Multiple sequence alignment - TraesCS7B01G210200

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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 TraesCS7B01G210200 chr7B 100.000 5730 0 0 1 5730 383727256 383732985 0.000000e+00 10582.0
1 TraesCS7B01G210200 chr7D 95.032 5676 186 39 26 5656 388690943 388696567 0.000000e+00 8831.0
2 TraesCS7B01G210200 chr7D 88.197 305 23 6 1567 1859 636296751 636297054 9.130000e-93 351.0
3 TraesCS7B01G210200 chr7D 87.960 299 17 5 1570 1859 635714668 635714380 9.200000e-88 335.0
4 TraesCS7B01G210200 chr7D 93.590 78 4 1 5653 5730 388696638 388696714 1.300000e-21 115.0
5 TraesCS7B01G210200 chr7A 95.175 4311 142 35 1444 5719 438850266 438854545 0.000000e+00 6748.0
6 TraesCS7B01G210200 chr7A 90.283 1307 72 30 95 1356 438848753 438850049 0.000000e+00 1659.0
7 TraesCS7B01G210200 chr7A 91.716 338 13 7 5402 5729 438854813 438855145 6.770000e-124 455.0
8 TraesCS7B01G210200 chr7A 90.378 291 17 3 1570 1859 471737806 471737526 7.010000e-99 372.0
9 TraesCS7B01G210200 chr5B 82.728 3109 372 94 2095 5138 540254072 540251064 0.000000e+00 2614.0
10 TraesCS7B01G210200 chr5B 83.908 261 37 4 1001 1260 540255348 540255092 1.590000e-60 244.0
11 TraesCS7B01G210200 chr5B 76.630 184 41 2 3129 3311 540252888 540253070 3.650000e-17 100.0
12 TraesCS7B01G210200 chr5A 83.729 2317 295 41 2573 4827 559809530 559807234 0.000000e+00 2115.0
13 TraesCS7B01G210200 chr5A 85.115 262 34 4 1001 1261 559811399 559811142 4.400000e-66 263.0
14 TraesCS7B01G210200 chr5A 75.543 184 38 7 3100 3278 559808758 559808939 3.680000e-12 84.2
15 TraesCS7B01G210200 chr5D 84.838 1451 170 20 3412 4827 443636059 443634624 0.000000e+00 1415.0
16 TraesCS7B01G210200 chr5D 90.654 535 26 7 1976 2508 393604706 393604194 0.000000e+00 689.0
17 TraesCS7B01G210200 chr5D 87.585 443 52 3 2573 3014 443636498 443636058 1.420000e-140 510.0
18 TraesCS7B01G210200 chr5D 81.765 340 46 9 1001 1328 443638476 443638141 2.630000e-68 270.0
19 TraesCS7B01G210200 chr5D 76.101 159 30 7 3144 3300 446268189 446268341 6.160000e-10 76.8
20 TraesCS7B01G210200 chr6A 90.675 1008 70 7 1976 2981 92339607 92340592 0.000000e+00 1319.0
21 TraesCS7B01G210200 chr3A 90.415 939 70 13 1859 2794 725009892 725008971 0.000000e+00 1218.0
22 TraesCS7B01G210200 chr3A 93.169 366 24 1 2148 2513 555513064 555512700 2.350000e-148 536.0
23 TraesCS7B01G210200 chr3A 85.085 295 19 6 1567 1860 343110874 343111144 1.570000e-70 278.0
24 TraesCS7B01G210200 chr3A 90.521 211 16 3 1654 1860 725010799 725010589 5.660000e-70 276.0
25 TraesCS7B01G210200 chr3A 80.000 100 12 8 3145 3240 485326342 485326247 3.710000e-07 67.6
26 TraesCS7B01G210200 chr4A 92.053 755 49 8 2043 2794 730355528 730356274 0.000000e+00 1051.0
27 TraesCS7B01G210200 chr4A 93.220 295 19 1 1567 1860 730354790 730355084 3.170000e-117 433.0
