Multiple sequence alignment - TraesCS5B01G273300

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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 TraesCS5B01G273300 chr5B 100.000 5094 0 0 1 5094 458714626 458719719 0.000000e+00 9407.0
1 TraesCS5B01G273300 chr5B 96.364 55 2 0 4255 4309 458719778 458719724 1.950000e-14 91.6
2 TraesCS5B01G273300 chr5B 95.652 46 1 1 3347 3392 556531459 556531415 7.070000e-09 73.1
3 TraesCS5B01G273300 chr5A 95.214 3197 108 16 1885 5064 482787000 482790168 0.000000e+00 5014.0
4 TraesCS5B01G273300 chr5A 93.478 966 39 9 832 1779 482785926 482786885 0.000000e+00 1413.0
5 TraesCS5B01G273300 chr5A 89.831 826 65 14 20 837 482779408 482780222 0.000000e+00 1042.0
6 TraesCS5B01G273300 chr5A 97.122 139 4 0 4171 4309 482790327 482790189 8.530000e-58 235.0
7 TraesCS5B01G273300 chr5A 94.340 53 3 0 575 627 482780057 482780109 1.180000e-11 82.4
8 TraesCS5B01G273300 chr5D 97.231 1589 41 3 3401 4988 382423077 382424663 0.000000e+00 2687.0
9 TraesCS5B01G273300 chr5D 94.463 1499 53 17 1885 3361 382421603 382423093 0.000000e+00 2281.0
10 TraesCS5B01G273300 chr5D 91.962 1468 68 15 451 1885 382420103 382421553 0.000000e+00 2012.0
11 TraesCS5B01G273300 chr5D 89.157 415 42 3 1 414 382419685 382420097 9.780000e-142 514.0
12 TraesCS5B01G273300 chr5D 96.296 54 2 0 671 724 382420225 382420278 7.020000e-14 89.8
13 TraesCS5B01G273300 chr5D 82.524 103 10 7 4364 4458 382423936 382424038 3.270000e-12 84.2
14 TraesCS5B01G273300 chr2B 83.478 115 15 3 449 563 607534668 607534558 2.510000e-18 104.0
15 TraesCS5B01G273300 chr2D 86.842 76 6 4 3320 3394 642502857 642502785 1.180000e-11 82.4
16 TraesCS5B01G273300 chr4A 84.706 85 6 6 3309 3392 694441436 694441514 1.520000e-10 78.7
17 TraesCS5B01G273300 chr7D 95.652 46 2 0 3356 3401 624044624 624044669 1.970000e-09 75.0
18 TraesCS5B01G273300 chr7D 95.652 46 2 0 3356 3401 624143807 624143852 1.970000e-09 75.0
19 TraesCS5B01G273300 chr7D 95.652 46 2 0 3356 3401 624232390 624232435 1.970000e-09 75.0
20 TraesCS5B01G273300 chr7D 100.000 29 0 0 455 483 605964247 605964275 3.000000e-03 54.7
21 TraesCS5B01G273300 chr7B 93.878 49 1 1 3351 3397 660545960 660545912 7.070000e-09 73.1
22 TraesCS5B01G273300 chr6A 93.617 47 2 1 3348 3394 591915747 591915702 9.150000e-08 69.4
23 TraesCS5B01G273300 chr1B 86.667 60 5 3 491 549 542764773 542764830 4.260000e-06 63.9
24 TraesCS5B01G273300 chr7A 100.000 29 0 0 455 483 698141589 698141617 3.000000e-03 54.7
25 TraesCS5B01G273300 chr3D 96.774 31 1 0 453 483 549330678 549330708 9.000000e-03 52.8


