Multiple sequence alignment - TraesCS1D01G028000

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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 TraesCS1D01G028000 chr1D 100.000 2216 0 0 1 2216 11126913 11124698 0.000000e+00 4093
1 TraesCS1D01G028000 chr1D 94.106 1476 44 11 682 2153 11042950 11041514 0.000000e+00 2204
2 TraesCS1D01G028000 chr1D 93.927 1482 46 12 677 2153 11091670 11090228 0.000000e+00 2198
3 TraesCS1D01G028000 chr1D 96.373 386 8 1 1 386 57943321 57943700 4.020000e-177 630
4 TraesCS1D01G028000 chr1D 85.151 431 42 14 410 831 11202517 11202100 2.630000e-114 422
5 TraesCS1D01G028000 chr1B 92.228 1827 82 31 407 2216 16481115 16479332 0.000000e+00 2532
6 TraesCS1D01G028000 chr1B 88.951 896 58 17 1340 2210 16647074 16646195 0.000000e+00 1068
7 TraesCS1D01G028000 chr1B 93.578 545 27 5 407 947 16653091 16652551 0.000000e+00 806
8 TraesCS1D01G028000 chr1B 95.430 372 14 2 974 1342 16652557 16652186 6.820000e-165 590
9 TraesCS1D01G028000 chr1B 84.455 431 44 15 410 831 16800627 16800211 9.530000e-109 403
10 TraesCS1D01G028000 chr1A 95.165 1489 46 6 740 2216 22631678 22633152 0.000000e+00 2327
11 TraesCS1D01G028000 chr1A 86.862 921 75 25 407 1314 12679814 12680701 0.000000e+00 989
12 TraesCS1D01G028000 chr1A 97.015 335 7 2 407 741 22631243 22631574 5.340000e-156 560
13 TraesCS1D01G028000 chr1A 93.333 330 20 2 1816 2144 12688629 12688957 9.200000e-134 486
14 TraesCS1D01G028000 chr1A 93.103 145 2 3 1682 1826 12686574 12686710 2.880000e-49 206
15 TraesCS1D01G028000 chr7B 86.862 921 75 25 407 1314 192779335 192780222 0.000000e+00 989
16 TraesCS1D01G028000 chr7B 93.103 145 2 3 1682 1826 192786095 192786231 2.880000e-49 206
17 TraesCS1D01G028000 chr2B 86.862 921 75 25 407 1314 47190949 47190062 0.000000e+00 989
18 TraesCS1D01G028000 chr2B 93.103 145 2 3 1682 1826 47184189 47184053 2.880000e-49 206
19 TraesCS1D01G028000 chrUn 90.925 562 35 9 407 965 351922397 351921849 0.000000e+00 741
20 TraesCS1D01G028000 chrUn 96.333 409 11 3 1 406 392473266 392472859 0.000000e+00 669
21 TraesCS1D01G028000 chrUn 85.030 334 38 6 985 1314 261624300 261624625 1.640000e-86 329
22 TraesCS1D01G028000 chr6D 98.030 406 8 0 1 406 2783787 2784192 0.000000e+00 706
23 TraesCS1D01G028000 chr7D 96.333 409 12 2 1 406 271461211 271460803 0.000000e+00 669
24 TraesCS1D01G028000 chr2D 96.333 409 11 3 1 406 43180760 43180353 0.000000e+00 669
25 TraesCS1D01G028000 chr2D 96.333 409 11 3 1 406 43201832 43201425 0.000000e+00 669
26 TraesCS1D01G028000 chr6B 94.866 409 18 2 1 406 196916475 196916883 8.630000e-179 636
27 TraesCS1D01G028000 chr5B 94.132 409 21 2 1 406 487486331 487486739 8.690000e-174 619
28 TraesCS1D01G028000 chr4A 93.643 409 23 2 1 406 163931858 163931450 1.880000e-170 608


