Multiple sequence alignment - TraesCS7D01G095200

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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 TraesCS7D01G095200 chr7D 100.000 2952 0 0 496 3447 57541678 57538727 0.000000e+00 5452.0
1 TraesCS7D01G095200 chr7D 93.072 765 32 3 825 1589 58054300 58055043 0.000000e+00 1099.0
2 TraesCS7D01G095200 chr7D 100.000 266 0 0 1 266 57542173 57541908 3.090000e-135 492.0
3 TraesCS7D01G095200 chr7D 88.804 393 38 4 2043 2435 58142773 58143159 8.650000e-131 477.0
4 TraesCS7D01G095200 chr7D 95.572 271 12 0 2190 2460 58055254 58055524 5.280000e-118 435.0
5 TraesCS7D01G095200 chr7D 87.989 358 40 3 2632 2988 58072477 58072832 1.480000e-113 420.0
6 TraesCS7D01G095200 chr7D 86.458 192 17 8 10 195 606540626 606540438 5.830000e-48 202.0
7 TraesCS7D01G095200 chr7D 87.574 169 15 6 2474 2639 58055592 58055757 1.260000e-44 191.0
8 TraesCS7D01G095200 chr7D 83.920 199 26 6 3 198 64016601 64016406 5.870000e-43 185.0
9 TraesCS7D01G095200 chr7A 94.796 2037 83 11 805 2834 61891982 61889962 0.000000e+00 3153.0
10 TraesCS7D01G095200 chr7A 91.461 1663 123 13 805 2460 62175953 62177603 0.000000e+00 2266.0
11 TraesCS7D01G095200 chr7A 94.814 617 27 4 2833 3447 61889800 61889187 0.000000e+00 957.0
12 TraesCS7D01G095200 chr7A 90.027 371 22 5 3088 3444 62469397 62469766 1.870000e-127 466.0
13 TraesCS7D01G095200 chr7A 89.577 307 14 2 496 802 61892313 61892025 1.170000e-99 374.0
14 TraesCS7D01G095200 chr7A 92.241 116 6 1 3088 3200 62179175 62179290 9.900000e-36 161.0
15 TraesCS7D01G095200 chr7A 88.235 68 2 4 199 266 61892474 61892413 3.690000e-10 76.8
16 TraesCS7D01G095200 chr4A 94.087 1539 72 9 936 2460 673856740 673858273 0.000000e+00 2320.0
17 TraesCS7D01G095200 chr4A 89.189 296 24 7 2459 2749 673858336 673858628 2.530000e-96 363.0
18 TraesCS7D01G095200 chrUn 90.769 195 16 2 3 195 105364890 105365084 3.410000e-65 259.0
19 TraesCS7D01G095200 chrUn 75.210 238 51 7 999 1229 8827108 8826872 4.700000e-19 106.0
20 TraesCS7D01G095200 chr3D 84.500 200 26 5 3 199 536239258 536239455 3.510000e-45 193.0
21 TraesCS7D01G095200 chr3B 84.500 200 25 6 3 198 743715926 743715729 3.510000e-45 193.0
22 TraesCS7D01G095200 chr3B 100.000 29 0 0 509 537 5320903 5320875 2.000000e-03 54.7
23 TraesCS7D01G095200 chr6D 85.185 189 24 4 10 195 427636388 427636575 1.260000e-44 191.0
24 TraesCS7D01G095200 chr6B 84.615 195 23 7 5 195 204770632 204770823 1.630000e-43 187.0
25 TraesCS7D01G095200 chr2B 83.500 200 29 4 3 199 748576191 748576389 2.110000e-42 183.0
26 TraesCS7D01G095200 chr1B 83.417 199 29 4 3 198 571068431 571068234 7.600000e-42 182.0
27 TraesCS7D01G095200 chr1B 72.643 541 113 31 994 1512 675648068 675648595 2.770000e-31 147.0
28 TraesCS7D01G095200 chr1D 71.538 650 142 37 994 1614 485249193 485249828 6.000000e-28 135.0
