Multiple sequence alignment - TraesCS5B01G215500

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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 TraesCS5B01G215500 chr5B 100.000 2849 0 0 1 2849 388482701 388479853 0.000000e+00 5262
1 TraesCS5B01G215500 chr5B 93.114 334 21 2 1073 1406 530609449 530609780 3.300000e-134 488
2 TraesCS5B01G215500 chr5D 90.181 2098 135 47 148 2185 332460449 332458363 0.000000e+00 2667
3 TraesCS5B01G215500 chr5D 91.441 701 27 6 2173 2849 332456861 332456170 0.000000e+00 931
4 TraesCS5B01G215500 chr5D 94.322 317 18 0 1090 1406 331842146 331841830 1.190000e-133 486
5 TraesCS5B01G215500 chr5A 89.846 1428 93 24 741 2118 433378864 433377439 0.000000e+00 1786
6 TraesCS5B01G215500 chr5A 92.439 701 27 5 2173 2849 433376525 433375827 0.000000e+00 977
7 TraesCS5B01G215500 chr4A 95.556 315 14 0 1092 1406 66148187 66147873 3.280000e-139 505
8 TraesCS5B01G215500 chr4B 95.238 315 15 0 1092 1406 471338310 471337996 1.520000e-137 499
9 TraesCS5B01G215500 chr6B 94.888 313 16 0 1094 1406 679983415 679983103 9.170000e-135 490
10 TraesCS5B01G215500 chr4D 94.118 323 17 2 1084 1406 384270924 384270604 9.170000e-135 490
11 TraesCS5B01G215500 chr1A 94.888 313 16 0 1094 1406 541343823 541344135 9.170000e-135 490


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 TraesCS5B01G215500 chr5B 388479853 388482701 2848 True 5262.0 5262 100.0000 1 2849 1 chr5B.!!$R1 2848
1 TraesCS5B01G215500 chr5D 332456170 332460449 4279 True 1799.0 2667 90.8110 148 2849 2 chr5D.!!$R2 2701
2 TraesCS5B01G215500 chr5A 433375827 433378864 3037 True 1381.5 1786 91.1425 741 2849 2 chr5A.!!$R1 2108

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
183 184 0.321346 CTTGTGGGTTTTCATGGGGC 59.679 55.000 0.00 0.0 0.0 5.80 F
189 190 0.608130 GGTTTTCATGGGGCCTGTTC 59.392 55.000 0.84 0.0 0.0 3.18 F
588 619 0.950836 CACCGTTTGAACTGCATGGA 59.049 50.000 0.00 0.0 0.0 3.41 F
764 797 1.490490 TCCCTGCTCGCTAAAATGGAT 59.510 47.619 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 1124 0.803768 CCGGACATCTTCTCGCTGTG 60.804 60.000 0.00 0.0 0.00 3.66 R
1341 1384 1.080366 GTACACGACGTCCATGGCA 60.080 57.895 10.58 0.0 0.00 4.92 R
1777 1860 1.129998 CTTGCAGCAGGAATTGTCTCG 59.870 52.381 0.00 0.0 0.00 4.04 R
2600 4260 1.000171 CAAGGCTGGAAAGAAGGCAAC 60.000 52.381 0.00 0.0 42.43 4.17 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 6.767524 ACACAACTCAACATAAAAGGTCAA 57.232 33.333 0.00 0.00 0.00 3.18
24 25 7.164230 ACACAACTCAACATAAAAGGTCAAA 57.836 32.000 0.00 0.00 0.00 2.69
25 26 7.781056 ACACAACTCAACATAAAAGGTCAAAT 58.219 30.769 0.00 0.00 0.00 2.32
26 27 7.920682 ACACAACTCAACATAAAAGGTCAAATC 59.079 33.333 0.00 0.00 0.00 2.17
27 28 7.382218 CACAACTCAACATAAAAGGTCAAATCC 59.618 37.037 0.00 0.00 0.00 3.01
28 29 6.590234 ACTCAACATAAAAGGTCAAATCCC 57.410 37.500 0.00 0.00 0.00 3.85
