Multiple sequence alignment - TraesCS2D01G248500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G248500 chr2D 100.000 9184 0 0 1 9184 293137775 293146958 0.000000e+00 16960.0
1 TraesCS2D01G248500 chr2D 80.690 145 14 9 2639 2780 191268532 191268665 5.870000e-17 100.0
2 TraesCS2D01G248500 chr2B 97.422 8534 164 18 1 8514 368953052 368961549 0.000000e+00 14489.0
3 TraesCS2D01G248500 chr2B 92.021 376 12 6 8812 9184 368972582 368972942 6.360000e-141 512.0
4 TraesCS2D01G248500 chr2B 85.714 56 8 0 7133 7188 367733288 367733233 9.960000e-05 60.2
5 TraesCS2D01G248500 chr2A 98.422 5515 70 7 1 5510 360415744 360421246 0.000000e+00 9686.0
6 TraesCS2D01G248500 chr2A 96.189 3254 90 8 5487 8717 360422238 360425480 0.000000e+00 5291.0
7 TraesCS2D01G248500 chr2A 95.733 375 14 1 8812 9184 360428475 360428849 3.670000e-168 603.0
8 TraesCS2D01G248500 chr2A 94.245 139 6 2 1688 1825 596470945 596470808 2.600000e-50 211.0
9 TraesCS2D01G248500 chr2A 93.525 139 7 2 1688 1825 596491023 596490886 1.210000e-48 206.0
10 TraesCS2D01G248500 chr2A 96.491 114 3 1 1872 1984 596470808 596470695 4.380000e-43 187.0
11 TraesCS2D01G248500 chr2A 95.690 116 4 1 1872 1986 596490886 596490771 1.570000e-42 185.0
12 TraesCS2D01G248500 chr2A 96.875 96 3 0 8721 8816 360427074 360427169 2.650000e-35 161.0
13 TraesCS2D01G248500 chr2A 75.706 177 31 9 2621 2795 175173623 175173457 2.750000e-10 78.7
14 TraesCS2D01G248500 chr2A 100.000 29 0 0 8673 8701 621486834 621486806 5.000000e-03 54.7
15 TraesCS2D01G248500 chr4D 81.495 281 45 7 2392 2666 51846613 51846892 3.340000e-54 224.0
16 TraesCS2D01G248500 chr4D 77.241 145 25 6 2638 2782 440873804 440873668 2.750000e-10 78.7
17 TraesCS2D01G248500 chr4D 100.000 29 0 0 8673 8701 373466786 373466758 5.000000e-03 54.7
18 TraesCS2D01G248500 chr5B 94.891 137 7 0 1685 1821 386158571 386158707 2.010000e-51 215.0
19 TraesCS2D01G248500 chr5B 95.041 121 5 1 1867 1986 386158706 386158826 1.220000e-43 189.0
20 TraesCS2D01G248500 chr5B 93.333 75 4 1 2101 2174 386158893 386158819 9.750000e-20 110.0
21 TraesCS2D01G248500 chr5B 92.308 39 3 0 8663 8701 220810912 220810950 1.000000e-03 56.5
22 TraesCS2D01G248500 chr6A 78.049 369 60 15 2347 2703 105844876 105845235 7.220000e-51 213.0
23 TraesCS2D01G248500 chr6A 76.309 401 59 19 2412 2779 149830216 149829819 2.040000e-41 182.0
24 TraesCS2D01G248500 chr5A 93.431 137 9 0 1685 1821 641422103 641422239 4.350000e-48 204.0