29 TraesCS7D01G095200 chr5D 100.000 29 0 0 509 537 548969161 548969189 2.000000e-03 54.7


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 TraesCS7D01G095200 chr7D 57538727 57542173 3446 True 2972.0 5452 100.000000 1 3447 2 chr7D.!!$R3 3446
1 TraesCS7D01G095200 chr7D 58054300 58055757 1457 False 575.0 1099 92.072667 825 2639 3 chr7D.!!$F3 1814
2 TraesCS7D01G095200 chr7A 62175953 62179290 3337 False 1213.5 2266 91.851000 805 3200 2 chr7A.!!$F2 2395
3 TraesCS7D01G095200 chr7A 61889187 61892474 3287 True 1140.2 3153 91.855500 199 3447 4 chr7A.!!$R1 3248
4 TraesCS7D01G095200 chr4A 673856740 673858628 1888 False 1341.5 2320 91.638000 936 2749 2 chr4A.!!$F1 1813

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
989 1033 0.029567 CTGATCTCACCTACCGACGC 59.97 60.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 3161 1.221414 AGCAAATCGAAGCTATCCGC 58.779 50.0 8.4 0.0 39.78 5.54 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
22 23 5.779806 CAGTCAACCTAACGGTCAAATAG 57.220 43.478 0.00 0.00 44.73 1.73
23 24 5.475719 CAGTCAACCTAACGGTCAAATAGA 58.524 41.667 0.00 0.00 44.73 1.98
24 25 5.347907 CAGTCAACCTAACGGTCAAATAGAC 59.652 44.000 0.00 0.00 44.73 2.59
37 38 6.549912 GTCAAATAGACGGTTTGTTTAGGT 57.450 37.500 0.00 0.00 37.53 3.08
38 39 6.368213 GTCAAATAGACGGTTTGTTTAGGTG 58.632 40.000 0.00 0.00 37.53 4.00
39 40 5.049267 TCAAATAGACGGTTTGTTTAGGTGC 60.049 40.000 0.00 0.00 37.70 5.01
40 41 1.223187 AGACGGTTTGTTTAGGTGCG 58.777 50.000 0.00 0.00 0.00 5.34
41 42 0.236449 GACGGTTTGTTTAGGTGCGG 59.764 55.000 0.00 0.00 0.00 5.69
42 43 1.167781 ACGGTTTGTTTAGGTGCGGG 61.168 55.000 0.00 0.00 0.00 6.13
43 44 1.287815 GGTTTGTTTAGGTGCGGGC 59.712 57.895 0.00 0.00 0.00 6.13
44 45 1.287815 GTTTGTTTAGGTGCGGGCC 59.712 57.895 0.00 0.00 0.00 5.80
45 46 1.904378 TTTGTTTAGGTGCGGGCCC 60.904 57.895 13.57 13.57 0.00 5.80
46 47 2.642183 TTTGTTTAGGTGCGGGCCCA 62.642 55.000 24.92 0.00 0.00 5.36
47 48 2.282603 GTTTAGGTGCGGGCCCAA 60.283 61.111 24.92 6.27 0.00 4.12
48 49 2.282603 TTTAGGTGCGGGCCCAAC 60.283 61.111 24.92 19.37 0.00 3.77
49 50 3.871850 TTTAGGTGCGGGCCCAACC 62.872 63.158 29.08 29.08 37.93 3.77
56 57 2.994699 CGGGCCCAACCTGTCATA 59.005 61.111 24.92 0.00 40.35 2.15
57 58 1.301623 CGGGCCCAACCTGTCATAA 59.698 57.895 24.92 0.00 40.35 1.90
58 59 0.106719 CGGGCCCAACCTGTCATAAT 60.107 55.000 24.92 0.00 40.35 1.28
59 60 1.692411 GGGCCCAACCTGTCATAATC 58.308 55.000 19.95 0.00 39.10 1.75
60 61 1.308998 GGCCCAACCTGTCATAATCG 58.691 55.000 0.00 0.00 34.51 3.34
61 62 0.663153 GCCCAACCTGTCATAATCGC 59.337 55.000 0.00 0.00 0.00 4.58
62 63 0.937304 CCCAACCTGTCATAATCGCG 59.063 55.000 0.00 0.00 0.00 5.87
63 64 1.472552 CCCAACCTGTCATAATCGCGA 60.473 52.381 13.09 13.09 0.00 5.87
