Multiple sequence alignment - TraesCS1D01G108800

Loading Multiple Alignment...

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 TraesCS1D01G108800 chr1D 100.000 5600 0 0 808 6407 101581338 101575739 0.000000e+00 10342.0
1 TraesCS1D01G108800 chr1D 100.000 408 0 0 1 408 101582145 101581738 0.000000e+00 754.0
2 TraesCS1D01G108800 chr1A 96.997 4229 89 22 2206 6407 103635223 103631006 0.000000e+00 7071.0
3 TraesCS1D01G108800 chr1A 92.936 1274 36 11 935 2170 103636467 103635210 0.000000e+00 1805.0
4 TraesCS1D01G108800 chr1A 91.617 334 14 5 81 408 103637064 103636739 3.520000e-122 449.0
5 TraesCS1D01G108800 chr1A 91.667 60 3 2 822 881 103636577 103636520 1.480000e-11 82.4
6 TraesCS1D01G108800 chr1B 95.927 4223 114 18 2206 6407 150063039 150058854 0.000000e+00 6793.0
7 TraesCS1D01G108800 chr1B 95.559 698 19 3 1481 2170 150063719 150063026 0.000000e+00 1107.0
8 TraesCS1D01G108800 chr1B 94.030 603 25 5 878 1472 150064381 150063782 0.000000e+00 904.0
9 TraesCS1D01G108800 chr1B 89.831 59 0 1 808 860 150064439 150064381 3.200000e-08 71.3
10 TraesCS1D01G108800 chr5A 94.444 72 4 0 6336 6407 672416360 672416431 1.890000e-20 111.0
11 TraesCS1D01G108800 chr5A 92.683 41 3 0 1478 1518 287520662 287520702 6.940000e-05 60.2
12 TraesCS1D01G108800 chr4B 94.444 72 4 0 6336 6407 630428564 630428493 1.890000e-20 111.0
13 TraesCS1D01G108800 chr7B 95.122 41 2 0 1478 1518 178570026 178569986 1.490000e-06 65.8
14 TraesCS1D01G108800 chr2D 93.182 44 2 1 1481 1523 145889927 145889970 5.360000e-06 63.9
15 TraesCS1D01G108800 chr6B 92.500 40 3 0 1478 1517 208476514 208476475 2.500000e-04 58.4
16 TraesCS1D01G108800 chr4D 94.595 37 2 0 6371 6407 490603480 490603444 2.500000e-04 58.4
17 TraesCS1D01G108800 chr7A 87.234 47 4 1 1479 1523 198948546 198948500 1.200000e-02 52.8


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 TraesCS1D01G108800 chr1D 101575739 101582145 6406 True 5548.000 10342 100.00000 1 6407 2 chr1D.!!$R1 6406
1 TraesCS1D01G108800 chr1A 103631006 103637064 6058 True 2351.850 7071 93.30425 81 6407 4 chr1A.!!$R1 6326
2 TraesCS1D01G108800 chr1B 150058854 150064439 5585 True 2218.825 6793 93.83675 808 6407 4 chr1B.!!$R1 5599

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
329 334 1.216122 GGAGAGCGATGTCATTGAGC 58.784 55.000 4.07 2.86 0.00 4.26 F
1704 1804 0.804156 CGTGGCAAAAGCACGGTTTT 60.804 50.000 0.00 1.25 38.50 2.43 F
2171 2305 1.031571 GCATCAGGCATGGACCGAAA 61.032 55.000 0.00 0.00 43.97 3.46 F
2172 2306 1.462616 CATCAGGCATGGACCGAAAA 58.537 50.000 0.00 0.00 33.69 2.29 F