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 TraesCS5B01G273300 chr5B 458714626 458719719 5093 False 9407.0 9407 100.000000 1 5094 1 chr5B.!!$F1 5093
1 TraesCS5B01G273300 chr5A 482785926 482790168 4242 False 3213.5 5014 94.346000 832 5064 2 chr5A.!!$F2 4232
2 TraesCS5B01G273300 chr5A 482779408 482780222 814 False 562.2 1042 92.085500 20 837 2 chr5A.!!$F1 817
3 TraesCS5B01G273300 chr5D 382419685 382424663 4978 False 1278.0 2687 91.938833 1 4988 6 chr5D.!!$F1 4987

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
337 340 0.249741 ACGTCCGTACTTTTGCTGCT 60.250 50.0 0.00 0.0 0.00 4.24 F
1162 1203 0.102481 CCCGTCCTCACAATACTCCG 59.898 60.0 0.00 0.0 0.00 4.63 F
2055 2155 0.948678 TTTTCTTTCGTCAAGCCCCG 59.051 50.0 0.00 0.0 31.70 5.73 F
2249 2350 0.184933 AGTCAGCCTAGGATCGAGCT 59.815 55.0 14.75 0.0 35.52 4.09 F
2835 2952 0.249120 TGGGTAGTGTCGCCATCAAG 59.751 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1696 0.466739 CATAGGCAAGGGCAGCATCA 60.467 55.0 0.00 0.00 43.71 3.07 R
2215 2316 0.755698 TGACTGGTCCGATCCTAGGC 60.756 60.0 2.96 0.00 0.00 3.93 R
3286 3403 0.035343 GAACCCTACAAGTCCAGGCC 60.035 60.0 0.00 0.00 0.00 5.19 R
3940 4059 0.522626 TCATGCGTGCCACATCAAAG 59.477 50.0 0.00 0.00 0.00 2.77 R
4668 4787 0.319405 AAGCTTGCCCATTGAGCAAC 59.681 50.0 0.96 0.25 44.95 4.17 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
39 40 2.009774 CCGAGGCAGTCCAACTTAATG 58.990 52.381 0.00 0.00 33.74 1.90
63 65 1.718280 AGAGGTTATCCCCATCGACC 58.282 55.000 0.00 0.00 0.00 4.79
100 102 1.533625 GCCAAGTTCCATGTGTAGCA 58.466 50.000 0.00 0.00 0.00 3.49
102 104 2.783135 CCAAGTTCCATGTGTAGCACT 58.217 47.619 0.90 0.00 35.11 4.40
124 126 1.546099 GGTATTGGGGAACGTGGTTGT 60.546 52.381 0.00 0.00 0.00 3.32
181 183 3.755483 GCCATCCACCTCAGATCCTAGTA 60.755 52.174 0.00 0.00 0.00 1.82
240 242 7.410120 AAGACATTGTCAAGTTCTTTTTCCT 57.590 32.000 18.57 0.00 34.60 3.36
245 247 6.834168 TTGTCAAGTTCTTTTTCCTTGAGT 57.166 33.333 0.00 0.00 43.67 3.41
320 323 5.183140 ACCCTTTTATGAGGAATTGACAACG 59.817 40.000 0.00 0.00 39.25 4.10
331 334 4.024641 GGAATTGACAACGTCCGTACTTTT 60.025 41.667 4.41 0.00 0.00 2.27
337 340 0.249741 ACGTCCGTACTTTTGCTGCT 60.250 50.000 0.00 0.00 0.00 4.24
339 342 1.654105 CGTCCGTACTTTTGCTGCTAG 59.346 52.381 0.00 0.00 0.00 3.42
340 343 2.670229 CGTCCGTACTTTTGCTGCTAGA 60.670 50.000 0.00 0.00 0.00 2.43
342 345 2.297880 TCCGTACTTTTGCTGCTAGACA 59.702 45.455 0.00 0.00 0.00 3.41
376 379 1.047002 CTCGAGAAGGATGCAGGGAT 58.953 55.000 6.58 0.00 0.00 3.85
