Multiple sequence alignment - TraesCS6A01G145700

Loading Multiple Alignment...

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 TraesCS6A01G145700 chr6A 100.000 4933 0 0 1 4933 124264607 124269539 0.000000e+00 9110.0
1 TraesCS6A01G145700 chr6A 86.103 698 50 31 22 700 124234938 124235607 0.000000e+00 708.0
2 TraesCS6A01G145700 chr6B 92.392 4929 227 71 73 4930 188665227 188670078 0.000000e+00 6889.0
3 TraesCS6A01G145700 chr6D 94.967 4073 134 34 911 4933 103000999 103005050 0.000000e+00 6320.0
4 TraesCS6A01G145700 chr6D 83.636 110 8 6 336 442 102994552 102994654 1.460000e-15 95.3
5 TraesCS6A01G145700 chr7D 85.321 109 14 2 3095 3202 606645666 606645559 1.450000e-20 111.0
6 TraesCS6A01G145700 chr7B 83.486 109 16 2 3095 3202 690869331 690869224 3.140000e-17 100.0
7 TraesCS6A01G145700 chr4D 100.000 32 0 0 4902 4933 212646545 212646514 5.330000e-05 60.2
8 TraesCS6A01G145700 chr1A 100.000 32 0 0 4902 4933 129868307 129868338 5.330000e-05 60.2
9 TraesCS6A01G145700 chr2A 100.000 31 0 0 4902 4932 110190186 110190156 1.920000e-04 58.4


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 TraesCS6A01G145700 chr6A 124264607 124269539 4932 False 9110 9110 100.000 1 4933 1 chr6A.!!$F2 4932
1 TraesCS6A01G145700 chr6A 124234938 124235607 669 False 708 708 86.103 22 700 1 chr6A.!!$F1 678
2 TraesCS6A01G145700 chr6B 188665227 188670078 4851 False 6889 6889 92.392 73 4930 1 chr6B.!!$F1 4857
3 TraesCS6A01G145700 chr6D 103000999 103005050 4051 False 6320 6320 94.967 911 4933 1 chr6D.!!$F2 4022

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
133 134 0.033504 TCCCAGACGAACTGTTCAGC 59.966 55.0 19.56 10.69 44.40 4.26 F
693 754 0.170561 AGCGGTAACAGCGACTAGTG 59.829 55.0 0.00 0.00 42.41 2.74 F
1327 1395 0.102300 ACAGCGTTGTTTTTCTGGGC 59.898 50.0 0.00 0.00 32.28 5.36 F
1349 1417 0.609957 TTGATTCTGGCCCTGTGCTG 60.610 55.0 0.00 0.00 40.92 4.41 F
1845 1920 0.893727 CCCAAGTGCCTAACCACCAC 60.894 60.0 0.00 0.00 36.38 4.16 F
2305 2383 1.609208 GGGTGCATGTATAAGGCCAG 58.391 55.0 5.01 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1376 0.102300 GCCCAGAAAAACAACGCTGT 59.898 50.000 0.00 0.0 37.39 4.40 R
1658 1733 0.253327 GTCGCCTCCCCTCAGATTTT 59.747 55.000 0.00 0.0 0.00 1.82 R
2659 2742 2.093973 ACCTATCCAACTTCACAGCTCG 60.094 50.000 0.00 0.0 0.00 5.03 R
3324 3409 3.826466 TGCATATACATCGCTCTTCTCG 58.174 45.455 0.00 0.0 0.00 4.04 R
3800 3900 0.960861 GTGGCCTGTAGCTTGGTTCC 60.961 60.000 3.32 0.0 43.05 3.62 R
3958 4060 1.176527 CCCACTGAATCGCCACATTT 58.823 50.000 0.00 0.0 0.00 2.32 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 0.319813 TGTGACATGCCTGACACTCG 60.320 55.000 20.69 0.00 44.81 4.18
58 59 6.935771 TCTAAAACCTTGTGATTTAAGGCGTA 59.064 34.615 3.80 0.00 46.89 4.42
60 61 4.281898 ACCTTGTGATTTAAGGCGTAGT 57.718 40.909 3.80 0.00 46.89 2.73
