Multiple sequence alignment - TraesCS3A01G104700

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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 TraesCS3A01G104700 chr3A 100.000 2516 0 0 1 2516 68126781 68129296 0.000000e+00 4647
1 TraesCS3A01G104700 chr3D 84.842 2619 160 94 44 2516 59261095 59263622 0.000000e+00 2418
2 TraesCS3A01G104700 chr3B 84.968 1876 113 71 131 1917 94864900 94866695 0.000000e+00 1746
3 TraesCS3A01G104700 chr3B 86.420 486 32 13 2042 2516 94866857 94867319 3.740000e-138 501
4 TraesCS3A01G104700 chr3B 86.111 72 7 1 1977 2045 94866746 94866817 9.650000e-10 75


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 TraesCS3A01G104700 chr3A 68126781 68129296 2515 False 4647 4647 100.000 1 2516 1 chr3A.!!$F1 2515
1 TraesCS3A01G104700 chr3D 59261095 59263622 2527 False 2418 2418 84.842 44 2516 1 chr3D.!!$F1 2472
2 TraesCS3A01G104700 chr3B 94864900 94867319 2419 False 774 1746 85.833 131 2516 3 chr3B.!!$F1 2385

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
90 91 0.110486 GTCCAGTTGCCCCAGAGAAA 59.89 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1809 0.03213 ATTGATGGACGGACCGATCG 59.968 55.0 23.38 8.51 42.61 3.69 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
36 37 4.489306 AACAGGTAGACTCTTATTGGGC 57.511 45.455 0.00 0.00 0.00 5.36
37 38 2.772515 ACAGGTAGACTCTTATTGGGCC 59.227 50.000 0.00 0.00 0.00 5.80
38 39 2.040178 AGGTAGACTCTTATTGGGCCG 58.960 52.381 0.00 0.00 0.00 6.13
39 40 1.070289 GGTAGACTCTTATTGGGCCGG 59.930 57.143 0.00 0.00 0.00 6.13
40 41 2.037144 GTAGACTCTTATTGGGCCGGA 58.963 52.381 5.05 0.00 0.00 5.14
41 42 1.807814 AGACTCTTATTGGGCCGGAT 58.192 50.000 5.05 0.00 0.00 4.18
42 43 2.972348 AGACTCTTATTGGGCCGGATA 58.028 47.619 5.05 0.00 0.00 2.59
90 91 0.110486 GTCCAGTTGCCCCAGAGAAA 59.890 55.000 0.00 0.00 0.00 2.52
112 113 1.882623 CCTTTTCTTGCTCGCTTCCTT 59.117 47.619 0.00 0.00 0.00 3.36
113 114 2.294512 CCTTTTCTTGCTCGCTTCCTTT 59.705 45.455 0.00 0.00 0.00 3.11
114 115 3.559504 CTTTTCTTGCTCGCTTCCTTTC 58.440 45.455 0.00 0.00 0.00 2.62
115 116 1.523758 TTCTTGCTCGCTTCCTTTCC 58.476 50.000 0.00 0.00 0.00 3.13
116 117 0.396435 TCTTGCTCGCTTCCTTTCCA 59.604 50.000 0.00 0.00 0.00 3.53
139 140 0.886490 CCGGTGTGCAGCTTCTTTCT 60.886 55.000 0.00 0.00 0.00 2.52
251 253 5.482908 CTGTACAGCTCACAAGGTTAATCT 58.517 41.667 10.54 0.00 0.00 2.40
252 254 5.479306 TGTACAGCTCACAAGGTTAATCTC 58.521 41.667 0.00 0.00 0.00 2.75
255 257 3.614616 CAGCTCACAAGGTTAATCTCGAC 59.385 47.826 0.00 0.00 0.00 4.20
256 258 3.511934 AGCTCACAAGGTTAATCTCGACT 59.488 43.478 0.00 0.00 0.00 4.18
390 397 2.158559 AGAGCAAAACACACACACACA 58.841 42.857 0.00 0.00 0.00 3.72
392 399 0.981240 GCAAAACACACACACACACG 59.019 50.000 0.00 0.00 0.00 4.49
