Multiple sequence alignment - TraesCS5D01G359100

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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 TraesCS5D01G359100 chr5D 100.000 3986 0 0 1 3986 438593678 438597663 0.000000e+00 7361.0
1 TraesCS5D01G359100 chr5D 96.117 3374 125 3 615 3983 438690766 438694138 0.000000e+00 5500.0
2 TraesCS5D01G359100 chr5D 86.545 602 60 10 2286 2876 438725606 438726197 0.000000e+00 643.0
3 TraesCS5D01G359100 chr5D 85.977 599 69 5 2286 2876 438661717 438662308 9.400000e-176 627.0
4 TraesCS5D01G359100 chr5D 91.954 174 13 1 298 470 438690320 438690493 3.980000e-60 243.0
5 TraesCS5D01G359100 chr5D 89.888 89 5 3 2900 2984 438662304 438662392 1.170000e-20 111.0
6 TraesCS5D01G359100 chr5A 94.116 3705 159 11 298 3983 554206502 554210166 0.000000e+00 5579.0
7 TraesCS5D01G359100 chr5A 85.199 527 68 7 2298 2820 554239367 554239887 2.110000e-147 532.0
8 TraesCS5D01G359100 chr5A 79.878 328 58 3 993 1314 554205694 554206019 2.400000e-57 233.0
9 TraesCS5D01G359100 chr5B 96.100 3128 96 3 669 3789 533499448 533502556 0.000000e+00 5077.0
10 TraesCS5D01G359100 chr5B 88.592 561 61 2 2286 2846 533526280 533526837 0.000000e+00 678.0
11 TraesCS5D01G359100 chr5B 86.364 572 68 7 2286 2848 533576315 533576885 2.040000e-172 616.0
12 TraesCS5D01G359100 chr5B 71.864 1379 352 25 1349 2700 511606172 511607541 8.140000e-97 364.0
13 TraesCS5D01G359100 chr5B 87.147 319 27 7 311 615 533499055 533499373 2.280000e-92 350.0
14 TraesCS5D01G359100 chr5B 88.406 207 13 2 3781 3976 533503436 533503642 5.150000e-59 239.0
15 TraesCS5D01G359100 chr5B 89.394 66 7 0 3894 3959 533526948 533527013 2.550000e-12 84.2


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 TraesCS5D01G359100 chr5D 438593678 438597663 3985 False 7361.000000 7361 100.0000 1 3986 1 chr5D.!!$F1 3985
1 TraesCS5D01G359100 chr5D 438690320 438694138 3818 False 2871.500000 5500 94.0355 298 3983 2 chr5D.!!$F4 3685
2 TraesCS5D01G359100 chr5D 438725606 438726197 591 False 643.000000 643 86.5450 2286 2876 1 chr5D.!!$F2 590
3 TraesCS5D01G359100 chr5D 438661717 438662392 675 False 369.000000 627 87.9325 2286 2984 2 chr5D.!!$F3 698
4 TraesCS5D01G359100 chr5A 554205694 554210166 4472 False 2906.000000 5579 86.9970 298 3983 2 chr5A.!!$F2 3685
5 TraesCS5D01G359100 chr5A 554239367 554239887 520 False 532.000000 532 85.1990 2298 2820 1 chr5A.!!$F1 522
6 TraesCS5D01G359100 chr5B 533499055 533503642 4587 False 1888.666667 5077 90.5510 311 3976 3 chr5B.!!$F3 3665
7 TraesCS5D01G359100 chr5B 533576315 533576885 570 False 616.000000 616 86.3640 2286 2848 1 chr5B.!!$F2 562
