Multiple sequence alignment - TraesCS2A01G290600

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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 TraesCS2A01G290600 chr2A 100.000 2402 0 0 1 2402 500772488 500770087 0.000000e+00 4436
1 TraesCS2A01G290600 chr2B 90.476 1344 96 19 923 2252 439366797 439365472 0.000000e+00 1744
2 TraesCS2A01G290600 chr2B 86.176 774 45 25 162 917 439367579 439366850 0.000000e+00 780
3 TraesCS2A01G290600 chr2D 87.893 859 79 11 922 1764 369762399 369761550 0.000000e+00 987
4 TraesCS2A01G290600 chr2D 92.939 524 28 7 1881 2402 369761433 369760917 0.000000e+00 754
5 TraesCS2A01G290600 chr2D 88.689 557 28 21 373 917 369762984 369762451 0.000000e+00 647
6 TraesCS2A01G290600 chr2D 92.708 384 28 0 1137 1520 398509627 398509244 2.700000e-154 555
7 TraesCS2A01G290600 chr2D 92.913 381 27 0 1137 1517 618885945 618886325 2.700000e-154 555
8 TraesCS2A01G290600 chr2D 92.188 384 30 0 1137 1520 152028510 152028127 5.840000e-151 544
9 TraesCS2A01G290600 chr2D 91.282 195 5 8 162 353 369763446 369763261 3.060000e-64 255
10 TraesCS2A01G290600 chr4D 89.835 787 50 9 749 1517 20901640 20902414 0.000000e+00 983
11 TraesCS2A01G290600 chr6A 92.388 381 29 0 1137 1517 603624363 603623983 5.840000e-151 544
12 TraesCS2A01G290600 chr6A 98.795 166 2 0 1 166 153681354 153681189 1.810000e-76 296
13 TraesCS2A01G290600 chr1D 92.188 384 30 0 1137 1520 383171472 383171089 5.840000e-151 544
14 TraesCS2A01G290600 chr6D 92.388 381 27 2 1137 1517 414105703 414106081 2.100000e-150 542
15 TraesCS2A01G290600 chr1A 88.043 460 31 7 726 1169 16029091 16029542 7.610000e-145 523
16 TraesCS2A01G290600 chr6B 98.795 166 2 0 1 166 149553664 149553499 1.810000e-76 296
17 TraesCS2A01G290600 chr6B 97.143 175 3 2 1 173 567540698 567540524 6.490000e-76 294
18 TraesCS2A01G290600 chr4A 98.795 166 2 0 1 166 572648807 572648972 1.810000e-76 296
19 TraesCS2A01G290600 chr1B 97.661 171 4 0 1 171 596317761 596317591 6.490000e-76 294
20 TraesCS2A01G290600 chr5B 97.126 174 3 2 1 174 18130442 18130271 2.340000e-75 292
21 TraesCS2A01G290600 chr3B 97.661 171 3 1 1 171 675607993 675607824 2.340000e-75 292
22 TraesCS2A01G290600 chr7B 94.652 187 8 2 1 185 150541533 150541347 3.020000e-74 289
23 TraesCS2A01G290600 chr4B 97.605 167 4 0 1 167 534409119 534409285 1.090000e-73 287


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 TraesCS2A01G290600 chr2A 500770087 500772488 2401 True 4436.00 4436 100.00000 1 2402 1 chr2A.!!$R1 2401
1 TraesCS2A01G290600 chr2B 439365472 439367579 2107 True 1262.00 1744 88.32600 162 2252 2 chr2B.!!$R1 2090
2 TraesCS2A01G290600 chr2D 369760917 369763446 2529 True 660.75 987 90.20075 162 2402 4 chr2D.!!$R3 2240
3 TraesCS2A01G290600 chr4D 20901640 20902414 774 False 983.00 983 89.83500 749 1517 1 chr4D.!!$F1 768

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
901 1195 0.405585 ACCACCAACCATCCTCCTTG 59.594 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 2318 1.681793 CTCAGGGGTGATGTACTACCG 59.318 57.143 0.0 0.0 37.85 4.02 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 4.957759 GTTACCATCACATAGCGGTTTT 57.042 40.909 0.00 0.00 32.81 2.43
22 23 4.905269 GTTACCATCACATAGCGGTTTTC 58.095 43.478 0.00 0.00 32.81 2.29
