Multiple sequence alignment - TraesCS7B01G229600

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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 TraesCS7B01G229600 chr7B 100.000 3381 0 0 1 3381 431664858 431661478 0.000000e+00 6244
1 TraesCS7B01G229600 chr7B 93.421 76 5 0 2932 3007 431661885 431661810 2.760000e-21 113
2 TraesCS7B01G229600 chr7B 93.421 76 5 0 2974 3049 431661927 431661852 2.760000e-21 113
3 TraesCS7B01G229600 chr7D 95.301 2490 72 7 916 3381 416238785 416236317 0.000000e+00 3908
4 TraesCS7B01G229600 chr7A 94.970 2505 80 9 904 3381 478503708 478501223 0.000000e+00 3886
5 TraesCS7B01G229600 chr7A 85.950 484 53 8 384 863 478504263 478503791 1.400000e-138 503
6 TraesCS7B01G229600 chr7A 92.105 76 6 0 2932 3007 478501630 478501555 1.280000e-19 108
7 TraesCS7B01G229600 chr2A 87.443 1314 116 25 1067 2359 727918573 727917288 0.000000e+00 1467
8 TraesCS7B01G229600 chr2A 79.960 499 80 18 1872 2358 727244915 727244425 1.930000e-92 350
9 TraesCS7B01G229600 chr2A 80.986 426 54 13 1237 1660 419652343 419652743 2.530000e-81 313
10 TraesCS7B01G229600 chr2A 79.876 323 61 4 1 322 18171437 18171756 2.030000e-57 233
11 TraesCS7B01G229600 chr2A 77.083 384 62 17 1133 1511 727245607 727245245 7.400000e-47 198
12 TraesCS7B01G229600 chr2B 86.186 1332 128 30 1067 2371 719294266 719292964 0.000000e+00 1389
13 TraesCS7B01G229600 chr2B 77.477 888 147 25 4 864 769483005 769483866 1.820000e-132 483
14 TraesCS7B01G229600 chr2B 78.672 497 90 14 1872 2358 718969535 718969045 1.960000e-82 316
15 TraesCS7B01G229600 chr2B 79.876 323 61 4 1 322 4552148 4551829 2.030000e-57 233
16 TraesCS7B01G229600 chr2B 77.403 385 59 20 1133 1511 718970224 718969862 1.590000e-48 204
17 TraesCS7B01G229600 chr4B 77.344 768 117 35 45 789 652895956 652895223 5.250000e-108 401
18 TraesCS7B01G229600 chr4B 80.751 426 55 13 1237 1660 612329486 612329886 1.180000e-79 307
19 TraesCS7B01G229600 chr2D 79.960 499 80 18 1872 2358 592791037 592790547 1.930000e-92 350
20 TraesCS7B01G229600 chr2D 77.953 381 64 14 1133 1511 592791729 592791367 1.580000e-53 220
21 TraesCS7B01G229600 chr5D 84.290 331 24 15 558 864 530014890 530015216 7.090000e-77 298
22 TraesCS7B01G229600 chr5D 85.976 164 20 3 402 563 529854691 529854853 4.490000e-39 172
23 TraesCS7B01G229600 chr1B 75.549 683 126 28 211 863 356981796 356982467 7.090000e-77 298
24 TraesCS7B01G229600 chr3A 74.481 674 135 25 249 894 138287844 138288508 1.200000e-64 257
25 TraesCS7B01G229600 chr3A 75.940 266 52 9 263 523 459862932 459863190 3.540000e-25 126
26 TraesCS7B01G229600 chr4A 79.876 323 61 4 1 322 89642257 89642576 2.030000e-57 233