8 TraesCS5D01G359100 chr5B 533526280 533527013 733 False 381.100000 678 88.9930 2286 3959 2 chr5B.!!$F4 1673
9 TraesCS5D01G359100 chr5B 511606172 511607541 1369 False 364.000000 364 71.8640 1349 2700 1 chr5B.!!$F1 1351

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
19 20 0.033601 ATCCTCTCGAGCCAGACACT 60.034 55.0 7.81 0.0 0.00 3.55 F
26 27 0.038251 CGAGCCAGACACTGTAGCAA 60.038 55.0 0.00 0.0 0.00 3.91 F
1088 1774 0.327480 ATGTCCATGGCCACCTCCTA 60.327 55.0 8.16 0.0 0.00 2.94 F
1178 1864 0.767375 ACCAGCATGACAAGTGACCT 59.233 50.0 0.00 0.0 39.69 3.85 F
2718 3460 1.065410 TTCCCCAGGACTTTGGAGCA 61.065 55.0 0.00 0.0 40.87 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1099 1785 1.065564 GCTCCTGCTGGATGTTTCTCT 60.066 52.381 13.33 0.00 42.29 3.10 R
1178 1864 1.134220 AGGAGTCCAGTCGTTTTGCAA 60.134 47.619 12.86 0.00 0.00 4.08 R
2086 2796 3.107402 AGCAGACAGATCTAAGGACCA 57.893 47.619 0.00 0.00 32.25 4.02 R
2735 3477 5.874831 TGATATGGTTTGCGAACAATACAC 58.125 37.500 15.03 12.56 35.12 2.90 R
3921 5570 0.469494 TTCAGTGAAGCACCAGCAGA 59.531 50.000 0.08 0.00 45.49 4.26 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
19 20 0.033601 ATCCTCTCGAGCCAGACACT 60.034 55.000 7.81 0.00 0.00 3.55
20 21 0.962855 TCCTCTCGAGCCAGACACTG 60.963 60.000 7.81 0.00 0.00 3.66
21 22 1.247419 CCTCTCGAGCCAGACACTGT 61.247 60.000 7.81 0.00 0.00 3.55
23 24 1.400142 CTCTCGAGCCAGACACTGTAG 59.600 57.143 7.81 0.00 0.00 2.74
24 25 0.179150 CTCGAGCCAGACACTGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
26 27 0.038251 CGAGCCAGACACTGTAGCAA 60.038 55.000 0.00 0.00 0.00 3.91
27 28 1.605457 CGAGCCAGACACTGTAGCAAA 60.605 52.381 0.00 0.00 0.00 3.68
28 29 1.801178 GAGCCAGACACTGTAGCAAAC 59.199 52.381 0.00 0.00 0.00 2.93
30 31 1.872237 GCCAGACACTGTAGCAAACGA 60.872 52.381 0.00 0.00 0.00 3.85
31 32 2.688507 CCAGACACTGTAGCAAACGAT 58.311 47.619 0.00 0.00 0.00 3.73
32 33 2.413112 CCAGACACTGTAGCAAACGATG 59.587 50.000 0.00 0.00 0.00 3.84
33 34 3.059884 CAGACACTGTAGCAAACGATGT 58.940 45.455 0.00 0.00 0.00 3.06
34 35 3.494626 CAGACACTGTAGCAAACGATGTT 59.505 43.478 0.00 0.00 0.00 2.71
35 36 4.024893 CAGACACTGTAGCAAACGATGTTT 60.025 41.667 0.00 0.00 0.00 2.83
36 37 4.574828 AGACACTGTAGCAAACGATGTTTT 59.425 37.500 0.00 0.00 0.00 2.43
39 40 4.440758 CACTGTAGCAAACGATGTTTTTGG 59.559 41.667 0.00 0.00 34.97 3.28
40 41 4.097286 ACTGTAGCAAACGATGTTTTTGGT 59.903 37.500 5.62 5.62 44.60 3.67
41 42 5.000012 TGTAGCAAACGATGTTTTTGGTT 58.000 34.783 5.62 0.00 40.82 3.67
42 43 5.411781 TGTAGCAAACGATGTTTTTGGTTT 58.588 33.333 5.62 0.00 40.82 3.27
43 44 5.869888 TGTAGCAAACGATGTTTTTGGTTTT 59.130 32.000 5.62 0.00 40.82 2.43
44 45 5.463499 AGCAAACGATGTTTTTGGTTTTC 57.537 34.783 0.00 0.00 40.82 2.29
