Multiple sequence alignment - TraesCS3D01G383200

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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 TraesCS3D01G383200 chr3D 100.000 2792 0 0 1 2792 498485388 498482597 0.000000e+00 5156.0
1 TraesCS3D01G383200 chr3D 84.128 1216 109 43 700 1855 498356697 498355506 0.000000e+00 1099.0
2 TraesCS3D01G383200 chr3D 82.937 1219 106 49 700 1853 498396144 498394963 0.000000e+00 1005.0
3 TraesCS3D01G383200 chr3D 83.599 1067 116 40 700 1728 498264926 498263881 0.000000e+00 946.0
4 TraesCS3D01G383200 chr3D 88.136 59 7 0 93 151 498427300 498427242 1.390000e-08 71.3
5 TraesCS3D01G383200 chr3A 89.266 1267 64 30 905 2147 638468044 638466826 0.000000e+00 1520.0
6 TraesCS3D01G383200 chr3A 91.182 1134 71 17 975 2092 638711570 638710450 0.000000e+00 1513.0
7 TraesCS3D01G383200 chr3A 83.759 1176 109 40 700 1843 638447349 638446224 0.000000e+00 1038.0
8 TraesCS3D01G383200 chr3A 90.815 577 34 14 1069 1636 638452987 638452421 0.000000e+00 754.0
9 TraesCS3D01G383200 chr3A 87.841 477 37 8 2087 2563 638707472 638707017 8.800000e-150 540.0
10 TraesCS3D01G383200 chr3A 89.809 157 11 3 475 629 638468305 638468152 2.190000e-46 196.0
11 TraesCS3D01G383200 chr3A 100.000 31 0 0 104 134 638705744 638705714 1.080000e-04 58.4
12 TraesCS3D01G383200 chr3B 88.472 1145 87 17 854 1966 659305667 659304536 0.000000e+00 1341.0
13 TraesCS3D01G383200 chr3B 85.536 1044 94 26 700 1724 659276400 659275395 0.000000e+00 1038.0
14 TraesCS3D01G383200 chr3B 85.667 914 68 23 2 869 659306579 659305683 0.000000e+00 904.0
15 TraesCS3D01G383200 chr3B 89.641 724 47 22 927 1631 659298281 659297567 0.000000e+00 896.0
16 TraesCS3D01G383200 chr3B 82.305 729 73 26 1967 2668 659304348 659303649 5.180000e-162 580.0
17 TraesCS3D01G383200 chr6B 79.539 347 43 21 2171 2501 314515594 314515260 3.620000e-54 222.0
18 TraesCS3D01G383200 chr6A 78.841 345 46 18 2171 2501 352618003 352617672 1.010000e-49 207.0
19 TraesCS3D01G383200 chr5A 81.714 175 20 7 2330 2497 556239006 556239175 4.850000e-28 135.0
20 TraesCS3D01G383200 chr5A 82.014 139 16 5 2366 2497 556299352 556299488 2.940000e-20 110.0
21 TraesCS3D01G383200 chr5A 82.014 139 16 5 2366 2497 556397865 556398001 2.940000e-20 110.0
22 TraesCS3D01G383200 chr4D 74.348 230 44 12 2283 2509 74408071 74408288 1.780000e-12 84.2
23 TraesCS3D01G383200 chr4B 73.913 230 44 13 2283 2509 106867653 106867869 8.290000e-11 78.7