442 454 0.323451 AGAAATGCTTCCCGAACCCC 60.323 55.000 0.00 0.00 31.28 4.95
468 480 4.451652 GTCCGTCCGTCCGTCGTC 62.452 72.222 0.00 0.00 37.94 4.20
469 481 4.687215 TCCGTCCGTCCGTCGTCT 62.687 66.667 0.00 0.00 37.94 4.18
473 485 4.334118 TCCGTCCGTCGTCTCCCA 62.334 66.667 0.00 0.00 37.94 4.37
476 488 2.911484 CGTCCGTCGTCTCCCACAA 61.911 63.158 0.00 0.00 34.52 3.33
483 498 1.669115 CGTCTCCCACAAGCCACAG 60.669 63.158 0.00 0.00 0.00 3.66
649 684 1.557443 GGTCAACAGCACCGACGAAG 61.557 60.000 0.00 0.00 0.00 3.79
651 686 1.300620 CAACAGCACCGACGAAGGA 60.301 57.895 7.84 0.00 34.73 3.36
657 692 0.790814 GCACCGACGAAGGAAGAAAG 59.209 55.000 7.84 0.00 34.73 2.62
659 694 2.750948 CACCGACGAAGGAAGAAAGAA 58.249 47.619 7.84 0.00 34.73 2.52
661 696 3.184581 CACCGACGAAGGAAGAAAGAAAG 59.815 47.826 7.84 0.00 34.73 2.62
859 938 0.622136 CCCCCGCCCTATATAAACCC 59.378 60.000 0.00 0.00 0.00 4.11
870 949 0.896923 TATAAACCCACGTGGACGCT 59.103 50.000 36.07 18.35 44.43 5.07
871 950 0.390735 ATAAACCCACGTGGACGCTC 60.391 55.000 36.07 0.00 44.43 5.03
906 991 3.626924 ACCACCACGCCTCACTCC 61.627 66.667 0.00 0.00 0.00 3.85
910 995 3.775654 CCACGCCTCACTCCCCTC 61.776 72.222 0.00 0.00 0.00 4.30
911 996 3.775654 CACGCCTCACTCCCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
918 1003 1.862138 TCACTCCCCTCCTCCTCCA 60.862 63.158 0.00 0.00 0.00 3.86
925 1010 2.063378 CCTCCTCCTCCACCTCTGC 61.063 68.421 0.00 0.00 0.00 4.26
951 1036 2.002018 TTCCACTTGGCGGTTCCCTT 62.002 55.000 0.00 0.00 34.44 3.95
953 1038 1.971695 CACTTGGCGGTTCCCTTCC 60.972 63.158 0.00 0.00 0.00 3.46
976 1070 3.117171 CTGAGTCGGCTGCTGTGC 61.117 66.667 8.55 3.20 0.00 4.57
987 1081 4.648626 GCTGTGCCTGTGGGAGCA 62.649 66.667 0.00 0.00 36.44 4.26
1110 1204 2.671682 GGAGGTGGTGGCTTCTCC 59.328 66.667 0.00 0.00 38.95 3.71
1136 1230 3.237741 GGCGGAGATGGAGGAGGG 61.238 72.222 0.00 0.00 0.00 4.30
1396 1490 2.280524 CCGAGCCCAACAACGACA 60.281 61.111 0.00 0.00 0.00 4.35
1397 1491 2.604174 CCGAGCCCAACAACGACAC 61.604 63.158 0.00 0.00 0.00 3.67
1405 1499 0.248458 CAACAACGACACCACCAAGC 60.248 55.000 0.00 0.00 0.00 4.01
1528 1637 1.455217 GAGTAGGGTAGGGCGCAGA 60.455 63.158 10.83 0.00 0.00 4.26
1541 1650 4.577246 GCAGAGCGCTCGGGTAGG 62.577 72.222 33.38 19.70 37.77 3.18
1542 1651 4.577246 CAGAGCGCTCGGGTAGGC 62.577 72.222 30.39 6.03 34.09 3.93
1559 1668 4.729856 CAAGGCAAGGCAAGGCGC 62.730 66.667 0.00 0.00 41.28 6.53
1728 1837 2.513666 TCCATCAATGCGGTCGGC 60.514 61.111 0.00 0.00 43.96 5.54
1782 1891 2.098117 CGAGGAAATGGAAATGGTGCTC 59.902 50.000 0.00 0.00 0.00 4.26
1829 1956 1.399343 GCTTTTGCGTCCGGTTTCTAC 60.399 52.381 0.00 0.00 34.86 2.59
1830 1957 2.140717 CTTTTGCGTCCGGTTTCTACT 58.859 47.619 0.00 0.00 0.00 2.57
1831 1958 1.504359 TTTGCGTCCGGTTTCTACTG 58.496 50.000 0.00 0.00 0.00 2.74
