Multiple sequence alignment - TraesCS5A01G147400

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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 TraesCS5A01G147400 chr5A 100.000 2348 0 0 1 2348 325185588 325183241 0.000000e+00 4337.0
1 TraesCS5A01G147400 chr5A 83.425 181 27 3 1832 2010 38034079 38034258 5.190000e-37 165.0
2 TraesCS5A01G147400 chr5A 94.681 94 5 0 1 94 41138939 41139032 1.880000e-31 147.0
3 TraesCS5A01G147400 chr5B 91.289 1722 94 12 94 1790 273460259 273458569 0.000000e+00 2298.0
4 TraesCS5A01G147400 chr5B 92.473 93 7 0 3 95 507606973 507606881 1.460000e-27 134.0
5 TraesCS5A01G147400 chr5B 88.298 94 11 0 1 94 65532060 65532153 1.910000e-21 113.0
6 TraesCS5A01G147400 chr5B 84.043 94 15 0 1 94 145013503 145013410 8.940000e-15 91.6
7 TraesCS5A01G147400 chr5B 97.500 40 1 0 1790 1829 421502396 421502357 4.190000e-08 69.4
8 TraesCS5A01G147400 chr5D 97.339 1090 27 1 702 1791 231787921 231789008 0.000000e+00 1851.0
9 TraesCS5A01G147400 chr5D 91.653 623 41 8 94 710 231785399 231786016 0.000000e+00 852.0
10 TraesCS5A01G147400 chr5D 85.851 523 55 9 1827 2348 540035724 540035220 2.660000e-149 538.0
11 TraesCS5A01G147400 chr3A 88.825 519 57 1 1830 2348 651595074 651594557 9.150000e-179 636.0
12 TraesCS5A01G147400 chr3A 96.842 95 3 0 1 95 741219104 741219010 2.420000e-35 159.0
13 TraesCS5A01G147400 chr3A 95.745 94 4 0 1 94 597175941 597176034 4.040000e-33 152.0
14 TraesCS5A01G147400 chr3A 100.000 38 0 0 1790 1827 8923422 8923385 1.160000e-08 71.3
15 TraesCS5A01G147400 chr6D 90.947 475 34 4 1876 2348 12662109 12661642 4.260000e-177 630.0
16 TraesCS5A01G147400 chr2A 88.054 519 59 2 1830 2348 105546067 105546582 1.540000e-171 612.0
17 TraesCS5A01G147400 chr2A 94.737 95 5 0 1 95 692595926 692595832 5.230000e-32 148.0
18 TraesCS5A01G147400 chr2A 95.349 43 1 1 1791 1833 690320023 690320064 1.510000e-07 67.6
19 TraesCS5A01G147400 chr3D 88.259 494 47 6 1830 2321 30354435 30353951 4.350000e-162 580.0
20 TraesCS5A01G147400 chr7A 87.305 512 50 8 1841 2348 653004668 653005168 2.620000e-159 571.0
21 TraesCS5A01G147400 chr7A 95.789 95 4 0 1 95 29244003 29243909 1.120000e-33 154.0
22 TraesCS5A01G147400 chr7A 97.297 37 1 0 1791 1827 429166826 429166862 1.950000e-06 63.9
23 TraesCS5A01G147400 chr2D 88.428 458 52 1 1830 2286 180997334 180996877 3.410000e-153 551.0
24 TraesCS5A01G147400 chr2D 97.727 88 2 0 1567 1654 34022967 34022880 4.040000e-33 152.0
25 TraesCS5A01G147400 chr7D 88.571 385 36 7 1940 2320 133493574 133493954 5.910000e-126 460.0
26 TraesCS5A01G147400 chr7D 88.571 385 36 7 1940 2320 133610925 133610545 5.910000e-126 460.0
27 TraesCS5A01G147400 chr7D 93.182 44 2 1 1784 1827 33656438 33656396 1.950000e-06 63.9
28 TraesCS5A01G147400 chr3B 93.684 95 6 0 1 95 697686589 697686495 2.430000e-30 143.0
29 TraesCS5A01G147400 chr3B 92.473 93 7 0 3 95 659526843 659526751 1.460000e-27 134.0
30 TraesCS5A01G147400 chr3B 95.238 42 1 1 1786 1827 22786985 22787025 5.420000e-07 65.8
31 TraesCS5A01G147400 chr2B 93.684 95 6 0 1 95 61343608 61343514 2.430000e-30 143.0
32 TraesCS5A01G147400 chr6B 92.632 95 7 0 1 95 102194647 102194741 1.130000e-28 137.0
33 TraesCS5A01G147400 chr6B 89.474 95 10 0 1 95 672655241 672655147 1.140000e-23 121.0
