Multiple sequence alignment - TraesCS5A01G101800

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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 TraesCS5A01G101800 chr5A 100.000 3828 0 0 682 4509 151244681 151248508 0.000000e+00 7070
1 TraesCS5A01G101800 chr5A 100.000 107 0 0 1 107 151244000 151244106 9.890000e-47 198
2 TraesCS5A01G101800 chr5B 96.575 3854 104 13 682 4509 143737079 143733228 0.000000e+00 6360
3 TraesCS5A01G101800 chr5B 87.226 501 44 11 3743 4227 143732771 143732275 1.830000e-153 553
4 TraesCS5A01G101800 chr5D 96.594 3523 56 17 682 4183 132433920 132430441 0.000000e+00 5782
5 TraesCS5A01G101800 chr5D 89.056 466 41 7 3771 4227 132429686 132429222 1.820000e-158 569
6 TraesCS5A01G101800 chr5D 93.089 246 16 1 4265 4509 132430442 132430197 4.290000e-95 359


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 TraesCS5A01G101800 chr5A 151244000 151248508 4508 False 3634.000000 7070 100.0000 1 4509 2 chr5A.!!$F1 4508
1 TraesCS5A01G101800 chr5B 143732275 143737079 4804 True 3456.500000 6360 91.9005 682 4509 2 chr5B.!!$R1 3827
2 TraesCS5A01G101800 chr5D 132429222 132433920 4698 True 2236.666667 5782 92.9130 682 4509 3 chr5D.!!$R1 3827

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
29 30 0.395173 ACCACTGTTTCAAAGCCGGT 60.395 50.0 1.90 0.0 0.00 5.28 F
1750 1761 0.476771 GGAAGGTCCTCCCAACAACA 59.523 55.0 0.00 0.0 32.53 3.33 F
2351 2365 0.915364 AGGAGTTCTCCATCTTGGCC 59.085 55.0 19.28 0.0 37.47 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 1965 1.213619 TCACATCCTTGATGCCCCCA 61.214 55.0 4.05 0.0 43.15 4.96 R
3119 3145 0.890542 GCTGCTGTGGTGACCATTGA 60.891 55.0 7.94 0.0 35.28 2.57 R
3759 3785 0.550914 AACAAGGAACCCTCAGTGCA 59.449 50.0 0.00 0.0 30.89 4.57 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
26 27 4.379339 TTTGTACCACTGTTTCAAAGCC 57.621 40.909 0.00 0.00 0.00 4.35
27 28 1.944024 TGTACCACTGTTTCAAAGCCG 59.056 47.619 0.00 0.00 0.00 5.52
28 29 1.265905 GTACCACTGTTTCAAAGCCGG 59.734 52.381 0.00 0.00 0.00 6.13
29 30 0.395173 ACCACTGTTTCAAAGCCGGT 60.395 50.000 1.90 0.00 0.00 5.28
30 31 1.134037 ACCACTGTTTCAAAGCCGGTA 60.134 47.619 1.90 0.00 0.00 4.02
31 32 2.159382 CCACTGTTTCAAAGCCGGTAT 58.841 47.619 1.90 0.00 0.00 2.73
32 33 2.161609 CCACTGTTTCAAAGCCGGTATC 59.838 50.000 1.90 0.00 0.00 2.24
33 34 2.811431 CACTGTTTCAAAGCCGGTATCA 59.189 45.455 1.90 0.00 0.00 2.15
34 35 3.440173 CACTGTTTCAAAGCCGGTATCAT 59.560 43.478 1.90 0.00 0.00 2.45
35 36 3.440173 ACTGTTTCAAAGCCGGTATCATG 59.560 43.478 1.90 0.00 0.00 3.07