27 TraesCS7B01G229600 chr3D 81.250 128 21 3 622 748 613963011 613962886 2.150000e-17 100


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 TraesCS7B01G229600 chr7B 431661478 431664858 3380 True 2156.666667 6244 95.614000 1 3381 3 chr7B.!!$R1 3380
1 TraesCS7B01G229600 chr7D 416236317 416238785 2468 True 3908.000000 3908 95.301000 916 3381 1 chr7D.!!$R1 2465
2 TraesCS7B01G229600 chr7A 478501223 478504263 3040 True 1499.000000 3886 91.008333 384 3381 3 chr7A.!!$R1 2997
3 TraesCS7B01G229600 chr2A 727917288 727918573 1285 True 1467.000000 1467 87.443000 1067 2359 1 chr2A.!!$R1 1292
4 TraesCS7B01G229600 chr2A 727244425 727245607 1182 True 274.000000 350 78.521500 1133 2358 2 chr2A.!!$R2 1225
5 TraesCS7B01G229600 chr2B 719292964 719294266 1302 True 1389.000000 1389 86.186000 1067 2371 1 chr2B.!!$R2 1304
6 TraesCS7B01G229600 chr2B 769483005 769483866 861 False 483.000000 483 77.477000 4 864 1 chr2B.!!$F1 860
7 TraesCS7B01G229600 chr2B 718969045 718970224 1179 True 260.000000 316 78.037500 1133 2358 2 chr2B.!!$R3 1225
8 TraesCS7B01G229600 chr4B 652895223 652895956 733 True 401.000000 401 77.344000 45 789 1 chr4B.!!$R1 744
9 TraesCS7B01G229600 chr2D 592790547 592791729 1182 True 285.000000 350 78.956500 1133 2358 2 chr2D.!!$R1 1225
10 TraesCS7B01G229600 chr1B 356981796 356982467 671 False 298.000000 298 75.549000 211 863 1 chr1B.!!$F1 652
11 TraesCS7B01G229600 chr3A 138287844 138288508 664 False 257.000000 257 74.481000 249 894 1 chr3A.!!$F1 645

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
307 308 0.035458 CTAGGAATAGGCAAGCGGGG 59.965 60.0 0.0 0.0 0.00 5.73 F
600 612 0.103208 GCTGTCCTCGACATGGGTAG 59.897 60.0 0.0 0.0 41.94 3.18 F
1235 1332 0.885879 ATCTACAACGCCGTCACAGA 59.114 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1982 1.002069 TGATGAACCCCTGCTTCCAT 58.998 50.000 0.00 0.00 0.00 3.41 R
1891 2024 1.007271 CGAGTTGAGCACCGACAGT 60.007 57.895 0.00 0.00 0.00 3.55 R
2757 2897 0.099968 CATGCTGGGCGTTTCAGATG 59.900 55.000 6.09 4.12 34.36 2.90 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
21 22 3.371034 TGAGAAGGTGGTCATATTCGGA 58.629 45.455 0.00 0.00 0.00 4.55
22 23 3.967326 TGAGAAGGTGGTCATATTCGGAT 59.033 43.478 0.00 0.00 0.00 4.18
30 31 4.216257 GTGGTCATATTCGGATGGATTTGG 59.784 45.833 0.00 0.00 0.00 3.28
32 33 3.191371 GTCATATTCGGATGGATTTGGCC 59.809 47.826 0.00 0.00 0.00 5.36
33 34 3.156293 CATATTCGGATGGATTTGGCCA 58.844 45.455 0.00 0.00 43.23 5.36
63 64 1.028330 ATGGTGGACTTGCTGATGCG 61.028 55.000 0.00 0.00 43.34 4.73
67 68 0.950555 TGGACTTGCTGATGCGTGTC 60.951 55.000 0.00 0.00 43.34 3.67
89 90 2.111162 CGGAGCTCGAGAGGTTGAT 58.889 57.895 18.75 0.00 42.43 2.57