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 TraesCS1D01G028000 chr1D 11124698 11126913 2215 True 4093.0 4093 100.000 1 2216 1 chr1D.!!$R3 2215
1 TraesCS1D01G028000 chr1D 11041514 11042950 1436 True 2204.0 2204 94.106 682 2153 1 chr1D.!!$R1 1471
2 TraesCS1D01G028000 chr1D 11090228 11091670 1442 True 2198.0 2198 93.927 677 2153 1 chr1D.!!$R2 1476
3 TraesCS1D01G028000 chr1B 16479332 16481115 1783 True 2532.0 2532 92.228 407 2216 1 chr1B.!!$R1 1809
4 TraesCS1D01G028000 chr1B 16646195 16647074 879 True 1068.0 1068 88.951 1340 2210 1 chr1B.!!$R2 870
5 TraesCS1D01G028000 chr1B 16652186 16653091 905 True 698.0 806 94.504 407 1342 2 chr1B.!!$R4 935
6 TraesCS1D01G028000 chr1A 22631243 22633152 1909 False 1443.5 2327 96.090 407 2216 2 chr1A.!!$F3 1809
7 TraesCS1D01G028000 chr1A 12679814 12680701 887 False 989.0 989 86.862 407 1314 1 chr1A.!!$F1 907
8 TraesCS1D01G028000 chr1A 12686574 12688957 2383 False 346.0 486 93.218 1682 2144 2 chr1A.!!$F2 462
9 TraesCS1D01G028000 chr7B 192779335 192780222 887 False 989.0 989 86.862 407 1314 1 chr7B.!!$F1 907
10 TraesCS1D01G028000 chr2B 47190062 47190949 887 True 989.0 989 86.862 407 1314 1 chr2B.!!$R2 907
11 TraesCS1D01G028000 chrUn 351921849 351922397 548 True 741.0 741 90.925 407 965 1 chrUn.!!$R1 558

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
124 125 0.036952 CTCCACACTGTAGCCACCAG 60.037 60.0 0.0 0.0 36.01 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1586 1.402968 CCGGTCTCTGCATCAAAATGG 59.597 52.381 0.0 0.0 33.19 3.16 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 4.225497 CCAAACTCCGCCAGATCC 57.775 61.111 0.00 0.00 0.00 3.36
18 19 1.299648 CCAAACTCCGCCAGATCCA 59.700 57.895 0.00 0.00 0.00 3.41
19 20 0.745845 CCAAACTCCGCCAGATCCAG 60.746 60.000 0.00 0.00 0.00 3.86
20 21 1.078143 AAACTCCGCCAGATCCAGC 60.078 57.895 0.00 0.00 0.00 4.85
26 27 2.268920 GCCAGATCCAGCGACCAA 59.731 61.111 0.00 0.00 0.00 3.67
27 28 2.109126 GCCAGATCCAGCGACCAAC 61.109 63.158 0.00 0.00 0.00 3.77
28 29 1.450312 CCAGATCCAGCGACCAACC 60.450 63.158 0.00 0.00 0.00 3.77
29 30 1.811266 CAGATCCAGCGACCAACCG 60.811 63.158 0.00 0.00 0.00 4.44
37 38 4.367023 CGACCAACCGCGGGAAGA 62.367 66.667 31.76 0.00 0.00 2.87
38 39 2.741211 GACCAACCGCGGGAAGAC 60.741 66.667 31.76 13.44 0.00 3.01
39 40 3.524648 GACCAACCGCGGGAAGACA 62.525 63.158 31.76 0.00 0.00 3.41
40 41 2.281208 CCAACCGCGGGAAGACAA 60.281 61.111 31.76 0.00 0.00 3.18
41 42 2.325082 CCAACCGCGGGAAGACAAG 61.325 63.158 31.76 9.12 0.00 3.16
42 43 2.668550 AACCGCGGGAAGACAAGC 60.669 61.111 31.76 0.00 0.00 4.01
46 47 3.793144 GCGGGAAGACAAGCGCAG 61.793 66.667 11.47 3.78 0.00 5.18
47 48 2.048222 CGGGAAGACAAGCGCAGA 60.048 61.111 11.47 0.00 0.00 4.26