29 30 6.074648 ACTCAACATAAAAGGTCAAATCCCA 58.925 36.000 0.00 0.00 0.00 4.37
30 31 6.725834 ACTCAACATAAAAGGTCAAATCCCAT 59.274 34.615 0.00 0.00 0.00 4.00
31 32 6.934056 TCAACATAAAAGGTCAAATCCCATG 58.066 36.000 0.00 0.00 0.00 3.66
32 33 6.496565 TCAACATAAAAGGTCAAATCCCATGT 59.503 34.615 0.00 0.00 0.00 3.21
33 34 7.671819 TCAACATAAAAGGTCAAATCCCATGTA 59.328 33.333 0.00 0.00 0.00 2.29
34 35 8.477256 CAACATAAAAGGTCAAATCCCATGTAT 58.523 33.333 0.00 0.00 0.00 2.29
35 36 8.237811 ACATAAAAGGTCAAATCCCATGTATC 57.762 34.615 0.00 0.00 0.00 2.24
36 37 5.835113 AAAAGGTCAAATCCCATGTATCG 57.165 39.130 0.00 0.00 0.00 2.92
37 38 4.503714 AAGGTCAAATCCCATGTATCGT 57.496 40.909 0.00 0.00 0.00 3.73
38 39 4.073293 AGGTCAAATCCCATGTATCGTC 57.927 45.455 0.00 0.00 0.00 4.20
39 40 3.139077 GGTCAAATCCCATGTATCGTCC 58.861 50.000 0.00 0.00 0.00 4.79
40 41 2.800544 GTCAAATCCCATGTATCGTCCG 59.199 50.000 0.00 0.00 0.00 4.79
41 42 2.432874 TCAAATCCCATGTATCGTCCGT 59.567 45.455 0.00 0.00 0.00 4.69
42 43 3.637694 TCAAATCCCATGTATCGTCCGTA 59.362 43.478 0.00 0.00 0.00 4.02
43 44 3.655276 AATCCCATGTATCGTCCGTAC 57.345 47.619 0.00 0.00 0.00 3.67
61 62 2.770164 ACGGAGTAAAATCAGCTGCT 57.230 45.000 9.47 0.00 41.94 4.24
62 63 2.622436 ACGGAGTAAAATCAGCTGCTC 58.378 47.619 9.47 8.52 41.94 4.26
63 64 2.028112 ACGGAGTAAAATCAGCTGCTCA 60.028 45.455 9.47 0.00 41.94 4.26
64 65 2.606725 CGGAGTAAAATCAGCTGCTCAG 59.393 50.000 9.47 5.71 0.00 3.35
74 75 4.383861 CTGCTCAGCTGCGGGACA 62.384 66.667 9.47 1.38 35.80 4.02
75 76 4.687215 TGCTCAGCTGCGGGACAC 62.687 66.667 9.47 0.00 35.36 3.67
77 78 4.767255 CTCAGCTGCGGGACACCC 62.767 72.222 9.47 0.00 41.09 4.61
98 99 4.701663 CACACGTGGATCTGCCTT 57.298 55.556 21.57 0.00 37.63 4.35
99 100 3.832704 CACACGTGGATCTGCCTTA 57.167 52.632 21.57 0.00 37.63 2.69
100 101 1.645034 CACACGTGGATCTGCCTTAG 58.355 55.000 21.57 0.00 37.63 2.18
101 102 1.204704 CACACGTGGATCTGCCTTAGA 59.795 52.381 21.57 0.00 40.37 2.10
103 104 2.159043 ACACGTGGATCTGCCTTAGATG 60.159 50.000 21.57 0.00 46.12 2.90
104 105 2.101415 CACGTGGATCTGCCTTAGATGA 59.899 50.000 7.95 0.00 46.12 2.92
105 106 2.968574 ACGTGGATCTGCCTTAGATGAT 59.031 45.455 0.00 0.00 46.12 2.45
106 107 3.389329 ACGTGGATCTGCCTTAGATGATT 59.611 43.478 0.00 0.00 46.12 2.57
107 108 3.744942 CGTGGATCTGCCTTAGATGATTG 59.255 47.826 0.00 0.00 46.12 2.67
108 109 4.712476 GTGGATCTGCCTTAGATGATTGT 58.288 43.478 0.00 0.00 46.12 2.71
109 110 4.514441 GTGGATCTGCCTTAGATGATTGTG 59.486 45.833 0.00 0.00 46.12 3.33
110 111 4.164796 TGGATCTGCCTTAGATGATTGTGT 59.835 41.667 0.00 0.00 46.12 3.72
111 112 5.128919 GGATCTGCCTTAGATGATTGTGTT 58.871 41.667 0.00 0.00 46.12 3.32
112 113 5.238214 GGATCTGCCTTAGATGATTGTGTTC 59.762 44.000 0.00 0.00 46.12 3.18
113 114 5.164620 TCTGCCTTAGATGATTGTGTTCA 57.835 39.130 0.00 0.00 0.00 3.18
114 115 5.559770 TCTGCCTTAGATGATTGTGTTCAA 58.440 37.500 0.00 0.00 37.98 2.69
