Multiple sequence alignment - TraesCS6B01G246900

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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 TraesCS6B01G246900 chr6B 100.000 2258 0 0 1 2258 439176873 439174616 0.000000e+00 4170.0
1 TraesCS6B01G246900 chr6A 92.272 1087 54 14 543 1603 397958982 397960064 0.000000e+00 1515.0
2 TraesCS6B01G246900 chr6A 91.071 448 15 6 35 469 397958248 397958683 1.160000e-162 582.0
3 TraesCS6B01G246900 chr6D 91.241 1096 64 13 543 1608 277252567 277253660 0.000000e+00 1463.0
4 TraesCS6B01G246900 chr6D 90.283 494 16 7 1 477 277252073 277252551 3.190000e-173 617.0
5 TraesCS6B01G246900 chr6D 85.773 485 56 7 1602 2081 83177240 83176764 3.350000e-138 501.0
6 TraesCS6B01G246900 chr6D 94.798 173 8 1 2087 2258 465174704 465174876 3.700000e-68 268.0
7 TraesCS6B01G246900 chr6D 88.525 61 5 2 1435 1494 277253511 277253570 3.110000e-09 73.1
8 TraesCS6B01G246900 chr5D 89.072 485 45 5 1602 2081 445868425 445867944 1.490000e-166 595.0
9 TraesCS6B01G246900 chr7D 88.636 484 46 5 1602 2078 599080052 599080533 4.180000e-162 580.0
10 TraesCS6B01G246900 chr2D 87.602 492 50 8 1595 2078 30431382 30430894 5.450000e-156 560.0
11 TraesCS6B01G246900 chr2D 94.706 170 8 1 2090 2258 30429239 30429070 1.720000e-66 263.0
12 TraesCS6B01G246900 chr4D 87.759 482 52 5 1602 2081 487405367 487404891 7.050000e-155 556.0
13 TraesCS6B01G246900 chr4D 87.631 477 46 6 1600 2070 133736208 133735739 1.970000e-150 542.0
14 TraesCS6B01G246900 chr4D 94.798 173 8 1 2087 2258 352572452 352572624 3.700000e-68 268.0
15 TraesCS6B01G246900 chr4D 93.529 170 10 1 2090 2258 487381445 487381276 3.720000e-63 252.0
16 TraesCS6B01G246900 chr1D 87.243 486 48 8 1603 2081 452531240 452530762 1.970000e-150 542.0
17 TraesCS6B01G246900 chr2B 85.979 485 54 7 1604 2082 160751965 160751489 7.200000e-140 507.0
18 TraesCS6B01G246900 chr3D 85.685 482 62 5 1600 2078 380529801 380530278 3.350000e-138 501.0
19 TraesCS6B01G246900 chrUn 95.294 170 7 1 2090 2258 262691728 262691559 3.700000e-68 268.0
20 TraesCS6B01G246900 chrUn 94.798 173 8 1 2087 2258 268714221 268714393 3.700000e-68 268.0
21 TraesCS6B01G246900 chr5B 93.064 173 8 2 2087 2258 419500675 419500844 1.340000e-62 250.0
22 TraesCS6B01G246900 chr4B 93.529 170 7 2 2090 2258 520189318 520189152 1.340000e-62 250.0
23 TraesCS6B01G246900 chr3B 93.529 170 7 3 2090 2258 625621525 625621359 1.340000e-62 250.0


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 TraesCS6B01G246900 chr6B 439174616 439176873 2257 True 4170.0 4170 100.000000 1 2258 1 chr6B.!!$R1 2257