45 46 4.932200 AGCAAACGATGTTTTTGGTTTTCA 59.068 33.333 0.00 0.00 40.82 2.69
46 47 5.063312 AGCAAACGATGTTTTTGGTTTTCAG 59.937 36.000 0.00 0.00 40.82 3.02
47 48 5.254842 CAAACGATGTTTTTGGTTTTCAGC 58.745 37.500 0.00 0.00 30.73 4.26
48 49 3.453424 ACGATGTTTTTGGTTTTCAGCC 58.547 40.909 0.00 0.00 0.00 4.85
49 50 2.470999 CGATGTTTTTGGTTTTCAGCCG 59.529 45.455 0.00 0.00 0.00 5.52
50 51 2.301577 TGTTTTTGGTTTTCAGCCGG 57.698 45.000 0.00 0.00 0.00 6.13
51 52 1.134670 TGTTTTTGGTTTTCAGCCGGG 60.135 47.619 2.18 0.00 0.00 5.73
55 56 1.196012 TTGGTTTTCAGCCGGGTTTT 58.804 45.000 1.64 0.00 0.00 2.43
57 58 2.385803 TGGTTTTCAGCCGGGTTTTAA 58.614 42.857 1.64 0.00 0.00 1.52
58 59 2.764572 TGGTTTTCAGCCGGGTTTTAAA 59.235 40.909 1.64 2.10 0.00 1.52
59 60 3.197116 TGGTTTTCAGCCGGGTTTTAAAA 59.803 39.130 1.64 8.78 0.00 1.52
60 61 3.805422 GGTTTTCAGCCGGGTTTTAAAAG 59.195 43.478 1.64 0.00 0.00 2.27
61 62 4.435425 GTTTTCAGCCGGGTTTTAAAAGT 58.565 39.130 1.64 0.00 0.00 2.66
62 63 5.451659 GGTTTTCAGCCGGGTTTTAAAAGTA 60.452 40.000 1.64 0.00 0.00 2.24
63 64 4.834357 TTCAGCCGGGTTTTAAAAGTAC 57.166 40.909 1.64 0.00 0.00 2.73
65 66 3.816523 TCAGCCGGGTTTTAAAAGTACAG 59.183 43.478 1.64 0.00 0.00 2.74
66 67 3.816523 CAGCCGGGTTTTAAAAGTACAGA 59.183 43.478 1.64 0.00 0.00 3.41
67 68 4.457949 CAGCCGGGTTTTAAAAGTACAGAT 59.542 41.667 1.64 0.00 0.00 2.90
68 69 4.457949 AGCCGGGTTTTAAAAGTACAGATG 59.542 41.667 0.00 0.00 0.00 2.90
69 70 4.456566 GCCGGGTTTTAAAAGTACAGATGA 59.543 41.667 2.18 0.00 0.00 2.92
70 71 5.391629 GCCGGGTTTTAAAAGTACAGATGAG 60.392 44.000 2.18 0.00 0.00 2.90
71 72 5.704053 CCGGGTTTTAAAAGTACAGATGAGT 59.296 40.000 0.00 0.00 0.00 3.41
72 73 6.206048 CCGGGTTTTAAAAGTACAGATGAGTT 59.794 38.462 0.00 0.00 0.00 3.01
73 74 7.255346 CCGGGTTTTAAAAGTACAGATGAGTTT 60.255 37.037 0.00 0.00 0.00 2.66
74 75 8.132995 CGGGTTTTAAAAGTACAGATGAGTTTT 58.867 33.333 0.00 0.00 0.00 2.43
88 89 9.903682 ACAGATGAGTTTTACAAATTTGAGATG 57.096 29.630 24.64 0.00 0.00 2.90
89 90 8.857216 CAGATGAGTTTTACAAATTTGAGATGC 58.143 33.333 24.64 10.99 0.00 3.91
91 92 7.048629 TGAGTTTTACAAATTTGAGATGCCA 57.951 32.000 24.64 10.50 0.00 4.92
93 94 7.437862 TGAGTTTTACAAATTTGAGATGCCAAC 59.562 33.333 24.64 14.67 0.00 3.77
94 95 7.271511 AGTTTTACAAATTTGAGATGCCAACA 58.728 30.769 24.64 0.00 0.00 3.33
95 96 7.768120 AGTTTTACAAATTTGAGATGCCAACAA 59.232 29.630 24.64 0.00 0.00 2.83
97 98 8.674263 TTTACAAATTTGAGATGCCAACAATT 57.326 26.923 24.64 0.00 0.00 2.32
98 99 8.674263 TTACAAATTTGAGATGCCAACAATTT 57.326 26.923 24.64 0.00 0.00 1.82
100 101 7.998580 ACAAATTTGAGATGCCAACAATTTTT 58.001 26.923 24.64 0.00 30.34 1.94
269 270 6.597262 AACAAGGAAAAATGTAAAAAGCCG 57.403 33.333 0.00 0.00 0.00 5.52
