Multiple sequence alignment - TraesCS7D01G207900

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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 TraesCS7D01G207900 chr7D 100.000 3805 0 0 1 3805 165480227 165484031 0.000000e+00 7027
1 TraesCS7D01G207900 chr7D 89.655 261 27 0 3448 3708 165506880 165507140 2.190000e-87 333
2 TraesCS7D01G207900 chr7D 90.769 195 18 0 380 574 92137948 92137754 1.050000e-65 261
3 TraesCS7D01G207900 chr7D 86.735 196 19 6 365 554 604465332 604465138 1.070000e-50 211
4 TraesCS7D01G207900 chr7A 90.793 3302 174 54 572 3797 167161231 167164478 0.000000e+00 4294
5 TraesCS7D01G207900 chr7A 88.889 261 29 0 3448 3708 167171585 167171845 4.740000e-84 322
6 TraesCS7D01G207900 chr7A 87.755 98 7 3 2659 2756 167163246 167163338 4.020000e-20 110
7 TraesCS7D01G207900 chr7B 90.765 3270 169 60 576 3797 128761122 128764306 0.000000e+00 4242
8 TraesCS7D01G207900 chr7B 89.272 261 28 0 3448 3708 128769659 128769919 1.020000e-85 327
9 TraesCS7D01G207900 chr3D 87.789 606 45 17 2 579 20143095 20143699 0.000000e+00 682
10 TraesCS7D01G207900 chr3D 88.095 588 50 8 2 570 501792126 501791540 0.000000e+00 680
11 TraesCS7D01G207900 chr6D 87.000 600 49 17 2 573 47079156 47078558 0.000000e+00 649
12 TraesCS7D01G207900 chr6D 89.459 370 31 3 2 363 445651619 445651250 9.630000e-126 460
13 TraesCS7D01G207900 chrUn 86.690 571 41 16 2 570 95314224 95314761 5.440000e-168 601
14 TraesCS7D01G207900 chr3A 85.974 549 52 18 1 526 670553902 670554448 7.140000e-157 564
15 TraesCS7D01G207900 chr2D 91.105 371 25 3 1 363 375356536 375356166 2.640000e-136 496
16 TraesCS7D01G207900 chr1D 90.000 370 25 4 1 363 468133291 468133655 5.760000e-128 468
17 TraesCS7D01G207900 chr1D 81.538 195 30 6 3518 3709 481408002 481408193 5.090000e-34 156
18 TraesCS7D01G207900 chr1D 80.208 192 26 12 3489 3676 481397989 481398172 2.380000e-27 134
19 TraesCS7D01G207900 chr2A 90.395 354 24 7 211 564 715798077 715797734 1.250000e-124 457
20 TraesCS7D01G207900 chr6B 89.971 349 28 5 2 347 45982286 45982630 9.700000e-121 444
21 TraesCS7D01G207900 chr4A 87.958 191 21 2 380 570 191755908 191755720 1.380000e-54 224
22 TraesCS7D01G207900 chr1A 87.192 203 19 5 371 570 554908143 554908341 1.380000e-54 224
23 TraesCS7D01G207900 chr1A 80.531 226 33 11 3488 3708 577886655 577886874 3.040000e-36 163
24 TraesCS7D01G207900 chr5D 86.341 205 25 2 366 570 37120195 37120396 1.780000e-53 220
25 TraesCS7D01G207900 chr5A 86.634 202 20 6 372 570 306909426 306909229 2.300000e-52 217
26 TraesCS7D01G207900 chr6A 80.882 272 44 6 1996 2261 528924193 528923924 1.390000e-49 207
27 TraesCS7D01G207900 chr1B 78.855 227 37 11 3488 3709 669784185 669784405 3.960000e-30 143