395 398 3.246880 GGTTGGGGTGGAGTCGGT 61.247 66.667 0.00 0.00 0.00 4.69
396 399 2.346365 GTTGGGGTGGAGTCGGTC 59.654 66.667 0.00 0.00 0.00 4.79
401 404 1.377725 GGGTGGAGTCGGTCGTCTA 60.378 63.158 0.00 0.00 0.00 2.59
433 436 0.801251 GACAGTGAGATTGCTGCCAC 59.199 55.000 0.00 0.00 36.26 5.01
436 439 0.390866 AGTGAGATTGCTGCCACTCG 60.391 55.000 0.00 0.00 35.15 4.18
493 496 8.610369 TCCATCCCATAATATAGTGTGCATTAA 58.390 33.333 0.00 0.00 0.00 1.40
521 524 9.598517 TTTTGCAAAAGTCAATCTTCATAAACT 57.401 25.926 20.46 0.00 35.02 2.66
524 527 9.033481 TGCAAAAGTCAATCTTCATAAACTTTG 57.967 29.630 0.00 0.00 37.12 2.77
847 865 3.304911 TTTTTGTGTGGGAGGATGACA 57.695 42.857 0.00 0.00 0.00 3.58
947 988 2.158842 CCATGTTGGAACCAAAAAGCCA 60.159 45.455 7.89 2.47 40.96 4.75
962 1003 2.434884 CCATCAACCAGCGAGCGT 60.435 61.111 0.00 0.00 0.00 5.07
1162 1203 0.102481 CCCGTCCTCACAATACTCCG 59.898 60.000 0.00 0.00 0.00 4.63
1267 1309 8.269424 CCATACTCGAATTCTAAACTGATTTCG 58.731 37.037 3.52 12.37 44.33 3.46
1335 1377 3.077556 AGATCGAACTGGGGCGCT 61.078 61.111 7.64 0.00 0.00 5.92
1500 1542 3.440127 CACCTAACAACAATCCCCCATT 58.560 45.455 0.00 0.00 0.00 3.16
1504 1546 5.020132 CCTAACAACAATCCCCCATTTGTA 58.980 41.667 0.00 0.00 35.09 2.41
1513 1555 4.249638 TCCCCCATTTGTATCTGGAAAG 57.750 45.455 0.00 0.00 34.24 2.62
1582 1624 2.354259 ACTGATTCTACTGCTGCTTGC 58.646 47.619 0.00 0.00 43.25 4.01
1654 1696 2.165998 GCTGCTCCTTCCATCTTTGTT 58.834 47.619 0.00 0.00 0.00 2.83
1694 1736 7.598869 CCTATGCATTCTATAAACTGAGCGTTA 59.401 37.037 3.54 0.00 33.90 3.18
1760 1802 4.159120 GACTCGCTTGAAATTTGGTAAGC 58.841 43.478 15.95 15.95 41.47 3.09
1761 1803 3.568007 ACTCGCTTGAAATTTGGTAAGCA 59.432 39.130 21.53 12.91 44.23 3.91
1787 1829 6.963796 ACTGCTTTGACATTGTCTTTAGAAG 58.036 36.000 17.26 15.63 33.15 2.85
1792 1834 7.173390 GCTTTGACATTGTCTTTAGAAGGTAGT 59.827 37.037 17.26 0.00 33.15 2.73
1881 1923 1.615424 AGGCCTACCCATCCGTGTT 60.615 57.895 1.29 0.00 36.11 3.32
2055 2155 0.948678 TTTTCTTTCGTCAAGCCCCG 59.051 50.000 0.00 0.00 31.70 5.73
2073 2173 4.155733 CCCACGGTGGCAGCGATA 62.156 66.667 41.06 0.00 42.41 2.92
2090 2191 3.679025 GCGATAGATCTGAGCTGATTTGG 59.321 47.826 5.18 0.00 39.76 3.28
2215 2316 2.330440 AAAAACAAAAGCCCAGCCAG 57.670 45.000 0.00 0.00 0.00 4.85
2218 2319 2.602568 CAAAAGCCCAGCCAGCCT 60.603 61.111 0.00 0.00 0.00 4.58
2249 2350 0.184933 AGTCAGCCTAGGATCGAGCT 59.815 55.000 14.75 0.00 35.52 4.09
2309 2414 1.308998 CTGACTTCCGGTGCACTTTT 58.691 50.000 17.98 0.00 0.00 2.27
2310 2415 1.002468 CTGACTTCCGGTGCACTTTTG 60.002 52.381 17.98 6.35 0.00 2.44
