Multiple sequence alignment - TraesCS5B01G409900

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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 TraesCS5B01G409900 chr5B 100.000 2664 0 0 468 3131 584999850 585002513 0.000000e+00 4920.0
1 TraesCS5B01G409900 chr5B 100.000 201 0 0 1 201 584999383 584999583 3.810000e-99 372.0
2 TraesCS5B01G409900 chr5B 94.167 120 7 0 2 121 297082445 297082564 1.920000e-42 183.0
3 TraesCS5B01G409900 chr5A 96.147 2336 85 5 667 2999 596559815 596562148 0.000000e+00 3810.0
4 TraesCS5B01G409900 chr5A 92.562 121 9 0 1 121 365049427 365049547 1.150000e-39 174.0
5 TraesCS5B01G409900 chr5A 95.652 92 4 0 3040 3131 596562145 596562236 7.000000e-32 148.0
6 TraesCS5B01G409900 chr5A 91.026 78 7 0 120 197 596559387 596559464 4.270000e-19 106.0
7 TraesCS5B01G409900 chr5D 94.388 2477 102 13 667 3128 477328266 477330720 0.000000e+00 3770.0
8 TraesCS5B01G409900 chr5D 96.933 163 4 1 468 629 477328017 477328179 3.980000e-69 272.0
9 TraesCS5B01G409900 chr5D 93.902 82 5 0 120 201 477327873 477327954 1.180000e-24 124.0
10 TraesCS5B01G409900 chr7A 93.388 121 8 0 1 121 645447835 645447955 2.480000e-41 180.0
11 TraesCS5B01G409900 chr7A 92.562 121 9 0 1 121 119956749 119956629 1.150000e-39 174.0
12 TraesCS5B01G409900 chr7A 92.562 121 9 0 1 121 195351430 195351310 1.150000e-39 174.0
13 TraesCS5B01G409900 chr7A 92.562 121 9 0 1 121 488808551 488808431 1.150000e-39 174.0
14 TraesCS5B01G409900 chr6A 93.388 121 8 0 1 121 568155747 568155867 2.480000e-41 180.0
15 TraesCS5B01G409900 chr3A 93.388 121 8 0 1 121 370091144 370091264 2.480000e-41 180.0
16 TraesCS5B01G409900 chr1B 92.562 121 9 0 1 121 539154462 539154342 1.150000e-39 174.0
17 TraesCS5B01G409900 chr3B 96.875 32 0 1 171 201 384311241 384311210 6.000000e-03 52.8


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 TraesCS5B01G409900 chr5B 584999383 585002513 3130 False 2646.000000 4920 100.000000 1 3131 2 chr5B.!!$F2 3130
1 TraesCS5B01G409900 chr5A 596559387 596562236 2849 False 1354.666667 3810 94.275000 120 3131 3 chr5A.!!$F2 3011
2 TraesCS5B01G409900 chr5D 477327873 477330720 2847 False 1388.666667 3770 95.074333 120 3128 3 chr5D.!!$F1 3008

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
