143 5.817816 CCTTTTCGATGCCATTAGTTCTACT 59.182 40.000 0.00 0.00 0.00 2.57
2863 10260 2.610859 GGCAGAGGGGAGGTGGAA 60.611 66.667 0.00 0.00 0.00 3.53
2900 10308 0.320508 GTCCCAACTCCCAACTCGAC 60.321 60.000 0.00 0.00 0.00 4.20
2908 10316 0.251297 TCCCAACTCGACCGGTAGAA 60.251 55.000 18.49 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.518303 AGAAATAGTACTTCGGGCAGGTT 59.482 43.478 0.00 0.00 0.00 3.50
2 3 3.385111 AGAGAAATAGTACTTCGGGCAGG 59.615 47.826 0.00 0.00 0.00 4.85
3 4 4.500035 GGAGAGAAATAGTACTTCGGGCAG 60.500 50.000 0.00 0.00 0.00 4.85
4 5 3.383825 GGAGAGAAATAGTACTTCGGGCA 59.616 47.826 0.00 0.00 0.00 5.36
5 6 3.550436 CGGAGAGAAATAGTACTTCGGGC 60.550 52.174 0.00 0.00 0.00 6.13
11 12 2.317973 GGGCCGGAGAGAAATAGTACT 58.682 52.381 5.05 0.00 0.00 2.73
12 13 1.343789 GGGGCCGGAGAGAAATAGTAC 59.656 57.143 5.05 0.00 0.00 2.73
13 14 1.713297 GGGGCCGGAGAGAAATAGTA 58.287 55.000 5.05 0.00 0.00 1.82
14 15 1.054978 GGGGGCCGGAGAGAAATAGT 61.055 60.000 5.05 0.00 0.00 2.12
15 16 1.755384 GGGGGCCGGAGAGAAATAG 59.245 63.158 5.05 0.00 0.00 1.73
16 17 2.138179 CGGGGGCCGGAGAGAAATA 61.138 63.158 5.05 0.00 44.15 1.40
49 3558 0.528924 TCGACGTGGATTTGATCGGT 59.471 50.000 0.00 0.00 33.66 4.69
50 3559 1.787155 GATCGACGTGGATTTGATCGG 59.213 52.381 14.57 0.00 33.66 4.18
91 3600 3.437642 TGGTTAGCCAGCAAAGCTT 57.562 47.368 0.00 0.00 41.83 3.74
107 3616 2.040939 AGATCATCCTCTGCTGACTGG 58.959 52.381 0.00 0.00 0.00 4.00
119 3628 0.876342 GTTCGTCGCCCAGATCATCC 60.876 60.000 0.00 0.00 0.00 3.51
120 3629 0.179111 TGTTCGTCGCCCAGATCATC 60.179 55.000 0.00 0.00 0.00 2.92
121 3630 0.249120 TTGTTCGTCGCCCAGATCAT 59.751 50.000 0.00 0.00 0.00 2.45
122 3631 0.034198 TTTGTTCGTCGCCCAGATCA 59.966 50.000 0.00 0.00 0.00 2.92
123 3632 1.369625 ATTTGTTCGTCGCCCAGATC 58.630 50.000 0.00 0.00 0.00 2.75
124 3633 1.821216 AATTTGTTCGTCGCCCAGAT 58.179 45.000 0.00 0.00 0.00 2.90
125 3634 2.070783 GTAATTTGTTCGTCGCCCAGA 58.929 47.619 0.00 0.00 0.00 3.86
126 3635 1.201877 CGTAATTTGTTCGTCGCCCAG 60.202 52.381 0.00 0.00 0.00 4.45
127 3636 0.791422 CGTAATTTGTTCGTCGCCCA 59.209 50.000 0.00 0.00 0.00 5.36
128 3637 0.519792 GCGTAATTTGTTCGTCGCCC 60.520 55.000 0.00 0.00 38.16 6.13
129 3638 2.907177 GCGTAATTTGTTCGTCGCC 58.093 52.632 0.00 0.00 38.16 5.54
130 3639 0.164217 TGGCGTAATTTGTTCGTCGC 59.836 50.000 0.00 0.00 42.32 5.19
131 3640 2.580729 TTGGCGTAATTTGTTCGTCG 57.419 45.000 0.00 0.00 31.65 5.12
133 3642 4.411327 CATGATTGGCGTAATTTGTTCGT 58.589 39.130 0.00 0.00 0.00 3.85
134 3643 3.240401 GCATGATTGGCGTAATTTGTTCG 59.760 43.478 0.00 0.00 0.00 3.95
163 3672 6.778834 TCTATCTAAACCATACACGGTCAA 57.221 37.500 0.00 0.00 38.76 3.18
209 3718 3.883744 GAGCACCACACCTCACCCG 62.884 68.421 0.00 0.00 0.00 5.28
215 3724 1.938657 CTCGATCGAGCACCACACCT 61.939 60.000 30.41 0.00 35.31 4.00
