Multiple sequence alignment - TraesCS1D01G054400

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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 TraesCS1D01G054400 chr1D 100.000 2754 0 0 1 2754 35789783 35787030 0.000000e+00 5086.0
1 TraesCS1D01G054400 chr1D 92.415 1437 83 12 147 1572 35901362 35899941 0.000000e+00 2026.0
2 TraesCS1D01G054400 chr1D 90.380 1289 93 16 591 1867 35927568 35926299 0.000000e+00 1664.0
3 TraesCS1D01G054400 chr1D 86.652 442 39 11 2320 2754 35871239 35870811 3.210000e-129 472.0
4 TraesCS1D01G054400 chr1D 89.643 280 29 0 2475 2754 35917799 35917520 9.380000e-95 357.0
5 TraesCS1D01G054400 chr1D 87.742 310 30 6 2452 2754 35816251 35815943 3.370000e-94 355.0
6 TraesCS1D01G054400 chr1B 91.764 1882 124 14 591 2454 54974229 54972361 0.000000e+00 2588.0
7 TraesCS1D01G054400 chr1B 91.301 1253 82 12 591 1826 55012758 55011516 0.000000e+00 1685.0
8 TraesCS1D01G054400 chr1B 81.395 1247 174 38 670 1880 55429229 55428005 0.000000e+00 965.0
9 TraesCS1D01G054400 chr1B 92.756 566 37 1 1889 2454 55011518 55010957 0.000000e+00 815.0
10 TraesCS1D01G054400 chr1B 90.504 337 27 2 2423 2754 54964848 54964512 9.050000e-120 440.0
11 TraesCS1D01G054400 chr1B 90.208 337 28 2 2423 2754 55008133 55007797 4.210000e-118 435.0
12 TraesCS1D01G054400 chr1B 82.284 429 47 16 171 590 360363518 360363926 7.300000e-91 344.0
13 TraesCS1D01G054400 chr1A 93.306 1733 70 23 145 1852 34861431 34859720 0.000000e+00 2516.0
14 TraesCS1D01G054400 chr1A 93.299 1731 70 25 145 1852 34708925 34707218 0.000000e+00 2512.0
15 TraesCS1D01G054400 chr1A 91.244 1302 76 20 591 1867 34886542 34885254 0.000000e+00 1738.0
16 TraesCS1D01G054400 chr1A 91.029 758 50 5 1377 2124 34536137 34535388 0.000000e+00 1007.0
17 TraesCS1D01G054400 chr1A 94.483 580 20 1 2175 2754 34535386 34534819 0.000000e+00 883.0
18 TraesCS1D01G054400 chr1A 91.544 272 22 1 2484 2754 34705834 34705563 9.310000e-100 374.0
19 TraesCS1D01G054400 chr1A 91.111 270 24 0 2485 2754 34878780 34878511 1.560000e-97 366.0
20 TraesCS1D01G054400 chr1A 98.305 59 1 0 2696 2754 34859160 34859102 1.350000e-18 104.0
21 TraesCS1D01G054400 chr4D 85.930 398 39 16 169 558 401955091 401954703 2.550000e-110 409.0
22 TraesCS1D01G054400 chr6B 84.309 427 48 8 166 589 668971484 668971074 1.540000e-107 399.0
23 TraesCS1D01G054400 chr2B 84.197 386 49 9 211 589 63092135 63092515 5.600000e-97 364.0
24 TraesCS1D01G054400 chr2B 92.414 145 11 0 1 145 520966503 520966647 1.000000e-49 207.0
25 TraesCS1D01G054400 chr2B 92.361 144 10 1 1 144 454345601 454345743 1.290000e-48 204.0
26 TraesCS1D01G054400 chr2B 91.724 145 10 2 1 144 41948265 41948408 1.670000e-47 200.0
27 TraesCS1D01G054400 chrUn 81.733 427 63 9 170 589 39240175 39239757 2.630000e-90 342.0
28 TraesCS1D01G054400 chr4A 80.706 425 64 14 164 581 456448927 456448514 5.730000e-82 315.0
29 TraesCS1D01G054400 chr7B 93.056 144 10 0 1 144 732302762 732302619 7.730000e-51 211.0
30 TraesCS1D01G054400 chr5B 91.724 145 12 0 1 145 689459407 689459263 4.650000e-48 202.0