36 37 3.680490 TGTTTCAAAGCCGGTATCATGA 58.320 40.909 1.90 0.00 0.00 3.07
37 38 4.269183 TGTTTCAAAGCCGGTATCATGAT 58.731 39.130 13.81 13.81 0.00 2.45
38 39 5.432645 TGTTTCAAAGCCGGTATCATGATA 58.567 37.500 11.49 11.49 0.00 2.15
39 40 5.883115 TGTTTCAAAGCCGGTATCATGATAA 59.117 36.000 16.97 0.00 0.00 1.75
40 41 6.545666 TGTTTCAAAGCCGGTATCATGATAAT 59.454 34.615 16.97 0.00 0.00 1.28
41 42 6.558771 TTCAAAGCCGGTATCATGATAATG 57.441 37.500 16.97 11.82 0.00 1.90
42 43 4.455533 TCAAAGCCGGTATCATGATAATGC 59.544 41.667 16.97 17.60 0.00 3.56
43 44 2.991250 AGCCGGTATCATGATAATGCC 58.009 47.619 16.97 12.85 0.00 4.40
44 45 2.573462 AGCCGGTATCATGATAATGCCT 59.427 45.455 16.97 8.75 0.00 4.75
45 46 3.774766 AGCCGGTATCATGATAATGCCTA 59.225 43.478 16.97 0.00 0.00 3.93
46 47 4.225042 AGCCGGTATCATGATAATGCCTAA 59.775 41.667 16.97 0.00 0.00 2.69
47 48 5.104360 AGCCGGTATCATGATAATGCCTAAT 60.104 40.000 16.97 2.43 0.00 1.73
48 49 5.590259 GCCGGTATCATGATAATGCCTAATT 59.410 40.000 16.97 0.00 0.00 1.40
49 50 6.095440 GCCGGTATCATGATAATGCCTAATTT 59.905 38.462 16.97 0.00 0.00 1.82
50 51 7.362920 GCCGGTATCATGATAATGCCTAATTTT 60.363 37.037 16.97 0.00 0.00 1.82
51 52 8.184192 CCGGTATCATGATAATGCCTAATTTTC 58.816 37.037 16.97 0.37 0.00 2.29
52 53 8.729756 CGGTATCATGATAATGCCTAATTTTCA 58.270 33.333 16.97 0.00 39.55 2.69
57 58 9.851686 TCATGATAATGCCTAATTTTCAGTACT 57.148 29.630 0.00 0.00 38.91 2.73
61 62 9.952188 GATAATGCCTAATTTTCAGTACTTTCC 57.048 33.333 0.00 0.00 0.00 3.13
62 63 7.775053 AATGCCTAATTTTCAGTACTTTCCA 57.225 32.000 0.00 0.00 0.00 3.53
63 64 6.569179 TGCCTAATTTTCAGTACTTTCCAC 57.431 37.500 0.00 0.00 0.00 4.02
64 65 6.065374 TGCCTAATTTTCAGTACTTTCCACA 58.935 36.000 0.00 0.00 0.00 4.17
65 66 6.719370 TGCCTAATTTTCAGTACTTTCCACAT 59.281 34.615 0.00 0.00 0.00 3.21
66 67 7.029563 GCCTAATTTTCAGTACTTTCCACATG 58.970 38.462 0.00 0.00 0.00 3.21
67 68 7.309194 GCCTAATTTTCAGTACTTTCCACATGT 60.309 37.037 0.00 0.00 0.00 3.21
68 69 8.023128 CCTAATTTTCAGTACTTTCCACATGTG 58.977 37.037 19.31 19.31 0.00 3.21
69 70 7.581213 AATTTTCAGTACTTTCCACATGTGA 57.419 32.000 27.46 10.46 0.00 3.58
70 71 7.765695 ATTTTCAGTACTTTCCACATGTGAT 57.234 32.000 27.46 9.23 0.00 3.06
71 72 6.558771 TTTCAGTACTTTCCACATGTGATG 57.441 37.500 27.46 11.51 0.00 3.07
72 73 4.578871 TCAGTACTTTCCACATGTGATGG 58.421 43.478 27.46 11.05 38.71 3.51
73 74 4.041567 TCAGTACTTTCCACATGTGATGGT 59.958 41.667 27.46 19.47 38.47 3.55
74 75 4.761739 CAGTACTTTCCACATGTGATGGTT 59.238 41.667 27.46 10.48 38.47 3.67
75 76 5.937540 CAGTACTTTCCACATGTGATGGTTA 59.062 40.000 27.46 9.51 38.47 2.85
