Multiple sequence alignment - TraesCS2D01G034400

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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 TraesCS2D01G034400 chr2D 100.000 2381 0 0 1 2381 13227655 13230035 0.000000e+00 4397.0
1 TraesCS2D01G034400 chr2D 94.000 50 3 0 229 278 263240544 263240593 2.540000e-10 76.8
2 TraesCS2D01G034400 chr2B 93.513 1711 81 16 57 1758 23877173 23878862 0.000000e+00 2518.0
3 TraesCS2D01G034400 chr2B 85.229 589 64 9 1813 2380 23878878 23879464 3.410000e-163 584.0
4 TraesCS2D01G034400 chr2B 90.323 62 4 1 225 284 796024274 796024213 1.960000e-11 80.5
5 TraesCS2D01G034400 chr2A 92.926 1442 77 14 345 1777 15269337 15270762 0.000000e+00 2074.0
6 TraesCS2D01G034400 chr2A 85.478 544 60 5 1844 2381 15271112 15271642 1.240000e-152 549.0
7 TraesCS2D01G034400 chr2A 90.057 352 21 8 1 351 15244792 15245130 6.040000e-121 444.0
8 TraesCS2D01G034400 chr4D 81.395 258 37 11 1141 1391 323354816 323354563 1.440000e-47 200.0
9 TraesCS2D01G034400 chr4B 81.124 249 37 10 1141 1383 403624662 403624418 8.690000e-45 191.0
10 TraesCS2D01G034400 chr4A 80.385 260 39 12 1141 1392 148757869 148758124 1.120000e-43 187.0
11 TraesCS2D01G034400 chr6D 97.917 48 1 0 225 272 65497125 65497172 1.520000e-12 84.2
12 TraesCS2D01G034400 chr3D 96.078 51 2 0 225 275 583869034 583868984 1.520000e-12 84.2
13 TraesCS2D01G034400 chr3B 96.078 51 2 0 225 275 548455904 548455854 1.520000e-12 84.2
14 TraesCS2D01G034400 chr5D 89.394 66 3 4 225 286 447626979 447626914 1.960000e-11 80.5
15 TraesCS2D01G034400 chr1A 91.525 59 3 2 225 281 430590387 430590329 1.960000e-11 80.5


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 TraesCS2D01G034400 chr2D 13227655 13230035 2380 False 4397.0 4397 100.000 1 2381 1 chr2D.!!$F1 2380
1 TraesCS2D01G034400 chr2B 23877173 23879464 2291 False 1551.0 2518 89.371 57 2380 2 chr2B.!!$F1 2323
2 TraesCS2D01G034400 chr2A 15269337 15271642 2305 False 1311.5 2074 89.202 345 2381 2 chr2A.!!$F2 2036

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
59 60 0.10741 AACCATTATTCTCCGGCGCA 60.107 50.0 10.83 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1823 0.320374 TGAAATCTGTTCGGCGGAGT 59.68 50.0 7.21 0.0 35.67 3.85 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
30 31 4.695217 TTTTAGACCACATCCAATTCGC 57.305 40.909 0.00 0.00 0.00 4.70
31 32 3.342377 TTAGACCACATCCAATTCGCA 57.658 42.857 0.00 0.00 0.00 5.10
32 33 2.425143 AGACCACATCCAATTCGCAT 57.575 45.000 0.00 0.00 0.00 4.73
33 34 3.558931 AGACCACATCCAATTCGCATA 57.441 42.857 0.00 0.00 0.00 3.14
34 35 4.090761 AGACCACATCCAATTCGCATAT 57.909 40.909 0.00 0.00 0.00 1.78
35 36 3.817084 AGACCACATCCAATTCGCATATG 59.183 43.478 0.00 0.00 0.00 1.78
36 37 3.554934 ACCACATCCAATTCGCATATGT 58.445 40.909 4.29 0.00 0.00 2.29
37 38 3.316029 ACCACATCCAATTCGCATATGTG 59.684 43.478 10.11 10.11 44.41 3.21
38 39 3.892522 CACATCCAATTCGCATATGTGG 58.107 45.455 16.02 9.42 42.25 4.17