23 24 3.066291 ACCATCACATAGCGGTTTTCA 57.934 42.857 0.00 0.00 0.00 2.69
24 25 3.417101 ACCATCACATAGCGGTTTTCAA 58.583 40.909 0.00 0.00 0.00 2.69
25 26 4.016444 ACCATCACATAGCGGTTTTCAAT 58.984 39.130 0.00 0.00 0.00 2.57
26 27 4.142403 ACCATCACATAGCGGTTTTCAATG 60.142 41.667 0.00 0.00 0.00 2.82
27 28 3.485947 TCACATAGCGGTTTTCAATGC 57.514 42.857 0.00 0.00 0.00 3.56
28 29 2.816672 TCACATAGCGGTTTTCAATGCA 59.183 40.909 0.00 0.00 0.00 3.96
29 30 3.443329 TCACATAGCGGTTTTCAATGCAT 59.557 39.130 0.00 0.00 0.00 3.96
30 31 4.637977 TCACATAGCGGTTTTCAATGCATA 59.362 37.500 0.00 0.00 0.00 3.14
31 32 5.124617 TCACATAGCGGTTTTCAATGCATAA 59.875 36.000 0.00 0.00 0.00 1.90
32 33 5.978919 CACATAGCGGTTTTCAATGCATAAT 59.021 36.000 0.00 0.00 0.00 1.28
33 34 5.978919 ACATAGCGGTTTTCAATGCATAATG 59.021 36.000 0.00 0.00 0.00 1.90
34 35 4.717233 AGCGGTTTTCAATGCATAATGA 57.283 36.364 0.00 0.00 0.00 2.57
35 36 4.675510 AGCGGTTTTCAATGCATAATGAG 58.324 39.130 0.00 0.00 0.00 2.90
36 37 4.158394 AGCGGTTTTCAATGCATAATGAGT 59.842 37.500 0.00 0.00 0.00 3.41
37 38 4.500477 GCGGTTTTCAATGCATAATGAGTC 59.500 41.667 0.00 0.00 0.00 3.36
38 39 5.677091 GCGGTTTTCAATGCATAATGAGTCT 60.677 40.000 0.00 0.00 0.00 3.24
39 40 6.458206 GCGGTTTTCAATGCATAATGAGTCTA 60.458 38.462 0.00 0.00 0.00 2.59
40 41 6.907212 CGGTTTTCAATGCATAATGAGTCTAC 59.093 38.462 0.00 0.00 0.00 2.59
41 42 7.413988 CGGTTTTCAATGCATAATGAGTCTACA 60.414 37.037 0.00 0.00 0.00 2.74
42 43 8.243426 GGTTTTCAATGCATAATGAGTCTACAA 58.757 33.333 0.00 0.00 0.00 2.41
43 44 9.624697 GTTTTCAATGCATAATGAGTCTACAAA 57.375 29.630 0.00 0.00 0.00 2.83
44 45 9.844790 TTTTCAATGCATAATGAGTCTACAAAG 57.155 29.630 0.00 0.00 0.00 2.77
45 46 8.565896 TTCAATGCATAATGAGTCTACAAAGT 57.434 30.769 0.00 0.00 0.00 2.66
46 47 9.665719 TTCAATGCATAATGAGTCTACAAAGTA 57.334 29.630 0.00 0.00 0.00 2.24
47 48 9.665719 TCAATGCATAATGAGTCTACAAAGTAA 57.334 29.630 0.00 0.00 0.00 2.24
58 59 9.162764 TGAGTCTACAAAGTAATAAATGAAGGC 57.837 33.333 0.00 0.00 0.00 4.35
59 60 9.162764 GAGTCTACAAAGTAATAAATGAAGGCA 57.837 33.333 0.00 0.00 0.00 4.75
60 61 9.515226 AGTCTACAAAGTAATAAATGAAGGCAA 57.485 29.630 0.00 0.00 0.00 4.52
61 62 9.556030 GTCTACAAAGTAATAAATGAAGGCAAC 57.444 33.333 0.00 0.00 0.00 4.17
76 77 3.067684 GGCAACTATGTTACCACACCT 57.932 47.619 0.00 0.00 35.03 4.00
77 78 4.210724 GGCAACTATGTTACCACACCTA 57.789 45.455 0.00 0.00 35.03 3.08
78 79 4.777463 GGCAACTATGTTACCACACCTAT 58.223 43.478 0.00 0.00 35.03 2.57
79 80 4.574828 GGCAACTATGTTACCACACCTATG 59.425 45.833 0.00 0.00 35.03 2.23
80 81 5.424757 GCAACTATGTTACCACACCTATGA 58.575 41.667 0.00 0.00 35.03 2.15
81 82 5.293569 GCAACTATGTTACCACACCTATGAC 59.706 44.000 0.00 0.00 35.03 3.06
82 83 6.403049 CAACTATGTTACCACACCTATGACA 58.597 40.000 0.00 0.00 35.03 3.58
83 84 5.974108 ACTATGTTACCACACCTATGACAC 58.026 41.667 0.00 0.00 35.03 3.67
84 85 5.720041 ACTATGTTACCACACCTATGACACT 59.280 40.000 0.00 0.00 35.03 3.55
85 86 6.893554 ACTATGTTACCACACCTATGACACTA 59.106 38.462 0.00 0.00 35.03 2.74
86 87 5.395682 TGTTACCACACCTATGACACTAC 57.604 43.478 0.00 0.00 0.00 2.73
87 88 4.221262 TGTTACCACACCTATGACACTACC 59.779 45.833 0.00 0.00 0.00 3.18
88 89 2.185387 ACCACACCTATGACACTACCC 58.815 52.381 0.00 0.00 0.00 3.69
89 90 2.184533 CCACACCTATGACACTACCCA 58.815 52.381 0.00 0.00 0.00 4.51