631 678 1.067974 CAATCGGCCCGGCGATATATA 59.932 52.381 23.99 0.00 0.0 0.86 F
632 679 1.629043 ATCGGCCCGGCGATATATAT 58.371 50.000 22.72 0.38 0.0 0.86 F
775 877 1.942677 TTCGTCACGCTGGAAAAAGA 58.057 45.000 0.00 0.00 0.0 2.52 F
1566 1673 2.338620 GTTGCAACGGGAAAGGGC 59.661 61.111 14.90 0.00 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1838 0.249868 TCACCAAAGTCTCCACTGCG 60.250 55.000 0.0 0.0 31.06 5.18 R
1802 1909 0.609151 TCCATTGCTGTTGCCATTGG 59.391 50.000 0.0 0.0 38.71 3.16 R
2112 2219 1.534163 GTTCAAGCGGTAACCAGGAAC 59.466 52.381 0.0 0.0 0.00 3.62 R
2817 2934 4.469945 AGACGGAGGAACTGAAATCCAATA 59.530 41.667 0.0 0.0 41.55 1.90 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
59 60 8.601243 AACATAATTTGTTTAGAAAGCGATCG 57.399 30.769 11.69 11.69 46.51 3.69
60 61 7.748847 ACATAATTTGTTTAGAAAGCGATCGT 58.251 30.769 17.81 0.26 33.74 3.73
61 62 8.875803 ACATAATTTGTTTAGAAAGCGATCGTA 58.124 29.630 17.81 0.00 33.74 3.43
62 63 9.697250 CATAATTTGTTTAGAAAGCGATCGTAA 57.303 29.630 17.81 3.98 0.00 3.18
63 64 9.916397 ATAATTTGTTTAGAAAGCGATCGTAAG 57.084 29.630 17.81 0.00 0.00 2.34
77 78 3.003394 TCGTAAGATTACCTCGGGTGA 57.997 47.619 5.90 0.00 45.01 4.02
78 79 3.559069 TCGTAAGATTACCTCGGGTGAT 58.441 45.455 5.90 3.33 45.01 3.06
79 80 3.317149 TCGTAAGATTACCTCGGGTGATG 59.683 47.826 5.30 0.00 45.01 3.07
80 81 3.317149 CGTAAGATTACCTCGGGTGATGA 59.683 47.826 5.30 0.00 36.23 2.92
81 82 4.202080 CGTAAGATTACCTCGGGTGATGAA 60.202 45.833 5.30 0.00 36.23 2.57
82 83 5.509163 CGTAAGATTACCTCGGGTGATGAAT 60.509 44.000 5.30 0.00 36.23 2.57
83 84 6.294342 CGTAAGATTACCTCGGGTGATGAATA 60.294 42.308 5.30 0.00 36.23 1.75
84 85 6.494666 AAGATTACCTCGGGTGATGAATAA 57.505 37.500 5.30 0.00 36.19 1.40
85 86 5.855045 AGATTACCTCGGGTGATGAATAAC 58.145 41.667 5.30 0.00 36.19 1.89
86 87 5.602978 AGATTACCTCGGGTGATGAATAACT 59.397 40.000 5.30 0.00 36.19 2.24
87 88 5.687166 TTACCTCGGGTGATGAATAACTT 57.313 39.130 5.90 0.00 36.19 2.66
88 89 6.795144 TTACCTCGGGTGATGAATAACTTA 57.205 37.500 5.90 0.00 36.19 2.24
89 90 5.888982 ACCTCGGGTGATGAATAACTTAT 57.111 39.130 0.00 0.00 32.98 1.73
90 91 6.248569 ACCTCGGGTGATGAATAACTTATT 57.751 37.500 0.00 0.00 32.98 1.40
91 92 6.055588 ACCTCGGGTGATGAATAACTTATTG 58.944 40.000 0.00 0.00 32.98 1.90
92 93 6.055588 CCTCGGGTGATGAATAACTTATTGT 58.944 40.000 0.00 0.00 0.00 2.71
