Multiple sequence alignment - TraesCS3D01G235400

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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 TraesCS3D01G235400 chr3D 100.000 3993 0 0 1 3993 325709748 325705756 0.000000e+00 7374
1 TraesCS3D01G235400 chr3D 90.294 340 29 3 1 339 141155090 141155426 3.660000e-120 442
2 TraesCS3D01G235400 chr3D 89.706 340 29 4 1 339 141149635 141149969 2.850000e-116 429
3 TraesCS3D01G235400 chr3D 84.615 234 34 2 504 736 470732433 470732201 8.630000e-57 231
4 TraesCS3D01G235400 chr3A 94.247 3320 149 23 73 3368 439457517 439460818 0.000000e+00 5035
5 TraesCS3D01G235400 chr3A 88.925 623 61 6 3369 3989 439464370 439464986 0.000000e+00 761
6 TraesCS3D01G235400 chr3B 95.273 2158 83 11 121 2275 423180573 423178432 0.000000e+00 3402
7 TraesCS3D01G235400 chr3B 92.334 1722 92 24 2272 3989 423178399 423176714 0.000000e+00 2412
8 TraesCS3D01G235400 chr5D 91.176 340 25 4 1 339 377566210 377566545 1.310000e-124 457
9 TraesCS3D01G235400 chr5D 89.736 341 29 5 1 339 319776417 319776753 7.930000e-117 431
10 TraesCS3D01G235400 chr5D 80.426 235 41 5 504 735 546034567 546034335 1.480000e-39 174
11 TraesCS3D01G235400 chr5D 77.500 240 47 7 500 735 431695452 431695216 1.940000e-28 137
12 TraesCS3D01G235400 chr6D 89.706 340 29 4 1 339 186861461 186861795 2.850000e-116 429
13 TraesCS3D01G235400 chr6D 87.921 356 36 6 1 355 243071978 243072327 2.870000e-111 412
14 TraesCS3D01G235400 chr4D 89.565 345 25 4 1 339 294000346 294000685 1.030000e-115 427
15 TraesCS3D01G235400 chr5A 89.412 340 31 4 1 339 667962354 667962689 1.330000e-114 424
16 TraesCS3D01G235400 chr5A 80.723 249 40 8 500 745 9463046 9463289 1.890000e-43 187
17 TraesCS3D01G235400 chr6B 81.818 242 40 4 507 745 534911418 534911178 2.430000e-47 200
18 TraesCS3D01G235400 chr2A 81.780 236 39 4 501 734 10505483 10505250 1.130000e-45 195
19 TraesCS3D01G235400 chr2B 80.851 235 43 1 504 736 369500049 369499815 2.450000e-42 183
20 TraesCS3D01G235400 chr2D 80.169 237 43 3 501 735 503574882 503575116 1.480000e-39 174
21 TraesCS3D01G235400 chr5B 77.928 222 45 4 500 719 522354263 522354044 6.960000e-28 135


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 TraesCS3D01G235400 chr3D 325705756 325709748 3992 True 7374 7374 100.0000 1 3993 1 chr3D.!!$R1 3992
1 TraesCS3D01G235400 chr3A 439457517 439464986 7469 False 2898 5035 91.5860 73 3989 2 chr3A.!!$F1 3916
2 TraesCS3D01G235400 chr3B 423176714 423180573 3859 True 2907 3402 93.8035 121 3989 2 chr3B.!!$R1 3868