271 272 5.163395 ACAAGGAAAAATGTAAAAAGCCGGA 60.163 36.000 5.05 0.00 0.00 5.14
272 273 4.878439 AGGAAAAATGTAAAAAGCCGGAC 58.122 39.130 5.05 0.00 0.00 4.79
273 274 4.342665 AGGAAAAATGTAAAAAGCCGGACA 59.657 37.500 5.05 0.00 0.00 4.02
274 275 4.684242 GGAAAAATGTAAAAAGCCGGACAG 59.316 41.667 5.05 0.00 0.00 3.51
275 276 5.508320 GGAAAAATGTAAAAAGCCGGACAGA 60.508 40.000 5.05 0.00 0.00 3.41
278 279 3.974871 TGTAAAAAGCCGGACAGAAAC 57.025 42.857 5.05 0.00 0.00 2.78
281 282 2.067365 AAAAGCCGGACAGAAACCTT 57.933 45.000 5.05 0.00 0.00 3.50
282 283 2.067365 AAAGCCGGACAGAAACCTTT 57.933 45.000 5.05 0.00 0.00 3.11
283 284 1.605753 AAGCCGGACAGAAACCTTTC 58.394 50.000 5.05 0.00 37.45 2.62
284 285 0.472471 AGCCGGACAGAAACCTTTCA 59.528 50.000 5.05 0.00 39.61 2.69
285 286 0.875059 GCCGGACAGAAACCTTTCAG 59.125 55.000 5.05 0.00 39.61 3.02
286 287 1.542547 GCCGGACAGAAACCTTTCAGA 60.543 52.381 5.05 0.00 39.61 3.27
287 288 2.846193 CCGGACAGAAACCTTTCAGAA 58.154 47.619 0.00 0.00 39.61 3.02
288 289 2.808543 CCGGACAGAAACCTTTCAGAAG 59.191 50.000 0.00 0.00 39.61 2.85
316 828 1.531602 GCCCAACTCACCTTGGCTT 60.532 57.895 0.00 0.00 39.67 4.35
359 872 3.441222 CCAGCAATTTGATGTAGTGAGCA 59.559 43.478 13.16 0.00 30.62 4.26
399 916 2.961424 CCCCCTCCACACAATCAAC 58.039 57.895 0.00 0.00 0.00 3.18
456 973 6.035542 GCAGATTTAGAGAACTCACTTAGCAC 59.964 42.308 4.64 0.00 0.00 4.40
474 992 5.864628 AGCACTAAAGCTTAGTTTGTAGC 57.135 39.130 0.00 3.77 43.70 3.58
475 993 5.305585 AGCACTAAAGCTTAGTTTGTAGCA 58.694 37.500 0.00 0.00 43.70 3.49
477 995 5.609088 CACTAAAGCTTAGTTTGTAGCACG 58.391 41.667 0.00 0.00 39.85 5.34
478 996 5.404366 CACTAAAGCTTAGTTTGTAGCACGA 59.596 40.000 0.00 0.00 39.85 4.35
479 997 5.987347 ACTAAAGCTTAGTTTGTAGCACGAA 59.013 36.000 0.00 0.00 39.85 3.85
520 1126 2.605837 TGTCCAGCTTCAAACGTACA 57.394 45.000 0.00 0.00 0.00 2.90
530 1136 3.610040 TCAAACGTACATGAGATGCCT 57.390 42.857 0.00 0.00 0.00 4.75
592 1198 4.344679 TGACAGAGGGAAAACAATTGCATT 59.655 37.500 5.05 0.18 0.00 3.56
616 1302 5.940470 TCCTTCATGGAAGAAAAAGCTAGAC 59.060 40.000 7.52 0.00 42.94 2.59
715 1401 3.342377 TGCTGATGGTTCCGACAATAA 57.658 42.857 0.00 0.00 0.00 1.40
937 1623 3.074412 GAGGAATTTTCAACCTCTCGCA 58.926 45.455 0.00 0.00 44.54 5.10
1016 1702 0.756442 ACAATGGCCACAGCAACACT 60.756 50.000 8.16 0.00 42.56 3.55
1088 1774 0.327480 ATGTCCATGGCCACCTCCTA 60.327 55.000 8.16 0.00 0.00 2.94
1098 1784 1.981495 GCCACCTCCTATTCCTATGCT 59.019 52.381 0.00 0.00 0.00 3.79
1099 1785 3.173965 GCCACCTCCTATTCCTATGCTA 58.826 50.000 0.00 0.00 0.00 3.49
1162 1848 1.609208 GCTGCTCTCCTTCAAAACCA 58.391 50.000 0.00 0.00 0.00 3.67