39 40 3.565063 CACATCCAATTCGCATATGTGGA 59.435 43.478 16.02 14.29 42.25 4.02
40 41 4.036616 CACATCCAATTCGCATATGTGGAA 59.963 41.667 16.02 13.69 42.25 3.53
41 42 4.644234 ACATCCAATTCGCATATGTGGAAA 59.356 37.500 16.02 4.76 41.54 3.13
42 43 4.630894 TCCAATTCGCATATGTGGAAAC 57.369 40.909 16.02 0.00 35.45 2.78
43 44 3.380004 TCCAATTCGCATATGTGGAAACC 59.620 43.478 16.02 0.00 35.45 3.27
44 45 3.130164 CCAATTCGCATATGTGGAAACCA 59.870 43.478 16.02 0.00 0.00 3.67
45 46 4.202141 CCAATTCGCATATGTGGAAACCAT 60.202 41.667 16.02 0.00 35.28 3.55
46 47 5.350633 CAATTCGCATATGTGGAAACCATT 58.649 37.500 16.02 3.66 35.28 3.16
47 48 6.460814 CCAATTCGCATATGTGGAAACCATTA 60.461 38.462 16.02 0.00 35.28 1.90
48 49 6.899393 ATTCGCATATGTGGAAACCATTAT 57.101 33.333 16.02 0.00 35.28 1.28
49 50 6.707440 TTCGCATATGTGGAAACCATTATT 57.293 33.333 16.02 0.00 35.28 1.40
50 51 6.312399 TCGCATATGTGGAAACCATTATTC 57.688 37.500 16.02 0.00 35.28 1.75
51 52 6.061441 TCGCATATGTGGAAACCATTATTCT 58.939 36.000 16.02 0.00 35.28 2.40
52 53 6.204688 TCGCATATGTGGAAACCATTATTCTC 59.795 38.462 16.02 0.00 35.28 2.87
53 54 6.568462 CGCATATGTGGAAACCATTATTCTCC 60.568 42.308 8.46 0.00 35.28 3.71
54 55 6.568462 GCATATGTGGAAACCATTATTCTCCG 60.568 42.308 4.29 0.00 35.28 4.63
55 56 3.616219 TGTGGAAACCATTATTCTCCGG 58.384 45.455 0.00 0.00 35.28 5.14
56 57 2.357952 GTGGAAACCATTATTCTCCGGC 59.642 50.000 0.00 0.00 35.28 6.13
57 58 1.602377 GGAAACCATTATTCTCCGGCG 59.398 52.381 0.00 0.00 0.00 6.46
58 59 1.002792 GAAACCATTATTCTCCGGCGC 60.003 52.381 0.00 0.00 0.00 6.53
59 60 0.107410 AACCATTATTCTCCGGCGCA 60.107 50.000 10.83 0.00 0.00 6.09
60 61 0.107410 ACCATTATTCTCCGGCGCAA 60.107 50.000 10.83 0.00 0.00 4.85
103 104 8.786826 TTTGTATCTAACACGGAATTTCTCAT 57.213 30.769 0.00 0.00 38.00 2.90
115 116 4.427312 GAATTTCTCATCAACATGCACCC 58.573 43.478 0.00 0.00 0.00 4.61
131 133 1.531149 CACCCAGAACGTGTGCTAAAG 59.469 52.381 0.00 0.00 0.00 1.85
134 136 2.479837 CCAGAACGTGTGCTAAAGACA 58.520 47.619 0.00 0.00 0.00 3.41
168 170 4.507756 GCAAAATGAAAACCACTCACTTCC 59.492 41.667 0.00 0.00 0.00 3.46
199 201 3.813166 CCAAGCCGAAAACAGAAAGTAGA 59.187 43.478 0.00 0.00 0.00 2.59
231 233 5.330455 TCTTGGTCTGCTTGATAGTGTAG 57.670 43.478 0.00 0.00 0.00 2.74
235 237 4.082190 TGGTCTGCTTGATAGTGTAGTGTC 60.082 45.833 0.00 0.00 0.00 3.67
242 244 6.071463 GCTTGATAGTGTAGTGTCAAAAACG 58.929 40.000 1.48 0.00 30.96 3.60
243 245 6.292703 GCTTGATAGTGTAGTGTCAAAAACGT 60.293 38.462 1.48 0.00 30.96 3.99
263 265 6.600882 ACGTTCTTATATTATGGGACGGAT 57.399 37.500 13.18 0.00 0.00 4.18
264 266 6.395629 ACGTTCTTATATTATGGGACGGATG 58.604 40.000 13.18 0.00 0.00 3.51
271 273 8.618240 TTATATTATGGGACGGATGGAGTATT 57.382 34.615 0.00 0.00 0.00 1.89
272 274 4.617253 TTATGGGACGGATGGAGTATTG 57.383 45.455 0.00 0.00 0.00 1.90
273 275 1.128200 TGGGACGGATGGAGTATTGG 58.872 55.000 0.00 0.00 0.00 3.16
274 276 1.343580 TGGGACGGATGGAGTATTGGA 60.344 52.381 0.00 0.00 0.00 3.53
275 277 1.344763 GGGACGGATGGAGTATTGGAG 59.655 57.143 0.00 0.00 0.00 3.86
