Multiple sequence alignment - TraesCS6B01G277400

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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 TraesCS6B01G277400 chr6B 100.000 4172 0 0 1 4172 501770019 501774190 0.000000e+00 7705.0
1 TraesCS6B01G277400 chr6B 89.143 175 18 1 3768 3942 487136353 487136180 2.530000e-52 217.0
2 TraesCS6B01G277400 chr6B 88.028 142 16 1 4012 4152 487136187 487136046 2.580000e-37 167.0
3 TraesCS6B01G277400 chr6B 93.976 83 3 1 3940 4020 135505596 135505678 1.570000e-24 124.0
4 TraesCS6B01G277400 chr6D 95.808 3626 70 19 577 4172 321776898 321773325 0.000000e+00 5779.0
5 TraesCS6B01G277400 chr6D 89.340 197 13 3 169 363 321777526 321777336 1.500000e-59 241.0
6 TraesCS6B01G277400 chr6D 88.050 159 7 5 374 525 321777294 321777141 1.190000e-40 178.0
7 TraesCS6B01G277400 chr6D 94.545 55 3 0 1 55 321777683 321777629 7.430000e-13 86.1
8 TraesCS6B01G277400 chr6A 95.185 3302 93 34 602 3877 459077453 459074192 0.000000e+00 5156.0
9 TraesCS6B01G277400 chr6A 88.557 201 11 6 169 363 459082038 459081844 2.510000e-57 233.0
10 TraesCS6B01G277400 chr6A 88.166 169 7 5 418 576 459077991 459077826 5.510000e-44 189.0
11 TraesCS6B01G277400 chr4B 88.571 175 19 1 3768 3942 471307836 471308009 1.180000e-50 211.0
12 TraesCS6B01G277400 chr7A 88.506 174 19 1 3769 3942 230300984 230301156 4.230000e-50 209.0
13 TraesCS6B01G277400 chr7A 88.068 176 20 1 3767 3942 204737055 204736881 1.520000e-49 207.0
14 TraesCS6B01G277400 chr5D 88.068 176 19 2 3767 3942 201311966 201312139 1.520000e-49 207.0
15 TraesCS6B01G277400 chr3B 88.000 175 20 1 3768 3942 254193186 254193013 5.470000e-49 206.0
16 TraesCS6B01G277400 chr5A 87.500 176 21 1 3767 3942 210535384 210535558 7.070000e-48 202.0
17 TraesCS6B01G277400 chr5A 87.857 140 16 1 4012 4150 178032247 178032386 3.340000e-36 163.0
18 TraesCS6B01G277400 chr5A 87.857 140 15 2 4012 4150 500045323 500045185 3.340000e-36 163.0
19 TraesCS6B01G277400 chr5A 85.806 155 19 3 4012 4163 444536783 444536937 1.200000e-35 161.0
20 TraesCS6B01G277400 chr1A 88.571 140 15 1 4012 4150 293712532 293712671 7.170000e-38 169.0
21 TraesCS6B01G277400 chr1A 95.556 45 1 1 2070 2114 569372540 569372497 2.080000e-08 71.3
22 TraesCS6B01G277400 chr2A 87.413 143 17 1 4012 4153 203459807 203459949 3.340000e-36 163.0
23 TraesCS6B01G277400 chr1D 87.857 140 16 1 4012 4150 226449897 226450036 3.340000e-36 163.0
24 TraesCS6B01G277400 chr1D 87.413 143 17 1 4012 4153 461273178 461273320 3.340000e-36 163.0
25 TraesCS6B01G277400 chr1D 91.111 90 6 1 3939 4026 3368845 3368756 2.040000e-23 121.0
26 TraesCS6B01G277400 chr4A 95.238 84 3 1 3938 4021 724795787 724795869 9.410000e-27 132.0
27 TraesCS6B01G277400 chr7D 92.473 93 4 2 3941 4030 29876456 29876364 3.380000e-26 130.0
28 TraesCS6B01G277400 chr7D 92.941 85 4 1 3938 4020 311882043 311882127 5.660000e-24 122.0