1178 1864 0.767375 ACCAGCATGACAAGTGACCT 59.233 50.000 0.00 0.00 39.69 3.85
1210 1896 2.132300 GACTCCTGGAGAGGCCATC 58.868 63.158 29.71 11.96 46.08 3.51
1257 1943 1.826054 CAACAACCGGACAGGCCAA 60.826 57.895 9.46 0.00 46.52 4.52
1296 1982 2.094597 CCGCAATGCCTTCATCAAAGAA 60.095 45.455 0.00 0.00 37.12 2.52
1302 1988 7.037438 GCAATGCCTTCATCAAAGAAGATAAA 58.963 34.615 5.34 0.00 46.18 1.40
1562 2254 1.614317 CCACCTTAACCTTGAGGCCAG 60.614 57.143 5.01 0.00 37.45 4.85
2086 2796 4.084223 CGGCGTGTACAAAGAGTAAATTGT 60.084 41.667 0.00 0.00 42.16 2.71
2152 2862 5.393962 CAAGCAGTATTAAGCAGTGGAAAC 58.606 41.667 0.00 0.00 0.00 2.78
2718 3460 1.065410 TTCCCCAGGACTTTGGAGCA 61.065 55.000 0.00 0.00 40.87 4.26
2719 3461 1.065410 TCCCCAGGACTTTGGAGCAA 61.065 55.000 0.00 0.00 40.87 3.91
3050 3804 3.154827 ACGTGGACATCAGGGAAATTT 57.845 42.857 0.00 0.00 35.71 1.82
3204 3958 4.679373 TTGGCCAACTTAAAAGCAATGA 57.321 36.364 16.05 0.00 0.00 2.57
3224 3978 9.956720 GCAATGACTCAATATAGCAAAATAAGT 57.043 29.630 0.00 0.00 0.00 2.24
3452 4206 5.449725 GCTGAAGCTTCTGAATATTTCCCAC 60.450 44.000 30.77 9.66 38.21 4.61
3534 4288 4.428209 TGATCTCTCATTCAACGAGCTTC 58.572 43.478 0.00 0.00 0.00 3.86
3688 4442 4.729227 TCGGCAACAACTATCTATGTGA 57.271 40.909 0.00 0.00 0.00 3.58
3824 5466 4.524328 GGACTTTGGATGGTCTTTGTCATT 59.476 41.667 0.00 0.00 33.46 2.57
3912 5561 1.808133 GCAAATGTCCGTGGCCAAAAA 60.808 47.619 7.24 0.00 0.00 1.94
3978 5631 3.271250 GCTTGGGCTTTCTGATCCA 57.729 52.632 0.00 0.00 35.22 3.41
3983 5636 0.915364 GGGCTTTCTGATCCACCTCT 59.085 55.000 0.00 0.00 0.00 3.69
3984 5637 1.283321 GGGCTTTCTGATCCACCTCTT 59.717 52.381 0.00 0.00 0.00 2.85
3985 5638 2.505819 GGGCTTTCTGATCCACCTCTTA 59.494 50.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.247419 ACAGTGTCTGGCTCGAGAGG 61.247 60.000 18.75 4.97 35.51 3.69
3 4 1.400142 CTACAGTGTCTGGCTCGAGAG 59.600 57.143 18.75 5.61 35.51 3.20
4 5 1.454201 CTACAGTGTCTGGCTCGAGA 58.546 55.000 18.75 0.00 35.51 4.04
5 6 0.179150 GCTACAGTGTCTGGCTCGAG 60.179 60.000 8.45 8.45 35.51 4.04
6 7 0.893727 TGCTACAGTGTCTGGCTCGA 60.894 55.000 0.00 0.00 35.51 4.04
7 8 0.038251 TTGCTACAGTGTCTGGCTCG 60.038 55.000 0.00 0.00 35.51 5.03
9 10 1.873903 CGTTTGCTACAGTGTCTGGCT 60.874 52.381 0.00 0.00 35.51 4.75
11 12 2.148916 TCGTTTGCTACAGTGTCTGG 57.851 50.000 0.00 0.00 35.51 3.86
13 14 3.386768 ACATCGTTTGCTACAGTGTCT 57.613 42.857 0.00 0.00 0.00 3.41
14 15 4.468095 AAACATCGTTTGCTACAGTGTC 57.532 40.909 0.00 0.00 0.00 3.67
15 16 4.893424 AAAACATCGTTTGCTACAGTGT 57.107 36.364 0.00 0.00 0.00 3.55
16 17 4.440758 CCAAAAACATCGTTTGCTACAGTG 59.559 41.667 0.00 0.00 35.13 3.66
19 20 4.640789 ACCAAAAACATCGTTTGCTACA 57.359 36.364 0.00 0.00 35.13 2.74