76 77 6.599244 CAGTACTTTCCACATGTGATGGTTAT 59.401 38.462 27.46 8.55 38.47 1.89
77 78 7.768582 CAGTACTTTCCACATGTGATGGTTATA 59.231 37.037 27.46 7.61 38.47 0.98
78 79 7.987458 AGTACTTTCCACATGTGATGGTTATAG 59.013 37.037 27.46 13.37 38.47 1.31
79 80 6.122277 ACTTTCCACATGTGATGGTTATAGG 58.878 40.000 27.46 6.30 38.47 2.57
80 81 5.708736 TTCCACATGTGATGGTTATAGGT 57.291 39.130 27.46 0.00 38.47 3.08
81 82 5.708736 TCCACATGTGATGGTTATAGGTT 57.291 39.130 27.46 0.00 38.47 3.50
82 83 5.680619 TCCACATGTGATGGTTATAGGTTC 58.319 41.667 27.46 0.00 38.47 3.62
83 84 5.428457 TCCACATGTGATGGTTATAGGTTCT 59.572 40.000 27.46 0.00 38.47 3.01
84 85 6.613679 TCCACATGTGATGGTTATAGGTTCTA 59.386 38.462 27.46 0.00 38.47 2.10
85 86 7.126573 TCCACATGTGATGGTTATAGGTTCTAA 59.873 37.037 27.46 0.00 38.47 2.10
86 87 7.773224 CCACATGTGATGGTTATAGGTTCTAAA 59.227 37.037 27.46 0.00 32.08 1.85
87 88 9.173021 CACATGTGATGGTTATAGGTTCTAAAA 57.827 33.333 21.64 0.00 33.60 1.52
88 89 9.174166 ACATGTGATGGTTATAGGTTCTAAAAC 57.826 33.333 0.00 0.00 32.55 2.43
89 90 9.396022 CATGTGATGGTTATAGGTTCTAAAACT 57.604 33.333 0.00 0.00 35.61 2.66
90 91 9.614792 ATGTGATGGTTATAGGTTCTAAAACTC 57.385 33.333 0.00 0.00 35.61 3.01
91 92 8.822805 TGTGATGGTTATAGGTTCTAAAACTCT 58.177 33.333 0.00 0.00 35.61 3.24
92 93 9.668497 GTGATGGTTATAGGTTCTAAAACTCTT 57.332 33.333 0.00 0.00 35.61 2.85
95 96 8.331730 TGGTTATAGGTTCTAAAACTCTTTGC 57.668 34.615 0.00 0.00 35.61 3.68
96 97 7.940137 TGGTTATAGGTTCTAAAACTCTTTGCA 59.060 33.333 0.00 0.00 35.61 4.08
97 98 8.789762 GGTTATAGGTTCTAAAACTCTTTGCAA 58.210 33.333 0.00 0.00 35.61 4.08
101 102 6.914259 AGGTTCTAAAACTCTTTGCAATAGC 58.086 36.000 0.00 0.00 37.10 2.97
102 103 6.717084 AGGTTCTAAAACTCTTTGCAATAGCT 59.283 34.615 0.00 0.00 37.31 3.32
103 104 7.883311 AGGTTCTAAAACTCTTTGCAATAGCTA 59.117 33.333 0.00 0.00 37.31 3.32
104 105 8.678199 GGTTCTAAAACTCTTTGCAATAGCTAT 58.322 33.333 0.00 0.00 37.31 2.97
968 973 1.738908 GCCTAAAAATCCACGCCGTAA 59.261 47.619 0.00 0.00 0.00 3.18
1198 1203 3.764237 TTTCTGTAGAAAGAACGCCCT 57.236 42.857 3.05 0.00 38.94 5.19
1460 1465 7.657023 AACGGTACTCTTTGACCTAATATCT 57.343 36.000 0.00 0.00 33.21 1.98
1490 1497 6.189859 TGTTCAGGAATCAGGAGCATAAATT 58.810 36.000 0.00 0.00 0.00 1.82
1750 1761 0.476771 GGAAGGTCCTCCCAACAACA 59.523 55.000 0.00 0.00 32.53 3.33
1951 1965 2.354821 GAGAGTTTTTGGTTCACGTGCT 59.645 45.455 11.67 0.00 0.00 4.40
2131 2145 2.490509 CCGGTGGATTTTGGGTAGAAAC 59.509 50.000 0.00 0.00 0.00 2.78
2246 2260 2.211806 GCAGATGAAGATGCTGACCTC 58.788 52.381 0.00 0.00 39.38 3.85
