Multiple sequence alignment - TraesCS3D01G438300

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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 TraesCS3D01G438300 chr3D 100.000 2536 0 0 1 2536 549000402 548997867 0.000000e+00 4684.0
1 TraesCS3D01G438300 chr3D 96.320 462 17 0 2075 2536 5537810 5537349 0.000000e+00 760.0
2 TraesCS3D01G438300 chr3D 89.388 490 46 5 806 1292 553357578 553358064 1.670000e-171 612.0
3 TraesCS3D01G438300 chr3D 87.500 496 55 6 806 1298 553405994 553406485 1.320000e-157 566.0
4 TraesCS3D01G438300 chr3D 89.974 389 33 3 518 906 553357146 553357528 4.870000e-137 497.0
5 TraesCS3D01G438300 chr3D 87.206 383 39 5 1299 1674 553358107 553358486 6.480000e-116 427.0
6 TraesCS3D01G438300 chr3D 89.450 218 18 5 214 431 553405447 553405659 1.160000e-68 270.0
7 TraesCS3D01G438300 chr3D 87.234 188 20 3 365 549 573906839 573906653 7.110000e-51 211.0
8 TraesCS3D01G438300 chr3A 96.627 919 29 2 379 1296 686281571 686280654 0.000000e+00 1524.0
9 TraesCS3D01G438300 chr3A 89.962 528 47 5 378 901 689523254 689523779 0.000000e+00 676.0
10 TraesCS3D01G438300 chr3A 91.340 485 35 6 420 901 689608205 689608685 0.000000e+00 656.0
11 TraesCS3D01G438300 chr3A 91.134 485 36 6 420 901 689578427 689578907 0.000000e+00 651.0
12 TraesCS3D01G438300 chr3A 96.615 384 12 1 1 383 686305784 686305401 9.900000e-179 636.0
13 TraesCS3D01G438300 chr3A 93.839 422 14 3 1299 1708 686280615 686280194 2.140000e-175 625.0
14 TraesCS3D01G438300 chr3A 88.732 497 48 7 806 1298 689660102 689660594 3.610000e-168 601.0
15 TraesCS3D01G438300 chr3A 88.732 497 48 7 806 1298 689662939 689663431 3.610000e-168 601.0
16 TraesCS3D01G438300 chr3A 87.949 473 49 4 822 1292 689523844 689524310 3.690000e-153 551.0
17 TraesCS3D01G438300 chr3A 87.949 473 49 4 822 1292 689608750 689609216 3.690000e-153 551.0
18 TraesCS3D01G438300 chr3A 86.318 497 61 7 806 1298 689867332 689867825 3.710000e-148 534.0
19 TraesCS3D01G438300 chr3A 88.462 390 39 4 518 906 689846534 689846918 1.370000e-127 466.0
20 TraesCS3D01G438300 chr3A 88.235 391 38 5 518 906 689866848 689867232 6.390000e-126 460.0
21 TraesCS3D01G438300 chr3A 88.372 387 38 5 515 900 689659666 689660046 2.300000e-125 459.0
22 TraesCS3D01G438300 chr3A 88.512 383 38 4 518 900 689662507 689662883 2.300000e-125 459.0
23 TraesCS3D01G438300 chr3A 85.050 301 34 6 1299 1592 689524353 689524649 1.910000e-76 296.0