276 278 2.040178 GGACGGATGGAGTATTGGAGT 58.960 52.381 0.00 0.00 0.00 3.85
277 279 3.228453 GGACGGATGGAGTATTGGAGTA 58.772 50.000 0.00 0.00 0.00 2.59
278 280 3.833070 GGACGGATGGAGTATTGGAGTAT 59.167 47.826 0.00 0.00 0.00 2.12
279 281 5.014858 GGACGGATGGAGTATTGGAGTATA 58.985 45.833 0.00 0.00 0.00 1.47
280 282 5.657302 GGACGGATGGAGTATTGGAGTATAT 59.343 44.000 0.00 0.00 0.00 0.86
281 283 6.405953 GGACGGATGGAGTATTGGAGTATATG 60.406 46.154 0.00 0.00 0.00 1.78
324 326 3.821033 GCTCTTCCCAACGCCATAATTAT 59.179 43.478 0.00 0.00 0.00 1.28
341 343 9.703892 CCATAATTATTTGGCCATTCGAAATTA 57.296 29.630 6.09 12.96 35.26 1.40
354 356 9.209175 GCCATTCGAAATTACACTTAGATAGAT 57.791 33.333 0.00 0.00 0.00 1.98
426 428 1.135139 CTCCAGTGACATGGTCCTACG 59.865 57.143 0.00 0.00 41.43 3.51
428 430 2.097036 CCAGTGACATGGTCCTACGTA 58.903 52.381 0.00 0.00 35.47 3.57
429 431 2.159282 CCAGTGACATGGTCCTACGTAC 60.159 54.545 0.00 0.00 35.47 3.67
430 432 2.490509 CAGTGACATGGTCCTACGTACA 59.509 50.000 0.00 0.00 0.00 2.90
431 433 3.130516 CAGTGACATGGTCCTACGTACAT 59.869 47.826 0.00 0.00 0.00 2.29
432 434 3.380637 AGTGACATGGTCCTACGTACATC 59.619 47.826 0.00 0.00 0.00 3.06
433 435 3.380637 GTGACATGGTCCTACGTACATCT 59.619 47.826 0.00 0.00 0.00 2.90
434 436 4.021229 TGACATGGTCCTACGTACATCTT 58.979 43.478 0.00 0.00 0.00 2.40
435 437 5.066893 GTGACATGGTCCTACGTACATCTTA 59.933 44.000 0.00 0.00 0.00 2.10
436 438 5.653330 TGACATGGTCCTACGTACATCTTAA 59.347 40.000 0.00 0.00 0.00 1.85
516 522 7.050493 ACCAGATGTAGGAGATATACCAGAT 57.950 40.000 0.00 0.00 0.00 2.90
599 605 3.000078 GCACAACATGAACCTCGTATACG 60.000 47.826 19.23 19.23 41.45 3.06
640 646 4.380843 TTTCTCACCAACATACACCCAT 57.619 40.909 0.00 0.00 0.00 4.00
649 655 0.650512 CATACACCCATGAACGCGTC 59.349 55.000 14.44 7.01 0.00 5.19
652 658 2.047274 ACCCATGAACGCGTCCAG 60.047 61.111 14.44 0.00 0.00 3.86
655 661 1.361668 CCCATGAACGCGTCCAGAAG 61.362 60.000 14.44 0.00 0.00 2.85
694 700 6.756074 TGTCAAAATGAAAATCACACACTTCC 59.244 34.615 0.00 0.00 0.00 3.46
769 776 4.866486 CAGTTGCTTGCCTGAAAAATATCC 59.134 41.667 0.00 0.00 0.00 2.59
770 777 4.774200 AGTTGCTTGCCTGAAAAATATCCT 59.226 37.500 0.00 0.00 0.00 3.24
790 802 3.642778 AATGAGACGACGTGGCCCG 62.643 63.158 4.58 11.48 44.03 6.13
821 833 2.158957 GCCCAGACATGATAGGAAACGA 60.159 50.000 0.00 0.00 0.00 3.85
834 846 2.286025 AGGAAACGAGTGCACGTAAAAC 59.714 45.455 12.01 3.51 45.83 2.43
837 849 1.494824 ACGAGTGCACGTAAAACCTC 58.505 50.000 12.01 0.00 44.72 3.85
945 957 0.519519 CCTTACCGCATCAAACGCAA 59.480 50.000 0.00 0.00 0.00 4.85
975 987 7.768807 TGTTACAGCCTAACCACATAAAATT 57.231 32.000 0.60 0.00 0.00 1.82
978 990 5.949735 ACAGCCTAACCACATAAAATTTCG 58.050 37.500 0.00 0.00 0.00 3.46
980 992 4.109766 GCCTAACCACATAAAATTTCGGC 58.890 43.478 0.00 0.00 0.00 5.54
1314 1326 0.390472 GGGACAAGCTCAAGGACTCG 60.390 60.000 0.00 0.00 0.00 4.18
1420 1432 1.591863 GGACGGCGGATAGTGAAGC 60.592 63.158 13.24 0.00 0.00 3.86