34 TraesCS5A01G147400 chr6B 87.234 94 12 0 1 94 1972588 1972681 8.870000e-20 108.0
35 TraesCS5A01G147400 chr6B 86.667 60 3 5 1791 1846 36361099 36361157 7.010000e-06 62.1
36 TraesCS5A01G147400 chr1B 92.632 95 7 0 1 95 635406155 635406249 1.130000e-28 137.0
37 TraesCS5A01G147400 chr1B 91.579 95 8 0 1 95 673466098 673466192 5.270000e-27 132.0
38 TraesCS5A01G147400 chr1B 88.298 94 11 0 1 94 299390840 299390747 1.910000e-21 113.0
39 TraesCS5A01G147400 chr1B 86.170 94 13 0 1 94 5719072 5718979 4.130000e-18 102.0
40 TraesCS5A01G147400 chr7B 90.526 95 9 0 1 95 633757990 633757896 2.450000e-25 126.0
41 TraesCS5A01G147400 chr7B 89.474 95 10 0 1 95 34132022 34131928 1.140000e-23 121.0
42 TraesCS5A01G147400 chr7B 93.023 43 2 1 1787 1829 163313534 163313493 7.010000e-06 62.1
43 TraesCS5A01G147400 chr4A 86.170 94 13 0 1 94 609321017 609321110 4.130000e-18 102.0
44 TraesCS5A01G147400 chr4A 84.043 94 15 0 1 94 617916904 617916811 8.940000e-15 91.6
45 TraesCS5A01G147400 chr4A 83.516 91 15 0 1 91 722256020 722256110 4.160000e-13 86.1
46 TraesCS5A01G147400 chr1D 97.500 40 0 1 1791 1829 420830253 420830214 1.510000e-07 67.6


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 TraesCS5A01G147400 chr5A 325183241 325185588 2347 True 4337.0 4337 100.000 1 2348 1 chr5A.!!$R1 2347
1 TraesCS5A01G147400 chr5B 273458569 273460259 1690 True 2298.0 2298 91.289 94 1790 1 chr5B.!!$R2 1696
2 TraesCS5A01G147400 chr5D 231785399 231789008 3609 False 1351.5 1851 94.496 94 1791 2 chr5D.!!$F1 1697
3 TraesCS5A01G147400 chr5D 540035220 540035724 504 True 538.0 538 85.851 1827 2348 1 chr5D.!!$R1 521
4 TraesCS5A01G147400 chr3A 651594557 651595074 517 True 636.0 636 88.825 1830 2348 1 chr3A.!!$R2 518
5 TraesCS5A01G147400 chr2A 105546067 105546582 515 False 612.0 612 88.054 1830 2348 1 chr2A.!!$F1 518
6 TraesCS5A01G147400 chr7A 653004668 653005168 500 False 571.0 571 87.305 1841 2348 1 chr7A.!!$F2 507

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
55 56 0.179468 GCCCTTGATACGCCCACTTA 59.821 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 3802 0.179084 GCAGATGCTTAGCCGGTACA 60.179 55.0 1.9 0.0 38.21 2.9 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
22 23 5.488262 TGTCATCCTCAAACTCAATCTGA 57.512 39.130 0.00 0.00 0.00 3.27
23 24 5.868454 TGTCATCCTCAAACTCAATCTGAA 58.132 37.500 0.00 0.00 0.00 3.02
24 25 5.936372 TGTCATCCTCAAACTCAATCTGAAG 59.064 40.000 0.00 0.00 0.00 3.02
25 26 5.353678 GTCATCCTCAAACTCAATCTGAAGG 59.646 44.000 0.00 0.00 0.00 3.46
26 27 4.982241 TCCTCAAACTCAATCTGAAGGT 57.018 40.909 0.00 0.00 0.00 3.50
27 28 5.310409 TCCTCAAACTCAATCTGAAGGTT 57.690 39.130 0.00 0.00 0.00 3.50
28 29 5.065914 TCCTCAAACTCAATCTGAAGGTTG 58.934 41.667 0.00 0.00 0.00 3.77
29 30 4.823989 CCTCAAACTCAATCTGAAGGTTGT 59.176 41.667 3.35 0.00 30.07 3.32
30 31 5.997746 CCTCAAACTCAATCTGAAGGTTGTA 59.002 40.000 3.35 0.00 30.07 2.41
31 32 6.486657 CCTCAAACTCAATCTGAAGGTTGTAA 59.513 38.462 3.35 0.00 30.07 2.41
32 33 7.013274 CCTCAAACTCAATCTGAAGGTTGTAAA 59.987 37.037 3.35 0.00 30.07 2.01
46 47 4.696899 GTTGTAAACCTGCCCTTGATAC 57.303 45.455 0.00 0.00 42.21 2.24
47 48 2.980568 TGTAAACCTGCCCTTGATACG 58.019 47.619 0.00 0.00 0.00 3.06