28 TraesCS7B01G210200 chr4A 80.909 110 17 4 3171 3279 37789799 37789905 3.680000e-12 84.2
29 TraesCS7B01G210200 chr3B 88.456 745 61 10 1964 2706 202532 203253 0.000000e+00 876.0
30 TraesCS7B01G210200 chr3B 85.714 294 23 4 1567 1859 448408021 448408296 5.620000e-75 292.0
31 TraesCS7B01G210200 chr3B 84.783 92 13 1 4023 4114 749022429 749022519 2.200000e-14 91.6
32 TraesCS7B01G210200 chr3B 76.821 151 25 9 3130 3276 20724773 20724629 6.160000e-10 76.8
33 TraesCS7B01G210200 chr2A 91.501 553 42 5 2189 2739 560574525 560575074 0.000000e+00 756.0
34 TraesCS7B01G210200 chr2A 91.409 291 14 3 1570 1859 312040117 312039837 6.960000e-104 388.0
35 TraesCS7B01G210200 chr2A 83.333 78 8 5 3145 3220 282727813 282727887 3.710000e-07 67.6
36 TraesCS7B01G210200 chr1B 91.466 539 36 5 1976 2513 292422696 292423225 0.000000e+00 732.0
37 TraesCS7B01G210200 chr1B 91.095 539 38 5 1976 2513 292348370 292348899 0.000000e+00 721.0
38 TraesCS7B01G210200 chr1B 92.800 375 25 2 2609 2981 292348896 292349270 5.050000e-150 542.0
39 TraesCS7B01G210200 chr1B 92.800 375 24 3 2609 2981 292423222 292423595 1.820000e-149 540.0
40 TraesCS7B01G210200 chrUn 92.246 374 28 1 2609 2981 49575793 49575420 3.930000e-146 529.0
41 TraesCS7B01G210200 chrUn 89.933 298 22 3 1976 2273 49576264 49575975 1.510000e-100 377.0
42 TraesCS7B01G210200 chr4D 91.065 291 15 3 1570 1859 289466603 289466323 3.240000e-102 383.0
43 TraesCS7B01G210200 chr3D 83.983 231 37 0 4345 4575 561708809 561709039 7.470000e-54 222.0
44 TraesCS7B01G210200 chr6B 76.812 138 26 6 3159 3293 717078113 717077979 7.960000e-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 TraesCS7B01G210200 chr7B 383727256 383732985 5729 False 10582.000000 10582 100.000000 1 5730 1 chr7B.!!$F1 5729
1 TraesCS7B01G210200 chr7D 388690943 388696714 5771 False 4473.000000 8831 94.311000 26 5730 2 chr7D.!!$F2 5704
2 TraesCS7B01G210200 chr7A 438848753 438855145 6392 False 2954.000000 6748 92.391333 95 5729 3 chr7A.!!$F1 5634
3 TraesCS7B01G210200 chr5B 540251064 540255348 4284 True 1429.000000 2614 83.318000 1001 5138 2 chr5B.!!$R1 4137
4 TraesCS7B01G210200 chr5A 559807234 559811399 4165 True 1189.000000 2115 84.422000 1001 4827 2 chr5A.!!$R1 3826
5 TraesCS7B01G210200 chr5D 443634624 443638476 3852 True 731.666667 1415 84.729333 1001 4827 3 chr5D.!!$R2 3826
6 TraesCS7B01G210200 chr5D 393604194 393604706 512 True 689.000000 689 90.654000 1976 2508 1 chr5D.!!$R1 532
7 TraesCS7B01G210200 chr6A 92339607 92340592 985 False 1319.000000 1319 90.675000 1976 2981 1 chr6A.!!$F1 1005
8 TraesCS7B01G210200 chr3A 725008971 725010799 1828 True 747.000000 1218 90.468000 1654 2794 2 chr3A.!!$R3 1140
9 TraesCS7B01G210200 chr4A 730354790 730356274 1484 False 742.000000 1051 92.636500 1567 2794 2 chr4A.!!$F2 1227
