Multiple sequence alignment - TraesCS2A01G148400

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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 TraesCS2A01G148400 chr2A 100.000 2441 0 0 1 2441 94317368 94319808 0.000000e+00 4508.0
1 TraesCS2A01G148400 chr2A 89.256 847 69 4 668 1495 94447034 94447877 0.000000e+00 1040.0
2 TraesCS2A01G148400 chr2A 91.554 663 49 5 1063 1721 94324405 94325064 0.000000e+00 907.0
3 TraesCS2A01G148400 chr2A 94.157 445 26 0 1528 1972 94447880 94448324 0.000000e+00 678.0
4 TraesCS2A01G148400 chr2A 94.150 359 19 2 2009 2367 94448333 94448689 1.650000e-151 545.0
5 TraesCS2A01G148400 chr2A 95.556 90 4 0 2352 2441 94449307 94449396 7.030000e-31 145.0
6 TraesCS2A01G148400 chr2A 92.593 54 4 0 531 584 90030216 90030163 7.240000e-11 78.7
7 TraesCS2A01G148400 chr2A 88.710 62 4 3 531 592 94291106 94291164 3.370000e-09 73.1
8 TraesCS2A01G148400 chr2D 89.046 1771 132 20 17 1755 96083452 96085192 0.000000e+00 2139.0
9 TraesCS2A01G148400 chr2D 88.770 1772 139 19 17 1755 96292905 96294649 0.000000e+00 2115.0
10 TraesCS2A01G148400 chr2D 88.045 1790 131 31 1 1755 95786627 95788368 0.000000e+00 2043.0
11 TraesCS2A01G148400 chr2D 88.667 1500 123 20 293 1755 95917196 95918685 0.000000e+00 1784.0
12 TraesCS2A01G148400 chr2D 83.624 287 34 3 1 286 95915137 95915411 8.660000e-65 257.0
13 TraesCS2A01G148400 chr2D 78.676 136 16 9 174 307 95786900 95787024 7.240000e-11 78.7
14 TraesCS2A01G148400 chrUn 88.845 1013 78 14 666 1655 17383315 17384315 0.000000e+00 1212.0
15 TraesCS2A01G148400 chrUn 87.812 681 58 11 1 668 17382620 17383288 0.000000e+00 774.0
16 TraesCS2A01G148400 chrUn 90.954 409 29 7 1218 1620 477994025 477993619 5.940000e-151 544.0
17 TraesCS2A01G148400 chr7A 77.778 162 30 5 750 908 574754198 574754356 7.190000e-16 95.3
18 TraesCS2A01G148400 chr7B 77.439 164 27 8 750 908 535614669 535614827 3.340000e-14 89.8
19 TraesCS2A01G148400 chr3A 87.013 77 6 2 1192 1266 628219365 628219291 1.560000e-12 84.2
20 TraesCS2A01G148400 chr3A 92.593 54 4 0 804 857 628219772 628219719 7.240000e-11 78.7
21 TraesCS2A01G148400 chr2B 90.323 62 3 3 531 592 147491598 147491656 7.240000e-11 78.7
22 TraesCS2A01G148400 chr6D 77.953 127 23 4 449 573 448595461 448595584 9.360000e-10 75.0
23 TraesCS2A01G148400 chr1D 93.333 45 3 0 1013 1057 62890537 62890581 1.570000e-07 67.6
24 TraesCS2A01G148400 chr1B 93.333 45 3 0 1013 1057 100422987 100423031 1.570000e-07 67.6


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 TraesCS2A01G148400 chr2A 94317368 94319808 2440 False 4508.00 4508 100.00000 1 2441 1 chr2A.!!$F2 2440
1 TraesCS2A01G148400 chr2A 94324405 94325064 659 False 907.00 907 91.55400 1063 1721 1 chr2A.!!$F3 658
2 TraesCS2A01G148400 chr2A 94447034 94449396 2362 False 602.00 1040 93.27975 668 2441 4 chr2A.!!$F4 1773