1832 1959 0.947180 TTGCGTCCGGTTTCTACTGC 60.947 55.000 0.00 0.87 0.00 4.40
1833 1960 1.080025 GCGTCCGGTTTCTACTGCT 60.080 57.895 0.00 0.00 0.00 4.24
1834 1961 1.352156 GCGTCCGGTTTCTACTGCTG 61.352 60.000 0.00 0.00 0.00 4.41
1835 1962 0.736325 CGTCCGGTTTCTACTGCTGG 60.736 60.000 0.00 0.00 0.00 4.85
1836 1963 1.019805 GTCCGGTTTCTACTGCTGGC 61.020 60.000 0.00 0.00 0.00 4.85
1837 1964 1.745489 CCGGTTTCTACTGCTGGCC 60.745 63.158 0.00 0.00 0.00 5.36
1838 1965 1.003839 CGGTTTCTACTGCTGGCCA 60.004 57.895 4.71 4.71 0.00 5.36
1858 1985 2.421424 CACTATGGCTCAGTTTTCCTGC 59.579 50.000 0.00 0.00 41.25 4.85
1865 1992 0.756294 TCAGTTTTCCTGCTCCGTGA 59.244 50.000 0.00 0.00 41.25 4.35
1866 1993 0.868406 CAGTTTTCCTGCTCCGTGAC 59.132 55.000 0.00 0.00 33.59 3.67
1867 1994 0.600255 AGTTTTCCTGCTCCGTGACG 60.600 55.000 0.00 0.00 0.00 4.35
1899 2029 0.179111 CTTGACTGGCCGATAGCGAA 60.179 55.000 0.00 0.00 45.17 4.70
1900 2030 0.464036 TTGACTGGCCGATAGCGAAT 59.536 50.000 0.00 0.00 45.17 3.34
1903 2033 1.069765 CTGGCCGATAGCGAATGGT 59.930 57.895 0.00 0.00 45.17 3.55
1926 2062 6.032094 GTGTTTGAATTCGATCGTACTCCTA 58.968 40.000 15.94 0.00 0.00 2.94
1931 2067 2.299993 TCGATCGTACTCCTACGTGT 57.700 50.000 15.94 0.00 45.14 4.49
1959 2109 0.538746 CCAACCTACCCAACCCACAC 60.539 60.000 0.00 0.00 0.00 3.82
1965 2115 2.423660 CCTACCCAACCCACACTCAAAA 60.424 50.000 0.00 0.00 0.00 2.44
1987 2137 1.280457 AAAAAGCAACCCAACCCACA 58.720 45.000 0.00 0.00 0.00 4.17
1988 2138 1.506025 AAAAGCAACCCAACCCACAT 58.494 45.000 0.00 0.00 0.00 3.21
1989 2139 1.506025 AAAGCAACCCAACCCACATT 58.494 45.000 0.00 0.00 0.00 2.71
1990 2140 2.390225 AAGCAACCCAACCCACATTA 57.610 45.000 0.00 0.00 0.00 1.90
1991 2141 2.390225 AGCAACCCAACCCACATTAA 57.610 45.000 0.00 0.00 0.00 1.40
1992 2142 2.683768 AGCAACCCAACCCACATTAAA 58.316 42.857 0.00 0.00 0.00 1.52
1993 2143 3.247162 AGCAACCCAACCCACATTAAAT 58.753 40.909 0.00 0.00 0.00 1.40
1994 2144 3.260632 AGCAACCCAACCCACATTAAATC 59.739 43.478 0.00 0.00 0.00 2.17
1995 2145 3.007398 GCAACCCAACCCACATTAAATCA 59.993 43.478 0.00 0.00 0.00 2.57
1996 2146 4.819769 CAACCCAACCCACATTAAATCAG 58.180 43.478 0.00 0.00 0.00 2.90
1997 2147 2.831526 ACCCAACCCACATTAAATCAGC 59.168 45.455 0.00 0.00 0.00 4.26
1998 2148 3.099141 CCCAACCCACATTAAATCAGCT 58.901 45.455 0.00 0.00 0.00 4.24
1999 2149 4.264172 ACCCAACCCACATTAAATCAGCTA 60.264 41.667 0.00 0.00 0.00 3.32
2004 2154 3.248602 CCCACATTAAATCAGCTAGCGTC 59.751 47.826 9.55 0.00 0.00 5.19
2009 2159 5.980116 ACATTAAATCAGCTAGCGTCTACAG 59.020 40.000 9.55 0.00 0.00 2.74
2011 2161 4.457834 AAATCAGCTAGCGTCTACAGTT 57.542 40.909 9.55 0.00 0.00 3.16
2015 2165 4.763073 TCAGCTAGCGTCTACAGTTAGTA 58.237 43.478 9.55 0.00 0.00 1.82