24 TraesCS3D01G383200 chr4A 73.568 227 44 12 2286 2509 513185441 513185228 3.860000e-09 73.1


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 TraesCS3D01G383200 chr3D 498482597 498485388 2791 True 5156.000000 5156 100.000000 1 2792 1 chr3D.!!$R5 2791
1 TraesCS3D01G383200 chr3D 498355506 498356697 1191 True 1099.000000 1099 84.128000 700 1855 1 chr3D.!!$R2 1155
2 TraesCS3D01G383200 chr3D 498394963 498396144 1181 True 1005.000000 1005 82.937000 700 1853 1 chr3D.!!$R3 1153
3 TraesCS3D01G383200 chr3D 498263881 498264926 1045 True 946.000000 946 83.599000 700 1728 1 chr3D.!!$R1 1028
4 TraesCS3D01G383200 chr3A 638446224 638447349 1125 True 1038.000000 1038 83.759000 700 1843 1 chr3A.!!$R1 1143
5 TraesCS3D01G383200 chr3A 638466826 638468305 1479 True 858.000000 1520 89.537500 475 2147 2 chr3A.!!$R3 1672
6 TraesCS3D01G383200 chr3A 638452421 638452987 566 True 754.000000 754 90.815000 1069 1636 1 chr3A.!!$R2 567
7 TraesCS3D01G383200 chr3A 638705714 638711570 5856 True 703.800000 1513 93.007667 104 2563 3 chr3A.!!$R4 2459
8 TraesCS3D01G383200 chr3B 659275395 659276400 1005 True 1038.000000 1038 85.536000 700 1724 1 chr3B.!!$R1 1024
9 TraesCS3D01G383200 chr3B 659303649 659306579 2930 True 941.666667 1341 85.481333 2 2668 3 chr3B.!!$R3 2666
10 TraesCS3D01G383200 chr3B 659297567 659298281 714 True 896.000000 896 89.641000 927 1631 1 chr3B.!!$R2 704

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
231 251 0.104671 TGCAATCATCAGATCGCCGA 59.895 50.0 0.0 0.0 33.15 5.54 F
900 1010 0.246635 TAAGCTTCGCCCAGTCACTC 59.753 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 1205 1.123861 AGCTGCTCTCTGGGTGTTGA 61.124 55.0 0.0 0.0 0.0 3.18 R
2135 5595 1.165907 TTCCTTGCGACTGTGCCTTG 61.166 55.0 0.0 0.0 0.0 3.61 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
23 24 4.148891 GGTCGCTCAAACTAAACAAATCG 58.851 43.478 0.00 0.00 0.00 3.34
25 26 2.583801 CGCTCAAACTAAACAAATCGCG 59.416 45.455 0.00 0.00 0.00 5.87
27 28 2.908626 CTCAAACTAAACAAATCGCGCC 59.091 45.455 0.00 0.00 0.00 6.53
43 44 1.895051 CGCCACCAAATCAAATCGAC 58.105 50.000 0.00 0.00 0.00 4.20
49 50 3.980775 CACCAAATCAAATCGACACCAAC 59.019 43.478 0.00 0.00 0.00 3.77
53 54 1.504359 TCAAATCGACACCAACGACC 58.496 50.000 0.00 0.00 42.37 4.79
57 58 4.289245 CGACACCAACGACCCGGT 62.289 66.667 0.00 0.00 35.27 5.28
68 69 3.308705 ACCCGGTGGTTCCTCGAC 61.309 66.667 0.00 0.00 44.75 4.20
