Multiple sequence alignment - TraesCS7A01G066800

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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 TraesCS7A01G066800 chr7A 100.000 2414 0 0 1 2414 33456037 33453624 0.000000e+00 4458
1 TraesCS7A01G066800 chr7A 81.297 663 100 15 982 1635 33448912 33448265 1.280000e-142 516
2 TraesCS7A01G066800 chr7A 79.098 665 111 15 983 1630 33425514 33424861 1.330000e-117 433
3 TraesCS7A01G066800 chr7A 90.654 321 27 3 651 969 33426218 33425899 7.980000e-115 424
4 TraesCS7A01G066800 chr7A 79.513 493 73 15 1920 2397 33448236 33447757 2.310000e-85 326
5 TraesCS7A01G066800 chr7A 80.678 295 51 5 662 953 733781103 733781394 8.680000e-55 224
6 TraesCS7A01G066800 chr7D 96.098 1435 53 2 982 2414 33105103 33103670 0.000000e+00 2337
7 TraesCS7A01G066800 chr7D 92.523 856 52 5 135 986 33106310 33105463 0.000000e+00 1216
8 TraesCS7A01G066800 chr7D 79.372 1338 189 57 982 2278 33098210 33096919 0.000000e+00 861
9 TraesCS7A01G066800 chr7D 75.853 1466 238 66 982 2382 33056492 33055078 7.280000e-180 640
10 TraesCS7A01G066800 chr7D 80.930 645 82 15 1128 1755 33095712 33095092 2.810000e-129 472
11 TraesCS7A01G066800 chr7D 79.794 485 69 23 1050 1527 33088279 33087817 2.310000e-85 326
12 TraesCS7A01G066800 chr7D 78.986 414 44 15 136 532 33096147 33095760 2.400000e-60 243
13 TraesCS7A01G066800 chr7D 94.161 137 8 0 1 137 3406149 3406285 2.430000e-50 209
14 TraesCS7A01G066800 chr7D 89.423 104 10 1 1640 1742 33087758 33087655 1.950000e-26 130
15 TraesCS7A01G066800 chr7D 91.463 82 5 2 2317 2397 33094913 33094833 7.050000e-21 111
16 TraesCS7A01G066800 chr4A 93.969 1426 60 12 982 2396 693490828 693489418 0.000000e+00 2134
17 TraesCS7A01G066800 chr4A 78.732 1467 221 49 982 2397 693451437 693450011 0.000000e+00 896
18 TraesCS7A01G066800 chr4A 93.642 346 22 0 641 986 693491542 693491197 3.560000e-143 518
19 TraesCS7A01G066800 chr4A 90.933 375 30 4 597 969 693445324 693444952 3.580000e-138 501
20 TraesCS7A01G066800 chr4A 79.484 697 106 25 978 1654 693444573 693443894 6.080000e-126 460
21 TraesCS7A01G066800 chr4A 87.371 388 24 9 620 984 693433372 693432987 2.870000e-114 422
22 TraesCS7A01G066800 chr4A 83.810 420 52 10 982 1390 693432601 693432187 3.760000e-103 385
23 TraesCS7A01G066800 chr4A 94.000 50 2 1 2349 2397 693431893 693431844 9.260000e-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 TraesCS7A01G066800 chr7A 33453624 33456037 2413 True 4458.00 4458 100.000000 1 2414 1 chr7A.!!$R1 2413
1 TraesCS7A01G066800 chr7A 33424861 33426218 1357 True 428.50 433 84.876000 651 1630 2 chr7A.!!$R2 979
2 TraesCS7A01G066800 chr7A 33447757 33448912 1155 True 421.00 516 80.405000 982 2397 2 chr7A.!!$R3 1415
3 TraesCS7A01G066800 chr7D 33103670 33106310 2640 True 1776.50 2337 94.310500 135 2414 2 chr7D.!!$R4 2279
4 TraesCS7A01G066800 chr7D 33055078 33056492 1414 True 640.00 640 75.853000 982 2382 1 chr7D.!!$R1 1400
