Multiple sequence alignment - TraesCS5A01G097300

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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 TraesCS5A01G097300 chr5A 100.000 2440 0 0 1 2440 138082189 138079750 0.000000e+00 4506.0
1 TraesCS5A01G097300 chr5A 90.209 1195 113 2 786 1977 469664656 469665849 0.000000e+00 1555.0
2 TraesCS5A01G097300 chr5A 100.000 291 0 0 2682 2972 138079508 138079218 3.370000e-149 538.0
3 TraesCS5A01G097300 chr5B 95.460 1586 72 0 392 1977 491849373 491850958 0.000000e+00 2531.0
4 TraesCS5A01G097300 chr5B 95.334 1586 74 0 392 1977 419520889 419522474 0.000000e+00 2519.0
5 TraesCS5A01G097300 chr5B 94.175 309 18 0 96 404 419520521 419520829 3.470000e-129 472.0
6 TraesCS5A01G097300 chr5B 90.291 309 20 4 96 404 491849015 491849313 2.150000e-106 396.0
7 TraesCS5A01G097300 chr5B 95.000 220 11 0 1989 2208 419522552 419522771 2.190000e-91 346.0
8 TraesCS5A01G097300 chr5B 94.977 219 10 1 1989 2207 491851036 491851253 2.840000e-90 342.0
9 TraesCS5A01G097300 chr3A 95.340 1588 71 1 392 1979 34994040 34992456 0.000000e+00 2519.0
10 TraesCS5A01G097300 chr3A 93.291 313 21 0 94 406 34994401 34994089 2.090000e-126 462.0
11 TraesCS5A01G097300 chr3A 93.991 233 14 0 1977 2209 34980919 34980687 1.310000e-93 353.0
12 TraesCS5A01G097300 chr2D 95.334 1586 74 0 392 1977 617965616 617967201 0.000000e+00 2519.0
13 TraesCS5A01G097300 chr2D 94.175 309 18 0 96 404 617965248 617965556 3.470000e-129 472.0
14 TraesCS5A01G097300 chr2D 96.364 220 8 0 1989 2208 116829788 116829569 2.180000e-96 363.0
15 TraesCS5A01G097300 chr2D 94.643 224 10 2 1989 2212 617967279 617967500 2.190000e-91 346.0
16 TraesCS5A01G097300 chr2D 86.709 316 35 4 92 404 101557302 101557613 7.890000e-91 344.0
17 TraesCS5A01G097300 chr2B 95.334 1586 74 0 392 1977 795980628 795982213 0.000000e+00 2519.0
18 TraesCS5A01G097300 chr2B 94.175 309 18 0 96 404 795980260 795980568 3.470000e-129 472.0
19 TraesCS5A01G097300 chr2B 94.954 218 10 1 1989 2206 795982291 795982507 1.020000e-89 340.0
20 TraesCS5A01G097300 chr5D 90.468 1238 110 7 743 1977 467262774 467264006 0.000000e+00 1626.0
21 TraesCS5A01G097300 chr5D 87.647 340 32 5 403 740 467262389 467262720 1.290000e-103 387.0
22 TraesCS5A01G097300 chr5D 87.907 215 22 4 96 309 467262123 467262334 1.770000e-62 250.0
23 TraesCS5A01G097300 chr7B 90.073 1229 118 2 743 1967 59646075 59644847 0.000000e+00 1591.0
24 TraesCS5A01G097300 chr7B 89.482 1236 122 6 743 1977 664079262 664078034 0.000000e+00 1555.0
25 TraesCS5A01G097300 chr7B 83.871 341 34 3 403 743 59646445 59646126 3.720000e-79 305.0
26 TraesCS5A01G097300 chr7B 90.783 217 18 2 96 312 59646711 59646497 3.750000e-74 289.0
27 TraesCS5A01G097300 chr7B 80.466 343 32 14 403 743 664079622 664079313 2.300000e-56 230.0
