Multiple sequence alignment - TraesCS5D01G364700

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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 TraesCS5D01G364700 chr5D 100.000 3568 0 0 1 3568 442092885 442096452 0.000000e+00 6589.0
1 TraesCS5D01G364700 chr5D 76.744 172 28 9 594 757 441930511 441930678 6.350000e-13 86.1
2 TraesCS5D01G364700 chr5A 87.909 1191 97 31 1689 2835 558321061 558322248 0.000000e+00 1358.0
3 TraesCS5D01G364700 chr5A 94.556 349 16 2 3222 3568 558323998 558324345 1.460000e-148 536.0
4 TraesCS5D01G364700 chr5A 89.817 383 31 5 2829 3209 558322277 558322653 5.360000e-133 484.0
5 TraesCS5D01G364700 chr5A 85.443 474 31 23 1139 1607 558320590 558321030 3.250000e-125 459.0
6 TraesCS5D01G364700 chr5B 91.568 925 46 14 1916 2835 538293221 538294118 0.000000e+00 1247.0
7 TraesCS5D01G364700 chr5B 96.622 740 21 2 2829 3568 538294147 538294882 0.000000e+00 1225.0
8 TraesCS5D01G364700 chr5B 87.196 1070 66 22 1 1057 538289955 538290966 0.000000e+00 1151.0
9 TraesCS5D01G364700 chr5B 91.358 648 28 15 1085 1719 538292390 538293022 0.000000e+00 861.0
10 TraesCS5D01G364700 chr5B 96.000 50 2 0 594 643 537967721 537967770 8.210000e-12 82.4
11 TraesCS5D01G364700 chr6D 82.993 294 23 16 2305 2580 123781100 123780816 1.280000e-59 241.0
12 TraesCS5D01G364700 chr6D 79.530 298 29 17 3288 3568 123779895 123779613 2.190000e-42 183.0
13 TraesCS5D01G364700 chr6A 82.770 296 20 18 2305 2580 157633228 157633512 5.960000e-58 235.0
14 TraesCS5D01G364700 chr6A 80.201 298 27 17 3288 3568 157634424 157634706 1.010000e-45 195.0
15 TraesCS5D01G364700 chr6B 82.313 294 25 16 2305 2580 218674523 218674239 2.770000e-56 230.0
16 TraesCS5D01G364700 chr6B 81.145 297 24 17 3289 3568 218672115 218671834 3.610000e-50 209.0


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 TraesCS5D01G364700 chr5D 442092885 442096452 3567 False 6589.00 6589 100.00000 1 3568 1 chr5D.!!$F2 3567
1 TraesCS5D01G364700 chr5A 558320590 558324345 3755 False 709.25 1358 89.43125 1139 3568 4 chr5A.!!$F1 2429
2 TraesCS5D01G364700 chr5B 538289955 538294882 4927 False 1121.00 1247 91.68600 1 3568 4 chr5B.!!$F2 3567
3 TraesCS5D01G364700 chr6D 123779613 123781100 1487 True 212.00 241 81.26150 2305 3568 2 chr6D.!!$R1 1263
4 TraesCS5D01G364700 chr6A 157633228 157634706 1478 False 215.00 235 81.48550 2305 3568 2 chr6A.!!$F1 1263
5 TraesCS5D01G364700 chr6B 218671834 218674523 2689 True 219.50 230 81.72900 2305 3568 2 chr6B.!!$R1 1263

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
913 924 0.095417 GCTAAGAACCGAGCTTTGCG 59.905 55.0 0.0 0.0 35.22 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2840 4405 0.107508 ATGCTCAGTGGATCCCGTTG 60.108 55.0 9.9 5.1 0.0 4.1 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
