Multiple sequence alignment - TraesCS7B01G470800

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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 TraesCS7B01G470800 chr7B 100.000 2868 0 0 1 2868 727187269 727184402 0.000000e+00 5297.0
1 TraesCS7B01G470800 chr7B 89.066 1628 114 36 793 2414 727391883 727393452 0.000000e+00 1962.0
2 TraesCS7B01G470800 chr7B 89.700 767 60 11 1995 2760 727326707 727325959 0.000000e+00 961.0
3 TraesCS7B01G470800 chr7B 84.314 918 79 22 794 1686 727328416 727327539 0.000000e+00 837.0
4 TraesCS7B01G470800 chr7B 78.577 1237 183 41 814 1995 727381898 727380689 0.000000e+00 741.0
5 TraesCS7B01G470800 chr7B 82.562 843 122 15 1000 1819 727654097 727653257 0.000000e+00 719.0
6 TraesCS7B01G470800 chr7B 83.051 708 88 24 78 774 727390970 727391656 5.250000e-172 614.0
7 TraesCS7B01G470800 chr7B 77.070 1208 188 44 846 1994 727397572 727398749 5.250000e-172 614.0
8 TraesCS7B01G470800 chr7B 86.783 401 20 6 1698 2090 727327052 727326677 1.590000e-112 416.0
9 TraesCS7B01G470800 chr7B 86.810 326 33 4 2474 2791 727393474 727393797 3.510000e-94 355.0
10 TraesCS7B01G470800 chr7B 76.327 735 106 38 1993 2721 727409502 727410174 5.920000e-87 331.0
11 TraesCS7B01G470800 chr7B 81.389 360 38 12 1661 1991 727683475 727683116 1.690000e-67 267.0
12 TraesCS7B01G470800 chr7B 93.750 160 10 0 2709 2868 727393879 727394038 1.030000e-59 241.0
13 TraesCS7B01G470800 chr7B 93.976 83 5 0 2709 2791 727393797 727393879 3.000000e-25 126.0
14 TraesCS7B01G470800 chr7B 81.410 156 13 7 1832 1972 727371257 727371103 2.340000e-21 113.0
15 TraesCS7B01G470800 chr7B 85.897 78 8 2 405 479 727657697 727657620 2.370000e-11 80.5
16 TraesCS7B01G470800 chr7D 90.057 1931 141 28 977 2868 626908991 626910909 0.000000e+00 2455.0
17 TraesCS7B01G470800 chr7D 81.094 1042 140 21 977 1972 626946393 626947423 0.000000e+00 780.0
18 TraesCS7B01G470800 chr7D 83.432 845 116 10 1000 1820 627059172 627060016 0.000000e+00 763.0
19 TraesCS7B01G470800 chr7D 83.829 841 97 14 1000 1819 627071307 627072129 0.000000e+00 763.0
20 TraesCS7B01G470800 chr7D 79.823 1016 158 28 992 1995 626922796 626923776 0.000000e+00 697.0
21 TraesCS7B01G470800 chr7D 85.333 525 43 12 274 774 626908002 626908516 1.970000e-141 512.0
22 TraesCS7B01G470800 chr7D 79.839 744 102 19 996 1715 627024011 627024730 1.530000e-137 499.0
23 TraesCS7B01G470800 chr7D 85.128 195 10 4 793 982 626908766 626908946 6.310000e-42 182.0
24 TraesCS7B01G470800 chr7D 85.714 84 9 2 398 478 627068868 627068951 5.090000e-13 86.1
25 TraesCS7B01G470800 chrUn 87.942 1244 73 30 793 1993 83608051 83609260 0.000000e+00 1395.0
26 TraesCS7B01G470800 chrUn 84.861 720 69 22 85 774 83607140 83607849 0.000000e+00 689.0