2077 2270 1.418264 TGAATCCAAGTTGGGTCGTGA 59.582 47.619 21.85 1.33 38.32 4.35
2078 2271 2.158740 TGAATCCAAGTTGGGTCGTGAA 60.159 45.455 21.85 0.54 38.32 3.18
2080 2273 0.834612 TCCAAGTTGGGTCGTGAAGT 59.165 50.000 21.85 0.00 38.32 3.01
2120 2317 2.158841 CGTGAACTAATTTCCACCGGTG 59.841 50.000 28.26 28.26 32.58 4.94
2126 2323 0.602562 AATTTCCACCGGTGCATGTG 59.397 50.000 29.75 15.17 0.00 3.21
2132 2329 2.349376 CCGGTGCATGTGGTGGTA 59.651 61.111 0.00 0.00 0.00 3.25
2138 2335 0.106894 TGCATGTGGTGGTACGTTCA 59.893 50.000 0.00 0.00 0.00 3.18
2149 2346 2.819019 TGGTACGTTCATGTCCTTCGTA 59.181 45.455 0.00 0.00 36.24 3.43
2156 2353 2.100197 TCATGTCCTTCGTAGTCTGGG 58.900 52.381 0.00 0.00 0.00 4.45
2188 2390 4.542833 TCCAAGAGGCAACGGTACGAAG 62.543 54.545 0.00 0.00 46.63 3.79
2245 2447 4.427661 GCGAGCGAGCACAGAGGT 62.428 66.667 0.00 0.00 37.05 3.85
2277 2479 0.182775 GGTGGTCTGTGGTTTCAGGT 59.817 55.000 0.00 0.00 36.25 4.00
2322 2524 0.806102 CATGCATTGCAAGCAGCCTC 60.806 55.000 16.46 2.38 46.36 4.70
2335 2547 3.221222 GCCTCCTGCGTGGATAGT 58.779 61.111 0.00 0.00 45.16 2.12
2354 2566 0.953727 TGCAGTGCAGGCTTTACTTG 59.046 50.000 15.37 0.00 33.32 3.16
2367 2579 4.467735 GCTTTACTTGCTTTCACTGTAGC 58.532 43.478 0.00 0.00 37.89 3.58
2403 2615 2.967473 GCAGACAGCAGCACAGCAG 61.967 63.158 0.00 0.00 44.79 4.24
2404 2616 1.301479 CAGACAGCAGCACAGCAGA 60.301 57.895 0.00 0.00 36.85 4.26
2405 2617 1.004799 AGACAGCAGCACAGCAGAG 60.005 57.895 0.00 0.00 36.85 3.35
2406 2618 2.668889 ACAGCAGCACAGCAGAGC 60.669 61.111 0.00 0.00 36.85 4.09
2407 2619 2.668550 CAGCAGCACAGCAGAGCA 60.669 61.111 0.85 0.00 36.85 4.26
2408 2620 2.668889 AGCAGCACAGCAGAGCAC 60.669 61.111 0.85 0.00 36.85 4.40
2409 2621 2.976350 GCAGCACAGCAGAGCACA 60.976 61.111 0.85 0.00 33.43 4.57
2410 2622 2.944429 CAGCACAGCAGAGCACAC 59.056 61.111 0.85 0.00 33.43 3.82
2411 2623 2.281345 AGCACAGCAGAGCACACC 60.281 61.111 0.85 0.00 33.43 4.16
2412 2624 2.592574 GCACAGCAGAGCACACCA 60.593 61.111 0.00 0.00 0.00 4.17
2437 2654 1.266718 TCAAAGGCAGCACGTTTCATC 59.733 47.619 0.00 0.00 34.20 2.92
2440 2657 0.534877 AGGCAGCACGTTTCATCACA 60.535 50.000 0.00 0.00 0.00 3.58
2445 2662 1.069022 AGCACGTTTCATCACACATGC 60.069 47.619 0.00 0.00 0.00 4.06
2446 2663 1.069022 GCACGTTTCATCACACATGCT 60.069 47.619 0.00 0.00 0.00 3.79
2447 2664 2.577450 CACGTTTCATCACACATGCTG 58.423 47.619 0.00 0.00 0.00 4.41
2448 2665 2.223845 CACGTTTCATCACACATGCTGA 59.776 45.455 0.00 0.00 0.00 4.26
2482 2707 1.153086 CACCACTATCAGGCCAGGC 60.153 63.158 5.01 1.26 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.710567 GCCCAATAAGAGTCTACCTGTTTTT 59.289 40.000 0.00 0.00 0.00 1.94
13 14 5.254115 GCCCAATAAGAGTCTACCTGTTTT 58.746 41.667 0.00 0.00 0.00 2.43
14 15 4.324331 GGCCCAATAAGAGTCTACCTGTTT 60.324 45.833 0.00 0.00 0.00 2.83