100 101 0.675522 GAGGTTGATCCGGGCGAAAA 60.676 55.000 0.00 0.00 41.99 2.29
109 110 0.602905 CCGGGCGAAAACTTGTCTCT 60.603 55.000 0.00 0.00 0.00 3.10
112 113 1.542547 GGGCGAAAACTTGTCTCTGGA 60.543 52.381 0.00 0.00 0.00 3.86
124 125 1.273886 GTCTCTGGAGTTTTCGGAGCT 59.726 52.381 0.00 0.00 0.00 4.09
125 126 2.492484 GTCTCTGGAGTTTTCGGAGCTA 59.508 50.000 0.00 0.00 0.00 3.32
160 161 2.110006 GAGCGCCATCTCCCTTCC 59.890 66.667 2.29 0.00 0.00 3.46
164 165 1.153289 CGCCATCTCCCTTCCTGTG 60.153 63.158 0.00 0.00 0.00 3.66
173 174 1.002134 CCTTCCTGTGGGCATCGTT 60.002 57.895 0.00 0.00 0.00 3.85
194 195 2.868964 AGGTACTCTCAGGCCCAATA 57.131 50.000 0.00 0.00 0.00 1.90
196 197 2.975489 AGGTACTCTCAGGCCCAATATG 59.025 50.000 0.00 0.00 0.00 1.78
197 198 2.706190 GGTACTCTCAGGCCCAATATGT 59.294 50.000 0.00 0.00 0.00 2.29
199 200 2.200081 ACTCTCAGGCCCAATATGTGT 58.800 47.619 0.00 0.00 0.00 3.72
202 203 3.384168 TCTCAGGCCCAATATGTGTAGT 58.616 45.455 0.00 0.00 0.00 2.73
206 207 4.227300 TCAGGCCCAATATGTGTAGTTTCT 59.773 41.667 0.00 0.00 0.00 2.52
208 209 4.227300 AGGCCCAATATGTGTAGTTTCTGA 59.773 41.667 0.00 0.00 0.00 3.27
209 210 4.947388 GGCCCAATATGTGTAGTTTCTGAA 59.053 41.667 0.00 0.00 0.00 3.02
237 238 1.566563 GATCCGTGTGATCGCATGC 59.433 57.895 20.82 7.91 40.53 4.06
242 243 1.353609 CGTGTGATCGCATGCTGACA 61.354 55.000 17.13 5.57 0.00 3.58
243 244 0.095935 GTGTGATCGCATGCTGACAC 59.904 55.000 17.13 20.20 0.00 3.67
293 294 2.290323 GGCTTTGTCTTTGGAGCTAGGA 60.290 50.000 0.00 0.00 35.53 2.94
296 297 5.186198 GCTTTGTCTTTGGAGCTAGGAATA 58.814 41.667 0.00 0.00 32.54 1.75
307 308 0.035458 CTAGGAATAGGCAAGCGGGG 59.965 60.000 0.00 0.00 0.00 5.73
330 332 0.327924 ATGGAAGATGGCGGTGTTGA 59.672 50.000 0.00 0.00 0.00 3.18
335 337 2.726691 GATGGCGGTGTTGACGTCG 61.727 63.158 11.62 0.00 39.10 5.12
336 338 4.953868 TGGCGGTGTTGACGTCGG 62.954 66.667 11.62 0.00 39.10 4.79
338 340 4.955774 GCGGTGTTGACGTCGGGT 62.956 66.667 11.62 0.00 0.00 5.28
348 350 1.803366 GACGTCGGGTCTTCTGTGGT 61.803 60.000 0.00 0.00 42.62 4.16
353 355 1.553248 TCGGGTCTTCTGTGGTAATGG 59.447 52.381 0.00 0.00 0.00 3.16
361 363 2.556766 TCTGTGGTAATGGTGATGGGA 58.443 47.619 0.00 0.00 0.00 4.37
371 373 2.545810 TGGTGATGGGAGTGTGTGATA 58.454 47.619 0.00 0.00 0.00 2.15
528 540 0.580104 CGTTCGGTGGTCTTTCACAC 59.420 55.000 0.00 0.00 39.27 3.82
531 543 0.105964 TCGGTGGTCTTTCACACTGG 59.894 55.000 0.00 0.00 42.72 4.00
554 566 4.005650 CAGCCTTGCATAGTTCTTCTTCA 58.994 43.478 0.00 0.00 0.00 3.02
593 605 2.355837 GTTGCGCTGTCCTCGACA 60.356 61.111 9.73 0.00 40.50 4.35
599 611 1.663379 CGCTGTCCTCGACATGGGTA 61.663 60.000 0.00 0.00 41.94 3.69
