Multiple sequence alignment - TraesCS4D01G284800

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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 TraesCS4D01G284800 chr4D 100.000 4835 0 0 1 4835 455750006 455745172 0.000000e+00 8929
1 TraesCS4D01G284800 chr4D 91.638 574 34 6 1 561 204707416 204706844 0.000000e+00 782
2 TraesCS4D01G284800 chr4B 94.939 2806 104 16 2043 4835 569632552 569629772 0.000000e+00 4361
3 TraesCS4D01G284800 chr4B 92.231 605 32 11 1447 2051 569633540 569632951 0.000000e+00 843
4 TraesCS4D01G284800 chr4B 88.626 633 30 12 839 1443 569634226 569633608 0.000000e+00 732
5 TraesCS4D01G284800 chr4B 83.333 252 16 12 561 810 569634510 569634283 4.900000e-50 209
6 TraesCS4D01G284800 chr4A 94.710 2741 110 19 1447 4164 11808897 11811625 0.000000e+00 4226
7 TraesCS4D01G284800 chr4A 95.065 689 25 4 4149 4835 11811644 11812325 0.000000e+00 1075
8 TraesCS4D01G284800 chr4A 90.453 618 32 14 639 1243 11807942 11808545 0.000000e+00 789
9 TraesCS4D01G284800 chr4A 84.861 251 14 8 1211 1443 11808551 11808795 1.050000e-56 231
10 TraesCS4D01G284800 chr1B 91.869 578 34 3 1 565 630541499 630540922 0.000000e+00 795
11 TraesCS4D01G284800 chr7D 93.955 397 13 2 3 388 236524448 236524844 1.500000e-164 590
12 TraesCS4D01G284800 chr7D 95.506 178 8 0 384 561 236577291 236577468 7.920000e-73 285
13 TraesCS4D01G284800 chr6D 94.422 251 12 1 313 561 446615787 446615537 7.590000e-103 385
14 TraesCS4D01G284800 chr6D 94.536 183 10 0 26 208 446616284 446616102 2.850000e-72 283
15 TraesCS4D01G284800 chr6D 90.141 142 13 1 1 142 446616357 446616217 2.970000e-42 183


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 TraesCS4D01G284800 chr4D 455745172 455750006 4834 True 8929.000000 8929 100.00000 1 4835 1 chr4D.!!$R2 4834
1 TraesCS4D01G284800 chr4D 204706844 204707416 572 True 782.000000 782 91.63800 1 561 1 chr4D.!!$R1 560
2 TraesCS4D01G284800 chr4B 569629772 569634510 4738 True 1536.250000 4361 89.78225 561 4835 4 chr4B.!!$R1 4274
3 TraesCS4D01G284800 chr4A 11807942 11812325 4383 False 1580.250000 4226 91.27225 639 4835 4 chr4A.!!$F1 4196
4 TraesCS4D01G284800 chr1B 630540922 630541499 577 True 795.000000 795 91.86900 1 565 1 chr1B.!!$R1 564
5 TraesCS4D01G284800 chr6D 446615537 446616357 820 True 283.666667 385 93.03300 1 561 3 chr6D.!!$R1 560

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
756 1024 0.105964 CTCCTCCTACCAGCCAGCTA 60.106 60.0 0.00 0.0 0.00 3.32 F
819 1090 0.248215 GCAGCAACACACACAGACAC 60.248 55.0 0.00 0.0 0.00 3.67 F