48 49 1.669265 GTAAACCTGCCCTTGATACGC 59.331 52.381 0.00 0.00 0.00 4.42
49 50 0.679960 AAACCTGCCCTTGATACGCC 60.680 55.000 0.00 0.00 0.00 5.68
50 51 2.203209 CCTGCCCTTGATACGCCC 60.203 66.667 0.00 0.00 0.00 6.13
51 52 2.589540 CTGCCCTTGATACGCCCA 59.410 61.111 0.00 0.00 0.00 5.36
52 53 1.819632 CTGCCCTTGATACGCCCAC 60.820 63.158 0.00 0.00 0.00 4.61
53 54 2.257409 CTGCCCTTGATACGCCCACT 62.257 60.000 0.00 0.00 0.00 4.00
54 55 1.077716 GCCCTTGATACGCCCACTT 60.078 57.895 0.00 0.00 0.00 3.16
55 56 0.179468 GCCCTTGATACGCCCACTTA 59.821 55.000 0.00 0.00 0.00 2.24
56 57 1.407712 GCCCTTGATACGCCCACTTAA 60.408 52.381 0.00 0.00 0.00 1.85
57 58 2.285977 CCCTTGATACGCCCACTTAAC 58.714 52.381 0.00 0.00 0.00 2.01
58 59 2.285977 CCTTGATACGCCCACTTAACC 58.714 52.381 0.00 0.00 0.00 2.85
59 60 2.355310 CCTTGATACGCCCACTTAACCA 60.355 50.000 0.00 0.00 0.00 3.67
60 61 2.389962 TGATACGCCCACTTAACCAC 57.610 50.000 0.00 0.00 0.00 4.16
61 62 1.624312 TGATACGCCCACTTAACCACA 59.376 47.619 0.00 0.00 0.00 4.17
62 63 2.237643 TGATACGCCCACTTAACCACAT 59.762 45.455 0.00 0.00 0.00 3.21
63 64 2.389962 TACGCCCACTTAACCACATC 57.610 50.000 0.00 0.00 0.00 3.06
64 65 0.398696 ACGCCCACTTAACCACATCA 59.601 50.000 0.00 0.00 0.00 3.07
65 66 1.086696 CGCCCACTTAACCACATCAG 58.913 55.000 0.00 0.00 0.00 2.90
66 67 1.463674 GCCCACTTAACCACATCAGG 58.536 55.000 0.00 0.00 0.00 3.86
67 68 1.463674 CCCACTTAACCACATCAGGC 58.536 55.000 0.00 0.00 0.00 4.85
68 69 1.271871 CCCACTTAACCACATCAGGCA 60.272 52.381 0.00 0.00 0.00 4.75
69 70 1.812571 CCACTTAACCACATCAGGCAC 59.187 52.381 0.00 0.00 0.00 5.01
70 71 2.503331 CACTTAACCACATCAGGCACA 58.497 47.619 0.00 0.00 0.00 4.57
71 72 2.884012 CACTTAACCACATCAGGCACAA 59.116 45.455 0.00 0.00 0.00 3.33
72 73 3.317711 CACTTAACCACATCAGGCACAAA 59.682 43.478 0.00 0.00 0.00 2.83
73 74 3.317993 ACTTAACCACATCAGGCACAAAC 59.682 43.478 0.00 0.00 0.00 2.93
74 75 2.071778 AACCACATCAGGCACAAACT 57.928 45.000 0.00 0.00 0.00 2.66
75 76 2.071778 ACCACATCAGGCACAAACTT 57.928 45.000 0.00 0.00 0.00 2.66
76 77 1.682854 ACCACATCAGGCACAAACTTG 59.317 47.619 0.00 0.00 0.00 3.16
77 78 1.955778 CCACATCAGGCACAAACTTGA 59.044 47.619 0.00 0.00 0.00 3.02
78 79 2.559668 CCACATCAGGCACAAACTTGAT 59.440 45.455 0.00 0.00 0.00 2.57
79 80 3.571571 CACATCAGGCACAAACTTGATG 58.428 45.455 13.18 13.18 39.05 3.07
80 81 3.005050 CACATCAGGCACAAACTTGATGT 59.995 43.478 14.29 14.29 44.62 3.06
81 82 3.254166 ACATCAGGCACAAACTTGATGTC 59.746 43.478 14.29 0.00 41.39 3.06
82 83 2.229792 TCAGGCACAAACTTGATGTCC 58.770 47.619 0.00 0.00 0.00 4.02
83 84 1.955778 CAGGCACAAACTTGATGTCCA 59.044 47.619 0.00 0.00 0.00 4.02
84 85 2.361757 CAGGCACAAACTTGATGTCCAA 59.638 45.455 0.00 0.00 0.00 3.53
85 86 3.030291 AGGCACAAACTTGATGTCCAAA 58.970 40.909 0.00 0.00 33.76 3.28
86 87 3.450457 AGGCACAAACTTGATGTCCAAAA 59.550 39.130 0.00 0.00 33.76 2.44
87 88 4.101430 AGGCACAAACTTGATGTCCAAAAT 59.899 37.500 0.00 0.00 33.76 1.82
88 89 5.304101 AGGCACAAACTTGATGTCCAAAATA 59.696 36.000 0.00 0.00 33.76 1.40
89 90 5.405269 GGCACAAACTTGATGTCCAAAATAC 59.595 40.000 0.00 0.00 33.76 1.89
90 91 6.215845 GCACAAACTTGATGTCCAAAATACT 58.784 36.000 0.00 0.00 33.76 2.12
91 92 6.144402 GCACAAACTTGATGTCCAAAATACTG 59.856 38.462 0.00 0.00 33.76 2.74
