Multiple sequence alignment - TraesCS5D01G131400

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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 TraesCS5D01G131400 chr5D 100.000 3302 0 0 1 3302 208541198 208537897 0.000000e+00 6098.0
1 TraesCS5D01G131400 chr4B 92.928 2814 153 21 325 3105 124040535 124043335 0.000000e+00 4052.0
2 TraesCS5D01G131400 chr4B 82.390 318 52 4 4 319 110444464 110444149 1.170000e-69 274.0
3 TraesCS5D01G131400 chr4B 88.095 168 16 3 1976 2140 666604754 666604920 2.600000e-46 196.0
4 TraesCS5D01G131400 chr3B 94.823 2009 94 8 338 2340 449840176 449842180 0.000000e+00 3125.0
5 TraesCS5D01G131400 chr3B 95.935 738 26 2 2337 3073 449845369 449846103 0.000000e+00 1194.0
6 TraesCS5D01G131400 chr3B 83.908 87 13 1 3020 3105 543187574 543187660 7.590000e-12 82.4
7 TraesCS5D01G131400 chr3B 81.928 83 10 3 3026 3105 15972529 15972609 7.650000e-07 65.8
8 TraesCS5D01G131400 chr3A 94.491 1797 51 19 330 2117 57909621 57911378 0.000000e+00 2726.0
9 TraesCS5D01G131400 chr3A 96.725 1496 42 5 627 2117 745551637 745553130 0.000000e+00 2484.0
10 TraesCS5D01G131400 chr3A 96.324 952 34 1 2154 3105 745553126 745554076 0.000000e+00 1563.0
11 TraesCS5D01G131400 chr3A 97.699 565 13 0 2154 2718 57911374 57911938 0.000000e+00 972.0
12 TraesCS5D01G131400 chr3A 96.947 524 15 1 2561 3084 57911935 57912457 0.000000e+00 878.0
13 TraesCS5D01G131400 chr3A 92.222 180 11 3 320 498 745550898 745551075 5.470000e-63 252.0
14 TraesCS5D01G131400 chr3A 92.857 98 6 1 536 632 745551083 745551180 1.240000e-29 141.0
15 TraesCS5D01G131400 chr5A 96.641 1280 39 2 656 1931 3457597 3456318 0.000000e+00 2122.0
16 TraesCS5D01G131400 chr5A 97.059 952 27 1 2154 3105 3455286 3454336 0.000000e+00 1602.0
17 TraesCS5D01G131400 chr5A 95.980 199 6 2 1924 2120 3455477 3455279 4.110000e-84 322.0
18 TraesCS5D01G131400 chr5A 98.315 178 2 1 3126 3302 269328379 269328202 8.900000e-81 311.0
19 TraesCS5D01G131400 chr5B 94.298 1175 40 8 1893 3052 31288055 31289217 0.000000e+00 1773.0
20 TraesCS5D01G131400 chr5B 94.128 1175 42 8 1893 3052 31195028 31196190 0.000000e+00 1762.0
21 TraesCS5D01G131400 chr5B 96.865 638 19 1 1254 1891 31287292 31287928 0.000000e+00 1066.0
22 TraesCS5D01G131400 chr5B 96.401 639 21 2 1254 1891 31194264 31194901 0.000000e+00 1051.0
23 TraesCS5D01G131400 chr5B 95.691 557 21 1 706 1259 31188517 31189073 0.000000e+00 893.0
24 TraesCS5D01G131400 chr5B 95.153 557 24 2 706 1259 31281546 31282102 0.000000e+00 876.0