3159 3304 0.324552 CATTTGCCCCTGGTGATGGA 60.325 55.000 0.00 0.00 0.00 3.41 F
3801 3953 0.954452 AGCAAAAGAAAGGAGGCACG 59.046 50.000 0.00 0.00 0.00 5.34 F
4632 4787 1.134367 CAGACTCGTCGGCCTATTTCA 59.866 52.381 0.00 0.00 34.09 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2336 0.039618 AAATCGGTCCATGCCTGGTT 59.960 50.000 7.98 0.0 43.61 3.67 R
2647 2786 0.179018 GCTACATCTCCCCCGCAAAT 60.179 55.000 0.00 0.0 0.00 2.32 R
3146 3291 2.603075 TTTTCTTCCATCACCAGGGG 57.397 50.000 0.00 0.0 0.00 4.79 R
3801 3953 4.383010 CCATAAAAAGGACCCTTTGCATCC 60.383 45.833 14.18 0.0 44.50 3.51 R
4365 4520 2.838202 GAGGGTAGTGGTTGATCCTCAA 59.162 50.000 0.00 0.0 40.18 3.02 R
5202 5363 1.211949 GGGGCTGCAAAGTAGATGGTA 59.788 52.381 0.50 0.0 0.00 3.25 R
6105 6268 2.548920 CCCAGACCTTGTCAGACTGTTC 60.549 54.545 1.59 0.0 34.60 3.18 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
41 42 3.461773 CCACCACGCGAGGAGGAT 61.462 66.667 29.74 5.37 41.43 3.24
42 43 2.202797 CACCACGCGAGGAGGATG 60.203 66.667 29.67 12.90 34.87 3.51
43 44 3.461773 ACCACGCGAGGAGGATGG 61.462 66.667 29.67 18.37 36.46 3.51
44 45 4.227134 CCACGCGAGGAGGATGGG 62.227 72.222 18.51 0.00 32.87 4.00
45 46 4.227134 CACGCGAGGAGGATGGGG 62.227 72.222 15.93 0.00 0.00 4.96
49 50 4.888325 CGAGGAGGATGGGGCCCT 62.888 72.222 25.93 9.44 36.57 5.19
79 80 4.697756 CCTCGCGGCCTTTGACCA 62.698 66.667 6.13 0.00 0.00 4.02
80 81 3.121030 CTCGCGGCCTTTGACCAG 61.121 66.667 6.13 0.00 0.00 4.00
81 82 3.589654 CTCGCGGCCTTTGACCAGA 62.590 63.158 6.13 0.00 0.00 3.86
82 83 3.121030 CGCGGCCTTTGACCAGAG 61.121 66.667 0.00 0.00 0.00 3.35
83 84 2.747855 GCGGCCTTTGACCAGAGG 60.748 66.667 0.00 2.49 35.90 3.69
86 87 2.032681 GCCTTTGACCAGAGGCGT 59.967 61.111 14.57 0.00 46.67 5.68
92 93 2.154798 TTGACCAGAGGCGTCTTCGG 62.155 60.000 6.10 8.66 37.56 4.30
125 126 4.537433 GGTGGCGGCTGCTCTAGG 62.537 72.222 18.85 0.00 42.25 3.02
126 127 4.537433 GTGGCGGCTGCTCTAGGG 62.537 72.222 18.85 0.00 42.25 3.53
149 150 4.517934 CCCGAGTCGCCCCTCCTA 62.518 72.222 7.12 0.00 0.00 2.94
162 163 2.439701 TCCTAGGAGCGACGTGGG 60.440 66.667 7.62 3.55 36.56 4.61
163 164 2.754658 CCTAGGAGCGACGTGGGT 60.755 66.667 1.05 0.59 31.81 4.51
164 165 2.490217 CTAGGAGCGACGTGGGTG 59.510 66.667 7.09 0.00 0.00 4.61
165 166 3.701604 CTAGGAGCGACGTGGGTGC 62.702 68.421 13.10 13.10 0.00 5.01
176 177 4.624364 TGGGTGCAGGCTGTCACG 62.624 66.667 25.07 0.90 34.20 4.35
235 240 7.979444 ATCGTAAATGGTCTTCTTTCTTCAA 57.021 32.000 0.00 0.00 0.00 2.69
296 301 4.625963 AGGGCCTACAAATTAGAGAGAGT 58.374 43.478 2.82 0.00 0.00 3.24
329 334 1.216122 GGAGAGCGATGTCATTGAGC 58.784 55.000 4.07 2.86 0.00 4.26