48 49 1.667830 CGGGAAGACAAGCGCAGAA 60.668 57.895 11.47 0.00 0.00 3.02
49 50 1.630244 CGGGAAGACAAGCGCAGAAG 61.630 60.000 11.47 0.00 0.00 2.85
50 51 1.499502 GGAAGACAAGCGCAGAAGC 59.500 57.895 11.47 0.00 37.42 3.86
61 62 3.452786 CAGAAGCGGAGGGAGCGA 61.453 66.667 0.00 0.00 40.04 4.93
62 63 2.680352 AGAAGCGGAGGGAGCGAA 60.680 61.111 0.00 0.00 40.04 4.70
63 64 2.060980 AGAAGCGGAGGGAGCGAAT 61.061 57.895 0.00 0.00 40.04 3.34
64 65 1.153349 GAAGCGGAGGGAGCGAATT 60.153 57.895 0.00 0.00 40.04 2.17
65 66 0.104304 GAAGCGGAGGGAGCGAATTA 59.896 55.000 0.00 0.00 40.04 1.40
66 67 0.105039 AAGCGGAGGGAGCGAATTAG 59.895 55.000 0.00 0.00 40.04 1.73
67 68 1.301009 GCGGAGGGAGCGAATTAGG 60.301 63.158 0.00 0.00 0.00 2.69
68 69 1.367840 CGGAGGGAGCGAATTAGGG 59.632 63.158 0.00 0.00 0.00 3.53
69 70 1.755384 GGAGGGAGCGAATTAGGGG 59.245 63.158 0.00 0.00 0.00 4.79
70 71 1.071642 GAGGGAGCGAATTAGGGGC 59.928 63.158 0.00 0.00 0.00 5.80
71 72 2.280865 GGGAGCGAATTAGGGGCG 60.281 66.667 0.00 0.00 0.00 6.13
72 73 2.280865 GGAGCGAATTAGGGGCGG 60.281 66.667 0.00 0.00 0.00 6.13
73 74 2.973052 GAGCGAATTAGGGGCGGC 60.973 66.667 0.00 0.00 0.00 6.53
74 75 3.750373 GAGCGAATTAGGGGCGGCA 62.750 63.158 12.47 0.00 0.00 5.69
75 76 2.826738 GCGAATTAGGGGCGGCAA 60.827 61.111 12.47 0.00 0.00 4.52
76 77 2.411504 GCGAATTAGGGGCGGCAAA 61.412 57.895 12.47 1.78 0.00 3.68
77 78 1.431845 CGAATTAGGGGCGGCAAAC 59.568 57.895 12.47 0.00 0.00 2.93
78 79 1.813859 GAATTAGGGGCGGCAAACC 59.186 57.895 12.47 2.38 0.00 3.27
79 80 0.683179 GAATTAGGGGCGGCAAACCT 60.683 55.000 12.47 11.06 38.40 3.50
80 81 0.683179 AATTAGGGGCGGCAAACCTC 60.683 55.000 12.47 0.00 35.84 3.85
81 82 2.567664 ATTAGGGGCGGCAAACCTCC 62.568 60.000 12.47 0.64 40.44 4.30
84 85 4.344865 GGGCGGCAAACCTCCAGA 62.345 66.667 12.47 0.00 43.27 3.86
85 86 2.044946 GGCGGCAAACCTCCAGAT 60.045 61.111 3.07 0.00 40.90 2.90
86 87 2.115291 GGCGGCAAACCTCCAGATC 61.115 63.158 3.07 0.00 40.90 2.75
87 88 1.078143 GCGGCAAACCTCCAGATCT 60.078 57.895 0.00 0.00 0.00 2.75
88 89 1.372087 GCGGCAAACCTCCAGATCTG 61.372 60.000 16.24 16.24 0.00 2.90
98 99 3.861341 CCAGATCTGGCGAGGAAAA 57.139 52.632 28.45 0.00 44.73 2.29
99 100 1.661341 CCAGATCTGGCGAGGAAAAG 58.339 55.000 28.45 1.31 44.73 2.27
100 101 1.661341 CAGATCTGGCGAGGAAAAGG 58.339 55.000 15.38 0.00 0.00 3.11
101 102 1.208052 CAGATCTGGCGAGGAAAAGGA 59.792 52.381 15.38 0.00 0.00 3.36
102 103 1.484240 AGATCTGGCGAGGAAAAGGAG 59.516 52.381 0.00 0.00 0.00 3.69
103 104 0.543749 ATCTGGCGAGGAAAAGGAGG 59.456 55.000 0.00 0.00 0.00 4.30
104 105 1.746991 CTGGCGAGGAAAAGGAGGC 60.747 63.158 0.00 0.00 0.00 4.70
105 106 2.438614 GGCGAGGAAAAGGAGGCC 60.439 66.667 0.00 0.00 0.00 5.19
106 107 2.671682 GCGAGGAAAAGGAGGCCT 59.328 61.111 3.86 3.86 33.87 5.19