64 65 2.483876 CCAACCTGTCATAATCGCGAT 58.516 47.619 17.62 17.62 0.00 4.58
65 66 2.476619 CCAACCTGTCATAATCGCGATC 59.523 50.000 23.92 10.03 0.00 3.69
66 67 3.123050 CAACCTGTCATAATCGCGATCA 58.877 45.455 23.92 8.70 0.00 2.92
67 68 3.452755 ACCTGTCATAATCGCGATCAA 57.547 42.857 23.92 14.30 0.00 2.57
68 69 3.123804 ACCTGTCATAATCGCGATCAAC 58.876 45.455 23.92 17.22 0.00 3.18
69 70 3.181475 ACCTGTCATAATCGCGATCAACT 60.181 43.478 23.92 9.33 0.00 3.16
70 71 3.804325 CCTGTCATAATCGCGATCAACTT 59.196 43.478 23.92 9.77 0.00 2.66
71 72 4.271049 CCTGTCATAATCGCGATCAACTTT 59.729 41.667 23.92 8.97 0.00 2.66
72 73 5.142635 TGTCATAATCGCGATCAACTTTG 57.857 39.130 23.92 11.92 0.00 2.77
73 74 4.867608 TGTCATAATCGCGATCAACTTTGA 59.132 37.500 23.92 14.05 42.14 2.69
74 75 5.350091 TGTCATAATCGCGATCAACTTTGAA 59.650 36.000 23.92 6.05 41.13 2.69
75 76 6.037062 TGTCATAATCGCGATCAACTTTGAAT 59.963 34.615 23.92 4.87 41.13 2.57
76 77 6.571520 GTCATAATCGCGATCAACTTTGAATC 59.428 38.462 23.92 3.40 41.13 2.52
77 78 4.944962 AATCGCGATCAACTTTGAATCA 57.055 36.364 23.92 0.00 41.13 2.57
78 79 3.722555 TCGCGATCAACTTTGAATCAC 57.277 42.857 3.71 0.00 41.13 3.06
79 80 3.325870 TCGCGATCAACTTTGAATCACT 58.674 40.909 3.71 0.00 41.13 3.41
80 81 3.745975 TCGCGATCAACTTTGAATCACTT 59.254 39.130 3.71 0.00 41.13 3.16
81 82 3.842428 CGCGATCAACTTTGAATCACTTG 59.158 43.478 0.00 0.00 41.13 3.16
82 83 4.377328 CGCGATCAACTTTGAATCACTTGA 60.377 41.667 0.00 1.21 41.13 3.02
83 84 5.634896 GCGATCAACTTTGAATCACTTGAT 58.365 37.500 8.79 8.79 41.13 2.57
84 85 5.510674 GCGATCAACTTTGAATCACTTGATG 59.489 40.000 12.22 7.83 41.13 3.07
85 86 6.621380 GCGATCAACTTTGAATCACTTGATGA 60.621 38.462 12.22 4.16 41.13 2.92
112 113 0.741915 TTTTTGAACAGCGGACCACC 59.258 50.000 0.00 0.00 0.00 4.61
113 114 1.104577 TTTTGAACAGCGGACCACCC 61.105 55.000 0.00 0.00 0.00 4.61
114 115 2.272230 TTTGAACAGCGGACCACCCA 62.272 55.000 0.00 0.00 34.14 4.51
115 116 2.668550 GAACAGCGGACCACCCAC 60.669 66.667 0.00 0.00 34.14 4.61
116 117 3.168528 AACAGCGGACCACCCACT 61.169 61.111 0.00 0.00 34.14 4.00
117 118 2.676163 GAACAGCGGACCACCCACTT 62.676 60.000 0.00 0.00 34.14 3.16
118 119 2.669569 CAGCGGACCACCCACTTG 60.670 66.667 0.00 0.00 34.14 3.16
119 120 3.953775 AGCGGACCACCCACTTGG 61.954 66.667 0.00 0.00 43.04 3.61
136 137 8.857694 CCCACTTGGTAGTTATCTAAGAAAAA 57.142 34.615 0.00 0.00 30.26 1.94
243 244 4.505217 GCAGCGCATCGTCGGTTG 62.505 66.667 11.47 0.00 38.18 3.77
257 258 1.984026 GGTTGACAATGGGGGCTGG 60.984 63.158 0.00 0.00 0.00 4.85
258 259 2.283821 TTGACAATGGGGGCTGGC 60.284 61.111 0.00 0.00 0.00 4.85
259 260 3.157733 TTGACAATGGGGGCTGGCA 62.158 57.895 2.88 0.00 0.00 4.92
563 564 1.579626 GACTACGAACCGACGAGCG 60.580 63.158 0.00 0.00 40.47 5.03
626 627 2.036929 GCAAGCAGGGGATAGGAGAGA 61.037 57.143 0.00 0.00 0.00 3.10
656 657 2.985139 GACGAAGAAGAAACCCTGTACG 59.015 50.000 0.00 0.00 0.00 3.67