31 TraesCS1D01G054400 chr3B 91.724 145 12 0 1 145 819309883 819309739 4.650000e-48 202.0
32 TraesCS1D01G054400 chr3B 91.667 144 12 0 2 145 817225005 817225148 1.670000e-47 200.0
33 TraesCS1D01G054400 chr5A 91.667 144 12 0 1 144 303403786 303403929 1.670000e-47 200.0
34 TraesCS1D01G054400 chr4B 91.667 144 12 0 1 144 141251922 141252065 1.670000e-47 200.0
35 TraesCS1D01G054400 chr6A 97.143 35 1 0 2232 2266 473616718 473616684 2.960000e-05 60.2


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 TraesCS1D01G054400 chr1D 35787030 35789783 2753 True 5086.000000 5086 100.000000 1 2754 1 chr1D.!!$R1 2753
1 TraesCS1D01G054400 chr1D 35899941 35901362 1421 True 2026.000000 2026 92.415000 147 1572 1 chr1D.!!$R4 1425
2 TraesCS1D01G054400 chr1D 35926299 35927568 1269 True 1664.000000 1664 90.380000 591 1867 1 chr1D.!!$R6 1276
3 TraesCS1D01G054400 chr1B 54972361 54974229 1868 True 2588.000000 2588 91.764000 591 2454 1 chr1B.!!$R2 1863
4 TraesCS1D01G054400 chr1B 55007797 55012758 4961 True 978.333333 1685 91.421667 591 2754 3 chr1B.!!$R4 2163
5 TraesCS1D01G054400 chr1B 55428005 55429229 1224 True 965.000000 965 81.395000 670 1880 1 chr1B.!!$R3 1210
6 TraesCS1D01G054400 chr1A 34885254 34886542 1288 True 1738.000000 1738 91.244000 591 1867 1 chr1A.!!$R2 1276
7 TraesCS1D01G054400 chr1A 34705563 34708925 3362 True 1443.000000 2512 92.421500 145 2754 2 chr1A.!!$R4 2609
8 TraesCS1D01G054400 chr1A 34859102 34861431 2329 True 1310.000000 2516 95.805500 145 2754 2 chr1A.!!$R5 2609
9 TraesCS1D01G054400 chr1A 34534819 34536137 1318 True 945.000000 1007 92.756000 1377 2754 2 chr1A.!!$R3 1377

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
33 34 0.451783 GGCGTTTCTATGTTGGGCAG 59.548 55.0 0.0 0.0 0.0 4.85 F
62 63 0.948678 GGACTGTGGCGTTGCTAAAA 59.051 50.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1370 1433 2.401766 GCGCCAATGAGACACCCAG 61.402 63.158 0.0 0.0 0.00 4.45 R
1921 1996 2.428890 GAGATGTCTGGTCACCACTAGG 59.571 54.545 0.0 0.0 42.21 3.02 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
17 18 3.584052 ACGCTAGCTACCTCGGCG 61.584 66.667 19.20 19.20 43.82 6.46
18 19 3.584052 CGCTAGCTACCTCGGCGT 61.584 66.667 13.93 0.00 38.07 5.68
19 20 2.806237 GCTAGCTACCTCGGCGTT 59.194 61.111 7.70 0.00 34.52 4.84
20 21 1.141234 GCTAGCTACCTCGGCGTTT 59.859 57.895 7.70 0.00 34.52 3.60
21 22 0.870735 GCTAGCTACCTCGGCGTTTC 60.871 60.000 7.70 0.00 34.52 2.78
22 23 0.739561 CTAGCTACCTCGGCGTTTCT 59.260 55.000 6.85 0.00 34.52 2.52
23 24 1.945394 CTAGCTACCTCGGCGTTTCTA 59.055 52.381 6.85 0.87 34.52 2.10
24 25 1.400737 AGCTACCTCGGCGTTTCTAT 58.599 50.000 6.85 0.00 34.52 1.98
25 26 1.067212 AGCTACCTCGGCGTTTCTATG 59.933 52.381 6.85 0.00 34.52 2.23
26 27 1.202382 GCTACCTCGGCGTTTCTATGT 60.202 52.381 6.85 0.00 0.00 2.29
27 28 2.737679 GCTACCTCGGCGTTTCTATGTT 60.738 50.000 6.85 0.00 0.00 2.71
28 29 1.722011 ACCTCGGCGTTTCTATGTTG 58.278 50.000 6.85 0.00 0.00 3.33
29 30 1.006832 CCTCGGCGTTTCTATGTTGG 58.993 55.000 6.85 0.00 0.00 3.77
30 31 1.006832 CTCGGCGTTTCTATGTTGGG 58.993 55.000 6.85 0.00 0.00 4.12