61 62 5.410355 ACCTTGTGATTTAAGGCGTAGTA 57.590 39.130 3.80 0.00 46.89 1.82
62 63 5.416947 ACCTTGTGATTTAAGGCGTAGTAG 58.583 41.667 3.80 0.00 46.89 2.57
63 64 5.046807 ACCTTGTGATTTAAGGCGTAGTAGT 60.047 40.000 3.80 0.00 46.89 2.73
64 65 6.153340 ACCTTGTGATTTAAGGCGTAGTAGTA 59.847 38.462 3.80 0.00 46.89 1.82
65 66 6.696148 CCTTGTGATTTAAGGCGTAGTAGTAG 59.304 42.308 0.00 0.00 38.38 2.57
66 67 5.585390 TGTGATTTAAGGCGTAGTAGTAGC 58.415 41.667 0.00 0.00 0.00 3.58
118 119 2.430382 GAAACGTCTGCCTCGTCCCA 62.430 60.000 0.00 0.00 40.69 4.37
133 134 0.033504 TCCCAGACGAACTGTTCAGC 59.966 55.000 19.56 10.69 44.40 4.26
149 150 0.798776 CAGCGCCGAATCAATATCCC 59.201 55.000 2.29 0.00 0.00 3.85
179 180 2.617788 CCCCATTTGACTTCATGTCCGA 60.618 50.000 0.00 0.00 44.75 4.55
189 190 3.325870 CTTCATGTCCGAAGTGCTAACA 58.674 45.455 0.00 0.00 38.07 2.41
216 217 4.269312 CGTTTCTGCAGATCAATCAATCG 58.731 43.478 19.04 7.75 0.00 3.34
293 295 2.874780 CGAGCACTGTACCGACGC 60.875 66.667 0.00 0.00 0.00 5.19
390 392 2.138595 GTGTACCACCAGTCCACCA 58.861 57.895 0.00 0.00 0.00 4.17
557 591 3.490759 CAGTCGTGCACCGCATCC 61.491 66.667 12.15 0.00 41.91 3.51
558 592 4.760047 AGTCGTGCACCGCATCCC 62.760 66.667 12.15 0.00 41.91 3.85
559 593 4.760047 GTCGTGCACCGCATCCCT 62.760 66.667 12.15 0.00 41.91 4.20
560 594 4.451150 TCGTGCACCGCATCCCTC 62.451 66.667 12.15 0.00 41.91 4.30
561 595 4.457496 CGTGCACCGCATCCCTCT 62.457 66.667 12.15 0.00 41.91 3.69
562 596 2.512515 GTGCACCGCATCCCTCTC 60.513 66.667 5.22 0.00 41.91 3.20
563 597 3.785859 TGCACCGCATCCCTCTCC 61.786 66.667 0.00 0.00 31.71 3.71
564 598 4.554036 GCACCGCATCCCTCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
565 599 2.765807 CACCGCATCCCTCTCCCT 60.766 66.667 0.00 0.00 0.00 4.20
566 600 2.444895 ACCGCATCCCTCTCCCTC 60.445 66.667 0.00 0.00 0.00 4.30
567 601 2.123077 CCGCATCCCTCTCCCTCT 60.123 66.667 0.00 0.00 0.00 3.69
568 602 2.206536 CCGCATCCCTCTCCCTCTC 61.207 68.421 0.00 0.00 0.00 3.20
693 754 0.170561 AGCGGTAACAGCGACTAGTG 59.829 55.000 0.00 0.00 42.41 2.74
852 913 1.204941 GTATCTTGTCAGACCGGCACT 59.795 52.381 0.00 0.00 0.00 4.40
895 956 0.543749 CATTGTCTCCTCCCCAGGAC 59.456 60.000 0.00 0.00 44.75 3.85
896 957 0.621862 ATTGTCTCCTCCCCAGGACC 60.622 60.000 0.00 0.00 44.75 4.46
897 958 2.043527 TTGTCTCCTCCCCAGGACCA 62.044 60.000 0.00 0.00 44.75 4.02
898 959 1.687493 GTCTCCTCCCCAGGACCAG 60.687 68.421 0.00 0.00 44.75 4.00
899 960 3.086600 CTCCTCCCCAGGACCAGC 61.087 72.222 0.00 0.00 44.75 4.85
923 984 1.494721 AGCCCAGGAGTAGAGAGAGAG 59.505 57.143 0.00 0.00 0.00 3.20
924 985 1.493022 GCCCAGGAGTAGAGAGAGAGA 59.507 57.143 0.00 0.00 0.00 3.10
925 986 2.092103 GCCCAGGAGTAGAGAGAGAGAA 60.092 54.545 0.00 0.00 0.00 2.87
926 987 3.820557 CCCAGGAGTAGAGAGAGAGAAG 58.179 54.545 0.00 0.00 0.00 2.85
927 988 3.214328 CCAGGAGTAGAGAGAGAGAAGC 58.786 54.545 0.00 0.00 0.00 3.86
928 989 3.117888 CCAGGAGTAGAGAGAGAGAAGCT 60.118 52.174 0.00 0.00 0.00 3.74