240 3749 6.088824 AGCAAAGCGTAAAAGAGAATGAATG 58.911 36.000 0.00 0.00 0.00 2.67
241 3750 6.259550 AGCAAAGCGTAAAAGAGAATGAAT 57.740 33.333 0.00 0.00 0.00 2.57
242 3751 5.689383 AGCAAAGCGTAAAAGAGAATGAA 57.311 34.783 0.00 0.00 0.00 2.57
243 3752 5.689383 AAGCAAAGCGTAAAAGAGAATGA 57.311 34.783 0.00 0.00 0.00 2.57
244 3753 5.387752 GCAAAGCAAAGCGTAAAAGAGAATG 60.388 40.000 0.00 0.00 0.00 2.67
278 3787 1.304052 CCAACGGGATGGAAAGGCA 60.304 57.895 0.00 0.00 43.54 4.75
328 3837 3.931907 TCCCCACTTGTTATCTGGATG 57.068 47.619 0.00 0.00 0.00 3.51
346 3855 2.009681 TTTCTCCAAGCCCCTTTTCC 57.990 50.000 0.00 0.00 0.00 3.13
347 3856 2.288213 CGTTTTCTCCAAGCCCCTTTTC 60.288 50.000 0.00 0.00 0.00 2.29
348 3857 1.686587 CGTTTTCTCCAAGCCCCTTTT 59.313 47.619 0.00 0.00 0.00 2.27
349 3858 1.328279 CGTTTTCTCCAAGCCCCTTT 58.672 50.000 0.00 0.00 0.00 3.11
351 3860 0.537371 CACGTTTTCTCCAAGCCCCT 60.537 55.000 0.00 0.00 0.00 4.79
353 3862 1.468914 GATCACGTTTTCTCCAAGCCC 59.531 52.381 0.00 0.00 0.00 5.19
354 3863 1.128692 CGATCACGTTTTCTCCAAGCC 59.871 52.381 0.00 0.00 34.56 4.35
357 3866 2.139917 CACCGATCACGTTTTCTCCAA 58.860 47.619 0.00 0.00 37.88 3.53
360 3869 2.603560 GGATCACCGATCACGTTTTCTC 59.396 50.000 6.33 0.00 40.50 2.87
394 3911 2.919328 GCTGCCACCTTTGCCCTT 60.919 61.111 0.00 0.00 0.00 3.95
418 3935 2.047179 GCGAGTTGGGACACCCTC 60.047 66.667 8.34 2.13 45.70 4.30
509 4049 1.330521 CCGAGATAATTGGTGTTGCCG 59.669 52.381 0.00 0.00 41.21 5.69
514 4054 2.494471 TCACGACCGAGATAATTGGTGT 59.506 45.455 0.00 0.00 46.69 4.16
692 4246 2.029623 GCCATGCCAATGAGACTTCAT 58.970 47.619 0.00 0.00 45.92 2.57
693 4247 1.466856 GCCATGCCAATGAGACTTCA 58.533 50.000 0.00 0.00 35.67 3.02
711 4265 4.265073 AGAGTTCATTGGTGAATACAGGC 58.735 43.478 0.00 0.00 45.46 4.85
783 4349 4.180377 TCATTCCCGAGTATAGTCCACT 57.820 45.455 1.88 0.00 0.00 4.00
794 4360 2.357009 CTCTGCCATTTTCATTCCCGAG 59.643 50.000 0.00 0.00 0.00 4.63
797 4363 3.624777 TCTCTCTGCCATTTTCATTCCC 58.375 45.455 0.00 0.00 0.00 3.97
808 5089 0.326522 TAGCCCCATTCTCTCTGCCA 60.327 55.000 0.00 0.00 0.00 4.92
827 5108 1.338389 GGCATGTTTTCATTGCTGGCT 60.338 47.619 0.00 0.00 38.64 4.75
828 5109 1.081094 GGCATGTTTTCATTGCTGGC 58.919 50.000 0.00 0.00 38.64 4.85
829 5110 2.070783 GTGGCATGTTTTCATTGCTGG 58.929 47.619 0.00 0.00 38.64 4.85
830 5111 2.734606 CTGTGGCATGTTTTCATTGCTG 59.265 45.455 0.00 0.00 38.64 4.41
851 5132 4.335400 TTGTCCTGCCTTGAAAAATTCC 57.665 40.909 0.00 0.00 0.00 3.01
852 5133 4.152938 GCATTGTCCTGCCTTGAAAAATTC 59.847 41.667 0.00 0.00 36.10 2.17
854 5135 3.071312 TGCATTGTCCTGCCTTGAAAAAT 59.929 39.130 0.00 0.00 41.58 1.82
855 5136 2.433604 TGCATTGTCCTGCCTTGAAAAA 59.566 40.909 0.00 0.00 41.58 1.94
865 5150 1.399714 ATGAGCCATGCATTGTCCTG 58.600 50.000 0.00 0.00 0.00 3.86
870 5155 2.855660 TTCGAATGAGCCATGCATTG 57.144 45.000 0.00 0.00 36.19 2.82