2394 2499 2.033448 GTGATGTCGTTGGGGCCA 59.967 61.111 4.39 0.00 0.00 5.36
2404 2509 1.078891 TTGGGGCCATGCAATCACT 59.921 52.632 4.39 0.00 0.00 3.41
2733 2850 6.041511 CGAACCCAATATGATTGCAATTTCA 58.958 36.000 14.33 9.41 0.00 2.69
2735 2852 6.795144 ACCCAATATGATTGCAATTTCAGA 57.205 33.333 14.33 6.61 0.00 3.27
2835 2952 0.249120 TGGGTAGTGTCGCCATCAAG 59.751 55.000 0.00 0.00 0.00 3.02
2900 3017 1.185618 TAGCAGTCACGTTGGGAGCT 61.186 55.000 0.00 0.00 34.84 4.09
2914 3031 3.798954 GAGCTATTCGGCCGCTGCT 62.799 63.158 23.51 24.70 37.74 4.24
2982 3099 1.691434 GGCAAAGGGTCATGGAAAACA 59.309 47.619 0.00 0.00 0.00 2.83
2999 3116 3.565214 ACGTGCCCCATGTCACCA 61.565 61.111 0.00 0.00 0.00 4.17
3034 3151 3.886505 CGGGATAGAGGCTATAGTCATCC 59.113 52.174 7.19 10.02 0.00 3.51
3070 3187 1.673920 GAGGAGTCTCTCGCGAAGATT 59.326 52.381 11.33 12.57 37.07 2.40
3103 3220 6.209589 CCAAGAAGATATAGCTAGGTACTGCA 59.790 42.308 3.24 0.00 41.52 4.41
3105 3222 7.639113 AGAAGATATAGCTAGGTACTGCATC 57.361 40.000 3.24 5.41 41.52 3.91
3165 3282 0.828677 AGGCAATGACCGTACCCTAC 59.171 55.000 0.00 0.00 33.69 3.18
3179 3296 0.976073 CCCTACGGAGTCATGTGGGT 60.976 60.000 13.66 0.00 43.93 4.51
3203 3320 3.737032 TGTTCGGACACACTGTGATAA 57.263 42.857 16.30 1.91 36.96 1.75
3260 3377 4.160329 AGGAGGATAAGTTGTGACACAGA 58.840 43.478 8.55 0.00 0.00 3.41
3286 3403 2.689983 GCACCATGTTGAAATAGAGGGG 59.310 50.000 0.00 0.00 0.00 4.79
3287 3404 3.290710 CACCATGTTGAAATAGAGGGGG 58.709 50.000 0.00 0.00 0.00 5.40
3354 3471 4.981812 TGGACTAGGAGCGAGTGATATAA 58.018 43.478 0.00 0.00 0.00 0.98
3359 3476 7.542824 GGACTAGGAGCGAGTGATATAATTTTC 59.457 40.741 0.00 0.00 0.00 2.29
3360 3477 8.184304 ACTAGGAGCGAGTGATATAATTTTCT 57.816 34.615 0.00 0.00 0.00 2.52
3397 3515 5.450818 TGGGCATGTTTCCTAGTAAATCT 57.549 39.130 0.00 0.00 0.00 2.40
3864 3983 6.701841 TGTTACTGTTCTTCTCACTGACATTC 59.298 38.462 0.00 0.00 0.00 2.67
4218 4337 3.380142 CCATGGTTGTGTACAGTTTTGC 58.620 45.455 2.57 0.00 0.00 3.68
4296 4415 4.325028 TGAAGAGCATTTGCAATGTGTT 57.675 36.364 0.00 0.17 45.16 3.32
4324 4443 7.522236 GCATTCTTTTAAAGTCTGTAACAGCCT 60.522 37.037 4.53 0.00 0.00 4.58
4332 4451 3.194542 AGTCTGTAACAGCCTGATGAGAC 59.805 47.826 0.00 3.44 0.00 3.36
4335 4454 1.134371 GTAACAGCCTGATGAGACCCC 60.134 57.143 0.00 0.00 0.00 4.95
4340 4459 2.374504 CAGCCTGATGAGACCCCATATT 59.625 50.000 0.00 0.00 0.00 1.28
4601 4720 6.985117 TGGAGGAAAAATTGAGATTGTTCAG 58.015 36.000 4.87 0.00 40.03 3.02
4668 4787 5.215252 ACTGTATATCCGAGTCCAAATGG 57.785 43.478 0.00 0.00 0.00 3.16
4725 4845 4.927425 CCTTGACAATTTGGAATTCAGCAG 59.073 41.667 7.93 0.00 0.00 4.24
