Multiple sequence alignment - TraesCS2D01G555400

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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 TraesCS2D01G555400 chr2D 100.000 3295 0 0 1 3295 629448193 629444899 0.000000e+00 6085.0
1 TraesCS2D01G555400 chr2D 86.609 463 50 8 650 1101 118223544 118224005 4.910000e-138 501.0
2 TraesCS2D01G555400 chr3A 95.893 3117 111 13 193 3295 733321645 733324758 0.000000e+00 5031.0
3 TraesCS2D01G555400 chr3A 95.497 3087 97 13 224 3295 535169835 535166776 0.000000e+00 4892.0
4 TraesCS2D01G555400 chr3A 94.545 55 3 0 200 254 671355444 671355390 5.860000e-13 86.1
5 TraesCS2D01G555400 chr2B 95.879 3106 115 11 200 3295 477604210 477601108 0.000000e+00 5014.0
6 TraesCS2D01G555400 chr2B 95.811 3103 109 8 200 3295 424379626 424382714 0.000000e+00 4990.0
7 TraesCS2D01G555400 chr2B 84.885 827 87 17 1813 2627 728626005 728626805 0.000000e+00 800.0
8 TraesCS2D01G555400 chrUn 95.065 3100 114 19 204 3295 178180859 178183927 0.000000e+00 4841.0
9 TraesCS2D01G555400 chr5D 91.915 1781 119 8 909 2666 456631233 456633011 0.000000e+00 2468.0
10 TraesCS2D01G555400 chr5D 84.960 1609 174 31 1103 2672 250404888 250403309 0.000000e+00 1568.0
11 TraesCS2D01G555400 chr5D 86.420 729 64 10 210 911 456630195 456630915 0.000000e+00 765.0
12 TraesCS2D01G555400 chr5D 89.456 607 59 5 2691 3295 456633692 456634295 0.000000e+00 761.0
13 TraesCS2D01G555400 chr7A 94.997 1559 63 7 204 1755 713723218 713724768 0.000000e+00 2433.0
14 TraesCS2D01G555400 chr7A 84.494 445 55 12 2493 2930 713729703 713730140 8.450000e-116 427.0
15 TraesCS2D01G555400 chr7A 86.076 79 8 3 204 281 705547840 705547916 7.580000e-12 82.4
16 TraesCS2D01G555400 chr5B 84.658 1610 177 37 1103 2672 588572490 588570911 0.000000e+00 1541.0
17 TraesCS2D01G555400 chr5B 91.724 1015 63 4 982 1975 558449528 558450542 0.000000e+00 1389.0
18 TraesCS2D01G555400 chr5B 90.642 716 47 10 941 1636 558448807 558449522 0.000000e+00 933.0
19 TraesCS2D01G555400 chr5B 88.193 703 67 5 1970 2672 558452115 558452801 0.000000e+00 824.0
20 TraesCS2D01G555400 chr5B 89.769 606 54 4 2692 3295 558554925 558555524 0.000000e+00 769.0
21 TraesCS2D01G555400 chr5B 89.253 549 55 4 2750 3295 558546974 558547521 0.000000e+00 684.0
22 TraesCS2D01G555400 chr7D 91.644 1113 81 8 1296 2401 90192097 90190990 0.000000e+00 1530.0
23 TraesCS2D01G555400 chr7D 86.988 1122 97 25 204 1300 90240218 90239121 0.000000e+00 1218.0
24 TraesCS2D01G555400 chr7D 90.429 606 49 8 2691 3295 90183427 90182830 0.000000e+00 789.0
25 TraesCS2D01G555400 chr7D 89.873 237 22 2 2412 2648 90184356 90184122 1.490000e-78 303.0


