Multiple sequence alignment - TraesCS1D01G139900

Loading Multiple Alignment...

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 TraesCS1D01G139900 chr1D 100.000 2618 0 0 1 2618 192664058 192661441 0.000000e+00 4835.0
1 TraesCS1D01G139900 chr1D 86.316 380 41 10 6 379 148836153 148836527 1.130000e-108 403.0
2 TraesCS1D01G139900 chr1A 95.596 1317 35 10 833 2147 238870651 238869356 0.000000e+00 2089.0
3 TraesCS1D01G139900 chr1A 94.715 492 14 4 2130 2618 238869342 238868860 0.000000e+00 754.0
4 TraesCS1D01G139900 chr1A 86.700 594 74 4 1 593 238872733 238872144 0.000000e+00 654.0
5 TraesCS1D01G139900 chr1A 85.901 383 46 8 1 379 203705397 203705019 4.060000e-108 401.0
6 TraesCS1D01G139900 chr4D 87.013 385 40 10 1 379 144770941 144771321 2.410000e-115 425.0
7 TraesCS1D01G139900 chr4D 87.139 381 37 11 6 379 403953590 403953215 3.120000e-114 422.0
8 TraesCS1D01G139900 chr5D 86.614 381 45 6 1 379 457398727 457399103 1.450000e-112 416.0
9 TraesCS1D01G139900 chr5A 86.579 380 41 10 6 379 227979772 227980147 6.740000e-111 411.0
10 TraesCS1D01G139900 chr5A 95.238 42 2 0 2145 2186 359344150 359344191 1.680000e-07 67.6
11 TraesCS1D01G139900 chr5B 86.198 384 43 9 1 379 210766314 210765936 8.720000e-110 407.0
12 TraesCS1D01G139900 chr5B 94.595 37 1 1 2150 2186 185514063 185514028 3.640000e-04 56.5
13 TraesCS1D01G139900 chr3D 85.938 384 44 9 1 379 239209133 239208755 4.060000e-108 401.0
14 TraesCS1D01G139900 chr7B 89.362 47 4 1 2145 2190 163503940 163503986 1.010000e-04 58.4
15 TraesCS1D01G139900 chr2B 90.698 43 4 0 2146 2188 773173767 773173809 1.010000e-04 58.4
16 TraesCS1D01G139900 chr2B 92.500 40 2 1 2149 2188 748082374 748082336 3.640000e-04 56.5
17 TraesCS1D01G139900 chr2B 92.500 40 2 1 2149 2188 748341681 748341643 3.640000e-04 56.5


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 TraesCS1D01G139900 chr1D 192661441 192664058 2617 True 4835.000000 4835 100.000 1 2618 1 chr1D.!!$R1 2617
1 TraesCS1D01G139900 chr1A 238868860 238872733 3873 True 1165.666667 2089 92.337 1 2618 3 chr1A.!!$R2 2617

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
488 490 0.034337 TAGTGTCCAGGCCGTTCAAC 59.966 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 3089 0.031585 CGATGATTAAGGACGCGGGA 59.968 55.0 12.47 0.0 0.0 5.14 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 1.068474 CAACTCTTAGGGCGTCGTTG 58.932 55.000 0.00 0.00 0.00 4.10
42 43 6.655930 TGTAGACTTGGGTTTTGTTTAGACT 58.344 36.000 0.00 0.00 0.00 3.24
60 61 7.900782 TTAGACTAAAGTTCACCATAGTTGC 57.099 36.000 0.00 0.00 0.00 4.17
75 76 2.307309 TTGCAACTCGCGTCCTTCG 61.307 57.895 5.77 0.00 46.97 3.79
79 80 0.111266 CAACTCGCGTCCTTCGTTTG 60.111 55.000 5.77 0.00 42.13 2.93
96 97 1.658994 TTGTGTTCAACGACCAGACC 58.341 50.000 0.00 0.00 0.00 3.85
102 103 1.116308 TCAACGACCAGACCAAGACA 58.884 50.000 0.00 0.00 0.00 3.41