3 TraesCS2A01G148400 chr2D 96083452 96085192 1740 False 2139.00 2139 89.04600 17 1755 1 chr2D.!!$F1 1738
4 TraesCS2A01G148400 chr2D 96292905 96294649 1744 False 2115.00 2115 88.77000 17 1755 1 chr2D.!!$F2 1738
5 TraesCS2A01G148400 chr2D 95786627 95788368 1741 False 1060.85 2043 83.36050 1 1755 2 chr2D.!!$F3 1754
6 TraesCS2A01G148400 chr2D 95915137 95918685 3548 False 1020.50 1784 86.14550 1 1755 2 chr2D.!!$F4 1754
7 TraesCS2A01G148400 chrUn 17382620 17384315 1695 False 993.00 1212 88.32850 1 1655 2 chrUn.!!$F1 1654

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
148 149 0.031917 TACACCTATCCCAAGCCCGA 60.032 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 3862 0.180642 ATGGAGTGCATGGCAGAGAG 59.819 55.0 0.0 0.0 40.08 3.2 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
43 44 1.534729 TCGAGCAAGAGTAGCTGACA 58.465 50.000 0.00 0.00 43.58 3.58
107 108 2.968206 GTACTCGGTTCCGTGGCT 59.032 61.111 15.78 1.15 0.00 4.75
115 116 2.597217 TTCCGTGGCTTGCCAAGG 60.597 61.111 31.35 31.35 39.96 3.61
121 122 2.272146 GGCTTGCCAAGGATCCGA 59.728 61.111 5.98 0.00 0.00 4.55
143 144 1.120530 ACGGCTACACCTATCCCAAG 58.879 55.000 0.00 0.00 35.61 3.61
144 145 0.249911 CGGCTACACCTATCCCAAGC 60.250 60.000 0.00 0.00 35.61 4.01
145 146 0.108774 GGCTACACCTATCCCAAGCC 59.891 60.000 0.00 0.00 42.40 4.35
146 147 0.108774 GCTACACCTATCCCAAGCCC 59.891 60.000 0.00 0.00 0.00 5.19
147 148 0.393077 CTACACCTATCCCAAGCCCG 59.607 60.000 0.00 0.00 0.00 6.13
148 149 0.031917 TACACCTATCCCAAGCCCGA 60.032 55.000 0.00 0.00 0.00 5.14
167 168 0.697854 ACCCCACTCCCATCATACCC 60.698 60.000 0.00 0.00 0.00 3.69
168 169 0.401979 CCCCACTCCCATCATACCCT 60.402 60.000 0.00 0.00 0.00 4.34
179 180 4.424867 ATACCCTCGCCCCCACCA 62.425 66.667 0.00 0.00 0.00 4.17
192 193 4.003788 CACCACCGGCGACTCCTT 62.004 66.667 9.30 0.00 0.00 3.36
209 211 1.961180 CTTCGTCGAGCCTTCCCCAT 61.961 60.000 0.00 0.00 0.00 4.00
217 219 2.308722 GCCTTCCCCATCTCCACCA 61.309 63.158 0.00 0.00 0.00 4.17
219 221 0.916358 CCTTCCCCATCTCCACCAGT 60.916 60.000 0.00 0.00 0.00 4.00
228 230 3.370104 CATCTCCACCAGTTACTCCTCT 58.630 50.000 0.00 0.00 0.00 3.69
240 242 2.041508 TCCTCTGCCCAGCCCTAG 60.042 66.667 0.00 0.00 0.00 3.02
282 284 2.941025 CACCCCCACTCCCACCAT 60.941 66.667 0.00 0.00 0.00 3.55
308 2088 2.513897 CGCCCCCATCGGTTTCTC 60.514 66.667 0.00 0.00 0.00 2.87
319 2099 2.265096 GGTTTCTCCTCCGACGAGT 58.735 57.895 0.00 0.00 33.93 4.18
341 2127 2.781174 CCTACTCCACCTCCTACTCTCT 59.219 54.545 0.00 0.00 0.00 3.10
343 2129 1.567175 ACTCCACCTCCTACTCTCTCC 59.433 57.143 0.00 0.00 0.00 3.71
353 2139 1.581923 TACTCTCTCCCCGAGCCCTT 61.582 60.000 0.00 0.00 39.70 3.95
366 2152 2.367378 CCCTTCTCCTACCCCGGT 59.633 66.667 0.00 0.00 0.00 5.28
375 2161 0.542232 CCTACCCCGGTCTATCCCAG 60.542 65.000 0.00 0.00 0.00 4.45
391 2183 4.918360 AGCCCCACTCCCACCACA 62.918 66.667 0.00 0.00 0.00 4.17