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 TraesCS7D01G207900 chr7D 165480227 165484031 3804 False 7027 7027 100.000 1 3805 1 chr7D.!!$F1 3804
1 TraesCS7D01G207900 chr7A 167161231 167164478 3247 False 2202 4294 89.274 572 3797 2 chr7A.!!$F2 3225
2 TraesCS7D01G207900 chr7B 128761122 128764306 3184 False 4242 4242 90.765 576 3797 1 chr7B.!!$F1 3221
3 TraesCS7D01G207900 chr3D 20143095 20143699 604 False 682 682 87.789 2 579 1 chr3D.!!$F1 577
4 TraesCS7D01G207900 chr3D 501791540 501792126 586 True 680 680 88.095 2 570 1 chr3D.!!$R1 568
5 TraesCS7D01G207900 chr6D 47078558 47079156 598 True 649 649 87.000 2 573 1 chr6D.!!$R1 571
6 TraesCS7D01G207900 chrUn 95314224 95314761 537 False 601 601 86.690 2 570 1 chrUn.!!$F1 568
7 TraesCS7D01G207900 chr3A 670553902 670554448 546 False 564 564 85.974 1 526 1 chr3A.!!$F1 525

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
649 682 0.249398 ACCACGCTACCCAAGACATC 59.751 55.000 0.00 0.00 0.00 3.06 F
864 900 1.005805 ACTAGGAAATGCCATGGTGCA 59.994 47.619 14.67 6.33 46.94 4.57 F
1959 2036 0.172803 GGCCGAACGATGTCAGTAGT 59.827 55.000 0.00 0.00 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2009 0.172803 ACTACTGACATCGTTCGGCC 59.827 55.0 0.00 0.0 0.00 6.13 R
2297 2374 0.463654 GCGGCCATGTCCAGTATTCA 60.464 55.0 2.24 0.0 0.00 2.57 R
2987 3109 0.304705 CCACGATAAAGCCGATGCAC 59.695 55.0 0.00 0.0 41.13 4.57 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
23 24 2.107141 AGCTATCGCTTCCCGCAC 59.893 61.111 0.00 0.00 46.47 5.34
54 55 3.606886 GAGGAACAGTTCTTCGCCA 57.393 52.632 13.13 0.00 0.00 5.69
57 58 1.141053 AGGAACAGTTCTTCGCCAAGT 59.859 47.619 13.13 0.00 0.00 3.16
70 71 2.592993 CCAAGTGGAGGGCGGAGAA 61.593 63.158 0.00 0.00 37.39 2.87
94 95 1.869824 AAGAGGAGGGAGGAGCGAGT 61.870 60.000 0.00 0.00 0.00 4.18
103 105 1.152943 AGGAGCGAGTGCCTATCGA 60.153 57.895 6.50 0.00 42.76 3.59
104 106 0.752009 AGGAGCGAGTGCCTATCGAA 60.752 55.000 6.50 0.00 42.76 3.71
139 141 1.604693 CGGAAGGCGGTCGCTAAATAT 60.605 52.381 15.04 0.00 41.60 1.28
171 173 2.039624 AGATGCGTCCTCCTGGGT 59.960 61.111 1.23 0.00 36.25 4.51
216 219 1.060622 CTACGCTCAGACGTCGGAC 59.939 63.158 14.65 10.52 44.43 4.79
217 220 1.360194 CTACGCTCAGACGTCGGACT 61.360 60.000 14.65 3.04 44.43 3.85
246 255 2.795297 GAGGCAGAGTCCGAGTCG 59.205 66.667 5.29 5.29 0.00 4.18
325 334 9.433153 TGACGAACTATGAACTATCTATCGTAT 57.567 33.333 0.00 0.00 40.60 3.06
351 360 7.445707 TGAGAAGACTATGAACTATCTACGCAT 59.554 37.037 0.00 0.00 0.00 4.73
405 424 9.970395 AACCAAATATGTATCGAATCGTAGTAA 57.030 29.630 1.52 0.00 0.00 2.24
529 560 1.069765 CCCGGCGCTGTATTCTGAT 59.930 57.895 16.49 0.00 0.00 2.90
540 571 4.494199 GCTGTATTCTGATTTTTAGCGCGT 60.494 41.667 8.43 0.00 0.00 6.01
565 596 0.645868 GTTGCGCGGATGTTAGAGAC 59.354 55.000 8.83 0.00 0.00 3.36
