Multiple sequence alignment - TraesCS6A01G247000

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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 TraesCS6A01G247000 chr6A 100.000 2350 0 0 942 3291 457685762 457688111 0.000000e+00 4340.0
1 TraesCS6A01G247000 chr6A 100.000 564 0 0 1 564 457684821 457685384 0.000000e+00 1042.0
2 TraesCS6A01G247000 chr6D 89.883 1789 115 24 1478 3225 320228505 320230268 0.000000e+00 2241.0
3 TraesCS6A01G247000 chr6D 94.718 568 22 5 1 564 320227394 320227957 0.000000e+00 876.0
4 TraesCS6A01G247000 chr6D 92.150 535 32 7 942 1473 320227999 320228526 0.000000e+00 747.0
5 TraesCS6A01G247000 chr6B 94.090 846 38 10 2015 2856 502483469 502482632 0.000000e+00 1275.0
6 TraesCS6A01G247000 chr6B 90.619 970 72 11 943 1906 502484579 502483623 0.000000e+00 1269.0
7 TraesCS6A01G247000 chr6B 94.867 565 21 5 1 561 502485183 502484623 0.000000e+00 876.0
8 TraesCS6A01G247000 chr6B 90.355 197 16 2 3094 3289 502482633 502482439 4.210000e-64 255.0
9 TraesCS6A01G247000 chr6B 97.826 46 1 0 1974 2019 502483528 502483483 2.720000e-11 80.5
10 TraesCS6A01G247000 chr2D 82.182 275 49 0 1098 1372 523028490 523028764 1.530000e-58 237.0
11 TraesCS6A01G247000 chr2B 82.182 275 49 0 1098 1372 616934591 616934865 1.530000e-58 237.0
12 TraesCS6A01G247000 chr2B 87.179 156 18 2 2138 2292 616934972 616935126 3.380000e-40 176.0
13 TraesCS6A01G247000 chr2B 75.983 229 49 6 1147 1372 290519771 290519996 2.680000e-21 113.0
14 TraesCS6A01G247000 chr2A 82.182 275 49 0 1098 1372 668242743 668243017 1.530000e-58 237.0
15 TraesCS6A01G247000 chr2A 87.097 155 20 0 2138 2292 668243107 668243261 3.380000e-40 176.0
16 TraesCS6A01G247000 chr4D 85.263 95 14 0 1279 1373 387441858 387441952 7.520000e-17 99.0
17 TraesCS6A01G247000 chr4B 85.263 95 14 0 1279 1373 475811323 475811417 7.520000e-17 99.0
18 TraesCS6A01G247000 chr4A 85.263 95 14 0 1279 1373 68689450 68689544 7.520000e-17 99.0


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 TraesCS6A01G247000 chr6A 457684821 457688111 3290 False 2691.0 4340 100.000000 1 3291 2 chr6A.!!$F1 3290
1 TraesCS6A01G247000 chr6D 320227394 320230268 2874 False 1288.0 2241 92.250333 1 3225 3 chr6D.!!$F1 3224
2 TraesCS6A01G247000 chr6B 502482439 502485183 2744 True 751.1 1275 93.551400 1 3289 5 chr6B.!!$R1 3288
3 TraesCS6A01G247000 chr2B 616934591 616935126 535 False 206.5 237 84.680500 1098 2292 2 chr2B.!!$F2 1194
4 TraesCS6A01G247000 chr2A 668242743 668243261 518 False 206.5 237 84.639500 1098 2292 2 chr2A.!!$F1 1194

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
56 57 0.603707 TGTTTGAGCTTGAGCCGGAG 60.604 55.000 5.05 0.0 43.38 4.63 F