1443 1812 0.543277 TCGCTCTGGAAGGCATGAAT 59.457 50.0 0.00 0.0 31.60 2.57 F
1923 2403 0.109723 ACGGCTGCCAAAGAGGTTTA 59.890 50.0 20.29 0.0 40.61 2.01 F
2561 3449 0.249120 TTCCTGTGGTCCTGCATACG 59.751 55.0 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 2139 1.265095 GCCACCATGTCGCATATCTTG 59.735 52.381 0.00 0.00 0.00 3.02 R
1923 2403 1.620819 AGTGCTCGAATCTGTTGGACT 59.379 47.619 0.00 0.00 0.00 3.85 R
3085 3983 2.092429 TGAATAGTCAGGATTGCACCCC 60.092 50.000 0.91 0.00 0.00 4.95 R
3756 4654 0.179119 CGTGGGGGTTAGCGTAGAAG 60.179 60.000 0.00 0.00 0.00 2.85 R
4105 5006 0.249238 TTGTTCACCGTGGCAATTGC 60.249 50.000 22.47 22.47 41.14 3.56 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 1.305219 GCCATGGCTGTCGCTTGTTA 61.305 55.000 29.98 0.00 38.26 2.41
38 87 2.105528 GTTAGATCGCCGCCGGAA 59.894 61.111 7.68 0.00 34.56 4.30
113 162 4.742201 GCTCCTCTCGCAACGGCA 62.742 66.667 0.00 0.00 41.24 5.69
174 223 0.538516 GCTCCTCCTCTCCTCGCATA 60.539 60.000 0.00 0.00 0.00 3.14
401 664 1.070758 TGAGAAGAAGGTGAGTGGTGC 59.929 52.381 0.00 0.00 0.00 5.01
414 677 2.898343 GGTGCGTGTGGGTCGTTT 60.898 61.111 0.00 0.00 0.00 3.60
456 719 0.599991 AACGATGTTGCTCGCTGACA 60.600 50.000 0.00 2.26 42.35 3.58
568 831 6.349033 CGGGAGTTATTGATTCCGAAAAACTT 60.349 38.462 0.00 0.00 39.83 2.66
594 857 9.581099 TTGAAAATCACAAAGTCTAGAAAAACC 57.419 29.630 0.00 0.00 0.00 3.27
595 858 8.966868 TGAAAATCACAAAGTCTAGAAAAACCT 58.033 29.630 0.00 0.00 0.00 3.50
599 862 5.995897 TCACAAAGTCTAGAAAAACCTAGCC 59.004 40.000 0.00 0.00 36.84 3.93
600 863 5.998363 CACAAAGTCTAGAAAAACCTAGCCT 59.002 40.000 0.00 0.00 36.84 4.58
601 864 7.015877 TCACAAAGTCTAGAAAAACCTAGCCTA 59.984 37.037 0.00 0.00 36.84 3.93
604 867 6.930068 AGTCTAGAAAAACCTAGCCTACAA 57.070 37.500 0.00 0.00 36.84 2.41
614 877 0.755698 TAGCCTACAAGAGCTCCCCG 60.756 60.000 10.93 1.15 40.56 5.73
625 888 1.079057 GCTCCCCGAGTCTTGGAAC 60.079 63.158 7.82 0.00 31.39 3.62
626 889 1.545706 GCTCCCCGAGTCTTGGAACT 61.546 60.000 7.82 0.00 31.39 3.01
641 904 1.641577 GAACTGCCCGTCTCATGTAC 58.358 55.000 0.00 0.00 0.00 2.90
642 905 1.204941 GAACTGCCCGTCTCATGTACT 59.795 52.381 0.00 0.00 0.00 2.73
643 906 1.267121 ACTGCCCGTCTCATGTACTT 58.733 50.000 0.00 0.00 0.00 2.24
656 919 3.056107 TCATGTACTTACTCCACCAGTGC 60.056 47.826 0.00 0.00 36.43 4.40
662 925 1.406860 TACTCCACCAGTGCAGTGCA 61.407 55.000 15.37 15.37 36.43 4.57
715 978 3.809832 CACACTTAGCCAAGGATAATCCG 59.190 47.826 0.00 0.00 42.75 4.18
719 982 2.332063 AGCCAAGGATAATCCGTGTG 57.668 50.000 0.00 0.00 43.22 3.82
756 1024 0.105964 CTCCTCCTACCAGCCAGCTA 60.106 60.000 0.00 0.00 0.00 3.32