416 2208 2.687566 CCCCACCGGCTTCTACCT 60.688 66.667 0.00 0.00 0.00 3.08
423 2215 0.396695 CCGGCTTCTACCTCTACCCA 60.397 60.000 0.00 0.00 0.00 4.51
584 2383 4.700213 GCTTTGTCCAGGTACACATACATT 59.300 41.667 0.00 0.00 32.40 2.71
587 2386 5.084818 TGTCCAGGTACACATACATTCAG 57.915 43.478 0.00 0.00 32.40 3.02
610 2411 4.739046 CGCAAGTGAAGTTTGAGAGATT 57.261 40.909 0.00 0.00 0.00 2.40
611 2412 4.461405 CGCAAGTGAAGTTTGAGAGATTG 58.539 43.478 0.00 0.00 0.00 2.67
615 2416 7.201591 CGCAAGTGAAGTTTGAGAGATTGATAT 60.202 37.037 0.00 0.00 0.00 1.63
616 2417 9.102757 GCAAGTGAAGTTTGAGAGATTGATATA 57.897 33.333 0.00 0.00 0.00 0.86
618 2419 8.864069 AGTGAAGTTTGAGAGATTGATATACG 57.136 34.615 0.00 0.00 0.00 3.06
619 2420 7.436673 AGTGAAGTTTGAGAGATTGATATACGC 59.563 37.037 0.00 0.00 0.00 4.42
620 2421 6.701841 TGAAGTTTGAGAGATTGATATACGCC 59.298 38.462 0.00 0.00 0.00 5.68
621 2422 6.412362 AGTTTGAGAGATTGATATACGCCT 57.588 37.500 0.00 0.00 0.00 5.52
622 2423 7.526142 AGTTTGAGAGATTGATATACGCCTA 57.474 36.000 0.00 0.00 0.00 3.93
665 2496 6.710597 TGAGAAGCTAACTATGGTATCGTT 57.289 37.500 0.00 0.00 0.00 3.85
679 2510 1.981256 ATCGTTGCTTTCAGGGTTGT 58.019 45.000 0.00 0.00 0.00 3.32
694 2525 1.677217 GGTTGTGATGCCTCTGTCCTC 60.677 57.143 0.00 0.00 0.00 3.71
733 2564 1.078143 GCCTGAACCGGAGATGCTT 60.078 57.895 9.46 0.00 0.00 3.91
929 2777 2.442272 ACGGATGAGACCCTCCCG 60.442 66.667 9.16 9.16 39.80 5.14
935 2783 0.252742 ATGAGACCCTCCCGAACCTT 60.253 55.000 0.00 0.00 0.00 3.50
944 2792 2.933834 CCGAACCTTCCCCCACCT 60.934 66.667 0.00 0.00 0.00 4.00
956 2804 2.268076 CCCACCTTTCGCCAACCTG 61.268 63.158 0.00 0.00 0.00 4.00
961 2809 1.628846 ACCTTTCGCCAACCTGACTAT 59.371 47.619 0.00 0.00 0.00 2.12
974 2822 6.406370 CAACCTGACTATCCTCACACAAATA 58.594 40.000 0.00 0.00 0.00 1.40
1000 2848 2.586425 CAAGAAGGGACTCAGCCAAAA 58.414 47.619 0.00 0.00 38.49 2.44
1001 2849 3.160269 CAAGAAGGGACTCAGCCAAAAT 58.840 45.455 0.00 0.00 38.49 1.82
1003 2851 2.108952 AGAAGGGACTCAGCCAAAATGT 59.891 45.455 0.00 0.00 38.49 2.71
1011 2861 0.031857 CAGCCAAAATGTCGGTTGCA 59.968 50.000 0.00 0.00 0.00 4.08
1098 2948 0.462937 CCAACGACAACTCCACCACA 60.463 55.000 0.00 0.00 0.00 4.17
1113 2963 2.173669 CACATCGATGGACGCCACC 61.174 63.158 28.09 0.00 42.26 4.61
1131 2981 1.608717 CCTACGCTGGGAAGCTGACT 61.609 60.000 0.00 0.00 0.00 3.41
1158 3008 2.063979 CCCTGCCGGTAGTGATCCA 61.064 63.158 18.86 0.00 0.00 3.41
1356 3206 0.617935 TCGAGGATGCCATGGTGAAA 59.382 50.000 14.67 0.00 0.00 2.69
1368 3218 4.686670 GCCATGGTGAAAATGGGCAATATT 60.687 41.667 14.67 0.00 44.13 1.28
1473 3324 6.211584 TCAAGGGTGGAGACTATATATTCAGC 59.788 42.308 3.24 0.00 0.00 4.26
1478 3329 4.462834 TGGAGACTATATATTCAGCCGTGG 59.537 45.833 3.24 0.00 0.00 4.94
1485 3336 2.715737 TATTCAGCCGTGGTTTTTGC 57.284 45.000 0.00 0.00 0.00 3.68
1505 3360 1.338105 CGTGTGCCTTCTGATCTTCCA 60.338 52.381 0.00 0.00 0.00 3.53