2311 2325 2.371841 AGGATGTTGACAGTGCCTGTAA 59.628 45.455 7.69 0.00 45.44 2.41
2351 2365 0.915364 AGGAGTTCTCCATCTTGGCC 59.085 55.000 19.28 0.00 37.47 5.36
2622 2636 4.142381 GGTTGATACTTTGTCCATGGCTTC 60.142 45.833 6.96 0.43 0.00 3.86
2629 2643 1.909700 TGTCCATGGCTTCCAACTTC 58.090 50.000 6.96 0.00 36.95 3.01
2818 2844 4.670221 GCTGAAGCAATGGTAGAAGAAACG 60.670 45.833 0.00 0.00 41.59 3.60
2986 3012 4.095932 GCATCATCATCAAACTCTCAGCAA 59.904 41.667 0.00 0.00 0.00 3.91
3019 3045 1.202452 GCACTTTCCAAGTTTGCTGCT 60.202 47.619 0.00 0.00 40.46 4.24
3119 3145 1.743995 GCCTTCGTACCAATGCCGT 60.744 57.895 0.00 0.00 0.00 5.68
3759 3785 5.521735 GTGTAGTGCATCGATGAAAGAGATT 59.478 40.000 29.20 7.11 0.00 2.40
3892 3918 9.897744 CTACTAATGAAATTTTGAAGCTGTTGA 57.102 29.630 0.00 0.00 37.87 3.18
3910 3936 5.437060 TGTTGAAAAAGGACTAGTCAGCTT 58.563 37.500 23.91 15.46 0.00 3.74
3914 3940 7.672983 TGAAAAAGGACTAGTCAGCTTTATG 57.327 36.000 23.91 0.00 0.00 1.90
3949 3975 6.775594 ATACTTCCACTCCCAAAATTTAGC 57.224 37.500 0.00 0.00 0.00 3.09
3955 3981 5.418840 TCCACTCCCAAAATTTAGCTCATTC 59.581 40.000 0.00 0.00 0.00 2.67
4075 4101 6.897966 AGTGAGATCCATGAACCTAAGAACTA 59.102 38.462 0.00 0.00 0.00 2.24
4212 4238 4.262420 GCCTTTCTAAATTGGTGGAGCAAA 60.262 41.667 0.00 0.00 0.00 3.68
4280 4308 8.253810 ACCGATCACTATCAATATGATTACCAG 58.746 37.037 0.00 0.00 38.26 4.00
4282 4310 8.253810 CGATCACTATCAATATGATTACCAGGT 58.746 37.037 0.00 0.00 38.26 4.00
4292 4320 4.274602 TGATTACCAGGTTGCGTCTTAA 57.725 40.909 0.00 0.00 0.00 1.85
4359 4387 7.457868 CGCTATAAAAATACTTTTGTCCGTCA 58.542 34.615 0.00 0.00 35.50 4.35
4370 4398 6.114767 ACTTTTGTCCGTCAGGTAAGTTTTA 58.885 36.000 0.00 0.00 39.05 1.52
4378 4406 6.070995 TCCGTCAGGTAAGTTTTATCTGTCAT 60.071 38.462 8.49 0.00 39.05 3.06
4405 4433 6.239148 GCAGTTTTCAATTTTCTTCCTCCTCT 60.239 38.462 0.00 0.00 0.00 3.69
4440 4468 4.592351 TGGGCAGATTTTGATTTTCCTTGA 59.408 37.500 0.00 0.00 0.00 3.02
4444 4472 6.402875 GGCAGATTTTGATTTTCCTTGAATGC 60.403 38.462 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.301002 GGCTTTGAAACAGTGGTACAAATTATA 58.699 33.333 9.86 0.00 44.16 0.98
1 2 7.151976 GGCTTTGAAACAGTGGTACAAATTAT 58.848 34.615 9.86 0.00 44.16 1.28
2 3 6.508777 GGCTTTGAAACAGTGGTACAAATTA 58.491 36.000 9.86 0.00 44.16 1.40
3 4 5.356426 GGCTTTGAAACAGTGGTACAAATT 58.644 37.500 9.86 0.00 44.16 1.82
4 5 4.499019 CGGCTTTGAAACAGTGGTACAAAT 60.499 41.667 9.86 0.00 44.16 2.32
5 6 3.181495 CGGCTTTGAAACAGTGGTACAAA 60.181 43.478 0.00 3.24 44.16 2.83