31 32 7.283127 ACTGAAAACGCTTGTGGAATATATGAT 59.717 33.333 0.00 0.00 0.00 2.45
73 74 5.982890 ATTGAAATGAAACTAGTGTGGGG 57.017 39.130 0.00 0.00 0.00 4.96
93 94 7.399765 TGTGGGGTATCTTGAAATGATTGAAAT 59.600 33.333 0.00 0.00 32.45 2.17
228 229 9.624697 TGAAATTTGTGCTTGAATTACATAGAC 57.375 29.630 0.00 0.00 0.00 2.59
322 323 5.794687 TGTGTATTGAAATTACTGAGGCG 57.205 39.130 0.00 0.00 0.00 5.52
341 342 9.173939 CTGAGGCGTATCATTCAAAAATATTTC 57.826 33.333 0.10 0.00 0.00 2.17
409 411 7.545362 AACTGAGAAATGTGCTGACATATAC 57.455 36.000 0.00 0.00 42.30 1.47
413 415 9.433153 CTGAGAAATGTGCTGACATATACATAT 57.567 33.333 0.00 0.00 42.30 1.78
441 443 8.495148 GTTCATAACATTCCAAATTGGTGAAAC 58.505 33.333 12.28 4.61 39.03 2.78
442 444 6.865726 TCATAACATTCCAAATTGGTGAAACG 59.134 34.615 12.28 0.00 39.03 3.60
443 445 3.988819 ACATTCCAAATTGGTGAAACGG 58.011 40.909 12.28 0.00 39.03 4.44
444 446 3.639094 ACATTCCAAATTGGTGAAACGGA 59.361 39.130 12.28 0.00 39.03 4.69
445 447 4.236935 CATTCCAAATTGGTGAAACGGAG 58.763 43.478 12.28 0.00 39.03 4.63
447 449 3.761897 TCCAAATTGGTGAAACGGAGAT 58.238 40.909 12.28 0.00 39.03 2.75
448 450 4.912586 TCCAAATTGGTGAAACGGAGATA 58.087 39.130 12.28 0.00 39.03 1.98
450 452 5.949354 TCCAAATTGGTGAAACGGAGATAAT 59.051 36.000 12.28 0.00 39.03 1.28
451 453 6.435904 TCCAAATTGGTGAAACGGAGATAATT 59.564 34.615 12.28 0.00 39.03 1.40
452 454 6.531240 CCAAATTGGTGAAACGGAGATAATTG 59.469 38.462 3.34 0.00 38.12 2.32
455 457 6.885952 TTGGTGAAACGGAGATAATTGAAA 57.114 33.333 0.00 0.00 38.12 2.69
456 458 7.461182 TTGGTGAAACGGAGATAATTGAAAT 57.539 32.000 0.00 0.00 38.12 2.17
457 459 7.083875 TGGTGAAACGGAGATAATTGAAATC 57.916 36.000 0.00 0.00 38.12 2.17
458 460 6.657117 TGGTGAAACGGAGATAATTGAAATCA 59.343 34.615 0.00 0.00 38.12 2.57
459 461 7.175816 TGGTGAAACGGAGATAATTGAAATCAA 59.824 33.333 0.00 0.00 38.12 2.57
460 462 8.026607 GGTGAAACGGAGATAATTGAAATCAAA 58.973 33.333 0.00 0.00 37.22 2.69
461 463 9.573133 GTGAAACGGAGATAATTGAAATCAAAT 57.427 29.630 0.00 0.00 39.55 2.32
467 469 9.903682 CGGAGATAATTGAAATCAAATATTGCT 57.096 29.630 0.00 0.00 39.55 3.91
612 623 3.193479 GGGTGTGAAACTGATTTGGGATC 59.807 47.826 0.00 0.00 38.04 3.36
615 626 5.006386 GTGTGAAACTGATTTGGGATCTCT 58.994 41.667 0.00 0.00 38.04 3.10
698 709 8.862325 TCATTTATTTGTGTGAAGTATCTGGT 57.138 30.769 0.00 0.00 0.00 4.00
699 710 9.295825 TCATTTATTTGTGTGAAGTATCTGGTT 57.704 29.630 0.00 0.00 0.00 3.67
700 711 9.912634 CATTTATTTGTGTGAAGTATCTGGTTT 57.087 29.630 0.00 0.00 0.00 3.27
701 712 9.912634 ATTTATTTGTGTGAAGTATCTGGTTTG 57.087 29.630 0.00 0.00 0.00 2.93
702 713 8.684386 TTATTTGTGTGAAGTATCTGGTTTGA 57.316 30.769 0.00 0.00 0.00 2.69
703 714 7.581213 ATTTGTGTGAAGTATCTGGTTTGAA 57.419 32.000 0.00 0.00 0.00 2.69