92 93 7.424803 CACAAACTTGATGTCCAAAATACTGA 58.575 34.615 0.00 0.00 33.76 3.41
99 100 4.649267 TGTCCAAAATACTGACCCATCA 57.351 40.909 0.00 0.00 0.00 3.07
110 111 2.231478 CTGACCCATCAACGTACTGTCT 59.769 50.000 0.00 0.00 33.30 3.41
154 155 1.998222 ATCCCTAGTTAGAGCCCGTC 58.002 55.000 0.00 0.00 0.00 4.79
217 218 5.182001 CGACCAGATGTCTTTCCAAAATCTT 59.818 40.000 0.00 0.00 42.13 2.40
225 226 9.399403 GATGTCTTTCCAAAATCTTGTACTTTC 57.601 33.333 0.00 0.00 0.00 2.62
237 238 6.139679 TCTTGTACTTTCTCCAATCCCAAT 57.860 37.500 0.00 0.00 0.00 3.16
276 277 8.940952 CCTACTAACAAAAAGATCCTCTTTCAG 58.059 37.037 2.81 2.27 45.19 3.02
296 297 5.065914 TCAGTCTGATCAAACCTTTCCAAG 58.934 41.667 0.00 0.00 0.00 3.61
301 302 2.151502 TCAAACCTTTCCAAGTGGCA 57.848 45.000 0.00 0.00 34.44 4.92
338 339 8.480133 TTGTCTAGAGAAAGAGTTTTAGACCT 57.520 34.615 0.00 0.00 31.58 3.85
380 381 8.324163 AGTACTTTTTGCCATACTAGTTTCAG 57.676 34.615 0.00 0.00 0.00 3.02
387 388 8.911918 TTTGCCATACTAGTTTCAGTTAAAGA 57.088 30.769 0.00 0.00 0.00 2.52
424 425 3.162202 TGTTGAGCAACCATGTGTTTG 57.838 42.857 10.54 0.00 40.46 2.93
448 449 8.190326 TGTAATATGAAGATCCTCAATACCGT 57.810 34.615 0.00 0.00 0.00 4.83
473 474 2.358510 CCTTTGGTCCCATGGATGACAT 60.359 50.000 15.22 0.00 41.57 3.06
481 482 5.163519 GGTCCCATGGATGACATAAAACTTG 60.164 44.000 15.22 0.00 37.84 3.16
488 489 5.048083 TGGATGACATAAAACTTGCCACTTC 60.048 40.000 0.00 0.00 0.00 3.01
567 574 3.127548 CCGCTTATGTTCATCACTTTGCT 59.872 43.478 0.00 0.00 0.00 3.91
608 615 8.815565 TGTGAAGGAAGTGCCAATATTTAATA 57.184 30.769 0.00 0.00 40.02 0.98
609 616 9.420118 TGTGAAGGAAGTGCCAATATTTAATAT 57.580 29.630 0.00 0.00 40.02 1.28
896 2841 2.707257 CGAACCCCTATTTAAGCCCCTA 59.293 50.000 0.00 0.00 0.00 3.53
903 2848 5.515008 CCCCTATTTAAGCCCCTACATTCTC 60.515 48.000 0.00 0.00 0.00 2.87
905 2850 5.073144 CCTATTTAAGCCCCTACATTCTCCA 59.927 44.000 0.00 0.00 0.00 3.86
926 2871 2.912956 ACTACATTCTCCACACCACCAT 59.087 45.455 0.00 0.00 0.00 3.55
1235 3180 0.036010 GCTTGCTACTGCCTCAAGGA 60.036 55.000 0.00 0.00 38.05 3.36
1236 3181 1.407989 GCTTGCTACTGCCTCAAGGAT 60.408 52.381 0.00 0.00 38.05 3.24
1243 3188 1.069823 ACTGCCTCAAGGATATCGCTG 59.930 52.381 0.00 0.59 37.39 5.18
1246 3191 1.606737 GCCTCAAGGATATCGCTGGTC 60.607 57.143 0.00 0.00 37.39 4.02
1264 3209 2.076100 GTCGCATCCACAATCTCAACA 58.924 47.619 0.00 0.00 0.00 3.33
1333 3278 2.171003 ACCACATCAGTCTCGACATCA 58.829 47.619 0.00 0.00 0.00 3.07
1402 3347 8.925161 ACATTCATCCACGTAAAATTTATTGG 57.075 30.769 9.04 9.04 0.00 3.16
1639 3584 6.718294 TCAGTATCTGTGTACCTGAGAGTTA 58.282 40.000 0.00 0.00 32.61 2.24
1707 3652 0.510359 CAGCTCGTTCTGTTCAGTGC 59.490 55.000 0.00 0.00 0.00 4.40
1771 3716 4.905456 TCCTTCCATCCGGTATTAGTTGAT 59.095 41.667 0.00 0.00 0.00 2.57
1780 3725 4.634004 CCGGTATTAGTTGATGCTCAAACA 59.366 41.667 0.00 0.00 38.22 2.83
1791 3736 8.427276 AGTTGATGCTCAAACAGATATATCTGA 58.573 33.333 37.76 21.02 45.89 3.27
1792 3737 8.710551 GTTGATGCTCAAACAGATATATCTGAG 58.289 37.037 37.76 27.66 45.89 3.35
1793 3738 8.427276 TTGATGCTCAAACAGATATATCTGAGT 58.573 33.333 37.76 25.61 43.78 3.41
1827 3772 6.723298 AAACTACCACAATTCATGAAACCA 57.277 33.333 13.09 0.00 0.00 3.67