72 73 3.308705 GGTGGTTCCTCGACCGGT 61.309 66.667 6.92 6.92 42.83 5.28
87 88 1.360551 CGGTGGCTCGGAGTGATAG 59.639 63.158 6.90 0.00 0.00 2.08
89 90 0.824759 GGTGGCTCGGAGTGATAGTT 59.175 55.000 6.90 0.00 0.00 2.24
90 91 1.202428 GGTGGCTCGGAGTGATAGTTC 60.202 57.143 6.90 0.00 0.00 3.01
91 92 1.112113 TGGCTCGGAGTGATAGTTCC 58.888 55.000 6.90 0.00 0.00 3.62
210 230 4.799824 GCCCGCGCATGTGCAAAT 62.800 61.111 29.19 0.00 42.21 2.32
231 251 0.104671 TGCAATCATCAGATCGCCGA 59.895 50.000 0.00 0.00 33.15 5.54
245 265 4.485834 CCGACCGATTGGCGACGA 62.486 66.667 14.98 0.00 44.57 4.20
275 295 2.281208 TGCAGTGGTAACGTGGCC 60.281 61.111 0.00 0.00 42.51 5.36
287 307 1.198759 ACGTGGCCTTGTATGGGAGT 61.199 55.000 3.32 0.00 0.00 3.85
288 308 0.828022 CGTGGCCTTGTATGGGAGTA 59.172 55.000 3.32 0.00 0.00 2.59
289 309 1.472728 CGTGGCCTTGTATGGGAGTAC 60.473 57.143 3.32 0.00 0.00 2.73
290 310 1.838077 GTGGCCTTGTATGGGAGTACT 59.162 52.381 3.32 0.00 0.00 2.73
291 311 2.116238 TGGCCTTGTATGGGAGTACTC 58.884 52.381 14.87 14.87 0.00 2.59
320 340 4.911514 ATTATCGTGGTTTTGTATGGCC 57.088 40.909 0.00 0.00 0.00 5.36
322 342 2.208132 TCGTGGTTTTGTATGGCCAT 57.792 45.000 24.45 24.45 33.20 4.40
339 359 1.495878 CATCTAGCTCGGTGCATGTC 58.504 55.000 4.74 0.00 45.94 3.06
349 369 1.602311 GGTGCATGTCCATCTCATCC 58.398 55.000 0.00 0.00 0.00 3.51
353 373 1.051008 CATGTCCATCTCATCCCGGA 58.949 55.000 0.73 0.00 0.00 5.14
361 381 1.040646 TCTCATCCCGGACATGCTAC 58.959 55.000 0.73 0.00 0.00 3.58
366 386 0.251916 TCCCGGACATGCTACAAAGG 59.748 55.000 0.73 0.00 0.00 3.11
371 391 2.159099 CGGACATGCTACAAAGGCTAGA 60.159 50.000 0.00 0.00 0.00 2.43
384 404 1.574925 GCTAGACGCCGATCGATCA 59.425 57.895 24.40 2.82 41.67 2.92
540 561 8.041323 AGTAAATCACTCGACCAACTTTATCAT 58.959 33.333 0.00 0.00 28.33 2.45
574 595 4.557690 CGTATGTGGTTAGAGACGAAACAG 59.442 45.833 0.00 0.00 37.00 3.16
597 620 6.807230 CAGTTTTAGCAGTACGTAGACTTCAT 59.193 38.462 0.00 0.00 0.00 2.57
600 623 8.493547 GTTTTAGCAGTACGTAGACTTCATTTT 58.506 33.333 0.00 0.00 0.00 1.82
601 624 7.576750 TTAGCAGTACGTAGACTTCATTTTG 57.423 36.000 0.00 0.00 0.00 2.44
605 628 2.433436 ACGTAGACTTCATTTTGGGGC 58.567 47.619 0.00 0.00 0.00 5.80
618 641 0.741915 TTGGGGCAAAAGTTGTCGAC 59.258 50.000 9.11 9.11 35.72 4.20
636 659 2.919229 CGACAATACGGTACACCAGTTC 59.081 50.000 0.00 0.00 35.14 3.01
637 660 2.919229 GACAATACGGTACACCAGTTCG 59.081 50.000 0.00 0.00 35.14 3.95