28 TraesCS5A01G097300 chr4B 95.533 291 11 2 2682 2972 59832152 59831864 5.800000e-127 464.0
29 TraesCS5A01G097300 chr4B 95.111 225 11 0 2216 2440 59832488 59832264 3.640000e-94 355.0
30 TraesCS5A01G097300 chr1B 95.533 291 12 1 2682 2972 167884660 167884371 5.800000e-127 464.0
31 TraesCS5A01G097300 chr1B 94.222 225 13 0 2216 2440 167884996 167884772 7.890000e-91 344.0
32 TraesCS5A01G097300 chr6D 96.818 220 7 0 1989 2208 39090285 39090504 4.680000e-98 368.0
33 TraesCS5A01G097300 chr4A 89.369 301 20 5 2682 2972 677617544 677617842 4.680000e-98 368.0
34 TraesCS5A01G097300 chr4A 97.087 103 2 1 2217 2319 677617350 677617451 3.940000e-39 172.0
35 TraesCS5A01G097300 chr4A 97.222 36 0 1 1 36 677617312 677617346 3.200000e-05 60.2
36 TraesCS5A01G097300 chr6B 90.411 292 9 7 2682 2972 701237749 701237476 1.680000e-97 366.0
37 TraesCS5A01G097300 chr6B 95.154 227 11 0 2214 2440 701238087 701237861 2.820000e-95 359.0
38 TraesCS5A01G097300 chrUn 95.890 219 9 0 1989 2207 8839892 8839674 3.640000e-94 355.0
39 TraesCS5A01G097300 chr3B 93.182 220 15 0 1989 2208 98009330 98009549 1.030000e-84 324.0
40 TraesCS5A01G097300 chr7A 89.140 221 22 2 596 816 727383508 727383290 1.050000e-69 274.0


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 TraesCS5A01G097300 chr5A 138079218 138082189 2971 True 2522.000000 4506 100.000000 1 2972 2 chr5A.!!$R1 2971
1 TraesCS5A01G097300 chr5A 469664656 469665849 1193 False 1555.000000 1555 90.209000 786 1977 1 chr5A.!!$F1 1191
2 TraesCS5A01G097300 chr5B 419520521 419522771 2250 False 1112.333333 2519 94.836333 96 2208 3 chr5B.!!$F1 2112
3 TraesCS5A01G097300 chr5B 491849015 491851253 2238 False 1089.666667 2531 93.576000 96 2207 3 chr5B.!!$F2 2111
4 TraesCS5A01G097300 chr3A 34992456 34994401 1945 True 1490.500000 2519 94.315500 94 1979 2 chr3A.!!$R2 1885
5 TraesCS5A01G097300 chr2D 617965248 617967500 2252 False 1112.333333 2519 94.717333 96 2212 3 chr2D.!!$F2 2116
6 TraesCS5A01G097300 chr2B 795980260 795982507 2247 False 1110.333333 2519 94.821000 96 2206 3 chr2B.!!$F1 2110
7 TraesCS5A01G097300 chr5D 467262123 467264006 1883 False 754.333333 1626 88.674000 96 1977 3 chr5D.!!$F1 1881
8 TraesCS5A01G097300 chr7B 664078034 664079622 1588 True 892.500000 1555 84.974000 403 1977 2 chr7B.!!$R2 1574
9 TraesCS5A01G097300 chr7B 59644847 59646711 1864 True 728.333333 1591 88.242333 96 1967 3 chr7B.!!$R1 1871
10 TraesCS5A01G097300 chr4B 59831864 59832488 624 True 409.500000 464 95.322000 2216 2972 2 chr4B.!!$R1 756
11 TraesCS5A01G097300 chr1B 167884371 167884996 625 True 404.000000 464 94.877500 2216 2972 2 chr1B.!!$R1 756
12 TraesCS5A01G097300 chr4A 677617312 677617842 530 False 200.066667 368 94.559333 1 2972 3 chr4A.!!$F1 2971