15 16 3.200165 GGCCCAATAAGAGTCTACCTGTT 59.800 47.826 0.00 0.00 0.00 3.16
16 17 2.772515 GGCCCAATAAGAGTCTACCTGT 59.227 50.000 0.00 0.00 0.00 4.00
17 18 2.224066 CGGCCCAATAAGAGTCTACCTG 60.224 54.545 0.00 0.00 0.00 4.00
18 19 2.040178 CGGCCCAATAAGAGTCTACCT 58.960 52.381 0.00 0.00 0.00 3.08
19 20 1.070289 CCGGCCCAATAAGAGTCTACC 59.930 57.143 0.00 0.00 0.00 3.18
20 21 2.037144 TCCGGCCCAATAAGAGTCTAC 58.963 52.381 0.00 0.00 0.00 2.59
21 22 2.464796 TCCGGCCCAATAAGAGTCTA 57.535 50.000 0.00 0.00 0.00 2.59
22 23 1.807814 ATCCGGCCCAATAAGAGTCT 58.192 50.000 0.00 0.00 0.00 3.24
23 24 2.028020 CCTATCCGGCCCAATAAGAGTC 60.028 54.545 0.00 0.00 0.00 3.36
24 25 1.978580 CCTATCCGGCCCAATAAGAGT 59.021 52.381 0.00 0.00 0.00 3.24
25 26 2.770164 CCTATCCGGCCCAATAAGAG 57.230 55.000 0.00 0.00 0.00 2.85
36 37 3.164269 AGTGGCAGGCCTATCCGG 61.164 66.667 3.98 0.00 40.77 5.14
37 38 2.109799 CAGTGGCAGGCCTATCCG 59.890 66.667 3.98 0.00 40.77 4.18
38 39 2.512896 CCAGTGGCAGGCCTATCC 59.487 66.667 3.98 10.98 36.94 2.59
39 40 2.512896 CCCAGTGGCAGGCCTATC 59.487 66.667 3.98 0.23 36.94 2.08
90 91 1.239347 GAAGCGAGCAAGAAAAGGGT 58.761 50.000 0.00 0.00 0.00 4.34
105 106 1.453928 CCGGGGATGGAAAGGAAGC 60.454 63.158 0.00 0.00 0.00 3.86
112 113 3.253061 TGCACACCGGGGATGGAA 61.253 61.111 12.96 0.00 0.00 3.53
113 114 3.716195 CTGCACACCGGGGATGGA 61.716 66.667 12.96 5.37 0.00 3.41
115 116 3.925630 AAGCTGCACACCGGGGATG 62.926 63.158 12.96 6.27 0.00 3.51
116 117 3.628646 GAAGCTGCACACCGGGGAT 62.629 63.158 12.96 0.00 0.00 3.85
174 176 3.243636 GGAGAGGTTTTACACGAGTGTCA 60.244 47.826 12.54 0.00 43.74 3.58
208 210 1.013524 GCGCGTTACCCTTTCGGTTA 61.014 55.000 8.43 0.00 45.36 2.85
209 211 2.319841 GCGCGTTACCCTTTCGGTT 61.320 57.895 8.43 0.00 45.36 4.44
213 215 0.390209 TACAGGCGCGTTACCCTTTC 60.390 55.000 8.43 0.00 0.00 2.62
218 220 2.450345 GCTGTACAGGCGCGTTACC 61.450 63.158 23.95 0.00 0.00 2.85
286 292 2.664185 CCGATCTCCTGCATGCCG 60.664 66.667 16.68 9.00 0.00 5.69
310 316 2.597217 CTGCGGGGCTGTTTTGGA 60.597 61.111 0.00 0.00 0.00 3.53
340 347 1.066587 TTTTCGTTGGCGCCTTTGG 59.933 52.632 29.70 14.26 38.14 3.28
463 475 1.668151 GTGGCTTGTGGGAGACGAC 60.668 63.158 0.00 0.00 39.85 4.34
464 476 2.099652 CTGTGGCTTGTGGGAGACGA 62.100 60.000 0.00 0.00 0.00 4.20
465 477 1.669115 CTGTGGCTTGTGGGAGACG 60.669 63.158 0.00 0.00 0.00 4.18
466 478 1.968540 GCTGTGGCTTGTGGGAGAC 60.969 63.158 0.00 0.00 35.22 3.36
467 479 2.431683 GCTGTGGCTTGTGGGAGA 59.568 61.111 0.00 0.00 35.22 3.71
468 480 3.052082 CGCTGTGGCTTGTGGGAG 61.052 66.667 0.00 0.00 36.09 4.30
469 481 4.641645 CCGCTGTGGCTTGTGGGA 62.642 66.667 0.00 0.00 36.09 4.37
661 696 4.533318 GGGTGGGGAAAGAAACCC 57.467 61.111 0.00 0.00 45.29 4.11