25 TraesCS2D01G248500 chr5A 97.391 115 2 1 1867 1980 641422238 641422352 2.620000e-45 195.0
26 TraesCS2D01G248500 chr5A 90.741 54 2 1 2229 2279 441340456 441340403 1.650000e-07 69.4
27 TraesCS2D01G248500 chr5A 82.895 76 10 1 2229 2301 386651570 386651495 2.140000e-06 65.8
28 TraesCS2D01G248500 chr7A 96.522 115 3 1 1867 1980 449719774 449719888 1.220000e-43 189.0
29 TraesCS2D01G248500 chr7A 90.780 141 9 1 1685 1821 449719635 449719775 1.570000e-42 185.0
30 TraesCS2D01G248500 chr7A 98.182 55 1 0 2106 2160 449719941 449719887 7.590000e-16 97.1
31 TraesCS2D01G248500 chr6B 76.382 398 58 21 2412 2776 214090047 214090441 2.040000e-41 182.0
32 TraesCS2D01G248500 chr1D 81.633 196 23 8 2515 2703 36625186 36624997 5.740000e-32 150.0
33 TraesCS2D01G248500 chr3D 80.800 125 14 10 2666 2781 481730122 481730245 1.270000e-13 89.8
34 TraesCS2D01G248500 chr3A 77.241 145 25 6 2635 2779 300159138 300159002 2.750000e-10 78.7
35 TraesCS2D01G248500 chr4A 76.190 168 24 14 2625 2787 312170832 312170676 3.560000e-09 75.0
36 TraesCS2D01G248500 chr5D 79.646 113 13 6 2229 2332 270718277 270718388 1.280000e-08 73.1
37 TraesCS2D01G248500 chr5D 89.655 58 2 2 2229 2283 563512364 563512420 4.600000e-08 71.3
38 TraesCS2D01G248500 chr3B 90.909 55 2 1 2229 2280 529141559 529141613 4.600000e-08 71.3
39 TraesCS2D01G248500 chr3B 97.059 34 1 0 8668 8701 829125224 829125257 3.580000e-04 58.4
40 TraesCS2D01G248500 chr3B 100.000 29 0 0 8673 8701 808987701 808987673 5.000000e-03 54.7
41 TraesCS2D01G248500 chr7D 90.741 54 2 1 2229 2279 86255577 86255524 1.650000e-07 69.4
42 TraesCS2D01G248500 chr7D 100.000 31 0 0 8671 8701 606306653 606306623 3.580000e-04 58.4
43 TraesCS2D01G248500 chr7D 100.000 29 0 0 8673 8701 136315481 136315453 5.000000e-03 54.7
44 TraesCS2D01G248500 chr6D 84.286 70 11 0 2711 2780 8091084 8091153 1.650000e-07 69.4
45 TraesCS2D01G248500 chr6D 100.000 29 0 0 8673 8701 144264815 144264787 5.000000e-03 54.7
46 TraesCS2D01G248500 chrUn 89.130 46 2 2 2752 2795 373670914 373670870 5.000000e-03 54.7
47 TraesCS2D01G248500 chr1A 78.652 89 14 3 2229 2314 226446208 226446122 5.000000e-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 TraesCS2D01G248500 chr2D 293137775 293146958 9183 False 16960.00 16960 100.00000 1 9184 1 chr2D.!!$F2 9183
1 TraesCS2D01G248500 chr2B 368953052 368961549 8497 False 14489.00 14489 97.42200 1 8514 1 chr2B.!!$F1 8513
2 TraesCS2D01G248500 chr2A 360415744 360428849 13105 False 3935.25 9686 96.80475 1 9184 4 chr2A.!!$F1 9183