600 612 0.103208 GCTGTCCTCGACATGGGTAG 59.897 60.000 0.00 0.00 41.94 3.18
601 613 1.475403 CTGTCCTCGACATGGGTAGT 58.525 55.000 0.00 0.00 41.94 2.73
611 623 3.489398 CGACATGGGTAGTAGCTGAGTTC 60.489 52.174 0.00 0.00 0.00 3.01
670 682 1.271163 TGAAGGTTGGGTCGATGTTCC 60.271 52.381 0.00 0.00 0.00 3.62
704 717 1.213013 GAGTCGCTTGCTCGGAGAA 59.787 57.895 9.69 0.00 34.09 2.87
707 720 1.476891 AGTCGCTTGCTCGGAGAATAA 59.523 47.619 9.69 0.00 34.09 1.40
750 780 1.063174 GAAGAAGTGATGCCGATGTGC 59.937 52.381 0.00 0.00 0.00 4.57
758 788 1.779025 ATGCCGATGTGCGATCTTGC 61.779 55.000 0.00 0.00 44.57 4.01
796 839 2.281208 GTTGTGTGGGTGCCGCTA 60.281 61.111 0.00 0.00 34.70 4.26
808 851 3.578456 CCGCTAGGCAGTTTGTGG 58.422 61.111 0.00 0.00 0.00 4.17
844 889 7.269316 CCGGTTTTTATTAATTAACTGGGCAT 58.731 34.615 18.73 0.00 41.32 4.40
847 926 9.529325 GGTTTTTATTAATTAACTGGGCATCTC 57.471 33.333 0.00 0.00 0.00 2.75
854 933 2.969628 AACTGGGCATCTCTTCTACG 57.030 50.000 0.00 0.00 0.00 3.51
859 938 4.406003 ACTGGGCATCTCTTCTACGTAATT 59.594 41.667 0.00 0.00 0.00 1.40
867 946 9.250624 GCATCTCTTCTACGTAATTAATGTCTT 57.749 33.333 0.00 0.00 0.00 3.01
886 965 5.875930 GTCTTTTGACTCCGTTTGAAAAGA 58.124 37.500 0.00 0.00 45.55 2.52
887 966 6.319399 GTCTTTTGACTCCGTTTGAAAAGAA 58.681 36.000 0.00 0.00 45.55 2.52
888 967 6.250739 GTCTTTTGACTCCGTTTGAAAAGAAC 59.749 38.462 0.00 0.00 45.55 3.01
889 968 5.630661 TTTGACTCCGTTTGAAAAGAACA 57.369 34.783 0.00 0.00 0.00 3.18
890 969 4.609691 TGACTCCGTTTGAAAAGAACAC 57.390 40.909 0.00 0.00 0.00 3.32
892 971 4.698304 TGACTCCGTTTGAAAAGAACACTT 59.302 37.500 0.00 0.00 0.00 3.16
894 973 3.765026 TCCGTTTGAAAAGAACACTTGC 58.235 40.909 0.00 0.00 0.00 4.01
895 974 3.191581 TCCGTTTGAAAAGAACACTTGCA 59.808 39.130 0.00 0.00 0.00 4.08
896 975 3.923461 CCGTTTGAAAAGAACACTTGCAA 59.077 39.130 0.00 0.00 0.00 4.08
898 977 4.856487 CGTTTGAAAAGAACACTTGCAAGA 59.144 37.500 32.50 3.08 0.00 3.02
899 978 5.344665 CGTTTGAAAAGAACACTTGCAAGAA 59.655 36.000 32.50 9.49 0.00 2.52
900 979 6.128956 CGTTTGAAAAGAACACTTGCAAGAAA 60.129 34.615 32.50 14.81 0.00 2.52
902 981 6.266168 TGAAAAGAACACTTGCAAGAAAGA 57.734 33.333 32.50 0.00 0.00 2.52
903 982 6.866480 TGAAAAGAACACTTGCAAGAAAGAT 58.134 32.000 32.50 15.65 0.00 2.40
904 983 6.753279 TGAAAAGAACACTTGCAAGAAAGATG 59.247 34.615 32.50 20.98 0.00 2.90
914 993 3.311966 GCAAGAAAGATGCACAAAGTCC 58.688 45.455 0.00 0.00 43.29 3.85
1233 1330 1.011968 GCATCTACAACGCCGTCACA 61.012 55.000 0.00 0.00 0.00 3.58
1235 1332 0.885879 ATCTACAACGCCGTCACAGA 59.114 50.000 0.00 0.00 0.00 3.41
1245 1342 1.162698 CCGTCACAGACCTCGTCTAA 58.837 55.000 0.00 0.00 41.37 2.10
1251 1348 1.339438 ACAGACCTCGTCTAAGGCGTA 60.339 52.381 0.00 0.00 41.37 4.42