13 TraesCS5A01G097300 chr6B 701237476 701238087 611 True 362.500000 366 92.782500 2214 2972 2 chr6B.!!$R1 758

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
863 999 0.036388 CCGCCTCCTGTAGCTTTTCA 60.036 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2124 0.099082 TCGCAACGAAACCACCAAAC 59.901 50.0 0.0 0.0 31.06 2.93 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
31 32 9.436957 ACTATCTTATTCAGAACGAAAATGTGT 57.563 29.630 0.00 0.00 37.12 3.72
38 39 6.403333 TCAGAACGAAAATGTGTATAGTGC 57.597 37.500 0.00 0.00 0.00 4.40
39 40 5.061684 TCAGAACGAAAATGTGTATAGTGCG 59.938 40.000 0.00 0.00 0.00 5.34
40 41 3.651562 ACGAAAATGTGTATAGTGCGC 57.348 42.857 0.00 0.00 0.00 6.09
41 42 2.997303 ACGAAAATGTGTATAGTGCGCA 59.003 40.909 5.66 5.66 0.00 6.09
42 43 3.621268 ACGAAAATGTGTATAGTGCGCAT 59.379 39.130 15.91 5.37 38.54 4.73
43 44 3.961860 CGAAAATGTGTATAGTGCGCATG 59.038 43.478 15.91 0.00 37.18 4.06
44 45 3.969117 AAATGTGTATAGTGCGCATGG 57.031 42.857 15.91 0.00 37.18 3.66
45 46 1.882912 ATGTGTATAGTGCGCATGGG 58.117 50.000 15.91 5.19 35.95 4.00
46 47 0.539518 TGTGTATAGTGCGCATGGGT 59.460 50.000 15.91 2.77 0.00 4.51
47 48 1.757699 TGTGTATAGTGCGCATGGGTA 59.242 47.619 15.91 3.70 0.00 3.69
48 49 2.168728 TGTGTATAGTGCGCATGGGTAA 59.831 45.455 15.91 0.00 0.00 2.85
49 50 3.199677 GTGTATAGTGCGCATGGGTAAA 58.800 45.455 15.91 0.00 0.00 2.01
50 51 3.623960 GTGTATAGTGCGCATGGGTAAAA 59.376 43.478 15.91 0.00 0.00 1.52
51 52 3.874543 TGTATAGTGCGCATGGGTAAAAG 59.125 43.478 15.91 0.00 0.00 2.27
52 53 2.772077 TAGTGCGCATGGGTAAAAGA 57.228 45.000 15.91 0.00 0.00 2.52
53 54 1.904287 AGTGCGCATGGGTAAAAGAA 58.096 45.000 15.91 0.00 0.00 2.52
54 55 2.446435 AGTGCGCATGGGTAAAAGAAT 58.554 42.857 15.91 0.00 0.00 2.40
55 56 2.423538 AGTGCGCATGGGTAAAAGAATC 59.576 45.455 15.91 0.00 0.00 2.52
56 57 1.400142 TGCGCATGGGTAAAAGAATCG 59.600 47.619 5.66 0.00 0.00 3.34
57 58 1.400494 GCGCATGGGTAAAAGAATCGT 59.600 47.619 11.82 0.00 0.00 3.73
58 59 2.610374 GCGCATGGGTAAAAGAATCGTA 59.390 45.455 11.82 0.00 0.00 3.43
59 60 3.250040 GCGCATGGGTAAAAGAATCGTAT 59.750 43.478 11.82 0.00 0.00 3.06
60 61 4.261031 GCGCATGGGTAAAAGAATCGTATT 60.261 41.667 11.82 0.00 0.00 1.89
61 62 5.204833 CGCATGGGTAAAAGAATCGTATTG 58.795 41.667 0.68 0.00 0.00 1.90
62 63 5.519722 GCATGGGTAAAAGAATCGTATTGG 58.480 41.667 0.00 0.00 0.00 3.16
63 64 5.298276 GCATGGGTAAAAGAATCGTATTGGA 59.702 40.000 0.00 0.00 0.00 3.53
64 65 6.513393 GCATGGGTAAAAGAATCGTATTGGAG 60.513 42.308 0.00 0.00 0.00 3.86
65 66 5.433526 TGGGTAAAAGAATCGTATTGGAGG 58.566 41.667 0.00 0.00 0.00 4.30
66 67 4.820173 GGGTAAAAGAATCGTATTGGAGGG 59.180 45.833 0.00 0.00 0.00 4.30
67 68 4.820173 GGTAAAAGAATCGTATTGGAGGGG 59.180 45.833 0.00 0.00 0.00 4.79
68 69 2.640316 AAGAATCGTATTGGAGGGGC 57.360 50.000 0.00 0.00 0.00 5.80