570 601 0.930742 GCGGATGTTAGAGACGCTCG 60.931 60.000 0.00 0.00 46.02 5.03
590 621 3.434641 TCGTAGCGTCCTATTTCTATCGG 59.565 47.826 0.00 0.00 0.00 4.18
591 622 2.726832 AGCGTCCTATTTCTATCGGC 57.273 50.000 0.00 0.00 0.00 5.54
592 623 1.272769 AGCGTCCTATTTCTATCGGCC 59.727 52.381 0.00 0.00 0.00 6.13
614 645 0.999406 CGTAGTCGCATTCCAACCAG 59.001 55.000 0.00 0.00 0.00 4.00
616 647 2.695359 GTAGTCGCATTCCAACCAGAA 58.305 47.619 0.00 0.00 0.00 3.02
618 649 2.795329 AGTCGCATTCCAACCAGAATT 58.205 42.857 0.00 0.00 34.19 2.17
642 673 2.031919 CTTGCACCACGCTACCCA 59.968 61.111 0.00 0.00 43.06 4.51
644 675 1.577328 CTTGCACCACGCTACCCAAG 61.577 60.000 0.00 0.00 43.06 3.61
649 682 0.249398 ACCACGCTACCCAAGACATC 59.751 55.000 0.00 0.00 0.00 3.06
663 696 3.791973 AGACATCAAAAACCGTTTGCA 57.208 38.095 0.00 0.00 0.00 4.08
688 721 2.225727 GGAGAACGACATTTCCACAACC 59.774 50.000 0.00 0.00 0.00 3.77
791 824 3.181487 ACACGATTAGCCATTGCAATTCC 60.181 43.478 9.83 3.51 41.13 3.01
855 891 1.852633 AGGCCCAAACTAGGAAATGC 58.147 50.000 0.00 0.00 0.00 3.56
862 898 3.119029 CCAAACTAGGAAATGCCATGGTG 60.119 47.826 14.67 0.00 40.02 4.17
863 899 1.767759 ACTAGGAAATGCCATGGTGC 58.232 50.000 14.67 0.00 40.02 5.01
864 900 1.005805 ACTAGGAAATGCCATGGTGCA 59.994 47.619 14.67 6.33 46.94 4.57
954 994 1.978617 CCACCAATCACCACCAGCC 60.979 63.158 0.00 0.00 0.00 4.85
982 1034 2.046892 CACAAGCACCGAGGAGGG 60.047 66.667 0.00 0.00 46.96 4.30
1098 1150 4.103103 GCGGCGACAAAGAAGGCC 62.103 66.667 12.98 0.00 42.14 5.19
1254 1306 1.383109 TGGCAGGACCATCGGAGAT 60.383 57.895 0.00 0.00 46.36 2.75
1265 1317 4.624913 ACCATCGGAGATATCATGGGTAT 58.375 43.478 18.97 1.78 45.12 2.73
1312 1367 5.187381 ACATCCACATGAATGGCAAAATGTA 59.813 36.000 0.00 0.86 39.85 2.29
1414 1475 1.572085 GACCGACGACGAGGTTCTCA 61.572 60.000 17.71 0.00 41.51 3.27
1422 1483 2.048127 GAGGTTCTCAGCGGCGTT 60.048 61.111 9.37 0.00 0.00 4.84
1490 1551 1.514087 TCGTAAGCGATGGACCCAC 59.486 57.895 0.00 0.00 42.81 4.61
1499 1560 1.405526 CGATGGACCCACGATGTTTCT 60.406 52.381 0.00 0.00 0.00 2.52
1504 1565 2.028020 GGACCCACGATGTTTCTTCTCT 60.028 50.000 0.00 0.00 0.00 3.10
1715 1780 2.159226 CCAGATCGGACTTGGTACAGTC 60.159 54.545 5.05 5.05 36.64 3.51
1751 1816 5.184287 TGATTTGCTTCAGCTGATCAATCAA 59.816 36.000 24.18 17.89 38.80 2.57
1940 2009 2.353145 CGTAAGACGGGCCGATCG 60.353 66.667 35.78 22.64 38.08 3.69
1958 2035 0.866061 CGGCCGAACGATGTCAGTAG 60.866 60.000 24.07 0.00 35.47 2.57
1959 2036 0.172803 GGCCGAACGATGTCAGTAGT 59.827 55.000 0.00 0.00 0.00 2.73
1960 2037 1.402968 GGCCGAACGATGTCAGTAGTA 59.597 52.381 0.00 0.00 0.00 1.82
1961 2038 2.541178 GGCCGAACGATGTCAGTAGTAG 60.541 54.545 0.00 0.00 0.00 2.57
1962 2039 2.097142 GCCGAACGATGTCAGTAGTAGT 59.903 50.000 0.00 0.00 0.00 2.73