6 7 2.356382 CGGCTTTGAAACAGTGGTACAA 59.644 45.455 0.00 0.00 44.16 2.41
7 8 1.944024 CGGCTTTGAAACAGTGGTACA 59.056 47.619 0.00 0.00 0.00 2.90
8 9 1.265905 CCGGCTTTGAAACAGTGGTAC 59.734 52.381 0.00 0.00 0.00 3.34
9 10 1.134037 ACCGGCTTTGAAACAGTGGTA 60.134 47.619 0.00 0.00 0.00 3.25
10 11 0.395173 ACCGGCTTTGAAACAGTGGT 60.395 50.000 0.00 0.00 0.00 4.16
11 12 1.600023 TACCGGCTTTGAAACAGTGG 58.400 50.000 0.00 0.00 0.00 4.00
12 13 2.811431 TGATACCGGCTTTGAAACAGTG 59.189 45.455 0.00 0.00 0.00 3.66
13 14 3.134574 TGATACCGGCTTTGAAACAGT 57.865 42.857 0.00 0.00 0.00 3.55
14 15 3.689161 TCATGATACCGGCTTTGAAACAG 59.311 43.478 0.00 0.00 0.00 3.16
15 16 3.680490 TCATGATACCGGCTTTGAAACA 58.320 40.909 0.00 0.00 0.00 2.83
16 17 4.900635 ATCATGATACCGGCTTTGAAAC 57.099 40.909 6.36 0.00 0.00 2.78
17 18 6.514870 GCATTATCATGATACCGGCTTTGAAA 60.515 38.462 15.10 0.00 31.07 2.69
18 19 5.048782 GCATTATCATGATACCGGCTTTGAA 60.049 40.000 15.10 0.00 31.07 2.69
19 20 4.455533 GCATTATCATGATACCGGCTTTGA 59.544 41.667 15.10 0.00 31.07 2.69
20 21 4.379813 GGCATTATCATGATACCGGCTTTG 60.380 45.833 15.10 6.02 31.07 2.77
21 22 3.758554 GGCATTATCATGATACCGGCTTT 59.241 43.478 15.10 0.00 31.07 3.51
22 23 3.009473 AGGCATTATCATGATACCGGCTT 59.991 43.478 23.72 17.04 31.01 4.35
23 24 2.573462 AGGCATTATCATGATACCGGCT 59.427 45.455 23.72 23.72 31.07 5.52
24 25 2.991250 AGGCATTATCATGATACCGGC 58.009 47.619 21.07 21.07 31.07 6.13
25 26 7.630242 AAATTAGGCATTATCATGATACCGG 57.370 36.000 15.10 0.00 31.07 5.28
26 27 8.729756 TGAAAATTAGGCATTATCATGATACCG 58.270 33.333 15.10 10.06 31.07 4.02
31 32 9.851686 AGTACTGAAAATTAGGCATTATCATGA 57.148 29.630 0.00 0.00 31.07 3.07
35 36 9.952188 GGAAAGTACTGAAAATTAGGCATTATC 57.048 33.333 0.00 0.00 0.00 1.75
36 37 9.474313 TGGAAAGTACTGAAAATTAGGCATTAT 57.526 29.630 0.00 0.00 0.00 1.28
37 38 8.736244 GTGGAAAGTACTGAAAATTAGGCATTA 58.264 33.333 0.00 0.00 0.00 1.90
38 39 7.232534 TGTGGAAAGTACTGAAAATTAGGCATT 59.767 33.333 0.00 0.00 0.00 3.56
39 40 6.719370 TGTGGAAAGTACTGAAAATTAGGCAT 59.281 34.615 0.00 0.00 0.00 4.40
40 41 6.065374 TGTGGAAAGTACTGAAAATTAGGCA 58.935 36.000 0.00 0.00 0.00 4.75
41 42 6.569179 TGTGGAAAGTACTGAAAATTAGGC 57.431 37.500 0.00 0.00 0.00 3.93
42 43 8.023128 CACATGTGGAAAGTACTGAAAATTAGG 58.977 37.037 18.51 0.00 0.00 2.69
43 44 8.783093 TCACATGTGGAAAGTACTGAAAATTAG 58.217 33.333 25.16 0.00 0.00 1.73
44 45 8.684386 TCACATGTGGAAAGTACTGAAAATTA 57.316 30.769 25.16 0.00 0.00 1.40
45 46 7.581213 TCACATGTGGAAAGTACTGAAAATT 57.419 32.000 25.16 0.00 0.00 1.82
46 47 7.309377 CCATCACATGTGGAAAGTACTGAAAAT 60.309 37.037 25.16 3.68 39.12 1.82