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
357 358 0.764890 AGACCCACTTAACAGCTGCA 59.235 50.0 15.27 0.00 0.0 4.41 F
684 685 0.984230 AGGATTTGTGGCCTCTCGAA 59.016 50.0 3.32 1.17 0.0 3.71 F
2191 2195 0.854218 TAGCAGAGTAGGAGAGGGGG 59.146 60.0 0.00 0.00 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2193 0.608035 TCCAAACAGATTCCGTGCCC 60.608 55.0 0.00 0.0 0.00 5.36 R
2253 2257 0.761702 ACACCCTACCCGTGAACACT 60.762 55.0 3.51 0.0 35.17 3.55 R
3306 3362 0.109226 CTCGTCGACCCAAAGAGACC 60.109 60.0 10.58 0.0 0.00 3.85 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
53 54 3.741476 GCGCACCCTTGAGGCTTG 61.741 66.667 0.30 0.00 40.58 4.01
54 55 2.281761 CGCACCCTTGAGGCTTGT 60.282 61.111 0.00 0.00 40.58 3.16
55 56 2.620112 CGCACCCTTGAGGCTTGTG 61.620 63.158 0.00 0.00 40.58 3.33
56 57 2.270986 GCACCCTTGAGGCTTGTGG 61.271 63.158 0.00 0.00 40.58 4.17
57 58 2.116125 ACCCTTGAGGCTTGTGGC 59.884 61.111 0.00 0.00 40.58 5.01
66 67 2.045536 GCTTGTGGCCTCCTCTGG 60.046 66.667 3.32 0.00 34.27 3.86
67 68 2.596851 GCTTGTGGCCTCCTCTGGA 61.597 63.158 3.32 0.00 34.27 3.86
68 69 1.298014 CTTGTGGCCTCCTCTGGAC 59.702 63.158 3.32 0.00 35.14 4.02
69 70 1.152030 TTGTGGCCTCCTCTGGACT 60.152 57.895 3.32 0.00 35.73 3.85
70 71 1.194781 TTGTGGCCTCCTCTGGACTC 61.195 60.000 3.32 0.00 35.73 3.36
71 72 1.305718 GTGGCCTCCTCTGGACTCT 60.306 63.158 3.32 0.00 35.73 3.24
75 76 0.823460 GCCTCCTCTGGACTCTTCTG 59.177 60.000 0.00 0.00 0.00 3.02
103 104 0.963962 TCCAAGTCACGTAGGTGTCC 59.036 55.000 14.78 7.49 44.68 4.02
105 106 1.067776 CCAAGTCACGTAGGTGTCCTC 60.068 57.143 14.78 5.41 44.68 3.71
106 107 1.887198 CAAGTCACGTAGGTGTCCTCT 59.113 52.381 14.78 7.28 44.68 3.69
115 116 0.838122 AGGTGTCCTCTGGTCCAAGG 60.838 60.000 11.80 11.80 0.00 3.61
176 177 8.850452 CGTTTGATAATCCTTTTCTGTAAAAGC 58.150 33.333 5.31 0.00 46.84 3.51
187 188 7.065683 CCTTTTCTGTAAAAGCCAAAAACATGT 59.934 33.333 0.00 0.00 46.84 3.21
188 189 9.092876 CTTTTCTGTAAAAGCCAAAAACATGTA 57.907 29.630 0.00 0.00 43.68 2.29
189 190 8.641499 TTTCTGTAAAAGCCAAAAACATGTAG 57.359 30.769 0.00 0.00 0.00 2.74
234 235 6.925934 TGGGCTCTAGGTTAATAGGTTAGTA 58.074 40.000 0.00 0.00 0.00 1.82
235 236 7.541967 TGGGCTCTAGGTTAATAGGTTAGTAT 58.458 38.462 0.00 0.00 0.00 2.12
236 237 8.681584 TGGGCTCTAGGTTAATAGGTTAGTATA 58.318 37.037 0.00 0.00 0.00 1.47
354 355 3.119101 CGTATCAGACCCACTTAACAGCT 60.119 47.826 0.00 0.00 0.00 4.24
357 358 0.764890 AGACCCACTTAACAGCTGCA 59.235 50.000 15.27 0.00 0.00 4.41
372 373 1.202651 GCTGCACGGGGTATATCAACT 60.203 52.381 0.00 0.00 0.00 3.16