1828 3773 6.916360 AACTACCACAATTCATGAAACCAT 57.084 33.333 13.09 0.00 0.00 3.55
1851 3796 2.619646 GCAAACTCCTTTTTACCGGTGA 59.380 45.455 19.93 6.00 0.00 4.02
1903 3849 1.491127 CACTTTGCGATTCGTGCGA 59.509 52.632 8.03 0.00 34.24 5.10
1907 3853 1.834178 CTTTGCGATTCGTGCGATTTC 59.166 47.619 8.03 0.00 34.24 2.17
1909 3855 1.016653 TGCGATTCGTGCGATTTCCA 61.017 50.000 8.03 0.00 34.24 3.53
1918 3864 2.700773 GCGATTTCCAGGCCCACAC 61.701 63.158 0.00 0.00 0.00 3.82
1940 3886 7.594015 CACACCTCACGTATATTAGTGTATTCC 59.406 40.741 9.21 0.00 39.25 3.01
1944 3890 7.813148 CCTCACGTATATTAGTGTATTCCCAAG 59.187 40.741 9.21 0.05 39.25 3.61
1954 3900 0.925558 TATTCCCAAGGAGCATGGCA 59.074 50.000 0.00 0.00 36.58 4.92
1966 3913 4.038763 AGGAGCATGGCATATTCAACATTG 59.961 41.667 0.00 0.00 0.00 2.82
1972 3919 5.918426 TGGCATATTCAACATTGTGTCAT 57.082 34.783 0.00 0.00 0.00 3.06
2026 3975 6.595682 AGTAGTACTTTATGCATGCCTGATT 58.404 36.000 16.68 0.00 0.00 2.57
2040 3989 6.522946 CATGCCTGATTCATTCTCTCTTCTA 58.477 40.000 0.00 0.00 0.00 2.10
2053 4002 6.497785 TCTCTCTTCTAGTTCACGTAAAGG 57.502 41.667 0.00 0.00 0.00 3.11
2059 4008 5.648178 TCTAGTTCACGTAAAGGTGCATA 57.352 39.130 0.00 0.00 37.83 3.14
2277 4226 9.468532 GTTTTCTGAAATAAGTGAAATCAGCTT 57.531 29.630 3.31 4.50 37.89 3.74
2279 4228 9.683069 TTTCTGAAATAAGTGAAATCAGCTTTC 57.317 29.630 0.00 0.00 43.05 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.488262 TCAGATTGAGTTTGAGGATGACA 57.512 39.130 0.00 0.00 0.00 3.58
3 4 5.251764 ACCTTCAGATTGAGTTTGAGGATG 58.748 41.667 0.00 0.00 0.00 3.51
4 5 5.511386 ACCTTCAGATTGAGTTTGAGGAT 57.489 39.130 0.00 0.00 0.00 3.24
5 6 4.982241 ACCTTCAGATTGAGTTTGAGGA 57.018 40.909 0.00 0.00 0.00 3.71
6 7 4.823989 ACAACCTTCAGATTGAGTTTGAGG 59.176 41.667 0.00 0.00 0.00 3.86
7 8 7.496529 TTACAACCTTCAGATTGAGTTTGAG 57.503 36.000 0.00 0.00 0.00 3.02
8 9 7.703328 GTTTACAACCTTCAGATTGAGTTTGA 58.297 34.615 0.00 0.00 0.00 2.69
9 10 7.914537 GTTTACAACCTTCAGATTGAGTTTG 57.085 36.000 0.00 0.00 0.00 2.93
25 26 3.126343 CGTATCAAGGGCAGGTTTACAAC 59.874 47.826 0.00 0.00 0.00 3.32
26 27 3.340034 CGTATCAAGGGCAGGTTTACAA 58.660 45.455 0.00 0.00 0.00 2.41
27 28 2.937873 GCGTATCAAGGGCAGGTTTACA 60.938 50.000 0.00 0.00 0.00 2.41
28 29 1.669265 GCGTATCAAGGGCAGGTTTAC 59.331 52.381 0.00 0.00 0.00 2.01
29 30 1.407712 GGCGTATCAAGGGCAGGTTTA 60.408 52.381 0.00 0.00 36.18 2.01
30 31 0.679960 GGCGTATCAAGGGCAGGTTT 60.680 55.000 0.00 0.00 36.18 3.27
31 32 1.077716 GGCGTATCAAGGGCAGGTT 60.078 57.895 0.00 0.00 36.18 3.50
32 33 2.590092 GGCGTATCAAGGGCAGGT 59.410 61.111 0.00 0.00 36.18 4.00
33 34 2.203209 GGGCGTATCAAGGGCAGG 60.203 66.667 0.00 0.00 37.76 4.85
34 35 1.819632 GTGGGCGTATCAAGGGCAG 60.820 63.158 0.00 0.00 37.76 4.85
35 36 1.847798 AAGTGGGCGTATCAAGGGCA 61.848 55.000 0.00 0.00 37.76 5.36
36 37 0.179468 TAAGTGGGCGTATCAAGGGC 59.821 55.000 0.00 0.00 35.46 5.19
37 38 2.285977 GTTAAGTGGGCGTATCAAGGG 58.714 52.381 0.00 0.00 0.00 3.95
38 39 2.285977 GGTTAAGTGGGCGTATCAAGG 58.714 52.381 0.00 0.00 0.00 3.61
39 40 2.676342 GTGGTTAAGTGGGCGTATCAAG 59.324 50.000 0.00 0.00 0.00 3.02
40 41 2.038689 TGTGGTTAAGTGGGCGTATCAA 59.961 45.455 0.00 0.00 0.00 2.57
41 42 1.624312 TGTGGTTAAGTGGGCGTATCA 59.376 47.619 0.00 0.00 0.00 2.15