104 105 2.069273 CAACGACCAGACCAAGACATC 58.931 52.381 0.00 0.00 0.00 3.06
106 107 1.000955 ACGACCAGACCAAGACATCAC 59.999 52.381 0.00 0.00 0.00 3.06
108 109 2.693069 GACCAGACCAAGACATCACAG 58.307 52.381 0.00 0.00 0.00 3.66
110 111 2.301296 ACCAGACCAAGACATCACAGAG 59.699 50.000 0.00 0.00 0.00 3.35
111 112 2.344950 CAGACCAAGACATCACAGAGC 58.655 52.381 0.00 0.00 0.00 4.09
116 117 2.344950 CAAGACATCACAGAGCCTCAC 58.655 52.381 0.00 0.00 0.00 3.51
128 129 5.293814 CACAGAGCCTCACTTTGATCAATAG 59.706 44.000 9.40 11.69 34.59 1.73
129 130 5.188555 ACAGAGCCTCACTTTGATCAATAGA 59.811 40.000 9.40 6.87 34.59 1.98
132 133 7.282675 CAGAGCCTCACTTTGATCAATAGATTT 59.717 37.037 9.40 0.00 32.13 2.17
158 159 9.911788 TTCTCTCTCTTAAATTTGCAATATCCT 57.088 29.630 0.00 0.00 0.00 3.24
176 177 9.674824 CAATATCCTAATTGCAATCTCAGTTTC 57.325 33.333 13.38 0.00 30.59 2.78
181 182 7.882791 TCCTAATTGCAATCTCAGTTTCTTACA 59.117 33.333 13.38 0.00 0.00 2.41
190 191 8.777413 CAATCTCAGTTTCTTACATGTTCTTCA 58.223 33.333 2.30 0.00 0.00 3.02
222 223 3.639094 AGGAAATAGACCCTCGTGATCAG 59.361 47.826 0.00 0.00 0.00 2.90
236 237 1.576356 GATCAGGTTGATCGTGCTCC 58.424 55.000 3.54 0.00 43.11 4.70
250 251 1.448893 GCTCCGGCGTGGTCAATAA 60.449 57.895 6.01 0.00 39.52 1.40
251 252 0.814010 GCTCCGGCGTGGTCAATAAT 60.814 55.000 6.01 0.00 39.52 1.28
257 258 2.481276 CGGCGTGGTCAATAATCTCTCA 60.481 50.000 0.00 0.00 0.00 3.27
280 281 8.988064 TCAGAGTTAGTTTAGTGATTGCTAAG 57.012 34.615 0.00 0.00 33.16 2.18
283 284 5.581085 AGTTAGTTTAGTGATTGCTAAGGCG 59.419 40.000 0.00 0.00 42.25 5.52
284 285 2.678336 AGTTTAGTGATTGCTAAGGCGC 59.322 45.455 0.00 0.00 42.25 6.53
287 288 1.084370 AGTGATTGCTAAGGCGCGAC 61.084 55.000 12.10 7.34 42.25 5.19
291 292 0.810031 ATTGCTAAGGCGCGACGATT 60.810 50.000 12.10 0.00 42.25 3.34
305 306 2.344441 CGACGATTGTATGTTCGCAGTT 59.656 45.455 0.00 0.00 38.91 3.16
325 326 2.942710 TGGATCGTCAAAGTCGACTTC 58.057 47.619 29.82 17.01 40.07 3.01
329 330 1.679680 TCGTCAAAGTCGACTTCCACT 59.320 47.619 29.82 12.71 34.61 4.00
336 337 5.875910 TCAAAGTCGACTTCCACTAAAAACA 59.124 36.000 29.82 2.08 34.61 2.83
344 345 8.981647 TCGACTTCCACTAAAAACAATAGTTAC 58.018 33.333 0.00 0.00 36.84 2.50
379 380 2.916089 GACGAGAAACTTTCGCCTCTAC 59.084 50.000 0.00 0.00 41.57 2.59
381 382 2.260481 GAGAAACTTTCGCCTCTACCG 58.740 52.381 0.00 0.00 34.02 4.02
390 391 0.814410 CGCCTCTACCGAGAGCACTA 60.814 60.000 0.00 0.00 46.97 2.74
392 393 1.310904 CCTCTACCGAGAGCACTACC 58.689 60.000 0.00 0.00 46.97 3.18
396 397 1.142465 CTACCGAGAGCACTACCCCTA 59.858 57.143 0.00 0.00 0.00 3.53
410 412 2.813908 CCTACTTGCCGCCGTCAC 60.814 66.667 0.00 0.00 0.00 3.67
448 450 1.308216 CCTCCCCATCCACCTCCTT 60.308 63.158 0.00 0.00 0.00 3.36
449 451 1.348775 CCTCCCCATCCACCTCCTTC 61.349 65.000 0.00 0.00 0.00 3.46
485 487 0.462047 CCATAGTGTCCAGGCCGTTC 60.462 60.000 0.00 0.00 0.00 3.95
488 490 0.034337 TAGTGTCCAGGCCGTTCAAC 59.966 55.000 0.00 0.00 0.00 3.18