74 75 1.203052 GAGAACACCGGGAATCGTGTA 59.797 52.381 6.32 0.0 34.50 2.90 F
1940 1951 1.166531 GGGCAGTTTTCAGCGTGACT 61.167 55.000 0.00 0.0 32.98 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1611 0.823460 AAGTGGCAAAGGGTGTGTTG 59.177 50.000 0.00 0.0 0.0 3.33 R
1953 1964 2.025037 ACAGCATATGGCCTTTTCTGGA 60.025 45.455 3.32 0.0 46.5 3.86 R
3243 3386 0.105039 CTGGACTATCTTCGGGGTGC 59.895 60.000 0.00 0.0 0.0 5.01 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
56 57 0.603707 TGTTTGAGCTTGAGCCGGAG 60.604 55.000 5.05 0.00 43.38 4.63
70 71 4.515404 GGAGAACACCGGGAATCG 57.485 61.111 6.32 0.00 38.88 3.34
74 75 1.203052 GAGAACACCGGGAATCGTGTA 59.797 52.381 6.32 0.00 34.50 2.90
126 127 4.405680 ACAGATGGAACGATGTTCAGGATA 59.594 41.667 11.39 0.00 0.00 2.59
129 130 4.336889 TGGAACGATGTTCAGGATATCC 57.663 45.455 14.41 14.41 0.00 2.59
147 148 3.281727 TCCGGAAAATGATGGGAAGAG 57.718 47.619 0.00 0.00 0.00 2.85
152 153 3.053320 GGAAAATGATGGGAAGAGAGGGT 60.053 47.826 0.00 0.00 0.00 4.34
189 190 2.093658 GGATCTAGTTTGGTCGAGGCAA 60.094 50.000 0.00 0.00 0.00 4.52
241 242 2.996621 AGAATGTAAGTCTTGCACTCGC 59.003 45.455 5.43 0.00 38.70 5.03
251 252 2.159240 TCTTGCACTCGCGTCAGATATT 60.159 45.455 5.77 0.00 42.97 1.28
261 262 4.443063 TCGCGTCAGATATTATCAAAACGG 59.557 41.667 5.77 12.64 33.93 4.44
356 358 3.735240 TGTTTTGATGCTGCAACGATTTC 59.265 39.130 6.36 0.00 0.00 2.17
406 408 2.098298 GTGGTAGCGCGCATGTTG 59.902 61.111 35.10 0.00 0.00 3.33
472 477 1.368268 TTGGTCAAAAGCCCCTCCCT 61.368 55.000 0.00 0.00 0.00 4.20
490 495 1.371337 CTGGACGTGGTGGCATCATG 61.371 60.000 18.21 18.21 0.00 3.07
984 989 3.748568 CGAGAAAGGAAGGAAGGAAACAG 59.251 47.826 0.00 0.00 0.00 3.16
1010 1015 2.991250 AGCATCAACCATGGTGAGTAC 58.009 47.619 20.60 8.76 41.89 2.73
1014 1019 1.977854 TCAACCATGGTGAGTACAGCT 59.022 47.619 20.60 0.00 43.81 4.24
1028 1033 4.826556 AGTACAGCTCAACCTCATTCTTC 58.173 43.478 0.00 0.00 0.00 2.87
1086 1092 4.481463 GGTGTGTGTTAACATGTTATGGC 58.519 43.478 18.69 12.32 38.92 4.40
1088 1094 3.168193 GTGTGTTAACATGTTATGGCGC 58.832 45.455 18.69 16.87 38.92 6.53
1089 1095 2.162608 TGTGTTAACATGTTATGGCGCC 59.837 45.455 22.73 22.73 33.60 6.53
1100 1106 2.196997 TATGGCGCCTCCTTGTTGCT 62.197 55.000 29.70 1.76 35.26 3.91
1117 1123 1.207377 GCTAGTCGAATTCCGCGTCC 61.207 60.000 4.92 0.00 38.37 4.79
1136 1142 2.404186 GGAATGGCCGTTTCCGACC 61.404 63.158 18.52 8.76 37.10 4.79
1400 1406 6.038161 CCTGCTCGGATCACAAATATTGTTTA 59.962 38.462 0.00 0.00 36.94 2.01
1487 1495 1.251251 ATGAAAGGCAGTTGCTGGTC 58.749 50.000 3.88 0.18 41.70 4.02
1503 1511 8.592809 AGTTGCTGGTCCAAATTTATGAATTTA 58.407 29.630 7.77 0.00 42.14 1.40
1506 1514 8.250332 TGCTGGTCCAAATTTATGAATTTAGAC 58.750 33.333 19.21 19.21 45.25 2.59