10 TraesCS7B01G210200 chr3B 202532 203253 721 False 876.000000 876 88.456000 1964 2706 1 chr3B.!!$F1 742
11 TraesCS7B01G210200 chr2A 560574525 560575074 549 False 756.000000 756 91.501000 2189 2739 1 chr2A.!!$F2 550
12 TraesCS7B01G210200 chr1B 292422696 292423595 899 False 636.000000 732 92.133000 1976 2981 2 chr1B.!!$F2 1005
13 TraesCS7B01G210200 chr1B 292348370 292349270 900 False 631.500000 721 91.947500 1976 2981 2 chr1B.!!$F1 1005
14 TraesCS7B01G210200 chrUn 49575420 49576264 844 True 453.000000 529 91.089500 1976 2981 2 chrUn.!!$R1 1005

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
162 164 0.531090 TGTACGTGGCTTTGTCGCTT 60.531 50.0 0.0 0.0 0.00 4.68 F
1224 1300 0.256752 TCGATTCCCCGTACCTGAGA 59.743 55.0 0.0 0.0 0.00 3.27 F
2887 4354 0.523335 CCGCAAACGCCATTCTAAGC 60.523 55.0 0.0 0.0 38.22 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1610 0.471591 TGGGGGTACACACGTTAGGT 60.472 55.0 0.0 0.00 0.00 3.08 R
2921 4388 1.061905 ACTGCATATAGGCCCAGGCA 61.062 55.0 11.5 3.63 44.11 4.75 R
4870 6421 0.246635 GCGAGTTCCTTGGCTCTACA 59.753 55.0 0.0 0.00 0.00 2.74 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
22 23 2.685017 TCCACGAGGAGGCTGCAT 60.685 61.111 9.23 0.00 39.61 3.96
23 24 2.270205 CCACGAGGAGGCTGCATT 59.730 61.111 9.23 0.00 36.89 3.56
24 25 2.110967 CCACGAGGAGGCTGCATTG 61.111 63.158 9.23 1.60 36.89 2.82
71 72 4.694037 GCTTTACAAACTGTTACCCGAGAT 59.306 41.667 0.00 0.00 0.00 2.75
76 77 4.181578 CAAACTGTTACCCGAGATGTAGG 58.818 47.826 0.00 0.00 0.00 3.18
88 89 3.617263 CGAGATGTAGGGTTTGTAGTTGC 59.383 47.826 0.00 0.00 0.00 4.17
92 93 2.706723 TGTAGGGTTTGTAGTTGCTGGA 59.293 45.455 0.00 0.00 0.00 3.86
113 114 2.745968 TGAGCACCCCTTTTCTTGTTT 58.254 42.857 0.00 0.00 0.00 2.83
162 164 0.531090 TGTACGTGGCTTTGTCGCTT 60.531 50.000 0.00 0.00 0.00 4.68
196 198 8.368857 GTCGATGAAATGATACGTGATCTTATG 58.631 37.037 0.00 0.00 35.37 1.90
205 207 6.363357 TGATACGTGATCTTATGAATTCGCTG 59.637 38.462 0.00 0.00 35.37 5.18
211 218 7.163195 CGTGATCTTATGAATTCGCTGAAAAAG 59.837 37.037 0.04 0.00 0.00 2.27
223 230 5.474825 TCGCTGAAAAAGGAAAACAAAAGT 58.525 33.333 0.00 0.00 0.00 2.66
228 235 7.183580 TGAAAAAGGAAAACAAAAGTGTGTG 57.816 32.000 0.00 0.00 38.27 3.82
234 241 4.803613 GGAAAACAAAAGTGTGTGCTTAGG 59.196 41.667 0.00 0.00 38.27 2.69
271 278 6.811253 GGAGAAAACCCACAAAAACTTTTT 57.189 33.333 0.00 0.00 0.00 1.94
299 306 7.309438 GGAAGAGTTTTGGAGTAATCTTTGCAT 60.309 37.037 0.00 0.00 0.00 3.96
306 313 4.227300 TGGAGTAATCTTTGCATAGGGTGT 59.773 41.667 4.23 0.00 0.00 4.16
410 438 3.754323 CAGGTTTGCCAAATGATGCATTT 59.246 39.130 0.00 0.00 43.71 2.32
411 439 4.216687 CAGGTTTGCCAAATGATGCATTTT 59.783 37.500 0.00 0.00 40.60 1.82
583 617 1.285950 GCAAGCTCGAAACCAACCC 59.714 57.895 0.00 0.00 0.00 4.11
619 686 1.182667 TACATGCACGCACTAGAGGT 58.817 50.000 0.00 0.00 0.00 3.85