392 397 4.946784 ACGGGTACTACGTTACACTAAG 57.053 45.455 9.72 0.00 42.70 2.18
885 907 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
886 908 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
887 909 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
888 910 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
892 914 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
951 992 3.066621 GCATACTCTCTCTCTCCACAGTG 59.933 52.174 0.00 0.00 0.00 3.66
1482 1561 9.566432 AAGTACTGTACTGTACACTACTAAGTT 57.434 33.333 32.06 18.14 43.65 2.66
1483 1562 8.997323 AGTACTGTACTGTACACTACTAAGTTG 58.003 37.037 32.06 13.40 43.65 3.16
1589 1689 6.220930 TCATTATACATCTGCCTAACGTTCC 58.779 40.000 2.82 0.00 0.00 3.62
1621 1721 7.325660 TCTTAATCCTGCAAGCATTAAGAAG 57.674 36.000 21.25 11.04 39.45 2.85
1639 1739 5.424121 AGAAGACCTTCAAACATGAAACG 57.576 39.130 11.80 0.00 41.84 3.60
1704 1804 0.804156 CGTGGCAAAAGCACGGTTTT 60.804 50.000 0.00 1.25 38.50 2.43
1705 1805 1.534175 CGTGGCAAAAGCACGGTTTTA 60.534 47.619 6.63 0.00 38.50 1.52
1706 1806 1.855978 GTGGCAAAAGCACGGTTTTAC 59.144 47.619 6.63 1.89 0.00 2.01
1988 2099 7.148407 CCACTTAACCAACTGACTATGTTGATC 60.148 40.741 8.01 0.00 45.27 2.92
1991 2102 8.918202 TTAACCAACTGACTATGTTGATCTTT 57.082 30.769 8.01 0.25 45.27 2.52
2170 2304 1.451927 GCATCAGGCATGGACCGAA 60.452 57.895 0.00 0.00 43.97 4.30
2171 2305 1.031571 GCATCAGGCATGGACCGAAA 61.032 55.000 0.00 0.00 43.97 3.46
2172 2306 1.462616 CATCAGGCATGGACCGAAAA 58.537 50.000 0.00 0.00 33.69 2.29
2191 2325 4.806640 AAAAATCAGGCATGAACCGATT 57.193 36.364 4.62 0.00 39.39 3.34
2192 2326 4.806640 AAAATCAGGCATGAACCGATTT 57.193 36.364 4.62 0.00 40.92 2.17
2193 2327 4.806640 AAATCAGGCATGAACCGATTTT 57.193 36.364 4.62 0.00 38.55 1.82
2194 2328 4.806640 AATCAGGCATGAACCGATTTTT 57.193 36.364 4.62 0.00 39.39 1.94
2226 2360 3.968649 CAGGCATGGACCGATTTATTTG 58.031 45.455 0.00 0.00 33.69 2.32
2227 2361 2.362077 AGGCATGGACCGATTTATTTGC 59.638 45.455 0.00 0.00 33.69 3.68
2228 2362 2.100584 GGCATGGACCGATTTATTTGCA 59.899 45.455 0.00 0.00 0.00 4.08
2456 2591 3.628032 TCTTGTTTTGCCGTGTTGTGATA 59.372 39.130 0.00 0.00 0.00 2.15
2605 2743 7.867403 GTGGACAGTTGTTGAATGAATACAAAT 59.133 33.333 0.00 0.00 33.96 2.32
2606 2744 7.866898 TGGACAGTTGTTGAATGAATACAAATG 59.133 33.333 11.56 11.56 46.97 2.32
2726 2866 8.246180 GTGCTACCGTATATGCCTATTAGTTTA 58.754 37.037 0.00 0.00 0.00 2.01
3146 3291 2.760092 TGCCTGGGAAAGATACATTTGC 59.240 45.455 0.00 0.00 0.00 3.68
3159 3304 0.324552 CATTTGCCCCTGGTGATGGA 60.325 55.000 0.00 0.00 0.00 3.41