107 108 1.450491 GCGAGGAAAAGGAGGCCTC 60.450 63.158 25.59 25.59 43.73 4.70
118 119 1.219393 GAGGCCTCCACACTGTAGC 59.781 63.158 23.19 0.00 0.00 3.58
119 120 2.245438 GAGGCCTCCACACTGTAGCC 62.245 65.000 23.19 0.00 40.79 3.93
120 121 2.592993 GGCCTCCACACTGTAGCCA 61.593 63.158 0.00 0.00 40.20 4.75
121 122 1.376037 GCCTCCACACTGTAGCCAC 60.376 63.158 0.00 0.00 0.00 5.01
122 123 1.296715 CCTCCACACTGTAGCCACC 59.703 63.158 0.00 0.00 0.00 4.61
123 124 1.480212 CCTCCACACTGTAGCCACCA 61.480 60.000 0.00 0.00 0.00 4.17
124 125 0.036952 CTCCACACTGTAGCCACCAG 60.037 60.000 0.00 0.00 36.01 4.00
125 126 1.003355 CCACACTGTAGCCACCAGG 60.003 63.158 0.00 0.00 34.16 4.45
165 166 4.803426 CAGTCGAGGACGCCAGCC 62.803 72.222 0.00 0.00 37.67 4.85
167 168 4.803426 GTCGAGGACGCCAGCCAG 62.803 72.222 0.00 0.00 39.58 4.85
169 170 4.504916 CGAGGACGCCAGCCAGAG 62.505 72.222 0.00 0.00 0.00 3.35
170 171 4.828925 GAGGACGCCAGCCAGAGC 62.829 72.222 0.00 0.00 40.32 4.09
201 202 3.186047 CGTTCAGGGCTAACGGCG 61.186 66.667 4.80 4.80 44.49 6.46
202 203 2.263540 GTTCAGGGCTAACGGCGA 59.736 61.111 16.62 0.00 42.94 5.54
203 204 2.098831 GTTCAGGGCTAACGGCGAC 61.099 63.158 16.62 0.00 42.94 5.19
251 252 1.005156 GATCCAGATCCTCCGCTGC 60.005 63.158 0.00 0.00 31.76 5.25
252 253 1.752358 GATCCAGATCCTCCGCTGCA 61.752 60.000 0.00 0.00 31.76 4.41
253 254 1.756408 ATCCAGATCCTCCGCTGCAG 61.756 60.000 10.11 10.11 0.00 4.41
254 255 2.108566 CAGATCCTCCGCTGCAGG 59.891 66.667 17.12 5.50 0.00 4.85
255 256 2.042537 AGATCCTCCGCTGCAGGA 60.043 61.111 17.12 10.73 44.46 3.86
265 266 4.504916 CTGCAGGAGCGACGAGGG 62.505 72.222 5.57 0.00 46.23 4.30
330 331 3.374402 ACCTCAGGTGGCGACGAG 61.374 66.667 0.00 0.00 32.98 4.18
331 332 4.135153 CCTCAGGTGGCGACGAGG 62.135 72.222 8.08 8.08 39.20 4.63
332 333 3.062466 CTCAGGTGGCGACGAGGA 61.062 66.667 0.00 0.00 0.00 3.71
333 334 3.057547 CTCAGGTGGCGACGAGGAG 62.058 68.421 0.00 0.00 0.00 3.69
334 335 4.135153 CAGGTGGCGACGAGGAGG 62.135 72.222 0.00 0.00 0.00 4.30
337 338 3.827898 GTGGCGACGAGGAGGGAG 61.828 72.222 0.00 0.00 0.00 4.30
338 339 4.043100 TGGCGACGAGGAGGGAGA 62.043 66.667 0.00 0.00 0.00 3.71
339 340 3.213402 GGCGACGAGGAGGGAGAG 61.213 72.222 0.00 0.00 0.00 3.20
340 341 3.213402 GCGACGAGGAGGGAGAGG 61.213 72.222 0.00 0.00 0.00 3.69
341 342 2.590645 CGACGAGGAGGGAGAGGA 59.409 66.667 0.00 0.00 0.00 3.71
342 343 1.525077 CGACGAGGAGGGAGAGGAG 60.525 68.421 0.00 0.00 0.00 3.69
343 344 1.152839 GACGAGGAGGGAGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
344 345 1.928714 GACGAGGAGGGAGAGGAGGT 61.929 65.000 0.00 0.00 0.00 3.85
345 346 1.454847 CGAGGAGGGAGAGGAGGTG 60.455 68.421 0.00 0.00 0.00 4.00
346 347 1.700985 GAGGAGGGAGAGGAGGTGT 59.299 63.158 0.00 0.00 0.00 4.16