375 376 1.068127 GCACGGGGTATATCAACTCGT 59.932 52.381 0.00 0.00 32.60 4.18
376 377 2.739292 CACGGGGTATATCAACTCGTG 58.261 52.381 10.82 10.82 38.98 4.35
383 384 5.106237 GGGGTATATCAACTCGTGCTACTAG 60.106 48.000 0.00 0.00 0.00 2.57
390 391 4.153655 TCAACTCGTGCTACTAGTACACTG 59.846 45.833 22.19 18.47 29.68 3.66
480 481 4.382254 CGCCAGTGGTATTTGTCTACCTAA 60.382 45.833 11.74 0.00 41.54 2.69
544 545 6.133356 AGAGATTAGGGAGTTAAGAGGAGTG 58.867 44.000 0.00 0.00 0.00 3.51
558 559 4.237018 AGAGGAGTGGGTAGTTTTTACCA 58.763 43.478 5.78 0.00 39.31 3.25
559 560 4.850386 AGAGGAGTGGGTAGTTTTTACCAT 59.150 41.667 5.78 0.00 39.31 3.55
621 622 1.066605 GTCAACTATAGCCGCTCCGAA 59.933 52.381 0.00 0.00 0.00 4.30
648 649 5.985911 ACTACTGTTGTGTGGTTAAACTCT 58.014 37.500 0.00 0.00 0.00 3.24
684 685 0.984230 AGGATTTGTGGCCTCTCGAA 59.016 50.000 3.32 1.17 0.00 3.71
880 882 2.959357 GCCACTCTCTGCACGTTGC 61.959 63.158 3.44 3.44 45.29 4.17
1047 1049 1.188219 TGCTGGTCACCACTCTCTCC 61.188 60.000 0.00 0.00 0.00 3.71
1260 1262 2.687935 GTTCTTCAACAAGGTTCAGGCA 59.312 45.455 0.00 0.00 32.14 4.75
1603 1605 1.450025 GTCCAAGAATTCCACGTCCC 58.550 55.000 0.65 0.00 0.00 4.46
1754 1756 1.821753 TCTGCACTCTCCTAGAACTGC 59.178 52.381 0.00 0.00 31.77 4.40
1835 1838 1.409064 TGATCTGCTGTAGGGCGTAAG 59.591 52.381 0.00 0.00 43.44 2.34
1871 1874 5.632034 ACAGTTCCCCATAATTCTCCTAC 57.368 43.478 0.00 0.00 0.00 3.18
1908 1912 2.924105 GCTGGCAGTCCCAACAAGC 61.924 63.158 17.16 0.00 44.81 4.01
2103 2107 4.143115 CGTTCTGCTGAATTCACGTACAAT 60.143 41.667 9.40 0.00 34.40 2.71
2114 2118 2.036217 TCACGTACAATCCGACAACCTT 59.964 45.455 0.00 0.00 0.00 3.50
2189 2193 2.441750 AGAGTAGCAGAGTAGGAGAGGG 59.558 54.545 0.00 0.00 0.00 4.30
2190 2194 1.497286 AGTAGCAGAGTAGGAGAGGGG 59.503 57.143 0.00 0.00 0.00 4.79
2191 2195 0.854218 TAGCAGAGTAGGAGAGGGGG 59.146 60.000 0.00 0.00 0.00 5.40
2228 2232 5.867330 TGGATTTTGGAACATCTGCATTTT 58.133 33.333 0.00 0.00 39.30 1.82
2229 2233 5.933463 TGGATTTTGGAACATCTGCATTTTC 59.067 36.000 0.00 0.00 39.30 2.29
2230 2234 5.933463 GGATTTTGGAACATCTGCATTTTCA 59.067 36.000 0.00 0.00 39.30 2.69
2231 2235 6.596497 GGATTTTGGAACATCTGCATTTTCAT 59.404 34.615 0.00 0.00 39.30 2.57
2232 2236 7.765360 GGATTTTGGAACATCTGCATTTTCATA 59.235 33.333 0.00 0.00 39.30 2.15
2233 2237 7.887996 TTTTGGAACATCTGCATTTTCATAC 57.112 32.000 0.00 0.00 39.30 2.39
2298 2337 7.175073 CTTTATGAGCATCTGTGACTATGTG 57.825 40.000 0.00 0.00 34.92 3.21
2299 2338 2.897436 TGAGCATCTGTGACTATGTGC 58.103 47.619 0.00 0.00 34.92 4.57