31 32 1.022451 TCGGCGTTTCTATGTTGGGC 61.022 55.000 6.85 0.00 0.00 5.36
32 33 1.302383 CGGCGTTTCTATGTTGGGCA 61.302 55.000 0.00 0.00 0.00 5.36
33 34 0.451783 GGCGTTTCTATGTTGGGCAG 59.548 55.000 0.00 0.00 0.00 4.85
34 35 1.448985 GCGTTTCTATGTTGGGCAGA 58.551 50.000 0.00 0.00 0.00 4.26
35 36 1.810151 GCGTTTCTATGTTGGGCAGAA 59.190 47.619 0.00 0.00 0.00 3.02
36 37 2.227865 GCGTTTCTATGTTGGGCAGAAA 59.772 45.455 0.00 0.00 36.27 2.52
38 39 3.821841 GTTTCTATGTTGGGCAGAAACG 58.178 45.455 9.81 0.00 44.66 3.60
39 40 1.448985 TCTATGTTGGGCAGAAACGC 58.551 50.000 0.00 0.00 0.00 4.84
48 49 3.777925 CAGAAACGCCGCGGACTG 61.778 66.667 33.48 22.87 0.00 3.51
49 50 4.295119 AGAAACGCCGCGGACTGT 62.295 61.111 33.48 21.05 0.00 3.55
50 51 4.072088 GAAACGCCGCGGACTGTG 62.072 66.667 33.48 14.72 0.00 3.66
59 60 2.048597 CGGACTGTGGCGTTGCTA 60.049 61.111 0.00 0.00 0.00 3.49
60 61 1.666553 CGGACTGTGGCGTTGCTAA 60.667 57.895 0.00 0.00 0.00 3.09
61 62 1.225376 CGGACTGTGGCGTTGCTAAA 61.225 55.000 0.00 0.00 0.00 1.85
62 63 0.948678 GGACTGTGGCGTTGCTAAAA 59.051 50.000 0.00 0.00 0.00 1.52
63 64 1.069227 GGACTGTGGCGTTGCTAAAAG 60.069 52.381 0.00 0.00 0.00 2.27
64 65 1.871039 GACTGTGGCGTTGCTAAAAGA 59.129 47.619 0.00 0.00 0.00 2.52
65 66 1.873591 ACTGTGGCGTTGCTAAAAGAG 59.126 47.619 0.00 0.00 0.00 2.85
66 67 1.873591 CTGTGGCGTTGCTAAAAGAGT 59.126 47.619 0.00 0.00 0.00 3.24
67 68 1.871039 TGTGGCGTTGCTAAAAGAGTC 59.129 47.619 0.00 0.00 0.00 3.36
68 69 1.871039 GTGGCGTTGCTAAAAGAGTCA 59.129 47.619 0.00 0.00 0.00 3.41
69 70 2.096218 GTGGCGTTGCTAAAAGAGTCAG 60.096 50.000 0.00 0.00 0.00 3.51
70 71 2.224185 TGGCGTTGCTAAAAGAGTCAGA 60.224 45.455 0.00 0.00 0.00 3.27
71 72 3.003480 GGCGTTGCTAAAAGAGTCAGAT 58.997 45.455 0.00 0.00 0.00 2.90
72 73 3.062774 GGCGTTGCTAAAAGAGTCAGATC 59.937 47.826 0.00 0.00 0.00 2.75
73 74 3.241804 GCGTTGCTAAAAGAGTCAGATCG 60.242 47.826 0.00 0.00 0.00 3.69
74 75 3.921021 CGTTGCTAAAAGAGTCAGATCGT 59.079 43.478 0.00 0.00 0.00 3.73
75 76 4.201532 CGTTGCTAAAAGAGTCAGATCGTG 60.202 45.833 0.00 0.00 0.00 4.35
76 77 4.783764 TGCTAAAAGAGTCAGATCGTGA 57.216 40.909 0.00 0.00 0.00 4.35
77 78 5.134202 TGCTAAAAGAGTCAGATCGTGAA 57.866 39.130 0.00 0.00 36.74 3.18
78 79 5.538118 TGCTAAAAGAGTCAGATCGTGAAA 58.462 37.500 0.00 0.00 36.74 2.69
79 80 6.166279 TGCTAAAAGAGTCAGATCGTGAAAT 58.834 36.000 0.00 0.00 36.74 2.17
80 81 7.320399 TGCTAAAAGAGTCAGATCGTGAAATA 58.680 34.615 0.00 0.00 36.74 1.40
81 82 7.275779 TGCTAAAAGAGTCAGATCGTGAAATAC 59.724 37.037 0.00 0.00 36.74 1.89
82 83 7.489757 GCTAAAAGAGTCAGATCGTGAAATACT 59.510 37.037 0.00 0.00 36.74 2.12
83 84 9.360093 CTAAAAGAGTCAGATCGTGAAATACTT 57.640 33.333 0.00 0.00 36.74 2.24
84 85 8.608844 AAAAGAGTCAGATCGTGAAATACTTT 57.391 30.769 0.00 0.00 36.74 2.66
85 86 7.820044 AAGAGTCAGATCGTGAAATACTTTC 57.180 36.000 0.00 0.00 36.74 2.62
86 87 6.925211 AGAGTCAGATCGTGAAATACTTTCA 58.075 36.000 0.00 0.00 46.68 2.69
99 100 8.827177 TGAAATACTTTCATGTCGAGTTTAGT 57.173 30.769 0.00 0.00 44.21 2.24
100 101 9.268268 TGAAATACTTTCATGTCGAGTTTAGTT 57.732 29.630 0.00 0.00 44.21 2.24