1275 1372 2.354729 CCGGTCCAGCCCATGAAA 59.645 61.111 0.00 0.00 0.00 2.69
1357 1454 2.293318 ATCCTCACAGCCGCCTTCA 61.293 57.895 0.00 0.00 0.00 3.02
1407 1504 1.062845 GCTCGTCTACTGGCTCGTC 59.937 63.158 0.00 0.00 0.00 4.20
1408 1505 1.722677 CTCGTCTACTGGCTCGTCC 59.277 63.158 0.00 0.00 0.00 4.79
1409 1506 1.716826 CTCGTCTACTGGCTCGTCCC 61.717 65.000 0.00 0.00 0.00 4.46
1410 1507 2.799371 GTCTACTGGCTCGTCCCG 59.201 66.667 0.00 0.00 0.00 5.14
1411 1508 3.138798 TCTACTGGCTCGTCCCGC 61.139 66.667 0.00 0.00 0.00 6.13
1412 1509 3.141488 CTACTGGCTCGTCCCGCT 61.141 66.667 0.00 0.00 0.00 5.52
1413 1510 3.127352 CTACTGGCTCGTCCCGCTC 62.127 68.421 0.00 0.00 0.00 5.03
1419 1516 3.382832 CTCGTCCCGCTCCCACTT 61.383 66.667 0.00 0.00 0.00 3.16
1420 1517 2.920912 TCGTCCCGCTCCCACTTT 60.921 61.111 0.00 0.00 0.00 2.66
1421 1518 2.032071 CGTCCCGCTCCCACTTTT 59.968 61.111 0.00 0.00 0.00 2.27
1422 1519 2.325082 CGTCCCGCTCCCACTTTTG 61.325 63.158 0.00 0.00 0.00 2.44
1602 1702 2.320587 CCGCCCTATGCTTCATCGC 61.321 63.158 0.00 0.00 38.05 4.58
1683 1795 3.202829 AGGAAACAACAGCCGTTCTTA 57.797 42.857 0.00 0.00 31.13 2.10
1849 1982 2.421314 CACATATCGCGGGAGGCA 59.579 61.111 6.13 0.00 43.84 4.75
2278 2414 1.445066 CGTCATGCTCGTCTGCACT 60.445 57.895 3.09 0.00 46.33 4.40
2563 2703 5.762218 AGCTTCACTAATGTCTATTGCATCC 59.238 40.000 0.00 0.00 0.00 3.51
2602 2742 0.824595 TTCTCCTGTCGACAACCGGA 60.825 55.000 20.49 20.37 38.79 5.14
2611 2751 0.601558 CGACAACCGGAGAAGGAGAA 59.398 55.000 9.46 0.00 34.73 2.87
2616 2756 2.011122 ACCGGAGAAGGAGAAGACAA 57.989 50.000 9.46 0.00 34.73 3.18
2675 2815 1.758280 TCGGTACATTACTTCGGCCAT 59.242 47.619 2.24 0.00 0.00 4.40
2689 2829 1.031571 GGCCATTGAACATCCGAGCA 61.032 55.000 0.00 0.00 0.00 4.26
2697 2837 0.392998 AACATCCGAGCACCATGGAC 60.393 55.000 21.47 10.28 33.91 4.02
2704 2844 3.127533 GCACCATGGACGACTGGC 61.128 66.667 21.47 6.25 35.88 4.85
2725 2865 3.084579 GATGCTTCGACTGGTGCG 58.915 61.111 0.00 0.00 0.00 5.34
2728 2868 3.782244 GCTTCGACTGGTGCGCAG 61.782 66.667 12.22 0.60 0.00 5.18
2729 2869 3.114616 CTTCGACTGGTGCGCAGG 61.115 66.667 12.22 6.90 0.00 4.85
2752 2892 1.438814 GCTTGCACCAGCTTTGTGT 59.561 52.632 13.22 0.00 42.74 3.72
2757 2897 0.308993 GCACCAGCTTTGTGTCTGTC 59.691 55.000 13.22 0.00 37.91 3.51
2983 3138 1.279152 CAGAGTTCTGAGCATCGCTG 58.721 55.000 2.97 0.00 46.59 5.18
2989 3144 1.521010 CTGAGCATCGCTGGACTGG 60.521 63.158 0.00 0.00 39.88 4.00
3025 3180 1.144565 CGGAGTTCTGAGCATCGCTG 61.145 60.000 0.00 0.00 39.88 5.18
3241 3396 2.792290 CGTGGCGCATTCAGACTCG 61.792 63.158 10.83 0.00 0.00 4.18