69 70 0.765510 AGAATCGTATTGGAGGGGCC 59.234 55.000 0.00 0.00 37.10 5.80
70 71 0.765510 GAATCGTATTGGAGGGGCCT 59.234 55.000 0.84 0.00 37.63 5.19
71 72 1.975680 GAATCGTATTGGAGGGGCCTA 59.024 52.381 0.84 0.00 37.63 3.93
72 73 1.349067 ATCGTATTGGAGGGGCCTAC 58.651 55.000 0.84 0.00 37.63 3.18
73 74 0.263765 TCGTATTGGAGGGGCCTACT 59.736 55.000 0.84 0.28 37.63 2.57
74 75 0.680061 CGTATTGGAGGGGCCTACTC 59.320 60.000 16.61 16.61 37.63 2.59
75 76 1.758123 CGTATTGGAGGGGCCTACTCT 60.758 57.143 21.74 7.80 37.63 3.24
76 77 2.409570 GTATTGGAGGGGCCTACTCTT 58.590 52.381 21.74 12.72 37.63 2.85
77 78 1.216990 ATTGGAGGGGCCTACTCTTG 58.783 55.000 21.74 0.00 37.63 3.02
78 79 1.562672 TTGGAGGGGCCTACTCTTGC 61.563 60.000 21.74 10.36 37.63 4.01
84 85 3.478540 GGCCTACTCTTGCCGATTT 57.521 52.632 0.00 0.00 38.00 2.17
85 86 1.300481 GGCCTACTCTTGCCGATTTC 58.700 55.000 0.00 0.00 38.00 2.17
86 87 1.134371 GGCCTACTCTTGCCGATTTCT 60.134 52.381 0.00 0.00 38.00 2.52
87 88 2.205911 GCCTACTCTTGCCGATTTCTC 58.794 52.381 0.00 0.00 0.00 2.87
88 89 2.159028 GCCTACTCTTGCCGATTTCTCT 60.159 50.000 0.00 0.00 0.00 3.10
89 90 3.068307 GCCTACTCTTGCCGATTTCTCTA 59.932 47.826 0.00 0.00 0.00 2.43
90 91 4.794655 GCCTACTCTTGCCGATTTCTCTAG 60.795 50.000 0.00 0.00 0.00 2.43
91 92 4.580995 CCTACTCTTGCCGATTTCTCTAGA 59.419 45.833 0.00 0.00 0.00 2.43
92 93 4.647424 ACTCTTGCCGATTTCTCTAGAG 57.353 45.455 13.98 13.98 35.09 2.43
222 223 3.953775 CCCTCGTTGCCTGTGGGT 61.954 66.667 0.00 0.00 35.79 4.51
228 229 0.457851 CGTTGCCTGTGGGTTTCAAA 59.542 50.000 0.00 0.00 34.45 2.69
260 261 1.007271 CGCCGCCATCTCTATCGTT 60.007 57.895 0.00 0.00 0.00 3.85
372 373 1.074775 GGTGTTGGTGATGCCTCCA 59.925 57.895 0.00 0.00 38.35 3.86
383 384 4.212913 GCCTCCATGCGAGCTCGA 62.213 66.667 38.74 23.38 43.02 4.04
463 536 1.216444 GCTGCTGTCGACATCCTGA 59.784 57.895 20.40 0.00 0.00 3.86
527 600 1.067416 GCTCGCGTCCATCACCATA 59.933 57.895 5.77 0.00 0.00 2.74
543 616 0.539438 CATAGAGCTCGCTCCCCTCT 60.539 60.000 14.83 0.00 43.70 3.69
782 917 2.768253 TGCTTCCATCGTGATGAAGT 57.232 45.000 11.35 0.00 41.20 3.01
863 999 0.036388 CCGCCTCCTGTAGCTTTTCA 60.036 55.000 0.00 0.00 0.00 2.69
893 1029 2.819984 ATCAATGTGCGGCGTTCCCT 62.820 55.000 9.37 0.00 0.00 4.20
942 1078 0.959553 GGTGTCTCTGTCGAGGTCAA 59.040 55.000 0.00 0.00 37.86 3.18
956 1092 1.372499 GTCAACGCGCACACTCCTA 60.372 57.895 5.73 0.00 0.00 2.94
1002 1138 1.293924 GCCTTCGATCTGGACACATG 58.706 55.000 4.14 0.00 0.00 3.21
1003 1139 1.134699 GCCTTCGATCTGGACACATGA 60.135 52.381 0.00 0.00 0.00 3.07
1126 1262 1.142465 AGTTCCGGTCTATCTCGGCTA 59.858 52.381 0.00 0.00 45.31 3.93
1387 1523 0.758734 TGCTACAGCCTGTCAGTTGT 59.241 50.000 0.00 10.86 41.18 3.32
1550 1686 0.193574 TCTCTTGGAGGGGACTTGGT 59.806 55.000 0.00 0.00 44.43 3.67
1609 1745 2.203337 AGCCGCTTGCCTTTGTGA 60.203 55.556 0.00 0.00 42.71 3.58