29 TraesCS6B01G277400 chr7B 93.182 88 5 1 3941 4027 84186515 84186602 1.220000e-25 128.0
30 TraesCS6B01G277400 chr3D 92.941 85 4 1 3941 4025 169888215 169888133 5.660000e-24 122.0
31 TraesCS6B01G277400 chr3D 92.045 88 3 4 3939 4024 169888138 169888223 2.040000e-23 121.0
32 TraesCS6B01G277400 chr2D 83.036 112 11 3 3941 4045 14625957 14626067 1.230000e-15 95.3


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 TraesCS6B01G277400 chr6B 501770019 501774190 4171 False 7705.000000 7705 100.00000 1 4172 1 chr6B.!!$F2 4171
1 TraesCS6B01G277400 chr6D 321773325 321777683 4358 True 1571.025000 5779 91.93575 1 4172 4 chr6D.!!$R1 4171
2 TraesCS6B01G277400 chr6A 459074192 459082038 7846 True 1859.333333 5156 90.63600 169 3877 3 chr6A.!!$R1 3708


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
538 4378 0.106519 AGGAGGCAGAGAGAGAGAGC 60.107 60.0 0.0 0.0 0.0 4.09 F
1794 6023 0.182299 CCTTCTTCATGCCCCTCTCC 59.818 60.0 0.0 0.0 0.0 3.71 F
1938 6167 0.254178 CCCTGCTACATGGCTCACTT 59.746 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 6027 0.179100 CGCTGGTTGTGATCGGAGAT 60.179 55.0 0.0 0.0 45.12 2.75 R
2916 7145 0.664166 CAGCAAACACATTCCGCCAC 60.664 55.0 0.0 0.0 0.00 5.01 R
3905 8143 5.241728 GGTTTCTAGCATCCACTCAAACTTT 59.758 40.0 0.0 0.0 0.00 2.66 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
53 54 3.072184 AGAGCAGCCGAAAAGGATATGAT 59.928 43.478 0.00 0.00 45.00 2.45
54 55 4.284490 AGAGCAGCCGAAAAGGATATGATA 59.716 41.667 0.00 0.00 45.00 2.15
55 56 4.319177 AGCAGCCGAAAAGGATATGATAC 58.681 43.478 0.00 0.00 45.00 2.24
56 57 4.040952 AGCAGCCGAAAAGGATATGATACT 59.959 41.667 0.00 0.00 45.00 2.12
57 58 4.153117 GCAGCCGAAAAGGATATGATACTG 59.847 45.833 0.00 0.00 45.00 2.74
58 59 4.692625 CAGCCGAAAAGGATATGATACTGG 59.307 45.833 0.00 0.00 45.00 4.00
59 60 4.593206 AGCCGAAAAGGATATGATACTGGA 59.407 41.667 0.00 0.00 45.00 3.86
60 61 4.932200 GCCGAAAAGGATATGATACTGGAG 59.068 45.833 0.00 0.00 45.00 3.86
61 62 4.932200 CCGAAAAGGATATGATACTGGAGC 59.068 45.833 0.00 0.00 45.00 4.70
62 63 5.511373 CCGAAAAGGATATGATACTGGAGCA 60.511 44.000 0.00 0.00 45.00 4.26
63 64 5.636965 CGAAAAGGATATGATACTGGAGCAG 59.363 44.000 0.00 0.00 37.52 4.24
91 92 5.232463 AGCTGTGTTTAAAATGGCAAGATG 58.768 37.500 0.00 0.00 0.00 2.90
92 93 4.143052 GCTGTGTTTAAAATGGCAAGATGC 60.143 41.667 0.00 0.00 44.08 3.91
93 94 5.212532 TGTGTTTAAAATGGCAAGATGCT 57.787 34.783 2.00 0.00 44.28 3.79
94 95 6.338214 TGTGTTTAAAATGGCAAGATGCTA 57.662 33.333 2.00 0.00 44.28 3.49
95 96 6.389091 TGTGTTTAAAATGGCAAGATGCTAG 58.611 36.000 2.00 0.00 44.28 3.42
96 97 6.015519 TGTGTTTAAAATGGCAAGATGCTAGT 60.016 34.615 2.00 0.00 44.28 2.57
97 98 7.175816 TGTGTTTAAAATGGCAAGATGCTAGTA 59.824 33.333 2.00 0.00 44.28 1.82
98 99 7.698130 GTGTTTAAAATGGCAAGATGCTAGTAG 59.302 37.037 2.00 0.00 44.28 2.57
99 100 7.393234 TGTTTAAAATGGCAAGATGCTAGTAGT 59.607 33.333 2.00 0.00 44.28 2.73
100 101 8.889717 GTTTAAAATGGCAAGATGCTAGTAGTA 58.110 33.333 2.00 0.00 44.28 1.82