1550 1558 4.880120 CACCTCTGCATGTTAGATCAATGT 59.120 41.667 0.00 0.00 0.00 2.71
1552 1560 6.202379 CACCTCTGCATGTTAGATCAATGTAG 59.798 42.308 0.00 2.85 0.00 2.74
1593 1604 7.826690 TCTTTATCATTTGGTTTCTACAAGCC 58.173 34.615 0.00 0.00 33.46 4.35
1600 1611 8.250332 TCATTTGGTTTCTACAAGCCATAATTC 58.750 33.333 0.00 0.00 42.09 2.17
1620 1631 2.028130 CAACACACCCTTTGCCACTTA 58.972 47.619 0.00 0.00 0.00 2.24
1622 1633 2.957474 ACACACCCTTTGCCACTTATT 58.043 42.857 0.00 0.00 0.00 1.40
1630 1641 3.989817 CCTTTGCCACTTATTGAGCAAAC 59.010 43.478 4.99 0.00 42.02 2.93
1634 1645 4.651778 TGCCACTTATTGAGCAAACTAGT 58.348 39.130 0.00 0.00 30.98 2.57
1635 1646 4.455533 TGCCACTTATTGAGCAAACTAGTG 59.544 41.667 0.00 12.11 30.98 2.74
1693 1704 5.046878 TCGTTTCATATAACACTGGTGACCT 60.047 40.000 2.11 0.00 0.00 3.85
1696 1707 7.332430 CGTTTCATATAACACTGGTGACCTAAA 59.668 37.037 2.11 0.00 0.00 1.85
1725 1736 7.809331 TGTAATTTTGTTAGATCAGCTTGCAAG 59.191 33.333 22.44 22.44 0.00 4.01
1730 1741 2.592102 AGATCAGCTTGCAAGGGAAA 57.408 45.000 27.10 0.00 0.00 3.13
1736 1747 1.460273 GCTTGCAAGGGAAACGGGAA 61.460 55.000 27.10 0.00 0.00 3.97
1741 1752 1.975660 CAAGGGAAACGGGAAGACAA 58.024 50.000 0.00 0.00 0.00 3.18
1764 1775 7.279313 ACAATTACTAGCTTATTTACCACACGG 59.721 37.037 0.00 0.00 38.77 4.94
1765 1776 6.528537 TTACTAGCTTATTTACCACACGGA 57.471 37.500 0.00 0.00 35.59 4.69
1768 1779 6.412214 ACTAGCTTATTTACCACACGGAAAT 58.588 36.000 0.00 0.00 35.59 2.17
1772 1783 5.646577 TTATTTACCACACGGAAATTGGG 57.353 39.130 0.00 0.00 34.41 4.12
1777 1788 1.892474 CCACACGGAAATTGGGAACAT 59.108 47.619 0.00 0.00 42.32 2.71
1802 1813 4.090761 TCCAATGTAGGAAGCATGGATC 57.909 45.455 0.00 0.00 33.93 3.36
1811 1822 6.823689 TGTAGGAAGCATGGATCTTAAGAAAC 59.176 38.462 9.71 6.07 0.00 2.78
1813 1824 6.488715 AGGAAGCATGGATCTTAAGAAACTT 58.511 36.000 9.71 6.94 0.00 2.66
1906 1917 4.704057 GGAAGACATGCCTTGATCTTTTCT 59.296 41.667 0.00 0.00 31.58 2.52
1907 1918 5.882557 GGAAGACATGCCTTGATCTTTTCTA 59.117 40.000 0.00 0.00 31.58 2.10
1909 1920 5.189180 AGACATGCCTTGATCTTTTCTACC 58.811 41.667 0.00 0.00 0.00 3.18
1934 1945 1.544724 TATGGTGGGCAGTTTTCAGC 58.455 50.000 0.00 0.00 0.00 4.26
1940 1951 1.166531 GGGCAGTTTTCAGCGTGACT 61.167 55.000 0.00 0.00 32.98 3.41
1946 1957 4.031028 CAGTTTTCAGCGTGACTTCAAAG 58.969 43.478 0.00 0.00 0.00 2.77
1947 1958 3.689649 AGTTTTCAGCGTGACTTCAAAGT 59.310 39.130 0.00 0.00 43.16 2.66
1948 1959 4.873827 AGTTTTCAGCGTGACTTCAAAGTA 59.126 37.500 0.00 0.00 39.88 2.24
1949 1960 5.353123 AGTTTTCAGCGTGACTTCAAAGTAA 59.647 36.000 0.00 0.00 39.88 2.24
1953 1964 4.873827 TCAGCGTGACTTCAAAGTAAAACT 59.126 37.500 0.00 0.00 39.88 2.66