93 94 6.202954 CCTCGGGTGATGAATAACTTATTGTC 59.797 42.308 0.00 0.00 0.00 3.18
94 95 6.053005 TCGGGTGATGAATAACTTATTGTCC 58.947 40.000 0.00 0.00 0.00 4.02
95 96 5.820423 CGGGTGATGAATAACTTATTGTCCA 59.180 40.000 0.00 0.00 0.00 4.02
96 97 6.238374 CGGGTGATGAATAACTTATTGTCCAC 60.238 42.308 0.00 4.28 0.00 4.02
97 98 6.039382 GGGTGATGAATAACTTATTGTCCACC 59.961 42.308 17.50 17.50 36.97 4.61
98 99 6.039382 GGTGATGAATAACTTATTGTCCACCC 59.961 42.308 16.22 6.48 34.56 4.61
99 100 6.828785 GTGATGAATAACTTATTGTCCACCCT 59.171 38.462 0.00 0.00 0.00 4.34
100 101 6.828273 TGATGAATAACTTATTGTCCACCCTG 59.172 38.462 0.00 0.00 0.00 4.45
101 102 6.381498 TGAATAACTTATTGTCCACCCTGA 57.619 37.500 0.00 0.00 0.00 3.86
102 103 6.414732 TGAATAACTTATTGTCCACCCTGAG 58.585 40.000 0.00 0.00 0.00 3.35
103 104 6.012858 TGAATAACTTATTGTCCACCCTGAGT 60.013 38.462 0.00 0.00 0.00 3.41
104 105 3.703001 ACTTATTGTCCACCCTGAGTG 57.297 47.619 0.00 0.00 46.83 3.51
118 119 5.978814 ACCCTGAGTGATGAATAGTAACAC 58.021 41.667 0.00 0.00 0.00 3.32
132 133 8.111545 TGAATAGTAACACTACTCCCTCTGTTA 58.888 37.037 0.00 0.00 39.23 2.41
133 134 7.878547 ATAGTAACACTACTCCCTCTGTTAC 57.121 40.000 10.27 10.27 44.85 2.50
197 198 2.544844 TGGAACGGAGGGAGTAGAAT 57.455 50.000 0.00 0.00 0.00 2.40
199 200 3.178865 TGGAACGGAGGGAGTAGAATTT 58.821 45.455 0.00 0.00 0.00 1.82
529 537 8.017946 CCTTAGAAGCTGATGTTTTACAAGTTC 58.982 37.037 0.00 0.00 0.00 3.01
561 602 5.119125 GGAATGATGTTTTACAAAGCTGCAC 59.881 40.000 1.02 0.00 0.00 4.57
629 676 1.216977 CAATCGGCCCGGCGATATA 59.783 57.895 23.99 0.00 0.00 0.86
631 678 1.067974 CAATCGGCCCGGCGATATATA 59.932 52.381 23.99 0.00 0.00 0.86
632 679 1.629043 ATCGGCCCGGCGATATATAT 58.371 50.000 22.72 0.38 0.00 0.86
633 680 2.275134 TCGGCCCGGCGATATATATA 57.725 50.000 9.30 0.00 0.00 0.86
647 706 6.399039 GCGATATATATATTTGCGAGAAGGCG 60.399 42.308 13.59 6.95 35.06 5.52
652 711 4.732285 ATATTTGCGAGAAGGCGTTATG 57.268 40.909 0.00 0.00 35.06 1.90
654 713 2.658373 TTGCGAGAAGGCGTTATGTA 57.342 45.000 0.00 0.00 35.06 2.29
656 715 3.994204 TGCGAGAAGGCGTTATGTATA 57.006 42.857 0.00 0.00 35.06 1.47
659 718 3.913163 GCGAGAAGGCGTTATGTATAGTC 59.087 47.826 0.00 0.00 0.00 2.59
660 719 4.474113 CGAGAAGGCGTTATGTATAGTCC 58.526 47.826 0.00 0.00 0.00 3.85
661 720 4.023450 CGAGAAGGCGTTATGTATAGTCCA 60.023 45.833 0.00 0.00 0.00 4.02