347 348 0.686112 GAGGAGGGAGAGGAGGTGTG 60.686 65.000 0.00 0.00 0.00 3.82
348 349 1.687493 GGAGGGAGAGGAGGTGTGG 60.687 68.421 0.00 0.00 0.00 4.17
349 350 1.687493 GAGGGAGAGGAGGTGTGGG 60.687 68.421 0.00 0.00 0.00 4.61
350 351 2.689034 GGGAGAGGAGGTGTGGGG 60.689 72.222 0.00 0.00 0.00 4.96
351 352 2.689034 GGAGAGGAGGTGTGGGGG 60.689 72.222 0.00 0.00 0.00 5.40
352 353 2.450243 GAGAGGAGGTGTGGGGGA 59.550 66.667 0.00 0.00 0.00 4.81
353 354 1.687493 GAGAGGAGGTGTGGGGGAG 60.687 68.421 0.00 0.00 0.00 4.30
354 355 2.689034 GAGGAGGTGTGGGGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
372 373 4.137872 CGGCGCTCGGAAACCCTA 62.138 66.667 7.64 0.00 34.75 3.53
373 374 2.202892 GGCGCTCGGAAACCCTAG 60.203 66.667 7.64 0.00 0.00 3.02
374 375 2.890961 GCGCTCGGAAACCCTAGC 60.891 66.667 0.00 0.00 38.67 3.42
375 376 2.202892 CGCTCGGAAACCCTAGCC 60.203 66.667 0.00 0.00 38.80 3.93
376 377 2.202892 GCTCGGAAACCCTAGCCG 60.203 66.667 0.00 0.00 46.08 5.52
377 378 2.202892 CTCGGAAACCCTAGCCGC 60.203 66.667 0.00 0.00 44.45 6.53
378 379 3.735037 CTCGGAAACCCTAGCCGCC 62.735 68.421 0.00 0.00 44.45 6.13
584 585 5.278169 GCATTCAAGACCATATCAATTCGCT 60.278 40.000 0.00 0.00 0.00 4.93
588 589 4.881019 AGACCATATCAATTCGCTAGCT 57.119 40.909 13.93 0.00 0.00 3.32
589 590 5.984695 AGACCATATCAATTCGCTAGCTA 57.015 39.130 13.93 0.00 0.00 3.32
692 695 3.828451 ACCTTGCTACTAGAACGTACCAA 59.172 43.478 0.00 0.00 0.00 3.67
763 872 6.662414 ATACATTACTCGACCAATGTGTTG 57.338 37.500 21.74 7.00 43.41 3.33
777 886 3.435105 TGTGTTGTGCAAATCAAGTCC 57.565 42.857 0.00 0.00 0.00 3.85
781 890 2.064434 TGTGCAAATCAAGTCCCACA 57.936 45.000 0.00 0.00 0.00 4.17
792 901 2.899838 TCCCACACACAGCGCAAC 60.900 61.111 11.47 0.00 0.00 4.17
988 1123 4.380087 CGATCGATCTCAAGTTATCAACCG 59.620 45.833 22.43 0.93 0.00 4.44
994 1129 2.416547 CTCAAGTTATCAACCGGTGCTG 59.583 50.000 8.52 3.18 0.00 4.41
1307 1448 9.905713 ATGGAGAAATAAAGAAGTATGCAAGTA 57.094 29.630 0.00 0.00 0.00 2.24
1443 1586 8.141835 TCGTATAATAATATGGATGCATGCAC 57.858 34.615 25.37 16.53 0.00 4.57
1505 1655 0.246360 TCGTGTGCTTGATCGGTCAT 59.754 50.000 0.00 0.00 33.56 3.06
1563 1742 4.101114 TCCAGGGTAGATTAAGACAAGCA 58.899 43.478 0.00 0.00 0.00 3.91
1832 3962 2.805353 CTGCCGAACCAGACGTCG 60.805 66.667 10.46 5.16 34.77 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.745845 CTGGATCTGGCGGAGTTTGG 60.746 60.000 1.04 0.00 0.00 3.28
1 2 1.372087 GCTGGATCTGGCGGAGTTTG 61.372 60.000 1.04 0.00 0.00 2.93
2 3 1.078143 GCTGGATCTGGCGGAGTTT 60.078 57.895 1.04 0.00 0.00 2.66
3 4 2.586792 GCTGGATCTGGCGGAGTT 59.413 61.111 1.04 0.00 0.00 3.01
4 5 3.842923 CGCTGGATCTGGCGGAGT 61.843 66.667 19.49 0.00 46.42 3.85
9 10 2.109126 GTTGGTCGCTGGATCTGGC 61.109 63.158 0.00 0.00 0.00 4.85