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
562 565 6.499699 AGGTTGATCTCTATTCTATGGATGCA 59.500 38.462 0.00 0.00 0.00 3.96 F
1010 1015 0.407139 AGAAGTGCCATGGAGCCTTT 59.593 50.000 18.40 1.25 0.00 3.11 F
1047 1052 1.152902 ACTGAAGCAAGCTGGCACA 60.153 52.632 17.28 13.83 35.83 4.57 F
2856 2863 1.906574 ACTAATGTCTCGGGCCTTTCA 59.093 47.619 0.84 0.00 0.00 2.69 F
3523 3530 1.273267 ACCTGCTGATGTCACCCTCTA 60.273 52.381 0.00 0.00 0.00 2.43 F
4979 4986 8.221251 AGGGTTCTAAGAAACAGAAGAAGAAAT 58.779 33.333 0.00 0.00 32.81 2.17 F
5465 5474 0.109179 TCGTGTTTATCCGTGACCCG 60.109 55.000 0.00 0.00 0.00 5.28 F
5508 6533 0.178981 ATGCTTGGCTGTGTCTTGGT 60.179 50.000 0.00 0.00 0.00 3.67 F
6213 7239 0.456221 CGTTGTACTCGGGCTCATCT 59.544 55.000 0.00 0.00 0.00 2.90 F
6764 7790 0.036164 TCCACAACGCAGGCATAACT 59.964 50.000 0.00 0.00 0.00 2.24 F
7955 8983 0.036732 TTGAGCAGGAGAAACGGCAT 59.963 50.000 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 2321 4.202441 CCATCAGGTAGAAAGGAATGGTG 58.798 47.826 0.00 0.0 0.00 4.17 R
2856 2863 7.446625 AGCATGAGAAATGAGACTTTTAACACT 59.553 33.333 0.00 0.0 0.00 3.55 R
3086 3093 2.078849 TGTTGCTGGAGACACATACG 57.921 50.000 0.00 0.0 35.60 3.06 R
4873 4880 1.869767 AGCTCTGCAAGTTCACTTTCG 59.130 47.619 0.00 0.0 33.11 3.46 R
4979 4986 0.599558 GATTGTGCTGCCTGCTTGAA 59.400 50.000 0.00 0.0 43.37 2.69 R
6357 7383 0.034380 TAGTAGCCTCGCCTCACTGT 60.034 55.000 0.00 0.0 0.00 3.55 R
6698 7724 1.045407 ACCGTCTGTAAAGCCACTCA 58.955 50.000 0.00 0.0 0.00 3.41 R
6725 7751 1.666011 GACGGAGCCACAGTCAAGA 59.334 57.895 6.84 0.0 41.88 3.02 R
7955 8983 1.069090 GTGGGAGACAACGCTGTGA 59.931 57.895 0.00 0.0 35.30 3.58 R
7959 8987 1.367840 GACTGTGGGAGACAACGCT 59.632 57.895 0.00 0.0 32.80 5.07 R
8893 12846 1.154035 GACGCGGCCCAAGATTTTG 60.154 57.895 12.47 0.0 0.00 2.44 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
562 565 6.499699 AGGTTGATCTCTATTCTATGGATGCA 59.500 38.462 0.00 0.00 0.00 3.96
1010 1015 0.407139 AGAAGTGCCATGGAGCCTTT 59.593 50.000 18.40 1.25 0.00 3.11
1019 1024 3.326297 GCCATGGAGCCTTTAGTATCTCT 59.674 47.826 18.40 0.00 0.00 3.10
1031 1036 2.060383 TATCTCTGCCAGGCGCACT 61.060 57.895 10.83 0.02 44.64 4.40
1047 1052 1.152902 ACTGAAGCAAGCTGGCACA 60.153 52.632 17.28 13.83 35.83 4.57
2253 2260 2.598192 CACAAACCTCAAAACACAAGCG 59.402 45.455 0.00 0.00 0.00 4.68
2326 2333 7.607991 TCTTCTAAATGAGTCACCATTCCTTTC 59.392 37.037 0.00 0.00 35.86 2.62