662 721 5.335740 CGAGAAGGCGTTATGTATAGTCCAT 60.336 44.000 0.00 0.00 0.00 3.41
663 722 6.128090 CGAGAAGGCGTTATGTATAGTCCATA 60.128 42.308 0.00 0.00 0.00 2.74
664 723 7.415318 CGAGAAGGCGTTATGTATAGTCCATAT 60.415 40.741 0.00 0.00 0.00 1.78
775 877 1.942677 TTCGTCACGCTGGAAAAAGA 58.057 45.000 0.00 0.00 0.00 2.52
776 878 1.942677 TCGTCACGCTGGAAAAAGAA 58.057 45.000 0.00 0.00 0.00 2.52
893 996 4.471726 CGACTCCGCCGCGTAACT 62.472 66.667 12.58 0.00 0.00 2.24
1308 1415 4.436998 GAGGTCTCCGCCACCGTG 62.437 72.222 0.00 0.00 39.13 4.94
1566 1673 2.338620 GTTGCAACGGGAAAGGGC 59.661 61.111 14.90 0.00 0.00 5.19
1653 1760 8.034313 ACAAGACCATACACATCAATACCTAT 57.966 34.615 0.00 0.00 0.00 2.57
1731 1838 2.584791 CTTGTTTCAGTATGCAACGGC 58.415 47.619 0.00 0.00 45.33 5.68
1787 1894 6.426646 AGTTATCTCCAAGGCCAATAGTAG 57.573 41.667 5.01 0.00 0.00 2.57
1788 1895 5.308237 AGTTATCTCCAAGGCCAATAGTAGG 59.692 44.000 5.01 0.00 0.00 3.18
2112 2219 2.414559 GCATGTGTTGAATGGAACTCGG 60.415 50.000 0.00 0.00 0.00 4.63
2357 2465 1.021202 TGAGAAAGTGTGTTTGCGGG 58.979 50.000 0.00 0.00 0.00 6.13
2462 2570 7.250569 TCATCAATATCGAAAGTTTTTCTGGC 58.749 34.615 0.00 0.00 0.00 4.85
2546 2654 8.731275 TGTTTTTCAACTATCTTCTGTTCTCA 57.269 30.769 0.00 0.00 33.58 3.27
2619 2728 7.336427 TGAATGCTTTGTTTGGATTCAAAGTTT 59.664 29.630 15.60 11.14 44.86 2.66
2694 2803 5.191124 TCCATCCTGTGTAGTGTACTAGAGA 59.809 44.000 0.00 0.00 0.00 3.10
2702 2811 9.344772 CTGTGTAGTGTACTAGAGATTCCTAAT 57.655 37.037 0.00 0.00 0.00 1.73
2756 2865 9.903682 CATATTGAATGGGATCTTACAAACATC 57.096 33.333 0.00 0.00 0.00 3.06
2758 2867 7.959658 TTGAATGGGATCTTACAAACATCAT 57.040 32.000 0.00 0.00 0.00 2.45
2795 2904 2.173519 CATTGTCCCATGAAAGTGCCT 58.826 47.619 0.00 0.00 0.00 4.75
2817 2934 8.058847 TGCCTCCCAAAGATAAAATACTAACAT 58.941 33.333 0.00 0.00 0.00 2.71
2861 2978 7.010183 CCGTCTTAGTTTACATGATACAGTTGG 59.990 40.741 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 7.748847 ACGATCGCTTTCTAAACAAATTATGT 58.251 30.769 16.60 0.00 46.82 2.29
36 37 9.697250 TTACGATCGCTTTCTAAACAAATTATG 57.303 29.630 16.60 0.00 0.00 1.90
37 38 9.916397 CTTACGATCGCTTTCTAAACAAATTAT 57.084 29.630 16.60 0.00 0.00 1.28
38 39 9.142515 TCTTACGATCGCTTTCTAAACAAATTA 57.857 29.630 16.60 0.00 0.00 1.40