2339 2391 8.800370 TTGCATGTCATATAGGAGTGTTAAAA 57.200 30.769 0.00 0.00 0.00 1.52
2340 2392 8.437360 TGCATGTCATATAGGAGTGTTAAAAG 57.563 34.615 0.00 0.00 0.00 2.27
2719 2771 2.964925 GTGGACACGCGCAAGTCA 60.965 61.111 24.77 12.25 36.50 3.41
2995 3047 2.423577 GGTAACCTTGCGTTGTGATCT 58.576 47.619 0.00 0.00 35.79 2.75
2999 3051 3.626028 ACCTTGCGTTGTGATCTTTTC 57.374 42.857 0.00 0.00 0.00 2.29
3004 3056 5.173854 CCTTGCGTTGTGATCTTTTCTTTTC 59.826 40.000 0.00 0.00 0.00 2.29
3005 3057 5.499139 TGCGTTGTGATCTTTTCTTTTCT 57.501 34.783 0.00 0.00 0.00 2.52
3006 3058 5.890334 TGCGTTGTGATCTTTTCTTTTCTT 58.110 33.333 0.00 0.00 0.00 2.52
3007 3059 6.329496 TGCGTTGTGATCTTTTCTTTTCTTT 58.671 32.000 0.00 0.00 0.00 2.52
3042 3098 5.029654 TCGTTGAAAGGCTTTTTACGAAAC 58.970 37.500 30.65 19.64 38.99 2.78
3077 3133 6.018669 CCTCTTATCGAAAATGTAAGCTGGTC 60.019 42.308 0.00 0.00 0.00 4.02
3291 3347 2.034685 GGACAAAGTTGAACAAGCTCCC 59.965 50.000 0.00 0.00 0.00 4.30
3292 3348 2.687935 GACAAAGTTGAACAAGCTCCCA 59.312 45.455 0.00 0.00 0.00 4.37
3366 3422 0.953471 TTGTTGACGGCAAGATCGGG 60.953 55.000 2.40 0.00 34.01 5.14
3384 6990 3.066342 TCGGGCGTTAGACTCTTTAGATG 59.934 47.826 0.00 0.00 0.00 2.90
3400 7006 6.706270 TCTTTAGATGGACTCAAGTGTTCAAC 59.294 38.462 0.00 0.00 33.19 3.18
3403 7009 3.469008 TGGACTCAAGTGTTCAACGAT 57.531 42.857 0.00 0.00 0.00 3.73
3435 7041 2.358957 CCATTGGCGTTGATCTTCAGA 58.641 47.619 0.00 0.00 0.00 3.27
3444 7050 1.649321 TGATCTTCAGAGGCACCTGT 58.351 50.000 0.00 0.00 35.71 4.00
3504 7110 2.009774 CTCCTTATGGAAGTGGCAACG 58.990 52.381 0.00 0.00 42.66 4.10
3511 7117 3.236618 GAAGTGGCAACGACGGTGC 62.237 63.158 29.32 29.32 42.51 5.01
3512 7118 4.539083 AGTGGCAACGACGGTGCA 62.539 61.111 36.08 20.94 42.51 4.57
3530 7136 1.730064 GCATCGACGCCTAGTTTTGAA 59.270 47.619 0.00 0.00 0.00 2.69
3540 7146 5.186409 ACGCCTAGTTTTGAAGATGGTAGTA 59.814 40.000 0.00 0.00 0.00 1.82
3561 7167 1.001633 GTTGTACGGTGGTCCAGTGAT 59.998 52.381 0.00 0.00 0.00 3.06
3565 7171 0.984230 ACGGTGGTCCAGTGATCATT 59.016 50.000 0.00 0.00 33.26 2.57
3684 7290 5.529791 GGAAAGGAAACCAGTTTTCTTAGC 58.470 41.667 15.48 11.19 45.09 3.09
3686 7292 5.774498 AAGGAAACCAGTTTTCTTAGCAG 57.226 39.130 13.91 0.00 44.29 4.24
3728 7335 6.605471 AGAATAAAACCAGCTTTTTAGGGG 57.395 37.500 8.79 0.00 35.05 4.79
3741 7348 5.047943 GCTTTTTAGGGGAGAGAAGAAAACC 60.048 44.000 0.00 0.00 0.00 3.27
3766 7373 6.146347 CAGCTAAACTAGAAGAAAACGAAGCT 59.854 38.462 0.00 0.00 35.92 3.74
3916 7524 1.675310 CTTGCGATGAGGGGTGCAA 60.675 57.895 0.00 0.00 44.34 4.08