90 91 2.093658 CCACACCTATGACACTACCCAC 60.094 54.545 0.00 0.00 0.00 4.61
91 92 2.832129 CACACCTATGACACTACCCACT 59.168 50.000 0.00 0.00 0.00 4.00
92 93 4.021229 CACACCTATGACACTACCCACTA 58.979 47.826 0.00 0.00 0.00 2.74
93 94 4.649674 CACACCTATGACACTACCCACTAT 59.350 45.833 0.00 0.00 0.00 2.12
94 95 5.831525 CACACCTATGACACTACCCACTATA 59.168 44.000 0.00 0.00 0.00 1.31
95 96 6.322969 CACACCTATGACACTACCCACTATAA 59.677 42.308 0.00 0.00 0.00 0.98
96 97 6.899075 ACACCTATGACACTACCCACTATAAA 59.101 38.462 0.00 0.00 0.00 1.40
97 98 7.069578 ACACCTATGACACTACCCACTATAAAG 59.930 40.741 0.00 0.00 0.00 1.85
98 99 6.553852 ACCTATGACACTACCCACTATAAAGG 59.446 42.308 0.00 0.00 0.00 3.11
99 100 6.553852 CCTATGACACTACCCACTATAAAGGT 59.446 42.308 0.00 0.00 37.69 3.50
100 101 7.727186 CCTATGACACTACCCACTATAAAGGTA 59.273 40.741 0.00 0.00 35.02 3.08
151 152 8.558973 TGTTACTAGTCTAAGTTACTCTCCAC 57.441 38.462 0.00 0.00 31.82 4.02
152 153 8.381636 TGTTACTAGTCTAAGTTACTCTCCACT 58.618 37.037 0.00 0.00 31.82 4.00
153 154 9.883142 GTTACTAGTCTAAGTTACTCTCCACTA 57.117 37.037 0.00 0.00 0.00 2.74
155 156 8.967664 ACTAGTCTAAGTTACTCTCCACTATG 57.032 38.462 0.00 0.00 0.00 2.23
156 157 8.770322 ACTAGTCTAAGTTACTCTCCACTATGA 58.230 37.037 0.00 0.00 0.00 2.15
157 158 7.868906 AGTCTAAGTTACTCTCCACTATGAC 57.131 40.000 0.00 0.00 0.00 3.06
158 159 6.829811 AGTCTAAGTTACTCTCCACTATGACC 59.170 42.308 0.00 0.00 31.22 4.02
159 160 6.602406 GTCTAAGTTACTCTCCACTATGACCA 59.398 42.308 0.00 0.00 0.00 4.02
160 161 5.923733 AAGTTACTCTCCACTATGACCAG 57.076 43.478 0.00 0.00 0.00 4.00
295 296 1.450531 GATGCTGCCATGCTGGGTAC 61.451 60.000 0.00 0.00 38.19 3.34
296 297 1.929860 ATGCTGCCATGCTGGGTACT 61.930 55.000 0.00 0.00 38.19 2.73
297 298 2.117156 GCTGCCATGCTGGGTACTG 61.117 63.158 4.65 0.00 38.19 2.74
298 299 1.300963 CTGCCATGCTGGGTACTGT 59.699 57.895 4.65 0.00 38.19 3.55
299 300 0.541392 CTGCCATGCTGGGTACTGTA 59.459 55.000 4.65 0.00 38.19 2.74
300 301 1.141657 CTGCCATGCTGGGTACTGTAT 59.858 52.381 4.65 0.00 38.19 2.29
345 346 2.471743 GTCGAGTGCTATCCATTAACGC 59.528 50.000 0.00 0.00 0.00 4.84
346 347 2.100087 TCGAGTGCTATCCATTAACGCA 59.900 45.455 0.00 0.00 0.00 5.24
348 349 3.717707 GAGTGCTATCCATTAACGCAGA 58.282 45.455 0.00 0.00 0.00 4.26
366 640 7.883229 ACGCAGAAAAAGAAAAAGAAAAAGA 57.117 28.000 0.00 0.00 0.00 2.52
367 641 8.305441 ACGCAGAAAAAGAAAAAGAAAAAGAA 57.695 26.923 0.00 0.00 0.00 2.52
368 642 8.769891 ACGCAGAAAAAGAAAAAGAAAAAGAAA 58.230 25.926 0.00 0.00 0.00 2.52
369 643 9.592720 CGCAGAAAAAGAAAAAGAAAAAGAAAA 57.407 25.926 0.00 0.00 0.00 2.29
397 671 1.276622 CCCAGTGGTAGTAGGTTGCT 58.723 55.000 8.74 0.00 0.00 3.91
423 697 2.049618 GCTCTAGCCGCGATGGAG 60.050 66.667 8.23 13.88 42.00 3.86
424 698 2.851071 GCTCTAGCCGCGATGGAGT 61.851 63.158 20.04 0.00 42.00 3.85
437 711 1.961180 ATGGAGTAGTCTGTGGGCGC 61.961 60.000 0.00 0.00 0.00 6.53
787 1072 4.651503 CCCTCTTGCAGATTTCTAGGTAGA 59.348 45.833 0.00 0.00 0.00 2.59
796 1081 6.459573 GCAGATTTCTAGGTAGAGTGACTCTG 60.460 46.154 24.52 7.91 41.37 3.35
799 1084 3.879998 TCTAGGTAGAGTGACTCTGCTG 58.120 50.000 25.85 17.34 41.71 4.41
818 1103 5.555017 TGCTGCTAATCTCAAGTTCTTTCT 58.445 37.500 0.00 0.00 0.00 2.52
827 1112 8.744568 AATCTCAAGTTCTTTCTGTTCTTCTT 57.255 30.769 0.00 0.00 0.00 2.52