2346 2353 6.264744 CCTTTCTACCTGATGGTCTACGATTA 59.735 42.308 0.00 0.00 44.78 1.75
2808 2815 2.621055 TGTGCCAATGAAGCGTAAAGTT 59.379 40.909 0.00 0.00 0.00 2.66
2856 2863 1.906574 ACTAATGTCTCGGGCCTTTCA 59.093 47.619 0.84 0.00 0.00 2.69
3086 3093 4.455533 TCAAACAGAGGTATGTGTGAATGC 59.544 41.667 0.00 0.00 43.00 3.56
3108 3115 4.371786 CGTATGTGTCTCCAGCAACATAT 58.628 43.478 0.00 0.00 32.80 1.78
3523 3530 1.273267 ACCTGCTGATGTCACCCTCTA 60.273 52.381 0.00 0.00 0.00 2.43
4979 4986 8.221251 AGGGTTCTAAGAAACAGAAGAAGAAAT 58.779 33.333 0.00 0.00 32.81 2.17
5012 5019 5.407995 GCAGCACAATCTGATATTACCTCTC 59.592 44.000 0.00 0.00 36.19 3.20
5442 5451 5.712917 GGTGACCAGTGGTATAATTTTGGAA 59.287 40.000 16.72 0.00 35.25 3.53
5465 5474 0.109179 TCGTGTTTATCCGTGACCCG 60.109 55.000 0.00 0.00 0.00 5.28
5508 6533 0.178981 ATGCTTGGCTGTGTCTTGGT 60.179 50.000 0.00 0.00 0.00 3.67
5509 6534 1.102809 TGCTTGGCTGTGTCTTGGTG 61.103 55.000 0.00 0.00 0.00 4.17
5510 6535 0.819259 GCTTGGCTGTGTCTTGGTGA 60.819 55.000 0.00 0.00 0.00 4.02
5538 6563 7.159322 TGTTTGACTAAGTTTTGCACCTTTA 57.841 32.000 0.00 0.00 0.00 1.85
5661 6686 8.302438 AGGCAGAATATCTTGTTTCTTTCTTTG 58.698 33.333 0.00 0.00 29.85 2.77
5795 6820 4.851639 AGACTGATTAATCTGGCCAACT 57.148 40.909 21.04 11.32 34.63 3.16
5810 6835 3.487372 GCCAACTGGTTTTCTTAGGTCT 58.513 45.455 0.00 0.00 37.57 3.85
5856 6882 2.286563 CACTAACACATGCACGAACACA 59.713 45.455 0.00 0.00 0.00 3.72
6053 7079 2.852075 TGCCCTTTGGTCCCTCGT 60.852 61.111 0.00 0.00 0.00 4.18
6054 7080 1.536907 TGCCCTTTGGTCCCTCGTA 60.537 57.895 0.00 0.00 0.00 3.43
6062 7088 3.741476 GTCCCTCGTACGTGCCGT 61.741 66.667 16.05 5.58 44.35 5.68
6213 7239 0.456221 CGTTGTACTCGGGCTCATCT 59.544 55.000 0.00 0.00 0.00 2.90
6324 7350 1.339151 GGATGGAGACGCTGAAAAGGT 60.339 52.381 0.00 0.00 0.00 3.50
6357 7383 1.503994 CACAACACCACAACACGCA 59.496 52.632 0.00 0.00 0.00 5.24
6589 7615 4.148825 GCATCCGGTGGCGACTCT 62.149 66.667 0.00 0.00 0.00 3.24
6711 7737 2.839486 CACCTCTGAGTGGCTTTACA 57.161 50.000 3.66 0.00 33.95 2.41
6761 7787 1.078497 CCTCCACAACGCAGGCATA 60.078 57.895 0.00 0.00 0.00 3.14
6764 7790 0.036164 TCCACAACGCAGGCATAACT 59.964 50.000 0.00 0.00 0.00 2.24
6806 7832 1.271001 CCAGCCTCCATTGCATCGATA 60.271 52.381 0.00 0.00 0.00 2.92
6877 7903 1.386533 GCAACATCCTGGTGATCTGG 58.613 55.000 0.00 0.00 37.20 3.86
6888 7914 1.555075 GGTGATCTGGCCTGAGTGTTA 59.445 52.381 18.00 0.00 0.00 2.41
7443 8470 6.136541 TCAAAGAAGAAGAACAAGAAAGGC 57.863 37.500 0.00 0.00 0.00 4.35