27 TraesCS7B01G470800 chrUn 87.387 111 7 4 1892 1995 83628650 83628760 1.400000e-23 121.0
28 TraesCS7B01G470800 chr7A 83.473 835 122 6 1000 1819 722482162 722482995 0.000000e+00 763.0
29 TraesCS7B01G470800 chr7A 80.294 883 126 27 1993 2868 722415806 722416647 8.730000e-175 623.0
30 TraesCS7B01G470800 chr7A 94.118 153 9 0 1000 1152 722572110 722572262 1.720000e-57 233.0
31 TraesCS7B01G470800 chr7A 83.871 93 11 3 390 478 722566132 722566224 5.090000e-13 86.1


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 TraesCS7B01G470800 chr7B 727184402 727187269 2867 True 5297.000000 5297 100.000000 1 2868 1 chr7B.!!$R1 2867
1 TraesCS7B01G470800 chr7B 727380689 727381898 1209 True 741.000000 741 78.577000 814 1995 1 chr7B.!!$R3 1181
2 TraesCS7B01G470800 chr7B 727325959 727328416 2457 True 738.000000 961 86.932333 794 2760 3 chr7B.!!$R5 1966
3 TraesCS7B01G470800 chr7B 727390970 727398749 7779 False 652.000000 1962 87.287167 78 2868 6 chr7B.!!$F2 2790
4 TraesCS7B01G470800 chr7B 727653257 727657697 4440 True 399.750000 719 84.229500 405 1819 2 chr7B.!!$R6 1414
5 TraesCS7B01G470800 chr7B 727409502 727410174 672 False 331.000000 331 76.327000 1993 2721 1 chr7B.!!$F1 728
6 TraesCS7B01G470800 chr7D 626908002 626910909 2907 False 1049.666667 2455 86.839333 274 2868 3 chr7D.!!$F5 2594
7 TraesCS7B01G470800 chr7D 626946393 626947423 1030 False 780.000000 780 81.094000 977 1972 1 chr7D.!!$F2 995
8 TraesCS7B01G470800 chr7D 627059172 627060016 844 False 763.000000 763 83.432000 1000 1820 1 chr7D.!!$F4 820
9 TraesCS7B01G470800 chr7D 626922796 626923776 980 False 697.000000 697 79.823000 992 1995 1 chr7D.!!$F1 1003
10 TraesCS7B01G470800 chr7D 627024011 627024730 719 False 499.000000 499 79.839000 996 1715 1 chr7D.!!$F3 719
11 TraesCS7B01G470800 chr7D 627068868 627072129 3261 False 424.550000 763 84.771500 398 1819 2 chr7D.!!$F6 1421
12 TraesCS7B01G470800 chrUn 83607140 83609260 2120 False 1042.000000 1395 86.401500 85 1993 2 chrUn.!!$F2 1908
13 TraesCS7B01G470800 chr7A 722482162 722482995 833 False 763.000000 763 83.473000 1000 1819 1 chr7A.!!$F2 819
14 TraesCS7B01G470800 chr7A 722415806 722416647 841 False 623.000000 623 80.294000 1993 2868 1 chr7A.!!$F1 875

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
785 4074 0.179936 GCTAGCAGCAACCTCCTCAT 59.82 55.0 10.63 0.0 41.89 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 6286 0.306533 AAAAACATATAGGCGCCGCG 59.693 50.0 23.2 8.83 0.0 6.46 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
35 36 3.814268 GCCATCCAACGCGTGCAT 61.814 61.111 14.98 1.57 0.00 3.96
36 37 2.468670 GCCATCCAACGCGTGCATA 61.469 57.895 14.98 0.00 0.00 3.14