1 TraesCS6B01G246900 chr6A 397958248 397960064 1816 False 1048.5 1515 91.671500 35 1603 2 chr6A.!!$F1 1568
2 TraesCS6B01G246900 chr6D 277252073 277253660 1587 False 717.7 1463 90.016333 1 1608 3 chr6D.!!$F2 1607
3 TraesCS6B01G246900 chr2D 30429070 30431382 2312 True 411.5 560 91.154000 1595 2258 2 chr2D.!!$R1 663

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
492 789 0.035881 CTCTCACTTGGCTTGCTGGA 59.964 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 4079 0.108615 ATCACGTGAAGCTCGGAAGG 60.109 55.0 24.13 0.0 0.0 3.46 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
133 139 1.290955 CGCGAACTGTCCCTTGGTA 59.709 57.895 0.00 0.00 0.00 3.25
134 140 1.012486 CGCGAACTGTCCCTTGGTAC 61.012 60.000 0.00 0.00 0.00 3.34
135 141 0.320697 GCGAACTGTCCCTTGGTACT 59.679 55.000 0.00 0.00 0.00 2.73
153 159 3.499050 GCAGACTGCAGAGCCATG 58.501 61.111 23.35 11.80 44.26 3.66
224 230 1.282570 CAACCTGCGTGATTTGCGT 59.717 52.632 0.00 0.00 34.24 5.24
251 261 1.999648 AAATGGCCTCACAAAGCTCA 58.000 45.000 3.32 0.00 0.00 4.26
256 266 1.612726 GGCCTCACAAAGCTCAGATGT 60.613 52.381 0.00 0.00 0.00 3.06
257 267 2.157738 GCCTCACAAAGCTCAGATGTT 58.842 47.619 0.00 0.00 0.00 2.71
258 268 2.161211 GCCTCACAAAGCTCAGATGTTC 59.839 50.000 0.00 0.00 0.00 3.18
259 269 2.414481 CCTCACAAAGCTCAGATGTTCG 59.586 50.000 0.00 0.00 0.00 3.95
260 270 1.800586 TCACAAAGCTCAGATGTTCGC 59.199 47.619 0.00 0.00 0.00 4.70
261 271 1.532437 CACAAAGCTCAGATGTTCGCA 59.468 47.619 0.00 0.00 0.00 5.10
262 272 1.802960 ACAAAGCTCAGATGTTCGCAG 59.197 47.619 0.00 0.00 0.00 5.18
263 273 1.129998 CAAAGCTCAGATGTTCGCAGG 59.870 52.381 0.00 0.00 0.00 4.85
264 274 1.023513 AAGCTCAGATGTTCGCAGGC 61.024 55.000 0.00 0.00 0.00 4.85
283 293 4.624117 TCGATCGGCGATGCGGTC 62.624 66.667 29.20 12.47 45.59 4.79
329 339 2.161855 ACAAAATCCAAGCGCATCTCA 58.838 42.857 11.47 0.00 0.00 3.27
368 378 2.048597 CCGTGCCGTAGCTCACAA 60.049 61.111 0.00 0.00 40.80 3.33
448 470 3.264193 TCCCGGTTACTCTACAGTCTACA 59.736 47.826 0.00 0.00 33.62 2.74
484 781 4.544242 GCTTAATTAGCTCTCACTTGGC 57.456 45.455 0.00 0.00 46.77 4.52
485 782 4.195416 GCTTAATTAGCTCTCACTTGGCT 58.805 43.478 0.00 0.00 46.77 4.75
486 783 4.637977 GCTTAATTAGCTCTCACTTGGCTT 59.362 41.667 0.00 0.00 46.77 4.35
487 784 5.448360 GCTTAATTAGCTCTCACTTGGCTTG 60.448 44.000 0.00 0.00 46.77 4.01
488 785 1.813513 TTAGCTCTCACTTGGCTTGC 58.186 50.000 0.00 0.00 37.50 4.01
489 786 0.979665 TAGCTCTCACTTGGCTTGCT 59.020 50.000 0.00 0.00 37.50 3.91