25 TraesCS5D01G131400 chr5B 80.884 1177 138 46 1976 3105 140948478 140947342 0.000000e+00 846.0
26 TraesCS5D01G131400 chr5B 89.637 386 14 9 321 704 31272129 31272490 4.990000e-128 468.0
27 TraesCS5D01G131400 chr5B 89.378 386 15 9 321 704 31187415 31187776 2.320000e-126 462.0
28 TraesCS5D01G131400 chr5B 91.223 319 28 0 1 319 222129178 222128860 5.060000e-118 435.0
29 TraesCS5D01G131400 chr5B 91.542 201 8 3 3108 3302 222128677 222128480 5.430000e-68 268.0
30 TraesCS5D01G131400 chr5B 96.262 107 2 2 329 435 31187029 31187133 1.220000e-39 174.0
31 TraesCS5D01G131400 chr6A 80.714 1177 140 44 1976 3105 21656028 21654892 0.000000e+00 835.0
32 TraesCS5D01G131400 chr7A 87.651 664 67 4 736 1384 726603353 726602690 0.000000e+00 758.0
33 TraesCS5D01G131400 chr6D 83.725 596 61 14 1976 2552 306006485 306007063 6.270000e-147 531.0
34 TraesCS5D01G131400 chr6D 81.962 316 55 2 5 319 97573448 97573762 1.950000e-67 267.0
35 TraesCS5D01G131400 chr1B 88.338 343 37 2 874 1213 667240458 667240116 3.070000e-110 409.0
36 TraesCS5D01G131400 chr1B 84.127 315 49 1 4 317 61964895 61965209 1.490000e-78 303.0
37 TraesCS5D01G131400 chr1B 83.178 321 52 2 1 319 573580049 573580369 3.220000e-75 292.0
38 TraesCS5D01G131400 chr7D 87.353 340 34 4 1640 1975 32159065 32159399 6.690000e-102 381.0
39 TraesCS5D01G131400 chr7D 82.919 322 50 5 1 319 60277789 60277470 5.390000e-73 285.0
40 TraesCS5D01G131400 chr2D 82.039 412 63 9 1486 1890 472475028 472474621 1.130000e-89 340.0
41 TraesCS5D01G131400 chr2D 87.379 103 13 0 2714 2816 37139629 37139731 5.790000e-23 119.0
42 TraesCS5D01G131400 chr1D 84.277 318 48 2 4 320 477505110 477504794 3.200000e-80 309.0
43 TraesCS5D01G131400 chr1D 83.226 310 48 4 6 313 387422591 387422898 6.980000e-72 281.0
44 TraesCS5D01G131400 chr6B 90.610 213 20 0 2293 2505 19603232 19603020 1.940000e-72 283.0
45 TraesCS5D01G131400 chr2B 82.334 317 55 1 4 319 153128398 153128082 1.170000e-69 274.0
46 TraesCS5D01G131400 chr7B 88.095 168 16 3 1976 2140 634287391 634287557 2.600000e-46 196.0


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 TraesCS5D01G131400 chr5D 208537897 208541198 3301 True 6098.000000 6098 100.0000 1 3302 1 chr5D.!!$R1 3301
1 TraesCS5D01G131400 chr4B 124040535 124043335 2800 False 4052.000000 4052 92.9280 325 3105 1 chr4B.!!$F1 2780
2 TraesCS5D01G131400 chr3B 449840176 449846103 5927 False 2159.500000 3125 95.3790 338 3073 2 chr3B.!!$F3 2735
3 TraesCS5D01G131400 chr3A 57909621 57912457 2836 False 1525.333333 2726 96.3790 330 3084 3 chr3A.!!$F1 2754