37 38 1.987704 GCCATCCAACGCGTGCATAA 61.988 55.000 14.98 0.00 0.00 1.90
38 39 0.248054 CCATCCAACGCGTGCATAAC 60.248 55.000 14.98 0.00 0.00 1.89
39 40 0.248054 CATCCAACGCGTGCATAACC 60.248 55.000 14.98 0.00 0.00 2.85
40 41 1.701545 ATCCAACGCGTGCATAACCG 61.702 55.000 14.98 0.00 0.00 4.44
41 42 2.573167 CAACGCGTGCATAACCGC 60.573 61.111 14.98 9.19 46.10 5.68
42 43 3.795342 AACGCGTGCATAACCGCC 61.795 61.111 14.98 0.00 46.83 6.13
43 44 4.752879 ACGCGTGCATAACCGCCT 62.753 61.111 12.93 0.00 46.83 5.52
44 45 4.222589 CGCGTGCATAACCGCCTG 62.223 66.667 13.02 0.00 46.83 4.85
45 46 4.536687 GCGTGCATAACCGCCTGC 62.537 66.667 8.12 0.00 43.96 4.85
46 47 3.876198 CGTGCATAACCGCCTGCC 61.876 66.667 0.00 0.00 37.59 4.85
47 48 2.749839 GTGCATAACCGCCTGCCA 60.750 61.111 0.00 0.00 37.59 4.92
48 49 2.034843 TGCATAACCGCCTGCCAA 59.965 55.556 0.00 0.00 37.59 4.52
49 50 2.339556 TGCATAACCGCCTGCCAAC 61.340 57.895 0.00 0.00 37.59 3.77
50 51 3.063743 GCATAACCGCCTGCCAACC 62.064 63.158 0.00 0.00 32.15 3.77
51 52 2.044352 ATAACCGCCTGCCAACCC 60.044 61.111 0.00 0.00 0.00 4.11
52 53 3.655350 ATAACCGCCTGCCAACCCC 62.655 63.158 0.00 0.00 0.00 4.95
68 69 4.374584 CCCCAAATCCCCGCCACA 62.375 66.667 0.00 0.00 0.00 4.17
69 70 2.043046 CCCAAATCCCCGCCACAT 60.043 61.111 0.00 0.00 0.00 3.21
70 71 2.127232 CCCAAATCCCCGCCACATC 61.127 63.158 0.00 0.00 0.00 3.06
71 72 2.480610 CCAAATCCCCGCCACATCG 61.481 63.158 0.00 0.00 0.00 3.84
72 73 2.828549 AAATCCCCGCCACATCGC 60.829 61.111 0.00 0.00 0.00 4.58
73 74 4.875713 AATCCCCGCCACATCGCC 62.876 66.667 0.00 0.00 0.00 5.54
76 77 4.169696 CCCCGCCACATCGCCTTA 62.170 66.667 0.00 0.00 0.00 2.69
77 78 2.895372 CCCGCCACATCGCCTTAC 60.895 66.667 0.00 0.00 0.00 2.34
78 79 2.895372 CCGCCACATCGCCTTACC 60.895 66.667 0.00 0.00 0.00 2.85
79 80 2.895372 CGCCACATCGCCTTACCC 60.895 66.667 0.00 0.00 0.00 3.69
80 81 2.590092 GCCACATCGCCTTACCCT 59.410 61.111 0.00 0.00 0.00 4.34
81 82 1.819632 GCCACATCGCCTTACCCTG 60.820 63.158 0.00 0.00 0.00 4.45
82 83 1.904771 CCACATCGCCTTACCCTGA 59.095 57.895 0.00 0.00 0.00 3.86
83 84 0.251916 CCACATCGCCTTACCCTGAA 59.748 55.000 0.00 0.00 0.00 3.02
87 88 1.207089 CATCGCCTTACCCTGAACTGA 59.793 52.381 0.00 0.00 0.00 3.41
104 105 7.068593 CCTGAACTGATCATCTCTCTAAGTCTT 59.931 40.741 0.00 0.00 37.44 3.01
116 117 9.793259 ATCTCTCTAAGTCTTATGTTCTCTAGG 57.207 37.037 0.00 0.00 0.00 3.02
122 123 5.697067 AGTCTTATGTTCTCTAGGGTCGAT 58.303 41.667 0.00 0.00 0.00 3.59
138 139 1.296715 GATGACGACCCTGCACCTT 59.703 57.895 0.00 0.00 0.00 3.50
139 140 0.741221 GATGACGACCCTGCACCTTC 60.741 60.000 0.00 0.00 0.00 3.46
142 143 0.321653 GACGACCCTGCACCTTCAAT 60.322 55.000 0.00 0.00 0.00 2.57
164 165 0.398318 GCACCAGTCAACCCTCTTCT 59.602 55.000 0.00 0.00 0.00 2.85