690 691 0.328926 TTAATCGGGTGGTTGGGGAC 59.671 55.000 0.00 0.00 0.00 4.46
799 800 0.035036 TACACGAAATTGGGTGCGGA 59.965 50.000 8.59 0.00 37.68 5.54
802 803 1.740585 CACGAAATTGGGTGCGGATAA 59.259 47.619 0.00 0.00 0.00 1.75
803 804 2.014128 ACGAAATTGGGTGCGGATAAG 58.986 47.619 0.00 0.00 0.00 1.73
815 856 4.202020 GGTGCGGATAAGGGAAAAGATTTC 60.202 45.833 0.00 0.00 0.00 2.17
823 864 1.130561 GGGAAAAGATTTCGCCGTCTG 59.869 52.381 8.26 0.00 0.00 3.51
852 893 2.865119 TGTGTCCGTAGAGTCCTACA 57.135 50.000 0.00 0.00 44.22 2.74
853 894 2.708051 TGTGTCCGTAGAGTCCTACAG 58.292 52.381 0.00 0.00 44.22 2.74
980 1024 2.166459 TGTTCCACGATCTGATCTCACC 59.834 50.000 15.16 0.33 0.00 4.02
989 1033 0.029567 CTGATCTCACCTACCGACGC 59.970 60.000 0.00 0.00 0.00 5.19
1302 1350 1.006571 CACGGACTACTGCAACGGT 60.007 57.895 0.00 0.00 0.00 4.83
1312 1360 0.671781 CTGCAACGGTCTCCTCTTGG 60.672 60.000 0.00 0.00 0.00 3.61
1320 1368 2.484770 CGGTCTCCTCTTGGTTGAAACA 60.485 50.000 0.00 0.00 34.23 2.83
1520 1568 2.731721 CGACGTGGCGTGCAGTAA 60.732 61.111 0.00 0.00 41.37 2.24
1539 1587 2.656069 GGAGTGGCCACCTTCGCTA 61.656 63.158 32.29 0.00 36.34 4.26
1638 1686 1.003580 ACAATGGCCGACATGAACTCT 59.996 47.619 0.00 0.00 40.44 3.24
1662 1710 8.556589 TCTGACTTTAATTCTGATGGGGAATTA 58.443 33.333 0.00 0.00 41.66 1.40
1716 1767 7.125391 TCTATGTCCCTTTAAGGCATGAAAAT 58.875 34.615 5.29 0.00 32.73 1.82
1733 1784 8.719648 GCATGAAAATGGTGATTTTGTTATGAA 58.280 29.630 0.00 0.00 41.06 2.57
1936 2004 5.544176 AGGGGTCTATTGTGTACAGGATATG 59.456 44.000 0.00 0.00 0.00 1.78
2033 2101 3.696051 TGAAATATGCTTTGAGACAGCCC 59.304 43.478 0.00 0.00 36.33 5.19
2081 2149 1.833630 GTGGACCATGGATCTCACAGA 59.166 52.381 21.47 0.00 0.00 3.41
2101 2169 3.882888 AGACGCTTCAACAAAAGGAATCA 59.117 39.130 0.00 0.00 0.00 2.57
2158 2226 8.076178 GCAAATAAATACAACGAGGCAATATCT 58.924 33.333 0.00 0.00 0.00 1.98
2314 2382 7.449704 GCCCTTTTCCATGATGATTATAGAAGT 59.550 37.037 0.00 0.00 0.00 3.01
2615 2992 7.280205 CGGGTTAACATTCTTTGTAAGCTATCT 59.720 37.037 8.10 0.00 37.68 1.98
2656 3033 8.455598 TTTTTAATTATGTAGCGAACAAAGGC 57.544 30.769 0.00 0.00 42.70 4.35
2728 3105 8.958119 TTAAAGACTTTGATATATGCCGAACT 57.042 30.769 10.80 0.00 0.00 3.01
2766 3143 4.837972 AGATTACCAAAGAGTCTTCCTGC 58.162 43.478 5.70 0.00 0.00 4.85
2784 3161 1.421410 GCATGTAAGGGTCGTGCGAG 61.421 60.000 0.00 0.00 37.91 5.03
2802 3195 3.736581 GCGGATAGCTTCGATTTGC 57.263 52.632 0.00 0.00 44.04 3.68
2843 3399 4.521146 AGCTGCTCTACTAATTTGCATGT 58.479 39.130 0.00 0.00 33.02 3.21
2856 3412 5.824904 ATTTGCATGTGATGTCTCTAACC 57.175 39.130 0.00 0.00 0.00 2.85
2884 3440 2.643551 ACTGTGCAACCAGGCATATAC 58.356 47.619 8.97 0.00 46.92 1.47
2915 3472 9.985730 AAAAGAGTGATATCAGCAAAAATTCAA 57.014 25.926 5.42 0.00 0.00 2.69