102 103 9.878599 AAATACTTTCATGTCGAGTTTAGTTTG 57.121 29.630 0.00 0.00 0.00 2.93
103 104 6.920569 ACTTTCATGTCGAGTTTAGTTTGT 57.079 33.333 0.00 0.00 0.00 2.83
104 105 6.715464 ACTTTCATGTCGAGTTTAGTTTGTG 58.285 36.000 0.00 0.00 0.00 3.33
105 106 6.537301 ACTTTCATGTCGAGTTTAGTTTGTGA 59.463 34.615 0.00 0.00 0.00 3.58
106 107 5.900339 TCATGTCGAGTTTAGTTTGTGAC 57.100 39.130 0.00 0.00 0.00 3.67
107 108 5.353111 TCATGTCGAGTTTAGTTTGTGACA 58.647 37.500 0.00 0.00 38.98 3.58
108 109 5.813157 TCATGTCGAGTTTAGTTTGTGACAA 59.187 36.000 0.00 0.00 38.25 3.18
109 110 6.314152 TCATGTCGAGTTTAGTTTGTGACAAA 59.686 34.615 6.66 6.66 38.25 2.83
110 111 6.102006 TGTCGAGTTTAGTTTGTGACAAAG 57.898 37.500 11.54 0.00 32.48 2.77
111 112 5.640357 TGTCGAGTTTAGTTTGTGACAAAGT 59.360 36.000 20.69 20.69 32.48 2.66
112 113 6.148150 TGTCGAGTTTAGTTTGTGACAAAGTT 59.852 34.615 21.87 11.16 32.48 2.66
113 114 7.019418 GTCGAGTTTAGTTTGTGACAAAGTTT 58.981 34.615 21.87 8.87 0.00 2.66
114 115 7.007099 GTCGAGTTTAGTTTGTGACAAAGTTTG 59.993 37.037 21.87 14.13 0.00 2.93
115 116 6.237201 CGAGTTTAGTTTGTGACAAAGTTTGC 60.237 38.462 21.87 12.54 0.00 3.68
116 117 6.687604 AGTTTAGTTTGTGACAAAGTTTGCT 58.312 32.000 21.87 12.42 0.00 3.91
117 118 6.586082 AGTTTAGTTTGTGACAAAGTTTGCTG 59.414 34.615 21.87 0.00 0.00 4.41
118 119 4.782019 AGTTTGTGACAAAGTTTGCTGA 57.218 36.364 11.54 0.00 0.00 4.26
119 120 5.329035 AGTTTGTGACAAAGTTTGCTGAT 57.671 34.783 11.54 0.00 0.00 2.90
120 121 6.449635 AGTTTGTGACAAAGTTTGCTGATA 57.550 33.333 11.54 0.00 0.00 2.15
121 122 6.862209 AGTTTGTGACAAAGTTTGCTGATAA 58.138 32.000 11.54 2.72 0.00 1.75
122 123 6.974622 AGTTTGTGACAAAGTTTGCTGATAAG 59.025 34.615 11.54 0.00 0.00 1.73
123 124 5.437289 TGTGACAAAGTTTGCTGATAAGG 57.563 39.130 15.59 0.00 0.00 2.69
124 125 4.887071 TGTGACAAAGTTTGCTGATAAGGT 59.113 37.500 15.59 0.00 0.00 3.50
125 126 5.008613 TGTGACAAAGTTTGCTGATAAGGTC 59.991 40.000 15.59 3.17 0.00 3.85
126 127 5.008613 GTGACAAAGTTTGCTGATAAGGTCA 59.991 40.000 15.59 5.69 35.05 4.02
140 141 5.869344 TGATAAGGTCAGAACAGTGATTTCG 59.131 40.000 0.00 0.00 31.80 3.46
141 142 3.045601 AGGTCAGAACAGTGATTTCGG 57.954 47.619 0.00 0.00 0.00 4.30
142 143 1.464997 GGTCAGAACAGTGATTTCGGC 59.535 52.381 0.00 0.00 0.00 5.54
143 144 1.464997 GTCAGAACAGTGATTTCGGCC 59.535 52.381 0.00 0.00 0.00 6.13
175 176 7.824779 ACAAGTTAGCCCTTTAATAGTGAGAAG 59.175 37.037 0.00 0.00 0.00 2.85
217 218 5.888105 CTCACTGGAGCTTGAATATTTTGG 58.112 41.667 0.00 0.00 33.67 3.28
247 251 8.532977 AATCAAAATTCATACTTTCCGGTTTG 57.467 30.769 0.00 0.02 0.00 2.93
486 503 8.744568 TGTGTGTTATGCCTTCATAAATATCA 57.255 30.769 0.00 0.00 44.22 2.15
588 607 3.317150 CCGGACTCCAAAAGCAATTTTC 58.683 45.455 0.00 0.00 0.00 2.29
589 608 3.243704 CCGGACTCCAAAAGCAATTTTCA 60.244 43.478 0.00 0.00 0.00 2.69
640 659 2.787249 CTGCATCGCCAAGTTCCG 59.213 61.111 0.00 0.00 0.00 4.30
662 681 2.705658 TCTGGTTCAAGTGTGGAGACAT 59.294 45.455 0.00 0.00 46.14 3.06
716 739 6.411376 ACGAATATGACCTGTTCAAACCATA 58.589 36.000 0.00 0.00 37.92 2.74
885 929 8.188501 TCTTCCTCCATGTCCCTATATATACT 57.811 38.462 0.00 0.00 0.00 2.12