167 168 2.104792 CACCAGTCAACCCTCTTCTTCA 59.895 50.000 0.00 0.00 0.00 3.02
229 230 0.959553 TCACCAACGTCCAGTCTCTC 59.040 55.000 0.00 0.00 0.00 3.20
275 276 3.976758 TCGACAGTCATCGACGGT 58.023 55.556 0.41 0.00 45.84 4.83
289 291 0.935196 GACGGTGTTGCTCTCGTTTT 59.065 50.000 0.00 0.00 35.91 2.43
290 292 1.329599 GACGGTGTTGCTCTCGTTTTT 59.670 47.619 0.00 0.00 35.91 1.94
299 301 1.725931 GCTCTCGTTTTTGGCATCGTG 60.726 52.381 0.00 0.00 0.00 4.35
301 303 2.416547 CTCTCGTTTTTGGCATCGTGAT 59.583 45.455 0.00 0.00 0.00 3.06
316 318 4.182693 TCGTGATTAATCAAGTGACGGT 57.817 40.909 24.55 0.00 38.75 4.83
331 333 5.607477 AGTGACGGTAGTGAAATTTTCAGA 58.393 37.500 12.02 1.26 41.01 3.27
377 385 1.154169 CATGCATGTGGTGTGCGTC 60.154 57.895 18.91 0.00 45.37 5.19
455 468 3.496884 ACGCATAAGACAAAATCACACGT 59.503 39.130 0.00 0.00 0.00 4.49
457 470 5.350365 ACGCATAAGACAAAATCACACGTAT 59.650 36.000 0.00 0.00 0.00 3.06
487 500 0.445436 GATTGTTGCGGAGTGCTCAG 59.555 55.000 1.41 0.00 46.63 3.35
497 517 0.833287 GAGTGCTCAGCCTTCCCATA 59.167 55.000 0.00 0.00 0.00 2.74
510 533 0.780637 TCCCATAGATCTCCTCGCCT 59.219 55.000 0.00 0.00 0.00 5.52
513 536 2.025793 CCCATAGATCTCCTCGCCTCTA 60.026 54.545 0.00 0.00 0.00 2.43
518 565 0.539438 ATCTCCTCGCCTCTAGCCTG 60.539 60.000 0.00 0.00 38.78 4.85
523 570 2.333225 CGCCTCTAGCCTGCGTAG 59.667 66.667 10.85 0.00 43.12 3.51
525 572 2.128507 GCCTCTAGCCTGCGTAGGT 61.129 63.158 21.31 10.28 46.41 3.08
653 718 2.038295 GACCTGGACTCATCATCCATCC 59.962 54.545 0.00 0.00 45.27 3.51
654 719 2.052468 CCTGGACTCATCATCCATCCA 58.948 52.381 0.00 0.00 45.27 3.41
655 720 2.440627 CCTGGACTCATCATCCATCCAA 59.559 50.000 0.00 0.00 45.27 3.53
656 721 3.496337 CCTGGACTCATCATCCATCCAAG 60.496 52.174 0.00 0.00 45.27 3.61
696 2429 2.434185 TCCGTGTTCCGCTGCATC 60.434 61.111 0.00 0.00 34.38 3.91
784 4073 0.906756 AGCTAGCAGCAACCTCCTCA 60.907 55.000 18.83 0.00 45.56 3.86
785 4074 0.179936 GCTAGCAGCAACCTCCTCAT 59.820 55.000 10.63 0.00 41.89 2.90
786 4075 1.809651 GCTAGCAGCAACCTCCTCATC 60.810 57.143 10.63 0.00 41.89 2.92
787 4076 1.761784 CTAGCAGCAACCTCCTCATCT 59.238 52.381 0.00 0.00 0.00 2.90
788 4077 0.540923 AGCAGCAACCTCCTCATCTC 59.459 55.000 0.00 0.00 0.00 2.75
789 4078 0.809241 GCAGCAACCTCCTCATCTCG 60.809 60.000 0.00 0.00 0.00 4.04
790 4079 0.534412 CAGCAACCTCCTCATCTCGT 59.466 55.000 0.00 0.00 0.00 4.18
791 4080 0.534412 AGCAACCTCCTCATCTCGTG 59.466 55.000 0.00 0.00 0.00 4.35
1041 4415 3.036819 CTCCATCTCATTCCCTCTGACA 58.963 50.000 0.00 0.00 0.00 3.58
1065 4439 1.261238 CGAGGTCCTTCTCCAAGCCT 61.261 60.000 0.00 0.00 0.00 4.58
1197 4613 2.817834 GCCAACATCCACGCGCTA 60.818 61.111 5.73 0.00 0.00 4.26