5 TraesCS7A01G066800 chr7D 33094833 33098210 3377 True 421.75 861 82.687750 136 2397 4 chr7D.!!$R3 2261
6 TraesCS7A01G066800 chr7D 33087655 33088279 624 True 228.00 326 84.608500 1050 1742 2 chr7D.!!$R2 692
7 TraesCS7A01G066800 chr4A 693489418 693491542 2124 True 1326.00 2134 93.805500 641 2396 2 chr4A.!!$R4 1755
8 TraesCS7A01G066800 chr4A 693450011 693451437 1426 True 896.00 896 78.732000 982 2397 1 chr4A.!!$R1 1415
9 TraesCS7A01G066800 chr4A 693443894 693445324 1430 True 480.50 501 85.208500 597 1654 2 chr4A.!!$R3 1057
10 TraesCS7A01G066800 chr4A 693431844 693433372 1528 True 294.00 422 88.393667 620 2397 3 chr4A.!!$R2 1777

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
43 44 0.036010 CTTCCTGAATGTCGGGTGCT 60.036 55.0 3.08 0.0 43.49 4.40 F
278 279 0.042188 CTGGTTGAGTTTCGTGTGCG 60.042 55.0 0.00 0.0 39.92 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1048 1465 1.000739 CCACAATGGCCATGTCCCT 59.999 57.895 21.63 0.00 0.00 4.20 R
1547 1997 1.187567 AACTTGGGAGTTGGCCATGC 61.188 55.000 6.09 2.32 44.27 4.06 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
21 22 3.702330 GTTAGGTGTTGTTGTTCCTTGC 58.298 45.455 0.00 0.00 0.00 4.01
22 23 2.143876 AGGTGTTGTTGTTCCTTGCT 57.856 45.000 0.00 0.00 0.00 3.91
23 24 2.024414 AGGTGTTGTTGTTCCTTGCTC 58.976 47.619 0.00 0.00 0.00 4.26
24 25 1.067060 GGTGTTGTTGTTCCTTGCTCC 59.933 52.381 0.00 0.00 0.00 4.70
25 26 2.024414 GTGTTGTTGTTCCTTGCTCCT 58.976 47.619 0.00 0.00 0.00 3.69
26 27 2.427095 GTGTTGTTGTTCCTTGCTCCTT 59.573 45.455 0.00 0.00 0.00 3.36
27 28 2.687935 TGTTGTTGTTCCTTGCTCCTTC 59.312 45.455 0.00 0.00 0.00 3.46
28 29 1.981256 TGTTGTTCCTTGCTCCTTCC 58.019 50.000 0.00 0.00 0.00 3.46
29 30 1.494721 TGTTGTTCCTTGCTCCTTCCT 59.505 47.619 0.00 0.00 0.00 3.36
30 31 1.882623 GTTGTTCCTTGCTCCTTCCTG 59.117 52.381 0.00 0.00 0.00 3.86
31 32 1.434188 TGTTCCTTGCTCCTTCCTGA 58.566 50.000 0.00 0.00 0.00 3.86
32 33 1.774254 TGTTCCTTGCTCCTTCCTGAA 59.226 47.619 0.00 0.00 0.00 3.02
33 34 2.376518 TGTTCCTTGCTCCTTCCTGAAT 59.623 45.455 0.00 0.00 0.00 2.57
34 35 2.751806 GTTCCTTGCTCCTTCCTGAATG 59.248 50.000 0.00 0.00 0.00 2.67
35 36 1.988107 TCCTTGCTCCTTCCTGAATGT 59.012 47.619 0.00 0.00 0.00 2.71
36 37 2.026822 TCCTTGCTCCTTCCTGAATGTC 60.027 50.000 0.00 0.00 0.00 3.06
37 38 2.005451 CTTGCTCCTTCCTGAATGTCG 58.995 52.381 0.00 0.00 0.00 4.35
38 39 0.250234 TGCTCCTTCCTGAATGTCGG 59.750 55.000 0.00 0.00 0.00 4.79
39 40 0.462759 GCTCCTTCCTGAATGTCGGG 60.463 60.000 0.00 0.00 44.41 5.14
40 41 0.905357 CTCCTTCCTGAATGTCGGGT 59.095 55.000 3.08 0.00 43.49 5.28
41 42 0.613260 TCCTTCCTGAATGTCGGGTG 59.387 55.000 3.08 0.00 43.49 4.61
42 43 1.026718 CCTTCCTGAATGTCGGGTGC 61.027 60.000 3.08 0.00 43.49 5.01
43 44 0.036010 CTTCCTGAATGTCGGGTGCT 60.036 55.000 3.08 0.00 43.49 4.40
44 45 1.207089 CTTCCTGAATGTCGGGTGCTA 59.793 52.381 3.08 0.00 43.49 3.49
45 46 1.496060 TCCTGAATGTCGGGTGCTAT 58.504 50.000 3.08 0.00 43.49 2.97
46 47 1.138859 TCCTGAATGTCGGGTGCTATG 59.861 52.381 3.08 0.00 43.49 2.23