833 1118 5.526846 AGTTCTTTCTGTTCTTCTTCTGCTG 59.473 40.000 0.00 0.00 0.00 4.41
835 1120 3.482156 TTCTGTTCTTCTTCTGCTGCT 57.518 42.857 0.00 0.00 0.00 4.24
836 1121 3.482156 TCTGTTCTTCTTCTGCTGCTT 57.518 42.857 0.00 0.00 0.00 3.91
837 1122 3.813443 TCTGTTCTTCTTCTGCTGCTTT 58.187 40.909 0.00 0.00 0.00 3.51
892 1186 2.235016 GCAACTGATTACCACCAACCA 58.765 47.619 0.00 0.00 0.00 3.67
901 1195 0.405585 ACCACCAACCATCCTCCTTG 59.594 55.000 0.00 0.00 0.00 3.61
988 1332 7.095024 GGAACGAATCATGTATTTACTCGAG 57.905 40.000 11.84 11.84 0.00 4.04
1027 1380 2.023673 TGCAGAAACAGGAAACACAGG 58.976 47.619 0.00 0.00 0.00 4.00
1030 1383 1.133482 AGAAACAGGAAACACAGGGGG 60.133 52.381 0.00 0.00 0.00 5.40
1155 1514 0.744874 CCAAGAATACGCGGAGGAGA 59.255 55.000 12.47 0.00 0.00 3.71
1209 1571 0.884704 GCCACAGACTCGCTTCCAAA 60.885 55.000 0.00 0.00 0.00 3.28
1218 1580 1.868997 CGCTTCCAAATGCGTCTGT 59.131 52.632 0.00 0.00 46.09 3.41
1263 1625 2.034879 CAAGTGCCGCTTCCATCGT 61.035 57.895 0.00 0.00 34.69 3.73
1281 1649 2.228480 TACCAACTCCCAGGGCCAC 61.228 63.158 6.18 0.00 0.00 5.01
1282 1650 4.722700 CCAACTCCCAGGGCCACG 62.723 72.222 6.18 0.00 0.00 4.94
1283 1651 4.722700 CAACTCCCAGGGCCACGG 62.723 72.222 6.18 5.52 0.00 4.94
1385 1753 1.840650 CATCCTCCTCCTCCGGCAT 60.841 63.158 0.00 0.00 0.00 4.40
1423 1791 2.268920 GCCCAAGCATCGGTCTCA 59.731 61.111 0.00 0.00 39.53 3.27
1435 1803 4.574013 GCATCGGTCTCAAGAATCAAGAAT 59.426 41.667 0.00 0.00 0.00 2.40
1442 1810 5.523188 GTCTCAAGAATCAAGAATGCTCGAT 59.477 40.000 0.00 0.00 0.00 3.59
1443 1811 5.522824 TCTCAAGAATCAAGAATGCTCGATG 59.477 40.000 0.00 0.00 0.00 3.84
1452 1820 4.933505 AGAATGCTCGATGATGAAGAGA 57.066 40.909 0.00 0.00 34.13 3.10
1523 1891 3.004419 TCCCTCGATGTATTGTGTCGATC 59.996 47.826 0.00 0.00 42.65 3.69
1603 1981 5.165961 TGAATCGAATGGACTTTCCTCTT 57.834 39.130 0.00 0.00 37.46 2.85
1650 2028 0.106967 GCTTCTCCCCACCCTTCATC 60.107 60.000 0.00 0.00 0.00 2.92
1660 2038 2.158842 CCACCCTTCATCTGAGATGGAC 60.159 54.545 21.27 0.00 35.44 4.02
1666 2045 5.489249 CCTTCATCTGAGATGGACCATATG 58.511 45.833 21.27 7.07 35.44 1.78
1684 2065 1.938585 TGGGTCAGAGGATTTCGAGT 58.061 50.000 0.00 0.00 0.00 4.18
1686 2067 2.233922 TGGGTCAGAGGATTTCGAGTTC 59.766 50.000 0.00 0.00 0.00 3.01
1754 2135 9.448294 GCTTCTTGCAAGATTTAAGATCTTATG 57.552 33.333 28.89 11.50 42.31 1.90
1810 2230 2.433970 AGTTGGAGGAGCATCTCTTAGC 59.566 50.000 6.34 0.00 34.39 3.09
1849 2272 3.018856 TGCAAATGAGCCAACCAGATAG 58.981 45.455 0.00 0.00 0.00 2.08
1859 2282 3.681874 GCCAACCAGATAGAACAGGGTAC 60.682 52.174 0.00 0.00 0.00 3.34
1864 2287 6.051179 ACCAGATAGAACAGGGTACTTTTC 57.949 41.667 0.00 0.00 34.38 2.29
1866 2289 6.272558 ACCAGATAGAACAGGGTACTTTTCTT 59.727 38.462 2.00 0.00 39.99 2.52
1867 2290 7.168905 CCAGATAGAACAGGGTACTTTTCTTT 58.831 38.462 2.00 0.00 39.99 2.52
1868 2291 7.665974 CCAGATAGAACAGGGTACTTTTCTTTT 59.334 37.037 2.00 0.00 39.99 2.27
1869 2292 8.722394 CAGATAGAACAGGGTACTTTTCTTTTC 58.278 37.037 2.00 1.62 39.99 2.29
1870 2293 8.661345 AGATAGAACAGGGTACTTTTCTTTTCT 58.339 33.333 2.00 3.47 39.99 2.52
1871 2294 9.286170 GATAGAACAGGGTACTTTTCTTTTCTT 57.714 33.333 2.00 3.52 39.99 2.52
1895 2318 4.813027 TGAAACGTATGACAGGGTACTTC 58.187 43.478 0.00 0.00 0.00 3.01