847 926 3.645884 CGTCCACGTGGGTTTATATAGG 58.354 50.000 33.40 13.70 38.11 2.57
906 991 1.382420 CAGAGGTGGAGGAGGAGGG 60.382 68.421 0.00 0.00 0.00 4.30
910 995 0.251634 GAAAGCAGAGGTGGAGGAGG 59.748 60.000 0.00 0.00 0.00 4.30
911 996 0.979665 TGAAAGCAGAGGTGGAGGAG 59.020 55.000 0.00 0.00 0.00 3.69
918 1003 2.262423 GTGGAACTGAAAGCAGAGGT 57.738 50.000 0.00 0.00 45.17 3.85
951 1036 0.967887 CAGCCGACTCAGAGGAAGGA 60.968 60.000 11.07 0.00 0.00 3.36
953 1038 1.153667 GCAGCCGACTCAGAGGAAG 60.154 63.158 1.53 0.00 0.00 3.46
977 1071 2.579201 CTACCGGTGCTCCCACAG 59.421 66.667 19.93 0.00 43.88 3.66
978 1072 3.000819 CCTACCGGTGCTCCCACA 61.001 66.667 19.93 0.00 43.88 4.17
979 1073 3.782443 CCCTACCGGTGCTCCCAC 61.782 72.222 19.93 0.00 41.32 4.61
980 1074 4.326227 ACCCTACCGGTGCTCCCA 62.326 66.667 19.93 0.00 46.09 4.37
989 1083 1.075525 TCCTCCATCCACCCTACCG 60.076 63.158 0.00 0.00 0.00 4.02
1098 1192 2.069776 CTTCCAGGAGAAGCCACCA 58.930 57.895 0.00 0.00 45.38 4.17
1110 1204 1.445095 CATCTCCGCCTCCTTCCAG 59.555 63.158 0.00 0.00 0.00 3.86
1136 1230 2.123382 CGTACTCCTCCCCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
1314 1408 2.436646 GTGTCCACGGAGGCCATG 60.437 66.667 5.01 0.00 37.29 3.66
1387 1481 1.381165 GGCTTGGTGGTGTCGTTGTT 61.381 55.000 0.00 0.00 0.00 2.83
1388 1482 1.822186 GGCTTGGTGGTGTCGTTGT 60.822 57.895 0.00 0.00 0.00 3.32
1389 1483 2.892334 CGGCTTGGTGGTGTCGTTG 61.892 63.158 0.00 0.00 0.00 4.10
1390 1484 2.590575 CGGCTTGGTGGTGTCGTT 60.591 61.111 0.00 0.00 0.00 3.85
1528 1637 4.148825 CTTGCCTACCCGAGCGCT 62.149 66.667 11.27 11.27 0.00 5.92
1533 1642 2.668632 CTTGCCTTGCCTACCCGA 59.331 61.111 0.00 0.00 0.00 5.14
1534 1643 2.438434 CCTTGCCTTGCCTACCCG 60.438 66.667 0.00 0.00 0.00 5.28
1537 1646 1.598701 CCTTGCCTTGCCTTGCCTAC 61.599 60.000 0.00 0.00 0.00 3.18
1538 1647 1.304381 CCTTGCCTTGCCTTGCCTA 60.304 57.895 0.00 0.00 0.00 3.93
1539 1648 2.602568 CCTTGCCTTGCCTTGCCT 60.603 61.111 0.00 0.00 0.00 4.75
1540 1649 4.383861 GCCTTGCCTTGCCTTGCC 62.384 66.667 0.00 0.00 0.00 4.52
1541 1650 4.729856 CGCCTTGCCTTGCCTTGC 62.730 66.667 0.00 0.00 0.00 4.01
1542 1651 4.729856 GCGCCTTGCCTTGCCTTG 62.730 66.667 0.00 0.00 37.76 3.61
1697 1806 3.138930 ATGGACGGACCGATCGCTG 62.139 63.158 23.38 4.71 42.61 5.18
1698 1807 2.833582 ATGGACGGACCGATCGCT 60.834 61.111 23.38 0.00 42.61 4.93
1699 1808 2.354773 GATGGACGGACCGATCGC 60.355 66.667 23.38 6.58 42.61 4.58
1700 1809 0.032130 ATTGATGGACGGACCGATCG 59.968 55.000 23.38 8.51 42.61 3.69
1701 1810 1.502231 CATTGATGGACGGACCGATC 58.498 55.000 23.38 13.83 42.61 3.69
1712 1821 3.585990 GGCCGACCGCATTGATGG 61.586 66.667 0.00 0.00 40.31 3.51
1737 1846 2.978010 CACCCCTCAACGCACCAC 60.978 66.667 0.00 0.00 0.00 4.16
1738 1847 3.164977 TCACCCCTCAACGCACCA 61.165 61.111 0.00 0.00 0.00 4.17