20 21 5.959652 AAACCAAAAACATCGTTTGCTAC 57.040 34.783 0.00 0.00 35.13 3.58
21 22 6.100004 TGAAAACCAAAAACATCGTTTGCTA 58.900 32.000 0.00 0.00 35.13 3.49
23 24 5.209944 TGAAAACCAAAAACATCGTTTGC 57.790 34.783 0.00 0.00 35.13 3.68
24 25 5.254842 GCTGAAAACCAAAAACATCGTTTG 58.745 37.500 0.00 0.00 36.03 2.93
26 27 3.868661 GGCTGAAAACCAAAAACATCGTT 59.131 39.130 0.00 0.00 0.00 3.85
27 28 3.453424 GGCTGAAAACCAAAAACATCGT 58.547 40.909 0.00 0.00 0.00 3.73
28 29 2.470999 CGGCTGAAAACCAAAAACATCG 59.529 45.455 0.00 0.00 0.00 3.84
30 31 2.484594 CCCGGCTGAAAACCAAAAACAT 60.485 45.455 0.00 0.00 0.00 2.71
31 32 1.134670 CCCGGCTGAAAACCAAAAACA 60.135 47.619 0.00 0.00 0.00 2.83
32 33 1.134640 ACCCGGCTGAAAACCAAAAAC 60.135 47.619 0.00 0.00 0.00 2.43
33 34 1.196012 ACCCGGCTGAAAACCAAAAA 58.804 45.000 0.00 0.00 0.00 1.94
34 35 1.196012 AACCCGGCTGAAAACCAAAA 58.804 45.000 0.00 0.00 0.00 2.44
35 36 1.196012 AAACCCGGCTGAAAACCAAA 58.804 45.000 0.00 0.00 0.00 3.28
36 37 1.196012 AAAACCCGGCTGAAAACCAA 58.804 45.000 0.00 0.00 0.00 3.67
39 40 4.435425 ACTTTTAAAACCCGGCTGAAAAC 58.565 39.130 0.00 0.00 0.00 2.43
40 41 4.739587 ACTTTTAAAACCCGGCTGAAAA 57.260 36.364 0.00 0.00 0.00 2.29
41 42 4.643784 TGTACTTTTAAAACCCGGCTGAAA 59.356 37.500 0.00 0.00 0.00 2.69
42 43 4.205587 TGTACTTTTAAAACCCGGCTGAA 58.794 39.130 0.00 0.00 0.00 3.02
43 44 3.816523 CTGTACTTTTAAAACCCGGCTGA 59.183 43.478 0.00 0.00 0.00 4.26
44 45 3.816523 TCTGTACTTTTAAAACCCGGCTG 59.183 43.478 0.00 0.00 0.00 4.85
45 46 4.089408 TCTGTACTTTTAAAACCCGGCT 57.911 40.909 0.00 0.00 0.00 5.52
46 47 4.456566 TCATCTGTACTTTTAAAACCCGGC 59.543 41.667 0.00 0.00 0.00 6.13
47 48 5.704053 ACTCATCTGTACTTTTAAAACCCGG 59.296 40.000 0.00 0.00 0.00 5.73
48 49 6.796705 ACTCATCTGTACTTTTAAAACCCG 57.203 37.500 0.00 0.00 0.00 5.28
62 63 9.903682 CATCTCAAATTTGTAAAACTCATCTGT 57.096 29.630 17.47 0.00 0.00 3.41
63 64 8.857216 GCATCTCAAATTTGTAAAACTCATCTG 58.143 33.333 17.47 2.32 0.00 2.90
65 66 7.814107 TGGCATCTCAAATTTGTAAAACTCATC 59.186 33.333 17.47 1.46 0.00 2.92
66 67 7.669427 TGGCATCTCAAATTTGTAAAACTCAT 58.331 30.769 17.47 0.00 0.00 2.90
67 68 7.048629 TGGCATCTCAAATTTGTAAAACTCA 57.951 32.000 17.47 7.21 0.00 3.41
68 69 7.437862 TGTTGGCATCTCAAATTTGTAAAACTC 59.562 33.333 17.47 5.00 0.00 3.01
69 70 7.271511 TGTTGGCATCTCAAATTTGTAAAACT 58.728 30.769 17.47 0.00 0.00 2.66
70 71 7.475771 TGTTGGCATCTCAAATTTGTAAAAC 57.524 32.000 17.47 12.84 0.00 2.43
71 72 8.674263 ATTGTTGGCATCTCAAATTTGTAAAA 57.326 26.923 17.47 3.07 0.00 1.52
72 73 8.674263 AATTGTTGGCATCTCAAATTTGTAAA 57.326 26.923 17.47 5.39 0.00 2.01
73 74 8.674263 AAATTGTTGGCATCTCAAATTTGTAA 57.326 26.923 17.47 7.75 0.00 2.41