10 11 1.450312 GGTTGGTCGCTGGATCTGG 60.450 63.158 0.00 0.00 0.00 3.86
11 12 1.811266 CGGTTGGTCGCTGGATCTG 60.811 63.158 0.00 0.00 0.00 2.90
12 13 2.579201 CGGTTGGTCGCTGGATCT 59.421 61.111 0.00 0.00 0.00 2.75
20 21 4.367023 TCTTCCCGCGGTTGGTCG 62.367 66.667 26.12 7.54 0.00 4.79
21 22 2.741211 GTCTTCCCGCGGTTGGTC 60.741 66.667 26.12 7.77 0.00 4.02
22 23 3.109592 TTGTCTTCCCGCGGTTGGT 62.110 57.895 26.12 0.00 0.00 3.67
23 24 2.281208 TTGTCTTCCCGCGGTTGG 60.281 61.111 26.12 13.11 0.00 3.77
24 25 2.966309 GCTTGTCTTCCCGCGGTTG 61.966 63.158 26.12 13.56 0.00 3.77
25 26 2.668550 GCTTGTCTTCCCGCGGTT 60.669 61.111 26.12 0.00 0.00 4.44
29 30 3.793144 CTGCGCTTGTCTTCCCGC 61.793 66.667 9.73 0.00 45.99 6.13
30 31 1.630244 CTTCTGCGCTTGTCTTCCCG 61.630 60.000 9.73 0.00 0.00 5.14
31 32 1.916697 GCTTCTGCGCTTGTCTTCCC 61.917 60.000 9.73 0.00 0.00 3.97
32 33 1.499502 GCTTCTGCGCTTGTCTTCC 59.500 57.895 9.73 0.00 0.00 3.46
44 45 2.303549 ATTCGCTCCCTCCGCTTCTG 62.304 60.000 0.00 0.00 0.00 3.02
45 46 1.617947 AATTCGCTCCCTCCGCTTCT 61.618 55.000 0.00 0.00 0.00 2.85
46 47 0.104304 TAATTCGCTCCCTCCGCTTC 59.896 55.000 0.00 0.00 0.00 3.86
47 48 0.105039 CTAATTCGCTCCCTCCGCTT 59.895 55.000 0.00 0.00 0.00 4.68
48 49 1.742768 CTAATTCGCTCCCTCCGCT 59.257 57.895 0.00 0.00 0.00 5.52
49 50 1.301009 CCTAATTCGCTCCCTCCGC 60.301 63.158 0.00 0.00 0.00 5.54
50 51 1.367840 CCCTAATTCGCTCCCTCCG 59.632 63.158 0.00 0.00 0.00 4.63
51 52 1.755384 CCCCTAATTCGCTCCCTCC 59.245 63.158 0.00 0.00 0.00 4.30
52 53 1.071642 GCCCCTAATTCGCTCCCTC 59.928 63.158 0.00 0.00 0.00 4.30
53 54 2.808206 CGCCCCTAATTCGCTCCCT 61.808 63.158 0.00 0.00 0.00 4.20
54 55 2.280865 CGCCCCTAATTCGCTCCC 60.281 66.667 0.00 0.00 0.00 4.30
55 56 2.280865 CCGCCCCTAATTCGCTCC 60.281 66.667 0.00 0.00 0.00 4.70
56 57 2.973052 GCCGCCCCTAATTCGCTC 60.973 66.667 0.00 0.00 0.00 5.03
57 58 2.830186 TTTGCCGCCCCTAATTCGCT 62.830 55.000 0.00 0.00 0.00 4.93
58 59 2.411504 TTTGCCGCCCCTAATTCGC 61.412 57.895 0.00 0.00 0.00 4.70
59 60 1.431845 GTTTGCCGCCCCTAATTCG 59.568 57.895 0.00 0.00 0.00 3.34
60 61 0.683179 AGGTTTGCCGCCCCTAATTC 60.683 55.000 0.00 0.00 40.50 2.17
61 62 0.683179 GAGGTTTGCCGCCCCTAATT 60.683 55.000 0.00 0.00 40.50 1.40
62 63 1.076995 GAGGTTTGCCGCCCCTAAT 60.077 57.895 0.00 0.00 40.50 1.73
63 64 2.353573 GAGGTTTGCCGCCCCTAA 59.646 61.111 0.00 0.00 40.50 2.69
69 70 1.078143 AGATCTGGAGGTTTGCCGC 60.078 57.895 0.00 0.00 40.50 6.53
70 71 2.772739 CAGATCTGGAGGTTTGCCG 58.227 57.895 15.38 0.00 40.50 5.69
81 82 1.208052 TCCTTTTCCTCGCCAGATCTG 59.792 52.381 16.24 16.24 0.00 2.90
82 83 1.484240 CTCCTTTTCCTCGCCAGATCT 59.516 52.381 0.00 0.00 0.00 2.75
83 84 1.474143 CCTCCTTTTCCTCGCCAGATC 60.474 57.143 0.00 0.00 0.00 2.75