1621 1634 1.069258 GGGTATGGTGTAGAGGCGC 59.931 63.158 0.00 0.00 0.00 6.53
1647 1660 6.657875 AGTCTGATCCTCCTTTTCCATTAAG 58.342 40.000 0.00 0.00 0.00 1.85
1679 1692 3.600388 AGCTCTAAAAACCTGACATCCG 58.400 45.455 0.00 0.00 0.00 4.18
1695 1708 3.374058 ACATCCGAATTTTAGCACTTCCG 59.626 43.478 0.00 0.00 0.00 4.30
1696 1709 2.352388 TCCGAATTTTAGCACTTCCGG 58.648 47.619 0.00 0.00 0.00 5.14
1698 1711 2.095372 CCGAATTTTAGCACTTCCGGTC 59.905 50.000 0.00 0.00 0.00 4.79
1726 1739 3.879295 CTGTTTTAGCCATCGGATCACAT 59.121 43.478 0.00 0.00 0.00 3.21
1734 1747 0.744057 ATCGGATCACATTGCACGCA 60.744 50.000 0.00 0.00 0.00 5.24
1760 1773 0.467384 AGCAATCTGATAGCCACGCT 59.533 50.000 0.00 0.00 43.41 5.07
1777 1790 3.990469 CACGCTAGACTTTGAGATGTGTT 59.010 43.478 0.00 0.00 0.00 3.32
1778 1791 4.449068 CACGCTAGACTTTGAGATGTGTTT 59.551 41.667 0.00 0.00 0.00 2.83
1779 1792 4.449068 ACGCTAGACTTTGAGATGTGTTTG 59.551 41.667 0.00 0.00 0.00 2.93
1780 1793 4.143030 CGCTAGACTTTGAGATGTGTTTGG 60.143 45.833 0.00 0.00 0.00 3.28
1781 1794 4.757149 GCTAGACTTTGAGATGTGTTTGGT 59.243 41.667 0.00 0.00 0.00 3.67
1785 1798 2.286365 TTGAGATGTGTTTGGTCCCC 57.714 50.000 0.00 0.00 0.00 4.81
1786 1799 0.404040 TGAGATGTGTTTGGTCCCCC 59.596 55.000 0.00 0.00 0.00 5.40
1787 1800 0.404040 GAGATGTGTTTGGTCCCCCA 59.596 55.000 0.00 0.00 39.65 4.96
1788 1801 0.112412 AGATGTGTTTGGTCCCCCAC 59.888 55.000 0.00 0.00 41.67 4.61
1789 1802 0.112412 GATGTGTTTGGTCCCCCACT 59.888 55.000 4.80 0.00 41.67 4.00
1790 1803 0.112412 ATGTGTTTGGTCCCCCACTC 59.888 55.000 4.80 0.00 41.67 3.51
1791 1804 1.282653 TGTGTTTGGTCCCCCACTCA 61.283 55.000 4.80 0.00 41.67 3.41
1792 1805 0.822121 GTGTTTGGTCCCCCACTCAC 60.822 60.000 0.00 0.00 41.67 3.51
1793 1806 1.228459 GTTTGGTCCCCCACTCACC 60.228 63.158 0.00 0.00 41.67 4.02
1794 1807 1.698116 TTTGGTCCCCCACTCACCA 60.698 57.895 0.00 0.00 41.67 4.17
1795 1808 2.002018 TTTGGTCCCCCACTCACCAC 62.002 60.000 0.00 0.00 41.67 4.16
1796 1809 3.647771 GGTCCCCCACTCACCACC 61.648 72.222 0.00 0.00 0.00 4.61
1797 1810 3.647771 GTCCCCCACTCACCACCC 61.648 72.222 0.00 0.00 0.00 4.61
1798 1811 4.995058 TCCCCCACTCACCACCCC 62.995 72.222 0.00 0.00 0.00 4.95
1821 1834 3.103911 CACACGACTCCGCCGAAC 61.104 66.667 0.00 0.00 39.95 3.95
1824 1837 2.981909 ACGACTCCGCCGAACAGA 60.982 61.111 0.00 0.00 39.95 3.41
1846 2142 2.031516 CAGTGAACTCGGCAGCCAG 61.032 63.158 13.30 10.63 0.00 4.85
1867 2166 2.165301 CGCGGATTCGACCAGTTCC 61.165 63.158 0.00 0.00 39.00 3.62
1870 2169 1.153429 GGATTCGACCAGTTCCCGG 60.153 63.158 0.00 0.00 0.00 5.73
1916 2215 4.680237 CGCCAGTTGTGCTCCCGA 62.680 66.667 0.00 0.00 0.00 5.14
1983 2283 1.248785 TACTCTGCGGCGTCCTTCTT 61.249 55.000 9.37 0.00 0.00 2.52
2030 2333 1.329906 CTGTCTTGCGGAATGATGAGC 59.670 52.381 0.00 0.00 0.00 4.26
2070 2390 2.123248 TTTCCTCGCCATGTCCTGCA 62.123 55.000 0.00 0.00 0.00 4.41
2071 2391 1.913951 TTCCTCGCCATGTCCTGCAT 61.914 55.000 0.00 0.00 38.60 3.96
2096 2416 1.414919 GTATCGTGCCTCCATACCCAA 59.585 52.381 0.00 0.00 0.00 4.12