757 1025 0.105964 TCCTCCTACCAGCCAGCTAG 60.106 60.000 0.00 0.00 0.00 3.42
768 1038 0.883833 GCCAGCTAGCAACAACACAT 59.116 50.000 18.83 0.00 0.00 3.21
815 1086 2.328989 CCGCAGCAACACACACAG 59.671 61.111 0.00 0.00 0.00 3.66
818 1089 1.704387 CGCAGCAACACACACAGACA 61.704 55.000 0.00 0.00 0.00 3.41
819 1090 0.248215 GCAGCAACACACACAGACAC 60.248 55.000 0.00 0.00 0.00 3.67
820 1091 1.085893 CAGCAACACACACAGACACA 58.914 50.000 0.00 0.00 0.00 3.72
821 1092 1.468127 CAGCAACACACACAGACACAA 59.532 47.619 0.00 0.00 0.00 3.33
822 1093 2.095314 CAGCAACACACACAGACACAAA 60.095 45.455 0.00 0.00 0.00 2.83
824 1095 2.351253 GCAACACACACAGACACAAACA 60.351 45.455 0.00 0.00 0.00 2.83
826 1097 2.499197 ACACACACAGACACAAACACA 58.501 42.857 0.00 0.00 0.00 3.72
828 1099 2.225255 CACACACAGACACAAACACACA 59.775 45.455 0.00 0.00 0.00 3.72
830 1101 2.225255 CACACAGACACAAACACACACA 59.775 45.455 0.00 0.00 0.00 3.72
999 1306 4.827087 CGGCTGTGAGGCTGCGAT 62.827 66.667 0.00 0.00 42.12 4.58
1193 1500 2.203153 AAGTGCGTGCCTTTCCGT 60.203 55.556 0.00 0.00 0.00 4.69
1202 1509 3.610821 GCGTGCCTTTCCGTCTTATTTTT 60.611 43.478 0.00 0.00 0.00 1.94
1203 1510 3.911964 CGTGCCTTTCCGTCTTATTTTTG 59.088 43.478 0.00 0.00 0.00 2.44
1204 1511 4.555906 CGTGCCTTTCCGTCTTATTTTTGT 60.556 41.667 0.00 0.00 0.00 2.83
1248 1594 8.798748 AATTTTATCGATTAGTGTCTACGAGG 57.201 34.615 1.71 0.00 36.49 4.63
1298 1651 9.282247 CAACTTTGAAATGATACATGTAAGAGC 57.718 33.333 10.14 0.91 0.00 4.09
1300 1653 7.549134 ACTTTGAAATGATACATGTAAGAGCGA 59.451 33.333 10.14 0.00 0.00 4.93
1310 1663 3.811722 TGTAAGAGCGAGTGCATTTTG 57.188 42.857 0.00 0.00 46.23 2.44
1333 1686 3.088532 TGATCACCCTTTCCCAAATTCG 58.911 45.455 0.00 0.00 0.00 3.34
1356 1709 4.980339 ACCAATTTTCCTGCCAAAGAAT 57.020 36.364 0.00 0.00 0.00 2.40
1357 1710 6.349777 CGTACCAATTTTCCTGCCAAAGAATA 60.350 38.462 0.00 0.00 0.00 1.75
1358 1711 5.793817 ACCAATTTTCCTGCCAAAGAATAC 58.206 37.500 0.00 0.00 0.00 1.89
1359 1712 5.178061 CCAATTTTCCTGCCAAAGAATACC 58.822 41.667 0.00 0.00 0.00 2.73
1370 1739 6.586344 TGCCAAAGAATACCAATTTGTGAAA 58.414 32.000 0.00 0.00 33.13 2.69
1381 1750 4.383010 CCAATTTGTGAAATTAGAGGGGCC 60.383 45.833 0.00 0.00 38.97 5.80
1443 1812 0.543277 TCGCTCTGGAAGGCATGAAT 59.457 50.000 0.00 0.00 31.60 2.57
1444 1813 1.065199 TCGCTCTGGAAGGCATGAATT 60.065 47.619 0.00 0.00 31.60 2.17
1477 1949 9.942850 TCAAGATGTTACTATTTCAGTCAATCA 57.057 29.630 0.00 0.00 38.80 2.57
1579 2059 5.359860 TCTTAATCAGATGCGTTCAGAGGTA 59.640 40.000 0.00 0.00 0.00 3.08
1580 2060 2.941453 TCAGATGCGTTCAGAGGTAC 57.059 50.000 0.00 0.00 0.00 3.34