1739 1848 2.358737 CTCACCCCTCAACGCACC 60.359 66.667 0.00 0.00 0.00 5.01
1836 1963 3.356529 AGGAAAACTGAGCCATAGTGG 57.643 47.619 0.00 0.00 41.55 4.00
1858 1985 0.790814 GAGAAAAAGGCGTCACGGAG 59.209 55.000 0.00 0.00 0.00 4.63
1865 1992 0.534203 TCAAGGCGAGAAAAAGGCGT 60.534 50.000 0.00 0.00 38.03 5.68
1866 1993 0.110192 GTCAAGGCGAGAAAAAGGCG 60.110 55.000 0.00 0.00 38.03 5.52
1867 1994 1.068954 CAGTCAAGGCGAGAAAAAGGC 60.069 52.381 0.00 0.00 0.00 4.35
1899 2029 5.175859 AGTACGATCGAATTCAAACACCAT 58.824 37.500 24.34 0.00 0.00 3.55
1900 2030 4.562082 AGTACGATCGAATTCAAACACCA 58.438 39.130 24.34 0.00 0.00 4.17
1903 2033 5.068234 AGGAGTACGATCGAATTCAAACA 57.932 39.130 24.34 0.00 0.00 2.83
1926 2062 0.379316 GGTTGGCGAAAGAAACACGT 59.621 50.000 0.00 0.00 32.73 4.49
1931 2067 1.143277 TGGGTAGGTTGGCGAAAGAAA 59.857 47.619 0.00 0.00 0.00 2.52
1968 2118 1.280457 TGTGGGTTGGGTTGCTTTTT 58.720 45.000 0.00 0.00 0.00 1.94
1970 2120 1.506025 AATGTGGGTTGGGTTGCTTT 58.494 45.000 0.00 0.00 0.00 3.51
1971 2121 2.390225 TAATGTGGGTTGGGTTGCTT 57.610 45.000 0.00 0.00 0.00 3.91
1972 2122 2.390225 TTAATGTGGGTTGGGTTGCT 57.610 45.000 0.00 0.00 0.00 3.91
1973 2123 3.007398 TGATTTAATGTGGGTTGGGTTGC 59.993 43.478 0.00 0.00 0.00 4.17
1974 2124 4.819769 CTGATTTAATGTGGGTTGGGTTG 58.180 43.478 0.00 0.00 0.00 3.77
1976 2126 2.831526 GCTGATTTAATGTGGGTTGGGT 59.168 45.455 0.00 0.00 0.00 4.51
1977 2127 3.099141 AGCTGATTTAATGTGGGTTGGG 58.901 45.455 0.00 0.00 0.00 4.12
1978 2128 4.202050 GCTAGCTGATTTAATGTGGGTTGG 60.202 45.833 7.70 0.00 0.00 3.77
1979 2129 4.496341 CGCTAGCTGATTTAATGTGGGTTG 60.496 45.833 13.93 0.00 0.00 3.77
1980 2130 3.627577 CGCTAGCTGATTTAATGTGGGTT 59.372 43.478 13.93 0.00 0.00 4.11
1981 2131 3.206150 CGCTAGCTGATTTAATGTGGGT 58.794 45.455 13.93 0.00 0.00 4.51
1982 2132 3.206150 ACGCTAGCTGATTTAATGTGGG 58.794 45.455 13.93 0.00 0.00 4.61
1983 2133 4.122776 AGACGCTAGCTGATTTAATGTGG 58.877 43.478 13.93 0.00 0.00 4.17
1986 2136 5.980116 ACTGTAGACGCTAGCTGATTTAATG 59.020 40.000 13.93 0.00 0.00 1.90
1987 2137 6.150396 ACTGTAGACGCTAGCTGATTTAAT 57.850 37.500 13.93 0.00 0.00 1.40
1988 2138 5.578005 ACTGTAGACGCTAGCTGATTTAA 57.422 39.130 13.93 0.00 0.00 1.52
1989 2139 5.578005 AACTGTAGACGCTAGCTGATTTA 57.422 39.130 13.93 0.00 0.00 1.40
1990 2140 4.457834 AACTGTAGACGCTAGCTGATTT 57.542 40.909 13.93 0.00 0.00 2.17
1991 2141 4.641094 ACTAACTGTAGACGCTAGCTGATT 59.359 41.667 13.93 0.00 0.00 2.57
1992 2142 4.200874 ACTAACTGTAGACGCTAGCTGAT 58.799 43.478 13.93 0.00 0.00 2.90
1993 2143 3.607741 ACTAACTGTAGACGCTAGCTGA 58.392 45.455 13.93 0.00 0.00 4.26
2009 2159 7.321153 TCTGAGATTGGTTAACAGCTACTAAC 58.679 38.462 8.10 8.09 0.00 2.34
2011 2161 6.663953 ACTCTGAGATTGGTTAACAGCTACTA 59.336 38.462 12.44 0.00 0.00 1.82