101 102 8.662781 TTAAAATGGCAAGATGCTAGTAGTAG 57.337 34.615 0.00 0.00 44.28 2.57
117 118 8.160521 CTAGTAGTAGCATGATGAGTACAAGT 57.839 38.462 0.00 0.00 0.00 3.16
118 119 7.033530 AGTAGTAGCATGATGAGTACAAGTC 57.966 40.000 0.00 0.00 0.00 3.01
119 120 6.831353 AGTAGTAGCATGATGAGTACAAGTCT 59.169 38.462 0.00 0.00 0.00 3.24
120 121 5.900425 AGTAGCATGATGAGTACAAGTCTG 58.100 41.667 0.00 0.00 0.00 3.51
159 160 4.142902 TGTTATTTTTCAGCTCAGCTACGC 60.143 41.667 0.00 0.00 36.40 4.42
160 161 2.169832 TTTTTCAGCTCAGCTACGCT 57.830 45.000 0.00 3.27 36.40 5.07
161 162 2.169832 TTTTCAGCTCAGCTACGCTT 57.830 45.000 0.00 0.00 36.40 4.68
162 163 2.169832 TTTCAGCTCAGCTACGCTTT 57.830 45.000 0.00 0.00 36.40 3.51
163 164 2.169832 TTCAGCTCAGCTACGCTTTT 57.830 45.000 0.00 0.00 36.40 2.27
164 165 3.313012 TTCAGCTCAGCTACGCTTTTA 57.687 42.857 0.00 0.00 36.40 1.52
166 167 3.861840 TCAGCTCAGCTACGCTTTTAAT 58.138 40.909 0.00 0.00 36.40 1.40
167 168 3.618594 TCAGCTCAGCTACGCTTTTAATG 59.381 43.478 0.00 0.00 36.40 1.90
189 215 6.861065 TGTAAGGCTCCGATTTTAATGATC 57.139 37.500 0.00 0.00 0.00 2.92
199 229 2.071778 TTTAATGATCTGCCTGCCCC 57.928 50.000 0.00 0.00 0.00 5.80
204 234 3.011517 ATCTGCCTGCCCCTCGTT 61.012 61.111 0.00 0.00 0.00 3.85
205 235 3.335356 ATCTGCCTGCCCCTCGTTG 62.335 63.158 0.00 0.00 0.00 4.10
222 252 2.926200 CGTTGCCACAATCTCAGTCTAG 59.074 50.000 0.00 0.00 0.00 2.43
233 263 2.309162 TCTCAGTCTAGGGCAGTACTGT 59.691 50.000 23.44 7.20 40.18 3.55
236 266 2.164624 CAGTCTAGGGCAGTACTGTCAC 59.835 54.545 27.67 18.52 36.81 3.67
237 267 2.041891 AGTCTAGGGCAGTACTGTCACT 59.958 50.000 27.67 23.73 36.81 3.41
334 366 0.535102 ACAGCCGTCAAAGTCCCAAG 60.535 55.000 0.00 0.00 0.00 3.61
356 388 3.560068 GGATTTCTCGCGGTCAATACAAT 59.440 43.478 6.13 0.00 0.00 2.71
363 395 2.132762 GCGGTCAATACAATACCTCCG 58.867 52.381 0.00 0.00 39.71 4.63
364 396 2.223876 GCGGTCAATACAATACCTCCGA 60.224 50.000 0.00 0.00 39.17 4.55
367 399 3.067180 GGTCAATACAATACCTCCGACGA 59.933 47.826 0.00 0.00 0.00 4.20
369 401 3.949754 TCAATACAATACCTCCGACGACT 59.050 43.478 0.00 0.00 0.00 4.18
370 402 5.008019 GTCAATACAATACCTCCGACGACTA 59.992 44.000 0.00 0.00 0.00 2.59
371 403 5.237996 TCAATACAATACCTCCGACGACTAG 59.762 44.000 0.00 0.00 0.00 2.57
372 404 2.996631 ACAATACCTCCGACGACTAGT 58.003 47.619 0.00 0.00 0.00 2.57
381 451 3.068574 GACGACTAGTCTCGGCTCT 57.931 57.895 20.34 0.00 46.13 4.09
405 475 8.103305 TCTCTGCAATAATTTTGGTCTCTACTT 58.897 33.333 0.00 0.00 0.00 2.24
407 477 7.336931 TCTGCAATAATTTTGGTCTCTACTTCC 59.663 37.037 0.00 0.00 0.00 3.46
408 478 6.377146 TGCAATAATTTTGGTCTCTACTTCCC 59.623 38.462 0.00 0.00 0.00 3.97
409 479 6.458342 GCAATAATTTTGGTCTCTACTTCCCG 60.458 42.308 0.00 0.00 0.00 5.14
410 480 2.467566 TTTTGGTCTCTACTTCCCGC 57.532 50.000 0.00 0.00 0.00 6.13
411 481 0.245539 TTTGGTCTCTACTTCCCGCG 59.754 55.000 0.00 0.00 0.00 6.46
412 482 0.896940 TTGGTCTCTACTTCCCGCGT 60.897 55.000 4.92 0.00 0.00 6.01