4 TraesCS5D01G131400 chr3A 745550898 745554076 3178 False 1110.000000 2484 94.5320 320 3105 4 chr3A.!!$F2 2785
5 TraesCS5D01G131400 chr5A 3454336 3457597 3261 True 1348.666667 2122 96.5600 656 3105 3 chr5A.!!$R2 2449
6 TraesCS5D01G131400 chr5B 31287292 31289217 1925 False 1419.500000 1773 95.5815 1254 3052 2 chr5B.!!$F5 1798
7 TraesCS5D01G131400 chr5B 31194264 31196190 1926 False 1406.500000 1762 95.2645 1254 3052 2 chr5B.!!$F4 1798
8 TraesCS5D01G131400 chr5B 31281546 31282102 556 False 876.000000 876 95.1530 706 1259 1 chr5B.!!$F2 553
9 TraesCS5D01G131400 chr5B 140947342 140948478 1136 True 846.000000 846 80.8840 1976 3105 1 chr5B.!!$R1 1129
10 TraesCS5D01G131400 chr5B 31187029 31189073 2044 False 509.666667 893 93.7770 321 1259 3 chr5B.!!$F3 938
11 TraesCS5D01G131400 chr5B 222128480 222129178 698 True 351.500000 435 91.3825 1 3302 2 chr5B.!!$R2 3301
12 TraesCS5D01G131400 chr6A 21654892 21656028 1136 True 835.000000 835 80.7140 1976 3105 1 chr6A.!!$R1 1129
13 TraesCS5D01G131400 chr7A 726602690 726603353 663 True 758.000000 758 87.6510 736 1384 1 chr7A.!!$R1 648
14 TraesCS5D01G131400 chr6D 306006485 306007063 578 False 531.000000 531 83.7250 1976 2552 1 chr6D.!!$F2 576

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
319 320 0.958876 GTTCGGTTGTCCATGGACCC 60.959 60.0 36.27 29.46 43.97 4.46 F
1127 2435 0.608130 TCCATGGACTCACTTCACCG 59.392 55.0 11.44 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 4374 0.582005 GCGCGTGAAGACTTGTCTTT 59.418 50.0 15.94 2.14 0.0 2.52 R
2998 8811 0.884704 TCCAAACGAGCAAGAGTGGC 60.885 55.0 0.00 0.00 0.0 5.01 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
24 25 1.419374 CTCCTCAAGTTCGTTCGTGG 58.581 55.000 0.00 0.00 0.00 4.94
25 26 1.000607 CTCCTCAAGTTCGTTCGTGGA 60.001 52.381 0.00 0.00 0.00 4.02
72 73 1.965754 ATTCCTGCCAGCTCCTCGAC 61.966 60.000 0.00 0.00 0.00 4.20
93 94 1.337541 GCGACGAGGTTAGGGTTTCTT 60.338 52.381 0.00 0.00 0.00 2.52
121 122 3.366724 GTGTATGCAACGACGAGATTTGA 59.633 43.478 0.00 0.00 0.00 2.69
124 125 1.128507 TGCAACGACGAGATTTGATGC 59.871 47.619 0.00 0.00 0.00 3.91
136 137 5.344128 CGAGATTTGATGCTTGGTTTTTCAG 59.656 40.000 0.00 0.00 0.00 3.02
157 158 6.585416 TCAGATCGATTCAAGGATTCAATGA 58.415 36.000 0.00 0.00 0.00 2.57
166 167 4.452114 TCAAGGATTCAATGACAACGACTG 59.548 41.667 0.00 0.00 0.00 3.51
177 178 2.513259 AACGACTGGGCTCCCGAAA 61.513 57.895 0.00 0.00 39.42 3.46
178 179 2.125512 CGACTGGGCTCCCGAAAG 60.126 66.667 0.00 0.00 39.42 2.62
254 255 2.727392 CGGCTCCGGTATGGGAACA 61.727 63.158 0.00 0.00 39.59 3.18