7748 8775 1.301244 CACCTGCTCGTGCTGTTCT 60.301 57.895 11.19 0.00 40.48 3.01
7815 8842 1.191535 CCTCACCCAACCTATCACGA 58.808 55.000 0.00 0.00 0.00 4.35
7955 8983 0.036732 TTGAGCAGGAGAAACGGCAT 59.963 50.000 0.00 0.00 0.00 4.40
7959 8987 0.955428 GCAGGAGAAACGGCATCACA 60.955 55.000 0.00 0.00 0.00 3.58
8197 9225 1.758122 TCTAGGATGAGCTGCCGCA 60.758 57.895 2.05 0.00 39.10 5.69
8238 9266 6.531948 CGGAAGAGTTAGTCATCTTGTTTAGG 59.468 42.308 0.00 0.00 35.93 2.69
8239 9267 6.314152 GGAAGAGTTAGTCATCTTGTTTAGGC 59.686 42.308 0.00 0.00 35.93 3.93
8240 9268 6.613153 AGAGTTAGTCATCTTGTTTAGGCT 57.387 37.500 0.00 0.00 0.00 4.58
8241 9269 6.635755 AGAGTTAGTCATCTTGTTTAGGCTC 58.364 40.000 0.00 0.00 0.00 4.70
8242 9270 6.211584 AGAGTTAGTCATCTTGTTTAGGCTCA 59.788 38.462 0.00 0.00 0.00 4.26
8243 9271 6.402222 AGTTAGTCATCTTGTTTAGGCTCAG 58.598 40.000 0.00 0.00 0.00 3.35
8603 9656 4.322349 CCTTCTACTCCCTCTGTTCACAAG 60.322 50.000 0.00 0.00 0.00 3.16
8608 9661 5.923733 ACTCCCTCTGTTCACAAGTATAG 57.076 43.478 0.00 0.00 0.00 1.31
8611 9664 6.071278 ACTCCCTCTGTTCACAAGTATAGAAC 60.071 42.308 0.00 0.00 41.42 3.01
8675 9728 8.947055 AATAAAATTTCATTACCATGTGCTCC 57.053 30.769 0.00 0.00 0.00 4.70
8680 9733 3.653164 TCATTACCATGTGCTCCCTCTA 58.347 45.455 0.00 0.00 0.00 2.43
8685 9738 1.427809 CATGTGCTCCCTCTATCCCA 58.572 55.000 0.00 0.00 0.00 4.37
8697 9750 7.787424 GCTCCCTCTATCCCATAATATAAGAGT 59.213 40.741 0.00 0.00 0.00 3.24
8717 9770 4.607239 AGTGTTCTAGAACGGAGGGAATA 58.393 43.478 26.35 6.75 43.94 1.75
8718 9771 4.645588 AGTGTTCTAGAACGGAGGGAATAG 59.354 45.833 26.35 0.00 43.94 1.73
8719 9772 4.401837 GTGTTCTAGAACGGAGGGAATAGT 59.598 45.833 26.35 0.00 43.94 2.12
8873 12826 5.179452 AGGACTTTGTTATACACTGGCAT 57.821 39.130 0.00 0.00 0.00 4.40
8888 12841 1.020861 GGCATCGTGCTGTCATGACA 61.021 55.000 26.33 26.33 44.28 3.58
8903 12856 6.916440 TGTCATGACAGAATCAAAATCTTGG 58.084 36.000 24.56 0.00 41.93 3.61
8915 12868 1.175983 AATCTTGGGCCGCGTCAAAA 61.176 50.000 4.92 0.00 0.00 2.44
8948 12901 4.900635 ATCTTGCGGATTGTGGATTTAC 57.099 40.909 0.00 0.00 0.00 2.01
8953 12906 1.668751 CGGATTGTGGATTTACACGGG 59.331 52.381 0.00 0.00 44.21 5.28
9007 12962 4.654262 AGTAAAGACCAGAGAAACTGTGGA 59.346 41.667 19.18 0.00 46.28 4.02
9023 12978 6.641169 ACTGTGGAAAAGAGAAAAGAATCC 57.359 37.500 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.860022 AGAGCTACTTTTTGGCCATATGT 58.140 39.130 6.09 9.11 0.00 2.29
56 57 6.058183 CACTAGAGCTACTTTTTGGCCATAT 58.942 40.000 6.09 0.00 0.00 1.78