1963 2040 3.310774 GCCGAACGATGTCAGTAGTAGTA 59.689 47.826 0.00 0.00 0.00 1.82
1964 2041 4.201851 GCCGAACGATGTCAGTAGTAGTAA 60.202 45.833 0.00 0.00 0.00 2.24
1965 2042 5.261661 CCGAACGATGTCAGTAGTAGTAAC 58.738 45.833 0.00 0.00 0.00 2.50
1966 2043 5.163824 CCGAACGATGTCAGTAGTAGTAACA 60.164 44.000 0.00 0.00 0.00 2.41
1967 2044 5.731723 CGAACGATGTCAGTAGTAGTAACAC 59.268 44.000 0.00 0.00 0.00 3.32
1968 2045 5.213913 ACGATGTCAGTAGTAGTAACACG 57.786 43.478 0.00 0.00 0.00 4.49
1969 2046 4.692625 ACGATGTCAGTAGTAGTAACACGT 59.307 41.667 0.00 4.18 0.00 4.49
1970 2047 5.869344 ACGATGTCAGTAGTAGTAACACGTA 59.131 40.000 6.95 0.00 31.18 3.57
1984 2061 2.004017 ACACGTACCATTGCCGTAATG 58.996 47.619 2.40 2.40 44.67 1.90
2029 2106 2.694829 ATCTCGGGGCGCGTAATGTC 62.695 60.000 23.46 0.00 0.00 3.06
2044 2121 2.358737 GTCTGGTTCACGGGGCTG 60.359 66.667 0.00 0.00 0.00 4.85
2297 2374 0.250038 ACGCACTGTCTGTCTTGCAT 60.250 50.000 0.00 0.00 34.49 3.96
2298 2375 0.165295 CGCACTGTCTGTCTTGCATG 59.835 55.000 0.00 0.00 34.49 4.06
2299 2376 1.516161 GCACTGTCTGTCTTGCATGA 58.484 50.000 0.00 0.00 34.97 3.07
2300 2377 1.875514 GCACTGTCTGTCTTGCATGAA 59.124 47.619 3.51 0.00 34.97 2.57
2301 2378 2.486982 GCACTGTCTGTCTTGCATGAAT 59.513 45.455 3.51 0.00 34.97 2.57
2302 2379 3.686241 GCACTGTCTGTCTTGCATGAATA 59.314 43.478 3.51 0.00 34.97 1.75
2303 2380 4.436584 GCACTGTCTGTCTTGCATGAATAC 60.437 45.833 3.51 3.99 34.97 1.89
2304 2381 4.934001 CACTGTCTGTCTTGCATGAATACT 59.066 41.667 3.51 0.00 0.00 2.12
2305 2382 4.934001 ACTGTCTGTCTTGCATGAATACTG 59.066 41.667 3.51 8.98 0.00 2.74
2306 2383 4.256110 TGTCTGTCTTGCATGAATACTGG 58.744 43.478 3.51 0.00 0.00 4.00
2307 2384 4.020307 TGTCTGTCTTGCATGAATACTGGA 60.020 41.667 3.51 0.00 0.00 3.86
2308 2385 4.331168 GTCTGTCTTGCATGAATACTGGAC 59.669 45.833 3.51 3.76 0.00 4.02
2309 2386 4.020307 TCTGTCTTGCATGAATACTGGACA 60.020 41.667 3.51 0.00 0.00 4.02
2310 2387 4.847198 TGTCTTGCATGAATACTGGACAT 58.153 39.130 3.51 0.00 0.00 3.06
2311 2388 4.637091 TGTCTTGCATGAATACTGGACATG 59.363 41.667 3.51 0.00 42.60 3.21
2312 2389 4.036027 GTCTTGCATGAATACTGGACATGG 59.964 45.833 3.51 0.00 40.83 3.66
2313 2390 2.300433 TGCATGAATACTGGACATGGC 58.700 47.619 0.00 0.00 40.83 4.40
2314 2391 1.610522 GCATGAATACTGGACATGGCC 59.389 52.381 12.04 12.04 40.83 5.36
2330 2407 2.281070 CCGCGAGCTAATGGCCAT 60.281 61.111 14.09 14.09 43.05 4.40
2331 2408 1.893808 CCGCGAGCTAATGGCCATT 60.894 57.895 32.59 32.59 43.05 3.16
2345 2422 1.512926 GCCATTATTCGATCCGTGCT 58.487 50.000 0.00 0.00 0.00 4.40
2346 2423 1.873591 GCCATTATTCGATCCGTGCTT 59.126 47.619 0.00 0.00 0.00 3.91
2465 2542 2.029964 TTCGTGTTCTGGGACGCC 59.970 61.111 0.00 0.00 35.53 5.68
2742 2822 2.176546 CTGTGAATGGCAACGGCG 59.823 61.111 4.80 4.80 42.47 6.46