3022 3579 5.507637 ACGAGACCTTAGAAACTAGATCCA 58.492 41.667 0.00 0.00 0.00 3.41
3045 3604 4.869215 TGTTGATACGTCCAACGACTTTA 58.131 39.130 21.18 7.00 46.05 1.85
3050 3609 7.424227 TGATACGTCCAACGACTTTATTTTT 57.576 32.000 6.48 0.00 46.05 1.94
3248 4496 4.158394 GGCTGGAAAGTGCAAAGATATCAA 59.842 41.667 5.32 0.00 0.00 2.57
3249 4497 5.336690 GGCTGGAAAGTGCAAAGATATCAAA 60.337 40.000 5.32 0.00 0.00 2.69
3258 4506 8.854614 AGTGCAAAGATATCAAAGTCTTAGTT 57.145 30.769 5.32 0.00 33.76 2.24
3377 4625 4.682401 GGGCAAAAATAACAGTAACAACCG 59.318 41.667 0.00 0.00 0.00 4.44
3392 4640 1.818060 CAACCGAAATGGCCAGATCAA 59.182 47.619 13.05 0.00 43.94 2.57
3415 4663 8.736244 TCAAGCTGTTATTTAATTTGTAGGGTC 58.264 33.333 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.515330 ACCGTCTATTTGACCGTTAGG 57.485 47.619 0.00 0.00 42.49 2.69
8 9 4.687483 ACAAACCGTCTATTTGACCGTTAG 59.313 41.667 4.57 0.00 42.97 2.34
9 10 4.630111 ACAAACCGTCTATTTGACCGTTA 58.370 39.130 4.57 0.00 42.97 3.18
10 11 3.469739 ACAAACCGTCTATTTGACCGTT 58.530 40.909 4.57 0.74 44.66 4.44
11 12 3.116079 ACAAACCGTCTATTTGACCGT 57.884 42.857 4.57 0.00 42.49 4.83
12 13 4.477302 AAACAAACCGTCTATTTGACCG 57.523 40.909 4.57 0.00 42.49 4.79
13 14 5.471116 ACCTAAACAAACCGTCTATTTGACC 59.529 40.000 4.57 0.00 42.49 4.02
14 15 6.368213 CACCTAAACAAACCGTCTATTTGAC 58.632 40.000 4.57 0.00 39.01 3.18
15 16 5.049267 GCACCTAAACAAACCGTCTATTTGA 60.049 40.000 4.57 0.00 39.01 2.69
16 17 5.151389 GCACCTAAACAAACCGTCTATTTG 58.849 41.667 0.00 0.00 41.81 2.32
17 18 4.083696 CGCACCTAAACAAACCGTCTATTT 60.084 41.667 0.00 0.00 0.00 1.40
18 19 3.434299 CGCACCTAAACAAACCGTCTATT 59.566 43.478 0.00 0.00 0.00 1.73
19 20 2.997986 CGCACCTAAACAAACCGTCTAT 59.002 45.455 0.00 0.00 0.00 1.98
20 21 2.406130 CGCACCTAAACAAACCGTCTA 58.594 47.619 0.00 0.00 0.00 2.59
21 22 1.223187 CGCACCTAAACAAACCGTCT 58.777 50.000 0.00 0.00 0.00 4.18
22 23 0.236449 CCGCACCTAAACAAACCGTC 59.764 55.000 0.00 0.00 0.00 4.79
23 24 1.167781 CCCGCACCTAAACAAACCGT 61.168 55.000 0.00 0.00 0.00 4.83
24 25 1.577421 CCCGCACCTAAACAAACCG 59.423 57.895 0.00 0.00 0.00 4.44
25 26 1.287815 GCCCGCACCTAAACAAACC 59.712 57.895 0.00 0.00 0.00 3.27
26 27 1.287815 GGCCCGCACCTAAACAAAC 59.712 57.895 0.00 0.00 0.00 2.93
27 28 1.904378 GGGCCCGCACCTAAACAAA 60.904 57.895 5.69 0.00 0.00 2.83
28 29 2.282603 GGGCCCGCACCTAAACAA 60.283 61.111 5.69 0.00 0.00 2.83
29 30 3.134703 TTGGGCCCGCACCTAAACA 62.135 57.895 19.37 0.00 0.00 2.83
30 31 2.282603 TTGGGCCCGCACCTAAAC 60.283 61.111 19.37 0.00 0.00 2.01
31 32 2.282603 GTTGGGCCCGCACCTAAA 60.283 61.111 19.37 0.00 31.25 1.85
32 33 4.354162 GGTTGGGCCCGCACCTAA 62.354 66.667 28.71 10.54 0.00 2.69
38 39 2.830186 TTATGACAGGTTGGGCCCGC 62.830 60.000 19.37 12.84 38.26 6.13
39 40 0.106719 ATTATGACAGGTTGGGCCCG 60.107 55.000 19.37 4.36 38.26 6.13