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 TraesCS2D01G555400 chr2D 629444899 629448193 3294 True 6085.000000 6085 100.000000 1 3295 1 chr2D.!!$R1 3294
1 TraesCS2D01G555400 chr3A 733321645 733324758 3113 False 5031.000000 5031 95.893000 193 3295 1 chr3A.!!$F1 3102
2 TraesCS2D01G555400 chr3A 535166776 535169835 3059 True 4892.000000 4892 95.497000 224 3295 1 chr3A.!!$R1 3071
3 TraesCS2D01G555400 chr2B 477601108 477604210 3102 True 5014.000000 5014 95.879000 200 3295 1 chr2B.!!$R1 3095
4 TraesCS2D01G555400 chr2B 424379626 424382714 3088 False 4990.000000 4990 95.811000 200 3295 1 chr2B.!!$F1 3095
5 TraesCS2D01G555400 chr2B 728626005 728626805 800 False 800.000000 800 84.885000 1813 2627 1 chr2B.!!$F2 814
6 TraesCS2D01G555400 chrUn 178180859 178183927 3068 False 4841.000000 4841 95.065000 204 3295 1 chrUn.!!$F1 3091
7 TraesCS2D01G555400 chr5D 250403309 250404888 1579 True 1568.000000 1568 84.960000 1103 2672 1 chr5D.!!$R1 1569
8 TraesCS2D01G555400 chr5D 456630195 456634295 4100 False 1331.333333 2468 89.263667 210 3295 3 chr5D.!!$F1 3085
9 TraesCS2D01G555400 chr7A 713723218 713724768 1550 False 2433.000000 2433 94.997000 204 1755 1 chr7A.!!$F2 1551
10 TraesCS2D01G555400 chr5B 588570911 588572490 1579 True 1541.000000 1541 84.658000 1103 2672 1 chr5B.!!$R1 1569
11 TraesCS2D01G555400 chr5B 558448807 558452801 3994 False 1048.666667 1389 90.186333 941 2672 3 chr5B.!!$F3 1731
12 TraesCS2D01G555400 chr5B 558554925 558555524 599 False 769.000000 769 89.769000 2692 3295 1 chr5B.!!$F2 603
13 TraesCS2D01G555400 chr5B 558546974 558547521 547 False 684.000000 684 89.253000 2750 3295 1 chr5B.!!$F1 545
14 TraesCS2D01G555400 chr7D 90190990 90192097 1107 True 1530.000000 1530 91.644000 1296 2401 1 chr7D.!!$R1 1105
15 TraesCS2D01G555400 chr7D 90239121 90240218 1097 True 1218.000000 1218 86.988000 204 1300 1 chr7D.!!$R2 1096
16 TraesCS2D01G555400 chr7D 90182830 90184356 1526 True 546.000000 789 90.151000 2412 3295 2 chr7D.!!$R3 883

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
556 582 2.041922 TCCCACCATCTCCCCGAG 60.042 66.667 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 5150 0.904649 TCACGAAGGACATGCCAGAT 59.095 50.0 8.58 0.0 40.02 2.9 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 8.934507 TTACATTCCTTTTGTACTGTTTTTGG 57.065 30.769 0.00 0.00 29.60 3.28
42 43 6.941857 ACATTCCTTTTGTACTGTTTTTGGT 58.058 32.000 0.00 0.00 0.00 3.67
43 44 7.390823 ACATTCCTTTTGTACTGTTTTTGGTT 58.609 30.769 0.00 0.00 0.00 3.67
44 45 7.333174 ACATTCCTTTTGTACTGTTTTTGGTTG 59.667 33.333 0.00 0.00 0.00 3.77