42 43 2.389962 TGTGGTTAAGTGGGCGTATC 57.610 50.000 0.00 0.00 0.00 2.24
43 44 2.237643 TGATGTGGTTAAGTGGGCGTAT 59.762 45.455 0.00 0.00 0.00 3.06
44 45 1.624312 TGATGTGGTTAAGTGGGCGTA 59.376 47.619 0.00 0.00 0.00 4.42
45 46 0.398696 TGATGTGGTTAAGTGGGCGT 59.601 50.000 0.00 0.00 0.00 5.68
46 47 1.086696 CTGATGTGGTTAAGTGGGCG 58.913 55.000 0.00 0.00 0.00 6.13
47 48 1.463674 CCTGATGTGGTTAAGTGGGC 58.536 55.000 0.00 0.00 0.00 5.36
48 49 1.271871 TGCCTGATGTGGTTAAGTGGG 60.272 52.381 0.00 0.00 0.00 4.61
49 50 1.812571 GTGCCTGATGTGGTTAAGTGG 59.187 52.381 0.00 0.00 0.00 4.00
50 51 2.503331 TGTGCCTGATGTGGTTAAGTG 58.497 47.619 0.00 0.00 0.00 3.16
51 52 2.949177 TGTGCCTGATGTGGTTAAGT 57.051 45.000 0.00 0.00 0.00 2.24
52 53 3.569701 AGTTTGTGCCTGATGTGGTTAAG 59.430 43.478 0.00 0.00 0.00 1.85
53 54 3.561143 AGTTTGTGCCTGATGTGGTTAA 58.439 40.909 0.00 0.00 0.00 2.01
54 55 3.222173 AGTTTGTGCCTGATGTGGTTA 57.778 42.857 0.00 0.00 0.00 2.85
55 56 2.071778 AGTTTGTGCCTGATGTGGTT 57.928 45.000 0.00 0.00 0.00 3.67
56 57 1.682854 CAAGTTTGTGCCTGATGTGGT 59.317 47.619 0.00 0.00 0.00 4.16
57 58 1.955778 TCAAGTTTGTGCCTGATGTGG 59.044 47.619 0.00 0.00 0.00 4.17
58 59 3.005050 ACATCAAGTTTGTGCCTGATGTG 59.995 43.478 14.04 0.00 42.91 3.21
59 60 3.225104 ACATCAAGTTTGTGCCTGATGT 58.775 40.909 10.04 10.04 40.72 3.06
60 61 3.366679 GGACATCAAGTTTGTGCCTGATG 60.367 47.826 8.88 8.88 39.05 3.07
61 62 2.821969 GGACATCAAGTTTGTGCCTGAT 59.178 45.455 0.00 0.00 30.07 2.90
62 63 2.229792 GGACATCAAGTTTGTGCCTGA 58.770 47.619 0.00 0.00 30.07 3.86
63 64 1.955778 TGGACATCAAGTTTGTGCCTG 59.044 47.619 0.00 0.00 34.85 4.85
64 65 2.363306 TGGACATCAAGTTTGTGCCT 57.637 45.000 0.00 0.00 34.85 4.75
65 66 3.451141 TTTGGACATCAAGTTTGTGCC 57.549 42.857 0.00 0.00 36.62 5.01
66 67 6.144402 CAGTATTTTGGACATCAAGTTTGTGC 59.856 38.462 0.00 0.00 36.62 4.57
67 68 7.379529 GTCAGTATTTTGGACATCAAGTTTGTG 59.620 37.037 0.00 0.00 36.62 3.33
68 69 7.425606 GTCAGTATTTTGGACATCAAGTTTGT 58.574 34.615 0.00 0.00 36.62 2.83
69 70 6.863126 GGTCAGTATTTTGGACATCAAGTTTG 59.137 38.462 0.00 0.00 36.62 2.93
70 71 6.015434 GGGTCAGTATTTTGGACATCAAGTTT 60.015 38.462 0.00 0.00 36.62 2.66
71 72 5.476945 GGGTCAGTATTTTGGACATCAAGTT 59.523 40.000 0.00 0.00 36.62 2.66
72 73 5.010282 GGGTCAGTATTTTGGACATCAAGT 58.990 41.667 0.00 0.00 36.62 3.16
73 74 5.009631 TGGGTCAGTATTTTGGACATCAAG 58.990 41.667 0.00 0.00 36.62 3.02
74 75 4.991776 TGGGTCAGTATTTTGGACATCAA 58.008 39.130 0.00 0.00 33.26 2.57
75 76 4.649267 TGGGTCAGTATTTTGGACATCA 57.351 40.909 0.00 0.00 33.26 3.07
76 77 5.192927 TGATGGGTCAGTATTTTGGACATC 58.807 41.667 0.00 0.00 33.26 3.06
77 78 5.191727 TGATGGGTCAGTATTTTGGACAT 57.808 39.130 0.00 0.00 33.26 3.06
78 79 4.649267 TGATGGGTCAGTATTTTGGACA 57.351 40.909 0.00 0.00 33.26 4.02
79 80 4.142687 CGTTGATGGGTCAGTATTTTGGAC 60.143 45.833 0.00 0.00 35.39 4.02
80 81 4.006989 CGTTGATGGGTCAGTATTTTGGA 58.993 43.478 0.00 0.00 35.39 3.53
81 82 3.756434 ACGTTGATGGGTCAGTATTTTGG 59.244 43.478 0.00 0.00 35.39 3.28
82 83 5.642063 AGTACGTTGATGGGTCAGTATTTTG 59.358 40.000 0.00 0.00 35.39 2.44
83 84 5.642063 CAGTACGTTGATGGGTCAGTATTTT 59.358 40.000 0.00 0.00 35.39 1.82
84 85 5.175859 CAGTACGTTGATGGGTCAGTATTT 58.824 41.667 0.00 0.00 35.39 1.40