2103 2426 1.602237 CTCCATACCCAACACCGCT 59.398 57.895 0.00 0.00 0.00 5.52
2106 2429 0.322098 CCATACCCAACACCGCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
2110 2433 1.371183 CCCAACACCGCTTCAGAGA 59.629 57.895 0.00 0.00 0.00 3.10
2112 2435 1.207089 CCCAACACCGCTTCAGAGATA 59.793 52.381 0.00 0.00 0.00 1.98
2175 2498 0.925720 AGGATTCCTCCCCCATTGCA 60.926 55.000 0.00 0.00 43.21 4.08
2182 2505 1.215173 CCTCCCCCATTGCATCTAACA 59.785 52.381 0.00 0.00 0.00 2.41
2289 2612 1.306141 AGGTCCCAGCAATCGAGGA 60.306 57.895 0.00 0.00 0.00 3.71
2327 2650 1.254026 AGGACATGAGTCGGTTCGAA 58.746 50.000 0.00 0.00 45.92 3.71
2339 2662 2.589442 TTCGAAAACACGGGCGCT 60.589 55.556 7.64 0.00 0.00 5.92
2351 2674 2.544698 GGGCGCTATCGTCGACTCT 61.545 63.158 14.70 2.90 42.10 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.520874 TGCGAATTGGATGTGGTCTAAAAA 59.479 37.500 0.00 0.00 30.60 1.94
9 10 4.075682 TGCGAATTGGATGTGGTCTAAAA 58.924 39.130 0.00 0.00 30.60 1.52
10 11 3.680490 TGCGAATTGGATGTGGTCTAAA 58.320 40.909 0.00 0.00 30.60 1.85
11 12 3.342377 TGCGAATTGGATGTGGTCTAA 57.658 42.857 0.00 0.00 0.00 2.10
12 13 3.558931 ATGCGAATTGGATGTGGTCTA 57.441 42.857 0.00 0.00 0.00 2.59
13 14 2.425143 ATGCGAATTGGATGTGGTCT 57.575 45.000 0.00 0.00 0.00 3.85
14 15 3.565482 ACATATGCGAATTGGATGTGGTC 59.435 43.478 1.58 0.00 40.98 4.02
15 16 3.316029 CACATATGCGAATTGGATGTGGT 59.684 43.478 9.19 0.00 40.98 4.16
16 17 3.892522 CACATATGCGAATTGGATGTGG 58.107 45.455 9.19 0.00 40.98 4.17
17 18 3.565063 TCCACATATGCGAATTGGATGTG 59.435 43.478 9.88 9.88 44.47 3.21
18 19 3.819368 TCCACATATGCGAATTGGATGT 58.181 40.909 7.69 0.00 31.19 3.06
19 20 4.834357 TTCCACATATGCGAATTGGATG 57.166 40.909 11.60 0.00 36.25 3.51
20 21 4.037923 GGTTTCCACATATGCGAATTGGAT 59.962 41.667 11.60 0.00 36.25 3.41
21 22 3.380004 GGTTTCCACATATGCGAATTGGA 59.620 43.478 7.69 7.69 34.46 3.53
22 23 3.130164 TGGTTTCCACATATGCGAATTGG 59.870 43.478 1.58 2.68 0.00 3.16
23 24 4.368874 TGGTTTCCACATATGCGAATTG 57.631 40.909 1.58 0.00 0.00 2.32
24 25 5.596836 AATGGTTTCCACATATGCGAATT 57.403 34.783 1.58 0.00 35.80 2.17
25 26 6.899393 ATAATGGTTTCCACATATGCGAAT 57.101 33.333 1.58 0.00 35.80 3.34
26 27 6.545666 AGAATAATGGTTTCCACATATGCGAA 59.454 34.615 1.58 2.12 35.80 4.70
27 28 6.061441 AGAATAATGGTTTCCACATATGCGA 58.939 36.000 1.58 0.00 35.80 5.10
28 29 6.317789 AGAATAATGGTTTCCACATATGCG 57.682 37.500 1.58 0.00 35.80 4.73
29 30 6.568462 CGGAGAATAATGGTTTCCACATATGC 60.568 42.308 1.58 0.00 35.80 3.14
30 31 6.072508 CCGGAGAATAATGGTTTCCACATATG 60.073 42.308 0.00 0.00 35.80 1.78
31 32 6.003950 CCGGAGAATAATGGTTTCCACATAT 58.996 40.000 0.00 0.00 35.80 1.78
32 33 5.373222 CCGGAGAATAATGGTTTCCACATA 58.627 41.667 0.00 0.00 35.80 2.29
33 34 4.207165 CCGGAGAATAATGGTTTCCACAT 58.793 43.478 0.00 0.00 35.80 3.21
34 35 3.616219 CCGGAGAATAATGGTTTCCACA 58.384 45.455 0.00 0.00 35.80 4.17
35 36 2.357952 GCCGGAGAATAATGGTTTCCAC 59.642 50.000 5.05 0.00 35.80 4.02