1550 3406 1.504359 TTCGCTCGTCGGTTCATTTT 58.496 45.000 0.00 0.00 39.05 1.82
1617 3473 0.388907 CGGGCAATGCTTTTCACTGG 60.389 55.000 4.82 0.00 0.00 4.00
1755 3613 3.118738 CCTAGAGTGTGTATGGTCAACCC 60.119 52.174 0.00 0.00 34.29 4.11
1801 3659 4.523173 CCTTTTCTTTTGAGGGAGGGTAAC 59.477 45.833 0.00 0.00 0.00 2.50
1803 3661 4.799715 TTCTTTTGAGGGAGGGTAACAA 57.200 40.909 0.00 0.00 39.74 2.83
1836 3694 8.485976 ACTAAGTGCTCTATCAAAATCAGTTC 57.514 34.615 0.00 0.00 0.00 3.01
1846 3704 8.474831 TCTATCAAAATCAGTTCGTATGAAGGA 58.525 33.333 0.00 0.00 33.98 3.36
1847 3705 6.721571 TCAAAATCAGTTCGTATGAAGGAC 57.278 37.500 0.00 0.00 33.98 3.85
1871 3729 4.342665 CCCTACTTCTTACTCCTAAGCCAG 59.657 50.000 0.00 0.00 30.85 4.85
1899 3757 2.783510 TCTGGTTCCTCCCTTTTCAGTT 59.216 45.455 0.00 0.00 34.77 3.16
1956 3814 7.768582 TGTGAAACATCTTGTCTTCTTCTTGTA 59.231 33.333 0.00 0.00 45.67 2.41
1972 3830 7.704271 TCTTCTTGTATCGGTGTCTAATACTG 58.296 38.462 0.00 0.00 0.00 2.74
1974 3832 7.400599 TCTTGTATCGGTGTCTAATACTGTT 57.599 36.000 0.00 0.00 0.00 3.16
1975 3833 7.833786 TCTTGTATCGGTGTCTAATACTGTTT 58.166 34.615 0.00 0.00 0.00 2.83
1976 3834 7.758076 TCTTGTATCGGTGTCTAATACTGTTTG 59.242 37.037 0.00 0.00 0.00 2.93
1977 3835 6.334989 TGTATCGGTGTCTAATACTGTTTGG 58.665 40.000 0.00 0.00 0.00 3.28
1978 3836 4.877378 TCGGTGTCTAATACTGTTTGGT 57.123 40.909 0.00 0.00 0.00 3.67
1979 3837 5.217978 TCGGTGTCTAATACTGTTTGGTT 57.782 39.130 0.00 0.00 0.00 3.67
1980 3838 5.613329 TCGGTGTCTAATACTGTTTGGTTT 58.387 37.500 0.00 0.00 0.00 3.27
1981 3839 6.757237 TCGGTGTCTAATACTGTTTGGTTTA 58.243 36.000 0.00 0.00 0.00 2.01
1982 3840 7.388437 TCGGTGTCTAATACTGTTTGGTTTAT 58.612 34.615 0.00 0.00 0.00 1.40
1983 3841 7.546667 TCGGTGTCTAATACTGTTTGGTTTATC 59.453 37.037 0.00 0.00 0.00 1.75
1984 3842 7.332430 CGGTGTCTAATACTGTTTGGTTTATCA 59.668 37.037 0.00 0.00 0.00 2.15
1985 3843 9.174166 GGTGTCTAATACTGTTTGGTTTATCAT 57.826 33.333 0.00 0.00 0.00 2.45
1986 3844 9.988350 GTGTCTAATACTGTTTGGTTTATCATG 57.012 33.333 0.00 0.00 0.00 3.07
1987 3845 8.673711 TGTCTAATACTGTTTGGTTTATCATGC 58.326 33.333 0.00 0.00 0.00 4.06
1988 3846 8.673711 GTCTAATACTGTTTGGTTTATCATGCA 58.326 33.333 0.00 0.00 0.00 3.96
1989 3847 9.407380 TCTAATACTGTTTGGTTTATCATGCAT 57.593 29.630 0.00 0.00 0.00 3.96
1990 3848 9.454585 CTAATACTGTTTGGTTTATCATGCATG 57.545 33.333 21.07 21.07 0.00 4.06
1991 3849 5.726980 ACTGTTTGGTTTATCATGCATGT 57.273 34.783 25.43 15.34 0.00 3.21
1992 3850 5.713025 ACTGTTTGGTTTATCATGCATGTC 58.287 37.500 25.43 11.91 0.00 3.06
1993 3851 5.477984 ACTGTTTGGTTTATCATGCATGTCT 59.522 36.000 25.43 16.39 0.00 3.41
1994 3852 5.953183 TGTTTGGTTTATCATGCATGTCTC 58.047 37.500 25.43 12.52 0.00 3.36
1995 3853 5.711506 TGTTTGGTTTATCATGCATGTCTCT 59.288 36.000 25.43 11.78 0.00 3.10
1996 3854 6.209192 TGTTTGGTTTATCATGCATGTCTCTT 59.791 34.615 25.43 9.68 0.00 2.85