644 711 3.031964 GCTGCACTTACTGCCAGCG 62.032 63.158 0.00 0.00 46.51 5.18
786 853 4.563061 GTTCTCCGGTTGGCGTATATAAT 58.437 43.478 0.00 0.00 34.14 1.28
830 897 2.759973 TCGCTGGCTCCGAGGAAT 60.760 61.111 0.00 0.00 0.00 3.01
941 1008 1.737793 CGGAATCGGGGAGAGTTTTTG 59.262 52.381 0.00 0.00 0.00 2.44
945 1012 5.677567 GGAATCGGGGAGAGTTTTTGTATA 58.322 41.667 0.00 0.00 0.00 1.47
966 1033 2.359975 GGTGTCTGGCTTTCCGGG 60.360 66.667 0.00 0.00 39.31 5.73
1219 1295 2.414594 CGGTCGATTCCCCGTACC 59.585 66.667 4.14 0.00 39.38 3.34
1224 1300 0.256752 TCGATTCCCCGTACCTGAGA 59.743 55.000 0.00 0.00 0.00 3.27
1348 1456 1.341976 ACCAATCGGGCTGGCTAAATT 60.342 47.619 0.00 0.00 42.05 1.82
1418 1624 4.992319 CCTGATTTTCACCTAACGTGTGTA 59.008 41.667 4.64 0.00 43.51 2.90
1431 1638 3.253838 GTGTACCCCCAGTGCCCA 61.254 66.667 0.00 0.00 0.00 5.36
1525 1765 2.164422 GGCTGCCTCAATTGTTAAGACC 59.836 50.000 12.43 0.00 0.00 3.85
1546 1788 3.178267 CACAGCGCTCTTTTGTGAAAAA 58.822 40.909 18.81 0.00 43.68 1.94
1615 1872 3.173953 TGGGCCTGAGTCAATTCATTT 57.826 42.857 4.53 0.00 0.00 2.32
1733 1995 3.868757 TCACCAAATCCTCGAGTAGTG 57.131 47.619 12.31 9.12 0.00 2.74
1828 2094 5.245977 TCACACCATCTTCAGTTGTATCAGA 59.754 40.000 0.00 0.00 0.00 3.27
1830 2096 5.934625 ACACCATCTTCAGTTGTATCAGAAC 59.065 40.000 0.00 0.00 0.00 3.01
2055 3306 6.486253 ACTGCACTATTATGTTTGTGTCTG 57.514 37.500 0.00 0.00 33.44 3.51
2653 4116 9.899661 ACATTTGTGTATGAATAGTTAGCCTAA 57.100 29.630 0.00 0.00 0.00 2.69
2852 4319 5.093457 GGCAAGGTAATAAAAGTCTTTCGC 58.907 41.667 0.00 0.00 0.00 4.70
2887 4354 0.523335 CCGCAAACGCCATTCTAAGC 60.523 55.000 0.00 0.00 38.22 3.09
3020 4487 6.182627 ACTTATCAAGCTGATGTGGATTTCA 58.817 36.000 8.40 0.00 37.70 2.69
3125 4599 3.554324 CCCTCCGTTCAAATATACACACG 59.446 47.826 0.00 0.00 0.00 4.49
3131 4606 3.897141 TCAAATATACACACGCCCTCA 57.103 42.857 0.00 0.00 0.00 3.86
3141 4616 3.118956 ACACACGCCCTCAAATTTTGAAA 60.119 39.130 12.62 0.00 39.58 2.69
3445 4936 5.419788 TCATGCATCATTTCCAGTAAAGCTT 59.580 36.000 0.00 0.00 0.00 3.74
3697 5191 2.915869 ACACTCCCTTCTCCCATAACA 58.084 47.619 0.00 0.00 0.00 2.41
3830 5324 1.066002 TGCAAGCTTCAGTTTCAGTGC 59.934 47.619 0.00 0.00 0.00 4.40
4061 5555 4.009675 GGACAGACCAAATATCAGCACAA 58.990 43.478 0.00 0.00 38.79 3.33
4136 5633 2.159043 ACCATGGATGCTAGTGAGAACG 60.159 50.000 21.47 0.00 0.00 3.95
4166 5669 0.898326 GGGGTTGGTTGATGGTGGTC 60.898 60.000 0.00 0.00 0.00 4.02
4189 5692 2.672996 GCGTGGGCTGACATGGTT 60.673 61.111 0.00 0.00 35.83 3.67
4414 5932 1.083015 CGTGAACCGGAGTTTTGCG 60.083 57.895 9.46 0.00 35.94 4.85
4606 6133 0.546267 ATGGACACTCTCAGGGTGCT 60.546 55.000 3.92 0.00 40.93 4.40
4699 6226 1.281419 TGCGGGTCTTCCAGGAAATA 58.719 50.000 2.72 0.00 34.36 1.40
4748 6277 8.599055 TGCATAGCTACATCTTTATTCTTCAG 57.401 34.615 0.00 0.00 0.00 3.02
4856 6407 4.096833 TCAATGCAACAATCATGTAGAGCC 59.903 41.667 0.00 0.00 39.40 4.70