1818 1961 2.670934 CTTGGCCGCTTGCTCACT 60.671 61.111 0.00 0.00 40.92 3.41
1896 2039 2.823747 GGAGGTTTCTACGGGCAAAATT 59.176 45.455 0.00 0.00 0.00 1.82
1903 2046 6.072342 GGTTTCTACGGGCAAAATTAAGAAGA 60.072 38.462 0.00 0.00 0.00 2.87
1912 2055 6.533012 GGGCAAAATTAAGAAGATGAAGAAGC 59.467 38.462 0.00 0.00 0.00 3.86
1923 2066 4.555689 AGATGAAGAAGCCTATCAGGAGT 58.444 43.478 0.00 0.00 37.67 3.85
1941 2084 5.304101 CAGGAGTATAGGCAAGAAGACTGAT 59.696 44.000 0.00 0.00 35.25 2.90
1958 2101 2.868583 CTGATGTCATTAGGAAGGCGTG 59.131 50.000 0.00 0.00 0.00 5.34
1979 2122 1.718757 GCGGCTGCTTAATGGAGTGG 61.719 60.000 11.21 0.00 38.39 4.00
1980 2123 1.718757 CGGCTGCTTAATGGAGTGGC 61.719 60.000 0.00 0.00 36.43 5.01
1981 2124 1.718757 GGCTGCTTAATGGAGTGGCG 61.719 60.000 0.00 0.00 36.43 5.69
1983 2126 1.453155 CTGCTTAATGGAGTGGCGTT 58.547 50.000 0.00 0.00 0.00 4.84
1984 2127 1.812571 CTGCTTAATGGAGTGGCGTTT 59.187 47.619 0.00 0.00 0.00 3.60
1986 2129 1.135402 GCTTAATGGAGTGGCGTTTGG 60.135 52.381 0.00 0.00 0.00 3.28
1987 2130 2.159382 CTTAATGGAGTGGCGTTTGGT 58.841 47.619 0.00 0.00 0.00 3.67
2011 2220 3.617540 TTCGTTGCGATGTCATTTTGT 57.382 38.095 0.00 0.00 35.23 2.83
2017 2226 1.812571 GCGATGTCATTTTGTGAGGGT 59.187 47.619 0.00 0.00 37.56 4.34
2020 2229 4.229096 CGATGTCATTTTGTGAGGGTTTG 58.771 43.478 0.00 0.00 37.56 2.93
2058 2267 2.619177 TGTATGTTTGTTGGGTTGACCG 59.381 45.455 0.00 0.00 44.64 4.79
2120 2329 7.041372 GCATGTGGTCTATATGTATCGGTTTTT 60.041 37.037 0.00 0.00 31.17 1.94
2125 2334 5.761234 GTCTATATGTATCGGTTTTTGCCCA 59.239 40.000 0.00 0.00 0.00 5.36
2133 2342 1.577468 GGTTTTTGCCCAGTTTTCCG 58.423 50.000 0.00 0.00 0.00 4.30
2157 2366 7.312899 CGTTAATTAACTGGGCAATTCTCTTT 58.687 34.615 22.57 0.00 34.12 2.52
2199 2408 3.121362 GCAAATCTTTTGCCTTCGTTTCG 60.121 43.478 12.74 0.00 39.38 3.46
2256 2466 9.656040 TGATTAATTTGCATGCAATAGAAGTTT 57.344 25.926 32.27 18.09 35.70 2.66
2309 2519 5.724328 TGGTGCTACTCATAAGAACTTCAG 58.276 41.667 0.00 0.00 0.00 3.02
2336 2546 9.150348 GAAAGAAAAGAAAAAGGAACATGTTGA 57.850 29.630 17.58 0.00 0.00 3.18
2340 2550 9.706846 GAAAAGAAAAAGGAACATGTTGAATTG 57.293 29.630 17.58 0.00 0.00 2.32
2347 2557 6.422776 AGGAACATGTTGAATTGATACGTC 57.577 37.500 17.58 0.00 0.00 4.34
2434 2644 5.105554 GGAGCTCTAAGTTGAGTCTGAATCA 60.106 44.000 14.64 3.33 36.51 2.57
2738 2948 5.244178 ACCCTTCGCTAGATGGTTATTAGAG 59.756 44.000 0.00 0.00 39.36 2.43
2743 2953 5.241064 TCGCTAGATGGTTATTAGAGGTCAC 59.759 44.000 0.00 0.00 0.00 3.67
2759 2969 3.458487 AGGTCACTGTTGGTTAGGAAAGT 59.542 43.478 0.00 0.00 0.00 2.66
2815 3025 5.591877 GCCATTTATTCAGTGGACAGAATCT 59.408 40.000 1.10 0.00 34.56 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.409718 TCTTTTACCCATGCGCACTATA 57.590 40.909 14.90 0.00 0.00 1.31