1590 2070 3.800506 CGTTCAGAGGTACGTTGTCTTTT 59.199 43.478 0.00 0.00 33.73 2.27
1599 2079 5.689068 AGGTACGTTGTCTTTTCTTACTTCG 59.311 40.000 0.00 0.00 0.00 3.79
1602 2082 3.246699 CGTTGTCTTTTCTTACTTCGGCA 59.753 43.478 0.00 0.00 0.00 5.69
1603 2083 4.524749 GTTGTCTTTTCTTACTTCGGCAC 58.475 43.478 0.00 0.00 0.00 5.01
1630 2110 5.975988 ATCCTAGCTTTCCCATTCTAACA 57.024 39.130 0.00 0.00 0.00 2.41
1636 2116 4.043435 AGCTTTCCCATTCTAACACTTCCT 59.957 41.667 0.00 0.00 0.00 3.36
1638 2118 4.993705 TTCCCATTCTAACACTTCCTGT 57.006 40.909 0.00 0.00 32.89 4.00
1646 2126 6.827586 TTCTAACACTTCCTGTTGTTTTGT 57.172 33.333 0.00 0.00 43.38 2.83
1653 2133 6.260936 ACACTTCCTGTTGTTTTGTATCTCTG 59.739 38.462 0.00 0.00 0.00 3.35
1659 2139 9.431887 TCCTGTTGTTTTGTATCTCTGTTATAC 57.568 33.333 0.00 0.00 0.00 1.47
1686 2166 2.282391 GACATGGTGGCAGTGGCA 60.282 61.111 16.56 16.56 43.71 4.92
1713 2193 2.812011 GCTAAACCTCACGATGGTTGTT 59.188 45.455 10.93 1.96 45.99 2.83
1754 2234 0.907486 TTCTGGGCTGATCAGAGGTG 59.093 55.000 27.04 12.50 41.57 4.00
1786 2266 4.462508 TCTTGAAGAGGTGCTCTATGTG 57.537 45.455 0.00 0.00 40.28 3.21
1923 2403 0.109723 ACGGCTGCCAAAGAGGTTTA 59.890 50.000 20.29 0.00 40.61 2.01
1937 2417 4.822026 AGAGGTTTAGTCCAACAGATTCG 58.178 43.478 0.00 0.00 0.00 3.34
2006 2486 1.846007 ACTTGCACCAGGTTTGTCAA 58.154 45.000 0.00 0.00 0.00 3.18
2085 2972 3.193267 AGTCTCTCACTTGTGCAGATCTC 59.807 47.826 0.00 0.00 26.56 2.75
2383 3270 6.861055 TCAAAAGAATGAGGTACAATTTTCGC 59.139 34.615 0.00 0.00 0.00 4.70
2391 3278 4.890088 AGGTACAATTTTCGCTGTACAGA 58.110 39.130 27.08 5.29 46.39 3.41
2561 3449 0.249120 TTCCTGTGGTCCTGCATACG 59.751 55.000 0.00 0.00 0.00 3.06
3033 3930 5.220397 GCTTTTCCAAAACTTGTAAGTGTGC 60.220 40.000 0.00 0.00 39.66 4.57
3049 3946 2.888834 GTGCCCAACACTTTGTCAAT 57.111 45.000 0.00 0.00 46.41 2.57
3085 3983 7.026562 TGTTCATTTTCGTGGCAATAACTATG 58.973 34.615 0.00 0.00 0.00 2.23
3087 3985 4.974368 TTTTCGTGGCAATAACTATGGG 57.026 40.909 0.00 0.00 0.00 4.00
3089 3987 1.841277 TCGTGGCAATAACTATGGGGT 59.159 47.619 0.00 0.00 0.00 4.95
3090 3988 1.946768 CGTGGCAATAACTATGGGGTG 59.053 52.381 0.00 0.00 0.00 4.61
3091 3989 1.681264 GTGGCAATAACTATGGGGTGC 59.319 52.381 0.00 0.00 0.00 5.01
3092 3990 1.286257 TGGCAATAACTATGGGGTGCA 59.714 47.619 0.00 0.00 33.66 4.57
3093 3991 2.291865 TGGCAATAACTATGGGGTGCAA 60.292 45.455 0.00 0.00 33.66 4.08
3162 4060 2.360165 CTGCTTGCAGTTTCTGACCTTT 59.640 45.455 13.89 0.00 32.44 3.11
3182 4080 3.431673 TCATGCCATGTGTCCAAAGTA 57.568 42.857 4.31 0.00 0.00 2.24