512 514 1.372087 GCAAGATCGGTTCCTGCTGG 61.372 60.000 2.58 2.58 38.53 4.85
517 519 1.672881 GATCGGTTCCTGCTGGATTTG 59.327 52.381 13.72 6.21 42.81 2.32
524 526 0.674581 CCTGCTGGATTTGCACTCGA 60.675 55.000 2.92 0.00 36.37 4.04
530 532 0.449388 GGATTTGCACTCGAGCCAAG 59.551 55.000 13.61 1.10 0.00 3.61
537 539 1.336240 GCACTCGAGCCAAGCATTTTT 60.336 47.619 13.61 0.00 0.00 1.94
540 542 2.287788 ACTCGAGCCAAGCATTTTTGTG 60.288 45.455 13.61 0.00 0.00 3.33
547 549 4.523943 AGCCAAGCATTTTTGTGTGATAGA 59.476 37.500 0.00 0.00 0.00 1.98
559 561 6.633500 TTGTGTGATAGAGGAAACCAAAAG 57.367 37.500 0.00 0.00 0.00 2.27
565 567 0.881796 GAGGAAACCAAAAGGAGCGG 59.118 55.000 0.00 0.00 0.00 5.52
566 568 0.539669 AGGAAACCAAAAGGAGCGGG 60.540 55.000 0.00 0.00 0.00 6.13
567 569 1.532604 GGAAACCAAAAGGAGCGGGG 61.533 60.000 0.00 0.00 0.00 5.73
568 570 1.532604 GAAACCAAAAGGAGCGGGGG 61.533 60.000 0.00 0.00 0.00 5.40
574 576 0.539669 AAAAGGAGCGGGGGAAACTG 60.540 55.000 0.00 0.00 0.00 3.16
589 591 5.130477 GGGGAAACTGAGAATATGAGGTACA 59.870 44.000 0.00 0.00 0.00 2.90
593 595 5.878406 ACTGAGAATATGAGGTACAAGGG 57.122 43.478 0.00 0.00 0.00 3.95
594 596 4.656112 ACTGAGAATATGAGGTACAAGGGG 59.344 45.833 0.00 0.00 0.00 4.79
598 1889 6.011981 TGAGAATATGAGGTACAAGGGGTTTT 60.012 38.462 0.00 0.00 0.00 2.43
602 1893 4.376225 TGAGGTACAAGGGGTTTTTAGG 57.624 45.455 0.00 0.00 0.00 2.69
608 1899 0.412244 AAGGGGTTTTTAGGGGGAGC 59.588 55.000 0.00 0.00 0.00 4.70
613 1904 0.039764 GTTTTTAGGGGGAGCAGGCT 59.960 55.000 0.00 0.00 0.00 4.58
614 1905 1.283905 GTTTTTAGGGGGAGCAGGCTA 59.716 52.381 0.00 0.00 0.00 3.93
633 1924 3.188048 GCTATTCTGCGGGATCTGAAATG 59.812 47.826 0.00 0.00 0.00 2.32
637 1928 2.027285 TCTGCGGGATCTGAAATGAACA 60.027 45.455 0.00 0.00 0.00 3.18
675 1967 5.430886 ACCGTAAAGCGAGGGTTATTTTAT 58.569 37.500 0.00 0.00 44.77 1.40
680 1972 8.645487 CGTAAAGCGAGGGTTATTTTATAGATC 58.355 37.037 0.00 0.00 44.77 2.75
704 1997 1.400530 CCTTTACGAGGGATCCGGCT 61.401 60.000 5.45 0.00 42.26 5.52
719 2012 0.388907 CGGCTGGGCAAGATTTGTTG 60.389 55.000 0.00 0.00 0.00 3.33
730 2023 5.624344 CAAGATTTGTTGCAGATGACTCT 57.376 39.130 0.00 0.00 0.00 3.24
731 2024 5.629097 CAAGATTTGTTGCAGATGACTCTC 58.371 41.667 0.00 0.00 0.00 3.20
732 2025 4.903054 AGATTTGTTGCAGATGACTCTCA 58.097 39.130 0.00 0.00 0.00 3.27
733 2026 4.936411 AGATTTGTTGCAGATGACTCTCAG 59.064 41.667 0.00 0.00 0.00 3.35
734 2027 2.090400 TGTTGCAGATGACTCTCAGC 57.910 50.000 0.00 0.00 31.96 4.26
735 2028 0.997932 GTTGCAGATGACTCTCAGCG 59.002 55.000 0.00 0.00 37.94 5.18
736 2029 0.738762 TTGCAGATGACTCTCAGCGC 60.739 55.000 0.00 0.00 37.94 5.92
752 2045 1.517361 CGCTCAGTGGTGGCTATCA 59.483 57.895 0.00 0.00 0.00 2.15
777 2070 2.966516 AGGGACTCGAAAGAAGTCAACT 59.033 45.455 5.71 0.91 41.32 3.16
812 2105 8.879427 ATTTTAGCAAATACTCCCTGTAAACT 57.121 30.769 0.00 0.00 34.45 2.66