255 256 2.246761 CGGCTCCGGTATGGGAACAA 62.247 60.000 0.00 0.00 38.98 2.83
268 269 3.515286 GAACAACGAAAGCGGCGCA 62.515 57.895 35.02 0.00 43.17 6.09
319 320 0.958876 GTTCGGTTGTCCATGGACCC 60.959 60.000 36.27 29.46 43.97 4.46
321 322 2.602676 CGGTTGTCCATGGACCCCT 61.603 63.158 36.27 0.00 43.97 4.79
322 323 1.303282 GGTTGTCCATGGACCCCTC 59.697 63.158 36.27 23.67 43.97 4.30
327 328 1.051556 GTCCATGGACCCCTCTCTCC 61.052 65.000 31.37 4.75 39.08 3.71
408 473 1.153208 GGTCGACGAGGAGGAGCTA 60.153 63.158 9.92 0.00 0.00 3.32
620 711 4.664640 CGCGCACAATTTCGTCTTAGTTTA 60.665 41.667 8.75 0.00 0.00 2.01
632 723 4.857588 CGTCTTAGTTTATGACAAGCGACT 59.142 41.667 0.00 0.00 33.77 4.18
699 1252 6.849502 TCGAGATCTGTTTGTTCGTTATAGT 58.150 36.000 0.00 0.00 33.35 2.12
750 2042 2.615912 GCTGCTGCTTCTATCCGAAAAT 59.384 45.455 8.53 0.00 36.03 1.82
805 2097 5.928264 AGCATTCTCCAGTTGTTTTATTTGC 59.072 36.000 0.00 0.00 0.00 3.68
814 2106 2.386249 TGTTTTATTTGCGAACGCCAC 58.614 42.857 16.27 3.20 41.09 5.01
1074 2379 1.337354 TGCTTCAACGACTTCGCCATA 60.337 47.619 0.00 0.00 44.43 2.74
1127 2435 0.608130 TCCATGGACTCACTTCACCG 59.392 55.000 11.44 0.00 0.00 4.94
1213 2522 6.372659 AGCTGATTGATTCGAGTTTTGTATGT 59.627 34.615 0.00 0.00 0.00 2.29
1231 2540 2.323599 TGTAGATGCAGAGGGAGATGG 58.676 52.381 0.00 0.00 0.00 3.51
1472 2781 9.701098 TTATGTTTATATGGTCTAACGACATCC 57.299 33.333 0.00 0.00 42.05 3.51
1593 2902 5.597813 AAACTAACGATCAAACTGCAGAG 57.402 39.130 23.35 9.98 0.00 3.35
1883 3262 7.224362 TGAACAAAACATGATTTTGCTAACCTG 59.776 33.333 22.43 5.49 41.66 4.00
1891 3270 7.537715 CATGATTTTGCTAACCTGTCATGTAA 58.462 34.615 12.33 0.00 37.66 2.41
2070 4426 1.308998 CCTTGCCTCTGTCGTTGTTT 58.691 50.000 0.00 0.00 0.00 2.83
2331 4707 9.534565 TTAGCTACTGATTCACAATCTATCAAC 57.465 33.333 0.00 0.00 38.72 3.18
2544 8155 0.107654 CTAGGTTTCGGCTTCCTGGG 60.108 60.000 0.00 0.00 33.34 4.45
2811 8608 0.035439 TTGGAGATCGCCCACCTTTC 60.035 55.000 13.44 0.00 32.58 2.62
2817 8614 1.550130 ATCGCCCACCTTTCGGAGAA 61.550 55.000 0.00 0.00 45.90 2.87
2818 8615 1.302192 CGCCCACCTTTCGGAGAAA 60.302 57.895 0.00 0.00 45.90 2.52
2848 8646 4.023707 CCTTGACTTGAACAGTTGGATGTC 60.024 45.833 0.00 0.00 35.01 3.06
2976 8786 0.788995 CACTCTTCTGCTGCAGTTCG 59.211 55.000 27.24 16.82 32.61 3.95
3064 8880 3.605056 CAGTTTGATTAGTGCGCACATTG 59.395 43.478 39.21 20.69 0.00 2.82
3118 8934 4.307443 GCCACTAGCAAAAAGAAACTGT 57.693 40.909 0.00 0.00 42.97 3.55
3119 8935 4.044426 GCCACTAGCAAAAAGAAACTGTG 58.956 43.478 0.00 0.00 42.97 3.66