4863 6414 4.922206 ACAATCATGTAGAGCCAAGGAAA 58.078 39.130 0.00 0.00 38.24 3.13
4864 6415 4.702131 ACAATCATGTAGAGCCAAGGAAAC 59.298 41.667 0.00 0.00 38.24 2.78
4865 6416 4.574674 ATCATGTAGAGCCAAGGAAACA 57.425 40.909 0.00 0.00 0.00 2.83
4866 6417 4.365514 TCATGTAGAGCCAAGGAAACAA 57.634 40.909 0.00 0.00 0.00 2.83
4867 6418 4.922206 TCATGTAGAGCCAAGGAAACAAT 58.078 39.130 0.00 0.00 0.00 2.71
4868 6419 4.943705 TCATGTAGAGCCAAGGAAACAATC 59.056 41.667 0.00 0.00 0.00 2.67
4869 6420 4.365514 TGTAGAGCCAAGGAAACAATCA 57.634 40.909 0.00 0.00 0.00 2.57
4870 6421 4.922206 TGTAGAGCCAAGGAAACAATCAT 58.078 39.130 0.00 0.00 0.00 2.45
4871 6422 4.701651 TGTAGAGCCAAGGAAACAATCATG 59.298 41.667 0.00 0.00 0.00 3.07
4872 6423 3.771216 AGAGCCAAGGAAACAATCATGT 58.229 40.909 0.00 0.00 43.14 3.21
4873 6424 4.922206 AGAGCCAAGGAAACAATCATGTA 58.078 39.130 0.00 0.00 39.40 2.29
4874 6425 4.946157 AGAGCCAAGGAAACAATCATGTAG 59.054 41.667 0.00 0.00 39.40 2.74
4875 6426 4.922206 AGCCAAGGAAACAATCATGTAGA 58.078 39.130 0.00 0.00 39.40 2.59
4876 6427 4.946157 AGCCAAGGAAACAATCATGTAGAG 59.054 41.667 0.00 0.00 39.40 2.43
4877 6428 4.439289 GCCAAGGAAACAATCATGTAGAGC 60.439 45.833 0.00 0.00 39.40 4.09
4878 6429 4.096984 CCAAGGAAACAATCATGTAGAGCC 59.903 45.833 0.00 0.00 39.40 4.70
4879 6430 4.574674 AGGAAACAATCATGTAGAGCCA 57.425 40.909 0.00 0.00 39.40 4.75
4880 6431 4.922206 AGGAAACAATCATGTAGAGCCAA 58.078 39.130 0.00 0.00 39.40 4.52
4881 6432 4.946157 AGGAAACAATCATGTAGAGCCAAG 59.054 41.667 0.00 0.00 39.40 3.61
4882 6433 4.096984 GGAAACAATCATGTAGAGCCAAGG 59.903 45.833 0.00 0.00 39.40 3.61
4883 6434 4.574674 AACAATCATGTAGAGCCAAGGA 57.425 40.909 0.00 0.00 39.40 3.36
4884 6435 4.574674 ACAATCATGTAGAGCCAAGGAA 57.425 40.909 0.00 0.00 38.24 3.36
4925 6480 7.777440 TCACTGGTCCATATTATTAACAATGCA 59.223 33.333 0.00 0.00 0.00 3.96
4926 6481 7.862372 CACTGGTCCATATTATTAACAATGCAC 59.138 37.037 0.00 0.00 0.00 4.57
4928 6483 8.532186 TGGTCCATATTATTAACAATGCACTT 57.468 30.769 0.00 0.00 0.00 3.16
4929 6484 8.976353 TGGTCCATATTATTAACAATGCACTTT 58.024 29.630 0.00 0.00 0.00 2.66
4952 6517 8.833231 TTTCTTCAAATCCAAGTAGACAGTAG 57.167 34.615 0.00 0.00 0.00 2.57
4953 6518 7.540474 TCTTCAAATCCAAGTAGACAGTAGT 57.460 36.000 0.00 0.00 0.00 2.73
4954 6519 8.645814 TCTTCAAATCCAAGTAGACAGTAGTA 57.354 34.615 0.00 0.00 0.00 1.82
5173 6746 0.166814 GAGCACATGTGGTTTCTCGC 59.833 55.000 29.63 13.44 41.93 5.03
5234 6807 2.669364 CAGAGACAAGCAATGGCAAAC 58.331 47.619 0.00 0.00 40.75 2.93
5236 6809 1.001378 GAGACAAGCAATGGCAAACGT 60.001 47.619 0.00 0.00 40.75 3.99
5288 6861 1.069668 TGCATCGATCTGCATAGTGCT 59.930 47.619 9.58 0.00 46.76 4.40
5412 6985 1.076192 AGCAATGGCAGCCTTGAGT 59.924 52.632 21.34 9.28 44.61 3.41
5439 7012 3.190849 CATCCTGACCAGCACGCG 61.191 66.667 3.53 3.53 0.00 6.01