813 2106 9.969001 ATTTTAGCAAATACTCCCTGTAAACTA 57.031 29.630 0.00 0.00 34.45 2.24
814 2107 9.796180 TTTTAGCAAATACTCCCTGTAAACTAA 57.204 29.630 0.00 0.00 34.45 2.24
815 2108 8.782339 TTAGCAAATACTCCCTGTAAACTAAC 57.218 34.615 0.00 0.00 34.45 2.34
816 2109 6.775708 AGCAAATACTCCCTGTAAACTAACA 58.224 36.000 0.00 0.00 34.45 2.41
817 2110 7.228590 AGCAAATACTCCCTGTAAACTAACAA 58.771 34.615 0.00 0.00 34.45 2.83
818 2111 7.722285 AGCAAATACTCCCTGTAAACTAACAAA 59.278 33.333 0.00 0.00 34.45 2.83
819 2112 8.354426 GCAAATACTCCCTGTAAACTAACAAAA 58.646 33.333 0.00 0.00 34.45 2.44
876 2169 3.448660 GGAAGATTGAAATGTTGGAGGGG 59.551 47.826 0.00 0.00 0.00 4.79
1243 2536 2.564553 CTTCTTCCCGCTCGGTCCTG 62.565 65.000 7.59 0.00 0.00 3.86
1252 2545 2.601666 TCGGTCCTGCTGCTGTCT 60.602 61.111 0.00 0.00 0.00 3.41
1275 2568 4.066139 GGCTGGGCCCCATTCACT 62.066 66.667 22.27 0.00 44.06 3.41
1284 2577 1.342374 GCCCCATTCACTCCCTTCAAT 60.342 52.381 0.00 0.00 0.00 2.57
1293 2586 3.420482 CCCTTCAATCCCGCCCCT 61.420 66.667 0.00 0.00 0.00 4.79
1461 2754 1.144936 GGAGGAGAAGGCATCCACG 59.855 63.158 6.25 0.00 39.47 4.94
1466 2759 2.227089 GAGAAGGCATCCACGGTCGT 62.227 60.000 0.00 0.00 0.00 4.34
1619 2912 3.808466 TCTCCAAGAGATTCCGTGATG 57.192 47.619 0.00 0.00 33.35 3.07
1661 2954 1.014352 GCCTTTTGATCATACCGCGT 58.986 50.000 4.92 0.00 0.00 6.01
1672 2965 4.970662 TCATACCGCGTTTAAGACTAGT 57.029 40.909 4.92 0.00 0.00 2.57
1673 2966 6.260714 TGATCATACCGCGTTTAAGACTAGTA 59.739 38.462 4.92 0.00 0.00 1.82
1678 2971 8.847567 CATACCGCGTTTAAGACTAGTATAATG 58.152 37.037 4.92 0.00 0.00 1.90
1723 3016 6.239515 GGTTCGAATATGGGGATGTTAGTACT 60.240 42.308 0.00 0.00 0.00 2.73
1773 3066 6.423182 TCTGATGGAAATGTAGGGTTTTAGG 58.577 40.000 0.00 0.00 0.00 2.69
1792 3085 1.680249 GGGGTTGAAGAGCTGCTAAGG 60.680 57.143 0.15 0.00 0.00 2.69
1794 3087 2.236395 GGGTTGAAGAGCTGCTAAGGTA 59.764 50.000 0.15 0.00 33.19 3.08
1796 3089 4.518249 GGTTGAAGAGCTGCTAAGGTATT 58.482 43.478 0.15 0.00 38.02 1.89
1798 3091 4.408182 TGAAGAGCTGCTAAGGTATTCC 57.592 45.455 0.15 0.00 46.63 3.01
1799 3092 3.134804 TGAAGAGCTGCTAAGGTATTCCC 59.865 47.826 0.15 0.00 46.63 3.97
1836 3129 1.363885 GACCGTGGCCGTGGAAATAC 61.364 60.000 19.24 0.00 0.00 1.89
1907 3200 2.596346 TCCATGCCTTTTGTCATGTGT 58.404 42.857 0.00 0.00 38.63 3.72
1912 3205 1.869342 GCCTTTTGTCATGTGTGTGGC 60.869 52.381 0.00 0.00 0.00 5.01
1957 3250 2.565841 GGTGTCCTCTGGCATAATGTC 58.434 52.381 0.00 0.00 0.00 3.06
1988 3281 5.048504 TCGCTCATTTTGCTTCTTTCATCTT 60.049 36.000 0.00 0.00 0.00 2.40
1989 3282 5.060569 CGCTCATTTTGCTTCTTTCATCTTG 59.939 40.000 0.00 0.00 0.00 3.02
2027 3320 4.142071 TGTGCAGGAGAGATCACAGTAATC 60.142 45.833 0.00 0.00 34.87 1.75
2038 3332 8.641499 GAGATCACAGTAATCTCGAAGAAAAT 57.359 34.615 0.00 0.00 39.69 1.82
2039 3333 9.092876 GAGATCACAGTAATCTCGAAGAAAATT 57.907 33.333 0.00 0.00 39.69 1.82
2068 3362 5.767269 TCATTTTGCTCAATGCTCGTAAAA 58.233 33.333 4.12 0.00 43.37 1.52