433 4263 2.771089 ACTTGCATACAGTCCACACAG 58.229 47.619 0.00 0.00 0.00 3.66
442 4272 6.072728 GCATACAGTCCACACAGACAAATAAA 60.073 38.462 0.00 0.00 39.34 1.40
538 4378 0.106519 AGGAGGCAGAGAGAGAGAGC 60.107 60.000 0.00 0.00 0.00 4.09
566 4406 1.610624 GCAGACTGAAAACGATGGGGA 60.611 52.381 6.65 0.00 0.00 4.81
634 4821 2.825836 GCACGCATCCAGGGAAGG 60.826 66.667 0.00 0.00 0.00 3.46
635 4822 2.989639 CACGCATCCAGGGAAGGA 59.010 61.111 0.00 0.00 43.01 3.36
636 4823 1.153289 CACGCATCCAGGGAAGGAG 60.153 63.158 0.00 0.00 41.90 3.69
657 4846 5.246203 GGAGATAGCAGTAGAGAGAGAGAGA 59.754 48.000 0.00 0.00 0.00 3.10
659 4848 6.077993 AGATAGCAGTAGAGAGAGAGAGAGA 58.922 44.000 0.00 0.00 0.00 3.10
660 4849 4.679373 AGCAGTAGAGAGAGAGAGAGAG 57.321 50.000 0.00 0.00 0.00 3.20
661 4850 4.290093 AGCAGTAGAGAGAGAGAGAGAGA 58.710 47.826 0.00 0.00 0.00 3.10
703 4892 0.326595 ACAGCGAGGACAGAGAGAGA 59.673 55.000 0.00 0.00 0.00 3.10
704 4893 1.016627 CAGCGAGGACAGAGAGAGAG 58.983 60.000 0.00 0.00 0.00 3.20
705 4894 0.748005 AGCGAGGACAGAGAGAGAGC 60.748 60.000 0.00 0.00 0.00 4.09
706 4895 2.013807 CGAGGACAGAGAGAGAGCG 58.986 63.158 0.00 0.00 0.00 5.03
707 4896 0.461163 CGAGGACAGAGAGAGAGCGA 60.461 60.000 0.00 0.00 0.00 4.93
708 4897 1.299541 GAGGACAGAGAGAGAGCGAG 58.700 60.000 0.00 0.00 0.00 5.03
709 4898 0.748005 AGGACAGAGAGAGAGCGAGC 60.748 60.000 0.00 0.00 0.00 5.03
710 4899 1.351707 GACAGAGAGAGAGCGAGCG 59.648 63.158 0.00 0.00 0.00 5.03
711 4900 1.078778 ACAGAGAGAGAGCGAGCGA 60.079 57.895 0.00 0.00 0.00 4.93
712 4901 1.089481 ACAGAGAGAGAGCGAGCGAG 61.089 60.000 0.00 0.00 0.00 5.03
713 4902 2.180204 AGAGAGAGAGCGAGCGAGC 61.180 63.158 0.00 0.00 37.41 5.03
714 4903 2.437537 AGAGAGAGCGAGCGAGCA 60.438 61.111 9.01 0.00 40.15 4.26
715 4904 2.024588 GAGAGAGCGAGCGAGCAG 59.975 66.667 9.01 0.00 40.15 4.24
742 4931 3.309296 GGGAGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
747 4936 3.312890 AGAGAGAGAGAGAGAGAGGAGG 58.687 54.545 0.00 0.00 0.00 4.30
839 5030 3.387050 CCTCCCTGTACCCTGTTGTATAC 59.613 52.174 0.00 0.00 0.00 1.47
840 5031 4.287552 CTCCCTGTACCCTGTTGTATACT 58.712 47.826 4.17 0.00 0.00 2.12
841 5032 4.284178 TCCCTGTACCCTGTTGTATACTC 58.716 47.826 4.17 0.00 0.00 2.59
842 5033 4.016851 TCCCTGTACCCTGTTGTATACTCT 60.017 45.833 4.17 0.00 0.00 3.24
843 5034 4.341520 CCCTGTACCCTGTTGTATACTCTC 59.658 50.000 4.17 0.00 0.00 3.20
844 5035 5.202004 CCTGTACCCTGTTGTATACTCTCT 58.798 45.833 4.17 0.00 0.00 3.10
845 5036 5.299782 CCTGTACCCTGTTGTATACTCTCTC 59.700 48.000 4.17 0.00 0.00 3.20
846 5037 6.075949 TGTACCCTGTTGTATACTCTCTCT 57.924 41.667 4.17 0.00 0.00 3.10
847 5038 6.120905 TGTACCCTGTTGTATACTCTCTCTC 58.879 44.000 4.17 0.00 0.00 3.20
848 5039 5.459982 ACCCTGTTGTATACTCTCTCTCT 57.540 43.478 4.17 0.00 0.00 3.10
887 5079 1.381327 CCAGGTAGGAAGCGAGGGA 60.381 63.158 0.00 0.00 41.22 4.20
888 5080 1.395826 CCAGGTAGGAAGCGAGGGAG 61.396 65.000 0.00 0.00 41.22 4.30