5466 7040 4.821589 GACGCCGCCAGCTAAGCT 62.822 66.667 6.37 0.00 40.77 3.74
5485 7059 1.887242 GAAGGTGGCGCGATATGCA 60.887 57.895 12.10 0.00 46.97 3.96
5491 7065 2.175078 GCGCGATATGCATGCCTG 59.825 61.111 16.68 1.17 46.97 4.85
5540 7702 4.102210 TGCTCCAACCAATTCATCCAAAAA 59.898 37.500 0.00 0.00 0.00 1.94
5541 7703 5.221884 TGCTCCAACCAATTCATCCAAAAAT 60.222 36.000 0.00 0.00 0.00 1.82
5546 7716 9.632638 TCCAACCAATTCATCCAAAAATAAAAA 57.367 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.187946 GCCTCCTCGTGGATGGTG 59.812 66.667 6.68 0.00 42.29 4.17
1 2 2.039624 AGCCTCCTCGTGGATGGT 59.960 61.111 6.68 7.18 42.29 3.55
2 3 2.503061 CAGCCTCCTCGTGGATGG 59.497 66.667 6.68 11.38 42.29 3.51
3 4 2.202987 GCAGCCTCCTCGTGGATG 60.203 66.667 6.68 5.53 42.29 3.51
4 5 1.630126 AATGCAGCCTCCTCGTGGAT 61.630 55.000 6.68 0.00 42.29 3.41
5 6 2.293318 AATGCAGCCTCCTCGTGGA 61.293 57.895 6.00 6.00 40.69 4.02
6 7 2.110967 CAATGCAGCCTCCTCGTGG 61.111 63.158 0.00 0.00 0.00 4.94
7 8 2.758089 GCAATGCAGCCTCCTCGTG 61.758 63.158 0.00 0.00 0.00 4.35
8 9 2.437359 GCAATGCAGCCTCCTCGT 60.437 61.111 0.00 0.00 0.00 4.18
9 10 3.570638 CGCAATGCAGCCTCCTCG 61.571 66.667 5.91 0.00 0.00 4.63
10 11 3.207669 CCGCAATGCAGCCTCCTC 61.208 66.667 5.91 0.00 0.00 3.71
11 12 4.809496 CCCGCAATGCAGCCTCCT 62.809 66.667 5.91 0.00 0.00 3.69
17 18 3.515286 CTCTGGCCCGCAATGCAG 61.515 66.667 5.91 0.00 0.00 4.41
18 19 3.866379 AACTCTGGCCCGCAATGCA 62.866 57.895 5.91 0.00 0.00 3.96
19 20 3.064324 AACTCTGGCCCGCAATGC 61.064 61.111 0.00 0.00 0.00 3.56
20 21 2.703798 CCAACTCTGGCCCGCAATG 61.704 63.158 0.00 0.00 35.39 2.82
21 22 2.361610 CCAACTCTGGCCCGCAAT 60.362 61.111 0.00 0.00 35.39 3.56
22 23 3.551496 CTCCAACTCTGGCCCGCAA 62.551 63.158 0.00 0.00 43.17 4.85
23 24 4.020617 CTCCAACTCTGGCCCGCA 62.021 66.667 0.00 0.00 43.17 5.69
30 31 2.952714 CCCTTTGGCTCCAACTCTG 58.047 57.895 0.00 0.00 35.46 3.35
47 48 3.140623 TCGGGTAACAGTTTGTAAAGCC 58.859 45.455 0.00 0.00 39.74 4.35
55 56 3.197116 CCCTACATCTCGGGTAACAGTTT 59.803 47.826 0.00 0.00 35.65 2.66
71 72 2.706723 TCCAGCAACTACAAACCCTACA 59.293 45.455 0.00 0.00 0.00 2.74
88 89 1.005215 AGAAAAGGGGTGCTCATCCAG 59.995 52.381 1.16 0.00 31.60 3.86
92 93 2.683211 ACAAGAAAAGGGGTGCTCAT 57.317 45.000 0.00 0.00 0.00 2.90
134 136 2.431942 CCACGTACACACTCCGGC 60.432 66.667 0.00 0.00 0.00 6.13
137 139 0.865769 CAAAGCCACGTACACACTCC 59.134 55.000 0.00 0.00 0.00 3.85
162 164 1.478916 TCATTTCATCGACGGGTAGCA 59.521 47.619 0.00 0.00 0.00 3.49
196 198 6.582437 TTGTTTTCCTTTTTCAGCGAATTC 57.418 33.333 0.00 0.00 0.00 2.17
205 207 6.073276 AGCACACACTTTTGTTTTCCTTTTTC 60.073 34.615 0.00 0.00 31.66 2.29
211 218 4.803613 CCTAAGCACACACTTTTGTTTTCC 59.196 41.667 0.00 0.00 31.66 3.13
223 230 1.213182 TGTGGGTTTCCTAAGCACACA 59.787 47.619 7.38 7.38 38.94 3.72
271 278 7.470009 GCAAAGATTACTCCAAAACTCTTCCAA 60.470 37.037 0.00 0.00 0.00 3.53