39 40 8.025243 TCTTACGATCGCTTTCTAAACAAATT 57.975 30.769 16.60 0.00 0.00 1.82
40 41 7.591006 TCTTACGATCGCTTTCTAAACAAAT 57.409 32.000 16.60 0.00 0.00 2.32
41 42 7.591006 ATCTTACGATCGCTTTCTAAACAAA 57.409 32.000 16.60 0.00 0.00 2.83
42 43 7.591006 AATCTTACGATCGCTTTCTAAACAA 57.409 32.000 16.60 0.00 0.00 2.83
43 44 7.221452 GGTAATCTTACGATCGCTTTCTAAACA 59.779 37.037 16.60 0.00 34.50 2.83
44 45 7.434602 AGGTAATCTTACGATCGCTTTCTAAAC 59.565 37.037 16.60 5.11 34.50 2.01
45 46 7.486647 AGGTAATCTTACGATCGCTTTCTAAA 58.513 34.615 16.60 0.00 34.50 1.85
46 47 7.035840 AGGTAATCTTACGATCGCTTTCTAA 57.964 36.000 16.60 4.99 34.50 2.10
47 48 6.565435 CGAGGTAATCTTACGATCGCTTTCTA 60.565 42.308 16.60 0.00 37.02 2.10
48 49 5.517322 AGGTAATCTTACGATCGCTTTCT 57.483 39.130 16.60 0.00 34.50 2.52
49 50 4.379204 CGAGGTAATCTTACGATCGCTTTC 59.621 45.833 16.60 0.00 37.02 2.62
50 51 4.288531 CGAGGTAATCTTACGATCGCTTT 58.711 43.478 16.60 4.55 37.02 3.51
51 52 3.304525 CCGAGGTAATCTTACGATCGCTT 60.305 47.826 16.60 0.00 39.81 4.68
52 53 2.225963 CCGAGGTAATCTTACGATCGCT 59.774 50.000 16.60 5.20 39.81 4.93
53 54 2.582687 CCGAGGTAATCTTACGATCGC 58.417 52.381 16.60 0.00 39.81 4.58
54 55 2.551459 ACCCGAGGTAATCTTACGATCG 59.449 50.000 14.88 14.88 40.33 3.69
55 56 3.567164 TCACCCGAGGTAATCTTACGATC 59.433 47.826 0.00 0.00 32.11 3.69
56 57 3.559069 TCACCCGAGGTAATCTTACGAT 58.441 45.455 0.00 0.00 32.11 3.73
57 58 3.003394 TCACCCGAGGTAATCTTACGA 57.997 47.619 0.00 0.00 32.11 3.43
58 59 3.317149 TCATCACCCGAGGTAATCTTACG 59.683 47.826 0.00 0.00 32.11 3.18
59 60 4.931661 TCATCACCCGAGGTAATCTTAC 57.068 45.455 0.00 0.00 32.11 2.34
60 61 7.289317 AGTTATTCATCACCCGAGGTAATCTTA 59.711 37.037 0.00 0.00 32.11 2.10
61 62 6.099845 AGTTATTCATCACCCGAGGTAATCTT 59.900 38.462 0.00 0.00 32.11 2.40
62 63 5.602978 AGTTATTCATCACCCGAGGTAATCT 59.397 40.000 0.00 0.00 32.11 2.40
63 64 5.855045 AGTTATTCATCACCCGAGGTAATC 58.145 41.667 0.00 0.00 32.11 1.75
64 65 5.888982 AGTTATTCATCACCCGAGGTAAT 57.111 39.130 0.00 0.00 32.11 1.89
65 66 5.687166 AAGTTATTCATCACCCGAGGTAA 57.313 39.130 0.00 0.00 32.11 2.85
66 67 6.989155 ATAAGTTATTCATCACCCGAGGTA 57.011 37.500 0.00 0.00 32.11 3.08
67 68 5.888982 ATAAGTTATTCATCACCCGAGGT 57.111 39.130 0.00 0.00 35.62 3.85
68 69 6.055588 ACAATAAGTTATTCATCACCCGAGG 58.944 40.000 5.10 0.00 0.00 4.63