47 48 1.134401 CCTGAATGTCGGGTGCTATGT 60.134 52.381 0.00 0.00 38.13 2.29
48 49 1.935873 CTGAATGTCGGGTGCTATGTG 59.064 52.381 0.00 0.00 0.00 3.21
49 50 1.277842 TGAATGTCGGGTGCTATGTGT 59.722 47.619 0.00 0.00 0.00 3.72
50 51 2.290008 TGAATGTCGGGTGCTATGTGTT 60.290 45.455 0.00 0.00 0.00 3.32
51 52 1.737838 ATGTCGGGTGCTATGTGTTG 58.262 50.000 0.00 0.00 0.00 3.33
52 53 0.394938 TGTCGGGTGCTATGTGTTGT 59.605 50.000 0.00 0.00 0.00 3.32
53 54 1.619332 TGTCGGGTGCTATGTGTTGTA 59.381 47.619 0.00 0.00 0.00 2.41
54 55 1.997606 GTCGGGTGCTATGTGTTGTAC 59.002 52.381 0.00 0.00 0.00 2.90
55 56 1.066716 TCGGGTGCTATGTGTTGTACC 60.067 52.381 0.00 0.00 38.06 3.34
57 58 1.365699 GGTGCTATGTGTTGTACCCG 58.634 55.000 0.00 0.00 33.72 5.28
58 59 1.338389 GGTGCTATGTGTTGTACCCGT 60.338 52.381 0.00 0.00 33.72 5.28
59 60 1.997606 GTGCTATGTGTTGTACCCGTC 59.002 52.381 0.00 0.00 0.00 4.79
60 61 1.274596 GCTATGTGTTGTACCCGTCG 58.725 55.000 0.00 0.00 0.00 5.12
61 62 1.403249 GCTATGTGTTGTACCCGTCGT 60.403 52.381 0.00 0.00 0.00 4.34
62 63 2.256174 CTATGTGTTGTACCCGTCGTG 58.744 52.381 0.00 0.00 0.00 4.35
63 64 0.390124 ATGTGTTGTACCCGTCGTGT 59.610 50.000 0.00 0.00 0.00 4.49
64 65 0.175302 TGTGTTGTACCCGTCGTGTT 59.825 50.000 0.00 0.00 0.00 3.32
65 66 0.578211 GTGTTGTACCCGTCGTGTTG 59.422 55.000 0.00 0.00 0.00 3.33
66 67 0.175302 TGTTGTACCCGTCGTGTTGT 59.825 50.000 0.00 0.00 0.00 3.32
67 68 1.406898 TGTTGTACCCGTCGTGTTGTA 59.593 47.619 0.00 0.00 0.00 2.41
68 69 2.035704 TGTTGTACCCGTCGTGTTGTAT 59.964 45.455 0.00 0.00 0.00 2.29
69 70 2.634982 TGTACCCGTCGTGTTGTATC 57.365 50.000 0.00 0.00 0.00 2.24
70 71 2.161855 TGTACCCGTCGTGTTGTATCT 58.838 47.619 0.00 0.00 0.00 1.98
71 72 2.162208 TGTACCCGTCGTGTTGTATCTC 59.838 50.000 0.00 0.00 0.00 2.75
72 73 1.250328 ACCCGTCGTGTTGTATCTCA 58.750 50.000 0.00 0.00 0.00 3.27
73 74 1.068055 ACCCGTCGTGTTGTATCTCAC 60.068 52.381 0.00 0.00 0.00 3.51
74 75 1.201647 CCCGTCGTGTTGTATCTCACT 59.798 52.381 0.00 0.00 33.07 3.41
75 76 2.516923 CCGTCGTGTTGTATCTCACTC 58.483 52.381 0.00 0.00 33.07 3.51
76 77 2.161808 CCGTCGTGTTGTATCTCACTCT 59.838 50.000 0.00 0.00 33.07 3.24
77 78 3.366070 CCGTCGTGTTGTATCTCACTCTT 60.366 47.826 0.00 0.00 33.07 2.85
78 79 4.142752 CCGTCGTGTTGTATCTCACTCTTA 60.143 45.833 0.00 0.00 33.07 2.10
79 80 5.448768 CCGTCGTGTTGTATCTCACTCTTAT 60.449 44.000 0.00 0.00 33.07 1.73
80 81 6.028368 CGTCGTGTTGTATCTCACTCTTATT 58.972 40.000 0.00 0.00 33.07 1.40
81 82 6.527023 CGTCGTGTTGTATCTCACTCTTATTT 59.473 38.462 0.00 0.00 33.07 1.40
82 83 7.695201 CGTCGTGTTGTATCTCACTCTTATTTA 59.305 37.037 0.00 0.00 33.07 1.40
83 84 9.517609 GTCGTGTTGTATCTCACTCTTATTTAT 57.482 33.333 0.00 0.00 33.07 1.40
101 102 9.696917 CTTATTTATAATGGAATTGGTTCAGGC 57.303 33.333 0.00 0.00 36.99 4.85
102 103 6.478512 TTTATAATGGAATTGGTTCAGGCC 57.521 37.500 0.00 0.00 36.99 5.19
103 104 1.185315 AATGGAATTGGTTCAGGCCG 58.815 50.000 0.00 0.00 33.44 6.13
104 105 0.684153 ATGGAATTGGTTCAGGCCGG 60.684 55.000 0.00 0.00 36.01 6.13
105 106 2.710902 GGAATTGGTTCAGGCCGGC 61.711 63.158 21.18 21.18 36.01 6.13