490 787 0.605860 AGCTCTCACTTGGCTTGCTG 60.606 55.000 0.00 0.00 31.81 4.41
491 788 1.584380 GCTCTCACTTGGCTTGCTGG 61.584 60.000 0.00 0.00 0.00 4.85
492 789 0.035881 CTCTCACTTGGCTTGCTGGA 59.964 55.000 0.00 0.00 0.00 3.86
493 790 0.694771 TCTCACTTGGCTTGCTGGAT 59.305 50.000 0.00 0.00 0.00 3.41
494 791 1.093159 CTCACTTGGCTTGCTGGATC 58.907 55.000 0.00 0.00 0.00 3.36
495 792 0.694771 TCACTTGGCTTGCTGGATCT 59.305 50.000 0.00 0.00 0.00 2.75
510 807 3.603532 TGGATCTGTTGATGCTGAACTC 58.396 45.455 0.00 0.00 40.95 3.01
513 810 3.599730 TCTGTTGATGCTGAACTCGAT 57.400 42.857 0.00 0.00 0.00 3.59
514 811 4.718940 TCTGTTGATGCTGAACTCGATA 57.281 40.909 0.00 0.00 0.00 2.92
515 812 4.676546 TCTGTTGATGCTGAACTCGATAG 58.323 43.478 0.00 0.00 0.00 2.08
516 813 6.734324 GATCTGTTGATGCTGAACTCGATAGA 60.734 42.308 0.00 0.00 36.91 1.98
517 814 4.424626 TGTTGATGCTGAACTCGATAGAC 58.575 43.478 0.00 0.00 42.67 2.59
518 815 3.717400 TGATGCTGAACTCGATAGACC 57.283 47.619 0.00 0.00 42.67 3.85
519 816 2.033424 TGATGCTGAACTCGATAGACCG 59.967 50.000 0.00 0.00 42.67 4.79
520 817 0.738975 TGCTGAACTCGATAGACCGG 59.261 55.000 0.00 0.00 42.67 5.28
521 818 1.022735 GCTGAACTCGATAGACCGGA 58.977 55.000 9.46 0.00 42.67 5.14
522 819 1.268640 GCTGAACTCGATAGACCGGAC 60.269 57.143 9.46 0.10 42.67 4.79
523 820 2.290464 CTGAACTCGATAGACCGGACT 58.710 52.381 9.46 10.97 42.67 3.85
524 821 2.683867 CTGAACTCGATAGACCGGACTT 59.316 50.000 12.68 0.00 42.67 3.01
525 822 3.087031 TGAACTCGATAGACCGGACTTT 58.913 45.455 12.68 3.81 42.67 2.66
526 823 3.508793 TGAACTCGATAGACCGGACTTTT 59.491 43.478 12.68 0.00 42.67 2.27
527 824 4.021719 TGAACTCGATAGACCGGACTTTTT 60.022 41.667 12.68 0.00 42.67 1.94
606 903 3.739300 ACAGTTTTCTCGGTAACATGACG 59.261 43.478 0.00 0.00 0.00 4.35
610 907 4.517952 TTTCTCGGTAACATGACGGTAA 57.482 40.909 0.00 0.00 0.00 2.85
681 978 2.516906 TCAAGTCCAAGATGCATGCAA 58.483 42.857 26.68 8.49 0.00 4.08
697 994 2.833794 TGCAAAAGACAAGCGTAGACT 58.166 42.857 0.00 0.00 0.00 3.24
707 1004 3.317149 ACAAGCGTAGACTGTGTACAAGA 59.683 43.478 14.45 0.00 0.00 3.02
737 1035 0.674895 CTGGCCTCCTGGTTTTCTCG 60.675 60.000 3.32 0.00 35.27 4.04
739 1037 1.302511 GCCTCCTGGTTTTCTCGCA 60.303 57.895 0.00 0.00 35.27 5.10
741 1039 0.321671 CCTCCTGGTTTTCTCGCAGA 59.678 55.000 0.00 0.00 0.00 4.26
764 1066 1.980951 TAAAGGCATGCAAGCTCGCG 61.981 55.000 21.36 0.00 33.35 5.87
826 1128 1.076265 TCCGGCCTGCTAGCTAGAA 60.076 57.895 25.15 13.71 0.00 2.10
848 1150 5.888982 AGTTTTCTCTAGTCCAGGAACAA 57.111 39.130 0.00 0.00 0.00 2.83