45 46 6.347859 TCCTTTTGTACTGTTTTTGGTTGT 57.652 33.333 0.00 0.00 0.00 3.32
46 47 6.391537 TCCTTTTGTACTGTTTTTGGTTGTC 58.608 36.000 0.00 0.00 0.00 3.18
47 48 6.209788 TCCTTTTGTACTGTTTTTGGTTGTCT 59.790 34.615 0.00 0.00 0.00 3.41
48 49 6.871492 CCTTTTGTACTGTTTTTGGTTGTCTT 59.129 34.615 0.00 0.00 0.00 3.01
49 50 7.386573 CCTTTTGTACTGTTTTTGGTTGTCTTT 59.613 33.333 0.00 0.00 0.00 2.52
50 51 8.664211 TTTTGTACTGTTTTTGGTTGTCTTTT 57.336 26.923 0.00 0.00 0.00 2.27
51 52 7.644986 TTGTACTGTTTTTGGTTGTCTTTTG 57.355 32.000 0.00 0.00 0.00 2.44
52 53 6.982852 TGTACTGTTTTTGGTTGTCTTTTGA 58.017 32.000 0.00 0.00 0.00 2.69
53 54 7.607250 TGTACTGTTTTTGGTTGTCTTTTGAT 58.393 30.769 0.00 0.00 0.00 2.57
54 55 8.091449 TGTACTGTTTTTGGTTGTCTTTTGATT 58.909 29.630 0.00 0.00 0.00 2.57
55 56 7.977789 ACTGTTTTTGGTTGTCTTTTGATTT 57.022 28.000 0.00 0.00 0.00 2.17
57 58 9.495572 ACTGTTTTTGGTTGTCTTTTGATTTAA 57.504 25.926 0.00 0.00 0.00 1.52
84 85 8.950208 TTTTTATTTCGTTTCCTTTGTTCCAT 57.050 26.923 0.00 0.00 0.00 3.41
85 86 8.950208 TTTTATTTCGTTTCCTTTGTTCCATT 57.050 26.923 0.00 0.00 0.00 3.16
86 87 8.950208 TTTATTTCGTTTCCTTTGTTCCATTT 57.050 26.923 0.00 0.00 0.00 2.32
88 89 7.940178 ATTTCGTTTCCTTTGTTCCATTTAC 57.060 32.000 0.00 0.00 0.00 2.01
89 90 6.702716 TTCGTTTCCTTTGTTCCATTTACT 57.297 33.333 0.00 0.00 0.00 2.24
90 91 6.702716 TCGTTTCCTTTGTTCCATTTACTT 57.297 33.333 0.00 0.00 0.00 2.24
91 92 7.102847 TCGTTTCCTTTGTTCCATTTACTTT 57.897 32.000 0.00 0.00 0.00 2.66
92 93 6.975772 TCGTTTCCTTTGTTCCATTTACTTTG 59.024 34.615 0.00 0.00 0.00 2.77
93 94 6.200097 CGTTTCCTTTGTTCCATTTACTTTGG 59.800 38.462 0.00 0.00 35.45 3.28
94 95 6.800072 TTCCTTTGTTCCATTTACTTTGGT 57.200 33.333 0.00 0.00 35.64 3.67
95 96 6.800072 TCCTTTGTTCCATTTACTTTGGTT 57.200 33.333 0.00 0.00 35.64 3.67
96 97 7.189079 TCCTTTGTTCCATTTACTTTGGTTT 57.811 32.000 0.00 0.00 35.64 3.27
97 98 7.625469 TCCTTTGTTCCATTTACTTTGGTTTT 58.375 30.769 0.00 0.00 35.64 2.43
98 99 7.766738 TCCTTTGTTCCATTTACTTTGGTTTTC 59.233 33.333 0.00 0.00 35.64 2.29
99 100 7.768582 CCTTTGTTCCATTTACTTTGGTTTTCT 59.231 33.333 0.00 0.00 35.64 2.52
100 101 9.161629 CTTTGTTCCATTTACTTTGGTTTTCTT 57.838 29.630 0.00 0.00 35.64 2.52
101 102 9.508642 TTTGTTCCATTTACTTTGGTTTTCTTT 57.491 25.926 0.00 0.00 35.64 2.52
102 103 8.485976 TGTTCCATTTACTTTGGTTTTCTTTG 57.514 30.769 0.00 0.00 35.64 2.77
103 104 8.097662 TGTTCCATTTACTTTGGTTTTCTTTGT 58.902 29.630 0.00 0.00 35.64 2.83
104 105 8.941977 GTTCCATTTACTTTGGTTTTCTTTGTT 58.058 29.630 0.00 0.00 35.64 2.83
105 106 9.508642 TTCCATTTACTTTGGTTTTCTTTGTTT 57.491 25.926 0.00 0.00 35.64 2.83