704 715 7.397892 TTTGTGTGAAGTATCTGGTTTGAAA 57.602 32.000 0.00 0.00 0.00 2.69
705 716 6.371809 TGTGTGAAGTATCTGGTTTGAAAC 57.628 37.500 0.00 0.00 0.00 2.78
706 717 5.883115 TGTGTGAAGTATCTGGTTTGAAACA 59.117 36.000 10.53 0.00 0.00 2.83
831 842 4.024670 AGGTAGAGTACTTAAGTGCCCTG 58.975 47.826 18.56 0.00 0.00 4.45
844 855 3.042481 GCCCTGGCATATTTCCTCC 57.958 57.895 2.58 0.00 41.49 4.30
866 877 2.103373 GCTAGGACACTGACAGATGGA 58.897 52.381 10.08 0.00 0.00 3.41
902 913 3.813073 GCACGTACGTATGCTAAGAAC 57.187 47.619 22.34 0.00 38.84 3.01
911 922 3.000322 CGTATGCTAAGAACCGAGCTTTG 60.000 47.826 0.00 0.00 39.54 2.77
912 923 1.156736 TGCTAAGAACCGAGCTTTGC 58.843 50.000 0.00 0.00 42.00 3.68
913 924 0.095417 GCTAAGAACCGAGCTTTGCG 59.905 55.000 0.00 0.00 35.22 4.85
921 932 1.638467 CGAGCTTTGCGGCTACATC 59.362 57.895 0.00 0.00 43.20 3.06
924 935 0.807667 AGCTTTGCGGCTACATCGAG 60.808 55.000 0.00 0.00 41.16 4.04
933 944 3.713288 CGGCTACATCGAGGAACAATTA 58.287 45.455 3.06 0.00 0.00 1.40
953 964 1.373590 CGGATGTTTTACGGCCTGGG 61.374 60.000 0.00 0.00 0.00 4.45
1000 1011 5.308825 ACATTCAGAGGGGCGATTAATTAG 58.691 41.667 0.00 0.00 0.00 1.73
1013 1024 6.370166 GGCGATTAATTAGGAGGAGAAGATTG 59.630 42.308 0.00 0.00 0.00 2.67
1037 1048 6.705381 TGTTTAGGCAAATTGATTGAAACAGG 59.295 34.615 0.00 0.00 41.85 4.00
1049 1060 0.868406 GAAACAGGACAGCTCAACCG 59.132 55.000 0.00 0.00 0.00 4.44
1057 1068 1.445582 CAGCTCAACCGGTCCGTAC 60.446 63.158 8.04 0.00 0.00 3.67
1066 2452 1.239296 CCGGTCCGTACAGTCTGTGA 61.239 60.000 16.03 1.49 0.00 3.58
1072 2458 1.215647 GTACAGTCTGTGAGCCGGG 59.784 63.158 16.03 0.00 0.00 5.73
1116 2523 2.442272 CCGATCCCCGTGTCCTCT 60.442 66.667 0.00 0.00 36.31 3.69
1262 2677 3.041940 CTCCGCCGCGTTCTGTTT 61.042 61.111 12.58 0.00 0.00 2.83
1272 2687 2.062519 GCGTTCTGTTTGTCTCTCTCC 58.937 52.381 0.00 0.00 0.00 3.71
1278 2693 1.964223 TGTTTGTCTCTCTCCTCGCTT 59.036 47.619 0.00 0.00 0.00 4.68
1286 2706 0.106719 CTCTCCTCGCTTCTCCTCCT 60.107 60.000 0.00 0.00 0.00 3.69
1489 2913 1.005630 CGATCGATTCCCCTGAGCC 60.006 63.158 10.26 0.00 0.00 4.70
1608 3032 1.003233 GGAGGAACTGGCTGGTGTC 60.003 63.158 0.00 0.00 41.55 3.67
1625 3051 4.196971 GGTGTCTGGATGTATGTAAACCC 58.803 47.826 0.00 0.00 0.00 4.11
1627 3053 5.129815 GGTGTCTGGATGTATGTAAACCCTA 59.870 44.000 0.00 0.00 0.00 3.53
1628 3054 6.047231 GTGTCTGGATGTATGTAAACCCTAC 58.953 44.000 0.00 0.00 0.00 3.18
1630 3056 6.127168 TGTCTGGATGTATGTAAACCCTACAG 60.127 42.308 0.00 0.00 0.00 2.74
1631 3057 5.962031 TCTGGATGTATGTAAACCCTACAGT 59.038 40.000 0.00 0.00 0.00 3.55
1633 3059 5.722441 TGGATGTATGTAAACCCTACAGTGA 59.278 40.000 0.00 0.00 0.00 3.41
1641 3070 8.650143 ATGTAAACCCTACAGTGATCAATTTT 57.350 30.769 0.00 0.00 0.00 1.82