1955 1966 4.272748 AGCGTGACTTCAAAGTAAAACTCC 59.727 41.667 0.00 0.00 39.88 3.85
1957 1968 5.738370 CGTGACTTCAAAGTAAAACTCCAG 58.262 41.667 0.00 0.00 39.88 3.86
1969 2007 6.494059 AGTAAAACTCCAGAAAAGGCCATAT 58.506 36.000 5.01 0.00 0.00 1.78
1970 2008 5.665916 AAAACTCCAGAAAAGGCCATATG 57.334 39.130 5.01 0.00 0.00 1.78
2021 2077 0.390078 CAGTGCTCTGGAGTCTGCAG 60.390 60.000 14.88 14.88 37.15 4.41
2070 2144 5.171337 GTGTAAATGCACGACAAAACAGAAG 59.829 40.000 0.00 0.00 0.00 2.85
2083 2157 4.373156 AAACAGAAGTGGTTCCTGCTAT 57.627 40.909 0.00 0.00 32.48 2.97
2091 2165 3.084786 GTGGTTCCTGCTATTTTCAGCT 58.915 45.455 0.00 0.00 42.30 4.24
2108 2182 0.308993 GCTGAAAACTGAAGCAGCGT 59.691 50.000 0.00 0.00 43.43 5.07
2109 2183 1.268743 GCTGAAAACTGAAGCAGCGTT 60.269 47.619 0.00 0.00 43.43 4.84
2110 2184 2.796032 GCTGAAAACTGAAGCAGCGTTT 60.796 45.455 0.00 0.00 43.43 3.60
2308 2432 5.984695 TCTGAAGAAGAGAAAATCCGAGA 57.015 39.130 0.00 0.00 0.00 4.04
2309 2433 6.346477 TCTGAAGAAGAGAAAATCCGAGAA 57.654 37.500 0.00 0.00 0.00 2.87
2331 2455 3.691609 ACAGCTACTTACTACGTACACCC 59.308 47.826 0.00 0.00 0.00 4.61
2335 2459 4.096984 GCTACTTACTACGTACACCCACAT 59.903 45.833 0.00 0.00 0.00 3.21
2339 2463 2.250031 ACTACGTACACCCACATCCAA 58.750 47.619 0.00 0.00 0.00 3.53
2340 2464 2.633967 ACTACGTACACCCACATCCAAA 59.366 45.455 0.00 0.00 0.00 3.28
2368 2493 1.688884 AGGAGCAGAGGAGGCCTTC 60.689 63.158 6.77 3.97 31.76 3.46
2369 2494 1.992277 GGAGCAGAGGAGGCCTTCA 60.992 63.158 15.31 0.00 31.76 3.02
2375 2500 1.227497 GAGGAGGCCTTCATCTGCG 60.227 63.158 15.31 0.00 33.87 5.18
2418 2543 0.032217 TCCCCATCCATTTTCCCTGC 60.032 55.000 0.00 0.00 0.00 4.85
2437 2562 1.135286 GCCATTCTTTTCCTGGAAGCG 60.135 52.381 9.42 5.10 31.38 4.68
2443 2568 0.951558 TTTTCCTGGAAGCGAAGTGC 59.048 50.000 9.42 0.00 46.98 4.40
2484 2609 4.759693 TGTATGCCGTCTTCATTCTTGTTT 59.240 37.500 0.00 0.00 0.00 2.83
2539 2665 9.804758 ACTACTGCTGTAAACTAGAACATATTC 57.195 33.333 4.91 0.00 34.78 1.75
2561 2687 3.663995 CATTTGATGCCAGGTGTGAAA 57.336 42.857 0.00 0.00 0.00 2.69
2609 2735 7.273381 CGCCGATTTTCACAAAAGAAGATTTAT 59.727 33.333 0.00 0.00 33.22 1.40
2634 2760 7.595819 TTTATCCCATCTGTTGTTCTTGTTT 57.404 32.000 0.00 0.00 0.00 2.83
2637 2763 6.817765 TCCCATCTGTTGTTCTTGTTTATC 57.182 37.500 0.00 0.00 0.00 1.75
2646 2772 7.284074 TGTTGTTCTTGTTTATCTACTTCCCA 58.716 34.615 0.00 0.00 0.00 4.37
2763 2890 4.484236 TGCGCAATTGTTCCTTCAAATAG 58.516 39.130 8.16 0.00 0.00 1.73
2775 2902 9.431887 TGTTCCTTCAAATAGTTGTACTACATC 57.568 33.333 10.09 0.00 32.84 3.06
2868 2996 4.930963 AGAGACGATTACTCTGCAATCTG 58.069 43.478 0.00 0.00 42.20 2.90
2869 2997 4.047822 GAGACGATTACTCTGCAATCTGG 58.952 47.826 0.00 0.00 31.49 3.86