24 TraesCS3D01G438300 chr3A 95.676 185 4 3 1844 2026 686278900 686278718 6.860000e-76 294.0
25 TraesCS3D01G438300 chr3A 84.718 301 35 6 1299 1592 689579481 689579777 8.880000e-75 291.0
26 TraesCS3D01G438300 chr3A 84.718 301 35 6 1299 1592 689609259 689609555 8.880000e-75 291.0
27 TraesCS3D01G438300 chr3A 92.308 156 9 3 1801 1954 689579774 689579928 4.250000e-53 219.0
28 TraesCS3D01G438300 chr3A 92.308 156 9 3 1801 1954 689609552 689609706 4.250000e-53 219.0
29 TraesCS3D01G438300 chr3A 94.366 142 6 2 1708 1848 686279892 686279752 1.530000e-52 217.0
30 TraesCS3D01G438300 chr3A 84.360 211 29 4 267 475 689846322 689846530 1.190000e-48 204.0
31 TraesCS3D01G438300 chr3A 84.360 211 30 3 267 476 689866637 689866845 1.190000e-48 204.0
32 TraesCS3D01G438300 chr3B 93.430 1035 47 10 808 1834 728295448 728294427 0.000000e+00 1515.0
33 TraesCS3D01G438300 chr3B 95.922 515 20 1 92 605 728308326 728307812 0.000000e+00 833.0
34 TraesCS3D01G438300 chr3B 96.795 468 14 1 2069 2535 772443147 772442680 0.000000e+00 780.0
35 TraesCS3D01G438300 chr3B 94.587 351 17 2 2069 2418 545671839 545672188 2.220000e-150 542.0
36 TraesCS3D01G438300 chr3B 88.327 257 28 2 2280 2536 699538051 699538305 8.810000e-80 307.0
37 TraesCS3D01G438300 chr3B 92.350 183 10 3 1846 2026 728293849 728293669 9.000000e-65 257.0
38 TraesCS3D01G438300 chr3B 98.214 56 1 0 2024 2079 545671702 545671757 5.770000e-17 99.0
39 TraesCS3D01G438300 chr3B 96.552 58 2 0 2023 2080 772443285 772443228 2.080000e-16 97.1
40 TraesCS3D01G438300 chr2B 95.879 461 19 0 2075 2535 767646862 767647322 0.000000e+00 747.0
41 TraesCS3D01G438300 chr2B 96.296 54 2 0 2027 2080 767646744 767646797 3.470000e-14 89.8
42 TraesCS3D01G438300 chr7A 95.455 462 21 0 2075 2536 669862740 669863201 0.000000e+00 737.0
43 TraesCS3D01G438300 chr4A 94.872 468 23 1 2069 2535 658860958 658860491 0.000000e+00 730.0
44 TraesCS3D01G438300 chr4A 96.721 61 2 0 2020 2080 658861099 658861039 4.460000e-18 102.0
45 TraesCS3D01G438300 chr1B 89.979 469 28 4 2069 2536 670368840 670368390 2.810000e-164 588.0
46 TraesCS3D01G438300 chr1B 85.580 319 33 6 2229 2536 125712068 125712384 3.150000e-84 322.0
47 TraesCS3D01G438300 chr6A 95.092 163 8 0 2374 2536 49737981 49737819 9.000000e-65 257.0
48 TraesCS3D01G438300 chr6A 89.130 138 8 2 2075 2206 49738120 49737984 5.610000e-37 165.0
49 TraesCS3D01G438300 chr7B 89.820 167 15 2 2077 2242 78675708 78675543 1.980000e-51 213.0