1511 4928 1.069378 CTGAACCTCGTCGCCGTTAC 61.069 60.000 0.00 0.00 35.01 2.50
1669 5089 2.033194 CCGTTCGCAAGGAAGTCCC 61.033 63.158 0.00 0.00 34.69 4.46
1741 5639 2.428569 GCTTCGACGAGTGCGACA 60.429 61.111 8.70 0.00 41.64 4.35
1827 5725 3.235200 GCCCACCATCTAGTCATCTAGT 58.765 50.000 2.84 0.00 42.88 2.57
2047 5979 2.871096 TACCCGTTTCATTTCCAGCT 57.129 45.000 0.00 0.00 0.00 4.24
2048 5980 2.871096 ACCCGTTTCATTTCCAGCTA 57.129 45.000 0.00 0.00 0.00 3.32
2049 5981 2.711542 ACCCGTTTCATTTCCAGCTAG 58.288 47.619 0.00 0.00 0.00 3.42
2050 5982 1.401905 CCCGTTTCATTTCCAGCTAGC 59.598 52.381 6.62 6.62 0.00 3.42
2059 5991 3.940209 TTTCCAGCTAGCCAACAATTG 57.060 42.857 12.13 3.24 0.00 2.32
2245 6241 2.863809 ACTTGATCACACCCTCAAACC 58.136 47.619 0.00 0.00 31.40 3.27
2254 6250 2.900546 ACACCCTCAAACCAAACAAACA 59.099 40.909 0.00 0.00 0.00 2.83
2269 6266 7.123547 ACCAAACAAACAAATAGTCCAAGAAGA 59.876 33.333 0.00 0.00 0.00 2.87
2289 6286 4.488879 AGAGGTAAACCGATAAACGTGAC 58.511 43.478 0.00 0.00 42.08 3.67
2303 6300 2.049526 TGACGCGGCGCCTATATG 60.050 61.111 27.87 13.71 0.00 1.78
2305 6302 1.663702 GACGCGGCGCCTATATGTT 60.664 57.895 27.87 0.00 0.00 2.71
2338 6335 1.067213 TCGCTGATGTCGTTGATCCAA 60.067 47.619 0.00 0.00 0.00 3.53
2342 6339 4.672542 CGCTGATGTCGTTGATCCAATTTT 60.673 41.667 0.00 0.00 0.00 1.82
2347 6344 4.942852 TGTCGTTGATCCAATTTTGCTTT 58.057 34.783 0.00 0.00 0.00 3.51
2385 6382 3.070018 GCAGCTAATCAACACTGTCAGT 58.930 45.455 0.00 0.00 32.65 3.41
2426 6423 2.229792 CACCAAAGCAAGCCAGTCTAA 58.770 47.619 0.00 0.00 0.00 2.10
2466 6470 7.822822 GCTAGGTTTCTTGGTTTTGTATAGAGA 59.177 37.037 0.00 0.00 0.00 3.10
2470 6474 8.504815 GGTTTCTTGGTTTTGTATAGAGAGAAC 58.495 37.037 0.00 0.00 0.00 3.01
2550 6554 6.902224 TCATATTGTAAGGTGTGATGAACG 57.098 37.500 0.00 0.00 0.00 3.95
2552 6556 7.548967 TCATATTGTAAGGTGTGATGAACGTA 58.451 34.615 0.00 0.00 0.00 3.57
2687 6704 8.323567 CCTTAAGGTTTTACATACCCTAGTTCA 58.676 37.037 13.83 0.00 36.27 3.18
2753 6852 2.344535 GCTCAATGCCAACACACCT 58.655 52.632 0.00 0.00 35.15 4.00
2770 6951 4.582656 CACACCTGATACAAACCCAAAAGA 59.417 41.667 0.00 0.00 0.00 2.52
2773 6954 6.326323 ACACCTGATACAAACCCAAAAGAATT 59.674 34.615 0.00 0.00 0.00 2.17
2808 6989 1.536766 CGAAACACATGCCACACTCAT 59.463 47.619 0.00 0.00 0.00 2.90
2821 7002 5.170021 GCCACACTCATAAAATGCATGAAA 58.830 37.500 0.00 0.00 32.20 2.69
2853 7034 1.153005 CCAGATGCAAGGCTCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.987704 TTATGCACGCGTTGGATGGC 61.988 55.000 10.22 9.94 36.80 4.40
19 20 0.248054 GTTATGCACGCGTTGGATGG 60.248 55.000 10.22 0.00 36.80 3.51
20 21 0.248054 GGTTATGCACGCGTTGGATG 60.248 55.000 10.22 0.00 36.80 3.51
21 22 1.701545 CGGTTATGCACGCGTTGGAT 61.702 55.000 10.22 14.62 39.99 3.41