946 991 2.077413 CGCAAGCAGTTCTTCTCTCT 57.923 50.000 0.00 0.00 31.27 3.10
947 992 2.411904 CGCAAGCAGTTCTTCTCTCTT 58.588 47.619 0.00 0.00 31.27 2.85
948 993 2.411409 CGCAAGCAGTTCTTCTCTCTTC 59.589 50.000 0.00 0.00 31.27 2.87
949 994 3.663025 GCAAGCAGTTCTTCTCTCTTCT 58.337 45.455 0.00 0.00 31.27 2.85
1370 1433 0.521735 GATTGCCGGGTTGAACACTC 59.478 55.000 2.18 0.00 0.00 3.51
1921 1996 0.823356 TGTGGCCAAGGCAAAGAGAC 60.823 55.000 7.24 0.00 44.11 3.36
1938 2013 3.863120 ACCTAGTGGTGACCAGACA 57.137 52.632 3.58 0.00 46.51 3.41
1941 2016 2.225394 ACCTAGTGGTGACCAGACATCT 60.225 50.000 3.58 0.00 46.51 2.90
2016 2137 2.096220 ACTGCTGAAGTGCTGATCAG 57.904 50.000 18.84 18.84 44.66 2.90
2046 2174 5.366460 AAGCAGAGATACTGATCATTGGTG 58.634 41.667 0.00 0.00 44.93 4.17
2048 2176 7.129539 AAGCAGAGATACTGATCATTGGTGTG 61.130 42.308 0.00 0.00 44.93 3.82
2107 2235 3.550820 TGTGTTGTTGTATGCTTGGAGT 58.449 40.909 0.00 0.00 0.00 3.85
2173 2301 5.104735 ACGAGGATAGGAAATTTCTTCAGCT 60.105 40.000 17.42 8.37 0.00 4.24
2234 2366 8.589629 CGAATTTTCCATGATTGCTAAAGAAAG 58.410 33.333 0.00 0.00 0.00 2.62
2235 2367 9.643693 GAATTTTCCATGATTGCTAAAGAAAGA 57.356 29.630 0.00 0.00 0.00 2.52
2238 2370 9.829507 TTTTCCATGATTGCTAAAGAAAGAAAA 57.170 25.926 0.00 0.00 0.00 2.29
2266 2398 7.092716 GTCATCCTTGAACAACATAAATTGCT 58.907 34.615 0.00 0.00 32.48 3.91
2273 2405 6.215121 TGAACAACATAAATTGCTGTGGAAG 58.785 36.000 2.80 0.00 34.89 3.46
2289 2421 1.737793 GGAAGGCGTTCGATTTGTCAT 59.262 47.619 12.65 0.00 32.92 3.06
2421 2690 5.473162 CCCATGGACGAAAAGAATATGCATA 59.527 40.000 15.22 9.27 0.00 3.14
2433 2702 7.767745 AAGAATATGCATATCAGACATAGCG 57.232 36.000 19.35 0.00 30.31 4.26
2580 6134 4.760047 ACGGTGGCGCAGATGGAC 62.760 66.667 10.83 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.584052 CGCCGAGGTAGCTAGCGT 61.584 66.667 23.49 6.00 41.78 5.07
2 3 0.870735 GAAACGCCGAGGTAGCTAGC 60.871 60.000 15.19 15.19 0.00 3.42
3 4 0.739561 AGAAACGCCGAGGTAGCTAG 59.260 55.000 0.00 0.00 0.00 3.42
4 5 2.042686 TAGAAACGCCGAGGTAGCTA 57.957 50.000 0.00 0.00 0.00 3.32
5 6 1.067212 CATAGAAACGCCGAGGTAGCT 59.933 52.381 0.00 0.00 0.00 3.32
6 7 1.202382 ACATAGAAACGCCGAGGTAGC 60.202 52.381 0.00 0.00 0.00 3.58
7 8 2.858344 CAACATAGAAACGCCGAGGTAG 59.142 50.000 0.00 0.00 0.00 3.18
8 9 2.417651 CCAACATAGAAACGCCGAGGTA 60.418 50.000 0.00 0.00 0.00 3.08
9 10 1.674817 CCAACATAGAAACGCCGAGGT 60.675 52.381 0.00 0.00 0.00 3.85
10 11 1.006832 CCAACATAGAAACGCCGAGG 58.993 55.000 0.00 0.00 0.00 4.63
11 12 1.006832 CCCAACATAGAAACGCCGAG 58.993 55.000 0.00 0.00 0.00 4.63
12 13 1.022451 GCCCAACATAGAAACGCCGA 61.022 55.000 0.00 0.00 0.00 5.54
13 14 1.302383 TGCCCAACATAGAAACGCCG 61.302 55.000 0.00 0.00 0.00 6.46
14 15 0.451783 CTGCCCAACATAGAAACGCC 59.548 55.000 0.00 0.00 0.00 5.68
15 16 1.448985 TCTGCCCAACATAGAAACGC 58.551 50.000 0.00 0.00 0.00 4.84
16 17 3.821841 GTTTCTGCCCAACATAGAAACG 58.178 45.455 11.75 0.00 45.66 3.60
18 19 2.227865 GCGTTTCTGCCCAACATAGAAA 59.772 45.455 0.00 0.00 37.91 2.52
19 20 1.810151 GCGTTTCTGCCCAACATAGAA 59.190 47.619 0.00 0.00 0.00 2.10