2027 2456 3.052082 CACTTCACTGCCAGCCCG 61.052 66.667 0.00 0.00 0.00 6.13
2058 2487 4.613031 GCTGTCTTGATTAAGCGTTTGTTC 59.387 41.667 0.00 0.00 33.82 3.18
2273 2702 4.271049 ACCGATCTAAACATGAGATTTGCG 59.729 41.667 0.00 0.00 33.71 4.85
2274 2703 4.271049 CCGATCTAAACATGAGATTTGCGT 59.729 41.667 0.00 0.00 33.71 5.24
2275 2704 5.193216 CGATCTAAACATGAGATTTGCGTG 58.807 41.667 0.00 0.00 33.71 5.34
2276 2705 5.005682 CGATCTAAACATGAGATTTGCGTGA 59.994 40.000 0.00 0.00 33.71 4.35
2277 2706 5.784750 TCTAAACATGAGATTTGCGTGAG 57.215 39.130 0.00 0.00 0.00 3.51
2280 2709 4.928661 AACATGAGATTTGCGTGAGTAC 57.071 40.909 0.00 0.00 0.00 2.73
2298 2727 7.044901 CGTGAGTACGTACTGTCAATATTCAAG 60.045 40.741 31.91 17.44 44.99 3.02
2303 2732 9.525409 GTACGTACTGTCAATATTCAAGGTAAT 57.475 33.333 18.47 0.00 0.00 1.89
2331 2760 3.842732 TCAAACTCGAGTAAGCGATCA 57.157 42.857 20.39 0.00 39.85 2.92
2354 2783 3.805207 ACTCCACCGTATGCTATTTTCC 58.195 45.455 0.00 0.00 0.00 3.13
2356 2785 1.871039 CCACCGTATGCTATTTTCCCG 59.129 52.381 0.00 0.00 0.00 5.14
2359 2788 3.001939 CACCGTATGCTATTTTCCCGTTC 59.998 47.826 0.00 0.00 0.00 3.95
2368 2797 7.455641 TGCTATTTTCCCGTTCTTAATTCAA 57.544 32.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.393680 TGAAAACCGCTATGTGATGGTAAC 59.606 41.667 0.00 0.00 33.45 2.50
1 2 4.580868 TGAAAACCGCTATGTGATGGTAA 58.419 39.130 0.00 0.00 33.45 2.85
2 3 4.209307 TGAAAACCGCTATGTGATGGTA 57.791 40.909 0.00 0.00 33.45 3.25
3 4 3.066291 TGAAAACCGCTATGTGATGGT 57.934 42.857 0.00 0.00 35.90 3.55
4 5 4.353737 CATTGAAAACCGCTATGTGATGG 58.646 43.478 0.00 0.00 0.00 3.51
5 6 3.792956 GCATTGAAAACCGCTATGTGATG 59.207 43.478 0.00 0.00 0.00 3.07
6 7 3.443329 TGCATTGAAAACCGCTATGTGAT 59.557 39.130 0.00 0.00 0.00 3.06
7 8 2.816672 TGCATTGAAAACCGCTATGTGA 59.183 40.909 0.00 0.00 0.00 3.58
8 9 3.214697 TGCATTGAAAACCGCTATGTG 57.785 42.857 0.00 0.00 0.00 3.21
9 10 5.574891 TTATGCATTGAAAACCGCTATGT 57.425 34.783 3.54 0.00 0.00 2.29
10 11 6.207928 TCATTATGCATTGAAAACCGCTATG 58.792 36.000 3.54 0.00 0.00 2.23
11 12 6.039717 ACTCATTATGCATTGAAAACCGCTAT 59.960 34.615 3.54 0.00 0.00 2.97
12 13 5.356751 ACTCATTATGCATTGAAAACCGCTA 59.643 36.000 3.54 0.00 0.00 4.26
13 14 4.158394 ACTCATTATGCATTGAAAACCGCT 59.842 37.500 3.54 0.00 0.00 5.52
14 15 4.423732 ACTCATTATGCATTGAAAACCGC 58.576 39.130 3.54 0.00 0.00 5.68
15 16 5.883661 AGACTCATTATGCATTGAAAACCG 58.116 37.500 3.54 0.00 0.00 4.44
16 17 7.761409 TGTAGACTCATTATGCATTGAAAACC 58.239 34.615 3.54 0.00 0.00 3.27
17 18 9.624697 TTTGTAGACTCATTATGCATTGAAAAC 57.375 29.630 3.54 0.56 0.00 2.43
18 19 9.844790 CTTTGTAGACTCATTATGCATTGAAAA 57.155 29.630 3.54 0.00 0.00 2.29
19 20 9.013229 ACTTTGTAGACTCATTATGCATTGAAA 57.987 29.630 3.54 0.00 0.00 2.69
20 21 8.565896 ACTTTGTAGACTCATTATGCATTGAA 57.434 30.769 3.54 0.00 0.00 2.69
21 22 9.665719 TTACTTTGTAGACTCATTATGCATTGA 57.334 29.630 3.54 2.16 0.00 2.57
32 33 9.162764 GCCTTCATTTATTACTTTGTAGACTCA 57.837 33.333 0.00 0.00 0.00 3.41
33 34 9.162764 TGCCTTCATTTATTACTTTGTAGACTC 57.837 33.333 0.00 0.00 0.00 3.36
34 35 9.515226 TTGCCTTCATTTATTACTTTGTAGACT 57.485 29.630 0.00 0.00 0.00 3.24
35 36 9.556030 GTTGCCTTCATTTATTACTTTGTAGAC 57.444 33.333 0.00 0.00 0.00 2.59
36 37 9.515226 AGTTGCCTTCATTTATTACTTTGTAGA 57.485 29.630 0.00 0.00 0.00 2.59