50 TraesCS3D01G438300 chr2D 86.243 189 20 6 361 548 650651782 650651965 1.540000e-47 200.0
51 TraesCS3D01G438300 chr6D 98.148 54 1 0 2023 2076 378380166 378380219 7.470000e-16 95.3


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 TraesCS3D01G438300 chr3D 548997867 549000402 2535 True 4684.000000 4684 100.000000 1 2536 1 chr3D.!!$R2 2535
1 TraesCS3D01G438300 chr3D 553357146 553358486 1340 False 512.000000 612 88.856000 518 1674 3 chr3D.!!$F1 1156
2 TraesCS3D01G438300 chr3D 553405447 553406485 1038 False 418.000000 566 88.475000 214 1298 2 chr3D.!!$F2 1084
3 TraesCS3D01G438300 chr3A 686278718 686281571 2853 True 665.000000 1524 95.127000 379 2026 4 chr3A.!!$R2 1647
4 TraesCS3D01G438300 chr3A 689659666 689663431 3765 False 530.000000 601 88.587000 515 1298 4 chr3A.!!$F4 783
5 TraesCS3D01G438300 chr3A 689523254 689524649 1395 False 507.666667 676 87.653667 378 1592 3 chr3A.!!$F1 1214
6 TraesCS3D01G438300 chr3A 689608205 689609706 1501 False 429.250000 656 89.078750 420 1954 4 chr3A.!!$F3 1534
7 TraesCS3D01G438300 chr3A 689866637 689867825 1188 False 399.333333 534 86.304333 267 1298 3 chr3A.!!$F6 1031
8 TraesCS3D01G438300 chr3A 689578427 689579928 1501 False 387.000000 651 89.386667 420 1954 3 chr3A.!!$F2 1534
9 TraesCS3D01G438300 chr3A 689846322 689846918 596 False 335.000000 466 86.411000 267 906 2 chr3A.!!$F5 639
10 TraesCS3D01G438300 chr3B 728293669 728295448 1779 True 886.000000 1515 92.890000 808 2026 2 chr3B.!!$R2 1218
11 TraesCS3D01G438300 chr3B 728307812 728308326 514 True 833.000000 833 95.922000 92 605 1 chr3B.!!$R1 513
12 TraesCS3D01G438300 chr3B 772442680 772443285 605 True 438.550000 780 96.673500 2023 2535 2 chr3B.!!$R3 512
13 TraesCS3D01G438300 chr2B 767646744 767647322 578 False 418.400000 747 96.087500 2027 2535 2 chr2B.!!$F1 508
14 TraesCS3D01G438300 chr4A 658860491 658861099 608 True 416.000000 730 95.796500 2020 2535 2 chr4A.!!$R1 515

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
85 86 0.535553 TCGGGTTTTTCAGGTTCGGG 60.536 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 4278 1.832608 CATCGATGGGAGGGACCGA 60.833 63.158 17.96 0.0 40.11 4.69 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
21 22 4.519540 CCATGAGTTGAAACCCGAATTT 57.480 40.909 0.00 0.00 0.00 1.82
22 23 4.485163 CCATGAGTTGAAACCCGAATTTC 58.515 43.478 0.00 4.84 38.77 2.17