942 1009 1.005805 AGAAGCTGAGAGAGGCTGAGA 59.994 52.381 0.00 0.00 38.91 3.27
1271 1338 2.747460 TGCAGCTGGATCAACGCC 60.747 61.111 17.12 0.00 0.00 5.68
1276 1344 1.135575 CAGCTGGATCAACGCCTTTTC 60.136 52.381 5.57 0.00 0.00 2.29
1281 1349 4.229876 CTGGATCAACGCCTTTTCTTTTC 58.770 43.478 0.00 0.00 0.00 2.29
1308 1376 3.243035 CCGTGTTCATTGTCTTCTTGCAA 60.243 43.478 0.00 0.00 0.00 4.08
1310 1378 4.671377 GTGTTCATTGTCTTCTTGCAACA 58.329 39.130 0.00 0.00 0.00 3.33
1311 1379 4.736793 GTGTTCATTGTCTTCTTGCAACAG 59.263 41.667 0.00 0.00 0.00 3.16
1312 1380 3.631145 TCATTGTCTTCTTGCAACAGC 57.369 42.857 0.00 0.00 0.00 4.40
1315 1383 1.378531 TGTCTTCTTGCAACAGCGTT 58.621 45.000 0.00 0.00 0.00 4.84
1316 1384 1.063912 TGTCTTCTTGCAACAGCGTTG 59.936 47.619 14.44 14.44 0.00 4.10
1322 1390 2.920490 TCTTGCAACAGCGTTGTTTTTC 59.080 40.909 15.47 8.16 45.01 2.29
1323 1391 2.645730 TGCAACAGCGTTGTTTTTCT 57.354 40.000 15.47 0.00 45.01 2.52
1327 1395 0.102300 ACAGCGTTGTTTTTCTGGGC 59.898 50.000 0.00 0.00 32.28 5.36
1330 1398 1.744320 GCGTTGTTTTTCTGGGCCCT 61.744 55.000 25.70 0.00 0.00 5.19
1338 1406 2.220653 TTTCTGGGCCCTTGATTCTG 57.779 50.000 25.70 2.96 0.00 3.02
1349 1417 0.609957 TTGATTCTGGCCCTGTGCTG 60.610 55.000 0.00 0.00 40.92 4.41
1350 1418 2.362120 ATTCTGGCCCTGTGCTGC 60.362 61.111 0.00 0.00 40.92 5.25
1428 1496 0.973632 TCTTGCCTGCTTCGTCCTTA 59.026 50.000 0.00 0.00 0.00 2.69
1436 1504 4.253685 CCTGCTTCGTCCTTATTTCAGAA 58.746 43.478 0.00 0.00 0.00 3.02
1596 1671 2.660362 CGAGCGCACAGTTCTTTCTTTC 60.660 50.000 11.47 0.00 0.00 2.62
1603 1678 4.222114 CACAGTTCTTTCTTTCGGAATGC 58.778 43.478 0.00 0.00 33.53 3.56
1605 1680 4.023707 ACAGTTCTTTCTTTCGGAATGCTG 60.024 41.667 0.00 0.00 33.53 4.41
1614 1689 3.866883 TTCGGAATGCTGGGAAAAATC 57.133 42.857 0.00 0.00 0.00 2.17
1620 1695 4.706962 GGAATGCTGGGAAAAATCACTACT 59.293 41.667 0.00 0.00 0.00 2.57
1621 1696 5.885912 GGAATGCTGGGAAAAATCACTACTA 59.114 40.000 0.00 0.00 0.00 1.82
1624 1699 6.614694 TGCTGGGAAAAATCACTACTACTA 57.385 37.500 0.00 0.00 0.00 1.82
1625 1700 6.403878 TGCTGGGAAAAATCACTACTACTAC 58.596 40.000 0.00 0.00 0.00 2.73
1626 1701 5.816258 GCTGGGAAAAATCACTACTACTACC 59.184 44.000 0.00 0.00 0.00 3.18
1627 1702 6.575649 GCTGGGAAAAATCACTACTACTACCA 60.576 42.308 0.00 0.00 0.00 3.25
1628 1703 6.942976 TGGGAAAAATCACTACTACTACCAG 58.057 40.000 0.00 0.00 0.00 4.00
1629 1704 6.499350 TGGGAAAAATCACTACTACTACCAGT 59.501 38.462 0.00 0.00 0.00 4.00
1630 1705 7.675195 TGGGAAAAATCACTACTACTACCAGTA 59.325 37.037 0.00 0.00 0.00 2.74
1658 1733 7.697352 CATTTTGTGCTCATAAAACTTGTCA 57.303 32.000 6.67 0.00 34.94 3.58
1672 1747 4.026356 ACTTGTCAAAATCTGAGGGGAG 57.974 45.455 0.00 0.00 33.60 4.30
1699 1774 2.411904 CAAGGATCCTGCTAAGATCGC 58.588 52.381 17.02 0.00 40.93 4.58
1735 1810 8.406172 TCAATTAAAGTGTTGCTGTTTCTTTC 57.594 30.769 0.00 0.00 32.01 2.62