3361 3516 7.341769 TCTTCATCCTTCTTTTCCAAAAACTCA 59.658 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.310769 CATCCGAATATGACCACCTTCTC 58.689 47.826 0.00 0.00 0.00 2.87
2 3 3.071602 CCATCCGAATATGACCACCTTCT 59.928 47.826 0.00 0.00 0.00 2.85
5 6 2.689658 TCCATCCGAATATGACCACCT 58.310 47.619 0.00 0.00 0.00 4.00
14 15 3.156293 CATGGCCAAATCCATCCGAATA 58.844 45.455 10.96 0.00 44.63 1.75
17 18 0.550432 TCATGGCCAAATCCATCCGA 59.450 50.000 10.96 0.00 44.63 4.55
32 33 1.679680 GTCCACCATTGAGCCATCATG 59.320 52.381 0.00 0.00 34.73 3.07
33 34 1.567649 AGTCCACCATTGAGCCATCAT 59.432 47.619 0.00 0.00 34.73 2.45
36 37 1.843368 CAAGTCCACCATTGAGCCAT 58.157 50.000 0.00 0.00 0.00 4.40
43 44 1.180029 GCATCAGCAAGTCCACCATT 58.820 50.000 0.00 0.00 41.58 3.16
48 49 0.950555 GACACGCATCAGCAAGTCCA 60.951 55.000 0.00 0.00 42.27 4.02
63 64 1.875813 CTCGAGCTCCGCATGACAC 60.876 63.158 8.47 0.00 38.37 3.67
67 68 2.027314 CCTCTCGAGCTCCGCATG 59.973 66.667 7.81 0.00 38.37 4.06
89 90 0.601841 GAGACAAGTTTTCGCCCGGA 60.602 55.000 0.73 0.00 0.00 5.14
100 101 2.698797 TCCGAAAACTCCAGAGACAAGT 59.301 45.455 0.70 0.00 0.00 3.16
109 110 0.108804 CGCTAGCTCCGAAAACTCCA 60.109 55.000 13.93 0.00 0.00 3.86
112 113 1.471676 CCATCGCTAGCTCCGAAAACT 60.472 52.381 13.93 0.00 38.31 2.66
117 118 3.966104 CGCCATCGCTAGCTCCGA 61.966 66.667 13.93 11.18 39.24 4.55
160 161 0.249120 TACCTCAACGATGCCCACAG 59.751 55.000 0.00 0.00 0.00 3.66
164 165 0.824759 AGAGTACCTCAACGATGCCC 59.175 55.000 0.00 0.00 32.06 5.36
187 188 5.880332 TCTTCAGAAACTACACATATTGGGC 59.120 40.000 0.00 0.00 0.00 5.36
188 189 7.921786 TTCTTCAGAAACTACACATATTGGG 57.078 36.000 0.00 0.00 0.00 4.12
202 203 6.015350 ACACGGATCTAGAGTTTCTTCAGAAA 60.015 38.462 0.00 0.00 41.29 2.52
206 207 4.765339 TCACACGGATCTAGAGTTTCTTCA 59.235 41.667 0.00 0.00 0.00 3.02
208 209 5.923733 ATCACACGGATCTAGAGTTTCTT 57.076 39.130 0.00 0.00 0.00 2.52
233 234 0.388134 GCCAAAGCAGTGTCAGCATG 60.388 55.000 0.00 0.00 39.53 4.06
235 236 1.453562 TGCCAAAGCAGTGTCAGCA 60.454 52.632 0.00 0.00 46.52 4.41
330 332 0.538057 TACCACAGAAGACCCGACGT 60.538 55.000 0.00 0.00 0.00 4.34
335 337 2.304761 TCACCATTACCACAGAAGACCC 59.695 50.000 0.00 0.00 0.00 4.46
336 338 3.695830 TCACCATTACCACAGAAGACC 57.304 47.619 0.00 0.00 0.00 3.85
338 340 3.054434 CCCATCACCATTACCACAGAAGA 60.054 47.826 0.00 0.00 0.00 2.87
348 350 2.909662 TCACACACTCCCATCACCATTA 59.090 45.455 0.00 0.00 0.00 1.90
353 355 3.384668 CGATATCACACACTCCCATCAC 58.615 50.000 3.12 0.00 0.00 3.06
361 363 1.065701 GCGTCTCCGATATCACACACT 59.934 52.381 3.12 0.00 35.63 3.55
371 373 1.226974 CCATTGTCGCGTCTCCGAT 60.227 57.895 5.77 0.00 39.67 4.18
432 437 0.673437 ACCACAACAAAATGAGCCGG 59.327 50.000 0.00 0.00 0.00 6.13