23 24 4.485163 CATGAGTTGAAACCCGAATTTCC 58.515 43.478 8.36 0.00 37.72 3.13
24 25 2.888414 TGAGTTGAAACCCGAATTTCCC 59.112 45.455 8.36 1.42 37.72 3.97
25 26 2.888414 GAGTTGAAACCCGAATTTCCCA 59.112 45.455 8.36 0.00 37.72 4.37
26 27 3.301274 AGTTGAAACCCGAATTTCCCAA 58.699 40.909 8.36 0.00 37.72 4.12
27 28 3.707102 AGTTGAAACCCGAATTTCCCAAA 59.293 39.130 8.36 0.00 37.72 3.28
28 29 4.346709 AGTTGAAACCCGAATTTCCCAAAT 59.653 37.500 8.36 0.00 37.72 2.32
29 30 5.540719 AGTTGAAACCCGAATTTCCCAAATA 59.459 36.000 8.36 0.00 37.72 1.40
30 31 6.042208 AGTTGAAACCCGAATTTCCCAAATAA 59.958 34.615 8.36 0.00 37.72 1.40
31 32 6.420913 TGAAACCCGAATTTCCCAAATAAA 57.579 33.333 8.36 0.00 37.72 1.40
32 33 6.827727 TGAAACCCGAATTTCCCAAATAAAA 58.172 32.000 8.36 0.00 37.72 1.52
33 34 7.454225 TGAAACCCGAATTTCCCAAATAAAAT 58.546 30.769 8.36 0.00 37.72 1.82
34 35 7.939588 TGAAACCCGAATTTCCCAAATAAAATT 59.060 29.630 8.36 0.00 37.72 1.82
35 36 8.698973 AAACCCGAATTTCCCAAATAAAATTT 57.301 26.923 0.00 0.00 35.72 1.82
36 37 7.680442 ACCCGAATTTCCCAAATAAAATTTG 57.320 32.000 5.56 5.56 35.72 2.32
37 38 6.657117 ACCCGAATTTCCCAAATAAAATTTGG 59.343 34.615 19.92 19.92 46.72 3.28
56 57 9.554395 AAATTTGGGTTTCTAAATTGTTACCTG 57.446 29.630 0.00 0.00 41.23 4.00
57 58 7.899648 TTTGGGTTTCTAAATTGTTACCTGA 57.100 32.000 0.00 0.00 0.00 3.86
58 59 8.485578 TTTGGGTTTCTAAATTGTTACCTGAT 57.514 30.769 0.00 0.00 0.00 2.90
59 60 8.485578 TTGGGTTTCTAAATTGTTACCTGATT 57.514 30.769 0.00 0.00 0.00 2.57
60 61 8.485578 TGGGTTTCTAAATTGTTACCTGATTT 57.514 30.769 0.00 0.00 0.00 2.17
61 62 9.589461 TGGGTTTCTAAATTGTTACCTGATTTA 57.411 29.630 0.00 0.00 0.00 1.40
68 69 9.755064 CTAAATTGTTACCTGATTTAGTGTTCG 57.245 33.333 11.42 0.00 38.02 3.95
69 70 6.737254 ATTGTTACCTGATTTAGTGTTCGG 57.263 37.500 0.00 0.00 0.00 4.30
70 71 4.571919 TGTTACCTGATTTAGTGTTCGGG 58.428 43.478 0.00 0.00 42.98 5.14
75 76 5.447624 CCTGATTTAGTGTTCGGGTTTTT 57.552 39.130 0.00 0.00 34.28 1.94
76 77 5.458015 CCTGATTTAGTGTTCGGGTTTTTC 58.542 41.667 0.00 0.00 34.28 2.29
77 78 5.009210 CCTGATTTAGTGTTCGGGTTTTTCA 59.991 40.000 0.00 0.00 34.28 2.69
78 79 6.067263 TGATTTAGTGTTCGGGTTTTTCAG 57.933 37.500 0.00 0.00 0.00 3.02
79 80 4.904253 TTTAGTGTTCGGGTTTTTCAGG 57.096 40.909 0.00 0.00 0.00 3.86
80 81 2.430248 AGTGTTCGGGTTTTTCAGGT 57.570 45.000 0.00 0.00 0.00 4.00
81 82 2.730382 AGTGTTCGGGTTTTTCAGGTT 58.270 42.857 0.00 0.00 0.00 3.50