36 37 2.650322 GCCGGAGAATAATGGTTTCCA 58.350 47.619 5.05 0.00 38.19 3.53
37 38 1.602377 CGCCGGAGAATAATGGTTTCC 59.398 52.381 5.05 0.00 0.00 3.13
38 39 1.002792 GCGCCGGAGAATAATGGTTTC 60.003 52.381 10.31 0.00 0.00 2.78
39 40 1.021968 GCGCCGGAGAATAATGGTTT 58.978 50.000 10.31 0.00 0.00 3.27
40 41 0.107410 TGCGCCGGAGAATAATGGTT 60.107 50.000 10.31 0.00 0.00 3.67
41 42 0.107410 TTGCGCCGGAGAATAATGGT 60.107 50.000 10.31 0.00 0.00 3.55
42 43 1.238439 ATTGCGCCGGAGAATAATGG 58.762 50.000 10.31 0.00 0.00 3.16
43 44 3.684305 TCATATTGCGCCGGAGAATAATG 59.316 43.478 10.31 5.64 0.00 1.90
44 45 3.937814 TCATATTGCGCCGGAGAATAAT 58.062 40.909 10.31 8.56 0.00 1.28
45 46 3.394674 TCATATTGCGCCGGAGAATAA 57.605 42.857 10.31 0.42 0.00 1.40
46 47 3.064207 GTTCATATTGCGCCGGAGAATA 58.936 45.455 10.31 10.55 0.00 1.75
47 48 1.873591 GTTCATATTGCGCCGGAGAAT 59.126 47.619 10.31 8.61 0.00 2.40
48 49 1.295792 GTTCATATTGCGCCGGAGAA 58.704 50.000 10.31 0.00 0.00 2.87
49 50 0.531974 GGTTCATATTGCGCCGGAGA 60.532 55.000 10.31 0.00 0.00 3.71
50 51 0.532862 AGGTTCATATTGCGCCGGAG 60.533 55.000 5.05 1.55 0.00 4.63
51 52 0.531974 GAGGTTCATATTGCGCCGGA 60.532 55.000 5.05 0.00 0.00 5.14
52 53 1.831389 CGAGGTTCATATTGCGCCGG 61.831 60.000 4.18 0.00 0.00 6.13
53 54 1.151777 ACGAGGTTCATATTGCGCCG 61.152 55.000 4.18 0.00 0.00 6.46
54 55 1.860676 TACGAGGTTCATATTGCGCC 58.139 50.000 4.18 0.00 0.00 6.53
55 56 7.464830 AATATATACGAGGTTCATATTGCGC 57.535 36.000 0.00 0.00 0.00 6.09
56 57 8.869897 ACAAATATATACGAGGTTCATATTGCG 58.130 33.333 0.00 0.00 0.00 4.85
86 87 6.622679 GCATGTTGATGAGAAATTCCGTGTTA 60.623 38.462 0.00 0.00 0.00 2.41
103 104 0.179032 ACGTTCTGGGTGCATGTTGA 60.179 50.000 0.00 0.00 0.00 3.18
115 116 3.123804 ACTGTCTTTAGCACACGTTCTG 58.876 45.455 0.00 0.00 0.00 3.02
168 170 1.167851 TTTCGGCTTGGCAAGATGAG 58.832 50.000 30.45 16.46 0.00 2.90
199 201 7.765695 TCAAGCAGACCAAGAAGATATTTTT 57.234 32.000 0.00 0.00 0.00 1.94
218 220 6.071463 CGTTTTTGACACTACACTATCAAGC 58.929 40.000 0.00 0.00 32.90 4.01
231 233 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
235 237 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
242 244 6.942976 TCCATCCGTCCCATAATATAAGAAC 58.057 40.000 0.00 0.00 0.00 3.01
243 245 6.729100 ACTCCATCCGTCCCATAATATAAGAA 59.271 38.462 0.00 0.00 0.00 2.52
255 257 1.344763 CTCCAATACTCCATCCGTCCC 59.655 57.143 0.00 0.00 0.00 4.46
263 265 8.647796 CAACTTACCATATACTCCAATACTCCA 58.352 37.037 0.00 0.00 0.00 3.86
264 266 8.867097 TCAACTTACCATATACTCCAATACTCC 58.133 37.037 0.00 0.00 0.00 3.85
271 273 5.301045 CCGTCTCAACTTACCATATACTCCA 59.699 44.000 0.00 0.00 0.00 3.86
272 274 5.278858 CCCGTCTCAACTTACCATATACTCC 60.279 48.000 0.00 0.00 0.00 3.85
273 275 5.301298 ACCCGTCTCAACTTACCATATACTC 59.699 44.000 0.00 0.00 0.00 2.59
274 276 5.206587 ACCCGTCTCAACTTACCATATACT 58.793 41.667 0.00 0.00 0.00 2.12
275 277 5.508657 GGACCCGTCTCAACTTACCATATAC 60.509 48.000 0.00 0.00 0.00 1.47
276 278 4.586001 GGACCCGTCTCAACTTACCATATA 59.414 45.833 0.00 0.00 0.00 0.86