2817 2897 2.353889 CAGCCTTGAACAATCCGATCAG 59.646 50.000 0.00 0.00 0.00 2.90
2840 2934 2.129555 GACAGACCCTGTGCCACCAT 62.130 60.000 4.14 0.00 45.44 3.55
2872 2966 3.852471 CACATTTTCGTGTCTCGTTCA 57.148 42.857 0.00 0.00 40.80 3.18
2888 2982 3.562973 TCGTTCATCTCCACTATACGTCC 59.437 47.826 0.00 0.00 0.00 4.79
2898 2992 4.957954 TCCACTATACGTCCATACCAAACT 59.042 41.667 0.00 0.00 0.00 2.66
2899 2993 5.422970 TCCACTATACGTCCATACCAAACTT 59.577 40.000 0.00 0.00 0.00 2.66
2908 3006 6.815142 ACGTCCATACCAAACTTAATGTACTC 59.185 38.462 0.00 0.00 0.00 2.59
2909 3007 6.020121 CGTCCATACCAAACTTAATGTACTCG 60.020 42.308 0.00 0.00 0.00 4.18
2921 3019 0.250424 TGTACTCGGACACTCGGTGA 60.250 55.000 10.46 0.00 36.96 4.02
2922 3020 0.877071 GTACTCGGACACTCGGTGAA 59.123 55.000 10.46 0.00 36.96 3.18
2923 3021 1.471684 GTACTCGGACACTCGGTGAAT 59.528 52.381 10.46 0.00 36.96 2.57
2924 3022 0.966920 ACTCGGACACTCGGTGAATT 59.033 50.000 10.46 0.00 36.96 2.17
2925 3023 2.165167 ACTCGGACACTCGGTGAATTA 58.835 47.619 10.46 0.00 36.96 1.40
2926 3024 2.559668 ACTCGGACACTCGGTGAATTAA 59.440 45.455 10.46 0.00 36.96 1.40
2927 3025 3.179830 CTCGGACACTCGGTGAATTAAG 58.820 50.000 10.46 0.00 36.96 1.85
2928 3026 2.559668 TCGGACACTCGGTGAATTAAGT 59.440 45.455 10.46 0.00 36.96 2.24
2929 3027 2.921754 CGGACACTCGGTGAATTAAGTC 59.078 50.000 10.46 0.00 36.96 3.01
2930 3028 3.613193 CGGACACTCGGTGAATTAAGTCA 60.613 47.826 0.56 0.56 36.96 3.41
2987 3109 3.313012 TGATTCCTAGGTCACAACGTG 57.687 47.619 9.08 0.00 34.45 4.49
3025 3147 2.030562 GCATATCCCGTCCCCGTG 59.969 66.667 0.00 0.00 0.00 4.94
3079 3201 4.440250 CCATCTCCGACTCGATTTACAACT 60.440 45.833 0.00 0.00 0.00 3.16
3133 3255 0.036306 CAGTACCGGCTTCCCTGTTT 59.964 55.000 0.00 0.00 30.60 2.83
3136 3258 1.538512 GTACCGGCTTCCCTGTTTTTC 59.461 52.381 0.00 0.00 30.60 2.29
3165 3287 2.568623 AAAATCTCTGCGTCCCAACT 57.431 45.000 0.00 0.00 0.00 3.16
3169 3291 1.153939 CTCTGCGTCCCAACTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
3285 3408 1.666054 GCTTCTGCTCTTGATCCCTG 58.334 55.000 0.00 0.00 36.03 4.45
3286 3409 1.666054 CTTCTGCTCTTGATCCCTGC 58.334 55.000 0.00 0.00 0.00 4.85
3302 3425 0.678048 CTGCTGTGGGGTTCTTAGCC 60.678 60.000 0.00 0.00 41.36 3.93
3619 3751 0.109458 TACTGCATCGACGTGTGGAC 60.109 55.000 0.00 0.00 0.00 4.02
3744 3876 4.672587 TTCTAGAGGCGCTGATATGTTT 57.327 40.909 7.64 0.00 0.00 2.83
3769 3902 2.541556 AGCCGATCTCGCTAAACTTTC 58.458 47.619 2.53 0.00 38.18 2.62
3775 3908 6.238130 GCCGATCTCGCTAAACTTTCTTAATT 60.238 38.462 0.00 0.00 38.18 1.40
3800 3933 9.850198 TTACCAATAGTGTTTACAGGTACTTTT 57.150 29.630 0.00 0.00 34.60 2.27
3801 3934 8.756486 ACCAATAGTGTTTACAGGTACTTTTT 57.244 30.769 0.00 0.00 34.60 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.600420 CTGTTCCTCGTTGATGATGTCG 59.400 50.000 0.00 0.00 0.00 4.35