22 23 2.384309 CGGTTATGCACGCGTTGGA 61.384 57.895 10.22 7.25 0.00 3.53
23 24 2.097538 CGGTTATGCACGCGTTGG 59.902 61.111 10.22 0.00 0.00 3.77
24 25 2.573167 GCGGTTATGCACGCGTTG 60.573 61.111 10.22 6.68 46.58 4.10
29 30 3.876198 GGCAGGCGGTTATGCACG 61.876 66.667 0.00 0.00 44.37 5.34
30 31 2.339556 TTGGCAGGCGGTTATGCAC 61.340 57.895 0.00 0.00 44.37 4.57
31 32 2.034843 TTGGCAGGCGGTTATGCA 59.965 55.556 0.00 0.00 44.37 3.96
32 33 2.489751 GTTGGCAGGCGGTTATGC 59.510 61.111 0.00 0.00 41.80 3.14
33 34 2.414785 GGGTTGGCAGGCGGTTATG 61.415 63.158 0.00 0.00 0.00 1.90
34 35 2.044352 GGGTTGGCAGGCGGTTAT 60.044 61.111 0.00 0.00 0.00 1.89
35 36 4.354162 GGGGTTGGCAGGCGGTTA 62.354 66.667 0.00 0.00 0.00 2.85
51 52 3.677480 ATGTGGCGGGGATTTGGGG 62.677 63.158 0.00 0.00 0.00 4.96
52 53 2.043046 ATGTGGCGGGGATTTGGG 60.043 61.111 0.00 0.00 0.00 4.12
53 54 2.480610 CGATGTGGCGGGGATTTGG 61.481 63.158 0.00 0.00 0.00 3.28
54 55 3.110139 CGATGTGGCGGGGATTTG 58.890 61.111 0.00 0.00 0.00 2.32
55 56 2.828549 GCGATGTGGCGGGGATTT 60.829 61.111 0.00 0.00 0.00 2.17
56 57 4.875713 GGCGATGTGGCGGGGATT 62.876 66.667 0.00 0.00 0.00 3.01
63 64 1.819632 CAGGGTAAGGCGATGTGGC 60.820 63.158 0.00 0.00 45.27 5.01
64 65 0.251916 TTCAGGGTAAGGCGATGTGG 59.748 55.000 0.00 0.00 0.00 4.17
65 66 1.066143 AGTTCAGGGTAAGGCGATGTG 60.066 52.381 0.00 0.00 0.00 3.21
66 67 1.066143 CAGTTCAGGGTAAGGCGATGT 60.066 52.381 0.00 0.00 0.00 3.06
67 68 1.207089 TCAGTTCAGGGTAAGGCGATG 59.793 52.381 0.00 0.00 0.00 3.84
68 69 1.568504 TCAGTTCAGGGTAAGGCGAT 58.431 50.000 0.00 0.00 0.00 4.58
69 70 1.480954 GATCAGTTCAGGGTAAGGCGA 59.519 52.381 0.00 0.00 0.00 5.54
70 71 1.207089 TGATCAGTTCAGGGTAAGGCG 59.793 52.381 0.00 0.00 0.00 5.52
71 72 3.135530 AGATGATCAGTTCAGGGTAAGGC 59.864 47.826 0.09 0.00 37.89 4.35
72 73 4.653341 AGAGATGATCAGTTCAGGGTAAGG 59.347 45.833 0.09 0.00 37.89 2.69
73 74 5.598005 AGAGAGATGATCAGTTCAGGGTAAG 59.402 44.000 0.09 0.00 37.89 2.34
74 75 5.523588 AGAGAGATGATCAGTTCAGGGTAA 58.476 41.667 0.09 0.00 37.89 2.85
75 76 5.136068 AGAGAGATGATCAGTTCAGGGTA 57.864 43.478 0.09 0.00 37.89 3.69
76 77 3.992999 AGAGAGATGATCAGTTCAGGGT 58.007 45.455 0.09 0.00 37.89 4.34
77 78 5.598005 ACTTAGAGAGATGATCAGTTCAGGG 59.402 44.000 0.09 0.00 37.89 4.45
78 79 6.547141 AGACTTAGAGAGATGATCAGTTCAGG 59.453 42.308 0.09 0.00 37.89 3.86
79 80 7.572523 AGACTTAGAGAGATGATCAGTTCAG 57.427 40.000 0.09 0.00 37.89 3.02
80 81 7.953005 AAGACTTAGAGAGATGATCAGTTCA 57.047 36.000 0.09 0.00 39.12 3.18
81 82 9.897744 CATAAGACTTAGAGAGATGATCAGTTC 57.102 37.037 0.09 1.18 0.00 3.01
82 83 9.420118 ACATAAGACTTAGAGAGATGATCAGTT 57.580 33.333 0.09 0.00 0.00 3.16
83 84 8.995027 ACATAAGACTTAGAGAGATGATCAGT 57.005 34.615 0.09 0.00 0.00 3.41