665 690 6.717997 TCCAGATGAACAGTACAGTACTTACA 59.282 38.462 10.80 11.13 36.76 2.41
668 693 9.723447 CAGATGAACAGTACAGTACTTACATAG 57.277 37.037 10.80 1.46 36.76 2.23
756 817 1.153745 AGATGCAGAGACCGCGTTC 60.154 57.895 4.92 0.00 0.00 3.95
757 818 2.507102 ATGCAGAGACCGCGTTCG 60.507 61.111 4.92 0.00 0.00 3.95
758 819 3.282745 ATGCAGAGACCGCGTTCGT 62.283 57.895 4.92 0.00 0.00 3.85
759 820 2.733593 GCAGAGACCGCGTTCGTT 60.734 61.111 4.92 0.00 0.00 3.85
760 821 1.443194 GCAGAGACCGCGTTCGTTA 60.443 57.895 4.92 0.00 0.00 3.18
761 822 1.671880 GCAGAGACCGCGTTCGTTAC 61.672 60.000 4.92 0.00 0.00 2.50
762 823 1.069378 CAGAGACCGCGTTCGTTACC 61.069 60.000 4.92 0.00 0.00 2.85
763 824 1.081242 GAGACCGCGTTCGTTACCA 60.081 57.895 4.92 0.00 0.00 3.25
764 825 1.339946 GAGACCGCGTTCGTTACCAC 61.340 60.000 4.92 0.00 0.00 4.16
765 826 1.372128 GACCGCGTTCGTTACCACT 60.372 57.895 4.92 0.00 0.00 4.00
766 827 0.940991 GACCGCGTTCGTTACCACTT 60.941 55.000 4.92 0.00 0.00 3.16
787 855 2.937689 ACCTCCCCATGTGCTGCT 60.938 61.111 0.00 0.00 0.00 4.24
788 856 2.124403 CCTCCCCATGTGCTGCTC 60.124 66.667 0.00 0.00 0.00 4.26
789 857 2.124403 CTCCCCATGTGCTGCTCC 60.124 66.667 0.00 0.00 0.00 4.70
790 858 4.100084 TCCCCATGTGCTGCTCCG 62.100 66.667 0.00 0.00 0.00 4.63
791 859 4.415150 CCCCATGTGCTGCTCCGT 62.415 66.667 0.00 0.00 0.00 4.69
792 860 2.360350 CCCATGTGCTGCTCCGTT 60.360 61.111 0.00 0.00 0.00 4.44
793 861 1.973281 CCCATGTGCTGCTCCGTTT 60.973 57.895 0.00 0.00 0.00 3.60
818 887 0.809385 GCATCAGCAACAGCAGACAT 59.191 50.000 0.00 0.00 41.58 3.06
869 948 6.308282 CACTCGATTAACGCTAATCTATTCCC 59.692 42.308 14.76 0.00 40.87 3.97
892 1002 2.942648 ATTCCCGCTAAGCTTCGCCC 62.943 60.000 16.51 0.00 0.00 6.13
899 1009 0.247736 CTAAGCTTCGCCCAGTCACT 59.752 55.000 0.00 0.00 0.00 3.41
900 1010 0.246635 TAAGCTTCGCCCAGTCACTC 59.753 55.000 0.00 0.00 0.00 3.51
901 1011 2.771763 AAGCTTCGCCCAGTCACTCG 62.772 60.000 0.00 0.00 0.00 4.18
902 1012 2.651361 CTTCGCCCAGTCACTCGT 59.349 61.111 0.00 0.00 0.00 4.18
903 1013 1.734477 CTTCGCCCAGTCACTCGTG 60.734 63.158 0.00 0.00 0.00 4.35
1041 1205 1.744368 CATCAAGCCTCACGCAGCT 60.744 57.895 0.00 0.00 42.40 4.24
1187 1393 2.586792 GAGCCGGTCCAAGAGCAT 59.413 61.111 1.90 0.00 0.00 3.79
1188 1394 1.817099 GAGCCGGTCCAAGAGCATG 60.817 63.158 1.90 0.00 0.00 4.06
1189 1395 2.825836 GCCGGTCCAAGAGCATGG 60.826 66.667 1.90 0.00 42.12 3.66
1190 1396 2.671070 CCGGTCCAAGAGCATGGT 59.329 61.111 0.00 0.00 41.46 3.55