2071 3365 1.468520 TGCTCAATGCTCGTAAAAGCC 59.531 47.619 0.00 0.00 41.77 4.35
2110 3404 4.740268 TCAAATTTCTGAGATGCATGCAC 58.260 39.130 25.37 16.77 0.00 4.57
2200 3526 1.937899 GCACCAACAACAGTACGAGTT 59.062 47.619 0.00 1.53 0.00 3.01
2266 3592 7.397192 ACAGCAGGATTTAAGTTTGTTCCATAT 59.603 33.333 0.00 0.00 0.00 1.78
2267 3593 7.917505 CAGCAGGATTTAAGTTTGTTCCATATC 59.082 37.037 0.00 0.00 0.00 1.63
2290 3616 6.340522 TCGTCATCTTGCAGAATTGATAGAA 58.659 36.000 0.00 0.00 0.00 2.10
2292 3618 8.143835 TCGTCATCTTGCAGAATTGATAGAATA 58.856 33.333 0.00 0.00 0.00 1.75
2409 3738 2.159170 GCCTTACGCTGACTTCTCATCT 60.159 50.000 0.00 0.00 0.00 2.90
2458 3787 3.922171 AGGTTCTCATGATCAGTTCCC 57.078 47.619 0.09 0.00 0.00 3.97
2542 3871 9.691362 TTGGATTCTAGTTTTGAAATAAACTGC 57.309 29.630 10.98 0.00 45.36 4.40
2565 3894 5.678871 GCATCAGGATGTCGTCTTACTTACA 60.679 44.000 10.69 0.00 40.80 2.41
2574 3903 7.830940 TGTCGTCTTACTTACAAAGAAACAA 57.169 32.000 0.00 0.00 34.86 2.83
2575 3904 8.254178 TGTCGTCTTACTTACAAAGAAACAAA 57.746 30.769 0.00 0.00 34.86 2.83
2576 3905 8.719648 TGTCGTCTTACTTACAAAGAAACAAAA 58.280 29.630 0.00 0.00 34.86 2.44
2577 3906 9.545611 GTCGTCTTACTTACAAAGAAACAAAAA 57.454 29.630 0.00 0.00 34.86 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.741706 TCTACAACGACGCCCTAAGAG 59.258 52.381 0.00 0.00 0.00 2.85
19 20 8.667076 TTAGTCTAAACAAAACCCAAGTCTAC 57.333 34.615 0.00 0.00 0.00 2.59
42 43 5.178623 CGAGTTGCAACTATGGTGAACTTTA 59.821 40.000 31.20 0.00 39.88 1.85
75 76 2.223180 GGTCTGGTCGTTGAACACAAAC 60.223 50.000 0.00 0.00 0.00 2.93
79 80 1.597663 CTTGGTCTGGTCGTTGAACAC 59.402 52.381 0.00 0.00 28.71 3.32
96 97 2.028294 AGTGAGGCTCTGTGATGTCTTG 60.028 50.000 16.72 0.00 0.00 3.02
102 103 3.262660 TGATCAAAGTGAGGCTCTGTGAT 59.737 43.478 16.72 16.85 41.05 3.06
104 105 3.049708 TGATCAAAGTGAGGCTCTGTG 57.950 47.619 16.72 8.31 0.00 3.66
106 107 5.668471 TCTATTGATCAAAGTGAGGCTCTG 58.332 41.667 16.72 5.58 0.00 3.35
108 109 7.565323 AAATCTATTGATCAAAGTGAGGCTC 57.435 36.000 13.09 7.79 31.51 4.70
110 111 7.994194 AGAAAATCTATTGATCAAAGTGAGGC 58.006 34.615 13.09 0.00 31.51 4.70
111 112 9.393512 AGAGAAAATCTATTGATCAAAGTGAGG 57.606 33.333 13.09 0.00 36.10 3.86
132 133 9.911788 AGGATATTGCAAATTTAAGAGAGAGAA 57.088 29.630 1.71 0.00 0.00 2.87
152 153 9.638176 AAGAAACTGAGATTGCAATTAGGATAT 57.362 29.630 14.33 0.00 0.00 1.63
158 159 9.013229 ACATGTAAGAAACTGAGATTGCAATTA 57.987 29.630 14.33 2.74 0.00 1.40
159 160 7.889469 ACATGTAAGAAACTGAGATTGCAATT 58.111 30.769 14.33 3.59 0.00 2.32
161 162 6.882610 ACATGTAAGAAACTGAGATTGCAA 57.117 33.333 0.00 0.00 0.00 4.08
162 163 6.712095 AGAACATGTAAGAAACTGAGATTGCA 59.288 34.615 0.00 0.00 0.00 4.08
172 173 8.482429 CAAGCAAATGAAGAACATGTAAGAAAC 58.518 33.333 0.00 0.00 39.39 2.78
176 177 5.921976 TGCAAGCAAATGAAGAACATGTAAG 59.078 36.000 0.00 0.00 39.39 2.34