84 85 0.543749 CCTCCTTTTCCTCGCCAGAT 59.456 55.000 0.00 0.00 0.00 2.90
85 86 1.983224 CCTCCTTTTCCTCGCCAGA 59.017 57.895 0.00 0.00 0.00 3.86
86 87 1.746991 GCCTCCTTTTCCTCGCCAG 60.747 63.158 0.00 0.00 0.00 4.85
87 88 2.351276 GCCTCCTTTTCCTCGCCA 59.649 61.111 0.00 0.00 0.00 5.69
88 89 2.438614 GGCCTCCTTTTCCTCGCC 60.439 66.667 0.00 0.00 0.00 5.54
89 90 1.450491 GAGGCCTCCTTTTCCTCGC 60.450 63.158 23.19 0.00 37.28 5.03
90 91 1.222113 GGAGGCCTCCTTTTCCTCG 59.778 63.158 39.99 0.00 45.57 4.63
100 101 1.219393 GCTACAGTGTGGAGGCCTC 59.781 63.158 25.59 25.59 0.00 4.70
101 102 3.393360 GCTACAGTGTGGAGGCCT 58.607 61.111 3.86 3.86 0.00 5.19
104 105 1.296715 GGTGGCTACAGTGTGGAGG 59.703 63.158 11.32 0.00 0.00 4.30
105 106 0.036952 CTGGTGGCTACAGTGTGGAG 60.037 60.000 11.32 0.00 0.00 3.86
106 107 1.480212 CCTGGTGGCTACAGTGTGGA 61.480 60.000 11.32 0.00 34.16 4.02
107 108 1.003355 CCTGGTGGCTACAGTGTGG 60.003 63.158 5.88 3.64 34.16 4.17
108 109 4.701663 CCTGGTGGCTACAGTGTG 57.298 61.111 5.88 0.00 34.16 3.82
148 149 4.803426 GGCTGGCGTCCTCGACTG 62.803 72.222 0.00 0.00 46.49 3.51
150 151 4.803426 CTGGCTGGCGTCCTCGAC 62.803 72.222 0.00 0.00 46.54 4.20
152 153 4.504916 CTCTGGCTGGCGTCCTCG 62.505 72.222 0.00 0.00 40.37 4.63
153 154 4.828925 GCTCTGGCTGGCGTCCTC 62.829 72.222 0.00 0.00 35.22 3.71
185 186 2.098831 GTCGCCGTTAGCCCTGAAC 61.099 63.158 0.00 0.00 38.78 3.18
186 187 2.263540 GTCGCCGTTAGCCCTGAA 59.736 61.111 0.00 0.00 38.78 3.02
187 188 4.124351 CGTCGCCGTTAGCCCTGA 62.124 66.667 0.00 0.00 38.78 3.86
233 234 1.005156 GCAGCGGAGGATCTGGATC 60.005 63.158 2.24 2.24 43.35 3.36
234 235 1.756408 CTGCAGCGGAGGATCTGGAT 61.756 60.000 0.00 0.00 43.35 3.41
235 236 2.364186 TGCAGCGGAGGATCTGGA 60.364 61.111 0.00 0.00 43.35 3.86
236 237 2.108566 CTGCAGCGGAGGATCTGG 59.891 66.667 0.00 0.00 43.35 3.86
237 238 2.108566 CCTGCAGCGGAGGATCTG 59.891 66.667 8.66 0.00 46.81 2.90
238 239 2.042537 TCCTGCAGCGGAGGATCT 60.043 61.111 8.66 0.00 34.49 2.75
239 240 2.420890 CTCCTGCAGCGGAGGATC 59.579 66.667 19.84 0.00 45.53 3.36
248 249 4.504916 CCCTCGTCGCTCCTGCAG 62.505 72.222 6.78 6.78 39.64 4.41
313 314 3.374402 CTCGTCGCCACCTGAGGT 61.374 66.667 0.00 0.00 35.62 3.85
314 315 4.135153 CCTCGTCGCCACCTGAGG 62.135 72.222 0.00 0.00 41.82 3.86
315 316 3.057547 CTCCTCGTCGCCACCTGAG 62.058 68.421 0.00 0.00 0.00 3.35
316 317 3.062466 CTCCTCGTCGCCACCTGA 61.062 66.667 0.00 0.00 0.00 3.86
317 318 4.135153 CCTCCTCGTCGCCACCTG 62.135 72.222 0.00 0.00 0.00 4.00
320 321 3.827898 CTCCCTCCTCGTCGCCAC 61.828 72.222 0.00 0.00 0.00 5.01
321 322 3.997400 CTCTCCCTCCTCGTCGCCA 62.997 68.421 0.00 0.00 0.00 5.69
322 323 3.213402 CTCTCCCTCCTCGTCGCC 61.213 72.222 0.00 0.00 0.00 5.54
323 324 3.213402 CCTCTCCCTCCTCGTCGC 61.213 72.222 0.00 0.00 0.00 5.19