1739 1814 3.214328 AGTGTTGCTGTTTCTTTCGGAT 58.786 40.909 0.00 0.00 0.00 4.18
1808 1883 3.915437 TCGAAAAGGTTGATCTTTGCC 57.085 42.857 0.00 0.00 37.09 4.52
1845 1920 0.893727 CCCAAGTGCCTAACCACCAC 60.894 60.000 0.00 0.00 36.38 4.16
1979 2054 2.861006 GTCCTCGCCGTGCTTTTC 59.139 61.111 0.00 0.00 0.00 2.29
2065 2140 4.161377 AGGTCTTGATACTCTTCTTGCTCC 59.839 45.833 0.00 0.00 0.00 4.70
2093 2168 5.841957 AATTGGTTCTGATGTATCCAAGC 57.158 39.130 0.00 0.00 40.67 4.01
2291 2369 2.818274 GTCGGTGGATTCGGGTGC 60.818 66.667 0.00 0.00 0.00 5.01
2292 2370 3.315140 TCGGTGGATTCGGGTGCA 61.315 61.111 0.00 0.00 0.00 4.57
2305 2383 1.609208 GGGTGCATGTATAAGGCCAG 58.391 55.000 5.01 0.00 0.00 4.85
2351 2429 3.959991 GAAGAGGCTGGGGTGCGAC 62.960 68.421 0.00 0.00 0.00 5.19
2375 2453 5.751028 CGGACAGGAGTATGAGAAAGAATTC 59.249 44.000 0.00 0.00 35.70 2.17
2631 2714 8.047310 ACACTCCCATTAAATTATCTCGAGTTT 58.953 33.333 13.13 8.09 0.00 2.66
2642 2725 8.833231 AATTATCTCGAGTTTCTTGTCTGAAA 57.167 30.769 13.13 0.00 34.05 2.69
2929 3012 2.030007 CGAACACTGCAATCCACCAATT 60.030 45.455 0.00 0.00 0.00 2.32
2999 3082 6.588719 TTAATGCAAAGGTATGACTGCTTT 57.411 33.333 0.00 0.00 36.49 3.51
3262 3345 8.713271 GTGATTCTCTTTGTAGACTAAACCTTG 58.287 37.037 0.00 0.00 0.00 3.61
3301 3384 8.109705 TGTTCTACTCTAATTACGTGTAACCA 57.890 34.615 0.00 0.00 0.00 3.67
3495 3580 6.259550 AGAATTGATCCAGTTAAACAGTGC 57.740 37.500 0.00 0.00 0.00 4.40
3516 3601 4.246409 CGGAAATTCGCTAGAACACTTC 57.754 45.455 0.00 0.00 39.48 3.01
3537 3622 5.913137 TCAATTATTCACCGCCTGAATTT 57.087 34.783 10.73 0.47 45.89 1.82
3562 3647 4.757149 GCAGATAAGTTCCATTCGCCTAAT 59.243 41.667 0.00 0.00 0.00 1.73
3698 3783 3.841643 CACTTGTACCAAGTACTACCCG 58.158 50.000 9.13 0.00 39.49 5.28
3710 3795 6.392354 CAAGTACTACCCGTCACTGAAATTA 58.608 40.000 0.00 0.00 0.00 1.40
3857 3957 2.626950 CCACTCTCTGATTCCCCTGGTA 60.627 54.545 0.00 0.00 0.00 3.25
3925 4025 2.159653 GCGCGACACAAAATCAATCTCT 60.160 45.455 12.10 0.00 0.00 3.10
3943 4043 9.017509 TCAATCTCTGTGCTGAGAAATAAAAAT 57.982 29.630 11.72 0.00 44.94 1.82
3958 4060 7.898636 AGAAATAAAAATGAGGGGTACAATCCA 59.101 33.333 0.00 0.00 0.00 3.41
3984 4086 0.745845 GCGATTCAGTGGGCTCACAT 60.746 55.000 21.13 3.11 45.91 3.21
4211 4315 1.933021 ATTTTCCCCCGTCCTTTTCC 58.067 50.000 0.00 0.00 0.00 3.13
4258 4362 9.378597 CGCTGTATAGATTTGAAGATTTTCATG 57.621 33.333 0.00 0.00 42.60 3.07
4395 4499 3.725490 TGAAGAATGAGCCATGAGATCG 58.275 45.455 0.00 0.00 0.00 3.69
4400 4504 1.194218 TGAGCCATGAGATCGGTTGA 58.806 50.000 0.00 0.00 0.00 3.18
4446 4550 3.438360 CCTTGTTCACACTCTTGTTTGC 58.562 45.455 0.00 0.00 31.66 3.68
4456 4566 4.096382 ACACTCTTGTTTGCACTTTGTAGG 59.904 41.667 0.00 0.00 28.43 3.18
4514 4628 8.909708 TTCTGTACAAGTTGCAATATAAATGC 57.090 30.769 0.59 6.87 44.08 3.56
4603 4723 2.871096 AGCCACCGGATTAGACAAAA 57.129 45.000 9.46 0.00 0.00 2.44