4789 4909 2.846193 TGACAAAGTTGGAGGCACTAC 58.154 47.619 0.00 0.00 41.55 2.73
4816 4936 6.795144 AGATGCATTGGGTTCATTTGATAA 57.205 33.333 0.00 0.00 0.00 1.75
4875 4995 4.778213 ATTGCACTATAGTCCACCATGT 57.222 40.909 1.26 0.00 0.00 3.21
4959 5079 4.213270 TGAAGGTACTCAAAAGTTCATGCG 59.787 41.667 0.00 0.00 38.49 4.73
4970 5090 1.474478 AGTTCATGCGAGACTCGACAT 59.526 47.619 28.43 24.21 43.74 3.06
5001 5121 7.599998 GCTGTTGACAAAACCATATTGATTCTT 59.400 33.333 0.00 0.00 0.00 2.52
5002 5122 9.132521 CTGTTGACAAAACCATATTGATTCTTC 57.867 33.333 0.00 0.00 0.00 2.87
5003 5123 7.807433 TGTTGACAAAACCATATTGATTCTTCG 59.193 33.333 0.00 0.00 0.00 3.79
5040 5160 6.016276 ACAATTACCCTTCTGCAACTTGTTAG 60.016 38.462 0.00 0.00 0.00 2.34
5064 5184 3.744238 ACAGTTTGGTTTGTATTGGCC 57.256 42.857 0.00 0.00 0.00 5.36
5065 5185 3.304829 ACAGTTTGGTTTGTATTGGCCT 58.695 40.909 3.32 0.00 0.00 5.19
5066 5186 4.475345 ACAGTTTGGTTTGTATTGGCCTA 58.525 39.130 3.32 0.00 0.00 3.93
5067 5187 5.083821 ACAGTTTGGTTTGTATTGGCCTAT 58.916 37.500 3.32 4.11 0.00 2.57
5068 5188 5.542251 ACAGTTTGGTTTGTATTGGCCTATT 59.458 36.000 4.63 0.00 0.00 1.73
5069 5189 5.868801 CAGTTTGGTTTGTATTGGCCTATTG 59.131 40.000 4.63 0.00 0.00 1.90
5070 5190 5.542251 AGTTTGGTTTGTATTGGCCTATTGT 59.458 36.000 4.63 0.00 0.00 2.71
5071 5191 5.652994 TTGGTTTGTATTGGCCTATTGTC 57.347 39.130 4.63 0.00 0.00 3.18
5072 5192 4.020543 TGGTTTGTATTGGCCTATTGTCC 58.979 43.478 4.63 2.87 0.00 4.02
5073 5193 3.383505 GGTTTGTATTGGCCTATTGTCCC 59.616 47.826 4.63 0.00 0.00 4.46
5074 5194 4.278310 GTTTGTATTGGCCTATTGTCCCT 58.722 43.478 4.63 0.00 0.00 4.20
5075 5195 5.442391 GTTTGTATTGGCCTATTGTCCCTA 58.558 41.667 4.63 0.00 0.00 3.53
5076 5196 4.974645 TGTATTGGCCTATTGTCCCTAG 57.025 45.455 4.63 0.00 0.00 3.02
5077 5197 2.959465 ATTGGCCTATTGTCCCTAGC 57.041 50.000 3.32 0.00 0.00 3.42
5078 5198 1.893315 TTGGCCTATTGTCCCTAGCT 58.107 50.000 3.32 0.00 0.00 3.32
5079 5199 1.131638 TGGCCTATTGTCCCTAGCTG 58.868 55.000 3.32 0.00 0.00 4.24
5080 5200 1.343985 TGGCCTATTGTCCCTAGCTGA 60.344 52.381 3.32 0.00 0.00 4.26
5081 5201 1.981495 GGCCTATTGTCCCTAGCTGAT 59.019 52.381 0.00 0.00 0.00 2.90
5082 5202 2.373502 GGCCTATTGTCCCTAGCTGATT 59.626 50.000 0.00 0.00 0.00 2.57
5083 5203 3.181439 GGCCTATTGTCCCTAGCTGATTT 60.181 47.826 0.00 0.00 0.00 2.17
5084 5204 4.041691 GGCCTATTGTCCCTAGCTGATTTA 59.958 45.833 0.00 0.00 0.00 1.40
5085 5205 5.241662 GCCTATTGTCCCTAGCTGATTTAG 58.758 45.833 0.00 0.00 0.00 1.85
5086 5206 5.799213 CCTATTGTCCCTAGCTGATTTAGG 58.201 45.833 0.00 0.00 37.92 2.69