3120 8936 4.202010 GCCACTAGCAAAAAGAAACTGTGA 60.202 41.667 0.00 0.00 42.97 3.58
3121 8937 5.678616 GCCACTAGCAAAAAGAAACTGTGAA 60.679 40.000 0.00 0.00 42.97 3.18
3122 8938 5.743872 CCACTAGCAAAAAGAAACTGTGAAC 59.256 40.000 0.00 0.00 0.00 3.18
3123 8939 6.321717 CACTAGCAAAAAGAAACTGTGAACA 58.678 36.000 0.00 0.00 0.00 3.18
3124 8940 6.974622 CACTAGCAAAAAGAAACTGTGAACAT 59.025 34.615 0.00 0.00 0.00 2.71
3125 8941 7.489113 CACTAGCAAAAAGAAACTGTGAACATT 59.511 33.333 0.00 0.00 0.00 2.71
3126 8942 8.682710 ACTAGCAAAAAGAAACTGTGAACATTA 58.317 29.630 0.00 0.00 0.00 1.90
3127 8943 7.755582 AGCAAAAAGAAACTGTGAACATTAC 57.244 32.000 0.00 0.00 0.00 1.89
3128 8944 7.547227 AGCAAAAAGAAACTGTGAACATTACT 58.453 30.769 0.00 0.00 0.00 2.24
3129 8945 8.682710 AGCAAAAAGAAACTGTGAACATTACTA 58.317 29.630 0.00 0.00 0.00 1.82
3130 8946 8.958043 GCAAAAAGAAACTGTGAACATTACTAG 58.042 33.333 0.00 0.00 0.00 2.57
3135 8951 8.034058 AGAAACTGTGAACATTACTAGAATGC 57.966 34.615 0.00 0.00 0.00 3.56
3136 8952 6.408858 AACTGTGAACATTACTAGAATGCG 57.591 37.500 0.00 0.00 0.00 4.73
3137 8953 5.720202 ACTGTGAACATTACTAGAATGCGA 58.280 37.500 0.00 0.00 0.00 5.10
3138 8954 6.163476 ACTGTGAACATTACTAGAATGCGAA 58.837 36.000 0.00 0.00 0.00 4.70
3139 8955 6.818644 ACTGTGAACATTACTAGAATGCGAAT 59.181 34.615 0.00 0.00 0.00 3.34
3140 8956 7.010552 ACTGTGAACATTACTAGAATGCGAATC 59.989 37.037 0.00 1.55 0.00 2.52
3141 8957 6.816140 TGTGAACATTACTAGAATGCGAATCA 59.184 34.615 0.00 3.76 0.00 2.57
3142 8958 7.495606 TGTGAACATTACTAGAATGCGAATCAT 59.504 33.333 0.00 0.00 36.87 2.45
3143 8959 8.006590 GTGAACATTACTAGAATGCGAATCATC 58.993 37.037 0.00 0.00 33.40 2.92
3144 8960 7.928167 TGAACATTACTAGAATGCGAATCATCT 59.072 33.333 0.00 0.00 33.40 2.90
3145 8961 7.649370 ACATTACTAGAATGCGAATCATCTG 57.351 36.000 0.00 0.00 33.40 2.90
3146 8962 6.146837 ACATTACTAGAATGCGAATCATCTGC 59.853 38.462 0.00 0.00 33.40 4.26
3147 8963 3.397482 ACTAGAATGCGAATCATCTGCC 58.603 45.455 0.00 0.00 33.40 4.85
3148 8964 2.336945 AGAATGCGAATCATCTGCCA 57.663 45.000 0.00 0.00 33.40 4.92
3149 8965 2.219458 AGAATGCGAATCATCTGCCAG 58.781 47.619 0.00 0.00 33.40 4.85
3150 8966 0.666913 AATGCGAATCATCTGCCAGC 59.333 50.000 0.00 0.00 33.40 4.85
3151 8967 0.179026 ATGCGAATCATCTGCCAGCT 60.179 50.000 0.00 0.00 0.00 4.24
3152 8968 0.812811 TGCGAATCATCTGCCAGCTC 60.813 55.000 0.00 0.00 0.00 4.09
3153 8969 1.829349 GCGAATCATCTGCCAGCTCG 61.829 60.000 0.00 0.00 0.00 5.03
3154 8970 0.249197 CGAATCATCTGCCAGCTCGA 60.249 55.000 0.00 0.00 0.00 4.04