85 86 4.222145 ACAGTACGTTGATGGGTCAGTATT 59.778 41.667 0.00 0.00 35.39 1.89
86 87 3.767673 ACAGTACGTTGATGGGTCAGTAT 59.232 43.478 0.00 0.00 35.39 2.12
87 88 3.159472 ACAGTACGTTGATGGGTCAGTA 58.841 45.455 0.00 0.00 35.39 2.74
88 89 1.968493 ACAGTACGTTGATGGGTCAGT 59.032 47.619 0.00 0.00 35.39 3.41
89 90 2.231478 AGACAGTACGTTGATGGGTCAG 59.769 50.000 0.00 0.00 35.39 3.51
90 91 2.230508 GAGACAGTACGTTGATGGGTCA 59.769 50.000 0.00 0.00 0.00 4.02
91 92 2.230508 TGAGACAGTACGTTGATGGGTC 59.769 50.000 0.00 0.00 0.00 4.46
92 93 2.231478 CTGAGACAGTACGTTGATGGGT 59.769 50.000 0.00 0.00 0.00 4.51
99 100 1.269998 GCTCCACTGAGACAGTACGTT 59.730 52.381 0.00 0.00 43.43 3.99
110 111 0.543277 GGACATCATGGCTCCACTGA 59.457 55.000 0.00 0.00 0.00 3.41
154 155 1.126846 GTTGTGAGATGCCGAGTTTCG 59.873 52.381 0.00 0.00 40.07 3.46
194 195 6.015940 ACAAGATTTTGGAAAGACATCTGGTC 60.016 38.462 0.57 0.00 41.58 4.02
217 218 5.253330 GTCATTGGGATTGGAGAAAGTACA 58.747 41.667 0.00 0.00 0.00 2.90
225 226 3.375299 GTCTTTCGTCATTGGGATTGGAG 59.625 47.826 0.00 0.00 0.00 3.86
237 238 2.827921 GTTAGTAGGGGGTCTTTCGTCA 59.172 50.000 0.00 0.00 0.00 4.35
296 297 1.003718 AAGCCTACGGACTTGCCAC 60.004 57.895 0.00 0.00 35.94 5.01
301 302 3.018149 CTCTAGACAAGCCTACGGACTT 58.982 50.000 0.00 0.00 0.00 3.01
338 339 9.856162 AAAAAGTACTTCCTAACAAATACCTCA 57.144 29.630 8.95 0.00 0.00 3.86
380 381 9.087424 ACAAATGTCTTTTCAAGCTTCTTTAAC 57.913 29.630 0.00 0.00 0.00 2.01
387 388 5.521372 GCTCAACAAATGTCTTTTCAAGCTT 59.479 36.000 0.00 0.00 0.00 3.74
424 425 8.304596 TCACGGTATTGAGGATCTTCATATTAC 58.695 37.037 8.52 10.43 34.92 1.89
473 474 4.379339 AAAAGCGAAGTGGCAAGTTTTA 57.621 36.364 0.00 0.00 34.64 1.52
567 574 9.859427 CTTCCTTCACATATGCAAAATTTTCTA 57.141 29.630 1.58 0.00 0.00 2.10
574 581 4.321899 GGCACTTCCTTCACATATGCAAAA 60.322 41.667 1.58 0.00 33.24 2.44
684 691 3.848726 CGCAAGGGCAACATCTTTAATT 58.151 40.909 0.00 0.00 41.24 1.40
866 2811 3.955524 AATAGGGGTTCGAGAGAGAGA 57.044 47.619 0.00 0.00 43.69 3.10
867 2812 5.508320 GCTTAAATAGGGGTTCGAGAGAGAG 60.508 48.000 0.00 0.00 43.69 3.20
896 2841 4.532126 TGTGGAGAATGTAGTGGAGAATGT 59.468 41.667 0.00 0.00 0.00 2.71
903 2848 2.615493 GGTGGTGTGGAGAATGTAGTGG 60.615 54.545 0.00 0.00 0.00 4.00
905 2850 2.334977 TGGTGGTGTGGAGAATGTAGT 58.665 47.619 0.00 0.00 0.00 2.73
926 2871 1.552337 GGTGGAGAGATGAGCAACTCA 59.448 52.381 9.88 0.00 44.99 3.41
1175 3120 2.203209 GCGCCTGGTTATGGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
1222 3167 2.297315 CAGCGATATCCTTGAGGCAGTA 59.703 50.000 0.00 0.00 34.44 2.74
1243 3188 1.398390 GTTGAGATTGTGGATGCGACC 59.602 52.381 0.00 0.00 0.00 4.79
1246 3191 2.159476 CCTTGTTGAGATTGTGGATGCG 60.159 50.000 0.00 0.00 0.00 4.73
1303 3248 2.103263 GACTGATGTGGTATGGGAGGTC 59.897 54.545 0.00 0.00 0.00 3.85
1707 3652 4.859798 GTGAGGAAACAGAGATAAGTCACG 59.140 45.833 0.00 0.00 0.00 4.35
1802 3747 7.560368 TGGTTTCATGAATTGTGGTAGTTTTT 58.440 30.769 9.40 0.00 0.00 1.94
1803 3748 7.118496 TGGTTTCATGAATTGTGGTAGTTTT 57.882 32.000 9.40 0.00 0.00 2.43
1804 3749 6.723298 TGGTTTCATGAATTGTGGTAGTTT 57.277 33.333 9.40 0.00 0.00 2.66
1805 3750 6.349280 CGATGGTTTCATGAATTGTGGTAGTT 60.349 38.462 9.40 0.00 32.98 2.24