3507 3657 3.354948 ACTGGTGCAGCAATAGAATGA 57.645 42.857 20.60 0.00 34.37 2.57
3664 3815 7.654022 TTTGTTGGAAAACAGAATAACCTCT 57.346 32.000 0.00 0.00 33.73 3.69
3801 3953 0.954452 AGCAAAAGAAAGGAGGCACG 59.046 50.000 0.00 0.00 0.00 5.34
4365 4520 2.390225 AACTGACAGTGACTCCCTCT 57.610 50.000 9.33 0.00 0.00 3.69
4475 4630 1.613928 TGGTAGCGGTGGGAATCCA 60.614 57.895 0.09 0.00 41.58 3.41
4632 4787 1.134367 CAGACTCGTCGGCCTATTTCA 59.866 52.381 0.00 0.00 34.09 2.69
4800 4958 5.938125 GGACCAACCATAAATACTCGCATAT 59.062 40.000 0.00 0.00 38.79 1.78
4926 5086 8.083828 ACATAAGACTATCTGATTGGACACTT 57.916 34.615 0.00 2.79 0.00 3.16
4959 5119 6.243216 ACTAGTTTACCAAGACACTCCAAA 57.757 37.500 0.00 0.00 0.00 3.28
5000 5161 4.741928 AAACCCACTACTGGATTTCCTT 57.258 40.909 0.00 0.00 40.55 3.36
5032 5193 5.205056 TCTTACCAGTTGTCACCCAAAAAT 58.795 37.500 0.00 0.00 34.07 1.82
5059 5220 5.928839 CACATCTGAAGCTGTGTAAGTTAGT 59.071 40.000 6.20 0.00 37.39 2.24
5069 5230 5.346281 GCTGTGTAAGTTAGTCTAACAGCAG 59.654 44.000 21.92 19.39 46.16 4.24
5513 5674 3.549794 ACAGCTATTGCCAGAAATCTCC 58.450 45.455 0.00 0.00 40.80 3.71
5685 5848 4.023707 CCTTACAGCAAAGTCTTCCACAAG 60.024 45.833 0.00 0.00 0.00 3.16
5958 6121 8.855110 TCCAATTTTCTAAATTGAAGTGTGCTA 58.145 29.630 20.65 0.00 39.36 3.49
6020 6183 5.950544 ACTATAGCACCAGGTATTTGTGA 57.049 39.130 0.00 0.00 39.12 3.58
6040 6203 7.827819 TGTGAAGTACTTACTATTCATGTGC 57.172 36.000 8.42 0.00 34.99 4.57
6051 6214 5.482908 ACTATTCATGTGCGGGATTAGATC 58.517 41.667 0.00 0.00 0.00 2.75
6086 6249 2.949177 TACAGAGAAAAGGCTTGGCA 57.051 45.000 0.00 0.00 0.00 4.92
6096 6259 2.341176 GCTTGGCACCCTGCTTTG 59.659 61.111 0.00 0.00 44.28 2.77
6317 6486 0.471617 GCTGATCCCATAGCACTGGT 59.528 55.000 4.12 0.00 39.67 4.00
6353 6522 4.846779 TGTTAGTTTGGATGTCTTTGGC 57.153 40.909 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.461773 ATCCTCCTCGCGTGGTGG 61.462 66.667 32.20 32.20 40.94 4.61
25 26 2.202797 CATCCTCCTCGCGTGGTG 60.203 66.667 25.10 22.14 0.00 4.17
26 27 3.461773 CCATCCTCCTCGCGTGGT 61.462 66.667 25.10 4.65 0.00 4.16
27 28 4.227134 CCCATCCTCCTCGCGTGG 62.227 72.222 20.92 20.92 0.00 4.94
28 29 4.227134 CCCCATCCTCCTCGCGTG 62.227 72.222 5.77 2.75 0.00 5.34
32 33 4.888325 AGGGCCCCATCCTCCTCG 62.888 72.222 21.43 0.00 0.00 4.63
33 34 2.851588 GAGGGCCCCATCCTCCTC 60.852 72.222 21.43 2.14 43.71 3.71
34 35 4.888325 CGAGGGCCCCATCCTCCT 62.888 72.222 21.43 0.00 46.01 3.69
63 64 3.121030 CTGGTCAAAGGCCGCGAG 61.121 66.667 8.23 0.00 0.00 5.03
64 65 3.589654 CTCTGGTCAAAGGCCGCGA 62.590 63.158 8.23 0.00 0.00 5.87
65 66 3.121030 CTCTGGTCAAAGGCCGCG 61.121 66.667 0.00 0.00 0.00 6.46