889 5081 1.075896 AGGTAGGAAGCGAGGGAGG 60.076 63.158 0.00 0.00 0.00 4.30
890 5082 2.134933 GGTAGGAAGCGAGGGAGGG 61.135 68.421 0.00 0.00 0.00 4.30
1341 5558 4.193893 TGGGATGCCATGCTCGGG 62.194 66.667 0.00 0.00 0.00 5.14
1470 5687 2.507102 CCGCTCGTCGACAATGCT 60.507 61.111 17.16 0.00 41.67 3.79
1713 5930 1.001641 CACAAAGCCCCCTCTCCTG 60.002 63.158 0.00 0.00 0.00 3.86
1743 5960 1.885871 GCATGGCCTCTTCAACCAC 59.114 57.895 3.32 0.00 35.99 4.16
1750 5967 1.348036 GCCTCTTCAACCACTACCAGT 59.652 52.381 0.00 0.00 0.00 4.00
1792 6021 0.918310 AGCCTTCTTCATGCCCCTCT 60.918 55.000 0.00 0.00 0.00 3.69
1794 6023 0.182299 CCTTCTTCATGCCCCTCTCC 59.818 60.000 0.00 0.00 0.00 3.71
1798 6027 0.984961 CTTCATGCCCCTCTCCTCCA 60.985 60.000 0.00 0.00 0.00 3.86
1881 6110 0.727970 CAGACGACCTCTACCTCACG 59.272 60.000 0.00 0.00 0.00 4.35
1938 6167 0.254178 CCCTGCTACATGGCTCACTT 59.746 55.000 0.00 0.00 0.00 3.16
2262 6491 1.258676 ACAAGTCCTTCTCCGACCTC 58.741 55.000 0.00 0.00 0.00 3.85
2622 6851 1.075542 CTGGCGACGAAATTGTAGCA 58.924 50.000 0.00 0.00 41.55 3.49
2664 6893 4.735132 GCTCGTGCACCACCGCTA 62.735 66.667 12.15 0.00 39.41 4.26
2742 6971 0.757512 ATGGAGCTGATCGTGCTGAT 59.242 50.000 16.20 6.74 41.30 2.90
2883 7112 1.134367 CCAAGAGTCGAAGATGCGGTA 59.866 52.381 0.00 0.00 40.67 4.02
3630 7864 6.299805 TGCCTAGATGTTTAGAGACAACAT 57.700 37.500 0.00 0.00 45.60 2.71
3644 7878 9.587772 TTAGAGACAACATAGCAGAATCTTTAC 57.412 33.333 0.00 0.00 0.00 2.01
3759 7997 6.159988 GTCTATATGATGACCTGTACTTGCC 58.840 44.000 0.00 0.00 0.00 4.52
3852 8090 5.532557 TGTCATGCTCATCTAAATCCTACG 58.467 41.667 0.00 0.00 0.00 3.51
3932 8170 2.237143 TGAGTGGATGCTAGAAACCCTG 59.763 50.000 0.00 0.00 0.00 4.45
3968 8206 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.830744 TTCGAGGAAACTTGTCTTGGA 57.169 42.857 0.00 0.00 44.43 3.53
7 8 4.035675 AGCTTTTCGAGGAAACTTGTCTTG 59.964 41.667 0.00 0.00 44.43 3.02
45 46 7.069331 AGCTATTACTGCTCCAGTATCATATCC 59.931 40.741 5.97 0.00 44.85 2.59
53 54 4.023980 ACACAGCTATTACTGCTCCAGTA 58.976 43.478 1.18 1.18 43.46 2.74
55 56 3.533606 ACACAGCTATTACTGCTCCAG 57.466 47.619 0.00 0.00 41.60 3.86
56 57 3.981071 AACACAGCTATTACTGCTCCA 57.019 42.857 0.00 0.00 41.60 3.86
57 58 6.737254 TTTAAACACAGCTATTACTGCTCC 57.263 37.500 0.00 0.00 41.60 4.70
58 59 7.698130 CCATTTTAAACACAGCTATTACTGCTC 59.302 37.037 0.00 0.00 41.60 4.26
59 60 7.538575 CCATTTTAAACACAGCTATTACTGCT 58.461 34.615 0.00 0.00 41.60 4.24
60 61 6.253512 GCCATTTTAAACACAGCTATTACTGC 59.746 38.462 0.00 0.00 41.60 4.40
61 62 7.312154 TGCCATTTTAAACACAGCTATTACTG 58.688 34.615 0.00 0.00 43.59 2.74
62 63 7.461182 TGCCATTTTAAACACAGCTATTACT 57.539 32.000 0.00 0.00 0.00 2.24
63 64 8.026607 TCTTGCCATTTTAAACACAGCTATTAC 58.973 33.333 0.00 0.00 0.00 1.89
66 67 6.588719 TCTTGCCATTTTAAACACAGCTAT 57.411 33.333 0.00 0.00 0.00 2.97
72 73 6.389906 ACTAGCATCTTGCCATTTTAAACAC 58.610 36.000 0.00 0.00 46.52 3.32