1662 3091 1.811965 CGTTTCTCCCATGTTGCATCA 59.188 47.619 0.00 0.00 0.00 3.07
1676 3105 4.060205 GTTGCATCAGAATGGCTTTGTTT 58.940 39.130 0.00 0.00 36.16 2.83
1726 3155 4.142271 GGAGTTGTGATCATCTCGACTCTT 60.142 45.833 26.05 2.99 44.65 2.85
1727 3156 4.992688 AGTTGTGATCATCTCGACTCTTC 58.007 43.478 0.00 0.00 31.03 2.87
1728 3157 4.704540 AGTTGTGATCATCTCGACTCTTCT 59.295 41.667 0.00 0.00 31.03 2.85
1738 3170 4.799678 TCTCGACTCTTCTTAAACAGCTG 58.200 43.478 13.48 13.48 0.00 4.24
1740 3172 2.996621 CGACTCTTCTTAAACAGCTGGG 59.003 50.000 19.93 2.76 0.00 4.45
1741 3173 2.744741 GACTCTTCTTAAACAGCTGGGC 59.255 50.000 19.93 0.00 0.00 5.36
1779 3238 1.873591 GTTCCTGTGAAATGCGTCAGT 59.126 47.619 0.00 0.00 30.79 3.41
1785 3244 2.135139 GTGAAATGCGTCAGTGACTCA 58.865 47.619 17.70 17.70 31.81 3.41
1786 3245 2.543848 GTGAAATGCGTCAGTGACTCAA 59.456 45.455 19.13 6.01 31.04 3.02
1787 3246 2.543848 TGAAATGCGTCAGTGACTCAAC 59.456 45.455 19.13 13.59 31.04 3.18
1788 3247 2.238942 AATGCGTCAGTGACTCAACA 57.761 45.000 19.13 12.59 31.04 3.33
1789 3248 2.238942 ATGCGTCAGTGACTCAACAA 57.761 45.000 19.13 0.00 31.04 2.83
1790 3249 2.238942 TGCGTCAGTGACTCAACAAT 57.761 45.000 20.64 0.00 0.00 2.71
1794 3255 2.476619 CGTCAGTGACTCAACAATGTCC 59.523 50.000 20.64 0.00 37.20 4.02
1803 3264 6.260050 GTGACTCAACAATGTCCTCAACTAAA 59.740 38.462 0.00 0.00 32.67 1.85
1805 3266 7.027778 ACTCAACAATGTCCTCAACTAAAAC 57.972 36.000 0.00 0.00 0.00 2.43
1816 3277 8.598916 TGTCCTCAACTAAAACTATATTGTCCA 58.401 33.333 0.00 0.00 0.00 4.02
1817 3278 9.444600 GTCCTCAACTAAAACTATATTGTCCAA 57.555 33.333 0.00 0.00 0.00 3.53
1826 3287 5.947228 ACTATATTGTCCAATTCATGCCG 57.053 39.130 0.00 0.00 32.50 5.69
1827 3288 3.648339 ATATTGTCCAATTCATGCCGC 57.352 42.857 0.00 0.00 32.50 6.53
1841 3302 2.031919 CCGCAGCCACTGTTACCA 59.968 61.111 0.00 0.00 33.43 3.25
1856 3317 1.671979 TACCAGTATGCTCGTAGCGT 58.328 50.000 6.77 6.77 46.26 5.07
1872 3333 5.177881 TCGTAGCGTCATTAACAACAAACAT 59.822 36.000 0.00 0.00 0.00 2.71
1873 3334 5.280446 CGTAGCGTCATTAACAACAAACATG 59.720 40.000 0.00 0.00 0.00 3.21
1876 3337 4.088496 GCGTCATTAACAACAAACATGAGC 59.912 41.667 0.00 0.00 0.00 4.26
1882 3343 2.808244 ACAACAAACATGAGCAAACCG 58.192 42.857 0.00 0.00 0.00 4.44
1914 3375 3.653344 GCTATAGCGTCCATGTGAATGA 58.347 45.455 9.40 0.00 0.00 2.57
1930 3412 5.009811 TGTGAATGATGCAAGTTCAATGACA 59.990 36.000 11.74 3.37 34.04 3.58
1941 3423 5.443185 AGTTCAATGACAGTTTGACATGG 57.557 39.130 0.00 0.00 33.39 3.66
1944 3426 4.650734 TCAATGACAGTTTGACATGGCTA 58.349 39.130 0.00 0.00 33.39 3.93
1958 3440 4.962155 ACATGGCTAACCTAAGATGTAGC 58.038 43.478 0.00 0.00 36.63 3.58
1963 3445 4.202472 GGCTAACCTAAGATGTAGCCCATT 60.202 45.833 9.02 0.00 42.99 3.16
2003 3490 0.657840 GCTGCGTACCTAAATGGCTG 59.342 55.000 0.00 0.00 40.22 4.85