74 75 8.674263 AAAATTGTTGGCATCTCAAATTTGTA 57.326 26.923 17.47 8.08 0.00 2.41
243 244 8.604890 CGGCTTTTTACATTTTTCCTTGTTTTA 58.395 29.630 0.00 0.00 0.00 1.52
244 245 7.414651 CCGGCTTTTTACATTTTTCCTTGTTTT 60.415 33.333 0.00 0.00 0.00 2.43
245 246 6.037720 CCGGCTTTTTACATTTTTCCTTGTTT 59.962 34.615 0.00 0.00 0.00 2.83
247 248 5.053811 CCGGCTTTTTACATTTTTCCTTGT 58.946 37.500 0.00 0.00 0.00 3.16
248 249 5.176774 GTCCGGCTTTTTACATTTTTCCTTG 59.823 40.000 0.00 0.00 0.00 3.61
249 250 5.163395 TGTCCGGCTTTTTACATTTTTCCTT 60.163 36.000 0.00 0.00 0.00 3.36
250 251 4.342665 TGTCCGGCTTTTTACATTTTTCCT 59.657 37.500 0.00 0.00 0.00 3.36
251 252 4.623002 TGTCCGGCTTTTTACATTTTTCC 58.377 39.130 0.00 0.00 0.00 3.13
254 255 5.523438 TTCTGTCCGGCTTTTTACATTTT 57.477 34.783 0.00 0.00 0.00 1.82
257 258 3.254903 GGTTTCTGTCCGGCTTTTTACAT 59.745 43.478 0.00 0.00 0.00 2.29
258 259 2.619646 GGTTTCTGTCCGGCTTTTTACA 59.380 45.455 0.00 0.00 0.00 2.41
259 260 2.882761 AGGTTTCTGTCCGGCTTTTTAC 59.117 45.455 0.00 0.00 0.00 2.01
260 261 3.217681 AGGTTTCTGTCCGGCTTTTTA 57.782 42.857 0.00 0.00 0.00 1.52
262 263 2.067365 AAGGTTTCTGTCCGGCTTTT 57.933 45.000 0.00 0.00 0.00 2.27
264 265 1.133915 TGAAAGGTTTCTGTCCGGCTT 60.134 47.619 0.00 0.00 38.02 4.35
265 266 0.472471 TGAAAGGTTTCTGTCCGGCT 59.528 50.000 0.00 0.00 38.02 5.52
266 267 0.875059 CTGAAAGGTTTCTGTCCGGC 59.125 55.000 0.00 0.00 38.02 6.13
268 269 2.808543 CCTTCTGAAAGGTTTCTGTCCG 59.191 50.000 4.19 0.00 46.10 4.79
290 291 1.072505 GTGAGTTGGGCTTCGGGAA 59.927 57.895 0.00 0.00 0.00 3.97
291 292 2.747686 GTGAGTTGGGCTTCGGGA 59.252 61.111 0.00 0.00 0.00 5.14
292 293 2.359975 GGTGAGTTGGGCTTCGGG 60.360 66.667 0.00 0.00 0.00 5.14
293 294 1.073199 AAGGTGAGTTGGGCTTCGG 59.927 57.895 0.00 0.00 0.00 4.30
294 295 1.237285 CCAAGGTGAGTTGGGCTTCG 61.237 60.000 0.00 0.00 43.02 3.79
295 296 1.527433 GCCAAGGTGAGTTGGGCTTC 61.527 60.000 4.85 0.00 46.31 3.86
296 297 1.531602 GCCAAGGTGAGTTGGGCTT 60.532 57.895 4.85 0.00 46.31 4.35
316 828 1.803998 CGATTCGCAGAAGAGGCATCA 60.804 52.381 0.00 0.00 45.90 3.07
330 843 2.114056 CATCAAATTGCTGGCGATTCG 58.886 47.619 8.30 0.62 0.00 3.34
338 851 4.690184 TGCTCACTACATCAAATTGCTG 57.310 40.909 0.00 0.00 0.00 4.41
382 899 1.073763 TCTGTTGATTGTGTGGAGGGG 59.926 52.381 0.00 0.00 0.00 4.79
399 916 5.408299 TCCAACATGTGTAATCGTCTTTCTG 59.592 40.000 0.00 0.00 0.00 3.02
439 956 5.245075 AGCTTTAGTGCTAAGTGAGTTCTCT 59.755 40.000 1.53 0.00 42.10 3.10
456 973 6.297353 GTTCGTGCTACAAACTAAGCTTTAG 58.703 40.000 3.20 0.00 39.53 1.85
470 988 0.606604 TTCCCTCAGGTTCGTGCTAC 59.393 55.000 0.00 0.00 0.00 3.58
473 991 0.591659 GTTTTCCCTCAGGTTCGTGC 59.408 55.000 0.00 0.00 0.00 5.34