858 1160 1.422024 TCCAGGAACAATGAAACCCGA 59.578 47.619 0.00 0.00 0.00 5.14
864 1166 4.469945 AGGAACAATGAAACCCGATCTAGA 59.530 41.667 0.00 0.00 0.00 2.43
917 1228 0.246635 TTCCGCTGAGCCTGTAACTC 59.753 55.000 0.00 0.00 34.62 3.01
920 1231 1.608717 CGCTGAGCCTGTAACTCCCT 61.609 60.000 0.00 0.00 32.98 4.20
924 1235 1.116308 GAGCCTGTAACTCCCTCTCC 58.884 60.000 0.00 0.00 0.00 3.71
927 1238 1.897647 GCCTGTAACTCCCTCTCCAGT 60.898 57.143 0.00 0.00 0.00 4.00
930 1241 0.173708 GTAACTCCCTCTCCAGTGCG 59.826 60.000 0.00 0.00 0.00 5.34
969 1286 0.757188 ATGCTGCTAGGCTACGTCCT 60.757 55.000 0.00 0.00 40.21 3.85
986 1303 4.223032 ACGTCCTACTTTCACCATTGATCT 59.777 41.667 0.00 0.00 0.00 2.75
1018 1335 4.138487 CCTATGAGGTCCAGTTGGTTAC 57.862 50.000 0.00 0.00 36.34 2.50
1031 1348 2.125793 GTTACCCACTCCGGCGTC 60.126 66.667 6.01 0.00 0.00 5.19
1078 1395 4.577677 TTTGCGCTGCCCCTGTGA 62.578 61.111 9.73 0.00 0.00 3.58
1142 1459 2.935238 GCCTTCTCAATAGCCACGACAA 60.935 50.000 0.00 0.00 0.00 3.18
1316 1637 2.856720 GCAGAGCAGTAGTAGCATCGAC 60.857 54.545 0.00 0.00 0.00 4.20
1470 1802 6.650120 TCCCTCTTGATCTATGTTTTGGTAC 58.350 40.000 0.00 0.00 0.00 3.34
1494 1826 8.380742 ACTCTTCCCTCTTGATCTATGTTTTA 57.619 34.615 0.00 0.00 0.00 1.52
1518 1850 7.736447 AGTATTTTGGTAGCTTGATCTATGC 57.264 36.000 0.00 0.00 0.00 3.14
1576 1913 1.746470 CCGGGTCAAGGTTGTATTCC 58.254 55.000 0.00 0.00 0.00 3.01
1586 1923 2.027469 AGGTTGTATTCCTTGTCCGGTC 60.027 50.000 0.00 0.00 30.18 4.79
1608 1945 7.043325 CGGTCTTGTATAGTTTGTTAGAGCATC 60.043 40.741 0.00 0.00 0.00 3.91
1620 1957 2.475666 GAGCATCTCCAACAGCCAC 58.524 57.895 0.00 0.00 0.00 5.01
1655 1992 1.345410 CGCCGTAAATTTGCCCTTTG 58.655 50.000 0.00 0.00 0.00 2.77
1660 1997 3.057174 CCGTAAATTTGCCCTTTGTAGCA 60.057 43.478 0.00 0.00 37.18 3.49
1667 2004 2.398554 CCCTTTGTAGCATGCGCGT 61.399 57.895 13.01 0.00 45.49 6.01
1671 2008 2.223249 CCTTTGTAGCATGCGCGTAATT 60.223 45.455 13.01 0.00 45.49 1.40
1672 2009 3.425404 CTTTGTAGCATGCGCGTAATTT 58.575 40.909 13.01 0.00 45.49 1.82
1687 2024 3.370103 CGTAATTTGTAGAGGGGCTCCAA 60.370 47.826 4.79 0.00 34.83 3.53
1688 2025 4.686122 CGTAATTTGTAGAGGGGCTCCAAT 60.686 45.833 4.79 0.00 34.83 3.16
1690 2027 1.965414 TTGTAGAGGGGCTCCAATGA 58.035 50.000 4.79 0.00 34.83 2.57
1699 2036 1.081509 GCTCCAATGAACGCGCAAA 60.082 52.632 5.73 0.00 0.00 3.68
1700 2037 1.067199 GCTCCAATGAACGCGCAAAG 61.067 55.000 5.73 0.00 0.00 2.77
1701 2038 1.067199 CTCCAATGAACGCGCAAAGC 61.067 55.000 5.73 0.00 43.95 3.51
1727 2065 2.334838 CGGTAATATAGAGTTGGGCGC 58.665 52.381 0.00 0.00 0.00 6.53