106 107 3.051392 GAATTGGTTCAGGCCGGCG 62.051 63.158 22.54 7.85 34.41 6.46
107 108 3.860930 AATTGGTTCAGGCCGGCGT 62.861 57.895 22.54 20.09 0.00 5.68
108 109 2.472414 AATTGGTTCAGGCCGGCGTA 62.472 55.000 23.15 4.02 0.00 4.42
109 110 2.472414 ATTGGTTCAGGCCGGCGTAA 62.472 55.000 23.15 12.63 0.00 3.18
110 111 2.358984 GGTTCAGGCCGGCGTAAA 60.359 61.111 23.15 11.77 0.00 2.01
111 112 2.683859 GGTTCAGGCCGGCGTAAAC 61.684 63.158 24.06 24.06 0.00 2.01
112 113 2.358984 TTCAGGCCGGCGTAAACC 60.359 61.111 23.15 5.54 0.00 3.27
113 114 3.905437 TTCAGGCCGGCGTAAACCC 62.905 63.158 23.15 4.68 0.00 4.11
114 115 4.708386 CAGGCCGGCGTAAACCCA 62.708 66.667 23.15 0.00 0.00 4.51
115 116 4.710167 AGGCCGGCGTAAACCCAC 62.710 66.667 22.26 2.03 0.00 4.61
118 119 4.685467 CCGGCGTAAACCCACCGT 62.685 66.667 6.01 0.00 44.14 4.83
119 120 2.261052 CGGCGTAAACCCACCGTA 59.739 61.111 0.00 0.00 40.77 4.02
120 121 1.806758 CGGCGTAAACCCACCGTAG 60.807 63.158 0.00 0.00 40.77 3.51
121 122 2.102438 GGCGTAAACCCACCGTAGC 61.102 63.158 0.00 0.00 0.00 3.58
122 123 1.374505 GCGTAAACCCACCGTAGCA 60.375 57.895 0.00 0.00 0.00 3.49
123 124 1.629345 GCGTAAACCCACCGTAGCAC 61.629 60.000 0.00 0.00 0.00 4.40
124 125 1.015607 CGTAAACCCACCGTAGCACC 61.016 60.000 0.00 0.00 0.00 5.01
125 126 1.015607 GTAAACCCACCGTAGCACCG 61.016 60.000 0.00 0.00 0.00 4.94
126 127 1.470996 TAAACCCACCGTAGCACCGT 61.471 55.000 0.00 0.00 0.00 4.83
127 128 2.328155 AAACCCACCGTAGCACCGTT 62.328 55.000 0.00 0.00 0.00 4.44
128 129 1.470996 AACCCACCGTAGCACCGTTA 61.471 55.000 0.00 0.00 0.00 3.18
129 130 1.292860 CCCACCGTAGCACCGTTAA 59.707 57.895 0.00 0.00 0.00 2.01
130 131 0.320596 CCCACCGTAGCACCGTTAAA 60.321 55.000 0.00 0.00 0.00 1.52
131 132 1.510776 CCACCGTAGCACCGTTAAAA 58.489 50.000 0.00 0.00 0.00 1.52
132 133 1.872313 CCACCGTAGCACCGTTAAAAA 59.128 47.619 0.00 0.00 0.00 1.94
162 163 2.455674 TATCACTTCGCAACAGCTGT 57.544 45.000 15.25 15.25 0.00 4.40
167 168 1.071605 CTTCGCAACAGCTGTAGACC 58.928 55.000 22.01 7.78 0.00 3.85
174 175 2.105006 ACAGCTGTAGACCTGCAATG 57.895 50.000 20.16 0.00 40.25 2.82
182 183 1.675641 GACCTGCAATGGCGTCCTT 60.676 57.895 0.00 0.00 45.35 3.36
192 193 3.864789 ATGGCGTCCTTATTTCTCCAT 57.135 42.857 0.00 0.00 0.00 3.41
224 225 2.176148 TGTCGTCACATAGGGATAGGGA 59.824 50.000 0.00 0.00 0.00 4.20
233 234 0.104934 AGGGATAGGGATTGCCGTCT 60.105 55.000 3.48 0.00 33.56 4.18
249 250 2.821366 CTCGGGCGATGCTGCTTT 60.821 61.111 0.00 0.00 34.52 3.51
264 265 1.322442 GCTTTCCAACTGCTCTGGTT 58.678 50.000 0.00 0.00 35.30 3.67
268 269 1.131638 TCCAACTGCTCTGGTTGAGT 58.868 50.000 7.96 0.00 44.58 3.41
278 279 0.042188 CTGGTTGAGTTTCGTGTGCG 60.042 55.000 0.00 0.00 39.92 5.34
279 280 1.368850 GGTTGAGTTTCGTGTGCGC 60.369 57.895 0.00 0.00 38.14 6.09
321 326 1.081242 CTCGGCCATGTGTTGTTGC 60.081 57.895 2.24 0.00 0.00 4.17
327 332 1.321474 CCATGTGTTGTTGCTGGACT 58.679 50.000 0.00 0.00 0.00 3.85
365 370 4.445385 GTGCATGAACACATTTCTTTCACC 59.555 41.667 0.00 0.00 40.40 4.02