47 48 6.016360 CCATCACATGTGGAAAGTACTGAAAA 60.016 38.462 25.16 1.24 39.12 2.29
48 49 5.473162 CCATCACATGTGGAAAGTACTGAAA 59.527 40.000 25.16 1.69 39.12 2.69
49 50 5.003160 CCATCACATGTGGAAAGTACTGAA 58.997 41.667 25.16 1.91 39.12 3.02
50 51 4.041567 ACCATCACATGTGGAAAGTACTGA 59.958 41.667 25.16 2.45 39.12 3.41
51 52 4.326826 ACCATCACATGTGGAAAGTACTG 58.673 43.478 25.16 9.84 39.12 2.74
52 53 4.640771 ACCATCACATGTGGAAAGTACT 57.359 40.909 25.16 0.00 39.12 2.73
53 54 7.226720 CCTATAACCATCACATGTGGAAAGTAC 59.773 40.741 25.16 0.00 39.12 2.73
54 55 7.092623 ACCTATAACCATCACATGTGGAAAGTA 60.093 37.037 25.16 12.72 39.12 2.24
55 56 6.122277 CCTATAACCATCACATGTGGAAAGT 58.878 40.000 25.16 14.51 39.12 2.66
56 57 6.122277 ACCTATAACCATCACATGTGGAAAG 58.878 40.000 25.16 13.91 39.12 2.62
57 58 6.073447 ACCTATAACCATCACATGTGGAAA 57.927 37.500 25.16 7.10 39.12 3.13
58 59 5.708736 ACCTATAACCATCACATGTGGAA 57.291 39.130 25.16 7.89 39.12 3.53
59 60 5.428457 AGAACCTATAACCATCACATGTGGA 59.572 40.000 25.16 12.59 39.12 4.02
60 61 5.684704 AGAACCTATAACCATCACATGTGG 58.315 41.667 25.16 12.47 42.55 4.17
61 62 8.731275 TTTAGAACCTATAACCATCACATGTG 57.269 34.615 20.18 20.18 0.00 3.21
62 63 9.174166 GTTTTAGAACCTATAACCATCACATGT 57.826 33.333 0.00 0.00 0.00 3.21
63 64 9.396022 AGTTTTAGAACCTATAACCATCACATG 57.604 33.333 0.00 0.00 36.39 3.21
64 65 9.614792 GAGTTTTAGAACCTATAACCATCACAT 57.385 33.333 0.00 0.00 36.39 3.21
65 66 8.822805 AGAGTTTTAGAACCTATAACCATCACA 58.177 33.333 0.00 0.00 36.39 3.58
66 67 9.668497 AAGAGTTTTAGAACCTATAACCATCAC 57.332 33.333 0.00 0.00 36.39 3.06
69 70 8.957466 GCAAAGAGTTTTAGAACCTATAACCAT 58.043 33.333 0.00 0.00 36.39 3.55
70 71 7.940137 TGCAAAGAGTTTTAGAACCTATAACCA 59.060 33.333 0.00 0.00 36.39 3.67
71 72 8.331730 TGCAAAGAGTTTTAGAACCTATAACC 57.668 34.615 0.00 0.00 36.39 2.85
75 76 8.678199 GCTATTGCAAAGAGTTTTAGAACCTAT 58.322 33.333 1.71 0.00 37.51 2.57
76 77 7.883311 AGCTATTGCAAAGAGTTTTAGAACCTA 59.117 33.333 1.71 0.00 37.51 3.08
77 78 6.717084 AGCTATTGCAAAGAGTTTTAGAACCT 59.283 34.615 1.71 0.00 37.51 3.50
78 79 6.914259 AGCTATTGCAAAGAGTTTTAGAACC 58.086 36.000 1.71 0.00 37.51 3.62
935 940 1.742308 TTTAGGCTGTGAGGGAGGTT 58.258 50.000 0.00 0.00 0.00 3.50
1460 1465 5.104402 TGCTCCTGATTCCTGAACATATCAA 60.104 40.000 0.00 0.00 37.67 2.57
1511 1518 8.243426 GCAACAACAAGATCATGGTAAGAAATA 58.757 33.333 2.59 0.00 0.00 1.40
1750 1761 6.431234 CACCCTTTTCAGCTACATCTTTAAGT 59.569 38.462 0.00 0.00 0.00 2.24
1951 1965 1.213619 TCACATCCTTGATGCCCCCA 61.214 55.000 4.05 0.00 43.15 4.96