3155 8971 1.604947 CGAATCATCTGCCAGCTCGAT 60.605 52.381 0.00 0.00 0.00 3.59
3156 8972 2.067766 GAATCATCTGCCAGCTCGATC 58.932 52.381 0.00 0.00 0.00 3.69
3157 8973 1.340088 ATCATCTGCCAGCTCGATCT 58.660 50.000 0.00 0.00 0.00 2.75
3158 8974 0.388294 TCATCTGCCAGCTCGATCTG 59.612 55.000 9.32 9.32 0.00 2.90
3159 8975 1.069427 ATCTGCCAGCTCGATCTGC 59.931 57.895 10.79 7.16 32.87 4.26
3160 8976 1.401318 ATCTGCCAGCTCGATCTGCT 61.401 55.000 10.79 0.86 42.06 4.24
3161 8977 1.153409 CTGCCAGCTCGATCTGCTT 60.153 57.895 10.79 0.00 38.92 3.91
3162 8978 1.152989 CTGCCAGCTCGATCTGCTTC 61.153 60.000 10.79 3.15 38.92 3.86
3163 8979 1.143620 GCCAGCTCGATCTGCTTCT 59.856 57.895 10.79 0.00 38.92 2.85
3164 8980 0.387202 GCCAGCTCGATCTGCTTCTA 59.613 55.000 10.79 0.00 38.92 2.10
3165 8981 1.202463 GCCAGCTCGATCTGCTTCTAA 60.202 52.381 10.79 0.00 38.92 2.10
3166 8982 2.739932 GCCAGCTCGATCTGCTTCTAAA 60.740 50.000 10.79 0.00 38.92 1.85
3167 8983 3.525537 CCAGCTCGATCTGCTTCTAAAA 58.474 45.455 10.79 0.00 38.92 1.52
3168 8984 3.935203 CCAGCTCGATCTGCTTCTAAAAA 59.065 43.478 10.79 0.00 38.92 1.94
3213 9029 3.659092 CCGGCAAGCAAGCGACAA 61.659 61.111 0.00 0.00 34.64 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.292292 GGAGCTCCGTCTAATCTGTCTC 59.708 54.545 19.06 0.00 0.00 3.36
25 26 2.303175 GGAGCTCCGTCTAATCTGTCT 58.697 52.381 19.06 0.00 0.00 3.41
72 73 1.074872 GAAACCCTAACCTCGTCGCG 61.075 60.000 0.00 0.00 0.00 5.87
76 77 2.288640 CGACAAGAAACCCTAACCTCGT 60.289 50.000 0.00 0.00 0.00 4.18
93 94 1.133407 GTCGTTGCATACACACGACA 58.867 50.000 27.39 1.39 46.97 4.35
121 122 5.183713 TGAATCGATCTGAAAAACCAAGCAT 59.816 36.000 0.00 0.00 0.00 3.79
124 125 6.072508 TCCTTGAATCGATCTGAAAAACCAAG 60.073 38.462 0.00 0.00 0.00 3.61
136 137 6.609237 TGTCATTGAATCCTTGAATCGATC 57.391 37.500 0.00 0.00 0.00 3.69
157 158 4.003788 CGGGAGCCCAGTCGTTGT 62.004 66.667 6.34 0.00 35.37 3.32
207 208 1.182667 TGTCGATGACAGTCGGGATT 58.817 50.000 0.00 0.00 41.74 3.01
214 215 2.868044 GCTTGACCTTGTCGATGACAGT 60.868 50.000 0.00 0.00 43.69 3.55
245 246 1.444836 CCGCTTTCGTTGTTCCCATA 58.555 50.000 0.00 0.00 0.00 2.74
254 255 4.147322 CGATGCGCCGCTTTCGTT 62.147 61.111 21.13 0.00 33.08 3.85
268 269 2.109799 CCAGAATGAGCCGCCGAT 59.890 61.111 0.00 0.00 39.69 4.18
278 279 3.520862 ATTGCCGCCGCCAGAATG 61.521 61.111 0.00 0.00 0.00 2.67
279 280 3.520862 CATTGCCGCCGCCAGAAT 61.521 61.111 0.00 0.00 0.00 2.40
304 305 1.208165 AGAGGGGTCCATGGACAACC 61.208 60.000 38.83 36.24 46.20 3.77
319 320 0.478507 GAGAGAGGGAGGGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