40 41 1.692411 GATTATGACAGGTTGGGCCC 58.308 55.000 17.59 17.59 38.26 5.80
41 42 1.308998 CGATTATGACAGGTTGGGCC 58.691 55.000 0.00 0.00 37.58 5.80
42 43 0.663153 GCGATTATGACAGGTTGGGC 59.337 55.000 0.00 0.00 0.00 5.36
43 44 0.937304 CGCGATTATGACAGGTTGGG 59.063 55.000 0.00 0.00 0.00 4.12
44 45 1.934589 TCGCGATTATGACAGGTTGG 58.065 50.000 3.71 0.00 0.00 3.77
45 46 3.123050 TGATCGCGATTATGACAGGTTG 58.877 45.455 24.55 0.00 0.00 3.77
46 47 3.452755 TGATCGCGATTATGACAGGTT 57.547 42.857 24.55 0.00 0.00 3.50
47 48 3.123804 GTTGATCGCGATTATGACAGGT 58.876 45.455 24.55 0.00 0.00 4.00
48 49 3.384668 AGTTGATCGCGATTATGACAGG 58.615 45.455 24.55 0.00 0.00 4.00
49 50 5.005682 TCAAAGTTGATCGCGATTATGACAG 59.994 40.000 24.55 11.75 31.01 3.51
50 51 4.867608 TCAAAGTTGATCGCGATTATGACA 59.132 37.500 24.55 13.24 31.01 3.58
51 52 5.389642 TCAAAGTTGATCGCGATTATGAC 57.610 39.130 24.55 14.83 31.01 3.06
52 53 6.257630 TGATTCAAAGTTGATCGCGATTATGA 59.742 34.615 24.55 16.06 37.00 2.15
53 54 6.355405 GTGATTCAAAGTTGATCGCGATTATG 59.645 38.462 24.55 13.95 37.00 1.90
54 55 6.258727 AGTGATTCAAAGTTGATCGCGATTAT 59.741 34.615 24.55 0.35 37.00 1.28
55 56 5.580691 AGTGATTCAAAGTTGATCGCGATTA 59.419 36.000 24.55 17.25 37.00 1.75
56 57 4.393062 AGTGATTCAAAGTTGATCGCGATT 59.607 37.500 24.55 4.27 37.00 3.34
57 58 3.935203 AGTGATTCAAAGTTGATCGCGAT 59.065 39.130 23.97 23.97 37.00 4.58
58 59 3.325870 AGTGATTCAAAGTTGATCGCGA 58.674 40.909 13.09 13.09 37.00 5.87
59 60 3.729526 AGTGATTCAAAGTTGATCGCG 57.270 42.857 0.00 0.00 37.00 5.87
60 61 5.034554 TCAAGTGATTCAAAGTTGATCGC 57.965 39.130 0.00 2.68 37.00 4.58
61 62 6.834876 TCATCAAGTGATTCAAAGTTGATCG 58.165 36.000 13.41 10.75 42.90 3.69
93 94 0.741915 GGTGGTCCGCTGTTCAAAAA 59.258 50.000 1.66 0.00 0.00 1.94
94 95 1.104577 GGGTGGTCCGCTGTTCAAAA 61.105 55.000 1.66 0.00 33.83 2.44
95 96 1.527380 GGGTGGTCCGCTGTTCAAA 60.527 57.895 1.66 0.00 33.83 2.69
96 97 2.112297 GGGTGGTCCGCTGTTCAA 59.888 61.111 1.66 0.00 33.83 2.69
97 98 3.164977 TGGGTGGTCCGCTGTTCA 61.165 61.111 1.66 0.00 38.76 3.18
98 99 2.668550 GTGGGTGGTCCGCTGTTC 60.669 66.667 1.66 0.00 42.62 3.18
111 112 8.857694 TTTTTCTTAGATAACTACCAAGTGGG 57.142 34.615 1.69 0.00 44.81 4.61
177 178 9.927081 CCTGGGGAATAAATAGCATAAATCTAT 57.073 33.333 0.00 0.00 0.00 1.98
178 179 9.122954 TCCTGGGGAATAAATAGCATAAATCTA 57.877 33.333 0.00 0.00 0.00 1.98
179 180 8.000171 TCCTGGGGAATAAATAGCATAAATCT 58.000 34.615 0.00 0.00 0.00 2.40
180 181 8.109634 TCTCCTGGGGAATAAATAGCATAAATC 58.890 37.037 0.00 0.00 0.00 2.17
181 182 8.000171 TCTCCTGGGGAATAAATAGCATAAAT 58.000 34.615 0.00 0.00 0.00 1.40
182 183 7.401060 TCTCCTGGGGAATAAATAGCATAAA 57.599 36.000 0.00 0.00 0.00 1.40
183 184 7.405292 CATCTCCTGGGGAATAAATAGCATAA 58.595 38.462 0.00 0.00 0.00 1.90
184 185 6.069440 CCATCTCCTGGGGAATAAATAGCATA 60.069 42.308 0.00 0.00 41.82 3.14