4661 4781 4.508124 GGTCCGCTTTCTGAACAGTATATG 59.492 45.833 1.73 0.00 0.00 1.78
4681 4801 4.890158 TGTGACATGTACATGGACTCTT 57.110 40.909 33.32 15.96 42.91 2.85
4699 4819 7.671819 TGGACTCTTGAGAATCTTAGAAAGAGA 59.328 37.037 20.79 3.28 41.95 3.10
4731 4851 5.695851 AGCAAGTGAATCTTACAAGGTTG 57.304 39.130 0.00 0.00 34.66 3.77
4840 4960 1.880675 CGTCATAGACTCATAGGCCGT 59.119 52.381 0.00 0.00 0.00 5.68
4876 4997 2.233271 GGGGGTATGCATGTCTGATTG 58.767 52.381 10.16 0.00 0.00 2.67
4887 5008 5.941647 TGCATGTCTGATTGTATATGGGATG 59.058 40.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.189285 GCATGTCACACAAAAACAGCTT 58.811 40.909 0.00 0.00 0.00 3.74
3 4 3.117794 CAGGCATGTCACACAAAAACAG 58.882 45.455 0.00 0.00 0.00 3.16
4 5 2.757314 TCAGGCATGTCACACAAAAACA 59.243 40.909 0.00 0.00 0.00 2.83
5 6 3.115554 GTCAGGCATGTCACACAAAAAC 58.884 45.455 0.00 0.00 0.00 2.43
6 7 2.757314 TGTCAGGCATGTCACACAAAAA 59.243 40.909 0.00 0.00 0.00 1.94
7 8 2.098934 GTGTCAGGCATGTCACACAAAA 59.901 45.455 20.90 0.00 42.70 2.44
8 9 1.675483 GTGTCAGGCATGTCACACAAA 59.325 47.619 20.90 0.00 42.70 2.83
9 10 1.134128 AGTGTCAGGCATGTCACACAA 60.134 47.619 25.88 0.00 44.72 3.33
10 11 0.469494 AGTGTCAGGCATGTCACACA 59.531 50.000 25.88 8.81 44.72 3.72
11 12 1.151668 GAGTGTCAGGCATGTCACAC 58.848 55.000 25.88 19.92 44.72 3.82
12 13 0.319813 CGAGTGTCAGGCATGTCACA 60.320 55.000 25.88 9.86 44.72 3.58
13 14 0.038251 TCGAGTGTCAGGCATGTCAC 60.038 55.000 18.78 18.78 43.26 3.67
14 15 0.897621 ATCGAGTGTCAGGCATGTCA 59.102 50.000 0.00 0.00 0.00 3.58
15 16 1.135915 AGATCGAGTGTCAGGCATGTC 59.864 52.381 0.00 0.00 0.00 3.06
16 17 1.189752 AGATCGAGTGTCAGGCATGT 58.810 50.000 0.00 0.00 0.00 3.21
17 18 3.443099 TTAGATCGAGTGTCAGGCATG 57.557 47.619 0.00 0.00 0.00 4.06
18 19 4.184629 GTTTTAGATCGAGTGTCAGGCAT 58.815 43.478 0.00 0.00 0.00 4.40
19 20 3.585862 GTTTTAGATCGAGTGTCAGGCA 58.414 45.455 0.00 0.00 0.00 4.75
20 21 2.930682 GGTTTTAGATCGAGTGTCAGGC 59.069 50.000 0.00 0.00 0.00 4.85
31 32 6.967199 CGCCTTAAATCACAAGGTTTTAGATC 59.033 38.462 3.27 0.00 43.83 2.75
58 59 2.446285 CCACCCCTACTAGGCTACTACT 59.554 54.545 0.00 0.00 32.73 2.57
60 61 1.146566 GCCACCCCTACTAGGCTACTA 59.853 57.143 0.00 0.00 43.70 1.82
61 62 0.105607 GCCACCCCTACTAGGCTACT 60.106 60.000 0.00 0.00 43.70 2.57
62 63 2.438730 GCCACCCCTACTAGGCTAC 58.561 63.158 0.00 0.00 43.70 3.58
66 67 1.003051 ACCTGCCACCCCTACTAGG 59.997 63.158 0.00 0.00 34.30 3.02
67 68 0.325296 TCACCTGCCACCCCTACTAG 60.325 60.000 0.00 0.00 0.00 2.57
118 119 1.664965 GGCGCTGAACAGTTCGTCT 60.665 57.895 7.64 0.00 0.00 4.18
121 122 1.626654 ATTCGGCGCTGAACAGTTCG 61.627 55.000 32.72 12.20 0.00 3.95
133 134 1.442769 CCAGGGATATTGATTCGGCG 58.557 55.000 0.00 0.00 0.00 6.46
179 180 1.951602 GAAACGGGGTTGTTAGCACTT 59.048 47.619 0.00 0.00 0.00 3.16
189 190 0.400213 TGATCTGCAGAAACGGGGTT 59.600 50.000 22.50 0.18 0.00 4.11