5087 5207 5.544176 CCTATTGTCCCTAGCTGATTTAGGA 59.456 44.000 0.00 0.00 40.12 2.94
5088 5208 5.975988 ATTGTCCCTAGCTGATTTAGGAA 57.024 39.130 0.00 0.00 40.12 3.36
5089 5209 5.975988 TTGTCCCTAGCTGATTTAGGAAT 57.024 39.130 0.00 0.00 40.12 3.01
5090 5210 5.552870 TGTCCCTAGCTGATTTAGGAATC 57.447 43.478 0.00 0.00 40.12 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.475135 GGACTGCCTCGGCCCTTC 62.475 72.222 5.33 0.00 41.09 3.46
39 40 3.578716 TCGATGGGGATAACCTCTTCATC 59.421 47.826 5.75 5.72 39.80 2.92
63 65 1.901650 GCGAGGGTGTTCTTTCAGCG 61.902 60.000 0.00 0.00 36.79 5.18
100 102 1.271707 CCACGTTCCCCAATACCAAGT 60.272 52.381 0.00 0.00 0.00 3.16
102 104 0.772384 ACCACGTTCCCCAATACCAA 59.228 50.000 0.00 0.00 0.00 3.67
124 126 6.691754 TCAACATAAACAAGACTTTCAGCA 57.308 33.333 0.00 0.00 0.00 4.41
181 183 6.407202 GCGGACATGGATTAACTAATAGGAT 58.593 40.000 0.00 0.00 0.00 3.24
203 205 2.939103 CAATGTCTTCCTCCTAAAGGCG 59.061 50.000 0.00 0.00 45.78 5.52
240 242 6.567687 TGTGTTGAGAAAGTTGAAACTCAA 57.432 33.333 0.00 0.00 43.79 3.02
245 247 7.873719 TTAGGATGTGTTGAGAAAGTTGAAA 57.126 32.000 0.00 0.00 0.00 2.69
320 323 2.666994 GTCTAGCAGCAAAAGTACGGAC 59.333 50.000 0.00 0.00 0.00 4.79
337 340 1.684734 GGCTTCGGGGGACTGTCTA 60.685 63.158 7.85 0.00 38.16 2.59
339 342 4.097361 GGGCTTCGGGGGACTGTC 62.097 72.222 0.00 0.00 38.16 3.51
368 371 3.671410 CCCCAACCCATCCCTGCA 61.671 66.667 0.00 0.00 0.00 4.41
376 379 3.246112 CGACTCCACCCCAACCCA 61.246 66.667 0.00 0.00 0.00 4.51
395 398 4.264253 TGTCGGGAGTATTTTCTAGACGA 58.736 43.478 0.00 0.00 0.00 4.20
396 399 4.096081 ACTGTCGGGAGTATTTTCTAGACG 59.904 45.833 0.00 0.00 0.00 4.18
401 404 4.087182 TCTCACTGTCGGGAGTATTTTCT 58.913 43.478 0.00 0.00 32.93 2.52
595 598 8.451908 GGTACCAAATCAATAGCATTAGACTT 57.548 34.615 7.15 0.00 0.00 3.01
684 688 9.770097 AATCAATAACATTAGACTCGTCATGAT 57.230 29.630 0.00 0.00 0.00 2.45
706 710 7.194112 TGTGAACATCTAGGATACCAAATCA 57.806 36.000 0.00 0.00 37.17 2.57
813 831 9.249053 TCCCACACAAAAATAATAATCTTGCTA 57.751 29.630 0.00 0.00 0.00 3.49
819 837 8.912988 TCATCCTCCCACACAAAAATAATAATC 58.087 33.333 0.00 0.00 0.00 1.75
847 865 1.831736 CCTGGTACTCCGAGTTCCATT 59.168 52.381 22.93 0.00 43.33 3.16
935 963 2.485302 GCTGGTTGATGGCTTTTTGGTT 60.485 45.455 0.00 0.00 0.00 3.67
947 988 0.458543 CTGTACGCTCGCTGGTTGAT 60.459 55.000 0.00 0.00 0.00 2.57
1104 1145 3.391382 CCTCGTGTCCCCCTGGTC 61.391 72.222 0.00 0.00 0.00 4.02
1162 1203 2.409870 CCAACGCCCATGGAGCTTC 61.410 63.158 15.22 0.00 40.56 3.86
1249 1290 6.902417 GCTACAGCGAAATCAGTTTAGAATTC 59.098 38.462 0.00 0.00 0.00 2.17