32 33 3.275617 TCTTTTACCCATGCGCACTAT 57.724 42.857 14.90 0.46 0.00 2.12
33 34 2.772077 TCTTTTACCCATGCGCACTA 57.228 45.000 14.90 0.00 0.00 2.74
34 35 1.904287 TTCTTTTACCCATGCGCACT 58.096 45.000 14.90 0.00 0.00 4.40
35 36 2.791158 CGATTCTTTTACCCATGCGCAC 60.791 50.000 14.90 0.00 0.00 5.34
36 37 1.400142 CGATTCTTTTACCCATGCGCA 59.600 47.619 14.96 14.96 0.00 6.09
37 38 1.400494 ACGATTCTTTTACCCATGCGC 59.600 47.619 0.00 0.00 0.00 6.09
38 39 5.204833 CAATACGATTCTTTTACCCATGCG 58.795 41.667 0.00 0.00 0.00 4.73
39 40 5.298276 TCCAATACGATTCTTTTACCCATGC 59.702 40.000 0.00 0.00 0.00 4.06
40 41 6.017109 CCTCCAATACGATTCTTTTACCCATG 60.017 42.308 0.00 0.00 0.00 3.66
41 42 6.062095 CCTCCAATACGATTCTTTTACCCAT 58.938 40.000 0.00 0.00 0.00 4.00
42 43 5.433526 CCTCCAATACGATTCTTTTACCCA 58.566 41.667 0.00 0.00 0.00 4.51
43 44 4.820173 CCCTCCAATACGATTCTTTTACCC 59.180 45.833 0.00 0.00 0.00 3.69
44 45 4.820173 CCCCTCCAATACGATTCTTTTACC 59.180 45.833 0.00 0.00 0.00 2.85
45 46 4.275196 GCCCCTCCAATACGATTCTTTTAC 59.725 45.833 0.00 0.00 0.00 2.01
46 47 4.457466 GCCCCTCCAATACGATTCTTTTA 58.543 43.478 0.00 0.00 0.00 1.52
47 48 3.288092 GCCCCTCCAATACGATTCTTTT 58.712 45.455 0.00 0.00 0.00 2.27
48 49 2.422945 GGCCCCTCCAATACGATTCTTT 60.423 50.000 0.00 0.00 34.01 2.52
49 50 1.143073 GGCCCCTCCAATACGATTCTT 59.857 52.381 0.00 0.00 34.01 2.52
50 51 0.765510 GGCCCCTCCAATACGATTCT 59.234 55.000 0.00 0.00 34.01 2.40
51 52 0.765510 AGGCCCCTCCAATACGATTC 59.234 55.000 0.00 0.00 37.29 2.52
52 53 1.697982 GTAGGCCCCTCCAATACGATT 59.302 52.381 0.00 0.00 37.29 3.34
53 54 1.132817 AGTAGGCCCCTCCAATACGAT 60.133 52.381 0.00 0.00 37.29 3.73
54 55 0.263765 AGTAGGCCCCTCCAATACGA 59.736 55.000 0.00 0.00 37.29 3.43
55 56 0.680061 GAGTAGGCCCCTCCAATACG 59.320 60.000 0.00 0.00 37.29 3.06
56 57 2.104669 AGAGTAGGCCCCTCCAATAC 57.895 55.000 14.77 2.54 37.29 1.89
57 58 2.408565 CAAGAGTAGGCCCCTCCAATA 58.591 52.381 14.77 0.00 37.29 1.90
58 59 1.216990 CAAGAGTAGGCCCCTCCAAT 58.783 55.000 14.77 1.66 37.29 3.16
59 60 1.562672 GCAAGAGTAGGCCCCTCCAA 61.563 60.000 14.77 0.00 37.29 3.53
60 61 1.995626 GCAAGAGTAGGCCCCTCCA 60.996 63.158 14.77 0.00 37.29 3.86
61 62 2.747443 GGCAAGAGTAGGCCCCTCC 61.747 68.421 14.77 2.27 44.53 4.30
62 63 2.911928 GGCAAGAGTAGGCCCCTC 59.088 66.667 11.28 11.28 44.53 4.30
66 67 1.134371 AGAAATCGGCAAGAGTAGGCC 60.134 52.381 0.00 0.00 46.80 5.19
67 68 2.159028 AGAGAAATCGGCAAGAGTAGGC 60.159 50.000 0.00 0.00 0.00 3.93
68 69 3.810310 AGAGAAATCGGCAAGAGTAGG 57.190 47.619 0.00 0.00 0.00 3.18
69 70 5.757886 CTCTAGAGAAATCGGCAAGAGTAG 58.242 45.833 15.05 0.00 0.00 2.57
70 71 4.036971 GCTCTAGAGAAATCGGCAAGAGTA 59.963 45.833 24.24 0.00 33.23 2.59
71 72 3.181480 GCTCTAGAGAAATCGGCAAGAGT 60.181 47.826 24.24 0.00 33.23 3.24