216 217 5.969435 GGAACCGATTTTCATTTAATCCGTC 59.031 40.000 0.00 0.00 0.00 4.79
383 385 1.033746 CCATGGATGCTGTGGTGGAC 61.034 60.000 5.56 0.00 0.00 4.02
384 386 1.303948 CCATGGATGCTGTGGTGGA 59.696 57.895 5.56 0.00 0.00 4.02
385 387 1.755395 CCCATGGATGCTGTGGTGG 60.755 63.158 15.22 0.00 0.00 4.61
386 388 0.750546 CTCCCATGGATGCTGTGGTG 60.751 60.000 15.22 0.00 0.00 4.17
387 389 1.611419 CTCCCATGGATGCTGTGGT 59.389 57.895 15.22 0.00 0.00 4.16
388 390 1.152819 CCTCCCATGGATGCTGTGG 60.153 63.158 15.22 2.26 0.00 4.17
389 391 1.152819 CCCTCCCATGGATGCTGTG 60.153 63.158 15.22 0.00 0.00 3.66
390 392 1.308128 TCCCTCCCATGGATGCTGT 60.308 57.895 15.22 0.00 0.00 4.40
557 591 1.541672 GGAGAGGGAGAGGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
558 592 1.541672 GGGAGAGGGAGAGGGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
559 593 2.015726 GGGGAGAGGGAGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
560 594 2.612251 GGGGAGAGGGAGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
561 595 3.430497 CGGGGAGAGGGAGAGGGA 61.430 72.222 0.00 0.00 0.00 4.20
562 596 4.548513 CCGGGGAGAGGGAGAGGG 62.549 77.778 0.00 0.00 0.00 4.30
563 597 3.742248 GACCGGGGAGAGGGAGAGG 62.742 73.684 6.32 0.00 0.00 3.69
564 598 2.123640 GACCGGGGAGAGGGAGAG 60.124 72.222 6.32 0.00 0.00 3.20
565 599 3.752167 GGACCGGGGAGAGGGAGA 61.752 72.222 6.32 0.00 0.00 3.71
566 600 3.756783 AGGACCGGGGAGAGGGAG 61.757 72.222 6.32 0.00 0.00 4.30
567 601 4.075793 CAGGACCGGGGAGAGGGA 62.076 72.222 6.32 0.00 0.00 4.20
753 814 2.231380 TGGCCTTGTCCTCTTCCCC 61.231 63.158 3.32 0.00 0.00 4.81
754 815 1.002011 GTGGCCTTGTCCTCTTCCC 60.002 63.158 3.32 0.00 0.00 3.97
761 822 0.890996 CAGTTGGAGTGGCCTTGTCC 60.891 60.000 3.32 8.03 37.63 4.02
852 913 2.682856 GACAACAAGAACACAAGAGCCA 59.317 45.455 0.00 0.00 0.00 4.75
895 956 4.421515 CTCCTGGGCTGGTGCTGG 62.422 72.222 0.00 0.00 39.59 4.85
896 957 2.249413 CTACTCCTGGGCTGGTGCTG 62.249 65.000 0.00 0.00 39.59 4.41
897 958 1.992277 CTACTCCTGGGCTGGTGCT 60.992 63.158 0.00 0.00 39.59 4.40
898 959 1.965754 CTCTACTCCTGGGCTGGTGC 61.966 65.000 0.00 0.00 38.76 5.01
899 960 0.324738 TCTCTACTCCTGGGCTGGTG 60.325 60.000 0.00 0.00 0.00 4.17
923 984 1.473258 TCTCAGCCTCTCTCAGCTTC 58.527 55.000 0.00 0.00 37.18 3.86
924 985 1.935799 TTCTCAGCCTCTCTCAGCTT 58.064 50.000 0.00 0.00 37.18 3.74
925 986 1.826720 CTTTCTCAGCCTCTCTCAGCT 59.173 52.381 0.00 0.00 40.89 4.24
926 987 1.824230 TCTTTCTCAGCCTCTCTCAGC 59.176 52.381 0.00 0.00 0.00 4.26
927 988 3.119029 CCTTCTTTCTCAGCCTCTCTCAG 60.119 52.174 0.00 0.00 0.00 3.35
928 989 2.830923 CCTTCTTTCTCAGCCTCTCTCA 59.169 50.000 0.00 0.00 0.00 3.27
942 1009 3.260632 GCCTCTGTCTTCTCTCCTTCTTT 59.739 47.826 0.00 0.00 0.00 2.52
1044 1111 3.697045 AGATGACGAAGAGGTAGAAGGTG 59.303 47.826 0.00 0.00 0.00 4.00
1254 1321 2.747460 GGCGTTGATCCAGCTGCA 60.747 61.111 8.66 0.00 0.00 4.41