406 411 7.260603 GGAGGGAAAATCATTAATGTTGTCAG 58.739 38.462 14.97 0.00 0.00 3.51
451 456 8.867935 TGTGAAGTTAACATTGTTGTCAAAATG 58.132 29.630 12.30 14.02 39.26 2.32
579 584 6.605119 AGTAGCTAAAATGGCTGGTATCATT 58.395 36.000 0.00 0.00 40.52 2.57
581 586 6.152932 AGCTAAAATGGCTGGTATCATTTG 57.847 37.500 0.00 0.00 41.15 2.32
585 590 5.796424 AAATGGCTGGTATCATTTGGATC 57.204 39.130 0.00 0.00 40.68 3.36
966 992 3.567579 TTTTCAGCCCCCGCCTCAG 62.568 63.158 0.00 0.00 34.57 3.35
1018 1435 3.323403 CAGGATGGAGTTCTCCACTATCC 59.677 52.174 21.70 22.20 43.37 2.59
1023 1440 3.271225 TGGAGTTCTCCACTATCCACCTA 59.729 47.826 16.47 0.00 35.01 3.08
1048 1465 3.242867 CCTCCACCTGGCTCTTATATGA 58.757 50.000 0.00 0.00 34.44 2.15
1101 1518 4.530553 GGAAGGTTTGGGATGTTTACCATT 59.469 41.667 0.00 0.00 36.48 3.16
1287 1727 3.278574 TCCAAAAGATGATAGGCCAACG 58.721 45.455 5.01 0.00 0.00 4.10
1439 1880 1.620822 AAGCTTGCCCTCGATTTTGT 58.379 45.000 0.00 0.00 0.00 2.83
1449 1890 7.259290 TGCCCTCGATTTTGTATTTCTTATC 57.741 36.000 0.00 0.00 0.00 1.75
1547 1997 1.006832 CGGTCCTGAATTAACGCTGG 58.993 55.000 0.00 0.00 0.00 4.85
1569 4430 0.111639 TGGCCAACTCCCAAGTTACC 59.888 55.000 0.61 0.00 43.99 2.85
1584 4445 6.602009 CCCAAGTTACCTTCAACCCTTTATAG 59.398 42.308 0.00 0.00 0.00 1.31
1613 4474 7.684670 TCACTCATATTGCTTGTCGTTATTTC 58.315 34.615 0.00 0.00 0.00 2.17
1761 4666 7.383102 AGAAACAGTAACCAGCATTCTTATG 57.617 36.000 0.00 0.00 34.76 1.90
1843 4786 3.073356 TCTTGTACATTTTCCCCTCCGTT 59.927 43.478 0.00 0.00 0.00 4.44
1889 4832 3.678529 GCTTCTGCTAGGTCCTTTCAGAG 60.679 52.174 17.20 13.86 35.52 3.35
1891 4834 3.093057 TCTGCTAGGTCCTTTCAGAGTC 58.907 50.000 15.11 0.00 31.07 3.36
1903 4846 5.926542 TCCTTTCAGAGTCGTTACATTCTTG 59.073 40.000 0.00 0.00 0.00 3.02
1917 4860 7.060979 CGTTACATTCTTGTCACCAATTGATTG 59.939 37.037 7.12 3.82 36.32 2.67
2086 5029 6.417044 GTGCATCATGTCTAATGAATTCTTGC 59.583 38.462 7.05 4.64 32.64 4.01
2170 5113 2.184830 CCAGCTGGCATCATCACCG 61.185 63.158 22.33 0.00 0.00 4.94
2185 5128 3.232213 TCACCGAGTTATCAAGTCTGC 57.768 47.619 0.00 0.00 0.00 4.26
2215 5160 8.902806 TGTTAGGTGGAATAGCTATGATTTTTG 58.097 33.333 7.09 0.00 39.01 2.44
2235 5180 1.267806 GGTGCAGTCAATTGACCACAG 59.732 52.381 31.47 22.42 45.85 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.024414 GAGCAAGGAACAACAACACCT 58.976 47.619 0.00 0.00 0.00 4.00
4 5 1.067060 GGAGCAAGGAACAACAACACC 59.933 52.381 0.00 0.00 0.00 4.16
5 6 2.024414 AGGAGCAAGGAACAACAACAC 58.976 47.619 0.00 0.00 0.00 3.32
7 8 2.034685 GGAAGGAGCAAGGAACAACAAC 59.965 50.000 0.00 0.00 0.00 3.32
8 9 2.091885 AGGAAGGAGCAAGGAACAACAA 60.092 45.455 0.00 0.00 0.00 2.83
9 10 1.494721 AGGAAGGAGCAAGGAACAACA 59.505 47.619 0.00 0.00 0.00 3.33
10 11 1.882623 CAGGAAGGAGCAAGGAACAAC 59.117 52.381 0.00 0.00 0.00 3.32
11 12 1.774254 TCAGGAAGGAGCAAGGAACAA 59.226 47.619 0.00 0.00 0.00 2.83
12 13 1.434188 TCAGGAAGGAGCAAGGAACA 58.566 50.000 0.00 0.00 0.00 3.18
13 14 2.568623 TTCAGGAAGGAGCAAGGAAC 57.431 50.000 0.00 0.00 0.00 3.62