72 73 3.181482 TGCTCTAGAGAAATCGGCAAGAG 60.181 47.826 24.24 0.00 33.70 2.85
73 74 2.760650 TGCTCTAGAGAAATCGGCAAGA 59.239 45.455 24.24 0.00 0.00 3.02
74 75 3.122297 CTGCTCTAGAGAAATCGGCAAG 58.878 50.000 24.24 3.95 0.00 4.01
75 76 2.760650 TCTGCTCTAGAGAAATCGGCAA 59.239 45.455 24.24 2.06 0.00 4.52
76 77 2.099921 GTCTGCTCTAGAGAAATCGGCA 59.900 50.000 24.24 11.80 35.70 5.69
77 78 2.544903 GGTCTGCTCTAGAGAAATCGGC 60.545 54.545 24.24 7.43 35.70 5.54
78 79 2.035321 GGGTCTGCTCTAGAGAAATCGG 59.965 54.545 24.24 10.43 35.70 4.18
79 80 2.287308 CGGGTCTGCTCTAGAGAAATCG 60.287 54.545 24.24 13.58 35.70 3.34
80 81 2.952978 TCGGGTCTGCTCTAGAGAAATC 59.047 50.000 24.24 8.44 35.70 2.17
81 82 2.691011 GTCGGGTCTGCTCTAGAGAAAT 59.309 50.000 24.24 0.00 35.70 2.17
82 83 2.093106 GTCGGGTCTGCTCTAGAGAAA 58.907 52.381 24.24 9.51 35.70 2.52
83 84 1.682394 GGTCGGGTCTGCTCTAGAGAA 60.682 57.143 24.24 12.65 35.70 2.87
84 85 0.107116 GGTCGGGTCTGCTCTAGAGA 60.107 60.000 24.24 7.73 35.70 3.10
85 86 1.104577 GGGTCGGGTCTGCTCTAGAG 61.105 65.000 15.85 15.85 35.70 2.43
86 87 1.076923 GGGTCGGGTCTGCTCTAGA 60.077 63.158 0.00 0.00 0.00 2.43
87 88 2.128507 GGGGTCGGGTCTGCTCTAG 61.129 68.421 0.00 0.00 0.00 2.43
88 89 2.043248 GGGGTCGGGTCTGCTCTA 60.043 66.667 0.00 0.00 0.00 2.43
222 223 1.015868 GGACGACAACCGGTTTGAAA 58.984 50.000 19.55 0.00 43.93 2.69
260 261 1.762957 GATCCAGATCTGACCGGGAAA 59.237 52.381 24.62 0.00 35.04 3.13
316 317 3.341629 CTGGGTGGGCAGGTCCAT 61.342 66.667 0.00 0.00 39.26 3.41
358 359 1.750018 CGCATGGAGGCATCACCAA 60.750 57.895 0.00 0.00 43.14 3.67
527 600 2.441901 CAGAGGGGAGCGAGCTCT 60.442 66.667 22.37 5.12 42.38 4.09
780 915 2.887783 ACACTCGAGAACATCAGTCACT 59.112 45.455 21.68 0.00 0.00 3.41
782 917 2.884639 TCACACTCGAGAACATCAGTCA 59.115 45.455 21.68 0.00 0.00 3.41
854 990 1.280710 TGGAAGGGCGATGAAAAGCTA 59.719 47.619 0.00 0.00 0.00 3.32
863 999 1.683943 CACATTGATGGAAGGGCGAT 58.316 50.000 0.00 0.00 0.00 4.58
893 1029 4.069232 CTCTCAGCCACGCCGGAA 62.069 66.667 5.05 0.00 36.56 4.30
942 1078 2.258591 CTGTAGGAGTGTGCGCGT 59.741 61.111 8.43 0.00 0.00 6.01
1002 1138 2.568696 TAGCATGACAGAAGCGAGTC 57.431 50.000 0.00 0.00 35.37 3.36
1003 1139 2.493675 TCTTAGCATGACAGAAGCGAGT 59.506 45.455 0.00 0.00 0.00 4.18
1043 1179 2.409055 GCATGACATTGGAGCGGCA 61.409 57.895 1.45 0.00 0.00 5.69
1126 1262 1.603455 CCACCAACCCGACATGCTT 60.603 57.895 0.00 0.00 0.00 3.91
1197 1333 1.377229 CGCCCTCCCCAAAACACTA 59.623 57.895 0.00 0.00 0.00 2.74
1226 1362 1.614317 GCACCACCTCTAGTTTGGCAT 60.614 52.381 6.87 0.00 33.25 4.40
1550 1686 1.375908 GAGGTCGCAGTTGGCATCA 60.376 57.895 0.00 0.00 45.17 3.07
1818 1961 1.228644 ACAAGCTGCATCCAAGCCA 60.229 52.632 1.02 0.00 0.00 4.75
1896 2039 6.841229 TCCTGATAGGCTTCTTCATCTTCTTA 59.159 38.462 0.00 0.00 34.61 2.10