1271 1338 2.028876 ACACGGGGGTGAAAAGAAAAG 58.971 47.619 0.62 0.00 0.00 2.27
1276 1344 1.616159 ATGAACACGGGGGTGAAAAG 58.384 50.000 0.62 0.00 0.00 2.27
1281 1349 0.250727 AGACAATGAACACGGGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
1308 1376 0.102300 GCCCAGAAAAACAACGCTGT 59.898 50.000 0.00 0.00 37.39 4.40
1310 1378 1.739667 GGCCCAGAAAAACAACGCT 59.260 52.632 0.00 0.00 0.00 5.07
1311 1379 1.300620 GGGCCCAGAAAAACAACGC 60.301 57.895 19.95 0.00 0.00 4.84
1312 1380 0.750249 AAGGGCCCAGAAAAACAACG 59.250 50.000 27.56 0.00 0.00 4.10
1315 1383 2.397044 ATCAAGGGCCCAGAAAAACA 57.603 45.000 27.56 0.00 0.00 2.83
1316 1384 2.899900 AGAATCAAGGGCCCAGAAAAAC 59.100 45.455 27.56 13.38 0.00 2.43
1322 1390 1.755783 GCCAGAATCAAGGGCCCAG 60.756 63.158 27.56 16.94 41.90 4.45
1323 1391 2.360191 GCCAGAATCAAGGGCCCA 59.640 61.111 27.56 2.74 41.90 5.36
1327 1395 0.682209 CACAGGGCCAGAATCAAGGG 60.682 60.000 6.18 0.00 0.00 3.95
1330 1398 0.609957 CAGCACAGGGCCAGAATCAA 60.610 55.000 6.18 0.00 46.50 2.57
1386 1454 7.748677 AGAGAATGTTTCCCCAAATTTGAAAT 58.251 30.769 19.86 0.00 31.35 2.17
1428 1496 7.386848 CCAAATCAGCACTGAAATTTCTGAAAT 59.613 33.333 26.21 9.76 43.58 2.17
1436 1504 3.007182 CCCACCAAATCAGCACTGAAATT 59.993 43.478 4.14 0.67 43.58 1.82
1527 1596 5.835911 GAAAAGATTCCTTTGCTCAAAGC 57.164 39.130 14.99 0.00 44.76 3.51
1596 1671 2.493278 AGTGATTTTTCCCAGCATTCCG 59.507 45.455 0.00 0.00 0.00 4.30
1603 1678 6.942976 TGGTAGTAGTAGTGATTTTTCCCAG 58.057 40.000 0.00 0.00 0.00 4.45
1605 1680 6.944096 ACTGGTAGTAGTAGTGATTTTTCCC 58.056 40.000 0.00 0.00 0.00 3.97
1658 1733 0.253327 GTCGCCTCCCCTCAGATTTT 59.747 55.000 0.00 0.00 0.00 1.82
1672 1747 2.892425 CAGGATCCTTGCGTCGCC 60.892 66.667 13.00 0.00 0.00 5.54
1699 1774 9.532697 GCAACACTTTAATTGAATTTAATGCAG 57.467 29.630 0.00 0.00 29.14 4.41
1735 1810 5.072040 ACCTTCTTTTGCCATTAAATCCG 57.928 39.130 0.00 0.00 0.00 4.18
1739 1814 4.819088 GCCAAACCTTCTTTTGCCATTAAA 59.181 37.500 0.00 0.00 35.48 1.52
1808 1883 1.227118 GGTGTTTGGTTGGGCGTTG 60.227 57.895 0.00 0.00 0.00 4.10
1845 1920 1.750399 CACGGAGGCAAATGGAGGG 60.750 63.158 0.00 0.00 0.00 4.30
1901 1976 1.462616 TAATCTGCCTGCGCAAATGT 58.537 45.000 13.05 0.00 46.66 2.71
1952 2027 1.300233 GGCGAGGACGATCATCACC 60.300 63.158 0.00 0.00 42.66 4.02
2007 2082 2.154798 TTGAAGTCGTCTGGGGCTCG 62.155 60.000 0.00 0.00 0.00 5.03
2012 2087 0.679505 TGTCCTTGAAGTCGTCTGGG 59.320 55.000 0.00 0.00 0.00 4.45
2065 2140 6.315144 TGGATACATCAGAACCAATTAACACG 59.685 38.462 0.00 0.00 46.17 4.49
2093 2168 6.749578 CACATCAGTAGCTAACTCACTTACTG 59.250 42.308 0.00 0.00 35.76 2.74
2291 2369 5.593909 TCCATCAAAACTGGCCTTATACATG 59.406 40.000 3.32 0.00 33.56 3.21
2292 2370 5.765510 TCCATCAAAACTGGCCTTATACAT 58.234 37.500 3.32 0.00 33.56 2.29
2305 2383 2.607038 GCGACAAACCCTCCATCAAAAC 60.607 50.000 0.00 0.00 0.00 2.43