179 180 4.304110 CTGCAAGCAAATGAAGAACATGT 58.696 39.130 0.00 0.00 39.39 3.21
181 182 3.575256 TCCTGCAAGCAAATGAAGAACAT 59.425 39.130 0.00 0.00 41.45 2.71
190 191 3.448660 GGGTCTATTTCCTGCAAGCAAAT 59.551 43.478 0.00 0.00 0.00 2.32
236 237 2.128035 GAGAGATTATTGACCACGCCG 58.872 52.381 0.00 0.00 0.00 6.46
250 251 7.978975 GCAATCACTAAACTAACTCTGAGAGAT 59.021 37.037 17.71 7.02 33.32 2.75
251 252 7.177568 AGCAATCACTAAACTAACTCTGAGAGA 59.822 37.037 17.71 0.00 33.32 3.10
257 258 6.819146 GCCTTAGCAATCACTAAACTAACTCT 59.181 38.462 0.00 0.00 39.53 3.24
270 271 2.164663 CGTCGCGCCTTAGCAATCA 61.165 57.895 0.00 0.00 39.83 2.57
280 281 0.043310 GAACATACAATCGTCGCGCC 60.043 55.000 0.00 0.00 0.00 6.53
283 284 0.643310 TGCGAACATACAATCGTCGC 59.357 50.000 9.25 9.25 44.08 5.19
284 285 1.917955 ACTGCGAACATACAATCGTCG 59.082 47.619 0.00 0.00 41.01 5.12
287 288 2.670905 TCCAACTGCGAACATACAATCG 59.329 45.455 0.00 0.00 41.81 3.34
291 292 2.267426 CGATCCAACTGCGAACATACA 58.733 47.619 0.00 0.00 0.00 2.29
305 306 2.352421 GGAAGTCGACTTTGACGATCCA 60.352 50.000 30.22 0.00 43.42 3.41
325 326 9.226606 TGAGATGGTAACTATTGTTTTTAGTGG 57.773 33.333 0.00 0.00 37.59 4.00
336 337 8.258007 TCGTCTTTTGATGAGATGGTAACTATT 58.742 33.333 0.00 0.00 39.36 1.73
354 355 3.604065 GGCGAAAGTTTCTCGTCTTTT 57.396 42.857 13.56 0.00 37.90 2.27
379 380 0.106619 AGTAGGGGTAGTGCTCTCGG 60.107 60.000 0.00 0.00 0.00 4.63
381 382 1.137282 GCAAGTAGGGGTAGTGCTCTC 59.863 57.143 0.00 0.00 32.43 3.20
392 393 4.077184 TGACGGCGGCAAGTAGGG 62.077 66.667 15.88 0.00 0.00 3.53
413 415 4.500116 GCACGCGAGGAGGAGGTC 62.500 72.222 15.93 0.00 0.00 3.85
440 442 2.498078 GGAGTTCTAGTGGAAGGAGGTG 59.502 54.545 0.00 0.00 34.23 4.00
441 443 2.822697 GGAGTTCTAGTGGAAGGAGGT 58.177 52.381 0.00 0.00 34.23 3.85
448 450 1.202964 TGGTGTCGGAGTTCTAGTGGA 60.203 52.381 0.00 0.00 0.00 4.02
449 451 1.254026 TGGTGTCGGAGTTCTAGTGG 58.746 55.000 0.00 0.00 0.00 4.00
485 487 4.851114 CCGATCTTGCGCGCGTTG 62.851 66.667 32.35 20.59 0.00 4.10
488 490 4.559386 GAACCGATCTTGCGCGCG 62.559 66.667 28.44 28.44 0.00 6.86
491 493 3.093278 CAGGAACCGATCTTGCGC 58.907 61.111 0.00 0.00 0.00 6.09
512 514 0.179179 GCTTGGCTCGAGTGCAAATC 60.179 55.000 15.13 0.00 34.04 2.17
517 519 0.242017 AAAATGCTTGGCTCGAGTGC 59.758 50.000 15.13 13.49 0.00 4.40
524 526 3.756933 ATCACACAAAAATGCTTGGCT 57.243 38.095 0.00 0.00 0.00 4.75
530 532 5.863935 GGTTTCCTCTATCACACAAAAATGC 59.136 40.000 0.00 0.00 0.00 3.56
537 539 5.070001 CCTTTTGGTTTCCTCTATCACACA 58.930 41.667 0.00 0.00 34.07 3.72
540 542 4.396478 GCTCCTTTTGGTTTCCTCTATCAC 59.604 45.833 0.00 0.00 41.38 3.06
547 549 0.539669 CCCGCTCCTTTTGGTTTCCT 60.540 55.000 0.00 0.00 41.38 3.36
559 561 1.838073 TTCTCAGTTTCCCCCGCTCC 61.838 60.000 0.00 0.00 0.00 4.70
565 567 4.779993 ACCTCATATTCTCAGTTTCCCC 57.220 45.455 0.00 0.00 0.00 4.81
566 568 6.235231 TGTACCTCATATTCTCAGTTTCCC 57.765 41.667 0.00 0.00 0.00 3.97