14 15 2.376518 ACATTCAGGAAGGAGCAAGGAA 59.623 45.455 0.18 0.00 0.00 3.36
15 16 1.988107 ACATTCAGGAAGGAGCAAGGA 59.012 47.619 0.18 0.00 0.00 3.36
16 17 2.363683 GACATTCAGGAAGGAGCAAGG 58.636 52.381 0.18 0.00 0.00 3.61
17 18 2.005451 CGACATTCAGGAAGGAGCAAG 58.995 52.381 0.18 0.00 0.00 4.01
18 19 1.339055 CCGACATTCAGGAAGGAGCAA 60.339 52.381 0.18 0.00 0.00 3.91
19 20 0.250234 CCGACATTCAGGAAGGAGCA 59.750 55.000 0.18 0.00 0.00 4.26
20 21 0.462759 CCCGACATTCAGGAAGGAGC 60.463 60.000 0.18 0.00 0.00 4.70
21 22 0.905357 ACCCGACATTCAGGAAGGAG 59.095 55.000 0.18 0.00 0.00 3.69
22 23 0.613260 CACCCGACATTCAGGAAGGA 59.387 55.000 0.18 0.00 0.00 3.36
23 24 1.026718 GCACCCGACATTCAGGAAGG 61.027 60.000 0.00 0.00 0.00 3.46
24 25 0.036010 AGCACCCGACATTCAGGAAG 60.036 55.000 0.00 0.00 0.00 3.46
25 26 1.271856 TAGCACCCGACATTCAGGAA 58.728 50.000 0.00 0.00 0.00 3.36
26 27 1.138859 CATAGCACCCGACATTCAGGA 59.861 52.381 0.00 0.00 0.00 3.86
27 28 1.134401 ACATAGCACCCGACATTCAGG 60.134 52.381 0.00 0.00 0.00 3.86
28 29 1.935873 CACATAGCACCCGACATTCAG 59.064 52.381 0.00 0.00 0.00 3.02
29 30 1.277842 ACACATAGCACCCGACATTCA 59.722 47.619 0.00 0.00 0.00 2.57
30 31 2.024176 ACACATAGCACCCGACATTC 57.976 50.000 0.00 0.00 0.00 2.67
31 32 2.083774 CAACACATAGCACCCGACATT 58.916 47.619 0.00 0.00 0.00 2.71
32 33 1.003118 ACAACACATAGCACCCGACAT 59.997 47.619 0.00 0.00 0.00 3.06
33 34 0.394938 ACAACACATAGCACCCGACA 59.605 50.000 0.00 0.00 0.00 4.35
34 35 1.997606 GTACAACACATAGCACCCGAC 59.002 52.381 0.00 0.00 0.00 4.79
35 36 1.066716 GGTACAACACATAGCACCCGA 60.067 52.381 0.00 0.00 0.00 5.14
36 37 1.365699 GGTACAACACATAGCACCCG 58.634 55.000 0.00 0.00 0.00 5.28
37 38 1.746470 GGGTACAACACATAGCACCC 58.254 55.000 0.00 0.00 38.94 4.61
38 39 1.338389 ACGGGTACAACACATAGCACC 60.338 52.381 0.00 0.00 0.00 5.01
39 40 1.997606 GACGGGTACAACACATAGCAC 59.002 52.381 0.00 0.00 0.00 4.40
40 41 1.403116 CGACGGGTACAACACATAGCA 60.403 52.381 0.00 0.00 0.00 3.49
41 42 1.274596 CGACGGGTACAACACATAGC 58.725 55.000 0.00 0.00 0.00 2.97
42 43 2.256174 CACGACGGGTACAACACATAG 58.744 52.381 0.00 0.00 0.00 2.23
43 44 1.612950 ACACGACGGGTACAACACATA 59.387 47.619 0.00 0.00 0.00 2.29
44 45 0.390124 ACACGACGGGTACAACACAT 59.610 50.000 0.00 0.00 0.00 3.21
45 46 0.175302 AACACGACGGGTACAACACA 59.825 50.000 1.61 0.00 0.00 3.72
46 47 0.578211 CAACACGACGGGTACAACAC 59.422 55.000 1.61 0.00 0.00 3.32
47 48 0.175302 ACAACACGACGGGTACAACA 59.825 50.000 1.61 0.00 0.00 3.33
48 49 2.132740 TACAACACGACGGGTACAAC 57.867 50.000 1.61 0.00 0.00 3.32
49 50 2.557924 AGATACAACACGACGGGTACAA 59.442 45.455 1.61 0.00 0.00 2.41
50 51 2.161855 AGATACAACACGACGGGTACA 58.838 47.619 1.61 0.00 0.00 2.90
51 52 2.162208 TGAGATACAACACGACGGGTAC 59.838 50.000 1.61 0.00 0.00 3.34
52 53 2.162208 GTGAGATACAACACGACGGGTA 59.838 50.000 1.61 0.00 0.00 3.69
53 54 1.068055 GTGAGATACAACACGACGGGT 60.068 52.381 0.00 0.00 0.00 5.28
54 55 1.201647 AGTGAGATACAACACGACGGG 59.798 52.381 0.00 0.00 41.22 5.28