91 92 6.561737 TGTACTCATCATGCTACTACTAGC 57.438 41.667 0.00 0.00 45.19 3.42
92 93 8.160521 ACTTGTACTCATCATGCTACTACTAG 57.839 38.462 0.00 0.00 0.00 2.57
93 94 7.993758 AGACTTGTACTCATCATGCTACTACTA 59.006 37.037 0.00 0.00 0.00 1.82
94 95 6.831353 AGACTTGTACTCATCATGCTACTACT 59.169 38.462 0.00 0.00 0.00 2.57
95 96 6.915300 CAGACTTGTACTCATCATGCTACTAC 59.085 42.308 0.00 0.00 0.00 2.73
96 97 6.603599 ACAGACTTGTACTCATCATGCTACTA 59.396 38.462 0.00 0.00 35.25 1.82
97 98 5.420421 ACAGACTTGTACTCATCATGCTACT 59.580 40.000 0.00 0.00 35.25 2.57
98 99 5.655488 ACAGACTTGTACTCATCATGCTAC 58.345 41.667 0.00 0.00 35.25 3.58
99 100 5.921962 ACAGACTTGTACTCATCATGCTA 57.078 39.130 0.00 0.00 35.25 3.49
100 101 4.815533 ACAGACTTGTACTCATCATGCT 57.184 40.909 0.00 0.00 35.25 3.79
101 102 6.968131 TTTACAGACTTGTACTCATCATGC 57.032 37.500 0.00 0.00 39.44 4.06
133 134 7.684670 CGTAGCTGAGCTGAAAAATAACAATA 58.315 34.615 18.79 0.00 40.10 1.90
160 161 9.796120 CATTAAAATCGGAGCCTTACATTAAAA 57.204 29.630 0.00 0.00 0.00 1.52
161 162 9.179909 TCATTAAAATCGGAGCCTTACATTAAA 57.820 29.630 0.00 0.00 0.00 1.52
162 163 8.740123 TCATTAAAATCGGAGCCTTACATTAA 57.260 30.769 0.00 0.00 0.00 1.40
163 164 8.918202 ATCATTAAAATCGGAGCCTTACATTA 57.082 30.769 0.00 0.00 0.00 1.90
164 165 7.721399 AGATCATTAAAATCGGAGCCTTACATT 59.279 33.333 0.00 0.00 0.00 2.71
166 167 6.483307 CAGATCATTAAAATCGGAGCCTTACA 59.517 38.462 0.00 0.00 0.00 2.41
167 168 6.566753 GCAGATCATTAAAATCGGAGCCTTAC 60.567 42.308 0.00 0.00 0.00 2.34
199 229 1.728971 GACTGAGATTGTGGCAACGAG 59.271 52.381 0.00 0.00 42.51 4.18
204 234 1.833630 CCCTAGACTGAGATTGTGGCA 59.166 52.381 0.00 0.00 0.00 4.92
205 235 1.474143 GCCCTAGACTGAGATTGTGGC 60.474 57.143 0.00 0.00 0.00 5.01
206 236 1.833630 TGCCCTAGACTGAGATTGTGG 59.166 52.381 0.00 0.00 0.00 4.17
222 252 1.376037 GCCAGTGACAGTACTGCCC 60.376 63.158 22.90 14.88 45.21 5.36
233 263 0.534873 TAATGCTACAGCGCCAGTGA 59.465 50.000 2.29 0.00 45.83 3.41
236 266 0.527600 TCGTAATGCTACAGCGCCAG 60.528 55.000 2.29 0.00 45.83 4.85
237 267 0.804544 GTCGTAATGCTACAGCGCCA 60.805 55.000 2.29 0.00 45.83 5.69
238 268 0.804544 TGTCGTAATGCTACAGCGCC 60.805 55.000 2.29 0.00 45.83 6.53
302 332 2.724174 GACGGCTGTTTTGTTATGTTGC 59.276 45.455 0.00 0.00 0.00 4.17
334 366 2.546778 TGTATTGACCGCGAGAAATCC 58.453 47.619 8.23 0.00 0.00 3.01
363 395 0.932399 GAGAGCCGAGACTAGTCGTC 59.068 60.000 17.07 13.26 43.17 4.20
364 396 0.538118 AGAGAGCCGAGACTAGTCGT 59.462 55.000 17.07 5.93 38.32 4.34
367 399 0.034960 TGCAGAGAGCCGAGACTAGT 60.035 55.000 0.00 0.00 44.83 2.57
369 401 1.769026 ATTGCAGAGAGCCGAGACTA 58.231 50.000 0.00 0.00 44.83 2.59
370 402 1.769026 TATTGCAGAGAGCCGAGACT 58.231 50.000 0.00 0.00 44.83 3.24
371 403 2.586258 TTATTGCAGAGAGCCGAGAC 57.414 50.000 0.00 0.00 44.83 3.36
372 404 3.827008 AATTATTGCAGAGAGCCGAGA 57.173 42.857 0.00 0.00 44.83 4.04
376 446 4.400567 AGACCAAAATTATTGCAGAGAGCC 59.599 41.667 0.00 0.00 44.83 4.70