567 569 6.763610 CCTTGTACCTCATATTCTCAGTTTCC 59.236 42.308 0.00 0.00 0.00 3.13
568 570 6.763610 CCCTTGTACCTCATATTCTCAGTTTC 59.236 42.308 0.00 0.00 0.00 2.78
574 576 5.632034 AACCCCTTGTACCTCATATTCTC 57.368 43.478 0.00 0.00 0.00 2.87
589 591 0.412244 GCTCCCCCTAAAAACCCCTT 59.588 55.000 0.00 0.00 0.00 3.95
593 595 0.970937 GCCTGCTCCCCCTAAAAACC 60.971 60.000 0.00 0.00 0.00 3.27
594 596 0.039764 AGCCTGCTCCCCCTAAAAAC 59.960 55.000 0.00 0.00 0.00 2.43
598 1889 1.061346 AGAATAGCCTGCTCCCCCTAA 60.061 52.381 0.00 0.00 0.00 2.69
608 1899 0.683973 AGATCCCGCAGAATAGCCTG 59.316 55.000 0.00 0.00 37.23 4.85
613 1904 4.687901 TCATTTCAGATCCCGCAGAATA 57.312 40.909 0.00 0.00 0.00 1.75
614 1905 3.565764 TCATTTCAGATCCCGCAGAAT 57.434 42.857 0.00 0.00 0.00 2.40
647 1938 1.202675 ACCCTCGCTTTACGGTTTTGA 60.203 47.619 0.00 0.00 43.89 2.69
655 1946 8.645487 CGATCTATAAAATAACCCTCGCTTTAC 58.355 37.037 0.00 0.00 0.00 2.01
675 1967 2.228059 CCTCGTAAAGGCTCCGATCTA 58.772 52.381 4.67 0.00 38.67 1.98
680 1972 0.032267 GATCCCTCGTAAAGGCTCCG 59.968 60.000 0.00 0.00 44.71 4.63
704 1997 1.702182 TCTGCAACAAATCTTGCCCA 58.298 45.000 1.64 0.00 45.13 5.36
719 2012 0.871163 GAGCGCTGAGAGTCATCTGC 60.871 60.000 18.48 0.00 39.86 4.26
724 2017 1.583477 CACTGAGCGCTGAGAGTCA 59.417 57.895 30.94 12.77 0.00 3.41
730 2023 4.687215 GCCACCACTGAGCGCTGA 62.687 66.667 18.48 5.01 0.00 4.26
731 2024 2.584261 ATAGCCACCACTGAGCGCTG 62.584 60.000 18.48 3.12 0.00 5.18
732 2025 2.303549 GATAGCCACCACTGAGCGCT 62.304 60.000 11.27 11.27 0.00 5.92
733 2026 1.884926 GATAGCCACCACTGAGCGC 60.885 63.158 0.00 0.00 0.00 5.92
734 2027 0.529337 CTGATAGCCACCACTGAGCG 60.529 60.000 0.00 0.00 0.00 5.03
735 2028 0.179062 CCTGATAGCCACCACTGAGC 60.179 60.000 0.00 0.00 0.00 4.26
736 2029 1.489481 TCCTGATAGCCACCACTGAG 58.511 55.000 0.00 0.00 0.00 3.35
752 2045 2.563620 GACTTCTTTCGAGTCCCTTCCT 59.436 50.000 0.00 0.00 38.02 3.36
823 2116 5.246307 ACTCTTTAATACTCCCTGTGCAAC 58.754 41.667 0.00 0.00 37.35 4.17
824 2117 5.499004 ACTCTTTAATACTCCCTGTGCAA 57.501 39.130 0.00 0.00 0.00 4.08
825 2118 5.012664 TCAACTCTTTAATACTCCCTGTGCA 59.987 40.000 0.00 0.00 0.00 4.57
826 2119 5.488341 TCAACTCTTTAATACTCCCTGTGC 58.512 41.667 0.00 0.00 0.00 4.57
827 2120 8.043710 AGATTCAACTCTTTAATACTCCCTGTG 58.956 37.037 0.00 0.00 0.00 3.66
828 2121 8.043710 CAGATTCAACTCTTTAATACTCCCTGT 58.956 37.037 0.00 0.00 0.00 4.00
829 2122 7.497249 CCAGATTCAACTCTTTAATACTCCCTG 59.503 40.741 0.00 0.00 0.00 4.45
830 2123 7.403231 TCCAGATTCAACTCTTTAATACTCCCT 59.597 37.037 0.00 0.00 0.00 4.20
831 2124 7.565680 TCCAGATTCAACTCTTTAATACTCCC 58.434 38.462 0.00 0.00 0.00 4.30
859 2152 4.412060 TTACCCCCTCCAACATTTCAAT 57.588 40.909 0.00 0.00 0.00 2.57
876 2169 6.207417 GGGTAAAGGGTACTTTTCAGTTTACC 59.793 42.308 11.11 11.11 44.26 2.85
894 2187 3.495753 GGATAATAACGCCGTGGGTAAAG 59.504 47.826 0.00 0.00 0.00 1.85