115 116 5.412594 TCTGCCTTAGATGATTGTGTTCAAC 59.587 40.000 0.00 0.00 36.33 3.18
116 117 5.069318 TGCCTTAGATGATTGTGTTCAACA 58.931 37.500 0.00 0.00 36.33 3.33
145 146 4.400529 TTTCTTCTTCACTTTTTGCCCC 57.599 40.909 0.00 0.00 0.00 5.80
146 147 3.025322 TCTTCTTCACTTTTTGCCCCA 57.975 42.857 0.00 0.00 0.00 4.96
151 152 3.966665 TCTTCACTTTTTGCCCCATTTCT 59.033 39.130 0.00 0.00 0.00 2.52
159 160 5.356291 TTTTGCCCCATTTCTTCATATGG 57.644 39.130 2.13 0.00 40.82 2.74
170 171 6.588719 TTTCTTCATATGGGTTTCTTGTGG 57.411 37.500 2.13 0.00 0.00 4.17
176 177 5.245075 TCATATGGGTTTCTTGTGGGTTTTC 59.755 40.000 2.13 0.00 0.00 2.29
178 179 3.379452 TGGGTTTCTTGTGGGTTTTCAT 58.621 40.909 0.00 0.00 0.00 2.57
183 184 0.321346 CTTGTGGGTTTTCATGGGGC 59.679 55.000 0.00 0.00 0.00 5.80
184 185 1.124477 TTGTGGGTTTTCATGGGGCC 61.124 55.000 0.00 0.00 0.00 5.80
185 186 1.229177 GTGGGTTTTCATGGGGCCT 60.229 57.895 0.84 0.00 0.00 5.19
186 187 1.229145 TGGGTTTTCATGGGGCCTG 60.229 57.895 0.84 0.00 0.00 4.85
188 189 0.835971 GGGTTTTCATGGGGCCTGTT 60.836 55.000 0.84 0.00 0.00 3.16
189 190 0.608130 GGTTTTCATGGGGCCTGTTC 59.392 55.000 0.84 0.00 0.00 3.18
191 192 2.556559 GGTTTTCATGGGGCCTGTTCTA 60.557 50.000 0.84 0.00 0.00 2.10
193 194 3.297134 TTTCATGGGGCCTGTTCTATC 57.703 47.619 0.84 0.00 0.00 2.08
194 195 1.140312 TCATGGGGCCTGTTCTATCC 58.860 55.000 0.84 0.00 0.00 2.59
196 197 1.496429 CATGGGGCCTGTTCTATCCTT 59.504 52.381 0.84 0.00 0.00 3.36
197 198 1.681229 TGGGGCCTGTTCTATCCTTT 58.319 50.000 0.84 0.00 0.00 3.11
291 311 5.945191 TCACATGGATGTTTTCTAGAATGCA 59.055 36.000 5.89 8.78 39.39 3.96
319 339 6.747125 TCAATTTCTAATGTTGCACACACAT 58.253 32.000 0.00 0.00 38.61 3.21
323 343 7.840342 TTTCTAATGTTGCACACACATTTTT 57.160 28.000 17.83 5.64 38.61 1.94
324 344 7.462109 TTCTAATGTTGCACACACATTTTTC 57.538 32.000 17.83 0.00 38.61 2.29
325 345 6.567959 TCTAATGTTGCACACACATTTTTCA 58.432 32.000 17.83 2.63 38.61 2.69
326 346 7.208777 TCTAATGTTGCACACACATTTTTCAT 58.791 30.769 17.83 0.00 38.61 2.57
330 350 9.656040 AATGTTGCACACACATTTTTCATATAT 57.344 25.926 9.03 0.00 38.61 0.86
378 398 5.562705 TGAACGTTTTGTTTGAAACACAC 57.437 34.783 10.72 9.52 42.09 3.82
380 400 2.981140 ACGTTTTGTTTGAAACACACGG 59.019 40.909 29.94 19.16 45.64 4.94
389 409 3.479505 TGAAACACACGGACAACTTTG 57.520 42.857 0.00 0.00 0.00 2.77
391 411 3.253677 TGAAACACACGGACAACTTTGTT 59.746 39.130 0.00 0.00 42.43 2.83
393 413 4.609691 AACACACGGACAACTTTGTTAG 57.390 40.909 0.00 0.00 42.43 2.34
394 414 3.602483 ACACACGGACAACTTTGTTAGT 58.398 40.909 0.00 0.00 42.43 2.24
458 489 8.612619 AGTACCTGAACATTTTCTATAAATGCG 58.387 33.333 9.48 0.00 40.35 4.73
465 496 7.276953 ACATTTTCTATAAATGCGCAAACAC 57.723 32.000 17.11 0.00 40.35 3.32
468 499 7.561237 TTTTCTATAAATGCGCAAACACTTC 57.439 32.000 17.11 0.00 0.00 3.01
474 505 5.635549 AAATGCGCAAACACTTCTAAAAC 57.364 34.783 17.11 0.00 0.00 2.43
480 511 8.481974 TGCGCAAACACTTCTAAAACTATATA 57.518 30.769 8.16 0.00 0.00 0.86