82 83 2.686405 AGTGTTCGGGTTTTTCAGGTTC 59.314 45.455 0.00 0.00 0.00 3.62
83 84 1.671845 TGTTCGGGTTTTTCAGGTTCG 59.328 47.619 0.00 0.00 0.00 3.95
84 85 1.002142 GTTCGGGTTTTTCAGGTTCGG 60.002 52.381 0.00 0.00 0.00 4.30
85 86 0.535553 TCGGGTTTTTCAGGTTCGGG 60.536 55.000 0.00 0.00 0.00 5.14
86 87 0.535553 CGGGTTTTTCAGGTTCGGGA 60.536 55.000 0.00 0.00 0.00 5.14
87 88 1.884928 CGGGTTTTTCAGGTTCGGGAT 60.885 52.381 0.00 0.00 0.00 3.85
88 89 2.616001 CGGGTTTTTCAGGTTCGGGATA 60.616 50.000 0.00 0.00 0.00 2.59
89 90 2.751259 GGGTTTTTCAGGTTCGGGATAC 59.249 50.000 0.00 0.00 0.00 2.24
90 91 3.414269 GGTTTTTCAGGTTCGGGATACA 58.586 45.455 0.00 0.00 39.74 2.29
110 111 1.835267 GGGTTCGGGTTTGGGCTTT 60.835 57.895 0.00 0.00 0.00 3.51
152 153 1.331214 CATGAGTGGTGCCCTTGTTT 58.669 50.000 0.00 0.00 0.00 2.83
169 170 2.158534 TGTTTGTCATGGCCTGGTTAGT 60.159 45.455 3.32 0.00 0.00 2.24
189 190 4.775236 AGTCAGACTAGAAAATCATGGCC 58.225 43.478 0.00 0.00 0.00 5.36
204 205 2.561478 TGGCCAGACCTTGTTTAGAC 57.439 50.000 0.00 0.00 40.22 2.59
233 234 6.998673 GGATACTTACTAAGCCAAATGACCAT 59.001 38.462 0.00 0.00 0.00 3.55
309 310 7.829706 AGTATTAGGTTGGAAGATCCTTCAAAC 59.170 37.037 15.21 15.21 37.46 2.93
341 342 0.961019 GCACAAAGCCCTCAATGACA 59.039 50.000 0.00 0.00 37.23 3.58
374 376 9.838339 TGTTATCTTCTTATTTCAGGATTCCTC 57.162 33.333 0.98 0.00 0.00 3.71
621 625 7.863375 CCTTAACATAATTTGTTTTCCACGACA 59.137 33.333 10.04 0.00 46.51 4.35
626 630 7.221838 ACATAATTTGTTTTCCACGACAAGTTG 59.778 33.333 0.00 0.00 36.68 3.16
1171 1477 9.461312 TTCTGGTGCACATATTAATTCTAAGTT 57.539 29.630 20.43 0.00 0.00 2.66
1272 1578 1.681327 GGGGCCTGTCAGTACGAGA 60.681 63.158 0.84 0.00 0.00 4.04
1282 1588 3.887110 TGTCAGTACGAGAACTTCAAGGA 59.113 43.478 0.00 0.00 0.00 3.36
1348 1693 3.579709 AGAGAAAGACGTGCATGTGTAG 58.420 45.455 18.17 0.00 0.00 2.74
1574 1929 9.182214 TGGAAAATGATTTCAATAAGAGAGGAG 57.818 33.333 3.97 0.00 45.53 3.69
1714 2590 3.118186 CCTTACGATCCCATGTACCCAAA 60.118 47.826 0.00 0.00 0.00 3.28
1723 2599 4.017808 CCCATGTACCCAAAACCGATTTA 58.982 43.478 0.00 0.00 0.00 1.40
1769 2647 1.470051 ACGAGCCAACACCTGTTTTT 58.530 45.000 0.00 0.00 35.83 1.94
1791 2670 6.841781 TTCCCCTAAAAATGCTAGACCTAT 57.158 37.500 0.00 0.00 0.00 2.57
1843 2722 6.842437 TCCATCTCTAATTAATCTCCTCCG 57.158 41.667 0.00 0.00 0.00 4.63
1976 4278 1.073199 CCTTGTGCGACCCTTCCTT 59.927 57.895 0.00 0.00 0.00 3.36
2255 4713 4.172807 TCTCTTTAACTGCCCCTCCTAAA 58.827 43.478 0.00 0.00 0.00 1.85