381 451 7.336931 GGAAGTAGAGACCAAAATTATTGCAGA 59.663 37.037 0.00 0.00 0.00 4.26
405 475 0.179121 CTGTATGCAAGTACGCGGGA 60.179 55.000 12.47 0.00 33.35 5.14
407 477 0.921347 GACTGTATGCAAGTACGCGG 59.079 55.000 12.47 0.00 33.35 6.46
408 478 0.921347 GGACTGTATGCAAGTACGCG 59.079 55.000 3.53 3.53 33.35 6.01
409 479 1.659098 GTGGACTGTATGCAAGTACGC 59.341 52.381 0.00 0.00 0.00 4.42
410 480 2.666508 GTGTGGACTGTATGCAAGTACG 59.333 50.000 0.00 0.00 0.00 3.67
411 481 3.659786 TGTGTGGACTGTATGCAAGTAC 58.340 45.455 0.00 0.00 0.00 2.73
412 482 3.576550 TCTGTGTGGACTGTATGCAAGTA 59.423 43.478 0.00 0.00 0.00 2.24
433 4263 3.310501 GCAATGCATGGGCTTTATTTGTC 59.689 43.478 14.52 0.00 41.91 3.18
442 4272 3.142838 GACGGCAATGCATGGGCT 61.143 61.111 23.92 11.97 41.91 5.19
514 4348 1.360852 TCTCTCTCTGCCTCCTTCCTT 59.639 52.381 0.00 0.00 0.00 3.36
515 4349 1.006813 TCTCTCTCTGCCTCCTTCCT 58.993 55.000 0.00 0.00 0.00 3.36
521 4355 2.024918 CGCTCTCTCTCTCTGCCTC 58.975 63.158 0.00 0.00 0.00 4.70
538 4378 2.644078 GTTTTCAGTCTGCTTCAAGCG 58.356 47.619 4.57 0.00 46.26 4.68
566 4406 1.522900 CTCCCCCTCTCTCTCTCTCT 58.477 60.000 0.00 0.00 0.00 3.10
634 4821 6.209589 TCTCTCTCTCTCTCTACTGCTATCTC 59.790 46.154 0.00 0.00 0.00 2.75
635 4822 6.077993 TCTCTCTCTCTCTCTACTGCTATCT 58.922 44.000 0.00 0.00 0.00 1.98
636 4823 6.209589 TCTCTCTCTCTCTCTCTACTGCTATC 59.790 46.154 0.00 0.00 0.00 2.08
657 4846 0.251386 TGTGGCCTCGTCTCTTCTCT 60.251 55.000 3.32 0.00 0.00 3.10
659 4848 1.536943 GGTGTGGCCTCGTCTCTTCT 61.537 60.000 3.32 0.00 0.00 2.85
660 4849 1.079750 GGTGTGGCCTCGTCTCTTC 60.080 63.158 3.32 0.00 0.00 2.87
661 4850 1.837051 TGGTGTGGCCTCGTCTCTT 60.837 57.895 3.32 0.00 38.35 2.85
703 4892 4.495336 CTCTGCTGCTCGCTCGCT 62.495 66.667 0.00 0.00 40.11 4.93
705 4894 4.869440 CCCTCTGCTGCTCGCTCG 62.869 72.222 0.00 0.00 40.11 5.03
706 4895 4.527583 CCCCTCTGCTGCTCGCTC 62.528 72.222 0.00 0.00 40.11 5.03
708 4897 4.527583 CTCCCCTCTGCTGCTCGC 62.528 72.222 0.00 0.00 39.77 5.03
709 4898 2.757508 TCTCCCCTCTGCTGCTCG 60.758 66.667 0.00 0.00 0.00 5.03
710 4899 1.381056 TCTCTCCCCTCTGCTGCTC 60.381 63.158 0.00 0.00 0.00 4.26
711 4900 1.381599 CTCTCTCCCCTCTGCTGCT 60.382 63.158 0.00 0.00 0.00 4.24
712 4901 1.381056 TCTCTCTCCCCTCTGCTGC 60.381 63.158 0.00 0.00 0.00 5.25
713 4902 0.258484 TCTCTCTCTCCCCTCTGCTG 59.742 60.000 0.00 0.00 0.00 4.41
714 4903 0.552848 CTCTCTCTCTCCCCTCTGCT 59.447 60.000 0.00 0.00 0.00 4.24
715 4904 0.550914 TCTCTCTCTCTCCCCTCTGC 59.449 60.000 0.00 0.00 0.00 4.26
716 4905 2.105477 CTCTCTCTCTCTCTCCCCTCTG 59.895 59.091 0.00 0.00 0.00 3.35
721 4910 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
819 5008 4.016851 AGAGTATACAACAGGGTACAGGGA 60.017 45.833 5.50 0.00 0.00 4.20
823 5014 6.069556 AGAGAGAGAGTATACAACAGGGTACA 60.070 42.308 5.50 0.00 0.00 2.90
839 5030 2.101415 TGCGAGAGAGAGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
840 5031 2.107366 TGCGAGAGAGAGAGAGAGAGA 58.893 52.381 0.00 0.00 0.00 3.10