277 279 3.387050 GGACCCGTCTCAACTTACCATAT 59.613 47.826 0.00 0.00 0.00 1.78
278 280 2.762327 GGACCCGTCTCAACTTACCATA 59.238 50.000 0.00 0.00 0.00 2.74
279 281 1.553704 GGACCCGTCTCAACTTACCAT 59.446 52.381 0.00 0.00 0.00 3.55
280 282 0.971386 GGACCCGTCTCAACTTACCA 59.029 55.000 0.00 0.00 0.00 3.25
281 283 1.264295 AGGACCCGTCTCAACTTACC 58.736 55.000 0.00 0.00 0.00 2.85
324 326 5.461032 AAGTGTAATTTCGAATGGCCAAA 57.539 34.783 10.96 0.00 0.00 3.28
341 343 7.121315 GCCAAAGAAAACCATCTATCTAAGTGT 59.879 37.037 0.00 0.00 0.00 3.55
354 356 0.383949 GCGAGTGCCAAAGAAAACCA 59.616 50.000 0.00 0.00 33.98 3.67
426 428 4.816925 GCAGAGGTCCCAATTAAGATGTAC 59.183 45.833 0.00 0.00 0.00 2.90
428 430 3.525199 AGCAGAGGTCCCAATTAAGATGT 59.475 43.478 0.00 0.00 0.00 3.06
429 431 4.133078 GAGCAGAGGTCCCAATTAAGATG 58.867 47.826 0.00 0.00 0.00 2.90
430 432 3.137360 GGAGCAGAGGTCCCAATTAAGAT 59.863 47.826 3.93 0.00 43.62 2.40
431 433 2.505819 GGAGCAGAGGTCCCAATTAAGA 59.494 50.000 3.93 0.00 43.62 2.10
432 434 2.924421 GGAGCAGAGGTCCCAATTAAG 58.076 52.381 3.93 0.00 43.62 1.85
538 544 2.715046 ACAGATGCGAATTGGATGTGT 58.285 42.857 0.00 0.00 46.03 3.72
599 605 1.799544 ACCCGTGTTGGATACGAAAC 58.200 50.000 0.00 0.00 43.82 2.78
640 646 3.450507 TCCTTCTGGACGCGTTCA 58.549 55.556 21.11 21.11 37.46 3.18
649 655 2.290641 CACGGAAAAACTGTCCTTCTGG 59.709 50.000 12.58 4.75 35.72 3.86
652 658 2.940410 TGACACGGAAAAACTGTCCTTC 59.060 45.455 0.00 0.00 35.72 3.46
655 661 3.768468 TTTGACACGGAAAAACTGTCC 57.232 42.857 0.00 0.00 35.72 4.02
661 667 7.331934 TGTGATTTTCATTTTGACACGGAAAAA 59.668 29.630 0.00 0.00 39.85 1.94
666 672 5.039984 TGTGTGATTTTCATTTTGACACGG 58.960 37.500 0.00 0.00 0.00 4.94
694 700 1.333636 ACGATTGGCAGGAGGAGGAG 61.334 60.000 0.00 0.00 0.00 3.69
769 776 1.078759 GGCCACGTCGTCTCATTGAG 61.079 60.000 7.38 7.38 0.00 3.02
770 777 1.080093 GGCCACGTCGTCTCATTGA 60.080 57.895 0.00 0.00 0.00 2.57
790 802 0.394352 ATGTCTGGGCCAATCGTTCC 60.394 55.000 8.04 0.00 0.00 3.62
821 833 0.250597 GGGGAGGTTTTACGTGCACT 60.251 55.000 16.19 4.64 0.00 4.40
945 957 3.881089 GTGGTTAGGCTGTAACAAGTTGT 59.119 43.478 1.64 1.64 0.00 3.32
975 987 3.315140 TGTGGTGGATCGGCCGAA 61.315 61.111 34.66 14.02 40.66 4.30
978 990 4.796495 GGGTGTGGTGGATCGGCC 62.796 72.222 0.00 0.00 37.10 6.13
980 992 2.268920 CAGGGTGTGGTGGATCGG 59.731 66.667 0.00 0.00 0.00 4.18
1314 1326 1.031029 AGTAGTTCTCGAGCGGGTCC 61.031 60.000 7.81 0.00 0.00 4.46
1420 1432 1.507141 GCCAAGAACACCACGTCCAG 61.507 60.000 0.00 0.00 0.00 3.86
1621 1634 2.497675 TGGAAAAGGAGGATCAGACTCG 59.502 50.000 0.00 0.00 36.25 4.18
1653 1666 5.048846 TGTCAGGTTTTTAGAGCTTCCTT 57.951 39.130 0.00 0.00 0.00 3.36
1654 1667 4.706842 TGTCAGGTTTTTAGAGCTTCCT 57.293 40.909 0.00 0.00 0.00 3.36
1679 1692 2.997986 TCGACCGGAAGTGCTAAAATTC 59.002 45.455 9.46 0.00 0.00 2.17
1695 1708 3.652018 GCTAAAACAGCGTTCGACC 57.348 52.632 0.00 0.00 41.37 4.79