2053 3540 4.039245 TGGAGTCTGGAGAGTAAACTGTTG 59.961 45.833 0.00 0.00 0.00 3.33
2062 3549 5.334414 GGAGAGTAAACTGTTGCACATTCTG 60.334 44.000 0.00 0.00 0.00 3.02
2084 3573 4.083855 TGCATCACAGACGAGAAAAATCAC 60.084 41.667 0.00 0.00 0.00 3.06
2086 3575 4.066646 TCACAGACGAGAAAAATCACCA 57.933 40.909 0.00 0.00 0.00 4.17
2137 3626 9.725019 AATGACAAGTATCAGATGAGTTTGTTA 57.275 29.630 9.37 7.07 30.97 2.41
2170 3659 6.222038 ACTCGTGGAGCTAAAGATAATTCA 57.778 37.500 0.00 0.00 32.04 2.57
2272 3762 2.999355 CAGCTGAGTTTGTTCTAGAGCC 59.001 50.000 8.42 0.00 0.00 4.70
2297 3787 4.398358 CACTCACGGACCTAAAGATAGTCA 59.602 45.833 0.00 0.00 0.00 3.41
2415 3914 1.959226 GGAAACGCCGTGCTCTTCA 60.959 57.895 0.00 0.00 0.00 3.02
2429 3928 2.094417 GCTCTTCATACCTGTTTGCGAC 59.906 50.000 0.00 0.00 0.00 5.19
2435 3934 3.932710 TCATACCTGTTTGCGACAAGATC 59.067 43.478 0.00 0.00 37.93 2.75
2489 3995 2.427506 GCAACCAAACAGACCCTAGAG 58.572 52.381 0.00 0.00 0.00 2.43
2582 4093 0.244721 TCCAGACACTGCACTCATCG 59.755 55.000 0.00 0.00 0.00 3.84
2803 4325 6.380995 TGTTTTGCATTAAGCTACTCATGTG 58.619 36.000 0.00 0.00 45.94 3.21
2820 4342 8.891671 ACTCATGTGATTAAAACAGCAAAAAT 57.108 26.923 0.94 0.00 0.00 1.82
2840 4405 7.477144 AAAATAACAGTTTTACTTTGCTGCC 57.523 32.000 0.00 0.00 32.65 4.85
2876 4441 7.601073 CTGAGCATAGTCAGTTCATACAAAA 57.399 36.000 0.00 0.00 39.39 2.44
2948 4513 1.000394 CTTGCCAAAACCTTTACCCGG 60.000 52.381 0.00 0.00 0.00 5.73
2957 4522 0.534873 CCTTTACCCGGGCATTTTGG 59.465 55.000 24.08 12.02 0.00 3.28
3050 4660 4.934602 CCAGCAAAACCAAGACAAAAGAAA 59.065 37.500 0.00 0.00 0.00 2.52
3070 4680 5.827797 AGAAACATTCTCAACAGCCTTAACA 59.172 36.000 0.00 0.00 34.07 2.41
3073 4683 6.259550 ACATTCTCAACAGCCTTAACAATC 57.740 37.500 0.00 0.00 0.00 2.67
3279 7595 9.530129 CTTCGAAGAAAACATACATAAACTGAC 57.470 33.333 20.74 0.00 45.90 3.51
3443 7759 5.220931 GCTATCCAGAATACAAGTTTGCAGG 60.221 44.000 0.00 0.00 0.00 4.85
3454 7770 4.705023 ACAAGTTTGCAGGTGTTAGAGTTT 59.295 37.500 0.00 0.00 0.00 2.66
3518 7850 3.366679 CGAGTTCTTTCACTAAGCCCGTA 60.367 47.826 0.00 0.00 33.66 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.482743 GCAATAACATCATATATTCCACAAGCG 59.517 37.037 0.00 0.00 0.00 4.68
201 202 9.844790 TCTATGTAATTCAAGCACAAATTTCAG 57.155 29.630 0.00 0.00 29.53 3.02
208 209 9.394767 ACATATGTCTATGTAATTCAAGCACAA 57.605 29.630 1.41 0.00 44.85 3.33
306 307 6.821160 TGAATGATACGCCTCAGTAATTTCAA 59.179 34.615 0.00 0.00 0.00 2.69
341 342 9.409312 TCACAACTTGCATATTTCACTTATTTG 57.591 29.630 0.00 0.00 0.00 2.32
413 415 8.642935 TCACCAATTTGGAATGTTATGAACTA 57.357 30.769 22.19 0.00 40.96 2.24
414 416 7.537596 TCACCAATTTGGAATGTTATGAACT 57.462 32.000 22.19 0.00 40.96 3.01