2264 4722 4.154942 CTGCCCCTCCTAAATTTATGCAT 58.845 43.478 3.79 3.79 0.00 3.96
2391 6107 4.793071 CAAAAATACATGTGTGCCGAAGA 58.207 39.130 9.11 0.00 0.00 2.87
2421 6137 5.442391 ACTCTGGTTGTTTGGTTTAAGCTA 58.558 37.500 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.485163 GGAAATTCGGGTTTCAACTCATG 58.515 43.478 13.03 0.00 39.33 3.07
3 4 2.888414 GGGAAATTCGGGTTTCAACTCA 59.112 45.455 13.03 0.00 39.33 3.41
4 5 2.888414 TGGGAAATTCGGGTTTCAACTC 59.112 45.455 13.03 0.00 39.33 3.01
5 6 2.952116 TGGGAAATTCGGGTTTCAACT 58.048 42.857 13.03 0.00 39.33 3.16
6 7 3.737032 TTGGGAAATTCGGGTTTCAAC 57.263 42.857 13.03 7.59 39.33 3.18
7 8 4.965200 ATTTGGGAAATTCGGGTTTCAA 57.035 36.364 13.03 3.00 39.33 2.69
8 9 6.420913 TTTATTTGGGAAATTCGGGTTTCA 57.579 33.333 13.03 0.00 39.33 2.69
9 10 7.915293 ATTTTATTTGGGAAATTCGGGTTTC 57.085 32.000 5.27 5.27 37.37 2.78
10 11 8.572185 CAAATTTTATTTGGGAAATTCGGGTTT 58.428 29.630 4.59 0.00 35.14 3.27
11 12 7.175816 CCAAATTTTATTTGGGAAATTCGGGTT 59.824 33.333 18.97 0.00 43.88 4.11
12 13 6.657117 CCAAATTTTATTTGGGAAATTCGGGT 59.343 34.615 18.97 0.00 43.88 5.28
13 14 7.082700 CCAAATTTTATTTGGGAAATTCGGG 57.917 36.000 18.97 0.00 43.88 5.14
30 31 9.554395 CAGGTAACAATTTAGAAACCCAAATTT 57.446 29.630 0.00 0.00 33.23 1.82
31 32 8.929487 TCAGGTAACAATTTAGAAACCCAAATT 58.071 29.630 0.00 0.00 35.30 1.82
32 33 8.485578 TCAGGTAACAATTTAGAAACCCAAAT 57.514 30.769 0.00 0.00 41.41 2.32
33 34 7.899648 TCAGGTAACAATTTAGAAACCCAAA 57.100 32.000 0.00 0.00 41.41 3.28
34 35 8.485578 AATCAGGTAACAATTTAGAAACCCAA 57.514 30.769 0.00 0.00 41.41 4.12
35 36 8.485578 AAATCAGGTAACAATTTAGAAACCCA 57.514 30.769 0.00 0.00 41.41 4.51
43 44 8.723311 CCGAACACTAAATCAGGTAACAATTTA 58.277 33.333 0.00 0.24 36.18 1.40
44 45 7.308951 CCCGAACACTAAATCAGGTAACAATTT 60.309 37.037 0.00 0.00 37.75 1.82
45 46 6.150474 CCCGAACACTAAATCAGGTAACAATT 59.850 38.462 0.00 0.00 41.41 2.32
46 47 5.646360 CCCGAACACTAAATCAGGTAACAAT 59.354 40.000 0.00 0.00 41.41 2.71
47 48 4.998672 CCCGAACACTAAATCAGGTAACAA 59.001 41.667 0.00 0.00 41.41 2.83
48 49 4.040706 ACCCGAACACTAAATCAGGTAACA 59.959 41.667 0.00 0.00 41.41 2.41
49 50 4.572909 ACCCGAACACTAAATCAGGTAAC 58.427 43.478 0.00 0.00 0.00 2.50
50 51 4.895668 ACCCGAACACTAAATCAGGTAA 57.104 40.909 0.00 0.00 0.00 2.85
51 52 4.895668 AACCCGAACACTAAATCAGGTA 57.104 40.909 0.00 0.00 0.00 3.08