55 56 2.161808 AGAGTGAGATACAACACGACGG 59.838 50.000 0.00 0.00 41.22 4.79
56 57 3.473093 AGAGTGAGATACAACACGACG 57.527 47.619 0.00 0.00 41.22 5.12
57 58 7.813852 AAATAAGAGTGAGATACAACACGAC 57.186 36.000 0.00 0.00 41.22 4.34
75 76 9.696917 GCCTGAACCAATTCCATTATAAATAAG 57.303 33.333 0.00 0.00 33.49 1.73
76 77 8.646900 GGCCTGAACCAATTCCATTATAAATAA 58.353 33.333 0.00 0.00 33.49 1.40
77 78 7.040062 CGGCCTGAACCAATTCCATTATAAATA 60.040 37.037 0.00 0.00 33.49 1.40
78 79 6.239289 CGGCCTGAACCAATTCCATTATAAAT 60.239 38.462 0.00 0.00 33.49 1.40
79 80 5.068460 CGGCCTGAACCAATTCCATTATAAA 59.932 40.000 0.00 0.00 33.49 1.40
80 81 4.582656 CGGCCTGAACCAATTCCATTATAA 59.417 41.667 0.00 0.00 33.49 0.98
81 82 4.141287 CGGCCTGAACCAATTCCATTATA 58.859 43.478 0.00 0.00 33.49 0.98
82 83 2.958355 CGGCCTGAACCAATTCCATTAT 59.042 45.455 0.00 0.00 33.49 1.28
83 84 2.374184 CGGCCTGAACCAATTCCATTA 58.626 47.619 0.00 0.00 33.49 1.90
84 85 1.185315 CGGCCTGAACCAATTCCATT 58.815 50.000 0.00 0.00 33.49 3.16
85 86 0.684153 CCGGCCTGAACCAATTCCAT 60.684 55.000 0.00 0.00 33.49 3.41
86 87 1.304052 CCGGCCTGAACCAATTCCA 60.304 57.895 0.00 0.00 33.49 3.53
87 88 2.710902 GCCGGCCTGAACCAATTCC 61.711 63.158 18.11 0.00 33.49 3.01
88 89 2.885113 GCCGGCCTGAACCAATTC 59.115 61.111 18.11 0.00 35.18 2.17
89 90 2.472414 TACGCCGGCCTGAACCAATT 62.472 55.000 23.46 0.00 0.00 2.32
90 91 2.472414 TTACGCCGGCCTGAACCAAT 62.472 55.000 23.46 0.00 0.00 3.16
91 92 2.677765 TTTACGCCGGCCTGAACCAA 62.678 55.000 23.46 0.99 0.00 3.67
92 93 3.179888 TTTACGCCGGCCTGAACCA 62.180 57.895 23.46 0.00 0.00 3.67
93 94 2.358984 TTTACGCCGGCCTGAACC 60.359 61.111 23.46 0.00 0.00 3.62
94 95 2.683859 GGTTTACGCCGGCCTGAAC 61.684 63.158 23.46 21.38 0.00 3.18
95 96 2.358984 GGTTTACGCCGGCCTGAA 60.359 61.111 23.46 9.98 0.00 3.02
96 97 4.397832 GGGTTTACGCCGGCCTGA 62.398 66.667 23.46 2.61 0.00 3.86
97 98 4.708386 TGGGTTTACGCCGGCCTG 62.708 66.667 23.46 10.83 0.00 4.85
98 99 4.710167 GTGGGTTTACGCCGGCCT 62.710 66.667 23.46 12.81 0.00 5.19
103 104 2.102438 GCTACGGTGGGTTTACGCC 61.102 63.158 0.00 0.00 37.66 5.68
104 105 1.374505 TGCTACGGTGGGTTTACGC 60.375 57.895 0.00 0.00 0.00 4.42
105 106 1.015607 GGTGCTACGGTGGGTTTACG 61.016 60.000 0.00 0.00 0.00 3.18
106 107 1.015607 CGGTGCTACGGTGGGTTTAC 61.016 60.000 0.00 0.00 0.00 2.01
107 108 1.292860 CGGTGCTACGGTGGGTTTA 59.707 57.895 0.00 0.00 0.00 2.01
108 109 2.031465 CGGTGCTACGGTGGGTTT 59.969 61.111 0.00 0.00 0.00 3.27
109 110 1.470996 TAACGGTGCTACGGTGGGTT 61.471 55.000 1.43 0.00 38.39 4.11
110 111 1.470996 TTAACGGTGCTACGGTGGGT 61.471 55.000 1.43 0.00 38.39 4.51
111 112 0.320596 TTTAACGGTGCTACGGTGGG 60.321 55.000 1.43 0.00 38.39 4.61
112 113 1.510776 TTTTAACGGTGCTACGGTGG 58.489 50.000 1.43 0.00 38.39 4.61
131 132 4.764823 TGCGAAGTGATAAGGGTCATTTTT 59.235 37.500 0.00 0.00 29.55 1.94
132 133 4.331968 TGCGAAGTGATAAGGGTCATTTT 58.668 39.130 0.00 0.00 29.55 1.82
133 134 3.950397 TGCGAAGTGATAAGGGTCATTT 58.050 40.909 0.00 0.00 31.71 2.32