415 417 8.495148 GTTTCACCAATTTGGAATGTTATGAAC 58.505 33.333 22.19 9.74 40.96 3.18
416 418 7.383572 CGTTTCACCAATTTGGAATGTTATGAA 59.616 33.333 22.19 15.05 40.96 2.57
417 419 6.865726 CGTTTCACCAATTTGGAATGTTATGA 59.134 34.615 22.19 10.08 40.96 2.15
418 420 6.090628 CCGTTTCACCAATTTGGAATGTTATG 59.909 38.462 22.19 7.90 40.96 1.90
420 422 5.302059 TCCGTTTCACCAATTTGGAATGTTA 59.698 36.000 22.19 1.87 40.96 2.41
441 443 9.903682 AGCAATATTTGATTTCAATTATCTCCG 57.096 29.630 7.71 0.00 33.69 4.63
570 581 7.493320 CACACCCTGATTTCCATAAATGAAATG 59.507 37.037 3.19 0.00 35.41 2.32
612 623 5.954296 AGTGGTGTCAATCATTTCAAGAG 57.046 39.130 0.00 0.00 0.00 2.85
646 657 8.763049 TTCAGTTACTCACACAAATAGATGAG 57.237 34.615 0.00 0.00 43.47 2.90
647 658 9.725019 ATTTCAGTTACTCACACAAATAGATGA 57.275 29.630 0.00 0.00 0.00 2.92
648 659 9.979270 GATTTCAGTTACTCACACAAATAGATG 57.021 33.333 0.00 0.00 0.00 2.90
649 660 9.725019 TGATTTCAGTTACTCACACAAATAGAT 57.275 29.630 0.00 0.00 0.00 1.98
650 661 9.725019 ATGATTTCAGTTACTCACACAAATAGA 57.275 29.630 0.00 0.00 0.00 1.98
684 695 7.581213 AATGTTTCAAACCAGATACTTCACA 57.419 32.000 0.00 0.00 0.00 3.58
693 704 9.528018 GAGTTATTTCAAATGTTTCAAACCAGA 57.472 29.630 0.00 0.00 0.00 3.86
814 825 2.025589 GCCAGGGCACTTAAGTACTC 57.974 55.000 8.04 2.06 41.49 2.59
831 842 2.639839 TCCTAGCAGGAGGAAATATGCC 59.360 50.000 0.00 0.00 42.90 4.40
844 855 2.159128 CCATCTGTCAGTGTCCTAGCAG 60.159 54.545 0.00 0.00 0.00 4.24
885 896 3.286576 CTCGGTTCTTAGCATACGTACG 58.713 50.000 15.01 15.01 0.00 3.67
886 897 3.041492 GCTCGGTTCTTAGCATACGTAC 58.959 50.000 0.00 0.00 38.63 3.67
887 898 2.947652 AGCTCGGTTCTTAGCATACGTA 59.052 45.455 0.00 0.00 41.32 3.57
888 899 1.749634 AGCTCGGTTCTTAGCATACGT 59.250 47.619 0.00 0.00 41.32 3.57
911 922 0.459585 TTGTTCCTCGATGTAGCCGC 60.460 55.000 0.00 0.00 0.00 6.53
912 923 2.225068 ATTGTTCCTCGATGTAGCCG 57.775 50.000 0.00 0.00 0.00 5.52
913 924 3.489785 CGTAATTGTTCCTCGATGTAGCC 59.510 47.826 0.00 0.00 0.00 3.93
921 932 4.939509 AAACATCCGTAATTGTTCCTCG 57.060 40.909 0.00 0.00 35.09 4.63
924 935 5.326292 CCGTAAAACATCCGTAATTGTTCC 58.674 41.667 0.00 0.00 35.09 3.62
933 944 0.675522 CCAGGCCGTAAAACATCCGT 60.676 55.000 0.00 0.00 0.00 4.69
971 982 1.743772 CGCCCCTCTGAATGTAACTGG 60.744 57.143 0.00 0.00 0.00 4.00
1000 1011 4.222124 TGCCTAAACAATCTTCTCCTCC 57.778 45.455 0.00 0.00 0.00 4.30
1013 1024 6.928492 TCCTGTTTCAATCAATTTGCCTAAAC 59.072 34.615 0.00 0.00 35.16 2.01
1019 1030 4.151157 GCTGTCCTGTTTCAATCAATTTGC 59.849 41.667 0.00 0.00 35.16 3.68
1037 1048 1.870055 TACGGACCGGTTGAGCTGTC 61.870 60.000 20.00 0.00 0.00 3.51
1049 1060 0.109226 GCTCACAGACTGTACGGACC 60.109 60.000 8.02 0.00 0.00 4.46
1057 1068 4.767255 GCCCCGGCTCACAGACTG 62.767 72.222 0.00 0.00 38.26 3.51