1749 2087 2.584970 TCCGAATCGCCATCACGC 60.585 61.111 0.00 0.00 0.00 5.34
1766 2104 1.846849 CGCGGTGTGTATTTGGTGCA 61.847 55.000 0.00 0.00 0.00 4.57
1799 2137 2.710971 CGACACACTCAAGCGCTCG 61.711 63.158 12.06 0.00 0.00 5.03
1838 2176 4.077184 CTACCTTCGCCCCGCACA 62.077 66.667 0.00 0.00 0.00 4.57
1872 2210 1.910580 AATTGACCCGATGGACGCCT 61.911 55.000 0.00 0.00 41.07 5.52
1911 2249 1.139095 CCCTTCCTACAGTCGCGAC 59.861 63.158 31.30 31.30 0.00 5.19
1913 2251 1.139095 CTTCCTACAGTCGCGACCC 59.861 63.158 34.08 12.47 0.00 4.46
1914 2252 2.280823 CTTCCTACAGTCGCGACCCC 62.281 65.000 34.08 11.65 0.00 4.95
2037 2381 3.770040 CGGATGACCTCGGTGGCA 61.770 66.667 0.00 0.00 40.22 4.92
2123 4110 2.202919 CGTGATGAGGATGCGGCA 60.203 61.111 4.58 4.58 0.00 5.69
2168 4155 0.733729 AATCGTCTTCGGAGGAGTCG 59.266 55.000 0.00 0.00 41.29 4.18
2208 4195 0.248702 GGATGAAGACGAGGACGAGC 60.249 60.000 0.00 0.00 42.66 5.03
2209 4196 0.736053 GATGAAGACGAGGACGAGCT 59.264 55.000 0.00 0.00 42.66 4.09
2211 4198 0.241213 TGAAGACGAGGACGAGCTTG 59.759 55.000 0.00 0.00 42.66 4.01
2213 4200 1.179814 AAGACGAGGACGAGCTTGGT 61.180 55.000 5.79 0.00 42.66 3.67
2215 4202 0.524862 GACGAGGACGAGCTTGGTTA 59.475 55.000 5.79 0.00 42.66 2.85
2224 4212 3.674997 ACGAGCTTGGTTATTGATGTGT 58.325 40.909 5.79 0.00 0.00 3.72
2250 4238 3.311322 TCGTTTGTGTCATGAACTTGGTC 59.689 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.591594 GGCTGTAGCTTGCGCGATA 60.592 57.895 12.10 0.00 42.32 2.92
8 9 2.892425 GGCTGTAGCTTGCGCGAT 60.892 61.111 12.10 0.00 42.32 4.58
152 158 6.588719 AACTAACCTTGCTTTATTCATGCA 57.411 33.333 0.00 0.00 33.79 3.96
153 159 9.586435 AATTAACTAACCTTGCTTTATTCATGC 57.414 29.630 0.00 0.00 0.00 4.06
251 261 0.176680 ATCGAAGCCTGCGAACATCT 59.823 50.000 0.00 0.00 41.52 2.90
256 266 2.202743 CCGATCGAAGCCTGCGAA 60.203 61.111 18.66 0.00 41.52 4.70
257 267 4.873129 GCCGATCGAAGCCTGCGA 62.873 66.667 18.66 0.00 42.48 5.10
259 269 4.873129 TCGCCGATCGAAGCCTGC 62.873 66.667 18.66 9.27 45.36 4.85
283 293 1.069636 GTTTGCAACTGCTCTCTTCGG 60.070 52.381 0.00 0.00 42.66 4.30
329 339 1.000955 GATCGAAGGTATGCCACGGAT 59.999 52.381 16.09 8.80 37.40 4.18
410 428 3.197116 ACCGGGATTTCAACACCTACTAG 59.803 47.826 6.32 0.00 0.00 2.57
448 470 5.437191 AATTAAGCACCCTAAGCTACTGT 57.563 39.130 0.00 0.00 42.53 3.55
477 774 0.809385 CAGATCCAGCAAGCCAAGTG 59.191 55.000 0.00 0.00 0.00 3.16
478 775 0.403271 ACAGATCCAGCAAGCCAAGT 59.597 50.000 0.00 0.00 0.00 3.16
479 776 1.201647 CAACAGATCCAGCAAGCCAAG 59.798 52.381 0.00 0.00 0.00 3.61
480 777 1.202915 TCAACAGATCCAGCAAGCCAA 60.203 47.619 0.00 0.00 0.00 4.52