880 5165 4.806247 GTGGGAGTATCACTTTCGAATGAG 59.194 45.833 17.09 9.75 41.12 2.90
924 5209 7.041107 GCTTAATCAGGTGGAGAGATATGATC 58.959 42.308 0.00 0.00 0.00 2.92
933 5218 2.551270 AGTGGCTTAATCAGGTGGAGA 58.449 47.619 0.00 0.00 0.00 3.71
945 5231 2.771943 CTGGGATACTCCAAGTGGCTTA 59.228 50.000 0.00 0.00 38.64 3.09
992 5289 0.254638 TAGGGAGGGAGGAGGGAAGA 60.255 60.000 0.00 0.00 0.00 2.87
994 5291 1.962570 GCTAGGGAGGGAGGAGGGAA 61.963 65.000 0.00 0.00 0.00 3.97
995 5292 2.404750 GCTAGGGAGGGAGGAGGGA 61.405 68.421 0.00 0.00 0.00 4.20
996 5293 2.202899 GCTAGGGAGGGAGGAGGG 59.797 72.222 0.00 0.00 0.00 4.30
1013 5333 0.605589 GTCTCTGTGTGGAGTGGGAG 59.394 60.000 0.00 0.00 35.11 4.30
1040 5360 0.035176 GATGAGATGAGAGCAGGGGC 59.965 60.000 0.00 0.00 41.61 5.80
1041 5361 1.719529 AGATGAGATGAGAGCAGGGG 58.280 55.000 0.00 0.00 0.00 4.79
1043 5363 3.493002 GGACAAGATGAGATGAGAGCAGG 60.493 52.174 0.00 0.00 0.00 4.85
1045 5365 2.433604 GGGACAAGATGAGATGAGAGCA 59.566 50.000 0.00 0.00 0.00 4.26
1046 5366 2.433604 TGGGACAAGATGAGATGAGAGC 59.566 50.000 0.00 0.00 31.92 4.09
1051 5371 3.450096 TCTCTGTGGGACAAGATGAGATG 59.550 47.826 0.00 0.00 44.16 2.90
1060 5380 1.474320 CGTTGGTTCTCTGTGGGACAA 60.474 52.381 0.00 0.00 44.16 3.18
1679 6025 2.970639 GGAGACGCTACTGTGCCA 59.029 61.111 0.00 0.00 0.00 4.92
1775 6135 0.179034 CTACCTGCTGGCCAAGATCC 60.179 60.000 7.01 0.00 36.63 3.36
1855 6217 5.475220 TGGGTGATAATGTTACCAACACAAG 59.525 40.000 0.00 0.00 45.50 3.16
1913 6275 6.367421 TGAAATTGATTTGAAAGTACCGTCG 58.633 36.000 0.00 0.00 0.00 5.12
1956 6319 6.187682 TCCTTTTTCACTTTTCTGAGTTCCT 58.812 36.000 0.00 0.00 0.00 3.36
1969 6332 6.594159 CCACGTCTGTATATTCCTTTTTCACT 59.406 38.462 0.00 0.00 0.00 3.41
1983 6346 0.966875 TACGGCACCCACGTCTGTAT 60.967 55.000 0.00 0.00 44.37 2.29
2009 6372 1.438710 CGCGCGCTTTATGTATGCC 60.439 57.895 30.48 0.00 0.00 4.40
2100 6465 1.359459 CCCTCTTGCGGTAAAGCGAC 61.359 60.000 5.64 0.00 40.67 5.19
2128 6493 1.725641 TGATCGGCACTTGATCACAC 58.274 50.000 0.00 0.00 45.37 3.82
2276 6698 1.138247 GCCCGGAGTACGTACTGTG 59.862 63.158 31.91 21.80 42.24 3.66
2401 6885 2.206576 GGGTAGCCCATCATCATTCC 57.793 55.000 0.00 0.00 44.65 3.01
2546 9865 1.789078 GACGTGGATCCATGCATGCC 61.789 60.000 30.24 16.96 38.52 4.40
2611 9936 1.691434 CTCCCTCCTGATTGGTAGCTC 59.309 57.143 0.00 0.00 37.07 4.09
2615 9940 0.722676 ACCCTCCCTCCTGATTGGTA 59.277 55.000 0.00 0.00 37.07 3.25
2639 9994 6.436218 ACCCATCACAAAATTTTACTCCTACC 59.564 38.462 2.44 0.00 0.00 3.18
2769 10142 8.146412 TGTTATCTAGATGACAATCATGGTGAG 58.854 37.037 23.82 0.00 37.20 3.51
2770 10143 8.021898 TGTTATCTAGATGACAATCATGGTGA 57.978 34.615 23.82 1.26 37.20 4.02
2863 10260 4.760220 ATGCCCCCTCCCCGAGTT 62.760 66.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.