3477 4375 9.700831 AGATATAGTGTGTACATATAGCCATCA 57.299 33.333 0.00 0.00 0.00 3.07
3631 4529 7.487509 GTCGGAAACTAGTTGAACTTATAGACC 59.512 40.741 9.34 0.60 0.00 3.85
3720 4618 2.732658 GTCCAACCGTCCTGTCGT 59.267 61.111 0.00 0.00 0.00 4.34
3744 4642 3.289076 GAAACTCGAAAACAAGCCGAAG 58.711 45.455 0.00 0.00 31.59 3.79
3935 4833 4.505300 CGATGATCGTTTAACCGATGTTG 58.495 43.478 12.97 2.04 46.85 3.33
3936 4834 4.550063 CGATGATCGTTTAACCGATGTTGG 60.550 45.833 12.97 0.00 46.85 3.77
3955 4853 3.334691 TGGCAGTGTTCTGTTGTATAGC 58.665 45.455 0.00 0.00 43.05 2.97
3969 4867 5.475564 TGTTGTATAGCCCAGGTTTTTCTTC 59.524 40.000 0.00 0.00 0.00 2.87
3980 4879 7.255977 GCCCAGGTTTTTCTTCTTCTTTCTATT 60.256 37.037 0.00 0.00 0.00 1.73
4021 4920 3.959535 TTGAAGCTTGCCAAAATAGGG 57.040 42.857 2.10 0.00 0.00 3.53
4047 4946 6.761242 AGGAGGCTTTGTGTAAATTTTTGTTC 59.239 34.615 0.00 0.00 0.00 3.18
4121 5022 1.539157 TATGCAATTGCCACGGTGAA 58.461 45.000 26.94 6.63 41.18 3.18
4125 5026 1.486439 CAATTGCCACGGTGAACAAC 58.514 50.000 10.28 0.00 0.00 3.32
4126 5027 0.387565 AATTGCCACGGTGAACAACC 59.612 50.000 10.28 0.00 46.60 3.77
4147 5048 4.827284 ACCGAGAGACATTTTGGTTTCATT 59.173 37.500 0.00 0.00 0.00 2.57
4182 5117 9.594936 TTATTTTTCCTAAACTCCTCATTTCCA 57.405 29.630 0.00 0.00 0.00 3.53
4184 5119 7.703058 TTTTCCTAAACTCCTCATTTCCATC 57.297 36.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 223 4.736896 GCGTTCCCCTTCGTCGCT 62.737 66.667 0.00 0.00 42.88 4.93
401 664 2.962786 TCGCAAACGACCCACACG 60.963 61.111 0.00 0.00 45.12 4.49
414 677 1.533731 GGGAAAACAGAAATCGTCGCA 59.466 47.619 0.00 0.00 0.00 5.10
456 719 4.101448 GCAGTGGACCCGAGCCAT 62.101 66.667 0.00 0.00 37.81 4.40
511 774 7.614192 ACAGTATTTTAGAATTTGGGTCCGAAT 59.386 33.333 0.00 0.00 0.00 3.34
568 831 9.581099 GGTTTTTCTAGACTTTGTGATTTTCAA 57.419 29.630 0.00 0.00 0.00 2.69
592 855 1.689892 GGGAGCTCTTGTAGGCTAGGT 60.690 57.143 14.64 0.00 39.05 3.08
594 857 1.044611 GGGGAGCTCTTGTAGGCTAG 58.955 60.000 14.64 0.00 39.05 3.42
595 858 0.755698 CGGGGAGCTCTTGTAGGCTA 60.756 60.000 14.64 0.00 39.05 3.93
596 859 2.060980 CGGGGAGCTCTTGTAGGCT 61.061 63.158 14.64 0.00 41.88 4.58
599 862 0.741915 GACTCGGGGAGCTCTTGTAG 59.258 60.000 14.64 9.14 32.04 2.74
600 863 0.331954 AGACTCGGGGAGCTCTTGTA 59.668 55.000 14.64 0.00 32.04 2.41
601 864 0.543174 AAGACTCGGGGAGCTCTTGT 60.543 55.000 14.64 5.58 32.89 3.16
604 867 1.684049 CCAAGACTCGGGGAGCTCT 60.684 63.158 14.64 0.00 32.04 4.09
614 877 0.670854 GACGGGCAGTTCCAAGACTC 60.671 60.000 0.00 0.00 36.21 3.36
625 888 2.427453 AGTAAGTACATGAGACGGGCAG 59.573 50.000 0.00 0.00 0.00 4.85