44 45 9.946165 GGTAACATAGTTGCCTTCATTTATTAC 57.054 33.333 9.36 0.00 0.00 1.89
45 46 9.688091 TGGTAACATAGTTGCCTTCATTTATTA 57.312 29.630 16.08 0.00 46.17 0.98
46 47 8.588290 TGGTAACATAGTTGCCTTCATTTATT 57.412 30.769 16.08 0.00 46.17 1.40
65 66 4.382362 GGGTAGTGTCATAGGTGTGGTAAC 60.382 50.000 0.00 0.00 0.00 2.50
66 67 3.770933 GGGTAGTGTCATAGGTGTGGTAA 59.229 47.826 0.00 0.00 0.00 2.85
67 68 3.245694 TGGGTAGTGTCATAGGTGTGGTA 60.246 47.826 0.00 0.00 0.00 3.25
68 69 2.185387 GGGTAGTGTCATAGGTGTGGT 58.815 52.381 0.00 0.00 0.00 4.16
69 70 2.093658 GTGGGTAGTGTCATAGGTGTGG 60.094 54.545 0.00 0.00 0.00 4.17
70 71 2.832129 AGTGGGTAGTGTCATAGGTGTG 59.168 50.000 0.00 0.00 0.00 3.82
71 72 3.185880 AGTGGGTAGTGTCATAGGTGT 57.814 47.619 0.00 0.00 0.00 4.16
72 73 6.971726 TTATAGTGGGTAGTGTCATAGGTG 57.028 41.667 0.00 0.00 0.00 4.00
73 74 6.553852 CCTTTATAGTGGGTAGTGTCATAGGT 59.446 42.308 0.00 0.00 0.00 3.08
74 75 6.553852 ACCTTTATAGTGGGTAGTGTCATAGG 59.446 42.308 0.00 0.00 0.00 2.57
75 76 7.598759 ACCTTTATAGTGGGTAGTGTCATAG 57.401 40.000 0.00 0.00 0.00 2.23
76 77 8.701908 CTACCTTTATAGTGGGTAGTGTCATA 57.298 38.462 14.51 0.00 44.30 2.15
77 78 7.598759 CTACCTTTATAGTGGGTAGTGTCAT 57.401 40.000 14.51 0.00 44.30 3.06
125 126 9.176460 GTGGAGAGTAACTTAGACTAGTAACAT 57.824 37.037 0.00 0.00 0.00 2.71
126 127 8.381636 AGTGGAGAGTAACTTAGACTAGTAACA 58.618 37.037 0.00 0.00 0.00 2.41
127 128 8.791327 AGTGGAGAGTAACTTAGACTAGTAAC 57.209 38.462 0.00 0.00 0.00 2.50
130 131 8.770322 TCATAGTGGAGAGTAACTTAGACTAGT 58.230 37.037 0.00 0.00 0.00 2.57
131 132 9.048446 GTCATAGTGGAGAGTAACTTAGACTAG 57.952 40.741 0.00 0.00 31.58 2.57
132 133 7.992033 GGTCATAGTGGAGAGTAACTTAGACTA 59.008 40.741 0.00 0.00 33.27 2.59
133 134 6.829811 GGTCATAGTGGAGAGTAACTTAGACT 59.170 42.308 0.00 0.00 33.27 3.24
134 135 6.602406 TGGTCATAGTGGAGAGTAACTTAGAC 59.398 42.308 0.00 0.00 32.58 2.59
135 136 6.728411 TGGTCATAGTGGAGAGTAACTTAGA 58.272 40.000 0.00 0.00 0.00 2.10
136 137 6.460399 GCTGGTCATAGTGGAGAGTAACTTAG 60.460 46.154 0.00 0.00 0.00 2.18
137 138 5.360144 GCTGGTCATAGTGGAGAGTAACTTA 59.640 44.000 0.00 0.00 0.00 2.24
138 139 4.160626 GCTGGTCATAGTGGAGAGTAACTT 59.839 45.833 0.00 0.00 0.00 2.66
139 140 3.702045 GCTGGTCATAGTGGAGAGTAACT 59.298 47.826 0.00 0.00 0.00 2.24
140 141 3.181474 GGCTGGTCATAGTGGAGAGTAAC 60.181 52.174 0.00 0.00 0.00 2.50
141 142 3.031736 GGCTGGTCATAGTGGAGAGTAA 58.968 50.000 0.00 0.00 0.00 2.24
142 143 2.245028 AGGCTGGTCATAGTGGAGAGTA 59.755 50.000 0.00 0.00 0.00 2.59
143 144 1.007721 AGGCTGGTCATAGTGGAGAGT 59.992 52.381 0.00 0.00 0.00 3.24
144 145 1.786937 AGGCTGGTCATAGTGGAGAG 58.213 55.000 0.00 0.00 0.00 3.20
145 146 3.031736 GTTAGGCTGGTCATAGTGGAGA 58.968 50.000 0.00 0.00 0.00 3.71
146 147 2.223829 CGTTAGGCTGGTCATAGTGGAG 60.224 54.545 0.00 0.00 0.00 3.86
147 148 1.754803 CGTTAGGCTGGTCATAGTGGA 59.245 52.381 0.00 0.00 0.00 4.02
148 149 1.480954 ACGTTAGGCTGGTCATAGTGG 59.519 52.381 0.00 0.00 0.00 4.00
149 150 2.540515 CACGTTAGGCTGGTCATAGTG 58.459 52.381 0.00 0.00 0.00 2.74
150 151 1.480954 CCACGTTAGGCTGGTCATAGT 59.519 52.381 0.00 0.00 0.00 2.12
151 152 2.225068 CCACGTTAGGCTGGTCATAG 57.775 55.000 0.00 0.00 0.00 2.23
265 266 1.512996 GGCAGCATCCATCGGTCATG 61.513 60.000 0.00 0.00 0.00 3.07
295 296 2.011947 TCGTGACGTCCTACCATACAG 58.988 52.381 14.12 0.03 0.00 2.74