54 55 2.294078 CCTTCTCCGCCCTCCACTT 61.294 63.158 0.00 0.00 0.00 3.16
70 71 2.042435 CCTCCCTCCTCTTCGCCT 60.042 66.667 0.00 0.00 0.00 5.52
94 95 1.739035 CGCTTGTCCTTTCGATAGGCA 60.739 52.381 16.35 14.15 34.80 4.75
103 105 2.604174 CCGCGTTCGCTTGTCCTTT 61.604 57.895 14.92 0.00 0.00 3.11
104 106 2.981977 TTCCGCGTTCGCTTGTCCTT 62.982 55.000 14.92 0.00 0.00 3.36
139 141 1.269102 GCATCTCCTAGCGCTTCGTTA 60.269 52.381 18.68 0.00 0.00 3.18
216 219 0.387202 CTGCCTCGGTGATGTCCTAG 59.613 60.000 0.00 0.00 0.00 3.02
217 220 0.033503 TCTGCCTCGGTGATGTCCTA 60.034 55.000 0.00 0.00 0.00 2.94
246 255 5.932661 ACGAAAAACTACTACTACTCGTCC 58.067 41.667 0.00 0.00 33.32 4.79
325 334 6.766467 TGCGTAGATAGTTCATAGTCTTCTCA 59.234 38.462 0.00 0.00 0.00 3.27
377 396 8.358148 ACTACGATTCGATACATATTTGGTTCT 58.642 33.333 13.95 0.00 0.00 3.01
555 586 2.759538 GCTACGAGCGTCTCTAACAT 57.240 50.000 0.00 0.00 0.00 2.71
570 601 3.500014 GCCGATAGAAATAGGACGCTAC 58.500 50.000 0.00 0.00 39.76 3.58
590 621 2.588034 GAATGCGACTACGGGGGC 60.588 66.667 0.00 0.00 40.15 5.80
591 622 2.108362 GGAATGCGACTACGGGGG 59.892 66.667 0.00 0.00 40.15 5.40
592 623 1.087771 GTTGGAATGCGACTACGGGG 61.088 60.000 0.00 0.00 40.15 5.73
614 645 2.351738 CGTGGTGCAAGGAAGGAAATTC 60.352 50.000 0.00 0.00 37.17 2.17
616 647 1.247567 CGTGGTGCAAGGAAGGAAAT 58.752 50.000 0.00 0.00 0.00 2.17
618 649 1.896660 GCGTGGTGCAAGGAAGGAA 60.897 57.895 0.00 0.00 45.45 3.36
642 673 4.116747 TGCAAACGGTTTTTGATGTCTT 57.883 36.364 2.79 0.00 0.00 3.01
644 675 4.109050 TCTTGCAAACGGTTTTTGATGTC 58.891 39.130 2.79 0.00 0.00 3.06
649 682 3.115554 CTCCTCTTGCAAACGGTTTTTG 58.884 45.455 2.79 0.00 0.00 2.44
663 696 3.071023 TGTGGAAATGTCGTTCTCCTCTT 59.929 43.478 7.23 0.00 0.00 2.85
688 721 0.036952 CTGAGGTGGTAGCTGTGGTG 60.037 60.000 0.00 0.00 0.00 4.17
791 824 0.959867 TGCGATTGGGTGTGGTGATG 60.960 55.000 0.00 0.00 0.00 3.07
862 898 3.181967 CAGCGAGCGTAGGTGTGC 61.182 66.667 0.00 0.00 39.88 4.57
863 899 3.181967 GCAGCGAGCGTAGGTGTG 61.182 66.667 9.31 0.00 39.88 3.82
954 994 0.031178 GTGCTTGTGTTGGGCAAGAG 59.969 55.000 8.95 0.00 44.29 2.85
1098 1150 2.674177 GCCGAATATGTAGATCACCGGG 60.674 54.545 6.32 0.00 36.55 5.73
1254 1306 5.163205 ACAAGCAGCTTACATACCCATGATA 60.163 40.000 7.52 0.00 35.96 2.15
1265 1317 2.549754 GAGCAGAAACAAGCAGCTTACA 59.450 45.455 7.52 0.00 35.36 2.41
1312 1367 4.801247 GCAAACCCCCGAATAAAACACATT 60.801 41.667 0.00 0.00 0.00 2.71
1443 1504 0.454620 CGGTCTCGTTGAGAAGTCCG 60.455 60.000 9.13 9.13 40.59 4.79
1483 1544 2.028020 AGAGAAGAAACATCGTGGGTCC 60.028 50.000 0.00 0.00 0.00 4.46
1486 1547 2.668457 CGAAGAGAAGAAACATCGTGGG 59.332 50.000 0.00 0.00 0.00 4.61