626 889 2.426024 GAGTAAGTACATGAGACGGGCA 59.574 50.000 0.00 0.00 0.00 5.36
685 948 2.472695 TGGCTAAGTGTGTGATCACC 57.527 50.000 22.85 14.28 43.26 4.02
700 963 1.837439 TCACACGGATTATCCTTGGCT 59.163 47.619 19.65 0.00 39.83 4.75
715 978 4.043200 GGCGGCTTGGCTTCACAC 62.043 66.667 0.00 0.00 40.72 3.82
756 1024 0.822811 TTGTGGCATGTGTTGTTGCT 59.177 45.000 0.00 0.00 38.88 3.91
757 1025 1.649664 TTTGTGGCATGTGTTGTTGC 58.350 45.000 0.00 0.00 38.14 4.17
768 1038 1.520342 GCGTTTGGCTTTTGTGGCA 60.520 52.632 0.00 0.00 40.80 4.92
815 1086 3.262420 AGAGAGTGTGTGTGTTTGTGTC 58.738 45.455 0.00 0.00 0.00 3.67
818 1089 3.055819 ACAGAGAGAGTGTGTGTGTTTGT 60.056 43.478 0.00 0.00 29.56 2.83
819 1090 3.308053 CACAGAGAGAGTGTGTGTGTTTG 59.692 47.826 0.00 0.00 43.87 2.93
820 1091 3.525537 CACAGAGAGAGTGTGTGTGTTT 58.474 45.455 0.00 0.00 43.87 2.83
821 1092 3.170791 CACAGAGAGAGTGTGTGTGTT 57.829 47.619 0.00 0.00 43.87 3.32
822 1093 2.879002 CACAGAGAGAGTGTGTGTGT 57.121 50.000 0.00 0.00 43.87 3.72
830 1101 0.390860 GGCACACACACAGAGAGAGT 59.609 55.000 0.00 0.00 0.00 3.24
861 1164 1.020437 GATCTTGTTGGCCTAGCTGC 58.980 55.000 3.32 0.00 0.00 5.25
951 1258 3.409959 GATCGGCGCCGGCATTTTT 62.410 57.895 44.95 22.32 42.47 1.94
998 1305 4.626081 GCCTGGACCGCGCCATAT 62.626 66.667 5.90 0.00 37.30 1.78
1193 1500 8.685838 AGCCAGTAGTAACAACAAAAATAAGA 57.314 30.769 0.00 0.00 0.00 2.10
1239 1546 9.583765 AACTTTATCACTTATTTCCTCGTAGAC 57.416 33.333 0.00 0.00 0.00 2.59
1272 1625 9.282247 GCTCTTACATGTATCATTTCAAAGTTG 57.718 33.333 6.36 0.00 0.00 3.16
1273 1626 8.177663 CGCTCTTACATGTATCATTTCAAAGTT 58.822 33.333 6.36 0.00 0.00 2.66
1274 1627 7.549134 TCGCTCTTACATGTATCATTTCAAAGT 59.451 33.333 6.36 0.00 0.00 2.66
1275 1628 7.909267 TCGCTCTTACATGTATCATTTCAAAG 58.091 34.615 6.36 0.00 0.00 2.77
1298 1651 2.855180 GTGATCACCAAAATGCACTCG 58.145 47.619 15.31 0.00 0.00 4.18
1333 1686 4.864704 TCTTTGGCAGGAAAATTGGTAC 57.135 40.909 0.00 0.00 0.00 3.34
1356 1709 5.420739 GCCCCTCTAATTTCACAAATTGGTA 59.579 40.000 0.00 0.00 41.01 3.25
1357 1710 4.222810 GCCCCTCTAATTTCACAAATTGGT 59.777 41.667 0.00 0.00 41.01 3.67
1358 1711 4.383010 GGCCCCTCTAATTTCACAAATTGG 60.383 45.833 0.00 2.34 41.01 3.16
1359 1712 4.677779 CGGCCCCTCTAATTTCACAAATTG 60.678 45.833 0.00 0.00 41.01 2.32
1370 1739 2.770048 AGCAGCGGCCCCTCTAAT 60.770 61.111 4.82 0.00 42.56 1.73
1381 1750 0.096628 CAGCTAAGCTTTCAGCAGCG 59.903 55.000 20.52 9.04 45.56 5.18
1477 1949 1.877443 GTCGCAATTACTGTTGGTGGT 59.123 47.619 0.00 0.00 0.00 4.16