2870 2998 3.701542 AGACGATTACTCTGCAATCTGGA 59.298 43.478 0.00 0.00 31.49 3.86
2871 2999 4.160439 AGACGATTACTCTGCAATCTGGAA 59.840 41.667 0.00 0.00 31.49 3.53
2900 3028 4.984161 AGAGTGCATTGCAACATTTACAAC 59.016 37.500 13.94 0.00 41.47 3.32
2921 3049 6.995091 ACAACATCTTCAGCTCTAGAAGTTTT 59.005 34.615 10.98 4.55 42.35 2.43
2929 3057 2.930682 GCTCTAGAAGTTTTCGGCGAAT 59.069 45.455 24.33 8.34 34.02 3.34
2993 3124 1.296392 CACCTCCTTGCCGACATCA 59.704 57.895 0.00 0.00 0.00 3.07
3195 3338 2.813474 CGGCATCGTGGAAGCGAA 60.813 61.111 0.00 0.00 44.38 4.70
3220 3363 3.728373 GAGGTGAACCCCGGCCAT 61.728 66.667 2.24 0.00 36.42 4.40
3231 3374 3.722295 CGGCCATGTTGCGTCGTT 61.722 61.111 2.24 0.00 0.00 3.85
3232 3375 2.175811 GGCCATGTTGCGTCGTTC 59.824 61.111 0.00 0.00 0.00 3.95
3235 3378 2.202171 CATGTTGCGTCGTTCGGC 60.202 61.111 0.00 0.00 40.26 5.54
3236 3379 3.773630 ATGTTGCGTCGTTCGGCG 61.774 61.111 14.67 14.67 40.26 6.46
3239 3382 3.694394 TTGCGTCGTTCGGCGTTC 61.694 61.111 19.38 5.60 42.13 3.95
3243 3386 3.110178 GTCGTTCGGCGTTCCCAG 61.110 66.667 6.85 0.00 42.13 4.45
3289 3433 3.316573 GAACTCCTCGGGGCAGTGG 62.317 68.421 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.603707 TCCGGCTCAAGCTCAAACAG 60.604 55.000 0.00 0.00 41.70 3.16
38 39 0.320771 TCTCCGGCTCAAGCTCAAAC 60.321 55.000 0.00 0.00 41.70 2.93
56 57 1.067354 AGTACACGATTCCCGGTGTTC 60.067 52.381 0.00 0.00 43.93 3.18
70 71 5.701290 GCATATATGTTCCCAAGGAGTACAC 59.299 44.000 14.14 0.00 31.21 2.90
74 75 4.747931 GCAGCATATATGTTCCCAAGGAGT 60.748 45.833 14.14 0.00 31.21 3.85
126 127 3.459598 TCTCTTCCCATCATTTTCCGGAT 59.540 43.478 4.15 0.00 0.00 4.18
129 130 3.209410 CCTCTCTTCCCATCATTTTCCG 58.791 50.000 0.00 0.00 0.00 4.30
147 148 2.622436 CGGTTCTTTGATGAGACCCTC 58.378 52.381 0.00 0.00 0.00 4.30
152 153 3.107601 AGATCCCGGTTCTTTGATGAGA 58.892 45.455 0.00 0.00 0.00 3.27
189 190 1.202758 TGTTCGGCATTGTTCAGACCT 60.203 47.619 0.00 0.00 0.00 3.85
241 242 8.889849 AAAAACCGTTTTGATAATATCTGACG 57.110 30.769 9.98 12.84 35.58 4.35
301 303 7.752518 TGGGGTGGTGTATATTTACTCTTAA 57.247 36.000 0.00 0.00 0.00 1.85
302 304 7.348801 ACATGGGGTGGTGTATATTTACTCTTA 59.651 37.037 0.00 0.00 0.00 2.10
314 316 0.119561 AGGGTACATGGGGTGGTGTA 59.880 55.000 0.00 0.00 0.00 2.90
321 323 2.883026 TCAAAACAAGGGTACATGGGG 58.117 47.619 0.00 0.00 0.00 4.96
356 358 0.334676 AGACAGACCCTCCCTCAGAG 59.665 60.000 0.00 0.00 42.83 3.35
406 408 3.430236 CCAGAAACTTTTGTGTCCAACCC 60.430 47.826 0.00 0.00 37.38 4.11
472 477 1.377072 CATGATGCCACCACGTCCA 60.377 57.895 0.00 0.00 0.00 4.02
490 495 0.695347 AATATAGGGAGGCCTGCTGC 59.305 55.000 24.77 8.42 40.16 5.25
984 989 2.165030 CACCATGGTTGATGCTTTCTCC 59.835 50.000 16.84 0.00 0.00 3.71