20 21 1.448985 GCGTTTCTGCCCAACATAGA 58.551 50.000 0.00 0.00 0.00 1.98
21 22 3.996825 GCGTTTCTGCCCAACATAG 57.003 52.632 0.00 0.00 0.00 2.23
31 32 3.777925 CAGTCCGCGGCGTTTCTG 61.778 66.667 23.51 19.78 0.00 3.02
32 33 4.295119 ACAGTCCGCGGCGTTTCT 62.295 61.111 23.51 12.80 0.00 2.52
33 34 4.072088 CACAGTCCGCGGCGTTTC 62.072 66.667 23.51 10.72 0.00 2.78
42 43 1.225376 TTTAGCAACGCCACAGTCCG 61.225 55.000 0.00 0.00 0.00 4.79
43 44 0.948678 TTTTAGCAACGCCACAGTCC 59.051 50.000 0.00 0.00 0.00 3.85
44 45 1.871039 TCTTTTAGCAACGCCACAGTC 59.129 47.619 0.00 0.00 0.00 3.51
45 46 1.873591 CTCTTTTAGCAACGCCACAGT 59.126 47.619 0.00 0.00 0.00 3.55
46 47 1.873591 ACTCTTTTAGCAACGCCACAG 59.126 47.619 0.00 0.00 0.00 3.66
47 48 1.871039 GACTCTTTTAGCAACGCCACA 59.129 47.619 0.00 0.00 0.00 4.17
48 49 1.871039 TGACTCTTTTAGCAACGCCAC 59.129 47.619 0.00 0.00 0.00 5.01
49 50 2.143122 CTGACTCTTTTAGCAACGCCA 58.857 47.619 0.00 0.00 0.00 5.69
50 51 2.413837 TCTGACTCTTTTAGCAACGCC 58.586 47.619 0.00 0.00 0.00 5.68
51 52 3.241804 CGATCTGACTCTTTTAGCAACGC 60.242 47.826 0.00 0.00 0.00 4.84
52 53 3.921021 ACGATCTGACTCTTTTAGCAACG 59.079 43.478 0.00 0.00 0.00 4.10
53 54 4.923871 TCACGATCTGACTCTTTTAGCAAC 59.076 41.667 0.00 0.00 0.00 4.17
54 55 5.134202 TCACGATCTGACTCTTTTAGCAA 57.866 39.130 0.00 0.00 0.00 3.91
55 56 4.783764 TCACGATCTGACTCTTTTAGCA 57.216 40.909 0.00 0.00 0.00 3.49
56 57 6.654793 ATTTCACGATCTGACTCTTTTAGC 57.345 37.500 0.00 0.00 0.00 3.09
57 58 8.918961 AGTATTTCACGATCTGACTCTTTTAG 57.081 34.615 0.00 0.00 0.00 1.85
58 59 9.706691 AAAGTATTTCACGATCTGACTCTTTTA 57.293 29.630 0.00 0.00 27.08 1.52
59 60 8.608844 AAAGTATTTCACGATCTGACTCTTTT 57.391 30.769 0.00 0.00 27.08 2.27
76 77 9.878599 CAAACTAAACTCGACATGAAAGTATTT 57.121 29.630 0.00 0.00 43.98 1.40
77 78 9.052759 ACAAACTAAACTCGACATGAAAGTATT 57.947 29.630 0.00 0.95 0.00 1.89
78 79 8.495949 CACAAACTAAACTCGACATGAAAGTAT 58.504 33.333 0.00 0.00 0.00 2.12
79 80 7.707464 TCACAAACTAAACTCGACATGAAAGTA 59.293 33.333 0.00 0.00 0.00 2.24
80 81 6.537301 TCACAAACTAAACTCGACATGAAAGT 59.463 34.615 0.00 0.00 0.00 2.66
81 82 6.846283 GTCACAAACTAAACTCGACATGAAAG 59.154 38.462 0.00 0.00 0.00 2.62
82 83 6.314152 TGTCACAAACTAAACTCGACATGAAA 59.686 34.615 0.00 0.00 0.00 2.69
83 84 5.813157 TGTCACAAACTAAACTCGACATGAA 59.187 36.000 0.00 0.00 0.00 2.57
84 85 5.353111 TGTCACAAACTAAACTCGACATGA 58.647 37.500 0.00 0.00 0.00 3.07
85 86 5.651172 TGTCACAAACTAAACTCGACATG 57.349 39.130 0.00 0.00 0.00 3.21
86 87 6.315393 ACTTTGTCACAAACTAAACTCGACAT 59.685 34.615 0.00 0.00 32.45 3.06
87 88 5.640357 ACTTTGTCACAAACTAAACTCGACA 59.360 36.000 0.00 0.00 0.00 4.35
88 89 6.103222 ACTTTGTCACAAACTAAACTCGAC 57.897 37.500 0.00 0.00 0.00 4.20
89 90 6.730960 AACTTTGTCACAAACTAAACTCGA 57.269 33.333 0.00 0.00 0.00 4.04
90 91 6.237201 GCAAACTTTGTCACAAACTAAACTCG 60.237 38.462 0.00 0.00 0.00 4.18
91 92 6.806739 AGCAAACTTTGTCACAAACTAAACTC 59.193 34.615 0.00 0.00 0.00 3.01
92 93 6.586082 CAGCAAACTTTGTCACAAACTAAACT 59.414 34.615 0.00 0.00 0.00 2.66