1490 1551 7.510630 ACAATTAACGAAGAGAAGAAACATCG 58.489 34.615 0.00 0.00 36.45 3.84
1499 1560 6.612247 TTCTGCAACAATTAACGAAGAGAA 57.388 33.333 0.00 0.00 0.00 2.87
1559 1620 2.016961 CAAGATCGCATTGACCCCG 58.983 57.895 0.00 0.00 0.00 5.73
1940 2009 0.172803 ACTACTGACATCGTTCGGCC 59.827 55.000 0.00 0.00 0.00 6.13
1958 2035 2.599973 CGGCAATGGTACGTGTTACTAC 59.400 50.000 0.00 0.00 0.00 2.73
1959 2036 2.230992 ACGGCAATGGTACGTGTTACTA 59.769 45.455 0.00 0.00 39.64 1.82
1960 2037 1.001181 ACGGCAATGGTACGTGTTACT 59.999 47.619 0.00 0.00 39.64 2.24
1961 2038 1.431496 ACGGCAATGGTACGTGTTAC 58.569 50.000 0.00 0.00 39.64 2.50
1962 2039 3.309961 TTACGGCAATGGTACGTGTTA 57.690 42.857 0.00 0.00 41.40 2.41
1963 2040 2.166821 TTACGGCAATGGTACGTGTT 57.833 45.000 0.00 0.00 41.40 3.32
1964 2041 2.004017 CATTACGGCAATGGTACGTGT 58.996 47.619 0.00 0.00 40.41 4.49
1965 2042 2.272678 TCATTACGGCAATGGTACGTG 58.727 47.619 0.00 0.00 43.68 4.49
1966 2043 2.676632 TCATTACGGCAATGGTACGT 57.323 45.000 10.88 0.00 43.68 3.57
1967 2044 4.545823 AAATCATTACGGCAATGGTACG 57.454 40.909 10.88 0.00 43.68 3.67
1968 2045 5.646606 ACAAAATCATTACGGCAATGGTAC 58.353 37.500 10.88 0.00 43.68 3.34
1969 2046 5.906113 ACAAAATCATTACGGCAATGGTA 57.094 34.783 10.88 0.00 43.68 3.25
1970 2047 4.799564 ACAAAATCATTACGGCAATGGT 57.200 36.364 10.88 2.73 43.68 3.55
1984 2061 3.054878 CAGCCTCTGCACAAACAAAATC 58.945 45.455 0.00 0.00 41.13 2.17
2297 2374 0.463654 GCGGCCATGTCCAGTATTCA 60.464 55.000 2.24 0.00 0.00 2.57
2298 2375 1.498865 CGCGGCCATGTCCAGTATTC 61.499 60.000 2.24 0.00 0.00 1.75
2299 2376 1.523711 CGCGGCCATGTCCAGTATT 60.524 57.895 2.24 0.00 0.00 1.89
2300 2377 2.108976 CGCGGCCATGTCCAGTAT 59.891 61.111 2.24 0.00 0.00 2.12
2301 2378 3.071837 TCGCGGCCATGTCCAGTA 61.072 61.111 6.13 0.00 0.00 2.74
2302 2379 4.457496 CTCGCGGCCATGTCCAGT 62.457 66.667 6.13 0.00 0.00 4.00
2305 2382 2.996168 ATTAGCTCGCGGCCATGTCC 62.996 60.000 6.13 0.00 43.05 4.02
2306 2383 1.595382 ATTAGCTCGCGGCCATGTC 60.595 57.895 6.13 0.00 43.05 3.06
2307 2384 1.889105 CATTAGCTCGCGGCCATGT 60.889 57.895 6.13 0.00 43.05 3.21
2308 2385 2.610694 CCATTAGCTCGCGGCCATG 61.611 63.158 6.13 13.12 43.05 3.66
2309 2386 2.281070 CCATTAGCTCGCGGCCAT 60.281 61.111 6.13 1.17 43.05 4.40
2313 2390 0.602638 TAATGGCCATTAGCTCGCGG 60.603 55.000 30.39 0.00 43.05 6.46
2314 2391 1.442769 ATAATGGCCATTAGCTCGCG 58.557 50.000 34.95 0.00 43.05 5.87
2327 2404 2.872245 ACAAGCACGGATCGAATAATGG 59.128 45.455 0.00 0.00 0.00 3.16
2329 2406 2.287915 GCACAAGCACGGATCGAATAAT 59.712 45.455 0.00 0.00 41.58 1.28
2330 2407 1.663643 GCACAAGCACGGATCGAATAA 59.336 47.619 0.00 0.00 41.58 1.40
2331 2408 1.286501 GCACAAGCACGGATCGAATA 58.713 50.000 0.00 0.00 41.58 1.75
2345 2422 0.741574 ACGTCGTGAAACCTGCACAA 60.742 50.000 0.00 0.00 36.06 3.33