955 2248 4.821589 GAGACGCGGGGAAGCTGG 62.822 72.222 12.47 0.00 34.40 4.85
956 2249 3.708220 GAGAGACGCGGGGAAGCTG 62.708 68.421 12.47 0.00 34.40 4.24
957 2250 3.453679 GAGAGACGCGGGGAAGCT 61.454 66.667 12.47 0.00 34.40 3.74
1043 2336 1.519455 GTCCAGAATGCCTCGTCGG 60.519 63.158 0.00 0.00 31.97 4.79
1243 2536 1.020333 CAGCCTTCAGAGACAGCAGC 61.020 60.000 0.00 0.00 0.00 5.25
1248 2541 2.596851 GGCCCAGCCTTCAGAGACA 61.597 63.158 0.00 0.00 46.69 3.41
1275 2568 3.416880 GGGGCGGGATTGAAGGGA 61.417 66.667 0.00 0.00 0.00 4.20
1461 2754 1.084370 CGGCCTTGAGATTGACGACC 61.084 60.000 0.00 0.00 0.00 4.79
1466 2759 0.826715 CTCTCCGGCCTTGAGATTGA 59.173 55.000 18.85 1.65 38.16 2.57
1619 2912 3.084786 CAACCTTTCTTCTCACCCATCC 58.915 50.000 0.00 0.00 0.00 3.51
1692 2985 5.488919 ACATCCCCATATTCGAACCATCTAT 59.511 40.000 0.00 0.00 0.00 1.98
1695 2988 4.021102 ACATCCCCATATTCGAACCATC 57.979 45.455 0.00 0.00 0.00 3.51
1723 3016 6.446318 ACTAAACCAAAGTACGACGATTACA 58.554 36.000 0.00 0.00 0.00 2.41
1773 3066 1.003696 ACCTTAGCAGCTCTTCAACCC 59.996 52.381 0.00 0.00 0.00 4.11
1792 3085 3.102052 TGATTAAGGACGCGGGAATAC 57.898 47.619 12.47 0.00 0.00 1.89
1794 3087 2.767505 GATGATTAAGGACGCGGGAAT 58.232 47.619 12.47 1.74 0.00 3.01
1796 3089 0.031585 CGATGATTAAGGACGCGGGA 59.968 55.000 12.47 0.00 0.00 5.14
1797 3090 0.249322 ACGATGATTAAGGACGCGGG 60.249 55.000 12.47 0.00 0.00 6.13
1798 3091 0.852777 CACGATGATTAAGGACGCGG 59.147 55.000 12.47 0.00 0.00 6.46
1799 3092 1.517276 GTCACGATGATTAAGGACGCG 59.483 52.381 3.53 3.53 0.00 6.01
1836 3129 0.527565 CCAAAAGGAGCCACATTCCG 59.472 55.000 0.00 0.00 39.77 4.30
1838 3131 1.273327 CACCCAAAAGGAGCCACATTC 59.727 52.381 0.00 0.00 39.89 2.67
1907 3200 5.628797 TCATCAGATTAATACAGGCCACA 57.371 39.130 5.01 0.00 0.00 4.17
1912 3205 7.498239 CCCTGCATATCATCAGATTAATACAGG 59.502 40.741 0.00 0.00 35.56 4.00
1957 3250 4.447054 AGAAGCAAAATGAGCGAGATATCG 59.553 41.667 5.13 5.13 37.01 2.92
1988 3281 1.339055 GCACAAGAGAGCACATACCCA 60.339 52.381 0.00 0.00 0.00 4.51
1989 3282 1.339055 TGCACAAGAGAGCACATACCC 60.339 52.381 0.00 0.00 36.40 3.69
2071 3365 2.327200 TGAGAGCAATCCAGCATCAG 57.673 50.000 0.00 0.00 36.85 2.90
2103 3397 1.176527 AGGTATTGGTGTGTGCATGC 58.823 50.000 11.82 11.82 0.00 4.06
2104 3398 2.819019 TCAAGGTATTGGTGTGTGCATG 59.181 45.455 0.00 0.00 37.02 4.06
2110 3404 9.357652 CTAAATTCAATTCAAGGTATTGGTGTG 57.642 33.333 0.00 0.00 37.02 3.82
2266 3592 5.906073 TCTATCAATTCTGCAAGATGACGA 58.094 37.500 0.00 0.00 46.36 4.20
2267 3593 6.594284 TTCTATCAATTCTGCAAGATGACG 57.406 37.500 0.00 0.00 46.36 4.35
2391 3720 2.747989 ACGAGATGAGAAGTCAGCGTAA 59.252 45.455 0.00 0.00 44.26 3.18
2409 3738 1.686355 AAACCTTGCAACATCCACGA 58.314 45.000 0.00 0.00 0.00 4.35
2542 3871 5.891451 TGTAAGTAAGACGACATCCTGATG 58.109 41.667 5.60 5.60 44.15 3.07


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

AutoCloner maintained by Alex Coulton.