1903 2046 6.667414 CCTATACTCCTGATAGGCTTCTTCAT 59.333 42.308 0.00 0.00 39.58 2.57
1912 2055 6.013379 TCTTCTTGCCTATACTCCTGATAGG 58.987 44.000 4.60 4.60 46.10 2.57
1923 2066 6.737720 ATGACATCAGTCTTCTTGCCTATA 57.262 37.500 0.00 0.00 45.20 1.31
1941 2084 0.739462 CGCACGCCTTCCTAATGACA 60.739 55.000 0.00 0.00 0.00 3.58
1958 2101 3.173390 CTCCATTAAGCAGCCGCGC 62.173 63.158 0.00 0.00 45.49 6.86
1979 2122 1.476235 GCAACGAAACCACCAAACGC 61.476 55.000 0.00 0.00 0.00 4.84
1980 2123 1.197368 CGCAACGAAACCACCAAACG 61.197 55.000 0.00 0.00 0.00 3.60
1981 2124 0.099082 TCGCAACGAAACCACCAAAC 59.901 50.000 0.00 0.00 31.06 2.93
1983 2126 0.309302 CATCGCAACGAAACCACCAA 59.691 50.000 0.00 0.00 39.99 3.67
1984 2127 0.816018 ACATCGCAACGAAACCACCA 60.816 50.000 0.00 0.00 39.99 4.17
1986 2129 0.584396 TGACATCGCAACGAAACCAC 59.416 50.000 0.00 0.00 39.99 4.16
1987 2130 1.518325 ATGACATCGCAACGAAACCA 58.482 45.000 0.00 0.00 39.99 3.67
2011 2220 0.820871 GCAACAACCACAAACCCTCA 59.179 50.000 0.00 0.00 0.00 3.86
2017 2226 5.016051 ACATAACATGCAACAACCACAAA 57.984 34.783 0.00 0.00 0.00 2.83
2020 2229 5.708948 ACATACATAACATGCAACAACCAC 58.291 37.500 0.00 0.00 0.00 4.16
2058 2267 4.137543 AGAAAGAAACTCCATGACACCAC 58.862 43.478 0.00 0.00 0.00 4.16
2120 2329 4.828387 AGTTAATTAACGGAAAACTGGGCA 59.172 37.500 19.92 0.00 40.96 5.36
2125 2334 4.828387 TGCCCAGTTAATTAACGGAAAACT 59.172 37.500 26.78 10.10 40.96 2.66
2133 2342 9.489084 AAAAAGAGAATTGCCCAGTTAATTAAC 57.511 29.630 18.77 18.77 36.46 2.01
2157 2366 9.950680 GATTTGCCTCATCGATTAATTAAGAAA 57.049 29.630 3.94 0.00 0.00 2.52
2208 2417 5.990996 TCAAGGCAGTTTTGGAATCATTTTC 59.009 36.000 0.00 0.00 0.00 2.29
2210 2419 5.549742 TCAAGGCAGTTTTGGAATCATTT 57.450 34.783 0.00 0.00 0.00 2.32
2211 2420 5.750352 ATCAAGGCAGTTTTGGAATCATT 57.250 34.783 0.00 0.00 0.00 2.57
2212 2421 5.750352 AATCAAGGCAGTTTTGGAATCAT 57.250 34.783 0.00 0.00 0.00 2.45
2256 2466 8.840833 AAAACTTAAAACTTGGAGCAAGAAAA 57.159 26.923 0.00 0.00 43.42 2.29
2274 2484 7.817418 ATGAGTAGCACCAAAGAAAAACTTA 57.183 32.000 0.00 0.00 37.93 2.24
2309 2519 8.390354 CAACATGTTCCTTTTTCTTTTCTTTCC 58.610 33.333 8.48 0.00 0.00 3.13
2336 2546 5.660460 TCAGCACACATAGACGTATCAATT 58.340 37.500 0.00 0.00 0.00 2.32
2340 2550 3.426859 GCATCAGCACACATAGACGTATC 59.573 47.826 0.00 0.00 41.58 2.24
2367 2577 1.809547 CGTATGCCATGTGACCACAAA 59.190 47.619 6.95 0.00 45.41 2.83
2689 2899 3.117625 AGTTCCGGAAAAAGGGAAGAGTT 60.118 43.478 20.79 0.00 42.68 3.01
2738 2948 3.816994 ACTTTCCTAACCAACAGTGACC 58.183 45.455 0.00 0.00 0.00 4.02
2743 2953 8.739972 AGCATAATTTACTTTCCTAACCAACAG 58.260 33.333 0.00 0.00 0.00 3.16
2815 3025 4.568072 TTTTCTAGCATCTAGGCAACCA 57.432 40.909 1.51 0.00 35.83 3.67


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

AutoCloner maintained by Alex Coulton.