481 778 0.401356 TCAACAGATCCAGCAAGCCA 59.599 50.000 0.00 0.00 0.00 4.75
482 779 1.404391 CATCAACAGATCCAGCAAGCC 59.596 52.381 0.00 0.00 0.00 4.35
483 780 1.202268 GCATCAACAGATCCAGCAAGC 60.202 52.381 0.00 0.00 0.00 4.01
484 781 2.097629 CAGCATCAACAGATCCAGCAAG 59.902 50.000 0.00 0.00 0.00 4.01
485 782 2.089201 CAGCATCAACAGATCCAGCAA 58.911 47.619 0.00 0.00 0.00 3.91
486 783 1.279846 TCAGCATCAACAGATCCAGCA 59.720 47.619 0.00 0.00 0.00 4.41
487 784 2.034104 TCAGCATCAACAGATCCAGC 57.966 50.000 0.00 0.00 0.00 4.85
488 785 3.607741 AGTTCAGCATCAACAGATCCAG 58.392 45.455 0.00 0.00 0.00 3.86
489 786 3.603532 GAGTTCAGCATCAACAGATCCA 58.396 45.455 0.00 0.00 0.00 3.41
490 787 2.606725 CGAGTTCAGCATCAACAGATCC 59.393 50.000 0.00 0.00 0.00 3.36
491 788 3.515630 TCGAGTTCAGCATCAACAGATC 58.484 45.455 0.00 0.00 0.00 2.75
492 789 3.599730 TCGAGTTCAGCATCAACAGAT 57.400 42.857 0.00 0.00 0.00 2.90
493 790 3.599730 ATCGAGTTCAGCATCAACAGA 57.400 42.857 0.00 0.00 0.00 3.41
494 791 4.502282 GTCTATCGAGTTCAGCATCAACAG 59.498 45.833 0.00 0.00 0.00 3.16
495 792 4.424626 GTCTATCGAGTTCAGCATCAACA 58.575 43.478 0.00 0.00 0.00 3.33
527 824 4.449743 CGGTCTATCACTGTTTCGGAAAAA 59.550 41.667 4.46 0.00 0.00 1.94
528 825 3.991773 CGGTCTATCACTGTTTCGGAAAA 59.008 43.478 4.46 0.00 0.00 2.29
529 826 3.581755 CGGTCTATCACTGTTTCGGAAA 58.418 45.455 0.00 0.00 0.00 3.13
530 827 2.094390 CCGGTCTATCACTGTTTCGGAA 60.094 50.000 0.00 0.00 38.64 4.30
531 828 1.475280 CCGGTCTATCACTGTTTCGGA 59.525 52.381 0.00 0.00 38.64 4.55
532 829 1.475280 TCCGGTCTATCACTGTTTCGG 59.525 52.381 0.00 0.00 37.82 4.30
533 830 2.163815 AGTCCGGTCTATCACTGTTTCG 59.836 50.000 0.00 0.00 0.00 3.46
534 831 3.870633 AGTCCGGTCTATCACTGTTTC 57.129 47.619 0.00 0.00 0.00 2.78
535 832 3.306780 CCAAGTCCGGTCTATCACTGTTT 60.307 47.826 0.37 0.00 0.00 2.83
536 833 2.233922 CCAAGTCCGGTCTATCACTGTT 59.766 50.000 0.37 0.00 0.00 3.16
537 834 1.825474 CCAAGTCCGGTCTATCACTGT 59.175 52.381 0.37 0.00 0.00 3.55
538 835 1.471676 GCCAAGTCCGGTCTATCACTG 60.472 57.143 0.37 0.00 0.00 3.66
539 836 0.824759 GCCAAGTCCGGTCTATCACT 59.175 55.000 0.37 0.00 0.00 3.41
540 837 0.824759 AGCCAAGTCCGGTCTATCAC 59.175 55.000 0.37 0.00 0.00 3.06
541 838 1.207089 CAAGCCAAGTCCGGTCTATCA 59.793 52.381 0.37 0.00 0.00 2.15
542 839 1.941325 CAAGCCAAGTCCGGTCTATC 58.059 55.000 0.37 0.00 0.00 2.08
543 840 0.107654 GCAAGCCAAGTCCGGTCTAT 60.108 55.000 0.37 0.00 0.00 1.98
544 841 1.192146 AGCAAGCCAAGTCCGGTCTA 61.192 55.000 0.37 0.00 0.00 2.59