3918 7526 3.499737 GCGATGAGGGGTGCAACG 61.500 66.667 0.00 0.00 38.12 4.10
3932 7540 1.873165 CAACGCCCGTGCTTTGTAT 59.127 52.632 0.91 0.00 40.70 2.29
3968 7576 2.729491 GCCGCACGAAACAAAGGC 60.729 61.111 0.00 0.00 37.61 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.741476 CAAGCCTCAAGGGTGCGC 61.741 66.667 0.00 0.00 46.73 6.09
37 38 2.281761 ACAAGCCTCAAGGGTGCG 60.282 61.111 0.67 0.00 46.73 5.34
38 39 2.270986 CCACAAGCCTCAAGGGTGC 61.271 63.158 0.67 0.00 46.73 5.01
39 40 2.270986 GCCACAAGCCTCAAGGGTG 61.271 63.158 0.67 0.00 46.73 4.61
49 50 2.045536 CCAGAGGAGGCCACAAGC 60.046 66.667 5.01 0.00 42.60 4.01
50 51 1.197430 AGTCCAGAGGAGGCCACAAG 61.197 60.000 5.01 0.00 29.39 3.16
51 52 1.152030 AGTCCAGAGGAGGCCACAA 60.152 57.895 5.01 0.00 29.39 3.33
52 53 1.610673 GAGTCCAGAGGAGGCCACA 60.611 63.158 5.01 0.00 29.39 4.17
53 54 0.907230 AAGAGTCCAGAGGAGGCCAC 60.907 60.000 5.01 0.00 29.39 5.01
54 55 0.616111 GAAGAGTCCAGAGGAGGCCA 60.616 60.000 5.01 0.00 29.39 5.36
55 56 0.325203 AGAAGAGTCCAGAGGAGGCC 60.325 60.000 0.00 0.00 29.39 5.19
56 57 0.823460 CAGAAGAGTCCAGAGGAGGC 59.177 60.000 0.00 0.00 29.39 4.70
57 58 2.099405 GTCAGAAGAGTCCAGAGGAGG 58.901 57.143 0.00 0.00 29.39 4.30
58 59 2.099405 GGTCAGAAGAGTCCAGAGGAG 58.901 57.143 0.00 0.00 29.39 3.69
59 60 1.272760 GGGTCAGAAGAGTCCAGAGGA 60.273 57.143 0.00 0.00 0.00 3.71
60 61 1.190643 GGGTCAGAAGAGTCCAGAGG 58.809 60.000 0.00 0.00 0.00 3.69
61 62 2.099405 GAGGGTCAGAAGAGTCCAGAG 58.901 57.143 0.00 0.00 0.00 3.35
62 63 1.713647 AGAGGGTCAGAAGAGTCCAGA 59.286 52.381 0.00 0.00 0.00 3.86
63 64 2.099405 GAGAGGGTCAGAAGAGTCCAG 58.901 57.143 0.00 0.00 0.00 3.86
64 65 1.713647 AGAGAGGGTCAGAAGAGTCCA 59.286 52.381 0.00 0.00 0.00 4.02
65 66 2.375146 GAGAGAGGGTCAGAAGAGTCC 58.625 57.143 0.00 0.00 0.00 3.85
66 67 2.291282 TGGAGAGAGGGTCAGAAGAGTC 60.291 54.545 0.00 0.00 0.00 3.36
67 68 1.713647 TGGAGAGAGGGTCAGAAGAGT 59.286 52.381 0.00 0.00 0.00 3.24
68 69 2.523325 TGGAGAGAGGGTCAGAAGAG 57.477 55.000 0.00 0.00 0.00 2.85
69 70 2.110899 ACTTGGAGAGAGGGTCAGAAGA 59.889 50.000 0.00 0.00 0.00 2.87
70 71 2.495669 GACTTGGAGAGAGGGTCAGAAG 59.504 54.545 0.00 0.00 0.00 2.85
71 72 2.158310 TGACTTGGAGAGAGGGTCAGAA 60.158 50.000 0.00 0.00 33.74 3.02
75 76 0.528470 CGTGACTTGGAGAGAGGGTC 59.472 60.000 0.00 0.00 0.00 4.46
103 104 4.592942 TGATGATTTTCCTTGGACCAGAG 58.407 43.478 0.00 0.00 0.00 3.35
105 106 7.123247 ACTTTATGATGATTTTCCTTGGACCAG 59.877 37.037 0.00 0.00 0.00 4.00
106 107 6.953520 ACTTTATGATGATTTTCCTTGGACCA 59.046 34.615 0.00 0.00 0.00 4.02