321 322 1.010793 AGAGAGAGAGGGAGGGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
322 323 1.421646 GAGAGAGAGAGGGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
327 328 2.126882 TCTGAGAGAGAGAGAGGGAGG 58.873 57.143 0.00 0.00 0.00 4.30
595 686 2.111932 AAGACGAAATTGTGCGCGCA 62.112 50.000 33.09 33.09 0.00 6.09
604 695 7.117236 TCGCTTGTCATAAACTAAGACGAAATT 59.883 33.333 0.00 0.00 35.09 1.82
620 711 0.894141 AGAGCTCAGTCGCTTGTCAT 59.106 50.000 17.77 0.00 41.08 3.06
750 2042 3.683365 TGTGCAATCTAGTTCTGCAGA 57.317 42.857 13.74 13.74 46.16 4.26
1213 2522 2.021262 CCCATCTCCCTCTGCATCTA 57.979 55.000 0.00 0.00 0.00 1.98
1231 2540 3.307339 CCTCCTTATAAGATCCAGCAGCC 60.307 52.174 14.28 0.00 0.00 4.85
2021 4374 0.582005 GCGCGTGAAGACTTGTCTTT 59.418 50.000 15.94 2.14 0.00 2.52
2073 4429 8.465999 TGACAGCAGTTTTATTCTTCAGAAAAA 58.534 29.630 0.00 0.00 37.61 1.94
2086 4446 5.165961 AGAGCCTAATGACAGCAGTTTTA 57.834 39.130 0.00 0.00 0.00 1.52
2198 4560 8.836268 AAATGGTACTGTGTAACTAAAATCGA 57.164 30.769 0.00 0.00 38.04 3.59
2331 4707 5.987953 CACACACAGATACATGAAGATAGGG 59.012 44.000 0.00 0.00 0.00 3.53
2811 8608 3.665190 AGTCAAGGTTTAGCTTTCTCCG 58.335 45.455 0.00 0.00 0.00 4.63
2817 8614 5.193679 ACTGTTCAAGTCAAGGTTTAGCTT 58.806 37.500 0.00 0.00 31.64 3.74
2818 8615 4.781934 ACTGTTCAAGTCAAGGTTTAGCT 58.218 39.130 0.00 0.00 31.64 3.32
2848 8646 5.243981 AGTTGGATGACTGATCACAGAAAG 58.756 41.667 0.00 0.00 46.03 2.62
2998 8811 0.884704 TCCAAACGAGCAAGAGTGGC 60.885 55.000 0.00 0.00 0.00 5.01
3004 8820 3.243035 TGTTGACAATCCAAACGAGCAAG 60.243 43.478 0.00 0.00 0.00 4.01
3045 8861 2.594321 GCAATGTGCGCACTAATCAAA 58.406 42.857 37.59 18.89 31.71 2.69
3109 8925 8.507249 GCATTCTAGTAATGTTCACAGTTTCTT 58.493 33.333 13.14 0.00 0.00 2.52
3110 8926 7.148573 CGCATTCTAGTAATGTTCACAGTTTCT 60.149 37.037 13.14 0.00 0.00 2.52
3111 8927 6.955963 CGCATTCTAGTAATGTTCACAGTTTC 59.044 38.462 13.14 0.00 0.00 2.78
3112 8928 6.649141 TCGCATTCTAGTAATGTTCACAGTTT 59.351 34.615 13.14 0.00 0.00 2.66
3113 8929 6.163476 TCGCATTCTAGTAATGTTCACAGTT 58.837 36.000 13.14 0.00 0.00 3.16
3114 8930 5.720202 TCGCATTCTAGTAATGTTCACAGT 58.280 37.500 13.14 0.00 0.00 3.55
3115 8931 6.647212 TTCGCATTCTAGTAATGTTCACAG 57.353 37.500 13.14 0.00 0.00 3.66
3116 8932 6.816140 TGATTCGCATTCTAGTAATGTTCACA 59.184 34.615 13.14 0.00 0.00 3.58
3117 8933 7.234187 TGATTCGCATTCTAGTAATGTTCAC 57.766 36.000 13.14 5.99 0.00 3.18
3118 8934 7.928167 AGATGATTCGCATTCTAGTAATGTTCA 59.072 33.333 13.14 11.59 37.34 3.18