1997 3855 6.839124 TTGGTTTATCATGCATGTCTCTTT 57.161 33.333 25.43 8.09 0.00 2.52
1998 3856 7.936496 TTGGTTTATCATGCATGTCTCTTTA 57.064 32.000 25.43 5.50 0.00 1.85
1999 3857 8.523915 TTGGTTTATCATGCATGTCTCTTTAT 57.476 30.769 25.43 12.54 0.00 1.40
2000 3858 8.523915 TGGTTTATCATGCATGTCTCTTTATT 57.476 30.769 25.43 4.37 0.00 1.40
2001 3859 8.970020 TGGTTTATCATGCATGTCTCTTTATTT 58.030 29.630 25.43 3.00 0.00 1.40
2002 3860 9.807649 GGTTTATCATGCATGTCTCTTTATTTT 57.192 29.630 25.43 0.00 0.00 1.82
2005 3863 7.893124 ATCATGCATGTCTCTTTATTTTCCT 57.107 32.000 25.43 0.00 0.00 3.36
2006 3864 7.325660 TCATGCATGTCTCTTTATTTTCCTC 57.674 36.000 25.43 0.00 0.00 3.71
2007 3865 7.114754 TCATGCATGTCTCTTTATTTTCCTCT 58.885 34.615 25.43 0.00 0.00 3.69
2019 3877 0.694771 TTTCCTCTCTGCCATGCACT 59.305 50.000 0.00 0.00 33.79 4.40
2020 3878 0.251354 TTCCTCTCTGCCATGCACTC 59.749 55.000 0.00 0.00 33.79 3.51
2055 3913 7.414436 TCCACATCTTTTGTTAGAAAACTTCG 58.586 34.615 0.00 0.00 36.00 3.79
2094 3952 1.907807 GTGCACTTTGGCCCATCCA 60.908 57.895 10.32 0.00 44.85 3.41
2121 3979 4.245660 TGAACAAGAAGCTTATGACTCCG 58.754 43.478 16.35 1.05 0.00 4.63
2139 3997 3.511699 TCCGTGAATCTGAAGATTGTCG 58.488 45.455 10.23 12.76 44.14 4.35
2214 4072 7.903995 AGCAGTTCAAATTTTTCAAAAGACA 57.096 28.000 0.00 0.00 0.00 3.41
2218 4076 9.316859 CAGTTCAAATTTTTCAAAAGACACAAC 57.683 29.630 0.00 0.00 0.00 3.32
2251 4109 2.031333 GCAGACTTGAGCACTTTTCCTG 60.031 50.000 0.00 0.00 0.00 3.86
2253 4111 3.003068 CAGACTTGAGCACTTTTCCTGTG 59.997 47.826 0.00 0.00 38.36 3.66
2278 4136 1.405821 GCGAGAGGAATCGAAGAAGGA 59.594 52.381 0.00 0.00 45.56 3.36
2279 4137 2.542824 GCGAGAGGAATCGAAGAAGGAG 60.543 54.545 0.00 0.00 45.56 3.69
2280 4138 2.034053 CGAGAGGAATCGAAGAAGGAGG 59.966 54.545 0.00 0.00 45.56 4.30
2327 4185 6.483974 TGATTTGAAAATGCAAGCATCTTTGT 59.516 30.769 8.14 0.00 35.31 2.83
2333 4191 7.495279 TGAAAATGCAAGCATCTTTGTAAAGTT 59.505 29.630 8.14 0.00 37.31 2.66
2340 4198 7.116805 GCAAGCATCTTTGTAAAGTTTTGCTAT 59.883 33.333 20.81 13.76 41.77 2.97
2358 4216 6.682423 TGCTATGTCATACATGAAACAAGG 57.318 37.500 0.00 0.00 39.53 3.61
2382 4873 7.560991 AGGGCACATGATATTATCAGACAAAAA 59.439 33.333 11.77 0.00 43.53 1.94
2409 4900 5.915196 GCATTACTTGTGGACAAAGTTTCTC 59.085 40.000 0.00 0.00 35.15 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.224548 TGCTCGATCGAGGGAAGATAGA 60.225 50.000 38.18 5.94 42.19 1.98
11 12 2.271944 TGCTCGATCGAGGGAAGATA 57.728 50.000 38.18 10.15 42.19 1.98
43 44 1.519719 GCCATCTTCCTCTGCTCGT 59.480 57.895 0.00 0.00 0.00 4.18
92 93 2.030562 CAAGCCACGGAACCGAGT 59.969 61.111 20.14 0.00 42.83 4.18
107 108 0.174845 CGTAGTCGGATCCTTGGCAA 59.825 55.000 10.75 0.00 0.00 4.52
121 122 1.216175 TGGGATAGGTGTAGCCGTAGT 59.784 52.381 0.00 0.00 43.70 2.73
144 145 3.480133 GATGGGAGTGGGGTCGGG 61.480 72.222 0.00 0.00 0.00 5.14
145 146 0.762842 TATGATGGGAGTGGGGTCGG 60.763 60.000 0.00 0.00 0.00 4.79