276 283 7.337942 CCTATGCAAAGATTACTCCAAAACTCT 59.662 37.037 0.00 0.00 0.00 3.24
286 293 4.227300 TGGACACCCTATGCAAAGATTACT 59.773 41.667 0.00 0.00 0.00 2.24
372 400 4.993705 AACCTGGGAGTTCTGATGTTTA 57.006 40.909 0.00 0.00 0.00 2.01
466 495 0.738389 ACAACCTTGCTTCACCGTTG 59.262 50.000 0.00 0.00 39.70 4.10
644 711 2.277503 CGTTCGCTCGCGTACTAGC 61.278 63.158 16.67 6.74 37.53 3.42
786 853 0.389426 GAAGCAGAACGAACGGCCTA 60.389 55.000 0.00 0.00 0.00 3.93
830 897 1.665679 GATCGCATCCGCAAGAAGAAA 59.334 47.619 0.00 0.00 43.02 2.52
941 1008 0.464452 AAGCCAGACACCGCCTATAC 59.536 55.000 0.00 0.00 0.00 1.47
945 1012 2.032681 GAAAGCCAGACACCGCCT 59.967 61.111 0.00 0.00 0.00 5.52
1219 1295 2.884685 CGCCTGCTTCGCTCTCAG 60.885 66.667 0.00 0.00 0.00 3.35
1279 1361 4.261572 CGCTCAATTTTGGAACCTGAAGAA 60.262 41.667 0.00 0.00 0.00 2.52
1405 1610 0.471591 TGGGGGTACACACGTTAGGT 60.472 55.000 0.00 0.00 0.00 3.08
1418 1624 3.803311 TACACTGGGCACTGGGGGT 62.803 63.158 0.00 0.00 0.00 4.95
1431 1638 7.393796 AGCACTAACTGTTATCACTAGTACACT 59.606 37.037 0.00 0.00 0.00 3.55
1525 1765 2.473530 TTTCACAAAAGAGCGCTGTG 57.526 45.000 18.48 18.06 41.47 3.66
1546 1788 3.389983 CCAGGAAAATGGATGCCAATGAT 59.610 43.478 0.00 0.00 43.57 2.45
1733 1995 2.703007 ACTGCATCCTTCTCTCCCATAC 59.297 50.000 0.00 0.00 0.00 2.39
1928 2989 5.193679 AGACATATGTAGAAGGGCAAAACC 58.806 41.667 8.71 0.00 37.93 3.27
2055 3306 5.048224 TGAGCACCTGTTACAACTACTAGTC 60.048 44.000 0.00 0.00 0.00 2.59
2852 4319 1.811965 TGCGGGACAAATGAAGATGTG 59.188 47.619 0.00 0.00 0.00 3.21
2887 4354 2.787994 ACCTTCATGACAAAGCAGAGG 58.212 47.619 0.00 0.00 0.00 3.69
2921 4388 1.061905 ACTGCATATAGGCCCAGGCA 61.062 55.000 11.50 3.63 44.11 4.75
3002 4469 6.094464 TGTCTAATGAAATCCACATCAGCTTG 59.906 38.462 0.00 0.00 0.00 4.01
3220 4698 4.104102 AGAGTTACACCATTGGAAACCTCA 59.896 41.667 10.37 0.00 0.00 3.86
3445 4936 3.754965 AGCAGCTGGATTTAGTTGAACA 58.245 40.909 17.12 0.00 31.40 3.18
3589 5083 4.258543 TGCAGTTGTAAGGTATAGGTTGC 58.741 43.478 0.00 0.00 0.00 4.17
3697 5191 7.901029 TCTGTGAATCTTTAGACTTCATCTGT 58.099 34.615 7.42 0.00 38.49 3.41
3830 5324 3.724508 ATCCTCACGCTTCTCTGTATG 57.275 47.619 0.00 0.00 0.00 2.39
4061 5555 6.538263 AGCTAGGAGTTTGAACTTGATTCTT 58.462 36.000 0.00 0.00 39.88 2.52
4115 5609 2.159043 CGTTCTCACTAGCATCCATGGT 60.159 50.000 12.58 0.00 41.93 3.55
4136 5633 2.270986 CCAACCCCTCTTGCACAGC 61.271 63.158 0.00 0.00 0.00 4.40
4166 5669 1.577328 ATGTCAGCCCACGCTTTTCG 61.577 55.000 0.00 0.00 45.55 3.46
4189 5692 0.251354 GCTGCTGTTCATCCTCCTCA 59.749 55.000 0.00 0.00 0.00 3.86
4414 5932 1.153208 CCATGCTGGAGCTGTCCTC 60.153 63.158 0.00 0.00 44.30 3.71
4606 6133 1.855295 TAGTGGCCTCGGTGTGATTA 58.145 50.000 3.32 0.00 0.00 1.75
4660 6187 2.671070 CGGTTCTGTGGCCTCCAT 59.329 61.111 3.32 0.00 35.28 3.41