112 113 7.802738 ACTTTGGTTTTCTTTGTTTACTTTGC 58.197 30.769 0.00 0.00 0.00 3.68
113 114 7.659799 ACTTTGGTTTTCTTTGTTTACTTTGCT 59.340 29.630 0.00 0.00 0.00 3.91
114 115 7.971183 TTGGTTTTCTTTGTTTACTTTGCTT 57.029 28.000 0.00 0.00 0.00 3.91
115 116 7.589574 TGGTTTTCTTTGTTTACTTTGCTTC 57.410 32.000 0.00 0.00 0.00 3.86
116 117 7.382898 TGGTTTTCTTTGTTTACTTTGCTTCT 58.617 30.769 0.00 0.00 0.00 2.85
117 118 7.544217 TGGTTTTCTTTGTTTACTTTGCTTCTC 59.456 33.333 0.00 0.00 0.00 2.87
118 119 7.759886 GGTTTTCTTTGTTTACTTTGCTTCTCT 59.240 33.333 0.00 0.00 0.00 3.10
119 120 8.799091 GTTTTCTTTGTTTACTTTGCTTCTCTC 58.201 33.333 0.00 0.00 0.00 3.20
120 121 6.619801 TCTTTGTTTACTTTGCTTCTCTCC 57.380 37.500 0.00 0.00 0.00 3.71
121 122 6.357367 TCTTTGTTTACTTTGCTTCTCTCCT 58.643 36.000 0.00 0.00 0.00 3.69
122 123 6.828785 TCTTTGTTTACTTTGCTTCTCTCCTT 59.171 34.615 0.00 0.00 0.00 3.36
123 124 6.377327 TTGTTTACTTTGCTTCTCTCCTTG 57.623 37.500 0.00 0.00 0.00 3.61
124 125 4.821805 TGTTTACTTTGCTTCTCTCCTTGG 59.178 41.667 0.00 0.00 0.00 3.61
125 126 4.706842 TTACTTTGCTTCTCTCCTTGGT 57.293 40.909 0.00 0.00 0.00 3.67
126 127 3.584733 ACTTTGCTTCTCTCCTTGGTT 57.415 42.857 0.00 0.00 0.00 3.67
127 128 3.903467 ACTTTGCTTCTCTCCTTGGTTT 58.097 40.909 0.00 0.00 0.00 3.27
128 129 3.885901 ACTTTGCTTCTCTCCTTGGTTTC 59.114 43.478 0.00 0.00 0.00 2.78
129 130 3.864789 TTGCTTCTCTCCTTGGTTTCT 57.135 42.857 0.00 0.00 0.00 2.52
130 131 4.974645 TTGCTTCTCTCCTTGGTTTCTA 57.025 40.909 0.00 0.00 0.00 2.10
131 132 5.505181 TTGCTTCTCTCCTTGGTTTCTAT 57.495 39.130 0.00 0.00 0.00 1.98
132 133 5.091261 TGCTTCTCTCCTTGGTTTCTATC 57.909 43.478 0.00 0.00 0.00 2.08
133 134 4.116238 GCTTCTCTCCTTGGTTTCTATCG 58.884 47.826 0.00 0.00 0.00 2.92
134 135 4.688021 CTTCTCTCCTTGGTTTCTATCGG 58.312 47.826 0.00 0.00 0.00 4.18
135 136 3.709587 TCTCTCCTTGGTTTCTATCGGT 58.290 45.455 0.00 0.00 0.00 4.69
136 137 4.094476 TCTCTCCTTGGTTTCTATCGGTT 58.906 43.478 0.00 0.00 0.00 4.44
137 138 4.530946 TCTCTCCTTGGTTTCTATCGGTTT 59.469 41.667 0.00 0.00 0.00 3.27
138 139 5.012768 TCTCTCCTTGGTTTCTATCGGTTTT 59.987 40.000 0.00 0.00 0.00 2.43
139 140 5.627135 TCTCCTTGGTTTCTATCGGTTTTT 58.373 37.500 0.00 0.00 0.00 1.94
170 171 9.658799 TTCTCCTTTTGTATAGAAACAGAGATG 57.341 33.333 17.47 3.28 0.00 2.90
171 172 8.816894 TCTCCTTTTGTATAGAAACAGAGATGT 58.183 33.333 14.73 0.00 0.00 3.06
172 173 9.442047 CTCCTTTTGTATAGAAACAGAGATGTT 57.558 33.333 12.28 0.00 0.00 2.71
173 174 9.793259 TCCTTTTGTATAGAAACAGAGATGTTT 57.207 29.630 6.08 6.08 43.77 2.83
288 289 4.067913 TGATCACGCGGCTGCTGA 62.068 61.111 17.03 17.63 39.65 4.26