841 5032 2.205074 GTGCGAGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 0.00 3.20
842 5033 1.470805 CGTGCGAGAGAGAGAGAGAGA 60.471 57.143 0.00 0.00 0.00 3.10
843 5034 0.930310 CGTGCGAGAGAGAGAGAGAG 59.070 60.000 0.00 0.00 0.00 3.20
844 5035 1.087202 GCGTGCGAGAGAGAGAGAGA 61.087 60.000 0.00 0.00 0.00 3.10
845 5036 1.351707 GCGTGCGAGAGAGAGAGAG 59.648 63.158 0.00 0.00 0.00 3.20
846 5037 2.109739 GGCGTGCGAGAGAGAGAGA 61.110 63.158 0.00 0.00 0.00 3.10
847 5038 2.321668 CTGGCGTGCGAGAGAGAGAG 62.322 65.000 0.00 0.00 0.00 3.20
848 5039 2.359975 TGGCGTGCGAGAGAGAGA 60.360 61.111 0.00 0.00 0.00 3.10
874 5066 1.230497 CTCCCTCCCTCGCTTCCTA 59.770 63.158 0.00 0.00 0.00 2.94
878 5070 3.684628 TCCCTCCCTCCCTCGCTT 61.685 66.667 0.00 0.00 0.00 4.68
887 5079 3.773154 GGCTCTCCCTCCCTCCCT 61.773 72.222 0.00 0.00 0.00 4.20
888 5080 4.095400 TGGCTCTCCCTCCCTCCC 62.095 72.222 0.00 0.00 0.00 4.30
889 5081 2.766229 GTGGCTCTCCCTCCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
890 5082 1.383803 ATGTGGCTCTCCCTCCCTC 60.384 63.158 0.00 0.00 0.00 4.30
1470 5687 2.186903 GAGAATCCGAAGCCGCCA 59.813 61.111 0.00 0.00 0.00 5.69
1601 5818 2.768492 GCCGAGGATGCTTTGCTGG 61.768 63.158 0.00 0.00 0.00 4.85
1698 5915 2.615288 CCCAGGAGAGGGGGCTTT 60.615 66.667 0.00 0.00 45.60 3.51
1743 5960 2.499685 GGCGGCTGGTACTGGTAG 59.500 66.667 0.00 0.00 0.00 3.18
1792 6021 1.757118 GTTGTGATCGGAGATGGAGGA 59.243 52.381 0.00 0.00 45.12 3.71
1794 6023 1.482182 TGGTTGTGATCGGAGATGGAG 59.518 52.381 0.00 0.00 45.12 3.86
1798 6027 0.179100 CGCTGGTTGTGATCGGAGAT 60.179 55.000 0.00 0.00 45.12 2.75
1881 6110 2.388232 CGTGCCTAGGTGGTTTCGC 61.388 63.158 11.31 0.00 38.35 4.70
1938 6167 3.706373 GGCTGGAGCTGGAACGGA 61.706 66.667 0.00 0.00 41.70 4.69
2433 6662 1.081641 CAGCTTCAGCAACGGCAAG 60.082 57.895 0.75 0.00 45.16 4.01
2622 6851 1.062488 AACCAACAGGGAGGCTCACT 61.062 55.000 15.01 15.01 41.15 3.41
2742 6971 0.827925 AGTGCTGTGAGAACGGGAGA 60.828 55.000 0.00 0.00 0.00 3.71
2916 7145 0.664166 CAGCAAACACATTCCGCCAC 60.664 55.000 0.00 0.00 0.00 5.01
3759 7997 5.942826 GGATCAAAAGAGGCCCTATTCTATG 59.057 44.000 0.00 0.00 0.00 2.23
3819 8057 6.645790 AGATGAGCATGACATTTTAATCCC 57.354 37.500 0.00 0.00 0.00 3.85
3852 8090 6.601741 TGCAATCAAACAACCAAAAATCTC 57.398 33.333 0.00 0.00 0.00 2.75
3905 8143 5.241728 GGTTTCTAGCATCCACTCAAACTTT 59.758 40.000 0.00 0.00 0.00 2.66
3986 8224 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
3987 8225 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
3988 8226 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
3989 8227 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
3990 8228 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
4056 8301 7.537596 TGTTGGTTGTTTGATTCATAGGATT 57.462 32.000 0.00 0.00 0.00 3.01



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

AutoCloner maintained by Alex Coulton.