52 53 3.782656 AACCCGAACACTAAATCAGGT 57.217 42.857 0.00 0.00 0.00 4.00
53 54 5.009210 TGAAAAACCCGAACACTAAATCAGG 59.991 40.000 0.00 0.00 0.00 3.86
54 55 6.067263 TGAAAAACCCGAACACTAAATCAG 57.933 37.500 0.00 0.00 0.00 2.90
55 56 5.009210 CCTGAAAAACCCGAACACTAAATCA 59.991 40.000 0.00 0.00 0.00 2.57
56 57 5.009310 ACCTGAAAAACCCGAACACTAAATC 59.991 40.000 0.00 0.00 0.00 2.17
57 58 4.891168 ACCTGAAAAACCCGAACACTAAAT 59.109 37.500 0.00 0.00 0.00 1.40
58 59 4.271661 ACCTGAAAAACCCGAACACTAAA 58.728 39.130 0.00 0.00 0.00 1.85
59 60 3.888583 ACCTGAAAAACCCGAACACTAA 58.111 40.909 0.00 0.00 0.00 2.24
60 61 3.564053 ACCTGAAAAACCCGAACACTA 57.436 42.857 0.00 0.00 0.00 2.74
61 62 2.430248 ACCTGAAAAACCCGAACACT 57.570 45.000 0.00 0.00 0.00 3.55
62 63 2.540157 CGAACCTGAAAAACCCGAACAC 60.540 50.000 0.00 0.00 0.00 3.32
63 64 1.671845 CGAACCTGAAAAACCCGAACA 59.328 47.619 0.00 0.00 0.00 3.18
64 65 1.002142 CCGAACCTGAAAAACCCGAAC 60.002 52.381 0.00 0.00 0.00 3.95
65 66 1.310904 CCGAACCTGAAAAACCCGAA 58.689 50.000 0.00 0.00 0.00 4.30
66 67 0.535553 CCCGAACCTGAAAAACCCGA 60.536 55.000 0.00 0.00 0.00 5.14
67 68 0.535553 TCCCGAACCTGAAAAACCCG 60.536 55.000 0.00 0.00 0.00 5.28
68 69 1.919240 ATCCCGAACCTGAAAAACCC 58.081 50.000 0.00 0.00 0.00 4.11
69 70 3.189910 GTGTATCCCGAACCTGAAAAACC 59.810 47.826 0.00 0.00 0.00 3.27
70 71 3.120442 CGTGTATCCCGAACCTGAAAAAC 60.120 47.826 0.00 0.00 0.00 2.43
71 72 3.068560 CGTGTATCCCGAACCTGAAAAA 58.931 45.455 0.00 0.00 0.00 1.94
72 73 2.613474 CCGTGTATCCCGAACCTGAAAA 60.613 50.000 0.00 0.00 0.00 2.29
73 74 1.066716 CCGTGTATCCCGAACCTGAAA 60.067 52.381 0.00 0.00 0.00 2.69
74 75 0.533491 CCGTGTATCCCGAACCTGAA 59.467 55.000 0.00 0.00 0.00 3.02
75 76 1.324740 CCCGTGTATCCCGAACCTGA 61.325 60.000 0.00 0.00 0.00 3.86
76 77 1.143183 CCCGTGTATCCCGAACCTG 59.857 63.158 0.00 0.00 0.00 4.00
77 78 0.906282 AACCCGTGTATCCCGAACCT 60.906 55.000 0.00 0.00 0.00 3.50
78 79 0.460811 GAACCCGTGTATCCCGAACC 60.461 60.000 0.00 0.00 0.00 3.62
79 80 0.803380 CGAACCCGTGTATCCCGAAC 60.803 60.000 0.00 0.00 0.00 3.95
80 81 1.512230 CGAACCCGTGTATCCCGAA 59.488 57.895 0.00 0.00 0.00 4.30
81 82 2.417257 CCGAACCCGTGTATCCCGA 61.417 63.158 0.00 0.00 0.00 5.14
82 83 2.105528 CCGAACCCGTGTATCCCG 59.894 66.667 0.00 0.00 0.00 5.14
83 84 1.902765 AACCCGAACCCGTGTATCCC 61.903 60.000 0.00 0.00 0.00 3.85
84 85 0.036105 AAACCCGAACCCGTGTATCC 60.036 55.000 0.00 0.00 0.00 2.59
85 86 1.081094 CAAACCCGAACCCGTGTATC 58.919 55.000 0.00 0.00 0.00 2.24