1579 2059 3.246936 GCCGAAGTAAGAAAAGACAACGT 59.753 43.478 0.00 0.00 0.00 3.99
1580 2060 3.246699 TGCCGAAGTAAGAAAAGACAACG 59.753 43.478 0.00 0.00 0.00 4.10
1590 2070 3.260884 AGGATTGAAGTGCCGAAGTAAGA 59.739 43.478 0.00 0.00 0.00 2.10
1599 2079 2.685388 GGAAAGCTAGGATTGAAGTGCC 59.315 50.000 0.00 0.00 0.00 5.01
1602 2082 4.870021 ATGGGAAAGCTAGGATTGAAGT 57.130 40.909 0.00 0.00 0.00 3.01
1603 2083 5.444176 AGAATGGGAAAGCTAGGATTGAAG 58.556 41.667 0.00 0.00 0.00 3.02
1630 2110 6.357367 ACAGAGATACAAAACAACAGGAAGT 58.643 36.000 0.00 0.00 0.00 3.01
1646 2126 9.010029 TGTCGCATATCTTGTATAACAGAGATA 57.990 33.333 11.10 11.10 35.18 1.98
1653 2133 6.128553 CCACCATGTCGCATATCTTGTATAAC 60.129 42.308 0.00 0.00 0.00 1.89
1658 2138 2.564771 CCACCATGTCGCATATCTTGT 58.435 47.619 0.00 0.00 0.00 3.16
1659 2139 1.265095 GCCACCATGTCGCATATCTTG 59.735 52.381 0.00 0.00 0.00 3.02
1668 2148 3.434319 GCCACTGCCACCATGTCG 61.434 66.667 0.00 0.00 0.00 4.35
1686 2166 2.228138 TCGTGAGGTTTAGCAAACGT 57.772 45.000 6.65 6.65 42.29 3.99
1713 2193 5.752036 ATGATCTCTTGTCAAGTTCTGGA 57.248 39.130 12.30 5.31 0.00 3.86
1719 2199 4.841422 CCCAGAATGATCTCTTGTCAAGT 58.159 43.478 12.30 0.00 39.69 3.16
1754 2234 5.166398 CACCTCTTCAAGAAAATGGAATGC 58.834 41.667 0.00 0.00 0.00 3.56
1786 2266 6.759827 TCGCTTAAGATATCAACCTGGTTAAC 59.240 38.462 12.53 0.00 0.00 2.01
1844 2324 5.428496 AATGCCTCACATCAAATATGTCG 57.572 39.130 0.00 0.00 38.34 4.35
1923 2403 1.620819 AGTGCTCGAATCTGTTGGACT 59.379 47.619 0.00 0.00 0.00 3.85
1937 2417 3.430218 GTGACATGTCAAGTGTAGTGCTC 59.570 47.826 29.42 9.31 41.85 4.26
2006 2486 3.135530 GCAAGAGTGGATCCCAGATAAGT 59.864 47.826 9.90 0.00 32.34 2.24
2085 2972 7.119699 TGACTTTATATTTGCTGAAGAGTGGTG 59.880 37.037 0.00 0.00 0.00 4.17
2383 3270 6.455647 TGATGTTAGGTGAAAGTCTGTACAG 58.544 40.000 17.17 17.17 0.00 2.74
2417 3304 4.989279 TTCAATATCCAAAAGGCTGCTC 57.011 40.909 0.00 0.00 0.00 4.26
2495 3382 6.978343 TGTCACCATTGCTAGTATTTGTAC 57.022 37.500 0.00 0.00 0.00 2.90
2500 3387 7.739825 ACATCTATGTCACCATTGCTAGTATT 58.260 34.615 0.00 0.00 35.87 1.89
2534 3421 3.403038 CAGGACCACAGGAACAAACTAG 58.597 50.000 0.00 0.00 0.00 2.57
2705 3600 8.978874 ATGGCACTTATACAATTTGACTATGA 57.021 30.769 2.79 0.00 0.00 2.15
2720 3615 6.506538 AGACCAAGATAAGATGGCACTTAT 57.493 37.500 16.81 16.81 43.12 1.73
3049 3946 5.689514 CACGAAAATGAACAAGCCAATGTAA 59.310 36.000 0.00 0.00 32.02 2.41
3085 3983 2.092429 TGAATAGTCAGGATTGCACCCC 60.092 50.000 0.91 0.00 0.00 4.95
3087 3985 5.585390 CAATTGAATAGTCAGGATTGCACC 58.415 41.667 0.00 0.00 34.49 5.01