1806 3751 5.123820 CGATGGTTTCATGAATTGTGGTAGT 59.876 40.000 9.40 0.00 32.98 2.73
1807 3752 5.572211 CGATGGTTTCATGAATTGTGGTAG 58.428 41.667 9.40 0.00 32.98 3.18
1808 3753 4.142491 GCGATGGTTTCATGAATTGTGGTA 60.142 41.667 9.40 0.00 32.98 3.25
1809 3754 3.367292 GCGATGGTTTCATGAATTGTGGT 60.367 43.478 9.40 0.00 32.98 4.16
1810 3755 3.181397 GCGATGGTTTCATGAATTGTGG 58.819 45.455 9.40 0.00 32.98 4.17
1811 3756 3.835779 TGCGATGGTTTCATGAATTGTG 58.164 40.909 9.40 0.00 32.98 3.33
1812 3757 4.517952 TTGCGATGGTTTCATGAATTGT 57.482 36.364 9.40 0.00 32.98 2.71
1813 3758 4.925054 AGTTTGCGATGGTTTCATGAATTG 59.075 37.500 9.40 0.00 32.98 2.32
1814 3759 5.138125 AGTTTGCGATGGTTTCATGAATT 57.862 34.783 9.40 0.00 32.98 2.17
1815 3760 4.380867 GGAGTTTGCGATGGTTTCATGAAT 60.381 41.667 9.40 0.00 32.98 2.57
1816 3761 3.057596 GGAGTTTGCGATGGTTTCATGAA 60.058 43.478 3.38 3.38 32.98 2.57
1817 3762 2.487762 GGAGTTTGCGATGGTTTCATGA 59.512 45.455 0.00 0.00 32.98 3.07
1818 3763 2.489329 AGGAGTTTGCGATGGTTTCATG 59.511 45.455 0.00 0.00 32.98 3.07
1819 3764 2.795329 AGGAGTTTGCGATGGTTTCAT 58.205 42.857 0.00 0.00 36.09 2.57
1820 3765 2.270352 AGGAGTTTGCGATGGTTTCA 57.730 45.000 0.00 0.00 0.00 2.69
1821 3766 3.643159 AAAGGAGTTTGCGATGGTTTC 57.357 42.857 0.00 0.00 0.00 2.78
1822 3767 4.400529 AAAAAGGAGTTTGCGATGGTTT 57.599 36.364 0.00 0.00 0.00 3.27
1823 3768 4.261867 GGTAAAAAGGAGTTTGCGATGGTT 60.262 41.667 0.00 0.00 0.00 3.67
1824 3769 3.254903 GGTAAAAAGGAGTTTGCGATGGT 59.745 43.478 0.00 0.00 0.00 3.55
1825 3770 3.669557 CGGTAAAAAGGAGTTTGCGATGG 60.670 47.826 0.00 0.00 0.00 3.51
1826 3771 3.488489 CGGTAAAAAGGAGTTTGCGATG 58.512 45.455 0.00 0.00 0.00 3.84
1827 3772 2.486592 CCGGTAAAAAGGAGTTTGCGAT 59.513 45.455 0.00 0.00 0.00 4.58
1828 3773 1.874872 CCGGTAAAAAGGAGTTTGCGA 59.125 47.619 0.00 0.00 0.00 5.10
1851 3796 2.024590 GCTTAGCCGGTACATCCCGT 62.025 60.000 1.90 0.00 46.66 5.28
1857 3802 0.179084 GCAGATGCTTAGCCGGTACA 60.179 55.000 1.90 0.00 38.21 2.90
1903 3849 1.384191 GAGGTGTGGGCCTGGAAAT 59.616 57.895 4.53 0.00 39.34 2.17
1907 3853 4.704833 CGTGAGGTGTGGGCCTGG 62.705 72.222 4.53 0.00 39.34 4.45
1909 3855 0.324923 TATACGTGAGGTGTGGGCCT 60.325 55.000 4.53 0.00 42.53 5.19
1918 3864 7.223260 TGGGAATACACTAATATACGTGAGG 57.777 40.000 0.00 0.00 35.23 3.86
1940 3886 2.589720 TGAATATGCCATGCTCCTTGG 58.410 47.619 0.00 0.00 37.31 3.61
1944 3890 4.202182 ACAATGTTGAATATGCCATGCTCC 60.202 41.667 0.00 0.00 0.00 4.70
1966 3913 3.397482 GACCTGCCATCTGATATGACAC 58.603 50.000 0.00 0.00 0.00 3.67
2012 3961 4.981812 AGAGAATGAATCAGGCATGCATA 58.018 39.130 21.36 3.97 0.00 3.14
2020 3969 7.706179 GTGAACTAGAAGAGAGAATGAATCAGG 59.294 40.741 0.00 0.00 0.00 3.86
2026 3975 7.683437 TTACGTGAACTAGAAGAGAGAATGA 57.317 36.000 0.00 0.00 0.00 2.57
2040 3989 3.374058 GCATATGCACCTTTACGTGAACT 59.626 43.478 22.84 0.00 41.59 3.01
2059 4008 3.057736 GCAGGATTTAATCTCGCATGCAT 60.058 43.478 19.57 0.00 0.00 3.96
2153 4102 7.769044 GTCTTGGTGCTAGGAGTTCAAATATAA 59.231 37.037 0.00 0.00 0.00 0.98
2169 4118 3.857157 TGTTCTAAAGGTCTTGGTGCT 57.143 42.857 0.00 0.00 0.00 4.40
2172 4121 6.187727 TGATCTTGTTCTAAAGGTCTTGGT 57.812 37.500 0.00 0.00 38.02 3.67


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

AutoCloner maintained by Alex Coulton.