2015 2165 4.323104 GGACTCTGAGATTGGTTAACAGCT 60.323 45.833 12.44 0.00 0.00 4.24
2016 2166 3.935828 GGACTCTGAGATTGGTTAACAGC 59.064 47.826 12.44 0.00 0.00 4.40
2077 2270 2.577593 GGCCGAGACGCCTAACTT 59.422 61.111 0.00 0.00 46.10 2.66
2100 2297 2.095415 GCACCGGTGGAAATTAGTTCAC 60.095 50.000 34.58 10.35 38.06 3.18
2120 2317 1.130373 CATGAACGTACCACCACATGC 59.870 52.381 0.00 0.00 0.00 4.06
2126 2323 2.344025 GAAGGACATGAACGTACCACC 58.656 52.381 0.00 0.00 0.00 4.61
2129 2326 2.358939 ACGAAGGACATGAACGTACC 57.641 50.000 0.00 0.00 35.49 3.34
2132 2329 2.818432 AGACTACGAAGGACATGAACGT 59.182 45.455 0.00 6.21 40.23 3.99
2138 2335 0.824759 GCCCAGACTACGAAGGACAT 59.175 55.000 0.00 0.00 0.00 3.06
2149 2346 1.202698 GGAATCTAATGCGCCCAGACT 60.203 52.381 4.18 0.00 0.00 3.24
2156 2353 1.265365 GCCTCTTGGAATCTAATGCGC 59.735 52.381 0.00 0.00 34.57 6.09
2197 2399 0.625316 TGGCTATCCATGTTGCCTGT 59.375 50.000 9.54 0.00 45.11 4.00
2277 2479 1.209261 TGCCGTGGAAGCTGATGATAA 59.791 47.619 0.00 0.00 0.00 1.75
2309 2511 2.987547 GCAGGAGGCTGCTTGCAA 60.988 61.111 19.69 0.00 46.04 4.08
2326 2528 1.086067 CCTGCACTGCACTATCCACG 61.086 60.000 0.00 0.00 33.79 4.94
2335 2547 0.953727 CAAGTAAAGCCTGCACTGCA 59.046 50.000 3.11 3.11 36.92 4.41
2354 2566 3.058639 CCTGAAACTGCTACAGTGAAAGC 60.059 47.826 13.20 13.20 44.62 3.51
2389 2601 2.668889 GCTCTGCTGTGCTGCTGT 60.669 61.111 10.03 0.00 34.27 4.40
2391 2603 2.668889 GTGCTCTGCTGTGCTGCT 60.669 61.111 16.89 0.00 34.18 4.24
2403 2615 0.947244 CTTTGACCTGTGGTGTGCTC 59.053 55.000 0.00 0.00 35.25 4.26
2404 2616 0.466189 CCTTTGACCTGTGGTGTGCT 60.466 55.000 0.00 0.00 35.25 4.40
2405 2617 2.032981 CCTTTGACCTGTGGTGTGC 58.967 57.895 0.00 0.00 35.25 4.57
2406 2618 0.751277 TGCCTTTGACCTGTGGTGTG 60.751 55.000 0.00 0.00 35.25 3.82
2407 2619 0.466189 CTGCCTTTGACCTGTGGTGT 60.466 55.000 0.00 0.00 35.25 4.16
2408 2620 1.799258 GCTGCCTTTGACCTGTGGTG 61.799 60.000 0.00 0.00 35.25 4.17
2409 2621 1.529244 GCTGCCTTTGACCTGTGGT 60.529 57.895 0.00 0.00 39.44 4.16
2410 2622 1.529010 TGCTGCCTTTGACCTGTGG 60.529 57.895 0.00 0.00 0.00 4.17
2411 2623 1.656441 GTGCTGCCTTTGACCTGTG 59.344 57.895 0.00 0.00 0.00 3.66
2412 2624 1.893808 CGTGCTGCCTTTGACCTGT 60.894 57.895 0.00 0.00 0.00 4.00
2445 2662 0.661552 GGTAGCTGCATGCATGTCAG 59.338 55.000 30.51 30.51 45.94 3.51
2446 2663 0.035247 TGGTAGCTGCATGCATGTCA 60.035 50.000 26.79 22.09 45.94 3.58
2447 2664 0.379669 GTGGTAGCTGCATGCATGTC 59.620 55.000 26.79 18.98 45.94 3.06
2448 2665 1.033746 GGTGGTAGCTGCATGCATGT 61.034 55.000 26.79 13.89 45.94 3.21
2482 2707 4.148825 AGAAGCACGGCGGCTAGG 62.149 66.667 20.24 2.35 45.07 3.02


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

AutoCloner maintained by Alex Coulton.