66 67 2.747855 CCTCTGGTCAAAGGCCGC 60.748 66.667 0.00 0.00 0.00 6.53
70 71 0.035458 AAGACGCCTCTGGTCAAAGG 59.965 55.000 0.00 0.00 36.87 3.11
71 72 1.433534 GAAGACGCCTCTGGTCAAAG 58.566 55.000 0.00 0.00 36.87 2.77
72 73 0.319555 CGAAGACGCCTCTGGTCAAA 60.320 55.000 0.00 0.00 36.87 2.69
73 74 1.289066 CGAAGACGCCTCTGGTCAA 59.711 57.895 0.00 0.00 36.87 3.18
74 75 2.636412 CCGAAGACGCCTCTGGTCA 61.636 63.158 0.00 0.00 36.87 4.02
75 76 2.182030 CCGAAGACGCCTCTGGTC 59.818 66.667 0.00 0.00 38.29 4.02
76 77 4.070552 GCCGAAGACGCCTCTGGT 62.071 66.667 0.00 0.00 38.29 4.00
113 114 2.501610 GGAACCCTAGAGCAGCCG 59.498 66.667 0.00 0.00 0.00 5.52
147 148 2.490217 CACCCACGTCGCTCCTAG 59.510 66.667 0.00 0.00 0.00 3.02
162 163 4.314440 TCCCGTGACAGCCTGCAC 62.314 66.667 8.60 8.60 0.00 4.57
163 164 4.314440 GTCCCGTGACAGCCTGCA 62.314 66.667 0.00 0.00 41.37 4.41
165 166 2.507110 AATCGTCCCGTGACAGCCTG 62.507 60.000 0.00 0.00 41.85 4.85
166 167 2.283529 AATCGTCCCGTGACAGCCT 61.284 57.895 0.00 0.00 41.85 4.58
167 168 2.100631 CAATCGTCCCGTGACAGCC 61.101 63.158 0.00 0.00 41.85 4.85
168 169 0.460284 ATCAATCGTCCCGTGACAGC 60.460 55.000 0.00 0.00 41.85 4.40
176 177 2.135933 GTCGGATTGATCAATCGTCCC 58.864 52.381 32.05 22.26 46.11 4.46
235 240 4.262420 GCAGAAATGGGTTGTGTTTATGGT 60.262 41.667 0.00 0.00 33.03 3.55
296 301 1.622725 GCTCTCCCTTCCCCTCTGTTA 60.623 57.143 0.00 0.00 0.00 2.41
329 334 8.494347 GTCATGAGCTTAATTGTCTATGCTTAG 58.506 37.037 0.00 0.14 33.68 2.18
1476 1555 5.569413 AGACGTTTTTGCAGTTCAACTTAG 58.431 37.500 0.00 0.00 33.73 2.18
1479 1558 4.434713 AAGACGTTTTTGCAGTTCAACT 57.565 36.364 0.00 0.00 33.73 3.16
1480 1559 8.502161 AATATAAGACGTTTTTGCAGTTCAAC 57.498 30.769 0.00 0.00 33.73 3.18
1589 1689 4.619160 GCTTGCAGGATTAAGAAACCCTTG 60.619 45.833 0.00 0.00 36.34 3.61
1621 1721 5.668558 AGTACGTTTCATGTTTGAAGGTC 57.331 39.130 0.00 0.00 42.60 3.85
1639 1739 3.492829 GGGCCTGAATACAGCACTAGTAC 60.493 52.174 0.84 0.00 42.25 2.73
1704 1804 6.318144 GCTGACCAGACTGTTATGTAGTAGTA 59.682 42.308 0.93 0.00 0.00 1.82
1705 1805 5.125739 GCTGACCAGACTGTTATGTAGTAGT 59.874 44.000 0.93 0.00 0.00 2.73
1706 1806 5.358442 AGCTGACCAGACTGTTATGTAGTAG 59.642 44.000 0.93 0.00 0.00 2.57
1947 2055 2.046604 TGGCACTGCTGCTAGCTG 60.047 61.111 17.23 16.92 42.97 4.24
1988 2099 4.572985 ACCACATCACATTCACACAAAG 57.427 40.909 0.00 0.00 0.00 2.77
1991 2102 3.490590 GCAAACCACATCACATTCACACA 60.491 43.478 0.00 0.00 0.00 3.72
2170 2304 4.806640 AATCGGTTCATGCCTGATTTTT 57.193 36.364 11.40 0.00 32.27 1.94
2171 2305 4.806640 AAATCGGTTCATGCCTGATTTT 57.193 36.364 18.69 9.17 37.90 1.82