86 87 0.321830 CCAAACCCGAACCCGTGTAT 60.322 55.000 0.00 0.00 0.00 2.29
87 88 1.071128 CCAAACCCGAACCCGTGTA 59.929 57.895 0.00 0.00 0.00 2.90
88 89 2.203238 CCAAACCCGAACCCGTGT 60.203 61.111 0.00 0.00 0.00 4.49
89 90 2.981350 CCCAAACCCGAACCCGTG 60.981 66.667 0.00 0.00 0.00 4.94
90 91 4.960866 GCCCAAACCCGAACCCGT 62.961 66.667 0.00 0.00 0.00 5.28
152 153 1.278985 CTGACTAACCAGGCCATGACA 59.721 52.381 5.01 0.00 0.00 3.58
169 170 4.471025 TCTGGCCATGATTTTCTAGTCTGA 59.529 41.667 5.51 0.00 0.00 3.27
189 190 7.162082 AGTATCCAAAGTCTAAACAAGGTCTG 58.838 38.462 0.00 0.00 0.00 3.51
204 205 8.398665 GTCATTTGGCTTAGTAAGTATCCAAAG 58.601 37.037 24.89 19.53 43.89 2.77
233 234 3.521560 GCTAACATGGAGTCGATCAACA 58.478 45.455 0.00 0.00 0.00 3.33
309 310 1.733402 TTTGTGCTTCAACGCCCAGG 61.733 55.000 0.00 0.00 35.61 4.45
374 376 4.974368 AGTCCTTAGTCGACTGAGATTG 57.026 45.455 32.33 18.92 39.14 2.67
887 992 6.754702 CATTCAATGCCTTAGAGGATATGG 57.245 41.667 0.00 0.00 37.67 2.74
1095 1400 9.681692 CGATTGATCTAAAATTGCATGGAATTA 57.318 29.630 23.36 10.03 0.00 1.40
1132 1438 8.752005 ATGTGCACCAGAAAATTATAGTACAT 57.248 30.769 15.69 0.00 0.00 2.29
1171 1477 2.584064 CCTCCGCACCTGCATGTA 59.416 61.111 0.00 0.00 42.21 2.29
1194 1500 2.031163 GCTAGGGGCCGTGCATAG 59.969 66.667 9.43 0.00 34.27 2.23
1272 1578 2.644798 AGCAGTACCCATCCTTGAAGTT 59.355 45.455 0.00 0.00 0.00 2.66
1348 1693 4.405358 TGGGGTTTTTCCTGCATTCATATC 59.595 41.667 0.00 0.00 36.25 1.63
1476 1828 3.982576 TTTCTTCTTGTTTTCTCCCGC 57.017 42.857 0.00 0.00 0.00 6.13
1714 2590 7.148137 GGTGTTGTATGAGGAAATAAATCGGTT 60.148 37.037 0.00 0.00 0.00 4.44
1723 2599 4.343231 TGCATGGTGTTGTATGAGGAAAT 58.657 39.130 0.00 0.00 0.00 2.17
1769 2647 5.908831 TCATAGGTCTAGCATTTTTAGGGGA 59.091 40.000 0.00 0.00 0.00 4.81
1843 2722 2.678471 CCCACAATGAAATTCAGGGC 57.322 50.000 5.28 0.00 39.66 5.19
1940 4242 5.357032 CACAAGGGAAAAAGGATAACGCTAT 59.643 40.000 0.00 0.00 0.00 2.97
1976 4278 1.832608 CATCGATGGGAGGGACCGA 60.833 63.158 17.96 0.00 40.11 4.69
2264 4722 8.613482 TGACCGAAATTATCATTTAAATACGCA 58.387 29.630 0.00 0.00 32.35 5.24
2277 4735 8.446599 TCCTAAAAATCCTGACCGAAATTATC 57.553 34.615 0.00 0.00 0.00 1.75
2391 6107 3.951680 ACCAAACAACCAGAGTTCGAATT 59.048 39.130 0.00 0.00 32.45 2.17
2421 6137 6.265422 GGTTGATTTATTGGTTGGCTAGCTAT 59.735 38.462 15.72 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.