482 513 9.931210 GCGCAAACACTTCTAAAACTATATAAT 57.069 29.630 0.30 0.00 0.00 1.28
517 548 8.751302 ACCCGTGAACATTTATTTTACATTTC 57.249 30.769 0.00 0.00 0.00 2.17
582 613 3.691049 ATGTGAACACCGTTTGAACTG 57.309 42.857 2.46 0.00 0.00 3.16
588 619 0.950836 CACCGTTTGAACTGCATGGA 59.049 50.000 0.00 0.00 0.00 3.41
596 627 5.689514 CGTTTGAACTGCATGGACATTTTTA 59.310 36.000 0.00 0.00 0.00 1.52
599 630 8.558700 GTTTGAACTGCATGGACATTTTTAAAT 58.441 29.630 0.00 0.00 0.00 1.40
601 632 7.440198 TGAACTGCATGGACATTTTTAAATGA 58.560 30.769 19.12 0.88 46.72 2.57
602 633 8.095792 TGAACTGCATGGACATTTTTAAATGAT 58.904 29.630 19.12 6.21 46.72 2.45
603 634 8.483307 AACTGCATGGACATTTTTAAATGATC 57.517 30.769 19.12 12.88 46.72 2.92
604 635 7.844009 ACTGCATGGACATTTTTAAATGATCT 58.156 30.769 19.12 0.30 46.72 2.75
661 694 8.204160 AGGGGAAAACAAAATGAAAAAGTAGAG 58.796 33.333 0.00 0.00 0.00 2.43
764 797 1.490490 TCCCTGCTCGCTAAAATGGAT 59.510 47.619 0.00 0.00 0.00 3.41
765 798 1.605710 CCCTGCTCGCTAAAATGGATG 59.394 52.381 0.00 0.00 0.00 3.51
774 807 2.223805 GCTAAAATGGATGGGCGGAAAG 60.224 50.000 0.00 0.00 0.00 2.62
799 832 2.760159 GCGCTATTTTCCGCTGCCA 61.760 57.895 0.00 0.00 46.14 4.92
803 837 2.322999 CTATTTTCCGCTGCCACGCC 62.323 60.000 0.00 0.00 0.00 5.68
882 916 2.046285 CCCCATCCAACGGCTCAAC 61.046 63.158 0.00 0.00 0.00 3.18
997 1038 3.730761 CACCAGCCTCGCAGCAAC 61.731 66.667 0.00 0.00 34.23 4.17
1026 1068 3.866582 CGGCTCCATCCCTCCCAC 61.867 72.222 0.00 0.00 0.00 4.61
1057 1099 2.237392 CCCAATTCCTTCGTCTTCCTCT 59.763 50.000 0.00 0.00 0.00 3.69
1081 1124 2.947890 GACGCACACAGCAGAGCAC 61.948 63.158 0.00 0.00 46.13 4.40
1083 1126 2.635899 GCACACAGCAGAGCACAC 59.364 61.111 0.00 0.00 44.79 3.82
1430 1478 3.859411 AGCTAGCTTCAGTGTGTCTAC 57.141 47.619 12.68 0.00 0.00 2.59
1444 1492 2.052690 TCTACCAGGTCGCTGCTCC 61.053 63.158 0.00 0.06 0.00 4.70
1483 1533 7.571059 GCCTGTGGTTTAATTTAATGCTTGTTG 60.571 37.037 0.00 0.00 0.00 3.33
1491 1541 9.474920 TTTAATTTAATGCTTGTTGTGAGGAAG 57.525 29.630 0.00 0.00 0.00 3.46
1497 1547 3.077359 GCTTGTTGTGAGGAAGTGCTAT 58.923 45.455 0.00 0.00 0.00 2.97
1519 1570 7.094634 GCTATCTGGATTTGTTTCTCTGTTCAA 60.095 37.037 0.00 0.00 0.00 2.69
1534 1585 3.521560 TGTTCAATATCGTCAGTCCAGC 58.478 45.455 0.00 0.00 0.00 4.85
1537 1588 2.700371 TCAATATCGTCAGTCCAGCCAT 59.300 45.455 0.00 0.00 0.00 4.40
1538 1589 3.134623 TCAATATCGTCAGTCCAGCCATT 59.865 43.478 0.00 0.00 0.00 3.16
1595 1646 3.826157 TCTTTTCATTCGGTCCTGCAAAT 59.174 39.130 0.00 0.00 0.00 2.32
1625 1676 5.239351 TGGCAAATTTGTCATCTGGATTTG 58.761 37.500 21.18 0.00 37.97 2.32
1627 1678 5.702209 GGCAAATTTGTCATCTGGATTTGTT 59.298 36.000 17.76 0.00 38.99 2.83
1638 1689 4.804108 TCTGGATTTGTTTACCATTTGCG 58.196 39.130 0.00 0.00 33.08 4.85
1639 1690 4.279671 TCTGGATTTGTTTACCATTTGCGT 59.720 37.500 0.00 0.00 33.08 5.24
1701 1755 2.686558 TTGCAGTGTGATTTTCTCGC 57.313 45.000 0.00 0.00 34.82 5.03