439 444 5.536161 AGCTATGACTTCACCACAACAAAAT 59.464 36.000 0.00 0.00 0.00 1.82
554 566 5.828299 CTTCGACTCTGAAGGATAGTTCT 57.172 43.478 0.00 0.00 41.32 3.01
593 605 2.032620 CCGAACTCAGCTACTACCCAT 58.967 52.381 0.00 0.00 0.00 4.00
599 611 0.898320 ATGTGCCGAACTCAGCTACT 59.102 50.000 0.00 0.00 0.00 2.57
600 612 1.002366 CATGTGCCGAACTCAGCTAC 58.998 55.000 0.00 0.00 0.00 3.58
601 613 0.740868 GCATGTGCCGAACTCAGCTA 60.741 55.000 0.00 0.00 34.31 3.32
670 682 2.586900 GACTCCGACTTCGTCAAAGAG 58.413 52.381 0.00 0.00 38.44 2.85
750 780 3.798954 GAGGGCCTCGGCAAGATCG 62.799 68.421 19.53 0.00 44.11 3.69
758 788 2.045280 CTCACATAGAGGGCCTCGG 58.955 63.158 27.11 21.74 40.84 4.63
796 839 0.534873 AAAAACGCCACAAACTGCCT 59.465 45.000 0.00 0.00 0.00 4.75
849 928 9.362539 GGAGTCAAAAGACATTAATTACGTAGA 57.637 33.333 0.00 0.00 0.00 2.59
854 933 9.113876 CAAACGGAGTCAAAAGACATTAATTAC 57.886 33.333 0.00 0.00 45.00 1.89
859 938 6.928979 TTCAAACGGAGTCAAAAGACATTA 57.071 33.333 0.00 0.00 45.00 1.90
867 946 5.182380 AGTGTTCTTTTCAAACGGAGTCAAA 59.818 36.000 0.00 0.00 45.00 2.69
868 947 4.698304 AGTGTTCTTTTCAAACGGAGTCAA 59.302 37.500 0.00 0.00 45.00 3.18
873 952 3.191581 TGCAAGTGTTCTTTTCAAACGGA 59.808 39.130 0.00 0.00 0.00 4.69
875 954 4.856487 TCTTGCAAGTGTTCTTTTCAAACG 59.144 37.500 25.19 0.00 0.00 3.60
876 955 6.704512 TTCTTGCAAGTGTTCTTTTCAAAC 57.295 33.333 25.19 0.00 0.00 2.93
877 956 7.151308 TCTTTCTTGCAAGTGTTCTTTTCAAA 58.849 30.769 25.19 13.03 0.00 2.69
878 957 6.686630 TCTTTCTTGCAAGTGTTCTTTTCAA 58.313 32.000 25.19 6.10 0.00 2.69
879 958 6.266168 TCTTTCTTGCAAGTGTTCTTTTCA 57.734 33.333 25.19 0.00 0.00 2.69
880 959 6.292008 GCATCTTTCTTGCAAGTGTTCTTTTC 60.292 38.462 25.19 5.86 39.90 2.29
883 962 4.098349 TGCATCTTTCTTGCAAGTGTTCTT 59.902 37.500 25.19 5.66 46.48 2.52
884 963 3.633525 TGCATCTTTCTTGCAAGTGTTCT 59.366 39.130 25.19 7.01 46.48 3.01
894 973 3.305608 GGGGACTTTGTGCATCTTTCTTG 60.306 47.826 0.00 0.00 0.00 3.02
895 974 2.893489 GGGGACTTTGTGCATCTTTCTT 59.107 45.455 0.00 0.00 0.00 2.52
896 975 2.519013 GGGGACTTTGTGCATCTTTCT 58.481 47.619 0.00 0.00 0.00 2.52
898 977 1.147817 AGGGGGACTTTGTGCATCTTT 59.852 47.619 0.00 0.00 0.00 2.52
899 978 0.779997 AGGGGGACTTTGTGCATCTT 59.220 50.000 0.00 0.00 0.00 2.40
900 979 0.329596 GAGGGGGACTTTGTGCATCT 59.670 55.000 0.00 0.00 0.00 2.90
902 981 1.142688 AGGAGGGGGACTTTGTGCAT 61.143 55.000 0.00 0.00 0.00 3.96
903 982 0.474854 TAGGAGGGGGACTTTGTGCA 60.475 55.000 0.00 0.00 0.00 4.57
904 983 0.919710 ATAGGAGGGGGACTTTGTGC 59.080 55.000 0.00 0.00 0.00 4.57
906 985 4.415846 GGATTTATAGGAGGGGGACTTTGT 59.584 45.833 0.00 0.00 0.00 2.83