2351 2429 4.720649 TTCTTTCTCATACTCCTGTCCG 57.279 45.455 0.00 0.00 0.00 4.79
2375 2453 4.494484 TGTAGAACACAATCATCACCTCG 58.506 43.478 0.00 0.00 32.95 4.63
2399 2482 8.958119 AGACAACAATCTGAAAACAACTAGTA 57.042 30.769 0.00 0.00 0.00 1.82
2400 2483 7.865706 AGACAACAATCTGAAAACAACTAGT 57.134 32.000 0.00 0.00 0.00 2.57
2642 2725 8.902806 TCACAGCTCGATATAATTTCCATTTTT 58.097 29.630 0.00 0.00 0.00 1.94
2659 2742 2.093973 ACCTATCCAACTTCACAGCTCG 60.094 50.000 0.00 0.00 0.00 5.03
3262 3345 6.388278 AGAGTAGAACATCGTCCTTGTAAAC 58.612 40.000 0.00 0.00 0.00 2.01
3301 3384 4.137543 GTCAACTTCCCTGAATTCAGTGT 58.862 43.478 29.03 19.70 42.27 3.55
3324 3409 3.826466 TGCATATACATCGCTCTTCTCG 58.174 45.455 0.00 0.00 0.00 4.04
3495 3580 3.678072 TGAAGTGTTCTAGCGAATTTCCG 59.322 43.478 0.00 0.00 0.00 4.30
3537 3622 2.288666 GCGAATGGAACTTATCTGCCA 58.711 47.619 0.00 0.00 34.45 4.92
3562 3647 7.560991 ACCCAAATATGTCAGATGCTAATGAAA 59.439 33.333 0.00 0.00 0.00 2.69
3613 3698 2.172293 AGGGAGCTTGGATCTGTCAATC 59.828 50.000 0.00 0.00 0.00 2.67
3741 3827 4.111375 AGGTAGCGAAGTAGTTGTGATG 57.889 45.455 0.00 0.00 0.00 3.07
3742 3828 4.803098 AAGGTAGCGAAGTAGTTGTGAT 57.197 40.909 0.00 0.00 0.00 3.06
3800 3900 0.960861 GTGGCCTGTAGCTTGGTTCC 60.961 60.000 3.32 0.00 43.05 3.62
3857 3957 1.930656 CCCTCCAAGGTCCATGGGT 60.931 63.158 13.02 0.00 38.54 4.51
3913 4013 6.889301 TTTCTCAGCACAGAGATTGATTTT 57.111 33.333 4.67 0.00 43.67 1.82
3925 4025 5.185635 CCCCTCATTTTTATTTCTCAGCACA 59.814 40.000 0.00 0.00 0.00 4.57
3943 4043 3.696045 CACATTTGGATTGTACCCCTCA 58.304 45.455 0.00 0.00 0.00 3.86
3958 4060 1.176527 CCCACTGAATCGCCACATTT 58.823 50.000 0.00 0.00 0.00 2.32
3984 4086 4.649674 AGGCTATCTGAACTATTTGGACGA 59.350 41.667 0.00 0.00 0.00 4.20
4211 4315 3.548818 CGGTGTTCAGAGCCAAAGAAAAG 60.549 47.826 0.00 0.00 0.00 2.27
4258 4362 4.183865 GGGGCAAGTATTTCTTTCATTGC 58.816 43.478 0.00 0.00 41.67 3.56
4395 4499 1.298014 CTCCCTGAGCCACTCAACC 59.702 63.158 0.00 0.00 40.18 3.77
4400 4504 1.072965 CAAAGAACTCCCTGAGCCACT 59.927 52.381 0.00 0.00 32.04 4.00
4478 4592 7.083858 GCAACTTGTACAGAATGCATTTCTAA 58.916 34.615 14.33 3.36 42.98 2.10
4514 4628 3.877508 ACAGGTCTCGTTGGAAAAAGAAG 59.122 43.478 0.00 0.00 0.00 2.85
4603 4723 5.163893 CGTCGCACCTAATTAACAATGAAGT 60.164 40.000 0.00 0.00 0.00 3.01
4639 4759 5.005779 CACATATACTGTTCAGAAAGCGGAC 59.994 44.000 6.83 0.00 35.29 4.79
4661 4781 4.820897 TCAAGAGTCCATGTACATGTCAC 58.179 43.478 29.25 24.37 37.11 3.67
4704 4824 7.224297 ACCTTGTAAGATTCACTTGCTTAAGA 58.776 34.615 6.67 0.00 40.85 2.10
4731 4851 0.954452 CTGTTTCCCACAGCTCAACC 59.046 55.000 0.00 0.00 46.70 3.77
4840 4960 2.673114 CCCAGCGCGCTTTTTCGTA 61.673 57.895 34.58 0.00 0.00 3.43
4887 5008 5.062528 CCTCCAGCTTCTAAATGAGAATCC 58.937 45.833 0.00 0.00 43.39 3.01


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

AutoCloner maintained by Alex Coulton.