311 322 2.847327 TCTGCACAGGAGAAGGAAAG 57.153 50.000 0.00 0.00 0.00 2.62
369 387 4.392166 TCCTACCCAGCTCCGCCA 62.392 66.667 0.00 0.00 0.00 5.69
556 582 2.041922 TCCCACCATCTCCCCGAG 60.042 66.667 0.00 0.00 0.00 4.63
673 718 4.602696 CCGTCGCCGCCTACTACG 62.603 72.222 0.00 0.00 0.00 3.51
829 875 7.661847 TGAAAAATTCCTTCTCTGAAGTCCTAC 59.338 37.037 6.57 0.00 0.00 3.18
833 879 6.749036 TTCCTTCTCTGAAGTCCTACTTTT 57.251 37.500 6.57 0.00 38.80 2.27
834 880 7.850935 TTCCTTCTCTGAAGTCCTACTTTTA 57.149 36.000 6.57 0.00 38.80 1.52
1140 1511 3.374058 GTGCACCGTTTCAGCTACATATT 59.626 43.478 5.22 0.00 0.00 1.28
1185 1556 3.107661 GCTGCACAAACATGGCGC 61.108 61.111 0.00 0.00 0.00 6.53
1259 1631 3.871463 GCCTTGAGACCAGTTGACATGAT 60.871 47.826 0.00 0.00 0.00 2.45
1333 1739 2.300152 CAGCTTGGTCACTTCTAGTGGA 59.700 50.000 6.96 0.00 45.94 4.02
2408 5110 1.274167 CAACATGGCTTGCCACTGATT 59.726 47.619 17.22 6.14 0.00 2.57
2432 5134 9.918630 ATTGACTTTGATTGATTTTACCTGAAG 57.081 29.630 0.00 0.00 0.00 3.02
2448 5150 2.981977 GAAGTCGGGTTGTGGTCGCA 62.982 60.000 0.00 0.00 0.00 5.10
2556 5276 2.138595 ACCACGCTAACCAGGTCAA 58.861 52.632 0.00 0.00 0.00 3.18
2557 5277 0.034896 ACCACGCTAACCAGGTCAAG 59.965 55.000 0.00 0.00 0.00 3.02
2885 6268 6.839124 ACCGATACCCGATAACATACATAA 57.161 37.500 0.00 0.00 41.76 1.90
2894 6277 6.258287 CCCGATAACATACATAAAAACACCGA 59.742 38.462 0.00 0.00 0.00 4.69
3218 6605 4.263068 GGTAATACATGAGCTGCATACCCT 60.263 45.833 0.00 0.00 34.82 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.372369 CCAAAAACAGTACAAAAGGAATGTAAA 57.628 29.630 0.00 0.00 35.21 2.01
16 17 8.532819 ACCAAAAACAGTACAAAAGGAATGTAA 58.467 29.630 0.00 0.00 35.21 2.41
17 18 8.068892 ACCAAAAACAGTACAAAAGGAATGTA 57.931 30.769 0.00 0.00 32.27 2.29
18 19 6.941857 ACCAAAAACAGTACAAAAGGAATGT 58.058 32.000 0.00 0.00 34.81 2.71
19 20 7.333174 ACAACCAAAAACAGTACAAAAGGAATG 59.667 33.333 0.00 0.00 0.00 2.67
20 21 7.390823 ACAACCAAAAACAGTACAAAAGGAAT 58.609 30.769 0.00 0.00 0.00 3.01
21 22 6.760291 ACAACCAAAAACAGTACAAAAGGAA 58.240 32.000 0.00 0.00 0.00 3.36
22 23 6.209788 AGACAACCAAAAACAGTACAAAAGGA 59.790 34.615 0.00 0.00 0.00 3.36
23 24 6.394809 AGACAACCAAAAACAGTACAAAAGG 58.605 36.000 0.00 0.00 0.00 3.11
24 25 7.883229 AAGACAACCAAAAACAGTACAAAAG 57.117 32.000 0.00 0.00 0.00 2.27
25 26 8.552034 CAAAAGACAACCAAAAACAGTACAAAA 58.448 29.630 0.00 0.00 0.00 2.44
26 27 7.926555 TCAAAAGACAACCAAAAACAGTACAAA 59.073 29.630 0.00 0.00 0.00 2.83
27 28 7.434492 TCAAAAGACAACCAAAAACAGTACAA 58.566 30.769 0.00 0.00 0.00 2.41
28 29 6.982852 TCAAAAGACAACCAAAAACAGTACA 58.017 32.000 0.00 0.00 0.00 2.90