907 986 4.665483 AGGATTTATAGGAGGGGGACTTTG 59.335 45.833 0.00 0.00 0.00 2.77
908 987 4.665483 CAGGATTTATAGGAGGGGGACTTT 59.335 45.833 0.00 0.00 0.00 2.66
909 988 4.243643 CAGGATTTATAGGAGGGGGACTT 58.756 47.826 0.00 0.00 0.00 3.01
911 990 2.306219 GCAGGATTTATAGGAGGGGGAC 59.694 54.545 0.00 0.00 0.00 4.46
912 991 2.089638 TGCAGGATTTATAGGAGGGGGA 60.090 50.000 0.00 0.00 0.00 4.81
913 992 2.040412 GTGCAGGATTTATAGGAGGGGG 59.960 54.545 0.00 0.00 0.00 5.40
914 993 2.040412 GGTGCAGGATTTATAGGAGGGG 59.960 54.545 0.00 0.00 0.00 4.79
1042 1133 2.193536 GTTGCTTGGTGCCTCCGTT 61.194 57.895 0.00 0.00 42.00 4.44
1233 1330 1.377536 GTACGCCTTAGACGAGGTCT 58.622 55.000 0.00 3.52 45.54 3.85
1235 1332 1.034292 GGGTACGCCTTAGACGAGGT 61.034 60.000 0.00 0.00 39.11 3.85
1305 1402 1.480789 TCTCCGGGATGTCGAATGAA 58.519 50.000 0.00 0.00 0.00 2.57
1347 1444 2.366167 AGGAGGATGAAGGCGGCT 60.366 61.111 5.25 5.25 0.00 5.52
1357 1454 2.519780 GACGCCGAGGAGGAGGAT 60.520 66.667 0.00 0.00 44.78 3.24
1407 1504 3.373565 GGCAAAAGTGGGAGCGGG 61.374 66.667 0.00 0.00 0.00 6.13
1408 1505 3.373565 GGGCAAAAGTGGGAGCGG 61.374 66.667 0.00 0.00 0.00 5.52
1409 1506 3.737172 CGGGCAAAAGTGGGAGCG 61.737 66.667 0.00 0.00 0.00 5.03
1410 1507 4.056125 GCGGGCAAAAGTGGGAGC 62.056 66.667 0.00 0.00 0.00 4.70
1411 1508 2.282462 AGCGGGCAAAAGTGGGAG 60.282 61.111 0.00 0.00 0.00 4.30
1412 1509 2.282180 GAGCGGGCAAAAGTGGGA 60.282 61.111 0.00 0.00 0.00 4.37
1413 1510 3.373565 GGAGCGGGCAAAAGTGGG 61.374 66.667 0.00 0.00 0.00 4.61
1414 1511 3.373565 GGGAGCGGGCAAAAGTGG 61.374 66.667 0.00 0.00 0.00 4.00
1415 1512 3.373565 GGGGAGCGGGCAAAAGTG 61.374 66.667 0.00 0.00 0.00 3.16
1849 1982 1.002069 TGATGAACCCCTGCTTCCAT 58.998 50.000 0.00 0.00 0.00 3.41
1891 2024 1.007271 CGAGTTGAGCACCGACAGT 60.007 57.895 0.00 0.00 0.00 3.55
2563 2703 2.738743 AGGAATGGTAACCATGGCAAG 58.261 47.619 13.04 0.00 44.40 4.01
2602 2742 4.704057 GCCATTGATTTGTCTTCTCCTTCT 59.296 41.667 0.00 0.00 0.00 2.85
2611 2751 0.813184 CTGGCGCCATTGATTTGTCT 59.187 50.000 32.87 0.00 0.00 3.41
2616 2756 0.682209 AGAAGCTGGCGCCATTGATT 60.682 50.000 32.87 24.56 36.60 2.57
2675 2815 1.452110 CATGGTGCTCGGATGTTCAA 58.548 50.000 0.00 0.00 0.00 2.69
2689 2829 4.082523 CCGCCAGTCGTCCATGGT 62.083 66.667 12.58 0.00 38.91 3.55
2752 2892 0.684535 TGGGCGTTTCAGATGACAGA 59.315 50.000 0.00 0.00 0.00 3.41
2757 2897 0.099968 CATGCTGGGCGTTTCAGATG 59.900 55.000 6.09 4.12 34.36 2.90
2983 3138 2.488153 GTCACAAAATAGCACCCAGTCC 59.512 50.000 0.00 0.00 0.00 3.85
2989 3144 2.673368 CTCCGAGTCACAAAATAGCACC 59.327 50.000 0.00 0.00 0.00 5.01
3025 3180 1.071699 TCACAAAGTAGCACCCAGTCC 59.928 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.