606 903 6.597672 TGGTGACATGACATATTCAACTTACC 59.402 38.462 13.01 6.09 37.92 2.85
681 978 3.454371 ACACAGTCTACGCTTGTCTTT 57.546 42.857 0.00 0.00 0.00 2.52
697 994 4.159693 CAGTAGGCCACTATCTTGTACACA 59.840 45.833 5.01 0.00 34.98 3.72
737 1035 3.063045 GCTTGCATGCCTTTAATTTCTGC 59.937 43.478 16.68 0.00 0.00 4.26
739 1037 4.676196 CGAGCTTGCATGCCTTTAATTTCT 60.676 41.667 19.99 0.57 0.00 2.52
741 1039 3.514645 CGAGCTTGCATGCCTTTAATTT 58.485 40.909 19.99 0.00 0.00 1.82
765 1067 2.452813 CGGTTCCTTGCGTGATCCG 61.453 63.158 5.43 5.43 38.35 4.18
771 1073 0.179078 TGTACAACGGTTCCTTGCGT 60.179 50.000 0.00 0.00 0.00 5.24
826 1128 5.888982 TTGTTCCTGGACTAGAGAAAACT 57.111 39.130 0.00 0.00 0.00 2.66
848 1150 2.683768 AGGCTCTAGATCGGGTTTCAT 58.316 47.619 0.00 0.00 0.00 2.57
858 1160 7.516209 TGGTTATATAAACCCAAGGCTCTAGAT 59.484 37.037 8.05 0.00 39.54 1.98
864 1166 4.457466 CGTGGTTATATAAACCCAAGGCT 58.543 43.478 8.05 0.00 39.54 4.58
898 1209 0.246635 GAGTTACAGGCTCAGCGGAA 59.753 55.000 0.00 0.00 33.45 4.30
917 1228 4.504916 CGAGCGCACTGGAGAGGG 62.505 72.222 11.47 0.00 0.00 4.30
920 1231 4.426112 CAGCGAGCGCACTGGAGA 62.426 66.667 17.68 0.00 44.88 3.71
969 1286 6.998074 AGTTGTTGAGATCAATGGTGAAAGTA 59.002 34.615 0.00 0.00 37.30 2.24
1031 1348 1.271934 CTATGATGAGCAGGGAGACGG 59.728 57.143 0.00 0.00 0.00 4.79
1033 1350 1.336702 CGCTATGATGAGCAGGGAGAC 60.337 57.143 0.00 0.00 42.99 3.36
1316 1637 2.891941 TTTATCAGGGCAGGGCAGCG 62.892 60.000 0.00 0.00 34.64 5.18
1470 1802 8.482128 ACTAAAACATAGATCAAGAGGGAAGAG 58.518 37.037 0.00 0.00 0.00 2.85
1494 1826 7.512992 AGCATAGATCAAGCTACCAAAATACT 58.487 34.615 4.96 0.00 36.73 2.12
1518 1850 4.442706 ACTTGTCCATACTATCCGCAAAG 58.557 43.478 0.00 0.00 0.00 2.77
1576 1913 5.235516 ACAAACTATACAAGACCGGACAAG 58.764 41.667 9.46 0.40 0.00 3.16
1580 1917 6.626623 GCTCTAACAAACTATACAAGACCGGA 60.627 42.308 9.46 0.00 0.00 5.14
1583 1920 7.982354 AGATGCTCTAACAAACTATACAAGACC 59.018 37.037 0.00 0.00 0.00 3.85
1586 1923 7.981789 TGGAGATGCTCTAACAAACTATACAAG 59.018 37.037 0.00 0.00 0.00 3.16
1608 1945 1.453155 ATTTAGCGTGGCTGTTGGAG 58.547 50.000 0.00 0.00 40.10 3.86
1631 1968 2.205842 GCAAATTTACGGCGCGACG 61.206 57.895 36.13 36.13 40.31 5.12
1633 1970 2.481464 GGCAAATTTACGGCGCGA 59.519 55.556 12.10 0.00 0.00 5.87
1641 1978 4.502962 GCATGCTACAAAGGGCAAATTTA 58.497 39.130 11.37 0.00 41.90 1.40
1655 1992 2.452006 ACAAATTACGCGCATGCTAC 57.548 45.000 17.13 6.83 39.65 3.58
1660 1997 2.210116 CCCTCTACAAATTACGCGCAT 58.790 47.619 5.73 0.00 0.00 4.73
1672 2009 1.559682 GTTCATTGGAGCCCCTCTACA 59.440 52.381 0.00 0.00 32.60 2.74