324 325 1.525077 CTCCTCTCCCTCCTCGTCG 60.525 68.421 0.00 0.00 0.00 5.12
325 326 1.152839 CCTCCTCTCCCTCCTCGTC 60.153 68.421 0.00 0.00 0.00 4.20
326 327 1.931705 ACCTCCTCTCCCTCCTCGT 60.932 63.158 0.00 0.00 0.00 4.18
327 328 1.454847 CACCTCCTCTCCCTCCTCG 60.455 68.421 0.00 0.00 0.00 4.63
328 329 0.686112 CACACCTCCTCTCCCTCCTC 60.686 65.000 0.00 0.00 0.00 3.71
329 330 1.390125 CACACCTCCTCTCCCTCCT 59.610 63.158 0.00 0.00 0.00 3.69
330 331 1.687493 CCACACCTCCTCTCCCTCC 60.687 68.421 0.00 0.00 0.00 4.30
331 332 1.687493 CCCACACCTCCTCTCCCTC 60.687 68.421 0.00 0.00 0.00 4.30
332 333 2.452114 CCCACACCTCCTCTCCCT 59.548 66.667 0.00 0.00 0.00 4.20
333 334 2.689034 CCCCACACCTCCTCTCCC 60.689 72.222 0.00 0.00 0.00 4.30
334 335 2.689034 CCCCCACACCTCCTCTCC 60.689 72.222 0.00 0.00 0.00 3.71
335 336 1.687493 CTCCCCCACACCTCCTCTC 60.687 68.421 0.00 0.00 0.00 3.20
336 337 2.452114 CTCCCCCACACCTCCTCT 59.548 66.667 0.00 0.00 0.00 3.69
337 338 2.689034 CCTCCCCCACACCTCCTC 60.689 72.222 0.00 0.00 0.00 3.71
355 356 4.137872 TAGGGTTTCCGAGCGCCG 62.138 66.667 2.29 7.65 38.33 6.46
356 357 2.202892 CTAGGGTTTCCGAGCGCC 60.203 66.667 2.29 0.00 38.33 6.53
360 361 2.202892 GCGGCTAGGGTTTCCGAG 60.203 66.667 9.59 0.00 45.53 4.63
361 362 3.777910 GGCGGCTAGGGTTTCCGA 61.778 66.667 9.59 0.00 45.53 4.55
393 394 2.298411 TTATTTACCGGTCGCCTGAC 57.702 50.000 12.40 0.00 44.72 3.51
394 395 4.877378 ATATTATTTACCGGTCGCCTGA 57.123 40.909 12.40 0.00 0.00 3.86
395 396 7.977853 ACTATAATATTATTTACCGGTCGCCTG 59.022 37.037 12.40 0.00 0.00 4.85
396 397 8.071177 ACTATAATATTATTTACCGGTCGCCT 57.929 34.615 12.40 0.00 0.00 5.52
397 398 9.801873 TTACTATAATATTATTTACCGGTCGCC 57.198 33.333 12.40 0.00 0.00 5.54
692 695 5.537674 GGTAGCATCTTCATTTTCCATCCAT 59.462 40.000 0.00 0.00 0.00 3.41
709 713 5.871834 AGAGAGATTACGAGTAGGTAGCAT 58.128 41.667 0.00 0.00 0.00 3.79
746 855 2.139917 GCACAACACATTGGTCGAGTA 58.860 47.619 0.00 0.00 40.42 2.59
763 872 1.680735 TGTGTGGGACTTGATTTGCAC 59.319 47.619 0.00 0.00 0.00 4.57
777 886 0.179140 AAAAGTTGCGCTGTGTGTGG 60.179 50.000 9.73 0.00 0.00 4.17
792 901 4.495349 CGATGATTGACAGGCTAGCAAAAG 60.495 45.833 18.24 5.24 0.00 2.27
988 1123 0.723981 GAACTCATCTTCGCAGCACC 59.276 55.000 0.00 0.00 0.00 5.01
1307 1448 3.350219 AGGACCGATTAAGCACACATT 57.650 42.857 0.00 0.00 0.00 2.71
1443 1586 1.402968 CCGGTCTCTGCATCAAAATGG 59.597 52.381 0.00 0.00 33.19 3.16
1505 1655 5.709631 AGTTTGGCACATACACATACATGAA 59.290 36.000 0.00 0.00 42.66 2.57
1832 3962 4.112341 ACGTCGCCGGTAGCACTC 62.112 66.667 1.90 0.00 44.04 3.51
1877 4007 2.286732 AGCTTGGGAGGGATGCCT 60.287 61.111 4.97 4.97 0.00 4.75


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

AutoCloner maintained by Alex Coulton.