197 198 1.071385 AGAGCCCAGTGTCAGTTTCTG 59.929 52.381 0.00 0.00 0.00 3.02
354 355 1.067974 CGAGTTGATATACCCCGTGCA 59.932 52.381 0.00 0.00 0.00 4.57
357 358 1.068127 GCACGAGTTGATATACCCCGT 59.932 52.381 0.00 0.00 0.00 5.28
372 373 3.935203 GGTACAGTGTACTAGTAGCACGA 59.065 47.826 27.94 12.53 38.10 4.35
375 376 4.914983 ACAGGTACAGTGTACTAGTAGCA 58.085 43.478 27.94 2.13 38.36 3.49
376 377 5.007528 GCTACAGGTACAGTGTACTAGTAGC 59.992 48.000 38.21 38.21 40.08 3.58
383 384 2.415090 CCACGCTACAGGTACAGTGTAC 60.415 54.545 22.81 22.81 33.87 2.90
390 391 0.390735 CAACCCCACGCTACAGGTAC 60.391 60.000 0.00 0.00 30.63 3.34
480 481 2.963101 GCCACTACAAGGAAAAACCCTT 59.037 45.455 0.00 0.00 46.91 3.95
490 491 3.558931 TGACCATATGCCACTACAAGG 57.441 47.619 0.00 0.00 0.00 3.61
493 494 6.247229 ACTAAATGACCATATGCCACTACA 57.753 37.500 0.00 0.00 0.00 2.74
621 622 6.882678 AGTTTAACCACACAACAGTAGTTCTT 59.117 34.615 0.00 0.00 35.28 2.52
648 649 2.531771 TCCTCGATACAAGGTGGAACA 58.468 47.619 0.00 0.00 39.98 3.18
880 882 3.007920 AGCTCTCCCACAGGCCAG 61.008 66.667 5.01 0.00 0.00 4.85
1425 1427 3.728373 ACAATGTCCCGCCTCCCC 61.728 66.667 0.00 0.00 0.00 4.81
1603 1605 1.487231 CGCTTCGTCTGTTGAACCG 59.513 57.895 0.00 0.00 0.00 4.44
1835 1838 1.467342 GAACTGTTTATGCCGGTGGAC 59.533 52.381 1.90 0.00 0.00 4.02
1908 1912 2.554775 CAGCAGCACAACAGCGAG 59.445 61.111 0.00 0.00 40.15 5.03
2103 2107 3.830744 TCAGAAAGAAAGGTTGTCGGA 57.169 42.857 0.00 0.00 0.00 4.55
2114 2118 5.132502 ACACCATGTGATGTTCAGAAAGAA 58.867 37.500 0.49 0.00 36.96 2.52
2189 2193 0.608035 TCCAAACAGATTCCGTGCCC 60.608 55.000 0.00 0.00 0.00 5.36
2190 2194 1.463674 ATCCAAACAGATTCCGTGCC 58.536 50.000 0.00 0.00 0.00 5.01
2191 2195 3.575965 AAATCCAAACAGATTCCGTGC 57.424 42.857 0.00 0.00 35.40 5.34
2253 2257 0.761702 ACACCCTACCCGTGAACACT 60.762 55.000 3.51 0.00 35.17 3.55
2288 2327 3.536158 TTTTCAAGCGCACATAGTCAC 57.464 42.857 11.47 0.00 0.00 3.67
2320 2372 8.483758 TCCTTCCTTTTAACACTCCTATATGAC 58.516 37.037 0.00 0.00 0.00 3.06
2339 2391 1.637553 AGCATGTGATGGTTCCTTCCT 59.362 47.619 0.00 0.00 37.84 3.36
2340 2392 2.019984 GAGCATGTGATGGTTCCTTCC 58.980 52.381 0.00 0.00 41.77 3.46
2719 2771 1.558233 CCTTCTCCTTGAGGTACGGT 58.442 55.000 0.00 0.00 36.34 4.83
2764 2816 2.509336 CCGTGCAAGTAGCCCTCG 60.509 66.667 0.00 0.00 44.83 4.63
3006 3058 5.768317 CCTTTCAACGATCTTAGGCAAAAA 58.232 37.500 0.00 0.00 0.00 1.94
3007 3059 4.320935 GCCTTTCAACGATCTTAGGCAAAA 60.321 41.667 14.51 0.00 45.73 2.44