4699 6226 7.857569 CAACATTTTGCTTCATCTCATTTGTT 58.142 30.769 0.00 0.00 0.00 2.83
4748 6277 5.924825 AGTAAGAACTTACATCAACGGTGAC 59.075 40.000 21.49 0.00 45.79 3.67
4856 6407 4.701651 TGGCTCTACATGATTGTTTCCTTG 59.298 41.667 0.00 0.00 37.28 3.61
4863 6414 4.018960 AGTTCCTTGGCTCTACATGATTGT 60.019 41.667 0.00 0.00 39.98 2.71
4864 6415 4.521146 AGTTCCTTGGCTCTACATGATTG 58.479 43.478 0.00 0.00 0.00 2.67
4865 6416 4.681781 CGAGTTCCTTGGCTCTACATGATT 60.682 45.833 0.00 0.00 0.00 2.57
4866 6417 3.181471 CGAGTTCCTTGGCTCTACATGAT 60.181 47.826 0.00 0.00 0.00 2.45
4867 6418 2.166459 CGAGTTCCTTGGCTCTACATGA 59.834 50.000 0.00 0.00 0.00 3.07
4868 6419 2.544685 CGAGTTCCTTGGCTCTACATG 58.455 52.381 0.00 0.00 0.00 3.21
4869 6420 1.134670 GCGAGTTCCTTGGCTCTACAT 60.135 52.381 0.00 0.00 0.00 2.29
4870 6421 0.246635 GCGAGTTCCTTGGCTCTACA 59.753 55.000 0.00 0.00 0.00 2.74
4871 6422 0.460459 GGCGAGTTCCTTGGCTCTAC 60.460 60.000 0.00 0.00 37.44 2.59
4872 6423 1.898154 GGCGAGTTCCTTGGCTCTA 59.102 57.895 0.00 0.00 37.44 2.43
4873 6424 2.665603 GGCGAGTTCCTTGGCTCT 59.334 61.111 0.00 0.00 37.44 4.09
4874 6425 2.781595 TTCGGCGAGTTCCTTGGCTC 62.782 60.000 10.46 0.00 38.16 4.70
4875 6426 2.185310 ATTCGGCGAGTTCCTTGGCT 62.185 55.000 10.46 0.00 38.16 4.75
4876 6427 0.461339 TATTCGGCGAGTTCCTTGGC 60.461 55.000 10.94 0.00 37.12 4.52
4877 6428 2.135933 GATATTCGGCGAGTTCCTTGG 58.864 52.381 10.94 0.00 0.00 3.61
4878 6429 2.821546 TGATATTCGGCGAGTTCCTTG 58.178 47.619 10.94 0.00 0.00 3.61
4879 6430 3.069586 TGATGATATTCGGCGAGTTCCTT 59.930 43.478 10.94 1.36 0.00 3.36
4880 6431 2.628178 TGATGATATTCGGCGAGTTCCT 59.372 45.455 10.94 1.94 0.00 3.36
4881 6432 2.731976 GTGATGATATTCGGCGAGTTCC 59.268 50.000 10.94 3.59 0.00 3.62
4882 6433 3.426859 CAGTGATGATATTCGGCGAGTTC 59.573 47.826 10.94 9.35 0.00 3.01
4883 6434 3.384668 CAGTGATGATATTCGGCGAGTT 58.615 45.455 10.94 4.87 0.00 3.01
4884 6435 2.288457 CCAGTGATGATATTCGGCGAGT 60.288 50.000 10.46 10.45 0.00 4.18
4923 6478 6.017109 TGTCTACTTGGATTTGAAGAAAGTGC 60.017 38.462 0.00 0.00 33.37 4.40
4925 6480 7.283329 ACTGTCTACTTGGATTTGAAGAAAGT 58.717 34.615 0.00 0.00 35.39 2.66
4926 6481 7.736447 ACTGTCTACTTGGATTTGAAGAAAG 57.264 36.000 0.00 0.00 0.00 2.62
4928 6483 7.963532 ACTACTGTCTACTTGGATTTGAAGAA 58.036 34.615 0.00 0.00 0.00 2.52
4929 6484 7.540474 ACTACTGTCTACTTGGATTTGAAGA 57.460 36.000 0.00 0.00 0.00 2.87
4961 6526 9.403110 GACAAAGGAAAAATATATATGCAGCTG 57.597 33.333 10.11 10.11 0.00 4.24
5173 6746 0.249784 AGATGTCTAGCCATGCAGCG 60.250 55.000 0.00 0.00 38.01 5.18
5466 7040 1.887242 GCATATCGCGCCACCTTCA 60.887 57.895 0.00 0.00 0.00 3.02
5546 7716 2.597510 GGCCGGCAGGTCAGTTTT 60.598 61.111 30.85 0.00 43.06 2.43
5580 7750 3.713902 CCACATTAGGGCTAGCTGG 57.286 57.895 15.72 8.63 0.00 4.85


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

AutoCloner maintained by Alex Coulton.