3091 3989 6.750501 CACTTGCAATTGAATAGTCAGGATTG 59.249 38.462 11.11 11.46 36.02 2.67
3092 3990 6.660521 TCACTTGCAATTGAATAGTCAGGATT 59.339 34.615 16.30 0.00 34.49 3.01
3093 3991 6.182627 TCACTTGCAATTGAATAGTCAGGAT 58.817 36.000 16.30 0.00 34.49 3.24
3162 4060 2.291209 ACTTTGGACACATGGCATGA 57.709 45.000 32.74 8.15 0.00 3.07
3182 4080 3.521727 GTCCATACAGGGGGAGTATCAT 58.478 50.000 0.00 0.00 35.29 2.45
3465 4363 5.704053 TCTTGTTGCAGATGATGGCTATATG 59.296 40.000 0.00 0.00 0.00 1.78
3477 4375 5.967088 ACTAGTACGAATCTTGTTGCAGAT 58.033 37.500 0.00 0.00 34.78 2.90
3606 4504 7.395489 AGGTCTATAAGTTCAACTAGTTTCCGA 59.605 37.037 5.07 0.00 0.00 4.55
3631 4529 6.692681 CAGGAAATTGTCTTGTTGTTGTACAG 59.307 38.462 0.00 0.00 0.00 2.74
3720 4618 1.600485 GGCTTGTTTTCGAGTTTCCGA 59.400 47.619 0.00 0.00 36.70 4.55
3723 4621 3.289076 CTTCGGCTTGTTTTCGAGTTTC 58.711 45.455 0.00 0.00 34.33 2.78
3744 4642 3.224269 AGCGTAGAAGTAATCCTCCTCC 58.776 50.000 0.00 0.00 0.00 4.30
3756 4654 0.179119 CGTGGGGGTTAGCGTAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
3935 4833 2.678336 GGCTATACAACAGAACACTGCC 59.322 50.000 0.00 0.00 35.31 4.85
3936 4834 2.678336 GGGCTATACAACAGAACACTGC 59.322 50.000 0.00 0.00 35.31 4.40
3955 4853 7.767250 ATAGAAAGAAGAAGAAAAACCTGGG 57.233 36.000 0.00 0.00 0.00 4.45
3969 4867 7.993101 TGAATGGATTGCAGAATAGAAAGAAG 58.007 34.615 0.00 0.00 0.00 2.85
3980 4879 9.373603 CTTCAAAATAAATGAATGGATTGCAGA 57.626 29.630 0.00 0.00 36.30 4.26
4021 4920 6.280643 ACAAAAATTTACACAAAGCCTCCTC 58.719 36.000 0.00 0.00 0.00 3.71
4047 4946 1.136474 TGAACAATAGCGCAAACGACG 60.136 47.619 11.47 0.00 43.93 5.12
4088 4989 5.822519 GCAATTGCATATCCCTTCCGATATA 59.177 40.000 25.36 0.00 41.59 0.86
4105 5006 0.249238 TTGTTCACCGTGGCAATTGC 60.249 50.000 22.47 22.47 41.14 3.56
4121 5022 3.208747 ACCAAAATGTCTCTCGGTTGT 57.791 42.857 0.00 0.00 0.00 3.32
4125 5026 5.376854 AATGAAACCAAAATGTCTCTCGG 57.623 39.130 0.00 0.00 0.00 4.63
4126 5027 7.535258 CACTTAATGAAACCAAAATGTCTCTCG 59.465 37.037 0.00 0.00 0.00 4.04
4167 5068 6.779539 GGATAATGGATGGAAATGAGGAGTTT 59.220 38.462 0.00 0.00 0.00 2.66
4182 5117 6.371278 AGAAAGCTTCACATGGATAATGGAT 58.629 36.000 0.00 0.00 40.94 3.41
4184 5119 5.826737 AGAGAAAGCTTCACATGGATAATGG 59.173 40.000 0.00 0.00 40.94 3.16
4320 5257 2.683933 GGAGGACAAGGCTCGGGA 60.684 66.667 0.00 0.00 0.00 5.14
4385 5322 3.340782 GGTAAAGGGGGCCGGGAA 61.341 66.667 2.18 0.00 0.00 3.97
4621 5558 2.245159 TCATCGACATCTTCATGGCC 57.755 50.000 0.00 0.00 33.90 5.36


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

AutoCloner maintained by Alex Coulton.