1744 1822 3.353557 TGGAACTGTACTCTGACGCTAT 58.646 45.455 0.00 0.00 0.00 2.97
1777 1860 5.283457 ACTCTGTAATAGGCAACATCTCC 57.717 43.478 0.00 0.00 41.41 3.71
1901 1994 0.877213 GGTTAACGCGTCCGGCATAT 60.877 55.000 14.44 0.00 43.84 1.78
2062 2158 7.333528 TCAGCATTAACAACTTCAGTTTCTT 57.666 32.000 0.00 0.00 35.83 2.52
2118 2214 5.228665 GGAACTGTTGGAGTACAAGACTAC 58.771 45.833 0.00 0.00 40.38 2.73
2120 2216 5.455056 ACTGTTGGAGTACAAGACTACTG 57.545 43.478 0.00 0.00 40.13 2.74
2213 3825 2.824880 CCCTCCACCAAACGACCCA 61.825 63.158 0.00 0.00 0.00 4.51
2293 3905 2.368011 CCCCCTTCCTCCGGAGAAC 61.368 68.421 33.39 0.00 31.21 3.01
2301 3913 2.573369 TCCTCCGGAGAACTAAGATCG 58.427 52.381 33.39 11.74 0.00 3.69
2389 4049 7.028131 AGATGGATTGAGAGGGGTATTAAGAT 58.972 38.462 0.00 0.00 0.00 2.40
2471 4131 3.984508 ATAGTCGTCAATCAGGTACGG 57.015 47.619 0.00 0.00 37.24 4.02
2485 4145 4.992319 TCAGGTACGGAACATTGTTAAGTG 59.008 41.667 15.46 4.65 0.00 3.16
2490 4150 2.816337 CGGAACATTGTTAAGTGGGGGT 60.816 50.000 1.15 0.00 0.00 4.95
2535 4195 6.749118 GGCTTCAAAGTAGCATTGTTCATAAG 59.251 38.462 0.00 0.00 40.42 1.73
2600 4260 5.998981 ACCTGATGGATTAGACTAGTCTACG 59.001 44.000 28.43 13.46 38.21 3.51
2618 4278 0.890996 CGTTGCCTTCTTTCCAGCCT 60.891 55.000 0.00 0.00 0.00 4.58
2711 4371 4.634012 TTACCCTGCAACACTCTAACAT 57.366 40.909 0.00 0.00 0.00 2.71
2739 4399 2.364324 ACTCCGAAGTAGTCAACAAGCA 59.636 45.455 0.00 0.00 32.59 3.91
2799 4459 0.178068 AAGTCCGTGAATCCCATCCG 59.822 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.767524 TTGACCTTTTATGTTGAGTTGTGT 57.232 33.333 0.00 0.00 0.00 3.72
1 2 7.382218 GGATTTGACCTTTTATGTTGAGTTGTG 59.618 37.037 0.00 0.00 0.00 3.33
2 3 7.433680 GGATTTGACCTTTTATGTTGAGTTGT 58.566 34.615 0.00 0.00 0.00 3.32
3 4 6.868339 GGGATTTGACCTTTTATGTTGAGTTG 59.132 38.462 0.00 0.00 0.00 3.16
4 5 6.553100 TGGGATTTGACCTTTTATGTTGAGTT 59.447 34.615 0.00 0.00 0.00 3.01
5 6 6.074648 TGGGATTTGACCTTTTATGTTGAGT 58.925 36.000 0.00 0.00 0.00 3.41
6 7 6.588719 TGGGATTTGACCTTTTATGTTGAG 57.411 37.500 0.00 0.00 0.00 3.02
7 8 6.496565 ACATGGGATTTGACCTTTTATGTTGA 59.503 34.615 0.00 0.00 0.00 3.18
8 9 6.700352 ACATGGGATTTGACCTTTTATGTTG 58.300 36.000 0.00 0.00 0.00 3.33
9 10 6.933514 ACATGGGATTTGACCTTTTATGTT 57.066 33.333 0.00 0.00 0.00 2.71
10 11 7.013274 CGATACATGGGATTTGACCTTTTATGT 59.987 37.037 0.00 0.00 0.00 2.29
11 12 7.013274 ACGATACATGGGATTTGACCTTTTATG 59.987 37.037 0.00 0.00 0.00 1.90
12 13 7.060421 ACGATACATGGGATTTGACCTTTTAT 58.940 34.615 0.00 0.00 0.00 1.40
13 14 6.419791 ACGATACATGGGATTTGACCTTTTA 58.580 36.000 0.00 0.00 0.00 1.52
14 15 5.261216 ACGATACATGGGATTTGACCTTTT 58.739 37.500 0.00 0.00 0.00 2.27
15 16 4.855340 ACGATACATGGGATTTGACCTTT 58.145 39.130 0.00 0.00 0.00 3.11
16 17 4.451900 GACGATACATGGGATTTGACCTT 58.548 43.478 0.00 0.00 0.00 3.50
17 18 3.181454 GGACGATACATGGGATTTGACCT 60.181 47.826 0.00 0.00 0.00 3.85