69 70 6.202954 GGACAATAAGTTATTCATCACCCGAG 59.797 42.308 5.10 0.00 0.00 4.63
70 71 6.053005 GGACAATAAGTTATTCATCACCCGA 58.947 40.000 5.10 0.00 0.00 5.14
71 72 5.820423 TGGACAATAAGTTATTCATCACCCG 59.180 40.000 5.10 0.00 0.00 5.28
72 73 6.039382 GGTGGACAATAAGTTATTCATCACCC 59.961 42.308 23.79 15.85 35.04 4.61
73 74 6.039382 GGGTGGACAATAAGTTATTCATCACC 59.961 42.308 24.93 24.93 37.44 4.02
74 75 6.828785 AGGGTGGACAATAAGTTATTCATCAC 59.171 38.462 5.10 12.14 0.00 3.06
75 76 6.828273 CAGGGTGGACAATAAGTTATTCATCA 59.172 38.462 5.10 2.06 0.00 3.07
76 77 7.054124 TCAGGGTGGACAATAAGTTATTCATC 58.946 38.462 5.10 6.52 0.00 2.92
77 78 6.969043 TCAGGGTGGACAATAAGTTATTCAT 58.031 36.000 5.10 0.00 0.00 2.57
78 79 6.012858 ACTCAGGGTGGACAATAAGTTATTCA 60.013 38.462 5.10 0.00 0.00 2.57
79 80 6.316390 CACTCAGGGTGGACAATAAGTTATTC 59.684 42.308 5.10 0.00 41.90 1.75
80 81 6.012858 TCACTCAGGGTGGACAATAAGTTATT 60.013 38.462 0.00 2.10 45.38 1.40
81 82 5.487488 TCACTCAGGGTGGACAATAAGTTAT 59.513 40.000 0.00 0.00 45.38 1.89
82 83 4.841813 TCACTCAGGGTGGACAATAAGTTA 59.158 41.667 0.00 0.00 45.38 2.24
83 84 3.650942 TCACTCAGGGTGGACAATAAGTT 59.349 43.478 0.00 0.00 45.38 2.66
84 85 3.248024 TCACTCAGGGTGGACAATAAGT 58.752 45.455 0.00 0.00 45.38 2.24
85 86 3.981071 TCACTCAGGGTGGACAATAAG 57.019 47.619 0.00 0.00 45.38 1.73
86 87 3.843619 TCATCACTCAGGGTGGACAATAA 59.156 43.478 0.00 0.00 45.38 1.40
87 88 3.449918 TCATCACTCAGGGTGGACAATA 58.550 45.455 0.00 0.00 45.38 1.90
88 89 2.269023 TCATCACTCAGGGTGGACAAT 58.731 47.619 0.00 0.00 45.38 2.71
89 90 1.728323 TCATCACTCAGGGTGGACAA 58.272 50.000 0.00 0.00 45.38 3.18
90 91 1.728323 TTCATCACTCAGGGTGGACA 58.272 50.000 0.00 0.00 45.38 4.02
91 92 3.452627 ACTATTCATCACTCAGGGTGGAC 59.547 47.826 0.00 0.00 45.38 4.02
92 93 3.724478 ACTATTCATCACTCAGGGTGGA 58.276 45.455 0.00 0.00 45.38 4.02
93 94 5.104941 TGTTACTATTCATCACTCAGGGTGG 60.105 44.000 0.00 0.00 45.38 4.61
94 95 5.812642 GTGTTACTATTCATCACTCAGGGTG 59.187 44.000 0.00 0.00 46.60 4.61
95 96 5.721960 AGTGTTACTATTCATCACTCAGGGT 59.278 40.000 0.00 0.00 34.87 4.34
96 97 6.227298 AGTGTTACTATTCATCACTCAGGG 57.773 41.667 0.00 0.00 34.87 4.45
97 98 8.001881 AGTAGTGTTACTATTCATCACTCAGG 57.998 38.462 0.00 0.00 38.35 3.86
98 99 8.132362 GGAGTAGTGTTACTATTCATCACTCAG 58.868 40.741 11.81 0.00 38.65 3.35