296 297 2.011947 CTCGTGACGTCCTACCATACA 58.988 52.381 14.12 0.00 0.00 2.29
297 298 2.012673 ACTCGTGACGTCCTACCATAC 58.987 52.381 14.12 1.19 0.00 2.39
298 299 2.408271 ACTCGTGACGTCCTACCATA 57.592 50.000 14.12 0.00 0.00 2.74
299 300 2.012673 GTACTCGTGACGTCCTACCAT 58.987 52.381 14.12 0.00 0.00 3.55
300 301 1.002430 AGTACTCGTGACGTCCTACCA 59.998 52.381 14.12 0.00 0.00 3.25
364 638 3.774766 ACCACTGGGCTTTTTCTTTTTCT 59.225 39.130 0.00 0.00 37.90 2.52
365 639 4.137116 ACCACTGGGCTTTTTCTTTTTC 57.863 40.909 0.00 0.00 37.90 2.29
366 640 4.714802 ACTACCACTGGGCTTTTTCTTTTT 59.285 37.500 0.00 0.00 37.90 1.94
367 641 4.286707 ACTACCACTGGGCTTTTTCTTTT 58.713 39.130 0.00 0.00 37.90 2.27
368 642 3.910989 ACTACCACTGGGCTTTTTCTTT 58.089 40.909 0.00 0.00 37.90 2.52
369 643 3.595190 ACTACCACTGGGCTTTTTCTT 57.405 42.857 0.00 0.00 37.90 2.52
370 644 3.009143 CCTACTACCACTGGGCTTTTTCT 59.991 47.826 0.00 0.00 37.90 2.52
371 645 3.244805 ACCTACTACCACTGGGCTTTTTC 60.245 47.826 0.00 0.00 37.90 2.29
372 646 2.714793 ACCTACTACCACTGGGCTTTTT 59.285 45.455 0.00 0.00 37.90 1.94
373 647 2.345560 ACCTACTACCACTGGGCTTTT 58.654 47.619 0.00 0.00 37.90 2.27
374 648 2.039879 CAACCTACTACCACTGGGCTTT 59.960 50.000 0.00 0.00 37.90 3.51
375 649 1.628846 CAACCTACTACCACTGGGCTT 59.371 52.381 0.00 0.00 37.90 4.35
376 650 1.276622 CAACCTACTACCACTGGGCT 58.723 55.000 0.00 0.00 37.90 5.19
377 651 0.392595 GCAACCTACTACCACTGGGC 60.393 60.000 0.00 0.00 37.90 5.36
378 652 1.066143 CAGCAACCTACTACCACTGGG 60.066 57.143 0.00 0.00 41.29 4.45
406 680 1.516365 TACTCCATCGCGGCTAGAGC 61.516 60.000 6.13 0.00 41.14 4.09
419 693 2.646175 GCGCCCACAGACTACTCCA 61.646 63.158 0.00 0.00 0.00 3.86
422 696 3.391382 GGGCGCCCACAGACTACT 61.391 66.667 40.73 0.00 35.81 2.57
423 697 4.468689 GGGGCGCCCACAGACTAC 62.469 72.222 44.46 22.62 44.65 2.73
667 952 0.179067 CCCTCGCTTTATACGGGCAA 60.179 55.000 0.00 0.00 0.00 4.52
787 1072 3.095332 TGAGATTAGCAGCAGAGTCACT 58.905 45.455 0.00 0.00 0.00 3.41
796 1081 5.411053 ACAGAAAGAACTTGAGATTAGCAGC 59.589 40.000 0.00 0.00 0.00 5.25
799 1084 7.665561 AGAACAGAAAGAACTTGAGATTAGC 57.334 36.000 0.00 0.00 0.00 3.09
818 1103 3.813443 AGAAAGCAGCAGAAGAAGAACA 58.187 40.909 0.00 0.00 0.00 3.18
827 1112 6.710295 TGAAAATAACACTAGAAAGCAGCAGA 59.290 34.615 0.00 0.00 0.00 4.26
833 1118 7.203255 ACAGGTGAAAATAACACTAGAAAGC 57.797 36.000 0.00 0.00 38.20 3.51
835 1120 9.787435 ACATACAGGTGAAAATAACACTAGAAA 57.213 29.630 0.00 0.00 38.20 2.52
836 1121 9.214957 CACATACAGGTGAAAATAACACTAGAA 57.785 33.333 0.00 0.00 41.32 2.10
837 1122 7.333423 GCACATACAGGTGAAAATAACACTAGA 59.667 37.037 0.00 0.00 41.32 2.43
892 1186 2.176798 TCAACAACCCAACAAGGAGGAT 59.823 45.455 0.00 0.00 41.22 3.24
901 1195 5.557866 AGGAGTACTAATCAACAACCCAAC 58.442 41.667 0.00 0.00 0.00 3.77
905 1199 8.880750 GTTCATTAGGAGTACTAATCAACAACC 58.119 37.037 15.04 0.00 46.36 3.77
932 1273 5.646577 ATAACCCGAGATTTAGATCGAGG 57.353 43.478 0.00 3.95 41.40 4.63
987 1331 4.610945 GCATAGGCATTGAATTTAACGCT 58.389 39.130 0.98 0.00 40.72 5.07
988 1332 4.954238 GCATAGGCATTGAATTTAACGC 57.046 40.909 0.00 0.00 40.72 4.84
1013 1366 1.152546 GCCCCCTGTGTTTCCTGTT 60.153 57.895 0.00 0.00 0.00 3.16
1027 1380 0.904394 TTGGAAGCCATTTCTGCCCC 60.904 55.000 0.00 0.00 36.03 5.80