1699 2036 1.800315 CTATATTACCGCGCGCGCT 60.800 57.895 45.97 35.49 39.32 5.92
1700 2037 1.730593 CTCTATATTACCGCGCGCGC 61.731 60.000 45.06 42.65 38.24 6.86
1701 2038 0.453950 ACTCTATATTACCGCGCGCG 60.454 55.000 43.73 43.73 39.44 6.86
1709 2046 1.725164 GCGCGCCCAACTCTATATTAC 59.275 52.381 23.24 0.00 0.00 1.89
1710 2047 1.667756 CGCGCGCCCAACTCTATATTA 60.668 52.381 27.72 0.00 0.00 0.98
1711 2048 0.944311 CGCGCGCCCAACTCTATATT 60.944 55.000 27.72 0.00 0.00 1.28
1749 2087 0.239879 GGTGCACCAAATACACACCG 59.760 55.000 31.23 0.00 41.21 4.94
1751 2089 0.239879 CGGGTGCACCAAATACACAC 59.760 55.000 35.78 14.93 40.22 3.82
1778 2116 3.030308 CGCTTGAGTGTGTCGCGT 61.030 61.111 5.77 0.00 39.07 6.01
1783 2121 3.038417 GCGAGCGCTTGAGTGTGT 61.038 61.111 29.00 0.00 38.26 3.72
1822 2160 4.382320 GTGTGCGGGGCGAAGGTA 62.382 66.667 0.00 0.00 0.00 3.08
1852 2190 1.436983 GGCGTCCATCGGGTCAATTC 61.437 60.000 0.00 0.00 40.26 2.17
1888 2226 0.818296 CGACTGTAGGAAGGGGTGAG 59.182 60.000 0.00 0.00 0.00 3.51
1889 2227 1.255667 GCGACTGTAGGAAGGGGTGA 61.256 60.000 0.00 0.00 0.00 4.02
1890 2228 1.218316 GCGACTGTAGGAAGGGGTG 59.782 63.158 0.00 0.00 0.00 4.61
1891 2229 2.348888 CGCGACTGTAGGAAGGGGT 61.349 63.158 0.00 0.00 0.00 4.95
1892 2230 2.050350 TCGCGACTGTAGGAAGGGG 61.050 63.158 3.71 0.00 0.00 4.79
2082 2426 3.966026 CTCGGAAGGTGTCGGACGC 62.966 68.421 13.14 13.14 32.55 5.19
2085 2429 1.874345 GAAGCTCGGAAGGTGTCGGA 61.874 60.000 0.00 0.00 34.63 4.55
2086 2430 1.446272 GAAGCTCGGAAGGTGTCGG 60.446 63.158 0.00 0.00 32.35 4.79
2087 2431 1.009389 GTGAAGCTCGGAAGGTGTCG 61.009 60.000 0.00 0.00 32.35 4.35
2088 2432 1.009389 CGTGAAGCTCGGAAGGTGTC 61.009 60.000 0.00 0.00 32.35 3.67
2092 4079 0.108615 ATCACGTGAAGCTCGGAAGG 60.109 55.000 24.13 0.00 0.00 3.46
2097 4084 0.171231 TCCTCATCACGTGAAGCTCG 59.829 55.000 24.13 9.33 36.14 5.03
2123 4110 1.448540 CTCCTCTTCATTGCCGCGT 60.449 57.895 4.92 0.00 0.00 6.01
2168 4155 3.306641 CCTCATCTTCCTCCGATTCATCC 60.307 52.174 0.00 0.00 0.00 3.51
2208 4195 6.241207 ACGAAAGACACATCAATAACCAAG 57.759 37.500 0.00 0.00 0.00 3.61
2209 4196 6.627395 AACGAAAGACACATCAATAACCAA 57.373 33.333 0.00 0.00 0.00 3.67
2211 4198 6.359617 CACAAACGAAAGACACATCAATAACC 59.640 38.462 0.00 0.00 0.00 2.85
2213 4200 7.022055 ACACAAACGAAAGACACATCAATAA 57.978 32.000 0.00 0.00 0.00 1.40
2215 4202 5.065859 TGACACAAACGAAAGACACATCAAT 59.934 36.000 0.00 0.00 0.00 2.57
2224 4212 5.448496 CCAAGTTCATGACACAAACGAAAGA 60.448 40.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.