1276 1318 2.203126 GGGGAATCAGGCGAGCAG 60.203 66.667 0.00 0.00 0.00 4.24
1500 1542 6.009589 TCCATTGCTTTCTTTCCAGATACAA 58.990 36.000 0.00 0.00 0.00 2.41
1504 1546 5.776716 TCTTTCCATTGCTTTCTTTCCAGAT 59.223 36.000 0.00 0.00 0.00 2.90
1513 1555 3.881937 ATGGCTCTTTCCATTGCTTTC 57.118 42.857 0.00 0.00 44.04 2.62
1582 1624 4.023707 CCAAGAAAAGCACCTACAGAAGTG 60.024 45.833 0.00 0.00 37.05 3.16
1654 1696 0.466739 CATAGGCAAGGGCAGCATCA 60.467 55.000 0.00 0.00 43.71 3.07
1694 1736 4.148825 GCGCACCTCCGAGGACAT 62.149 66.667 21.89 0.00 37.67 3.06
1760 1802 8.032952 TCTAAAGACAATGTCAAAGCAGTATG 57.967 34.615 16.38 0.00 35.08 2.39
1761 1803 8.621532 TTCTAAAGACAATGTCAAAGCAGTAT 57.378 30.769 16.38 0.00 34.60 2.12
1838 1880 3.556004 GGGCACTATAGAATGCTCTCACC 60.556 52.174 6.78 0.00 39.36 4.02
1840 1882 3.070159 GTGGGCACTATAGAATGCTCTCA 59.930 47.826 14.41 8.67 43.13 3.27
1841 1883 3.070159 TGTGGGCACTATAGAATGCTCTC 59.930 47.826 14.41 11.77 43.13 3.20
1869 1911 2.656069 CCCTCGAACACGGATGGGT 61.656 63.158 0.00 0.00 32.60 4.51
1881 1923 1.306141 AATCAGGACCAGCCCTCGA 60.306 57.895 0.00 0.00 37.37 4.04
2017 2110 2.358737 GTGGAACAGGGCTCCGTG 60.359 66.667 7.03 7.03 41.80 4.94
2019 2112 2.411765 AAAGGTGGAACAGGGCTCCG 62.412 60.000 0.00 0.00 41.80 4.63
2073 2173 2.762887 TCGACCAAATCAGCTCAGATCT 59.237 45.455 0.00 0.00 0.00 2.75
2090 2191 1.537562 GGTGGTATTGGTCCGATCGAC 60.538 57.143 18.66 12.55 41.15 4.20
2208 2309 2.739784 CGATCCTAGGCTGGCTGG 59.260 66.667 14.70 11.07 0.00 4.85
2215 2316 0.755698 TGACTGGTCCGATCCTAGGC 60.756 60.000 2.96 0.00 0.00 3.93
2218 2319 0.755698 GGCTGACTGGTCCGATCCTA 60.756 60.000 0.00 0.00 0.00 2.94
2249 2350 1.377202 GATGGCTTGGCTTGTCCGA 60.377 57.895 0.00 0.00 37.80 4.55
2309 2414 2.088423 AGCTCGTTTCCAACAACAACA 58.912 42.857 0.00 0.00 0.00 3.33
2310 2415 2.844122 AGCTCGTTTCCAACAACAAC 57.156 45.000 0.00 0.00 0.00 3.32
2394 2499 5.072741 ACTAAACCAAGACAGTGATTGCAT 58.927 37.500 0.00 0.00 0.00 3.96
2404 2509 5.655532 CCTAGCCTAGTACTAAACCAAGACA 59.344 44.000 3.76 0.00 0.00 3.41
2454 2563 5.230097 CGCAGATATATATAGCACACAACCG 59.770 44.000 10.48 0.00 0.00 4.44
2741 2858 2.775890 CTGCTTTCTATCGGGATGCAT 58.224 47.619 0.00 0.00 0.00 3.96
2809 2926 1.687123 GGCGACACTACCCATAGATGT 59.313 52.381 0.00 0.00 32.23 3.06
2811 2928 2.082140 TGGCGACACTACCCATAGAT 57.918 50.000 0.00 0.00 33.40 1.98
2835 2952 1.419374 CGGATGCCTAATACGCAGTC 58.581 55.000 0.00 0.00 43.93 3.51
2900 3017 1.748329 ATCTCAGCAGCGGCCGAATA 61.748 55.000 33.48 6.08 42.56 1.75