185 186 5.281401 CCATCTCCTGGGGAATAAATAGCAT 60.281 44.000 0.00 0.00 41.82 3.79
186 187 4.043310 CCATCTCCTGGGGAATAAATAGCA 59.957 45.833 0.00 0.00 41.82 3.49
187 188 4.593956 CCATCTCCTGGGGAATAAATAGC 58.406 47.826 0.00 0.00 41.82 2.97
188 189 4.593956 GCCATCTCCTGGGGAATAAATAG 58.406 47.826 0.00 0.00 46.06 1.73
189 190 4.657814 GCCATCTCCTGGGGAATAAATA 57.342 45.455 0.00 0.00 46.06 1.40
190 191 3.532641 GCCATCTCCTGGGGAATAAAT 57.467 47.619 0.00 0.00 46.06 1.40
228 229 2.809601 GTCAACCGACGATGCGCT 60.810 61.111 9.73 0.00 31.07 5.92
235 236 2.038269 CCCCCATTGTCAACCGACG 61.038 63.158 0.00 0.00 45.80 5.12
236 237 2.340328 GCCCCCATTGTCAACCGAC 61.340 63.158 0.00 0.00 42.93 4.79
237 238 2.034999 GCCCCCATTGTCAACCGA 59.965 61.111 0.00 0.00 0.00 4.69
238 239 2.035626 AGCCCCCATTGTCAACCG 59.964 61.111 0.00 0.00 0.00 4.44
239 240 1.984026 CCAGCCCCCATTGTCAACC 60.984 63.158 0.00 0.00 0.00 3.77
243 244 2.757099 CTGCCAGCCCCCATTGTC 60.757 66.667 0.00 0.00 0.00 3.18
600 601 0.107703 TATCCCCTGCTTGCTTGACG 60.108 55.000 0.00 0.00 0.00 4.35
601 602 1.673168 CTATCCCCTGCTTGCTTGAC 58.327 55.000 0.00 0.00 0.00 3.18
602 603 0.548031 CCTATCCCCTGCTTGCTTGA 59.452 55.000 0.00 0.00 0.00 3.02
603 604 0.548031 TCCTATCCCCTGCTTGCTTG 59.452 55.000 0.00 0.00 0.00 4.01
604 605 0.842635 CTCCTATCCCCTGCTTGCTT 59.157 55.000 0.00 0.00 0.00 3.91
605 606 0.030705 TCTCCTATCCCCTGCTTGCT 60.031 55.000 0.00 0.00 0.00 3.91
606 607 0.396060 CTCTCCTATCCCCTGCTTGC 59.604 60.000 0.00 0.00 0.00 4.01
607 608 2.094100 TCTCTCCTATCCCCTGCTTG 57.906 55.000 0.00 0.00 0.00 4.01
608 609 2.022527 AGTTCTCTCCTATCCCCTGCTT 60.023 50.000 0.00 0.00 0.00 3.91
609 610 1.578215 AGTTCTCTCCTATCCCCTGCT 59.422 52.381 0.00 0.00 0.00 4.24
610 611 1.691434 CAGTTCTCTCCTATCCCCTGC 59.309 57.143 0.00 0.00 0.00 4.85
611 612 1.691434 GCAGTTCTCTCCTATCCCCTG 59.309 57.143 0.00 0.00 0.00 4.45
612 613 1.413808 GGCAGTTCTCTCCTATCCCCT 60.414 57.143 0.00 0.00 0.00 4.79
613 614 1.052617 GGCAGTTCTCTCCTATCCCC 58.947 60.000 0.00 0.00 0.00 4.81
614 615 0.676736 CGGCAGTTCTCTCCTATCCC 59.323 60.000 0.00 0.00 0.00 3.85
615 616 0.032815 GCGGCAGTTCTCTCCTATCC 59.967 60.000 0.00 0.00 0.00 2.59
616 617 0.318275 CGCGGCAGTTCTCTCCTATC 60.318 60.000 0.00 0.00 0.00 2.08
626 627 2.022129 CTTCTTCGTCGCGGCAGTT 61.022 57.895 12.89 0.00 0.00 3.16
656 657 3.630101 CGATTAAGTCGCTAACTCTCCC 58.370 50.000 0.00 0.00 44.33 4.30
690 691 1.935917 CACCCGCACGATACGTACG 60.936 63.158 15.01 15.01 44.69 3.67
759 760 4.657075 ACACTAGCCGAACAAAAATACG 57.343 40.909 0.00 0.00 0.00 3.06
799 800 3.617284 ACGGCGAAATCTTTTCCCTTAT 58.383 40.909 16.62 0.00 0.00 1.73
802 803 1.003233 AGACGGCGAAATCTTTTCCCT 59.997 47.619 16.62 0.00 0.00 4.20
803 804 1.130561 CAGACGGCGAAATCTTTTCCC 59.869 52.381 16.62 0.00 0.00 3.97