99 100 7.068348 GGGAGTAGTGTTACTATTCATCACTCA 59.932 40.741 11.81 0.00 38.65 3.41
100 101 7.285858 AGGGAGTAGTGTTACTATTCATCACTC 59.714 40.741 11.81 5.83 38.65 3.51
101 102 7.126733 AGGGAGTAGTGTTACTATTCATCACT 58.873 38.462 11.81 0.00 38.65 3.41
102 103 7.285858 AGAGGGAGTAGTGTTACTATTCATCAC 59.714 40.741 11.81 0.00 38.65 3.06
103 104 7.285629 CAGAGGGAGTAGTGTTACTATTCATCA 59.714 40.741 11.81 0.00 38.65 3.07
104 105 7.285858 ACAGAGGGAGTAGTGTTACTATTCATC 59.714 40.741 11.81 9.38 38.65 2.92
105 106 7.126733 ACAGAGGGAGTAGTGTTACTATTCAT 58.873 38.462 11.81 2.50 38.65 2.57
106 107 6.491383 ACAGAGGGAGTAGTGTTACTATTCA 58.509 40.000 11.81 0.00 38.65 2.57
107 108 7.407393 AACAGAGGGAGTAGTGTTACTATTC 57.593 40.000 3.68 3.68 40.21 1.75
108 109 8.291191 GTAACAGAGGGAGTAGTGTTACTATT 57.709 38.462 14.15 0.00 46.15 1.73
109 110 7.878547 GTAACAGAGGGAGTAGTGTTACTAT 57.121 40.000 14.15 0.00 46.15 2.12
113 114 8.834004 ATTATGTAACAGAGGGAGTAGTGTTA 57.166 34.615 0.00 0.00 34.92 2.41
114 115 7.735326 ATTATGTAACAGAGGGAGTAGTGTT 57.265 36.000 0.00 0.00 37.00 3.32
115 116 7.735326 AATTATGTAACAGAGGGAGTAGTGT 57.265 36.000 0.00 0.00 0.00 3.55
116 117 9.698309 CATAATTATGTAACAGAGGGAGTAGTG 57.302 37.037 16.03 0.00 0.00 2.74
117 118 8.871125 CCATAATTATGTAACAGAGGGAGTAGT 58.129 37.037 21.20 0.00 31.82 2.73
118 119 8.871125 ACCATAATTATGTAACAGAGGGAGTAG 58.129 37.037 21.20 5.49 31.82 2.57
132 133 8.806146 GGCCTAAAATCATGACCATAATTATGT 58.194 33.333 21.20 11.26 31.82 2.29
133 134 8.805175 TGGCCTAAAATCATGACCATAATTATG 58.195 33.333 17.11 17.11 0.00 1.90
156 157 7.826690 TCCATAGAGTTTAGTTCAAATTTGGC 58.173 34.615 17.90 11.16 0.00 4.52
498 506 5.573337 AAACATCAGCTTCTAAGGCATTC 57.427 39.130 0.00 0.00 0.00 2.67
561 602 0.457443 TCTGTCTCTACATGCAGGCG 59.543 55.000 0.00 0.00 34.37 5.52
629 676 5.932303 ACATAACGCCTTCTCGCAAATATAT 59.068 36.000 0.00 0.00 0.00 0.86
631 678 4.127171 ACATAACGCCTTCTCGCAAATAT 58.873 39.130 0.00 0.00 0.00 1.28
632 679 3.527533 ACATAACGCCTTCTCGCAAATA 58.472 40.909 0.00 0.00 0.00 1.40
633 680 2.356135 ACATAACGCCTTCTCGCAAAT 58.644 42.857 0.00 0.00 0.00 2.32
652 711 7.434492 AGCCGCAATATGTATATGGACTATAC 58.566 38.462 0.00 0.00 41.74 1.47
654 713 6.098266 TGAGCCGCAATATGTATATGGACTAT 59.902 38.462 0.00 0.00 0.00 2.12