146 147 0.393077 GTATGATGGGAGTGGGGTCG 59.607 60.000 0.00 0.00 0.00 4.79
147 148 0.765510 GGTATGATGGGAGTGGGGTC 59.234 60.000 0.00 0.00 0.00 4.46
148 149 0.697854 GGGTATGATGGGAGTGGGGT 60.698 60.000 0.00 0.00 0.00 4.95
185 186 0.179158 GAAGGCTCGACGAAGGAGTC 60.179 60.000 0.00 0.00 36.40 3.36
192 193 2.363795 ATGGGGAAGGCTCGACGA 60.364 61.111 0.00 0.00 0.00 4.20
195 196 1.762460 GGAGATGGGGAAGGCTCGA 60.762 63.158 0.00 0.00 0.00 4.04
209 211 2.808919 CAGAGGAGTAACTGGTGGAGA 58.191 52.381 0.00 0.00 0.00 3.71
217 219 1.268283 GGCTGGGCAGAGGAGTAACT 61.268 60.000 0.00 0.00 0.00 2.24
219 221 1.995626 GGGCTGGGCAGAGGAGTAA 60.996 63.158 0.00 0.00 0.00 2.24
248 250 2.529753 GGGATAGCCCGGGGTAGA 59.470 66.667 33.98 18.06 46.48 2.59
265 267 2.941025 ATGGTGGGAGTGGGGGTG 60.941 66.667 0.00 0.00 0.00 4.61
267 269 4.447342 GCATGGTGGGAGTGGGGG 62.447 72.222 0.00 0.00 0.00 5.40
308 2088 0.814812 GGAGTAGGACTCGTCGGAGG 60.815 65.000 0.73 0.00 45.96 4.30
319 2099 2.778850 GAGAGTAGGAGGTGGAGTAGGA 59.221 54.545 0.00 0.00 0.00 2.94
341 2127 2.322156 TAGGAGAAGGGCTCGGGGA 61.322 63.158 0.00 0.00 44.91 4.81
343 2129 2.134933 GGTAGGAGAAGGGCTCGGG 61.135 68.421 0.00 0.00 44.91 5.14
353 2139 0.776176 GGATAGACCGGGGTAGGAGA 59.224 60.000 6.32 0.00 34.73 3.71
366 2152 1.074471 GGAGTGGGGCTGGGATAGA 60.074 63.158 0.00 0.00 0.00 1.98
375 2161 4.660938 GTGTGGTGGGAGTGGGGC 62.661 72.222 0.00 0.00 0.00 5.80
416 2208 1.306141 CAGGTGGAGGCTGGGTAGA 60.306 63.158 0.00 0.00 0.00 2.59
423 2215 3.644606 CAGTGGCAGGTGGAGGCT 61.645 66.667 0.00 0.00 0.00 4.58
544 2343 1.621992 AGCAGTCGTGGAAGAAGAGA 58.378 50.000 0.00 0.00 0.00 3.10
584 2383 2.866156 CTCAAACTTCACTTGCGTCTGA 59.134 45.455 0.00 0.00 0.00 3.27
587 2386 3.123804 TCTCTCAAACTTCACTTGCGTC 58.876 45.455 0.00 0.00 0.00 5.19
610 2411 5.243060 AGTGCACAACTATAGGCGTATATCA 59.757 40.000 21.04 0.00 37.36 2.15
611 2412 5.573282 CAGTGCACAACTATAGGCGTATATC 59.427 44.000 21.04 0.00 36.83 1.63
615 2416 2.737359 GCAGTGCACAACTATAGGCGTA 60.737 50.000 21.04 0.00 36.83 4.42
616 2417 2.007049 GCAGTGCACAACTATAGGCGT 61.007 52.381 21.04 0.00 36.83 5.68
618 2419 1.737838 TGCAGTGCACAACTATAGGC 58.262 50.000 21.04 9.34 36.83 3.93
665 2496 0.961019 GCATCACAACCCTGAAAGCA 59.039 50.000 0.00 0.00 0.00 3.91
679 2510 0.041684 TCAGGAGGACAGAGGCATCA 59.958 55.000 0.00 0.00 0.00 3.07
708 2539 2.597217 CCGGTTCAGGCTTGCCAA 60.597 61.111 14.54 0.00 0.00 4.52
808 2639 4.357947 GCGCAGGAGACGACACCA 62.358 66.667 0.30 0.00 0.00 4.17
910 2741 1.381327 GGGAGGGTCTCATCCGTCA 60.381 63.158 7.53 0.00 44.27 4.35
929 2777 0.608308 CGAAAGGTGGGGGAAGGTTC 60.608 60.000 0.00 0.00 0.00 3.62
935 2783 3.179339 TTGGCGAAAGGTGGGGGA 61.179 61.111 0.00 0.00 0.00 4.81
944 2792 1.906574 AGGATAGTCAGGTTGGCGAAA 59.093 47.619 0.00 0.00 0.00 3.46
956 2804 5.177696 GGCGAATATTTGTGTGAGGATAGTC 59.822 44.000 4.60 0.00 0.00 2.59