93 94 6.584563 TCAGCAAACTTTGTCACAAACTAAAC 59.415 34.615 0.00 0.00 0.00 2.01
94 95 6.682746 TCAGCAAACTTTGTCACAAACTAAA 58.317 32.000 0.00 0.00 0.00 1.85
95 96 6.260870 TCAGCAAACTTTGTCACAAACTAA 57.739 33.333 0.00 0.00 0.00 2.24
96 97 5.888691 TCAGCAAACTTTGTCACAAACTA 57.111 34.783 0.00 0.00 0.00 2.24
97 98 4.782019 TCAGCAAACTTTGTCACAAACT 57.218 36.364 0.00 0.00 0.00 2.66
98 99 6.198966 CCTTATCAGCAAACTTTGTCACAAAC 59.801 38.462 0.00 0.00 0.00 2.93
99 100 6.127479 ACCTTATCAGCAAACTTTGTCACAAA 60.127 34.615 2.24 2.24 0.00 2.83
100 101 5.359576 ACCTTATCAGCAAACTTTGTCACAA 59.640 36.000 3.48 0.00 0.00 3.33
101 102 4.887071 ACCTTATCAGCAAACTTTGTCACA 59.113 37.500 3.48 0.00 0.00 3.58
102 103 5.008613 TGACCTTATCAGCAAACTTTGTCAC 59.991 40.000 3.48 0.00 31.91 3.67
103 104 5.129634 TGACCTTATCAGCAAACTTTGTCA 58.870 37.500 3.48 0.00 31.91 3.58
104 105 5.689383 TGACCTTATCAGCAAACTTTGTC 57.311 39.130 3.48 0.00 31.91 3.18
116 117 5.869344 CGAAATCACTGTTCTGACCTTATCA 59.131 40.000 0.00 0.00 35.45 2.15
117 118 5.292101 CCGAAATCACTGTTCTGACCTTATC 59.708 44.000 0.00 0.00 0.00 1.75
118 119 5.178797 CCGAAATCACTGTTCTGACCTTAT 58.821 41.667 0.00 0.00 0.00 1.73
119 120 4.566004 CCGAAATCACTGTTCTGACCTTA 58.434 43.478 0.00 0.00 0.00 2.69
120 121 3.403038 CCGAAATCACTGTTCTGACCTT 58.597 45.455 0.00 0.00 0.00 3.50
121 122 2.872038 GCCGAAATCACTGTTCTGACCT 60.872 50.000 0.00 0.00 0.00 3.85
122 123 1.464997 GCCGAAATCACTGTTCTGACC 59.535 52.381 0.00 0.00 0.00 4.02
123 124 1.464997 GGCCGAAATCACTGTTCTGAC 59.535 52.381 0.00 0.00 0.00 3.51
124 125 1.347707 AGGCCGAAATCACTGTTCTGA 59.652 47.619 0.00 0.00 0.00 3.27
125 126 1.466167 CAGGCCGAAATCACTGTTCTG 59.534 52.381 0.00 0.00 0.00 3.02
126 127 1.072331 ACAGGCCGAAATCACTGTTCT 59.928 47.619 0.00 0.00 41.03 3.01
127 128 1.523758 ACAGGCCGAAATCACTGTTC 58.476 50.000 0.00 0.00 41.03 3.18
128 129 1.981256 AACAGGCCGAAATCACTGTT 58.019 45.000 0.00 0.00 46.11 3.16
129 130 1.981256 AAACAGGCCGAAATCACTGT 58.019 45.000 0.00 0.00 45.34 3.55
130 131 2.811431 TGTAAACAGGCCGAAATCACTG 59.189 45.455 0.00 0.00 37.01 3.66
131 132 3.134574 TGTAAACAGGCCGAAATCACT 57.865 42.857 0.00 0.00 0.00 3.41
132 133 3.252458 ACTTGTAAACAGGCCGAAATCAC 59.748 43.478 0.00 0.00 0.00 3.06
133 134 3.482436 ACTTGTAAACAGGCCGAAATCA 58.518 40.909 0.00 0.00 0.00 2.57
134 135 4.499037 AACTTGTAAACAGGCCGAAATC 57.501 40.909 0.00 0.00 0.00 2.17
135 136 4.082949 GCTAACTTGTAAACAGGCCGAAAT 60.083 41.667 0.00 0.00 0.00 2.17
136 137 3.251487 GCTAACTTGTAAACAGGCCGAAA 59.749 43.478 0.00 0.00 0.00 3.46
137 138 2.809696 GCTAACTTGTAAACAGGCCGAA 59.190 45.455 0.00 0.00 0.00 4.30
138 139 2.419667 GCTAACTTGTAAACAGGCCGA 58.580 47.619 0.00 0.00 0.00 5.54
139 140 1.467342 GGCTAACTTGTAAACAGGCCG 59.533 52.381 0.00 0.00 0.00 6.13
140 141 1.816835 GGGCTAACTTGTAAACAGGCC 59.183 52.381 0.00 0.00 43.62 5.19
141 142 2.791655 AGGGCTAACTTGTAAACAGGC 58.208 47.619 0.00 0.00 0.00 4.85
142 143 6.887626 TTAAAGGGCTAACTTGTAAACAGG 57.112 37.500 0.00 0.00 0.00 4.00
143 144 9.227777 ACTATTAAAGGGCTAACTTGTAAACAG 57.772 33.333 0.00 0.00 0.00 3.16
175 176 1.838568 GCTCGGTCACCAAAACGACC 61.839 60.000 0.00 0.00 46.88 4.79