57 58 5.045869 ACACTAGAGCTACTTTTTGGCCATA 60.046 40.000 6.09 0.00 0.00 2.74
112 113 2.110011 AGGTGACCAGGTGGCTATTTTT 59.890 45.455 3.63 0.00 39.32 1.94
118 119 1.152118 TACAGGTGACCAGGTGGCT 60.152 57.895 3.63 0.00 39.32 4.75
562 565 7.095183 TCCAAATGGGATGCTAGATAAAGAT 57.905 36.000 0.00 0.00 42.15 2.40
1010 1015 2.041976 GCGCCTGGCAGAGATACTA 58.958 57.895 20.29 0.00 42.87 1.82
1031 1036 2.545596 CGTGTGCCAGCTTGCTTCA 61.546 57.895 11.53 7.62 0.00 3.02
1047 1052 1.066858 CATCCAGTACAAGGTCTGCGT 60.067 52.381 0.00 0.00 0.00 5.24
2314 2321 4.202441 CCATCAGGTAGAAAGGAATGGTG 58.798 47.826 0.00 0.00 0.00 4.17
2856 2863 7.446625 AGCATGAGAAATGAGACTTTTAACACT 59.553 33.333 0.00 0.00 0.00 3.55
3086 3093 2.078849 TGTTGCTGGAGACACATACG 57.921 50.000 0.00 0.00 35.60 3.06
3108 3115 9.906660 CCATAAGCACACTGTAAATTTTAGAAA 57.093 29.630 0.00 0.00 0.00 2.52
3402 3409 4.273235 TGATATTTTGCTGCAGATACACCG 59.727 41.667 20.43 0.00 0.00 4.94
3523 3530 1.331214 CCCAAGTGAACACCTGCAAT 58.669 50.000 1.11 0.00 0.00 3.56
4873 4880 1.869767 AGCTCTGCAAGTTCACTTTCG 59.130 47.619 0.00 0.00 33.11 3.46
4979 4986 0.599558 GATTGTGCTGCCTGCTTGAA 59.400 50.000 0.00 0.00 43.37 2.69
5012 5019 2.941720 GCTCCTTGTCCTCATGCTTTAG 59.058 50.000 0.00 0.00 0.00 1.85
5442 5451 2.613691 GTCACGGATAAACACGACCAT 58.386 47.619 0.00 0.00 0.00 3.55
5498 5507 4.075682 TCAAACAAACTCACCAAGACACA 58.924 39.130 0.00 0.00 0.00 3.72
5508 6533 6.584563 GTGCAAAACTTAGTCAAACAAACTCA 59.415 34.615 0.00 0.00 0.00 3.41
5509 6534 6.034577 GGTGCAAAACTTAGTCAAACAAACTC 59.965 38.462 0.00 0.00 0.00 3.01
5510 6535 5.867174 GGTGCAAAACTTAGTCAAACAAACT 59.133 36.000 0.00 0.00 0.00 2.66
5703 6728 7.567250 TCTGTTAGATGGGGTATAATCTGTCAA 59.433 37.037 0.00 0.00 34.91 3.18
5795 6820 4.862371 ACAAACCAGACCTAAGAAAACCA 58.138 39.130 0.00 0.00 0.00 3.67
5856 6882 1.542187 GGTACAGCGTGGAGGACCTT 61.542 60.000 0.00 0.00 37.04 3.50
5891 6917 1.880027 AGCCAAACCGACAGATGTTTC 59.120 47.619 0.00 0.00 32.60 2.78
6251 7277 2.489073 CCTTTGCAGGTAAACCTCCAGT 60.489 50.000 0.00 0.00 46.65 4.00
6324 7350 1.640593 TTGTGGCTGGACAGGAACCA 61.641 55.000 1.01 0.00 35.96 3.67
6357 7383 0.034380 TAGTAGCCTCGCCTCACTGT 60.034 55.000 0.00 0.00 0.00 3.55
6548 7574 1.688735 CACACTTCTCACCACCAGAGA 59.311 52.381 0.00 0.00 40.20 3.10
6589 7615 2.257371 GCAGTGGACTACGACGCA 59.743 61.111 0.00 0.00 0.00 5.24
6698 7724 1.045407 ACCGTCTGTAAAGCCACTCA 58.955 50.000 0.00 0.00 0.00 3.41