87 88 9.866655 AGAGAACATAAGACTTAGAGAGATGAT 57.133 33.333 0.73 0.00 0.00 2.45
104 105 3.813724 CGTCATCGACCCTAGAGAACATA 59.186 47.826 0.00 0.00 39.71 2.29
122 123 1.691195 TTGAAGGTGCAGGGTCGTCA 61.691 55.000 0.00 0.00 0.00 4.35
138 139 1.545428 GGGTTGACTGGTGCAGATTGA 60.545 52.381 0.00 0.00 35.18 2.57
139 140 0.883833 GGGTTGACTGGTGCAGATTG 59.116 55.000 0.00 0.00 35.18 2.67
142 143 0.764369 AGAGGGTTGACTGGTGCAGA 60.764 55.000 0.00 0.00 35.18 4.26
167 168 3.733507 TAGATGGAGCCGCGGAGGT 62.734 63.158 33.48 12.93 43.70 3.85
229 230 2.758089 GCTGAGCCATGACCTTGCG 61.758 63.158 0.00 0.00 0.00 4.85
250 251 1.601914 CGATGACTGTCGACCACAACA 60.602 52.381 14.12 6.77 44.06 3.33
271 272 1.063469 CAAAAACGAGAGCAACACCGT 59.937 47.619 0.00 0.00 36.77 4.83
275 276 1.098869 TGCCAAAAACGAGAGCAACA 58.901 45.000 0.00 0.00 0.00 3.33
289 291 4.940654 TCACTTGATTAATCACGATGCCAA 59.059 37.500 24.23 5.66 36.36 4.52
290 292 4.332543 GTCACTTGATTAATCACGATGCCA 59.667 41.667 24.23 6.31 36.36 4.92
299 301 7.591006 TTTCACTACCGTCACTTGATTAATC 57.409 36.000 8.60 8.60 0.00 1.75
301 303 7.972832 AATTTCACTACCGTCACTTGATTAA 57.027 32.000 0.00 0.00 0.00 1.40
316 318 7.074653 ACCTAGGTGTCTGAAAATTTCACTA 57.925 36.000 15.42 3.96 35.46 2.74
331 333 5.705609 CATGTTTTGCTAAACCTAGGTGT 57.294 39.130 17.14 13.50 42.39 4.16
377 385 4.986659 TCGTTTCGTTTAGGGAGAGAAAAG 59.013 41.667 0.00 0.00 33.39 2.27
487 500 1.548269 CGAGGAGATCTATGGGAAGGC 59.452 57.143 0.00 0.00 0.00 4.35
490 510 1.148027 AGGCGAGGAGATCTATGGGAA 59.852 52.381 0.00 0.00 0.00 3.97
497 517 0.251165 GGCTAGAGGCGAGGAGATCT 60.251 60.000 0.00 0.00 42.94 2.75
518 565 2.028883 GCACGACTATTTTGACCTACGC 59.971 50.000 0.00 0.00 0.00 4.42
523 570 0.725117 CGGGCACGACTATTTTGACC 59.275 55.000 0.00 0.00 44.60 4.02
525 572 0.320858 TGCGGGCACGACTATTTTGA 60.321 50.000 15.48 0.00 44.60 2.69
617 682 0.966920 AGGTCATCCTCAACGAACGT 59.033 50.000 0.00 0.00 40.58 3.99
621 686 0.895530 GTCCAGGTCATCCTCAACGA 59.104 55.000 0.00 0.00 43.07 3.85
653 718 3.116300 CACGATCTACCGTTGGATCTTG 58.884 50.000 4.87 1.95 41.29 3.02
654 719 2.100916 CCACGATCTACCGTTGGATCTT 59.899 50.000 4.87 0.00 41.29 2.40
655 720 1.681793 CCACGATCTACCGTTGGATCT 59.318 52.381 4.87 0.00 41.29 2.75
656 721 1.679680 TCCACGATCTACCGTTGGATC 59.320 52.381 0.00 0.00 41.29 3.36
696 2429 0.107508 ATGACTCATTGGGCAGGACG 60.108 55.000 0.00 0.00 0.00 4.79
784 4073 1.032657 CGGTGGAGGAGACACGAGAT 61.033 60.000 0.00 0.00 39.69 2.75
785 4074 1.674651 CGGTGGAGGAGACACGAGA 60.675 63.158 0.00 0.00 39.69 4.04
786 4075 2.701780 CCGGTGGAGGAGACACGAG 61.702 68.421 0.00 0.00 39.69 4.18
787 4076 2.675423 CCGGTGGAGGAGACACGA 60.675 66.667 0.00 0.00 39.69 4.35