2982 3099 3.551496 CTGGTGACATGGGGCACGT 62.551 63.158 0.00 0.00 41.51 4.49
2999 3116 5.081032 CCTCTATCCCGACTATTTTCCTCT 58.919 45.833 0.00 0.00 0.00 3.69
3070 3187 5.945310 AGCTATATCTTCTTGGCATCCAAA 58.055 37.500 0.00 0.00 43.44 3.28
3179 3296 2.362717 TCACAGTGTGTCCGAACATGTA 59.637 45.455 22.29 0.00 37.81 2.29
3207 3324 2.080693 GCCAACAATGATCGTGGTGTA 58.919 47.619 11.96 0.00 31.40 2.90
3260 3377 5.380043 CTCTATTTCAACATGGTGCCCTAT 58.620 41.667 5.66 0.00 0.00 2.57
3286 3403 0.035343 GAACCCTACAAGTCCAGGCC 60.035 60.000 0.00 0.00 0.00 5.19
3287 3404 0.984995 AGAACCCTACAAGTCCAGGC 59.015 55.000 0.00 0.00 0.00 4.85
3375 3493 5.450818 AGATTTACTAGGAAACATGCCCA 57.549 39.130 1.11 0.00 0.00 5.36
3525 3644 8.582437 TCGAACAACTAATAAGAGAAAAGGAGA 58.418 33.333 0.00 0.00 0.00 3.71
3751 3870 7.592938 CATAACAACATAACCAAAGCTCAGAA 58.407 34.615 0.00 0.00 0.00 3.02
3825 3944 8.615878 AGAACAGTAACAACAGCATATAAACA 57.384 30.769 0.00 0.00 0.00 2.83
3837 3956 5.810587 TGTCAGTGAGAAGAACAGTAACAAC 59.189 40.000 0.00 0.00 0.00 3.32
3864 3983 8.519492 AAAATGGTTGATGACAAACTAAATCG 57.481 30.769 0.00 0.00 43.37 3.34
3940 4059 0.522626 TCATGCGTGCCACATCAAAG 59.477 50.000 0.00 0.00 0.00 2.77
4296 4415 8.504005 GCTGTTACAGACTTTAAAAGAATGCTA 58.496 33.333 17.40 0.00 32.44 3.49
4324 4443 5.415065 ACTATGGAATATGGGGTCTCATCA 58.585 41.667 0.00 0.00 0.00 3.07
4601 4720 8.668353 TCATTATTTCTGCTGATCTTGTACAAC 58.332 33.333 3.59 0.00 0.00 3.32
4656 4775 1.522668 TGAGCAACCATTTGGACTCG 58.477 50.000 3.01 0.00 36.60 4.18
4668 4787 0.319405 AAGCTTGCCCATTGAGCAAC 59.681 50.000 0.96 0.25 44.95 4.17
4904 5024 9.611284 TTCATAAATCTGAAAATGAAGTTGTCG 57.389 29.630 7.97 0.00 34.34 4.35
4959 5079 2.408050 ACAGCACAAATGTCGAGTCTC 58.592 47.619 0.00 0.00 0.00 3.36
4970 5090 3.667497 TGGTTTTGTCAACAGCACAAA 57.333 38.095 0.00 0.00 41.05 2.83
5001 5121 9.321562 GAAGGGTAATTGTATTTATTCTGACGA 57.678 33.333 0.00 0.00 0.00 4.20
5002 5122 9.326413 AGAAGGGTAATTGTATTTATTCTGACG 57.674 33.333 0.00 0.00 0.00 4.35
5064 5184 6.672266 TCCTAAATCAGCTAGGGACAATAG 57.328 41.667 0.00 0.00 37.18 1.73
5065 5185 7.292356 TGATTCCTAAATCAGCTAGGGACAATA 59.708 37.037 0.00 0.00 44.94 1.90
5066 5186 5.975988 TTCCTAAATCAGCTAGGGACAAT 57.024 39.130 0.00 0.00 37.18 2.71
5067 5187 5.428457 TGATTCCTAAATCAGCTAGGGACAA 59.572 40.000 0.00 0.00 44.94 3.18
5068 5188 4.968719 TGATTCCTAAATCAGCTAGGGACA 59.031 41.667 0.00 0.00 44.94 4.02
5069 5189 5.552870 TGATTCCTAAATCAGCTAGGGAC 57.447 43.478 0.00 0.00 44.94 4.46


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

AutoCloner maintained by Alex Coulton.