29 30 8.474006 AATCAAAAGACAACCAAAAACAGTAC 57.526 30.769 0.00 0.00 0.00 2.73
31 32 7.977789 AAATCAAAAGACAACCAAAAACAGT 57.022 28.000 0.00 0.00 0.00 3.55
78 79 8.487313 ACAAAGAAAACCAAAGTAAATGGAAC 57.513 30.769 0.00 0.00 40.56 3.62
79 80 9.508642 AAACAAAGAAAACCAAAGTAAATGGAA 57.491 25.926 0.00 0.00 40.56 3.53
86 87 8.927721 GCAAAGTAAACAAAGAAAACCAAAGTA 58.072 29.630 0.00 0.00 0.00 2.24
87 88 7.659799 AGCAAAGTAAACAAAGAAAACCAAAGT 59.340 29.630 0.00 0.00 0.00 2.66
88 89 8.028540 AGCAAAGTAAACAAAGAAAACCAAAG 57.971 30.769 0.00 0.00 0.00 2.77
89 90 7.971183 AGCAAAGTAAACAAAGAAAACCAAA 57.029 28.000 0.00 0.00 0.00 3.28
90 91 7.875554 AGAAGCAAAGTAAACAAAGAAAACCAA 59.124 29.630 0.00 0.00 0.00 3.67
91 92 7.382898 AGAAGCAAAGTAAACAAAGAAAACCA 58.617 30.769 0.00 0.00 0.00 3.67
92 93 7.759886 AGAGAAGCAAAGTAAACAAAGAAAACC 59.240 33.333 0.00 0.00 0.00 3.27
93 94 8.689251 AGAGAAGCAAAGTAAACAAAGAAAAC 57.311 30.769 0.00 0.00 0.00 2.43
94 95 7.973944 GGAGAGAAGCAAAGTAAACAAAGAAAA 59.026 33.333 0.00 0.00 0.00 2.29
95 96 7.339466 AGGAGAGAAGCAAAGTAAACAAAGAAA 59.661 33.333 0.00 0.00 0.00 2.52
96 97 6.828785 AGGAGAGAAGCAAAGTAAACAAAGAA 59.171 34.615 0.00 0.00 0.00 2.52
97 98 6.357367 AGGAGAGAAGCAAAGTAAACAAAGA 58.643 36.000 0.00 0.00 0.00 2.52
98 99 6.625873 AGGAGAGAAGCAAAGTAAACAAAG 57.374 37.500 0.00 0.00 0.00 2.77
99 100 6.183360 CCAAGGAGAGAAGCAAAGTAAACAAA 60.183 38.462 0.00 0.00 0.00 2.83
100 101 5.299279 CCAAGGAGAGAAGCAAAGTAAACAA 59.701 40.000 0.00 0.00 0.00 2.83
101 102 4.821805 CCAAGGAGAGAAGCAAAGTAAACA 59.178 41.667 0.00 0.00 0.00 2.83
102 103 4.822350 ACCAAGGAGAGAAGCAAAGTAAAC 59.178 41.667 0.00 0.00 0.00 2.01
103 104 5.048846 ACCAAGGAGAGAAGCAAAGTAAA 57.951 39.130 0.00 0.00 0.00 2.01
104 105 4.706842 ACCAAGGAGAGAAGCAAAGTAA 57.293 40.909 0.00 0.00 0.00 2.24
105 106 4.706842 AACCAAGGAGAGAAGCAAAGTA 57.293 40.909 0.00 0.00 0.00 2.24
106 107 3.584733 AACCAAGGAGAGAAGCAAAGT 57.415 42.857 0.00 0.00 0.00 2.66
107 108 4.140536 AGAAACCAAGGAGAGAAGCAAAG 58.859 43.478 0.00 0.00 0.00 2.77
108 109 4.170468 AGAAACCAAGGAGAGAAGCAAA 57.830 40.909 0.00 0.00 0.00 3.68
109 110 3.864789 AGAAACCAAGGAGAGAAGCAA 57.135 42.857 0.00 0.00 0.00 3.91
110 111 4.382040 CGATAGAAACCAAGGAGAGAAGCA 60.382 45.833 0.00 0.00 39.76 3.91
111 112 4.116238 CGATAGAAACCAAGGAGAGAAGC 58.884 47.826 0.00 0.00 39.76 3.86
112 113 4.160626 ACCGATAGAAACCAAGGAGAGAAG 59.839 45.833 0.00 0.00 39.76 2.85
113 114 4.094476 ACCGATAGAAACCAAGGAGAGAA 58.906 43.478 0.00 0.00 39.76 2.87
114 115 3.709587 ACCGATAGAAACCAAGGAGAGA 58.290 45.455 0.00 0.00 39.76 3.10