961 2809 3.342377 TGGCGAATATTTGTGTGAGGA 57.658 42.857 4.60 0.00 0.00 3.71
974 2822 0.984230 TGAGTCCCTTCTTGGCGAAT 59.016 50.000 0.00 0.00 0.00 3.34
1041 2891 2.286523 ACGGAAGGAGGAGCAGTGG 61.287 63.158 0.00 0.00 0.00 4.00
1098 2948 1.740285 GTAGGTGGCGTCCATCGAT 59.260 57.895 0.00 0.00 40.09 3.59
1158 3008 3.307906 TAGTCCTGCGGCACCGTT 61.308 61.111 11.27 0.00 42.09 4.44
1356 3206 4.870636 TCTTCACCTCAATATTGCCCATT 58.129 39.130 10.76 0.00 0.00 3.16
1368 3218 3.706055 GGTGCTGTTCTTCACCTCA 57.294 52.632 4.31 0.00 46.90 3.86
1473 3324 2.227568 GCACACGCAAAAACCACGG 61.228 57.895 0.00 0.00 38.36 4.94
1478 3329 1.199624 CAGAAGGCACACGCAAAAAC 58.800 50.000 0.00 0.00 41.24 2.43
1485 3336 1.338105 TGGAAGATCAGAAGGCACACG 60.338 52.381 0.00 0.00 0.00 4.49
1533 3388 3.061563 TGAATAAAATGAACCGACGAGCG 59.938 43.478 0.00 0.00 40.47 5.03
1758 3616 1.808945 GAGTGTTTGCATCCAGTCAGG 59.191 52.381 13.35 0.00 39.47 3.86
1759 3617 1.808945 GGAGTGTTTGCATCCAGTCAG 59.191 52.381 17.75 0.00 33.57 3.51
1773 3631 4.464947 CTCCCTCAAAAGAAAAGGAGTGT 58.535 43.478 0.00 0.00 36.87 3.55
1774 3632 3.823304 CCTCCCTCAAAAGAAAAGGAGTG 59.177 47.826 0.00 0.00 39.43 3.51
1801 3659 8.932945 TGATAGAGCACTTAGTAGAATTGTTG 57.067 34.615 0.00 0.00 0.00 3.33
1803 3661 9.944376 TTTTGATAGAGCACTTAGTAGAATTGT 57.056 29.630 0.00 0.00 0.00 2.71
1836 3694 3.297736 AGAAGTAGGGGTCCTTCATACG 58.702 50.000 0.00 0.00 39.61 3.06
1846 3704 4.288398 GCTTAGGAGTAAGAAGTAGGGGT 58.712 47.826 0.00 0.00 38.39 4.95
1847 3705 3.642377 GGCTTAGGAGTAAGAAGTAGGGG 59.358 52.174 0.00 0.00 38.39 4.79
1899 3757 9.566432 AAACCAAAAATATGCCAGATGTAAAAA 57.434 25.926 0.00 0.00 0.00 1.94
1956 3814 5.416271 ACCAAACAGTATTAGACACCGAT 57.584 39.130 0.00 0.00 0.00 4.18
1972 3830 6.199937 AGAGACATGCATGATAAACCAAAC 57.800 37.500 32.75 10.91 0.00 2.93
1974 3832 6.839124 AAAGAGACATGCATGATAAACCAA 57.161 33.333 32.75 0.00 0.00 3.67
1975 3833 8.523915 AATAAAGAGACATGCATGATAAACCA 57.476 30.769 32.75 12.78 0.00 3.67
1976 3834 9.807649 AAAATAAAGAGACATGCATGATAAACC 57.192 29.630 32.75 14.22 0.00 3.27
1979 3837 9.412460 AGGAAAATAAAGAGACATGCATGATAA 57.588 29.630 32.75 10.74 0.00 1.75
1980 3838 8.985315 AGGAAAATAAAGAGACATGCATGATA 57.015 30.769 32.75 14.57 0.00 2.15
1981 3839 7.778853 AGAGGAAAATAAAGAGACATGCATGAT 59.221 33.333 32.75 20.01 0.00 2.45
1982 3840 7.114754 AGAGGAAAATAAAGAGACATGCATGA 58.885 34.615 32.75 9.14 0.00 3.07
1983 3841 7.282675 AGAGAGGAAAATAAAGAGACATGCATG 59.717 37.037 25.09 25.09 0.00 4.06
1984 3842 7.282675 CAGAGAGGAAAATAAAGAGACATGCAT 59.717 37.037 0.00 0.00 0.00 3.96
1985 3843 6.596888 CAGAGAGGAAAATAAAGAGACATGCA 59.403 38.462 0.00 0.00 0.00 3.96
1986 3844 6.458070 GCAGAGAGGAAAATAAAGAGACATGC 60.458 42.308 0.00 0.00 0.00 4.06
1987 3845 6.038050 GGCAGAGAGGAAAATAAAGAGACATG 59.962 42.308 0.00 0.00 0.00 3.21
1988 3846 6.118852 GGCAGAGAGGAAAATAAAGAGACAT 58.881 40.000 0.00 0.00 0.00 3.06