1010 1015 2.746362 GTGGAAGAATGAGGTTGAGCTG 59.254 50.000 0.00 0.00 0.00 4.24
1028 1033 2.288395 GGTTCCTTGAACAGCATTGTGG 60.288 50.000 9.01 0.00 43.54 4.17
1061 1067 2.738587 ACATGTTAACACACACCCCA 57.261 45.000 11.22 0.00 35.03 4.96
1067 1073 3.168193 GCGCCATAACATGTTAACACAC 58.832 45.455 21.57 8.61 35.03 3.82
1086 1092 1.078759 CGACTAGCAACAAGGAGGCG 61.079 60.000 0.00 0.00 33.45 5.52
1088 1094 2.743636 TTCGACTAGCAACAAGGAGG 57.256 50.000 0.00 0.00 0.00 4.30
1089 1095 3.619038 GGAATTCGACTAGCAACAAGGAG 59.381 47.826 0.00 0.00 0.00 3.69
1100 1106 1.063006 CGGACGCGGAATTCGACTA 59.937 57.895 12.47 0.00 42.43 2.59
1131 1137 1.608590 ACTTGAGTTTGCATTGGTCGG 59.391 47.619 0.00 0.00 0.00 4.79
1136 1142 3.318839 TCCTGGAACTTGAGTTTGCATTG 59.681 43.478 0.00 0.00 38.56 2.82
1258 1264 2.490509 CAAGCAGGCTGTGAAATCATCA 59.509 45.455 17.16 0.00 35.05 3.07
1416 1424 8.565896 ACTATGAAAATGCAACACTCTATGAA 57.434 30.769 0.00 0.00 0.00 2.57
1457 1465 7.340232 AGCAACTGCCTTTCATAAGATTGAATA 59.660 33.333 0.00 0.00 43.38 1.75
1487 1495 9.463443 GAATCCCGTCTAAATTCATAAATTTGG 57.537 33.333 0.00 0.00 43.32 3.28
1503 1511 6.884295 TGATTTTATCAAACTGAATCCCGTCT 59.116 34.615 0.00 0.00 36.11 4.18
1506 1514 6.095440 AGGTGATTTTATCAAACTGAATCCCG 59.905 38.462 0.00 0.00 41.69 5.14
1569 1577 7.601856 TGGCTTGTAGAAACCAAATGATAAAG 58.398 34.615 0.00 0.00 0.00 1.85
1593 1604 4.244862 GGCAAAGGGTGTGTTGAATTATG 58.755 43.478 0.00 0.00 0.00 1.90
1600 1611 0.823460 AAGTGGCAAAGGGTGTGTTG 59.177 50.000 0.00 0.00 0.00 3.33
1620 1631 7.093814 TGGAATAAATGCACTAGTTTGCTCAAT 60.094 33.333 6.85 0.00 43.41 2.57
1622 1633 5.709631 TGGAATAAATGCACTAGTTTGCTCA 59.290 36.000 6.85 0.00 43.41 4.26
1630 1641 6.095300 TGTGGACAATGGAATAAATGCACTAG 59.905 38.462 0.00 0.00 29.39 2.57
1634 1645 5.735285 TTGTGGACAATGGAATAAATGCA 57.265 34.783 0.00 0.00 0.00 3.96
1635 1646 7.432350 TTTTTGTGGACAATGGAATAAATGC 57.568 32.000 0.00 0.00 35.55 3.56
1666 1677 7.493320 GGTCACCAGTGTTATATGAAACGAATA 59.507 37.037 0.00 0.00 31.76 1.75
1670 1681 5.175859 AGGTCACCAGTGTTATATGAAACG 58.824 41.667 0.00 0.00 31.76 3.60
1680 1691 2.508300 ACAGGTTTAGGTCACCAGTGTT 59.492 45.455 0.00 0.00 36.67 3.32
1685 1696 6.130569 ACAAAATTACAGGTTTAGGTCACCA 58.869 36.000 0.00 0.00 36.67 4.17
1693 1704 9.515226 AGCTGATCTAACAAAATTACAGGTTTA 57.485 29.630 0.00 0.00 32.34 2.01
1696 1707 7.575720 GCAAGCTGATCTAACAAAATTACAGGT 60.576 37.037 0.00 0.00 36.63 4.00
1725 1736 3.682696 AGTAATTGTCTTCCCGTTTCCC 58.317 45.455 0.00 0.00 0.00 3.97
1730 1741 4.820894 AAGCTAGTAATTGTCTTCCCGT 57.179 40.909 0.00 0.00 0.00 5.28
1736 1747 9.379791 GTGTGGTAAATAAGCTAGTAATTGTCT 57.620 33.333 0.00 0.00 0.00 3.41