474 992 1.873591 CTGTTTTCCCTCAGGTTCGTG 59.126 52.381 0.00 0.00 0.00 4.35
475 993 1.202770 CCTGTTTTCCCTCAGGTTCGT 60.203 52.381 3.38 0.00 44.19 3.85
520 1126 1.417145 GCAGAGGAAGAGGCATCTCAT 59.583 52.381 0.00 0.00 42.34 2.90
530 1136 4.245660 CATTTTACAGTCGCAGAGGAAGA 58.754 43.478 0.00 0.00 36.95 2.87
572 1178 4.020839 AGGAATGCAATTGTTTTCCCTCTG 60.021 41.667 25.44 0.00 36.07 3.35
609 1215 4.689612 TTTCAGTTGAACCAGTCTAGCT 57.310 40.909 0.00 0.00 33.13 3.32
616 1302 8.327941 TCTATCTTGATTTTCAGTTGAACCAG 57.672 34.615 0.00 0.00 33.13 4.00
649 1335 0.042131 TAATGACCGGGACCCAGACT 59.958 55.000 12.15 0.00 0.00 3.24
650 1336 0.177373 GTAATGACCGGGACCCAGAC 59.823 60.000 12.15 0.00 0.00 3.51
651 1337 0.252330 TGTAATGACCGGGACCCAGA 60.252 55.000 12.15 0.00 0.00 3.86
715 1401 6.935167 ACAAGAGGAAGAAATTTGTGTTGTT 58.065 32.000 0.00 0.00 31.34 2.83
841 1527 6.073314 AGGGTCAAGTAAGAGTAGTAACACA 58.927 40.000 0.00 0.00 0.00 3.72
937 1623 6.017109 GGAATGTATACGGTGAATTGCTTGAT 60.017 38.462 0.00 0.00 0.00 2.57
1088 1774 6.743773 GCTGGATGTTTCTCTAGCATAGGAAT 60.744 42.308 4.78 0.00 45.91 3.01
1098 1784 2.169352 GCTCCTGCTGGATGTTTCTCTA 59.831 50.000 13.33 0.00 42.29 2.43
1099 1785 1.065564 GCTCCTGCTGGATGTTTCTCT 60.066 52.381 13.33 0.00 42.29 3.10
1178 1864 1.134220 AGGAGTCCAGTCGTTTTGCAA 60.134 47.619 12.86 0.00 0.00 4.08
1257 1943 1.589113 GAGGCTGAGCTTGACGACT 59.411 57.895 3.72 0.00 0.00 4.18
1302 1988 3.553904 AGGCATGCACCAAACAAATTTT 58.446 36.364 21.36 0.00 0.00 1.82
1305 1991 1.693062 TGAGGCATGCACCAAACAAAT 59.307 42.857 21.36 0.00 0.00 2.32
1423 2115 6.548321 AGAATTTTGGTATGGTCACACCTAA 58.452 36.000 0.00 0.00 39.58 2.69
1562 2254 6.959361 TGCAAAAGAGTATCAGAGAAAACAC 58.041 36.000 0.00 0.00 37.82 3.32
2086 2796 3.107402 AGCAGACAGATCTAAGGACCA 57.893 47.619 0.00 0.00 32.25 4.02
2735 3477 5.874831 TGATATGGTTTGCGAACAATACAC 58.125 37.500 15.03 12.56 35.12 2.90
3050 3804 8.233868 CGTAACAACAGAAATGACAAATATGGA 58.766 33.333 0.00 0.00 0.00 3.41
3062 3816 8.220755 ACATATTATGCCGTAACAACAGAAAT 57.779 30.769 3.52 0.00 0.00 2.17
3224 3978 2.505819 GCTCTCCAAGGGGTTATCAGAA 59.494 50.000 0.00 0.00 34.93 3.02
3688 4442 1.149711 AGCTCATGGATAGAGGAGGCT 59.850 52.381 0.00 0.00 33.72 4.58
3723 4477 4.190001 CCTTCATGGTGATCTTCAGTCAG 58.810 47.826 0.00 0.00 0.00 3.51
3777 4531 2.199535 AAACCCTGCAGCAAGCCT 59.800 55.556 8.66 0.00 44.83 4.58
3782 4536 2.186160 CGTGACAAACCCTGCAGCA 61.186 57.895 8.66 0.00 0.00 4.41
3824 5466 4.963373 TCCAGGTCTTCACGAATAACAAA 58.037 39.130 0.00 0.00 0.00 2.83
3921 5570 0.469494 TTCAGTGAAGCACCAGCAGA 59.531 50.000 0.08 0.00 45.49 4.26


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

AutoCloner maintained by Alex Coulton.