115 116 4.473477 AACCGATAGAAACCAAGGAGAG 57.527 45.455 0.00 0.00 39.76 3.20
116 117 4.903045 AAACCGATAGAAACCAAGGAGA 57.097 40.909 0.00 0.00 39.76 3.71
117 118 5.959618 AAAAACCGATAGAAACCAAGGAG 57.040 39.130 0.00 0.00 39.76 3.69
144 145 9.658799 CATCTCTGTTTCTATACAAAAGGAGAA 57.341 33.333 9.14 0.00 33.46 2.87
145 146 8.816894 ACATCTCTGTTTCTATACAAAAGGAGA 58.183 33.333 8.15 8.15 33.86 3.71
146 147 9.442047 AACATCTCTGTTTCTATACAAAAGGAG 57.558 33.333 0.00 0.00 43.05 3.69
196 197 9.416794 CAGTTGCCACATACATATTTTGTTAAA 57.583 29.630 0.00 0.00 39.87 1.52
198 199 8.026026 CACAGTTGCCACATACATATTTTGTTA 58.974 33.333 0.00 0.00 39.87 2.41
202 203 6.389091 CACACAGTTGCCACATACATATTTT 58.611 36.000 0.00 0.00 0.00 1.82
288 289 0.534412 CCTTCTCCTGTGCAGATCGT 59.466 55.000 0.02 0.00 0.00 3.73
311 322 2.524569 GAGATAAGGCTCCTGTCAGC 57.475 55.000 0.00 0.00 38.84 4.26
369 387 3.740128 GAGATGGGTGCGTGGCGAT 62.740 63.158 0.00 0.00 0.00 4.58
556 582 0.736325 CCCGACGATGACTTGTGGAC 60.736 60.000 0.00 0.00 0.00 4.02
673 718 1.204941 ACCATAAGCTCACCTGTCGAC 59.795 52.381 9.11 9.11 0.00 4.20
829 875 9.801873 TTTTTGAAGACTTCTGTCCATTAAAAG 57.198 29.630 16.02 0.00 43.91 2.27
833 879 8.576442 GGAATTTTTGAAGACTTCTGTCCATTA 58.424 33.333 16.02 0.00 43.91 1.90
834 880 7.069826 TGGAATTTTTGAAGACTTCTGTCCATT 59.930 33.333 16.02 7.97 43.91 3.16
958 1327 2.881403 GCACCATGATCAGGAACCTGTT 60.881 50.000 18.60 11.73 43.96 3.16
1140 1511 0.110486 GGTCTTGAGGCCCTTTCACA 59.890 55.000 0.00 0.00 0.00 3.58
1185 1556 0.533755 GTCAGCCCCAAGATCGATGG 60.534 60.000 0.54 12.26 37.71 3.51
1259 1631 5.223449 ACTTCCTCGGAACAAAATACTCA 57.777 39.130 0.00 0.00 0.00 3.41
1333 1739 5.277683 GCAAAGTGATCGTTATCATGCTGAT 60.278 40.000 5.58 4.45 43.87 2.90
1772 2865 5.882557 AGATCGGATTAAAAATGCTGACACT 59.117 36.000 0.00 0.00 0.00 3.55
1852 2949 7.475015 TCAAAGTTATCAAGCTGACATATTGC 58.525 34.615 0.00 0.00 0.00 3.56
2243 4921 1.338105 TGGATGAAGCTGAAGACCACG 60.338 52.381 0.00 0.00 0.00 4.94
2408 5110 8.463930 ACTTCAGGTAAAATCAATCAAAGTCA 57.536 30.769 0.00 0.00 0.00 3.41
2432 5134 2.358247 ATGCGACCACAACCCGAC 60.358 61.111 0.00 0.00 0.00 4.79
2448 5150 0.904649 TCACGAAGGACATGCCAGAT 59.095 50.000 8.58 0.00 40.02 2.90
2556 5276 5.089970 TCTTAGCACAAGCATGATGTACT 57.910 39.130 0.00 3.47 45.49 2.73
2557 5277 5.998454 ATCTTAGCACAAGCATGATGTAC 57.002 39.130 0.00 0.00 45.49 2.90
2885 6268 4.701171 TGTTCAAAGTTACCTCGGTGTTTT 59.299 37.500 0.00 0.00 0.00 2.43
2894 6277 6.844097 TTTTTCCACTGTTCAAAGTTACCT 57.156 33.333 0.00 0.00 0.00 3.08
3088 6473 1.269413 ACTTATCGGGTATGCGGTTCG 60.269 52.381 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.