2172 2306 4.806640 AAAATCGGTTCATGCCTGATTT 57.193 36.364 18.69 18.69 40.18 2.17
2196 2330 1.691434 GGTCCATGCCTGGTTCAAAAA 59.309 47.619 7.98 0.00 43.61 1.94
2197 2331 1.337118 GGTCCATGCCTGGTTCAAAA 58.663 50.000 7.98 0.00 43.61 2.44
2198 2332 0.893270 CGGTCCATGCCTGGTTCAAA 60.893 55.000 7.98 0.00 43.61 2.69
2199 2333 1.303236 CGGTCCATGCCTGGTTCAA 60.303 57.895 7.98 0.00 43.61 2.69
2200 2334 1.561769 ATCGGTCCATGCCTGGTTCA 61.562 55.000 7.98 0.00 43.61 3.18
2201 2335 0.394352 AATCGGTCCATGCCTGGTTC 60.394 55.000 7.98 3.12 43.61 3.62
2202 2336 0.039618 AAATCGGTCCATGCCTGGTT 59.960 50.000 7.98 0.00 43.61 3.67
2203 2337 0.916086 TAAATCGGTCCATGCCTGGT 59.084 50.000 7.98 0.00 43.61 4.00
2204 2338 2.276732 ATAAATCGGTCCATGCCTGG 57.723 50.000 0.78 0.78 44.64 4.45
2205 2339 3.796504 GCAAATAAATCGGTCCATGCCTG 60.797 47.826 0.00 0.00 0.00 4.85
2206 2340 2.362077 GCAAATAAATCGGTCCATGCCT 59.638 45.455 0.00 0.00 0.00 4.75
2207 2341 2.100584 TGCAAATAAATCGGTCCATGCC 59.899 45.455 0.00 0.00 0.00 4.40
2208 2342 3.435105 TGCAAATAAATCGGTCCATGC 57.565 42.857 0.00 0.00 0.00 4.06
2209 2343 4.362279 CCTTGCAAATAAATCGGTCCATG 58.638 43.478 0.00 0.00 0.00 3.66
2210 2344 3.181476 GCCTTGCAAATAAATCGGTCCAT 60.181 43.478 0.00 0.00 0.00 3.41
2211 2345 2.165437 GCCTTGCAAATAAATCGGTCCA 59.835 45.455 0.00 0.00 0.00 4.02
2212 2346 2.165437 TGCCTTGCAAATAAATCGGTCC 59.835 45.455 0.00 0.00 34.76 4.46
2213 2347 3.438360 CTGCCTTGCAAATAAATCGGTC 58.562 45.455 0.00 0.00 38.41 4.79
2214 2348 2.166254 CCTGCCTTGCAAATAAATCGGT 59.834 45.455 0.00 0.00 38.41 4.69
2215 2349 2.426738 TCCTGCCTTGCAAATAAATCGG 59.573 45.455 0.00 0.00 38.41 4.18
2216 2350 3.129287 AGTCCTGCCTTGCAAATAAATCG 59.871 43.478 0.00 0.00 38.41 3.34
2217 2351 4.725790 AGTCCTGCCTTGCAAATAAATC 57.274 40.909 0.00 0.00 38.41 2.17
2218 2352 4.098501 GCTAGTCCTGCCTTGCAAATAAAT 59.901 41.667 0.00 0.00 38.41 1.40
2219 2353 3.443681 GCTAGTCCTGCCTTGCAAATAAA 59.556 43.478 0.00 0.00 38.41 1.40
2220 2354 3.016736 GCTAGTCCTGCCTTGCAAATAA 58.983 45.455 0.00 0.00 38.41 1.40
2221 2355 2.239654 AGCTAGTCCTGCCTTGCAAATA 59.760 45.455 0.00 0.00 38.41 1.40
2222 2356 1.005215 AGCTAGTCCTGCCTTGCAAAT 59.995 47.619 0.00 0.00 38.41 2.32
2223 2357 0.401738 AGCTAGTCCTGCCTTGCAAA 59.598 50.000 0.00 0.00 38.41 3.68
2224 2358 1.208052 CTAGCTAGTCCTGCCTTGCAA 59.792 52.381 12.92 0.00 38.41 4.08
2225 2359 0.826715 CTAGCTAGTCCTGCCTTGCA 59.173 55.000 12.92 0.00 35.94 4.08
2226 2360 0.531753 GCTAGCTAGTCCTGCCTTGC 60.532 60.000 21.62 0.56 34.07 4.01
2227 2361 1.118838 AGCTAGCTAGTCCTGCCTTG 58.881 55.000 17.69 0.00 0.00 3.61