1260 1469 2.722201 GCGGATCGAGTGGGAGGTT 61.722 63.158 0.00 0.00 0.00 3.50
1605 1829 3.341629 CTCATGGGGGTGCCCTGT 61.342 66.667 7.26 0.00 44.66 4.00
1657 1916 0.809241 CCCATCAGCTGTTCTCGCTC 60.809 60.000 14.67 0.00 35.07 5.03
1662 1921 1.069204 TCAGCTGTTCTCGCTCTTTGT 59.931 47.619 14.67 0.00 35.07 2.83
1682 1947 1.161843 TTTGGGCGAAGATCGGTTTC 58.838 50.000 1.64 0.00 40.84 2.78
1690 1955 1.464997 GAAGATCGGTTTCAGGTGTGC 59.535 52.381 0.00 0.00 0.00 4.57
1881 2164 7.194607 ACAGTGATTGTGTTTTCTACAGATG 57.805 36.000 0.00 0.00 38.99 2.90
1882 2165 6.082338 CAGTGATTGTGTTTTCTACAGATGC 58.918 40.000 0.00 0.00 37.45 3.91
1883 2166 5.082059 GTGATTGTGTTTTCTACAGATGCG 58.918 41.667 0.00 0.00 37.45 4.73
1884 2167 4.754618 TGATTGTGTTTTCTACAGATGCGT 59.245 37.500 0.00 0.00 37.45 5.24
1885 2168 5.929415 TGATTGTGTTTTCTACAGATGCGTA 59.071 36.000 0.00 0.00 37.45 4.42
1886 2169 5.585500 TTGTGTTTTCTACAGATGCGTAC 57.415 39.130 0.00 0.00 37.45 3.67
1930 2213 3.278574 GTTGCTGGCTCCATGTACATTA 58.721 45.455 5.37 0.00 0.00 1.90
1955 2238 6.844696 TTCGATGGAATTAGCAATACAGTC 57.155 37.500 0.00 0.00 0.00 3.51
1959 2242 4.523083 TGGAATTAGCAATACAGTCCACC 58.477 43.478 0.00 0.00 0.00 4.61
1961 2244 4.523083 GAATTAGCAATACAGTCCACCCA 58.477 43.478 0.00 0.00 0.00 4.51
1962 2245 3.343941 TTAGCAATACAGTCCACCCAC 57.656 47.619 0.00 0.00 0.00 4.61
2135 5595 1.949525 ACAGTCAGTTTCACACATGCC 59.050 47.619 0.00 0.00 0.00 4.40
2159 5619 1.537202 GCACAGTCGCAAGGAAATCTT 59.463 47.619 0.00 0.00 35.79 2.40
2173 5633 4.466370 AGGAAATCTTCATGTACTCCACGA 59.534 41.667 0.00 0.00 0.00 4.35
2183 5643 6.884832 TCATGTACTCCACGAAAATTCCTAT 58.115 36.000 0.00 0.00 0.00 2.57
2190 5650 3.066760 CCACGAAAATTCCTATTGGAGCC 59.933 47.826 0.00 0.00 44.24 4.70
2560 6032 5.201910 TCGTGAACAGTTTCTAAATTTGCG 58.798 37.500 0.00 0.00 32.36 4.85
2579 6051 7.993821 TTTGCGAACAATTTCTAAATTCACA 57.006 28.000 0.00 0.00 36.52 3.58
2741 6217 4.360951 TTTTCGCTTCCCTTCCTCTTTA 57.639 40.909 0.00 0.00 0.00 1.85
2743 6219 4.569719 TTCGCTTCCCTTCCTCTTTATT 57.430 40.909 0.00 0.00 0.00 1.40
2787 6263 1.768684 GCCGAGGCCCAATAGGATCA 61.769 60.000 0.00 0.00 38.24 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.170116 TCGATTTGATTTGGTGGCGC 59.830 50.000 0.00 0.00 0.00 6.53
25 26 2.595386 GTGTCGATTTGATTTGGTGGC 58.405 47.619 0.00 0.00 0.00 5.01
27 28 3.913548 TGGTGTCGATTTGATTTGGTG 57.086 42.857 0.00 0.00 0.00 4.17