1723 1736 2.228582 TGCTTTTAGATGCGTGCAATGT 59.771 40.909 0.00 0.00 0.00 2.71
1726 1739 3.191162 AGATTGCTTTTAGATGCGTGCAA 59.809 39.130 0.00 0.00 43.09 4.08
1734 1747 5.468072 CGTGGCTATCAGATTGCTTTTAGAT 59.532 40.000 15.30 0.00 0.00 1.98
1760 1773 5.305585 GGACCAAACACATCTCAAAGTCTA 58.694 41.667 0.00 0.00 0.00 2.59
1780 1793 3.647771 GGGTGGTGAGTGGGGGAC 61.648 72.222 0.00 0.00 0.00 4.46
1781 1794 4.995058 GGGGTGGTGAGTGGGGGA 62.995 72.222 0.00 0.00 0.00 4.81
1809 1822 1.000145 GAAATCTGTTCGGCGGAGTC 59.000 55.000 7.21 0.00 35.67 3.36
1810 1823 0.320374 TGAAATCTGTTCGGCGGAGT 59.680 50.000 7.21 0.00 35.67 3.85
1811 1824 1.002366 CTGAAATCTGTTCGGCGGAG 58.998 55.000 7.21 0.63 35.67 4.63
1812 1825 0.320374 ACTGAAATCTGTTCGGCGGA 59.680 50.000 7.21 0.00 36.82 5.54
1813 1826 0.443869 CACTGAAATCTGTTCGGCGG 59.556 55.000 7.21 0.00 0.00 6.13
1814 1827 1.428448 TCACTGAAATCTGTTCGGCG 58.572 50.000 0.00 0.00 0.00 6.46
1815 1828 2.808543 AGTTCACTGAAATCTGTTCGGC 59.191 45.455 0.00 0.00 0.00 5.54
1821 1834 2.414481 CTGCCGAGTTCACTGAAATCTG 59.586 50.000 15.32 10.86 34.97 2.90
1824 1837 1.160137 GCTGCCGAGTTCACTGAAAT 58.840 50.000 0.00 0.00 0.00 2.17
1867 2166 3.121030 CTCAAGCCAGTTCGCCGG 61.121 66.667 0.00 0.00 0.00 6.13
1870 2169 1.301716 TGACCTCAAGCCAGTTCGC 60.302 57.895 0.00 0.00 0.00 4.70
1923 2222 1.219124 CGACAGGTGGATCTGTGGG 59.781 63.158 0.00 0.00 46.76 4.61
1924 2223 1.219124 CCGACAGGTGGATCTGTGG 59.781 63.158 0.00 0.00 46.76 4.17
1928 2227 3.461773 CGGCCGACAGGTGGATCT 61.462 66.667 24.07 0.00 40.50 2.75
2070 2390 1.337384 TGGAGGCACGATACCAGCAT 61.337 55.000 0.00 0.00 0.00 3.79
2071 2391 1.337384 ATGGAGGCACGATACCAGCA 61.337 55.000 0.00 0.00 35.84 4.41
2078 2398 0.180406 GTTGGGTATGGAGGCACGAT 59.820 55.000 0.00 0.00 0.00 3.73
2096 2416 0.456221 CGGTATCTCTGAAGCGGTGT 59.544 55.000 0.00 0.00 33.22 4.16
2103 2426 0.105658 CCTCCCCCGGTATCTCTGAA 60.106 60.000 0.00 0.00 0.00 3.02
2106 2429 2.201771 GCCTCCCCCGGTATCTCT 59.798 66.667 0.00 0.00 0.00 3.10
2171 2494 1.725641 CGCTGACCTGTTAGATGCAA 58.274 50.000 0.00 0.00 0.00 4.08
2173 2496 1.432270 GGCGCTGACCTGTTAGATGC 61.432 60.000 7.64 0.00 0.00 3.91
2175 2498 0.833287 ATGGCGCTGACCTGTTAGAT 59.167 50.000 7.64 0.00 0.00 1.98
2182 2505 3.984193 GAGGCAATGGCGCTGACCT 62.984 63.158 7.64 8.97 42.47 3.85
2252 2575 1.735198 CGACGCCGCCAAAGACTTA 60.735 57.895 0.00 0.00 0.00 2.24
2275 2598 1.153086 CCCTTCCTCGATTGCTGGG 60.153 63.158 0.00 0.00 0.00 4.45
2279 2602 1.653151 GTACACCCTTCCTCGATTGC 58.347 55.000 0.00 0.00 0.00 3.56
2289 2612 2.608678 GGTCCCCCGTACACCCTT 60.609 66.667 0.00 0.00 0.00 3.95
2307 2630 1.254026 TCGAACCGACTCATGTCCTT 58.746 50.000 0.00 0.00 39.94 3.36
2318 2641 2.246042 GCCCGTGTTTTCGAACCGA 61.246 57.895 0.00 0.00 0.00 4.69
2327 2650 1.808390 GACGATAGCGCCCGTGTTT 60.808 57.895 21.62 0.00 42.48 2.83
2351 2674 2.621526 ACCAGCATATATGACGACGTCA 59.378 45.455 30.90 30.90 46.90 4.35


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

AutoCloner maintained by Alex Coulton.