3042 3098 8.993121 ACATTTTCGATAAGAGGCAGTATTATG 58.007 33.333 0.00 0.00 0.00 1.90
3077 3133 9.893305 AATATTTGACGGTAAAAAGTTCAGAAG 57.107 29.630 0.00 0.00 0.00 2.85
3171 3227 3.419264 TTCGGTGCAAACATATCATGC 57.581 42.857 0.00 0.00 40.45 4.06
3236 3292 1.294857 GAGGAGAATCGCAAGGCTTC 58.705 55.000 0.00 0.00 34.37 3.86
3292 3348 6.118170 CCAAAGAGACCACATGAATCTATGT 58.882 40.000 0.00 0.00 41.77 2.29
3306 3362 0.109226 CTCGTCGACCCAAAGAGACC 60.109 60.000 10.58 0.00 0.00 3.85
3349 3405 2.750888 GCCCGATCTTGCCGTCAAC 61.751 63.158 0.00 0.00 0.00 3.18
3357 3413 1.405821 AGAGTCTAACGCCCGATCTTG 59.594 52.381 0.00 0.00 0.00 3.02
3366 3422 5.163642 TGAGTCCATCTAAAGAGTCTAACGC 60.164 44.000 0.00 0.00 34.22 4.84
3370 6976 6.948886 ACACTTGAGTCCATCTAAAGAGTCTA 59.051 38.462 0.00 0.00 34.73 2.59
3384 6990 3.184581 GTCATCGTTGAACACTTGAGTCC 59.815 47.826 0.00 0.00 32.48 3.85
3400 7006 1.775039 AATGGCCGCAATCGTCATCG 61.775 55.000 0.00 0.00 38.55 3.84
3403 7009 2.405805 CCAATGGCCGCAATCGTCA 61.406 57.895 0.00 0.00 0.00 4.35
3418 7024 1.945819 GCCTCTGAAGATCAACGCCAA 60.946 52.381 0.00 0.00 0.00 4.52
3427 7033 3.378512 TCATACAGGTGCCTCTGAAGAT 58.621 45.455 9.91 0.00 38.11 2.40
3435 7041 5.416952 CAGAAAAATCTTCATACAGGTGCCT 59.583 40.000 0.00 0.00 0.00 4.75
3478 7084 1.211457 CACTTCCATAAGGAGCTGGCT 59.789 52.381 0.00 0.00 46.74 4.75
3504 7110 3.405592 TAGGCGTCGATGCACCGTC 62.406 63.158 29.46 12.81 36.28 4.79
3511 7117 3.250744 TCTTCAAAACTAGGCGTCGATG 58.749 45.455 0.00 0.00 0.00 3.84
3512 7118 3.587797 TCTTCAAAACTAGGCGTCGAT 57.412 42.857 0.00 0.00 0.00 3.59
3519 7125 8.095169 ACAACTACTACCATCTTCAAAACTAGG 58.905 37.037 0.00 0.00 0.00 3.02
3530 7136 3.698040 CCACCGTACAACTACTACCATCT 59.302 47.826 0.00 0.00 0.00 2.90
3540 7146 0.391597 CACTGGACCACCGTACAACT 59.608 55.000 0.00 0.00 39.42 3.16
3718 7325 6.068670 TGGTTTTCTTCTCTCCCCTAAAAAG 58.931 40.000 0.00 0.00 0.00 2.27
3723 7330 2.572104 GCTGGTTTTCTTCTCTCCCCTA 59.428 50.000 0.00 0.00 0.00 3.53
3728 7335 7.379750 TCTAGTTTAGCTGGTTTTCTTCTCTC 58.620 38.462 0.00 0.00 0.00 3.20
3741 7348 6.146347 AGCTTCGTTTTCTTCTAGTTTAGCTG 59.854 38.462 0.00 0.00 33.27 4.24
3918 7526 0.663153 GGATGATACAAAGCACGGGC 59.337 55.000 0.00 0.00 41.61 6.13
3927 7535 4.456535 CGGTACCATTTGGGATGATACAA 58.543 43.478 13.54 0.00 41.15 2.41
3932 7540 0.548989 CCCGGTACCATTTGGGATGA 59.451 55.000 15.71 0.00 44.88 2.92
3968 7576 0.384309 ATGAAGCGCATCAAGCATGG 59.616 50.000 20.21 0.00 46.13 3.66


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

AutoCloner maintained by Alex Coulton.