1072 2458 3.127352 CTGGGAGTAGACGCGAGCC 62.127 68.421 15.93 4.03 0.00 4.70
1078 2464 3.066481 GGTTAGTTAGCTGGGAGTAGACG 59.934 52.174 0.00 0.00 0.00 4.18
1116 2523 3.430497 CGGAGGAGGGAGGGAGGA 61.430 72.222 0.00 0.00 0.00 3.71
1246 2661 3.342627 CAAACAGAACGCGGCGGA 61.343 61.111 27.37 0.00 0.00 5.54
1262 2677 1.680555 GGAGAAGCGAGGAGAGAGACA 60.681 57.143 0.00 0.00 0.00 3.41
1272 2687 2.584673 TCCAAGGAGGAGAAGCGAG 58.415 57.895 0.00 0.00 43.07 5.03
1278 2693 7.941238 GATTCATTAATCAATCCAAGGAGGAGA 59.059 37.037 0.79 0.00 44.43 3.71
1286 2706 6.896860 ACACCCAGATTCATTAATCAATCCAA 59.103 34.615 8.30 0.00 43.44 3.53
1415 2839 0.532573 TGGAGTCGATGAAGTCCTGC 59.467 55.000 0.00 0.00 39.20 4.85
1505 2929 1.143305 CAGAACAGAGACCACAAGCG 58.857 55.000 0.00 0.00 0.00 4.68
1513 2937 0.249489 ACGCACCACAGAACAGAGAC 60.249 55.000 0.00 0.00 0.00 3.36
1608 3032 6.049149 CACTGTAGGGTTTACATACATCCAG 58.951 44.000 0.00 0.00 0.00 3.86
1625 3051 7.237173 GGAGAAACGAAAATTGATCACTGTAG 58.763 38.462 0.00 0.00 0.00 2.74
1627 3053 5.048713 GGGAGAAACGAAAATTGATCACTGT 60.049 40.000 0.00 0.00 0.00 3.55
1628 3054 5.048782 TGGGAGAAACGAAAATTGATCACTG 60.049 40.000 0.00 0.00 0.00 3.66
1630 3056 5.371115 TGGGAGAAACGAAAATTGATCAC 57.629 39.130 0.00 0.00 0.00 3.06
1631 3057 5.476599 ACATGGGAGAAACGAAAATTGATCA 59.523 36.000 0.00 0.00 0.00 2.92
1633 3059 5.982890 ACATGGGAGAAACGAAAATTGAT 57.017 34.783 0.00 0.00 0.00 2.57
1641 3070 2.083774 GATGCAACATGGGAGAAACGA 58.916 47.619 0.00 0.00 0.00 3.85
1676 3105 2.979814 ATAATACACGAGCACTGGCA 57.020 45.000 0.00 0.00 44.61 4.92
1726 3155 6.889722 AGTTTATTATGCCCAGCTGTTTAAGA 59.110 34.615 13.81 0.00 0.00 2.10
1727 3156 6.974622 CAGTTTATTATGCCCAGCTGTTTAAG 59.025 38.462 13.81 0.00 0.00 1.85
1728 3157 6.627065 GCAGTTTATTATGCCCAGCTGTTTAA 60.627 38.462 13.81 5.29 36.41 1.52
1738 3170 1.946768 TGCGAGCAGTTTATTATGCCC 59.053 47.619 0.00 0.00 43.60 5.36
1774 3233 3.733337 AGGACATTGTTGAGTCACTGAC 58.267 45.455 0.38 0.38 36.50 3.51
1779 3238 4.422073 AGTTGAGGACATTGTTGAGTCA 57.578 40.909 0.00 0.00 36.50 3.41
1789 3248 9.614792 GGACAATATAGTTTTAGTTGAGGACAT 57.385 33.333 0.00 0.00 0.00 3.06
1790 3249 8.598916 TGGACAATATAGTTTTAGTTGAGGACA 58.401 33.333 0.00 0.00 0.00 4.02
1803 3264 5.278463 GCGGCATGAATTGGACAATATAGTT 60.278 40.000 0.00 0.00 0.00 2.24
1805 3266 4.216042 TGCGGCATGAATTGGACAATATAG 59.784 41.667 0.00 0.00 0.00 1.31
1809 3270 1.135527 CTGCGGCATGAATTGGACAAT 59.864 47.619 1.75 0.00 0.00 2.71
1816 3277 1.679977 AGTGGCTGCGGCATGAATT 60.680 52.632 21.31 0.00 40.92 2.17
1817 3278 2.044650 AGTGGCTGCGGCATGAAT 60.045 55.556 21.31 0.00 40.92 2.57
1841 3302 4.201980 TGTTAATGACGCTACGAGCATACT 60.202 41.667 7.47 0.00 42.58 2.12
1856 3317 6.478344 GGTTTGCTCATGTTTGTTGTTAATGA 59.522 34.615 0.00 0.00 0.00 2.57