1741 1752 7.116075 TCCGTGTGGTAAATAAGCTAGTAAT 57.884 36.000 0.00 0.00 36.30 1.89
1764 1775 9.533253 CTACATTGGATTTATGTTCCCAATTTC 57.467 33.333 0.00 0.00 44.41 2.17
1765 1776 8.485392 CCTACATTGGATTTATGTTCCCAATTT 58.515 33.333 0.00 0.00 44.41 1.82
1768 1779 6.736581 TCCTACATTGGATTTATGTTCCCAA 58.263 36.000 0.00 0.00 42.16 4.12
1772 1783 7.333528 TGCTTCCTACATTGGATTTATGTTC 57.666 36.000 0.00 0.00 37.42 3.18
1777 1788 6.012337 TCCATGCTTCCTACATTGGATTTA 57.988 37.500 0.00 0.00 35.83 1.40
1786 1797 6.560003 TTCTTAAGATCCATGCTTCCTACA 57.440 37.500 5.89 0.00 0.00 2.74
1871 1882 3.659786 CATGTCTTCCTTGGTGTTACGA 58.340 45.455 0.00 0.00 0.00 3.43
1906 1917 6.773583 AAACTGCCCACCATAATATAGGTA 57.226 37.500 0.00 0.00 36.07 3.08
1907 1918 5.663158 AAACTGCCCACCATAATATAGGT 57.337 39.130 0.00 0.00 39.10 3.08
1909 1920 6.294176 GCTGAAAACTGCCCACCATAATATAG 60.294 42.308 0.00 0.00 0.00 1.31
1918 1929 2.193536 ACGCTGAAAACTGCCCACC 61.194 57.895 0.00 0.00 0.00 4.61
1934 1945 5.522460 TCTGGAGTTTTACTTTGAAGTCACG 59.478 40.000 0.00 0.00 40.37 4.35
1940 1951 6.406512 GGCCTTTTCTGGAGTTTTACTTTGAA 60.407 38.462 0.00 0.00 0.00 2.69
1946 1957 6.564328 CATATGGCCTTTTCTGGAGTTTTAC 58.436 40.000 3.32 0.00 0.00 2.01
1947 1958 5.127031 GCATATGGCCTTTTCTGGAGTTTTA 59.873 40.000 3.32 0.00 36.11 1.52
1948 1959 4.081476 GCATATGGCCTTTTCTGGAGTTTT 60.081 41.667 3.32 0.00 36.11 2.43
1949 1960 3.448660 GCATATGGCCTTTTCTGGAGTTT 59.551 43.478 3.32 0.00 36.11 2.66
1953 1964 2.025037 ACAGCATATGGCCTTTTCTGGA 60.025 45.455 3.32 0.00 46.50 3.86
1955 1966 4.159135 AGAAACAGCATATGGCCTTTTCTG 59.841 41.667 3.32 7.63 45.44 3.02
1957 1968 4.725790 AGAAACAGCATATGGCCTTTTC 57.274 40.909 3.32 8.33 46.50 2.29
1969 2007 3.003689 GCAGCTTGTTAGAAGAAACAGCA 59.996 43.478 0.00 0.00 40.29 4.41
1970 2008 3.251972 AGCAGCTTGTTAGAAGAAACAGC 59.748 43.478 0.00 0.00 40.29 4.40
2021 2077 7.328737 ACGATCATGCTTAAGGATTTACGATAC 59.671 37.037 22.62 10.88 26.83 2.24
2070 2144 3.084786 AGCTGAAAATAGCAGGAACCAC 58.915 45.455 0.00 0.00 46.07 4.16
2091 2165 3.502191 AAAACGCTGCTTCAGTTTTCA 57.498 38.095 9.36 0.00 42.28 2.69
2297 2421 6.100668 AGTAAGTAGCTGTTCTCGGATTTTC 58.899 40.000 0.00 0.00 0.00 2.29
2298 2422 6.038997 AGTAAGTAGCTGTTCTCGGATTTT 57.961 37.500 0.00 0.00 0.00 1.82
2302 2426 3.620374 CGTAGTAAGTAGCTGTTCTCGGA 59.380 47.826 0.00 0.00 0.00 4.55
2331 2455 0.251297 TGCTCCTGGGTTTGGATGTG 60.251 55.000 0.00 0.00 32.56 3.21
2335 2459 1.463214 TCCTGCTCCTGGGTTTGGA 60.463 57.895 0.00 0.00 0.00 3.53
2339 2463 2.530151 TGCTCCTGCTCCTGGGTT 60.530 61.111 0.00 0.00 40.48 4.11
2340 2464 3.007920 CTGCTCCTGCTCCTGGGT 61.008 66.667 0.00 0.00 40.48 4.51
2375 2500 3.435186 GCAAGAACAGGAGCCGGC 61.435 66.667 21.89 21.89 0.00 6.13