6725 7751 1.666011 GACGGAGCCACAGTCAAGA 59.334 57.895 6.84 0.00 41.88 3.02
6764 7790 2.451191 TGGAGACAAGGCACAGCCA 61.451 57.895 11.06 0.00 44.29 4.75
7193 8220 9.866655 AGAAATGCCTACATAAATAGGATCAAA 57.133 29.630 2.94 0.00 44.12 2.69
7225 8252 9.260002 ACAAAACGATGATTAAAGCAAAGAAAT 57.740 25.926 0.00 0.00 0.00 2.17
7443 8470 3.486841 CACTCAAAAACAATGACAAGCCG 59.513 43.478 0.00 0.00 0.00 5.52
7748 8775 2.168521 CTCTTATCCCCTTCGTGAGCAA 59.831 50.000 0.00 0.00 0.00 3.91
7815 8842 2.834549 CTGTATGTCCCTGAGTGAAGGT 59.165 50.000 0.00 0.00 35.34 3.50
7878 8905 9.710979 TTGTTATATTGCTGTAAGAAAATACGC 57.289 29.630 0.00 0.00 33.13 4.42
7955 8983 1.069090 GTGGGAGACAACGCTGTGA 59.931 57.895 0.00 0.00 35.30 3.58
7959 8987 1.367840 GACTGTGGGAGACAACGCT 59.632 57.895 0.00 0.00 32.80 5.07
8147 9175 1.634960 TGATCCTCACGGTGGTGTAA 58.365 50.000 8.50 0.00 44.68 2.41
8197 9225 3.801997 CGGGATTGAGGCCAGGCT 61.802 66.667 12.43 1.67 0.00 4.58
8238 9266 3.791586 GGGAGGGTGAGCCTGAGC 61.792 72.222 8.45 0.00 40.32 4.26
8239 9267 3.465403 CGGGAGGGTGAGCCTGAG 61.465 72.222 8.45 0.00 32.05 3.35
8240 9268 3.846405 AACGGGAGGGTGAGCCTGA 62.846 63.158 8.45 0.00 34.57 3.86
8241 9269 3.322466 AACGGGAGGGTGAGCCTG 61.322 66.667 8.45 0.00 36.60 4.85
8242 9270 3.322466 CAACGGGAGGGTGAGCCT 61.322 66.667 1.18 1.18 34.45 4.58
8608 9661 7.727017 ACTTGTATGATAAGTCGAAAACGTTC 58.273 34.615 0.00 0.00 33.28 3.95
8671 9724 7.787424 ACTCTTATATTATGGGATAGAGGGAGC 59.213 40.741 0.00 0.00 0.00 4.70
8673 9726 8.633724 ACACTCTTATATTATGGGATAGAGGGA 58.366 37.037 0.00 0.00 0.00 4.20
8697 9750 4.607239 ACTATTCCCTCCGTTCTAGAACA 58.393 43.478 29.95 14.42 41.20 3.18
8704 9757 7.603024 CCATTTCTTATACTATTCCCTCCGTTC 59.397 40.741 0.00 0.00 0.00 3.95
8707 9760 7.005709 ACCATTTCTTATACTATTCCCTCCG 57.994 40.000 0.00 0.00 0.00 4.63
8756 11399 8.429237 AAAATGGAAAACTATGTATGGGTTGA 57.571 30.769 0.00 0.00 0.00 3.18
8888 12841 1.478105 GCGGCCCAAGATTTTGATTCT 59.522 47.619 0.00 0.00 36.36 2.40
8893 12846 1.154035 GACGCGGCCCAAGATTTTG 60.154 57.895 12.47 0.00 0.00 2.44
8917 12870 8.474025 TCCACAATCCGCAAGATATAAAAATTT 58.526 29.630 0.00 0.00 43.02 1.82
8918 12871 8.006298 TCCACAATCCGCAAGATATAAAAATT 57.994 30.769 0.00 0.00 43.02 1.82
8919 12872 7.581213 TCCACAATCCGCAAGATATAAAAAT 57.419 32.000 0.00 0.00 43.02 1.82
8923 12876 7.717436 TGTAAATCCACAATCCGCAAGATATAA 59.283 33.333 0.00 0.00 43.02 0.98
8953 12906 8.637281 TGAACGAAGAATTTAAAGGGTTTTTC 57.363 30.769 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.