788 4077 4.436998 GCCGGTGGAGGAGACACG 62.437 72.222 1.90 0.00 39.69 4.49
789 4078 4.436998 CGCCGGTGGAGGAGACAC 62.437 72.222 7.26 0.00 38.10 3.67
844 4137 2.826738 GGTGGTTGCACGTGTGGT 60.827 61.111 18.38 0.00 0.00 4.16
990 4364 0.181114 TGGGAGCCATTTCGATGGAG 59.819 55.000 9.29 0.00 44.39 3.86
1158 4574 2.520536 GCCGGCTGGTATGGAGGAT 61.521 63.158 22.15 0.00 37.67 3.24
1463 4880 2.599645 CTTGGTGGAGATGGCGGAGG 62.600 65.000 0.00 0.00 0.00 4.30
1650 5067 1.301479 GGACTTCCTTGCGAACGGT 60.301 57.895 0.00 0.00 0.00 4.83
1651 5068 2.033194 GGGACTTCCTTGCGAACGG 61.033 63.158 0.00 0.00 35.95 4.44
1686 5109 2.636412 CCTCTCCACGTTCGCCTCA 61.636 63.158 0.00 0.00 0.00 3.86
1694 5592 4.363990 CGTGCAGCCTCTCCACGT 62.364 66.667 2.42 0.00 45.08 4.49
2047 5979 7.391554 GGATATATTGCTCTCAATTGTTGGCTA 59.608 37.037 5.13 5.76 42.51 3.93
2048 5980 6.208204 GGATATATTGCTCTCAATTGTTGGCT 59.792 38.462 5.13 0.00 42.51 4.75
2049 5981 6.016024 TGGATATATTGCTCTCAATTGTTGGC 60.016 38.462 5.13 8.53 42.51 4.52
2050 5982 7.514784 TGGATATATTGCTCTCAATTGTTGG 57.485 36.000 5.13 0.00 42.51 3.77
2059 5991 7.012704 TCACAAAAGCTTGGATATATTGCTCTC 59.987 37.037 0.00 0.00 36.82 3.20
2124 6114 6.810911 TGAAAGTAAGCTTGTTAATTTGGCA 58.189 32.000 9.86 0.00 34.71 4.92
2245 6241 7.649306 CCTCTTCTTGGACTATTTGTTTGTTTG 59.351 37.037 0.00 0.00 0.00 2.93
2254 6250 6.013984 TCGGTTTACCTCTTCTTGGACTATTT 60.014 38.462 0.00 0.00 0.00 1.40
2269 6266 3.244976 CGTCACGTTTATCGGTTTACCT 58.755 45.455 0.00 0.00 44.69 3.08
2289 6286 0.306533 AAAAACATATAGGCGCCGCG 59.693 50.000 23.20 8.83 0.00 6.46
2314 6311 2.088763 CAACGACATCAGCGACGCT 61.089 57.895 18.46 18.46 40.77 5.07
2342 6339 7.213216 TGCTGTTCTAATGTCAAATAAAGCA 57.787 32.000 0.00 0.00 33.69 3.91
2347 6344 8.737168 ATTAGCTGCTGTTCTAATGTCAAATA 57.263 30.769 13.43 0.00 35.03 1.40
2363 6360 3.244353 ACTGACAGTGTTGATTAGCTGCT 60.244 43.478 7.47 7.57 32.65 4.24
2385 6382 4.342665 GTGTTAAAATTCCAAGTGTCCCCA 59.657 41.667 0.00 0.00 0.00 4.96
2401 6398 2.763448 ACTGGCTTGCTTTGGTGTTAAA 59.237 40.909 0.00 0.00 0.00 1.52
2538 6542 3.570926 TCAGACTACGTTCATCACACC 57.429 47.619 0.00 0.00 0.00 4.16
2550 6554 6.649141 TGTGTTATGGACAATGTTCAGACTAC 59.351 38.462 0.00 0.00 40.65 2.73
2552 6556 5.620206 TGTGTTATGGACAATGTTCAGACT 58.380 37.500 0.00 0.00 40.65 3.24
2632 6644 2.033194 GCTAAAGTCGGGCAAGCGT 61.033 57.895 0.00 0.00 0.00 5.07
2687 6704 9.661563 TCAAGTACCGTGTATTTTATTCTCATT 57.338 29.630 0.00 0.00 0.00 2.57
2753 6852 7.441017 CCAAGAATTCTTTTGGGTTTGTATCA 58.559 34.615 18.16 0.00 40.11 2.15
2808 6989 9.628746 CGGATGATCATATTTTCATGCATTTTA 57.371 29.630 8.54 0.00 39.75 1.52


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

AutoCloner maintained by Alex Coulton.