2418 2543 2.436417 TCGCTTCCAGGAAAAGAATGG 58.564 47.619 2.72 0.00 35.30 3.16
2437 2562 4.387256 GTCTCATACAGAACACAGCACTTC 59.613 45.833 0.00 0.00 30.72 3.01
2443 2568 5.518128 GCATACAGTCTCATACAGAACACAG 59.482 44.000 0.00 0.00 30.72 3.66
2484 2609 2.519780 GCACCAAACACGGGGGAA 60.520 61.111 0.00 0.00 0.00 3.97
2552 2678 2.795329 CCACATTAGGCTTTCACACCT 58.205 47.619 0.00 0.00 40.24 4.00
2609 2735 7.595819 AACAAGAACAACAGATGGGATAAAA 57.404 32.000 0.00 0.00 0.00 1.52
2616 2742 8.553459 AGTAGATAAACAAGAACAACAGATGG 57.447 34.615 0.00 0.00 0.00 3.51
2634 2760 7.785028 ACAGATCACAGTATTGGGAAGTAGATA 59.215 37.037 0.00 0.00 40.86 1.98
2637 2763 6.097554 AGACAGATCACAGTATTGGGAAGTAG 59.902 42.308 0.00 0.00 40.86 2.57
2671 2797 1.566018 CGACGGCAAAGGTTCCTGAC 61.566 60.000 0.00 0.00 0.00 3.51
2763 2890 3.370061 GCCCAGAAACGATGTAGTACAAC 59.630 47.826 7.16 3.59 0.00 3.32
2775 2902 2.743636 TCTACTCTTGCCCAGAAACG 57.256 50.000 0.00 0.00 0.00 3.60
2868 2996 1.200948 GCAATGCACTCTGTTCCTTCC 59.799 52.381 0.00 0.00 0.00 3.46
2869 2997 1.881973 TGCAATGCACTCTGTTCCTTC 59.118 47.619 2.72 0.00 31.71 3.46
2870 2998 1.985473 TGCAATGCACTCTGTTCCTT 58.015 45.000 2.72 0.00 31.71 3.36
2871 2999 1.610522 GTTGCAATGCACTCTGTTCCT 59.389 47.619 7.72 0.00 38.71 3.36
2900 3028 5.290643 CCGAAAACTTCTAGAGCTGAAGATG 59.709 44.000 16.77 11.26 42.37 2.90
2921 3049 5.237048 TGATGATCAATTCATATTCGCCGA 58.763 37.500 0.00 0.00 45.29 5.54
2929 3057 7.550597 AGGAGTAGCTGATGATCAATTCATA 57.449 36.000 0.00 0.00 45.29 2.15
3008 3139 2.048127 GCCGACGCCTCAAACTCT 60.048 61.111 0.00 0.00 0.00 3.24
3009 3140 3.479269 CGCCGACGCCTCAAACTC 61.479 66.667 0.00 0.00 0.00 3.01
3010 3141 3.509137 TTCGCCGACGCCTCAAACT 62.509 57.895 0.00 0.00 39.84 2.66
3012 3143 3.039588 GTTCGCCGACGCCTCAAA 61.040 61.111 0.00 0.00 39.84 2.69
3055 3198 2.031516 CCAGACAAGCAGCTGACGG 61.032 63.158 20.43 7.68 34.06 4.79
3058 3201 0.535780 CAACCCAGACAAGCAGCTGA 60.536 55.000 20.43 0.00 34.06 4.26
3063 3206 1.808531 GCATGCAACCCAGACAAGCA 61.809 55.000 14.21 0.00 39.79 3.91
3189 3332 4.394712 CCTCCCTGCCGTTCGCTT 62.395 66.667 0.00 0.00 38.78 4.68
3195 3338 3.637273 GGTTCACCTCCCTGCCGT 61.637 66.667 0.00 0.00 0.00 5.68
3235 3378 4.323477 TTCGGGGTGCTGGGAACG 62.323 66.667 0.00 0.00 0.00 3.95
3236 3379 2.198304 ATCTTCGGGGTGCTGGGAAC 62.198 60.000 0.00 0.00 0.00 3.62
3237 3380 0.619255 TATCTTCGGGGTGCTGGGAA 60.619 55.000 0.00 0.00 0.00 3.97
3239 3382 1.338136 ACTATCTTCGGGGTGCTGGG 61.338 60.000 0.00 0.00 0.00 4.45
3242 3385 0.325296 TGGACTATCTTCGGGGTGCT 60.325 55.000 0.00 0.00 0.00 4.40
3243 3386 0.105039 CTGGACTATCTTCGGGGTGC 59.895 60.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.