291 298 9.132923 TCACCCTAAAAATTTACACACATACAA 57.867 29.630 0.00 0.00 0.00 2.41
413 423 1.686052 GTTGAAATGAGGGGTGTGCAA 59.314 47.619 0.00 0.00 0.00 4.08
414 424 1.327303 GTTGAAATGAGGGGTGTGCA 58.673 50.000 0.00 0.00 0.00 4.57
420 430 4.173256 GCAAAATACGTTGAAATGAGGGG 58.827 43.478 0.00 0.00 0.00 4.79
640 659 2.158957 TGTCTCCACACTTGAACCAGAC 60.159 50.000 0.00 0.00 0.00 3.51
662 681 3.891977 ACTAGCTCTCTTGTCTTGTGTCA 59.108 43.478 0.00 0.00 0.00 3.58
716 739 7.016661 TCTCACCCTCTCTTTTAATTTCTCTGT 59.983 37.037 0.00 0.00 0.00 3.41
885 929 0.771127 CAAAGGGTTGGAGGAGACCA 59.229 55.000 0.00 0.00 37.68 4.02
922 967 2.233007 GAAGAACTGCTTGCGCTCGG 62.233 60.000 9.73 5.54 36.83 4.63
943 988 5.866633 GTGTGTTTGATCAGGTAGAGAAGAG 59.133 44.000 0.00 0.00 0.00 2.85
944 989 5.540337 AGTGTGTTTGATCAGGTAGAGAAGA 59.460 40.000 0.00 0.00 0.00 2.87
945 990 5.788450 AGTGTGTTTGATCAGGTAGAGAAG 58.212 41.667 0.00 0.00 0.00 2.85
946 991 5.808366 AGTGTGTTTGATCAGGTAGAGAA 57.192 39.130 0.00 0.00 0.00 2.87
947 992 5.304357 TCAAGTGTGTTTGATCAGGTAGAGA 59.696 40.000 0.00 0.00 32.39 3.10
948 993 5.541845 TCAAGTGTGTTTGATCAGGTAGAG 58.458 41.667 0.00 0.00 32.39 2.43
949 994 5.545063 TCAAGTGTGTTTGATCAGGTAGA 57.455 39.130 0.00 0.00 32.39 2.59
1370 1433 2.401766 GCGCCAATGAGACACCCAG 61.402 63.158 0.00 0.00 0.00 4.45
1803 1874 9.567917 CGATATCGTAAAGAAACACACATAATG 57.432 33.333 17.06 0.00 34.11 1.90
1881 1956 6.481976 CCACACGTTGTACATAATCCACATAT 59.518 38.462 0.00 0.00 0.00 1.78
1921 1996 2.428890 GAGATGTCTGGTCACCACTAGG 59.571 54.545 0.00 0.00 42.21 3.02
2016 2137 5.583854 TGATCAGTATCTCTGCTTTTCTTGC 59.416 40.000 0.00 0.00 43.32 4.01
2046 2174 8.450964 TCTTTATTAGCTTACATCTTTGCACAC 58.549 33.333 0.00 0.00 0.00 3.82
2048 2176 9.278734 GTTCTTTATTAGCTTACATCTTTGCAC 57.721 33.333 0.00 0.00 0.00 4.57
2082 2210 6.264292 ACTCCAAGCATACAACAACACAATAA 59.736 34.615 0.00 0.00 0.00 1.40
2090 2218 5.312895 ACATACACTCCAAGCATACAACAA 58.687 37.500 0.00 0.00 0.00 2.83
2107 2235 5.236695 TGAAAAACGTTCGATTGGACATACA 59.763 36.000 0.00 0.00 0.00 2.29
2153 2281 6.017523 GTGCTAGCTGAAGAAATTTCCTATCC 60.018 42.308 17.23 1.62 0.00 2.59
2173 2301 0.323302 TGTCAGGATTTGCCGTGCTA 59.677 50.000 0.00 0.00 43.43 3.49
2234 2366 7.951530 ATGTTGTTCAAGGATGACAATTTTC 57.048 32.000 0.00 0.00 34.61 2.29
2235 2367 9.829507 TTTATGTTGTTCAAGGATGACAATTTT 57.170 25.926 0.00 0.00 34.61 1.82
2238 2370 9.426837 CAATTTATGTTGTTCAAGGATGACAAT 57.573 29.630 0.00 0.00 34.61 2.71
2239 2371 7.384660 GCAATTTATGTTGTTCAAGGATGACAA 59.615 33.333 0.00 0.00 34.61 3.18
2266 2398 0.871722 CAAATCGAACGCCTTCCACA 59.128 50.000 0.00 0.00 0.00 4.17
2273 2405 1.062587 CCAGATGACAAATCGAACGCC 59.937 52.381 0.00 0.00 0.00 5.68
2289 2421 6.234920 TCGTTCTTGGATTTTGATAACCAGA 58.765 36.000 0.00 0.00 33.85 3.86
2421 2690 2.924185 GCATGGCGCTATGTCTGAT 58.076 52.632 30.74 0.00 37.77 2.90
2580 6134 1.043116 TCCTCGTAGGCATGGTCCTG 61.043 60.000 2.35 0.00 37.01 3.86


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

AutoCloner maintained by Alex Coulton.