18 19 3.139077 GGACGATACATGGGATTTGACC 58.861 50.000 0.00 0.00 0.00 4.02
19 20 2.800544 CGGACGATACATGGGATTTGAC 59.199 50.000 0.00 0.00 0.00 3.18
20 21 2.432874 ACGGACGATACATGGGATTTGA 59.567 45.455 0.00 0.00 0.00 2.69
21 22 2.833794 ACGGACGATACATGGGATTTG 58.166 47.619 0.00 0.00 0.00 2.32
22 23 3.986277 GTACGGACGATACATGGGATTT 58.014 45.455 0.00 0.00 0.00 2.17
23 24 3.655276 GTACGGACGATACATGGGATT 57.345 47.619 0.00 0.00 0.00 3.01
36 37 2.856557 GCTGATTTTACTCCGTACGGAC 59.143 50.000 32.61 20.66 39.76 4.79
37 38 2.756760 AGCTGATTTTACTCCGTACGGA 59.243 45.455 33.55 33.55 42.90 4.69
38 39 2.858344 CAGCTGATTTTACTCCGTACGG 59.142 50.000 28.66 28.66 0.00 4.02
39 40 2.281762 GCAGCTGATTTTACTCCGTACG 59.718 50.000 20.43 8.69 0.00 3.67
40 41 3.522553 AGCAGCTGATTTTACTCCGTAC 58.477 45.455 20.43 0.00 0.00 3.67
41 42 3.194755 TGAGCAGCTGATTTTACTCCGTA 59.805 43.478 20.43 0.00 0.00 4.02
42 43 2.028112 TGAGCAGCTGATTTTACTCCGT 60.028 45.455 20.43 0.00 0.00 4.69
43 44 2.606725 CTGAGCAGCTGATTTTACTCCG 59.393 50.000 20.43 5.87 0.00 4.63
57 58 4.383861 TGTCCCGCAGCTGAGCAG 62.384 66.667 20.43 8.70 0.00 4.24
58 59 4.687215 GTGTCCCGCAGCTGAGCA 62.687 66.667 20.43 4.89 0.00 4.26
60 61 4.767255 GGGTGTCCCGCAGCTGAG 62.767 72.222 20.43 15.45 44.46 3.35
80 81 5.308984 ATCTAAGGCAGATCCACGTGTGG 62.309 52.174 15.65 12.91 40.09 4.17
81 82 1.204704 TCTAAGGCAGATCCACGTGTG 59.795 52.381 15.65 7.18 37.29 3.82
82 83 1.557099 TCTAAGGCAGATCCACGTGT 58.443 50.000 15.65 0.00 37.29 4.49
83 84 2.101415 TCATCTAAGGCAGATCCACGTG 59.899 50.000 9.08 9.08 42.40 4.49
84 85 2.388735 TCATCTAAGGCAGATCCACGT 58.611 47.619 0.00 0.00 42.40 4.49
85 86 3.674528 ATCATCTAAGGCAGATCCACG 57.325 47.619 0.00 0.00 42.40 4.94
86 87 4.514441 CACAATCATCTAAGGCAGATCCAC 59.486 45.833 0.00 0.00 42.40 4.02
87 88 4.164796 ACACAATCATCTAAGGCAGATCCA 59.835 41.667 0.00 0.00 42.40 3.41
88 89 4.712476 ACACAATCATCTAAGGCAGATCC 58.288 43.478 0.00 0.00 42.40 3.36
89 90 5.819379 TGAACACAATCATCTAAGGCAGATC 59.181 40.000 0.00 0.00 42.40 2.75
90 91 5.748402 TGAACACAATCATCTAAGGCAGAT 58.252 37.500 0.00 0.00 45.35 2.90
91 92 5.164620 TGAACACAATCATCTAAGGCAGA 57.835 39.130 0.00 0.00 37.79 4.26
92 93 5.181811 TGTTGAACACAATCATCTAAGGCAG 59.818 40.000 0.00 0.00 29.87 4.85
93 94 5.069318 TGTTGAACACAATCATCTAAGGCA 58.931 37.500 0.00 0.00 29.87 4.75
94 95 5.627499 TGTTGAACACAATCATCTAAGGC 57.373 39.130 0.00 0.00 29.87 4.35
122 123 5.182487 GGGGCAAAAAGTGAAGAAGAAAAA 58.818 37.500 0.00 0.00 0.00 1.94
123 124 4.223923 TGGGGCAAAAAGTGAAGAAGAAAA 59.776 37.500 0.00 0.00 0.00 2.29
124 125 3.772025 TGGGGCAAAAAGTGAAGAAGAAA 59.228 39.130 0.00 0.00 0.00 2.52
125 126 3.370104 TGGGGCAAAAAGTGAAGAAGAA 58.630 40.909 0.00 0.00 0.00 2.52
126 127 3.025322 TGGGGCAAAAAGTGAAGAAGA 57.975 42.857 0.00 0.00 0.00 2.87
127 128 4.341366 AATGGGGCAAAAAGTGAAGAAG 57.659 40.909 0.00 0.00 0.00 2.85