57 58 3.307906 CCACCGGTCGAGGAACCA 61.308 66.667 2.59 0.00 39.43 3.67
72 73 1.112113 GGAACTATCACTCCGAGCCA 58.888 55.000 0.00 0.00 0.00 4.75
80 81 0.537188 CTGTGCGGGGAACTATCACT 59.463 55.000 0.00 0.00 0.00 3.41
82 83 0.249120 CACTGTGCGGGGAACTATCA 59.751 55.000 0.00 0.00 0.00 2.15
83 84 1.090052 GCACTGTGCGGGGAACTATC 61.090 60.000 17.93 0.00 31.71 2.08
84 85 1.078426 GCACTGTGCGGGGAACTAT 60.078 57.895 17.93 0.00 31.71 2.12
85 86 2.345991 GCACTGTGCGGGGAACTA 59.654 61.111 17.93 0.00 31.71 2.24
134 154 3.067833 GTTCCATTTAGCCTATCGGAGC 58.932 50.000 0.00 0.00 0.00 4.70
135 155 4.608948 AGTTCCATTTAGCCTATCGGAG 57.391 45.455 0.00 0.00 0.00 4.63
193 213 4.799824 ATTTGCACATGCGCGGGC 62.800 61.111 18.81 18.81 45.83 6.13
205 225 3.729217 CGATCTGATGATTGCACATTTGC 59.271 43.478 0.00 0.00 40.18 3.68
231 251 1.087771 GGATTTCGTCGCCAATCGGT 61.088 55.000 9.55 0.00 39.05 4.69
239 259 0.179200 ACGCATTTGGATTTCGTCGC 60.179 50.000 0.00 0.00 0.00 5.19
244 264 1.987770 CACTGCACGCATTTGGATTTC 59.012 47.619 0.00 0.00 0.00 2.17
245 265 1.337074 CCACTGCACGCATTTGGATTT 60.337 47.619 12.43 0.00 33.29 2.17
306 326 3.053693 AGCTAGATGGCCATACAAAACCA 60.054 43.478 20.84 0.00 36.43 3.67
319 339 0.105593 ACATGCACCGAGCTAGATGG 59.894 55.000 0.00 0.00 45.94 3.51
320 340 1.495878 GACATGCACCGAGCTAGATG 58.504 55.000 0.00 0.00 45.94 2.90
322 342 0.970427 TGGACATGCACCGAGCTAGA 60.970 55.000 0.00 0.00 45.94 2.43
339 359 0.604780 GCATGTCCGGGATGAGATGG 60.605 60.000 16.12 0.00 36.73 3.51
349 369 0.392998 AGCCTTTGTAGCATGTCCGG 60.393 55.000 0.00 0.00 0.00 5.14
353 373 2.893637 CGTCTAGCCTTTGTAGCATGT 58.106 47.619 0.00 0.00 0.00 3.21
384 404 4.741239 ACCTGACCCCCTGCCGAT 62.741 66.667 0.00 0.00 0.00 4.18
390 410 3.402681 CGCATCACCTGACCCCCT 61.403 66.667 0.00 0.00 0.00 4.79
434 455 1.970917 GCGAGCATGTGGACTTTCCG 61.971 60.000 0.00 0.00 40.17 4.30
540 561 1.503091 CACATACGTCCGTGTCCGA 59.497 57.895 1.98 0.00 35.63 4.55
574 595 7.578169 AATGAAGTCTACGTACTGCTAAAAC 57.422 36.000 0.00 0.00 0.00 2.43
597 620 1.825474 TCGACAACTTTTGCCCCAAAA 59.175 42.857 3.46 3.46 40.41 2.44
600 623 0.394488 TGTCGACAACTTTTGCCCCA 60.394 50.000 17.62 0.00 0.00 4.96
601 624 0.741915 TTGTCGACAACTTTTGCCCC 59.258 50.000 26.53 0.00 0.00 5.80
605 628 4.461992 ACCGTATTGTCGACAACTTTTG 57.538 40.909 31.87 20.52 38.86 2.44
618 641 2.264813 CCGAACTGGTGTACCGTATTG 58.735 52.381 0.00 0.00 39.43 1.90