1882 3343 1.215655 CGCTATAGCTGTCCGTTGCC 61.216 60.000 21.98 0.00 39.32 4.52
1890 3351 2.031870 TCACATGGACGCTATAGCTGT 58.968 47.619 21.98 19.77 39.32 4.40
1897 3358 2.212652 GCATCATTCACATGGACGCTA 58.787 47.619 0.00 0.00 0.00 4.26
1903 3364 4.443913 TGAACTTGCATCATTCACATGG 57.556 40.909 0.00 0.00 0.00 3.66
1904 3365 6.034577 GTCATTGAACTTGCATCATTCACATG 59.965 38.462 7.17 12.10 32.21 3.21
1914 3375 5.163530 TGTCAAACTGTCATTGAACTTGCAT 60.164 36.000 0.00 0.00 38.44 3.96
1930 3412 5.499004 TCTTAGGTTAGCCATGTCAAACT 57.501 39.130 0.00 0.00 37.19 2.66
1941 3423 4.625607 ATGGGCTACATCTTAGGTTAGC 57.374 45.455 0.00 0.00 33.53 3.09
1944 3426 6.576778 AACTAATGGGCTACATCTTAGGTT 57.423 37.500 0.00 0.00 39.40 3.50
1958 3440 5.123979 GGTTCTTGAAGCTGTAACTAATGGG 59.876 44.000 5.43 0.00 0.00 4.00
1963 3445 4.040461 AGCTGGTTCTTGAAGCTGTAACTA 59.960 41.667 16.52 0.00 45.36 2.24
2003 3490 4.402056 TGTATCCGGGAATCAAGTCTTC 57.598 45.455 0.00 0.00 0.00 2.87
2062 3549 4.398247 GTGATTTTTCTCGTCTGTGATGC 58.602 43.478 0.00 0.00 0.00 3.91
2084 3573 5.069119 TGGTAGATACTAGCAGTTCATGTGG 59.931 44.000 6.58 0.00 0.00 4.17
2086 3575 6.551227 TGATGGTAGATACTAGCAGTTCATGT 59.449 38.462 14.26 0.00 29.74 3.21
2137 3626 1.338200 GCTCCACGAGTCCAACTTGAT 60.338 52.381 1.37 0.00 33.76 2.57
2170 3659 9.498176 GGGGATATTTATATTGTTGTCGTTACT 57.502 33.333 0.00 0.00 0.00 2.24
2272 3762 0.242825 TCTTTAGGTCCGTGAGTGCG 59.757 55.000 0.00 0.00 0.00 5.34
2297 3787 0.898320 ACAGTTAGATGCAGGCGACT 59.102 50.000 0.00 0.00 46.44 4.18
2415 3914 2.930040 CGATCTTGTCGCAAACAGGTAT 59.070 45.455 0.00 0.00 44.33 2.73
2429 3928 3.448686 ACGCCTAAGAACATCGATCTTG 58.551 45.455 9.51 0.00 37.67 3.02
2435 3934 5.458015 TGTATCATACGCCTAAGAACATCG 58.542 41.667 0.00 0.00 0.00 3.84
2489 3995 6.428159 TCTCCAAAGCAGAGTAAGTTTGATTC 59.572 38.462 0.00 0.00 32.65 2.52
2688 4202 0.988145 TGACCATAGGGAAGGGCCAG 60.988 60.000 6.18 0.00 38.95 4.85
2820 4342 5.344884 GTTGGCAGCAAAGTAAAACTGTTA 58.655 37.500 0.00 0.00 32.65 2.41
2840 4405 0.107508 ATGCTCAGTGGATCCCGTTG 60.108 55.000 9.90 5.10 0.00 4.10
2876 4441 6.929606 GGTAAGATCCAGTATATTTGCTCGTT 59.070 38.462 0.00 0.00 0.00 3.85
2957 4522 1.700042 AATGATCGCAGGAGTCCCCC 61.700 60.000 5.25 0.00 34.66 5.40
3050 4660 5.106555 CGATTGTTAAGGCTGTTGAGAATGT 60.107 40.000 0.00 0.00 0.00 2.71
3070 4680 8.244113 GGTTGTTCATAAAAAGGAGAATCGATT 58.756 33.333 11.20 11.20 34.37 3.34
3073 4683 6.908825 TGGTTGTTCATAAAAAGGAGAATCG 58.091 36.000 0.00 0.00 34.37 3.34
3279 7595 0.950836 TCACCGTTTCCAAGCATGTG 59.049 50.000 0.00 0.00 0.00 3.21
3518 7850 3.993658 TCTCTCTACATACCCCCATGT 57.006 47.619 0.00 0.00 41.88 3.21
3527 7859 6.715347 TGCATTGCTACTTCTCTCTACATA 57.285 37.500 10.49 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.