3119 8935 8.219769 CAGATGATTCGCATTCTAGTAATGTTC 58.780 37.037 13.14 8.28 37.34 3.18
3120 8936 7.307632 GCAGATGATTCGCATTCTAGTAATGTT 60.308 37.037 13.14 1.89 37.34 2.71
3121 8937 6.146837 GCAGATGATTCGCATTCTAGTAATGT 59.853 38.462 13.14 0.00 37.34 2.71
3122 8938 6.401903 GGCAGATGATTCGCATTCTAGTAATG 60.402 42.308 9.33 9.33 37.34 1.90
3123 8939 5.641209 GGCAGATGATTCGCATTCTAGTAAT 59.359 40.000 0.00 0.00 37.34 1.89
3124 8940 4.991056 GGCAGATGATTCGCATTCTAGTAA 59.009 41.667 0.00 0.00 37.34 2.24
3125 8941 4.039124 TGGCAGATGATTCGCATTCTAGTA 59.961 41.667 0.00 0.00 37.34 1.82
3126 8942 3.181462 TGGCAGATGATTCGCATTCTAGT 60.181 43.478 0.00 0.00 37.34 2.57
3127 8943 3.396560 TGGCAGATGATTCGCATTCTAG 58.603 45.455 0.00 0.00 37.34 2.43
3128 8944 3.396560 CTGGCAGATGATTCGCATTCTA 58.603 45.455 9.42 0.00 37.34 2.10
3129 8945 2.219458 CTGGCAGATGATTCGCATTCT 58.781 47.619 9.42 0.00 37.34 2.40
3130 8946 1.334779 GCTGGCAGATGATTCGCATTC 60.335 52.381 20.86 0.00 37.34 2.67
3131 8947 0.666913 GCTGGCAGATGATTCGCATT 59.333 50.000 20.86 0.00 37.34 3.56
3132 8948 0.179026 AGCTGGCAGATGATTCGCAT 60.179 50.000 20.86 0.00 40.77 4.73
3133 8949 0.812811 GAGCTGGCAGATGATTCGCA 60.813 55.000 20.86 0.00 0.00 5.10
3134 8950 1.829349 CGAGCTGGCAGATGATTCGC 61.829 60.000 20.86 0.00 0.00 4.70
3135 8951 0.249197 TCGAGCTGGCAGATGATTCG 60.249 55.000 20.86 17.03 0.00 3.34
3136 8952 2.067766 GATCGAGCTGGCAGATGATTC 58.932 52.381 20.86 4.14 0.00 2.52
3137 8953 1.693062 AGATCGAGCTGGCAGATGATT 59.307 47.619 20.86 0.00 0.00 2.57
3138 8954 1.001068 CAGATCGAGCTGGCAGATGAT 59.999 52.381 22.80 16.95 32.26 2.45
3139 8955 0.388294 CAGATCGAGCTGGCAGATGA 59.612 55.000 22.80 12.76 32.26 2.92
3140 8956 1.222766 GCAGATCGAGCTGGCAGATG 61.223 60.000 30.05 6.14 36.41 2.90
3141 8957 1.069427 GCAGATCGAGCTGGCAGAT 59.931 57.895 30.05 13.42 36.41 2.90
3142 8958 1.611474 AAGCAGATCGAGCTGGCAGA 61.611 55.000 30.05 0.00 42.53 4.26
3143 8959 1.152989 GAAGCAGATCGAGCTGGCAG 61.153 60.000 30.05 10.94 42.53 4.85
3144 8960 1.153489 GAAGCAGATCGAGCTGGCA 60.153 57.895 30.05 0.00 42.53 4.92
3145 8961 0.387202 TAGAAGCAGATCGAGCTGGC 59.613 55.000 30.05 21.68 42.53 4.85
3146 8962 2.879002 TTAGAAGCAGATCGAGCTGG 57.121 50.000 30.05 13.43 42.53 4.85
3166 8982 3.443588 GGTGACGCCAGCCTTTTT 58.556 55.556 0.00 0.00 37.17 1.94
3212 9028 3.660865 GACAGTTATGTCGGTTGGAGTT 58.339 45.455 0.00 0.00 46.01 3.01
3213 9029 3.314541 GACAGTTATGTCGGTTGGAGT 57.685 47.619 0.00 0.00 46.01 3.85


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

AutoCloner maintained by Alex Coulton.