668 693 9.113876 CGTTTGTTTCCATTTGTTTACTCTATC 57.886 33.333 0.00 0.00 0.00 2.08
698 723 1.617947 GGAATCCTCTCACCGGCTGT 61.618 60.000 0.00 0.00 0.00 4.40
756 817 1.066645 GGGAGGTGGTAAGTGGTAACG 60.067 57.143 0.00 0.00 42.51 3.18
757 818 1.280133 GGGGAGGTGGTAAGTGGTAAC 59.720 57.143 0.00 0.00 0.00 2.50
758 819 1.132462 TGGGGAGGTGGTAAGTGGTAA 60.132 52.381 0.00 0.00 0.00 2.85
759 820 0.492730 TGGGGAGGTGGTAAGTGGTA 59.507 55.000 0.00 0.00 0.00 3.25
760 821 0.178843 ATGGGGAGGTGGTAAGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
761 822 0.255890 CATGGGGAGGTGGTAAGTGG 59.744 60.000 0.00 0.00 0.00 4.00
762 823 0.991920 ACATGGGGAGGTGGTAAGTG 59.008 55.000 0.00 0.00 0.00 3.16
763 824 0.991920 CACATGGGGAGGTGGTAAGT 59.008 55.000 0.00 0.00 0.00 2.24
764 825 0.394352 GCACATGGGGAGGTGGTAAG 60.394 60.000 0.00 0.00 35.58 2.34
765 826 0.844661 AGCACATGGGGAGGTGGTAA 60.845 55.000 0.00 0.00 43.26 2.85
766 827 1.229820 AGCACATGGGGAGGTGGTA 60.230 57.895 0.00 0.00 43.26 3.25
790 858 0.452784 GTTGCTGATGCGACGGAAAC 60.453 55.000 0.00 0.00 42.88 2.78
791 859 1.866237 GTTGCTGATGCGACGGAAA 59.134 52.632 0.00 0.00 42.88 3.13
792 860 3.561429 GTTGCTGATGCGACGGAA 58.439 55.556 0.00 0.00 42.88 4.30
818 887 4.988065 GCTGAGTTAGGCGACACA 57.012 55.556 0.00 0.00 0.00 3.72
869 948 1.587547 GAAGCTTAGCGGGAATGGAG 58.412 55.000 0.00 0.00 0.00 3.86
892 1002 6.699204 AGAATTAAGATATGCACGAGTGACTG 59.301 38.462 7.50 0.00 0.00 3.51
899 1009 8.506168 AAAAAGGAGAATTAAGATATGCACGA 57.494 30.769 0.00 0.00 0.00 4.35
947 1080 2.272918 GAAGTCGCGACAGAGAGGGG 62.273 65.000 37.85 0.00 0.00 4.79
1041 1205 1.123861 AGCTGCTCTCTGGGTGTTGA 61.124 55.000 0.00 0.00 0.00 3.18
1294 1503 4.471726 GTCGTCATCGTCCGGCGT 62.472 66.667 16.00 3.62 42.13 5.68
1605 1829 5.333581 TCTTAGACTTGGATGAAGGAGTGA 58.666 41.667 0.00 0.00 35.78 3.41
1657 1916 2.584791 CGATCTTCGCCCAAAACAAAG 58.415 47.619 0.00 0.00 31.14 2.77
1662 1921 1.538075 GAAACCGATCTTCGCCCAAAA 59.462 47.619 0.00 0.00 38.82 2.44
1682 1947 4.389077 GCTAACACTTAACTAGCACACCTG 59.611 45.833 0.00 0.00 38.33 4.00
1690 1955 7.602517 AAGAATGCAGCTAACACTTAACTAG 57.397 36.000 0.00 0.00 0.00 2.57
1877 2160 3.444034 AGACACACATGTAGTACGCATCT 59.556 43.478 0.00 0.00 39.95 2.90
1878 2161 3.770666 AGACACACATGTAGTACGCATC 58.229 45.455 0.00 0.00 39.95 3.91
1879 2162 3.868757 AGACACACATGTAGTACGCAT 57.131 42.857 0.00 1.01 39.95 4.73
1880 2163 3.653539 AAGACACACATGTAGTACGCA 57.346 42.857 0.00 0.00 39.95 5.24