2346 2423 1.149361 GACGTCGTGAAACCTGCACA 61.149 55.000 0.63 0.00 36.06 4.57
2465 2542 2.181021 GCGTCGGAGGTGTGGTAG 59.819 66.667 0.00 0.00 0.00 3.18
2795 2875 2.027285 TGATCGGATTGTTCAAGGCTGA 60.027 45.455 0.00 0.00 0.00 4.26
2817 2897 2.359230 GCACAGGGTCTGTCTGCC 60.359 66.667 0.00 0.00 43.43 4.85
2840 2934 1.003331 GAAAATGTGTCGACGTTGCCA 60.003 47.619 11.62 2.76 31.34 4.92
2872 2966 4.994282 TGGTATGGACGTATAGTGGAGAT 58.006 43.478 0.00 0.00 0.00 2.75
2888 2982 6.814644 TGTCCGAGTACATTAAGTTTGGTATG 59.185 38.462 0.00 0.00 0.00 2.39
2898 2992 3.084039 ACCGAGTGTCCGAGTACATTAA 58.916 45.455 0.00 0.00 0.00 1.40
2899 2993 2.421073 CACCGAGTGTCCGAGTACATTA 59.579 50.000 0.00 0.00 0.00 1.90
2908 3006 2.921754 GACTTAATTCACCGAGTGTCCG 59.078 50.000 4.33 0.00 34.79 4.79
2909 3007 3.921677 TGACTTAATTCACCGAGTGTCC 58.078 45.455 4.33 0.00 34.79 4.02
2924 3022 8.454106 GCTCTCTGCTTTGATTAATTTGACTTA 58.546 33.333 0.00 0.00 38.95 2.24
2925 3023 7.040201 TGCTCTCTGCTTTGATTAATTTGACTT 60.040 33.333 0.00 0.00 43.37 3.01
2926 3024 6.432162 TGCTCTCTGCTTTGATTAATTTGACT 59.568 34.615 0.00 0.00 43.37 3.41
2927 3025 6.615088 TGCTCTCTGCTTTGATTAATTTGAC 58.385 36.000 0.00 0.00 43.37 3.18
2928 3026 6.656270 TCTGCTCTCTGCTTTGATTAATTTGA 59.344 34.615 0.00 0.00 43.37 2.69
2929 3027 6.849502 TCTGCTCTCTGCTTTGATTAATTTG 58.150 36.000 0.00 0.00 43.37 2.32
2930 3028 7.642082 ATCTGCTCTCTGCTTTGATTAATTT 57.358 32.000 0.00 0.00 43.37 1.82
2958 3056 4.896482 GTGACCTAGGAATCATACTCTGGT 59.104 45.833 17.98 0.00 0.00 4.00
2960 3058 6.276847 GTTGTGACCTAGGAATCATACTCTG 58.723 44.000 17.98 0.00 0.00 3.35
2987 3109 0.304705 CCACGATAAAGCCGATGCAC 59.695 55.000 0.00 0.00 41.13 4.57
2991 3113 0.464036 TGCTCCACGATAAAGCCGAT 59.536 50.000 0.00 0.00 35.12 4.18
3050 3172 1.439644 GAGTCGGAGATGGGTGCTC 59.560 63.158 0.00 0.00 40.67 4.26
3079 3201 0.683828 TACGTATTCGGGAGTGGCCA 60.684 55.000 0.00 0.00 41.85 5.36
3165 3287 2.993220 CGATTTTGGATGTGTGACGAGA 59.007 45.455 0.00 0.00 0.00 4.04
3169 3291 4.466828 CTTGTCGATTTTGGATGTGTGAC 58.533 43.478 0.00 0.00 0.00 3.67
3285 3408 1.745489 CGGCTAAGAACCCCACAGC 60.745 63.158 0.00 0.00 0.00 4.40
3286 3409 1.745489 GCGGCTAAGAACCCCACAG 60.745 63.158 0.00 0.00 0.00 3.66
3302 3425 3.372676 GAGGCACACTGCGATTGCG 62.373 63.158 0.00 0.00 46.21 4.85
3344 3467 4.030452 GCGTTTGCTTCTGCCGCT 62.030 61.111 0.00 0.00 41.64 5.52
3393 3516 1.434696 GTTCAATGGCCGCCATCAG 59.565 57.895 25.27 19.62 44.40 2.90
3619 3751 1.294659 GCAGGTGGTCTTGCTCTTCG 61.295 60.000 0.00 0.00 42.25 3.79
3744 3876 4.501071 AGTTTAGCGAGATCGGCTAAAAA 58.499 39.130 30.98 19.47 42.85 1.94
3775 3908 9.850198 AAAAAGTACCTGTAAACACTATTGGTA 57.150 29.630 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.