141 142 2.738846 ACAGCTGTTGCGAAGTGATAAG 59.261 45.455 15.25 0.00 45.42 1.73
151 152 2.449548 CAGGTCTACAGCTGTTGCG 58.550 57.895 27.06 13.97 42.33 4.85
162 163 1.220749 GGACGCCATTGCAGGTCTA 59.779 57.895 0.00 0.00 37.32 2.59
167 168 2.684881 AGAAATAAGGACGCCATTGCAG 59.315 45.455 0.00 0.00 37.32 4.41
174 175 6.445357 TTTTAATGGAGAAATAAGGACGCC 57.555 37.500 0.00 0.00 0.00 5.68
233 234 2.819595 GAAAGCAGCATCGCCCGA 60.820 61.111 0.00 0.00 0.00 5.14
264 265 1.087202 AACAGCGCACACGAAACTCA 61.087 50.000 11.47 0.00 43.93 3.41
268 269 1.585002 GCAAACAGCGCACACGAAA 60.585 52.632 11.47 0.00 43.93 3.46
311 316 1.472082 CAACAGTCCAGCAACAACACA 59.528 47.619 0.00 0.00 0.00 3.72
327 332 0.682532 TGCACCAAAGACTGCCAACA 60.683 50.000 0.00 0.00 31.97 3.33
365 370 1.625818 CCTCCCCTTGATCTTATCCCG 59.374 57.143 0.00 0.00 0.00 5.14
406 411 6.524101 TCACATTAAATTAGGAAACCAGGC 57.476 37.500 0.00 0.00 0.00 4.85
468 473 9.295825 TGATTTAGGAACAACATTGATTGTACT 57.704 29.630 0.00 3.45 42.01 2.73
469 474 9.906660 TTGATTTAGGAACAACATTGATTGTAC 57.093 29.630 0.00 0.00 42.01 2.90
552 557 7.570132 TGATACCAGCCATTTTAGCTACTTTA 58.430 34.615 0.00 0.00 38.95 1.85
553 558 6.423182 TGATACCAGCCATTTTAGCTACTTT 58.577 36.000 0.00 0.00 38.95 2.66
581 586 0.393077 ACCACGATTCGGATGGATCC 59.607 55.000 19.21 4.20 43.65 3.36
865 883 2.876645 GAGAAGTCTGCGTCGGCG 60.877 66.667 4.29 4.29 44.10 6.46
1018 1435 1.553690 CCAGGTGGAGGTGGTAGGTG 61.554 65.000 0.00 0.00 37.39 4.00
1023 1440 2.930562 GAGCCAGGTGGAGGTGGT 60.931 66.667 0.00 0.00 36.10 4.16
1048 1465 1.000739 CCACAATGGCCATGTCCCT 59.999 57.895 21.63 0.00 0.00 4.20
1101 1518 5.120399 ACACCACGTTTAACTTGATCAGAA 58.880 37.500 3.07 0.00 0.00 3.02
1287 1727 8.424918 TGGAGATCCAGTGAAAAATAGTCTATC 58.575 37.037 0.00 0.00 42.01 2.08
1449 1890 9.783256 CATATTGTAATGTCATATGGATGCAAG 57.217 33.333 2.13 0.00 32.62 4.01
1547 1997 1.187567 AACTTGGGAGTTGGCCATGC 61.188 55.000 6.09 2.32 44.27 4.06
1569 4430 7.837863 TGAGTGAGTACTATAAAGGGTTGAAG 58.162 38.462 0.00 0.00 37.25 3.02
1584 4445 5.103000 ACGACAAGCAATATGAGTGAGTAC 58.897 41.667 0.00 0.00 0.00 2.73
1613 4474 8.644318 AACTACTAACCATTAGAATAGCAACG 57.356 34.615 2.65 0.00 36.73 4.10
1748 4653 6.146184 CGTACTATTCACCATAAGAATGCTGG 59.854 42.308 0.00 0.00 36.45 4.85
1761 4666 2.953466 TCCTGTGCGTACTATTCACC 57.047 50.000 4.97 0.00 0.00 4.02
1903 4846 5.569059 CGAACTAAAGCAATCAATTGGTGAC 59.431 40.000 5.42 0.00 46.62 3.67
1917 4860 5.006941 TCACCACAAAGTAACGAACTAAAGC 59.993 40.000 0.00 0.00 37.50 3.51
2086 5029 1.876156 GTGAGTCTCACCAGCCAAAAG 59.124 52.381 20.54 0.00 41.37 2.27
2170 5113 3.931578 ACACCAGCAGACTTGATAACTC 58.068 45.455 0.00 0.00 0.00 3.01
2185 5128 3.914426 AGCTATTCCACCTAACACCAG 57.086 47.619 0.00 0.00 0.00 4.00
2215 5160 1.267806 CTGTGGTCAATTGACTGCACC 59.732 52.381 31.81 19.52 44.20 5.01
2235 5180 8.364129 ACACATAAATTTGAACATTCAACCAC 57.636 30.769 6.55 0.00 45.99 4.16


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

AutoCloner maintained by Alex Coulton.