656 715 4.222810 TGAGCCGCAATATGTATATGGACT 59.777 41.667 0.00 0.00 0.00 3.85
659 718 3.306973 CGTGAGCCGCAATATGTATATGG 59.693 47.826 0.00 0.00 0.00 2.74
660 719 4.173256 TCGTGAGCCGCAATATGTATATG 58.827 43.478 0.00 0.00 36.19 1.78
661 720 4.450082 TCGTGAGCCGCAATATGTATAT 57.550 40.909 0.00 0.00 36.19 0.86
662 721 3.926821 TCGTGAGCCGCAATATGTATA 57.073 42.857 0.00 0.00 36.19 1.47
663 722 2.812358 TCGTGAGCCGCAATATGTAT 57.188 45.000 0.00 0.00 36.19 2.29
664 723 2.469826 CTTCGTGAGCCGCAATATGTA 58.530 47.619 0.00 0.00 36.19 2.29
893 996 1.298340 CTGCCGTGATGGGTTGGTA 59.702 57.895 0.00 0.00 38.63 3.25
1194 1301 4.816984 TCGGAGGAGACGAGGGCC 62.817 72.222 0.00 0.00 35.12 5.80
1230 1337 3.098377 GAGCTCGTCGGAGTCGGAC 62.098 68.421 18.32 18.32 42.53 4.79
1566 1673 0.745845 AGCTGCTAATCGCCTTGTGG 60.746 55.000 0.00 0.00 38.05 4.17
1653 1760 1.593787 CCCTTCGAAGAGCTGCTCA 59.406 57.895 29.49 7.87 38.43 4.26
1731 1838 0.249868 TCACCAAAGTCTCCACTGCG 60.250 55.000 0.00 0.00 31.06 5.18
1787 1894 3.795877 CCATTGGCATTGTTATCCAACC 58.204 45.455 8.42 0.00 42.02 3.77
1802 1909 0.609151 TCCATTGCTGTTGCCATTGG 59.391 50.000 0.00 0.00 38.71 3.16
1893 2000 6.403866 ACATCAAGCACAAAATTCCTGTTA 57.596 33.333 0.00 0.00 0.00 2.41
2112 2219 1.534163 GTTCAAGCGGTAACCAGGAAC 59.466 52.381 0.00 0.00 0.00 3.62
2357 2465 7.775120 ACAACACATCTCCATTCCAAATAATC 58.225 34.615 0.00 0.00 0.00 1.75
2462 2570 7.716612 AGAAAACAAGACAATTAGGAAACCAG 58.283 34.615 0.00 0.00 0.00 4.00
2538 2646 6.965500 GCTATGTTTGACATCATTGAGAACAG 59.035 38.462 0.00 0.00 39.88 3.16
2546 2654 7.067494 GGAGGTTAAGCTATGTTTGACATCATT 59.933 37.037 7.26 0.00 39.88 2.57
2653 2762 8.061304 ACAGGATGGATAAAAGGTTGTTATCAT 58.939 33.333 6.53 0.00 43.62 2.45
2658 2767 5.393866 ACACAGGATGGATAAAAGGTTGTT 58.606 37.500 0.00 0.00 43.62 2.83
2666 2775 8.057011 TCTAGTACACTACACAGGATGGATAAA 58.943 37.037 0.00 0.00 43.62 1.40
2756 2865 5.235831 ACAATGCATCGACATCACTAGAATG 59.764 40.000 0.00 2.45 0.00 2.67
2758 2867 4.758688 ACAATGCATCGACATCACTAGAA 58.241 39.130 0.00 0.00 0.00 2.10
2817 2934 4.469945 AGACGGAGGAACTGAAATCCAATA 59.530 41.667 0.00 0.00 41.55 1.90
2861 2978 6.912591 CACCAGTATGTCAAAAACTGTTTCTC 59.087 38.462 6.20 0.00 39.17 2.87


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

AutoCloner maintained by Alex Coulton.