1030 1383 2.159517 CGTAGTTGGAAGCCATTTCTGC 60.160 50.000 0.00 0.00 36.03 4.26
1263 1625 2.208640 TGGCCCTGGGAGTTGGTA 59.791 61.111 19.27 0.00 0.00 3.25
1385 1753 4.034258 GTCACTGGGTCGCGACGA 62.034 66.667 30.99 19.90 0.00 4.20
1419 1787 5.077134 TCGAGCATTCTTGATTCTTGAGA 57.923 39.130 0.00 0.00 0.00 3.27
1423 1791 6.053650 TCATCATCGAGCATTCTTGATTCTT 58.946 36.000 0.00 0.00 40.62 2.52
1435 1803 3.067883 CCTTCTCTCTTCATCATCGAGCA 59.932 47.826 0.00 0.00 0.00 4.26
1442 1810 6.864151 TGATCTTTCCTTCTCTCTTCATCA 57.136 37.500 0.00 0.00 0.00 3.07
1629 2007 1.065410 TGAAGGGTGGGGAGAAGCAA 61.065 55.000 0.00 0.00 0.00 3.91
1660 2038 3.324846 TCGAAATCCTCTGACCCATATGG 59.675 47.826 15.41 15.41 41.37 2.74
1666 2045 2.735762 CGAACTCGAAATCCTCTGACCC 60.736 54.545 0.00 0.00 43.02 4.46
1675 2056 2.132762 ACACCACACGAACTCGAAATC 58.867 47.619 6.05 0.00 43.02 2.17
1678 2059 1.135527 AGAACACCACACGAACTCGAA 59.864 47.619 6.05 0.00 43.02 3.71
1679 2060 0.742505 AGAACACCACACGAACTCGA 59.257 50.000 6.05 0.00 43.02 4.04
1680 2061 1.129326 GAGAACACCACACGAACTCG 58.871 55.000 0.00 0.00 46.33 4.18
1684 2065 2.093921 TCACAAGAGAACACCACACGAA 60.094 45.455 0.00 0.00 0.00 3.85
1686 2067 1.934589 TCACAAGAGAACACCACACG 58.065 50.000 0.00 0.00 0.00 4.49
1849 2272 8.248253 TCAAAAGAAAAGAAAAGTACCCTGTTC 58.752 33.333 0.00 0.00 35.46 3.18
1864 2287 6.636850 CCCTGTCATACGTTTCAAAAGAAAAG 59.363 38.462 0.00 0.00 0.00 2.27
1866 2289 5.591067 ACCCTGTCATACGTTTCAAAAGAAA 59.409 36.000 0.00 0.00 0.00 2.52
1867 2290 5.127491 ACCCTGTCATACGTTTCAAAAGAA 58.873 37.500 0.00 0.00 0.00 2.52
1868 2291 4.710324 ACCCTGTCATACGTTTCAAAAGA 58.290 39.130 0.00 0.00 0.00 2.52
1869 2292 5.699458 AGTACCCTGTCATACGTTTCAAAAG 59.301 40.000 0.00 0.00 0.00 2.27
1870 2293 5.613329 AGTACCCTGTCATACGTTTCAAAA 58.387 37.500 0.00 0.00 0.00 2.44
1871 2294 5.217978 AGTACCCTGTCATACGTTTCAAA 57.782 39.130 0.00 0.00 0.00 2.69
1895 2318 1.681793 CTCAGGGGTGATGTACTACCG 59.318 57.143 0.00 0.00 37.85 4.02
2027 2456 4.378874 GCTTAATCAAGACAGCACCAGAAC 60.379 45.833 0.00 0.00 33.20 3.01
2169 2598 4.127171 TCTTGATTGCCTACGAAATAGCC 58.873 43.478 0.00 0.00 0.00 3.93
2273 2702 7.220300 CCTTGAATATTGACAGTACGTACTCAC 59.780 40.741 25.10 20.19 33.46 3.51
2274 2703 7.094075 ACCTTGAATATTGACAGTACGTACTCA 60.094 37.037 25.10 18.04 33.46 3.41
2275 2704 7.256286 ACCTTGAATATTGACAGTACGTACTC 58.744 38.462 25.10 15.65 33.46 2.59
2276 2705 7.166691 ACCTTGAATATTGACAGTACGTACT 57.833 36.000 22.45 22.45 36.90 2.73
2277 2706 8.915871 TTACCTTGAATATTGACAGTACGTAC 57.084 34.615 18.10 18.10 0.00 3.67
2303 2732 7.252708 TCGCTTACTCGAGTTTGATATTGTTA 58.747 34.615 25.44 0.00 34.09 2.41
2313 2742 3.440872 AGTCTGATCGCTTACTCGAGTTT 59.559 43.478 25.44 1.29 42.14 2.66
2331 2760 4.443034 GGAAAATAGCATACGGTGGAGTCT 60.443 45.833 0.00 0.00 0.00 3.24
2354 2783 7.910162 CAGGTACATGAATTGAATTAAGAACGG 59.090 37.037 0.00 0.00 0.00 4.44
2356 2785 8.243426 TGCAGGTACATGAATTGAATTAAGAAC 58.757 33.333 12.53 0.00 0.00 3.01
2359 2788 6.974622 GGTGCAGGTACATGAATTGAATTAAG 59.025 38.462 12.53 0.00 0.00 1.85
2368 2797 4.160252 GGAAATTGGTGCAGGTACATGAAT 59.840 41.667 12.53 0.00 0.00 2.57
2372 2801 3.245229 TGAGGAAATTGGTGCAGGTACAT 60.245 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.