852 893 2.264005 AGTACATCGATCCGAGCTCT 57.736 50.000 12.85 0.00 39.91 4.09
853 894 3.365164 GGTAAGTACATCGATCCGAGCTC 60.365 52.174 2.73 2.73 39.91 4.09
980 1024 4.143333 CCACCCCAGCGTCGGTAG 62.143 72.222 0.00 0.00 0.00 3.18
989 1033 0.394762 CATGTCCATGTCCACCCCAG 60.395 60.000 0.00 0.00 34.23 4.45
1209 1255 2.222217 GGTGATGTAGCGCGTCGTC 61.222 63.158 8.43 16.21 35.92 4.20
1302 1350 3.454447 TGTCTGTTTCAACCAAGAGGAGA 59.546 43.478 0.00 0.00 38.69 3.71
1312 1360 1.067060 GGCCACCTTGTCTGTTTCAAC 59.933 52.381 0.00 0.00 0.00 3.18
1320 1368 2.520968 GGGTTGGCCACCTTGTCT 59.479 61.111 19.69 0.00 46.38 3.41
1520 1568 4.021925 GCGAAGGTGGCCACTCCT 62.022 66.667 33.91 22.06 42.20 3.69
1539 1587 6.124340 TGAGGAGAAAACATGCATGACATAT 58.876 36.000 32.75 14.46 36.64 1.78
1662 1710 1.033574 GCCAGTGAGCGGAGTAGTAT 58.966 55.000 0.00 0.00 0.00 2.12
1733 1784 9.730705 TGTGTAATTGTGAGTAGTAGTAGTACT 57.269 33.333 16.10 16.10 42.49 2.73
1817 1885 9.241317 GTCATTCCATAATTTTATTCTGCACAG 57.759 33.333 0.00 0.00 0.00 3.66
1936 2004 1.317613 TAAATGTGCATCGGCCATCC 58.682 50.000 2.24 0.00 40.13 3.51
2017 2085 1.377725 CCGGGCTGTCTCAAAGCAT 60.378 57.895 0.00 0.00 42.69 3.79
2033 2101 5.005394 CACGTTTACAAGGATATGTTCTCCG 59.995 44.000 0.00 0.00 37.88 4.63
2081 2149 4.853924 ATGATTCCTTTTGTTGAAGCGT 57.146 36.364 0.00 0.00 29.74 5.07
2101 2169 3.564225 GGTTGACGTCTTCTTCCAACAAT 59.436 43.478 17.92 0.00 38.92 2.71
2158 2226 9.478238 TCAGAATCCCATTCAAAATCATCTTTA 57.522 29.630 0.00 0.00 41.71 1.85
2622 2999 9.607988 TCGCTACATAATTAAAAAGAATCAGGA 57.392 29.630 0.00 0.00 0.00 3.86
2656 3033 6.128634 GGAAATTACTGGTCTGTTCGTTACTG 60.129 42.308 0.00 0.00 0.00 2.74
2766 3143 1.421410 GCTCGCACGACCCTTACATG 61.421 60.000 0.00 0.00 0.00 3.21
2784 3161 1.221414 AGCAAATCGAAGCTATCCGC 58.779 50.000 8.40 0.00 39.78 5.54
2802 3195 8.970691 AGCAGCTTTACACACAAAATATAAAG 57.029 30.769 0.00 0.00 36.41 1.85
2843 3399 7.330946 CACAGTTAAATTCGGTTAGAGACATCA 59.669 37.037 0.00 0.00 0.00 3.07
2856 3412 3.564511 CCTGGTTGCACAGTTAAATTCG 58.435 45.455 3.87 0.00 36.75 3.34
2884 3440 8.578308 TTTTGCTGATATCACTCTTTTGTTTG 57.422 30.769 0.00 0.00 0.00 2.93
2942 3499 7.058525 TCAATTGGACTGATGATTTGAGCTAT 58.941 34.615 5.42 0.00 0.00 2.97
2995 3552 5.311265 TCTAGTTTCTAAGGTCTCGTCACA 58.689 41.667 0.00 0.00 0.00 3.58
2997 3554 5.589452 GGATCTAGTTTCTAAGGTCTCGTCA 59.411 44.000 0.00 0.00 0.00 4.35
3050 3609 3.955551 GGTCCTGGTAACTTTTGACCAAA 59.044 43.478 0.00 0.00 45.03 3.28
3051 3610 3.053544 TGGTCCTGGTAACTTTTGACCAA 60.054 43.478 6.71 0.00 45.03 3.67
3052 3611 2.510382 TGGTCCTGGTAACTTTTGACCA 59.490 45.455 5.14 5.14 43.23 4.02
3377 4625 2.097825 ACAGCTTGATCTGGCCATTTC 58.902 47.619 5.51 7.04 38.36 2.17
3392 4640 8.107095 TCAGACCCTACAAATTAAATAACAGCT 58.893 33.333 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.