1989 3847 5.013079 TGGCAGAGAGGAAAATAAAGAGACA 59.987 40.000 0.00 0.00 0.00 3.41
1990 3848 5.491982 TGGCAGAGAGGAAAATAAAGAGAC 58.508 41.667 0.00 0.00 0.00 3.36
1991 3849 5.762179 TGGCAGAGAGGAAAATAAAGAGA 57.238 39.130 0.00 0.00 0.00 3.10
1992 3850 5.221009 GCATGGCAGAGAGGAAAATAAAGAG 60.221 44.000 0.00 0.00 0.00 2.85
1993 3851 4.641989 GCATGGCAGAGAGGAAAATAAAGA 59.358 41.667 0.00 0.00 0.00 2.52
1994 3852 4.400251 TGCATGGCAGAGAGGAAAATAAAG 59.600 41.667 0.00 0.00 33.32 1.85
1995 3853 4.158394 GTGCATGGCAGAGAGGAAAATAAA 59.842 41.667 0.00 0.00 40.08 1.40
1996 3854 3.696051 GTGCATGGCAGAGAGGAAAATAA 59.304 43.478 0.00 0.00 40.08 1.40
1997 3855 3.054139 AGTGCATGGCAGAGAGGAAAATA 60.054 43.478 0.00 0.00 40.08 1.40
1998 3856 2.097825 GTGCATGGCAGAGAGGAAAAT 58.902 47.619 0.00 0.00 40.08 1.82
1999 3857 1.074405 AGTGCATGGCAGAGAGGAAAA 59.926 47.619 0.00 0.00 40.08 2.29
2000 3858 0.694771 AGTGCATGGCAGAGAGGAAA 59.305 50.000 0.00 0.00 40.08 3.13
2001 3859 0.251354 GAGTGCATGGCAGAGAGGAA 59.749 55.000 0.00 0.00 40.08 3.36
2002 3860 1.620739 GGAGTGCATGGCAGAGAGGA 61.621 60.000 0.00 0.00 40.08 3.71
2003 3861 1.153208 GGAGTGCATGGCAGAGAGG 60.153 63.158 0.00 0.00 40.08 3.69
2004 3862 0.180642 ATGGAGTGCATGGCAGAGAG 59.819 55.000 0.00 0.00 40.08 3.20
2005 3863 0.622136 AATGGAGTGCATGGCAGAGA 59.378 50.000 0.00 0.00 40.08 3.10
2006 3864 2.158856 TCTAATGGAGTGCATGGCAGAG 60.159 50.000 0.00 0.00 40.08 3.35
2007 3865 1.839354 TCTAATGGAGTGCATGGCAGA 59.161 47.619 0.00 0.00 40.08 4.26
2019 3877 8.421249 AACAAAAGATGTGGATTTCTAATGGA 57.579 30.769 0.00 0.00 42.99 3.41
2020 3878 9.793252 CTAACAAAAGATGTGGATTTCTAATGG 57.207 33.333 0.00 0.00 42.99 3.16
2077 3935 2.525075 TGGATGGGCCAAAGTGCA 59.475 55.556 11.89 2.15 45.87 4.57
2094 3952 8.084684 GGAGTCATAAGCTTCTTGTTCAATTTT 58.915 33.333 0.00 0.00 0.00 1.82
2095 3953 7.573843 CGGAGTCATAAGCTTCTTGTTCAATTT 60.574 37.037 0.00 0.00 0.00 1.82
2121 3979 4.499183 AGTCCGACAATCTTCAGATTCAC 58.501 43.478 0.40 0.00 42.41 3.18
2166 4024 7.334421 GCTTATAGAATCTCTGTTTGTGGTTGA 59.666 37.037 0.00 0.00 0.00 3.18
2251 4109 0.716108 CGATTCCTCTCGCACAACAC 59.284 55.000 0.00 0.00 0.00 3.32
2253 4111 1.656095 CTTCGATTCCTCTCGCACAAC 59.344 52.381 0.00 0.00 38.52 3.32
2278 4136 7.060421 CACTATATGTTCCACAAAATACCCCT 58.940 38.462 0.00 0.00 0.00 4.79
2279 4137 7.057894 TCACTATATGTTCCACAAAATACCCC 58.942 38.462 0.00 0.00 0.00 4.95
2280 4138 8.691661 ATCACTATATGTTCCACAAAATACCC 57.308 34.615 0.00 0.00 0.00 3.69
2333 4191 7.362834 CCCTTGTTTCATGTATGACATAGCAAA 60.363 37.037 0.00 0.00 36.53 3.68
2340 4198 3.505680 GTGCCCTTGTTTCATGTATGACA 59.494 43.478 0.00 0.00 36.36 3.58
2382 4873 5.789643 ACTTTGTCCACAAGTAATGCATT 57.210 34.783 17.56 17.56 37.15 3.56
2394 4885 4.083802 CGAATGGAGAGAAACTTTGTCCAC 60.084 45.833 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.