128 129 4.408596 AGAAATGGGGCAAAAAGTGAAGAA 59.591 37.500 0.00 0.00 0.00 2.52
129 130 3.966665 AGAAATGGGGCAAAAAGTGAAGA 59.033 39.130 0.00 0.00 0.00 2.87
130 131 4.341366 AGAAATGGGGCAAAAAGTGAAG 57.659 40.909 0.00 0.00 0.00 3.02
131 132 4.163078 TGAAGAAATGGGGCAAAAAGTGAA 59.837 37.500 0.00 0.00 0.00 3.18
132 133 3.708631 TGAAGAAATGGGGCAAAAAGTGA 59.291 39.130 0.00 0.00 0.00 3.41
133 134 4.070630 TGAAGAAATGGGGCAAAAAGTG 57.929 40.909 0.00 0.00 0.00 3.16
134 135 4.980339 ATGAAGAAATGGGGCAAAAAGT 57.020 36.364 0.00 0.00 0.00 2.66
135 136 5.818857 CCATATGAAGAAATGGGGCAAAAAG 59.181 40.000 3.65 0.00 39.23 2.27
136 137 5.743117 CCATATGAAGAAATGGGGCAAAAA 58.257 37.500 3.65 0.00 39.23 1.94
137 138 5.356291 CCATATGAAGAAATGGGGCAAAA 57.644 39.130 3.65 0.00 39.23 2.44
144 145 7.037438 CACAAGAAACCCATATGAAGAAATGG 58.963 38.462 3.65 0.00 42.02 3.16
145 146 7.037438 CCACAAGAAACCCATATGAAGAAATG 58.963 38.462 3.65 0.00 0.00 2.32
146 147 6.155049 CCCACAAGAAACCCATATGAAGAAAT 59.845 38.462 3.65 0.00 0.00 2.17
151 152 4.396357 ACCCACAAGAAACCCATATGAA 57.604 40.909 3.65 0.00 0.00 2.57
159 160 3.494223 CCCATGAAAACCCACAAGAAACC 60.494 47.826 0.00 0.00 0.00 3.27
170 171 0.608130 GAACAGGCCCCATGAAAACC 59.392 55.000 0.00 0.00 0.00 3.27
176 177 1.143813 AGGATAGAACAGGCCCCATG 58.856 55.000 0.00 0.00 0.00 3.66
178 179 1.681229 AAAGGATAGAACAGGCCCCA 58.319 50.000 0.00 0.00 0.00 4.96
285 305 8.273557 GCAACATTAGAAATTGATCATGCATTC 58.726 33.333 0.00 0.00 0.00 2.67
356 376 4.146616 CGTGTGTTTCAAACAAAACGTTCA 59.853 37.500 22.70 7.29 44.16 3.18
361 381 3.982058 TGTCCGTGTGTTTCAAACAAAAC 59.018 39.130 4.02 5.94 44.16 2.43
366 386 3.481112 AGTTGTCCGTGTGTTTCAAAC 57.519 42.857 0.00 0.00 0.00 2.93
433 464 7.376072 GCGCATTTATAGAAAATGTTCAGGTAC 59.624 37.037 0.30 0.00 39.25 3.34
437 468 7.739022 TTGCGCATTTATAGAAAATGTTCAG 57.261 32.000 12.75 3.88 39.25 3.02
438 469 7.596621 TGTTTGCGCATTTATAGAAAATGTTCA 59.403 29.630 12.75 7.24 39.25 3.18
573 604 5.989551 AAAAATGTCCATGCAGTTCAAAC 57.010 34.783 0.00 0.00 0.00 2.93
582 613 9.585099 TGTTAGATCATTTAAAAATGTCCATGC 57.415 29.630 13.58 4.84 44.66 4.06
596 627 8.561738 ACGGTCTAAAACATGTTAGATCATTT 57.438 30.769 17.70 8.11 40.03 2.32
599 630 6.370442 CCAACGGTCTAAAACATGTTAGATCA 59.630 38.462 17.70 0.00 40.03 2.92
600 631 6.592607 TCCAACGGTCTAAAACATGTTAGATC 59.407 38.462 12.39 11.22 41.09 2.75
601 632 6.469410 TCCAACGGTCTAAAACATGTTAGAT 58.531 36.000 12.39 4.17 41.09 1.98
602 633 5.856156 TCCAACGGTCTAAAACATGTTAGA 58.144 37.500 12.39 9.26 37.69 2.10
603 634 6.548441 TTCCAACGGTCTAAAACATGTTAG 57.452 37.500 12.39 6.78 33.16 2.34
604 635 8.795842 ATATTCCAACGGTCTAAAACATGTTA 57.204 30.769 12.39 0.00 0.00 2.41
774 807 0.234884 CGGAAAATAGCGCGGGAATC 59.765 55.000 8.83 0.00 0.00 2.52
882 916 2.434884 AAGTGTGCGAGCGATGGG 60.435 61.111 0.00 0.00 0.00 4.00
997 1038 0.897863 TGGAGCCGAATTGGTTTGGG 60.898 55.000 0.00 0.00 39.03 4.12