2228 2362 2.593026 CTAGCTAGCTAGTCCTGCCTT 58.407 52.381 34.41 6.75 40.68 4.35
2512 2647 8.909708 TCACTTTGGCTTGAATTATATTTTCG 57.090 30.769 0.00 0.00 0.00 3.46
2631 2770 9.990360 CCCCCGCAAATAAATAAATAAATTAGT 57.010 29.630 0.00 0.00 0.00 2.24
2647 2786 0.179018 GCTACATCTCCCCCGCAAAT 60.179 55.000 0.00 0.00 0.00 2.32
2651 2790 0.247736 CATAGCTACATCTCCCCCGC 59.752 60.000 0.00 0.00 0.00 6.13
2652 2791 1.633774 ACATAGCTACATCTCCCCCG 58.366 55.000 0.00 0.00 0.00 5.73
3146 3291 2.603075 TTTTCTTCCATCACCAGGGG 57.397 50.000 0.00 0.00 0.00 4.79
3159 3304 6.208204 AGCTTAACATCTGTGAGCATTTTCTT 59.792 34.615 16.49 0.00 39.21 2.52
3507 3657 5.998363 GGATGGTTCAACTTTCTTGTACTCT 59.002 40.000 0.00 0.00 0.00 3.24
3643 3793 8.817100 CAAAAAGAGGTTATTCTGTTTTCCAAC 58.183 33.333 0.00 0.00 38.66 3.77
3664 3815 8.367156 CCCTCTCCTTTTATTTGATGACAAAAA 58.633 33.333 0.00 0.00 46.77 1.94
3801 3953 4.383010 CCATAAAAAGGACCCTTTGCATCC 60.383 45.833 14.18 0.00 44.50 3.51
4365 4520 2.838202 GAGGGTAGTGGTTGATCCTCAA 59.162 50.000 0.00 0.00 40.18 3.02
4632 4787 5.183530 TGAAGGAGATCACCAACATTGAT 57.816 39.130 12.05 0.00 36.37 2.57
4822 4980 4.900635 GTTCATATGAACCGCTGGAAAT 57.099 40.909 30.37 0.00 46.42 2.17
4929 5089 8.747538 AGTGTCTTGGTAAACTAGTTTTCAAT 57.252 30.769 25.07 11.87 34.23 2.57
5000 5161 5.244626 GTGACAACTGGTAAGAGGGTACTTA 59.755 44.000 0.00 0.00 0.00 2.24
5059 5220 7.187824 AGGATTAGTGATTTCTGCTGTTAGA 57.812 36.000 0.00 0.00 0.00 2.10
5115 5276 3.391296 TCAGAGCCTGAAAAGTACAAGGT 59.609 43.478 0.00 0.00 37.57 3.50
5202 5363 1.211949 GGGGCTGCAAAGTAGATGGTA 59.788 52.381 0.50 0.00 0.00 3.25
5513 5674 6.019881 CACACACACTACACCATCATAATACG 60.020 42.308 0.00 0.00 0.00 3.06
5685 5848 9.660180 ATTTGAATTTAGAGTTAGGTCTCACTC 57.340 33.333 4.60 4.60 39.92 3.51
5985 6148 5.290386 GGTGCTATAGTACCTTGTGCTTAG 58.710 45.833 27.40 0.00 45.69 2.18
6020 6183 5.128171 TCCCGCACATGAATAGTAAGTACTT 59.872 40.000 13.68 13.68 37.73 2.24
6038 6201 2.693591 AGAAACTCGATCTAATCCCGCA 59.306 45.455 0.00 0.00 0.00 5.69
6040 6203 6.074544 ACTAAGAAACTCGATCTAATCCCG 57.925 41.667 0.00 0.00 0.00 5.14
6096 6259 3.639538 TGTCAGACTGTTCGCTTTCTAC 58.360 45.455 1.59 0.00 0.00 2.59
6105 6268 2.548920 CCCAGACCTTGTCAGACTGTTC 60.549 54.545 1.59 0.00 34.60 3.18
6162 6330 7.814264 ATGTTGAGTTTCATGACTCTCTTTT 57.186 32.000 20.10 6.76 44.99 2.27
6163 6331 7.814264 AATGTTGAGTTTCATGACTCTCTTT 57.186 32.000 20.10 12.52 44.99 2.52
6166 6334 7.589221 GTGAAAATGTTGAGTTTCATGACTCTC 59.411 37.037 13.87 14.68 45.21 3.20
6317 6486 7.984050 TCCAAACTAACAAAATCAAAGCAATGA 59.016 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.