2183 2197 3.868077 GCAACGCAGATACAATTCTCTCT 59.132 43.478 0.00 0.00 0.00 3.10
2246 2260 4.337763 GCATAGATGTCTTGCAGTTTTCG 58.662 43.478 10.31 0.00 36.40 3.46
2311 2325 6.181908 TCCTGTTAACAAACAGTACCTTTGT 58.818 36.000 10.03 11.69 46.54 2.83
2351 2365 5.034554 ACATCACAAAACATGCTAAGACG 57.965 39.130 0.00 0.00 0.00 4.18
2598 2612 3.010584 AGCCATGGACAAAGTATCAACCT 59.989 43.478 18.40 0.00 0.00 3.50
2622 2636 4.330250 ACACAGATCCAAGATGAAGTTGG 58.670 43.478 0.00 0.00 45.18 3.77
2818 2844 2.568090 CTCCGTTGCATGTTGGCC 59.432 61.111 0.00 0.00 0.00 5.36
2986 3012 4.922206 TGGAAAGTGCAGATTGGAGTATT 58.078 39.130 0.00 0.00 0.00 1.89
3019 3045 6.340522 TGAGCGTATCTCAGATGAATTTTCA 58.659 36.000 0.00 0.00 46.34 2.69
3119 3145 0.890542 GCTGCTGTGGTGACCATTGA 60.891 55.000 7.94 0.00 35.28 2.57
3759 3785 0.550914 AACAAGGAACCCTCAGTGCA 59.449 50.000 0.00 0.00 30.89 4.57
3822 3848 3.185594 CACAAATGGAAACTTGCTGCATG 59.814 43.478 13.31 13.31 0.00 4.06
3878 3904 6.036577 AGTCCTTTTTCAACAGCTTCAAAA 57.963 33.333 0.00 0.00 0.00 2.44
3892 3918 6.072452 GCACATAAAGCTGACTAGTCCTTTTT 60.072 38.462 23.58 19.40 0.00 1.94
3910 3936 7.367285 GTGGAAGTATTTCAAGTTGCACATAA 58.633 34.615 10.12 0.00 45.35 1.90
3914 3940 5.438761 AGTGGAAGTATTTCAAGTTGCAC 57.561 39.130 7.69 7.69 45.98 4.57
3949 3975 7.326454 TGAAGAACAGGAAGTATGAGAATGAG 58.674 38.462 0.00 0.00 0.00 2.90
3955 3981 8.037758 ACTACATTGAAGAACAGGAAGTATGAG 58.962 37.037 0.00 0.00 0.00 2.90
3999 4025 9.048446 GTCTGGTGTAGTTTTACTCATTTACAA 57.952 33.333 0.00 0.00 0.00 2.41
4018 4044 3.814842 TGCAAGTTTAGTGATGTCTGGTG 59.185 43.478 0.00 0.00 0.00 4.17
4192 4218 8.744568 AAAAATTTGCTCCACCAATTTAGAAA 57.255 26.923 0.00 0.00 0.00 2.52
4231 4259 8.953990 CGGTTAGAAACTTGTAAATTTGTTCAG 58.046 33.333 0.00 0.00 0.00 3.02
4234 4262 9.673454 GATCGGTTAGAAACTTGTAAATTTGTT 57.327 29.630 0.00 0.00 0.00 2.83
4280 4308 8.911247 ATTTTGATCTTATTTAAGACGCAACC 57.089 30.769 13.01 0.00 44.30 3.77
4359 4387 6.942576 ACTGCAATGACAGATAAAACTTACCT 59.057 34.615 10.68 0.00 40.25 3.08
4370 4398 7.929785 AGAAAATTGAAAACTGCAATGACAGAT 59.070 29.630 10.68 0.00 40.25 2.90
4378 4406 6.048509 GGAGGAAGAAAATTGAAAACTGCAA 58.951 36.000 0.00 0.00 0.00 4.08
4417 4445 4.592351 TCAAGGAAAATCAAAATCTGCCCA 59.408 37.500 0.00 0.00 0.00 5.36
4440 4468 0.539051 CTCGACCAGAAGAGGGCATT 59.461 55.000 0.00 0.00 35.99 3.56
4444 4472 1.339610 CATAGCTCGACCAGAAGAGGG 59.660 57.143 0.00 0.00 35.19 4.30


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

AutoCloner maintained by Alex Coulton.