1026 1068 4.220602 ACGAAGGAATTGGGGATTTTTCTG 59.779 41.667 0.00 0.00 0.00 3.02
1081 1124 0.803768 CCGGACATCTTCTCGCTGTG 60.804 60.000 0.00 0.00 0.00 3.66
1083 1126 1.227089 CCCGGACATCTTCTCGCTG 60.227 63.158 0.73 0.00 0.00 5.18
1341 1384 1.080366 GTACACGACGTCCATGGCA 60.080 57.895 10.58 0.00 0.00 4.92
1444 1492 2.202388 CAGGCACAAGCATTCGCG 60.202 61.111 0.00 0.00 45.49 5.87
1483 1533 4.414337 AATCCAGATAGCACTTCCTCAC 57.586 45.455 0.00 0.00 0.00 3.51
1491 1541 5.645497 ACAGAGAAACAAATCCAGATAGCAC 59.355 40.000 0.00 0.00 0.00 4.40
1497 1547 8.868522 ATATTGAACAGAGAAACAAATCCAGA 57.131 30.769 0.00 0.00 0.00 3.86
1519 1570 2.808202 GCAATGGCTGGACTGACGATAT 60.808 50.000 0.00 0.00 36.96 1.63
1534 1585 3.671433 CGGTGTCAAATCAGAAGCAATGG 60.671 47.826 0.00 0.00 0.00 3.16
1537 1588 2.571212 ACGGTGTCAAATCAGAAGCAA 58.429 42.857 0.00 0.00 0.00 3.91
1538 1589 2.254546 ACGGTGTCAAATCAGAAGCA 57.745 45.000 0.00 0.00 0.00 3.91
1551 1602 4.712122 ATTTCACAAACTCAAACGGTGT 57.288 36.364 0.00 0.00 0.00 4.16
1595 1646 6.294675 CCAGATGACAAATTTGCCAAGTTAGA 60.295 38.462 18.12 0.00 0.00 2.10
1668 1722 7.094508 TCACACTGCAATTTAGTTTCAGAAA 57.905 32.000 0.00 0.00 0.00 2.52
1669 1723 6.691754 TCACACTGCAATTTAGTTTCAGAA 57.308 33.333 0.00 0.00 0.00 3.02
1701 1755 2.721274 AGCAGCTATGAGCATACTCG 57.279 50.000 0.00 0.00 46.69 4.18
1744 1822 7.109501 TGCCTATTACAGAGTAAATGCTTTCA 58.890 34.615 0.00 0.00 0.00 2.69
1777 1860 1.129998 CTTGCAGCAGGAATTGTCTCG 59.870 52.381 0.00 0.00 0.00 4.04
1892 1985 3.069586 CAGGTCAAGTTCTATATGCCGGA 59.930 47.826 5.05 0.00 0.00 5.14
1894 1987 4.060038 ACAGGTCAAGTTCTATATGCCG 57.940 45.455 0.00 0.00 0.00 5.69
2163 2259 5.046231 AGGTATTCTCCCAGACAAAGAACTC 60.046 44.000 0.00 0.00 32.22 3.01
2213 3825 4.038883 AGCTTCGTGTTGTACCTAAAGTCT 59.961 41.667 0.00 0.00 0.00 3.24
2293 3905 3.138205 AGTGACTCGCAACGATCTTAG 57.862 47.619 0.00 0.00 34.61 2.18
2301 3913 2.423892 TCATCCTCTAGTGACTCGCAAC 59.576 50.000 0.00 0.00 0.00 4.17
2389 4049 4.467084 CCCAGGCGCCGAAGCTAA 62.467 66.667 23.20 0.00 36.60 3.09
2465 4125 3.437741 CCCACTTAACAATGTTCCGTACC 59.562 47.826 0.22 0.00 0.00 3.34
2471 4131 4.828387 TGTTACCCCCACTTAACAATGTTC 59.172 41.667 0.22 0.00 35.69 3.18
2490 4150 2.438411 CAATAGGGCAAACGGGTGTTA 58.562 47.619 0.00 0.00 37.31 2.41
2535 4195 1.667724 CGACATGGACAGATCCTTTGC 59.332 52.381 0.00 0.00 46.43 3.68
2600 4260 1.000171 CAAGGCTGGAAAGAAGGCAAC 60.000 52.381 0.00 0.00 42.43 4.17
2618 4278 1.234821 GCAACTTGGACGACCATCAA 58.765 50.000 7.61 0.00 46.34 2.57
2655 4315 4.278170 ACTCGAATTTTCTTCATGCCACAA 59.722 37.500 0.00 0.00 0.00 3.33
2711 4371 5.302568 TGTTGACTACTTCGGAGTTCCTTTA 59.697 40.000 0.00 0.00 37.33 1.85
2739 4399 3.586470 TGGTCAGTAAACATGGTTGGT 57.414 42.857 6.16 0.00 0.00 3.67
2813 4473 2.727123 TGGGAGAAGCTTGTTGAACA 57.273 45.000 2.10 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.