1881 2164 6.530534 AGAATAAAGACACACATGTAGTACGC 59.469 38.462 0.00 0.00 39.95 4.42
1882 2165 8.462143 AAGAATAAAGACACACATGTAGTACG 57.538 34.615 0.00 0.00 39.95 3.67
1884 2167 9.772973 ACAAAGAATAAAGACACACATGTAGTA 57.227 29.630 0.00 0.00 39.95 1.82
1885 2168 8.677148 ACAAAGAATAAAGACACACATGTAGT 57.323 30.769 0.00 0.00 39.95 2.73
1886 2169 9.385902 CAACAAAGAATAAAGACACACATGTAG 57.614 33.333 0.00 0.00 39.95 2.74
1930 2213 7.041098 GGACTGTATTGCTAATTCCATCGAAAT 60.041 37.037 0.00 0.00 0.00 2.17
1959 2242 7.633621 CAAGAAATGTATATGTAGCACAGTGG 58.366 38.462 1.84 0.00 0.00 4.00
1961 2244 6.823182 TGCAAGAAATGTATATGTAGCACAGT 59.177 34.615 0.00 0.00 0.00 3.55
1962 2245 7.250445 TGCAAGAAATGTATATGTAGCACAG 57.750 36.000 0.00 0.00 0.00 3.66
2075 2552 6.671614 TGTCTTAAATATAGTTGGCCGTTG 57.328 37.500 0.00 0.00 0.00 4.10
2135 5595 1.165907 TTCCTTGCGACTGTGCCTTG 61.166 55.000 0.00 0.00 0.00 3.61
2159 5619 5.160607 AGGAATTTTCGTGGAGTACATGA 57.839 39.130 0.00 0.00 43.20 3.07
2173 5633 3.956848 GCTCAGGCTCCAATAGGAATTTT 59.043 43.478 0.00 0.00 45.19 1.82
2274 5740 7.855784 ACAAGTAGTATACATCCATGATCCA 57.144 36.000 5.50 0.00 46.26 3.41
2309 5775 9.599322 GTAGCTCATAAAAATATTTCGTCATGG 57.401 33.333 0.10 0.44 0.00 3.66
2350 5819 9.595823 AGTACATATGCTAGAAATACGTGTTTT 57.404 29.630 11.77 4.93 0.00 2.43
2534 6006 6.691388 GCAAATTTAGAAACTGTTCACGAACT 59.309 34.615 11.01 0.00 41.67 3.01
2535 6007 6.343924 CGCAAATTTAGAAACTGTTCACGAAC 60.344 38.462 2.89 2.89 41.50 3.95
2536 6008 5.679355 CGCAAATTTAGAAACTGTTCACGAA 59.321 36.000 0.00 0.00 36.09 3.85
2537 6009 5.006844 TCGCAAATTTAGAAACTGTTCACGA 59.993 36.000 0.00 0.00 36.09 4.35
2538 6010 5.201910 TCGCAAATTTAGAAACTGTTCACG 58.798 37.500 0.00 0.00 36.09 4.35
2539 6011 6.470877 TGTTCGCAAATTTAGAAACTGTTCAC 59.529 34.615 9.09 0.00 36.09 3.18
2540 6012 6.556212 TGTTCGCAAATTTAGAAACTGTTCA 58.444 32.000 9.09 1.92 36.09 3.18
2541 6013 7.444558 TTGTTCGCAAATTTAGAAACTGTTC 57.555 32.000 9.09 0.00 33.58 3.18
2542 6014 8.419076 AATTGTTCGCAAATTTAGAAACTGTT 57.581 26.923 9.09 0.00 40.90 3.16
2543 6015 8.419076 AAATTGTTCGCAAATTTAGAAACTGT 57.581 26.923 9.09 0.00 40.90 3.55
2544 6016 8.755018 AGAAATTGTTCGCAAATTTAGAAACTG 58.245 29.630 9.09 0.00 40.90 3.16
2723 6199 4.569719 AAATAAAGAGGAAGGGAAGCGA 57.430 40.909 0.00 0.00 0.00 4.93
2724 6200 5.644977 AAAAATAAAGAGGAAGGGAAGCG 57.355 39.130 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.